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
TraesCS7A01G095000
chr7A
100.000
2688
0
0
1
2688
57964024
57961337
0.000000e+00
4964
1
TraesCS7A01G095000
chr6A
97.593
2701
45
8
1
2688
315406070
315408763
0.000000e+00
4610
2
TraesCS7A01G095000
chr6A
87.769
1161
92
23
1220
2344
70063906
70065052
0.000000e+00
1312
3
TraesCS7A01G095000
chr6A
89.866
671
42
14
396
1047
70063245
70063908
0.000000e+00
839
4
TraesCS7A01G095000
chr4B
96.213
1637
55
5
1057
2688
633178312
633176678
0.000000e+00
2673
5
TraesCS7A01G095000
chr4B
96.993
1031
24
1
1
1024
633179339
633178309
0.000000e+00
1725
6
TraesCS7A01G095000
chr4B
87.166
1161
99
23
1220
2344
125739564
125740710
0.000000e+00
1273
7
TraesCS7A01G095000
chr3D
87.984
2222
168
47
396
2561
33867197
33865019
0.000000e+00
2532
8
TraesCS7A01G095000
chr2A
86.461
2105
195
45
502
2557
552865042
552862979
0.000000e+00
2226
9
TraesCS7A01G095000
chr2A
85.913
575
46
19
1831
2373
445929320
445928749
4.990000e-162
580
10
TraesCS7A01G095000
chr2A
96.721
122
4
0
2562
2683
552862569
552862448
1.260000e-48
204
11
TraesCS7A01G095000
chr7B
88.881
1484
105
19
396
1855
1757851
1759298
0.000000e+00
1772
12
TraesCS7A01G095000
chr7B
88.538
1012
79
19
1395
2373
693933330
693932323
0.000000e+00
1192
13
TraesCS7A01G095000
chr7B
95.935
123
5
0
2561
2683
693932036
693931914
1.630000e-47
200
14
TraesCS7A01G095000
chr5A
98.138
913
9
2
1
905
436605109
436606021
0.000000e+00
1585
15
TraesCS7A01G095000
chr5A
98.049
615
10
2
2076
2688
436608120
436608734
0.000000e+00
1068
16
TraesCS7A01G095000
chr1A
87.931
1102
98
23
505
1595
517327301
517328378
0.000000e+00
1266
17
TraesCS7A01G095000
chr1A
96.000
125
5
0
2559
2683
517330339
517330463
1.260000e-48
204
18
TraesCS7A01G095000
chr1A
90.833
120
8
1
396
512
517325761
517325880
9.960000e-35
158
19
TraesCS7A01G095000
chr4D
86.524
1165
90
32
1220
2344
487999872
488001009
0.000000e+00
1219
20
TraesCS7A01G095000
chr4D
89.655
667
45
15
396
1047
487999217
487999874
0.000000e+00
828
21
TraesCS7A01G095000
chr3B
87.587
1007
79
16
1395
2366
8745307
8744312
0.000000e+00
1125
22
TraesCS7A01G095000
chr3B
96.748
123
4
0
2561
2683
8744019
8743897
3.510000e-49
206
23
TraesCS7A01G095000
chr3B
93.333
75
5
0
1
75
778415504
778415578
7.870000e-21
111
24
TraesCS7A01G095000
chr3A
88.213
806
80
11
798
1596
36801821
36801024
0.000000e+00
948
25
TraesCS7A01G095000
chr3A
85.692
643
55
15
1780
2390
324102842
324102205
0.000000e+00
643
26
TraesCS7A01G095000
chr3A
83.709
577
62
16
2014
2561
36800548
36799975
1.430000e-142
516
27
TraesCS7A01G095000
chr4A
87.219
579
50
17
1809
2373
293331393
293330825
2.920000e-179
638
28
TraesCS7A01G095000
chr2B
92.058
277
19
3
2288
2563
541601751
541602025
1.170000e-103
387
29
TraesCS7A01G095000
chr2B
94.444
126
7
0
2563
2688
541602343
541602468
7.590000e-46
195
30
TraesCS7A01G095000
chr5D
97.541
122
3
0
2562
2683
548609866
548609987
2.710000e-50
209
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
TraesCS7A01G095000
chr7A
57961337
57964024
2687
True
4964.000000
4964
100.0000
1
2688
1
chr7A.!!$R1
2687
1
TraesCS7A01G095000
chr6A
315406070
315408763
2693
False
4610.000000
4610
97.5930
1
2688
1
chr6A.!!$F1
2687
2
TraesCS7A01G095000
chr6A
70063245
70065052
1807
False
1075.500000
1312
88.8175
396
2344
2
chr6A.!!$F2
1948
3
TraesCS7A01G095000
chr4B
633176678
633179339
2661
True
2199.000000
2673
96.6030
1
2688
2
chr4B.!!$R1
2687
4
TraesCS7A01G095000
chr4B
125739564
125740710
1146
False
1273.000000
1273
87.1660
1220
2344
1
chr4B.!!$F1
1124
5
TraesCS7A01G095000
chr3D
33865019
33867197
2178
True
2532.000000
2532
87.9840
396
2561
1
chr3D.!!$R1
2165
6
TraesCS7A01G095000
chr2A
552862448
552865042
2594
True
1215.000000
2226
91.5910
502
2683
2
chr2A.!!$R2
2181
7
TraesCS7A01G095000
chr2A
445928749
445929320
571
True
580.000000
580
85.9130
1831
2373
1
chr2A.!!$R1
542
8
TraesCS7A01G095000
chr7B
1757851
1759298
1447
False
1772.000000
1772
88.8810
396
1855
1
chr7B.!!$F1
1459
9
TraesCS7A01G095000
chr7B
693931914
693933330
1416
True
696.000000
1192
92.2365
1395
2683
2
chr7B.!!$R1
1288
10
TraesCS7A01G095000
chr5A
436605109
436608734
3625
False
1326.500000
1585
98.0935
1
2688
2
chr5A.!!$F1
2687
11
TraesCS7A01G095000
chr1A
517325761
517330463
4702
False
542.666667
1266
91.5880
396
2683
3
chr1A.!!$F1
2287
12
TraesCS7A01G095000
chr4D
487999217
488001009
1792
False
1023.500000
1219
88.0895
396
2344
2
chr4D.!!$F1
1948
13
TraesCS7A01G095000
chr3B
8743897
8745307
1410
True
665.500000
1125
92.1675
1395
2683
2
chr3B.!!$R1
1288
14
TraesCS7A01G095000
chr3A
36799975
36801821
1846
True
732.000000
948
85.9610
798
2561
2
chr3A.!!$R2
1763
15
TraesCS7A01G095000
chr3A
324102205
324102842
637
True
643.000000
643
85.6920
1780
2390
1
chr3A.!!$R1
610
16
TraesCS7A01G095000
chr4A
293330825
293331393
568
True
638.000000
638
87.2190
1809
2373
1
chr4A.!!$R1
564
17
TraesCS7A01G095000
chr2B
541601751
541602468
717
False
291.000000
387
93.2510
2288
2688
2
chr2B.!!$F1
400
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.