Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016242.1 Corchorus capsularis cultivar CVL-1 contig16263, 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, 799
Length: 1333
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Found at i:551 original size:14 final size:14
Alignment explanation
Indices: 532--558 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
522 TTTGCTTTTT
532 TATATATACATATA
1 TATATATACATATA
546 TATATATACATAT
1 TATATATACATAT
559 TTTCCACTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATATACATATA
Found at i:1026 original size:12 final size:12
Alignment explanation
Indices: 1009--1033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
999 AAAGAGTCAT
1009 GGTTTTCAAAAA
1 GGTTTTCAAAAA
1021 GGTTTTCAAAAA
1 GGTTTTCAAAAA
1033 G
1 G
1034 AGTCATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (12 bp):
GGTTTTCAAAAA
Found at i:1047 original size:19 final size:18
Alignment explanation
Indices: 991--1050 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
981 TGATAAAATG
991 GTTTTCAAAAAGAGTCAT
1 GTTTTCAAAAAGAGTCAT
1009 GGTTTTC-AAAA-AG----
1 -GTTTTCAAAAAGAGTCAT
1022 GTTTTCAAAAAGAGTCAT
1 GTTTTCAAAAAGAGTCAT
1040 GATTTTCAAAA
1 G-TTTTCAAAA
1051 GGTTTTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
12 6 0.18
13 4 0.12
14 2 0.06
17 2 0.06
18 5 0.15
19 15 0.44
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (18 bp):
GTTTTCAAAAAGAGTCAT
Found at i:1047 original size:75 final size:75
Alignment explanation
Indices: 945--1100 Score: 235
Period size: 75 Copynumber: 2.1 Consensus size: 75
935 GAGCAACGAT
* * *
945 GGTTTTCAAAAAATAGTCATGGCTTTCAAAAGGTTTTGATAAAATGG-TTTTCAAAAAGAGTCAT
1 GGTTTTCAAAAAAGAGTCATGACTTTCAAAAGGTTTTAATAAAA-GGATTTTCAAAAAGAGTCAT
1009 GGTTTTCAAAAA
65 GGTTTTC-AAAA
* *
1021 GGTTTTC-AAAAAGAGTCATGATTTTCAAAAGGTTTTAATAAAAGGATTTTCAAAAAGAGTCTTG
1 GGTTTTCAAAAAAGAGTCATGACTTTCAAAAGGTTTTAATAAAAGGATTTTCAAAAAGAGTCATG
1085 GTTTTCAAAA
66 GTTTTCAAAA
1095 GGTTTT
1 GGTTTT
1101 GATAAAATGT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
74 12 0.16
75 55 0.74
76 7 0.09
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (75 bp):
GGTTTTCAAAAAAGAGTCATGACTTTCAAAAGGTTTTAATAAAAGGATTTTCAAAAAGAGTCATG
GTTTTCAAAA
Found at i:1064 original size:31 final size:31
Alignment explanation
Indices: 985--1056 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
975 AGGTTTTGAT
* *
985 AAAATGGTTTTCAAAAAGAGTCATGGTTTTC
1 AAAAAGGTTTTCAAAAAGAGTCATGATTTTC
1016 AAAAAGGTTTTCAAAAAGAGTCATGATTTTC
1 AAAAAGGTTTTCAAAAAGAGTCATGATTTTC
1047 -AAAAGGTTTT
1 AAAAAGGTTTT
1057 AATAAAAGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 10 0.26
31 29 0.74
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (31 bp):
AAAAAGGTTTTCAAAAAGAGTCATGATTTTC
Done.