Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1632
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: 29739
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Found at i:1252 original size:27 final size:26
Alignment explanation
Indices: 1204--1263 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
1194 AGCGAGTTGC
*
1204 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
1231 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
1257 CAGATAT
1 CAGATAT
1264 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:3896 original size:19 final size:20
Alignment explanation
Indices: 3872--3909 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3862 GGTACCACCA
3872 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
3891 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
3910 ACCACACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:6985 original size:13 final size:14
Alignment explanation
Indices: 6967--6996 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6957 TTCATATGAA
6967 TTATGA-ATTTATG
1 TTATGATATTTATG
6980 TTATGATATTTATG
1 TTATGATATTTATG
6994 TTA
1 TTA
6997 GAAAGTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (14 bp):
TTATGATATTTATG
Found at i:10949 original size:23 final size:24
Alignment explanation
Indices: 10912--10957 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
10902 TATGTGTTTA
10912 TTCTTATTTCATTTATCTATCTTT
1 TTCTTATTTCATTTATCTATCTTT
*
10936 TTCTTATTT-GTTTATCTATCTT
1 TTCTTATTTCATTTATCTATCTT
10958 CATAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.67
Consensus pattern (24 bp):
TTCTTATTTCATTTATCTATCTTT
Found at i:11430 original size:41 final size:42
Alignment explanation
Indices: 11369--11496 Score: 154
Period size: 44 Copynumber: 3.0 Consensus size: 42
11359 GTTGATAATC
*
11369 TTTCATATCACGTTGTCATGGTATCTTCAA-ATGGTCTTACACA
1 TTTCAT-TCAGGTTGTCATGGTATCTTCAACATGGTCTTA-ACA
*
11412 -TTCATTCAGGTTGCCATGGTATCTTTCAACCATGGTCTTAACA
1 TTTCATTCAGGTTGTCATGGTATC-TTCAA-CATGGTCTTAACA
* *
11455 TTTCATTCAGGTTGTAATGGTAT-TTCAACCATGATCTTAACA
1 TTTCATTCAGGTTGTCATGGTATCTTCAA-CATGGTCTTAACA
11497 GGACATTTCA
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
41 16 0.21
42 28 0.37
43 3 0.04
44 29 0.38
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (42 bp):
TTTCATTCAGGTTGTCATGGTATCTTCAACATGGTCTTAACA
Found at i:11460 original size:44 final size:44
Alignment explanation
Indices: 11369--11496 Score: 160
Period size: 42 Copynumber: 3.0 Consensus size: 44
11359 GTTGATAATC
*
11369 TTTCATATCACGTTGTCATGGTATC-TTCAA--ATGGTCTTACACA
1 TTTCAT-TCAGGTTGTCATGGTATCTTTCAACCATGGTCTTA-ACA
*
11412 -TTCATTCAGGTTGCCATGGTATCTTTCAACCATGGTCTTAACA
1 TTTCATTCAGGTTGTCATGGTATCTTTCAACCATGGTCTTAACA
* *
11455 TTTCATTCAGGTTGTAATGGTA--TTTCAACCATGATCTTAACA
1 TTTCATTCAGGTTGTCATGGTATCTTTCAACCATGGTCTTAACA
11497 GGACATTTCA
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
41 16 0.21
42 29 0.38
43 3 0.04
44 28 0.37
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (44 bp):
TTTCATTCAGGTTGTCATGGTATCTTTCAACCATGGTCTTAACA
Found at i:17772 original size:42 final size:41
Alignment explanation
Indices: 17507--17868 Score: 226
Period size: 41 Copynumber: 8.6 Consensus size: 41
17497 CAGCATGATT
* * * * *
17507 TGCTCTTT-GGGACCTAGCCCGGATATAAACACCAGCGCG-A
1 TGCTCTTTCGGGACTTAGCCCGGATA-CATCACTAGCACGAA
* * * * *
17547 TGCTCTTTCGAGG-TTTAGCATC-GATATATTACTTGCACGAA
1 TGCTCTTTCG-GGACTTAGC-CCGGATACATCACTAGCACGAA
* *
17588 TGCTC-TTCGGAACTTAGCCCCCGGATACAATGCACTTAGCATGAA
1 TGCTCTTTCGGGACTTAG--CCCGGATAC-AT-CAC-TAGCACGAA
* *
17633 TGCTC-TTCGGGACCTGTAGTCC-GATAC-TCACTA-CATTTGAA
1 TGCTCTTTCGGGA-CT-TAGCCCGGATACATCACTAGCA--CGAA
* * *
17674 TGCTCTTCCGAGACTTGAGTCCAGGATACATCACTAGCACGAA
1 TGCTCTTTCGGGACTT-AG-CCCGGATACATCACTAGCACGAA
* * *
17717 TGCTCTGTCGGGACTTAGCCCCGGATACATCA-TCGCATGAA
1 TGCTCTTTCGGGACTTAG-CCCGGATACATCACTAGCACGAA
* *
17758 TGCTCCTTTTGGGACTTAGCCCGGGTACATCACTAGCACGAA
1 TGCT-CTTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
17800 TGCTC-TTCGGGACTTA-CCCGGGTACATCACTAGCATGAAA
1 TGCTCTTTCGGGACTTAGCCCGGATACATCACTAGCACG-AA
*
17840 TGGCGCTGCTTCGGGACTTTAGCCCGGAT
1 T-GCTCT--TTCGGGAC-TTAGCCCGGAT
17869 GCCATCGTCG
Statistics
Matches: 253, Mismatches: 39, Indels: 54
0.73 0.11 0.16
Matches are distributed among these distances:
39 23 0.09
40 39 0.15
41 59 0.23
42 52 0.21
43 23 0.09
44 21 0.08
45 25 0.10
46 8 0.03
47 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (41 bp):
TGCTCTTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Done.