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
TraesCS4A01G463500
chr4A
100.000
2537
0
0
1
2537
727191709
727189173
0.000000e+00
4686.0
1
TraesCS4A01G463500
chr4A
98.961
770
8
0
716
1485
727127425
727128194
0.000000e+00
1378.0
2
TraesCS4A01G463500
chr4A
89.972
718
67
5
1
715
707310518
707311233
0.000000e+00
922.0
3
TraesCS4A01G463500
chr4A
89.972
718
47
4
1780
2474
722748687
722749402
0.000000e+00
904.0
4
TraesCS4A01G463500
chr4A
87.057
649
78
6
70
715
415864472
415865117
0.000000e+00
728.0
5
TraesCS4A01G463500
chr5D
89.526
1098
65
9
1486
2537
437846108
437847201
0.000000e+00
1345.0
6
TraesCS4A01G463500
chr5D
89.061
1097
74
6
1486
2537
31910418
31911513
0.000000e+00
1319.0
7
TraesCS4A01G463500
chr1D
89.517
1097
67
8
1486
2537
411599421
411598328
0.000000e+00
1345.0
8
TraesCS4A01G463500
chr1D
85.792
549
75
3
937
1482
7510036
7510584
1.690000e-161
579.0
9
TraesCS4A01G463500
chr1D
88.043
184
18
1
946
1125
7037788
7037605
5.500000e-52
215.0
10
TraesCS4A01G463500
chr1D
85.135
74
11
0
716
789
423268641
423268714
2.710000e-10
76.8
11
TraesCS4A01G463500
chr6B
89.416
1096
71
6
1486
2537
559381934
559383028
0.000000e+00
1339.0
12
TraesCS4A01G463500
chr6B
94.469
687
35
2
1486
2170
288066434
288065749
0.000000e+00
1055.0
13
TraesCS4A01G463500
chr6B
73.923
441
85
18
1051
1485
712331924
712332340
1.570000e-32
150.0
14
TraesCS4A01G463500
chr2B
89.440
1089
76
11
1486
2537
764707700
764706614
0.000000e+00
1338.0
15
TraesCS4A01G463500
chr2B
90.138
943
63
7
1555
2474
269168361
269169296
0.000000e+00
1199.0
16
TraesCS4A01G463500
chr2B
84.270
623
78
13
874
1485
72589275
72588662
7.820000e-165
590.0
17
TraesCS4A01G463500
chr2B
85.405
185
14
11
2362
2537
791838501
791838321
2.010000e-41
180.0
18
TraesCS4A01G463500
chr2B
84.865
185
15
5
2362
2537
773896991
773896811
9.330000e-40
174.0
19
TraesCS4A01G463500
chr5B
89.325
1096
70
8
1486
2537
555101499
555100407
0.000000e+00
1332.0
20
TraesCS4A01G463500
chr5B
81.188
202
21
12
2349
2537
532304401
532304598
2.030000e-31
147.0
21
TraesCS4A01G463500
chr7D
89.101
1101
68
21
1486
2537
618623600
618624697
0.000000e+00
1321.0
22
TraesCS4A01G463500
chr7D
91.415
431
32
5
290
715
34033707
34034137
1.010000e-163
586.0
23
TraesCS4A01G463500
chr3B
88.788
1097
71
7
1486
2537
684799930
684798841
0.000000e+00
1297.0
24
TraesCS4A01G463500
chr3B
88.423
1097
76
14
1486
2537
381827672
381826582
0.000000e+00
1275.0
25
TraesCS4A01G463500
chr3B
89.226
891
61
10
1486
2350
20033624
20032743
0.000000e+00
1081.0
26
TraesCS4A01G463500
chr3B
88.889
891
63
12
1486
2350
75546960
75546080
0.000000e+00
1064.0
27
TraesCS4A01G463500
chr3B
88.444
900
60
5
1681
2537
150149707
150150605
0.000000e+00
1046.0
28
TraesCS4A01G463500
chr7B
88.605
1097
76
7
1486
2537
681604031
681605123
0.000000e+00
1288.0
29
TraesCS4A01G463500
chr7B
89.280
681
57
11
38
715
677206769
677206102
0.000000e+00
839.0
30
TraesCS4A01G463500
chr7B
86.646
659
77
9
70
719
692869303
692869959
0.000000e+00
719.0
31
TraesCS4A01G463500
chr7B
91.837
294
24
0
2181
2474
712746742
712746449
6.530000e-111
411.0
32
TraesCS4A01G463500
chr7B
91.781
146
11
1
42
187
126098535
126098391
4.280000e-48
202.0
33
TraesCS4A01G463500
chr7B
86.486
185
12
10
2362
2537
711161774
711161594
9.260000e-45
191.0
34
TraesCS4A01G463500
chr7B
85.946
185
13
11
2362
2537
684005963
684006143
4.310000e-43
185.0
35
TraesCS4A01G463500
chr7B
84.865
185
15
11
2362
2537
732487102
732487282
9.330000e-40
174.0
36
TraesCS4A01G463500
chr1B
89.371
715
60
5
1
713
62416192
62415492
0.000000e+00
885.0
37
TraesCS4A01G463500
chr1B
84.544
537
74
5
957
1485
9712665
9712130
8.040000e-145
523.0
38
TraesCS4A01G463500
chr1B
85.405
185
14
11
2362
2537
35009158
35009338
2.010000e-41
180.0
39
TraesCS4A01G463500
chr1B
81.564
179
16
10
2362
2537
13252795
13252631
5.690000e-27
132.0
40
TraesCS4A01G463500
chr3A
88.472
720
72
10
1
715
705217039
705216326
0.000000e+00
859.0
41
TraesCS4A01G463500
chr3D
86.320
731
81
8
1
715
480013744
480013017
0.000000e+00
778.0
42
TraesCS4A01G463500
chr7A
86.447
546
62
12
178
715
26043068
26043609
2.810000e-164
588.0
43
TraesCS4A01G463500
chr7A
84.416
77
12
0
716
792
479838154
479838230
2.710000e-10
76.8
44
TraesCS4A01G463500
chr7A
84.507
71
11
0
719
789
39429973
39429903
1.260000e-08
71.3
45
TraesCS4A01G463500
chr2D
83.706
626
79
13
874
1485
45548014
45547398
1.020000e-158
569.0
46
TraesCS4A01G463500
chr2D
84.000
75
12
0
716
790
27669327
27669401
3.500000e-09
73.1
47
TraesCS4A01G463500
chr2D
93.617
47
3
0
747
793
32771399
32771353
1.260000e-08
71.3
48
TraesCS4A01G463500
chr2A
83.333
570
86
9
151
715
612360603
612361168
3.740000e-143
518.0
49
TraesCS4A01G463500
chr5A
85.787
197
16
5
1
187
522592373
522592567
5.540000e-47
198.0
50
TraesCS4A01G463500
chr4B
85.946
185
13
11
2362
2537
605923224
605923404
4.310000e-43
185.0
51
TraesCS4A01G463500
chr1A
81.333
75
14
0
716
790
445446204
445446278
7.580000e-06
62.1
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
TraesCS4A01G463500
chr4A
727189173
727191709
2536
True
4686
4686
100.000
1
2537
1
chr4A.!!$R1
2536
1
TraesCS4A01G463500
chr4A
727127425
727128194
769
False
1378
1378
98.961
716
1485
1
chr4A.!!$F4
769
2
TraesCS4A01G463500
chr4A
707310518
707311233
715
False
922
922
89.972
1
715
1
chr4A.!!$F2
714
3
TraesCS4A01G463500
chr4A
722748687
722749402
715
False
904
904
89.972
1780
2474
1
chr4A.!!$F3
694
4
TraesCS4A01G463500
chr4A
415864472
415865117
645
False
728
728
87.057
70
715
1
chr4A.!!$F1
645
5
TraesCS4A01G463500
chr5D
437846108
437847201
1093
False
1345
1345
89.526
1486
2537
1
chr5D.!!$F2
1051
6
TraesCS4A01G463500
chr5D
31910418
31911513
1095
False
1319
1319
89.061
1486
2537
1
chr5D.!!$F1
1051
7
TraesCS4A01G463500
chr1D
411598328
411599421
1093
True
1345
1345
89.517
1486
2537
1
chr1D.!!$R2
1051
8
TraesCS4A01G463500
chr1D
7510036
7510584
548
False
579
579
85.792
937
1482
1
chr1D.!!$F1
545
9
TraesCS4A01G463500
chr6B
559381934
559383028
1094
False
1339
1339
89.416
1486
2537
1
chr6B.!!$F1
1051
10
TraesCS4A01G463500
chr6B
288065749
288066434
685
True
1055
1055
94.469
1486
2170
1
chr6B.!!$R1
684
11
TraesCS4A01G463500
chr2B
764706614
764707700
1086
True
1338
1338
89.440
1486
2537
1
chr2B.!!$R2
1051
12
TraesCS4A01G463500
chr2B
269168361
269169296
935
False
1199
1199
90.138
1555
2474
1
chr2B.!!$F1
919
13
TraesCS4A01G463500
chr2B
72588662
72589275
613
True
590
590
84.270
874
1485
1
chr2B.!!$R1
611
14
TraesCS4A01G463500
chr5B
555100407
555101499
1092
True
1332
1332
89.325
1486
2537
1
chr5B.!!$R1
1051
15
TraesCS4A01G463500
chr7D
618623600
618624697
1097
False
1321
1321
89.101
1486
2537
1
chr7D.!!$F2
1051
16
TraesCS4A01G463500
chr3B
684798841
684799930
1089
True
1297
1297
88.788
1486
2537
1
chr3B.!!$R4
1051
17
TraesCS4A01G463500
chr3B
381826582
381827672
1090
True
1275
1275
88.423
1486
2537
1
chr3B.!!$R3
1051
18
TraesCS4A01G463500
chr3B
20032743
20033624
881
True
1081
1081
89.226
1486
2350
1
chr3B.!!$R1
864
19
TraesCS4A01G463500
chr3B
75546080
75546960
880
True
1064
1064
88.889
1486
2350
1
chr3B.!!$R2
864
20
TraesCS4A01G463500
chr3B
150149707
150150605
898
False
1046
1046
88.444
1681
2537
1
chr3B.!!$F1
856
21
TraesCS4A01G463500
chr7B
681604031
681605123
1092
False
1288
1288
88.605
1486
2537
1
chr7B.!!$F1
1051
22
TraesCS4A01G463500
chr7B
677206102
677206769
667
True
839
839
89.280
38
715
1
chr7B.!!$R2
677
23
TraesCS4A01G463500
chr7B
692869303
692869959
656
False
719
719
86.646
70
719
1
chr7B.!!$F3
649
24
TraesCS4A01G463500
chr1B
62415492
62416192
700
True
885
885
89.371
1
713
1
chr1B.!!$R3
712
25
TraesCS4A01G463500
chr1B
9712130
9712665
535
True
523
523
84.544
957
1485
1
chr1B.!!$R1
528
26
TraesCS4A01G463500
chr3A
705216326
705217039
713
True
859
859
88.472
1
715
1
chr3A.!!$R1
714
27
TraesCS4A01G463500
chr3D
480013017
480013744
727
True
778
778
86.320
1
715
1
chr3D.!!$R1
714
28
TraesCS4A01G463500
chr7A
26043068
26043609
541
False
588
588
86.447
178
715
1
chr7A.!!$F1
537
29
TraesCS4A01G463500
chr2D
45547398
45548014
616
True
569
569
83.706
874
1485
1
chr2D.!!$R2
611
30
TraesCS4A01G463500
chr2A
612360603
612361168
565
False
518
518
83.333
151
715
1
chr2A.!!$F1
564
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.