Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011208.1 Corchorus capsularis cultivar CVL-1 contig11229, 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: 14746
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:2225 original size:2 final size:2
Alignment explanation
Indices: 2218--2248 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2208 CTTTTGCAAG
*
2218 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2249 ATACCTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
AT
Found at i:7433 original size:31 final size:31
Alignment explanation
Indices: 7368--7526 Score: 147
Period size: 31 Copynumber: 5.4 Consensus size: 31
7358 TTTGTGCACA
* * * ** *
7368 TGGCATGCCACGTGCCATTTTTTGAAACATG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
*
7399 TGGCATGCCACGTGTCACTTTTTGGTACACG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
* *
7430 TGGCGTGACATGTGTCACTTTTTGGTACA--
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
* *
7459 T---GTGGCAC--G--ACTTTTTGGTACATG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
*
7483 TGGCGTGCCACATGTCACTTTTTGGTACACG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
7514 TGGCGTGCCACGT
1 TGGCGTGCCACGT
7527 CGGACACCGT
Statistics
Matches: 106, Mismatches: 13, Indels: 18
0.77 0.09 0.13
Matches are distributed among these distances:
22 13 0.12
24 2 0.02
26 5 0.05
27 6 0.06
29 2 0.02
31 78 0.74
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (31 bp):
TGGCGTGCCACGTGTCACTTTTTGGTACACG
Found at i:7477 original size:53 final size:53
Alignment explanation
Indices: 7415--7517 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
7405 GCCACGTGTC
** *
7415 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
7468 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
7518 GTGCCACGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:9249 original size:15 final size:15
Alignment explanation
Indices: 9229--9265 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
9219 ATCTGAAATA
9229 CTTCAGATATTGATT
1 CTTCAGATATTGATT
*
9244 CTTCAGATCTTGATT
1 CTTCAGATATTGATT
9259 CTTCAGA
1 CTTCAGA
9266 GTTTTCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (15 bp):
CTTCAGATATTGATT
Found at i:9278 original size:15 final size:16
Alignment explanation
Indices: 9260--9289 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9250 ATCTTGATTC
9260 TTCAGAG-TTTTCTGT
1 TTCAGAGCTTTTCTGT
9275 TTCAGAGCTTTTCTG
1 TTCAGAGCTTTTCTG
9290 CCTTCTGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.17, G:0.20, T:0.50
Consensus pattern (16 bp):
TTCAGAGCTTTTCTGT
Found at i:14033 original size:63 final size:63
Alignment explanation
Indices: 13812--14126 Score: 516
Period size: 63 Copynumber: 5.0 Consensus size: 63
13802 GGGGGTTTTT
* *
13812 TTTTTTTTTTG-GCTCTAACTTTTGCCTAAGCCGTCTTTTGTAGGATTTTCAACTTAGCGAGC
1 TTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
*
13874 -----TTTTTGTGCTCTAACTTTTGCCTAAGCTGTCCTTTGCAGGATTTTCAACTTAGCGAGC
1 TTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
*
13932 TTTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCTGTCCTTTGCAGGATTTTCAACTTAGCGAGC
1 -TTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
13996 TTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
1 TTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
*
14059 TTTTTTTTTTTTGTGCTCTAACTTTTGCCTAAGTCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
1 --TTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
14124 TTT
1 TTT
14127 GCAAGTAGTT
Statistics
Matches: 239, Mismatches: 5, Indels: 17
0.92 0.02 0.07
Matches are distributed among these distances:
57 6 0.03
58 48 0.20
63 65 0.27
64 58 0.24
65 62 0.26
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (63 bp):
TTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
Done.