Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009316.1 Corchorus capsularis cultivar CVL-1 contig09337, 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: 4500
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:338 original size:34 final size:36
Alignment explanation
Indices: 299--379 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 36
289 AGAGGAAGTG
299 ATCAGTA-G-AATTAAGAGTAAAAGTAAAAGGA-GTA
1 ATCAGTAGGTAATTAAGAGTAAAAGT-AAAGGAGGTA
333 ATCAGTAAAATGGTAATTAAGAGTAAAAGTAAAGGAGGTA
1 ATCAGT---A-GGTAATTAAGAGTAAAAGTAAAGGAGGTA
373 ATCAGTA
1 ATCAGTA
380 AATCGGTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
34 6 0.15
37 2 0.05
39 7 0.17
40 25 0.62
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.22
Consensus pattern (36 bp):
ATCAGTAGGTAATTAAGAGTAAAAGTAAAGGAGGTA
Found at i:485 original size:32 final size:33
Alignment explanation
Indices: 425--507 Score: 125
Period size: 32 Copynumber: 2.5 Consensus size: 33
415 AGTAATCGGT
425 AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
*
458 AAAGAGTAAAAT-G-ACAAATGGTGATTAAATTC
1 AAAGAGTAAAATAGTA-AAATGGTAATTAAATTC
490 AAAGAGTGAAAATAGTAA
1 AAAGAGT-AAAATAGTAA
508 TTAAATTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 1 0.02
32 24 0.53
33 17 0.38
34 2 0.04
35 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.18, T:0.24
Consensus pattern (33 bp):
AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
Found at i:510 original size:26 final size:26
Alignment explanation
Indices: 440--534 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 26
430 GTAAAATAGT
*
440 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATAGTAATTAAATTCAAAGAG-----TG
* *
471 ACAAATGGTGATTAAATTCAAAGAGTG
1 A-AAATAGTAATTAAATTCAAAGAGTG
498 AAAATAGTAATTAAATTCAAGAGAGT-
1 AAAATAGTAATTAAATTCAA-AGAGTG
524 AAAATAGTAAT
1 AAAATAGTAAT
535 CAGTAAAGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
26 28 0.47
27 8 0.14
31 1 0.02
32 22 0.37
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (26 bp):
AAAATAGTAATTAAATTCAAAGAGTG
Found at i:566 original size:28 final size:28
Alignment explanation
Indices: 529--600 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
519 AGAGTAAAAT
529 AGTAATCAGTAAAGAGGAAAAA-GTAAA
1 AGTAATCAGTAAAGAGGAAAAAGGTAAA
*
556 GAGTAATCAGTAAA-AGTAAAAATGGTAAA
1 -AGTAATCAGTAAAGAGGAAAAA-GGTAAA
*
585 AGTAATTAGTAAAGAG
1 AGTAATCAGTAAAGAG
601 TAATCAGCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.18
28 25 0.64
29 7 0.18
ACGTcount: A:0.56, C:0.03, G:0.22, T:0.19
Consensus pattern (28 bp):
AGTAATCAGTAAAGAGGAAAAAGGTAAA
Found at i:567 original size:14 final size:14
Alignment explanation
Indices: 529--607 Score: 72
Period size: 14 Copynumber: 5.6 Consensus size: 14
519 AGAGTAAAAT
529 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
* **
543 AGGAAAAAGTAAAG
1 AGTAATCAGTAAAG
557 AGTAATCAGTAAA-
1 AGTAATCAGTAAAG
**
570 AGTAAAAATGGTAAA-
1 AGTAATCA--GTAAAG
*
585 AGTAATTAGTAAAG
1 AGTAATCAGTAAAG
599 AGTAATCAG
1 AGTAATCAG
608 CGAAAAGTAA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
13 11 0.22
14 29 0.57
15 11 0.22
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:603 original size:42 final size:44
Alignment explanation
Indices: 550--632 Score: 134
Period size: 43 Copynumber: 1.9 Consensus size: 44
540 AAGAGGAAAA
* *
550 AGTAAAGAGTAATCAG-TAAAAGTAAAAATGGTAAA-AGTAATT
1 AGTAAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAGAGTAATT
592 AGTAAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAGAGTA
1 AGTAAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAGAGTA
633 GTAAAAGGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 16 0.43
43 17 0.46
44 4 0.11
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (44 bp):
AGTAAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAGAGTAATT
Found at i:654 original size:40 final size:42
Alignment explanation
Indices: 553--657 Score: 112
Period size: 43 Copynumber: 2.5 Consensus size: 42
543 AGGAAAAAGT
* * *
553 AAAGAGTAATCAG-TAAAAGTAAAAATGGTAAAAGTAATTAG
1 AAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAAGTAAGTAG
594 TAAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAGAGT-AGTA-
1 -AAAGAGTAATCAGCGAAAAGTAAAAATGGCAAA-AGTAAGTAG
*
636 AAAG-GTATTCAG-GCAAAAGTAA
1 AAAGAGTAATCAGCG-AAAAGTAA
658 TCAGTAAAGG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 1 0.02
40 15 0.27
41 4 0.07
42 13 0.23
43 20 0.36
44 3 0.05
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.19
Consensus pattern (42 bp):
AAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAAGTAAGTAG
Found at i:713 original size:21 final size:22
Alignment explanation
Indices: 676--774 Score: 89
Period size: 22 Copynumber: 4.6 Consensus size: 22
666 GGAAGAATGA
*
676 TAAAGAGT-AAAGGGTAATCAG
1 TAAAGAGTCAAATGGTAATCAG
697 T-AAGAG-CAAGATGGTAATCAG
1 TAAAGAGTCAA-ATGGTAATCAG
*
718 TAAAGAGTCAAATAGTAATCAG
1 TAAAGAGTCAAATGGTAATCAG
* * * *
740 CAAAAAGT-AAGAAGGCAATCAG
1 TAAAGAGTCAA-ATGGTAATCAG
*
762 TAAAGAGTGAAAT
1 TAAAGAGTCAAAT
775 ATTAAGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
20 7 0.11
21 14 0.23
22 36 0.58
23 5 0.08
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.18
Consensus pattern (22 bp):
TAAAGAGTCAAATGGTAATCAG
Found at i:720 original size:35 final size:35
Alignment explanation
Indices: 654--722 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
644 TCAGGCAAAA
* *
654 GTAATCAGTAAAGGAAGAATGATAAAGAGTAAAGG
1 GTAATCAGTAAAGCAAGAATGATAAACAGTAAAGG
* *
689 GTAATCAGTAAGAGCAAG-ATGGTAATCAGTAAAG
1 GTAATCAGTAA-AGCAAGAATGATAAACAGTAAAG
723 AGTCAAATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 24 0.83
36 5 0.17
ACGTcount: A:0.48, C:0.06, G:0.28, T:0.19
Consensus pattern (35 bp):
GTAATCAGTAAAGCAAGAATGATAAACAGTAAAGG
Found at i:821 original size:14 final size:14
Alignment explanation
Indices: 782--831 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
772 AATATTAAGA
782 GTAAAAAGGTAAAATG
1 GTAAAAA-GTAAAA-G
798 GTAAAAAGTAAAAG
1 GTAAAAAGTAAAAG
** *
812 GTAATCAGTAAAGG
1 GTAAAAAGTAAAAG
826 GTAAAA
1 GTAAAA
832 TGGTAATTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 16 0.55
15 6 0.21
16 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.24, T:0.18
Consensus pattern (14 bp):
GTAAAAAGTAAAAG
Found at i:836 original size:22 final size:22
Alignment explanation
Indices: 798--866 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
788 AGGTAAAATG
798 GTAAAAAGTAAAA-GGTAATCA
1 GTAAAAAGTAAAATGGTAATCA
** *
819 GTAAAGGGTAAAATGGTAATTA
1 GTAAAAAGTAAAATGGTAATCA
* *
841 GTAAAAAGTAAGATGGCAATCA
1 GTAAAAAGTAAAATGGTAATCA
863 GTAA
1 GTAA
867 GAAGAGGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 11 0.28
22 28 0.72
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.22
Consensus pattern (22 bp):
GTAAAAAGTAAAATGGTAATCA
Done.