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
TraesCS6B01G453000
chr6B
100.000
3552
0
0
1
3552
711664352
711667903
0.000000e+00
6560.0
1
TraesCS6B01G453000
chr6B
92.176
1815
126
10
794
2597
711695145
711693336
0.000000e+00
2551.0
2
TraesCS6B01G453000
chr6B
99.857
698
0
1
2856
3552
626660592
626659895
0.000000e+00
1282.0
3
TraesCS6B01G453000
chr6B
85.767
1082
120
13
1518
2577
142099024
142097955
0.000000e+00
1114.0
4
TraesCS6B01G453000
chr6B
89.646
367
25
5
2365
2722
711496362
711496000
4.180000e-124
455.0
5
TraesCS6B01G453000
chr6B
85.511
421
40
13
49
460
711695818
711695410
1.520000e-113
420.0
6
TraesCS6B01G453000
chr6B
95.652
69
2
1
487
555
711695410
711695343
3.750000e-20
110.0
7
TraesCS6B01G453000
chr6D
95.835
1969
72
4
897
2856
466544004
466545971
0.000000e+00
3173.0
8
TraesCS6B01G453000
chr6D
91.004
1812
129
14
797
2597
466551955
466550167
0.000000e+00
2412.0
9
TraesCS6B01G453000
chr6D
87.049
1637
168
20
1093
2696
466528255
466526630
0.000000e+00
1808.0
10
TraesCS6B01G453000
chr6D
85.218
1813
198
32
810
2573
67326881
67325090
0.000000e+00
1799.0
11
TraesCS6B01G453000
chr6D
89.629
916
44
12
1
898
466541326
466542208
0.000000e+00
1118.0
12
TraesCS6B01G453000
chr6D
80.105
191
25
10
282
465
466552937
466552753
2.880000e-26
130.0
13
TraesCS6B01G453000
chr6D
92.405
79
6
0
204
282
466552971
466552893
2.900000e-21
113.0
14
TraesCS6B01G453000
chr6D
91.892
74
6
0
2646
2719
67325061
67324988
1.740000e-18
104.0
15
TraesCS6B01G453000
chr6A
83.530
1949
248
34
654
2566
84700129
84698218
0.000000e+00
1753.0
16
TraesCS6B01G453000
chr6A
84.298
484
40
12
2213
2694
612578285
612577836
1.170000e-119
440.0
17
TraesCS6B01G453000
chr5A
90.909
1166
96
7
584
1739
46959204
46960369
0.000000e+00
1557.0
18
TraesCS6B01G453000
chr5A
88.843
242
19
4
12
247
46720111
46720350
1.250000e-74
291.0
19
TraesCS6B01G453000
chr5A
85.171
263
16
6
272
511
46882912
46883174
7.610000e-62
248.0
20
TraesCS6B01G453000
chr7A
80.652
1964
311
49
794
2722
219396792
219398721
0.000000e+00
1458.0
21
TraesCS6B01G453000
chr7A
84.658
1271
158
23
677
1923
668061902
668063159
0.000000e+00
1232.0
22
TraesCS6B01G453000
chr2D
83.106
1610
227
21
857
2444
493883369
493881783
0.000000e+00
1424.0
23
TraesCS6B01G453000
chr2D
85.897
78
9
2
282
359
414974286
414974211
8.170000e-12
82.4
24
TraesCS6B01G453000
chr2A
82.921
1616
234
20
851
2444
639694681
639696276
0.000000e+00
1417.0
25
TraesCS6B01G453000
chr2A
88.160
625
63
8
1969
2590
581963984
581963368
0.000000e+00
734.0
26
TraesCS6B01G453000
chr2A
84.722
144
12
5
2723
2856
2616072
2615929
6.190000e-28
135.0
27
TraesCS6B01G453000
chr2A
82.550
149
14
6
2719
2856
2614229
2614376
1.730000e-23
121.0
28
TraesCS6B01G453000
chr2A
82.639
144
14
5
2724
2856
23941100
23941243
2.240000e-22
117.0
29
TraesCS6B01G453000
chr2A
85.714
70
8
2
290
359
581966257
581966190
4.920000e-09
73.1
30
TraesCS6B01G453000
chr7D
88.319
1190
124
11
758
1936
576658036
576659221
0.000000e+00
1413.0
31
TraesCS6B01G453000
chr7D
86.262
626
76
8
1969
2590
576661160
576661779
0.000000e+00
671.0
32
TraesCS6B01G453000
chr7D
93.103
87
6
0
204
290
576657406
576657492
1.040000e-25
128.0
33
TraesCS6B01G453000
chr3B
100.000
698
0
0
2855
3552
292383483
292384180
0.000000e+00
1290.0
34
TraesCS6B01G453000
chr3B
99.857
700
1
0
2853
3552
292391560
292392259
0.000000e+00
1288.0
35
TraesCS6B01G453000
chr2B
99.857
700
1
0
2853
3552
451176083
451176782
0.000000e+00
1288.0
36
TraesCS6B01G453000
chr2B
99.857
697
1
0
2856
3552
443046355
443047051
0.000000e+00
1282.0
37
TraesCS6B01G453000
chr2B
99.715
701
1
1
2853
3552
443054430
443055130
0.000000e+00
1282.0
38
TraesCS6B01G453000
chr2B
81.079
1390
226
25
583
1947
246574409
246575786
0.000000e+00
1075.0
39
TraesCS6B01G453000
chr2B
82.857
140
20
4
237
374
246569990
246570127
4.820000e-24
122.0
40
TraesCS6B01G453000
chrUn
99.857
697
1
0
2856
3552
245665600
245664904
0.000000e+00
1282.0
41
TraesCS6B01G453000
chr5B
99.428
699
3
1
2855
3552
37237225
37236527
0.000000e+00
1267.0
42
TraesCS6B01G453000
chr5B
99.287
701
1
1
2856
3552
37229140
37228440
0.000000e+00
1264.0
43
TraesCS6B01G453000
chr1A
82.993
147
16
3
2722
2859
533777439
533777293
1.340000e-24
124.0
44
TraesCS6B01G453000
chr1A
82.069
145
15
6
2723
2856
533772558
533772702
2.900000e-21
113.0
45
TraesCS6B01G453000
chr1B
80.128
156
17
7
2717
2859
54923812
54923658
1.740000e-18
104.0
46
TraesCS6B01G453000
chr1B
90.278
72
7
0
2788
2859
54940643
54940572
1.050000e-15
95.3
47
TraesCS6B01G453000
chr7B
79.167
144
20
6
2726
2859
630605620
630605477
1.360000e-14
91.6
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
TraesCS6B01G453000
chr6B
711664352
711667903
3551
False
6560.000000
6560
100.000
1
3552
1
chr6B.!!$F1
3551
1
TraesCS6B01G453000
chr6B
626659895
626660592
697
True
1282.000000
1282
99.857
2856
3552
1
chr6B.!!$R2
696
2
TraesCS6B01G453000
chr6B
142097955
142099024
1069
True
1114.000000
1114
85.767
1518
2577
1
chr6B.!!$R1
1059
3
TraesCS6B01G453000
chr6B
711693336
711695818
2482
True
1027.000000
2551
91.113
49
2597
3
chr6B.!!$R4
2548
4
TraesCS6B01G453000
chr6D
466541326
466545971
4645
False
2145.500000
3173
92.732
1
2856
2
chr6D.!!$F1
2855
5
TraesCS6B01G453000
chr6D
466526630
466528255
1625
True
1808.000000
1808
87.049
1093
2696
1
chr6D.!!$R1
1603
6
TraesCS6B01G453000
chr6D
67324988
67326881
1893
True
951.500000
1799
88.555
810
2719
2
chr6D.!!$R2
1909
7
TraesCS6B01G453000
chr6D
466550167
466552971
2804
True
885.000000
2412
87.838
204
2597
3
chr6D.!!$R3
2393
8
TraesCS6B01G453000
chr6A
84698218
84700129
1911
True
1753.000000
1753
83.530
654
2566
1
chr6A.!!$R1
1912
9
TraesCS6B01G453000
chr5A
46959204
46960369
1165
False
1557.000000
1557
90.909
584
1739
1
chr5A.!!$F3
1155
10
TraesCS6B01G453000
chr7A
219396792
219398721
1929
False
1458.000000
1458
80.652
794
2722
1
chr7A.!!$F1
1928
11
TraesCS6B01G453000
chr7A
668061902
668063159
1257
False
1232.000000
1232
84.658
677
1923
1
chr7A.!!$F2
1246
12
TraesCS6B01G453000
chr2D
493881783
493883369
1586
True
1424.000000
1424
83.106
857
2444
1
chr2D.!!$R2
1587
13
TraesCS6B01G453000
chr2A
639694681
639696276
1595
False
1417.000000
1417
82.921
851
2444
1
chr2A.!!$F3
1593
14
TraesCS6B01G453000
chr2A
581963368
581966257
2889
True
403.550000
734
86.937
290
2590
2
chr2A.!!$R2
2300
15
TraesCS6B01G453000
chr7D
576657406
576661779
4373
False
737.333333
1413
89.228
204
2590
3
chr7D.!!$F1
2386
16
TraesCS6B01G453000
chr3B
292383483
292384180
697
False
1290.000000
1290
100.000
2855
3552
1
chr3B.!!$F1
697
17
TraesCS6B01G453000
chr3B
292391560
292392259
699
False
1288.000000
1288
99.857
2853
3552
1
chr3B.!!$F2
699
18
TraesCS6B01G453000
chr2B
451176083
451176782
699
False
1288.000000
1288
99.857
2853
3552
1
chr2B.!!$F5
699
19
TraesCS6B01G453000
chr2B
443046355
443047051
696
False
1282.000000
1282
99.857
2856
3552
1
chr2B.!!$F3
696
20
TraesCS6B01G453000
chr2B
443054430
443055130
700
False
1282.000000
1282
99.715
2853
3552
1
chr2B.!!$F4
699
21
TraesCS6B01G453000
chr2B
246574409
246575786
1377
False
1075.000000
1075
81.079
583
1947
1
chr2B.!!$F2
1364
22
TraesCS6B01G453000
chrUn
245664904
245665600
696
True
1282.000000
1282
99.857
2856
3552
1
chrUn.!!$R1
696
23
TraesCS6B01G453000
chr5B
37236527
37237225
698
True
1267.000000
1267
99.428
2855
3552
1
chr5B.!!$R2
697
24
TraesCS6B01G453000
chr5B
37228440
37229140
700
True
1264.000000
1264
99.287
2856
3552
1
chr5B.!!$R1
696
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.