Multiple sequence alignment - TraesCS3A01G367800

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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 TraesCS3A01G367800 chr3A 100.000 3104 0 0 1 3104 616710546 616713649 0.000000e+00 5733.0
1 TraesCS3A01G367800 chr3A 82.812 64 7 3 13 73 608142469 608142407 2.000000e-03 54.7
2 TraesCS3A01G367800 chr3D 92.079 1982 89 20 2 1917 474431454 474433433 0.000000e+00 2728.0
3 TraesCS3A01G367800 chr3D 94.084 862 43 6 1791 2646 474433343 474434202 0.000000e+00 1303.0
4 TraesCS3A01G367800 chr3D 90.127 395 21 7 2723 3104 474434211 474434600 5.980000e-137 497.0
5 TraesCS3A01G367800 chr3D 88.596 114 10 1 1775 1885 474433366 474433479 5.400000e-28 135.0
6 TraesCS3A01G367800 chr3D 86.667 75 7 1 1775 1846 474433405 474433479 2.570000e-11 80.5
7 TraesCS3A01G367800 chr3B 90.891 1965 101 21 2 1917 630590572 630592507 0.000000e+00 2566.0
8 TraesCS3A01G367800 chr3B 93.035 804 37 5 1791 2593 630592420 630593205 0.000000e+00 1157.0
9 TraesCS3A01G367800 chr3B 91.810 525 25 8 2592 3104 630593287 630593805 0.000000e+00 715.0
10 TraesCS3A01G367800 chr3B 95.745 47 2 0 1775 1821 630592479 630592525 3.320000e-10 76.8
11 TraesCS3A01G367800 chr7D 88.525 61 5 2 17 75 29758791 29758731 4.290000e-09 73.1
12 TraesCS3A01G367800 chr1D 81.522 92 9 8 17 103 399180346 399180258 5.550000e-08 69.4
13 TraesCS3A01G367800 chr1D 86.792 53 5 2 336 387 489744764 489744713 1.200000e-04 58.4
14 TraesCS3A01G367800 chr1D 90.476 42 3 1 17 58 429590973 429590933 2.000000e-03 54.7
15 TraesCS3A01G367800 chr5D 83.117 77 8 3 5 77 128650998 128650923 7.180000e-07 65.8
16 TraesCS3A01G367800 chr5D 83.824 68 6 5 9 72 528555003 528554937 3.340000e-05 60.2
17 TraesCS3A01G367800 chr7B 100.000 28 0 0 16 43 417620454 417620427 6.000000e-03 52.8


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 TraesCS3A01G367800 chr3A 616710546 616713649 3103 False 5733.0 5733 100.00000 1 3104 1 chr3A.!!$F1 3103
1 TraesCS3A01G367800 chr3D 474431454 474434600 3146 False 948.7 2728 90.31060 2 3104 5 chr3D.!!$F1 3102
2 TraesCS3A01G367800 chr3B 630590572 630593805 3233 False 1128.7 2566 92.87025 2 3104 4 chr3B.!!$F1 3102

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
976 1044 2.132996 CCCCACACCAAAGCAAGCA 61.133 57.895 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2836 3045 0.035343 GGACTAGGGTGAGTTTGCCC 60.035 60.0 0.0 0.0 45.16 5.36 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
90 92 5.408880 TGTTTTTATTCGGATTTTCCCCC 57.591 39.130 0.00 0.00 31.13 5.40
91 93 5.088026 TGTTTTTATTCGGATTTTCCCCCT 58.912 37.500 0.00 0.00 31.13 4.79
92 94 5.544562 TGTTTTTATTCGGATTTTCCCCCTT 59.455 36.000 0.00 0.00 31.13 3.95
179 187 8.092687 AGAATTCATGAAGTTTTCCAAATCCAG 58.907 33.333 14.54 0.00 0.00 3.86
181 189 5.147032 TCATGAAGTTTTCCAAATCCAGGT 58.853 37.500 0.00 0.00 0.00 4.00
412 439 5.888724 TGACGCCATTTTATTTAATCTGGGA 59.111 36.000 0.00 0.00 0.00 4.37
454 481 8.283340 TGAATATTTTTAAAAACCGGTCAACG 57.717 30.769 15.35 0.00 43.80 4.10
544 571 7.488322 TGAAATCCGGGAACATTATTCAAATC 58.512 34.615 0.00 0.00 0.00 2.17
659 687 9.780186 AAAATTTTGGAACATTTATTAACCCGA 57.220 25.926 1.75 0.00 39.30 5.14
660 688 9.780186 AAATTTTGGAACATTTATTAACCCGAA 57.220 25.926 0.00 0.00 39.30 4.30
769 817 6.448207 TGACATGCCGATCATTTTTAATGA 57.552 33.333 4.72 4.72 31.79 2.57
775 823 5.576384 TGCCGATCATTTTTAATGAAGCAAC 59.424 36.000 16.17 5.12 33.09 4.17
792 840 8.539770 TGAAGCAACAAATAAAACACAAAAGA 57.460 26.923 0.00 0.00 0.00 2.52
976 1044 2.132996 CCCCACACCAAAGCAAGCA 61.133 57.895 0.00 0.00 0.00 3.91
1016 1090 3.727258 CATGGCTTCCCCGTCCCA 61.727 66.667 0.00 0.00 35.87 4.37
1596 1670 1.381191 TCCTGAGCCGCAGTATCCA 60.381 57.895 0.00 0.00 43.33 3.41
1692 1766 2.092699 GGACCAGTACTACCGTCCTAGT 60.093 54.545 20.84 0.55 41.36 2.57
1734 1811 0.738975 CGCCTCCATCTCAGTACGAA 59.261 55.000 0.00 0.00 0.00 3.85
1773 1850 0.904649 CACCTGTGGAGTATGGCAGA 59.095 55.000 0.00 0.00 0.00 4.26
1824 1901 1.131638 TGACTGGGCAGTATGATCCC 58.868 55.000 0.00 0.00 42.66 3.85
1887 2003 1.122019 GGACTGAGGGTGTGACTGGT 61.122 60.000 0.00 0.00 0.00 4.00
1919 2035 2.285743 AGGAAGGACTGAGGGGGC 60.286 66.667 0.00 0.00 0.00 5.80
1920 2036 2.610859 GGAAGGACTGAGGGGGCA 60.611 66.667 0.00 0.00 0.00 5.36
2114 2230 4.709886 TCGAGAGTATTGATGGGAGTTCAA 59.290 41.667 0.00 0.00 37.49 2.69
2118 2234 5.249393 AGAGTATTGATGGGAGTTCAAGTGT 59.751 40.000 0.00 0.00 36.60 3.55
2139 2255 0.035317 TGAGGATGCGCTGTGAGTTT 59.965 50.000 9.73 0.00 0.00 2.66
2263 2379 4.241999 GTGCTTATGGCCTGCGCG 62.242 66.667 3.32 0.00 40.92 6.86
2390 2507 9.877178 CTTAAGTCTGTTCCATTAGTATCTGTT 57.123 33.333 0.00 0.00 0.00 3.16
2418 2535 2.102109 TTGGTGCTTGGCATTGCAGG 62.102 55.000 14.50 0.90 41.91 4.85
2519 2638 6.346477 TGCTTCTACACTCAAATCTACACT 57.654 37.500 0.00 0.00 0.00 3.55
2522 2641 6.647067 GCTTCTACACTCAAATCTACACTTGT 59.353 38.462 0.00 0.00 0.00 3.16
2556 2675 3.060070 GCATTTTGCTGCAGTGTTTTCTC 60.060 43.478 16.64 0.00 40.96 2.87
2562 2681 3.375610 TGCTGCAGTGTTTTCTCGTTTTA 59.624 39.130 16.64 0.00 0.00 1.52
2566 2685 5.507077 TGCAGTGTTTTCTCGTTTTATGTC 58.493 37.500 0.00 0.00 0.00 3.06
2569 2688 7.041712 TGCAGTGTTTTCTCGTTTTATGTCATA 60.042 33.333 0.00 0.00 0.00 2.15
2573 2692 8.071368 GTGTTTTCTCGTTTTATGTCATAACCA 58.929 33.333 4.71 0.00 0.00 3.67
2623 2825 3.441572 AGCCACAATATGTTCAGAGTTGC 59.558 43.478 0.00 0.00 0.00 4.17
2671 2873 5.974108 ACGTAGTGTAATTGGTAATGCTCT 58.026 37.500 0.00 0.00 42.51 4.09
2672 2874 5.810587 ACGTAGTGTAATTGGTAATGCTCTG 59.189 40.000 0.00 0.00 42.51 3.35
2703 2905 5.189736 AGTGAATGTGACCCATAGAAAGCTA 59.810 40.000 0.00 0.00 31.97 3.32
2704 2906 6.058183 GTGAATGTGACCCATAGAAAGCTAT 58.942 40.000 0.00 0.00 37.83 2.97
2705 2907 7.071196 AGTGAATGTGACCCATAGAAAGCTATA 59.929 37.037 0.00 0.00 35.58 1.31
2707 2909 8.097038 TGAATGTGACCCATAGAAAGCTATATC 58.903 37.037 0.00 0.00 35.58 1.63
2712 2914 9.343539 GTGACCCATAGAAAGCTATATCTTTTT 57.656 33.333 3.23 0.89 36.50 1.94
2745 2947 6.201044 CGGAAAACATACGAAGCTAGATTGAT 59.799 38.462 0.00 0.00 0.00 2.57
2754 2956 3.251479 AGCTAGATTGATGTTGCACGA 57.749 42.857 0.00 0.00 0.00 4.35
2778 2980 7.008266 CGAATTTGTTTCAGAATAAATCCACCG 59.992 37.037 6.43 5.48 36.10 4.94
2796 2998 4.142556 CCACCGTAATGGGAAACAATGTAC 60.143 45.833 0.00 0.00 44.64 2.90
2825 3034 9.981114 AGATTTTGTACACCTCCAAATTTTAAG 57.019 29.630 0.00 0.00 31.20 1.85
2833 3042 4.280929 ACCTCCAAATTTTAAGCACCTGAC 59.719 41.667 0.00 0.00 0.00 3.51
2834 3043 4.524328 CCTCCAAATTTTAAGCACCTGACT 59.476 41.667 0.00 0.00 0.00 3.41
2835 3044 5.011023 CCTCCAAATTTTAAGCACCTGACTT 59.989 40.000 0.00 0.00 0.00 3.01
2836 3045 5.841810 TCCAAATTTTAAGCACCTGACTTG 58.158 37.500 0.00 0.00 0.00 3.16
2857 3067 1.351350 GGCAAACTCACCCTAGTCCTT 59.649 52.381 0.00 0.00 0.00 3.36
2927 3137 2.948979 TGTTTTGCTGGACTCGAAATGT 59.051 40.909 0.00 0.00 0.00 2.71
2949 3159 6.676950 TGTGAAATAACATTGCACTTACTGG 58.323 36.000 10.57 0.00 0.00 4.00
3025 3239 4.686091 GGAACCTTTTTGCTTTGCATACTC 59.314 41.667 0.00 0.00 38.76 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.774908 ACCGTTGGGGGAGAAAATCA 59.225 50.000 0.00 0.00 41.60 2.57
92 94 9.869757 TTCAAAAAGGGAAAACAAAAACAAAAA 57.130 22.222 0.00 0.00 0.00 1.94
97 103 8.300286 TGGATTTCAAAAAGGGAAAACAAAAAC 58.700 29.630 0.00 0.00 37.74 2.43
102 108 6.893583 TCATGGATTTCAAAAAGGGAAAACA 58.106 32.000 0.00 0.00 37.74 2.83
103 109 7.498900 AGTTCATGGATTTCAAAAAGGGAAAAC 59.501 33.333 0.00 0.00 37.74 2.43
107 113 6.745794 AAGTTCATGGATTTCAAAAAGGGA 57.254 33.333 0.00 0.00 0.00 4.20
153 161 7.965718 TGGATTTGGAAAACTTCATGAATTCT 58.034 30.769 8.96 0.00 0.00 2.40
255 263 7.278135 TGTTCATGAATTTGAAAATTGACCCA 58.722 30.769 12.12 0.00 38.64 4.51
344 371 9.145865 GTATTTCAAAAATTGCTCCCGAATTTA 57.854 29.630 0.00 0.00 32.94 1.40
544 571 8.693504 GTTCGCATATTTGAATAATGTTCATGG 58.306 33.333 0.00 0.00 0.00 3.66
653 681 7.121315 TCCAAATTTGAAAAATGTTTTCGGGTT 59.879 29.630 19.86 1.83 0.00 4.11
655 683 7.020914 TCCAAATTTGAAAAATGTTTTCGGG 57.979 32.000 19.86 0.00 0.00 5.14
656 684 7.965107 TGTTCCAAATTTGAAAAATGTTTTCGG 59.035 29.630 19.86 0.00 0.00 4.30
691 739 8.486383 CACGTATTTGCAAAAGAAAAATCATGA 58.514 29.630 17.19 0.00 0.00 3.07
693 741 8.586570 TCACGTATTTGCAAAAGAAAAATCAT 57.413 26.923 17.19 0.00 0.00 2.45
695 743 9.516091 GATTCACGTATTTGCAAAAGAAAAATC 57.484 29.630 17.19 15.68 0.00 2.17
696 744 8.213812 CGATTCACGTATTTGCAAAAGAAAAAT 58.786 29.630 17.19 11.49 37.22 1.82
698 746 7.088097 CGATTCACGTATTTGCAAAAGAAAA 57.912 32.000 17.19 6.74 37.22 2.29
699 747 6.667981 CGATTCACGTATTTGCAAAAGAAA 57.332 33.333 17.19 10.60 37.22 2.52
749 797 5.749588 TGCTTCATTAAAAATGATCGGCATG 59.250 36.000 15.07 0.00 37.28 4.06
792 840 5.294356 GCCCCTGTTTATTTCTTTCGTTTT 58.706 37.500 0.00 0.00 0.00 2.43
898 946 3.329542 GACCTGCTTGATCCCCGCA 62.330 63.158 0.00 0.00 0.00 5.69
900 948 2.202932 CGACCTGCTTGATCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
901 949 2.514824 GCGACCTGCTTGATCCCC 60.515 66.667 0.00 0.00 41.73 4.81
902 950 2.514824 GGCGACCTGCTTGATCCC 60.515 66.667 0.00 0.00 45.43 3.85
903 951 1.522580 GAGGCGACCTGCTTGATCC 60.523 63.158 2.98 0.00 45.43 3.36
976 1044 1.985116 GGGGAGCTCTGACCTTCGT 60.985 63.158 14.64 0.00 0.00 3.85
1016 1090 2.272170 TGGAGAGGGGAGGGGGATT 61.272 63.158 0.00 0.00 0.00 3.01
1425 1499 3.999297 GAGGAGGTCGCGGAGAGGT 62.999 68.421 6.13 0.00 0.00 3.85
1596 1670 2.788589 GGGGAGGAGGAAGGAGGT 59.211 66.667 0.00 0.00 0.00 3.85
1671 1745 2.570135 CTAGGACGGTAGTACTGGTCC 58.430 57.143 24.61 24.61 42.67 4.46
1692 1766 1.304630 TGGCGCAGAGTAGTACCCA 60.305 57.895 10.83 0.00 0.00 4.51
1722 1799 4.098044 CCTGTGGTGTATTCGTACTGAGAT 59.902 45.833 0.00 0.00 0.00 2.75
1734 1811 1.082954 AGAGGGCCCTGTGGTGTAT 59.917 57.895 34.59 0.00 0.00 2.29
1767 1844 2.302733 TCTTTGCTCATACTGTCTGCCA 59.697 45.455 0.00 0.00 0.00 4.92
1773 1850 3.840666 TCCTTCCTCTTTGCTCATACTGT 59.159 43.478 0.00 0.00 0.00 3.55
1824 1901 2.366916 AGTCACACCTTCAGTCCTTCTG 59.633 50.000 0.00 0.00 44.85 3.02
1887 2003 5.960811 AGTCCTTCCTCTTTGATCATACTGA 59.039 40.000 0.00 0.00 0.00 3.41
1896 2012 2.260822 CCCTCAGTCCTTCCTCTTTGA 58.739 52.381 0.00 0.00 0.00 2.69
1919 2035 1.927174 CATACCTTTCGCTCGGAGTTG 59.073 52.381 6.90 0.00 0.00 3.16
1920 2036 1.134788 CCATACCTTTCGCTCGGAGTT 60.135 52.381 6.90 0.00 0.00 3.01
2114 2230 1.375140 CAGCGCATCCTCACACACT 60.375 57.895 11.47 0.00 0.00 3.55
2118 2234 1.079612 CTCACAGCGCATCCTCACA 60.080 57.895 11.47 0.00 0.00 3.58
2139 2255 7.040478 CCACATTAACAGGAATTGAGAAGAACA 60.040 37.037 0.00 0.00 0.00 3.18
2239 2355 0.038744 AGGCCATAAGCACAAGCACT 59.961 50.000 5.01 0.00 46.50 4.40
2390 2507 1.892474 GCCAAGCACCAAACCAGATAA 59.108 47.619 0.00 0.00 0.00 1.75
2459 2576 4.436242 TTTGGTACGCTGTTCAACAAAA 57.564 36.364 0.00 0.00 0.00 2.44
2547 2666 8.071368 TGGTTATGACATAAAACGAGAAAACAC 58.929 33.333 9.47 0.00 0.00 3.32
2556 2675 5.965334 GCTCACATGGTTATGACATAAAACG 59.035 40.000 9.47 2.37 37.73 3.60
2562 2681 3.650281 TGGCTCACATGGTTATGACAT 57.350 42.857 0.00 0.00 37.73 3.06
2566 2685 6.455360 AAATACTTGGCTCACATGGTTATG 57.545 37.500 0.00 0.00 40.24 1.90
2569 2688 3.440173 CGAAATACTTGGCTCACATGGTT 59.560 43.478 0.00 0.00 0.00 3.67
2573 2692 5.086104 AGTACGAAATACTTGGCTCACAT 57.914 39.130 0.00 0.00 41.71 3.21
2606 2808 4.097437 AGCATGGCAACTCTGAACATATTG 59.903 41.667 0.00 0.00 37.61 1.90
2623 2825 4.157289 ACTGCAAGATAAACTGAAGCATGG 59.843 41.667 0.00 0.00 37.43 3.66
2671 2873 2.303022 GGGTCACATTCACTCTCCTTCA 59.697 50.000 0.00 0.00 0.00 3.02
2672 2874 2.303022 TGGGTCACATTCACTCTCCTTC 59.697 50.000 0.00 0.00 0.00 3.46
2714 2916 3.731717 GCTTCGTATGTTTTCCGCAAAAA 59.268 39.130 0.00 0.00 33.17 1.94
2720 2922 5.518847 TCAATCTAGCTTCGTATGTTTTCCG 59.481 40.000 0.00 0.00 0.00 4.30
2731 2933 3.542875 CGTGCAACATCAATCTAGCTTCG 60.543 47.826 0.00 0.00 35.74 3.79
2745 2947 4.362932 TCTGAAACAAATTCGTGCAACA 57.637 36.364 0.00 0.00 41.18 3.33
2754 2956 7.666623 ACGGTGGATTTATTCTGAAACAAATT 58.333 30.769 12.03 0.00 0.00 1.82
2778 2980 4.393680 TCTGCGTACATTGTTTCCCATTAC 59.606 41.667 0.00 0.00 0.00 1.89
2796 2998 2.422597 TGGAGGTGTACAAAATCTGCG 58.577 47.619 0.00 0.00 0.00 5.18
2825 3034 1.109323 AGTTTGCCCAAGTCAGGTGC 61.109 55.000 0.00 0.00 0.00 5.01
2836 3045 0.035343 GGACTAGGGTGAGTTTGCCC 60.035 60.000 0.00 0.00 45.16 5.36
2857 3067 5.165961 ACAAGAGCTCCTAAATAGCACAA 57.834 39.130 10.93 0.00 42.62 3.33
2898 3108 3.634910 GAGTCCAGCAAAACAAAGGGTAA 59.365 43.478 0.00 0.00 0.00 2.85
2927 3137 6.714810 AGTCCAGTAAGTGCAATGTTATTTCA 59.285 34.615 0.00 0.00 0.00 2.69
2949 3159 3.957497 TGGAAGCTCTGAGAATCCTAGTC 59.043 47.826 22.00 3.27 0.00 2.59


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

AutoCloner maintained by Alex Coulton.