Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004837.1 Corchorus capsularis cultivar CVL-1 contig04855, 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: 12144
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:709 original size:2 final size:2
Alignment explanation
Indices: 702--726 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
692 TACAGTTAAT
702 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
727 TTCCTTCTTC
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:1112 original size:31 final size:30
Alignment explanation
Indices: 1077--1142 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
1067 TAATTAAGTT
** *
1077 CCTAACGTTGCAAAATCGGCTTAAATCAGTC
1 CCTAACGTTAAAAAATCGGCTCAAATCAG-C
1108 CCTAACGTTAAAAAATCGGCTCAAATCAGC
1 CCTAACGTTAAAAAATCGGCTCAAATCAGC
1138 CCTAA
1 CCTAA
1143 TATTTTGAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (30 bp):
CCTAACGTTAAAAAATCGGCTCAAATCAGC
Found at i:1921 original size:34 final size:34
Alignment explanation
Indices: 1882--1993 Score: 106
Period size: 34 Copynumber: 3.3 Consensus size: 34
1872 GAAAAGAGCT
*
1882 GGTCGCGACCCGCGTCACGACCCGCCCATGGCTG
1 GGTCGCGACCCGCGTCGCGACCCGCCCATGGCTG
* * *
1916 GGTCGCGATCCGCGT-GCGACCCGTCTCATGGGATG
1 GGTCGCGACCCGCGTCGCGACCCG-CCCAT-GGCTG
* *
1951 GGTCACG-CCCAG-ATCGCGACCCGCACCATGGCT-
1 GGTCGCGACCC-GCGTCGCGACCCGC-CCATGGCTG
1984 GGTCGCGACC
1 GGTCGCGACC
1994 AGAGCTTTTC
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
33 13 0.21
34 27 0.44
35 22 0.35
ACGTcount: A:0.13, C:0.39, G:0.33, T:0.14
Consensus pattern (34 bp):
GGTCGCGACCCGCGTCGCGACCCGCCCATGGCTG
Found at i:3981 original size:12 final size:12
Alignment explanation
Indices: 3964--3988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3954 AATTAACTAA
3964 CTCTCAATTTAG
1 CTCTCAATTTAG
3976 CTCTCAATTTAG
1 CTCTCAATTTAG
3988 C
1 C
3989 AATAAGTTAG
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:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (12 bp):
CTCTCAATTTAG
Found at i:4140 original size:28 final size:29
Alignment explanation
Indices: 4086--4142 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
4076 GCTACATTTC
4086 AATTATATAGCTTAAGCATTTTTAGTAAT
1 AATTATATAGCTTAAGCATTTTTAGTAAT
*
4115 AATTATATGGCTT-AGCATTTTTAGTAAT
1 AATTATATAGCTTAAGCATTTTTAGTAAT
4143 GGGTCTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (29 bp):
AATTATATAGCTTAAGCATTTTTAGTAAT
Found at i:6569 original size:47 final size:47
Alignment explanation
Indices: 6515--6613 Score: 180
Period size: 47 Copynumber: 2.1 Consensus size: 47
6505 ATAACATACT
6515 AAGTTATATTAAGTCAGGATAGTCAATAATTAAATGTTAAAAATGTA
1 AAGTTATATTAAGTCAGGATAGTCAATAATTAAATGTTAAAAATGTA
*
6562 AAGTTATATTAAGTCAGGTTAGTCAATAATTAAATGTTAAAAATGTA
1 AAGTTATATTAAGTCAGGATAGTCAATAATTAAATGTTAAAAATGTA
*
6609 TAGTT
1 AAGTT
6614 TTGTTGAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.36
Consensus pattern (47 bp):
AAGTTATATTAAGTCAGGATAGTCAATAATTAAATGTTAAAAATGTA
Found at i:7345 original size:21 final size:21
Alignment explanation
Indices: 7319--7374 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
7309 AAAAAATGAT
7319 AATCAGTAAAGAGTAATAGAA
1 AATCAGTAAAGAGTAATAGAA
**
7340 AATCAGT-AAGAAGTAATAGTG
1 AATCAGTAAAG-AGTAATAGAA
7361 AA-CAGTAAA-AGTAA
1 AATCAGTAAAGAGTAA
7375 AAAAGGGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 5 0.16
20 7 0.23
21 19 0.61
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (21 bp):
AATCAGTAAAGAGTAATAGAA
Found at i:7536 original size:25 final size:26
Alignment explanation
Indices: 7489--7540 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
7479 GGTAATAGTA
7489 ATCAGTAAAGTCAGTAATTAAGAGTC
1 ATCAGTAAAGTCAGTAATTAAGAGTC
7515 ATCAGTAAA-TC-GATAATTAAGAGTC
1 ATCAGTAAAGTCAG-TAATTAAGAGTC
7540 A
1 A
7541 AAATGATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 1 0.04
25 15 0.60
26 9 0.36
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (26 bp):
ATCAGTAAAGTCAGTAATTAAGAGTC
Found at i:7647 original size:16 final size:16
Alignment explanation
Indices: 7626--7656 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
7616 GTAATCAAGA
7626 GAAGTAATCAGTAAAG
1 GAAGTAATCAGTAAAG
7642 GAAGTAATCAGTAAA
1 GAAGTAATCAGTAAA
7657 ATGGTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (16 bp):
GAAGTAATCAGTAAAG
Found at i:7824 original size:26 final size:25
Alignment explanation
Indices: 7781--7848 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
7771 CAAAGAGTAA
* *
7781 AATGACAAATGGTGATTAAATTCAAAG
1 AATGA-AAATAGTAATTAAATTC-AAG
*
7808 AATGAAAATAGTAATTAAGTTCAAG
1 AATGAAAATAGTAATTAAATTCAAG
**
7833 AGGGTAAAATAGTAAT
1 AATG-AAAATAGTAAT
7849 CAGTAAAGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 5 0.14
26 25 0.71
27 5 0.14
ACGTcount: A:0.50, C:0.04, G:0.19, T:0.26
Consensus pattern (25 bp):
AATGAAAATAGTAATTAAATTCAAG
Found at i:7881 original size:14 final size:14
Alignment explanation
Indices: 7843--7888 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
7833 AGGGTAAAAT
7843 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
* **
7857 AGAAAAAAGTAAAG
1 AGTAATCAGTAAAG
7871 AGTAATCAGTAAA-
1 AGTAATCAGTAAAG
7884 AGTAA
1 AGTAA
7889 AAATGGCAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 5 0.19
14 21 0.81
ACGTcount: A:0.59, C:0.04, G:0.20, T:0.17
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:7948 original size:21 final size:21
Alignment explanation
Indices: 7919--7970 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
7909 AAGTAATCGG
7919 GTAAT-AGTAATCAGTAAAAGA
1 GTAATCAGTAA-CAGTAAAAGA
* *
7940 -TAATCAGTAAGAGTAAAATA
1 GTAATCAGTAACAGTAAAAGA
7960 GTAATCAGTAA
1 GTAATCAGTAA
7971 GAGCAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (21 bp):
GTAATCAGTAACAGTAAAAGA
Found at i:7971 original size:21 final size:21
Alignment explanation
Indices: 7931--7998 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
7921 AATAGTAATC
*
7931 AGTAAAAGA-TAATCAGTAAG
1 AGTAAAATAGTAATCAGTAAG
7951 AGTAAAATAGTAATCAGTAAG
1 AGTAAAATAGTAATCAGTAAG
* *
7972 AGCAAAATGGTAAT-AGGTAAAG
1 AGTAAAATAGTAATCA-GT-AAG
7994 AGTAA
1 AGTAA
7999 TCAGTAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.22
21 25 0.61
22 7 0.17
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.21
Consensus pattern (21 bp):
AGTAAAATAGTAATCAGTAAG
Found at i:8005 original size:21 final size:22
Alignment explanation
Indices: 7981--8027 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
7971 GAGCAAAATG
7981 GTAATAG-GT-AAAGAGTAATCA
1 GTAATAGAGTAAAAG-GTAATCA
*
8002 GTAA-AGAGTAAAAGGTGATCA
1 GTAATAGAGTAAAAGGTAATCA
8023 GTAAT
1 GTAAT
8028 TCAAAGAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 2 0.09
21 16 0.73
22 4 0.18
ACGTcount: A:0.47, C:0.04, G:0.26, T:0.23
Consensus pattern (22 bp):
GTAATAGAGTAAAAGGTAATCA
Found at i:8109 original size:28 final size:29
Alignment explanation
Indices: 8060--8130 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
8050 GTATAAGAGG
8060 AAAAGAAGAGTAA--AAAGTGGTAATCAAT
1 AAAAG-AGAGTAAGGAAAGTGGTAATCAAT
* *
8088 AAAAGAGAGTAAGGAAAG-GGTAATTAGT
1 AAAAGAGAGTAAGGAAAGTGGTAATCAAT
8116 AAAA-AGAGT-AGGAAA
1 AAAAGAGAGTAAGGAAA
8131 AGAGTAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 6 0.15
27 12 0.31
28 17 0.44
29 4 0.10
ACGTcount: A:0.56, C:0.01, G:0.27, T:0.15
Consensus pattern (29 bp):
AAAAGAGAGTAAGGAAAGTGGTAATCAAT
Found at i:11252 original size:12 final size:12
Alignment explanation
Indices: 11235--11269 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11225 TTGAGAAAAA
*
11235 TATTTTCCTTGG
1 TATTTTCCTTAG
*
11247 TATTTTCCATAG
1 TATTTTCCTTAG
11259 TATTTTCCTTA
1 TATTTTCCTTA
11270 ACACCAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (12 bp):
TATTTTCCTTAG
Found at i:11356 original size:17 final size:17
Alignment explanation
Indices: 11326--11359 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11316 TGATTTCAAT
11326 TTTCCCTAAAATTTTCC
1 TTTCCCTAAAATTTTCC
* *
11343 TTTCCTTAATATTTTCC
1 TTTCCCTAAAATTTTCC
11360 CTAATACCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTCCCTAAAATTTTCC
Done.