Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011505.1 Corchorus capsularis cultivar CVL-1 contig11526, 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: 14673
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Found at i:153 original size:2 final size:2
Alignment explanation
Indices: 146--171 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
136 ATTTATAATA
146 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
172 TAATGTGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:593 original size:11 final size:11
Alignment explanation
Indices: 577--613 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
567 GTTCTTTTTA
577 AATATATATAT
1 AATATATATAT
588 AATATATATAT
1 AATATATATAT
* *
599 ATTATTTATAT
1 AATATATATAT
610 AATA
1 AATA
614 ATAATTCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AATATATATAT
Found at i:596 original size:13 final size:13
Alignment explanation
Indices: 578--616 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
568 TTCTTTTTAA
578 ATATATATATAAT
1 ATATATATATAAT
*
591 ATATATATATTAT
1 ATATATATATAAT
*
604 TTATATA-ATAAT
1 ATATATATATAAT
616 A
1 A
617 ATTCACATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATATATAAT
Found at i:846 original size:64 final size:64
Alignment explanation
Indices: 719--839 Score: 233
Period size: 64 Copynumber: 1.9 Consensus size: 64
709 AGGAACCACA
719 TGCACGTTCGAGGTTTCGGACCAGCCACGTTGTTTGCAGCCGCCTTCTTAATTGAGAGAGGTTT
1 TGCACGTTCGAGGTTTCGGACCAGCCACGTTGTTTGCAGCCGCCTTCTTAATTGAGAGAGGTTT
*
783 TGCACGTTCGAGGTTTCTGACCAGCCACGTTGTTTGCAGCCGCCTTCTTAATTGAGA
1 TGCACGTTCGAGGTTTCGGACCAGCCACGTTGTTTGCAGCCGCCTTCTTAATTGAGA
840 CGGGTTTGGC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.31
Consensus pattern (64 bp):
TGCACGTTCGAGGTTTCGGACCAGCCACGTTGTTTGCAGCCGCCTTCTTAATTGAGAGAGGTTT
Found at i:1385 original size:84 final size:85
Alignment explanation
Indices: 1217--1388 Score: 301
Period size: 84 Copynumber: 2.0 Consensus size: 85
1207 TCCTCAACAA
* *
1217 TCTCCCCCGATTTACATGTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCCGTTAAGTCTTAAG
1 TCTCCCCCAATTTACATGTGAGTCCTCATCTCTCCCCCGT--GGCCCAACCCATTAAGTCTTAAG
1282 CCAATTACCGGCTATCCAAGAC
64 CCAATTACCGGCTATCCAAGAC
1304 TCTCCCCCAATTTACATGTGAGTCCTCATCTCTCCCCCGT-GCCCAACCCATTAAGTCTTAAGCC
1 TCTCCCCCAATTTACATGTGAGTCCTCATCTCTCCCCCGTGGCCCAACCCATTAAGTCTTAAGCC
1368 AATTACCGGCTATCCAAGAC
66 AATTACCGGCTATCCAAGAC
1388 T
1 T
1389 TAACCCCTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
84 44 0.53
87 39 0.47
ACGTcount: A:0.22, C:0.38, G:0.14, T:0.26
Consensus pattern (85 bp):
TCTCCCCCAATTTACATGTGAGTCCTCATCTCTCCCCCGTGGCCCAACCCATTAAGTCTTAAGCC
AATTACCGGCTATCCAAGAC
Found at i:1496 original size:77 final size:77
Alignment explanation
Indices: 1369--1511 Score: 277
Period size: 77 Copynumber: 1.9 Consensus size: 77
1359 TCTTAAGCCA
1369 ATTACCGGCTATCCAAGACTTAACCCCTGGAGTGGTACAAGCTACGAACACTCCAACAATCGCAC
1 ATTACCGGCTATCCAAGACTTAACCCCTGGAGTGGTACAAGCTACGAACACTCCAACAATCGCAC
1434 AGACCCAACCCG
66 AGACCCAACCCG
*
1446 ATTACCGGCTATCCAAGACTTAACCCTTGGAGTGGTACAAGCTACGAACACTCCAACAATCGCAC
1 ATTACCGGCTATCCAAGACTTAACCCCTGGAGTGGTACAAGCTACGAACACTCCAACAATCGCAC
1511 A
66 A
1512 CCCCTGGTGG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 65 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (77 bp):
ATTACCGGCTATCCAAGACTTAACCCCTGGAGTGGTACAAGCTACGAACACTCCAACAATCGCAC
AGACCCAACCCG
Found at i:4168 original size:26 final size:26
Alignment explanation
Indices: 4116--4168 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
4106 AATTCACTAC
* * * *
4116 AAATTAACTACTACTTTTTTTTTTTT
1 AAATCAACTACTACTATTATTTATTT
4142 AAATCAACTACTACTATTATTTATTT
1 AAATCAACTACTACTATTATTTATTT
4168 A
1 A
4169 CACATTAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (26 bp):
AAATCAACTACTACTATTATTTATTT
Found at i:6757 original size:37 final size:35
Alignment explanation
Indices: 6699--6767 Score: 111
Period size: 37 Copynumber: 1.9 Consensus size: 35
6689 GTGAGTCAAA
6699 GTCATGCCAGAATTAGATAAATACGTATTGCGAAG
1 GTCATGCCAGAATTAGATAAATACGTATTGCGAAG
*
6734 GTCATGCCAGATCATTAGATAAATACGTGTTGCG
1 GTCATGCCAGA--ATTAGATAAATACGTATTGCG
6768 CGCAGGGTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 11 0.35
37 20 0.65
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (35 bp):
GTCATGCCAGAATTAGATAAATACGTATTGCGAAG
Found at i:9385 original size:28 final size:28
Alignment explanation
Indices: 9345--9409 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
9335 ATCCCTAACA
*
9345 ATCTCCCCCGATTCACTTGTGAGTCCTC
1 ATCTCTCCCGATTCACTTGTGAGTCCTC
9373 ATCTCTCCCGATTCACTTGTGAGTCCTC
1 ATCTCTCCCGATTCACTTGTGAGTCCTC
9401 ATCTCTCCC
1 ATCTCTCCC
9410 CCGTGCAGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.14, C:0.40, G:0.12, T:0.34
Consensus pattern (28 bp):
ATCTCTCCCGATTCACTTGTGAGTCCTC
Found at i:11021 original size:29 final size:29
Alignment explanation
Indices: 10979--11036 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
10969 TCTTCGAAGT
10979 ACCTCTCAAGTATCTGAAGATCCACGCTC
1 ACCTCTCAAGTATCTGAAGATCCACGCTC
*
11008 ACCTCTCAAGTATCTGAAGATCTACGCTC
1 ACCTCTCAAGTATCTGAAGATCCACGCTC
11037 TGATACCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.26
Consensus pattern (29 bp):
ACCTCTCAAGTATCTGAAGATCCACGCTC
Found at i:14390 original size:22 final size:22
Alignment explanation
Indices: 14365--14441 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
14355 TTGAGGTATT
*
14365 CAAAATTCC-TTAGAGAGGTTAA
1 CAAAATTCCATAAGA-AGGTTAA
*
14387 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTCCATAAGAAGGTTAA
* * * **
14409 AAAAATT-TATAAAAAGGTTCT
1 CAAAATTCCATAAGAAGGTTAA
*
14430 CGAAATTCCATA
1 CAAAATTCCATA
14442 GTATCATTAT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 15 0.35
22 24 0.56
23 4 0.09
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.29
Consensus pattern (22 bp):
CAAAATTCCATAAGAAGGTTAA
Found at i:14420 original size:21 final size:22
Alignment explanation
Indices: 14380--14427 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
14370 TTCCTTAGAG
* *
14380 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAAA
14402 AGGTTAAAAAAATTT-ATAAAA
1 AGGTTAAAAAAATTTCATAAAA
14423 AGGTT
1 AGGTT
14428 CTCGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.29
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAAA
Done.