Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014803.1 Corchorus olitorius cultivar O-4 contig14836, 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: 36872
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Found at i:6101 original size:30 final size:30
Alignment explanation
Indices: 6030--6102 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
6020 AATAAAATTA
* *
6030 TGGCAAAGCCCATTGAAAACTGCAAATCCG
1 TGGCAAAGCCCGTTGAAAACTGCAAAACCG
6060 TGGCAAAGCCCGTTGAAAACT-CTAAAACCG
1 TGGCAAAGCCCGTTGAAAACTGC-AAAACCG
*
6090 TGGCAAGGCCCGT
1 TGGCAAAGCCCGT
6103 CGCCAACTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 1 0.03
30 38 0.97
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.16
Consensus pattern (30 bp):
TGGCAAAGCCCGTTGAAAACTGCAAAACCG
Found at i:8004 original size:76 final size:76
Alignment explanation
Indices: 7910--8061 Score: 191
Period size: 76 Copynumber: 2.0 Consensus size: 76
7900 TGATGAGCTA
* * *
7910 TGACACAGCCCATCTGGGTGATCAGGCGAAA-CACATGGGT-CTTAAGACAAACCATGTGGGCAC
1 TGACACAGCCCACCTGGGTGATCAAGC-AAACCACATGGGTGCTCAAGAC-AACCATGTGGGCAC
7973 CCAGCTGGAGTCG
64 CCAGCTGGAGTCG
* ** * *
7986 TGACACTGCCCACCTGGGTTCTCAAGCAAACCACATGGGTGCTCAAGGCAACCATGTGGGCGCCC
1 TGACACAGCCCACCTGGGTGATCAAGCAAACCACATGGGTGCTCAAGACAACCATGTGGGCACCC
*
8051 AGGTGGAGTCG
66 AGCTGGAGTCG
8062 GGGTCCTTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
75 3 0.05
76 56 0.86
77 6 0.09
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.17
Consensus pattern (76 bp):
TGACACAGCCCACCTGGGTGATCAAGCAAACCACATGGGTGCTCAAGACAACCATGTGGGCACCC
AGCTGGAGTCG
Found at i:12800 original size:21 final size:21
Alignment explanation
Indices: 12775--12826 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
12765 GCAAATAATC
*
12775 TTTTCAATTTGGTCCTTACAT
1 TTTTCAATTTGATCCTTACAT
12796 TTTTCAATTTGATCCTTACAT
1 TTTTCAATTTGATCCTTACAT
12817 TTTTCAATTT
1 TTTTCAATTT
12827 TTCAATTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.17, G:0.06, T:0.56
Consensus pattern (21 bp):
TTTTCAATTTGATCCTTACAT
Found at i:13606 original size:23 final size:24
Alignment explanation
Indices: 13580--13635 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
13570 ATATATATAT
13580 ATGCAA-AGGACAAAAAAGAAACC
1 ATGCAAGAGGACAAAAAAGAAACC
* *
13603 ATGCACAAGAGGACAAAGAAGAGACC
1 ATG--CAAGAGGACAAAAAAGAAACC
13629 ATGCAAG
1 ATGCAAG
13636 CACGGTACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 3 0.11
24 4 0.14
25 3 0.11
26 18 0.64
ACGTcount: A:0.54, C:0.18, G:0.23, T:0.05
Consensus pattern (24 bp):
ATGCAAGAGGACAAAAAAGAAACC
Found at i:20184 original size:29 final size:30
Alignment explanation
Indices: 20120--20186 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
20110 GGCTTCGTCT
* * * *
20120 TGGACATTGGCACATGAACAATGAACGTCC
1 TGGACATTGCCAAATGAACAACGAACGCCC
20150 TGGACATTGCCAAATGAAC-ACGAACGCCC
1 TGGACATTGCCAAATGAACAACGAACGCCC
20179 TGGACATT
1 TGGACATT
20187 ACCATCGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.19
Consensus pattern (30 bp):
TGGACATTGCCAAATGAACAACGAACGCCC
Found at i:20209 original size:29 final size:29
Alignment explanation
Indices: 20142--20212 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
20132 CATGAACAAT
* *
20142 GAACGTCCTGGACATTGCCAAATGAACAC
1 GAACGTCCTGGACATTACCAAAGGAACAC
* **
20171 GAACGCCCTGGACATTACCATCGGAACAC
1 GAACGTCCTGGACATTACCAAAGGAACAC
**
20200 GTTCGTCCTGGAC
1 GAACGTCCTGGAC
20213 TTCGCCACAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (29 bp):
GAACGTCCTGGACATTACCAAAGGAACAC
Found at i:28739 original size:6 final size:6
Alignment explanation
Indices: 28728--28752 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28718 GTGGCTCAAT
28728 ATGATC ATGATC ATGATC ATGATC A
1 ATGATC ATGATC ATGATC ATGATC A
28753 GTTTGGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
ATGATC
Done.