Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013654.1 Corchorus olitorius cultivar O-4 contig13687, 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: 29897
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4501 original size:24 final size:24
Alignment explanation
Indices: 4474--4519 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
4464 ATTAAACATC
*
4474 TCAAGATATTGAGAGATATTTTAT
1 TCAACATATTGAGAGATATTTTAT
4498 TCAACATATTGAGAGATATTTT
1 TCAACATATTGAGAGATATTTT
4520 GATTATATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (24 bp):
TCAACATATTGAGAGATATTTTAT
Found at i:8652 original size:123 final size:123
Alignment explanation
Indices: 8462--8706 Score: 341
Period size: 123 Copynumber: 1.9 Consensus size: 123
8452 ATTTTTATAG
* *
8462 TTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGATTTTTA-CCAT
1 TTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATGATTTTTATAC-T
8526 TTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTTACAA
65 TTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTTACAA
*
8585 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-ACCTATTTTATT
1 TTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATGA--T-TTTTA--
* *
8649 TTTACCGTTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATATA
61 --TA-C-TTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATA
8707 TTTCTTAAAT
Statistics
Matches: 107, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
122 1 0.01
123 50 0.47
124 1 0.01
125 5 0.05
131 50 0.47
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (123 bp):
TTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATGATTTTTATACTT
TTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTTACAA
Found at i:8699 original size:131 final size:123
Alignment explanation
Indices: 8462--8706 Score: 373
Period size: 131 Copynumber: 1.9 Consensus size: 123
8452 ATTTTTATAG
8462 TTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGATTTTTACCATT
1 TTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGATTTTTACCATT
8527 TTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTTACAA
66 TTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTTACAA
* *
8585 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTATTT
1 TTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T---TA--TGATTT
* * *
8650 TTACCGTTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATATA
58 TTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATA
8707 TTTCTTAAAT
Statistics
Matches: 109, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
123 45 0.41
124 1 0.01
125 1 0.01
126 1 0.01
129 2 0.02
131 59 0.54
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (123 bp):
TTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGATTTTTACCATT
TTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTTACAA
Found at i:17501 original size:30 final size:30
Alignment explanation
Indices: 17423--17523 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 30
17413 GCTCCACCGT
**
17423 AGGATGTACAGGTAGATGTTCCACTGCCGC
1 AGGATGTACAGACAGATGTTCCACTGCCGC
* * * * *
17453 AAGATTTACAAACTGATGTTCCTCTGCCGC
1 AGGATGTACAGACAGATGTTCCACTGCCGC
* * * *
17483 GGGATGTACAGACAGATGTTTCATTGCCGT
1 AGGATGTACAGACAGATGTTCCACTGCCGC
*
17513 AGGATTTACAG
1 AGGATGTACAG
17524 CTGGCTGTTA
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (30 bp):
AGGATGTACAGACAGATGTTCCACTGCCGC
Found at i:19344 original size:17 final size:17
Alignment explanation
Indices: 19322--19354 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19312 ATTTGTAAAG
19322 TTGTTACACTAGATAGT
1 TTGTTACACTAGATAGT
*
19339 TTGTTAGACTAGATAG
1 TTGTTACACTAGATAG
19355 CTCTATGTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (17 bp):
TTGTTACACTAGATAGT
Found at i:25076 original size:18 final size:18
Alignment explanation
Indices: 25053--25087 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25043 CATTACTTCA
25053 TTAAAAGCCCACTATTCC
1 TTAAAAGCCCACTATTCC
*
25071 TTAAAAGCCCATTATTC
1 TTAAAAGCCCACTATTC
25088 ACAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (18 bp):
TTAAAAGCCCACTATTCC
Found at i:25699 original size:161 final size:161
Alignment explanation
Indices: 25434--25755 Score: 608
Period size: 161 Copynumber: 2.0 Consensus size: 161
25424 TTTTGGTTTG
*
25434 TACAAAAGTCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
1 TACAAAAGTCCACTATGTGACAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
25499 TCCTTGTATGGTGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATTGA
66 TCCTTGTATGGTGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATTGA
*
25564 GACAACCTACAGTTCTTACCGTGTCTTTATT
131 GACAACCTACAGTTCTCACCGTGTCTTTATT
25595 TACAAAAGTCCACTATGTGACAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
1 TACAAAAGTCCACTATGTGACAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
25660 TCCTTGTATGGTGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATTGA
66 TCCTTGTATGGTGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATTGA
* *
25725 GACAACCTATAGTTCTCACCTTGTCTTTATT
131 GACAACCTACAGTTCTCACCGTGTCTTTATT
25756 ATTATGATAT
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 157 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (161 bp):
TACAAAAGTCCACTATGTGACAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
TCCTTGTATGGTGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATTGA
GACAACCTACAGTTCTCACCGTGTCTTTATT
Found at i:26185 original size:21 final size:20
Alignment explanation
Indices: 26159--26197 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
26149 CCTTAAATCT
*
26159 ATTATTTATTTATCTATTTCC
1 ATTATTTATTCAT-TATTTCC
26180 ATTATTTATTCATTATTT
1 ATTATTTATTCATTATTT
26198 ATTAAAGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTATTTATTCATTATTTCC
Found at i:26493 original size:20 final size:21
Alignment explanation
Indices: 26468--26508 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
26458 TTGAAGGGAA
26468 TCTTGT-CATAAGCATTAAAT
1 TCTTGTCCATAAGCATTAAAT
* *
26488 TCTTGTCCTTGAGCATTAAAT
1 TCTTGTCCATAAGCATTAAAT
26509 GCTGATGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTTGTCCATAAGCATTAAAT
Done.