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
TraesCS4A01G402800
chr4A
100.000
4528
0
0
660
5187
676531333
676526806
0.000000e+00
8362.0
1
TraesCS4A01G402800
chr4A
94.509
692
29
5
3641
4324
676456501
676455811
0.000000e+00
1059.0
2
TraesCS4A01G402800
chr4A
100.000
424
0
0
1
424
676531992
676531569
0.000000e+00
784.0
3
TraesCS4A01G402800
chr4A
92.131
305
16
2
3015
3318
676456804
676456507
1.730000e-114
424.0
4
TraesCS4A01G402800
chr4A
89.764
254
18
4
4089
4334
676362453
676362200
8.380000e-83
318.0
5
TraesCS4A01G402800
chr4A
94.702
151
6
2
2865
3015
676493861
676493713
3.120000e-57
233.0
6
TraesCS4A01G402800
chr4A
93.377
151
7
3
2865
3015
676457046
676456899
2.430000e-53
220.0
7
TraesCS4A01G402800
chr7A
90.067
2668
190
42
660
3304
63707710
63710325
0.000000e+00
3389.0
8
TraesCS4A01G402800
chr7A
88.798
1223
86
28
3015
4217
63578469
63577278
0.000000e+00
1452.0
9
TraesCS4A01G402800
chr7A
94.199
724
36
5
3641
4361
63710345
63711065
0.000000e+00
1099.0
10
TraesCS4A01G402800
chr7A
89.868
681
54
11
3643
4310
63554185
63553507
0.000000e+00
861.0
11
TraesCS4A01G402800
chr7A
83.490
533
67
14
4668
5187
642589630
642590154
1.310000e-130
477.0
12
TraesCS4A01G402800
chr7A
87.028
424
35
10
1
424
63707264
63707667
1.320000e-125
460.0
13
TraesCS4A01G402800
chr7A
92.715
151
7
3
2865
3015
63578710
63578564
1.130000e-51
215.0
14
TraesCS4A01G402800
chr7A
81.373
204
34
3
4398
4600
662397870
662397670
4.160000e-36
163.0
15
TraesCS4A01G402800
chr7D
87.610
2728
180
72
691
3304
59094285
59091602
0.000000e+00
3020.0
16
TraesCS4A01G402800
chr7D
89.518
1183
85
19
3075
4228
58993480
58992308
0.000000e+00
1461.0
17
TraesCS4A01G402800
chr7D
94.498
727
34
3
3641
4362
59091582
59090857
0.000000e+00
1116.0
18
TraesCS4A01G402800
chr7D
86.261
575
64
11
3643
4209
58938018
58937451
1.230000e-170
610.0
19
TraesCS4A01G402800
chr7D
84.061
527
72
10
4668
5185
348188504
348187981
1.000000e-136
497.0
20
TraesCS4A01G402800
chr7D
92.216
334
13
4
12
340
59095037
59094712
1.320000e-125
460.0
21
TraesCS4A01G402800
chr7D
81.550
542
75
11
4668
5187
531111878
531112416
1.730000e-114
424.0
22
TraesCS4A01G402800
chr7D
95.364
151
6
1
2865
3015
58994051
58993902
6.710000e-59
239.0
23
TraesCS4A01G402800
chr7D
96.825
63
2
0
3015
3077
58993802
58993740
7.100000e-19
106.0
24
TraesCS4A01G402800
chr3A
84.146
492
75
3
4668
5158
123902091
123902580
1.690000e-129
473.0
25
TraesCS4A01G402800
chr3D
83.142
522
63
11
4668
5187
61043705
61044203
2.200000e-123
453.0
26
TraesCS4A01G402800
chr3D
86.581
313
30
8
3320
3622
30368890
30369200
8.320000e-88
335.0
27
TraesCS4A01G402800
chr3D
100.000
28
0
0
3821
3848
154754800
154754773
9.000000e-03
52.8
28
TraesCS4A01G402800
chr3D
100.000
28
0
0
3821
3848
369031623
369031596
9.000000e-03
52.8
29
TraesCS4A01G402800
chr2B
82.453
530
78
12
4668
5187
212569371
212568847
2.850000e-122
449.0
30
TraesCS4A01G402800
chr2B
82.143
504
86
4
4686
5187
65868792
65868291
3.710000e-116
429.0
31
TraesCS4A01G402800
chr2B
87.543
289
30
4
3316
3600
403120335
403120049
3.870000e-86
329.0
32
TraesCS4A01G402800
chr2B
81.882
287
42
8
4399
4679
212569692
212569410
3.120000e-57
233.0
33
TraesCS4A01G402800
chr2B
81.435
237
38
6
4955
5187
513813294
513813060
6.860000e-44
189.0
34
TraesCS4A01G402800
chr2A
82.353
544
70
13
4668
5187
14441362
14440821
2.850000e-122
449.0
35
TraesCS4A01G402800
chr3B
81.992
522
82
6
4668
5187
818996172
818995661
2.870000e-117
433.0
36
TraesCS4A01G402800
chr4D
80.917
545
78
18
4668
5187
451301201
451300658
1.740000e-109
407.0
37
TraesCS4A01G402800
chr5B
85.752
379
52
2
4672
5049
641802753
641802376
2.910000e-107
399.0
38
TraesCS4A01G402800
chr5B
87.456
287
25
8
3319
3599
661526293
661526012
2.330000e-83
320.0
39
TraesCS4A01G402800
chr5B
83.243
185
30
1
4433
4617
519455897
519456080
8.930000e-38
169.0
40
TraesCS4A01G402800
chr5B
83.815
173
27
1
5013
5185
423354062
423354233
4.160000e-36
163.0
41
TraesCS4A01G402800
chr5D
85.789
380
49
5
4671
5048
456588269
456587893
1.050000e-106
398.0
42
TraesCS4A01G402800
chr5D
81.855
248
31
9
4443
4679
430167690
430167934
4.100000e-46
196.0
43
TraesCS4A01G402800
chr6A
86.799
303
24
12
3342
3634
578072349
578072053
1.800000e-84
324.0
44
TraesCS4A01G402800
chr6A
79.181
293
47
9
4398
4679
503928465
503928176
1.910000e-44
191.0
45
TraesCS4A01G402800
chr6D
86.755
302
25
9
3342
3634
431316560
431316265
6.480000e-84
322.0
46
TraesCS4A01G402800
chr6D
80.769
286
43
7
4399
4679
57466723
57466445
4.070000e-51
213.0
47
TraesCS4A01G402800
chr6D
100.000
28
0
0
3821
3848
169248727
169248754
9.000000e-03
52.8
48
TraesCS4A01G402800
chr1B
85.231
325
35
8
3319
3634
622600937
622600617
6.480000e-84
322.0
49
TraesCS4A01G402800
chr1B
84.239
184
22
5
5007
5187
513146232
513146053
6.910000e-39
172.0
50
TraesCS4A01G402800
chr1A
84.308
325
32
13
3319
3634
547341633
547341319
3.040000e-77
300.0
51
TraesCS4A01G402800
chr1D
83.451
284
39
6
4399
4677
180248256
180248536
1.850000e-64
257.0
52
TraesCS4A01G402800
chr1D
83.404
235
33
6
4385
4617
180246421
180246651
4.070000e-51
213.0
53
TraesCS4A01G402800
chr2D
77.525
396
69
15
4799
5187
517342664
517342282
2.430000e-53
220.0
54
TraesCS4A01G402800
chr4B
80.420
286
50
4
4399
4679
88399673
88399957
4.070000e-51
213.0
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
TraesCS4A01G402800
chr4A
676526806
676531992
5186
True
4573.000000
8362
100.000000
1
5187
2
chr4A.!!$R4
5186
1
TraesCS4A01G402800
chr4A
676455811
676457046
1235
True
567.666667
1059
93.339000
2865
4324
3
chr4A.!!$R3
1459
2
TraesCS4A01G402800
chr7A
63707264
63711065
3801
False
1649.333333
3389
90.431333
1
4361
3
chr7A.!!$F2
4360
3
TraesCS4A01G402800
chr7A
63553507
63554185
678
True
861.000000
861
89.868000
3643
4310
1
chr7A.!!$R1
667
4
TraesCS4A01G402800
chr7A
63577278
63578710
1432
True
833.500000
1452
90.756500
2865
4217
2
chr7A.!!$R3
1352
5
TraesCS4A01G402800
chr7A
642589630
642590154
524
False
477.000000
477
83.490000
4668
5187
1
chr7A.!!$F1
519
6
TraesCS4A01G402800
chr7D
59090857
59095037
4180
True
1532.000000
3020
91.441333
12
4362
3
chr7D.!!$R4
4350
7
TraesCS4A01G402800
chr7D
58937451
58938018
567
True
610.000000
610
86.261000
3643
4209
1
chr7D.!!$R1
566
8
TraesCS4A01G402800
chr7D
58992308
58994051
1743
True
602.000000
1461
93.902333
2865
4228
3
chr7D.!!$R3
1363
9
TraesCS4A01G402800
chr7D
348187981
348188504
523
True
497.000000
497
84.061000
4668
5185
1
chr7D.!!$R2
517
10
TraesCS4A01G402800
chr7D
531111878
531112416
538
False
424.000000
424
81.550000
4668
5187
1
chr7D.!!$F1
519
11
TraesCS4A01G402800
chr2B
65868291
65868792
501
True
429.000000
429
82.143000
4686
5187
1
chr2B.!!$R1
501
12
TraesCS4A01G402800
chr2B
212568847
212569692
845
True
341.000000
449
82.167500
4399
5187
2
chr2B.!!$R4
788
13
TraesCS4A01G402800
chr2A
14440821
14441362
541
True
449.000000
449
82.353000
4668
5187
1
chr2A.!!$R1
519
14
TraesCS4A01G402800
chr3B
818995661
818996172
511
True
433.000000
433
81.992000
4668
5187
1
chr3B.!!$R1
519
15
TraesCS4A01G402800
chr4D
451300658
451301201
543
True
407.000000
407
80.917000
4668
5187
1
chr4D.!!$R1
519
16
TraesCS4A01G402800
chr1D
180246421
180248536
2115
False
235.000000
257
83.427500
4385
4677
2
chr1D.!!$F1
292
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.