Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011987.1 Corchorus capsularis cultivar CVL-1 contig12008, 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: 77106
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:23001 original size:314 final size:314
Alignment explanation
Indices: 22432--23046 Score: 1194
Period size: 314 Copynumber: 2.0 Consensus size: 314
22422 AAATATCAAG
22432 TGTAAAATGTGTAATATGCATGTAAGATGAGGTTTTTACTATTGAACTATATGCACTAAATGAAG
1 TGTAAAATGTGTAATATGCATGTAAGATGAGGTTTTTACTATTGAACTATATGCACTAAATGAAG
22497 AATTTGCTAATTATATCTTGAAGATTCTGAGAGGGGCATGTCATGCAGATGTTTTGAAACAAAAA
66 AATTTGCTAATTATATCTTGAAGATTCTGAGAGGGGCATGTCATGCAGATGTTTTGAAACAAAAA
**
22562 ATGTGCATTTCTTTGTCATCCCATTAAAAATGTATGTATTGGTTAGCTAAATTATAGGTGTCTTG
131 ATGTGCATTTCTTTGTCATCCCATTAAAAATGTATGTATCAGTTAGCTAAATTATAGGTGTCTTG
22627 AAGACCAAATCAAATATGCTAAATTCTCAATTAGCAAAAGTATATTTGGTATCAATCTTGTTGAT
196 AAGACCAAATCAAATATGCTAAATTCTCAATTAGCAAAAGTATATTTGGTATCAATCTTGTTGAT
22692 ATCTAAGTACCTAGTGTCATTATATGTGTAATATGGAAAGAGGTGTAATATGCA
261 ATCTAAGTACCTAGTGTCATTATATGTGTAATATGGAAAGAGGTGTAATATGCA
*
22746 TGTAAAATGTGTAATATGCATGTAAGATGAGGTTTTTACTATTGAACTGTATGCACTAAATGAAG
1 TGTAAAATGTGTAATATGCATGTAAGATGAGGTTTTTACTATTGAACTATATGCACTAAATGAAG
22811 AATTTGCTAATTATATCTTGAAGATTCTGAGAGGGGCATGTCATGCAGATGTTTTGAAACAAAAA
66 AATTTGCTAATTATATCTTGAAGATTCTGAGAGGGGCATGTCATGCAGATGTTTTGAAACAAAAA
*
22876 ATGTGCATTTCTTTGTCATCCCATTAGAAATGTATGTATCAGTTAGCTAAATTATAGGTGTCTTG
131 ATGTGCATTTCTTTGTCATCCCATTAAAAATGTATGTATCAGTTAGCTAAATTATAGGTGTCTTG
22941 AAGACCAAATCAAATATGCTAAATTCTCAATTAGCAAAAGTATATTTGGTATCAATCTTGTTGAT
196 AAGACCAAATCAAATATGCTAAATTCTCAATTAGCAAAAGTATATTTGGTATCAATCTTGTTGAT
23006 ATCTAAGTACCTAGTGTCATTATATGTGTAATATGGAAAGA
261 ATCTAAGTACCTAGTGTCATTATATGTGTAATATGGAAAGA
23047 TGTGGGCTTA
Statistics
Matches: 297, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
314 297 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36
Consensus pattern (314 bp):
TGTAAAATGTGTAATATGCATGTAAGATGAGGTTTTTACTATTGAACTATATGCACTAAATGAAG
AATTTGCTAATTATATCTTGAAGATTCTGAGAGGGGCATGTCATGCAGATGTTTTGAAACAAAAA
ATGTGCATTTCTTTGTCATCCCATTAAAAATGTATGTATCAGTTAGCTAAATTATAGGTGTCTTG
AAGACCAAATCAAATATGCTAAATTCTCAATTAGCAAAAGTATATTTGGTATCAATCTTGTTGAT
ATCTAAGTACCTAGTGTCATTATATGTGTAATATGGAAAGAGGTGTAATATGCA
Found at i:56702 original size:20 final size:20
Alignment explanation
Indices: 56658--56703 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
56648 ATTAAGTTAG
56658 AAAA-TAATAATATATATAT
1 AAAATTAATAATATATATAT
* *
56677 ATAATTAATAATA-ATATCCT
1 AAAATTAATAATATATAT-AT
56697 AAAATTA
1 AAAATTA
56704 TCAGGAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTAATAATATATATAT
Found at i:56753 original size:23 final size:23
Alignment explanation
Indices: 56723--56767 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
56713 CTAGGAAAAA
56723 GCTTTTTTCCTTCTGAATCAGAT
1 GCTTTTTTCCTTCTGAATCAGAT
*
56746 GCTTTTTTCTTTCTGAATCAGA
1 GCTTTTTTCCTTCTGAATCAGA
56768 CGACGTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.13, T:0.49
Consensus pattern (23 bp):
GCTTTTTTCCTTCTGAATCAGAT
Done.