Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016774.1 Corchorus olitorius cultivar O-4 contig16807, 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: 10059
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Found at i:545 original size:21 final size:21
Alignment explanation
Indices: 521--577 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
511 ACTAAACATC
521 TGAGGCAGGCACAAGAAGAAA
1 TGAGGCAGGCACAAGAAGAAA
* ** * * *
542 TGAGACATTCGCAAGATGAGA
1 TGAGGCAGGCACAAGAAGAAA
*
563 TGAGGCAGGAACAAG
1 TGAGGCAGGCACAAG
578 GTGTTATAAA
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.14, G:0.33, T:0.11
Consensus pattern (21 bp):
TGAGGCAGGCACAAGAAGAAA
Found at i:8718 original size:54 final size:54
Alignment explanation
Indices: 8631--8739 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
8621 GAAACAGGTG
* *
8631 TTCAGATGATCCAGTGCGATCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
1 TTCAAATGATCCAGTGCGATCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
* * *
8685 TTCAAATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGATGATTAGAGTTGATC
1 TTCAAATGATCCAGTGCGATCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
8739 T
1 T
8740 CGTTTCAAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (54 bp):
TTCAAATGATCCAGTGCGATCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
Found at i:8749 original size:35 final size:35
Alignment explanation
Indices: 8704--9090 Score: 494
Period size: 35 Copynumber: 11.0 Consensus size: 35
8694 TCCAGTGCGG
* *
8704 TCATTCCAAGAAGTTTTCGATGATTAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
*
8739 TCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
8774 TCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* **
8809 TTC-TTTCAGGAAGTTTTTTTTATGATCAGAGTTGATC
1 -TCATTTCAAGAAG--TTTTCGATGATCAGAGTTGATC
** **
8846 TCATTTTCAAG-TTTTTTTTATGATCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTTCGATGATCAGAGTTGATC
*
8881 TTATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
8916 TCGTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * **
8951 TCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
*
8986 TCATTTTCAAGATGTTTT--ATGATCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
9020 TCATTTCAAGAAGTTTGCGGTGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
*
9055 TCATTTCAAGAAGTTTTCGGTGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
9090 T
1 T
9091 TCACATTGAT
Statistics
Matches: 314, Mismatches: 29, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
33 12 0.04
34 26 0.08
35 235 0.75
36 16 0.05
37 19 0.06
38 6 0.02
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
Found at i:8884 original size:18 final size:18
Alignment explanation
Indices: 8828--8884 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
8818 GAAGTTTTTT
8828 TTATGATCAGAGTTGATC
1 TTATGATCAGAGTTGATC
* ** ** *
8846 TCATTTTCA-AGTTTTTT
1 TTATGATCAGAGTTGATC
8863 TTATGATCAGAGTTGATC
1 TTATGATCAGAGTTGATC
8881 TTAT
1 TTAT
8885 TTCAAGAAGT
Statistics
Matches: 26, Mismatches: 12, Indels: 2
0.65 0.30 0.05
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.49
Consensus pattern (18 bp):
TTATGATCAGAGTTGATC
Found at i:8960 original size:142 final size:139
Alignment explanation
Indices: 8723--9090 Score: 610
Period size: 142 Copynumber: 2.6 Consensus size: 139
8713 GAAGTTTTCG
* *
8723 ATGATTAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGT
1 ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGT
*
8788 TTTCGGTGATCAGAGTTGATCTTCTTTCAGGAAGTTTTTTTTATGATCAGAGTTGATCTCATTTT
66 TTTCGGTGATCAGAGTTGATCTCCTTTCAGGAAG--TTTTTTATGATCAGAGTTGATCTCATTTT
* *
8853 CAAGTTTTTTTT
129 CAAG-ATGTTTT
*
8865 ATGATCAGAGTTGATCTTATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGT
1 ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGT
* *
8930 TTTTGATGATCAGAGTTGATCTCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATCTCATTTTCA
66 TTTCGGTGATCAGAGTTGATCTCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATCTCATTTTCA
8995 AGATGTTTT
131 AGATGTTTT
* * *
9004 ATGATCAGAGTTGATCTCATTTCAAGAAGTTTGCGGTGATCAGAGTTGATCTCATTTCAAGAAGT
1 ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGT
9069 TTTCGGTGATCAGAGTTGATCT
66 TTTCGGTGATCAGAGTTGATCT
9091 TCACATTGAT
Statistics
Matches: 212, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
139 86 0.41
140 33 0.16
142 93 0.44
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.41
Consensus pattern (139 bp):
ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGT
TTTCGGTGATCAGAGTTGATCTCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATCTCATTTTCA
AGATGTTTT
Done.