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
TraesCS7B01G274000
chr7B
100.000
2549
0
0
1
2549
503342316
503344864
0.000000e+00
4708
1
TraesCS7B01G274000
chr7B
93.154
1373
63
11
605
1953
54520694
54519329
0.000000e+00
1986
2
TraesCS7B01G274000
chr7B
97.162
599
16
1
2
599
120521140
120521738
0.000000e+00
1011
3
TraesCS7B01G274000
chr7B
97.157
598
17
0
2
599
230952804
230953401
0.000000e+00
1011
4
TraesCS7B01G274000
chr7B
94.975
597
30
0
1953
2549
54518754
54518158
0.000000e+00
937
5
TraesCS7B01G274000
chr7B
94.807
597
30
1
1953
2549
503451475
503452070
0.000000e+00
929
6
TraesCS7B01G274000
chr7B
94.482
598
32
1
1953
2549
129567443
129566846
0.000000e+00
920
7
TraesCS7B01G274000
chr2D
94.199
1379
55
4
600
1953
610930657
610932035
0.000000e+00
2080
8
TraesCS7B01G274000
chr2D
93.388
242
12
3
1715
1953
435213918
435214158
3.120000e-94
355
9
TraesCS7B01G274000
chr2D
93.004
243
12
4
1715
1953
299993296
299993537
1.450000e-92
350
10
TraesCS7B01G274000
chr4A
93.198
1382
62
9
595
1949
738255679
738257055
0.000000e+00
2002
11
TraesCS7B01G274000
chr4A
93.438
1341
53
12
636
1949
598584614
598583282
0.000000e+00
1956
12
TraesCS7B01G274000
chr4A
92.975
242
12
5
1715
1953
603145878
603145639
5.220000e-92
348
13
TraesCS7B01G274000
chr6B
92.934
1387
73
3
592
1953
527993585
527992199
0.000000e+00
1995
14
TraesCS7B01G274000
chr6B
93.854
602
32
3
1953
2549
271093705
271093104
0.000000e+00
902
15
TraesCS7B01G274000
chr1B
92.899
1380
72
4
600
1953
582666189
582664810
0.000000e+00
1982
16
TraesCS7B01G274000
chr1B
96.990
598
18
0
2
599
263605734
263605137
0.000000e+00
1005
17
TraesCS7B01G274000
chr1B
96.990
598
18
0
2
599
355016384
355015787
0.000000e+00
1005
18
TraesCS7B01G274000
chr1B
94.807
597
30
1
1953
2549
575858376
575857781
0.000000e+00
929
19
TraesCS7B01G274000
chr1B
94.186
602
30
2
1953
2549
130647139
130647740
0.000000e+00
913
20
TraesCS7B01G274000
chr1B
93.854
602
32
3
1953
2549
616701883
616701282
0.000000e+00
902
21
TraesCS7B01G274000
chr1B
94.088
592
35
0
1958
2549
372944966
372944375
0.000000e+00
900
22
TraesCS7B01G274000
chr4B
92.754
1380
76
3
598
1953
534922953
534921574
0.000000e+00
1973
23
TraesCS7B01G274000
chr4B
92.442
1376
80
4
600
1953
546331516
546330143
0.000000e+00
1943
24
TraesCS7B01G274000
chr4B
94.027
1038
41
3
937
1953
656537814
656536777
0.000000e+00
1554
25
TraesCS7B01G274000
chr4B
96.990
598
18
0
2
599
286005241
286005838
0.000000e+00
1005
26
TraesCS7B01G274000
chr4B
95.477
597
27
0
1953
2549
642721451
642720855
0.000000e+00
953
27
TraesCS7B01G274000
chr4B
94.640
597
32
0
1953
2549
100009642
100009046
0.000000e+00
926
28
TraesCS7B01G274000
chr4B
94.305
597
34
0
1953
2549
656536206
656535610
0.000000e+00
915
29
TraesCS7B01G274000
chr4B
94.137
597
35
0
1953
2549
80651699
80651103
0.000000e+00
909
30
TraesCS7B01G274000
chr4B
93.970
597
36
0
1953
2549
657231530
657230934
0.000000e+00
904
31
TraesCS7B01G274000
chr4B
93.802
597
37
0
1953
2549
648879449
648878853
0.000000e+00
898
32
TraesCS7B01G274000
chr4B
93.667
600
35
2
1953
2549
89563717
89564316
0.000000e+00
894
33
TraesCS7B01G274000
chr4B
93.478
598
39
0
1952
2549
585996882
585997479
0.000000e+00
889
34
TraesCS7B01G274000
chr3B
92.213
1387
76
7
595
1953
792939413
792940795
0.000000e+00
1934
35
TraesCS7B01G274000
chr3B
94.472
597
32
1
1953
2549
804663007
804663602
0.000000e+00
918
36
TraesCS7B01G274000
chrUn
91.737
1416
60
23
595
1953
60558704
60560119
0.000000e+00
1914
37
TraesCS7B01G274000
chrUn
92.664
1036
53
4
937
1949
37355410
37354375
0.000000e+00
1471
38
TraesCS7B01G274000
chrUn
92.664
1036
53
4
937
1949
287430937
287429902
0.000000e+00
1471
39
TraesCS7B01G274000
chrUn
93.189
602
36
3
1953
2549
60560698
60561299
0.000000e+00
880
40
TraesCS7B01G274000
chrUn
91.820
599
47
1
1953
2549
37353797
37353199
0.000000e+00
833
41
TraesCS7B01G274000
chrUn
91.820
599
47
1
1953
2549
287429324
287428726
0.000000e+00
833
42
TraesCS7B01G274000
chrUn
92.105
570
36
2
1987
2548
93724282
93723714
0.000000e+00
795
43
TraesCS7B01G274000
chrUn
92.091
569
34
3
1988
2548
302376021
302376586
0.000000e+00
791
44
TraesCS7B01G274000
chrUn
91.449
573
33
5
1987
2548
88422502
88423069
0.000000e+00
773
45
TraesCS7B01G274000
chrUn
91.274
573
34
5
1987
2548
284637032
284637599
0.000000e+00
767
46
TraesCS7B01G274000
chrUn
91.274
573
34
5
1987
2548
443236731
443236164
0.000000e+00
767
47
TraesCS7B01G274000
chrUn
90.925
573
36
5
1987
2548
231574982
231575549
0.000000e+00
756
48
TraesCS7B01G274000
chrUn
90.409
563
39
8
1987
2548
43127339
43126791
0.000000e+00
726
49
TraesCS7B01G274000
chrUn
92.593
243
12
5
1715
1953
93725161
93724921
6.750000e-91
344
50
TraesCS7B01G274000
chrUn
91.770
243
14
5
1715
1953
175763458
175763698
1.460000e-87
333
51
TraesCS7B01G274000
chrUn
91.770
243
14
6
1715
1953
353552469
353552229
1.460000e-87
333
52
TraesCS7B01G274000
chrUn
91.736
242
16
3
1715
1953
368601967
368602207
1.460000e-87
333
53
TraesCS7B01G274000
chrUn
95.631
206
8
1
1749
1953
302375245
302375450
1.890000e-86
329
54
TraesCS7B01G274000
chrUn
91.701
241
13
6
1716
1951
88505651
88505889
6.800000e-86
327
55
TraesCS7B01G274000
chrUn
91.358
243
15
5
1715
1953
406119632
406119872
6.800000e-86
327
56
TraesCS7B01G274000
chr5B
97.492
598
15
0
2
599
166970159
166969562
0.000000e+00
1022
57
TraesCS7B01G274000
chr5B
97.329
599
14
2
2
599
635961513
635960916
0.000000e+00
1016
58
TraesCS7B01G274000
chr5B
97.157
598
17
0
2
599
377466413
377465816
0.000000e+00
1011
59
TraesCS7B01G274000
chr2B
96.833
600
15
3
2
599
364979591
364980188
0.000000e+00
1000
60
TraesCS7B01G274000
chr2B
95.310
597
28
0
1953
2549
62452909
62453505
0.000000e+00
948
61
TraesCS7B01G274000
chr2B
94.975
597
30
0
1953
2549
666073796
666073200
0.000000e+00
937
62
TraesCS7B01G274000
chr6D
92.105
570
32
5
1987
2548
52519527
52518963
0.000000e+00
791
63
TraesCS7B01G274000
chr6D
92.562
242
14
3
1715
1953
277566066
277565826
6.750000e-91
344
64
TraesCS7B01G274000
chr6D
92.181
243
14
4
1715
1953
52520403
52520162
3.140000e-89
339
65
TraesCS7B01G274000
chr6D
92.181
243
14
4
1715
1953
109964552
109964793
3.140000e-89
339
66
TraesCS7B01G274000
chr5D
92.077
568
32
5
1987
2546
324811521
324812083
0.000000e+00
787
67
TraesCS7B01G274000
chr5D
91.930
570
33
5
1987
2548
559992019
559991455
0.000000e+00
785
68
TraesCS7B01G274000
chr5D
93.004
243
12
4
1715
1953
482330823
482330582
1.450000e-92
350
69
TraesCS7B01G274000
chr5D
92.975
242
12
5
1715
1953
336263967
336264206
5.220000e-92
348
70
TraesCS7B01G274000
chr5D
92.562
242
14
4
1715
1953
336309630
336309390
6.750000e-91
344
71
TraesCS7B01G274000
chr5D
92.181
243
14
4
1715
1953
324810634
324810875
3.140000e-89
339
72
TraesCS7B01G274000
chr5D
92.181
243
14
4
1715
1953
559992904
559992663
3.140000e-89
339
73
TraesCS7B01G274000
chr1A
91.623
573
32
5
1987
2548
71841835
71842402
0.000000e+00
778
74
TraesCS7B01G274000
chr1A
91.449
573
33
5
1987
2548
72557070
72557637
0.000000e+00
773
75
TraesCS7B01G274000
chr7D
93.033
244
11
4
1715
1953
577660118
577659876
4.030000e-93
351
76
TraesCS7B01G274000
chr7D
92.623
244
12
6
1715
1953
604917259
604917501
1.880000e-91
346
77
TraesCS7B01G274000
chr7D
92.593
243
12
6
1715
1953
574725776
574725536
6.750000e-91
344
78
TraesCS7B01G274000
chr7A
92.975
242
13
4
1715
1953
112660534
112660294
1.450000e-92
350
79
TraesCS7B01G274000
chr3D
92.593
243
12
6
1715
1953
475107990
475108230
6.750000e-91
344
80
TraesCS7B01G274000
chr3D
92.213
244
13
5
1715
1953
410900936
410901178
8.730000e-90
340
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
TraesCS7B01G274000
chr7B
503342316
503344864
2548
False
4708.0
4708
100.0000
1
2549
1
chr7B.!!$F3
2548
1
TraesCS7B01G274000
chr7B
54518158
54520694
2536
True
1461.5
1986
94.0645
605
2549
2
chr7B.!!$R2
1944
2
TraesCS7B01G274000
chr7B
120521140
120521738
598
False
1011.0
1011
97.1620
2
599
1
chr7B.!!$F1
597
3
TraesCS7B01G274000
chr7B
230952804
230953401
597
False
1011.0
1011
97.1570
2
599
1
chr7B.!!$F2
597
4
TraesCS7B01G274000
chr7B
503451475
503452070
595
False
929.0
929
94.8070
1953
2549
1
chr7B.!!$F4
596
5
TraesCS7B01G274000
chr7B
129566846
129567443
597
True
920.0
920
94.4820
1953
2549
1
chr7B.!!$R1
596
6
TraesCS7B01G274000
chr2D
610930657
610932035
1378
False
2080.0
2080
94.1990
600
1953
1
chr2D.!!$F3
1353
7
TraesCS7B01G274000
chr4A
738255679
738257055
1376
False
2002.0
2002
93.1980
595
1949
1
chr4A.!!$F1
1354
8
TraesCS7B01G274000
chr4A
598583282
598584614
1332
True
1956.0
1956
93.4380
636
1949
1
chr4A.!!$R1
1313
9
TraesCS7B01G274000
chr6B
527992199
527993585
1386
True
1995.0
1995
92.9340
592
1953
1
chr6B.!!$R2
1361
10
TraesCS7B01G274000
chr6B
271093104
271093705
601
True
902.0
902
93.8540
1953
2549
1
chr6B.!!$R1
596
11
TraesCS7B01G274000
chr1B
582664810
582666189
1379
True
1982.0
1982
92.8990
600
1953
1
chr1B.!!$R5
1353
12
TraesCS7B01G274000
chr1B
263605137
263605734
597
True
1005.0
1005
96.9900
2
599
1
chr1B.!!$R1
597
13
TraesCS7B01G274000
chr1B
355015787
355016384
597
True
1005.0
1005
96.9900
2
599
1
chr1B.!!$R2
597
14
TraesCS7B01G274000
chr1B
575857781
575858376
595
True
929.0
929
94.8070
1953
2549
1
chr1B.!!$R4
596
15
TraesCS7B01G274000
chr1B
130647139
130647740
601
False
913.0
913
94.1860
1953
2549
1
chr1B.!!$F1
596
16
TraesCS7B01G274000
chr1B
616701282
616701883
601
True
902.0
902
93.8540
1953
2549
1
chr1B.!!$R6
596
17
TraesCS7B01G274000
chr1B
372944375
372944966
591
True
900.0
900
94.0880
1958
2549
1
chr1B.!!$R3
591
18
TraesCS7B01G274000
chr4B
534921574
534922953
1379
True
1973.0
1973
92.7540
598
1953
1
chr4B.!!$R3
1355
19
TraesCS7B01G274000
chr4B
546330143
546331516
1373
True
1943.0
1943
92.4420
600
1953
1
chr4B.!!$R4
1353
20
TraesCS7B01G274000
chr4B
656535610
656537814
2204
True
1234.5
1554
94.1660
937
2549
2
chr4B.!!$R8
1612
21
TraesCS7B01G274000
chr4B
286005241
286005838
597
False
1005.0
1005
96.9900
2
599
1
chr4B.!!$F2
597
22
TraesCS7B01G274000
chr4B
642720855
642721451
596
True
953.0
953
95.4770
1953
2549
1
chr4B.!!$R5
596
23
TraesCS7B01G274000
chr4B
100009046
100009642
596
True
926.0
926
94.6400
1953
2549
1
chr4B.!!$R2
596
24
TraesCS7B01G274000
chr4B
80651103
80651699
596
True
909.0
909
94.1370
1953
2549
1
chr4B.!!$R1
596
25
TraesCS7B01G274000
chr4B
657230934
657231530
596
True
904.0
904
93.9700
1953
2549
1
chr4B.!!$R7
596
26
TraesCS7B01G274000
chr4B
648878853
648879449
596
True
898.0
898
93.8020
1953
2549
1
chr4B.!!$R6
596
27
TraesCS7B01G274000
chr4B
89563717
89564316
599
False
894.0
894
93.6670
1953
2549
1
chr4B.!!$F1
596
28
TraesCS7B01G274000
chr4B
585996882
585997479
597
False
889.0
889
93.4780
1952
2549
1
chr4B.!!$F3
597
29
TraesCS7B01G274000
chr3B
792939413
792940795
1382
False
1934.0
1934
92.2130
595
1953
1
chr3B.!!$F1
1358
30
TraesCS7B01G274000
chr3B
804663007
804663602
595
False
918.0
918
94.4720
1953
2549
1
chr3B.!!$F2
596
31
TraesCS7B01G274000
chrUn
60558704
60561299
2595
False
1397.0
1914
92.4630
595
2549
2
chrUn.!!$F8
1954
32
TraesCS7B01G274000
chrUn
37353199
37355410
2211
True
1152.0
1471
92.2420
937
2549
2
chrUn.!!$R4
1612
33
TraesCS7B01G274000
chrUn
287428726
287430937
2211
True
1152.0
1471
92.2420
937
2549
2
chrUn.!!$R6
1612
34
TraesCS7B01G274000
chrUn
88422502
88423069
567
False
773.0
773
91.4490
1987
2548
1
chrUn.!!$F1
561
35
TraesCS7B01G274000
chrUn
284637032
284637599
567
False
767.0
767
91.2740
1987
2548
1
chrUn.!!$F5
561
36
TraesCS7B01G274000
chrUn
443236164
443236731
567
True
767.0
767
91.2740
1987
2548
1
chrUn.!!$R3
561
37
TraesCS7B01G274000
chrUn
231574982
231575549
567
False
756.0
756
90.9250
1987
2548
1
chrUn.!!$F4
561
38
TraesCS7B01G274000
chrUn
43126791
43127339
548
True
726.0
726
90.4090
1987
2548
1
chrUn.!!$R1
561
39
TraesCS7B01G274000
chrUn
93723714
93725161
1447
True
569.5
795
92.3490
1715
2548
2
chrUn.!!$R5
833
40
TraesCS7B01G274000
chrUn
302375245
302376586
1341
False
560.0
791
93.8610
1749
2548
2
chrUn.!!$F9
799
41
TraesCS7B01G274000
chr5B
166969562
166970159
597
True
1022.0
1022
97.4920
2
599
1
chr5B.!!$R1
597
42
TraesCS7B01G274000
chr5B
635960916
635961513
597
True
1016.0
1016
97.3290
2
599
1
chr5B.!!$R3
597
43
TraesCS7B01G274000
chr5B
377465816
377466413
597
True
1011.0
1011
97.1570
2
599
1
chr5B.!!$R2
597
44
TraesCS7B01G274000
chr2B
364979591
364980188
597
False
1000.0
1000
96.8330
2
599
1
chr2B.!!$F2
597
45
TraesCS7B01G274000
chr2B
62452909
62453505
596
False
948.0
948
95.3100
1953
2549
1
chr2B.!!$F1
596
46
TraesCS7B01G274000
chr2B
666073200
666073796
596
True
937.0
937
94.9750
1953
2549
1
chr2B.!!$R1
596
47
TraesCS7B01G274000
chr6D
52518963
52520403
1440
True
565.0
791
92.1430
1715
2548
2
chr6D.!!$R2
833
48
TraesCS7B01G274000
chr5D
324810634
324812083
1449
False
563.0
787
92.1290
1715
2546
2
chr5D.!!$F2
831
49
TraesCS7B01G274000
chr5D
559991455
559992904
1449
True
562.0
785
92.0555
1715
2548
2
chr5D.!!$R3
833
50
TraesCS7B01G274000
chr1A
71841835
71842402
567
False
778.0
778
91.6230
1987
2548
1
chr1A.!!$F1
561
51
TraesCS7B01G274000
chr1A
72557070
72557637
567
False
773.0
773
91.4490
1987
2548
1
chr1A.!!$F2
561
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.