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
TraesCS4B01G124400
chr4B
100.000
5228
0
0
1
5228
149725558
149720331
0.000000e+00
9655
1
TraesCS4B01G124400
chr4D
96.211
4566
118
20
72
4604
105933259
105928716
0.000000e+00
7422
2
TraesCS4B01G124400
chr4A
96.492
2195
62
9
2425
4604
470099066
470101260
0.000000e+00
3613
3
TraesCS4B01G124400
chr4A
97.216
1868
42
8
285
2148
470097201
470099062
0.000000e+00
3153
4
TraesCS4B01G124400
chr1A
91.684
986
43
13
2015
2973
541979960
541978987
0.000000e+00
1330
5
TraesCS4B01G124400
chr1A
98.728
629
7
1
4601
5228
562129796
562130424
0.000000e+00
1116
6
TraesCS4B01G124400
chr1A
85.263
285
41
1
4601
4884
562130607
562130323
5.120000e-75
292
7
TraesCS4B01G124400
chr7B
98.882
626
7
0
4603
5228
539931152
539930527
0.000000e+00
1118
8
TraesCS4B01G124400
chr7B
86.380
279
37
1
4606
4884
539930351
539930628
2.370000e-78
303
9
TraesCS4B01G124400
chr6B
98.878
624
7
0
4605
5228
702811222
702810599
0.000000e+00
1114
10
TraesCS4B01G124400
chr7A
98.558
624
9
0
4605
5228
55920055
55920678
0.000000e+00
1103
11
TraesCS4B01G124400
chr7A
98.403
626
10
0
4603
5228
706401276
706400651
0.000000e+00
1101
12
TraesCS4B01G124400
chr7A
92.424
330
17
2
368
697
486211093
486210772
1.030000e-126
464
13
TraesCS4B01G124400
chr7A
85.663
279
39
1
4606
4884
55920854
55920577
5.120000e-75
292
14
TraesCS4B01G124400
chr7A
95.082
183
8
1
588
769
226469548
226469366
2.380000e-73
287
15
TraesCS4B01G124400
chr3B
88.850
565
49
6
1
554
26069540
26068979
0.000000e+00
682
16
TraesCS4B01G124400
chr3B
88.850
565
48
7
1
554
25933411
25932851
0.000000e+00
680
17
TraesCS4B01G124400
chr3B
88.673
565
50
6
1
554
26258597
26258036
0.000000e+00
676
18
TraesCS4B01G124400
chr3B
83.511
564
47
16
1
554
25999522
25998995
7.870000e-133
484
19
TraesCS4B01G124400
chr3B
83.481
563
49
14
1
554
26187088
26186561
7.870000e-133
484
20
TraesCS4B01G124400
chr3B
88.144
388
33
5
1
377
26297149
26296764
2.870000e-122
449
21
TraesCS4B01G124400
chr3B
87.887
388
34
5
1
377
26337815
26337430
1.340000e-120
444
22
TraesCS4B01G124400
chr3B
90.000
330
23
3
233
554
26337367
26337040
8.100000e-113
418
23
TraesCS4B01G124400
chr3B
90.000
330
22
4
233
554
26296653
26296327
2.910000e-112
416
24
TraesCS4B01G124400
chr6D
89.054
539
45
5
1
527
4673509
4672973
0.000000e+00
656
25
TraesCS4B01G124400
chr5D
90.574
488
33
5
77
554
512453675
512454159
7.390000e-178
634
26
TraesCS4B01G124400
chr5D
95.604
182
7
1
588
768
512454972
512455153
1.840000e-74
291
27
TraesCS4B01G124400
chr2B
88.048
502
45
7
3
494
431576710
431577206
9.760000e-162
580
28
TraesCS4B01G124400
chr2B
96.237
186
6
1
588
772
431578063
431578248
2.370000e-78
303
29
TraesCS4B01G124400
chr2B
95.135
185
8
1
588
771
123303073
123302889
1.840000e-74
291
30
TraesCS4B01G124400
chr7D
84.880
291
40
4
4601
4890
9829239
9829526
1.840000e-74
291
31
TraesCS4B01G124400
chr5A
95.109
184
8
1
588
770
78445823
78446006
6.620000e-74
289
32
TraesCS4B01G124400
chr2A
95.556
180
7
1
588
766
766574341
766574520
2.380000e-73
287
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
TraesCS4B01G124400
chr4B
149720331
149725558
5227
True
9655.0
9655
100.0000
1
5228
1
chr4B.!!$R1
5227
1
TraesCS4B01G124400
chr4D
105928716
105933259
4543
True
7422.0
7422
96.2110
72
4604
1
chr4D.!!$R1
4532
2
TraesCS4B01G124400
chr4A
470097201
470101260
4059
False
3383.0
3613
96.8540
285
4604
2
chr4A.!!$F1
4319
3
TraesCS4B01G124400
chr1A
541978987
541979960
973
True
1330.0
1330
91.6840
2015
2973
1
chr1A.!!$R1
958
4
TraesCS4B01G124400
chr1A
562129796
562130424
628
False
1116.0
1116
98.7280
4601
5228
1
chr1A.!!$F1
627
5
TraesCS4B01G124400
chr7B
539930527
539931152
625
True
1118.0
1118
98.8820
4603
5228
1
chr7B.!!$R1
625
6
TraesCS4B01G124400
chr6B
702810599
702811222
623
True
1114.0
1114
98.8780
4605
5228
1
chr6B.!!$R1
623
7
TraesCS4B01G124400
chr7A
55920055
55920678
623
False
1103.0
1103
98.5580
4605
5228
1
chr7A.!!$F1
623
8
TraesCS4B01G124400
chr7A
706400651
706401276
625
True
1101.0
1101
98.4030
4603
5228
1
chr7A.!!$R4
625
9
TraesCS4B01G124400
chr3B
26068979
26069540
561
True
682.0
682
88.8500
1
554
1
chr3B.!!$R3
553
10
TraesCS4B01G124400
chr3B
25932851
25933411
560
True
680.0
680
88.8500
1
554
1
chr3B.!!$R1
553
11
TraesCS4B01G124400
chr3B
26258036
26258597
561
True
676.0
676
88.6730
1
554
1
chr3B.!!$R5
553
12
TraesCS4B01G124400
chr3B
25998995
25999522
527
True
484.0
484
83.5110
1
554
1
chr3B.!!$R2
553
13
TraesCS4B01G124400
chr3B
26186561
26187088
527
True
484.0
484
83.4810
1
554
1
chr3B.!!$R4
553
14
TraesCS4B01G124400
chr3B
26296327
26297149
822
True
432.5
449
89.0720
1
554
2
chr3B.!!$R6
553
15
TraesCS4B01G124400
chr3B
26337040
26337815
775
True
431.0
444
88.9435
1
554
2
chr3B.!!$R7
553
16
TraesCS4B01G124400
chr6D
4672973
4673509
536
True
656.0
656
89.0540
1
527
1
chr6D.!!$R1
526
17
TraesCS4B01G124400
chr5D
512453675
512455153
1478
False
462.5
634
93.0890
77
768
2
chr5D.!!$F1
691
18
TraesCS4B01G124400
chr2B
431576710
431578248
1538
False
441.5
580
92.1425
3
772
2
chr2B.!!$F1
769
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.