Multiple sequence alignment - TraesCS5D01G142400

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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 TraesCS5D01G142400 chr5D 100.000 2942 0 0 818 3759 228509090 228512031 0 5433
1 TraesCS5D01G142400 chr5D 96.960 2928 81 8 818 3739 212865101 212868026 0 4907
2 TraesCS5D01G142400 chr5D 100.000 451 0 0 1 451 228508273 228508723 0 833
3 TraesCS5D01G142400 chr5D 98.013 453 7 2 1 451 167753580 167753128 0 785
4 TraesCS5D01G142400 chr5D 98.013 453 7 2 1 451 212864594 212865046 0 785
5 TraesCS5D01G142400 chr4D 97.217 2946 75 7 818 3759 52454552 52457494 0 4979
6 TraesCS5D01G142400 chr4D 98.451 452 6 1 1 451 52454047 52454498 0 795
7 TraesCS5D01G142400 chr4D 98.230 452 7 1 1 451 348411114 348410663 0 789
8 TraesCS5D01G142400 chr4D 97.357 454 9 3 1 451 381424393 381424846 0 769
9 TraesCS5D01G142400 chr1D 96.877 2946 83 8 818 3759 134443605 134446545 0 4922
10 TraesCS5D01G142400 chr1D 91.017 2950 235 26 820 3759 49643783 49640854 0 3952
11 TraesCS5D01G142400 chr1D 98.234 453 6 2 1 451 134443095 134443547 0 791
12 TraesCS5D01G142400 chr6D 91.307 2945 231 19 820 3759 126403120 126406044 0 3997
13 TraesCS5D01G142400 chr5B 90.278 2952 252 24 820 3759 192377174 192374246 0 3829
14 TraesCS5D01G142400 chr5B 89.938 2922 267 21 846 3759 575796600 575799502 0 3742
15 TraesCS5D01G142400 chr1B 89.837 2952 272 20 820 3759 341106729 341109664 0 3764
16 TraesCS5D01G142400 chr2A 89.614 2956 263 30 820 3759 121062453 121065380 0 3718
17 TraesCS5D01G142400 chr7D 98.664 449 5 1 1 448 369866757 369867205 0 795
18 TraesCS5D01G142400 chr7D 97.788 452 9 1 1 451 251598447 251597996 0 778
19 TraesCS5D01G142400 chr3D 98.230 452 7 1 1 451 588806240 588805789 0 789


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 TraesCS5D01G142400 chr5D 228508273 228512031 3758 False 3133.0 5433 100.0000 1 3759 2 chr5D.!!$F2 3758
1 TraesCS5D01G142400 chr5D 212864594 212868026 3432 False 2846.0 4907 97.4865 1 3739 2 chr5D.!!$F1 3738
2 TraesCS5D01G142400 chr4D 52454047 52457494 3447 False 2887.0 4979 97.8340 1 3759 2 chr4D.!!$F2 3758
3 TraesCS5D01G142400 chr1D 49640854 49643783 2929 True 3952.0 3952 91.0170 820 3759 1 chr1D.!!$R1 2939
4 TraesCS5D01G142400 chr1D 134443095 134446545 3450 False 2856.5 4922 97.5555 1 3759 2 chr1D.!!$F1 3758
5 TraesCS5D01G142400 chr6D 126403120 126406044 2924 False 3997.0 3997 91.3070 820 3759 1 chr6D.!!$F1 2939
6 TraesCS5D01G142400 chr5B 192374246 192377174 2928 True 3829.0 3829 90.2780 820 3759 1 chr5B.!!$R1 2939
7 TraesCS5D01G142400 chr5B 575796600 575799502 2902 False 3742.0 3742 89.9380 846 3759 1 chr5B.!!$F1 2913
8 TraesCS5D01G142400 chr1B 341106729 341109664 2935 False 3764.0 3764 89.8370 820 3759 1 chr1B.!!$F1 2939
9 TraesCS5D01G142400 chr2A 121062453 121065380 2927 False 3718.0 3718 89.6140 820 3759 1 chr2A.!!$F1 2939

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
844 848 3.445096 AGTTTGCAATTGTCTGATAGGGC 59.555 43.478 7.4 0.0 0.00 5.19 F
1400 1405 0.033208 TTCCCCATCCTGGTGAATGC 60.033 55.000 0.0 0.0 35.17 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2756 2781 0.541063 TGTGTGTCGGGAAGCTCCTA 60.541 55.0 0.0 0.0 36.57 2.94 R
3041 3066 0.331954 TCGAACCTCCTCCTAGCAGT 59.668 55.0 0.0 0.0 0.00 4.40 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
157 159 6.112734 AGTACATTCGCCTTTGAATATGTGA 58.887 36.000 0.00 0.0 36.46 3.58
341 345 6.477053 TCATTTTCACCCTGACATTTTTGA 57.523 33.333 0.00 0.0 0.00 2.69
844 848 3.445096 AGTTTGCAATTGTCTGATAGGGC 59.555 43.478 7.40 0.0 0.00 5.19
1014 1019 0.400381 TGGGGATGCAGGCTCTGATA 60.400 55.000 6.40 0.0 32.44 2.15
1177 1182 0.457851 CCGCGGAGAGATCAAAGTCT 59.542 55.000 24.07 0.0 0.00 3.24
1400 1405 0.033208 TTCCCCATCCTGGTGAATGC 60.033 55.000 0.00 0.0 35.17 3.56
1684 1690 3.801114 ACTCTTTTTGCAAACACTCCC 57.199 42.857 12.39 0.0 0.00 4.30
1849 1859 1.286501 TTGACGGATCATGCGTTAGC 58.713 50.000 5.39 0.0 46.52 3.09
1850 1860 0.459899 TGACGGATCATGCGTTAGCT 59.540 50.000 5.39 0.0 46.52 3.32
1851 1861 1.134818 TGACGGATCATGCGTTAGCTT 60.135 47.619 5.39 0.0 46.52 3.74
2621 2646 0.674581 CGGAATGACCAGCTTGCTCA 60.675 55.000 0.00 0.0 38.90 4.26
2644 2669 0.923358 AGTTGGTTGAGGGTTGGACA 59.077 50.000 0.00 0.0 0.00 4.02
2756 2781 1.198637 GGTACGACTACAACAGCTCGT 59.801 52.381 0.00 0.0 41.08 4.18
2783 2808 2.455674 TCCCGACACACAAGATGAAG 57.544 50.000 0.00 0.0 0.00 3.02
2893 2918 0.690762 GTGCAGGTGGTAAGAAGGGA 59.309 55.000 0.00 0.0 0.00 4.20
2953 2978 1.181741 AACAGACAGCTGCGAGAGGA 61.182 55.000 15.27 0.0 46.26 3.71
3010 3035 4.432741 GAGGTTGGGCAGGGCTCC 62.433 72.222 0.00 0.0 0.00 4.70
3118 3145 2.136026 ACAGACTGACCCCCTTTTTCT 58.864 47.619 10.08 0.0 0.00 2.52
3122 3149 4.038042 CAGACTGACCCCCTTTTTCTTTTC 59.962 45.833 0.00 0.0 0.00 2.29
3123 3150 4.079154 AGACTGACCCCCTTTTTCTTTTCT 60.079 41.667 0.00 0.0 0.00 2.52
3198 3227 3.879295 GCCTCTTTCTTATATGTGCAGCA 59.121 43.478 0.00 0.0 0.00 4.41
3206 3235 1.431488 ATATGTGCAGCAAGGCGACG 61.431 55.000 0.00 0.0 36.28 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
341 345 6.626623 GCCATTCTGCTGATGTAAGAACAAAT 60.627 38.462 0.00 0.00 39.58 2.32
844 848 5.476599 TGTTTCACCATCATGAAGGTTTAGG 59.523 40.000 19.80 9.12 39.68 2.69
1014 1019 3.340814 AGATTCTTGCACCGAACATCT 57.659 42.857 0.08 0.00 0.00 2.90
1400 1405 8.923270 AGGAAAAATGAAGGAGTAGAGATAGAG 58.077 37.037 0.00 0.00 0.00 2.43
2621 2646 1.133482 CCAACCCTCAACCAACTTCCT 60.133 52.381 0.00 0.00 0.00 3.36
2644 2669 2.158696 GCTGTCAGAGCCATTAAGGGAT 60.159 50.000 11.08 2.46 42.54 3.85
2707 2732 1.172180 AACCAGTTGGCCGATGTGTG 61.172 55.000 0.00 0.00 39.32 3.82
2756 2781 0.541063 TGTGTGTCGGGAAGCTCCTA 60.541 55.000 0.00 0.00 36.57 2.94
2783 2808 2.351641 CGAGAGCAGCATCTCCATCTAC 60.352 54.545 13.26 0.00 42.34 2.59
2893 2918 1.633945 GGGACATCTGGTACACCCTTT 59.366 52.381 0.00 0.00 35.03 3.11
3010 3035 2.104170 GTCCTAGGTCTCTTGACAGGG 58.896 57.143 9.08 0.00 44.61 4.45
3041 3066 0.331954 TCGAACCTCCTCCTAGCAGT 59.668 55.000 0.00 0.00 0.00 4.40
3198 3227 2.678934 TCCACTAGCCGTCGCCTT 60.679 61.111 0.00 0.00 34.57 4.35
3206 3235 0.815734 TAACTGCTCGTCCACTAGCC 59.184 55.000 1.11 0.00 37.97 3.93


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

AutoCloner maintained by Alex Coulton.