Multiple sequence alignment - TraesCS2D01G565800

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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 TraesCS2D01G565800 chr2D 100.000 3797 0 0 1 3797 635287946 635284150 0 7012
1 TraesCS2D01G565800 chr2D 97.895 3801 72 6 1 3797 635313967 635310171 0 6569
2 TraesCS2D01G565800 chr2B 96.182 3798 130 9 7 3795 779425760 779421969 0 6196
3 TraesCS2D01G565800 chr2B 96.156 3798 130 10 7 3795 779393606 779389816 0 6191
4 TraesCS2D01G565800 chr2B 96.103 3798 131 10 7 3795 779412857 779409068 0 6178
5 TraesCS2D01G565800 chr2B 96.103 3798 131 10 7 3795 779419306 779415517 0 6178
6 TraesCS2D01G565800 chr2B 96.051 3798 133 10 7 3795 779432215 779428426 0 6167
7 TraesCS2D01G565800 chr2B 95.841 3799 137 15 7 3795 779490133 779486346 0 6120
8 TraesCS2D01G565800 chr2B 95.718 3807 144 15 1 3795 779483690 779479891 0 6109
9 TraesCS2D01G565800 chrUn 95.978 3804 136 11 1 3795 280844157 280847952 0 6161


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 TraesCS2D01G565800 chr2D 635284150 635287946 3796 True 7012.00 7012 100.00000 1 3797 1 chr2D.!!$R1 3796
1 TraesCS2D01G565800 chr2D 635310171 635313967 3796 True 6569.00 6569 97.89500 1 3797 1 chr2D.!!$R2 3796
2 TraesCS2D01G565800 chr2B 779389816 779393606 3790 True 6191.00 6191 96.15600 7 3795 1 chr2B.!!$R1 3788
3 TraesCS2D01G565800 chr2B 779409068 779432215 23147 True 6179.75 6196 96.10975 7 3795 4 chr2B.!!$R2 3788
4 TraesCS2D01G565800 chr2B 779479891 779490133 10242 True 6114.50 6120 95.77950 1 3795 2 chr2B.!!$R3 3794
5 TraesCS2D01G565800 chrUn 280844157 280847952 3795 False 6161.00 6161 95.97800 1 3795 1 chrUn.!!$F1 3794

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
72 73 1.768275 TGCTCCACTTCTCCTGTTCAA 59.232 47.619 0.0 0.0 0.00 2.69 F
1002 13915 1.016627 CCCCATACACAAGCATGTCG 58.983 55.000 0.0 0.0 37.82 4.35 F
2015 14930 0.036732 GGGATGACACTTGCTCACCA 59.963 55.000 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1017 13930 1.203523 TCCAGTGTTTGTGTGTTTGCC 59.796 47.619 0.00 0.0 0.00 4.52 R
2377 21746 3.987220 GCCACATATTTGTCGTGCTTTTT 59.013 39.130 0.00 0.0 32.34 1.94 R
3044 28862 6.868339 CGATGGATGTAGTGAACTATGCATTA 59.132 38.462 3.54 0.0 32.23 1.90 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
66 67 2.499289 CTGTATGTGCTCCACTTCTCCT 59.501 50.000 0.00 0.00 35.11 3.69
72 73 1.768275 TGCTCCACTTCTCCTGTTCAA 59.232 47.619 0.00 0.00 0.00 2.69
146 6602 4.494484 GAACCAGACAAGTTTGCAAAACT 58.506 39.130 14.67 10.65 0.00 2.66
165 6621 2.159128 ACTGCATCGAGACAGGATTGAG 60.159 50.000 18.55 1.11 38.25 3.02
482 6940 2.678190 CGGGGGCAAAACAAAAACTGAA 60.678 45.455 0.00 0.00 0.00 3.02
658 13568 9.565090 TTGGAAATCAGACTTATCCTTATCATG 57.435 33.333 0.00 0.00 0.00 3.07
725 13635 6.957631 TGGAGTAGTAATTGTCATTGGTGAT 58.042 36.000 0.00 0.00 36.60 3.06
740 13650 3.355378 TGGTGATGATGCGAAAGGAAAT 58.645 40.909 0.00 0.00 32.68 2.17
846 13756 8.598202 TCCTACCTATTTTGTATCAGTACACA 57.402 34.615 0.00 0.00 40.40 3.72
949 13862 7.789202 TTTCATCCCTCAATCCATAAAACAA 57.211 32.000 0.00 0.00 0.00 2.83
963 13876 5.887035 CCATAAAACAAATTGGCCCATGAAT 59.113 36.000 0.00 0.00 0.00 2.57
993 13906 6.328934 CCAGTATATATATGCCCCCATACACA 59.671 42.308 5.44 0.00 36.79 3.72
1002 13915 1.016627 CCCCATACACAAGCATGTCG 58.983 55.000 0.00 0.00 37.82 4.35
1017 13930 1.790755 TGTCGTCCAAAGTTCATCGG 58.209 50.000 0.00 0.00 0.00 4.18
1376 14289 7.439157 TCAACATTCAACCAAAGTATCTCAG 57.561 36.000 0.00 0.00 0.00 3.35
1560 14473 4.848357 ACTTTCCAGGTGATGTTATCCAG 58.152 43.478 0.00 0.00 0.00 3.86
1590 14503 3.431486 GCTACAAGTCAGGCAAGAGCTAT 60.431 47.826 0.00 0.00 41.70 2.97
1629 14542 1.667724 GTCATTGGATCTGGCAACTCG 59.332 52.381 0.00 0.00 37.61 4.18
2015 14930 0.036732 GGGATGACACTTGCTCACCA 59.963 55.000 0.00 0.00 0.00 4.17
2021 14936 1.728971 GACACTTGCTCACCATCTTCG 59.271 52.381 0.00 0.00 0.00 3.79
2524 21893 4.142093 GGTGAGAGCATGTTAAATGGCAAT 60.142 41.667 0.00 0.00 0.00 3.56
3043 28861 7.630082 AGGTAGTAATCACATCAGCCTAAAAA 58.370 34.615 0.00 0.00 0.00 1.94
3044 28862 8.275040 AGGTAGTAATCACATCAGCCTAAAAAT 58.725 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.646522 ATTTGCCTAACAGAATAATCCACTAAT 57.353 29.630 0.00 0.00 0.00 1.73
66 67 5.055812 GGAACTTCCATGCAAAATTGAACA 58.944 37.500 2.62 0.00 36.28 3.18
93 94 9.154847 CTGACTGACACAGATTAATCACAATTA 57.845 33.333 17.56 0.00 37.54 1.40
146 6602 2.102578 TCTCAATCCTGTCTCGATGCA 58.897 47.619 0.00 0.00 0.00 3.96
413 6871 0.107897 TGGTGTCAACACAACGAGCT 60.108 50.000 14.72 0.00 44.07 4.09
482 6940 3.243771 CCTCTGGTTCAGTTGTAAGACGT 60.244 47.826 0.00 0.00 32.61 4.34
559 7017 6.232581 TGTGGATGACAAAAGGAAACAAAT 57.767 33.333 0.00 0.00 0.00 2.32
560 7018 5.667539 TGTGGATGACAAAAGGAAACAAA 57.332 34.783 0.00 0.00 0.00 2.83
626 13536 7.177878 AGGATAAGTCTGATTTCCAAACACAT 58.822 34.615 0.00 0.00 0.00 3.21
658 13568 6.268825 TCCTCTTTGTATGCGATATAGGAC 57.731 41.667 0.00 0.00 0.00 3.85
702 13612 7.047891 TCATCACCAATGACAATTACTACTCC 58.952 38.462 0.00 0.00 39.52 3.85
725 13635 6.507958 TCATGTTTATTTCCTTTCGCATCA 57.492 33.333 0.00 0.00 0.00 3.07
846 13756 1.021968 GAGCCGTTGTTGGTTGAAGT 58.978 50.000 0.00 0.00 0.00 3.01
949 13862 3.899360 CTGGTATCATTCATGGGCCAATT 59.101 43.478 11.89 0.00 0.00 2.32
963 13876 6.698670 TGGGGGCATATATATACTGGTATCA 58.301 40.000 0.00 0.00 0.00 2.15
993 13906 2.571212 TGAACTTTGGACGACATGCTT 58.429 42.857 0.00 0.00 0.00 3.91
1002 13915 1.243902 TTGCCCGATGAACTTTGGAC 58.756 50.000 0.00 0.00 0.00 4.02
1017 13930 1.203523 TCCAGTGTTTGTGTGTTTGCC 59.796 47.619 0.00 0.00 0.00 4.52
1376 14289 2.265739 TGGATGACTCCACGCTGC 59.734 61.111 0.00 0.00 46.95 5.25
1560 14473 2.933056 GCCTGACTTGTAGCTTGAGGAC 60.933 54.545 0.00 0.00 0.00 3.85
1590 14503 4.661222 TGACCAATACATTCTTGCCAGAA 58.339 39.130 2.25 2.25 43.45 3.02
1629 14542 3.321968 GGTCATAAGCAATTTCCATCCCC 59.678 47.826 0.00 0.00 0.00 4.81
1674 14587 2.470257 CGGGCTTCGTATAACAATCGAC 59.530 50.000 0.00 0.00 33.38 4.20
1979 14894 5.126384 GTCATCCCCAAACGAATTAATTCCA 59.874 40.000 20.01 0.00 33.28 3.53
2015 14930 9.482627 GTTTATCCACTAGATTCAATCGAAGAT 57.517 33.333 9.15 4.09 37.66 2.40
2377 21746 3.987220 GCCACATATTTGTCGTGCTTTTT 59.013 39.130 0.00 0.00 32.34 1.94
3043 28861 7.547019 CGATGGATGTAGTGAACTATGCATTAT 59.453 37.037 3.54 0.00 32.23 1.28
3044 28862 6.868339 CGATGGATGTAGTGAACTATGCATTA 59.132 38.462 3.54 0.00 32.23 1.90


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

AutoCloner maintained by Alex Coulton.