Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014749.1 Corchorus olitorius cultivar O-4 contig14782, 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: 33080
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:9998 original size:18 final size:18
Alignment explanation
Indices: 9971--10008 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
9961 TAGACCCTAA
9971 TCACTGTCATCATCCTCG
1 TCACTGTCATCATCCTCG
*
9989 TCACTTTCATCATCCTCG
1 TCACTGTCATCATCCTCG
10007 TC
1 TC
10009 GCCTTCGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.39, G:0.08, T:0.37
Consensus pattern (18 bp):
TCACTGTCATCATCCTCG
Found at i:11976 original size:21 final size:21
Alignment explanation
Indices: 11952--12009 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 21
11942 GCTGCTCTAA
11952 TAATCTCATCTGTACAATATC
1 TAATCTCATCTGTACAATATC
* * *
11973 TAATCTAATCTGTAC-A-GTG
1 TAATCTCATCTGTACAATATC
*
11992 TAATTTCATCTGTACAAT
1 TAATCTCATCTGTACAAT
12010 TGTTAAACAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 14 0.47
20 2 0.07
21 14 0.47
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (21 bp):
TAATCTCATCTGTACAATATC
Found at i:12720 original size:21 final size:22
Alignment explanation
Indices: 12696--12737 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12686 CTGACTACGT
12696 GGCA-TTTTTAGCTGACGTGGA
1 GGCATTTTTTAGCTGACGTGGA
*
12717 GGCATTTTTTGGCTGACGTGG
1 GGCATTTTTTAGCTGACGTGG
12738 CGTAGGTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.14, C:0.14, G:0.36, T:0.36
Consensus pattern (22 bp):
GGCATTTTTTAGCTGACGTGGA
Found at i:13851 original size:14 final size:14
Alignment explanation
Indices: 13820--13853 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13810 TTTCTTTTAA
*
13820 TTTTTTCCTTTTTC
1 TTTTTTCCGTTTTC
*
13834 TTTTTTCCGTTTTG
1 TTTTTTCCGTTTTC
13848 TTTTTT
1 TTTTTT
13854 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTTTTCCGTTTTC
Found at i:16731 original size:39 final size:40
Alignment explanation
Indices: 16677--16756 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
16667 TATTATGTTG
*
16677 GAATAGTGAATTTCTGACTTTCTGTAATG-TTCTCTATGA
1 GAATAGTGAATTTCTGACTTTCTATAATGATTCTCTATGA
*
16716 GAATATTGAATTTCTGACTTTCTATAATGACTTCTCTATGA
1 GAATAGTGAATTTCTGACTTTCTATAATGA-TTCTCTATGA
16757 AATTTGGAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 27 0.73
41 10 0.27
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.44
Consensus pattern (40 bp):
GAATAGTGAATTTCTGACTTTCTATAATGATTCTCTATGA
Found at i:22009 original size:2 final size:2
Alignment explanation
Indices: 22002--22044 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
21992 CATCACATGA
* * *
22002 AT AT AT AT AT AT AT AT AT AT GT AT AT AT GT AT CAA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
22045 GGAGATTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 33 0.97
3 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24343 original size:14 final size:14
Alignment explanation
Indices: 24324--24358 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
24314 AATTATTAAC
24324 GATGTATAGGATTT
1 GATGTATAGGATTT
24338 GATGTATAGGATTT
1 GATGTATAGGATTT
*
24352 AATGTAT
1 GATGTAT
24359 TGACAATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (14 bp):
GATGTATAGGATTT
Found at i:24664 original size:15 final size:15
Alignment explanation
Indices: 24646--24676 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24636 CAAGGGCTGA
*
24646 AATTAATTAATTATT
1 AATTAAATAATTATT
24661 AATTAAATAATTATT
1 AATTAAATAATTATT
24676 A
1 A
24677 TTTTCTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAAATAATTATT
Done.