Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020060.1 Corchorus olitorius cultivar O-4 contig20093, 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: 20505
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:3784 original size:21 final size:20
Alignment explanation
Indices: 3754--3797 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
3744 TCTTGTAATC
3754 TAAAATTATTATAAA-AGTTA
1 TAAAATTATTA-AAATAGTTA
3774 TAAAAGTTATTAAAATAGTTA
1 TAAAA-TTATTAAAATAGTTA
3795 TAA
1 TAA
3798 TGCATTCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (20 bp):
TAAAATTATTAAAATAGTTA
Found at i:8195 original size:17 final size:16
Alignment explanation
Indices: 8146--8195 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
8136 GCTAGTTCGA
*
8146 TTGAATTGATTTTTGC
1 TTGAATTTATTTTTGC
* *
8162 TTGCATGTTATTATTGC
1 TTGAAT-TTATTTTTGC
8179 TTGAATTTAGTTTTTGC
1 TTGAATTTA-TTTTTGC
8196 ATTTAGTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (16 bp):
TTGAATTTATTTTTGC
Found at i:10807 original size:28 final size:28
Alignment explanation
Indices: 10756--11060 Score: 317
Period size: 28 Copynumber: 10.8 Consensus size: 28
10746 TTTTGCGAAC
* *
10756 CCAAAGGCATTTTGGTCATTTTTGCATAT
1 CCAAGGGCATTTTGGTCA-TTTTGCACAT
* *
10785 CTAAGGGCATTTTGGTCATTTTGCGCAT
1 CCAAGGGCATTTTGGTCATTTTGCACAT
* * *
10813 CCGAGGGCATTTTGATCATTTTGCGCAT
1 CCAAGGGCATTTTGGTCATTTTGCACAT
*
10841 CCAAGGGCATTTTGGTCATTTTGCGCAT
1 CCAAGGGCATTTTGGTCATTTTGCACAT
* *
10869 CCAAGGGCATTTTGATCATTTTGCGCAT
1 CCAAGGGCATTTTGGTCATTTTGCACAT
*
10897 CCAAGGGCATTTTGGTCATTTTACGCATAT
1 CCAAGGGCATTTTGGTCATTTT--GCACAT
* * *
10927 CTAGGGGCATTTCGGTCATTTTGCACAT
1 CCAAGGGCATTTTGGTCATTTTGCACAT
* *
10955 CCAAGGGCATTTTGGTCATTTTTACTCAT
1 CCAAGGGCATTTTGGTCA-TTTTGCACAT
* * * *
10984 CTAGGGGCATTTCGATCATTTTTGCACAT
1 CCAAGGGCATTTTGGTCA-TTTTGCACAT
* * * *
11013 CTAGGGGCATTTTGGTCA-TTT-CGCGT
1 CCAAGGGCATTTTGGTCATTTTGCACAT
* *
11039 CCAGGGGCATTTTGATCATTTT
1 CCAAGGGCATTTTGGTCATTTT
11061 TTTGCATACT
Statistics
Matches: 238, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
26 19 0.08
27 6 0.03
28 127 0.53
29 63 0.26
30 23 0.10
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (28 bp):
CCAAGGGCATTTTGGTCATTTTGCACAT
Found at i:10859 original size:56 final size:57
Alignment explanation
Indices: 10761--11060 Score: 369
Period size: 56 Copynumber: 5.3 Consensus size: 57
10751 CGAACCCAAA
* * * * *
10761 GGCATTTTGGTCATTTTTGCATATCTAAGGGCATTTTGGTCATTTTGCGCATCCGA-G
1 GGCATTTTGATCA-TTTTGCACATCCAAGGGCATTTTGGTCATTTTACGCATCCTAGG
* * *
10818 GGCATTTTGATCATTTTGCGCATCCAAGGGCATTTTGGTCATTTTGCGCATCC-AAG
1 GGCATTTTGATCATTTTGCACATCCAAGGGCATTTTGGTCATTTTACGCATCCTAGG
* *
10874 GGCATTTTGATCATTTTGCGCATCCAAGGGCATTTTGGTCATTTTACGCATATCTAGG
1 GGCATTTTGATCATTTTGCACATCCAAGGGCATTTTGGTCATTTTACGCAT-CCTAGG
* * *
10932 GGCATTTCGGTCATTTTGCACATCCAAGGGCATTTTGGTCATTTTTACTCAT-CTAGG
1 GGCATTTTGATCATTTTGCACATCCAAGGGCATTTTGGTCA-TTTTACGCATCCTAGG
* * * *
10989 GGCATTTCGATCATTTTTGCACATCTAGGGGCATTTTGGTCA-TTT-CGCGTCC-AGG
1 GGCATTTTGATCA-TTTTGCACATCCAAGGGCATTTTGGTCATTTTACGCATCCTAGG
11044 GGCATTTTGATCATTTT
1 GGCATTTTGATCATTTT
11061 TTTGCATACT
Statistics
Matches: 220, Mismatches: 17, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
54 4 0.02
55 19 0.09
56 92 0.42
57 30 0.14
58 66 0.30
59 9 0.04
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (57 bp):
GGCATTTTGATCATTTTGCACATCCAAGGGCATTTTGGTCATTTTACGCATCCTAGG
Found at i:11047 original size:142 final size:141
Alignment explanation
Indices: 10746--11060 Score: 391
Period size: 142 Copynumber: 2.2 Consensus size: 141
10736 TAATTGACAT
* * * * * *
10746 TTTTGCGAACCCAAAGGCATTTTGGTCATTTTTGCATATCTAAGGGCATTTTGGTCATTTTGCGC
1 TTTTGCGCATCCAAGGGCATTTTGGTCATTTTCGCATATCTAAGGGCATTTCGGTCATTTTGCAC
* * * * *
10811 ATCCGAGGGCATTTTGATCATTTTGCGCATCCAAGGGCATTTTGGTCATTTTGCGCATCCAAGGG
66 ATCCAAGGGCATTTTGATCATTTTACGCATCCAAGGGCATTTCGATCATTTTGCACATCCAAGGG
10876 CATTTTGATCA
131 CATTTTGATCA
*
10887 TTTTGCGCATCCAAGGGCATTTTGGTCATTTTACGCATATCTAGGGGCATTTCGGTCATTTTGCA
1 TTTTGCGCATCCAAGGGCATTTTGGTCATTTT-CGCATATCTAAGGGCATTTCGGTCATTTTGCA
* * * * * *
10952 CATCCAAGGGCATTTTGGTCATTTTTACTCATCTAGGGGCATTTCGATCATTTTTGCACATCTAG
65 CATCCAAGGGCATTTTGATCA-TTTTACGCATCCAAGGGCATTTCGATCA-TTTTGCACATCCAA
*
11017 GGGCATTTTGGTCA
128 GGGCATTTTGATCA
* * *
11031 -TTT-CGCGTCCAGGGGCATTTTGATCATTTT
1 TTTTGCGCATCCAAGGGCATTTTGGTCATTTT
11061 TTTGCATACT
Statistics
Matches: 149, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
141 29 0.19
142 71 0.48
143 25 0.17
144 24 0.16
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (141 bp):
TTTTGCGCATCCAAGGGCATTTTGGTCATTTTCGCATATCTAAGGGCATTTCGGTCATTTTGCAC
ATCCAAGGGCATTTTGATCATTTTACGCATCCAAGGGCATTTCGATCATTTTGCACATCCAAGGG
CATTTTGATCA
Found at i:11063 original size:86 final size:86
Alignment explanation
Indices: 10761--11061 Score: 351
Period size: 84 Copynumber: 3.5 Consensus size: 86
10751 CGAACCCAAA
** * * * *
10761 GGCATTTTGGTCATTTTTGCATATCTAAGGGCATTTTGGTCA-TTTTGCGCATCCGAGGGCATTT
1 GGCATTTTGGTCA-TTTTGCGCATCCAAGGGCATTTTGATCATTTTTACGCATCCAAGGGCATTT
* * *
10825 TGATCA-TTTTGCGCATCCAAG
65 TGATCATTTTTGCACATCTAGG
*
10846 GGCATTTTGGTCATTTTGCGCATCCAAGGGCATTTTGATCA-TTTTGCGCATCCAAGGGCATTTT
1 GGCATTTTGGTCATTTTGCGCATCCAAGGGCATTTTGATCATTTTTACGCATCCAAGGGCATTTT
* * *
10910 GGTCATTTTACGCATATCTAGG
66 GATCATTTT-TGCACATCTAGG
* * * * * * *
10932 GGCATTTCGGTCATTTTGCACATCCAAGGGCATTTTGGTCATTTTTACTCATCTAGGGGCATTTC
1 GGCATTTTGGTCATTTTGCGCATCCAAGGGCATTTTGATCATTTTTACGCATCCAAGGGCATTTT
10997 GATCATTTTTGCACATCTAGG
66 GATCATTTTTGCACATCTAGG
* *
11018 GGCATTTTGGTCA-TTT-CGCGTCCAGGGGCATTTTGATCATTTTT
1 GGCATTTTGGTCATTTTGCGCATCCAAGGGCATTTTGATCATTTTT
11062 TTGCATACTC
Statistics
Matches: 186, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
84 74 0.40
85 19 0.10
86 67 0.36
87 26 0.14
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (86 bp):
GGCATTTTGGTCATTTTGCGCATCCAAGGGCATTTTGATCATTTTTACGCATCCAAGGGCATTTT
GATCATTTTTGCACATCTAGG
Found at i:16219 original size:20 final size:20
Alignment explanation
Indices: 16188--16233 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
16178 TTATGATTTT
*
16188 TTTA-TAATTATTAGTGTTA
1 TTTATTAATTATTAGTATTA
16207 -TTATTAATATATTAGTATTA
1 TTTATTAAT-TATTAGTATTA
16227 TTTATTA
1 TTTATTA
16234 TGTATTGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 10 0.43
21 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTATTAATTATTAGTATTA
Done.