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
TraesCS4A01G316100
chr4A
100.000
2880
0
0
1
2880
606338516
606341395
0.000000e+00
5319.0
1
TraesCS4A01G316100
chr4A
76.000
550
70
31
1244
1735
605750936
605750391
8.030000e-56
228.0
2
TraesCS4A01G316100
chr4A
86.408
206
15
4
979
1184
605765450
605765258
2.250000e-51
213.0
3
TraesCS4A01G316100
chr4A
92.969
128
8
1
2748
2875
89954254
89954380
4.900000e-43
185.0
4
TraesCS4A01G316100
chr4A
87.302
63
5
2
378
438
641983627
641983566
5.150000e-08
69.4
5
TraesCS4A01G316100
chr4A
95.238
42
1
1
394
435
405552412
405552452
6.660000e-07
65.8
6
TraesCS4A01G316100
chr3A
97.608
1672
18
13
1210
2880
744098214
744096564
0.000000e+00
2846.0
7
TraesCS4A01G316100
chr3A
90.909
132
5
2
62
186
671091475
671091344
1.370000e-38
171.0
8
TraesCS4A01G316100
chr5D
92.655
708
32
8
501
1197
564787954
564788652
0.000000e+00
1002.0
9
TraesCS4A01G316100
chr5D
91.877
714
39
11
1319
2018
564789293
564790001
0.000000e+00
979.0
10
TraesCS4A01G316100
chr5D
93.598
453
20
4
63
506
564777931
564778383
0.000000e+00
667.0
11
TraesCS4A01G316100
chr5D
81.349
697
85
23
1343
2014
564750898
564750222
2.540000e-145
525.0
12
TraesCS4A01G316100
chr5D
80.505
554
85
19
1395
1934
564748123
564747579
1.240000e-108
403.0
13
TraesCS4A01G316100
chr5D
78.211
615
106
21
1237
1832
483810778
483811383
4.530000e-98
368.0
14
TraesCS4A01G316100
chr5D
89.493
276
20
7
2075
2347
564789992
564790261
9.880000e-90
340.0
15
TraesCS4A01G316100
chr5D
78.284
571
85
19
1395
1934
557283556
557282994
5.950000e-87
331.0
16
TraesCS4A01G316100
chr5D
87.372
293
28
6
911
1197
564749144
564748855
7.690000e-86
327.0
17
TraesCS4A01G316100
chr5D
83.333
318
26
10
894
1197
564752258
564751954
4.730000e-68
268.0
18
TraesCS4A01G316100
chr5D
80.741
270
23
13
931
1197
528280011
528279768
1.760000e-42
183.0
19
TraesCS4A01G316100
chr5D
92.188
128
3
2
63
183
503278045
503278172
1.060000e-39
174.0
20
TraesCS4A01G316100
chr5D
88.679
106
11
1
1212
1317
564751480
564751376
8.380000e-26
128.0
21
TraesCS4A01G316100
chr5D
79.275
193
30
7
2193
2376
557323794
557323603
3.010000e-25
126.0
22
TraesCS4A01G316100
chr5D
79.275
193
30
7
2193
2376
557354644
557354453
3.010000e-25
126.0
23
TraesCS4A01G316100
chr5D
79.275
193
30
7
2193
2376
557375082
557374891
3.010000e-25
126.0
24
TraesCS4A01G316100
chr5D
79.275
193
30
7
2193
2376
564726991
564726800
3.010000e-25
126.0
25
TraesCS4A01G316100
chr5D
92.308
65
4
1
1
64
564777845
564777909
1.100000e-14
91.6
26
TraesCS4A01G316100
chr5B
80.537
447
77
7
1389
1832
595019210
595019649
4.600000e-88
335.0
27
TraesCS4A01G316100
chr5B
81.984
383
56
9
1645
2014
708657461
708657079
2.150000e-81
313.0
28
TraesCS4A01G316100
chr5B
84.229
279
24
8
926
1197
708657809
708657544
1.320000e-63
254.0
29
TraesCS4A01G316100
chr5B
87.895
190
21
2
510
698
270633570
270633758
3.740000e-54
222.0
30
TraesCS4A01G316100
chr5B
81.675
191
24
7
1008
1197
683655323
683655503
6.430000e-32
148.0
31
TraesCS4A01G316100
chr5B
96.000
50
2
0
1267
1316
708611036
708610987
6.610000e-12
82.4
32
TraesCS4A01G316100
chr5B
94.000
50
3
0
1267
1316
708453526
708453477
3.080000e-10
76.8
33
TraesCS4A01G316100
chr5B
94.000
50
3
0
1267
1316
708532949
708532900
3.080000e-10
76.8
34
TraesCS4A01G316100
chr5B
94.000
50
3
0
1267
1316
708570544
708570495
3.080000e-10
76.8
35
TraesCS4A01G316100
chr5B
100.000
32
0
0
306
337
34245266
34245235
3.100000e-05
60.2
36
TraesCS4A01G316100
chr5A
76.708
644
118
23
1210
1832
605249725
605250357
2.140000e-86
329.0
37
TraesCS4A01G316100
chr5A
84.667
300
34
5
901
1197
656216714
656216424
3.630000e-74
289.0
38
TraesCS4A01G316100
chr5A
96.053
152
6
0
186
337
16595222
16595373
6.160000e-62
248.0
39
TraesCS4A01G316100
chr5A
94.872
39
2
0
2496
2534
445200108
445200070
8.620000e-06
62.1
40
TraesCS4A01G316100
chr7A
77.027
592
119
12
1256
1838
91497366
91497949
9.950000e-85
324.0
41
TraesCS4A01G316100
chr7A
87.958
191
21
2
508
697
30660910
30660721
1.040000e-54
224.0
42
TraesCS4A01G316100
chr1D
91.053
190
16
1
508
696
457175411
457175600
3.680000e-64
255.0
43
TraesCS4A01G316100
chr1D
90.476
189
14
3
513
700
28560008
28560193
2.220000e-61
246.0
44
TraesCS4A01G316100
chr1D
86.154
130
14
2
2752
2878
481407315
481407187
1.390000e-28
137.0
45
TraesCS4A01G316100
chr6B
96.644
149
5
0
189
337
394516587
394516439
6.160000e-62
248.0
46
TraesCS4A01G316100
chr6B
87.786
131
15
1
2748
2878
528290249
528290378
4.970000e-33
152.0
47
TraesCS4A01G316100
chr6B
81.818
66
12
0
2497
2562
469832167
469832102
4.010000e-04
56.5
48
TraesCS4A01G316100
chr2D
94.079
152
9
0
186
337
391003874
391004025
6.210000e-57
231.0
49
TraesCS4A01G316100
chr2D
90.341
176
15
2
530
704
647674776
647674602
2.230000e-56
230.0
50
TraesCS4A01G316100
chr2D
78.818
203
30
4
509
698
536924678
536924476
1.080000e-24
124.0
51
TraesCS4A01G316100
chr1B
92.857
154
11
0
184
337
583604398
583604551
1.040000e-54
224.0
52
TraesCS4A01G316100
chr1B
90.909
44
4
0
2493
2536
152317639
152317682
3.100000e-05
60.2
53
TraesCS4A01G316100
chr1B
90.909
44
4
0
2493
2536
170294825
170294868
3.100000e-05
60.2
54
TraesCS4A01G316100
chr4D
89.143
175
17
2
530
703
258893484
258893657
1.740000e-52
217.0
55
TraesCS4A01G316100
chr4D
90.179
112
4
2
82
186
19928737
19928626
3.870000e-29
139.0
56
TraesCS4A01G316100
chr3D
86.911
191
23
2
510
698
43776890
43776700
2.250000e-51
213.0
57
TraesCS4A01G316100
chr3D
88.571
175
18
2
530
702
317203565
317203391
8.080000e-51
211.0
58
TraesCS4A01G316100
chr3D
83.916
143
21
2
1056
1197
609232339
609232480
5.010000e-28
135.0
59
TraesCS4A01G316100
chr3D
97.222
36
0
1
504
538
317203604
317203569
3.100000e-05
60.2
60
TraesCS4A01G316100
chr1A
90.789
152
14
0
186
337
115873604
115873755
1.350000e-48
204.0
61
TraesCS4A01G316100
chr1A
95.238
42
2
0
394
435
104385886
104385845
1.850000e-07
67.6
62
TraesCS4A01G316100
chrUn
92.188
128
3
2
63
183
346596313
346596440
1.060000e-39
174.0
63
TraesCS4A01G316100
chrUn
91.406
128
4
2
63
183
93409450
93409577
4.940000e-38
169.0
64
TraesCS4A01G316100
chrUn
91.406
128
4
2
63
183
216518421
216518548
4.940000e-38
169.0
65
TraesCS4A01G316100
chrUn
91.406
128
4
2
63
183
216521809
216521936
4.940000e-38
169.0
66
TraesCS4A01G316100
chrUn
90.840
131
5
2
63
186
422745236
422745106
4.940000e-38
169.0
67
TraesCS4A01G316100
chrUn
79.275
193
30
7
2193
2376
376645900
376645709
3.010000e-25
126.0
68
TraesCS4A01G316100
chrUn
79.275
193
30
7
2193
2376
404505858
404505667
3.010000e-25
126.0
69
TraesCS4A01G316100
chrUn
94.545
55
3
0
189
243
417578679
417578625
5.110000e-13
86.1
70
TraesCS4A01G316100
chr6D
90.840
131
5
2
63
186
168251719
168251589
4.940000e-38
169.0
71
TraesCS4A01G316100
chr6D
95.960
99
4
0
62
160
263916310
263916212
8.260000e-36
161.0
72
TraesCS4A01G316100
chr2A
81.951
205
25
3
506
698
749834235
749834439
2.300000e-36
163.0
73
TraesCS4A01G316100
chr2A
88.281
128
14
1
2751
2878
605336137
605336011
4.970000e-33
152.0
74
TraesCS4A01G316100
chr2A
97.059
34
1
0
2491
2524
778141018
778141051
1.110000e-04
58.4
75
TraesCS4A01G316100
chr4B
88.722
133
13
2
2746
2877
632331106
632331237
8.260000e-36
161.0
76
TraesCS4A01G316100
chr4B
86.466
133
17
1
2746
2877
632393713
632393845
8.320000e-31
145.0
77
TraesCS4A01G316100
chr4B
83.969
131
20
1
2748
2878
43183205
43183334
1.080000e-24
124.0
78
TraesCS4A01G316100
chr4B
93.878
49
2
1
398
446
611405370
611405417
3.980000e-09
73.1
79
TraesCS4A01G316100
chr3B
82.051
195
27
6
1009
1196
819948241
819948434
2.970000e-35
159.0
80
TraesCS4A01G316100
chr3B
85.827
127
17
1
2752
2878
573644005
573644130
1.800000e-27
134.0
81
TraesCS4A01G316100
chr3B
90.909
44
4
0
2493
2536
171510073
171510116
3.100000e-05
60.2
82
TraesCS4A01G316100
chr7D
94.828
58
3
0
186
243
626728076
626728133
1.100000e-14
91.6
83
TraesCS4A01G316100
chr7D
94.545
55
3
0
189
243
382069763
382069709
5.110000e-13
86.1
84
TraesCS4A01G316100
chr7D
92.683
41
3
0
2497
2537
203884881
203884921
3.100000e-05
60.2
85
TraesCS4A01G316100
chr6A
84.932
73
10
1
2491
2562
6024638
6024710
3.980000e-09
73.1
86
TraesCS4A01G316100
chr6A
100.000
32
0
0
306
337
289136212
289136181
3.100000e-05
60.2
87
TraesCS4A01G316100
chr6A
100.000
32
0
0
306
337
608866863
608866832
3.100000e-05
60.2
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
TraesCS4A01G316100
chr4A
606338516
606341395
2879
False
5319.000000
5319
100.000000
1
2880
1
chr4A.!!$F3
2879
1
TraesCS4A01G316100
chr4A
605750391
605750936
545
True
228.000000
228
76.000000
1244
1735
1
chr4A.!!$R1
491
2
TraesCS4A01G316100
chr3A
744096564
744098214
1650
True
2846.000000
2846
97.608000
1210
2880
1
chr3A.!!$R2
1670
3
TraesCS4A01G316100
chr5D
564787954
564790261
2307
False
773.666667
1002
91.341667
501
2347
3
chr5D.!!$F4
1846
4
TraesCS4A01G316100
chr5D
564777845
564778383
538
False
379.300000
667
92.953000
1
506
2
chr5D.!!$F3
505
5
TraesCS4A01G316100
chr5D
483810778
483811383
605
False
368.000000
368
78.211000
1237
1832
1
chr5D.!!$F1
595
6
TraesCS4A01G316100
chr5D
557282994
557283556
562
True
331.000000
331
78.284000
1395
1934
1
chr5D.!!$R2
539
7
TraesCS4A01G316100
chr5D
564747579
564752258
4679
True
330.200000
525
84.247600
894
2014
5
chr5D.!!$R7
1120
8
TraesCS4A01G316100
chr5B
708657079
708657809
730
True
283.500000
313
83.106500
926
2014
2
chr5B.!!$R6
1088
9
TraesCS4A01G316100
chr5A
605249725
605250357
632
False
329.000000
329
76.708000
1210
1832
1
chr5A.!!$F2
622
10
TraesCS4A01G316100
chr7A
91497366
91497949
583
False
324.000000
324
77.027000
1256
1838
1
chr7A.!!$F1
582
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.