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
TraesCS2B01G419600
chr2B
100.000
3007
0
0
1
3007
601214156
601211150
0.000000e+00
5553.0
1
TraesCS2B01G419600
chr2B
88.145
523
38
8
1
499
760834097
760834619
4.290000e-168
601.0
2
TraesCS2B01G419600
chr2B
87.380
523
42
3
1
499
601268472
601267950
2.010000e-161
579.0
3
TraesCS2B01G419600
chr2A
91.625
2376
120
44
501
2862
655220121
655217811
0.000000e+00
3212.0
4
TraesCS2B01G419600
chr2A
80.196
510
61
22
1
499
764651638
764652118
2.220000e-91
346.0
5
TraesCS2B01G419600
chr2D
93.523
1621
53
20
565
2157
512043697
512042101
0.000000e+00
2364.0
6
TraesCS2B01G419600
chr2D
87.520
625
72
6
2370
2991
512041245
512040624
0.000000e+00
717.0
7
TraesCS2B01G419600
chr2D
82.486
531
58
18
1
499
624182002
624182529
1.660000e-117
433.0
8
TraesCS2B01G419600
chr2D
88.660
194
13
6
2155
2340
512041809
512041617
8.390000e-56
228.0
9
TraesCS2B01G419600
chr2D
78.333
360
69
8
2588
2942
469462350
469461995
1.080000e-54
224.0
10
TraesCS2B01G419600
chr7B
87.954
523
39
7
1
499
48241242
48241764
2.000000e-166
595.0
11
TraesCS2B01G419600
chr7B
86.857
525
40
11
1
499
669324892
669324371
7.280000e-156
560.0
12
TraesCS2B01G419600
chr1B
87.791
516
43
7
1
499
463815751
463816263
1.200000e-163
586.0
13
TraesCS2B01G419600
chr6B
87.380
523
42
7
1
499
122789725
122790247
2.010000e-161
579.0
14
TraesCS2B01G419600
chr6B
86.807
523
44
10
1
499
216445352
216445873
7.280000e-156
560.0
15
TraesCS2B01G419600
chr6B
95.000
100
5
0
400
499
500214359
500214260
1.120000e-34
158.0
16
TraesCS2B01G419600
chr3B
86.616
523
44
9
1
499
130133374
130133894
3.390000e-154
555.0
17
TraesCS2B01G419600
chr3B
91.294
402
33
2
1
400
130182066
130182467
5.670000e-152
547.0
18
TraesCS2B01G419600
chr3B
93.000
100
7
0
401
500
563405210
563405111
2.420000e-31
147.0
19
TraesCS2B01G419600
chr3B
84.483
116
16
2
2378
2493
548368762
548368649
2.450000e-21
113.0
20
TraesCS2B01G419600
chr3B
87.000
100
10
3
2377
2475
548549254
548549157
3.170000e-20
110.0
21
TraesCS2B01G419600
chr3B
82.906
117
17
3
2377
2493
548835645
548835532
5.300000e-18
102.0
22
TraesCS2B01G419600
chr3B
80.909
110
17
3
2384
2493
279689683
279689788
1.920000e-12
84.2
23
TraesCS2B01G419600
chr7D
82.409
523
59
14
1
499
268557554
268557041
2.770000e-115
425.0
24
TraesCS2B01G419600
chr7D
81.768
181
28
5
2562
2738
596552548
596552369
2.420000e-31
147.0
25
TraesCS2B01G419600
chr4B
80.626
511
57
25
1
499
4554413
4554893
1.030000e-94
357.0
26
TraesCS2B01G419600
chrUn
81.410
468
45
20
56
499
35183239
35183688
7.980000e-91
344.0
27
TraesCS2B01G419600
chrUn
81.410
468
45
20
56
499
35188960
35189409
7.980000e-91
344.0
28
TraesCS2B01G419600
chrUn
81.622
185
27
7
2564
2743
50980036
50979854
2.420000e-31
147.0
29
TraesCS2B01G419600
chrUn
80.909
110
21
0
2384
2493
29719278
29719169
1.480000e-13
87.9
30
TraesCS2B01G419600
chr5D
80.387
362
47
12
162
499
559885813
559886174
1.380000e-63
254.0
31
TraesCS2B01G419600
chr5D
83.246
191
27
5
1029
1215
352219256
352219445
1.430000e-38
171.0
32
TraesCS2B01G419600
chr5D
80.303
198
33
6
1025
1219
353478115
353478309
8.690000e-31
145.0
33
TraesCS2B01G419600
chr5B
83.511
188
26
5
1032
1215
416851121
416850935
1.430000e-38
171.0
34
TraesCS2B01G419600
chr5B
80.808
198
32
6
1025
1219
417438511
417438705
1.870000e-32
150.0
35
TraesCS2B01G419600
chr5B
100.000
28
0
0
2507
2534
529664620
529664647
5.000000e-03
52.8
36
TraesCS2B01G419600
chr5A
82.447
188
28
5
1032
1215
453877101
453876915
3.100000e-35
159.0
37
TraesCS2B01G419600
chr5A
78.846
208
37
7
1025
1228
454397162
454397366
1.880000e-27
134.0
38
TraesCS2B01G419600
chr5A
79.562
137
17
6
2324
2460
241189878
241189753
1.480000e-13
87.9
39
TraesCS2B01G419600
chr5A
79.091
110
23
0
2384
2493
706151684
706151575
3.210000e-10
76.8
40
TraesCS2B01G419600
chr3D
81.522
184
28
6
2560
2738
232920781
232920963
2.420000e-31
147.0
41
TraesCS2B01G419600
chr1D
81.319
182
28
6
2562
2738
149050458
149050278
3.120000e-30
143.0
42
TraesCS2B01G419600
chr1D
80.769
182
29
6
2562
2738
288788329
288788149
1.450000e-28
137.0
43
TraesCS2B01G419600
chr4A
81.765
170
26
5
2562
2727
716524144
716524312
1.450000e-28
137.0
44
TraesCS2B01G419600
chr4A
76.238
202
42
6
1029
1227
19622498
19622300
5.300000e-18
102.0
45
TraesCS2B01G419600
chr6D
75.665
263
52
8
2507
2757
447442087
447441825
1.460000e-23
121.0
46
TraesCS2B01G419600
chr4D
74.619
197
41
9
1032
1225
506340126
506339936
8.940000e-11
78.7
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
TraesCS2B01G419600
chr2B
601211150
601214156
3006
True
5553
5553
100.000
1
3007
1
chr2B.!!$R1
3006
1
TraesCS2B01G419600
chr2B
760834097
760834619
522
False
601
601
88.145
1
499
1
chr2B.!!$F1
498
2
TraesCS2B01G419600
chr2B
601267950
601268472
522
True
579
579
87.380
1
499
1
chr2B.!!$R2
498
3
TraesCS2B01G419600
chr2A
655217811
655220121
2310
True
3212
3212
91.625
501
2862
1
chr2A.!!$R1
2361
4
TraesCS2B01G419600
chr2D
512040624
512043697
3073
True
1103
2364
89.901
565
2991
3
chr2D.!!$R2
2426
5
TraesCS2B01G419600
chr2D
624182002
624182529
527
False
433
433
82.486
1
499
1
chr2D.!!$F1
498
6
TraesCS2B01G419600
chr7B
48241242
48241764
522
False
595
595
87.954
1
499
1
chr7B.!!$F1
498
7
TraesCS2B01G419600
chr7B
669324371
669324892
521
True
560
560
86.857
1
499
1
chr7B.!!$R1
498
8
TraesCS2B01G419600
chr1B
463815751
463816263
512
False
586
586
87.791
1
499
1
chr1B.!!$F1
498
9
TraesCS2B01G419600
chr6B
122789725
122790247
522
False
579
579
87.380
1
499
1
chr6B.!!$F1
498
10
TraesCS2B01G419600
chr6B
216445352
216445873
521
False
560
560
86.807
1
499
1
chr6B.!!$F2
498
11
TraesCS2B01G419600
chr3B
130133374
130133894
520
False
555
555
86.616
1
499
1
chr3B.!!$F1
498
12
TraesCS2B01G419600
chr7D
268557041
268557554
513
True
425
425
82.409
1
499
1
chr7D.!!$R1
498
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.