Multiple sequence alignment - TraesCS5A01G439200

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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 TraesCS5A01G439200 chr5A 100.000 2540 0 0 784 3323 620857106 620859645 0.000000e+00 4691.0
1 TraesCS5A01G439200 chr5A 100.000 428 0 0 1 428 620856323 620856750 0.000000e+00 791.0
2 TraesCS5A01G439200 chr5B 92.590 2591 84 42 786 3323 615586964 615589499 0.000000e+00 3622.0
3 TraesCS5A01G439200 chr5B 90.909 429 19 9 4 428 615586522 615586934 2.900000e-155 558.0
4 TraesCS5A01G439200 chr5B 96.078 51 2 0 5 55 615694126 615694176 2.120000e-12 84.2
5 TraesCS5A01G439200 chr5D 91.876 2622 78 52 784 3323 496846275 496848843 0.000000e+00 3537.0
6 TraesCS5A01G439200 chr5D 94.393 428 20 4 3 428 496845823 496846248 0.000000e+00 654.0
7 TraesCS5A01G439200 chr4A 75.527 237 52 6 1832 2064 17675970 17676204 9.750000e-21 111.0
8 TraesCS5A01G439200 chr4B 74.783 230 54 4 1842 2069 561386130 561385903 2.110000e-17 100.0
9 TraesCS5A01G439200 chr4D 74.153 236 57 4 1832 2064 449055621 449055387 9.810000e-16 95.3


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 TraesCS5A01G439200 chr5A 620856323 620859645 3322 False 2741.0 4691 100.0000 1 3323 2 chr5A.!!$F1 3322
1 TraesCS5A01G439200 chr5B 615586522 615589499 2977 False 2090.0 3622 91.7495 4 3323 2 chr5B.!!$F2 3319
2 TraesCS5A01G439200 chr5D 496845823 496848843 3020 False 2095.5 3537 93.1345 3 3323 2 chr5D.!!$F1 3320

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
169 173 0.178990 GAAAGGGCCGGCCATTATCT 60.179 55.0 42.58 29.25 39.36 1.98 F
406 414 0.685097 TGTGAAAAGGAGACGGGGAG 59.315 55.0 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 1784 0.105408 GGGGAATACGCCGAGCTTAA 59.895 55.0 0.0 0.0 39.24 1.85 R
2331 2394 0.035820 TTATTTTGTCCGCCTCGCCT 60.036 50.0 0.0 0.0 0.00 5.52 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
120 124 0.535102 CCCAGCGCGAAATCCCTATT 60.535 55.000 12.10 0.00 0.00 1.73
121 125 0.868406 CCAGCGCGAAATCCCTATTC 59.132 55.000 12.10 0.00 0.00 1.75
123 127 1.528586 CAGCGCGAAATCCCTATTCTG 59.471 52.381 12.10 0.00 0.00 3.02
154 158 1.035932 CAGCAGATGGCCCTGGAAAG 61.036 60.000 10.59 0.00 46.50 2.62
169 173 0.178990 GAAAGGGCCGGCCATTATCT 60.179 55.000 42.58 29.25 39.36 1.98
365 370 1.074248 GCTCCCCTCCCGTTTGAAA 59.926 57.895 0.00 0.00 0.00 2.69
406 414 0.685097 TGTGAAAAGGAGACGGGGAG 59.315 55.000 0.00 0.00 0.00 4.30
855 870 2.156098 CAGTAGAGGGCGTCCTATCTC 58.844 57.143 9.57 2.67 45.05 2.75
881 896 2.025589 TTTTCTGCGTGTGTGTGGTA 57.974 45.000 0.00 0.00 0.00 3.25
884 899 1.110518 TCTGCGTGTGTGTGGTAGGA 61.111 55.000 0.00 0.00 0.00 2.94
905 920 2.426023 GTGGTTGCAGTCGGGACT 59.574 61.111 0.00 0.00 43.61 3.85
1023 1038 4.722700 TTCCAGCTCAAGGCCGGC 62.723 66.667 21.18 21.18 43.05 6.13
1179 1227 2.131067 GGAGAAGGAGGAGAGGCCG 61.131 68.421 0.00 0.00 43.43 6.13
1181 1229 2.364448 GAAGGAGGAGAGGCCGGT 60.364 66.667 1.90 0.00 43.43 5.28
1420 1468 5.351740 GCACTCAAGGTACTACTGGAATTTC 59.648 44.000 0.00 0.00 38.49 2.17
1727 1783 2.022195 CGTCCTCCTCGATTCACCTAA 58.978 52.381 0.00 0.00 0.00 2.69
1728 1784 2.623889 CGTCCTCCTCGATTCACCTAAT 59.376 50.000 0.00 0.00 0.00 1.73
1729 1785 3.068307 CGTCCTCCTCGATTCACCTAATT 59.932 47.826 0.00 0.00 0.00 1.40
1730 1786 4.277672 CGTCCTCCTCGATTCACCTAATTA 59.722 45.833 0.00 0.00 0.00 1.40
1731 1787 5.221185 CGTCCTCCTCGATTCACCTAATTAA 60.221 44.000 0.00 0.00 0.00 1.40
1733 1789 4.991687 CCTCCTCGATTCACCTAATTAAGC 59.008 45.833 0.00 0.00 0.00 3.09
1736 1792 4.681942 CCTCGATTCACCTAATTAAGCTCG 59.318 45.833 0.00 0.00 0.00 5.03
1737 1793 4.617959 TCGATTCACCTAATTAAGCTCGG 58.382 43.478 0.00 0.00 0.00 4.63
1738 1794 3.184581 CGATTCACCTAATTAAGCTCGGC 59.815 47.826 0.00 0.00 0.00 5.54
1778 1834 2.687566 CAGGGGCTTACCGGACCT 60.688 66.667 9.46 2.34 41.60 3.85
1779 1835 2.687566 AGGGGCTTACCGGACCTG 60.688 66.667 9.46 0.00 41.60 4.00
1818 1878 4.779819 GAGTACATCGACGCCGTT 57.220 55.556 0.00 0.00 37.05 4.44
1932 1992 3.645975 CTGCCGCCGTTGTTCGTT 61.646 61.111 0.00 0.00 37.94 3.85
2195 2258 2.124570 CATGAACCAGAGCGGGGG 60.125 66.667 0.00 0.00 40.22 5.40
2235 2298 1.822990 GAGAAGATCACGGTGGTGGTA 59.177 52.381 8.50 0.00 44.50 3.25
2328 2391 4.803426 GCCGTCCTCTGAGCGTGG 62.803 72.222 0.00 1.25 0.00 4.94
2329 2392 4.803426 CCGTCCTCTGAGCGTGGC 62.803 72.222 0.00 0.00 0.00 5.01
2331 2394 3.749064 GTCCTCTGAGCGTGGCGA 61.749 66.667 0.00 0.00 0.00 5.54
2524 2594 1.768077 ACTCCCATCCCCTAGCAGC 60.768 63.158 0.00 0.00 0.00 5.25
2640 2714 2.192187 CCCTCCCGCCGACTAGTAC 61.192 68.421 0.00 0.00 0.00 2.73
2672 2746 3.103742 AGCTGTAAGAGAAGAAGAGGGG 58.896 50.000 0.00 0.00 34.07 4.79
2799 2879 4.108699 TGGTGCTTGTTATTGCTATTGC 57.891 40.909 0.00 0.00 40.20 3.56
2800 2880 3.763360 TGGTGCTTGTTATTGCTATTGCT 59.237 39.130 0.00 0.00 40.48 3.91
2801 2881 4.946772 TGGTGCTTGTTATTGCTATTGCTA 59.053 37.500 0.00 0.00 40.48 3.49
2802 2882 5.593909 TGGTGCTTGTTATTGCTATTGCTAT 59.406 36.000 0.00 0.86 40.48 2.97
2803 2883 6.096705 TGGTGCTTGTTATTGCTATTGCTATT 59.903 34.615 1.31 0.00 40.48 1.73
2804 2884 6.418819 GGTGCTTGTTATTGCTATTGCTATTG 59.581 38.462 1.31 0.00 40.48 1.90
2805 2885 5.978919 TGCTTGTTATTGCTATTGCTATTGC 59.021 36.000 7.53 7.53 40.48 3.56
2806 2886 6.183360 TGCTTGTTATTGCTATTGCTATTGCT 60.183 34.615 14.39 0.00 40.48 3.91
2807 2887 7.013178 TGCTTGTTATTGCTATTGCTATTGCTA 59.987 33.333 14.39 8.34 40.48 3.49
2808 2888 8.025445 GCTTGTTATTGCTATTGCTATTGCTAT 58.975 33.333 14.39 14.04 40.48 2.97
2809 2889 9.903682 CTTGTTATTGCTATTGCTATTGCTATT 57.096 29.630 14.28 4.18 40.48 1.73
2810 2890 9.681692 TTGTTATTGCTATTGCTATTGCTATTG 57.318 29.630 14.28 1.57 40.48 1.90
2811 2891 7.809331 TGTTATTGCTATTGCTATTGCTATTGC 59.191 33.333 18.00 18.00 46.17 3.56
2812 2892 6.585695 ATTGCTATTGCTATTGCTATTGCT 57.414 33.333 22.49 8.10 46.15 3.91
2813 2893 7.692460 ATTGCTATTGCTATTGCTATTGCTA 57.308 32.000 22.49 18.05 46.15 3.49
2814 2894 7.692460 TTGCTATTGCTATTGCTATTGCTAT 57.308 32.000 22.49 14.04 46.15 2.97
2815 2895 7.692460 TGCTATTGCTATTGCTATTGCTATT 57.308 32.000 22.49 4.18 46.15 1.73
2816 2896 7.532571 TGCTATTGCTATTGCTATTGCTATTG 58.467 34.615 22.49 13.37 46.15 1.90
2817 2897 6.471519 GCTATTGCTATTGCTATTGCTATTGC 59.528 38.462 20.39 20.39 46.17 3.56
2818 2898 6.585695 ATTGCTATTGCTATTGCTATTGCT 57.414 33.333 22.49 8.10 46.15 3.91
2819 2899 7.692460 ATTGCTATTGCTATTGCTATTGCTA 57.308 32.000 22.49 18.05 46.15 3.49
2820 2900 7.692460 TTGCTATTGCTATTGCTATTGCTAT 57.308 32.000 22.49 14.04 46.15 2.97
2821 2901 7.692460 TGCTATTGCTATTGCTATTGCTATT 57.308 32.000 22.49 4.18 46.15 1.73
2822 2902 7.532571 TGCTATTGCTATTGCTATTGCTATTG 58.467 34.615 22.49 13.37 46.15 1.90
2846 2926 7.153315 TGAAGAGATGATGAACTATGATGAGC 58.847 38.462 0.00 0.00 0.00 4.26
2875 2955 7.671495 ATTCAAGTTTATGCCATGTTTTTCC 57.329 32.000 0.00 0.00 0.00 3.13
2888 2968 1.882623 GTTTTTCCCCACTCTGCTCTG 59.117 52.381 0.00 0.00 0.00 3.35
2890 2970 2.454832 TTTCCCCACTCTGCTCTGCG 62.455 60.000 0.00 0.00 0.00 5.18
2930 3033 2.896801 GAACTGTGTGGCGCTGGTG 61.897 63.158 7.64 0.00 0.00 4.17
3028 3131 3.589881 GGGAGCACGCCATGATGC 61.590 66.667 8.11 8.11 42.39 3.91
3040 3143 2.753966 ATGATGCACAGCCGAACGC 61.754 57.895 0.00 0.00 37.98 4.84
3065 3176 1.068333 CATTCACCTGGCCGAAACAAG 60.068 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 124 2.686470 CTGGAGCTCAGGGGCAGA 60.686 66.667 17.19 0.00 39.76 4.26
121 125 4.486503 GCTGGAGCTCAGGGGCAG 62.487 72.222 17.19 13.77 43.54 4.85
123 127 4.486503 CTGCTGGAGCTCAGGGGC 62.487 72.222 17.19 13.38 43.54 5.80
154 158 2.282462 CCAGATAATGGCCGGCCC 60.282 66.667 41.75 26.08 43.83 5.80
169 173 2.124540 ATGCCCATTTTGCCCCCA 59.875 55.556 0.00 0.00 0.00 4.96
317 322 2.723334 TAAAGGGCTCAGGTGGGGGT 62.723 60.000 0.00 0.00 0.00 4.95
365 370 1.823169 TTACAAGCGAGCGAAGGGGT 61.823 55.000 0.00 0.00 0.00 4.95
864 879 0.249699 CCTACCACACACACGCAGAA 60.250 55.000 0.00 0.00 0.00 3.02
865 880 1.110518 TCCTACCACACACACGCAGA 61.111 55.000 0.00 0.00 0.00 4.26
869 884 1.733041 CGCTCCTACCACACACACG 60.733 63.158 0.00 0.00 0.00 4.49
881 896 3.537206 GACTGCAACCACCGCTCCT 62.537 63.158 0.00 0.00 0.00 3.69
884 899 4.988598 CCGACTGCAACCACCGCT 62.989 66.667 0.00 0.00 0.00 5.52
905 920 0.107116 GTTACACACCACCACCACCA 60.107 55.000 0.00 0.00 0.00 4.17
906 921 0.181824 AGTTACACACCACCACCACC 59.818 55.000 0.00 0.00 0.00 4.61
907 922 1.305201 CAGTTACACACCACCACCAC 58.695 55.000 0.00 0.00 0.00 4.16
1406 1454 3.804036 CCATGCGGAAATTCCAGTAGTA 58.196 45.455 13.04 0.00 35.91 1.82
1407 1455 2.643551 CCATGCGGAAATTCCAGTAGT 58.356 47.619 13.04 0.00 35.91 2.73
1408 1456 1.334869 GCCATGCGGAAATTCCAGTAG 59.665 52.381 13.04 0.00 35.91 2.57
1701 1751 0.397254 AATCGAGGAGGACGGGATGT 60.397 55.000 0.00 0.00 0.00 3.06
1727 1783 1.270678 GGGGAATACGCCGAGCTTAAT 60.271 52.381 0.00 0.00 39.24 1.40
1728 1784 0.105408 GGGGAATACGCCGAGCTTAA 59.895 55.000 0.00 0.00 39.24 1.85
1729 1785 1.744014 GGGGAATACGCCGAGCTTA 59.256 57.895 0.00 0.00 39.24 3.09
1730 1786 2.504519 GGGGAATACGCCGAGCTT 59.495 61.111 0.00 0.00 39.24 3.74
1737 1793 0.668535 GCCATGAAAGGGGAATACGC 59.331 55.000 0.00 0.00 38.99 4.42
1738 1794 2.051334 TGCCATGAAAGGGGAATACG 57.949 50.000 0.00 0.00 32.67 3.06
1778 1834 0.965866 CTCCCCTGCGTAGACAGACA 60.966 60.000 0.53 0.00 40.25 3.41
1779 1835 1.810532 CTCCCCTGCGTAGACAGAC 59.189 63.158 0.53 0.00 40.25 3.51
1818 1878 3.691342 CTCGCTCCGTCCCCAACA 61.691 66.667 0.00 0.00 0.00 3.33
2115 2178 3.649986 GCCGTCGCAGTTGCAGTT 61.650 61.111 4.84 0.00 42.21 3.16
2154 2217 4.785512 AGCAGCTCGAACTCGCCG 62.786 66.667 0.00 0.00 39.60 6.46
2329 2392 4.735132 TTTGTCCGCCTCGCCTCG 62.735 66.667 0.00 0.00 0.00 4.63
2330 2393 0.461339 TATTTTGTCCGCCTCGCCTC 60.461 55.000 0.00 0.00 0.00 4.70
2331 2394 0.035820 TTATTTTGTCCGCCTCGCCT 60.036 50.000 0.00 0.00 0.00 5.52
2504 2570 0.692419 CTGCTAGGGGATGGGAGTGT 60.692 60.000 0.00 0.00 0.00 3.55
2513 2579 2.072487 GGATGGTGCTGCTAGGGGA 61.072 63.158 0.00 0.00 0.00 4.81
2524 2594 5.048504 CGAAATTAATGGAGGATGGATGGTG 60.049 44.000 0.00 0.00 0.00 4.17
2699 2773 2.344950 CTACAGGCAAGCAGAGAACAG 58.655 52.381 0.00 0.00 0.00 3.16
2799 2879 9.770503 CTTCAATAGCAATAGCAATAGCAATAG 57.229 33.333 0.00 0.00 45.49 1.73
2800 2880 9.506018 TCTTCAATAGCAATAGCAATAGCAATA 57.494 29.630 0.00 0.00 45.49 1.90
2801 2881 8.400184 TCTTCAATAGCAATAGCAATAGCAAT 57.600 30.769 0.00 0.00 45.49 3.56
2802 2882 7.716560 TCTCTTCAATAGCAATAGCAATAGCAA 59.283 33.333 0.00 0.00 45.49 3.91
2803 2883 7.219322 TCTCTTCAATAGCAATAGCAATAGCA 58.781 34.615 0.00 0.00 45.49 3.49
2804 2884 7.664082 TCTCTTCAATAGCAATAGCAATAGC 57.336 36.000 0.00 0.00 45.49 2.97
2805 2885 9.433153 TCATCTCTTCAATAGCAATAGCAATAG 57.567 33.333 0.00 0.00 45.49 1.73
2806 2886 9.955102 ATCATCTCTTCAATAGCAATAGCAATA 57.045 29.630 0.00 0.00 45.49 1.90
2807 2887 8.731605 CATCATCTCTTCAATAGCAATAGCAAT 58.268 33.333 0.00 0.00 45.49 3.56
2808 2888 7.935210 TCATCATCTCTTCAATAGCAATAGCAA 59.065 33.333 0.00 0.00 45.49 3.91
2809 2889 7.447594 TCATCATCTCTTCAATAGCAATAGCA 58.552 34.615 0.00 0.00 45.49 3.49
2810 2890 7.902387 TCATCATCTCTTCAATAGCAATAGC 57.098 36.000 0.00 0.00 42.56 2.97
2811 2891 9.491675 AGTTCATCATCTCTTCAATAGCAATAG 57.508 33.333 0.00 0.00 0.00 1.73
2814 2894 9.269453 CATAGTTCATCATCTCTTCAATAGCAA 57.731 33.333 0.00 0.00 0.00 3.91
2815 2895 8.645110 TCATAGTTCATCATCTCTTCAATAGCA 58.355 33.333 0.00 0.00 0.00 3.49
2816 2896 9.656040 ATCATAGTTCATCATCTCTTCAATAGC 57.344 33.333 0.00 0.00 0.00 2.97
2819 2899 9.713713 CTCATCATAGTTCATCATCTCTTCAAT 57.286 33.333 0.00 0.00 0.00 2.57
2820 2900 7.656542 GCTCATCATAGTTCATCATCTCTTCAA 59.343 37.037 0.00 0.00 0.00 2.69
2821 2901 7.153315 GCTCATCATAGTTCATCATCTCTTCA 58.847 38.462 0.00 0.00 0.00 3.02
2822 2902 7.153315 TGCTCATCATAGTTCATCATCTCTTC 58.847 38.462 0.00 0.00 0.00 2.87
2888 2968 1.672363 TCACTCAATTCATCATGCCGC 59.328 47.619 0.00 0.00 0.00 6.53
2890 2970 2.034305 GGCTCACTCAATTCATCATGCC 59.966 50.000 0.00 0.00 0.00 4.40
2930 3033 0.391130 TGGCGGATCACAGTAACAGC 60.391 55.000 0.00 0.00 0.00 4.40
2932 3035 1.552792 TCATGGCGGATCACAGTAACA 59.447 47.619 0.00 0.00 0.00 2.41
2933 3036 2.309528 TCATGGCGGATCACAGTAAC 57.690 50.000 0.00 0.00 0.00 2.50
3040 3143 1.889105 CGGCCAGGTGAATGATCGG 60.889 63.158 2.24 0.00 0.00 4.18
3065 3176 2.818132 CCCTCATCAGTCCTCGCC 59.182 66.667 0.00 0.00 0.00 5.54
3167 3283 4.343814 CCGCATTCCCCACCTTATTTTAAT 59.656 41.667 0.00 0.00 0.00 1.40
3277 3394 3.356639 GAGTCGCGATGGTGGCAGA 62.357 63.158 14.06 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.