Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016274.1 Corchorus olitorius cultivar O-4 contig16307, 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: 137053
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:4463 original size:1 final size:1
Alignment explanation
Indices: 4417--4456 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
4407 AAACCTTGGC
***
4417 AAAAAAAAAAAAAAAAAAAAAAAAGGTAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4457 TTAAAAAGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.93, C:0.00, G:0.05, T:0.03
Consensus pattern (1 bp):
A
Found at i:11098 original size:23 final size:23
Alignment explanation
Indices: 11072--11116 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
11062 ACAACTTGAT
11072 TTCCCTAAAACATCAAAGTATTA
1 TTCCCTAAAACATCAAAGTATTA
11095 TTCCCTAAAACATCAAAGTATT
1 TTCCCTAAAACATCAAAGTATT
11117 TTGAAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.31
Consensus pattern (23 bp):
TTCCCTAAAACATCAAAGTATTA
Found at i:13375 original size:19 final size:19
Alignment explanation
Indices: 13344--13381 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
13334 CCTCATTCTT
13344 TTTTGTGAAAACATATATTA
1 TTTTGTGAAAACAT-TATTA
13364 TTTTGT-AAAACATTATTA
1 TTTTGTGAAAACATTATTA
13382 AGGAAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (19 bp):
TTTTGTGAAAACATTATTA
Found at i:15704 original size:19 final size:21
Alignment explanation
Indices: 15664--15706 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
15654 AATTTTTAAG
15664 TAAAAATTTAATATATATAAA
1 TAAAAATTTAATATATATAAA
15685 TAAAAATTTAATAT-TA-AAA
1 TAAAAATTTAATATATATAAA
15704 TAA
1 TAA
15707 TTAATTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 2 0.09
21 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAAATTTAATATATATAAA
Found at i:34593 original size:16 final size:16
Alignment explanation
Indices: 34574--34621 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
34564 TTTGGCATCG
*
34574 TTTTCGTTTTTTTTGA
1 TTTTCGTTTTTTTTCA
*
34590 TTTTTGTTTTTGTTTCA
1 TTTTCGTTTTT-TTTCA
34607 TTTTCGTTTTGTTTT
1 TTTTCGTTTT-TTTT
34622 TATTGCGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 10 0.37
17 16 0.59
18 1 0.04
ACGTcount: A:0.04, C:0.06, G:0.12, T:0.77
Consensus pattern (16 bp):
TTTTCGTTTTTTTTCA
Found at i:40694 original size:26 final size:26
Alignment explanation
Indices: 40660--40714 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
40650 TATAAATTAC
*
40660 TAAGCACACTAGTGCTCATGATCAAT
1 TAAGAACACTAGTGCTCATGATCAAT
40686 TAAGAACACTAGTGCTCATGATCAAT
1 TAAGAACACTAGTGCTCATGATCAAT
40712 TAA
1 TAA
40715 TTCGTTGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (26 bp):
TAAGAACACTAGTGCTCATGATCAAT
Found at i:41840 original size:33 final size:33
Alignment explanation
Indices: 41798--41863 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
41788 GATGAGATTC
41798 AGCAAAGTTAGGGTCGGATGTTAGAGAATTCCA
1 AGCAAAGTTAGGGTCGGATGTTAGAGAATTCCA
*
41831 AGCAAAGTTAGGGTCGGATGTTGGAGAATTCCA
1 AGCAAAGTTAGGGTCGGATGTTAGAGAATTCCA
41864 TGGCCTGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (33 bp):
AGCAAAGTTAGGGTCGGATGTTAGAGAATTCCA
Found at i:42497 original size:42 final size:42
Alignment explanation
Indices: 42438--42523 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
42428 CGTACGCAGC
*
42438 CGCCCTCATTGGTAGACTCACCCACCAAACCCAGACTCAGGT
1 CGCCCTCATTGGTAGACTCACCCACCAAACCCAGACCCAGGT
42480 CGCCCTCATTGGTAGACTCACCCACCAAACCCAGACCCAGGT
1 CGCCCTCATTGGTAGACTCACCCACCAAACCCAGACCCAGGT
42522 CG
1 CG
42524 AATCCGGATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.42, G:0.17, T:0.15
Consensus pattern (42 bp):
CGCCCTCATTGGTAGACTCACCCACCAAACCCAGACCCAGGT
Found at i:43707 original size:24 final size:23
Alignment explanation
Indices: 43670--43714 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
43660 TTTAGTGAGA
43670 GATAAAGATAAAAGATTGAGTTTG
1 GATAAAGATAAAAGA-TGAGTTTG
43694 GATAAAGA-ACAAAGATGAGTT
1 GATAAAGATA-AAAGATGAGTT
43715 GAAGAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.24
Consensus pattern (23 bp):
GATAAAGATAAAAGATGAGTTTG
Found at i:48086 original size:20 final size:20
Alignment explanation
Indices: 48045--48087 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
48035 CTCTCACAAG
* *
48045 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
48065 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
48085 TTT
1 TTT
48088 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:50444 original size:18 final size:19
Alignment explanation
Indices: 50421--50459 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
50411 TTCAAGTCAA
*
50421 AATGAACCCAT-TAAGCAC
1 AATGAACACATATAAGCAC
50439 AATGAACACATATAAGCAC
1 AATGAACACATATAAGCAC
50458 AA
1 AA
50460 AAGATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (19 bp):
AATGAACACATATAAGCAC
Found at i:53643 original size:20 final size:20
Alignment explanation
Indices: 53602--53644 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
53592 CTCTCACAAG
* *
53602 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
53622 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
53642 TTT
1 TTT
53645 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:75741 original size:28 final size:28
Alignment explanation
Indices: 75708--75778 Score: 133
Period size: 28 Copynumber: 2.5 Consensus size: 28
75698 GTAGAAACAT
75708 AACTATACTTATTAGCATCCTTAAAAAA
1 AACTATACTTATTAGCATCCTTAAAAAA
*
75736 AACTATACTTATTAGCATCCTTGAAAAA
1 AACTATACTTATTAGCATCCTTAAAAAA
75764 AACTATACTTATTAG
1 AACTATACTTATTAG
75779 TAAACCGATC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.34
Consensus pattern (28 bp):
AACTATACTTATTAGCATCCTTAAAAAA
Found at i:98720 original size:41 final size:40
Alignment explanation
Indices: 98641--98724 Score: 91
Period size: 41 Copynumber: 2.1 Consensus size: 40
98631 CTTTTCCTTC
* * * *
98641 TTTTTCTTTTCTTTGCTTTTCTTTTTAGCTCTTCTCTTTCT
1 TTTTTCTTTTCTTTCCTTCTCTTTTTAGCTCATATCTTT-T
98682 TTTTTCTTCTTC-TTCCTTCTCTTCTTTAGCT-ATATCTTTT
1 TTTTTCTT-TTCTTTCCTTCTCTT-TTTAGCTCATATCTTTT
98722 TTT
1 TTT
98725 ATGTGAAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
40 4 0.11
41 23 0.62
42 10 0.27
ACGTcount: A:0.05, C:0.23, G:0.04, T:0.69
Consensus pattern (40 bp):
TTTTTCTTTTCTTTCCTTCTCTTTTTAGCTCATATCTTTT
Found at i:107305 original size:42 final size:42
Alignment explanation
Indices: 107246--107332 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
107236 CAATTCATGG
107246 GCACTAGCTACTCGTTTAAGCCCAGTCTAGATTGATTAATGT
1 GCACTAGCTACTCGTTTAAGCCCAGTCTAGATTGATTAATGT
107288 GCACTAGCTACTCGTTTAAGCCCAGTCTAGATTGATTAATGT
1 GCACTAGCTACTCGTTTAAGCCCAGTCTAGATTGATTAATGT
107330 GCA
1 GCA
107333 ATTACCACTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (42 bp):
GCACTAGCTACTCGTTTAAGCCCAGTCTAGATTGATTAATGT
Found at i:107317 original size:23 final size:23
Alignment explanation
Indices: 107249--107317 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 23
107239 TTCATGGGCA
107249 CTAGCTACTCGTTTAAGCCCAGT
1 CTAGCTACTCGTTTAAGCCCAGT
* * **
107272 CTAG--A-TTGATTAATGTGCA--
1 CTAGCTACTCGTTTAA-GCCCAGT
107291 CTAGCTACTCGTTTAAGCCCAGT
1 CTAGCTACTCGTTTAAGCCCAGT
107314 CTAG
1 CTAG
107318 ATTGATTAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 4 0.12
20 6 0.19
21 8 0.25
22 6 0.19
23 8 0.25
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (23 bp):
CTAGCTACTCGTTTAAGCCCAGT
Found at i:109216 original size:40 final size:40
Alignment explanation
Indices: 109161--109242 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
109151 CCTTCCTTTT
*
109161 ATGAAAAAAATTGAGATAAGATTTGTCCACGTAACAATGG
1 ATGAAAAAAATTGAGATAAGATCTGTCCACGTAACAATGG
* *
109201 ATGAAAAATATTGAGATAAGATCTGTCCTCGTAACAATGG
1 ATGAAAAAAATTGAGATAAGATCTGTCCACGTAACAATGG
109241 AT
1 AT
109243 CAGGCAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.27
Consensus pattern (40 bp):
ATGAAAAAAATTGAGATAAGATCTGTCCACGTAACAATGG
Found at i:112170 original size:19 final size:20
Alignment explanation
Indices: 112135--112175 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
112125 AAAAAGAATC
112135 TTTGTAATATATGTGTGTGTT
1 TTTGTAATATA-GTGTGTGTT
112156 TTTGTAATATA-TGTGTGTT
1 TTTGTAATATAGTGTGTGTT
112175 T
1 T
112176 AATAAGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.59
Consensus pattern (20 bp):
TTTGTAATATAGTGTGTGTT
Found at i:112762 original size:131 final size:131
Alignment explanation
Indices: 112582--112835 Score: 354
Period size: 131 Copynumber: 1.9 Consensus size: 131
112572 TCATTTATCC
* * * *
112582 AAATTTTAATATATCTAAGTTTTTTTAATTAAATTAGTAAAATGATAAAAA-TAAATTAAG-TAT
1 AAATTCTAATATATATAAG-TTTTTTAATTAAAATAATAAAATGATAAAAATTAAATT--GTTAT
* *
112645 AAGGATATAAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGTATAT
63 AAAGATATAAGATTTAAGTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGTATAT
112710 TTAAA
127 TTAAA
112715 AAATTCTAATATATATAAG-TTTTTAATTAAAATAATAAAAT-AGTAAAAATTAAATTGTTATAA
1 AAATTCTAATATATATAAGTTTTTTAATTAAAATAATAAAATGA-TAAAAATTAAATTGTTATAA
* * *
112778 AGATATTAGATTTAAGTAAATACAAATAGATTTTTTAGTTGAGTAAAATTATAAAAGT
65 AGATATAAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGT
112836 TTAAACAATG
Statistics
Matches: 109, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
130 37 0.34
131 49 0.45
132 6 0.06
133 17 0.16
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.39
Consensus pattern (131 bp):
AAATTCTAATATATATAAGTTTTTTAATTAAAATAATAAAATGATAAAAATTAAATTGTTATAAA
GATATAAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGTATATTTAA
A
Found at i:117057 original size:9 final size:8
Alignment explanation
Indices: 117028--117055 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
117018 TTTATTGAAA
117028 TTTTGTTT
1 TTTTGTTT
117036 TTTTGTTT
1 TTTTGTTT
117044 TTTTGTTT
1 TTTTGTTT
117052 TTTT
1 TTTT
117056 TGATTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTGTTT
Found at i:130733 original size:20 final size:20
Alignment explanation
Indices: 130704--130741 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
130694 ATTAAAGGGC
*
130704 TTATTTCAGTTTAAGCAGGT
1 TTATTCCAGTTTAAGCAGGT
130724 TTATTCCAGTTTAAGCAG
1 TTATTCCAGTTTAAGCAG
130742 ATTTTAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (20 bp):
TTATTCCAGTTTAAGCAGGT
Found at i:136337 original size:21 final size:19
Alignment explanation
Indices: 136311--136368 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
136301 GCTGCTTTAA
*
136311 TAATCTCATTTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
136332 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
136351 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
136369 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Done.