Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1725
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 620
Length: 1034
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Found at i:984 original size:478 final size:472
Alignment explanation
Indices: 8--1034 Score: 1356
Period size: 478 Copynumber: 2.2 Consensus size: 472
1 GGGCCTG
*
8 CAAATGAGAC-ATAT-GGATTCTAGT-ATGATATTCATTCTTTTTCTGGTAAAGCACTAC-AACA
1 CAAATGAGACAATATGGGATTCTAGTAATGATCTTCATTCTTTTTCTGGTAAAGCACTACAAACA
* *
69 CATTCTCTTCTTTAGGACAAAAGAACATTGAAGTTTTTCGTTTGCATGGAAATCTGTTCTTCGCC
66 CATTCTCATCTTTAGGACAAAAGAACATTGAAGTTTTTCGTTTGCATGAAAATCTGTTCTTCGCC
134 CTATTTTCCTCAAAATGAAAGTTCACCCTTGAAGAAGACAGCCATCGATTCCCTAACAGTCTCCT
131 CTATTTTCCTCAAAATGAAAGTTCACCCTTGAAGAAGACAGCCATCGATTCCCTAACAGTCTCCT
199 TTCTTTTCAAGATTAGGAAGCCAAAACACATGCTATTGTTAGGATACCCGACAGTGATGCTTTGG
196 TTCTTTTCAAGATTAGGAAGCCAAAACACATGCTATTGTTAGGATACCCGACAGTGATGCTTTGG
** * *
264 TGTCTCAAGAAAGCCTTTCTTTCACGTCATTTTGATAGAATCAACGTTTGTCTCTTAAATATGCA
261 TGTCTCAAGAAAGCCTTTCTCACACGTCATTTTGATAGAATCAACGTTTGTCTATTAAATAAGCA
* *
329 GAACATTAATACTCAAACTAATCCTCATTCTTTTTAGATTTAGGCACCATAAACATAGTCTCTCA
326 GAACATTAATACTCAAACTAATCCTCATTCCTTTTAGATTGAGGCACCATAAACATAGTCTCTCA
* * *
394 TTAGGATACACGATATTGATGCTTTGGTTTCGCAACAAAGGCTTTTTTTTCCCACCAATCGTTGT
391 TTAGGATACACGATACTGATGCTTTGGTTTCGCAACAAAGGC-ATTTTTTCCCACCAATCGCTGT
459 AAAGTCTAAGTTCTGCCA
455 AAAGTCTAAGTTCTGCCA
* * ***
477 CAAATGAGATAATA-GTTGATTCTAGTAATGATCTTCATTCTTTTTCCAATAAAGCAACTACAAA
1 CAAATGAGACAATATG-GGATTCTAGTAATGATCTTCATTCTTTTTCTGGTAAAGC-ACTAC-AA
* * * * * *
541 ACACATTCTCATCTTTAGGACAAAAG-ACTTTGAAGTTTTTCTTTTTC-TTAAAATCTTTTCTTT
63 ACACATTCTCATCTTTAGGACAAAAGAACATTGAAGTTTTTCGTTTGCATGAAAATCTGTTCTTC
* * * * *
604 GCTCTA-TTTCCTTAAAATGAAGGTTCATCCCTTGAATAAGACAAG-GATCG-TTCTCCTAACAA
128 GCCCTATTTTCCTCAAAATGAAAGTTCA-CCCTTGAAGAAGAC-AGCCATCGATTC-CCTAAC-A
*
666 G-CTCCTTTTCTTTTCAAGATTGGGAAG-CAAAACACATTGCTATTGTTTTAGGAATACCCGACA
189 GTCTCC-TTTCTTTTCAAGATTAGGAAGCCAAAACACA-TGCTATTG--TTAGG-ATACCCGACA
* * *
729 TTGAT-CTTTGGTGTCTCAAGAAAGCTTTTCTCACACTTCACGTTTTTGATAGAATCAACGTTTG
249 GTGATGCTTTGGTGTCTCAAGAAAGCCTTTCTCACACGTCA---TTTTGATAGAATCAACGTTTG
* * *
793 TCTATTAAATAAGCCGAACATTAA-A-TCAAAGCTAATCCTTATTCCTTTTAGATTGAGGCCCCA
311 TCTATTAAATAAGCAGAACATTAATACTCAAA-CTAATCCTCATTCCTTTTAGATTGAGGCACCA
* *
856 T-AATATAG-CTCTCATTAGGAGATACACGATACTGATGCTTTGGTTTCGCAA-TAAGG-ATTTT
375 TAAACATAGTCTCTCATTA-G-GATACACGATACTGATGCTTTGGTTTCGCAACAAAGGCATTTT
**
917 TTCCCACCAATCGCTGTAAAGTCTAAGTTCGTTGCGT
438 TTCCCACCAATCGCTGTAAAGTCTAAGTTC--TGCCA
954 CAAATGAGACAAATATGGGATTCTAGTAATGATC-TCATTCTTTTTCTGGTAAAGCACTACAAAC
1 CAAATGAGAC-AATATGGGATTCTAGTAATGATCTTCATTCTTTTTCTGGTAAAGCACTACAAAC
*
1018 ACATTCTCCTCTTTAGG
65 ACATTCTCATCTTTAGG
Statistics
Matches: 487, Mismatches: 45, Indels: 46
0.84 0.08 0.08
Matches are distributed among these distances:
469 9 0.02
470 3 0.01
471 9 0.02
472 46 0.09
473 58 0.12
474 50 0.10
475 79 0.16
476 50 0.10
477 60 0.12
478 80 0.16
479 43 0.09
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (472 bp):
CAAATGAGACAATATGGGATTCTAGTAATGATCTTCATTCTTTTTCTGGTAAAGCACTACAAACA
CATTCTCATCTTTAGGACAAAAGAACATTGAAGTTTTTCGTTTGCATGAAAATCTGTTCTTCGCC
CTATTTTCCTCAAAATGAAAGTTCACCCTTGAAGAAGACAGCCATCGATTCCCTAACAGTCTCCT
TTCTTTTCAAGATTAGGAAGCCAAAACACATGCTATTGTTAGGATACCCGACAGTGATGCTTTGG
TGTCTCAAGAAAGCCTTTCTCACACGTCATTTTGATAGAATCAACGTTTGTCTATTAAATAAGCA
GAACATTAATACTCAAACTAATCCTCATTCCTTTTAGATTGAGGCACCATAAACATAGTCTCTCA
TTAGGATACACGATACTGATGCTTTGGTTTCGCAACAAAGGCATTTTTTCCCACCAATCGCTGTA
AAGTCTAAGTTCTGCCA
Done.