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
TraesCS2D01G035300
chr2D
100.000
2873
0
0
1
2873
13523161
13520289
0.000000e+00
5306
1
TraesCS2D01G035300
chr5A
95.765
2810
70
10
69
2873
115998062
115995297
0.000000e+00
4484
2
TraesCS2D01G035300
chr5A
89.109
101
5
5
1
98
59640816
59640719
1.400000e-23
121
3
TraesCS2D01G035300
chr5A
95.890
73
3
0
1
73
623489234
623489306
5.030000e-23
119
4
TraesCS2D01G035300
chr3D
95.410
2854
59
13
72
2873
376078866
376076033
0.000000e+00
4479
5
TraesCS2D01G035300
chr2A
93.271
2556
104
26
66
2568
613242146
613239606
0.000000e+00
3705
6
TraesCS2D01G035300
chr2A
90.681
998
50
8
69
1025
175030954
175031949
0.000000e+00
1288
7
TraesCS2D01G035300
chr3B
97.267
2086
31
3
799
2870
7318875
7320948
0.000000e+00
3513
8
TraesCS2D01G035300
chr3B
96.209
633
17
5
69
695
7318251
7318882
0.000000e+00
1029
9
TraesCS2D01G035300
chr3B
97.260
73
2
0
1
73
571304662
571304590
1.080000e-24
124
10
TraesCS2D01G035300
chr4B
97.172
2086
33
3
802
2873
595724640
595722567
0.000000e+00
3502
11
TraesCS2D01G035300
chr4B
96.209
633
17
4
69
695
595725267
595724636
0.000000e+00
1029
12
TraesCS2D01G035300
chr4B
96.000
75
3
0
1
75
669976369
669976443
3.890000e-24
122
13
TraesCS2D01G035300
chr2B
94.401
2161
84
11
730
2873
796755226
796753086
0.000000e+00
3286
14
TraesCS2D01G035300
chr2B
96.750
1723
29
4
1161
2871
33473353
33471646
0.000000e+00
2846
15
TraesCS2D01G035300
chr2B
95.920
1103
39
5
69
1167
33482917
33481817
0.000000e+00
1783
16
TraesCS2D01G035300
chr2B
97.260
73
2
0
1
73
98313345
98313273
1.080000e-24
124
17
TraesCS2D01G035300
chr2B
93.750
80
5
0
1
80
505492685
505492764
1.400000e-23
121
18
TraesCS2D01G035300
chr5D
95.836
1561
37
4
69
1601
431181776
431180216
0.000000e+00
2497
19
TraesCS2D01G035300
chr5D
97.261
1278
23
1
1596
2873
431176774
431175509
0.000000e+00
2156
20
TraesCS2D01G035300
chr5D
98.592
71
1
0
1
71
446523418
446523488
3.010000e-25
126
21
TraesCS2D01G035300
chr7A
89.539
1931
135
20
986
2873
542714785
542716691
0.000000e+00
2385
22
TraesCS2D01G035300
chr6A
93.746
1391
50
9
93
1475
367769262
367767901
0.000000e+00
2052
23
TraesCS2D01G035300
chr6A
98.020
909
17
1
1470
2378
367765375
367764468
0.000000e+00
1578
24
TraesCS2D01G035300
chr6A
96.337
819
28
1
598
1414
34076960
34077778
0.000000e+00
1345
25
TraesCS2D01G035300
chr6B
91.876
1354
82
12
1536
2873
18466278
18467619
0.000000e+00
1866
26
TraesCS2D01G035300
chr6B
91.728
1354
84
11
1536
2873
18463099
18461758
0.000000e+00
1855
27
TraesCS2D01G035300
chr6B
94.872
78
4
0
1
78
158187326
158187249
3.890000e-24
122
28
TraesCS2D01G035300
chr7B
91.485
1327
67
24
524
1819
33410168
33411479
0.000000e+00
1783
29
TraesCS2D01G035300
chr5B
97.678
689
14
1
802
1488
322287388
322286700
0.000000e+00
1182
30
TraesCS2D01G035300
chr5B
96.825
630
16
4
69
695
322288012
322287384
0.000000e+00
1050
31
TraesCS2D01G035300
chr3A
92.683
82
5
1
1
82
724078625
724078545
1.810000e-22
117
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
TraesCS2D01G035300
chr2D
13520289
13523161
2872
True
5306.0
5306
100.0000
1
2873
1
chr2D.!!$R1
2872
1
TraesCS2D01G035300
chr5A
115995297
115998062
2765
True
4484.0
4484
95.7650
69
2873
1
chr5A.!!$R2
2804
2
TraesCS2D01G035300
chr3D
376076033
376078866
2833
True
4479.0
4479
95.4100
72
2873
1
chr3D.!!$R1
2801
3
TraesCS2D01G035300
chr2A
613239606
613242146
2540
True
3705.0
3705
93.2710
66
2568
1
chr2A.!!$R1
2502
4
TraesCS2D01G035300
chr2A
175030954
175031949
995
False
1288.0
1288
90.6810
69
1025
1
chr2A.!!$F1
956
5
TraesCS2D01G035300
chr3B
7318251
7320948
2697
False
2271.0
3513
96.7380
69
2870
2
chr3B.!!$F1
2801
6
TraesCS2D01G035300
chr4B
595722567
595725267
2700
True
2265.5
3502
96.6905
69
2873
2
chr4B.!!$R1
2804
7
TraesCS2D01G035300
chr2B
796753086
796755226
2140
True
3286.0
3286
94.4010
730
2873
1
chr2B.!!$R4
2143
8
TraesCS2D01G035300
chr2B
33471646
33473353
1707
True
2846.0
2846
96.7500
1161
2871
1
chr2B.!!$R1
1710
9
TraesCS2D01G035300
chr2B
33481817
33482917
1100
True
1783.0
1783
95.9200
69
1167
1
chr2B.!!$R2
1098
10
TraesCS2D01G035300
chr5D
431175509
431181776
6267
True
2326.5
2497
96.5485
69
2873
2
chr5D.!!$R1
2804
11
TraesCS2D01G035300
chr7A
542714785
542716691
1906
False
2385.0
2385
89.5390
986
2873
1
chr7A.!!$F1
1887
12
TraesCS2D01G035300
chr6A
367764468
367769262
4794
True
1815.0
2052
95.8830
93
2378
2
chr6A.!!$R1
2285
13
TraesCS2D01G035300
chr6A
34076960
34077778
818
False
1345.0
1345
96.3370
598
1414
1
chr6A.!!$F1
816
14
TraesCS2D01G035300
chr6B
18466278
18467619
1341
False
1866.0
1866
91.8760
1536
2873
1
chr6B.!!$F1
1337
15
TraesCS2D01G035300
chr6B
18461758
18463099
1341
True
1855.0
1855
91.7280
1536
2873
1
chr6B.!!$R1
1337
16
TraesCS2D01G035300
chr7B
33410168
33411479
1311
False
1783.0
1783
91.4850
524
1819
1
chr7B.!!$F1
1295
17
TraesCS2D01G035300
chr5B
322286700
322288012
1312
True
1116.0
1182
97.2515
69
1488
2
chr5B.!!$R1
1419
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.