Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017420.1 Corchorus olitorius cultivar O-4 contig17453, 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: 42772
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3114 original size:14 final size:15
Alignment explanation
Indices: 3081--3114 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3071 TTAATGCTGA
3081 CTTTGGGCCTTATGG
1 CTTTGGGCCTTATGG
*
3096 CTTTGGGCTTTAT-G
1 CTTTGGGCCTTATGG
3110 CTTTG
1 CTTTG
3115 AACTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.06, C:0.18, G:0.29, T:0.47
Consensus pattern (15 bp):
CTTTGGGCCTTATGG
Found at i:6249 original size:27 final size:26
Alignment explanation
Indices: 6209--6266 Score: 98
Period size: 27 Copynumber: 2.2 Consensus size: 26
6199 AACTAAAACC
6209 GAAAATGACGGGAACTTTCCCAATTT
1 GAAAATGACGGGAACTTTCCCAATTT
*
6235 GAAAACTGATGGGAACTTTCCCAATTT
1 GAAAA-TGACGGGAACTTTCCCAATTT
6262 GAAAA
1 GAAAA
6267 GGAGCTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (26 bp):
GAAAATGACGGGAACTTTCCCAATTT
Found at i:7161 original size:34 final size:34
Alignment explanation
Indices: 7123--7187 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
7113 ATTTACTTTA
7123 AACTAAAGCGAACATCAATCAGGAGTAAATTATT
1 AACTAAAGCGAACATCAATCAGGAGTAAATTATT
7157 AACTAAAGCGAACATCAATCAGGAGTAAATT
1 AACTAAAGCGAACATCAATCAGGAGTAAATT
7188 GAAAAAAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (34 bp):
AACTAAAGCGAACATCAATCAGGAGTAAATTATT
Found at i:29264 original size:12 final size:12
Alignment explanation
Indices: 29247--29271 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29237 ACTCTTCAGA
29247 TTGTGTAGATTT
1 TTGTGTAGATTT
29259 TTGTGTAGATTT
1 TTGTGTAGATTT
29271 T
1 T
29272 GATTCTTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (12 bp):
TTGTGTAGATTT
Found at i:30585 original size:13 final size:13
Alignment explanation
Indices: 30567--30592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30557 CACTCCCTCC
30567 GTCCGAATTATAT
1 GTCCGAATTATAT
30580 GTCCGAATTATAT
1 GTCCGAATTATAT
30593 ATAGGGTAAA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GTCCGAATTATAT
Found at i:37533 original size:30 final size:31
Alignment explanation
Indices: 37456--37526 Score: 110
Period size: 30 Copynumber: 2.3 Consensus size: 31
37446 ATTTTTGGCC
*
37456 ACCAATTTGAGGCTAAACCTTTCAAAATTTG
1 ACCAATTTGAGGCTAAACCTTTCAAAAATTG
37487 -CTCAATTTGAGGCTAAACC-TTCAAAAATTG
1 AC-CAATTTGAGGCTAAACCTTTCAAAAATTG
37517 ACCAATTTGA
1 ACCAATTTGA
37527 ACCTAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.31
Consensus pattern (31 bp):
ACCAATTTGAGGCTAAACCTTTCAAAAATTG
Found at i:41578 original size:29 final size:30
Alignment explanation
Indices: 41536--41604 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
41526 TTCCATCTTC
*
41536 TTTGTCCCCTGAACTTCAA-TTTCGGACAT
1 TTTGCCCCCTGAACTTCAATTTTCGGACAT
* *
41565 TTTGCCCCCTGAACTTCAATTTTGGGACGT
1 TTTGCCCCCTGAACTTCAATTTTCGGACAT
41595 TTTGCCCCCT
1 TTTGCCCCCT
41605 CAGCCTAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.38
Consensus pattern (30 bp):
TTTGCCCCCTGAACTTCAATTTTCGGACAT
Found at i:41813 original size:29 final size:30
Alignment explanation
Indices: 41745--41816 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
41735 CCTGAGTGGG
*
41745 AAAACGTCCCAAAATTGAAGTTCAGGGGGGC
1 AAAACGT-CCAAAAGTGAAGTTCAGGGGGGC
*
41776 AAAATGTCCAAAAGTGAAGTTCA-GGGGGC
1 AAAACGTCCAAAAGTGAAGTTCAGGGGGGC
41805 AAAACGTCCAAA
1 AAAACGTCCAAA
41817 CGTTACAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 17 0.45
30 15 0.39
31 6 0.16
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.15
Consensus pattern (30 bp):
AAAACGTCCAAAAGTGAAGTTCAGGGGGGC
Done.