Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012151.1 Corchorus capsularis cultivar CVL-1 contig12172, 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: 48698
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:11849 original size:13 final size:13
Alignment explanation
Indices: 11831--11855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11821 AAAAATAGTA
11831 ATATATATATATG
1 ATATATATATATG
11844 ATATATATATAT
1 ATATATATATAT
11856 ATTGGATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
ATATATATATATG
Found at i:12932 original size:13 final size:12
Alignment explanation
Indices: 12903--12935 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
12893 ATTGAATATG
12903 TTTTTTT-ATAA
1 TTTTTTTAATAA
12914 TTTTTTTAATAA
1 TTTTTTTAATAA
12926 TTATTTTTAA
1 TT-TTTTTAA
12936 GACTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 6 0.30
13 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTTAATAA
Found at i:14489 original size:20 final size:21
Alignment explanation
Indices: 14464--14503 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
14454 TAGGTCAACC
14464 CAAGTGAAGACT-TTCATTTG
1 CAAGTGAAGACTCTTCATTTG
14484 CAAGTGAAGACTCTTCATTT
1 CAAGTGAAGACTCTTCATTT
14504 AATTTAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
CAAGTGAAGACTCTTCATTTG
Found at i:14588 original size:51 final size:51
Alignment explanation
Indices: 14512--14615 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
14502 TTAATTTAAA
14512 ACAGATTAGACTAGTATATATAAGTATGAATGTTAAGAAACTTTTAGATCG
1 ACAGATTAGACTAGTATATATAAGTATGAATGTTAAGAAACTTTTAGATCG
*
14563 ACAGATTAGACTAGTATATATAAGTATGAGTGTTAAGAAACTTTTAGATCG
1 ACAGATTAGACTAGTATATATAAGTATGAATGTTAAGAAACTTTTAGATCG
14614 AC
1 AC
14616 GATGATATCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (51 bp):
ACAGATTAGACTAGTATATATAAGTATGAATGTTAAGAAACTTTTAGATCG
Found at i:16649 original size:18 final size:18
Alignment explanation
Indices: 16626--16665 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
16616 TTTGTTGCAT
16626 CATCAGATGAATAAGATG
1 CATCAGATGAATAAGATG
*
16644 CATCAGATGAATAAGATT
1 CATCAGATGAATAAGATG
16662 CATC
1 CATC
16666 TGCATCAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (18 bp):
CATCAGATGAATAAGATG
Found at i:18716 original size:28 final size:28
Alignment explanation
Indices: 18653--18732 Score: 108
Period size: 28 Copynumber: 2.8 Consensus size: 28
18643 GTTTAATATC
18653 CAAATT-AGCCCCTTAACTATTCATTTTGGGA
1 CAAATTGA-CCCCTTAACT-TT--TTTTGGGA
18684 CAAATTGACCCCTTAACTTTTTTTGGGA
1 CAAATTGACCCCTTAACTTTTTTTGGGA
*
18712 CAAATTGGCCCCTTAACTTTT
1 CAAATTGACCCCTTAACTTTT
18733 AAAAACGAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
28 28 0.60
30 2 0.04
31 16 0.34
32 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (28 bp):
CAAATTGACCCCTTAACTTTTTTTGGGA
Found at i:21722 original size:28 final size:28
Alignment explanation
Indices: 21690--21743 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
21680 ACCCCATCCA
21690 GTATCCA-GGTCTTTGCCTTAACTAATTC
1 GTATCCAGGGT-TTTGCCTTAACTAATTC
21718 GTATCCAGGGTTTTGCCTTAACTAAT
1 GTATCCAGGGTTTTGCCTTAACTAAT
21744 CCGGATACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (28 bp):
GTATCCAGGGTTTTGCCTTAACTAATTC
Found at i:21810 original size:27 final size:28
Alignment explanation
Indices: 21772--21827 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
21762 GCGCACCTGA
*
21772 TTATGGTGAGTGAGTCTACCAAC-GGGG
1 TTATAGTGAGTGAGTCTACCAACAGGGG
21799 TTATAGTGAGTGAGTCTACCAACAGGGG
1 TTATAGTGAGTGAGTCTACCAACAGGGG
21827 T
1 T
21828 AGCTGCGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.27
Consensus pattern (28 bp):
TTATAGTGAGTGAGTCTACCAACAGGGG
Found at i:26344 original size:2 final size:2
Alignment explanation
Indices: 26337--26361 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26327 AGGTGTTTTC
26337 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
26362 GTTAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30731 original size:78 final size:78
Alignment explanation
Indices: 30645--30891 Score: 388
Period size: 78 Copynumber: 3.2 Consensus size: 78
30635 AGTTTTTAAT
30645 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAGAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAGAAATAGA
30710 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
30723 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAGAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAGAAATAGA
30788 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * * ** * * * *
30801 TAAAATAGTAAAAAGGTAAAATAAAATAGTTATAAAGATAAAATATTTAATTAAATAAAAATAAA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAGAAATAGA
*
30866 ATTTTTAGTTGAG
66 GTTTTTAGTTGAG
30879 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
30892 ACCTAAGCAA
Statistics
Matches: 158, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
78 156 0.99
79 2 0.01
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAGAAATAGA
GTTTTTAGTTGAG
Found at i:30827 original size:21 final size:22
Alignment explanation
Indices: 30801--30845 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
30791 TTTAGTTGAG
*
30801 TAAAATAG-TAAAAAGGTAAAA
1 TAAAATAGTTAAAAAGATAAAA
*
30822 TAAAATAGTTATAAAGATAAAA
1 TAAAATAGTTAAAAAGATAAAA
30844 TA
1 TA
30846 TTTAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.24
Consensus pattern (22 bp):
TAAAATAGTTAAAAAGATAAAA
Found at i:30858 original size:17 final size:16
Alignment explanation
Indices: 30817--30860 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
30807 AGTAAAAAGG
30817 TAAAATAAAATAGTTA
1 TAAAATAAAATAGTTA
*
30833 TAAAGATAAAATATTTAA
1 TAAA-ATAAAATAGTT-A
*
30851 TTAAATAAAA
1 TAAAATAAAA
30861 ATAAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAAAATAAAATAGTTA
Found at i:37874 original size:15 final size:15
Alignment explanation
Indices: 37854--37884 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
37844 ACCATGATAC
37854 GATGGTAGGAGTGGT
1 GATGGTAGGAGTGGT
37869 GATGGTAGGAGTGGT
1 GATGGTAGGAGTGGT
37884 G
1 G
37885 CATACATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.55, T:0.26
Consensus pattern (15 bp):
GATGGTAGGAGTGGT
Done.