Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013389.1 Corchorus olitorius cultivar O-4 contig13422, 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, 746
Length: 1244
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Found at i:860 original size:36 final size:36
Alignment explanation
Indices: 772--1063 Score: 310
Period size: 36 Copynumber: 8.0 Consensus size: 36
762 AATGTTTTTG
*
772 ATGGGAACTTTCCCACTTTGAAAAC-T-AAAACTGAAA
1 ATGGGAACTTTCCCAATTTGAAAACTTAAAAACTG--A
* *
808 ATGACGGGAACTTTCCCTAAATTGAAAAC-TAAAACCTGA
1 AT---GGGAACTTTCCC-AATTTGAAAACTTAAAAACTGA
* *
847 ATGGGAACTTTCCCAATTTGAAAACTTTGAAAACTGG
1 ATGGGAACTTTCCCAATTTGAAAAC-TTAAAAACTGA
884 ATGGGAACTTTCCCAATTTG-AAACTTAAAAAAACTG-
1 ATGGGAACTTTCCCAATTTGAAAACTT--AAAAACTGA
* * *
920 GTGGGAACTTTCCC-ATTTAAAAACTTTGAAAACTGA
1 ATGGGAACTTTCCCAATTTGAAAAC-TTAAAAACTGA
956 ATGGGAACTTTCCCAATTTGAAAACTTAAAAAACTG-
1 ATGGGAACTTTCCCAATTTGAAAACTT-AAAAACTGA
* * * * *
992 GTGGGAACTTTACCAATTTAAAAACTTTGAAAATTGA
1 ATGGGAACTTTCCCAATTTGAAAAC-TTAAAAACTGA
1029 ATGGGAACTTTCCCAATTTGAAAACTTAAAAACTG
1 ATGGGAACTTTCCCAATTTGAAAACTTAAAAACTG
1064 GTGGGATTCT
Statistics
Matches: 216, Mismatches: 24, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
35 23 0.11
36 86 0.40
37 76 0.35
39 15 0.07
40 10 0.05
41 6 0.03
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (36 bp):
ATGGGAACTTTCCCAATTTGAAAACTTAAAAACTGA
Found at i:933 original size:73 final size:73
Alignment explanation
Indices: 813--1069 Score: 389
Period size: 72 Copynumber: 3.5 Consensus size: 73
803 TGAAAATGAC
* * * *
813 GGGAACTTTCCCTAAATTGAAAAC-T-AAAACCTGAATGGGAACTTTCCCAATTTGAAAACTTTG
1 GGGAACTTTCCC-AATTTGAAAACTTAAAAAACTG-GTGGGAACTTTCCCAATTTAAAAACTTTG
*
876 AAAACTGGAT
64 AAAACTGAAT
886 GGGAACTTTCCCAATTTG-AAACTTAAAAAAACTGGTGGGAACTTTCCC-ATTTAAAAACTTTGA
1 GGGAACTTTCCCAATTTGAAAACTT-AAAAAACTGGTGGGAACTTTCCCAATTTAAAAACTTTGA
949 AAACTGAAT
65 AAACTGAAT
*
958 GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGAACTTTACCAATTTAAAAACTTTGAA
1 GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGAACTTTCCCAATTTAAAAACTTTGAA
*
1023 AATTGAAT
66 AACTGAAT
1031 GGGAACTTTCCCAATTTGAAAACTT-AAAAACTGGTGGGA
1 GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGA
1070 TTCTTTTTGA
Statistics
Matches: 172, Mismatches: 7, Indels: 11
0.91 0.04 0.06
Matches are distributed among these distances:
71 4 0.02
72 82 0.48
73 79 0.46
74 7 0.04
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (73 bp):
GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGAACTTTCCCAATTTAAAAACTTTGAA
AACTGAAT
Found at i:952 original size:72 final size:72
Alignment explanation
Indices: 813--1069 Score: 378
Period size: 73 Copynumber: 3.6 Consensus size: 72
803 TGAAAATGAC
* * * *
813 GGGAACTTTCCCTAAATTGAAAAC-T-AAAACCTGAATGGGAACTTTCCCAATTTGAAAACTTTG
1 GGGAACTTTCCC-AATTTGAAAACTTAAAAAACTG-GTGGGAACTTTCCC-ATTTAAAAACTTTG
*
876 AAAACTGGAT
63 AAAACTGAAT
886 GGGAACTTTCCCAATTTG-AAACTTAAAAAAACTGGTGGGAACTTTCCCATTTAAAAACTTTGAA
1 GGGAACTTTCCCAATTTGAAAACTT-AAAAAACTGGTGGGAACTTTCCCATTTAAAAACTTTGAA
950 AACTGAAT
65 AACTGAAT
*
958 GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGAACTTTACCAATTTAAAAACTTTGAA
1 GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGAACTTT-CCCATTTAAAAACTTTGAA
*
1023 AATTGAAT
65 AACTGAAT
1031 GGGAACTTTCCCAATTTGAAAACTT-AAAAACTGGTGGGA
1 GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGA
1070 TTCTTTTTGA
Statistics
Matches: 172, Mismatches: 7, Indels: 11
0.91 0.04 0.06
Matches are distributed among these distances:
71 4 0.02
72 80 0.47
73 81 0.47
74 7 0.04
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (72 bp):
GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGAACTTTCCCATTTAAAAACTTTGAAA
ACTGAAT
Done.