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
TraesCS5B01G142800
chr5B
100.000
2426
0
0
1
2426
269953849
269951424
0.000000e+00
4481.0
1
TraesCS5B01G142800
chr5B
92.632
190
14
0
753
942
269946783
269946972
8.550000e-70
274.0
2
TraesCS5B01G142800
chr5B
88.021
192
22
1
749
940
524222928
524222738
2.430000e-55
226.0
3
TraesCS5B01G142800
chr5B
93.919
148
7
2
2280
2426
60086230
60086084
3.140000e-54
222.0
4
TraesCS5B01G142800
chr5D
95.312
1536
55
6
756
2276
338408062
338409595
0.000000e+00
2422.0
5
TraesCS5B01G142800
chr5D
95.055
1537
60
5
755
2276
476457964
476456429
0.000000e+00
2403.0
6
TraesCS5B01G142800
chr5D
90.893
582
35
9
1039
1617
565257986
565258552
0.000000e+00
765.0
7
TraesCS5B01G142800
chr5D
85.095
577
68
8
1039
1611
565239015
565238453
7.520000e-160
573.0
8
TraesCS5B01G142800
chr3B
97.786
768
13
4
1
767
51966944
51966180
0.000000e+00
1321.0
9
TraesCS5B01G142800
chr3B
98.141
753
13
1
1
753
776030216
776030967
0.000000e+00
1312.0
10
TraesCS5B01G142800
chr3B
85.347
389
36
8
47
435
741653732
741653365
1.360000e-102
383.0
11
TraesCS5B01G142800
chr3B
97.619
42
1
0
447
488
741653284
741653243
3.350000e-09
73.1
12
TraesCS5B01G142800
chr4B
97.347
754
12
1
1
754
613015839
613015094
0.000000e+00
1275.0
13
TraesCS5B01G142800
chr1B
97.458
708
17
1
47
754
634164010
634163304
0.000000e+00
1206.0
14
TraesCS5B01G142800
chr4A
96.823
661
21
0
1616
2276
689848516
689849176
0.000000e+00
1105.0
15
TraesCS5B01G142800
chr4A
85.590
576
61
9
1039
1611
606648226
606647670
3.480000e-163
584.0
16
TraesCS5B01G142800
chr4A
95.833
72
2
1
970
1041
689847592
689847662
5.480000e-22
115.0
17
TraesCS5B01G142800
chr7D
96.520
661
23
0
1616
2276
35182927
35182267
0.000000e+00
1094.0
18
TraesCS5B01G142800
chr7D
89.637
193
18
2
749
940
207790331
207790140
6.700000e-61
244.0
19
TraesCS5B01G142800
chr7D
89.157
83
6
2
962
1041
35183863
35183781
1.530000e-17
100.0
20
TraesCS5B01G142800
chr7A
96.218
661
25
0
1616
2276
35396703
35396043
0.000000e+00
1083.0
21
TraesCS5B01G142800
chr7A
92.391
368
25
2
1
366
705292905
705293271
2.760000e-144
521.0
22
TraesCS5B01G142800
chr7A
91.667
372
22
3
397
760
705293272
705293642
7.740000e-140
507.0
23
TraesCS5B01G142800
chr7A
90.110
91
4
4
956
1041
35397647
35397557
1.970000e-21
113.0
24
TraesCS5B01G142800
chr2B
91.777
754
45
2
1
754
53731151
53731887
0.000000e+00
1033.0
25
TraesCS5B01G142800
chr2B
91.766
753
45
2
1
753
53729499
53730234
0.000000e+00
1031.0
26
TraesCS5B01G142800
chr2B
92.431
436
33
0
319
754
53754616
53755051
7.370000e-175
623.0
27
TraesCS5B01G142800
chr1A
96.471
510
6
1
245
754
61118369
61118866
0.000000e+00
832.0
28
TraesCS5B01G142800
chr1A
98.095
420
8
0
1
420
61117894
61118313
0.000000e+00
732.0
29
TraesCS5B01G142800
chr1A
90.857
175
16
0
753
927
508205710
508205536
4.030000e-58
235.0
30
TraesCS5B01G142800
chr1A
91.304
138
12
0
1
138
61117189
61117326
3.180000e-44
189.0
31
TraesCS5B01G142800
chr6B
96.599
147
3
2
2281
2426
369526057
369525912
2.410000e-60
243.0
32
TraesCS5B01G142800
chr6B
93.878
147
7
2
2281
2426
305957628
305957773
1.130000e-53
220.0
33
TraesCS5B01G142800
chr7B
88.776
196
20
2
748
942
88338323
88338517
3.120000e-59
239.0
34
TraesCS5B01G142800
chr7B
93.038
158
8
3
2271
2426
578788603
578788447
6.750000e-56
228.0
35
TraesCS5B01G142800
chr7B
91.463
164
9
5
2266
2426
654207720
654207559
1.130000e-53
220.0
36
TraesCS5B01G142800
chr6A
88.144
194
22
1
749
942
91164657
91164465
1.880000e-56
230.0
37
TraesCS5B01G142800
chr4D
87.692
195
23
1
747
940
30392894
30393088
2.430000e-55
226.0
38
TraesCS5B01G142800
chrUn
93.878
147
6
3
2281
2426
344735187
344735043
4.060000e-53
219.0
39
TraesCS5B01G142800
chr3A
93.878
147
6
3
2281
2426
738564523
738564667
4.060000e-53
219.0
40
TraesCS5B01G142800
chr3A
93.197
147
8
2
2281
2426
738664681
738664826
5.250000e-52
215.0
41
TraesCS5B01G142800
chr3A
93.197
147
7
3
2281
2426
738491981
738492125
1.890000e-51
213.0
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
TraesCS5B01G142800
chr5B
269951424
269953849
2425
True
4481.000000
4481
100.0000
1
2426
1
chr5B.!!$R2
2425
1
TraesCS5B01G142800
chr5D
338408062
338409595
1533
False
2422.000000
2422
95.3120
756
2276
1
chr5D.!!$F1
1520
2
TraesCS5B01G142800
chr5D
476456429
476457964
1535
True
2403.000000
2403
95.0550
755
2276
1
chr5D.!!$R1
1521
3
TraesCS5B01G142800
chr5D
565257986
565258552
566
False
765.000000
765
90.8930
1039
1617
1
chr5D.!!$F2
578
4
TraesCS5B01G142800
chr5D
565238453
565239015
562
True
573.000000
573
85.0950
1039
1611
1
chr5D.!!$R2
572
5
TraesCS5B01G142800
chr3B
51966180
51966944
764
True
1321.000000
1321
97.7860
1
767
1
chr3B.!!$R1
766
6
TraesCS5B01G142800
chr3B
776030216
776030967
751
False
1312.000000
1312
98.1410
1
753
1
chr3B.!!$F1
752
7
TraesCS5B01G142800
chr4B
613015094
613015839
745
True
1275.000000
1275
97.3470
1
754
1
chr4B.!!$R1
753
8
TraesCS5B01G142800
chr1B
634163304
634164010
706
True
1206.000000
1206
97.4580
47
754
1
chr1B.!!$R1
707
9
TraesCS5B01G142800
chr4A
689847592
689849176
1584
False
610.000000
1105
96.3280
970
2276
2
chr4A.!!$F1
1306
10
TraesCS5B01G142800
chr4A
606647670
606648226
556
True
584.000000
584
85.5900
1039
1611
1
chr4A.!!$R1
572
11
TraesCS5B01G142800
chr7D
35182267
35183863
1596
True
597.000000
1094
92.8385
962
2276
2
chr7D.!!$R2
1314
12
TraesCS5B01G142800
chr7A
35396043
35397647
1604
True
598.000000
1083
93.1640
956
2276
2
chr7A.!!$R1
1320
13
TraesCS5B01G142800
chr7A
705292905
705293642
737
False
514.000000
521
92.0290
1
760
2
chr7A.!!$F1
759
14
TraesCS5B01G142800
chr2B
53729499
53731887
2388
False
1032.000000
1033
91.7715
1
754
2
chr2B.!!$F2
753
15
TraesCS5B01G142800
chr1A
61117189
61118866
1677
False
584.333333
832
95.2900
1
754
3
chr1A.!!$F1
753
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.