Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010681.1 Corchorus olitorius cultivar O-4 contig10713, 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: 17353
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Found at i:16012 original size:54 final size:54
Alignment explanation
Indices: 15888--16058 Score: 207
Period size: 54 Copynumber: 3.1 Consensus size: 54
15878 GTGCGGTCTT
* * * *
15888 TTGATCCTCAAATGATTCAGTGCGGTCATTCCAAGAAGTTTTTTTTTAAGGATCAGAG
1 TTGATACTCAGATGATCCAGTGCGGTCATTCCAAGAAG----TTTTTAATGATCAGAG
* * *
15946 TTGATCCTCAGATGATCCAGTGCGGTCATTCCAACAAGTTTTTAATGATTAGAG
1 TTGATACTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAGAG
* * * *
16000 TTGATATTCAGATGATCCAGTGCGGTCGTTTCAAGAAGTTTTCAATGATCAGAG
1 TTGATACTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAGAG
16054 TTGAT
1 TTGAT
16059 CTCGTTTCAA
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
54 66 0.65
58 35 0.35
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (54 bp):
TTGATACTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAGAG
Found at i:16389 original size:70 final size:69
Alignment explanation
Indices: 16028--16621 Score: 768
Period size: 69 Copynumber: 8.5 Consensus size: 69
16018 AGTGCGGTCG
* * *
16028 TTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTTA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTT-GATGATCAGAGTTGA
16093 TCT-A
65 TCTCA
*
16097 GTTTCAAGAAGTTTTCGATGATCAGAGTTGA--TCATTTTAAGAAGTTTTGATGATCAGAGTTGA
1 -TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTGATGATCAGAGTTGA
*
16160 TCTCC
65 TCTCA
* *
16165 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCACATTTTAAGAAGTTTTGATGATCAGAGTTGAT
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTGATGATCAGAGTTGAT
*
16230 CGCA
66 CTCA
* * * * *
16234 TTTCAA-AAGTTTTTGATGATCAGAGTTGATCACATTTTAAGAAGTTTTGATCATCAGGGTTGAT
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTGATGATCAGAGTTGAT
*
16298 CGCA
66 CTCA
*
16302 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATAATCAGAGTTGA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTT-GATGATCAGAGTTGA
16367 TCTCA
65 TCTCA
* *
16372 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTCTTCGATGATCAGAGTTGA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGT-TTTGATGATCAGAGTTGA
16437 TCTCA
65 TCTCA
* * *
16442 TTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCCTTTTAAGAAGTTTTTG-TCGATCAGAGTTG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAG-TTTTGAT-GATCAGAGTTG
16505 ATCTCA
64 ATCTCA
** * * *
16511 TTTCAAGAAGTTTTTTTTTATGGTCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTTTTTATGATC
1 TTTCAAGAAG---TTTTCGATGATCAGAGTTGATCTCATTTCAAGAAG------TTTTGATGATC
*
16576 AGAGTTGATCTTA
57 AGAGTTGATCTCA
*
16589 TTTCAAGAAATTTTCGATGATCAGAGTTGATCT
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
16622 TCACATTGAT
Statistics
Matches: 474, Mismatches: 32, Indels: 31
0.88 0.06 0.06
Matches are distributed among these distances:
67 47 0.10
68 81 0.17
69 136 0.29
70 125 0.26
71 2 0.00
72 4 0.01
73 28 0.06
75 20 0.04
78 30 0.06
79 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.40
Consensus pattern (69 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTGATGATCAGAGTTGAT
CTCA
Found at i:16622 original size:35 final size:35
Alignment explanation
Indices: 16028--16621 Score: 774
Period size: 35 Copynumber: 16.9 Consensus size: 35
16018 AGTGCGGTCG
* *
16028 TTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
16063 TTTCAAGAAGTTTTCGATGATCAGAGTTTATCT-A
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
16097 GTTTCAAGAAGTTTTCGATGATCAGAGTTGA--TCA
1 -TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
16131 TTTTAAGAAGTTTT-GATGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
16165 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCACA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
16200 TTTTAAGAAGTTTT-GATGATCAGAGTTGATCGCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
16234 TTTCAA-AAGTTTTTGATGATCAGAGTTGATCACA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* * * *
16268 TTTTAAGAAGTTTT-GATCATCAGGGTTGATCGCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
16302 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
16337 TTTCAAGAAGTTTTCGATAATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
16372 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
16407 TTTCAAGAAGTCTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
16442 TTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
16476 TTTTAAGAAGTTTTTG-TCGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGAT-GATCAGAGTTGATCTCA
** * *
16511 TTTCAAGAAGTTTTTTTTTATGGTCAGAGTTGATCTCC
1 TTTCAAGAAG---TTTTCGATGATCAGAGTTGATCTCA
** *
16549 TTTCAAGAAGTTTTTTTTTTTATGATCAGAGTTGATCTTA
1 TTTCAAGAAG-----TTTTCGATGATCAGAGTTGATCTCA
*
16589 TTTCAAGAAATTTTCGATGATCAGAGTTGATCT
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
16622 TCACATTGAT
Statistics
Matches: 501, Mismatches: 42, Indels: 32
0.87 0.07 0.06
Matches are distributed among these distances:
32 15 0.03
33 21 0.04
34 126 0.25
35 274 0.55
38 30 0.06
39 1 0.00
40 34 0.07
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.40
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
Done.