Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024677.1 Corchorus olitorius cultivar O-4 contig24710, 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: 13949
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:229 original size:23 final size:23
Alignment explanation
Indices: 198--241 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
188 GCCGACATGG
* *
198 TTGCCTTGAGCACCCATGTGGTT
1 TTGCCTTGAGAACCCAGGTGGTT
*
221 TTGCTTTGAGAACCCAGGTGG
1 TTGCCTTGAGAACCCAGGTGG
242 GCAGTGTCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.32
Consensus pattern (23 bp):
TTGCCTTGAGAACCCAGGTGGTT
Found at i:1307 original size:28 final size:26
Alignment explanation
Indices: 1252--1301 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1242 ATGATTTAGG
*
1252 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACACCCTTTTTCTTTTGA
* *
1278 GGTTACTAACACTCTTTTTTTTTT
1 GGTTACTAACACCCTTTTTCTTTT
1302 CAGAGGGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.54
Consensus pattern (26 bp):
GGTTACTAACACCCTTTTTCTTTTGA
Found at i:5019 original size:9 final size:10
Alignment explanation
Indices: 4986--5030 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
4976 TAAAGAGAAT
4986 TATGTGAAGG
1 TATGTGAAGG
4996 TATGTGAAGG
1 TATGTGAAGG
5006 TATGTGAA-G
1 TATGTGAAGG
5015 TATGTG-AGG
1 TATGTGAAGG
5024 TATGTGA
1 TATGTGA
5031 TTTGTGTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 1 0.03
9 14 0.42
10 18 0.55
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (10 bp):
TATGTGAAGG
Found at i:5026 original size:18 final size:20
Alignment explanation
Indices: 4986--5030 Score: 76
Period size: 18 Copynumber: 2.4 Consensus size: 20
4976 TAAAGAGAAT
4986 TATGTGAAGGTATGTGAAGG
1 TATGTGAAGGTATGTGAAGG
5006 TATGTGAA-GTATGTG-AGG
1 TATGTGAAGGTATGTGAAGG
5024 TATGTGA
1 TATGTGA
5031 TTTGTGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 10 0.40
19 7 0.28
20 8 0.32
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (20 bp):
TATGTGAAGGTATGTGAAGG
Found at i:7472 original size:21 final size:21
Alignment explanation
Indices: 7446--7491 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
7436 CGGGTATGTG
**
7446 ACGGGCATGGCCGGTGGTGGC
1 ACGGGCATAACCGGTGGTGGC
*
7467 ACGGGCTTAACCGGTGGTGGC
1 ACGGGCATAACCGGTGGTGGC
7488 ACGG
1 ACGG
7492 TGGATGGTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.24, G:0.48, T:0.15
Consensus pattern (21 bp):
ACGGGCATAACCGGTGGTGGC
Found at i:10631 original size:14 final size:15
Alignment explanation
Indices: 10612--10643 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
10602 AGCTTCCTAG
10612 AAAAACTAAAAA-AA
1 AAAAACTAAAAAGAA
10626 AAAAACTAAAAAGAA
1 AAAAACTAAAAAGAA
10641 AAA
1 AAA
10644 TTGTTAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (15 bp):
AAAAACTAAAAAGAA
Found at i:11133 original size:15 final size:16
Alignment explanation
Indices: 11109--11148 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
11099 AGAGGTTGAA
*
11109 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
11124 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
11140 AGAAAACAA
1 AGAAAACAA
11149 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:11951 original size:10 final size:10
Alignment explanation
Indices: 11936--11970 Score: 56
Period size: 9 Copynumber: 3.7 Consensus size: 10
11926 TAAAGAGAAT
11936 TATGTGAAGG
1 TATGTGAAGG
11946 TATGTGAA-G
1 TATGTGAAGG
11955 TATGTG-AGG
1 TATGTGAAGG
11964 TATGTGA
1 TATGTGA
11971 TTTGTGTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.04
9 14 0.61
10 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.34
Consensus pattern (10 bp):
TATGTGAAGG
Found at i:13889 original size:76 final size:76
Alignment explanation
Indices: 13752--13903 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
13742 ACAAGGACCC
* * *
13752 CGACTCCACCTGGGCGCCGACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
13817 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
13828 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
13890 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
13904 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.29, G:0.30, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.