Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020795.1 Corchorus olitorius cultivar O-4 contig20828, 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: 58408
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:265 original size:29 final size:30
Alignment explanation
Indices: 205--282 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
195 GAGTTTTTAA
* *
205 CCAACCCATTGTAGTTCTTAAAAATAATTC
1 CCAAACCATTGTACTTCTTAAAAATAATTC
* *
235 CCAAACCATTGTACTT-TTAGAATTAATTC
1 CCAAACCATTGTACTTCTTAAAAATAATTC
* *
264 CCAAACTATTGTATTTCTT
1 CCAAACCATTGTACTTCTT
283 GCCACATCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 25 0.61
30 16 0.39
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.38
Consensus pattern (30 bp):
CCAAACCATTGTACTTCTTAAAAATAATTC
Found at i:1457 original size:30 final size:29
Alignment explanation
Indices: 1387--1463 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
1377 GGATGTGGCA
*
1387 AAAAATACAAT-GTTATGGGAATTAATTTT
1 AAAAGTACAATGGTT-TGGGAATTAATTTT
* *
1416 AAAAGTACAATGGTTTGGGGATTATTTTT
1 AAAAGTACAATGGTTTGGGAATTAATTTT
*
1445 AAGAATTACAATGGTTTGG
1 AA-AAGTACAATGGTTTGG
1464 TCAAAAACTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 24 0.57
30 18 0.43
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (29 bp):
AAAAGTACAATGGTTTGGGAATTAATTTT
Found at i:5393 original size:7 final size:7
Alignment explanation
Indices: 5381--5413 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
5371 CGTGCTTTTC
5381 TTTTCTT
1 TTTTCTT
5388 TTTTCTT
1 TTTTCTT
5395 TTTTCTT
1 TTTTCTT
5402 TTTTCTT
1 TTTTCTT
5409 TTTTC
1 TTTTC
5414 ATACTTCGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTCTT
Found at i:5814 original size:30 final size:30
Alignment explanation
Indices: 5778--5842 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
5768 AATCTACTTC
5778 TTTGAATAATTTTCTATTCGAATTAAATTG
1 TTTGAATAATTTTCTATTCGAATTAAATTG
5808 TTTGAATAATTTTCTATTCGAATTAAATTG
1 TTTGAATAATTTTCTATTCGAATTAAATTG
5838 TTTGA
1 TTTGA
5843 TACGTAGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.06, G:0.11, T:0.51
Consensus pattern (30 bp):
TTTGAATAATTTTCTATTCGAATTAAATTG
Found at i:7151 original size:21 final size:19
Alignment explanation
Indices: 7124--7182 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 19
7114 CGCTGCTCTA
7124 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
*
7143 ATCTAATCTAATCTGTACAGT
1 A--TAATCTCATCTGTACAGT
*
7164 ATAATCTCATATGTACAGT
1 ATAATCTCATCTGTACAGT
7183 TGCTAAATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 17 0.49
21 18 0.51
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:7283 original size:8 final size:8
Alignment explanation
Indices: 7270--7299 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
7260 GGAGTTTGAG
7270 TTTTTTTA
1 TTTTTTTA
7278 -TTTTTTA
1 TTTTTTTA
7285 TTTTTTTA
1 TTTTTTTA
7293 TTTTTTT
1 TTTTTTT
7300 TCTTCTTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:7290 original size:15 final size:15
Alignment explanation
Indices: 7270--7298 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7260 GGAGTTTGAG
7270 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
7285 TTTTTTTATTTTTT
1 TTTTTTTATTTTTT
7299 TTCTTCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:10647 original size:33 final size:33
Alignment explanation
Indices: 10605--10668 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
10595 ACTCCAACAG
* ** *
10605 TTTTACACGTGGCCTCCACATAATTACCCACAT
1 TTTTACACGTGCCCAACACATAAATACCCACAT
10638 TTTTACACGTGCCCAACACATAAATACCCAC
1 TTTTACACGTGCCCAACACATAAATACCCAC
10669 TCTAAATCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.34, G:0.08, T:0.27
Consensus pattern (33 bp):
TTTTACACGTGCCCAACACATAAATACCCACAT
Found at i:13322 original size:16 final size:16
Alignment explanation
Indices: 13301--13332 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13291 TTCGCATGAC
13301 GAGTTCTATATACTTA
1 GAGTTCTATATACTTA
13317 GAGTTCTATATACTTA
1 GAGTTCTATATACTTA
13333 ACGTGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
GAGTTCTATATACTTA
Found at i:14595 original size:29 final size:29
Alignment explanation
Indices: 14543--14598 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
14533 GGATCTAAAC
*
14543 AAATTGATTTTGTAAATGCCAAAAAAAAT
1 AAATTGATTTTGTAAATGACAAAAAAAAT
* *
14572 AAATTGATTTTGTATATGAGAAAAAAA
1 AAATTGATTTTGTAAATGACAAAAAAA
14599 GGGAATAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (29 bp):
AAATTGATTTTGTAAATGACAAAAAAAAT
Found at i:18591 original size:37 final size:37
Alignment explanation
Indices: 18541--18614 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
18531 CTAGTTTGCT
18541 ATACCTCCAATTTGGGCAAGACTCCTCTGCAAATTAG
1 ATACCTCCAATTTGGGCAAGACTCCTCTGCAAATTAG
*
18578 ATACCTCCAATTTGGGCAAGGCTCCTCTGCAAATTAG
1 ATACCTCCAATTTGGGCAAGACTCCTCTGCAAATTAG
18615 TTAATGTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (37 bp):
ATACCTCCAATTTGGGCAAGACTCCTCTGCAAATTAG
Found at i:21254 original size:22 final size:22
Alignment explanation
Indices: 21226--21268 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
21216 AAAGAATATA
21226 ATATTAAGCAAACATTCTGTTT
1 ATATTAAGCAAACATTCTGTTT
21248 ATATTAAGCAAACATTCTGTT
1 ATATTAAGCAAACATTCTGTT
21269 GGGTAAGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
ATATTAAGCAAACATTCTGTTT
Found at i:30480 original size:27 final size:27
Alignment explanation
Indices: 30442--30494 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
30432 CTCTAAAAAA
*
30442 AGTTTTAAAAGTGGTAATTAGAAAGAG
1 AGTTGTAAAAGTGGTAATTAGAAAGAG
30469 AGTTGTAAAAGTGGTAATTAGAAAGA
1 AGTTGTAAAAGTGGTAATTAGAAAGA
30495 AATTAAGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.28
Consensus pattern (27 bp):
AGTTGTAAAAGTGGTAATTAGAAAGAG
Found at i:33051 original size:28 final size:27
Alignment explanation
Indices: 33009--33063 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
32999 ACTGAGACTA
*
33009 GACTCGAAACTGACTCGAAAAAACAAACT
1 GACTCGAAACCGACTC--AAAAACAAACT
33038 GACTC-AAACCGACTCAAAAACAAACT
1 GACTCGAAACCGACTCAAAAACAAACT
33064 CAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.49, C:0.27, G:0.11, T:0.13
Consensus pattern (27 bp):
GACTCGAAACCGACTCAAAAACAAACT
Found at i:44923 original size:11 final size:11
Alignment explanation
Indices: 44907--44936 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
44897 CTGTTTTTTG
44907 TTTTTGTTTCA
1 TTTTTGTTTCA
*
44918 TTTTTGTTTTA
1 TTTTTGTTTCA
44929 TTTTTGTT
1 TTTTTGTT
44937 GCGCTGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.03, G:0.10, T:0.80
Consensus pattern (11 bp):
TTTTTGTTTCA
Found at i:46167 original size:27 final size:27
Alignment explanation
Indices: 46137--46189 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
46127 ATAAAAGTAA
46137 GTTGTCTAACTATCTTGATTTATAATT
1 GTTGTCTAACTATCTTGATTTATAATT
46164 GTTGTCTAACTATCTTGATTTATAAT
1 GTTGTCTAACTATCTTGATTTATAAT
46190 GGTGGATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (27 bp):
GTTGTCTAACTATCTTGATTTATAATT
Done.