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
TraesCS2A01G094200
chr2A
100.000
3828
0
0
1
3828
47920634
47916807
0.000000e+00
7070.0
1
TraesCS2A01G094200
chr2A
87.772
1333
109
34
1660
2978
61286431
61287723
0.000000e+00
1509.0
2
TraesCS2A01G094200
chr2A
88.305
761
42
19
728
1478
61285008
61285731
0.000000e+00
869.0
3
TraesCS2A01G094200
chr2A
85.876
177
13
2
1483
1659
61286231
61286395
1.090000e-40
178.0
4
TraesCS2A01G094200
chr2A
78.346
254
44
6
3499
3745
485315128
485315377
1.840000e-33
154.0
5
TraesCS2A01G094200
chr2D
96.823
1983
39
16
1483
3455
44088211
44086243
0.000000e+00
3291.0
6
TraesCS2A01G094200
chr2D
86.114
1642
131
50
1483
3050
60752791
60754409
0.000000e+00
1679.0
7
TraesCS2A01G094200
chr2D
94.567
773
13
6
726
1479
44089460
44088698
0.000000e+00
1168.0
8
TraesCS2A01G094200
chr2D
88.792
687
26
13
728
1402
60751548
60752195
0.000000e+00
795.0
9
TraesCS2A01G094200
chr2D
92.946
241
11
3
3540
3779
44086112
44085877
2.830000e-91
346.0
10
TraesCS2A01G094200
chr2D
78.906
256
40
10
3498
3745
422089788
422089539
1.100000e-35
161.0
11
TraesCS2A01G094200
chr2B
96.070
1603
22
6
1485
3077
69501476
69499905
0.000000e+00
2573.0
12
TraesCS2A01G094200
chr2B
96.073
713
24
2
1656
2367
94926715
94927424
0.000000e+00
1158.0
13
TraesCS2A01G094200
chr2B
91.823
746
9
11
739
1479
69502695
69501997
0.000000e+00
992.0
14
TraesCS2A01G094200
chr2B
90.382
707
36
14
777
1479
94925316
94925994
0.000000e+00
900.0
15
TraesCS2A01G094200
chr2B
87.129
707
82
9
1653
2355
601333874
601334575
0.000000e+00
793.0
16
TraesCS2A01G094200
chr2B
87.318
686
81
6
1
685
622754820
622755500
0.000000e+00
780.0
17
TraesCS2A01G094200
chr2B
85.983
692
88
5
1
685
511692496
511693185
0.000000e+00
732.0
18
TraesCS2A01G094200
chr2B
89.514
391
24
4
3449
3827
69499550
69499165
2.680000e-131
479.0
19
TraesCS2A01G094200
chr2B
86.207
377
30
11
2606
2976
94927651
94928011
4.640000e-104
388.0
20
TraesCS2A01G094200
chr2B
93.388
242
12
2
3109
3346
69499915
69499674
4.700000e-94
355.0
21
TraesCS2A01G094200
chr2B
91.573
178
12
2
1483
1659
94926505
94926680
3.820000e-60
243.0
22
TraesCS2A01G094200
chr2B
77.344
256
45
8
3477
3726
659650396
659650644
5.160000e-29
139.0
23
TraesCS2A01G094200
chr2B
95.556
45
0
2
3411
3455
69499671
69499629
1.910000e-08
71.3
24
TraesCS2A01G094200
chr5B
86.464
857
91
20
1535
2381
457989685
457990526
0.000000e+00
917.0
25
TraesCS2A01G094200
chr5B
87.609
686
79
6
1
685
320855422
320854742
0.000000e+00
791.0
26
TraesCS2A01G094200
chr5B
78.390
236
40
8
3498
3726
325061401
325061170
3.990000e-30
143.0
27
TraesCS2A01G094200
chr5B
91.304
46
4
0
2978
3023
457990614
457990659
3.190000e-06
63.9
28
TraesCS2A01G094200
chr1D
88.873
683
70
6
3
683
263894786
263894108
0.000000e+00
835.0
29
TraesCS2A01G094200
chr1D
91.163
215
18
1
876
1089
269496886
269496672
1.350000e-74
291.0
30
TraesCS2A01G094200
chr3B
88.484
686
72
7
1
685
242421124
242421803
0.000000e+00
822.0
31
TraesCS2A01G094200
chr3B
86.257
684
86
7
4
685
553197071
553196394
0.000000e+00
736.0
32
TraesCS2A01G094200
chr3B
90.210
143
11
3
1
143
216200989
216201128
2.350000e-42
183.0
33
TraesCS2A01G094200
chr6B
86.880
686
71
13
2
685
535592209
535591541
0.000000e+00
750.0
34
TraesCS2A01G094200
chr6B
87.203
547
64
5
1830
2374
157480015
157479473
5.430000e-173
617.0
35
TraesCS2A01G094200
chr6B
89.394
132
13
1
1757
1887
157480137
157480006
8.510000e-37
165.0
36
TraesCS2A01G094200
chr6B
76.894
264
44
9
3492
3745
548131180
548131436
2.400000e-27
134.0
37
TraesCS2A01G094200
chr6B
95.238
42
2
0
2978
3019
157476399
157476358
2.470000e-07
67.6
38
TraesCS2A01G094200
chr6B
95.238
42
2
0
2978
3019
157478529
157478488
2.470000e-07
67.6
39
TraesCS2A01G094200
chr6B
95.238
42
2
0
2978
3019
157479378
157479337
2.470000e-07
67.6
40
TraesCS2A01G094200
chr4B
86.053
674
77
14
1
669
190831736
190832397
0.000000e+00
708.0
41
TraesCS2A01G094200
chr7D
84.626
709
83
15
1
687
178180458
178181162
0.000000e+00
682.0
42
TraesCS2A01G094200
chr3D
89.414
529
27
9
956
1479
473415338
473414834
1.160000e-179
640.0
43
TraesCS2A01G094200
chr3D
90.698
215
19
1
876
1089
275444650
275444864
6.260000e-73
285.0
44
TraesCS2A01G094200
chr4D
89.015
528
30
9
956
1479
499921221
499920718
2.510000e-176
628.0
45
TraesCS2A01G094200
chr4D
92.754
138
9
1
985
1121
295434961
295434824
8.390000e-47
198.0
46
TraesCS2A01G094200
chr5A
87.666
527
36
15
956
1479
612651936
612652436
1.530000e-163
586.0
47
TraesCS2A01G094200
chr5A
86.641
524
42
12
960
1479
232875101
232874602
4.320000e-154
555.0
48
TraesCS2A01G094200
chr7B
86.767
529
41
11
956
1479
629183109
629183613
2.580000e-156
562.0
49
TraesCS2A01G094200
chr7B
86.767
529
41
15
956
1479
629199523
629200027
2.580000e-156
562.0
50
TraesCS2A01G094200
chr7B
85.305
524
49
7
960
1479
596280753
596281252
2.040000e-142
516.0
51
TraesCS2A01G094200
chr7B
83.465
254
13
8
956
1204
619196852
619197081
3.880000e-50
209.0
52
TraesCS2A01G094200
chr1A
86.767
529
41
8
956
1479
414218133
414218637
2.580000e-156
562.0
53
TraesCS2A01G094200
chr4A
90.394
406
34
4
1978
2381
703283603
703283201
2.620000e-146
529.0
54
TraesCS2A01G094200
chr3A
90.654
214
19
1
877
1089
596107659
596107872
2.250000e-72
283.0
55
TraesCS2A01G094200
chr3A
78.970
233
33
10
3499
3726
146203166
146202945
1.110000e-30
145.0
56
TraesCS2A01G094200
chr6D
80.282
213
33
6
3510
3718
423771269
423771476
6.620000e-33
152.0
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
TraesCS2A01G094200
chr2A
47916807
47920634
3827
True
7070.000000
7070
100.000000
1
3828
1
chr2A.!!$R1
3827
1
TraesCS2A01G094200
chr2A
61285008
61287723
2715
False
852.000000
1509
87.317667
728
2978
3
chr2A.!!$F2
2250
2
TraesCS2A01G094200
chr2D
44085877
44089460
3583
True
1601.666667
3291
94.778667
726
3779
3
chr2D.!!$R2
3053
3
TraesCS2A01G094200
chr2D
60751548
60754409
2861
False
1237.000000
1679
87.453000
728
3050
2
chr2D.!!$F1
2322
4
TraesCS2A01G094200
chr2B
69499165
69502695
3530
True
894.060000
2573
93.270200
739
3827
5
chr2B.!!$R1
3088
5
TraesCS2A01G094200
chr2B
601333874
601334575
701
False
793.000000
793
87.129000
1653
2355
1
chr2B.!!$F2
702
6
TraesCS2A01G094200
chr2B
622754820
622755500
680
False
780.000000
780
87.318000
1
685
1
chr2B.!!$F3
684
7
TraesCS2A01G094200
chr2B
511692496
511693185
689
False
732.000000
732
85.983000
1
685
1
chr2B.!!$F1
684
8
TraesCS2A01G094200
chr2B
94925316
94928011
2695
False
672.250000
1158
91.058750
777
2976
4
chr2B.!!$F5
2199
9
TraesCS2A01G094200
chr5B
320854742
320855422
680
True
791.000000
791
87.609000
1
685
1
chr5B.!!$R1
684
10
TraesCS2A01G094200
chr5B
457989685
457990659
974
False
490.450000
917
88.884000
1535
3023
2
chr5B.!!$F1
1488
11
TraesCS2A01G094200
chr1D
263894108
263894786
678
True
835.000000
835
88.873000
3
683
1
chr1D.!!$R1
680
12
TraesCS2A01G094200
chr3B
242421124
242421803
679
False
822.000000
822
88.484000
1
685
1
chr3B.!!$F2
684
13
TraesCS2A01G094200
chr3B
553196394
553197071
677
True
736.000000
736
86.257000
4
685
1
chr3B.!!$R1
681
14
TraesCS2A01G094200
chr6B
535591541
535592209
668
True
750.000000
750
86.880000
2
685
1
chr6B.!!$R1
683
15
TraesCS2A01G094200
chr4B
190831736
190832397
661
False
708.000000
708
86.053000
1
669
1
chr4B.!!$F1
668
16
TraesCS2A01G094200
chr7D
178180458
178181162
704
False
682.000000
682
84.626000
1
687
1
chr7D.!!$F1
686
17
TraesCS2A01G094200
chr3D
473414834
473415338
504
True
640.000000
640
89.414000
956
1479
1
chr3D.!!$R1
523
18
TraesCS2A01G094200
chr4D
499920718
499921221
503
True
628.000000
628
89.015000
956
1479
1
chr4D.!!$R2
523
19
TraesCS2A01G094200
chr5A
612651936
612652436
500
False
586.000000
586
87.666000
956
1479
1
chr5A.!!$F1
523
20
TraesCS2A01G094200
chr7B
629183109
629183613
504
False
562.000000
562
86.767000
956
1479
1
chr7B.!!$F3
523
21
TraesCS2A01G094200
chr7B
629199523
629200027
504
False
562.000000
562
86.767000
956
1479
1
chr7B.!!$F4
523
22
TraesCS2A01G094200
chr1A
414218133
414218637
504
False
562.000000
562
86.767000
956
1479
1
chr1A.!!$F1
523
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.