Multiple sequence alignment - TraesCS3A01G004000

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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 TraesCS3A01G004000 chr3A 100.000 3340 0 0 1 3340 2135501 2138840 0 6168
1 TraesCS3A01G004000 chr3A 98.683 3340 43 1 1 3340 4125021 4128359 0 5923
2 TraesCS3A01G004000 chr3A 98.563 3340 47 1 1 3340 3072441 3075779 0 5901
3 TraesCS3A01G004000 chr3A 98.533 3340 48 1 1 3340 2602872 2606210 0 5895
4 TraesCS3A01G004000 chr3A 98.323 3340 55 1 1 3340 5139520 5142858 0 5856
5 TraesCS3A01G004000 chr3A 98.054 3340 62 3 1 3340 2434132 2437468 0 5805
6 TraesCS3A01G004000 chr3A 97.934 3340 68 1 1 3340 5486096 5489434 0 5784
7 TraesCS3A01G004000 chr3A 97.904 3340 68 2 1 3340 2913746 2917083 0 5779
8 TraesCS3A01G004000 chr3A 97.904 3339 69 1 1 3339 3433583 3436920 0 5777
9 TraesCS3A01G004000 chr3A 97.814 3340 71 2 1 3340 4490261 4493598 0 5762


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 TraesCS3A01G004000 chr3A 2135501 2138840 3339 False 6168 6168 100.000 1 3340 1 chr3A.!!$F1 3339
1 TraesCS3A01G004000 chr3A 4125021 4128359 3338 False 5923 5923 98.683 1 3340 1 chr3A.!!$F7 3339
2 TraesCS3A01G004000 chr3A 3072441 3075779 3338 False 5901 5901 98.563 1 3340 1 chr3A.!!$F5 3339
3 TraesCS3A01G004000 chr3A 2602872 2606210 3338 False 5895 5895 98.533 1 3340 1 chr3A.!!$F3 3339
4 TraesCS3A01G004000 chr3A 5139520 5142858 3338 False 5856 5856 98.323 1 3340 1 chr3A.!!$F9 3339
5 TraesCS3A01G004000 chr3A 2434132 2437468 3336 False 5805 5805 98.054 1 3340 1 chr3A.!!$F2 3339
6 TraesCS3A01G004000 chr3A 5486096 5489434 3338 False 5784 5784 97.934 1 3340 1 chr3A.!!$F10 3339
7 TraesCS3A01G004000 chr3A 2913746 2917083 3337 False 5779 5779 97.904 1 3340 1 chr3A.!!$F4 3339
8 TraesCS3A01G004000 chr3A 3433583 3436920 3337 False 5777 5777 97.904 1 3339 1 chr3A.!!$F6 3338
9 TraesCS3A01G004000 chr3A 4490261 4493598 3337 False 5762 5762 97.814 1 3340 1 chr3A.!!$F8 3339

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
46 47 2.101415 GCCATGAGGTATTTTTGAGGGC 59.899 50.0 0.0 0.0 37.19 5.19 F
1050 1052 0.819582 CATGCACCAATGTCCTTCCC 59.180 55.0 0.0 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1750 1752 1.268999 GCACAACATGAAACTTCGGCA 60.269 47.619 0.0 0.0 0.0 5.69 R
2902 2904 1.522668 TTTCATTCACGCCAGACCAG 58.477 50.000 0.0 0.0 0.0 4.00 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
46 47 2.101415 GCCATGAGGTATTTTTGAGGGC 59.899 50.000 0.00 0.00 37.19 5.19
104 105 8.880991 TGACCAGATAGAGTAGTTTACTTCTT 57.119 34.615 0.00 0.00 39.59 2.52
219 220 2.281484 TCAAGGCGTCTGTTGGGC 60.281 61.111 0.00 0.00 0.00 5.36
509 510 8.825745 ACAAGCAATTTAATGAAACGAATTGTT 58.174 25.926 8.79 1.58 44.59 2.83
710 712 6.350445 CCATCTGAAGAAGTTAAAACATGGGG 60.350 42.308 0.00 0.00 0.00 4.96
1050 1052 0.819582 CATGCACCAATGTCCTTCCC 59.180 55.000 0.00 0.00 0.00 3.97
1139 1141 3.154710 CCCTGGAACTCCAAAAACCTAC 58.845 50.000 0.00 0.00 46.97 3.18
1642 1644 6.697395 TCTCTCAGAAAAATCACCGACATTA 58.303 36.000 0.00 0.00 0.00 1.90
1644 1646 7.492669 TCTCTCAGAAAAATCACCGACATTATC 59.507 37.037 0.00 0.00 0.00 1.75
1841 1843 9.892444 TCCTAACCTTGTCTATTTATCCATAGA 57.108 33.333 0.00 0.00 34.01 1.98
2747 2749 8.655901 TGACACCCTATATAGTGCATGAATAAA 58.344 33.333 8.92 0.00 37.51 1.40
2882 2884 6.151648 GCATCTCTAGACATCTCTATCTTGCT 59.848 42.308 0.00 0.00 0.00 3.91
2902 2904 4.277672 TGCTAGTCGTATGAGGTGGTTATC 59.722 45.833 0.00 0.00 0.00 1.75
2921 2923 1.071542 TCTGGTCTGGCGTGAATGAAA 59.928 47.619 0.00 0.00 0.00 2.69
2922 2924 2.086869 CTGGTCTGGCGTGAATGAAAT 58.913 47.619 0.00 0.00 0.00 2.17
3106 3108 4.201812 CGACATTTCAATTGTATCAGCGGT 60.202 41.667 5.13 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 5.440610 AGGTGGGAAACATTTAGATAGCAG 58.559 41.667 0.00 0.00 0.00 4.24
104 105 1.112315 ACATGGCAAGGCGGTGAAAA 61.112 50.000 0.00 0.00 0.00 2.29
219 220 8.472413 ACCATAAATTTCTTCATTGGATCACAG 58.528 33.333 0.00 0.00 0.00 3.66
1050 1052 2.256117 AAGTCCAAGGAACAAGGTCG 57.744 50.000 0.00 0.00 0.00 4.79
1283 1285 6.963234 TTGGCTACAAAAGGGAACCAATGAC 61.963 44.000 0.00 0.00 42.87 3.06
1642 1644 2.582636 GGCCTCCATGGTATAATGGGAT 59.417 50.000 12.58 0.00 46.17 3.85
1644 1646 1.995542 AGGCCTCCATGGTATAATGGG 59.004 52.381 12.58 5.25 46.17 4.00
1750 1752 1.268999 GCACAACATGAAACTTCGGCA 60.269 47.619 0.00 0.00 0.00 5.69
1841 1843 5.556915 TGTTTTCGGTAGATGAAACCTCAT 58.443 37.500 0.00 0.00 45.34 2.90
2747 2749 7.559897 AGGTAATTCAACGGATGGTATTCAAAT 59.440 33.333 0.00 0.00 0.00 2.32
2882 2884 4.825634 CCAGATAACCACCTCATACGACTA 59.174 45.833 0.00 0.00 0.00 2.59
2902 2904 1.522668 TTTCATTCACGCCAGACCAG 58.477 50.000 0.00 0.00 0.00 4.00
2921 2923 8.260818 AGCAACATGATACTACTACAACTTCAT 58.739 33.333 0.00 0.00 0.00 2.57
2922 2924 7.611770 AGCAACATGATACTACTACAACTTCA 58.388 34.615 0.00 0.00 0.00 3.02
3106 3108 2.616842 GTTTTCGCCTTTCTCCACTGAA 59.383 45.455 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.