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
TraesCS2B01G612800
chr2B
100.000
1972
0
0
1
1972
792039800
792041771
0.000000e+00
3642.0
1
TraesCS2B01G612800
chr2B
99.544
1972
9
0
1
1972
791956050
791958021
0.000000e+00
3592.0
2
TraesCS2B01G612800
chr2B
100.000
1516
0
0
2389
3904
792042188
792043703
0.000000e+00
2800.0
3
TraesCS2B01G612800
chr2B
99.538
1516
4
1
2389
3904
791958787
791960299
0.000000e+00
2758.0
4
TraesCS2B01G612800
chr2B
97.736
530
9
2
3209
3738
791980479
791981005
0.000000e+00
909.0
5
TraesCS2B01G612800
chr2B
96.014
276
9
2
2937
3212
791966111
791966384
7.690000e-122
448.0
6
TraesCS2B01G612800
chr2B
98.990
99
1
0
3806
3904
791981003
791981101
1.110000e-40
178.0
7
TraesCS2B01G612800
chr2B
78.261
230
45
4
2447
2675
704292567
704292792
4.070000e-30
143.0
8
TraesCS2B01G612800
chr2B
78.505
214
42
3
103
313
212183045
212182833
1.890000e-28
137.0
9
TraesCS2B01G612800
chr4D
82.521
698
76
16
4
662
494059513
494058823
4.380000e-159
571.0
10
TraesCS2B01G612800
chr4D
80.693
202
34
4
10
207
7913248
7913048
6.760000e-33
152.0
11
TraesCS2B01G612800
chr6A
79.129
551
68
18
1
512
597696602
597697144
1.740000e-88
337.0
12
TraesCS2B01G612800
chr2D
76.632
475
81
21
1477
1946
584530851
584531300
6.520000e-58
235.0
13
TraesCS2B01G612800
chr2D
76.842
380
65
15
1019
1394
584539434
584539794
3.980000e-45
193.0
14
TraesCS2B01G612800
chr2D
75.306
409
72
17
994
1394
584533241
584533628
6.710000e-38
169.0
15
TraesCS2B01G612800
chr2D
79.039
229
43
4
2447
2674
584540566
584540790
6.760000e-33
152.0
16
TraesCS2B01G612800
chr7B
78.302
318
60
7
3
313
607524308
607523993
3.080000e-46
196.0
17
TraesCS2B01G612800
chr2A
80.913
241
44
2
2437
2675
718575720
718575960
5.150000e-44
189.0
18
TraesCS2B01G612800
chr2A
78.947
228
41
6
2447
2672
718722823
718723045
8.740000e-32
148.0
19
TraesCS2B01G612800
chr1B
92.453
106
7
1
3800
3904
12086029
12086134
2.430000e-32
150.0
20
TraesCS2B01G612800
chr1B
91.346
104
8
1
3802
3904
12078891
12078994
1.460000e-29
141.0
21
TraesCS2B01G612800
chr1B
91.346
104
8
1
3802
3904
12084053
12083950
1.460000e-29
141.0
22
TraesCS2B01G612800
chr1B
90.385
104
9
1
3802
3904
12049531
12049634
6.800000e-28
135.0
23
TraesCS2B01G612800
chr1B
90.385
104
9
1
3802
3904
12057800
12057903
6.800000e-28
135.0
24
TraesCS2B01G612800
chr1B
90.385
104
9
1
3802
3904
12061195
12061298
6.800000e-28
135.0
25
TraesCS2B01G612800
chr1B
76.033
121
27
2
3091
3210
532484882
532485001
1.170000e-05
62.1
26
TraesCS2B01G612800
chr5A
81.283
187
27
6
666
850
433189284
433189104
1.130000e-30
145.0
27
TraesCS2B01G612800
chr4A
80.952
189
28
6
664
850
328252982
328252800
4.070000e-30
143.0
28
TraesCS2B01G612800
chr3B
91.262
103
8
1
3803
3904
771664024
771663922
5.260000e-29
139.0
29
TraesCS2B01G612800
chr3B
84.906
106
16
0
745
850
578627333
578627228
1.480000e-19
108.0
30
TraesCS2B01G612800
chr7D
78.261
207
40
4
4
207
415792540
415792744
1.140000e-25
128.0
31
TraesCS2B01G612800
chr1A
86.792
106
14
0
745
850
570128160
570128055
6.850000e-23
119.0
32
TraesCS2B01G612800
chrUn
83.654
104
16
1
67
169
68151722
68151619
3.210000e-16
97.1
33
TraesCS2B01G612800
chr1D
71.161
534
112
27
3052
3581
232139657
232140152
1.150000e-15
95.3
34
TraesCS2B01G612800
chr1D
92.000
50
4
0
745
794
479209182
479209231
1.950000e-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
TraesCS2B01G612800
chr2B
792039800
792043703
3903
False
3221.0
3642
100.000
1
3904
2
chr2B.!!$F5
3903
1
TraesCS2B01G612800
chr2B
791956050
791960299
4249
False
3175.0
3592
99.541
1
3904
2
chr2B.!!$F3
3903
2
TraesCS2B01G612800
chr2B
791980479
791981101
622
False
543.5
909
98.363
3209
3904
2
chr2B.!!$F4
695
3
TraesCS2B01G612800
chr4D
494058823
494059513
690
True
571.0
571
82.521
4
662
1
chr4D.!!$R2
658
4
TraesCS2B01G612800
chr6A
597696602
597697144
542
False
337.0
337
79.129
1
512
1
chr6A.!!$F1
511
5
TraesCS2B01G612800
chr2D
584530851
584533628
2777
False
202.0
235
75.969
994
1946
2
chr2D.!!$F1
952
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.