Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold271
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: 77494
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:7279 original size:79 final size:81
Alignment explanation
Indices: 7139--7323 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
7129 TTGAATGATG
* *
7139 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
*
7203 TGTGTGAGATACTA-A
66 TGTGCGAGATACTATA
* * * ** *
7218 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGGAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
7280 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
7298 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
7324 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 55 0.62
80 33 0.37
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:7330 original size:40 final size:40
Alignment explanation
Indices: 7139--7323 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
7129 TTGAATGATG
* * * *
7139 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
7179 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
7219 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
7258 TCCGGGTTAAGTCCCGGAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
7299 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
7324 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28576 original size:25 final size:25
Alignment explanation
Indices: 28523--28587 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
28513 ATGAATATGT
* * *
28523 ATGCTCATACGAGCTGTGAATTGGT
1 ATGCTCATACGAGCTGAGAATCGGC
28548 ATGCTCATACGAGCTGA-AGATCGGC
1 ATGCTCATACGAGCTGAGA-ATCGGC
28573 ATGCTC-TCACGAGCT
1 ATGCTCAT-ACGAGCT
28588 ATAAATCGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.06
25 33 0.94
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (25 bp):
ATGCTCATACGAGCTGAGAATCGGC
Found at i:28595 original size:25 final size:25
Alignment explanation
Indices: 28567--28618 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
28557 CGAGCTGAAG
28567 ATCGGCATGCTCTCACGAGCTATAA
1 ATCGGCATGCTCTCACGAGCTATAA
* *
28592 ATCGGTATGCTCTCACGATCTATAA
1 ATCGGCATGCTCTCACGAGCTATAA
28617 AT
1 AT
28619 AAATAACCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (25 bp):
ATCGGCATGCTCTCACGAGCTATAA
Found at i:31000 original size:68 final size:68
Alignment explanation
Indices: 30850--31007 Score: 151
Period size: 68 Copynumber: 2.3 Consensus size: 68
30840 CTAGCCAATT
* * *
30850 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TAGAATCACACATGCGACCTAGCTACA
**
30915 TTTA
65 CATA
* * * *
30919 TCTCTCCCCTAGCTCTCTTGTCTACATGG-GATACATC-C-AGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTAGAATCACACATGCGACCTAGCTA
30981 CTACATA
63 C-ACATA
*
30988 GTATCTCGTAGCTTTCTTGT
1 -TATCTCGTAGCTCTCTTGT
31008 ACACATGATG
Statistics
Matches: 72, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
68 34 0.47
69 7 0.10
70 6 0.08
71 25 0.35
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTAGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:41113 original size:8 final size:8
Alignment explanation
Indices: 41100--41131 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
41090 CTAGATCGGC
41100 AAAAGCCG
1 AAAAGCCG
41108 AAAAGCCG
1 AAAAGCCG
*
41116 AAATGCCG
1 AAAAGCCG
41124 AAAAGCCG
1 AAAAGCCG
41132 GTATTTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:41393 original size:26 final size:25
Alignment explanation
Indices: 41364--41422 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
41354 ATTTACTAAA
*
41364 ATACCCCAAGTATAAAAATTACCATT
1 ATACCCCAAGT-GAAAAATTACCATT
* * *
41390 ATACCCTTAGGTGCAAAATTACCATT
1 ATACCC-CAAGTGAAAAATTACCATT
41416 ATACCCC
1 ATACCCC
41423 TAGGGTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (25 bp):
ATACCCCAAGTGAAAAATTACCATT
Found at i:41588 original size:27 final size:28
Alignment explanation
Indices: 41530--41591 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
41520 GAGGAAACGT
* *
41530 TCTGGTGGCTCTGCCACAAATATCTGTT
1 TCTGGTGGCTCTACCACAAATATCTGTA
*
41558 TCTGGTGGCTCTACCA-TAATATCTGTA
1 TCTGGTGGCTCTACCACAAATATCTGTA
41585 TCTGGTG
1 TCTGGTG
41592 ACTTTGTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (28 bp):
TCTGGTGGCTCTACCACAAATATCTGTA
Found at i:45305 original size:27 final size:27
Alignment explanation
Indices: 45275--45332 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
45265 ACTAAAATAT
45275 CCCTAAGTATG-AAAATTACCATTATAC
1 CCCTAAG-ATGCAAAATTACCATTATAC
*
45302 CCCT-AGGTGCAAAATTACCATTATAC
1 CCCTAAGATGCAAAATTACCATTATAC
45328 CCCTA
1 CCCTA
45333 GGGTTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 2 0.07
26 22 0.79
27 4 0.14
ACGTcount: A:0.36, C:0.28, G:0.09, T:0.28
Consensus pattern (27 bp):
CCCTAAGATGCAAAATTACCATTATAC
Found at i:45486 original size:27 final size:27
Alignment explanation
Indices: 45437--45520 Score: 123
Period size: 27 Copynumber: 3.1 Consensus size: 27
45427 GGAGGAAGTG
45437 TTCTGGTGGCTCTACCACAAATATCTGT
1 TTCTGGTGGCTCTACCAC-AATATCTGT
*
45465 TTCTGGTGGCTCTGCCACAATATCTGT
1 TTCTGGTGGCTCTACCACAATATCTGT
* * *
45492 ATCTGGTGACTCTATCACAATATCTGT
1 TTCTGGTGGCTCTACCACAATATCTGT
45519 TT
1 TT
45521 TGGCAGCCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
27 33 0.66
28 17 0.34
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (27 bp):
TTCTGGTGGCTCTACCACAATATCTGT
Found at i:46520 original size:13 final size:13
Alignment explanation
Indices: 46498--46530 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
46488 AAGGGTTTGT
46498 TTAT-TAAACTAA
1 TTATCTAAACTAA
46510 TTATCTAAACTAA
1 TTATCTAAACTAA
*
46523 TTAACTAA
1 TTATCTAA
46531 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:49109 original size:33 final size:32
Alignment explanation
Indices: 49058--49119 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
49048 ACGAAGTCAC
* *
49058 CAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGATACAGATATTGTGGCGAAGCCACCAGAA
* *
49090 CAGATATATATATATGTGGCGAAGCCACCA
1 CAGATACAGATAT-TGTGGCGAAGCCACCA
49120 AATTGCAGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 11 0.44
33 14 0.56
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (32 bp):
CAGATACAGATATTGTGGCGAAGCCACCAGAA
Found at i:49870 original size:27 final size:27
Alignment explanation
Indices: 49840--50039 Score: 199
Period size: 27 Copynumber: 7.4 Consensus size: 27
49830 TGGGCAAAAT
* * *
49840 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
49867 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
49894 GG-AATTCCTACGCTACAAGGGTATTTC
1 GGTAATT-CTACCCTACAAGGGTATTTC
* * * *
49921 GGTAATTCTATCCTAGAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
49948 GATAATTCTACCCTA-TAGGCGTATTTC
1 GGTAATTCTACCCTACAAGG-GTATTTC
** *
49975 AATAATTCTACCGTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
50002 GGTAATTCTACCTTAC-AGGAGTAGTTC
1 GGTAATTCTACCCTACAAGG-GTATTTC
*
50029 AGTAATTCTAC
1 GGTAATTCTAC
50040 AACTTATCCA
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 9 0.06
27 128 0.89
28 7 0.05
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:65507 original size:25 final size:25
Alignment explanation
Indices: 65479--65552 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
65469 TCATGAACAT
*
65479 GTATGCTCATATGAGCTATGAATCG
1 GTATGCTCATATGAGCTATAAATCG
* *
65504 GTATCCTCATTTGAGCTA-AAGATCG
1 GTATGCTCATATGAGCTATAA-ATCG
65529 GTATGCTC-TCATGAGCTATAAATC
1 GTATGCTCAT-ATGAGCTATAAATC
65553 AGTAACCCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
24 2 0.05
25 37 0.90
26 2 0.05
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (25 bp):
GTATGCTCATATGAGCTATAAATCG
Found at i:72550 original size:40 final size:39
Alignment explanation
Indices: 72479--72685 Score: 292
Period size: 40 Copynumber: 5.2 Consensus size: 39
72469 CCTTCGGGGT
*
72479 TTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTCGAGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCG-GAC
* *
72518 TTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCCGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTT-CGGAC
* *
72558 TTGGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGAC
72598 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGAC
* *
72638 TTAGCCCGGATATAGTAACTCCCACAAATGCCTTCGGGC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGAC
72677 TTAGCCCGG
1 TTAGCCCGG
72686 TTATCAATCC
Statistics
Matches: 155, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
39 18 0.12
40 135 0.87
41 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (39 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGAC
Done.