Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold624
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: 37714
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Found at i:3570 original size:16 final size:16
Alignment explanation
Indices: 3546--3596 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
3536 AGTAATCGGC
*
3546 AAATCCCGAAAAGCCG
1 AAATGCCGAAAAGCCG
*
3562 AAATGCCGAAAAGTCG
1 AAATGCCGAAAAGCCG
* * *
3578 AAATGACAAAAAGCTG
1 AAATGCCGAAAAGCCG
3594 AAA
1 AAA
3597 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.10
Consensus pattern (16 bp):
AAATGCCGAAAAGCCG
Found at i:3858 original size:28 final size:28
Alignment explanation
Indices: 3809--3892 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
3799 GAGCATGACT
*
3809 GTAAATGTGATTTGGGCCTAATGGGCCAC
1 GTAAATGTGA-ATGGGCCTAATGGGCCAC
3838 GTAAATGTGAATGGGCCTAATGGGCCAC
1 GTAAATGTGAATGGGCCTAATGGGCCAC
3866 GTAAATGTGAATGGGCCTAATGGGCCA
1 GTAAATGTGAATGGGCCTAATGGGCCA
3893 TATGAAAGAG
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 44 0.81
29 10 0.19
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
GTAAATGTGAATGGGCCTAATGGGCCAC
Found at i:3911 original size:56 final size:56
Alignment explanation
Indices: 3809--3919 Score: 127
Period size: 56 Copynumber: 2.0 Consensus size: 56
3799 GAGCATGACT
* * * *
3809 GTAAATGTGATTTGGGCCTAATGGGCCACGTAAATGTGAATGGGCCTAATGGGCCAC
1 GTAAATGTGATATGGGCCTAATGGGCCACATAAATGAGAATAGGCCT-ATGGGCCAC
* * *
3866 GTAAATGTGA-ATGGGCCTAATGGGCCATATGAAA-GAGATTAGGCCTGTGGGCCA
1 GTAAATGTGATATGGGCCTAATGGGCCACAT-AAATGAGAATAGGCCTATGGGCCA
3920 TATATAGGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
55 7 0.15
56 26 0.57
57 13 0.28
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.23
Consensus pattern (56 bp):
GTAAATGTGATATGGGCCTAATGGGCCACATAAATGAGAATAGGCCTATGGGCCAC
Found at i:5604 original size:40 final size:38
Alignment explanation
Indices: 5512--5607 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 38
5502 CTATCTCGGT
*
5512 ATCGCACACTTAGTGCCTCATATAGCCGAAACCATTCTA
1 ATCGCACACTTAGTG-CTCATATAGCCGAAACCATTCGA
* * *
5551 ATTGGCACCCTTAGTGCT-ATTTATAGCCGAAACTATTTCGA
1 A-TCGCACACTTAGTGCTCA--TATAGCCGAAACCA-TTCGA
5592 ATCGCACACTTAGTGC
1 ATCGCACACTTAGTGC
5608 CGAACACAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
38 1 0.02
39 3 0.06
40 38 0.81
41 5 0.11
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (38 bp):
ATCGCACACTTAGTGCTCATATAGCCGAAACCATTCGA
Found at i:11715 original size:39 final size:39
Alignment explanation
Indices: 11628--11823 Score: 245
Period size: 39 Copynumber: 5.0 Consensus size: 39
11618 CAAATCCAAT
* * *
11628 CACCACCAC-AAAGCATGCGGGACTTTAAGCCCGGATATAA
1 CACCAGCACGAAAGCCTTCGGGAC-TT-AGCCCGGATATAA
* *
11668 TACCAGCAC-AAAGCCTACGGGACTTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTTCGGGAC-TTAGCCCGGATATAA
* * *
11707 CACTAGCACGAATGCCTTCGGGACTTAGCCCAGATATAA
1 CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
* *
11746 CACCAGCACGAATGCCTTTGGGACTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
11785 CACCAGCACGAATA-CCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAA-AGCCTTCGGGACTTAGCCCGGATATAA
11824 TTCTCCATTA
Statistics
Matches: 140, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 106 0.76
40 34 0.24
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (39 bp):
CACCAGCACGAAAGCCTTCGGGACTTAGCCCGGATATAA
Found at i:13152 original size:68 final size:67
Alignment explanation
Indices: 13106--13263 Score: 280
Period size: 68 Copynumber: 2.3 Consensus size: 67
13096 ATACTATATA
13106 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACG-GAGAGATA
13171 AAT
65 AAT
13174 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACG-GAGAGATA
13239 AAT
65 AAT
* *
13242 GTAGCTAGGTCGCATGAGTGAT
1 GTAGCTAGGTCACATGTGTGAT
13264 TCCAAGTAAA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 88 1.00
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (67 bp):
GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGGAGAGATAA
AT
Found at i:20206 original size:39 final size:39
Alignment explanation
Indices: 20152--20392 Score: 385
Period size: 39 Copynumber: 6.2 Consensus size: 39
20142 TTTAAGCCTT
* * *
20152 GATATAATACCAGCAC-AAAGCCTACGGGACTTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCCG
20191 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
20230 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
* * *
20269 GATATAACACCAGCACGAGTGCCTTCGGGTCTGAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
* *
20308 GATATAACACCAACATGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
*
20347 GATACAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
20386 GATATAA
1 GATATAA
20393 TTCTCCATTA
Statistics
Matches: 186, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 174 0.94
40 12 0.06
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.18
Consensus pattern (39 bp):
GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
Found at i:26065 original size:78 final size:78
Alignment explanation
Indices: 25952--26190 Score: 385
Period size: 77 Copynumber: 3.1 Consensus size: 78
25942 TTTAAGCCTT
* * *
25952 GATATAATACCAGCAC-AAAGCCTACGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 GATATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
26016 CGGGACTTAGCCCG
65 CGGGACTTAGCCCG
26030 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
*
26095 GGGTC-TAGCCCG
66 GGGACTTAGCCCG
* * *
26107 GATATAACACCAACATGAATGCCTTCGGGACTTAG-CCGGATACAACACCAGCACGAATGCCTTC
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
26171 GGGACTTAGCCCG
66 GGGACTTAGCCCG
26184 GATATAA
1 GATATAA
26191 TTCTCCATTA
Statistics
Matches: 151, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
76 32 0.21
77 54 0.36
78 53 0.35
79 12 0.08
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.18
Consensus pattern (78 bp):
GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
GGGACTTAGCCCG
Found at i:26113 original size:38 final size:39
Alignment explanation
Indices: 25952--26190 Score: 385
Period size: 39 Copynumber: 6.2 Consensus size: 39
25942 TTTAAGCCTT
* * *
25952 GATATAATACCAGCAC-AAAGCCTACGGGACTTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCCG
25991 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
26030 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
*
26069 GATATAACACCAGCACGAATGCCTTCGGGTC-TAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
* *
26107 GATATAACACCAACATGAATGCCTTCGGGACTTAG-CCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
*
26145 GATACAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
26184 GATATAA
1 GATATAA
26191 TTCTCCATTA
Statistics
Matches: 186, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
38 70 0.38
39 104 0.56
40 12 0.06
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.18
Consensus pattern (39 bp):
GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
Found at i:31787 original size:39 final size:39
Alignment explanation
Indices: 31733--31973 Score: 403
Period size: 39 Copynumber: 6.2 Consensus size: 39
31723 TTTAAGCCTT
* * *
31733 GATATAATACCAGCAC-AAAGCCTACGGGACTTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCCG
31772 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
31811 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
*
31850 GATATAACACCAGCACGAATGCCTTCGGGTCTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
* *
31889 GATATAACACCAACATGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
*
31928 GATACAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
1 GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
31967 GATATAA
1 GATATAA
31974 TTCTCCATTA
Statistics
Matches: 190, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 178 0.94
40 12 0.06
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (39 bp):
GATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG
Found at i:37581 original size:39 final size:39
Alignment explanation
Indices: 37556--37713 Score: 282
Period size: 39 Copynumber: 4.1 Consensus size: 39
37546 CAAGCCGAAT
37556 GGGACTTTAGCCC-GATATAACACCAGCACGAATGCCTTC
1 GGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTTC
37595 GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
1 GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
37634 GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
1 GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
* *
37673 GGGACTTAGCCCGGATATAACACCAACATGAATGCCTTC
1 GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
37712 GG
1 GG
37714 A
Statistics
Matches: 116, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
38 7 0.06
39 109 0.94
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (39 bp):
GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
Done.