Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010140.1 Corchorus capsularis cultivar CVL-1 contig10161, 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: 3795
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Found at i:2191 original size:35 final size:35
Alignment explanation
Indices: 2156--2823 Score: 1083
Period size: 35 Copynumber: 19.1 Consensus size: 35
2146 GTGCGGTCAT
2156 TTTC-AGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
2190 TTCCAAGAAGTTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAG-TTTTCAGAGGTCAGAGTTGATCTCA
2226 TTTCAAGAAG-TTTCTAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTC-AGAGGTCAGAGTTGATCTCA
* *
2261 TTCCAAGAAGTTTTCAGAGGTCAAAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
2296 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCCCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
2331 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* * *
2366 TATCAGGAACTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
2401 -TTCTAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTC-AAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
2436 TTTCAAGCAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
2471 TTCCAAGCAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
2506 TTTCAAGCAA-TTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAG-AAGTTTTCAGAGGTCAGAGTTGATCTCA
*
2541 TTTCAAGCAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* * *
2576 TTCCAAGAAGTTTACAGAGGTTAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
2611 TTTCAAGCAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* * *
2646 TTCCAAGAAGTTTACAGAGGTTAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
2681 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
2716 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
2751 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
2786 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
2821 TTT
1 TTT
2824 TCAGTATTTT
Statistics
Matches: 588, Mismatches: 38, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
34 10 0.02
35 536 0.91
36 42 0.07
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
Found at i:2845 original size:35 final size:35
Alignment explanation
Indices: 2806--3067 Score: 391
Period size: 35 Copynumber: 7.5 Consensus size: 35
2796 TTTTCAGAGG
* *
2806 TCAGAGTTGATCTCATTTTCAGTATTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
2841 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
2876 TCATAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
2911 TCAGAGTTGATCGCATTTTCAATAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
2946 TCAGAGTTGATCGCATTTTCAGTAGTTACCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * * *
2981 TCAGAGTTG-CCGCATTTTCAATATTTTGCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
3015 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
3050 TCAGAGGTGATCTCATTT
1 TCAGAGTTGATCGCATTT
3068 CAAGAAATTC
Statistics
Matches: 206, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
34 29 0.14
35 177 0.86
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (35 bp):
TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
Found at i:3559 original size:28 final size:28
Alignment explanation
Indices: 3518--3572 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
3508 GACAGCCAAT
* * *
3518 ACACACACATAGAGAGATAGAGAGATAG
1 ACACAAACACAGAGAGACAGAGAGATAG
3546 ACACAAACACAGAGAGACAGAGAGATA
1 ACACAAACACAGAGAGACAGAGAGATA
3573 CACCGGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.53, C:0.16, G:0.24, T:0.07
Consensus pattern (28 bp):
ACACAAACACAGAGAGACAGAGAGATAG
Done.