Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007787.1 Corchorus capsularis cultivar CVL-1 contig07808, 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: 70407
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1114 original size:30 final size:32
Alignment explanation
Indices: 1056--1122 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 32
1046 ATTTTTTCCG
* * *
1056 ATTGTACCCTTATTTTTAAAATATATTTCT-A
1 ATTGTACCCTTATTCTAAAAACATATTTCTAA
1087 ATTGTACCCTT-TTCTAAAAACATATTTCTAA
1 ATTGTACCCTTATTCTAAAAACATATTTCTAA
1118 ATTGT
1 ATTGT
1123 CATTACTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (32 bp):
ATTGTACCCTTATTCTAAAAACATATTTCTAA
Found at i:1401 original size:22 final size:22
Alignment explanation
Indices: 1349--1578 Score: 152
Period size: 22 Copynumber: 10.5 Consensus size: 22
1339 TAAGGAGTAG
*
1349 CAAAATTTGATAGAAG-G-TTAT
1 CAAAATTTCATA-AAGTGATTAT
*
1370 C-AAATCTCATAAAGTGATTAT
1 CAAAATTTCATAAAGTGATTAT
* * *
1391 CGAAATTTCATAGAGATCGGGTTAT
1 CAAAATTTCATAAAG-T--GATTAT
1416 CAAAATTT-ATAGAAG-GATTAT
1 CAAAATTTCATA-AAGTGATTAT
** *
1437 CAAAATTTCATAGTGTTATTAT
1 CAAAATTTCATAAAGTGATTAT
*
1459 CAAAATTTC--AAAGCGAGGTTAT
1 CAAAATTTCATAAAGTGA--TTAT
* *
1481 CAAAATTACATAATGTGATTAT
1 CAAAATTTCATAAAGTGATTAT
* * * * *
1503 CAGAATTTCATAAAGGGGTCAA
1 CAAAATTTCATAAAGTGATTAT
* * *
1525 CAAAATTTTATAAAGAGGTTAT
1 CAAAATTTCATAAAGTGATTAT
1547 CAAAATTTCATAAAGATG-TTAT
1 CAAAATTTCATAAAG-TGATTAT
*
1569 CAAATTTTCA
1 CAAAATTTCA
1579 AACAAAATTT
Statistics
Matches: 162, Mismatches: 33, Indels: 27
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.02
20 12 0.07
21 20 0.12
22 103 0.64
23 2 0.01
24 8 0.05
25 14 0.09
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAAAGTGATTAT
Found at i:1771 original size:22 final size:22
Alignment explanation
Indices: 1743--2258 Score: 167
Period size: 22 Copynumber: 23.7 Consensus size: 22
1733 TCAGCGAGGA
1743 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
1765 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
1787 TTTCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
1808 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
1831 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
1853 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
1875 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
1891 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
1913 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
1936 TATCAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
* *
1959 TATCAAAATTTCATAGCGAA-AT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
1981 TATCACAATTTCATGGTG-TGAT
1 TATCAAAATTTCAT-ATGAAGGT
*
2003 TATCAAAATTTCAGAGTGTAA--T
1 TATCAAAATTTCATA-TG-AAGGT
* * *
2025 TA-CTAACAA-TTCAGATGGAGTT
1 TATC-AA-AATTTCATATGAAGGT
* * * ** *
2047 TTTTAAATTTTCATAACATGGT
1 TATCAAAATTTCATATGAAGGT
* * **
2069 TATCAACATATCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
*
2092 TATCAAAATTTCAT-TGGAAAGT
1 TATCAAAATTTCATAT-GAAGGT
*
2114 TATCAAAATTTCATATTG-AGCT
1 TATCAAAATTTCATA-TGAAGGT
* * *
2136 CT-TCAAAATTTCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * * **
2158 TAACCAAATTTTATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
2180 TA-AAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
2200 TCTCAAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
2222 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
2244 TATCAAAATTTCATA
1 TATCAAAATTTCATA
2259 ATGGGATCAT
Statistics
Matches: 367, Mismatches: 88, Indels: 78
0.69 0.17 0.15
Matches are distributed among these distances:
16 9 0.02
17 2 0.01
18 2 0.01
20 16 0.04
21 25 0.07
22 248 0.68
23 61 0.17
24 3 0.01
25 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:1940 original size:23 final size:23
Alignment explanation
Indices: 1890--1974 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
1880 AAATTTGTAG
* *
1890 TTATCAAGATTTCATAAGAAAG--
1 TTATCAAAATTTTAT-AGAAAGAT
** *
1912 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGAAAGAT
1935 TTATCAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGAAAGAT
*
1958 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
1975 CGAAATTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
21 4 0.08
22 13 0.25
23 36 0.68
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAAAGAT
Found at i:1984 original size:45 final size:45
Alignment explanation
Indices: 1890--1994 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 45
1880 AAATTTGTAG
* * * **
1890 TTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGCGAGAA
*
1935 TTATCAAAATTTTAT-AGAAAGATTTATCAAAATTTCATAGCGA-AA
1 TTATCAAAATTTCATAAGAAAG--TTATCAAAATTTCATAGCGAGAA
*
1980 TTATCACAATTTCAT
1 TTATCAAAATTTCAT
1995 GGTGTGATTA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 6 0.12
45 26 0.52
46 18 0.36
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (45 bp):
TTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGCGAGAA
Found at i:2209 original size:21 final size:20
Alignment explanation
Indices: 2162--2200 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2152 GGAGGTTAAC
*
2162 CAAATTTTATAAAAAGGTTA
1 CAAAATTTATAAAAAGGTTA
*
2182 AAAAATTTATAAAAAGGTT
1 CAAAATTTATAAAAAGGTT
2201 CTCAAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (20 bp):
CAAAATTTATAAAAAGGTTA
Found at i:3036 original size:3 final size:3
Alignment explanation
Indices: 3030--3070 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3020 TTTTTTTTTG
3030 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3071 GGAAAACAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6377 original size:1 final size:1
Alignment explanation
Indices: 6371--6395 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
6361 GTTCAAAAGT
6371 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
6396 CTTTCTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20635 original size:7 final size:7
Alignment explanation
Indices: 20623--20652 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
20613 TTGAACACAA
20623 CCAAAAT
1 CCAAAAT
20630 CCAAAAT
1 CCAAAAT
20637 CCAAAAT
1 CCAAAAT
20644 CCAAAAT
1 CCAAAAT
20651 CC
1 CC
20653 TTCCGCCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.13
Consensus pattern (7 bp):
CCAAAAT
Found at i:21091 original size:26 final size:28
Alignment explanation
Indices: 21038--21092 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
21028 TTTCTTTAGT
21038 AAGTAAATAATAATTCATATGGATACCAA
1 AAGTAAATAATAATTCATATGGA-ACCAA
21067 AAGTAAAT-ATAATTCATATGG-ACCAA
1 AAGTAAATAATAATTCATATGGAACCAA
21093 TCGGTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 5 0.19
28 13 0.50
29 8 0.31
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (28 bp):
AAGTAAATAATAATTCATATGGAACCAA
Found at i:27511 original size:83 final size:83
Alignment explanation
Indices: 27372--27539 Score: 327
Period size: 83 Copynumber: 2.0 Consensus size: 83
27362 CTGTTGCATA
27372 AAACTGCAAAATGGAACTTTGATTTACCACTACTTATAGGAGGCAAATGAAAAGGCAATAAGGAA
1 AAACTGCAAAATGGAACTTTGATTTACCACTACTTATAGGAGGCAAATGAAAAGGCAATAAGGAA
27437 TGAAATACGACTCAAATG
66 TGAAATACGACTCAAATG
27455 AAACTGCAAAATGGAACTTTGATTTACCACTACTTATAGGAGGCAAATGAAAAGGCAATAAGGAA
1 AAACTGCAAAATGGAACTTTGATTTACCACTACTTATAGGAGGCAAATGAAAAGGCAATAAGGAA
*
27520 TGAAATACGACTCGAATG
66 TGAAATACGACTCAAATG
27538 AA
1 AA
27540 CAAAAACAAG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (83 bp):
AAACTGCAAAATGGAACTTTGATTTACCACTACTTATAGGAGGCAAATGAAAAGGCAATAAGGAA
TGAAATACGACTCAAATG
Found at i:33454 original size:19 final size:20
Alignment explanation
Indices: 33419--33465 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
33409 TTATCTTTCA
33419 TGTATTCACAAAAAAAA-AT
1 TGTATTCACAAAAAAAATAT
*
33438 TGTATTCA-AATATAAAATAT
1 TGTATTCACAA-AAAAAATAT
*
33458 TGTGTTCA
1 TGTATTCA
33466 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 9 0.38
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (20 bp):
TGTATTCACAAAAAAAATAT
Found at i:33851 original size:21 final size:21
Alignment explanation
Indices: 33822--33864 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
33812 GGTCTTAGGT
* *
33822 TCAATTCTCACGGGATGTGAG
1 TCAACTCTCACGGAATGTGAG
33843 TCAACTCTCACGGAATGTGAG
1 TCAACTCTCACGGAATGTGAG
33864 T
1 T
33865 TTATTTGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
TCAACTCTCACGGAATGTGAG
Found at i:39226 original size:21 final size:21
Alignment explanation
Indices: 39202--39241 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39192 TCGAGAGTCA
39202 TTAGATCAATG-GTTCAATTCG
1 TTAGATCAATGTG-TCAATTCG
*
39223 TTAGATTAATGTGTCAATT
1 TTAGATCAATGTGTCAATT
39242 GTTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (21 bp):
TTAGATCAATGTGTCAATTCG
Found at i:40630 original size:12 final size:12
Alignment explanation
Indices: 40599--40638 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
40589 TATTTAACCA
* *
40599 TATATATCTATA
1 TATATATGTATG
40611 TATATATGTATG
1 TATATATGTATG
40623 TATATATGTATG
1 TATATATGTATG
40635 TATA
1 TATA
40639 ATAAACACGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (12 bp):
TATATATGTATG
Found at i:42524 original size:2 final size:2
Alignment explanation
Indices: 42519--42553 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
42509 AATTAGTAAT
42519 TA TA TA GTA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42554 CCATAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:42528 original size:11 final size:12
Alignment explanation
Indices: 42512--42548 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42502 TGTATATAAT
42512 TAGTAAT-TATA
1 TAGTAATATATA
42523 TAGTAATATATA
1 TAGTAATATATA
42535 TA-TATATATATA
1 TAGTA-ATATATA
42547 TA
1 TA
42549 TATATCCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (12 bp):
TAGTAATATATA
Found at i:44981 original size:7 final size:7
Alignment explanation
Indices: 44969--45003 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
44959 CATCCAAAAA
44969 CAAACTT
1 CAAACTT
44976 CAAACTT
1 CAAACTT
44983 CAAACTT
1 CAAACTT
*
44990 GAAACTT
1 CAAACTT
*
44997 GAAACTT
1 CAAACTT
45004 TTACTTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (7 bp):
CAAACTT
Found at i:45318 original size:6 final size:6
Alignment explanation
Indices: 45309--45333 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45299 AAACACAAAC
45309 AGTCTG AGTCTG AGTCTG AGTCTG A
1 AGTCTG AGTCTG AGTCTG AGTCTG A
45334 CTGACAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (6 bp):
AGTCTG
Found at i:49273 original size:6 final size:6
Alignment explanation
Indices: 49262--49286 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
49252 CAGACCAGAA
49262 TGTATC TGTATC TGTATC TGTATC T
1 TGTATC TGTATC TGTATC TGTATC T
49287 AAGTGGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTATC
Found at i:60031 original size:2 final size:2
Alignment explanation
Indices: 60024--60050 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60014 GATTGTTAAT
60024 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
60051 TTTTGCTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.