Multiple sequence alignment - TraesCS5D01G475300

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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 TraesCS5D01G475300 chr5D 100.000 2648 0 0 1 2648 515026104 515023457 0.000000e+00 4891
1 TraesCS5D01G475300 chr5D 96.524 2647 87 4 4 2648 514996744 514994101 0.000000e+00 4373
2 TraesCS5D01G475300 chr5D 94.534 2653 136 6 1 2648 514948902 514946254 0.000000e+00 4087
3 TraesCS5D01G475300 chr5D 93.545 2649 161 7 1 2648 514975310 514972671 0.000000e+00 3936
4 TraesCS5D01G475300 chr5B 90.157 2550 214 18 1 2536 647699122 647696596 0.000000e+00 3284
5 TraesCS5D01G475300 chr5B 90.145 2547 217 18 1 2536 647781500 647778977 0.000000e+00 3282
6 TraesCS5D01G475300 chr5B 91.947 2049 152 6 4 2042 647405851 647403806 0.000000e+00 2857
7 TraesCS5D01G475300 chr5B 92.002 1938 137 11 235 2166 647464822 647462897 0.000000e+00 2704
8 TraesCS5D01G475300 chr5A 89.014 2303 235 14 244 2537 643042713 643040420 0.000000e+00 2835
9 TraesCS5D01G475300 chr5A 89.206 2140 218 8 244 2375 643029622 643027488 0.000000e+00 2660
10 TraesCS5D01G475300 chr7A 92.035 226 18 0 15 240 655561825 655562050 4.250000e-83 318
11 TraesCS5D01G475300 chr1D 91.111 225 20 0 15 239 8737635 8737411 3.310000e-79 305
12 TraesCS5D01G475300 chr1D 89.167 240 26 0 1 240 251889169 251888930 1.540000e-77 300
13 TraesCS5D01G475300 chr1D 82.482 137 15 8 2501 2632 31698411 31698279 7.750000e-21 111
14 TraesCS5D01G475300 chr3B 88.710 186 17 4 2354 2537 798284704 798284887 9.540000e-55 224
15 TraesCS5D01G475300 chr3B 88.889 180 16 4 2360 2537 275698107 275698284 4.440000e-53 219
16 TraesCS5D01G475300 chr2A 79.592 294 48 7 2360 2644 41641645 41641355 1.610000e-47 200
17 TraesCS5D01G475300 chr2A 85.156 128 17 2 2517 2644 232389570 232389445 2.140000e-26 130
18 TraesCS5D01G475300 chr6D 84.247 146 19 3 2501 2643 340975550 340975406 3.550000e-29 139


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 TraesCS5D01G475300 chr5D 515023457 515026104 2647 True 4891 4891 100.000 1 2648 1 chr5D.!!$R4 2647
1 TraesCS5D01G475300 chr5D 514994101 514996744 2643 True 4373 4373 96.524 4 2648 1 chr5D.!!$R3 2644
2 TraesCS5D01G475300 chr5D 514946254 514948902 2648 True 4087 4087 94.534 1 2648 1 chr5D.!!$R1 2647
3 TraesCS5D01G475300 chr5D 514972671 514975310 2639 True 3936 3936 93.545 1 2648 1 chr5D.!!$R2 2647
4 TraesCS5D01G475300 chr5B 647696596 647699122 2526 True 3284 3284 90.157 1 2536 1 chr5B.!!$R3 2535
5 TraesCS5D01G475300 chr5B 647778977 647781500 2523 True 3282 3282 90.145 1 2536 1 chr5B.!!$R4 2535
6 TraesCS5D01G475300 chr5B 647403806 647405851 2045 True 2857 2857 91.947 4 2042 1 chr5B.!!$R1 2038
7 TraesCS5D01G475300 chr5B 647462897 647464822 1925 True 2704 2704 92.002 235 2166 1 chr5B.!!$R2 1931
8 TraesCS5D01G475300 chr5A 643040420 643042713 2293 True 2835 2835 89.014 244 2537 1 chr5A.!!$R2 2293
9 TraesCS5D01G475300 chr5A 643027488 643029622 2134 True 2660 2660 89.206 244 2375 1 chr5A.!!$R1 2131

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
324 331 0.035458 CGGAGTTTTCACAGAGGGCT 59.965 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2314 1.204113 AGGAACTCCAAGGGCAGAGG 61.204 60.0 0.0 0.0 38.89 3.69 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
211 213 7.988028 GGTGAAATACTAGCCTTGAAGACTATT 59.012 37.037 0.00 0.00 0.00 1.73
214 216 4.143986 ACTAGCCTTGAAGACTATTGCC 57.856 45.455 0.00 0.00 0.00 4.52
290 292 5.876460 GGTTAGTTTAGGGCTAATTTCGTCA 59.124 40.000 0.00 0.00 32.01 4.35
317 324 3.128349 GAGTAGTTGCGGAGTTTTCACA 58.872 45.455 0.00 0.00 0.00 3.58
324 331 0.035458 CGGAGTTTTCACAGAGGGCT 59.965 55.000 0.00 0.00 0.00 5.19
443 455 3.282831 ACTGCTTTGTTAACCAATCGC 57.717 42.857 2.48 0.20 31.81 4.58
501 513 9.794719 ACCTAGCCTAAAATTCTTATATGAACC 57.205 33.333 3.35 0.00 0.00 3.62
664 685 7.070571 AGTCAAGATTAGGGACTTCTCCTTATG 59.929 40.741 0.00 0.00 38.69 1.90
857 879 6.547510 AGATTATGTAAGTTGGAGGATTTGGC 59.452 38.462 0.00 0.00 0.00 4.52
858 880 3.806949 TGTAAGTTGGAGGATTTGGCT 57.193 42.857 0.00 0.00 0.00 4.75
1043 1076 8.190784 CCACTATTTCACTTTTCTGTTCTTGTT 58.809 33.333 0.00 0.00 0.00 2.83
1079 1112 2.262423 AGAAGTCAAGAGCAACACCC 57.738 50.000 0.00 0.00 0.00 4.61
1131 1164 2.925416 TTTGGTGCTGCTTCTGGCCA 62.925 55.000 4.71 4.71 40.92 5.36
1245 1278 2.994995 ACATCCAGTCCGGCGACA 60.995 61.111 9.30 0.00 41.87 4.35
1278 1311 9.862371 GTGAGAACTCTAAAGATCAAGTGATTA 57.138 33.333 0.00 0.00 34.37 1.75
1307 1340 8.367911 TGTTCTTGATGTCTATACTGTGTTCTT 58.632 33.333 0.00 0.00 0.00 2.52
1371 1404 2.487762 CAACCCGAGTATGCACAATGTT 59.512 45.455 0.00 0.00 0.00 2.71
1623 1657 4.024218 GCTAGCTCATGATGAATTGGTGAC 60.024 45.833 7.70 0.00 0.00 3.67
1792 1832 4.511826 GGGCAAACGATTATGAAGGTCTAG 59.488 45.833 0.00 0.00 0.00 2.43
1811 1851 2.910199 AGCACAGTCATATGCATTCGT 58.090 42.857 3.54 0.00 44.59 3.85
1815 1855 4.318333 GCACAGTCATATGCATTCGTAGTG 60.318 45.833 3.54 8.82 41.65 2.74
2132 2174 1.780919 AGGGTAGGTTTTGGACTGCTT 59.219 47.619 0.00 0.00 0.00 3.91
2146 2188 3.128242 GGACTGCTTCACTCCATGATTTG 59.872 47.826 0.00 0.00 37.11 2.32
2271 2314 0.034477 CCACTTCACCCACCATACCC 60.034 60.000 0.00 0.00 0.00 3.69
2640 2692 8.376270 GCACCTTATATTAAGTAACAGAGGGAT 58.624 37.037 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 8.632679 CCAAAGAATATTTATGAGCCTTAGCAA 58.367 33.333 0.00 0.00 43.56 3.91
197 199 2.620585 GGATGGCAATAGTCTTCAAGGC 59.379 50.000 0.00 0.00 0.00 4.35
211 213 2.338809 CCTCAAGTATAGGGGATGGCA 58.661 52.381 0.00 0.00 0.00 4.92
290 292 2.180276 ACTCCGCAACTACTCCTGATT 58.820 47.619 0.00 0.00 0.00 2.57
324 331 1.475403 GAGACGATGACCTCAAGGGA 58.525 55.000 0.29 0.00 40.27 4.20
443 455 6.292328 GGAACAATTGAAAAAGAAAAGAGCCG 60.292 38.462 13.59 0.00 0.00 5.52
501 513 8.653338 CAGAAGTTGGAAAATTGAATGCATTAG 58.347 33.333 12.97 0.00 32.38 1.73
502 514 8.366401 TCAGAAGTTGGAAAATTGAATGCATTA 58.634 29.630 12.97 0.00 32.38 1.90
503 515 7.218614 TCAGAAGTTGGAAAATTGAATGCATT 58.781 30.769 12.83 12.83 32.38 3.56
504 516 6.761312 TCAGAAGTTGGAAAATTGAATGCAT 58.239 32.000 0.00 0.00 32.38 3.96
505 517 6.159299 TCAGAAGTTGGAAAATTGAATGCA 57.841 33.333 0.00 0.00 32.38 3.96
506 518 7.481275 TTTCAGAAGTTGGAAAATTGAATGC 57.519 32.000 0.00 0.00 32.38 3.56
787 808 6.826231 TGAACGAGGATGCATTTATTTCCTAA 59.174 34.615 0.00 0.00 38.71 2.69
839 861 2.164422 GCAGCCAAATCCTCCAACTTAC 59.836 50.000 0.00 0.00 0.00 2.34
1043 1076 7.165460 TGACTTCTTGTTGATACCGAAGATA 57.835 36.000 0.00 0.00 35.79 1.98
1079 1112 2.568090 GTTGCCCGTGCCATTGAG 59.432 61.111 0.00 0.00 36.33 3.02
1205 1238 3.095347 GCCACTCTCCCATCCGGAC 62.095 68.421 6.12 0.00 34.86 4.79
1245 1278 5.489792 TCTTTAGAGTTCTCACCAAGCAT 57.510 39.130 2.64 0.00 0.00 3.79
1278 1311 7.671302 ACACAGTATAGACATCAAGAACAACT 58.329 34.615 0.00 0.00 0.00 3.16
1371 1404 3.160585 CCTTCTCCCACCTGCACA 58.839 61.111 0.00 0.00 0.00 4.57
1792 1832 3.804325 ACTACGAATGCATATGACTGTGC 59.196 43.478 6.97 0.00 39.73 4.57
1829 1869 4.442192 GGGTGCTTTGTACATTTGGTGAAA 60.442 41.667 0.00 0.00 0.00 2.69
1934 1975 3.148279 GGTCAGGACGGCTCCGAT 61.148 66.667 15.95 0.00 42.22 4.18
2067 2109 5.363939 GGAGCATATCCTATATGTGAAGGC 58.636 45.833 8.32 0.00 45.64 4.35
2132 2174 6.611613 AACTCTACTCAAATCATGGAGTGA 57.388 37.500 11.32 3.52 43.78 3.41
2146 2188 8.496751 GTTGAGGTGTTTGAAATAACTCTACTC 58.503 37.037 20.45 8.13 38.39 2.59
2271 2314 1.204113 AGGAACTCCAAGGGCAGAGG 61.204 60.000 0.00 0.00 38.89 3.69


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

AutoCloner maintained by Alex Coulton.