Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014150.1 Corchorus olitorius cultivar O-4 contig14183, 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: 22092
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:294 original size:50 final size:48
Alignment explanation
Indices: 204--343 Score: 137
Period size: 50 Copynumber: 2.9 Consensus size: 48
194 CAAGCAATCC
* **
204 TTTACTTTTCA-CTGCAC-TTTTCTCAA-TTTTACTACAAAATTGAACAT
1 TTTAATTTTCATC-GCACTTTTTCTCAATTTTTAAGACAAAATTGAAC-T
* * *
251 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TCGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACT
* *
300 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAATTTTCATCGCACTTTTTCTCAATTTTTAAGACAAAATTGA
344 TTGGCACGCT
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
46 5 0.06
47 17 0.22
48 16 0.21
49 17 0.22
50 22 0.29
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (48 bp):
TTTAATTTTCATCGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
Found at i:4238 original size:15 final size:14
Alignment explanation
Indices: 4218--4247 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4208 ACCCGAGCAA
4218 TCCTTTTCCATTCCT
1 TCCTTTTCC-TTCCT
4233 TCCTTTTCCTTCCT
1 TCCTTTTCCTTCCT
4247 T
1 T
4248 ATCTTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (14 bp):
TCCTTTTCCTTCCT
Found at i:5318 original size:2 final size:2
Alignment explanation
Indices: 5311--5346 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5301 CTACGTTAGT
5311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5347 AATGCTTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6816 original size:27 final size:27
Alignment explanation
Indices: 6786--6870 Score: 136
Period size: 27 Copynumber: 3.1 Consensus size: 27
6776 AAATTAAAGG
6786 TGGACTTGCAAATGACCAAAATGCCCC
1 TGGACTTGCAAATGACCAAAATGCCCC
*
6813 TGGACATGCAAATGACCAAAATGCCCC
1 TGGACTTGCAAATGACCAAAATGCCCC
*
6840 AGGA-TGTGCAAATGACCAAAATGCCCC
1 TGGACT-TGCAAATGACCAAAATGCCCC
6867 TGGA
1 TGGA
6871 TGACCCTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.16
Consensus pattern (27 bp):
TGGACTTGCAAATGACCAAAATGCCCC
Found at i:7222 original size:78 final size:78
Alignment explanation
Indices: 7131--7286 Score: 267
Period size: 78 Copynumber: 2.0 Consensus size: 78
7121 AGATTTATAG
* *
7131 TTTTACTCAACTAAAAACTCTAGTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTAGTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
*
7196 TACCATTTTACTA
66 TACCATTTAACTA
* *
7209 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATTTAATATCTTTATAACTATTTCAGTT
1 TTTTACTCAACTAAAAACTCTAGTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
7274 TACCATTTAACTA
66 TACCATTTAACTA
7287 CTTCAACTAG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.49
Consensus pattern (78 bp):
TTTTACTCAACTAAAAACTCTAGTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
TACCATTTAACTA
Found at i:13729 original size:52 final size:52
Alignment explanation
Indices: 13659--13762 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
13649 CTCAATCTAC
* * * * * *
13659 ATAGATAACAAATGATTCATCAATGCACTCGGTTGAATGTTGTGTTAGTTTT
1 ATAGACAAAAAATCATTCATCAATGCACTCAGTTGAATGGTGTGTCAGTTTT
* *
13711 ATAGACAAAAAATCATTCATTAATGCACTCAGTTTAATGGTGTGTCAGTTTT
1 ATAGACAAAAAATCATTCATCAATGCACTCAGTTGAATGGTGTGTCAGTTTT
13763 GTTGTCTGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (52 bp):
ATAGACAAAAAATCATTCATCAATGCACTCAGTTGAATGGTGTGTCAGTTTT
Found at i:21838 original size:42 final size:43
Alignment explanation
Indices: 21787--21880 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
21777 AGTGTGTTAC
* *
21787 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
21828 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
*
21873 TTAATATT
1 CTAATATT
21881 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Done.