Multiple sequence alignment - TraesCS3A01G257700
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BLAST Results
BLAST Results - Input Sequence
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
TraesCS3A01G257700
chr3A
100.000
3635
0
0
1
3635
479473776
479477410
0.000000e+00
6713
1
TraesCS3A01G257700
chr3A
99.286
140
1
0
2706
2845
479471374
479471235
1.680000e-63
254
2
TraesCS3A01G257700
chr3D
97.219
2697
49
8
8
2684
360039516
360042206
0.000000e+00
4542
3
TraesCS3A01G257700
chr3D
96.744
952
31
0
2684
3635
360042235
360043186
0.000000e+00
1587
4
TraesCS3A01G257700
chr3B
94.684
2709
105
19
8
2684
466099547
466102248
0.000000e+00
4169
5
TraesCS3A01G257700
chr3B
95.925
957
38
1
2679
3635
466102272
466103227
0.000000e+00
1550
BLAST Results - HSPs grouped
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
TraesCS3A01G257700
chr3A
479473776
479477410
3634
False
6713.0
6713
100.0000
1
3635
1
chr3A.!!$F1
3634
1
TraesCS3A01G257700
chr3D
360039516
360043186
3670
False
3064.5
4542
96.9815
8
3635
2
chr3D.!!$F1
3627
2
TraesCS3A01G257700
chr3B
466099547
466103227
3680
False
2859.5
4169
95.3045
8
3635
2
chr3B.!!$F1
3627
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
242
243
0.250901
GGAGCCAAGTTCCTTCAGCA
60.251
55.000
0.00
0.0
30.11
4.41
F
1268
1291
1.666553
CGACTTTACAGCGGGTGCA
60.667
57.895
7.17
0.0
46.23
4.57
F
2056
2079
2.857186
TGCTGCAGACCTTGATAACA
57.143
45.000
20.43
0.0
0.00
2.41
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1908
1931
0.251634
TGCTCACCAACAGACACACA
59.748
50.000
0.0
0.0
0.00
3.72
R
2131
2155
3.004839
TGGATACGAGATAAGCAGCAGAC
59.995
47.826
0.0
0.0
42.51
3.51
R
3525
3594
2.496070
TCCAGGGACGACTAATGTTGAG
59.504
50.000
0.0
0.0
0.00
3.02
R
All possible primers
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
91
92
4.275524
AGCTCGACTGCTTGCTTC
57.724
55.556
0.00
0.00
40.93
3.86
116
117
4.175962
AGTTGGGACCTCTAAATCTTCCA
58.824
43.478
0.00
0.00
0.00
3.53
142
143
2.991190
TCGGTAAAATCTGCACGAAGTC
59.009
45.455
0.00
0.00
41.61
3.01
167
168
2.227388
CAGTTTTGCCTACAGCCTTCTG
59.773
50.000
0.00
0.00
45.71
3.02
177
178
0.534412
CAGCCTTCTGTCCAGATCGT
59.466
55.000
0.00
0.00
37.29
3.73
226
227
2.870175
AGAGACATAGATGACCCGGAG
58.130
52.381
0.73
0.00
0.00
4.63
242
243
0.250901
GGAGCCAAGTTCCTTCAGCA
60.251
55.000
0.00
0.00
30.11
4.41
254
255
1.876156
CCTTCAGCACGAGAAGCTTTT
59.124
47.619
0.00
0.00
41.14
2.27
257
258
2.688507
TCAGCACGAGAAGCTTTTAGG
58.311
47.619
0.00
0.00
41.14
2.69
262
263
1.716172
GAGAAGCTTTTAGGCGGCG
59.284
57.895
0.51
0.51
37.29
6.46
321
322
4.037803
CACCACAAGAAATTGACATGTCCA
59.962
41.667
22.85
12.96
0.00
4.02
382
386
3.476552
TGCCTTAATTCCGATGGATCAC
58.523
45.455
0.00
0.00
0.00
3.06
601
622
5.711506
ACAGAATGATGCACTACAAATCCAA
59.288
36.000
0.00
0.00
39.69
3.53
638
660
8.564574
CATAAAGTTTGCAGTGTTACTAAAGGA
58.435
33.333
0.00
0.00
0.00
3.36
1101
1124
7.309499
CCTCTATTCCAGCGTAATCAGAAGTAT
60.309
40.741
0.00
0.00
0.00
2.12
1242
1265
8.466798
GCCACTAATGAAAACACCAATATAGTT
58.533
33.333
0.00
0.00
0.00
2.24
1268
1291
1.666553
CGACTTTACAGCGGGTGCA
60.667
57.895
7.17
0.00
46.23
4.57
1371
1394
3.894427
ACACACCATCAATTACAAGGCAA
59.106
39.130
0.00
0.00
0.00
4.52
1689
1712
3.146066
GCTGAACAGGGTATTTGACACA
58.854
45.455
3.99
0.00
31.73
3.72
1908
1931
3.453679
GGAAGGCTCTCCGCGACT
61.454
66.667
8.23
0.00
40.44
4.18
2034
2057
3.441572
AGAAGAAAATGGACAATGAGCCG
59.558
43.478
0.00
0.00
0.00
5.52
2056
2079
2.857186
TGCTGCAGACCTTGATAACA
57.143
45.000
20.43
0.00
0.00
2.41
2131
2155
6.403333
TTTGTACTTAACATGCGCTTCTAG
57.597
37.500
9.73
1.01
38.10
2.43
2246
2275
7.413000
GCACGACAAAGAGCTAATAATTTCTCA
60.413
37.037
0.00
0.00
0.00
3.27
2499
2531
4.891168
TCCATATGCAACAGCAAATCAGAT
59.109
37.500
0.00
0.00
42.37
2.90
2538
2570
3.133003
TGAAAGAGATGGGGAAGATCGAC
59.867
47.826
0.00
0.00
0.00
4.20
2794
2863
5.350365
TGTCGTATACAATTGAACTTGGAGC
59.650
40.000
13.59
0.00
34.29
4.70
2796
2865
4.260212
CGTATACAATTGAACTTGGAGCCG
60.260
45.833
13.59
0.00
0.00
5.52
2810
2879
6.646267
ACTTGGAGCCGTATTTCTTGTAATA
58.354
36.000
0.00
0.00
0.00
0.98
2825
2894
6.894682
TCTTGTAATATGGTTGGTCATAGCA
58.105
36.000
0.00
0.00
33.69
3.49
2974
3043
4.888326
AGAAAGAGACAGAGCTTGACAT
57.112
40.909
0.00
0.00
0.00
3.06
3076
3145
4.825085
TCGCAATCCTGGAAAAGTTAGTTT
59.175
37.500
0.00
0.00
0.00
2.66
3117
3186
0.897863
TTCGGTTTGGGGATGCCAAG
60.898
55.000
5.30
0.00
0.00
3.61
3164
3233
6.606234
TTAGTGCATTTGTGACTTTTCGTA
57.394
33.333
0.00
0.00
0.00
3.43
3166
3235
4.334203
AGTGCATTTGTGACTTTTCGTACA
59.666
37.500
0.00
0.00
0.00
2.90
3287
3356
4.479158
TCTTTTGCTAATTGGGAACTGGT
58.521
39.130
0.00
0.00
0.00
4.00
3387
3456
2.158559
TCCATGATGTTTGTTGGGTCG
58.841
47.619
0.00
0.00
0.00
4.79
3504
3573
4.698304
TCATCAATTTTACCGGAGAACACC
59.302
41.667
9.46
0.00
0.00
4.16
3525
3594
4.351111
ACCCTTATATGGTCATTGGAGTCC
59.649
45.833
0.73
0.73
0.00
3.85
3532
3601
2.644299
TGGTCATTGGAGTCCTCAACAT
59.356
45.455
11.33
0.00
0.00
2.71
3536
3605
5.491982
GTCATTGGAGTCCTCAACATTAGT
58.508
41.667
11.33
0.00
0.00
2.24
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
1.608055
CAGAGTTTGTGGCCACATCA
58.392
50.000
37.97
24.93
41.52
3.07
1
2
0.883833
CCAGAGTTTGTGGCCACATC
59.116
55.000
37.97
30.49
41.52
3.06
2
3
0.478072
TCCAGAGTTTGTGGCCACAT
59.522
50.000
37.97
24.58
41.52
3.21
3
4
0.478072
ATCCAGAGTTTGTGGCCACA
59.522
50.000
34.74
34.74
39.98
4.17
4
5
2.084546
GTATCCAGAGTTTGTGGCCAC
58.915
52.381
29.67
29.67
34.77
5.01
5
6
1.702401
TGTATCCAGAGTTTGTGGCCA
59.298
47.619
0.00
0.00
34.77
5.36
6
7
2.359900
CTGTATCCAGAGTTTGTGGCC
58.640
52.381
0.00
0.00
41.50
5.36
7
8
2.027192
TCCTGTATCCAGAGTTTGTGGC
60.027
50.000
0.00
0.00
41.50
5.01
8
9
3.981071
TCCTGTATCCAGAGTTTGTGG
57.019
47.619
0.00
0.00
41.50
4.17
9
10
7.331026
TCTTTATCCTGTATCCAGAGTTTGTG
58.669
38.462
0.00
0.00
41.50
3.33
91
92
2.766828
AGATTTAGAGGTCCCAACTCCG
59.233
50.000
0.00
0.00
35.58
4.63
116
117
2.993899
CGTGCAGATTTTACCGAAGACT
59.006
45.455
0.00
0.00
0.00
3.24
142
143
1.463444
GGCTGTAGGCAAAACTGTACG
59.537
52.381
0.01
0.00
44.01
3.67
167
168
5.416013
TCTGTATGGATCATACGATCTGGAC
59.584
44.000
11.81
0.00
46.69
4.02
168
169
5.416013
GTCTGTATGGATCATACGATCTGGA
59.584
44.000
11.81
3.26
46.69
3.86
177
178
3.572682
GGTCGGTGTCTGTATGGATCATA
59.427
47.826
0.00
0.00
0.00
2.15
242
243
1.019805
GCCGCCTAAAAGCTTCTCGT
61.020
55.000
0.00
0.00
0.00
4.18
254
255
2.278989
GTACGATTGCGCCGCCTA
60.279
61.111
6.63
0.00
42.48
3.93
257
258
3.627218
GAGGTACGATTGCGCCGC
61.627
66.667
4.18
0.00
42.48
6.53
262
263
0.179081
GGTGAGGGAGGTACGATTGC
60.179
60.000
0.00
0.00
0.00
3.56
321
322
0.532862
CCGTTCTGCAACTGGAGTGT
60.533
55.000
0.00
0.00
34.87
3.55
601
622
4.168760
GCAAACTTTATGCTGAGCGATTT
58.831
39.130
0.00
0.00
40.64
2.17
638
660
1.694696
GCGGGGGATTCTCACTTCTAT
59.305
52.381
0.00
0.00
0.00
1.98
1242
1265
0.947180
GCTGTAAAGTCGGCGTGGAA
60.947
55.000
6.85
0.00
0.00
3.53
1371
1394
8.478775
TGTATAGGATGACACTAACAATAGCT
57.521
34.615
0.00
0.00
31.96
3.32
1689
1712
7.558161
TTTCTTTTCAGCATCGATCATGTAT
57.442
32.000
0.00
0.00
34.56
2.29
1908
1931
0.251634
TGCTCACCAACAGACACACA
59.748
50.000
0.00
0.00
0.00
3.72
2034
2057
1.742761
TATCAAGGTCTGCAGCAAGC
58.257
50.000
9.47
2.17
45.96
4.01
2056
2079
7.645058
ATTTACAATACCTTACAGCTGCATT
57.355
32.000
15.27
0.00
0.00
3.56
2131
2155
3.004839
TGGATACGAGATAAGCAGCAGAC
59.995
47.826
0.00
0.00
42.51
3.51
2246
2275
8.132995
CGTGTTTGGTAAAAGACTAAAAGGAAT
58.867
33.333
0.00
0.00
39.88
3.01
2499
2531
9.896645
ATCTCTTTCAGCTTGTAGATCATAAAA
57.103
29.630
0.00
0.00
0.00
1.52
2538
2570
4.605968
AGATCATCGTGACATCTTTCTCG
58.394
43.478
0.00
0.00
34.55
4.04
2794
2863
7.281324
TGACCAACCATATTACAAGAAATACGG
59.719
37.037
0.00
0.00
32.25
4.02
2810
2879
3.766545
AGTTGTTGCTATGACCAACCAT
58.233
40.909
0.00
0.00
41.33
3.55
2825
2894
8.706322
ATATGTAAAGAAACCCTGAAGTTGTT
57.294
30.769
0.00
0.00
0.00
2.83
2829
2898
9.588096
AGAAAATATGTAAAGAAACCCTGAAGT
57.412
29.630
0.00
0.00
0.00
3.01
2974
3043
8.763356
GCAAACTACAAAACATTGAATTCATCA
58.237
29.630
9.40
0.00
35.85
3.07
3076
3145
6.201615
CGAATATGCTTGAGCTTCATTACAGA
59.798
38.462
4.44
0.00
42.66
3.41
3164
3233
3.588569
AGGTTAGTCTTGAAGGAGGTGT
58.411
45.455
0.00
0.00
0.00
4.16
3166
3235
4.908481
AGAAAGGTTAGTCTTGAAGGAGGT
59.092
41.667
0.00
0.00
0.00
3.85
3387
3456
3.376546
GCTTCACATTCTCCAAGGATCAC
59.623
47.826
0.00
0.00
0.00
3.06
3452
3521
6.402222
GTGGATGAGACTAGTGATTCAAACT
58.598
40.000
0.00
0.00
0.00
2.66
3504
3573
5.307976
TGAGGACTCCAATGACCATATAAGG
59.692
44.000
0.00
0.00
0.00
2.69
3525
3594
2.496070
TCCAGGGACGACTAATGTTGAG
59.504
50.000
0.00
0.00
0.00
3.02
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.