Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005607.1 Corchorus capsularis cultivar CVL-1 contig05625, 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: 7327
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:509 original size:13 final size:12
Alignment explanation
Indices: 485--535 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
475 AATTTCCCAT
485 AAAAAA-AAAGA
1 AAAAAAGAAAGA
496 AAAAAAGAAGAGA
1 AAAAAAGAA-AGA
* *
509 AAAAGAGAAAAA
1 AAAAAAGAAAGA
521 AGAAAAAGAGAAGA
1 A-AAAAAGA-AAGA
535 A
1 A
536 GCAGTGATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 6 0.19
12 5 0.16
13 17 0.53
14 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:643 original size:46 final size:45
Alignment explanation
Indices: 542--646 Score: 167
Period size: 45 Copynumber: 2.3 Consensus size: 45
532 AGAAGCAGTG
*
542 ATGG-TTTTCAAAAAGAGTCATGGATTTCAAAAGGTGTTAATAAA
1 ATGGTTTTTCAAAAAGAGTCATGGATTTCAAAAAGTGTTAATAAA
* *
586 ATGGTTTTTCAAAAAGAGTCATGGTTTTCAAAAAGTGTTAATATA
1 ATGGTTTTTCAAAAAGAGTCATGGATTTCAAAAAGTGTTAATAAA
631 ATGGTTTTTTCAAAAA
1 ATGG-TTTTTCAAAAA
647 AAAATAGTCA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 4 0.07
45 41 0.73
46 11 0.20
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (45 bp):
ATGGTTTTTCAAAAAGAGTCATGGATTTCAAAAAGTGTTAATAAA
Found at i:1072 original size:27 final size:26
Alignment explanation
Indices: 1042--1095 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1032 AAAGAGGAGG
*
1042 AAAAAGTGAAAATTGAAAGTGAAAGGA
1 AAAAAGTGAAAA-TAAAAGTGAAAGGA
* *
1069 AAAAATTGAAAATAAAAGTGGAAGGA
1 AAAAAGTGAAAATAAAAGTGAAAGGA
1095 A
1 A
1096 GAGTGAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (26 bp):
AAAAAGTGAAAATAAAAGTGAAAGGA
Found at i:1422 original size:26 final size:27
Alignment explanation
Indices: 1385--1440 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
1375 AGGTGCATGG
1385 AAGAAAAGAAGAAAAAAAGAA-AAGAA
1 AAGAAAAGAAGAAAAAAAGAAGAAGAA
*
1411 AAGAGAAA-AAGAAAAAGAGAATGAAGAA
1 AAGA-AAAGAAGAAAAAAAGAA-GAAGAA
1439 AA
1 AA
1441 AGGCTCGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 16 0.62
27 3 0.12
28 7 0.27
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (27 bp):
AAGAAAAGAAGAAAAAAAGAAGAAGAA
Found at i:1442 original size:21 final size:21
Alignment explanation
Indices: 1385--1442 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1375 AGGTGCATGG
*
1385 AAGAAAAGAAGAAAAAAAGAA
1 AAGAAAAGAAGAAAAAGAGAA
1406 AAGAAAAG-AGAAAAAGA-AA
1 AAGAAAAGAAGAAAAAGAGAA
*
1425 AAGAGAATGAAGAAAAAG
1 AAGA-AAAGAAGAAAAAG
1443 GCTCGAGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.18
20 11 0.33
21 16 0.48
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (21 bp):
AAGAAAAGAAGAAAAAGAGAA
Found at i:2052 original size:28 final size:29
Alignment explanation
Indices: 1998--2053 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
1988 AGTAAAAGAG
1998 TCTTTCAAAGCATACTATTCAAGTCAGAA
1 TCTTTCAAAGCATACTATTCAAGTCAGAA
*
2027 TCTTTCAAAGCA-AGTATTCAAGTCAGA
1 TCTTTCAAAGCATACTATTCAAGTCAGA
2054 TCTAGGGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (29 bp):
TCTTTCAAAGCATACTATTCAAGTCAGAA
Found at i:2428 original size:69 final size:69
Alignment explanation
Indices: 2282--2429 Score: 190
Period size: 69 Copynumber: 2.1 Consensus size: 69
2272 CGAATGCTCC
** * *
2282 GGCTTTTCCACAAACCAAACTCGTTTCCACACGAGTCAGTTTAGCCTTGGTTCCGTCCAAGCATT
1 GGCTTTTCCACAAACCAAACTCGTTTCCACACGAGTCAGTCCAGCCTTGGTTCCATCCAAGCATA
*
2347 CAGG
66 CAGA
* * * *
2351 GGCATTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAGGCA-
1 GGCTTTTCCACAAACCAAACTCGTTTCCACACGAGTCAG-TCCAGCCTTGGTTCCATCCAAGCAT
*
2415 AGAGA
65 ACAGA
2420 GGCTTTTCCA
1 GGCTTTTCCA
2430 TAAGTGATCG
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
69 48 0.72
70 19 0.28
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (69 bp):
GGCTTTTCCACAAACCAAACTCGTTTCCACACGAGTCAGTCCAGCCTTGGTTCCATCCAAGCATA
CAGA
Found at i:2675 original size:11 final size:11
Alignment explanation
Indices: 2659--2690 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2649 GAAGTTTGTG
2659 TTTGAAGATTA
1 TTTGAAGATTA
*
2670 TTTGAAGATAA
1 TTTGAAGATTA
2681 TTTGAAGATT
1 TTTGAAGATT
2691 TGAAAACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:6587 original size:12 final size:12
Alignment explanation
Indices: 6566--6607 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
6556 TTTTCTAACA
6566 TTTTTA-TTTTC
1 TTTTTAGTTTTC
6577 TTTTTAGTTTTC
1 TTTTTAGTTTTC
* **
6589 TTTCTCTTTTTC
1 TTTTTAGTTTTC
6601 TTTTTAG
1 TTTTTAG
6608 GATTTCAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.76
Consensus pattern (12 bp):
TTTTTAGTTTTC
Found at i:7061 original size:21 final size:21
Alignment explanation
Indices: 7031--7071 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7021 TATGATTCAT
7031 ATGCTATGAA-TGCTATGATTG
1 ATGCTATGAATTGCT-TGATTG
*
7052 ATGCTTTGAATTGCTTGATT
1 ATGCTATGAATTGCTTGATT
7072 TGCTTGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (21 bp):
ATGCTATGAATTGCTTGATTG
Done.