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
TraesCS2A01G327800
chr2A
100.000
2432
0
0
1
2432
559608315
559610746
0.000000e+00
4492.0
1
TraesCS2A01G327800
chr2A
86.765
68
9
0
414
481
753732759
753732692
2.590000e-10
76.8
2
TraesCS2A01G327800
chr2B
92.641
2052
100
29
4
2006
505007635
505005586
0.000000e+00
2905.0
3
TraesCS2A01G327800
chr2B
96.966
758
21
1
757
1512
512305954
512306711
0.000000e+00
1271.0
4
TraesCS2A01G327800
chr2B
91.886
875
37
13
1517
2376
512306775
512307630
0.000000e+00
1192.0
5
TraesCS2A01G327800
chr2B
94.221
571
30
3
1
570
512305389
512305957
0.000000e+00
869.0
6
TraesCS2A01G327800
chr2B
85.042
361
22
8
2025
2376
505005599
505005262
3.000000e-89
339.0
7
TraesCS2A01G327800
chr2D
94.486
1886
80
16
1
1867
427971060
427969180
0.000000e+00
2885.0
8
TraesCS2A01G327800
chr2D
90.305
361
26
2
2025
2376
427969005
427968645
4.740000e-127
464.0
9
TraesCS2A01G327800
chr2D
91.275
149
9
2
1860
2005
427969140
427968993
1.470000e-47
200.0
10
TraesCS2A01G327800
chr7D
80.128
312
57
4
1112
1419
41800439
41800749
6.760000e-56
228.0
11
TraesCS2A01G327800
chr7A
79.868
303
61
0
1112
1414
41449777
41450079
3.150000e-54
222.0
12
TraesCS2A01G327800
chr7A
92.453
53
4
0
418
470
96392796
96392848
2.590000e-10
76.8
13
TraesCS2A01G327800
chr4B
84.211
95
11
4
38
129
566977080
566977173
3.330000e-14
89.8
14
TraesCS2A01G327800
chr4B
92.727
55
3
1
196
249
35522828
35522774
7.210000e-11
78.7
15
TraesCS2A01G327800
chr4B
86.765
68
9
0
418
485
75348064
75347997
2.590000e-10
76.8
16
TraesCS2A01G327800
chr5B
93.103
58
3
1
194
250
300394509
300394452
1.550000e-12
84.2
17
TraesCS2A01G327800
chr5B
92.157
51
3
1
200
249
347698722
347698672
1.210000e-08
71.3
18
TraesCS2A01G327800
chr4D
92.982
57
3
1
194
249
23422741
23422685
5.570000e-12
82.4
19
TraesCS2A01G327800
chr4A
92.727
55
3
1
196
249
578537010
578537064
7.210000e-11
78.7
20
TraesCS2A01G327800
chr4A
80.220
91
14
4
384
472
522458223
522458135
5.610000e-07
65.8
21
TraesCS2A01G327800
chr3A
84.286
70
11
0
414
483
340409981
340409912
4.340000e-08
69.4
22
TraesCS2A01G327800
chr3A
80.645
93
10
6
384
472
200913203
200913291
5.610000e-07
65.8
23
TraesCS2A01G327800
chr1A
82.716
81
9
2
73
148
238683290
238683210
1.560000e-07
67.6
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
TraesCS2A01G327800
chr2A
559608315
559610746
2431
False
4492.000000
4492
100.000000
1
2432
1
chr2A.!!$F1
2431
1
TraesCS2A01G327800
chr2B
505005262
505007635
2373
True
1622.000000
2905
88.841500
4
2376
2
chr2B.!!$R1
2372
2
TraesCS2A01G327800
chr2B
512305389
512307630
2241
False
1110.666667
1271
94.357667
1
2376
3
chr2B.!!$F1
2375
3
TraesCS2A01G327800
chr2D
427968645
427971060
2415
True
1183.000000
2885
92.022000
1
2376
3
chr2D.!!$R1
2375
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.