Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018393.1 Corchorus olitorius cultivar O-4 contig18426, 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: 17146
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Found at i:1905 original size:228 final size:223
Alignment explanation
Indices: 1483--1933 Score: 699
Period size: 228 Copynumber: 2.0 Consensus size: 223
1473 ATTATCATAT
*
1483 GAGTCAATTTTTATAGATTGTTTTTTTGCTCTGTAAATGTGAACGCGCTTTCGGTGGATTTAAAT
1 GAGTCAATTTTTATAGATTG-TTTTTTGCTCTGTAAATGTGAACGCACTTTCGGTGGATTTAAAT
* *
1548 ATAATAAATATGATTTATGAGGTTATGGAGTGATGGAATACGAATCGGTTCAGTGTAATCGCATG
65 ATAATAAATATGATTTATGAGGTTATAGAGTGATGGAATACGAATCGGTTCAGTGTAACCGCATG
* *
1613 TGAGAAATGACTAAAACGGGGCGATAAGGTCGTCTCAGGTTAAAAGTTAGAAGGAGCGTTTAGTA
130 TGAGAAATGACTAAAACGGGGCGATAAGGTCGTCCCAGGTTAAAAGTTAGAAGGAGCATTTAGTA
**
1678 ATTTCACCTGGTTAAAAAAATAATATGTA
195 ATTTCACCTAATTAAAAAAATAATATGTA
* * *
1707 GAGTCAATTTTTATAGA-TG-TTTTTGCTCTGTAAATGTGAACGCATTTTCTGTGGGTTTAAATA
1 GAGTCAATTTTTATAGATTGTTTTTTGCTCTGTAAATGTGAACGCACTTTCGGTGGATTTAAATA
*
1770 TAATAAATATGATTTATGAGTTATAGTCTTATAGAGTGATGGAATACGAATCGGTTTAGTGTAAC
66 TAATAAATATGATTTATGAG-----G--TTATAGAGTGATGGAATACGAATCGGTTCAGTGTAAC
*
1835 CGCATGTGAGAAATGACTAAAACGGGGCGATAAGGTCGTCCCAGGTTAAAAGTTAGAATGAGCAT
124 CGCATGTGAGAAATGACTAAAACGGGGCGATAAGGTCGTCCCAGGTTAAAAGTTAGAAGGAGCAT
*
1900 TTAGTAATTTCACCTAATTACAAAAATAATATGT
189 TTAGTAATTTCACCTAATTAAAAAAATAATATGT
1934 GGAATATATA
Statistics
Matches: 207, Mismatches: 13, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
221 60 0.29
223 2 0.01
224 17 0.08
226 1 0.00
228 127 0.61
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (223 bp):
GAGTCAATTTTTATAGATTGTTTTTTGCTCTGTAAATGTGAACGCACTTTCGGTGGATTTAAATA
TAATAAATATGATTTATGAGGTTATAGAGTGATGGAATACGAATCGGTTCAGTGTAACCGCATGT
GAGAAATGACTAAAACGGGGCGATAAGGTCGTCCCAGGTTAAAAGTTAGAAGGAGCATTTAGTAA
TTTCACCTAATTAAAAAAATAATATGTA
Found at i:10625 original size:6 final size:6
Alignment explanation
Indices: 10611--10645 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
10601 CTGCGACTAG
* *
10611 GGCTAC GGCTGC GGCTAC GGCTGC GGCTAC GGCTA
1 GGCTAC GGCTAC GGCTAC GGCTAC GGCTAC GGCTA
10646 TAACGACGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.11, C:0.31, G:0.40, T:0.17
Consensus pattern (6 bp):
GGCTAC
Found at i:10628 original size:12 final size:12
Alignment explanation
Indices: 10611--10644 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
10601 CTGCGACTAG
10611 GGCTACGGCTGC
1 GGCTACGGCTGC
10623 GGCTACGGCTGC
1 GGCTACGGCTGC
10635 GGCTACGGCT
1 GGCTACGGCT
10645 ATAACGACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.09, C:0.32, G:0.41, T:0.18
Consensus pattern (12 bp):
GGCTACGGCTGC
Found at i:10643 original size:18 final size:18
Alignment explanation
Indices: 10601--10645 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
10591 AGGGGTTTTA
* *
10601 CTGCGACTAGGGCTACGG
1 CTGCGGCTACGGCTACGG
*
10619 CTGCGGCTACGGCTGCGG
1 CTGCGGCTACGGCTACGG
*
10637 CTACGGCTA
1 CTGCGGCTA
10646 TAACGACGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.31, G:0.38, T:0.18
Consensus pattern (18 bp):
CTGCGGCTACGGCTACGG
Found at i:11355 original size:36 final size:36
Alignment explanation
Indices: 11272--11357 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
11262 GCCCGAGCTC
*
11272 CTACTTATGCTTCTCCGAGAAGATCTTACAGGACTT
1 CTACTTATGCTTCTCCGAGAAGATCTCACAGGACTT
* * * *
11308 CTGC-TAGTGCTTCTCCGAGAAGATCTCCCTGGGCTT
1 CTACTTA-TGCTTCTCCGAGAAGATCTCACAGGACTT
11344 CTACTTATGCTTCT
1 CTACTTATGCTTCT
11358 TTTCGAAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
35 2 0.05
36 38 0.90
37 2 0.05
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (36 bp):
CTACTTATGCTTCTCCGAGAAGATCTCACAGGACTT
Found at i:11583 original size:39 final size:39
Alignment explanation
Indices: 11475--11690 Score: 240
Period size: 39 Copynumber: 5.6 Consensus size: 39
11465 TTCTTCTAGA
* * *
11475 AACTGGGCTCCTGCTAATGCTTCTTTGAGAACGTGATCG
1 AACTGGGCTCCTGCTAATGCTTCTTTGAGAATGTGCTCT
*
11514 AACTGGGCTCCTGC---TGCTTCTTTGGGAATGTGCTCT
1 AACTGGGCTCCTGCTAATGCTTCTTTGAGAATGTGCTCT
*
11550 AACTGGGCTCCTGCTAAGGCTTCTTTGAGAATGTGCTCT
1 AACTGGGCTCCTGCTAATGCTTCTTTGAGAATGTGCTCT
* * ** * **
11589 TACTGGGCTCCTACCGATGGTTCTGGGAGAATGTGCTCT
1 AACTGGGCTCCTGCTAATGCTTCTTTGAGAATGTGCTCT
* * ** *
11628 AGCAGGGCTCCTGCCGATGCTTCTTCGAGAATGTGCTCT
1 AACTGGGCTCCTGCTAATGCTTCTTTGAGAATGTGCTCT
* *
11667 AGCTGGGCTCCTGCTGATGCTTCT
1 AACTGGGCTCCTGCTAATGCTTCT
11691 ACTCTTTCTA
Statistics
Matches: 151, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
36 32 0.21
39 119 0.79
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.32
Consensus pattern (39 bp):
AACTGGGCTCCTGCTAATGCTTCTTTGAGAATGTGCTCT
Found at i:16950 original size:4 final size:4
Alignment explanation
Indices: 16941--17011 Score: 79
Period size: 4 Copynumber: 17.8 Consensus size: 4
16931 TAAAGTGATA
* * *
16941 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
16989 ATGT ATAT GTAT GTAT GTAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATA
17012 ATTAAAGCTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:16952 original size:6 final size:6
Alignment explanation
Indices: 16941--17011 Score: 79
Period size: 6 Copynumber: 11.8 Consensus size: 6
16931 TAAAGTGATA
* * *
16941 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT GTATGT ATGTAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
16989 ATGTAT ATGTAT GTATGT ATATA
1 ATATAT ATATAT ATATAT ATATA
17012 ATTAAAGCTC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (6 bp):
ATATAT
Found at i:16966 original size:20 final size:20
Alignment explanation
Indices: 16941--17011 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
16931 TAAAGTGATA
*
16941 ATATATATATATATATATAT
1 ATATATATATATATATGTAT
16961 ATATATATATATATATGTAT
1 ATATATATATATATATGTAT
* * *
16981 GTATGTATATGTATATGTAT
1 ATATATATATATATATGTAT
* *
17001 GTATGTATATA
1 ATATATATATA
17012 ATTAAAGCTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
ATATATATATATATATGTAT
Done.