Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006825.1 Corchorus capsularis cultivar CVL-1 contig06846, 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: 25730
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:475 original size:10 final size:10
Alignment explanation
Indices: 455--501 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
445 AGGCCAACTT
455 GAGAGAAAAAA
1 GAGA-AAAAAA
*
466 GGGAAAAAAA
1 GAGAAAAAAA
*
476 AAGAAAAAAA
1 GAGAAAAAAA
486 GA-AAAAAAA
1 GAGAAAAAAA
*
495 AAGAAAA
1 GAGAAAA
502 GAAAATTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 8 0.27
10 19 0.63
11 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
GAGAAAAAAA
Found at i:482 original size:8 final size:8
Alignment explanation
Indices: 471--506 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
461 AAAAAGGGAA
471 AAAAAAAG
1 AAAAAAAG
479 AAAAAAAG
1 AAAAAAAG
487 AAAAAAA-
1 AAAAAAAG
494 AAAGAAAAG
1 AAA-AAAAG
503 AAAA
1 AAAA
507 TTTCTTCAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 3 0.12
8 20 0.77
9 3 0.12
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:482 original size:19 final size:19
Alignment explanation
Indices: 458--501 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
448 CCAACTTGAG
* *
458 AGAAAAAAGGGAAAAAAAA
1 AGAAAAAAAGAAAAAAAAA
477 AGAAAAAAAGAAAAAAAAA
1 AGAAAAAAAGAAAAAAAAA
496 AGAAAA
1 AGAAAA
502 GAAAATTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AGAAAAAAAGAAAAAAAAA
Found at i:493 original size:11 final size:11
Alignment explanation
Indices: 469--506 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
459 GAAAAAAGGG
*
469 AAAAAAA-AAG
1 AAAAAAAGAAA
479 AAAAAAAGAAA
1 AAAAAAAGAAA
490 AAAAAAAGAAA
1 AAAAAAAGAAA
501 AGAAAA
1 A-AAAA
507 TTTCTTCAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 7 0.28
11 14 0.56
12 4 0.16
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:6145 original size:3 final size:3
Alignment explanation
Indices: 6132--6171 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
6122 TTGCAGAAAT
6132 TAA TCAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
6172 GCCCTTTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:10631 original size:14 final size:14
Alignment explanation
Indices: 10612--10642 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10602 AACTACTTAG
*
10612 AAATTATTAAAAAA
1 AAATTAATAAAAAA
10626 AAATTAATAAAAAA
1 AAATTAATAAAAAA
10640 AAA
1 AAA
10643 AGGACAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATTAATAAAAAA
Found at i:17214 original size:31 final size:31
Alignment explanation
Indices: 17176--17335 Score: 158
Period size: 31 Copynumber: 5.2 Consensus size: 31
17166 AAGTCGTGCT
* * *
17176 ACGTGTACCAAAAAGTGACATTTGTCACGTC
1 ACGTGTACCAAAAAGTGACATGTGGCACGCC
* * *
17207 ACGTGTACAAAAAAGTGTCATGTGCCACGCC
1 ACGTGTACCAAAAAGTGACATGTGGCACGCC
* * * *
17238 ACATGTACAAAAAAGTGACACGTGGCATGCC
1 ACGTGTACCAAAAAGTGACATGTGGCACGCC
* * * * *
17269 ACGGGTGCCAAAAAGTGACACGTGGCATGTC
1 ACGTGTACCAAAAAGTGACATGTGGCACGCC
** *
17300 ACGTGTTTCAAAAAGTGACATGTGGCATGCC
1 ACGTGTACCAAAAAGTGACATGTGGCACGCC
17331 ACGTG
1 ACGTG
17336 CACGAAAGGA
Statistics
Matches: 109, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 109 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.21
Consensus pattern (31 bp):
ACGTGTACCAAAAAGTGACATGTGGCACGCC
Found at i:22520 original size:7 final size:7
Alignment explanation
Indices: 22508--22544 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
22498 GTTTGGTTGT
22508 GAATTGA
1 GAATTGA
22515 GAATTGA
1 GAATTGA
22522 GAATTGA
1 GAATTGA
22529 GAATTGA
1 GAATTGA
22536 GAATTGA
1 GAATTGA
22543 GA
1 GA
22545 TACTAAGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (7 bp):
GAATTGA
Found at i:23689 original size:26 final size:26
Alignment explanation
Indices: 23660--23727 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
23650 TTCCTTTCTT
23660 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
23686 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
23712 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
23728 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:24088 original size:21 final size:21
Alignment explanation
Indices: 24059--24103 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
24049 CAAAAATTAT
**
24059 AAAAAGGGGACGGTATTTAGC
1 AAAAAGGGGACGGTAAATAGC
* *
24080 AAAAGGGGGGCGGTAAATAGC
1 AAAAAGGGGACGGTAAATAGC
24101 AAA
1 AAA
24104 CCCCAAATTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.36, T:0.13
Consensus pattern (21 bp):
AAAAAGGGGACGGTAAATAGC
Done.