Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011414.1 Corchorus capsularis cultivar CVL-1 contig11435, 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: 22727
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Found at i:1461 original size:3 final size:3
Alignment explanation
Indices: 1453--1498 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
1443 CTCTCTTCCC
* *
1453 ACA ACA ACA AAA ACA AAA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1499 GAACGAACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:2448 original size:32 final size:34
Alignment explanation
Indices: 2378--2457 Score: 119
Period size: 32 Copynumber: 2.4 Consensus size: 34
2368 AAATCATTCT
*
2378 TTTGTCCATATATAGGTCTTTTCCTTTTTGCCAGAA
1 TTTGTCCATATATAGGTC-TTT-CTTTTGGCCAGAA
2414 TTTGTCCATATATAGGTC-TT-TTTTGGCCAGAA
1 TTTGTCCATATATAGGTCTTTCTTTTGGCCAGAA
2446 TTTGTCCATATA
1 TTTGTCCATATA
2458 GGTCAACAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
32 23 0.53
34 2 0.05
36 18 0.42
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.46
Consensus pattern (34 bp):
TTTGTCCATATATAGGTCTTTCTTTTGGCCAGAA
Found at i:2821 original size:5 final size:5
Alignment explanation
Indices: 2811--2842 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
2801 TTATTAGTCC
2811 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
2843 AGCTTATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:5352 original size:15 final size:15
Alignment explanation
Indices: 5332--5361 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5322 TTTCAAGGTT
*
5332 TTAGAAGATTTGAAG
1 TTAGAAAATTTGAAG
5347 TTAGAAAATTTGAAG
1 TTAGAAAATTTGAAG
5362 AAAATGAAAT
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:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
TTAGAAAATTTGAAG
Found at i:5423 original size:60 final size:61
Alignment explanation
Indices: 5313--5436 Score: 187
Period size: 60 Copynumber: 2.0 Consensus size: 61
5303 TGAAAACTTG
* *
5313 AGGTTTTAGTTTCAAGGTTTTAGAAGATTTGAAGTTAGAAAATTTGAAGAAAATGAAATAA
1 AGGTTTTAGTTTCAAGGTTTTACAAGATTTGAAGTTAGAAAATTTAAAGAAAATGAAATAA
* * * *
5374 AGGTTTTAGTTTGAAGG-TTTACAGGATTTGAAGTTAGAAAGTTTAAAGAAAATGAAGTAA
1 AGGTTTTAGTTTCAAGGTTTTACAAGATTTGAAGTTAGAAAATTTAAAGAAAATGAAATAA
5434 AGG
1 AGG
5437 GCAATAGGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 41 0.72
61 16 0.28
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (61 bp):
AGGTTTTAGTTTCAAGGTTTTACAAGATTTGAAGTTAGAAAATTTAAAGAAAATGAAATAA
Found at i:6209 original size:21 final size:21
Alignment explanation
Indices: 6167--6209 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6157 CCGACTGAAA
**
6167 TCGGTTTCGGTCGGTTGTCAG
1 TCGGTTTCGGTCGGTTAACAG
* *
6188 TCGGTTTCGGTTGTTTAACAG
1 TCGGTTTCGGTCGGTTAACAG
6209 T
1 T
6210 TGATTTTAGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.09, C:0.16, G:0.33, T:0.42
Consensus pattern (21 bp):
TCGGTTTCGGTCGGTTAACAG
Found at i:8917 original size:21 final size:21
Alignment explanation
Indices: 8891--8935 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8881 AGCAAAGGGG
*
8891 TTTGCTAAAGACCGCCCCCCT
1 TTTGCTAAACACCGCCCCCCT
* *
8912 TTTGCTAAACACCGCTCTCCT
1 TTTGCTAAACACCGCCCCCCT
8933 TTT
1 TTT
8936 TATAATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.38, G:0.11, T:0.33
Consensus pattern (21 bp):
TTTGCTAAACACCGCCCCCCT
Found at i:9533 original size:23 final size:22
Alignment explanation
Indices: 9489--9533 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
9479 TTAAATTTTT
*
9489 TTTAAAAATAAATTTTGGAAAA
1 TTTAAAAATAAATTTTGCAAAA
* *
9511 TTTAAAACTTAAATTTTTCAAAA
1 TTTAAAA-ATAAATTTTGCAAAA
9534 CATATTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TTTAAAAATAAATTTTGCAAAA
Found at i:9556 original size:15 final size:14
Alignment explanation
Indices: 9523--9561 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
9513 TAAAACTTAA
*
9523 ATTTTTCAAAACAT
1 ATTTTTTAAAACAT
9537 ATTTTTTAAAACAT
1 ATTTTTTAAAACAT
9551 ATTTTTTAAAA
1 ATTTTTTAAAA
9562 TTTTAATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTTTTAAAACAT
Found at i:11191 original size:21 final size:20
Alignment explanation
Indices: 11150--11191 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
11140 GCATGTAATT
*
11150 AACTAATTCATGAACCCAAA
1 AACTAATTCATGAACCAAAA
*
11170 AACTAATTCATTGAACTAAAA
1 AACTAATTCA-TGAACCAAAA
11191 A
1 A
11192 TTTATTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (20 bp):
AACTAATTCATGAACCAAAA
Found at i:11326 original size:14 final size:14
Alignment explanation
Indices: 11307--11365 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 14
11297 AGGTCAAAGA
11307 TTATATAAAATAAT
1 TTATATAAAATAAT
11321 TTATAT---ATAAT
1 TTATATAAAATAAT
** *
11332 TTATATAATCTTA-
1 TTATATAAAATAAT
11345 TTA-ATAAAATAAT
1 TTATATAAAATAAT
11358 TTATATAA
1 TTATATAA
11366 TCTTATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
11 11 0.31
12 6 0.17
13 6 0.17
14 12 0.34
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATATAAAATAAT
Found at i:11376 original size:35 final size:38
Alignment explanation
Indices: 11306--11382 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 38
11296 CAGGTCAAAG
*
11306 ATTATATAAAATAATTTATATATAATTTATATAATCTT
1 ATTATATAAAATAATTTATATATAATTTATATAATCAT
11344 ATTA-ATAAAATAA-TT-TATATAATCTTAT-TAATCAT
1 ATTATATAAAATAATTTATATATAAT-TTATATAATCAT
11379 ATTA
1 ATTA
11383 GTCCAATCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
35 18 0.49
36 6 0.16
37 9 0.24
38 4 0.11
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (38 bp):
ATTATATAAAATAATTTATATATAATTTATATAATCAT
Found at i:11831 original size:2 final size:2
Alignment explanation
Indices: 11824--11872 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
11814 ACCGACCGAC
* *
11824 TA TA TA TA TA TA T- TA -A TA AA TA TA TT TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11863 TA TA TA TA TA
1 TA TA TA TA TA
11873 CTATTCATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18459 original size:29 final size:29
Alignment explanation
Indices: 18392--18459 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
18382 GAAGTATTTT
*
18392 TTAATTAATTATGTTTTTAGGATAATTAA
1 TTAATGAATTATGTTTTTAGGATAATTAA
* * *
18421 TTAATTAATTATG-TTTTAGGGTTAATTAT
1 TTAATGAATTATGTTTTTA-GGATAATTAA
*
18450 TTTATGAATT
1 TTAATGAATT
18460 TAAAATACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (29 bp):
TTAATGAATTATGTTTTTAGGATAATTAA
Found at i:21095 original size:24 final size:26
Alignment explanation
Indices: 21059--21108 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
21049 AGGTTACACC
21059 TTCATGTGGTGAAGAA-AACAACAAA
1 TTCATGTGGTGAAGAAGAACAACAAA
*
21084 TTCATG-GGTGAAGAAGAAGAACAAA
1 TTCATGTGGTGAAGAAGAACAACAAA
21109 ATGAGTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.48, C:0.10, G:0.24, T:0.18
Consensus pattern (26 bp):
TTCATGTGGTGAAGAAGAACAACAAA
Done.