Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023167.1 Corchorus olitorius cultivar O-4 contig23200, 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: 20559
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--36 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 GTT
4 TA TA 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 TA TA T
37 TAATTATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6934 original size:23 final size:23
Alignment explanation
Indices: 6900--6949 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
6890 AGGATATCGT
6900 AAAA-ACTCTCTCTTAAATTGTG
1 AAAACACTCTCTCTTAAATTGTG
6922 AAAACACTCTCTCTTAAATTGTG
1 AAAACACTCTCTCTTAAATTGTG
6945 AAAAC
1 AAAAC
6950 GGAAAGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (23 bp):
AAAACACTCTCTCTTAAATTGTG
Found at i:7453 original size:191 final size:197
Alignment explanation
Indices: 6935--7468 Score: 651
Period size: 201 Copynumber: 2.7 Consensus size: 197
6925 ACACTCTCTC
* * * * * *
6935 TTAAATTGTGAAAACGGAAAGGATAAATATCGTAAAAATTCTCTTTTAAATTTAACATT-TTTAA
1 TTAAATTGTCAGAAC-GAAAGGATAGATATCGTAAAAATTCTCTCTTAAATTTAACCTTACTTAA
* * * * *
6999 TTTTATATTAGATACCAATAAATTTATATTAAGCACGTAAT-TTTTTCTAGTTTTTCACAAATTT
65 TCTTATA-TAGATACCAATAAATTTATATTAAGCACGAAATATTTTT-TAGTTTTTGATAAATTA
* * *
7063 TATTGGATTTAATAGAGTTATTGATGTGACATTTAGATTATGAGTTATGACACTTAACACTACTG
128 TATTGGATTAAATAGAGTTACTGATATGACATTTAGA-TA-GAGTTATGACACTTAACACTACTG
7128 TTTGTAT
191 TTTGTAT
* * * *
7135 TTAAATTGTGAGAACGAAATGGATAGATATCATAAAAACTCTCTCTTAAACTTAACCTTACTTAA
1 TTAAATTGTCAGAACGAAA-GGATAGATATCGTAAAAATTCTCTCTTAAATTTAACCTTACTTAA
*
7200 TGTTATATTAGATACCAATAAATTTATATTAAGCAC-ATAATATTTTTTAGTTTTTGATAAATTA
65 TCTTATA-TAGATACCAATAAATTTATATTAAGCACGA-AATATTTTTTAGTTTTTGATAAATTA
* * * **
7264 CATTGGATTGAATAGAGTTACTGATAT-AGCATTTA-A-A-A-TT-TGACATTTAATGGC-ACTG
128 TATTGGATTAAATAGAGTTACTGATATGA-CATTTAGATAGAGTTATGACACTTAA-CACTACTG
7322 TTTGTAT
191 TTTGTAT
* *
7329 TTCAATTGTCTGAACAGAAAGGATAGATATCGTAAAAATTCTCTCTTAAATTTAACCTTACTTAA
1 TTAAATTGTCAGAAC-GAAAGGATAGATATCGTAAAAATTCTCTCTTAAATTTAACCTTACTTAA
7394 TCTTATA-A-ATACCAATAAATTTATATTAAGCACGAAATATTTTTTAGTTTTTGATAAATTATA
65 TCTTATATAGATACCAATAAATTTATATTAAGCACGAAATATTTTTTAGTTTTTGATAAATTATA
7457 TTGGATTAAATA
130 TTGGATTAAATA
7469 CTAATGTGGT
Statistics
Matches: 297, Mismatches: 29, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
191 63 0.21
192 2 0.01
194 80 0.27
195 7 0.02
196 1 0.00
198 1 0.00
199 4 0.01
200 49 0.16
201 85 0.29
202 5 0.02
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (197 bp):
TTAAATTGTCAGAACGAAAGGATAGATATCGTAAAAATTCTCTCTTAAATTTAACCTTACTTAAT
CTTATATAGATACCAATAAATTTATATTAAGCACGAAATATTTTTTAGTTTTTGATAAATTATAT
TGGATTAAATAGAGTTACTGATATGACATTTAGATAGAGTTATGACACTTAACACTACTGTTTGT
AT
Found at i:8942 original size:172 final size:172
Alignment explanation
Indices: 8656--8999 Score: 600
Period size: 172 Copynumber: 2.0 Consensus size: 172
8646 TTGAGCAAAG
8656 AAAAACTCATTAATTTGCTTGTTATTGAAACCTAAAATACAGTACAACATCGACCCAGATGTTGT
1 AAAAACTCATTAATTTGCTTGTTATTGAAACCTAAAATACAGTACAACATCGACCCAGATGTTGT
* * *
8721 CAACTTCTGCCCAGAAGTTGGCTTATTGAAAAGAGAACAAGAATTGCAGGAAAATTTCGGCCCAG
66 CAACTTCTGCCCAGAAGTTGGCCTATTGAAAAGAGAACAAGAATTGCAGGAAAACTTCAGCCCAG
8786 AACTTGTTCCA-CTTCGGGACAGAAGTTGTTGCGCAGGACAAC
131 AACTTGTT-CAGCTTCGGGACAGAAGTTGTTGCGCAGGACAAC
*
8828 AAAAACTCATTAATTTGCTTGTTATTGAAACCTAAAATACAGTACAACATCGGCCCAGATGTTGT
1 AAAAACTCATTAATTTGCTTGTTATTGAAACCTAAAATACAGTACAACATCGACCCAGATGTTGT
* *
8893 CAACTTCTGCCCAGAAGTTGGCCTGTTGAAAAGAGAACAAGAATTGCAGGACAACTTCAGCCCAG
66 CAACTTCTGCCCAGAAGTTGGCCTATTGAAAAGAGAACAAGAATTGCAGGAAAACTTCAGCCCAG
* *
8958 AACTTGTTCAGCTTTGGGACAGAAGTTGTTGTGCAGGACAAC
131 AACTTGTTCAGCTTCGGGACAGAAGTTGTTGCGCAGGACAAC
9000 TTCGGCCCAG
Statistics
Matches: 163, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
171 2 0.01
172 161 0.99
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (172 bp):
AAAAACTCATTAATTTGCTTGTTATTGAAACCTAAAATACAGTACAACATCGACCCAGATGTTGT
CAACTTCTGCCCAGAAGTTGGCCTATTGAAAAGAGAACAAGAATTGCAGGAAAACTTCAGCCCAG
AACTTGTTCAGCTTCGGGACAGAAGTTGTTGCGCAGGACAAC
Found at i:9001 original size:52 final size:52
Alignment explanation
Indices: 8937--9040 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
8927 GAACAAGAAT
* *
8937 TGCAGGACAACTTCAGCCCAGAACTTGTTCAGCTTTGGGACAGAAGTTGTTG
1 TGCAGGACAACTTCAGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTG
*
8989 TGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTG
1 TGCAGGACAACTTCAGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTG
9041 CGGAAAGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (52 bp):
TGCAGGACAACTTCAGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTG
Found at i:9032 original size:22 final size:22
Alignment explanation
Indices: 8996--9039 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8986 TTGTGCAGGA
*
8996 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
9018 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
9040 GCGGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Found at i:12027 original size:22 final size:22
Alignment explanation
Indices: 11991--12034 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11981 AATTGCAGGA
**
11991 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGAACAGAACTTGTT
*
12013 CAACTTCGGAACAGAAGTTGTT
1 CAACTTCGGAACAGAACTTGTT
12035 GCGCAGGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (22 bp):
CAACTTCGGAACAGAACTTGTT
Found at i:12048 original size:52 final size:52
Alignment explanation
Indices: 11985--12089 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
11975 AACAAGAATT
11985 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCG-GAACAGAAGTTGTTGC
1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGAG-ACAGAAGTTGTTGC
12037 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGAGACAGAAGTTGTTGC
1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGAGACAGAAGTTGTTGC
12089 G
1 G
12090 GAAAGAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
52 51 0.98
53 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.23
Consensus pattern (52 bp):
GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGAGACAGAAGTTGTTGC
Found at i:14393 original size:18 final size:19
Alignment explanation
Indices: 14370--14418 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
14360 TGGAATTTTT
14370 AATAATAATTATTTAA-TA
1 AATAATAATTATTTAATTA
14388 AATAATAATTATTTAATTA
1 AATAATAATTATTTAATTA
*
14407 ATTAATTAATTA
1 AATAA-TAATTA
14419 ATTTCAGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 16 0.57
19 6 0.21
20 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAATAATTATTTAATTA
Found at i:14440 original size:4 final size:4
Alignment explanation
Indices: 14375--14421 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
14365 TTTTTAATAA
* * *
14375 TAAT TATT TAA- TAAA TAA- TAAT TATT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
14421 T
1 T
14422 TCAGCCCTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 6 0.16
4 31 0.84
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TAAT
Found at i:16271 original size:15 final size:15
Alignment explanation
Indices: 16251--16281 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16241 GATTAACATG
16251 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
16266 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
16281 T
1 T
16282 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:17357 original size:16 final size:16
Alignment explanation
Indices: 17332--17384 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
17322 TGAAATTTTT
*
17332 TTTTGTAAAA-AACTAA
1 TTTTGGAAAATAA-TAA
17348 TTTTGGAAAATAATAA
1 TTTTGGAAAATAATAA
17364 TTTTGGAAAATAATAA
1 TTTTGGAAAATAATAA
17380 TTTTG
1 TTTTG
17385 CAATGTGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
16 33 0.94
17 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (16 bp):
TTTTGGAAAATAATAA
Found at i:18949 original size:3 final size:3
Alignment explanation
Indices: 18941--18981 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
18931 TTAACTCTTT
18941 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18982 GGGTTTCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Done.