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
TraesCS3B01G544800
chr3B
100.000
3237
0
0
1
3237
782173537
782170301
0.000000e+00
5978
1
TraesCS3B01G544800
chr3B
99.012
3238
31
1
1
3237
782256039
782252802
0.000000e+00
5801
2
TraesCS3B01G544800
chr3B
98.950
3238
27
2
1
3237
782214630
782211399
0.000000e+00
5784
3
TraesCS3B01G544800
chr3B
98.888
3238
25
4
1
3237
782297852
782294625
0.000000e+00
5770
4
TraesCS3B01G544800
chr5A
95.976
2187
51
20
663
2845
457099661
457101814
0.000000e+00
3517
5
TraesCS3B01G544800
chr5A
98.204
668
11
1
1
667
457098964
457099631
0.000000e+00
1166
6
TraesCS3B01G544800
chr5A
91.031
669
58
2
1
667
390556910
390557578
0.000000e+00
902
7
TraesCS3B01G544800
chr5A
87.835
485
50
7
1080
1558
390558240
390558721
7.840000e-156
560
8
TraesCS3B01G544800
chr7B
95.932
2188
51
21
663
2846
505221664
505219511
0.000000e+00
3513
9
TraesCS3B01G544800
chr7B
98.054
668
12
1
1
667
505222361
505221694
0.000000e+00
1160
10
TraesCS3B01G544800
chr2A
89.055
2211
172
32
663
2848
21632184
21634349
0.000000e+00
2678
11
TraesCS3B01G544800
chr2A
91.330
669
56
2
1
667
180214796
180214128
0.000000e+00
913
12
TraesCS3B01G544800
chr4A
97.937
1406
28
1
1440
2845
27194815
27193411
0.000000e+00
2435
13
TraesCS3B01G544800
chr4A
90.939
1810
131
18
1047
2844
698013234
698011446
0.000000e+00
2403
14
TraesCS3B01G544800
chr4D
97.597
1165
27
1
1682
2846
505348746
505347583
0.000000e+00
1995
15
TraesCS3B01G544800
chr4D
97.902
143
3
0
885
1027
505348908
505348766
6.930000e-62
248
16
TraesCS3B01G544800
chr4B
97.517
1168
28
1
1679
2846
42255569
42256735
0.000000e+00
1995
17
TraesCS3B01G544800
chr4B
97.902
143
3
0
885
1027
42255410
42255552
6.930000e-62
248
18
TraesCS3B01G544800
chr3D
97.597
1165
27
1
1682
2846
562176038
562174875
0.000000e+00
1995
19
TraesCS3B01G544800
chr3D
92.417
211
10
2
3033
3237
585878463
585878253
2.440000e-76
296
20
TraesCS3B01G544800
chr3D
95.506
178
8
0
2845
3022
585878710
585878533
5.290000e-73
285
21
TraesCS3B01G544800
chr6B
91.181
669
57
2
1
667
532351327
532351995
0.000000e+00
907
22
TraesCS3B01G544800
chr7A
91.031
669
58
2
1
667
31808115
31808783
0.000000e+00
902
23
TraesCS3B01G544800
chr7A
87.423
485
52
7
1080
1558
31809315
31809796
1.700000e-152
549
24
TraesCS3B01G544800
chr1B
88.796
714
74
4
1568
2280
150371624
150370916
0.000000e+00
870
25
TraesCS3B01G544800
chr5D
97.902
143
3
0
885
1027
468179801
468179659
6.930000e-62
248
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
TraesCS3B01G544800
chr3B
782170301
782173537
3236
True
5978.0
5978
100.0000
1
3237
1
chr3B.!!$R1
3236
1
TraesCS3B01G544800
chr3B
782252802
782256039
3237
True
5801.0
5801
99.0120
1
3237
1
chr3B.!!$R3
3236
2
TraesCS3B01G544800
chr3B
782211399
782214630
3231
True
5784.0
5784
98.9500
1
3237
1
chr3B.!!$R2
3236
3
TraesCS3B01G544800
chr3B
782294625
782297852
3227
True
5770.0
5770
98.8880
1
3237
1
chr3B.!!$R4
3236
4
TraesCS3B01G544800
chr5A
457098964
457101814
2850
False
2341.5
3517
97.0900
1
2845
2
chr5A.!!$F2
2844
5
TraesCS3B01G544800
chr5A
390556910
390558721
1811
False
731.0
902
89.4330
1
1558
2
chr5A.!!$F1
1557
6
TraesCS3B01G544800
chr7B
505219511
505222361
2850
True
2336.5
3513
96.9930
1
2846
2
chr7B.!!$R1
2845
7
TraesCS3B01G544800
chr2A
21632184
21634349
2165
False
2678.0
2678
89.0550
663
2848
1
chr2A.!!$F1
2185
8
TraesCS3B01G544800
chr2A
180214128
180214796
668
True
913.0
913
91.3300
1
667
1
chr2A.!!$R1
666
9
TraesCS3B01G544800
chr4A
27193411
27194815
1404
True
2435.0
2435
97.9370
1440
2845
1
chr4A.!!$R1
1405
10
TraesCS3B01G544800
chr4A
698011446
698013234
1788
True
2403.0
2403
90.9390
1047
2844
1
chr4A.!!$R2
1797
11
TraesCS3B01G544800
chr4D
505347583
505348908
1325
True
1121.5
1995
97.7495
885
2846
2
chr4D.!!$R1
1961
12
TraesCS3B01G544800
chr4B
42255410
42256735
1325
False
1121.5
1995
97.7095
885
2846
2
chr4B.!!$F1
1961
13
TraesCS3B01G544800
chr3D
562174875
562176038
1163
True
1995.0
1995
97.5970
1682
2846
1
chr3D.!!$R1
1164
14
TraesCS3B01G544800
chr6B
532351327
532351995
668
False
907.0
907
91.1810
1
667
1
chr6B.!!$F1
666
15
TraesCS3B01G544800
chr7A
31808115
31809796
1681
False
725.5
902
89.2270
1
1558
2
chr7A.!!$F1
1557
16
TraesCS3B01G544800
chr1B
150370916
150371624
708
True
870.0
870
88.7960
1568
2280
1
chr1B.!!$R1
712
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.