Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011773.1 Corchorus capsularis cultivar CVL-1 contig11794, 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: 12755
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:973 original size:35 final size:35
Alignment explanation
Indices: 927--996 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
917 CTTTATCTTC
927 TTATGTCTTAAGATTAATTTACATGTGGCTTCCTT
1 TTATGTCTTAAGATTAATTTACATGTGGCTTCCTT
962 TTATGTCTTAAGATTAATTTACATGTGGCTTCCTT
1 TTATGTCTTAAGATTAATTTACATGTGGCTTCCTT
997 GGAAAGTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (35 bp):
TTATGTCTTAAGATTAATTTACATGTGGCTTCCTT
Found at i:7491 original size:2 final size:2
Alignment explanation
Indices: 7484--7512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7474 CATGCTTTAT
7484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7513 TTCTGTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7640 original size:3 final size:3
Alignment explanation
Indices: 7634--7663 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
7624 TTTTGTGAAA
7634 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
7664 AAATATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:9099 original size:19 final size:20
Alignment explanation
Indices: 9072--9129 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 20
9062 ATAATTAATT
9072 TACCTTATTCATGTTATATA
1 TACCTTATTCATGTTATATA
*
9092 TA-CTTATT-A-GTTAAAT-
1 TACCTTATTCATGTTATATA
9108 TACCTTATTCATGTTATATA
1 TACCTTATTCATGTTATATA
9128 TA
1 TA
9130 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 2 0.06
17 12 0.38
18 2 0.06
19 12 0.38
20 4 0.12
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (20 bp):
TACCTTATTCATGTTATATA
Found at i:9114 original size:17 final size:19
Alignment explanation
Indices: 9066--9123 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
9056 TACTTTATAA
*
9066 TTAATTTACCTTATTCATG
1 TTAAATTACCTTATTCATG
*
9085 TTATATATA-CTTATT-A-G
1 TTAAAT-TACCTTATTCATG
9102 TTAAATTACCTTATTCATG
1 TTAAATTACCTTATTCATG
9121 TTA
1 TTA
9124 TATATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.06
17 12 0.38
18 2 0.06
19 14 0.44
20 2 0.06
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (19 bp):
TTAAATTACCTTATTCATG
Found at i:10616 original size:20 final size:20
Alignment explanation
Indices: 10591--10628 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10581 ATAAACAGTG
10591 GTCCCTAACGTTTTATTATA
1 GTCCCTAACGTTTTATTATA
10611 GTCCCTAACGTTTTATTA
1 GTCCCTAACGTTTTATTA
10629 GTGTTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.45
Consensus pattern (20 bp):
GTCCCTAACGTTTTATTATA
Found at i:11712 original size:21 final size:21
Alignment explanation
Indices: 11686--11728 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
11676 GGTCTTAGAT
*
11686 TCAACTCTCACGGAATGTGAG
1 TCAACTCTCACGGAATATGAG
11707 TCAACTCTCACGGAATATGAG
1 TCAACTCTCACGGAATATGAG
11728 T
1 T
11729 TTATTTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (21 bp):
TCAACTCTCACGGAATATGAG
Found at i:11831 original size:30 final size:30
Alignment explanation
Indices: 11791--11857 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
11781 GGCATAGAGA
11791 TTTATTTGAATTGTAATGAGATTTCATTGGG
1 TTTA-TTGAATTGTAATGAGATTTCATTGGG
11822 TTTATTGAATTGTAATGAGATTTCATTGGG
1 TTTATTGAATTGTAATGAGATTTCATTGGG
11852 TTTATT
1 TTTATT
11858 TGTTGGCTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.25, C:0.03, G:0.21, T:0.51
Consensus pattern (30 bp):
TTTATTGAATTGTAATGAGATTTCATTGGG
Found at i:12730 original size:33 final size:30
Alignment explanation
Indices: 12672--12755 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 30
12662 AAAGACACGT
*
12672 GACATGTGTC-CTTTT-GTGCACGTGGCATGCG
1 GACATGTGTCACTTTTGGTACACGTGGC--G-G
* *
12703 GCCATGTGTCACTTTTGGTACACGTGGCGT
1 GACATGTGTCACTTTTGGTACACGTGGCGG
12733 GACATGTGTCACCTTTTGGTACA
1 GACATGTGTCA-CTTTTGGTACA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 10 0.22
31 21 0.46
32 5 0.11
33 10 0.22
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33
Consensus pattern (30 bp):
GACATGTGTCACTTTTGGTACACGTGGCGG
Done.