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
TraesCS4A01G128700
chr4A
100.000
2504
0
0
1
2504
165711374
165713877
0.000000e+00
4625.0
1
TraesCS4A01G128700
chr4A
87.119
854
105
5
1652
2501
602857669
602858521
0.000000e+00
963.0
2
TraesCS4A01G128700
chr4D
94.277
1625
66
15
1
1608
309510193
309508579
0.000000e+00
2460.0
3
TraesCS4A01G128700
chr3A
90.738
799
71
3
1705
2502
716571190
716571986
0.000000e+00
1062.0
4
TraesCS4A01G128700
chr3A
92.958
71
4
1
330
399
440635038
440634968
4.410000e-18
102.0
5
TraesCS4A01G128700
chr3A
92.857
56
4
0
483
538
7457454
7457509
5.740000e-12
82.4
6
TraesCS4A01G128700
chr3A
92.857
56
4
0
483
538
7463999
7464054
5.740000e-12
82.4
7
TraesCS4A01G128700
chr4B
87.660
859
93
8
1652
2502
626519369
626520222
0.000000e+00
987.0
8
TraesCS4A01G128700
chr4B
89.920
754
29
18
200
944
386222989
386222274
0.000000e+00
928.0
9
TraesCS4A01G128700
chr4B
92.799
611
38
1
1009
1613
386213995
386213385
0.000000e+00
880.0
10
TraesCS4A01G128700
chr4B
92.799
611
38
1
1009
1613
386218774
386218164
0.000000e+00
880.0
11
TraesCS4A01G128700
chr4B
92.799
611
38
1
1009
1613
386220595
386219985
0.000000e+00
880.0
12
TraesCS4A01G128700
chr4B
92.635
611
39
1
1009
1613
386216953
386216343
0.000000e+00
874.0
13
TraesCS4A01G128700
chr4B
90.276
689
32
15
1
688
386223651
386222997
0.000000e+00
869.0
14
TraesCS4A01G128700
chr4B
84.923
849
119
9
1655
2498
581951118
581951962
0.000000e+00
850.0
15
TraesCS4A01G128700
chr4B
100.000
55
0
0
963
1017
386222277
386222223
4.410000e-18
102.0
16
TraesCS4A01G128700
chr3B
86.845
859
103
10
1652
2504
707575050
707575904
0.000000e+00
952.0
17
TraesCS4A01G128700
chr3B
91.549
71
5
1
330
399
422472529
422472599
2.050000e-16
97.1
18
TraesCS4A01G128700
chr3B
97.674
43
1
0
1614
1656
386062145
386062187
9.610000e-10
75.0
19
TraesCS4A01G128700
chr7B
85.631
856
110
13
1655
2503
678291106
678290257
0.000000e+00
887.0
20
TraesCS4A01G128700
chr7B
83.274
849
117
8
1656
2502
633679450
633678625
0.000000e+00
758.0
21
TraesCS4A01G128700
chr7B
91.667
48
2
2
1610
1657
113068064
113068019
5.780000e-07
65.8
22
TraesCS4A01G128700
chr2B
85.263
855
112
13
1656
2503
778804277
778803430
0.000000e+00
869.0
23
TraesCS4A01G128700
chr2B
89.362
47
4
1
310
356
493968981
493969026
9.670000e-05
58.4
24
TraesCS4A01G128700
chr7A
89.164
646
68
2
1860
2504
28408308
28408952
0.000000e+00
804.0
25
TraesCS4A01G128700
chr7A
89.320
206
18
4
1655
1860
28359010
28359211
3.200000e-64
255.0
26
TraesCS4A01G128700
chr7A
90.141
71
6
1
330
399
68881102
68881172
9.540000e-15
91.6
27
TraesCS4A01G128700
chr7A
97.917
48
1
0
483
530
693453467
693453420
1.600000e-12
84.2
28
TraesCS4A01G128700
chr5A
85.275
781
92
10
1655
2431
4227036
4226275
0.000000e+00
784.0
29
TraesCS4A01G128700
chr5A
95.455
44
0
1
1615
1656
82867948
82867905
4.470000e-08
69.4
30
TraesCS4A01G128700
chr5A
88.000
50
4
2
314
362
474916870
474916918
9.670000e-05
58.4
31
TraesCS4A01G128700
chr5A
84.211
57
5
3
302
355
629924936
629924991
5.000000e-03
52.8
32
TraesCS4A01G128700
chr1A
89.342
441
41
6
1656
2095
533287131
533286696
1.310000e-152
549.0
33
TraesCS4A01G128700
chr1A
75.926
540
118
9
1856
2389
9954883
9955416
1.480000e-67
267.0
34
TraesCS4A01G128700
chr6B
89.773
88
7
2
314
399
541936638
541936725
7.320000e-21
111.0
35
TraesCS4A01G128700
chr6B
88.235
51
4
2
1605
1655
212623484
212623436
2.690000e-05
60.2
36
TraesCS4A01G128700
chr6A
88.636
88
8
2
314
399
501479274
501479361
3.410000e-19
106.0
37
TraesCS4A01G128700
chr7D
91.781
73
4
2
330
401
46702663
46702734
1.580000e-17
100.0
38
TraesCS4A01G128700
chr7D
90.541
74
4
2
330
400
184573430
184573357
7.370000e-16
95.3
39
TraesCS4A01G128700
chr7D
91.379
58
3
2
483
539
168580908
168580852
7.430000e-11
78.7
40
TraesCS4A01G128700
chr7D
91.304
46
3
1
314
359
4643978
4644022
7.480000e-06
62.1
41
TraesCS4A01G128700
chrUn
96.491
57
2
0
1009
1065
414074371
414074315
7.370000e-16
95.3
42
TraesCS4A01G128700
chr1D
90.541
74
4
2
329
401
464799795
464799724
7.370000e-16
95.3
43
TraesCS4A01G128700
chr3D
94.444
54
1
2
486
537
272290707
272290760
5.740000e-12
82.4
44
TraesCS4A01G128700
chr2D
91.228
57
4
1
475
531
7229333
7229278
2.670000e-10
76.8
45
TraesCS4A01G128700
chr1B
95.745
47
2
0
1610
1656
196649297
196649251
2.670000e-10
76.8
46
TraesCS4A01G128700
chr1B
93.617
47
3
0
1610
1656
196628972
196628926
1.240000e-08
71.3
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
TraesCS4A01G128700
chr4A
165711374
165713877
2503
False
4625.000000
4625
100.000000
1
2504
1
chr4A.!!$F1
2503
1
TraesCS4A01G128700
chr4A
602857669
602858521
852
False
963.000000
963
87.119000
1652
2501
1
chr4A.!!$F2
849
2
TraesCS4A01G128700
chr4D
309508579
309510193
1614
True
2460.000000
2460
94.277000
1
1608
1
chr4D.!!$R1
1607
3
TraesCS4A01G128700
chr3A
716571190
716571986
796
False
1062.000000
1062
90.738000
1705
2502
1
chr3A.!!$F3
797
4
TraesCS4A01G128700
chr4B
626519369
626520222
853
False
987.000000
987
87.660000
1652
2502
1
chr4B.!!$F2
850
5
TraesCS4A01G128700
chr4B
581951118
581951962
844
False
850.000000
850
84.923000
1655
2498
1
chr4B.!!$F1
843
6
TraesCS4A01G128700
chr4B
386213385
386223651
10266
True
773.285714
928
93.032571
1
1613
7
chr4B.!!$R1
1612
7
TraesCS4A01G128700
chr3B
707575050
707575904
854
False
952.000000
952
86.845000
1652
2504
1
chr3B.!!$F3
852
8
TraesCS4A01G128700
chr7B
678290257
678291106
849
True
887.000000
887
85.631000
1655
2503
1
chr7B.!!$R3
848
9
TraesCS4A01G128700
chr7B
633678625
633679450
825
True
758.000000
758
83.274000
1656
2502
1
chr7B.!!$R2
846
10
TraesCS4A01G128700
chr2B
778803430
778804277
847
True
869.000000
869
85.263000
1656
2503
1
chr2B.!!$R1
847
11
TraesCS4A01G128700
chr7A
28408308
28408952
644
False
804.000000
804
89.164000
1860
2504
1
chr7A.!!$F2
644
12
TraesCS4A01G128700
chr5A
4226275
4227036
761
True
784.000000
784
85.275000
1655
2431
1
chr5A.!!$R1
776
13
TraesCS4A01G128700
chr1A
9954883
9955416
533
False
267.000000
267
75.926000
1856
2389
1
chr1A.!!$F1
533
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.