Multiple sequence alignment - TraesCS3A01G189500

Loading Multiple Alignment...

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 TraesCS3A01G189500 chr3A 100.000 2414 0 0 1 2414 233024160 233021747 0.000000e+00 4458.0
1 TraesCS3A01G189500 chr3D 93.917 2433 112 26 1 2414 183136780 183134365 0.000000e+00 3640.0
2 TraesCS3A01G189500 chr3B 92.830 1604 78 27 565 2142 262079442 262077850 0.000000e+00 2290.0
3 TraesCS3A01G189500 chr3B 92.287 363 23 3 171 531 262080392 262080033 5.950000e-141 510.0
4 TraesCS3A01G189500 chr3B 91.700 253 18 2 2165 2414 262077857 262077605 4.940000e-92 348.0
5 TraesCS3A01G189500 chr3B 87.879 165 4 4 1 162 262081316 262081165 1.910000e-41 180.0
6 TraesCS3A01G189500 chr5D 80.435 92 7 7 1577 1659 60145782 60145871 2.590000e-05 60.2
7 TraesCS3A01G189500 chr1D 97.222 36 0 1 1892 1926 294204605 294204640 2.590000e-05 60.2
8 TraesCS3A01G189500 chr1B 97.143 35 1 0 1358 1392 645519335 645519301 2.590000e-05 60.2


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 TraesCS3A01G189500 chr3A 233021747 233024160 2413 True 4458 4458 100.000 1 2414 1 chr3A.!!$R1 2413
1 TraesCS3A01G189500 chr3D 183134365 183136780 2415 True 3640 3640 93.917 1 2414 1 chr3D.!!$R1 2413
2 TraesCS3A01G189500 chr3B 262077605 262081316 3711 True 832 2290 91.174 1 2414 4 chr3B.!!$R1 2413

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
188 956 0.030235 CAATGATGCCATCACTGCGG 59.97 55.0 10.06 0.0 43.01 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 2778 1.522676 CTTATCGTACATGCAGCACGG 59.477 52.381 14.97 0.0 37.59 4.94 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
65 66 2.920524 ACATACACGACACACCCAAAA 58.079 42.857 0.00 0.0 0.00 2.44
66 67 3.280295 ACATACACGACACACCCAAAAA 58.720 40.909 0.00 0.0 0.00 1.94
67 68 3.886505 ACATACACGACACACCCAAAAAT 59.113 39.130 0.00 0.0 0.00 1.82
108 109 1.643880 TGCACACGATGATGCACTAG 58.356 50.000 0.00 0.0 46.63 2.57
151 152 4.055360 CGACCGCCACATATGATCTTAAA 58.945 43.478 10.38 0.0 0.00 1.52
188 956 0.030235 CAATGATGCCATCACTGCGG 59.970 55.000 10.06 0.0 43.01 5.69
225 993 5.032863 CGCCATTGAAGAATCTCATGAAAC 58.967 41.667 0.00 0.0 0.00 2.78
304 1074 0.109643 GCATTGTGCGAAGTGATGCA 60.110 50.000 0.00 0.0 41.92 3.96
386 1156 3.952535 ACTGAAATGAACTCGTTTGTGC 58.047 40.909 1.66 0.0 35.40 4.57
393 1163 4.643385 CTCGTTTGTGCGCGCGTT 62.643 61.111 32.35 0.0 0.00 4.84
413 1183 5.560148 CGTTAGAGCACACATATTTTGACC 58.440 41.667 0.00 0.0 0.00 4.02
451 1221 4.207019 GCCAATATTAACGAACATGCTTGC 59.793 41.667 0.00 0.0 0.00 4.01
488 1258 7.187824 AGCTCTATTGACAGGTAATTCAAGA 57.812 36.000 0.00 0.0 35.25 3.02
586 1913 4.091365 CAGCTCGATGAAACGTGTAAATCA 59.909 41.667 0.00 0.0 34.70 2.57
595 1922 4.419522 AACGTGTAAATCAGCCACAATC 57.580 40.909 0.00 0.0 0.00 2.67
596 1923 2.415168 ACGTGTAAATCAGCCACAATCG 59.585 45.455 0.00 0.0 0.00 3.34
597 1924 2.785679 GTGTAAATCAGCCACAATCGC 58.214 47.619 0.00 0.0 0.00 4.58
598 1925 2.420022 GTGTAAATCAGCCACAATCGCT 59.580 45.455 0.00 0.0 36.91 4.93
600 1927 4.094294 GTGTAAATCAGCCACAATCGCTAA 59.906 41.667 0.00 0.0 33.91 3.09
601 1928 4.332543 TGTAAATCAGCCACAATCGCTAAG 59.667 41.667 0.00 0.0 33.91 2.18
605 1932 3.407698 TCAGCCACAATCGCTAAGAAAA 58.592 40.909 0.00 0.0 33.91 2.29
616 1944 8.875803 ACAATCGCTAAGAAAATCGTGTAATTA 58.124 29.630 0.00 0.0 0.00 1.40
617 1945 9.864034 CAATCGCTAAGAAAATCGTGTAATTAT 57.136 29.630 0.00 0.0 0.00 1.28
693 2021 1.713246 CAACACAACAGTGCGACGT 59.287 52.632 0.00 0.0 36.74 4.34
726 2060 3.858989 CACGCACGCACACACACA 61.859 61.111 0.00 0.0 0.00 3.72
727 2061 3.860125 ACGCACGCACACACACAC 61.860 61.111 0.00 0.0 0.00 3.82
861 2211 5.983720 GCGTCACTTCACACTATATAATGGT 59.016 40.000 0.00 0.0 0.00 3.55
862 2212 7.143340 GCGTCACTTCACACTATATAATGGTA 58.857 38.462 0.00 0.0 0.00 3.25
863 2213 7.650504 GCGTCACTTCACACTATATAATGGTAA 59.349 37.037 0.00 0.0 0.00 2.85
864 2214 8.965172 CGTCACTTCACACTATATAATGGTAAC 58.035 37.037 0.00 0.0 0.00 2.50
865 2215 8.965172 GTCACTTCACACTATATAATGGTAACG 58.035 37.037 0.00 0.0 42.51 3.18
866 2216 8.139350 TCACTTCACACTATATAATGGTAACGG 58.861 37.037 0.00 0.0 42.51 4.44
1036 2389 0.900647 CTCGGTTCCTCTCCTGGTGT 60.901 60.000 0.00 0.0 0.00 4.16
1068 2421 0.900182 TCTCCTGCTTCTTCCTCGCA 60.900 55.000 0.00 0.0 0.00 5.10
1425 2778 5.941948 ACCCGCATTAAGAGTTATTATGC 57.058 39.130 0.00 0.0 0.00 3.14
1518 2871 9.890629 ATTAAGCATATATATCATCACCACGTT 57.109 29.630 0.00 0.0 0.00 3.99
1589 2942 9.762381 TTGGTTGATAATAACAAATACTCCCTT 57.238 29.630 0.00 0.0 32.22 3.95
1590 2943 9.403583 TGGTTGATAATAACAAATACTCCCTTC 57.596 33.333 0.00 0.0 32.22 3.46
1591 2944 9.628500 GGTTGATAATAACAAATACTCCCTTCT 57.372 33.333 0.00 0.0 32.22 2.85
1707 3061 4.840271 AGCATGTTTCATCTCTGTCATCA 58.160 39.130 0.00 0.0 0.00 3.07
1740 3094 1.561542 AGGCCGAGTCAATCCAAATCT 59.438 47.619 0.00 0.0 0.00 2.40
2015 3372 5.163703 TGGTTTCCATGCATATAACGACAAC 60.164 40.000 0.00 0.0 0.00 3.32
2040 3397 8.404000 ACTTGATTCATTCTTGACAATCATAGC 58.596 33.333 0.00 0.0 32.06 2.97
2052 3409 6.394809 TGACAATCATAGCGTCTCTTTAACA 58.605 36.000 0.00 0.0 0.00 2.41
2062 3419 5.992217 AGCGTCTCTTTAACAAACATCTCTT 59.008 36.000 0.00 0.0 0.00 2.85
2101 3459 7.090953 AGACAATAACTTTCAAACCGAAACA 57.909 32.000 0.00 0.0 38.72 2.83
2135 3494 1.112113 TCTACCTCATTCTCGGCACC 58.888 55.000 0.00 0.0 0.00 5.01
2218 3577 6.403636 CCATCCTGTCAAAATCTTTACTTCCG 60.404 42.308 0.00 0.0 0.00 4.30
2334 3695 7.807977 AAGTGTGATCTTTCTCTTGCTTTTA 57.192 32.000 0.00 0.0 0.00 1.52
2346 3707 7.621428 TCTCTTGCTTTTATTCTTCATGGAG 57.379 36.000 0.00 0.0 0.00 3.86
2348 3709 7.551974 TCTCTTGCTTTTATTCTTCATGGAGAG 59.448 37.037 3.35 0.0 0.00 3.20
2370 3731 6.067217 AGTAAGTGACTATTTCATTGGGCT 57.933 37.500 0.00 0.0 36.27 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.805744 TGTATCCTCTCCTCTTTAGTCCC 58.194 47.826 0.00 0.00 0.00 4.46
65 66 7.171337 GCATGTTGTTCCATCTTGTTTGTTATT 59.829 33.333 0.00 0.00 0.00 1.40
66 67 6.646240 GCATGTTGTTCCATCTTGTTTGTTAT 59.354 34.615 0.00 0.00 0.00 1.89
67 68 5.982516 GCATGTTGTTCCATCTTGTTTGTTA 59.017 36.000 0.00 0.00 0.00 2.41
108 109 0.534203 TGGAGGGTTTGTCGACTTGC 60.534 55.000 17.92 6.22 0.00 4.01
151 152 4.225942 TCATTGCTGAGTCCTCCAAGTTAT 59.774 41.667 0.00 0.00 0.00 1.89
225 993 1.948104 TGTTTGTGTCCTTGTCTCGG 58.052 50.000 0.00 0.00 0.00 4.63
304 1074 4.314440 TTCGCCGGCTCAGCTGTT 62.314 61.111 26.68 0.00 32.22 3.16
386 1156 1.137459 TATGTGTGCTCTAACGCGCG 61.137 55.000 30.96 30.96 43.07 6.86
393 1163 5.123820 GCAAGGTCAAAATATGTGTGCTCTA 59.876 40.000 0.00 0.00 0.00 2.43
413 1183 1.175983 TTGGCAAAGGTACCGGCAAG 61.176 55.000 19.00 5.99 39.90 4.01
470 1240 7.038302 TGGTCTAGTCTTGAATTACCTGTCAAT 60.038 37.037 0.00 0.00 33.45 2.57
472 1242 5.778241 TGGTCTAGTCTTGAATTACCTGTCA 59.222 40.000 0.00 0.00 0.00 3.58
488 1258 0.978146 ATTCGGCAGCCTGGTCTAGT 60.978 55.000 10.54 0.00 0.00 2.57
586 1913 3.063997 CGATTTTCTTAGCGATTGTGGCT 59.936 43.478 0.00 0.00 44.35 4.75
595 1922 7.792508 GTCCATAATTACACGATTTTCTTAGCG 59.207 37.037 0.00 0.00 0.00 4.26
596 1923 7.792508 CGTCCATAATTACACGATTTTCTTAGC 59.207 37.037 7.39 0.00 34.06 3.09
597 1924 9.027129 TCGTCCATAATTACACGATTTTCTTAG 57.973 33.333 10.56 0.00 36.39 2.18
598 1925 8.929827 TCGTCCATAATTACACGATTTTCTTA 57.070 30.769 10.56 0.00 36.39 2.10
616 1944 1.867233 GAGTGCGCAAATATCGTCCAT 59.133 47.619 14.00 0.00 0.00 3.41
617 1945 1.286501 GAGTGCGCAAATATCGTCCA 58.713 50.000 14.00 0.00 0.00 4.02
658 1986 2.026157 GCGCCGTGATCTCGATCA 59.974 61.111 18.20 5.53 44.83 2.92
716 2050 2.234613 ACGCTATGTGTGTGTGTGC 58.765 52.632 0.00 0.00 38.09 4.57
726 2060 1.475280 ACGTCCACATACACGCTATGT 59.525 47.619 1.36 1.36 46.06 2.29
727 2061 2.203800 ACGTCCACATACACGCTATG 57.796 50.000 0.00 0.23 39.73 2.23
865 2215 0.391597 TTTGTGACAGACGGGTCTCC 59.608 55.000 0.00 0.00 37.98 3.71
866 2216 1.068741 AGTTTGTGACAGACGGGTCTC 59.931 52.381 0.32 3.35 37.98 3.36
879 2229 1.662044 GCCTTGGCCTCAGTTTGTG 59.338 57.895 3.32 0.00 0.00 3.33
1036 2389 1.539869 AGGAGAGGAAGGCCAGCAA 60.540 57.895 5.01 0.00 36.29 3.91
1068 2421 2.137523 GTCAATCCGTACAAACCGTGT 58.862 47.619 0.00 0.00 44.82 4.49
1122 2475 2.224967 GGCAAATATGAGGAGGATGGCT 60.225 50.000 0.00 0.00 0.00 4.75
1425 2778 1.522676 CTTATCGTACATGCAGCACGG 59.477 52.381 14.97 0.00 37.59 4.94
1503 2856 5.182487 TGTTTAGCAACGTGGTGATGATAT 58.818 37.500 0.00 0.00 35.40 1.63
1504 2857 4.570930 TGTTTAGCAACGTGGTGATGATA 58.429 39.130 0.00 0.00 35.40 2.15
1505 2858 3.407698 TGTTTAGCAACGTGGTGATGAT 58.592 40.909 0.00 0.00 35.40 2.45
1506 2859 2.839975 TGTTTAGCAACGTGGTGATGA 58.160 42.857 0.00 0.00 35.40 2.92
1509 2862 2.839975 TGATGTTTAGCAACGTGGTGA 58.160 42.857 0.00 0.00 35.40 4.02
1515 2868 9.507280 AAATTAAGATCATGATGTTTAGCAACG 57.493 29.630 21.75 0.00 35.40 4.10
1687 3040 7.187480 GTGATTGATGACAGAGATGAAACATG 58.813 38.462 0.00 0.00 0.00 3.21
1740 3094 9.906660 GAACCAAACATATTGAAGATTACAACA 57.093 29.630 0.00 0.00 0.00 3.33
1882 3236 7.842887 ACTAGTAAAAATAAAGGTGGGCAAA 57.157 32.000 0.00 0.00 0.00 3.68
1884 3238 7.005296 TCAACTAGTAAAAATAAAGGTGGGCA 58.995 34.615 0.00 0.00 0.00 5.36
1886 3240 9.855021 CATTCAACTAGTAAAAATAAAGGTGGG 57.145 33.333 0.00 0.00 0.00 4.61
2015 3372 7.586664 CGCTATGATTGTCAAGAATGAATCAAG 59.413 37.037 0.00 0.00 35.00 3.02
2040 3397 7.644986 AGAAGAGATGTTTGTTAAAGAGACG 57.355 36.000 0.00 0.00 0.00 4.18
2078 3435 7.253850 GGTTGTTTCGGTTTGAAAGTTATTGTC 60.254 37.037 0.00 0.00 46.85 3.18
2101 3459 3.587951 GAGGTAGAAGGAAAAGAGGGGTT 59.412 47.826 0.00 0.00 0.00 4.11
2135 3494 5.051891 AGATTTTGAAAAGACGGCTCATG 57.948 39.130 0.00 0.00 0.00 3.07
2177 3536 5.181748 CAGGATGGAAGTAAAGTCTTCTGG 58.818 45.833 6.44 0.00 42.19 3.86
2178 3537 5.799213 ACAGGATGGAAGTAAAGTCTTCTG 58.201 41.667 6.44 0.00 43.62 3.02
2334 3695 6.865834 AGTCACTTACTCTCCATGAAGAAT 57.134 37.500 0.00 0.00 30.33 2.40
2346 3707 6.116126 AGCCCAATGAAATAGTCACTTACTC 58.884 40.000 0.00 0.00 39.72 2.59
2348 3709 6.759497 AAGCCCAATGAAATAGTCACTTAC 57.241 37.500 0.00 0.00 39.72 2.34
2370 3731 2.097791 GGGCACCGCGTTTGATTAATAA 59.902 45.455 4.92 0.00 40.86 1.40


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

AutoCloner maintained by Alex Coulton.