Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007668.1 Corchorus capsularis cultivar CVL-1 contig07689, 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: 7125
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:5179 original size:13 final size:13
Alignment explanation
Indices: 5161--5185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5151 TTCAATGTTC
5161 TAAATATTATTTA
1 TAAATATTATTTA
5174 TAAATATTATTT
1 TAAATATTATTT
5186 GGAATTTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:5463 original size:22 final size:22
Alignment explanation
Indices: 5438--5999 Score: 218
Period size: 22 Copynumber: 25.7 Consensus size: 22
5428 ATGATCTCGT
5438 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCA
* ***
5460 TATGAAATTTTAATAATGAT-A
1 TATGAAATTTTGATAACCTTCA
* * **
5481 TTAT-AGAATTTCGAGAACCTTTT
1 -TATGA-AATTTTGATAACCTTCA
** *
5504 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCA
* * *
5526 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCA
* *
5548 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-A
5570 TATGAAATTTTGATAA-CTTCCCA
1 TATGAAATTTTGATAACCTT--CA
**
5593 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTTCA
* * *
5614 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTTCA
* * * *
5637 TATGATATATTGATAACC-ACGT
1 TATGAAATTTTGATAACCTTC-A
* * * *
5659 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTTCA
* *
5681 TATG-AATTGTT-AGTAATC-ACA
1 TATGAAATT-TTGA-TAACCTTCA
* * *
5702 CTCTGAAATTTTGATAATC-ACA
1 -TATGAAATTTTGATAACCTTCA
* *
5724 CTATGAAATTGTGATAACC-TCGC
1 -TATGAAATTTTGATAACCTTC-A
* *
5747 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCA
*
5770 TAT-AAGATTTTGATAAACTTCCCA
1 TATGAA-ATTTTGATAACCTT--CA
* * *
5794 -ATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCA
*
5815 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTTCA
* *
5832 TA-CAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCA
**
5853 TATGATTTTTTGATAACC-TCA
1 TATGAAATTTTGATAACCTTCA
* * * *
5874 TTATGAAATTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTTCA
* * *
5897 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTTCA
* *
5919 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCA
* * **
5941 TATGAAATTCTGA-AAACTAAA
1 TATGAAATTTTGATAACCTTCA
*
5962 CTATGAAATTTTGATATCCTTCA
1 -TATGAAATTTTGATAACCTTCA
5985 TATGAAATTTTGATA
1 TATGAAATTTTGATA
6000 TCCTCCCTGA
Statistics
Matches: 405, Mismatches: 94, Indels: 82
0.70 0.16 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 1 0.00
20 1 0.00
21 27 0.07
22 291 0.72
23 66 0.16
24 6 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:5779 original size:23 final size:23
Alignment explanation
Indices: 5751--5808 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
5741 CCTCGCTATG
*
5751 AAATTTTGATAAATCTT-CCTATA
1 AAATTTTGATAAA-CTTCCCAATA
*
5774 AGATTTTGATAAACTTCCCAATA
1 AAATTTTGATAAACTTCCCAATA
5797 AAATTTTGATAA
1 AAATTTTGATAA
5809 CTTTCTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (23 bp):
AAATTTTGATAAACTTCCCAATA
Found at i:6000 original size:22 final size:22
Alignment explanation
Indices: 5835--6038 Score: 109
Period size: 22 Copynumber: 9.5 Consensus size: 22
5825 TGATAACTAC
* *
5835 AAATTTTGATAACCTTCCTATG
1 AAATTTTGATATCCTTCATATG
** *
5857 ATTTTTTGATAACC-TCATTATG
1 AAATTTTGATATCCTTCA-TATG
* * *
5879 AAATTTTGTTAAT-CTCCCTATG
1 AAATTTTGAT-ATCCTTCATATG
* * *
5901 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGATATCCTTCA-TATG
* * *
5923 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATATCCTTCATATG
* ** **
5945 AAATTCTGA-AAACTAAACTATG
1 AAATTTTGATATCCTTCA-TATG
5967 AAATTTTGATATCCTTCATATG
1 AAATTTTGATATCCTTCATATG
**
5989 AAATTTTGATATCC-TC-CCTG
1 AAATTTTGATATCCTTCATATG
* *
6009 AAATTTTGATATTC-TC-TCTG
1 AAATTTTGATATCCTTCATATG
6029 AAATTTTGAT
1 AAATTTTGAT
6039 TACTCCATAA
Statistics
Matches: 140, Mismatches: 34, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
20 30 0.21
21 8 0.06
22 96 0.69
23 6 0.04
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (22 bp):
AAATTTTGATATCCTTCATATG
Found at i:6012 original size:20 final size:20
Alignment explanation
Indices: 5965--6038 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
5955 AACTAAACTA
*
5965 TGAAATTTTGATATCCTTCATA
1 TGAAATTTTGATATCC-TC-TC
*
5987 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCTC
*
6007 TGAAATTTTGATATTCTCTC
1 TGAAATTTTGATATCCTCTC
6027 TGAAATTTTGAT
1 TGAAATTTTGAT
6039 TACTCCATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 30 0.62
21 2 0.04
22 16 0.33
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCTC
Found at i:6169 original size:22 final size:22
Alignment explanation
Indices: 6143--6312 Score: 71
Period size: 22 Copynumber: 7.8 Consensus size: 22
6133 AATCACATTT
* *
6143 TGAAAATTTGGTAACCTTTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
6165 TGAAATTTTGATAACGTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
6187 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
6209 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* * *
6231 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
* ** **
6253 TGAAATTTTGATAACAACACTA
1 TGAAAATTTGATAACCTCTTTA
* *
6275 TG-AAATTTCGATAATCACTTTA
1 TGAAAATTT-GATAACCTCTTTA
*
6297 TG-AGATTTGATAACCT
1 TGAAAATTTGATAACCT
6313 TCTATCAAAT
Statistics
Matches: 108, Mismatches: 33, Indels: 15
0.69 0.21 0.10
Matches are distributed among these distances:
21 17 0.16
22 85 0.79
23 6 0.06
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:6259 original size:66 final size:65
Alignment explanation
Indices: 6162--6326 Score: 158
Period size: 66 Copynumber: 2.5 Consensus size: 65
6152 GGTAACCTTT
* * * * ** *
6162 TTATGAAATTTTGATAACGTCTTTATAAAATTTTGTTGACCCCTCTATGAAA-TTCTGATAATCA
1 TTATG-AATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTTC-GATAATCA
6226 CA
64 CA
*
6228 TTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTCGATAATCA
1 TTATG-AATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTTCGATAATCA
*
6292 CT
64 CA
* *
6294 TTATGAGA-TTTGATAACCTTC-TATCAAATTTTG
1 TTATGA-ATTTTGATAACCTCCTTATAAAATTTTG
6327 GTGCTCCTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 1 0.01
64 10 0.12
65 12 0.14
66 55 0.66
67 5 0.06
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (65 bp):
TTATGAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTTCGATAATCACA
Found at i:6378 original size:22 final size:21
Alignment explanation
Indices: 6349--6488 Score: 74
Period size: 22 Copynumber: 6.4 Consensus size: 21
6339 AAATTGAGAC
6349 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* * *
6370 TTTTGATAAGCACATTATAAAA
1 TTTTGATAACCTCA-TATGAAA
*
6392 TTTTGATAACCTC-TCCATTAAA
1 TTTTGATAACCTCAT--ATGAAA
* *
6414 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
*
6436 TTTTGTTAA-CTACACTATGAAA
1 TTTTGATAACCT-CA-TATGAAA
* *
6458 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
6480 TTTTGATAA
1 TTTTGATAA
6489 TCTCTTTGAT
Statistics
Matches: 91, Mismatches: 15, Indels: 25
0.69 0.11 0.19
Matches are distributed among these distances:
20 1 0.01
21 11 0.12
22 73 0.80
23 6 0.07
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:6634 original size:22 final size:22
Alignment explanation
Indices: 6553--6737 Score: 110
Period size: 22 Copynumber: 8.3 Consensus size: 22
6543 AAAAAAAAAA
* * **
6553 AACCACCCTATGGAATTTCAAT
1 AACCACACTATGAAATTTTGAT
* *
6575 AACCA-ATCTAAGAAATTTTAAT
1 AACCACA-CTATGAAATTTTGAT
*
6597 AACCTGATC-CTATGAAATTTTGGT
1 AACC--A-CACTATGAAATTTTGAT
6621 AACCACACTATGAAATTTTGAT
1 AACCACACTATGAAATTTTGAT
** *
6643 AACTTTCA-TATGAAATTTTGGT
1 AAC-CACACTATGAAATTTTGAT
* * * *
6665 GACCATACTATGGAGTTTTGAT
1 AACCACACTATGAAATTTTGAT
* * *
6687 AACCTC-CTCATGAAATTATAAT
1 AACCACACT-ATGAAATTTTGAT
6709 AACCATCA-TATGAAATTTTGAT
1 AACCA-CACTATGAAATTTTGAT
*
6731 AAGCACA
1 AACCACA
6738 TAGAGACAAG
Statistics
Matches: 123, Mismatches: 29, Indels: 23
0.70 0.17 0.13
Matches are distributed among these distances:
21 6 0.05
22 96 0.78
23 4 0.03
24 17 0.14
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (22 bp):
AACCACACTATGAAATTTTGAT
Found at i:6675 original size:44 final size:43
Alignment explanation
Indices: 6607--6732 Score: 137
Period size: 44 Copynumber: 2.9 Consensus size: 43
6597 AACCTGATCC
* *
6607 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTTCA
1 TATGAAATTTTGGTAACCATACTATGAAATTTTGATAAC-CTCA
* * * *
6651 TATGAAATTTTGGTGACCATACTATGGAGTTTTGATAACCTCC
1 TATGAAATTTTGGTAACCATACTATGAAATTTTGATAACCTCA
* **
6694 TCATGAAATTATAATAACCAT-CATATGAAATTTTGATAA
1 T-ATGAAATTTTGGTAACCATAC-TATGAAATTTTGATAA
6733 GCACATAGAG
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 4 0.06
44 64 0.94
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (43 bp):
TATGAAATTTTGGTAACCATACTATGAAATTTTGATAACCTCA
Done.