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
TraesCS7A01G303600
chr7A
100.000
3147
0
0
1
3147
427287223
427290369
0.000000e+00
5812.0
1
TraesCS7A01G303600
chr7A
97.347
490
12
1
2444
2933
483967089
483967577
0.000000e+00
832.0
2
TraesCS7A01G303600
chr7A
98.605
215
3
0
2933
3147
483967710
483967924
6.370000e-102
381.0
3
TraesCS7A01G303600
chr7A
96.744
215
7
0
2933
3147
91944009
91943795
2.980000e-95
359.0
4
TraesCS7A01G303600
chr7A
95.161
62
2
1
901
962
690577116
690577056
2.580000e-16
97.1
5
TraesCS7A01G303600
chr7D
96.972
1486
38
4
964
2444
378850290
378851773
0.000000e+00
2488.0
6
TraesCS7A01G303600
chr7D
96.881
513
12
4
403
913
378849654
378850164
0.000000e+00
856.0
7
TraesCS7A01G303600
chr7D
94.377
409
16
3
1
409
378844112
378844513
3.450000e-174
621.0
8
TraesCS7A01G303600
chr7B
96.433
1486
45
4
964
2444
374313263
374314745
0.000000e+00
2444.0
9
TraesCS7A01G303600
chr7B
93.974
531
12
8
1
527
374310942
374311456
0.000000e+00
785.0
10
TraesCS7A01G303600
chr7B
97.767
403
7
2
513
913
374312735
374313137
0.000000e+00
693.0
11
TraesCS7A01G303600
chr7B
98.246
57
1
0
909
965
742237421
742237477
2.000000e-17
100.0
12
TraesCS7A01G303600
chr2A
94.896
1489
66
5
964
2444
338279451
338280937
0.000000e+00
2320.0
13
TraesCS7A01G303600
chr2A
94.633
913
33
7
1
904
338278334
338279239
0.000000e+00
1400.0
14
TraesCS7A01G303600
chr2A
95.492
488
22
0
2446
2933
51989373
51988886
0.000000e+00
780.0
15
TraesCS7A01G303600
chr4A
97.551
490
12
0
2444
2933
248946181
248945692
0.000000e+00
839.0
16
TraesCS7A01G303600
chr4A
95.918
490
20
0
2444
2933
681182802
681183291
0.000000e+00
795.0
17
TraesCS7A01G303600
chr4A
98.605
215
3
0
2933
3147
248945559
248945345
6.370000e-102
381.0
18
TraesCS7A01G303600
chr6A
95.910
489
20
0
2445
2933
122740813
122740325
0.000000e+00
793.0
19
TraesCS7A01G303600
chr6A
97.209
215
6
0
2933
3147
199998136
199997922
6.410000e-97
364.0
20
TraesCS7A01G303600
chr6A
95.082
61
3
0
909
969
234180579
234180639
2.580000e-16
97.1
21
TraesCS7A01G303600
chr1A
96.099
487
18
1
2447
2933
588758849
588759334
0.000000e+00
793.0
22
TraesCS7A01G303600
chr1A
95.297
489
23
0
2445
2933
590638246
590637758
0.000000e+00
776.0
23
TraesCS7A01G303600
chr1A
97.209
215
6
0
2933
3147
588759467
588759681
6.410000e-97
364.0
24
TraesCS7A01G303600
chr1A
96.744
215
7
0
2933
3147
590637625
590637411
2.980000e-95
359.0
25
TraesCS7A01G303600
chr1A
95.349
215
10
0
2933
3147
319312582
319312796
3.010000e-90
342.0
26
TraesCS7A01G303600
chr3A
94.898
490
25
0
2444
2933
665992751
665993240
0.000000e+00
767.0
27
TraesCS7A01G303600
chr3A
95.349
215
10
0
2933
3147
665993373
665993587
3.010000e-90
342.0
28
TraesCS7A01G303600
chr5A
94.705
491
26
0
2443
2933
567573054
567572564
0.000000e+00
763.0
29
TraesCS7A01G303600
chr5A
92.537
67
4
1
897
962
37840741
37840675
9.290000e-16
95.3
30
TraesCS7A01G303600
chr5B
96.744
215
7
0
2933
3147
15662389
15662603
2.980000e-95
359.0
31
TraesCS7A01G303600
chr6B
98.305
59
1
0
909
967
438925123
438925065
1.540000e-18
104.0
32
TraesCS7A01G303600
chr4B
100.000
54
0
0
909
962
462230904
462230957
2.000000e-17
100.0
33
TraesCS7A01G303600
chr4B
100.000
54
0
0
909
962
635421675
635421622
2.000000e-17
100.0
34
TraesCS7A01G303600
chr4B
95.082
61
3
0
909
969
142056602
142056542
2.580000e-16
97.1
35
TraesCS7A01G303600
chr1B
100.000
54
0
0
909
962
524303610
524303557
2.000000e-17
100.0
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
TraesCS7A01G303600
chr7A
427287223
427290369
3146
False
5812.000000
5812
100.0000
1
3147
1
chr7A.!!$F1
3146
1
TraesCS7A01G303600
chr7A
483967089
483967924
835
False
606.500000
832
97.9760
2444
3147
2
chr7A.!!$F2
703
2
TraesCS7A01G303600
chr7D
378849654
378851773
2119
False
1672.000000
2488
96.9265
403
2444
2
chr7D.!!$F2
2041
3
TraesCS7A01G303600
chr7B
374310942
374314745
3803
False
1307.333333
2444
96.0580
1
2444
3
chr7B.!!$F2
2443
4
TraesCS7A01G303600
chr2A
338278334
338280937
2603
False
1860.000000
2320
94.7645
1
2444
2
chr2A.!!$F1
2443
5
TraesCS7A01G303600
chr4A
248945345
248946181
836
True
610.000000
839
98.0780
2444
3147
2
chr4A.!!$R1
703
6
TraesCS7A01G303600
chr1A
588758849
588759681
832
False
578.500000
793
96.6540
2447
3147
2
chr1A.!!$F2
700
7
TraesCS7A01G303600
chr1A
590637411
590638246
835
True
567.500000
776
96.0205
2445
3147
2
chr1A.!!$R1
702
8
TraesCS7A01G303600
chr3A
665992751
665993587
836
False
554.500000
767
95.1235
2444
3147
2
chr3A.!!$F1
703
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.