Hyper Stacks 1994 May

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MacBinary | 1994-04-27 | 40.8 KB | [STAK/WILD]
open in:
MacOS 8.1 extracted |
Win98 extracted |
DOS extracted
view JSON data |
view as text

This file was processed as: MacBinary (archive/macBinary).

You can browse this item here: HyperPCR
Confidence	Program	Detection	Match Type	Support
`100%`	dexvert	HyperCard Stack `(archive/hypercard)`	idMeta	Supported
`10%`	dexvert	MacBinary `(archive/macBinary)`	fallback	Supported
`100%`	file	MacBinary II, inited, Wed Aug 5 05:15:08 1992, modified Wed Apr 27 09:04:21 1994, creator HyperCard, type HyperCard stack, 40960 bytes "HyperPCR" , at 0xa080 582 bytes resource	default (weak)
`99%`	file	data	default
`74%`	TrID	Mac HyperCard stack (MacBinary)	default
`25%`	TrID	MacBinary 2	default (weak)
`100%`	lsar	MacBinary	default
id metadata
key	value
macFileType	`[STAK]`
macFileCreator	`[WILD]`
hex view
+--------+-------------------------+-------------------------+--------+--------+
|00000000| 00 08 48 79 70 65 72 50 | 43 52 00 00 00 00 00 00 |..HyperP|CR......|
|00000010| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000020| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000030| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000040| 00 53 54 41 4b 57 49 4c | 44 01 00 00 00 00 00 00 |.STAKWIL|D.......|
|00000050| 00 00 00 00 00 a0 00 00 | 00 02 46 a6 a5 4c 9c a9 |........|..F..L..|
|00000060| e4 13 55 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |..U.....|........|
|00000070| 00 00 00 00 00 00 00 00 | 00 00 81 81 a8 c1 00 00 |........|........|
|00000080| 00 00 08 00 53 54 41 4b | ff ff ff ff 00 00 00 00 |....STAK|........|
|00000090| 00 00 00 0a 00 00 a0 00 | 00 00 08 00 00 00 00 00 |........|........|
|000000a0| 00 00 00 00 00 00 00 01 | 00 00 0a d7 00 00 00 02 |........|........|
|000000b0| 00 00 0b 81 00 00 11 ed | 00 00 00 04 00 00 64 80 |........|......d.|
|000000c0| 00 00 09 f5 00 00 00 00 | 00 05 00 00 10 00 00 00 |........|........|
|000000d0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000000e0| 02 00 80 00 02 00 80 00 | 02 00 80 00 02 10 80 01 |........|........|
|000000f0| dd b0 a2 eb 00 00 00 00 | 00 35 00 10 01 8b 02 10 |........|.5......|
|00000100| 00 00 00 00 02 70 03 40 | 00 00 00 00 00 00 00 00 |.....p.@|........|
|00000110| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000120| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000130| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000140| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000150| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000160| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000170| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000180| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000190| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000001a0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000001b0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000001c0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000001d0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000001e0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000001f0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000200| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000210| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000220| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000230| 00 00 0d 6e 00 00 0c 0b | 01 56 02 00 00 00 00 00 |...n....|.V......|
|00000240| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000250| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000260| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000270| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000280| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000290| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000002a0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000002b0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000002c0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000002d0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000002e0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000002f0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000300| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000310| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000320| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000330| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000340| 00 00 00 00 00 00 00 00 | 80 00 00 00 08 00 00 00 |........|........|
|00000350| 88 00 22 00 88 00 22 00 | 88 88 22 22 88 88 22 22 |.."...".|..""..""|
|00000360| 88 aa 22 aa 88 aa 22 aa | cc aa 33 aa cc aa 33 aa |.."...".|..3...3.|
|00000370| ee aa bb aa ee aa bb aa | ee bb bb ee ee bb bb ee |........|........|
|00000380| ff bb ff ee ff bb ff ee | ff bb ff ff ff bb ff ff |........|........|
|00000390| 80 10 02 20 01 08 40 04 | ff ff ff ff ff ff ff ff |... ..@.|........|
|000003a0| 88 22 88 22 88 22 88 22 | 11 22 44 88 11 22 44 88 |."."."."|."D.."D.|
|000003b0| c4 80 0c 68 43 02 30 26 | b1 30 03 1b d8 c0 0c 8d |...hC.0&|.0......|
|000003c0| aa 00 aa 00 aa 00 aa 00 | 88 22 55 22 88 22 55 22 |........|."U"."U"|
|000003d0| 88 55 22 55 88 55 22 55 | 77 dd 77 dd 77 dd 77 dd |.U"U.U"U|w.w.w.w.|
|000003e0| 80 00 00 00 00 00 00 00 | aa 55 aa 55 aa 55 aa 55 |........|.U.U.U.U|
|000003f0| 03 84 48 30 0c 02 01 01 | 82 44 39 44 82 01 01 01 |..H0....|.D9D....|
|00000400| 88 14 22 41 88 41 22 14 | 80 80 41 3e 08 08 14 e3 |.."A.A".|..A>....|
|00000410| 22 04 8c 74 22 17 98 10 | be 80 88 08 eb 08 88 80 |"..t"...|........|
|00000420| 25 c8 32 89 64 24 4c 92 | a2 9c 41 be 2a c9 14 eb |%.2.d$L.|..A.*...|
|00000430| 40 a0 00 00 04 0a 00 00 | 80 40 20 00 02 04 08 00 |@.......|.@ .....|
|00000440| aa 00 80 00 88 00 80 00 | ff 80 80 80 80 80 80 80 |........|........|
|00000450| 08 1c 22 c1 80 01 02 04 | ff 80 80 80 ff 08 08 08 |..".....|........|
|00000460| f8 74 22 47 8f 17 22 71 | bf 00 bf bf b0 b0 b0 b0 |.t"G.."q|........|
|00000470| ff 7f be 5d a2 41 80 00 | fa f5 fa f5 a0 50 a0 50 |...].A..|.....P.P|
|00000480| 00 00 1a 40 00 00 12 20 | 00 00 2e 60 00 00 07 60 |...@... |...`...`|
|00000490| 00 00 37 a0 00 00 19 c0 | 00 00 6e a0 00 00 31 40 |..7.....|..n...1@|
|000004a0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000004b0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000004c0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000004d0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000004e0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000004f0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000500| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000510| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000520| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000530| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000540| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000550| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000560| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000570| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000580| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000590| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000005a0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000005b0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000005c0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000005d0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000005e0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000005f0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000600| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000610| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000620| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000630| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000640| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000650| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000660| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000670| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000680| 6f 6e 20 63 6c 6f 73 65 | 53 74 61 63 6b 0d 73 65 |on close|Stack.se|
|00000690| 74 20 74 68 65 20 73 74 | 79 6c 65 20 6f 66 20 63 |t the st|yle of c|
|000006a0| 64 20 66 6c 64 20 34 20 | 74 6f 20 22 72 65 63 74 |d fld 4 |to "rect|
|000006b0| 61 6e 67 6c 65 22 0d 70 | 75 74 20 22 32 22 20 69 |angle".p|ut "2" i|
|000006c0| 6e 74 6f 20 63 64 20 66 | 6c 64 20 38 0d 70 75 74 |nto cd f|ld 8.put|
|000006d0| 20 22 34 22 20 69 6e 74 | 6f 20 63 64 20 66 6c 64 | "4" int|o cd fld|
|000006e0| 20 39 0d 65 6e 64 20 63 | 6c 6f 73 65 53 74 61 63 | 9.end c|loseStac|
|000006f0| 6b 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |k.......|........|
|00000700| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000710| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000720| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000730| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000740| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000750| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000760| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000770| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000780| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000790| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000007a0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000007b0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000007c0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000007d0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000007e0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000007f0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000800| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000810| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000820| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000830| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000840| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000850| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000860| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000870| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000880| 00 00 02 00 4d 41 53 54 | ff ff ff ff 00 00 00 00 |....MAST|........|
|00000890| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000008a0| 00 01 63 b5 00 01 b3 f5 | 00 00 94 d7 00 02 8b 81 |..c.....|........|
|000008b0| 00 01 ae 0b 00 01 b1 6e | 00 00 00 00 00 00 00 00 |.......n|........|
|000008c0| 00 00 96 3a 00 00 50 ed | 00 00 54 11 00 00 00 00 |...:..P.|..T.....|
|000008d0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000008e0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000008f0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000900| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000910| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000920| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000930| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000940| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000950| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000960| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000970| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000980| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000990| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000009a0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000009b0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000009c0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000009d0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000009e0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000009f0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000a00| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000a10| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000a20| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000a30| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000a40| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000a50| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000a60| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000a70| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000a80| 00 00 00 80 4c 49 53 54 | 00 00 11 ed 00 00 00 00 |....LIST|........|
|00000a90| 00 00 00 01 00 00 08 00 | 00 00 00 02 00 70 00 02 |........|.....p..|
|00000aa0| 00 1b 00 03 20 00 02 44 | 00 00 00 02 00 00 00 00 |.... ..D|........|
|00000ab0| 00 00 12 11 00 02 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000ac0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000ad0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000ae0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000af0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000b00| 00 00 08 00 50 41 47 45 | 00 00 12 11 00 00 00 00 |....PAGE|........|
|00000b10| 00 00 11 ed 44 00 02 35 | 00 00 0b 81 60 12 82 88 |....D..5|....`...|
|00000b20| 51 40 88 0e 10 01 c4 00 | 00 44 00 a2 0a 20 03 08 |Q@......|.D... ..|
|00000b30| 44 00 79 00 00 20 00 00 | a5 30 10 a2 14 10 02 00 |D.y.. ..|.0......|
|00000b40| 00 00 49 81 0c e0 05 00 | 80 00 59 80 08 14 08 20 |..I.....|..Y.... |
|00000b50| 83 00 18 00 05 40 0e 38 | 83 8c 7d c0 08 44 01 32 |.....@.8|..}..D.2|
|00000b60| 80 84 02 0c 40 20 1a 60 | 02 00 00 40 08 80 14 5a |....@ .`|...@...Z|
|00000b70| 82 90 00 00 08 00 04 00 | 0a 20 01 46 00 35 04 42 |........|. .F.5.B|
|00000b80| 00 30 03 0a 28 c3 04 00 | 00 00 10 3a 20 5e 0a e1 |.0..(...|...: ^..|
|00000b90| 42 9a 55 df b8 28 0a bf | b9 f9 3f c8 1a 28 9c 8e |B.U..(..|..?..(..|
|00000ba0| 19 df 59 39 13 25 b9 1d | 04 27 1c c6 f7 56 cc f5 |..Y9.%..|.'...V..|
|00000bb0| c9 d9 df ef 8f 13 c8 ba | b5 ea a5 e9 f7 b3 e0 43 |........|.......C|
|00000bc0| 08 94 97 69 71 2a 63 82 | 00 ac c8 6d 7f ef 74 d3 |...iq*c.|...m..t.|
|00000bd0| 3d c1 6f 84 98 f0 b1 f0 | 3b 87 69 bc 0a f5 ea ee |=.o.....|;.i.....|
|00000be0| b5 ea c9 f5 5a 2a 97 c5 | a9 75 ab 2f 2a be 75 5a |....Z*..|.u./*.uZ|
|00000bf0| 0f dc e3 67 b9 b2 3b c8 | 00 00 00 00 00 00 00 00 |...g..;.|........|
|00000c00| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000c10| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000c20| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000c30| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000c40| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000c50| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000c60| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000c70| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000c80| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000c90| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000ca0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000cb0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000cc0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000cd0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000ce0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000cf0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000d00| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000d10| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000d20| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000d30| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000d40| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000d50| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000d60| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000d70| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000d80| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000d90| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000da0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000db0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000dc0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000dd0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000de0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000df0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000e00| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000e10| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000e20| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000e30| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000e40| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000e50| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000e60| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000e70| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000e80| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000e90| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000ea0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000eb0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000ec0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000ed0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000ee0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000ef0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000f00| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000f10| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000f20| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000f30| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000f40| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000f50| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000f60| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000f70| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000f80| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000f90| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000fa0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000fb0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000fc0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000fd0| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
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|00001330| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
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|00001390| 00 00 00 10 00 00 00 00 | 00 72 00 02 01 00 01 3b |........|.r.....;|
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|00001410| 00 00 00 01 05 3e 00 03 | 05 43 00 01 05 69 00 03 |.....>..|.C...i..|
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|000017e0| 74 6f 6e 20 22 43 6c 65 | 61 72 22 20 63 6c 65 61 |ton "Cle|ar" clea|
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|000018d0| 73 65 20 63 61 6c 63 75 | 6c 61 74 69 6f 6e 73 2e |se calcu|lations.|
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|00001910| 20 6f 76 65 72 6c 61 70 | 20 61 6e 64 20 6d 69 6e | overlap| and min|
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|00001930| 65 6d 20 6f 66 20 34 20 | 62 61 73 65 20 70 61 69 |em of 4 |base pai|
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|00001950| 65 64 20 61 73 20 6e 65 | 65 64 65 64 2e 0d 0d 31 |ed as ne|eded...1|
|00001960| 2e 20 52 79 63 68 6c 69 | 6b 20 65 74 20 61 6c 20 |. Rychli|k et al |
|00001970| 20 28 31 39 39 30 29 20 | 4e 41 52 20 31 38 2c 20 | (1990) |NAR 18, |
|00001980| 36 34 30 39 2d 36 34 31 | 32 2e 0d 32 2e 20 46 72 |6409-641|2..2. Fr|
|00001990| 65 69 65 72 20 65 74 20 | 61 6c 20 20 28 31 39 38 |eier et |al  (198|
|000019a0| 36 29 2c 20 50 4e 41 53 | 20 38 33 2c 20 39 33 37 |6), PNAS| 83, 937|
|000019b0| 33 2d 39 33 37 37 2e 0d | 33 2e 20 42 72 65 73 6c |3-9377..|3. Bresl|
|000019c0| 61 75 65 72 20 65 74 20 | 61 6c 20 20 28 31 39 38 |auer et |al  (198|
|000019d0| 36 29 2c 20 50 4e 41 53 | 20 38 33 2c 20 33 37 34 |6), PNAS| 83, 374|
|000019e0| 36 2d 33 37 35 30 2e 0d | 34 2e 20 52 79 63 68 6c |6-3750..|4. Rychl|
|000019f0| 69 6b 2c 20 57 2e 2c 20 | 61 6e 64 20 52 68 6f 61 |ik, W., |and Rhoa|
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|00001a60| 41 6c 62 61 6e 79 20 43 | 41 20 39 34 37 31 30 00 |Albany C|A 94710.|
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|00001ad0| 0f 46 72 65 65 20 4f 62 | 6a 65 63 74 20 20 20 20 |.Free Ob|ject    |
|00001ae0| 00 00 00 00 00 00 00 01 | 00 16 00 0c 01 00 00 10 |........|........|
|00001af0| 00 00 00 00 00 22 00 12 | 02 04 00 40 01 12 00 4f |....."..|...@...O|
|00001b00| 01 f6 00 00 00 00 00 00 | 00 01 00 16 00 0c 01 00 |........|........|
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|00001b20| 00 fd 01 f7 00 00 00 00 | 00 00 00 01 00 16 00 0c |........|........|
|00001b30| 01 00 00 10 00 00 00 00 | 00 22 00 0b 02 04 01 14 |........|."......|
|00001b40| 01 de 01 25 01 f7 00 02 | 00 00 00 00 00 00 00 16 |...%....|........|
|00001b50| 00 0e 00 00 00 12 00 00 | 00 00 00 22 00 10 02 04 |........|..."....|
|00001b60| 01 02 01 de 01 13 01 f7 | 00 02 00 00 00 00 00 00 |........|........|
|00001b70| 00 16 00 0e 00 00 00 12 | 00 00 00 00 00 76 00 14 |........|.....v..|
|00001b80| 01 00 01 03 00 56 01 19 | 00 99 a0 02 00 00 00 00 |.....V..|........|
|00001b90| 00 01 00 00 00 0c 00 00 | 00 10 43 6c 65 61 72 00 |........|..Clear.|
|00001ba0| 00 6f 6e 20 6d 6f 75 73 | 65 55 70 0d 72 65 70 65 |.on mous|eUp.repe|
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|00001c00| 00 13 00 74 67 74 67 74 | 63 74 63 74 67 67 67 61 |...tgtgt|ctctggga|
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|00001c50| 47 43 54 43 47 47 54 41 | 43 43 43 47 47 47 61 61 |GCTCGGTA|CCCGGGaa|
|00001c60| 74 74 67 74 67 61 67 63 | 67 63 74 63 61 63 61 61 |ttgtgagc|gctcacaa|
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|00001c80| 61 61 63 61 61 74 74 74 | 63 61 63 61 63 61 67 67 |aacaattt|cacacagg|
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|00001cb0| 2e 00 ff ee 00 0b 00 54 | 6d 20 3d 20 34 35 2e 36 |.......T|m = 45.6|
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|00001da0| 74 65 73 20 6d 65 6c 74 | 69 6e 67 20 74 65 6d 70 |tes melt|ing temp|
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|00001dc0| 47 20 2b 20 43 0d 72 65 | 74 75 72 6e 20 28 2e 34 |G + C.re|turn (.4|
|00001dd0| 31 20 2a 20 75 29 20 2b | 20 36 34 2e 39 20 2d 20 |1 * u) +| 64.9 - |
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|00001e50| 70 75 74 20 22 67 63 22 | 20 69 6e 74 6f 20 62 61 |put "gc"| into ba|
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|00002390| 74 68 65 4f 6c 69 67 6f | 29 20 69 6e 74 6f 20 69 |theOligo|) into i|
|000023a0| 74 73 4c 65 6e 67 74 68 | 0d 72 65 70 65 61 74 20 |tsLength|.repeat |
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|000023d0| 72 65 70 65 61 74 20 77 | 69 74 68 20 7a 20 3d 20 |repeat w|ith z = |
|000023e0| 30 20 74 6f 20 69 74 73 | 4c 65 6e 67 74 68 20 2d |0 to its|Length -|
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|00002430| 20 7a 20 2b 20 79 20 2b | 20 31 20 6f 66 20 c2 0d | z + y +| 1 of ..|
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|00002460| 70 65 61 74 0d 65 6c 73 | 65 0d 69 66 20 7a 20 3c |peat.els|e.if z <|
|00002470| 20 73 74 65 6d 53 69 7a | 65 20 74 68 65 6e 20 65 | stemSiz|e then e|
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|000024a0| 66 20 6f 6c 69 67 6f 20 | 22 20 26 20 69 74 73 4e |f oligo |" & itsN|
|000024b0| 75 6d 62 65 72 20 26 26 | 20 22 70 61 69 72 73 20 |umber &&| "pairs |
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|00002540| 20 63 64 20 66 6c 64 20 | 34 20 3e 20 32 30 31 20 | cd fld |4 > 201 |
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|000025b0| 61 6e 64 20 66 20 69 73 | 20 22 63 22 20 74 68 65 |and f is| "c" the|
|000025c0| 6e 20 72 65 74 75 72 6e | 20 22 74 72 75 65 22 0d |n return| "true".|
|000025d0| 69 66 20 65 20 69 73 20 | 22 63 22 20 61 6e 64 20 |if e is |"c" and |
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|00002610| 20 22 74 22 20 74 68 65 | 6e 20 72 65 74 75 72 6e | "t" the|n return|
|00002620| 20 22 74 72 75 65 22 0d | 69 66 20 65 20 69 73 20 | "true".|if e is |
|00002630| 22 74 22 20 61 6e 64 20 | 66 20 69 73 20 22 61 22 |"t" and |f is "a"|
|00002640| 20 74 68 65 6e 20 72 65 | 74 75 72 6e 20 22 74 72 | then re|turn "tr|
|00002650| 75 65 22 0d 65 6e 64 20 | 70 61 69 72 69 6e 67 0d |ue".end |pairing.|
|00002660| 0d 66 75 6e 63 74 69 6f | 6e 20 64 48 20 78 2c 79 |.functio|n dH x,y|
|00002670| 0d 2d 2d 20 72 65 74 75 | 72 6e 73 20 65 6e 74 68 |.-- retu|rns enth|
|00002680| 61 6c 70 69 65 73 20 6f | 66 20 61 64 6a 61 63 65 |alpies o|f adjace|
|00002690| 6e 74 20 70 61 69 72 73 | 0d 69 66 20 78 20 69 73 |nt pairs|.if x is|
|000026a0| 20 22 61 22 20 74 68 65 | 6e 0d 69 66 20 79 20 69 | "a" the|n.if y i|
|000026b0| 73 20 22 61 22 20 74 68 | 65 6e 20 72 65 74 75 72 |s "a" th|en retur|
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|000026d0| 22 74 22 20 74 68 65 6e | 20 72 65 74 75 72 6e 20 |"t" then| return |
|000026e0| 22 38 2e 36 22 0d 69 66 | 20 79 20 69 73 20 22 67 |"8.6".if| y is "g|
|000026f0| 22 20 74 68 65 6e 20 72 | 65 74 75 72 6e 20 22 37 |" then r|eturn "7|
|00002700| 2e 38 22 0d 69 66 20 79 | 20 69 73 20 22 63 22 20 |.8".if y| is "c" |
|00002710| 74 68 65 6e 20 72 65 74 | 75 72 6e 20 22 36 2e 35 |then ret|urn "6.5|
|00002720| 22 0d 65 6e 64 20 69 66 | 0d 69 66 20 78 20 69 73 |".end if|.if x is|
|00002730| 20 22 74 22 20 74 68 65 | 6e 0d 69 66 20 79 20 69 | "t" the|n.if y i|
|00002740| 73 20 22 61 22 20 74 68 | 65 6e 20 72 65 74 75 72 |s "a" th|en retur|
|00002750| 6e 20 22 36 22 0d 69 66 | 20 79 20 69 73 20 22 74 |n "6".if| y is "t|
|00002760| 22 20 74 68 65 6e 20 72 | 65 74 75 72 6e 20 22 39 |" then r|eturn "9|
|00002770| 2e 31 22 0d 69 66 20 79 | 20 69 73 20 22 67 22 20 |.1".if y| is "g" |
|00002780| 74 68 65 6e 20 72 65 74 | 75 72 6e 20 22 35 2e 38 |then ret|urn "5.8|
|00002790| 22 0d 69 66 20 79 20 69 | 73 20 22 63 22 20 74 68 |".if y i|s "c" th|
|000027a0| 65 6e 20 72 65 74 75 72 | 6e 20 22 35 2e 36 22 0d |en retur|n "5.6".|
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|000027c0| 67 22 20 74 68 65 6e 0d | 69 66 20 79 20 69 73 20 |g" then.|if y is |
|000027d0| 22 61 22 20 74 68 65 6e | 20 72 65 74 75 72 6e 20 |"a" then| return |
|000027e0| 22 35 2e 36 22 0d 69 66 | 20 79 20 69 73 20 22 74 |"5.6".if| y is "t|
|000027f0| 22 20 74 68 65 6e 20 72 | 65 74 75 72 6e 20 22 36 |" then r|eturn "6|
|00002800| 2e 35 22 0d 69 66 20 79 | 20 69 73 20 22 67 22 20 |.5".if y| is "g" |
|00002810| 74 68 65 6e 20 72 65 74 | 75 72 6e 20 22 31 31 22 |then ret|urn "11"|
|00002820| 0d 69 66 20 79 20 69 73 | 20 22 63 22 20 74 68 65 |.if y is| "c" the|
|00002830| 6e 20 72 65 74 75 72 6e | 20 22 31 31 2e 31 22 0d |n return| "11.1".|
|00002840| 65 6e 64 20 69 66 0d 69 | 66 20 78 20 69 73 20 22 |end if.i|f x is "|
|00002850| 63 22 20 74 68 65 6e 0d | 69 66 20 79 20 69 73 20 |c" then.|if y is |
|00002860| 22 61 22 20 74 68 65 6e | 20 72 65 74 75 72 6e 20 |"a" then| return |
|00002870| 22 35 2e 38 22 0d 69 66 | 20 79 20 69 73 20 22 74 |"5.8".if| y is "t|
|00002880| 22 20 74 68 65 6e 20 72 | 65 74 75 72 6e 20 22 37 |" then r|eturn "7|
|00002890| 2e 38 22 0d 69 66 20 79 | 20 69 73 20 22 67 22 20 |.8".if y| is "g" |
|000028a0| 74 68 65 6e 20 72 65 74 | 75 72 6e 20 22 31 31 2e |then ret|urn "11.|
|000028b0| 39 22 0d 69 66 20 79 20 | 69 73 20 22 63 22 20 74 |9".if y |is "c" t|
|000028c0| 68 65 6e 20 72 65 74 75 | 72 6e 20 22 31 31 22 0d |hen retu|rn "11".|
|000028d0| 65 6e 64 20 69 66 0d 65 | 6e 64 20 64 48 0d 0d 66 |end if.e|nd dH..f|
|000028e0| 75 6e 63 74 69 6f 6e 20 | 64 53 20 78 2c 79 0d 2d |unction |dS x,y.-|
|000028f0| 2d 20 72 65 74 75 72 6e | 73 20 65 6e 74 72 6f 70 |- return|s entrop|
|00002900| 69 65 73 20 6f 66 20 61 | 64 6a 61 63 65 6e 74 20 |ies of a|djacent |
|00002910| 70 61 69 72 73 0d 69 66 | 20 78 20 69 73 20 22 61 |pairs.if| x is "a|
|00002920| 22 20 74 68 65 6e 0d 69 | 66 20 79 20 69 73 20 22 |" then.i|f y is "|
|00002930| 61 22 20 74 68 65 6e 20 | 72 65 74 75 72 6e 20 22 |a" then |return "|
|00002940| 32 34 22 0d 69 66 20 79 | 20 69 73 20 22 74 22 20 |24".if y| is "t" |
|00002950| 74 68 65 6e 20 72 65 74 | 75 72 6e 20 22 32 33 2e |then ret|urn "23.|
|00002960| 39 22 0d 69 66 20 79 20 | 69 73 20 22 67 22 20 74 |9".if y |is "g" t|
|00002970| 68 65 6e 20 72 65 74 75 | 72 6e 20 22 32 30 2e 38 |hen retu|rn "20.8|
|00002980| 22 0d 69 66 20 79 20 69 | 73 20 22 63 22 20 74 68 |".if y i|s "c" th|
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|000029b0| 22 74 22 20 74 68 65 6e | 0d 69 66 20 79 20 69 73 |"t" then|.if y is|
|000029c0| 20 22 61 22 20 74 68 65 | 6e 20 72 65 74 75 72 6e | "a" the|n return|
|000029d0| 20 22 31 36 2e 39 22 0d | 69 66 20 79 20 69 73 20 | "16.9".|if y is |
|000029e0| 22 74 22 20 74 68 65 6e | 20 72 65 74 75 72 6e 20 |"t" then| return |
|000029f0| 22 32 34 22 0d 69 66 20 | 79 20 69 73 20 22 67 22 |"24".if |y is "g"|
|00002a00| 20 74 68 65 6e 20 72 65 | 74 75 72 6e 20 22 31 32 | then re|turn "12|
|00002a10| 2e 39 22 0d 69 66 20 79 | 20 69 73 20 22 63 22 20 |.9".if y| is "c" |
|00002a20| 74 68 65 6e 20 72 65 74 | 75 72 6e 20 22 31 33 2e |then ret|urn "13.|
|00002a30| 35 22 0d 65 6e 64 20 69 | 66 0d 69 66 20 78 20 69 |5".end i|f.if x i|
|00002a40| 73 20 22 67 22 20 74 68 | 65 6e 0d 69 66 20 79 20 |s "g" th|en.if y |
|00002a50| 69 73 20 22 61 22 20 74 | 68 65 6e 20 72 65 74 75 |is "a" t|hen retu|
|00002a60| 72 6e 20 22 31 33 2e 35 | 22 0d 69 66 20 79 20 69 |rn "13.5|".if y i|
|00002a70| 73 20 22 74 22 20 74 68 | 65 6e 20 72 65 74 75 72 |s "t" th|en retur|
|00002a80| 6e 20 22 31 37 2e 33 22 | 0d 69 66 20 79 20 69 73 |n "17.3"|.if y is|
|00002a90| 20 22 67 22 20 74 68 65 | 6e 20 72 65 74 75 72 6e | "g" the|n return|
|00002aa0| 20 22 32 36 2e 36 22 0d | 69 66 20 79 20 69 73 20 | "26.6".|if y is |
|00002ab0| 22 63 22 20 74 68 65 6e | 20 72 65 74 75 72 6e 20 |"c" then| return |
|00002ac0| 22 32 36 2e 37 22 0d 65 | 6e 64 20 69 66 0d 69 66 |"26.7".e|nd if.if|
|00002ad0| 20 78 20 69 73 20 22 63 | 22 20 74 68 65 6e 0d 69 | x is "c|" then.i|
|00002ae0| 66 20 79 20 69 73 20 22 | 61 22 20 74 68 65 6e 20 |f y is "|a" then |
|00002af0| 72 65 74 75 72 6e 20 22 | 31 32 2e 39 22 0d 69 66 |return "|12.9".if|
|00002b00| 20 79 20 69 73 20 22 74 | 22 20 74 68 65 6e 20 72 | y is "t|" then r|
|00002b10| 65 74 75 72 6e 20 22 32 | 30 2e 38 22 0d 69 66 20 |eturn "2|0.8".if |
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|00002b30| 74 75 72 6e 20 22 32 37 | 2e 38 22 0d 69 66 20 79 |turn "27|.8".if y|
|00002b40| 20 69 73 20 22 63 22 20 | 74 68 65 6e 20 72 65 74 | is "c" |then ret|
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|00002b70| 65 72 74 4d 65 20 78 0d | 70 75 74 20 77 6f 72 64 |ertMe x.|put word|
|00002b80| 20 31 20 6f 66 20 63 64 | 20 66 6c 64 20 78 20 69 | 1 of cd| fld x i|
|00002b90| 6e 74 6f 20 73 74 72 61 | 6e 64 6f 6e 65 0d 70 75 |nto stra|ndone.pu|
|00002ba0| 74 20 65 6d 70 74 79 20 | 69 6e 74 6f 20 73 74 72 |t empty |into str|
|00002bb0| 61 6e 64 74 77 6f 0d 72 | 65 70 65 61 74 20 77 69 |andtwo.r|epeat wi|
|00002bc0| 74 68 20 7a 20 3d 20 31 | 20 74 6f 20 74 68 65 20 |th z = 1| to the |
|00002bd0| 6e 75 6d 62 65 72 20 6f | 66 20 63 68 61 72 73 20 |number o|f chars |
|00002be0| 69 6e 20 73 74 72 61 6e | 64 6f 6e 65 0d 70 75 74 |in stran|done.put|
|00002bf0| 20 69 6e 76 65 72 74 28 | 63 68 61 72 20 7a 20 6f | invert(|char z o|
|00002c00| 66 20 73 74 72 61 6e 64 | 6f 6e 65 29 20 62 65 66 |f strand|one) bef|
|00002c10| 6f 72 65 20 73 74 72 61 | 6e 64 74 77 6f 0d 65 6e |ore stra|ndtwo.en|
|00002c20| 64 20 72 65 70 65 61 74 | 0d 70 75 74 20 73 74 72 |d repeat|.put str|
|00002c30| 61 6e 64 74 77 6f 20 69 | 6e 74 6f 20 63 64 20 66 |andtwo i|nto cd f|
|00002c40| 6c 64 20 78 0d 65 6e 64 | 20 69 6e 76 65 72 74 4d |ld x.end| invertM|
|00002c50| 65 0d 0d 66 75 6e 63 74 | 69 6f 6e 20 69 6e 76 65 |e..funct|ion inve|
|00002c60| 72 74 20 78 0d 69 66 20 | 78 20 69 73 20 22 67 22 |rt x.if |x is "g"|
|00002c70| 20 74 68 65 6e 20 72 65 | 74 75 72 6e 20 22 63 22 | then re|turn "c"|
|00002c80| 0d 69 66 20 78 20 69 73 | 20 22 61 22 20 74 68 65 |.if x is| "a" the|
|00002c90| 6e 20 72 65 74 75 72 6e | 20 22 74 22 0d 69 66 20 |n return| "t".if |
|00002ca0| 78 20 69 73 20 22 74 22 | 20 74 68 65 6e 20 72 65 |x is "t"| then re|
|00002cb0| 74 75 72 6e 20 22 61 22 | 0d 69 66 20 78 20 69 73 |turn "a"|.if x is|
|00002cc0| 20 22 63 22 20 74 68 65 | 6e 20 72 65 74 75 72 6e | "c" the|n return|
|00002cd0| 20 22 67 22 0d 65 6e 64 | 20 69 6e 76 65 72 74 00 | "g".end| invert.|
|00002ce0| 00 00 02 00 42 4d 41 50 | 00 00 08 b5 00 00 00 00 |....BMAP|........|
|00002cf0| 00 00 00 00 00 01 00 00 | 00 00 00 00 01 56 02 00 |........|.....V..|
|00002d00| 00 00 00 00 00 00 00 00 | 00 1b 00 07 01 22 01 d8 |........|....."..|
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|00002d40| 2e 0f c0 e1 0a 11 0c e1 | 1f 60 e1 0a a2 85 20 01 |........|.`.... .|
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|00002d80| 80 e2 0c 3d 10 00 40 e2 | 0c a2 85 3d 20 00 20 e2 |...=..@.|...= . .|
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|00002f00| 00 00 12 11 00 00 0a d7 | 00 02 00 03 00 00 00 94 |........|........|
|00002f10| 00 01 00 00 06 5a 00 22 | 00 01 02 00 00 15 00 02 |.....Z."|........|
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|00002f80| 76 69 73 75 61 6c 20 73 | 68 72 69 6e 6b 20 74 6f |visual s|hrink to|
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|00002fb0| 00 00 00 01 05 43 00 03 | 05 48 00 01 05 6e 00 03 |.....C..|.H...n..|
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|000031d0| 61 6c 6c 20 66 69 65 6c | 64 73 20 6f 6e 20 74 6f |all fiel|ds on to|
|000031e0| 70 2e 20 43 6f 6d 6d 61 | 6e 64 2d 63 6c 69 63 6b |p. Comma|nd-click|
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|00003390| 20 63 6c 65 61 72 73 20 | 74 68 65 20 66 69 65 6c | clears |the fiel|
|000033a0| 64 73 20 73 68 6f 77 69 | 6e 67 20 74 68 65 20 54 |ds showi|ng the T|
|000033b0| 6d 27 73 2e 0d 0d 48 79 | 70 65 72 50 43 52 20 61 |m's...Hy|perPCR a|
|000033c0| 75 74 6f 6d 61 74 69 63 | 61 6c 6c 79 20 63 68 65 |utomatic|ally che|
|000033d0| 63 6b 73 20 66 6f 72 20 | 63 6f 6d 70 6c 65 6d 65 |cks for |compleme|
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|000034c0| 64 20 6d 69 6e 69 6d 75 | 6d 20 69 6e 74 65 72 6e |d minimu|m intern|
|000034d0| 61 6c 20 73 74 65 6d 20 | 6f 66 20 34 20 62 61 73 |al stem |of 4 bas|
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|00003530| 32 2e 20 46 72 65 69 65 | 72 20 65 74 20 61 6c 20 |2. Freie|r et al |
|00003540| 20 28 31 39 38 36 29 2c | 20 50 4e 41 53 20 38 33 | (1986),| PNAS 83|
|00003550| 2c 20 39 33 37 33 2d 39 | 33 37 37 2e 0d 33 2e 20 |, 9373-9|377..3. |
|00003560| 42 72 65 73 6c 61 75 65 | 72 20 65 74 20 61 6c 20 |Breslaue|r et al |
|00003570| 20 28 31 39 38 36 29 2c | 20 50 4e 41 53 20 38 33 | (1986),| PNAS 83|
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|00003a20| 70 75 74 20 4f 6c 69 67 | 6f 22 20 26 20 6a 20 26 |put Olig|o" & j &|
|00003a30| 26 20 22 69 6e 74 6f 20 | 63 64 20 66 6c 64 22 20 |& "into |cd fld" |
|00003a40| 26 26 20 6a 0d 65 6e 64 | 20 72 65 70 65 61 74 0d |&& j.end| repeat.|
|00003a50| 73 65 74 20 6e 75 6d 62 | 65 72 46 6f 72 6d 61 74 |set numb|erFormat|
|00003a60| 20 74 6f 20 22 30 30 2e | 30 22 0d 73 65 74 20 73 | to "00.|0".set s|
|00003a70| 74 79 6c 65 20 6f 66 20 | 63 64 20 66 6c 64 20 34 |tyle of |cd fld 4|
|00003a80| 20 74 6f 20 22 72 65 63 | 74 61 6e 67 6c 65 22 0d | to "rec|tangle".|
|00003a90| 69 66 20 77 6f 72 64 20 | 31 20 6f 66 20 63 64 20 |if word |1 of cd |
|00003aa0| 66 6c 64 20 33 20 69 73 | 20 65 6d 70 74 79 20 74 |fld 3 is| empty t|
|00003ab0| 68 65 6e 0d 61 73 6b 20 | 22 45 73 74 69 6d 61 74 |hen.ask |"Estimat|
|00003ac0| 65 64 20 25 47 43 20 6f | 66 20 74 65 6d 70 6c 61 |ed %GC o|f templa|
|00003ad0| 74 65 3f 22 0d 69 66 20 | 69 74 20 69 73 20 65 6d |te?".if |it is em|
|00003ae0| 70 74 79 20 74 68 65 6e | 20 65 78 69 74 20 6d 6f |pty then| exit mo|
|00003af0| 75 73 65 55 70 0d 70 75 | 74 20 69 74 20 69 6e 74 |useUp.pu|t it int|
|00003b00| 6f 20 70 65 72 63 65 6e | 74 47 61 6e 64 43 0d 61 |o percen|tGandC.a|
|00003b10| 73 6b 20 22 45 73 74 69 | 6d 61 74 65 64 20 6c 65 |sk "Esti|mated le|
|00003b20| 6e 67 74 68 20 6f 66 20 | 70 72 6f 64 75 63 74 3f |ngth of |product?|
|00003b30| 22 0d 69 66 20 69 74 20 | 69 73 20 65 6d 70 74 79 |".if it |is empty|
|00003b40| 20 74 68 65 6e 20 65 78 | 69 74 20 6d 6f 75 73 65 | then ex|it mouse|
|00003b50| 55 70 0d 70 75 74 20 69 | 74 20 69 6e 74 6f 20 70 |Up.put i|t into p|
|00003b60| 72 6f 64 75 63 74 4c 0d | 65 6c 73 65 0d 72 65 70 |roductL.|else.rep|
|00003b70| 65 61 74 20 77 69 74 68 | 20 7a 20 3d 20 31 20 74 |eat with| z = 1 t|
|00003b80| 6f 20 6e 75 6d 62 65 72 | 20 6f 66 20 77 6f 72 64 |o number| of word|
|00003b90| 73 20 69 6e 20 63 64 20 | 66 6c 64 20 33 0d 70 75 |s in cd |fld 3.pu|
|00003ba0| 74 20 77 6f 72 64 20 7a | 20 6f 66 20 63 64 20 66 |t word z| of cd f|
|00003bb0| 6c 64 20 33 20 61 66 74 | 65 72 20 74 65 6d 70 6c |ld 3 aft|er templ|
|00003bc0| 61 74 65 0d 65 6e 64 20 | 72 65 70 65 61 74 0d 70 |ate.end |repeat.p|
|00003bd0| 75 74 20 70 65 72 63 65 | 6e 74 47 43 28 74 65 6d |ut perce|ntGC(tem|
|00003be0| 70 6c 61 74 65 29 20 69 | 6e 74 6f 20 70 65 72 63 |plate) i|nto perc|
|00003bf0| 65 6e 74 47 61 6e 64 43 | 0d 70 75 74 20 6c 65 6e |entGandC|.put len|
|00003c00| 67 74 68 28 74 65 6d 70 | 6c 61 74 65 29 20 69 6e |gth(temp|late) in|
|00003c10| 74 6f 20 70 72 6f 64 75 | 63 74 4c 0d 65 6e 64 20 |to produ|ctL.end |
|00003c20| 69 66 0d 70 75 74 20 70 | 72 6f 64 75 63 74 54 65 |if.put p|roductTe|
|00003c30| 6d 70 28 70 65 72 63 65 | 6e 74 47 61 6e 64 43 2c |mp(perce|ntGandC,|
|00003c40| 70 72 6f 64 75 63 74 4c | 29 20 69 6e 74 6f 20 70 |productL|) into p|
|00003c50| 54 65 6d 70 0d 69 66 20 | 77 6f 72 64 20 31 20 6f |Temp.if |word 1 o|
|00003c60| 66 20 63 64 20 66 6c 64 | 20 33 20 69 73 20 65 6d |f cd fld| 3 is em|
|00003c70| 70 74 79 20 74 68 65 6e | 0d 70 75 74 20 22 54 6d |pty then|.put "Tm|
|00003c80| 20 6f 66 20 65 73 74 69 | 6d 61 74 65 64 20 70 72 | of esti|mated pr|
|00003c90| 6f 64 75 63 74 20 3d 20 | 22 20 26 20 70 54 65 6d |oduct = |" & pTem|
|00003ca0| 70 20 26 20 22 2e 22 20 | 26 20 72 65 74 75 72 6e |p & "." |& return|
|00003cb0| 20 69 6e 74 6f 20 63 64 | 20 66 6c 64 20 37 0d 65 | into cd| fld 7.e|
|00003cc0| 6c 73 65 0d 70 75 74 20 | 22 54 6d 20 3d 20 22 20 |lse.put |"Tm = " |
|00003cd0| 26 20 70 54 65 6d 70 20 | 26 20 22 2e 22 20 26 20 |& pTemp |& "." & |
|00003ce0| 72 65 74 75 72 6e 20 69 | 6e 74 6f 20 63 64 20 66 |return i|nto cd f|
|00003cf0| 6c 64 20 37 0d 65 6e 64 | 20 69 66 0d 70 75 74 20 |ld 7.end| if.put |
|00003d00| 6f 6c 69 67 6f 54 65 6d | 70 28 4f 6c 69 67 6f 31 |oligoTem|p(Oligo1|
|00003d10| 29 20 69 6e 74 6f 20 6f | 6e 65 54 65 6d 70 0d 70 |) into o|neTemp.p|
|00003d20| 75 74 20 22 54 6d 20 3d | 20 22 20 26 20 6f 6e 65 |ut "Tm =| " & one|
|00003d30| 54 65 6d 70 20 2d 20 31 | 34 20 26 20 22 2e 22 20 |Temp - 1|4 & "." |
|00003d40| 69 6e 74 6f 20 63 64 20 | 66 6c 64 20 35 0d 70 75 |into cd |fld 5.pu|
|00003d50| 74 20 6f 6c 69 67 6f 54 | 65 6d 70 28 4f 6c 69 67 |t oligoT|emp(Olig|
|00003d60| 6f 32 29 20 69 6e 74 6f | 20 74 77 6f 54 65 6d 70 |o2) into| twoTemp|
|00003d70| 0d 70 75 74 20 22 54 6d | 20 3d 20 22 20 26 20 74 |.put "Tm| = " & t|
|00003d80| 77 6f 54 65 6d 70 20 2d | 20 31 34 20 26 20 22 2e |woTemp -| 14 & ".|
|00003d90| 22 20 69 6e 74 6f 20 63 | 64 20 66 6c 64 20 36 0d |" into c|d fld 6.|
|00003da0| 69 66 20 6f 6e 65 54 65 | 6d 70 20 3e 3d 20 74 77 |if oneTe|mp >= tw|
|00003db0| 6f 54 65 6d 70 20 74 68 | 65 6e 0d 70 75 74 20 2e |oTemp th|en.put .|
|00003dc0| 33 20 2a 20 74 77 6f 54 | 65 6d 70 20 2b 20 2e 37 |3 * twoT|emp + .7|
|00003dd0| 20 2a 20 70 54 65 6d 70 | 20 2d 20 32 32 2e 39 20 | * pTemp| - 22.9 |
|00003de0| 69 6e 74 6f 20 54 6f 70 | 74 0d 65 6c 73 65 0d 70 |into Top|t.else.p|
|00003df0| 75 74 20 2e 33 20 2a 20 | 6f 6e 65 54 65 6d 70 20 |ut .3 * |oneTemp |
|00003e00| 2b 20 2e 37 20 2a 20 70 | 54 65 6d 70 20 2d 20 32 |+ .7 * p|Temp - 2|
|00003e10| 32 2e 39 20 69 6e 74 6f | 20 54 6f 70 74 0d 65 6e |2.9 into| Topt.en|
|00003e20| 64 20 69 66 0d 70 75 74 | 20 22 4f 70 74 69 6d 61 |d if.put| "Optima|
|00003e30| 6c 20 61 6e 6e 65 61 6c | 69 6e 67 20 74 65 6d 70 |l anneal|ing temp|
|00003e40| 65 72 61 74 75 72 65 20 | 69 73 20 22 20 26 20 54 |erature |is " & T|
|00003e50| 6f 70 74 20 26 20 22 2e | 22 20 69 6e 74 6f 20 63 |opt & ".|" into c|
|00003e60| 64 20 66 6c 64 20 34 0d | 63 68 65 63 6b 50 61 69 |d fld 4.|checkPai|
|00003e70| 72 20 4f 6c 69 67 6f 31 | 2c 4f 6c 69 67 6f 32 0d |r Oligo1|,Oligo2.|
|00003e80| 72 65 70 65 61 74 20 77 | 69 74 68 20 74 20 3d 20 |repeat w|ith t = |
|00003e90| 31 20 74 6f 20 32 0d 63 | 68 65 63 6b 53 74 65 6d |1 to 2.c|heckStem|
|00003ea0| 20 77 6f 72 64 20 31 20 | 6f 66 20 63 64 20 66 6c | word 1 |of cd fl|
|00003eb0| 64 20 39 2c 77 6f 72 64 | 20 31 20 6f 66 20 63 64 |d 9,word| 1 of cd|
|00003ec0| 20 66 6c 64 20 74 2c 74 | 0d 65 6e 64 20 72 65 70 | fld t,t|.end rep|
|00003ed0| 65 61 74 0d 65 6e 64 20 | 6d 6f 75 73 65 55 70 0d |eat.end |mouseUp.|
|00003ee0| 0d 00 00 7c 00 0a 01 00 | 01 03 00 08 01 19 00 4b |...|....|.......K|
|00003ef0| a0 02 00 00 00 00 00 01 | 00 00 00 0c 00 00 00 10 |........|........|
|00003f00| 3f 00 00 6f 6e 20 6d 6f | 75 73 65 55 70 0d 76 69 |?..on mo|useUp.vi|
|00003f10| 73 75 61 6c 20 73 68 72 | 69 6e 6b 20 74 6f 20 62 |sual shr|ink to b|
|00003f20| 6f 74 74 6f 6d 20 74 6f | 20 67 72 65 79 0d 76 69 |ottom to| grey.vi|
|00003f30| 73 75 61 6c 20 73 68 72 | 69 6e 6b 20 74 6f 20 62 |sual shr|ink to b|
|00003f40| 6f 74 74 6f 6d 0d 67 6f | 20 63 64 20 32 0d 65 6e |ottom.go| cd 2.en|
|00003f50| 64 20 6d 6f 75 73 65 55 | 70 0d 0d 0d 00 00 00 54 |d mouseU|p......T|
|00003f60| 00 0e 01 00 01 03 00 a3 | 01 19 00 e6 a0 02 00 00 |........|........|
|00003f70| 00 00 00 01 00 00 00 0c | 00 00 00 10 4f 70 65 6e |........|....Open|
|00003f80| 20 66 69 6c 65 00 00 6f | 6e 20 6d 6f 75 73 65 55 | file..o|n mouseU|
|00003f90| 70 0d 6f 70 65 6e 20 61 | 70 70 6c 69 63 61 74 69 |p.open a|pplicati|
|00003fa0| 6f 6e 0d 65 6e 64 20 6d | 6f 75 73 65 55 70 0d 0d |on.end m|ouseUp..|
|00003fb0| 0d 00 00 22 00 11 02 04 | 00 40 00 15 00 4f 00 f9 |..."....|.@...O..|
|00003fc0| 00 00 00 00 00 00 00 01 | 00 16 00 0c 01 00 00 10 |........|........|
|00003fd0| 00 00 00 00 00 22 00 12 | 02 04 00 40 01 12 00 4f |....."..|...@...O|
|00003fe0| 01 f6 00 00 00 00 00 00 | 00 01 00 16 00 0c 01 00 |........|........|
|00003ff0| 00 10 00 00 00 00 00 22 | 00 13 02 04 00 ee 00 09 |......."|........|
|00004000| 00 fd 01 f7 00 00 00 00 | 00 00 00 01 00 16 00 0c |........|........|
|00004010| 01 00 00 10 00 00 00 00 | 00 22 00 0b 02 04 01 14 |........|."......|
|00004020| 01 de 01 25 01 f7 00 02 | 00 00 00 00 00 00 00 16 |...%....|........|
|00004030| 00 0e 00 00 00 12 00 00 | 00 00 00 22 00 10 02 04 |........|..."....|
|00004040| 01 02 01 de 01 13 01 f7 | 00 02 00 00 00 00 00 00 |........|........|
|00004050| 00 16 00 0e 00 00 00 12 | 00 00 00 00 00 76 00 14 |........|.....v..|
|00004060| 01 00 01 03 00 56 01 19 | 00 99 a0 02 00 00 00 00 |.....V..|........|
|00004070| 00 01 00 00 00 0c 00 00 | 00 10 43 6c 65 61 72 00 |........|..Clear.|
|00004080| 00 6f 6e 20 6d 6f 75 73 | 65 55 70 0d 72 65 70 65 |.on mous|eUp.repe|
|00004090| 61 74 20 77 69 74 68 20 | 65 20 3d 20 34 20 74 6f |at with |e = 4 to|
|000040a0| 20 37 0d 70 75 74 20 65 | 6d 70 74 79 20 69 6e 74 | 7.put e|mpty int|
|000040b0| 6f 20 63 64 20 66 6c 64 | 20 65 0d 65 6e 64 20 72 |o cd fld| e.end r|
|000040c0| 65 70 65 61 74 0d 65 6e | 64 20 6d 6f 75 73 65 55 |epeat.en|d mouseU|
|000040d0| 70 00 ff f5 00 02 00 32 | ff f0 00 02 00 34 ff fe |p......2|.....4..|
|000040e0| 00 15 00 61 61 74 74 67 | 74 67 61 67 63 67 63 74 |...aattg|tgagcgct|
|000040f0| 63 61 63 61 61 74 74 00 | ff fd 00 59 00 61 67 63 |cacaatt.|...Y.agc|
|00004100| 67 67 61 74 61 61 63 61 | 61 74 74 74 63 61 63 61 |ggataaca|atttcaca|
|00004110| 63 61 67 67 61 41 41 43 | 41 47 43 54 41 54 47 41 |caggaAAC|AGCTATGA|
|00004120| 43 43 41 54 47 41 54 54 | 41 43 47 41 41 54 54 43 |CCATGATT|ACGAATTC|
|00004130| 47 41 47 43 54 43 47 47 | 54 41 43 43 43 47 47 47 |GAGCTCGG|TACCCGGG|
|00004140| 61 61 74 74 67 74 67 61 | 67 63 67 63 74 63 61 63 |aattgtga|gcgctcac|
|00004150| 61 61 74 74 0d 00 ff ff | 00 19 00 61 67 63 67 67 |aatt....|...agcgg|
|00004160| 61 74 61 61 63 61 61 74 | 74 74 63 61 63 61 63 61 |ataacaat|ttcacaca|
|00004170| 67 67 61 00 ff ed 00 0c | 00 54 6d 20 3d 20 37 36 |gga.....|.Tm = 76|
|00004180| 2e 30 2e 0d ff ef 00 0b | 00 54 6d 20 3d 20 35 36 |.0......|.Tm = 56|
|00004190| 2e 36 2e 00 ff ee 00 0b | 00 54 6d 20 3d 20 34 39 |.6......|.Tm = 49|
|000041a0| 2e 39 2e 00 ff fc 00 27 | 00 4f 70 74 69 6d 61 6c |.9.....'|.Optimal|
|000041b0| 20 61 6e 6e 65 61 6c 69 | 6e 67 20 74 65 6d 70 65 | anneali|ng tempe|
|000041c0| 72 61 74 75 72 65 20 69 | 73 20 34 39 2e 35 2e 00 |rature i|s 49.5..|
|000041d0| 00 66 75 6e 63 74 69 6f | 6e 20 6f 6c 69 67 6f 54 |.functio|n oligoT|
|000041e0| 65 6d 70 20 78 0d 2d 2d | 20 63 61 6c 63 75 6c 61 |emp x.--| calcula|
|000041f0| 74 65 73 20 6d 65 6c 74 | 69 6e 67 20 74 65 6d 70 |tes melt|ing temp|
|00004200| 2e 0d 2d 2d 20 77 69 74 | 68 20 6e 65 61 72 65 73 |..-- wit|h neares|
|00004210| 74 20 6e 65 69 67 68 62 | 6f 72 20 64 61 74 61 0d |t neighb|or data.|
|00004220| 72 65 74 75 72 6e 20 28 | 64 65 6c 74 61 48 28 78 |return (|deltaH(x|
|00004230| 29 2f 28 64 65 6c 74 61 | 53 28 78 29 20 2d 20 34 |)/(delta|S(x) - 4|
|00004240| 36 2e 36 38 29 29 20 2d | 20 32 38 30 2e 37 35 0d |6.68)) -| 280.75.|
|00004250| 65 6e 64 20 6f 6c 69 67 | 6f 54 65 6d 70 0d 0d 66 |end olig|oTemp..f|
|00004260| 75 6e 63 74 69 6f 6e 20 | 70 72 6f 64 75 63 74 54 |unction |productT|
|00004270| 65 6d 70 20 75 2c 6f 0d | 2d 2d 20 63 61 6c 63 75 |emp u,o.|-- calcu|
|00004280| 6c 61 74 65 73 20 6d 65 | 6c 74 69 6e 67 20 74 65 |lates me|lting te|
|00004290| 6d 70 2e 0d 2d 2d 20 62 | 79 20 70 65 72 63 65 6e |mp..-- b|y percen|
|000042a0| 74 20 47 20 2b 20 43 0d | 72 65 74 75 72 6e 20 28 |t G + C.|return (|
|000042b0| 2e 34 31 20 2a 20 75 29 | 20 2b 20 36 34 2e 39 20 |.41 * u)| + 64.9 |
|000042c0| 2d 20 36 37 35 2f 6f 0d | 65 6e 64 20 70 72 6f 64 |- 675/o.|end prod|
|000042d0| 75 63 74 54 65 6d 70 0d | 0d 66 75 6e 63 74 69 6f |uctTemp.|.functio|
|000042e0| 6e 20 70 65 72 63 65 6e | 74 47 43 20 61 0d 2d 2d |n percen|tGC a.--|
|000042f0| 20 63 61 6c 63 75 6c 61 | 74 65 73 20 25 20 47 43 | calcula|tes % GC|
|00004300| 0d 73 65 74 20 6e 75 6d | 62 65 72 46 6f 72 6d 61 |.set num|berForma|
|00004310| 74 20 74 6f 20 22 30 30 | 2e 30 22 0d 70 75 74 20 |t to "00|.0".put |
|00004320| 22 30 22 20 69 6e 74 6f | 20 6e 75 6d 62 65 72 47 |"0" into| numberG|
|00004330| 43 0d 70 75 74 20 22 67 | 63 22 20 69 6e 74 6f 20 |C.put "g|c" into |
|00004340| 62 61 73 65 73 0d 72 65 | 70 65 61 74 20 77 69 74 |bases.re|peat wit|
|00004350| 68 20 62 61 73 65 20 3d | 20 31 20 74 6f 20 32 0d |h base =| 1 to 2.|
|00004360| 72 65 70 65 61 74 20 75 | 6e 74 69 6c 20 6f 66 66 |repeat u|ntil off|
|00004370| 73 65 74 28 63 68 61 72 | 20 62 61 73 65 20 6f 66 |set(char| base of|
|00004380| 20 62 61 73 65 73 2c 61 | 29 20 3d 20 30 0d 64 65 | bases,a|) = 0.de|
|00004390| 6c 65 74 65 20 63 68 61 | 72 20 6f 66 66 73 65 74 |lete cha|r offset|
|000043a0| 28 63 68 61 72 20 62 61 | 73 65 20 6f 66 20 62 61 |(char ba|se of ba|
|000043b0| 73 65 73 2c 61 29 20 6f | 66 20 61 0d 61 64 64 20 |ses,a) o|f a.add |
|000043c0| 31 20 74 6f 20 6e 75 6d | 62 65 72 47 43 0d 65 6e |1 to num|berGC.en|
|000043d0| 64 20 72 65 70 65 61 74 | 0d 65 6e 64 20 72 65 70 |d repeat|.end rep|
|000043e0| 65 61 74 0d 72 65 74 75 | 72 6e 20 31 30 30 20 2a |eat.retu|rn 100 *|
|000043f0| 20 6e 75 6d 62 65 72 47 | 43 2f 28 6e 75 6d 62 65 | numberG|C/(numbe|
|00004400| 72 20 6f 66 20 63 68 61 | 72 73 20 69 6e 20 61 20 |r of cha|rs in a |
|00004410| 2b 20 6e 75 6d 62 65 72 | 47 43 29 0d 65 6e 64 20 |+ number|GC).end |
|00004420| 70 65 72 63 65 6e 74 47 | 43 0d 0d 66 75 6e 63 74 |percentG|C..funct|
|00004430| 69 6f 6e 20 64 65 6c 74 | 61 48 20 78 0d 2d 2d 20 |ion delt|aH x.-- |
|00004440| 63 61 6c 63 75 6c 61 74 | 65 73 20 74 6f 74 61 6c |calculat|es total|
|00004450| 20 65 6e 74 68 61 6c 70 | 79 20 6f 66 20 66 6f 72 | enthalp|y of for|
|00004460| 6d 61 74 69 6f 6e 0d 70 | 75 74 20 22 30 22 20 69 |mation.p|ut "0" i|
|00004470| 6e 74 6f 20 61 0d 72 65 | 70 65 61 74 20 77 69 74 |nto a.re|peat wit|
|00004480| 68 20 62 20 3d 20 31 20 | 74 6f 20 6e 75 6d 62 65 |h b = 1 |to numbe|
|00004490| 72 20 6f 66 20 63 68 61 | 72 73 20 69 6e 20 78 20 |r of cha|rs in x |
|000044a0| 2d 20 31 0d 61 64 64 20 | 64 48 28 63 68 61 72 20 |- 1.add |dH(char |
|000044b0| 62 20 6f 66 20 78 2c 63 | 68 61 72 20 62 20 2b 20 |b of x,c|har b + |
|000044c0| 31 20 6f 66 20 78 29 20 | 74 6f 20 61 0d 65 6e 64 |1 of x) |to a.end|
|000044d0| 20 72 65 70 65 61 74 0d | 72 65 74 75 72 6e 20 2d | repeat.|return -|
|000044e0| 28 31 30 30 30 20 2a 20 | 61 29 0d 65 6e 64 20 64 |(1000 * |a).end d|
|000044f0| 65 6c 74 61 48 0d 0d 66 | 75 6e 63 74 69 6f 6e 20 |eltaH..f|unction |
|00004500| 64 65 6c 74 61 53 20 78 | 0d 2d 2d 20 63 61 6c 63 |deltaS x|.-- calc|
|00004510| 75 6c 61 74 65 73 20 74 | 6f 74 61 6c 20 65 6e 74 |ulates t|otal ent|
|00004520| 72 6f 70 79 20 6f 66 20 | 66 6f 72 6d 61 74 69 6f |ropy of |formatio|
|00004530| 6e 0d 2d 2d 20 22 31 30 | 2e 38 22 20 69 73 20 74 |n.-- "10|.8" is t|
|00004540| 68 65 20 65 6e 74 72 6f | 70 79 20 6f 66 20 68 65 |he entro|py of he|
|00004550| 6c 69 78 20 69 6e 69 74 | 69 61 74 69 6f 6e 0d 70 |lix init|iation.p|
|00004560| 75 74 20 22 30 22 20 69 | 6e 74 6f 20 61 0d 72 65 |ut "0" i|nto a.re|
|00004570| 70 65 61 74 20 77 69 74 | 68 20 62 20 3d 20 31 20 |peat wit|h b = 1 |
|00004580| 74 6f 20 6e 75 6d 62 65 | 72 20 6f 66 20 63 68 61 |to numbe|r of cha|
|00004590| 72 73 20 69 6e 20 78 20 | 2d 20 31 0d 61 64 64 20 |rs in x |- 1.add |
|000045a0| 64 53 28 63 68 61 72 20 | 62 20 6f 66 20 78 2c 63 |dS(char |b of x,c|
|000045b0| 68 61 72 20 62 20 2b 20 | 31 20 6f 66 20 78 29 20 |har b + |1 of x) |
|000045c0| 74 6f 20 61 0d 65 6e 64 | 20 72 65 70 65 61 74 0d |to a.end| repeat.|
|000045d0| 72 65 74 75 72 6e 20 2d | 20 61 20 2d 20 31 30 2e |return -| a - 10.|
|000045e0| 38 0d 65 6e 64 20 64 65 | 6c 74 61 53 0d 0d 6f 6e |8.end de|ltaS..on|
|000045f0| 20 63 68 65 63 6b 50 61 | 69 72 20 61 2c 62 0d 2d | checkPa|ir a,b.-|
|00004600| 2d 20 63 68 65 63 6b 73 | 20 66 6f 72 20 70 61 69 |- checks| for pai|
|00004610| 72 69 6e 67 20 62 65 74 | 77 65 65 6e 20 33 27 20 |ring bet|ween 3' |
|00004620| 65 6e 64 73 20 6f 66 20 | 74 77 6f 20 6f 6c 69 67 |ends of |two olig|
|00004630| 6f 73 0d 70 75 74 20 77 | 6f 72 64 20 31 20 6f 66 |os.put w|ord 1 of|
|00004640| 20 63 64 20 66 6c 64 20 | 38 20 69 6e 74 6f 20 63 | cd fld |8 into c|
|00004650| 6f 6d 70 4e 75 6d 0d 72 | 65 70 65 61 74 20 77 69 |ompNum.r|epeat wi|
|00004660| 74 68 20 7a 20 3d 20 31 | 20 74 6f 20 63 6f 6d 70 |th z = 1| to comp|
|00004670| 4e 75 6d 0d 69 66 20 70 | 61 69 72 69 6e 67 28 63 |Num.if p|airing(c|
|00004680| 68 61 72 20 28 6e 75 6d | 62 65 72 20 6f 66 20 63 |har (num|ber of c|
|00004690| 68 61 72 73 20 69 6e 20 | 61 20 2d 20 7a 20 2b 20 |hars in |a - z + |
|000046a0| 31 29 20 6f 66 20 61 2c | c2 0d 63 68 61 72 20 28 |1) of a,|..char (|
|000046b0| 6e 75 6d 62 65 72 20 6f | 66 20 63 68 61 72 73 20 |number o|f chars |
|000046c0| 69 6e 20 62 20 2d 20 63 | 6f 6d 70 4e 75 6d 20 2b |in b - c|ompNum +|
|000046d0| 20 7a 20 29 20 6f 66 20 | 62 29 20 c2 0d 69 73 20 | z ) of |b) ..is |
|000046e0| 6e 6f 74 20 22 74 72 75 | 65 22 20 74 68 65 6e 20 |not "tru|e" then |
|000046f0| 65 78 69 74 20 63 68 65 | 63 6b 50 61 69 72 0d 65 |exit che|ckPair.e|
|00004700| 6e 64 20 72 65 70 65 61 | 74 0d 70 75 74 20 22 20 |nd repea|t.put " |
|00004710| 54 68 65 73 65 20 6f 6c | 69 67 6f 6e 75 63 6c 65 |These ol|igonucle|
|00004720| 6f 74 69 64 65 73 20 61 | 72 65 20 63 6f 6d 70 6c |otides a|re compl|
|00004730| 65 6d 65 6e 74 61 72 79 | 20 61 74 20 74 68 65 69 |ementary| at thei|
|00004740| 72 20 33 27 20 65 6e 64 | 73 22 20 c2 0d 26 26 20 |r 3' end|s" ..&& |
|00004750| 22 28 22 20 26 20 63 6f | 6d 70 4e 75 6d 20 26 26 |"(" & co|mpNum &&|
|00004760| 20 22 62 61 73 65 20 6f | 76 65 72 6c 61 70 29 2e | "base o|verlap).|
|00004770| 22 20 61 66 74 65 72 20 | 63 64 20 66 6c 64 20 34 |" after |cd fld 4|
|00004780| 0d 65 6e 64 20 63 68 65 | 63 6b 50 61 69 72 0d 0d |.end che|ckPair..|
|00004790| 6f 6e 20 63 68 65 63 6b | 53 74 65 6d 20 73 74 65 |on check|Stem ste|
|000047a0| 6d 53 69 7a 65 2c 74 68 | 65 4f 6c 69 67 6f 2c 69 |mSize,th|eOligo,i|
|000047b0| 74 73 4e 75 6d 62 65 72 | 0d 2d 2d 20 63 68 65 63 |tsNumber|.-- chec|
|000047c0| 6b 73 20 66 6f 72 20 73 | 74 65 6d 20 2d 20 6c 6f |ks for s|tem - lo|
|000047d0| 6f 70 20 73 74 72 75 63 | 74 75 72 65 73 0d 2d 2d |op struc|tures.--|
|000047e0| 20 6d 69 6e 69 6d 75 6d | 20 6c 6f 6f 70 20 73 69 | minimum| loop si|
|000047f0| 7a 65 20 69 73 20 33 0d | 73 65 74 20 6e 75 6d 62 |ze is 3.|set numb|
|00004800| 65 72 46 6f 72 6d 61 74 | 20 74 6f 20 22 30 22 0d |erFormat| to "0".|
|00004810| 70 75 74 20 32 20 2a 20 | 73 74 65 6d 53 69 7a 65 |put 2 * |stemSize|
|00004820| 20 2b 20 33 20 69 6e 74 | 6f 20 68 61 69 72 50 0d | + 3 int|o hairP.|
|00004830| 69 66 20 6c 65 6e 67 74 | 68 28 74 68 65 4f 6c 69 |if lengt|h(theOli|
|00004840| 67 6f 29 20 3c 20 68 61 | 69 72 50 20 74 68 65 6e |go) < ha|irP then|
|00004850| 20 65 78 69 74 20 63 68 | 65 63 6b 53 74 65 6d 20 | exit ch|eckStem |
|00004860| 65 6c 73 65 20 c2 0d 70 | 75 74 20 6c 65 6e 67 74 |else ..p|ut lengt|
|00004870| 68 28 74 68 65 4f 6c 69 | 67 6f 29 20 69 6e 74 6f |h(theOli|go) into|
|00004880| 20 69 74 73 4c 65 6e 67 | 74 68 0d 72 65 70 65 61 | itsLeng|th.repea|
|00004890| 74 20 77 69 74 68 20 79 | 20 3d 20 30 20 74 6f 20 |t with y| = 0 to |
|000048a0| 69 74 73 4c 65 6e 67 74 | 68 20 2d 20 68 61 69 72 |itsLengt|h - hair|
|000048b0| 50 0d 72 65 70 65 61 74 | 20 77 69 74 68 20 7a 20 |P.repeat| with z |
|000048c0| 3d 20 30 20 74 6f 20 69 | 74 73 4c 65 6e 67 74 68 |= 0 to i|tsLength|
|000048d0| 20 2d 20 73 74 65 6d 53 | 69 7a 65 20 2d 20 34 20 | - stemS|ize - 4 |
|000048e0| 2d 20 79 0d 69 66 20 70 | 61 69 72 69 6e 67 28 63 |- y.if p|airing(c|
|000048f0| 68 61 72 20 69 74 73 4c | 65 6e 67 74 68 20 2d 20 |har itsL|ength - |
|00004900| 7a 20 6f 66 20 74 68 65 | 4f 6c 69 67 6f 2c 63 68 |z of the|Oligo,ch|
|00004910| 61 72 20 7a 20 2b 20 79 | 20 2b 20 31 20 6f 66 20 |ar z + y| + 1 of |
|00004920| c2 0d 74 68 65 4f 6c 69 | 67 6f 29 20 69 73 20 22 |..theOli|go) is "|
|00004930| 74 72 75 65 22 20 74 68 | 65 6e 0d 6e 65 78 74 20 |true" th|en.next |
|00004940| 72 65 70 65 61 74 0d 65 | 6c 73 65 0d 69 66 20 7a |repeat.e|lse.if z|
|00004950| 20 3c 20 73 74 65 6d 53 | 69 7a 65 20 74 68 65 6e | < stemS|ize then|
|00004960| 20 65 78 69 74 20 72 65 | 70 65 61 74 0d 65 6e 64 | exit re|peat.end|
|00004970| 20 69 66 0d 70 75 74 20 | 22 20 33 27 20 65 6e 64 | if.put |" 3' end|
|00004980| 20 6f 66 20 6f 6c 69 67 | 6f 20 22 20 26 20 69 74 | of olig|o " & it|
|00004990| 73 4e 75 6d 62 65 72 20 | 26 26 20 22 70 61 69 72 |sNumber |&& "pair|
|000049a0| 73 20 74 6f 20 70 6f 73 | 69 74 69 6f 6e 73 20 22 |s to pos|itions "|
|000049b0| 20 c2 0d 26 20 79 20 2b | 20 31 20 26 20 22 20 74 | ..& y +| 1 & " t|
|000049c0| 6f 20 22 20 26 20 79 20 | 2b 20 7a 20 26 20 22 20 |o " & y |+ z & " |
|000049d0| 6f 66 20 69 74 73 65 6c | 66 2e 22 20 61 66 74 65 |of itsel|f." afte|
|000049e0| 72 20 63 64 20 66 6c 64 | 20 34 0d 65 78 69 74 20 |r cd fld| 4.exit |
|000049f0| 72 65 70 65 61 74 0d 65 | 6e 64 20 72 65 70 65 61 |repeat.e|nd repea|
|00004a00| 74 0d 65 6e 64 20 72 65 | 70 65 61 74 0d 69 66 20 |t.end re|peat.if |
|00004a10| 6e 75 6d 62 65 72 20 6f | 66 20 63 68 61 72 73 20 |number o|f chars |
|00004a20| 69 6e 20 63 64 20 66 6c | 64 20 34 20 3e 20 32 30 |in cd fl|d 4 > 20|
|00004a30| 31 20 74 68 65 6e 20 73 | 65 74 20 74 68 65 20 73 |1 then s|et the s|
|00004a40| 74 79 6c 65 20 6f 66 20 | 63 64 20 c2 0d 66 6c 64 |tyle of |cd ..fld|
|00004a50| 20 34 20 74 6f 20 22 73 | 63 72 6f 6c 6c 69 6e 67 | 4 to "s|crolling|
|00004a60| 22 0d 65 6e 64 20 63 68 | 65 63 6b 53 74 65 6d 0d |".end ch|eckStem.|
|00004a70| 0d 66 75 6e 63 74 69 6f | 6e 20 70 61 69 72 69 6e |.functio|n pairin|
|00004a80| 67 20 65 2c 66 0d 69 66 | 20 65 20 69 73 20 22 67 |g e,f.if| e is "g|
|00004a90| 22 20 61 6e 64 20 66 20 | 69 73 20 22 63 22 20 74 |" and f |is "c" t|
|00004aa0| 68 65 6e 20 72 65 74 75 | 72 6e 20 22 74 72 75 65 |hen retu|rn "true|
|00004ab0| 22 0d 69 66 20 65 20 69 | 73 20 22 63 22 20 61 6e |".if e i|s "c" an|
|00004ac0| 64 20 66 20 69 73 20 22 | 67 22 20 74 68 65 6e 20 |d f is "|g" then |
|00004ad0| 72 65 74 75 72 6e 20 22 | 74 72 75 65 22 0d 69 66 |return "|true".if|
|00004ae0| 20 65 20 69 73 20 22 61 | 22 20 61 6e 64 20 66 20 | e is "a|" and f |
|00004af0| 69 73 20 22 74 22 20 74 | 68 65 6e 20 72 65 74 75 |is "t" t|hen retu|
|00004b00| 72 6e 20 22 74 72 75 65 | 22 0d 69 66 20 65 20 69 |rn "true|".if e i|
|00004b10| 73 20 22 74 22 20 61 6e | 64 20 66 20 69 73 20 22 |s "t" an|d f is "|
|00004b20| 61 22 20 74 68 65 6e 20 | 72 65 74 75 72 6e 20 22 |a" then |return "|
|00004b30| 74 72 75 65 22 0d 65 6e | 64 20 70 61 69 72 69 6e |true".en|d pairin|
|00004b40| 67 0d 0d 66 75 6e 63 74 | 69 6f 6e 20 64 48 20 78 |g..funct|ion dH x|
|00004b50| 2c 79 0d 2d 2d 20 72 65 | 74 75 72 6e 73 20 65 6e |,y.-- re|turns en|
|00004b60| 74 68 61 6c 70 69 65 73 | 20 6f 66 20 61 64 6a 61 |thalpies| of adja|
|00004b70| 63 65 6e 74 20 70 61 69 | 72 73 0d 69 66 20 78 20 |cent pai|rs.if x |
|00004b80| 69 73 20 22 61 22 20 74 | 68 65 6e 0d 69 66 20 79 |is "a" t|hen.if y|
|00004b90| 20 69 73 20 22 61 22 20 | 74 68 65 6e 20 72 65 74 | is "a" |then ret|
|00004ba0| 75 72 6e 20 22 39 2e 31 | 22 0d 69 66 20 79 20 69 |urn "9.1|".if y i|
|00004bb0| 73 20 22 74 22 20 74 68 | 65 6e 20 72 65 74 75 72 |s "t" th|en retur|
|00004bc0| 6e 20 22 38 2e 36 22 0d | 69 66 20 79 20 69 73 20 |n "8.6".|if y is |
|00004bd0| 22 67 22 20 74 68 65 6e | 20 72 65 74 75 72 6e 20 |"g" then| return |
|00004be0| 22 37 2e 38 22 0d 69 66 | 20 79 20 69 73 20 22 63 |"7.8".if| y is "c|
|00004bf0| 22 20 74 68 65 6e 20 72 | 65 74 75 72 6e 20 22 36 |" then r|eturn "6|
|00004c00| 2e 35 22 0d 65 6e 64 20 | 69 66 0d 69 66 20 78 20 |.5".end |if.if x |
|00004c10| 69 73 20 22 74 22 20 74 | 68 65 6e 0d 69 66 20 79 |is "t" t|hen.if y|
|00004c20| 20 69 73 20 22 61 22 20 | 74 68 65 6e 20 72 65 74 | is "a" |then ret|
|00004c30| 75 72 6e 20 22 36 22 0d | 69 66 20 79 20 69 73 20 |urn "6".|if y is |
|00004c40| 22 74 22 20 74 68 65 6e | 20 72 65 74 75 72 6e 20 |"t" then| return |
|00004c50| 22 39 2e 31 22 0d 69 66 | 20 79 20 69 73 20 22 67 |"9.1".if| y is "g|
|00004c60| 22 20 74 68 65 6e 20 72 | 65 74 75 72 6e 20 22 35 |" then r|eturn "5|
|00004c70| 2e 38 22 0d 69 66 20 79 | 20 69 73 20 22 63 22 20 |.8".if y| is "c" |
|00004c80| 74 68 65 6e 20 72 65 74 | 75 72 6e 20 22 35 2e 36 |then ret|urn "5.6|
|00004c90| 22 0d 65 6e 64 20 69 66 | 0d 69 66 20 78 20 69 73 |".end if|.if x is|
|00004ca0| 20 22 67 22 20 74 68 65 | 6e 0d 69 66 20 79 20 69 | "g" the|n.if y i|
|00004cb0| 73 20 22 61 22 20 74 68 | 65 6e 20 72 65 74 75 72 |s "a" th|en retur|
|00004cc0| 6e 20 22 35 2e 36 22 0d | 69 66 20 79 20 69 73 20 |n "5.6".|if y is |
|00004cd0| 22 74 22 20 74 68 65 6e | 20 72 65 74 75 72 6e 20 |"t" then| return |
|00004ce0| 22 36 2e 35 22 0d 69 66 | 20 79 20 69 73 20 22 67 |"6.5".if| y is "g|
|00004cf0| 22 20 74 68 65 6e 20 72 | 65 74 75 72 6e 20 22 31 |" then r|eturn "1|
|00004d00| 31 22 0d 69 66 20 79 20 | 69 73 20 22 63 22 20 74 |1".if y |is "c" t|
|00004d10| 68 65 6e 20 72 65 74 75 | 72 6e 20 22 31 31 2e 31 |hen retu|rn "11.1|
|00004d20| 22 0d 65 6e 64 20 69 66 | 0d 69 66 20 78 20 69 73 |".end if|.if x is|
|00004d30| 20 22 63 22 20 74 68 65 | 6e 0d 69 66 20 79 20 69 | "c" the|n.if y i|
|00004d40| 73 20 22 61 22 20 74 68 | 65 6e 20 72 65 74 75 72 |s "a" th|en retur|
|00004d50| 6e 20 22 35 2e 38 22 0d | 69 66 20 79 20 69 73 20 |n "5.8".|if y is |
|00004d60| 22 74 22 20 74 68 65 6e | 20 72 65 74 75 72 6e 20 |"t" then| return |
|00004d70| 22 37 2e 38 22 0d 69 66 | 20 79 20 69 73 20 22 67 |"7.8".if| y is "g|
|00004d80| 22 20 74 68 65 6e 20 72 | 65 74 75 72 6e 20 22 31 |" then r|eturn "1|
|00004d90| 31 2e 39 22 0d 69 66 20 | 79 20 69 73 20 22 63 22 |1.9".if |y is "c"|
|00004da0| 20 74 68 65 6e 20 72 65 | 74 75 72 6e 20 22 31 31 | then re|turn "11|
|00004db0| 22 0d 65 6e 64 20 69 66 | 0d 65 6e 64 20 64 48 0d |".end if|.end dH.|
|00004dc0| 0d 66 75 6e 63 74 69 6f | 6e 20 64 53 20 78 2c 79 |.functio|n dS x,y|
|00004dd0| 0d 2d 2d 20 72 65 74 75 | 72 6e 73 20 65 6e 74 72 |.-- retu|rns entr|
|00004de0| 6f 70 69 65 73 20 6f 66 | 20 61 64 6a 61 63 65 6e |opies of| adjacen|
|00004df0| 74 20 70 61 69 72 73 0d | 69 66 20 78 20 69 73 20 |t pairs.|if x is |
|00004e00| 22 61 22 20 74 68 65 6e | 0d 69 66 20 79 20 69 73 |"a" then|.if y is|
|00004e10| 20 22 61 22 20 74 68 65 | 6e 20 72 65 74 75 72 6e | "a" the|n return|
|00004e20| 20 22 32 34 22 0d 69 66 | 20 79 20 69 73 20 22 74 | "24".if| y is "t|
|00004e30| 22 20 74 68 65 6e 20 72 | 65 74 75 72 6e 20 22 32 |" then r|eturn "2|
|00004e40| 33 2e 39 22 0d 69 66 20 | 79 20 69 73 20 22 67 22 |3.9".if |y is "g"|
|00004e50| 20 74 68 65 6e 20 72 65 | 74 75 72 6e 20 22 32 30 | then re|turn "20|
|00004e60| 2e 38 22 0d 69 66 20 79 | 20 69 73 20 22 63 22 20 |.8".if y| is "c" |
|00004e70| 74 68 65 6e 20 72 65 74 | 75 72 6e 20 22 31 37 2e |then ret|urn "17.|
|00004e80| 33 22 0d 65 6e 64 20 69 | 66 0d 69 66 20 78 20 69 |3".end i|f.if x i|
|00004e90| 73 20 22 74 22 20 74 68 | 65 6e 0d 69 66 20 79 20 |s "t" th|en.if y |
|00004ea0| 69 73 20 22 61 22 20 74 | 68 65 6e 20 72 65 74 75 |is "a" t|hen retu|
|00004eb0| 72 6e 20 22 31 36 2e 39 | 22 0d 69 66 20 79 20 69 |rn "16.9|".if y i|
|00004ec0| 73 20 22 74 22 20 74 68 | 65 6e 20 72 65 74 75 72 |s "t" th|en retur|
|00004ed0| 6e 20 22 32 34 22 0d 69 | 66 20 79 20 69 73 20 22 |n "24".i|f y is "|
|00004ee0| 67 22 20 74 68 65 6e 20 | 72 65 74 75 72 6e 20 22 |g" then |return "|
|00004ef0| 31 32 2e 39 22 0d 69 66 | 20 79 20 69 73 20 22 63 |12.9".if| y is "c|
|00004f00| 22 20 74 68 65 6e 20 72 | 65 74 75 72 6e 20 22 31 |" then r|eturn "1|
|00004f10| 33 2e 35 22 0d 65 6e 64 | 20 69 66 0d 69 66 20 78 |3.5".end| if.if x|
|00004f20| 20 69 73 20 22 67 22 20 | 74 68 65 6e 0d 69 66 20 | is "g" |then.if |
|00004f30| 79 20 69 73 20 22 61 22 | 20 74 68 65 6e 20 72 65 |y is "a"| then re|
|00004f40| 74 75 72 6e 20 22 31 33 | 2e 35 22 0d 69 66 20 79 |turn "13|.5".if y|
|00004f50| 20 69 73 20 22 74 22 20 | 74 68 65 6e 20 72 65 74 | is "t" |then ret|
|00004f60| 75 72 6e 20 22 31 37 2e | 33 22 0d 69 66 20 79 20 |urn "17.|3".if y |
|00004f70| 69 73 20 22 67 22 20 74 | 68 65 6e 20 72 65 74 75 |is "g" t|hen retu|
|00004f80| 72 6e 20 22 32 36 2e 36 | 22 0d 69 66 20 79 20 69 |rn "26.6|".if y i|
|00004f90| 73 20 22 63 22 20 74 68 | 65 6e 20 72 65 74 75 72 |s "c" th|en retur|
|00004fa0| 6e 20 22 32 36 2e 37 22 | 0d 65 6e 64 20 69 66 0d |n "26.7"|.end if.|
|00004fb0| 69 66 20 78 20 69 73 20 | 22 63 22 20 74 68 65 6e |if x is |"c" then|
|00004fc0| 0d 69 66 20 79 20 69 73 | 20 22 61 22 20 74 68 65 |.if y is| "a" the|
|00004fd0| 6e 20 72 65 74 75 72 6e | 20 22 31 32 2e 39 22 0d |n return| "12.9".|
|00004fe0| 69 66 20 79 20 69 73 20 | 22 74 22 20 74 68 65 6e |if y is |"t" then|
|00004ff0| 20 72 65 74 75 72 6e 20 | 22 32 30 2e 38 22 0d 69 | return |"20.8".i|
|00005000| 66 20 79 20 69 73 20 22 | 67 22 20 74 68 65 6e 20 |f y is "|g" then |
|00005010| 72 65 74 75 72 6e 20 22 | 32 37 2e 38 22 0d 69 66 |return "|27.8".if|
|00005020| 20 79 20 69 73 20 22 63 | 22 20 74 68 65 6e 20 72 | y is "c|" then r|
|00005030| 65 74 75 72 6e 20 22 32 | 36 2e 36 22 0d 65 6e 64 |eturn "2|6.6".end|
|00005040| 20 69 66 0d 65 6e 64 20 | 64 53 0d 0d 6f 6e 20 69 | if.end |dS..on i|
|00005050| 6e 76 65 72 74 4d 65 20 | 78 0d 70 75 74 20 77 6f |nvertMe |x.put wo|
|00005060| 72 64 20 31 20 6f 66 20 | 63 64 20 66 6c 64 20 78 |rd 1 of |cd fld x|
|00005070| 20 69 6e 74 6f 20 73 74 | 72 61 6e 64 6f 6e 65 0d | into st|randone.|
|00005080| 70 75 74 20 65 6d 70 74 | 79 20 69 6e 74 6f 20 73 |put empt|y into s|
|00005090| 74 72 61 6e 64 74 77 6f | 0d 72 65 70 65 61 74 20 |trandtwo|.repeat |
|000050a0| 77 69 74 68 20 7a 20 3d | 20 31 20 74 6f 20 74 68 |with z =| 1 to th|
|000050b0| 65 20 6e 75 6d 62 65 72 | 20 6f 66 20 63 68 61 72 |e number| of char|
|000050c0| 73 20 69 6e 20 73 74 72 | 61 6e 64 6f 6e 65 0d 70 |s in str|andone.p|
|000050d0| 75 74 20 69 6e 76 65 72 | 74 28 63 68 61 72 20 7a |ut inver|t(char z|
|000050e0| 20 6f 66 20 73 74 72 61 | 6e 64 6f 6e 65 29 20 62 | of stra|ndone) b|
|000050f0| 65 66 6f 72 65 20 73 74 | 72 61 6e 64 74 77 6f 0d |efore st|randtwo.|
|00005100| 65 6e 64 20 72 65 70 65 | 61 74 0d 70 75 74 20 73 |end repe|at.put s|
|00005110| 74 72 61 6e 64 74 77 6f | 20 69 6e 74 6f 20 63 64 |trandtwo| into cd|
|00005120| 20 66 6c 64 20 78 0d 65 | 6e 64 20 69 6e 76 65 72 | fld x.e|nd inver|
|00005130| 74 4d 65 0d 0d 66 75 6e | 63 74 69 6f 6e 20 69 6e |tMe..fun|ction in|
|00005140| 76 65 72 74 20 78 0d 69 | 66 20 78 20 69 73 20 22 |vert x.i|f x is "|
|00005150| 67 22 20 74 68 65 6e 20 | 72 65 74 75 72 6e 20 22 |g" then |return "|
|00005160| 63 22 0d 69 66 20 78 20 | 69 73 20 22 61 22 20 74 |c".if x |is "a" t|
|00005170| 68 65 6e 20 72 65 74 75 | 72 6e 20 22 74 22 0d 69 |hen retu|rn "t".i|
|00005180| 66 20 78 20 69 73 20 22 | 74 22 20 74 68 65 6e 20 |f x is "|t" then |
|00005190| 72 65 74 75 72 6e 20 22 | 61 22 0d 69 66 20 78 20 |return "|a".if x |
|000051a0| 69 73 20 22 63 22 20 74 | 68 65 6e 20 72 65 74 75 |is "c" t|hen retu|
|000051b0| 72 6e 20 22 67 22 0d 65 | 6e 64 20 69 6e 76 65 72 |rn "g".e|nd inver|
|000051c0| 74 00 00 00 00 48 00 08 | f7 60 00 00 00 40 42 4b |t....H..|.`...@BK|
|000051d0| 47 44 00 00 f7 60 00 00 | 00 40 42 4b 47 44 00 00 |GD...`..|.@BKGD..|
|000051e0| 00 00 1d 40 43 41 52 44 | 00 00 0b 81 00 00 00 00 |...@CARD|........|
|000051f0| 00 00 08 b5 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00005200| 00 00 12 11 00 00 0a d7 | 00 0d 00 14 00 00 08 a2 |........|........|
|00005210| 00 05 00 00 01 80 00 46 | 00 01 02 04 00 1b 00 15 |.......F|........|
|00005220| 00 40 00 f9 00 02 00 00 | 00 00 00 00 00 16 00 0c |.@......|........|
|00005230| 00 00 00 10 00 00 6f 6e | 20 6d 6f 75 73 65 44 6f |......on| mouseDo|
|00005240| 77 6e 0d 69 6e 76 65 72 | 74 4d 65 20 31 0d 65 6e |wn.inver|tMe 1.en|
|00005250| 64 20 6d 6f 75 73 65 44 | 6f 77 6e 00 00 46 00 02 |d mouseD|own..F..|
|00005260| 02 04 00 1b 01 12 00 40 | 01 f6 00 02 00 00 00 00 |.......@|........|
|00005270| 00 00 00 16 00 0c 00 00 | 00 10 00 00 6f 6e 20 6d |........|....on m|
|00005280| 6f 75 73 65 44 6f 77 6e | 0d 69 6e 76 65 72 74 4d |ouseDown|.invertM|
|00005290| 65 20 32 0d 65 6e 64 20 | 6d 6f 75 73 65 44 6f 77 |e 2.end |mouseDow|
|000052a0| 6e 00 00 22 00 03 02 04 | 00 51 00 09 00 ee 01 f7 |n.."....|.Q......|
|000052b0| 00 07 00 00 00 00 00 00 | 00 16 00 0c 00 00 00 10 |........|........|
|000052c0| 00 00 00 00 00 22 00 04 | 02 04 01 2a 00 07 01 52 |....."..|...*...R|
|000052d0| 01 f7 00 02 00 00 00 00 | 00 00 00 16 00 0c 21 00 |........|......!.|
|000052e0| 00 10 00 00 00 00 05 bc | 00 08 01 00 01 03 00 f0 |........|........|
|000052f0| 01 19 01 33 a0 02 00 00 | 00 00 00 01 00 00 00 0c |...3....|........|
|00005300| 00 00 00 10 43 61 6c 63 | 75 6c 61 74 65 00 00 6f |....Calc|ulate..o|
|00005310| 6e 20 6d 6f 75 73 65 55 | 70 0d 73 65 74 20 63 75 |n mouseU|p.set cu|
|00005320| 72 73 6f 72 20 74 6f 20 | 34 0d 73 65 74 20 73 63 |rsor to |4.set sc|
|00005330| 72 6f 6c 6c 20 6f 66 20 | 63 64 20 66 6c 64 20 33 |roll of |cd fld 3|
|00005340| 20 74 6f 20 22 30 22 0d | 72 65 70 65 61 74 20 77 | to "0".|repeat w|
|00005350| 69 74 68 20 6a 20 3d 20 | 31 20 74 6f 20 32 0d 72 |ith j = |1 to 2.r|
|00005360| 65 70 65 61 74 20 77 69 | 74 68 20 73 20 3d 20 31 |epeat wi|th s = 1|
|00005370| 20 74 6f 20 6e 75 6d 62 | 65 72 20 6f 66 20 77 6f | to numb|er of wo|
|00005380| 72 64 73 20 69 6e 20 63 | 64 20 66 6c 64 20 6a 0d |rds in c|d fld j.|
|00005390| 64 6f 20 22 70 75 74 20 | 77 6f 72 64 22 20 26 26 |do "put |word" &&|
|000053a0| 20 73 20 26 26 20 22 6f | 66 20 63 64 20 66 6c 64 | s && "o|f cd fld|
|000053b0| 22 20 26 26 20 6a 20 26 | 26 20 22 61 66 74 65 72 |" && j &|& "after|
|000053c0| 22 20 26 26 20 22 4f 6c | 69 67 6f 22 20 26 20 6a |" && "Ol|igo" & j|
|000053d0| 0d 65 6e 64 20 72 65 70 | 65 61 74 0d 64 6f 20 22 |.end rep|eat.do "|
|000053e0| 70 75 74 20 4f 6c 69 67 | 6f 22 20 26 20 6a 20 26 |put Olig|o" & j &|
|000053f0| 26 20 22 69 6e 74 6f 20 | 63 64 20 66 6c 64 22 20 |& "into |cd fld" |
|00005400| 26 26 20 6a 0d 65 6e 64 | 20 72 65 70 65 61 74 0d |&& j.end| repeat.|
|00005410| 73 65 74 20 6e 75 6d 62 | 65 72 46 6f 72 6d 61 74 |set numb|erFormat|
|00005420| 20 74 6f 20 22 30 30 2e | 30 22 0d 73 65 74 20 73 | to "00.|0".set s|
|00005430| 74 79 6c 65 20 6f 66 20 | 63 64 20 66 6c 64 20 34 |tyle of |cd fld 4|
|00005440| 20 74 6f 20 22 72 65 63 | 74 61 6e 67 6c 65 22 0d | to "rec|tangle".|
|00005450| 69 66 20 77 6f 72 64 20 | 31 20 6f 66 20 63 64 20 |if word |1 of cd |
|00005460| 66 6c 64 20 33 20 69 73 | 20 65 6d 70 74 79 20 74 |fld 3 is| empty t|
|00005470| 68 65 6e 0d 61 73 6b 20 | 22 45 73 74 69 6d 61 74 |hen.ask |"Estimat|
|00005480| 65 64 20 25 47 43 20 6f | 66 20 74 65 6d 70 6c 61 |ed %GC o|f templa|
|00005490| 74 65 3f 22 0d 69 66 20 | 69 74 20 69 73 20 65 6d |te?".if |it is em|
|000054a0| 70 74 79 20 74 68 65 6e | 20 65 78 69 74 20 6d 6f |pty then| exit mo|
|000054b0| 75 73 65 55 70 0d 70 75 | 74 20 69 74 20 69 6e 74 |useUp.pu|t it int|
|000054c0| 6f 20 70 65 72 63 65 6e | 74 47 61 6e 64 43 0d 61 |o percen|tGandC.a|
|000054d0| 73 6b 20 22 45 73 74 69 | 6d 61 74 65 64 20 6c 65 |sk "Esti|mated le|
|000054e0| 6e 67 74 68 20 6f 66 20 | 70 72 6f 64 75 63 74 3f |ngth of |product?|
|000054f0| 22 0d 69 66 20 69 74 20 | 69 73 20 65 6d 70 74 79 |".if it |is empty|
|00005500| 20 74 68 65 6e 20 65 78 | 69 74 20 6d 6f 75 73 65 | then ex|it mouse|
|00005510| 55 70 0d 70 75 74 20 69 | 74 20 69 6e 74 6f 20 70 |Up.put i|t into p|
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|000059b0| 00 10 00 00 00 00 00 22 | 00 13 02 04 00 ee 00 09 |......."|........|
|000059c0| 00 fd 01 f7 00 00 00 00 | 00 00 00 01 00 16 00 0c |........|........|
|000059d0| 01 00 00 10 00 00 00 00 | 00 22 00 0b 02 04 01 14 |........|."......|
|000059e0| 01 de 01 25 01 f7 00 02 | 00 00 00 00 00 00 00 16 |...%....|........|
|000059f0| 00 0e 00 00 00 12 00 00 | 00 00 00 22 00 10 02 04 |........|..."....|
|00005a00| 01 02 01 de 01 13 01 f7 | 00 02 00 00 00 00 00 00 |........|........|
|00005a10| 00 16 00 0e 00 00 00 12 | 00 00 00 00 00 9c 00 14 |........|........|
|00005a20| 01 00 01 03 00 56 01 19 | 00 99 a0 02 00 00 00 00 |.....V..|........|
|00005a30| 00 01 00 00 00 0c 00 00 | 00 10 43 6c 65 61 72 00 |........|..Clear.|
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|00005b20| 43 54 43 43 43 54 54 54 | 47 47 43 43 47 43 54 43 |CTCCCTTT|GGCCGCTC|
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|00005b40| 47 0d 54 41 41 54 47 43 | 54 54 54 54 41 43 54 47 |G.TAATGC|TTTTACTG|
|00005b50| 47 43 43 54 47 43 54 43 | 43 43 54 54 41 54 43 47 |GCCTGCTC|CCTTATCG|
|00005b60| 47 47 41 41 47 43 47 47 | 47 47 43 47 43 41 54 43 |GGAAGCGG|GGCGCATC|
|00005b70| 41 54 41 54 43 41 41 41 | 54 47 41 43 47 43 47 43 |ATATCAAA|TGACGCGC|
|00005b80| 43 47 43 54 47 54 41 41 | 41 47 54 47 54 54 41 43 |CGCTGTAA|AGTGTTAC|
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|00005be0| 63 63 67 0d 74 61 74 61 | 67 67 61 61 67 63 67 67 |ccg.tata|ggaagcgg|
|00005bf0| 67 67 67 67 67 63 74 61 | 74 74 67 63 63 74 67 63 |gggggcta|ttgcctgc|
|00005c00| 74 63 63 61 74 63 67 61 | 67 61 74 67 67 67 63 74 |tccatcga|gatgggct|
|00005c10| 61 63 63 61 63 67 63 61 | 63 74 74 63 63 74 74 61 |accacgca|cttcctta|
|00005c20| 74 61 61 67 63 74 61 61 | 67 67 63 61 74 67 67 63 |taagctaa|ggcatggc|
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|00005d40| 0d 66 75 6e 63 74 69 6f | 6e 20 70 65 72 63 65 6e |.functio|n percen|
|00005d50| 74 47 43 20 61 0d 2d 2d | 20 63 61 6c 63 75 6c 61 |tGC a.--| calcula|
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|00005e50| 72 6e 20 31 30 30 20 2a | 20 6e 75 6d 62 65 72 47 |rn 100 *| numberG|
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|00005e90| 43 0d 0d 66 75 6e 63 74 | 69 6f 6e 20 64 65 6c 74 |C..funct|ion delt|
|00005ea0| 61 48 20 78 0d 2d 2d 20 | 63 61 6c 63 75 6c 61 74 |aH x.-- |calculat|
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|00005ed0| 75 74 20 22 30 22 20 69 | 6e 74 6f 20 61 0d 72 65 |ut "0" i|nto a.re|
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|00005f00| 72 73 20 69 6e 20 78 20 | 2d 20 31 0d 61 64 64 20 |rs in x |- 1.add |
|00005f10| 64 48 28 63 68 61 72 20 | 62 20 6f 66 20 78 2c 63 |dH(char |b of x,c|
|00005f20| 68 61 72 20 62 20 2b 20 | 31 20 6f 66 20 78 29 20 |har b + |1 of x) |
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|00005f40| 72 65 74 75 72 6e 20 2d | 28 31 30 30 30 20 2a 20 |return -|(1000 * |
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|00005f60| 75 6e 63 74 69 6f 6e 20 | 64 65 6c 74 61 53 20 78 |unction |deltaS x|
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|00005f80| 6f 74 61 6c 20 65 6e 74 | 72 6f 70 79 20 6f 66 20 |otal ent|ropy of |
|00005f90| 66 6f 72 6d 61 74 69 6f | 6e 0d 2d 2d 20 22 31 30 |formatio|n.-- "10|
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|00006000| 2d 20 31 0d 61 64 64 20 | 64 53 28 63 68 61 72 20 |- 1.add |dS(char |
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|000060e0| 74 68 20 66 20 3d 20 31 | 20 74 6f 20 6c 65 6e 67 |th f = 1| to leng|
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|00006160| 65 70 65 61 74 20 77 69 | 74 68 20 78 20 3d 20 63 |epeat wi|th x = c|
|00006170| 6f 6d 70 4e 75 6d 20 74 | 6f 20 31 30 30 0d 69 66 |ompNum t|o 100.if|
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|000061c0| 68 20 79 20 3d 20 31 20 | 74 6f 20 78 0d 69 66 20 |h y = 1 |to x.if |
|000061d0| 70 61 69 72 69 6e 67 28 | 63 68 61 72 20 79 20 6f |pairing(|char y o|
|000061e0| 66 20 61 61 2c 63 68 61 | 72 20 78 20 2d 20 79 20 |f aa,cha|r x - y |
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|00006270| 22 28 22 20 26 20 78 20 | 26 26 20 22 62 61 73 65 |"(" & x |&& "base|
|00006280| 20 6f 76 65 72 6c 61 70 | 29 2e 22 20 61 66 74 65 | overlap|)." afte|
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|000062a0| 65 70 65 61 74 0d 65 6e | 64 20 72 65 70 65 61 74 |epeat.en|d repeat|
|000062b0| 0d 65 6e 64 20 63 68 65 | 63 6b 50 61 69 72 0d 0d |.end che|ckPair..|
|000062c0| 6f 6e 20 63 68 65 63 6b | 53 74 65 6d 20 73 74 65 |on check|Stem ste|
|000062d0| 6d 53 69 7a 65 2c 74 68 | 65 4f 6c 69 67 6f 2c 69 |mSize,th|eOligo,i|
|000062e0| 74 73 4e 75 6d 62 65 72 | 0d 2d 2d 20 63 68 65 63 |tsNumber|.-- chec|
|000062f0| 6b 73 20 66 6f 72 20 73 | 74 65 6d 20 2d 20 6c 6f |ks for s|tem - lo|
|00006300| 6f 70 20 73 74 72 75 63 | 74 75 72 65 73 0d 2d 2d |op struc|tures.--|
|00006310| 20 6d 69 6e 69 6d 75 6d | 20 6c 6f 6f 70 20 73 69 | minimum| loop si|
|00006320| 7a 65 20 69 73 20 33 0d | 73 65 74 20 6e 75 6d 62 |ze is 3.|set numb|
|00006330| 65 72 46 6f 72 6d 61 74 | 20 74 6f 20 22 30 22 0d |erFormat| to "0".|
|00006340| 70 75 74 20 32 20 2a 20 | 73 74 65 6d 53 69 7a 65 |put 2 * |stemSize|
|00006350| 20 2b 20 33 20 69 6e 74 | 6f 20 68 61 69 72 50 0d | + 3 int|o hairP.|
|00006360| 69 66 20 6c 65 6e 67 74 | 68 28 74 68 65 4f 6c 69 |if lengt|h(theOli|
|00006370| 67 6f 29 20 3c 20 68 61 | 69 72 50 20 74 68 65 6e |go) < ha|irP then|
|00006380| 20 65 78 69 74 20 63 68 | 65 63 6b 53 74 65 6d 20 | exit ch|eckStem |
|00006390| 65 6c 73 65 20 c2 0d 70 | 75 74 20 6c 65 6e 67 74 |else ..p|ut lengt|
|000063a0| 68 28 74 68 65 4f 6c 69 | 67 6f 29 20 69 6e 74 6f |h(theOli|go) into|
|000063b0| 20 69 74 73 4c 65 6e 67 | 74 68 0d 72 65 70 65 61 | itsLeng|th.repea|
|000063c0| 74 20 77 69 74 68 20 79 | 20 3d 20 30 20 74 6f 20 |t with y| = 0 to |
|000063d0| 69 74 73 4c 65 6e 67 74 | 68 20 2d 20 68 61 69 72 |itsLengt|h - hair|
|000063e0| 50 0d 72 65 70 65 61 74 | 20 77 69 74 68 20 7a 20 |P.repeat| with z |
|000063f0| 3d 20 30 20 74 6f 20 69 | 74 73 4c 65 6e 67 74 68 |= 0 to i|tsLength|
+--------+-------------------------+-------------------------+--------+--------+
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