Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015038.1 Corchorus capsularis cultivar CVL-1 contig15059, 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: 42480
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5034 original size:14 final size:14
Alignment explanation
Indices: 5015--5043 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5005 TGGGAAGAAG
5015 GAGCAAAACCTCAT
1 GAGCAAAACCTCAT
5029 GAGCAAAACCTCAT
1 GAGCAAAACCTCAT
5043 G
1 G
5044 GATTTAAGAA
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:0.41, C:0.28, G:0.17, T:0.14
Consensus pattern (14 bp):
GAGCAAAACCTCAT
Found at i:8512 original size:86 final size:85
Alignment explanation
Indices: 8327--8574 Score: 353
Period size: 83 Copynumber: 3.0 Consensus size: 85
8317 ACATTACCAA
* *
8327 AAAATTGACCCCAAATTTGATCCTCCATGACGTGTTGTTACATGATTGGTTCAG--ACTGATCCC
1 AAAATTGACCCAAAATTTGGTCCTCCATGACGTGTTGTTACATGATTGGTTCAGCAACTGATCCC
* *
8390 ACTACTATTTAAGTGAGGTT
66 ACCACTATTTAAGTGGGGTT
* *
8410 AAAATTGACCCAAAATTTGGTCTTTCATGACGTGTTGTTACATGATTGGTTCAGCAAGCTGATCC
1 AAAATTGACCCAAAATTTGGTCCTCCATGACGTGTTGTTACATGATTGGTTCAGCAA-CTGATCC
*
8475 TACCACTATTTAAGTGGGGTT
65 CACCACTATTTAAGTGGGGTT
* **
8496 AAAATTGACCCGAAATTTGGTCCTCCATGAC--G-TGTTACACAATTGGTTCAGCAAACTGATCC
1 AAAATTGACCCAAAATTTGGTCCTCCATGACGTGTTGTTACATGATTGGTTCAGC-AACTGATCC
8558 CACCACTATTTAAGTGG
65 CACCACTATTTAAGTGG
8575 TGTTTTTGCT
Statistics
Matches: 148, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
83 91 0.61
84 3 0.02
85 1 0.01
86 53 0.36
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (85 bp):
AAAATTGACCCAAAATTTGGTCCTCCATGACGTGTTGTTACATGATTGGTTCAGCAACTGATCCC
ACCACTATTTAAGTGGGGTT
Found at i:16283 original size:46 final size:46
Alignment explanation
Indices: 16231--16328 Score: 180
Period size: 46 Copynumber: 2.2 Consensus size: 46
16221 AATAATTTTG
16231 TTATTTCCTTTTGTTACCCTCTCCTCTGTATTGGAACCAGGGGTTC
1 TTATTTCCTTTTGTTACCCTCTCCTCTGTATTGGAACCAGGGGTTC
*
16277 TTATTTCCTTTTGTTACCCTCTCCTCTGTATTGGAATCAGGGGTTC
1 TTATTTCCTTTTGTTACCCTCTCCTCTGTATTGGAACCAGGGGTTC
16323 TT-TTTC
1 TTATTTC
16329 TAGTAGTAGC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 4 0.08
46 47 0.92
ACGTcount: A:0.12, C:0.24, G:0.16, T:0.47
Consensus pattern (46 bp):
TTATTTCCTTTTGTTACCCTCTCCTCTGTATTGGAACCAGGGGTTC
Found at i:22464 original size:24 final size:24
Alignment explanation
Indices: 22437--22486 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
22427 CTAGTACAAA
22437 AGGTTGTTACAAAAGGAACAAAGC
1 AGGTTGTTACAAAAGGAACAAAGC
22461 AGGTTGTTACAAAAGGAACAAAGC
1 AGGTTGTTACAAAAGGAACAAAGC
22485 AG
1 AG
22487 AGAACTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.26, T:0.16
Consensus pattern (24 bp):
AGGTTGTTACAAAAGGAACAAAGC
Found at i:24690 original size:53 final size:53
Alignment explanation
Indices: 24610--24716 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
24600 ACAATATCCT
24610 GCAAAATGTCAGTTAATAACTCCTTAGGACATCCAGTAACTTTTGAAGAAAGA
1 GCAAAATGTCAGTTAATAACTCCTTAGGACATCCAGTAACTTTTGAAGAAAGA
24663 GCAAAATGTCAGTTAATAACTCCTTAGGACATCCAGTAACTTTTGAAGAAAGA
1 GCAAAATGTCAGTTAATAACTCCTTAGGACATCCAGTAACTTTTGAAGAAAGA
24716 G
1 G
24717 ATAGCCTCGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (53 bp):
GCAAAATGTCAGTTAATAACTCCTTAGGACATCCAGTAACTTTTGAAGAAAGA
Found at i:25442 original size:11 final size:11
Alignment explanation
Indices: 25426--25455 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
25416 CGTTACGCAT
25426 CCTGGTTGCAC
1 CCTGGTTGCAC
25437 CCTGGTTGCAC
1 CCTGGTTGCAC
25448 CCTGGTTG
1 CCTGGTTG
25456 GGTCAGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.07, C:0.33, G:0.30, T:0.30
Consensus pattern (11 bp):
CCTGGTTGCAC
Found at i:27230 original size:19 final size:19
Alignment explanation
Indices: 27206--27244 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
27196 AATTTGTCTC
27206 TTGAATTAATTATGAACTA
1 TTGAATTAATTATGAACTA
27225 TTGAATTAATTATGAACTA
1 TTGAATTAATTATGAACTA
27244 T
1 T
27245 AAATCGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (19 bp):
TTGAATTAATTATGAACTA
Done.