Multiple sequence alignment - TraesCS3A01G513400

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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 TraesCS3A01G513400 chr3A 100.000 2213 0 0 1 2213 732640178 732637966 0.000000e+00 4087
1 TraesCS3A01G513400 chr3D 96.460 2147 58 6 1 2130 603427890 603430035 0.000000e+00 3528
2 TraesCS3A01G513400 chr3D 85.599 1729 194 23 1 1691 587379789 587378078 0.000000e+00 1762
3 TraesCS3A01G513400 chr3D 75.219 1142 242 34 161 1277 586002865 586003990 9.120000e-139 503
4 TraesCS3A01G513400 chr3D 95.789 95 3 1 2120 2213 603430064 603430158 3.810000e-33 152
5 TraesCS3A01G513400 chr3B 85.286 1733 202 31 1 1691 784432599 784430878 0.000000e+00 1738
6 TraesCS3A01G513400 chr6B 77.201 443 91 10 831 1270 664822281 664821846 1.310000e-62 250
7 TraesCS3A01G513400 chr2A 86.170 94 12 1 2120 2213 391541232 391541140 1.400000e-17 100


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 TraesCS3A01G513400 chr3A 732637966 732640178 2212 True 4087 4087 100.0000 1 2213 1 chr3A.!!$R1 2212
1 TraesCS3A01G513400 chr3D 603427890 603430158 2268 False 1840 3528 96.1245 1 2213 2 chr3D.!!$F2 2212
2 TraesCS3A01G513400 chr3D 587378078 587379789 1711 True 1762 1762 85.5990 1 1691 1 chr3D.!!$R1 1690
3 TraesCS3A01G513400 chr3D 586002865 586003990 1125 False 503 503 75.2190 161 1277 1 chr3D.!!$F1 1116
4 TraesCS3A01G513400 chr3B 784430878 784432599 1721 True 1738 1738 85.2860 1 1691 1 chr3B.!!$R1 1690

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
84 85 1.001974 TCACTGGTGATAGCTTTGCGT 59.998 47.619 0.0 0.0 34.14 5.24 F
91 92 2.484264 GTGATAGCTTTGCGTGGTTTCT 59.516 45.455 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1075 1117 2.016318 TGGAGTGACAAGCTTGTTGTG 58.984 47.619 31.58 7.21 42.43 3.33 R
1974 2021 3.117474 TGGTTGGGTGGACAAATAGTTCA 60.117 43.478 0.00 0.00 31.67 3.18 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
84 85 1.001974 TCACTGGTGATAGCTTTGCGT 59.998 47.619 0.00 0.00 34.14 5.24
91 92 2.484264 GTGATAGCTTTGCGTGGTTTCT 59.516 45.455 0.00 0.00 0.00 2.52
388 409 9.941325 TCAATGCAATTTATGGTTTTCTACATT 57.059 25.926 0.00 0.00 31.22 2.71
747 786 7.913674 ATATCTTCAGAGGAACAGAAACAAC 57.086 36.000 0.00 0.00 0.00 3.32
868 910 3.814268 CGGCGAATTGGTGGCTGG 61.814 66.667 0.00 0.00 0.00 4.85
931 973 8.997323 CAAGTTCACTCTTCTCTCACATTAAAT 58.003 33.333 0.00 0.00 0.00 1.40
1019 1061 2.621556 ATGGGTAGTGGGCATTTTGT 57.378 45.000 0.00 0.00 0.00 2.83
1075 1117 5.416952 AGAAACATCCAGATTGTTGACATCC 59.583 40.000 0.00 0.00 0.00 3.51
1134 1176 7.514721 ACCTTCTTGGAACTAGTGATAAAACA 58.485 34.615 0.00 0.00 39.71 2.83
1284 1326 9.744468 GTTGGACATTTACATAATTATTGGGAC 57.256 33.333 0.00 0.00 0.00 4.46
1319 1361 9.180678 CATTCAAGTTTTTAATGTGGTGAGTAC 57.819 33.333 0.00 0.00 0.00 2.73
1516 1558 4.221703 AGGTACAAAGTCCTCATGTGAGAG 59.778 45.833 11.47 2.47 44.74 3.20
1598 1641 7.465989 CGTTGACCTTGTAAACTTTGTTCTTA 58.534 34.615 0.00 0.00 0.00 2.10
1707 1750 2.886523 CTCCTTTGACAGCCATCAAACA 59.113 45.455 8.52 0.00 42.32 2.83
1758 1801 1.075374 TGAGCCTAGCCCACAAAACAT 59.925 47.619 0.00 0.00 0.00 2.71
1771 1814 4.134379 ACAAAACATGCCATTGTGACAA 57.866 36.364 0.00 0.00 36.03 3.18
1776 1819 6.696441 AAACATGCCATTGTGACAAATTTT 57.304 29.167 0.62 0.00 0.00 1.82
1812 1856 5.711506 TGTTAGAACATCACATGCATTTCCT 59.288 36.000 0.00 0.00 33.17 3.36
1866 1911 1.152830 GAAGCCCAAACACCCTCCA 59.847 57.895 0.00 0.00 0.00 3.86
1884 1931 2.105821 TCCACCCAAAGGTCAACAGTAG 59.894 50.000 0.00 0.00 46.45 2.57
1890 1937 4.275936 CCCAAAGGTCAACAGTAGAACTTG 59.724 45.833 0.00 0.00 41.93 3.16
2150 2237 6.864421 ACATGTTACTCCCTCTATCCATCTA 58.136 40.000 0.00 0.00 0.00 1.98
2181 2268 6.404293 GGCCTAATGCATTTTTCGAGACTAAA 60.404 38.462 18.75 0.00 43.89 1.85
2189 2276 6.308041 GCATTTTTCGAGACTAAATTTGACCC 59.692 38.462 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 5.941555 ATTACCCAAACAACAAGAAACCA 57.058 34.783 0.00 0.00 0.00 3.67
388 409 3.766591 CACATGCACCCCCTGTAAATTAA 59.233 43.478 0.00 0.00 0.00 1.40
643 681 4.769688 TGCGTATGTGAATCTCCTTGAAT 58.230 39.130 0.00 0.00 0.00 2.57
747 786 5.525012 TGCTAAATATCTAGTGTGCTTGCAG 59.475 40.000 0.00 0.00 0.00 4.41
937 979 4.044065 ACCACCCCAGTATGAGAAAATTCA 59.956 41.667 0.00 0.00 39.69 2.57
1019 1061 2.939640 GCTTTTCCATACCCTTCAGCGA 60.940 50.000 0.00 0.00 0.00 4.93
1075 1117 2.016318 TGGAGTGACAAGCTTGTTGTG 58.984 47.619 31.58 7.21 42.43 3.33
1152 1194 9.657419 TGCATACCATGATTATCAACTACATAG 57.343 33.333 0.00 0.00 0.00 2.23
1319 1361 3.293337 TGCCTTGATGGGATTGATGAAG 58.707 45.455 0.00 0.00 36.00 3.02
1516 1558 5.736951 ATGTGTCTAATAGGAGATCTGCC 57.263 43.478 11.06 6.84 0.00 4.85
1598 1641 8.768501 TTTAGTGTCAGTATATGTCATCCTCT 57.231 34.615 0.00 0.00 29.60 3.69
1671 1714 8.876275 TGTCAAAGGAGATTTCAAATTTGAAG 57.124 30.769 27.52 15.98 46.68 3.02
1707 1750 5.012354 AGCCAATGGAAGAACATGTTGAAAT 59.988 36.000 17.58 0.00 0.00 2.17
1758 1801 5.426504 ACAGAAAAATTTGTCACAATGGCA 58.573 33.333 10.98 0.00 0.00 4.92
1884 1931 5.235305 TCAAGAAGTTTGACAGCAAGTTC 57.765 39.130 0.84 0.84 35.04 3.01
1890 1937 8.801715 TTATGAATTTCAAGAAGTTTGACAGC 57.198 30.769 2.68 0.00 0.00 4.40
1974 2021 3.117474 TGGTTGGGTGGACAAATAGTTCA 60.117 43.478 0.00 0.00 31.67 3.18
2123 2170 4.341235 TGGATAGAGGGAGTAACATGTTCG 59.659 45.833 15.85 0.00 0.00 3.95
2150 2237 5.304101 TCGAAAAATGCATTAGGCCCATTAT 59.696 36.000 13.39 0.00 43.89 1.28


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

AutoCloner maintained by Alex Coulton.