Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002680.1 Corchorus olitorius cultivar O-4 contig02682, 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: 2049
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:393 original size:65 final size:65
Alignment explanation
Indices: 289--521 Score: 362
Period size: 65 Copynumber: 3.5 Consensus size: 65
279 TAAAAAGACA
*
289 ACCTGTCTGAGGTCGAAATT-AGAACTGAGAAAGACCTGTCTGAGATATGGAACTGAAAGATAAA
1 ACCTGTCTGAGGTCGAAATTGA-AACTGAGAAAGACCTGTCTGAGATCTGGAACTGAAAGATAAA
353 G
65 G
354 ACCTGTCTGAGGTCGAAATTGAAACTGAGAAAGACCTGTCTGAGATCTGGAACTGAAAGATAAAG
1 ACCTGTCTGAGGTCGAAATTGAAACTGAGAAAGACCTGTCTGAGATCTGGAACTGAAAGATAAAG
*
419 ACCTATCTGAGGTC-AAGATTGAAACTGAGAAAGAATGACCTGTCTGAGATCTGGAACTGAAAGA
1 ACCTGTCTGAGGTCGAA-ATTGAAACTGAG--A-AA-GACCTGTCTGAGATCTGGAACTGAAAGA
483 TAAAG
61 TAAAG
* *
488 ATCTGTCTGAGGTCAAAATTGAAACTGAGAAAGA
1 ACCTGTCTGAGGTCGAAATTGAAACTGAGAAAGA
522 ATGACCTGTT
Statistics
Matches: 157, Mismatches: 4, Indels: 14
0.90 0.02 0.08
Matches are distributed among these distances:
64 2 0.01
65 89 0.57
66 3 0.02
67 2 0.01
68 2 0.01
69 57 0.36
70 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (65 bp):
ACCTGTCTGAGGTCGAAATTGAAACTGAGAAAGACCTGTCTGAGATCTGGAACTGAAAGATAAAG
Found at i:459 original size:37 final size:36
Alignment explanation
Indices: 353--530 Score: 123
Period size: 37 Copynumber: 5.2 Consensus size: 36
343 GAAAGATAAA
353 GACCTGTCTGAGGTCGAAATTGAAACTGAG--A-AA-
1 GACCTGTCTGAGGTC-AAATTGAAACTGAGAAAGAAT
* * * *
386 GACCTGTCTGAGATC----TGGAACTGA-AAGATAAA
1 GACCTGTCTGAGGTCAAATTGAAACTGAGAA-AGAAT
*
418 GACCTATCTGAGGTCAAGATTGAAACTGAGAAAGAAT
1 GACCTGTCTGAGGTCAA-ATTGAAACTGAGAAAGAAT
* * * *
455 GACCTGTCTGAGATC----TGGAACTGA-AAGATAAA
1 GACCTGTCTGAGGTCAAATTGAAACTGAGAA-AGAAT
*
487 GATCTGTCTGAGGTCAAAATTGAAACTGAGAAAGAAT
1 GACCTGTCTGAGGTC-AAATTGAAACTGAGAAAGAAT
524 GACCTGT
1 GACCTGT
531 TTCCACTCAA
Statistics
Matches: 109, Mismatches: 18, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
28 8 0.07
30 1 0.01
31 4 0.04
32 37 0.34
33 14 0.13
37 41 0.38
38 4 0.04
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (36 bp):
GACCTGTCTGAGGTCAAATTGAAACTGAGAAAGAAT
Found at i:572 original size:39 final size:39
Alignment explanation
Indices: 512--1030 Score: 804
Period size: 39 Copynumber: 13.5 Consensus size: 39
502 AAAATTGAAA
* *
512 CTGAGAAAGAATGACCTGTTTCCACTCAACTTTGATAAATA
1 CTGA-AAAG-ATGACCTGTTTCCAGTCAACTTTGATAAATG
*
553 CTAAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
592 CTGAAAAGATGACCTGTTTCCAGT---C------AAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
*
622 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAGTG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
* * *
661 CTGGAAAGATGACCTGTTTCTAGTCAACTTTGATAAATA
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
*
700 CTGAAAAGATGACCTGTTTCCAGTCAATTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
*
739 GTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
778 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
* *
817 CTGGAAAGATGACCTGTTTCCAGTCAACTTTGATAAATA
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
*
856 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATA
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
*
895 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATA
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
* *
934 CTGAAAAGATGATCTGTTTCCAGTCAATTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
* *
973 GTGAAAAGATGACCTGTTTCCAGTCAATTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
1012 CTGAAAAGATGACCTGTTT
1 CTGAAAAGATGACCTGTTT
1031 GAATGCTTTA
Statistics
Matches: 444, Mismatches: 25, Indels: 20
0.91 0.05 0.04
Matches are distributed among these distances:
30 29 0.07
33 1 0.00
36 1 0.00
39 406 0.91
40 4 0.01
41 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (39 bp):
CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
Found at i:623 original size:30 final size:30
Alignment explanation
Indices: 587--648 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
577 CAACTTTGAT
587 AAATGCTGAAAAGATGACCTGTTTCCAGTC
1 AAATGCTGAAAAGATGACCTGTTTCCAGTC
617 AAATGCTGAAAAGATGACCTGTTTCCAGTC
1 AAATGCTGAAAAGATGACCTGTTTCCAGTC
647 AA
1 AA
649 CTTTGATAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (30 bp):
AAATGCTGAAAAGATGACCTGTTTCCAGTC
Done.