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
TraesCS7D01G493200
chr7D
100.000
3233
0
0
1
3233
601392538
601389306
0.000000e+00
5971
1
TraesCS7D01G493200
chr7D
73.338
1309
285
41
989
2269
601494377
601493105
2.980000e-115
425
2
TraesCS7D01G493200
chr7D
72.570
1327
296
49
989
2286
601439652
601438365
3.940000e-99
372
3
TraesCS7D01G493200
chr7D
74.094
552
115
19
996
1530
601914896
601915436
5.470000e-48
202
4
TraesCS7D01G493200
chr7A
94.268
2669
104
23
579
3233
693035918
693033285
0.000000e+00
4036
5
TraesCS7D01G493200
chr7A
94.159
2671
106
21
579
3233
693062165
693059529
0.000000e+00
4023
6
TraesCS7D01G493200
chr7A
93.783
2670
106
22
579
3233
693088755
693086131
0.000000e+00
3956
7
TraesCS7D01G493200
chr7A
94.843
2230
85
14
653
2878
693134139
693131936
0.000000e+00
3454
8
TraesCS7D01G493200
chr7A
80.066
602
58
33
1
557
693134900
693134316
1.090000e-104
390
9
TraesCS7D01G493200
chr7A
80.354
509
52
29
110
580
693062710
693062212
3.090000e-90
342
10
TraesCS7D01G493200
chr7A
79.764
509
55
28
110
580
693089300
693088802
3.110000e-85
326
11
TraesCS7D01G493200
chr7A
76.210
496
105
11
996
1483
693492733
693493223
1.930000e-62
250
12
TraesCS7D01G493200
chr7B
90.000
2030
121
36
285
2279
680351696
680349714
0.000000e+00
2549
13
TraesCS7D01G493200
chr7B
91.546
970
57
11
2274
3233
680349669
680348715
0.000000e+00
1314
14
TraesCS7D01G493200
chr7B
85.896
787
92
6
1499
2284
680369914
680369146
0.000000e+00
821
15
TraesCS7D01G493200
chr7B
92.431
436
22
4
626
1060
680408196
680407771
2.130000e-171
612
16
TraesCS7D01G493200
chr7B
91.743
436
25
4
626
1060
680439544
680439119
2.150000e-166
595
17
TraesCS7D01G493200
chr7B
90.367
436
23
10
626
1060
680468133
680467716
3.640000e-154
555
18
TraesCS7D01G493200
chr7B
89.752
322
33
0
1180
1501
680382029
680381708
2.320000e-111
412
19
TraesCS7D01G493200
chr7B
73.070
1088
241
35
1151
2222
600720662
600721713
4.000000e-89
339
20
TraesCS7D01G493200
chr7B
86.102
295
29
7
1
283
680468570
680468276
1.130000e-79
307
21
TraesCS7D01G493200
chr7B
87.008
254
29
4
1
250
680439834
680439581
1.900000e-72
283
22
TraesCS7D01G493200
chr7B
86.957
230
26
4
25
250
680408462
680408233
4.140000e-64
255
23
TraesCS7D01G493200
chr7B
94.444
162
9
0
1052
1213
680466382
680466221
1.930000e-62
250
24
TraesCS7D01G493200
chr7B
91.975
162
13
0
1052
1213
680437715
680437554
9.020000e-56
228
25
TraesCS7D01G493200
chr3D
85.464
970
100
20
2275
3233
11144084
11143145
0.000000e+00
972
26
TraesCS7D01G493200
chr3D
83.687
613
75
12
2625
3232
11077708
11077116
3.640000e-154
555
27
TraesCS7D01G493200
chr3D
87.421
159
13
6
15
168
91710772
91710928
3.310000e-40
176
28
TraesCS7D01G493200
chr3D
86.228
167
15
7
8
168
553037749
553037913
1.190000e-39
174
29
TraesCS7D01G493200
chr3A
84.568
972
112
13
2275
3233
18780319
18779373
0.000000e+00
929
30
TraesCS7D01G493200
chr3A
83.608
970
111
23
2275
3228
18168135
18167198
0.000000e+00
867
31
TraesCS7D01G493200
chr3A
73.629
1331
285
39
971
2269
53204168
53205464
1.370000e-123
453
32
TraesCS7D01G493200
chr3B
84.691
405
43
10
2274
2670
25618993
25618600
1.410000e-103
387
33
TraesCS7D01G493200
chr3B
83.607
305
40
6
2274
2576
15761981
15762277
8.830000e-71
278
34
TraesCS7D01G493200
chr2D
72.481
1330
281
61
989
2280
33544542
33545824
1.850000e-92
350
35
TraesCS7D01G493200
chr2D
72.168
1333
286
61
989
2280
33340686
33341974
8.650000e-86
327
36
TraesCS7D01G493200
chr6D
86.585
164
15
6
11
169
431160668
431160829
1.190000e-39
174
37
TraesCS7D01G493200
chr4B
86.503
163
16
6
11
168
653312688
653312527
1.190000e-39
174
38
TraesCS7D01G493200
chrUn
85.294
170
20
4
4
169
426802960
426802792
1.540000e-38
171
39
TraesCS7D01G493200
chr5D
84.444
180
19
6
7
181
123459907
123460082
5.550000e-38
169
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
TraesCS7D01G493200
chr7D
601389306
601392538
3232
True
5971.000000
5971
100.000000
1
3233
1
chr7D.!!$R1
3232
1
TraesCS7D01G493200
chr7D
601493105
601494377
1272
True
425.000000
425
73.338000
989
2269
1
chr7D.!!$R3
1280
2
TraesCS7D01G493200
chr7D
601438365
601439652
1287
True
372.000000
372
72.570000
989
2286
1
chr7D.!!$R2
1297
3
TraesCS7D01G493200
chr7D
601914896
601915436
540
False
202.000000
202
74.094000
996
1530
1
chr7D.!!$F1
534
4
TraesCS7D01G493200
chr7A
693033285
693035918
2633
True
4036.000000
4036
94.268000
579
3233
1
chr7A.!!$R1
2654
5
TraesCS7D01G493200
chr7A
693059529
693062710
3181
True
2182.500000
4023
87.256500
110
3233
2
chr7A.!!$R2
3123
6
TraesCS7D01G493200
chr7A
693086131
693089300
3169
True
2141.000000
3956
86.773500
110
3233
2
chr7A.!!$R3
3123
7
TraesCS7D01G493200
chr7A
693131936
693134900
2964
True
1922.000000
3454
87.454500
1
2878
2
chr7A.!!$R4
2877
8
TraesCS7D01G493200
chr7B
680348715
680351696
2981
True
1931.500000
2549
90.773000
285
3233
2
chr7B.!!$R3
2948
9
TraesCS7D01G493200
chr7B
680369146
680369914
768
True
821.000000
821
85.896000
1499
2284
1
chr7B.!!$R1
785
10
TraesCS7D01G493200
chr7B
680407771
680408462
691
True
433.500000
612
89.694000
25
1060
2
chr7B.!!$R4
1035
11
TraesCS7D01G493200
chr7B
680466221
680468570
2349
True
370.666667
555
90.304333
1
1213
3
chr7B.!!$R6
1212
12
TraesCS7D01G493200
chr7B
680437554
680439834
2280
True
368.666667
595
90.242000
1
1213
3
chr7B.!!$R5
1212
13
TraesCS7D01G493200
chr7B
600720662
600721713
1051
False
339.000000
339
73.070000
1151
2222
1
chr7B.!!$F1
1071
14
TraesCS7D01G493200
chr3D
11143145
11144084
939
True
972.000000
972
85.464000
2275
3233
1
chr3D.!!$R2
958
15
TraesCS7D01G493200
chr3D
11077116
11077708
592
True
555.000000
555
83.687000
2625
3232
1
chr3D.!!$R1
607
16
TraesCS7D01G493200
chr3A
18779373
18780319
946
True
929.000000
929
84.568000
2275
3233
1
chr3A.!!$R2
958
17
TraesCS7D01G493200
chr3A
18167198
18168135
937
True
867.000000
867
83.608000
2275
3228
1
chr3A.!!$R1
953
18
TraesCS7D01G493200
chr3A
53204168
53205464
1296
False
453.000000
453
73.629000
971
2269
1
chr3A.!!$F1
1298
19
TraesCS7D01G493200
chr2D
33544542
33545824
1282
False
350.000000
350
72.481000
989
2280
1
chr2D.!!$F2
1291
20
TraesCS7D01G493200
chr2D
33340686
33341974
1288
False
327.000000
327
72.168000
989
2280
1
chr2D.!!$F1
1291
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.