Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020097.1 Corchorus olitorius cultivar O-4 contig20130, 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: 26947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3218 original size:25 final size:26
Alignment explanation
Indices: 3181--3229 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
3171 GTGGATGATA
3181 TTAACTTAGGATTTCTCATTTCCTAT
1 TTAACTTAGGATTTCTCATTTCCTAT
*
3207 TTAA-TTATGATTTCTCATTTCCT
1 TTAACTTAGGATTTCTCATTTCCT
3230 TATTATTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.53
Consensus pattern (26 bp):
TTAACTTAGGATTTCTCATTTCCTAT
Found at i:6055 original size:23 final size:24
Alignment explanation
Indices: 5993--6055 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 24
5983 GAAAAATTTT
5993 ATACTATTTGATATCCAATTTGTAC
1 ATACTATTT-ATATCCAATTTGTAC
*
6018 ATACTTATAGATATATCCAATTTGTAC
1 ATAC-TAT--TTATATCCAATTTGTAC
6045 ATA-TATTTATA
1 ATACTATTTATA
6056 GAATCTCGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
23 4 0.12
25 7 0.21
26 3 0.09
27 18 0.55
28 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (24 bp):
ATACTATTTATATCCAATTTGTAC
Found at i:6865 original size:22 final size:23
Alignment explanation
Indices: 6839--6887 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
6829 GTTAAGTCAA
6839 TAAAAAATA-TTTTTTAATTA-T
1 TAAAAAATATTTTTTTAATTACT
*
6860 TAAAAAGTATTTTTTTAATTACT
1 TAAAAAATATTTTTTTAATTACT
6883 TAAAA
1 TAAAA
6888 TAAAAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.32
22 11 0.44
23 6 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAAATATTTTTTTAATTACT
Found at i:8128 original size:19 final size:19
Alignment explanation
Indices: 8104--8140 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8094 AGCTTAGGAC
8104 ATAATGCAATAAAGTTTAA
1 ATAATGCAATAAAGTTTAA
*
8123 ATAATGCAATGAAGTTTA
1 ATAATGCAATAAAGTTTA
8141 GGCAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (19 bp):
ATAATGCAATAAAGTTTAA
Found at i:8840 original size:45 final size:42
Alignment explanation
Indices: 8791--8900 Score: 130
Period size: 45 Copynumber: 2.5 Consensus size: 42
8781 TTTCCAGGCA
* * * *
8791 TTTCAACTTCTTCAATTGGATTTCCAACATCATCATCTACTGGAT
1 TTTCAACTCCTTCAACTGGATTTCCAAAACCATC-TCT--TGGAT
* *
8836 TTTCAACTCCATCAACTGGATTTTCAAAACCATCTCTTGGAT
1 TTTCAACTCCTTCAACTGGATTTCCAAAACCATCTCTTGGAT
*
8878 TTTCAACTCCTTCAACTAGATTT
1 TTTCAACTCCTTCAACTGGATTT
8901 TCTTTCTCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 26 0.46
44 3 0.05
45 28 0.49
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.39
Consensus pattern (42 bp):
TTTCAACTCCTTCAACTGGATTTCCAAAACCATCTCTTGGAT
Found at i:8853 original size:21 final size:21
Alignment explanation
Indices: 8791--8902 Score: 91
Period size: 21 Copynumber: 5.2 Consensus size: 21
8781 TTTCCAGGCA
* * *
8791 TTTCAACTTCTTCAATTGGAT
1 TTTCAACTCCATCAACTGGAT
* *
8812 TTCCAACATCATCATCTACTGGAT
1 TTTCAAC-TC--CATCAACTGGAT
8836 TTTCAACTCCATCAACTGGAT
1 TTTCAACTCCATCAACTGGAT
** *
8857 TTTCAAAACCATC-TCTTGGAT
1 TTTCAACTCCATCAAC-TGGAT
* *
8878 TTTCAACTCCTTCAACTAGAT
1 TTTCAACTCCATCAACTGGAT
8899 TTTC
1 TTTC
8903 TTTCTCATAT
Statistics
Matches: 71, Mismatches: 15, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.01
21 51 0.72
22 2 0.03
23 2 0.03
24 15 0.21
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.39
Consensus pattern (21 bp):
TTTCAACTCCATCAACTGGAT
Found at i:19674 original size:53 final size:53
Alignment explanation
Indices: 19611--19773 Score: 290
Period size: 53 Copynumber: 3.1 Consensus size: 53
19601 TGTTTATTCA
*
19611 ATTGAACCTATTAAATAAGCACGCATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
* * *
19664 ATTGAACCTATGAAATAAGCACACATACCAAATAATACAAAATCCAATAAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
19717 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
19770 ATTG
1 ATTG
19774 GATTTAAAGA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 103 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:20138 original size:20 final size:20
Alignment explanation
Indices: 20113--20150 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
20103 CATTTCCTAG
20113 ATTAATTTCTAATTGAGTAA
1 ATTAATTTCTAATTGAGTAA
20133 ATTAATTTCTAATTGAGT
1 ATTAATTTCTAATTGAGT
20151 TGAATTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (20 bp):
ATTAATTTCTAATTGAGTAA
Done.