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
TraesCS4B01G312500
chr4B
100.000
2609
0
0
1
2609
602293337
602290729
0.000000e+00
4819
1
TraesCS4B01G312500
chr4B
90.177
1812
123
30
840
2608
194219979
194221778
0.000000e+00
2309
2
TraesCS4B01G312500
chr4B
87.630
865
55
30
1
850
194219098
194219925
0.000000e+00
957
3
TraesCS4B01G312500
chr6D
91.682
2633
154
33
1
2608
14045561
14048153
0.000000e+00
3589
4
TraesCS4B01G312500
chr5D
90.964
2634
154
39
1
2608
373747708
373750283
0.000000e+00
3469
5
TraesCS4B01G312500
chr6A
86.556
2648
258
54
1
2608
74674998
74677587
0.000000e+00
2828
6
TraesCS4B01G312500
chr5B
91.553
2060
135
19
558
2608
445131422
445133451
0.000000e+00
2804
7
TraesCS4B01G312500
chr5B
90.929
1797
118
24
854
2608
420718032
420719825
0.000000e+00
2374
8
TraesCS4B01G312500
chr5B
90.221
1810
124
29
840
2608
179227840
179229637
0.000000e+00
2313
9
TraesCS4B01G312500
chr5B
88.051
862
54
22
1
850
179226962
179227786
0.000000e+00
976
10
TraesCS4B01G312500
chr5B
87.963
864
54
26
1
850
406870655
406869828
0.000000e+00
974
11
TraesCS4B01G312500
chr5B
87.826
575
51
10
1
562
445111491
445112059
0.000000e+00
656
12
TraesCS4B01G312500
chr2D
93.764
1764
99
9
849
2608
617164184
617162428
0.000000e+00
2638
13
TraesCS4B01G312500
chr2D
93.140
860
39
12
1
850
617165088
617164239
0.000000e+00
1243
14
TraesCS4B01G312500
chr1D
93.718
1767
97
12
848
2608
485158460
485160218
0.000000e+00
2636
15
TraesCS4B01G312500
chr1D
94.416
591
27
5
263
850
485157818
485158405
0.000000e+00
904
16
TraesCS4B01G312500
chr2A
92.325
1772
104
18
848
2608
17676655
17674905
0.000000e+00
2490
17
TraesCS4B01G312500
chr2A
87.935
862
54
23
1
850
719453738
719454561
0.000000e+00
970
18
TraesCS4B01G312500
chr2A
87.703
862
58
23
1
850
43380232
43381057
0.000000e+00
961
19
TraesCS4B01G312500
chr2A
94.247
591
29
4
263
850
17677299
17676711
0.000000e+00
898
20
TraesCS4B01G312500
chr7B
90.558
1811
122
26
840
2608
68098241
68100044
0.000000e+00
2351
21
TraesCS4B01G312500
chr7B
88.079
864
52
24
1
850
528879444
528880270
0.000000e+00
977
22
TraesCS4B01G312500
chr3B
90.492
1809
123
23
840
2608
552478977
552480776
0.000000e+00
2342
23
TraesCS4B01G312500
chr3B
88.208
865
52
23
1
851
552478097
552478925
0.000000e+00
987
24
TraesCS4B01G312500
chr7A
90.387
1810
121
29
840
2608
171419456
171421253
0.000000e+00
2329
25
TraesCS4B01G312500
chr7A
85.681
866
53
35
1
850
171418592
171419402
0.000000e+00
846
26
TraesCS4B01G312500
chr1A
90.306
1795
126
29
854
2608
567477295
567475509
0.000000e+00
2307
27
TraesCS4B01G312500
chr1A
85.658
509
36
21
2131
2608
567471887
567471385
3.880000e-138
501
28
TraesCS4B01G312500
chr6B
87.963
864
53
26
1
850
704850743
704849917
0.000000e+00
972
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
TraesCS4B01G312500
chr4B
602290729
602293337
2608
True
4819.0
4819
100.0000
1
2609
1
chr4B.!!$R1
2608
1
TraesCS4B01G312500
chr4B
194219098
194221778
2680
False
1633.0
2309
88.9035
1
2608
2
chr4B.!!$F1
2607
2
TraesCS4B01G312500
chr6D
14045561
14048153
2592
False
3589.0
3589
91.6820
1
2608
1
chr6D.!!$F1
2607
3
TraesCS4B01G312500
chr5D
373747708
373750283
2575
False
3469.0
3469
90.9640
1
2608
1
chr5D.!!$F1
2607
4
TraesCS4B01G312500
chr6A
74674998
74677587
2589
False
2828.0
2828
86.5560
1
2608
1
chr6A.!!$F1
2607
5
TraesCS4B01G312500
chr5B
445131422
445133451
2029
False
2804.0
2804
91.5530
558
2608
1
chr5B.!!$F3
2050
6
TraesCS4B01G312500
chr5B
420718032
420719825
1793
False
2374.0
2374
90.9290
854
2608
1
chr5B.!!$F1
1754
7
TraesCS4B01G312500
chr5B
179226962
179229637
2675
False
1644.5
2313
89.1360
1
2608
2
chr5B.!!$F4
2607
8
TraesCS4B01G312500
chr5B
406869828
406870655
827
True
974.0
974
87.9630
1
850
1
chr5B.!!$R1
849
9
TraesCS4B01G312500
chr5B
445111491
445112059
568
False
656.0
656
87.8260
1
562
1
chr5B.!!$F2
561
10
TraesCS4B01G312500
chr2D
617162428
617165088
2660
True
1940.5
2638
93.4520
1
2608
2
chr2D.!!$R1
2607
11
TraesCS4B01G312500
chr1D
485157818
485160218
2400
False
1770.0
2636
94.0670
263
2608
2
chr1D.!!$F1
2345
12
TraesCS4B01G312500
chr2A
17674905
17677299
2394
True
1694.0
2490
93.2860
263
2608
2
chr2A.!!$R1
2345
13
TraesCS4B01G312500
chr2A
719453738
719454561
823
False
970.0
970
87.9350
1
850
1
chr2A.!!$F2
849
14
TraesCS4B01G312500
chr2A
43380232
43381057
825
False
961.0
961
87.7030
1
850
1
chr2A.!!$F1
849
15
TraesCS4B01G312500
chr7B
68098241
68100044
1803
False
2351.0
2351
90.5580
840
2608
1
chr7B.!!$F1
1768
16
TraesCS4B01G312500
chr7B
528879444
528880270
826
False
977.0
977
88.0790
1
850
1
chr7B.!!$F2
849
17
TraesCS4B01G312500
chr3B
552478097
552480776
2679
False
1664.5
2342
89.3500
1
2608
2
chr3B.!!$F1
2607
18
TraesCS4B01G312500
chr7A
171418592
171421253
2661
False
1587.5
2329
88.0340
1
2608
2
chr7A.!!$F1
2607
19
TraesCS4B01G312500
chr1A
567471385
567477295
5910
True
1404.0
2307
87.9820
854
2608
2
chr1A.!!$R1
1754
20
TraesCS4B01G312500
chr6B
704849917
704850743
826
True
972.0
972
87.9630
1
850
1
chr6B.!!$R1
849
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.