Multiple sequence alignment - TraesCS5D01G041200

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 TraesCS5D01G041200 chr5D 100.000 2896 0 0 1 2896 41771250 41768355 0 5349
1 TraesCS5D01G041200 chr5D 95.882 2841 110 4 1 2839 350369417 350366582 0 4591
2 TraesCS5D01G041200 chr5D 95.107 2841 127 6 1 2838 320660717 320663548 0 4466
3 TraesCS5D01G041200 chr5D 94.519 2846 142 7 1 2837 134489641 134486801 0 4379
4 TraesCS5D01G041200 chr5D 94.382 2848 144 8 1 2839 530733314 530736154 0 4359
5 TraesCS5D01G041200 chr7D 95.918 2842 108 7 1 2838 550636001 550638838 0 4599
6 TraesCS5D01G041200 chr5B 95.011 2846 135 4 1 2840 184289059 184291903 0 4462
7 TraesCS5D01G041200 chr6B 94.482 2845 145 6 1 2837 197818314 197815474 0 4373
8 TraesCS5D01G041200 chr6B 94.480 2844 146 5 5 2838 681901036 681903878 0 4372
9 TraesCS5D01G041200 chr6B 94.339 2844 152 5 1 2835 521149628 521146785 0 4351


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 TraesCS5D01G041200 chr5D 41768355 41771250 2895 True 5349 5349 100.000 1 2896 1 chr5D.!!$R1 2895
1 TraesCS5D01G041200 chr5D 350366582 350369417 2835 True 4591 4591 95.882 1 2839 1 chr5D.!!$R3 2838
2 TraesCS5D01G041200 chr5D 320660717 320663548 2831 False 4466 4466 95.107 1 2838 1 chr5D.!!$F1 2837
3 TraesCS5D01G041200 chr5D 134486801 134489641 2840 True 4379 4379 94.519 1 2837 1 chr5D.!!$R2 2836
4 TraesCS5D01G041200 chr5D 530733314 530736154 2840 False 4359 4359 94.382 1 2839 1 chr5D.!!$F2 2838
5 TraesCS5D01G041200 chr7D 550636001 550638838 2837 False 4599 4599 95.918 1 2838 1 chr7D.!!$F1 2837
6 TraesCS5D01G041200 chr5B 184289059 184291903 2844 False 4462 4462 95.011 1 2840 1 chr5B.!!$F1 2839
7 TraesCS5D01G041200 chr6B 197815474 197818314 2840 True 4373 4373 94.482 1 2837 1 chr6B.!!$R1 2836
8 TraesCS5D01G041200 chr6B 681901036 681903878 2842 False 4372 4372 94.480 5 2838 1 chr6B.!!$F1 2833
9 TraesCS5D01G041200 chr6B 521146785 521149628 2843 True 4351 4351 94.339 1 2835 1 chr6B.!!$R2 2834

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
169 172 0.108138 CCATTCTTCCTCCGTTCGCT 60.108 55.0 0.00 0.00 0.00 4.93 F
1029 1048 0.534203 AGCCGTTCATGTCCACGTTT 60.534 50.0 11.87 0.71 34.47 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1403 0.834687 AACTCAGCGTCCCTTGGGTA 60.835 55.0 5.51 0.0 0.00 3.69 R
2852 2875 0.106519 CTTCCCTTCCCGGATGCAAT 60.107 55.0 0.73 0.0 33.16 3.56 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
169 172 0.108138 CCATTCTTCCTCCGTTCGCT 60.108 55.000 0.00 0.00 0.00 4.93
178 181 2.048503 CCGTTCGCTCTTTCCCGT 60.049 61.111 0.00 0.00 0.00 5.28
233 236 3.849951 ATCTTCATCGGCCGGCGT 61.850 61.111 27.83 9.24 0.00 5.68
281 284 1.361668 CGGCGTTCATCTTCCACCAG 61.362 60.000 0.00 0.00 0.00 4.00
311 314 2.033141 TCCTCAAGCTGCAGCCAC 59.967 61.111 34.39 8.53 43.38 5.01
408 411 5.372343 AGATGCATGGTTGATTAGTGGTA 57.628 39.130 2.46 0.00 0.00 3.25
415 418 6.488006 GCATGGTTGATTAGTGGTATGATCTT 59.512 38.462 0.00 0.00 0.00 2.40
419 422 8.106462 TGGTTGATTAGTGGTATGATCTTTGAA 58.894 33.333 0.00 0.00 0.00 2.69
465 468 2.159254 CGGTTGCAATTTGTGATAGGGG 60.159 50.000 0.59 0.00 0.00 4.79
601 604 7.971183 TGTAGCATGTTGTTTGTTGTAGATA 57.029 32.000 0.00 0.00 0.00 1.98
734 738 2.235155 TCCGGTATGTTGTGTGCTATGT 59.765 45.455 0.00 0.00 0.00 2.29
773 777 4.501571 GCTACGATTGTAGGACATGACCAT 60.502 45.833 19.70 0.77 46.72 3.55
891 895 2.095212 TGATTCAGAGGTGTTCGAGTCG 60.095 50.000 6.09 6.09 0.00 4.18
919 923 2.428530 CTCTATGTGCCAGTAGTGCTCA 59.571 50.000 0.00 0.00 36.74 4.26
1029 1048 0.534203 AGCCGTTCATGTCCACGTTT 60.534 50.000 11.87 0.71 34.47 3.60
1137 1157 1.068588 CAGGTGTTCGAGTTCTGTGGA 59.931 52.381 0.00 0.00 0.00 4.02
1374 1394 6.020678 GCAACTAACAACACTTGTGTTTCATC 60.021 38.462 15.46 0.00 44.59 2.92
1383 1403 5.163195 ACACTTGTGTTTCATCCTTAGGACT 60.163 40.000 1.74 0.00 32.98 3.85
1629 1650 1.342975 GGAAGAGGAAGAGAGGAGGCT 60.343 57.143 0.00 0.00 0.00 4.58
1643 1664 1.433121 GAGGCTTGATGGAGGAGGAT 58.567 55.000 0.00 0.00 0.00 3.24
1735 1756 1.755393 GACGTCCACCCTGACCTGTT 61.755 60.000 3.51 0.00 31.35 3.16
1782 1803 1.750780 AGCGACGAGGCTCTCATGA 60.751 57.895 13.50 0.00 39.61 3.07
2046 2067 6.395426 TTGGTGAGGTGGTATATACTAACG 57.605 41.667 12.54 0.00 28.83 3.18
2065 2086 1.688772 GCCTCATGCTGATGGTGAAT 58.311 50.000 0.00 0.00 36.87 2.57
2089 2110 0.323725 GGTGGTAGGACGACACCCTA 60.324 60.000 0.00 0.00 46.90 3.53
2255 2276 1.220529 TCAACTCTTGCTCTTGTGCG 58.779 50.000 0.00 0.00 35.36 5.34
2297 2318 1.068474 GTGTTCATCGGTGAGGTTCG 58.932 55.000 0.00 0.00 35.39 3.95
2312 2333 5.127682 GTGAGGTTCGAGGGGTTTATAGTTA 59.872 44.000 0.00 0.00 0.00 2.24
2332 2353 1.941377 ATGGGAAGAAGCCAATGCAA 58.059 45.000 0.00 0.00 41.13 4.08
2379 2400 7.411808 ACAACTATAGAGGGTTCAAGACTAGA 58.588 38.462 6.78 0.00 0.00 2.43
2382 2403 7.588169 ACTATAGAGGGTTCAAGACTAGACAT 58.412 38.462 6.78 0.00 0.00 3.06
2406 2427 1.801178 GCAGAACAAGCTTACTTCGCT 59.199 47.619 0.00 0.00 39.94 4.93
2451 2474 0.465460 GTGGACAGTGCCAAGGTTGA 60.465 55.000 7.71 0.00 40.20 3.18
2453 2476 1.341482 TGGACAGTGCCAAGGTTGAAA 60.341 47.619 4.08 0.00 34.31 2.69
2491 2514 2.301870 TGCTAAGGTGGATCGTCAGTTT 59.698 45.455 0.00 0.00 0.00 2.66
2568 2591 1.294138 GGCGTTGGTGTGCTAGGTA 59.706 57.895 0.00 0.00 0.00 3.08
2662 2685 0.673644 GTGTTCATGTGCCGCTAGGT 60.674 55.000 0.00 0.00 40.50 3.08
2726 2749 0.784495 ACAGGGACTAGGGACACAGA 59.216 55.000 0.00 0.00 36.02 3.41
2769 2792 3.004862 ACGTATTAGGGCCTGTTTTTCG 58.995 45.455 18.53 15.00 0.00 3.46
2793 2816 0.991920 CCAGGCTGGGTTAAGAAGGA 59.008 55.000 26.34 0.00 32.67 3.36
2797 2820 4.597507 CCAGGCTGGGTTAAGAAGGATATA 59.402 45.833 26.34 0.00 32.67 0.86
2802 2825 7.516209 AGGCTGGGTTAAGAAGGATATACAATA 59.484 37.037 0.00 0.00 0.00 1.90
2806 2829 9.096823 TGGGTTAAGAAGGATATACAATACGAT 57.903 33.333 0.00 0.00 0.00 3.73
2840 2863 0.874175 GAAACCAAACACGCCCTTGC 60.874 55.000 0.00 0.00 0.00 4.01
2841 2864 2.304901 AAACCAAACACGCCCTTGCC 62.305 55.000 0.00 0.00 0.00 4.52
2842 2865 4.341502 CCAAACACGCCCTTGCCG 62.342 66.667 0.00 0.00 0.00 5.69
2843 2866 3.283684 CAAACACGCCCTTGCCGA 61.284 61.111 0.00 0.00 0.00 5.54
2844 2867 3.284449 AAACACGCCCTTGCCGAC 61.284 61.111 0.00 0.00 0.00 4.79
2858 2881 2.505982 CGACCCCTCGGATTGCAT 59.494 61.111 0.00 0.00 36.16 3.96
2859 2882 1.595382 CGACCCCTCGGATTGCATC 60.595 63.158 0.00 0.00 36.16 3.91
2860 2883 1.227973 GACCCCTCGGATTGCATCC 60.228 63.158 5.39 5.39 46.22 3.51
2867 2890 4.164258 GGATTGCATCCGGGAAGG 57.836 61.111 0.00 0.00 40.13 3.46
2868 2891 1.529244 GGATTGCATCCGGGAAGGG 60.529 63.158 0.00 0.00 40.13 3.95
2869 2892 1.531748 GATTGCATCCGGGAAGGGA 59.468 57.895 0.00 0.00 41.52 4.20
2870 2893 0.106719 GATTGCATCCGGGAAGGGAA 60.107 55.000 0.00 4.57 40.09 3.97
2871 2894 0.106519 ATTGCATCCGGGAAGGGAAG 60.107 55.000 0.00 0.00 40.09 3.46
2872 2895 2.193248 GCATCCGGGAAGGGAAGG 59.807 66.667 0.00 0.00 40.09 3.46
2873 2896 2.919043 CATCCGGGAAGGGAAGGG 59.081 66.667 0.00 0.00 40.09 3.95
2874 2897 3.097162 ATCCGGGAAGGGAAGGGC 61.097 66.667 0.00 0.00 40.09 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 68 0.254747 ATCCTCCCGCCGATTTTTCA 59.745 50.000 0.00 0.00 0.00 2.69
115 118 1.608154 GGTGAGGGAGGGGCTAAAC 59.392 63.158 0.00 0.00 0.00 2.01
233 236 3.282745 GAGCTCTGACGCCGTGGAA 62.283 63.158 6.43 0.00 0.00 3.53
311 314 1.363744 GATTGAACTCACAGAGGCCG 58.636 55.000 0.00 0.00 33.35 6.13
381 384 7.016563 ACCACTAATCAACCATGCATCTAGATA 59.983 37.037 4.54 0.00 0.00 1.98
408 411 7.121382 ACCAACCATATCAGTTCAAAGATCAT 58.879 34.615 0.00 0.00 0.00 2.45
415 418 4.406456 AGCAACCAACCATATCAGTTCAA 58.594 39.130 0.00 0.00 0.00 2.69
419 422 3.885297 GCATAGCAACCAACCATATCAGT 59.115 43.478 0.00 0.00 0.00 3.41
465 468 4.572389 CCTACCACATGCTTGAACATCTAC 59.428 45.833 6.60 0.00 0.00 2.59
601 604 7.160049 CAGACAATCTATGAGCAGGAACATAT 58.840 38.462 0.00 0.00 0.00 1.78
734 738 1.798223 GTAGCACGCATTGACAGTGAA 59.202 47.619 1.52 0.00 38.06 3.18
891 895 1.771255 ACTGGCACATAGAGGGAATCC 59.229 52.381 0.00 0.00 38.20 3.01
919 923 0.964358 GCAGCAGGAGTTGGCTCAAT 60.964 55.000 0.00 0.00 43.37 2.57
1029 1048 2.874086 CTCACACATCTTGTTCAGCACA 59.126 45.455 0.00 0.00 35.67 4.57
1172 1192 1.166129 TCGACTTCTCCACTTCCTCG 58.834 55.000 0.00 0.00 0.00 4.63
1305 1325 4.225267 GGACAGTATGAAAAGGAAGAGGGA 59.775 45.833 0.00 0.00 39.69 4.20
1383 1403 0.834687 AACTCAGCGTCCCTTGGGTA 60.835 55.000 5.51 0.00 0.00 3.69
1629 1650 5.848369 AGACATTGATATCCTCCTCCATCAA 59.152 40.000 0.00 0.00 40.57 2.57
1643 1664 5.416639 AGTCATGCTGCAAAAGACATTGATA 59.583 36.000 24.81 0.00 31.84 2.15
1735 1756 2.359850 GGGTCATGACAGCGCCAA 60.360 61.111 26.47 0.00 0.00 4.52
1782 1803 3.067091 CAGGTGGCTGAGAGCTGT 58.933 61.111 0.00 0.00 41.99 4.40
2065 2086 1.005867 GTCGTCCTACCACCGCAAA 60.006 57.895 0.00 0.00 0.00 3.68
2089 2110 3.825908 ACCTACCACCACATCCAAAAT 57.174 42.857 0.00 0.00 0.00 1.82
2297 2318 7.145474 TCTTCCCATTAACTATAAACCCCTC 57.855 40.000 0.00 0.00 0.00 4.30
2312 2333 1.941377 TGCATTGGCTTCTTCCCATT 58.059 45.000 0.00 0.00 41.91 3.16
2332 2353 3.605634 TGTTGCTATACGATGCCACTTT 58.394 40.909 0.00 0.00 0.00 2.66
2379 2400 1.325355 AAGCTTGTTCTGCTGCATGT 58.675 45.000 1.31 0.00 41.03 3.21
2382 2403 2.260844 AGTAAGCTTGTTCTGCTGCA 57.739 45.000 9.86 0.88 41.03 4.41
2451 2474 2.099756 GCAGCTTCCACTTTGACAGTTT 59.900 45.455 0.00 0.00 30.92 2.66
2453 2476 1.133976 AGCAGCTTCCACTTTGACAGT 60.134 47.619 0.00 0.00 35.35 3.55
2491 2514 0.767375 AGTTCTTCAGCTTCAGGCCA 59.233 50.000 5.01 0.00 43.05 5.36
2568 2591 5.068636 GGTGAGCTTATCCACAATGATCAT 58.931 41.667 1.18 1.18 35.13 2.45
2662 2685 0.392336 GTTTGGTTGGCTGCATTGGA 59.608 50.000 0.50 0.00 0.00 3.53
2797 2820 6.932400 TCAGTTTGGAACAGTAATCGTATTGT 59.068 34.615 0.00 0.00 42.39 2.71
2802 2825 5.008316 GGTTTCAGTTTGGAACAGTAATCGT 59.992 40.000 2.92 0.00 42.39 3.73
2806 2829 6.015350 TGTTTGGTTTCAGTTTGGAACAGTAA 60.015 34.615 2.92 0.00 42.39 2.24
2841 2864 1.595382 GATGCAATCCGAGGGGTCG 60.595 63.158 0.00 0.00 37.38 4.79
2842 2865 4.464262 GATGCAATCCGAGGGGTC 57.536 61.111 0.00 0.00 37.38 4.46
2851 2874 0.106719 TTCCCTTCCCGGATGCAATC 60.107 55.000 0.73 0.00 44.55 2.67
2852 2875 0.106519 CTTCCCTTCCCGGATGCAAT 60.107 55.000 0.73 0.00 33.16 3.56
2853 2876 1.302949 CTTCCCTTCCCGGATGCAA 59.697 57.895 0.73 0.00 33.16 4.08
2854 2877 2.679342 CCTTCCCTTCCCGGATGCA 61.679 63.158 0.73 0.00 33.16 3.96
2855 2878 2.193248 CCTTCCCTTCCCGGATGC 59.807 66.667 0.73 0.00 33.16 3.91
2856 2879 2.919043 CCCTTCCCTTCCCGGATG 59.081 66.667 0.73 0.00 33.16 3.51
2857 2880 3.097162 GCCCTTCCCTTCCCGGAT 61.097 66.667 0.73 0.00 33.16 4.18


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

AutoCloner maintained by Alex Coulton.