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
TraesCS1A01G068900
chr1A
100.000
3791
0
0
1
3791
50541079
50537289
0.000000e+00
7001.0
1
TraesCS1A01G068900
chr1A
97.797
2451
48
2
509
2958
589112791
589115236
0.000000e+00
4222.0
2
TraesCS1A01G068900
chr1A
94.915
177
7
2
1
175
544170784
544170960
3.730000e-70
276.0
3
TraesCS1A01G068900
chr1A
94.318
176
9
1
1
175
444429460
444429635
6.240000e-68
268.0
4
TraesCS1A01G068900
chr1A
75.591
254
37
14
1831
2080
521671854
521671622
6.700000e-18
102.0
5
TraesCS1A01G068900
chr4B
92.362
2998
161
36
4
2957
58970446
58973419
0.000000e+00
4205.0
6
TraesCS1A01G068900
chr4B
80.348
748
85
29
2956
3655
457871852
457872585
9.390000e-141
510.0
7
TraesCS1A01G068900
chr7B
94.772
2257
94
7
707
2959
743663367
743661131
0.000000e+00
3493.0
8
TraesCS1A01G068900
chr7B
84.581
454
46
12
65
505
743663805
743663363
2.710000e-116
429.0
9
TraesCS1A01G068900
chr1B
93.683
2248
79
15
753
2956
667284154
667286382
0.000000e+00
3306.0
10
TraesCS1A01G068900
chr1B
81.095
767
81
27
2952
3668
491728874
491729626
4.280000e-154
555.0
11
TraesCS1A01G068900
chr1B
80.341
763
87
26
2956
3668
161314466
161315215
1.560000e-143
520.0
12
TraesCS1A01G068900
chr7A
97.460
1181
17
4
1778
2957
15675975
15677143
0.000000e+00
2002.0
13
TraesCS1A01G068900
chr7A
99.137
1043
8
1
714
1755
15674937
15675979
0.000000e+00
1875.0
14
TraesCS1A01G068900
chr7A
96.267
643
11
5
1
635
15668756
15669393
0.000000e+00
1042.0
15
TraesCS1A01G068900
chr7A
97.778
90
2
0
631
720
15674712
15674801
5.070000e-34
156.0
16
TraesCS1A01G068900
chr4A
95.018
843
21
2
2969
3791
65656039
65655198
0.000000e+00
1304.0
17
TraesCS1A01G068900
chr4A
95.455
176
7
1
1
175
430273630
430273455
2.880000e-71
279.0
18
TraesCS1A01G068900
chr4A
92.655
177
11
2
1
175
543404681
543404505
1.750000e-63
254.0
19
TraesCS1A01G068900
chr4A
80.297
269
40
8
1
257
690247254
690246987
1.390000e-44
191.0
20
TraesCS1A01G068900
chr5D
89.524
525
47
5
2450
2967
560484109
560484632
0.000000e+00
658.0
21
TraesCS1A01G068900
chr5D
83.088
136
16
2
1618
1753
501504090
501503962
2.390000e-22
117.0
22
TraesCS1A01G068900
chr3B
80.183
767
83
31
2956
3668
42267613
42268364
9.390000e-141
510.0
23
TraesCS1A01G068900
chr6B
80.267
750
83
29
2971
3668
95573136
95572400
4.370000e-139
505.0
24
TraesCS1A01G068900
chr6B
87.069
116
10
5
2970
3085
461154828
461154718
3.980000e-25
126.0
25
TraesCS1A01G068900
chr2D
86.429
420
48
4
2544
2959
23162390
23162804
5.770000e-123
451.0
26
TraesCS1A01G068900
chr3D
85.882
425
51
4
2539
2959
589558498
589558079
9.660000e-121
444.0
27
TraesCS1A01G068900
chr3D
84.969
326
34
7
3346
3668
15453747
15454060
2.200000e-82
316.0
28
TraesCS1A01G068900
chr5B
84.742
426
55
5
2539
2960
280594433
280594014
5.860000e-113
418.0
29
TraesCS1A01G068900
chr5B
76.127
377
29
19
1620
1956
633142923
633143278
1.420000e-29
141.0
30
TraesCS1A01G068900
chr7D
75.658
760
124
39
1053
1761
476109821
476110570
4.720000e-84
322.0
31
TraesCS1A01G068900
chr7D
74.307
541
91
30
1053
1550
49288339
49287804
6.470000e-43
185.0
32
TraesCS1A01G068900
chr7D
74.307
541
91
30
1053
1550
49309888
49309353
6.470000e-43
185.0
33
TraesCS1A01G068900
chr7D
89.344
122
12
1
2956
3076
72067468
72067589
6.560000e-33
152.0
34
TraesCS1A01G068900
chr7D
83.217
143
16
4
1053
1189
593881739
593881879
1.430000e-24
124.0
35
TraesCS1A01G068900
chr4D
80.244
410
46
10
2969
3352
295417317
295417717
3.730000e-70
276.0
36
TraesCS1A01G068900
chrUn
78.870
407
69
10
1349
1745
69739359
69738960
3.760000e-65
259.0
37
TraesCS1A01G068900
chr3A
82.132
319
41
6
3351
3668
731513677
731513374
3.760000e-65
259.0
38
TraesCS1A01G068900
chr2A
77.860
271
48
9
1
261
192132419
192132151
1.410000e-34
158.0
39
TraesCS1A01G068900
chr5A
80.882
136
19
6
1618
1753
599487118
599486990
2.410000e-17
100.0
40
TraesCS1A01G068900
chr5A
75.862
145
20
7
1609
1753
625702704
625702833
4.090000e-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
TraesCS1A01G068900
chr1A
50537289
50541079
3790
True
7001.000000
7001
100.0000
1
3791
1
chr1A.!!$R1
3790
1
TraesCS1A01G068900
chr1A
589112791
589115236
2445
False
4222.000000
4222
97.7970
509
2958
1
chr1A.!!$F3
2449
2
TraesCS1A01G068900
chr4B
58970446
58973419
2973
False
4205.000000
4205
92.3620
4
2957
1
chr4B.!!$F1
2953
3
TraesCS1A01G068900
chr4B
457871852
457872585
733
False
510.000000
510
80.3480
2956
3655
1
chr4B.!!$F2
699
4
TraesCS1A01G068900
chr7B
743661131
743663805
2674
True
1961.000000
3493
89.6765
65
2959
2
chr7B.!!$R1
2894
5
TraesCS1A01G068900
chr1B
667284154
667286382
2228
False
3306.000000
3306
93.6830
753
2956
1
chr1B.!!$F3
2203
6
TraesCS1A01G068900
chr1B
491728874
491729626
752
False
555.000000
555
81.0950
2952
3668
1
chr1B.!!$F2
716
7
TraesCS1A01G068900
chr1B
161314466
161315215
749
False
520.000000
520
80.3410
2956
3668
1
chr1B.!!$F1
712
8
TraesCS1A01G068900
chr7A
15674712
15677143
2431
False
1344.333333
2002
98.1250
631
2957
3
chr7A.!!$F2
2326
9
TraesCS1A01G068900
chr7A
15668756
15669393
637
False
1042.000000
1042
96.2670
1
635
1
chr7A.!!$F1
634
10
TraesCS1A01G068900
chr4A
65655198
65656039
841
True
1304.000000
1304
95.0180
2969
3791
1
chr4A.!!$R1
822
11
TraesCS1A01G068900
chr5D
560484109
560484632
523
False
658.000000
658
89.5240
2450
2967
1
chr5D.!!$F1
517
12
TraesCS1A01G068900
chr3B
42267613
42268364
751
False
510.000000
510
80.1830
2956
3668
1
chr3B.!!$F1
712
13
TraesCS1A01G068900
chr6B
95572400
95573136
736
True
505.000000
505
80.2670
2971
3668
1
chr6B.!!$R1
697
14
TraesCS1A01G068900
chr7D
476109821
476110570
749
False
322.000000
322
75.6580
1053
1761
1
chr7D.!!$F2
708
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.