Multiple sequence alignment - TraesCS3D01G505200

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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 TraesCS3D01G505200 chr3D 100.000 3007 0 0 1 3007 592607060 592610066 0.000000e+00 5553
1 TraesCS3D01G505200 chr3D 85.967 1582 169 31 1372 2908 592576741 592578314 0.000000e+00 1642
2 TraesCS3D01G505200 chr3D 89.753 527 44 8 714 1231 592575668 592576193 0.000000e+00 665
3 TraesCS3D01G505200 chr3A 96.274 3033 76 13 1 3007 723662790 723659769 0.000000e+00 4940
4 TraesCS3D01G505200 chr3A 86.096 1647 173 34 1307 2908 724023043 724021408 0.000000e+00 1722
5 TraesCS3D01G505200 chr3A 89.456 294 25 4 725 1012 724023572 724023279 1.700000e-97 366
6 TraesCS3D01G505200 chr3B 95.439 2346 79 10 3 2341 794545455 794543131 0.000000e+00 3714
7 TraesCS3D01G505200 chr3B 85.547 1619 180 35 1307 2882 794840188 794838581 0.000000e+00 1644
8 TraesCS3D01G505200 chr3B 86.152 1372 144 23 1307 2641 794593154 794591792 0.000000e+00 1439
9 TraesCS3D01G505200 chr3B 90.974 698 31 11 2330 3007 794541617 794540932 0.000000e+00 911
10 TraesCS3D01G505200 chr3B 90.520 538 43 5 725 1254 794593677 794593140 0.000000e+00 704
11 TraesCS3D01G505200 chr3B 90.149 538 45 5 725 1254 794840711 794840174 0.000000e+00 693
12 TraesCS3D01G505200 chr3B 84.211 266 35 5 380 640 794841070 794840807 4.980000e-63 252


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 TraesCS3D01G505200 chr3D 592607060 592610066 3006 False 5553.0 5553 100.000000 1 3007 1 chr3D.!!$F1 3006
1 TraesCS3D01G505200 chr3D 592575668 592578314 2646 False 1153.5 1642 87.860000 714 2908 2 chr3D.!!$F2 2194
2 TraesCS3D01G505200 chr3A 723659769 723662790 3021 True 4940.0 4940 96.274000 1 3007 1 chr3A.!!$R1 3006
3 TraesCS3D01G505200 chr3A 724021408 724023572 2164 True 1044.0 1722 87.776000 725 2908 2 chr3A.!!$R2 2183
4 TraesCS3D01G505200 chr3B 794540932 794545455 4523 True 2312.5 3714 93.206500 3 3007 2 chr3B.!!$R1 3004
5 TraesCS3D01G505200 chr3B 794591792 794593677 1885 True 1071.5 1439 88.336000 725 2641 2 chr3B.!!$R2 1916
6 TraesCS3D01G505200 chr3B 794838581 794841070 2489 True 863.0 1644 86.635667 380 2882 3 chr3B.!!$R3 2502

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
851 903 0.178068 TATGCGGGCCTGTCTTTCTC 59.822 55.0 14.55 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2674 4786 1.620819 GAGCTGGTTGGAGTCTTCAGA 59.379 52.381 0.0 0.0 0.0 3.27 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
205 206 8.582657 TCGTTTATTCCCCAGAAAATTCATAA 57.417 30.769 0.00 0.00 35.09 1.90
223 225 5.551233 TCATAAAGCTCAAATAGGATCCCG 58.449 41.667 8.55 0.00 0.00 5.14
288 290 0.178876 TGGATGAACAGAGGACCCCA 60.179 55.000 0.00 0.00 0.00 4.96
710 733 6.634805 TGGCATTTGTGTCACTAAAGAAAAA 58.365 32.000 4.27 0.00 0.00 1.94
851 903 0.178068 TATGCGGGCCTGTCTTTCTC 59.822 55.000 14.55 0.00 0.00 2.87
1217 1274 6.081693 GGTGAACAACGTTATGATTTGGTAC 58.918 40.000 0.00 0.00 0.00 3.34
1278 1803 7.690454 TTATCTATGAACTTGGGGATCTTGA 57.310 36.000 0.00 0.00 0.00 3.02
1423 1957 3.132289 TGGATCGATCTACCTTTGTGTCC 59.868 47.826 23.96 5.67 0.00 4.02
1622 2156 0.511653 CTGCGATCAAGGCATCATCG 59.488 55.000 7.99 7.99 41.92 3.84
1752 2290 6.820152 ACTTACCCCGTGTTATTAGTTCATTC 59.180 38.462 0.00 0.00 0.00 2.67
1816 2360 6.484977 GGAATCAAAGAGGATATGAGGACAAC 59.515 42.308 0.00 0.00 0.00 3.32
1916 2460 4.757149 GGTAACAATGAAGAGAGTTGCAGT 59.243 41.667 0.00 0.00 0.00 4.40
2389 4477 5.355910 GGGACGCACATTCCTTTTTATTAGA 59.644 40.000 0.00 0.00 33.17 2.10
2674 4786 1.500108 CAAATTGCGCACCACACAAT 58.500 45.000 11.12 0.00 35.59 2.71
2715 4830 2.356382 CCTCGTCACTACTTAGCTGGAG 59.644 54.545 0.00 0.00 0.00 3.86
2719 4834 1.195115 CACTACTTAGCTGGAGGCCA 58.805 55.000 5.01 0.00 43.05 5.36
2738 4853 3.002965 GCCAAGTAAATTCCGAATACCCG 59.997 47.826 0.00 0.00 0.00 5.28
2744 4859 1.105457 ATTCCGAATACCCGTCGTCA 58.895 50.000 0.00 0.00 36.77 4.35
2811 4932 1.971695 GCCAAAAGGGGACAGGTCG 60.972 63.158 0.00 0.00 37.04 4.79
2812 4933 1.454539 CCAAAAGGGGACAGGTCGT 59.545 57.895 0.00 0.00 0.00 4.34
2813 4934 0.889186 CCAAAAGGGGACAGGTCGTG 60.889 60.000 0.00 0.00 0.00 4.35
2814 4935 0.107831 CAAAAGGGGACAGGTCGTGA 59.892 55.000 0.00 0.00 0.00 4.35
2815 4936 1.064825 AAAAGGGGACAGGTCGTGAT 58.935 50.000 0.00 0.00 0.00 3.06
2816 4937 1.064825 AAAGGGGACAGGTCGTGATT 58.935 50.000 0.00 0.00 0.00 2.57
2872 5001 3.084786 CACTTTGATCCTTTCCCTGACC 58.915 50.000 0.00 0.00 0.00 4.02
2882 5011 6.039415 TCCTTTCCCTGACCTACATAGTAT 57.961 41.667 0.00 0.00 0.00 2.12
2909 5040 6.996879 CCCATCAATAGACTGAATGTGATTCT 59.003 38.462 0.00 0.00 39.96 2.40
2910 5041 8.152898 CCCATCAATAGACTGAATGTGATTCTA 58.847 37.037 0.00 0.00 39.96 2.10
2927 5058 7.232534 TGTGATTCTAAAATGGTTAACCTGCTT 59.767 33.333 24.78 16.09 36.82 3.91
2935 5066 7.865706 AAATGGTTAACCTGCTTAGTATCTG 57.134 36.000 24.78 0.00 36.82 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 206 2.408565 TCCGGGATCCTATTTGAGCTT 58.591 47.619 12.58 0.00 0.00 3.74
223 225 6.156083 AGAGGCTATATCTTGCTAGGAAATCC 59.844 42.308 0.00 0.00 0.00 3.01
288 290 1.689273 GCAAGAGATCCCCGATACACT 59.311 52.381 0.00 0.00 0.00 3.55
710 733 6.088883 GGAATACATTTCGCGTGAACAAATTT 59.911 34.615 11.68 3.17 32.71 1.82
1423 1957 8.279970 TCCATAAGTTAATTCATGTTGGTCAG 57.720 34.615 0.00 0.00 0.00 3.51
1622 2156 7.252708 TGCAAATCTCACAATTGTATGATGAC 58.747 34.615 19.59 14.36 0.00 3.06
1816 2360 7.875041 AGTCAATAATATCTCCAATCGGAACAG 59.125 37.037 0.00 0.00 42.21 3.16
2077 2621 9.360093 CTTATTTTGTTCAAAACCTTACACACA 57.640 29.630 11.99 0.00 0.00 3.72
2389 4477 2.424601 CTCCATGCATGTCATCCGTTTT 59.575 45.455 24.58 0.00 31.79 2.43
2674 4786 1.620819 GAGCTGGTTGGAGTCTTCAGA 59.379 52.381 0.00 0.00 0.00 3.27
2715 4830 3.317149 GGGTATTCGGAATTTACTTGGCC 59.683 47.826 8.76 0.00 0.00 5.36
2719 4834 4.114794 CGACGGGTATTCGGAATTTACTT 58.885 43.478 8.76 0.00 32.66 2.24
2811 4932 9.185192 CTAAAGAAACAAAACCTCATCAATCAC 57.815 33.333 0.00 0.00 0.00 3.06
2812 4933 7.867403 GCTAAAGAAACAAAACCTCATCAATCA 59.133 33.333 0.00 0.00 0.00 2.57
2813 4934 7.867403 TGCTAAAGAAACAAAACCTCATCAATC 59.133 33.333 0.00 0.00 0.00 2.67
2814 4935 7.725251 TGCTAAAGAAACAAAACCTCATCAAT 58.275 30.769 0.00 0.00 0.00 2.57
2815 4936 7.106439 TGCTAAAGAAACAAAACCTCATCAA 57.894 32.000 0.00 0.00 0.00 2.57
2816 4937 6.239008 CCTGCTAAAGAAACAAAACCTCATCA 60.239 38.462 0.00 0.00 0.00 3.07
2872 5001 7.978414 CAGTCTATTGATGGGCATACTATGTAG 59.022 40.741 0.00 0.00 0.00 2.74
2882 5011 4.080413 TCACATTCAGTCTATTGATGGGCA 60.080 41.667 0.00 0.00 0.00 5.36
2909 5040 9.391006 CAGATACTAAGCAGGTTAACCATTTTA 57.609 33.333 26.26 17.61 38.89 1.52
2910 5041 7.888546 ACAGATACTAAGCAGGTTAACCATTTT 59.111 33.333 26.26 17.45 38.89 1.82
2935 5066 6.701400 AGTGCATGTGTTCCATTTTTCTTTAC 59.299 34.615 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.