Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021218.1 Corchorus olitorius cultivar O-4 contig21251, 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: 10134
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:377 original size:201 final size:201
Alignment explanation
Indices: 2--641 Score: 912
Period size: 201 Copynumber: 3.2 Consensus size: 201
1 T
2 GGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATT-AA-ATATTTAATTAA
1 GGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTAATTAA
* * * * * * * *
65 TTATGAAATGGGGGTATATGTCAACCTCTTAACCCACTTACGGAGTCTAAAATTTACACTAACAT
66 TTATGAAAT-GAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAA
* * * *
130 TGAATTGTATAATAATCCTATAAGAAAAAGTATACAATACACCGTCAGTGGAGTTTAGCAGACTG
130 TGTATTGTATAATAATCCAAAAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTG
195 CACATGC
195 CACATGC
* * **
202 GGGGTTTAAGGGTTAACATGTGTCCTCTTAGGGAATATGTATTAATATTAAATATATTTTCTTAA
1 GGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTAATTAA
* *
267 TTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATAGAGTCCAAAATTTACACTGACAGT
66 TTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAAT
* * * * *
332 GTATTGTATAATAATTCAAGAAGAAGAATTATACAATAAACCGTCACTGGAGTTTAGCAGACTGC
131 GTATTGTATAATAATCCAAAAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGC
**
397 ATGTGC
196 ACATGC
* *
403 GGGGTTTAAGGGTCGACATGTGTCCCC-TAGGGGAATATATATTAATATTAAATATATTTAATTA
1 GGGGTTTAAGGGTTGACATGTGTCCCCTTA-GGGAATATGTATTAATATTAAATATATTTAATTA
* *
467 ATTATGAAATGAGGTATGTGTCAACTTCTTAACACGCTTATGGAGTCCAAAATTTGCACTGACAA
65 ATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAA
*
532 TGTATTGTATAATAATCCTAAAAAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
130 TGTATTGTATAATAATCC-AAAAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
597 G--CATGC
194 GCACATGC
* *
603 GCGAGATTTAAGGGTTGACATGTTTCCCCTTAGGGAATA
1 G-G-GGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
642 GTTTTGTATA
Statistics
Matches: 389, Mismatches: 44, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
200 53 0.14
201 244 0.63
202 90 0.23
203 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (201 bp):
GGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTAATTAA
TTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAAT
GTATTGTATAATAATCCAAAAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGC
ACATGC
Found at i:1171 original size:13 final size:13
Alignment explanation
Indices: 1155--1179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1145 AATACTAAAA
1155 TATAATAAGTTTT
1 TATAATAAGTTTT
1168 TATAATAAGTTT
1 TATAATAAGTTT
1180 AATAATAAAT
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:0.08, T:0.52
Consensus pattern (13 bp):
TATAATAAGTTTT
Found at i:2118 original size:22 final size:21
Alignment explanation
Indices: 2093--2163 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
2083 TCTAACAATA
2093 TTAATAAAGTCACTAAAAAAAC
1 TTAATAAAGTCACT-AAAAAAC
* *
2115 TTAA-AGAAGTTACTATAAAAC
1 TTAATA-AAGTCACTAAAAAAC
** * *
2136 TTAACGAGGTCACTAAAATAC
1 TTAATAAAGTCACTAAAAAAC
2157 TTAATAA
1 TTAATAA
2164 GATTAAGATT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 27 0.71
22 11 0.29
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (21 bp):
TTAATAAAGTCACTAAAAAAC
Found at i:2272 original size:21 final size:21
Alignment explanation
Indices: 2248--2433 Score: 67
Period size: 21 Copynumber: 8.6 Consensus size: 21
2238 ATGGTTCCTA
2248 AAAAACTTAATAAGGTTATTT
1 AAAAACTTAATAAGGTTATTT
* *
2269 AAAAACTTTATAA--TTAGTT
1 AAAAACTTAATAAGGTTATTT
* * * *
2288 -AAAAGTTTATAAGATTATTA
1 AAAAACTTAATAAGGTTATTT
* * * * *
2308 AAATAAATTGATTATGTTA-CT
1 AAA-AACTTAATAAGGTTATTT
* * *
2329 AAAAAGGTTTAATAAAGTTA-GT
1 AAAAA--CTTAATAAGGTTATTT
*
2351 AAAAACTTAATTATAAGGAAATATATT
1 AAAAACTT-A--ATAAGG--TTAT-TT
* ** *
2378 AAAAATCTTAATATGGTTCCTA
1 AAAAA-CTTAATAAGGTTATTT
2400 AAAAACTTAATAAGGTTATTT
1 AAAAACTTAATAAGGTTATTT
*
2421 AAAAACTTTATAA
1 AAAAACTTAATAA
2434 TTAGTTAAAA
Statistics
Matches: 120, Mismatches: 31, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
18 11 0.09
19 5 0.04
20 8 0.07
21 42 0.35
22 31 0.26
23 6 0.05
25 7 0.06
27 7 0.06
28 3 0.03
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (21 bp):
AAAAACTTAATAAGGTTATTT
Found at i:2273 original size:70 final size:70
Alignment explanation
Indices: 2199--2434 Score: 197
Period size: 70 Copynumber: 3.2 Consensus size: 70
2189 TGATTAATAA
*
2199 AAAAACTTAATAATAAGGAAATATATTAAGAACCTTAATATGGTTCCTAAAAAACTTAATAAGGT
1 AAAAACTTAATAATAAGGAAATATATTAAGAATCTTAATATGGTTCCTAAAAAACTTAATAAGGT
2264 TATTT
66 TATTT
* * * * * * *
2269 AAAAACTTTATAATTAGTTAAA-AGTTTATAAGATTATTAAAATAAATTGATTATGTTACTAAAA
1 AAAAACTTAATAATAAG-GAAATA-TAT-TAAGAATCTT--AAT--A-TG-----GTTCCTAAAA
** * *
2333 AGGTTTAATAAAGTTA-GT
53 A-ACTTAATAAGGTTATTT
* *
2351 AAAAACTTAATTATAAGGAAATATATTAAAAATCTTAATATGGTTCCTAAAAAACTTAATAAGGT
1 AAAAACTTAATAATAAGGAAATATATTAAGAATCTTAATATGGTTCCTAAAAAACTTAATAAGGT
2416 TATTT
66 TATTT
*
2421 AAAAACTTTATAAT
1 AAAAACTTAATAAT
2435 TAGTTAAAAG
Statistics
Matches: 123, Mismatches: 27, Indels: 32
0.68 0.15 0.18
Matches are distributed among these distances:
69 11 0.09
70 39 0.32
71 5 0.04
72 7 0.06
74 3 0.02
75 2 0.02
76 2 0.02
77 2 0.02
78 3 0.02
80 7 0.06
81 5 0.04
82 26 0.21
83 11 0.09
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (70 bp):
AAAAACTTAATAATAAGGAAATATATTAAGAATCTTAATATGGTTCCTAAAAAACTTAATAAGGT
TATTT
Found at i:2443 original size:19 final size:20
Alignment explanation
Indices: 2400--2443 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
2390 ATGGTTCCTA
*
2400 AAAAACTTAATAAGGTTATTT
1 AAAAACTTAATAA-GTTAGTT
*
2421 AAAAACTTTATAA-TTAGTT
1 AAAAACTTAATAAGTTAGTT
2440 AAAA
1 AAAA
2444 GTTTATAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
21 12 0.57
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (20 bp):
AAAAACTTAATAAGTTAGTT
Found at i:2513 original size:152 final size:152
Alignment explanation
Indices: 2199--2503 Score: 583
Period size: 152 Copynumber: 2.0 Consensus size: 152
2189 TGATTAATAA
*
2199 AAAAACTTAATAATAAGGAAATATATTAAGAACCTTAATATGGTTCCTAAAAAACTTAATAAGGT
1 AAAAACTTAATAATAAGGAAATATATTAAAAACCTTAATATGGTTCCTAAAAAACTTAATAAGGT
2264 TATTTAAAAACTTTATAATTAGTTAAAAGTTTATAAGATTATTAAAATAAATTGATTATGTTACT
66 TATTTAAAAACTTTATAATTAGTTAAAAGTTTATAAGATTATTAAAATAAATTGATTATGTTACT
2329 AAAAAGGTTTAATAAAGTTAGT
131 AAAAAGGTTTAATAAAGTTAGT
* *
2351 AAAAACTTAATTATAAGGAAATATATTAAAAATCTTAATATGGTTCCTAAAAAACTTAATAAGGT
1 AAAAACTTAATAATAAGGAAATATATTAAAAACCTTAATATGGTTCCTAAAAAACTTAATAAGGT
2416 TATTTAAAAACTTTATAATTAGTTAAAAGTTTATAAGATTATTAAAATAAATTGATTATGTTACT
66 TATTTAAAAACTTTATAATTAGTTAAAAGTTTATAAGATTATTAAAATAAATTGATTATGTTACT
2481 AAAAAGGTTTAATAAAGTTAGT
131 AAAAAGGTTTAATAAAGTTAGT
2503 A
1 A
2504 CAATATTAAT
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
152 150 1.00
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (152 bp):
AAAAACTTAATAATAAGGAAATATATTAAAAACCTTAATATGGTTCCTAAAAAACTTAATAAGGT
TATTTAAAAACTTTATAATTAGTTAAAAGTTTATAAGATTATTAAAATAAATTGATTATGTTACT
AAAAAGGTTTAATAAAGTTAGT
Found at i:2525 original size:20 final size:19
Alignment explanation
Indices: 2489--2530 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
2479 CTAAAAAGGT
*
2489 TTAATAAAGTTAGTACAATA
1 TTAATAAAGTTACTACAA-A
2509 TTAATAACA-TTACTACAAA
1 TTAATAA-AGTTACTACAAA
2528 TTA
1 TTA
2531 TCAAGGTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 15 0.75
21 1 0.05
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (19 bp):
TTAATAAAGTTACTACAAA
Found at i:2559 original size:19 final size:19
Alignment explanation
Indices: 2537--2585 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2527 ATTATCAAGG
* *
2537 TTACTAAAAATCTCTAAAA
1 TTACTAAAAACCTATAAAA
*
2556 TTACTGAAAAACCTATTAAA
1 TTACT-AAAAACCTATAAAA
*
2576 TTATTAAAAA
1 TTACTAAAAA
2586 AGCTTAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (19 bp):
TTACTAAAAACCTATAAAA
Found at i:6375 original size:22 final size:23
Alignment explanation
Indices: 6336--6378 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
6326 AATCCTAATC
6336 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
6359 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
6379 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:9278 original size:30 final size:31
Alignment explanation
Indices: 9244--9320 Score: 115
Period size: 30 Copynumber: 2.5 Consensus size: 31
9234 TAATGACAAA
9244 ATCAGAATTC-TCTCCTTCACAAACAAAGAG
1 ATCAGAATTCTTCTCCTTCACAAACAAAGAG
9274 ATCAGAA-TCTTCTCCTTCACAAACAAAGAG
1 ATCAGAATTCTTCTCCTTCACAAACAAAGAG
*
9304 ATCGGAA-TCTTCCTCCT
1 ATCAGAATTCTT-CTCCT
9321 CGTCATACTC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 2 0.05
30 37 0.84
31 5 0.11
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.26
Consensus pattern (31 bp):
ATCAGAATTCTTCTCCTTCACAAACAAAGAG
Found at i:10056 original size:22 final size:23
Alignment explanation
Indices: 10017--10059 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
10007 AATCCTAATC
10017 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
10040 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
10060 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Done.