Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019534.1 Corchorus olitorius cultivar O-4 contig19567, 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: 39089
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:167 original size:30 final size:27
Alignment explanation
Indices: 134--216 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 27
124 ATACCACTAA
* *
134 TAATTATTATTATTATAATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
*
161 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATA--A-TAATAATAAGTT
191 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
217 CTAAATTAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.45
28 1 0.02
29 1 0.02
30 25 0.51
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Found at i:510 original size:6 final size:6
Alignment explanation
Indices: 492--521 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
482 GTTTAGACTT
492 ATATAG TATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATA
522 TATTCTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:8614 original size:21 final size:22
Alignment explanation
Indices: 8590--8633 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
8580 TGGAGATCGG
8590 GAGAAT-TTATCGGAAGAAAAA
1 GAGAATGTTATCGGAAGAAAAA
8611 GAGAATGAGTTATCGGAAGAAAA
1 GAGAAT--GTTATCGGAAGAAAA
8634 GGGAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
24 14 0.70
ACGTcount: A:0.50, C:0.05, G:0.27, T:0.18
Consensus pattern (22 bp):
GAGAATGTTATCGGAAGAAAAA
Found at i:8895 original size:13 final size:13
Alignment explanation
Indices: 8877--8903 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8867 CTGACTTCTC
8877 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
8890 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
8903 C
1 C
8904 AAATATCGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
CTTTTTTCTTTTT
Found at i:9251 original size:31 final size:31
Alignment explanation
Indices: 9213--9296 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
9203 TTAAAACTTT
*
9213 ATCAATTTAGTCCTTGTACTCATAAGATTTG
1 ATCAATTTAGTCCTTGTACTCATAAGATTAG
* *
9244 ATCAATTTAGTTCC-TATACTCATAATATTAG
1 ATCAATTTAG-TCCTTGTACTCATAAGATTAG
*
9275 ATCAATTTAGTCATTGTACTCA
1 ATCAATTTAGTCCTTGTACTCA
9297 CAAGTGGGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 2 0.04
31 41 0.89
32 3 0.07
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.42
Consensus pattern (31 bp):
ATCAATTTAGTCCTTGTACTCATAAGATTAG
Found at i:11973 original size:23 final size:23
Alignment explanation
Indices: 11926--11974 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
11916 AGAAATTTAG
* * * *
11926 CTTTATAGAGTTGATTGTTTGAA
1 CTTTATAGAGATGACTATTTAAA
11949 CTTTATAGAGATGACTATTTAAA
1 CTTTATAGAGATGACTATTTAAA
11972 CTT
1 CTT
11975 AGAAATTTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (23 bp):
CTTTATAGAGATGACTATTTAAA
Found at i:13113 original size:2 final size:2
Alignment explanation
Indices: 13106--13132 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13096 ATATTTGATG
13106 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 T
13133 TACAAATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24443 original size:4 final size:4
Alignment explanation
Indices: 24434--24477 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
24424 TTGCATGATT
* * *
24434 TTTA TTTA TTTA TTTA ATTA TTTA -TTA TATA TTTA ATTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
24478 CTTTTACTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:24466 original size:19 final size:19
Alignment explanation
Indices: 24434--24477 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
24424 TTGCATGATT
*
24434 TTTATTTATTTATTTAATTA
1 TTTA-TTATATATTTAATTA
24454 TTTATTATATATTTAATTA
1 TTTATTATATATTTAATTA
24473 TTTAT
1 TTTAT
24478 CTTTTACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTATATATTTAATTA
Found at i:24566 original size:103 final size:103
Alignment explanation
Indices: 24384--24590 Score: 396
Period size: 103 Copynumber: 2.0 Consensus size: 103
24374 ATAAATCTTC
*
24384 AAAGTTGGATGTAAGTCACTGCAACTGAATCTCTCATGGTTTGCATGATTTTTATTTATTTATTT
1 AAAGTTGGATGTAAGTCACTGCAACTGAATCTCTCATGGTTTGCATGATTTCTATTTATTTATTT
*
24449 AATTATTTATTATATATTTAATTATTTATCTTTTACTA
66 AATTATTTAGTATATATTTAATTATTTATCTTTTACTA
24487 AAAGTTGGATGTAAGTCACTGCAACTGAATCTCTCATGGTTTGCATGATTTCTATTTATTTATTT
1 AAAGTTGGATGTAAGTCACTGCAACTGAATCTCTCATGGTTTGCATGATTTCTATTTATTTATTT
24552 AATTATTTAGTATATATTTAATTATTTATCTTTTACTA
66 AATTATTTAGTATATATTTAATTATTTATCTTTTACTA
24590 A
1 A
24591 GCATCACACT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.49
Consensus pattern (103 bp):
AAAGTTGGATGTAAGTCACTGCAACTGAATCTCTCATGGTTTGCATGATTTCTATTTATTTATTT
AATTATTTAGTATATATTTAATTATTTATCTTTTACTA
Found at i:35035 original size:11 final size:11
Alignment explanation
Indices: 35021--35047 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
35011 TTTTCTCTTT
35021 TTTTTTTTATC
1 TTTTTTTTATC
35032 TTTTTTTTATC
1 TTTTTTTTATC
35043 TTTTT
1 TTTTT
35048 GGGGAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTATC
Found at i:35038 original size:14 final size:14
Alignment explanation
Indices: 35003--35039 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
34993 CATTGCTTTG
* *
35003 CTTTTTTGTTTTCT
1 CTTTTTTTTTTTAT
35017 CTTTTTTTTTTTAT
1 CTTTTTTTTTTTAT
35031 CTTTTTTTT
1 CTTTTTTTT
35040 ATCTTTTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (14 bp):
CTTTTTTTTTTTAT
Found at i:37463 original size:18 final size:18
Alignment explanation
Indices: 37440--37478 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
37430 AAATAACTAA
37440 ATAAAAATAATAAATCGC
1 ATAAAAATAATAAATCGC
37458 ATAAAAATAATAAATCGC
1 ATAAAAATAATAAATCGC
37476 ATA
1 ATA
37479 TTAATCTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (18 bp):
ATAAAAATAATAAATCGC
Found at i:38208 original size:273 final size:273
Alignment explanation
Indices: 37721--38266 Score: 1038
Period size: 273 Copynumber: 2.0 Consensus size: 273
37711 CTAACTTGGC
* *
37721 TTTTCTTGCAACTCTTTTTTTCTTTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATCCATCGA
1 TTTTCTTGCAACTCCTTTTTTCGTTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATCCATCGA
*
37786 GCATAATTAAGTCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTATTCTTGAGC
66 GCATAATTAAATCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTATTCTTGAGC
37851 TTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTT
131 TTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTT
*
37916 GCAATTTCTTTGATTAACTCGGCATTTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGT
196 GCAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGT
*
37981 TGTAGATATCAGT
261 TATAGATATCAGT
37994 TTTTCTTGCAACTCCTTTTTTCGTTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATCCATCGA
1 TTTTCTTGCAACTCCTTTTTTCGTTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATCCATCGA
*
38059 GCATAATTAAATCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAGC
66 GCATAATTAAATCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTATTCTTGAGC
38124 TTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTT
131 TTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTT
38189 GCAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGT
196 GCAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGT
38254 TATAGATATCAGT
261 TATAGATATCAGT
38267 GCTAGTTCCA
Statistics
Matches: 267, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
273 267 1.00
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (273 bp):
TTTTCTTGCAACTCCTTTTTTCGTTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATCCATCGA
GCATAATTAAATCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTATTCTTGAGC
TTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTT
GCAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGT
TATAGATATCAGT
Done.