Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016236.1 Corchorus capsularis cultivar CVL-1 contig16257, 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: 24116
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Found at i:2607 original size:223 final size:223
Alignment explanation
Indices: 2219--2664 Score: 793
Period size: 223 Copynumber: 2.0 Consensus size: 223
2209 CTAATTCATT
2219 GTCATTTTCAGGCCTATCATATCAAAACCCAAATCAGGAACAACAATGCCAGCTACACAACATTA
1 GTCATTTTCAGGCCTATCATATCAAAACCCAAATCAGGAACAACAATGCCAGCTACACAACATTA
2284 ATTTTCAAAATTTCTCAATTTTCACACTGCCTACAACCAAATACTACCAAACTCCACATTACCTT
66 ATTTTCAAAATTTCTCAATTTTCACACTGCCTACAACCAAATACTACCAAACTCCACATTACCTT
2349 CGAAATGGGTATTCGGGAGGCAGACAATAAATGACCAAAAGTGGAAATTGAAGAACAAATCTGAA
131 CGAAATGGGTATTCGGGAGGCAGACAATAAATGACCAAAAGTGGAAATTGAAGAACAAATCTGAA
* *
2414 ATTCCATATATCACCACTAGAACTAAAA
196 ATTCCATATATCACCACCAAAACTAAAA
**
2442 GTCATTTTCAGGCCTATCATATCAAAATTCAAATCAGGAACAACAATGCCAGCTACACAACATTA
1 GTCATTTTCAGGCCTATCATATCAAAACCCAAATCAGGAACAACAATGCCAGCTACACAACATTA
* *
2507 ATTTTCAGAATTTCTCAATTTTCACATTGCCTACAACCAAATACTACCAAACTCCACATTACCTT
66 ATTTTCAAAATTTCTCAATTTTCACACTGCCTACAACCAAATACTACCAAACTCCACATTACCTT
* * *
2572 CGAAATGGGTATTGGGGAGGCAGGCAATAAATGACCAAAAGTGTAAATTGAAGAACAAATCTGAA
131 CGAAATGGGTATTCGGGAGGCAGACAATAAATGACCAAAAGTGGAAATTGAAGAACAAATCTGAA
* *
2637 ATTCTATATATCATCACCAAAACTAAAA
196 ATTCCATATATCACCACCAAAACTAAAA
2665 ATTGAACCAT
Statistics
Matches: 212, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
223 212 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.25
Consensus pattern (223 bp):
GTCATTTTCAGGCCTATCATATCAAAACCCAAATCAGGAACAACAATGCCAGCTACACAACATTA
ATTTTCAAAATTTCTCAATTTTCACACTGCCTACAACCAAATACTACCAAACTCCACATTACCTT
CGAAATGGGTATTCGGGAGGCAGACAATAAATGACCAAAAGTGGAAATTGAAGAACAAATCTGAA
ATTCCATATATCACCACCAAAACTAAAA
Found at i:5329 original size:26 final size:26
Alignment explanation
Indices: 5300--5355 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
5290 ACCAAAAGAC
*
5300 AACAACGCCAAAATTAGCTCAACAAA
1 AACAACACCAAAATTAGCTCAACAAA
* **
5326 AACAGCACCAACTTTAGCTCAACAAA
1 AACAACACCAAAATTAGCTCAACAAA
5352 AACA
1 AACA
5356 GACGAAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.52, C:0.29, G:0.07, T:0.12
Consensus pattern (26 bp):
AACAACACCAAAATTAGCTCAACAAA
Found at i:11880 original size:14 final size:14
Alignment explanation
Indices: 11861--11896 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11851 TGTCCTTAGA
*
11861 CTCATCTCTTTCAG
1 CTCATCTCTTTAAG
11875 CTCATCTCTTTAAG
1 CTCATCTCTTTAAG
*
11889 CTCCTCTC
1 CTCATCTC
11897 CTAGGCCGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.39, G:0.06, T:0.42
Consensus pattern (14 bp):
CTCATCTCTTTAAG
Found at i:14248 original size:12 final size:12
Alignment explanation
Indices: 14231--14255 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14221 AAAGTTGGGA
14231 AAGAAAAAGAAG
1 AAGAAAAAGAAG
14243 AAGAAAAAGAAG
1 AAGAAAAAGAAG
14255 A
1 A
14256 GATGATGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAG
Found at i:15989 original size:22 final size:22
Alignment explanation
Indices: 15944--15989 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
15934 CTAAAAACAC
* *
15944 AAATACATATAAAATAGTGTAA
1 AAATACACATAAAATAGTGAAA
15966 AAATACACATAAAAATAGT-AAA
1 AAATACACAT-AAAATAGTGAAA
15988 AA
1 AA
15990 GCATAGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.22
Consensus pattern (22 bp):
AAATACACATAAAATAGTGAAA
Found at i:19422 original size:29 final size:30
Alignment explanation
Indices: 19368--19438 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
19358 CAAATTATCT
* *
19368 ATCAATTAACTAGCAAATAATTGCAATTCA
1 ATCAATCAACTAGCAAATAATGGCAATTCA
*
19398 ATCAATCAA-TAGCAAGAT-ATGGCAATTGAA
1 ATCAATCAACTAGCAA-ATAATGGCAATT-CA
19428 ATCAA-CAACTA
1 ATCAATCAACTA
19439 AAAGATAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 17 0.49
30 18 0.51
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (30 bp):
ATCAATCAACTAGCAAATAATGGCAATTCA
Found at i:22465 original size:6 final size:6
Alignment explanation
Indices: 22456--22488 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
22446 AAAGCAAAGC
22456 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
22489 GCAGATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:22500 original size:12 final size:13
Alignment explanation
Indices: 22485--22529 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
22475 AATCTAAATC
22485 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
22497 TAAAGCAAATTAA
1 TAAAGCAGATTAA
22510 TAAAGCAGATTAA
1 TAAAGCAGATTAA
22523 TAAAGCA
1 TAAAGCA
22530 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:22536 original size:25 final size:25
Alignment explanation
Indices: 22485--22537 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
22475 AATCTAAATC
*
22485 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
22510 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
22535 TAA
1 TAA
22538 TTAAAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Done.