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
TraesCS4B01G252700
chr4B
100.000
3676
0
0
1
3676
518678176
518674501
0.000000e+00
6789.0
1
TraesCS4B01G252700
chr4B
89.301
2860
283
16
831
3676
629035296
629038146
0.000000e+00
3565.0
2
TraesCS4B01G252700
chr4B
89.126
2860
291
15
831
3676
628997834
629000687
0.000000e+00
3541.0
3
TraesCS4B01G252700
chr7B
97.751
2846
63
1
831
3676
636946493
636943649
0.000000e+00
4900.0
4
TraesCS4B01G252700
chr7B
98.020
1768
34
1
1909
3676
641051055
641049289
0.000000e+00
3070.0
5
TraesCS4B01G252700
chr7B
97.332
1087
28
1
831
1917
641060603
641059518
0.000000e+00
1845.0
6
TraesCS4B01G252700
chr7B
97.561
41
1
0
3
43
588875616
588875576
1.830000e-08
71.3
7
TraesCS4B01G252700
chr7B
100.000
37
0
0
1
37
460329685
460329721
6.590000e-08
69.4
8
TraesCS4B01G252700
chr2A
95.645
2847
112
7
831
3676
3401203
3404038
0.000000e+00
4560.0
9
TraesCS4B01G252700
chr2A
95.258
1961
83
5
1716
3676
768722807
768724757
0.000000e+00
3097.0
10
TraesCS4B01G252700
chr5B
95.327
2846
121
5
831
3676
617246429
617243596
0.000000e+00
4508.0
11
TraesCS4B01G252700
chr3B
95.116
2846
126
8
831
3676
819518361
819515529
0.000000e+00
4473.0
12
TraesCS4B01G252700
chr1B
88.663
2858
302
16
834
3676
61171416
61168566
0.000000e+00
3463.0
13
TraesCS4B01G252700
chr4D
87.640
2856
328
21
830
3676
363205455
363208294
0.000000e+00
3295.0
14
TraesCS4B01G252700
chr4D
94.095
796
46
1
35
830
421556065
421555271
0.000000e+00
1208.0
15
TraesCS4B01G252700
chr6A
95.161
1922
83
5
1755
3676
162459117
162461028
0.000000e+00
3025.0
16
TraesCS4B01G252700
chr6A
97.561
41
0
1
2
42
558988370
558988331
6.590000e-08
69.4
17
TraesCS4B01G252700
chr6A
100.000
35
0
0
2
36
6196552
6196586
8.520000e-07
65.8
18
TraesCS4B01G252700
chr4A
93.400
803
42
7
34
830
42262328
42263125
0.000000e+00
1179.0
19
TraesCS4B01G252700
chr2B
95.833
48
0
2
1
48
49902947
49902902
3.940000e-10
76.8
20
TraesCS4B01G252700
chr2B
95.455
44
2
0
2
45
659694595
659694638
1.830000e-08
71.3
21
TraesCS4B01G252700
chr7A
97.561
41
1
0
2
42
198617054
198617094
1.830000e-08
71.3
22
TraesCS4B01G252700
chr2D
97.561
41
1
0
1
41
566129307
566129267
1.830000e-08
71.3
23
TraesCS4B01G252700
chr3A
95.455
44
0
2
2
44
722282142
722282100
6.590000e-08
69.4
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
TraesCS4B01G252700
chr4B
518674501
518678176
3675
True
6789
6789
100.000
1
3676
1
chr4B.!!$R1
3675
1
TraesCS4B01G252700
chr4B
629035296
629038146
2850
False
3565
3565
89.301
831
3676
1
chr4B.!!$F2
2845
2
TraesCS4B01G252700
chr4B
628997834
629000687
2853
False
3541
3541
89.126
831
3676
1
chr4B.!!$F1
2845
3
TraesCS4B01G252700
chr7B
636943649
636946493
2844
True
4900
4900
97.751
831
3676
1
chr7B.!!$R2
2845
4
TraesCS4B01G252700
chr7B
641049289
641051055
1766
True
3070
3070
98.020
1909
3676
1
chr7B.!!$R3
1767
5
TraesCS4B01G252700
chr7B
641059518
641060603
1085
True
1845
1845
97.332
831
1917
1
chr7B.!!$R4
1086
6
TraesCS4B01G252700
chr2A
3401203
3404038
2835
False
4560
4560
95.645
831
3676
1
chr2A.!!$F1
2845
7
TraesCS4B01G252700
chr2A
768722807
768724757
1950
False
3097
3097
95.258
1716
3676
1
chr2A.!!$F2
1960
8
TraesCS4B01G252700
chr5B
617243596
617246429
2833
True
4508
4508
95.327
831
3676
1
chr5B.!!$R1
2845
9
TraesCS4B01G252700
chr3B
819515529
819518361
2832
True
4473
4473
95.116
831
3676
1
chr3B.!!$R1
2845
10
TraesCS4B01G252700
chr1B
61168566
61171416
2850
True
3463
3463
88.663
834
3676
1
chr1B.!!$R1
2842
11
TraesCS4B01G252700
chr4D
363205455
363208294
2839
False
3295
3295
87.640
830
3676
1
chr4D.!!$F1
2846
12
TraesCS4B01G252700
chr4D
421555271
421556065
794
True
1208
1208
94.095
35
830
1
chr4D.!!$R1
795
13
TraesCS4B01G252700
chr6A
162459117
162461028
1911
False
3025
3025
95.161
1755
3676
1
chr6A.!!$F2
1921
14
TraesCS4B01G252700
chr4A
42262328
42263125
797
False
1179
1179
93.400
34
830
1
chr4A.!!$F1
796
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.