Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006913.1 Corchorus capsularis cultivar CVL-1 contig06934, 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: 23149
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:205 original size:10 final size:10
Alignment explanation
Indices: 190--214 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
180 GTTGCTGCAC
190 AATTCCAGAA
1 AATTCCAGAA
200 AATTCCAGAA
1 AATTCCAGAA
210 AATTC
1 AATTC
215 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:1154 original size:6 final size:6
Alignment explanation
Indices: 1143--1178 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
1133 ATTAATTTGC
1143 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA
1179 ATTGCTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TTTAGA
Found at i:1507 original size:34 final size:35
Alignment explanation
Indices: 1460--1529 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1450 TCCAAGAATT
* *
1460 AGTTTTT-GTTTTTTCCGTTTTTTCTAAAAAAAAA
1 AGTTTTTCCTTTTTTCCGATTTTTCTAAAAAAAAA
1494 AGTTTTTCCTTTTTTCCGATTTTTCTAAAAAAAAA
1 AGTTTTTCCTTTTTTCCGATTTTTCTAAAAAAAAA
1529 A
1 A
1530 AAAGATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 7 0.21
35 26 0.79
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.50
Consensus pattern (35 bp):
AGTTTTTCCTTTTTTCCGATTTTTCTAAAAAAAAA
Found at i:1641 original size:35 final size:35
Alignment explanation
Indices: 1575--1641 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
1565 TTGCGCCGAT
* *
1575 TAAAAAAAAAATTCTTTTCCGTTTTTCCTTTTAAA
1 TAAAAAAAAAATTATTTTCCGTTTCTCCTTTTAAA
** * *
1610 TAAAAAAAATTTTATTTTCTGTTTCTGCTTTT
1 TAAAAAAAAAATTATTTTCCGTTTCTCCTTTT
1642 TATTTTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (35 bp):
TAAAAAAAAAATTATTTTCCGTTTCTCCTTTTAAA
Found at i:5129 original size:23 final size:23
Alignment explanation
Indices: 5096--5140 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5086 CATCACTGTG
5096 CCATGCCCGGCCT-TGTCCGCGCA
1 CCATGCCCGGCCTATG-CCGCGCA
*
5119 CCATGCTCGGCCTATGCCGCGC
1 CCATGCCCGGCCTATGCCGCGC
5141 CATCCGTGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.09, C:0.47, G:0.27, T:0.18
Consensus pattern (23 bp):
CCATGCCCGGCCTATGCCGCGCA
Found at i:15047 original size:25 final size:24
Alignment explanation
Indices: 15002--15050 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
14992 CGACCGACTA
*
15002 ATTATATAATATAATTTTAAAAAT
1 ATTATATAATATAATTATAAAAAT
15026 ATTATAT-ATATATATTCATAAAAAT
1 ATTATATAATATA-ATT-ATAAAAAT
15051 TCAGAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 10 0.45
25 7 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTATATAATATAATTATAAAAAT
Found at i:15145 original size:18 final size:18
Alignment explanation
Indices: 15114--15149 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
15104 CCTAAGATTG
15114 ATTTTTCCTCTCTCTCTT
1 ATTTTTCCTCTCTCTCTT
15132 ATTTTCTCCT-TCTCTCTT
1 ATTTT-TCCTCTCTCTCTT
15150 CGAAACCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTCCTCTCTCTCTT
Found at i:16801 original size:26 final size:26
Alignment explanation
Indices: 16720--16794 Score: 118
Period size: 24 Copynumber: 3.0 Consensus size: 26
16710 ATGTGCCGTA
16720 TCATGGCAACCAAGTCCCCACATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
* *
16746 TCATGGTAACCAAGT-GCC-CATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
16770 TCATGGCAACCAAGTCCCCACATGG
1 TCATGGCAACCAAGTCCCCACATGG
16795 AATATGGAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.47
25 4 0.09
26 19 0.44
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.17
Consensus pattern (26 bp):
TCATGGCAACCAAGTCCCCACATGGC
Found at i:18640 original size:32 final size:33
Alignment explanation
Indices: 18570--18650 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
18560 CTTACGACAA
*
18570 TGGAGATTTGCGGCAATGGTGAGATACAACTAC
1 TGGAGATTTGCGGCAGTGGTGAGATACAACTAC
* ** *
18603 T-GAGATTTGCAGCAGTGGTGAGATACGGCT-G
1 TGGAGATTTGCGGCAGTGGTGAGATACAACTAC
18634 TGGAGATTTGCGGCAGT
1 TGGAGATTTGCGGCAGT
18651 AGGTAGTGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 1 0.02
32 39 0.95
33 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.36, T:0.26
Consensus pattern (33 bp):
TGGAGATTTGCGGCAGTGGTGAGATACAACTAC
Found at i:18787 original size:16 final size:16
Alignment explanation
Indices: 18736--18787 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
18726 ACATACGACT
*
18736 GTGGAGATTTGCGGCA
1 GTGGAGATTTACGGCA
* ** **
18752 GTGGTGAGATACGGTT
1 GTGGAGATTTACGGCA
18768 GTGGAGATTTACGGCA
1 GTGGAGATTTACGGCA
18784 GTGG
1 GTGG
18788 TGGGATATGG
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.19, C:0.10, G:0.44, T:0.27
Consensus pattern (16 bp):
GTGGAGATTTACGGCA
Found at i:18848 original size:32 final size:32
Alignment explanation
Indices: 18704--18849 Score: 193
Period size: 32 Copynumber: 4.6 Consensus size: 32
18694 GCTTACGACA
* * * *
18704 GTGGAGATTTGTGGCAATGGTGACATACGACT
1 GTGGAGATTTGCGGCAGTGGTGAGATACGGCT
*
18736 GTGGAGATTTGCGGCAGTGGTGAGATACGGTT
1 GTGGAGATTTGCGGCAGTGGTGAGATACGGCT
* * *
18768 GTGGAGATTTACGGCAGTGGTGGGATATGGCT
1 GTGGAGATTTGCGGCAGTGGTGAGATACGGCT
* *
18800 GTGGAGATTTGCGGCAGTGCTGAGATATGGCT
1 GTGGAGATTTGCGGCAGTGGTGAGATACGGCT
*
18832 ATGGAGATTTGCGGCAGT
1 GTGGAGATTTGCGGCAGT
18850 AGGTAGTGGA
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 101 1.00
ACGTcount: A:0.21, C:0.11, G:0.40, T:0.28
Consensus pattern (32 bp):
GTGGAGATTTGCGGCAGTGGTGAGATACGGCT
Found at i:19085 original size:16 final size:16
Alignment explanation
Indices: 19036--19087 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
19026 AGCAATGCCA
*
19036 CACCCAAGCGATGTTG
1 CACCCAAGCGATGTCG
* **
19052 CATCCAAGCGATACCG
1 CACCCAAGCGATGTCG
19068 CACCCAAGCGATGTCG
1 CACCCAAGCGATGTCG
19084 CACC
1 CACC
19088 ATAGTAAATG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.27, C:0.38, G:0.21, T:0.13
Consensus pattern (16 bp):
CACCCAAGCGATGTCG
Found at i:19338 original size:50 final size:50
Alignment explanation
Indices: 19188--19463 Score: 337
Period size: 50 Copynumber: 5.5 Consensus size: 50
19178 CGACAATGAC
* * * *
19188 GAGATGCGGCATCAAACATTATGGCAT-AAGAGGTCTATGGCGTAATGACAT
1 GAGATGCGGCGTCAAACATTATGGCATCAA-AAGTCTATGGCATAA-GGCAT
*
19239 GAGACGCGGCGTCAAACATTATGGCATC--AAGTCTATGGCATAAGGCAT
1 GAGATGCGGCGTCAAACATTATGGCATCAAAAGTCTATGGCATAAGGCAT
* * *
19287 GAGATGTGGCGTCAAACATTACGACATCAAAAGTCTATGGCATAAGGCAT
1 GAGATGCGGCGTCAAACATTATGGCATCAAAAGTCTATGGCATAAGGCAT
* *
19337 GAGATGCGGTGTCAAACATTATGGCAT-AAGAATTCTATGGCATAAGGCAT
1 GAGATGCGGCGTCAAACATTATGGCATCAA-AAGTCTATGGCATAAGGCAT
* * * *
19387 GAGATGCGGCGTCAAACATTACGGCTTCAGAAGTCTATGGCATAAGACAT
1 GAGATGCGGCGTCAAACATTATGGCATCAAAAGTCTATGGCATAAGGCAT
*
19437 GAGATGCGGCATCAGATAC-TTATGGCA
1 GAGATGCGGCGTCA-A-ACATTATGGCA
19464 CAAGACATGA
Statistics
Matches: 195, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
48 28 0.14
49 15 0.08
50 117 0.60
51 33 0.17
52 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (50 bp):
GAGATGCGGCGTCAAACATTATGGCATCAAAAGTCTATGGCATAAGGCAT
Found at i:19613 original size:15 final size:15
Alignment explanation
Indices: 19593--19622 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19583 AACTGCGGGA
*
19593 GCTACGGTATAAGTC
1 GCTACGGCATAAGTC
19608 GCTACGGCATAAGTC
1 GCTACGGCATAAGTC
19623 CCAACCGCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (15 bp):
GCTACGGCATAAGTC
Found at i:19647 original size:42 final size:42
Alignment explanation
Indices: 19566--19649 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
19556 AAGTCCCAAA
* * **
19566 GCTATGGCATAACTCCCAACTGCGGGAGCTACGGTATAAGTC
1 GCTACGGCATAACTCCCAACCGCGGGAGCTACGAAATAAGTC
* *
19608 GCTACGGCATAAGTCCCAACCGCGGGAGCTATGAAATAAGTC
1 GCTACGGCATAACTCCCAACCGCGGGAGCTACGAAATAAGTC
19650 CCTAGAGCCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (42 bp):
GCTACGGCATAACTCCCAACCGCGGGAGCTACGAAATAAGTC
Found at i:22448 original size:50 final size:50
Alignment explanation
Indices: 22380--22581 Score: 309
Period size: 50 Copynumber: 4.0 Consensus size: 50
22370 ATGTGCCGTA
* *
22380 TCATGGCAACCAAGTCCCCACATGGCTCAAGGTAACCAAGT-CCC-CATGGC
1 TCATGGCAACCAAGT-CCC-CATGGCTCATGGCAACCAAGTCCCCACATGGC
22430 TCATGGCAACCAAGTCCCCACATGGCTCATGGCAACCAAGTCCCCACATGGC
1 TCATGGCAACCAAGT-CCC-CATGGCTCATGGCAACCAAGTCCCCACATGGC
*
22482 TCATGGCAACTCAAGTGCCCATGGCTCATGGCAACCAAGTCCCCACATGGC
1 TCATGGCAAC-CAAGTCCCCATGGCTCATGGCAACCAAGTCCCCACATGGC
*
22533 TCATGGCAACCAAGTGCCCATGGCTCATGGCAACCAAGTCCCCACATGG
1 TCATGGCAACCAAGTCCCCATGGCTCATGGCAACCAAGTCCCCACATGG
22582 AATATGGAAC
Statistics
Matches: 146, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
50 78 0.53
51 45 0.31
52 18 0.12
53 5 0.03
ACGTcount: A:0.27, C:0.36, G:0.21, T:0.16
Consensus pattern (50 bp):
TCATGGCAACCAAGTCCCCATGGCTCATGGCAACCAAGTCCCCACATGGC
Found at i:22588 original size:26 final size:26
Alignment explanation
Indices: 22380--22581 Score: 317
Period size: 26 Copynumber: 8.0 Consensus size: 26
22370 ATGTGCCGTA
22380 TCATGGCAACCAAGTCCCCACATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
* *
22406 TCAAGGTAACCAAGT-CCC-CATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
22430 TCATGGCAACCAAGTCCCCACATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
22456 TCATGGCAACCAAGTCCCCACATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
*
22482 TCATGGCAACTCAAGT-GCC-CATGGC
1 TCATGGCAAC-CAAGTCCCCACATGGC
22507 TCATGGCAACCAAGTCCCCACATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
*
22533 TCATGGCAACCAAGT-GCC-CATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
22557 TCATGGCAACCAAGTCCCCACATGG
1 TCATGGCAACCAAGTCCCCACATGG
22582 AATATGGAAC
Statistics
Matches: 161, Mismatches: 8, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
24 45 0.28
25 28 0.17
26 83 0.52
27 5 0.03
ACGTcount: A:0.27, C:0.36, G:0.21, T:0.16
Consensus pattern (26 bp):
TCATGGCAACCAAGTCCCCACATGGC
Done.