Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_6943
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, 1000
Length: 5000
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Found at i:1016 original size:17 final size:19
Alignment explanation
Indices: 980--1020 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
970 CCCCATTTTA
*
980 ATTTATTTTTCAATAAAAT
1 ATTTATTTTTCAAAAAAAT
999 ATTTA-TTTT-AAAAAAAT
1 ATTTATTTTTCAAAAAAAT
1016 ATTTA
1 ATTTA
1021 AAACCATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 4 0.19
19 5 0.24
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTATTTTTCAAAAAAAT
Found at i:1786 original size:513 final size:512
Alignment explanation
Indices: 1--1982 Score: 3186
Period size: 512 Copynumber: 3.9 Consensus size: 512
* *
1 TAAAACCAT-AAA-TGATTTCTCTAAAATA-TTTTATTTT-CAGAAAATTATTTACCGATTTTTA
1 TAAAACCATAAAATTGATTTCTCTAAAATATTTTTATTTTCCGGAATATTATTTACCGATTTTTA
* * *
62 AATGAAATTAAGCTAACTAATTTTTTTTCAAAAGAAATAACTAGTAAACCTGATTAACTCCTAGC
66 AATAAAATTAAGCTAACTAA-TTTTTTTAAAAAGAAATGACTAGTAAACC-GATTAACTCCTAGC
127 TTTCACCCGAAACTCGATAAACTTACTCAAAACTAGTAGACCTATTTTTAGGGCA-TTACAAACA
129 TTTCACCCGAAACTCGATAAACTTACTCAAAACTAGTAGACCTATTTTTAGGG-AGTTACAAACA
* *
191 CAACATACTTTGGAAAATTTGCGATTACAAGCAGGTTTGGACAATTAGGATTGTGATCAAGGAGC
193 CAACATACTTTGGAAAATTTGCGATTACAAGTAGGTTTGGACAATTAGGATTGTGATCGAGGAGC
* * *
256 TTCTATCAAAGATAAGCAGAATTTGGTGGTTTGGAAAGGAAAGAGGAAAATATTGGGTGATACTC
258 TTCTATCAAAGATAAGCAGAATTTGGTGGTCTGGAAAGGAAAAAGGAAAATATTGGGCGATACTC
* * *
321 CCGCGGAAGAATTTGTGTCAGCCTAAAAGGATGGGGTTATTAGTATTCATGATATTAGTGATATT
323 CCGTGGAAGAATTTGTGTCAGCCTAAAAGGATGGGGGTATTAGTATTCATGATATTCGTGATATT
* *
386 TTTCTAAAAATATTTTTATTTTCCGGAATATTAAATACCTATTAAGTTAATATTGTAACTTCTCT
388 TTTCTAAAAATATTTTTATTTTCCGGAATATTATATACCTATTTAGTTAATATTGTAACTTCTCT
* *
451 AAATTAAACCCCATTTTAATTTATTTTTCAATAAAATATTTATTTTAACC-AAAAATATT
453 CAATGAAACCCCATTTTAATTTATTTTTCAATAAAATATTTATTTTAACCAAAAAATATT
510 TAAAACCATAAAATTGATTTCTCTAAAATATTTTTATTTTCCGGAATATTATTTACCGATTTTTA
1 TAAAACCATAAAATTGATTTCTCTAAAATATTTTTATTTTCCGGAATATTATTTACCGATTTTTA
* *
575 AATGAAATTAAGCTAACTAATTTTTTTAAAAAGAAATGACTAGTAAACCCGATTAACACCTAGCT
66 AATAAAATTAAGCTAACTAATTTTTTTAAAAAGAAATGACTAGTAAA-CCGATTAACTCCTAGCT
*
640 TTCACCCGAAACTCGATAAACTTACTCAAAACTAGTAGACCTATTTTTAGGGCGTTACAAACACA
130 TTCACCCGAAACTCGATAAACTTACTCAAAACTAGTAGACCTATTTTTAGGGAGTTACAAACACA
705 ACATACTTTGGAAAATTTGCGATTACAAGTAGGTTTGGACAATTAGGATTGTGATCGAGGAGCTT
195 ACATACTTTGGAAAATTTGCGATTACAAGTAGGTTTGGACAATTAGGATTGTGATCGAGGAGCTT
* ** * * * *
770 GTATGGAAGATAAGTAGAATTTGGTGGTGTGGAAAGAAAAAAGGAAAATATTGGGCGATACTCCT
260 CTATCAAAGATAAGCAGAATTTGGTGGTCTGGAAAGGAAAAAGGAAAATATTGGGCGATACTCCC
*
835 GTGGAAGAATTTGTGTCAGCCTAAAAGGATAGGGGTATTAGTATTCATGATATTCGTGATATTTT
325 GTGGAAGAATTTGTGTCAGCCTAAAAGGATGGGGGTATTAGTATTCATGATATTCGTGATATTTT
* *
900 TCTAAAAATA-TTTTATTTTCTGGAATATTATATACCTATTTAGTTAATAATGTAACTTCTCTCA
390 TCTAAAAATATTTTTATTTTCCGGAATATTATATACCTATTTAGTTAATATTGTAACTTCTCTCA
964 ATGAAACCCCATTTTAATTTATTTTTCAATAAAATATTTATTTT-A--AAAAAATATT
455 ATGAAACCCCATTTTAATTTATTTTTCAATAAAATATTTATTTTAACCAAAAAATATT
*
1019 TAAAACCATAAAATTGATTTCTCTAAAAATATTTTTATTTTCCGGAATATTATTTATCGA--TTT
1 TAAAACCATAAAATTGATTTCTCT-AAAATATTTTTATTTTCCGGAATATTATTTACCGATTTTT
*
1082 AAA-AAAATTAAGCTAACTAATTTTTTTAAAAAGAAATGACTAGTAAACTCGATTAACTCGTAGC
65 AAATAAAATTAAGCTAACTAATTTTTTTAAAAAGAAATGACTAGTAAAC-CGATTAACTCCTAGC
* * * *
1146 TTTCACCCG-GACCCGATAAACTCACTCAAAACTAGTAGACCTATTTTTAGGGCGTTACAAACAC
129 TTTCACCCGAAACTCGATAAACTTACTCAAAACTAGTAGACCTATTTTTAGGGAGTTACAAACAC
* * *
1210 AACATACTTTGGAAAATTTGCGATTAGAAGTATGCTTGGACAATTAGGATTGTGATCGAGGAGCT
194 AACATACTTTGGAAAATTTGCGATTACAAGTAGGTTTGGACAATTAGGATTGTGATCGAGGAGCT
* * *
1275 TCTATCAAAGATAAGCATAATTTGATGGTCTAGAAAGGAAAAAGGAAAATATTGGGCGATACTCC
259 TCTATCAAAGATAAGCAGAATTTGGTGGTCTGGAAAGGAAAAAGGAAAATATTGGGCGATACTCC
1340 CGTGGAAGAATTTGTGTCAGCCTAAAAGGATGGGGGTATTAGTATTCATGATATTCGTGATATTT
324 CGTGGAAGAATTTGTGTCAGCCTAAAAGGATGGGGGTATTAGTATTCATGATATTCGTGATATTT
1405 TTCTAAAAATATTTTTATTTTCCGGAATATTATATACCTATTTAGTTAATATTGTAACTTCTCTC
389 TTCTAAAAATATTTTTATTTTCCGGAATATTATATACCTATTTAGTTAATATTGTAACTTCTCTC
*
1470 AATGAAATCCCATTTTAATTTATTTTTCAATAAAATATTTATTTTAACCAAAAAATATT
454 AATGAAACCCCATTTTAATTTATTTTTCAATAAAATATTTATTTTAACCAAAAAATATT
* * *
1529 TAAAACCATAAAATTGATTTCTCTAAAAATATTTTTATTTTTCGGAATATTATTTATCGATTTTA
1 TAAAACCATAAAATTGATTTCTCT-AAAATATTTTTATTTTCCGGAATATTATTTACCGATTTTT
** *
1594 AAATAAAATTAAGCTAACT-ATTTTTTTTTAAAGAAATGACTAGTAAAGCCAATTAACTCCTAGC
65 AAATAAAATTAAGCTAACTAATTTTTTTAAAAAGAAATGACTAGTAAA-CCGATTAACTCCTAGC
* * *
1658 TTTCACCCGGAAC-CTGATAAACTTACTCAAAATTAGTATACCTATTTTTAGGGAGTTACAAACA
129 TTTCACCCGAAACTC-GATAAACTTACTCAAAACTAGTAGACCTATTTTTAGGGAGTTACAAACA
* *
1722 CAACATACTTTGGAAAATTTGTGATTACTAGTAGGTTTGGACAATTAGGATTGTGATCGAGGAGC
193 CAACATACTTTGGAAAATTTGCGATTACAAGTAGGTTTGGACAATTAGGATTGTGATCGAGGAGC
* * * *** *
1787 TTCTATGAAAGATAAGTAGAATTTGGTGGGCTGGAAAGGAACGGGGAAAATATTAGGCGATACTC
258 TTCTATCAAAGATAAGCAGAATTTGGTGGTCTGGAAAGGAAAAAGGAAAATATTGGGCGATACTC
* *
1852 CCGTGGAAGAATTTGTGTCAGCCTTAAAGGATGGGGGTATTAGTATTCATGATATTCGTGGTATT
323 CCGTGGAAGAATTTGTGTCAGCCTAAAAGGATGGGGGTATTAGTATTCATGATATTCGTGATATT
* *
1917 TTTTTAAAAATATTTTTATTTTCCGAAATATTATATACCTATTTAGTTAATATTGTAACTTCTCT
388 TTTCTAAAAATATTTTTATTTTCCGGAATATTATATACCTATTTAGTTAATATTGTAACTTCTCT
1982 C
453 C
1983 TATAGACACT
Statistics
Matches: 1373, Mismatches: 81, Indels: 34
0.92 0.05 0.02
Matches are distributed among these distances:
506 245 0.18
507 160 0.12
508 7 0.01
509 42 0.03
510 107 0.08
511 108 0.08
512 355 0.26
513 349 0.25
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (512 bp):
TAAAACCATAAAATTGATTTCTCTAAAATATTTTTATTTTCCGGAATATTATTTACCGATTTTTA
AATAAAATTAAGCTAACTAATTTTTTTAAAAAGAAATGACTAGTAAACCGATTAACTCCTAGCTT
TCACCCGAAACTCGATAAACTTACTCAAAACTAGTAGACCTATTTTTAGGGAGTTACAAACACAA
CATACTTTGGAAAATTTGCGATTACAAGTAGGTTTGGACAATTAGGATTGTGATCGAGGAGCTTC
TATCAAAGATAAGCAGAATTTGGTGGTCTGGAAAGGAAAAAGGAAAATATTGGGCGATACTCCCG
TGGAAGAATTTGTGTCAGCCTAAAAGGATGGGGGTATTAGTATTCATGATATTCGTGATATTTTT
CTAAAAATATTTTTATTTTCCGGAATATTATATACCTATTTAGTTAATATTGTAACTTCTCTCAA
TGAAACCCCATTTTAATTTATTTTTCAATAAAATATTTATTTTAACCAAAAAATATT
Found at i:2263 original size:17 final size:19
Alignment explanation
Indices: 2166--2256 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
2156 ATAATCTTCA
2166 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2185 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2204 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
2221 ATGAT-TACAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2239 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
2257 AGATATGATT
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 36 0.53
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:2282 original size:22 final size:22
Alignment explanation
Indices: 2166--2279 Score: 87
Period size: 19 Copynumber: 5.8 Consensus size: 22
2156 ATAATCTTCA
2166 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
2185 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
2204 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
*
2221 ATGAT-TACAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
2239 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
2261 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
2280 GATTTAATTT
Statistics
Matches: 85, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
17 16 0.19
18 16 0.19
19 33 0.39
22 8 0.09
23 12 0.14
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:2569 original size:17 final size:17
Alignment explanation
Indices: 2545--2579 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2535 TGTTTCCCTG
*
2545 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
2563 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
2580 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Done.