Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2454
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: 23322
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2897 original size:68 final size:68
Alignment explanation
Indices: 2747--2897 Score: 155
Period size: 68 Copynumber: 2.2 Consensus size: 68
2737 CTAGCCAATT
* * *
2747 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACA
**
2812 TTTA
65 CATA
* * *
2816 TCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTA
2878 CTACATA
63 C-ACATA
2885 GTATCTCGTAGCT
1 -TATCTCGTAGCT
2898 TTCTAGTACA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
68 29 0.43
69 7 0.10
70 6 0.09
71 26 0.38
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:6418 original size:27 final size:27
Alignment explanation
Indices: 6388--6543 Score: 206
Period size: 27 Copynumber: 5.8 Consensus size: 27
6378 ATTACCAAAG
*
6388 TACCCCCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
6415 TACCCTCAATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
6442 TACCCTTGATTTACAGAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
* **
6469 TACCCTCGATTTATAGAATTACTACTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
6496 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
6523 TACCCTCGATTTACAAAATTA
1 TACCCTCGATTTACAGAATTA
6544 GTAAAATACC
Statistics
Matches: 109, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
26 1 0.01
27 107 0.98
28 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:6435 original size:54 final size:54
Alignment explanation
Indices: 6395--6571 Score: 248
Period size: 54 Copynumber: 3.3 Consensus size: 54
6385 AAGTACCCCC
* *
6395 GATTTACAGAATTACTGTTTTACCCTCAATTTATAGAATTACTATTTTACCCTT
1 GATTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACTAATTTACCCTT
*
6449 GATTTACAGAATTA-TCGTTTTACCCTCGATTTATAGAATTACTACTTTACCCTT
1 GATTTACAGAATTACT-GTTTTACCCTCGATTTATAGAATTACTAATTTACCCTT
* * * **
6503 GATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTAGTAAAATACCCTT
1 GATTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACTAATTTACCCTT
* *
6557 GGTTTACAAAATTAC
1 GATTTACAGAATTAC
6572 CAAAATACCC
Statistics
Matches: 111, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.01
54 109 0.98
55 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.41
Consensus pattern (54 bp):
GATTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACTAATTTACCCTT
Found at i:6554 original size:81 final size:81
Alignment explanation
Indices: 6365--6571 Score: 202
Period size: 81 Copynumber: 2.6 Consensus size: 81
6355 TTGAAATACT
* * ** * * ** *
6365 CTCGACTTATAAAATTACCAAAGTACCCCCGATTTACAGAATTACTGTTTTACCCTCAATTTATA
1 CTCGATTTACAAAATTAGTAAAATACCCTCGATTTACAGAATTACTACTTTACCCTCAATTTACA
6430 GAATTACTATTTTACC
66 GAATTACTATTTTACC
* * ** * **
6446 CTTGATTTACAGAATTATCGT--TTTACCCTCGATTTATAGAATTACTACTTTACCCTTGATTTA
1 CTCGATTTACAAAATTA--GTAAAATACCCTCGATTTACAGAATTACTACTTTACCCTCAATTTA
*
6509 CAGAATTACTGTTTTACC
64 CAGAATTACTATTTTACC
* * *
6527 CTCGATTTACAAAATTAGTAAAATACCCTTGGTTTACAAAATTAC
1 CTCGATTTACAAAATTAGTAAAATACCCTCGATTTACAGAATTAC
6572 CAAAATACCC
Statistics
Matches: 98, Mismatches: 24, Indels: 8
0.75 0.18 0.06
Matches are distributed among these distances:
79 2 0.02
81 96 0.98
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (81 bp):
CTCGATTTACAAAATTAGTAAAATACCCTCGATTTACAGAATTACTACTTTACCCTCAATTTACA
GAATTACTATTTTACC
Found at i:6581 original size:54 final size:53
Alignment explanation
Indices: 6523--6832 Score: 168
Period size: 54 Copynumber: 5.7 Consensus size: 53
6513 ATTACTGTTT
*
6523 TACCCTCGATTTACAAAATTAGTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTT-CAAAATTACCAAAA
* * * * * *
6577 TACCCTCGA-TCAGTAAAATTACCAAAATACAC-TGGTCTGT-AAAATTGCTAAAA
1 TACCCTCGATTTA-CAAAATTACTAAAATACCCTTGGT-T-TCAAAATTACCAAAA
* ** * * * * *
6630 TACCC-CTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAGTTACCAAAA
1 TACCCTCGA-TTTACAAAATTACTAAAATACCCTTGGTTT-CAAAATTACCAAAA
* *** * **
6684 TACCACT-GGTTTGTGAAATTA-TCGAAATACCCTTAATTTCTAAAATTACCAAAA
1 TACC-CTCGATTTACAAAATTACT-AAAATACCCTTGGTTTC-AAAATTACCAAAA
* * **
6738 TACCC-CTAATTTACAAAATTA-TAGAAATACCCTTGACTTTCTAAAAATTATAAAAA
1 TACCCTC-GATTTACAAAATTACTA-AAATACCCTTG-GTTTC--AAAATTACCAAAA
* * * *
6794 TACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTT
6833 GTAGATTTAC
Statistics
Matches: 196, Mismatches: 41, Indels: 37
0.72 0.15 0.14
Matches are distributed among these distances:
52 3 0.02
53 42 0.21
54 103 0.53
55 9 0.05
56 38 0.19
57 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (53 bp):
TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTCAAAATTACCAAAA
Found at i:6648 original size:80 final size:80
Alignment explanation
Indices: 6537--6743 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 80
6527 CTCGATTTAC
* *
6537 AAAATTAGTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGA-TCAGTAAAATTACCA
1 AAAATT-GTAAAATACCCTTAGTTTATAAAATTACCAAAATACCC-CGAGTCAGTAAAATTACCA
6601 AAATA-CACTGGTCTGT
64 AAATACCACTGGTCTGT
* * * ** *
6617 AAAATTGCTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAGTTACCAA
1 AAAATTG-TAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCGAGTCAGTAAAATTACCAA
*
6682 AATACCACTGGTTTGT
65 AATACCACTGGTCTGT
* * * * *
6698 GAAATTATCGAAATACCCTTAATTTCTAAAATTACCAAAATACCCC
1 AAAATTGT-AAAATACCCTTAGTTTATAAAATTACCAAAATACCCC
6744 TAATTTACAA
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
79 3 0.03
80 57 0.53
81 48 0.44
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (80 bp):
AAAATTGTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCGAGTCAGTAAAATTACCAAA
ATACCACTGGTCTGT
Found at i:6738 original size:81 final size:81
Alignment explanation
Indices: 6537--6745 Score: 239
Period size: 81 Copynumber: 2.6 Consensus size: 81
6527 CTCGATTTAC
* *
6537 AAAATTAG-TAAAATACCCTTGGTTTAC-AAAATTACCAAAATA-CCCTCGATCAGTAAAATTAC
1 AAAATT-GCTAAAATACCCTTAGTTT-CTAAAATTACCAAAATACCCCTAGATCAGTAAAATTAC
6599 CAAAATACACTGGTCTGT
64 CAAAATACACTGGTCTGT
* * ** *
6617 AAAATTGCTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAG-TTTGTAAAGTTACCA
1 AAAATTGCTAAAATACCCTTAGTTTCTAAAATTACCAAAATACCCCTAGATCAGTAAAATTACCA
*
6681 AAATACCACTGGTTTGT
66 AAATA-CACTGGTCTGT
* * * *
6698 GAAATT-ATCGAAATACCCTTAATTTCTAAAATTACCAAAATACCCCTA
1 AAAATTGCT-AAAATACCCTTAGTTTCTAAAATTACCAAAATACCCCTA
6746 ATTTACAAAA
Statistics
Matches: 110, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
79 1 0.01
80 54 0.49
81 55 0.50
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (81 bp):
AAAATTGCTAAAATACCCTTAGTTTCTAAAATTACCAAAATACCCCTAGATCAGTAAAATTACCA
AAATACACTGGTCTGT
Found at i:6829 original size:27 final size:27
Alignment explanation
Indices: 6496--6832 Score: 141
Period size: 27 Copynumber: 12.4 Consensus size: 27
6486 ATTACTACTT
* * ****
6496 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTTGGTTTACAAAATTACTAAAA
* * *
6523 TACCCTCGATTTACAAAATTAGTAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
*
6550 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* * * * *
6577 TACCC-TCGATCAGTAAAATTACCAAAA
1 TACCCTTGGTTTA-CAAAATTACTAAAA
* * ** *
6604 TACAC-TGGTCTGTAAAATTGCTAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* * ** *
6630 TACCCCTAGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* * ** * *
6657 TACCCCTAGTTTGTAAAGTTACCAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
*** *
6684 TACCAC-TGGTTTGTGAAATTA-TCGAAA
1 TACC-CTTGGTTTACAAAATTACT-AAAA
** *
6711 TACCCTTAATTT-CTAAAATTACCAAAA
1 TACCCTTGGTTTAC-AAAATTACTAAAA
* **
6738 TACCCCTAATTTACAAAATTA-TAGAAA
1 TACCCTTGGTTTACAAAATTACTA-AAA
*
6765 TACCCTTGACTTT-CTAAAAATTA-TAAAAA
1 TACCCTTG-GTTTAC--AAAATTACT-AAAA
* *
6794 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
6821 TACCCTTGGTTT
1 TACCCTTGGTTT
6833 GTAGATTTAC
Statistics
Matches: 246, Mismatches: 49, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
26 22 0.09
27 195 0.79
28 9 0.04
29 19 0.08
30 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTACTAAAA
Found at i:7799 original size:52 final size:50
Alignment explanation
Indices: 7722--7845 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 50
7712 GGAGGAAGCG
7722 CAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTAC
1 CAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTAC
7773 CAAAATGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTAC
1 CAAAA-GGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTAC
7824 CGAAAAGGGCTT-TGCCCCAGTT
1 C-AAAAGGGCTTATGCCCCAGTT
7846 ATTAAAGAGG
Statistics
Matches: 71, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
50 10 0.14
51 25 0.35
52 36 0.51
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (50 bp):
CAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTAC
Found at i:7820 original size:25 final size:26
Alignment explanation
Indices: 7723--7845 Score: 180
Period size: 26 Copynumber: 4.8 Consensus size: 26
7713 GAGGAAGCGC
*
7723 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
7749 AAAAGGGCTTATGCCCCAGTTTA-CC
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
7774 AAAATGGGCTTATGCCCCAGTTTATTG
1 AAAA-GGGCTTATGCCCCAGTTTATCG
*
7801 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
7826 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
7846 ATTAAAGAGG
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
25 37 0.42
26 48 0.54
27 4 0.04
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATCG
Found at i:8101 original size:31 final size:31
Alignment explanation
Indices: 8063--8167 Score: 192
Period size: 31 Copynumber: 3.4 Consensus size: 31
8053 GTTTACAATA
*
8063 AAGGCTTCGGCCCAGAGATATGATTTATGAT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
8094 AAGGCTTCGGCCCAGTGATATGATTTATGAT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
*
8125 AAGGCTTCGGCCCAGTGATATGATTTATGAA
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
8156 AAGGCTTCGGCC
1 AAGGCTTCGGCC
8168 TAGTAACCGT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (31 bp):
AAGGCTTCGGCCCAGTGATATGATTTATGAT
Found at i:10679 original size:39 final size:39
Alignment explanation
Indices: 10625--10775 Score: 248
Period size: 39 Copynumber: 3.9 Consensus size: 39
10615 AGTGATGAAG
* *
10625 TATATCCGGACTTAAGGTCTGCAGGATATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
10664 TATATCCGGACTTAAGGTCCGCAAGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
10703 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTAGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* *
10742 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCT
10776 AAAATATGTC
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 105 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:18890 original size:39 final size:39
Alignment explanation
Indices: 18836--18961 Score: 189
Period size: 39 Copynumber: 3.2 Consensus size: 39
18826 AGTGATGAAG
*
18836 TATATCCGGACTTAAGGTCCGTAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
18875 TATATCTGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * *
18914 TATAACCGGACTTAAGGTCCACAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
18953 TATGTCCGG
1 TATATCCGG
18962 GTTAAAGTCC
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:18975 original size:39 final size:39
Alignment explanation
Indices: 18836--18979 Score: 128
Period size: 39 Copynumber: 3.7 Consensus size: 39
18826 AGTGATGAAG
* * ** * *
18836 TATATCCGGACTTAAGGTCCGTAGGCTATGTGCTGGAAT
1 TATAACCGGACTTAAAGTCCACAGGCTACGTGCTGGAAA
* * * * * *
18875 TATATCTGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATAACCGGACTTAAAGTCCACAGGCTACGTGCTGGAAA
*
18914 TATAACCGGACTTAAGGTCCACAGGCTACGTGCTGGAAA
1 TATAACCGGACTTAAAGTCCACAGGCTACGTGCTGGAAA
** *
18953 TATGTCCGG-GTTAAAGTCCCACAGGCT
1 TATAACCGGACTTAAAGT-CCACAGGCT
18980 TCGAGCTAGT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 6 0.06
39 87 0.94
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
TATAACCGGACTTAAAGTCCACAGGCTACGTGCTGGAAA
Found at i:18978 original size:78 final size:78
Alignment explanation
Indices: 18836--18979 Score: 182
Period size: 78 Copynumber: 1.8 Consensus size: 78
18826 AGTGATGAAG
* ** * * * * *
18836 TATATCCGGACTTAAGGTCCGTAGGCTATGTGCTGGAATTATATCTGGACTTAAGGTCCGCAGGC
1 TATAACCGGACTTAAGGTCCACAGGCTACGTGCTGGAAATATATCCGGACTTAAAGTCCACAGGC
18901 TATGTGCTGGAAT
66 TATGTGCTGGAAT
* *
18914 TATAACCGGACTTAAGGTCCACAGGCTACGTGCTGGAAATATGTCCGG-GTTAAAGTCCCACAGG
1 TATAACCGGACTTAAGGTCCACAGGCTACGTGCTGGAAATATATCCGGACTTAAAGT-CCACAGG
18978 CT
65 CT
18980 TCGAGCTAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
77 6 0.11
78 49 0.89
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (78 bp):
TATAACCGGACTTAAGGTCCACAGGCTACGTGCTGGAAATATATCCGGACTTAAAGTCCACAGGC
TATGTGCTGGAAT
Done.