Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009380.1 Corchorus capsularis cultivar CVL-1 contig09401, 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: 37609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:713 original size:29 final size:30
Alignment explanation
Indices: 667--724 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
657 GTTAGGTTGA
667 GGGGGCAAAAAGTCCCAAAATTGAAGTTCG
1 GGGGGCAAAAAGTCCCAAAATTGAAGTTCG
* *
697 GGGGGCAAAATGT-CCAAGATTGAAGTTC
1 GGGGGCAAAAAGTCCCAAAATTGAAGTTC
725 ATTCAGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (30 bp):
GGGGGCAAAAAGTCCCAAAATTGAAGTTCG
Found at i:14787 original size:138 final size:138
Alignment explanation
Indices: 14539--14813 Score: 487
Period size: 138 Copynumber: 2.0 Consensus size: 138
14529 GTGATTATAA
*
14539 ATTAAAAGGGTACCTGAACCTACATTCCAAGCAGTTATCCATTCTGATATCAAGTAAAACTAAGC
1 ATTAAAAGGGTACCTGAACCTACATTCCAAGCAGTTATCCATTCTGATATCAACTAAAACTAAGC
* *
14604 TACCAACTATGGAAAAAATTGCAAATGAAGTTTTGGTACGCCAATAGTAAGTATAAATCATAGTA
66 TACCAACTACGGAAAAAATTGCAAATGAAGTTTTGGCACGCCAATAGTAAGTATAAATCATAGTA
14669 ATTATTAG
131 ATTATTAG
* *
14677 ATTAAAAGGGTACCTGAACCTACATTCCAAGCAGTTATCCATTGTGATATCAACTAAACCTAAGC
1 ATTAAAAGGGTACCTGAACCTACATTCCAAGCAGTTATCCATTCTGATATCAACTAAAACTAAGC
* *
14742 TACCAACTACGGAAAAAGTTGCAAATGAAGTTTTGGCATGCCAATAGTAAGTATAAATCATAGTA
66 TACCAACTACGGAAAAAATTGCAAATGAAGTTTTGGCACGCCAATAGTAAGTATAAATCATAGTA
14807 ATTATTA
131 ATTATTA
14814 ATGCAGCTAC
Statistics
Matches: 130, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
138 130 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (138 bp):
ATTAAAAGGGTACCTGAACCTACATTCCAAGCAGTTATCCATTCTGATATCAACTAAAACTAAGC
TACCAACTACGGAAAAAATTGCAAATGAAGTTTTGGCACGCCAATAGTAAGTATAAATCATAGTA
ATTATTAG
Found at i:19725 original size:16 final size:17
Alignment explanation
Indices: 19704--19736 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19694 CCTTTAATGC
19704 TATATAAACAAT-TTGT
1 TATATAAACAATCTTGT
*
19720 TATATATACAATCTTGT
1 TATATAAACAATCTTGT
19737 AACTTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TATATAAACAATCTTGT
Found at i:21998 original size:7 final size:7
Alignment explanation
Indices: 21988--22014 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
21978 CGTGTTTTCA
21988 TTTTTGT
1 TTTTTGT
21995 TTTTTGT
1 TTTTTGT
22002 TTTTTGT
1 TTTTTGT
22009 TTTTTG
1 TTTTTG
22015 GGTATTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (7 bp):
TTTTTGT
Found at i:26173 original size:177 final size:178
Alignment explanation
Indices: 25872--26404 Score: 1025
Period size: 177 Copynumber: 3.0 Consensus size: 178
25862 GGGGGGGGGG
25872 GGGGCTTGAACGTGGTCATTACTTGAGTTTCTTGATGCTAGGTTGATGTTCTGTGGAAACTTAGT
1 GGGG-TTGAACGTGGTCATTACTTGAGTTTCTTGATGCTAGGTTGATGTTCTGTGGAAACTTAGT
*
25937 TGTTGATTTGGATATGCCATGATCAATTCATCCAATATGCAATCCCCAACCTGATCTCAC-TTTT
65 TGTTGATTTGGATATGCCATGATCAATTCATCCAATATGCAATCCCCAACCTAATCTCACTTTTT
*
26001 CAAATTCCAATAAAAAGCAACTTCACCTTGAAATTATCCAGGAGTTACA
130 CAAATTCCAATAAAAAGCAACTTCTCCTTGAAATTATCCAGGAGTTACA
26050 GGGGTTGAACGTGGTCATTACTTGAGTTTCTTGATGCTAGGTTGATGTTCTGTGGAAACTTAGTT
1 GGGGTTGAACGTGGTCATTACTTGAGTTTCTTGATGCTAGGTTGATGTTCTGTGGAAACTTAGTT
26115 GTTGATTTGGATATGCCATGATCAATTCATCCAATATGCAATCCCCAACCTAATCTCACTTTTTC
66 GTTGATTTGGATATGCCATGATCAATTCATCCAATATGCAATCCCCAACCTAATCTCACTTTTTC
26180 AAATTCCAATAAAAAGCAACTTCTCCTTGAAATTATCCAGGAGTTACA
131 AAATTCCAATAAAAAGCAACTTCTCCTTGAAATTATCCAGGAGTTACA
26228 -GGGTTGAACGTGGTCATTACTTGAGTTTCTTGATGCTAGGTTGATGTTCTGTGGAAACTTAGTT
1 GGGGTTGAACGTGGTCATTACTTGAGTTTCTTGATGCTAGGTTGATGTTCTGTGGAAACTTAGTT
26292 GTTGATTTGGATATGCCATGATCAATTCATCCAATATGCAATCCCCAACCTAATCTCACTTTTTC
66 GTTGATTTGGATATGCCATGATCAATTCATCCAATATGCAATCCCCAACCTAATCTCACTTTTTC
26357 AAATTCCAATAAAAAGCAACTTCTCCTTGAAATTATCCAGGAGTTACA
131 AAATTCCAATAAAAAGCAACTTCTCCTTGAAATTATCCAGGAGTTACA
26405 AATTTTACAT
Statistics
Matches: 352, Mismatches: 2, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
177 296 0.84
178 56 0.16
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (178 bp):
GGGGTTGAACGTGGTCATTACTTGAGTTTCTTGATGCTAGGTTGATGTTCTGTGGAAACTTAGTT
GTTGATTTGGATATGCCATGATCAATTCATCCAATATGCAATCCCCAACCTAATCTCACTTTTTC
AAATTCCAATAAAAAGCAACTTCTCCTTGAAATTATCCAGGAGTTACA
Found at i:26595 original size:33 final size:33
Alignment explanation
Indices: 26553--26647 Score: 165
Period size: 33 Copynumber: 2.9 Consensus size: 33
26543 ATCAGCATGG
26553 ATGCCACCTCAGTCGA-TGCCTTATGCATCGGGA
1 ATGCCACCTCAGTC-ACTGCCTTATGCATCGGGA
*
26586 ATGCCACCTCAGTCACTGCCTTATGCATCTGGA
1 ATGCCACCTCAGTCACTGCCTTATGCATCGGGA
26619 ATGCCACCTCAGTCACTGCCTTATGCATC
1 ATGCCACCTCAGTCACTGCCTTATGCATC
26648 AGCAATTCCG
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 1 0.02
33 59 0.98
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (33 bp):
ATGCCACCTCAGTCACTGCCTTATGCATCGGGA
Done.