Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005267.1 Corchorus capsularis cultivar CVL-1 contig05285, 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, 907
Length: 1513
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:596 original size:26 final size:27
Alignment explanation
Indices: 555--605 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
545 CCAAGTCGTT
*
555 ACAACAACCAAGCTTTCCTCAAGCTTG
1 ACAACAACCAAGCTTTCCCCAAGCTTG
*
582 ACAAC-ACCGAGCTTTCCCCAAGCT
1 ACAACAACCAAGCTTTCCCCAAGCT
606 CAAACAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.31, C:0.37, G:0.12, T:0.20
Consensus pattern (27 bp):
ACAACAACCAAGCTTTCCCCAAGCTTG
Found at i:612 original size:27 final size:27
Alignment explanation
Indices: 555--612 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
545 CCAAGTCGTT
* **
555 ACAACAACCAAGCTTTCCTCAAGCTTG
1 ACAACAACCAAGCTTTCCCCAAGCTAA
*
582 ACAAC-ACCGAGCTTTCCCCAAGCTCAA
1 ACAACAACCAAGCTTTCCCCAAGCT-AA
609 ACAA
1 ACAA
613 GTGCTCCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.36, C:0.36, G:0.10, T:0.17
Consensus pattern (27 bp):
ACAACAACCAAGCTTTCCCCAAGCTAA
Found at i:620 original size:21 final size:21
Alignment explanation
Indices: 596--671 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 21
586 CACCGAGCTT
596 TCCCCAAGCTCAAACAAGTGC
1 TCCCCAAGCTCAAACAAGTGC
*
617 TCCCCACACTGATCTCAAACCTAAGCT-T
1 TCCCCA-A--G--CTCAAA-C-AAG-TGC
645 TCCCCAAGCTCAAACAAGTGC
1 TCCCCAAGCTCAAACAAGTGC
666 TCCCCA
1 TCCCCA
672 CACTGATCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
20 1 0.02
21 15 0.34
22 2 0.05
23 6 0.14
24 1 0.02
25 1 0.02
26 6 0.14
27 2 0.05
28 9 0.20
29 1 0.02
ACGTcount: A:0.30, C:0.41, G:0.11, T:0.18
Consensus pattern (21 bp):
TCCCCAAGCTCAAACAAGTGC
Found at i:633 original size:26 final size:26
Alignment explanation
Indices: 604--685 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 26
594 TTTCCCCAAG
604 CTCAAACAAGTGCTCCCCACACTGAT
1 CTCAAACAAGTGCTCCCCACACTGAT
*
630 CTCAAACCTAAGCT-TTCCCCA-A--G--
1 CTCAAA-C-AAG-TGCTCCCCACACTGAT
653 CTCAAACAAGTGCTCCCCACACTGAT
1 CTCAAACAAGTGCTCCCCACACTGAT
679 CTCAAAC
1 CTCAAAC
686 CTAAGCTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
20 1 0.02
21 9 0.20
22 2 0.04
23 6 0.13
24 1 0.02
25 1 0.02
26 13 0.29
27 2 0.04
28 9 0.20
29 1 0.02
ACGTcount: A:0.32, C:0.39, G:0.10, T:0.20
Consensus pattern (26 bp):
CTCAAACAAGTGCTCCCCACACTGAT
Found at i:644 original size:49 final size:49
Alignment explanation
Indices: 591--725 Score: 243
Period size: 49 Copynumber: 2.7 Consensus size: 49
581 GACAACACCG
591 AGCTTTCCCCAAGCTCAAACAAGTGCTCCCCACACTGATCTCAAACCTA
1 AGCTTTCCCCAAGCTCAAACAAGTGCTCCCCACACTGATCTCAAACCTA
640 AGCTTTCCCCAAGCTCAAACAAGTGCTCCCCACACTGATCTCAAACCTA
1 AGCTTTCCCCAAGCTCAAACAAGTGCTCCCCACACTGATCTCAAACCTA
* *
689 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACT
1 AGCTTTCCCCAAGCTCA-AACAAGTGCTCCCCACACT
726 AATTACAATC
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
49 65 0.78
50 18 0.22
ACGTcount: A:0.29, C:0.39, G:0.12, T:0.21
Consensus pattern (49 bp):
AGCTTTCCCCAAGCTCAAACAAGTGCTCCCCACACTGATCTCAAACCTA
Found at i:659 original size:23 final size:23
Alignment explanation
Indices: 630--703 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 23
620 CCACACTGAT
630 CTCAAACCTAAGCTTTCCCCAAG
1 CTCAAACCTAAGCTTTCCCCAAG
*
653 CTCAAA-C-AAG-TGCTCCCCACACTG
1 CTCAAACCTAAGCT-TTCCCCA-A--G
677 ATCTCAAACCTAAGCTTTCCCCAAG
1 --CTCAAACCTAAGCTTTCCCCAAG
702 CT
1 CT
704 TAGAACAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 18
0.67 0.03 0.30
Matches are distributed among these distances:
20 1 0.03
21 9 0.22
22 2 0.05
23 8 0.20
24 1 0.03
25 1 0.03
26 6 0.15
27 2 0.05
28 9 0.22
29 1 0.03
ACGTcount: A:0.30, C:0.39, G:0.09, T:0.22
Consensus pattern (23 bp):
CTCAAACCTAAGCTTTCCCCAAG
Done.