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
TraesCS1A01G360100
chr1A
100.000
2312
0
0
1
2312
541461785
541459474
0.000000e+00
4270.0
1
TraesCS1A01G360100
chr1A
85.070
1641
131
52
715
2302
541343537
541345116
0.000000e+00
1568.0
2
TraesCS1A01G360100
chr1A
97.053
543
15
1
772
1313
543928135
543928677
0.000000e+00
913.0
3
TraesCS1A01G360100
chr1A
84.574
564
49
12
1
546
456652610
456653153
2.030000e-145
525.0
4
TraesCS1A01G360100
chr1A
87.088
364
37
5
1898
2255
456654523
456654882
9.950000e-109
403.0
5
TraesCS1A01G360100
chr1A
87.748
302
26
7
274
574
541343194
541343485
2.200000e-90
342.0
6
TraesCS1A01G360100
chr1A
89.796
98
8
2
478
574
487572594
487572690
8.670000e-25
124.0
7
TraesCS1A01G360100
chr1A
78.981
157
14
13
1432
1574
456654119
456654270
3.160000e-14
89.8
8
TraesCS1A01G360100
chr3D
85.880
1381
108
37
713
2020
114881015
114879649
0.000000e+00
1389.0
9
TraesCS1A01G360100
chr3D
89.394
198
17
3
2117
2312
114879611
114879416
1.770000e-61
246.0
10
TraesCS1A01G360100
chr3A
83.537
1555
131
40
713
2153
111104418
111102875
0.000000e+00
1338.0
11
TraesCS1A01G360100
chr1D
86.411
1251
97
41
704
1896
445367113
445365878
0.000000e+00
1301.0
12
TraesCS1A01G360100
chr1D
86.137
1183
112
29
735
1896
355827820
355828971
0.000000e+00
1229.0
13
TraesCS1A01G360100
chr1D
86.862
784
72
20
729
1494
388603359
388604129
0.000000e+00
848.0
14
TraesCS1A01G360100
chr1D
88.663
591
44
10
1
574
446438816
446439400
0.000000e+00
699.0
15
TraesCS1A01G360100
chr1D
85.336
566
56
10
4
546
355827007
355827568
5.580000e-156
560.0
16
TraesCS1A01G360100
chr1D
88.389
422
38
7
1899
2312
355829003
355829421
4.440000e-137
497.0
17
TraesCS1A01G360100
chr1D
88.337
403
33
5
1902
2302
446477087
446477477
2.690000e-129
472.0
18
TraesCS1A01G360100
chr1D
79.470
151
22
7
1330
1480
394490842
394490701
5.260000e-17
99.0
19
TraesCS1A01G360100
chr1B
86.422
1171
89
37
738
1855
607317032
607315879
0.000000e+00
1218.0
20
TraesCS1A01G360100
chr1B
88.317
1010
70
20
733
1702
608043027
608042026
0.000000e+00
1168.0
21
TraesCS1A01G360100
chr1B
84.459
1229
96
51
733
1896
610892995
610894193
0.000000e+00
1123.0
22
TraesCS1A01G360100
chr1B
86.727
987
84
27
733
1704
608335898
608334944
0.000000e+00
1053.0
23
TraesCS1A01G360100
chr1B
87.500
584
47
11
1
565
610562475
610563051
0.000000e+00
651.0
24
TraesCS1A01G360100
chr1B
87.593
403
34
6
1902
2302
610894225
610894613
9.740000e-124
453.0
25
TraesCS1A01G360100
chr1B
88.411
302
28
3
275
574
608353397
608353101
7.860000e-95
357.0
26
TraesCS1A01G360100
chr1B
85.185
270
26
8
1898
2156
608042012
608041746
4.900000e-67
265.0
27
TraesCS1A01G360100
chr1B
88.776
98
9
2
478
574
521768233
521768329
4.040000e-23
119.0
28
TraesCS1A01G360100
chr3B
84.759
374
34
8
1939
2312
168137276
168136926
1.020000e-93
353.0
29
TraesCS1A01G360100
chr6A
89.401
217
17
4
334
548
67140679
67140467
3.790000e-68
268.0
30
TraesCS1A01G360100
chr6D
86.550
171
18
4
392
560
47871571
47871738
1.410000e-42
183.0
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
TraesCS1A01G360100
chr1A
541459474
541461785
2311
True
4270.000000
4270
100.000000
1
2312
1
chr1A.!!$R1
2311
1
TraesCS1A01G360100
chr1A
541343194
541345116
1922
False
955.000000
1568
86.409000
274
2302
2
chr1A.!!$F4
2028
2
TraesCS1A01G360100
chr1A
543928135
543928677
542
False
913.000000
913
97.053000
772
1313
1
chr1A.!!$F2
541
3
TraesCS1A01G360100
chr1A
456652610
456654882
2272
False
339.266667
525
83.547667
1
2255
3
chr1A.!!$F3
2254
4
TraesCS1A01G360100
chr3D
114879416
114881015
1599
True
817.500000
1389
87.637000
713
2312
2
chr3D.!!$R1
1599
5
TraesCS1A01G360100
chr3A
111102875
111104418
1543
True
1338.000000
1338
83.537000
713
2153
1
chr3A.!!$R1
1440
6
TraesCS1A01G360100
chr1D
445365878
445367113
1235
True
1301.000000
1301
86.411000
704
1896
1
chr1D.!!$R2
1192
7
TraesCS1A01G360100
chr1D
388603359
388604129
770
False
848.000000
848
86.862000
729
1494
1
chr1D.!!$F1
765
8
TraesCS1A01G360100
chr1D
355827007
355829421
2414
False
762.000000
1229
86.620667
4
2312
3
chr1D.!!$F4
2308
9
TraesCS1A01G360100
chr1D
446438816
446439400
584
False
699.000000
699
88.663000
1
574
1
chr1D.!!$F2
573
10
TraesCS1A01G360100
chr1B
607315879
607317032
1153
True
1218.000000
1218
86.422000
738
1855
1
chr1B.!!$R1
1117
11
TraesCS1A01G360100
chr1B
608334944
608335898
954
True
1053.000000
1053
86.727000
733
1704
1
chr1B.!!$R2
971
12
TraesCS1A01G360100
chr1B
610892995
610894613
1618
False
788.000000
1123
86.026000
733
2302
2
chr1B.!!$F3
1569
13
TraesCS1A01G360100
chr1B
608041746
608043027
1281
True
716.500000
1168
86.751000
733
2156
2
chr1B.!!$R4
1423
14
TraesCS1A01G360100
chr1B
610562475
610563051
576
False
651.000000
651
87.500000
1
565
1
chr1B.!!$F2
564
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.