Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005671.1 Corchorus capsularis cultivar CVL-1 contig05689, 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: 1952
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Found at i:820 original size:35 final size:35
Alignment explanation
Indices: 780--1140 Score: 577
Period size: 35 Copynumber: 10.3 Consensus size: 35
770 TTTTAAGAAG
780 CAGAGTTGATCTCATATCAAGAAGTTTTCAGAGGT
1 CAGAGTTGATCTCATATCAAGAAGTTTTCAGAGGT
*
815 CAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGT
1 CAGAGTTGATCTCATATCAAGAAGTTTTCAGAGGT
* *
850 CAGAGTTGATCTCGTATCAAGAAGTTTTCAGACGT
1 CAGAGTTGATCTCATATCAAGAAGTTTTCAGAGGT
*
885 CAGAGTTGATCTCATATCAAGAAGTTTTCACAGGT
1 CAGAGTTGATCTCATATCAAGAAGTTTTCAGAGGT
920 CAGAGTTGATCTCAT-TCCAAGAAGTTTTCAGAGGT
1 CAGAGTTGATCTCATAT-CAAGAAGTTTTCAGAGGT
955 CAGAGTTGATCTCAT-TCCAAGAAGTTTTCAGAGGT
1 CAGAGTTGATCTCATAT-CAAGAAGTTTTCAGAGGT
990 CAGAGTTGATCTCAT-TCCAAGAAGTTTTCAGAGGT
1 CAGAGTTGATCTCATAT-CAAGAAGTTTTCAGAGGT
*
1025 CAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGT
1 CAGAGTTGATCTCATATCAAGAAGTTTTCAGAGGT
*
1060 CAGAGTTGATCTCATATCAAGAAGTTTTCAAAGGT
1 CAGAGTTGATCTCATATCAAGAAGTTTTCAGAGGT
* * *
1095 CAGAGTTGATCTCATTTCAAGAAGTTTCCA-ACGAT
1 CAGAGTTGATCTCATATCAAGAAGTTTTCAGA-GGT
1130 CAGAGTTGATC
1 CAGAGTTGATC
1141 GCATTTTCAG
Statistics
Matches: 310, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
34 2 0.01
35 307 0.99
36 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (35 bp):
CAGAGTTGATCTCATATCAAGAAGTTTTCAGAGGT
Found at i:1146 original size:35 final size:35
Alignment explanation
Indices: 780--1419 Score: 524
Period size: 35 Copynumber: 18.3 Consensus size: 35
770 TTTTAAGAAG
* * *
780 CAGAGTTGATCTCATATCAAGAAGTTTTCAGA-GGT
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCA-ACGAT
* *
815 CAGAGTTGATCTCATTTCAAGAAGTTTTCAGA-GGT
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCA-ACGAT
* * *
850 CAGAGTTGATCTCGTATCAAGAAGTTTTCAGACG-T
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCA-ACGAT
* * *
885 CAGAGTTGATCTCATATCAAGAAGTTTTC-ACAGGT
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCAAC-GAT
* * *
920 CAGAGTTGATCTCATTCCAAGAAGTTTTCAGA-GGT
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCA-ACGAT
* * *
955 CAGAGTTGATCTCATTCCAAGAAGTTTTCAGA-GGT
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCA-ACGAT
* * *
990 CAGAGTTGATCTCATTCCAAGAAGTTTTCAGA-GGT
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCA-ACGAT
* *
1025 CAGAGTTGATCTCATTTCAAGAAGTTTTCAGA-GGT
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCA-ACGAT
* * * *
1060 CAGAGTTGATCTCATATCAAGAAGTTTTCAAAGGT
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCAACGAT
1095 CAGAGTTGATCTCATTTCAAGAAGTTTCCAACGAT
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCAACGAT
* * *
1130 CAGAGTTGATCGCATTTTC-AGTATTTTCCAACGAT
1 CAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACGAT
* * * *
1165 CAGAGTTGATCGCATTTTC-AGTATTTTCCAACAAT
1 CAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACGAT
* * * *
1200 CAGAGTTGATCGCATTTTC-AGTATTTTCC-ATGAT
1 CAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACGAT
* * *
1234 CAGAGTTGATCGCATTTTC-AGTAGTTTCCAATGAT
1 CAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACGAT
* * *
1269 CGGAGTTGAT-TGCATTTTC-AGTATTTTCCAACGAT
1 CAGAGTTGATCT-CA-TTTCAAGAAGTTTCCAACGAT
*
1304 CAGAGTTGATCGT-ATTTTC-AGTAGTTTCCAACGAT
1 CAGAGTTGATC-TCA-TTTCAAGAAGTTTCCAACGAT
* * * *
1339 CAAAGTTGATCACATTTTC-AGTAGTTTCCAACAAT
1 CAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACGAT
* * * * *
1374 TAGAGGTGATCTCATTTCAAGAAATTTCCGATGAT
1 CAGAGTTGATCTCATTTCAAGAAGTTTCCAACGAT
1409 CAGAGTTGATC
1 CAGAGTTGATC
1420 CAGAGGAGTT
Statistics
Matches: 553, Mismatches: 39, Indels: 26
0.89 0.06 0.04
Matches are distributed among these distances:
33 2 0.00
34 37 0.07
35 507 0.92
36 5 0.01
37 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (35 bp):
CAGAGTTGATCTCATTTCAAGAAGTTTCCAACGAT
Found at i:1275 original size:139 final size:139
Alignment explanation
Indices: 1094--1419 Score: 456
Period size: 139 Copynumber: 2.3 Consensus size: 139
1084 TTTTCAAAGG
*
1094 TCAGAGTTGATCTCATTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
1 TCAGAGTTGATCGCATTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
* * * *
1159 AACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACAATCAGAGTTGATCGCATTTTCAGTAT
66 AACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACAATCAAAGTTGATCACATTTTCAGTAG
1224 TTTCCATGA
131 TTTCCATGA
* * * *
1233 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAATGATCGGAGTTGATTGCATTTTCAGTATTTTC
1 TCAGAGTTGATCGCA-TTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
* *
1297 CAACGATCAGAGTTGATCGTATTTTCAGTAGTTTCCAACGATCAAAGTTGATCACATTTTCAGTA
65 CAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACAATCAAAGTTGATCACATTTTCAGTA
**
1362 GTTTCCAACAA
130 GTTTCC-ATGA
* * * * * *
1373 TTAGAGGTGATCTCATTTCAAGAAATTTCCGATGATCAGAGTTGATC
1 TCAGAGTTGATCGCATTTCAAGAAGTTTCCAACGATCAGAGTTGATC
1420 CAGAGGAGTT
Statistics
Matches: 163, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
139 123 0.75
140 40 0.25
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (139 bp):
TCAGAGTTGATCGCATTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
AACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACAATCAAAGTTGATCACATTTTCAGTAG
TTTCCATGA
Done.