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
TraesCS2A01G024100
chr2A
100.000
2551
0
0
1
2551
11689939
11692489
0.000000e+00
4674.0
1
TraesCS2A01G024100
chr2A
98.848
1042
6
2
562
1597
11649443
11650484
0.000000e+00
1853.0
2
TraesCS2A01G024100
chr2A
99.543
875
4
0
1677
2551
11650663
11651537
0.000000e+00
1594.0
3
TraesCS2A01G024100
chr2A
95.365
561
9
5
1
561
11666309
11666852
0.000000e+00
876.0
4
TraesCS2A01G024100
chr2A
91.444
561
46
2
1
561
18846321
18846879
0.000000e+00
769.0
5
TraesCS2A01G024100
chr2A
91.376
545
45
2
19
561
19399460
19400004
0.000000e+00
745.0
6
TraesCS2A01G024100
chr2A
92.593
378
27
1
3
380
18856569
18856945
2.230000e-150
542.0
7
TraesCS2A01G024100
chr2A
92.287
363
27
1
59
420
19380665
19381027
4.870000e-142
514.0
8
TraesCS2A01G024100
chr2A
89.444
360
37
1
22
380
20739701
20739342
1.080000e-123
453.0
9
TraesCS2A01G024100
chr2A
85.387
349
46
5
1
348
18810248
18809904
8.680000e-95
357.0
10
TraesCS2A01G024100
chr2A
86.562
320
30
9
240
556
19380893
19381202
8.740000e-90
340.0
11
TraesCS2A01G024100
chr2A
89.850
266
17
8
305
561
18856823
18857087
1.460000e-87
333.0
12
TraesCS2A01G024100
chr2A
83.959
293
37
7
286
569
20739483
20739192
3.230000e-69
272.0
13
TraesCS2A01G024100
chr2A
84.615
273
32
8
298
561
11954621
11954350
1.950000e-66
263.0
14
TraesCS2A01G024100
chr2D
88.868
1051
68
16
562
1597
10986138
10987154
0.000000e+00
1247.0
15
TraesCS2A01G024100
chr2D
84.698
745
75
19
855
1580
11029930
11030654
0.000000e+00
708.0
16
TraesCS2A01G024100
chr2D
83.673
343
33
9
1260
1597
11023122
11023446
4.120000e-78
302.0
17
TraesCS2A01G024100
chr2D
90.811
185
15
2
673
855
11029863
11030047
1.960000e-61
246.0
18
TraesCS2A01G024100
chr2D
85.246
244
17
5
911
1149
11022762
11022991
1.530000e-57
233.0
19
TraesCS2A01G024100
chr2D
87.395
119
11
1
853
967
10986320
10986438
1.590000e-27
134.0
20
TraesCS2A01G024100
chr2B
89.354
789
53
12
824
1587
16828594
16829376
0.000000e+00
963.0
21
TraesCS2A01G024100
chr2B
81.842
749
94
22
853
1589
16847446
16848164
2.190000e-165
592.0
22
TraesCS2A01G024100
chr2B
82.065
184
29
4
100
282
130964347
130964527
1.220000e-33
154.0
23
TraesCS2A01G024100
chrUn
84.923
849
85
18
765
1589
12174227
12175056
0.000000e+00
819.0
24
TraesCS2A01G024100
chrUn
84.362
697
66
24
911
1587
12171134
12171807
0.000000e+00
643.0
25
TraesCS2A01G024100
chrUn
86.136
339
26
9
911
1244
467992733
467993055
1.880000e-91
346.0
26
TraesCS2A01G024100
chrUn
90.000
120
10
2
737
855
12174314
12174432
1.220000e-33
154.0
27
TraesCS2A01G024100
chrUn
90.625
96
8
1
1608
1703
49432526
49432620
2.660000e-25
126.0
28
TraesCS2A01G024100
chr6A
97.603
292
7
0
2260
2551
498822837
498823128
3.790000e-138
501.0
29
TraesCS2A01G024100
chr6A
96.000
300
12
0
2252
2551
371769775
371770074
2.950000e-134
488.0
30
TraesCS2A01G024100
chr6A
83.835
266
29
10
298
559
611973215
611972960
9.120000e-60
241.0
31
TraesCS2A01G024100
chr6A
82.686
283
32
14
284
561
25358988
25359258
4.240000e-58
235.0
32
TraesCS2A01G024100
chr6A
83.271
269
30
11
298
561
611984880
611984622
1.530000e-57
233.0
33
TraesCS2A01G024100
chr5A
97.586
290
7
0
2262
2551
7268552
7268841
4.900000e-137
497.0
34
TraesCS2A01G024100
chr5A
97.586
290
7
0
2262
2551
614280372
614280661
4.900000e-137
497.0
35
TraesCS2A01G024100
chr4A
97.586
290
7
0
2262
2551
181210618
181210907
4.900000e-137
497.0
36
TraesCS2A01G024100
chr4A
97.586
290
7
0
2262
2551
479878479
479878190
4.900000e-137
497.0
37
TraesCS2A01G024100
chr3A
97.586
290
7
0
2262
2551
661546101
661546390
4.900000e-137
497.0
38
TraesCS2A01G024100
chr3A
97.251
291
8
0
2261
2551
388900518
388900228
6.340000e-136
494.0
39
TraesCS2A01G024100
chr3A
84.073
383
61
0
1875
2257
11828755
11829137
1.110000e-98
370.0
40
TraesCS2A01G024100
chr3A
90.114
263
26
0
1618
1880
676751108
676750846
2.430000e-90
342.0
41
TraesCS2A01G024100
chr7A
97.260
292
7
1
2261
2551
128508281
128507990
6.340000e-136
494.0
42
TraesCS2A01G024100
chr7A
83.733
375
59
2
1884
2257
51829395
51829022
1.120000e-93
353.0
43
TraesCS2A01G024100
chr7A
83.827
371
58
2
1884
2253
51870612
51870243
4.040000e-93
351.0
44
TraesCS2A01G024100
chr7A
77.073
205
39
6
1976
2178
17719408
17719606
7.460000e-21
111.0
45
TraesCS2A01G024100
chr1A
86.423
383
52
0
1875
2257
544918779
544918397
1.090000e-113
420.0
46
TraesCS2A01G024100
chr1B
90.813
283
24
2
1608
1889
629493890
629493609
6.660000e-101
377.0
47
TraesCS2A01G024100
chr1B
91.579
95
7
1
1608
1702
613028602
613028509
2.060000e-26
130.0
48
TraesCS2A01G024100
chr5B
82.677
381
61
5
1
379
310340142
310339765
1.460000e-87
333.0
49
TraesCS2A01G024100
chr5B
85.567
291
29
10
283
561
310103676
310103387
2.480000e-75
292.0
50
TraesCS2A01G024100
chr5B
84.536
291
32
10
283
561
310339908
310339619
2.500000e-70
276.0
51
TraesCS2A01G024100
chr3D
96.104
154
6
0
1727
1880
2525575
2525422
4.210000e-63
252.0
52
TraesCS2A01G024100
chr3D
93.617
141
8
1
1875
2014
2525066
2524926
2.570000e-50
209.0
53
TraesCS2A01G024100
chr6B
88.525
61
6
1
1642
1702
149619134
149619193
3.520000e-09
73.1
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
TraesCS2A01G024100
chr2A
11689939
11692489
2550
False
4674.000000
4674
100.000000
1
2551
1
chr2A.!!$F2
2550
1
TraesCS2A01G024100
chr2A
11649443
11651537
2094
False
1723.500000
1853
99.195500
562
2551
2
chr2A.!!$F5
1989
2
TraesCS2A01G024100
chr2A
11666309
11666852
543
False
876.000000
876
95.365000
1
561
1
chr2A.!!$F1
560
3
TraesCS2A01G024100
chr2A
18846321
18846879
558
False
769.000000
769
91.444000
1
561
1
chr2A.!!$F3
560
4
TraesCS2A01G024100
chr2A
19399460
19400004
544
False
745.000000
745
91.376000
19
561
1
chr2A.!!$F4
542
5
TraesCS2A01G024100
chr2A
18856569
18857087
518
False
437.500000
542
91.221500
3
561
2
chr2A.!!$F6
558
6
TraesCS2A01G024100
chr2A
19380665
19381202
537
False
427.000000
514
89.424500
59
556
2
chr2A.!!$F7
497
7
TraesCS2A01G024100
chr2A
20739192
20739701
509
True
362.500000
453
86.701500
22
569
2
chr2A.!!$R3
547
8
TraesCS2A01G024100
chr2D
10986138
10987154
1016
False
690.500000
1247
88.131500
562
1597
2
chr2D.!!$F1
1035
9
TraesCS2A01G024100
chr2D
11029863
11030654
791
False
477.000000
708
87.754500
673
1580
2
chr2D.!!$F3
907
10
TraesCS2A01G024100
chr2D
11022762
11023446
684
False
267.500000
302
84.459500
911
1597
2
chr2D.!!$F2
686
11
TraesCS2A01G024100
chr2B
16828594
16829376
782
False
963.000000
963
89.354000
824
1587
1
chr2B.!!$F1
763
12
TraesCS2A01G024100
chr2B
16847446
16848164
718
False
592.000000
592
81.842000
853
1589
1
chr2B.!!$F2
736
13
TraesCS2A01G024100
chrUn
12171134
12175056
3922
False
538.666667
819
86.428333
737
1589
3
chrUn.!!$F3
852
14
TraesCS2A01G024100
chr5B
310339619
310340142
523
True
304.500000
333
83.606500
1
561
2
chr5B.!!$R2
560
15
TraesCS2A01G024100
chr3D
2524926
2525575
649
True
230.500000
252
94.860500
1727
2014
2
chr3D.!!$R1
287
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.