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
TraesCS5D01G364000
chr5D
100.000
3062
0
0
1
3062
441569725
441566664
0.000000e+00
5655.0
1
TraesCS5D01G364000
chr5D
96.522
1639
40
7
961
2592
490431474
490429846
0.000000e+00
2695.0
2
TraesCS5D01G364000
chr5D
97.417
968
22
3
1
965
490437499
490436532
0.000000e+00
1646.0
3
TraesCS5D01G364000
chr5D
84.122
296
16
10
2728
3002
490428869
490428584
1.090000e-64
257.0
4
TraesCS5D01G364000
chr5D
98.601
143
2
0
2590
2732
490429795
490429653
1.410000e-63
254.0
5
TraesCS5D01G364000
chr7D
92.280
2474
108
17
1
2434
44717253
44714823
0.000000e+00
3434.0
6
TraesCS5D01G364000
chr7D
87.213
305
24
5
2295
2591
44714828
44714531
1.760000e-87
333.0
7
TraesCS5D01G364000
chr6D
91.004
2579
111
35
1
2536
28310675
28308175
0.000000e+00
3365.0
8
TraesCS5D01G364000
chr6D
92.636
1548
65
17
657
2194
420225684
420224176
0.000000e+00
2182.0
9
TraesCS5D01G364000
chr6D
95.695
302
9
3
1
302
420228666
420228369
1.650000e-132
483.0
10
TraesCS5D01G364000
chr6D
96.503
143
5
0
2590
2732
28308092
28307950
1.420000e-58
237.0
11
TraesCS5D01G364000
chr6D
92.547
161
8
2
1286
1442
13922058
13922218
8.540000e-56
228.0
12
TraesCS5D01G364000
chr6D
98.148
54
1
0
2197
2250
420224149
420224096
9.040000e-16
95.3
13
TraesCS5D01G364000
chr6A
90.314
2612
120
44
1
2584
29577371
29579877
0.000000e+00
3299.0
14
TraesCS5D01G364000
chr6A
95.000
40
2
0
3023
3062
504621352
504621313
2.550000e-06
63.9
15
TraesCS5D01G364000
chr5A
92.238
2332
98
19
306
2592
611977603
611975310
0.000000e+00
3227.0
16
TraesCS5D01G364000
chr5A
96.013
301
9
2
1
301
611978599
611978302
1.280000e-133
486.0
17
TraesCS5D01G364000
chr5A
97.203
143
3
1
2590
2732
611974472
611974331
1.100000e-59
241.0
18
TraesCS5D01G364000
chr5A
88.889
189
16
4
2728
2911
611973619
611973431
8.540000e-56
228.0
19
TraesCS5D01G364000
chr7A
94.004
2118
78
15
1
2110
47295307
47293231
0.000000e+00
3162.0
20
TraesCS5D01G364000
chr7A
85.225
555
43
20
2065
2591
47293235
47292692
4.490000e-148
534.0
21
TraesCS5D01G364000
chr5B
92.004
2276
90
23
359
2592
604858080
604855855
0.000000e+00
3110.0
22
TraesCS5D01G364000
chr5B
95.801
381
14
1
1
381
604871988
604872366
5.610000e-172
614.0
23
TraesCS5D01G364000
chr5B
95.745
141
6
0
2590
2730
604855804
604855664
8.540000e-56
228.0
24
TraesCS5D01G364000
chr4A
94.702
302
13
2
1
302
581493262
581492964
1.660000e-127
466.0
25
TraesCS5D01G364000
chr4A
100.000
37
0
0
3024
3060
457286100
457286136
5.480000e-08
69.4
26
TraesCS5D01G364000
chr4A
97.368
38
1
0
3023
3060
292923732
292923695
7.090000e-07
65.8
27
TraesCS5D01G364000
chr4A
97.143
35
1
0
3026
3060
617910491
617910457
3.300000e-05
60.2
28
TraesCS5D01G364000
chr3A
78.808
604
65
34
1737
2292
128521175
128520587
6.280000e-92
348.0
29
TraesCS5D01G364000
chr6B
90.496
242
21
1
561
802
25279063
25279302
4.930000e-83
318.0
30
TraesCS5D01G364000
chr6B
100.000
36
0
0
3025
3060
107879847
107879812
1.970000e-07
67.6
31
TraesCS5D01G364000
chr1A
95.882
170
6
1
2026
2194
389877111
389877280
1.080000e-69
274.0
32
TraesCS5D01G364000
chr1A
92.708
96
4
1
2197
2292
389877472
389877564
5.330000e-28
135.0
33
TraesCS5D01G364000
chr1A
93.023
43
3
0
3018
3060
384069743
384069701
2.550000e-06
63.9
34
TraesCS5D01G364000
chr1A
100.000
29
0
0
2915
2943
113250781
113250809
2.000000e-03
54.7
35
TraesCS5D01G364000
chr2B
82.935
293
38
5
294
575
138115682
138115391
1.410000e-63
254.0
36
TraesCS5D01G364000
chr2B
97.368
38
1
0
3025
3062
420197799
420197762
7.090000e-07
65.8
37
TraesCS5D01G364000
chr2B
95.000
40
1
1
3021
3060
677017674
677017712
9.170000e-06
62.1
38
TraesCS5D01G364000
chr1D
82.958
311
24
15
1737
2041
310148264
310148551
1.410000e-63
254.0
39
TraesCS5D01G364000
chr4D
87.560
209
19
3
918
1125
55035065
55035267
5.100000e-58
235.0
40
TraesCS5D01G364000
chr4D
94.595
37
2
0
2837
2873
322259936
322259972
1.190000e-04
58.4
41
TraesCS5D01G364000
chr2A
85.882
170
21
1
402
568
46323254
46323085
8.720000e-41
178.0
42
TraesCS5D01G364000
chr7B
89.583
48
3
2
3014
3060
130268589
130268635
3.300000e-05
60.2
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
TraesCS5D01G364000
chr5D
441566664
441569725
3061
True
5655.000000
5655
100.000000
1
3062
1
chr5D.!!$R1
3061
1
TraesCS5D01G364000
chr5D
490436532
490437499
967
True
1646.000000
1646
97.417000
1
965
1
chr5D.!!$R2
964
2
TraesCS5D01G364000
chr5D
490428584
490431474
2890
True
1068.666667
2695
93.081667
961
3002
3
chr5D.!!$R3
2041
3
TraesCS5D01G364000
chr7D
44714531
44717253
2722
True
1883.500000
3434
89.746500
1
2591
2
chr7D.!!$R1
2590
4
TraesCS5D01G364000
chr6D
28307950
28310675
2725
True
1801.000000
3365
93.753500
1
2732
2
chr6D.!!$R1
2731
5
TraesCS5D01G364000
chr6D
420224096
420228666
4570
True
920.100000
2182
95.493000
1
2250
3
chr6D.!!$R2
2249
6
TraesCS5D01G364000
chr6A
29577371
29579877
2506
False
3299.000000
3299
90.314000
1
2584
1
chr6A.!!$F1
2583
7
TraesCS5D01G364000
chr5A
611973431
611978599
5168
True
1045.500000
3227
93.585750
1
2911
4
chr5A.!!$R1
2910
8
TraesCS5D01G364000
chr7A
47292692
47295307
2615
True
1848.000000
3162
89.614500
1
2591
2
chr7A.!!$R1
2590
9
TraesCS5D01G364000
chr5B
604855664
604858080
2416
True
1669.000000
3110
93.874500
359
2730
2
chr5B.!!$R1
2371
10
TraesCS5D01G364000
chr3A
128520587
128521175
588
True
348.000000
348
78.808000
1737
2292
1
chr3A.!!$R1
555
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.