Multiple sequence alignment - TraesCS2B01G305500

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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 TraesCS2B01G305500 chr2B 100.000 2789 0 0 1 2789 435628368 435631156 0.000000e+00 5151.0
1 TraesCS2B01G305500 chr2A 94.643 2072 62 19 305 2366 496562131 496564163 0.000000e+00 3166.0
2 TraesCS2B01G305500 chr2A 91.343 335 21 5 2457 2789 496564159 496564487 4.240000e-123 451.0
3 TraesCS2B01G305500 chr2A 88.889 99 7 4 1 97 496561913 496562009 4.880000e-23 119.0
4 TraesCS2B01G305500 chr2D 94.564 1913 77 13 1 1907 367088054 367089945 0.000000e+00 2931.0
5 TraesCS2B01G305500 chr2D 90.939 607 42 10 2193 2789 367093609 367094212 0.000000e+00 804.0
6 TraesCS2B01G305500 chr2D 93.354 316 10 5 1891 2197 367089957 367090270 9.100000e-125 457.0
7 TraesCS2B01G305500 chr6A 77.160 162 18 10 145 290 58406416 58406258 2.980000e-10 76.8
8 TraesCS2B01G305500 chr6A 77.160 162 18 10 145 290 58422937 58422779 2.980000e-10 76.8
9 TraesCS2B01G305500 chr7B 86.885 61 7 1 129 189 721070049 721069990 1.790000e-07 67.6
10 TraesCS2B01G305500 chr3B 97.297 37 0 1 1018 1053 605335690 605335654 8.340000e-06 62.1


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 TraesCS2B01G305500 chr2B 435628368 435631156 2788 False 5151.000000 5151 100.000000 1 2789 1 chr2B.!!$F1 2788
1 TraesCS2B01G305500 chr2A 496561913 496564487 2574 False 1245.333333 3166 91.625000 1 2789 3 chr2A.!!$F1 2788
2 TraesCS2B01G305500 chr2D 367088054 367094212 6158 False 1397.333333 2931 92.952333 1 2789 3 chr2D.!!$F1 2788

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
801 810 0.399075 AACCTCCACCCCACTTAACG 59.601 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2446 5848 0.842635 ATGAGTTGGGGATGCCTCTC 59.157 55.0 2.19 9.56 0.0 3.2 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
46 47 9.788960 GTAAAATGCAATAAAACCAAACCAAAA 57.211 25.926 0.00 0.00 0.00 2.44
78 79 3.601443 AAGACGAACTGAGCATAGCTT 57.399 42.857 0.00 0.00 39.88 3.74
83 84 6.385843 AGACGAACTGAGCATAGCTTATATG 58.614 40.000 0.00 0.00 39.88 1.78
104 105 5.687166 TGGTTAGGTTTCTTATGACGGAT 57.313 39.130 0.00 0.00 0.00 4.18
143 144 3.386768 TGTCTTAGACTTGGCACTGAC 57.613 47.619 13.86 0.00 33.15 3.51
156 157 2.669434 GGCACTGACGCTCGTATTTTTA 59.331 45.455 0.00 0.00 0.00 1.52
157 158 3.483085 GGCACTGACGCTCGTATTTTTAC 60.483 47.826 0.00 0.00 0.00 2.01
158 159 3.367025 GCACTGACGCTCGTATTTTTACT 59.633 43.478 0.00 0.00 0.00 2.24
159 160 4.721226 GCACTGACGCTCGTATTTTTACTG 60.721 45.833 0.00 0.00 0.00 2.74
199 200 3.588955 TGACGATGTTCAATCAGTGAGG 58.411 45.455 0.00 0.00 37.61 3.86
207 210 4.082125 GTTCAATCAGTGAGGGGATGTTT 58.918 43.478 0.00 0.00 37.61 2.83
261 269 5.698832 TCAAAATGTTTTGCCAGTATCTCG 58.301 37.500 12.21 0.00 45.35 4.04
275 284 4.457257 CAGTATCTCGGATGTGCTCATAGA 59.543 45.833 0.32 1.90 34.06 1.98
287 296 4.711846 TGTGCTCATAGAGGTAAGATGTGT 59.288 41.667 0.00 0.00 0.00 3.72
288 297 5.046529 GTGCTCATAGAGGTAAGATGTGTG 58.953 45.833 0.00 0.00 0.00 3.82
289 298 4.711846 TGCTCATAGAGGTAAGATGTGTGT 59.288 41.667 0.00 0.00 0.00 3.72
290 299 5.046529 GCTCATAGAGGTAAGATGTGTGTG 58.953 45.833 0.00 0.00 0.00 3.82
291 300 5.394663 GCTCATAGAGGTAAGATGTGTGTGT 60.395 44.000 0.00 0.00 0.00 3.72
292 301 5.965922 TCATAGAGGTAAGATGTGTGTGTG 58.034 41.667 0.00 0.00 0.00 3.82
293 302 3.045601 AGAGGTAAGATGTGTGTGTGC 57.954 47.619 0.00 0.00 0.00 4.57
294 303 2.076863 GAGGTAAGATGTGTGTGTGCC 58.923 52.381 0.00 0.00 0.00 5.01
295 304 1.419762 AGGTAAGATGTGTGTGTGCCA 59.580 47.619 0.00 0.00 0.00 4.92
296 305 1.806542 GGTAAGATGTGTGTGTGCCAG 59.193 52.381 0.00 0.00 0.00 4.85
297 306 2.494059 GTAAGATGTGTGTGTGCCAGT 58.506 47.619 0.00 0.00 0.00 4.00
298 307 1.311859 AAGATGTGTGTGTGCCAGTG 58.688 50.000 0.00 0.00 0.00 3.66
299 308 0.469494 AGATGTGTGTGTGCCAGTGA 59.531 50.000 0.00 0.00 0.00 3.41
300 309 1.072806 AGATGTGTGTGTGCCAGTGAT 59.927 47.619 0.00 0.00 0.00 3.06
315 324 4.568956 CCAGTGATGTGTGTGTTCATAGA 58.431 43.478 0.00 0.00 0.00 1.98
328 337 6.970043 GTGTGTTCATAGAGATGAGTGTAGAC 59.030 42.308 0.00 0.00 43.03 2.59
329 338 6.659242 TGTGTTCATAGAGATGAGTGTAGACA 59.341 38.462 0.00 0.00 43.03 3.41
331 340 7.647318 GTGTTCATAGAGATGAGTGTAGACATG 59.353 40.741 0.00 0.00 43.03 3.21
350 359 7.899973 AGACATGTATGATGTATGTGAGCATA 58.100 34.615 0.00 0.00 35.35 3.14
362 371 7.102993 TGTATGTGAGCATATGTGTTTGTACT 58.897 34.615 4.29 0.00 39.49 2.73
372 381 8.073768 GCATATGTGTTTGTACTGTGTTTAACT 58.926 33.333 4.29 0.00 0.00 2.24
415 424 2.916702 TAAGTGGATGCGCATGAGAT 57.083 45.000 30.76 12.28 0.00 2.75
424 433 2.009051 TGCGCATGAGATGACGAATTT 58.991 42.857 5.66 0.00 33.68 1.82
479 488 8.803201 TCTATAATTGAAGATGCTGTTACTCG 57.197 34.615 0.00 0.00 0.00 4.18
583 592 2.032528 CAAAGCGACCTCTGCCCA 59.967 61.111 0.00 0.00 0.00 5.36
717 726 8.840321 TGATTGATTAACAAAAGGAGCTATAGC 58.160 33.333 17.33 17.33 42.03 2.97
718 727 8.752005 ATTGATTAACAAAAGGAGCTATAGCA 57.248 30.769 26.07 1.46 41.95 3.49
719 728 7.792374 TGATTAACAAAAGGAGCTATAGCAG 57.208 36.000 26.07 9.17 45.16 4.24
720 729 7.338710 TGATTAACAAAAGGAGCTATAGCAGT 58.661 34.615 26.07 6.86 45.16 4.40
721 730 8.482943 TGATTAACAAAAGGAGCTATAGCAGTA 58.517 33.333 26.07 2.60 45.16 2.74
722 731 8.894768 ATTAACAAAAGGAGCTATAGCAGTAG 57.105 34.615 26.07 11.26 45.16 2.57
747 756 2.460918 CACATAACGACGGATCACCTC 58.539 52.381 0.00 0.00 0.00 3.85
763 772 5.068234 TCACCTCGTTAACTAATCCTGTG 57.932 43.478 3.71 2.27 0.00 3.66
801 810 0.399075 AACCTCCACCCCACTTAACG 59.601 55.000 0.00 0.00 0.00 3.18
874 883 0.682209 GCAGCATCCATCCAACCACT 60.682 55.000 0.00 0.00 0.00 4.00
941 950 1.902508 ACGACCAACACATCCATCTCT 59.097 47.619 0.00 0.00 0.00 3.10
946 955 3.265221 ACCAACACATCCATCTCTCACAT 59.735 43.478 0.00 0.00 0.00 3.21
955 964 4.344104 TCCATCTCTCACATAGTCACACA 58.656 43.478 0.00 0.00 0.00 3.72
956 965 4.158579 TCCATCTCTCACATAGTCACACAC 59.841 45.833 0.00 0.00 0.00 3.82
960 969 4.216472 TCTCTCACATAGTCACACACACTC 59.784 45.833 0.00 0.00 0.00 3.51
1494 1506 2.756400 GGTGCCCCTGACATGTCA 59.244 61.111 26.33 26.33 38.06 3.58
1797 1809 6.986904 TCCTACTACTACTGATATGATGCG 57.013 41.667 0.00 0.00 0.00 4.73
1964 2004 3.066621 TGCGTCCTTTTTCATATCATGGC 59.933 43.478 0.00 0.00 0.00 4.40
2124 2172 3.546815 GCTGGCGCTTCAGTGTAATATTG 60.547 47.826 7.64 0.00 37.12 1.90
2152 2204 6.358118 TGTTATGATGATTTACCTGTTCGC 57.642 37.500 0.00 0.00 0.00 4.70
2168 2221 3.056107 TGTTCGCTGTTATTACTCCTGCT 60.056 43.478 0.00 0.00 0.00 4.24
2175 2228 6.907212 CGCTGTTATTACTCCTGCTTATTTTG 59.093 38.462 0.00 0.00 0.00 2.44
2177 2230 7.628366 GCTGTTATTACTCCTGCTTATTTTGCA 60.628 37.037 0.00 0.00 38.81 4.08
2212 5608 1.816835 CAGATGTTCTGCCAATGTGCT 59.183 47.619 0.00 0.00 37.72 4.40
2301 5700 1.192312 GTGCACACACACATACACTCG 59.808 52.381 13.17 0.00 46.61 4.18
2383 5785 6.835819 TCCCGATCTATATTCCACTTACTG 57.164 41.667 0.00 0.00 0.00 2.74
2396 5798 4.710375 TCCACTTACTGTCTCCAGGATTAC 59.290 45.833 0.00 0.00 43.36 1.89
2397 5799 4.466370 CCACTTACTGTCTCCAGGATTACA 59.534 45.833 4.99 4.99 43.36 2.41
2420 5822 8.904099 ACAGAGCAAAGTATTTTAGTTACACT 57.096 30.769 0.00 0.00 35.03 3.55
2446 5848 8.055279 TGTTCTTGCTTTTATGAGGGATAAAG 57.945 34.615 0.00 0.00 37.72 1.85
2494 5897 4.317488 TCGGGTGAACAGTATAACCAAAC 58.683 43.478 0.00 0.00 34.18 2.93
2495 5898 3.437741 CGGGTGAACAGTATAACCAAACC 59.562 47.826 0.00 0.00 34.18 3.27
2579 5984 3.054948 TCATCACCAGCTGACATTCATGA 60.055 43.478 17.39 10.44 0.00 3.07
2618 6023 9.933723 AAAGAAATTGATCCTCCAAAATGTTAG 57.066 29.630 0.00 0.00 0.00 2.34
2776 6182 3.383761 GGTGATGAAACTTTGCAACCAG 58.616 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 6.105397 TCAGTTCGTCTTACCTTTGGTTAT 57.895 37.500 0.00 0.00 37.09 1.89
78 79 8.481492 TCCGTCATAAGAAACCTAACCATATA 57.519 34.615 0.00 0.00 0.00 0.86
83 84 5.055144 GGATCCGTCATAAGAAACCTAACC 58.945 45.833 0.00 0.00 0.00 2.85
104 105 2.369860 ACATGAACTCTGTTGAGCTGGA 59.630 45.455 0.00 0.00 43.85 3.86
171 172 5.406780 ACTGATTGAACATCGTCAGAAAGTC 59.593 40.000 15.19 0.00 40.30 3.01
175 176 4.881920 TCACTGATTGAACATCGTCAGAA 58.118 39.130 15.19 4.91 40.30 3.02
190 191 1.210478 CGGAAACATCCCCTCACTGAT 59.790 52.381 0.00 0.00 0.00 2.90
192 193 0.324943 ACGGAAACATCCCCTCACTG 59.675 55.000 0.00 0.00 0.00 3.66
261 269 5.011533 ACATCTTACCTCTATGAGCACATCC 59.988 44.000 0.00 0.00 37.87 3.51
275 284 1.419762 TGGCACACACACATCTTACCT 59.580 47.619 0.00 0.00 0.00 3.08
287 296 0.107263 ACACACATCACTGGCACACA 60.107 50.000 0.00 0.00 0.00 3.72
288 297 0.308684 CACACACATCACTGGCACAC 59.691 55.000 0.00 0.00 0.00 3.82
289 298 0.107263 ACACACACATCACTGGCACA 60.107 50.000 0.00 0.00 0.00 4.57
290 299 1.002468 GAACACACACATCACTGGCAC 60.002 52.381 0.00 0.00 0.00 5.01
291 300 1.308047 GAACACACACATCACTGGCA 58.692 50.000 0.00 0.00 0.00 4.92
292 301 1.308047 TGAACACACACATCACTGGC 58.692 50.000 0.00 0.00 0.00 4.85
293 302 4.568956 TCTATGAACACACACATCACTGG 58.431 43.478 0.00 0.00 0.00 4.00
294 303 5.473039 TCTCTATGAACACACACATCACTG 58.527 41.667 0.00 0.00 0.00 3.66
295 304 5.728637 TCTCTATGAACACACACATCACT 57.271 39.130 0.00 0.00 0.00 3.41
296 305 6.101997 TCATCTCTATGAACACACACATCAC 58.898 40.000 0.00 0.00 39.20 3.06
297 306 6.071165 ACTCATCTCTATGAACACACACATCA 60.071 38.462 0.00 0.00 41.57 3.07
298 307 6.255237 CACTCATCTCTATGAACACACACATC 59.745 42.308 0.00 0.00 41.57 3.06
299 308 6.104665 CACTCATCTCTATGAACACACACAT 58.895 40.000 0.00 0.00 41.57 3.21
300 309 5.011023 ACACTCATCTCTATGAACACACACA 59.989 40.000 0.00 0.00 41.57 3.72
315 324 7.594351 ACATCATACATGTCTACACTCATCT 57.406 36.000 0.00 0.00 0.00 2.90
328 337 8.388103 CACATATGCTCACATACATCATACATG 58.612 37.037 1.58 0.00 41.50 3.21
329 338 8.098912 ACACATATGCTCACATACATCATACAT 58.901 33.333 1.58 0.00 41.50 2.29
331 340 7.895975 ACACATATGCTCACATACATCATAC 57.104 36.000 1.58 0.00 41.50 2.39
350 359 9.699703 AAAAAGTTAAACACAGTACAAACACAT 57.300 25.926 0.00 0.00 0.00 3.21
404 413 1.655484 AATTCGTCATCTCATGCGCA 58.345 45.000 14.96 14.96 32.54 6.09
479 488 7.521585 GCAAGTAGGGCACATGGTTTTATATAC 60.522 40.741 0.00 0.00 0.00 1.47
583 592 0.466963 TGATCGATCACAGGCATGCT 59.533 50.000 23.99 0.11 0.00 3.79
717 726 3.036633 CGTCGTTATGTGCTAGCTACTG 58.963 50.000 17.23 0.00 0.00 2.74
718 727 2.033049 CCGTCGTTATGTGCTAGCTACT 59.967 50.000 17.23 2.52 0.00 2.57
719 728 2.032550 TCCGTCGTTATGTGCTAGCTAC 59.967 50.000 17.23 12.72 0.00 3.58
720 729 2.291365 TCCGTCGTTATGTGCTAGCTA 58.709 47.619 17.23 5.45 0.00 3.32
721 730 1.100510 TCCGTCGTTATGTGCTAGCT 58.899 50.000 17.23 0.00 0.00 3.32
722 731 2.052157 GATCCGTCGTTATGTGCTAGC 58.948 52.381 8.10 8.10 0.00 3.42
747 756 5.812642 AGCTCATTCACAGGATTAGTTAACG 59.187 40.000 0.00 0.00 0.00 3.18
763 772 1.466856 TGGCCATGACAAGCTCATTC 58.533 50.000 0.00 0.00 37.53 2.67
801 810 1.000607 GCGGGAAAGTGAAAAGGGTTC 60.001 52.381 0.00 0.00 0.00 3.62
874 883 3.263425 GGAGGTCAGAGGTGGTTGAAATA 59.737 47.826 0.00 0.00 0.00 1.40
941 950 4.145052 AGAGAGTGTGTGTGACTATGTGA 58.855 43.478 0.00 0.00 0.00 3.58
946 955 5.106118 GCAATAGAGAGAGTGTGTGTGACTA 60.106 44.000 0.00 0.00 0.00 2.59
955 964 3.768757 AGAGCAAGCAATAGAGAGAGTGT 59.231 43.478 0.00 0.00 0.00 3.55
956 965 4.114073 CAGAGCAAGCAATAGAGAGAGTG 58.886 47.826 0.00 0.00 0.00 3.51
960 969 5.410746 TCAAAACAGAGCAAGCAATAGAGAG 59.589 40.000 0.00 0.00 0.00 3.20
2031 2079 8.213489 AGGCCCAAAATAAAATAAAAAGAGGA 57.787 30.769 0.00 0.00 0.00 3.71
2033 2081 9.671279 ATGAGGCCCAAAATAAAATAAAAAGAG 57.329 29.630 0.00 0.00 0.00 2.85
2037 2085 8.097662 ACGAATGAGGCCCAAAATAAAATAAAA 58.902 29.630 0.00 0.00 0.00 1.52
2041 2089 5.675684 ACGAATGAGGCCCAAAATAAAAT 57.324 34.783 0.00 0.00 0.00 1.82
2044 2092 5.067153 CACATACGAATGAGGCCCAAAATAA 59.933 40.000 0.00 0.00 36.54 1.40
2045 2093 4.578516 CACATACGAATGAGGCCCAAAATA 59.421 41.667 0.00 0.00 36.54 1.40
2124 2172 7.807977 ACAGGTAAATCATCATAACATGGAC 57.192 36.000 0.00 0.00 0.00 4.02
2152 2204 7.761409 TGCAAAATAAGCAGGAGTAATAACAG 58.239 34.615 0.00 0.00 37.02 3.16
2168 2221 6.765036 TGGCAGTGAAAGAAAATGCAAAATAA 59.235 30.769 0.00 0.00 38.63 1.40
2175 2228 3.648339 TCTGGCAGTGAAAGAAAATGC 57.352 42.857 15.27 0.00 36.16 3.56
2177 2230 5.537674 AGAACATCTGGCAGTGAAAGAAAAT 59.462 36.000 15.27 0.00 0.00 1.82
2261 5659 6.140108 GTGCACGTACTATGTTTTGAAAACAG 59.860 38.462 25.16 16.43 33.18 3.16
2301 5700 3.306166 GTGAGCGTGTGTGTCCATAATAC 59.694 47.826 0.00 0.00 0.00 1.89
2383 5785 3.895232 TTGCTCTGTAATCCTGGAGAC 57.105 47.619 1.52 3.54 0.00 3.36
2420 5822 8.415950 TTTATCCCTCATAAAAGCAAGAACAA 57.584 30.769 0.00 0.00 34.53 2.83
2428 5830 5.471797 GCCTCTCTTTATCCCTCATAAAAGC 59.528 44.000 0.00 0.00 36.66 3.51
2446 5848 0.842635 ATGAGTTGGGGATGCCTCTC 59.157 55.000 2.19 9.56 0.00 3.20
2579 5984 8.136800 GGATCAATTTCTTTTTGCCATGTTTTT 58.863 29.630 0.00 0.00 0.00 1.94
2595 6000 7.550712 AGCTAACATTTTGGAGGATCAATTTC 58.449 34.615 0.00 0.00 36.25 2.17
2598 6003 6.664816 TGAAGCTAACATTTTGGAGGATCAAT 59.335 34.615 0.00 0.00 36.25 2.57
2656 6062 5.703978 ATGGATGACATTCGTGAAAAACA 57.296 34.783 0.00 0.00 35.97 2.83
2733 6139 5.943416 ACCGAATGACATTCATGGAAAACTA 59.057 36.000 24.26 0.00 37.15 2.24
2743 6149 5.003160 AGTTTCATCACCGAATGACATTCA 58.997 37.500 24.26 8.39 41.24 2.57


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

AutoCloner maintained by Alex Coulton.