Multiple sequence alignment - TraesCS5D01G446400

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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 TraesCS5D01G446400 chr5D 100.000 3343 0 0 1 3343 496845494 496848836 0.000000e+00 6174.0
1 TraesCS5D01G446400 chr5B 92.032 3376 137 61 1 3331 615586187 615589475 0.000000e+00 4623.0
2 TraesCS5D01G446400 chr5B 93.103 58 4 0 325 382 615694119 615694176 5.940000e-13 86.1
3 TraesCS5D01G446400 chr5A 91.855 2615 78 52 782 3343 620857106 620859638 0.000000e+00 3524.0
4 TraesCS5D01G446400 chr5A 89.677 775 56 15 1 755 620855980 620856750 0.000000e+00 966.0
5 TraesCS5D01G446400 chr4A 75.785 223 50 4 1870 2090 17675984 17676204 3.530000e-20 110.0
6 TraesCS5D01G446400 chr4B 74.783 230 54 4 1868 2095 561386130 561385903 2.120000e-17 100.0
7 TraesCS5D01G446400 chr4D 74.324 222 55 2 1870 2090 449055607 449055387 3.550000e-15 93.5


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 TraesCS5D01G446400 chr5D 496845494 496848836 3342 False 6174 6174 100.000 1 3343 1 chr5D.!!$F1 3342
1 TraesCS5D01G446400 chr5B 615586187 615589475 3288 False 4623 4623 92.032 1 3331 1 chr5B.!!$F1 3330
2 TraesCS5D01G446400 chr5A 620855980 620859638 3658 False 2245 3524 90.766 1 3343 2 chr5A.!!$F1 3342

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
44 45 1.203758 GTTGCGGGTAAATTGGGAAGG 59.796 52.381 0.0 0.0 0.00 3.46 F
1717 2106 0.333993 AGACTAAGTCCTACCCCGCA 59.666 55.000 0.0 0.0 32.18 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 2189 0.879400 GCGTAGACGGAGAGGATCGA 60.879 60.0 3.97 0.0 39.30 3.59 R
3158 3608 0.531974 GCGCCACCGGATAGAATGAA 60.532 55.0 9.46 0.0 34.32 2.57 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
38 39 1.718711 CTTTGCGTTGCGGGTAAATTG 59.281 47.619 0.00 0.00 0.00 2.32
44 45 1.203758 GTTGCGGGTAAATTGGGAAGG 59.796 52.381 0.00 0.00 0.00 3.46
52 53 5.625886 CGGGTAAATTGGGAAGGGAATTTTC 60.626 44.000 0.00 0.00 34.42 2.29
111 112 1.385743 GCAGTCGTAGTACAACTTGCG 59.614 52.381 0.38 0.00 0.00 4.85
118 119 3.245754 CGTAGTACAACTTGCGTTTTCCA 59.754 43.478 0.38 0.00 0.00 3.53
119 120 4.260294 CGTAGTACAACTTGCGTTTTCCAA 60.260 41.667 0.38 0.00 0.00 3.53
120 121 4.287238 AGTACAACTTGCGTTTTCCAAG 57.713 40.909 0.00 0.00 43.98 3.61
121 122 3.942748 AGTACAACTTGCGTTTTCCAAGA 59.057 39.130 8.01 0.00 41.64 3.02
242 268 1.674221 CCCTGCTCAAAAGTCCTCTCG 60.674 57.143 0.00 0.00 0.00 4.04
244 270 2.231478 CCTGCTCAAAAGTCCTCTCGTA 59.769 50.000 0.00 0.00 0.00 3.43
266 293 3.131755 ACTTACGTATGGACTAGGCCAAC 59.868 47.826 24.47 19.13 42.16 3.77
308 341 8.613922 ATCCAATCCAACCAGAAAAGATAAAT 57.386 30.769 0.00 0.00 0.00 1.40
383 421 3.886505 CAGTAGTCCCTCACTATCCAGTC 59.113 52.174 0.00 0.00 39.90 3.51
444 483 4.483243 TCCCAGCGCGAAATCCCC 62.483 66.667 12.10 0.00 0.00 4.81
519 558 2.457778 GCAAAATGGGCATGCGCAG 61.458 57.895 35.93 25.26 42.04 5.18
848 1219 4.208686 GGCAGTAGAGGGCGTCCG 62.209 72.222 0.00 0.00 38.33 4.79
849 1220 3.450115 GCAGTAGAGGGCGTCCGT 61.450 66.667 0.00 0.00 38.33 4.69
850 1221 2.799371 CAGTAGAGGGCGTCCGTC 59.201 66.667 0.00 5.41 38.54 4.79
857 1228 3.040844 GGGCGTCCGTCCTATCTC 58.959 66.667 2.48 0.00 36.84 2.75
858 1229 1.528776 GGGCGTCCGTCCTATCTCT 60.529 63.158 2.48 0.00 36.84 3.10
1018 1394 1.986575 GATGCCGTTCCAGCTCAAGC 61.987 60.000 0.00 0.00 42.49 4.01
1526 1915 1.286880 CTTTCCCTTTGCGTGCAGG 59.713 57.895 1.01 1.01 0.00 4.85
1543 1932 4.389576 GGTTTGGTGCAGAGCGCG 62.390 66.667 0.00 0.00 46.97 6.86
1702 2091 2.676822 TCGCGCTGGGAGAAGACT 60.677 61.111 5.56 0.00 0.00 3.24
1717 2106 0.333993 AGACTAAGTCCTACCCCGCA 59.666 55.000 0.00 0.00 32.18 5.69
1751 2141 1.320344 CCCGTCCTCCTCGATTCACA 61.320 60.000 0.00 0.00 0.00 3.58
1763 2153 1.268589 CGATTCACATACGCTCGGTCT 60.269 52.381 0.00 0.00 0.00 3.85
1764 2154 2.032290 CGATTCACATACGCTCGGTCTA 60.032 50.000 0.00 0.00 0.00 2.59
1792 2184 2.165643 TTTCATGGCATGGCAGGGGA 62.166 55.000 30.13 21.79 0.00 4.81
1796 2188 0.562177 ATGGCATGGCAGGGGATTAA 59.438 50.000 27.02 0.00 0.00 1.40
1797 2189 0.562177 TGGCATGGCAGGGGATTAAT 59.438 50.000 19.43 0.00 0.00 1.40
1798 2190 1.260544 GGCATGGCAGGGGATTAATC 58.739 55.000 15.47 6.93 0.00 1.75
1801 2193 2.881403 GCATGGCAGGGGATTAATCGAT 60.881 50.000 9.32 0.00 0.00 3.59
1804 2196 1.630878 GGCAGGGGATTAATCGATCCT 59.369 52.381 9.32 12.22 44.17 3.24
1805 2197 2.355209 GGCAGGGGATTAATCGATCCTC 60.355 54.545 16.09 0.00 45.46 3.71
1808 2200 3.897141 GGGGATTAATCGATCCTCTCC 57.103 52.381 9.32 1.49 42.42 3.71
1858 2253 4.388499 CGTGGTTGGGGACGGAGG 62.388 72.222 0.00 0.00 31.84 4.30
2219 2620 1.450312 CATGAACAGGAGCGGGGTC 60.450 63.158 0.00 0.00 0.00 4.46
2536 2952 4.007323 ACTCGCCCACCCCCTAGT 62.007 66.667 0.00 0.00 0.00 2.57
2629 3045 1.675641 GCCGTGGAGCTTTGGTGAT 60.676 57.895 0.00 0.00 0.00 3.06
2652 3068 4.485530 ACCCCCTCCCGCCGAATA 62.486 66.667 0.00 0.00 0.00 1.75
2653 3069 3.626924 CCCCCTCCCGCCGAATAG 61.627 72.222 0.00 0.00 0.00 1.73
2800 3220 9.924650 GAGTTGTTATATAATCTTATGGACGGT 57.075 33.333 0.00 0.00 0.00 4.83
2801 3221 9.924650 AGTTGTTATATAATCTTATGGACGGTC 57.075 33.333 0.00 0.00 0.00 4.79
2816 3236 1.806542 ACGGTCTGCTTGTTATTGCTG 59.193 47.619 0.00 0.00 0.00 4.41
2882 3329 4.955811 TGTTTTTCTCCACTCTGCTCTA 57.044 40.909 0.00 0.00 0.00 2.43
2884 3331 4.345257 TGTTTTTCTCCACTCTGCTCTACT 59.655 41.667 0.00 0.00 0.00 2.57
2885 3332 5.538813 TGTTTTTCTCCACTCTGCTCTACTA 59.461 40.000 0.00 0.00 0.00 1.82
2886 3333 5.646577 TTTTCTCCACTCTGCTCTACTAC 57.353 43.478 0.00 0.00 0.00 2.73
2887 3334 4.577988 TTCTCCACTCTGCTCTACTACT 57.422 45.455 0.00 0.00 0.00 2.57
2899 3346 5.536260 TGCTCTACTACTGCATGATGAATC 58.464 41.667 0.00 0.00 0.00 2.52
2904 3351 3.744942 ACTACTGCATGATGAATCGATGC 59.255 43.478 0.00 0.00 39.51 3.91
2906 3353 2.946990 ACTGCATGATGAATCGATGCAA 59.053 40.909 10.89 0.00 43.58 4.08
3153 3603 1.269831 GCCCGTCTATCCAGTAAGCAG 60.270 57.143 0.00 0.00 0.00 4.24
3154 3604 2.307768 CCCGTCTATCCAGTAAGCAGA 58.692 52.381 0.00 0.00 0.00 4.26
3155 3605 2.294791 CCCGTCTATCCAGTAAGCAGAG 59.705 54.545 0.00 0.00 0.00 3.35
3156 3606 2.952978 CCGTCTATCCAGTAAGCAGAGT 59.047 50.000 0.00 0.00 0.00 3.24
3158 3608 3.378742 CGTCTATCCAGTAAGCAGAGTGT 59.621 47.826 0.00 0.00 0.00 3.55
3159 3609 4.142359 CGTCTATCCAGTAAGCAGAGTGTT 60.142 45.833 0.00 0.00 0.00 3.32
3160 3610 5.344884 GTCTATCCAGTAAGCAGAGTGTTC 58.655 45.833 0.00 0.00 0.00 3.18
3190 3640 0.928229 GTGGCGCGTCGAATAAATCT 59.072 50.000 6.09 0.00 0.00 2.40
3191 3641 2.121786 GTGGCGCGTCGAATAAATCTA 58.878 47.619 6.09 0.00 0.00 1.98
3213 3664 4.680407 AGGGTTAAAATAAGGTGGGGAAC 58.320 43.478 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.718711 CAATTTACCCGCAACGCAAAG 59.281 47.619 0.00 0.00 0.00 2.77
38 39 2.766263 GGACCATGAAAATTCCCTTCCC 59.234 50.000 0.00 0.00 0.00 3.97
44 45 3.388552 AGGGAGGACCATGAAAATTCC 57.611 47.619 0.00 0.00 43.89 3.01
52 53 4.946157 GCATCATATTTAGGGAGGACCATG 59.054 45.833 0.00 0.00 43.89 3.66
256 282 2.148768 GTTTTAGCGTGTTGGCCTAGT 58.851 47.619 3.32 0.00 0.00 2.57
335 373 2.224257 TGCTACCGACCCGTTTAAAAGT 60.224 45.455 0.47 0.00 0.00 2.66
383 421 2.343758 CGTGAGGTGTGGAGTGGG 59.656 66.667 0.00 0.00 0.00 4.61
444 483 1.347050 CTGGAGCTCAGGGGTATGATG 59.653 57.143 17.19 0.00 39.76 3.07
477 516 0.374758 CGATGATGGTCTGCCGTTTG 59.625 55.000 0.00 0.00 37.67 2.93
681 720 0.892358 GAAGGGGGTTCAAACGGGAC 60.892 60.000 0.00 0.00 34.97 4.46
774 817 1.878948 GCGGGCGGCTGGTTATTATTA 60.879 52.381 20.56 0.00 39.11 0.98
776 819 1.599797 GCGGGCGGCTGGTTATTAT 60.600 57.895 20.56 0.00 39.11 1.28
867 1238 1.586422 CCAACCACACACACAGAGAG 58.414 55.000 0.00 0.00 0.00 3.20
1176 1561 1.681486 CCTCCTTCTCCCGCTCCTTC 61.681 65.000 0.00 0.00 0.00 3.46
1526 1915 4.389576 CGCGCTCTGCACCAAACC 62.390 66.667 5.56 0.00 46.97 3.27
1601 1990 1.675641 CCTTTCCCTTGCAGGTCCG 60.676 63.158 0.00 0.00 31.93 4.79
1702 2091 4.368003 CCTGCGGGGTAGGACTTA 57.632 61.111 2.57 0.00 37.63 2.24
1717 2106 2.970640 GGACGGGATAGATTTGGTACCT 59.029 50.000 14.36 0.00 0.00 3.08
1724 2113 2.158505 TCGAGGAGGACGGGATAGATTT 60.159 50.000 0.00 0.00 0.00 2.17
1725 2114 1.424302 TCGAGGAGGACGGGATAGATT 59.576 52.381 0.00 0.00 0.00 2.40
1726 2115 1.065647 TCGAGGAGGACGGGATAGAT 58.934 55.000 0.00 0.00 0.00 1.98
1727 2116 1.065647 ATCGAGGAGGACGGGATAGA 58.934 55.000 0.00 0.00 0.00 1.98
1728 2117 1.813786 GAATCGAGGAGGACGGGATAG 59.186 57.143 0.00 0.00 0.00 2.08
1729 2118 1.144298 TGAATCGAGGAGGACGGGATA 59.856 52.381 0.00 0.00 0.00 2.59
1751 2141 3.022406 GGGGAATATAGACCGAGCGTAT 58.978 50.000 0.00 0.00 0.00 3.06
1763 2153 4.676109 CCATGCCATGAAAGGGGAATATA 58.324 43.478 6.18 0.00 45.20 0.86
1764 2154 3.513517 CCATGCCATGAAAGGGGAATAT 58.486 45.455 6.18 0.00 45.20 1.28
1792 2184 4.392445 CGTAGACGGAGAGGATCGATTAAT 59.608 45.833 0.00 0.00 36.34 1.40
1796 2188 1.798283 CGTAGACGGAGAGGATCGAT 58.202 55.000 0.00 0.00 36.34 3.59
1797 2189 0.879400 GCGTAGACGGAGAGGATCGA 60.879 60.000 3.97 0.00 39.30 3.59
1798 2190 1.158484 TGCGTAGACGGAGAGGATCG 61.158 60.000 3.97 0.00 39.30 3.69
1806 2198 2.439701 CTCCCCTGCGTAGACGGA 60.440 66.667 0.53 5.62 40.23 4.69
1807 2199 4.208686 GCTCCCCTGCGTAGACGG 62.209 72.222 0.53 0.81 40.23 4.79
1808 2200 3.449227 TGCTCCCCTGCGTAGACG 61.449 66.667 0.53 0.00 43.27 4.18
1858 2253 4.899239 CCTCCACGATCAGCCGCC 62.899 72.222 0.00 0.00 0.00 6.13
1860 2255 2.202797 CACCTCCACGATCAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
1976 2371 1.605058 CCACGGACACGATCTTCCCT 61.605 60.000 0.00 0.00 44.60 4.20
2456 2865 2.265647 ACACGGAAACACCAAAAACG 57.734 45.000 0.00 0.00 38.90 3.60
2523 2937 0.762082 GGTACTACTAGGGGGTGGGC 60.762 65.000 0.00 0.00 0.00 5.36
2525 2939 2.606378 GATGGTACTACTAGGGGGTGG 58.394 57.143 0.00 0.00 0.00 4.61
2527 2941 2.229523 TGGATGGTACTACTAGGGGGT 58.770 52.381 0.00 0.00 0.00 4.95
2536 2952 7.888514 AATTAATGGAGGATGGATGGTACTA 57.111 36.000 0.00 0.00 0.00 1.82
2797 3217 1.806542 ACAGCAATAACAAGCAGACCG 59.193 47.619 0.00 0.00 0.00 4.79
2800 3220 4.821260 TCTTCAACAGCAATAACAAGCAGA 59.179 37.500 0.00 0.00 0.00 4.26
2801 3221 5.049198 TCTCTTCAACAGCAATAACAAGCAG 60.049 40.000 0.00 0.00 0.00 4.24
2816 3236 9.809096 TTACTCATCATAGTTCATCTCTTCAAC 57.191 33.333 0.00 0.00 0.00 3.18
2853 3300 5.359009 CAGAGTGGAGAAAAACATGGCATAT 59.641 40.000 0.00 0.00 0.00 1.78
2882 3329 3.744942 GCATCGATTCATCATGCAGTAGT 59.255 43.478 0.00 0.00 39.21 2.73
2884 3331 3.731089 TGCATCGATTCATCATGCAGTA 58.269 40.909 16.44 0.00 41.62 2.74
2885 3332 2.567985 TGCATCGATTCATCATGCAGT 58.432 42.857 16.44 0.00 41.62 4.40
2886 3333 3.297472 GTTGCATCGATTCATCATGCAG 58.703 45.455 18.18 0.00 44.21 4.41
2887 3334 2.286536 CGTTGCATCGATTCATCATGCA 60.287 45.455 11.75 16.44 43.11 3.96
2899 3346 3.551485 TCAAGTGTATCATCGTTGCATCG 59.449 43.478 10.93 10.93 0.00 3.84
2904 3351 4.032217 GCTCACTCAAGTGTATCATCGTTG 59.968 45.833 9.82 0.00 45.76 4.10
2906 3353 3.429547 GGCTCACTCAAGTGTATCATCGT 60.430 47.826 9.82 0.00 45.76 3.73
2913 3360 1.961394 AGTTCGGCTCACTCAAGTGTA 59.039 47.619 9.82 0.00 45.76 2.90
2943 3390 2.739292 CGGATCACAGTAATGGTACCG 58.261 52.381 7.57 0.00 0.00 4.02
3153 3603 3.458189 CCACCGGATAGAATGAACACTC 58.542 50.000 9.46 0.00 0.00 3.51
3154 3604 2.420129 GCCACCGGATAGAATGAACACT 60.420 50.000 9.46 0.00 0.00 3.55
3155 3605 1.940613 GCCACCGGATAGAATGAACAC 59.059 52.381 9.46 0.00 0.00 3.32
3156 3606 1.472552 CGCCACCGGATAGAATGAACA 60.473 52.381 9.46 0.00 0.00 3.18
3158 3608 0.531974 GCGCCACCGGATAGAATGAA 60.532 55.000 9.46 0.00 34.32 2.57
3159 3609 1.069090 GCGCCACCGGATAGAATGA 59.931 57.895 9.46 0.00 34.32 2.57
3160 3610 2.310233 CGCGCCACCGGATAGAATG 61.310 63.158 9.46 0.00 34.32 2.67
3190 3640 5.573296 CGTTCCCCACCTTATTTTAACCCTA 60.573 44.000 0.00 0.00 0.00 3.53
3191 3641 4.680407 GTTCCCCACCTTATTTTAACCCT 58.320 43.478 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.