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
TraesCS5A01G319500
chr5A
100.000
2480
0
0
1
2480
531398023
531395544
0.000000e+00
4580.0
1
TraesCS5A01G319500
chr5A
89.401
217
20
3
364
578
644353263
644353048
1.130000e-68
270.0
2
TraesCS5A01G319500
chr5A
96.471
85
3
0
2117
2201
531395823
531395907
9.250000e-30
141.0
3
TraesCS5A01G319500
chr5A
95.455
88
4
0
2114
2201
660790603
660790516
9.250000e-30
141.0
4
TraesCS5A01G319500
chr6A
96.657
2483
56
10
1
2480
604196224
604198682
0.000000e+00
4100.0
5
TraesCS5A01G319500
chr6A
91.163
215
17
2
363
576
25623555
25623342
8.680000e-75
291.0
6
TraesCS5A01G319500
chr6A
96.471
85
3
0
2117
2201
604198404
604198320
9.250000e-30
141.0
7
TraesCS5A01G319500
chr6B
88.753
818
64
13
977
1784
695834260
695835059
0.000000e+00
976.0
8
TraesCS5A01G319500
chr6B
86.182
550
70
6
1561
2108
649107899
649108444
7.640000e-165
590.0
9
TraesCS5A01G319500
chr6B
79.770
781
137
12
794
1563
649107009
649107779
4.660000e-152
547.0
10
TraesCS5A01G319500
chr6B
95.575
339
13
1
1781
2117
695840337
695840675
2.170000e-150
542.0
11
TraesCS5A01G319500
chr6B
97.849
279
6
0
2202
2480
695840677
695840955
1.330000e-132
483.0
12
TraesCS5A01G319500
chr6B
83.991
431
45
11
573
979
695821021
695821451
2.310000e-105
392.0
13
TraesCS5A01G319500
chr6B
88.433
268
31
0
2200
2467
649108452
649108719
8.550000e-85
324.0
14
TraesCS5A01G319500
chr6B
90.476
210
19
1
364
572
9364946
9365155
2.430000e-70
276.0
15
TraesCS5A01G319500
chr6B
95.455
88
4
0
2117
2204
187829333
187829246
9.250000e-30
141.0
16
TraesCS5A01G319500
chr6B
90.909
88
8
0
278
365
695820946
695821033
4.330000e-23
119.0
17
TraesCS5A01G319500
chr6D
94.737
342
11
2
1785
2119
457265074
457265415
2.180000e-145
525.0
18
TraesCS5A01G319500
chr6D
83.929
560
65
8
1561
2119
430706333
430706868
1.700000e-141
512.0
19
TraesCS5A01G319500
chr6D
97.509
281
7
0
2200
2480
457265413
457265693
4.800000e-132
481.0
20
TraesCS5A01G319500
chr6D
88.693
283
30
1
2200
2480
430706866
430707148
6.570000e-91
344.0
21
TraesCS5A01G319500
chr6D
91.441
222
13
1
573
794
457260266
457260481
1.440000e-77
300.0
22
TraesCS5A01G319500
chr6D
95.833
72
3
0
290
361
457260203
457260274
1.560000e-22
117.0
23
TraesCS5A01G319500
chr3A
90.821
207
18
1
364
569
290712318
290712524
2.430000e-70
276.0
24
TraesCS5A01G319500
chrUn
90.777
206
17
2
369
573
63263791
63263587
8.740000e-70
274.0
25
TraesCS5A01G319500
chrUn
95.402
87
4
0
2115
2201
100223737
100223823
3.330000e-29
139.0
26
TraesCS5A01G319500
chr4A
90.000
210
20
1
364
572
604639722
604639513
1.130000e-68
270.0
27
TraesCS5A01G319500
chr1A
90.000
210
20
1
364
572
402617218
402617427
1.130000e-68
270.0
28
TraesCS5A01G319500
chr1A
90.000
210
17
2
363
572
551528255
551528460
4.070000e-68
268.0
29
TraesCS5A01G319500
chr1B
96.591
88
3
0
2114
2201
328029465
328029552
1.990000e-31
147.0
30
TraesCS5A01G319500
chr2A
95.506
89
4
0
2113
2201
569281160
569281072
2.570000e-30
143.0
31
TraesCS5A01G319500
chr2A
96.471
85
3
0
2117
2201
709027584
709027668
9.250000e-30
141.0
32
TraesCS5A01G319500
chr3D
94.286
35
2
0
943
977
596080945
596080911
1.000000e-03
54.7
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
TraesCS5A01G319500
chr5A
531395544
531398023
2479
True
4580.0
4580
100.000
1
2480
1
chr5A.!!$R1
2479
1
TraesCS5A01G319500
chr6A
604196224
604198682
2458
False
4100.0
4100
96.657
1
2480
1
chr6A.!!$F1
2479
2
TraesCS5A01G319500
chr6B
695834260
695835059
799
False
976.0
976
88.753
977
1784
1
chr6B.!!$F2
807
3
TraesCS5A01G319500
chr6B
695840337
695840955
618
False
512.5
542
96.712
1781
2480
2
chr6B.!!$F5
699
4
TraesCS5A01G319500
chr6B
649107009
649108719
1710
False
487.0
590
84.795
794
2467
3
chr6B.!!$F3
1673
5
TraesCS5A01G319500
chr6B
695820946
695821451
505
False
255.5
392
87.450
278
979
2
chr6B.!!$F4
701
6
TraesCS5A01G319500
chr6D
457265074
457265693
619
False
503.0
525
96.123
1785
2480
2
chr6D.!!$F3
695
7
TraesCS5A01G319500
chr6D
430706333
430707148
815
False
428.0
512
86.311
1561
2480
2
chr6D.!!$F1
919
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.