Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017611.1 Corchorus olitorius cultivar O-4 contig17644, whole genome shotgun sequence
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: 13679
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:1208 original size:9 final size:9
Alignment explanation
Indices: 1194--1219 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1184 ATAAACACAT
1194 TTAATTTCA
1 TTAATTTCA
1203 TTAATTTCA
1 TTAATTTCA
1212 TTAATTTC
1 TTAATTTC
1220 CTAATTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58
Consensus pattern (9 bp):
TTAATTTCA
Found at i:7655 original size:54 final size:54
Alignment explanation
Indices: 7591--7698 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
7581 AGGTGATTTT
*
7591 AGTCATCTAATGTTCAAACGCACTTTTTAAGCGCAAAATCACCTAAAGATTAGC
1 AGTCATCTAATGTCCAAACGCACTTTTTAAGCGCAAAATCACCTAAAGATTAGC
*
7645 AGTCATCTAATGTCCAAACGCACTTTTTAAGCGCAAAATCACTTAAAGATTAGC
1 AGTCATCTAATGTCCAAACGCACTTTTTAAGCGCAAAATCACCTAAAGATTAGC
7699 TTTTCAGGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (54 bp):
AGTCATCTAATGTCCAAACGCACTTTTTAAGCGCAAAATCACCTAAAGATTAGC
Found at i:8232 original size:28 final size:28
Alignment explanation
Indices: 8201--8256 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
8191 TAGTTTTTGT
8201 TTAAGTGCTACACACTTTAGAGGAGGAA
1 TTAAGTGCTACACACTTTAGAGGAGGAA
8229 TTAAGTGCTACACACTTTAGAGGAGGAA
1 TTAAGTGCTACACACTTTAGAGGAGGAA
8257 ACAAAATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (28 bp):
TTAAGTGCTACACACTTTAGAGGAGGAA
Found at i:9983 original size:17 final size:18
Alignment explanation
Indices: 9954--9987 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
9944 ACTTTATTTA
9954 TATCAATTTTAAAAAAAT
1 TATCAATTTTAAAAAAAT
9972 TATCAA-TTTAAAAAAA
1 TATCAATTTTAAAAAAA
9988 ACCCTCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
TATCAATTTTAAAAAAAT
Found at i:9988 original size:18 final size:18
Alignment explanation
Indices: 9954--9988 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9944 ACTTTATTTA
*
9954 TATCAATTTTAAAAAAAT
1 TATCAATTTAAAAAAAAT
9972 TATCAATTTAAAAAAAA
1 TATCAATTTAAAAAAAA
9989 CCCTCTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
TATCAATTTAAAAAAAAT
Found at i:10349 original size:29 final size:30
Alignment explanation
Indices: 10289--10368 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
10279 GCTAAATACC
* * *
10289 CAAAAAAATCCCTTATATTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
10320 CAAAATAATCCCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
* *
10349 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
10369 CAAAAATGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 25 0.57
31 19 0.43
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:10587 original size:31 final size:31
Alignment explanation
Indices: 10492--10577 Score: 154
Period size: 31 Copynumber: 2.8 Consensus size: 31
10482 AAGGGACTGA
10492 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
*
10523 TTTGTCCCAAAAGAAAAGCATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
*
10554 TTTGTCCCAAAAGAAAAATATAAG
1 TTTGTCCCAAAAGAAAAACATAAG
10578 AGAAGTTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Found at i:10899 original size:37 final size:37
Alignment explanation
Indices: 10849--10939 Score: 166
Period size: 37 Copynumber: 2.5 Consensus size: 37
10839 TATATTTAAA
10849 AAACAAGCCCTTAACATTACGTGACTCTGTTTTCTAG
1 AAACAAGCCCTTAACATTACGTGACTCTGTTTTCTAG
10886 AAACAAGCCCTTAACATTACGTGACTCTGTTTTCTAG
1 AAACAAGCCCTTAACATTACGTGACTCTGTTTTCTAG
10923 AAACAAG-CCTCTAACAT
1 AAACAAGCCCT-TAACAT
10940 ATTTAATCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
36 3 0.06
37 50 0.94
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (37 bp):
AAACAAGCCCTTAACATTACGTGACTCTGTTTTCTAG
Found at i:11397 original size:126 final size:125
Alignment explanation
Indices: 11229--11467 Score: 320
Period size: 126 Copynumber: 1.9 Consensus size: 125
11219 CTTATTTTTC
* * **
11229 AAATATATTTTTTAAATACAATTTTTAAACTTTTATAATTTTACTCAATTAAAAACTCTATTTTT
1 AAATATATTTCTTAAATACAATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
*
11294 ATTTAATCAAA-TCTAATATATTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
66 ATTTAATCAAATTC-AATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
* * ** *
11354 AAATATATTTCTTAAATGAC-ATTATTTAAACTTTTACAGTTTTATTTTACCAAAAATTCTATTT
1 AAATATATTTCTTAAAT-ACAATT-TTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTT
* * *
11418 TTGTTTAATTAAATTCAATATTTTTATAACTATTTTATCTTTACCATTTT
64 TTATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTT
11468 TTTAGGGAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
125 19 0.19
126 77 0.79
127 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.53
Consensus pattern (125 bp):
AAATATATTTCTTAAATACAATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
ATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:11573 original size:15 final size:15
Alignment explanation
Indices: 11553--11584 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11543 AAAGGAGGAG
11553 AAGGAAAAAAGAAAA
1 AAGGAAAAAAGAAAA
*
11568 AAGGAAAAAGGAAAA
1 AAGGAAAAAAGAAAA
11583 AA
1 AA
11585 ATCAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGGAAAAAAGAAAA
Found at i:11574 original size:8 final size:8
Alignment explanation
Indices: 11553--11584 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
11543 AAAGGAGGAG
11553 AAGGAAAA
1 AAGGAAAA
11561 AA-GAAAA
1 AAGGAAAA
11568 AAGG-AAA
1 AAGGAAAA
11575 AAGGAAAA
1 AAGGAAAA
11583 AA
1 AA
11585 ATCAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.64
8 8 0.36
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAGGAAAA
Found at i:11709 original size:31 final size:32
Alignment explanation
Indices: 11626--11709 Score: 127
Period size: 31 Copynumber: 2.7 Consensus size: 32
11616 ACTAAATACT
* *
11626 AAAAAAATCCCTAATGTTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTTATTTTGGGAC
11658 AAAAAAATCCCTTATG-TTTTTATTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTTATTTTGGGAC
*
11689 AAAAAAA-CCTTTATGTTTTTT
1 AAAAAAATCCCTTATGTTTTTT
11710 TATGGACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
30 7 0.15
31 26 0.54
32 15 0.31
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (32 bp):
AAAAAAATCCCTTATGTTTTTTATTTTGGGAC
Done.