Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012725.1 Corchorus olitorius cultivar O-4 contig12758, 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: 47819
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:5868 original size:18 final size:17
Alignment explanation
Indices: 5845--5882 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
5835 CCCAAATTAC
5845 TTATGGAAATTAGAGAAA
1 TTATGGAAATTAG-GAAA
5863 TTATGGAAATTAGGAAA
1 TTATGGAAATTAGGAAA
5880 TTA
1 TTA
5883 AATGAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (17 bp):
TTATGGAAATTAGGAAA
Found at i:5880 original size:8 final size:8
Alignment explanation
Indices: 5849--5882 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
5839 AATTACTTAT
5849 GGAAATTA
1 GGAAATTA
5857 GAGAAATTA
1 G-GAAATTA
5866 TGGAAATTA
1 -GGAAATTA
5875 GGAAATTA
1 GGAAATTA
5883 AATGAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 9 0.38
9 14 0.58
10 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (8 bp):
GGAAATTA
Found at i:7299 original size:48 final size:47
Alignment explanation
Indices: 7162--7303 Score: 185
Period size: 49 Copynumber: 3.0 Consensus size: 47
7152 CAAGCAATCC
** *
7162 TTTATTTTTACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTATTTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGATCT
7209 TTTATTTTTACTTGCACCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTATTTTTAC-TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGATCT
* * ** *
7258 TTTAATTTTCACTGCACTTTTTATCAATTTTTTGGATAAAATTGAT
1 TTT-ATTTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGAT
7304 TGGCACGCTC
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
47 11 0.13
48 30 0.36
49 36 0.43
50 7 0.08
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.51
Consensus pattern (47 bp):
TTTATTTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGATCT
Found at i:21131 original size:13 final size:13
Alignment explanation
Indices: 21113--21138 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21103 CTTGGCATGA
21113 GTGATGATTTTTG
1 GTGATGATTTTTG
21126 GTGATGATTTTTG
1 GTGATGATTTTTG
21139 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:21515 original size:19 final size:19
Alignment explanation
Indices: 21493--21540 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
21483 GGACTGAAAT
21493 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
21512 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
21531 TAATT-ATTAT
1 TAATTAATTAT
21541 CAAAAATCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:32239 original size:210 final size:210
Alignment explanation
Indices: 31962--32396 Score: 649
Period size: 210 Copynumber: 2.1 Consensus size: 210
31952 AGTAAAAATG
* * *
31962 TCAGCTTTCAAACCTCTTTCAGCCATTAGATCCAAAACCTCAACGGCTTCTTCAGTTCTCCTTTC
1 TCAGGTTTCAAACCTCTTTCAGCCATTAGATCCAAAACCACAACGGCTTCCTCAGTTCTCCTTTC
* *
32027 CTTGCAAAGAGCATAAATTATAGAGTTGAAAGTAACCACATTTGGCTGTACTCCTCCTTCCATCA
66 CTTGCAAAGAGCATAAATAATACAGTTGAAAGTAACCACATTTGGCTGTACTCCTCCTTCCATCA
* *
32092 TTCTGTTAAACAAGCTTGTCACTTCTTTCCATCGATTTGA-AAGACAAAACCCGT-GGATTACAG
131 TTCTGTTAAACAAGCTTGTCACTTCTTTCCATCGACTT-ACAAGACAAAACCC-TCGGATCACAG
*
32155 AATTATAGGTGACGACA
194 AATTATAGGTGAAGACA
* * * * *
32172 TCAGGTTTCACACCTCTTTCCGCCATTAGATCTAACACCACAATGGCTTCCTCAGTTCTCCTTTC
1 TCAGGTTTCAAACCTCTTTCAGCCATTAGATCCAAAACCACAACGGCTTCCTCAGTTCTCCTTTC
* * *
32237 CTTGCAAATAGCATCAATAATACAGTTGAAAGTTACCACATTTGGCTGTACTCCTCCTTCCATCA
66 CTTGCAAAGAGCATAAATAATACAGTTGAAAGTAACCACATTTGGCTGTACTCCTCCTTCCATCA
* * * *
32302 TTCTGTTAAACAAGCTTGTCGCTTCTTTCCATTGACTTACAAGACAAAATCCTCGGATCATAGAA
131 TTCTGTTAAACAAGCTTGTCACTTCTTTCCATCGACTTACAAGACAAAACCCTCGGATCACAGAA
32367 TTATAGGTGAAGACA
196 TTATAGGTGAAGACA
*
32382 TCTGGTTTCAAACCT
1 TCAGGTTTCAAACCT
32397 TTTTGAGTCA
Statistics
Matches: 201, Mismatches: 22, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
209 2 0.01
210 199 0.99
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (210 bp):
TCAGGTTTCAAACCTCTTTCAGCCATTAGATCCAAAACCACAACGGCTTCCTCAGTTCTCCTTTC
CTTGCAAAGAGCATAAATAATACAGTTGAAAGTAACCACATTTGGCTGTACTCCTCCTTCCATCA
TTCTGTTAAACAAGCTTGTCACTTCTTTCCATCGACTTACAAGACAAAACCCTCGGATCACAGAA
TTATAGGTGAAGACA
Found at i:32450 original size:210 final size:210
Alignment explanation
Indices: 31962--32452 Score: 589
Period size: 210 Copynumber: 2.3 Consensus size: 210
31952 AGTAAAAATG
* * * * * * * *
31962 TCAGCTTTCAAACCTCTTTCAGCCATTAGATCCAAAACCTCAACGGCTTCTTCAGTTCTCCTTTC
1 TCAGGTTTCAAACCTCTTTCAGCCATCAGATCAAAAACCACAATGCCTTCCTCAGGTCTCCTTTC
* *
32027 CTTGCAAAGAGCATAAATTATAGAGTTGAAAGTAACCACATTTGGCTGTACTCCTCCTTCCATCA
66 CTTGCAAAGAGCATAAATAATACAGTTGAAAGTAACCACATTTGGCTGTACTCCTCCTTCCATCA
* *
32092 TTCTGTTAAACAAGCTTGTCACTTCTTTCCATCGATTTGAAAGACAAAACCCGTGGATTACAGAA
131 TTCTGTTAAACAAGCTTGTCACTTCTTTCCATCGACTTGAAAGACAAAACCCGTGGATCACAGAA
*
32157 TTATAGGTGACGACA
196 TTATAGGTGAAGACA
* * * * * * *
32172 TCAGGTTTCACACCTCTTTCCGCCATTAGATCTAACACCACAATGGCTTCCTCAGTTCTCCTTTC
1 TCAGGTTTCAAACCTCTTTCAGCCATCAGATCAAAAACCACAATGCCTTCCTCAGGTCTCCTTTC
* * *
32237 CTTGCAAATAGCATCAATAATACAGTTGAAAGTTACCACATTTGGCTGTACTCCTCCTTCCATCA
66 CTTGCAAAGAGCATAAATAATACAGTTGAAAGTAACCACATTTGGCTGTACTCCTCCTTCCATCA
* * * *
32302 TTCTGTTAAACAAGCTTGTCGCTTCTTTCCATTGACTT-ACAAGACAAAATCC-TCGGATCATAG
131 TTCTGTTAAACAAGCTTGTCACTTCTTTCCATCGACTTGA-AAGACAAAACCCGT-GGATCACAG
32365 AATTATAGGTGAAGACA
194 AATTATAGGTGAAGACA
* * * * * *
32382 TCTGGTTTCAAACCTTTTTGAGTCATCA-ATTCCAAAAATTCA-AATGCCTTCC-C-GGTCTTCT
1 TCAGGTTTCAAACCTCTTTCAGCCATCAGA-T-CAAAAA-CCACAATGCCTTCCTCAGGTCTCCT
32443 CTTCCTTGCA
63 -TTCCTTGCA
32453 TAAAATATCA
Statistics
Matches: 242, Mismatches: 33, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
209 9 0.04
210 218 0.90
211 13 0.05
212 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (210 bp):
TCAGGTTTCAAACCTCTTTCAGCCATCAGATCAAAAACCACAATGCCTTCCTCAGGTCTCCTTTC
CTTGCAAAGAGCATAAATAATACAGTTGAAAGTAACCACATTTGGCTGTACTCCTCCTTCCATCA
TTCTGTTAAACAAGCTTGTCACTTCTTTCCATCGACTTGAAAGACAAAACCCGTGGATCACAGAA
TTATAGGTGAAGACA
Found at i:47019 original size:7 final size:8
Alignment explanation
Indices: 47003--47030 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
46993 ATTTTAGCTC
47003 TTCTTTTT
1 TTCTTTTT
47011 TTCTTTTT
1 TTCTTTTT
47019 TTCTTTTT
1 TTCTTTTT
47027 TTCT
1 TTCT
47031 CTTGGCCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTCTTTTT
Done.