Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012024.1 Corchorus capsularis cultivar CVL-1 contig12045, 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, 953
Length: 1589
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Found at i:798 original size:35 final size:35
Alignment explanation
Indices: 520--797 Score: 520
Period size: 35 Copynumber: 7.9 Consensus size: 35
510 AGCTCATTGG
*
520 AAGAAGTTTTCAGAGGTCAGAGTTGACCTCATTCC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
555 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
590 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
*
625 AAGGAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
*
660 AAGCAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
695 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
*
730 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
765 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATT
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATT
798 TTCAGTATTT
Statistics
Matches: 238, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 238 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (35 bp):
AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
Found at i:820 original size:35 final size:35
Alignment explanation
Indices: 746--1002 Score: 286
Period size: 35 Copynumber: 7.3 Consensus size: 35
736 TTTTCAGAGG
* * * *
746 TCAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GG
1 TCAGAGTTGATCACATTTTC-AGTAGTTTCCA-ACGA
* *
781 TCAGAGTTGATCTCATTTTCAGTATTTTCCAACGA
1 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGA
*
816 TCAGAGTTGATCACATTTTCAGTATTTTCCAACGA
1 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGA
* * *
851 TCAGAGTTTATCACATTTTCAGAAGTTTCCAACAA
1 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGA
*
886 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGA
*
921 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGA
* ** * * * * *
956 TTAGAGGCGATCTCA-TTTCAAGAAATTTCCGATGA
1 TCAGAGTTGATCACATTTTC-AGTAGTTTCCAACGA
991 TCAGAGTTGATC
1 TCAGAGTTGATC
1003 CAGAGGAGTT
Statistics
Matches: 192, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
34 5 0.03
35 183 0.95
36 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (35 bp):
TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGA
Found at i:820 original size:105 final size:105
Alignment explanation
Indices: 520--832 Score: 488
Period size: 105 Copynumber: 3.0 Consensus size: 105
510 AGCTCATTGG
*
520 AAGAAGTTTTCAGAGGTCAGAGTTGACCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
* *
585 ATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
66 ATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCACATTCC
* *
625 AAGGAGTTTTCAGAGGTCAGAGTTGATCTCATTCCAAGCAGTTTTCAGAGGTCAGAGTTGATCTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
* *
690 ATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCC
66 ATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCACATTCC
*
730 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
* *
795 ATTTTC-AGTA-TTTTCCA-ACGATCAGAGTTGATCACATT
66 A-TTCCAAGAAGTTTT-CAGA-GATCAGAGTTGATCACATT
833 TTCAGTATTT
Statistics
Matches: 195, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
104 5 0.03
105 187 0.96
106 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (105 bp):
AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTC
ATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCACATTCC
Found at i:855 original size:105 final size:105
Alignment explanation
Indices: 524--1002 Score: 444
Period size: 105 Copynumber: 4.6 Consensus size: 105
514 CATTGGAAGA
* * *
524 AGTTTTCAGAGGTCAGAGTTGACCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTC
1 AGTTTTCAGAGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTC
* * *
589 CAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCCAAGG
66 CAAGAAGTTTTCAGAGATCAGAGTTGATCACATTCCAAGT
* * *
629 AGTTTTCAGAGGTCAGAGTTGATCTCATTCCAAGCAGTTTTCAGAGGTCAGAGTTGATCTCATTC
1 AGTTTTCAGAGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTC
* * *
694 CAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCCAAGA
66 CAAGAAGTTTTCAGAGATCAGAGTTGATCACATTCCAAGT
*
734 AGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTT
1 AGTTTTCAGAGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA-TT
* * *
799 TC-AGTA-TTTTCCA-ACGATCAGAGTTGATCACATTTTC-AGT
65 CCAAGAAGTTTT-CAGA-GATCAGAGTTGATCACA-TTCCAAGT
* * * ** *
839 A-TTTTCCA-ACGATCAGAGTTTATCACATTTTC-AGAAGTTTCCA-ACAATCAGAGTTGATCGC
1 AGTTTT-CAGA-GATCAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTC
* * * *
900 ATTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATCACATTTTC-AGT
62 A-TTCCAAGAAGTTTTCAGA-GATCAGAGTTGATCACA-TTCCAAGT
* * * ** * * *
944 AGTTTCCA-ACAATTAGAGGCGATCTCATTTCAAGAA-ATTTCCGATGATCAGAGTTGATC
1 AGTTTTCAGA-GATCAGAGTTGATCTCATTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
1003 CAGAGGAGTT
Statistics
Matches: 331, Mismatches: 31, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
104 18 0.05
105 297 0.90
106 16 0.05
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (105 bp):
AGTTTTCAGAGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTC
CAAGAAGTTTTCAGAGATCAGAGTTGATCACATTCCAAGT
Done.