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
TraesCS7A01G286500
chr7A
100.000
2200
0
0
1
2200
335986010
335988209
0.000000e+00
4063
1
TraesCS7A01G286500
chr7B
93.832
2221
104
11
1
2191
339214980
339212763
0.000000e+00
3312
2
TraesCS7A01G286500
chr7B
89.189
111
9
3
328
436
71616749
71616640
3.810000e-28
135
3
TraesCS7A01G286500
chr7B
87.826
115
11
3
327
439
687407540
687407427
4.930000e-27
132
4
TraesCS7A01G286500
chr7D
93.551
2233
106
15
1
2200
295320916
295318689
0.000000e+00
3291
5
TraesCS7A01G286500
chr7D
78.821
916
159
22
1298
2198
290613598
290612703
3.150000e-163
584
6
TraesCS7A01G286500
chr7D
90.452
199
16
2
110
305
237412849
237412651
2.170000e-65
259
7
TraesCS7A01G286500
chr7D
95.455
88
3
1
327
414
237412577
237412663
2.950000e-29
139
8
TraesCS7A01G286500
chr4A
80.690
1854
286
42
400
2198
637695869
637697705
0.000000e+00
1375
9
TraesCS7A01G286500
chr4A
79.890
726
131
13
395
1113
736383797
736383080
3.240000e-143
518
10
TraesCS7A01G286500
chr4A
89.756
205
19
2
109
311
3883728
3883524
6.020000e-66
261
11
TraesCS7A01G286500
chr5A
78.777
1701
294
46
551
2198
328833899
328832213
0.000000e+00
1079
12
TraesCS7A01G286500
chr5A
86.307
796
105
2
1407
2198
331754570
331753775
0.000000e+00
863
13
TraesCS7A01G286500
chr1A
86.381
771
97
5
1435
2198
30263380
30262611
0.000000e+00
835
14
TraesCS7A01G286500
chr1A
78.743
668
133
6
498
1160
137881721
137882384
2.590000e-119
438
15
TraesCS7A01G286500
chr2B
85.342
805
105
5
1407
2198
358767128
358766324
0.000000e+00
821
16
TraesCS7A01G286500
chr2B
90.909
198
16
2
110
305
603410181
603410378
4.660000e-67
265
17
TraesCS7A01G286500
chr2B
94.681
94
3
2
322
414
603410458
603410366
6.330000e-31
145
18
TraesCS7A01G286500
chr2A
85.440
728
99
5
1468
2190
25260546
25259821
0.000000e+00
750
19
TraesCS7A01G286500
chr2A
85.363
731
95
10
1468
2190
25213340
25212614
0.000000e+00
747
20
TraesCS7A01G286500
chr2A
91.133
203
13
5
106
305
716504308
716504108
1.000000e-68
270
21
TraesCS7A01G286500
chr1D
80.729
768
135
12
395
1155
382734975
382735736
8.750000e-164
586
22
TraesCS7A01G286500
chr1D
78.431
663
134
7
503
1160
24583862
24583204
7.260000e-115
424
23
TraesCS7A01G286500
chr5B
81.590
717
122
8
399
1110
37785229
37785940
3.150000e-163
584
24
TraesCS7A01G286500
chr5B
81.111
720
126
10
399
1113
18343486
18342772
3.170000e-158
568
25
TraesCS7A01G286500
chr3B
90.955
199
16
2
109
305
696745240
696745042
1.290000e-67
267
26
TraesCS7A01G286500
chr3B
96.552
87
2
1
328
414
817426341
817426256
2.280000e-30
143
27
TraesCS7A01G286500
chr3B
95.455
88
3
1
327
414
763250315
763250401
2.950000e-29
139
28
TraesCS7A01G286500
chr5D
89.950
199
20
0
107
305
2748814
2749012
7.790000e-65
257
29
TraesCS7A01G286500
chr6B
88.372
215
20
5
106
318
67465713
67465502
1.010000e-63
254
30
TraesCS7A01G286500
chr4B
93.617
94
4
2
322
414
187444236
187444328
2.950000e-29
139
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
TraesCS7A01G286500
chr7A
335986010
335988209
2199
False
4063
4063
100.000
1
2200
1
chr7A.!!$F1
2199
1
TraesCS7A01G286500
chr7B
339212763
339214980
2217
True
3312
3312
93.832
1
2191
1
chr7B.!!$R2
2190
2
TraesCS7A01G286500
chr7D
295318689
295320916
2227
True
3291
3291
93.551
1
2200
1
chr7D.!!$R3
2199
3
TraesCS7A01G286500
chr7D
290612703
290613598
895
True
584
584
78.821
1298
2198
1
chr7D.!!$R2
900
4
TraesCS7A01G286500
chr4A
637695869
637697705
1836
False
1375
1375
80.690
400
2198
1
chr4A.!!$F1
1798
5
TraesCS7A01G286500
chr4A
736383080
736383797
717
True
518
518
79.890
395
1113
1
chr4A.!!$R2
718
6
TraesCS7A01G286500
chr5A
328832213
328833899
1686
True
1079
1079
78.777
551
2198
1
chr5A.!!$R1
1647
7
TraesCS7A01G286500
chr5A
331753775
331754570
795
True
863
863
86.307
1407
2198
1
chr5A.!!$R2
791
8
TraesCS7A01G286500
chr1A
30262611
30263380
769
True
835
835
86.381
1435
2198
1
chr1A.!!$R1
763
9
TraesCS7A01G286500
chr1A
137881721
137882384
663
False
438
438
78.743
498
1160
1
chr1A.!!$F1
662
10
TraesCS7A01G286500
chr2B
358766324
358767128
804
True
821
821
85.342
1407
2198
1
chr2B.!!$R1
791
11
TraesCS7A01G286500
chr2A
25259821
25260546
725
True
750
750
85.440
1468
2190
1
chr2A.!!$R2
722
12
TraesCS7A01G286500
chr2A
25212614
25213340
726
True
747
747
85.363
1468
2190
1
chr2A.!!$R1
722
13
TraesCS7A01G286500
chr1D
382734975
382735736
761
False
586
586
80.729
395
1155
1
chr1D.!!$F1
760
14
TraesCS7A01G286500
chr1D
24583204
24583862
658
True
424
424
78.431
503
1160
1
chr1D.!!$R1
657
15
TraesCS7A01G286500
chr5B
37785229
37785940
711
False
584
584
81.590
399
1110
1
chr5B.!!$F1
711
16
TraesCS7A01G286500
chr5B
18342772
18343486
714
True
568
568
81.111
399
1113
1
chr5B.!!$R1
714
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.