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
TraesCS7A01G249600
chr7A
100.000
4538
0
0
1
4538
232373691
232378228
0.000000e+00
8381.0
1
TraesCS7A01G249600
chr7B
96.326
4028
132
10
516
4538
179924775
179920759
0.000000e+00
6604.0
2
TraesCS7A01G249600
chr7B
94.444
36
2
0
672
707
545045875
545045910
6.340000e-04
56.5
3
TraesCS7A01G249600
chr7D
96.751
3355
82
10
666
4002
219827843
219831188
0.000000e+00
5566.0
4
TraesCS7A01G249600
chr7D
96.512
516
11
5
4024
4538
219831181
219831690
0.000000e+00
846.0
5
TraesCS7A01G249600
chr7D
90.577
520
43
6
3
520
561454482
561453967
0.000000e+00
684.0
6
TraesCS7A01G249600
chr7D
97.059
102
3
0
516
617
219827747
219827848
6.040000e-39
172.0
7
TraesCS7A01G249600
chr5A
89.103
1872
183
12
1792
3652
36373689
36371828
0.000000e+00
2307.0
8
TraesCS7A01G249600
chr5A
87.597
387
42
1
1457
1837
36374069
36373683
1.160000e-120
444.0
9
TraesCS7A01G249600
chr5B
89.800
1598
131
21
1891
3466
45823892
45822305
0.000000e+00
2019.0
10
TraesCS7A01G249600
chr5B
88.550
1214
86
24
2409
3613
45650531
45649362
0.000000e+00
1423.0
11
TraesCS7A01G249600
chr5B
87.265
903
98
9
1456
2356
45651412
45650525
0.000000e+00
1014.0
12
TraesCS7A01G249600
chr5B
89.382
518
46
7
4
512
606750399
606750916
1.060000e-180
643.0
13
TraesCS7A01G249600
chr5B
87.402
381
34
3
1464
1844
45824263
45823897
4.200000e-115
425.0
14
TraesCS7A01G249600
chr3A
94.737
513
24
3
1
512
28563903
28564413
0.000000e+00
795.0
15
TraesCS7A01G249600
chr3A
86.873
518
56
9
3
516
698745228
698744719
1.830000e-158
569.0
16
TraesCS7A01G249600
chr3A
81.778
225
23
11
4308
4514
732483538
732483314
6.040000e-39
172.0
17
TraesCS7A01G249600
chr4D
93.359
527
32
3
3
528
482726133
482726657
0.000000e+00
776.0
18
TraesCS7A01G249600
chr5D
87.829
608
61
4
1456
2061
45601344
45600748
0.000000e+00
701.0
19
TraesCS7A01G249600
chr5D
92.229
489
28
6
2394
2874
45598901
45598415
0.000000e+00
684.0
20
TraesCS7A01G249600
chr5D
89.286
280
25
2
2065
2340
45599371
45599093
3.360000e-91
346.0
21
TraesCS7A01G249600
chr5D
89.000
100
2
1
2908
3007
45598411
45598321
1.030000e-21
115.0
22
TraesCS7A01G249600
chr5D
91.358
81
6
1
958
1038
45601422
45601343
4.800000e-20
110.0
23
TraesCS7A01G249600
chr6B
89.808
520
43
9
3
513
515192862
515193380
0.000000e+00
658.0
24
TraesCS7A01G249600
chr6B
88.952
525
46
11
3
517
702298180
702298702
4.950000e-179
638.0
25
TraesCS7A01G249600
chr6B
100.000
30
0
0
678
707
44923302
44923273
6.340000e-04
56.5
26
TraesCS7A01G249600
chr4B
89.883
514
48
2
3
512
31480208
31479695
0.000000e+00
658.0
27
TraesCS7A01G249600
chr3B
88.213
526
51
8
2
519
743338986
743338464
6.450000e-173
617.0
28
TraesCS7A01G249600
chr3B
87.597
129
15
1
4387
4514
810282997
810282869
1.020000e-31
148.0
29
TraesCS7A01G249600
chr3B
94.000
50
2
1
625
673
708025197
708025148
1.750000e-09
75.0
30
TraesCS7A01G249600
chr3D
81.778
225
23
10
4308
4514
603590324
603590548
6.040000e-39
172.0
31
TraesCS7A01G249600
chr6D
80.531
226
25
11
4308
4514
455720994
455720769
6.080000e-34
156.0
32
TraesCS7A01G249600
chr2B
83.735
166
22
4
4006
4166
93039790
93039625
7.860000e-33
152.0
33
TraesCS7A01G249600
chr6A
79.556
225
28
10
4308
4514
590781026
590781250
1.320000e-30
145.0
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
TraesCS7A01G249600
chr7A
232373691
232378228
4537
False
8381.000000
8381
100.0000
1
4538
1
chr7A.!!$F1
4537
1
TraesCS7A01G249600
chr7B
179920759
179924775
4016
True
6604.000000
6604
96.3260
516
4538
1
chr7B.!!$R1
4022
2
TraesCS7A01G249600
chr7D
219827747
219831690
3943
False
2194.666667
5566
96.7740
516
4538
3
chr7D.!!$F1
4022
3
TraesCS7A01G249600
chr7D
561453967
561454482
515
True
684.000000
684
90.5770
3
520
1
chr7D.!!$R1
517
4
TraesCS7A01G249600
chr5A
36371828
36374069
2241
True
1375.500000
2307
88.3500
1457
3652
2
chr5A.!!$R1
2195
5
TraesCS7A01G249600
chr5B
45822305
45824263
1958
True
1222.000000
2019
88.6010
1464
3466
2
chr5B.!!$R2
2002
6
TraesCS7A01G249600
chr5B
45649362
45651412
2050
True
1218.500000
1423
87.9075
1456
3613
2
chr5B.!!$R1
2157
7
TraesCS7A01G249600
chr5B
606750399
606750916
517
False
643.000000
643
89.3820
4
512
1
chr5B.!!$F1
508
8
TraesCS7A01G249600
chr3A
28563903
28564413
510
False
795.000000
795
94.7370
1
512
1
chr3A.!!$F1
511
9
TraesCS7A01G249600
chr3A
698744719
698745228
509
True
569.000000
569
86.8730
3
516
1
chr3A.!!$R1
513
10
TraesCS7A01G249600
chr4D
482726133
482726657
524
False
776.000000
776
93.3590
3
528
1
chr4D.!!$F1
525
11
TraesCS7A01G249600
chr5D
45598321
45601422
3101
True
391.200000
701
89.9404
958
3007
5
chr5D.!!$R1
2049
12
TraesCS7A01G249600
chr6B
515192862
515193380
518
False
658.000000
658
89.8080
3
513
1
chr6B.!!$F1
510
13
TraesCS7A01G249600
chr6B
702298180
702298702
522
False
638.000000
638
88.9520
3
517
1
chr6B.!!$F2
514
14
TraesCS7A01G249600
chr4B
31479695
31480208
513
True
658.000000
658
89.8830
3
512
1
chr4B.!!$R1
509
15
TraesCS7A01G249600
chr3B
743338464
743338986
522
True
617.000000
617
88.2130
2
519
1
chr3B.!!$R2
517
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.