Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012632.1 Corchorus capsularis cultivar CVL-1 contig12653, 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: 49556
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Found at i:133 original size:33 final size:33
Alignment explanation
Indices: 87--166 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
77 GGCGCGAGAG
* **
87 ACCGGCCATGCGACTTTGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
* *
120 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
*
153 ACCGGCTACGCGAC
1 ACCGGCCACGCGAC
167 ATGGACATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.21, C:0.40, G:0.29, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
Found at i:181 original size:33 final size:32
Alignment explanation
Indices: 109--193 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 32
99 ACTTTGAGAA
*
109 GCCCGGCCAACACCGGCCACGCGACTCGGAGAT
1 GCCCGGCC-ACACCGGCCACGCGACTCGGACAT
*
142 GCCCGGCCATCACCGGCTACGCGACAT-GGACAT
1 GCCCGGCCA-CACCGGCCACGCGAC-TCGGACAT
*
175 GTCCGGCCACAACCGGCCA
1 GCCCGGCCAC-ACCGGCCA
194 TCGCTTGGCG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 2 0.04
33 42 0.93
34 1 0.02
ACGTcount: A:0.21, C:0.42, G:0.28, T:0.08
Consensus pattern (32 bp):
GCCCGGCCACACCGGCCACGCGACTCGGACAT
Found at i:13002 original size:25 final size:25
Alignment explanation
Indices: 12974--13024 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
12964 ATTCATTTAA
12974 AGCATTACAACCAAAGTTTGGATTC
1 AGCATTACAACCAAAGTTTGGATTC
* * * *
12999 AGCATTATAGCCAACGTTTGGTTTC
1 AGCATTACAACCAAAGTTTGGATTC
13024 A
1 A
13025 TTACATCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (25 bp):
AGCATTACAACCAAAGTTTGGATTC
Found at i:17760 original size:22 final size:21
Alignment explanation
Indices: 17734--17854 Score: 118
Period size: 22 Copynumber: 5.6 Consensus size: 21
17724 CCTCGGTTGA
17734 AATTTTGATAACAGCCCTATAT
1 AATTTTGATAAC-GCCCTATAT
*
17756 AATTTTGATAACGACCCTCTAT
1 AATTTTGATAACG-CCCTATAT
* * * * *
17778 AGTTTTAATAAC-CTCGATTGT
1 AATTTTGATAACGCCCTA-TAT
17799 AATTTTGATAACAGCCCTATAT
1 AATTTTGATAAC-GCCCTATAT
*
17821 AATTTTGATAACGACCCTTTAT
1 AATTTTGATAACG-CCCTATAT
*
17843 AGTTTTGATAAC
1 AATTTTGATAAC
17855 CTCATGGGAT
Statistics
Matches: 80, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.03
21 14 0.17
22 61 0.76
23 3 0.04
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (21 bp):
AATTTTGATAACGCCCTATAT
Found at i:17824 original size:65 final size:65
Alignment explanation
Indices: 17715--17857 Score: 241
Period size: 65 Copynumber: 2.2 Consensus size: 65
17705 ATAGCACCAA
* *
17715 TTTTTATAACCTCGGTTGAAATTTTGATAACAGCCCTATATAATTTTGATAACGACCCTCTATAG
1 TTTTAATAACCTCGATTGAAATTTTGATAACAGCCCTATATAATTTTGATAACGACCCTCTATAG
* *
17780 TTTTAATAACCTCGATTGTAATTTTGATAACAGCCCTATATAATTTTGATAACGACCCTTTATAG
1 TTTTAATAACCTCGATTGAAATTTTGATAACAGCCCTATATAATTTTGATAACGACCCTCTATAG
*
17845 TTTTGATAACCTC
1 TTTTAATAACCTC
17858 ATGGGATTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 73 1.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (65 bp):
TTTTAATAACCTCGATTGAAATTTTGATAACAGCCCTATATAATTTTGATAACGACCCTCTATAG
Found at i:17961 original size:22 final size:22
Alignment explanation
Indices: 17931--17983 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
17921 TCTTATGAGG
*
17931 TTTTGATAACAATACTTTGTAA
1 TTTTCATAACAATACTTTGTAA
* * *
17953 TTTTTATAACTATCCTTTGTAA
1 TTTTCATAACAATACTTTGTAA
17975 TTTTCATAA
1 TTTTCATAA
17984 ACACTTTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (22 bp):
TTTTCATAACAATACTTTGTAA
Found at i:18385 original size:29 final size:29
Alignment explanation
Indices: 18329--18386 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
18319 AGAGGTAATC
* * *
18329 AAATTTACAATATCTTCTATTCTCAAAAA
1 AAATTTACAATAGCTTCTACTCTAAAAAA
18358 AAATTTACAATAGCTTCTTACT-TAAAAAA
1 AAATTTACAATAGCTTC-TACTCTAAAAAA
18387 CTATATAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.36
Consensus pattern (29 bp):
AAATTTACAATAGCTTCTACTCTAAAAAA
Found at i:28542 original size:22 final size:21
Alignment explanation
Indices: 28516--28567 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
28506 AAATTGCATA
28516 GAAAATTTGC-ATTAAATTTTAC
1 GAAAATTTGCGA--AAATTTTAC
28538 GAAAATTTTGCGAAAATTTTAC
1 GAAAA-TTTGCGAAAATTTTAC
28560 GAAAATTT
1 GAAAATTT
28568 TAAATTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.11
22 19 0.68
23 5 0.18
24 1 0.04
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (21 bp):
GAAAATTTGCGAAAATTTTAC
Found at i:28543 original size:11 final size:11
Alignment explanation
Indices: 28529--28569 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
28519 AATTTGCATT
28529 AAATTTTACGA
1 AAATTTTACGA
*
28540 AAATTTTGCGA
1 AAATTTTACGA
28551 AAATTTTACGA
1 AAATTTTACGA
28562 AAATTTTA
1 AAATTTTA
28570 AATTTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (11 bp):
AAATTTTACGA
Found at i:33242 original size:120 final size:119
Alignment explanation
Indices: 33094--33375 Score: 429
Period size: 120 Copynumber: 2.3 Consensus size: 119
33084 CTCCAAGTCC
33094 TTGCCCCCCAAGTCTTTCATCGATGAGACCAATTGGAGCCATGACTGGTTGGTTGTTCACCTGAT
1 TTGCCCCCCAAGTCTTTCATCGATGAGACCAATT-GAGCCATGACTGGTTGGTTGTTCACCTGAT
* *
33159 GATTGACTTGTTGAAGAGGCAGAGCACCGGGCTAGGCACCAAGCAGTTGTTGGTT
65 GATTGACTTGTTGAAAAGGCAGAGCACCGGGCTAGGCACCAAGCAGTTGATGGTT
* *
33214 TTGCCCCCCAAGTCTTTCATCGATGAGACCAATCTGAGCCATGACTTGTTGGTTGTTCATCTGAT
1 TTGCCCCCCAAGTCTTTCATCGATGAGACCAAT-TGAGCCATGACTGGTTGGTTGTTCACCTGAT
* * *
33279 GGTTGACTTGTTGAAAAGGCAGAGCATCGGGCTGGGCACCAAGCAGTTGATGGTT
65 GATTGACTTGTTGAAAAGGCAGAGCACCGGGCTAGGCACCAAGCAGTTGATGGTT
* * * * *
33334 TTGCCCTCCGAGTCCTTCTTCGATGAGACCAATCCGAGCCAT
1 TTGCCCCCCAAGTCTTTCATCGATGAGACCAAT-TGAGCCAT
33376 AATGCTTTCT
Statistics
Matches: 149, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
120 148 0.99
121 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (119 bp):
TTGCCCCCCAAGTCTTTCATCGATGAGACCAATTGAGCCATGACTGGTTGGTTGTTCACCTGATG
ATTGACTTGTTGAAAAGGCAGAGCACCGGGCTAGGCACCAAGCAGTTGATGGTT
Found at i:38603 original size:15 final size:15
Alignment explanation
Indices: 38582--38622 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
38572 GTTTCTTCTA
38582 AAAAAAATTGTGTCGG
1 AAAAAAATTGTGTC-G
38598 AAAAAAAATTGTGTCG
1 -AAAAAAATTGTGTCG
*
38614 AAATAAATT
1 AAAAAAATT
38623 TAGGATTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 14 0.61
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (15 bp):
AAAAAAATTGTGTCG
Found at i:38603 original size:17 final size:17
Alignment explanation
Indices: 38581--38613 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
38571 CGTTTCTTCT
38581 AAAAAAAATTGTGTCGG
1 AAAAAAAATTGTGTCGG
38598 AAAAAAAATTGTGTCG
1 AAAAAAAATTGTGTCG
38614 AAATAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.24
Consensus pattern (17 bp):
AAAAAAAATTGTGTCGG
Found at i:39726 original size:15 final size:15
Alignment explanation
Indices: 39706--39734 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39696 CTTGCCGAAC
39706 CAGAAGATGAGCCAG
1 CAGAAGATGAGCCAG
39721 CAGAAGATGAGCCA
1 CAGAAGATGAGCCA
39735 CAAAAAGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.31, T:0.07
Consensus pattern (15 bp):
CAGAAGATGAGCCAG
Found at i:42553 original size:11 final size:11
Alignment explanation
Indices: 42537--42568 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
42527 GAAGTTCATG
42537 TTTGAAGATTA
1 TTTGAAGATTA
*
42548 TTTGAAGATAA
1 TTTGAAGATTA
42559 TTTGAAGATT
1 TTTGAAGATT
42569 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:42565 original size:22 final size:22
Alignment explanation
Indices: 42537--42596 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
42527 GAAGTTCATG
*
42537 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
42559 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
42578 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
42597 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:42571 original size:19 final size:18
Alignment explanation
Indices: 42547--42584 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
42537 TTTGAAGATT
*
42547 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
42566 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
42584 A
1 A
42585 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:44906 original size:242 final size:242
Alignment explanation
Indices: 44481--44956 Score: 943
Period size: 242 Copynumber: 2.0 Consensus size: 242
44471 AACTGAGTGC
44481 TGTAAAGTTCCTTTCTCTATAGGGAAGTATAATTATGAAGTTTACTGCGATGTGGTTGATATGGA
1 TGTAAAGTTCCTTTCTCTATAGGGAAGTATAATTATGAAGTTTACTGCGATGTGGTTGATATGGA
44546 TGTTTGTCAGTTCTTGCTTGAAAGACCTTGGCAGTATGATCTTGATGTTTTGCATTTAGGCAGGA
66 TGTTTGTCAGTTCTTGCTTGAAAGACCTTGGCAGTATGATCTTGATGTTTTGCATTTAGGCAGGA
44611 GTAACCAATATCGATTCGAAAAAAATGGTGAAAAATTTCTCTTGTTGCCTATGCAGAAGAGTGAT
131 GTAACCAATATCGATTCGAAAAAAATGGTGAAAAATTTCTCTTGTTGCCTATGCAGAAGAGTGAT
44676 AAATCAAAGGAGCAGAAAACCTTCCTGTATGTGGCTAAGTATAATTA
196 AAATCAAAGGAGCAGAAAACCTTCCTGTATGTGGCTAAGTATAATTA
44723 TGTAAAGTTCCTTTCTCTATAGGGAAGTATAATTATGAAGTTTACTGCGATGTGGTTGATATGGA
1 TGTAAAGTTCCTTTCTCTATAGGGAAGTATAATTATGAAGTTTACTGCGATGTGGTTGATATGGA
44788 TGTTTGTCAGTTCTTGCTTGAAAGACCTTGGCAGTATGATCTTGATGTTTTGCATTTAGGCAGGA
66 TGTTTGTCAGTTCTTGCTTGAAAGACCTTGGCAGTATGATCTTGATGTTTTGCATTTAGGCAGGA
*
44853 GTAACCAATATCGGTTCGAAAAAAATGGTGAAAAATTTCTCTTGTTGCCTATGCAGAAGAGTGAT
131 GTAACCAATATCGATTCGAAAAAAATGGTGAAAAATTTCTCTTGTTGCCTATGCAGAAGAGTGAT
44918 AAATCAAAGGAGCAGAAAACCTTCCTGTATGTGGCTAAG
196 AAATCAAAGGAGCAGAAAACCTTCCTGTATGTGGCTAAG
44957 GATTTCGGTT
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
242 233 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (242 bp):
TGTAAAGTTCCTTTCTCTATAGGGAAGTATAATTATGAAGTTTACTGCGATGTGGTTGATATGGA
TGTTTGTCAGTTCTTGCTTGAAAGACCTTGGCAGTATGATCTTGATGTTTTGCATTTAGGCAGGA
GTAACCAATATCGATTCGAAAAAAATGGTGAAAAATTTCTCTTGTTGCCTATGCAGAAGAGTGAT
AAATCAAAGGAGCAGAAAACCTTCCTGTATGTGGCTAAGTATAATTA
Done.