Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011051.1 Corchorus capsularis cultivar CVL-1 contig11072, 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: 39063
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 1--97 Score: 162
Period size: 2 Copynumber: 49.5 Consensus size: 2
1 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
41 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
83 TC CC TC CC TC TC TC T
1 TC TC TC TC TC TC TC T
98 TTTCCCCTTT
Statistics
Matches: 89, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
1 2 0.02
2 87 0.98
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:12076 original size:5 final size:5
Alignment explanation
Indices: 12066--12091 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12056 TTAGACACAC
12066 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
12092 GGAGATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:12185 original size:2 final size:2
Alignment explanation
Indices: 12178--12208 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12168 ATCGTCCATT
12178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12209 TCCTTCACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17456 original size:10 final size:11
Alignment explanation
Indices: 17437--17461 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17427 CTAATTTGTC
17437 TTTTGTTTTTT
1 TTTTGTTTTTT
17448 TTTTGTTTTTT
1 TTTTGTTTTTT
17459 TTT
1 TTT
17462 ACAGATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:18025 original size:2 final size:2
Alignment explanation
Indices: 18018--18046 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18008 TGACCCTGGC
18018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18047 GTGTGAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27349 original size:92 final size:92
Alignment explanation
Indices: 27207--27385 Score: 250
Period size: 92 Copynumber: 1.9 Consensus size: 92
27197 CATTATTGGT
** * * * *
27207 GGAAAGCAGTATTTGGTGGTCATATTGGGTCTGGACTAATCTGGAATCAAGTTTTGTTGGTAGAC
1 GGAAAGCAGTATTTGGTGGTCATATTGCATCTGCACTAATCCGGAATCAAGCTGTGTTGGTAGAC
* *
27272 CCATATTGGGTCTGGACTAATCCTGGC
66 CCATATTAGGTCTGGACAAATCCTGGC
* * * *
27299 GGAAAGCGGTATTTGGTGGTCATGTTGCATCTGCACTAATCCGGAGTCAAGCTGTGTTGGTATAC
1 GGAAAGCAGTATTTGGTGGTCATATTGCATCTGCACTAATCCGGAATCAAGCTGTGTTGGTAGAC
27364 CCATATTAGGTCTGGACAAATC
66 CCATATTAGGTCTGGACAAATC
27386 TGGAGTTGAG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (92 bp):
GGAAAGCAGTATTTGGTGGTCATATTGCATCTGCACTAATCCGGAATCAAGCTGTGTTGGTAGAC
CCATATTAGGTCTGGACAAATCCTGGC
Found at i:31310 original size:30 final size:31
Alignment explanation
Indices: 31276--31333 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
31266 AGCCATAAAG
31276 GGGTTAATTTAGCT-AAATTGGCCAATTCAA
1 GGGTTAATTTAGCTAAAATTGGCCAATTCAA
* * *
31306 GGGTTTATTTAGTTAAAATTGGCGAATT
1 GGGTTAATTTAGCTAAAATTGGCCAATT
31334 TAATGTCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (31 bp):
GGGTTAATTTAGCTAAAATTGGCCAATTCAA
Found at i:37058 original size:51 final size:51
Alignment explanation
Indices: 37000--37103 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
36990 TTGATCCAAC
37000 CCTTTATTATTGATTTAATGGATAAATAATTAGATATATTACCCCTATGAT
1 CCTTTATTATTGATTTAATGGATAAATAATTAGATATATTACCCCTATGAT
*
37051 CCTTTATTATTGATTTAATGGATAAATTATTAGATATATTACCCCTATGAT
1 CCTTTATTATTGATTTAATGGATAAATAATTAGATATATTACCCCTATGAT
37102 CC
1 CC
37104 ATGGTATCAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (51 bp):
CCTTTATTATTGATTTAATGGATAAATAATTAGATATATTACCCCTATGAT
Done.