Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015369.1 Corchorus capsularis cultivar CVL-1 contig15390, 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: 42316
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:315 original size:87 final size:87
Alignment explanation
Indices: 207--522 Score: 571
Period size: 87 Copynumber: 3.6 Consensus size: 87
197 ATTGTTAAAA
* *
207 TAATAATGAGAAAATTTTCTAAATCTTGCCAACTTGTGGGAGATTTAGGAGATATTTTAAGAAAT
1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
272 AAATAAATTATAAAGATTGAGC
66 AAATAAATTATAAAGATTGAGC
294 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
*
359 AAATAAATTACAAAGATTGAGC
66 AAATAAATTATAAAGATTGAGC
381 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
*
446 AAATAAATTATAAAGATTGAGT
66 AAATAAATTATAAAGATTGAGC
*
468 TAATGAA-GAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
1 TAAT-AATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATAT
523 AGAATAGGAA
Statistics
Matches: 222, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
87 220 0.99
88 2 0.01
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (87 bp):
TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
AAATAAATTATAAAGATTGAGC
Found at i:6182 original size:23 final size:23
Alignment explanation
Indices: 6132--6175 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
6122 TCTCTATAGT
6132 TTCTTTGAATACTCACAAGCAAA
1 TTCTTTGAATACTCACAAGCAAA
6155 TTCTTTGAATACTCACAAGCA
1 TTCTTTGAATACTCACAAGCA
6176 TGATCTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (23 bp):
TTCTTTGAATACTCACAAGCAAA
Found at i:6275 original size:13 final size:13
Alignment explanation
Indices: 6257--6281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6247 GCTTATTAAT
6257 TATTATTAATTAG
1 TATTATTAATTAG
6270 TATTATTAATTA
1 TATTATTAATTA
6282 AATAAAATAA
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TATTATTAATTAG
Found at i:6694 original size:23 final size:23
Alignment explanation
Indices: 6668--6715 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
6658 GGATCATCCA
* *
6668 TTAAGACAAAGAAATAGTACAGT
1 TTAAGAAAAAAAAATAGTACAGT
*
6691 TTAATAAAAAAAAATAGTACAGT
1 TTAAGAAAAAAAAATAGTACAGT
6714 TT
1 TT
6716 GTAGAGCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.27
Consensus pattern (23 bp):
TTAAGAAAAAAAAATAGTACAGT
Found at i:20544 original size:16 final size:16
Alignment explanation
Indices: 20525--20569 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
20515 TTCTTCTCCA
20525 TATTCTGTTGTCTCTC
1 TATTCTGTTGTCTCTC
20541 TATTCTGTTGTCTCTC
1 TATTCTGTTGTCTCTC
20557 TATTCTGTTGTCT
1 TATTCTGTTGTCT
20570 TTTCCATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.07, C:0.22, G:0.13, T:0.58
Consensus pattern (16 bp):
TATTCTGTTGTCTCTC
Found at i:26679 original size:31 final size:31
Alignment explanation
Indices: 26643--26704 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
26633 CCATCAGATG
26643 GGGTTTCAATGTGTATATTGTTGGTACCTAT
1 GGGTTTCAATGTGTATATTGTTGGTACCTAT
26674 GGGTTTCAATGTGTATATTGTTGGTACCTAT
1 GGGTTTCAATGTGTATATTGTTGGTACCTAT
26705 CGCTTTGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.45
Consensus pattern (31 bp):
GGGTTTCAATGTGTATATTGTTGGTACCTAT
Found at i:27082 original size:107 final size:105
Alignment explanation
Indices: 26854--27117 Score: 406
Period size: 107 Copynumber: 2.5 Consensus size: 105
26844 AATTTTTCTA
** *
26854 ACCCTTAAAATAAAAATTTTAATTTTAATTT-GGACTAAACTTAGTG-AATTAATTATATATTTT
1 ACCCTTAAAATAAAAA-TAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTT
* *
26917 ATTTCTAAAATCCTATAACAATATTATTAATTATGGAATTT
65 ATTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* * *
26958 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
*
27023 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
27065 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
27118 GGCTAAACTT
Statistics
Matches: 146, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
103 12 0.08
104 30 0.21
105 35 0.24
107 69 0.47
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:27602 original size:24 final size:24
Alignment explanation
Indices: 27575--27622 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
27565 TGGTTTTAAA
27575 AACCTTTTGGAATGAATTTATACG
1 AACCTTTTGGAATGAATTTATACG
27599 AACCTTTTGGAATGAATTTATACG
1 AACCTTTTGGAATGAATTTATACG
27623 TGGTTGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (24 bp):
AACCTTTTGGAATGAATTTATACG
Found at i:37818 original size:17 final size:17
Alignment explanation
Indices: 37793--37825 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
37783 TAGGAGAAAA
*
37793 AAAATGCTTTTAGTTGT
1 AAAAGGCTTTTAGTTGT
37810 AAAAGGCTTTTAGTTG
1 AAAAGGCTTTTAGTTG
37826 ACAAGACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (17 bp):
AAAAGGCTTTTAGTTGT
Found at i:38975 original size:23 final size:22
Alignment explanation
Indices: 38931--38994 Score: 92
Period size: 23 Copynumber: 2.9 Consensus size: 22
38921 AAAGGGAGCA
*
38931 TGTTAAAAACAAGGGTTGTTTT
1 TGTTAAAAACAAGGGCTGTTTT
38953 TGTTAAAAACAAGGGCTGCTTTT
1 TGTTAAAAACAAGGGCTG-TTTT
* *
38976 TATTAAAAACAGGGGCTGT
1 TGTTAAAAACAAGGGCTGT
38995 AATCATATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 18 0.47
23 20 0.53
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.34
Consensus pattern (22 bp):
TGTTAAAAACAAGGGCTGTTTT
Found at i:39062 original size:84 final size:84
Alignment explanation
Indices: 38953--39146 Score: 327
Period size: 84 Copynumber: 2.3 Consensus size: 84
38943 GGGTTGTTTT
* *
38953 TGTTAAAAACAAGGGCTGCTTTTTATTAAAAACAGGGGCTGTAATCATATGAGAATATGTTTTGG
1 TGTTAAAAACAGGGGCTG-TTTTTATTAAAAACAGGGGCTGTAATCATATGACAATATGTTTTGG
39018 ATCATTATTACACAGAAGCA
65 ATCATTATTACACAGAAGCA
* *
39038 TGTTAATAAA-AGGGGCTGTTTTTATTAAGAACAGGGGCTGTAATCATATTACAATATGTTTTGG
1 TGTTAA-AAACAGGGGCTGTTTTTATTAAAAACAGGGGCTGTAATCATATGACAATATGTTTTGG
39102 ATCATTATTACACAGAAGCA
65 ATCATTATTACACAGAAGCA
39122 TGTTAAAAACAGGGGCTGTTTTTAT
1 TGTTAAAAACAGGGGCTGTTTTTAT
39147 GTTATAAGAT
Statistics
Matches: 103, Mismatches: 4, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
83 3 0.03
84 84 0.82
85 13 0.13
86 3 0.03
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.34
Consensus pattern (84 bp):
TGTTAAAAACAGGGGCTGTTTTTATTAAAAACAGGGGCTGTAATCATATGACAATATGTTTTGGA
TCATTATTACACAGAAGCA
Done.