Multiple sequence alignment - TraesCS2B01G285700

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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 TraesCS2B01G285700 chr2B 100.000 4236 0 0 1 4236 393464081 393468316 0.000000e+00 7823
1 TraesCS2B01G285700 chr2B 84.635 397 59 2 1 396 472899379 472899774 1.100000e-105 394
2 TraesCS2B01G285700 chr2D 95.974 4297 79 31 1 4236 324594122 324598385 0.000000e+00 6890
3 TraesCS2B01G285700 chr2A 94.724 3639 92 30 669 4236 394021163 394017554 0.000000e+00 5565
4 TraesCS2B01G285700 chr2A 93.818 647 27 3 1 634 394021921 394021275 0.000000e+00 961
5 TraesCS2B01G285700 chr2A 83.375 397 64 2 1 396 536624535 536624930 2.410000e-97 366


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 TraesCS2B01G285700 chr2B 393464081 393468316 4235 False 7823 7823 100.000 1 4236 1 chr2B.!!$F1 4235
1 TraesCS2B01G285700 chr2D 324594122 324598385 4263 False 6890 6890 95.974 1 4236 1 chr2D.!!$F1 4235
2 TraesCS2B01G285700 chr2A 394017554 394021921 4367 True 3263 5565 94.271 1 4236 2 chr2A.!!$R1 4235

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
616 630 0.885879 TCCGTTCTAGTGCGATGTGT 59.114 50.0 9.54 0.0 0.0 3.72 F
1895 2042 0.395036 CACCCACAACTGAACCACCA 60.395 55.0 0.00 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2167 0.508213 GGCGACAATTTGCAAACTGC 59.492 50.0 19.81 15.32 45.29 4.40 R
3764 3955 0.240945 ACCAATGCACGCTAGTTTGC 59.759 50.0 9.97 9.97 39.33 3.68 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
20 21 2.722071 GCCTACTCGAAACGATCTCTG 58.278 52.381 0.00 0.00 34.61 3.35
185 186 1.845266 CGCACGTAGCAGAGATGATT 58.155 50.000 9.95 0.00 46.13 2.57
197 198 3.632604 CAGAGATGATTGAGCTGCCAATT 59.367 43.478 14.58 3.78 36.93 2.32
311 312 2.812499 GCCAAGACGGAGGCGATA 59.188 61.111 0.00 0.00 41.70 2.92
428 441 7.519032 TTTGTTCCCCAGTTAAATCTTACAG 57.481 36.000 0.00 0.00 0.00 2.74
444 457 4.767409 TCTTACAGTTGAGCTCTGCTAGAA 59.233 41.667 16.19 8.84 39.88 2.10
502 515 8.592105 TTATTTCTTCCTTGCAAATTGTCTTG 57.408 30.769 0.00 0.00 0.00 3.02
507 520 4.431809 TCCTTGCAAATTGTCTTGTGTTG 58.568 39.130 0.00 0.00 0.00 3.33
529 543 6.731292 TGGCTCTATAAAATGTCTAGCTCA 57.269 37.500 0.00 0.00 0.00 4.26
540 554 4.890158 TGTCTAGCTCATGGACAAGAAA 57.110 40.909 0.00 0.00 45.42 2.52
542 556 4.997395 TGTCTAGCTCATGGACAAGAAAAC 59.003 41.667 0.00 0.00 45.42 2.43
545 559 2.549754 AGCTCATGGACAAGAAAACACG 59.450 45.455 0.00 0.00 0.00 4.49
610 624 1.722011 ACCATTTCCGTTCTAGTGCG 58.278 50.000 0.00 0.00 0.00 5.34
616 630 0.885879 TCCGTTCTAGTGCGATGTGT 59.114 50.000 9.54 0.00 0.00 3.72
628 642 4.515191 AGTGCGATGTGTAATGTTCTGTTT 59.485 37.500 0.00 0.00 0.00 2.83
700 796 4.877823 TCACTGCAGTAATGCAAGATTAGG 59.122 41.667 21.20 7.97 44.88 2.69
714 811 5.600696 CAAGATTAGGTTGCTTGTTTGGTT 58.399 37.500 0.00 0.00 35.49 3.67
727 835 5.535783 GCTTGTTTGGTTAAAGGGGTTAGTA 59.464 40.000 0.00 0.00 0.00 1.82
753 861 1.833630 TGAGGTGGCAGATTAGTGGAG 59.166 52.381 0.00 0.00 0.00 3.86
754 862 2.111384 GAGGTGGCAGATTAGTGGAGA 58.889 52.381 0.00 0.00 0.00 3.71
835 943 2.539081 GGGTCAAGGGTCAAGGGCT 61.539 63.158 0.00 0.00 0.00 5.19
940 1048 1.706305 CCCCCACCCGCCTTTATATAA 59.294 52.381 0.00 0.00 0.00 0.98
1471 1594 6.418819 CAGGAAACAATGTTCATTCACAAGAC 59.581 38.462 0.00 0.00 0.00 3.01
1492 1619 9.265938 CAAGACATTGTACGTATTTCATTCTTG 57.734 33.333 15.35 15.35 0.00 3.02
1526 1665 7.010552 CAGCGAAAGAGTGCTACAGTATAAAAT 59.989 37.037 0.00 0.00 40.03 1.82
1658 1800 4.803426 GCTCTCCGCACCTCCACG 62.803 72.222 0.00 0.00 38.92 4.94
1864 2011 4.958581 TGCAAAGACTCCATCTCATCTCTA 59.041 41.667 0.00 0.00 36.27 2.43
1895 2042 0.395036 CACCCACAACTGAACCACCA 60.395 55.000 0.00 0.00 0.00 4.17
1896 2043 0.395173 ACCCACAACTGAACCACCAC 60.395 55.000 0.00 0.00 0.00 4.16
2002 2149 1.971357 AGTGTCGTTGGAAGGTCAGAT 59.029 47.619 0.00 0.00 0.00 2.90
2010 2157 4.273318 GTTGGAAGGTCAGATAAGGCAAT 58.727 43.478 0.00 0.00 0.00 3.56
2020 2167 5.048713 GTCAGATAAGGCAATTAATTCCCCG 60.049 44.000 4.42 0.00 0.00 5.73
2038 2186 0.159345 CGCAGTTTGCAAATTGTCGC 59.841 50.000 28.54 17.47 45.36 5.19
2047 2195 6.204495 AGTTTGCAAATTGTCGCCAAATAAAT 59.796 30.769 16.21 0.00 33.44 1.40
2066 2214 9.832445 AAATAAATCGTATGTAGGAACTGATGT 57.168 29.630 0.00 0.00 41.52 3.06
2170 2318 2.565841 GCTTCCAAGTCAGACACACTT 58.434 47.619 2.66 0.00 34.24 3.16
2266 2419 5.818857 TGTGTCACAATCATCATACCATCTG 59.181 40.000 2.31 0.00 0.00 2.90
2704 2879 4.323028 CCAAGTCAGTAATGAGGCTCAAGA 60.323 45.833 22.84 9.53 0.00 3.02
2724 2899 1.207329 AGGCCTGATTTCGACCACTAC 59.793 52.381 3.11 0.00 0.00 2.73
2872 3047 0.668535 GTTGGACAGGCAGTTGTTCC 59.331 55.000 0.00 0.00 0.00 3.62
3404 3579 8.803799 CCGTATTTAAATGCAAGGTTGTAATTC 58.196 33.333 15.33 0.00 0.00 2.17
3696 3887 4.648762 TCACCTTCATTCAGGAAAGCAAAA 59.351 37.500 0.00 0.00 37.39 2.44
3764 3955 4.507756 TCATGAGAGTCAACACAAACGAAG 59.492 41.667 0.00 0.00 0.00 3.79
4086 4278 1.148273 TCACCAACTCCAGTGCACC 59.852 57.895 14.63 0.00 33.90 5.01
4109 4301 1.355720 CTCTTCCACAAACCCTCCCAT 59.644 52.381 0.00 0.00 0.00 4.00
4111 4303 1.895131 CTTCCACAAACCCTCCCATTG 59.105 52.381 0.00 0.00 0.00 2.82
4194 4386 7.225931 TCGAGAATAATACCCAGCATTGTTTAC 59.774 37.037 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.319549 CCAAGAGCGGTTTCAAAGTACTTC 60.320 45.833 8.95 0.00 0.00 3.01
185 186 0.815095 CATGCTCAATTGGCAGCTCA 59.185 50.000 21.00 5.12 43.15 4.26
197 198 3.072211 CAGCTTCTTCTCAACATGCTCA 58.928 45.455 0.00 0.00 0.00 4.26
428 441 3.131933 TGGAGATTCTAGCAGAGCTCAAC 59.868 47.826 17.77 7.23 40.44 3.18
444 457 3.137913 CAGGGATTTCATGTCCTGGAGAT 59.862 47.826 0.00 0.00 42.12 2.75
502 515 6.763610 AGCTAGACATTTTATAGAGCCAACAC 59.236 38.462 0.00 0.00 0.00 3.32
507 520 6.593382 CCATGAGCTAGACATTTTATAGAGCC 59.407 42.308 0.00 0.00 0.00 4.70
529 543 3.020984 ACAACCGTGTTTTCTTGTCCAT 58.979 40.909 0.00 0.00 32.58 3.41
542 556 2.605338 CCATCAAGCAGAAACAACCGTG 60.605 50.000 0.00 0.00 0.00 4.94
545 559 4.320608 TTTCCATCAAGCAGAAACAACC 57.679 40.909 0.00 0.00 0.00 3.77
557 571 6.349280 GCAAGTGCTAACTGTATTTCCATCAA 60.349 38.462 0.00 0.00 36.51 2.57
637 656 0.250945 ACCCACACACACACACACAA 60.251 50.000 0.00 0.00 0.00 3.33
700 796 3.118555 ACCCCTTTAACCAAACAAGCAAC 60.119 43.478 0.00 0.00 0.00 4.17
714 811 4.100498 CCTCAATCGCTACTAACCCCTTTA 59.900 45.833 0.00 0.00 0.00 1.85
727 835 0.254178 AATCTGCCACCTCAATCGCT 59.746 50.000 0.00 0.00 0.00 4.93
753 861 1.017387 CTAATTTGGACCTGCGCCTC 58.983 55.000 4.18 0.00 0.00 4.70
754 862 1.032114 GCTAATTTGGACCTGCGCCT 61.032 55.000 4.18 0.00 0.00 5.52
835 943 0.171231 CGCATGTCTCGTCTTCTCCA 59.829 55.000 0.00 0.00 0.00 3.86
1471 1594 7.020602 TGCACAAGAATGAAATACGTACAATG 58.979 34.615 0.00 0.00 0.00 2.82
1492 1619 3.642008 CTCTTTCGCTGCGCTGCAC 62.642 63.158 33.73 10.56 33.79 4.57
1864 2011 4.918360 TGGGTGGGTGGGCAGACT 62.918 66.667 0.00 0.00 0.00 3.24
2002 2149 2.955660 CTGCGGGGAATTAATTGCCTTA 59.044 45.455 30.57 18.90 46.24 2.69
2020 2167 0.508213 GGCGACAATTTGCAAACTGC 59.492 50.000 19.81 15.32 45.29 4.40
2038 2186 8.657074 TCAGTTCCTACATACGATTTATTTGG 57.343 34.615 0.00 0.00 0.00 3.28
2047 2195 3.943381 ACGACATCAGTTCCTACATACGA 59.057 43.478 0.00 0.00 0.00 3.43
2170 2318 9.005777 GGTGAAATAAATACCTTGTTACTCACA 57.994 33.333 0.00 0.00 32.30 3.58
2198 2346 6.037172 GCACTAAGAGTTGAGTTGAGTTGAAA 59.963 38.462 0.00 0.00 0.00 2.69
2266 2419 4.507710 TGTCAATCTACACAATGAGCCTC 58.492 43.478 0.00 0.00 0.00 4.70
2704 2879 1.207329 GTAGTGGTCGAAATCAGGCCT 59.793 52.381 0.00 0.00 33.78 5.19
2724 2899 0.806102 ATTCGTCATCGGAACCAGCG 60.806 55.000 0.00 0.00 37.69 5.18
2836 3011 2.428171 CCAACTGAATGGAAATCGGCAT 59.572 45.455 0.00 0.00 43.54 4.40
2872 3047 4.037208 AGTTTGCATGAGACAAGAAACCTG 59.963 41.667 0.00 0.00 0.00 4.00
3404 3579 8.339714 TCATACTTTCCGTGAAACAGTAAAAAG 58.660 33.333 0.00 0.00 35.74 2.27
3408 3583 6.751157 TCTCATACTTTCCGTGAAACAGTAA 58.249 36.000 3.75 0.00 35.74 2.24
3696 3887 9.374711 TCTCTGGGGTGAAGTTTATTTAATTTT 57.625 29.630 0.00 0.00 0.00 1.82
3699 3890 8.950007 TTTCTCTGGGGTGAAGTTTATTTAAT 57.050 30.769 0.00 0.00 0.00 1.40
3764 3955 0.240945 ACCAATGCACGCTAGTTTGC 59.759 50.000 9.97 9.97 39.33 3.68
4086 4278 2.619074 GGGAGGGTTTGTGGAAGAGATG 60.619 54.545 0.00 0.00 0.00 2.90
4109 4301 4.933505 TCAAAGTTCCATTGCATGACAA 57.066 36.364 0.00 0.33 44.01 3.18
4111 4303 6.040166 AGGATATCAAAGTTCCATTGCATGAC 59.960 38.462 4.83 0.00 31.65 3.06
4194 4386 6.343703 TCTGATCCATCAAAGAGTACACATG 58.656 40.000 0.00 0.00 36.18 3.21


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

AutoCloner maintained by Alex Coulton.