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
TraesCS3B01G285900
chr3B
100.000
3267
0
0
1
3267
457636743
457633477
0.000000e+00
6034.0
1
TraesCS3B01G285900
chr3B
100.000
120
0
0
3426
3545
457633318
457633199
4.610000e-54
222.0
2
TraesCS3B01G285900
chr3A
93.015
2577
94
25
701
3247
475306657
475304137
0.000000e+00
3683.0
3
TraesCS3B01G285900
chr3A
94.958
119
6
0
3427
3545
475303676
475303558
1.680000e-43
187.0
4
TraesCS3B01G285900
chr3D
94.700
2302
58
28
692
2961
356624906
356622637
0.000000e+00
3517.0
5
TraesCS3B01G285900
chr3D
87.838
222
22
5
3045
3266
356622604
356622388
4.540000e-64
255.0
6
TraesCS3B01G285900
chr1D
91.041
1518
134
2
1019
2535
16504637
16506153
0.000000e+00
2049.0
7
TraesCS3B01G285900
chrUn
90.308
1558
145
5
979
2535
2669499
2667947
0.000000e+00
2036.0
8
TraesCS3B01G285900
chr2B
96.961
691
9
8
1
690
629109613
629108934
0.000000e+00
1149.0
9
TraesCS3B01G285900
chr2B
97.290
369
7
2
325
690
90434451
90434083
1.080000e-174
623.0
10
TraesCS3B01G285900
chr2B
99.123
342
3
0
1
342
90434719
90434378
1.810000e-172
616.0
11
TraesCS3B01G285900
chr1A
92.795
694
22
18
1
692
485328862
485328195
0.000000e+00
979.0
12
TraesCS3B01G285900
chr1A
97.003
367
10
1
325
690
507990244
507989878
1.810000e-172
616.0
13
TraesCS3B01G285900
chr1A
99.123
342
3
0
1
342
507990512
507990171
1.810000e-172
616.0
14
TraesCS3B01G285900
chr5A
89.870
691
31
18
1
690
666316558
666315906
0.000000e+00
852.0
15
TraesCS3B01G285900
chr7A
89.451
692
34
18
1
691
705282207
705281554
0.000000e+00
837.0
16
TraesCS3B01G285900
chr7A
96.486
370
11
2
325
693
556141482
556141850
8.410000e-171
610.0
17
TraesCS3B01G285900
chr7A
94.444
360
2
1
1
342
556141196
556141555
4.030000e-149
538.0
18
TraesCS3B01G285900
chr4A
99.708
342
1
0
1
342
3253562
3253221
8.350000e-176
627.0
19
TraesCS3B01G285900
chr4A
97.035
371
10
1
325
694
3253294
3252924
1.080000e-174
623.0
20
TraesCS3B01G285900
chr1B
99.415
342
2
0
1
342
30530562
30530221
3.890000e-174
621.0
21
TraesCS3B01G285900
chr1B
97.019
369
10
1
325
692
30530294
30529926
1.400000e-173
619.0
22
TraesCS3B01G285900
chr5B
97.003
367
10
1
325
690
448586784
448586418
1.810000e-172
616.0
23
TraesCS3B01G285900
chr7D
90.933
386
35
0
1322
1707
562417543
562417158
1.460000e-143
520.0
24
TraesCS3B01G285900
chr7D
94.805
154
8
0
1212
1365
562417691
562417538
1.270000e-59
241.0
25
TraesCS3B01G285900
chr4D
80.412
97
7
8
3103
3187
439697761
439697857
2.950000e-06
63.9
26
TraesCS3B01G285900
chr5D
100.000
29
0
0
3161
3189
369876175
369876203
2.000000e-03
54.7
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
TraesCS3B01G285900
chr3B
457633199
457636743
3544
True
3128.0
6034
100.0000
1
3545
2
chr3B.!!$R1
3544
1
TraesCS3B01G285900
chr3A
475303558
475306657
3099
True
1935.0
3683
93.9865
701
3545
2
chr3A.!!$R1
2844
2
TraesCS3B01G285900
chr3D
356622388
356624906
2518
True
1886.0
3517
91.2690
692
3266
2
chr3D.!!$R1
2574
3
TraesCS3B01G285900
chr1D
16504637
16506153
1516
False
2049.0
2049
91.0410
1019
2535
1
chr1D.!!$F1
1516
4
TraesCS3B01G285900
chrUn
2667947
2669499
1552
True
2036.0
2036
90.3080
979
2535
1
chrUn.!!$R1
1556
5
TraesCS3B01G285900
chr2B
629108934
629109613
679
True
1149.0
1149
96.9610
1
690
1
chr2B.!!$R1
689
6
TraesCS3B01G285900
chr2B
90434083
90434719
636
True
619.5
623
98.2065
1
690
2
chr2B.!!$R2
689
7
TraesCS3B01G285900
chr1A
485328195
485328862
667
True
979.0
979
92.7950
1
692
1
chr1A.!!$R1
691
8
TraesCS3B01G285900
chr1A
507989878
507990512
634
True
616.0
616
98.0630
1
690
2
chr1A.!!$R2
689
9
TraesCS3B01G285900
chr5A
666315906
666316558
652
True
852.0
852
89.8700
1
690
1
chr5A.!!$R1
689
10
TraesCS3B01G285900
chr7A
705281554
705282207
653
True
837.0
837
89.4510
1
691
1
chr7A.!!$R1
690
11
TraesCS3B01G285900
chr7A
556141196
556141850
654
False
574.0
610
95.4650
1
693
2
chr7A.!!$F1
692
12
TraesCS3B01G285900
chr4A
3252924
3253562
638
True
625.0
627
98.3715
1
694
2
chr4A.!!$R1
693
13
TraesCS3B01G285900
chr1B
30529926
30530562
636
True
620.0
621
98.2170
1
692
2
chr1B.!!$R1
691
14
TraesCS3B01G285900
chr7D
562417158
562417691
533
True
380.5
520
92.8690
1212
1707
2
chr7D.!!$R1
495
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.