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
TraesCS3A01G110700
chr3A
100.000
2747
0
0
1
2747
77707465
77710211
0.000000e+00
5073
1
TraesCS3A01G110700
chr3A
99.648
1990
7
0
1
1990
77593911
77595900
0.000000e+00
3637
2
TraesCS3A01G110700
chr3A
93.377
1389
44
14
630
1990
77548000
77549368
0.000000e+00
2012
3
TraesCS3A01G110700
chr3A
88.372
387
25
5
1992
2366
77595948
77596326
5.400000e-122
448
4
TraesCS3A01G110700
chr3A
86.923
390
26
11
1991
2366
77549416
77549794
5.470000e-112
414
5
TraesCS3A01G110700
chr3D
91.137
1399
73
13
630
1987
66552979
66554367
0.000000e+00
1849
6
TraesCS3A01G110700
chr3D
88.031
1529
124
33
763
2247
66561416
66562929
0.000000e+00
1755
7
TraesCS3A01G110700
chr3D
87.524
529
28
9
16
522
593291171
593290659
6.600000e-161
577
8
TraesCS3A01G110700
chr3D
89.791
382
30
6
1991
2366
66554418
66554796
5.320000e-132
481
9
TraesCS3A01G110700
chr3D
87.760
384
33
11
2365
2741
104393582
104393958
1.170000e-118
436
10
TraesCS3A01G110700
chr3D
96.250
160
5
1
609
768
66557693
66557851
7.550000e-66
261
11
TraesCS3A01G110700
chr3B
89.962
1315
85
16
630
1912
110735573
110736872
0.000000e+00
1653
12
TraesCS3A01G110700
chr3B
89.558
1063
59
10
609
1658
110741389
110742412
0.000000e+00
1301
13
TraesCS3A01G110700
chr3B
86.788
386
34
8
1993
2366
110738114
110738494
5.470000e-112
414
14
TraesCS3A01G110700
chr3B
78.534
573
68
32
1717
2247
110742413
110742972
2.640000e-85
326
15
TraesCS3A01G110700
chr4A
87.179
741
62
21
1037
1745
697432888
697433627
0.000000e+00
811
16
TraesCS3A01G110700
chr4A
86.803
735
64
20
1043
1745
697439333
697440066
0.000000e+00
789
17
TraesCS3A01G110700
chr4A
85.971
613
47
20
16
609
320492234
320491642
1.080000e-173
619
18
TraesCS3A01G110700
chr7D
90.397
604
42
9
16
609
104606032
104605435
0.000000e+00
780
19
TraesCS3A01G110700
chr7D
86.066
732
72
21
1044
1745
31101997
31101266
0.000000e+00
760
20
TraesCS3A01G110700
chr7D
88.960
625
36
8
16
609
576204498
576203876
0.000000e+00
741
21
TraesCS3A01G110700
chr7D
81.499
854
97
38
869
1679
31070934
31070099
0.000000e+00
645
22
TraesCS3A01G110700
chr7D
84.921
630
35
21
16
602
587445768
587446380
1.420000e-162
582
23
TraesCS3A01G110700
chr7D
84.628
631
33
21
16
602
460082150
460081540
1.100000e-158
569
24
TraesCS3A01G110700
chr7D
90.977
399
36
0
1347
1745
31055803
31055405
3.110000e-149
538
25
TraesCS3A01G110700
chr7D
88.946
389
31
9
2365
2747
134434668
134434286
1.150000e-128
470
26
TraesCS3A01G110700
chr7D
88.918
388
30
9
2365
2747
571725666
571725287
1.490000e-127
466
27
TraesCS3A01G110700
chr7D
92.941
85
6
0
1661
1745
31063506
31063422
1.030000e-24
124
28
TraesCS3A01G110700
chr7A
85.849
742
72
19
1037
1745
31511965
31511224
0.000000e+00
758
29
TraesCS3A01G110700
chr7A
87.814
558
45
8
16
550
717475968
717475411
1.390000e-177
632
30
TraesCS3A01G110700
chr2D
87.774
638
32
13
16
609
498283940
498283305
0.000000e+00
704
31
TraesCS3A01G110700
chr2D
85.474
654
32
22
16
608
638285405
638286056
8.350000e-175
623
32
TraesCS3A01G110700
chr2D
90.026
391
29
7
2365
2747
636073171
636073559
5.280000e-137
497
33
TraesCS3A01G110700
chr6A
87.844
617
49
8
17
608
613706071
613705456
0.000000e+00
701
34
TraesCS3A01G110700
chr6A
86.371
631
42
10
17
603
9496534
9495904
0.000000e+00
649
35
TraesCS3A01G110700
chr6A
85.737
638
45
19
17
608
14692092
14692729
1.390000e-177
632
36
TraesCS3A01G110700
chr6D
87.344
640
36
10
16
610
435883928
435883289
0.000000e+00
691
37
TraesCS3A01G110700
chr6D
83.254
633
42
30
16
612
30186090
30186694
8.720000e-145
523
38
TraesCS3A01G110700
chr6D
87.824
386
36
7
2367
2747
462288190
462288569
2.510000e-120
442
39
TraesCS3A01G110700
chr5A
86.499
637
42
10
17
609
698083744
698083108
0.000000e+00
660
40
TraesCS3A01G110700
chr5A
87.565
386
35
9
2365
2747
435701738
435702113
4.200000e-118
435
41
TraesCS3A01G110700
chr1D
85.344
655
33
12
16
608
236041849
236041196
1.080000e-173
619
42
TraesCS3A01G110700
chr1D
84.786
631
34
23
16
602
303062222
303062834
6.600000e-161
577
43
TraesCS3A01G110700
chrUn
85.038
655
32
18
16
608
137755614
137756264
8.410000e-170
606
44
TraesCS3A01G110700
chrUn
84.494
632
33
23
16
602
24613496
24614107
5.140000e-157
564
45
TraesCS3A01G110700
chrUn
84.202
633
34
23
16
602
24583212
24583824
3.090000e-154
555
46
TraesCS3A01G110700
chrUn
92.188
128
8
1
1778
1903
378540026
378540153
2.170000e-41
180
47
TraesCS3A01G110700
chrUn
92.188
128
8
1
1778
1903
378540992
378541119
2.170000e-41
180
48
TraesCS3A01G110700
chrUn
92.188
128
8
1
1778
1903
378541822
378541949
2.170000e-41
180
49
TraesCS3A01G110700
chrUn
92.188
128
8
1
1778
1903
378542788
378542915
2.170000e-41
180
50
TraesCS3A01G110700
chrUn
91.406
128
9
1
1778
1903
378540509
378540636
1.010000e-39
174
51
TraesCS3A01G110700
chrUn
91.406
128
9
1
1778
1903
378542305
378542432
1.010000e-39
174
52
TraesCS3A01G110700
chrUn
91.406
128
9
1
1778
1903
431546651
431546778
1.010000e-39
174
53
TraesCS3A01G110700
chrUn
91.406
128
9
1
1778
1903
443782976
443782849
1.010000e-39
174
54
TraesCS3A01G110700
chrUn
91.406
128
9
1
1778
1903
443783459
443783332
1.010000e-39
174
55
TraesCS3A01G110700
chr5D
84.748
636
36
19
16
609
437166127
437165511
5.100000e-162
580
56
TraesCS3A01G110700
chr5D
89.203
389
32
6
2365
2747
558062795
558062411
6.880000e-131
477
57
TraesCS3A01G110700
chr5D
86.737
377
39
4
19
386
496573372
496572998
2.550000e-110
409
58
TraesCS3A01G110700
chr5D
83.766
154
18
5
1037
1184
37207160
37207008
3.690000e-29
139
59
TraesCS3A01G110700
chr2A
89.231
390
32
8
2363
2747
768685154
768684770
1.910000e-131
479
60
TraesCS3A01G110700
chr4D
88.010
392
29
15
2365
2747
16929589
16929207
5.400000e-122
448
61
TraesCS3A01G110700
chr2B
93.750
128
6
1
1778
1903
49887407
49887534
1.000000e-44
191
62
TraesCS3A01G110700
chr2B
92.969
128
7
1
1778
1903
49890789
49890916
4.670000e-43
185
63
TraesCS3A01G110700
chr2B
92.188
128
8
1
1778
1903
49893204
49893331
2.170000e-41
180
64
TraesCS3A01G110700
chr2B
89.437
142
13
1
1778
1917
49888374
49888515
7.820000e-41
178
65
TraesCS3A01G110700
chr2B
89.437
142
13
1
1778
1917
49894652
49894793
7.820000e-41
178
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
TraesCS3A01G110700
chr3A
77707465
77710211
2746
False
5073.0
5073
100.00000
1
2747
1
chr3A.!!$F1
2746
1
TraesCS3A01G110700
chr3A
77593911
77596326
2415
False
2042.5
3637
94.01000
1
2366
2
chr3A.!!$F3
2365
2
TraesCS3A01G110700
chr3A
77548000
77549794
1794
False
1213.0
2012
90.15000
630
2366
2
chr3A.!!$F2
1736
3
TraesCS3A01G110700
chr3D
66552979
66562929
9950
False
1086.5
1849
91.30225
609
2366
4
chr3D.!!$F2
1757
4
TraesCS3A01G110700
chr3D
593290659
593291171
512
True
577.0
577
87.52400
16
522
1
chr3D.!!$R1
506
5
TraesCS3A01G110700
chr3B
110735573
110742972
7399
False
923.5
1653
86.21050
609
2366
4
chr3B.!!$F1
1757
6
TraesCS3A01G110700
chr4A
697432888
697433627
739
False
811.0
811
87.17900
1037
1745
1
chr4A.!!$F1
708
7
TraesCS3A01G110700
chr4A
697439333
697440066
733
False
789.0
789
86.80300
1043
1745
1
chr4A.!!$F2
702
8
TraesCS3A01G110700
chr4A
320491642
320492234
592
True
619.0
619
85.97100
16
609
1
chr4A.!!$R1
593
9
TraesCS3A01G110700
chr7D
104605435
104606032
597
True
780.0
780
90.39700
16
609
1
chr7D.!!$R5
593
10
TraesCS3A01G110700
chr7D
31101266
31101997
731
True
760.0
760
86.06600
1044
1745
1
chr7D.!!$R4
701
11
TraesCS3A01G110700
chr7D
576203876
576204498
622
True
741.0
741
88.96000
16
609
1
chr7D.!!$R9
593
12
TraesCS3A01G110700
chr7D
31070099
31070934
835
True
645.0
645
81.49900
869
1679
1
chr7D.!!$R3
810
13
TraesCS3A01G110700
chr7D
587445768
587446380
612
False
582.0
582
84.92100
16
602
1
chr7D.!!$F1
586
14
TraesCS3A01G110700
chr7D
460081540
460082150
610
True
569.0
569
84.62800
16
602
1
chr7D.!!$R7
586
15
TraesCS3A01G110700
chr7A
31511224
31511965
741
True
758.0
758
85.84900
1037
1745
1
chr7A.!!$R1
708
16
TraesCS3A01G110700
chr7A
717475411
717475968
557
True
632.0
632
87.81400
16
550
1
chr7A.!!$R2
534
17
TraesCS3A01G110700
chr2D
498283305
498283940
635
True
704.0
704
87.77400
16
609
1
chr2D.!!$R1
593
18
TraesCS3A01G110700
chr2D
638285405
638286056
651
False
623.0
623
85.47400
16
608
1
chr2D.!!$F2
592
19
TraesCS3A01G110700
chr6A
613705456
613706071
615
True
701.0
701
87.84400
17
608
1
chr6A.!!$R2
591
20
TraesCS3A01G110700
chr6A
9495904
9496534
630
True
649.0
649
86.37100
17
603
1
chr6A.!!$R1
586
21
TraesCS3A01G110700
chr6A
14692092
14692729
637
False
632.0
632
85.73700
17
608
1
chr6A.!!$F1
591
22
TraesCS3A01G110700
chr6D
435883289
435883928
639
True
691.0
691
87.34400
16
610
1
chr6D.!!$R1
594
23
TraesCS3A01G110700
chr6D
30186090
30186694
604
False
523.0
523
83.25400
16
612
1
chr6D.!!$F1
596
24
TraesCS3A01G110700
chr5A
698083108
698083744
636
True
660.0
660
86.49900
17
609
1
chr5A.!!$R1
592
25
TraesCS3A01G110700
chr1D
236041196
236041849
653
True
619.0
619
85.34400
16
608
1
chr1D.!!$R1
592
26
TraesCS3A01G110700
chr1D
303062222
303062834
612
False
577.0
577
84.78600
16
602
1
chr1D.!!$F1
586
27
TraesCS3A01G110700
chrUn
137755614
137756264
650
False
606.0
606
85.03800
16
608
1
chrUn.!!$F3
592
28
TraesCS3A01G110700
chrUn
24613496
24614107
611
False
564.0
564
84.49400
16
602
1
chrUn.!!$F2
586
29
TraesCS3A01G110700
chrUn
24583212
24583824
612
False
555.0
555
84.20200
16
602
1
chrUn.!!$F1
586
30
TraesCS3A01G110700
chr5D
437165511
437166127
616
True
580.0
580
84.74800
16
609
1
chr5D.!!$R2
593
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.