Multiple sequence alignment - TraesCS4B01G230700

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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 TraesCS4B01G230700 chr4B 100.000 2350 0 0 701 3050 481801117 481803466 0.000000e+00 4340
1 TraesCS4B01G230700 chr4B 100.000 338 0 0 1 338 481800417 481800754 2.580000e-175 625
2 TraesCS4B01G230700 chr4A 97.235 2351 55 7 701 3050 73541877 73544218 0.000000e+00 3973
3 TraesCS4B01G230700 chr4A 92.128 343 22 5 1 338 73541369 73541711 2.130000e-131 479
4 TraesCS4B01G230700 chr4D 97.239 2354 47 9 701 3050 392218846 392221185 0.000000e+00 3971
5 TraesCS4B01G230700 chr4D 94.562 331 15 3 11 338 392218349 392218679 2.710000e-140 508


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 TraesCS4B01G230700 chr4B 481800417 481803466 3049 False 2482.5 4340 100.0000 1 3050 2 chr4B.!!$F1 3049
1 TraesCS4B01G230700 chr4A 73541369 73544218 2849 False 2226.0 3973 94.6815 1 3050 2 chr4A.!!$F1 3049
2 TraesCS4B01G230700 chr4D 392218349 392221185 2836 False 2239.5 3971 95.9005 11 3050 2 chr4D.!!$F1 3039

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
840 846 0.830648 CCCTGCTTACGGATCCTTGA 59.169 55.0 10.75 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2086 1.008538 CCAAACTGCAGCGTTGGAC 60.009 57.895 32.12 0.0 0.0 4.02 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
43 45 6.417930 CGTCGATTGTAGATGCTCTAATTTCA 59.582 38.462 0.00 0.00 29.58 2.69
184 189 2.648143 TACCGCTTACACGTGGGGG 61.648 63.158 21.57 20.60 40.11 5.40
214 219 1.605202 GGCGTGGCATTTGTGTCAAAT 60.605 47.619 0.00 2.42 0.00 2.32
330 336 2.203126 CAAGGCGGCTCCATCTCC 60.203 66.667 13.70 0.00 37.29 3.71
840 846 0.830648 CCCTGCTTACGGATCCTTGA 59.169 55.000 10.75 0.00 0.00 3.02
873 879 8.897872 TTCTACTTGTTTTTCGAAATAGGTCT 57.102 30.769 12.12 0.00 0.00 3.85
883 889 4.286707 TCGAAATAGGTCTCAGGGATTGA 58.713 43.478 0.00 0.00 0.00 2.57
1305 1312 1.064296 GCAGCATCAGCATCAGCAC 59.936 57.895 0.00 0.00 45.49 4.40
1578 1585 2.887152 GGTTGAAGAGCATTCTGTGGTT 59.113 45.455 3.70 0.00 39.00 3.67
2079 2086 2.332063 ATGTTGATCGCCTTGTAGGG 57.668 50.000 0.00 0.00 35.37 3.53
2102 2109 1.447317 AACGCTGCAGTTTGGTCTGG 61.447 55.000 16.64 0.00 36.12 3.86
2157 2164 4.487019 AGACGTCTTTAGAAGTAGCTTGC 58.513 43.478 13.58 0.00 36.91 4.01
2519 2526 2.852449 TCCCCATGGATCTAAGCAAGTT 59.148 45.455 15.22 0.00 35.03 2.66
2560 2567 3.755112 TTGTTCCGATCTGGTGTTACA 57.245 42.857 3.97 0.00 39.52 2.41
2573 2580 1.265635 GTGTTACAATGCGCTGAACCA 59.734 47.619 9.73 0.00 0.00 3.67
2584 2591 5.440234 TGCGCTGAACCAAGTATTTTTAA 57.560 34.783 9.73 0.00 0.00 1.52
2616 2623 6.269307 GCCTCTACCTTAATACCTTGGACATA 59.731 42.308 0.00 0.00 0.00 2.29
2653 2660 5.067674 GCTCACCAATGGTTTGCATATCTTA 59.932 40.000 17.72 0.00 31.02 2.10
2728 2735 1.468914 GTGTTTGATCGCCCTTTCTCC 59.531 52.381 0.00 0.00 0.00 3.71
2839 2848 8.169977 AGAAAGAAAAACATCATCAGCAAGTA 57.830 30.769 0.00 0.00 0.00 2.24
2845 2854 4.134379 ACATCATCAGCAAGTAGACAGG 57.866 45.455 0.00 0.00 0.00 4.00
2935 2944 0.610232 GATCCTGCAAAGGTGTGGCT 60.610 55.000 0.00 0.00 0.00 4.75
3006 3015 2.765699 TGGGCCCAAAATAATGAAGCTC 59.234 45.455 26.33 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.289109 ATCGACGCTTCAAACCACCG 61.289 55.000 0.00 0.00 0.00 4.94
7 8 1.263217 ACAATCGACGCTTCAAACCAC 59.737 47.619 0.00 0.00 0.00 4.16
8 9 1.588674 ACAATCGACGCTTCAAACCA 58.411 45.000 0.00 0.00 0.00 3.67
16 17 2.126914 GAGCATCTACAATCGACGCT 57.873 50.000 0.00 0.00 0.00 5.07
115 119 1.128692 CCGAGCATCTCCAAACGAAAC 59.871 52.381 0.00 0.00 0.00 2.78
121 125 0.036732 AACTGCCGAGCATCTCCAAA 59.963 50.000 0.00 0.00 38.13 3.28
193 198 2.126888 GACACAAATGCCACGCCG 60.127 61.111 0.00 0.00 0.00 6.46
214 219 7.388437 AGAAAATGGCATATTTCTTTCTGCAA 58.612 30.769 18.48 0.00 41.79 4.08
862 868 4.372656 GTCAATCCCTGAGACCTATTTCG 58.627 47.826 0.00 0.00 33.60 3.46
873 879 1.639722 TTCCAGACGTCAATCCCTGA 58.360 50.000 19.50 0.16 0.00 3.86
883 889 1.167851 CACCATTGCATTCCAGACGT 58.832 50.000 0.00 0.00 0.00 4.34
1018 1025 1.027357 CCCCAATTCCGAATGCTCAG 58.973 55.000 0.00 0.00 0.00 3.35
1099 1106 2.983592 CTTTGTGTCCCGGTGGCC 60.984 66.667 0.00 0.00 0.00 5.36
1128 1135 1.234615 GCTGCAAGAAGGTGCCGTTA 61.235 55.000 0.00 0.00 44.26 3.18
1305 1312 4.584518 TGGTGGTGCTGGTGCTGG 62.585 66.667 0.00 0.00 40.48 4.85
1464 1471 1.820906 ACGCGCATCTGGCATCATT 60.821 52.632 5.73 0.00 45.17 2.57
2079 2086 1.008538 CCAAACTGCAGCGTTGGAC 60.009 57.895 32.12 0.00 0.00 4.02
2102 2109 5.112686 CAAGAGCAGGTACAGAGAATAACC 58.887 45.833 0.00 0.00 0.00 2.85
2499 2506 3.303351 AACTTGCTTAGATCCATGGGG 57.697 47.619 13.02 0.00 0.00 4.96
2500 2507 6.736794 GCATTTAACTTGCTTAGATCCATGGG 60.737 42.308 13.02 0.00 37.14 4.00
2519 2526 8.579850 AACAATGAGAAACTATCAGGCATTTA 57.420 30.769 0.00 0.00 29.67 1.40
2560 2567 4.519540 AAAATACTTGGTTCAGCGCATT 57.480 36.364 11.47 0.00 0.00 3.56
2573 2580 8.520351 GGTAGAGGCACACAATTAAAAATACTT 58.480 33.333 0.00 0.00 0.00 2.24
2584 2591 5.428783 AGGTATTAAGGTAGAGGCACACAAT 59.571 40.000 0.00 0.00 0.00 2.71
2625 2632 1.336240 GCAAACCATTGGTGAGCAGTC 60.336 52.381 21.43 1.78 36.65 3.51
2830 2839 1.694150 AGTTGCCTGTCTACTTGCTGA 59.306 47.619 0.00 0.00 0.00 4.26
2868 2877 2.034687 CTTGGGGGCACTCAGGTG 59.965 66.667 0.00 0.00 45.53 4.00
2935 2944 3.935371 TTTTTCACAAGGAGGCCCA 57.065 47.368 0.00 0.00 33.88 5.36
2969 2978 1.035139 CCCATGGCACCTATGAAAGC 58.965 55.000 6.09 0.00 0.00 3.51
3006 3015 8.340618 TCTTTCAGAAAGGAAAATGTATGGAG 57.659 34.615 20.70 0.00 39.01 3.86


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

AutoCloner maintained by Alex Coulton.