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
TraesCS1A01G349300
chr1A
100.000
3769
0
0
1
3769
534274543
534278311
0.000000e+00
6961.0
1
TraesCS1A01G349300
chr1A
76.193
2096
391
77
601
2629
9533173
9531119
0.000000e+00
1007.0
2
TraesCS1A01G349300
chr1A
86.667
240
25
2
3280
3519
534269035
534269267
3.730000e-65
259.0
3
TraesCS1A01G349300
chr1B
95.230
3061
86
25
1
3007
592367966
592364912
0.000000e+00
4789.0
4
TraesCS1A01G349300
chr1B
78.603
1804
327
48
719
2483
9647399
9649182
0.000000e+00
1138.0
5
TraesCS1A01G349300
chr1B
92.259
788
28
7
3008
3769
592364800
592364020
0.000000e+00
1086.0
6
TraesCS1A01G349300
chr1D
95.251
2843
76
19
1
2796
437293728
437290898
0.000000e+00
4447.0
7
TraesCS1A01G349300
chr1D
77.415
2019
365
71
672
2629
7371994
7373982
0.000000e+00
1118.0
8
TraesCS1A01G349300
chr1D
95.455
110
5
0
2819
2928
437290838
437290729
3.870000e-40
176.0
9
TraesCS1A01G349300
chr1D
97.674
43
1
0
3727
3769
437296516
437296474
1.450000e-09
75.0
10
TraesCS1A01G349300
chr5D
73.721
1271
256
58
719
1936
41878416
41877171
3.480000e-115
425.0
11
TraesCS1A01G349300
chr5D
90.123
81
7
1
2954
3033
366647761
366647681
1.850000e-18
104.0
12
TraesCS1A01G349300
chr5D
71.984
257
61
11
1397
1646
375586275
375586527
8.740000e-07
65.8
13
TraesCS1A01G349300
chr2B
80.962
478
70
13
719
1188
785984525
785984061
3.580000e-95
359.0
14
TraesCS1A01G349300
chr2B
78.044
501
90
16
719
1207
775385775
775386267
7.910000e-77
298.0
15
TraesCS1A01G349300
chr2B
80.952
147
12
5
245
391
772593830
772593700
6.660000e-18
102.0
16
TraesCS1A01G349300
chr2D
77.046
501
95
16
719
1207
631983088
631983580
1.730000e-68
270.0
17
TraesCS1A01G349300
chr3D
72.844
545
117
27
1415
1942
514680439
514679909
1.400000e-34
158.0
18
TraesCS1A01G349300
chr3B
72.364
550
115
28
1415
1944
676967355
676966823
5.080000e-29
139.0
19
TraesCS1A01G349300
chr7B
88.696
115
6
6
33
147
534805774
534805881
2.360000e-27
134.0
20
TraesCS1A01G349300
chr4D
92.857
56
4
0
192
247
368914487
368914432
8.680000e-12
82.4
21
TraesCS1A01G349300
chr5B
72.481
258
58
8
1397
1646
448314635
448314887
1.880000e-08
71.3
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
TraesCS1A01G349300
chr1A
534274543
534278311
3768
False
6961.0
6961
100.000000
1
3769
1
chr1A.!!$F2
3768
1
TraesCS1A01G349300
chr1A
9531119
9533173
2054
True
1007.0
1007
76.193000
601
2629
1
chr1A.!!$R1
2028
2
TraesCS1A01G349300
chr1B
592364020
592367966
3946
True
2937.5
4789
93.744500
1
3769
2
chr1B.!!$R1
3768
3
TraesCS1A01G349300
chr1B
9647399
9649182
1783
False
1138.0
1138
78.603000
719
2483
1
chr1B.!!$F1
1764
4
TraesCS1A01G349300
chr1D
437290729
437296516
5787
True
1566.0
4447
96.126667
1
3769
3
chr1D.!!$R1
3768
5
TraesCS1A01G349300
chr1D
7371994
7373982
1988
False
1118.0
1118
77.415000
672
2629
1
chr1D.!!$F1
1957
6
TraesCS1A01G349300
chr5D
41877171
41878416
1245
True
425.0
425
73.721000
719
1936
1
chr5D.!!$R1
1217
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.