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
TraesCS1B01G200500
chr1B
100.000
2639
0
0
1
2639
359220719
359218081
0.000000e+00
4874.0
1
TraesCS1B01G200500
chr2B
96.634
2644
73
9
1
2639
225325803
225323171
0.000000e+00
4375.0
2
TraesCS1B01G200500
chr2B
88.462
1846
173
33
812
2639
664329675
664327852
0.000000e+00
2193.0
3
TraesCS1B01G200500
chr4B
93.380
1858
82
21
812
2639
622502469
622500623
0.000000e+00
2712.0
4
TraesCS1B01G200500
chr4B
95.732
820
34
1
1
820
622503321
622502503
0.000000e+00
1319.0
5
TraesCS1B01G200500
chr6B
93.369
1855
80
11
814
2636
717731239
717733082
0.000000e+00
2704.0
6
TraesCS1B01G200500
chr6B
93.914
1216
48
3
812
2002
147949876
147948662
0.000000e+00
1812.0
7
TraesCS1B01G200500
chr6B
87.898
1413
134
26
812
2197
567117376
567115974
0.000000e+00
1628.0
8
TraesCS1B01G200500
chr6B
96.220
820
30
1
1
820
147950728
147949910
0.000000e+00
1341.0
9
TraesCS1B01G200500
chr6B
81.609
174
23
8
1904
2072
717732479
717732648
4.580000e-28
135.0
10
TraesCS1B01G200500
chr5B
88.063
1843
177
36
812
2636
529281267
529283084
0.000000e+00
2145.0
11
TraesCS1B01G200500
chr5B
88.467
1448
130
27
812
2253
575036921
575035505
0.000000e+00
1714.0
12
TraesCS1B01G200500
chr5B
96.711
821
24
2
1
820
659536099
659536917
0.000000e+00
1363.0
13
TraesCS1B01G200500
chr5B
95.122
820
38
1
1
820
649874453
649875270
0.000000e+00
1291.0
14
TraesCS1B01G200500
chr5B
88.372
516
32
2
1725
2214
659546441
659546954
1.750000e-166
595.0
15
TraesCS1B01G200500
chr5B
93.275
342
21
2
2300
2639
575025503
575025162
1.090000e-138
503.0
16
TraesCS1B01G200500
chr5B
92.128
343
26
1
2295
2636
649895559
649895901
1.420000e-132
483.0
17
TraesCS1B01G200500
chr5B
81.633
196
27
8
1882
2072
659546746
659546937
1.260000e-33
154.0
18
TraesCS1B01G200500
chr3D
87.554
1856
187
22
812
2636
558680114
558681956
0.000000e+00
2108.0
19
TraesCS1B01G200500
chr3D
95.833
816
33
1
1
816
558679262
558680076
0.000000e+00
1317.0
20
TraesCS1B01G200500
chr2D
88.600
1421
119
26
812
2199
12315260
12313850
0.000000e+00
1687.0
21
TraesCS1B01G200500
chr2D
95.488
820
36
1
1
820
12316100
12315282
0.000000e+00
1308.0
22
TraesCS1B01G200500
chr7B
91.156
1176
81
15
812
1983
36427258
36426102
0.000000e+00
1574.0
23
TraesCS1B01G200500
chr7B
91.908
346
27
1
2295
2639
36425868
36425523
1.420000e-132
483.0
24
TraesCS1B01G200500
chr7B
100.000
31
0
0
1882
1912
380703615
380703645
1.020000e-04
58.4
25
TraesCS1B01G200500
chr3B
95.610
820
35
1
1
820
71793798
71792980
0.000000e+00
1314.0
26
TraesCS1B01G200500
chr3B
90.000
720
46
3
1377
2072
10032856
10032139
0.000000e+00
907.0
27
TraesCS1B01G200500
chr3B
81.992
472
57
22
2011
2473
10032322
10031870
2.480000e-100
375.0
28
TraesCS1B01G200500
chr5D
95.343
816
37
1
1
816
387241738
387242552
0.000000e+00
1295.0
29
TraesCS1B01G200500
chr4D
83.518
813
105
21
1843
2639
473876286
473875487
0.000000e+00
732.0
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
TraesCS1B01G200500
chr1B
359218081
359220719
2638
True
4874.0
4874
100.0000
1
2639
1
chr1B.!!$R1
2638
1
TraesCS1B01G200500
chr2B
225323171
225325803
2632
True
4375.0
4375
96.6340
1
2639
1
chr2B.!!$R1
2638
2
TraesCS1B01G200500
chr2B
664327852
664329675
1823
True
2193.0
2193
88.4620
812
2639
1
chr2B.!!$R2
1827
3
TraesCS1B01G200500
chr4B
622500623
622503321
2698
True
2015.5
2712
94.5560
1
2639
2
chr4B.!!$R1
2638
4
TraesCS1B01G200500
chr6B
567115974
567117376
1402
True
1628.0
1628
87.8980
812
2197
1
chr6B.!!$R1
1385
5
TraesCS1B01G200500
chr6B
147948662
147950728
2066
True
1576.5
1812
95.0670
1
2002
2
chr6B.!!$R2
2001
6
TraesCS1B01G200500
chr6B
717731239
717733082
1843
False
1419.5
2704
87.4890
814
2636
2
chr6B.!!$F1
1822
7
TraesCS1B01G200500
chr5B
529281267
529283084
1817
False
2145.0
2145
88.0630
812
2636
1
chr5B.!!$F1
1824
8
TraesCS1B01G200500
chr5B
575035505
575036921
1416
True
1714.0
1714
88.4670
812
2253
1
chr5B.!!$R2
1441
9
TraesCS1B01G200500
chr5B
659536099
659536917
818
False
1363.0
1363
96.7110
1
820
1
chr5B.!!$F4
819
10
TraesCS1B01G200500
chr5B
649874453
649875270
817
False
1291.0
1291
95.1220
1
820
1
chr5B.!!$F2
819
11
TraesCS1B01G200500
chr5B
659546441
659546954
513
False
374.5
595
85.0025
1725
2214
2
chr5B.!!$F5
489
12
TraesCS1B01G200500
chr3D
558679262
558681956
2694
False
1712.5
2108
91.6935
1
2636
2
chr3D.!!$F1
2635
13
TraesCS1B01G200500
chr2D
12313850
12316100
2250
True
1497.5
1687
92.0440
1
2199
2
chr2D.!!$R1
2198
14
TraesCS1B01G200500
chr7B
36425523
36427258
1735
True
1028.5
1574
91.5320
812
2639
2
chr7B.!!$R1
1827
15
TraesCS1B01G200500
chr3B
71792980
71793798
818
True
1314.0
1314
95.6100
1
820
1
chr3B.!!$R1
819
16
TraesCS1B01G200500
chr3B
10031870
10032856
986
True
641.0
907
85.9960
1377
2473
2
chr3B.!!$R2
1096
17
TraesCS1B01G200500
chr5D
387241738
387242552
814
False
1295.0
1295
95.3430
1
816
1
chr5D.!!$F1
815
18
TraesCS1B01G200500
chr4D
473875487
473876286
799
True
732.0
732
83.5180
1843
2639
1
chr4D.!!$R1
796
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.