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
TraesCS4B01G134300
chr4B
100.000
2931
0
0
1
2931
175309594
175306664
0.000000e+00
5413.0
1
TraesCS4B01G134300
chr4B
97.389
1800
47
0
1
1800
531339287
531341086
0.000000e+00
3064.0
2
TraesCS4B01G134300
chr4B
95.325
1583
62
7
1355
2931
609105459
609103883
0.000000e+00
2503.0
3
TraesCS4B01G134300
chr4B
96.292
809
30
0
1
809
357795610
357794802
0.000000e+00
1328.0
4
TraesCS4B01G134300
chr4B
83.905
845
83
21
1
809
289622409
289623236
0.000000e+00
758.0
5
TraesCS4B01G134300
chr4B
94.819
386
16
2
2544
2929
172482537
172482918
1.500000e-167
599.0
6
TraesCS4B01G134300
chr4B
93.830
389
21
3
2544
2931
316994408
316994794
1.510000e-162
582.0
7
TraesCS4B01G134300
chr4B
93.995
383
21
2
2549
2931
491006787
491006407
1.960000e-161
579.0
8
TraesCS4B01G134300
chr7D
96.510
1748
48
5
809
2551
311619004
311620743
0.000000e+00
2878.0
9
TraesCS4B01G134300
chr7D
89.610
77
6
1
559
633
46354311
46354235
2.400000e-16
97.1
10
TraesCS4B01G134300
chr3A
96.294
1727
57
5
814
2535
361576865
361575141
0.000000e+00
2828.0
11
TraesCS4B01G134300
chr5B
96.912
1684
46
4
809
2487
209633858
209632176
0.000000e+00
2817.0
12
TraesCS4B01G134300
chr6A
95.757
1744
66
6
814
2551
197861226
197859485
0.000000e+00
2804.0
13
TraesCS4B01G134300
chr3B
95.538
1748
72
4
809
2551
371039713
371037967
0.000000e+00
2791.0
14
TraesCS4B01G134300
chr3B
85.885
836
86
18
1
808
9161158
9161989
0.000000e+00
861.0
15
TraesCS4B01G134300
chr5D
95.974
1689
56
9
809
2487
199084299
199085985
0.000000e+00
2732.0
16
TraesCS4B01G134300
chr5A
95.616
1688
64
8
809
2487
216692021
216693707
0.000000e+00
2699.0
17
TraesCS4B01G134300
chr4D
96.558
1627
50
4
906
2527
366045591
366047216
0.000000e+00
2689.0
18
TraesCS4B01G134300
chr4D
78.906
256
34
11
549
800
353417693
353417932
3.910000e-34
156.0
19
TraesCS4B01G134300
chr4D
77.912
249
34
11
557
800
194082388
194082156
5.100000e-28
135.0
20
TraesCS4B01G134300
chr4D
98.182
55
1
0
814
868
366045531
366045585
2.400000e-16
97.1
21
TraesCS4B01G134300
chr7B
96.044
809
31
1
1
809
397594023
397593216
0.000000e+00
1315.0
22
TraesCS4B01G134300
chr1B
86.374
844
72
20
1
809
646214099
646214934
0.000000e+00
881.0
23
TraesCS4B01G134300
chr1B
95.361
388
17
1
2544
2931
148510266
148510652
1.490000e-172
616.0
24
TraesCS4B01G134300
chr1B
94.588
388
19
2
2544
2931
358387001
358386616
1.500000e-167
599.0
25
TraesCS4B01G134300
chr1B
93.557
388
22
3
2544
2931
359605877
359606261
2.530000e-160
575.0
26
TraesCS4B01G134300
chr1B
93.299
388
24
2
2544
2931
193412123
193411738
3.280000e-159
571.0
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
TraesCS4B01G134300
chr4B
175306664
175309594
2930
True
5413.00
5413
100.000
1
2931
1
chr4B.!!$R1
2930
1
TraesCS4B01G134300
chr4B
531339287
531341086
1799
False
3064.00
3064
97.389
1
1800
1
chr4B.!!$F4
1799
2
TraesCS4B01G134300
chr4B
609103883
609105459
1576
True
2503.00
2503
95.325
1355
2931
1
chr4B.!!$R4
1576
3
TraesCS4B01G134300
chr4B
357794802
357795610
808
True
1328.00
1328
96.292
1
809
1
chr4B.!!$R2
808
4
TraesCS4B01G134300
chr4B
289622409
289623236
827
False
758.00
758
83.905
1
809
1
chr4B.!!$F2
808
5
TraesCS4B01G134300
chr7D
311619004
311620743
1739
False
2878.00
2878
96.510
809
2551
1
chr7D.!!$F1
1742
6
TraesCS4B01G134300
chr3A
361575141
361576865
1724
True
2828.00
2828
96.294
814
2535
1
chr3A.!!$R1
1721
7
TraesCS4B01G134300
chr5B
209632176
209633858
1682
True
2817.00
2817
96.912
809
2487
1
chr5B.!!$R1
1678
8
TraesCS4B01G134300
chr6A
197859485
197861226
1741
True
2804.00
2804
95.757
814
2551
1
chr6A.!!$R1
1737
9
TraesCS4B01G134300
chr3B
371037967
371039713
1746
True
2791.00
2791
95.538
809
2551
1
chr3B.!!$R1
1742
10
TraesCS4B01G134300
chr3B
9161158
9161989
831
False
861.00
861
85.885
1
808
1
chr3B.!!$F1
807
11
TraesCS4B01G134300
chr5D
199084299
199085985
1686
False
2732.00
2732
95.974
809
2487
1
chr5D.!!$F1
1678
12
TraesCS4B01G134300
chr5A
216692021
216693707
1686
False
2699.00
2699
95.616
809
2487
1
chr5A.!!$F1
1678
13
TraesCS4B01G134300
chr4D
366045531
366047216
1685
False
1393.05
2689
97.370
814
2527
2
chr4D.!!$F2
1713
14
TraesCS4B01G134300
chr7B
397593216
397594023
807
True
1315.00
1315
96.044
1
809
1
chr7B.!!$R1
808
15
TraesCS4B01G134300
chr1B
646214099
646214934
835
False
881.00
881
86.374
1
809
1
chr1B.!!$F3
808
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.