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
TraesCS2B01G161100
chr2B
100.000
2929
0
0
1
2929
134340627
134343555
0.000000e+00
5409
1
TraesCS2B01G161100
chr4D
95.385
2925
98
18
24
2929
85853476
85850570
0.000000e+00
4619
2
TraesCS2B01G161100
chr6D
96.080
2245
63
12
470
2697
440673101
440675337
0.000000e+00
3635
3
TraesCS2B01G161100
chr6D
92.993
1313
78
11
1624
2929
450189339
450188034
0.000000e+00
1903
4
TraesCS2B01G161100
chr6D
92.559
766
41
8
32
793
137153310
137152557
0.000000e+00
1085
5
TraesCS2B01G161100
chr6D
93.488
430
13
6
1
426
440672679
440673097
2.480000e-175
625
6
TraesCS2B01G161100
chr5D
95.477
2277
63
19
1
2275
27280088
27282326
0.000000e+00
3598
7
TraesCS2B01G161100
chr5D
95.821
1388
44
7
1071
2450
431973345
431974726
0.000000e+00
2230
8
TraesCS2B01G161100
chr5D
92.965
1322
79
11
1615
2929
127940012
127938698
0.000000e+00
1914
9
TraesCS2B01G161100
chr5D
93.809
743
37
6
22
762
431972612
431973347
0.000000e+00
1109
10
TraesCS2B01G161100
chr4A
94.022
1723
72
9
188
1900
658380915
658382616
0.000000e+00
2582
11
TraesCS2B01G161100
chr4A
92.417
211
10
4
2
208
658380799
658381007
2.210000e-76
296
12
TraesCS2B01G161100
chr2D
95.613
1550
49
8
470
2006
606091670
606090127
0.000000e+00
2468
13
TraesCS2B01G161100
chr2D
96.967
1220
30
5
1713
2929
29096343
29095128
0.000000e+00
2041
14
TraesCS2B01G161100
chr2D
94.322
1092
50
7
21
1110
29097426
29096345
0.000000e+00
1663
15
TraesCS2B01G161100
chr7D
93.090
1317
79
9
1615
2925
530740951
530739641
0.000000e+00
1917
16
TraesCS2B01G161100
chr7D
92.646
1319
83
11
1615
2926
340173622
340174933
0.000000e+00
1886
17
TraesCS2B01G161100
chr6A
95.299
1170
43
4
696
1857
163168206
163167041
0.000000e+00
1845
18
TraesCS2B01G161100
chr6A
91.840
625
40
4
25
647
163168820
163168205
0.000000e+00
861
19
TraesCS2B01G161100
chr7B
93.674
1154
43
14
1
1137
228799927
228801067
0.000000e+00
1700
20
TraesCS2B01G161100
chr7B
97.419
930
23
1
1176
2105
228801064
228801992
0.000000e+00
1583
21
TraesCS2B01G161100
chr7A
90.217
828
59
13
811
1626
41464795
41463978
0.000000e+00
1061
22
TraesCS2B01G161100
chr7A
89.806
824
58
14
811
1623
617598489
617599297
0.000000e+00
1033
23
TraesCS2B01G161100
chr2A
89.684
824
59
13
811
1623
756524456
756525264
0.000000e+00
1027
24
TraesCS2B01G161100
chr3D
94.839
465
15
4
784
1239
614089797
614089333
0.000000e+00
717
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
TraesCS2B01G161100
chr2B
134340627
134343555
2928
False
5409.0
5409
100.0000
1
2929
1
chr2B.!!$F1
2928
1
TraesCS2B01G161100
chr4D
85850570
85853476
2906
True
4619.0
4619
95.3850
24
2929
1
chr4D.!!$R1
2905
2
TraesCS2B01G161100
chr6D
440672679
440675337
2658
False
2130.0
3635
94.7840
1
2697
2
chr6D.!!$F1
2696
3
TraesCS2B01G161100
chr6D
450188034
450189339
1305
True
1903.0
1903
92.9930
1624
2929
1
chr6D.!!$R2
1305
4
TraesCS2B01G161100
chr6D
137152557
137153310
753
True
1085.0
1085
92.5590
32
793
1
chr6D.!!$R1
761
5
TraesCS2B01G161100
chr5D
27280088
27282326
2238
False
3598.0
3598
95.4770
1
2275
1
chr5D.!!$F1
2274
6
TraesCS2B01G161100
chr5D
127938698
127940012
1314
True
1914.0
1914
92.9650
1615
2929
1
chr5D.!!$R1
1314
7
TraesCS2B01G161100
chr5D
431972612
431974726
2114
False
1669.5
2230
94.8150
22
2450
2
chr5D.!!$F2
2428
8
TraesCS2B01G161100
chr4A
658380799
658382616
1817
False
1439.0
2582
93.2195
2
1900
2
chr4A.!!$F1
1898
9
TraesCS2B01G161100
chr2D
606090127
606091670
1543
True
2468.0
2468
95.6130
470
2006
1
chr2D.!!$R1
1536
10
TraesCS2B01G161100
chr2D
29095128
29097426
2298
True
1852.0
2041
95.6445
21
2929
2
chr2D.!!$R2
2908
11
TraesCS2B01G161100
chr7D
530739641
530740951
1310
True
1917.0
1917
93.0900
1615
2925
1
chr7D.!!$R1
1310
12
TraesCS2B01G161100
chr7D
340173622
340174933
1311
False
1886.0
1886
92.6460
1615
2926
1
chr7D.!!$F1
1311
13
TraesCS2B01G161100
chr6A
163167041
163168820
1779
True
1353.0
1845
93.5695
25
1857
2
chr6A.!!$R1
1832
14
TraesCS2B01G161100
chr7B
228799927
228801992
2065
False
1641.5
1700
95.5465
1
2105
2
chr7B.!!$F1
2104
15
TraesCS2B01G161100
chr7A
41463978
41464795
817
True
1061.0
1061
90.2170
811
1626
1
chr7A.!!$R1
815
16
TraesCS2B01G161100
chr7A
617598489
617599297
808
False
1033.0
1033
89.8060
811
1623
1
chr7A.!!$F1
812
17
TraesCS2B01G161100
chr2A
756524456
756525264
808
False
1027.0
1027
89.6840
811
1623
1
chr2A.!!$F1
812
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.