Multiple sequence alignment - TraesCS3B01G408300

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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 TraesCS3B01G408300 chr3B 100.000 2883 0 0 1 2883 643858899 643856017 0.000000e+00 5325
1 TraesCS3B01G408300 chr3D 91.204 2933 107 60 3 2865 481741518 481738667 0.000000e+00 3847
2 TraesCS3B01G408300 chr3A 87.649 2097 98 55 863 2883 624943152 624941141 0.000000e+00 2289
3 TraesCS3B01G408300 chr3A 88.655 476 32 15 1 458 624947997 624947526 6.980000e-156 560
4 TraesCS3B01G408300 chr1D 86.818 220 26 2 1610 1826 370885335 370885554 2.870000e-60 243
5 TraesCS3B01G408300 chr1B 86.818 220 26 2 1610 1826 494222761 494222980 2.870000e-60 243
6 TraesCS3B01G408300 chr1A 86.425 221 25 4 1610 1826 469645069 469645288 1.340000e-58 237


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 TraesCS3B01G408300 chr3B 643856017 643858899 2882 True 5325 5325 100.000 1 2883 1 chr3B.!!$R1 2882
1 TraesCS3B01G408300 chr3D 481738667 481741518 2851 True 3847 3847 91.204 3 2865 1 chr3D.!!$R1 2862
2 TraesCS3B01G408300 chr3A 624941141 624943152 2011 True 2289 2289 87.649 863 2883 1 chr3A.!!$R1 2020

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
372 373 0.107848 GGAATCGGTACTGTGGTGGG 60.108 60.0 0.64 0.0 0.0 4.61 F
627 628 0.167908 CGCTGCGCAGAAATTAACCA 59.832 50.0 40.21 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1882 0.311477 GCTAGCGGTAGGAGTGTAGC 59.689 60.0 22.24 4.89 0.00 3.58 R
2460 2560 0.235665 GACGTGACAACATGGCAGTG 59.764 55.0 0.00 0.00 35.04 3.66 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 9.803315 TTCATTTGACTCAGTATATGTACAGAC 57.197 33.333 0.33 0.00 33.09 3.51
53 54 9.692749 ATATGTACAGACGTCCAGTAAAATATG 57.307 33.333 13.01 2.08 0.00 1.78
78 79 6.463049 GCTGGGAGAGTATTAGATGCAGTTTA 60.463 42.308 0.00 0.00 0.00 2.01
79 80 7.618019 TGGGAGAGTATTAGATGCAGTTTAT 57.382 36.000 0.00 0.00 0.00 1.40
86 87 7.934457 AGTATTAGATGCAGTTTATTTGGCAG 58.066 34.615 0.00 0.00 39.95 4.85
94 95 4.606961 CAGTTTATTTGGCAGTTCACGTT 58.393 39.130 0.00 0.00 0.00 3.99
107 108 4.062293 AGTTCACGTTTCCATTCGATCAA 58.938 39.130 0.00 0.00 0.00 2.57
232 233 3.768468 TTAATTCTTTAAAGCGGCCGG 57.232 42.857 29.38 8.29 0.00 6.13
281 282 7.619328 CAGAATAACGCTGATATGATGCTATG 58.381 38.462 0.00 0.00 35.39 2.23
285 286 3.259123 ACGCTGATATGATGCTATGGACA 59.741 43.478 0.00 0.00 0.00 4.02
327 328 3.756434 GCCAATTGTTCAGCCAAGTACTA 59.244 43.478 4.43 0.00 0.00 1.82
329 330 5.003804 CCAATTGTTCAGCCAAGTACTACT 58.996 41.667 4.43 0.00 0.00 2.57
330 331 6.170506 CCAATTGTTCAGCCAAGTACTACTA 58.829 40.000 4.43 0.00 0.00 1.82
331 332 6.823689 CCAATTGTTCAGCCAAGTACTACTAT 59.176 38.462 4.43 0.00 0.00 2.12
337 338 6.208988 TCAGCCAAGTACTACTATTGTGAG 57.791 41.667 0.00 0.00 0.00 3.51
372 373 0.107848 GGAATCGGTACTGTGGTGGG 60.108 60.000 0.64 0.00 0.00 4.61
392 393 4.832823 TGGGTTGGGAAAAGAAAAGATCTC 59.167 41.667 0.00 0.00 37.42 2.75
519 520 1.001293 TCAGCAGCAGACTTTCGTCAT 59.999 47.619 0.00 0.00 42.73 3.06
545 546 2.613977 CCAAAGCCGTGACAAGATCTCT 60.614 50.000 0.00 0.00 0.00 3.10
566 567 1.171549 TTTTTACCGCCCGAACCACC 61.172 55.000 0.00 0.00 0.00 4.61
617 618 2.431430 TCTGAACTCGCTGCGCAG 60.431 61.111 32.83 32.83 0.00 5.18
627 628 0.167908 CGCTGCGCAGAAATTAACCA 59.832 50.000 40.21 0.00 0.00 3.67
655 656 0.758734 CCAGTCACACTCACAGGGAA 59.241 55.000 0.00 0.00 0.00 3.97
752 757 2.542618 GCACTGATGACTGATCGACGAT 60.543 50.000 10.78 10.78 33.17 3.73
813 824 2.702751 TTCCACACGTACACGCCTGG 62.703 60.000 10.60 10.60 44.43 4.45
814 825 3.411351 CACACGTACACGCCTGGC 61.411 66.667 9.11 9.11 44.43 4.85
846 857 1.335324 GCATTTTCACTTGCACGCTCT 60.335 47.619 0.00 0.00 38.72 4.09
897 908 4.679373 ATTATCCTCTTCACATGCTCGT 57.321 40.909 0.00 0.00 0.00 4.18
898 909 2.593346 ATCCTCTTCACATGCTCGTC 57.407 50.000 0.00 0.00 0.00 4.20
899 910 0.532573 TCCTCTTCACATGCTCGTCC 59.467 55.000 0.00 0.00 0.00 4.79
1064 1077 1.475169 CCACACTCCCAGCTCACTCA 61.475 60.000 0.00 0.00 0.00 3.41
1075 1088 0.241213 GCTCACTCACAGACGCACTA 59.759 55.000 0.00 0.00 0.00 2.74
1114 1141 3.382803 CTAGCCAGCCAAGCGAGCT 62.383 63.158 10.48 10.48 42.45 4.09
1115 1142 2.021068 CTAGCCAGCCAAGCGAGCTA 62.021 60.000 11.40 11.40 40.83 3.32
1116 1143 2.021068 TAGCCAGCCAAGCGAGCTAG 62.021 60.000 0.00 0.00 40.83 3.42
1180 1216 3.881019 AAGCCGTCGTCCAGGAGGA 62.881 63.158 7.83 7.83 43.21 3.71
1189 1225 1.229304 TCCAGGAGGAGCAGCTTCA 60.229 57.895 2.68 0.00 39.61 3.02
1452 1491 3.834799 CTGTACGAGGACCCCGCC 61.835 72.222 0.00 0.00 0.00 6.13
1815 1860 2.041265 GGCCTCTTCTCCCCTCCA 59.959 66.667 0.00 0.00 0.00 3.86
1821 1866 2.040442 TTCTCCCCTCCATCGCCA 59.960 61.111 0.00 0.00 0.00 5.69
1835 1880 2.182842 CGCCATGCCAGTTCTAGCC 61.183 63.158 0.00 0.00 0.00 3.93
1836 1881 1.077501 GCCATGCCAGTTCTAGCCA 60.078 57.895 0.00 0.00 0.00 4.75
1837 1882 1.099879 GCCATGCCAGTTCTAGCCAG 61.100 60.000 0.00 0.00 0.00 4.85
1838 1883 1.099879 CCATGCCAGTTCTAGCCAGC 61.100 60.000 0.00 0.00 0.00 4.85
1842 1887 0.537188 GCCAGTTCTAGCCAGCTACA 59.463 55.000 0.00 0.00 0.00 2.74
1851 1896 1.038130 AGCCAGCTACACTCCTACCG 61.038 60.000 0.00 0.00 0.00 4.02
1923 1981 3.188100 CGCACGCATCCACGTCAT 61.188 61.111 0.00 0.00 46.34 3.06
2003 2064 4.101645 TCCTAGTAGTAGCACCTGATCC 57.898 50.000 0.00 0.00 0.00 3.36
2013 2074 1.406069 GCACCTGATCCATCGTCAGTT 60.406 52.381 2.86 0.00 41.13 3.16
2014 2075 2.544685 CACCTGATCCATCGTCAGTTC 58.455 52.381 2.86 0.00 41.13 3.01
2057 2126 0.105593 CCTCCATGTCCATCACTCCG 59.894 60.000 0.00 0.00 0.00 4.63
2097 2166 2.391724 TTAATGGAGATCCCGGCCGC 62.392 60.000 22.85 5.89 37.93 6.53
2144 2213 2.861286 GCTCAAGCTAAGCTGAAAAGC 58.139 47.619 12.56 0.00 39.62 3.51
2146 2215 3.686726 GCTCAAGCTAAGCTGAAAAGCTA 59.313 43.478 12.56 0.16 45.61 3.32
2147 2216 4.201802 GCTCAAGCTAAGCTGAAAAGCTAG 60.202 45.833 12.56 8.86 45.61 3.42
2148 2217 3.686726 TCAAGCTAAGCTGAAAAGCTAGC 59.313 43.478 6.62 6.62 45.61 3.42
2269 2353 5.098893 TGTTTGTGTTTGTGCATCAAGTAC 58.901 37.500 0.00 0.96 37.35 2.73
2355 2448 6.201044 CGTCACTCATCTTTCACTGTTTTACT 59.799 38.462 0.00 0.00 0.00 2.24
2378 2477 4.341783 GCCACTGGACTGCTGGCT 62.342 66.667 0.00 0.00 46.05 4.75
2380 2479 1.220206 CCACTGGACTGCTGGCTAG 59.780 63.158 8.34 8.34 0.00 3.42
2440 2539 4.031765 CGTCCTGTCAACTCGTGAAATATG 59.968 45.833 0.00 0.00 38.23 1.78
2445 2544 5.053811 TGTCAACTCGTGAAATATGTGTGT 58.946 37.500 0.00 0.00 38.23 3.72
2460 2560 2.090524 GTGTACTACGTGCCGCACC 61.091 63.158 17.81 3.21 0.00 5.01
2461 2561 2.259204 GTACTACGTGCCGCACCA 59.741 61.111 17.81 5.18 0.00 4.17
2462 2562 2.090524 GTACTACGTGCCGCACCAC 61.091 63.158 17.81 4.79 0.00 4.16
2464 2564 2.480853 TACTACGTGCCGCACCACTG 62.481 60.000 17.81 6.27 33.60 3.66
2505 2605 1.595609 CTTTTCGTTCTCGTGCATGC 58.404 50.000 11.82 11.82 38.33 4.06
2506 2606 0.110867 TTTTCGTTCTCGTGCATGCG 60.111 50.000 14.09 0.00 38.33 4.73
2507 2607 1.218875 TTTCGTTCTCGTGCATGCGT 61.219 50.000 14.09 0.00 38.33 5.24
2508 2608 0.387494 TTCGTTCTCGTGCATGCGTA 60.387 50.000 14.09 0.00 38.33 4.42
2605 2732 1.361668 CCGAGGCTGATTTGTGTCCG 61.362 60.000 0.00 0.00 0.00 4.79
2700 2827 0.536915 GGCCTGGATGAGATTGGAGC 60.537 60.000 0.00 0.00 0.00 4.70
2736 2863 0.824109 AATCAACGGCTGGATCTCGA 59.176 50.000 0.00 0.00 0.00 4.04
2748 2875 0.247736 GATCTCGACACAGTGCCCTT 59.752 55.000 0.00 0.00 0.00 3.95
2781 2908 4.467084 GATTGCGTCGGGGCCTCA 62.467 66.667 1.96 0.00 0.00 3.86
2823 2950 2.338015 GGTCGACGGAGCCACAGTA 61.338 63.158 9.92 0.00 34.60 2.74
2866 2994 5.151454 TCATTGGGGTAAATTTTCACTGGT 58.849 37.500 0.00 0.00 0.00 4.00
2869 2997 3.141272 TGGGGTAAATTTTCACTGGTCCT 59.859 43.478 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.997482 ACGTCTGTACATATACTGAGTCAAAT 58.003 34.615 0.00 0.00 39.23 2.32
21 22 5.527951 ACTGGACGTCTGTACATATACTGAG 59.472 44.000 16.46 0.00 38.57 3.35
24 25 7.870509 TTTACTGGACGTCTGTACATATACT 57.129 36.000 16.46 0.00 38.57 2.12
53 54 3.323403 ACTGCATCTAATACTCTCCCAGC 59.677 47.826 0.00 0.00 0.00 4.85
61 62 7.557719 ACTGCCAAATAAACTGCATCTAATACT 59.442 33.333 0.00 0.00 32.53 2.12
78 79 2.028130 TGGAAACGTGAACTGCCAAAT 58.972 42.857 0.00 0.00 0.00 2.32
79 80 1.464734 TGGAAACGTGAACTGCCAAA 58.535 45.000 0.00 0.00 0.00 3.28
86 87 4.398549 TTGATCGAATGGAAACGTGAAC 57.601 40.909 0.00 0.00 0.00 3.18
119 120 1.965643 AGTACATAGCCGCCGGAAATA 59.034 47.619 7.68 0.00 0.00 1.40
125 126 0.729478 CGATCAGTACATAGCCGCCG 60.729 60.000 0.00 0.00 0.00 6.46
212 213 2.424246 CCCGGCCGCTTTAAAGAATTAA 59.576 45.455 22.85 0.00 0.00 1.40
232 233 6.615726 TGCTATATATGTATTCTTCCCCTCCC 59.384 42.308 0.00 0.00 0.00 4.30
293 294 7.201688 GGCTGAACAATTGGCTCTTTTTAAAAA 60.202 33.333 12.62 12.62 0.00 1.94
297 298 4.343526 TGGCTGAACAATTGGCTCTTTTTA 59.656 37.500 10.83 0.00 0.00 1.52
308 309 7.883311 ACAATAGTAGTACTTGGCTGAACAATT 59.117 33.333 8.40 0.00 0.00 2.32
343 344 5.468746 CACAGTACCGATTCCTTGAGAAAAA 59.531 40.000 0.00 0.00 38.21 1.94
357 358 1.749665 CAACCCACCACAGTACCGA 59.250 57.895 0.00 0.00 0.00 4.69
372 373 7.277174 TCAAGAGATCTTTTCTTTTCCCAAC 57.723 36.000 0.00 0.00 33.74 3.77
392 393 3.500299 TCTCTGTCGAGTCTCTGTTCAAG 59.500 47.826 0.00 0.00 38.45 3.02
519 520 4.274602 TCTTGTCACGGCTTTGGTAATA 57.725 40.909 0.00 0.00 0.00 0.98
617 618 3.492337 TGGACAGTGGGTGGTTAATTTC 58.508 45.455 0.00 0.00 0.00 2.17
627 628 0.691078 AGTGTGACTGGACAGTGGGT 60.691 55.000 10.08 0.00 42.66 4.51
655 656 1.820581 GGCTGCATGCATCAATGGT 59.179 52.632 22.97 0.00 45.15 3.55
715 716 1.097547 GTGCATGGCCGCAAGATAGT 61.098 55.000 6.91 0.00 45.14 2.12
716 717 0.816825 AGTGCATGGCCGCAAGATAG 60.817 55.000 6.91 0.00 45.14 2.08
814 825 0.590732 GAAAATGCATGCCGCGAGAG 60.591 55.000 16.68 0.00 46.97 3.20
846 857 1.304052 CTGGGTGAAAATGGGCCGA 60.304 57.895 0.00 0.00 0.00 5.54
851 862 1.304052 TCGGCCTGGGTGAAAATGG 60.304 57.895 0.00 0.00 0.00 3.16
853 864 1.674322 CGTCGGCCTGGGTGAAAAT 60.674 57.895 0.00 0.00 0.00 1.82
897 908 3.430497 CGGGGAGGAGGAGGAGGA 61.430 72.222 0.00 0.00 0.00 3.71
898 909 4.548513 CCGGGGAGGAGGAGGAGG 62.549 77.778 0.00 0.00 45.00 4.30
1064 1077 1.007734 CACCGTGTAGTGCGTCTGT 60.008 57.895 0.00 0.00 0.00 3.41
1075 1088 2.426023 GAGGAAGGTGCACCGTGT 59.574 61.111 29.65 18.84 42.08 4.49
1140 1167 2.669569 GACATGGCGTGGCAGTGT 60.670 61.111 7.92 6.71 35.22 3.55
1815 1860 0.533755 GCTAGAACTGGCATGGCGAT 60.534 55.000 15.27 1.61 37.02 4.58
1821 1866 1.139853 GTAGCTGGCTAGAACTGGCAT 59.860 52.381 0.00 0.00 38.96 4.40
1835 1880 1.604755 CTAGCGGTAGGAGTGTAGCTG 59.395 57.143 13.90 0.00 36.30 4.24
1836 1881 1.970092 CTAGCGGTAGGAGTGTAGCT 58.030 55.000 13.90 0.00 38.57 3.32
1837 1882 0.311477 GCTAGCGGTAGGAGTGTAGC 59.689 60.000 22.24 4.89 0.00 3.58
1838 1883 1.970092 AGCTAGCGGTAGGAGTGTAG 58.030 55.000 22.24 0.00 0.00 2.74
1842 1887 2.101082 GCTTTTAGCTAGCGGTAGGAGT 59.899 50.000 22.24 0.00 38.45 3.85
1914 1968 2.756760 GGTGGTAAGAGTATGACGTGGA 59.243 50.000 0.00 0.00 0.00 4.02
1917 1975 3.428532 ACTGGTGGTAAGAGTATGACGT 58.571 45.455 0.00 0.00 0.00 4.34
1923 1981 5.490357 AGGAGTAGTACTGGTGGTAAGAGTA 59.510 44.000 7.76 0.00 31.56 2.59
2003 2064 4.413087 AGCTAGTTAACGAACTGACGATG 58.587 43.478 0.00 0.00 45.74 3.84
2013 2074 3.873910 ACTACGGGTAGCTAGTTAACGA 58.126 45.455 15.49 0.00 36.66 3.85
2014 2075 4.811557 AGTACTACGGGTAGCTAGTTAACG 59.188 45.833 5.78 9.41 36.66 3.18
2144 2213 5.641209 GGATTACACCATCATGCTTAGCTAG 59.359 44.000 5.60 0.00 0.00 3.42
2145 2214 5.071653 TGGATTACACCATCATGCTTAGCTA 59.928 40.000 5.60 0.00 34.77 3.32
2146 2215 4.141413 TGGATTACACCATCATGCTTAGCT 60.141 41.667 5.60 0.00 34.77 3.32
2147 2216 4.136796 TGGATTACACCATCATGCTTAGC 58.863 43.478 0.00 0.00 34.77 3.09
2148 2217 6.698008 TTTGGATTACACCATCATGCTTAG 57.302 37.500 0.00 0.00 39.82 2.18
2269 2353 1.583856 CGACTGCATAACTAGTGCACG 59.416 52.381 12.01 0.00 46.76 5.34
2286 2379 1.583054 AAGGTTGAGCAGTGAACGAC 58.417 50.000 0.00 0.00 0.00 4.34
2315 2408 7.984050 AGATGAGTGACGATATGTTTCTTCAAT 59.016 33.333 0.00 0.00 0.00 2.57
2330 2423 5.409643 AAAACAGTGAAAGATGAGTGACG 57.590 39.130 0.00 0.00 0.00 4.35
2355 2448 1.302752 GCAGTCCAGTGGCATGTCA 60.303 57.895 3.51 0.00 0.00 3.58
2378 2477 4.602995 CAACAAAAGCAGCGGTAAAACTA 58.397 39.130 0.00 0.00 0.00 2.24
2380 2479 2.034086 GCAACAAAAGCAGCGGTAAAAC 60.034 45.455 0.00 0.00 0.00 2.43
2460 2560 0.235665 GACGTGACAACATGGCAGTG 59.764 55.000 0.00 0.00 35.04 3.66
2461 2561 0.884704 GGACGTGACAACATGGCAGT 60.885 55.000 0.00 0.00 42.42 4.40
2462 2562 0.884259 TGGACGTGACAACATGGCAG 60.884 55.000 0.00 0.00 42.42 4.85
2464 2564 0.881118 ATTGGACGTGACAACATGGC 59.119 50.000 0.00 0.00 40.10 4.40
2553 2656 3.403057 CACCTGGTTCACGACGCG 61.403 66.667 3.53 3.53 0.00 6.01
2554 2657 3.712881 GCACCTGGTTCACGACGC 61.713 66.667 0.00 0.00 0.00 5.19
2555 2658 1.433053 TTTGCACCTGGTTCACGACG 61.433 55.000 0.00 0.00 0.00 5.12
2556 2659 0.736053 TTTTGCACCTGGTTCACGAC 59.264 50.000 0.00 0.00 0.00 4.34
2557 2660 1.021202 CTTTTGCACCTGGTTCACGA 58.979 50.000 0.00 0.00 0.00 4.35
2605 2732 2.359967 AACTAGACGCTGGAGGGGC 61.360 63.158 0.00 0.00 36.06 5.80
2617 2744 2.479837 CCGCACAGTGAAACAACTAGA 58.520 47.619 4.15 0.00 41.43 2.43
2619 2746 1.588674 CCCGCACAGTGAAACAACTA 58.411 50.000 4.15 0.00 41.43 2.24
2673 2800 1.852157 TCATCCAGGCCCCAACAGT 60.852 57.895 0.00 0.00 0.00 3.55
2700 2827 4.569023 TCGCACGCCTGCTATCCG 62.569 66.667 6.13 0.00 41.77 4.18
2748 2875 0.467844 AATCAAGCCCACACAGTGCA 60.468 50.000 0.00 0.00 31.34 4.57
2764 2891 4.467084 TGAGGCCCCGACGCAATC 62.467 66.667 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.