Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009129.1 Corchorus olitorius cultivar O-4 contig09157, 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, 786
Length: 1311
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:866 original size:8 final size:8
Alignment explanation
Indices: 853--940 Score: 54
Period size: 8 Copynumber: 9.8 Consensus size: 8
843 TCAAAATGAC
853 ATATAAAA
1 ATATAAAA
861 ATATAAAA
1 ATATAAAA
869 ATATAATGAA
1 ATATAA--AA
879 ATCA-AAATGA
1 AT-ATAAA--A
889 CATATAAAA
1 -ATATAAAA
898 ATATAATGAA
1 ATATAA--AA
908 ATCA-AAATGA
1 AT-ATAAA--A
918 CATATAAAA
1 -ATATAAAA
927 ATATAAAA
1 ATATAAAA
935 ATATAA
1 ATATAA
941 TGAAATCAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
8 36 0.55
9 2 0.03
10 16 0.24
11 12 0.18
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (8 bp):
ATATAAAA
Found at i:893 original size:37 final size:37
Alignment explanation
Indices: 843--969 Score: 198
Period size: 37 Copynumber: 3.6 Consensus size: 37
833 CAGAGTCAAT
843 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
880 TCAAAATGAC--------ATATAAAAATATAATGAAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
909 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
946 TCAAAATGACATATAAAAATATAA
1 TCAAAATGACATATAAAAATATAA
970 TGAAATCAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 16
0.84 0.00 0.16
Matches are distributed among these distances:
29 29 0.35
37 53 0.65
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (37 bp):
TCAAAATGACATATAAAAATATAAAAATATAATGAAA
Found at i:894 original size:29 final size:29
Alignment explanation
Indices: 861--994 Score: 196
Period size: 29 Copynumber: 4.3 Consensus size: 29
851 ACATATAAAA
861 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
890 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
919 ATATAAAAATATAAAAATATAATGAAATCAAAATGAC
1 --------ATATAAAAATATAATGAAATCAAAATGAC
956 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
985 ATATAAAAAT
1 ATATAAAAAT
995 GACATATAAT
Statistics
Matches: 97, Mismatches: 0, Indels: 16
0.86 0.00 0.14
Matches are distributed among these distances:
29 68 0.70
37 29 0.30
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (29 bp):
ATATAAAAATATAATGAAATCAAAATGAC
Found at i:949 original size:66 final size:66
Alignment explanation
Indices: 843--994 Score: 304
Period size: 66 Copynumber: 2.3 Consensus size: 66
833 CAGAGTCAAT
843 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
908 A
66 A
909 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
974 A
66 A
975 TCAAAATGACATATAAAAAT
1 TCAAAATGACATATAAAAAT
995 GACATATAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 86 1.00
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.24
Consensus pattern (66 bp):
TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
A
Found at i:995 original size:13 final size:13
Alignment explanation
Indices: 977--1003 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
967 TAATGAAATC
977 AAAATGACATATA
1 AAAATGACATATA
990 AAAATGACATATA
1 AAAATGACATATA
1003 A
1 A
1004 TTAAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (13 bp):
AAAATGACATATA
Done.