Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_791
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: 46688
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Found at i:2609 original size:30 final size:30
Alignment explanation
Indices: 2570--2628 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2560 TTTTTCATAA
* *
2570 TATTAATTAT-AAATTTTTCTATTTATATTT
1 TATTAATTATCAAAGTATT-TATTTATATTT
*
2600 TATTTATTATCAAAGTATTTATTTATATT
1 TATTAATTATCAAAGTATTTATTTATATT
2629 ATACGTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (30 bp):
TATTAATTATCAAAGTATTTATTTATATTT
Found at i:11355 original size:45 final size:45
Alignment explanation
Indices: 11283--11411 Score: 177
Period size: 45 Copynumber: 2.9 Consensus size: 45
11273 TGACATAGTT
* * *
11283 CGCATGTATGAGTCTGCCATATCTATGAATCTTCTTTTATGAATC
1 CGCATGTATGAGTCCGCTATATCTATGAATCTTCTTCTATGAATC
* * *
11328 CGTATGTATGAGTCCACTATATTTATGAATCTTCTTCTATGAATC
1 CGCATGTATGAGTCCGCTATATCTATGAATCTTCTTCTATGAATC
* * *
11373 CGCATGTATGAGCCCGTTATATCTATGAATATTCTTCTA
1 CGCATGTATGAGTCCGCTATATCTATGAATCTTCTTCTA
11412 CAAATTTGAA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (45 bp):
CGCATGTATGAGTCCGCTATATCTATGAATCTTCTTCTATGAATC
Found at i:16848 original size:13 final size:12
Alignment explanation
Indices: 16821--16859 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16811 GCCTTATTTA
*
16821 TTTTATACAATT
1 TTTTATAAAATT
16833 TTTTATAAATATT
1 TTTTATAAA-ATT
*
16846 TTTTATATAATT
1 TTTTATAAAATT
16858 TT
1 TT
16860 GTTTTTCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTATAAAATT
Found at i:19346 original size:16 final size:17
Alignment explanation
Indices: 19315--19348 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
19305 TTTATCTAAT
19315 TATATTTAATAATTTTA
1 TATATTTAATAATTTTA
19332 TATATTTAA-AATTTTA
1 TATATTTAATAATTTTA
19348 T
1 T
19349 TAGTTAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTTAATAATTTTA
Found at i:23224 original size:18 final size:17
Alignment explanation
Indices: 23192--23235 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
23182 GGGTGAGAAG
23192 TAAAAGTTTAGGGGGAAA
1 TAAAAGTTTAGGGGG-AA
*
23210 TAAAAAGTTT-TGGGGAA
1 T-AAAAGTTTAGGGGGAA
23227 TAAAAGTTT
1 TAAAAGTTT
23236 GAGAGAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 5 0.21
19 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (17 bp):
TAAAAGTTTAGGGGGAA
Found at i:23367 original size:31 final size:31
Alignment explanation
Indices: 23327--23386 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
23317 AGAGGTGGGA
23327 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAAG
1 TGGGAAGGGAATAAAA-TTTTAGGGAAAAAAG
* * *
23359 TGGG-AGGGAGTAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAATTTTAGGGAAAAA
23387 TAAAATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 11 0.44
31 10 0.40
32 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAATTTTAGGGAAAAAAG
Found at i:24745 original size:18 final size:19
Alignment explanation
Indices: 24704--24745 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
24694 TTTATAAAAC
* *
24704 ATAATATTTAAAATATGAT
1 ATAATATTAAAAATATGAA
*
24723 GTAATATTAAAAATA-GAA
1 ATAATATTAAAAATATGAA
24741 ATAAT
1 ATAAT
24746 GGTATAAATG
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (19 bp):
ATAATATTAAAAATATGAA
Found at i:25369 original size:27 final size:27
Alignment explanation
Indices: 25331--25382 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
25321 TTAAGAGTTT
25331 ATGCAAATGAGTTTTCTAAAAAAAAAC
1 ATGCAAATGAGTTTTCTAAAAAAAAAC
25358 ATGCAAATGAGTTTTCTAAAAAAAA
1 ATGCAAATGAGTTTTCTAAAAAAAA
25383 CGTGTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.27
Consensus pattern (27 bp):
ATGCAAATGAGTTTTCTAAAAAAAAAC
Found at i:25459 original size:14 final size:13
Alignment explanation
Indices: 25430--25463 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
25420 AAACAATAAT
*
25430 AAATAATAAATTA
1 AAATAATAAATGA
25443 AAATAAGTAAATGA
1 AAATAA-TAAATGA
25457 AAATAAT
1 AAATAAT
25464 TATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (13 bp):
AAATAATAAATGA
Found at i:37663 original size:9 final size:9
Alignment explanation
Indices: 37651--37840 Score: 66
Period size: 10 Copynumber: 20.4 Consensus size: 9
37641 TTTTATTTTT
37651 TTTTTATAA
1 TTTTTATAA
37660 TTTTTATAA
1 TTTTTATAA
*
37669 GTTTATATCAA
1 -TTTTTAT-AA
* *
37680 TTTTAATAC
1 TTTTTATAA
*
37689 TTTTTATTA
1 TTTTTATAA
* *
37698 TTTTGTAGAC
1 TTTT-TATAA
* *
37708 TTTTAATATG
1 TTTTTATA-A
37718 TTTTTATAA
1 TTTTTATAA
*
37727 ATTTTA-AA
1 TTTTTATAA
* *
37735 CATTTTAAACA
1 -TTTTTATA-A
*
37746 TTTTTATTA
1 TTTTTATAA
* *
37755 GTTTTGTAA
1 TTTTTATAA
*
37764 TTCTT-TAA
1 TTTTTATAA
37772 TTTTTAATAA
1 TTTTT-ATAA
**
37782 TTTATTATTT
1 TTT-TTATAA
*
37792 TTTTTAT-T
1 TTTTTATAA
37800 TTTTTAT-A
1 TTTTTATAA
37808 -TTTTATAAA
1 TTTTTAT-AA
*
37817 TTTATATCAA
1 TTTTTAT-AA
*
37827 TTTTCATATA
1 TTTTTATA-A
37837 TTTT
1 TTTT
37841 AATATTTAAT
Statistics
Matches: 135, Mismatches: 32, Indels: 27
0.70 0.16 0.14
Matches are distributed among these distances:
7 6 0.04
8 17 0.13
9 49 0.36
10 58 0.43
11 5 0.04
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:37711 original size:28 final size:29
Alignment explanation
Indices: 37679--37763 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 29
37669 GTTTATATCA
*
37679 ATTTTAATACTTTTTATTATTTTGTAGAC
1 ATTTTAATACTTTTTATTATTTTGTAAAC
* * *
37708 -TTTTAATATGTTTTTATAAATTT-TAAAC
1 ATTTTAATA-CTTTTTATTATTTTGTAAAC
37736 ATTTTAA-ACATTTTTATTAGTTTTGTAA
1 ATTTTAATAC-TTTTTATTA-TTTTGTAA
37764 TTCTTTAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
28 21 0.48
29 20 0.45
30 3 0.07
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.58
Consensus pattern (29 bp):
ATTTTAATACTTTTTATTATTTTGTAAAC
Found at i:39728 original size:31 final size:31
Alignment explanation
Indices: 39651--39751 Score: 96
Period size: 37 Copynumber: 3.1 Consensus size: 31
39641 TGCCGATTTG
39651 CTCAGTTTCTGCCGATTTGCTCCCTCTGTTT
1 CTCAGTTTCTGCCGATTTGCTCCCTCTGTTT
** *
39682 CTTTCTTTTCTTTTCTGTCGATTTGCTCCCTCTGTTT
1 C--TC----AGTTTCTGCCGATTTGCTCCCTCTGTTT
*
39719 CTCAGTTTCTGCCGATTTGCGT-CTTCTGTTT
1 CTCAGTTTCTGCCGATTTGC-TCCCTCTGTTT
39750 CT
1 CT
39752 TTTCTTTTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
31 25 0.45
32 1 0.02
33 2 0.04
35 2 0.04
37 26 0.46
ACGTcount: A:0.05, C:0.29, G:0.15, T:0.51
Consensus pattern (31 bp):
CTCAGTTTCTGCCGATTTGCTCCCTCTGTTT
Found at i:41521 original size:23 final size:22
Alignment explanation
Indices: 41478--41536 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 22
41468 TTGTTTTGAT
41478 ATTGTTCTTGATTTGTTCTGGAA
1 ATTGTTCTTGA-TTGTTCTGGAA
41501 ATTGTT-TTGATTGTCTGCTGGAA
1 ATTGTTCTTGATTGT-T-CTGGAA
41524 ATTGTTCTTGATT
1 ATTGTTCTTGATT
41537 TGTTAGTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.12
22 5 0.15
23 18 0.55
24 6 0.18
ACGTcount: A:0.17, C:0.08, G:0.22, T:0.53
Consensus pattern (22 bp):
ATTGTTCTTGATTGTTCTGGAA
Found at i:42384 original size:31 final size:31
Alignment explanation
Indices: 42346--42409 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
42336 CCATCATTCT
*
42346 TTATTAAACCAAATCCTCATTCTTTATTTTA
1 TTATTAAACCAAATCCTCATTATTTATTTTA
42377 TTATTAAACCAAATCCTCATTATTTATTTTA
1 TTATTAAACCAAATCCTCATTATTTATTTTA
42408 TT
1 TT
42410 TGTTTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (31 bp):
TTATTAAACCAAATCCTCATTATTTATTTTA
Found at i:42483 original size:37 final size:37
Alignment explanation
Indices: 42433--42521 Score: 151
Period size: 37 Copynumber: 2.4 Consensus size: 37
42423 GAAAACCTTA
* *
42433 ATTAAATTAATCAATGTTCAAACTTTGAACATGCTTT
1 ATTAAACTAATCAATGTTAAAACTTTGAACATGCTTT
42470 ATTAAACTAATCAATGTTAAAACTTTGAACATGCTTT
1 ATTAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
42507 AATAAACTAATCAAT
1 ATTAAACTAATCAAT
42522 ATATTTATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (37 bp):
ATTAAACTAATCAATGTTAAAACTTTGAACATGCTTT
Found at i:42772 original size:33 final size:33
Alignment explanation
Indices: 42735--42800 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
42725 AATCTAACAA
42735 ATACCAACAATTAATTTTAGGTCAATTATACAT
1 ATACCAACAATTAATTTTAGGTCAATTATACAT
42768 ATACCAACAATTAATTTTAGGTCAATTATACAT
1 ATACCAACAATTAATTTTAGGTCAATTATACAT
42801 GCTTTATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (33 bp):
ATACCAACAATTAATTTTAGGTCAATTATACAT
Found at i:45938 original size:91 final size:90
Alignment explanation
Indices: 45791--45997 Score: 333
Period size: 91 Copynumber: 2.3 Consensus size: 90
45781 TTGATTTTAG
* *
45791 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
45856 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAA-TATTTTAAATTATA
*
45883 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
45948 TGTAATAATAATATTTTAAATTATA
66 TGTAATAATAATATTTTAAATTATA
*
45973 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
45998 GTTATAATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 37 0.34
91 55 0.51
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (90 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATATTTTAAATTATA
Found at i:45949 original size:28 final size:25
Alignment explanation
Indices: 45913--45972 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
45903 TATTATCAAG
* *
45913 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAA-TA-ATAATATT-TTA
*
45941 AATTATATGTAATAATAATATTTTA
1 AATTATATGAAATAATAATATTTTA
45966 AATTATA
1 AATTATA
45973 CAAATTCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 10 0.34
26 7 0.24
27 2 0.07
28 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
AATTATATGAAATAATAATATTTTA
Found at i:46013 original size:47 final size:45
Alignment explanation
Indices: 45865--46016 Score: 127
Period size: 47 Copynumber: 3.3 Consensus size: 45
45855 TATTTAATAT
*
45865 TAATTATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAA
1 TAATTATTTTAAATTATA-AAATTCATATAAGAAAATTTATTAT-AA
* * * **
45912 GAATT-TTATGAAATTAT-ATATT-AT-T-ATTAAATTATATGTAATAA
1 TAATTATT-TTAAATTATAAAATTCATATAAGAAAATT-TAT-T-ATAA
*
45956 TAA-TATTTTAAATTATACAAATTCATATAAGAAAATTTATTAGTTA
1 TAATTATTTTAAATTATA-AAATTCATATAAGAAAATTTATTA-TAA
46002 TAATTATTTTAAATT
1 TAATTATTTTAAATT
46017 TTATTAAATC
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
42 6 0.07
43 13 0.16
44 9 0.11
45 11 0.14
46 10 0.12
47 26 0.32
48 6 0.07
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.47
Consensus pattern (45 bp):
TAATTATTTTAAATTATAAAATTCATATAAGAAAATTTATTATAA
Found at i:46214 original size:119 final size:120
Alignment explanation
Indices: 46013--46425 Score: 712
Period size: 119 Copynumber: 3.5 Consensus size: 120
46003 AATTATTTTA
* *
46013 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
46077 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
46133 AATTTTATTAAATTATATATTTTAATTAAAATAT-TTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
46197 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
46252 AATTTTATTAAATTATATA-TTT--TTATAATATATTTAATAATAATTATGTT-AATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
*
46313 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
46368 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
46426 ATGATTAAAT
Statistics
Matches: 281, Mismatches: 5, Indels: 13
0.94 0.02 0.04
Matches are distributed among these distances:
116 91 0.32
117 21 0.07
118 3 0.01
119 126 0.45
120 37 0.13
121 3 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:46403 original size:16 final size:16
Alignment explanation
Indices: 46382--46423 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
46372 TTATTAAATT
*
46382 ATATATTTTAATTATA
1 ATATATTTTAATAATA
46398 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
46413 AT-TATGTTTAA
1 ATATAT-TTTAA
46424 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:46408 original size:15 final size:15
Alignment explanation
Indices: 46373--46414 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
46363 TTAAGAATTT
*
46373 TATTAAATTAT-ATA
1 TATTTAATTATAATA
46387 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
46401 TATTTAATAATAAT
1 TATTTAATTATAAT
46415 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Done.