Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024413.1 Corchorus olitorius cultivar O-4 contig24446, 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: 10976
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:407 original size:39 final size:40
Alignment explanation
Indices: 353--433 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
343 ATACCTAAGA
*
353 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
392 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
432 AT
1 AT
434 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:5081 original size:4 final size:4
Alignment explanation
Indices: 5048--5108 Score: 59
Period size: 4 Copynumber: 14.8 Consensus size: 4
5038 GCAGTAAAAT
* * * * *
5048 CATA CATG CATA TATA CAATA CATTA CATA CATA CATG CATG CATG CATA
1 CATA CATA CATA CATA C-ATA CA-TA CATA CATA CATA CATA CATA CATA
5098 CATA CATA CAT
1 CATA CATA CAT
5109 GTGTATATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
4 41 0.84
5 8 0.16
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:5141 original size:24 final size:24
Alignment explanation
Indices: 5073--5142 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
5063 ACAATACATT
* ** * *
5073 ACATACATACATGCATGCATGCAT
1 ACATACATACATGTATATATGTAC
*
5097 ACATACATACATGTGTATATGTAC
1 ACATACATACATGTATATATGTAC
*
5121 ACATACATACATGTATTTATGT
1 ACATACATACATGTATATATGT
5143 TGTATATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (24 bp):
ACATACATACATGTATATATGTAC
Found at i:6291 original size:16 final size:17
Alignment explanation
Indices: 6270--6305 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6260 TGAAGATTCC
*
6270 TTCTTTT-TTTTTTTTT
1 TTCTTTTCTTTTTTGTT
6286 TTCTTTTCTTTTTTGTT
1 TTCTTTTCTTTTTTGTT
6303 TTC
1 TTC
6306 AATTTGCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (17 bp):
TTCTTTTCTTTTTTGTT
Found at i:10845 original size:2 final size:2
Alignment explanation
Indices: 10838--10936 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
10828 TCAAAATACT
10838 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
10880 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
10922 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
10937 TATATATATA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:10941 original size:2 final size:2
Alignment explanation
Indices: 10936--10976 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
10926 ACACACACAC
10936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.