Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015595.1 Corchorus capsularis cultivar CVL-1 contig15616, 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: 36831
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Found at i:1233 original size:39 final size:39
Alignment explanation
Indices: 1140--1246 Score: 146
Period size: 39 Copynumber: 2.8 Consensus size: 39
1130 CAAATTTCCA
1140 AAAGTTTTAAATTTAGGGAAAGATCCCA-CCAAGTCTCC
1 AAAGTTTTAAATTTAGGGAAAGATCCCATCCAAGTCTCC
* * **
1178 CAAGTTTTAAATTTAGGGAAAGATCCCATCC-AGTTTTTT
1 AAAGTTTTAAATTTAGGGAAAGATCCCATCCAAG-TCTCC
*
1217 AAAGTTTTCAATTTAGGGAAAGATCCCATC
1 AAAGTTTTAAATTTAGGGAAAGATCCCATC
1247 AAAAGGTATT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 29 0.48
39 32 0.52
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (39 bp):
AAAGTTTTAAATTTAGGGAAAGATCCCATCCAAGTCTCC
Found at i:6482 original size:35 final size:35
Alignment explanation
Indices: 6406--6475 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
6396 TCCAAGAATT
**
6406 AGTTTTTGTTTTTTCCGTTTTTTCTAAAAAAAAAA
1 AGTTTTTCCTTTTTCCGTTTTTTCTAAAAAAAAAA
*
6441 AGTTTTTCCTTTTTCCGATTTTTT-TATAAAAAAAA
1 AGTTTTTCCTTTTTCCG-TTTTTTCTAAAAAAAAAA
6476 TATTTTTGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.51
Consensus pattern (35 bp):
AGTTTTTCCTTTTTCCGTTTTTTCTAAAAAAAAAA
Found at i:13132 original size:74 final size:74
Alignment explanation
Indices: 12997--13145 Score: 244
Period size: 74 Copynumber: 2.0 Consensus size: 74
12987 TATGTTTAAT
* *
12997 TATGGATGTTATTATTCGATACTTGTATTCAGAGTTTATGGTTTTATTCAGTGGTCAGTGGTATT
1 TATGCATGTTATTATTCGATACTTGTATTCAGAGTTTATGGTTTTATTCAGTAGTCAGTGGTATT
13062 TTCAAACAA
66 TTCAAACAA
* * *
13071 TATGCATGTTATTATTCGATGCTTGTATTCAGAGTTTATGGTTTTATTTAGTAGTCGGTGGTATT
1 TATGCATGTTATTATTCGATACTTGTATTCAGAGTTTATGGTTTTATTCAGTAGTCAGTGGTATT
*
13136 TTCAGACAA
66 TTCAAACAA
13145 T
1 T
13146 GTGTTTATGG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.46
Consensus pattern (74 bp):
TATGCATGTTATTATTCGATACTTGTATTCAGAGTTTATGGTTTTATTCAGTAGTCAGTGGTATT
TTCAAACAA
Found at i:13247 original size:19 final size:20
Alignment explanation
Indices: 13223--13262 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
13213 TTATTACTGG
13223 TATTCAG-AGATTATGGTAT
1 TATTCAGTAGATTATGGTAT
* *
13242 TATTCAGTAGTTTGTGGTAT
1 TATTCAGTAGATTATGGTAT
13262 T
1 T
13263 TTGGAGCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (20 bp):
TATTCAGTAGATTATGGTAT
Found at i:16204 original size:12 final size:12
Alignment explanation
Indices: 16187--16214 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
16177 ATGCATGGGA
16187 CATCGCACGAGC
1 CATCGCACGAGC
16199 CATCGCACGAGC
1 CATCGCACGAGC
16211 CATC
1 CATC
16215 CGGCTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.43, G:0.21, T:0.11
Consensus pattern (12 bp):
CATCGCACGAGC
Found at i:16233 original size:42 final size:42
Alignment explanation
Indices: 16187--16272 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
16177 ATGCATGGGA
* *
16187 CATCGCAC-GAGCCATCGCACGAGCCATCCGGCTACAACCGGC
1 CATCGCACAG-GCCATCGCACGAGCCATCCAGCCACAACCGGC
* *
16229 CATCGCACAGGCCATCGCATGGGCCATCCAGCCACAACCGGC
1 CATCGCACAGGCCATCGCACGAGCCATCCAGCCACAACCGGC
16271 CA
1 CA
16273 CTTGACCCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.43, G:0.23, T:0.09
Consensus pattern (42 bp):
CATCGCACAGGCCATCGCACGAGCCATCCAGCCACAACCGGC
Found at i:18738 original size:33 final size:32
Alignment explanation
Indices: 18643--18747 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 32
18633 AAGAAAAGAG
*
18643 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC
* * * * *
18676 TAATTTGAGTGTTGTTTACAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC
*
18709 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC
18742 TGTTTT
1 TGTTTT
18748 GAATGCTAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 3 0.05
33 50 0.86
34 5 0.09
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.46
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGATACTAAATC
Found at i:18761 original size:33 final size:34
Alignment explanation
Indices: 18696--18781 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 34
18686 GTTGTTTACA
* * **
18696 ATGACACTAAATCTGTTTT-AAGTGTTGTTTGTG
1 ATGAAACTAAATCTGTTTTGAAGTGCTAATTGTG
*
18729 ATGATACTAAATCTGTTTTGAA-TGCTAATTGTG
1 ATGAAACTAAATCTGTTTTGAAGTGCTAATTGTG
* *
18762 ATGAAAATAATTCTGTTTTG
1 ATGAAACTAAATCTGTTTTG
18782 GTTGATCATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (34 bp):
ATGAAACTAAATCTGTTTTGAAGTGCTAATTGTG
Found at i:18836 original size:33 final size:33
Alignment explanation
Indices: 18763--18836 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
18753 CTAATTGTGA
*
18763 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTATTTTGGTTGATCATAGCAT
**
18796 TTCAAATAATTCTATTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTATTTTGGTTGATCATAGCAT
18829 TGAAAATA
1 TGAAAATA
18837 GGACTGTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (33 bp):
TGAAAATAATTCTATTTTGGTTGATCATAGCAT
Found at i:18847 original size:33 final size:33
Alignment explanation
Indices: 18763--18848 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
18753 CTAATTGTGA
**
18763 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAAGACTGTTTTGGTTGATCATAGCAT
** ** *
18796 TTCAAATAATTCTATTTTGGTTGATCATAGCAT
1 TGAAAATAAGACTGTTTTGGTTGATCATAGCAT
*
18829 TGAAAATAGGACTGTTTTGG
1 TGAAAATAAGACTGTTTTGG
18849 GTAAAAAGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (33 bp):
TGAAAATAAGACTGTTTTGGTTGATCATAGCAT
Found at i:20708 original size:23 final size:23
Alignment explanation
Indices: 20678--20732 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
20668 AGGAGTTGAG
20678 GACCGGCCACCATCGCATGGAGC
1 GACCGGCCACCATCGCATGGAGC
20701 GACCGGCCACCATCGCATGGAGC
1 GACCGGCCACCATCGCATGGAGC
20724 -ACCCGGCCA
1 GA-CCGGCCA
20733 TGACCAGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.22, C:0.42, G:0.29, T:0.07
Consensus pattern (23 bp):
GACCGGCCACCATCGCATGGAGC
Found at i:20803 original size:30 final size:30
Alignment explanation
Indices: 20762--20826 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
20752 ACATCGCACA
*
20762 GGCCATCGCACGAGCCATCCGGCTACAACC
1 GGCCATCGCACGAGCCATCCGGCCACAACC
* *
20792 GGCCATTGCACGGGCCATCCGGCCACAACC
1 GGCCATCGCACGAGCCATCCGGCCACAACC
20822 GGCCA
1 GGCCA
20827 CTTGACCCTT
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:0.22, C:0.43, G:0.26, T:0.09
Consensus pattern (30 bp):
GGCCATCGCACGAGCCATCCGGCCACAACC
Done.