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
TraesCS1B01G058500
chr1B
100.000
2438
0
0
1
2438
40854586
40852149
0.000000e+00
4503
1
TraesCS1B01G058500
chr1B
87.198
414
20
14
1878
2291
40702885
40702505
8.000000e-120
440
2
TraesCS1B01G058500
chr1B
91.473
129
11
0
2288
2416
40700498
40700370
6.930000e-41
178
3
TraesCS1B01G058500
chr1B
87.288
118
8
6
1762
1878
642772607
642772496
7.080000e-26
128
4
TraesCS1B01G058500
chr6D
95.922
1888
63
9
1
1878
321115220
321117103
0.000000e+00
3048
5
TraesCS1B01G058500
chr1A
95.003
1881
89
5
1
1878
487768957
487770835
0.000000e+00
2948
6
TraesCS1B01G058500
chr1A
84.725
1892
259
23
1
1878
347624342
347626217
0.000000e+00
1866
7
TraesCS1B01G058500
chr1A
95.733
539
23
0
1878
2416
26590402
26589864
0.000000e+00
869
8
TraesCS1B01G058500
chr4B
90.122
1883
166
12
1
1878
642377834
642375967
0.000000e+00
2429
9
TraesCS1B01G058500
chr2D
87.507
1769
201
17
1
1758
610359089
610360848
0.000000e+00
2025
10
TraesCS1B01G058500
chr2D
86.408
103
7
6
1780
1878
610360904
610361003
3.320000e-19
106
11
TraesCS1B01G058500
chr1D
88.806
1599
173
5
1
1599
252296805
252298397
0.000000e+00
1956
12
TraesCS1B01G058500
chr1D
92.421
541
28
8
1878
2416
25464040
25463511
0.000000e+00
760
13
TraesCS1B01G058500
chr1D
91.159
328
17
4
1878
2205
25416818
25416503
3.720000e-118
435
14
TraesCS1B01G058500
chr1D
93.607
219
12
1
2200
2416
25411413
25411195
2.340000e-85
326
15
TraesCS1B01G058500
chr6B
85.989
1770
230
10
1
1760
617784100
617782339
0.000000e+00
1879
16
TraesCS1B01G058500
chr2A
84.733
1893
257
24
1
1878
146945604
146943729
0.000000e+00
1866
17
TraesCS1B01G058500
chr5B
84.972
1271
182
7
494
1760
357163716
357162451
0.000000e+00
1280
18
TraesCS1B01G058500
chr7B
81.858
226
30
9
1550
1773
606554084
606553868
1.930000e-41
180
19
TraesCS1B01G058500
chr7B
87.395
119
7
6
1765
1878
606553842
606553727
1.970000e-26
130
20
TraesCS1B01G058500
chr7B
90.110
91
3
5
1789
1878
720476585
720476500
1.980000e-21
113
21
TraesCS1B01G058500
chr3A
74.359
312
78
2
65
375
721978677
721978367
5.470000e-27
132
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
TraesCS1B01G058500
chr1B
40852149
40854586
2437
True
4503.0
4503
100.0000
1
2438
1
chr1B.!!$R1
2437
1
TraesCS1B01G058500
chr1B
40700370
40702885
2515
True
309.0
440
89.3355
1878
2416
2
chr1B.!!$R3
538
2
TraesCS1B01G058500
chr6D
321115220
321117103
1883
False
3048.0
3048
95.9220
1
1878
1
chr6D.!!$F1
1877
3
TraesCS1B01G058500
chr1A
487768957
487770835
1878
False
2948.0
2948
95.0030
1
1878
1
chr1A.!!$F2
1877
4
TraesCS1B01G058500
chr1A
347624342
347626217
1875
False
1866.0
1866
84.7250
1
1878
1
chr1A.!!$F1
1877
5
TraesCS1B01G058500
chr1A
26589864
26590402
538
True
869.0
869
95.7330
1878
2416
1
chr1A.!!$R1
538
6
TraesCS1B01G058500
chr4B
642375967
642377834
1867
True
2429.0
2429
90.1220
1
1878
1
chr4B.!!$R1
1877
7
TraesCS1B01G058500
chr2D
610359089
610361003
1914
False
1065.5
2025
86.9575
1
1878
2
chr2D.!!$F1
1877
8
TraesCS1B01G058500
chr1D
252296805
252298397
1592
False
1956.0
1956
88.8060
1
1599
1
chr1D.!!$F1
1598
9
TraesCS1B01G058500
chr1D
25463511
25464040
529
True
760.0
760
92.4210
1878
2416
1
chr1D.!!$R3
538
10
TraesCS1B01G058500
chr6B
617782339
617784100
1761
True
1879.0
1879
85.9890
1
1760
1
chr6B.!!$R1
1759
11
TraesCS1B01G058500
chr2A
146943729
146945604
1875
True
1866.0
1866
84.7330
1
1878
1
chr2A.!!$R1
1877
12
TraesCS1B01G058500
chr5B
357162451
357163716
1265
True
1280.0
1280
84.9720
494
1760
1
chr5B.!!$R1
1266
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.