Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3595
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: 58178
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:5488 original size:28 final size:28
Alignment explanation
Indices: 5456--5520 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
5446 ATTTACTAGA
*
5456 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
5484 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
5512 ATACCCCTA
1 ATACCCCTA
5521 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:5667 original size:28 final size:29
Alignment explanation
Indices: 5626--5688 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
5616 AGGAAGCGTC
*
5626 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTAT
5654 CTGGTGGC-ACTGCCACAAAATATCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGTAT
5683 CTGGTG
1 CTGGTG
5689 ACTCTGTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.75
29 7 0.22
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (29 bp):
CTGGTGGCTATGCCACAAAATATCTGTAT
Found at i:5699 original size:29 final size:28
Alignment explanation
Indices: 5636--5699 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
5626 CTGGTGGCTA
* *
5636 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
5664 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
5693 TGTCACA
1 TGCCACA
5700 TTTTCTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:14132 original size:39 final size:39
Alignment explanation
Indices: 13986--14215 Score: 162
Period size: 39 Copynumber: 5.8 Consensus size: 39
13976 CAATCACCAA
* *
13986 CACAAAGCCTACGGGTCTTTAAGCCCTGATATAATTCCAG
1 CACAAAGCCTACGGGACTTT-AGCCCGGATATAATTCCAG
* * ** * * *
14026 CATAGAGCCTGTGGGTCTTTAAGCTCGGATACAATTCCAG
1 CACAAAGCCTACGGGACTTT-AGCCCGGATATAATTCCAG
* * * ** *
14066 CACGAAGCCTGC-GGACCTTAAATCCGGATACAATTCCAG
1 CACAAAGCCTACGGGA-CTTTAGCCCGGATATAATTCCAG
**
14105 CACAAAGCCTACGGGACTTTAGCCCGGATATAACACCAG
1 CACAAAGCCTACGGGACTTTAGCCCGGATATAATTCCAG
* * **
14144 CACGAATGCCTTCAGGG-C-TTAGCCCGGATATAACACCAG
1 CAC-AAAGCCTAC-GGGACTTTAGCCCGGATATAATTCCAG
* * *
14183 CACGAATGCCTTCGAGAC-TTAGCCCGGATATAA
1 CAC-AAAGCCTACGGGACTTTAGCCCGGATATAA
14216 CACCATTATA
Statistics
Matches: 158, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
38 2 0.01
39 98 0.62
40 55 0.35
41 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (39 bp):
CACAAAGCCTACGGGACTTTAGCCCGGATATAATTCCAG
Found at i:14216 original size:39 final size:39
Alignment explanation
Indices: 14101--14220 Score: 172
Period size: 39 Copynumber: 3.1 Consensus size: 39
14091 GGATACAATT
* * *
14101 CCAGCAC-AAAGCCTACGGGACTTTAGCCCGGATATAACA
1 CCAGCACGAATGCCTTCGAGAC-TTAGCCCGGATATAACA
*
14140 CCAGCACGAATGCCTTC-AGGGCTTAGCCCGGATATAACA
1 CCAGCACGAATGCCTTCGA-GACTTAGCCCGGATATAACA
14179 CCAGCACGAATGCCTTCGAGACTTAGCCCGGATATAACA
1 CCAGCACGAATGCCTTCGAGACTTAGCCCGGATATAACA
14218 CCA
1 CCA
14221 TTATAAAGTC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
39 63 0.86
40 10 0.14
ACGTcount: A:0.31, C:0.32, G:0.21, T:0.17
Consensus pattern (39 bp):
CCAGCACGAATGCCTTCGAGACTTAGCCCGGATATAACA
Found at i:14326 original size:28 final size:28
Alignment explanation
Indices: 14293--14365 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
14283 ATTTAATCAT
14293 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTTGCACACTAAGTGTCATTC
* ** *
14321 TCAATATCTCACACATTAAGTGTCATTC
1 TCAATATTTTGCACACTAAGTGTCATTC
*
14349 TCAATATTTTGTACACT
1 TCAATATTTTGCACACT
14366 GAGTACCATA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (28 bp):
TCAATATTTTGCACACTAAGTGTCATTC
Found at i:20659 original size:40 final size:39
Alignment explanation
Indices: 20608--20791 Score: 169
Period size: 39 Copynumber: 4.7 Consensus size: 39
20598 CACCAACACA
* * * *
20608 AAGCCTACGGGTCTTTAAGCCCGGATATAATTCCAGCAT
1 AAGCCTGCGGGACTTTAAGCCCGGATACAATTCCAGCAC
* *
20647 ACAGCCTGCGGGTCTTTAAGCCCGAATACAATTCCAGCAC
1 A-AGCCTGCGGGACTTTAAGCCCGGATACAATTCCAGCAC
* * *
20687 GAAGCTTGC-GGACCTTAAGTCCGGATACAATTCCAGCAC
1 -AAGCCTGCGGGACTTTAAGCCCGGATACAATTCCAGCAC
* * **
20726 AAAGCCTGCGGGACTTT-AGCCTGGATATAACACCAGCAC
1 -AAGCCTGCGGGACTTTAAGCCCGGATACAATTCCAGCAC
*
20765 GAATGCCTTCGGGAC-TT-AGCCCGGATA
1 -AA-GCCTGCGGGACTTTAAGCCCGGATA
20792 TAACACCATT
Statistics
Matches: 121, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
39 64 0.53
40 56 0.46
41 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (39 bp):
AAGCCTGCGGGACTTTAAGCCCGGATACAATTCCAGCAC
Found at i:20752 original size:39 final size:39
Alignment explanation
Indices: 20604--20791 Score: 173
Period size: 40 Copynumber: 4.8 Consensus size: 39
20594 TAATCACCAA
* * *
20604 CACAAAGCCTACGGGTCTTTAAGCCCGGATATAATTCCAG
1 CACAAAGCCTGCGGGACTTT-AGCCCGGATACAATTCCAG
* * * *
20644 CATACAGCCTGCGGGTCTTTAAGCCCGAATACAATTCCAG
1 CACAAAGCCTGCGGGACTTT-AGCCCGGATACAATTCCAG
* * * *
20684 CACGAAGCTTGC-GGACCTTAAGTCCGGATACAATTCCAG
1 CACAAAGCCTGCGGGA-CTTTAGCCCGGATACAATTCCAG
* * **
20723 CACAAAGCCTGCGGGACTTTAGCCTGGATATAACACCAG
1 CACAAAGCCTGCGGGACTTTAGCCCGGATACAATTCCAG
* *
20762 CACGAATGCCTTCGGGAC-TTAGCCCGGATA
1 CAC-AAAGCCTGCGGGACTTTAGCCCGGATA
20792 TAACACCATT
Statistics
Matches: 121, Mismatches: 24, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
39 60 0.50
40 61 0.50
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (39 bp):
CACAAAGCCTGCGGGACTTTAGCCCGGATACAATTCCAG
Found at i:32911 original size:17 final size:17
Alignment explanation
Indices: 32891--32931 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
32881 TTAGTAAAGG
* *
32891 TTAAAATGGTAAAATGA
1 TTAAAATGATAAAATAA
32908 TTAAAATGATAAAATAA
1 TTAAAATGATAAAATAA
32925 TTAAAAT
1 TTAAAAT
32932 AAAGCCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (17 bp):
TTAAAATGATAAAATAA
Found at i:32914 original size:9 final size:9
Alignment explanation
Indices: 32891--32931 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
32881 TTAGTAAAGG
32891 TTAAAATG-
1 TTAAAATGA
*
32899 GTAAAATGA
1 TTAAAATGA
32908 TTAAAATGA
1 TTAAAATGA
*
32917 -TAAAATAA
1 TTAAAATGA
32925 TTAAAAT
1 TTAAAAT
32932 AAAGCCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
8 14 0.50
9 14 0.50
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (9 bp):
TTAAAATGA
Found at i:33868 original size:43 final size:43
Alignment explanation
Indices: 33786--33868 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
33776 AGTGATTACA
* * * *
33786 TGTAAGCCCATGTCTGAGACATTGGCATTGTATTGTGATTATG
1 TGTAAGACCATGTCAGAGACATTGGCATCGTATTATGATTATG
33829 TGTAAGACCATGTCCAG-GACATTGGCATCGT-TATATGATT
1 TGTAAGACCATGT-CAGAGACATTGGCATCGTAT-TATGATT
33869 TCGTATAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
42 1 0.03
43 31 0.91
44 2 0.06
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (43 bp):
TGTAAGACCATGTCAGAGACATTGGCATCGTATTATGATTATG
Found at i:35548 original size:27 final size:28
Alignment explanation
Indices: 35509--35561 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
35499 TGCCCTATTT
* *
35509 TCACACGATCTG-TGACACAGGCGTGCC
1 TCACACGACCTGTTCACACAGGCGTGCC
*
35536 TCACACGGCCTGTTCACACAGGCGTG
1 TCACACGACCTGTTCACACAGGCGTG
35562 TGACCCTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (28 bp):
TCACACGACCTGTTCACACAGGCGTGCC
Found at i:38398 original size:41 final size:41
Alignment explanation
Indices: 38315--38415 Score: 121
Period size: 41 Copynumber: 2.5 Consensus size: 41
38305 TGTGGATACT
* * * *
38315 CCACAGCTCATGTGAGAATCATCATGTAGCTACGTTCCGAC
1 CCACAGCTCGTGTGAGAAGCATCATGTAACTACATTCCGAC
* ** *
38356 CCACAGCTCGTGTGAGCAGCATCATGTAACTGTATTCTGAC
1 CCACAGCTCGTGTGAGAAGCATCATGTAACTACATTCCGAC
*
38397 CCACAGCTTGTGTGAGAAG
1 CCACAGCTCGTGTGAGAAG
38416 GCCCATTTTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (41 bp):
CCACAGCTCGTGTGAGAAGCATCATGTAACTACATTCCGAC
Found at i:51497 original size:39 final size:40
Alignment explanation
Indices: 51308--51490 Score: 189
Period size: 39 Copynumber: 4.7 Consensus size: 40
51298 TCGAATGATG
* * * *
51308 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
51348 TCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
51388 TTCGGTCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
51427 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
51467 -CC-GGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
51491 AACGAGTAGC
Statistics
Matches: 119, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
38 6 0.05
39 72 0.61
40 33 0.28
41 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:57095 original size:72 final size:68
Alignment explanation
Indices: 56951--57098 Score: 224
Period size: 72 Copynumber: 2.1 Consensus size: 68
56941 GGGAACATCA
*
56951 ACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCTTTCATTTCAAATATACAATGGATAT
1 ACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCTTTCATTTCAAAGATACAATGGATAT
57016 CGC
66 CGC
***
57019 ACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTGG
1 ACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAA-CCCCTTT--CATTTCAAAGATACAATGG
57084 ATATCGC
62 ATATCGC
57091 ACTTAGCA
1 ACTTAGCA
57099 CCACCAATGA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
68 15 0.21
69 20 0.28
70 7 0.10
72 30 0.42
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (68 bp):
ACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCTTTCATTTCAAAGATACAATGGATAT
CGC
Found at i:57134 original size:77 final size:70
Alignment explanation
Indices: 56951--57135 Score: 223
Period size: 72 Copynumber: 2.6 Consensus size: 70
56941 GGGAACATCA
*
56951 ACTTAGCAACCCCT-CGGGGAATCAGCACATAGCAA-CCCCTTTCATTTCAAATATACAATGGAT
1 ACTTAGCAACCCCTCCGGGGAATCAGCACATAGCAACCCCCTTTCATTTCAAAGATACAATGGAT
57014 ATCGC
66 ATCGC
* ***
57019 ACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTGG
1 ACTTAGCAACCCCTCCGGGGAATCAGCACATAGCAACCCCCTTT--CATTTCAAAGATACAATGG
57084 ATATCGC
64 ATATCGC
*
57091 ACTTAGC-ACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCC
1 ACTTAGCAACC-CC--T---CCGGGGAATCAGCACATAGCAACCCC
57136 TCGGGGAATC
Statistics
Matches: 100, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
68 14 0.14
69 20 0.20
70 7 0.07
71 3 0.03
72 31 0.31
74 1 0.01
77 24 0.24
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (70 bp):
ACTTAGCAACCCCTCCGGGGAATCAGCACATAGCAACCCCCTTTCATTTCAAAGATACAATGGAT
ATCGC
Found at i:57141 original size:26 final size:26
Alignment explanation
Indices: 57111--57162 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
57101 ACCAATGAAC
*
57111 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
57137 CGGGGAATCAGCACATAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
57163 TTCACATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:57200 original size:102 final size:103
Alignment explanation
Indices: 57017--57237 Score: 349
Period size: 102 Copynumber: 2.2 Consensus size: 103
57007 AATGGATATC
57017 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
57082 GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATATCGCACATAGCACCACCAATAAACC-GGGAATCA
57121 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
57184 GGATCA-CGCACATAGCACCACCCATAAATCGGGAATCA
66 GGAT-ATCGCACATAGCACCACCAATAAACCGGGAATCA
**
57222 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
57238 TTTATATACA
Statistics
Matches: 110, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
101 22 0.20
102 50 0.45
103 21 0.19
104 17 0.15
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATATCGCACATAGCACCACCAATAAACCGGGAATCA
Done.