Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012453.1 Corchorus olitorius cultivar O-4 contig12486, 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: 71302
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:6559 original size:130 final size:135
Alignment explanation
Indices: 6424--6667 Score: 354
Period size: 130 Copynumber: 1.8 Consensus size: 135
6414 CATTGTTTAA
* * *
6424 ACTTTTATAGTTTTATTCAACTAAAAACTCTAATTTTATTTATTTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
6485 -TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATATTAGAAATTTTTTA
66 TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATATTAGAAATTTTTTA
6549 AATAT
131 AATAT
*
6554 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--C
* * * *
6619 TATTTTATTTTTACCATTTTATTATTTTATTTTAAAAACTTATATATAT
64 TA-TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATAT
6668 TAGAATTTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
130 52 0.53
131 1 0.01
132 1 0.01
133 1 0.01
136 2 0.02
138 41 0.42
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (135 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATATTAGAAATTTTTTA
AATAT
Found at i:6707 original size:14 final size:13
Alignment explanation
Indices: 6671--6709 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
6661 TATATATTAG
6671 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
6684 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
6698 AATTTTTTAAAT
1 AATTTTTTAAAT
6710 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:29880 original size:167 final size:167
Alignment explanation
Indices: 29599--29934 Score: 631
Period size: 167 Copynumber: 2.0 Consensus size: 167
29589 TTTTTTACTT
*
29599 TAGGTTAGGACTTGAGGAATGCATCTACTAACTTGCTATTGCATTTTGAATATTTGTCAAGGATC
1 TAGGCTAGGACTTGAGGAATGCATCTACTAACTTGCTATTGCATTTTGAATATTTGTCAAGGATC
29664 TTTGTAGGCATTGGTTTTTTAAGTTTGATTGTAGATGAAATTGCTTTACTGTTGACAAAATGCAT
66 TTTGTAGGCATTGGTTTTTTAAGTTTGATTGTAGATGAAATTGCTTTACTGTTGACAAAATGCAT
29729 TAGGCAAGCATTTTATATTTCCTTGTTTCTTAGTCTG
131 TAGGCAAGCATTTTATATTTCCTTGTTTCTTAGTCTG
29766 TAGGCTAGGACTTGAGGAATGCATCTACTAACTTGCTATTGCATTTTGAATATTTGTCAAGGATC
1 TAGGCTAGGACTTGAGGAATGCATCTACTAACTTGCTATTGCATTTTGAATATTTGTCAAGGATC
29831 TTTG-ATGGCATTGGTTTTTTACA-TTTGATTGTAGATGAAATTGCTTTACTGTTGACAAAATGC
66 TTTGTA-GGCATTGGTTTTTTA-AGTTTGATTGTAGATGAAATTGCTTTACTGTTGACAAAATGC
29894 ATTAGGCAAGCATTTTATATTTCCTTGTTTCTTAGTCTG
129 ATTAGGCAAGCATTTTATATTTCCTTGTTTCTTAGTCTG
29933 TA
1 TA
29935 ATTTTCTTTT
Statistics
Matches: 166, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
166 1 0.01
167 164 0.99
168 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (167 bp):
TAGGCTAGGACTTGAGGAATGCATCTACTAACTTGCTATTGCATTTTGAATATTTGTCAAGGATC
TTTGTAGGCATTGGTTTTTTAAGTTTGATTGTAGATGAAATTGCTTTACTGTTGACAAAATGCAT
TAGGCAAGCATTTTATATTTCCTTGTTTCTTAGTCTG
Found at i:44673 original size:57 final size:56
Alignment explanation
Indices: 44583--44699 Score: 182
Period size: 57 Copynumber: 2.1 Consensus size: 56
44573 CTTTGTCTCC
*
44583 AAGGGCACCCAGAAGTTGAGTTCGGATCTTAGAATGGACGGAGTGGAATTATGGGA
1 AAGGGCACCCAAAAGTTGAGTTCGGATCTTAGAATGGACGGAGTGGAATTATGGGA
* *
44639 AAGGGCACCCCAAAAGTTGAGTTTGGAT-TCTAGAATGGATGGAGTGGAATTATGGGA
1 AAGGGCA-CCCAAAAGTTGAGTTCGGATCT-TAGAATGGACGGAGTGGAATTATGGGA
44696 AAGG
1 AAGG
44700 AGAAAGCTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
56 8 0.14
57 48 0.86
ACGTcount: A:0.32, C:0.11, G:0.35, T:0.22
Consensus pattern (56 bp):
AAGGGCACCCAAAAGTTGAGTTCGGATCTTAGAATGGACGGAGTGGAATTATGGGA
Found at i:50277 original size:55 final size:53
Alignment explanation
Indices: 50193--50304 Score: 172
Period size: 55 Copynumber: 2.1 Consensus size: 53
50183 CTTATTCTTA
50193 ATTATGGTTTTTGAATTAGACTTTATGCCAGATTATTATATGTA-AATTAACTTGC
1 ATTATGGTTTTTGAATTAGACTTTATGCCAGA-TA-TATAT-TATAATTAACTTGC
*
50248 ATTATGGTTTTTGAATTAGACTTTTTGCCAGATATATATTATTAATTAACTTGC
1 ATTATGGTTTTTGAATTAGACTTTATGCCAGATATATATTA-TAATTAACTTGC
50302 ATT
1 ATT
50305 TTTACATCAT
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
52 2 0.04
53 5 0.09
54 16 0.30
55 31 0.57
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.47
Consensus pattern (53 bp):
ATTATGGTTTTTGAATTAGACTTTATGCCAGATATATATTATAATTAACTTGC
Found at i:55815 original size:60 final size:60
Alignment explanation
Indices: 55740--55866 Score: 202
Period size: 60 Copynumber: 2.1 Consensus size: 60
55730 GCTAACCTTT
*
55740 AATT-TGAGGAAAATTAAAATTAAATCAACCAAGCAAGAATTGGCACATTATACATGGAA
1 AATTATGAGGAAAATTAAAATCAAATCAACCAAGCAAGAATTGGCACATTATACATGGAA
* * * *
55799 AATTATGAGGCAAATTATAATCAAATCAACTAAGCAAGAATTGGCACATTTTACATGGAA
1 AATTATGAGGAAAATTAAAATCAAATCAACCAAGCAAGAATTGGCACATTATACATGGAA
55859 AATTATGA
1 AATTATGA
55867 TATTAAAGGA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
59 4 0.06
60 58 0.94
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (60 bp):
AATTATGAGGAAAATTAAAATCAAATCAACCAAGCAAGAATTGGCACATTATACATGGAA
Found at i:62528 original size:32 final size:34
Alignment explanation
Indices: 62492--62560 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
62482 CTTCCTTAAA
62492 TTTATATCTATATA-AAAA-GTCTCAGATTGAAG
1 TTTATATCTATATATAAAAGGTCTCAGATTGAAG
62524 TTTATATCTATATATAAAAGGTCTCAGATTGAAG
1 TTTATATCTATATATAAAAGGTCTCAGATTGAAG
62558 TTT
1 TTT
62561 TAAATTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 14 0.40
33 4 0.11
34 17 0.49
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.41
Consensus pattern (34 bp):
TTTATATCTATATATAAAAGGTCTCAGATTGAAG
Done.