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
TraesCS3D01G220300
chr3D
100.000
2784
0
0
1
2784
300682632
300679849
0.000000e+00
5142.0
1
TraesCS3D01G220300
chr3D
90.788
749
44
7
1
739
531450005
531450738
0.000000e+00
977.0
2
TraesCS3D01G220300
chr3D
96.507
544
13
2
1988
2525
23089051
23089594
0.000000e+00
894.0
3
TraesCS3D01G220300
chr3D
86.739
739
64
19
1039
1773
300582749
300583457
0.000000e+00
791.0
4
TraesCS3D01G220300
chr3D
90.769
455
41
1
288
741
13266764
13267218
8.530000e-170
606.0
5
TraesCS3D01G220300
chr5A
96.750
800
23
2
1988
2784
700670943
700671742
0.000000e+00
1330.0
6
TraesCS3D01G220300
chr5A
94.022
552
31
1
1988
2537
510491606
510491055
0.000000e+00
835.0
7
TraesCS3D01G220300
chr2A
95.500
800
35
1
1986
2784
29273411
29274210
0.000000e+00
1277.0
8
TraesCS3D01G220300
chr2A
90.727
798
66
2
1988
2784
166634835
166635625
0.000000e+00
1057.0
9
TraesCS3D01G220300
chr3A
86.124
1254
86
41
772
1991
434786688
434787887
0.000000e+00
1271.0
10
TraesCS3D01G220300
chr3A
87.615
759
78
9
1
743
709502471
709503229
0.000000e+00
867.0
11
TraesCS3D01G220300
chr3A
86.939
758
84
8
1
743
709536867
709537624
0.000000e+00
837.0
12
TraesCS3D01G220300
chr3A
89.167
600
56
4
1048
1647
434822465
434821875
0.000000e+00
739.0
13
TraesCS3D01G220300
chr3A
86.875
160
9
3
772
930
434822721
434822573
4.770000e-38
169.0
14
TraesCS3D01G220300
chr4A
96.042
758
25
5
1988
2740
65715137
65714380
0.000000e+00
1229.0
15
TraesCS3D01G220300
chr4A
92.593
108
8
0
2674
2781
563213503
563213610
3.710000e-34
156.0
16
TraesCS3D01G220300
chr1D
94.587
739
37
3
1
739
307838465
307837730
0.000000e+00
1140.0
17
TraesCS3D01G220300
chr1D
90.885
746
58
5
1
739
426189918
426190660
0.000000e+00
992.0
18
TraesCS3D01G220300
chr3B
87.055
1012
54
35
772
1772
420419149
420420094
0.000000e+00
1072.0
19
TraesCS3D01G220300
chr3B
86.567
737
67
19
1039
1773
420776882
420776176
0.000000e+00
784.0
20
TraesCS3D01G220300
chr3B
90.832
469
42
1
276
743
119310952
119310484
6.550000e-176
627.0
21
TraesCS3D01G220300
chr6A
92.818
738
32
2
1988
2723
546926608
546925890
0.000000e+00
1050.0
22
TraesCS3D01G220300
chr6A
93.421
76
4
1
2710
2784
546925065
546924990
8.150000e-21
111.0
23
TraesCS3D01G220300
chr7D
92.297
740
51
6
1
739
259362761
259362027
0.000000e+00
1046.0
24
TraesCS3D01G220300
chr7D
87.129
101
12
1
1812
1912
450758907
450758808
2.270000e-21
113.0
25
TraesCS3D01G220300
chr4D
91.644
730
54
4
19
742
508246417
508247145
0.000000e+00
1003.0
26
TraesCS3D01G220300
chr4D
96.674
451
13
2
1988
2437
465183409
465182960
0.000000e+00
749.0
27
TraesCS3D01G220300
chr4D
91.837
441
30
2
1
435
505153543
505153103
6.590000e-171
610.0
28
TraesCS3D01G220300
chr4D
92.593
108
8
0
2674
2781
8622413
8622520
3.710000e-34
156.0
29
TraesCS3D01G220300
chr4D
81.905
105
13
6
1812
1913
24864673
24864774
1.780000e-12
84.2
30
TraesCS3D01G220300
chr5B
89.986
739
73
1
1
739
683086114
683085377
0.000000e+00
953.0
31
TraesCS3D01G220300
chr5B
87.755
98
12
0
1816
1913
352488715
352488618
6.300000e-22
115.0
32
TraesCS3D01G220300
chr4B
86.156
679
85
8
1
674
384286735
384287409
0.000000e+00
725.0
33
TraesCS3D01G220300
chr2B
91.209
455
36
3
287
739
138438679
138438227
1.420000e-172
616.0
34
TraesCS3D01G220300
chr2B
86.940
536
47
13
1988
2500
214319619
214320154
5.170000e-162
580.0
35
TraesCS3D01G220300
chr2B
86.611
239
29
2
2457
2692
612094906
612095144
7.650000e-66
261.0
36
TraesCS3D01G220300
chr2B
83.168
101
16
1
1812
1912
90702668
90702767
1.060000e-14
91.6
37
TraesCS3D01G220300
chr5D
92.481
399
26
2
1988
2384
519644328
519644724
4.020000e-158
568.0
38
TraesCS3D01G220300
chr6D
93.215
339
22
1
1
339
450536542
450536879
5.350000e-137
497.0
39
TraesCS3D01G220300
chrUn
92.593
108
8
0
2674
2781
269813601
269813708
3.710000e-34
156.0
40
TraesCS3D01G220300
chrUn
86.139
101
13
1
1812
1912
27746664
27746565
1.050000e-19
108.0
41
TraesCS3D01G220300
chr6B
85.567
97
14
0
1814
1910
299778652
299778556
4.910000e-18
102.0
42
TraesCS3D01G220300
chr2D
83.168
101
11
6
1815
1912
326251209
326251112
1.370000e-13
87.9
43
TraesCS3D01G220300
chr7B
82.653
98
15
1
1815
1912
635667774
635667679
4.940000e-13
86.1
44
TraesCS3D01G220300
chr7B
81.905
105
13
6
1812
1913
153667064
153667165
1.780000e-12
84.2
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
TraesCS3D01G220300
chr3D
300679849
300682632
2783
True
5142.0
5142
100.0000
1
2784
1
chr3D.!!$R1
2783
1
TraesCS3D01G220300
chr3D
531450005
531450738
733
False
977.0
977
90.7880
1
739
1
chr3D.!!$F4
738
2
TraesCS3D01G220300
chr3D
23089051
23089594
543
False
894.0
894
96.5070
1988
2525
1
chr3D.!!$F2
537
3
TraesCS3D01G220300
chr3D
300582749
300583457
708
False
791.0
791
86.7390
1039
1773
1
chr3D.!!$F3
734
4
TraesCS3D01G220300
chr5A
700670943
700671742
799
False
1330.0
1330
96.7500
1988
2784
1
chr5A.!!$F1
796
5
TraesCS3D01G220300
chr5A
510491055
510491606
551
True
835.0
835
94.0220
1988
2537
1
chr5A.!!$R1
549
6
TraesCS3D01G220300
chr2A
29273411
29274210
799
False
1277.0
1277
95.5000
1986
2784
1
chr2A.!!$F1
798
7
TraesCS3D01G220300
chr2A
166634835
166635625
790
False
1057.0
1057
90.7270
1988
2784
1
chr2A.!!$F2
796
8
TraesCS3D01G220300
chr3A
434786688
434787887
1199
False
1271.0
1271
86.1240
772
1991
1
chr3A.!!$F1
1219
9
TraesCS3D01G220300
chr3A
709502471
709503229
758
False
867.0
867
87.6150
1
743
1
chr3A.!!$F2
742
10
TraesCS3D01G220300
chr3A
709536867
709537624
757
False
837.0
837
86.9390
1
743
1
chr3A.!!$F3
742
11
TraesCS3D01G220300
chr3A
434821875
434822721
846
True
454.0
739
88.0210
772
1647
2
chr3A.!!$R1
875
12
TraesCS3D01G220300
chr4A
65714380
65715137
757
True
1229.0
1229
96.0420
1988
2740
1
chr4A.!!$R1
752
13
TraesCS3D01G220300
chr1D
307837730
307838465
735
True
1140.0
1140
94.5870
1
739
1
chr1D.!!$R1
738
14
TraesCS3D01G220300
chr1D
426189918
426190660
742
False
992.0
992
90.8850
1
739
1
chr1D.!!$F1
738
15
TraesCS3D01G220300
chr3B
420419149
420420094
945
False
1072.0
1072
87.0550
772
1772
1
chr3B.!!$F1
1000
16
TraesCS3D01G220300
chr3B
420776176
420776882
706
True
784.0
784
86.5670
1039
1773
1
chr3B.!!$R2
734
17
TraesCS3D01G220300
chr6A
546924990
546926608
1618
True
580.5
1050
93.1195
1988
2784
2
chr6A.!!$R1
796
18
TraesCS3D01G220300
chr7D
259362027
259362761
734
True
1046.0
1046
92.2970
1
739
1
chr7D.!!$R1
738
19
TraesCS3D01G220300
chr4D
508246417
508247145
728
False
1003.0
1003
91.6440
19
742
1
chr4D.!!$F3
723
20
TraesCS3D01G220300
chr5B
683085377
683086114
737
True
953.0
953
89.9860
1
739
1
chr5B.!!$R2
738
21
TraesCS3D01G220300
chr4B
384286735
384287409
674
False
725.0
725
86.1560
1
674
1
chr4B.!!$F1
673
22
TraesCS3D01G220300
chr2B
214319619
214320154
535
False
580.0
580
86.9400
1988
2500
1
chr2B.!!$F2
512
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.