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
TraesCS3B01G245700
chr3B
100.000
2480
0
0
1
2480
389719855
389722334
0
4580
1
TraesCS3B01G245700
chr3B
98.236
1701
28
2
1
1699
361795826
361797526
0
2974
2
TraesCS3B01G245700
chr3B
94.094
982
37
14
1518
2480
361797400
361798379
0
1472
3
TraesCS3B01G245700
chr2B
98.060
1701
31
2
1
1699
728070275
728068575
0
2957
4
TraesCS3B01G245700
chr2B
93.279
982
45
14
1518
2480
728068701
728067722
0
1428
5
TraesCS3B01G245700
chr4D
97.709
1702
35
4
1
1699
393458503
393460203
0
2924
6
TraesCS3B01G245700
chr4D
93.177
982
46
14
1518
2480
393460077
393461056
0
1423
7
TraesCS3B01G245700
chr6B
97.648
1701
35
3
1
1699
587366784
587365087
0
2915
8
TraesCS3B01G245700
chr6B
92.668
982
50
15
1518
2480
587365213
587364235
0
1395
9
TraesCS3B01G245700
chr3D
97.531
1701
37
4
1
1699
359527471
359525774
0
2904
10
TraesCS3B01G245700
chr3D
92.879
983
47
16
1518
2480
359525900
359524921
0
1406
11
TraesCS3B01G245700
chr1D
97.472
1701
40
3
1
1699
251020559
251022258
0
2900
12
TraesCS3B01G245700
chr1D
92.057
982
57
14
1518
2480
251022132
251023111
0
1362
13
TraesCS3B01G245700
chr5D
97.121
1702
46
3
1
1699
557793948
557795649
0
2868
14
TraesCS3B01G245700
chr5D
98.107
951
16
2
751
1699
565809433
565810383
0
1655
15
TraesCS3B01G245700
chr5D
92.879
983
46
17
1518
2480
557795578
557796556
0
1406
16
TraesCS3B01G245700
chr5D
92.472
983
51
16
1518
2480
565810257
565811236
0
1384
17
TraesCS3B01G245700
chr2D
96.945
1702
49
3
1
1699
621997763
621999464
0
2852
18
TraesCS3B01G245700
chr2D
92.981
983
46
16
1518
2480
621999393
622000372
0
1411
19
TraesCS3B01G245700
chr6A
94.734
1709
69
14
1
1699
583326530
583328227
0
2638
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
TraesCS3B01G245700
chr3B
389719855
389722334
2479
False
4580.0
4580
100.0000
1
2480
1
chr3B.!!$F1
2479
1
TraesCS3B01G245700
chr3B
361795826
361798379
2553
False
2223.0
2974
96.1650
1
2480
2
chr3B.!!$F2
2479
2
TraesCS3B01G245700
chr2B
728067722
728070275
2553
True
2192.5
2957
95.6695
1
2480
2
chr2B.!!$R1
2479
3
TraesCS3B01G245700
chr4D
393458503
393461056
2553
False
2173.5
2924
95.4430
1
2480
2
chr4D.!!$F1
2479
4
TraesCS3B01G245700
chr6B
587364235
587366784
2549
True
2155.0
2915
95.1580
1
2480
2
chr6B.!!$R1
2479
5
TraesCS3B01G245700
chr3D
359524921
359527471
2550
True
2155.0
2904
95.2050
1
2480
2
chr3D.!!$R1
2479
6
TraesCS3B01G245700
chr1D
251020559
251023111
2552
False
2131.0
2900
94.7645
1
2480
2
chr1D.!!$F1
2479
7
TraesCS3B01G245700
chr5D
557793948
557796556
2608
False
2137.0
2868
95.0000
1
2480
2
chr5D.!!$F1
2479
8
TraesCS3B01G245700
chr5D
565809433
565811236
1803
False
1519.5
1655
95.2895
751
2480
2
chr5D.!!$F2
1729
9
TraesCS3B01G245700
chr2D
621997763
622000372
2609
False
2131.5
2852
94.9630
1
2480
2
chr2D.!!$F1
2479
10
TraesCS3B01G245700
chr6A
583326530
583328227
1697
False
2638.0
2638
94.7340
1
1699
1
chr6A.!!$F1
1698
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.