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
TraesCS6D01G393700
chr6D
100.000
3305
0
0
1
3305
467321007
467317703
0.000000e+00
6104.0
1
TraesCS6D01G393700
chr6D
88.783
1364
127
10
1170
2521
467547307
467545958
0.000000e+00
1648.0
2
TraesCS6D01G393700
chr6D
93.452
672
36
3
1
670
467531914
467531249
0.000000e+00
990.0
3
TraesCS6D01G393700
chr6D
91.753
388
29
3
2813
3197
467539584
467539197
1.350000e-148
536.0
4
TraesCS6D01G393700
chr6D
91.643
359
24
1
2839
3197
467545808
467545456
2.960000e-135
492.0
5
TraesCS6D01G393700
chr6D
79.902
204
12
9
2630
2812
467539816
467539621
4.480000e-24
122.0
6
TraesCS6D01G393700
chr6D
82.171
129
7
11
2630
2756
467545941
467545827
2.710000e-16
97.1
7
TraesCS6D01G393700
chr6D
97.059
34
1
0
678
711
111432281
111432314
1.280000e-04
58.4
8
TraesCS6D01G393700
chr6D
97.059
34
1
0
678
711
253868275
253868242
1.280000e-04
58.4
9
TraesCS6D01G393700
chr6A
89.712
1808
138
19
673
2465
613773544
613771770
0.000000e+00
2265.0
10
TraesCS6D01G393700
chr6A
87.997
1233
122
16
1234
2456
613794014
613792798
0.000000e+00
1434.0
11
TraesCS6D01G393700
chr6A
87.667
673
63
15
4
670
390452159
390451501
0.000000e+00
765.0
12
TraesCS6D01G393700
chr6A
91.498
494
27
2
2811
3304
613771200
613770722
0.000000e+00
665.0
13
TraesCS6D01G393700
chr6A
87.572
346
16
10
2486
2812
613771582
613771245
3.110000e-100
375.0
14
TraesCS6D01G393700
chr6A
100.000
29
0
0
678
706
553729906
553729934
2.000000e-03
54.7
15
TraesCS6D01G393700
chr6B
86.150
1704
186
34
784
2451
712676349
712674660
0.000000e+00
1794.0
16
TraesCS6D01G393700
chr6B
87.274
1328
137
15
1139
2451
712804372
712803062
0.000000e+00
1487.0
17
TraesCS6D01G393700
chr6B
84.403
1449
187
17
1096
2522
63417970
63416539
0.000000e+00
1387.0
18
TraesCS6D01G393700
chr6B
83.649
740
70
25
2610
3305
712674404
712673672
0.000000e+00
649.0
19
TraesCS6D01G393700
chr4A
84.514
1214
132
22
1258
2461
705440066
705438899
0.000000e+00
1149.0
20
TraesCS6D01G393700
chr2B
88.226
654
65
8
19
670
655723055
655723698
0.000000e+00
771.0
21
TraesCS6D01G393700
chr2B
94.118
34
2
0
678
711
588690491
588690458
6.000000e-03
52.8
22
TraesCS6D01G393700
chr7A
87.761
670
67
10
4
670
728602380
728603037
0.000000e+00
769.0
23
TraesCS6D01G393700
chr7A
87.612
670
68
10
4
670
728597444
728596787
0.000000e+00
763.0
24
TraesCS6D01G393700
chr7A
87.519
673
64
15
4
670
720773449
720774107
0.000000e+00
760.0
25
TraesCS6D01G393700
chr7B
87.500
672
65
14
4
670
11243473
11242816
0.000000e+00
758.0
26
TraesCS6D01G393700
chr7B
94.118
34
2
0
678
711
68860505
68860472
6.000000e-03
52.8
27
TraesCS6D01G393700
chr1B
87.823
657
65
10
19
670
96296326
96296972
0.000000e+00
756.0
28
TraesCS6D01G393700
chr1A
87.092
674
67
15
4
670
451546970
451547630
0.000000e+00
745.0
29
TraesCS6D01G393700
chr4D
89.293
495
46
7
2814
3305
7779051
7779541
6.060000e-172
614.0
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
TraesCS6D01G393700
chr6D
467317703
467321007
3304
True
6104.000000
6104
100.000000
1
3305
1
chr6D.!!$R2
3304
1
TraesCS6D01G393700
chr6D
467531249
467531914
665
True
990.000000
990
93.452000
1
670
1
chr6D.!!$R3
669
2
TraesCS6D01G393700
chr6D
467545456
467547307
1851
True
745.700000
1648
87.532333
1170
3197
3
chr6D.!!$R5
2027
3
TraesCS6D01G393700
chr6D
467539197
467539816
619
True
329.000000
536
85.827500
2630
3197
2
chr6D.!!$R4
567
4
TraesCS6D01G393700
chr6A
613792798
613794014
1216
True
1434.000000
1434
87.997000
1234
2456
1
chr6A.!!$R2
1222
5
TraesCS6D01G393700
chr6A
613770722
613773544
2822
True
1101.666667
2265
89.594000
673
3304
3
chr6A.!!$R3
2631
6
TraesCS6D01G393700
chr6A
390451501
390452159
658
True
765.000000
765
87.667000
4
670
1
chr6A.!!$R1
666
7
TraesCS6D01G393700
chr6B
712803062
712804372
1310
True
1487.000000
1487
87.274000
1139
2451
1
chr6B.!!$R2
1312
8
TraesCS6D01G393700
chr6B
63416539
63417970
1431
True
1387.000000
1387
84.403000
1096
2522
1
chr6B.!!$R1
1426
9
TraesCS6D01G393700
chr6B
712673672
712676349
2677
True
1221.500000
1794
84.899500
784
3305
2
chr6B.!!$R3
2521
10
TraesCS6D01G393700
chr4A
705438899
705440066
1167
True
1149.000000
1149
84.514000
1258
2461
1
chr4A.!!$R1
1203
11
TraesCS6D01G393700
chr2B
655723055
655723698
643
False
771.000000
771
88.226000
19
670
1
chr2B.!!$F1
651
12
TraesCS6D01G393700
chr7A
728602380
728603037
657
False
769.000000
769
87.761000
4
670
1
chr7A.!!$F2
666
13
TraesCS6D01G393700
chr7A
728596787
728597444
657
True
763.000000
763
87.612000
4
670
1
chr7A.!!$R1
666
14
TraesCS6D01G393700
chr7A
720773449
720774107
658
False
760.000000
760
87.519000
4
670
1
chr7A.!!$F1
666
15
TraesCS6D01G393700
chr7B
11242816
11243473
657
True
758.000000
758
87.500000
4
670
1
chr7B.!!$R1
666
16
TraesCS6D01G393700
chr1B
96296326
96296972
646
False
756.000000
756
87.823000
19
670
1
chr1B.!!$F1
651
17
TraesCS6D01G393700
chr1A
451546970
451547630
660
False
745.000000
745
87.092000
4
670
1
chr1A.!!$F1
666
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.