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
TraesCS1B01G479900
chr1B
100.000
2487
0
0
1
2487
687422172
687424658
0.000000e+00
4593.0
1
TraesCS1B01G479900
chr1B
87.500
768
76
11
784
1545
687650811
687651564
0.000000e+00
869.0
2
TraesCS1B01G479900
chr1B
84.848
561
69
7
943
1492
687531415
687531970
3.620000e-153
551.0
3
TraesCS1B01G479900
chr1B
80.612
490
67
18
1
470
687650013
687650494
1.090000e-93
353.0
4
TraesCS1B01G479900
chr1B
85.909
220
18
7
18
225
687529924
687530142
3.220000e-54
222.0
5
TraesCS1B01G479900
chr1B
74.126
429
85
22
2069
2484
687518759
687519174
1.190000e-33
154.0
6
TraesCS1B01G479900
chr1B
92.727
55
3
1
1492
1545
687517610
687517664
7.370000e-11
78.7
7
TraesCS1B01G479900
chr1A
91.257
1201
63
12
644
1822
592851729
592852909
0.000000e+00
1598.0
8
TraesCS1B01G479900
chr1A
88.005
767
78
10
784
1545
593214593
593215350
0.000000e+00
894.0
9
TraesCS1B01G479900
chr1A
88.204
763
62
9
785
1545
592977811
592978547
0.000000e+00
885.0
10
TraesCS1B01G479900
chr1A
85.938
768
89
12
784
1545
593217691
593218445
0.000000e+00
802.0
11
TraesCS1B01G479900
chr1A
84.520
562
68
8
943
1491
592994271
592994826
2.810000e-149
538.0
12
TraesCS1B01G479900
chr1A
87.500
456
38
6
2041
2484
592853030
592853478
2.210000e-140
508.0
13
TraesCS1B01G479900
chr1A
81.719
640
55
32
20
644
592977052
592977644
6.220000e-131
477.0
14
TraesCS1B01G479900
chr1A
88.172
279
16
8
1
262
592851290
592851568
1.440000e-82
316.0
15
TraesCS1B01G479900
chr1A
82.369
363
51
10
1
354
593213787
593214145
1.120000e-78
303.0
16
TraesCS1B01G479900
chr1A
77.413
487
61
32
18
470
592923904
592924375
6.870000e-61
244.0
17
TraesCS1B01G479900
chr1A
92.361
144
10
1
495
638
592851610
592851752
1.170000e-48
204.0
18
TraesCS1B01G479900
chr1A
75.394
508
69
31
2011
2484
480927761
480928246
7.020000e-46
195.0
19
TraesCS1B01G479900
chr1A
77.259
343
50
16
1662
1987
593215418
593215749
2.540000e-40
176.0
20
TraesCS1B01G479900
chr1A
81.279
219
32
7
2275
2484
592981455
592981673
4.250000e-38
169.0
21
TraesCS1B01G479900
chr1A
75.211
355
47
16
1662
1987
593218513
593218855
2.010000e-26
130.0
22
TraesCS1B01G479900
chr1A
100.000
28
0
0
364
391
592851585
592851612
4.000000e-03
52.8
23
TraesCS1B01G479900
chr1D
91.603
917
47
9
933
1822
494169050
494169963
0.000000e+00
1240.0
24
TraesCS1B01G479900
chr1D
88.482
764
59
7
784
1545
494327892
494328628
0.000000e+00
896.0
25
TraesCS1B01G479900
chr1D
87.206
766
85
7
785
1545
494423993
494424750
0.000000e+00
859.0
26
TraesCS1B01G479900
chr1D
86.280
707
45
14
1823
2484
494169994
494170693
0.000000e+00
721.0
27
TraesCS1B01G479900
chr1D
83.993
556
73
6
937
1480
494306795
494307346
1.020000e-143
520.0
28
TraesCS1B01G479900
chr1D
90.343
321
16
10
1
313
494168153
494168466
8.280000e-110
407.0
29
TraesCS1B01G479900
chr1D
81.748
515
60
18
1
488
494423155
494423662
1.390000e-107
399.0
30
TraesCS1B01G479900
chr1D
91.093
247
12
8
118
355
494327251
494327496
2.390000e-85
326.0
31
TraesCS1B01G479900
chr1D
90.164
244
16
4
400
638
494168675
494168915
6.680000e-81
311.0
32
TraesCS1B01G479900
chr1D
78.980
490
49
37
18
478
494348366
494348830
4.050000e-73
285.0
33
TraesCS1B01G479900
chr1D
77.823
487
77
22
18
488
494305666
494306137
3.150000e-69
272.0
34
TraesCS1B01G479900
chr1D
91.411
163
11
2
644
805
494168892
494169052
1.160000e-53
220.0
35
TraesCS1B01G479900
chr1D
75.870
431
75
19
2065
2484
494425870
494426282
2.520000e-45
193.0
36
TraesCS1B01G479900
chr1D
77.746
355
47
19
1662
1987
494424818
494425169
3.270000e-44
189.0
37
TraesCS1B01G479900
chr1D
73.611
504
73
30
2014
2481
379800240
379800719
3.340000e-29
139.0
38
TraesCS1B01G479900
chr1D
100.000
46
0
0
312
357
494168628
494168673
4.410000e-13
86.1
39
TraesCS1B01G479900
chrUn
87.412
707
63
6
784
1490
358968056
358967376
0.000000e+00
789.0
40
TraesCS1B01G479900
chrUn
81.875
640
65
26
20
644
358968829
358968226
2.220000e-135
492.0
41
TraesCS1B01G479900
chr5D
84.397
141
20
2
2345
2484
468305548
468305409
1.200000e-28
137.0
42
TraesCS1B01G479900
chr4A
87.324
71
4
5
2411
2479
595865462
595865395
2.650000e-10
76.8
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
TraesCS1B01G479900
chr1B
687422172
687424658
2486
False
4593.000000
4593
100.0000
1
2487
1
chr1B.!!$F1
2486
1
TraesCS1B01G479900
chr1B
687650013
687651564
1551
False
611.000000
869
84.0560
1
1545
2
chr1B.!!$F4
1544
2
TraesCS1B01G479900
chr1B
687529924
687531970
2046
False
386.500000
551
85.3785
18
1492
2
chr1B.!!$F3
1474
3
TraesCS1B01G479900
chr1A
592994271
592994826
555
False
538.000000
538
84.5200
943
1491
1
chr1A.!!$F3
548
4
TraesCS1B01G479900
chr1A
592851290
592853478
2188
False
535.760000
1598
91.8580
1
2484
5
chr1A.!!$F4
2483
5
TraesCS1B01G479900
chr1A
592977052
592981673
4621
False
510.333333
885
83.7340
20
2484
3
chr1A.!!$F5
2464
6
TraesCS1B01G479900
chr1A
593213787
593218855
5068
False
461.000000
894
81.7564
1
1987
5
chr1A.!!$F6
1986
7
TraesCS1B01G479900
chr1D
494327251
494328628
1377
False
611.000000
896
89.7875
118
1545
2
chr1D.!!$F5
1427
8
TraesCS1B01G479900
chr1D
494168153
494170693
2540
False
497.516667
1240
91.6335
1
2484
6
chr1D.!!$F3
2483
9
TraesCS1B01G479900
chr1D
494423155
494426282
3127
False
410.000000
859
80.6425
1
2484
4
chr1D.!!$F6
2483
10
TraesCS1B01G479900
chr1D
494305666
494307346
1680
False
396.000000
520
80.9080
18
1480
2
chr1D.!!$F4
1462
11
TraesCS1B01G479900
chrUn
358967376
358968829
1453
True
640.500000
789
84.6435
20
1490
2
chrUn.!!$R1
1470
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.