Multiple sequence alignment - TraesCS3A01G073900

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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 TraesCS3A01G073900 chr3A 100.000 2911 0 0 1 2911 46070121 46067211 0.000000e+00 5376
1 TraesCS3A01G073900 chr3A 98.157 1519 26 1 1249 2765 46130318 46128800 0.000000e+00 2649
2 TraesCS3A01G073900 chr3A 98.150 1243 21 2 2 1242 46131529 46130287 0.000000e+00 2167
3 TraesCS3A01G073900 chr3A 98.728 786 10 0 1 786 46098255 46097470 0.000000e+00 1397
4 TraesCS3A01G073900 chr3A 94.574 387 17 1 2529 2911 670023842 670023456 1.930000e-166 595
5 TraesCS3A01G073900 chr3A 94.271 384 20 1 2528 2911 10025737 10025356 1.160000e-163 586
6 TraesCS3A01G073900 chr3A 84.121 529 79 4 1645 2173 46041808 46041285 9.310000e-140 507
7 TraesCS3A01G073900 chr1A 95.855 386 13 1 2529 2911 523342347 523342732 3.190000e-174 621
8 TraesCS3A01G073900 chr2A 95.116 389 13 3 2529 2911 761343590 761343202 2.480000e-170 608
9 TraesCS3A01G073900 chr2A 94.588 388 14 5 2529 2911 667311924 667312309 6.950000e-166 593
10 TraesCS3A01G073900 chr7A 95.039 383 16 2 2529 2911 18520142 18519763 1.490000e-167 599
11 TraesCS3A01G073900 chr7A 94.737 380 18 1 2532 2911 708538911 708538534 8.980000e-165 590
12 TraesCS3A01G073900 chr6A 94.560 386 18 2 2529 2911 22709774 22710159 6.950000e-166 593
13 TraesCS3A01G073900 chrUn 83.012 259 40 3 1915 2173 231007614 231007360 6.270000e-57 231
14 TraesCS3A01G073900 chrUn 83.012 259 40 3 1915 2173 238600759 238600505 6.270000e-57 231
15 TraesCS3A01G073900 chrUn 82.625 259 41 3 1915 2173 204471396 204471142 2.920000e-55 226
16 TraesCS3A01G073900 chrUn 82.625 259 41 3 1915 2173 306234040 306233786 2.920000e-55 226
17 TraesCS3A01G073900 chr7B 77.143 245 51 5 1336 1576 719106670 719106427 1.410000e-28 137


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 TraesCS3A01G073900 chr3A 46067211 46070121 2910 True 5376 5376 100.0000 1 2911 1 chr3A.!!$R3 2910
1 TraesCS3A01G073900 chr3A 46128800 46131529 2729 True 2408 2649 98.1535 2 2765 2 chr3A.!!$R6 2763
2 TraesCS3A01G073900 chr3A 46097470 46098255 785 True 1397 1397 98.7280 1 786 1 chr3A.!!$R4 785
3 TraesCS3A01G073900 chr3A 46041285 46041808 523 True 507 507 84.1210 1645 2173 1 chr3A.!!$R2 528

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
137 138 1.089920 GCTTGGTGCTACATGAGGTG 58.910 55.000 0.0 0.0 38.95 4.00 F
254 255 1.348036 AGGTTAGAGGCAAAGACGCTT 59.652 47.619 0.0 0.0 0.00 4.68 F
1133 1134 1.059942 GAGCGAAAAATTTGTGCCGG 58.940 50.000 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1130 1131 0.251165 AACAGTCCCAAATCCACCGG 60.251 55.0 0.0 0.00 0.0 5.28 R
1630 1631 0.819259 TTTGTCTGCTGTCCCTGTGC 60.819 55.0 0.0 0.00 0.0 4.57 R
2880 2883 0.023732 CGTAGCATCAACGAAGCACG 59.976 55.0 0.0 1.99 42.9 5.34 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
137 138 1.089920 GCTTGGTGCTACATGAGGTG 58.910 55.000 0.00 0.00 38.95 4.00
254 255 1.348036 AGGTTAGAGGCAAAGACGCTT 59.652 47.619 0.00 0.00 0.00 4.68
673 674 7.071196 TGTGGATCTAGCCTTCAGTTATGTATT 59.929 37.037 0.00 0.00 0.00 1.89
717 718 2.577563 TCTTCATGCTCCTGGATGGAAA 59.422 45.455 0.00 0.00 45.63 3.13
1126 1127 8.352942 ACAATTTCTCTGTAGAGCGAAAAATTT 58.647 29.630 8.87 0.00 41.80 1.82
1128 1129 6.861065 TTCTCTGTAGAGCGAAAAATTTGT 57.139 33.333 4.01 0.00 41.80 2.83
1130 1131 4.783242 TCTGTAGAGCGAAAAATTTGTGC 58.217 39.130 0.00 0.00 0.00 4.57
1132 1133 2.050477 AGAGCGAAAAATTTGTGCCG 57.950 45.000 0.00 0.00 0.00 5.69
1133 1134 1.059942 GAGCGAAAAATTTGTGCCGG 58.940 50.000 0.00 0.00 0.00 6.13
1214 1215 7.806180 ACTATCTCTACAACCAAAATGCCTAT 58.194 34.615 0.00 0.00 0.00 2.57
1215 1216 8.934697 ACTATCTCTACAACCAAAATGCCTATA 58.065 33.333 0.00 0.00 0.00 1.31
1216 1217 9.950496 CTATCTCTACAACCAAAATGCCTATAT 57.050 33.333 0.00 0.00 0.00 0.86
1641 1642 3.845781 ATACCATAAGCACAGGGACAG 57.154 47.619 0.00 0.00 0.00 3.51
1927 1928 4.940463 TCATAAACTATGAGTACGCACCC 58.060 43.478 0.00 0.00 40.09 4.61
2198 2199 5.448632 CCGGCTGTATAGGTTGTCAATTTTC 60.449 44.000 0.00 0.00 0.00 2.29
2312 2315 5.073311 ACACTAGTCATCAGTTATGCGTT 57.927 39.130 0.00 0.00 35.38 4.84
2567 2570 3.389983 CCTATTGTCCCGGTTCATAAGGA 59.610 47.826 0.00 0.00 0.00 3.36
2721 2724 0.856982 TTGGTCCCAGTTGGTTCCAT 59.143 50.000 10.75 0.00 38.35 3.41
2740 2743 1.453197 CAACCGGGACCAATAGGCC 60.453 63.158 6.32 0.00 39.06 5.19
2742 2745 1.632965 AACCGGGACCAATAGGCCTC 61.633 60.000 9.68 0.00 39.06 4.70
2765 2768 1.726853 GCGTCAGTATTTCTGTGGCT 58.273 50.000 0.00 0.00 43.97 4.75
2766 2769 1.394917 GCGTCAGTATTTCTGTGGCTG 59.605 52.381 0.00 0.00 43.97 4.85
2767 2770 2.002586 CGTCAGTATTTCTGTGGCTGG 58.997 52.381 0.00 0.00 43.97 4.85
2768 2771 2.353704 CGTCAGTATTTCTGTGGCTGGA 60.354 50.000 0.00 0.00 43.97 3.86
2769 2772 3.674997 GTCAGTATTTCTGTGGCTGGAA 58.325 45.455 0.00 0.00 43.97 3.53
2770 2773 4.265073 GTCAGTATTTCTGTGGCTGGAAT 58.735 43.478 0.00 0.00 43.97 3.01
2771 2774 4.702131 GTCAGTATTTCTGTGGCTGGAATT 59.298 41.667 0.00 0.00 43.97 2.17
2772 2775 5.183904 GTCAGTATTTCTGTGGCTGGAATTT 59.816 40.000 0.00 0.00 43.97 1.82
2773 2776 5.774690 TCAGTATTTCTGTGGCTGGAATTTT 59.225 36.000 0.00 0.00 43.97 1.82
2774 2777 6.267471 TCAGTATTTCTGTGGCTGGAATTTTT 59.733 34.615 0.00 0.00 43.97 1.94
2775 2778 6.366877 CAGTATTTCTGTGGCTGGAATTTTTG 59.633 38.462 0.00 0.00 39.17 2.44
2776 2779 4.751767 TTTCTGTGGCTGGAATTTTTGT 57.248 36.364 0.00 0.00 0.00 2.83
2777 2780 4.751767 TTCTGTGGCTGGAATTTTTGTT 57.248 36.364 0.00 0.00 0.00 2.83
2778 2781 4.751767 TCTGTGGCTGGAATTTTTGTTT 57.248 36.364 0.00 0.00 0.00 2.83
2779 2782 5.096443 TCTGTGGCTGGAATTTTTGTTTT 57.904 34.783 0.00 0.00 0.00 2.43
2780 2783 5.495640 TCTGTGGCTGGAATTTTTGTTTTT 58.504 33.333 0.00 0.00 0.00 1.94
2805 2808 2.528127 GGGGGTTGGGGGTTTTGG 60.528 66.667 0.00 0.00 0.00 3.28
2806 2809 2.528127 GGGGTTGGGGGTTTTGGG 60.528 66.667 0.00 0.00 0.00 4.12
2807 2810 2.528127 GGGTTGGGGGTTTTGGGG 60.528 66.667 0.00 0.00 0.00 4.96
2808 2811 2.528127 GGTTGGGGGTTTTGGGGG 60.528 66.667 0.00 0.00 0.00 5.40
2829 2832 7.907841 GGGGGTTAATTTAGGTGTTTCATAT 57.092 36.000 0.00 0.00 0.00 1.78
2830 2833 8.999905 GGGGGTTAATTTAGGTGTTTCATATA 57.000 34.615 0.00 0.00 0.00 0.86
2831 2834 9.596308 GGGGGTTAATTTAGGTGTTTCATATAT 57.404 33.333 0.00 0.00 0.00 0.86
2841 2844 9.899661 TTAGGTGTTTCATATATTGTGTTAGCT 57.100 29.630 0.00 0.00 0.00 3.32
2843 2846 9.547753 AGGTGTTTCATATATTGTGTTAGCTAG 57.452 33.333 0.00 0.00 0.00 3.42
2844 2847 8.283291 GGTGTTTCATATATTGTGTTAGCTAGC 58.717 37.037 6.62 6.62 0.00 3.42
2845 2848 9.046296 GTGTTTCATATATTGTGTTAGCTAGCT 57.954 33.333 23.12 23.12 0.00 3.32
2880 2883 4.953579 AGAGAAGTGTCCTCTCTTATGTCC 59.046 45.833 0.00 0.00 37.55 4.02
2881 2884 3.697045 AGAAGTGTCCTCTCTTATGTCCG 59.303 47.826 0.00 0.00 0.00 4.79
2882 2885 3.088789 AGTGTCCTCTCTTATGTCCGT 57.911 47.619 0.00 0.00 0.00 4.69
2883 2886 2.755655 AGTGTCCTCTCTTATGTCCGTG 59.244 50.000 0.00 0.00 0.00 4.94
2884 2887 1.476891 TGTCCTCTCTTATGTCCGTGC 59.523 52.381 0.00 0.00 0.00 5.34
2885 2888 1.751924 GTCCTCTCTTATGTCCGTGCT 59.248 52.381 0.00 0.00 0.00 4.40
2886 2889 2.166664 GTCCTCTCTTATGTCCGTGCTT 59.833 50.000 0.00 0.00 0.00 3.91
2887 2890 2.427453 TCCTCTCTTATGTCCGTGCTTC 59.573 50.000 0.00 0.00 0.00 3.86
2888 2891 2.455032 CTCTCTTATGTCCGTGCTTCG 58.545 52.381 0.00 0.00 39.52 3.79
2889 2892 1.816835 TCTCTTATGTCCGTGCTTCGT 59.183 47.619 1.89 0.00 37.94 3.85
2890 2893 2.230508 TCTCTTATGTCCGTGCTTCGTT 59.769 45.455 1.89 0.00 37.94 3.85
2891 2894 2.333926 TCTTATGTCCGTGCTTCGTTG 58.666 47.619 1.89 0.00 37.94 4.10
2892 2895 2.029739 TCTTATGTCCGTGCTTCGTTGA 60.030 45.455 1.89 0.00 37.94 3.18
2893 2896 2.665649 TATGTCCGTGCTTCGTTGAT 57.334 45.000 1.89 0.00 37.94 2.57
2894 2897 1.078709 ATGTCCGTGCTTCGTTGATG 58.921 50.000 1.89 0.00 37.94 3.07
2895 2898 1.132640 GTCCGTGCTTCGTTGATGC 59.867 57.895 0.00 0.00 37.94 3.91
2896 2899 1.005037 TCCGTGCTTCGTTGATGCT 60.005 52.632 6.30 0.00 37.94 3.79
2897 2900 0.245266 TCCGTGCTTCGTTGATGCTA 59.755 50.000 6.30 0.00 37.94 3.49
2898 2901 0.370273 CCGTGCTTCGTTGATGCTAC 59.630 55.000 6.30 3.05 37.94 3.58
2899 2902 0.023732 CGTGCTTCGTTGATGCTACG 59.976 55.000 6.30 9.47 40.23 3.51
2900 2903 1.068474 GTGCTTCGTTGATGCTACGT 58.932 50.000 0.00 0.00 39.84 3.57
2901 2904 2.256174 GTGCTTCGTTGATGCTACGTA 58.744 47.619 0.00 0.00 39.84 3.57
2902 2905 2.027688 GTGCTTCGTTGATGCTACGTAC 59.972 50.000 0.00 0.00 39.84 3.67
2903 2906 2.094906 TGCTTCGTTGATGCTACGTACT 60.095 45.455 0.00 0.00 39.84 2.73
2904 2907 3.127376 TGCTTCGTTGATGCTACGTACTA 59.873 43.478 0.00 0.00 39.84 1.82
2905 2908 4.201980 TGCTTCGTTGATGCTACGTACTAT 60.202 41.667 0.00 0.00 39.84 2.12
2906 2909 5.007921 TGCTTCGTTGATGCTACGTACTATA 59.992 40.000 0.00 0.00 39.84 1.31
2907 2910 5.339085 GCTTCGTTGATGCTACGTACTATAC 59.661 44.000 0.00 0.00 39.84 1.47
2908 2911 5.989551 TCGTTGATGCTACGTACTATACA 57.010 39.130 0.00 0.00 39.84 2.29
2909 2912 6.549912 TCGTTGATGCTACGTACTATACAT 57.450 37.500 0.00 0.00 39.84 2.29
2910 2913 7.656707 TCGTTGATGCTACGTACTATACATA 57.343 36.000 0.00 0.00 39.84 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 5.296035 CGGTACCAATTAGATCCAAGGAAAC 59.704 44.000 13.54 0.00 0.00 2.78
361 362 0.179020 CACTGCCCTGAGTGGTTGAA 60.179 55.000 0.00 0.00 39.85 2.69
773 774 0.600057 GCTGGCTTGTCAAAGGAAGG 59.400 55.000 0.00 0.00 33.68 3.46
1072 1073 6.470877 GTGATGTTCTCTAGAAGAGCTAAACG 59.529 42.308 6.67 0.00 42.04 3.60
1126 1127 2.282816 CCCAAATCCACCGGCACA 60.283 61.111 0.00 0.00 0.00 4.57
1128 1129 2.034999 GTCCCAAATCCACCGGCA 59.965 61.111 0.00 0.00 0.00 5.69
1130 1131 0.251165 AACAGTCCCAAATCCACCGG 60.251 55.000 0.00 0.00 0.00 5.28
1132 1133 3.492337 TGTAAACAGTCCCAAATCCACC 58.508 45.455 0.00 0.00 0.00 4.61
1133 1134 4.022329 CCTTGTAAACAGTCCCAAATCCAC 60.022 45.833 0.00 0.00 0.00 4.02
1630 1631 0.819259 TTTGTCTGCTGTCCCTGTGC 60.819 55.000 0.00 0.00 0.00 4.57
2198 2199 6.900189 TGCAAAATTTTGGCACATATTTCTG 58.100 32.000 27.60 3.14 39.30 3.02
2297 2300 2.810852 TGTGCAAACGCATAACTGATGA 59.189 40.909 0.00 0.00 42.51 2.92
2312 2315 2.549064 TTCTGAGCTAGCTTGTGCAA 57.451 45.000 20.42 5.14 42.74 4.08
2445 2448 2.107141 GCCAGACCCGGAGAATCG 59.893 66.667 0.73 0.00 34.37 3.34
2458 2461 2.325082 CCGGTTCGAAAGGTGCCAG 61.325 63.158 0.00 0.00 0.00 4.85
2526 2529 1.366679 GCCCGTTTTCTACTAGTGGC 58.633 55.000 5.39 3.03 0.00 5.01
2567 2570 0.179001 CTGGAACCGGGACAAAAGGT 60.179 55.000 6.32 0.00 40.50 3.50
2644 2647 2.124695 GCCCATCTGTCCCGGTTC 60.125 66.667 0.00 0.00 0.00 3.62
2721 2724 1.605453 GCCTATTGGTCCCGGTTGA 59.395 57.895 0.00 0.00 35.27 3.18
2740 2743 2.279582 AGAAATACTGACGCGTGGAG 57.720 50.000 20.70 15.38 0.00 3.86
2753 2756 6.418057 ACAAAAATTCCAGCCACAGAAATA 57.582 33.333 0.00 0.00 0.00 1.40
2788 2791 2.528127 CCAAAACCCCCAACCCCC 60.528 66.667 0.00 0.00 0.00 5.40
2789 2792 2.528127 CCCAAAACCCCCAACCCC 60.528 66.667 0.00 0.00 0.00 4.95
2790 2793 2.528127 CCCCAAAACCCCCAACCC 60.528 66.667 0.00 0.00 0.00 4.11
2791 2794 2.528127 CCCCCAAAACCCCCAACC 60.528 66.667 0.00 0.00 0.00 3.77
2805 2808 7.907841 ATATGAAACACCTAAATTAACCCCC 57.092 36.000 0.00 0.00 0.00 5.40
2815 2818 9.899661 AGCTAACACAATATATGAAACACCTAA 57.100 29.630 0.00 0.00 0.00 2.69
2817 2820 9.547753 CTAGCTAACACAATATATGAAACACCT 57.452 33.333 0.00 0.00 0.00 4.00
2818 2821 8.283291 GCTAGCTAACACAATATATGAAACACC 58.717 37.037 7.70 0.00 0.00 4.16
2819 2822 9.046296 AGCTAGCTAACACAATATATGAAACAC 57.954 33.333 17.69 0.00 0.00 3.32
2857 2860 4.953579 GGACATAAGAGAGGACACTTCTCT 59.046 45.833 7.43 7.43 43.56 3.10
2858 2861 4.201970 CGGACATAAGAGAGGACACTTCTC 60.202 50.000 0.00 0.00 0.00 2.87
2859 2862 3.697045 CGGACATAAGAGAGGACACTTCT 59.303 47.826 0.00 0.00 0.00 2.85
2860 2863 3.444388 ACGGACATAAGAGAGGACACTTC 59.556 47.826 0.00 0.00 0.00 3.01
2861 2864 3.193691 CACGGACATAAGAGAGGACACTT 59.806 47.826 0.00 0.00 0.00 3.16
2862 2865 2.755655 CACGGACATAAGAGAGGACACT 59.244 50.000 0.00 0.00 0.00 3.55
2863 2866 2.735762 GCACGGACATAAGAGAGGACAC 60.736 54.545 0.00 0.00 0.00 3.67
2864 2867 1.476891 GCACGGACATAAGAGAGGACA 59.523 52.381 0.00 0.00 0.00 4.02
2865 2868 1.751924 AGCACGGACATAAGAGAGGAC 59.248 52.381 0.00 0.00 0.00 3.85
2866 2869 2.145397 AGCACGGACATAAGAGAGGA 57.855 50.000 0.00 0.00 0.00 3.71
2867 2870 2.796383 CGAAGCACGGACATAAGAGAGG 60.796 54.545 0.00 0.00 38.46 3.69
2868 2871 2.455032 CGAAGCACGGACATAAGAGAG 58.545 52.381 0.00 0.00 38.46 3.20
2869 2872 2.561733 CGAAGCACGGACATAAGAGA 57.438 50.000 0.00 0.00 38.46 3.10
2880 2883 0.023732 CGTAGCATCAACGAAGCACG 59.976 55.000 0.00 1.99 42.90 5.34
2881 2884 1.068474 ACGTAGCATCAACGAAGCAC 58.932 50.000 2.27 0.00 42.90 4.40
2882 2885 2.094906 AGTACGTAGCATCAACGAAGCA 60.095 45.455 0.00 0.00 42.90 3.91
2883 2886 2.527100 AGTACGTAGCATCAACGAAGC 58.473 47.619 0.00 0.00 42.90 3.86
2884 2887 6.424683 TGTATAGTACGTAGCATCAACGAAG 58.575 40.000 0.00 0.00 42.90 3.79
2885 2888 6.362210 TGTATAGTACGTAGCATCAACGAA 57.638 37.500 0.00 0.00 42.90 3.85
2886 2889 5.989551 TGTATAGTACGTAGCATCAACGA 57.010 39.130 0.00 0.00 42.90 3.85


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

AutoCloner maintained by Alex Coulton.