Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_389
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: 80998
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Found at i:1582 original size:79 final size:80
Alignment explanation
Indices: 1458--1641 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 80
1448 GCTACTCGTT
* * *
1458 CAAATGCCTTCGAGACATAGCCCGG-TTATAGTAACTCGCACAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCG-GGCTTAGCCCGGAATATAGTAACTCGCACAATGCCTTC-GGATCTTAACCCG
* *
1521 GATTTAGTAAC-TCGCA
64 GATATAGTAACTTAGCA
* **
1537 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCAC-AATGCCTTCGGATCTTAACCCGG
* *
1601 ATATGGTCACTTAGCA
65 ATATAGTAACTTAGCA
1617 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
1642 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
78 25 0.28
79 46 0.51
80 19 0.21
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:1641 original size:40 final size:40
Alignment explanation
Indices: 1439--1641 Score: 220
Period size: 39 Copynumber: 5.1 Consensus size: 40
1429 CGGAATTTAA
** * *
1439 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGAGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1479 CCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
1518 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1557 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
1597 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
1637 CCGGA
1 CCGGA
1642 CATCATTCAA
Statistics
Matches: 138, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
38 2 0.01
39 67 0.49
40 57 0.41
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:4343 original size:12 final size:11
Alignment explanation
Indices: 4326--4369 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
4316 TTTAAAGAAT
4326 TTTTATTTTTTA
1 TTTTA-TTTTTA
4338 TTTTATTTTTA
1 TTTTATTTTTA
*
4349 TTTTCACTTTTA
1 TTTT-ATTTTTA
4361 TCTTTATTT
1 T-TTTATTT
4370 ATCTTCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 10 0.36
12 15 0.54
13 3 0.11
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:4359 original size:18 final size:17
Alignment explanation
Indices: 4324--4369 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
4314 TGTTTAAAGA
*
4324 ATTTTTATTTTTTATTTT
1 ATTTTTA-TTTTCATTTT
4342 ATTTTTATTTTCACTTTT
1 ATTTTTATTTTCA-TTTT
*
4360 ATCTTTATTT
1 ATTTTTATTT
4370 ATCTTCTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTATTTTCATTTT
Found at i:4419 original size:26 final size:25
Alignment explanation
Indices: 4367--4420 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
4357 TTTATCTTTA
*
4367 TTTATCTTCTTTAAGTACTTTTTAT
1 TTTATCTTCTTTAAGTACTTTTCAT
*
4392 TTTATTTTCATTTAA-TACTATTTCAT
1 TTTATCTTC-TTTAAGTACT-TTTCAT
4418 TTT
1 TTT
4421 TAGGTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTATCTTCTTTAAGTACTTTTCAT
Found at i:9909 original size:21 final size:20
Alignment explanation
Indices: 9885--9935 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
9875 TTTTATTTTA
*
9885 ATTTTTATTCTTTATTTCTT
1 ATTTTTATTCTTTATATCTT
9905 -TATTTTATATCTTTATATCTT
1 AT-TTTTAT-TCTTTATATCTT
9926 ATTTATTATT
1 ATTT-TTATT
9936 TTATTTTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.04
20 6 0.23
21 14 0.54
22 5 0.19
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTATTCTTTATATCTT
Found at i:9934 original size:27 final size:28
Alignment explanation
Indices: 9877--9939 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
9867 TTTCTTTATT
* *
9877 TTATTTTA-ATTTTTATTCTTTATTTCT
1 TTATTTTATATCTTTATTCTTTATTTCA
9904 TTATTTTATATCTTTATATC-TTATTT-A
1 TTATTTTATATCTTTAT-TCTTTATTTCA
9931 TTATTTTAT
1 TTATTTTAT
9940 TTTCAGCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 17 0.53
28 13 0.41
29 2 0.06
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (28 bp):
TTATTTTATATCTTTATTCTTTATTTCA
Found at i:10179 original size:14 final size:15
Alignment explanation
Indices: 10160--10188 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10150 TTATGTGTCC
10160 ATTGTTCTTT-TTCT
1 ATTGTTCTTTATTCT
10174 ATTGTTCTTTATTCT
1 ATTGTTCTTTATTCT
10189 TAGCTTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (15 bp):
ATTGTTCTTTATTCT
Found at i:16225 original size:21 final size:21
Alignment explanation
Indices: 16201--16250 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
16191 TGGATCAGCT
16201 CTTCTGTTAAGCTCTCACGAG
1 CTTCTGTTAAGCTCTCACGAG
16222 CTTCTGTTAAGCTCTCACGAG
1 CTTCTGTTAAGCTCTCACGAG
16243 CTTCTGTT
1 CTTCTGTT
16251 GGCATGTTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.38
Consensus pattern (21 bp):
CTTCTGTTAAGCTCTCACGAG
Found at i:22019 original size:92 final size:93
Alignment explanation
Indices: 21896--22071 Score: 239
Period size: 92 Copynumber: 1.9 Consensus size: 93
21886 TAGTATATCT
* * *
21896 ATGCTGATGTCATGTCCCAGACATGGTCTTACACTGACACATC-T-CGTAGCTGATGCATGTCCC
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACAC-TCATACGTAGCCGATGCATGTCCC
21959 AGACATGTCTTACACTAGCACTCGTCTCA
65 AGACATGTCTTACACTAGCACTCGTCTCA
* * * * *
21988 ATGCCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCTCATTATGTAGCCGATGCATGTCTC
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCA-TACGTAGCCGATGCATGTCCC
*
22053 GGACATGTCTTACACTAGC
65 AGACATGTCTTACACTAGC
22072 TCACACAAGC
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
91 2 0.03
92 35 0.49
93 1 0.01
94 34 0.47
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (93 bp):
ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCATACGTAGCCGATGCATGTCCCA
GACATGTCTTACACTAGCACTCGTCTCA
Found at i:26996 original size:30 final size:31
Alignment explanation
Indices: 26918--27000 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 31
26908 TCAATCTCAA
26918 CATAT-ACTGGGCCGAAGCCTTTGCATTATT
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
* * *
26948 CATGTCACTGGGCTGAAGCCTTTTCATTA-T
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
*
26978 CATATCACTGAGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
27001 ACTGTAAACG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 25 0.54
31 21 0.46
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTGCATTATT
Found at i:27255 original size:25 final size:25
Alignment explanation
Indices: 27222--27292 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
27212 CTCTTTTACT
* *
27222 AACTAGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
27247 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
27272 AACTGGAGCAAAAGCCCTTTT
1 AACTGGGGC-AAAGCCCTTTT
27293 GCATTTCCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 30 0.73
26 11 0.27
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:35131 original size:24 final size:24
Alignment explanation
Indices: 35098--35155 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
35088 CTGGAGGCCT
*
35098 AGCCTCTTTTAAT-AACTGGGGTAA
1 AGCCT-TTTTAATAAACTGGGGCAA
*
35122 AGCCCTTTTTGATAAACTGGGGCAA
1 AG-CCTTTTTAATAAACTGGGGCAA
35147 AGCCTTTTT
1 AGCCTTTTT
35156 CGGTAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 15 0.50
25 15 0.50
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (24 bp):
AGCCTTTTTAATAAACTGGGGCAA
Found at i:35139 original size:25 final size:26
Alignment explanation
Indices: 35111--35181 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
35101 CTCTTTTAAT
*
35111 AACTGGGGTAAAGCCCTTTTT-GATA
1 AACTGGGGAAAAGCCCTTTTTCGATA
* *
35136 AACTGGGGCAAAG-CCTTTTTCGGTA
1 AACTGGGGAAAAGCCCTTTTTCGATA
*
35161 AACTAGGGCAAAAGCCCTTTT
1 AACT-GGGGAAAAGCCCTTTT
35182 GCACTTCCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 7 0.18
25 19 0.49
26 7 0.18
27 6 0.15
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (26 bp):
AACTGGGGAAAAGCCCTTTTTCGATA
Found at i:42794 original size:30 final size:31
Alignment explanation
Indices: 42720--42802 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 31
42710 TCAATCTCAA
42720 CATAT-ACTGGGCCGAAGCCTTTGCATTATT
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
** * *
42750 CATGCCATTGGGCCGAAGCCTTTTCATTA-T
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
42780 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
42803 ACTGTAAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 24 0.53
31 21 0.47
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTGCATTATT
Found at i:43093 original size:26 final size:25
Alignment explanation
Indices: 43023--43093 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
43013 CTCTTTTAAT
* * *
43023 AACTGGGGTAAAGCCCTTTTTGATA
1 AACTGGAGCAAAGCCCTTTTCGATA
*
43048 AACTGGAGCAAAGCCCTTTTCGGTA
1 AACTGGAGCAAAGCCCTTTTCGATA
43073 AACTAGG-GCAAAAGCCCTTTT
1 AACT-GGAGC-AAAGCCCTTTT
43094 GCACTTCCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 27 0.68
26 13 0.32
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
AACTGGAGCAAAGCCCTTTTCGATA
Found at i:51350 original size:13 final size:13
Alignment explanation
Indices: 51332--51369 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
51322 AACAATGCCA
51332 GACACGACCGTGC
1 GACACGACCGTGC
51345 GACACGACCGTGC
1 GACACGACCGTGC
51358 GACACGACCGTG
1 GACACGACCGTG
51370 TGCACCCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.24, C:0.37, G:0.32, T:0.08
Consensus pattern (13 bp):
GACACGACCGTGC
Found at i:66597 original size:27 final size:27
Alignment explanation
Indices: 66549--66707 Score: 191
Period size: 27 Copynumber: 5.9 Consensus size: 27
66539 AGCGAGGCTG
* * *
66549 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGATA
*
66576 CATATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
66602 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
66629 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
66656 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
66683 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
66708 GACGCTTCCT
Statistics
Matches: 115, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.08
27 102 0.89
28 4 0.03
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:66708 original size:54 final size:54
Alignment explanation
Indices: 66549--66710 Score: 247
Period size: 54 Copynumber: 3.0 Consensus size: 54
66539 AGCGAGGCTG
* * * * * *
66549 CAGATAT-TGTGACAAAGTCACCAGAT-ACATATATTGTGGCAGAGCCACCAGAA
1 CAGATATATGTGGCAGAGCCACCAGATCAGATA-ATTGTGGCATAGCCACCAGGA
66602 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGA
1 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGA
66656 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGA
1 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGA
66710 C
1 C
66711 GCTTCCTCCA
Statistics
Matches: 101, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
53 7 0.07
54 90 0.89
55 4 0.04
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (54 bp):
CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGA
Found at i:68353 original size:25 final size:26
Alignment explanation
Indices: 68286--68392 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
68276 TGAAATGCCC
68286 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
68312 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* * *
68338 ATCATGGAATA-CTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
68363 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
68389 ATCA
1 ATCA
68393 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
25 22 0.30
26 51 0.70
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Done.