Multiple sequence alignment - TraesCS1A01G088500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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 TraesCS1A01G088500 chr1A 100.000 2645 0 0 1 2645 76803020 76800376 0 4885
1 TraesCS1A01G088500 chr6D 95.136 2652 121 8 1 2645 176863274 176860624 0 4176
2 TraesCS1A01G088500 chr1D 95.089 2647 103 12 1 2645 146652723 146650102 0 4143
3 TraesCS1A01G088500 chr1D 96.125 2245 85 2 402 2645 234887057 234889300 0 3663
4 TraesCS1A01G088500 chr2D 94.838 2654 127 10 1 2645 460883028 460885680 0 4133
5 TraesCS1A01G088500 chr2D 92.061 2683 165 27 1 2645 606997920 606995248 0 3731
6 TraesCS1A01G088500 chr2D 93.487 952 56 6 1 947 69925674 69926624 0 1410
7 TraesCS1A01G088500 chr4D 94.798 2653 125 10 1 2645 504396232 504398879 0 4122
8 TraesCS1A01G088500 chr7D 94.499 2654 136 9 1 2645 313358073 313360725 0 4084
9 TraesCS1A01G088500 chr3D 94.115 2651 141 9 1 2645 478618291 478615650 0 4017
10 TraesCS1A01G088500 chr3D 93.794 2675 132 17 1 2645 588796864 588799534 0 3989
11 TraesCS1A01G088500 chr4A 94.149 2649 127 6 1 2645 440203830 440206454 0 4008
12 TraesCS1A01G088500 chr5D 94.049 2655 124 16 1 2645 45858645 45856015 0 3997
13 TraesCS1A01G088500 chr5A 92.924 2671 136 17 1 2645 92461045 92463688 0 3836


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 TraesCS1A01G088500 chr1A 76800376 76803020 2644 True 4885 4885 100.000 1 2645 1 chr1A.!!$R1 2644
1 TraesCS1A01G088500 chr6D 176860624 176863274 2650 True 4176 4176 95.136 1 2645 1 chr6D.!!$R1 2644
2 TraesCS1A01G088500 chr1D 146650102 146652723 2621 True 4143 4143 95.089 1 2645 1 chr1D.!!$R1 2644
3 TraesCS1A01G088500 chr1D 234887057 234889300 2243 False 3663 3663 96.125 402 2645 1 chr1D.!!$F1 2243
4 TraesCS1A01G088500 chr2D 460883028 460885680 2652 False 4133 4133 94.838 1 2645 1 chr2D.!!$F2 2644
5 TraesCS1A01G088500 chr2D 606995248 606997920 2672 True 3731 3731 92.061 1 2645 1 chr2D.!!$R1 2644
6 TraesCS1A01G088500 chr2D 69925674 69926624 950 False 1410 1410 93.487 1 947 1 chr2D.!!$F1 946
7 TraesCS1A01G088500 chr4D 504396232 504398879 2647 False 4122 4122 94.798 1 2645 1 chr4D.!!$F1 2644
8 TraesCS1A01G088500 chr7D 313358073 313360725 2652 False 4084 4084 94.499 1 2645 1 chr7D.!!$F1 2644
9 TraesCS1A01G088500 chr3D 478615650 478618291 2641 True 4017 4017 94.115 1 2645 1 chr3D.!!$R1 2644
10 TraesCS1A01G088500 chr3D 588796864 588799534 2670 False 3989 3989 93.794 1 2645 1 chr3D.!!$F1 2644
11 TraesCS1A01G088500 chr4A 440203830 440206454 2624 False 4008 4008 94.149 1 2645 1 chr4A.!!$F1 2644
12 TraesCS1A01G088500 chr5D 45856015 45858645 2630 True 3997 3997 94.049 1 2645 1 chr5D.!!$R1 2644
13 TraesCS1A01G088500 chr5A 92461045 92463688 2643 False 3836 3836 92.924 1 2645 1 chr5A.!!$F1 2644

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.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
69 70 0.809385 ACGAGACGCTTGCTAGCTTA 59.191 50.000 17.23 3.02 45.51 3.09 F
976 1038 1.402968 TCTAGGTGGACGAACATACGC 59.597 52.381 0.00 0.00 36.70 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1264 1326 0.110486 ACGGCTTCCATGGTTGACTT 59.890 50.000 12.58 0.00 0.0 3.01 R
2605 2725 1.215382 CAATGGTCGTCGAGCTCCA 59.785 57.895 23.53 14.79 0.0 3.86 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.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.586344 TGAAAGGAGTTGGATGACTATGATC 58.414 40.000 0.00 0.00 0.00 2.92
28 29 6.156775 TGAAAGGAGTTGGATGACTATGATCA 59.843 38.462 0.00 0.00 0.00 2.92
69 70 0.809385 ACGAGACGCTTGCTAGCTTA 59.191 50.000 17.23 3.02 45.51 3.09
174 175 1.769733 TCAATGCTGTTTTGAAGCGC 58.230 45.000 0.00 0.00 43.88 5.92
255 257 2.918712 AAATACTGGGATCCGAGCTG 57.081 50.000 22.58 7.65 0.00 4.24
318 320 7.801104 TGCTAACATATTTACCAATGGAGAGA 58.199 34.615 6.16 0.00 0.00 3.10
566 576 2.031157 GCAGTTTGCCACGTTTACTCAT 60.031 45.455 0.00 0.00 37.42 2.90
590 600 3.573538 TGCAGTTACCATGTTTGCTCAAT 59.426 39.130 0.00 0.00 35.85 2.57
609 619 2.222007 TTGCAGTTGCCATGTTTGAC 57.778 45.000 1.06 0.00 41.18 3.18
615 625 3.249799 CAGTTGCCATGTTTGACGAACTA 59.750 43.478 7.10 0.00 39.08 2.24
621 631 4.261031 GCCATGTTTGACGAACTACAGTTT 60.261 41.667 7.10 0.00 38.56 2.66
623 633 5.440685 CATGTTTGACGAACTACAGTTTCC 58.559 41.667 7.10 0.00 38.56 3.13
705 763 6.054295 GGTATGGAATGCAAATGCCAAAATA 58.946 36.000 2.46 0.00 41.18 1.40
746 804 5.466393 GCCATGTTTAAATGAACTGCAGTTT 59.534 36.000 31.58 18.80 38.56 2.66
816 874 6.264292 TGCCATGTTTAATGAACTGTAGTTGT 59.736 34.615 1.35 0.00 38.56 3.32
922 984 3.953612 ACACAAAACTTGCAGATTCCAGA 59.046 39.130 0.00 0.00 0.00 3.86
958 1020 2.688507 CCAGCATGTACACGACTTTCT 58.311 47.619 0.00 0.00 0.00 2.52
976 1038 1.402968 TCTAGGTGGACGAACATACGC 59.597 52.381 0.00 0.00 36.70 4.42
1005 1067 1.490490 TGTTCTATCCTGGGCATGTCC 59.510 52.381 10.20 10.20 0.00 4.02
1091 1153 3.390135 GCGAATACTACTGCCAATGCTA 58.610 45.455 0.00 0.00 38.71 3.49
1207 1269 1.412710 GATGGACTTGGGACGCTGATA 59.587 52.381 0.00 0.00 0.00 2.15
1264 1326 3.514777 GTGCATGACGAGAGACCAA 57.485 52.632 0.00 0.00 0.00 3.67
1332 1394 6.825213 ACTATGCTGAACTAATTGATGAAGCA 59.175 34.615 8.71 8.71 42.97 3.91
1340 1402 6.519679 ACTAATTGATGAAGCATGCAAGAA 57.480 33.333 21.98 2.36 0.00 2.52
1373 1435 1.757682 AGGGTCGCAGAAAAACACAA 58.242 45.000 0.00 0.00 39.69 3.33
1393 1455 2.625639 AGAAGGCCCTCAAAAGAGAGA 58.374 47.619 3.68 0.00 37.87 3.10
1401 1463 4.946157 GCCCTCAAAAGAGAGATTGATGAA 59.054 41.667 0.00 0.00 37.87 2.57
1661 1723 3.749088 CCGTAAACAACATTGGAGCACTA 59.251 43.478 0.00 0.00 0.00 2.74
1848 1913 4.098349 TGAATCTGCCATGCAATTTCTACC 59.902 41.667 0.00 0.00 38.41 3.18
1850 1915 2.016318 CTGCCATGCAATTTCTACCGA 58.984 47.619 0.00 0.00 38.41 4.69
1851 1916 2.423185 CTGCCATGCAATTTCTACCGAA 59.577 45.455 0.00 0.00 38.41 4.30
1852 1917 3.023119 TGCCATGCAATTTCTACCGAAT 58.977 40.909 0.00 0.00 34.76 3.34
1853 1918 3.066621 TGCCATGCAATTTCTACCGAATC 59.933 43.478 0.00 0.00 34.76 2.52
1854 1919 3.550842 GCCATGCAATTTCTACCGAATCC 60.551 47.826 0.00 0.00 0.00 3.01
1855 1920 3.303990 CCATGCAATTTCTACCGAATCCG 60.304 47.826 0.00 0.00 0.00 4.18
1856 1921 1.668751 TGCAATTTCTACCGAATCCGC 59.331 47.619 0.00 0.00 0.00 5.54
1857 1922 1.002792 GCAATTTCTACCGAATCCGCC 60.003 52.381 0.00 0.00 0.00 6.13
1858 1923 2.285083 CAATTTCTACCGAATCCGCCA 58.715 47.619 0.00 0.00 0.00 5.69
1859 1924 2.878406 CAATTTCTACCGAATCCGCCAT 59.122 45.455 0.00 0.00 0.00 4.40
1860 1925 4.062293 CAATTTCTACCGAATCCGCCATA 58.938 43.478 0.00 0.00 0.00 2.74
1861 1926 2.806608 TTCTACCGAATCCGCCATAC 57.193 50.000 0.00 0.00 0.00 2.39
1862 1927 0.963962 TCTACCGAATCCGCCATACC 59.036 55.000 0.00 0.00 0.00 2.73
1863 1928 0.677288 CTACCGAATCCGCCATACCA 59.323 55.000 0.00 0.00 0.00 3.25
1864 1929 1.275291 CTACCGAATCCGCCATACCAT 59.725 52.381 0.00 0.00 0.00 3.55
1865 1930 0.472471 ACCGAATCCGCCATACCATT 59.528 50.000 0.00 0.00 0.00 3.16
1866 1931 1.133915 ACCGAATCCGCCATACCATTT 60.134 47.619 0.00 0.00 0.00 2.32
1867 1932 1.535462 CCGAATCCGCCATACCATTTC 59.465 52.381 0.00 0.00 0.00 2.17
1868 1933 2.494059 CGAATCCGCCATACCATTTCT 58.506 47.619 0.00 0.00 0.00 2.52
1869 1934 3.556213 CCGAATCCGCCATACCATTTCTA 60.556 47.826 0.00 0.00 0.00 2.10
1870 1935 3.432252 CGAATCCGCCATACCATTTCTAC 59.568 47.826 0.00 0.00 0.00 2.59
1871 1936 4.642429 GAATCCGCCATACCATTTCTACT 58.358 43.478 0.00 0.00 0.00 2.57
1872 1937 5.566032 CGAATCCGCCATACCATTTCTACTA 60.566 44.000 0.00 0.00 0.00 1.82
1910 2024 7.703621 CCATTTCTACTGAATTTGCCATGTTAG 59.296 37.037 0.00 0.00 31.56 2.34
1913 2027 7.144722 TCTACTGAATTTGCCATGTTAGTTG 57.855 36.000 0.00 0.00 0.00 3.16
2003 2117 0.250252 TCCATGTTCAGTCAGCGCAA 60.250 50.000 11.47 0.00 0.00 4.85
2076 2190 1.079197 TCTCGTGCATCAACCGCAT 60.079 52.632 0.00 0.00 42.32 4.73
2366 2484 0.814010 GTCACTCACACACCACCACC 60.814 60.000 0.00 0.00 0.00 4.61
2510 2630 3.921021 CCACGTGATCACTTGTACTTCTC 59.079 47.826 25.46 0.00 0.00 2.87
2515 2635 3.824443 TGATCACTTGTACTTCTCGGTGA 59.176 43.478 0.00 0.00 37.94 4.02
2605 2725 6.478512 ACCAGTTCCATGTGTAAATTTTGT 57.521 33.333 0.00 0.00 0.00 2.83
2633 2753 2.735444 CGACGACCATTGTAGCTGTGAT 60.735 50.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.850198 TGATATGTTTTGATCATAGTCATCCAA 57.150 29.630 0.00 0.00 32.43 3.53
19 20 9.685276 TTGGACTTGATATGTTTTGATCATAGT 57.315 29.630 0.00 0.00 32.27 2.12
27 28 6.381801 GTGGTCTTGGACTTGATATGTTTTG 58.618 40.000 0.00 0.00 32.47 2.44
28 29 5.181245 CGTGGTCTTGGACTTGATATGTTTT 59.819 40.000 0.00 0.00 32.47 2.43
69 70 2.158900 CCAGTACATTCGCTTCTCCCAT 60.159 50.000 0.00 0.00 0.00 4.00
174 175 0.603569 AGTTGTCAGGGCTCACGTAG 59.396 55.000 0.00 0.00 0.00 3.51
255 257 0.936297 CGGTGTTTGCTTCTTGCTGC 60.936 55.000 0.00 0.00 43.37 5.25
279 281 4.862902 TGTTAGCAATTTTGGCTGCTTA 57.137 36.364 3.40 0.00 46.71 3.09
318 320 5.876651 TGGTGTATATCTTGCTCATCTGT 57.123 39.130 0.00 0.00 0.00 3.41
566 576 2.813754 GAGCAAACATGGTAACTGCAGA 59.186 45.455 23.35 0.00 35.44 4.26
590 600 1.535649 CGTCAAACATGGCAACTGCAA 60.536 47.619 3.76 0.00 44.36 4.08
609 619 7.802738 TCATTAAACATGGAAACTGTAGTTCG 58.197 34.615 0.00 0.00 37.25 3.95
615 625 6.183360 TGCAGTTCATTAAACATGGAAACTGT 60.183 34.615 12.33 0.00 40.56 3.55
621 631 5.771469 CAACTGCAGTTCATTAAACATGGA 58.229 37.500 28.97 0.00 40.56 3.41
623 633 4.386652 GGCAACTGCAGTTCATTAAACATG 59.613 41.667 28.97 15.46 44.36 3.21
672 729 2.158430 TGCATTCCATACCATCATGGCT 60.158 45.455 2.52 0.00 44.47 4.75
705 763 6.648879 ACATGGCAACTACATAACAACTTT 57.351 33.333 0.00 0.00 37.61 2.66
746 804 5.691305 GCAACTGCAGTTCATTAAACATGAA 59.309 36.000 28.97 0.00 40.56 2.57
816 874 7.652727 TGGAATTACAATTCGTTCAAACATGA 58.347 30.769 0.00 0.00 44.43 3.07
922 984 4.540359 TGCTGGCATGCTTTATTTCTTT 57.460 36.364 18.92 0.00 0.00 2.52
958 1020 1.402968 GAGCGTATGTTCGTCCACCTA 59.597 52.381 0.00 0.00 0.00 3.08
976 1038 3.369892 CCCAGGATAGAACACACCTTGAG 60.370 52.174 0.00 0.00 0.00 3.02
1091 1153 2.329614 CCGCCCCGTTCGAATTTGT 61.330 57.895 0.00 0.00 0.00 2.83
1264 1326 0.110486 ACGGCTTCCATGGTTGACTT 59.890 50.000 12.58 0.00 0.00 3.01
1332 1394 3.617284 TGCTGTCTCATCATTCTTGCAT 58.383 40.909 0.00 0.00 0.00 3.96
1340 1402 1.134580 CGACCCTTGCTGTCTCATCAT 60.135 52.381 0.00 0.00 0.00 2.45
1373 1435 2.625639 TCTCTCTTTTGAGGGCCTTCT 58.374 47.619 16.82 0.00 46.46 2.85
1401 1463 4.288105 TCCTCAGCTTTCCTCTTCTTGATT 59.712 41.667 0.00 0.00 0.00 2.57
1661 1723 1.704628 TGTCACCATGGACCAAGTCAT 59.295 47.619 21.47 0.00 36.97 3.06
1848 1913 2.494059 AGAAATGGTATGGCGGATTCG 58.506 47.619 0.00 0.00 39.81 3.34
1850 1915 4.706842 AGTAGAAATGGTATGGCGGATT 57.293 40.909 0.00 0.00 0.00 3.01
1851 1916 5.818678 TTAGTAGAAATGGTATGGCGGAT 57.181 39.130 0.00 0.00 0.00 4.18
1852 1917 5.617528 TTTAGTAGAAATGGTATGGCGGA 57.382 39.130 0.00 0.00 0.00 5.54
1853 1918 6.147821 CAGATTTAGTAGAAATGGTATGGCGG 59.852 42.308 0.00 0.00 0.00 6.13
1854 1919 6.347725 GCAGATTTAGTAGAAATGGTATGGCG 60.348 42.308 0.00 0.00 0.00 5.69
1855 1920 6.072452 GGCAGATTTAGTAGAAATGGTATGGC 60.072 42.308 0.00 0.00 0.00 4.40
1856 1921 6.998074 TGGCAGATTTAGTAGAAATGGTATGG 59.002 38.462 0.00 0.00 0.00 2.74
1857 1922 8.509690 CATGGCAGATTTAGTAGAAATGGTATG 58.490 37.037 0.00 0.00 0.00 2.39
1858 1923 7.175641 GCATGGCAGATTTAGTAGAAATGGTAT 59.824 37.037 0.00 0.00 0.00 2.73
1859 1924 6.486657 GCATGGCAGATTTAGTAGAAATGGTA 59.513 38.462 0.00 0.00 0.00 3.25
1860 1925 5.300286 GCATGGCAGATTTAGTAGAAATGGT 59.700 40.000 0.00 0.00 0.00 3.55
1861 1926 5.278660 GGCATGGCAGATTTAGTAGAAATGG 60.279 44.000 15.47 0.00 0.00 3.16
1862 1927 5.300034 TGGCATGGCAGATTTAGTAGAAATG 59.700 40.000 19.43 0.00 0.00 2.32
1863 1928 5.448654 TGGCATGGCAGATTTAGTAGAAAT 58.551 37.500 19.43 0.00 0.00 2.17
1864 1929 4.854173 TGGCATGGCAGATTTAGTAGAAA 58.146 39.130 19.43 0.00 0.00 2.52
1865 1930 4.502105 TGGCATGGCAGATTTAGTAGAA 57.498 40.909 19.43 0.00 0.00 2.10
1866 1931 4.712051 ATGGCATGGCAGATTTAGTAGA 57.288 40.909 27.02 0.00 0.00 2.59
1867 1932 5.533903 AGAAATGGCATGGCAGATTTAGTAG 59.466 40.000 27.02 0.00 0.00 2.57
1868 1933 5.448654 AGAAATGGCATGGCAGATTTAGTA 58.551 37.500 27.02 0.00 0.00 1.82
1869 1934 4.284178 AGAAATGGCATGGCAGATTTAGT 58.716 39.130 27.02 11.41 0.00 2.24
1870 1935 4.931661 AGAAATGGCATGGCAGATTTAG 57.068 40.909 27.02 0.00 0.00 1.85
1871 1936 5.300034 CAGTAGAAATGGCATGGCAGATTTA 59.700 40.000 27.02 14.22 0.00 1.40
1872 1937 4.098960 CAGTAGAAATGGCATGGCAGATTT 59.901 41.667 27.02 22.02 0.00 2.17
1910 2024 5.643777 ACTAACATGGCAGATTCAGTACAAC 59.356 40.000 0.00 0.00 0.00 3.32
1913 2027 5.643777 ACAACTAACATGGCAGATTCAGTAC 59.356 40.000 0.00 0.00 0.00 2.73
1955 2069 4.154195 ACGCAATGAAGATTCAGTACAACC 59.846 41.667 1.32 0.00 41.08 3.77
2003 2117 9.461312 ACCACAATACAATATGTGTGACTAAAT 57.539 29.630 4.28 0.00 44.21 1.40
2146 2261 9.925268 GTGAAAGTTATCGTTCTTTCTTGTTTA 57.075 29.630 15.33 0.00 45.36 2.01
2291 2408 3.678056 CCTACTTAGGTGTGACAGCAA 57.322 47.619 17.69 8.26 38.69 3.91
2366 2484 2.027745 TCTCCCCGTAGCCTAGTATACG 60.028 54.545 14.05 14.05 43.32 3.06
2510 2630 1.871080 AGCTGTGAAGAAAGTCACCG 58.129 50.000 3.06 0.00 46.13 4.94
2515 2635 5.247110 TCATAGAGGAAGCTGTGAAGAAAGT 59.753 40.000 0.00 0.00 33.82 2.66
2605 2725 1.215382 CAATGGTCGTCGAGCTCCA 59.785 57.895 23.53 14.79 0.00 3.86


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.