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
TraesCS7D01G516700
chr7D
100.000
2423
0
0
1
2423
616067180
616069602
0.000000e+00
4475
1
TraesCS7D01G516700
chr7D
85.596
1208
101
21
457
1622
616102583
616103759
0.000000e+00
1199
2
TraesCS7D01G516700
chr7D
84.225
1122
114
20
568
1657
616055152
616056242
0.000000e+00
1033
3
TraesCS7D01G516700
chr7D
85.000
780
100
10
888
1655
616174087
616174861
0.000000e+00
776
4
TraesCS7D01G516700
chr7D
88.042
577
58
11
1111
1680
616075963
616076535
0.000000e+00
673
5
TraesCS7D01G516700
chr7D
88.411
535
60
2
1878
2411
34315235
34315768
0.000000e+00
643
6
TraesCS7D01G516700
chr7D
81.818
429
42
16
1
419
616102064
616102466
6.460000e-86
327
7
TraesCS7D01G516700
chr7D
92.073
164
11
2
420
582
616054970
616055132
1.870000e-56
230
8
TraesCS7D01G516700
chr7D
83.766
154
18
6
269
420
616166793
616166941
3.250000e-29
139
9
TraesCS7D01G516700
chr7B
86.460
1130
88
26
601
1699
709258218
709259313
0.000000e+00
1179
10
TraesCS7D01G516700
chr7B
85.272
1066
122
18
617
1655
709322868
709323925
0.000000e+00
1066
11
TraesCS7D01G516700
chr7B
91.190
420
34
3
1
419
709353622
709354039
3.500000e-158
568
12
TraesCS7D01G516700
chr7B
93.827
243
6
2
503
737
709354145
709354386
8.240000e-95
357
13
TraesCS7D01G516700
chr7B
85.263
190
14
9
406
586
709257978
709258162
1.480000e-42
183
14
TraesCS7D01G516700
chr7B
92.708
96
6
1
1
95
709257774
709257869
1.170000e-28
137
15
TraesCS7D01G516700
chr7A
86.229
1111
96
23
575
1655
708912817
708913900
0.000000e+00
1151
16
TraesCS7D01G516700
chr7A
89.782
871
73
9
776
1646
709028446
709029300
0.000000e+00
1101
17
TraesCS7D01G516700
chr7A
93.653
646
36
3
1782
2423
708920188
708920832
0.000000e+00
961
18
TraesCS7D01G516700
chr7A
84.298
898
110
15
776
1655
709141809
709142693
0.000000e+00
848
19
TraesCS7D01G516700
chr7A
80.851
1081
134
46
510
1551
709121410
709122456
0.000000e+00
782
20
TraesCS7D01G516700
chr7A
83.168
909
98
34
776
1655
709129343
709130225
0.000000e+00
780
21
TraesCS7D01G516700
chr7A
88.361
421
41
5
1
419
708918440
708918854
1.290000e-137
499
22
TraesCS7D01G516700
chr7A
88.000
425
38
6
1
419
708912140
708912557
7.780000e-135
490
23
TraesCS7D01G516700
chr7A
82.796
279
17
19
406
657
709028113
709028387
1.130000e-53
220
24
TraesCS7D01G516700
chr7A
84.043
188
19
7
581
765
708919110
708919289
1.150000e-38
171
25
TraesCS7D01G516700
chr1A
87.709
537
58
6
1878
2411
53416333
53416864
9.520000e-174
619
26
TraesCS7D01G516700
chr1A
84.423
520
70
9
1895
2411
516577339
516576828
3.600000e-138
501
27
TraesCS7D01G516700
chr1B
87.942
481
52
4
1933
2411
547598697
547599173
1.630000e-156
562
28
TraesCS7D01G516700
chr1B
85.287
401
52
2
2011
2404
28328643
28329043
8.070000e-110
407
29
TraesCS7D01G516700
chr3D
83.685
521
76
4
1892
2410
369807232
369806719
1.300000e-132
483
30
TraesCS7D01G516700
chr6D
78.231
294
58
6
1894
2185
88881422
88881133
1.480000e-42
183
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
TraesCS7D01G516700
chr7D
616067180
616069602
2422
False
4475.000000
4475
100.000000
1
2423
1
chr7D.!!$F2
2422
1
TraesCS7D01G516700
chr7D
616174087
616174861
774
False
776.000000
776
85.000000
888
1655
1
chr7D.!!$F5
767
2
TraesCS7D01G516700
chr7D
616102064
616103759
1695
False
763.000000
1199
83.707000
1
1622
2
chr7D.!!$F7
1621
3
TraesCS7D01G516700
chr7D
616075963
616076535
572
False
673.000000
673
88.042000
1111
1680
1
chr7D.!!$F3
569
4
TraesCS7D01G516700
chr7D
34315235
34315768
533
False
643.000000
643
88.411000
1878
2411
1
chr7D.!!$F1
533
5
TraesCS7D01G516700
chr7D
616054970
616056242
1272
False
631.500000
1033
88.149000
420
1657
2
chr7D.!!$F6
1237
6
TraesCS7D01G516700
chr7B
709322868
709323925
1057
False
1066.000000
1066
85.272000
617
1655
1
chr7B.!!$F1
1038
7
TraesCS7D01G516700
chr7B
709257774
709259313
1539
False
499.666667
1179
88.143667
1
1699
3
chr7B.!!$F2
1698
8
TraesCS7D01G516700
chr7B
709353622
709354386
764
False
462.500000
568
92.508500
1
737
2
chr7B.!!$F3
736
9
TraesCS7D01G516700
chr7A
709141809
709142693
884
False
848.000000
848
84.298000
776
1655
1
chr7A.!!$F3
879
10
TraesCS7D01G516700
chr7A
708912140
708913900
1760
False
820.500000
1151
87.114500
1
1655
2
chr7A.!!$F4
1654
11
TraesCS7D01G516700
chr7A
709121410
709122456
1046
False
782.000000
782
80.851000
510
1551
1
chr7A.!!$F1
1041
12
TraesCS7D01G516700
chr7A
709129343
709130225
882
False
780.000000
780
83.168000
776
1655
1
chr7A.!!$F2
879
13
TraesCS7D01G516700
chr7A
709028113
709029300
1187
False
660.500000
1101
86.289000
406
1646
2
chr7A.!!$F6
1240
14
TraesCS7D01G516700
chr7A
708918440
708920832
2392
False
543.666667
961
88.685667
1
2423
3
chr7A.!!$F5
2422
15
TraesCS7D01G516700
chr1A
53416333
53416864
531
False
619.000000
619
87.709000
1878
2411
1
chr1A.!!$F1
533
16
TraesCS7D01G516700
chr1A
516576828
516577339
511
True
501.000000
501
84.423000
1895
2411
1
chr1A.!!$R1
516
17
TraesCS7D01G516700
chr3D
369806719
369807232
513
True
483.000000
483
83.685000
1892
2410
1
chr3D.!!$R1
518
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.