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
TraesCS3B01G232700
chr3B
100.000
3452
0
0
1
3452
358582928
358586379
0.000000e+00
6375
1
TraesCS3B01G232700
chr3B
75.886
1016
174
51
747
1715
151818076
151817085
1.460000e-123
453
2
TraesCS3B01G232700
chr3B
73.725
1020
203
45
748
1715
151825355
151824349
4.270000e-89
339
3
TraesCS3B01G232700
chr4B
92.177
3464
242
23
1
3452
242358658
242362104
0.000000e+00
4868
4
TraesCS3B01G232700
chr4B
87.626
695
69
13
5
694
250846707
250846025
0.000000e+00
791
5
TraesCS3B01G232700
chr7B
91.027
3466
261
33
1
3452
266110661
266114090
0.000000e+00
4632
6
TraesCS3B01G232700
chr7B
92.133
2644
186
17
819
3452
152831848
152834479
0.000000e+00
3711
7
TraesCS3B01G232700
chr7B
91.583
2495
178
18
960
3446
173690141
173692611
0.000000e+00
3415
8
TraesCS3B01G232700
chr7B
92.636
774
49
5
6
777
152831080
152831847
0.000000e+00
1107
9
TraesCS3B01G232700
chr7B
91.865
713
51
6
1
711
173627015
173627722
0.000000e+00
989
10
TraesCS3B01G232700
chr7B
91.386
267
18
4
719
981
173689867
173690132
9.110000e-96
361
11
TraesCS3B01G232700
chr5B
91.067
2250
161
24
1213
3445
140684674
140686900
0.000000e+00
3005
12
TraesCS3B01G232700
chr5B
86.620
2160
251
22
1305
3450
69988188
69986053
0.000000e+00
2353
13
TraesCS3B01G232700
chr5B
78.588
2634
421
100
747
3264
400197949
400200555
0.000000e+00
1607
14
TraesCS3B01G232700
chr5B
92.816
696
43
6
1
693
140675179
140675870
0.000000e+00
1002
15
TraesCS3B01G232700
chr1A
86.121
2702
312
33
744
3401
174034841
174037523
0.000000e+00
2854
16
TraesCS3B01G232700
chr1A
85.035
2693
318
43
744
3389
174055572
174058226
0.000000e+00
2662
17
TraesCS3B01G232700
chr1A
85.847
2268
264
30
744
2971
223778710
223780960
0.000000e+00
2357
18
TraesCS3B01G232700
chr7D
86.121
2702
308
39
744
3401
289510101
289507423
0.000000e+00
2850
19
TraesCS3B01G232700
chr7D
85.300
932
91
23
2543
3447
287523874
287524786
0.000000e+00
920
20
TraesCS3B01G232700
chr7A
85.641
2716
325
35
736
3404
386956071
386953374
0.000000e+00
2795
21
TraesCS3B01G232700
chr1B
78.514
2625
432
89
744
3265
252930912
252933507
0.000000e+00
1602
22
TraesCS3B01G232700
chr2B
91.615
644
46
5
54
693
604436820
604436181
0.000000e+00
883
23
TraesCS3B01G232700
chr2B
89.755
693
54
13
7
693
346392936
346392255
0.000000e+00
870
24
TraesCS3B01G232700
chr6B
86.895
702
72
15
3
694
287343256
287342565
0.000000e+00
769
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
TraesCS3B01G232700
chr3B
358582928
358586379
3451
False
6375
6375
100.0000
1
3452
1
chr3B.!!$F1
3451
1
TraesCS3B01G232700
chr3B
151817085
151818076
991
True
453
453
75.8860
747
1715
1
chr3B.!!$R1
968
2
TraesCS3B01G232700
chr3B
151824349
151825355
1006
True
339
339
73.7250
748
1715
1
chr3B.!!$R2
967
3
TraesCS3B01G232700
chr4B
242358658
242362104
3446
False
4868
4868
92.1770
1
3452
1
chr4B.!!$F1
3451
4
TraesCS3B01G232700
chr4B
250846025
250846707
682
True
791
791
87.6260
5
694
1
chr4B.!!$R1
689
5
TraesCS3B01G232700
chr7B
266110661
266114090
3429
False
4632
4632
91.0270
1
3452
1
chr7B.!!$F2
3451
6
TraesCS3B01G232700
chr7B
152831080
152834479
3399
False
2409
3711
92.3845
6
3452
2
chr7B.!!$F3
3446
7
TraesCS3B01G232700
chr7B
173689867
173692611
2744
False
1888
3415
91.4845
719
3446
2
chr7B.!!$F4
2727
8
TraesCS3B01G232700
chr7B
173627015
173627722
707
False
989
989
91.8650
1
711
1
chr7B.!!$F1
710
9
TraesCS3B01G232700
chr5B
140684674
140686900
2226
False
3005
3005
91.0670
1213
3445
1
chr5B.!!$F2
2232
10
TraesCS3B01G232700
chr5B
69986053
69988188
2135
True
2353
2353
86.6200
1305
3450
1
chr5B.!!$R1
2145
11
TraesCS3B01G232700
chr5B
400197949
400200555
2606
False
1607
1607
78.5880
747
3264
1
chr5B.!!$F3
2517
12
TraesCS3B01G232700
chr5B
140675179
140675870
691
False
1002
1002
92.8160
1
693
1
chr5B.!!$F1
692
13
TraesCS3B01G232700
chr1A
174034841
174037523
2682
False
2854
2854
86.1210
744
3401
1
chr1A.!!$F1
2657
14
TraesCS3B01G232700
chr1A
174055572
174058226
2654
False
2662
2662
85.0350
744
3389
1
chr1A.!!$F2
2645
15
TraesCS3B01G232700
chr1A
223778710
223780960
2250
False
2357
2357
85.8470
744
2971
1
chr1A.!!$F3
2227
16
TraesCS3B01G232700
chr7D
289507423
289510101
2678
True
2850
2850
86.1210
744
3401
1
chr7D.!!$R1
2657
17
TraesCS3B01G232700
chr7D
287523874
287524786
912
False
920
920
85.3000
2543
3447
1
chr7D.!!$F1
904
18
TraesCS3B01G232700
chr7A
386953374
386956071
2697
True
2795
2795
85.6410
736
3404
1
chr7A.!!$R1
2668
19
TraesCS3B01G232700
chr1B
252930912
252933507
2595
False
1602
1602
78.5140
744
3265
1
chr1B.!!$F1
2521
20
TraesCS3B01G232700
chr2B
604436181
604436820
639
True
883
883
91.6150
54
693
1
chr2B.!!$R2
639
21
TraesCS3B01G232700
chr2B
346392255
346392936
681
True
870
870
89.7550
7
693
1
chr2B.!!$R1
686
22
TraesCS3B01G232700
chr6B
287342565
287343256
691
True
769
769
86.8950
3
694
1
chr6B.!!$R1
691
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.