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
TraesCS4A01G473800
chr4A
100.000
3630
0
0
1
3630
733641387
733637758
0.000000e+00
6704.0
1
TraesCS4A01G473800
chr4A
80.767
1591
230
43
902
2438
733672341
733670773
0.000000e+00
1173.0
2
TraesCS4A01G473800
chr4A
81.137
1442
232
26
1005
2435
733741333
733742745
0.000000e+00
1120.0
3
TraesCS4A01G473800
chr4A
80.971
762
123
14
1691
2438
733761474
733762227
5.220000e-163
584.0
4
TraesCS4A01G473800
chr4A
79.828
813
105
23
915
1687
733759891
733760684
4.120000e-149
538.0
5
TraesCS4A01G473800
chr4A
84.818
494
53
13
2586
3067
733762369
733762852
9.120000e-131
477.0
6
TraesCS4A01G473800
chr4A
80.866
277
30
14
2500
2768
733670686
733670425
2.860000e-46
196.0
7
TraesCS4A01G473800
chr4A
93.023
43
3
0
2456
2498
733670770
733670728
3.030000e-06
63.9
8
TraesCS4A01G473800
chr4A
96.970
33
1
0
2500
2532
733762318
733762350
5.060000e-04
56.5
9
TraesCS4A01G473800
chr7A
94.146
2528
86
18
822
3319
7669113
7671608
0.000000e+00
3792.0
10
TraesCS4A01G473800
chr7A
85.916
2265
235
39
822
3056
7633964
7636174
0.000000e+00
2338.0
11
TraesCS4A01G473800
chr7A
80.154
1426
214
32
1044
2438
7628830
7630217
0.000000e+00
1002.0
12
TraesCS4A01G473800
chr7A
86.332
717
67
19
2507
3206
7630309
7631011
0.000000e+00
752.0
13
TraesCS4A01G473800
chr7A
90.307
423
28
7
3081
3494
7636172
7636590
3.190000e-150
542.0
14
TraesCS4A01G473800
chr7A
74.653
576
90
34
2496
3046
7636623
7637167
1.710000e-48
204.0
15
TraesCS4A01G473800
chr7A
83.673
147
15
7
3490
3628
7636614
7636759
2.940000e-26
130.0
16
TraesCS4A01G473800
chr7A
83.740
123
12
5
697
815
401562162
401562280
3.830000e-20
110.0
17
TraesCS4A01G473800
chr7A
80.916
131
18
4
3503
3627
7670787
7670916
2.980000e-16
97.1
18
TraesCS4A01G473800
chr7A
78.740
127
25
2
1361
1486
118314007
118314132
2.320000e-12
84.2
19
TraesCS4A01G473800
chr7D
85.826
2681
276
54
842
3492
6582044
6584650
0.000000e+00
2750.0
20
TraesCS4A01G473800
chr7D
80.978
1472
218
38
1005
2438
6490983
6492430
0.000000e+00
1110.0
21
TraesCS4A01G473800
chr7D
85.503
676
73
15
2507
3168
6492522
6493186
0.000000e+00
682.0
22
TraesCS4A01G473800
chr7D
76.190
567
89
28
2496
3046
6584686
6585222
1.290000e-64
257.0
23
TraesCS4A01G473800
chr7D
84.564
149
14
3
3490
3630
6584677
6584824
4.890000e-29
139.0
24
TraesCS4A01G473800
chr7D
81.102
127
19
5
1354
1477
75806765
75806641
2.980000e-16
97.1
25
TraesCS4A01G473800
chr5A
98.762
808
8
2
1
808
115675917
115675112
0.000000e+00
1435.0
26
TraesCS4A01G473800
chr5A
86.789
545
66
6
70
610
490151321
490151863
1.440000e-168
603.0
27
TraesCS4A01G473800
chr7B
97.691
823
11
5
1
821
6678217
6679033
0.000000e+00
1408.0
28
TraesCS4A01G473800
chr2B
95.567
812
19
4
1
812
232258489
232257695
0.000000e+00
1284.0
29
TraesCS4A01G473800
chr2B
87.075
588
57
10
7
591
699915812
699915241
0.000000e+00
647.0
30
TraesCS4A01G473800
chr1B
95.086
814
21
7
1
814
628793970
628794764
0.000000e+00
1264.0
31
TraesCS4A01G473800
chr1B
86.364
110
8
5
708
814
646746166
646746061
2.960000e-21
113.0
32
TraesCS4A01G473800
chr1B
80.952
126
21
2
695
819
637911207
637911330
2.980000e-16
97.1
33
TraesCS4A01G473800
chr1B
77.070
157
34
2
1333
1488
643032683
643032528
4.990000e-14
89.8
34
TraesCS4A01G473800
chr1A
88.121
564
56
9
130
684
515149775
515150336
0.000000e+00
660.0
35
TraesCS4A01G473800
chr1A
87.922
563
58
8
130
684
514893510
514894070
0.000000e+00
654.0
36
TraesCS4A01G473800
chr1A
89.216
102
8
3
709
810
272003746
272003648
1.370000e-24
124.0
37
TraesCS4A01G473800
chr1A
82.517
143
21
4
708
849
244564554
244564693
4.920000e-24
122.0
38
TraesCS4A01G473800
chr2A
87.382
531
56
10
70
593
720971769
720972295
1.870000e-167
599.0
39
TraesCS4A01G473800
chr2A
93.333
45
3
0
1091
1135
752551786
752551830
2.340000e-07
67.6
40
TraesCS4A01G473800
chr6D
87.855
387
44
3
225
610
300218493
300218109
5.530000e-123
451.0
41
TraesCS4A01G473800
chr6D
86.747
83
11
0
3548
3630
7564070
7563988
3.860000e-15
93.5
42
TraesCS4A01G473800
chr3B
90.141
284
26
2
70
351
458263990
458263707
5.730000e-98
368.0
43
TraesCS4A01G473800
chr2D
89.147
129
14
0
1073
1201
440617045
440616917
1.040000e-35
161.0
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
TraesCS4A01G473800
chr4A
733637758
733641387
3629
True
6704.000000
6704
100.000000
1
3630
1
chr4A.!!$R1
3629
1
TraesCS4A01G473800
chr4A
733741333
733742745
1412
False
1120.000000
1120
81.137000
1005
2435
1
chr4A.!!$F1
1430
2
TraesCS4A01G473800
chr4A
733670425
733672341
1916
True
477.633333
1173
84.885333
902
2768
3
chr4A.!!$R2
1866
3
TraesCS4A01G473800
chr4A
733759891
733762852
2961
False
413.875000
584
85.646750
915
3067
4
chr4A.!!$F2
2152
4
TraesCS4A01G473800
chr7A
7669113
7671608
2495
False
1944.550000
3792
87.531000
822
3627
2
chr7A.!!$F4
2805
5
TraesCS4A01G473800
chr7A
7628830
7637167
8337
False
828.000000
2338
83.505833
822
3628
6
chr7A.!!$F3
2806
6
TraesCS4A01G473800
chr7D
6582044
6585222
3178
False
1048.666667
2750
82.193333
842
3630
3
chr7D.!!$F2
2788
7
TraesCS4A01G473800
chr7D
6490983
6493186
2203
False
896.000000
1110
83.240500
1005
3168
2
chr7D.!!$F1
2163
8
TraesCS4A01G473800
chr5A
115675112
115675917
805
True
1435.000000
1435
98.762000
1
808
1
chr5A.!!$R1
807
9
TraesCS4A01G473800
chr5A
490151321
490151863
542
False
603.000000
603
86.789000
70
610
1
chr5A.!!$F1
540
10
TraesCS4A01G473800
chr7B
6678217
6679033
816
False
1408.000000
1408
97.691000
1
821
1
chr7B.!!$F1
820
11
TraesCS4A01G473800
chr2B
232257695
232258489
794
True
1284.000000
1284
95.567000
1
812
1
chr2B.!!$R1
811
12
TraesCS4A01G473800
chr2B
699915241
699915812
571
True
647.000000
647
87.075000
7
591
1
chr2B.!!$R2
584
13
TraesCS4A01G473800
chr1B
628793970
628794764
794
False
1264.000000
1264
95.086000
1
814
1
chr1B.!!$F1
813
14
TraesCS4A01G473800
chr1A
515149775
515150336
561
False
660.000000
660
88.121000
130
684
1
chr1A.!!$F3
554
15
TraesCS4A01G473800
chr1A
514893510
514894070
560
False
654.000000
654
87.922000
130
684
1
chr1A.!!$F2
554
16
TraesCS4A01G473800
chr2A
720971769
720972295
526
False
599.000000
599
87.382000
70
593
1
chr2A.!!$F1
523
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.