Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020547.1 Corchorus olitorius cultivar O-4 contig20580, 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: 14874
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:248 original size:27 final size:27
Alignment explanation
Indices: 192--359 Score: 169
Period size: 27 Copynumber: 6.3 Consensus size: 27
182 AGTGAACTTA
* * * **
192 AAATGACCGAAATG-CCCTTAGTGTAA
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
218 AAATGACCAAGATGCCCCTGAATGTGT
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
245 AAATGACCAAAATGCCCCTGGATATGC
1 AAATGACCAAAATGCCCCTGAATGTGC
* * **
272 AAATGACCAAAATG-CCCTTAGTGTAA
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
298 AAATGACCAAGATGCCCCTGAATGTGT
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
325 AAATGACCAAAATGCCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGAATGTGC
352 AAATGACC
1 AAATGACC
360 CCAAAACCCC
Statistics
Matches: 115, Mismatches: 25, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
26 31 0.27
27 84 0.73
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATGTGC
Found at i:258 original size:53 final size:53
Alignment explanation
Indices: 191--359 Score: 151
Period size: 53 Copynumber: 3.2 Consensus size: 53
181 CAGTGAACTT
* * *
191 AAAATGACCGAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCTTAGTGTGAAAATGACCAAAATGCCCCTGAATGTG
* * * * * * * *
244 TAAATGACCAAAATGCCCCTGGATATGCAAATGACCAAAATG-CCCTTAGTGTA
1 AAAATGACCAAAATGCCCTTAG-TGTGAAAATGACCAAAATGCCCCTGAATGTG
* * * * * *
297 AAAATGACCAAGATGCCCCTGAATGTGTAAATGACCAAAATGCCCCTGGACGTG
1 AAAATGACCAAAATG-CCCTTAGTGTGAAAATGACCAAAATGCCCCTGAATGTG
*
351 CAAATGACC
1 AAAATGACC
360 CCAAAACCCC
Statistics
Matches: 88, Mismatches: 25, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
53 56 0.64
54 32 0.36
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (53 bp):
AAAATGACCAAAATGCCCTTAGTGTGAAAATGACCAAAATGCCCCTGAATGTG
Found at i:325 original size:80 final size:80
Alignment explanation
Indices: 192--359 Score: 309
Period size: 80 Copynumber: 2.1 Consensus size: 80
182 AGTGAACTTA
*
192 AAATGACCGAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTGTAAATGACCAAAA
1 AAATGACCAAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTGTAAATGACCAAAA
*
257 TGCCCCTGGATATGC
66 TGCCCCTGGACATGC
272 AAATGACCAAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTGTAAATGACCAAAA
1 AAATGACCAAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTGTAAATGACCAAAA
*
337 TGCCCCTGGACGTGC
66 TGCCCCTGGACATGC
352 AAATGACC
1 AAATGACC
360 CCAAAACCCC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 85 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (80 bp):
AAATGACCAAAATGCCCTTAGTGTAAAAATGACCAAGATGCCCCTGAATGTGTAAATGACCAAAA
TGCCCCTGGACATGC
Found at i:10846 original size:45 final size:44
Alignment explanation
Indices: 10797--10887 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 44
10787 CCAATTTTAA
10797 TTAATTTTAAATTTATTATTATTATTATAATTTTTTTACACTAAT
1 TTAATTTTAAATTTATTATTATTATTATAA-TTTTTTACACTAAT
10842 TTAATTTTAAATTTATTATTATTATTATAATTTTTTACACTAAT
1 TTAATTTTAAATTTATTATTATTATTATAATTTTTTACACTAAT
10886 TT
1 TT
10888 CTCTTTGAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 16 0.35
45 30 0.65
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (44 bp):
TTAATTTTAAATTTATTATTATTATTATAATTTTTTACACTAAT
Found at i:11194 original size:38 final size:39
Alignment explanation
Indices: 11147--11221 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
11137 AACACTAGCA
* ** * *
11147 GCCGTGACAGGCTTCTATCAGCAGCGAG-TTGCTGCTTT
1 GCCGCGACAGGCCGCTAGCAGCAGCGAGCCTGCTGCTTT
11185 GCCGCGACAGGCCGCTAGCAGCAGCGAGCCTGCTGCT
1 GCCGCGACAGGCCGCTAGCAGCAGCGAGCCTGCTGCT
11222 GTTCTTGCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 24 0.77
39 7 0.23
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.20
Consensus pattern (39 bp):
GCCGCGACAGGCCGCTAGCAGCAGCGAGCCTGCTGCTTT
Found at i:14425 original size:19 final size:18
Alignment explanation
Indices: 14401--14436 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14391 TGAAGACTTA
14401 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
14420 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
14437 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.