Multiple sequence alignment - TraesCS5D01G397100

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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 TraesCS5D01G397100 chr5D 100.000 2926 0 0 1 2926 464092836 464089911 0 5404
1 TraesCS5D01G397100 chr5B 91.973 2342 86 34 1 2289 571188554 571186262 0 3190
2 TraesCS5D01G397100 chr5B 95.294 595 23 5 2335 2926 571186261 571185669 0 939
3 TraesCS5D01G397100 chr5A 91.024 2206 112 37 1 2193 584519557 584517425 0 2898
4 TraesCS5D01G397100 chr5A 92.138 725 31 6 2212 2926 584517282 584516574 0 1000


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 TraesCS5D01G397100 chr5D 464089911 464092836 2925 True 5404.0 5404 100.0000 1 2926 1 chr5D.!!$R1 2925
1 TraesCS5D01G397100 chr5B 571185669 571188554 2885 True 2064.5 3190 93.6335 1 2926 2 chr5B.!!$R1 2925
2 TraesCS5D01G397100 chr5A 584516574 584519557 2983 True 1949.0 2898 91.5810 1 2926 2 chr5A.!!$R1 2925

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
166 170 0.249073 CCGATCTTGGCGAGGTACAG 60.249 60.0 0.97 0.0 0.0 2.74 F
820 854 0.606401 CACACGATCCACTGGGCTTT 60.606 55.0 0.00 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1717 0.601841 CACGAACAGGGTTACGGCTT 60.602 55.0 0.0 0.0 0.0 4.35 R
2556 2778 0.035152 TCGGTCTACAAGGCTCGGTA 60.035 55.0 0.0 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
25 26 3.988976 TTCCTCTCCCAAAGATGACAG 57.011 47.619 0.00 0.00 32.19 3.51
47 51 5.528690 CAGAATGGATCGAAAATCCTGCTAA 59.471 40.000 5.20 0.00 38.95 3.09
166 170 0.249073 CCGATCTTGGCGAGGTACAG 60.249 60.000 0.97 0.00 0.00 2.74
502 515 3.700538 AGAACTGCAGGCCAATAATTGA 58.299 40.909 19.93 0.00 0.00 2.57
532 545 6.039941 AGAGAATTCTACAGTAATCGGACAGG 59.960 42.308 8.25 0.00 0.00 4.00
820 854 0.606401 CACACGATCCACTGGGCTTT 60.606 55.000 0.00 0.00 0.00 3.51
824 858 1.019673 CGATCCACTGGGCTTTCATG 58.980 55.000 0.00 0.00 0.00 3.07
842 879 2.611800 TGGATCCCACCTGCTGCT 60.612 61.111 9.90 0.00 0.00 4.24
1203 1280 1.585521 GGTCCGCATCTACGTCGTG 60.586 63.158 8.47 0.00 0.00 4.35
1601 1678 1.369839 GCCTTACTCTTTCAGGCCGC 61.370 60.000 0.00 0.00 46.55 6.53
1659 1736 0.601841 AAGCCGTAACCCTGTTCGTG 60.602 55.000 0.00 0.00 0.00 4.35
1660 1737 2.030958 GCCGTAACCCTGTTCGTGG 61.031 63.158 0.00 0.00 0.00 4.94
1661 1738 1.667151 CCGTAACCCTGTTCGTGGA 59.333 57.895 0.00 0.00 0.00 4.02
1674 1751 0.809385 TCGTGGATTCGTGTCTCCTC 59.191 55.000 0.00 0.00 32.47 3.71
1675 1752 0.811915 CGTGGATTCGTGTCTCCTCT 59.188 55.000 0.00 0.00 32.47 3.69
1676 1753 1.468224 CGTGGATTCGTGTCTCCTCTG 60.468 57.143 0.00 0.00 32.47 3.35
1677 1754 1.546476 GTGGATTCGTGTCTCCTCTGT 59.454 52.381 0.00 0.00 32.47 3.41
1932 2013 0.602106 CGCCGATGCCTGATTCATCT 60.602 55.000 0.00 0.00 38.47 2.90
1933 2014 1.337167 CGCCGATGCCTGATTCATCTA 60.337 52.381 0.00 0.00 38.47 1.98
1937 2018 4.742417 CCGATGCCTGATTCATCTACTAG 58.258 47.826 0.00 0.00 38.47 2.57
1938 2019 4.172505 CGATGCCTGATTCATCTACTAGC 58.827 47.826 0.00 0.00 38.47 3.42
1942 2023 4.837298 TGCCTGATTCATCTACTAGCAGAT 59.163 41.667 0.00 0.00 35.60 2.90
1963 2047 1.165270 CTACCAAGAACCCTTTGCCG 58.835 55.000 0.00 0.00 0.00 5.69
2000 2084 1.727880 GGCAGCGTCGTTTTGTACATA 59.272 47.619 0.00 0.00 0.00 2.29
2001 2085 2.158058 GGCAGCGTCGTTTTGTACATAA 59.842 45.455 0.00 0.00 0.00 1.90
2002 2086 3.364167 GGCAGCGTCGTTTTGTACATAAA 60.364 43.478 0.00 0.00 0.00 1.40
2003 2087 3.596562 GCAGCGTCGTTTTGTACATAAAC 59.403 43.478 16.89 16.89 33.28 2.01
2046 2131 2.728007 AGCCCCAGAATTCAGTTAAGC 58.272 47.619 8.44 2.89 0.00 3.09
2118 2205 2.577606 TTTGATTGACATCACCGGGT 57.422 45.000 6.32 0.00 39.28 5.28
2163 2250 7.117667 GCTCAAATTACCCAAAACACAATAAGG 59.882 37.037 0.00 0.00 0.00 2.69
2169 2256 3.554752 CCCAAAACACAATAAGGCACCTG 60.555 47.826 0.00 0.00 0.00 4.00
2171 2258 4.202202 CCAAAACACAATAAGGCACCTGAA 60.202 41.667 0.00 0.00 0.00 3.02
2182 2269 9.252962 CAATAAGGCACCTGAAATTATTCAATC 57.747 33.333 0.00 0.00 44.64 2.67
2185 2272 7.814264 AGGCACCTGAAATTATTCAATCTAG 57.186 36.000 0.00 0.00 44.64 2.43
2186 2273 7.577303 AGGCACCTGAAATTATTCAATCTAGA 58.423 34.615 0.00 0.00 44.64 2.43
2202 2289 3.945346 TCTAGAAGCAAAATACGGCCAA 58.055 40.909 2.24 0.00 0.00 4.52
2217 2429 2.422127 CGGCCAAATTGAAGTAACCGAT 59.578 45.455 2.24 0.00 41.86 4.18
2267 2486 2.203337 GCCTCACAACCCACAGCA 60.203 61.111 0.00 0.00 0.00 4.41
2277 2496 2.260869 CCCACAGCACCTTTCACGG 61.261 63.158 0.00 0.00 0.00 4.94
2328 2547 1.885388 CAAATGATCCGCCGCCGTA 60.885 57.895 0.00 0.00 0.00 4.02
2331 2550 2.581208 AATGATCCGCCGCCGTACAA 62.581 55.000 0.00 0.00 0.00 2.41
2338 2557 1.213094 CGCCGCCGTACAATCCTAAG 61.213 60.000 0.00 0.00 0.00 2.18
2426 2647 4.494484 GCATCAACCCCAACAAATCTAAC 58.506 43.478 0.00 0.00 0.00 2.34
2493 2715 5.778241 TCTTTTCGCATGGGTAGATATCCTA 59.222 40.000 9.86 0.00 0.00 2.94
2515 2737 5.821516 AAACACATCACAAACCTAACGAA 57.178 34.783 0.00 0.00 0.00 3.85
2553 2775 2.093973 ACTCATGGAGCAGTCTTAACCG 60.094 50.000 0.00 0.00 32.04 4.44
2556 2778 3.197766 TCATGGAGCAGTCTTAACCGAAT 59.802 43.478 0.00 0.00 0.00 3.34
2577 2800 0.179134 CCGAGCCTTGTAGACCGAAG 60.179 60.000 0.00 0.00 0.00 3.79
2695 2918 3.011517 ATGTTCCCCAGCTCCGCT 61.012 61.111 0.00 0.00 40.77 5.52
2746 2969 0.473755 TGCCTTTGTTCTCTGGAGCA 59.526 50.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.537688 TCTGTCATCTTTGGGAGAGGAATT 59.462 41.667 0.00 0.00 45.83 2.17
5 6 3.520696 TCTGTCATCTTTGGGAGAGGAA 58.479 45.455 0.00 0.00 45.83 3.36
7 8 3.988976 TTCTGTCATCTTTGGGAGAGG 57.011 47.619 0.00 0.00 37.93 3.69
9 10 3.845992 TCCATTCTGTCATCTTTGGGAGA 59.154 43.478 0.00 0.00 39.13 3.71
12 13 3.562973 CGATCCATTCTGTCATCTTTGGG 59.437 47.826 0.00 0.00 0.00 4.12
25 26 6.377327 TTTAGCAGGATTTTCGATCCATTC 57.623 37.500 6.33 0.00 40.61 2.67
47 51 1.079490 TCCACTCCTCCTCAGTCCATT 59.921 52.381 0.00 0.00 0.00 3.16
502 515 7.721842 TCCGATTACTGTAGAATTCTCTCTGAT 59.278 37.037 12.24 0.78 32.70 2.90
788 822 2.903547 CGTGTGAGGCCCGGTTTTG 61.904 63.158 0.00 0.00 0.00 2.44
1416 1493 1.222113 GGGGAAGCCGAAGAGGAAG 59.778 63.158 0.00 0.00 45.00 3.46
1587 1664 2.543067 GATGGGCGGCCTGAAAGAGT 62.543 60.000 29.87 4.61 34.07 3.24
1640 1717 0.601841 CACGAACAGGGTTACGGCTT 60.602 55.000 0.00 0.00 0.00 4.35
1651 1728 1.986378 GAGACACGAATCCACGAACAG 59.014 52.381 0.00 0.00 37.03 3.16
1659 1736 2.096248 AGACAGAGGAGACACGAATCC 58.904 52.381 0.00 0.00 35.71 3.01
1660 1737 2.490115 ACAGACAGAGGAGACACGAATC 59.510 50.000 0.00 0.00 0.00 2.52
1661 1738 2.490115 GACAGACAGAGGAGACACGAAT 59.510 50.000 0.00 0.00 0.00 3.34
1932 2013 5.363005 GGGTTCTTGGTAGAATCTGCTAGTA 59.637 44.000 0.00 0.00 42.14 1.82
1933 2014 4.162509 GGGTTCTTGGTAGAATCTGCTAGT 59.837 45.833 0.00 0.00 42.14 2.57
1937 2018 3.636153 AGGGTTCTTGGTAGAATCTGC 57.364 47.619 0.00 0.00 42.14 4.26
1938 2019 4.156739 GCAAAGGGTTCTTGGTAGAATCTG 59.843 45.833 0.00 0.00 42.14 2.90
1942 2023 2.812613 CGGCAAAGGGTTCTTGGTAGAA 60.813 50.000 0.00 0.00 38.06 2.10
2000 2084 6.710692 GCTAAATAGCAATGCTGTTTGTTT 57.289 33.333 30.98 18.96 46.32 2.83
2105 2192 1.594833 GCTACACCCGGTGATGTCA 59.405 57.895 24.80 2.93 36.96 3.58
2118 2205 4.202346 TGAGCTGTGCATATAATGGCTACA 60.202 41.667 0.00 0.00 0.00 2.74
2163 2250 7.859875 GCTTCTAGATTGAATAATTTCAGGTGC 59.140 37.037 0.00 0.00 42.60 5.01
2182 2269 4.695217 TTTGGCCGTATTTTGCTTCTAG 57.305 40.909 0.00 0.00 0.00 2.43
2185 2272 4.241681 TCAATTTGGCCGTATTTTGCTTC 58.758 39.130 0.00 0.00 0.00 3.86
2186 2273 4.264460 TCAATTTGGCCGTATTTTGCTT 57.736 36.364 0.00 0.00 0.00 3.91
2197 2284 4.638865 ACTATCGGTTACTTCAATTTGGCC 59.361 41.667 0.00 0.00 0.00 5.36
2217 2429 4.323257 GCAGGCCTGAGGTACTTTTTACTA 60.323 45.833 37.21 0.00 41.55 1.82
2229 2441 4.479993 CTTCCGGCAGGCCTGAGG 62.480 72.222 37.21 33.46 37.47 3.86
2267 2486 1.227734 CGTGAACCCCGTGAAAGGT 60.228 57.895 0.00 0.00 38.27 3.50
2277 2496 3.183574 GCTTTGTTTTTATGCGTGAACCC 59.816 43.478 0.00 0.00 0.00 4.11
2352 2573 9.624373 ATTCTTTTGTACTATCAGAATCTGCAT 57.376 29.630 5.18 3.23 0.00 3.96
2426 2647 0.324943 ATGAGGTTGGTCGAACAGGG 59.675 55.000 2.09 0.00 36.12 4.45
2493 2715 5.124138 TGTTCGTTAGGTTTGTGATGTGTTT 59.876 36.000 0.00 0.00 0.00 2.83
2515 2737 2.705658 TGAGTGGGAAATGAGTGAGTGT 59.294 45.455 0.00 0.00 0.00 3.55
2544 2766 2.100418 AGGCTCGGTATTCGGTTAAGAC 59.900 50.000 0.00 0.00 39.77 3.01
2553 2775 2.543238 CGGTCTACAAGGCTCGGTATTC 60.543 54.545 0.00 0.00 0.00 1.75
2556 2778 0.035152 TCGGTCTACAAGGCTCGGTA 60.035 55.000 0.00 0.00 0.00 4.02
2577 2800 2.355209 CCTTCTAAGAAGTGAGGTGCCC 60.355 54.545 0.00 0.00 0.00 5.36
2836 3059 1.079819 GAAGCGTCCTACAGCTGCA 60.080 57.895 15.27 0.00 43.78 4.41


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

AutoCloner maintained by Alex Coulton.