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
TraesCS1A01G296800
chr1A
100.000
2533
0
0
1
2533
492001377
491998845
0.000000e+00
4678.0
1
TraesCS1A01G296800
chr1A
93.237
1109
73
2
1426
2533
575003036
575004143
0.000000e+00
1631.0
2
TraesCS1A01G296800
chr1A
89.379
612
54
3
1426
2035
575076928
575077530
0.000000e+00
760.0
3
TraesCS1A01G296800
chr1A
88.871
611
58
2
1426
2035
575036359
575036960
0.000000e+00
743.0
4
TraesCS1A01G296800
chr6B
89.874
2548
227
13
1
2533
184805786
184808317
0.000000e+00
3247.0
5
TraesCS1A01G296800
chr4A
89.385
2195
221
6
350
2533
640155809
640153616
0.000000e+00
2752.0
6
TraesCS1A01G296800
chr4A
87.458
1188
124
15
1353
2532
703403632
703402462
0.000000e+00
1345.0
7
TraesCS1A01G296800
chr4A
74.796
1349
276
50
3
1334
708315836
708317137
1.320000e-152
549.0
8
TraesCS1A01G296800
chr4A
89.062
320
29
1
1
320
640174222
640174535
2.360000e-105
392.0
9
TraesCS1A01G296800
chr4A
73.261
733
147
21
812
1525
16260171
16259469
3.280000e-54
222.0
10
TraesCS1A01G296800
chr3B
91.525
1357
101
7
1187
2533
513943182
513944534
0.000000e+00
1857.0
11
TraesCS1A01G296800
chr3B
91.965
1257
87
6
1287
2533
661544680
661543428
0.000000e+00
1749.0
12
TraesCS1A01G296800
chr1B
96.105
1027
37
3
1508
2533
266115589
266114565
0.000000e+00
1672.0
13
TraesCS1A01G296800
chr1B
94.872
39
2
0
785
823
667720111
667720149
7.570000e-06
62.1
14
TraesCS1A01G296800
chr4D
88.255
1175
124
12
1369
2533
118590139
118588969
0.000000e+00
1393.0
15
TraesCS1A01G296800
chr4D
86.545
550
59
6
840
1377
118592252
118591706
2.170000e-165
592.0
16
TraesCS1A01G296800
chr3A
94.595
888
46
2
1645
2531
120813948
120814834
0.000000e+00
1373.0
17
TraesCS1A01G296800
chr3A
80.876
251
42
4
1
251
82459029
82459273
2.570000e-45
193.0
18
TraesCS1A01G296800
chr7D
94.928
828
39
3
1707
2533
37927818
37926993
0.000000e+00
1293.0
19
TraesCS1A01G296800
chr6D
87.833
526
34
14
614
1135
455718412
455718911
7.800000e-165
590.0
20
TraesCS1A01G296800
chr4B
74.500
1349
282
48
2
1334
614060623
614061925
1.730000e-146
529.0
21
TraesCS1A01G296800
chr6A
77.622
429
90
2
1
429
52704743
52704321
3.230000e-64
255.0
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
TraesCS1A01G296800
chr1A
491998845
492001377
2532
True
4678.0
4678
100.000
1
2533
1
chr1A.!!$R1
2532
1
TraesCS1A01G296800
chr1A
575003036
575004143
1107
False
1631.0
1631
93.237
1426
2533
1
chr1A.!!$F1
1107
2
TraesCS1A01G296800
chr1A
575076928
575077530
602
False
760.0
760
89.379
1426
2035
1
chr1A.!!$F3
609
3
TraesCS1A01G296800
chr1A
575036359
575036960
601
False
743.0
743
88.871
1426
2035
1
chr1A.!!$F2
609
4
TraesCS1A01G296800
chr6B
184805786
184808317
2531
False
3247.0
3247
89.874
1
2533
1
chr6B.!!$F1
2532
5
TraesCS1A01G296800
chr4A
640153616
640155809
2193
True
2752.0
2752
89.385
350
2533
1
chr4A.!!$R2
2183
6
TraesCS1A01G296800
chr4A
703402462
703403632
1170
True
1345.0
1345
87.458
1353
2532
1
chr4A.!!$R3
1179
7
TraesCS1A01G296800
chr4A
708315836
708317137
1301
False
549.0
549
74.796
3
1334
1
chr4A.!!$F2
1331
8
TraesCS1A01G296800
chr4A
16259469
16260171
702
True
222.0
222
73.261
812
1525
1
chr4A.!!$R1
713
9
TraesCS1A01G296800
chr3B
513943182
513944534
1352
False
1857.0
1857
91.525
1187
2533
1
chr3B.!!$F1
1346
10
TraesCS1A01G296800
chr3B
661543428
661544680
1252
True
1749.0
1749
91.965
1287
2533
1
chr3B.!!$R1
1246
11
TraesCS1A01G296800
chr1B
266114565
266115589
1024
True
1672.0
1672
96.105
1508
2533
1
chr1B.!!$R1
1025
12
TraesCS1A01G296800
chr4D
118588969
118592252
3283
True
992.5
1393
87.400
840
2533
2
chr4D.!!$R1
1693
13
TraesCS1A01G296800
chr3A
120813948
120814834
886
False
1373.0
1373
94.595
1645
2531
1
chr3A.!!$F2
886
14
TraesCS1A01G296800
chr7D
37926993
37927818
825
True
1293.0
1293
94.928
1707
2533
1
chr7D.!!$R1
826
15
TraesCS1A01G296800
chr4B
614060623
614061925
1302
False
529.0
529
74.500
2
1334
1
chr4B.!!$F1
1332
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.