Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013956.1 Corchorus capsularis cultivar CVL-1 contig13977, 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: 32216
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:392 original size:32 final size:32
Alignment explanation
Indices: 308--392 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 32
298 GGAATTTTCT
308 GGATTTCTGCAGAAACTTCACCAGCAGATTTG
1 GGATTTCTGCAGAAACTTCACCAGCAGATTTG
** * *
340 GTCTTGACCT-AAGAAACTTCACCAGCAGATTTG
1 GGATT--TCTGCAGAAACTTCACCAGCAGATTTG
373 GGATTTCTGCAGAAACTTCA
1 GGATTTCTGCAGAAACTTCA
393 ATTTTCTGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
31 2 0.05
32 13 0.31
33 25 0.60
34 2 0.05
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (32 bp):
GGATTTCTGCAGAAACTTCACCAGCAGATTTG
Found at i:3088 original size:39 final size:36
Alignment explanation
Indices: 3015--3097 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 36
3005 ACACACGGGT
*
3015 ACTCTCTCAACACATAAAAGTCCCAAAAATATGGGC
1 ACTCTCTCAACACATAAAAGTCCCAAAAACATGGGC
*
3051 ACTCTCTCAACA-ATACACAAAGATCCCAAATACATGGGC
1 ACTCTCTCAACACAT--A-AAAG-TCCCAAAAACATGGGC
3090 -CTCCTCTC
1 ACT-CTCTC
3098 TCATACAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 2 0.05
36 12 0.30
37 1 0.03
38 6 0.15
39 19 0.47
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.20
Consensus pattern (36 bp):
ACTCTCTCAACACATAAAAGTCCCAAAAACATGGGC
Found at i:11152 original size:10 final size:10
Alignment explanation
Indices: 11137--11189 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
11127 GGCCAATCGA
11137 TGGCCGGTTG
1 TGGCCGGTTG
11147 TGGCCGGTTGG
1 TGGCCGGTT-G
** *
11158 TGCGCCAATCG
1 TG-GCCGGTTG
11169 ATGGCCGGTTG
1 -TGGCCGGTTG
11180 TGGCCGGTTG
1 TGGCCGGTTG
11190 CCCCATGCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 19 0.56
11 9 0.26
12 6 0.18
ACGTcount: A:0.06, C:0.23, G:0.45, T:0.26
Consensus pattern (10 bp):
TGGCCGGTTG
Found at i:16555 original size:16 final size:16
Alignment explanation
Indices: 16517--16620 Score: 70
Period size: 16 Copynumber: 6.6 Consensus size: 16
16507 CGGGCTCGGG
*
16517 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
*
16532 CTGGTTCGGG-ATTTTT
1 CGGGTTCGGGTA-TTTT
16548 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* ** **
16564 CGGGCTCTAGT-TAAGT
1 CGGGTTCGGGTAT-TTT
* * *
16580 CGGGCTCGGGTAATGT
1 CGGGTTCGGGTATTTT
*
16596 CGGGTTCGGATATTTT
1 CGGGTTCGGGTATTTT
16612 CGGGTTCGG
1 CGGGTTCGG
16621 TCTCGGGTCG
Statistics
Matches: 68, Mismatches: 16, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
14 1 0.01
15 10 0.15
16 56 0.82
17 1 0.01
ACGTcount: A:0.10, C:0.16, G:0.38, T:0.37
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:17652 original size:16 final size:16
Alignment explanation
Indices: 17633--17675 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
17623 TCAGGCTGCC
*
17633 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTAATT
**
17649 TCGGACTCGGGTAATT
1 TCGGGTTCGGGTAATT
17665 TCGGGTTCGGG
1 TCGGGTTCGGG
17676 CGGGTTCGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.40, T:0.35
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:24836 original size:22 final size:22
Alignment explanation
Indices: 24804--24888 Score: 143
Period size: 22 Copynumber: 3.9 Consensus size: 22
24794 CTAAAGATTA
* *
24804 TGGCCATGAGATTCGGCCATGA
1 TGGCCGTGAGATTCGGCCATGG
*
24826 TGACCGTGAGATTCGGCCATGG
1 TGGCCGTGAGATTCGGCCATGG
24848 TGGCCGTGAGATTCGGCCATGG
1 TGGCCGTGAGATTCGGCCATGG
24870 TGGCCGTGAGATTCGGCCA
1 TGGCCGTGAGATTCGGCCA
24889 AATAGTGGTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.22
Consensus pattern (22 bp):
TGGCCGTGAGATTCGGCCATGG
Found at i:25173 original size:43 final size:43
Alignment explanation
Indices: 25081--25202 Score: 217
Period size: 43 Copynumber: 2.8 Consensus size: 43
25071 TTTAAAAGGC
* *
25081 CATGTTGTCTTTTCAATTTGACCAAGGTGGCTGTGACAAAAAGT
1 CATGTTGGCTTTTCAATTTGACCAAGGCGG-TGTGACAAAAAGT
25125 CATGTTGGCTTTTCAATTTGACCAAGGCGGTGTGACAAAAAGT
1 CATGTTGGCTTTTCAATTTGACCAAGGCGGTGTGACAAAAAGT
25168 CATGTTGGCTTTTCAATTTGACCAAGGCGGTGTGA
1 CATGTTGGCTTTTCAATTTGACCAAGGCGGTGTGA
25203 AGGCAAATCA
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
43 48 0.63
44 28 0.37
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (43 bp):
CATGTTGGCTTTTCAATTTGACCAAGGCGGTGTGACAAAAAGT
Found at i:29649 original size:22 final size:22
Alignment explanation
Indices: 29623--29708 Score: 147
Period size: 22 Copynumber: 3.9 Consensus size: 22
29613 ACTAAAGACT
29623 GTGGCCGTGAGATTCGGCCATG
1 GTGGCCGTGAGATTCGGCCATG
*
29645 GTGGCCGTGAGATTCGACCATG
1 GTGGCCGTGAGATTCGGCCATG
29667 GTGGCCGTGAGATTCGGCCATG
1 GTGGCCGTGAGATTCGGCCATG
29689 GTGGTCC-TGAGATTCGGCCA
1 GTGG-CCGTGAGATTCGGCCA
29709 CATAATGGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
22 59 0.97
23 2 0.03
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.23
Consensus pattern (22 bp):
GTGGCCGTGAGATTCGGCCATG
Found at i:29884 original size:22 final size:22
Alignment explanation
Indices: 29859--29925 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
29849 GGGTTAGTAT
29859 GTGGTCGTGAGATTCGCCCATG
1 GTGGTCGTGAGATTCGCCCATG
* *
29881 GTGGTCATGAGATTTGGCCACATG
1 GTGGTCGTGAGA-TTCGCC-CATG
* *
29905 GTGGCCGTGAGATTCGACCAT
1 GTGGTCGTGAGATTCGCCCAT
29926 CGTTCAAAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
22 14 0.38
23 9 0.24
24 14 0.38
ACGTcount: A:0.18, C:0.21, G:0.34, T:0.27
Consensus pattern (22 bp):
GTGGTCGTGAGATTCGCCCATG
Found at i:29908 original size:24 final size:23
Alignment explanation
Indices: 29859--29918 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
29849 GGGTTAGTAT
29859 GTGGTCGTGAGA-TTCGCCCATG
1 GTGGTCGTGAGATTTCGCCCATG
* *
29881 GTGGTCATGAGATTTGGCCACATG
1 GTGGTCGTGAGATTTCGCC-CATG
*
29905 GTGGCCGTGAGATT
1 GTGGTCGTGAGATT
29919 CGACCATCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 11 0.34
23 5 0.16
24 16 0.50
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (23 bp):
GTGGTCGTGAGATTTCGCCCATG
Done.