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
TraesCS1B01G369900
chr1B
100.000
2315
0
0
1
2315
599764778
599767092
0.000000e+00
4276.0
1
TraesCS1B01G369900
chr1B
97.797
1816
39
1
1
1815
599635608
599637423
0.000000e+00
3131.0
2
TraesCS1B01G369900
chr1B
97.577
1816
43
1
1
1815
599706816
599708631
0.000000e+00
3109.0
3
TraesCS1B01G369900
chr1B
96.703
1820
45
4
1
1815
599836323
599838132
0.000000e+00
3014.0
4
TraesCS1B01G369900
chr1B
96.864
1371
36
4
450
1815
599925578
599926946
0.000000e+00
2287.0
5
TraesCS1B01G369900
chr1B
96.791
1371
39
2
450
1815
599982766
599984136
0.000000e+00
2283.0
6
TraesCS1B01G369900
chr1B
96.791
1153
34
3
664
1815
599577667
599578817
0.000000e+00
1921.0
7
TraesCS1B01G369900
chr1B
98.413
441
7
0
1
441
599982177
599982617
0.000000e+00
776.0
8
TraesCS1B01G369900
chr1B
97.585
414
9
1
1
414
599924862
599925274
0.000000e+00
708.0
9
TraesCS1B01G369900
chr1B
95.739
399
13
4
1
398
599577278
599577673
6.970000e-180
640.0
10
TraesCS1B01G369900
chr1B
93.421
304
11
4
2012
2314
599838179
599838474
2.110000e-120
442.0
11
TraesCS1B01G369900
chr1B
93.377
302
12
4
2014
2314
599578869
599579163
7.590000e-120
440.0
12
TraesCS1B01G369900
chr1B
93.046
302
14
3
2014
2314
599708682
599708977
3.530000e-118
435.0
13
TraesCS1B01G369900
chr1B
93.046
302
13
4
2014
2314
599926997
599927291
3.530000e-118
435.0
14
TraesCS1B01G369900
chr1B
93.046
302
13
4
2014
2314
599984188
599984482
3.530000e-118
435.0
15
TraesCS1B01G369900
chr1B
92.384
302
16
3
2014
2314
599637475
599637770
7.650000e-115
424.0
16
TraesCS1B01G369900
chr1B
96.226
53
0
1
1844
1896
599578816
599578866
4.100000e-13
86.1
17
TraesCS1B01G369900
chr1B
96.226
53
0
1
1844
1896
599637422
599637472
4.100000e-13
86.1
18
TraesCS1B01G369900
chr1B
96.226
53
0
1
1844
1896
599708630
599708680
4.100000e-13
86.1
19
TraesCS1B01G369900
chr1D
92.218
1889
103
20
39
1897
441739567
441741441
0.000000e+00
2634.0
20
TraesCS1B01G369900
chr1D
89.076
952
80
12
962
1896
441644236
441645180
0.000000e+00
1160.0
21
TraesCS1B01G369900
chr1D
92.055
793
22
8
1
784
441631902
441632662
0.000000e+00
1077.0
22
TraesCS1B01G369900
chr1D
89.869
306
26
5
2012
2314
441741440
441741743
2.790000e-104
388.0
23
TraesCS1B01G369900
chr1D
90.357
280
26
1
2
281
441577853
441578131
1.310000e-97
366.0
24
TraesCS1B01G369900
chr1D
94.366
142
7
1
829
969
441632663
441632804
1.390000e-52
217.0
25
TraesCS1B01G369900
chr1A
86.623
912
92
16
996
1894
536629864
536628970
0.000000e+00
981.0
26
TraesCS1B01G369900
chr1A
91.597
119
10
0
1896
2014
6470348
6470466
5.120000e-37
165.0
27
TraesCS1B01G369900
chr5B
92.800
125
9
0
1896
2020
28370052
28369928
5.080000e-42
182.0
28
TraesCS1B01G369900
chr2B
91.200
125
11
0
1889
2013
711198330
711198454
1.100000e-38
171.0
29
TraesCS1B01G369900
chr2B
88.571
140
10
6
1893
2028
643184615
643184752
5.120000e-37
165.0
30
TraesCS1B01G369900
chr2B
79.096
177
30
7
219
393
793021527
793021698
5.230000e-22
115.0
31
TraesCS1B01G369900
chr7A
91.736
121
8
2
1895
2013
222941734
222941854
1.420000e-37
167.0
32
TraesCS1B01G369900
chr2A
91.667
120
10
0
1896
2015
477056142
477056023
1.420000e-37
167.0
33
TraesCS1B01G369900
chr6B
91.525
118
10
0
1896
2013
617675165
617675282
1.840000e-36
163.0
34
TraesCS1B01G369900
chr3B
91.453
117
10
0
1896
2012
622399406
622399290
6.620000e-36
161.0
35
TraesCS1B01G369900
chr4D
90.244
123
11
1
1893
2015
338012720
338012841
2.380000e-35
159.0
36
TraesCS1B01G369900
chr2D
85.484
62
3
6
2151
2209
60586833
60586775
2.480000e-05
60.2
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
TraesCS1B01G369900
chr1B
599764778
599767092
2314
False
4276.000000
4276
100.000000
1
2315
1
chr1B.!!$F1
2314
1
TraesCS1B01G369900
chr1B
599836323
599838474
2151
False
1728.000000
3014
95.062000
1
2314
2
chr1B.!!$F5
2313
2
TraesCS1B01G369900
chr1B
599635608
599637770
2162
False
1213.700000
3131
95.469000
1
2314
3
chr1B.!!$F3
2313
3
TraesCS1B01G369900
chr1B
599706816
599708977
2161
False
1210.033333
3109
95.616333
1
2314
3
chr1B.!!$F4
2313
4
TraesCS1B01G369900
chr1B
599982177
599984482
2305
False
1164.666667
2283
96.083333
1
2314
3
chr1B.!!$F7
2313
5
TraesCS1B01G369900
chr1B
599924862
599927291
2429
False
1143.333333
2287
95.831667
1
2314
3
chr1B.!!$F6
2313
6
TraesCS1B01G369900
chr1B
599577278
599579163
1885
False
771.775000
1921
95.533250
1
2314
4
chr1B.!!$F2
2313
7
TraesCS1B01G369900
chr1D
441739567
441741743
2176
False
1511.000000
2634
91.043500
39
2314
2
chr1D.!!$F4
2275
8
TraesCS1B01G369900
chr1D
441644236
441645180
944
False
1160.000000
1160
89.076000
962
1896
1
chr1D.!!$F2
934
9
TraesCS1B01G369900
chr1D
441631902
441632804
902
False
647.000000
1077
93.210500
1
969
2
chr1D.!!$F3
968
10
TraesCS1B01G369900
chr1A
536628970
536629864
894
True
981.000000
981
86.623000
996
1894
1
chr1A.!!$R1
898
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.