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
TraesCS3B01G167700
chr3B
100.000
2410
0
0
1
2410
168141422
168139013
0.000000e+00
4451
1
TraesCS3B01G167700
chr3B
92.802
514
34
3
427
938
740109527
740109015
0.000000e+00
741
2
TraesCS3B01G167700
chr3B
97.045
440
9
3
4
442
740134384
740133948
0.000000e+00
737
3
TraesCS3B01G167700
chr3B
77.124
306
35
19
1478
1782
168146594
168146323
6.940000e-31
145
4
TraesCS3B01G167700
chr5A
99.152
943
8
0
1
943
580486727
580487669
0.000000e+00
1698
5
TraesCS3B01G167700
chr5B
99.254
938
7
0
1
938
6980660
6979723
0.000000e+00
1694
6
TraesCS3B01G167700
chr4B
98.825
936
11
0
1
936
156062257
156061322
0.000000e+00
1668
7
TraesCS3B01G167700
chr7A
94.866
935
38
4
4
938
635303471
635302547
0.000000e+00
1452
8
TraesCS3B01G167700
chr1A
94.872
936
37
5
4
938
570617924
570616999
0.000000e+00
1452
9
TraesCS3B01G167700
chr1B
96.756
863
27
1
1
863
58018837
58019698
0.000000e+00
1437
10
TraesCS3B01G167700
chr1B
89.041
657
47
18
978
1629
610560742
610561378
0.000000e+00
791
11
TraesCS3B01G167700
chr1B
87.318
686
51
25
966
1629
607429565
607428894
0.000000e+00
752
12
TraesCS3B01G167700
chr1B
87.406
667
51
27
975
1629
608053861
608053216
0.000000e+00
736
13
TraesCS3B01G167700
chr1B
85.640
578
55
24
1066
1629
608355308
608354745
1.240000e-162
582
14
TraesCS3B01G167700
chr3D
90.314
1115
59
21
936
2045
114883168
114882098
0.000000e+00
1415
15
TraesCS3B01G167700
chr3D
97.275
367
9
1
2044
2410
114882139
114881774
2.630000e-174
621
16
TraesCS3B01G167700
chr3D
89.209
139
11
3
1647
1782
114886349
114886212
1.150000e-38
171
17
TraesCS3B01G167700
chr3A
86.990
1153
86
32
936
2045
111106261
111105130
0.000000e+00
1240
18
TraesCS3B01G167700
chr3A
80.311
386
38
12
2044
2410
111105170
111104804
8.550000e-65
257
19
TraesCS3B01G167700
chr6A
89.417
926
50
18
936
1817
67142157
67141236
0.000000e+00
1123
20
TraesCS3B01G167700
chr6A
88.714
381
27
7
2044
2410
67141174
67140796
3.650000e-123
451
21
TraesCS3B01G167700
chr1D
88.462
702
55
19
936
1629
446437040
446437723
0.000000e+00
824
22
TraesCS3B01G167700
chr1D
88.106
681
44
21
966
1629
355825263
355825923
0.000000e+00
774
23
TraesCS3B01G167700
chr1D
96.861
446
12
2
972
1416
446558456
446558900
0.000000e+00
745
24
TraesCS3B01G167700
chr1D
90.909
110
6
3
1523
1629
445385151
445385043
6.940000e-31
145
25
TraesCS3B01G167700
chr2A
93.122
567
29
4
375
938
654669719
654670278
0.000000e+00
822
26
TraesCS3B01G167700
chr6D
94.007
534
25
3
936
1462
47812313
47812846
0.000000e+00
802
27
TraesCS3B01G167700
chr6D
88.378
370
26
9
2044
2403
47812986
47813348
1.710000e-116
429
28
TraesCS3B01G167700
chrUn
96.614
443
11
3
1
442
280091664
280092103
0.000000e+00
732
29
TraesCS3B01G167700
chrUn
95.964
446
18
0
493
938
389205956
389206401
0.000000e+00
725
30
TraesCS3B01G167700
chrUn
93.648
488
21
4
4
491
473163559
473163082
0.000000e+00
721
31
TraesCS3B01G167700
chr2B
87.183
671
51
23
972
1636
161026441
161027082
0.000000e+00
730
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
TraesCS3B01G167700
chr3B
168139013
168141422
2409
True
4451.000000
4451
100.0000
1
2410
1
chr3B.!!$R1
2409
1
TraesCS3B01G167700
chr3B
740109015
740109527
512
True
741.000000
741
92.8020
427
938
1
chr3B.!!$R3
511
2
TraesCS3B01G167700
chr5A
580486727
580487669
942
False
1698.000000
1698
99.1520
1
943
1
chr5A.!!$F1
942
3
TraesCS3B01G167700
chr5B
6979723
6980660
937
True
1694.000000
1694
99.2540
1
938
1
chr5B.!!$R1
937
4
TraesCS3B01G167700
chr4B
156061322
156062257
935
True
1668.000000
1668
98.8250
1
936
1
chr4B.!!$R1
935
5
TraesCS3B01G167700
chr7A
635302547
635303471
924
True
1452.000000
1452
94.8660
4
938
1
chr7A.!!$R1
934
6
TraesCS3B01G167700
chr1A
570616999
570617924
925
True
1452.000000
1452
94.8720
4
938
1
chr1A.!!$R1
934
7
TraesCS3B01G167700
chr1B
58018837
58019698
861
False
1437.000000
1437
96.7560
1
863
1
chr1B.!!$F1
862
8
TraesCS3B01G167700
chr1B
610560742
610561378
636
False
791.000000
791
89.0410
978
1629
1
chr1B.!!$F2
651
9
TraesCS3B01G167700
chr1B
607428894
607429565
671
True
752.000000
752
87.3180
966
1629
1
chr1B.!!$R1
663
10
TraesCS3B01G167700
chr1B
608053216
608053861
645
True
736.000000
736
87.4060
975
1629
1
chr1B.!!$R2
654
11
TraesCS3B01G167700
chr1B
608354745
608355308
563
True
582.000000
582
85.6400
1066
1629
1
chr1B.!!$R3
563
12
TraesCS3B01G167700
chr3D
114881774
114886349
4575
True
735.666667
1415
92.2660
936
2410
3
chr3D.!!$R1
1474
13
TraesCS3B01G167700
chr3A
111104804
111106261
1457
True
748.500000
1240
83.6505
936
2410
2
chr3A.!!$R1
1474
14
TraesCS3B01G167700
chr6A
67140796
67142157
1361
True
787.000000
1123
89.0655
936
2410
2
chr6A.!!$R1
1474
15
TraesCS3B01G167700
chr1D
446437040
446437723
683
False
824.000000
824
88.4620
936
1629
1
chr1D.!!$F2
693
16
TraesCS3B01G167700
chr1D
355825263
355825923
660
False
774.000000
774
88.1060
966
1629
1
chr1D.!!$F1
663
17
TraesCS3B01G167700
chr2A
654669719
654670278
559
False
822.000000
822
93.1220
375
938
1
chr2A.!!$F1
563
18
TraesCS3B01G167700
chr6D
47812313
47813348
1035
False
615.500000
802
91.1925
936
2403
2
chr6D.!!$F1
1467
19
TraesCS3B01G167700
chr2B
161026441
161027082
641
False
730.000000
730
87.1830
972
1636
1
chr2B.!!$F1
664
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.