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
TraesCS7A01G217800
chr7A
100.000
4991
0
0
1
4991
184325464
184330454
0.000000e+00
9217.0
1
TraesCS7A01G217800
chr7A
89.761
1885
146
27
2952
4801
184171484
184173356
0.000000e+00
2368.0
2
TraesCS7A01G217800
chr7A
88.940
1745
138
36
1069
2795
184316318
184318025
0.000000e+00
2102.0
3
TraesCS7A01G217800
chr7A
86.709
1738
170
24
1105
2795
184169694
184171417
0.000000e+00
1873.0
4
TraesCS7A01G217800
chr7A
93.841
828
48
1
3433
4257
184318576
184319403
0.000000e+00
1243.0
5
TraesCS7A01G217800
chr7A
86.297
613
59
14
4388
4991
184319401
184319997
1.170000e-180
643.0
6
TraesCS7A01G217800
chr7A
90.758
422
30
1
2989
3401
184318093
184318514
5.650000e-154
555.0
7
TraesCS7A01G217800
chr7A
84.987
373
30
15
76
435
184314991
184315350
6.150000e-94
355.0
8
TraesCS7A01G217800
chr7A
88.583
254
15
8
593
841
184315926
184316170
3.780000e-76
296.0
9
TraesCS7A01G217800
chr7A
90.000
210
14
5
899
1103
184316177
184316384
1.070000e-66
265.0
10
TraesCS7A01G217800
chr7A
86.154
65
9
0
3656
3720
184171165
184171229
2.490000e-08
71.3
11
TraesCS7A01G217800
chr7B
96.415
3124
96
7
1105
4216
145964954
145968073
0.000000e+00
5134.0
12
TraesCS7A01G217800
chr7B
93.869
2055
110
6
2950
4991
145933760
145935811
0.000000e+00
3083.0
13
TraesCS7A01G217800
chr7B
89.268
1789
144
27
2952
4702
145825838
145827616
0.000000e+00
2196.0
14
TraesCS7A01G217800
chr7B
86.583
1744
170
39
1105
2795
145824039
145825771
0.000000e+00
1866.0
15
TraesCS7A01G217800
chr7B
93.762
1074
55
3
1809
2879
145932595
145933659
0.000000e+00
1602.0
16
TraesCS7A01G217800
chr7B
88.586
990
58
24
593
1579
145931353
145932290
0.000000e+00
1151.0
17
TraesCS7A01G217800
chr7B
97.183
426
10
2
1
425
145963707
145964131
0.000000e+00
719.0
18
TraesCS7A01G217800
chr7B
93.846
260
10
2
488
741
145964141
145964400
2.180000e-103
387.0
19
TraesCS7A01G217800
chr7B
86.610
351
26
14
86
427
145930451
145930789
7.890000e-98
368.0
20
TraesCS7A01G217800
chr7B
96.988
166
5
0
938
1103
145964826
145964991
3.800000e-71
279.0
21
TraesCS7A01G217800
chr7B
86.154
130
16
2
4862
4991
145970364
145970491
6.740000e-29
139.0
22
TraesCS7A01G217800
chr7B
91.262
103
4
2
742
839
145964651
145964753
8.720000e-28
135.0
23
TraesCS7A01G217800
chr7D
95.402
3219
101
18
1809
4991
180071733
180074940
0.000000e+00
5081.0
24
TraesCS7A01G217800
chr7D
89.130
1978
156
36
840
2795
180013977
180015917
0.000000e+00
2407.0
25
TraesCS7A01G217800
chr7D
93.961
828
47
1
3433
4257
180016468
180017295
0.000000e+00
1249.0
26
TraesCS7A01G217800
chr7D
89.577
662
28
23
1
656
180069858
180070484
0.000000e+00
802.0
27
TraesCS7A01G217800
chr7D
96.842
475
15
0
1105
1579
180071041
180071515
0.000000e+00
795.0
28
TraesCS7A01G217800
chr7D
94.323
458
13
6
663
1109
180070632
180071087
0.000000e+00
689.0
29
TraesCS7A01G217800
chr7D
87.899
595
58
9
4388
4973
180017293
180017882
0.000000e+00
688.0
30
TraesCS7A01G217800
chr7D
90.284
422
32
1
2989
3401
180015985
180016406
1.220000e-150
544.0
31
TraesCS7A01G217800
chr4A
90.698
516
39
5
2331
2840
726121117
726120605
0.000000e+00
678.0
32
TraesCS7A01G217800
chr4A
89.685
349
36
0
2442
2790
726120487
726120139
3.540000e-121
446.0
33
TraesCS7A01G217800
chr4A
96.503
143
5
0
2950
3092
726120591
726120449
2.320000e-58
237.0
34
TraesCS7A01G217800
chr4A
89.947
189
10
1
3203
3391
726120143
726119964
8.350000e-58
235.0
35
TraesCS7A01G217800
chrUn
90.657
396
22
5
1765
2145
477165654
477165259
3.450000e-141
512.0
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
TraesCS7A01G217800
chr7A
184325464
184330454
4990
False
9217.000000
9217
100.000000
1
4991
1
chr7A.!!$F1
4990
1
TraesCS7A01G217800
chr7A
184169694
184173356
3662
False
1437.433333
2368
87.541333
1105
4801
3
chr7A.!!$F2
3696
2
TraesCS7A01G217800
chr7A
184314991
184319997
5006
False
779.857143
2102
89.058000
76
4991
7
chr7A.!!$F3
4915
3
TraesCS7A01G217800
chr7B
145824039
145827616
3577
False
2031.000000
2196
87.925500
1105
4702
2
chr7B.!!$F1
3597
4
TraesCS7A01G217800
chr7B
145930451
145935811
5360
False
1551.000000
3083
90.706750
86
4991
4
chr7B.!!$F2
4905
5
TraesCS7A01G217800
chr7B
145963707
145970491
6784
False
1132.166667
5134
93.641333
1
4991
6
chr7B.!!$F3
4990
6
TraesCS7A01G217800
chr7D
180069858
180074940
5082
False
1841.750000
5081
94.036000
1
4991
4
chr7D.!!$F2
4990
7
TraesCS7A01G217800
chr7D
180013977
180017882
3905
False
1222.000000
2407
90.318500
840
4973
4
chr7D.!!$F1
4133
8
TraesCS7A01G217800
chr4A
726119964
726121117
1153
True
399.000000
678
91.708250
2331
3391
4
chr4A.!!$R1
1060
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.