Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011737.1 Corchorus capsularis cultivar CVL-1 contig11758, 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: 37030
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:6210 original size:19 final size:19
Alignment explanation
Indices: 6186--6222 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6176 GAGGAAGAAT
* *
6186 AAGAACCTTTTCTTTTGTG
1 AAGAACCTCTTCATTTGTG
6205 AAGAACCTCTTCATTTGT
1 AAGAACCTCTTCATTTGT
6223 TTGCTTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (19 bp):
AAGAACCTCTTCATTTGTG
Found at i:18752 original size:24 final size:26
Alignment explanation
Indices: 18720--18772 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
18710 ATGCAATCTC
18720 TCATAGAAAGACA-C-CTTTTATGTT
1 TCATAGAAAGACATCTCTTTTATGTT
* *
18744 TCATAGAAATACATCTTTTTTATGTT
1 TCATAGAAAGACATCTCTTTTATGTT
18770 TCA
1 TCA
18773 ACAGATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.48
25 1 0.04
26 12 0.48
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (26 bp):
TCATAGAAAGACATCTCTTTTATGTT
Found at i:22783 original size:15 final size:15
Alignment explanation
Indices: 22763--22792 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22753 CCGTAGTGCC
*
22763 AAAATGCCACCAAAA
1 AAAATGACACCAAAA
22778 AAAATGACACCAAAA
1 AAAATGACACCAAAA
22793 TTTCCTGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.23, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAATGACACCAAAA
Found at i:22993 original size:2 final size:2
Alignment explanation
Indices: 22986--23012 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22976 TTGCTCTAAA
22986 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
23013 GCAATTCACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30407 original size:12 final size:12
Alignment explanation
Indices: 30387--30421 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
30377 TTTATAGATA
*
30387 TAGTCAGTTAAG
1 TAGTTAGTTAAG
30399 TAGTTAGTTAAG
1 TAGTTAGTTAAG
30411 TAGTTAAGTTA
1 TAGTT-AGTTA
30422 GTTTCATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.40
Consensus pattern (12 bp):
TAGTTAGTTAAG
Found at i:32061 original size:3 final size:3
Alignment explanation
Indices: 32041--32079 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
32031 GCAATAGACT
*
32041 ATA ATA ATTA ATC A-A ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
32080 TACTACTCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 28 0.88
4 3 0.09
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:33341 original size:13 final size:13
Alignment explanation
Indices: 33323--33360 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
33313 TTAATTATTA
*
33323 GGAGGGTCAAGTT
1 GGAGGGTCAAATT
33336 GGAGGGAT-AAATT
1 GGAGGG-TCAAATT
33349 GGAGGGTCAAAT
1 GGAGGGTCAAAT
33361 AGAATTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 1 0.05
13 20 0.91
14 1 0.05
ACGTcount: A:0.32, C:0.05, G:0.42, T:0.21
Consensus pattern (13 bp):
GGAGGGTCAAATT
Done.