Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004680.1 Corchorus capsularis cultivar CVL-1 contig04696, 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, 613
Length: 1022
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Found at i:537 original size:19 final size:18
Alignment explanation
Indices: 498--537 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
488 GTCCTTTCCC
**
498 TTTTTTTATCATTTTTTT
1 TTTTTTTATCATTTTCAT
516 TTTTTTTGATCATTTTCAT
1 TTTTTTT-ATCATTTTCAT
535 TTT
1 TTT
538 CCTCCTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTTTATCATTTTCAT
Found at i:843 original size:30 final size:30
Alignment explanation
Indices: 809--1010 Score: 170
Period size: 30 Copynumber: 6.0 Consensus size: 30
799 TTTGATTTCA
809 TTCTATTTCATTATATGGTATTACATAATT
1 TTCTATTTCATTATATGGTATTACATAATT
839 TTCTATTTCATTATATGGTATTACATAATT
1 TTCTATTTCATTATATGGTATTACATAATT
**
869 TTCTATTTCATTATATGGTATTATGTAATT
1 TTCTATTTCATTATATGGTATTACATAATT
* *
899 TTGATTTCATTCTATGTTCATTATATGGTATTACATAATT
1 TT-CTAT--TTC-A--TT-A-T--ATGGTATTACATAATT
*
939 TTGATTTCATTCTATTTCATTATATGGTATTACATAATT
1 T---TC------TATTTCATTATATGGTATTACATAATT
978 TTCTATGTTCATTATATGGTATTATCATAATT
1 TTCTAT-TTCATTATATGGTATTA-CATAATT
1010 T
1 T
1011 CATTCTATGT
Statistics
Matches: 142, Mismatches: 9, Indels: 40
0.74 0.05 0.21
Matches are distributed among these distances:
30 63 0.44
31 19 0.13
32 8 0.06
33 3 0.02
34 1 0.01
36 3 0.02
37 1 0.01
38 1 0.01
39 17 0.12
40 15 0.11
41 1 0.01
42 1 0.01
43 3 0.02
45 1 0.01
46 3 0.02
48 2 0.01
ACGTcount: A:0.28, C:0.09, G:0.08, T:0.54
Consensus pattern (30 bp):
TTCTATTTCATTATATGGTATTACATAATT
Found at i:890 original size:15 final size:15
Alignment explanation
Indices: 812--890 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
802 GATTTCATTC
812 TATTTCATTATATGG
1 TATTTCATTATATGG
* * * **
827 TATTACATAATTTTC
1 TATTTCATTATATGG
842 TATTTCATTATATGG
1 TATTTCATTATATGG
* * * **
857 TATTACATAATTTTC
1 TATTTCATTATATGG
872 TATTTCATTATATGG
1 TATTTCATTATATGG
887 TATT
1 TATT
891 ATGTAATTTT
Statistics
Matches: 44, Mismatches: 20, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (15 bp):
TATTTCATTATATGG
Found at i:919 original size:40 final size:39
Alignment explanation
Indices: 869--979 Score: 195
Period size: 40 Copynumber: 2.8 Consensus size: 39
859 TTACATAATT
**
869 TTCTATTTCATTATATGGTATTATGTAATTTTGATTTCA
1 TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
908 TTCTATGTTCATTATATGGTATTACATAATTTTGATTTCA
1 TTCTAT-TTCATTATATGGTATTACATAATTTTGATTTCA
948 TTCTATTTCATTATATGGTATTACATAATTTT
1 TTCTATTTCATTATATGGTATTACATAATTTT
980 CTATGTTCAT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
39 32 0.46
40 37 0.54
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (39 bp):
TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
Found at i:982 original size:70 final size:70
Alignment explanation
Indices: 789--1010 Score: 292
Period size: 70 Copynumber: 3.2 Consensus size: 70
779 CATAATTACA
789 ATTACATAATTTTGATTTCATTCTATTTCATTATATGGTATTACATAATTTTCTAT-TTCATTAT
1 ATTACATAATTTTGATTTCATTCTATTTCATTATATGGTATTACATAATTTTCTATGTTCATTAT
853 ATGGT
66 ATGGT
* * * * ** **
858 ATTACATAATTTTCTATTTCATTATATGGT-ATTATGTAAT-TTTGAT--TTCATTCTATGTTCA
1 ATTACATAATTTT-GATTTCATTCTAT-TTCATTATATGGTATTACATAATT--TTCTATGTTCA
919 TTATATGGT
62 TTATATGGT
928 ATTACATAATTTTGATTTCATTCTATTTCATTATATGGTATTACATAATTTTCTATGTTCATTAT
1 ATTACATAATTTTGATTTCATTCTATTTCATTATATGGTATTACATAATTTTCTATGTTCATTAT
993 ATGGT
66 ATGGT
998 ATTATCATAATTT
1 ATTA-CATAATTT
1011 CATTCTATGT
Statistics
Matches: 127, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
67 2 0.02
68 1 0.01
69 41 0.32
70 72 0.57
71 9 0.07
72 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (70 bp):
ATTACATAATTTTGATTTCATTCTATTTCATTATATGGTATTACATAATTTTCTATGTTCATTAT
ATGGT
Found at i:990 original size:31 final size:31
Alignment explanation
Indices: 948--1010 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
938 TTTGATTTCA
948 TTCTATTTCATTATATGGTATTA-CATAATT
1 TTCTATTTCATTATATGGTATTATCATAATT
978 TTCTATGTTCATTATATGGTATTATCATAATT
1 TTCTAT-TTCATTATATGGTATTATCATAATT
1010 T
1 T
1011 CATTCTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 6 0.19
31 17 0.55
32 8 0.26
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.54
Consensus pattern (31 bp):
TTCTATTTCATTATATGGTATTATCATAATT
Done.