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
TraesCS7A01G527100
chr7A
100.000
4184
0
0
1
4184
708514694
708510511
0.000000e+00
7727.0
1
TraesCS7A01G527100
chr7A
82.060
2252
317
53
945
3130
708505168
708502938
0.000000e+00
1840.0
2
TraesCS7A01G527100
chr7A
90.783
434
33
3
1
433
733088480
733088053
1.300000e-159
573.0
3
TraesCS7A01G527100
chr7A
90.952
210
19
0
1
210
18671143
18671352
2.460000e-72
283.0
4
TraesCS7A01G527100
chr7A
92.000
200
15
1
1
199
136441214
136441413
3.190000e-71
279.0
5
TraesCS7A01G527100
chr7A
92.268
194
15
0
258
451
18671347
18671540
4.120000e-70
276.0
6
TraesCS7A01G527100
chr7A
87.442
215
26
1
415
628
136441936
136442150
3.230000e-61
246.0
7
TraesCS7A01G527100
chr7A
92.105
152
10
2
477
628
708549590
708549441
3.280000e-51
213.0
8
TraesCS7A01G527100
chr7A
83.945
218
32
3
412
627
727122894
727123110
5.480000e-49
206.0
9
TraesCS7A01G527100
chr7D
95.165
3247
148
3
945
4182
615870597
615867351
0.000000e+00
5118.0
10
TraesCS7A01G527100
chr7D
85.097
1295
176
10
1779
3060
615879717
615878427
0.000000e+00
1306.0
11
TraesCS7A01G527100
chr7D
96.117
309
12
0
632
940
615874237
615873929
4.830000e-139
505.0
12
TraesCS7A01G527100
chr7D
84.653
404
52
6
1362
1763
615880155
615879760
1.090000e-105
394.0
13
TraesCS7A01G527100
chr7D
88.673
309
24
3
632
940
615888157
615887860
2.380000e-97
366.0
14
TraesCS7A01G527100
chr7D
79.215
433
39
21
3025
3415
615878405
615877982
1.930000e-63
254.0
15
TraesCS7A01G527100
chr7D
86.076
237
22
6
3925
4153
609407400
609407167
1.160000e-60
244.0
16
TraesCS7A01G527100
chr7D
85.654
237
24
5
3925
4153
609440205
609439971
1.500000e-59
241.0
17
TraesCS7A01G527100
chr7D
93.617
47
3
0
1323
1369
615870291
615870245
2.090000e-08
71.3
18
TraesCS7A01G527100
chr7B
93.932
3263
152
19
945
4182
708848511
708845270
0.000000e+00
4887.0
19
TraesCS7A01G527100
chr7B
84.286
700
103
5
1779
2475
708872981
708872286
0.000000e+00
676.0
20
TraesCS7A01G527100
chr7B
84.500
600
84
5
2470
3060
708867342
708866743
6.030000e-163
584.0
21
TraesCS7A01G527100
chr7B
83.408
446
66
3
1323
1763
708873466
708873024
1.400000e-109
407.0
22
TraesCS7A01G527100
chr7B
76.177
361
61
16
944
1299
708873758
708873418
2.590000e-37
167.0
23
TraesCS7A01G527100
chr7B
81.553
103
9
7
3196
3288
708866517
708866415
4.490000e-10
76.8
24
TraesCS7A01G527100
chr7B
93.617
47
3
0
1323
1369
708848211
708848165
2.090000e-08
71.3
25
TraesCS7A01G527100
chr7B
87.097
62
2
2
659
714
708855602
708855541
9.710000e-07
65.8
26
TraesCS7A01G527100
chr4B
93.632
424
26
1
1
424
449934684
449935106
2.120000e-177
632.0
27
TraesCS7A01G527100
chr4B
90.728
151
13
1
485
634
391155241
391155091
2.550000e-47
200.0
28
TraesCS7A01G527100
chr4D
92.048
415
23
4
1
405
431513112
431513526
3.630000e-160
575.0
29
TraesCS7A01G527100
chr6B
88.300
453
26
10
1
427
449621
450072
6.200000e-143
518.0
30
TraesCS7A01G527100
chr3D
94.769
325
17
0
1
325
592814755
592815079
1.340000e-139
507.0
31
TraesCS7A01G527100
chr3D
88.378
370
38
2
263
631
592815089
592815454
1.380000e-119
440.0
32
TraesCS7A01G527100
chr3D
80.645
279
40
9
360
631
522100408
522100679
1.970000e-48
204.0
33
TraesCS7A01G527100
chr1B
93.493
292
18
1
114
405
384303588
384303298
2.310000e-117
433.0
34
TraesCS7A01G527100
chr1B
82.182
275
36
8
360
628
84372257
84372524
1.510000e-54
224.0
35
TraesCS7A01G527100
chr1B
91.870
123
10
0
1
123
384331146
384331024
5.560000e-39
172.0
36
TraesCS7A01G527100
chr4A
84.184
392
27
20
1
392
176783784
176783428
8.610000e-92
348.0
37
TraesCS7A01G527100
chr4A
82.511
223
24
14
413
628
232898297
232898511
9.240000e-42
182.0
38
TraesCS7A01G527100
chr3B
80.727
275
35
15
368
626
159963980
159964252
9.180000e-47
198.0
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
TraesCS7A01G527100
chr7A
708510511
708514694
4183
True
7727.000000
7727
100.000000
1
4184
1
chr7A.!!$R2
4183
1
TraesCS7A01G527100
chr7A
708502938
708505168
2230
True
1840.000000
1840
82.060000
945
3130
1
chr7A.!!$R1
2185
2
TraesCS7A01G527100
chr7A
136441214
136442150
936
False
262.500000
279
89.721000
1
628
2
chr7A.!!$F3
627
3
TraesCS7A01G527100
chr7D
615867351
615880155
12804
True
1274.716667
5118
88.977333
632
4182
6
chr7D.!!$R4
3550
4
TraesCS7A01G527100
chr7B
708845270
708848511
3241
True
2479.150000
4887
93.774500
945
4182
2
chr7B.!!$R2
3237
5
TraesCS7A01G527100
chr7B
708872286
708873758
1472
True
416.666667
676
81.290333
944
2475
3
chr7B.!!$R4
1531
6
TraesCS7A01G527100
chr7B
708866415
708867342
927
True
330.400000
584
83.026500
2470
3288
2
chr7B.!!$R3
818
7
TraesCS7A01G527100
chr3D
592814755
592815454
699
False
473.500000
507
91.573500
1
631
2
chr3D.!!$F2
630
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.