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
TraesCS2D01G021500
chr2D
100.000
3774
0
0
1
3774
9885620
9881847
0.000000e+00
6970.0
1
TraesCS2D01G021500
chr2D
88.623
167
18
1
2799
2965
362930815
362930980
6.390000e-48
202.0
2
TraesCS2D01G021500
chr2A
91.550
1858
132
11
960
2793
21275651
21273795
0.000000e+00
2538.0
3
TraesCS2D01G021500
chr2A
92.842
936
57
4
1867
2793
9388549
9389483
0.000000e+00
1349.0
4
TraesCS2D01G021500
chr2A
92.283
933
59
6
1874
2793
9841327
9842259
0.000000e+00
1312.0
5
TraesCS2D01G021500
chr2A
93.266
698
47
0
1137
1834
9838779
9839476
0.000000e+00
1029.0
6
TraesCS2D01G021500
chr2A
89.263
801
66
14
2983
3772
9389544
9390335
0.000000e+00
985.0
7
TraesCS2D01G021500
chr2A
92.507
694
37
10
2952
3636
21273796
21273109
0.000000e+00
979.0
8
TraesCS2D01G021500
chr2A
88.889
801
69
14
2983
3772
9842320
9843111
0.000000e+00
968.0
9
TraesCS2D01G021500
chr2A
83.745
972
88
33
156
1096
9138990
9138058
0.000000e+00
856.0
10
TraesCS2D01G021500
chr2A
82.265
998
147
18
992
1980
682635637
682634661
0.000000e+00
835.0
11
TraesCS2D01G021500
chr2A
83.257
651
86
9
2136
2776
682634554
682633917
9.090000e-161
577.0
12
TraesCS2D01G021500
chr2A
81.930
653
36
34
1
611
9837821
9838433
9.480000e-131
477.0
13
TraesCS2D01G021500
chr2A
77.083
864
156
30
1093
1947
5927740
5928570
9.550000e-126
460.0
14
TraesCS2D01G021500
chr2A
82.278
316
45
10
306
611
21276208
21275894
2.890000e-66
263.0
15
TraesCS2D01G021500
chr2A
96.262
107
4
0
1093
1199
9137633
9137527
3.870000e-40
176.0
16
TraesCS2D01G021500
chr7D
80.711
928
173
3
1032
1953
177876599
177877526
0.000000e+00
717.0
17
TraesCS2D01G021500
chr7D
86.842
266
24
6
3506
3763
485106459
485106721
1.720000e-73
287.0
18
TraesCS2D01G021500
chr7D
86.792
265
24
6
3506
3762
199607137
199606876
6.170000e-73
285.0
19
TraesCS2D01G021500
chr7D
89.130
46
5
0
2465
2510
613717192
613717237
1.460000e-04
58.4
20
TraesCS2D01G021500
chr7A
79.721
932
172
11
1032
1953
181695885
181696809
0.000000e+00
658.0
21
TraesCS2D01G021500
chr7B
84.518
633
96
2
2136
2767
143811062
143811693
3.200000e-175
625.0
22
TraesCS2D01G021500
chr7B
83.651
367
60
0
1032
1398
143808268
143808634
2.790000e-91
346.0
23
TraesCS2D01G021500
chr7B
87.454
271
22
6
3500
3762
540063193
540063459
6.130000e-78
302.0
24
TraesCS2D01G021500
chr7B
87.719
57
7
0
403
459
242957324
242957380
2.430000e-07
67.6
25
TraesCS2D01G021500
chr3A
80.676
828
127
22
993
1802
46584135
46583323
2.490000e-171
612.0
26
TraesCS2D01G021500
chr3A
77.953
635
101
19
2136
2764
46583111
46582510
9.970000e-96
361.0
27
TraesCS2D01G021500
chr4A
87.023
262
27
5
3502
3762
352482009
352481754
4.770000e-74
289.0
28
TraesCS2D01G021500
chr2B
86.842
266
24
6
3508
3765
438744180
438743918
1.720000e-73
287.0
29
TraesCS2D01G021500
chr5B
85.556
270
26
7
3507
3767
527760621
527760356
1.730000e-68
270.0
30
TraesCS2D01G021500
chr5B
91.613
155
13
0
2799
2953
612672830
612672984
8.210000e-52
215.0
31
TraesCS2D01G021500
chr5B
90.446
157
15
0
2799
2955
46768871
46769027
1.370000e-49
207.0
32
TraesCS2D01G021500
chr3B
86.275
255
28
6
3520
3772
80104427
80104676
1.730000e-68
270.0
33
TraesCS2D01G021500
chr1D
85.771
253
26
3
3518
3762
338927406
338927156
3.740000e-65
259.0
34
TraesCS2D01G021500
chr1D
97.059
34
0
1
421
454
355428974
355429006
5.270000e-04
56.5
35
TraesCS2D01G021500
chr3D
85.271
258
27
11
3518
3772
50537805
50538054
4.840000e-64
255.0
36
TraesCS2D01G021500
chr1A
91.613
155
13
0
2799
2953
181769434
181769588
8.210000e-52
215.0
37
TraesCS2D01G021500
chr1A
79.828
233
39
8
378
608
343611205
343610979
3.020000e-36
163.0
38
TraesCS2D01G021500
chr1A
85.616
146
9
7
650
783
168443372
168443517
3.930000e-30
143.0
39
TraesCS2D01G021500
chrUn
90.506
158
15
0
2797
2954
96464816
96464973
3.820000e-50
209.0
40
TraesCS2D01G021500
chrUn
85.616
146
9
7
650
783
93417096
93417241
3.930000e-30
143.0
41
TraesCS2D01G021500
chrUn
85.616
146
9
7
650
783
278886248
278886393
3.930000e-30
143.0
42
TraesCS2D01G021500
chrUn
85.616
146
9
7
650
783
327660628
327660773
3.930000e-30
143.0
43
TraesCS2D01G021500
chr1B
89.024
164
18
0
2792
2955
49836448
49836285
1.780000e-48
204.0
44
TraesCS2D01G021500
chr1B
89.024
164
18
0
2792
2955
49838679
49838516
1.780000e-48
204.0
45
TraesCS2D01G021500
chr1B
89.024
164
18
0
2792
2955
49839423
49839260
1.780000e-48
204.0
46
TraesCS2D01G021500
chr4B
85.075
201
18
11
2772
2964
97894861
97895057
1.070000e-45
195.0
47
TraesCS2D01G021500
chr4B
85.616
146
9
7
650
783
642713950
642714095
3.930000e-30
143.0
48
TraesCS2D01G021500
chr4B
87.719
57
7
0
403
459
195383723
195383779
2.430000e-07
67.6
49
TraesCS2D01G021500
chr4B
85.965
57
8
0
403
459
160479313
160479369
1.130000e-05
62.1
50
TraesCS2D01G021500
chr5D
86.014
143
8
7
653
783
503213151
503213009
3.930000e-30
143.0
51
TraesCS2D01G021500
chr5D
81.053
95
18
0
1342
1436
522761316
522761222
4.040000e-10
76.8
52
TraesCS2D01G021500
chr4D
85.315
143
9
5
653
783
468230
468088
1.830000e-28
137.0
53
TraesCS2D01G021500
chr4D
85.315
143
9
7
653
783
19923712
19923570
1.830000e-28
137.0
54
TraesCS2D01G021500
chr5A
89.796
49
5
0
378
426
534988103
534988055
3.150000e-06
63.9
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
TraesCS2D01G021500
chr2D
9881847
9885620
3773
True
6970.0
6970
100.000000
1
3774
1
chr2D.!!$R1
3773
1
TraesCS2D01G021500
chr2A
21273109
21276208
3099
True
1260.0
2538
88.778333
306
3636
3
chr2A.!!$R2
3330
2
TraesCS2D01G021500
chr2A
9388549
9390335
1786
False
1167.0
1349
91.052500
1867
3772
2
chr2A.!!$F2
1905
3
TraesCS2D01G021500
chr2A
9837821
9843111
5290
False
946.5
1312
89.092000
1
3772
4
chr2A.!!$F3
3771
4
TraesCS2D01G021500
chr2A
682633917
682635637
1720
True
706.0
835
82.761000
992
2776
2
chr2A.!!$R3
1784
5
TraesCS2D01G021500
chr2A
9137527
9138990
1463
True
516.0
856
90.003500
156
1199
2
chr2A.!!$R1
1043
6
TraesCS2D01G021500
chr2A
5927740
5928570
830
False
460.0
460
77.083000
1093
1947
1
chr2A.!!$F1
854
7
TraesCS2D01G021500
chr7D
177876599
177877526
927
False
717.0
717
80.711000
1032
1953
1
chr7D.!!$F1
921
8
TraesCS2D01G021500
chr7A
181695885
181696809
924
False
658.0
658
79.721000
1032
1953
1
chr7A.!!$F1
921
9
TraesCS2D01G021500
chr7B
143808268
143811693
3425
False
485.5
625
84.084500
1032
2767
2
chr7B.!!$F3
1735
10
TraesCS2D01G021500
chr3A
46582510
46584135
1625
True
486.5
612
79.314500
993
2764
2
chr3A.!!$R1
1771
11
TraesCS2D01G021500
chr1B
49836285
49839423
3138
True
204.0
204
89.024000
2792
2955
3
chr1B.!!$R1
163
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.