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
TraesCS2A01G502900
chr2A
100.000
4086
0
0
1
4086
732544301
732548386
0.000000e+00
7546.0
1
TraesCS2A01G502900
chr2A
98.766
2107
22
3
1
2106
732506636
732508739
0.000000e+00
3744.0
2
TraesCS2A01G502900
chr2A
98.790
1074
10
1
1033
2106
732519371
732520441
0.000000e+00
1908.0
3
TraesCS2A01G502900
chr2A
79.899
995
165
25
2100
3079
729568253
729569227
0.000000e+00
697.0
4
TraesCS2A01G502900
chr2A
90.566
53
3
2
768
818
761182258
761182206
7.330000e-08
69.4
5
TraesCS2A01G502900
chr2A
97.222
36
1
0
3023
3058
766003288
766003253
1.230000e-05
62.1
6
TraesCS2A01G502900
chr2A
94.737
38
2
0
3023
3060
138517679
138517642
4.410000e-05
60.2
7
TraesCS2A01G502900
chr2D
97.079
2499
45
9
981
3465
598610718
598613202
0.000000e+00
4185.0
8
TraesCS2A01G502900
chr2D
95.140
926
19
10
1
917
598609189
598610097
0.000000e+00
1437.0
9
TraesCS2A01G502900
chr2D
97.826
460
10
0
3627
4086
598613384
598613843
0.000000e+00
795.0
10
TraesCS2A01G502900
chr2D
76.737
1281
242
44
1828
3079
595508346
595509599
0.000000e+00
664.0
11
TraesCS2A01G502900
chr2D
97.973
148
2
1
3482
3629
598613189
598613335
5.240000e-64
255.0
12
TraesCS2A01G502900
chr2D
95.833
48
1
1
902
949
598610611
598610657
4.380000e-10
76.8
13
TraesCS2A01G502900
chr2D
84.746
59
5
4
954
1011
598610650
598610705
5.710000e-04
56.5
14
TraesCS2A01G502900
chr2B
95.685
2132
62
10
1349
3465
726463639
726465755
0.000000e+00
3400.0
15
TraesCS2A01G502900
chr2B
93.991
466
24
3
3624
4086
726465919
726466383
0.000000e+00
702.0
16
TraesCS2A01G502900
chr2B
78.932
1049
180
31
2054
3079
723429673
723430703
0.000000e+00
675.0
17
TraesCS2A01G502900
chr2B
85.948
612
53
24
1
598
726462242
726462834
1.250000e-174
623.0
18
TraesCS2A01G502900
chr2B
96.633
297
10
0
981
1277
726463337
726463633
1.020000e-135
494.0
19
TraesCS2A01G502900
chr2B
90.233
215
16
4
409
619
726462687
726462900
4.020000e-70
276.0
20
TraesCS2A01G502900
chr2B
97.516
161
4
0
815
975
726463124
726463284
4.020000e-70
276.0
21
TraesCS2A01G502900
chr2B
84.524
252
23
14
485
727
726462805
726463049
6.830000e-58
235.0
22
TraesCS2A01G502900
chr2B
90.345
145
6
2
3482
3626
726465742
726465878
2.510000e-42
183.0
23
TraesCS2A01G502900
chr2B
97.778
45
1
0
766
810
726463054
726463098
1.220000e-10
78.7
24
TraesCS2A01G502900
chr7A
88.400
500
35
11
3600
4086
236860488
236859999
7.610000e-162
580.0
25
TraesCS2A01G502900
chr1A
74.291
1023
213
43
2102
3094
497887781
497886779
1.780000e-103
387.0
26
TraesCS2A01G502900
chr1A
83.962
106
11
5
644
747
72674902
72674801
3.360000e-16
97.1
27
TraesCS2A01G502900
chr6B
84.804
204
16
6
3770
3959
54416604
54416806
1.500000e-44
191.0
28
TraesCS2A01G502900
chr6B
88.889
90
9
1
3997
4086
515433500
515433588
4.320000e-20
110.0
29
TraesCS2A01G502900
chr6B
81.132
106
13
7
518
618
250593649
250593546
1.220000e-10
78.7
30
TraesCS2A01G502900
chr3B
80.435
138
23
3
489
624
750461345
750461210
7.230000e-18
102.0
31
TraesCS2A01G502900
chr7B
80.435
138
19
7
487
618
733542974
733543109
9.350000e-17
99.0
32
TraesCS2A01G502900
chr7B
74.632
272
44
16
488
739
7714978
7715244
3.360000e-16
97.1
33
TraesCS2A01G502900
chr7B
77.528
178
27
12
426
598
713436296
713436127
1.210000e-15
95.3
34
TraesCS2A01G502900
chr4D
75.319
235
42
14
394
618
113935270
113935042
9.350000e-17
99.0
35
TraesCS2A01G502900
chr5A
76.279
215
28
11
623
816
452280591
452280379
4.350000e-15
93.5
36
TraesCS2A01G502900
chr1B
81.651
109
14
3
2974
3079
540338366
540338261
7.280000e-13
86.1
37
TraesCS2A01G502900
chr5D
86.301
73
7
3
671
741
75723993
75724064
4.380000e-10
76.8
38
TraesCS2A01G502900
chr5B
94.737
38
1
1
671
707
84480812
84480849
1.590000e-04
58.4
39
TraesCS2A01G502900
chrUn
100.000
28
0
0
3501
3528
45828162
45828189
7.000000e-03
52.8
40
TraesCS2A01G502900
chrUn
100.000
28
0
0
3501
3528
323578085
323578058
7.000000e-03
52.8
41
TraesCS2A01G502900
chr3D
100.000
28
0
0
3501
3528
599436732
599436759
7.000000e-03
52.8
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
TraesCS2A01G502900
chr2A
732544301
732548386
4085
False
7546.000000
7546
100.000000
1
4086
1
chr2A.!!$F4
4085
1
TraesCS2A01G502900
chr2A
732506636
732508739
2103
False
3744.000000
3744
98.766000
1
2106
1
chr2A.!!$F2
2105
2
TraesCS2A01G502900
chr2A
732519371
732520441
1070
False
1908.000000
1908
98.790000
1033
2106
1
chr2A.!!$F3
1073
3
TraesCS2A01G502900
chr2A
729568253
729569227
974
False
697.000000
697
79.899000
2100
3079
1
chr2A.!!$F1
979
4
TraesCS2A01G502900
chr2D
598609189
598613843
4654
False
1134.216667
4185
94.766167
1
4086
6
chr2D.!!$F2
4085
5
TraesCS2A01G502900
chr2D
595508346
595509599
1253
False
664.000000
664
76.737000
1828
3079
1
chr2D.!!$F1
1251
6
TraesCS2A01G502900
chr2B
726462242
726466383
4141
False
696.411111
3400
92.517000
1
4086
9
chr2B.!!$F2
4085
7
TraesCS2A01G502900
chr2B
723429673
723430703
1030
False
675.000000
675
78.932000
2054
3079
1
chr2B.!!$F1
1025
8
TraesCS2A01G502900
chr1A
497886779
497887781
1002
True
387.000000
387
74.291000
2102
3094
1
chr1A.!!$R2
992
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.