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
TraesCS5A01G251900
chr5A
100.000
2708
0
0
1
2708
467670924
467673631
0.000000e+00
5001.0
1
TraesCS5A01G251900
chr5A
92.577
970
61
2
596
1555
467679352
467680320
0.000000e+00
1382.0
2
TraesCS5A01G251900
chr5A
86.721
979
103
21
1743
2706
438828653
438829619
0.000000e+00
1062.0
3
TraesCS5A01G251900
chr5A
95.798
595
23
1
1
595
467665058
467665650
0.000000e+00
959.0
4
TraesCS5A01G251900
chr5A
91.328
542
37
1
597
1128
359486909
359487450
0.000000e+00
732.0
5
TraesCS5A01G251900
chr5A
90.055
543
44
1
596
1128
359518570
359519112
0.000000e+00
695.0
6
TraesCS5A01G251900
chr5A
87.213
305
29
4
752
1046
217752002
217752306
3.340000e-89
339.0
7
TraesCS5A01G251900
chr5A
85.902
305
33
4
752
1046
217744093
217744397
1.560000e-82
316.0
8
TraesCS5A01G251900
chr5A
93.210
162
11
0
596
757
75561999
75562160
3.480000e-59
239.0
9
TraesCS5A01G251900
chr5A
91.781
73
6
0
782
854
191845584
191845512
4.770000e-18
102.0
10
TraesCS5A01G251900
chr1A
90.018
1102
78
20
1593
2683
250712114
250711034
0.000000e+00
1397.0
11
TraesCS5A01G251900
chr1A
89.655
1102
84
19
1593
2683
250695185
250694103
0.000000e+00
1376.0
12
TraesCS5A01G251900
chr1A
90.650
1016
68
16
1593
2599
250703354
250702357
0.000000e+00
1325.0
13
TraesCS5A01G251900
chr1A
90.340
911
81
6
1801
2704
35641349
35640439
0.000000e+00
1188.0
14
TraesCS5A01G251900
chr1A
90.792
543
39
2
596
1128
103722346
103721805
0.000000e+00
715.0
15
TraesCS5A01G251900
chr1A
90.467
514
39
1
625
1128
103730295
103729782
0.000000e+00
669.0
16
TraesCS5A01G251900
chr1A
91.099
191
11
5
1102
1290
93888973
93889159
1.240000e-63
254.0
17
TraesCS5A01G251900
chr1A
90.526
190
14
4
1102
1290
224724350
224724536
5.790000e-62
248.0
18
TraesCS5A01G251900
chr1A
89.529
191
12
7
1102
1290
224716161
224716345
4.510000e-58
235.0
19
TraesCS5A01G251900
chr3A
87.991
866
77
16
1733
2586
463563771
463562921
0.000000e+00
998.0
20
TraesCS5A01G251900
chr3A
95.134
596
25
3
1
595
313233273
313233865
0.000000e+00
937.0
21
TraesCS5A01G251900
chr3A
91.623
191
10
5
1102
1290
369017119
369016933
2.670000e-65
259.0
22
TraesCS5A01G251900
chr3A
91.304
115
10
0
2594
2708
279010310
279010196
1.000000e-34
158.0
23
TraesCS5A01G251900
chr3A
84.049
163
23
3
2544
2704
292882635
292882474
1.300000e-33
154.0
24
TraesCS5A01G251900
chr3A
84.810
158
16
4
2559
2708
659173303
659173146
4.670000e-33
152.0
25
TraesCS5A01G251900
chr3A
82.558
172
27
3
2535
2704
577265171
577265341
6.040000e-32
148.0
26
TraesCS5A01G251900
chr4A
85.378
978
113
23
1743
2703
108243744
108244708
0.000000e+00
987.0
27
TraesCS5A01G251900
chr4A
96.141
596
20
2
1
595
166606281
166605688
0.000000e+00
970.0
28
TraesCS5A01G251900
chr4A
95.294
595
24
1
1
595
183882266
183882856
0.000000e+00
941.0
29
TraesCS5A01G251900
chr4A
94.975
597
24
5
1
595
375423058
375423650
0.000000e+00
931.0
30
TraesCS5A01G251900
chr4A
90.370
540
42
5
596
1125
385918338
385918877
0.000000e+00
701.0
31
TraesCS5A01G251900
chr4A
90.018
541
44
1
596
1126
385926438
385926978
0.000000e+00
691.0
32
TraesCS5A01G251900
chr6A
85.031
982
110
31
1743
2703
240076577
240075612
0.000000e+00
965.0
33
TraesCS5A01G251900
chr6A
95.462
595
25
1
1
595
404424291
404424883
0.000000e+00
948.0
34
TraesCS5A01G251900
chr6A
95.302
596
25
2
1
595
589365363
589365956
0.000000e+00
942.0
35
TraesCS5A01G251900
chr6A
91.638
287
23
1
905
1190
545284466
545284180
1.950000e-106
396.0
36
TraesCS5A01G251900
chr2A
95.302
596
24
3
1
595
329499067
329499659
0.000000e+00
942.0
37
TraesCS5A01G251900
chr2A
95.302
596
25
2
1
595
425953003
425953596
0.000000e+00
942.0
38
TraesCS5A01G251900
chr2A
90.576
191
12
5
1102
1290
239451157
239451343
5.790000e-62
248.0
39
TraesCS5A01G251900
chr2A
91.758
182
10
4
1111
1290
244234387
244234565
5.790000e-62
248.0
40
TraesCS5A01G251900
chr2A
90.576
191
12
5
1102
1290
244247727
244247913
5.790000e-62
248.0
41
TraesCS5A01G251900
chr2A
90.052
191
13
5
1102
1290
239469637
239469823
2.690000e-60
243.0
42
TraesCS5A01G251900
chr2A
93.711
159
10
0
596
754
691898357
691898199
3.480000e-59
239.0
43
TraesCS5A01G251900
chr2A
91.453
117
10
0
1384
1500
344747219
344747335
7.760000e-36
161.0
44
TraesCS5A01G251900
chr2A
80.556
216
34
8
2484
2695
509115634
509115845
2.790000e-35
159.0
45
TraesCS5A01G251900
chr7A
83.925
1014
122
32
1714
2708
682809289
682808298
0.000000e+00
931.0
46
TraesCS5A01G251900
chr7A
91.289
287
25
0
904
1190
487606041
487606327
2.530000e-105
392.0
47
TraesCS5A01G251900
chr7A
88.325
197
19
4
597
791
261349663
261349469
1.620000e-57
233.0
48
TraesCS5A01G251900
chr7D
89.362
94
6
3
1398
1490
183949602
183949512
6.130000e-22
115.0
49
TraesCS5A01G251900
chr7D
88.298
94
7
3
1398
1490
148056874
148056964
2.850000e-20
110.0
50
TraesCS5A01G251900
chr7D
88.298
94
7
3
1398
1490
241486730
241486640
2.850000e-20
110.0
51
TraesCS5A01G251900
chr5D
89.362
94
6
3
1398
1490
214950031
214950121
6.130000e-22
115.0
52
TraesCS5A01G251900
chr4D
88.298
94
7
3
1398
1490
135951896
135951806
2.850000e-20
110.0
53
TraesCS5A01G251900
chr4D
88.298
94
7
3
1398
1490
191600021
191599931
2.850000e-20
110.0
54
TraesCS5A01G251900
chr4D
88.172
93
9
2
1398
1490
191607772
191607682
2.850000e-20
110.0
55
TraesCS5A01G251900
chr4D
85.556
90
11
2
846
935
73854654
73854741
2.870000e-15
93.5
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
TraesCS5A01G251900
chr5A
467670924
467673631
2707
False
5001
5001
100.000
1
2708
1
chr5A.!!$F8
2707
1
TraesCS5A01G251900
chr5A
467679352
467680320
968
False
1382
1382
92.577
596
1555
1
chr5A.!!$F9
959
2
TraesCS5A01G251900
chr5A
438828653
438829619
966
False
1062
1062
86.721
1743
2706
1
chr5A.!!$F6
963
3
TraesCS5A01G251900
chr5A
467665058
467665650
592
False
959
959
95.798
1
595
1
chr5A.!!$F7
594
4
TraesCS5A01G251900
chr5A
359486909
359487450
541
False
732
732
91.328
597
1128
1
chr5A.!!$F4
531
5
TraesCS5A01G251900
chr5A
359518570
359519112
542
False
695
695
90.055
596
1128
1
chr5A.!!$F5
532
6
TraesCS5A01G251900
chr1A
250711034
250712114
1080
True
1397
1397
90.018
1593
2683
1
chr1A.!!$R6
1090
7
TraesCS5A01G251900
chr1A
250694103
250695185
1082
True
1376
1376
89.655
1593
2683
1
chr1A.!!$R4
1090
8
TraesCS5A01G251900
chr1A
250702357
250703354
997
True
1325
1325
90.650
1593
2599
1
chr1A.!!$R5
1006
9
TraesCS5A01G251900
chr1A
35640439
35641349
910
True
1188
1188
90.340
1801
2704
1
chr1A.!!$R1
903
10
TraesCS5A01G251900
chr1A
103721805
103722346
541
True
715
715
90.792
596
1128
1
chr1A.!!$R2
532
11
TraesCS5A01G251900
chr1A
103729782
103730295
513
True
669
669
90.467
625
1128
1
chr1A.!!$R3
503
12
TraesCS5A01G251900
chr3A
463562921
463563771
850
True
998
998
87.991
1733
2586
1
chr3A.!!$R4
853
13
TraesCS5A01G251900
chr3A
313233273
313233865
592
False
937
937
95.134
1
595
1
chr3A.!!$F1
594
14
TraesCS5A01G251900
chr4A
108243744
108244708
964
False
987
987
85.378
1743
2703
1
chr4A.!!$F1
960
15
TraesCS5A01G251900
chr4A
166605688
166606281
593
True
970
970
96.141
1
595
1
chr4A.!!$R1
594
16
TraesCS5A01G251900
chr4A
183882266
183882856
590
False
941
941
95.294
1
595
1
chr4A.!!$F2
594
17
TraesCS5A01G251900
chr4A
375423058
375423650
592
False
931
931
94.975
1
595
1
chr4A.!!$F3
594
18
TraesCS5A01G251900
chr4A
385918338
385918877
539
False
701
701
90.370
596
1125
1
chr4A.!!$F4
529
19
TraesCS5A01G251900
chr4A
385926438
385926978
540
False
691
691
90.018
596
1126
1
chr4A.!!$F5
530
20
TraesCS5A01G251900
chr6A
240075612
240076577
965
True
965
965
85.031
1743
2703
1
chr6A.!!$R1
960
21
TraesCS5A01G251900
chr6A
404424291
404424883
592
False
948
948
95.462
1
595
1
chr6A.!!$F1
594
22
TraesCS5A01G251900
chr6A
589365363
589365956
593
False
942
942
95.302
1
595
1
chr6A.!!$F2
594
23
TraesCS5A01G251900
chr2A
329499067
329499659
592
False
942
942
95.302
1
595
1
chr2A.!!$F5
594
24
TraesCS5A01G251900
chr2A
425953003
425953596
593
False
942
942
95.302
1
595
1
chr2A.!!$F7
594
25
TraesCS5A01G251900
chr7A
682808298
682809289
991
True
931
931
83.925
1714
2708
1
chr7A.!!$R2
994
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.