Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023609.1 Corchorus olitorius cultivar O-4 contig23642, 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: 3290
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Found at i:2293 original size:51 final size:50
Alignment explanation
Indices: 2222--2455 Score: 364
Period size: 51 Copynumber: 4.7 Consensus size: 50
2212 AGAAGAGTGG
2222 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGA
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTTTAAGATTGA
* * *
2273 ATTGGTAGACATTTCGAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGA
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTTTAAGATTGA
* *
2324 ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGCTCC-TTTAAGATTGA
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA
* * *
2373 ATTGGAAGACAGTTCAAAGGATAAGGGGAAGACAGTCCTTTTGAGATTGA
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA
2423 ATTGGAAGA-AGTTCAAAGGATAAGCGGAAGACG
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACG
2456 ACCCTTTAAT
Statistics
Matches: 169, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
49 67 0.40
50 19 0.11
51 83 0.49
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (50 bp):
ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA
Found at i:2462 original size:49 final size:50
Alignment explanation
Indices: 2222--2487 Score: 319
Period size: 51 Copynumber: 5.3 Consensus size: 50
2212 AGAAGAGTGG
* *
2222 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGA
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGAC-GACCCTTTTAAGATTGA
* * * * *
2273 ATTGGTAGACATTTCGAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGA
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGAC-GACCCTTTTAAGATTGA
*
2324 ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACG-CTCC-TTTAAGATTGA
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGAC-CCTTTTAAGATTGA
* * *
2373 ATTGGAAGACAGTTCAAAGGATAAGGGGAAGAC-AGTCCTTTTGAGATTGA
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGA-CCCTTTTAAGATTGA
*
2423 ATTGGAAGA-AGTTCAAAGGATAAGCGGAAGACGACCC-TTTAATATT-A
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGACCCTTTTAAGATTGA
* *
2470 GATTGGAATACGGTTCAA
1 -ATTGGAAGACAGTTCAA
2488 GGAAATTGAT
Statistics
Matches: 192, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
47 1 0.01
48 15 0.08
49 75 0.39
50 22 0.11
51 79 0.41
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (50 bp):
ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGACCCTTTTAAGATTGA
Found at i:2477 original size:98 final size:99
Alignment explanation
Indices: 2222--2487 Score: 358
Period size: 98 Copynumber: 2.7 Consensus size: 99
2212 AGAAGAGTGG
* * *
2222 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGAATTGGTAGACATTT
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGAC-G-CC-CTTTAAGATTGAATTGGAAGACAGTT
* *
2287 CGAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGA
63 CAAAGGATAAGCGGAAGACAGTCCTTTTTAAGATTGA
*
2324 ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGCTCCTTTAAGATTGAATTGGAAGACAGTTCA
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGC-CCTTTAAGATTGAATTGGAAGACAGTTCA
* *
2389 AAGGATAAGGGGAAGACAGTCC-TTTTGAGATTGA
65 AAGGATAAGCGGAAGACAGTCCTTTTTAAGATTGA
* * *
2423 ATTGGAAGA-AGTTCAAAGGATAAGCGGAAGACGACCCTTTAATATT-AGATTGGAATACGGTTC
1 ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACG-CCCTTTAAGATTGA-ATTGGAAGACAGTTC
2486 AA
64 AA
2488 GGAAATTGAT
Statistics
Matches: 149, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
97 1 0.01
98 49 0.33
99 20 0.13
100 45 0.30
101 2 0.01
102 32 0.21
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (99 bp):
ATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGCCCTTTAAGATTGAATTGGAAGACAGTTCAA
AGGATAAGCGGAAGACAGTCCTTTTTAAGATTGA
Done.