Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
to extract flanking regions for cloning. If the result of the multiple sequence alignment is
not as expected, these results could be used for further investigation.
qseqid
sseqid
percentage.identical
alignment.length
no.mismatch
no.gap.openings
qstart
qend
sstart
send
evalue
bitscore
0
TraesCS3D01G305700
chr3D
100.000
3171
0
0
1
3171
419636634
419633464
0.000000e+00
5856.0
1
TraesCS3D01G305700
chr3D
99.117
3171
23
2
1
3171
355120147
355116982
0.000000e+00
5696.0
2
TraesCS3D01G305700
chr7D
99.022
3171
31
0
1
3171
575648113
575651283
0.000000e+00
5685.0
3
TraesCS3D01G305700
chr5D
98.581
3172
42
3
1
3171
564866755
564869924
0.000000e+00
5605.0
4
TraesCS3D01G305700
chr5D
98.171
3171
56
2
1
3171
409714061
409717229
0.000000e+00
5533.0
5
TraesCS3D01G305700
chr5D
99.197
1245
10
0
1
1245
90284646
90285890
0.000000e+00
2244.0
6
TraesCS3D01G305700
chr5D
99.330
1044
7
0
2128
3171
90285891
90286934
0.000000e+00
1890.0
7
TraesCS3D01G305700
chrUn
98.234
3171
56
0
1
3171
70176444
70173274
0.000000e+00
5546.0
8
TraesCS3D01G305700
chr6A
93.938
1600
90
4
855
2453
121671112
121672705
0.000000e+00
2410.0
9
TraesCS3D01G305700
chr6A
88.489
278
32
0
2761
3038
558144639
558144362
1.410000e-88
337.0
10
TraesCS3D01G305700
chr6A
96.094
128
5
0
3044
3171
121672811
121672938
3.210000e-50
209.0
11
TraesCS3D01G305700
chr6B
92.502
1547
91
9
929
2453
139417828
139416285
0.000000e+00
2191.0
12
TraesCS3D01G305700
chr6B
90.923
650
51
2
573
1220
707972939
707973582
0.000000e+00
867.0
13
TraesCS3D01G305700
chr6B
93.061
245
14
3
331
574
707972653
707972895
3.890000e-94
355.0
14
TraesCS3D01G305700
chr6B
88.129
278
33
0
2761
3038
100913703
100913426
6.560000e-87
331.0
15
TraesCS3D01G305700
chr6B
96.875
128
4
0
3044
3171
707975031
707975158
6.890000e-52
215.0
16
TraesCS3D01G305700
chr2B
93.681
1266
75
4
929
2193
652607746
652606485
0.000000e+00
1890.0
17
TraesCS3D01G305700
chr2B
96.313
217
8
0
2237
2453
652606483
652606267
1.080000e-94
357.0
18
TraesCS3D01G305700
chr3B
93.602
1266
76
4
929
2193
741391162
741389901
0.000000e+00
1884.0
19
TraesCS3D01G305700
chr2A
88.325
394
44
2
2125
2516
438725357
438724964
3.700000e-129
472.0
20
TraesCS3D01G305700
chr2A
94.776
134
7
0
3038
3171
744804129
744803996
3.210000e-50
209.0
21
TraesCS3D01G305700
chr3A
88.129
278
33
0
2761
3038
27732899
27733176
6.560000e-87
331.0
22
TraesCS3D01G305700
chr2D
75.085
590
105
25
2
568
88614489
88615059
1.470000e-58
237.0
23
TraesCS3D01G305700
chr1B
81.928
83
10
2
2573
2655
84368176
84368253
7.340000e-07
65.8
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
purely upstream or downstream may be removed if they don't overlap both primers.
query
scaffold
start
end
length
rev.comp
avg.bitscore
max.bitscore
avg.percent.identical
query.start
query.end
num_hsp
groupid
homo_length
0
TraesCS3D01G305700
chr3D
419633464
419636634
3170
True
5856.0
5856
100.000000
1
3171
1
chr3D.!!$R2
3170
1
TraesCS3D01G305700
chr3D
355116982
355120147
3165
True
5696.0
5696
99.117000
1
3171
1
chr3D.!!$R1
3170
2
TraesCS3D01G305700
chr7D
575648113
575651283
3170
False
5685.0
5685
99.022000
1
3171
1
chr7D.!!$F1
3170
3
TraesCS3D01G305700
chr5D
564866755
564869924
3169
False
5605.0
5605
98.581000
1
3171
1
chr5D.!!$F2
3170
4
TraesCS3D01G305700
chr5D
409714061
409717229
3168
False
5533.0
5533
98.171000
1
3171
1
chr5D.!!$F1
3170
5
TraesCS3D01G305700
chr5D
90284646
90286934
2288
False
2067.0
2244
99.263500
1
3171
2
chr5D.!!$F3
3170
6
TraesCS3D01G305700
chrUn
70173274
70176444
3170
True
5546.0
5546
98.234000
1
3171
1
chrUn.!!$R1
3170
7
TraesCS3D01G305700
chr6A
121671112
121672938
1826
False
1309.5
2410
95.016000
855
3171
2
chr6A.!!$F1
2316
8
TraesCS3D01G305700
chr6B
139416285
139417828
1543
True
2191.0
2191
92.502000
929
2453
1
chr6B.!!$R2
1524
9
TraesCS3D01G305700
chr6B
707972653
707975158
2505
False
479.0
867
93.619667
331
3171
3
chr6B.!!$F1
2840
10
TraesCS3D01G305700
chr2B
652606267
652607746
1479
True
1123.5
1890
94.997000
929
2453
2
chr2B.!!$R1
1524
11
TraesCS3D01G305700
chr3B
741389901
741391162
1261
True
1884.0
1884
93.602000
929
2193
1
chr3B.!!$R1
1264
12
TraesCS3D01G305700
chr2D
88614489
88615059
570
False
237.0
237
75.085000
2
568
1
chr2D.!!$F1
566
AutoCloner calculated primer pairs
These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
whilst remaining within the specified product range where possible.
Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
during PCR or sequencing,
these could be used as alternatives.