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
TraesCS6A01G065200
chr6A
100.000
3155
0
0
1
3155
34415594
34412440
0.000000e+00
5827.0
1
TraesCS6A01G065200
chr6A
99.570
2323
8
2
835
3155
34304058
34301736
0.000000e+00
4233.0
2
TraesCS6A01G065200
chr6A
89.194
620
57
7
835
1452
34239368
34238757
0.000000e+00
765.0
3
TraesCS6A01G065200
chr6A
84.913
749
100
9
1777
2517
34212425
34211682
0.000000e+00
745.0
4
TraesCS6A01G065200
chr6A
87.561
611
57
11
2
604
453947722
453948321
0.000000e+00
689.0
5
TraesCS6A01G065200
chr6A
85.895
631
46
22
2
604
147930760
147931375
1.600000e-177
632.0
6
TraesCS6A01G065200
chr6A
76.028
705
163
5
1568
2270
8393034
8392334
8.320000e-96
361.0
7
TraesCS6A01G065200
chr6A
85.503
338
48
1
1448
1784
34221416
34221079
5.010000e-93
351.0
8
TraesCS6A01G065200
chr6A
76.461
599
137
3
1673
2270
8395393
8394798
3.930000e-84
322.0
9
TraesCS6A01G065200
chr6A
87.500
64
7
1
2643
2705
34572615
34572552
4.370000e-09
73.1
10
TraesCS6A01G065200
chr6A
100.000
28
0
0
102
129
20136229
20136202
6.000000e-03
52.8
11
TraesCS6A01G065200
chrUn
96.813
2322
50
14
846
3155
102006774
102004465
0.000000e+00
3856.0
12
TraesCS6A01G065200
chrUn
90.030
1655
145
13
871
2517
101944386
101942744
0.000000e+00
2124.0
13
TraesCS6A01G065200
chr6B
97.093
2133
60
2
1025
3155
62709296
62707164
0.000000e+00
3594.0
14
TraesCS6A01G065200
chr6B
90.915
1596
136
7
927
2514
62389725
62391319
0.000000e+00
2135.0
15
TraesCS6A01G065200
chr6B
91.494
1493
100
15
1685
3155
62650861
62649374
0.000000e+00
2028.0
16
TraesCS6A01G065200
chr6B
77.150
1256
252
29
953
2187
13951684
13950443
0.000000e+00
697.0
17
TraesCS6A01G065200
chr6B
75.724
1174
236
34
1075
2230
14622648
14621506
7.700000e-151
544.0
18
TraesCS6A01G065200
chr6B
95.745
94
4
0
743
836
341543124
341543031
5.450000e-33
152.0
19
TraesCS6A01G065200
chr5A
94.089
609
30
5
1
606
439875466
439874861
0.000000e+00
920.0
20
TraesCS6A01G065200
chr3A
92.928
608
39
4
1
606
526515515
526514910
0.000000e+00
881.0
21
TraesCS6A01G065200
chr6D
77.623
1220
260
11
964
2179
8552824
8551614
0.000000e+00
728.0
22
TraesCS6A01G065200
chr1D
88.207
619
45
17
1
604
52289480
52290085
0.000000e+00
713.0
23
TraesCS6A01G065200
chr1D
100.000
30
0
0
96
125
44254593
44254622
4.400000e-04
56.5
24
TraesCS6A01G065200
chr1A
88.072
612
48
12
2
604
90999574
91000169
0.000000e+00
702.0
25
TraesCS6A01G065200
chr3D
86.688
616
58
15
1
606
382518271
382518872
0.000000e+00
662.0
26
TraesCS6A01G065200
chr3D
95.876
97
4
0
743
839
61180276
61180372
1.170000e-34
158.0
27
TraesCS6A01G065200
chr3B
76.475
1288
260
38
994
2262
761047743
761046480
0.000000e+00
660.0
28
TraesCS6A01G065200
chr3B
82.988
241
12
13
623
836
822551251
822551489
1.160000e-44
191.0
29
TraesCS6A01G065200
chr1B
85.871
637
52
20
1
604
612820841
612821472
0.000000e+00
643.0
30
TraesCS6A01G065200
chr7A
85.624
633
51
20
2
605
690983853
690983232
2.070000e-176
628.0
31
TraesCS6A01G065200
chr5D
94.737
95
5
0
743
837
189244370
189244276
7.050000e-32
148.0
32
TraesCS6A01G065200
chr4A
94.624
93
5
0
743
835
29016315
29016223
9.120000e-31
145.0
33
TraesCS6A01G065200
chr7B
78.205
156
17
10
668
808
739423083
739422930
2.020000e-12
84.2
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
TraesCS6A01G065200
chr6A
34412440
34415594
3154
True
5827.0
5827
100.0000
1
3155
1
chr6A.!!$R6
3154
1
TraesCS6A01G065200
chr6A
34301736
34304058
2322
True
4233.0
4233
99.5700
835
3155
1
chr6A.!!$R5
2320
2
TraesCS6A01G065200
chr6A
34238757
34239368
611
True
765.0
765
89.1940
835
1452
1
chr6A.!!$R4
617
3
TraesCS6A01G065200
chr6A
34211682
34212425
743
True
745.0
745
84.9130
1777
2517
1
chr6A.!!$R2
740
4
TraesCS6A01G065200
chr6A
453947722
453948321
599
False
689.0
689
87.5610
2
604
1
chr6A.!!$F2
602
5
TraesCS6A01G065200
chr6A
147930760
147931375
615
False
632.0
632
85.8950
2
604
1
chr6A.!!$F1
602
6
TraesCS6A01G065200
chr6A
8392334
8395393
3059
True
341.5
361
76.2445
1568
2270
2
chr6A.!!$R8
702
7
TraesCS6A01G065200
chrUn
102004465
102006774
2309
True
3856.0
3856
96.8130
846
3155
1
chrUn.!!$R2
2309
8
TraesCS6A01G065200
chrUn
101942744
101944386
1642
True
2124.0
2124
90.0300
871
2517
1
chrUn.!!$R1
1646
9
TraesCS6A01G065200
chr6B
62707164
62709296
2132
True
3594.0
3594
97.0930
1025
3155
1
chr6B.!!$R4
2130
10
TraesCS6A01G065200
chr6B
62389725
62391319
1594
False
2135.0
2135
90.9150
927
2514
1
chr6B.!!$F1
1587
11
TraesCS6A01G065200
chr6B
62649374
62650861
1487
True
2028.0
2028
91.4940
1685
3155
1
chr6B.!!$R3
1470
12
TraesCS6A01G065200
chr6B
13950443
13951684
1241
True
697.0
697
77.1500
953
2187
1
chr6B.!!$R1
1234
13
TraesCS6A01G065200
chr6B
14621506
14622648
1142
True
544.0
544
75.7240
1075
2230
1
chr6B.!!$R2
1155
14
TraesCS6A01G065200
chr5A
439874861
439875466
605
True
920.0
920
94.0890
1
606
1
chr5A.!!$R1
605
15
TraesCS6A01G065200
chr3A
526514910
526515515
605
True
881.0
881
92.9280
1
606
1
chr3A.!!$R1
605
16
TraesCS6A01G065200
chr6D
8551614
8552824
1210
True
728.0
728
77.6230
964
2179
1
chr6D.!!$R1
1215
17
TraesCS6A01G065200
chr1D
52289480
52290085
605
False
713.0
713
88.2070
1
604
1
chr1D.!!$F2
603
18
TraesCS6A01G065200
chr1A
90999574
91000169
595
False
702.0
702
88.0720
2
604
1
chr1A.!!$F1
602
19
TraesCS6A01G065200
chr3D
382518271
382518872
601
False
662.0
662
86.6880
1
606
1
chr3D.!!$F2
605
20
TraesCS6A01G065200
chr3B
761046480
761047743
1263
True
660.0
660
76.4750
994
2262
1
chr3B.!!$R1
1268
21
TraesCS6A01G065200
chr1B
612820841
612821472
631
False
643.0
643
85.8710
1
604
1
chr1B.!!$F1
603
22
TraesCS6A01G065200
chr7A
690983232
690983853
621
True
628.0
628
85.6240
2
605
1
chr7A.!!$R1
603
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.