Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020428.1 Corchorus olitorius cultivar O-4 contig20461, 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: 27033
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:14992 original size:2 final size:2
Alignment explanation
Indices: 14985--15019 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14975 AAGTAGTTAG
14985 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15020 GTTTGAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16039 original size:27 final size:26
Alignment explanation
Indices: 15985--16045 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
15975 CTAAATTGCC
15985 ATTATTTTAATAATAGAATAATTAAAAT
1 ATTA-TTTAATAATAGAAT-ATTAAAAT
16013 ATTATTTAATAATAGCAAT-TTAGAAAT
1 ATTATTTAATAATAG-AATATTA-AAAT
16040 A-TATTT
1 ATTATTT
16046 GAAAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 16 0.52
28 7 0.23
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (26 bp):
ATTATTTAATAATAGAATATTAAAAT
Found at i:16582 original size:26 final size:28
Alignment explanation
Indices: 16531--16584 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
16521 GTAATCAAAT
16531 TTATAATATCTTCTTATCTCAAAAAAAAA
1 TTATAATATCTTCTTATCT-AAAAAAAAA
*
16560 TTATAATATCTTCTTA-CTTAAAAAA
1 TTATAATATCTTCTTATCTAAAAAAA
16585 CAATATAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.25
28 2 0.08
29 16 0.67
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (28 bp):
TTATAATATCTTCTTATCTAAAAAAAAA
Found at i:17298 original size:44 final size:44
Alignment explanation
Indices: 17235--17319 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
17225 TAAATTTCAT
* *
17235 AATTATAGTCAATCTAGAATATCTTTTCATAATTTAAAAAATGC
1 AATTATAGTCAATCTAGAATATCTTTCCATAATTGAAAAAATGC
* *
17279 AATTATAGT-AGATTTAGAATATCTTTCCATAGTTGAAAAAA
1 AATTATAGTCA-ATCTAGAATATCTTTCCATAATTGAAAAAA
17320 CAAAGTGGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (44 bp):
AATTATAGTCAATCTAGAATATCTTTCCATAATTGAAAAAATGC
Found at i:17910 original size:21 final size:21
Alignment explanation
Indices: 17885--17925 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17875 ATATGTACCG
* *
17885 TATTTTATAATTAATTATATA
1 TATTTAATAATTAAATATATA
*
17906 TATTTAATATTTAAATATAT
1 TATTTAATAATTAAATATAT
17926 TCCCTACTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTAATAATTAAATATATA
Found at i:22036 original size:22 final size:22
Alignment explanation
Indices: 22011--22053 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
22001 GATATTTATA
*
22011 ATTTAT-ATTATATATATAATAT
1 ATTTATGA-TATATATAAAATAT
22033 ATTTATGATATATATAAAATA
1 ATTTATGATATATATAAAATA
22054 AATTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTTATGATATATATAAAATAT
Found at i:22049 original size:38 final size:40
Alignment explanation
Indices: 21997--22105 Score: 102
Period size: 38 Copynumber: 2.8 Consensus size: 40
21987 AACCGACCGA
*
21997 TTATGATATTTATAATTTATATTATATATA-TA-ATATAT
1 TTATGATATATATAATTTATATTATATATATTAGATATAT
** * * * * *
22035 TTATGATATATATAAAATAAATTATTTTTATTAGTTTTAT
1 TTATGATATATATAATTTATATTATATATATTAGATATAT
22075 TT-T-ATATATATAATTTATATT-TATATTATTA
1 TTATGATATATATAATTTATATTATATA-TATTA
22106 ATTCAGAAAG
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
37 2 0.04
38 44 0.80
39 3 0.05
40 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (40 bp):
TTATGATATATATAATTTATATTATATATATTAGATATAT
Found at i:22108 original size:19 final size:18
Alignment explanation
Indices: 22002--22100 Score: 63
Period size: 18 Copynumber: 5.2 Consensus size: 18
21992 ACCGATTATG
* *
22002 ATATTTATAATTTATATT
1 ATATATATAATTTATTTT
*
22020 ATATATATAATATATTTAT
1 ATATATATAATTTATTT-T
** **
22039 GATATATATAAAATAAATT
1 -ATATATATAATTTATTTT
* * *
22058 ATTTTTATTAGTTTTATTTT
1 ATATATA-TA-ATTTATTTT
22078 ATATATATAATTTATATTT
1 ATATATATAATTTAT-TTT
22097 ATAT
1 ATAT
22101 TATTAATTCA
Statistics
Matches: 60, Mismatches: 16, Indels: 9
0.71 0.19 0.11
Matches are distributed among these distances:
18 24 0.40
19 13 0.22
20 23 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATATATATAATTTATTTT
Done.