Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009615.1 Corchorus capsularis cultivar CVL-1 contig09636, 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: 46678
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8386 original size:13 final size:13
Alignment explanation
Indices: 8368--8392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8358 TAGATGAACA
8368 TACATAATGTATT
1 TACATAATGTATT
8381 TACATAATGTAT
1 TACATAATGTAT
8393 CTACTTGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TACATAATGTATT
Found at i:12005 original size:14 final size:14
Alignment explanation
Indices: 11986--12012 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11976 AACTAGCCTC
11986 AATTATGATCCATG
1 AATTATGATCCATG
12000 AATTATGATCCAT
1 AATTATGATCCAT
12013 CGCTCAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (14 bp):
AATTATGATCCATG
Found at i:15165 original size:14 final size:14
Alignment explanation
Indices: 15148--15176 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15138 ATATATATAT
15148 AGATATATAGCATA
1 AGATATATAGCATA
15162 AGATATATAGCATA
1 AGATATATAGCATA
15176 A
1 A
15177 TTTGCTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
AGATATATAGCATA
Found at i:18248 original size:28 final size:28
Alignment explanation
Indices: 18217--18284 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
18207 CCAGGACGTC
18217 TCCCTCTGGTATGGGAGAC-GAAAATTCT
1 TCCCTCTGGTATGGGAGACGGAAAA-TCT
** *
18245 TCCCTCTAATAAGGGAGACGGAAAATCT
1 TCCCTCTGGTATGGGAGACGGAAAATCT
18273 TCCCTCTGGTAT
1 TCCCTCTGGTAT
18285 ATCACACAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (28 bp):
TCCCTCTGGTATGGGAGACGGAAAATCT
Found at i:18744 original size:73 final size:73
Alignment explanation
Indices: 18663--18809 Score: 249
Period size: 73 Copynumber: 2.0 Consensus size: 73
18653 TCTTAAGTCC
* *
18663 AATAAGGCTGAAATTTCATCAGTAAACTTAGATTATCCTCATTAGACTAGGGGTAAAATTCTAAG
1 AATAAGGCTGAAATTTCATCAGTAAACTTAGATTATCCTCATAAGACTAGGGGTAAAAATCTAAG
18728 TAAAACCG
66 TAAAACCG
***
18736 AATAAGGCTGAAATTTCATCAGTCGGCTTAGATTATCCTCATAAGACTAGGGGTAAAAATCTAAG
1 AATAAGGCTGAAATTTCATCAGTAAACTTAGATTATCCTCATAAGACTAGGGGTAAAAATCTAAG
18801 TAAAACCG
66 TAAAACCG
18809 A
1 A
18810 GTTCTCCTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (73 bp):
AATAAGGCTGAAATTTCATCAGTAAACTTAGATTATCCTCATAAGACTAGGGGTAAAAATCTAAG
TAAAACCG
Found at i:19086 original size:156 final size:156
Alignment explanation
Indices: 18760--19228 Score: 658
Period size: 156 Copynumber: 3.0 Consensus size: 156
18750 TTCATCAGTC
* * * *
18760 GGCTTAGATTATC-CTCATAAGACTAGGGGTAAAAA-TCTAAGTAAAACCGAGTTCTCCTTTATG
1 GGCTTAGATTATCTC-CATAAGACTA-TGGAAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATG
* * *
18823 GTGAACTTGGTTTCTCTCCCCAAAGTATCCTTAACTGAAAAAACATGCATAAGTTTTTCATCTTA
64 GTGAACTTGGTTTCTCACCCCAAACTGTCCTTAACTG-AAAAACATGCATAAGTTTTTCATCTTA
* *
18888 AGTCTGATTGAGCTGAAACTTGGCCACGA
128 AGTCTGATTGAGATGAAACTTGGCCAAGA
* * *
18917 GGCTTAGATTATCTCCATAAGGCTATGGAAAAAATTCTACGTAAAACCGAGCTCTTCTTCATGGT
1 GGCTTAGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATGGT
*
18982 GAACTTGGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACGTGCATAAGTTTTTCAT-TCTAAG
66 GAACTTGGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACATGCATAAGTTTTTCATCT-TAAG
**
19046 TCCAATTGAGATGAAACTTGGCCAAG-
130 TCTGATTGAGATGAAACTTGGCCAAGA
* * * * *
19072 GGACTTAGATTATCTCCATAAAAATATGAAAAAAATTATAAGTAAAACCGAGCTCTCCTTGATGG
1 GG-CTTAGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATGG
* *
19137 TGAGCTTGGTTTCTCACCCCAAACTGTCCTTAATTGAAAAACATGCATAAGTTTTTCATCTTAAG
65 TGAACTTGGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACATGCATAAGTTTTTCATCTTAAG
*
19202 TCTGTTTGAGATGAAACTTGGCCAAGA
130 TCTGATTGAGATGAAACTTGGCCAAGA
19229 TGATCCTCAT
Statistics
Matches: 277, Mismatches: 29, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
155 3 0.01
156 192 0.69
157 81 0.29
158 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (156 bp):
GGCTTAGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATGGT
GAACTTGGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACATGCATAAGTTTTTCATCTTAAGT
CTGATTGAGATGAAACTTGGCCAAGA
Found at i:32388 original size:27 final size:29
Alignment explanation
Indices: 32350--32408 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
32340 AAGACTTTTT
32350 TTTTTTTTTGC-A-AGAGAAAAAAGACAC
1 TTTTTTTTTGCAATAGAGAAAAAAGACAC
32377 TTTTTTTTTGCAATAGAGAAAAAAGACAC
1 TTTTTTTTTGCAATAGAGAAAAAAGACAC
32406 TTT
1 TTT
32409 ATTAATCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 11 0.37
28 1 0.03
29 18 0.60
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (29 bp):
TTTTTTTTTGCAATAGAGAAAAAAGACAC
Found at i:36102 original size:18 final size:18
Alignment explanation
Indices: 36081--36117 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
36071 TGATTTTAAT
*
36081 TTTCCTTACAATTTTTCC
1 TTTCCCTACAATTTTTCC
*
36099 TTTCCCTACTATTTTTCC
1 TTTCCCTACAATTTTTCC
36117 T
1 T
36118 ACTTCCAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.30, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTCCCTACAATTTTTCC
Found at i:36291 original size:21 final size:21
Alignment explanation
Indices: 36265--36310 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
36255 TATCTAATAT
36265 ATTTATACTATGAAGATAGGA
1 ATTTATACTATGAAGATAGGA
36286 ATTTATACTATGAAGATAGGA
1 ATTTATACTATGAAGATAGGA
36307 ATTT
1 ATTT
36311 TAAGAGACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (21 bp):
ATTTATACTATGAAGATAGGA
Found at i:41336 original size:27 final size:27
Alignment explanation
Indices: 41282--41337 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
41272 TTAATCCTAT
*
41282 ATAATTTTCCAAATATTTTTTGGCGAA
1 ATAATTTTCCAAATATTTTTTGACGAA
* *
41309 ATAATTTT-CAAATTTTTATTTGATGAA
1 ATAATTTTCCAAATATTT-TTTGACGAA
41336 AT
1 AT
41338 TTTTCTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (27 bp):
ATAATTTTCCAAATATTTTTTGACGAA
Done.