Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1167
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, 951
Length: 1586
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:1389 original size:467 final size:471
Alignment explanation
Indices: 8--1586 Score: 2192
Period size: 468 Copynumber: 3.4 Consensus size: 471
1 TAAGTTT
* * * * * *
8 GTGCCTCAAATGAGACAAA-AAGGATTCTAGTAA-GATCTTCATTCATTTTGTGATTACGCACTA
1 GTGCTTCAAGTGAGACAAACAAGGACTCTAGTAACGATCTACATTAATTTTGTGATTAGGCACTA
* * * *
71 TAAACACATTC-TTCAGTT-GGATAAATGAGATTGATGA-TTT-TTTTGCATGGAAATCATTTCT
66 TAAATACATTCTTTC-GTTATGATAAATGATATTGATGACTTTCTTTTGCATGAAAATCATTTCT
* ** * *
132 TTACCCTATTTTCCTCAAAA-A-AAATTCATATCTGAATTACGACAATTATCGATGCTCGTAACT
130 TTACCCTATTTTCCTTAAAATACAAATTCATCCCTGAATTATGACAATTATCGATTCTCGTAACT
* * * *
195 GTCTCCATTCTTCTCAAGATTTGGAACTAAGAACCCATTCCCTTTAATTAGGATAAA--ATATTG
195 GTCTCCATTCTTTTCAAGATTTGGAACTAAGAACCCAATCCC-TTCA-TAGGATAAATGATATTT
* * *
258 ATGCTTTGGTGTCGCAAGAAAAGGTTTCCTCTCTACCGTATTTGTTAGAATCAAAGTCTG-CTCT
258 ATGCTTTGGTGTCGCAGGAAAAGGTTTCGTCTCTACCGT-TTTGTTAGAATCAAAGTTTGCCTCT
322 TAAATAAGACAAACATGAATAGTCATACTAATCCCTAATCTTTTAGGATTAGGCACTATCAACAT
322 TAAATAAGACAAACATGAATAGTCATACTAATCCCTAATCTTTTAGGATTAGGCACTATCAACAT
*
387 AGTCAACTCATTAGGATAGACGAAATTGATGCTTTGGATTCACAAGAATGGA-TTCCTCACTCCA
387 AGTCAACTCATTAGGATAGACGAAATTGATGCTTTGGATTCACAAGAATGGATTTCTTCACTCCA
*
451 ATTTCTGGAAAGTCCAAGTC
452 ATTTCTGGAAAGTCCAACTC
*
471 TGTGCTTTAAGTGAGACAAACAAGGACTCTAGTAACGATCTACATTAA-TTTGTGATTAGGCACT
1 -GTGCTTCAAGTGAGACAAACAAGGACTCTAGTAACGATCTACATTAATTTTGTGATTAGGCACT
* * * *
535 AAAAATACATTCTTTTCGTTACGATAAATGATATTAATGACTTTCTTTTGCATGAAAATCTTTTC
65 ATAAATACATTC-TTTCGTTATGATAAATGATATTGATGACTTTCTTTTGCATGAAAATCATTTC
*
600 TTTACCCTATTTTTCTTAAAATACAAA-TCAT-CCTGAATTATGACAATTATCGATTCTCGTAAC
129 TTTACCCTATTTTCCTTAAAATACAAATTCATCCCTGAATTATGACAATTATCGATTCTCGTAAC
* *
663 TGTCT-CATTCTTTTTCAAGATTTGGAACT-AGAACCCAATCCCTTCTTAGGAAATAATTGATA-
194 TGTCTCCATTC-TTTTCAAGATTTGGAACTAAGAACCCAATCCCTTCATAGG--ATAAATGATAT
725 TTA-GCTTTGGTGTCGCAGG-AAAGGTTTCGTCTCTAACCG-TTTGTTAGAAATCAAAAGTTTGC
256 TTATGCTTTGGTGTCGCAGGAAAAGGTTTCGTCTCT-ACCGTTTTGTTAG-AATC-AAAGTTTGC
*
787 CTCTTAAATAAG-CAAACATGAATAGTCATACTAATCCCTAATCTTTTAAGATTAGGCACTATCA
318 CTCTTAAATAAGACAAACATGAATAGTCATACTAATCCCTAATCTTTTAGGATTAGGCACTATCA
*
851 ACATAGTCAACTCATTAGGATAGACGAAATTGATGCTTTGGATGCACAAGAATGGATTTCTTCAC
383 ACATAGTCAACTCATTAGGATAGACGAAATTGATGCTTTGGATTCACAAGAATGGATTTCTTCAC
916 TCCAATTTCTGGAAAGTCCAACTC
448 TCCAATTTCTGGAAAGTCCAACTC
*
940 GTGCTTCAAGTGAGACAAACAAGGACTCTAGTAACGATCTACATTAATTTTGTGATTAGGCGCTA
1 GTGCTTCAAGTGAGACAAACAAGGACTCTAGTAACGATCTACATTAATTTTGTGATTAGGCACTA
*
1005 TAAATACATTCTTTTCGTTATGATAAATGCTA-TGATGAC-TTCTTTTTGCATGAAAATC-TTTC
66 TAAATACATTC-TTTCGTTATGATAAATGATATTGATGACTTTC-TTTTGCATGAAAATCATTTC
*
1067 -TTACCCTATGTT-CTTAAAATACAAATTCATCCCTGAATTAT-ACAATTATCGATTCTCGT-AC
129 TTTACCCTATTTTCCTTAAAATACAAATTCATCCCTGAATTATGACAATTATCGATTCTCGTAAC
1128 TGTCTCCATTCTTTTCAAGATTTGGAACTAAGAACCCAATCCCTTCATAGGATAAATGATATTTA
194 TGTCTCCATTCTTTTCAAGATTTGGAACTAAGAACCCAATCCCTTCATAGGATAAATGATATTTA
1193 TGCTTTGGTGTCGCAGGAAAAGGTTTCGTCTCTACCGTTTTTGTTAGAATC-AAGTTTGCCTCTT
259 TGCTTTGGTGTCGCAGGAAAAGGTTTCGTCTCTACCG-TTTTGTTAGAATCAAAGTTTGCCTCTT
*
1257 AAATAAGACAAAACATGAATAGTTATACTAATCCCTAATCTTTTAGGATTAGGCACTATCAACAT
323 AAATAAGAC-AAACATGAATAGTCATACTAATCCCTAATCTTTTAGGATTAGGCACTATCAACAT
* * *
1322 AGTCAACTCATCAGGA-AGACGAAATT-ATGCTTTGGATTCGCAAGAATGGATTTTTTCACTGTC
387 AGTCAACTCATTAGGATAGACGAAATTGATGCTTTGGATTCACAAGAATGGATTTCTTCAC--TC
** * *
1385 CAA-TTCTATAAAGTCTAAGTTC
450 CAATTTCTGGAAAGTCCAA-CTC
* * * * *
1407 GTGCTTCAA-AGAGACAAACAAGGATTCCAGTAACGATCTTCTTTAATTTTGTG-TTA-GCACTA
1 GTGCTTCAAGTGAGACAAACAAGGACTCTAGTAACGATCTACATTAATTTTGTGATTAGGCACTA
* * * *
1469 TAAAGACATTCTTTCGTTATGATAAATGA-ATATCATGACTTTTCTTTTGCAAGCAAATCA-TTC
66 TAAATACATTCTTTCGTTATGATAAATGATAT-TGATGAC-TTTCTTTTGCATGAAAATCATTTC
* *
1532 TTTACCCTATTTTCCTTAAAATAAAAATCCATCCCTGAATTATGAC-ATTATCGAT
129 TTTACCCTATTTTCCTTAAAATACAAATTCATCCCTGAATTATGACAATTATCGAT
Statistics
Matches: 1007, Mismatches: 65, Indels: 83
0.87 0.06 0.07
Matches are distributed among these distances:
462 1 0.00
463 17 0.02
464 46 0.05
465 148 0.15
466 179 0.18
467 195 0.19
468 233 0.23
469 177 0.18
470 8 0.01
471 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (471 bp):
GTGCTTCAAGTGAGACAAACAAGGACTCTAGTAACGATCTACATTAATTTTGTGATTAGGCACTA
TAAATACATTCTTTCGTTATGATAAATGATATTGATGACTTTCTTTTGCATGAAAATCATTTCTT
TACCCTATTTTCCTTAAAATACAAATTCATCCCTGAATTATGACAATTATCGATTCTCGTAACTG
TCTCCATTCTTTTCAAGATTTGGAACTAAGAACCCAATCCCTTCATAGGATAAATGATATTTATG
CTTTGGTGTCGCAGGAAAAGGTTTCGTCTCTACCGTTTTGTTAGAATCAAAGTTTGCCTCTTAAA
TAAGACAAACATGAATAGTCATACTAATCCCTAATCTTTTAGGATTAGGCACTATCAACATAGTC
AACTCATTAGGATAGACGAAATTGATGCTTTGGATTCACAAGAATGGATTTCTTCACTCCAATTT
CTGGAAAGTCCAACTC
Done.