Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2960
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: 36269
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2049 original size:29 final size:27
Alignment explanation
Indices: 1999--2055 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
1989 ATAATTTTAT
* * *
1999 ATAAATAAAAGGTGGTTTTAAAATTAAA
1 ATAAATAAAAGGAGATTATAAAA-TAAA
2027 ATAAAGTAAAAGGAGATTATAAAATAAA
1 ATAAA-TAAAAGGAGATTATAAAATAAA
2055 A
1 A
2056 GAAAAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (27 bp):
ATAAATAAAAGGAGATTATAAAATAAA
Found at i:6789 original size:16 final size:15
Alignment explanation
Indices: 6766--6795 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6756 ACGAAAATAG
6766 AAAGGAAAGAAAGAA
1 AAAGGAAAGAAAGAA
6781 AAAGAGAAAGAAAGA
1 AAAG-GAAAGAAAGA
6796 CGCAAGACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAGGAAAGAAAGAA
Found at i:7476 original size:5 final size:5
Alignment explanation
Indices: 7448--7494 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
7438 CACTTTGATT
* * *
7448 ATTGA ATTGA TTTAA AGTTG- ATTGA ATTGA ATTGA ATTGA AATGA AT
1 ATTGA ATTGA ATTGA A-TTGA ATTGA ATTGA ATTGA ATTGA ATTGA AT
7495 ATATGTGTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 3 0.09
5 29 0.85
6 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (5 bp):
ATTGA
Found at i:7539 original size:24 final size:24
Alignment explanation
Indices: 7512--7590 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
7502 TTAATATGAA
7512 ATTTGGATATTGAATATTGGTTGT
1 ATTTGGATATTGAATATTGGTTGT
* * * * * *
7536 ATTTGGAAAGTGAGTTAAT--ATGAA
1 ATTTGGATATTGA-ATATTGGTTG-T
7560 ATTTGGATATTGAATATTGGTTGT
1 ATTTGGATATTGAATATTGGTTGT
7584 ATTTGGA
1 ATTTGGA
7591 AAGTGAAATT
Statistics
Matches: 39, Mismatches: 12, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
23 5 0.13
24 29 0.74
25 5 0.13
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.44
Consensus pattern (24 bp):
ATTTGGATATTGAATATTGGTTGT
Found at i:7555 original size:48 final size:48
Alignment explanation
Indices: 7501--7596 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
7491 GAATATATGT
7501 GTTAATATGAAATTTGGATATTGAATATTGGTTGTATTTGGAAAGTGA
1 GTTAATATGAAATTTGGATATTGAATATTGGTTGTATTTGGAAAGTGA
7549 GTTAATATGAAATTTGGATATTGAATATTGGTTGTATTTGGAAAGTGA
1 GTTAATATGAAATTTGGATATTGAATATTGGTTGTATTTGGAAAGTGA
7597 AATTAAACTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (48 bp):
GTTAATATGAAATTTGGATATTGAATATTGGTTGTATTTGGAAAGTGA
Found at i:18424 original size:76 final size:77
Alignment explanation
Indices: 18332--18486 Score: 294
Period size: 76 Copynumber: 2.0 Consensus size: 77
18322 GTATTGGAAG
18332 AAAGTATTAACAGAATTGTTATTTCTAAGATTCCTATCA-TTGAAATGTCAGTACTTTGTTTTCA
1 AAAGTATTAACAGAATTGTTATTTCTAAGATTCCTATCATTTGAAATGTCAGTACTTTGTTTTCA
18396 AAATTTGCTAAT
66 AAATTTGCTAAT
*
18408 AAAGTATTAACAGAATTGTTATTTCTAAGATTCCTATCATTTGAGATGTCAGTACTTTGTTTTCA
1 AAAGTATTAACAGAATTGTTATTTCTAAGATTCCTATCATTTGAAATGTCAGTACTTTGTTTTCA
18473 AAATTTGCTAAT
66 AAATTTGCTAAT
18485 AA
1 AA
18487 CTAAGACTGA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
76 39 0.51
77 38 0.49
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (77 bp):
AAAGTATTAACAGAATTGTTATTTCTAAGATTCCTATCATTTGAAATGTCAGTACTTTGTTTTCA
AAATTTGCTAAT
Found at i:21067 original size:20 final size:21
Alignment explanation
Indices: 21042--21086 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
21032 GTGAGAACTT
21042 TAAAAT-AAAATAATG-AAAAA
1 TAAAATGAAAATAA-GAAAAAA
*
21062 TAAAATGAAAATTAGAAAAAA
1 TAAAATGAAAATAAGAAAAAA
21083 TAAA
1 TAAA
21087 TTGGTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
TAAAATGAAAATAAGAAAAAA
Found at i:27662 original size:19 final size:19
Alignment explanation
Indices: 27628--27674 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
27618 ACACAGGTAA
27628 TTTTAAAATTTTCAAAATAAT
1 TTTTAAAA-TTTCAAAAT-AT
27649 TTTTAAAA-TTCAAAATAT
1 TTTTAAAATTTCAAAATAT
*
27667 TTATAAAA
1 TTTTAAAA
27675 ATCCAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 9 0.36
19 8 0.32
21 8 0.32
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTAAAATTTCAAAATAT
Found at i:27673 original size:18 final size:18
Alignment explanation
Indices: 27638--27688 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
27628 TTTTAAAATT
*
27638 TTCAAAATAATTTTTAAAA
1 TTCAAAAT-ATTTATAAAA
27657 TTCAAAATATTTATAAAA
1 TTCAAAATATTTATAAAA
* *
27675 ATCCAAA-ATTTATA
1 TTCAAAATATTTATA
27689 TTTTTTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 7 0.24
18 14 0.48
19 8 0.28
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
TTCAAAATATTTATAAAA
Found at i:27675 original size:19 final size:19
Alignment explanation
Indices: 27625--27683 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
27615 ATTACACAGG
*
27625 TAATTTTAAAATTTTCAAAA
1 TAATTTTAAAA-ATTCAAAA
*
27645 TAATTTTTAAAATTCAAAA
1 TAATTTTAAAAATTCAAAA
*
27664 T-ATTTATAAAAATCCAAAA
1 TAATTT-TAAAAATTCAAAA
27683 T
1 T
27684 TTATATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.12
19 20 0.59
20 10 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTTTAAAAATTCAAAA
Found at i:27746 original size:20 final size:19
Alignment explanation
Indices: 27710--27765 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
27700 ATATAGAAAT
27710 TATAAAAAAATCCTAAAGAA
1 TATAAAAAAATCCTAAA-AA
**
27730 TATAAAAAAATGTTAAAAA
1 TATAAAAAAATCCTAAAAA
*
27749 -GTAAAAAAAT-CTAAAAA
1 TATAAAAAAATCCTAAAAA
27766 AAACCTAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 6 0.19
18 9 0.28
19 2 0.06
20 15 0.47
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (19 bp):
TATAAAAAAATCCTAAAAA
Done.