Multiple sequence alignment - TraesCS4A01G150600

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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 TraesCS4A01G150600 chr4A 100.000 3069 0 0 460 3528 296906229 296903161 0.000000e+00 5668
1 TraesCS4A01G150600 chr4A 100.000 189 0 0 1 189 296906688 296906500 2.020000e-92 350
2 TraesCS4A01G150600 chrUn 96.619 3076 69 9 460 3528 56132576 56129529 0.000000e+00 5072
3 TraesCS4A01G150600 chrUn 93.158 190 12 1 1 189 56132855 56132666 9.650000e-71 278
4 TraesCS4A01G150600 chr4D 96.564 3056 76 6 478 3521 180194385 180191347 0.000000e+00 5035
5 TraesCS4A01G150600 chr4D 93.011 186 12 1 1 185 180195025 180194840 1.610000e-68 270


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 TraesCS4A01G150600 chr4A 296903161 296906688 3527 True 3009.0 5668 100.0000 1 3528 2 chr4A.!!$R1 3527
1 TraesCS4A01G150600 chrUn 56129529 56132855 3326 True 2675.0 5072 94.8885 1 3528 2 chrUn.!!$R1 3527
2 TraesCS4A01G150600 chr4D 180191347 180195025 3678 True 2652.5 5035 94.7875 1 3521 2 chr4D.!!$R1 3520

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
788 960 0.240945 CAATTCCTGCGCTTTCGGTT 59.759 50.0 9.73 0.0 35.95 4.44 F
1507 1683 0.972134 CAGAGGCAGACTTCAGGACA 59.028 55.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2443 2619 0.684153 ATCCAAATGGGCTGGTTCCG 60.684 55.0 0.0 0.0 35.3 4.30 R
2767 2943 1.182667 GGCCAGTGTTGGTATTTCCC 58.817 55.0 0.0 0.0 46.8 3.97 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
88 89 9.887406 ACGTAGTTTTATTTTGAACCATTACAG 57.113 29.630 0.00 0.00 37.78 2.74
609 778 0.634465 GAAGGAGAGGAGGAGGAGGT 59.366 60.000 0.00 0.00 0.00 3.85
786 958 1.137404 CCAATTCCTGCGCTTTCGG 59.863 57.895 9.73 3.98 35.95 4.30
788 960 0.240945 CAATTCCTGCGCTTTCGGTT 59.759 50.000 9.73 0.00 35.95 4.44
990 1165 0.984230 CAGGTTGGAAGTAGGAGCCA 59.016 55.000 0.00 0.00 0.00 4.75
1298 1473 6.262944 TCCATGCTGTTATATTGCTTTGTAGG 59.737 38.462 0.00 0.00 0.00 3.18
1299 1474 6.441274 CATGCTGTTATATTGCTTTGTAGGG 58.559 40.000 0.00 0.00 0.00 3.53
1399 1575 1.406898 CCTAGAGACGATCAGCAAGCA 59.593 52.381 0.00 0.00 0.00 3.91
1507 1683 0.972134 CAGAGGCAGACTTCAGGACA 59.028 55.000 0.00 0.00 0.00 4.02
1543 1719 1.806542 GGCACGATCACTGATGTTGTT 59.193 47.619 0.00 0.00 0.00 2.83
1828 2004 2.195741 ATGGAATGAGGATGGATGCG 57.804 50.000 0.00 0.00 0.00 4.73
2080 2256 3.119459 TCAACTCACTGGCTCGTAATCTC 60.119 47.826 0.00 0.00 0.00 2.75
2185 2361 5.124776 TGGAATCGGGAATAACAATGTGAAC 59.875 40.000 0.00 0.00 0.00 3.18
2247 2423 3.006677 GGGCTATGGCAGTGGGAA 58.993 61.111 2.58 0.00 40.87 3.97
2260 2436 2.825532 CAGTGGGAACTTTGGTTATGGG 59.174 50.000 0.00 0.00 35.58 4.00
2281 2457 4.340263 GGTCGACTGAAAACAACTTCAAC 58.660 43.478 16.46 0.00 34.96 3.18
2290 2466 3.933861 AACAACTTCAACCTGAGTCCT 57.066 42.857 0.00 0.00 0.00 3.85
2392 2568 3.195698 GATTCGTCAGCGGGTGGC 61.196 66.667 7.42 4.26 44.05 5.01
2553 2729 8.410141 ACAGATAGAGGTTAGATCTTTTCTTCG 58.590 37.037 0.00 0.00 35.79 3.79
2579 2755 9.476202 GTTGTATTATCCTTGTGCTTTTCTTTT 57.524 29.630 0.00 0.00 0.00 2.27
2629 2805 4.581077 TCATGTACTAGCAGCATCAGAG 57.419 45.455 0.00 0.00 0.00 3.35
2642 2818 3.522750 AGCATCAGAGAAAGACCCTCAAT 59.477 43.478 0.00 0.00 33.25 2.57
2647 2823 5.940617 TCAGAGAAAGACCCTCAATTTTGA 58.059 37.500 0.00 0.00 35.57 2.69
2665 2841 4.981806 TTGAAACTTTCCACTGAACTGG 57.018 40.909 0.00 0.00 0.00 4.00
2695 2871 5.725110 AATGCTTAGACAATGTAGCTTCG 57.275 39.130 7.96 0.00 34.77 3.79
2703 2879 8.942338 TTAGACAATGTAGCTTCGAATATGTT 57.058 30.769 0.00 0.00 0.00 2.71
2714 2890 5.611374 CTTCGAATATGTTGTATCCCCTGT 58.389 41.667 0.00 0.00 0.00 4.00
2716 2892 3.498397 CGAATATGTTGTATCCCCTGTGC 59.502 47.826 0.00 0.00 0.00 4.57
2793 2969 1.042559 ACCAACACTGGCCTTGGTTG 61.043 55.000 18.91 19.62 46.67 3.77
2811 2987 3.821033 GGTTGTCCCAGGATAATGCATAC 59.179 47.826 0.00 0.00 0.00 2.39
2829 3005 7.213216 TGCATACATGTAGTTGTCACATTTT 57.787 32.000 11.91 0.00 34.39 1.82
2901 3077 8.758829 ACCATGATACAGAAGTTACTGTCATTA 58.241 33.333 10.12 3.44 46.36 1.90
2970 3146 3.179443 TCTACTTCATGTCCCAATCGC 57.821 47.619 0.00 0.00 0.00 4.58
3309 3485 8.091449 ACTGTCTTGTCCTAGAAACTTGATTAG 58.909 37.037 0.00 0.00 0.00 1.73
3311 3487 7.872993 TGTCTTGTCCTAGAAACTTGATTAGTG 59.127 37.037 0.00 0.00 37.12 2.74
3333 3509 7.421955 GTGTTTTTCACATTCAAACATTTGC 57.578 32.000 0.00 0.00 45.51 3.68
3355 3531 4.392138 GCCATCTGTGAACTTAACCTACAC 59.608 45.833 0.00 0.00 0.00 2.90
3411 3587 0.454600 CCATGAACTGCAGCCATGAC 59.545 55.000 33.54 14.82 39.86 3.06
3502 3679 8.158169 TCAACGATAACGAGGTGTATTAGTAT 57.842 34.615 0.00 0.00 42.66 2.12
3503 3680 8.071967 TCAACGATAACGAGGTGTATTAGTATG 58.928 37.037 0.00 0.00 42.66 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 1.858458 TGCTTATGCATACTCGCGTTC 59.142 47.619 5.74 0.00 45.31 3.95
609 778 2.349376 CATACCACGGCACCACCA 59.651 61.111 0.00 0.00 39.03 4.17
740 912 0.966875 ATGGAGCAGAATTTGGCGCA 60.967 50.000 10.83 0.00 34.54 6.09
786 958 1.971695 CCCGGCTCCAAGAACCAAC 60.972 63.158 0.00 0.00 0.00 3.77
788 960 4.344865 GCCCGGCTCCAAGAACCA 62.345 66.667 0.71 0.00 0.00 3.67
990 1165 2.841988 GCCTCCATCTCCGGCTCT 60.842 66.667 0.00 0.00 40.62 4.09
1323 1499 7.992033 ACAATCCAAACATTCTGAATTTTCCAA 59.008 29.630 0.00 0.00 0.00 3.53
1399 1575 0.764890 TGCCACCACTCTTGCTAAGT 59.235 50.000 0.00 0.00 0.00 2.24
1507 1683 3.505680 TCGTGCCAAACTGCTCAAAATAT 59.494 39.130 0.00 0.00 0.00 1.28
1828 2004 2.924421 CCTGATAGAAGCCCAAACCTC 58.076 52.381 0.00 0.00 0.00 3.85
2080 2256 4.510167 ATTGAGACCTGAATTACCCCAG 57.490 45.455 0.00 0.00 0.00 4.45
2247 2423 2.635915 TCAGTCGACCCATAACCAAAGT 59.364 45.455 13.01 0.00 0.00 2.66
2260 2436 4.094442 AGGTTGAAGTTGTTTTCAGTCGAC 59.906 41.667 7.70 7.70 38.25 4.20
2281 2457 1.134280 CCATAAGCACCAGGACTCAGG 60.134 57.143 0.00 0.00 0.00 3.86
2290 2466 2.375174 AGTGTTCCTTCCATAAGCACCA 59.625 45.455 0.00 0.00 28.77 4.17
2443 2619 0.684153 ATCCAAATGGGCTGGTTCCG 60.684 55.000 0.00 0.00 35.30 4.30
2553 2729 9.476202 AAAAGAAAAGCACAAGGATAATACAAC 57.524 29.630 0.00 0.00 0.00 3.32
2582 2758 9.730420 AACTAGTAGTTAAACATTTGCAAACTG 57.270 29.630 15.41 15.52 36.52 3.16
2629 2805 7.224753 GGAAAGTTTCAAAATTGAGGGTCTTTC 59.775 37.037 17.16 20.33 38.61 2.62
2642 2818 5.245075 ACCAGTTCAGTGGAAAGTTTCAAAA 59.755 36.000 17.16 0.00 40.44 2.44
2695 2871 4.718961 AGCACAGGGGATACAACATATTC 58.281 43.478 0.00 0.00 39.74 1.75
2703 2879 2.930950 GCATTTAGCACAGGGGATACA 58.069 47.619 0.00 0.00 44.79 2.29
2716 2892 7.037438 ACTTGAGCATTAACAATGGCATTTAG 58.963 34.615 10.65 2.79 39.31 1.85
2755 2931 9.787435 GTGTTGGTATTTCCCATACTGAATATA 57.213 33.333 0.00 0.00 33.60 0.86
2756 2932 8.502738 AGTGTTGGTATTTCCCATACTGAATAT 58.497 33.333 0.00 0.00 33.53 1.28
2757 2933 7.773224 CAGTGTTGGTATTTCCCATACTGAATA 59.227 37.037 14.81 0.00 44.56 1.75
2758 2934 6.603201 CAGTGTTGGTATTTCCCATACTGAAT 59.397 38.462 14.81 0.00 44.56 2.57
2759 2935 5.943416 CAGTGTTGGTATTTCCCATACTGAA 59.057 40.000 14.81 0.00 44.56 3.02
2760 2936 5.496556 CAGTGTTGGTATTTCCCATACTGA 58.503 41.667 14.81 0.00 44.56 3.41
2761 2937 4.640201 CCAGTGTTGGTATTTCCCATACTG 59.360 45.833 13.74 13.74 43.10 2.74
2762 2938 4.855340 CCAGTGTTGGTATTTCCCATACT 58.145 43.478 0.00 0.00 39.79 2.12
2763 2939 3.380320 GCCAGTGTTGGTATTTCCCATAC 59.620 47.826 0.00 0.00 46.80 2.39
2764 2940 3.626222 GGCCAGTGTTGGTATTTCCCATA 60.626 47.826 0.00 0.00 46.80 2.74
2765 2941 2.456577 GCCAGTGTTGGTATTTCCCAT 58.543 47.619 0.00 0.00 46.80 4.00
2766 2942 1.549037 GGCCAGTGTTGGTATTTCCCA 60.549 52.381 0.00 0.00 46.80 4.37
2767 2943 1.182667 GGCCAGTGTTGGTATTTCCC 58.817 55.000 0.00 0.00 46.80 3.97
2768 2944 2.215942 AGGCCAGTGTTGGTATTTCC 57.784 50.000 5.01 0.00 46.80 3.13
2769 2945 2.231235 CCAAGGCCAGTGTTGGTATTTC 59.769 50.000 12.35 0.00 46.80 2.17
2770 2946 2.247358 CCAAGGCCAGTGTTGGTATTT 58.753 47.619 12.35 0.00 46.80 1.40
2771 2947 1.923356 CCAAGGCCAGTGTTGGTATT 58.077 50.000 12.35 0.00 46.80 1.89
2793 2969 4.655963 ACATGTATGCATTATCCTGGGAC 58.344 43.478 3.54 0.00 31.99 4.46
2811 2987 6.803320 GGACATGAAAATGTGACAACTACATG 59.197 38.462 17.49 17.49 38.67 3.21
2829 3005 5.685861 GCCTGTCTAGATTTCATGGACATGA 60.686 44.000 10.75 10.75 45.30 3.07
2901 3077 7.972832 TGGTAACGACATCTTTTTAGTTCAT 57.027 32.000 0.00 0.00 42.51 2.57
2943 3119 5.854010 TGGGACATGAAGTAGATAGACAC 57.146 43.478 0.00 0.00 0.00 3.67
3039 3215 6.796426 TCATTTTCACGTAACAATTGGAACA 58.204 32.000 10.83 0.00 0.00 3.18
3067 3243 7.122048 TCCATCATAAACAACCATGAACCATA 58.878 34.615 0.00 0.00 34.96 2.74
3309 3485 6.468637 GGCAAATGTTTGAATGTGAAAAACAC 59.531 34.615 9.53 0.00 44.14 3.32
3311 3487 6.549952 TGGCAAATGTTTGAATGTGAAAAAC 58.450 32.000 9.53 0.00 40.55 2.43
3333 3509 4.935808 GGTGTAGGTTAAGTTCACAGATGG 59.064 45.833 0.00 0.00 0.00 3.51
3411 3587 3.705579 TGCACCAATTCTTTCATATGGGG 59.294 43.478 2.13 0.00 37.63 4.96
3502 3679 6.355747 TGGAGATACAACATGCATATTCACA 58.644 36.000 0.00 0.00 0.00 3.58
3503 3680 6.866010 TGGAGATACAACATGCATATTCAC 57.134 37.500 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.