Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023754.1 Corchorus olitorius cultivar O-4 contig23787, 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: 19699
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:927 original size:15 final size:15
Alignment explanation
Indices: 897--938 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
887 TTACTTTGCT
897 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
913 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
928 TTGCTTTCTGT
1 TTGTTTTCTGT
939 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:11525 original size:13 final size:13
Alignment explanation
Indices: 11507--11532 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11497 AAACATAGAC
11507 AGCAAAGCCAAAT
1 AGCAAAGCCAAAT
11520 AGCAAAGCCAAAT
1 AGCAAAGCCAAAT
11533 TGGTAGGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.15, T:0.08
Consensus pattern (13 bp):
AGCAAAGCCAAAT
Found at i:14124 original size:39 final size:39
Alignment explanation
Indices: 14072--14668 Score: 503
Period size: 39 Copynumber: 14.3 Consensus size: 39
14062 CCACATTTCT
* ** *
14072 AGTTTGCCCTTCCCCACCAGAAGGCATTGTTTAATTCCT
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTCCC
* * *
14111 AGTTTGCCCTTCCCCACCGAAAGGTGTTGTCTAAATTCGC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGT-TTAATTCCC
* * * *
14151 AATTTGTCCTTCCGCATCGGAAGGTGTTGTTTAAAGTCTGATTTACCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT--A-----A-TT-CCC
* *
14199 AGTTTGTCCTTCCTCACCGGAAGGTGTTGTTTAATTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTCCC
** *
14238 AGTTTGCCCTTCCATACCGGAAGGTGTTGTTTAATTCTC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTCCC
* *
14277 AGTTTGCCCTTCCCCACCAGAAGGTGTTGTCTAAATTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGT-TTAATTCCC
* * *
14317 AATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGATTTACC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT-A-----A-TTCCC
* * *
14363 AATTTGCCCTTCCTCACCGGAAGGTGTTGTCTAAATTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGT-TTAATTCCC
* *
14403 AATTTGCCCCTTCCCCATCGGAAGGTGTTGTTTAAAGTCTGATTTACCC
1 AGTTTG-CCCTTCCCCACCGGAAGGTGTTGTTT--A-----A-TT-CCC
* *
14452 AGTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTCCT
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTCCC
*
14491 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTCCT
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTCCC
14530 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTCCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATT-CCC
* * * *
14570 AGTTTGCACTTCCTCATCGGAAGGTGTTGTCTAAGTCTACCTTTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTG--T---T-TA--ATTCCC
* * *
14617 AGTTTGCCCTTCCCCGCCGGAAGGTGTTGTCTATATT-TC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA-ATTCCC
*
14656 AGTCTGCCCTTCC
1 AGTTTGCCCTTCC
14669 TAAGTAGAAG
Statistics
Matches: 463, Mismatches: 57, Indels: 76
0.78 0.10 0.13
Matches are distributed among these distances:
39 182 0.39
40 111 0.24
41 28 0.06
42 2 0.00
45 3 0.01
46 38 0.08
47 32 0.07
48 59 0.13
49 8 0.02
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (39 bp):
AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTCCC
Found at i:14346 original size:166 final size:167
Alignment explanation
Indices: 14072--14649 Score: 644
Period size: 166 Copynumber: 3.4 Consensus size: 167
14062 CCACATTTCT
* ** * *
14072 AGTTTGCCCTTCCCCACCAGAAGGCATTGTTTAA-TTCCT-AGTTTGCCCTTCCCCACCGAAAGG
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTACTCAGTTTGCCCTTCCCCACCGGAAGG
* * *
14135 TGTTGTCTAAATTCGCAATTTGTCCTTCCGCATCGGAAGGTGTTGTTTAAAGTCTGATTTACCCA
66 TGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AAGTCTGATTTACCCA
*
14200 GTTTGTCCTTCCTCACCGGAAGGTGTTGTTTAATTCCC
130 GTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTCCC
** *
14238 AGTTTGCCCTTCCATACCGGAAGGTGTTGTTTAA-TT-CTCAGTTTGCCCTTCCCCACCAGAAGG
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTACTCAGTTTGCCCTTCCCCACCGGAAGG
*
14301 TGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGATTTA-CCAA
66 TGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGATTTACCCAG
*
14365 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTAAATTCCC
131 TTTGCCCTTCCTCACCGGAAGGTGTTGT-TTAATTCCC
* * * *
14403 AATTTGCCCCTTCCCCATCGGAAGGTGTTGTTTAAAGTCTGATTTACCCAGTTTGCCCTTCCTCA
1 AGTTTG-CCCTTCCCCACCGGAAGGTGTTGTTT-AA----G--TTACTCAGTTTGCCCTTCCCCA
* * * *
14468 CCGGAAGGTGTTGT-TTAATTCCTAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT-A-----A-
58 CCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGAT
* *
14525 TT-CCTAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTCCCC
123 TTACCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATT-CCC
* * * * *
14570 AGTTTGCACTTCCTCATCGGAAGGTGTTGTCTAAGTCTACCTTTCCCAGTTTGCCCTTCCCCGCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGT-TA-C--T--CAGTTTGCCCTTCCCCACC
14635 GGAAGGTGTTGTCTA
60 GGAAGGTGTTGTCTA
14650 TATTTCAGTC
Statistics
Matches: 355, Mismatches: 36, Indels: 42
0.82 0.08 0.10
Matches are distributed among these distances:
159 1 0.00
160 2 0.01
161 2 0.01
164 30 0.08
165 58 0.16
166 150 0.42
167 41 0.12
168 1 0.00
173 1 0.00
174 39 0.11
175 30 0.08
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.35
Consensus pattern (167 bp):
AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTACTCAGTTTGCCCTTCCCCACCGGAAGG
TGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGATTTACCCAG
TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTCCC
Found at i:14590 original size:253 final size:252
Alignment explanation
Indices: 14113--14649 Score: 846
Period size: 253 Copynumber: 2.1 Consensus size: 252
14103 TAATTCCTAG
* * * *
14113 TTTGCCCTTCCCCACCGAAAGGTGTTGTCTAAATTCGCAATTTGTCCTTCCGCATCGGAAGGTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCGGAAGGTGT
*
14178 TGTTTAAAGTCTGATTTACCCAGTTTGTCCTTCCTCACCGGAAGGTGTTGTTTAATTCCCAGTTT
66 TGTTTAAAGTCTGATTTACCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTCCCAGTTT
*
14243 GCCCTTCCATACCGGAAGGTGTTGTTTAATTCTCAGTTTGCCCTTCCCCACCAGAAGGTGTTGTC
131 GCCCTTCCACACCGGAAGGTGTTGTTTAATTCTCAGTTTGCCCTTCCCCACCAGAAGGTGTTGTC
* *
14308 TAAATTCCCAATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTGA-TTTACCAA
196 TAAATTCCCAATTTGCACTTCCCCATCGGAAGGTGTTGTCTAAGTCT-ACTTTACCAA
*
14365 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCCTTCCCCATCGGAAGGTG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTG-CCCTTCCCCATCGGAAGGTG
*
14430 TTGTTTAAAGTCTGATTTACCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTCCTAGTT
65 TTGTTTAAAGTCTGATTTACCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTCCCAGTT
* *
14495 TGCCCTTCCCCACCGGAAGGTGTTGTTTAATTC-CTAGTTTGCCCTTCCCCACCGGAAGGTGTTG
130 TGCCCTTCCACACCGGAAGGTGTTGTTTAATTCTC-AGTTTGCCCTTCCCCACCAGAAGGTGTTG
* * * * *
14559 T-TTAATTCCCCAGTTTGCACTTCCTCATCGGAAGGTGTTGTCTAAGTCTACCTTTCCCAG
194 TCTAAATT-CCCAATTTGCACTTCCCCATCGGAAGGTGTTGTCTAAGTCTA-CTTTACCAA
*
14619 TTTGCCCTTCCCCGCCGGAAGGTGTTGTCTA
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTCTA
14650 TATTTCAGTC
Statistics
Matches: 261, Mismatches: 19, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
252 48 0.18
253 178 0.68
254 35 0.13
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (252 bp):
TTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCGGAAGGTGT
TGTTTAAAGTCTGATTTACCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTCCCAGTTT
GCCCTTCCACACCGGAAGGTGTTGTTTAATTCTCAGTTTGCCCTTCCCCACCAGAAGGTGTTGTC
TAAATTCCCAATTTGCACTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCAA
Found at i:15817 original size:207 final size:203
Alignment explanation
Indices: 15465--15877 Score: 646
Period size: 207 Copynumber: 2.0 Consensus size: 203
15455 AGTATGAACC
* * * *
15465 CAGAAACTATGAAACCTGTTAAAAGTTAAACAACGGAAAGTTAGTATCAATTTGTGTCAAACCCT
1 CAGAAACTATGAAACCTGTTAAAAGTTAAAAAAAGGAAAATTAATATCAATTTGTGTCAAACCCT
** *
15530 AAACAAATGAAATCAAAAACATATGAAATTTACAAGATTAGAGATTAAAAGCAAAACCGAAAGCA
66 AAACAAATGAAAAAAAAAACATATGAAATTCACAAGATTAGAGATTAAAAGCAAAACCGAAAGCA
* *
15595 AATTACCTTTCAATTGCAGAAAATGCAAAACTAGGGTTCCTGAATTCGAAAATTGTGGAATTTCA
131 AATTACCTTTCAATTGCAGAAAATGCAAAACTAGGGTTCATGAATTCGAAAATTGGGGAATTTCA
15660 ATTGCAATT
196 ATT-CAATT
* **
15669 CAGAAACTATGAAACCTGTTACAAGTTAAAAAATAGGAAAATTAATATTGATTTGTGTCAAACCC
1 CAGAAACTATGAAACCTGTTAAAAGTTAAAAAA-AGGAAAATTAATATCAATTTGTGTCAAACCC
*
15734 TAAACAAATGAATAAAAAAAAACATATGAAATTCACTAGATTAGAGATTAAAAGCAAAACCGAAA
65 TAAACAAATG-A-AAAAAAAAACATATGAAATTCACAAGATTAGAGATTAAAAGCAAAACCGAAA
* *
15799 GCAAATTACCTTTCAATTGCAGAAAATGCAAAACTAGGGTTTATGAATTCGAAAATTGGGGATTT
128 GCAAATTACCTTTCAATTGCAGAAAATGCAAAACTAGGGTTCATGAATTCGAAAATTGGGGAATT
*
15864 TCGATTCAATT
193 TCAATTCAATT
15875 CAG
1 CAG
15878 CAATTGACCG
Statistics
Matches: 190, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
204 31 0.16
205 36 0.19
206 9 0.05
207 114 0.60
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.26
Consensus pattern (203 bp):
CAGAAACTATGAAACCTGTTAAAAGTTAAAAAAAGGAAAATTAATATCAATTTGTGTCAAACCCT
AAACAAATGAAAAAAAAAACATATGAAATTCACAAGATTAGAGATTAAAAGCAAAACCGAAAGCA
AATTACCTTTCAATTGCAGAAAATGCAAAACTAGGGTTCATGAATTCGAAAATTGGGGAATTTCA
ATTCAATT
Found at i:17905 original size:15 final size:16
Alignment explanation
Indices: 17885--17917 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17875 CATTTTAAAT
*
17885 AAATTTAAGAA-TTAA
1 AAATTTAAAAATTTAA
17900 AAATTTAAAAATTTAA
1 AAATTTAAAAATTTAA
17916 AA
1 AA
17918 GCTGACCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AAATTTAAAAATTTAA
Found at i:17907 original size:8 final size:8
Alignment explanation
Indices: 17885--17917 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
17875 CATTTTAAAT
17885 AAATTTAA
1 AAATTTAA
*
17893 GAA-TTAA
1 AAATTTAA
17900 AAATTTAA
1 AAATTTAA
17908 AAATTTAA
1 AAATTTAA
17916 AA
1 AA
17918 GCTGACCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (8 bp):
AAATTTAA
Found at i:19033 original size:2 final size:2
Alignment explanation
Indices: 19026--19086 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
19016 TTAGGATTTT
* *
19026 TA TA TA TA T- TA TA TA T- TA TA AA TA TT TA TA TA 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
* *
19066 TA T- TA TA -A TT TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
19087 CAAAAAACAT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
1 4 0.09
2 43 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19130 original size:12 final size:13
Alignment explanation
Indices: 19026--19133 Score: 63
Period size: 12 Copynumber: 8.8 Consensus size: 13
19016 TTAGGATTTT
*
19026 TATATATATTATA
1 TATATATAATATA
19039 TAT-TATAA-ATA
1 TATATATAATATA
19050 T-T-TAT-ATATA
1 TATATATAATATA
*
19060 TATATATATTATA
1 TATATATAATATA
*
19073 -ATTTATAA-ATA
1 TATATATAATATA
* * *
19084 TATCAAAAAACATA
1 TAT-ATATAATATA
* *
19098 AATCAT-TCATATA
1 TAT-ATATAATATA
19111 TATATATAATATA
1 TATATATAATATA
19124 T-TATATAATA
1 TATATATAATA
19134 AATACTATTA
Statistics
Matches: 73, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
9 1 0.01
10 8 0.11
11 8 0.11
12 26 0.36
13 23 0.32
14 7 0.10
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (13 bp):
TATATATAATATA
Done.