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
TraesCS6B01G362000
chr6B
100.000
3611
0
0
1
3611
633729679
633733289
0.000000e+00
6669.0
1
TraesCS6B01G362000
chr6B
92.081
985
76
1
1638
2622
612744562
612743580
0.000000e+00
1386.0
2
TraesCS6B01G362000
chr6B
90.359
1058
94
3
1656
2705
612270839
612269782
0.000000e+00
1382.0
3
TraesCS6B01G362000
chr6B
95.374
843
27
7
2772
3606
672136840
672136002
0.000000e+00
1330.0
4
TraesCS6B01G362000
chr6B
92.634
543
37
2
993
1535
612745155
612744616
0.000000e+00
778.0
5
TraesCS6B01G362000
chr6B
92.669
532
36
2
999
1530
612271447
612270919
0.000000e+00
763.0
6
TraesCS6B01G362000
chr6B
83.268
257
17
13
618
860
612745620
612745376
2.820000e-51
213.0
7
TraesCS6B01G362000
chr6B
93.333
75
5
0
471
545
77458147
77458221
1.060000e-20
111.0
8
TraesCS6B01G362000
chr6B
79.688
128
18
5
618
744
612271904
612271784
6.420000e-13
86.1
9
TraesCS6B01G362000
chr6B
90.476
63
3
2
796
857
612271681
612271621
2.990000e-11
80.5
10
TraesCS6B01G362000
chr6D
94.428
2046
84
14
707
2739
420569439
420567411
0.000000e+00
3120.0
11
TraesCS6B01G362000
chr6D
94.075
2059
92
12
712
2746
420558956
420561008
0.000000e+00
3099.0
12
TraesCS6B01G362000
chr6D
89.988
1708
150
8
993
2693
408157089
408155396
0.000000e+00
2187.0
13
TraesCS6B01G362000
chr6D
88.889
1719
148
23
999
2705
59089086
59087399
0.000000e+00
2076.0
14
TraesCS6B01G362000
chr6D
90.227
440
40
2
1
438
420570415
420569977
4.040000e-159
571.0
15
TraesCS6B01G362000
chr6D
90.183
438
41
2
3
438
420556269
420556706
1.450000e-158
569.0
16
TraesCS6B01G362000
chr6D
80.620
387
25
19
619
971
408157554
408157184
1.660000e-63
254.0
17
TraesCS6B01G362000
chr6D
81.569
255
21
8
620
858
59089542
59089298
1.710000e-43
187.0
18
TraesCS6B01G362000
chr6D
93.023
43
3
0
663
705
420558890
420558932
3.010000e-06
63.9
19
TraesCS6B01G362000
chr6A
92.562
2178
107
23
618
2746
563484355
563486526
0.000000e+00
3073.0
20
TraesCS6B01G362000
chr6A
88.547
1720
150
25
999
2705
553913299
553911614
0.000000e+00
2041.0
21
TraesCS6B01G362000
chr6A
89.217
1660
136
25
993
2641
553766978
553765351
0.000000e+00
2034.0
22
TraesCS6B01G362000
chr6A
87.443
438
53
2
1
438
563483870
563484305
1.500000e-138
503.0
23
TraesCS6B01G362000
chr6A
76.444
225
20
15
593
789
553767320
553767101
1.380000e-14
91.6
24
TraesCS6B01G362000
chr2B
96.548
840
24
4
2769
3606
731337813
731338649
0.000000e+00
1386.0
25
TraesCS6B01G362000
chr2B
95.853
844
28
6
2764
3606
42269849
42269012
0.000000e+00
1358.0
26
TraesCS6B01G362000
chr1B
96.177
837
28
3
2772
3606
99630752
99631586
0.000000e+00
1365.0
27
TraesCS6B01G362000
chr1B
95.249
842
30
6
2770
3606
664950409
664951245
0.000000e+00
1325.0
28
TraesCS6B01G362000
chr1B
95.775
71
3
0
480
550
72877122
72877052
8.190000e-22
115.0
29
TraesCS6B01G362000
chr1B
95.775
71
2
1
480
550
60120532
60120601
2.950000e-21
113.0
30
TraesCS6B01G362000
chr4A
95.390
846
29
7
2763
3604
669838656
669839495
0.000000e+00
1338.0
31
TraesCS6B01G362000
chr7B
95.590
839
27
6
2772
3606
381868306
381867474
0.000000e+00
1336.0
32
TraesCS6B01G362000
chr4B
95.119
840
34
7
2772
3606
638436729
638435892
0.000000e+00
1317.0
33
TraesCS6B01G362000
chr4B
94.084
862
35
12
2751
3606
642451019
642450168
0.000000e+00
1295.0
34
TraesCS6B01G362000
chr5D
97.143
70
1
1
481
550
120391749
120391817
2.280000e-22
117.0
35
TraesCS6B01G362000
chr3D
95.833
72
2
1
480
550
105890063
105889992
8.190000e-22
115.0
36
TraesCS6B01G362000
chr3D
92.105
76
6
0
470
545
613828388
613828463
1.370000e-19
108.0
37
TraesCS6B01G362000
chr3B
96.970
66
2
0
480
545
24003074
24003009
1.060000e-20
111.0
38
TraesCS6B01G362000
chr7D
91.139
79
7
0
480
558
363554611
363554533
1.370000e-19
108.0
39
TraesCS6B01G362000
chr4D
90.361
83
6
2
480
561
424572459
424572378
1.370000e-19
108.0
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
TraesCS6B01G362000
chr6B
633729679
633733289
3610
False
6669.000000
6669
100.000000
1
3611
1
chr6B.!!$F2
3610
1
TraesCS6B01G362000
chr6B
672136002
672136840
838
True
1330.000000
1330
95.374000
2772
3606
1
chr6B.!!$R1
834
2
TraesCS6B01G362000
chr6B
612743580
612745620
2040
True
792.333333
1386
89.327667
618
2622
3
chr6B.!!$R3
2004
3
TraesCS6B01G362000
chr6B
612269782
612271904
2122
True
577.900000
1382
88.298000
618
2705
4
chr6B.!!$R2
2087
4
TraesCS6B01G362000
chr6D
420567411
420570415
3004
True
1845.500000
3120
92.327500
1
2739
2
chr6D.!!$R3
2738
5
TraesCS6B01G362000
chr6D
420556269
420561008
4739
False
1243.966667
3099
92.427000
3
2746
3
chr6D.!!$F1
2743
6
TraesCS6B01G362000
chr6D
408155396
408157554
2158
True
1220.500000
2187
85.304000
619
2693
2
chr6D.!!$R2
2074
7
TraesCS6B01G362000
chr6D
59087399
59089542
2143
True
1131.500000
2076
85.229000
620
2705
2
chr6D.!!$R1
2085
8
TraesCS6B01G362000
chr6A
553911614
553913299
1685
True
2041.000000
2041
88.547000
999
2705
1
chr6A.!!$R1
1706
9
TraesCS6B01G362000
chr6A
563483870
563486526
2656
False
1788.000000
3073
90.002500
1
2746
2
chr6A.!!$F1
2745
10
TraesCS6B01G362000
chr6A
553765351
553767320
1969
True
1062.800000
2034
82.830500
593
2641
2
chr6A.!!$R2
2048
11
TraesCS6B01G362000
chr2B
731337813
731338649
836
False
1386.000000
1386
96.548000
2769
3606
1
chr2B.!!$F1
837
12
TraesCS6B01G362000
chr2B
42269012
42269849
837
True
1358.000000
1358
95.853000
2764
3606
1
chr2B.!!$R1
842
13
TraesCS6B01G362000
chr1B
99630752
99631586
834
False
1365.000000
1365
96.177000
2772
3606
1
chr1B.!!$F2
834
14
TraesCS6B01G362000
chr1B
664950409
664951245
836
False
1325.000000
1325
95.249000
2770
3606
1
chr1B.!!$F3
836
15
TraesCS6B01G362000
chr4A
669838656
669839495
839
False
1338.000000
1338
95.390000
2763
3604
1
chr4A.!!$F1
841
16
TraesCS6B01G362000
chr7B
381867474
381868306
832
True
1336.000000
1336
95.590000
2772
3606
1
chr7B.!!$R1
834
17
TraesCS6B01G362000
chr4B
638435892
638436729
837
True
1317.000000
1317
95.119000
2772
3606
1
chr4B.!!$R1
834
18
TraesCS6B01G362000
chr4B
642450168
642451019
851
True
1295.000000
1295
94.084000
2751
3606
1
chr4B.!!$R2
855
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.