Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020569.1 Corchorus olitorius cultivar O-4 contig20602, 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: 15445
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Found at i:6621 original size:21 final size:21
Alignment explanation
Indices: 6595--6642 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6585 AAATAATTTC
6595 CGTAGCAAAT-GTAAATAAGCT
1 CGTAGCAAATAG-AAATAAGCT
* *
6616 CGTAGCAAATAGAAATATGTT
1 CGTAGCAAATAGAAATAAGCT
6637 CGTAGC
1 CGTAGC
6643 CATACGACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (21 bp):
CGTAGCAAATAGAAATAAGCT
Found at i:7453 original size:21 final size:21
Alignment explanation
Indices: 7429--7498 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 21
7419 TTACTAATTG
7429 AGAATGTCACAATAAATATTT
1 AGAATGTCACAATAAATATTT
7450 AGAACTG-C-CAATAAATATTGATT
1 AGAA-TGTCACAATAAATA-T--TT
*
7473 GAGAATGTCACAATATATATTT
1 -AGAATGTCACAATAAATATTT
7495 AGAA
1 AGAA
7499 CTACCAATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
20 9 0.22
21 10 0.24
22 4 0.10
23 4 0.10
24 6 0.15
25 8 0.20
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (21 bp):
AGAATGTCACAATAAATATTT
Found at i:13764 original size:26 final size:26
Alignment explanation
Indices: 13710--13761 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
13700 CAGAAGTACC
* * *
13710 GAAAAAGAAAAGAAAAAGGGAAGAAG
1 GAAAAAGAAAAGAAAAACGCAAAAAG
13736 GAAAAAG-AAAGAAAAACGCAAAAAG
1 GAAAAAGAAAAGAAAAACGCAAAAAG
13761 G
1 G
13762 GAATCATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.69, C:0.04, G:0.27, T:0.00
Consensus pattern (26 bp):
GAAAAAGAAAAGAAAAACGCAAAAAG
Found at i:15161 original size:35 final size:35
Alignment explanation
Indices: 15113--15288 Score: 221
Period size: 34 Copynumber: 4.9 Consensus size: 35
15103 AGCTGAAAAT
*
15113 GATGGGAACTTTCCCTAAATTGAAAAC-TAAAACCC
1 GATGGGAACTTTCCC-AATTTGAAAACTTAAAACCC
* *
15148 GGTGGGAACTTTCCCAATTTGAAAACTTAAAAACTC
1 GATGGGAACTTTCCCAATTTGAAAACTT-AAAACCC
* *
15184 GATGGGAACTTTCCCAATTTGAAAGC-TAAAACCT
1 GATGGGAACTTTCCCAATTTGAAAACTTAAAACCC
*
15218 GATGGGAACTTTCCCAATTTGAAAACTTAAAAAAAAACTC
1 GATGGGAACTTTCCCAATTTGAAAACTT-----AAAACCC
15258 GATGGGAACTTTCCCAATTTGAAAACTTAAA
1 GATGGGAACTTTCCCAATTTGAAAACTTAAA
15289 CCTGACGAAA
Statistics
Matches: 123, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
34 40 0.33
35 20 0.16
36 30 0.24
40 33 0.27
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (35 bp):
GATGGGAACTTTCCCAATTTGAAAACTTAAAACCC
Found at i:15222 original size:34 final size:34
Alignment explanation
Indices: 15076--15293 Score: 220
Period size: 34 Copynumber: 6.0 Consensus size: 34
15066 TTGTTTTTTT
* **
15076 TGGGAACTTTCCCACTTTGAAAACTAAAGCTGAAAATGA
1 TGGGAACTTTCCCAATTTGAAAACT-AA----AACCTGA
* * *
15115 TGGGAACTTTCCCTAAATTGAAAACTAAAACCCGG
1 TGGGAACTTTCCC-AATTTGAAAACTAAAACCTGA
*
15150 TGGGAACTTTCCCAATTTGAAAACTTAAAAACTCGA
1 TGGGAACTTTCCCAATTTGAAAAC-TAAAACCT-GA
*
15186 TGGGAACTTTCCCAATTTGAAAGCTAAAACCTGA
1 TGGGAACTTTCCCAATTTGAAAACTAAAACCTGA
*
15220 TGGGAACTTTCCCAATTTGAAAACTTAAAAAAAAACTCGA
1 TGGGAACTTTCCCAATTTGAAAAC-T----AAAACCT-GA
*
15260 TGGGAACTTTCCCAATTTGAAAACTTAAACCTGA
1 TGGGAACTTTCCCAATTTGAAAACTAAAACCTGA
15294 CGAAATAATT
Statistics
Matches: 154, Mismatches: 16, Indels: 23
0.80 0.08 0.12
Matches are distributed among these distances:
34 37 0.24
35 35 0.23
36 24 0.16
39 22 0.14
40 36 0.23
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (34 bp):
TGGGAACTTTCCCAATTTGAAAACTAAAACCTGA
Found at i:15255 original size:40 final size:39
Alignment explanation
Indices: 15141--15288 Score: 195
Period size: 36 Copynumber: 4.0 Consensus size: 39
15131 ATTGAAAACT
* *
15141 AAAACCCGGTGGGAACTTTCCCAATTTGAAAACTT---A
1 AAAACTCGATGGGAACTTTCCCAATTTGAAAACTTAAAA
*
15177 AAAACTCGATGGGAACTTTCCCAATTTGAAAGC-T---A
1 AAAACTCGATGGGAACTTTCCCAATTTGAAAACTTAAAA
*
15212 AAACCT-GATGGGAACTTTCCCAATTTGAAAACTTAAAAA
1 AAAACTCGATGGGAACTTTCCCAATTTGAAAACTT-AAAA
15251 AAAACTCGATGGGAACTTTCCCAATTTGAAAACTTAAA
1 AAAACTCGATGGGAACTTTCCCAATTTGAAAACTTAAA
15289 CCTGACGAAA
Statistics
Matches: 100, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
34 25 0.25
35 8 0.08
36 30 0.30
39 9 0.09
40 28 0.28
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.26
Consensus pattern (39 bp):
AAAACTCGATGGGAACTTTCCCAATTTGAAAACTTAAAA
Done.