Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016612.1 Corchorus olitorius cultivar O-4 contig16645, 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: 13147
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:1777 original size:33 final size:33
Alignment explanation
Indices: 1740--1925 Score: 198
Period size: 33 Copynumber: 5.6 Consensus size: 33
1730 AGAATTTGTT
1740 TCATCACAAACAACAC-CTAAAACAGATTTAGTG
1 TCATCACAAACAACACTC-AAAACAGATTTAGTG
** * * *
1773 TCATCACAAACAACACTCAAATTAGTTTTAATA
1 TCATCACAAACAACACTCAAAACAGATTTAGTG
1806 TCATCA-ATAACAACA-TCTAAAACAGATTTAGTG
1 TCATCACA-AACAACACTC-AAAACAGATTTAGTG
* ** * *
1839 TCATCGCAAACAACACTCAAATTAGGTTTAGTA
1 TCATCACAAACAACACTCAAAACAGATTTAGTG
* *
1872 TCATCACTAACAACACTCAAAACAGATTTCGTG
1 TCATCACAAACAACACTCAAAACAGATTTAGTG
**
1905 TCATTGCAAACAACACTCAAA
1 TCATCACAAACAACACTCAAA
1926 TTAGGTTCAG
Statistics
Matches: 123, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
32 3 0.02
33 116 0.94
34 4 0.03
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (33 bp):
TCATCACAAACAACACTCAAAACAGATTTAGTG
Found at i:1930 original size:66 final size:67
Alignment explanation
Indices: 1740--1932 Score: 302
Period size: 66 Copynumber: 2.9 Consensus size: 67
1730 AGAATTTGTT
* * *
1740 TCATCACAAACAACAC-CTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGTTTTAA
1 TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAA
1804 TA
66 TA
* *
1806 TCATCAATAACAACA-TCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAG
1 TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAA
1870 TA
66 TA
* *
1872 TCATCACTAACAACACTC-AAAACAGATTTCGTGTCATTGCAAACAACACTCAAATTAGGTT
1 TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTT
1933 CAGAATTACT
Statistics
Matches: 117, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
66 115 0.98
67 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.26
Consensus pattern (67 bp):
TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAA
TA
Found at i:2226 original size:31 final size:31
Alignment explanation
Indices: 2191--2262 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
2181 CTCCCAAGCA
*
2191 ACACATGACAAGCTCGCATTGGTAGCACATC
1 ACACAAGACAAGCTCGCATTGGTAGCACATC
2222 ACACAAGACAAGCTCGCATTGGTAGCACATC
1 ACACAAGACAAGCTCGCATTGGTAGCACATC
2253 ACACAAGACA
1 ACACAAGACA
2263 TCCTCTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.38, C:0.29, G:0.18, T:0.15
Consensus pattern (31 bp):
ACACAAGACAAGCTCGCATTGGTAGCACATC
Found at i:4421 original size:21 final size:21
Alignment explanation
Indices: 4397--4488 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
4387 CTTAGACAAT
*
4397 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4418 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4439 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4460 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
4481 TCCAATGA
1 TCCAATGA
4489 TCTCCTAGCA
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 3 0.04
21 66 0.96
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:4742 original size:21 final size:21
Alignment explanation
Indices: 4716--4761 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4706 TAGCTCTTGC
* * *
4716 TCTTCATTGGGCCTAATGGCA
1 TCTTCAATGGACCAAATGGCA
*
4737 TCTTCAATGGATCAAATGGCA
1 TCTTCAATGGACCAAATGGCA
4758 TCTT
1 TCTT
4762 AGGCAATTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (21 bp):
TCTTCAATGGACCAAATGGCA
Found at i:4793 original size:21 final size:21
Alignment explanation
Indices: 4769--4902 Score: 207
Period size: 21 Copynumber: 6.4 Consensus size: 21
4759 CTTAGGCAAT
* *
4769 TCCAATGAGCGTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4790 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
4811 TCCAATGAGCTTGGAACTTTC
1 TCCAATGAGCTTGGAACCTTC
*
4832 TCCAATGAGCTTGGAACCTTT
1 TCCAATGAGCTTGGAACCTTC
4853 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
4874 TCCACTGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
4895 TCCAATGA
1 TCCAATGA
4903 ACTACAAGCA
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 3 0.03
21 101 0.97
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Done.