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
TraesCS1B01G449100
chr1B
100.000
1818
0
0
1
1818
667929932
667931749
0.000000e+00
3358.0
1
TraesCS1B01G449100
chr1B
94.026
837
44
6
987
1818
668031092
668030257
0.000000e+00
1264.0
2
TraesCS1B01G449100
chr1B
93.590
858
32
5
971
1815
667975787
667974940
0.000000e+00
1258.0
3
TraesCS1B01G449100
chr1B
89.863
878
41
15
987
1818
667997259
667996384
0.000000e+00
1085.0
4
TraesCS1B01G449100
chr1B
88.650
511
30
9
25
535
667976868
667976386
4.360000e-167
597.0
5
TraesCS1B01G449100
chr1B
100.000
319
0
0
2052
2370
667931983
667932301
7.300000e-165
590.0
6
TraesCS1B01G449100
chr1B
86.914
512
43
4
25
535
668032018
668031530
9.570000e-154
553.0
7
TraesCS1B01G449100
chr1B
86.041
394
34
10
541
927
668031480
668031101
1.020000e-108
403.0
8
TraesCS1B01G449100
chr1B
85.025
394
34
11
541
927
667997641
667997266
6.180000e-101
377.0
9
TraesCS1B01G449100
chr1B
86.339
366
26
6
25
390
667998709
667998368
6.180000e-101
377.0
10
TraesCS1B01G449100
chr1B
90.288
278
15
6
2091
2368
667996249
667995984
1.040000e-93
353.0
11
TraesCS1B01G449100
chr1B
91.093
247
21
1
2092
2338
667974929
667974684
1.360000e-87
333.0
12
TraesCS1B01G449100
chr1B
91.393
244
19
2
2096
2338
668029993
668029751
1.360000e-87
333.0
13
TraesCS1B01G449100
chr1B
90.625
160
15
0
376
535
667997851
667997692
1.850000e-51
213.0
14
TraesCS1B01G449100
chr1B
89.262
149
8
3
538
679
667976326
667976179
1.870000e-41
180.0
15
TraesCS1B01G449100
chr1B
88.462
130
12
3
798
926
667975901
667975774
1.130000e-33
154.0
16
TraesCS1B01G449100
chr1D
91.134
1252
65
14
538
1772
479759853
479758631
0.000000e+00
1655.0
17
TraesCS1B01G449100
chr1D
87.074
1261
118
30
573
1818
479751245
479750015
0.000000e+00
1384.0
18
TraesCS1B01G449100
chr1D
91.194
511
33
7
25
535
479760412
479759914
0.000000e+00
684.0
19
TraesCS1B01G449100
chr1D
87.867
511
39
3
25
535
479751818
479751331
1.580000e-161
579.0
20
TraesCS1B01G449100
chr1D
93.145
248
16
1
2091
2338
479750004
479749758
1.730000e-96
363.0
21
TraesCS1B01G449100
chr1D
89.655
261
24
1
1018
1278
479737852
479737595
1.760000e-86
329.0
22
TraesCS1B01G449100
chr1D
93.151
146
10
0
2165
2310
479722321
479722176
5.130000e-52
215.0
23
TraesCS1B01G449100
chr1D
94.915
59
3
0
1760
1818
479758612
479758554
2.510000e-15
93.5
24
TraesCS1B01G449100
chr1D
80.488
123
19
5
1545
1663
479737354
479737233
3.240000e-14
89.8
25
TraesCS1B01G449100
chr1D
83.333
84
6
3
2295
2370
479722161
479722078
1.180000e-08
71.3
26
TraesCS1B01G449100
chr1A
89.016
1311
71
25
538
1818
576204012
576202745
0.000000e+00
1555.0
27
TraesCS1B01G449100
chr1A
89.043
1150
77
21
538
1661
576139619
576138493
0.000000e+00
1380.0
28
TraesCS1B01G449100
chr1A
88.824
510
33
11
26
533
576204561
576204074
2.610000e-169
604.0
29
TraesCS1B01G449100
chr1A
88.889
477
41
3
69
533
576140157
576139681
5.680000e-161
577.0
30
TraesCS1B01G449100
chr1A
85.833
360
43
6
1018
1370
576078231
576077873
2.220000e-100
375.0
31
TraesCS1B01G449100
chr1A
89.606
279
18
4
2092
2370
576138376
576138109
6.270000e-91
344.0
32
TraesCS1B01G449100
chr1A
91.600
250
20
1
2089
2338
576202736
576202488
6.270000e-91
344.0
33
TraesCS1B01G449100
chr1A
86.667
120
4
7
1699
1818
576138494
576138387
3.200000e-24
122.0
34
TraesCS1B01G449100
chr1A
81.452
124
16
7
1545
1663
576077757
576077636
6.970000e-16
95.3
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
TraesCS1B01G449100
chr1B
667929932
667932301
2369
False
1974.000000
3358
100.000000
1
2370
2
chr1B.!!$F1
2369
1
TraesCS1B01G449100
chr1B
668029751
668032018
2267
True
638.250000
1264
89.593500
25
2338
4
chr1B.!!$R3
2313
2
TraesCS1B01G449100
chr1B
667974684
667976868
2184
True
504.400000
1258
90.211400
25
2338
5
chr1B.!!$R1
2313
3
TraesCS1B01G449100
chr1B
667995984
667998709
2725
True
481.000000
1085
88.428000
25
2368
5
chr1B.!!$R2
2343
4
TraesCS1B01G449100
chr1D
479758554
479760412
1858
True
810.833333
1655
92.414333
25
1818
3
chr1D.!!$R4
1793
5
TraesCS1B01G449100
chr1D
479749758
479751818
2060
True
775.333333
1384
89.362000
25
2338
3
chr1D.!!$R3
2313
6
TraesCS1B01G449100
chr1D
479737233
479737852
619
True
209.400000
329
85.071500
1018
1663
2
chr1D.!!$R2
645
7
TraesCS1B01G449100
chr1A
576202488
576204561
2073
True
834.333333
1555
89.813333
26
2338
3
chr1A.!!$R3
2312
8
TraesCS1B01G449100
chr1A
576138109
576140157
2048
True
605.750000
1380
88.551250
69
2370
4
chr1A.!!$R2
2301
9
TraesCS1B01G449100
chr1A
576077636
576078231
595
True
235.150000
375
83.642500
1018
1663
2
chr1A.!!$R1
645
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.