Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015932.1 Corchorus capsularis cultivar CVL-1 contig15953, 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: 41267
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:2699 original size:4 final size:4
Alignment explanation
Indices: 2690--2717 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2680 ATAATAAGTA
2690 AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT
2718 GATTTTCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:7669 original size:33 final size:33
Alignment explanation
Indices: 7628--7701 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
7618 CTAAATGTGA
*
7628 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAAATCTGTTTTGGTTGATCATAGCAT
*
7661 TGAGAATAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAAATCTGTTTTGGTTGATCATAGCAT
7694 TGAAAATA
1 TGAAAATA
7702 GGACTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (33 bp):
TGAAAATAAATCTGTTTTGGTTGATCATAGCAT
Found at i:8124 original size:30 final size:30
Alignment explanation
Indices: 8088--8150 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
8078 TCTTCAAGGG
*
8088 GGAGGGAATGATGCACCCAA-GGCTTATCAT
1 GGAGGGAATGATGCA-CCAATGACTTATCAT
8118 GGAGGGAATGATGCACCAATGACTTATCAT
1 GGAGGGAATGATGCACCAATGACTTATCAT
8148 GGA
1 GGA
8151 CTTGAAGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (30 bp):
GGAGGGAATGATGCACCAATGACTTATCAT
Found at i:10846 original size:72 final size:72
Alignment explanation
Indices: 10767--10913 Score: 267
Period size: 72 Copynumber: 2.0 Consensus size: 72
10757 CTTGGACTAG
* *
10767 TTTTTCCCTAGCCCTTATGTTTGGACGAAAATTAGGTTTTATTTTTAGGATTTTGGTTGTTCCCT
1 TTTTTCCCTAGCCCTTATGTTTGGACGAAAATTAGGTTTTATTTTTAGAATTTTAGTTGTTCCCT
10832 ATGCCTA
66 ATGCCTA
*
10839 TTTTTCCCTAGTCCTTATGTTTGGACGAAAATTAGGTTTTATTTTTAGAATTTTAGTTGTTCCCT
1 TTTTTCCCTAGCCCTTATGTTTGGACGAAAATTAGGTTTTATTTTTAGAATTTTAGTTGTTCCCT
10904 ATGCCTA
66 ATGCCTA
10911 TTT
1 TTT
10914 AAAGGGACCA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (72 bp):
TTTTTCCCTAGCCCTTATGTTTGGACGAAAATTAGGTTTTATTTTTAGAATTTTAGTTGTTCCCT
ATGCCTA
Found at i:20656 original size:22 final size:23
Alignment explanation
Indices: 20623--20665 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
20613 GTATAATTAA
20623 AATAAAATTTAT-CATATAAACT
1 AATAAAATTTATGCATATAAACT
*
20645 AATAATAA-TTATGTATATAAA
1 AATAA-AATTTATGCATATAAA
20666 TAGCAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (23 bp):
AATAAAATTTATGCATATAAACT
Found at i:22014 original size:10 final size:10
Alignment explanation
Indices: 21999--22023 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
21989 TCCATTATTT
21999 TACAAGTTGA
1 TACAAGTTGA
22009 TACAAGTTGA
1 TACAAGTTGA
22019 TACAA
1 TACAA
22024 CCCTAAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (10 bp):
TACAAGTTGA
Found at i:23492 original size:2 final size:2
Alignment explanation
Indices: 23476--23512 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
23466 GTCTCTGATT
23476 TA TA CTA TA -A TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23513 ATAGACTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 28 0.88
3 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:24497 original size:16 final size:16
Alignment explanation
Indices: 24470--24513 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
24460 GTCGGGTTGA
24470 TCGGGTTCGGGTCATT
1 TCGGGTTCGGGTCATT
* *
24486 TTGGGTTTGGGTCATT
1 TCGGGTTCGGGTCATT
24502 TCGGGTTCGGGT
1 TCGGGTTCGGGT
24514 ACCCAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.14, G:0.41, T:0.41
Consensus pattern (16 bp):
TCGGGTTCGGGTCATT
Found at i:25632 original size:16 final size:16
Alignment explanation
Indices: 25613--25655 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
25603 CCCGAACTCG
25613 CCCGAATCCGAAACTA
1 CCCGAATCCGAAACTA
*
25629 CCCGAA-CCTGAAATTA
1 CCCGAATCC-GAAACTA
*
25645 CCCAAATCCGA
1 CCCGAATCCGA
25656 GGCTATCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.37, C:0.37, G:0.12, T:0.14
Consensus pattern (16 bp):
CCCGAATCCGAAACTA
Found at i:26666 original size:16 final size:16
Alignment explanation
Indices: 26618--26702 Score: 95
Period size: 15 Copynumber: 5.4 Consensus size: 16
26608 ACCTGAGCCT
* *
26618 GAACCAGAAAATACTC
1 GAACCCGAAAATACCC
26634 GAACCC-AAAATACCC
1 GAACCCGAAAATACCC
*
26649 GAATCCGACAAA-ACCC
1 GAACCCGA-AAATACCC
26665 GAACCCGAAAATACCC
1 GAACCCGAAAATACCC
**
26681 GAACCC-AAAACGCCC
1 GAACCCGAAAATACCC
26696 GAACCCG
1 GAACCCG
26703 CCCAATTGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
15 29 0.49
16 27 0.46
17 3 0.05
ACGTcount: A:0.44, C:0.38, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACCCGAAAATACCC
Found at i:26697 original size:31 final size:31
Alignment explanation
Indices: 26633--26702 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
26623 AGAAAATACT
26633 CGAACCC-AAAATACCCGAATCCGACAAAACC
1 CGAACCCGAAAATACCCGAATCC-ACAAAACC
26664 CGAACCCGAAAATACCCGAA-CC-CAAAACGCC
1 CGAACCCGAAAATACCCGAATCCACAAAA--CC
26695 CGAACCCG
1 CGAACCCG
26703 CCCAATTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
29 5 0.14
31 19 0.53
32 12 0.33
ACGTcount: A:0.41, C:0.41, G:0.13, T:0.04
Consensus pattern (31 bp):
CGAACCCGAAAATACCCGAATCCACAAAACC
Found at i:32600 original size:19 final size:19
Alignment explanation
Indices: 32576--32616 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
32566 AATTTGGTTC
32576 AATTCTGTTGTTACACAGG
1 AATTCTGTTGTTACACAGG
32595 AATTCTGTTGTTACACAGG
1 AATTCTGTTGTTACACAGG
32614 AAT
1 AAT
32617 CCACCTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (19 bp):
AATTCTGTTGTTACACAGG
Done.