Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010070.1 Corchorus capsularis cultivar CVL-1 contig10091, 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: 28506
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:255 original size:120 final size:120
Alignment explanation
Indices: 59--334 Score: 464
Period size: 120 Copynumber: 2.3 Consensus size: 120
49 TCGGCCTTGT
* *
59 CTGGCGCTCGCCAGTTAGCGTTGGGCCCCTTGGGGGCTTTGTCGTTCCCGCGCTTGGTCTGGGAT
1 CTGGCGCTCGCCAGTTGGCGTTGGGCCCCTT-GGGGCTTTGTCGTTCCCGCACTTGGTCTGGGAT
*
124 GGTCTGTGCCGATCGCCAGCCAGTCGGGGGCCATACTTAGTTAAGGCCGGCT-ATGC
65 GGTCTGTGCCGATCGCCAGCCAGTCGGGGGCCATACTTAGTCAAGGCCGG-TAATGC
*
180 CTGGCGCTCGCCAGTTGGCGTTGGGCCCCGTGGGGCTTTGTCGTTCCCGCACTTGGTCTGGGATG
1 CTGGCGCTCGCCAGTTGGCGTTGGGCCCCTTGGGGCTTTGTCGTTCCCGCACTTGGTCTGGGATG
245 GTCTGTGCCGATCGCCAGCCAGTCGGGGGCCATACTTAGTCAAGGCCGGTAATGC
66 GTCTGTGCCGATCGCCAGCCAGTCGGGGGCCATACTTAGTCAAGGCCGGTAATGC
* * *
300 CTGGTGCTTGCCACTTGGCGTTGGGCCCCTTGGGG
1 CTGGCGCTCGCCAGTTGGCGTTGGGCCCCTTGGGG
335 GCTTCATAAT
Statistics
Matches: 146, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
119 1 0.01
120 116 0.79
121 29 0.20
ACGTcount: A:0.09, C:0.29, G:0.36, T:0.25
Consensus pattern (120 bp):
CTGGCGCTCGCCAGTTGGCGTTGGGCCCCTTGGGGCTTTGTCGTTCCCGCACTTGGTCTGGGATG
GTCTGTGCCGATCGCCAGCCAGTCGGGGGCCATACTTAGTCAAGGCCGGTAATGC
Found at i:757 original size:34 final size:34
Alignment explanation
Indices: 719--788 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
709 TTGTTAATTT
*
719 CAAATTTCAAGAAAATGGGAAGGGTGCCGAACGC
1 CAAATTTCAAGAAAATGGGAAAGGTGCCGAACGC
*
753 CAAATTTCAAGAATATGGGAAAGGTGCCGAACGC
1 CAAATTTCAAGAAAATGGGAAAGGTGCCGAACGC
787 CA
1 CA
789 TGTGACTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.16
Consensus pattern (34 bp):
CAAATTTCAAGAAAATGGGAAAGGTGCCGAACGC
Found at i:4214 original size:17 final size:17
Alignment explanation
Indices: 4192--4226 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4182 GAAACAACTT
4192 ATTTGTTTTGGCTACGA
1 ATTTGTTTTGGCTACGA
4209 ATTTGTTTTGGCTACGA
1 ATTTGTTTTGGCTACGA
4226 A
1 A
4227 GAAGTTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (17 bp):
ATTTGTTTTGGCTACGA
Found at i:28364 original size:14 final size:14
Alignment explanation
Indices: 28347--28417 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
28337 TATTTTTATT
28347 TATATAAATATTAA
1 TATATAAATATTAA
**
28361 TATATATAATTATTTT
1 TATATA-AA-TATTAA
28377 TATATAAATATTAA
1 TATATAAATATTAA
* *
28391 AATATATATTATTAA
1 TATATA-AATATTAA
* *
28406 AATATATATATT
1 TATATAAATATT
28418 GTTTATGAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
14 19 0.41
15 17 0.37
16 10 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATAAATATTAA
Found at i:28368 original size:16 final size:16
Alignment explanation
Indices: 28347--28413 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 16
28337 TATTTTTATT
*
28347 TATATAAATATTAATA
1 TATATAAATATTAAAA
* **
28363 TATATAATTATT--TT
1 TATATAAATATTAAAA
28377 TATATAAATATTAAAA
1 TATATAAATATTAAAA
*
28393 TATAT-ATTATTAAAA
1 TATATAAATATTAAAA
28408 TATATA
1 TATATA
28414 TATTGTTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.29
15 14 0.33
16 16 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATAAATATTAAAA
Found at i:28379 original size:30 final size:29
Alignment explanation
Indices: 28303--28403 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 29
28293 TATGTTCATT
* *
28303 TATATTATTATATATATTATATATATAATAAT-
1 TATATTATT-TTTATA-TAAATAT-TAA-AATA
* *
28335 TATATTTTTATTTATATAAATATTAATATA
1 TATATTATT-TTTATATAAATATTAAAATA
28365 TATAATTATTTTTATATAAATATTAAAATA
1 TAT-ATTATTTTTATATAAATATTAAAATA
28395 TATATTATT
1 TATATTATT
28404 AAAATATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
29 8 0.13
30 28 0.46
31 11 0.18
32 14 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATTATTTTTATATAAATATTAAAATA
Done.