Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2906
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: 53622
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:4733 original size:40 final size:39
Alignment explanation
Indices: 4689--4912 Score: 236
Period size: 40 Copynumber: 5.7 Consensus size: 39
4679 GCCACTAGCT
*
4689 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
** * *
4729 CAAATGCCTTCAAGACTTCGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* *
4768 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * *
4808 CAAACGCCTT-TGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * * ** * *
4847 CGAATGCCTTCGGGACTTAGCCCAGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
4887 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
4913 TATCATCCGG
Statistics
Matches: 155, Mismatches: 25, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
39 72 0.46
40 83 0.54
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:4790 original size:79 final size:79
Alignment explanation
Indices: 4689--4869 Score: 247
Period size: 79 Copynumber: 2.3 Consensus size: 79
4679 GCCACTAGCT
* * * * *
4689 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCAAGACTTCGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACGCCTT-AAGACTTAGCCCGG
4754 -TATAATAACTCGCA
65 ATATAATAACTCGCA
* **
4768 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCACAAACGCCTTTGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACGCCTTAAGACTTAGCCCGGA
* *
4833 TATAGTAGCTCGCA
66 TATAATAACTCGCA
*
4847 CGAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
4870 AGAATTAGCC
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
78 11 0.12
79 79 0.88
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACGCCTTAAGACTTAGCCCGGA
TATAATAACTCGCA
Found at i:11817 original size:40 final size:39
Alignment explanation
Indices: 11773--11997 Score: 290
Period size: 40 Copynumber: 5.7 Consensus size: 39
11763 GCCACTAGCT
*
11773 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
11813 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* *
11852 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* *
11892 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * ** * *
11932 CGAATGCCTTCGGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
11972 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
11998 TATCATCCGA
Statistics
Matches: 167, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 40 0.24
40 127 0.76
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:14963 original size:40 final size:41
Alignment explanation
Indices: 14899--14994 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
14889 GACAATGTTT
* *
14899 GGCACTAAGTGTGCG-TTTCAAAATAGCTTCGGCTATAAAT-A
1 GGCACTAAGTGTGCGAATTCAAAATAGCTTAGGCTAT--ATGA
*
14940 -GCACTAAGTGTGCGAATT-GAAATAGCTTAGGCTATATGA
1 GGCACTAAGTGTGCGAATTCAAAATAGCTTAGGCTATATGA
14979 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
14995 TACCAATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
38 2 0.04
39 1 0.02
40 44 0.90
41 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (41 bp):
GGCACTAAGTGTGCGAATTCAAAATAGCTTAGGCTATATGA
Found at i:16282 original size:27 final size:26
Alignment explanation
Indices: 16224--16286 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
16214 ACAGTCGAAT
*
16224 TTTAATATGTCTTAGTTCATACATGT
1 TTTAATATGTCTTAGTTCATACATGA
* * *
16250 TGTTAATTTGTCTTAGTTTATTGCATGA
1 T-TTAATATGTCTTAGTTCA-TACATGA
16278 TTTAA-ATGT
1 TTTAATATGT
16287 GTCTTTGAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 4 0.13
27 20 0.67
28 6 0.20
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.52
Consensus pattern (26 bp):
TTTAATATGTCTTAGTTCATACATGA
Found at i:18238 original size:30 final size:31
Alignment explanation
Indices: 18204--18300 Score: 85
Period size: 30 Copynumber: 3.2 Consensus size: 31
18194 TAAACTAAAA
18204 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * * *
18234 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCTAAAGCTTTAGCTCGTGAGCTAAAGT
*
18264 TGAGCTAAAG-TTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAAGCTTTAGCTCGTGAGCT-AAAGT
18294 TGAGCTA
1 TGAGCTA
18301 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
30 44 0.88
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (31 bp):
TGAGCTAAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:22508 original size:46 final size:47
Alignment explanation
Indices: 22402--22523 Score: 140
Period size: 46 Copynumber: 2.6 Consensus size: 47
22392 TCCCTTCGAC
** * *
22402 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
*
22452 ATCGG-CTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 AT-GGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
22498 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
22524 CCGTCCTGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
45 2 0.03
46 32 0.50
50 28 0.44
51 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:28781 original size:26 final size:26
Alignment explanation
Indices: 28751--28801 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
28741 ACCAATGAAC
**
28751 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACAGAGCAACCCCT
28777 CGGGGAATCAGCACAGAGCAACCCC
1 CGGGGAATCAGCACAGAGCAACCCC
28802 CTTTTCACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.35, G:0.25, T:0.10
Consensus pattern (26 bp):
CGGGGAATCAGCACAGAGCAACCCCT
Found at i:28808 original size:104 final size:104
Alignment explanation
Indices: 28614--28880 Score: 430
Period size: 104 Copynumber: 2.6 Consensus size: 104
28604 TAACCGTTAT
* **
28614 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
28679 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACAGAGCAACCCCCTTTCACATTTCAAAGATA
*
28718 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
28782 AATCAGCACAGAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACAGAGCAACCCCC-TTTCACATTTCAAAGATA
* **
28822 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
28881 TTATATACAA
Statistics
Matches: 152, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
103 24 0.16
104 127 0.84
105 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACAGAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:29241 original size:29 final size:29
Alignment explanation
Indices: 29208--29271 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
29198 TAATCCACCA
29208 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
29237 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
29267 CCCAA
1 CCCAA
29272 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:29245 original size:30 final size:30
Alignment explanation
Indices: 29215--29271 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29205 CCACCCAACT
29215 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
29244 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
29272 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:33284 original size:29 final size:29
Alignment explanation
Indices: 33251--33324 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
33241 GTTGTGAGAT
* *
33251 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
33280 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
33309 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
33325 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:38285 original size:47 final size:47
Alignment explanation
Indices: 38135--38315 Score: 147
Period size: 47 Copynumber: 3.9 Consensus size: 47
38125 CACATTATGA
* * * *
38135 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGAAACGA-
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACAT-GAAA-TAT
* * * * * * * *
38183 GTGTTAGTATAAGA-CATGCCTGGGACAT-GCATAGGCTACGAGATGAT
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC-ATGAAAT-AT
38230 -AG-TCAGTGTAAGACCATGTCTGGGACATGGCATCGACATGAAATAT
1 GAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGACATGAAATAT
* * *
38276 GAGCTAGTGTGAGACCGTGTCTGGGACATGGCATCAACAT
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACAT
38316 CTTACCCATG
Statistics
Matches: 106, Mismatches: 19, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
45 1 0.01
46 22 0.21
47 66 0.62
48 17 0.16
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (47 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATGAAATAT
Found at i:44540 original size:47 final size:46
Alignment explanation
Indices: 44350--44549 Score: 162
Period size: 46 Copynumber: 4.3 Consensus size: 46
44340 TGAGAACCAA
* *
44350 TGTATGACCATGTTTGGGA-ATGGCATCGACATCGAG--ATGAGTTCTAG
1 TGTAAGACCATGTCTGGGACAT-GCATCGACAT-GAGATATGAG--CTAG
* * ** * *
44397 TGTAAGA-CATGTCTGGGACATGCATCGGCCTTGAGACGTAAGCCAG
1 TGTAAGACCATGTCTGGGACATGCATC-GACATGAGATATGAGCTAG
*
44443 TGTAAGA-CATGTCTGGGACATGCATCGACTATGAGATGAT-AG-TCAC
1 TGTAAGACCATGTCTGGGACATGCATCGAC-ATGAGAT-ATGAGCT-AG
* *
44489 TGTAAGACCATGTCTGGGACATGGCATCAACATGAAATATGAGCTAG
1 TGTAAGACCATGTCTGGGACAT-GCATCGACATGAGATATGAGCTAG
*
44536 TGTAAGACCGTGTC
1 TGTAAGACCATGTC
44550 CTTACCTACG
Statistics
Matches: 125, Mismatches: 17, Indels: 22
0.76 0.10 0.13
Matches are distributed among these distances:
45 2 0.02
46 64 0.51
47 48 0.38
48 11 0.09
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (46 bp):
TGTAAGACCATGTCTGGGACATGCATCGACATGAGATATGAGCTAG
Found at i:51487 original size:18 final size:17
Alignment explanation
Indices: 51461--51494 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
51451 CCATAATACG
51461 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
51479 GCCCGTGTGGCCCACA
1 GCCCATGTGGCCCACA
51495 AAGCCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Done.