Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007034.1 Corchorus capsularis cultivar CVL-1 contig07055, 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: 29662
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1351 original size:8 final size:8
Alignment explanation
Indices: 1323--1356 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1313 GAATCAGCTA
1323 TGAATTTT
1 TGAATTTT
*
1331 TGAAGTTTC
1 TGAA-TTTT
1340 TGAATTTT
1 TGAATTTT
1348 TGAATTTT
1 TGAATTTT
1356 T
1 T
1357 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:2332 original size:33 final size:33
Alignment explanation
Indices: 2261--2335 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
2251 AAAGGATCGT
* * *
2261 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCGT
1 GTGGCCGGTTGTAGCCGGCCATGGCCGAGTCGC
* *
2294 TTGGCCGGTTGTAGCCGGCCATGTCC-ATGTCGC
1 GTGGCCGGTTGTAGCCGGCCATGGCCGA-GTCGC
2327 GTGGCCGGT
1 GTGGCCGGT
2336 CTTGTGGCCG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.03
33 34 0.97
ACGTcount: A:0.07, C:0.27, G:0.43, T:0.24
Consensus pattern (33 bp):
GTGGCCGGTTGTAGCCGGCCATGGCCGAGTCGC
Found at i:6132 original size:21 final size:20
Alignment explanation
Indices: 6098--6141 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
6088 CTAGTCAGGA
6098 CCGGCCACAACCGCTCTACAG
1 CCGGCCACAACCGCT-TACAG
* * *
6119 CCGGCCATATCCGCTTATAG
1 CCGGCCACAACCGCTTACAG
6139 CCG
1 CCG
6142 TGTGACCACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.16
Consensus pattern (20 bp):
CCGGCCACAACCGCTTACAG
Found at i:8649 original size:15 final size:15
Alignment explanation
Indices: 8629--8659 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8619 AGGAAGCTCC
8629 TAAAGAAGTTAAAAT
1 TAAAGAAGTTAAAAT
8644 TAAAGAAGTTAAAAT
1 TAAAGAAGTTAAAAT
8659 T
1 T
8660 GGTACCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (15 bp):
TAAAGAAGTTAAAAT
Found at i:13505 original size:23 final size:23
Alignment explanation
Indices: 13447--13505 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
13437 TTAGCTAATT
*
13447 AAGAAAACTAAAGCAAAGTATAA
1 AAGAAAACTAAATCAAAGTATAA
* *
13470 AGGAAATCTAAATCAATA-TATAA
1 AAGAAAACTAAATCAA-AGTATAA
*
13493 AAGAAACCTAAAT
1 AAGAAAACTAAAT
13506 ATATGAAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (23 bp):
AAGAAAACTAAATCAAAGTATAA
Found at i:13508 original size:19 final size:19
Alignment explanation
Indices: 13484--13520 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13474 AATCTAAATC
13484 AATATATAAAAGAAACCTA
1 AATATATAAAAGAAACCTA
*
13503 AATATATGAAAGAAACCT
1 AATATATAAAAGAAACCT
13521 CCAACATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.08, T:0.22
Consensus pattern (19 bp):
AATATATAAAAGAAACCTA
Found at i:16179 original size:12 final size:12
Alignment explanation
Indices: 16162--16197 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
16152 GAAAAAATTT
*
16162 CAAAATTAGGTA
1 CAAAATTAAGTA
16174 CAAAATTAAGTA
1 CAAAATTAAGTA
*
16186 CAATATTAAGTA
1 CAAAATTAAGTA
16198 ATCACCATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (12 bp):
CAAAATTAAGTA
Found at i:22387 original size:19 final size:19
Alignment explanation
Indices: 22363--22399 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22353 AATCTAAATC
22363 AATATATAAAAGAAACCTA
1 AATATATAAAAGAAACCTA
*
22382 AATATATGAAAGAAACCT
1 AATATATAAAAGAAACCT
22400 CCAACATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.08, T:0.22
Consensus pattern (19 bp):
AATATATAAAAGAAACCTA
Found at i:26184 original size:26 final size:26
Alignment explanation
Indices: 26153--26242 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
26143 ATTATTCAAT
26153 TTACTGATTACTATCTTTTTACCTAA
1 TTACTGATTACTATCTTTTTACCTAA
*
26179 TTACTGATTTACTGAT-TATTATTACCTTGA
1 TTACTGA-TTACT-ATCT-TT-TTACC-TAA
* * * *
26209 CT-CTGATTAATCTCTTTTTACTTAA
1 TTACTGATTACTATCTTTTTACCTAA
26234 TTACTGATT
1 TTACTGATT
26243 TACTGATTAC
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
25 3 0.06
26 17 0.34
27 9 0.18
28 9 0.18
29 9 0.18
30 3 0.06
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.51
Consensus pattern (26 bp):
TTACTGATTACTATCTTTTTACCTAA
Found at i:26214 original size:29 final size:29
Alignment explanation
Indices: 26182--26271 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
26172 TACCTAATTA
26182 CTGATTTACTGATTATTATTACCTTGACT
1 CTGATTTACTGATTATTATTACCTTGACT
* * * *
26211 CTGA-TTA---ATCTCTTTTTA-CTTAATT
1 CTGATTTACTGAT-TATTATTACCTTGACT
*
26236 ACTGATTTACTGATTACTATTACCTTGACT
1 -CTGATTTACTGATTATTATTACCTTGACT
26266 CTGATT
1 CTGATT
26272 AATCTCTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 7 0.16
26 10 0.22
27 3 0.07
28 3 0.07
29 15 0.33
30 7 0.16
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (29 bp):
CTGATTTACTGATTATTATTACCTTGACT
Found at i:26225 original size:55 final size:55
Alignment explanation
Indices: 26156--26582 Score: 660
Period size: 55 Copynumber: 7.8 Consensus size: 55
26146 ATTCAATTTA
* * * *
26156 CTGATTACTATCTTTTTACCTAATTACTGATTTACTGATTATTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
26211 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
* *
26266 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATCACTACTA-CTCTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCT-TGACT
**
26321 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAATTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
* * *
26376 CTGATTAATCTCTTTTCACTTAATTACGGATTTACTGATTACTATTACTTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
* * * *
26431 CTGATTAACCTCTTTTTACTTGATTACTGATCTACTGATTACTATTACTTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
* *
26486 ATGATTAATCTCTTTTCACTTAATTACTGATTTACTGACTT-CTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGA-TTACTATTACCTTGACT
*
26541 CTGATTAATCTCTTTTTACTTAATTACTGGTTTACTGATTAC
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTAC
26583 CCTTTTACTT
Statistics
Matches: 342, Mismatches: 26, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
54 4 0.01
55 335 0.98
56 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
Found at i:26677 original size:15 final size:15
Alignment explanation
Indices: 26637--26671 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
26627 CATTTTCTTC
* *
26637 TTACAGATTAGCTTT
1 TTACTGATTACCTTT
26652 TTACTGATTACCTTT
1 TTACTGATTACCTTT
26667 TTACT
1 TTACT
26672 TCTTACTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (15 bp):
TTACTGATTACCTTT
Found at i:26702 original size:33 final size:32
Alignment explanation
Indices: 26652--26713 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
26642 GATTAGCTTT
26652 TTACTGATTACCTTTTTACTTCTTACTGATCTC
1 TTACTGATTACCTTTTTAC-TCTTACTGATCTC
* *
26685 TTACTGATTA-TTATTTTACTCTTGCTGAT
1 TTACTGATTACCT-TTTTACTCTTACTGAT
26714 TACCTTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 10 0.38
33 16 0.62
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.53
Consensus pattern (32 bp):
TTACTGATTACCTTTTTACTCTTACTGATCTC
Found at i:26736 original size:22 final size:22
Alignment explanation
Indices: 26571--26803 Score: 108
Period size: 22 Copynumber: 10.5 Consensus size: 22
26561 TAATTACTGG
26571 TTTACTGATTACCCTT-TTACTT
1 TTTACTGATTA-CCTTCTTACTT
* * *
26593 TTTACTGATTGCCTTTTTGCTT
1 TTTACTGATTACCTTCTTACTT
*
26615 TTTACTCATTACCATT-TT-CTT
1 TTTACTGATTACC-TTCTTACTT
* * * * *
26636 CTTACAGATTAGCTTTTTACTG
1 TTTACTGATTACCTTCTTACTT
* **
26658 ATTACCTTTTTA-CTTCTTACTGAT
1 TTTA-CTGATTACCTTCTTACT--T
* *
26682 CTCTTACTGATTA-TTATTTTAC-T
1 -T-TTACTGATTACCT-TCTTACTT
* *
26705 CTTGCTGATTACCTTCTTACTT
1 TTTACTGATTACCTTCTTACTT
* *
26727 TTTACTGATTA-CTACTTCACTC
1 TTTACTGATTACCTTCTT-ACTT
* *
26749 TTTACTAATTACCATT-TTACCT
1 TTTACTGATTACC-TTCTTACTT
*
26771 TTTACTGATTATCATTCTT--TT
1 TTTACTGATTA-CCTTCTTACTT
26792 TTTACTGATTAC
1 TTTACTGATTAC
26804 TATTTTACTA
Statistics
Matches: 159, Mismatches: 35, Indels: 36
0.69 0.15 0.16
Matches are distributed among these distances:
20 3 0.02
21 49 0.31
22 79 0.50
23 13 0.08
24 1 0.01
25 6 0.04
26 8 0.05
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTACTGATTACCTTCTTACTT
Found at i:26918 original size:31 final size:30
Alignment explanation
Indices: 26849--26918 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
26839 ACTTTACTTT
*
26849 TTACTGATTGCTTTTTCTAATTGAACTTAA
1 TTACTGATTACTTTTTCTAATTGAACTTAA
* * * *
26879 TCATTGATTATTTTTTCCTTATTGAACTTAA
1 TTACTGATTACTTTTT-CTAATTGAACTTAA
26910 TTACTGATT
1 TTACTGATT
26919 GCCCTTTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.53
Consensus pattern (30 bp):
TTACTGATTACTTTTTCTAATTGAACTTAA
Done.