Multiple sequence alignment - TraesCS2A01G219000

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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 TraesCS2A01G219000 chr2A 100.000 2631 0 0 1 2631 206116082 206118712 0.000000e+00 4859
1 TraesCS2A01G219000 chr2D 91.591 2652 117 40 1 2631 192157908 192155342 0.000000e+00 3565
2 TraesCS2A01G219000 chr2B 91.860 2408 112 34 1 2372 248155443 248157802 0.000000e+00 3284
3 TraesCS2A01G219000 chr2B 89.723 253 15 5 2371 2622 248157906 248158148 1.970000e-81 313


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 TraesCS2A01G219000 chr2A 206116082 206118712 2630 False 4859.0 4859 100.0000 1 2631 1 chr2A.!!$F1 2630
1 TraesCS2A01G219000 chr2D 192155342 192157908 2566 True 3565.0 3565 91.5910 1 2631 1 chr2D.!!$R1 2630
2 TraesCS2A01G219000 chr2B 248155443 248158148 2705 False 1798.5 3284 90.7915 1 2622 2 chr2B.!!$F1 2621

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
624 654 1.00243 AGAAGACATCAAAGCTCGCCA 59.998 47.619 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2156 0.250234 ATTCGCAGCTTGGAGTAGCA 59.75 50.0 0.0 0.0 43.68 3.49 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 38 3.615155 CCTTCTCCCTGATTCTTGGTTC 58.385 50.000 0.00 0.00 0.00 3.62
45 48 6.409005 CCCTGATTCTTGGTTCATCTCTATGT 60.409 42.308 0.00 0.00 34.50 2.29
67 70 5.237127 TGTTCTGTTGTTGATCTGCAGTTAG 59.763 40.000 14.67 0.00 0.00 2.34
70 74 5.466728 TCTGTTGTTGATCTGCAGTTAGTTC 59.533 40.000 14.67 5.18 0.00 3.01
80 84 7.342026 TGATCTGCAGTTAGTTCTGTATTAGGA 59.658 37.037 14.67 0.00 37.70 2.94
95 99 6.639938 TGTATTAGGATCCCCTTCTATGGAA 58.360 40.000 8.55 0.00 40.78 3.53
98 102 4.302004 AGGATCCCCTTCTATGGAAAGA 57.698 45.455 8.55 0.00 40.78 2.52
102 106 7.672223 AGGATCCCCTTCTATGGAAAGAATCC 61.672 46.154 8.55 10.97 44.32 3.01
140 144 3.953712 TCTTGACTTGCGATCCTGTTA 57.046 42.857 0.00 0.00 0.00 2.41
154 158 3.499338 TCCTGTTAGTCTTCCGTGGTTA 58.501 45.455 0.00 0.00 0.00 2.85
164 168 5.247792 AGTCTTCCGTGGTTATTTCTTAGGT 59.752 40.000 0.00 0.00 0.00 3.08
170 174 5.868801 CCGTGGTTATTTCTTAGGTCGTTTA 59.131 40.000 0.00 0.00 0.00 2.01
171 175 6.536224 CCGTGGTTATTTCTTAGGTCGTTTAT 59.464 38.462 0.00 0.00 0.00 1.40
179 183 4.526970 TCTTAGGTCGTTTATAGGGTCGT 58.473 43.478 0.00 0.00 0.00 4.34
228 232 6.214399 GTTCTCTTTCGACCCGTATTGATAT 58.786 40.000 0.00 0.00 0.00 1.63
235 239 3.314553 GACCCGTATTGATATGGTCGTG 58.685 50.000 8.13 0.00 37.66 4.35
237 241 3.243636 ACCCGTATTGATATGGTCGTGTC 60.244 47.826 8.13 0.00 37.66 3.67
240 244 5.278610 CCCGTATTGATATGGTCGTGTCTTA 60.279 44.000 8.13 0.00 37.66 2.10
242 246 7.362315 CCCGTATTGATATGGTCGTGTCTTATA 60.362 40.741 8.13 0.00 37.66 0.98
243 247 8.188799 CCGTATTGATATGGTCGTGTCTTATAT 58.811 37.037 1.76 0.00 35.22 0.86
275 287 7.993101 TCGGGTATAGATTTTGATATCTACGG 58.007 38.462 3.98 0.00 39.31 4.02
278 290 8.529476 GGGTATAGATTTTGATATCTACGGTGT 58.471 37.037 3.98 0.00 39.31 4.16
335 350 8.969121 TGATGCTATTTTTCTGTACAAACATG 57.031 30.769 0.00 0.00 34.37 3.21
348 363 8.046708 TCTGTACAAACATGGTATGATTAGCTT 58.953 33.333 0.00 0.00 34.37 3.74
377 392 8.488979 ACGTGTATTTTCATTTCGAAGAAAAG 57.511 30.769 22.13 14.41 44.18 2.27
378 393 8.126700 ACGTGTATTTTCATTTCGAAGAAAAGT 58.873 29.630 22.13 14.85 44.18 2.66
497 514 7.825681 TGTGATCTTGAAGTTGAAAGAAAACA 58.174 30.769 0.00 6.74 36.09 2.83
500 517 9.520204 TGATCTTGAAGTTGAAAGAAAACATTC 57.480 29.630 0.00 0.00 36.09 2.67
624 654 1.002430 AGAAGACATCAAAGCTCGCCA 59.998 47.619 0.00 0.00 0.00 5.69
663 693 5.437289 TGCTCCACTAGTTTTGTGAAATG 57.563 39.130 0.00 0.00 37.60 2.32
832 862 5.984233 TTAGCTGTATGAAATAAGCACCG 57.016 39.130 0.00 0.00 36.24 4.94
921 951 4.681744 GAAGCTGTCATTCACCTCTCTAG 58.318 47.826 0.00 0.00 0.00 2.43
956 986 7.917505 CCCTAATGATTCATTTTCTTACTGTGC 59.082 37.037 16.62 0.00 35.54 4.57
1350 1380 1.374560 TGGACAGGTGTGTTGAAACG 58.625 50.000 0.00 0.00 36.88 3.60
1373 1403 3.502211 ACAAGCAAACTCGTTATCCCTTG 59.498 43.478 0.00 0.00 35.73 3.61
1530 1564 5.440234 TCTCTTCATCTTATGCTCGGTAC 57.560 43.478 0.00 0.00 0.00 3.34
1554 1588 3.921119 TGCAGTTCACAAACATGGATC 57.079 42.857 0.00 0.00 37.88 3.36
1688 1723 2.416547 GCAGCTATATATTGGTGGTGCG 59.583 50.000 22.07 3.33 41.15 5.34
1860 1895 0.257039 CCCTCTCCCATCAAGGTTGG 59.743 60.000 0.00 0.00 34.66 3.77
1928 1963 3.296322 TTTGGTTTGACATTCGCCATC 57.704 42.857 0.00 0.00 0.00 3.51
1969 2004 6.153510 ACATCTAGTCTTGAACTGTATCTGCA 59.846 38.462 0.00 0.00 39.11 4.41
1970 2005 6.782082 TCTAGTCTTGAACTGTATCTGCAT 57.218 37.500 0.00 0.00 39.11 3.96
1971 2006 6.800543 TCTAGTCTTGAACTGTATCTGCATC 58.199 40.000 0.00 0.00 39.11 3.91
1972 2007 5.674052 AGTCTTGAACTGTATCTGCATCT 57.326 39.130 0.00 0.00 36.65 2.90
1973 2008 5.417811 AGTCTTGAACTGTATCTGCATCTG 58.582 41.667 0.00 0.00 36.65 2.90
1974 2009 4.033817 GTCTTGAACTGTATCTGCATCTGC 59.966 45.833 0.00 0.00 42.50 4.26
2057 2094 3.961408 GGCTCTTCTGGGTCTACTGAATA 59.039 47.826 0.00 0.00 0.00 1.75
2058 2095 4.202172 GGCTCTTCTGGGTCTACTGAATAC 60.202 50.000 0.00 0.00 0.00 1.89
2059 2096 4.647399 GCTCTTCTGGGTCTACTGAATACT 59.353 45.833 0.00 0.00 0.00 2.12
2060 2097 5.221165 GCTCTTCTGGGTCTACTGAATACTC 60.221 48.000 0.00 0.00 0.00 2.59
2119 2156 4.655647 CCAGTGCCTGGTGCTGCT 62.656 66.667 11.85 0.00 45.82 4.24
2165 2210 5.102953 TGGATCTCATTACTGTTTGAGGG 57.897 43.478 15.91 0.00 39.84 4.30
2169 2214 6.351881 GGATCTCATTACTGTTTGAGGGTACA 60.352 42.308 15.91 2.63 39.84 2.90
2239 2284 3.064958 CGCTTCCTATCTTACGTCAGACA 59.935 47.826 0.61 0.00 0.00 3.41
2240 2285 4.602995 GCTTCCTATCTTACGTCAGACAG 58.397 47.826 0.61 0.00 0.00 3.51
2270 2315 2.415893 CCGTTGATGCACTTTTGATCCC 60.416 50.000 0.00 0.00 0.00 3.85
2291 2336 0.657840 CGGAGGGCATCGACATTTTC 59.342 55.000 0.00 0.00 0.00 2.29
2314 2359 4.445699 GCTTGGATAGCTGGTCCG 57.554 61.111 13.39 3.85 46.77 4.79
2315 2360 1.522569 GCTTGGATAGCTGGTCCGT 59.477 57.895 13.39 0.00 46.77 4.69
2352 2397 1.359475 GACTGCCGGACCGAGATAC 59.641 63.158 17.49 0.00 0.00 2.24
2462 2612 0.757561 TGGTCTGACCTGGACGAACA 60.758 55.000 26.03 2.68 39.58 3.18
2468 2618 3.576982 TCTGACCTGGACGAACATTTAGT 59.423 43.478 0.00 0.00 0.00 2.24
2488 2638 0.249868 GGATGCGATTGGATGACCGA 60.250 55.000 0.00 0.00 39.42 4.69
2492 2642 0.103208 GCGATTGGATGACCGACTCT 59.897 55.000 0.00 0.00 39.42 3.24
2494 2644 1.405463 CGATTGGATGACCGACTCTCA 59.595 52.381 0.00 0.00 39.42 3.27
2505 2655 1.815613 CCGACTCTCACATCACTGTCT 59.184 52.381 0.00 0.00 31.62 3.41
2507 2657 2.485814 CGACTCTCACATCACTGTCTGA 59.514 50.000 0.00 0.00 31.62 3.27
2617 2769 8.667463 CAACAACAAAATCACCTTTTTCTCATT 58.333 29.630 0.00 0.00 34.80 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 20 4.107072 AGATGAACCAAGAATCAGGGAGA 58.893 43.478 0.00 0.00 0.00 3.71
21 24 6.590068 ACATAGAGATGAACCAAGAATCAGG 58.410 40.000 0.00 0.00 36.48 3.86
22 25 7.986320 AGAACATAGAGATGAACCAAGAATCAG 59.014 37.037 0.00 0.00 36.48 2.90
35 38 7.465647 GCAGATCAACAACAGAACATAGAGATG 60.466 40.741 0.00 0.00 39.16 2.90
45 48 5.368145 ACTAACTGCAGATCAACAACAGAA 58.632 37.500 23.35 0.00 32.67 3.02
67 70 7.310734 CCATAGAAGGGGATCCTAATACAGAAC 60.311 44.444 12.58 0.00 44.07 3.01
70 74 6.264528 TCCATAGAAGGGGATCCTAATACAG 58.735 44.000 12.58 0.00 44.07 2.74
80 84 4.042187 CGGATTCTTTCCATAGAAGGGGAT 59.958 45.833 0.00 0.00 45.78 3.85
102 106 8.768957 AGTCAAGATGAATCCATAATCATACG 57.231 34.615 0.00 0.00 36.45 3.06
140 144 5.247792 ACCTAAGAAATAACCACGGAAGACT 59.752 40.000 0.00 0.00 0.00 3.24
154 158 6.097412 ACGACCCTATAAACGACCTAAGAAAT 59.903 38.462 0.00 0.00 0.00 2.17
179 183 2.181125 TCCAAGAATACCTACACGGCA 58.819 47.619 0.00 0.00 35.61 5.69
228 232 7.362315 CCCGATTGTATATATAAGACACGACCA 60.362 40.741 10.35 0.00 0.00 4.02
348 363 8.468720 TCTTCGAAATGAAAATACACGTATGA 57.531 30.769 0.00 0.00 35.79 2.15
377 392 7.754851 TTATCCCCTTCACTCAAAAAGTTAC 57.245 36.000 0.00 0.00 35.45 2.50
378 393 8.950007 ATTTATCCCCTTCACTCAAAAAGTTA 57.050 30.769 0.00 0.00 35.45 2.24
390 406 5.222233 TGTCCTGACAAATTTATCCCCTTCA 60.222 40.000 0.00 0.00 38.56 3.02
421 437 5.411781 AGTGCAGTGCTAGTCTTAACATAC 58.588 41.667 17.60 0.78 0.00 2.39
497 514 5.705905 CGGAGTGGAGTTTTTCCTAAAGAAT 59.294 40.000 0.00 0.00 46.92 2.40
500 517 3.751698 CCGGAGTGGAGTTTTTCCTAAAG 59.248 47.826 0.00 0.00 46.92 1.85
554 577 9.754382 ACATGTGATTTTTATCATCCTTTATGC 57.246 29.630 0.00 0.00 35.38 3.14
663 693 7.060421 TGGACCTAAATGATTATGGAAGAACC 58.940 38.462 3.85 0.00 39.54 3.62
832 862 6.694411 CCACTGACTAAATAATTTGCATCAGC 59.306 38.462 6.55 0.00 36.60 4.26
872 902 4.846779 TTCTCATTTGTACAACCAAGCC 57.153 40.909 8.07 0.00 0.00 4.35
921 951 3.216800 TGAATCATTAGGGCATGCAGTC 58.783 45.455 21.36 8.41 0.00 3.51
956 986 4.601019 CAAAAGCTACACCAAGAACTGTG 58.399 43.478 0.00 0.00 38.44 3.66
1350 1380 3.335579 AGGGATAACGAGTTTGCTTGTC 58.664 45.455 0.00 0.00 38.35 3.18
1373 1403 4.749598 AGAAAATTGCGAAACAAATGGGAC 59.250 37.500 0.00 0.00 42.86 4.46
1530 1564 2.118683 CATGTTTGTGAACTGCAACCG 58.881 47.619 0.00 0.00 36.70 4.44
1554 1588 9.846248 TCGACACATATCATATTAGACATCTTG 57.154 33.333 0.00 0.00 0.00 3.02
1688 1723 5.333111 GCGCTAGCACACAACTAAATATACC 60.333 44.000 16.45 0.00 44.35 2.73
1740 1775 7.486551 GGCTATGCTAGATTTTCTGTATACTCG 59.513 40.741 4.17 0.00 0.00 4.18
1880 1915 2.857592 TACGAAGGATACCACGCTTC 57.142 50.000 0.00 0.00 38.81 3.86
1928 1963 2.028125 ATGTATCGACACCGGCTGGG 62.028 60.000 18.00 7.55 38.76 4.45
1969 2004 6.017026 CAGCATAATTCAGTCATCAAGCAGAT 60.017 38.462 0.00 0.00 37.48 2.90
1970 2005 5.296035 CAGCATAATTCAGTCATCAAGCAGA 59.704 40.000 0.00 0.00 0.00 4.26
1971 2006 5.511571 CAGCATAATTCAGTCATCAAGCAG 58.488 41.667 0.00 0.00 0.00 4.24
1972 2007 4.201980 GCAGCATAATTCAGTCATCAAGCA 60.202 41.667 0.00 0.00 0.00 3.91
1973 2008 4.288531 GCAGCATAATTCAGTCATCAAGC 58.711 43.478 0.00 0.00 0.00 4.01
1974 2009 4.579340 AGGCAGCATAATTCAGTCATCAAG 59.421 41.667 0.00 0.00 0.00 3.02
2037 2074 5.888724 TGAGTATTCAGTAGACCCAGAAGAG 59.111 44.000 0.00 0.00 0.00 2.85
2057 2094 3.118482 CCATGAATGAGGCTACAGTGAGT 60.118 47.826 0.00 0.00 0.00 3.41
2058 2095 3.464907 CCATGAATGAGGCTACAGTGAG 58.535 50.000 0.00 0.00 0.00 3.51
2059 2096 3.548745 CCATGAATGAGGCTACAGTGA 57.451 47.619 0.00 0.00 0.00 3.41
2118 2155 0.390340 TTCGCAGCTTGGAGTAGCAG 60.390 55.000 0.00 0.00 43.68 4.24
2119 2156 0.250234 ATTCGCAGCTTGGAGTAGCA 59.750 50.000 0.00 0.00 43.68 3.49
2165 2210 7.015877 GTGTGCAGAATAAAGCTAAACTGTAC 58.984 38.462 14.92 14.92 39.82 2.90
2169 2214 5.765182 ACAGTGTGCAGAATAAAGCTAAACT 59.235 36.000 0.00 0.00 0.00 2.66
2196 2241 4.065789 CGTTTCCCTGTTTTTAGAGAGCT 58.934 43.478 0.00 0.00 0.00 4.09
2239 2284 1.089920 GCATCAACGGTCAATGAGCT 58.910 50.000 10.85 0.00 0.00 4.09
2240 2285 0.804364 TGCATCAACGGTCAATGAGC 59.196 50.000 1.78 1.78 0.00 4.26
2270 2315 0.744414 AAATGTCGATGCCCTCCGTG 60.744 55.000 0.00 0.00 0.00 4.94
2283 2328 6.473397 CTATCCAAGCTATCCGAAAATGTC 57.527 41.667 0.00 0.00 0.00 3.06
2298 2343 0.824109 TGACGGACCAGCTATCCAAG 59.176 55.000 14.86 3.95 35.83 3.61
2299 2344 1.207089 CTTGACGGACCAGCTATCCAA 59.793 52.381 14.86 3.11 35.83 3.53
2462 2612 4.516698 GTCATCCAATCGCATCCACTAAAT 59.483 41.667 0.00 0.00 0.00 1.40
2468 2618 0.532640 CGGTCATCCAATCGCATCCA 60.533 55.000 0.00 0.00 0.00 3.41
2488 2638 3.638627 TGTTCAGACAGTGATGTGAGAGT 59.361 43.478 0.00 0.00 34.17 3.24
2505 2655 5.007234 CCAAAACGAACACAGTATCTGTTCA 59.993 40.000 10.90 0.00 42.59 3.18
2507 2657 5.120399 TCCAAAACGAACACAGTATCTGTT 58.880 37.500 0.00 0.00 42.59 3.16
2516 2666 2.096819 GCTGACTTCCAAAACGAACACA 59.903 45.455 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.