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
TraesCS5A01G195300
chr5A
100.000
2909
0
0
1
2909
398482353
398479445
0.000000e+00
5373.0
1
TraesCS5A01G195300
chr5A
95.602
2274
85
8
1
2270
524675876
524678138
0.000000e+00
3631.0
2
TraesCS5A01G195300
chr6A
96.744
2273
57
4
1
2270
494425301
494427559
0.000000e+00
3771.0
3
TraesCS5A01G195300
chr6A
96.612
2273
62
2
1
2270
554915089
554917349
0.000000e+00
3757.0
4
TraesCS5A01G195300
chr6A
95.599
1386
45
3
889
2270
591845756
591844383
0.000000e+00
2207.0
5
TraesCS5A01G195300
chr6A
95.530
1387
45
4
889
2270
480642668
480641294
0.000000e+00
2202.0
6
TraesCS5A01G195300
chr6A
95.523
1385
46
3
890
2270
87945940
87944568
0.000000e+00
2200.0
7
TraesCS5A01G195300
chr6A
98.301
471
8
0
2433
2903
608069916
608070386
0.000000e+00
826.0
8
TraesCS5A01G195300
chr6A
96.124
129
4
1
2305
2432
40644560
40644432
2.940000e-50
209.0
9
TraesCS5A01G195300
chr6A
96.124
129
4
1
2305
2432
87944569
87944441
2.940000e-50
209.0
10
TraesCS5A01G195300
chr6A
96.124
129
4
1
2305
2432
184603860
184603732
2.940000e-50
209.0
11
TraesCS5A01G195300
chr6A
96.124
129
4
1
2305
2432
494427558
494427686
2.940000e-50
209.0
12
TraesCS5A01G195300
chr6A
96.124
129
4
1
2305
2432
570893863
570893735
2.940000e-50
209.0
13
TraesCS5A01G195300
chr6A
84.974
193
26
3
2433
2623
457327744
457327553
2.960000e-45
193.0
14
TraesCS5A01G195300
chr2A
96.700
2273
52
7
1
2270
58510411
58508159
0.000000e+00
3760.0
15
TraesCS5A01G195300
chr2A
96.524
2273
64
5
1
2270
619881387
619879127
0.000000e+00
3746.0
16
TraesCS5A01G195300
chr2A
96.260
2273
67
5
1
2270
733070590
733072847
0.000000e+00
3711.0
17
TraesCS5A01G195300
chr2A
96.729
2018
49
4
1
2015
614204176
614206179
0.000000e+00
3345.0
18
TraesCS5A01G195300
chr2A
97.904
477
10
0
2433
2909
23986711
23986235
0.000000e+00
826.0
19
TraesCS5A01G195300
chr2A
98.097
473
8
1
2438
2909
497443854
497443382
0.000000e+00
822.0
20
TraesCS5A01G195300
chr2A
96.875
128
3
1
2305
2431
614220541
614220668
2.270000e-51
213.0
21
TraesCS5A01G195300
chr3A
96.394
2274
62
9
1
2270
745750331
745752588
0.000000e+00
3727.0
22
TraesCS5A01G195300
chr3A
85.714
196
25
3
2432
2626
631144851
631144658
1.370000e-48
204.0
23
TraesCS5A01G195300
chr5D
94.660
2191
99
14
85
2270
65964972
65967149
0.000000e+00
3382.0
24
TraesCS5A01G195300
chr2B
88.141
2243
195
39
40
2269
600066660
600064476
0.000000e+00
2603.0
25
TraesCS5A01G195300
chr2B
96.491
171
6
0
2738
2908
189610116
189610286
1.710000e-72
283.0
26
TraesCS5A01G195300
chr6B
95.671
1386
44
3
889
2270
21359701
21361074
0.000000e+00
2213.0
27
TraesCS5A01G195300
chr6B
91.904
457
23
5
2433
2875
9985349
9985805
6.840000e-176
627.0
28
TraesCS5A01G195300
chr6B
90.444
450
28
9
2433
2875
9497060
9496619
1.940000e-161
579.0
29
TraesCS5A01G195300
chr6B
100.000
43
0
0
2867
2909
9495395
9495353
2.400000e-11
80.5
30
TraesCS5A01G195300
chr4A
95.455
1386
47
3
889
2270
593047272
593048645
0.000000e+00
2196.0
31
TraesCS5A01G195300
chr4A
96.687
483
16
0
2427
2909
361830450
361830932
0.000000e+00
804.0
32
TraesCS5A01G195300
chr4A
96.899
129
3
1
2305
2432
66554744
66554872
6.310000e-52
215.0
33
TraesCS5A01G195300
chr7A
96.660
479
15
1
2432
2909
521917746
521918224
0.000000e+00
795.0
34
TraesCS5A01G195300
chrUn
91.685
457
24
5
2433
2875
75925406
75924950
3.180000e-174
621.0
35
TraesCS5A01G195300
chrUn
91.257
366
21
3
2433
2787
476308911
476308546
3.370000e-134
488.0
36
TraesCS5A01G195300
chrUn
96.124
129
4
1
2305
2432
422727139
422727267
2.940000e-50
209.0
37
TraesCS5A01G195300
chr3B
89.000
200
20
2
2433
2631
41040550
41040748
2.240000e-61
246.0
38
TraesCS5A01G195300
chr4B
96.124
129
4
1
2305
2432
14708371
14708499
2.940000e-50
209.0
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
TraesCS5A01G195300
chr5A
398479445
398482353
2908
True
5373.00
5373
100.0000
1
2909
1
chr5A.!!$R1
2908
1
TraesCS5A01G195300
chr5A
524675876
524678138
2262
False
3631.00
3631
95.6020
1
2270
1
chr5A.!!$F1
2269
2
TraesCS5A01G195300
chr6A
554915089
554917349
2260
False
3757.00
3757
96.6120
1
2270
1
chr6A.!!$F1
2269
3
TraesCS5A01G195300
chr6A
591844383
591845756
1373
True
2207.00
2207
95.5990
889
2270
1
chr6A.!!$R6
1381
4
TraesCS5A01G195300
chr6A
480641294
480642668
1374
True
2202.00
2202
95.5300
889
2270
1
chr6A.!!$R4
1381
5
TraesCS5A01G195300
chr6A
494425301
494427686
2385
False
1990.00
3771
96.4340
1
2432
2
chr6A.!!$F3
2431
6
TraesCS5A01G195300
chr6A
87944441
87945940
1499
True
1204.50
2200
95.8235
890
2432
2
chr6A.!!$R7
1542
7
TraesCS5A01G195300
chr2A
58508159
58510411
2252
True
3760.00
3760
96.7000
1
2270
1
chr2A.!!$R2
2269
8
TraesCS5A01G195300
chr2A
619879127
619881387
2260
True
3746.00
3746
96.5240
1
2270
1
chr2A.!!$R4
2269
9
TraesCS5A01G195300
chr2A
733070590
733072847
2257
False
3711.00
3711
96.2600
1
2270
1
chr2A.!!$F3
2269
10
TraesCS5A01G195300
chr2A
614204176
614206179
2003
False
3345.00
3345
96.7290
1
2015
1
chr2A.!!$F1
2014
11
TraesCS5A01G195300
chr3A
745750331
745752588
2257
False
3727.00
3727
96.3940
1
2270
1
chr3A.!!$F1
2269
12
TraesCS5A01G195300
chr5D
65964972
65967149
2177
False
3382.00
3382
94.6600
85
2270
1
chr5D.!!$F1
2185
13
TraesCS5A01G195300
chr2B
600064476
600066660
2184
True
2603.00
2603
88.1410
40
2269
1
chr2B.!!$R1
2229
14
TraesCS5A01G195300
chr6B
21359701
21361074
1373
False
2213.00
2213
95.6710
889
2270
1
chr6B.!!$F2
1381
15
TraesCS5A01G195300
chr6B
9495353
9497060
1707
True
329.75
579
95.2220
2433
2909
2
chr6B.!!$R1
476
16
TraesCS5A01G195300
chr4A
593047272
593048645
1373
False
2196.00
2196
95.4550
889
2270
1
chr4A.!!$F3
1381
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.