Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1756
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: 41030
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:9611 original size:23 final size:21
Alignment explanation
Indices: 9581--9623 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
9571 CAATTATCAT
9581 AAATTTAATTTGTATAATTAATA
1 AAATTTAA-TTGTA-AATTAATA
9604 AAATTTAATTGTAAATTAAT
1 AAATTTAATTGTAAATTAAT
9624 TTTTACCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
AAATTTAATTGTAAATTAATA
Found at i:11117 original size:14 final size:15
Alignment explanation
Indices: 11089--11119 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11079 CATTTTTTAT
11089 TTTTTTAATAGAAAA
1 TTTTTTAATAGAAAA
*
11104 TTTTTTAATAAAAAA
1 TTTTTTAATAGAAAA
11119 T
1 T
11120 GAAAACTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTTTTAATAGAAAA
Found at i:12020 original size:72 final size:72
Alignment explanation
Indices: 11926--12443 Score: 601
Period size: 72 Copynumber: 7.2 Consensus size: 72
11916 AAGAGTTTGA
* *
11926 AACAGTTAGACCTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACC
1 AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACC
11991 AATTTAG
66 AATTTAG
** * * * * *
11998 AACAGTTGGACTTATCCAATAACCAAATTCGTGGTATTATCCC-CTTAGAC-TGGGGAACATGAA
1 AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTA-CCTTAGGCAAC-TTAA
* *
12061 -GAGTTT-G
64 CCAATTTAG
*
12068 AAACAGTTGGACCTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
1 -AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
12133 CAATTTAG
65 CAATTTAG
* * ** * *
12141 AACAGTTGGACTTCTCCAATAACCAAATTCGTGGTCCTAT-CC-CCTAGACTGGGGGAACATGAA
1 AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTA-CCTTAGGCAAC-TTAA
* *
12204 -GAGTTT-G
64 CCAATTTAG
*
12211 AAACAGTTGGACATATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
1 -AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
12276 CAATTTAG
65 CAATTTAG
* * ** * *
12284 AACAGTTGGACTTCTCCAATAACCAAATTCGTGGTCCTAT-CC-CCTAGACTGGGGGAACATGAA
1 AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTA-CCTTAGGCAAC-TTAA
* *
12347 -GAGTTT-G
64 CCAATTTAG
*
12354 AAACAGTTGGACATATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
1 -AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
12419 CAATTTAG
65 CAATTTAG
12427 AACAGTTGGACTTATCC
1 AACAGTTGGACTTATCC
12444 TTTAATCAAA
Statistics
Matches: 367, Mismatches: 58, Indels: 42
0.79 0.12 0.09
Matches are distributed among these distances:
70 11 0.03
71 165 0.45
72 180 0.49
73 11 0.03
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (72 bp):
AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACC
AATTTAG
Found at i:12082 original size:143 final size:143
Alignment explanation
Indices: 11892--12443 Score: 1018
Period size: 143 Copynumber: 3.9 Consensus size: 143
11882 ATTACCGGTT
* *
11892 CTATCCCCTAGACT-GGGGAACATGAAGAGTTTGAAACAGTTAGACCTATCCAATAACCAAATTC
1 CTATCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACATATCCAATAACCAAATTC
11956 GTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTATCCAATAAC
66 GTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTATCCAATAAC
*
12021 CAAATTCGTGGTA
131 CAAATTCGTGGTC
* *
12034 TTATCCCCTTAGACT-GGGGAACATGAAGAGTTTGAAACAGTTGGACCTATCCAATAACCAAATT
1 CTATCCCC-TAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACATATCCAATAACCAAATT
*
12098 CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTCTCCAATAA
65 CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTATCCAATAA
12163 CCAAATTCGTGGTC
130 CCAAATTCGTGGTC
12177 CTATCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACATATCCAATAACCAAATTC
1 CTATCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACATATCCAATAACCAAATTC
*
12242 GTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTCTCCAATAAC
66 GTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTATCCAATAAC
12307 CAAATTCGTGGTC
131 CAAATTCGTGGTC
12320 CTATCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACATATCCAATAACCAAATTC
1 CTATCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACATATCCAATAACCAAATTC
12385 GTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTATCC
66 GTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTATCC
12444 TTTAATCAAA
Statistics
Matches: 401, Mismatches: 7, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
142 13 0.03
143 388 0.97
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (143 bp):
CTATCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACATATCCAATAACCAAATTC
GTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTATCCAATAAC
CAAATTCGTGGTC
Found at i:21432 original size:23 final size:23
Alignment explanation
Indices: 21406--21481 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
21396 ATAAGTGCCA
21406 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
21429 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
21452 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
21475 CACTGAT
1 CACTGAT
21482 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:21581 original size:8 final size:8
Alignment explanation
Indices: 21568--21596 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
21558 ACCCGGGACT
21568 CACTGTAA
1 CACTGTAA
21576 CACTGTAA
1 CACTGTAA
21584 CACTGTAA
1 CACTGTAA
21592 CACTG
1 CACTG
21597 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:21727 original size:18 final size:17
Alignment explanation
Indices: 21701--21739 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
21691 ATTTTCCTTC
21701 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
21718 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
21736 CACA
1 CACA
21740 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:23206 original size:17 final size:17
Alignment explanation
Indices: 23180--23221 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
23170 GGCTTACACT
*
23180 TTTGGTTTGTTCGCCAC
1 TTTGGCTTGTTCGCCAC
**
23197 TTTGGCTTGTTCTTCAC
1 TTTGGCTTGTTCGCCAC
23214 TTTGGCTT
1 TTTGGCTT
23222 ACATTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.05, C:0.21, G:0.21, T:0.52
Consensus pattern (17 bp):
TTTGGCTTGTTCGCCAC
Found at i:24339 original size:30 final size:30
Alignment explanation
Indices: 24282--24339 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
24272 AGAAGTTGAT
* **
24282 TTAAATTTTGAAATATGAAAATTAAAAGGA
1 TTAAATTTTCAAATATGAAAAGGAAAAGGA
24312 TTAAA-TTTCAAATATGTAAAAGGAAAAG
1 TTAAATTTTCAAATATG-AAAAGGAAAAG
24340 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (30 bp):
TTAAATTTTCAAATATGAAAAGGAAAAGGA
Found at i:27335 original size:32 final size:31
Alignment explanation
Indices: 27280--27345 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
27270 TTAAAAATAT
*
27280 AAAAAATATTTAAAATTTATTAAAAATTAGA
1 AAAAAAAATTTAAAATTTATTAAAAATTAGA
* * *
27311 AAAAAAAATTGTAAATTTTTTTAAAAATTATA
1 AAAAAAAATT-TAAAATTTATTAAAAATTAGA
27343 AAA
1 AAA
27346 TGCATCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAAAAATTTAAAATTTATTAAAAATTAGA
Found at i:27430 original size:20 final size:21
Alignment explanation
Indices: 27407--27461 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 21
27397 GATTTTTATT
27407 TTTTTATATATTTT-TTAC-AA
1 TTTTTATA-ATTTTGTTACTAA
*
27427 -TTTTATAATTTTGTTTCTAA
1 TTTTTATAATTTTGTTACTAA
27447 TTTTTAATAAATTTT
1 TTTTT-AT-AATTTT
27462 AGATGTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.17
19 10 0.34
20 2 0.07
21 4 0.14
22 2 0.07
23 6 0.21
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTATAATTTTGTTACTAA
Found at i:33683 original size:21 final size:21
Alignment explanation
Indices: 33657--33697 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33647 ATCTGCTCAA
* *
33657 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
33678 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
33698 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Done.