Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024836.1 Corchorus olitorius cultivar O-4 contig24869, 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: 28337
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:8264 original size:7 final size:7
Alignment explanation
Indices: 8252--8276 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8242 ACAATTGAGT
8252 TTTTCCC
1 TTTTCCC
8259 TTTTCCC
1 TTTTCCC
8266 TTTTCCC
1 TTTTCCC
8273 TTTT
1 TTTT
8277 AATTTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTCCC
Found at i:9074 original size:4 final size:4
Alignment explanation
Indices: 9065--9090 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
9055 TCTTTGAAAA
9065 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
9091 AAGAATAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:20664 original size:76 final size:76
Alignment explanation
Indices: 20527--20678 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
20517 ACAAGGACCC
* * *
20527 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGGACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAT
20592 GGGCGGTGTCA
66 GGGCGGTGTCA
* * * * *
20603 CGACTCCAGCTGGGTGCCCACTTGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGCACCCA
*
20665 GATGGGCTGTGTCA
63 GATGGGCGGTGTCA
20679 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAT
GGGCGGTGTCA
Found at i:21661 original size:28 final size:26
Alignment explanation
Indices: 21606--21655 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
21596 ATGATTTAGG
*
21606 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACGCCCTTTTTCTTTTGA
* *
21632 GGTTACTAACGCTCTTTTTTTTTT
1 GGTTACTAACGCCCTTTTTCTTTT
21656 CAGAGGGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.54
Consensus pattern (26 bp):
GGTTACTAACGCCCTTTTTCTTTTGA
Found at i:21727 original size:6 final size:6
Alignment explanation
Indices: 21712--21743 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
21702 GTTACTAACC
*
21712 TTATTA TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TT
21744 TCAAAGAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTATTT
Found at i:26560 original size:76 final size:76
Alignment explanation
Indices: 26423--26574 Score: 184
Period size: 76 Copynumber: 2.0 Consensus size: 76
26413 ACAAGGACCC
* *
26423 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
26488 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
26499 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
26561 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
26575 TAGCTCATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.06
76 55 0.85
77 6 0.09
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.