Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3525
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: 49489
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Found at i:1315 original size:33 final size:32
Alignment explanation
Indices: 1267--1348 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
1257 TTCTCAACTT
* * *
1267 ACTGGGCGGAAAGCCTTTGCAATTATTCATGTC
1 ACTGGGCCG-AAGCCTTTGCAATTATTAATATC
* *
1300 ACTTGGGCCGAAGCCTTTTCTATTATTAATATC
1 AC-TGGGCCGAAGCCTTTGCAATTATTAATATC
1333 ACTGGGCCG-AGCCTTT
1 ACTGGGCCGAAGCCTTT
1349 TACTTGACGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 7 0.16
32 7 0.16
33 23 0.53
34 6 0.14
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (32 bp):
ACTGGGCCGAAGCCTTTGCAATTATTAATATC
Found at i:1349 original size:31 final size:33
Alignment explanation
Indices: 1277--1349 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
1267 ACTGGGCGGA
* * *
1277 AAGCCTTTGCAATTATTCATGTCACTTGGGCCG
1 AAGCCTTTTCAATTATTAATATCACTTGGGCCG
*
1310 AAGCCTTTTCTATTATTAATATCAC-TGGGCCG
1 AAGCCTTTTCAATTATTAATATCACTTGGGCCG
1342 -AGCCTTTT
1 AAGCCTTTT
1350 ACTTGACGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 8 0.22
32 7 0.19
33 21 0.58
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (33 bp):
AAGCCTTTTCAATTATTAATATCACTTGGGCCG
Found at i:23233 original size:31 final size:31
Alignment explanation
Indices: 23187--23268 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 31
23177 TCAATCTCAA
*
23187 CATAT-ACTGGGCCGAAGCCTTTGCATTATT
1 CATATCACTAGGCCGAAGCCTTTGCATTATT
* *
23217 CATGTCACTAGGCCGAAGCCTTTTCATTATT
1 CATATCACTAGGCCGAAGCCTTTGCATTATT
*
23248 CATATCACTGGGCCGAAGCCT
1 CATATCACTAGGCCGAAGCCT
23269 CTTACTGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 4 0.09
31 42 0.91
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (31 bp):
CATATCACTAGGCCGAAGCCTTTGCATTATT
Found at i:23563 original size:25 final size:26
Alignment explanation
Indices: 23491--23586 Score: 117
Period size: 26 Copynumber: 3.8 Consensus size: 26
23481 CTCTTTTAAT
***
23491 AACTGGGGCAAAAGCCCTTTTTTATA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
23517 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
*
23543 AACTGGGAC-AAAGCCCTTTTCGGT-
1 AACTGGGGCAAAAGCCCTTTTCGGTA
* *
23567 AACTAGGGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
23587 GCACTTCCTC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
24 17 0.27
25 15 0.24
26 31 0.49
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AACTGGGGCAAAAGCCCTTTTCGGTA
Found at i:25952 original size:12 final size:12
Alignment explanation
Indices: 25937--25961 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25927 ACAGAAAATA
25937 ATAAAAATTTTC
1 ATAAAAATTTTC
25949 ATAAAAATTTTC
1 ATAAAAATTTTC
25961 A
1 A
25962 AACATACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAAAATTTTC
Found at i:28763 original size:33 final size:33
Alignment explanation
Indices: 28718--28782 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
28708 AGAAACAGTC
*
28718 TGGGCCTGAGCCC-ATCAAAGAAACAGTATCAGG
1 TGGGCCTAAGCCCAAT-AAAGAAACAGTATCAGG
* *
28751 TGGGCCTAAGCCCAATATAGAATCAGTATCAG
1 TGGGCCTAAGCCCAATAAAGAAACAGTATCAG
28783 ATGCAGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (33 bp):
TGGGCCTAAGCCCAATAAAGAAACAGTATCAGG
Found at i:31479 original size:56 final size:56
Alignment explanation
Indices: 31444--31851 Score: 552
Period size: 56 Copynumber: 7.3 Consensus size: 56
31434 CACATATCAA
* *
31444 AATCACATATCGATGCCAACGTATTAAATGTGGTCTTAGTCGCATACATATTTC-G
1 AATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAG
* *
31499 CATTCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCGG
1 -AATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAG
* * *
31556 AATCACATATCGATGCCAACATATTAAACGTGGTCTTAATCGCACACATATTTC-G
1 AATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAG
* * *
31611 AAATTACTTATTGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAG
1 -AATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAG
*
31668 AATCACATATCGATGCCAATGTATTAAAAT-TGGTCTTACTCGCACACATATTTCAG
1 AATCACATATCGATGCCAACGTATT-AAATGTGGTCTTACTCGCACACATATTTCAG
* * ** * **
31724 AATCACATATTGATGCCAACATATTAAACATGGTCTTACTCACACACATATTTTGG
1 AATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAG
* * * ** *
31780 AATCACATATTGATGCTAATGTATTAAACATGGTCTTACTCGTACACATATTTCAG
1 AATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAG
31836 AATCACATATCGATGC
1 AATCACATATCGATGC
31852 GAACTAAAAA
Statistics
Matches: 315, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
55 4 0.01
56 305 0.97
57 6 0.02
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (56 bp):
AATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAG
Found at i:31676 original size:168 final size:168
Alignment explanation
Indices: 31443--31851 Score: 615
Period size: 168 Copynumber: 2.4 Consensus size: 168
31433 ACACATATCA
* * * *
31443 AAATCACATATCGATGCCAACGTATTAAATGTGGTCTTAGTCGCATACATATTTC-GCATTCACA
1 AAATCACATATTGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAG-AATCACA
*
31507 TATCGATGCCAACGTATT-AAATGTGGTCTTACTCGCACACATATTTCGGAATCACATATCGATG
65 TATCGATGCCAACGTATTAAAAT-TGGTCTTACTCGCACACATATTTCAGAATCACATATCGATG
* *
31571 CCAACATATTAAACGTGGTCTTAATCGCACACATATTTCG
129 CCAACATATTAAACATGGTCTTAATCACACACATATTTCG
* *
31611 AAATTACTTATTGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAGAATCACAT
1 AAATCACATATTGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAGAATCACAT
* *
31676 ATCGATGCCAATGTATTAAAATTGGTCTTACTCGCACACATATTTCAGAATCACATATTGATGCC
66 ATCGATGCCAACGTATTAAAATTGGTCTTACTCGCACACATATTTCAGAATCACATATCGATGCC
* *
31741 AACATATTAAACATGGTCTTACTCACACACATATTTTG
131 AACATATTAAACATGGTCTTAATCACACACATATTTCG
* * * ** *
31779 GAATCACATATTGATGCTAATGTATTAAACATGGTCTTACTCGTACACATATTTCAGAATCACAT
1 AAATCACATATTGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAGAATCACAT
31844 ATCGATGC
66 ATCGATGC
31852 GAACTAAAAA
Statistics
Matches: 218, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
168 213 0.98
169 5 0.02
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (168 bp):
AAATCACATATTGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATTTCAGAATCACAT
ATCGATGCCAACGTATTAAAATTGGTCTTACTCGCACACATATTTCAGAATCACATATCGATGCC
AACATATTAAACATGGTCTTAATCACACACATATTTCG
Found at i:37190 original size:79 final size:80
Alignment explanation
Indices: 37054--37236 Score: 203
Period size: 79 Copynumber: 2.3 Consensus size: 80
37044 TCGAATGATG
* *
37054 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
*
37118 TGTGTGAGTTACTA-A
65 TGTGCGAGTTACTATA
* * * **
37133 TTCCGGGCTAAGCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
37196 TTGTGCGAGTTACTATA
64 TTGTGCGAGTTACTATA
* **
37213 ACCGGGCTATTTCCCGAAGGCATT
1 TCCGGGCTA-AGCCCGAAGGCATT
37237 TGAACGAGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.65
80 30 0.34
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTATA
Found at i:37245 original size:40 final size:40
Alignment explanation
Indices: 37054--37238 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
37044 TCGAATGATG
* * * *
37054 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
37094 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
37134 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
37173 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
**
37214 -CCGGGCTATTTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
37239 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 34 0.27
40 81 0.65
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:45154 original size:39 final size:39
Alignment explanation
Indices: 45056--45233 Score: 142
Period size: 37 Copynumber: 4.6 Consensus size: 39
45046 TCGAATGATG
*
45056 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG--AC--AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
45092 ATCCGGACTAAGATCCGAA-GCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAT
* *
45132 TCTGGGCTAAGCCCGAAGGCA-TT-TGCGA-TTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAT
*
45168 TCCGGGTTAAGTCCCTGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAG-CCC-GAAGGCATTTGTGCGAGTTACTAAT
* **
45208 AACCGGGCTATTCCCGAAGGCATTTG
1 -TCCGGGCTAAGCCCGAAGGCATTTG
45234 AACGAGTAGC
Statistics
Matches: 114, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
36 20 0.18
37 30 0.26
38 16 0.14
39 25 0.22
40 11 0.10
41 12 0.11
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:49414 original size:28 final size:26
Alignment explanation
Indices: 49359--49470 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
49349 AGCATGGCTG
* *
49359 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
49385 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* *
49413 CCAGAGCAGATATATGTGGCAGAACCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
49440 CTAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
49467 CCAG
1 CCAG
49471 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.08
27 50 0.68
28 17 0.23
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:49424 original size:54 final size:54
Alignment explanation
Indices: 49359--49470 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
49349 AGCATGGCTG
**
49359 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAACCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * *
49413 CCAGAGCAGATATATGTGGCAGAACCACTAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAACCACCAGATCAGATAATCGTGGCAGAGCCA
49467 CCAG
1 CCAG
49471 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 34 0.68
55 16 0.32
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAACCACCAGATCAGATAATCGTGGCAGAGCCA
Done.