Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002092.1 Corchorus capsularis cultivar CVL-1 contig02096, 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: 2060
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Found at i:770 original size:77 final size:75
Alignment explanation
Indices: 683--912 Score: 363
Period size: 75 Copynumber: 3.0 Consensus size: 75
673 TTTTTAATTA
683 AAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATGTAAAAATAGAGT
1 AAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTA--TAAAAATAGAGT
748 TTTTAGTTGAGT
64 TTTTAGTTGAGT
*
760 AAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTAT-ATAATAGAGTTT
1 AAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATAAAAATAGAGTTT
824 TTAGTTGAGT
66 TTAGTTGAGT
* * * * *
834 AAAATAATAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAAAAAATAGAGTT
1 -AAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATAAAAATAGAGTT
*
899 TTTAATTGAGT
65 TTTAGTTGAGT
910 AAA
1 AAA
913 ATTATAAAAA
Statistics
Matches: 143, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
74 21 0.15
75 51 0.36
76 20 0.14
77 51 0.36
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (75 bp):
AAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATAAAAATAGAGTTT
TTAGTTGAGT
Found at i:883 original size:75 final size:75
Alignment explanation
Indices: 681--921 Score: 358
Period size: 77 Copynumber: 3.2 Consensus size: 75
671 AGTTTTTAAT
*
681 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATGTAAAAATAGA
1 TAAAATAATAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTA--T-AAAATAGA
746 GTTTTTAGTTGAG
63 GTTTTTAGTTGAG
* *
759 T-AAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAATAGAGTT
1 TAAAATAATAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATAAAATAGAGTT
823 TTTAGTTGAG
66 TTTAGTTGAG
* * * *
833 TAAAATAATAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAAAAAATAGAGT
1 TAAAATAATAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATT-ATAAAATAGAGT
*
898 TTTTAATTGAG
65 TTTTAGTTGAG
*
909 TAAAATTATAAAA
1 TAAAATAATAAAA
922 ATCTAAACAA
Statistics
Matches: 152, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
74 21 0.14
75 47 0.31
76 32 0.21
77 51 0.34
78 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (75 bp):
TAAAATAATAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATAAAATAGAGTT
TTTAGTTGAG
Found at i:1029 original size:45 final size:45
Alignment explanation
Indices: 965--1058 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
955 CAAATAAGGG
965 TATAATAGACGATTCAAAAGTTTTACAGGTGAATGTACTTTTTAA
1 TATAATAGACGATTCAAAAGTTTTACAGGTGAATGTACTTTTTAA
*
1010 TATAATAGGCGATTCAAAAGTTTTACAGGTGAATGTACTTTTTAA
1 TATAATAGACGATTCAAAAGTTTTACAGGTGAATGTACTTTTTAA
1055 TATA
1 TATA
1059 GTATAGATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (45 bp):
TATAATAGACGATTCAAAAGTTTTACAGGTGAATGTACTTTTTAA
Found at i:1072 original size:2 final size:2
Alignment explanation
Indices: 1054--1096 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
1044 GTACTTTTTA
*
1054 AT AT AGT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1097 TGTTGTGGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Done.