Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016457.1 Corchorus capsularis cultivar CVL-1 contig16478, 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: 7558
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1653 original size:27 final size:27
Alignment explanation
Indices: 1576--1653 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
1566 GTGATTCTTA
* *
1576 AAAAATGACTAAAATGCCCCTGAGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
1603 AAAAATGACCAAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
* *
1630 AAAAATGACCAAAATACCCTTGGG
1 AAAAATGACCAAAATGCCCCTGGG
1654 CGACTCTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGGGTGC
Found at i:3404 original size:14 final size:14
Alignment explanation
Indices: 3385--3411 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3375 AGACTAGCCG
3385 ATTGGTCTAAAATT
1 ATTGGTCTAAAATT
3399 ATTGGTCTAAAAT
1 ATTGGTCTAAAAT
3412 AATTTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
ATTGGTCTAAAATT
Found at i:4844 original size:31 final size:31
Alignment explanation
Indices: 4806--4973 Score: 116
Period size: 31 Copynumber: 5.5 Consensus size: 31
4796 TAAGGCTAAT
4806 TGCTCAAATAAGGGCCTAACATTTTCCAAAA
1 TGCTCAAATAAGGGCCTAACATTTTCCAAAA
** * **
4837 TGCTCAAATAAGGATCTGATC-TTTT--AATT
1 TGCTCAAATAAGGGCCT-AACATTTTCCAAAA
* *
4866 TAGC-CAAATAAGGGCCTAAAATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACATTTTCCAAAA
* * * **
4897 TGCTCCAATAAGGGCCCAACCTTTT--AATT
1 TGCTCAAATAAGGGCCTAACATTTTCCAAAA
** * *
4926 TGGC-CAAATAAGGATCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACATTTTCCAAAA
4957 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
4974 CGCATCGAAA
Statistics
Matches: 98, Mismatches: 29, Indels: 20
0.67 0.20 0.14
Matches are distributed among these distances:
28 1 0.01
29 35 0.36
30 8 0.08
31 52 0.53
32 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACATTTTCCAAAA
Found at i:4970 original size:60 final size:60
Alignment explanation
Indices: 4810--4972 Score: 218
Period size: 60 Copynumber: 2.7 Consensus size: 60
4800 GCTAATTGCT
* ** ** *
4810 CAAATAAGGGCCTAACATTTTCCAAAATGCTCAAATAAGGATCTGATCTTTTAATTTAGC
1 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCCCAACCTTTTAATTTAGC
* * *
4870 CAAATAAGGGCCTAAAATTTGCCAAAATGCTCCAATAAGGGCCCAACCTTTTAATTTGGC
1 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCCCAACCTTTTAATTTAGC
** *
4930 CAAATAAGGATCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCC
4973 TCGCATCGAA
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 89 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCCCAACCTTTTAATTTAGC
Found at i:5052 original size:31 final size:31
Alignment explanation
Indices: 5014--5146 Score: 137
Period size: 31 Copynumber: 4.4 Consensus size: 31
5004 CTGACGCCAT
*
5014 GCCCTTATTTGAGCATTTTTGATAACATTAG
1 GCCCTTATTTGAGCATTTTCGATAACATTAG
*
5045 GCCCTTATTTGAGCATTTTCGATAACGTTAG
1 GCCCTTATTTGAGCATTTTCGATAACATTAG
* ** * * **
5076 ACCCTTATTTG-GCCAAATT--AAAAGATCGG
1 GCCCTTATTTGAG-CATTTTCGATAACATTAG
*
5105 GCCCTTATTTGAGCATTTTCGATAACGTTAG
1 GCCCTTATTTGAGCATTTTCGATAACATTAG
*
5136 GTCCTTATTTG
1 GCCCTTATTTG
5147 GCCAAATTAA
Statistics
Matches: 79, Mismatches: 19, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
29 19 0.24
30 2 0.03
31 58 0.73
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (31 bp):
GCCCTTATTTGAGCATTTTCGATAACATTAG
Found at i:5113 original size:60 final size:60
Alignment explanation
Indices: 5044--5206 Score: 267
Period size: 60 Copynumber: 2.7 Consensus size: 60
5034 GATAACATTA
5044 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
**
5104 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGTCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
*
5164 GGCCCTTATTTGAGCATTTTGGCA-AACGTT-GAGCCCTTATTTG
1 GGCCCTTATTTGAGCATTTTCG-ATAACGTTAGA-CCCTTATTTG
5207 AGCAATTAGC
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
59 1 0.01
60 94 0.98
61 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
Found at i:5115 original size:29 final size:29
Alignment explanation
Indices: 5077--5175 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
5067 TAACGTTAGA
5077 CCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGG
** * **
5106 CCCTTATTTGAG-CATTTTCGATAACG-TTAGG
1 CCCTTATTTG-GCCAAATT--A-AAAGATCGGG
*
5137 TCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGG
5166 CCCTTATTTG
1 CCCTTATTTG
5176 AGCATTTTGG
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 3 0.06
29 27 0.52
30 2 0.04
31 17 0.33
32 3 0.06
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCGGG
Done.