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
TraesCS2A01G104300
chr2A
100.000
4577
0
0
1
4577
57820660
57825236
0.000000e+00
8453.0
1
TraesCS2A01G104300
chr2A
79.657
467
73
15
1064
1516
758526616
758526158
2.660000e-82
316.0
2
TraesCS2A01G104300
chr2D
93.842
2842
115
18
814
3615
56192785
56195606
0.000000e+00
4224.0
3
TraesCS2A01G104300
chr2D
91.980
586
37
5
3993
4577
330881448
330880872
0.000000e+00
813.0
4
TraesCS2A01G104300
chr2D
88.462
468
46
7
4112
4577
469109167
469108706
4.000000e-155
558.0
5
TraesCS2A01G104300
chr2D
90.201
398
22
8
3614
3995
455349004
455349400
1.900000e-138
503.0
6
TraesCS2A01G104300
chr2D
89.447
398
24
9
3614
3995
330881879
330881484
1.910000e-133
486.0
7
TraesCS2A01G104300
chr2D
78.692
474
71
18
1064
1520
628016242
628015782
5.790000e-74
289.0
8
TraesCS2A01G104300
chr2D
88.043
92
3
4
3332
3415
14895275
14895366
8.100000e-18
102.0
9
TraesCS2A01G104300
chr2B
93.990
2030
88
7
871
2890
88926107
88928112
0.000000e+00
3042.0
10
TraesCS2A01G104300
chr2B
93.285
417
13
5
2918
3333
88928107
88928509
6.550000e-168
601.0
11
TraesCS2A01G104300
chr2B
93.780
209
9
3
3408
3615
88928510
88928715
1.240000e-80
311.0
12
TraesCS2A01G104300
chr2B
79.443
467
73
16
1064
1516
771160311
771159854
4.450000e-80
309.0
13
TraesCS2A01G104300
chr4A
98.274
811
14
0
1
811
16550968
16550158
0.000000e+00
1421.0
14
TraesCS2A01G104300
chr4A
74.274
999
197
43
1054
2016
45149893
45148919
2.600000e-97
366.0
15
TraesCS2A01G104300
chr4A
90.244
82
7
1
3332
3413
47742531
47742611
6.260000e-19
106.0
16
TraesCS2A01G104300
chr3A
97.660
812
15
2
1
812
44810572
44811379
0.000000e+00
1391.0
17
TraesCS2A01G104300
chr3A
95.544
763
29
3
4
765
390992851
390992093
0.000000e+00
1216.0
18
TraesCS2A01G104300
chr3A
97.833
600
13
0
1
600
289017453
289016854
0.000000e+00
1037.0
19
TraesCS2A01G104300
chr3A
97.833
600
13
0
1
600
289025589
289024990
0.000000e+00
1037.0
20
TraesCS2A01G104300
chr3A
98.558
208
3
0
604
811
289016825
289016618
7.230000e-98
368.0
21
TraesCS2A01G104300
chr5A
98.705
695
9
0
3883
4577
570478755
570479449
0.000000e+00
1234.0
22
TraesCS2A01G104300
chr5A
96.729
214
7
0
3718
3931
570478549
570478762
1.570000e-94
357.0
23
TraesCS2A01G104300
chr5A
100.000
85
0
0
3614
3698
564353832
564353748
1.700000e-34
158.0
24
TraesCS2A01G104300
chr5A
98.000
50
1
0
3614
3663
570478503
570478552
2.270000e-13
87.9
25
TraesCS2A01G104300
chrUn
97.833
600
13
0
1
600
288418886
288418287
0.000000e+00
1037.0
26
TraesCS2A01G104300
chrUn
88.913
469
44
7
4111
4577
96551843
96552305
5.140000e-159
571.0
27
TraesCS2A01G104300
chr5B
92.416
712
35
11
3883
4577
92571293
92572002
0.000000e+00
998.0
28
TraesCS2A01G104300
chr5B
94.062
320
16
3
3614
3931
92570982
92571300
2.480000e-132
483.0
29
TraesCS2A01G104300
chr6D
74.979
2378
397
122
1068
3333
19972457
19970166
0.000000e+00
913.0
30
TraesCS2A01G104300
chr6D
75.717
1849
339
67
1067
2862
16865447
16863656
0.000000e+00
826.0
31
TraesCS2A01G104300
chr6D
75.065
1929
330
79
885
2710
20399865
20401745
0.000000e+00
758.0
32
TraesCS2A01G104300
chr6D
75.912
1042
204
34
1039
2059
19714823
19713808
1.480000e-134
490.0
33
TraesCS2A01G104300
chr6D
92.727
55
4
0
2205
2259
20141294
20141240
3.800000e-11
80.5
34
TraesCS2A01G104300
chr4B
91.718
652
42
7
4
652
347549757
347549115
0.000000e+00
894.0
35
TraesCS2A01G104300
chr6B
75.318
1730
317
68
1040
2706
33737799
33736117
0.000000e+00
728.0
36
TraesCS2A01G104300
chr6B
75.702
1424
265
50
885
2265
34856604
34857989
4.990000e-179
638.0
37
TraesCS2A01G104300
chr6B
78.692
535
87
16
2343
2862
33736112
33735590
9.490000e-87
331.0
38
TraesCS2A01G104300
chr6B
87.755
98
4
4
3328
3417
8403545
8403642
1.740000e-19
108.0
39
TraesCS2A01G104300
chr6B
82.727
110
10
6
2206
2312
36138753
36138856
6.310000e-14
89.8
40
TraesCS2A01G104300
chr1A
74.747
1877
303
94
1039
2859
557138672
557140433
0.000000e+00
682.0
41
TraesCS2A01G104300
chr1A
88.273
469
46
8
4111
4577
461968019
461967558
1.860000e-153
553.0
42
TraesCS2A01G104300
chr6A
74.159
1873
333
91
1040
2841
69361730
69359938
4.990000e-179
638.0
43
TraesCS2A01G104300
chr6A
76.452
1240
229
42
1039
2263
19611706
19610515
8.420000e-172
614.0
44
TraesCS2A01G104300
chr6A
92.727
55
4
0
2205
2259
20203151
20203097
3.800000e-11
80.5
45
TraesCS2A01G104300
chr4D
85.269
577
65
18
4009
4577
459190009
459190573
1.100000e-160
577.0
46
TraesCS2A01G104300
chr4D
91.463
82
6
1
3332
3413
416070709
416070629
1.350000e-20
111.0
47
TraesCS2A01G104300
chr4D
88.764
89
3
4
3333
3414
261827582
261827494
8.100000e-18
102.0
48
TraesCS2A01G104300
chr7D
84.749
577
68
18
4009
4577
69947152
69947716
1.110000e-155
560.0
49
TraesCS2A01G104300
chr7B
84.000
575
69
19
4013
4577
551486049
551485488
8.720000e-147
531.0
50
TraesCS2A01G104300
chr3B
86.308
409
32
15
3610
3995
564171657
564172064
1.520000e-114
424.0
51
TraesCS2A01G104300
chr3B
90.449
178
14
3
3991
4167
564172098
564172273
9.900000e-57
231.0
52
TraesCS2A01G104300
chr7A
80.357
168
30
1
3615
3779
7966005
7965838
1.730000e-24
124.0
53
TraesCS2A01G104300
chr7A
79.762
168
31
1
3615
3779
8105223
8105056
8.040000e-23
119.0
54
TraesCS2A01G104300
chr5D
89.773
88
1
3
3333
3412
329276201
329276288
6.260000e-19
106.0
55
TraesCS2A01G104300
chr3D
86.869
99
5
4
3333
3423
384726625
384726723
2.250000e-18
104.0
56
TraesCS2A01G104300
chr3D
86.000
100
5
4
3326
3417
600605045
600605143
1.050000e-16
99.0
57
TraesCS2A01G104300
chr3D
100.000
29
0
0
783
811
90226483
90226511
2.000000e-03
54.7
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
TraesCS2A01G104300
chr2A
57820660
57825236
4576
False
8453.000000
8453
100.000000
1
4577
1
chr2A.!!$F1
4576
1
TraesCS2A01G104300
chr2D
56192785
56195606
2821
False
4224.000000
4224
93.842000
814
3615
1
chr2D.!!$F2
2801
2
TraesCS2A01G104300
chr2D
330880872
330881879
1007
True
649.500000
813
90.713500
3614
4577
2
chr2D.!!$R3
963
3
TraesCS2A01G104300
chr2B
88926107
88928715
2608
False
1318.000000
3042
93.685000
871
3615
3
chr2B.!!$F1
2744
4
TraesCS2A01G104300
chr4A
16550158
16550968
810
True
1421.000000
1421
98.274000
1
811
1
chr4A.!!$R1
810
5
TraesCS2A01G104300
chr4A
45148919
45149893
974
True
366.000000
366
74.274000
1054
2016
1
chr4A.!!$R2
962
6
TraesCS2A01G104300
chr3A
44810572
44811379
807
False
1391.000000
1391
97.660000
1
812
1
chr3A.!!$F1
811
7
TraesCS2A01G104300
chr3A
390992093
390992851
758
True
1216.000000
1216
95.544000
4
765
1
chr3A.!!$R2
761
8
TraesCS2A01G104300
chr3A
289024990
289025589
599
True
1037.000000
1037
97.833000
1
600
1
chr3A.!!$R1
599
9
TraesCS2A01G104300
chr3A
289016618
289017453
835
True
702.500000
1037
98.195500
1
811
2
chr3A.!!$R3
810
10
TraesCS2A01G104300
chr5A
570478503
570479449
946
False
559.633333
1234
97.811333
3614
4577
3
chr5A.!!$F1
963
11
TraesCS2A01G104300
chrUn
288418287
288418886
599
True
1037.000000
1037
97.833000
1
600
1
chrUn.!!$R1
599
12
TraesCS2A01G104300
chr5B
92570982
92572002
1020
False
740.500000
998
93.239000
3614
4577
2
chr5B.!!$F1
963
13
TraesCS2A01G104300
chr6D
19970166
19972457
2291
True
913.000000
913
74.979000
1068
3333
1
chr6D.!!$R3
2265
14
TraesCS2A01G104300
chr6D
16863656
16865447
1791
True
826.000000
826
75.717000
1067
2862
1
chr6D.!!$R1
1795
15
TraesCS2A01G104300
chr6D
20399865
20401745
1880
False
758.000000
758
75.065000
885
2710
1
chr6D.!!$F1
1825
16
TraesCS2A01G104300
chr6D
19713808
19714823
1015
True
490.000000
490
75.912000
1039
2059
1
chr6D.!!$R2
1020
17
TraesCS2A01G104300
chr4B
347549115
347549757
642
True
894.000000
894
91.718000
4
652
1
chr4B.!!$R1
648
18
TraesCS2A01G104300
chr6B
34856604
34857989
1385
False
638.000000
638
75.702000
885
2265
1
chr6B.!!$F2
1380
19
TraesCS2A01G104300
chr6B
33735590
33737799
2209
True
529.500000
728
77.005000
1040
2862
2
chr6B.!!$R1
1822
20
TraesCS2A01G104300
chr1A
557138672
557140433
1761
False
682.000000
682
74.747000
1039
2859
1
chr1A.!!$F1
1820
21
TraesCS2A01G104300
chr6A
69359938
69361730
1792
True
638.000000
638
74.159000
1040
2841
1
chr6A.!!$R3
1801
22
TraesCS2A01G104300
chr6A
19610515
19611706
1191
True
614.000000
614
76.452000
1039
2263
1
chr6A.!!$R1
1224
23
TraesCS2A01G104300
chr4D
459190009
459190573
564
False
577.000000
577
85.269000
4009
4577
1
chr4D.!!$F1
568
24
TraesCS2A01G104300
chr7D
69947152
69947716
564
False
560.000000
560
84.749000
4009
4577
1
chr7D.!!$F1
568
25
TraesCS2A01G104300
chr7B
551485488
551486049
561
True
531.000000
531
84.000000
4013
4577
1
chr7B.!!$R1
564
26
TraesCS2A01G104300
chr3B
564171657
564172273
616
False
327.500000
424
88.378500
3610
4167
2
chr3B.!!$F1
557
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.