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
TraesCS7A01G518600
chr7A
100.000
4521
0
0
1
4521
702406461
702410981
0.000000e+00
8349.0
1
TraesCS7A01G518600
chr7A
82.169
3006
346
113
1344
4248
702237702
702240618
0.000000e+00
2407.0
2
TraesCS7A01G518600
chr7A
82.619
1703
241
38
983
2664
688345399
688347067
0.000000e+00
1454.0
3
TraesCS7A01G518600
chr7A
80.451
1775
276
41
919
2666
702610715
702612445
0.000000e+00
1290.0
4
TraesCS7A01G518600
chr7D
94.135
2711
139
12
11
2713
612324829
612327527
0.000000e+00
4108.0
5
TraesCS7A01G518600
chr7D
87.881
3218
279
54
1348
4520
611871164
611868013
0.000000e+00
3679.0
6
TraesCS7A01G518600
chr7D
82.827
3523
373
132
838
4248
611857669
611854267
0.000000e+00
2940.0
7
TraesCS7A01G518600
chr7D
95.775
1775
56
7
2762
4521
612327527
612329297
0.000000e+00
2844.0
8
TraesCS7A01G518600
chr7D
83.150
2813
303
92
1333
4049
612287028
612289765
0.000000e+00
2410.0
9
TraesCS7A01G518600
chr7D
80.875
1783
269
41
922
2666
612403623
612405371
0.000000e+00
1338.0
10
TraesCS7A01G518600
chr7D
82.000
1600
223
39
983
2568
595346729
595348277
0.000000e+00
1299.0
11
TraesCS7A01G518600
chr7D
83.387
933
125
18
1713
2640
595348292
595349199
0.000000e+00
837.0
12
TraesCS7A01G518600
chr7D
80.756
582
72
22
3499
4070
612406090
612406641
6.990000e-113
418.0
13
TraesCS7A01G518600
chr7D
79.141
652
82
24
2863
3491
595349207
595349827
7.040000e-108
401.0
14
TraesCS7A01G518600
chr7D
85.340
191
27
1
3023
3212
612405483
612405673
3.570000e-46
196.0
15
TraesCS7A01G518600
chr7B
90.449
2136
138
28
2002
4102
701647730
701649834
0.000000e+00
2754.0
16
TraesCS7A01G518600
chr7B
85.281
2310
238
63
835
3118
701457396
701459629
0.000000e+00
2289.0
17
TraesCS7A01G518600
chr7B
89.511
1268
97
19
16
1275
701643732
701644971
0.000000e+00
1572.0
18
TraesCS7A01G518600
chr7B
81.872
1699
256
31
982
2666
672770098
672771758
0.000000e+00
1384.0
19
TraesCS7A01G518600
chr7B
95.553
742
33
0
1268
2009
701645934
701646675
0.000000e+00
1188.0
20
TraesCS7A01G518600
chr7B
91.957
373
24
2
4148
4520
701649833
701650199
6.700000e-143
518.0
21
TraesCS7A01G518600
chr7B
79.623
795
90
36
3308
4049
701459812
701460587
5.220000e-139
505.0
22
TraesCS7A01G518600
chrUn
84.301
758
85
22
829
1583
324305047
324304321
0.000000e+00
710.0
23
TraesCS7A01G518600
chrUn
84.169
758
86
22
829
1583
324358662
324357936
0.000000e+00
704.0
24
TraesCS7A01G518600
chrUn
84.450
746
76
26
835
1577
87707587
87708295
0.000000e+00
699.0
25
TraesCS7A01G518600
chrUn
78.987
790
96
34
3308
4044
368811829
368812601
4.090000e-130
475.0
26
TraesCS7A01G518600
chrUn
81.879
447
59
15
1586
2029
388947917
388948344
1.550000e-94
357.0
27
TraesCS7A01G518600
chrUn
94.915
59
1
1
4153
4209
465862360
465862302
1.730000e-14
91.6
28
TraesCS7A01G518600
chr4A
85.294
102
14
1
26
127
742062366
742062466
2.220000e-18
104.0
29
TraesCS7A01G518600
chr1B
84.524
84
8
4
2665
2745
327570073
327569992
1.350000e-10
78.7
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
TraesCS7A01G518600
chr7A
702406461
702410981
4520
False
8349.000000
8349
100.000000
1
4521
1
chr7A.!!$F3
4520
1
TraesCS7A01G518600
chr7A
702237702
702240618
2916
False
2407.000000
2407
82.169000
1344
4248
1
chr7A.!!$F2
2904
2
TraesCS7A01G518600
chr7A
688345399
688347067
1668
False
1454.000000
1454
82.619000
983
2664
1
chr7A.!!$F1
1681
3
TraesCS7A01G518600
chr7A
702610715
702612445
1730
False
1290.000000
1290
80.451000
919
2666
1
chr7A.!!$F4
1747
4
TraesCS7A01G518600
chr7D
611868013
611871164
3151
True
3679.000000
3679
87.881000
1348
4520
1
chr7D.!!$R2
3172
5
TraesCS7A01G518600
chr7D
612324829
612329297
4468
False
3476.000000
4108
94.955000
11
4521
2
chr7D.!!$F3
4510
6
TraesCS7A01G518600
chr7D
611854267
611857669
3402
True
2940.000000
2940
82.827000
838
4248
1
chr7D.!!$R1
3410
7
TraesCS7A01G518600
chr7D
612287028
612289765
2737
False
2410.000000
2410
83.150000
1333
4049
1
chr7D.!!$F1
2716
8
TraesCS7A01G518600
chr7D
595346729
595349827
3098
False
845.666667
1299
81.509333
983
3491
3
chr7D.!!$F2
2508
9
TraesCS7A01G518600
chr7D
612403623
612406641
3018
False
650.666667
1338
82.323667
922
4070
3
chr7D.!!$F4
3148
10
TraesCS7A01G518600
chr7B
701643732
701650199
6467
False
1508.000000
2754
91.867500
16
4520
4
chr7B.!!$F3
4504
11
TraesCS7A01G518600
chr7B
701457396
701460587
3191
False
1397.000000
2289
82.452000
835
4049
2
chr7B.!!$F2
3214
12
TraesCS7A01G518600
chr7B
672770098
672771758
1660
False
1384.000000
1384
81.872000
982
2666
1
chr7B.!!$F1
1684
13
TraesCS7A01G518600
chrUn
324304321
324305047
726
True
710.000000
710
84.301000
829
1583
1
chrUn.!!$R1
754
14
TraesCS7A01G518600
chrUn
324357936
324358662
726
True
704.000000
704
84.169000
829
1583
1
chrUn.!!$R2
754
15
TraesCS7A01G518600
chrUn
87707587
87708295
708
False
699.000000
699
84.450000
835
1577
1
chrUn.!!$F1
742
16
TraesCS7A01G518600
chrUn
368811829
368812601
772
False
475.000000
475
78.987000
3308
4044
1
chrUn.!!$F2
736
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.