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
TraesCS1B01G222800
chr1B
100.000
3547
0
0
1
3547
400419224
400415678
0.000000e+00
6551
1
TraesCS1B01G222800
chr1B
95.006
3384
125
20
2
3354
98650893
98654263
0.000000e+00
5273
2
TraesCS1B01G222800
chr1B
94.220
3391
141
19
2
3362
91432992
91429627
0.000000e+00
5125
3
TraesCS1B01G222800
chr1B
94.615
2804
132
5
452
3237
554927324
554930126
0.000000e+00
4324
4
TraesCS1B01G222800
chr1B
95.038
524
25
1
2
525
21723444
21722922
0.000000e+00
822
5
TraesCS1B01G222800
chr1B
94.724
398
18
2
3153
3547
98654101
98654498
1.810000e-172
616
6
TraesCS1B01G222800
chr1B
94.221
398
20
2
3153
3547
91429797
91429400
3.920000e-169
604
7
TraesCS1B01G222800
chr1B
92.911
395
23
3
3153
3547
613851050
613850661
1.430000e-158
569
8
TraesCS1B01G222800
chr2B
94.797
3575
153
11
2
3545
764626615
764630187
0.000000e+00
5541
9
TraesCS1B01G222800
chr2B
94.743
3367
144
15
2
3355
635824957
635828303
0.000000e+00
5206
10
TraesCS1B01G222800
chr2B
93.899
2852
155
8
452
3289
177298504
177295658
0.000000e+00
4285
11
TraesCS1B01G222800
chr2B
94.656
524
27
1
2
525
120664705
120665227
0.000000e+00
811
12
TraesCS1B01G222800
chr2B
92.932
382
26
1
3166
3547
635828156
635828536
4.000000e-154
555
13
TraesCS1B01G222800
chr2B
91.228
399
23
6
3159
3547
488089586
488089190
1.870000e-147
532
14
TraesCS1B01G222800
chr2B
90.609
394
34
1
3153
3546
775288707
775289097
1.460000e-143
520
15
TraesCS1B01G222800
chr2B
88.384
396
32
10
3153
3547
671840714
671841096
6.940000e-127
464
16
TraesCS1B01G222800
chr5B
95.641
3395
115
9
2
3365
419024693
419021301
0.000000e+00
5419
17
TraesCS1B01G222800
chr5B
94.993
2796
116
7
452
3237
92758939
92756158
0.000000e+00
4366
18
TraesCS1B01G222800
chr5B
94.923
2797
127
5
452
3237
230939116
230936324
0.000000e+00
4364
19
TraesCS1B01G222800
chr5B
91.414
396
27
4
3153
3547
584466583
584466194
1.450000e-148
536
20
TraesCS1B01G222800
chr6B
95.193
3391
123
16
2
3362
692886319
692882939
0.000000e+00
5323
21
TraesCS1B01G222800
chr4B
95.422
2796
117
4
452
3237
127610345
127607551
0.000000e+00
4444
22
TraesCS1B01G222800
chr4B
96.026
453
18
0
2
454
16598160
16597708
0.000000e+00
737
23
TraesCS1B01G222800
chr3B
94.594
2830
142
4
452
3270
746729923
746732752
0.000000e+00
4368
24
TraesCS1B01G222800
chr3B
93.214
2859
155
20
452
3293
729277506
729274670
0.000000e+00
4169
25
TraesCS1B01G222800
chr3B
94.177
395
18
4
3153
3547
729274578
729274189
6.550000e-167
597
26
TraesCS1B01G222800
chr7B
94.707
2796
138
3
452
3237
529760370
529763165
0.000000e+00
4335
27
TraesCS1B01G222800
chr4A
94.244
2832
147
5
452
3270
656384212
656381384
0.000000e+00
4313
28
TraesCS1B01G222800
chr4A
94.361
1667
84
5
452
2108
656176697
656175031
0.000000e+00
2549
29
TraesCS1B01G222800
chr2A
86.637
2013
215
30
452
2440
338675773
338673791
0.000000e+00
2178
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
TraesCS1B01G222800
chr1B
400415678
400419224
3546
True
6551.0
6551
100.0000
1
3547
1
chr1B.!!$R2
3546
1
TraesCS1B01G222800
chr1B
554927324
554930126
2802
False
4324.0
4324
94.6150
452
3237
1
chr1B.!!$F1
2785
2
TraesCS1B01G222800
chr1B
98650893
98654498
3605
False
2944.5
5273
94.8650
2
3547
2
chr1B.!!$F2
3545
3
TraesCS1B01G222800
chr1B
91429400
91432992
3592
True
2864.5
5125
94.2205
2
3547
2
chr1B.!!$R4
3545
4
TraesCS1B01G222800
chr1B
21722922
21723444
522
True
822.0
822
95.0380
2
525
1
chr1B.!!$R1
523
5
TraesCS1B01G222800
chr2B
764626615
764630187
3572
False
5541.0
5541
94.7970
2
3545
1
chr2B.!!$F3
3543
6
TraesCS1B01G222800
chr2B
177295658
177298504
2846
True
4285.0
4285
93.8990
452
3289
1
chr2B.!!$R1
2837
7
TraesCS1B01G222800
chr2B
635824957
635828536
3579
False
2880.5
5206
93.8375
2
3547
2
chr2B.!!$F5
3545
8
TraesCS1B01G222800
chr2B
120664705
120665227
522
False
811.0
811
94.6560
2
525
1
chr2B.!!$F1
523
9
TraesCS1B01G222800
chr5B
419021301
419024693
3392
True
5419.0
5419
95.6410
2
3365
1
chr5B.!!$R3
3363
10
TraesCS1B01G222800
chr5B
92756158
92758939
2781
True
4366.0
4366
94.9930
452
3237
1
chr5B.!!$R1
2785
11
TraesCS1B01G222800
chr5B
230936324
230939116
2792
True
4364.0
4364
94.9230
452
3237
1
chr5B.!!$R2
2785
12
TraesCS1B01G222800
chr6B
692882939
692886319
3380
True
5323.0
5323
95.1930
2
3362
1
chr6B.!!$R1
3360
13
TraesCS1B01G222800
chr4B
127607551
127610345
2794
True
4444.0
4444
95.4220
452
3237
1
chr4B.!!$R2
2785
14
TraesCS1B01G222800
chr3B
746729923
746732752
2829
False
4368.0
4368
94.5940
452
3270
1
chr3B.!!$F1
2818
15
TraesCS1B01G222800
chr3B
729274189
729277506
3317
True
2383.0
4169
93.6955
452
3547
2
chr3B.!!$R1
3095
16
TraesCS1B01G222800
chr7B
529760370
529763165
2795
False
4335.0
4335
94.7070
452
3237
1
chr7B.!!$F1
2785
17
TraesCS1B01G222800
chr4A
656381384
656384212
2828
True
4313.0
4313
94.2440
452
3270
1
chr4A.!!$R2
2818
18
TraesCS1B01G222800
chr4A
656175031
656176697
1666
True
2549.0
2549
94.3610
452
2108
1
chr4A.!!$R1
1656
19
TraesCS1B01G222800
chr2A
338673791
338675773
1982
True
2178.0
2178
86.6370
452
2440
1
chr2A.!!$R1
1988
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.