Multiple sequence alignment - TraesCS5D01G083500

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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 TraesCS5D01G083500 chr5D 100.000 3251 0 0 1 3251 87174903 87171653 0.000000e+00 6004
1 TraesCS5D01G083500 chr5D 82.692 156 27 0 1175 1330 412147729 412147574 4.370000e-29 139
2 TraesCS5D01G083500 chr5A 93.315 3306 125 28 1 3251 80156946 80153682 0.000000e+00 4793
3 TraesCS5D01G083500 chr5A 82.716 162 28 0 1169 1330 523879581 523879420 9.400000e-31 145
4 TraesCS5D01G083500 chr5B 93.180 3299 134 35 1 3251 93213637 93210382 0.000000e+00 4761
5 TraesCS5D01G083500 chr5B 82.099 162 29 0 1169 1330 495473502 495473341 4.370000e-29 139
6 TraesCS5D01G083500 chr4A 94.089 203 11 1 1137 1339 545106829 545106628 1.130000e-79 307
7 TraesCS5D01G083500 chr4D 92.965 199 13 1 1141 1339 51608624 51608821 4.100000e-74 289
8 TraesCS5D01G083500 chr6B 86.486 222 22 7 1162 1377 699018604 699018385 1.510000e-58 237
9 TraesCS5D01G083500 chr6D 85.973 221 23 7 1162 1376 459735469 459735251 2.520000e-56 230


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 TraesCS5D01G083500 chr5D 87171653 87174903 3250 True 6004 6004 100.000 1 3251 1 chr5D.!!$R1 3250
1 TraesCS5D01G083500 chr5A 80153682 80156946 3264 True 4793 4793 93.315 1 3251 1 chr5A.!!$R1 3250
2 TraesCS5D01G083500 chr5B 93210382 93213637 3255 True 4761 4761 93.180 1 3251 1 chr5B.!!$R1 3250

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
913 941 0.103937 CCTCATCCTCGCTTGTCTCC 59.896 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2548 2627 0.461961 CCCTCTCAACTCCGGCTAAG 59.538 60.0 0.0 0.0 0.0 2.18 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
18 19 2.832201 CCCCTCCCTCGTCGTACC 60.832 72.222 0.00 0.00 0.00 3.34
25 30 0.107508 CCCTCGTCGTACCAGACCTA 60.108 60.000 0.00 0.00 37.85 3.08
44 49 4.887655 ACCTAAATCATTTTCTTAGGCCGG 59.112 41.667 0.00 0.00 43.73 6.13
71 76 1.068434 ACAACCTGAAAATGCCAACCG 59.932 47.619 0.00 0.00 0.00 4.44
81 86 1.434188 ATGCCAACCGATCCCATCTA 58.566 50.000 0.00 0.00 0.00 1.98
228 236 3.447229 CGGGGTTAAAAATTGGAGCTCAT 59.553 43.478 17.19 0.00 0.00 2.90
233 241 5.127031 GGTTAAAAATTGGAGCTCATAGCCA 59.873 40.000 17.19 0.66 43.77 4.75
235 243 5.945144 AAAAATTGGAGCTCATAGCCATT 57.055 34.783 17.19 0.00 43.77 3.16
249 257 1.065491 AGCCATTATGACTTGACGGCA 60.065 47.619 0.00 0.00 40.58 5.69
320 328 6.970191 ACCCTATACAAACTTTGAGCCTTAT 58.030 36.000 8.55 0.00 0.00 1.73
321 329 7.054751 ACCCTATACAAACTTTGAGCCTTATC 58.945 38.462 8.55 0.00 0.00 1.75
400 412 3.118629 CCGATGAGGAATCAAAGAGGTCA 60.119 47.826 0.00 0.00 45.00 4.02
423 435 4.858935 TGAACTCAAAATTTCTTGGCTCG 58.141 39.130 0.00 0.00 0.00 5.03
724 738 7.254387 CCATTTGTTGAACACCACAATTTACAG 60.254 37.037 0.00 0.00 0.00 2.74
733 747 5.010922 ACACCACAATTTACAGATGCAATGT 59.989 36.000 12.05 12.05 34.62 2.71
735 749 7.093814 ACACCACAATTTACAGATGCAATGTAT 60.094 33.333 13.95 1.57 33.36 2.29
791 812 9.414295 CCATCACCATTAACAATATAAATGCAG 57.586 33.333 0.00 0.00 30.81 4.41
858 885 6.570672 ATGAATGCACAAATGAGCTATAGG 57.429 37.500 1.04 0.00 32.76 2.57
859 886 4.276678 TGAATGCACAAATGAGCTATAGGC 59.723 41.667 1.04 0.00 42.19 3.93
898 926 2.297033 GCAACAAAAGGCATCTTCCTCA 59.703 45.455 0.00 0.00 34.82 3.86
899 927 3.056322 GCAACAAAAGGCATCTTCCTCAT 60.056 43.478 0.00 0.00 34.82 2.90
900 928 4.741342 CAACAAAAGGCATCTTCCTCATC 58.259 43.478 0.00 0.00 34.82 2.92
901 929 3.359950 ACAAAAGGCATCTTCCTCATCC 58.640 45.455 0.00 0.00 34.82 3.51
902 930 3.011032 ACAAAAGGCATCTTCCTCATCCT 59.989 43.478 0.00 0.00 34.82 3.24
903 931 3.574354 AAAGGCATCTTCCTCATCCTC 57.426 47.619 0.00 0.00 34.82 3.71
904 932 1.047002 AGGCATCTTCCTCATCCTCG 58.953 55.000 0.00 0.00 0.00 4.63
905 933 0.602372 GGCATCTTCCTCATCCTCGC 60.602 60.000 0.00 0.00 0.00 5.03
906 934 0.392336 GCATCTTCCTCATCCTCGCT 59.608 55.000 0.00 0.00 0.00 4.93
907 935 1.202627 GCATCTTCCTCATCCTCGCTT 60.203 52.381 0.00 0.00 0.00 4.68
908 936 2.481854 CATCTTCCTCATCCTCGCTTG 58.518 52.381 0.00 0.00 0.00 4.01
909 937 1.561643 TCTTCCTCATCCTCGCTTGT 58.438 50.000 0.00 0.00 0.00 3.16
910 938 1.478510 TCTTCCTCATCCTCGCTTGTC 59.521 52.381 0.00 0.00 0.00 3.18
911 939 1.480137 CTTCCTCATCCTCGCTTGTCT 59.520 52.381 0.00 0.00 0.00 3.41
912 940 1.107114 TCCTCATCCTCGCTTGTCTC 58.893 55.000 0.00 0.00 0.00 3.36
913 941 0.103937 CCTCATCCTCGCTTGTCTCC 59.896 60.000 0.00 0.00 0.00 3.71
914 942 0.820226 CTCATCCTCGCTTGTCTCCA 59.180 55.000 0.00 0.00 0.00 3.86
915 943 0.532573 TCATCCTCGCTTGTCTCCAC 59.467 55.000 0.00 0.00 0.00 4.02
916 944 0.534412 CATCCTCGCTTGTCTCCACT 59.466 55.000 0.00 0.00 0.00 4.00
917 945 0.820871 ATCCTCGCTTGTCTCCACTC 59.179 55.000 0.00 0.00 0.00 3.51
918 946 1.216710 CCTCGCTTGTCTCCACTCC 59.783 63.158 0.00 0.00 0.00 3.85
919 947 1.254284 CCTCGCTTGTCTCCACTCCT 61.254 60.000 0.00 0.00 0.00 3.69
920 948 0.605589 CTCGCTTGTCTCCACTCCTT 59.394 55.000 0.00 0.00 0.00 3.36
921 949 0.603569 TCGCTTGTCTCCACTCCTTC 59.396 55.000 0.00 0.00 0.00 3.46
945 996 5.075344 CCTCTCCTCCCCTATATATACTCCC 59.925 52.000 0.00 0.00 0.00 4.30
1649 1718 0.617535 TCGCCAGAAATGGAGGAGGA 60.618 55.000 0.00 0.00 0.00 3.71
1653 1722 2.200081 CCAGAAATGGAGGAGGAGGAA 58.800 52.381 0.00 0.00 0.00 3.36
1671 1740 2.499693 GGAAGAAGAAGAGGTGGAGGAG 59.500 54.545 0.00 0.00 0.00 3.69
1726 1795 2.174334 CAGTTCATGGACAAGCCGG 58.826 57.895 6.96 0.00 40.66 6.13
2008 2077 2.359230 GCCGCAAGAAGCAGAGGT 60.359 61.111 0.00 0.00 46.13 3.85
2085 2157 1.690219 ATCATGGCACGGAGGAGGAC 61.690 60.000 0.00 0.00 0.00 3.85
2256 2328 1.701292 TGCTACATGGCATAGGCTGAT 59.299 47.619 0.00 0.00 40.87 2.90
2318 2390 2.428890 GGTTGTGTTGGTGTGGAATTCA 59.571 45.455 7.93 0.00 0.00 2.57
2512 2591 1.270826 CAGAGAACAGAGCCTTCGTCA 59.729 52.381 0.00 0.00 0.00 4.35
2601 2683 2.824936 CCCTTTTGTCATACATGGCACA 59.175 45.455 0.00 0.00 42.90 4.57
2772 2866 8.734386 GTTGAATTCCTCAAGTTCAGATATTGT 58.266 33.333 2.27 0.00 44.83 2.71
2775 2869 5.762179 TCCTCAAGTTCAGATATTGTGGT 57.238 39.130 12.55 0.00 38.27 4.16
3175 3280 0.035915 GAGGCCAGAAACCCTGTCTC 60.036 60.000 5.01 0.00 41.33 3.36
3176 3281 1.002011 GGCCAGAAACCCTGTCTCC 60.002 63.158 0.00 0.00 41.33 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.238484 CGGCCTAAGAAAATGATTTAGGTCTG 60.238 42.308 0.00 5.82 43.63 3.51
25 30 3.708451 ACCCGGCCTAAGAAAATGATTT 58.292 40.909 0.00 0.00 0.00 2.17
44 49 2.287644 GCATTTTCAGGTTGTTGCAACC 59.712 45.455 26.14 19.96 40.58 3.77
71 76 2.635427 GTCCCTCTGGTTAGATGGGATC 59.365 54.545 13.75 0.00 44.72 3.36
81 86 6.749036 ATTATATTTCTCGTCCCTCTGGTT 57.251 37.500 0.00 0.00 0.00 3.67
228 236 2.169561 TGCCGTCAAGTCATAATGGCTA 59.830 45.455 6.41 0.00 43.96 3.93
233 241 1.747206 GCCCTGCCGTCAAGTCATAAT 60.747 52.381 0.00 0.00 0.00 1.28
235 243 1.220749 GCCCTGCCGTCAAGTCATA 59.779 57.895 0.00 0.00 0.00 2.15
320 328 8.677300 GCAAGAAAGATGATTAAACCACTATGA 58.323 33.333 0.00 0.00 0.00 2.15
321 329 8.461222 TGCAAGAAAGATGATTAAACCACTATG 58.539 33.333 0.00 0.00 0.00 2.23
400 412 5.464168 CGAGCCAAGAAATTTTGAGTTCAT 58.536 37.500 0.00 0.00 0.00 2.57
423 435 5.882000 TGCATGGATACTCAATATGGTATGC 59.118 40.000 0.00 0.00 37.30 3.14
561 573 3.624861 GCCTAGTCATTGACAGGTTCATG 59.375 47.826 24.03 0.00 35.15 3.07
640 652 7.375834 TCTCTAGTTAATTCGTGTGTTCATGT 58.624 34.615 0.00 0.00 32.85 3.21
709 721 5.010922 ACATTGCATCTGTAAATTGTGGTGT 59.989 36.000 0.84 0.00 0.00 4.16
744 758 3.054655 GGGTTAGTAGCACTGATTGGGAA 60.055 47.826 0.00 0.00 0.00 3.97
855 882 0.454600 GTGTGTGCGCTACTAGCCTA 59.545 55.000 9.73 0.00 38.18 3.93
857 884 0.669318 TTGTGTGTGCGCTACTAGCC 60.669 55.000 9.73 0.00 38.18 3.93
858 885 0.716108 CTTGTGTGTGCGCTACTAGC 59.284 55.000 9.73 0.00 38.02 3.42
859 886 0.716108 GCTTGTGTGTGCGCTACTAG 59.284 55.000 9.73 9.90 0.00 2.57
862 890 0.657368 GTTGCTTGTGTGTGCGCTAC 60.657 55.000 9.73 8.79 0.00 3.58
867 895 1.660104 CCTTTTGTTGCTTGTGTGTGC 59.340 47.619 0.00 0.00 0.00 4.57
898 926 0.820871 GAGTGGAGACAAGCGAGGAT 59.179 55.000 0.00 0.00 46.06 3.24
899 927 1.251527 GGAGTGGAGACAAGCGAGGA 61.252 60.000 0.00 0.00 46.06 3.71
900 928 1.216710 GGAGTGGAGACAAGCGAGG 59.783 63.158 0.00 0.00 46.06 4.63
901 929 0.605589 AAGGAGTGGAGACAAGCGAG 59.394 55.000 0.00 0.00 46.06 5.03
902 930 0.603569 GAAGGAGTGGAGACAAGCGA 59.396 55.000 0.00 0.00 46.06 4.93
903 931 0.390472 GGAAGGAGTGGAGACAAGCG 60.390 60.000 0.00 0.00 46.06 4.68
904 932 0.980423 AGGAAGGAGTGGAGACAAGC 59.020 55.000 0.00 0.00 46.06 4.01
905 933 2.495669 GAGAGGAAGGAGTGGAGACAAG 59.504 54.545 0.00 0.00 46.06 3.16
906 934 2.530701 GAGAGGAAGGAGTGGAGACAA 58.469 52.381 0.00 0.00 46.06 3.18
907 935 1.272760 GGAGAGGAAGGAGTGGAGACA 60.273 57.143 0.00 0.00 38.70 3.41
908 936 1.006639 AGGAGAGGAAGGAGTGGAGAC 59.993 57.143 0.00 0.00 0.00 3.36
909 937 1.286553 GAGGAGAGGAAGGAGTGGAGA 59.713 57.143 0.00 0.00 0.00 3.71
910 938 1.687996 GGAGGAGAGGAAGGAGTGGAG 60.688 61.905 0.00 0.00 0.00 3.86
911 939 0.336737 GGAGGAGAGGAAGGAGTGGA 59.663 60.000 0.00 0.00 0.00 4.02
912 940 0.689412 GGGAGGAGAGGAAGGAGTGG 60.689 65.000 0.00 0.00 0.00 4.00
913 941 0.689412 GGGGAGGAGAGGAAGGAGTG 60.689 65.000 0.00 0.00 0.00 3.51
914 942 0.858139 AGGGGAGGAGAGGAAGGAGT 60.858 60.000 0.00 0.00 0.00 3.85
915 943 1.236708 TAGGGGAGGAGAGGAAGGAG 58.763 60.000 0.00 0.00 0.00 3.69
916 944 1.942882 ATAGGGGAGGAGAGGAAGGA 58.057 55.000 0.00 0.00 0.00 3.36
917 945 5.759773 ATATATAGGGGAGGAGAGGAAGG 57.240 47.826 0.00 0.00 0.00 3.46
918 946 7.422089 GGAGTATATATAGGGGAGGAGAGGAAG 60.422 48.148 0.00 0.00 0.00 3.46
919 947 6.393440 GGAGTATATATAGGGGAGGAGAGGAA 59.607 46.154 0.00 0.00 0.00 3.36
920 948 5.918277 GGAGTATATATAGGGGAGGAGAGGA 59.082 48.000 0.00 0.00 0.00 3.71
921 949 5.075344 GGGAGTATATATAGGGGAGGAGAGG 59.925 52.000 0.00 0.00 0.00 3.69
945 996 5.055812 GGCTGAAAAGAGATGATCAGGTAG 58.944 45.833 0.09 0.00 39.69 3.18
1051 1108 3.248171 GCCGACGTCGATGTCAGC 61.248 66.667 37.65 28.50 43.02 4.26
1649 1718 2.112691 TCCTCCACCTCTTCTTCTTCCT 59.887 50.000 0.00 0.00 0.00 3.36
1653 1722 1.719378 TCCTCCTCCACCTCTTCTTCT 59.281 52.381 0.00 0.00 0.00 2.85
1671 1740 2.499693 CTCCTCTTCCACCTCTTCTTCC 59.500 54.545 0.00 0.00 0.00 3.46
2085 2157 2.063266 TCTTGCACGTAAGCTTTACCG 58.937 47.619 3.20 7.81 45.62 4.02
2196 2268 2.029518 CTCCACAGCAGCACGTCA 59.970 61.111 0.00 0.00 0.00 4.35
2256 2328 4.855715 TGGAACACAACAACAAAACTGA 57.144 36.364 0.00 0.00 0.00 3.41
2413 2489 2.225491 GGTGCATGCAAGTTCGTTTCTA 59.775 45.455 24.58 0.00 0.00 2.10
2512 2591 2.933287 TGGAGGGGATGCAACGGT 60.933 61.111 0.00 0.00 0.00 4.83
2548 2627 0.461961 CCCTCTCAACTCCGGCTAAG 59.538 60.000 0.00 0.00 0.00 2.18
2601 2683 3.139397 TGTCCATGGGAAAACTGGTACTT 59.861 43.478 13.02 0.00 31.38 2.24
2731 2825 4.713824 ATTCAACTCCATGCATGAACAG 57.286 40.909 28.31 20.49 34.88 3.16
2840 2945 6.584184 CACACACACTGTTGTATAGAGAAGAG 59.416 42.308 0.00 0.00 33.30 2.85
3175 3280 1.830408 CTAGAGGAGGACAGCCGGG 60.830 68.421 2.18 0.00 39.96 5.73
3176 3281 2.494530 GCTAGAGGAGGACAGCCGG 61.495 68.421 0.00 0.00 39.96 6.13


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

AutoCloner maintained by Alex Coulton.