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
TraesCS2B01G622100
chr2B
100.000
3417
0
0
1
3417
796163563
796166979
0.000000e+00
6311.0
1
TraesCS2B01G622100
chr2B
82.110
218
34
3
1225
1440
797183223
797183437
7.530000e-42
182.0
2
TraesCS2B01G622100
chr2B
80.531
226
34
10
1225
1444
797240393
797240614
7.590000e-37
165.0
3
TraesCS2B01G622100
chr2B
88.596
114
9
2
2408
2518
794675503
794675391
5.950000e-28
135.0
4
TraesCS2B01G622100
chr2B
96.970
66
2
0
1521
1586
794677691
794677626
1.000000e-20
111.0
5
TraesCS2B01G622100
chr2D
95.818
2415
45
13
1043
3417
600580510
600578112
0.000000e+00
3849.0
6
TraesCS2B01G622100
chr2D
93.418
1018
44
6
40
1045
600587228
600586222
0.000000e+00
1487.0
7
TraesCS2B01G622100
chr2D
86.015
1094
80
28
1223
2257
636923158
636922079
0.000000e+00
1105.0
8
TraesCS2B01G622100
chr2D
82.301
226
30
8
1225
1444
638350811
638350590
1.620000e-43
187.0
9
TraesCS2B01G622100
chr2D
75.592
422
72
25
1680
2080
637385428
637385017
2.710000e-41
180.0
10
TraesCS2B01G622100
chr2D
100.000
38
0
0
3209
3246
600577627
600577590
1.700000e-08
71.3
11
TraesCS2B01G622100
chr2D
89.796
49
0
2
2648
2691
637370047
637370095
1.320000e-04
58.4
12
TraesCS2B01G622100
chr2A
91.330
1165
55
19
1
1131
761602606
761603758
0.000000e+00
1550.0
13
TraesCS2B01G622100
chr2A
92.880
632
40
3
1
627
761807859
761807228
0.000000e+00
913.0
14
TraesCS2B01G622100
chr2A
97.697
521
10
1
2108
2626
761777367
761776847
0.000000e+00
894.0
15
TraesCS2B01G622100
chr2A
83.791
765
67
23
1526
2257
762725798
762726538
0.000000e+00
673.0
16
TraesCS2B01G622100
chr2A
96.567
233
8
0
2788
3020
761776675
761776443
1.490000e-103
387.0
17
TraesCS2B01G622100
chr2A
84.638
345
26
7
1223
1540
762724772
762725116
5.500000e-83
318.0
18
TraesCS2B01G622100
chr2A
88.636
264
6
2
3177
3417
761776444
761776182
1.990000e-77
300.0
19
TraesCS2B01G622100
chr2A
89.431
246
14
9
1802
2044
761777634
761777398
1.990000e-77
300.0
20
TraesCS2B01G622100
chr2A
96.450
169
4
1
2592
2758
761776843
761776675
9.340000e-71
278.0
21
TraesCS2B01G622100
chr2A
95.062
162
5
2
1341
1499
761777858
761777697
5.660000e-63
252.0
22
TraesCS2B01G622100
chr2A
90.303
165
13
3
2696
2859
762867738
762867576
2.670000e-51
213.0
23
TraesCS2B01G622100
chr2A
83.186
226
35
3
1215
1438
762660132
762660356
1.610000e-48
204.0
24
TraesCS2B01G622100
chr2A
79.221
308
46
10
2917
3220
762847952
762847659
7.480000e-47
198.0
25
TraesCS2B01G622100
chr2A
100.000
82
0
0
1043
1124
761777997
761777916
5.910000e-33
152.0
26
TraesCS2B01G622100
chr2A
80.625
160
28
3
1443
1600
763862582
763862424
1.670000e-23
121.0
27
TraesCS2B01G622100
chr2A
93.939
66
4
0
1521
1586
762720706
762720771
2.170000e-17
100.0
28
TraesCS2B01G622100
chr2A
89.333
75
7
1
1184
1258
761603757
761603830
3.630000e-15
93.5
29
TraesCS2B01G622100
chr2A
95.238
42
2
0
2990
3031
762868062
762868021
2.200000e-07
67.6
30
TraesCS2B01G622100
chr2A
88.679
53
6
0
2990
3042
762695936
762695884
7.910000e-07
65.8
31
TraesCS2B01G622100
chr7A
83.569
1345
133
44
1223
2520
30271557
30272860
0.000000e+00
1179.0
32
TraesCS2B01G622100
chr7A
82.116
1068
88
49
1223
2252
30240689
30241691
0.000000e+00
819.0
33
TraesCS2B01G622100
chr7A
81.313
396
61
11
539
930
609380769
609380383
3.310000e-80
309.0
34
TraesCS2B01G622100
chr7A
93.564
202
13
0
2319
2520
30241696
30241897
5.540000e-78
302.0
35
TraesCS2B01G622100
chr7A
93.258
89
6
0
1121
1209
30271414
30271502
7.690000e-27
132.0
36
TraesCS2B01G622100
chr4A
85.277
1046
84
24
1305
2288
699189121
699188084
0.000000e+00
1014.0
37
TraesCS2B01G622100
chr4A
82.677
381
57
6
552
929
461709893
461710267
2.540000e-86
329.0
38
TraesCS2B01G622100
chr7D
83.598
1134
95
29
1223
2300
29984547
29985645
0.000000e+00
979.0
39
TraesCS2B01G622100
chr7D
84.197
386
41
11
551
930
386363147
386362776
1.170000e-94
357.0
40
TraesCS2B01G622100
chr7D
91.765
85
3
2
2779
2859
133938665
133938581
7.750000e-22
115.0
41
TraesCS2B01G622100
chr7D
100.000
32
0
0
2319
2350
29985643
29985674
3.680000e-05
60.2
42
TraesCS2B01G622100
chr5D
82.576
396
55
11
545
934
487173576
487173189
1.520000e-88
337.0
43
TraesCS2B01G622100
chr5D
87.111
225
18
5
1706
1926
440114468
440114685
9.470000e-61
244.0
44
TraesCS2B01G622100
chr5D
86.813
91
11
1
2567
2657
555493662
555493573
2.170000e-17
100.0
45
TraesCS2B01G622100
chr5D
97.143
35
0
1
2414
2448
296933487
296933454
1.320000e-04
58.4
46
TraesCS2B01G622100
chr4D
82.895
380
55
6
554
930
5663362
5662990
1.970000e-87
333.0
47
TraesCS2B01G622100
chr4D
85.714
133
14
5
239
367
81913131
81913262
5.950000e-28
135.0
48
TraesCS2B01G622100
chr4D
92.941
85
2
2
2779
2859
308853867
308853783
1.670000e-23
121.0
49
TraesCS2B01G622100
chr4D
83.333
90
4
3
2414
2493
308854012
308853924
4.730000e-09
73.1
50
TraesCS2B01G622100
chr6B
82.143
392
54
12
541
927
76179240
76179620
4.250000e-84
322.0
51
TraesCS2B01G622100
chr6B
88.608
158
16
2
224
379
644860528
644860685
1.250000e-44
191.0
52
TraesCS2B01G622100
chr7B
83.333
306
44
5
625
930
380542072
380541774
3.360000e-70
276.0
53
TraesCS2B01G622100
chr7B
90.090
111
10
1
2408
2518
746125024
746124915
3.550000e-30
143.0
54
TraesCS2B01G622100
chr7B
80.769
156
22
4
2360
2515
746126490
746126343
7.750000e-22
115.0
55
TraesCS2B01G622100
chrUn
85.062
241
20
11
2290
2522
396320461
396320229
7.370000e-57
231.0
56
TraesCS2B01G622100
chrUn
75.561
401
73
21
1677
2062
234390382
234390772
1.260000e-39
174.0
57
TraesCS2B01G622100
chrUn
88.095
126
10
5
2710
2831
396319993
396319869
9.880000e-31
145.0
58
TraesCS2B01G622100
chr6A
85.635
181
23
3
201
379
573269661
573269840
1.620000e-43
187.0
59
TraesCS2B01G622100
chr1D
92.941
85
2
2
2779
2859
255588985
255588901
1.670000e-23
121.0
60
TraesCS2B01G622100
chr1D
97.222
36
1
0
193
228
233306793
233306828
1.020000e-05
62.1
61
TraesCS2B01G622100
chr1B
94.030
67
4
0
2449
2515
7245434
7245368
6.030000e-18
102.0
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
TraesCS2B01G622100
chr2B
796163563
796166979
3416
False
6311.000000
6311
100.000000
1
3417
1
chr2B.!!$F1
3416
1
TraesCS2B01G622100
chr2D
600577590
600580510
2920
True
1960.150000
3849
97.909000
1043
3417
2
chr2D.!!$R5
2374
2
TraesCS2B01G622100
chr2D
600586222
600587228
1006
True
1487.000000
1487
93.418000
40
1045
1
chr2D.!!$R1
1005
3
TraesCS2B01G622100
chr2D
636922079
636923158
1079
True
1105.000000
1105
86.015000
1223
2257
1
chr2D.!!$R2
1034
4
TraesCS2B01G622100
chr2A
761807228
761807859
631
True
913.000000
913
92.880000
1
627
1
chr2A.!!$R1
626
5
TraesCS2B01G622100
chr2A
761602606
761603830
1224
False
821.750000
1550
90.331500
1
1258
2
chr2A.!!$F3
1257
6
TraesCS2B01G622100
chr2A
762724772
762726538
1766
False
495.500000
673
84.214500
1223
2257
2
chr2A.!!$F4
1034
7
TraesCS2B01G622100
chr2A
761776182
761777997
1815
True
366.142857
894
94.834714
1043
3417
7
chr2A.!!$R5
2374
8
TraesCS2B01G622100
chr7A
30271414
30272860
1446
False
655.500000
1179
88.413500
1121
2520
2
chr7A.!!$F2
1399
9
TraesCS2B01G622100
chr7A
30240689
30241897
1208
False
560.500000
819
87.840000
1223
2520
2
chr7A.!!$F1
1297
10
TraesCS2B01G622100
chr4A
699188084
699189121
1037
True
1014.000000
1014
85.277000
1305
2288
1
chr4A.!!$R1
983
11
TraesCS2B01G622100
chr7D
29984547
29985674
1127
False
519.600000
979
91.799000
1223
2350
2
chr7D.!!$F1
1127
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.