Multiple sequence alignment - TraesCS1A01G237500

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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 TraesCS1A01G237500 chr1A 100.000 2938 0 0 1 2938 423290439 423287502 0 5426
1 TraesCS1A01G237500 chr1A 97.924 2938 60 1 1 2938 423164927 423161991 0 5086
2 TraesCS1A01G237500 chr1A 96.947 2948 75 11 1 2938 423228545 423225603 0 4931
3 TraesCS1A01G237500 chr1A 93.238 2943 191 8 1 2938 424272050 424274989 0 4325
4 TraesCS1A01G237500 chr1A 92.551 2940 196 9 2 2922 424079681 424082616 0 4194
5 TraesCS1A01G237500 chr1A 91.697 2782 188 19 172 2923 423551901 423549133 0 3818
6 TraesCS1A01G237500 chr1A 93.020 2550 168 9 376 2923 423594764 423592223 0 3714
7 TraesCS1A01G237500 chr1A 92.953 2228 148 6 700 2923 423515655 423513433 0 3236
8 TraesCS1A01G237500 chr1A 92.594 2228 154 7 700 2923 423462692 423460472 0 3190
9 TraesCS1A01G237500 chr1A 93.327 2053 131 6 866 2915 424392568 424394617 0 3027
10 TraesCS1A01G237500 chr1A 91.260 881 68 7 1 874 424390717 424391595 0 1192
11 TraesCS1A01G237500 chr1A 90.899 868 67 4 2 857 423144467 423143600 0 1155
12 TraesCS1A01G237500 chr1A 90.542 867 71 5 2 857 423085783 423084917 0 1136
13 TraesCS1A01G237500 chr1A 90.789 836 65 4 34 857 423270124 423269289 0 1107
14 TraesCS1A01G237500 chr1A 89.158 867 72 6 2 857 423208267 423207412 0 1061
15 TraesCS1A01G237500 chr1B 89.229 2089 169 26 1 2040 435811514 435813595 0 2560


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 TraesCS1A01G237500 chr1A 423287502 423290439 2937 True 5426.0 5426 100.0000 1 2938 1 chr1A.!!$R7 2937
1 TraesCS1A01G237500 chr1A 423161991 423164927 2936 True 5086.0 5086 97.9240 1 2938 1 chr1A.!!$R3 2937
2 TraesCS1A01G237500 chr1A 423225603 423228545 2942 True 4931.0 4931 96.9470 1 2938 1 chr1A.!!$R5 2937
3 TraesCS1A01G237500 chr1A 424272050 424274989 2939 False 4325.0 4325 93.2380 1 2938 1 chr1A.!!$F2 2937
4 TraesCS1A01G237500 chr1A 424079681 424082616 2935 False 4194.0 4194 92.5510 2 2922 1 chr1A.!!$F1 2920
5 TraesCS1A01G237500 chr1A 423549133 423551901 2768 True 3818.0 3818 91.6970 172 2923 1 chr1A.!!$R10 2751
6 TraesCS1A01G237500 chr1A 423592223 423594764 2541 True 3714.0 3714 93.0200 376 2923 1 chr1A.!!$R11 2547
7 TraesCS1A01G237500 chr1A 423513433 423515655 2222 True 3236.0 3236 92.9530 700 2923 1 chr1A.!!$R9 2223
8 TraesCS1A01G237500 chr1A 423460472 423462692 2220 True 3190.0 3190 92.5940 700 2923 1 chr1A.!!$R8 2223
9 TraesCS1A01G237500 chr1A 424390717 424394617 3900 False 2109.5 3027 92.2935 1 2915 2 chr1A.!!$F3 2914
10 TraesCS1A01G237500 chr1A 423143600 423144467 867 True 1155.0 1155 90.8990 2 857 1 chr1A.!!$R2 855
11 TraesCS1A01G237500 chr1A 423084917 423085783 866 True 1136.0 1136 90.5420 2 857 1 chr1A.!!$R1 855
12 TraesCS1A01G237500 chr1A 423269289 423270124 835 True 1107.0 1107 90.7890 34 857 1 chr1A.!!$R6 823
13 TraesCS1A01G237500 chr1A 423207412 423208267 855 True 1061.0 1061 89.1580 2 857 1 chr1A.!!$R4 855
14 TraesCS1A01G237500 chr1B 435811514 435813595 2081 False 2560.0 2560 89.2290 1 2040 1 chr1B.!!$F1 2039

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
86 87 0.107831 CCTGTTTCAGGTTGGGACGA 59.892 55.0 7.55 0.0 45.82 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 3340 7.718753 CCTAGCTCTTGGTATCAAAGATGATTT 59.281 37.037 0.0 0.0 43.89 2.17 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
86 87 0.107831 CCTGTTTCAGGTTGGGACGA 59.892 55.000 7.55 0.00 45.82 4.20
233 237 3.785887 TCATGGGTAGAATAAAGCTGGGT 59.214 43.478 0.00 0.00 0.00 4.51
258 262 2.234896 ATGGTGGCAATTGGTCATGA 57.765 45.000 7.72 0.00 30.93 3.07
414 444 2.235898 GCCCCAAATGAAACCTGCATAA 59.764 45.455 0.00 0.00 0.00 1.90
766 810 7.169140 GGTTATTTTTAGGAGCCAATAAATGCG 59.831 37.037 0.00 0.00 0.00 4.73
937 1976 6.402442 GCAGGAATGAATAAAATGGCAAACAC 60.402 38.462 0.00 0.00 0.00 3.32
1182 2222 6.986817 TCTATTTACCAGAGCTTATCAACTGC 59.013 38.462 0.00 0.00 0.00 4.40
1392 2456 7.406104 AGGCAAGTATCTTTTTCCTCATACTT 58.594 34.615 0.00 0.00 40.93 2.24
1729 2795 4.389374 GAACAACAAGAGGTTCTGATGGA 58.611 43.478 0.00 0.00 40.12 3.41
1975 3043 9.578439 GAGCATTATGAATTGTTTTTCTAGCTT 57.422 29.630 0.00 0.00 0.00 3.74
2269 3340 8.317891 TCGACTTGAATAATTCTGTAGCAAAA 57.682 30.769 0.00 0.00 0.00 2.44
2367 3438 9.275398 AGATTCATTGTTATTGCACACAAAATT 57.725 25.926 8.87 0.07 39.77 1.82
2594 3665 6.702329 AGTGTTCTTTGAACTACCTGATAGG 58.298 40.000 11.06 0.00 42.49 2.57
2595 3666 5.875359 GTGTTCTTTGAACTACCTGATAGGG 59.125 44.000 11.06 0.00 40.58 3.53
2596 3667 5.546499 TGTTCTTTGAACTACCTGATAGGGT 59.454 40.000 11.06 0.00 40.58 4.34
2621 3692 4.082625 TGAATACTGCCTCAGTTGCATTTG 60.083 41.667 4.70 0.00 42.59 2.32
2746 3817 5.063204 CAGGTGTCTTCCAGTTATTTGTCA 58.937 41.667 0.00 0.00 0.00 3.58
2828 3900 9.079833 AGATCATCATATTTTTCAAAACTTGCG 57.920 29.630 0.00 0.00 0.00 4.85
2883 3955 0.035317 GACACTCTCACATGCACCCA 59.965 55.000 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 3.377253 AGTGATGATCTTGGCATGGTT 57.623 42.857 0.00 0.00 0.00 3.67
218 222 7.936847 CACCATTACATACCCAGCTTTATTCTA 59.063 37.037 0.00 0.00 0.00 2.10
233 237 4.604156 TGACCAATTGCCACCATTACATA 58.396 39.130 0.00 0.00 0.00 2.29
755 799 9.064804 CATATACACAATTAGCGCATTTATTGG 57.935 33.333 11.47 9.63 33.41 3.16
937 1976 2.103094 TGGCCGATTCTTGGAGTATCAG 59.897 50.000 0.00 0.00 36.25 2.90
2269 3340 7.718753 CCTAGCTCTTGGTATCAAAGATGATTT 59.281 37.037 0.00 0.00 43.89 2.17
2367 3438 0.833949 TGGACCATTGGTATGCGCTA 59.166 50.000 8.70 0.00 35.25 4.26
2594 3665 2.744202 CAACTGAGGCAGTATTCACACC 59.256 50.000 0.00 0.00 44.62 4.16
2595 3666 2.160417 GCAACTGAGGCAGTATTCACAC 59.840 50.000 0.00 0.00 44.62 3.82
2596 3667 2.224499 TGCAACTGAGGCAGTATTCACA 60.224 45.455 0.00 0.00 44.62 3.58
2746 3817 6.991531 ACACAAGAAAATGTAATGGCAACAAT 59.008 30.769 0.00 0.00 40.74 2.71
2828 3900 2.076863 CAATGGAGAAAGTGACCGGAC 58.923 52.381 9.46 1.07 0.00 4.79
2883 3955 2.949447 ACAAGAACTGGAAGGTGCAAT 58.051 42.857 0.00 0.00 39.30 3.56


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

AutoCloner maintained by Alex Coulton.