Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012174.1 Corchorus capsularis cultivar CVL-1 contig12195, 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: 20937
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:2336 original size:2 final size:2
Alignment explanation
Indices: 2329--2358 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2319 TAATTAATAG
2329 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2359 GATTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5631 original size:31 final size:30
Alignment explanation
Indices: 5529--5695 Score: 105
Period size: 31 Copynumber: 5.6 Consensus size: 30
5519 TTATGCTAAT
* *
5529 TGCTCAAATAAGAGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-CGAAAA
* * * **
5560 TGCTCAAATAAGGGTCCGATC-TTT-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTTCGAAAA
5589 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TCGAAAA
* * * **
5620 TGCTCAAATAAGGGCCCGATC-TTT-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTTCGAAAA
5649 TGGC-C-AATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TCGAAAA
*
5679 TGCTCAAATAAAGGCCT
1 TGCTCAAATAAGGGCCT
5696 GGTGTCAATT
Statistics
Matches: 101, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
27 4 0.04
28 14 0.14
29 22 0.22
30 12 0.12
31 41 0.41
32 8 0.08
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTCGAAAA
Found at i:5687 original size:59 final size:60
Alignment explanation
Indices: 5533--5694 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 60
5523 GCTAATTGCT
* * *
5533 CAAATAAGAGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
5593 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
5653 C-AATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAAGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
5695 TGGTGTCAAT
Statistics
Matches: 97, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
59 40 0.41
60 56 0.58
61 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:5758 original size:31 final size:31
Alignment explanation
Indices: 5723--5890 Score: 145
Period size: 31 Copynumber: 5.5 Consensus size: 31
5713 CGCGTGAGAC
5723 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
* ** *
5754 AGGCCCTTGTTTG-GCCAAATT--CAAA-GAT
1 AGGCCCTTATTTGAG-CATTTTGGCAAACGTT
*
5782 GGAGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AG-GCCCTTATTTGAGCATTTTGGCAAACGTT
** * *
5814 AGGCCCTTATTTG-GCCAAATT---AAAAGAT
1 AGGCCCTTATTTGAG-CATTTTGGCAAACGTT
*
5842 CGTGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AG-GCCCTTATTTGAGCATTTTGGCAAACGTT
*
5874 AAGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
5891 ATTAGCCTTT
Statistics
Matches: 104, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 9 0.09
29 33 0.32
30 4 0.04
31 50 0.48
32 8 0.08
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTT
Found at i:5793 original size:60 final size:60
Alignment explanation
Indices: 5725--5886 Score: 279
Period size: 60 Copynumber: 2.7 Consensus size: 60
5715 CGTGAGACAG
* * *
5725 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTGTTTGGCCAAATTCAAAGATGGA
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGA
*
5785 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGT
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGA
*
5845 GCCCTTATTTGAGCATTTTGGCAAACGTTAAGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
5887 AGCAATTAGC
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGA
Found at i:8973 original size:4 final size:4
Alignment explanation
Indices: 8964--8990 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
8954 CCGTGAGAGA
8964 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
8991 ATCTTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:9966 original size:20 final size:22
Alignment explanation
Indices: 9924--9971 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
9914 CCGTCTCCAC
* *
9924 TCTCTTCTTCTCTTCCTTTTCT
1 TCTCTTCTTCTCTCCCTTCTCT
9946 TCTCTTCTT-TC-CCCTTCTCT
1 TCTCTTCTTCTCTCCCTTCTCT
9966 TCTCTT
1 TCTCTT
9972 TTGAACCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 2 0.08
22 9 0.38
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (22 bp):
TCTCTTCTTCTCTCCCTTCTCT
Found at i:13752 original size:19 final size:20
Alignment explanation
Indices: 13706--13753 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
13696 TGTGGCACGC
*
13706 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
13728 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
13747 CACATGT
1 CACATGT
13754 CACACCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:13767 original size:53 final size:53
Alignment explanation
Indices: 13672--13775 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 53
13662 CGACGTGGCA
* * ** * *
13672 TGCCACGTGTACCAAAAAGTGATATGTGGCACGCCACATGTACCAAAAAGTCG
1 TGCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACAAAAAAGTCG
* *
13725 TGCCACATGTACCAAAAAGTGACACATGTCACACCACGTGTACAAAAAAGT
1 TGCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACAAAAAAGT
13776 GACACGTGGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (53 bp):
TGCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACAAAAAAGTCG
Found at i:14703 original size:25 final size:25
Alignment explanation
Indices: 14655--14720 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
14645 CTAAATATAA
* *
14655 AATAATGAAAACAATAA-AGAATCTT
1 AATAA-GAAAATAATAATAGAATCTC
14680 ATATAAGAAAATAATAATAG-ATCTC
1 A-ATAAGAAAATAATAATAGAATCTC
14705 AA-AA-AAAATAATAATA
1 AATAAGAAAATAATAATA
14721 AAATTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
22 12 0.32
23 2 0.05
24 1 0.03
25 16 0.43
26 6 0.16
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (25 bp):
AATAAGAAAATAATAATAGAATCTC
Found at i:15109 original size:30 final size:30
Alignment explanation
Indices: 15075--15133 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
15065 TCAACTAATT
15075 AATCAATCAAAAGTAATTAATATATTTCCC
1 AATCAATCAAAAGTAATTAATATATTTCCC
15105 AATCAATCAAAAGTAATTAATATATTTCC
1 AATCAATCAAAAGTAATTAATATATTTCC
15134 TTTTGTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.34
Consensus pattern (30 bp):
AATCAATCAAAAGTAATTAATATATTTCCC
Found at i:15241 original size:8 final size:8
Alignment explanation
Indices: 15222--15263 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
15212 ATAAGATTAC
15222 TATTACTAT
1 TATTA-TAT
15231 TATTATAT
1 TATTATAT
15239 TATTATAT
1 TATTATAT
*
15247 TATAATAT
1 TATTATAT
15255 ATATTATAT
1 -TATTATAT
15264 ATAATATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 18 0.60
9 12 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
TATTATAT
Found at i:15281 original size:14 final size:16
Alignment explanation
Indices: 15247--15283 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
15237 ATTATTATAT
*
15247 TATAATATATATTATA
1 TATAATATATATAATA
15263 TATAATATA-ATAATA
1 TATAATATATATAATA
15278 -ATAATA
1 TATAATA
15284 ATAACAACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 6 0.30
15 5 0.25
16 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATATATATAATA
Found at i:17246 original size:36 final size:36
Alignment explanation
Indices: 17206--17280 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
17196 GTGTAATATC
* * *
17206 TATGTAATCTTTTTATCTTTGACAATGTGGAAGCTT
1 TATGTAATATTGTTATATTTGACAATGTGGAAGCTT
**
17242 TATGTAATATTGTTATATTTGACAATGTGGCTGCTT
1 TATGTAATATTGTTATATTTGACAATGTGGAAGCTT
17278 TAT
1 TAT
17281 ATAAATGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.48
Consensus pattern (36 bp):
TATGTAATATTGTTATATTTGACAATGTGGAAGCTT
Found at i:18078 original size:20 final size:20
Alignment explanation
Indices: 18055--18098 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
18045 GTTATAGGTC
**
18055 ATGGCTTTAGGGTTTAGGAA
1 ATGGCTTTAGGAATTAGGAA
18075 ATGGCTTTAGGAATTAGGAA
1 ATGGCTTTAGGAATTAGGAA
18095 ATGG
1 ATGG
18099 GTATTGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.32
Consensus pattern (20 bp):
ATGGCTTTAGGAATTAGGAA
Found at i:20146 original size:29 final size:29
Alignment explanation
Indices: 20104--20181 Score: 147
Period size: 29 Copynumber: 2.7 Consensus size: 29
20094 ATTAAAGGAG
20104 CCGTCAATTGTGCTGACGTGGCAGTGACA
1 CCGTCAATTGTGCTGACGTGGCAGTGACA
20133 CCGTCAATTGTGCTGACGTGGCAGTGACA
1 CCGTCAATTGTGCTGACGTGGCAGTGACA
*
20162 CTGTCAATTGTGCTGACGTG
1 CCGTCAATTGTGCTGACGTG
20182 TCATCTGCCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.19, C:0.23, G:0.31, T:0.27
Consensus pattern (29 bp):
CCGTCAATTGTGCTGACGTGGCAGTGACA
Done.