Multiple sequence alignment - TraesCS3B01G170400

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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 TraesCS3B01G170400 chr3B 100.000 2837 0 0 1 2837 171311435 171314271 0 5240
1 TraesCS3B01G170400 chr3B 97.158 950 22 4 1891 2837 171305144 171306091 0 1600
2 TraesCS3B01G170400 chr1D 92.517 2873 156 27 2 2835 33122462 33125314 0 4060
3 TraesCS3B01G170400 chr1D 92.348 2875 161 28 1 2835 33178644 33175789 0 4036
4 TraesCS3B01G170400 chr1D 90.920 1685 99 24 1189 2835 33198410 33196742 0 2215
5 TraesCS3B01G170400 chr1D 93.875 849 43 8 1995 2835 33111450 33110603 0 1271
6 TraesCS3B01G170400 chr1D 93.640 849 44 8 1995 2835 33169983 33169137 0 1260
7 TraesCS3B01G170400 chr5B 91.827 2863 194 24 1 2835 544187297 544184447 0 3954
8 TraesCS3B01G170400 chr5B 93.713 843 37 13 2003 2837 544195004 544194170 0 1249
9 TraesCS3B01G170400 chr4B 94.580 2214 112 7 1 2208 647021709 647019498 0 3417
10 TraesCS3B01G170400 chr2B 96.028 2014 75 5 1 2014 791908651 791910659 0 3271
11 TraesCS3B01G170400 chr2B 95.879 2014 77 6 1 2012 542736942 542738951 0 3254
12 TraesCS3B01G170400 chr2B 95.780 2014 79 5 1 2014 791884166 791882159 0 3243
13 TraesCS3B01G170400 chr5A 95.941 2020 73 9 1 2014 21853806 21855822 0 3267
14 TraesCS3B01G170400 chr5A 95.689 2018 81 6 1 2018 21862121 21864132 0 3240
15 TraesCS3B01G170400 chr6A 95.887 2018 78 5 1 2018 531357174 531355162 0 3262
16 TraesCS3B01G170400 chr4A 95.782 2015 80 5 1 2014 59258887 59256877 0 3245
17 TraesCS3B01G170400 chr2D 92.200 2295 142 21 1 2289 536413 534150 0 3212
18 TraesCS3B01G170400 chr3D 92.136 852 53 11 1990 2835 190430008 190429165 0 1190


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 TraesCS3B01G170400 chr3B 171311435 171314271 2836 False 5240 5240 100.000 1 2837 1 chr3B.!!$F2 2836
1 TraesCS3B01G170400 chr3B 171305144 171306091 947 False 1600 1600 97.158 1891 2837 1 chr3B.!!$F1 946
2 TraesCS3B01G170400 chr1D 33122462 33125314 2852 False 4060 4060 92.517 2 2835 1 chr1D.!!$F1 2833
3 TraesCS3B01G170400 chr1D 33175789 33178644 2855 True 4036 4036 92.348 1 2835 1 chr1D.!!$R3 2834
4 TraesCS3B01G170400 chr1D 33196742 33198410 1668 True 2215 2215 90.920 1189 2835 1 chr1D.!!$R4 1646
5 TraesCS3B01G170400 chr1D 33110603 33111450 847 True 1271 1271 93.875 1995 2835 1 chr1D.!!$R1 840
6 TraesCS3B01G170400 chr1D 33169137 33169983 846 True 1260 1260 93.640 1995 2835 1 chr1D.!!$R2 840
7 TraesCS3B01G170400 chr5B 544184447 544187297 2850 True 3954 3954 91.827 1 2835 1 chr5B.!!$R1 2834
8 TraesCS3B01G170400 chr5B 544194170 544195004 834 True 1249 1249 93.713 2003 2837 1 chr5B.!!$R2 834
9 TraesCS3B01G170400 chr4B 647019498 647021709 2211 True 3417 3417 94.580 1 2208 1 chr4B.!!$R1 2207
10 TraesCS3B01G170400 chr2B 791908651 791910659 2008 False 3271 3271 96.028 1 2014 1 chr2B.!!$F2 2013
11 TraesCS3B01G170400 chr2B 542736942 542738951 2009 False 3254 3254 95.879 1 2012 1 chr2B.!!$F1 2011
12 TraesCS3B01G170400 chr2B 791882159 791884166 2007 True 3243 3243 95.780 1 2014 1 chr2B.!!$R1 2013
13 TraesCS3B01G170400 chr5A 21853806 21855822 2016 False 3267 3267 95.941 1 2014 1 chr5A.!!$F1 2013
14 TraesCS3B01G170400 chr5A 21862121 21864132 2011 False 3240 3240 95.689 1 2018 1 chr5A.!!$F2 2017
15 TraesCS3B01G170400 chr6A 531355162 531357174 2012 True 3262 3262 95.887 1 2018 1 chr6A.!!$R1 2017
16 TraesCS3B01G170400 chr4A 59256877 59258887 2010 True 3245 3245 95.782 1 2014 1 chr4A.!!$R1 2013
17 TraesCS3B01G170400 chr2D 534150 536413 2263 True 3212 3212 92.200 1 2289 1 chr2D.!!$R1 2288
18 TraesCS3B01G170400 chr3D 190429165 190430008 843 True 1190 1190 92.136 1990 2835 1 chr3D.!!$R1 845

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
652 655 1.338674 TGGGGTGCGATACTCAAACAG 60.339 52.381 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 2230 0.31716 TTGTCTGGCCTCTGTGTACG 59.683 55.0 3.32 0.0 0.0 3.67 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
31 32 9.665264 GTAAAAATGGCTAAAGAATCTATTCCG 57.335 33.333 0.00 0.00 37.51 4.30
120 121 5.064441 GCACCTGCACTATTTCAAAGAAT 57.936 39.130 0.00 0.00 41.59 2.40
414 415 9.796120 TGATAAAAAGGTTTTACAACAGTTCTG 57.204 29.630 0.00 0.00 34.15 3.02
436 437 2.612212 AGGAATTGTAAACTATGCGCGG 59.388 45.455 8.83 0.00 0.00 6.46
577 580 6.377429 GGGTCAAGAATTTAAAACCCCTAGAG 59.623 42.308 11.13 0.00 40.42 2.43
652 655 1.338674 TGGGGTGCGATACTCAAACAG 60.339 52.381 0.00 0.00 0.00 3.16
733 737 9.385902 GGAAGTTACAAATTAAAGACGGTAAAC 57.614 33.333 0.00 0.00 0.00 2.01
830 834 1.933181 CAGTGCGAACAGACTGTGAAA 59.067 47.619 9.33 0.00 35.78 2.69
904 908 7.725844 AGAAGATGGGTTTTATTTGAAGACACT 59.274 33.333 0.00 0.00 0.00 3.55
1007 1011 5.291128 GCATCAAATTTGCAGAAATGAGGAG 59.709 40.000 13.54 1.89 39.90 3.69
1018 1022 6.126681 TGCAGAAATGAGGAGAGGATTATTCA 60.127 38.462 0.00 0.00 0.00 2.57
1154 1158 8.995027 AGATGCATATTGGATAACTTTTGGTA 57.005 30.769 0.00 0.00 0.00 3.25
1255 1261 2.996631 ACAAAAATGTGCCAAAGCCAA 58.003 38.095 0.00 0.00 38.69 4.52
1256 1262 2.944349 ACAAAAATGTGCCAAAGCCAAG 59.056 40.909 0.00 0.00 38.69 3.61
1632 1642 6.406370 TGACCCTTTAGACAGTGAATACATG 58.594 40.000 0.00 0.00 0.00 3.21
1736 1746 8.776376 TTAAGGCAAGAAATGGATGAAAAATC 57.224 30.769 0.00 0.00 0.00 2.17
1840 1856 1.656818 GCAGCGGCCTGAATAAAGCA 61.657 55.000 0.00 0.00 41.77 3.91
1883 1899 2.333926 CTATCAATTATTCGGGCGCGA 58.666 47.619 23.01 23.01 0.00 5.87
1895 1911 1.461911 GGGCGCGAAGGACCTATACT 61.462 60.000 12.10 0.00 0.00 2.12
1984 2000 1.379044 GGCAGGGAAGACCACATGG 60.379 63.158 0.00 0.00 43.89 3.66
2066 2152 3.059597 GGCATGAATGTACGCATACACTC 60.060 47.826 0.00 0.00 44.11 3.51
2144 2230 0.320771 TGGCCGAAGAGCAAAGACTC 60.321 55.000 0.00 0.00 36.91 3.36
2160 2246 0.251209 ACTCGTACACAGAGGCCAGA 60.251 55.000 5.01 0.00 39.90 3.86
2173 2259 3.266772 AGAGGCCAGACAATTATCCACAA 59.733 43.478 5.01 0.00 0.00 3.33
2189 2275 1.955778 CACAAAGAGACAATGCCCACA 59.044 47.619 0.00 0.00 0.00 4.17
2245 2331 1.349688 TGAAGTTTGTCGGGGCACTAT 59.650 47.619 0.00 0.00 0.00 2.12
2302 2388 6.127054 ACGCATGCATCCCTACTACATATAAT 60.127 38.462 19.57 0.00 0.00 1.28
2748 2847 2.094286 AGAGTGGCGTCTGAATGAGAAG 60.094 50.000 0.00 0.00 33.59 2.85
2749 2848 1.066573 AGTGGCGTCTGAATGAGAAGG 60.067 52.381 0.00 0.00 31.27 3.46
2777 2876 2.094130 CCGTAGAGAAGTGTTCCCTTCC 60.094 54.545 0.00 0.00 41.45 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.192317 GCTGTCCACGGAATAGATTCTTT 58.808 43.478 2.44 0.00 37.00 2.52
31 32 3.831715 GGACAAGTAAATGCTGTCCAC 57.168 47.619 14.13 0.00 45.94 4.02
414 415 3.303132 CCGCGCATAGTTTACAATTCCTC 60.303 47.826 8.75 0.00 0.00 3.71
552 555 6.250711 TCTAGGGGTTTTAAATTCTTGACCC 58.749 40.000 13.16 13.16 44.73 4.46
652 655 7.759886 GCTTTTGGAGAGTATTTATTGGGTTTC 59.240 37.037 0.00 0.00 0.00 2.78
793 797 7.441890 TCGCACTGTAAATTCTTTAAATCCA 57.558 32.000 0.00 0.00 0.00 3.41
889 893 7.857456 TCCCAGCTATAGTGTCTTCAAATAAA 58.143 34.615 0.84 0.00 0.00 1.40
1007 1011 6.122277 TCATCCTTGTTGGTGAATAATCCTC 58.878 40.000 0.00 0.00 37.07 3.71
1018 1022 7.205515 AGAAGAGATATTCATCCTTGTTGGT 57.794 36.000 0.00 0.00 37.07 3.67
1255 1261 7.066781 TCTCCTTTTGGTATTTCAACCTTTCT 58.933 34.615 0.00 0.00 40.44 2.52
1256 1262 7.284919 TCTCCTTTTGGTATTTCAACCTTTC 57.715 36.000 0.00 0.00 40.44 2.62
1420 1427 4.231890 TCCTAATACCTTCCTTGCCCAAAT 59.768 41.667 0.00 0.00 0.00 2.32
1632 1642 8.531146 TCAAACCTTTTATCCATTTCTTGATCC 58.469 33.333 0.00 0.00 0.00 3.36
1883 1899 1.492176 TCGGGTCGAGTATAGGTCCTT 59.508 52.381 0.00 0.00 0.00 3.36
1895 1911 6.872020 GGAATTTCTATCAATATTCGGGTCGA 59.128 38.462 0.00 0.00 0.00 4.20
2144 2230 0.317160 TTGTCTGGCCTCTGTGTACG 59.683 55.000 3.32 0.00 0.00 3.67
2160 2246 6.350445 GGCATTGTCTCTTTGTGGATAATTGT 60.350 38.462 0.00 0.00 0.00 2.71
2173 2259 2.821969 GTTCATGTGGGCATTGTCTCTT 59.178 45.455 0.00 0.00 31.99 2.85
2245 2331 2.030717 GCGATGGATAAGAGCGAGAGAA 60.031 50.000 0.00 0.00 0.00 2.87
2302 2388 2.632996 CCGGGAGAATGCACCTCTTATA 59.367 50.000 15.11 0.00 0.00 0.98
2737 2836 1.815003 GGCCACAACCTTCTCATTCAG 59.185 52.381 0.00 0.00 0.00 3.02
2748 2847 0.320697 ACTTCTCTACGGCCACAACC 59.679 55.000 2.24 0.00 0.00 3.77
2749 2848 1.270147 ACACTTCTCTACGGCCACAAC 60.270 52.381 2.24 0.00 0.00 3.32
2777 2876 3.190738 TTCCCAGGCAGTTCCACCG 62.191 63.158 0.00 0.00 37.29 4.94


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

AutoCloner maintained by Alex Coulton.