Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016184.1 Corchorus capsularis cultivar CVL-1 contig16205, 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: 22297
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:168 original size:2 final size:2
Alignment explanation
Indices: 161--224 Score: 69
Period size: 2 Copynumber: 31.5 Consensus size: 2
151 GGCACCATAC
161 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TGA -A CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A T-A TA -TA
* *
203 TA TA TA T- TG TA GA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
225 TATCAGTCTA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
1 2 0.04
2 48 0.87
3 5 0.09
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:464 original size:20 final size:20
Alignment explanation
Indices: 436--480 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
426 GTTCTGTTGT
*
436 TTAATATCTAACGCAACGAC
1 TTAAGATCTAACGCAACGAC
456 TTAAGATCTAACGCAACGAC
1 TTAAGATCTAACGCAACGAC
476 TTAAG
1 TTAAG
481 TATCCGCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (20 bp):
TTAAGATCTAACGCAACGAC
Found at i:1773 original size:30 final size:30
Alignment explanation
Indices: 1737--1799 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
1727 ATCGCATGCA
1737 CCATCGCATGGGGCAACCG-GCCACAACCGG
1 CCATCGCATGGGGCAACCGCG-CACAACCGG
*
1767 CCATCGCATGGGGCATCCGCGCACAACCGG
1 CCATCGCATGGGGCAACCGCGCACAACCGG
1797 CCA
1 CCA
1800 ATGGATCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.22, C:0.41, G:0.29, T:0.08
Consensus pattern (30 bp):
CCATCGCATGGGGCAACCGCGCACAACCGG
Found at i:3184 original size:22 final size:22
Alignment explanation
Indices: 3156--3198 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3146 AAAATTGGAT
3156 CAAGTGGTACTAGGGTTTTTGA
1 CAAGTGGTACTAGGGTTTTTGA
3178 CAAGTGGTACTAGGGTTTTTG
1 CAAGTGGTACTAGGGTTTTTG
3199 CTAGTCGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.33, T:0.37
Consensus pattern (22 bp):
CAAGTGGTACTAGGGTTTTTGA
Found at i:5399 original size:33 final size:33
Alignment explanation
Indices: 5304--5406 Score: 118
Period size: 33 Copynumber: 3.1 Consensus size: 33
5294 GCAAAGAGTG
* * *
5304 TTTTAGATGTTGTTTGCGATGATACTAAACCTA
1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
* * *
5337 ATTT-GAGTGTTGTTTGCAATGACACTAAATCTA
1 TTTTAG-GTGTTGTTTGCGATGAAACTAAATCTA
* *
5370 TTTTAGGTGTTGTTTGTGATGAAACTAAATCTG
1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
5403 TTTT
1 TTTT
5407 GGATGCTAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
32 1 0.02
33 56 0.97
34 1 0.02
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (33 bp):
TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
Found at i:5492 original size:30 final size:31
Alignment explanation
Indices: 5422--5509 Score: 106
Period size: 30 Copynumber: 2.8 Consensus size: 31
5412 CTAACTGTGA
* *
5422 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGA--ATAGCAT
* *
5455 TGCAAATAATTCTGTTTTGGTTG-ATGGCAT
1 TGAAAATAATTCTGTTTTGGTTGAATAGCAT
*
5485 TGAAAATAATTCTGTTTTGGGTGAA
1 TGAAAATAATTCTGTTTTGGTTGAA
5510 AAGAAAGAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 27 0.56
31 1 0.02
33 20 0.42
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.40
Consensus pattern (31 bp):
TGAAAATAATTCTGTTTTGGTTGAATAGCAT
Found at i:7493 original size:23 final size:23
Alignment explanation
Indices: 7462--7508 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
7452 CAACTGGCCA
7462 CAACCGGCCATCGCATGGAGCAT
1 CAACCGGCCATCGCATGGAGCAT
* *
7485 CAACTGGCCATCGCATGGGGCAT
1 CAACCGGCCATCGCATGGAGCAT
7508 C
1 C
7509 CGCGCACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.34, G:0.28, T:0.15
Consensus pattern (23 bp):
CAACCGGCCATCGCATGGAGCAT
Found at i:8383 original size:2 final size:2
Alignment explanation
Indices: 8376--8529 Score: 308
Period size: 2 Copynumber: 77.0 Consensus size: 2
8366 TGATGTACTT
8376 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
8418 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
8460 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
8502 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
8530 TGGAGATCAG
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 152 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10934 original size:2 final size:2
Alignment explanation
Indices: 10927--10957 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10917 TAAATGTAAT
10927 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
10958 TATCAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:14389 original size:22 final size:23
Alignment explanation
Indices: 14364--14408 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
14354 AGTACTATGG
*
14364 GTTGAATTTGGTGCTG-AATTTT
1 GTTGAATCTGGTGCTGCAATTTT
*
14386 GTTGAATCTGGTGTTGCAATTTT
1 GTTGAATCTGGTGCTGCAATTTT
14409 TTTTCATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.49
Consensus pattern (23 bp):
GTTGAATCTGGTGCTGCAATTTT
Found at i:14754 original size:1 final size:1
Alignment explanation
Indices: 14715--14741 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
14705 CGGTGCTTAG
14715 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
14742 GCTAGTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16650 original size:166 final size:164
Alignment explanation
Indices: 16373--16872 Score: 637
Period size: 167 Copynumber: 3.0 Consensus size: 164
16363 GAGTCATTTG
* *
16373 TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTTAATAATCAAAAGTTAGGACATT
1 TCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
* * * * *
16438 TAAGTAATCTGCCAAGTAGGTAAAGATGAAAAAGATTACTTCTCTAACTCATCATCAATCCTTGA
65 TAAGTAATCTGCAAAGTAGGAAAAGATGAAAAA-AATAGTTCTCTAACTCATCATCAATCCTTGG
*
16503 TGGGGATCTTTTATTAATTCCACTATTCTATTCAAA
129 TGGGGATCTTTTAGTAATTCCACTATTCTATTCAAA
* * *
16539 TCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGAACATT
1 TCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
* ** * *
16604 TGAGTAATCTGCAAAGTAGGAAAAGATGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTG
65 TAAGTAATCTGCAAAGTAGGAAAAGATGAAAAAAAT-AGTTCTCTAACT-CATCATCAATCCTTG
* *
16669 GTAGGGATCTTTTAGTAATTCCACTACTCTATT-AAA
128 GTGGGGATCTTTTAGTAATTCCACTATTCTATTCAAA
16705 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 -TCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * ** * * **
16770 TTAAGTAACCTGCTAAGT-GCGAAAAGAAGAAAAAAAGTAGTTCTCTCGCTCCTCATTAATCCGG
64 TTAAGTAATCTGCAAAGTAG-GAAAAGATGAAAAAAA-TAGTTCTCTAACTCATCATCAATCCTT
*
16834 GGTGGGGATCTTTTAGTAATTCCAC-ATGTTTATTCAAA
127 GGTGGGGATCTTTTAGTAATTCCACTAT-TCTATTCAAA
16872 T
1 T
16873 AATATGTAGT
Statistics
Matches: 287, Mismatches: 39, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
165 3 0.01
166 141 0.49
167 142 0.49
168 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (164 bp):
TCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTT
AAGTAATCTGCAAAGTAGGAAAAGATGAAAAAAATAGTTCTCTAACTCATCATCAATCCTTGGTG
GGGATCTTTTAGTAATTCCACTATTCTATTCAAA
Found at i:17391 original size:132 final size:132
Alignment explanation
Indices: 17152--17534 Score: 572
Period size: 132 Copynumber: 2.9 Consensus size: 132
17142 ATTTGTCGTT
* * * *
17152 GCGACTTAATTTGT-GACTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGA
1 GCGACTTAATATGTCG-TTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTCAAGGTCACTGCGA
* * *
17216 AAATCAATTTA-TAAGATATATTAAGCAATGAATAACAATAGTCGTTGCGAAAAGAGTAAGATTT
65 AAATCAA-TTAGTAAAATATATTAAGCAATGACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTT
*
17280 CGCA
129 CACA
*
17284 GCGACTTAATATGTCGTTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTCAAGGTAACTGCGAA
1 GCGACTTAATATGTCGTTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTCAAGGTCACTGCGAA
* **
17349 AATCAATTAGTAAAATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTCA
66 AATCAATTAGTAAAATATATTAAGCAATGACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCA
17414 CA
131 CA
* * *
17416 ACGACTTAATATGTCGTTTCAAAAGTAATCATGTTTTTTGTAACAACTTTCAAGGTCACTGCGAA
1 GCGACTTAATATGTCGTTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTCAAGGTCACTGCGAA
* * *
17481 AATCAATTTGTAAAATATATTAAGAAATGACTAACAAAAGTCGTTACGAAAAGA
66 AATCAATTAGTAAAATATATTAAGCAATGACTAACAAAAGTCGTTGCGAAAAGA
17535 CTATGAATTC
Statistics
Matches: 228, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
131 3 0.01
132 224 0.98
133 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (132 bp):
GCGACTTAATATGTCGTTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTCAAGGTCACTGCGAA
AATCAATTAGTAAAATATATTAAGCAATGACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCA
CA
Done.