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
TraesCS2D01G250600
chr2D
100.000
2813
0
0
1
2813
299372028
299369216
0.000000e+00
5195.0
1
TraesCS2D01G250600
chr2D
81.933
238
39
4
2457
2690
568276185
568275948
6.150000e-47
198.0
2
TraesCS2D01G250600
chr2A
96.125
1471
41
4
872
2329
373421325
373419858
0.000000e+00
2386.0
3
TraesCS2D01G250600
chr2A
90.011
911
74
12
1
905
373422221
373421322
0.000000e+00
1162.0
4
TraesCS2D01G250600
chr2A
90.664
482
26
7
2335
2813
373418574
373418109
8.560000e-175
623.0
5
TraesCS2D01G250600
chr2A
85.106
235
31
3
1
234
446648675
446648444
1.300000e-58
237.0
6
TraesCS2D01G250600
chr2B
95.968
1389
45
7
656
2037
355885125
355886509
0.000000e+00
2244.0
7
TraesCS2D01G250600
chr2B
88.846
780
61
10
2037
2813
355929672
355930428
0.000000e+00
935.0
8
TraesCS2D01G250600
chr2B
91.793
658
47
5
1
654
355881901
355882555
0.000000e+00
909.0
9
TraesCS2D01G250600
chr2B
76.863
255
48
9
2200
2448
682943326
682943077
1.760000e-27
134.0
10
TraesCS2D01G250600
chr4D
87.225
227
25
3
1
225
346238699
346238923
3.600000e-64
255.0
11
TraesCS2D01G250600
chr4D
85.470
234
29
5
1
232
22595620
22595390
3.620000e-59
239.0
12
TraesCS2D01G250600
chr4D
81.526
249
41
5
2447
2690
223684547
223684795
1.710000e-47
200.0
13
TraesCS2D01G250600
chr3A
85.833
240
28
5
1
238
235321203
235320968
1.670000e-62
250.0
14
TraesCS2D01G250600
chr3A
86.325
117
14
2
2691
2805
118453746
118453630
2.940000e-25
126.0
15
TraesCS2D01G250600
chr3A
82.203
118
21
0
2690
2807
451480363
451480480
4.960000e-18
102.0
16
TraesCS2D01G250600
chr1B
85.897
234
29
2
1
234
305930050
305929821
2.160000e-61
246.0
17
TraesCS2D01G250600
chr1B
82.895
228
35
4
2467
2690
306251077
306250850
4.750000e-48
202.0
18
TraesCS2D01G250600
chr3B
85.897
234
28
5
1
232
323467735
323467505
7.780000e-61
244.0
19
TraesCS2D01G250600
chr3B
78.027
223
37
10
2232
2448
473061622
473061838
2.270000e-26
130.0
20
TraesCS2D01G250600
chr3B
77.674
215
36
10
2240
2448
829263417
829263625
1.370000e-23
121.0
21
TraesCS2D01G250600
chr1A
85.169
236
30
5
1
234
93554221
93554453
1.300000e-58
237.0
22
TraesCS2D01G250600
chr4A
93.966
116
7
0
2690
2805
64952771
64952886
2.880000e-40
176.0
23
TraesCS2D01G250600
chr4A
80.889
225
39
2
2470
2690
273333819
273333595
1.040000e-39
174.0
24
TraesCS2D01G250600
chr4A
82.243
107
12
5
2701
2805
142794706
142794605
4.990000e-13
86.1
25
TraesCS2D01G250600
chr5B
78.333
240
44
8
2457
2690
601856383
601856620
6.280000e-32
148.0
26
TraesCS2D01G250600
chr7B
77.823
248
45
9
2206
2448
553824778
553824536
8.120000e-31
145.0
27
TraesCS2D01G250600
chr7B
85.333
75
11
0
2372
2446
424646965
424646891
8.350000e-11
78.7
28
TraesCS2D01G250600
chr4B
77.470
253
43
12
2203
2448
184205540
184205785
3.780000e-29
139.0
29
TraesCS2D01G250600
chr4B
78.027
223
37
10
2232
2448
434108214
434108430
2.270000e-26
130.0
30
TraesCS2D01G250600
chr4B
85.000
80
7
4
2728
2805
407411912
407411988
3.000000e-10
76.8
31
TraesCS2D01G250600
chrUn
84.559
136
18
3
2556
2688
105264519
105264654
6.320000e-27
132.0
32
TraesCS2D01G250600
chrUn
89.831
59
4
2
2747
2805
221309202
221309258
1.080000e-09
75.0
33
TraesCS2D01G250600
chr6A
83.212
137
20
3
2555
2688
42182469
42182333
3.810000e-24
122.0
34
TraesCS2D01G250600
chr3D
83.761
117
12
6
2692
2805
126088793
126088905
1.380000e-18
104.0
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
TraesCS2D01G250600
chr2D
299369216
299372028
2812
True
5195.000000
5195
100.000000
1
2813
1
chr2D.!!$R1
2812
1
TraesCS2D01G250600
chr2A
373418109
373422221
4112
True
1390.333333
2386
92.266667
1
2813
3
chr2A.!!$R2
2812
2
TraesCS2D01G250600
chr2B
355881901
355886509
4608
False
1576.500000
2244
93.880500
1
2037
2
chr2B.!!$F2
2036
3
TraesCS2D01G250600
chr2B
355929672
355930428
756
False
935.000000
935
88.846000
2037
2813
1
chr2B.!!$F1
776
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.