Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2353
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: 35756
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:4864 original size:40 final size:40
Alignment explanation
Indices: 4782--4966 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
4772 GCTACTCGTT
* *
4782 CAAATGCCTTCGGGACAT-AGCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
4821 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
4861 CAAATGCCTTCAGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*** * * * *
4901 CAAATGCCTTC-GGATCTTGGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
4942 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
4967 CATCATTCAA
Statistics
Matches: 129, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
39 20 0.16
40 96 0.74
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:13405 original size:20 final size:20
Alignment explanation
Indices: 13380--13431 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
13370 AAGACATAGC
13380 ACACGCCCGTGTGCTTCAGG
1 ACACGCCCGTGTGCTTCAGG
13400 ACACGCCCGTGTGCTTCAGG
1 ACACGCCCGTGTGCTTCAGG
13420 ACACGCCCGTGT
1 ACACGCCCGTGT
13432 CCCCTACTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.37, G:0.29, T:0.19
Consensus pattern (20 bp):
ACACGCCCGTGTGCTTCAGG
Found at i:21175 original size:159 final size:155
Alignment explanation
Indices: 20890--21228 Score: 443
Period size: 159 Copynumber: 2.2 Consensus size: 155
20880 TGTTACATTT
* *
20890 TTATTTTTCAAAATCTAAACTTTC-TCATTTTTAAAAGAAAAACATTATTTTTTTAAAATATTAA
1 TTATTTTTCAAAATCTAAACTTTCTTCATTTTTAAAAGAAAAACACTATTTTTTTAAAAGATTAA
* * * * * *
20954 AGCTTTTATTTTGAAGTAGTTAAAAAAGAAATCAAAATTTTGTTTTAAAAATTTAAGCTTTCCTT
66 AGCTTTTACTTTCAAATAGTTAAAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTT
21019 TAAAATAACTA-AAAAAAAATAGATTC
131 TAAAATAACTAGAAAAAAAAT--ATTC
* ** *
21045 TTATTTTTCAAAATCTAAAATTTCTTTTTTTTTTAAAA-AAAAAGTACTATTTTTCTT-AAAGAT
1 TTATTTTTCAAAATCTAAACTTTC-TTCATTTTTAAAAGAAAAA-CACTATTTTT-TTAAAAGAT
21108 TAAAGCTTTTACTTTCAAATAGTTGAAAAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTT
63 TAAAGCTTTTACTTTCAAATAGTT--AAAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTT
* * *
21173 TCCTTTGAAATAACTAGAAAAAACATATTT
126 TCCTTTAAAATAACTAGAAAAAAAATATTC
21203 TTATTTTTTCAAAATCTAAACTTTCT
1 TTA-TTTTTCAAAATCTAAACTTTCT
21229 CCTTAAAAAA
Statistics
Matches: 160, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
155 23 0.14
156 5 0.03
157 44 0.28
158 9 0.06
159 71 0.44
160 8 0.05
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (155 bp):
TTATTTTTCAAAATCTAAACTTTCTTCATTTTTAAAAGAAAAACACTATTTTTTTAAAAGATTAA
AGCTTTTACTTTCAAATAGTTAAAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTT
TAAAATAACTAGAAAAAAAATATTC
Found at i:21643 original size:8 final size:8
Alignment explanation
Indices: 21625--21659 Score: 56
Period size: 7 Copynumber: 4.6 Consensus size: 8
21615 ATAGGCCCAA
21625 AAAAGAA-
1 AAAAGAAT
21632 AAAAGAAT
1 AAAAGAAT
21640 AAAAGAAT
1 AAAAGAAT
21648 AAAA-AAT
1 AAAAGAAT
21655 AAAAG
1 AAAAG
21660 TCTCAAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.54
8 12 0.46
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (8 bp):
AAAAGAAT
Found at i:21645 original size:15 final size:15
Alignment explanation
Indices: 21625--21659 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
21615 ATAGGCCCAA
21625 AAAAGAA-AAAAGAAT
1 AAAAGAATAAAA-AAT
21640 AAAAGAATAAAAAAT
1 AAAAGAATAAAAAAT
21655 AAAAG
1 AAAAG
21660 TCTCAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (15 bp):
AAAAGAATAAAAAAT
Found at i:24807 original size:252 final size:252
Alignment explanation
Indices: 24359--24865 Score: 969
Period size: 252 Copynumber: 2.0 Consensus size: 252
24349 TTCAATTGAA
*
24359 TCACTATTTTTTTCCTTCTCTATTTTGTTCCCTTTCAAAGATTCAGTTGGTGCTAAAGTATCATG
1 TCACTATTTTTTTCCTTCTCTATTTTGTTCCCTTTCAAAGATTCAGTTGGTGCTAAAGTATCACG
*
24424 CAAAATACCTGCCATTTGTCCTGCTGTTGGATCGTTCTTTTCTCTATTAATAACTTTCATCAAGT
66 CAAAATACCTGCCATTTCTCCTGCTGTTGGATCGTTCTTTTCTCTATTAATAACTTTCATCAAGT
*
24489 CCTCAATTCTTGAAGAACTTTTGGACGATGCATGCTTTTTTCCTGAAATAGTGGTTGCACTTGGC
131 CCTCAATTCTTGAAGAACTTTTGGACGATGCATGCTTTTTTCCTGAAATAGTGGTTGCAATTGGC
24554 CTTTGAACAGAAGTAGCAGTTCTGTTCCCAGGTAGATAGTTCATAATTTCAGACAAG
196 CTTTGAACAGAAGTAGCAGTTCTGTTCCCAGGTAGATAGTTCATAATTTCAGACAAG
*
24611 TCACTATTTTTTTCCTTCTCTATTTTGTTCCCTTTCGAAGATTCAGTTGGTGCTAAAGTATCACG
1 TCACTATTTTTTTCCTTCTCTATTTTGTTCCCTTTCAAAGATTCAGTTGGTGCTAAAGTATCACG
24676 CAAAATACCTGCCATTTCTCCTGCTGTTGGATCGTTCTTTTCTCTATTAATAACTTTCATCAAGT
66 CAAAATACCTGCCATTTCTCCTGCTGTTGGATCGTTCTTTTCTCTATTAATAACTTTCATCAAGT
*
24741 CCTCAATTCTTGAAGAACTTTTGGACGATGCATGCTTTTTTCTTGAAATAGTGGTTGCAATTGGC
131 CCTCAATTCTTGAAGAACTTTTGGACGATGCATGCTTTTTTCCTGAAATAGTGGTTGCAATTGGC
24806 CTTTGAACAGAAGTAGCAGTTCTGTTCCCAGGTAGATAGTTCATAATTTCAGACAAG
196 CTTTGAACAGAAGTAGCAGTTCTGTTCCCAGGTAGATAGTTCATAATTTCAGACAAG
24863 TCA
1 TCA
24866 TTTGTACCAT
Statistics
Matches: 250, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
252 250 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (252 bp):
TCACTATTTTTTTCCTTCTCTATTTTGTTCCCTTTCAAAGATTCAGTTGGTGCTAAAGTATCACG
CAAAATACCTGCCATTTCTCCTGCTGTTGGATCGTTCTTTTCTCTATTAATAACTTTCATCAAGT
CCTCAATTCTTGAAGAACTTTTGGACGATGCATGCTTTTTTCCTGAAATAGTGGTTGCAATTGGC
CTTTGAACAGAAGTAGCAGTTCTGTTCCCAGGTAGATAGTTCATAATTTCAGACAAG
Found at i:26724 original size:31 final size:31
Alignment explanation
Indices: 26690--26750 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
26680 TTATAGAAGT
* *
26690 AAAATTGCACTTTAATCCTTTTAAAATTATTA
1 AAAATT-CAATTTAATCCTTTAAAAATTATTA
*
26722 AAAATTTAATTTAATCCTTTAAAAATTAT
1 AAAATTCAATTTAATCCTTTAAAAATTAT
26751 AAAGGTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (31 bp):
AAAATTCAATTTAATCCTTTAAAAATTATTA
Found at i:32357 original size:17 final size:19
Alignment explanation
Indices: 32310--32358 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
32300 TGGGCTATTT
* *
32310 TGTAAAGTTGTAAAATAAG
1 TGTAAATTTGTGAAATAAG
*
32329 TGTAAATGTGTGAAATAA-
1 TGTAAATTTGTGAAATAAG
32347 T-TAAATTTGTGA
1 TGTAAATTTGTGA
32359 CGTGCTATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 10 0.38
18 1 0.04
19 15 0.58
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (19 bp):
TGTAAATTTGTGAAATAAG
Found at i:35243 original size:24 final size:24
Alignment explanation
Indices: 35211--35258 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35201 TGCCATTTTC
35211 ATAGTATTCACCAAATACTATATA
1 ATAGTATTCACCAAATACTATATA
35235 ATAGTATTCACCAAATACTATATA
1 ATAGTATTCACCAAATACTATATA
35259 CATTATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAGTATTCACCAAATACTATATA
Done.