Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019135.1 Corchorus olitorius cultivar O-4 contig19168, 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: 9176
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:1334 original size:22 final size:22
Alignment explanation
Indices: 1307--1349 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1297 ATATATATAT
1307 GCCTGTAATTAGTACATAATAA
1 GCCTGTAATTAGTACATAATAA
1329 GCCTGTAATTAGTACATAATA
1 GCCTGTAATTAGTACATAATA
1350 TATTACTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (22 bp):
GCCTGTAATTAGTACATAATAA
Found at i:3121 original size:327 final size:326
Alignment explanation
Indices: 2250--3363 Score: 1183
Period size: 335 Copynumber: 3.3 Consensus size: 326
2240 TTACCTAAAT
* *
2250 TTTTTGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAATATTGAAAGGTTTTTCACG
1 TTTTTGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGG-CTTTCACG
* * * *
2315 CTTCTAATATCGGTTTTCCTATTTTTTCCGAATTAATTTCTAGTTAAATCGAAACATGATTCAGA
65 CTTCTAATATCGTTTTTCCTATTTTTTCC-AATTAATTTCTAATTAAATCAAAATATGATTCAGA
* * *
2380 TGCTCGTAAAAACAAATCCTTAAATTCAATCTGGTTGAGATTTGGTTAGATGGATATAGATATTT
129 TGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTT
* *
2445 CAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCCGGGACCCCAAAACGCGTTTTTAGTCA
194 CAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGG--CCCAAAACGCGTTTTTAGCCA
* *
2510 AAAACTGTGATGATTAGTATACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAAACATTTCT
257 AAAACTGTGATGA-TAGTACACGATTTCGACTAAAATTTTGTAAAAATTGACACGAAACATTTCT
2575 CCTCAA
321 CCTCAA
* * * *
2581 TTTCTGGCCACCATATTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAAGGCTTCTCAC
1 TTT-TTGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTT-TCAC
* * * * *
2646 GCTTCTAATATTGTTTTTTTTTCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAACT-GGAT
64 GCTTCTAATATCG---TTTTTCCTA-TTTTTTCCAATTAATTTCTAATTAAATC-AAAATATGAT
* * *
2710 TGAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTCGTTAGATAAATATAGA
124 TCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
* * * *
2775 TATTCCAATGAGTCTTGGCGGCAAAAATCATGCAAAACTGAGCCGGG-CCAGAACGCGTTTTTAG
189 TATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCAAAACGCGTTTTTAG
* * *
2839 CCAAACA-TCGTGAT-A-ACGTACATGATTTCGACTAAAATTTTGTAAAAATTGACCCGGAAGA-
254 CCAAAAACT-GTGATGATA-GTACACGATTTCGACTAAAATTTTGTAAAAATTGACAC-GAA-AC
2900 ATTT-TCCTCAA
315 ATTTCTCCTCAA
* ** *
2911 TTTTTGACCACGATACTCATAAAAAATATATAATTCAACACTGAAAAGATTGAAAGGCTATTCAT
1 TTTTTG-CCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCT-TTCAC
* * *
2976 GCTTCTAATATCGTTTTTCCTATTTTTTCCATATTAATTCCTAATTGAATCAAAATATGATTCAT
64 GCTTCTAATATCGTTTTTCCTATTTTTTCCA-ATTAATTTCTAATTAAATCAAAATATGATTCAG
* * *
3041 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTAAGATTTGGTTAGATGAATATAGATATT
128 ATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATT
* * ** **
3106 TCAATGAGACTTGGCGTCAAAAATCGTGCAAAACTGAGGCAAGGCTCCGGAACGCGTTTTTA-CT
193 TCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGA-GCCGGGC-CCAAAACGCGTTTTTAGC-
* * * * * * * *
3170 TTTTATTAAAAAACCGTGATGGTTAATATACGATTTC-AGCTAAAATGTTGCAAAAATTGACCCG
255 -------CAAAAACTGTGAT-GATAGTACACGATTTCGA-CTAAAATTTTGTAAAAATTGACACG
*
3234 AGAA-ATATCTCCTCAA
311 A-AACATTTCTCCTCAA
* * * * * * *
3250 TTTTGGGTCACAATACTAATAAAAAATATATAACTCAATGCCAAAAAGACTG-AAGGACTTTTCA
1 TTTT-TGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGG-C-TTTCA
* * * *
3314 TGCTTCTAATATTGCTTTTCCTACCTTTTTCCGAATTGAA--TCTAATTAAA
63 CGCTTCTAATATCGTTTTTCCTA-TTTTTTCC-AATT-AATTTCTAATTAAA
3364 AAAATTATAT
Statistics
Matches: 658, Mismatches: 86, Indels: 70
0.81 0.11 0.09
Matches are distributed among these distances:
326 12 0.02
327 123 0.19
328 4 0.01
329 4 0.01
330 120 0.18
331 15 0.02
332 91 0.14
335 131 0.20
336 9 0.01
337 9 0.01
338 11 0.02
339 113 0.17
340 13 0.02
341 3 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (326 bp):
TTTTTGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTCACGC
TTCTAATATCGTTTTTCCTATTTTTTCCAATTAATTTCTAATTAAATCAAAATATGATTCAGATG
CTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCA
ATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCAAAACGCGTTTTTAGCCAAAAA
CTGTGATGATAGTACACGATTTCGACTAAAATTTTGTAAAAATTGACACGAAACATTTCTCCTCA
A
Found at i:4023 original size:27 final size:26
Alignment explanation
Indices: 3969--4029 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
3959 CTAAATTTTA
3969 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAAT-ATTAAAAT
3997 ATTATTTAATAATGGCAAT-TTAGAAAT
1 ATTATTTAATAATGG-AATATTA-AAAT
4024 A-TATTT
1 ATTATTT
4030 GAAAAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 16 0.52
28 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
ATTATTTAATAATGGAATATTAAAAT
Found at i:4454 original size:123 final size:127
Alignment explanation
Indices: 4315--4569 Score: 401
Period size: 131 Copynumber: 2.0 Consensus size: 127
4305 CATTGTTTAA
*
4315 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCGAATAT-CT-T-TA-
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCGAATATCCTATCTAT
4376 TAATTTTTACCATTTTACTACTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TAATTTTTACCATTTTACTACTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
4438 ACTTTTACAGTTTTACTCAAGTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTAATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCGAATATCCT-AT--C
* *
4503 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
63 TA-TTAATTTTTACCATTTTACTACTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
4568 T
127 T
4569 A
1 A
4570 TCTCTTAAAT
Statistics
Matches: 119, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
123 53 0.45
124 2 0.02
126 1 0.01
129 2 0.02
131 61 0.51
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (127 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCGAATATCCTATCTAT
TAATTTTTACCATTTTACTACTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:5166 original size:20 final size:22
Alignment explanation
Indices: 5119--5166 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
5109 ATGGTTAAAA
*
5119 TTATAACAATATGGATTTTATT
1 TTATAACAATATGAATTTTATT
**
5141 GAATAA-AATAT-AATTTTATT
1 TTATAACAATATGAATTTTATT
5161 TTATAA
1 TTATAA
5167 TTTTCTTGGG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 12 0.57
21 5 0.24
22 4 0.19
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (22 bp):
TTATAACAATATGAATTTTATT
Found at i:5217 original size:15 final size:16
Alignment explanation
Indices: 5177--5217 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5167 TTTTCTTGGG
*
5177 TCATTCGGGTTTTGAC
1 TCATTCGGGTTTAGAC
5193 TCA-TCTGGGTTTAGA-
1 TCATTC-GGGTTTAGAC
5208 TCATTCGGGT
1 TCATTCGGGT
5218 ATGCTGGGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.41
Consensus pattern (16 bp):
TCATTCGGGTTTAGAC
Found at i:5479 original size:21 final size:22
Alignment explanation
Indices: 5423--5486 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
5413 ACTATAGTAT
* * *
5423 CAAAAAATTATAGGGAGATTAA
1 CAAAACATCATAGGGAGGTTAA
* *
5445 CAAAATATCATAGGGAGGTTAT
1 CAAAACATCATAGGGAGGTTAA
5467 CAAAACA-CATAGGGAGGTTA
1 CAAAACATCATAGGGAGGTTA
5487 CATAATTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 13 0.35
22 24 0.65
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.22
Consensus pattern (22 bp):
CAAAACATCATAGGGAGGTTAA
Found at i:5498 original size:21 final size:20
Alignment explanation
Indices: 5432--5506 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 20
5422 TCAAAAAATT
*
5432 ATAGGGAGATTAACAAAATATC
1 ATAGGGAGGTT-AC-AAATATC
*
5454 ATAGGGAGGTTATCAAA-ACAC
1 ATAGGGAGGTTA-CAAATA-TC
*
5475 ATAGGGAGGTTACATAATTTC
1 ATAGGGAGGTTACA-AATATC
*
5496 ATAGGAAGGTT
1 ATAGGGAGGTT
5507 TATTAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
20 3 0.07
21 30 0.68
22 11 0.25
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.25
Consensus pattern (20 bp):
ATAGGGAGGTTACAAATATC
Found at i:5528 original size:23 final size:22
Alignment explanation
Indices: 5445--5630 Score: 118
Period size: 22 Copynumber: 8.5 Consensus size: 22
5435 GGGAGATTAA
* *
5445 CAAAATATCATAGGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
** *
5467 CAAAA-CACATAGGGAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
*
5487 CATAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
* **
5510 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
5532 CAAAGTTTCATATGG-AGTTTAT
1 CAAAATTTCATA-GGAAGGTTAT
* *
5554 CACAATTTAATAGGTAA--TTAT
1 CAAAATTTCATAGG-AAGGTTAT
* *
5575 CAGAATTTCATA--ACGTGATTAT
1 CAAAATTTCATAGGAAG-G-TTAT
*
5597 CAAAATTTAATAGGATA-GTTAT
1 CAAAATTTCATAGGA-AGGTTAT
5619 CAAAATTTCATA
1 CAAAATTTCATA
5631 AAAATATTCA
Statistics
Matches: 127, Mismatches: 24, Indels: 26
0.72 0.14 0.15
Matches are distributed among these distances:
18 1 0.01
20 4 0.03
21 38 0.30
22 66 0.52
23 17 0.13
24 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:5584 original size:43 final size:43
Alignment explanation
Indices: 5528--5631 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
5518 CATAGTTAGG
** * *
5528 TTATCAAAGTTTCATATGGAGTTTATCACAATTTAATAGG-TAA
1 TTATCAAA-TTTCATAACGAGATTATCAAAATTTAATAGGATAA
* *
5571 TTATCAGAATTTCATAACGTGATTATCAAAATTTAATAGGATAG
1 TTATCA-AATTTCATAACGAGATTATCAAAATTTAATAGGATAA
5615 TTATCAAAATTTCATAA
1 TTATC-AAATTTCATAA
5632 AAATATTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
43 32 0.62
44 19 0.37
45 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (43 bp):
TTATCAAATTTCATAACGAGATTATCAAAATTTAATAGGATAA
Found at i:6124 original size:58 final size:58
Alignment explanation
Indices: 6034--6152 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
6024 TGAGTATTGT
6034 CTAGAATTTTATTTTAAGAAAAAAAGAAAGAAACAATGAGTTCTAGGTGAAACTTATA
1 CTAGAATTTTATTTTAAGAAAAAAAGAAAGAAACAATGAGTTCTAGGTGAAACTTATA
6092 CTAGAATTTTATTTTAAGAAAAAAAGAAAGAAACAATGAGTTCTAGGTGAAACTTATA
1 CTAGAATTTTATTTTAAGAAAAAAAGAAAGAAACAATGAGTTCTAGGTGAAACTTATA
6150 CTA
1 CTA
6153 TGAAAGAGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (58 bp):
CTAGAATTTTATTTTAAGAAAAAAAGAAAGAAACAATGAGTTCTAGGTGAAACTTATA
Found at i:6165 original size:58 final size:57
Alignment explanation
Indices: 6044--6165 Score: 192
Period size: 58 Copynumber: 2.1 Consensus size: 57
6034 CTAGAATTTT
**
6044 ATTTTAAGAAAAAAAGAAAGAAACAATGAGTTCTAGGTGAAACTTATACTAGAATTTT
1 ATTTTAAGAAAAAAAGAAAGAAACAATGAGTTCTAGGTGAAACTTATACTAGAA-TAG
6102 ATTTTAAGAAAAAAAGAAAGAAACAATGAGTTCTAGGTGAAACTTATACTATGAA-AG
1 ATTTTAAGAAAAAAAGAAAGAAACAATGAGTTCTAGGTGAAACTTATACTA-GAATAG
6159 AGTTTTA
1 A-TTTTA
6166 TATATATATA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
57 1 0.02
58 56 0.93
59 3 0.05
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (57 bp):
ATTTTAAGAAAAAAAGAAAGAAACAATGAGTTCTAGGTGAAACTTATACTAGAATAG
Found at i:6248 original size:2 final size:2
Alignment explanation
Indices: 6241--6265 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6231 GATCGTAGCA
6241 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6266 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7406 original size:6 final size:6
Alignment explanation
Indices: 7395--7422 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
7385 TTTGGAAAGC
7395 ATTGTA ATTGTA ATTGTA ATTGTA ATTG
1 ATTGTA ATTGTA ATTGTA ATTGTA ATTG
7423 ACTAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (6 bp):
ATTGTA
Found at i:8046 original size:30 final size:30
Alignment explanation
Indices: 8010--8076 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
8000 AAAGAGGCTG
8010 CATACTTGTTTTTTGTTTCATTAAAAAGCA
1 CATACTTGTTTTTTGTTTCATTAAAAAGCA
8040 CATACTTGTTTTTTGTTTCATTAAAAAGCA
1 CATACTTGTTTTTTGTTTCATTAAAAAGCA
8070 CATACTT
1 CATACTT
8077 TCACCCTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (30 bp):
CATACTTGTTTTTTGTTTCATTAAAAAGCA
Done.