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
TraesCS7D01G271400
chr7D
100.000
3492
0
0
1
3492
259842392
259838901
0.000000e+00
6449
1
TraesCS7D01G271400
chr7D
88.453
433
44
6
1
430
596066420
596066849
5.170000e-143
518
2
TraesCS7D01G271400
chr7A
94.248
3077
78
34
469
3492
282370329
282367299
0.000000e+00
4610
3
TraesCS7D01G271400
chr7B
93.629
2637
100
28
1
2615
239361448
239364038
0.000000e+00
3877
4
TraesCS7D01G271400
chr7B
97.479
357
8
1
2678
3034
239364323
239364678
2.980000e-170
608
5
TraesCS7D01G271400
chr7B
89.613
491
19
14
3030
3492
239364715
239365201
2.320000e-166
595
6
TraesCS7D01G271400
chr7B
89.655
435
41
4
1
433
484274003
484273571
5.090000e-153
551
7
TraesCS7D01G271400
chr1D
88.736
435
45
4
1
433
136948629
136948197
2.390000e-146
529
8
TraesCS7D01G271400
chrUn
88.657
432
45
4
1
430
95231438
95231867
1.110000e-144
523
9
TraesCS7D01G271400
chr3A
88.276
435
47
4
1
433
562894286
562893854
5.170000e-143
518
10
TraesCS7D01G271400
chr3A
84.259
324
42
6
1
321
550459961
550460278
1.220000e-79
307
11
TraesCS7D01G271400
chr3A
90.385
156
15
0
1539
1694
718836827
718836672
4.570000e-49
206
12
TraesCS7D01G271400
chr5B
87.529
433
48
6
1
430
70694438
70694009
2.420000e-136
496
13
TraesCS7D01G271400
chr5B
87.248
149
19
0
1549
1697
504307100
504306952
1.670000e-38
171
14
TraesCS7D01G271400
chr6D
88.020
409
46
3
1
407
468582480
468582887
6.780000e-132
481
15
TraesCS7D01G271400
chr6B
86.806
432
51
6
1
430
10691309
10691736
8.770000e-131
477
16
TraesCS7D01G271400
chr3B
91.558
154
13
0
1541
1694
786970552
786970399
2.730000e-51
213
17
TraesCS7D01G271400
chr3D
90.909
154
14
0
1541
1694
588489280
588489127
1.270000e-49
207
18
TraesCS7D01G271400
chr5A
87.248
149
19
0
1549
1697
530302400
530302252
1.670000e-38
171
19
TraesCS7D01G271400
chr5D
86.577
149
20
0
1549
1697
417040861
417040713
7.750000e-37
165
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
TraesCS7D01G271400
chr7D
259838901
259842392
3491
True
6449.000000
6449
100.000000
1
3492
1
chr7D.!!$R1
3491
1
TraesCS7D01G271400
chr7A
282367299
282370329
3030
True
4610.000000
4610
94.248000
469
3492
1
chr7A.!!$R1
3023
2
TraesCS7D01G271400
chr7B
239361448
239365201
3753
False
1693.333333
3877
93.573667
1
3492
3
chr7B.!!$F1
3491
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.