Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019512.1 Corchorus olitorius cultivar O-4 contig19545, 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: 13435
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:136 original size:42 final size:42
Alignment explanation
Indices: 90--175 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
80 CTAAATGAGA
* * * *
90 AACAAATTATAAACAAGCTCATATTCCGTGAGAGTTGAACCT
1 AACAAATTACAAACAAACTCACATTCCGTGAGAATTGAACCT
*
132 AACAAATTACAAACAAACTCACATTGCGTGAGAATTGAACCT
1 AACAAATTACAAACAAACTCACATTCCGTGAGAATTGAACCT
174 AA
1 AA
176 GACCTCTTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (42 bp):
AACAAATTACAAACAAACTCACATTCCGTGAGAATTGAACCT
Found at i:5859 original size:21 final size:21
Alignment explanation
Indices: 5835--5884 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
5825 AGTGCTTAGG
5835 TGCCAGAACAGAGCAAATGTT
1 TGCCAGAACAGAGCAAATGTT
5856 TGCCAGAACAGAGCAAATGTT
1 TGCCAGAACAGAGCAAATGTT
5877 TGCCAGAA
1 TGCCAGAA
5885 GTTGAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (21 bp):
TGCCAGAACAGAGCAAATGTT
Found at i:10421 original size:28 final size:28
Alignment explanation
Indices: 10390--10465 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
10380 TTAAGATGTC
*
10390 AAAATTACTGTTTTACCCTTGGTCAACT
1 AAAATTACAGTTTTACCCTTGGTCAACT
* **
10418 AAAATTACCA-TTTTACCCCTGGTTGACT
1 AAAATTA-CAGTTTTACCCTTGGTCAACT
*
10446 -AAATTACAGTTTTGCCCTTG
1 AAAATTACAGTTTTACCCTTG
10466 AATGCCGGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.05
27 15 0.38
28 22 0.55
29 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (28 bp):
AAAATTACAGTTTTACCCTTGGTCAACT
Found at i:12044 original size:160 final size:160
Alignment explanation
Indices: 11780--12090 Score: 595
Period size: 160 Copynumber: 1.9 Consensus size: 160
11770 GCAAACTTCA
*
11780 GTATTTCAGATTTATTACTTAGTTCATGTTTTCGGTATTTTTTTATCTGGTATTGACGCTTCGTG
1 GTATTTCAGATTTATTACTCAGTTCATGTTTTCGGTATTTTTTTATCTGGTATTGACGCTTCGTG
11845 GAACCTCGGTGCGCGTGACCGGCCGACACGTGTTTCGAGGTAACATGGCGGTTGTCCGTGCTCGA
66 GAACCTCGGTGCGCGTGACCGGCCGACACGTGTTTCGAGGTAACATGGCGGTTGTCCGTGCTCGA
11910 CTTCCGGGTCGGGGCGTGACAATTTTATTG
131 CTTCCGGGTCGGGGCGTGACAATTTTATTG
11940 GTATTTCAGATTTATTACTCAGTTCATGTTTTCGGTATTTTTTTATCTGGTATTGACGCTTCGTG
1 GTATTTCAGATTTATTACTCAGTTCATGTTTTCGGTATTTTTTTATCTGGTATTGACGCTTCGTG
* *
12005 GAACCTCGGTGCGTGTGACCGGCCGGCACGTGTTTCGAGGTAACATGGCGGTTGTCCGTGCTCGA
66 GAACCTCGGTGCGCGTGACCGGCCGACACGTGTTTCGAGGTAACATGGCGGTTGTCCGTGCTCGA
12070 CTTCCGGGTCGGGGCGTGACA
131 CTTCCGGGTCGGGGCGTGACA
12091 GCTCGTTTGC
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 148 1.00
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (160 bp):
GTATTTCAGATTTATTACTCAGTTCATGTTTTCGGTATTTTTTTATCTGGTATTGACGCTTCGTG
GAACCTCGGTGCGCGTGACCGGCCGACACGTGTTTCGAGGTAACATGGCGGTTGTCCGTGCTCGA
CTTCCGGGTCGGGGCGTGACAATTTTATTG
Found at i:13336 original size:19 final size:19
Alignment explanation
Indices: 13308--13348 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13298 CACCTGCGAA
*
13308 AATAATTAATGAAT-ACATT
1 AATAAATAAT-AATAACATT
13327 AATAAATAATAATAACATT
1 AATAAATAATAATAACATT
13346 AAT
1 AAT
13349 TAATTAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
AATAAATAATAATAACATT
Done.