Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020894.1 Corchorus olitorius cultivar O-4 contig20927, 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: 22050
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:1939 original size:107 final size:106
Alignment explanation
Indices: 1690--1977 Score: 399
Period size: 107 Copynumber: 2.8 Consensus size: 106
1680 CTAACCCTTG
* * *
1690 AAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATATTATTTCTAA
1 AAATAAAA-ATTAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAA
* *
1753 AACCCTATAACAAT--ATTATAAATTATGGAATTTACCCTTA
65 AACCCTATAACAATAAATTATAAATTATGAAATTTACCCTCA
* * *
1793 AAAT-AAAATT-TTTTTAATTTGGAGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAA
1 AAATAAAAATTAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAA
* *
1856 ACCCTATAACAATAAATTATTAATTTTGAAATTTACCCTCA
66 ACCCTATAACAATAAATTATAAATTATGAAATTTACCCTCA
*
1897 AAATAAAAATTAAATTTTAGTTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAA
1 AAATAAAAATT-AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAA
* *
1962 AACTCTATAATAATAA
65 AACCCTATAACAATAA
1978 TAAAAAAAGA
Statistics
Matches: 162, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
100 9 0.06
101 16 0.10
102 39 0.24
103 4 0.02
104 26 0.16
105 6 0.04
107 62 0.38
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.42
Consensus pattern (106 bp):
AAATAAAAATTAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAA
ACCCTATAACAATAAATTATAAATTATGAAATTTACCCTCA
Found at i:13244 original size:22 final size:22
Alignment explanation
Indices: 13216--13265 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
13206 TATTGGGATT
13216 ACCTTTTGTGAAGTAAATAGGC
1 ACCTTTTGTGAAGTAAATAGGC
*
13238 ACCTTTTTTGAAGTAAATAGGC
1 ACCTTTTGTGAAGTAAATAGGC
13260 A-CTTTT
1 ACCTTTT
13266 CTTTTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (22 bp):
ACCTTTTGTGAAGTAAATAGGC
Found at i:14301 original size:56 final size:56
Alignment explanation
Indices: 14234--14344 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
14224 AAACAAACAA
14234 GTTAAAATTTTGACATATATTCCACCACATCTAATTAATTATTTATTAATATTAAG
1 GTTAAAATTTTGACATATATTCCACCACATCTAATTAATTATTTATTAATATTAAG
* *
14290 GTTAAAATTTTGACATATATTCCACCATATCTAATTAATTATTTCTTAATATTAA
1 GTTAAAATTTTGACATATATTCCACCACATCTAATTAATTATTTATTAATATTAA
14345 AGAATATATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.44
Consensus pattern (56 bp):
GTTAAAATTTTGACATATATTCCACCACATCTAATTAATTATTTATTAATATTAAG
Found at i:14355 original size:2 final size:2
Alignment explanation
Indices: 14348--14377 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
14338 ATATTAAAGA
*
14348 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14378 CTTAGCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14921 original size:20 final size:20
Alignment explanation
Indices: 14896--14933 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14886 TTTTCATAGT
*
14896 TAATTAATATATACTTATGG
1 TAATTAATATATAATTATGG
*
14916 TAATTATTATATAATTAT
1 TAATTAATATATAATTAT
14934 TATTATTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TAATTAATATATAATTATGG
Found at i:19023 original size:29 final size:31
Alignment explanation
Indices: 18969--19042 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
18959 TGTTTAATTA
* *
18969 AACTACCACTATAATATCTC-ATAAAATAAT
1 AACTACCACTATAATAGCTCAAAAAAATAAT
18999 -ACTACCACTATAAGTAGC-CAAAAAAATAAT
1 AACTACCACTATAA-TAGCTCAAAAAAATAAT
*
19029 AACCACCACTATAA
1 AACTACCACTATAA
19043 CTGTCATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 14 0.37
30 12 0.32
31 12 0.32
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (31 bp):
AACTACCACTATAATAGCTCAAAAAAATAAT
Found at i:20201 original size:37 final size:38
Alignment explanation
Indices: 20146--20224 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 38
20136 ATTATATACT
* *
20146 TGATCAACATACATGTCTTTTCATATAGACATAACTTTA
1 TGATCAACA-ACATGTCTTTCCAAATAGACATAACTTTA
20185 TGATCAAC-ACATGTCTTTCCAAATAGACATAACTTTA
1 TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA
20222 TGA
1 TGA
20225 ATAATTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 30 0.79
39 8 0.21
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (38 bp):
TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA
Found at i:22027 original size:26 final size:25
Alignment explanation
Indices: 21989--22040 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
21979 TTTCTTACAA
21989 AAATAATAGAAATAAACATTAGATAT
1 AAATAATAGAAATAAAC-TTAGATAT
* * * *
22015 AAATCATATAAATGAACTTATATAT
1 AAATAATAGAAATAAACTTAGATAT
22040 A
1 A
22041 TCTCATTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATAATAGAAATAAACTTAGATAT
Done.