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
TraesCS2A01G172900
chr2A
100.000
2207
0
0
1
2207
130179795
130177589
0.000000e+00
4076
1
TraesCS2A01G172900
chr5A
97.602
2210
49
3
1
2207
109299930
109302138
0.000000e+00
3784
2
TraesCS2A01G172900
chr2B
97.736
1767
37
2
443
2207
10667770
10669535
0.000000e+00
3038
3
TraesCS2A01G172900
chr2B
97.568
1768
39
3
443
2207
390975865
390974099
0.000000e+00
3024
4
TraesCS2A01G172900
chr2B
92.598
689
49
2
630
1317
588687074
588686387
0.000000e+00
989
5
TraesCS2A01G172900
chr2B
95.552
607
18
5
1391
1989
588686398
588685793
0.000000e+00
963
6
TraesCS2A01G172900
chr2B
92.908
564
34
5
755
1317
588685795
588685237
0.000000e+00
815
7
TraesCS2A01G172900
chr2B
96.573
321
11
0
1
321
10667453
10667773
1.160000e-147
532
8
TraesCS2A01G172900
chr2B
95.950
321
13
0
1
321
390976182
390975862
2.510000e-144
521
9
TraesCS2A01G172900
chr2B
92.798
361
25
1
1
361
406245957
406245598
2.510000e-144
521
10
TraesCS2A01G172900
chr2B
93.617
235
15
0
122
356
599848128
599847894
3.490000e-93
351
11
TraesCS2A01G172900
chr1B
97.631
1731
36
3
481
2207
674642150
674640421
0.000000e+00
2964
12
TraesCS2A01G172900
chr1B
93.711
318
19
1
1
318
198560107
198560423
1.980000e-130
475
13
TraesCS2A01G172900
chr1B
95.135
185
9
0
1
185
674654639
674654455
2.140000e-75
292
14
TraesCS2A01G172900
chr7D
90.975
1651
115
8
358
1995
301662742
301661113
0.000000e+00
2193
15
TraesCS2A01G172900
chr7D
94.192
637
25
1
927
1563
46096344
46096968
0.000000e+00
961
16
TraesCS2A01G172900
chr7D
92.813
654
37
5
1563
2207
46101977
46102629
0.000000e+00
939
17
TraesCS2A01G172900
chr7D
92.781
471
27
5
358
825
46086101
46086567
0.000000e+00
675
18
TraesCS2A01G172900
chr1D
93.925
1251
47
6
967
2207
252590495
252591726
0.000000e+00
1862
19
TraesCS2A01G172900
chr1D
91.542
402
13
9
358
744
252585942
252586337
3.230000e-148
534
20
TraesCS2A01G172900
chr7A
93.700
1254
49
7
967
2207
665832345
665831109
0.000000e+00
1851
21
TraesCS2A01G172900
chr7A
89.227
362
35
2
1
361
673020932
673021290
1.200000e-122
449
22
TraesCS2A01G172900
chr4A
92.308
1261
58
9
967
2207
713137572
713136331
0.000000e+00
1755
23
TraesCS2A01G172900
chr4A
91.629
442
27
3
1776
2207
504866808
504867249
8.720000e-169
603
24
TraesCS2A01G172900
chr6B
93.469
934
44
11
384
1314
26562138
26563057
0.000000e+00
1371
25
TraesCS2A01G172900
chr6A
91.796
963
44
11
358
1317
611535000
611534070
0.000000e+00
1308
26
TraesCS2A01G172900
chr6A
94.574
258
13
1
1951
2207
611533569
611533312
4.420000e-107
398
27
TraesCS2A01G172900
chr7B
92.179
358
26
1
1
358
620571908
620572263
2.530000e-139
505
28
TraesCS2A01G172900
chr5B
88.674
362
36
3
1
361
523137003
523137360
9.360000e-119
436
29
TraesCS2A01G172900
chr2D
96.104
77
3
0
285
361
628840856
628840932
2.300000e-25
126
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
TraesCS2A01G172900
chr2A
130177589
130179795
2206
True
4076.000000
4076
100.0000
1
2207
1
chr2A.!!$R1
2206
1
TraesCS2A01G172900
chr5A
109299930
109302138
2208
False
3784.000000
3784
97.6020
1
2207
1
chr5A.!!$F1
2206
2
TraesCS2A01G172900
chr2B
10667453
10669535
2082
False
1785.000000
3038
97.1545
1
2207
2
chr2B.!!$F1
2206
3
TraesCS2A01G172900
chr2B
390974099
390976182
2083
True
1772.500000
3024
96.7590
1
2207
2
chr2B.!!$R3
2206
4
TraesCS2A01G172900
chr2B
588685237
588687074
1837
True
922.333333
989
93.6860
630
1989
3
chr2B.!!$R4
1359
5
TraesCS2A01G172900
chr1B
674640421
674642150
1729
True
2964.000000
2964
97.6310
481
2207
1
chr1B.!!$R1
1726
6
TraesCS2A01G172900
chr7D
301661113
301662742
1629
True
2193.000000
2193
90.9750
358
1995
1
chr7D.!!$R1
1637
7
TraesCS2A01G172900
chr7D
46096344
46096968
624
False
961.000000
961
94.1920
927
1563
1
chr7D.!!$F2
636
8
TraesCS2A01G172900
chr7D
46101977
46102629
652
False
939.000000
939
92.8130
1563
2207
1
chr7D.!!$F3
644
9
TraesCS2A01G172900
chr1D
252590495
252591726
1231
False
1862.000000
1862
93.9250
967
2207
1
chr1D.!!$F2
1240
10
TraesCS2A01G172900
chr7A
665831109
665832345
1236
True
1851.000000
1851
93.7000
967
2207
1
chr7A.!!$R1
1240
11
TraesCS2A01G172900
chr4A
713136331
713137572
1241
True
1755.000000
1755
92.3080
967
2207
1
chr4A.!!$R1
1240
12
TraesCS2A01G172900
chr6B
26562138
26563057
919
False
1371.000000
1371
93.4690
384
1314
1
chr6B.!!$F1
930
13
TraesCS2A01G172900
chr6A
611533312
611535000
1688
True
853.000000
1308
93.1850
358
2207
2
chr6A.!!$R1
1849
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.