Multiple sequence alignment - TraesCS3D01G297500

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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 TraesCS3D01G297500 chr3D 100.000 2321 0 0 1 2321 410990961 410993281 0 4287
1 TraesCS3D01G297500 chr3B 95.116 2191 88 10 1 2184 537433690 537435868 0 3435
2 TraesCS3D01G297500 chr3A 94.560 1250 44 12 1 1247 540661911 540660683 0 1910
3 TraesCS3D01G297500 chr3A 94.799 1096 45 5 1232 2320 540660660 540659570 0 1698


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 TraesCS3D01G297500 chr3D 410990961 410993281 2320 False 4287 4287 100.0000 1 2321 1 chr3D.!!$F1 2320
1 TraesCS3D01G297500 chr3B 537433690 537435868 2178 False 3435 3435 95.1160 1 2184 1 chr3B.!!$F1 2183
2 TraesCS3D01G297500 chr3A 540659570 540661911 2341 True 1804 1910 94.6795 1 2320 2 chr3A.!!$R1 2319

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
159 161 0.673644 ACAGATTTCTTCCGTGCCCG 60.674 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1956 0.179121 CCATCGCGTGCCTAACAGTA 60.179 55.0 5.77 0.0 0.0 2.74 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
24 25 7.630242 TTAGTTGAAATTAGATGGCTGAAGG 57.370 36.000 0.00 0.00 0.00 3.46
81 83 8.786898 TGAGAAGAAGAATGAGGTAAACATTTG 58.213 33.333 0.00 0.00 37.96 2.32
84 86 7.288810 AGAAGAATGAGGTAAACATTTGCAA 57.711 32.000 0.00 0.00 37.96 4.08
114 116 1.188863 ACCGTGTATACTCCGGCTTT 58.811 50.000 25.00 10.66 45.49 3.51
136 138 1.358046 GATGAATGGCAAGGCGAGC 59.642 57.895 0.00 0.00 0.00 5.03
159 161 0.673644 ACAGATTTCTTCCGTGCCCG 60.674 55.000 0.00 0.00 0.00 6.13
197 199 2.717639 ACCACAGTTCAGAGCAGTTT 57.282 45.000 0.00 0.00 0.00 2.66
210 212 2.810852 GAGCAGTTTGGTTCAGAGAAGG 59.189 50.000 0.00 0.00 0.00 3.46
419 424 2.975799 GAAGTTGACGGCGCCCAA 60.976 61.111 23.46 17.74 0.00 4.12
822 827 1.751927 CTGCTTCATGGTGAGCCCC 60.752 63.158 12.11 0.00 0.00 5.80
1026 1031 2.668550 GCCAGGAACACGGTGGAC 60.669 66.667 13.48 5.74 32.60 4.02
1158 1166 4.462280 GGTAAGTCCACGCCCCCG 62.462 72.222 0.00 0.00 41.14 5.73
1170 1178 2.993471 GCCCCCGTTGTTGCTGATG 61.993 63.158 0.00 0.00 0.00 3.07
1229 1237 5.922739 TCAAACATCGCCATATATGTCAC 57.077 39.130 11.73 0.46 35.30 3.67
1827 1878 0.652592 CGCTCAGCCATAGGAAAACG 59.347 55.000 0.00 0.00 0.00 3.60
1829 1880 1.666189 GCTCAGCCATAGGAAAACGAC 59.334 52.381 0.00 0.00 0.00 4.34
1847 1898 1.065997 ACCCCCTGCAGTAAGTGGTT 61.066 55.000 13.81 0.00 0.00 3.67
1871 1922 3.855689 ATTTAGCGCAAGTGAAGCATT 57.144 38.095 11.47 0.00 41.68 3.56
1878 1929 1.664016 GCAAGTGAAGCATTGACACGG 60.664 52.381 0.00 0.00 33.40 4.94
1881 1932 1.070758 AGTGAAGCATTGACACGGTCT 59.929 47.619 5.77 0.00 33.40 3.85
1889 1940 3.427503 GCATTGACACGGTCTTATTTGGG 60.428 47.826 5.77 0.00 33.15 4.12
1890 1941 3.773418 TTGACACGGTCTTATTTGGGA 57.227 42.857 5.77 0.00 33.15 4.37
1893 1944 3.833650 TGACACGGTCTTATTTGGGAGTA 59.166 43.478 5.77 0.00 33.15 2.59
1894 1945 4.081862 TGACACGGTCTTATTTGGGAGTAG 60.082 45.833 5.77 0.00 33.15 2.57
1895 1946 3.195661 CACGGTCTTATTTGGGAGTAGC 58.804 50.000 0.00 0.00 0.00 3.58
1896 1947 3.105283 ACGGTCTTATTTGGGAGTAGCT 58.895 45.455 0.00 0.00 0.00 3.32
1898 1949 4.019591 ACGGTCTTATTTGGGAGTAGCTTT 60.020 41.667 0.00 0.00 0.00 3.51
1899 1950 4.941873 CGGTCTTATTTGGGAGTAGCTTTT 59.058 41.667 0.00 0.00 0.00 2.27
1900 1951 6.110707 CGGTCTTATTTGGGAGTAGCTTTTA 58.889 40.000 0.00 0.00 0.00 1.52
1902 1953 6.036844 GGTCTTATTTGGGAGTAGCTTTTACG 59.963 42.308 0.00 0.00 0.00 3.18
1903 1954 5.583457 TCTTATTTGGGAGTAGCTTTTACGC 59.417 40.000 0.00 0.00 0.00 4.42
1904 1955 3.412237 TTTGGGAGTAGCTTTTACGCT 57.588 42.857 0.00 0.00 43.83 5.07
1905 1956 3.412237 TTGGGAGTAGCTTTTACGCTT 57.588 42.857 0.00 0.00 41.30 4.68
1917 1968 4.668431 GCTTTTACGCTTACTGTTAGGCAC 60.668 45.833 0.00 0.00 30.61 5.01
1947 1998 1.002888 CCTAGCGAGATGGCCATGAAT 59.997 52.381 26.56 8.91 0.00 2.57
2157 2208 4.629200 GCAAAGGTCAGAGAGAACACTATG 59.371 45.833 0.00 0.00 35.97 2.23
2164 2215 6.127310 GGTCAGAGAGAACACTATGTACCATT 60.127 42.308 0.00 0.00 33.73 3.16
2262 2313 7.248743 ACATGGATTGAAGGAAATCATGTTT 57.751 32.000 0.00 0.00 36.26 2.83
2271 2322 4.808042 AGGAAATCATGTTTATCCAGGGG 58.192 43.478 14.68 0.00 32.47 4.79
2272 2323 4.482025 AGGAAATCATGTTTATCCAGGGGA 59.518 41.667 14.68 0.00 35.55 4.81
2273 2324 4.584743 GGAAATCATGTTTATCCAGGGGAC 59.415 45.833 0.00 0.00 32.98 4.46
2277 2328 4.855340 TCATGTTTATCCAGGGGACTTTC 58.145 43.478 0.00 0.00 40.21 2.62
2285 2336 1.699634 CCAGGGGACTTTCTTGTCTCA 59.300 52.381 0.00 0.00 39.10 3.27
2288 2339 3.008375 CAGGGGACTTTCTTGTCTCATCA 59.992 47.826 0.00 0.00 39.10 3.07
2290 2341 4.290722 AGGGGACTTTCTTGTCTCATCAAT 59.709 41.667 0.00 0.00 39.10 2.57
2312 2363 2.859165 TCATTCTCAGTTGGGTGTCC 57.141 50.000 0.00 0.00 0.00 4.02
2320 2371 4.030913 CTCAGTTGGGTGTCCTATTCCTA 58.969 47.826 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 46 3.505386 TCTTCTTCTCAACAGAGAGGCT 58.495 45.455 0.00 0.00 39.43 4.58
84 86 6.146673 CGGAGTATACACGGTTCTTTCTTTTT 59.853 38.462 5.50 0.00 0.00 1.94
89 91 3.442100 CCGGAGTATACACGGTTCTTTC 58.558 50.000 23.24 3.37 42.53 2.62
98 100 1.933853 CAGCAAAGCCGGAGTATACAC 59.066 52.381 5.05 0.00 0.00 2.90
103 105 0.901827 TCATCAGCAAAGCCGGAGTA 59.098 50.000 5.05 0.00 0.00 2.59
114 116 1.659622 CGCCTTGCCATTCATCAGCA 61.660 55.000 0.00 0.00 33.97 4.41
136 138 2.840974 ACGGAAGAAATCTGTGCGG 58.159 52.632 9.72 0.00 46.12 5.69
159 161 5.163395 TGTGGTTAATGTTTCAAAGTTCCCC 60.163 40.000 0.00 0.00 0.00 4.81
210 212 2.114411 TTGCGGGGTTGGTTCTCC 59.886 61.111 0.00 0.00 0.00 3.71
1011 1016 1.663702 GTCGTCCACCGTGTTCCTG 60.664 63.158 0.00 0.00 37.94 3.86
1026 1031 2.427540 GGATCCTGCCGATCTGGTCG 62.428 65.000 3.84 2.72 45.90 4.79
1102 1107 2.029288 CAGAGCGTGATGGCAACGT 61.029 57.895 12.72 0.93 42.51 3.99
1158 1166 1.734707 GCCTGCATCATCAGCAACAAC 60.735 52.381 0.00 0.00 42.17 3.32
1170 1178 0.322816 TCCTGAACAAGGCCTGCATC 60.323 55.000 5.69 5.40 46.92 3.91
1229 1237 6.257193 TGATCGACTCAATGATTGTTCATCTG 59.743 38.462 4.93 0.00 41.83 2.90
1791 1842 2.828868 GCCATGATACCCGGAGCA 59.171 61.111 0.73 0.00 0.00 4.26
1827 1878 1.299976 CCACTTACTGCAGGGGGTC 59.700 63.158 19.93 0.00 33.00 4.46
1829 1880 0.322546 GAACCACTTACTGCAGGGGG 60.323 60.000 19.93 13.51 42.47 5.40
1847 1898 3.004210 TGCTTCACTTGCGCTAAATTTGA 59.996 39.130 9.73 0.00 0.00 2.69
1871 1922 2.635915 ACTCCCAAATAAGACCGTGTCA 59.364 45.455 6.78 0.00 34.60 3.58
1878 1929 6.456584 GCGTAAAAGCTACTCCCAAATAAGAC 60.457 42.308 0.00 0.00 0.00 3.01
1881 1932 5.806366 GCGTAAAAGCTACTCCCAAATAA 57.194 39.130 0.00 0.00 0.00 1.40
1894 1945 3.434299 TGCCTAACAGTAAGCGTAAAAGC 59.566 43.478 0.00 0.00 37.41 3.51
1895 1946 4.433805 CGTGCCTAACAGTAAGCGTAAAAG 60.434 45.833 0.00 0.00 0.00 2.27
1896 1947 3.429543 CGTGCCTAACAGTAAGCGTAAAA 59.570 43.478 0.00 0.00 0.00 1.52
1898 1949 2.598589 CGTGCCTAACAGTAAGCGTAA 58.401 47.619 0.00 0.00 0.00 3.18
1899 1950 1.733389 GCGTGCCTAACAGTAAGCGTA 60.733 52.381 0.00 0.00 0.00 4.42
1900 1951 1.012486 GCGTGCCTAACAGTAAGCGT 61.012 55.000 0.00 0.00 0.00 5.07
1902 1953 0.734942 TCGCGTGCCTAACAGTAAGC 60.735 55.000 5.77 0.00 0.00 3.09
1903 1954 1.588404 CATCGCGTGCCTAACAGTAAG 59.412 52.381 5.77 0.00 0.00 2.34
1904 1955 1.635844 CATCGCGTGCCTAACAGTAA 58.364 50.000 5.77 0.00 0.00 2.24
1905 1956 0.179121 CCATCGCGTGCCTAACAGTA 60.179 55.000 5.77 0.00 0.00 2.74
1917 1968 3.888079 CTCGCTAGGCTCCATCGCG 62.888 68.421 0.00 0.00 44.63 5.87
1947 1998 1.214325 CGACATGTACACAGGCCGA 59.786 57.895 0.00 0.00 0.00 5.54
2157 2208 7.404671 ACATCCCTTCAATTTGTAATGGTAC 57.595 36.000 0.00 0.00 0.00 3.34
2164 2215 8.768397 ACTGACTATACATCCCTTCAATTTGTA 58.232 33.333 0.00 0.00 0.00 2.41
2247 2298 5.302823 CCCCTGGATAAACATGATTTCCTTC 59.697 44.000 0.00 0.00 0.00 3.46
2262 2313 3.775316 GAGACAAGAAAGTCCCCTGGATA 59.225 47.826 0.00 0.00 39.34 2.59
2271 2322 7.606858 TGATCATTGATGAGACAAGAAAGTC 57.393 36.000 3.32 0.00 40.64 3.01
2272 2323 8.577048 AATGATCATTGATGAGACAAGAAAGT 57.423 30.769 20.11 0.00 40.64 2.66
2273 2324 8.894731 AGAATGATCATTGATGAGACAAGAAAG 58.105 33.333 25.37 0.00 40.64 2.62
2277 2328 7.496263 ACTGAGAATGATCATTGATGAGACAAG 59.504 37.037 25.37 12.11 40.64 3.16
2285 2336 5.593095 CACCCAACTGAGAATGATCATTGAT 59.407 40.000 25.37 13.46 0.00 2.57
2288 2339 4.927049 ACACCCAACTGAGAATGATCATT 58.073 39.130 20.85 20.85 0.00 2.57
2290 2341 3.307691 GGACACCCAACTGAGAATGATCA 60.308 47.826 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.