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
TraesCS1A01G057800
chr1A
100.000
2690
0
0
1
2690
38358265
38360954
0.000000e+00
4968
1
TraesCS1A01G057800
chr1A
81.783
785
110
25
949
1713
37466614
37467385
6.320000e-176
627
2
TraesCS1A01G057800
chr1B
94.351
1788
73
16
1
1774
58539166
58540939
0.000000e+00
2717
3
TraesCS1A01G057800
chr1B
94.589
924
49
1
1768
2690
58540965
58541888
0.000000e+00
1428
4
TraesCS1A01G057800
chr1B
84.319
778
104
13
967
1737
58752942
58753708
0.000000e+00
745
5
TraesCS1A01G057800
chr1B
81.646
790
116
22
949
1721
57782649
57783426
1.760000e-176
628
6
TraesCS1A01G057800
chr1B
81.360
794
113
22
945
1721
58031466
58032241
4.920000e-172
614
7
TraesCS1A01G057800
chr1D
93.835
1249
50
12
536
1774
38654810
38656041
0.000000e+00
1855
8
TraesCS1A01G057800
chr1D
97.180
922
26
0
1769
2690
38656068
38656989
0.000000e+00
1559
9
TraesCS1A01G057800
chr1D
79.008
1210
210
32
949
2130
38250316
38251509
0.000000e+00
787
10
TraesCS1A01G057800
chr1D
93.333
495
13
5
1
494
38654213
38654688
0.000000e+00
713
11
TraesCS1A01G057800
chr1D
85.064
703
87
13
1041
1737
39651489
39652179
0.000000e+00
701
12
TraesCS1A01G057800
chr1D
81.392
790
118
23
949
1721
38294076
38294853
3.800000e-173
617
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
TraesCS1A01G057800
chr1A
38358265
38360954
2689
False
4968.000000
4968
100.000000
1
2690
1
chr1A.!!$F2
2689
1
TraesCS1A01G057800
chr1A
37466614
37467385
771
False
627.000000
627
81.783000
949
1713
1
chr1A.!!$F1
764
2
TraesCS1A01G057800
chr1B
58539166
58541888
2722
False
2072.500000
2717
94.470000
1
2690
2
chr1B.!!$F4
2689
3
TraesCS1A01G057800
chr1B
58752942
58753708
766
False
745.000000
745
84.319000
967
1737
1
chr1B.!!$F3
770
4
TraesCS1A01G057800
chr1B
57782649
57783426
777
False
628.000000
628
81.646000
949
1721
1
chr1B.!!$F1
772
5
TraesCS1A01G057800
chr1B
58031466
58032241
775
False
614.000000
614
81.360000
945
1721
1
chr1B.!!$F2
776
6
TraesCS1A01G057800
chr1D
38654213
38656989
2776
False
1375.666667
1855
94.782667
1
2690
3
chr1D.!!$F4
2689
7
TraesCS1A01G057800
chr1D
38250316
38251509
1193
False
787.000000
787
79.008000
949
2130
1
chr1D.!!$F1
1181
8
TraesCS1A01G057800
chr1D
39651489
39652179
690
False
701.000000
701
85.064000
1041
1737
1
chr1D.!!$F3
696
9
TraesCS1A01G057800
chr1D
38294076
38294853
777
False
617.000000
617
81.392000
949
1721
1
chr1D.!!$F2
772
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.