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
TraesCS5A01G027600
chr5A
100.000
3485
0
0
1
3485
23611561
23608077
0.000000e+00
6436.0
1
TraesCS5A01G027600
chr5A
98.901
910
7
1
2579
3485
483276588
483275679
0.000000e+00
1622.0
2
TraesCS5A01G027600
chr5D
97.984
2580
35
3
1
2578
30617433
30619997
0.000000e+00
4460.0
3
TraesCS5A01G027600
chr3A
96.415
1590
47
5
1
1587
692345338
692346920
0.000000e+00
2612.0
4
TraesCS5A01G027600
chr3A
99.116
905
8
0
2581
3485
91017013
91016109
0.000000e+00
1628.0
5
TraesCS5A01G027600
chr3A
98.681
910
11
1
2576
3485
277503239
277502331
0.000000e+00
1613.0
6
TraesCS5A01G027600
chr3A
94.975
995
50
0
1584
2578
692347223
692348217
0.000000e+00
1561.0
7
TraesCS5A01G027600
chr3A
90.909
99
8
1
853
950
26493779
26493681
7.850000e-27
132.0
8
TraesCS5A01G027600
chr6D
95.424
1617
64
4
1
1615
98090515
98092123
0.000000e+00
2567.0
9
TraesCS5A01G027600
chr6D
89.157
166
18
0
2334
2499
16667595
16667760
1.270000e-49
207.0
10
TraesCS5A01G027600
chr3D
99.224
902
7
0
2584
3485
496780412
496779511
0.000000e+00
1628.0
11
TraesCS5A01G027600
chr3D
93.651
63
4
0
1
63
33324816
33324878
1.030000e-15
95.3
12
TraesCS5A01G027600
chr1D
99.011
910
6
1
2579
3485
223524579
223523670
0.000000e+00
1628.0
13
TraesCS5A01G027600
chr1D
98.900
909
10
0
2577
3485
94050649
94051557
0.000000e+00
1624.0
14
TraesCS5A01G027600
chr1D
98.897
907
10
0
2579
3485
493220713
493219807
0.000000e+00
1620.0
15
TraesCS5A01G027600
chr1D
81.307
979
113
23
1616
2578
407296331
407297255
0.000000e+00
730.0
16
TraesCS5A01G027600
chr1D
91.200
125
11
0
2446
2570
4538335
4538211
1.660000e-38
171.0
17
TraesCS5A01G027600
chr1D
93.651
63
4
0
1
63
484189118
484189180
1.030000e-15
95.3
18
TraesCS5A01G027600
chr2A
98.901
910
7
1
2579
3485
624462226
624463135
0.000000e+00
1622.0
19
TraesCS5A01G027600
chr2A
98.686
913
9
1
2576
3485
19253317
19254229
0.000000e+00
1616.0
20
TraesCS5A01G027600
chr2A
85.098
255
32
3
993
1242
138143510
138143257
4.460000e-64
255.0
21
TraesCS5A01G027600
chr2A
93.056
144
10
0
127
270
509365173
509365030
9.800000e-51
211.0
22
TraesCS5A01G027600
chr3B
88.677
786
68
7
848
1615
672672706
672671924
0.000000e+00
939.0
23
TraesCS5A01G027600
chr3B
91.363
521
45
0
1686
2206
658558488
658557968
0.000000e+00
713.0
24
TraesCS5A01G027600
chr3B
86.312
263
32
3
373
633
747702963
747703223
2.050000e-72
283.0
25
TraesCS5A01G027600
chr3B
92.708
192
14
0
127
318
756654462
756654271
9.530000e-71
278.0
26
TraesCS5A01G027600
chr7A
85.798
683
64
9
953
1615
528294514
528293845
0.000000e+00
693.0
27
TraesCS5A01G027600
chr7A
90.099
101
9
1
850
950
528294703
528294604
2.820000e-26
130.0
28
TraesCS5A01G027600
chr5B
89.787
470
45
3
316
785
562105700
562105234
1.790000e-167
599.0
29
TraesCS5A01G027600
chr5B
91.919
99
7
1
853
950
65100978
65101076
1.690000e-28
137.0
30
TraesCS5A01G027600
chr5B
96.721
61
2
0
792
852
84732015
84731955
6.150000e-18
102.0
31
TraesCS5A01G027600
chr4B
91.315
426
37
0
316
741
527960132
527960557
1.800000e-162
582.0
32
TraesCS5A01G027600
chr4B
86.312
263
33
2
373
633
59873286
59873547
2.050000e-72
283.0
33
TraesCS5A01G027600
chr4B
90.104
192
16
1
127
318
14179412
14179224
2.690000e-61
246.0
34
TraesCS5A01G027600
chr7D
84.669
574
75
10
950
1514
561004951
561004382
8.450000e-156
560.0
35
TraesCS5A01G027600
chr7D
84.864
403
55
5
2181
2578
618033310
618032909
5.420000e-108
401.0
36
TraesCS5A01G027600
chr7D
92.929
99
6
1
853
950
159081320
159081222
3.630000e-30
143.0
37
TraesCS5A01G027600
chr2B
83.394
548
75
10
954
1491
234826355
234826896
8.690000e-136
494.0
38
TraesCS5A01G027600
chr2B
96.721
61
2
0
792
852
613039671
613039611
6.150000e-18
102.0
39
TraesCS5A01G027600
chr7B
86.265
415
54
3
954
1366
608904925
608904512
6.860000e-122
448.0
40
TraesCS5A01G027600
chr7B
87.805
205
23
1
373
575
60366993
60366789
4.500000e-59
239.0
41
TraesCS5A01G027600
chr7B
89.381
113
11
1
1269
1381
197700950
197701061
1.300000e-29
141.0
42
TraesCS5A01G027600
chr1B
79.236
602
71
28
1616
2202
547701776
547702338
1.530000e-98
370.0
43
TraesCS5A01G027600
chr1B
87.778
180
21
1
2334
2513
550223862
550223684
3.520000e-50
209.0
44
TraesCS5A01G027600
chr1B
90.625
64
4
2
136
197
570305928
570305991
2.230000e-12
84.2
45
TraesCS5A01G027600
chr6B
88.889
180
20
0
2334
2513
648198368
648198189
4.530000e-54
222.0
46
TraesCS5A01G027600
chr6B
87.778
180
22
0
2334
2513
563912440
563912261
9.800000e-51
211.0
47
TraesCS5A01G027600
chr2D
94.366
142
8
0
127
268
582153618
582153477
5.860000e-53
219.0
48
TraesCS5A01G027600
chr2D
92.000
125
10
0
2446
2570
220630646
220630770
3.570000e-40
176.0
49
TraesCS5A01G027600
chr2D
91.919
99
7
1
853
950
398665849
398665751
1.690000e-28
137.0
50
TraesCS5A01G027600
chr4A
92.361
144
11
0
127
270
435436975
435437118
4.560000e-49
206.0
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
TraesCS5A01G027600
chr5A
23608077
23611561
3484
True
6436.0
6436
100.0000
1
3485
1
chr5A.!!$R1
3484
1
TraesCS5A01G027600
chr5A
483275679
483276588
909
True
1622.0
1622
98.9010
2579
3485
1
chr5A.!!$R2
906
2
TraesCS5A01G027600
chr5D
30617433
30619997
2564
False
4460.0
4460
97.9840
1
2578
1
chr5D.!!$F1
2577
3
TraesCS5A01G027600
chr3A
692345338
692348217
2879
False
2086.5
2612
95.6950
1
2578
2
chr3A.!!$F1
2577
4
TraesCS5A01G027600
chr3A
91016109
91017013
904
True
1628.0
1628
99.1160
2581
3485
1
chr3A.!!$R2
904
5
TraesCS5A01G027600
chr3A
277502331
277503239
908
True
1613.0
1613
98.6810
2576
3485
1
chr3A.!!$R3
909
6
TraesCS5A01G027600
chr6D
98090515
98092123
1608
False
2567.0
2567
95.4240
1
1615
1
chr6D.!!$F2
1614
7
TraesCS5A01G027600
chr3D
496779511
496780412
901
True
1628.0
1628
99.2240
2584
3485
1
chr3D.!!$R1
901
8
TraesCS5A01G027600
chr1D
223523670
223524579
909
True
1628.0
1628
99.0110
2579
3485
1
chr1D.!!$R2
906
9
TraesCS5A01G027600
chr1D
94050649
94051557
908
False
1624.0
1624
98.9000
2577
3485
1
chr1D.!!$F1
908
10
TraesCS5A01G027600
chr1D
493219807
493220713
906
True
1620.0
1620
98.8970
2579
3485
1
chr1D.!!$R3
906
11
TraesCS5A01G027600
chr1D
407296331
407297255
924
False
730.0
730
81.3070
1616
2578
1
chr1D.!!$F2
962
12
TraesCS5A01G027600
chr2A
624462226
624463135
909
False
1622.0
1622
98.9010
2579
3485
1
chr2A.!!$F2
906
13
TraesCS5A01G027600
chr2A
19253317
19254229
912
False
1616.0
1616
98.6860
2576
3485
1
chr2A.!!$F1
909
14
TraesCS5A01G027600
chr3B
672671924
672672706
782
True
939.0
939
88.6770
848
1615
1
chr3B.!!$R2
767
15
TraesCS5A01G027600
chr3B
658557968
658558488
520
True
713.0
713
91.3630
1686
2206
1
chr3B.!!$R1
520
16
TraesCS5A01G027600
chr7A
528293845
528294703
858
True
411.5
693
87.9485
850
1615
2
chr7A.!!$R1
765
17
TraesCS5A01G027600
chr7D
561004382
561004951
569
True
560.0
560
84.6690
950
1514
1
chr7D.!!$R2
564
18
TraesCS5A01G027600
chr2B
234826355
234826896
541
False
494.0
494
83.3940
954
1491
1
chr2B.!!$F1
537
19
TraesCS5A01G027600
chr1B
547701776
547702338
562
False
370.0
370
79.2360
1616
2202
1
chr1B.!!$F1
586
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.