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
TraesCS7D01G392800
chr7D
100.000
3816
0
0
1
3816
507820799
507816984
0.000000e+00
7047.0
1
TraesCS7D01G392800
chr7D
84.706
170
24
2
489
657
37116840
37116672
6.560000e-38
169.0
2
TraesCS7D01G392800
chr7D
87.075
147
18
1
489
634
187306771
187306917
8.480000e-37
165.0
3
TraesCS7D01G392800
chr7D
82.955
176
24
6
483
655
122878015
122878187
1.840000e-33
154.0
4
TraesCS7D01G392800
chr7D
80.899
178
29
4
302
477
635027243
635027417
6.650000e-28
135.0
5
TraesCS7D01G392800
chr7A
95.203
2314
71
16
705
2991
577445297
577442997
0.000000e+00
3622.0
6
TraesCS7D01G392800
chr7A
92.365
668
43
6
1
667
577448275
577447615
0.000000e+00
944.0
7
TraesCS7D01G392800
chr7A
92.857
378
22
3
3443
3816
577442468
577442092
9.320000e-151
544.0
8
TraesCS7D01G392800
chr7A
90.333
300
15
7
3119
3415
577442840
577442552
7.740000e-102
381.0
9
TraesCS7D01G392800
chr7A
95.625
160
3
1
3026
3181
577442999
577442840
1.760000e-63
254.0
10
TraesCS7D01G392800
chr7A
85.393
178
25
1
301
478
32776508
32776684
2.340000e-42
183.0
11
TraesCS7D01G392800
chr7A
85.965
171
23
1
488
657
197136295
197136125
8.420000e-42
182.0
12
TraesCS7D01G392800
chr7A
85.882
170
20
2
313
478
681095249
681095080
1.090000e-40
178.0
13
TraesCS7D01G392800
chr7A
83.721
172
25
3
489
658
46194516
46194346
3.950000e-35
159.0
14
TraesCS7D01G392800
chr7A
97.059
34
1
0
3415
3448
577442534
577442501
1.480000e-04
58.4
15
TraesCS7D01G392800
chr7B
95.847
1228
37
8
1781
3004
536006213
536004996
0.000000e+00
1973.0
16
TraesCS7D01G392800
chr7B
95.311
1109
41
7
682
1784
536007438
536006335
0.000000e+00
1749.0
17
TraesCS7D01G392800
chr7B
91.270
504
37
4
165
667
536007921
536007424
0.000000e+00
680.0
18
TraesCS7D01G392800
chr7B
94.385
374
17
2
3444
3813
536004578
536004205
4.280000e-159
571.0
19
TraesCS7D01G392800
chr7B
86.595
373
26
10
3086
3448
536004970
536004612
1.290000e-104
390.0
20
TraesCS7D01G392800
chr7B
91.463
164
14
0
302
465
382332091
382331928
3.840000e-55
226.0
21
TraesCS7D01G392800
chr7B
88.950
181
19
1
301
480
626602343
626602523
4.960000e-54
222.0
22
TraesCS7D01G392800
chr7B
94.444
126
5
2
43
168
536010558
536010435
3.890000e-45
193.0
23
TraesCS7D01G392800
chr7B
83.237
173
24
5
489
658
11668534
11668364
1.840000e-33
154.0
24
TraesCS7D01G392800
chr3D
91.860
172
12
2
298
468
87926164
87925994
4.930000e-59
239.0
25
TraesCS7D01G392800
chr2D
92.216
167
10
3
299
464
296364046
296364210
2.290000e-57
233.0
26
TraesCS7D01G392800
chr2D
84.211
171
26
1
489
658
585134258
585134428
8.480000e-37
165.0
27
TraesCS7D01G392800
chr2D
94.737
38
2
0
441
478
602733434
602733397
4.120000e-05
60.2
28
TraesCS7D01G392800
chr2B
92.216
167
10
3
299
464
366017682
366017518
2.290000e-57
233.0
29
TraesCS7D01G392800
chr2B
87.151
179
20
3
302
477
578597865
578597687
2.320000e-47
200.0
30
TraesCS7D01G392800
chrUn
91.515
165
14
0
299
463
141680743
141680907
1.070000e-55
228.0
31
TraesCS7D01G392800
chr4D
89.714
175
18
0
301
475
117421353
117421179
1.380000e-54
224.0
32
TraesCS7D01G392800
chr3B
78.107
169
33
4
486
652
53476553
53476387
1.880000e-18
104.0
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
TraesCS7D01G392800
chr7D
507816984
507820799
3815
True
7047.000000
7047
100.000000
1
3816
1
chr7D.!!$R2
3815
1
TraesCS7D01G392800
chr7A
577442092
577448275
6183
True
967.233333
3622
93.907000
1
3816
6
chr7A.!!$R4
3815
2
TraesCS7D01G392800
chr7B
536004205
536010558
6353
True
926.000000
1973
92.975333
43
3813
6
chr7B.!!$R3
3770
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.