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
TraesCS2A01G447300
chr2A
100.000
3091
0
0
1
3091
696218214
696221304
0.000000e+00
5709.0
1
TraesCS2A01G447300
chr2A
90.080
1250
98
10
1609
2839
696307720
696308962
0.000000e+00
1598.0
2
TraesCS2A01G447300
chr2A
83.042
1657
146
65
714
2276
696040132
696041747
0.000000e+00
1378.0
3
TraesCS2A01G447300
chr2A
81.473
1371
146
58
968
2244
695999081
696000437
0.000000e+00
1026.0
4
TraesCS2A01G447300
chr2A
85.731
876
62
24
18
874
696286735
696287566
0.000000e+00
867.0
5
TraesCS2A01G447300
chr2A
88.700
646
39
11
970
1597
696307007
696307636
0.000000e+00
758.0
6
TraesCS2A01G447300
chr2A
81.279
219
33
7
2819
3035
696309130
696309342
1.470000e-38
171.0
7
TraesCS2A01G447300
chr2A
82.178
101
8
7
2145
2235
696826522
696826622
9.190000e-11
78.7
8
TraesCS2A01G447300
chr2D
94.211
2142
87
20
968
3091
556365460
556367582
0.000000e+00
3234.0
9
TraesCS2A01G447300
chr2D
92.514
2164
93
34
968
3091
556619104
556621238
0.000000e+00
3035.0
10
TraesCS2A01G447300
chr2D
91.869
1316
54
24
968
2256
556408004
556409293
0.000000e+00
1788.0
11
TraesCS2A01G447300
chr2D
94.982
1136
49
6
1960
3091
556333871
556335002
0.000000e+00
1775.0
12
TraesCS2A01G447300
chr2D
95.352
753
31
3
223
971
556364668
556365420
0.000000e+00
1194.0
13
TraesCS2A01G447300
chr2D
94.197
741
39
3
2253
2990
556411563
556412302
0.000000e+00
1127.0
14
TraesCS2A01G447300
chr2D
82.288
1355
133
51
968
2237
556267194
556268526
0.000000e+00
1074.0
15
TraesCS2A01G447300
chr2D
82.273
1320
137
43
996
2238
556350544
556351843
0.000000e+00
1051.0
16
TraesCS2A01G447300
chr2D
88.399
862
57
15
129
968
556407134
556407974
0.000000e+00
998.0
17
TraesCS2A01G447300
chr2D
84.551
958
83
30
573
1509
556317994
556318907
0.000000e+00
889.0
18
TraesCS2A01G447300
chr2D
87.053
811
66
26
999
1787
556642397
556643190
0.000000e+00
880.0
19
TraesCS2A01G447300
chr2D
79.381
970
100
55
1365
2237
556339260
556340226
2.650000e-165
592.0
20
TraesCS2A01G447300
chr2D
88.866
476
29
12
1504
1956
556333284
556333758
5.790000e-157
564.0
21
TraesCS2A01G447300
chr2D
75.468
481
50
25
188
623
556349767
556350224
4.100000e-39
172.0
22
TraesCS2A01G447300
chr2D
96.154
104
4
0
2988
3091
556421605
556421708
1.470000e-38
171.0
23
TraesCS2A01G447300
chr2D
80.791
177
26
6
476
649
556265743
556265914
6.950000e-27
132.0
24
TraesCS2A01G447300
chr2D
87.736
106
3
2
1
106
556364138
556364233
7.000000e-22
115.0
25
TraesCS2A01G447300
chr2D
100.000
31
0
0
478
508
556618663
556618693
1.200000e-04
58.4
26
TraesCS2A01G447300
chr2B
90.577
1422
95
17
968
2375
663885996
663887392
0.000000e+00
1847.0
27
TraesCS2A01G447300
chr2B
82.226
1294
140
46
987
2228
663838006
663839261
0.000000e+00
1033.0
28
TraesCS2A01G447300
chr2B
85.802
810
72
31
999
1787
663898756
663899543
0.000000e+00
819.0
29
TraesCS2A01G447300
chr2B
88.225
569
27
10
139
706
663885200
663885729
0.000000e+00
643.0
30
TraesCS2A01G447300
chr2B
85.781
429
44
8
2447
2871
663887609
663888024
3.660000e-119
438.0
31
TraesCS2A01G447300
chr2B
83.946
299
33
6
681
969
663828606
663828899
3.930000e-69
272.0
32
TraesCS2A01G447300
chr2B
87.805
205
25
0
129
333
663827807
663828011
1.110000e-59
241.0
33
TraesCS2A01G447300
chr2B
84.034
238
26
5
746
971
663885723
663885960
5.190000e-53
219.0
34
TraesCS2A01G447300
chr2B
93.548
93
6
0
2999
3091
663892710
663892802
4.160000e-29
139.0
35
TraesCS2A01G447300
chr2B
75.636
275
49
15
214
477
663835089
663835356
1.510000e-23
121.0
36
TraesCS2A01G447300
chr2B
93.220
59
2
1
2394
2450
663887439
663887497
5.490000e-13
86.1
37
TraesCS2A01G447300
chr2B
79.137
139
15
7
2145
2270
663900032
663900169
1.980000e-12
84.2
38
TraesCS2A01G447300
chr2B
86.250
80
6
4
574
653
663837575
663837649
7.100000e-12
82.4
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
TraesCS2A01G447300
chr2A
696218214
696221304
3090
False
5709.000000
5709
100.000000
1
3091
1
chr2A.!!$F3
3090
1
TraesCS2A01G447300
chr2A
696040132
696041747
1615
False
1378.000000
1378
83.042000
714
2276
1
chr2A.!!$F2
1562
2
TraesCS2A01G447300
chr2A
695999081
696000437
1356
False
1026.000000
1026
81.473000
968
2244
1
chr2A.!!$F1
1276
3
TraesCS2A01G447300
chr2A
696286735
696287566
831
False
867.000000
867
85.731000
18
874
1
chr2A.!!$F4
856
4
TraesCS2A01G447300
chr2A
696307007
696309342
2335
False
842.333333
1598
86.686333
970
3035
3
chr2A.!!$F6
2065
5
TraesCS2A01G447300
chr2D
556618663
556621238
2575
False
1546.700000
3035
96.257000
478
3091
2
chr2D.!!$F10
2613
6
TraesCS2A01G447300
chr2D
556364138
556367582
3444
False
1514.333333
3234
92.433000
1
3091
3
chr2D.!!$F8
3090
7
TraesCS2A01G447300
chr2D
556407134
556412302
5168
False
1304.333333
1788
91.488333
129
2990
3
chr2D.!!$F9
2861
8
TraesCS2A01G447300
chr2D
556333284
556335002
1718
False
1169.500000
1775
91.924000
1504
3091
2
chr2D.!!$F6
1587
9
TraesCS2A01G447300
chr2D
556317994
556318907
913
False
889.000000
889
84.551000
573
1509
1
chr2D.!!$F1
936
10
TraesCS2A01G447300
chr2D
556642397
556643190
793
False
880.000000
880
87.053000
999
1787
1
chr2D.!!$F4
788
11
TraesCS2A01G447300
chr2D
556349767
556351843
2076
False
611.500000
1051
78.870500
188
2238
2
chr2D.!!$F7
2050
12
TraesCS2A01G447300
chr2D
556265743
556268526
2783
False
603.000000
1074
81.539500
476
2237
2
chr2D.!!$F5
1761
13
TraesCS2A01G447300
chr2D
556339260
556340226
966
False
592.000000
592
79.381000
1365
2237
1
chr2D.!!$F2
872
14
TraesCS2A01G447300
chr2B
663885200
663888024
2824
False
646.620000
1847
88.367400
139
2871
5
chr2B.!!$F4
2732
15
TraesCS2A01G447300
chr2B
663898756
663900169
1413
False
451.600000
819
82.469500
999
2270
2
chr2B.!!$F5
1271
16
TraesCS2A01G447300
chr2B
663835089
663839261
4172
False
412.133333
1033
81.370667
214
2228
3
chr2B.!!$F3
2014
17
TraesCS2A01G447300
chr2B
663827807
663828899
1092
False
256.500000
272
85.875500
129
969
2
chr2B.!!$F2
840
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.