Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011083.1 Corchorus olitorius cultivar O-4 contig11116, 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: 2544
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Found at i:1668 original size:20 final size:20
Alignment explanation
Indices: 1643--2044 Score: 272
Period size: 20 Copynumber: 22.5 Consensus size: 20
1633 AGTGTCAAGG
1643 CCGAGTGCCATCGGCAAGTC
1 CCGAGTGCCATCGGCAAGTC
*
1663 CCGAGTGGCCATCGGCAACTC
1 CCGAGT-GCCATCGGCAAGTC
*
1684 CCGAGTG----C--CAAG-G
1 CCGAGTGCCATCGGCAAGTC
* *
1697 CCTAGTGCCATCGGCAAGTG
1 CCGAGTGCCATCGGCAAGTC
*
1717 CCGAGTG----C--CAAG-G
1 CCGAGTGCCATCGGCAAGTC
*
1730 CCTAGTGCCATCGGCAAGTC
1 CCGAGTGCCATCGGCAAGTC
*
1750 CCGAGTGCCATCGGCAACTC
1 CCGAGTGCCATCGGCAAGTC
*
1770 CCGAGTGCCATCGGCAACTC
1 CCGAGTGCCATCGGCAAGTC
*
1790 CCGAGTG----C--CAAG-G
1 CCGAGTGCCATCGGCAAGTC
* *
1803 CCTAGTGCCATCGGCAAGTG
1 CCGAGTGCCATCGGCAAGTC
*
1823 CCGAGTGCCATCGGCAAGTG
1 CCGAGTGCCATCGGCAAGTC
*
1843 TCGAGTGCCATCGGCAAGTC
1 CCGAGTGCCATCGGCAAGTC
1863 CCGAGTGCCATCGGCAAGTC
1 CCGAGTGCCATCGGCAAGTC
*
1883 CCGAGTG----C--CAA-TG
1 CCGAGTGCCATCGGCAAGTC
* *
1896 CCGAGTGCCATCGGCAGGTG
1 CCGAGTGCCATCGGCAAGTC
1916 CCGAGTGCCATCGGCAAGTC
1 CCGAGTGCCATCGGCAAGTC
*
1936 CCGAGTG----C--CAAG-G
1 CCGAGTGCCATCGGCAAGTC
1949 CCGAGTGCCATCGGCAAGTC
1 CCGAGTGCCATCGGCAAGTC
*
1969 CCGAGTG----C--CAAG-G
1 CCGAGTGCCATCGGCAAGTC
*
1982 CCGAGTGCCATCAGCAAGTC
1 CCGAGTGCCATCGGCAAGTC
*
2002 CCGAGTG----C--CAAG-G
1 CCGAGTGCCATCGGCAAGTC
2015 CCGAGTGCCATCGGCAAGTC
1 CCGAGTGCCATCGGCAAGTC
2035 CCGAGTGCCA
1 CCGAGTGCCA
2045 AGGCCGAGTG
Statistics
Matches: 306, Mismatches: 26, Indels: 100
0.71 0.06 0.23
Matches are distributed among these distances:
13 48 0.16
14 25 0.08
16 7 0.02
17 7 0.02
19 26 0.08
20 174 0.57
21 19 0.06
ACGTcount: A:0.21, C:0.34, G:0.31, T:0.14
Consensus pattern (20 bp):
CCGAGTGCCATCGGCAAGTC
Found at i:1712 original size:33 final size:33
Alignment explanation
Indices: 1663--2057 Score: 409
Period size: 33 Copynumber: 11.3 Consensus size: 33
1653 TCGGCAAGTC
*
1663 CCGAGTGGCCATCGGCAACTCCCGAGTGCCAAGG
1 CCGAGT-GCCATCGGCAAGTCCCGAGTGCCAAGG
* *
1697 CCTAGTGCCATCGGCAAGTGCCGAGTGCCAAGG
1 CCGAGTGCCATCGGCAAGTCCCGAGTGCCAAGG
* *
1730 CCTAGTGCCATCGGCAAGTCCCGAGTGCCATCGG
1 CCGAGTGCCATCGGCAAGTCCCGAGTGCCA-AGG
*
1764 CAACTCCCGAGTGCCATCGGCAACTCCCGAGTGCCAAGG
1 ------CCGAGTGCCATCGGCAAGTCCCGAGTGCCAAGG
* *
1803 CCTAGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTG
1 CCGAGTGCCATCGGCAAGTCCCGAGTG----C--CAAG-G
* *
1843 TCGAGTGCCATCGGCAAGTCCCGAGTGCCATCGG
1 CCGAGTGCCATCGGCAAGTCCCGAGTGCCA-AGG
* * * *
1877 -CAAGTCCCGAGT-GCCAA-TGCCGAGTGCCATCGGCAGGTG
1 CCGAGTGCC-A-TCGGCAAGTCCCGAGTGCCA-----A-G-G
1916 CCGAGTGCCATCGGCAAGTCCCGAGTGCCAAGG
1 CCGAGTGCCATCGGCAAGTCCCGAGTGCCAAGG
1949 CCGAGTGCCATCGGCAAGTCCCGAGTGCCAAGG
1 CCGAGTGCCATCGGCAAGTCCCGAGTGCCAAGG
*
1982 CCGAGTGCCATCAGCAAGTCCCGAGTGCCAAGG
1 CCGAGTGCCATCGGCAAGTCCCGAGTGCCAAGG
2015 CCGAGTGCCATCGGCAAGTCCCGAGTGCCAAGG
1 CCGAGTGCCATCGGCAAGTCCCGAGTGCCAAGG
2048 CCGAGTGCCA
1 CCGAGTGCCA
2058 AGGCCCAGTG
Statistics
Matches: 308, Mismatches: 27, Indels: 53
0.79 0.07 0.14
Matches are distributed among these distances:
33 203 0.66
34 16 0.05
35 3 0.01
36 1 0.00
37 1 0.00
38 2 0.01
39 12 0.04
40 70 0.23
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.14
Consensus pattern (33 bp):
CCGAGTGCCATCGGCAAGTCCCGAGTGCCAAGG
Found at i:1774 original size:53 final size:53
Alignment explanation
Indices: 1700--2057 Score: 312
Period size: 53 Copynumber: 6.8 Consensus size: 53
1690 GCCAAGGCCT
* *
1700 AGTGCCATCGGCAAGTGCCGAGTGCCAAGGCCTAGTGCCATCGGCAAGTCCCG
1 AGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCCCG
* * * * * * * *
1753 AGTGCCATCGGCAACTCCCGAGTGCCATCGG-CAACTCCCGAGT-GCCAAG-GCCT
1 AGTGCCATCGGCAAGTCCCGAGTGCCA-AGGCCGAGTGCC-A-TCGGCAAGTCCCG
* *
1806 AGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTGTCGAGTGCCATCGGCAAGTCCCG
1 AGTGCCATCGGCAAGTCCCGAGTG----C--CAAG-GCCGAGTGCCATCGGCAAGTCCCG
* * *
1866 AGTGCCATCGGCAAGTCCCGAGTGCCAATGCCGAGTGCCATCGGCAGGTGCCG
1 AGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCCCG
1919 AGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCCCG
1 AGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCCCG
* * * * *
1972 AGTG----C--CAAG-GCCGAGTGCCATCA-G-CAAGTCCCGAGT-GCCAAG-GCCG
1 AGTGCCATCGGCAAGTCCCGAGTGCCA--AGGCCGAGTGCC-A-TCGGCAAGTCCCG
2018 AGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCA
1 AGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCA
2058 AGGCCCAGTG
Statistics
Matches: 245, Mismatches: 34, Indels: 53
0.74 0.10 0.16
Matches are distributed among these distances:
46 23 0.09
47 11 0.04
48 2 0.01
49 1 0.00
50 1 0.00
51 1 0.00
52 6 0.02
53 145 0.59
54 11 0.04
55 1 0.00
56 1 0.00
57 1 0.00
58 2 0.01
59 9 0.04
60 30 0.12
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.14
Consensus pattern (53 bp):
AGTGCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTCCCG
Found at i:1987 original size:13 final size:13
Alignment explanation
Indices: 1969--2070 Score: 60
Period size: 13 Copynumber: 6.8 Consensus size: 13
1959 TCGGCAAGTC
1969 CCGAGTGCCAAGG
1 CCGAGTGCCAAGG
1982 CCGAGTGCCATCAGCAAG
1 CCGAGTGCCA--AG---G
2000 TCCCGAGTGCCAAGG
1 --CCGAGTGCCAAGG
*
2015 CCGAGTGCCATCGGCAAGT
1 CCGAGTG----C--CAAGG
2034 CCCGAGTGCCAAGG
1 CC-GAGTGCCAAGG
2048 CCGAGTGCCAAGG
1 CCGAGTGCCAAGG
*
2061 CCCAGTGCCA
1 CCGAGTGCCA
2071 CCAAGTGCCG
Statistics
Matches: 72, Mismatches: 3, Indels: 28
0.70 0.03 0.27
Matches are distributed among these distances:
13 37 0.51
14 6 0.08
15 3 0.04
16 1 0.01
17 1 0.01
18 3 0.04
19 6 0.08
20 15 0.21
ACGTcount: A:0.23, C:0.34, G:0.32, T:0.11
Consensus pattern (13 bp):
CCGAGTGCCAAGG
Done.