Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2740
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: 37531
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:4889 original size:19 final size:19
Alignment explanation
Indices: 4865--4954 Score: 150
Period size: 19 Copynumber: 4.9 Consensus size: 19
4855 ATCATATCTC
4865 CTAAGATTGCATATCATAT
1 CTAAGATTGCATATCATAT
4884 CTAAGATTGCA-ATCATAT
1 CTAAGATTGCATATCATAT
4902 CTAAGATTG--TATCATAT
1 CTAAGATTGCATATCATAT
*
4919 CTAATATTGCATATCATAT
1 CTAAGATTGCATATCATAT
4938 CTAAGATTGCATATCAT
1 CTAAGATTGCATATCAT
4955 TGAAGATTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
17 15 0.23
18 16 0.24
19 35 0.53
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
CTAAGATTGCATATCATAT
Found at i:4919 original size:35 final size:37
Alignment explanation
Indices: 4865--4954 Score: 139
Period size: 35 Copynumber: 2.4 Consensus size: 37
4855 ATCATATCTC
4865 CTAAGATTGCATATCATATCTAAGATTGCA-ATCATAT
1 CTAAGATTG-ATATCATATCTAAGATTGCATATCATAT
*
4902 CTAAGATTG-TATCATATCTAATATTGCATATCATAT
1 CTAAGATTGATATCATATCTAAGATTGCATATCATAT
4938 CTAAGATTGCATATCAT
1 CTAAGATTG-ATATCAT
4955 TGAAGATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
35 18 0.37
36 16 0.33
37 9 0.18
38 6 0.12
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CTAAGATTGATATCATATCTAAGATTGCATATCATAT
Found at i:13758 original size:23 final size:23
Alignment explanation
Indices: 13732--13781 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
13722 GTTAAAGGTG
*
13732 AAATTAATAA-AAACATAAAATAA
1 AAATTAA-AAGAAAAATAAAATAA
13755 AAA-TAAAAGTAAAAATAAAATAA
1 AAATTAAAAG-AAAAATAAAATAA
13778 AAAT
1 AAAT
13782 AAACATCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 2 0.09
22 3 0.13
23 18 0.78
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATTAAAAGAAAAATAAAATAA
Found at i:13759 original size:6 final size:6
Alignment explanation
Indices: 13737--13784 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
13727 AGGTGAAATT
* *
13737 AATAAA AACATAA AATAAA AATAAA AGTAAA AAT-AA AATAAA AATAAA
1 AATAAA AATA-AA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
13785 CATCATCATC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 5 0.14
6 26 0.72
7 5 0.14
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:13762 original size:11 final size:11
Alignment explanation
Indices: 13741--13784 Score: 70
Period size: 11 Copynumber: 3.8 Consensus size: 11
13731 GAAATTAATA
13741 AAAACATAAAAT
1 AAAA-ATAAAAT
13753 AAAAATAAAAGT
1 AAAAATAAAA-T
13765 AAAAATAAAAT
1 AAAAATAAAAT
13776 AAAAATAAA
1 AAAAATAAA
13785 CATCATCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.52
12 15 0.48
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:19130 original size:41 final size:41
Alignment explanation
Indices: 19045--19224 Score: 218
Period size: 41 Copynumber: 4.4 Consensus size: 41
19035 CGGCATTTTG
* * *
19045 GTAAAACGCCGTTAAAAA-CAAAGCAATAGCGGCGCTTTCG
1 GTAAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTTCA
* *
19085 GTAAAGCGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCA
1 GTAAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTTCA
* * * *
19126 GTAAAACGCCGCTAAAAACCAGAGAATTAGCGACGCTTTCT
1 GTAAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTTCA
* ** * *
19167 GTAAAACGCCGCTAAAAACCAAAGCATTAACAACACTTTCG
1 GTAAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTTCA
*
19208 GTAAAACGCCGTTAAAA
1 GTAAAACGCCGCTAAAA
19225 GTCATATAAC
Statistics
Matches: 123, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 16 0.13
41 107 0.87
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (41 bp):
GTAAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTTCA
Found at i:21713 original size:19 final size:19
Alignment explanation
Indices: 21678--21775 Score: 146
Period size: 19 Copynumber: 5.2 Consensus size: 19
21668 AGATTACAAG
*
21678 ATCATATCTTCAAGATTGCTT
1 ATCATATC-T-AAGATTGCAT
21699 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
21718 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
*
21735 ATCATATCTAAGATTGCGT
1 ATCATATCTAAGATTGCAT
21754 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
21773 ATC
1 ATC
21776 CTTAAAGATT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
17 17 0.23
19 47 0.64
20 1 0.01
21 8 0.11
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:21742 original size:36 final size:37
Alignment explanation
Indices: 21678--21775 Score: 144
Period size: 36 Copynumber: 2.6 Consensus size: 37
21668 AGATTACAAG
21678 ATCATATCTTCAAGATTGCTTATCATATCTAAGATTGCAT
1 ATCATATC-T-AAGATTGC-TATCATATCTAAGATTGCAT
*
21718 ATCATATCTAAGATTG-TATCATATCTAAGATTGCGT
1 ATCATATCTAAGATTGCTATCATATCTAAGATTGCAT
21754 ATCATATCTAAGATTGCATATC
1 ATCATATCTAAGATTGC-TATC
21776 CTTAAAGATT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
36 35 0.64
38 11 0.20
39 1 0.02
40 8 0.15
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (37 bp):
ATCATATCTAAGATTGCTATCATATCTAAGATTGCAT
Found at i:22292 original size:13 final size:14
Alignment explanation
Indices: 22265--22301 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
22255 TTAAAACTAT
22265 AACCCCTAAACCCC
1 AACCCCTAAACCCC
*
22279 AACCCTTAAA-CCC
1 AACCCCTAAACCCC
22292 AACCCCTAAA
1 AACCCCTAAA
22302 ACAATGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.41, C:0.49, G:0.00, T:0.11
Consensus pattern (14 bp):
AACCCCTAAACCCC
Found at i:22597 original size:15 final size:15
Alignment explanation
Indices: 22579--22682 Score: 95
Period size: 15 Copynumber: 7.0 Consensus size: 15
22569 AAATAAACTC
22579 AAAAAATTAAAATTT
1 AAAAAATTAAAATTT
*
22594 AAAAATTTAAAATTT
1 AAAAAATTAAAATTT
*
22609 -AAAATTTAAAATTT
1 AAAAAATTAAAATTT
* *
22623 -AAAAATAAAAATTA
1 AAAAAATTAAAATTT
* *
22637 AAAAAATAAAAACTT
1 AAAAAATTAAAATTT
* *
22652 AAAAACTTAAAAACTT
1 AAAAAATT-AAAATTT
* *
22668 AAAAATTTAATATTT
1 AAAAAATTAAAATTT
22683 TAGTCCATAT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
14 25 0.33
15 37 0.49
16 14 0.18
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAAATTAAAATTT
Found at i:22598 original size:8 final size:8
Alignment explanation
Indices: 22587--22677 Score: 95
Period size: 8 Copynumber: 12.1 Consensus size: 8
22577 TCAAAAAATT
22587 AAAATTTA
1 AAAATTTA
22595 AAAATTT-
1 AAAATTTA
22602 AAAATTT-
1 AAAATTTA
22609 AAAATTT-
1 AAAATTTA
22616 AAAATTTA
1 AAAATTTA
22624 AAAA--TA
1 AAAATTTA
22630 AAAA-TTA
1 AAAATTTA
**
22637 AAAAAATA
1 AAAATTTA
*
22645 AAAACTTA
1 AAAATTTA
*
22653 AAAACTTA
1 AAAATTTA
*
22661 AAAACTTA
1 AAAATTTA
22669 AAAATTTA
1 AAAATTTA
22677 A
1 A
22678 TATTTTAGTC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
6 6 0.08
7 27 0.36
8 43 0.57
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (8 bp):
AAAATTTA
Found at i:22647 original size:6 final size:7
Alignment explanation
Indices: 22580--22674 Score: 93
Period size: 7 Copynumber: 13.0 Consensus size: 7
22570 AATAAACTCA
22580 AAAAATT
1 AAAAATT
*
22587 AAAATTT
1 AAAAATT
22594 AAAAATTT
1 AAAAA-TT
*
22602 AAAATTT
1 AAAAATT
*
22609 AAAATTT
1 AAAAATT
*
22616 AAAATTT
1 AAAAATT
22623 AAAAA-T
1 AAAAATT
22629 AAAAATT
1 AAAAATT
*
22636 AAAAAAAT
1 -AAAAATT
22644 AAAAACTT
1 AAAAA-TT
22652 AAAAACTT
1 AAAAA-TT
22660 AAAAACTT
1 AAAAA-TT
22668 AAAAATT
1 AAAAATT
22675 TAATATTTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
6 6 0.08
7 38 0.49
8 34 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (7 bp):
AAAAATT
Found at i:22814 original size:21 final size:21
Alignment explanation
Indices: 22771--22814 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22761 TTTTAAATAA
**
22771 AAAAATAGAAAAAAATATGTT
1 AAAAATAGAAAAAAATAAATT
22792 AAAAAT-GAAAAAAATAAAATT
1 AAAAATAGAAAAAAAT-AAATT
22813 AA
1 AA
22815 GCAATAGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAAATAGAAAAAAATAAATT
Found at i:26621 original size:19 final size:19
Alignment explanation
Indices: 26598--26651 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
26588 ATTTAATCTA
26598 ATTTTTATTATT-TA-TTTT
1 ATTTTTATT-TTATATTTTT
*
26616 AGTTTTGATTTTATATTTTT
1 A-TTTTTATTTTATATTTTT
26636 ATTTTTATTTTA-ATTT
1 ATTTTTATTTTATATTT
26652 GATAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 7 0.23
19 19 0.61
20 5 0.16
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (19 bp):
ATTTTTATTTTATATTTTT
Found at i:26646 original size:6 final size:6
Alignment explanation
Indices: 26598--26651 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
26588 ATTTAATCTA
* *
26598 ATTTTT ATTATTT A-TTTT AGTTTTG ATTTTAT ATTTTT ATTTTT ATTTTA
1 ATTTTT ATT-TTT ATTTTT A-TTTTT ATTTT-T ATTTTT ATTTTT ATTTTT
26648 ATTT
1 ATTT
26652 GATAATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
5 4 0.10
6 24 0.59
7 13 0.32
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:31778 original size:5 final size:5
Alignment explanation
Indices: 31768--31799 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
31758 GGCTTTGTGA
31768 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
31800 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:31793 original size:9 final size:9
Alignment explanation
Indices: 31769--31799 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
31759 GCTTTGTGAA
31769 AAATAAAAT
1 AAATAAAAT
31778 AAAATAAAAT
1 -AAATAAAAT
31788 AAATAAAAT
1 AAATAAAAT
31797 AAA
1 AAA
31800 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:35595 original size:40 final size:40
Alignment explanation
Indices: 35565--35697 Score: 198
Period size: 40 Copynumber: 3.3 Consensus size: 40
35555 GCTACTCGTT
*
35565 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCA
*
35605 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-TTATAGTAACTCGCA
* *
35645 CAAATGCCTTCGGGACTTAACCCGAATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCG-GTTATAGTAACTCGCA
35685 CAAATGCCTTCGG
1 CAAATGCCTTCGG
35698 ATCTTAGTCC
Statistics
Matches: 88, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
40 86 0.98
41 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCA
Found at i:35677 original size:80 final size:81
Alignment explanation
Indices: 35565--35748 Score: 241
Period size: 80 Copynumber: 2.3 Consensus size: 81
35555 GCTACTCGTT
* *
35565 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
35629 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
35645 CAAATGCCTTCGGGACTTAACCCGAATT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCG-ATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
35709 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
35726 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
35749 GACATCATTC
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
79 3 0.03
80 78 0.86
81 10 0.11
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Done.