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
TraesCS7D01G117600
chr7D
100.000
2690
0
0
1
2690
72521229
72523918
0.000000e+00
4968.0
1
TraesCS7D01G117600
chr7D
82.411
1410
202
38
793
2185
592222477
592223857
0.000000e+00
1188.0
2
TraesCS7D01G117600
chr7D
80.284
1339
210
39
824
2142
591929629
591928325
0.000000e+00
961.0
3
TraesCS7D01G117600
chr7D
80.833
1273
191
36
899
2142
591909339
591908091
0.000000e+00
950.0
4
TraesCS7D01G117600
chr7D
80.660
1272
194
39
899
2142
591888598
591887351
0.000000e+00
939.0
5
TraesCS7D01G117600
chr7B
93.281
2173
109
16
83
2251
15715442
15713303
0.000000e+00
3169.0
6
TraesCS7D01G117600
chr7B
84.000
475
68
3
824
1295
670918656
670919125
1.470000e-122
449.0
7
TraesCS7D01G117600
chr7B
83.789
475
69
3
824
1295
670889206
670889675
6.830000e-121
444.0
8
TraesCS7D01G117600
chr7B
79.070
172
34
1
3
174
674759123
674759292
1.690000e-22
117.0
9
TraesCS7D01G117600
chr7A
96.968
1418
38
3
684
2097
77599492
77600908
0.000000e+00
2375.0
10
TraesCS7D01G117600
chr7A
96.341
656
18
5
2041
2690
77600901
77601556
0.000000e+00
1074.0
11
TraesCS7D01G117600
chr7A
81.515
1320
190
37
824
2123
683235129
683233844
0.000000e+00
1037.0
12
TraesCS7D01G117600
chr7A
79.863
1172
192
33
969
2123
683186143
683184999
0.000000e+00
817.0
13
TraesCS7D01G117600
chr7A
79.293
1188
208
32
969
2142
683144559
683143396
0.000000e+00
797.0
14
TraesCS7D01G117600
chr3D
90.717
237
20
2
2455
2690
14451696
14451931
5.590000e-82
315.0
15
TraesCS7D01G117600
chr3D
87.500
208
17
4
2251
2457
72364147
72363948
5.790000e-57
231.0
16
TraesCS7D01G117600
chr3D
84.337
83
9
3
2372
2452
572254643
572254563
7.980000e-11
78.7
17
TraesCS7D01G117600
chr4A
88.382
241
21
4
2457
2690
442790251
442790491
1.580000e-72
283.0
18
TraesCS7D01G117600
chr2D
88.745
231
25
1
2460
2690
440633538
440633309
5.670000e-72
281.0
19
TraesCS7D01G117600
chr6D
86.383
235
32
0
2456
2690
20266076
20266310
9.560000e-65
257.0
20
TraesCS7D01G117600
chr5D
85.776
232
32
1
2460
2690
288321069
288320838
7.440000e-61
244.0
21
TraesCS7D01G117600
chr5A
89.024
164
17
1
2455
2617
565626680
565626517
4.540000e-48
202.0
22
TraesCS7D01G117600
chr4D
82.203
236
30
6
2455
2690
491521125
491520902
2.730000e-45
193.0
23
TraesCS7D01G117600
chr3B
84.571
175
18
4
2456
2621
166131566
166131392
5.960000e-37
165.0
24
TraesCS7D01G117600
chr3B
93.617
47
2
1
2644
2690
166131390
166131345
4.810000e-08
69.4
25
TraesCS7D01G117600
chr3A
88.406
138
7
3
2318
2454
84658173
84658044
9.970000e-35
158.0
26
TraesCS7D01G117600
chr1D
86.420
81
9
2
2610
2690
443183386
443183464
1.330000e-13
87.9
27
TraesCS7D01G117600
chr2B
84.270
89
8
5
2372
2457
496604659
496604744
6.170000e-12
82.4
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
TraesCS7D01G117600
chr7D
72521229
72523918
2689
False
4968.0
4968
100.0000
1
2690
1
chr7D.!!$F1
2689
1
TraesCS7D01G117600
chr7D
592222477
592223857
1380
False
1188.0
1188
82.4110
793
2185
1
chr7D.!!$F2
1392
2
TraesCS7D01G117600
chr7D
591928325
591929629
1304
True
961.0
961
80.2840
824
2142
1
chr7D.!!$R3
1318
3
TraesCS7D01G117600
chr7D
591908091
591909339
1248
True
950.0
950
80.8330
899
2142
1
chr7D.!!$R2
1243
4
TraesCS7D01G117600
chr7D
591887351
591888598
1247
True
939.0
939
80.6600
899
2142
1
chr7D.!!$R1
1243
5
TraesCS7D01G117600
chr7B
15713303
15715442
2139
True
3169.0
3169
93.2810
83
2251
1
chr7B.!!$R1
2168
6
TraesCS7D01G117600
chr7A
77599492
77601556
2064
False
1724.5
2375
96.6545
684
2690
2
chr7A.!!$F1
2006
7
TraesCS7D01G117600
chr7A
683233844
683235129
1285
True
1037.0
1037
81.5150
824
2123
1
chr7A.!!$R3
1299
8
TraesCS7D01G117600
chr7A
683184999
683186143
1144
True
817.0
817
79.8630
969
2123
1
chr7A.!!$R2
1154
9
TraesCS7D01G117600
chr7A
683143396
683144559
1163
True
797.0
797
79.2930
969
2142
1
chr7A.!!$R1
1173
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.