Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016712.1 Corchorus olitorius cultivar O-4 contig16745, 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: 18601
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:787 original size:31 final size:26
Alignment explanation
Indices: 725--775 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
715 GAAAGCCCAA
725 AGAAATGGACTTGAACAAAAGATAAG
1 AGAAATGGACTTGAACAAAAGATAAG
*
751 AGAAATGGACTTGACCAAAAGATAA
1 AGAAATGGACTTGAACAAAAGATAA
776 AGGAGAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.53, C:0.10, G:0.22, T:0.16
Consensus pattern (26 bp):
AGAAATGGACTTGAACAAAAGATAAG
Found at i:2004 original size:12 final size:12
Alignment explanation
Indices: 1987--2072 Score: 127
Period size: 12 Copynumber: 7.2 Consensus size: 12
1977 CCCTATTTAC
1987 TTCCTCAACTCT
1 TTCCTCAACTCT
1999 TTCCTCAACTCT
1 TTCCTCAACTCT
*
2011 TTCTTCAACTCT
1 TTCCTCAACTCT
*
2023 TTCCTCAACTCC
1 TTCCTCAACTCT
*
2035 TTCTTCAACTCT
1 TTCCTCAACTCT
* *
2047 TTCATGAACTCT
1 TTCCTCAACTCT
2059 TTCCTCAACTCT
1 TTCCTCAACTCT
2071 TT
1 TT
2073 GTTCAACTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.17, C:0.37, G:0.01, T:0.44
Consensus pattern (12 bp):
TTCCTCAACTCT
Found at i:2043 original size:36 final size:36
Alignment explanation
Indices: 1987--2092 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
1977 CCCTATTTAC
*
1987 TTCCTCAACTCTTTCCTCAACTCTTTCTTCAACTCT
1 TTCCTCAACTCTTTCTTCAACTCTTTCTTCAACTCT
* * *
2023 TTCCTCAACTCCTTCTTCAACTCTTTCATGAACTCT
1 TTCCTCAACTCTTTCTTCAACTCTTTCTTCAACTCT
* * *
2059 TTCCTCAACTCTTTGTTCAACTGTTTGTTCAACT
1 TTCCTCAACTCTTTCTTCAACTCTTTCTTCAACT
2093 GGATCTGGAG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.18, C:0.34, G:0.04, T:0.44
Consensus pattern (36 bp):
TTCCTCAACTCTTTCTTCAACTCTTTCTTCAACTCT
Found at i:2078 original size:12 final size:12
Alignment explanation
Indices: 1991--2092 Score: 123
Period size: 12 Copynumber: 8.5 Consensus size: 12
1981 ATTTACTTCC
*
1991 TCAACTCTTTCC
1 TCAACTCTTTCT
2003 TCAACTCTTTCT
1 TCAACTCTTTCT
*
2015 TCAACTCTTTCC
1 TCAACTCTTTCT
*
2027 TCAACTCCTTCT
1 TCAACTCTTTCT
*
2039 TCAACTCTTTCA
1 TCAACTCTTTCT
* *
2051 TGAACTCTTTCC
1 TCAACTCTTTCT
*
2063 TCAACTCTTTGT
1 TCAACTCTTTCT
* *
2075 TCAACTGTTTGT
1 TCAACTCTTTCT
2087 TCAACT
1 TCAACT
2093 GGATCTGGAG
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 78 1.00
ACGTcount: A:0.19, C:0.33, G:0.04, T:0.44
Consensus pattern (12 bp):
TCAACTCTTTCT
Found at i:2253 original size:24 final size:23
Alignment explanation
Indices: 2221--2309 Score: 101
Period size: 24 Copynumber: 3.9 Consensus size: 23
2211 CAACTTCTGC
2221 AACATTTTCTTCTACATTTTCCA
1 AACATTTTCTTCTACATTTTCCA
* *
2244 TAACATTTTCTTATATATTTT-C-
1 -AACATTTTCTTCTACATTTTCCA
* * *
2266 AACACTTTCATCTACATCTTCCA
1 AACATTTTCTTCTACATTTTCCA
2289 CAACATTTTCTTCTACATTTT
1 -AACATTTTCTTCTACATTTT
2310 TACCCAATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
21 15 0.29
22 1 0.02
23 1 0.02
24 35 0.67
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.48
Consensus pattern (23 bp):
AACATTTTCTTCTACATTTTCCA
Found at i:2269 original size:45 final size:45
Alignment explanation
Indices: 2220--2309 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
2210 TCAACTTCTG
* * * * *
2220 CAACATTTTCTTCTACATTTTCCATAACATTTTCTTATATATTTT
1 CAACACTTTCATCTACATCTTCCACAACATTTTCTTATACATTTT
*
2265 CAACACTTTCATCTACATCTTCCACAACATTTTCTTCTACATTTT
1 CAACACTTTCATCTACATCTTCCACAACATTTTCTTATACATTTT
2310 TACCCAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.27, C:0.26, G:0.00, T:0.48
Consensus pattern (45 bp):
CAACACTTTCATCTACATCTTCCACAACATTTTCTTATACATTTT
Found at i:3442 original size:16 final size:16
Alignment explanation
Indices: 3421--3457 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3411 GGTTAATGGG
3421 TTTTTACTTTATTTTC
1 TTTTTACTTTATTTTC
*
3437 TTTTTATTTTATTTTC
1 TTTTTACTTTATTTTC
3453 TTTTT
1 TTTTT
3458 CCGCCAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTACTTTATTTTC
Found at i:3842 original size:16 final size:16
Alignment explanation
Indices: 3817--3849 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3807 GGCATAAAAA
3817 TTAAATA-TTTTTATT
1 TTAAATATTTTTTATT
3832 TTAATATATTTTTTATT
1 TTAA-ATATTTTTTATT
3849 T
1 T
3850 AATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 3 0.19
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTAAATATTTTTTATT
Found at i:9173 original size:27 final size:27
Alignment explanation
Indices: 9120--9173 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9110 CCCATGCCGG
9120 TTCAATAATTGTTACATTACATGAGTT
1 TTCAATAATTGTTACATTACATGAGTT
9147 TTCAATAATTGTTACATTACATGAGTT
1 TTCAATAATTGTTACATTACATGAGTT
9174 CTTAGGGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (27 bp):
TTCAATAATTGTTACATTACATGAGTT
Found at i:9621 original size:29 final size:28
Alignment explanation
Indices: 9582--9637 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
9572 GTTATTCCAC
*
9582 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
9611 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
9638 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Done.