Multiple sequence alignment - TraesCS5B01G219300

Loading Multiple Alignment...

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 TraesCS5B01G219300 chr5B 100.000 2237 0 0 1 2237 393576563 393578799 0.000000e+00 4132
1 TraesCS5B01G219300 chr5D 93.134 1777 53 16 510 2237 335750898 335752654 0.000000e+00 2542
2 TraesCS5B01G219300 chr5D 89.451 237 21 2 1 237 335750404 335750636 1.680000e-76 296
3 TraesCS5B01G219300 chr5D 93.229 192 8 2 329 519 335750687 335750874 6.080000e-71 278
4 TraesCS5B01G219300 chr5A 88.019 1444 56 39 1 1376 436879955 436881349 0.000000e+00 1600
5 TraesCS5B01G219300 chr5A 94.145 854 33 9 1390 2237 436881574 436882416 0.000000e+00 1284


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 TraesCS5B01G219300 chr5B 393576563 393578799 2236 False 4132.000000 4132 100.000 1 2237 1 chr5B.!!$F1 2236
1 TraesCS5B01G219300 chr5D 335750404 335752654 2250 False 1038.666667 2542 91.938 1 2237 3 chr5D.!!$F1 2236
2 TraesCS5B01G219300 chr5A 436879955 436882416 2461 False 1442.000000 1600 91.082 1 2237 2 chr5A.!!$F1 2236

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
162 163 0.10852 GCAAAGACCACATGCATGGG 60.109 55.0 29.41 26.21 44.81 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 2111 1.745087 CCAACACTGTGAGTTTGTGCT 59.255 47.619 15.86 0.0 35.33 4.4 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
35 36 9.642343 AATATAACTTTTACCCTTCTCCAATCC 57.358 33.333 0.00 0.00 0.00 3.01
46 47 5.013495 CCCTTCTCCAATCCTGATAAGCATA 59.987 44.000 0.00 0.00 0.00 3.14
47 48 6.171921 CCTTCTCCAATCCTGATAAGCATAG 58.828 44.000 0.00 0.00 0.00 2.23
48 49 5.752036 TCTCCAATCCTGATAAGCATAGG 57.248 43.478 0.00 0.00 0.00 2.57
58 59 7.350382 TCCTGATAAGCATAGGAGGACTATAG 58.650 42.308 0.00 0.00 40.42 1.31
101 102 4.262207 CGGCCACAGTGATAGATAGATTGT 60.262 45.833 2.24 0.00 0.00 2.71
118 119 3.878086 TTGTCGTCAATCTGCAGTTTC 57.122 42.857 14.67 0.00 0.00 2.78
128 129 8.368126 CGTCAATCTGCAGTTTCATTTAATTTC 58.632 33.333 14.67 0.00 0.00 2.17
159 160 0.892755 CTGGCAAAGACCACATGCAT 59.107 50.000 0.00 0.00 41.80 3.96
162 163 0.108520 GCAAAGACCACATGCATGGG 60.109 55.000 29.41 26.21 44.81 4.00
241 263 0.722799 GCGCTTGTTTCGAGCAAGAC 60.723 55.000 25.85 18.32 44.29 3.01
264 286 1.227380 ATCGGAAGACATCTGCGCC 60.227 57.895 4.18 0.00 46.97 6.53
295 317 7.975616 AGTGCTTTGCTGGTTTGTTTATATATG 59.024 33.333 0.00 0.00 0.00 1.78
298 320 6.782082 TTGCTGGTTTGTTTATATATGGCA 57.218 33.333 0.00 0.00 0.00 4.92
299 321 6.389830 TGCTGGTTTGTTTATATATGGCAG 57.610 37.500 0.00 0.00 0.00 4.85
300 322 5.221224 TGCTGGTTTGTTTATATATGGCAGC 60.221 40.000 0.00 0.00 0.00 5.25
301 323 5.772521 CTGGTTTGTTTATATATGGCAGCC 58.227 41.667 3.66 3.66 0.00 4.85
302 324 5.454062 TGGTTTGTTTATATATGGCAGCCT 58.546 37.500 14.15 0.35 0.00 4.58
303 325 5.896678 TGGTTTGTTTATATATGGCAGCCTT 59.103 36.000 14.15 9.31 0.00 4.35
304 326 7.063593 TGGTTTGTTTATATATGGCAGCCTTA 58.936 34.615 14.15 11.57 0.00 2.69
305 327 7.728083 TGGTTTGTTTATATATGGCAGCCTTAT 59.272 33.333 20.72 20.72 0.00 1.73
306 328 8.585018 GGTTTGTTTATATATGGCAGCCTTATT 58.415 33.333 21.80 13.38 0.00 1.40
313 335 5.653255 ATATGGCAGCCTTATTATAGGGG 57.347 43.478 14.15 0.00 35.74 4.79
318 340 4.265073 GCAGCCTTATTATAGGGGTCATG 58.735 47.826 1.98 0.00 32.93 3.07
337 359 3.130280 TGGCGATCGGTAGACTGTATA 57.870 47.619 18.30 0.00 0.00 1.47
463 488 6.998074 TCACTCTCACAAATTGGTGTCTAAAT 59.002 34.615 12.74 0.00 39.76 1.40
464 489 8.154203 TCACTCTCACAAATTGGTGTCTAAATA 58.846 33.333 12.74 0.00 39.76 1.40
519 544 5.719173 GCACTTGCACAATTATTTAAGGGA 58.281 37.500 0.00 0.00 41.59 4.20
553 612 1.075601 TCACATGGGAAAGAAGGCCT 58.924 50.000 0.00 0.00 0.00 5.19
574 633 8.693625 AGGCCTAAGCTAATTATATTAGGTACG 58.306 37.037 23.70 9.79 44.06 3.67
575 634 7.924947 GGCCTAAGCTAATTATATTAGGTACGG 59.075 40.741 23.70 13.12 44.06 4.02
576 635 8.689972 GCCTAAGCTAATTATATTAGGTACGGA 58.310 37.037 23.70 6.43 44.06 4.69
633 696 3.245803 ACCAGACCAGACCAGATAGTTCT 60.246 47.826 0.00 0.00 0.00 3.01
687 751 0.109086 ACGTGGAGCTGAGACAATCG 60.109 55.000 0.00 0.00 0.00 3.34
783 854 2.296658 GTTGCAAACGCCAAACAGG 58.703 52.632 0.00 0.00 36.92 4.00
794 865 1.823250 GCCAAACAGGGAGACACCATT 60.823 52.381 0.00 0.00 41.20 3.16
800 871 6.409695 CCAAACAGGGAGACACCATTCTATAT 60.410 42.308 0.00 0.00 41.20 0.86
878 979 1.145738 ACAGGTGAAACATCCCTTGCT 59.854 47.619 0.00 0.00 39.98 3.91
881 982 2.108952 AGGTGAAACATCCCTTGCTTCT 59.891 45.455 0.00 0.00 39.98 2.85
987 1095 1.491668 GGAGGGAGAAAGGGAGAGAC 58.508 60.000 0.00 0.00 0.00 3.36
1368 1476 0.733729 CTTGCCTGCTCATCTCTTGC 59.266 55.000 0.00 0.00 0.00 4.01
1785 2111 3.589735 TCTGTAACTTATTTGGGGCTCCA 59.410 43.478 0.00 0.00 42.25 3.86
1786 2112 3.947834 CTGTAACTTATTTGGGGCTCCAG 59.052 47.826 4.89 0.00 45.04 3.86
1824 2150 6.529125 GTGTTGGCAGATTCTTCAACATAATG 59.471 38.462 23.66 0.00 46.96 1.90
1860 2186 4.126437 TGGATAACACATAACAGATGCCG 58.874 43.478 0.00 0.00 0.00 5.69
1861 2187 4.127171 GGATAACACATAACAGATGCCGT 58.873 43.478 0.00 0.00 0.00 5.68
1949 2277 7.514721 ACAGAACTTATTTTAGTCAAGGTCCA 58.485 34.615 0.00 0.00 36.80 4.02
2002 2330 6.525578 TCTAACCATGTAAGATATAGGCGG 57.474 41.667 0.00 0.00 0.00 6.13
2127 2458 6.316140 TCAATGTTCGTCAATATTTCTCAGGG 59.684 38.462 0.00 0.00 0.00 4.45
2130 2461 6.001460 TGTTCGTCAATATTTCTCAGGGTTT 58.999 36.000 0.00 0.00 0.00 3.27
2156 2487 5.238214 CAGCTATCAGCAAGGAAATAAGTCC 59.762 44.000 0.38 0.00 45.56 3.85
2182 2513 4.196118 TGGTCTCTCTCCAGATCATCAT 57.804 45.455 0.00 0.00 27.86 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.796502 ATCAGGATTGGAGAAGGGTAAAA 57.203 39.130 0.00 0.00 0.00 1.52
35 36 7.350382 TCCTATAGTCCTCCTATGCTTATCAG 58.650 42.308 0.00 0.00 36.98 2.90
46 47 2.516277 ACTGCACTCCTATAGTCCTCCT 59.484 50.000 0.00 0.00 35.76 3.69
47 48 2.952116 ACTGCACTCCTATAGTCCTCC 58.048 52.381 0.00 0.00 35.76 4.30
48 49 5.414454 CAGATACTGCACTCCTATAGTCCTC 59.586 48.000 0.00 0.00 35.76 3.71
58 59 0.539051 AGTGCCAGATACTGCACTCC 59.461 55.000 11.07 0.00 41.30 3.85
77 78 3.223674 TCTATCTATCACTGTGGCCGA 57.776 47.619 8.11 2.44 0.00 5.54
101 102 6.552859 TTAAATGAAACTGCAGATTGACGA 57.447 33.333 23.35 0.00 0.00 4.20
117 118 4.717991 CTTGCGTCGTGGAAATTAAATGA 58.282 39.130 0.00 0.00 0.00 2.57
118 119 3.300590 GCTTGCGTCGTGGAAATTAAATG 59.699 43.478 0.00 0.00 0.00 2.32
145 146 0.542467 TGCCCATGCATGTGGTCTTT 60.542 50.000 24.58 0.00 44.23 2.52
159 160 3.368635 GCAATGATCACAAGAAATGCCCA 60.369 43.478 0.00 0.00 0.00 5.36
162 163 5.849357 TTTGCAATGATCACAAGAAATGC 57.151 34.783 0.00 1.38 0.00 3.56
192 193 2.315925 ATCACAATCATCGAACGGCT 57.684 45.000 0.00 0.00 0.00 5.52
264 286 2.050714 CCAGCAAAGCACTGCACG 60.051 61.111 12.01 3.34 45.18 5.34
274 296 7.175347 TGCCATATATAAACAAACCAGCAAA 57.825 32.000 0.00 0.00 0.00 3.68
295 317 2.642807 TGACCCCTATAATAAGGCTGCC 59.357 50.000 11.65 11.65 35.09 4.85
298 320 3.267031 GCCATGACCCCTATAATAAGGCT 59.733 47.826 0.00 0.00 35.09 4.58
299 321 3.621558 GCCATGACCCCTATAATAAGGC 58.378 50.000 0.00 0.00 35.09 4.35
300 322 3.517901 TCGCCATGACCCCTATAATAAGG 59.482 47.826 0.00 0.00 36.30 2.69
301 323 4.819105 TCGCCATGACCCCTATAATAAG 57.181 45.455 0.00 0.00 0.00 1.73
302 324 4.142026 CGATCGCCATGACCCCTATAATAA 60.142 45.833 0.26 0.00 0.00 1.40
303 325 3.383505 CGATCGCCATGACCCCTATAATA 59.616 47.826 0.26 0.00 0.00 0.98
304 326 2.168521 CGATCGCCATGACCCCTATAAT 59.831 50.000 0.26 0.00 0.00 1.28
305 327 1.548719 CGATCGCCATGACCCCTATAA 59.451 52.381 0.26 0.00 0.00 0.98
306 328 1.182667 CGATCGCCATGACCCCTATA 58.817 55.000 0.26 0.00 0.00 1.31
307 329 1.544825 CCGATCGCCATGACCCCTAT 61.545 60.000 10.32 0.00 0.00 2.57
308 330 2.207229 CCGATCGCCATGACCCCTA 61.207 63.158 10.32 0.00 0.00 3.53
309 331 2.939760 TACCGATCGCCATGACCCCT 62.940 60.000 10.32 0.00 0.00 4.79
313 335 0.669077 AGTCTACCGATCGCCATGAC 59.331 55.000 10.32 13.87 0.00 3.06
318 340 2.810274 TGTATACAGTCTACCGATCGCC 59.190 50.000 10.32 0.00 0.00 5.54
337 359 2.867624 CAGCATTATGCCCCTGTATGT 58.132 47.619 14.10 0.00 46.52 2.29
394 417 5.047731 TCGTTTTTAATGTTCCATCCATGCA 60.048 36.000 0.00 0.00 0.00 3.96
397 420 6.987386 TGTTCGTTTTTAATGTTCCATCCAT 58.013 32.000 0.00 0.00 0.00 3.41
398 421 6.392625 TGTTCGTTTTTAATGTTCCATCCA 57.607 33.333 0.00 0.00 0.00 3.41
399 422 7.142680 TCTTGTTCGTTTTTAATGTTCCATCC 58.857 34.615 0.00 0.00 0.00 3.51
400 423 8.742554 ATCTTGTTCGTTTTTAATGTTCCATC 57.257 30.769 0.00 0.00 0.00 3.51
416 439 5.869344 TGAACTGACAGGATTATCTTGTTCG 59.131 40.000 11.20 8.05 36.79 3.95
514 539 7.775053 TGTGATTTTAGTTAGCAATTCCCTT 57.225 32.000 0.00 0.00 0.00 3.95
519 544 7.716799 TCCCATGTGATTTTAGTTAGCAATT 57.283 32.000 0.00 0.00 0.00 2.32
584 643 8.783093 CCGGTGTACATATCAATGTCAAAATAT 58.217 33.333 0.00 0.00 42.92 1.28
585 644 7.988028 TCCGGTGTACATATCAATGTCAAAATA 59.012 33.333 0.00 0.00 42.92 1.40
588 647 5.583061 GTCCGGTGTACATATCAATGTCAAA 59.417 40.000 0.00 0.00 42.92 2.69
593 652 4.058124 CTGGTCCGGTGTACATATCAATG 58.942 47.826 0.00 0.00 39.17 2.82
659 723 7.939784 TGTCTCAGCTCCACGTATATTATAT 57.060 36.000 0.00 0.00 0.00 0.86
660 724 7.754851 TTGTCTCAGCTCCACGTATATTATA 57.245 36.000 0.00 0.00 0.00 0.98
687 751 2.035193 TCCGCTCAGCTGATCATCTAAC 59.965 50.000 18.63 0.00 0.00 2.34
783 854 7.036220 CGGTCATTATATAGAATGGTGTCTCC 58.964 42.308 17.70 10.66 37.41 3.71
794 865 3.423749 TGTCCGGCGGTCATTATATAGA 58.576 45.455 27.32 0.00 0.00 1.98
800 871 0.108520 GAACTGTCCGGCGGTCATTA 60.109 55.000 27.32 2.18 35.19 1.90
878 979 3.374540 GGGGGCGTATATATAGGGGAGAA 60.375 52.174 13.00 0.00 0.00 2.87
881 982 2.781403 GGGGGCGTATATATAGGGGA 57.219 55.000 13.00 0.00 0.00 4.81
987 1095 4.525996 TCCTTCTCATCTCTCTCTCTGTG 58.474 47.826 0.00 0.00 0.00 3.66
1376 1484 4.547532 CAGCTCACAAACGTAGTACTTCT 58.452 43.478 0.00 0.00 45.00 2.85
1377 1485 3.673809 CCAGCTCACAAACGTAGTACTTC 59.326 47.826 0.00 0.00 45.00 3.01
1378 1486 3.650139 CCAGCTCACAAACGTAGTACTT 58.350 45.455 0.00 0.00 45.00 2.24
1785 2111 1.745087 CCAACACTGTGAGTTTGTGCT 59.255 47.619 15.86 0.00 35.33 4.40
1786 2112 1.798813 GCCAACACTGTGAGTTTGTGC 60.799 52.381 15.86 10.16 35.33 4.57
1824 2150 8.668510 ATGTGTTATCCAAGATAGATCAACAC 57.331 34.615 10.99 10.99 37.90 3.32
1855 2181 6.870965 TCTTACATTTTTATTTTGCACGGCAT 59.129 30.769 0.00 0.00 38.76 4.40
1949 2277 3.569701 CCCACAGTTGTACTTGAAGCAAT 59.430 43.478 0.00 0.00 0.00 3.56
2127 2458 5.376854 TTTCCTTGCTGATAGCTGAAAAC 57.623 39.130 0.00 0.00 42.97 2.43
2130 2461 6.418101 ACTTATTTCCTTGCTGATAGCTGAA 58.582 36.000 0.00 0.69 42.97 3.02
2182 2513 1.529226 CAAGTGGGCATGTCGGTTAA 58.471 50.000 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.