Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006116.1 Corchorus capsularis cultivar CVL-1 contig06134, 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: 20043
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1236 original size:1 final size:1
Alignment explanation
Indices: 1225--1255 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
1215 TGTGTGTGTG
*
1225 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1256 CTCTCGTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:5033 original size:28 final size:30
Alignment explanation
Indices: 4974--5046 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 30
4964 CAAAAACTCG
* **
4974 TATGTTTGCATTGTTCTTTTTTTTTGAAAA
1 TATGTCTGCATTGTTCTTTTTTGATGAAAA
*
5004 TATGTCTGCATTGTT-TTTTTTGATG-GAA
1 TATGTCTGCATTGTTCTTTTTTGATGAAAA
5032 TATGTCTGCATTGTT
1 TATGTCTGCATTGTT
5047 ACACCTTAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 17 0.44
29 8 0.21
30 14 0.36
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (30 bp):
TATGTCTGCATTGTTCTTTTTTGATGAAAA
Found at i:10210 original size:26 final size:27
Alignment explanation
Indices: 10157--10210 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
10147 TTACTCAACT
***
10157 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTAAATGTAA
10184 AAAAACTCTATTTTTATTTAAAT-TAA
1 AAAAACTCTATTTTTATTTAAATGTAA
10210 A
1 A
10211 TCTAATATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTAAATGTAA
Found at i:15319 original size:105 final size:105
Alignment explanation
Indices: 15137--15349 Score: 408
Period size: 105 Copynumber: 2.0 Consensus size: 105
15127 GAGTAAAACG
15137 ATCTGTGAACTCACCGTTAACAACAACTGAAAAAGAAACTGAACGAACACAAAACATGATTAAAT
1 ATCTGTGAACTCACCGTTAACAACAACTGAAAAAGAAACTGAACGAACACAAAACATGATTAAAT
15202 CCACCCATTTACCATCAAAACCCAAGCGTCACATTATAAC
66 CCACCCATTTACCATCAAAACCCAAGCGTCACATTATAAC
*
15242 ATCTGTGAACTCACCGTTAACAACAACTGAAAAAGAAACTGAACGAACTCAAAACATGATTAAAT
1 ATCTGTGAACTCACCGTTAACAACAACTGAAAAAGAAACTGAACGAACACAAAACATGATTAAAT
*
15307 CCACCCATTTACCATCAAAACCCAAGCGTCGCATTATAAC
66 CCACCCATTTACCATCAAAACCCAAGCGTCACATTATAAC
15347 ATC
1 ATC
15350 CAGAAAATCC
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.20
Consensus pattern (105 bp):
ATCTGTGAACTCACCGTTAACAACAACTGAAAAAGAAACTGAACGAACACAAAACATGATTAAAT
CCACCCATTTACCATCAAAACCCAAGCGTCACATTATAAC
Found at i:15892 original size:22 final size:22
Alignment explanation
Indices: 15864--15909 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
15854 CAAAACTGAA
15864 TTAATTTATAATTTTTTTAGTT
1 TTAATTTATAATTTTTTTAGTT
15886 TTAATTTATAATTTTTTTAGTT
1 TTAATTTATAATTTTTTTAGTT
15908 TT
1 TT
15910 GCTGTACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
TTAATTTATAATTTTTTTAGTT
Found at i:18073 original size:27 final size:26
Alignment explanation
Indices: 17989--18078 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 26
17979 CCAAGGGGGT
17989 TATGGAGGGTACGGTGGACGTGGAGG
1 TATGGAGGGTACGGTGGACGTGGAGG
*
18015 TAACGGAGGGTACGGTGGACGTGGAGG
1 T-ATGGAGGGTACGGTGGACGTGGAGG
* *
18042 TTATGGAGGGTACGGTGGCCGTGGCGG
1 -TATGGAGGGTACGGTGGACGTGGAGG
18069 CTATGGAGGG
1 -TATGGAGGG
18079 CGCGGTGGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
26 1 0.02
27 55 0.96
28 1 0.02
ACGTcount: A:0.18, C:0.11, G:0.52, T:0.19
Consensus pattern (26 bp):
TATGGAGGGTACGGTGGACGTGGAGG
Found at i:18112 original size:18 final size:18
Alignment explanation
Indices: 18045--18114 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 18
18035 GTGGAGGTTA
*
18045 TGGAGGGTACGGTGGCCG
1 TGGAGGGTACGGTGGACG
* * * * *
18063 TGGCGGCTATGGAGGGCG
1 TGGAGGGTACGGTGGACG
* *
18081 CGGTGGGTACGGTGGACG
1 TGGAGGGTACGGTGGACG
*
18099 TGGAGGGTATGGTGGA
1 TGGAGGGTACGGTGGA
18115 GGCTGCGCCT
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.13, C:0.13, G:0.56, T:0.19
Consensus pattern (18 bp):
TGGAGGGTACGGTGGACG
Done.