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
TraesCS6A01G074400
chr6A
100.000
2699
0
0
1
2699
42390101
42387403
0.000000e+00
4985.0
1
TraesCS6A01G074400
chr6A
99.074
2700
15
2
1
2699
42209190
42206500
0.000000e+00
4839.0
2
TraesCS6A01G074400
chr6A
86.055
1929
214
23
574
2462
62489515
62487602
0.000000e+00
2021.0
3
TraesCS6A01G074400
chr6A
87.143
210
23
1
2334
2543
62659850
62659645
4.490000e-58
235.0
4
TraesCS6A01G074400
chrUn
92.428
1915
96
22
826
2699
105245674
105247580
0.000000e+00
2687.0
5
TraesCS6A01G074400
chrUn
93.955
579
24
4
1
576
105245010
105245580
0.000000e+00
865.0
6
TraesCS6A01G074400
chrUn
100.000
431
0
0
1
431
345248710
345248280
0.000000e+00
797.0
7
TraesCS6A01G074400
chr6D
87.090
2014
202
26
574
2543
53309609
53311608
0.000000e+00
2226.0
8
TraesCS6A01G074400
chr6D
86.959
2009
202
28
574
2543
51624458
51622471
0.000000e+00
2204.0
9
TraesCS6A01G074400
chr6D
91.065
582
44
7
1
578
53308991
53309568
0.000000e+00
780.0
10
TraesCS6A01G074400
chr6D
89.465
579
55
5
1
576
51625076
51624501
0.000000e+00
726.0
11
TraesCS6A01G074400
chr6D
86.567
67
9
0
1416
1482
52007920
52007986
1.040000e-09
75.0
12
TraesCS6A01G074400
chr6B
88.503
1783
172
12
574
2332
76598961
76597188
0.000000e+00
2126.0
13
TraesCS6A01G074400
chr6B
87.747
1771
191
11
574
2325
118823165
118821402
0.000000e+00
2045.0
14
TraesCS6A01G074400
chr6B
89.173
1367
119
16
970
2316
76733990
76732633
0.000000e+00
1677.0
15
TraesCS6A01G074400
chr6B
91.019
579
46
5
2
576
118823784
118823208
0.000000e+00
776.0
16
TraesCS6A01G074400
chr6B
90.690
580
46
6
1
576
76742411
76741836
0.000000e+00
765.0
17
TraesCS6A01G074400
chr6B
90.674
579
45
6
1
576
76599576
76599004
0.000000e+00
761.0
18
TraesCS6A01G074400
chr6B
84.564
298
41
2
2403
2699
76573228
76572935
9.450000e-75
291.0
19
TraesCS6A01G074400
chr6B
91.429
210
14
1
2334
2543
118784749
118784544
4.400000e-73
285.0
20
TraesCS6A01G074400
chr6B
90.411
73
7
0
2333
2405
76574722
76574650
2.210000e-16
97.1
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
TraesCS6A01G074400
chr6A
42387403
42390101
2698
True
4985.0
4985
100.0000
1
2699
1
chr6A.!!$R2
2698
1
TraesCS6A01G074400
chr6A
42206500
42209190
2690
True
4839.0
4839
99.0740
1
2699
1
chr6A.!!$R1
2698
2
TraesCS6A01G074400
chr6A
62487602
62489515
1913
True
2021.0
2021
86.0550
574
2462
1
chr6A.!!$R3
1888
3
TraesCS6A01G074400
chrUn
105245010
105247580
2570
False
1776.0
2687
93.1915
1
2699
2
chrUn.!!$F1
2698
4
TraesCS6A01G074400
chr6D
53308991
53311608
2617
False
1503.0
2226
89.0775
1
2543
2
chr6D.!!$F2
2542
5
TraesCS6A01G074400
chr6D
51622471
51625076
2605
True
1465.0
2204
88.2120
1
2543
2
chr6D.!!$R1
2542
6
TraesCS6A01G074400
chr6B
76732633
76733990
1357
True
1677.0
1677
89.1730
970
2316
1
chr6B.!!$R1
1346
7
TraesCS6A01G074400
chr6B
76597188
76599576
2388
True
1443.5
2126
89.5885
1
2332
2
chr6B.!!$R5
2331
8
TraesCS6A01G074400
chr6B
118821402
118823784
2382
True
1410.5
2045
89.3830
2
2325
2
chr6B.!!$R6
2323
9
TraesCS6A01G074400
chr6B
76741836
76742411
575
True
765.0
765
90.6900
1
576
1
chr6B.!!$R2
575
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.