Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018920.1 Corchorus olitorius cultivar O-4 contig18953, 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: 76823
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8571 original size:6 final size:6
Alignment explanation
Indices: 8560--8588 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
8550 ACAGAAGCTT
8560 AAAATG AAAATG AAAATG AAAATG AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAAT
8589 AAACATGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:14727 original size:15 final size:15
Alignment explanation
Indices: 14689--14731 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
14679 AATCCATAAT
**
14689 CATCATCTTCTTCTT
1 CATCATCTTCTTCAA
* *
14704 CTTCCTCTTCTTCAA
1 CATCATCTTCTTCAA
14719 CATCATCTTCTTC
1 CATCATCTTCTTC
14732 CTCGTTATCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.14, C:0.37, G:0.00, T:0.49
Consensus pattern (15 bp):
CATCATCTTCTTCAA
Found at i:16641 original size:28 final size:30
Alignment explanation
Indices: 16584--16654 Score: 101
Period size: 28 Copynumber: 2.4 Consensus size: 30
16574 ATACCCGGGA
16584 GGTCCCTCTACTTACACAAAAAAATCAATTT
1 GGTCCCTCTAC-TACACAAAAAAATCAATTT
*
16615 GGTCCCTCTACTA-A-AAAAATATCAATTT
1 GGTCCCTCTACTACACAAAAAAATCAATTT
*
16643 AGTCCCTCTACT
1 GGTCCCTCTACT
16655 TGTGAGATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 24 0.63
29 1 0.03
30 2 0.05
31 11 0.29
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (30 bp):
GGTCCCTCTACTACACAAAAAAATCAATTT
Found at i:17755 original size:29 final size:29
Alignment explanation
Indices: 17713--17786 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
17703 CTTGCTTGTT
17713 CGGTCACTCTATAACAGCGAAGGAAGATC
1 CGGTCACTCTATAACAGCGAAGGAAGATC
17742 CGGTCACTCTATAACAGCGAAGGAAGATC
1 CGGTCACTCTATAACAGCGAAGGAAGATC
17771 CGGTCACTCTATAACA
1 CGGTCACTCTATAACA
17787 AGGAGAAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.19
Consensus pattern (29 bp):
CGGTCACTCTATAACAGCGAAGGAAGATC
Found at i:18079 original size:31 final size:31
Alignment explanation
Indices: 18031--18103 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
18021 GTTATTAATT
*
18031 GGACTTAATTGAT-CCAATCTGACAAGAAGAG
1 GGACTAAATTG-TCCCAATCTGACAAGAAGAG
* * *
18062 GGATTAAATTGTCCCAATCTTACAAGTAGAG
1 GGACTAAATTGTCCCAATCTGACAAGAAGAG
18093 GGACTAAATTG
1 GGACTAAATTG
18104 ATCGTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (31 bp):
GGACTAAATTGTCCCAATCTGACAAGAAGAG
Found at i:19210 original size:60 final size:59
Alignment explanation
Indices: 19117--19242 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 59
19107 CTAATTGCTC
* * *
19117 AAATAGGTCCTGAACATATGAGCAAATGTTCAATTTAGGGCTCATGAC-TTTAATTTGGTT
1 AAATAGGTCCTGAACATATGAGAAAATGCTCAATTTAAGG-TCAT-ACTTTTAATTTGGTT
* * * *
19177 AAATATGTCCTTAACATATGCGAAAATGCTCAATTTAAGGTTATACTTTTAATTTGGTT
1 AAATAGGTCCTGAACATATGAGAAAATGCTCAATTTAAGGTCATACTTTTAATTTGGTT
19236 AAATAGG
1 AAATAGG
19243 GCCCTAATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 2 0.04
59 21 0.37
60 34 0.60
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (59 bp):
AAATAGGTCCTGAACATATGAGAAAATGCTCAATTTAAGGTCATACTTTTAATTTGGTT
Found at i:19829 original size:232 final size:234
Alignment explanation
Indices: 19416--19884 Score: 789
Period size: 232 Copynumber: 2.0 Consensus size: 234
19406 TGTTAGGGCT
* *
19416 CTATTTAACCAAGCTAAAAGTATAAGTTCTAAATTGAATCGGTATTTGAAAAAAAAAAAAAACTC
1 CTATTTAACCAAGCTAAAAGTATAAGCTCTAAATTGAATCAGTATTT----AAAAAAAAAAACTC
* * *
19481 TAAATTGAATATTTTCACATACGTTAAGAACCTATTTGAACGATCAACCTAAATTTTTACCTTTC
62 TAAATTGAATATTTTCACATACGTTAAGAACCCATTTGAACAATCAACCTAAATTTTTACCCTTC
*
19546 AATTAACTACTAAGTCGCATGCAATGGATACATTATAGTTTTC-ACAAAAAAAGATACATTATAG
127 AATTAACTACTAAGTCGCATGCAATGGATACATTATAGTTTTCAAAAAAAAAAGATACATTATAG
*
19610 TTCAAAAGGATAAATATTTAGGATGCGTTTGGTAATTGATACA
192 TTCAAAAGAATAAATATTTAGGATGCGTTTGGTAATTGATACA
19653 CTATTTAACCAAGCTAAAAGTATAAGCTCTAAATTGAATCAGTATTT-AAAAAAAAAACTCTAAA
1 CTATTTAACCAAGCTAAAAGTATAAGCTCTAAATTGAATCAGTATTTAAAAAAAAAAACTCTAAA
*
19717 TTGAATATTTTCACATATGTTAAGAACCCATTTGAACAATCAACCTAAATTTTTACCCTTCAATT
66 TTGAATATTTTCACATACGTTAAGAACCCATTTGAACAATCAACCTAAATTTTTACCCTTCAATT
* *
19782 AACTGCTAAGTCGCATGCAATGGATACATTATAGTTTTCAAAAAAAAAATATACATTATAGTTCA
131 AACTACTAAGTCGCATGCAATGGATACATTATAGTTTTCAAAAAAAAAAGATACATTATAGTTCA
*
19847 AAAGAATAAATATTTAGGATGTGTTTGGTAATTGATAC
196 AAAGAATAAATATTTAGGATGCGTTTGGTAATTGATAC
19885 TTTCTTTTTT
Statistics
Matches: 220, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
232 116 0.53
233 59 0.27
237 45 0.20
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (234 bp):
CTATTTAACCAAGCTAAAAGTATAAGCTCTAAATTGAATCAGTATTTAAAAAAAAAAACTCTAAA
TTGAATATTTTCACATACGTTAAGAACCCATTTGAACAATCAACCTAAATTTTTACCCTTCAATT
AACTACTAAGTCGCATGCAATGGATACATTATAGTTTTCAAAAAAAAAAGATACATTATAGTTCA
AAAGAATAAATATTTAGGATGCGTTTGGTAATTGATACA
Found at i:22695 original size:33 final size:33
Alignment explanation
Indices: 22658--22741 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
22648 CATGGCCTAC
*
22658 TCGCG-TGCGAGTCGCGACCGGGCCATGGTCAGG
1 TCGCGATGCG-GTCGCGACCGGACCATGGTCAGG
* *
22691 TCGCGATTCGGTCGGGACCGGACCATGGTCAGG
1 TCGCGATGCGGTCGCGACCGGACCATGGTCAGG
*
22724 TCGCGAT-CCGTCGCGACC
1 TCGCGATGCGGTCGCGACC
22742 CGCCTATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 9 0.20
33 33 0.73
34 3 0.07
ACGTcount: A:0.13, C:0.32, G:0.38, T:0.17
Consensus pattern (33 bp):
TCGCGATGCGGTCGCGACCGGACCATGGTCAGG
Found at i:23271 original size:23 final size:25
Alignment explanation
Indices: 23245--23293 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
23235 GTTCATCCAA
23245 CCACC-CTTCTCTCTTTGTG-GGCC
1 CCACCACTTCTCTCTTTGTGAGGCC
*
23268 CCACCATTTTCTCTCTTTGTGAGGCC
1 CCACCA-CTTCTCTCTTTGTGAGGCC
23294 ACACGTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
25 13 0.59
26 4 0.18
ACGTcount: A:0.08, C:0.39, G:0.16, T:0.37
Consensus pattern (25 bp):
CCACCACTTCTCTCTTTGTGAGGCC
Found at i:24104 original size:34 final size:34
Alignment explanation
Indices: 24066--24130 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
24056 GGGTTTGGAG
24066 TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
1 TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
24100 TCAAACCCCAAACATTTGAAAGTCAAACCAC
1 TCAAACCCCAAACATTTGAAAGTCAAACCAC
24131 ATTTTGACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.43, C:0.31, G:0.08, T:0.18
Consensus pattern (34 bp):
TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
Found at i:24134 original size:18 final size:18
Alignment explanation
Indices: 24077--24134 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
24067 CAAACCCCAA
24077 ACATTTGAAAGTCAAACC
1 ACATTTGAAAGTCAAACC
* * ** *
24095 ACGTTTCAAACCCCAA--
1 ACATTTGAAAGTCAAACC
24111 ACATTTGAAAGTCAAACC
1 ACATTTGAAAGTCAAACC
24129 ACATTT
1 ACATTT
24135 TGACCCCACT
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
16 11 0.39
18 17 0.61
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (18 bp):
ACATTTGAAAGTCAAACC
Found at i:25117 original size:21 final size:21
Alignment explanation
Indices: 25091--25219 Score: 177
Period size: 21 Copynumber: 6.1 Consensus size: 21
25081 TTAATGTGTC
*
25091 GACTATCAAAATTTGGGGTTT
1 GACTATCAAACTTTGGGGTTT
25112 GACTATCAAACTTTGGGGTTT
1 GACTATCAAACTTTGGGGTTT
* *
25133 GACTTTCAAACTATGGGGTTT
1 GACTATCAAACTTTGGGGTTT
* *
25154 GACTTTCAAACTATGGGGTTT
1 GACTATCAAACTTTGGGGTTT
*
25175 GACTATCAAAATTTGGGGTTT
1 GACTATCAAACTTTGGGGTTT
** *
25196 GACTATCATCCTTTGTGGTTT
1 GACTATCAAACTTTGGGGTTT
25217 GAC
1 GAC
25220 CATGTATGTA
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 98 1.00
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (21 bp):
GACTATCAAACTTTGGGGTTT
Found at i:25990 original size:13 final size:13
Alignment explanation
Indices: 25972--26018 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
25962 AAAAAGAGAG
25972 AGAGAGAGGAAGA
1 AGAGAGAGGAAGA
25985 AGAGAGA-GAA-A
1 AGAGAGAGGAAGA
*
25996 TAGCGGAGAGGAAGA
1 -AG-AGAGAGGAAGA
26011 AGAGAGAG
1 AGAGAGAG
26019 AAATATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.04
12 5 0.18
13 16 0.57
14 5 0.18
15 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.45, T:0.02
Consensus pattern (13 bp):
AGAGAGAGGAAGA
Found at i:52055 original size:19 final size:20
Alignment explanation
Indices: 52031--52078 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
52021 ATGGTTGAAC
*
52031 ATTAATATATAT-TATTATA
1 ATTAATATATATATAATATA
52050 ATTAATATATATATAATATA
1 ATTAATATATATATAATATA
52070 A-TAATATAT
1 ATTAATATAT
52079 GCACTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTAATATATATATAATATA
Found at i:52076 original size:15 final size:15
Alignment explanation
Indices: 52033--52078 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
52023 GGTTGAACAT
*
52033 TAATAT-ATATTATTA
1 TAATATAATAATA-TA
52048 TAAT-TAATATATATA
1 TAATATAATA-ATATA
52063 TAATATAATAATATA
1 TAATATAATAATATA
52078 T
1 T
52079 GCACTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 1 0.04
15 19 0.70
16 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATATAATAATATA
Found at i:53328 original size:24 final size:24
Alignment explanation
Indices: 53291--53351 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
53281 AGGAGTTTTT
**
53291 TAAAATTTTTTTTTTTTAGAAAAG
1 TAAAATTTAATTTTTTTAGAAAAG
* * *
53315 TAAAATTTAATTTTTTTATAACAT
1 TAAAATTTAATTTTTTTAGAAAAG
53339 TAAAATTTAATTT
1 TAAAATTTAATTT
53352 AGAAGATGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (24 bp):
TAAAATTTAATTTTTTTAGAAAAG
Found at i:63196 original size:21 final size:21
Alignment explanation
Indices: 63170--63211 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
63160 AAGAACCTGC
63170 CCCAAAAAGTTCAAAGGATAA
1 CCCAAAAAGTTCAAAGGATAA
*
63191 CCCAAAAAGTTCGAAGGATAA
1 CCCAAAAAGTTCAAAGGATAA
63212 AAAGGCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (21 bp):
CCCAAAAAGTTCAAAGGATAA
Found at i:69409 original size:2 final size:2
Alignment explanation
Indices: 69402--69492 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
69392 TGATCTTTCT
69402 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
69444 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
69486 TC TC TC T
1 TC TC TC T
69493 TTCCATAAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:72284 original size:21 final size:19
Alignment explanation
Indices: 72255--72294 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
72245 TTTAATCAAA
72255 GCTCATTTTAATCCCTAATT
1 GCTCATTTTAA-CCCTAATT
*
72275 GCTCAATTTTAAGCCTAATT
1 GCTC-ATTTTAACCCTAATT
72295 TGTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.42
Consensus pattern (19 bp):
GCTCATTTTAACCCTAATT
Found at i:73611 original size:29 final size:29
Alignment explanation
Indices: 73569--73641 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
73559 AATCATATAT
73569 ATGATAATTAGTTAAATTTTTTTCCCACA
1 ATGATAATTAGTTAAATTTTTTTCCCACA
* **
73598 ATGATAATTAGTTAATTTTTTTTGGCACA
1 ATGATAATTAGTTAAATTTTTTTCCCACA
*
73627 ATCATAATTAGTTAA
1 ATGATAATTAGTTAA
73642 TTAATTAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (29 bp):
ATGATAATTAGTTAAATTTTTTTCCCACA
Done.