Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024756.1 Corchorus olitorius cultivar O-4 contig24789, 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: 7774
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Found at i:495 original size:13 final size:13
Alignment explanation
Indices: 462--514 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
452 GCACCCAAAA
*
462 CATTTAT-TAAAA
1 CATTTATATAAAG
474 CATTT-TATAAAG
1 CATTTATATAAAG
486 CATTTATATAAAG
1 CATTTATATAAAG
*
499 CAGTTATA-AAA-
1 CATTTATATAAAG
510 CATTT
1 CATTT
515 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:728 original size:19 final size:19
Alignment explanation
Indices: 687--728 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
677 TAGATCATAG
* *
687 CAAAACCAAGATAATCAAT
1 CAAAACCAAGATAATAAAC
*
706 CAAAACCGAGATAATAAAC
1 CAAAACCAAGATAATAAAC
725 CAAA
1 CAAA
729 TCAATCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.21, G:0.07, T:0.12
Consensus pattern (19 bp):
CAAAACCAAGATAATAAAC
Found at i:1913 original size:35 final size:35
Alignment explanation
Indices: 1871--1990 Score: 186
Period size: 35 Copynumber: 3.4 Consensus size: 35
1861 GCCAAAGCAG
*
1871 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTAC
1 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC
* *
1906 TGAGCCGCGCGGGCCAAGGCCAAGCGCTGGCCTGC
1 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC
* *
1941 TGGGCCGCGCAGGCCAAGGCCATGCGTTGGCCTGC
1 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC
*
1976 TGGGCCGCGCTGGCC
1 TGGGCCGCGCGGGCC
1991 TGCTGGGCTG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 77 1.00
ACGTcount: A:0.11, C:0.37, G:0.41, T:0.12
Consensus pattern (35 bp):
TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC
Found at i:1991 original size:18 final size:18
Alignment explanation
Indices: 1929--2008 Score: 67
Period size: 18 Copynumber: 4.5 Consensus size: 18
1919 CCAAGGCCAA
1929 GCGCTGGCCTGCTGGGCC
1 GCGCTGGCCTGCTGGGCC
* **
1947 GCGCAGG-C--CAAGGCC
1 GCGCTGGCCTGCTGGGCC
*
1962 ATGCGTTGGCCTGCTGGGCC
1 --GCGCTGGCCTGCTGGGCC
*
1982 GCGCTGGCCTGCTGGGCT
1 GCGCTGGCCTGCTGGGCC
*
2000 GCGCAGGCC
1 GCGCTGGCC
2009 AGGCCCTAGC
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
15 5 0.11
17 6 0.13
18 31 0.66
20 5 0.11
ACGTcount: A:0.06, C:0.36, G:0.42, T:0.15
Consensus pattern (18 bp):
GCGCTGGCCTGCTGGGCC
Found at i:2048 original size:3 final size:3
Alignment explanation
Indices: 2040--2072 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2030 TTACTTTTCT
*
2040 TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2073 CTCATCCGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:6788 original size:12 final size:13
Alignment explanation
Indices: 6771--6807 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
6761 TTATGCACCC
6771 AAAACATTTAT-T
1 AAAACATTTATAT
6783 AAAACATTT-TAT
1 AAAACATTTATAT
*
6795 AAAGCATTTATAT
1 AAAACATTTATAT
6808 GAAGCAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 1 0.05
12 18 0.82
13 3 0.14
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (13 bp):
AAAACATTTATAT
Found at i:7041 original size:19 final size:19
Alignment explanation
Indices: 7000--7041 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6990 TAGATCATAG
* *
7000 CAAAACCAAGATAATCAAT
1 CAAAACCAAGATAATAAAC
*
7019 CAAAACCGAGATAATAAAC
1 CAAAACCAAGATAATAAAC
7038 CAAA
1 CAAA
7042 TCAATCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.21, G:0.07, T:0.12
Consensus pattern (19 bp):
CAAAACCAAGATAATAAAC
Done.