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
TraesCS1A01G253500
chr1A
100.000
3477
0
0
1
3477
445501535
445505011
0.000000e+00
6421.0
1
TraesCS1A01G253500
chr1A
92.208
77
5
1
3398
3474
52534532
52534607
1.320000e-19
108.0
2
TraesCS1A01G253500
chr1D
96.503
2574
71
9
81
2646
345374101
345376663
0.000000e+00
4237.0
3
TraesCS1A01G253500
chr1D
80.000
450
70
11
2948
3380
161036260
161035814
7.240000e-82
315.0
4
TraesCS1A01G253500
chr1D
84.571
175
17
5
3208
3382
407697174
407697338
7.720000e-37
165.0
5
TraesCS1A01G253500
chr1D
87.500
72
8
1
3398
3468
161035823
161035752
8.000000e-12
82.4
6
TraesCS1A01G253500
chr1B
92.732
2917
115
41
104
2947
465390286
465387394
0.000000e+00
4122.0
7
TraesCS1A01G253500
chr6A
87.829
797
86
8
1707
2495
15542478
15543271
0.000000e+00
924.0
8
TraesCS1A01G253500
chr6A
85.279
788
95
14
1722
2495
15457423
15456643
0.000000e+00
793.0
9
TraesCS1A01G253500
chr6A
83.061
797
124
7
1708
2495
15491582
15490788
0.000000e+00
713.0
10
TraesCS1A01G253500
chr6A
84.395
628
86
6
1006
1630
15540721
15541339
1.070000e-169
606.0
11
TraesCS1A01G253500
chr6A
84.286
630
85
8
1006
1634
15461668
15461052
1.380000e-168
603.0
12
TraesCS1A01G253500
chr6A
86.574
432
48
8
2948
3375
428726029
428725604
5.250000e-128
468.0
13
TraesCS1A01G253500
chr6A
90.000
80
7
1
3398
3477
428725608
428725530
6.140000e-18
102.0
14
TraesCS1A01G253500
chr6D
86.879
785
94
7
1707
2485
14241306
14242087
0.000000e+00
870.0
15
TraesCS1A01G253500
chr6D
85.554
803
95
13
1707
2495
14201992
14201197
0.000000e+00
821.0
16
TraesCS1A01G253500
chr6D
84.036
783
112
10
1723
2495
14231354
14230575
0.000000e+00
741.0
17
TraesCS1A01G253500
chr6D
84.945
631
82
7
1006
1634
14203504
14202885
8.190000e-176
627.0
18
TraesCS1A01G253500
chr6D
84.420
629
86
6
1006
1631
14239438
14240057
2.970000e-170
608.0
19
TraesCS1A01G253500
chr6D
82.306
633
92
7
1006
1634
14232267
14231651
6.610000e-147
531.0
20
TraesCS1A01G253500
chr6D
85.143
175
16
5
3208
3382
9827095
9827259
1.660000e-38
171.0
21
TraesCS1A01G253500
chr6D
93.827
81
4
1
3398
3477
9827248
9827328
1.700000e-23
121.0
22
TraesCS1A01G253500
chr6B
86.233
799
97
8
1707
2495
26004656
26005451
0.000000e+00
854.0
23
TraesCS1A01G253500
chr6B
85.480
792
98
9
1707
2491
26120974
26120193
0.000000e+00
809.0
24
TraesCS1A01G253500
chr6B
84.444
630
87
5
1006
1634
25976120
25975501
8.250000e-171
610.0
25
TraesCS1A01G253500
chr6B
82.989
629
92
6
1006
1631
26001816
26002432
3.920000e-154
555.0
26
TraesCS1A01G253500
chr6B
81.538
195
33
2
1006
1197
26123565
26123371
1.290000e-34
158.0
27
TraesCS1A01G253500
chr4A
92.906
437
28
3
2946
3382
141117840
141117407
1.760000e-177
632.0
28
TraesCS1A01G253500
chr4A
93.976
83
4
1
3396
3477
141117420
141117338
1.310000e-24
124.0
29
TraesCS1A01G253500
chr7A
92.575
431
30
2
2952
3382
150269993
150270421
4.930000e-173
617.0
30
TraesCS1A01G253500
chr7A
89.885
435
28
4
2948
3382
586324176
586324594
2.360000e-151
545.0
31
TraesCS1A01G253500
chr7A
89.165
443
27
6
2943
3382
644711434
644711858
1.840000e-147
532.0
32
TraesCS1A01G253500
chr7A
93.976
83
4
1
3396
3477
586324581
586324663
1.310000e-24
124.0
33
TraesCS1A01G253500
chr7A
94.444
36
2
0
1546
1581
93488862
93488897
4.850000e-04
56.5
34
TraesCS1A01G253500
chr5A
91.800
439
32
4
2944
3382
11242933
11243367
2.970000e-170
608.0
35
TraesCS1A01G253500
chr5A
92.771
83
5
1
3396
3477
11243354
11243436
6.100000e-23
119.0
36
TraesCS1A01G253500
chr4B
78.479
618
102
21
1006
1600
629852590
629853199
3.280000e-100
375.0
37
TraesCS1A01G253500
chr3D
81.153
451
61
13
2944
3377
374271095
374271538
1.200000e-89
340.0
38
TraesCS1A01G253500
chr3D
85.246
61
7
1
3408
3468
374271543
374271601
1.040000e-05
62.1
39
TraesCS1A01G253500
chr3A
81.152
382
56
10
2948
3317
746626354
746625977
3.390000e-75
292.0
40
TraesCS1A01G253500
chr3A
90.196
51
3
2
2875
2923
88212816
88212766
8.060000e-07
65.8
41
TraesCS1A01G253500
chr7D
84.571
175
17
5
3208
3382
536156490
536156654
7.720000e-37
165.0
42
TraesCS1A01G253500
chr7D
91.358
81
6
1
3398
3477
536156643
536156723
3.670000e-20
110.0
43
TraesCS1A01G253500
chr2A
92.683
41
3
0
2891
2931
14171894
14171934
3.750000e-05
60.2
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
TraesCS1A01G253500
chr1A
445501535
445505011
3476
False
6421.00
6421
100.0000
1
3477
1
chr1A.!!$F2
3476
1
TraesCS1A01G253500
chr1D
345374101
345376663
2562
False
4237.00
4237
96.5030
81
2646
1
chr1D.!!$F1
2565
2
TraesCS1A01G253500
chr1B
465387394
465390286
2892
True
4122.00
4122
92.7320
104
2947
1
chr1B.!!$R1
2843
3
TraesCS1A01G253500
chr6A
15540721
15543271
2550
False
765.00
924
86.1120
1006
2495
2
chr6A.!!$F1
1489
4
TraesCS1A01G253500
chr6A
15490788
15491582
794
True
713.00
713
83.0610
1708
2495
1
chr6A.!!$R1
787
5
TraesCS1A01G253500
chr6A
15456643
15461668
5025
True
698.00
793
84.7825
1006
2495
2
chr6A.!!$R2
1489
6
TraesCS1A01G253500
chr6D
14239438
14242087
2649
False
739.00
870
85.6495
1006
2485
2
chr6D.!!$F2
1479
7
TraesCS1A01G253500
chr6D
14201197
14203504
2307
True
724.00
821
85.2495
1006
2495
2
chr6D.!!$R1
1489
8
TraesCS1A01G253500
chr6D
14230575
14232267
1692
True
636.00
741
83.1710
1006
2495
2
chr6D.!!$R2
1489
9
TraesCS1A01G253500
chr6B
26001816
26005451
3635
False
704.50
854
84.6110
1006
2495
2
chr6B.!!$F1
1489
10
TraesCS1A01G253500
chr6B
25975501
25976120
619
True
610.00
610
84.4440
1006
1634
1
chr6B.!!$R1
628
11
TraesCS1A01G253500
chr6B
26120193
26123565
3372
True
483.50
809
83.5090
1006
2491
2
chr6B.!!$R2
1485
12
TraesCS1A01G253500
chr4A
141117338
141117840
502
True
378.00
632
93.4410
2946
3477
2
chr4A.!!$R1
531
13
TraesCS1A01G253500
chr5A
11242933
11243436
503
False
363.50
608
92.2855
2944
3477
2
chr5A.!!$F1
533
14
TraesCS1A01G253500
chr4B
629852590
629853199
609
False
375.00
375
78.4790
1006
1600
1
chr4B.!!$F1
594
15
TraesCS1A01G253500
chr3D
374271095
374271601
506
False
201.05
340
83.1995
2944
3468
2
chr3D.!!$F1
524
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.