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
TraesCS5D01G184800
chr5D
100.000
4152
0
0
1
4152
287018426
287014275
0.000000e+00
7668.0
1
TraesCS5D01G184800
chr5D
82.550
298
26
11
3632
3916
286949778
286949494
5.360000e-59
239.0
2
TraesCS5D01G184800
chr5A
92.330
2073
70
39
1
2033
379095135
379093112
0.000000e+00
2865.0
3
TraesCS5D01G184800
chr5A
90.786
1704
79
25
2076
3710
379093015
379091321
0.000000e+00
2206.0
4
TraesCS5D01G184800
chr5A
90.431
418
18
9
3755
4152
379091315
379090900
7.900000e-147
531.0
5
TraesCS5D01G184800
chr5A
81.546
401
32
20
3793
4152
379040890
379040491
4.060000e-75
292.0
6
TraesCS5D01G184800
chr5A
93.443
61
4
0
3633
3693
379041067
379041007
1.590000e-14
91.6
7
TraesCS5D01G184800
chr5B
94.463
1752
41
20
639
2360
325965694
325963969
0.000000e+00
2647.0
8
TraesCS5D01G184800
chr5B
94.195
1068
44
3
2358
3424
325962814
325961764
0.000000e+00
1613.0
9
TraesCS5D01G184800
chr5B
95.944
641
23
3
4
641
325966438
325965798
0.000000e+00
1037.0
10
TraesCS5D01G184800
chr5B
91.086
718
33
13
3462
4152
325961758
325961045
0.000000e+00
942.0
11
TraesCS5D01G184800
chr5B
78.727
550
51
30
3636
4152
325943098
325942582
1.450000e-79
307.0
12
TraesCS5D01G184800
chr7D
88.388
1197
96
22
666
1855
37659440
37660600
0.000000e+00
1400.0
13
TraesCS5D01G184800
chr7D
87.668
746
69
10
811
1553
37625515
37626240
0.000000e+00
846.0
14
TraesCS5D01G184800
chr7D
79.048
630
78
28
2496
3101
37661234
37661833
2.340000e-102
383.0
15
TraesCS5D01G184800
chr7D
80.916
131
11
8
1912
2035
37660618
37660741
1.590000e-14
91.6
16
TraesCS5D01G184800
chr3D
88.230
1198
97
23
666
1855
25527112
25525951
0.000000e+00
1391.0
17
TraesCS5D01G184800
chr3D
79.348
644
77
30
2496
3101
25525317
25524692
6.470000e-108
401.0
18
TraesCS5D01G184800
chr3D
81.250
128
10
8
1915
2035
25525930
25525810
1.590000e-14
91.6
19
TraesCS5D01G184800
chr2A
88.137
1197
95
26
666
1849
720388432
720387270
0.000000e+00
1380.0
20
TraesCS5D01G184800
chr2A
88.263
639
58
11
919
1553
720354044
720353419
0.000000e+00
749.0
21
TraesCS5D01G184800
chr2A
76.774
930
102
46
2248
3101
720386640
720385749
2.310000e-112
416.0
22
TraesCS5D01G184800
chr2A
80.469
128
11
8
1915
2035
720387260
720387140
7.400000e-13
86.1
23
TraesCS5D01G184800
chr4A
89.559
1044
79
15
814
1851
687321183
687320164
0.000000e+00
1297.0
24
TraesCS5D01G184800
chr4A
76.661
587
66
27
2248
2770
687319504
687318925
4.120000e-65
259.0
25
TraesCS5D01G184800
chr4A
87.611
113
13
1
2048
2160
687319757
687319646
3.370000e-26
130.0
26
TraesCS5D01G184800
chr4A
80.469
128
11
9
1915
2035
687320139
687320019
7.400000e-13
86.1
27
TraesCS5D01G184800
chr2D
100.000
44
0
0
1869
1912
220960589
220960632
9.570000e-12
82.4
28
TraesCS5D01G184800
chr2B
96.000
50
2
0
1863
1912
291598899
291598948
9.570000e-12
82.4
29
TraesCS5D01G184800
chr2B
97.778
45
0
1
1869
1912
291588749
291588793
4.450000e-10
76.8
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
TraesCS5D01G184800
chr5D
287014275
287018426
4151
True
7668.000000
7668
100.000000
1
4152
1
chr5D.!!$R2
4151
1
TraesCS5D01G184800
chr5A
379090900
379095135
4235
True
1867.333333
2865
91.182333
1
4152
3
chr5A.!!$R2
4151
2
TraesCS5D01G184800
chr5B
325961045
325966438
5393
True
1559.750000
2647
93.922000
4
4152
4
chr5B.!!$R2
4148
3
TraesCS5D01G184800
chr5B
325942582
325943098
516
True
307.000000
307
78.727000
3636
4152
1
chr5B.!!$R1
516
4
TraesCS5D01G184800
chr7D
37625515
37626240
725
False
846.000000
846
87.668000
811
1553
1
chr7D.!!$F1
742
5
TraesCS5D01G184800
chr7D
37659440
37661833
2393
False
624.866667
1400
82.784000
666
3101
3
chr7D.!!$F2
2435
6
TraesCS5D01G184800
chr3D
25524692
25527112
2420
True
627.866667
1391
82.942667
666
3101
3
chr3D.!!$R1
2435
7
TraesCS5D01G184800
chr2A
720353419
720354044
625
True
749.000000
749
88.263000
919
1553
1
chr2A.!!$R1
634
8
TraesCS5D01G184800
chr2A
720385749
720388432
2683
True
627.366667
1380
81.793333
666
3101
3
chr2A.!!$R2
2435
9
TraesCS5D01G184800
chr4A
687318925
687321183
2258
True
443.025000
1297
83.575000
814
2770
4
chr4A.!!$R1
1956
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.