Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007764.1 Corchorus capsularis cultivar CVL-1 contig07785, 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: 63783
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:634 original size:332 final size:333
Alignment explanation
Indices: 1--1438 Score: 1923
Period size: 332 Copynumber: 4.3 Consensus size: 333
1 TTGGATTTATGGATTTG-TTTTAACGAACATCAGAAACCGATTTCATTTTCATTAGAAATTAATT
1 TTGGATTTATGGATTTGTTTTTAA-GAACATCAGAAACCGATTTCATTTTCATTAGAAATTAATT
* * *
65 CAGAAAAAAATAGAAAAATCTATGTT--AAGAGTGACAAACCCTTATATCTTTTTGGCGTTGATT
65 CAGAAAAAAATAGGAAAATCGATGTTAGAAGAGTGACAAACCCTTATATCTTTTTGGCGTTGAAT
* *
128 TATATATTTTTTATGAGTATTTCGGCCAAAAATTAAGGAAATATATTTCGGGTCAATTTTTGCAA
130 TATATATTTTTTATGAGTATTTCGGCCAAAAAATAAGGAAAAATATTTCGGGTCAATTTTTGCAA
* *
193 AATTTTTA-CCAAAATCGTGC-ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGACC
195 AA-TTTTAGCCAAAATCGT-CTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCC
* *
256 CGGCTCAGTTTTGCGTGATTTTTGACGTCAAGACTTCTTGAAATATCTATATTCATGTAACTAAA
258 CGGCTCAGTTTTGCGTGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATGTAACTAAA
*
321 TCTCAGCCACG
323 TCTCAGCCACA
332 TTGGATTTATGGATTTGTTTTTAAGAACATCAGAAACCGATTTCATTTTCATTAGAAATTAATTC
1 TTGGATTTATGGATTTGTTTTTAAGAACATCAGAAACCGATTTCATTTTCATTAGAAATTAATTC
*
397 AGAAAAAAAATAGGAAAATCGATGTTAGAAGAGTGACAAACCTTTATATCTTTTTGGCGTTGAAT
66 AG-AAAAAAATAGGAAAATCGATGTTAGAAGAGTGACAAACCCTTATATCTTTTTGGCGTTGAAT
*
462 TATATATTTTTTATGAGTATTTCGG-CAAAAAATAAGGAAAAATATTTCGGATCAATTTTTGCAA
130 TATATATTTTTTATGAGTATTTCGGCCAAAAAATAAGGAAAAATATTTCGGGTCAATTTTTGCAA
* *
526 AATTTTAGCCGAAATCGTCTACTAA-CATCATC-GTTTTTGGCTAAAAATGCGTTCCGGGGCCCC
195 AATTTTAGCCAAAATCGTCTACTAACCATCA-CAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCC
** * * ** *
589 GGCTCAGTTTTGTTTGATTTTTGGTGTCGAGACTCCTTGAAATATCTATATTCATGTGCCCAAAT
259 GGCTCAGTTTTGCGTGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATGTAACTAAAT
* *
654 TTCAGCCAAA
324 CTCAGCCACA
* * * * * *
664 TTGGATTTATGGATTTGTTTTTACGAACATTAAAAATCGATTTCTTTTTCATTAGAATTTAATTC
1 TTGGATTTATGGATTTGTTTTTAAGAACATCAGAAACCGATTTCATTTTCATTAGAAATTAATTC
* * *
729 AGAAAAAAATAGGAAAATCAATGTTAGAAGAGTGACAAACCCTTATATCTTTTAGGCTTTTGAAT
66 AGAAAAAAATAGGAAAATCGATGTTAGAAGAGTGACAAACCCTTATATCTTTTTGGC-GTTGAAT
* * * *
794 TATATATTTTTTATGAGTATTTCAGCAAAAAAATTGAGGAAAAATATTTCGGGTCAATTTTCGCA
130 TATATATTTTTTATGAGTATTTCGGCCAAAAAA-TAAGGAAAAATATTTCGGGTCAATTTTTGCA
* * *
859 AAATTTTAGCCGAAATCGTGTACTATCCATCACTA-TTTTTGGCTAAAAACGCGTTCCGGGGCCC
194 AAATTTTAGCCAAAATCGTCTACTAACCATCAC-AGTTTTTGGCTAAAAACGCGTTCCGGGGCCC
* * * *
923 CGGCTTAGTTTTGCATGATTTTTGGCGTCAAGACTTCTTGAAATATCTATATTCATGTATCTAAA
258 CGGCTCAGTTTTGCGTGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATGTAACTAAA
* *
988 TCTCGGCCACG
323 TCTCAGCCACA
* * * *
999 TTGGATTTATGGATTTGTTTTTAAAAACATCAGAAGCCGTTTTAATTTTCATTAGAAATTAATTC
1 TTGGATTTATGGATTTGTTTTTAAGAACATCAGAAACCGATTTCATTTTCATTAGAAATTAATTC
*
1064 AGAAAAAAATAGGAAAATCGATGTTAGAAGAGTGACAAACCCTTATATCTTTTTAGCGTTGAA-T
66 AGAAAAAAATAGGAAAATCGATGTTAGAAGAGTGACAAACCCTTATATCTTTTTGGCGTTGAATT
* * *
1128 -TATATTTTTTATGAGTTTTTCGGCCAAAAATTGAA-GAAAAATATTTCGGGTTTAATTTTTGCA
131 ATATATTTTTTATGAGTATTTCGGCCAAAAAAT-AAGGAAAAATATTTCGGG-TCAATTTTTGCA
* * * * *
1191 AAATTTTAGCCAAAATCATGTACTAACCATCACAGTTTTTGAATTTTGACTAAAACCGTGTTTCG
194 AAATTTTAGCCAAAATCGTCTACTAACCATCACAGTTTTTG------G-CTAAAAACGCGTTCCG
* * * * *
1256 GTGCCCCGGCTCAGTTTTGCGTGATTTTTTGTGCCGAA-ACTCCTTGAAATTTCTATATTCATGT
252 GGGCCCCGGCTCAGTTTTGCGTGATTTTTGGCGTC-AAGACTCCTTGAAATATCTATATTCATGT
* *
1320 AACTAAATCTCAGTCATA
316 AACTAAATCTCAGCCACA
** * * * * * *
1338 TTGGATTTAAAGATTTTTTTTTTTACGAGCATCAGAAACCGTTTTCAATTTCATTAGAAATTACT
1 TTGGATTTATGGA--TTTGTTTTTAAGAACATCAGAAACCGATTTCATTTTCATTAGAAATTAAT
* *
1403 TTAG-AAAAAATAGGAAAATCGATGTAAGAAGAGTGA
64 TCAGAAAAAAATAGGAAAATCGATGTTAGAAGAGTGA
1439 TATTTTTTGG
Statistics
Matches: 976, Mismatches: 105, Indels: 43
0.87 0.09 0.04
Matches are distributed among these distances:
331 129 0.13
332 295 0.30
333 60 0.06
334 118 0.12
335 205 0.21
338 1 0.00
339 90 0.09
340 33 0.03
341 45 0.05
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (333 bp):
TTGGATTTATGGATTTGTTTTTAAGAACATCAGAAACCGATTTCATTTTCATTAGAAATTAATTC
AGAAAAAAATAGGAAAATCGATGTTAGAAGAGTGACAAACCCTTATATCTTTTTGGCGTTGAATT
ATATATTTTTTATGAGTATTTCGGCCAAAAAATAAGGAAAAATATTTCGGGTCAATTTTTGCAAA
ATTTTAGCCAAAATCGTCTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGG
CTCAGTTTTGCGTGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATGTAACTAAATCT
CAGCCACA
Found at i:12343 original size:30 final size:29
Alignment explanation
Indices: 12270--12343 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
12260 GTAGCGTCTA
*
12270 GACGTTTTGCCCCCCAAACTTCAATCTTG
1 GACGTTTTGCCCCCTAAACTTCAATCTTG
* * * *
12299 GACATTTTGTCCCCTGAACTTCAATTTTGG
1 GACGTTTTGCCCCCTAAACTTCAATCTT-G
12329 GACGTTTTGCCCCCT
1 GACGTTTTGCCCCCT
12344 CAACCTAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (29 bp):
GACGTTTTGCCCCCTAAACTTCAATCTTG
Found at i:12546 original size:29 final size:30
Alignment explanation
Indices: 12478--12547 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
12468 CGTTAGGTTG
*
12478 AGGGGGCAAAATGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAATATCCCAAAATTGAAGTTC
* *
12508 ATGGGGCAAAATAT-CCAAGATTGAAGTTC
1 AGGGGGCAAAATATCCCAAAATTGAAGTTC
12537 -GGGGGACAAAA
1 AGGGGG-CAAAA
12548 CATCTAGACG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.11
29 19 0.54
30 12 0.34
ACGTcount: A:0.39, C:0.14, G:0.29, T:0.19
Consensus pattern (30 bp):
AGGGGGCAAAATATCCCAAAATTGAAGTTC
Found at i:54989 original size:2 final size:2
Alignment explanation
Indices: 54982--55047 Score: 93
Period size: 2 Copynumber: 34.5 Consensus size: 2
54972 AACAGTGTAT
*
54982 TA TA TA TA TA TA TA TA TA AA TA TA -A TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
55022 TA TA TA TA AA TA TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
55048 CGCTGTCATT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
1 3 0.05
2 54 0.95
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:55018 original size:30 final size:29
Alignment explanation
Indices: 54984--55047 Score: 119
Period size: 30 Copynumber: 2.2 Consensus size: 29
54974 CAGTGTATTA
54984 TATATATATATATATAAATATAATATATAA
1 TATATATATATATATAAATATAATATAT-A
55014 TATATATATATATATAAATATAATATATA
1 TATATATATATATATAAATATAATATATA
55043 TATAT
1 TATAT
55048 CGCTGTCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 6 0.18
30 28 0.82
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TATATATATATATATAAATATAATATATA
Found at i:59833 original size:22 final size:22
Alignment explanation
Indices: 59807--59851 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
59797 CTGGATTTTC
59807 TTTGGCAGCATTTCTTGAGACT
1 TTTGGCAGCATTTCTTGAGACT
59829 TTTGGCAGCATTTCTTGAGACT
1 TTTGGCAGCATTTCTTGAGACT
59851 T
1 T
59852 GTTATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (22 bp):
TTTGGCAGCATTTCTTGAGACT
Done.