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
TraesCS3A01G221300
chr3A
100.000
2525
0
0
1
2525
410246583
410249107
0.000000e+00
4663.0
1
TraesCS3A01G221300
chr3A
90.765
1646
141
6
57
1691
410233246
410234891
0.000000e+00
2187.0
2
TraesCS3A01G221300
chr3A
93.021
874
54
5
1656
2525
410234891
410235761
0.000000e+00
1269.0
3
TraesCS3A01G221300
chr3A
76.129
775
119
50
47
790
423435150
423435889
1.860000e-91
346.0
4
TraesCS3A01G221300
chr3A
87.365
277
29
6
2252
2525
456030979
456031252
1.890000e-81
313.0
5
TraesCS3A01G221300
chr3A
75.584
385
70
16
1719
2089
502392926
502393300
4.320000e-38
169.0
6
TraesCS3A01G221300
chr3A
88.971
136
14
1
1115
1250
332131610
332131744
1.550000e-37
167.0
7
TraesCS3A01G221300
chr3A
87.591
137
16
1
1115
1251
258704893
258704758
9.350000e-35
158.0
8
TraesCS3A01G221300
chr3A
85.926
135
18
1
1115
1249
332141470
332141603
2.620000e-30
143.0
9
TraesCS3A01G221300
chr3A
78.571
140
23
7
1776
1911
333277079
333277215
4.480000e-13
86.1
10
TraesCS3A01G221300
chr3A
79.762
84
16
1
1372
1454
675286946
675286863
2.710000e-05
60.2
11
TraesCS3A01G221300
chr5B
81.972
710
95
27
1
698
205797269
205797957
2.820000e-159
571.0
12
TraesCS3A01G221300
chr3B
83.770
573
63
23
128
684
239019141
239019699
1.340000e-142
516.0
13
TraesCS3A01G221300
chr3B
83.566
572
66
21
128
684
239027273
239027831
6.230000e-141
510.0
14
TraesCS3A01G221300
chr3B
77.273
440
68
28
286
709
712372671
712373094
1.950000e-56
230.0
15
TraesCS3A01G221300
chr3B
75.556
315
57
15
1782
2090
616471280
616470980
1.220000e-28
137.0
16
TraesCS3A01G221300
chr4D
80.791
708
90
30
1844
2525
191323145
191322458
1.730000e-141
512.0
17
TraesCS3A01G221300
chr4D
79.858
705
101
26
1844
2525
191304282
191303596
6.320000e-131
477.0
18
TraesCS3A01G221300
chr4D
75.181
415
74
19
1696
2091
41201448
41201852
4.320000e-38
169.0
19
TraesCS3A01G221300
chr4D
85.256
156
10
5
1115
1268
239119486
239119630
5.630000e-32
148.0
20
TraesCS3A01G221300
chr6B
81.231
666
93
28
1
652
113042336
113042983
2.240000e-140
508.0
21
TraesCS3A01G221300
chr6B
76.291
755
123
43
47
760
100400396
100401135
4.000000e-93
351.0
22
TraesCS3A01G221300
chr6B
83.673
147
20
3
1311
1454
331121786
331121931
4.380000e-28
135.0
23
TraesCS3A01G221300
chr3D
82.010
617
93
16
47
652
356760957
356760348
2.240000e-140
508.0
24
TraesCS3A01G221300
chr3D
83.274
562
75
19
101
651
356727563
356727010
1.350000e-137
499.0
25
TraesCS3A01G221300
chr3D
75.644
776
123
51
1
749
146534952
146534216
2.420000e-85
326.0
26
TraesCS3A01G221300
chr3D
79.710
414
58
17
1806
2205
164918757
164919158
2.470000e-70
276.0
27
TraesCS3A01G221300
chr3D
78.632
351
62
10
1753
2095
254210363
254210708
1.180000e-53
220.0
28
TraesCS3A01G221300
chr7B
80.301
665
101
26
1
652
300976668
300976021
2.270000e-130
475.0
29
TraesCS3A01G221300
chr7B
79.549
665
105
28
1
652
300984322
300983676
1.780000e-121
446.0
30
TraesCS3A01G221300
chr7B
86.335
161
20
1
1820
1980
207844552
207844394
9.280000e-40
174.0
31
TraesCS3A01G221300
chr7B
97.059
34
1
0
1732
1765
582761228
582761261
9.760000e-05
58.4
32
TraesCS3A01G221300
chr7D
90.461
304
27
2
1450
1751
360474179
360473876
1.410000e-107
399.0
33
TraesCS3A01G221300
chr7D
83.582
134
20
2
1844
1977
360473839
360473708
9.480000e-25
124.0
34
TraesCS3A01G221300
chr2B
76.548
759
121
43
57
790
193778279
193777553
1.850000e-96
363.0
35
TraesCS3A01G221300
chr2B
76.282
156
25
10
1965
2116
366011726
366011579
3.480000e-09
73.1
36
TraesCS3A01G221300
chr2A
80.370
433
62
19
2103
2525
310297856
310297437
8.770000e-80
307.0
37
TraesCS3A01G221300
chr2A
82.222
270
36
10
1936
2205
273918936
273918679
3.270000e-54
222.0
38
TraesCS3A01G221300
chr2A
85.946
185
25
1
1450
1633
216320969
216320785
1.980000e-46
196.0
39
TraesCS3A01G221300
chr2A
87.681
138
16
1
1493
1629
224395513
224395376
2.600000e-35
159.0
40
TraesCS3A01G221300
chr2A
83.824
136
21
1
1115
1250
233616389
233616523
7.330000e-26
128.0
41
TraesCS3A01G221300
chr2A
76.423
246
43
14
1853
2094
469074510
469074276
4.410000e-23
119.0
42
TraesCS3A01G221300
chr2A
87.805
82
10
0
752
833
352386599
352386680
2.070000e-16
97.1
43
TraesCS3A01G221300
chr2A
78.571
140
23
7
1776
1911
326750
326886
4.480000e-13
86.1
44
TraesCS3A01G221300
chr1A
80.046
431
68
14
2103
2525
179773878
179774298
1.130000e-78
303.0
45
TraesCS3A01G221300
chr1A
84.385
301
41
5
2228
2525
179984427
179984130
8.840000e-75
291.0
46
TraesCS3A01G221300
chr1A
89.781
137
14
0
1114
1250
302862579
302862443
2.580000e-40
176.0
47
TraesCS3A01G221300
chr1A
86.538
156
21
0
877
1032
141258914
141259069
3.340000e-39
172.0
48
TraesCS3A01G221300
chr1A
89.051
137
15
0
1114
1250
302870642
302870506
1.200000e-38
171.0
49
TraesCS3A01G221300
chr1A
84.694
98
7
6
1363
1454
208397128
208397033
9.620000e-15
91.6
50
TraesCS3A01G221300
chr2D
83.923
311
44
6
2212
2519
69423405
69423712
2.460000e-75
292.0
51
TraesCS3A01G221300
chr5D
78.555
429
75
16
2106
2525
47678421
47678001
1.490000e-67
267.0
52
TraesCS3A01G221300
chr5D
79.827
347
57
12
2185
2525
47685549
47685210
9.030000e-60
241.0
53
TraesCS3A01G221300
chr1B
78.082
438
72
20
1820
2241
508292574
508292145
3.220000e-64
255.0
54
TraesCS3A01G221300
chr1B
75.676
481
84
23
1777
2241
530008319
530008782
2.550000e-50
209.0
55
TraesCS3A01G221300
chr1B
78.549
317
58
9
1928
2241
530016509
530016818
1.530000e-47
200.0
56
TraesCS3A01G221300
chrUn
92.614
176
13
0
1576
1751
92433944
92433769
1.160000e-63
254.0
57
TraesCS3A01G221300
chr7A
82.079
279
41
8
1965
2241
252474241
252474512
1.950000e-56
230.0
58
TraesCS3A01G221300
chr7A
86.628
172
18
4
1459
1629
325548469
325548302
4.290000e-43
185.0
59
TraesCS3A01G221300
chr7A
75.862
145
27
7
1953
2095
309719017
309718879
1.620000e-07
67.6
60
TraesCS3A01G221300
chr7A
86.667
60
6
2
702
760
552281952
552282010
5.830000e-07
65.8
61
TraesCS3A01G221300
chr4A
87.500
176
21
1
1459
1633
166507264
166507089
4.260000e-48
202.0
62
TraesCS3A01G221300
chr4A
87.500
136
16
1
1115
1250
347530056
347530190
3.360000e-34
156.0
63
TraesCS3A01G221300
chr4A
89.157
83
8
1
747
829
357613141
357613222
4.440000e-18
102.0
64
TraesCS3A01G221300
chr4A
89.157
83
8
1
747
829
357621129
357621210
4.440000e-18
102.0
65
TraesCS3A01G221300
chr4A
85.714
91
7
4
1363
1453
248259519
248259603
9.620000e-15
91.6
66
TraesCS3A01G221300
chr4A
93.220
59
4
0
1738
1796
370358557
370358499
1.240000e-13
87.9
67
TraesCS3A01G221300
chr4A
95.349
43
2
0
1753
1795
393416975
393417017
4.510000e-08
69.4
68
TraesCS3A01G221300
chr4A
81.176
85
13
3
1372
1454
526176640
526176723
5.830000e-07
65.8
69
TraesCS3A01G221300
chr4A
100.000
30
0
0
1372
1401
526208833
526208862
3.510000e-04
56.5
70
TraesCS3A01G221300
chr6A
82.581
155
24
3
1115
1267
240638544
240638391
1.580000e-27
134.0
71
TraesCS3A01G221300
chr6A
90.526
95
6
1
1312
1403
303769365
303769271
3.410000e-24
122.0
72
TraesCS3A01G221300
chr6A
87.952
83
9
1
747
829
322600017
322600098
2.070000e-16
97.1
73
TraesCS3A01G221300
chr6A
86.747
83
10
1
747
829
322607971
322608052
9.620000e-15
91.6
74
TraesCS3A01G221300
chr6A
72.022
361
79
19
1812
2166
244508728
244509072
1.240000e-13
87.9
75
TraesCS3A01G221300
chr6A
100.000
30
0
0
1698
1727
325824640
325824611
3.510000e-04
56.5
76
TraesCS3A01G221300
chr5A
87.952
83
9
1
747
829
169131919
169131838
2.070000e-16
97.1
77
TraesCS3A01G221300
chr1D
88.889
54
5
1
1372
1424
340375182
340375235
5.830000e-07
65.8
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
TraesCS3A01G221300
chr3A
410246583
410249107
2524
False
4663
4663
100.000
1
2525
1
chr3A.!!$F4
2524
1
TraesCS3A01G221300
chr3A
410233246
410235761
2515
False
1728
2187
91.893
57
2525
2
chr3A.!!$F8
2468
2
TraesCS3A01G221300
chr3A
423435150
423435889
739
False
346
346
76.129
47
790
1
chr3A.!!$F5
743
3
TraesCS3A01G221300
chr5B
205797269
205797957
688
False
571
571
81.972
1
698
1
chr5B.!!$F1
697
4
TraesCS3A01G221300
chr3B
239019141
239019699
558
False
516
516
83.770
128
684
1
chr3B.!!$F1
556
5
TraesCS3A01G221300
chr3B
239027273
239027831
558
False
510
510
83.566
128
684
1
chr3B.!!$F2
556
6
TraesCS3A01G221300
chr4D
191322458
191323145
687
True
512
512
80.791
1844
2525
1
chr4D.!!$R2
681
7
TraesCS3A01G221300
chr4D
191303596
191304282
686
True
477
477
79.858
1844
2525
1
chr4D.!!$R1
681
8
TraesCS3A01G221300
chr6B
113042336
113042983
647
False
508
508
81.231
1
652
1
chr6B.!!$F2
651
9
TraesCS3A01G221300
chr6B
100400396
100401135
739
False
351
351
76.291
47
760
1
chr6B.!!$F1
713
10
TraesCS3A01G221300
chr3D
356760348
356760957
609
True
508
508
82.010
47
652
1
chr3D.!!$R3
605
11
TraesCS3A01G221300
chr3D
356727010
356727563
553
True
499
499
83.274
101
651
1
chr3D.!!$R2
550
12
TraesCS3A01G221300
chr3D
146534216
146534952
736
True
326
326
75.644
1
749
1
chr3D.!!$R1
748
13
TraesCS3A01G221300
chr7B
300976021
300976668
647
True
475
475
80.301
1
652
1
chr7B.!!$R2
651
14
TraesCS3A01G221300
chr7B
300983676
300984322
646
True
446
446
79.549
1
652
1
chr7B.!!$R3
651
15
TraesCS3A01G221300
chr2B
193777553
193778279
726
True
363
363
76.548
57
790
1
chr2B.!!$R1
733
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.