Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013839.1 Corchorus capsularis cultivar CVL-1 contig13860, 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: 12575
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Found at i:3961 original size:60 final size:59
Alignment explanation
Indices: 3897--4138 Score: 299
Period size: 60 Copynumber: 4.0 Consensus size: 59
3887 ATACAAACCC
* * * * * *
3897 CCAACAACTCCAACACCACC-AACCAAGCCACCCACAACTCCAGCACCTCC-TTACAAGCCA
1 CCAACAACTCCAGCACCGCCTTA-CAAGCCACCAACAACCCCAGCTCCTCCATT--AAGCCA
*
3957 CCAACAACTCCAGCACCGCCTTACAAGCCACCAACCACCCCAGCTCCTCCAGTTAAGCCA
1 CCAACAACTCCAGCACCGCCTTACAAGCCACCAACAACCCCAGCTCCTCCA-TTAAGCCA
*
4017 CCAACAACTCCAGCACCGCCTTACAAACCACCAACAACCCCAGCTCCTCCAGTTAAGCCA
1 CCAACAACTCCAGCACCGCCTTACAAGCCACCAACAACCCCAGCTCCTCCA-TTAAGCCA
** * * *
4077 CCAACAACTCCTTCACCGCCTTACAAACCACCAACAACTCCAGCTCCTCCAGTCAAGCCA
1 CCAACAACTCCAGCACCGCCTTACAAGCCACCAACAACCCCAGCTCCTCCA-TTAAGCCA
4137 CC
1 CC
4139 TTACAAGGCA
Statistics
Matches: 166, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
60 163 0.98
61 1 0.01
62 2 0.01
ACGTcount: A:0.33, C:0.48, G:0.07, T:0.12
Consensus pattern (59 bp):
CCAACAACTCCAGCACCGCCTTACAAGCCACCAACAACCCCAGCTCCTCCATTAAGCCA
Found at i:4138 original size:30 final size:30
Alignment explanation
Indices: 3888--4126 Score: 227
Period size: 30 Copynumber: 8.0 Consensus size: 30
3878 TACTCCCCCA
* * * *
3888 TACAAACCCCCAACAACTCCAACACCACC-
1 TACAAGCCACCAACAACTCCAGCACCTCCT
* *
3917 AACCAAGCCACCCACAACTCCAGCACCTCCT
1 TA-CAAGCCACCAACAACTCCAGCACCTCCT
*
3948 TACAAGCCACCAACAACTCCAGCACCGCCT
1 TACAAGCCACCAACAACTCCAGCACCTCCT
* * *
3978 TACAAGCCACCAACCACCCCAGCTCCTCCAGT
1 TACAAGCCACCAACAACTCCAGCACCTCC--T
*
4010 T--AAGCCACCAACAACTCCAGCACCGCCT
1 TACAAGCCACCAACAACTCCAGCACCTCCT
* * *
4038 TACAAACCACCAACAACCCCAGCTCCTCCAGT
1 TACAAGCCACCAACAACTCCAGCACCTCC--T
** *
4070 T--AAGCCACCAACAACTCCTTCACCGCCT
1 TACAAGCCACCAACAACTCCAGCACCTCCT
* *
4098 TACAAACCACCAACAACTCCAGCTCCTCC
1 TACAAGCCACCAACAACTCCAGCACCTCC
4127 AGTCAAGCCA
Statistics
Matches: 168, Mismatches: 32, Indels: 19
0.77 0.15 0.09
Matches are distributed among these distances:
28 4 0.02
29 1 0.01
30 158 0.94
31 1 0.01
32 4 0.02
ACGTcount: A:0.33, C:0.49, G:0.07, T:0.12
Consensus pattern (30 bp):
TACAAGCCACCAACAACTCCAGCACCTCCT
Found at i:4874 original size:11 final size:11
Alignment explanation
Indices: 4858--4906 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
4848 TTCTAAATAT
4858 AATATATAAAA
1 AATATATAAAA
*
4869 AATATATTAAA
1 AATATATAAAA
4880 AATATA-AAAA
1 AATATATAAAA
*
4890 AATATTTAGAAA
1 AATATATA-AAA
4902 AATAT
1 AATAT
4907 TTTTACCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 8 0.24
11 17 0.52
12 8 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AATATATAAAA
Found at i:4883 original size:22 final size:22
Alignment explanation
Indices: 4858--4906 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
4848 TTCTAAATAT
4858 AATATATAAAAAATATATTA-AA
1 AATATATAAAAAATAT-TTAGAA
4880 AATATA-AAAAAATATTTAGAA
1 AATATATAAAAAATATTTAGAA
4901 AA-ATAT
1 AATATAT
4907 TTTTACCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.24
21 13 0.52
22 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AATATATAAAAAATATTTAGAA
Found at i:4980 original size:16 final size:16
Alignment explanation
Indices: 4961--5000 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
4951 AATATTCAGT
4961 CTCTCAAATAGTTTTC
1 CTCTCAAATAGTTTTC
4977 CTCTCAAATAGTTTTC
1 CTCTCAAATAGTTTTC
4993 CTC-CAAAT
1 CTCTCAAAT
5001 GGTATGCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.40
Consensus pattern (16 bp):
CTCTCAAATAGTTTTC
Found at i:6350 original size:16 final size:17
Alignment explanation
Indices: 6325--6362 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
6315 CTAATTTGGA
6325 TTGCTTAGAGT-TT-AT
1 TTGCTTAGAGTCTTAAT
6340 TTGCATTAGAGTCTTAAT
1 TTGC-TTAGAGTCTTAAT
6358 TTGCT
1 TTGCT
6363 AATAGAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 3 0.15
18 6 0.30
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (17 bp):
TTGCTTAGAGTCTTAAT
Done.