Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018802.1 Corchorus olitorius cultivar O-4 contig18835, 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: 8071
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4644 original size:38 final size:36
Alignment explanation
Indices: 4565--4645 Score: 92
Period size: 39 Copynumber: 2.2 Consensus size: 36
4555 GAAAAATCCG
* *
4565 ACCTAAAGGAAACCCAACCCAAAAAAAAAAAAAATTG
1 ACCTGAAGGAAACCCAACCCAAAAAAAAAAAAAA-TA
*
4602 ACCTGAAGGAAACCTGAACCCCAAAAAAAAAAAGAAA-A
1 ACCTGAAGGAAACC-CAA-CCCAAAAAAAAAAA-AAATA
4640 ACCTGA
1 ACCTGA
4646 TTGAGCCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 13 0.34
38 8 0.21
39 14 0.37
40 3 0.08
ACGTcount: A:0.59, C:0.22, G:0.11, T:0.07
Consensus pattern (36 bp):
ACCTGAAGGAAACCCAACCCAAAAAAAAAAAAAATA
Found at i:4829 original size:7 final size:7
Alignment explanation
Indices: 4819--4854 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
4809 ATTAATTTAG
4819 AATTAAA
1 AATTAAA
4826 AATTAAA
1 AATTAAA
4833 AATTAAA
1 AATTAAA
4840 AATTAAA
1 AATTAAA
*
4847 AATGAAA
1 AATTAAA
4854 A
1 A
4855 TTCAGATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (7 bp):
AATTAAA
Found at i:4843 original size:21 final size:20
Alignment explanation
Indices: 4819--4879 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
4809 ATTAATTTAG
4819 AATTAAAAATTAAAAATTAAA
1 AATTAAAAA-TAAAAATTAAA
* * *
4840 AATTAAAAATGAAAATTCAG
1 AATTAAAAATAAAAATTAAA
*
4860 ATTTAATAAATAAAAATTAA
1 AATTAA-AAATAAAAATTAA
4880 TAGAAATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (20 bp):
AATTAAAAATAAAAATTAAA
Found at i:5113 original size:93 final size:93
Alignment explanation
Indices: 5011--5193 Score: 276
Period size: 93 Copynumber: 2.0 Consensus size: 93
5001 CCATTAATTA
* * * * *
5011 TACTTTTATAGTTTTAGTCCACTAAAAACTCTAATTTTATTTAATTAAATCTAATGTCCTTATAA
1 TACTTTTATAGTTTGACTCAACTAAAAACTCTAATTTTATCTAATTAAATCTAATATCCTTATAA
* *
5076 CTATTTCATTTTTATCATTTTACTATTT
66 CTATTTCATTTTTACCATATTACTATTT
* *
5104 TACTTTTATAGTTTGACTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAC
1 TACTTTTATAGTTTGACTCAACTAAAAACTCTAATTTTATCTAATTAAATCTAATATCCTTATAA
*
5169 CTATTTTATTTTTACCATATTACTA
66 CTATTTCATTTTTACCATATTACTA
5194 ATCTATACTA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (93 bp):
TACTTTTATAGTTTGACTCAACTAAAAACTCTAATTTTATCTAATTAAATCTAATATCCTTATAA
CTATTTCATTTTTACCATATTACTATTT
Found at i:5265 original size:31 final size:31
Alignment explanation
Indices: 5227--5288 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5217 GAGTTTTGTA
5227 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
*
5258 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
5289 TTTTGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCACCTATTATACCCTTATT
Found at i:5426 original size:93 final size:93
Alignment explanation
Indices: 5324--5508 Score: 298
Period size: 93 Copynumber: 2.0 Consensus size: 93
5314 TTGTTTAAAT
* * *
5324 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTGATTAAATATAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTATATTTTTATTTAATTAAATATAATATCCTTATAACTA
* *
5389 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
* *
5417 TTTTATAGTTTTACTCAACTAAAAACTATATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTATATTTTTATTTAATTAAATATAATATCCTTATAACTA
*
5482 TTTTATTTTTACGATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
5509 ATTAAAAAGT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.52
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTATATTTTTATTTAATTAAATATAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:6648 original size:41 final size:44
Alignment explanation
Indices: 6603--6698 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 44
6593 AAAGTGCATT
*
6603 ATCTAA-ATTCTA-C-TCCATCTCTAGGTAATTCATCAAAATAA
1 ATCTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAA
*
6644 ATCTAATATTCTACTCTTCCATCTCTAGATAATTCATCAAAATAT
1 ATCTAATATTCTAC-CTTCCATCTCTAGATAATTCATCAAAATAA
*
6689 AGCTAATATT
1 ATCTAATATT
6699 AATCGTTGCT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
41 6 0.12
42 6 0.12
44 1 0.02
45 35 0.73
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (44 bp):
ATCTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAA
Found at i:8003 original size:13 final size:13
Alignment explanation
Indices: 7961--8005 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
7951 TCATGCACCC
*
7961 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
7975 AAAACCATTT-AT
1 AAAACAATTTAAT
7987 AAAACAATTTAAT
1 AAAACAATTTAAT
8000 AAAACA
1 AAAACA
8006 GTAATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACAATTTAAT
Done.