Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013882.1 Corchorus capsularis cultivar CVL-1 contig13903, 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: 26830
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:1742 original size:33 final size:33
Alignment explanation
Indices: 1662--1754 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
1652 GCTGATGACC
* *
1662 GTATCGTGCCGCCCCAGGAGGGCGACAGGCCGTG
1 GTAT-GTGCCGCCCCAGGAGGGCGGCAGGCCATG
*
1696 GTATGTGCTGCCCCAGGAGGGCGGCATGAGCCATG
1 GTATGTGCCGCCCCAGGAGGGCGGCA-G-GCCATG
*
1731 GT-T-TGCCGCCCCAAGAGGGCGGCA
1 GTATGTGCCGCCCCAGGAGGGCGGCA
1755 AATGCCACGG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 39 0.75
34 6 0.12
35 7 0.13
ACGTcount: A:0.16, C:0.30, G:0.40, T:0.14
Consensus pattern (33 bp):
GTATGTGCCGCCCCAGGAGGGCGGCAGGCCATG
Found at i:3036 original size:21 final size:20
Alignment explanation
Indices: 3010--3051 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3000 TCTTGAAGGC
*
3010 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGA-CAA
*
3031 TTGAAGAGCATTGAAGACAA
1 TTGAAGACCATTGAAGACAA
3051 T
1 T
3052 AAGCAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGAAGACCATTGAAGACAA
Found at i:11973 original size:30 final size:30
Alignment explanation
Indices: 11937--12001 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
11927 TCCCTCAGAA
* *
11937 TCTGAGCCTCTCTCTAAAGCTCTCTCTCCC
1 TCTGAGCCTCTCCCTAAAGCTCTCGCTCCC
*
11967 TCTGAGCCTCTCCCTGAAGCTCTCGCTCCC
1 TCTGAGCCTCTCCCTAAAGCTCTCGCTCCC
11997 TCTGA
1 TCTGA
12002 AGCTCAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.12, C:0.43, G:0.14, T:0.31
Consensus pattern (30 bp):
TCTGAGCCTCTCCCTAAAGCTCTCGCTCCC
Found at i:12003 original size:18 final size:17
Alignment explanation
Indices: 11943--12006 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 17
11933 AGAATCTGAG
* *
11943 CCTCTCTCTAAAGCTCT
1 CCTCCCTCTGAAGCTCT
11960 CTCTCCCTCTG-AGC-CT
1 C-CTCCCTCTGAAGCTCT
11976 -CT-CC-CTGAAGCTCT
1 CCTCCCTCTGAAGCTCT
11990 CGCTCCCTCTGAAGCTC
1 C-CTCCCTCTGAAGCTC
12007 AACCTCTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
12 3 0.08
13 5 0.13
14 4 0.11
16 4 0.11
17 6 0.16
18 16 0.42
ACGTcount: A:0.12, C:0.45, G:0.12, T:0.30
Consensus pattern (17 bp):
CCTCCCTCTGAAGCTCT
Found at i:12200 original size:18 final size:18
Alignment explanation
Indices: 12150--12206 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
12140 ATTAATCGTA
*
12150 AATAAACTAATTAAAACT
1 AATAAACTAATTAACACT
* *
12168 AATAAAATAATTAACCCT
1 AATAAACTAATTAACACT
* *
12186 AATAAACTATTTAACAAT
1 AATAAACTAATTAACACT
12204 AAT
1 AAT
12207 TAATGTTACT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAACTAATTAACACT
Found at i:12659 original size:15 final size:15
Alignment explanation
Indices: 12639--12672 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
12629 ATTTAGAGGT
*
12639 TGTTTGAAGTAAAGA
1 TGTTTGAAATAAAGA
12654 TGTTTGAAATAAAGA
1 TGTTTGAAATAAAGA
12669 TGTT
1 TGTT
12673 AGTTTGAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (15 bp):
TGTTTGAAATAAAGA
Found at i:13878 original size:33 final size:32
Alignment explanation
Indices: 13836--13914 Score: 99
Period size: 30 Copynumber: 2.5 Consensus size: 32
13826 CCTAGTTTAG
13836 GTGTTGTTTGCGATGACACTAAATCTGCTTTGA
1 GTGTTGTTTG-GATGACACTAAATCTGCTTTGA
** *
13869 GTGTTGTTT-G-TGACACTAGTTCTGTTTTGA
1 GTGTTGTTTGGATGACACTAAATCTGCTTTGA
13899 GTGTTGTTTGTGATGA
1 GTGTTGTTTG-GATGA
13915 TAAAACAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 26 0.65
31 1 0.03
32 1 0.03
33 12 0.30
ACGTcount: A:0.16, C:0.10, G:0.28, T:0.46
Consensus pattern (32 bp):
GTGTTGTTTGGATGACACTAAATCTGCTTTGA
Found at i:20127 original size:33 final size:33
Alignment explanation
Indices: 20051--20163 Score: 140
Period size: 33 Copynumber: 3.4 Consensus size: 33
20041 TAGACAAAGG
* *
20051 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT
** * *
20084 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
20117 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT
20150 GTCGCGTGGCCGGT
1 GTCGCGTGGCCGGT
20164 CTTGTCTCCG
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
32 3 0.04
33 65 0.96
ACGTcount: A:0.08, C:0.27, G:0.42, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Found at i:26292 original size:33 final size:33
Alignment explanation
Indices: 26216--26328 Score: 131
Period size: 33 Copynumber: 3.4 Consensus size: 33
26206 TAGACAAAGG
* *
26216 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT
** * *
26249 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
26282 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT
*
26315 ATCGCGTGGCCGGT
1 GTCGCGTGGCCGGT
26329 CTTGTCTCCG
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
32 3 0.04
33 64 0.96
ACGTcount: A:0.09, C:0.27, G:0.41, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Done.