Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016105.1 Corchorus olitorius cultivar O-4 contig16138, 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: 36971
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5472 original size:109 final size:109
Alignment explanation
Indices: 5281--5498 Score: 375
Period size: 109 Copynumber: 2.0 Consensus size: 109
5271 TAGTCATTTT
*
5281 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGAACTTTGTATTATTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGAACTTTGTATTATTTGGTATGTATGCTT
5346 ATTTAATAGGTTCAATTGAATAAACAACACAATTAACAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAACAATAATA
* *
5390 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCA-TTTCGTATTGTTTGGTATGTATGCT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGAACTTT-GTATTATTTGGTATGTATGCT
* *
5454 TATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
65 TATTTAATAGGTTCAATTGAATAAACAACACAATTAACAATAATA
5499 TATATAATAG
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
108 3 0.03
109 100 0.97
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (109 bp):
GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGAACTTTGTATTATTTGGTATGTATGCTT
ATTTAATAGGTTCAATTGAATAAACAACACAATTAACAATAATA
Found at i:12665 original size:13 final size:13
Alignment explanation
Indices: 12647--12672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12637 TATAGAGTAT
12647 AAAGATAAAGATA
1 AAAGATAAAGATA
12660 AAAGATAAAGATA
1 AAAGATAAAGATA
12673 TATTTCCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAGATAAAGATA
Found at i:13229 original size:11 final size:11
Alignment explanation
Indices: 13215--13252 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13205 ATTCATAACA
13215 AATTTATAATT
1 AATTTATAATT
13226 AATTTATAATT
1 AATTTATAATT
13237 -ATTTGATAATT
1 AATTT-ATAATT
*
13248 TATTT
1 AATTT
13253 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:22130 original size:62 final size:61
Alignment explanation
Indices: 22014--22136 Score: 219
Period size: 61 Copynumber: 2.0 Consensus size: 61
22004 TTTTATTCAA
*
22014 CTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTATACCTATTTTATTTTTACCAT
1 CTAAAAACTCTATTTTTATTTAATTAAATCCAATATCTTATACCTATTTTATTTTTACCAT
*
22075 CTAAAAACTCTATTTTTATTTAATTAAATCCAATATCCTTCTACCTATTTTATTTTTACCAT
1 CTAAAAACTCTATTTTTATTTAATTAAATCCAATAT-CTTATACCTATTTTATTTTTACCAT
22137 TTTACTAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 35 0.59
62 24 0.41
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (61 bp):
CTAAAAACTCTATTTTTATTTAATTAAATCCAATATCTTATACCTATTTTATTTTTACCAT
Found at i:24759 original size:15 final size:16
Alignment explanation
Indices: 24733--24763 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
24723 ACTGATTTAG
24733 TATTTATTCATATAAT
1 TATTTATTCATATAAT
24749 TATTT-TTCATATAAT
1 TATTTATTCATATAAT
24764 GAAGTTTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTATTCATATAAT
Found at i:24983 original size:19 final size:19
Alignment explanation
Indices: 24956--25001 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
24946 GTTCGGATTG
*
24956 TTTTTTTTGTTTTT-TGTT
1 TTTTTTTTGTTTTTGAGTT
24974 TTTGTTTTTGTTTTTGAGTT
1 TTT-TTTTTGTTTTTGAGTT
24994 TTTTTTTT
1 TTTTTTTT
25002 CGGTCAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 16 0.64
20 6 0.24
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (19 bp):
TTTTTTTTGTTTTTGAGTT
Found at i:25001 original size:6 final size:6
Alignment explanation
Indices: 24959--24989 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
24949 CGGATTGTTT
24959 TTTTTG TTTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG
24990 AGTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:25312 original size:49 final size:50
Alignment explanation
Indices: 25254--25350 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 50
25244 TCAGATCAAC
25254 AAGAAGGAACCAATGTTATGT-GAAGGAGCTTGCTTAATTAT-GAGATCAG
1 AAGAAGGAACCAATGTTATGTGGAA-GAGCTTGCTTAATTATGGAGATCAG
*
25303 AAGAAGGAACTAATGTTATGTGGAAGAGCTTGCTTAATTATGGAGATC
1 AAGAAGGAACCAATGTTATGTGGAAGAGCTTGCTTAATTATGGAGATC
25351 CGGGAGTTAG
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
49 36 0.80
50 9 0.20
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (50 bp):
AAGAAGGAACCAATGTTATGTGGAAGAGCTTGCTTAATTATGGAGATCAG
Found at i:25490 original size:36 final size:36
Alignment explanation
Indices: 25443--25511 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
25433 ACTCTTTAAT
25443 TGATTGAATCTACAACTAAAAAAAAAACACAATGGA
1 TGATTGAATCTACAACTAAAAAAAAAACACAATGGA
* *
25479 TGATTGAATCTACTACTAAAAAAAAACCACAAT
1 TGATTGAATCTACAACTAAAAAAAAAACACAAT
25512 CGATCACGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.54, C:0.16, G:0.09, T:0.22
Consensus pattern (36 bp):
TGATTGAATCTACAACTAAAAAAAAAACACAATGGA
Found at i:25742 original size:18 final size:18
Alignment explanation
Indices: 25716--25750 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25706 ATTATTAGAT
25716 AAATAATAATAATTTTTG
1 AAATAATAATAATTTTTG
* *
25734 AAATTATAATTATTTTT
1 AAATAATAATAATTTTT
25751 ATTTCATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATAATAATAATTTTTG
Found at i:27180 original size:51 final size:51
Alignment explanation
Indices: 27080--27187 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 51
27070 TCCTTCAATA
** * **
27080 TTCTCTTGTTTAGATCTTGTCTCCGGACACCCAAACACTCTTTTAGTGTTT
1 TTCTCTTGTTTAGATCTTGTCTCCGGACACAAAAACACTCGTACAGTGTTT
*
27131 TTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACT-GTACACGTGTTT
1 TTCTCTTGTTT-AGATCTTGTCTCCGGACACAAAAACACTCGTACA-GTGTTT
*
27182 CTCTCT
1 TTCTCT
27188 CAGCAATAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
50 2 0.04
51 45 0.94
52 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (51 bp):
TTCTCTTGTTTAGATCTTGTCTCCGGACACAAAAACACTCGTACAGTGTTT
Done.