Multiple sequence alignment - TraesCS3B01G419100
Loading Multiple Alignment...
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
TraesCS3B01G419100
chr3B
100.000
2723
0
0
1
2723
655637430
655640152
0.000000e+00
5029.0
1
TraesCS3B01G419100
chr3D
89.240
2119
163
38
7
2090
496681619
496683707
0.000000e+00
2590.0
2
TraesCS3B01G419100
chr3D
88.832
394
12
7
2334
2723
496686022
496686387
3.200000e-124
455.0
3
TraesCS3B01G419100
chr3D
84.906
212
22
5
8
217
496681160
496681363
3.550000e-49
206.0
4
TraesCS3B01G419100
chr3D
89.600
125
13
0
2119
2243
496684730
496684854
2.810000e-35
159.0
5
TraesCS3B01G419100
chr3D
100.000
37
0
0
2087
2123
496684418
496684454
4.870000e-08
69.4
6
TraesCS3B01G419100
chr3A
91.887
1516
82
18
453
1948
638201609
638200115
0.000000e+00
2080.0
7
TraesCS3B01G419100
chr3A
84.924
524
48
12
1937
2457
638200096
638199601
4.050000e-138
501.0
8
TraesCS3B01G419100
chr3A
97.531
243
5
1
159
400
638201851
638201609
5.420000e-112
414.0
9
TraesCS3B01G419100
chr3A
91.007
278
14
8
2449
2723
638199374
638199105
5.540000e-97
364.0
10
TraesCS3B01G419100
chr3A
96.203
158
5
1
4
160
638202090
638201933
9.670000e-65
257.0
11
TraesCS3B01G419100
chr5A
78.037
601
82
25
1197
1749
322836770
322837368
1.560000e-87
333.0
12
TraesCS3B01G419100
chr4A
77.704
601
84
24
1197
1749
507597711
507598309
3.380000e-84
322.0
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
TraesCS3B01G419100
chr3B
655637430
655640152
2722
False
5029.00
5029
100.0000
1
2723
1
chr3B.!!$F1
2722
1
TraesCS3B01G419100
chr3D
496681160
496686387
5227
False
695.88
2590
90.5156
7
2723
5
chr3D.!!$F1
2716
2
TraesCS3B01G419100
chr3A
638199105
638202090
2985
True
723.20
2080
92.3104
4
2723
5
chr3A.!!$R1
2719
3
TraesCS3B01G419100
chr5A
322836770
322837368
598
False
333.00
333
78.0370
1197
1749
1
chr5A.!!$F1
552
4
TraesCS3B01G419100
chr4A
507597711
507598309
598
False
322.00
322
77.7040
1197
1749
1
chr4A.!!$F1
552
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
790
1359
0.319297
GCCTTTTCTTGTGCAGCTGG
60.319
55.0
17.12
0.0
0.0
4.85
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2163
3848
0.17668
GAAGCTGCCTCCATCTCGAA
59.823
55.0
0.0
0.0
0.0
3.71
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
206
753
6.449635
TGTTTTGTGATTTCTGTGCTAAGT
57.550
33.333
0.00
0.00
0.00
2.24
292
845
1.531058
GCGTGGTGTGTTGACAAGTTC
60.531
52.381
0.00
0.00
32.49
3.01
377
931
2.754472
TGTTCAGATTGTCACTGTCCG
58.246
47.619
0.00
0.00
36.81
4.79
400
954
2.076863
CCACCTAAAAACGAGCCTCTG
58.923
52.381
0.00
0.00
0.00
3.35
405
959
1.620822
AAAAACGAGCCTCTGCCAAT
58.379
45.000
0.00
0.00
38.69
3.16
407
961
1.620822
AAACGAGCCTCTGCCAATTT
58.379
45.000
0.00
0.00
38.69
1.82
408
962
0.883833
AACGAGCCTCTGCCAATTTG
59.116
50.000
0.00
0.00
38.69
2.32
420
974
4.883585
TCTGCCAATTTGTGATACTCATCC
59.116
41.667
0.00
0.00
0.00
3.51
488
1044
1.512926
AGCACGAAATTTGAGTCGCT
58.487
45.000
0.00
5.23
40.95
4.93
489
1045
1.873591
AGCACGAAATTTGAGTCGCTT
59.126
42.857
0.00
0.00
40.95
4.68
595
1160
0.326927
CGGACCCCTTAAAGCCTTCA
59.673
55.000
0.00
0.00
0.00
3.02
636
1201
2.623535
TGAAGGCATGCATCATTTTGC
58.376
42.857
21.36
0.00
43.07
3.68
789
1358
0.386476
TGCCTTTTCTTGTGCAGCTG
59.614
50.000
10.11
10.11
0.00
4.24
790
1359
0.319297
GCCTTTTCTTGTGCAGCTGG
60.319
55.000
17.12
0.00
0.00
4.85
869
1438
2.664851
TGCGCCGTTTGTCTCCAG
60.665
61.111
4.18
0.00
0.00
3.86
970
1545
4.430007
CAGCCATACACGTACATGTAGTT
58.570
43.478
5.62
0.00
38.43
2.24
971
1546
4.503007
CAGCCATACACGTACATGTAGTTC
59.497
45.833
5.62
0.00
38.43
3.01
973
1548
4.678574
GCCATACACGTACATGTAGTTCCA
60.679
45.833
5.62
0.00
38.43
3.53
979
1554
3.259064
CGTACATGTAGTTCCACCTTGG
58.741
50.000
5.62
0.00
39.43
3.61
1004
1581
4.437930
GGAAATCTTCCGAGTTTGCATGAG
60.438
45.833
0.00
0.00
40.59
2.90
1115
1692
1.273886
GGAGTCCAGCGTCTTCTTCTT
59.726
52.381
3.60
0.00
0.00
2.52
1116
1693
2.289133
GGAGTCCAGCGTCTTCTTCTTT
60.289
50.000
3.60
0.00
0.00
2.52
1139
1716
4.308458
CGTGACGTCCAGGGCCAA
62.308
66.667
14.12
0.00
0.00
4.52
1140
1717
2.358737
GTGACGTCCAGGGCCAAG
60.359
66.667
14.12
0.00
0.00
3.61
1164
1744
1.001597
GACAGGCTATCGTACTTCCGG
60.002
57.143
0.00
0.00
0.00
5.14
1302
1883
1.153086
GGTCCTTGCAGCCGATGAT
60.153
57.895
0.00
0.00
0.00
2.45
1388
1982
2.957489
CGTCCGTGACACGTGCAA
60.957
61.111
25.18
0.00
40.58
4.08
1389
1983
2.624264
GTCCGTGACACGTGCAAC
59.376
61.111
25.18
13.19
40.58
4.17
1500
2094
0.739462
CGGCTGCAAACTCGATGGTA
60.739
55.000
0.50
0.00
0.00
3.25
1501
2095
1.668419
GGCTGCAAACTCGATGGTAT
58.332
50.000
0.50
0.00
0.00
2.73
1556
2158
4.069232
CAAGGACGAGGAGGCGCA
62.069
66.667
10.83
0.00
33.86
6.09
1668
2288
2.980233
GTGGTGCTGTGCCTGGTC
60.980
66.667
0.00
0.00
0.00
4.02
1805
2441
4.919168
CGTCGTCTTATTGTACTTCACCAA
59.081
41.667
0.00
0.00
0.00
3.67
1815
2451
3.830178
TGTACTTCACCAACTAGCTAGCA
59.170
43.478
20.91
3.08
0.00
3.49
1816
2452
3.601443
ACTTCACCAACTAGCTAGCAG
57.399
47.619
20.91
14.32
0.00
4.24
1817
2453
2.275318
CTTCACCAACTAGCTAGCAGC
58.725
52.381
20.91
0.00
42.84
5.25
1862
2498
2.673862
GGAAAGAAACTAAGCTCCGAGC
59.326
50.000
12.80
12.80
42.84
5.03
1871
2507
4.921834
GCTCCGAGCTTAGCTTGT
57.078
55.556
18.99
0.00
39.88
3.16
1872
2508
3.145228
GCTCCGAGCTTAGCTTGTT
57.855
52.632
18.99
0.00
39.88
2.83
1873
2509
0.723981
GCTCCGAGCTTAGCTTGTTG
59.276
55.000
18.99
12.25
39.88
3.33
1874
2510
0.723981
CTCCGAGCTTAGCTTGTTGC
59.276
55.000
18.99
0.41
39.88
4.17
1897
2533
6.133392
GCTGCTGCGACGATTAATTTATTTA
58.867
36.000
0.00
0.00
0.00
1.40
1920
2573
4.084013
ACGTAGTTGCATGCTAAGAAACAC
60.084
41.667
20.33
12.84
37.78
3.32
1935
2626
4.649692
AGAAACACATCTCATGCTTCTGT
58.350
39.130
0.00
0.00
30.49
3.41
1959
2650
7.094420
TGTTCATCGTCATGTCCAAATAACAAT
60.094
33.333
0.00
0.00
0.00
2.71
1998
2689
4.081406
TGAATTGTCAGTTCATCCTTGGG
58.919
43.478
6.67
0.00
31.07
4.12
2002
2693
0.613260
TCAGTTCATCCTTGGGACGG
59.387
55.000
0.00
0.00
32.98
4.79
2070
2761
1.440938
TTTTGACAACCGGCCTGTCG
61.441
55.000
24.58
1.36
45.10
4.35
2129
3814
1.881973
TGAGGTGCATCAGAAAACAGC
59.118
47.619
0.00
0.00
0.00
4.40
2245
3930
5.606505
GGAACCCTATGAAATCTCTCTGTC
58.393
45.833
0.00
0.00
0.00
3.51
2248
3933
3.553922
CCCTATGAAATCTCTCTGTCGCC
60.554
52.174
0.00
0.00
0.00
5.54
2255
3941
1.256812
TCTCTCTGTCGCCACAATGA
58.743
50.000
0.00
0.00
29.82
2.57
2280
4768
3.181479
CGCTGCTAGTGATAACCCAGTAA
60.181
47.826
0.00
0.00
0.00
2.24
2299
4787
6.272318
CAGTAAAGAACACCTTGAATTGCAA
58.728
36.000
0.00
0.00
34.79
4.08
2300
4788
6.756074
CAGTAAAGAACACCTTGAATTGCAAA
59.244
34.615
1.71
0.00
35.74
3.68
2301
4789
7.277539
CAGTAAAGAACACCTTGAATTGCAAAA
59.722
33.333
1.71
0.00
35.74
2.44
2302
4790
7.821846
AGTAAAGAACACCTTGAATTGCAAAAA
59.178
29.630
1.71
0.00
35.74
1.94
2400
5162
3.425404
GCAAAGTATACACCGCAATGTG
58.575
45.455
5.50
0.00
42.05
3.21
2487
5485
5.439721
CTGGGGTAGTTGATGAATGATTCA
58.560
41.667
10.65
10.65
45.01
2.57
2490
5488
6.896860
TGGGGTAGTTGATGAATGATTCAAAT
59.103
34.615
12.36
0.00
43.95
2.32
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
3.942829
CAGAGCTGTGAAATCTGGGTAA
58.057
45.455
4.50
0.00
37.41
2.85
1
2
3.616956
CAGAGCTGTGAAATCTGGGTA
57.383
47.619
4.50
0.00
37.41
3.69
2
3
2.486472
CAGAGCTGTGAAATCTGGGT
57.514
50.000
4.50
0.00
37.41
4.51
13
14
8.011795
CATAATTATATGTGGCTCCAGAGCTGT
61.012
40.741
18.54
5.89
42.39
4.40
206
753
4.734398
AGACAAAAACCAGCAATGACAA
57.266
36.364
0.00
0.00
0.00
3.18
292
845
7.148623
GGAACATCACTAGTAGGAAAAAGAACG
60.149
40.741
1.45
0.00
0.00
3.95
346
899
4.130118
ACAATCTGAACAAGTCACCTGTC
58.870
43.478
0.00
0.00
31.13
3.51
377
931
1.162698
GGCTCGTTTTTAGGTGGTCC
58.837
55.000
0.00
0.00
0.00
4.46
420
974
1.264288
GCAGAACCGAAACAAGTGGAG
59.736
52.381
0.00
0.00
0.00
3.86
483
1039
1.070776
GTGAGTCAAAACGGAAGCGAC
60.071
52.381
0.00
0.00
0.00
5.19
488
1044
3.469739
GGTTAGGTGAGTCAAAACGGAA
58.530
45.455
0.00
0.00
0.00
4.30
489
1045
2.224354
GGGTTAGGTGAGTCAAAACGGA
60.224
50.000
0.00
0.00
0.00
4.69
569
1134
2.878526
GCTTTAAGGGGTCCGATGTTGT
60.879
50.000
0.00
0.00
0.00
3.32
595
1160
1.076632
TGTGGTTTTCGGCCTTGGT
60.077
52.632
0.00
0.00
0.00
3.67
636
1201
0.029035
GAAGCGCCATCTTGATGCAG
59.971
55.000
2.29
2.94
0.00
4.41
789
1358
9.965824
ATGATTTCGGTTTTCATATAATGTTCC
57.034
29.630
0.00
0.00
0.00
3.62
971
1546
0.811281
GAAGATTTCCGCCAAGGTGG
59.189
55.000
12.54
12.54
46.45
4.61
973
1548
3.266240
GGAAGATTTCCGCCAAGGT
57.734
52.632
0.00
0.00
40.59
3.50
1076
1653
4.373116
GGCCGTCACCTTCGCTGA
62.373
66.667
0.00
0.00
0.00
4.26
1136
1713
1.482593
ACGATAGCCTGTCCTTCTTGG
59.517
52.381
0.00
0.00
42.67
3.61
1138
1715
3.633418
AGTACGATAGCCTGTCCTTCTT
58.367
45.455
0.00
0.00
42.67
2.52
1139
1716
3.300239
AGTACGATAGCCTGTCCTTCT
57.700
47.619
0.00
0.00
42.67
2.85
1140
1717
3.243468
GGAAGTACGATAGCCTGTCCTTC
60.243
52.174
0.00
0.00
42.67
3.46
1164
1744
4.373116
TCGCCAACCTCGCTGGAC
62.373
66.667
1.32
0.00
39.71
4.02
1345
1939
3.437795
GAAGCGGACGACCTCGGA
61.438
66.667
1.72
0.00
44.95
4.55
1389
1983
4.559063
CTCCTCCTGGGCATGGCG
62.559
72.222
13.76
0.00
34.39
5.69
1495
2089
2.826702
GTCGCCGGGGAATACCAT
59.173
61.111
24.36
0.00
42.91
3.55
1533
2131
1.248785
CCTCCTCGTCCTTGTCGGAA
61.249
60.000
0.00
0.00
45.32
4.30
1668
2288
2.047274
ATCCACACGCCGAACAGG
60.047
61.111
0.00
0.00
44.97
4.00
1765
2398
2.269241
GGAGAAGGCCTTCGTGGG
59.731
66.667
34.27
0.00
43.97
4.61
1786
2419
7.097834
AGCTAGTTGGTGAAGTACAATAAGAC
58.902
38.462
0.00
0.00
0.00
3.01
1866
2502
2.428071
GTCGCAGCAGCAACAAGC
60.428
61.111
0.82
0.00
42.27
4.01
1867
2503
1.904852
ATCGTCGCAGCAGCAACAAG
61.905
55.000
0.82
0.00
42.27
3.16
1868
2504
1.506309
AATCGTCGCAGCAGCAACAA
61.506
50.000
0.82
0.00
42.27
2.83
1869
2505
0.669012
TAATCGTCGCAGCAGCAACA
60.669
50.000
0.82
0.00
42.27
3.33
1870
2506
0.442310
TTAATCGTCGCAGCAGCAAC
59.558
50.000
0.82
0.00
42.27
4.17
1871
2507
1.368641
ATTAATCGTCGCAGCAGCAA
58.631
45.000
0.82
0.00
42.27
3.91
1872
2508
1.368641
AATTAATCGTCGCAGCAGCA
58.631
45.000
0.82
0.00
42.27
4.41
1873
2509
2.458592
AAATTAATCGTCGCAGCAGC
57.541
45.000
0.00
0.00
37.42
5.25
1874
2510
6.297641
CGTAAATAAATTAATCGTCGCAGCAG
59.702
38.462
0.00
0.00
0.00
4.24
1875
2511
6.124099
CGTAAATAAATTAATCGTCGCAGCA
58.876
36.000
0.00
0.00
0.00
4.41
1876
2512
6.124759
ACGTAAATAAATTAATCGTCGCAGC
58.875
36.000
0.00
0.00
0.00
5.25
1877
2513
8.474577
ACTACGTAAATAAATTAATCGTCGCAG
58.525
33.333
0.00
0.00
0.00
5.18
1878
2514
8.338985
ACTACGTAAATAAATTAATCGTCGCA
57.661
30.769
0.00
0.00
0.00
5.10
1879
2515
9.074316
CAACTACGTAAATAAATTAATCGTCGC
57.926
33.333
0.00
0.00
0.00
5.19
1880
2516
9.074316
GCAACTACGTAAATAAATTAATCGTCG
57.926
33.333
0.00
0.00
0.00
5.12
1881
2517
9.904647
TGCAACTACGTAAATAAATTAATCGTC
57.095
29.630
0.00
0.00
0.00
4.20
1897
2533
4.062293
TGTTTCTTAGCATGCAACTACGT
58.938
39.130
21.98
0.00
0.00
3.57
1912
2565
5.068636
ACAGAAGCATGAGATGTGTTTCTT
58.931
37.500
0.00
0.00
42.15
2.52
1920
2573
3.869832
ACGATGAACAGAAGCATGAGATG
59.130
43.478
0.00
0.00
0.00
2.90
1935
2626
6.809630
TTGTTATTTGGACATGACGATGAA
57.190
33.333
0.00
0.00
33.36
2.57
1959
2650
2.136298
TCACAACAACCTTCTGCCAA
57.864
45.000
0.00
0.00
0.00
4.52
1998
2689
0.716108
CTGAAAGACATCGCACCGTC
59.284
55.000
0.00
0.00
34.07
4.79
2002
2693
1.421485
CCGCTGAAAGACATCGCAC
59.579
57.895
0.00
0.00
36.90
5.34
2140
3825
6.097915
AGACTTTAACAGCTACAGCAGTAA
57.902
37.500
3.70
0.00
45.16
2.24
2149
3834
5.417894
TCCATCTCGAAGACTTTAACAGCTA
59.582
40.000
0.00
0.00
0.00
3.32
2157
3842
1.902508
TGCCTCCATCTCGAAGACTTT
59.097
47.619
0.00
0.00
0.00
2.66
2163
3848
0.176680
GAAGCTGCCTCCATCTCGAA
59.823
55.000
0.00
0.00
0.00
3.71
2220
3905
4.657969
CAGAGAGATTTCATAGGGTTCCCT
59.342
45.833
15.19
15.19
40.06
4.20
2223
3908
5.285651
CGACAGAGAGATTTCATAGGGTTC
58.714
45.833
0.00
0.00
0.00
3.62
2227
3912
3.068732
TGGCGACAGAGAGATTTCATAGG
59.931
47.826
0.00
0.00
35.01
2.57
2229
3914
3.447229
TGTGGCGACAGAGAGATTTCATA
59.553
43.478
0.00
0.00
44.46
2.15
2248
3933
1.346197
CTAGCAGCGCGTCATTGTG
59.654
57.895
8.43
0.00
0.00
3.33
2255
3941
0.527817
GGTTATCACTAGCAGCGCGT
60.528
55.000
8.43
0.00
0.00
6.01
2400
5162
1.293179
GGTCTGCAAATGGCCCAAC
59.707
57.895
0.00
0.00
43.89
3.77
2507
5508
1.600957
AGCTCGATTGATTGCCATTCG
59.399
47.619
0.00
0.00
45.08
3.34
2586
5588
6.248569
AGTCATAGGTTGGTAGGGTTATTG
57.751
41.667
0.00
0.00
0.00
1.90
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.