Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007253.1 Corchorus capsularis cultivar CVL-1 contig07274, 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: 18568
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:8946 original size:42 final size:41
Alignment explanation
Indices: 8799--8951 Score: 193
Period size: 43 Copynumber: 3.7 Consensus size: 41
8789 CCTTTTTAAA
* *
8799 CAATTGAAAACTGTAAAGTTGTTGGAATGCTTTCCCTTGGGAG
1 CAATTGAAAACTGTAAAGTTGTTGGAATGC--CCCCTTGTGAG
* *
8842 CAATTGAAAA-TG-AAAGCTGTTGGAATACCCCCTTTGTGAG
1 CAATTGAAAACTGTAAAGTTGTTGGAATGCCCCC-TTGTGAG
8882 CAATTTGAAAACTGTAAAGTTGTTGGAATGCCCCCTCTGTGAG
1 CAA-TTGAAAACTGTAAAGTTGTTGGAATGCCCCCT-TGTGAG
* *
8925 CAAGTGAAAACTGAAAAGTTGTTGGAA
1 CAATTGAAAACTGTAAAGTTGTTGGAA
8952 AACTGAAAAG
Statistics
Matches: 97, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
39 3 0.03
40 9 0.09
41 21 0.22
42 27 0.28
43 37 0.38
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (41 bp):
CAATTGAAAACTGTAAAGTTGTTGGAATGCCCCCTTGTGAG
Found at i:8954 original size:19 final size:19
Alignment explanation
Indices: 8930--8989 Score: 102
Period size: 19 Copynumber: 3.2 Consensus size: 19
8920 GTGAGCAAGT
8930 GAAAACTGAAAAGTTGTTG
1 GAAAACTGAAAAGTTGTTG
8949 GAAAACTGAAAAGTTGTTG
1 GAAAACTGAAAAGTTGTTG
**
8968 GAACGCTGAAAAGTTGTTG
1 GAAAACTGAAAAGTTGTTG
8987 GAA
1 GAA
8990 TGTCTCCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (19 bp):
GAAAACTGAAAAGTTGTTG
Found at i:9019 original size:81 final size:80
Alignment explanation
Indices: 8897--9051 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 80
8887 TGAAAACTGT
*
8897 AAAGTTGTTGGAATGCCCCCTCTGTGAGCAAGTGAAAACTGAAAAGTTGTTGGAAAACTGAAAAG
1 AAAGTTGTTGGAATGCCCCCTCTGGGAGCAAGTGAAAACTGAAAAGTTGTTGGAAAACTGAAAAG
8962 TTGTTGGAACGCTGA
66 TTGTTGGAACGCTGA
* * * **
8977 AAAGTTGTTGGAATGTCTCCTTTTGGGAGC-AGCTGAAAACTGAAAAGTTGTTGGAATGCTGAAA
1 AAAGTTGTTGGAATG-CCCCCTCTGGGAGCAAG-TGAAAACTGAAAAGTTGTTGGAAAACTGAAA
9041 AGTTGTTGGAA
64 AGTTGTTGGAA
9052 TGTCTCCTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 17 0.25
81 50 0.75
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (80 bp):
AAAGTTGTTGGAATGCCCCCTCTGGGAGCAAGTGAAAACTGAAAAGTTGTTGGAAAACTGAAAAG
TTGTTGGAACGCTGA
Found at i:9040 original size:19 final size:19
Alignment explanation
Indices: 9016--9053 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9006 CAGCTGAAAA
9016 CTGAAAAGTTGTTGGAATG
1 CTGAAAAGTTGTTGGAATG
9035 CTGAAAAGTTGTTGGAATG
1 CTGAAAAGTTGTTGGAATG
9054 TCTCCTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (19 bp):
CTGAAAAGTTGTTGGAATG
Found at i:9095 original size:62 final size:62
Alignment explanation
Indices: 8949--9096 Score: 287
Period size: 62 Copynumber: 2.4 Consensus size: 62
8939 AAAGTTGTTG
*
8949 GAAAACTGAAAAGTTGTTGGAACGCTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCT
1 GAAAACTGAAAAGTTGTTGGAATGCTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCT
9011 GAAAACTGAAAAGTTGTTGGAATGCTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCT
1 GAAAACTGAAAAGTTGTTGGAATGCTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCT
9073 GAAAACTGAAAAGTTGTTGGAATG
1 GAAAACTGAAAAGTTGTTGGAATG
9097 TCTCCTTTTG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 85 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (62 bp):
GAAAACTGAAAAGTTGTTGGAATGCTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCT
Found at i:9096 original size:43 final size:43
Alignment explanation
Indices: 9035--9139 Score: 210
Period size: 43 Copynumber: 2.4 Consensus size: 43
9025 TGTTGGAATG
9035 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAA
1 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAA
9078 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAA
1 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAA
9121 CTGAAAAGTTGTTGGAATG
1 CTGAAAAGTTGTTGGAATG
9140 CTGAAAAGTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (43 bp):
CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAA
Found at i:9112 original size:105 final size:105
Alignment explanation
Indices: 8973--9227 Score: 458
Period size: 105 Copynumber: 2.4 Consensus size: 105
8963 TGTTGGAACG
8973 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAACTGAAAAGTTGTTGGAATGCTG
1 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAACTGAAAAGTTGTTGGAATGCTG
*
9038 AAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAA
66 AAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAACTGAAAA
9078 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAACTGAAAAGTTGTTGGAATGCTG
1 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAACTGAAAAGTTGTTGGAATGCTG
9143 AAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAACTGAAAA
66 AAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAACTGAAAA
* * * *
9183 CTGAAAAGTTGTTGGAATG-CCCCTCTTGGGAGCAACCGAAAACTG
1 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAACTG
9228 CTGAAAGATG
Statistics
Matches: 145, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
104 22 0.15
105 123 0.85
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (105 bp):
CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAACTGAAAAGTTGTTGGAATGCTG
AAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAACTGAAAA
Found at i:9144 original size:62 final size:62
Alignment explanation
Indices: 9078--9202 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
9068 CAGCTGAAAA
*
9078 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAGCTGAAAACTGAAAAGTTGTTGGAATG
1 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAACTGAAAACTGAAAAGTTGTTGGAATG
9140 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAACTGAAAACTGAAAAGTTGTTGGAATG
1 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAACTGAAAACTGAAAAGTTGTTGGAATG
9202 C
1 C
9203 CCCTCTTGGG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (62 bp):
CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAACTGAAAACTGAAAAGTTGTTGGAATG
Found at i:9145 original size:19 final size:19
Alignment explanation
Indices: 9121--9158 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9111 CAGCTGAAAA
9121 CTGAAAAGTTGTTGGAATG
1 CTGAAAAGTTGTTGGAATG
9140 CTGAAAAGTTGTTGGAATG
1 CTGAAAAGTTGTTGGAATG
9159 TCTCCTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (19 bp):
CTGAAAAGTTGTTGGAATG
Found at i:9225 original size:42 final size:43
Alignment explanation
Indices: 9140--9227 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 43
9130 TGTTGGAATG
* * *
9140 CTGAAAAGTTGTTGGAATGTCTCCTTTTGGGAGCAACTGAAAA
1 CTGAAAAGTTGTTGGAATGTCCCCTCTTGGGAGCAACCGAAAA
9183 CTGAAAAGTTGTTGGAATG-CCCCTCTTGGGAGCAACCGAAAA
1 CTGAAAAGTTGTTGGAATGTCCCCTCTTGGGAGCAACCGAAAA
9225 CTG
1 CTG
9228 CTGAAAGATG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 23 0.55
43 19 0.45
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (43 bp):
CTGAAAAGTTGTTGGAATGTCCCCTCTTGGGAGCAACCGAAAA
Found at i:9285 original size:38 final size:38
Alignment explanation
Indices: 9223--9305 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
9213 AGCAACCGAA
* *
9223 AACTGCTGAAAGATGACCCATTTCCAATCGATCTTGAT
1 AACTGTTGAAAGACGACCCATTTCCAATCGATCTTGAT
** *
9261 AACTGTTGAAAGACGACCTGTTTCCAGTCGATCTTGAT
1 AACTGTTGAAAGACGACCCATTTCCAATCGATCTTGAT
9299 AACTGTT
1 AACTGTT
9306 TTCAGATGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (38 bp):
AACTGTTGAAAGACGACCCATTTCCAATCGATCTTGAT
Found at i:10933 original size:20 final size:21
Alignment explanation
Indices: 10908--10960 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
10898 ACTAGCGCTG
*
10908 GGCG-CCCATGTGCTATGCTT
1 GGCGACCCATGTGCTATGCCT
* * *
10928 GGCGCCCCATGTGGTTTGCCT
1 GGCGACCCATGTGCTATGCCT
10949 GGCGACCCATGT
1 GGCGACCCATGT
10961 ACTCCAGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.09, C:0.32, G:0.32, T:0.26
Consensus pattern (21 bp):
GGCGACCCATGTGCTATGCCT
Found at i:12043 original size:15 final size:15
Alignment explanation
Indices: 12020--12050 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12010 CAATGAATTA
12020 ATTAATATTTTTTTT
1 ATTAATATTTTTTTT
*
12035 ATTATTATTTTTTTT
1 ATTAATATTTTTTTT
12050 A
1 A
12051 GCAAGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTAATATTTTTTTT
Found at i:14473 original size:13 final size:13
Alignment explanation
Indices: 14455--14482 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
14445 GGTAACATCG
14455 GCATGGCATGGGT
1 GCATGGCATGGGT
14468 GCATGGCATGGGT
1 GCATGGCATGGGT
14481 GC
1 GC
14483 TGTCAGCGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.18, G:0.46, T:0.21
Consensus pattern (13 bp):
GCATGGCATGGGT
Found at i:14693 original size:19 final size:20
Alignment explanation
Indices: 14655--14693 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
14645 GCTTGGTCGC
* *
14655 TTTGCTTCCAAATTTCAATT
1 TTTGCTACCAAATCTCAATT
14675 TTTGCTACCAAA-CTCAATT
1 TTTGCTACCAAATCTCAATT
14694 CCGATTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTGCTACCAAATCTCAATT
Found at i:18408 original size:13 final size:13
Alignment explanation
Indices: 18390--18423 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
18380 TAATTATTGT
18390 TTGCTTTATTAAA
1 TTGCTTTATTAAA
*
18403 TTGCTTTATTAAT
1 TTGCTTTATTAAA
18416 TTGCTTTA
1 TTGCTTTA
18424 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (13 bp):
TTGCTTTATTAAA
Found at i:18431 original size:6 final size:6
Alignment explanation
Indices: 18420--18446 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18410 ATTAATTTGC
18420 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
18447 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Done.