Multiple sequence alignment - TraesCS5A01G383500

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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 TraesCS5A01G383500 chr5A 100.000 2264 0 0 1 2264 581139958 581137695 0.000000e+00 4181
1 TraesCS5A01G383500 chr5B 94.372 2292 90 21 1 2264 567020835 567018555 0.000000e+00 3482
2 TraesCS5A01G383500 chr5D 94.340 2297 83 20 1 2264 460941788 460944070 0.000000e+00 3478
3 TraesCS5A01G383500 chr7D 80.702 342 64 2 3 343 531083939 531084279 4.790000e-67 265
4 TraesCS5A01G383500 chr7B 81.346 327 59 2 3 328 571575714 571576039 4.790000e-67 265
5 TraesCS5A01G383500 chr7A 80.702 342 64 2 3 343 611496398 611496738 4.790000e-67 265


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 TraesCS5A01G383500 chr5A 581137695 581139958 2263 True 4181 4181 100.000 1 2264 1 chr5A.!!$R1 2263
1 TraesCS5A01G383500 chr5B 567018555 567020835 2280 True 3482 3482 94.372 1 2264 1 chr5B.!!$R1 2263
2 TraesCS5A01G383500 chr5D 460941788 460944070 2282 False 3478 3478 94.340 1 2264 1 chr5D.!!$F1 2263

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
858 864 0.105593 TCGATGCTTGAGATCCTGCC 59.894 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 1966 0.03213 TCCTCATGCTTATCGCCGTC 59.968 55.0 0.0 0.0 38.05 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
541 545 3.285215 TAGCCGATCGAGACGCCC 61.285 66.667 18.66 0.00 0.00 6.13
581 585 3.023119 TCTGGAACTGCAAGCAAGAAAA 58.977 40.909 0.00 0.00 37.60 2.29
589 593 6.594284 ACTGCAAGCAAGAAAATTTTCTTC 57.406 33.333 33.29 27.06 45.61 2.87
590 594 6.343703 ACTGCAAGCAAGAAAATTTTCTTCT 58.656 32.000 33.29 28.30 45.61 2.85
591 595 6.478016 ACTGCAAGCAAGAAAATTTTCTTCTC 59.522 34.615 33.29 27.35 45.61 2.87
611 617 4.644234 TCTCAAACTTCATTGACCAAGCAA 59.356 37.500 0.00 0.00 35.55 3.91
614 620 3.375782 ACTTCATTGACCAAGCAAAGC 57.624 42.857 0.00 0.00 0.00 3.51
721 727 1.649815 CTTCCCGTCGATCTCTCCG 59.350 63.158 0.00 0.00 0.00 4.63
726 732 0.860533 CCGTCGATCTCTCCGTAGAC 59.139 60.000 0.00 0.00 0.00 2.59
858 864 0.105593 TCGATGCTTGAGATCCTGCC 59.894 55.000 0.00 0.00 0.00 4.85
869 876 1.064832 AGATCCTGCCAAAGAAGCTCC 60.065 52.381 0.00 0.00 0.00 4.70
877 884 2.299867 GCCAAAGAAGCTCCCATTTCAA 59.700 45.455 0.00 0.00 0.00 2.69
892 902 4.612614 CCATTTCAACACGAGTTTTCATCG 59.387 41.667 0.00 0.00 45.54 3.84
909 920 5.389859 TCATCGGTGAAAATTTCAATGCT 57.610 34.783 10.27 0.00 42.15 3.79
911 922 4.844998 TCGGTGAAAATTTCAATGCTCA 57.155 36.364 10.27 0.00 42.15 4.26
912 923 4.797471 TCGGTGAAAATTTCAATGCTCAG 58.203 39.130 10.27 0.00 42.15 3.35
914 925 4.855388 CGGTGAAAATTTCAATGCTCAGAG 59.145 41.667 10.27 0.00 42.15 3.35
916 927 5.279156 GGTGAAAATTTCAATGCTCAGAGGT 60.279 40.000 10.27 0.00 42.15 3.85
918 929 5.535783 TGAAAATTTCAATGCTCAGAGGTGA 59.464 36.000 5.87 0.00 36.59 4.02
958 993 2.373169 TGGCTCATCTGAACCTTCTGTT 59.627 45.455 1.64 0.00 40.81 3.16
1085 1120 3.537874 GACGAGGACCCCCATCCG 61.538 72.222 0.00 0.00 44.22 4.18
1404 1439 3.798878 CGATGTAACCTGCATGACAGTAG 59.201 47.826 13.67 4.82 45.68 2.57
1461 1504 6.396829 AGGAGAAGAAACAATCCAGTTTTG 57.603 37.500 0.00 0.00 41.48 2.44
1621 1664 2.791927 CTCTGACCGCGATGACGA 59.208 61.111 8.23 0.00 42.66 4.20
1641 1684 4.429212 CCCACACCGATGTCGCGA 62.429 66.667 3.71 3.71 36.72 5.87
1772 1815 8.752005 AGGAAAATTCATATTGATTCCTTCGA 57.248 30.769 5.46 0.00 37.56 3.71
1773 1816 9.359653 AGGAAAATTCATATTGATTCCTTCGAT 57.640 29.630 5.46 0.00 37.56 3.59
1791 1834 6.425114 CCTTCGATTCGATCATGGAAAGTAAT 59.575 38.462 9.96 0.00 35.23 1.89
1793 1836 7.786178 TCGATTCGATCATGGAAAGTAATTT 57.214 32.000 4.29 0.00 0.00 1.82
1799 1842 8.833231 TCGATCATGGAAAGTAATTTAGGATC 57.167 34.615 4.00 4.00 0.00 3.36
1815 1861 9.920946 AATTTAGGATCCACACTGTAATTGTAT 57.079 29.630 15.82 0.00 0.00 2.29
1852 1903 2.202544 GTCTCGAGCCACTCTGCG 60.203 66.667 7.81 0.00 36.02 5.18
1950 2001 0.745845 AGGATGTTGATGTCCAGCGC 60.746 55.000 0.00 0.00 36.96 5.92
1951 2002 1.349627 GATGTTGATGTCCAGCGCG 59.650 57.895 0.00 0.00 0.00 6.86
2036 2087 3.970410 CCAGCCACTGCAGGGGAA 61.970 66.667 39.55 0.00 40.32 3.97
2178 2229 0.320771 CCGTTGAGGACCTTCACTGG 60.321 60.000 0.00 0.00 45.00 4.00
2185 2236 0.818040 GGACCTTCACTGGTGCGTTT 60.818 55.000 0.00 0.00 41.00 3.60
2239 2290 9.647797 TTGAGATCGACTTGTAATTAAGCTTTA 57.352 29.630 3.20 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
541 545 5.942236 TCCAGAAAGAATGAATGGTCTGAAG 59.058 40.000 0.00 0.00 35.57 3.02
581 585 8.010733 TGGTCAATGAAGTTTGAGAAGAAAAT 57.989 30.769 0.00 0.00 36.34 1.82
589 593 4.572985 TGCTTGGTCAATGAAGTTTGAG 57.427 40.909 0.00 0.00 36.34 3.02
590 594 4.998671 TTGCTTGGTCAATGAAGTTTGA 57.001 36.364 0.00 0.00 33.32 2.69
591 595 4.025480 GCTTTGCTTGGTCAATGAAGTTTG 60.025 41.667 0.00 0.00 0.00 2.93
604 610 2.243602 ACATTTGGTGCTTTGCTTGG 57.756 45.000 0.00 0.00 0.00 3.61
611 617 4.605640 AGCAAACATACATTTGGTGCTT 57.394 36.364 2.39 0.00 45.88 3.91
777 783 1.643832 GCGCAGTCGAAATCCATCC 59.356 57.895 0.30 0.00 38.10 3.51
858 864 4.301628 GTGTTGAAATGGGAGCTTCTTTG 58.698 43.478 0.00 0.00 0.00 2.77
869 876 4.612614 CGATGAAAACTCGTGTTGAAATGG 59.387 41.667 3.24 0.00 36.39 3.16
877 884 2.519377 TCACCGATGAAAACTCGTGT 57.481 45.000 0.00 0.00 34.36 4.49
892 902 5.166398 CCTCTGAGCATTGAAATTTTCACC 58.834 41.667 11.30 3.92 39.87 4.02
902 913 3.708403 ATGTTCACCTCTGAGCATTGA 57.292 42.857 0.00 0.00 43.70 2.57
903 914 3.624861 GGTATGTTCACCTCTGAGCATTG 59.375 47.826 5.52 0.00 43.70 2.82
905 916 2.840038 TGGTATGTTCACCTCTGAGCAT 59.160 45.455 0.00 5.53 46.68 3.79
906 917 2.234661 CTGGTATGTTCACCTCTGAGCA 59.765 50.000 0.00 0.00 41.37 4.26
907 918 2.234908 ACTGGTATGTTCACCTCTGAGC 59.765 50.000 0.00 0.00 39.50 4.26
909 920 5.778241 TCTTTACTGGTATGTTCACCTCTGA 59.222 40.000 0.00 0.00 39.50 3.27
911 922 6.497259 TCTTCTTTACTGGTATGTTCACCTCT 59.503 38.462 0.00 0.00 39.50 3.69
912 923 6.698380 TCTTCTTTACTGGTATGTTCACCTC 58.302 40.000 0.00 0.00 39.50 3.85
914 925 6.316390 CCATCTTCTTTACTGGTATGTTCACC 59.684 42.308 0.00 0.00 39.20 4.02
916 927 5.880332 GCCATCTTCTTTACTGGTATGTTCA 59.120 40.000 0.00 0.00 0.00 3.18
918 929 6.067217 AGCCATCTTCTTTACTGGTATGTT 57.933 37.500 0.00 0.00 0.00 2.71
1374 1409 0.172578 CAGGTTACATCGCCGTGAGA 59.827 55.000 0.00 0.00 0.00 3.27
1404 1439 0.391661 TTCTTGCGGTGATCTGAGCC 60.392 55.000 0.00 0.00 0.00 4.70
1461 1504 1.012486 CGCTCAACTTGGACGGTACC 61.012 60.000 0.16 0.16 0.00 3.34
1621 1664 4.735132 CGACATCGGTGTGGGCGT 62.735 66.667 5.76 0.00 39.09 5.68
1641 1684 2.355481 GGCGAGGTCGTCAACGTT 60.355 61.111 0.00 0.00 44.43 3.99
1768 1811 7.786178 AATTACTTTCCATGATCGAATCGAA 57.214 32.000 10.12 0.00 39.99 3.71
1769 1812 7.786178 AAATTACTTTCCATGATCGAATCGA 57.214 32.000 8.12 8.12 41.13 3.59
1770 1813 8.223769 CCTAAATTACTTTCCATGATCGAATCG 58.776 37.037 0.00 0.00 0.00 3.34
1771 1814 9.273016 TCCTAAATTACTTTCCATGATCGAATC 57.727 33.333 0.00 0.00 0.00 2.52
1772 1815 9.799106 ATCCTAAATTACTTTCCATGATCGAAT 57.201 29.630 0.00 0.00 0.00 3.34
1773 1816 9.273016 GATCCTAAATTACTTTCCATGATCGAA 57.727 33.333 0.00 0.00 0.00 3.71
1793 1836 8.426489 GGTAATACAATTACAGTGTGGATCCTA 58.574 37.037 14.23 0.00 0.00 2.94
1799 1842 6.657541 ACCAAGGTAATACAATTACAGTGTGG 59.342 38.462 5.88 12.30 0.00 4.17
1815 1861 1.074775 CTGGCCTGCACCAAGGTAA 59.925 57.895 3.32 0.00 39.86 2.85
1852 1903 0.966920 TCGTCTTCCTCTTCACCACC 59.033 55.000 0.00 0.00 0.00 4.61
1915 1966 0.032130 TCCTCATGCTTATCGCCGTC 59.968 55.000 0.00 0.00 38.05 4.79
2239 2290 6.018469 TCTGAACCCAAAATCTCCATGAAAT 58.982 36.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.