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
TraesCS4B01G317200
chr4B
100.000
3578
0
0
1
3578
606910149
606906572
0.000000e+00
6608.0
1
TraesCS4B01G317200
chr4B
92.284
1918
117
15
892
2780
606867820
606865905
0.000000e+00
2693.0
2
TraesCS4B01G317200
chr4B
92.952
1816
115
10
974
2780
606828487
606826676
0.000000e+00
2632.0
3
TraesCS4B01G317200
chr4B
95.995
799
29
3
2780
3578
658554709
658555504
0.000000e+00
1295.0
4
TraesCS4B01G317200
chr4B
92.974
797
54
2
2782
3578
267659128
267659922
0.000000e+00
1160.0
5
TraesCS4B01G317200
chr4B
84.728
478
55
13
346
819
606869415
606868952
2.520000e-126
462.0
6
TraesCS4B01G317200
chr4D
94.751
2515
106
9
278
2779
479677171
479674670
0.000000e+00
3890.0
7
TraesCS4B01G317200
chr4D
90.887
2030
124
31
341
2328
479639438
479637428
0.000000e+00
2667.0
8
TraesCS4B01G317200
chr4D
96.263
1579
59
0
972
2550
479637327
479635749
0.000000e+00
2590.0
9
TraesCS4B01G317200
chr4D
89.437
142
12
3
36
176
479677307
479677168
3.670000e-40
176.0
10
TraesCS4B01G317200
chr4D
92.593
108
8
0
175
282
371212212
371212105
4.780000e-34
156.0
11
TraesCS4B01G317200
chr4A
94.248
2434
125
9
282
2711
686140840
686138418
0.000000e+00
3705.0
12
TraesCS4B01G317200
chr4A
91.327
2087
116
32
512
2550
685941526
685939457
0.000000e+00
2791.0
13
TraesCS4B01G317200
chr4A
91.826
1933
117
23
780
2677
686170408
686168482
0.000000e+00
2656.0
14
TraesCS4B01G317200
chr4A
94.743
1655
70
4
913
2550
685998857
685997203
0.000000e+00
2558.0
15
TraesCS4B01G317200
chr4A
80.477
461
48
22
278
725
686171148
686170717
7.460000e-82
315.0
16
TraesCS4B01G317200
chr4A
96.774
93
3
0
74
166
686140926
686140834
4.780000e-34
156.0
17
TraesCS4B01G317200
chr4A
90.123
81
6
2
4
82
686144202
686144122
1.760000e-18
104.0
18
TraesCS4B01G317200
chrUn
93.695
1824
99
8
972
2780
61732957
61731135
0.000000e+00
2717.0
19
TraesCS4B01G317200
chrUn
90.703
2033
123
35
339
2328
61735067
61733058
0.000000e+00
2647.0
20
TraesCS4B01G317200
chr7B
95.995
799
28
4
2780
3578
610641075
610641869
0.000000e+00
1295.0
21
TraesCS4B01G317200
chr7B
94.618
799
43
0
2780
3578
594132363
594133161
0.000000e+00
1238.0
22
TraesCS4B01G317200
chr5A
93.750
800
49
1
2779
3578
602045162
602044364
0.000000e+00
1199.0
23
TraesCS4B01G317200
chr5A
92.866
799
56
1
2780
3578
130313758
130312961
0.000000e+00
1158.0
24
TraesCS4B01G317200
chr2B
92.453
795
58
2
2784
3578
618881247
618880455
0.000000e+00
1134.0
25
TraesCS4B01G317200
chr1B
92.221
797
61
1
2782
3578
614170806
614170011
0.000000e+00
1127.0
26
TraesCS4B01G317200
chr1B
93.407
91
6
0
192
282
530049977
530050067
6.230000e-28
135.0
27
TraesCS4B01G317200
chr3B
92.405
790
59
1
2782
3571
50675180
50674392
0.000000e+00
1125.0
28
TraesCS4B01G317200
chr3B
91.667
108
9
0
175
282
371351472
371351365
2.230000e-32
150.0
29
TraesCS4B01G317200
chr3B
87.755
98
12
0
175
272
59221542
59221639
8.120000e-22
115.0
30
TraesCS4B01G317200
chr5B
88.983
118
3
1
175
282
517216988
517217105
1.730000e-28
137.0
31
TraesCS4B01G317200
chr6B
88.785
107
12
0
175
281
461267535
461267641
8.060000e-27
132.0
32
TraesCS4B01G317200
chr6B
85.714
119
7
1
173
281
260542968
260542850
2.260000e-22
117.0
33
TraesCS4B01G317200
chr7D
87.288
118
5
1
174
281
50726612
50726729
3.750000e-25
126.0
34
TraesCS4B01G317200
chr6D
95.946
74
3
0
211
284
382078450
382078523
1.740000e-23
121.0
35
TraesCS4B01G317200
chr3D
84.091
132
10
2
175
296
292034861
292034731
2.260000e-22
117.0
36
TraesCS4B01G317200
chr7A
84.034
119
9
1
174
282
200511784
200511902
4.890000e-19
106.0
37
TraesCS4B01G317200
chr5D
85.075
67
9
1
175
241
319101276
319101211
2.310000e-07
67.6
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
TraesCS4B01G317200
chr4B
606906572
606910149
3577
True
6608.000000
6608
100.0000
1
3578
1
chr4B.!!$R2
3577
1
TraesCS4B01G317200
chr4B
606826676
606828487
1811
True
2632.000000
2632
92.9520
974
2780
1
chr4B.!!$R1
1806
2
TraesCS4B01G317200
chr4B
606865905
606869415
3510
True
1577.500000
2693
88.5060
346
2780
2
chr4B.!!$R3
2434
3
TraesCS4B01G317200
chr4B
658554709
658555504
795
False
1295.000000
1295
95.9950
2780
3578
1
chr4B.!!$F2
798
4
TraesCS4B01G317200
chr4B
267659128
267659922
794
False
1160.000000
1160
92.9740
2782
3578
1
chr4B.!!$F1
796
5
TraesCS4B01G317200
chr4D
479635749
479639438
3689
True
2628.500000
2667
93.5750
341
2550
2
chr4D.!!$R2
2209
6
TraesCS4B01G317200
chr4D
479674670
479677307
2637
True
2033.000000
3890
92.0940
36
2779
2
chr4D.!!$R3
2743
7
TraesCS4B01G317200
chr4A
685939457
685941526
2069
True
2791.000000
2791
91.3270
512
2550
1
chr4A.!!$R1
2038
8
TraesCS4B01G317200
chr4A
685997203
685998857
1654
True
2558.000000
2558
94.7430
913
2550
1
chr4A.!!$R2
1637
9
TraesCS4B01G317200
chr4A
686168482
686171148
2666
True
1485.500000
2656
86.1515
278
2677
2
chr4A.!!$R4
2399
10
TraesCS4B01G317200
chr4A
686138418
686144202
5784
True
1321.666667
3705
93.7150
4
2711
3
chr4A.!!$R3
2707
11
TraesCS4B01G317200
chrUn
61731135
61735067
3932
True
2682.000000
2717
92.1990
339
2780
2
chrUn.!!$R1
2441
12
TraesCS4B01G317200
chr7B
610641075
610641869
794
False
1295.000000
1295
95.9950
2780
3578
1
chr7B.!!$F2
798
13
TraesCS4B01G317200
chr7B
594132363
594133161
798
False
1238.000000
1238
94.6180
2780
3578
1
chr7B.!!$F1
798
14
TraesCS4B01G317200
chr5A
602044364
602045162
798
True
1199.000000
1199
93.7500
2779
3578
1
chr5A.!!$R2
799
15
TraesCS4B01G317200
chr5A
130312961
130313758
797
True
1158.000000
1158
92.8660
2780
3578
1
chr5A.!!$R1
798
16
TraesCS4B01G317200
chr2B
618880455
618881247
792
True
1134.000000
1134
92.4530
2784
3578
1
chr2B.!!$R1
794
17
TraesCS4B01G317200
chr1B
614170011
614170806
795
True
1127.000000
1127
92.2210
2782
3578
1
chr1B.!!$R1
796
18
TraesCS4B01G317200
chr3B
50674392
50675180
788
True
1125.000000
1125
92.4050
2782
3571
1
chr3B.!!$R1
789
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.