Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014031.1 Corchorus capsularis cultivar CVL-1 contig14052, 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: 24480
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:6849 original size:6 final size:6
Alignment explanation
Indices: 6838--6881 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
6828 ACAGTAAGTT
* * *
6838 CTTTTC CTTTTC CTTTTA CTTTT- CATTTC CTTTTC TTTTTC CTT
1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTT
6882 CCGTGAGTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (6 bp):
CTTTTC
Found at i:6877 original size:17 final size:17
Alignment explanation
Indices: 6836--6878 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
6826 CAACAGTAAG
* *
6836 TTCTTTTCCTTTTCCTT
1 TTCTTTTTCATTTCCTT
6853 TTAC-TTTTCATTTCCTT
1 TT-CTTTTTCATTTCCTT
6870 TTCTTTTTC
1 TTCTTTTTC
6879 CTTCCGTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCTTTTTCATTTCCTT
Found at i:8712 original size:27 final size:26
Alignment explanation
Indices: 8676--8792 Score: 164
Period size: 27 Copynumber: 4.3 Consensus size: 26
8666 GTCTTCTCTC
8676 CCCACTTCGACCCCA-AGTTTGGATCCT
1 CCCACTTCGACCCCACAG--TGGATCCT
8703 CCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCA-CAGTGGATCCT
8730 CCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCA-CAGTGGATCCT
**
8757 CCCACTTCGATTCCAGCAGTGGATCCT
1 CCCACTTCGACCCCA-CAGTGGATCCT
8784 CCCACTTCG
1 CCCACTTCG
8793 CCTATAGTGG
Statistics
Matches: 86, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
27 84 0.98
29 2 0.02
ACGTcount: A:0.18, C:0.43, G:0.17, T:0.22
Consensus pattern (26 bp):
CCCACTTCGACCCCACAGTGGATCCT
Found at i:8735 original size:54 final size:53
Alignment explanation
Indices: 8676--8792 Score: 182
Period size: 54 Copynumber: 2.2 Consensus size: 53
8666 GTCTTCTCTC
8676 CCCACTTCGACCCCA-AGTTTGGATCCTCCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCACAG--TGGATCCTCCCACTTCGACCCCAGCAGTGGATCCT
**
8730 CCCACTTCGACCCCAGCAGTGGATCCTCCCACTTCGATTCCAGCAGTGGATCCT
1 CCCACTTCGACCCCA-CAGTGGATCCTCCCACTTCGACCCCAGCAGTGGATCCT
8784 CCCACTTCG
1 CCCACTTCG
8793 CCTATAGTGG
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
54 57 0.97
56 2 0.03
ACGTcount: A:0.18, C:0.43, G:0.17, T:0.22
Consensus pattern (53 bp):
CCCACTTCGACCCCACAGTGGATCCTCCCACTTCGACCCCAGCAGTGGATCCT
Found at i:9623 original size:17 final size:17
Alignment explanation
Indices: 9601--9635 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9591 GAAAAAGTGC
9601 ATTCTTGGTGGCACATT
1 ATTCTTGGTGGCACATT
* *
9618 ATTCTTGTTGGCATATT
1 ATTCTTGGTGGCACATT
9635 A
1 A
9636 ACATTATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (17 bp):
ATTCTTGGTGGCACATT
Found at i:11240 original size:33 final size:33
Alignment explanation
Indices: 11170--11250 Score: 112
Period size: 32 Copynumber: 2.5 Consensus size: 33
11160 GGATATAACG
* *
11170 TTATATAGCGGCGTCTGAAGAACAAAACGCCGC
1 TTATATAGCGGCGTCTGAAAAAAAAAACGCCGC
*
11203 -TATATAACGGCGTCTGAAAAAAATAAACGCC-C
1 TTATATAGCGGCGTCTGAAAAAAA-AAACGCCGC
11235 TTATATAGCGGCGTCT
1 TTATATAGCGGCGTCT
11251 AAATAACCAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 21 0.50
33 21 0.50
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (33 bp):
TTATATAGCGGCGTCTGAAAAAAAAAACGCCGC
Found at i:11362 original size:24 final size:24
Alignment explanation
Indices: 11326--11395 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
11316 AGGGGCGTCT
*
11326 GGGCGTCTAGACGCCACTATTT-C
1 GGGCGTCTAGACGCCACTATTTAA
* *
11349 GCGGCGTCTCGACGCCACCATTTAA
1 G-GGCGTCTAGACGCCACTATTTAA
* *
11374 GGGCGTCTGGACGCCGCTATTT
1 GGGCGTCTAGACGCCACTATTT
11396 GCAATTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 1 0.03
24 37 0.95
25 1 0.03
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (24 bp):
GGGCGTCTAGACGCCACTATTTAA
Found at i:12199 original size:17 final size:17
Alignment explanation
Indices: 12177--12215 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12167 CTGTCCCCTG
* *
12177 ATCACTGGTGACCTTGC
1 ATCACTGATGACCTTAC
*
12194 ATCACTGATGATCTTAC
1 ATCACTGATGACCTTAC
12211 ATCAC
1 ATCAC
12216 CAGTGGTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (17 bp):
ATCACTGATGACCTTAC
Found at i:13056 original size:45 final size:45
Alignment explanation
Indices: 13005--13092 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
12995 TAATAGAATA
13005 GTGGAATTACTAAAAGATCCCTACCCC-GAATTAATGATAAGCTAG
1 GTGGAATTACTAAAAGATCCCTACCCCAG-ATTAATGATAAGCTAG
*
13050 GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATGAGCT
1 GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATAAGCT
13093 GGAGAAGTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 40 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATAAGCTAG
Found at i:14353 original size:166 final size:167
Alignment explanation
Indices: 14070--14416 Score: 482
Period size: 166 Copynumber: 2.1 Consensus size: 167
14060 CAAGGCTTGC
* * *
14070 TTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAAATCCCTACCAAAACTTG
1 TTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTACTAAAAAATCCCCACCAAAACTTG
* ** * * * * *
14135 CTTTTGGAGCTAGAGAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTA
66 ATGATGGAGCTAGAGAAATAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATATCCTA
* * *
14200 ACTTTTGATTCTTGAGGGGAATAAATTAGTAATCTTT
131 ACTTTTGATTCTTGAGGGGAATAAATAACTAAACTTT
* * * *
14237 TTGGTCATTTCTCAATGGACTTGAATGGAGTAGTGGAATTACTAAAAGATCCCCATCAAGGA-TT
1 TTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTACTAAAAAATCCCCACCAA-AACTT
*
14301 GATGAT-GAGGTAGAGAAATAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATATCCT
65 GATGATGGAGCTAGAGAAATAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATATCCT
* *
14365 AACTTTTTATTCTTGAGGGGATTAAATAACTAAACTTT
130 AACTTTTGATTCTTGAGGGGAATAAATAACTAAACTTT
14403 TTGGTCATTTCTCA
1 TTGGTCATTTCTCA
14417 TTTCTCAATT
Statistics
Matches: 158, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
166 99 0.63
167 58 0.37
168 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (167 bp):
TTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTACTAAAAAATCCCCACCAAAACTTG
ATGATGGAGCTAGAGAAATAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATATCCTA
ACTTTTGATTCTTGAGGGGAATAAATAACTAAACTTT
Found at i:18217 original size:19 final size:19
Alignment explanation
Indices: 18193--18238 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
18183 TTTTCTTTAT
18193 AATTAAATAAT-AATAAATA
1 AATTAAA-AATAAATAAATA
* *
18212 AATTAAAATTAAATTAATA
1 AATTAAAAATAAATAAATA
18231 AATTAAAA
1 AATTAAAA
18239 TTAACTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTAAAAATAAATAAATA
Found at i:18239 original size:25 final size:24
Alignment explanation
Indices: 18193--18242 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
18183 TTTTCTTTAT
18193 AATTAAATAATAATAAATAAATTAA
1 AATTAAAT-ATAATAAATAAATTAA
18218 AATTAAAT-TAATAAATTAAAATTAA
1 AATTAAATATAATAAA-T-AAATTAA
18243 CTTATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.30
24 1 0.04
25 15 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTAAATATAATAAATAAATTAA
Found at i:18367 original size:19 final size:20
Alignment explanation
Indices: 18328--18363 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
18318 ATTTTTAAGT
18328 AAAAATATAATATATAAATA
1 AAAAATATAATATATAAATA
18348 AAAAAT-TAATAT-TAAA
1 AAAAATATAATATATAAA
18364 ATAATTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATATAATATATAAATA
Found at i:18466 original size:11 final size:11
Alignment explanation
Indices: 18450--18476 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
18440 GTACTAAAAT
18450 CCCTACCCTAA
1 CCCTACCCTAA
18461 CCCTACCCTAA
1 CCCTACCCTAA
18472 CCCTA
1 CCCTA
18477 TTATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.56, G:0.00, T:0.19
Consensus pattern (11 bp):
CCCTACCCTAA
Found at i:21059 original size:14 final size:14
Alignment explanation
Indices: 21022--21052 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
21012 TGGTGGCCGC
21022 AGCACACCCAGTTT
1 AGCACACCCAGTTT
21036 AGCACACCCAGTTT
1 AGCACACCCAGTTT
21050 AGC
1 AGC
21053 TCCCCCATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.19
Consensus pattern (14 bp):
AGCACACCCAGTTT
Found at i:22391 original size:8 final size:7
Alignment explanation
Indices: 22360--22443 Score: 81
Period size: 6 Copynumber: 12.4 Consensus size: 7
22350 ATTATCCCAA
*
22360 TTTTCCA
1 TTTTCCT
22367 TTTTCCTT
1 TTTTCC-T
22375 TTATTCCT
1 TT-TTCCT
22383 TATTTCCT
1 T-TTTCCT
22391 TTTT-CT
1 TTTTCCT
22397 TTTT-CT
1 TTTTCCT
*
22403 TTTTCCC
1 TTTTCCT
22410 TTTT-CT
1 TTTTCCT
22416 TTTTCC-
1 TTTTCCT
22422 TTTTCC-
1 TTTTCCT
22428 TTTTCC-
1 TTTTCCT
22434 TTTTCCT
1 TTTTCCT
22441 TTT
1 TTT
22444 CTTCATTTAT
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
6 35 0.51
7 18 0.26
8 10 0.15
9 5 0.07
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTCCT
Found at i:22400 original size:6 final size:6
Alignment explanation
Indices: 22389--22479 Score: 67
Period size: 6 Copynumber: 15.2 Consensus size: 6
22379 TCCTTATTTC
* * * *
22389 CTTTTT CTTTTT CTTTTT CCCTTTT CTTTTT CCTTTT CCTTTT CCTTTT
1 CTTTTT CTTTTT CTTTTT -CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
* ** * * * *
22438 CCTTTT CTTCAT -TTATT CTTCTT CTTCTT CTTTTT TTTTTT C
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C
22480 CCTGATTGGG
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
5 3 0.04
6 63 0.89
7 5 0.07
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:22413 original size:19 final size:19
Alignment explanation
Indices: 22385--22444 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
22375 TTATTCCTTA
* *
22385 TTTCCTTTTTCTTTTTCTT
1 TTTCCCTTTTCTTTTTCCT
22404 TTTCCCTTTTCTTTTTCCT
1 TTTCCCTTTTCTTTTTCCT
*
22423 TTT-CCTTTTCCTTTTCCT
1 TTTCCCTTTTCTTTTTCCT
22441 TTTC
1 TTTC
22445 TTCATTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 17 0.46
19 20 0.54
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCCCTTTTCTTTTTCCT
Found at i:22425 original size:25 final size:24
Alignment explanation
Indices: 22391--22446 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
22381 CTTATTTCCT
* *
22391 TTTTCTTTTTCTTTTTCCCTTTTCT
1 TTTTCTTTTTCCTTTT-CCTTTTCC
*
22416 TTTTCCTTTTCCTTTTCCTTTTCC
1 TTTTCTTTTTCCTTTTCCTTTTCC
22440 TTTTCTT
1 TTTTCTT
22447 CATTTATTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTCTTTTTCCTTTTCCTTTTCC
Done.