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
TraesCS7A01G511400
chr7A
100.000
3099
0
0
1
3099
699089814
699092912
0.000000e+00
5723.0
1
TraesCS7A01G511400
chr7A
74.864
736
167
13
1383
2108
699066830
699067557
4.990000e-83
318.0
2
TraesCS7A01G511400
chr7A
85.366
205
27
3
2878
3080
727814870
727815073
3.130000e-50
209.0
3
TraesCS7A01G511400
chr7B
90.652
1380
80
11
773
2121
691457935
691459296
0.000000e+00
1788.0
4
TraesCS7A01G511400
chr7B
94.109
696
39
2
2386
3080
733785064
733784370
0.000000e+00
1057.0
5
TraesCS7A01G511400
chr7B
91.860
258
17
1
2121
2378
691459394
691459647
1.060000e-94
357.0
6
TraesCS7A01G511400
chr7B
83.251
203
32
2
1900
2101
691275732
691275531
5.280000e-43
185.0
7
TraesCS7A01G511400
chr7B
81.604
212
23
6
2542
2747
430842207
430842408
8.890000e-36
161.0
8
TraesCS7A01G511400
chr7B
97.143
35
1
0
3065
3099
742762455
742762489
3.340000e-05
60.2
9
TraesCS7A01G511400
chr7B
97.143
35
1
0
3065
3099
742801788
742801822
3.340000e-05
60.2
10
TraesCS7A01G511400
chr4A
97.320
709
19
0
2391
3099
564699811
564700519
0.000000e+00
1205.0
11
TraesCS7A01G511400
chr4A
96.232
690
26
0
2391
3080
625074029
625073340
0.000000e+00
1131.0
12
TraesCS7A01G511400
chr4A
93.878
147
8
1
645
791
94991762
94991617
1.450000e-53
220.0
13
TraesCS7A01G511400
chr2A
95.672
670
28
1
2411
3080
58007378
58008046
0.000000e+00
1075.0
14
TraesCS7A01G511400
chr2A
95.320
641
30
0
1
641
749458995
749458355
0.000000e+00
1018.0
15
TraesCS7A01G511400
chr2A
95.171
642
29
2
1
641
560676531
560677171
0.000000e+00
1013.0
16
TraesCS7A01G511400
chr2A
93.292
641
42
1
1
641
459001125
459001764
0.000000e+00
944.0
17
TraesCS7A01G511400
chr2A
96.429
140
4
1
634
772
127160888
127160749
2.400000e-56
230.0
18
TraesCS7A01G511400
chr2A
96.377
138
4
1
634
770
560677278
560677415
3.110000e-55
226.0
19
TraesCS7A01G511400
chr2A
94.161
137
8
0
645
781
206083151
206083015
3.130000e-50
209.0
20
TraesCS7A01G511400
chr2A
92.361
144
10
1
634
776
749457902
749457759
1.460000e-48
204.0
21
TraesCS7A01G511400
chr1A
94.228
641
34
3
1
641
399819698
399820335
0.000000e+00
976.0
22
TraesCS7A01G511400
chr5A
94.072
641
36
2
1
641
482761373
482762011
0.000000e+00
972.0
23
TraesCS7A01G511400
chr5A
94.373
622
34
1
1
622
591677553
591676933
0.000000e+00
953.0
24
TraesCS7A01G511400
chr5A
95.035
141
3
4
634
772
482762125
482762263
5.200000e-53
219.0
25
TraesCS7A01G511400
chr6A
93.916
641
37
2
1
641
54974668
54975306
0.000000e+00
966.0
26
TraesCS7A01G511400
chr6A
93.760
641
39
1
1
641
22756828
22757467
0.000000e+00
961.0
27
TraesCS7A01G511400
chr6A
95.714
140
5
1
634
772
22757575
22757714
1.120000e-54
224.0
28
TraesCS7A01G511400
chr6A
95.000
140
6
1
634
772
54975413
54975552
5.200000e-53
219.0
29
TraesCS7A01G511400
chr6A
92.517
147
7
4
645
790
103976411
103976268
1.130000e-49
207.0
30
TraesCS7A01G511400
chr3B
93.281
640
41
2
2
641
708795528
708796165
0.000000e+00
942.0
31
TraesCS7A01G511400
chr3B
74.038
1117
244
37
1018
2113
555156081
555154990
6.180000e-112
414.0
32
TraesCS7A01G511400
chr3B
96.212
132
5
0
645
776
64548255
64548124
1.870000e-52
217.0
33
TraesCS7A01G511400
chr3B
76.562
384
44
25
2386
2753
90739424
90739071
5.310000e-38
169.0
34
TraesCS7A01G511400
chr1B
81.831
699
114
9
2391
3080
209564368
209565062
2.680000e-160
575.0
35
TraesCS7A01G511400
chr1B
96.992
133
4
0
645
777
581115126
581115258
1.120000e-54
224.0
36
TraesCS7A01G511400
chr2B
92.333
300
23
0
2781
3080
778832238
778831939
7.940000e-116
427.0
37
TraesCS7A01G511400
chr3A
80.274
583
78
22
2474
3037
700757908
700757344
3.720000e-109
405.0
38
TraesCS7A01G511400
chr3A
78.727
550
101
10
1569
2115
563395108
563395644
1.370000e-93
353.0
39
TraesCS7A01G511400
chr7D
79.318
440
51
20
2391
2812
638269451
638269034
3.940000e-69
272.0
40
TraesCS7A01G511400
chr7D
100.000
35
0
0
3065
3099
82466992
82466958
7.170000e-07
65.8
41
TraesCS7A01G511400
chr4B
94.928
138
6
1
634
770
1738519
1738382
6.730000e-52
215.0
42
TraesCS7A01G511400
chr4B
93.151
146
9
1
645
789
11437328
11437183
2.420000e-51
213.0
43
TraesCS7A01G511400
chr5B
93.056
144
9
1
634
776
360408745
360408602
3.130000e-50
209.0
44
TraesCS7A01G511400
chr5B
93.571
140
8
1
634
772
44136461
44136600
1.130000e-49
207.0
45
TraesCS7A01G511400
chr3D
77.657
367
41
25
2391
2743
160722832
160723171
5.280000e-43
185.0
46
TraesCS7A01G511400
chr3D
97.143
35
1
0
3065
3099
454669735
454669701
3.340000e-05
60.2
47
TraesCS7A01G511400
chr6D
95.238
42
2
0
2706
2747
414095571
414095612
1.990000e-07
67.6
48
TraesCS7A01G511400
chrUn
100.000
32
0
0
3068
3099
334693055
334693024
3.340000e-05
60.2
49
TraesCS7A01G511400
chrUn
97.143
35
1
0
3065
3099
335123900
335123934
3.340000e-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
TraesCS7A01G511400
chr7A
699089814
699092912
3098
False
5723.0
5723
100.0000
1
3099
1
chr7A.!!$F2
3098
1
TraesCS7A01G511400
chr7A
699066830
699067557
727
False
318.0
318
74.8640
1383
2108
1
chr7A.!!$F1
725
2
TraesCS7A01G511400
chr7B
691457935
691459647
1712
False
1072.5
1788
91.2560
773
2378
2
chr7B.!!$F4
1605
3
TraesCS7A01G511400
chr7B
733784370
733785064
694
True
1057.0
1057
94.1090
2386
3080
1
chr7B.!!$R2
694
4
TraesCS7A01G511400
chr4A
564699811
564700519
708
False
1205.0
1205
97.3200
2391
3099
1
chr4A.!!$F1
708
5
TraesCS7A01G511400
chr4A
625073340
625074029
689
True
1131.0
1131
96.2320
2391
3080
1
chr4A.!!$R2
689
6
TraesCS7A01G511400
chr2A
58007378
58008046
668
False
1075.0
1075
95.6720
2411
3080
1
chr2A.!!$F1
669
7
TraesCS7A01G511400
chr2A
459001125
459001764
639
False
944.0
944
93.2920
1
641
1
chr2A.!!$F2
640
8
TraesCS7A01G511400
chr2A
560676531
560677415
884
False
619.5
1013
95.7740
1
770
2
chr2A.!!$F3
769
9
TraesCS7A01G511400
chr2A
749457759
749458995
1236
True
611.0
1018
93.8405
1
776
2
chr2A.!!$R3
775
10
TraesCS7A01G511400
chr1A
399819698
399820335
637
False
976.0
976
94.2280
1
641
1
chr1A.!!$F1
640
11
TraesCS7A01G511400
chr5A
591676933
591677553
620
True
953.0
953
94.3730
1
622
1
chr5A.!!$R1
621
12
TraesCS7A01G511400
chr5A
482761373
482762263
890
False
595.5
972
94.5535
1
772
2
chr5A.!!$F1
771
13
TraesCS7A01G511400
chr6A
22756828
22757714
886
False
592.5
961
94.7370
1
772
2
chr6A.!!$F1
771
14
TraesCS7A01G511400
chr6A
54974668
54975552
884
False
592.5
966
94.4580
1
772
2
chr6A.!!$F2
771
15
TraesCS7A01G511400
chr3B
708795528
708796165
637
False
942.0
942
93.2810
2
641
1
chr3B.!!$F1
639
16
TraesCS7A01G511400
chr3B
555154990
555156081
1091
True
414.0
414
74.0380
1018
2113
1
chr3B.!!$R3
1095
17
TraesCS7A01G511400
chr1B
209564368
209565062
694
False
575.0
575
81.8310
2391
3080
1
chr1B.!!$F1
689
18
TraesCS7A01G511400
chr3A
700757344
700757908
564
True
405.0
405
80.2740
2474
3037
1
chr3A.!!$R1
563
19
TraesCS7A01G511400
chr3A
563395108
563395644
536
False
353.0
353
78.7270
1569
2115
1
chr3A.!!$F1
546
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.