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
TraesCS2D01G224700
chr2D
100.000
2723
0
0
1
2723
192187457
192184735
0.000000e+00
5029.0
1
TraesCS2D01G224700
chr2D
88.825
698
50
10
88
759
142021229
142020534
0.000000e+00
832.0
2
TraesCS2D01G224700
chr2D
89.453
512
28
9
275
761
448510445
448509935
8.280000e-175
623.0
3
TraesCS2D01G224700
chr2D
89.301
458
30
10
1
457
391337582
391338021
8.520000e-155
556.0
4
TraesCS2D01G224700
chr2B
95.031
966
17
10
763
1724
248136860
248137798
0.000000e+00
1489.0
5
TraesCS2D01G224700
chr2B
85.517
725
66
20
68
759
134248566
134247848
0.000000e+00
721.0
6
TraesCS2D01G224700
chr2B
88.124
421
26
9
2326
2723
248138502
248138921
1.900000e-131
479.0
7
TraesCS2D01G224700
chr2B
81.534
639
35
22
1749
2333
248137795
248138404
1.490000e-122
449.0
8
TraesCS2D01G224700
chr2B
77.538
325
55
12
1003
1319
728398394
728398080
2.150000e-41
180.0
9
TraesCS2D01G224700
chr2A
96.875
832
16
4
903
1734
205910830
205911651
0.000000e+00
1384.0
10
TraesCS2D01G224700
chr2A
94.581
609
25
4
2121
2723
205913954
205914560
0.000000e+00
935.0
11
TraesCS2D01G224700
chr2A
89.700
534
28
3
253
759
68539839
68540372
0.000000e+00
656.0
12
TraesCS2D01G224700
chr2A
91.756
279
14
5
1849
2122
205913596
205913870
1.980000e-101
379.0
13
TraesCS2D01G224700
chr2A
94.286
105
5
1
1733
1836
205913305
205913409
2.810000e-35
159.0
14
TraesCS2D01G224700
chr2A
97.561
41
0
1
795
835
205910709
205910748
4.870000e-08
69.4
15
TraesCS2D01G224700
chr1D
89.313
786
47
11
1
759
40864289
40863514
0.000000e+00
952.0
16
TraesCS2D01G224700
chr1D
88.604
781
52
16
5
759
410251368
410250599
0.000000e+00
915.0
17
TraesCS2D01G224700
chr1D
91.941
546
38
5
65
608
62438383
62437842
0.000000e+00
760.0
18
TraesCS2D01G224700
chr1D
83.004
253
37
3
1067
1319
262341552
262341798
9.810000e-55
224.0
19
TraesCS2D01G224700
chr4A
90.669
718
43
9
56
759
95193263
95193970
0.000000e+00
933.0
20
TraesCS2D01G224700
chr4A
87.006
785
66
12
1
759
507919028
507918254
0.000000e+00
852.0
21
TraesCS2D01G224700
chr4A
87.258
722
54
18
1
695
123254390
123253680
0.000000e+00
789.0
22
TraesCS2D01G224700
chr4A
82.592
787
61
26
1
759
712564496
712565234
2.300000e-175
625.0
23
TraesCS2D01G224700
chr4A
82.500
440
55
6
1
427
685796407
685796837
1.540000e-97
366.0
24
TraesCS2D01G224700
chr4A
74.102
668
134
29
1003
1651
5115255
5114608
3.500000e-59
239.0
25
TraesCS2D01G224700
chr6D
88.662
785
44
19
1
762
300294186
300294948
0.000000e+00
915.0
26
TraesCS2D01G224700
chr6D
89.124
708
37
9
1
695
414103764
414104444
0.000000e+00
845.0
27
TraesCS2D01G224700
chr6D
89.029
556
48
5
1
543
141140942
141141497
0.000000e+00
676.0
28
TraesCS2D01G224700
chr6D
95.652
69
3
0
693
761
33214604
33214672
7.970000e-21
111.0
29
TraesCS2D01G224700
chr7B
91.266
561
32
6
1
547
162112742
162112185
0.000000e+00
749.0
30
TraesCS2D01G224700
chr7B
86.027
730
62
14
64
761
440217043
440217764
0.000000e+00
747.0
31
TraesCS2D01G224700
chr7B
82.881
590
40
29
199
762
439255195
439255749
8.820000e-130
473.0
32
TraesCS2D01G224700
chr7B
95.714
70
3
0
693
762
72981989
72982058
2.220000e-21
113.0
33
TraesCS2D01G224700
chr5B
83.611
781
66
21
10
761
454692513
454691766
0.000000e+00
676.0
34
TraesCS2D01G224700
chr5B
75.371
337
65
13
994
1321
17952349
17952676
2.180000e-31
147.0
35
TraesCS2D01G224700
chr3D
83.919
740
62
25
64
762
355894578
355895301
0.000000e+00
654.0
36
TraesCS2D01G224700
chr3D
88.934
244
26
1
2480
2723
570840246
570840004
1.580000e-77
300.0
37
TraesCS2D01G224700
chr5D
84.202
652
65
17
64
695
50861091
50861724
1.400000e-167
599.0
38
TraesCS2D01G224700
chr5D
76.398
322
62
10
1003
1319
25042321
25042633
7.800000e-36
161.0
39
TraesCS2D01G224700
chr5D
93.671
79
3
2
693
771
375200331
375200255
1.710000e-22
117.0
40
TraesCS2D01G224700
chr3B
82.166
757
67
27
32
761
460110443
460111158
3.020000e-164
588.0
41
TraesCS2D01G224700
chr3A
78.771
716
115
22
990
1687
107047935
107048631
1.920000e-121
446.0
42
TraesCS2D01G224700
chr3A
88.800
250
27
1
2474
2723
703844009
703844257
3.410000e-79
305.0
43
TraesCS2D01G224700
chr1A
75.079
634
128
25
1003
1623
337658533
337657917
4.470000e-68
268.0
44
TraesCS2D01G224700
chr1A
81.176
255
38
6
1067
1319
337629745
337629499
2.140000e-46
196.0
45
TraesCS2D01G224700
chr1B
75.000
632
129
24
1003
1623
349547301
349546688
5.780000e-67
265.0
46
TraesCS2D01G224700
chr4D
74.595
618
120
26
1003
1605
465357896
465358491
1.260000e-58
237.0
47
TraesCS2D01G224700
chr6B
84.000
150
10
5
625
761
663708546
663708694
6.120000e-27
132.0
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
TraesCS2D01G224700
chr2D
192184735
192187457
2722
True
5029.000000
5029
100.000000
1
2723
1
chr2D.!!$R2
2722
1
TraesCS2D01G224700
chr2D
142020534
142021229
695
True
832.000000
832
88.825000
88
759
1
chr2D.!!$R1
671
2
TraesCS2D01G224700
chr2D
448509935
448510445
510
True
623.000000
623
89.453000
275
761
1
chr2D.!!$R3
486
3
TraesCS2D01G224700
chr2B
248136860
248138921
2061
False
805.666667
1489
88.229667
763
2723
3
chr2B.!!$F1
1960
4
TraesCS2D01G224700
chr2B
134247848
134248566
718
True
721.000000
721
85.517000
68
759
1
chr2B.!!$R1
691
5
TraesCS2D01G224700
chr2A
68539839
68540372
533
False
656.000000
656
89.700000
253
759
1
chr2A.!!$F1
506
6
TraesCS2D01G224700
chr2A
205910709
205914560
3851
False
585.280000
1384
95.011800
795
2723
5
chr2A.!!$F2
1928
7
TraesCS2D01G224700
chr1D
40863514
40864289
775
True
952.000000
952
89.313000
1
759
1
chr1D.!!$R1
758
8
TraesCS2D01G224700
chr1D
410250599
410251368
769
True
915.000000
915
88.604000
5
759
1
chr1D.!!$R3
754
9
TraesCS2D01G224700
chr1D
62437842
62438383
541
True
760.000000
760
91.941000
65
608
1
chr1D.!!$R2
543
10
TraesCS2D01G224700
chr4A
95193263
95193970
707
False
933.000000
933
90.669000
56
759
1
chr4A.!!$F1
703
11
TraesCS2D01G224700
chr4A
507918254
507919028
774
True
852.000000
852
87.006000
1
759
1
chr4A.!!$R3
758
12
TraesCS2D01G224700
chr4A
123253680
123254390
710
True
789.000000
789
87.258000
1
695
1
chr4A.!!$R2
694
13
TraesCS2D01G224700
chr4A
712564496
712565234
738
False
625.000000
625
82.592000
1
759
1
chr4A.!!$F3
758
14
TraesCS2D01G224700
chr4A
5114608
5115255
647
True
239.000000
239
74.102000
1003
1651
1
chr4A.!!$R1
648
15
TraesCS2D01G224700
chr6D
300294186
300294948
762
False
915.000000
915
88.662000
1
762
1
chr6D.!!$F3
761
16
TraesCS2D01G224700
chr6D
414103764
414104444
680
False
845.000000
845
89.124000
1
695
1
chr6D.!!$F4
694
17
TraesCS2D01G224700
chr6D
141140942
141141497
555
False
676.000000
676
89.029000
1
543
1
chr6D.!!$F2
542
18
TraesCS2D01G224700
chr7B
162112185
162112742
557
True
749.000000
749
91.266000
1
547
1
chr7B.!!$R1
546
19
TraesCS2D01G224700
chr7B
440217043
440217764
721
False
747.000000
747
86.027000
64
761
1
chr7B.!!$F3
697
20
TraesCS2D01G224700
chr7B
439255195
439255749
554
False
473.000000
473
82.881000
199
762
1
chr7B.!!$F2
563
21
TraesCS2D01G224700
chr5B
454691766
454692513
747
True
676.000000
676
83.611000
10
761
1
chr5B.!!$R1
751
22
TraesCS2D01G224700
chr3D
355894578
355895301
723
False
654.000000
654
83.919000
64
762
1
chr3D.!!$F1
698
23
TraesCS2D01G224700
chr5D
50861091
50861724
633
False
599.000000
599
84.202000
64
695
1
chr5D.!!$F2
631
24
TraesCS2D01G224700
chr3B
460110443
460111158
715
False
588.000000
588
82.166000
32
761
1
chr3B.!!$F1
729
25
TraesCS2D01G224700
chr3A
107047935
107048631
696
False
446.000000
446
78.771000
990
1687
1
chr3A.!!$F1
697
26
TraesCS2D01G224700
chr1A
337657917
337658533
616
True
268.000000
268
75.079000
1003
1623
1
chr1A.!!$R2
620
27
TraesCS2D01G224700
chr1B
349546688
349547301
613
True
265.000000
265
75.000000
1003
1623
1
chr1B.!!$R1
620
28
TraesCS2D01G224700
chr4D
465357896
465358491
595
False
237.000000
237
74.595000
1003
1605
1
chr4D.!!$F1
602
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.