Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004439.1 Corchorus capsularis cultivar CVL-1 contig04447, 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, 601
Length: 1002
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Found at i:675 original size:38 final size:38
Alignment explanation
Indices: 624--700 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
614 GGAACGCCTT
624 ATTGTATTGTATGTATTTGTTGACACGTTAGATTTTGA
1 ATTGTATTGTATGTATTTGTTGACACGTTAGATTTTGA
662 ATTGTATTGTATGTATTTGTTGACACGTTAGATTTTGA
1 ATTGTATTGTATGTATTTGTTGACACGTTAGATTTTGA
700 A
1 A
701 AAAACAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.25, C:0.05, G:0.21, T:0.49
Consensus pattern (38 bp):
ATTGTATTGTATGTATTTGTTGACACGTTAGATTTTGA
Found at i:737 original size:13 final size:14
Alignment explanation
Indices: 718--777 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 14
708 AGATAGATCT
718 TTTCATAAACAGAA
1 TTTCATAAACAGAA
*
732 -TTCATAAACATAA
1 TTTCATAAACAGAA
*
745 TTTCAT--ACATAA
1 TTTCATAAACAGAA
*
757 TTTCAT--ACATAA
1 TTTCATAAACAGAA
769 TTTCATAAA
1 TTTCATAAA
778 TTTTTATTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
12 24 0.57
13 12 0.29
14 6 0.14
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (14 bp):
TTTCATAAACAGAA
Found at i:756 original size:12 final size:12
Alignment explanation
Indices: 739--775 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
729 GAATTCATAA
739 ACATAATTTCAT
1 ACATAATTTCAT
751 ACATAATTTCAT
1 ACATAATTTCAT
763 ACATAATTTCAT
1 ACATAATTTCAT
775 A
1 A
776 AATTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (12 bp):
ACATAATTTCAT
Found at i:850 original size:14 final size:14
Alignment explanation
Indices: 831--859 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
821 AGATAGAAAA
831 TCAAAAATATATTC
1 TCAAAAATATATTC
845 TCAAAAATATATTC
1 TCAAAAATATATTC
859 T
1 T
860 AACTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (14 bp):
TCAAAAATATATTC
Found at i:867 original size:25 final size:24
Alignment explanation
Indices: 838--894 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
828 AAATCAAAAA
*
838 TATATTCTCAAAAATATATTCTAAC
1 TATATTAT-AAAAATATATTCTAAC
863 TATA-TATAAAAATATATTCTAAC
1 TATATTATAAAAATATATTCTAAC
886 TATA-TATAA
1 TATATTATAA
895 TAGAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 25 0.81
24 2 0.06
25 4 0.13
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (24 bp):
TATATTATAAAAATATATTCTAAC
Found at i:874 original size:23 final size:23
Alignment explanation
Indices: 847--894 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
837 ATATATTCTC
847 AAAAATATATTCTAACTATATAT
1 AAAAATATATTCTAACTATATAT
870 AAAAATATATTCTAACTATATAT
1 AAAAATATATTCTAACTATATAT
893 AA
1 AA
895 TAGAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAAATATATTCTAACTATATAT
Found at i:929 original size:14 final size:14
Alignment explanation
Indices: 894--964 Score: 67
Period size: 14 Copynumber: 5.1 Consensus size: 14
884 ACTATATATA
894 ATAGAATAAATAGAATT
1 ATAGAAT-AA-AGAA-T
911 ATAGAATAAAGAAT
1 ATAGAATAAAGAAT
*
925 ATAGAAT-AATAA-
1 ATAGAATAAAGAAT
* *
937 ATAGAATATAGAAA
1 ATAGAATAAAGAAT
951 ATAGAATAAA-AAT
1 ATAGAATAAAGAAT
964 A
1 A
965 AATTTCGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
12 7 0.15
13 10 0.21
14 17 0.36
15 4 0.09
16 2 0.04
17 7 0.15
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (14 bp):
ATAGAATAAAGAAT
Found at i:942 original size:26 final size:25
Alignment explanation
Indices: 911--964 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
901 AAATAGAATT
*
911 ATAGAATAAAGAATATAGAATAATAA
1 ATAGAATAAAGAAAATAGAATAA-AA
*
937 ATAGAATATAGAAAATAGAATAAAA
1 ATAGAATAAAGAAAATAGAATAAAA
962 ATA
1 ATA
965 AATTTCGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (25 bp):
ATAGAATAAAGAAAATAGAATAAAA
Found at i:944 original size:19 final size:19
Alignment explanation
Indices: 920--958 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
910 TATAGAATAA
920 AGAATATAGAATAATA-AAT
1 AGAATATAGAA-AATAGAAT
939 AGAATATAGAAAATAGAAT
1 AGAATATAGAAAATAGAAT
958 A
1 A
959 AAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (19 bp):
AGAATATAGAAAATAGAAT
Done.