Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000900.1 Corchorus capsularis cultivar CVL-1 contig00900, 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: 6203
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3142 original size:31 final size:31
Alignment explanation
Indices: 3103--3237 Score: 141
Period size: 31 Copynumber: 4.4 Consensus size: 31
3093 TTAATTTGGC
*
3103 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATACT
* * * * ** **
3134 TAAATAAGGGCCCGATC-TT-T-TAATTTGGT
1 CAAATAAGGG-CCTAACGTTATCGAAAATACT
*
3163 CAAATAAGGGCCTAACATTATCGAAAATACT
1 CAAATAAGGGCCTAACGTTATCGAAAATACT
*
3194 CAAATAAGGGCCTAATGTTATCGAAAATACT
1 CAAATAAGGGCCTAACGTTATCGAAAATACT
3225 CAAATAAGGGCCT
1 CAAATAAGGGCCT
3238 GGTGTCAATT
Statistics
Matches: 83, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
28 4 0.05
29 16 0.19
30 2 0.02
31 57 0.69
32 4 0.05
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATACT
Found at i:3157 original size:60 final size:60
Alignment explanation
Indices: 3042--3205 Score: 231
Period size: 60 Copynumber: 2.7 Consensus size: 60
3032 GCTAATTGCT
* * *
3042 CAAATAAGGGTCTAATGTT-TGCCAAAATGCTAAAATAAGGGTCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTAAAATAAGGG-CCCGATCTTTTAATTTGGC
* *
3103 CAAATAAGGGCCTAACGTTATCGAAAATGCTTAAATAAGGGCCCGATCTTTTAATTTGGT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTAAAATAAGGGCCCGATCTTTTAATTTGGC
* * *
3163 CAAATAAGGGCCTAACATTATCGAAAATACTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTAAAATAAGGGCC
3206 TAATGTTATC
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
60 58 0.62
61 35 0.37
62 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTAAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:3302 original size:31 final size:31
Alignment explanation
Indices: 3267--3432 Score: 132
Period size: 31 Copynumber: 5.5 Consensus size: 31
3257 CGTGAGACAA
*
3267 GCCCTTATTTGAGCATTTTGGCAAATGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
** **
3298 GCCCTTATTTG-GCCAAATT--CAAA-GATGGG
1 GCCCTTATTTGAG-CATTTTGGCAAACG-TTAG
* *
3327 GCCCTTATTTGAACATTTTGGAAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
** * *
3358 GCCCTTATTTG-GCCAAATT---AAAAGATCAG
1 GCCCTTATTTGAG-CATTTTGGCAAACG-TTAG
3387 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
*
3418 GTCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
3433 ATTAGCCGAT
Statistics
Matches: 103, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 5 0.05
29 39 0.38
30 2 0.02
31 52 0.50
32 5 0.05
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAG
Found at i:3334 original size:60 final size:60
Alignment explanation
Indices: 3267--3428 Score: 261
Period size: 60 Copynumber: 2.7 Consensus size: 60
3257 CGTGAGACAA
* * **
3267 GCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTCAAAGATGGG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
* *
3327 GCCCTTATTTGAACATTTTGGAAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
*
3387 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGTCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
3429 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
Found at i:3390 original size:29 final size:29
Alignment explanation
Indices: 3296--3397 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
3286 GGCAAATGTT
* *
3296 AGGCCCTTATTTGGCCAAATTCAAAGATG
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
* ** ** *
3325 GGGCCCTTATTTGAACATTTTGGAAAACG-TT
1 AGGCCCTTATTTGGCCAAATT--AAAA-GATC
3356 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
3385 AGGCCCTTATTTG
1 AGGCCCTTATTTG
3398 AGCATTTTGG
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
28 1 0.02
29 34 0.61
31 20 0.36
32 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:5585 original size:15 final size:15
Alignment explanation
Indices: 5567--5607 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
5557 TCGATTATTA
5567 ATAAAAAATAAAATT
1 ATAAAAAATAAAATT
5582 ATAAAAAGA-AAAATT
1 ATAAAAA-ATAAAATT
5597 ATAAAAGAATA
1 ATAAAA-AATA
5608 TATTAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (15 bp):
ATAAAAAATAAAATT
Done.