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
TraesCS5A01G409500
chr5A
100.000
3227
0
0
1
3227
599161689
599158463
0.000000e+00
5960.0
1
TraesCS5A01G409500
chr5A
97.586
580
13
1
2449
3027
502916247
502916826
0.000000e+00
992.0
2
TraesCS5A01G409500
chr5A
81.032
775
86
22
1
732
436638984
436638228
7.820000e-156
560.0
3
TraesCS5A01G409500
chr5A
85.976
164
11
5
3033
3196
589317238
589317389
7.160000e-37
165.0
4
TraesCS5A01G409500
chr5A
91.525
59
5
0
2449
2507
604236176
604236234
7.420000e-12
82.4
5
TraesCS5A01G409500
chr5D
95.326
1626
56
4
823
2448
480458423
480456818
0.000000e+00
2564.0
6
TraesCS5A01G409500
chr5D
77.347
671
99
24
78
705
89386598
89387258
6.630000e-92
348.0
7
TraesCS5A01G409500
chr5D
87.981
208
11
4
3027
3227
480456833
480456633
1.940000e-57
233.0
8
TraesCS5A01G409500
chr5B
95.334
1436
62
5
990
2421
588621313
588619879
0.000000e+00
2276.0
9
TraesCS5A01G409500
chr5B
91.226
1379
83
19
823
2168
588581083
588579710
0.000000e+00
1842.0
10
TraesCS5A01G409500
chr5B
95.122
287
10
2
2166
2448
588577267
588576981
1.770000e-122
449.0
11
TraesCS5A01G409500
chr5B
86.802
197
15
5
3027
3219
588576997
588576808
3.260000e-50
209.0
12
TraesCS5A01G409500
chr5B
95.349
129
6
0
832
960
588641416
588641288
4.220000e-49
206.0
13
TraesCS5A01G409500
chr5B
82.353
119
21
0
1067
1185
589349248
589349130
1.580000e-18
104.0
14
TraesCS5A01G409500
chr5B
87.013
77
8
2
2444
2519
322131295
322131370
5.740000e-13
86.1
15
TraesCS5A01G409500
chr3B
98.793
580
6
1
2449
3027
661422054
661422633
0.000000e+00
1031.0
16
TraesCS5A01G409500
chr3B
78.755
739
115
16
62
769
174452914
174452187
1.060000e-124
457.0
17
TraesCS5A01G409500
chr3B
83.019
106
11
4
2449
2548
794762484
794762588
4.430000e-14
89.8
18
TraesCS5A01G409500
chr4A
97.927
579
12
0
2449
3027
482411837
482411259
0.000000e+00
1003.0
19
TraesCS5A01G409500
chr4A
84.112
856
87
16
1
814
677961497
677962345
0.000000e+00
782.0
20
TraesCS5A01G409500
chr4A
74.926
674
122
23
96
739
117950172
117949516
6.860000e-67
265.0
21
TraesCS5A01G409500
chr4A
94.545
55
3
0
2453
2507
131994515
131994461
5.740000e-13
86.1
22
TraesCS5A01G409500
chr1B
97.445
587
14
1
2442
3027
301752160
301752746
0.000000e+00
1000.0
23
TraesCS5A01G409500
chr2A
97.432
584
14
1
2444
3027
226565551
226564969
0.000000e+00
994.0
24
TraesCS5A01G409500
chr2A
85.444
845
80
12
1
814
762932690
762931858
0.000000e+00
839.0
25
TraesCS5A01G409500
chr2B
97.586
580
12
2
2449
3027
797940479
797941057
0.000000e+00
992.0
26
TraesCS5A01G409500
chr2B
97.265
585
11
3
2448
3027
133941327
133941911
0.000000e+00
987.0
27
TraesCS5A01G409500
chr2B
83.537
820
82
22
1
777
452910188
452910997
0.000000e+00
717.0
28
TraesCS5A01G409500
chr2B
82.110
654
71
24
7
622
93117470
93116825
4.770000e-143
518.0
29
TraesCS5A01G409500
chr4D
86.799
856
63
13
7
820
476308324
476307477
0.000000e+00
909.0
30
TraesCS5A01G409500
chr4D
79.396
762
104
26
1
726
121853087
121853831
3.740000e-134
488.0
31
TraesCS5A01G409500
chr4D
78.291
714
118
21
79
770
82327201
82327899
2.980000e-115
425.0
32
TraesCS5A01G409500
chr4D
82.237
152
13
4
3033
3182
259881547
259881408
5.660000e-23
119.0
33
TraesCS5A01G409500
chr7A
83.232
823
83
20
1
777
540868436
540869249
0.000000e+00
704.0
34
TraesCS5A01G409500
chr7A
80.892
785
96
20
1
740
425772067
425772842
1.300000e-158
569.0
35
TraesCS5A01G409500
chr7A
78.826
562
83
18
84
612
675325254
675324696
2.380000e-91
346.0
36
TraesCS5A01G409500
chr1D
82.360
822
91
18
1
777
37201998
37202810
0.000000e+00
665.0
37
TraesCS5A01G409500
chr6B
82.886
783
83
21
1
740
76215767
76214993
0.000000e+00
656.0
38
TraesCS5A01G409500
chr6D
81.763
828
87
26
1
777
36260929
36260115
4.540000e-178
634.0
39
TraesCS5A01G409500
chr6D
83.333
150
13
3
3033
3182
469093980
469093843
9.400000e-26
128.0
40
TraesCS5A01G409500
chr6D
73.871
310
47
19
375
670
23042176
23041887
3.430000e-15
93.5
41
TraesCS5A01G409500
chr4B
82.796
744
91
19
47
770
17829824
17830550
5.880000e-177
630.0
42
TraesCS5A01G409500
chr7D
82.078
770
93
12
1
738
87984321
87985077
1.650000e-172
616.0
43
TraesCS5A01G409500
chr7D
79.536
733
121
14
45
760
398003018
398003738
2.240000e-136
496.0
44
TraesCS5A01G409500
chr7D
92.063
63
5
0
2445
2507
125453046
125453108
4.430000e-14
89.8
45
TraesCS5A01G409500
chr7D
92.727
55
4
0
2449
2503
511084655
511084709
2.670000e-11
80.5
46
TraesCS5A01G409500
chr2D
83.676
680
83
14
47
706
592290155
592289484
1.650000e-172
616.0
47
TraesCS5A01G409500
chr2D
82.405
682
76
23
1
652
95408376
95409043
3.640000e-154
555.0
48
TraesCS5A01G409500
chr2D
83.729
590
63
10
1
559
385567898
385568485
7.930000e-146
527.0
49
TraesCS5A01G409500
chr2D
90.476
63
4
2
2445
2507
382441980
382442040
7.420000e-12
82.4
50
TraesCS5A01G409500
chr6A
81.997
661
72
25
1
622
46134638
46133986
4.770000e-143
518.0
51
TraesCS5A01G409500
chrUn
81.364
660
79
27
1
622
269554304
269553651
6.220000e-137
497.0
52
TraesCS5A01G409500
chr7B
82.017
595
74
13
1
562
24414606
24414012
2.910000e-130
475.0
53
TraesCS5A01G409500
chr3D
79.028
720
104
22
84
768
46267719
46267012
1.770000e-122
449.0
54
TraesCS5A01G409500
chr3D
79.185
687
99
21
78
732
588201006
588201680
1.370000e-118
436.0
55
TraesCS5A01G409500
chr3D
83.696
92
11
3
3105
3196
581721196
581721109
2.060000e-12
84.2
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
TraesCS5A01G409500
chr5A
599158463
599161689
3226
True
5960.000000
5960
100.0000
1
3227
1
chr5A.!!$R2
3226
1
TraesCS5A01G409500
chr5A
502916247
502916826
579
False
992.000000
992
97.5860
2449
3027
1
chr5A.!!$F1
578
2
TraesCS5A01G409500
chr5A
436638228
436638984
756
True
560.000000
560
81.0320
1
732
1
chr5A.!!$R1
731
3
TraesCS5A01G409500
chr5D
480456633
480458423
1790
True
1398.500000
2564
91.6535
823
3227
2
chr5D.!!$R1
2404
4
TraesCS5A01G409500
chr5D
89386598
89387258
660
False
348.000000
348
77.3470
78
705
1
chr5D.!!$F1
627
5
TraesCS5A01G409500
chr5B
588619879
588621313
1434
True
2276.000000
2276
95.3340
990
2421
1
chr5B.!!$R1
1431
6
TraesCS5A01G409500
chr5B
588576808
588581083
4275
True
833.333333
1842
91.0500
823
3219
3
chr5B.!!$R4
2396
7
TraesCS5A01G409500
chr3B
661422054
661422633
579
False
1031.000000
1031
98.7930
2449
3027
1
chr3B.!!$F1
578
8
TraesCS5A01G409500
chr3B
174452187
174452914
727
True
457.000000
457
78.7550
62
769
1
chr3B.!!$R1
707
9
TraesCS5A01G409500
chr4A
482411259
482411837
578
True
1003.000000
1003
97.9270
2449
3027
1
chr4A.!!$R3
578
10
TraesCS5A01G409500
chr4A
677961497
677962345
848
False
782.000000
782
84.1120
1
814
1
chr4A.!!$F1
813
11
TraesCS5A01G409500
chr4A
117949516
117950172
656
True
265.000000
265
74.9260
96
739
1
chr4A.!!$R1
643
12
TraesCS5A01G409500
chr1B
301752160
301752746
586
False
1000.000000
1000
97.4450
2442
3027
1
chr1B.!!$F1
585
13
TraesCS5A01G409500
chr2A
226564969
226565551
582
True
994.000000
994
97.4320
2444
3027
1
chr2A.!!$R1
583
14
TraesCS5A01G409500
chr2A
762931858
762932690
832
True
839.000000
839
85.4440
1
814
1
chr2A.!!$R2
813
15
TraesCS5A01G409500
chr2B
797940479
797941057
578
False
992.000000
992
97.5860
2449
3027
1
chr2B.!!$F3
578
16
TraesCS5A01G409500
chr2B
133941327
133941911
584
False
987.000000
987
97.2650
2448
3027
1
chr2B.!!$F1
579
17
TraesCS5A01G409500
chr2B
452910188
452910997
809
False
717.000000
717
83.5370
1
777
1
chr2B.!!$F2
776
18
TraesCS5A01G409500
chr2B
93116825
93117470
645
True
518.000000
518
82.1100
7
622
1
chr2B.!!$R1
615
19
TraesCS5A01G409500
chr4D
476307477
476308324
847
True
909.000000
909
86.7990
7
820
1
chr4D.!!$R2
813
20
TraesCS5A01G409500
chr4D
121853087
121853831
744
False
488.000000
488
79.3960
1
726
1
chr4D.!!$F2
725
21
TraesCS5A01G409500
chr4D
82327201
82327899
698
False
425.000000
425
78.2910
79
770
1
chr4D.!!$F1
691
22
TraesCS5A01G409500
chr7A
540868436
540869249
813
False
704.000000
704
83.2320
1
777
1
chr7A.!!$F2
776
23
TraesCS5A01G409500
chr7A
425772067
425772842
775
False
569.000000
569
80.8920
1
740
1
chr7A.!!$F1
739
24
TraesCS5A01G409500
chr7A
675324696
675325254
558
True
346.000000
346
78.8260
84
612
1
chr7A.!!$R1
528
25
TraesCS5A01G409500
chr1D
37201998
37202810
812
False
665.000000
665
82.3600
1
777
1
chr1D.!!$F1
776
26
TraesCS5A01G409500
chr6B
76214993
76215767
774
True
656.000000
656
82.8860
1
740
1
chr6B.!!$R1
739
27
TraesCS5A01G409500
chr6D
36260115
36260929
814
True
634.000000
634
81.7630
1
777
1
chr6D.!!$R2
776
28
TraesCS5A01G409500
chr4B
17829824
17830550
726
False
630.000000
630
82.7960
47
770
1
chr4B.!!$F1
723
29
TraesCS5A01G409500
chr7D
87984321
87985077
756
False
616.000000
616
82.0780
1
738
1
chr7D.!!$F1
737
30
TraesCS5A01G409500
chr7D
398003018
398003738
720
False
496.000000
496
79.5360
45
760
1
chr7D.!!$F3
715
31
TraesCS5A01G409500
chr2D
592289484
592290155
671
True
616.000000
616
83.6760
47
706
1
chr2D.!!$R1
659
32
TraesCS5A01G409500
chr2D
95408376
95409043
667
False
555.000000
555
82.4050
1
652
1
chr2D.!!$F1
651
33
TraesCS5A01G409500
chr2D
385567898
385568485
587
False
527.000000
527
83.7290
1
559
1
chr2D.!!$F3
558
34
TraesCS5A01G409500
chr6A
46133986
46134638
652
True
518.000000
518
81.9970
1
622
1
chr6A.!!$R1
621
35
TraesCS5A01G409500
chrUn
269553651
269554304
653
True
497.000000
497
81.3640
1
622
1
chrUn.!!$R1
621
36
TraesCS5A01G409500
chr7B
24414012
24414606
594
True
475.000000
475
82.0170
1
562
1
chr7B.!!$R1
561
37
TraesCS5A01G409500
chr3D
46267012
46267719
707
True
449.000000
449
79.0280
84
768
1
chr3D.!!$R1
684
38
TraesCS5A01G409500
chr3D
588201006
588201680
674
False
436.000000
436
79.1850
78
732
1
chr3D.!!$F1
654
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.