Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014289.1 Corchorus capsularis cultivar CVL-1 contig14310, 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: 9894
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:6571 original size:12 final size:12
Alignment explanation
Indices: 6554--6578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6544 TCAAAGCCTC
6554 ACCACTATATAT
1 ACCACTATATAT
6566 ACCACTATATAT
1 ACCACTATATAT
6578 A
1 A
6579 GTGGAGTTGA
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:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ACCACTATATAT
Found at i:7473 original size:9 final size:9
Alignment explanation
Indices: 7459--7492 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
7449 TTAGGAGTGT
7459 TGCAATCAG
1 TGCAATCAG
7468 TGCAATCAG
1 TGCAATCAG
7477 TGCAAATCAG
1 TGC-AATCAG
7487 TGCAAT
1 TGCAAT
7493 GCCTATAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (9 bp):
TGCAATCAG
Found at i:7486 original size:10 final size:10
Alignment explanation
Indices: 7462--7491 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
7452 GGAGTGTTGC
7462 AATCAGTGC-
1 AATCAGTGCA
7471 AATCAGTGCA
1 AATCAGTGCA
7481 AATCAGTGCA
1 AATCAGTGCA
7491 A
1 A
7492 TGCCTATAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (10 bp):
AATCAGTGCA
Found at i:7552 original size:40 final size:40
Alignment explanation
Indices: 7489--7629 Score: 137
Period size: 40 Copynumber: 3.6 Consensus size: 40
7479 CAAATCAGTG
*
7489 CAATGCCTATAGCCTATGAAGCTTAAAAAGAAAATGCTTA
1 CAATGCCTATAGCCTATGAAGCTTAAAAAGAAAAGGCTTA
* * * * *
7529 CAATGCCTATAGCCAATGTAGCTT-GAAAG--AGGGCGTA
1 CAATGCCTATAGCCTATGAAGCTTAAAAAGAAAAGGCTTA
* *
7566 CAACGCCTATAGCCTATGCAGCTTAAAAA-AAAAGGGCTTA
1 CAATGCCTATAGCCTATGAAGCTTAAAAAGAAAA-GGCTTA
* * * *
7606 CTATGCCTACAGCCTTTGCAGCTT
1 CAATGCCTATAGCCTATGAAGCTT
7630 TACAACGTCT
Statistics
Matches: 81, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
37 26 0.32
38 3 0.04
39 5 0.06
40 47 0.58
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (40 bp):
CAATGCCTATAGCCTATGAAGCTTAAAAAGAAAAGGCTTA
Found at i:7654 original size:29 final size:29
Alignment explanation
Indices: 7612--7720 Score: 110
Period size: 29 Copynumber: 3.6 Consensus size: 29
7602 CTTACTATGC
* *
7612 CTACAGCCTTTGCAGCTTTACAACGTCTA
1 CTACAGCCTATGCAGCTTTACAACGCCTA
* * * * *
7641 CTACAGTCTATGCAGCTTAAAAAAAAGGCTTA
1 CTACAGCCTATGCAGCTT---TACAACGCCTA
7673 CTATCAGCCTATGCAGCTTTACAACGCCTA
1 CTA-CAGCCTATGCAGCTTTACAACGCCTA
*
7703 CTACAGTCTATGCAGCTT
1 CTACAGCCTATGCAGCTT
7721 AAAGAAGGCT
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
29 30 0.48
30 10 0.16
32 9 0.14
33 14 0.22
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (29 bp):
CTACAGCCTATGCAGCTTTACAACGCCTA
Found at i:7779 original size:65 final size:65
Alignment explanation
Indices: 7564--7800 Score: 265
Period size: 62 Copynumber: 3.7 Consensus size: 65
7554 AAAGAGGGCG
*
7564 TACAACGCCTA-T--AGCCTATGCAGCTTAAAAAAAAAGGGCTTACTATGCCTACAGCCTTTGCA
1 TACAACGCCTACTACAGCCTATGCAGCTT--AAAAAAA-GGCTTACTA-GCCTACAGCCTATGCA
7626 GCTT
62 GCTT
* *
7630 TACAACGTCTACTACAGTCTATGCAGCTTAAAAAAAAGGCTTACTA---T-CAGCCTATGCAGCT
1 TACAACGCCTACTACAGCCTATGCAGCTT-AAAAAAAGGCTTACTAGCCTACAGCCTATGCAGCT
7691 T
65 T
* * * *
7692 TACAACGCCTACTACAGTCTATGCAGCTT-AAAGAAGGCTTACTACGCCTACAGTCTATGCAGTT
1 TACAACGCCTACTACAGCCTATGCAGCTTAAAAAAAGGCTTACTA-GCCTACAGCCTATGCAGCT
7756 T
65 T
* * *
7757 TGCAACGCCTACTATAGCCTATGCATCTTAAAAAAAGGGCTTAC
1 TACAACGCCTACTACAGCCTATGCAGCTTAAAAAAA-GGCTTAC
7801 AATGCCTATA
Statistics
Matches: 149, Mismatches: 12, Indels: 19
0.83 0.07 0.11
Matches are distributed among these distances:
60 14 0.09
62 42 0.28
63 1 0.01
64 1 0.01
65 38 0.26
66 15 0.10
67 17 0.11
68 8 0.05
69 13 0.09
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (65 bp):
TACAACGCCTACTACAGCCTATGCAGCTTAAAAAAAGGCTTACTAGCCTACAGCCTATGCAGCTT
Found at i:8352 original size:47 final size:45
Alignment explanation
Indices: 8299--8624 Score: 286
Period size: 45 Copynumber: 7.2 Consensus size: 45
8289 ATCACCTTCC
8299 TCCAACAATAAAAATTTATACGCTCTTTCCAACATGATGGTGGCGCT
1 TCCAACAAT-AAAATTTATACGCTC-TTCCAACATGATGGTGGCGCT
* * ** * *
8346 TCCAACAATAAAATTTTTATGCGATTCCAACACGGTGGGGTGGCGCT
1 TCCAACAATAAAATTTATACGCTCTTCCAACATGAT--GGTGGCGCT
* ** * * * *
8393 TCCAACAGACAAAACCTATACTCACTTCCAACATGATGGTGACGCC
1 TCCAACA-ATAAAATTTATACGCTCTTCCAACATGATGGTGGCGCT
*
8439 TCCAATCACAAAAAATTTATACGCTCTTTCCAACATGATGGTGGCGCT
1 TCCAA-CA-ATAAAATTTATACGCTC-TTCCAACATGATGGTGGCGCT
* * *
8487 TCCAACAAT-AAATTTATATGCGCTTCCAACATGATTGTGGCGCCT
1 TCCAACAATAAAATTTATACGCTCTTCCAACATGATGGTGGCG-CT
* * *
8532 T-CAATC-ACAAAATTTATACACTCTTCCAACATGAGGGTGGCGCT
1 TCCAA-CAATAAAATTTATACGCTCTTCCAACATGATGGTGGCGCT
* * * * * *
8576 TCCAGCGATAAAATTCATATGCGCTTCCAAC---ATGGTTGCGCT
1 TCCAACAATAAAATTTATACGCTCTTCCAACATGATGGTGGCGCT
8618 TCCAACA
1 TCCAACA
8625 TGATGCTGAA
Statistics
Matches: 223, Mismatches: 46, Indels: 25
0.76 0.16 0.09
Matches are distributed among these distances:
42 14 0.06
44 26 0.12
45 75 0.34
46 24 0.11
47 41 0.18
48 43 0.19
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (45 bp):
TCCAACAATAAAATTTATACGCTCTTCCAACATGATGGTGGCGCT
Found at i:8617 original size:17 final size:17
Alignment explanation
Indices: 8595--8664 Score: 86
Period size: 17 Copynumber: 3.9 Consensus size: 17
8585 AAAATTCATA
8595 TGCGCTTCCAACATGGT
1 TGCGCTTCCAACATGGT
*
8612 TGCGCTTCCAACATGATGC
1 TGCGCTTCCAACATG--GT
*
8631 TGAAGCTTCCAACATGGT
1 TG-CGCTTCCAACATGGT
8649 TGCGCTTTCCAACATG
1 TGCGC-TTCCAACATG
8665 ATGCTAATGC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
17 17 0.38
18 13 0.29
19 3 0.07
20 12 0.27
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (17 bp):
TGCGCTTCCAACATGGT
Found at i:8640 original size:20 final size:20
Alignment explanation
Indices: 8615--8681 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
8605 ACATGGTTGC
8615 GCTTCCAACATGATGCTGAA
1 GCTTCCAACATGATGCTGAA
* *
8635 GCTTCCAACATG--GTTG-C
1 GCTTCCAACATGATGCTGAA
8652 GCTTTCCAACATGATGCT-AA
1 GC-TTCCAACATGATGCTGAA
8672 TGCTTCCAAC
1 -GCTTCCAAC
8682 GGAGAGAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
17 2 0.05
18 13 0.34
20 21 0.55
21 2 0.05
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (20 bp):
GCTTCCAACATGATGCTGAA
Found at i:8648 original size:37 final size:38
Alignment explanation
Indices: 8598--8681 Score: 145
Period size: 38 Copynumber: 2.2 Consensus size: 38
8588 ATTCATATGC
8598 GCTTCCAACATGGTTGCGC-TTCCAACATGATGCTGAA-
1 GCTTCCAACATGGTTGCGCTTTCCAACATGATGCT-AAT
8635 GCTTCCAACATGGTTGCGCTTTCCAACATGATGCTAAT
1 GCTTCCAACATGGTTGCGCTTTCCAACATGATGCTAAT
8673 GCTTCCAAC
1 GCTTCCAAC
8682 GGAGAGAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
37 21 0.47
38 24 0.53
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (38 bp):
GCTTCCAACATGGTTGCGCTTTCCAACATGATGCTAAT
Found at i:8890 original size:45 final size:45
Alignment explanation
Indices: 8833--9103 Score: 296
Period size: 45 Copynumber: 5.9 Consensus size: 45
8823 CTCTTCCAGG
* ** * * *
8833 GTGGTGGCGCTTCCAACGACATTATTTATACTCTCCTCCAACATGA
1 GTGGTGGCGCTTCCAATGACAAGAATTATACCCTCTTCCAACAT-A
* *
8879 G-GTTGGCGCTTCCAATGATAAGAATTATACCCTCTTCCAACATA
1 GTGGTGGCGCTTCCAATGACAAGAATTATACCCTCTTCCAACATA
* * *
8923 GTGGTGGTGCTTCCAATGAGAA-AATTTATACCCACTTCCAACATA
1 GTGGTGGCGCTTCCAATGACAAGAA-TTATACCCTCTTCCAACATA
*
8968 GTGGTGGCGCTTCCAATGACAAGAATTATACTCTCTTCCAACAT-
1 GTGGTGGCGCTTCCAATGACAAGAATTATACCCTCTTCCAACATA
* * *
9012 GATGGTGGCGTTTCCAATGGCAAGAATTATATCCTCTTCCAACATA
1 G-TGGTGGCGCTTCCAATGACAAGAATTATACCCTCTTCCAACATA
*
9058 GTGGTGGTGCTGGTGCTTCCAATGACAAGAATTATACTCTCTTCCA
1 GTGGT-G-GC----GCTTCCAATGACAAGAATTATACCCTCTTCCA
9104 CATGGTGTTG
Statistics
Matches: 190, Mismatches: 24, Indels: 17
0.82 0.10 0.07
Matches are distributed among these distances:
44 5 0.03
45 150 0.79
46 5 0.03
47 2 0.01
51 28 0.15
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (45 bp):
GTGGTGGCGCTTCCAATGACAAGAATTATACCCTCTTCCAACATA
Found at i:9384 original size:36 final size:36
Alignment explanation
Indices: 9344--9460 Score: 155
Period size: 36 Copynumber: 3.2 Consensus size: 36
9334 GCTCTGTTTC
* * *
9344 TGGCTATAATGCTGATGGCCTAAGTCGCCTAATCTT
1 TGGCTATAATGCCGATGGCCTAAGTCGCCCAATATT
* *
9380 TGGCTATAATGCCGATGGCCTAAGTCGCCCAAAAAT
1 TGGCTATAATGCCGATGGCCTAAGTCGCCCAATATT
* *
9416 TGGCTATAAAGCCGCTGGCC-ATAGTCGCCCAATATT
1 TGGCTATAATGCCGATGGCCTA-AGTCGCCCAATATT
9452 TGGCTATAA
1 TGGCTATAA
9461 CGCCACTGAC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
35 1 0.01
36 70 0.99
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (36 bp):
TGGCTATAATGCCGATGGCCTAAGTCGCCCAATATT
Found at i:9756 original size:46 final size:46
Alignment explanation
Indices: 9620--9762 Score: 180
Period size: 46 Copynumber: 3.1 Consensus size: 46
9610 AGGAGATGCA
* **
9620 TCTTATATGAGCACCCTTCTTCAGAAAG-ATTACTCTATACAATAGC
1 TCTTATGTGAGCACCCTTCTTCAGAAAGAATT-CTCTATACGGTAGC
* * * *
9666 TCTTATGTGAGCACACTTCTTCAGAAAGAATACTCTACATGGTAGC
1 TCTTATGTGAGCACCCTTCTTCAGAAAGAATTCTCTATACGGTAGC
* *
9712 TCTTATGTGAGCACCCATCTCCAGAAAGAATTCTCTATACGGTAGCC
1 TCTTATGTGAGCACCCTTCTTCAGAAAGAATTCTCTATACGGTAG-C
9759 TCTT
1 TCTT
9763 GCAACGCATT
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
46 75 0.91
47 7 0.09
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (46 bp):
TCTTATGTGAGCACCCTTCTTCAGAAAGAATTCTCTATACGGTAGC
Done.