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
TraesCS7B01G361100
chr7B
100.000
2390
0
0
1
2390
623271718
623269329
0.000000e+00
4414.0
1
TraesCS7B01G361100
chr7B
94.576
1899
85
12
177
2070
623485940
623484055
0.000000e+00
2920.0
2
TraesCS7B01G361100
chr7B
92.357
2041
126
17
167
2198
623059946
623057927
0.000000e+00
2878.0
3
TraesCS7B01G361100
chr7B
92.308
1963
114
11
237
2198
623102632
623100706
0.000000e+00
2754.0
4
TraesCS7B01G361100
chr7B
93.846
1170
56
8
231
1388
623373593
623372428
0.000000e+00
1748.0
5
TraesCS7B01G361100
chr7B
94.832
1103
51
4
1101
2198
586929659
586930760
0.000000e+00
1716.0
6
TraesCS7B01G361100
chr7B
93.134
1005
63
4
269
1267
623537885
623536881
0.000000e+00
1469.0
7
TraesCS7B01G361100
chr7B
92.654
1021
69
3
249
1267
623523444
623522428
0.000000e+00
1465.0
8
TraesCS7B01G361100
chr7B
95.005
921
43
2
1281
2198
623522372
623521452
0.000000e+00
1443.0
9
TraesCS7B01G361100
chr7B
94.886
919
46
1
1281
2198
623504495
623503577
0.000000e+00
1435.0
10
TraesCS7B01G361100
chr7B
94.565
920
48
2
1281
2198
623536811
623535892
0.000000e+00
1421.0
11
TraesCS7B01G361100
chr7B
91.546
970
48
11
1441
2389
623372415
623371459
0.000000e+00
1306.0
12
TraesCS7B01G361100
chr7B
91.892
777
58
3
249
1025
623540120
623539349
0.000000e+00
1081.0
13
TraesCS7B01G361100
chr7B
91.938
769
58
2
249
1017
623508332
623507568
0.000000e+00
1074.0
14
TraesCS7B01G361100
chr7B
85.373
335
37
7
1
333
623486006
623485682
1.060000e-88
337.0
15
TraesCS7B01G361100
chr7B
86.321
212
8
13
2199
2390
623521490
623521280
6.690000e-51
211.0
16
TraesCS7B01G361100
chr7B
85.849
212
9
13
2199
2390
623503615
623503405
3.110000e-49
206.0
17
TraesCS7B01G361100
chr7B
86.124
209
8
13
2202
2390
623535927
623535720
3.110000e-49
206.0
18
TraesCS7B01G361100
chr7B
84.906
212
11
2
2199
2390
586930722
586930932
6.740000e-46
195.0
19
TraesCS7B01G361100
chr7B
83.568
213
13
3
2199
2390
623057965
623057754
1.890000e-41
180.0
20
TraesCS7B01G361100
chr7D
92.853
1861
104
17
351
2198
568236268
568234424
0.000000e+00
2673.0
21
TraesCS7B01G361100
chr7D
83.159
1342
191
21
455
1771
568185804
568184473
0.000000e+00
1194.0
22
TraesCS7B01G361100
chr7D
83.333
210
14
2
2201
2390
568234460
568234252
8.780000e-40
174.0
23
TraesCS7B01G361100
chr2B
83.962
106
17
0
2199
2304
524517363
524517468
4.200000e-18
102.0
24
TraesCS7B01G361100
chr1B
81.818
110
14
5
2199
2304
553802603
553802710
1.180000e-13
87.9
25
TraesCS7B01G361100
chr4A
100.000
32
0
0
2264
2295
191794166
191794197
2.570000e-05
60.2
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
TraesCS7B01G361100
chr7B
623269329
623271718
2389
True
4414.000000
4414
100.000000
1
2390
1
chr7B.!!$R2
2389
1
TraesCS7B01G361100
chr7B
623100706
623102632
1926
True
2754.000000
2754
92.308000
237
2198
1
chr7B.!!$R1
1961
2
TraesCS7B01G361100
chr7B
623484055
623486006
1951
True
1628.500000
2920
89.974500
1
2070
2
chr7B.!!$R5
2069
3
TraesCS7B01G361100
chr7B
623057754
623059946
2192
True
1529.000000
2878
87.962500
167
2390
2
chr7B.!!$R3
2223
4
TraesCS7B01G361100
chr7B
623371459
623373593
2134
True
1527.000000
1748
92.696000
231
2389
2
chr7B.!!$R4
2158
5
TraesCS7B01G361100
chr7B
623535720
623540120
4400
True
1044.250000
1469
91.428750
249
2390
4
chr7B.!!$R8
2141
6
TraesCS7B01G361100
chr7B
623521280
623523444
2164
True
1039.666667
1465
91.326667
249
2390
3
chr7B.!!$R7
2141
7
TraesCS7B01G361100
chr7B
586929659
586930932
1273
False
955.500000
1716
89.869000
1101
2390
2
chr7B.!!$F1
1289
8
TraesCS7B01G361100
chr7B
623503405
623508332
4927
True
905.000000
1435
90.891000
249
2390
3
chr7B.!!$R6
2141
9
TraesCS7B01G361100
chr7D
568234252
568236268
2016
True
1423.500000
2673
88.093000
351
2390
2
chr7D.!!$R2
2039
10
TraesCS7B01G361100
chr7D
568184473
568185804
1331
True
1194.000000
1194
83.159000
455
1771
1
chr7D.!!$R1
1316
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.