Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016441.1 Corchorus capsularis cultivar CVL-1 contig16462, 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: 7830
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Found at i:69 original size:24 final size:24
Alignment explanation
Indices: 37--84 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
27 TTTAAAAAAA
*
37 TCTAAATAGCGGCGTCTCGACGCC
1 TCTAAATAGCGGCGTCTAGACGCC
61 TCTAAATAGCGGCGTCTAGACGCC
1 TCTAAATAGCGGCGTCTAGACGCC
85 GCTGTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.21
Consensus pattern (24 bp):
TCTAAATAGCGGCGTCTAGACGCC
Found at i:281 original size:31 final size:31
Alignment explanation
Indices: 246--320 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
236 GCGCCTTGTC
246 AGACGCCGCTATTCTAAATAGCGGCGTTTTT
1 AGACGCCGCTATTCTAAATAGCGGCGTTTTT
277 AGACGCCGCTATTCTAAATAGCGGCGTTTTT
1 AGACGCCGCTATTCTAAATAGCGGCGTTTTT
*
308 AAACGCCGCTATT
1 AGACGCCGCTATT
321 TTACTGTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (31 bp):
AGACGCCGCTATTCTAAATAGCGGCGTTTTT
Found at i:2902 original size:19 final size:18
Alignment explanation
Indices: 2869--2904 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2859 TTGAAATAAT
2869 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
2887 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
2905 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:4378 original size:21 final size:20
Alignment explanation
Indices: 4348--4400 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
4338 ACTAGCGCTG
*
4348 GGCGCCCATGTGGTATGCTT
1 GGCGCCCATGTGGTATGCCT
*
4368 GGCGCCCCATGTGGTTTGCCT
1 GGCG-CCCATGTGGTATGCCT
*
4389 CGCGACCCATGT
1 GGCG-CCCATGT
4401 ACTCCAGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.09, C:0.32, G:0.32, T:0.26
Consensus pattern (20 bp):
GGCGCCCATGTGGTATGCCT
Found at i:6467 original size:33 final size:33
Alignment explanation
Indices: 6442--6527 Score: 165
Period size: 33 Copynumber: 2.6 Consensus size: 33
6432 GCCGGTTGTA
6442 GCCGGACATGTCCATGTCGCGTGGCCGGTGATG
1 GCCGGACATGTCCATGTCGCGTGGCCGGTGATG
6475 GCCGGACATGTCCATGTCGCGTGGCCGGTGATG
1 GCCGGACATGTCCATGTCGCGTGGCCGGTGATG
6508 GCCGGACATGTCCATG-CGCG
1 GCCGGACATGTCCATGTCGCG
6528 GCTTCTCCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 4 0.08
33 49 0.92
ACGTcount: A:0.13, C:0.29, G:0.38, T:0.20
Consensus pattern (33 bp):
GCCGGACATGTCCATGTCGCGTGGCCGGTGATG
Found at i:6477 original size:66 final size:65
Alignment explanation
Indices: 6396--6527 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 65
6386 AAAGGGTTGT
* **
6396 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCGTTTGGCCGGTTG-TAGCCGGACATGTCCATGT
1 GTGGCCGGTTGTGGCCGGACATGGCC-ATGTCGCGTGGCCGG-TGATAGCCGGACATGTCCATG-
6459 CGC
63 CGC
* *
6462 GTGGCCGG-TGATGGCCGGACATGTCCATGTCGCGTGGCCGGTGATGGCCGGACATGTCCATGCG
1 GTGGCCGGTTG-TGGCCGGACATGGCCATGTCGCGTGGCCGGTGATAGCCGGACATGTCCATGCG
6526 C
65 C
6527 G
1 G
6528 GCTTCTCCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
65 9 0.16
66 49 0.84
ACGTcount: A:0.11, C:0.27, G:0.41, T:0.22
Consensus pattern (65 bp):
GTGGCCGGTTGTGGCCGGACATGGCCATGTCGCGTGGCCGGTGATAGCCGGACATGTCCATGCGC
Done.