Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016933.1 Corchorus olitorius cultivar O-4 contig16966, 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: 9141
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Found at i:190 original size:30 final size:31
Alignment explanation
Indices: 56--173 Score: 218
Period size: 31 Copynumber: 3.8 Consensus size: 31
46 ACTAAATACT
*
56 AAAAAATCCCTAATGTTTTTCTTTTGGGACA
1 AAAAAATCCCTTATGTTTTTCTTTTGGGACA
87 AAAAAATCCCTTATGTTTTTCTTTTGGGACA
1 AAAAAATCCCTTATGTTTTTCTTTTGGGACA
118 AAAAAATCCCTTATGTTTTTCTTTTGGGACA
1 AAAAAATCCCTTATGTTTTTCTTTTGGGACA
*
149 AAAAAATCCCTTATGTTTTTTTTTT
1 AAAAAATCCCTTATGTTTTTCTTTT
174 TGACAAATTA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (31 bp):
AAAAAATCCCTTATGTTTTTCTTTTGGGACA
Found at i:366 original size:29 final size:30
Alignment explanation
Indices: 324--397 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
314 CTCATTTTTG
* *
324 AAACGTAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
*
353 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
384 AAACATAAGGGATT
1 AAACATAAGGGATT
398 TTTCTGGGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 25 0.62
31 15 0.38
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:7789 original size:78 final size:78
Alignment explanation
Indices: 7597--8093 Score: 740
Period size: 78 Copynumber: 6.4 Consensus size: 78
7587 GAAAAAAATA
* * *
7597 AAACGATCGTCTCCTTTGAGAC--TTTCGTCACAAACGGCCAAACACCAGCCTTGGTGTCCCCGT
1 AAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCTCGGTGTCCCCGT
7660 AT-AAAA-AAACG
66 ATAAAAATAAACG
*
7671 AAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCT-TGTCGTCCCCG
1 AAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCTCGGT-GTCCCCG
7735 TATAAAAATAAACG
65 TATAAAAATAAACG
* * * *
7749 AAACGATTGTCTCCATTGAGACTGTTTCGTCACAAGCGGCCGAACACCAGCCTCGGTGTTCCCAT
1 AAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCTCGGTGTCCCCGT
*
7814 ATAAAAATAAATG
66 ATAAAAATAAACG
*
7827 AAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCT-TGTCGT-CCCG
1 AAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCTCGGT-GTCCCCG
7890 TATAAAAATAAACG
65 TATAAAAATAAACG
* * * *
7904 AAACGATTGTCTCCATTGAGACTGTTTCGTCACAAGCGGCCGAACACCAGCCTCGGTGTTCCCAT
1 AAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCTCGGTGTCCCCGT
*
7969 ATAAAAATAAATG
66 ATAAAAATAAACG
7982 AAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCTCGGTGTCCCCGT
1 AAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCTCGGTGTCCCCGT
*
8047 ATAAAAATAAATG
66 ATAAAAATAAACG
* * *
8060 AAACGAACGTC-CCTATTGAGACCGTTTCATCACA
1 AAACGATCGTCTCC-ATTGAGACTGTTTCGTCACA
8094 GATAAAAACA
Statistics
Matches: 387, Mismatches: 26, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
74 21 0.05
75 2 0.01
76 38 0.10
77 77 0.20
78 247 0.64
79 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (78 bp):
AAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCTCGGTGTCCCCGT
ATAAAAATAAACG
Found at i:8025 original size:233 final size:231
Alignment explanation
Indices: 7588--8093 Score: 772
Period size: 233 Copynumber: 2.2 Consensus size: 231
7578 GAAATTTTGG
* *
7588 AAAA-AAATAAAACGATCGTCTCCTTTGAGAC-TTTCGTCACAAACGGCCAAACACCAGCCTTGG
1 AAAATAAATGAAACGATCGTCTCCATTGAGACGTTTCGTCACAAACGGCCAAACACCAGCCTTGG
7651 TGTCCCCGTATAAAAAAACGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAAC
66 TGTCCCCGTATAAAAAAACGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAAC
* * *
7716 ACCAGCCTTGTCGTCCCCGTATAAAAATAAACGAAACGATTGTCTCCATTGAGACTGTTTCGTCA
131 ACCAGCCTGGTCGTCCCCATATAAAAATAAACGAAACGATCGTCTCCATTGAGACTGTTTCGTCA
* *
7781 CAAGCGGCCGAACACCAGCCTCGGTGTTCCCATATA
196 CAAACGGCCGAACACCAGCCTCGGTGTCCCCATATA
*
7817 AAAATAAATGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCCTT-
1 AAAATAAATGAAACGATCGTCTCCATTGAGAC-GTTTCGTCACAAACGGCCAAACACCAGCCTTG
* *
7881 GTCGT-CCCGTATAAAAATAAACGAAACGATTGTCTCCATTGAGACTGTTTCGTCACAAGCGGCC
65 GT-GTCCCCGTAT-AAAA-AAACGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCC
* *
7945 GAACACCAGCCTCGGT-GTTCCCATATAAAAATAAATGAAACGATCGTCTCCATTGAGACTGTTT
127 GAACACCAGCCT-GGTCGTCCCCATATAAAAATAAACGAAACGATCGTCTCCATTGAGACTGTTT
*
8009 CGTCACAAACGGCCGAACACCAGCCTCGGTGTCCCCGTATA
191 CGTCACAAACGGCCGAACACCAGCCTCGGTGTCCCCATATA
* *
8050 AAAATAAATGAAACGAACGTC-CCTATTGAGACCGTTTCATCACA
1 AAAATAAATGAAACGATCGTCTCC-ATTGAGA-CGTTTCGTCACA
8094 GATAAAAACA
Statistics
Matches: 253, Mismatches: 15, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
229 4 0.02
230 25 0.10
231 9 0.04
232 37 0.15
233 175 0.69
234 3 0.01
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (231 bp):
AAAATAAATGAAACGATCGTCTCCATTGAGACGTTTCGTCACAAACGGCCAAACACCAGCCTTGG
TGTCCCCGTATAAAAAAACGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAAC
ACCAGCCTGGTCGTCCCCATATAAAAATAAACGAAACGATCGTCTCCATTGAGACTGTTTCGTCA
CAAACGGCCGAACACCAGCCTCGGTGTCCCCATATA
Found at i:8133 original size:155 final size:156
Alignment explanation
Indices: 7597--8093 Score: 801
Period size: 155 Copynumber: 3.2 Consensus size: 156
7587 GAAAAAAATA
* * * * * * *
7597 AAACGATCGTCTCCTTTGAGAC--TTTCGTCACAAACGGCCAAACACCAGCCTTGGTGTCCCCGT
1 AAACGATTGTCTCCATTGAGACTGTTTCGTCACAAGCGGCCGAACACCAGCCTCGGTGTTCCCAT
*
7660 AT-AAAA-AAACGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCC
66 ATAAAAATAAATGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCC
7723 TTGTCGTCCCCGTATAAAAATAAACG
131 TTGTCGTCCCCGTATAAAAATAAACG
7749 AAACGATTGTCTCCATTGAGACTGTTTCGTCACAAGCGGCCGAACACCAGCCTCGGTGTTCCCAT
1 AAACGATTGTCTCCATTGAGACTGTTTCGTCACAAGCGGCCGAACACCAGCCTCGGTGTTCCCAT
7814 ATAAAAATAAATGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCC
66 ATAAAAATAAATGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCC
7879 TTGTCGT-CCCGTATAAAAATAAACG
131 TTGTCGTCCCCGTATAAAAATAAACG
7904 AAACGATTGTCTCCATTGAGACTGTTTCGTCACAAGCGGCCGAACACCAGCCTCGGTGTTCCCAT
1 AAACGATTGTCTCCATTGAGACTGTTTCGTCACAAGCGGCCGAACACCAGCCTCGGTGTTCCCAT
7969 ATAAAAATAAATGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCC
66 ATAAAAATAAATGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCC
* *
8034 TCGGT-GTCCCCGTATAAAAATAAATG
131 T-TGTCGTCCCCGTATAAAAATAAACG
** * *
8060 AAACGAACGTC-CCTATTGAGACCGTTTCATCACA
1 AAACGATTGTCTCC-ATTGAGACTGTTTCGTCACA
8094 GATAAAAACA
Statistics
Matches: 324, Mismatches: 14, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
152 20 0.06
154 38 0.12
155 157 0.48
156 109 0.34
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (156 bp):
AAACGATTGTCTCCATTGAGACTGTTTCGTCACAAGCGGCCGAACACCAGCCTCGGTGTTCCCAT
ATAAAAATAAATGAAACGATCGTCTCCATTGAGACTGTTTCGTCACAAACGGCCGAACACCAGCC
TTGTCGTCCCCGTATAAAAATAAACG
Done.