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
TraesCS7A01G344800
chr7A
100.000
2558
0
0
1
2558
506855620
506853063
0.000000e+00
4724.0
1
TraesCS7A01G344800
chr7A
92.487
945
69
1
624
1568
507014137
507013195
0.000000e+00
1351.0
2
TraesCS7A01G344800
chr7A
91.657
863
57
7
704
1566
507022558
507021711
0.000000e+00
1181.0
3
TraesCS7A01G344800
chr7A
94.435
575
15
4
1
558
311314226
311313652
0.000000e+00
869.0
4
TraesCS7A01G344800
chr7A
90.874
515
41
4
2048
2558
507013199
507012687
0.000000e+00
686.0
5
TraesCS7A01G344800
chr7A
85.915
284
23
3
2127
2408
507021608
507021340
1.160000e-73
287.0
6
TraesCS7A01G344800
chr7A
91.150
113
8
1
2448
2558
507021339
507021227
4.410000e-33
152.0
7
TraesCS7A01G344800
chr7A
93.103
58
2
2
566
621
159420754
159420811
1.630000e-12
84.2
8
TraesCS7A01G344800
chr7B
92.308
949
59
5
621
1568
443690443
443691378
0.000000e+00
1336.0
9
TraesCS7A01G344800
chr7B
81.690
426
59
13
2065
2474
443703796
443704218
1.130000e-88
337.0
10
TraesCS7A01G344800
chr7D
90.542
941
71
9
629
1568
426450670
426451593
0.000000e+00
1229.0
11
TraesCS7A01G344800
chr7D
88.347
944
79
14
631
1571
426496726
426497641
0.000000e+00
1105.0
12
TraesCS7A01G344800
chr7D
89.315
861
69
13
631
1487
426518134
426518975
0.000000e+00
1059.0
13
TraesCS7A01G344800
chr7D
88.667
803
74
10
683
1482
426553869
426554657
0.000000e+00
963.0
14
TraesCS7A01G344800
chr7D
85.437
927
100
22
621
1541
426644388
426645285
0.000000e+00
931.0
15
TraesCS7A01G344800
chr7D
81.092
513
68
18
2070
2558
426633753
426634260
1.440000e-102
383.0
16
TraesCS7A01G344800
chr7D
75.962
520
61
30
2071
2558
426554748
426555235
2.580000e-50
209.0
17
TraesCS7A01G344800
chr7D
75.105
474
60
25
2114
2558
426491906
426492350
4.380000e-38
169.0
18
TraesCS7A01G344800
chr7D
89.552
134
10
4
2070
2201
426519041
426519172
1.570000e-37
167.0
19
TraesCS7A01G344800
chr7D
78.629
248
34
12
1809
2047
574111567
574111804
2.050000e-31
147.0
20
TraesCS7A01G344800
chr7D
78.543
247
34
12
1809
2046
574112945
574113181
7.380000e-31
145.0
21
TraesCS7A01G344800
chr2B
89.261
866
79
9
708
1571
753835088
753835941
0.000000e+00
1072.0
22
TraesCS7A01G344800
chr4A
97.173
566
12
4
1
562
616598916
616599481
0.000000e+00
953.0
23
TraesCS7A01G344800
chr4A
97.951
488
8
1
1566
2053
563506034
563505549
0.000000e+00
845.0
24
TraesCS7A01G344800
chr4A
97.536
487
12
0
1568
2054
563504657
563504171
0.000000e+00
833.0
25
TraesCS7A01G344800
chr4A
93.103
580
15
4
1
556
123864895
123864317
0.000000e+00
826.0
26
TraesCS7A01G344800
chr4A
90.643
513
26
8
9
502
615010700
615010191
0.000000e+00
662.0
27
TraesCS7A01G344800
chr1A
96.986
564
14
3
1
562
365614153
365614715
0.000000e+00
944.0
28
TraesCS7A01G344800
chr1A
90.963
509
29
7
7
502
267389267
267389771
0.000000e+00
669.0
29
TraesCS7A01G344800
chr5A
95.164
579
11
3
1
562
281142534
281143112
0.000000e+00
898.0
30
TraesCS7A01G344800
chr5A
93.939
297
12
5
1568
1861
14957800
14958093
6.490000e-121
444.0
31
TraesCS7A01G344800
chr5A
93.311
299
12
6
1568
1861
14959199
14959494
3.910000e-118
435.0
32
TraesCS7A01G344800
chr3A
94.671
563
13
5
15
562
494060270
494060830
0.000000e+00
857.0
33
TraesCS7A01G344800
chr6D
92.769
567
28
10
7
566
470580464
470581024
0.000000e+00
808.0
34
TraesCS7A01G344800
chr6D
85.113
309
21
14
1568
1861
437416747
437416449
2.490000e-75
292.0
35
TraesCS7A01G344800
chr6D
93.333
60
3
1
563
621
353366131
353366190
1.260000e-13
87.9
36
TraesCS7A01G344800
chrUn
90.328
548
29
8
29
556
314590133
314590676
0.000000e+00
697.0
37
TraesCS7A01G344800
chrUn
90.328
548
29
8
29
556
382905215
382904672
0.000000e+00
697.0
38
TraesCS7A01G344800
chrUn
79.352
247
32
12
1809
2046
111045143
111045379
3.410000e-34
156.0
39
TraesCS7A01G344800
chr5B
91.068
515
26
5
61
558
9345686
9345175
0.000000e+00
678.0
40
TraesCS7A01G344800
chr5B
81.250
80
12
3
554
633
28207790
28207714
7.640000e-06
62.1
41
TraesCS7A01G344800
chr4B
92.442
344
22
3
1568
1910
65967523
65967183
2.960000e-134
488.0
42
TraesCS7A01G344800
chr5D
79.839
248
31
12
1809
2047
8962613
8962850
2.040000e-36
163.0
43
TraesCS7A01G344800
chr5D
77.823
248
34
14
1809
2046
8963991
8964227
1.600000e-27
134.0
44
TraesCS7A01G344800
chr1D
78.516
256
35
13
1809
2054
460841953
460841708
1.590000e-32
150.0
45
TraesCS7A01G344800
chr1D
94.828
58
2
1
566
622
84705343
84705286
3.510000e-14
89.8
46
TraesCS7A01G344800
chr3D
78.543
247
34
12
1809
2046
6034239
6034475
7.380000e-31
145.0
47
TraesCS7A01G344800
chr1B
88.235
102
11
1
1656
1757
7229620
7229520
1.240000e-23
121.0
48
TraesCS7A01G344800
chr1B
91.071
56
4
1
566
620
368203707
368203652
9.820000e-10
75.0
49
TraesCS7A01G344800
chr6A
86.916
107
5
6
1649
1755
612106143
612106240
7.480000e-21
111.0
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
TraesCS7A01G344800
chr7A
506853063
506855620
2557
True
4724.0
4724
100.0000
1
2558
1
chr7A.!!$R2
2557
1
TraesCS7A01G344800
chr7A
507012687
507014137
1450
True
1018.5
1351
91.6805
624
2558
2
chr7A.!!$R3
1934
2
TraesCS7A01G344800
chr7A
311313652
311314226
574
True
869.0
869
94.4350
1
558
1
chr7A.!!$R1
557
3
TraesCS7A01G344800
chr7A
507021227
507022558
1331
True
540.0
1181
89.5740
704
2558
3
chr7A.!!$R4
1854
4
TraesCS7A01G344800
chr7B
443690443
443691378
935
False
1336.0
1336
92.3080
621
1568
1
chr7B.!!$F1
947
5
TraesCS7A01G344800
chr7D
426450670
426451593
923
False
1229.0
1229
90.5420
629
1568
1
chr7D.!!$F1
939
6
TraesCS7A01G344800
chr7D
426496726
426497641
915
False
1105.0
1105
88.3470
631
1571
1
chr7D.!!$F3
940
7
TraesCS7A01G344800
chr7D
426644388
426645285
897
False
931.0
931
85.4370
621
1541
1
chr7D.!!$F5
920
8
TraesCS7A01G344800
chr7D
426518134
426519172
1038
False
613.0
1059
89.4335
631
2201
2
chr7D.!!$F6
1570
9
TraesCS7A01G344800
chr7D
426553869
426555235
1366
False
586.0
963
82.3145
683
2558
2
chr7D.!!$F7
1875
10
TraesCS7A01G344800
chr7D
426633753
426634260
507
False
383.0
383
81.0920
2070
2558
1
chr7D.!!$F4
488
11
TraesCS7A01G344800
chr2B
753835088
753835941
853
False
1072.0
1072
89.2610
708
1571
1
chr2B.!!$F1
863
12
TraesCS7A01G344800
chr4A
616598916
616599481
565
False
953.0
953
97.1730
1
562
1
chr4A.!!$F1
561
13
TraesCS7A01G344800
chr4A
563504171
563506034
1863
True
839.0
845
97.7435
1566
2054
2
chr4A.!!$R3
488
14
TraesCS7A01G344800
chr4A
123864317
123864895
578
True
826.0
826
93.1030
1
556
1
chr4A.!!$R1
555
15
TraesCS7A01G344800
chr4A
615010191
615010700
509
True
662.0
662
90.6430
9
502
1
chr4A.!!$R2
493
16
TraesCS7A01G344800
chr1A
365614153
365614715
562
False
944.0
944
96.9860
1
562
1
chr1A.!!$F2
561
17
TraesCS7A01G344800
chr1A
267389267
267389771
504
False
669.0
669
90.9630
7
502
1
chr1A.!!$F1
495
18
TraesCS7A01G344800
chr5A
281142534
281143112
578
False
898.0
898
95.1640
1
562
1
chr5A.!!$F1
561
19
TraesCS7A01G344800
chr5A
14957800
14959494
1694
False
439.5
444
93.6250
1568
1861
2
chr5A.!!$F2
293
20
TraesCS7A01G344800
chr3A
494060270
494060830
560
False
857.0
857
94.6710
15
562
1
chr3A.!!$F1
547
21
TraesCS7A01G344800
chr6D
470580464
470581024
560
False
808.0
808
92.7690
7
566
1
chr6D.!!$F2
559
22
TraesCS7A01G344800
chrUn
314590133
314590676
543
False
697.0
697
90.3280
29
556
1
chrUn.!!$F2
527
23
TraesCS7A01G344800
chrUn
382904672
382905215
543
True
697.0
697
90.3280
29
556
1
chrUn.!!$R1
527
24
TraesCS7A01G344800
chr5B
9345175
9345686
511
True
678.0
678
91.0680
61
558
1
chr5B.!!$R1
497
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.