Multiple sequence alignment - TraesCS4D01G146500

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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 TraesCS4D01G146500 chr4D 100.000 2827 0 0 1 2827 135035953 135033127 0 5221
1 TraesCS4D01G146500 chr7B 97.566 2835 59 5 1 2826 698140160 698142993 0 4844
2 TraesCS4D01G146500 chrUn 97.533 2837 59 5 1 2827 223706934 223704099 0 4841
3 TraesCS4D01G146500 chr1B 97.531 2835 61 5 1 2827 683734142 683731309 0 4839
4 TraesCS4D01G146500 chr6D 97.492 2831 65 5 1 2827 430481761 430484589 0 4830
5 TraesCS4D01G146500 chr2A 97.489 2827 59 6 1 2817 605912877 605910053 0 4817
6 TraesCS4D01G146500 chr1A 97.349 2829 72 3 1 2827 278500835 278503662 0 4806
7 TraesCS4D01G146500 chr5B 97.317 2833 69 4 1 2827 713082218 713079387 0 4804
8 TraesCS4D01G146500 chr2D 97.243 2829 69 4 1 2827 634995176 634997997 0 4783


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 TraesCS4D01G146500 chr4D 135033127 135035953 2826 True 5221 5221 100.000 1 2827 1 chr4D.!!$R1 2826
1 TraesCS4D01G146500 chr7B 698140160 698142993 2833 False 4844 4844 97.566 1 2826 1 chr7B.!!$F1 2825
2 TraesCS4D01G146500 chrUn 223704099 223706934 2835 True 4841 4841 97.533 1 2827 1 chrUn.!!$R1 2826
3 TraesCS4D01G146500 chr1B 683731309 683734142 2833 True 4839 4839 97.531 1 2827 1 chr1B.!!$R1 2826
4 TraesCS4D01G146500 chr6D 430481761 430484589 2828 False 4830 4830 97.492 1 2827 1 chr6D.!!$F1 2826
5 TraesCS4D01G146500 chr2A 605910053 605912877 2824 True 4817 4817 97.489 1 2817 1 chr2A.!!$R1 2816
6 TraesCS4D01G146500 chr1A 278500835 278503662 2827 False 4806 4806 97.349 1 2827 1 chr1A.!!$F1 2826
7 TraesCS4D01G146500 chr5B 713079387 713082218 2831 True 4804 4804 97.317 1 2827 1 chr5B.!!$R1 2826
8 TraesCS4D01G146500 chr2D 634995176 634997997 2821 False 4783 4783 97.243 1 2827 1 chr2D.!!$F1 2826

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
430 431 2.094957 AGACAGAAGTAAGACGAGCTGC 60.095 50.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2246 0.250467 CCCCCATTCTATGCTGACCG 60.25 60.0 0.0 0.0 0.0 4.79 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
54 55 3.604582 AGAGGCTCATACAGAAAGCAAC 58.395 45.455 18.26 0.00 37.78 4.17
98 99 4.876107 AGACCACAGCCTATTATTCAAACG 59.124 41.667 0.00 0.00 0.00 3.60
120 121 4.253685 GACAAAGGATCCGTCTTTCATCA 58.746 43.478 5.98 0.00 32.72 3.07
267 268 6.409704 CATCTCACTCAGACCCTTTTGAATA 58.590 40.000 0.00 0.00 32.26 1.75
282 283 9.184523 CCCTTTTGAATATAGTGGATAACAACA 57.815 33.333 0.00 0.00 0.00 3.33
430 431 2.094957 AGACAGAAGTAAGACGAGCTGC 60.095 50.000 0.00 0.00 0.00 5.25
522 523 8.255905 GTCATTGATCAAGAAGGAAATCCAAAT 58.744 33.333 14.54 0.00 38.89 2.32
617 618 8.652290 AGCTCCTGAGGTATTAAAAATACTAGG 58.348 37.037 0.00 12.51 37.39 3.02
849 850 8.857694 TCTAAAACCATAGGGAAAGTAACAAG 57.142 34.615 0.00 0.00 38.05 3.16
1045 1046 7.723616 TCTTCTTTTTCATTACTTCCATGGTCA 59.276 33.333 12.58 0.00 0.00 4.02
1090 1091 4.027132 CCGTACTATTGAAATGGTTCGTCG 60.027 45.833 14.19 7.79 38.38 5.12
1134 1135 5.059833 GCCTCTTCTTCCAATGGTACTATG 58.940 45.833 0.00 0.00 0.00 2.23
1148 1149 9.877178 CAATGGTACTATGATTCCTATTCCTAC 57.123 37.037 0.00 0.00 0.00 3.18
1204 1205 4.422073 AGGAAATTCATACGCTCCATGA 57.578 40.909 0.00 0.00 0.00 3.07
1312 1313 3.564644 TGCTTTATTTCGTTTCGTTCCCA 59.435 39.130 0.00 0.00 0.00 4.37
1419 1420 4.153835 CGTACTCTCTTCTCTTTACCACGT 59.846 45.833 0.00 0.00 0.00 4.49
1430 1431 4.084287 TCTTTACCACGTGATAGGTCAGT 58.916 43.478 19.30 6.07 39.31 3.41
1572 1573 2.668632 CCTGTAGCTTTCCCCGCA 59.331 61.111 0.00 0.00 0.00 5.69
1632 1638 1.211190 GAAAGCGGGCTTGAAGCTG 59.789 57.895 17.59 11.03 41.99 4.24
1909 1915 6.331307 ACCTTGATAGGAAGATGGCTTATTCT 59.669 38.462 7.55 0.00 45.05 2.40
2454 2465 6.557253 ACATATTATATTAGCCGCCTATCCCA 59.443 38.462 0.00 0.00 0.00 4.37
2483 2494 5.339200 GGACTGGGATGGAATAGAAAGAACA 60.339 44.000 0.00 0.00 0.00 3.18
2507 2518 0.964358 GCAGCAAGCAAGGGATGAGT 60.964 55.000 0.00 0.00 44.79 3.41
2518 2529 0.961019 GGGATGAGTGCTTTGTTGCA 59.039 50.000 0.00 0.00 41.05 4.08
2625 2637 3.813606 TTCCTGTCCGTCCCGACCA 62.814 63.158 0.00 0.00 31.35 4.02
2689 2701 2.435693 GGCCCGAGCTGTATGAGGT 61.436 63.158 0.00 0.00 39.73 3.85
2747 2760 0.034574 ACCCTGCAATAATGGTGCGA 60.035 50.000 0.00 0.00 45.27 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.679944 CGATATTGGGCTATGGGCTGG 60.680 57.143 1.86 0.00 41.46 4.85
98 99 4.253685 TGATGAAAGACGGATCCTTTGTC 58.746 43.478 10.75 10.07 34.33 3.18
120 121 4.655762 TGTTCGATCGAGAAGATTGGAT 57.344 40.909 18.54 0.00 40.26 3.41
267 268 4.164221 CCCCACTCTGTTGTTATCCACTAT 59.836 45.833 0.00 0.00 0.00 2.12
282 283 2.398588 TCAATTCGATAGCCCCACTCT 58.601 47.619 0.00 0.00 0.00 3.24
430 431 8.705134 TGAGTTCTTTACATGTACGTACAATTG 58.295 33.333 30.46 25.68 39.99 2.32
522 523 1.673920 GCACCAAAAACTCGAGTTCCA 59.326 47.619 29.82 0.00 37.25 3.53
826 827 8.442374 AGACTTGTTACTTTCCCTATGGTTTTA 58.558 33.333 0.00 0.00 0.00 1.52
849 850 4.922791 GCACGTGCCAAGAAAGAC 57.077 55.556 30.12 0.00 34.31 3.01
924 925 2.248280 AGTGTTCACAACGCATACCA 57.752 45.000 5.74 0.00 44.15 3.25
1090 1091 2.093447 CACCAGTGGGAACATCTCTACC 60.093 54.545 15.21 0.00 46.14 3.18
1134 1135 7.403671 GGAATAAAGGGGTAGGAATAGGAATC 58.596 42.308 0.00 0.00 0.00 2.52
1181 1182 4.576053 TCATGGAGCGTATGAATTTCCTTG 59.424 41.667 0.00 0.00 35.53 3.61
1204 1205 3.356290 ACACTCCACTTTTTGCTCTGTT 58.644 40.909 0.00 0.00 0.00 3.16
1419 1420 2.164422 CTCACGCTTCACTGACCTATCA 59.836 50.000 0.00 0.00 0.00 2.15
1632 1638 2.098831 GGCTCGTTGGTAAGGCGAC 61.099 63.158 0.00 0.00 0.00 5.19
1694 1700 8.350722 CCTCCATGTGAAATAGAAAGATTCATG 58.649 37.037 0.00 0.00 35.70 3.07
1909 1915 6.416415 TCCTTACCCTTATGCACGAATTTTA 58.584 36.000 0.00 0.00 0.00 1.52
1972 1978 1.352156 GCACTAGGTGTTTCCGAGCG 61.352 60.000 0.00 0.00 41.68 5.03
1986 1992 3.506455 GTCTCTCAGTGTGGTTAGCACTA 59.494 47.826 15.65 0.00 44.43 2.74
2240 2246 0.250467 CCCCCATTCTATGCTGACCG 60.250 60.000 0.00 0.00 0.00 4.79
2411 2417 0.454620 GTGCAGTAGTCGTCGTCTGG 60.455 60.000 2.08 0.00 0.00 3.86
2454 2465 4.570926 TCTATTCCATCCCAGTCCATTCT 58.429 43.478 0.00 0.00 0.00 2.40
2483 2494 2.263741 CCCTTGCTTGCTGCTTCGT 61.264 57.895 0.00 0.00 43.37 3.85
2507 2518 2.412525 CGCAGGTGCAACAAAGCA 59.587 55.556 3.64 0.00 43.35 3.91
2518 2529 1.200020 GCAAGAAAACTATGCGCAGGT 59.800 47.619 18.32 14.71 0.00 4.00
2562 2574 0.897621 AAGCAAGCTTATTGCCCCAC 59.102 50.000 5.34 0.00 45.98 4.61
2625 2637 2.753029 GGAGACCCAACTGCTGCT 59.247 61.111 0.00 0.00 0.00 4.24
2689 2701 1.464608 CGTACGTGGGACGAGTTTCTA 59.535 52.381 7.22 0.00 46.05 2.10
2775 2788 4.884668 AGGGAAATCGTTGAGTGAACTA 57.115 40.909 0.00 0.00 31.70 2.24


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

AutoCloner maintained by Alex Coulton.