Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3539
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: 32815
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:994 original size:20 final size:20
Alignment explanation
Indices: 964--1008 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
954 CTGTTTTATT
964 ATGGG-CCAACTGTATTAAA
1 ATGGGCCCAACTGTATTAAA
* *
983 ATGGGCCCAACTGTGTTAAT
1 ATGGGCCCAACTGTATTAAA
1003 ATGGGC
1 ATGGGC
1009 AAGACCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTAAA
Found at i:4645 original size:27 final size:26
Alignment explanation
Indices: 4607--4666 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
4597 CCACATATAT
* *
4607 ATATATGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
4633 ATATCTGTATCTGGTGACTTTGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
4660 ATATCTG
1 ATATCTG
4667 GCAGCCTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:5536 original size:799 final size:798
Alignment explanation
Indices: 3999--5597 Score: 3130
Period size: 799 Copynumber: 2.0 Consensus size: 798
3989 ACTTGTGTGA
3999 TGGTTGGATTAGTTGACGTGGATTTATGTTAGTTATCGTTAATTCGTAAGTCTAATGTGTTAGTG
1 TGGTTGGATTAGTTGACGTGGATTTATGTTAGTTATCGTTAATTCGTAAGTCTAATGTGTTAGTG
4064 ATTGATTGTAGGATTATCGCGTGGGAGATATCGTCATTAATCGTCATCAACCAGGTGTGTAAACG
66 ATTGATTGTAGGATTATCGCGTGGGAGATATCGTCATTAATCGTCATCAACCAGGTGTGTAAACG
4129 ATACCCTCCCTTAGACTGAATCAGTAAAAGCCGAAATACCGAAAGTTGTTATTTTGTGAACTCGC
131 ATACCCTCCCTTAGACTGAATCAGTAAAAGCCGAAATACCGAAAGTTGTTATTTTGTGAACTCGC
*
4194 GAGCGTGCGAGCACTCGTGAGACAGTTGTTAATGAATATAGTGCATTTGGATGATTAGAGTGCAA
196 GAGCGTGCAAGCACTCGTGAGACAGTTGTTAATGAATATAGTGCATTTGGATGATTAGAGTGCAA
4259 AGTGTGCATTTTCGTGTACAACGGTATTTTTGGCTTAATAGGCCGAAAGCGGGCCAATGGGCCAA
261 AGTGTGCATTTTCGTGTACAACGGTATTTTTGGCTTAATAGGCCGAAAGCGGGCCAATGGGCCAA
4324 CGGGCCCACTTTGGTAAAAAAACGGGGTAAGTACTTCTGATTACTTGGTAAACGTTAGAATGAAC
326 CGGGCCCACTTTGGTAAAAAAACGGGGTAAGTACTTCTGATTACTTGGTAAACGTTAGAATGAAC
4389 ATGAAACCTTAGAAATAGGTAATAATTATTGAAATACCGTTATGCATGCAAAATTACGATTTTAC
391 ATGAAACCTTAGAAATAGGTAATAATTATTGAAATACCGTTATGCATGCAAAATTACGATTTTAC
4454 CCCTAGGGTTATTTTTTTCTGAAACGCATGATGTTCTGTTTATGTATACGTATGCCATGACATAT
456 CCCTAGGGTTATTTTTTTCTGAAACGCATGATGTTCTGTTTATGTATACGTATGCCATGACATAT
4519 TATTTCTGTTGCATGGGACGTGGGTTTATATTGATAGAGGAAGCATTTTGGCAGCCTCACTACAA
521 TATTTCTGTTGCATGGGACGTGGGTTTATATTGATAGAGGAAGCATTTTGGCAGCCTCACTACAA
4584 TTTGGTCGCCTCGCCACATATATATATATGTTCTGGTGGCCTAGCCACAATATCTGTATCTGGTG
586 TTTGGTCGCCTCGCCACA-ATATATATATGTTCTGGTGGCCTAGCCACAATATCTGTATCTGGTG
4649 ACTTTGTCACAATATCTGGCAGCCTCACTACAATTTTTGTGTGTGTAGCAGTTGGGTGGGTCGAG
650 ACTTTGTCACAATATCTGGCAGCCTCACTACAATTTTTGTGTGTGTAGCAGTTGGGTGGGTCGAG
4714 TAGTCTCCCCACATGGTGTAAGGCTGGTACGGGGGTGTTATGGATGGCTCTGGGTTGGGATTTCT
715 TAGTCTCCCCACATGGTGTAAGGCTGGTACGGGGGTGTTATGGATGGCTCTGGGTTGGGATTTCT
4779 GCTTTCATGATATATTTGT
780 GCTTTCATGATATATTTGT
4798 TGGTTGGATTAGTTGACGTGGATTTATGTTAGTTATCGTTAATTCGTAAGTCTAATGTGTTAGTG
1 TGGTTGGATTAGTTGACGTGGATTTATGTTAGTTATCGTTAATTCGTAAGTCTAATGTGTTAGTG
4863 ATTGATTGTAGGATTATCGCGTGGGAGATATCGTCATTAATCGTCATCAACCAGGTGTGTAAACG
66 ATTGATTGTAGGATTATCGCGTGGGAGATATCGTCATTAATCGTCATCAACCAGGTGTGTAAACG
4928 ATACCCTCCCTTAGACTGAATCAGTAAAAGCCGAAATACCGAAAAGTTGTTATTTTGTGAACTCG
131 ATACCCTCCCTTAGACTGAATCAGTAAAAGCCGAAATACCG-AAAGTTGTTATTTTGTGAACTCG
4993 CGAGCGTGCAAGCACTCGTGAGACAGTTGTTAATGAATATAGTGCATTTGGATGATTAGAGTGCA
195 CGAGCGTGCAAGCACTCGTGAGACAGTTGTTAATGAATATAGTGCATTTGGATGATTAGAGTGCA
5058 AAGTGTGCATTTTCGTGTACAACGGTATTTTTGGGCTTAATAGGCCGAAAGCGGGCCAATGGGCC
260 AAGTGTGCATTTTCGTGTACAACGGTATTTTT-GGCTTAATAGGCCGAAAGCGGGCCAATGGGCC
5123 AACGGGCCCACTTTGGTAAAAAAACGGGGTAAGTACTTCTGATTACTTGGTAAACGTTAGAATGA
324 AACGGGCCCACTTTGGTAAAAAAACGGGGTAAGTACTTCTGATTACTTGGTAAACGTTAGAATGA
*
5188 GCATGAAACCTTAGAAATAGGTAATAATTATTGAAATACCGTTATGCATGCAAAATTACGATTTT
389 ACATGAAACCTTAGAAATAGGTAATAATTATTGAAATACCGTTATGCATGCAAAATTACGATTTT
5253 ACCCCTAGGGTTATTTTTTTCTGAAACGCATGATGTTCTGTTTATGTATACGTATGCCATGACAT
454 ACCCCTAGGGTTATTTTTTTCTGAAACGCATGATGTTCTGTTTATGTATACGTATGCCATGACAT
5318 ATTATTTCTGTTGCATGGGACGTGGGTTTATATTGATAGAGGAAGCATTTTGGCAGCCTCACTAC
519 ATTATTTCTGTTGCATGGGACGTGGGTTTATATTGATAGAGGAAGCATTTTGGCAGCCTCACTAC
5383 AATTTGGTCGCCTCGCCAC-ATATATATATGTTCTGGTGGCCTAGCCACAATATCTGTATCTGGT
584 AATTTGGTCGCCTCGCCACAATATATATATGTTCTGGTGGCCTAGCCACAATATCTGTATCTGGT
5447 GACTTTGTCACAATATCTGGCAGCCTCACTACAA-TTTTGTGGTGTGTAGCAGTTGGGTGGGTCG
649 GACTTTGTCACAATATCTGGCAGCCTCACTACAATTTTTGT-GTGTGTAGCAGTTGGGTGGGTCG
5511 AGTAGTCTCCCCACATGGTGTAAGGCTGGTACGGGGGTGTTATGGATGGCTCTGGGTTGGGATTT
713 AGTAGTCTCCCCACATGGTGTAAGGCTGGTACGGGGGTGTTATGGATGGCTCTGGGTTGGGATTT
5576 CTGCTTTCATGATATATTTGT
778 CTGCTTTCATGATATATTTGT
5597 T
1 T
5598 TTGTATCTGC
Statistics
Matches: 795, Mismatches: 2, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
798 6 0.01
799 360 0.45
800 119 0.15
801 310 0.39
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (798 bp):
TGGTTGGATTAGTTGACGTGGATTTATGTTAGTTATCGTTAATTCGTAAGTCTAATGTGTTAGTG
ATTGATTGTAGGATTATCGCGTGGGAGATATCGTCATTAATCGTCATCAACCAGGTGTGTAAACG
ATACCCTCCCTTAGACTGAATCAGTAAAAGCCGAAATACCGAAAGTTGTTATTTTGTGAACTCGC
GAGCGTGCAAGCACTCGTGAGACAGTTGTTAATGAATATAGTGCATTTGGATGATTAGAGTGCAA
AGTGTGCATTTTCGTGTACAACGGTATTTTTGGCTTAATAGGCCGAAAGCGGGCCAATGGGCCAA
CGGGCCCACTTTGGTAAAAAAACGGGGTAAGTACTTCTGATTACTTGGTAAACGTTAGAATGAAC
ATGAAACCTTAGAAATAGGTAATAATTATTGAAATACCGTTATGCATGCAAAATTACGATTTTAC
CCCTAGGGTTATTTTTTTCTGAAACGCATGATGTTCTGTTTATGTATACGTATGCCATGACATAT
TATTTCTGTTGCATGGGACGTGGGTTTATATTGATAGAGGAAGCATTTTGGCAGCCTCACTACAA
TTTGGTCGCCTCGCCACAATATATATATGTTCTGGTGGCCTAGCCACAATATCTGTATCTGGTGA
CTTTGTCACAATATCTGGCAGCCTCACTACAATTTTTGTGTGTGTAGCAGTTGGGTGGGTCGAGT
AGTCTCCCCACATGGTGTAAGGCTGGTACGGGGGTGTTATGGATGGCTCTGGGTTGGGATTTCTG
CTTTCATGATATATTTGT
Found at i:12960 original size:30 final size:30
Alignment explanation
Indices: 12924--12981 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
12914 ATAGCCTAAA
12924 GATTGATAAACCGGCTTTTCATTCAACTAC
1 GATTGATAAACCGGCTTTTCATTCAACTAC
*
12954 GATTGATAAACTGGCTTTTCATTCAACT
1 GATTGATAAACCGGCTTTTCATTCAACT
12982 GCTGTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (30 bp):
GATTGATAAACCGGCTTTTCATTCAACTAC
Found at i:15795 original size:67 final size:67
Alignment explanation
Indices: 15687--15816 Score: 260
Period size: 67 Copynumber: 1.9 Consensus size: 67
15677 AGAATATACG
15687 CTTGTTAAGGGATTTAGAAAGTTAAAAGTGGACATTGAAATATGCATTACTATATTCAGTTGAGG
1 CTTGTTAAGGGATTTAGAAAGTTAAAAGTGGACATTGAAATATGCATTACTATATTCAGTTGAGG
15752 TT
66 TT
15754 CTTGTTAAGGGATTTAGAAAGTTAAAAGTGGACATTGAAATATGCATTACTATATTCAGTTGA
1 CTTGTTAAGGGATTTAGAAAGTTAAAAGTGGACATTGAAATATGCATTACTATATTCAGTTGA
15817 TTTTGTAAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (67 bp):
CTTGTTAAGGGATTTAGAAAGTTAAAAGTGGACATTGAAATATGCATTACTATATTCAGTTGAGG
TT
Found at i:17708 original size:49 final size:48
Alignment explanation
Indices: 17589--17806 Score: 149
Period size: 49 Copynumber: 4.5 Consensus size: 48
17579 ATGCCGACGC
* * ** * * *
17589 CATGTCCCAGTCATGGTCTTACACTGGCTAGCATAT-TAGA-ATTGATG
1 CATGTCCCAGACA-GGTCTTACACTGACTTTCATATATCGAGGTCGATG
* * *
17636 TCATGTCCTAGACAGATCTTACACTGACTTTCATATATCGAGGCCGATG
1 -CATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGTCGATG
* * * * * * *
17685 CTATGTCCCAAACAGGTCTTACACTGGCTCTCATTTATCG-GTATTGTTG
1 C-ATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG-GTCGATG
* *
17734 CCATGTCCCAGACAGGTCTTATACT-AGCTTGT-ATATCTCGAGGTCGATG
1 -CATGTCCCAGACAGGTCTTACACTGA-CTT-TCATATATCGAGGTCGATG
* *
17783 CATGCCCCAGACATGTCTTACACT
1 CATGTCCCAGACAGGTCTTACACT
17807 AGCTCTCGTC
Statistics
Matches: 130, Mismatches: 32, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
47 18 0.14
48 37 0.28
49 72 0.55
50 3 0.02
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (48 bp):
CATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGTCGATG
Found at i:17754 original size:98 final size:97
Alignment explanation
Indices: 17637--17813 Score: 232
Period size: 98 Copynumber: 1.8 Consensus size: 97
17627 GAATTGATGT
* *
17637 CATGTCCTAGACAGATCTTACACT-GACTT-TCATATATCGAGGCCGATGCTATGTCCCAAACAG
1 CATGTCCCAGACAGATCTTACACTAG-CTTGT-ATATATCGAGGCCGATGC-ATGCCCCAAACAG
*
17700 GTCTTACACTGGCTCTCATTTATCGGTATTGTTGC
63 GTCTTACACTAGCTCTCATTTATCGGTATTGTTGC
* * * * * *
17735 CATGTCCCAGACAGGTCTTATACTAGCTTGTATATCTCGAGGTCGATGCATGCCCCAGACATGTC
1 CATGTCCCAGACAGATCTTACACTAGCTTGTATATATCGAGGCCGATGCATGCCCCAAACAGGTC
17800 TTACACTAGCTCTC
66 TTACACTAGCTCTC
17814 GTCTCAATGT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
97 26 0.38
98 40 0.59
99 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (97 bp):
CATGTCCCAGACAGATCTTACACTAGCTTGTATATATCGAGGCCGATGCATGCCCCAAACAGGTC
TTACACTAGCTCTCATTTATCGGTATTGTTGC
Found at i:22533 original size:39 final size:39
Alignment explanation
Indices: 22358--22540 Score: 179
Period size: 40 Copynumber: 4.6 Consensus size: 39
22348 TTGAATGCTG
* * * * * *
22358 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
22398 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
22438 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
22478 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
22517 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
22541 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 37 0.31
40 75 0.62
41 9 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:22537 original size:79 final size:81
Alignment explanation
Indices: 22359--22540 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 81
22349 TGAATGCTGT
* * * *
22359 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCCTTT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTCAATAAATCCGGACTAAGATCCGAAGGCCATT
*
22423 GTGCGAGATACTAAAT
66 GTGCGAGATACTAAAA
* * * **
22439 CCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTCATTAAATCCGGGTTAAG-TCCCGAAGG-CAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTCAATAAATCCGGACTAAGAT-CCGAAGGCCAT
* *
22501 TGTGTGAGTTACTAAAA
65 TGTGCGAGATACTAAAA
*
22518 CCGGGCTATGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
22541 TGAACGAGGA
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
79 38 0.44
80 42 0.49
81 6 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTCAATAAATCCGGACTAAGATCCGAAGGCCATT
GTGCGAGATACTAAAA
Done.