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
TraesCS5A01G012400
chr5A
100.000
2969
0
0
1
2969
8072743
8075711
0.000000e+00
5483
1
TraesCS5A01G012400
chr5A
90.387
1966
137
25
1022
2969
8112494
8114425
0.000000e+00
2536
2
TraesCS5A01G012400
chr5A
85.670
1298
140
23
1574
2846
8063709
8064985
0.000000e+00
1325
3
TraesCS5A01G012400
chr5A
90.446
628
49
6
910
1532
8063086
8063707
0.000000e+00
817
4
TraesCS5A01G012400
chr5A
95.385
325
12
1
30
351
8089875
8090199
5.670000e-142
514
5
TraesCS5A01G012400
chr5A
92.632
285
20
1
346
629
304124381
304124097
2.750000e-110
409
6
TraesCS5A01G012400
chr5A
92.975
242
12
2
623
860
8090196
8090436
6.090000e-92
348
7
TraesCS5A01G012400
chr5A
98.876
89
1
0
904
992
8112412
8112500
3.060000e-35
159
8
TraesCS5A01G012400
chr5D
95.455
1540
59
5
1
1532
10066668
10068204
0.000000e+00
2446
9
TraesCS5A01G012400
chr5D
95.205
1439
54
10
1545
2969
10068189
10069626
0.000000e+00
2261
10
TraesCS5A01G012400
chr5D
85.981
1234
137
19
1574
2780
10042913
10044137
0.000000e+00
1288
11
TraesCS5A01G012400
chr5D
90.363
633
51
8
904
1532
10042285
10042911
0.000000e+00
822
12
TraesCS5A01G012400
chr5D
90.135
223
21
1
663
884
10041975
10042197
3.740000e-74
289
13
TraesCS5A01G012400
chr5D
79.902
204
40
1
1307
1509
10469338
10469541
6.630000e-32
148
14
TraesCS5A01G012400
chr5B
88.217
1307
114
25
1577
2854
10169602
10168307
0.000000e+00
1524
15
TraesCS5A01G012400
chr5B
86.712
1317
128
26
1545
2838
42154599
42153307
0.000000e+00
1419
16
TraesCS5A01G012400
chr5B
93.513
632
38
2
904
1532
10170238
10169607
0.000000e+00
937
17
TraesCS5A01G012400
chr5B
88.855
664
59
7
1604
2266
10263526
10262877
0.000000e+00
802
18
TraesCS5A01G012400
chr5B
88.766
632
63
5
908
1532
42155214
42154584
0.000000e+00
767
19
TraesCS5A01G012400
chr5B
85.669
635
57
12
931
1532
10264199
10263566
3.230000e-179
638
20
TraesCS5A01G012400
chr5B
92.285
337
23
1
1
334
10170918
10170582
2.680000e-130
475
21
TraesCS5A01G012400
chr5B
90.135
223
16
2
663
884
10264552
10264335
4.840000e-73
285
22
TraesCS5A01G012400
chr5B
89.362
141
15
0
699
839
42155423
42155283
8.460000e-41
178
23
TraesCS5A01G012400
chr4D
94.286
280
15
1
348
626
332376560
332376281
7.610000e-116
427
24
TraesCS5A01G012400
chr4D
89.062
192
19
2
2648
2837
19876856
19877047
1.380000e-58
237
25
TraesCS5A01G012400
chrUn
93.190
279
18
1
348
625
87719602
87719880
2.750000e-110
409
26
TraesCS5A01G012400
chrUn
89.062
192
19
2
2648
2837
469402981
469402790
1.380000e-58
237
27
TraesCS5A01G012400
chr7B
93.190
279
18
1
348
625
713698461
713698739
2.750000e-110
409
28
TraesCS5A01G012400
chr6D
93.190
279
18
1
346
623
99228735
99228457
2.750000e-110
409
29
TraesCS5A01G012400
chr6B
93.190
279
17
2
346
623
183603024
183602747
2.750000e-110
409
30
TraesCS5A01G012400
chr2A
92.857
280
19
1
347
625
214842242
214842521
3.560000e-109
405
31
TraesCS5A01G012400
chr2A
92.281
285
21
1
346
629
167149586
167149302
1.280000e-108
403
32
TraesCS5A01G012400
chr1D
89.005
191
20
1
2648
2837
51863670
51863480
4.950000e-58
235
33
TraesCS5A01G012400
chr1A
89.005
191
19
2
2648
2837
154075006
154075195
4.950000e-58
235
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
TraesCS5A01G012400
chr5A
8072743
8075711
2968
False
5483.000000
5483
100.000000
1
2969
1
chr5A.!!$F1
2968
1
TraesCS5A01G012400
chr5A
8112412
8114425
2013
False
1347.500000
2536
94.631500
904
2969
2
chr5A.!!$F4
2065
2
TraesCS5A01G012400
chr5A
8063086
8064985
1899
False
1071.000000
1325
88.058000
910
2846
2
chr5A.!!$F2
1936
3
TraesCS5A01G012400
chr5A
8089875
8090436
561
False
431.000000
514
94.180000
30
860
2
chr5A.!!$F3
830
4
TraesCS5A01G012400
chr5D
10066668
10069626
2958
False
2353.500000
2446
95.330000
1
2969
2
chr5D.!!$F3
2968
5
TraesCS5A01G012400
chr5D
10041975
10044137
2162
False
799.666667
1288
88.826333
663
2780
3
chr5D.!!$F2
2117
6
TraesCS5A01G012400
chr5B
10168307
10170918
2611
True
978.666667
1524
91.338333
1
2854
3
chr5B.!!$R1
2853
7
TraesCS5A01G012400
chr5B
42153307
42155423
2116
True
788.000000
1419
88.280000
699
2838
3
chr5B.!!$R3
2139
8
TraesCS5A01G012400
chr5B
10262877
10264552
1675
True
575.000000
802
88.219667
663
2266
3
chr5B.!!$R2
1603
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.