Multiple sequence alignment - TraesCS6B01G189400

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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 TraesCS6B01G189400 chr6B 100.000 2579 0 0 1 2579 219213610 219216188 0.000000e+00 4763.0
1 TraesCS6B01G189400 chr6D 93.911 2595 122 20 3 2579 124141938 124144514 0.000000e+00 3884.0
2 TraesCS6B01G189400 chr6A 89.769 1906 117 27 3 1898 157029475 157027638 0.000000e+00 2368.0
3 TraesCS6B01G189400 chr6A 92.522 575 37 6 2009 2579 157027645 157027073 0.000000e+00 819.0
4 TraesCS6B01G189400 chr5A 86.458 96 12 1 1900 1994 455462912 455462817 1.260000e-18 104.0
5 TraesCS6B01G189400 chr5A 96.970 33 1 0 1962 1994 646567061 646567093 3.590000e-04 56.5
6 TraesCS6B01G189400 chr4A 89.796 49 4 1 1941 1989 87411137 87411184 7.710000e-06 62.1
7 TraesCS6B01G189400 chr1D 100.000 33 0 0 1961 1993 39996930 39996962 7.710000e-06 62.1
8 TraesCS6B01G189400 chr5B 97.059 34 1 0 1961 1994 654901918 654901951 9.970000e-05 58.4


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 TraesCS6B01G189400 chr6B 219213610 219216188 2578 False 4763.0 4763 100.0000 1 2579 1 chr6B.!!$F1 2578
1 TraesCS6B01G189400 chr6D 124141938 124144514 2576 False 3884.0 3884 93.9110 3 2579 1 chr6D.!!$F1 2576
2 TraesCS6B01G189400 chr6A 157027073 157029475 2402 True 1593.5 2368 91.1455 3 2579 2 chr6A.!!$R1 2576

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
404 415 0.036294 GCCCTGTAGGTCTGGTTCAC 60.036 60.0 0.00 0.00 38.26 3.18 F
839 860 0.305922 ATATGCTTCTTCTTGCGCGC 59.694 50.0 27.26 27.26 0.00 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1332 1355 0.392706 TCTCTTCAGACTTTGCGGCA 59.607 50.000 0.0 0.0 0.0 5.69 R
2324 2352 2.683933 GGGTTGGAGAGCGGGAGA 60.684 66.667 0.0 0.0 0.0 3.71 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
75 76 1.526917 GAGATCCCCCGCCAACATG 60.527 63.158 0.00 0.00 0.00 3.21
126 127 2.105930 GCGGGTTTGTTTGCTGCA 59.894 55.556 0.00 0.00 0.00 4.41
209 210 3.055312 CCCTGGGTTAACTAGTGAAGACC 60.055 52.174 3.97 1.22 0.00 3.85
292 301 2.180017 GCTTCATGTGCCTTGCCG 59.820 61.111 0.00 0.00 0.00 5.69
300 309 4.947147 TGCCTTGCCGTGGGTGAC 62.947 66.667 0.00 0.00 0.00 3.67
330 339 2.203470 TTTAGGTTTTAGGGTGGGCG 57.797 50.000 0.00 0.00 0.00 6.13
358 369 0.321564 TCTCACCCCGCTGTCATTTG 60.322 55.000 0.00 0.00 0.00 2.32
404 415 0.036294 GCCCTGTAGGTCTGGTTCAC 60.036 60.000 0.00 0.00 38.26 3.18
411 422 5.304686 TGTAGGTCTGGTTCACAATCTTT 57.695 39.130 0.00 0.00 0.00 2.52
412 423 5.690865 TGTAGGTCTGGTTCACAATCTTTT 58.309 37.500 0.00 0.00 0.00 2.27
427 438 2.857483 TCTTTTGCCCGTGAGATTGAA 58.143 42.857 0.00 0.00 0.00 2.69
434 445 1.011904 CGTGAGATTGAATGCGGCG 60.012 57.895 0.51 0.51 0.00 6.46
457 468 1.089920 CACTGGGTGAGCTGTAATGC 58.910 55.000 0.00 0.00 35.23 3.56
472 483 0.396695 AATGCTCTGGCTCATTGGGG 60.397 55.000 0.00 0.00 39.59 4.96
508 519 4.140536 GAGATTGAATCCCCCAGTTCATC 58.859 47.826 0.75 0.00 34.60 2.92
516 527 3.803340 TCCCCCAGTTCATCTACTTCTT 58.197 45.455 0.00 0.00 0.00 2.52
572 583 6.763355 TCTCATGGAATAGAGGAACTTATGC 58.237 40.000 0.00 0.00 41.55 3.14
588 599 2.359230 GCTGCTCGCCCTTGTCTT 60.359 61.111 0.00 0.00 0.00 3.01
697 710 1.811359 CTTCTTTTCTGGCAGCTGAGG 59.189 52.381 20.43 6.28 0.00 3.86
700 713 2.079925 CTTTTCTGGCAGCTGAGGTAC 58.920 52.381 20.43 0.00 0.00 3.34
723 736 3.127721 GCTGAGCATTTAGTTCCAAGTCC 59.872 47.826 0.00 0.00 0.00 3.85
741 761 6.363626 CCAAGTCCAATATCTCTAAATCGTCG 59.636 42.308 0.00 0.00 0.00 5.12
746 766 7.537991 GTCCAATATCTCTAAATCGTCGGTTAG 59.462 40.741 0.00 0.95 0.00 2.34
752 772 2.172851 AAATCGTCGGTTAGGTTGCA 57.827 45.000 0.00 0.00 0.00 4.08
764 785 5.006746 CGGTTAGGTTGCATCTAAGCTTAAG 59.993 44.000 24.19 0.00 40.81 1.85
772 793 7.764901 GGTTGCATCTAAGCTTAAGTAGTTACT 59.235 37.037 7.74 0.00 34.99 2.24
810 831 6.727824 TCTGTTTAGCTGCTCTTATTTGAC 57.272 37.500 4.91 0.00 0.00 3.18
839 860 0.305922 ATATGCTTCTTCTTGCGCGC 59.694 50.000 27.26 27.26 0.00 6.86
897 920 3.506455 GCAGGAGATTTCCATGGATCATG 59.494 47.826 17.06 18.20 46.64 3.07
942 965 2.677524 GTGCAGGGCAGCCAATCA 60.678 61.111 15.19 4.08 40.08 2.57
957 980 5.649395 CAGCCAATCATTAGTTTCTTCTCCA 59.351 40.000 0.00 0.00 0.00 3.86
989 1012 7.084486 GCTATATTTTTGTGCCAATACCTAGC 58.916 38.462 0.00 0.00 0.00 3.42
1108 1131 3.788766 CCGAGGCCGCAAAAGACG 61.789 66.667 7.44 0.00 0.00 4.18
1179 1202 2.777969 GCCACCAGCATCAGAGAAG 58.222 57.895 0.00 0.00 42.97 2.85
1260 1283 1.687682 CCAGCTCTCCTTCTCAGGCTA 60.688 57.143 0.00 0.00 40.58 3.93
1368 1391 5.297776 TGAAGAGAAAAAGGCTGAGAAGTTG 59.702 40.000 0.00 0.00 0.00 3.16
1374 1397 6.551227 AGAAAAAGGCTGAGAAGTTGGTATTT 59.449 34.615 0.00 0.00 0.00 1.40
1577 1600 1.696884 TGGTGTTGCTGTGATGGAGTA 59.303 47.619 0.00 0.00 0.00 2.59
1591 1614 6.603201 TGTGATGGAGTAAAGGATCAAATTCC 59.397 38.462 0.00 0.00 35.90 3.01
1592 1615 6.603201 GTGATGGAGTAAAGGATCAAATTCCA 59.397 38.462 0.00 0.32 38.32 3.53
1657 1680 1.107114 GGAGCATTCGAGGTCTGAGA 58.893 55.000 4.18 0.00 36.33 3.27
1707 1730 3.463944 ACTTGTGACAGGTAACGAAAGG 58.536 45.455 0.00 0.00 46.39 3.11
1736 1759 9.360093 GATGCGAACTAGATATTTAGTTGCTAT 57.640 33.333 20.19 16.88 42.38 2.97
1827 1853 3.058224 GGAACTGGGTGAAAGAAATGTCG 60.058 47.826 0.00 0.00 0.00 4.35
1828 1854 3.485463 ACTGGGTGAAAGAAATGTCGA 57.515 42.857 0.00 0.00 0.00 4.20
1829 1855 3.139077 ACTGGGTGAAAGAAATGTCGAC 58.861 45.455 9.11 9.11 0.00 4.20
1830 1856 2.139917 TGGGTGAAAGAAATGTCGACG 58.860 47.619 11.62 0.00 0.00 5.12
1831 1857 1.136057 GGGTGAAAGAAATGTCGACGC 60.136 52.381 11.62 0.15 0.00 5.19
1832 1858 1.798813 GGTGAAAGAAATGTCGACGCT 59.201 47.619 11.62 2.67 0.00 5.07
1833 1859 2.411547 GGTGAAAGAAATGTCGACGCTG 60.412 50.000 11.62 0.00 0.00 5.18
1834 1860 2.221055 GTGAAAGAAATGTCGACGCTGT 59.779 45.455 11.62 0.46 0.00 4.40
1915 1941 7.465353 TCATTTTGGATTTTGCTACAGATCA 57.535 32.000 0.00 0.00 0.00 2.92
1918 1944 9.158233 CATTTTGGATTTTGCTACAGATCAAAT 57.842 29.630 0.00 0.00 32.92 2.32
1923 1949 5.465532 TTTTGCTACAGATCAAATGCCAA 57.534 34.783 0.00 0.00 32.92 4.52
1949 1975 2.894763 TAGCATGGCAAATGGAATGC 57.105 45.000 0.00 0.00 44.56 3.56
1972 1998 5.490159 CCCAAGATGGCAAATTATGTTGTT 58.510 37.500 0.00 0.00 35.79 2.83
1973 1999 5.352016 CCCAAGATGGCAAATTATGTTGTTG 59.648 40.000 0.00 0.00 35.79 3.33
1974 2000 5.163834 CCAAGATGGCAAATTATGTTGTTGC 60.164 40.000 0.00 0.00 45.48 4.17
1982 2008 5.401550 CAAATTATGTTGTTGCGAGGATGT 58.598 37.500 0.00 0.00 0.00 3.06
1994 2020 4.797471 TGCGAGGATGTCAATTTTCTTTG 58.203 39.130 0.00 0.00 0.00 2.77
2006 2032 5.530543 TCAATTTTCTTTGCCAAACATTCCC 59.469 36.000 0.00 0.00 0.00 3.97
2014 2040 2.830923 TGCCAAACATTCCCGATCATTT 59.169 40.909 0.00 0.00 0.00 2.32
2049 2075 5.220567 CCTTTTGGTGTTTGATTTGAAACGG 60.221 40.000 0.00 0.00 38.46 4.44
2060 2086 5.292765 TGATTTGAAACGGCTTGCAATTTA 58.707 33.333 0.00 0.00 0.00 1.40
2062 2088 6.426328 TGATTTGAAACGGCTTGCAATTTATT 59.574 30.769 0.00 0.00 0.00 1.40
2064 2090 5.588568 TGAAACGGCTTGCAATTTATTTG 57.411 34.783 0.00 0.00 38.43 2.32
2173 2200 5.512060 GCATATCCTCATTCAGCCTAGTGAA 60.512 44.000 0.00 0.00 40.68 3.18
2220 2248 8.988934 GCTATCAGTTTCATATAAACGAATCCA 58.011 33.333 0.00 0.00 35.42 3.41
2312 2340 2.897207 CTGTAATCCGCCGGGTCA 59.103 61.111 1.90 0.00 33.83 4.02
2324 2352 3.728373 GGGTCACCGGGAATGCCT 61.728 66.667 6.32 0.00 0.00 4.75
2549 2577 0.744414 CCACCGTGATCGCCATTTCT 60.744 55.000 0.00 0.00 35.54 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 3.918253 TTGATGCCCCACCACGAGC 62.918 63.158 0.00 0.00 0.00 5.03
126 127 5.081728 TGGTAATATATGCTACTCCACCGT 58.918 41.667 0.00 0.00 0.00 4.83
164 165 2.011947 GGACCTAACGAAATTTCCGGG 58.988 52.381 12.54 11.06 0.00 5.73
209 210 1.537776 GCATCGATCTCACACTCCCAG 60.538 57.143 0.00 0.00 0.00 4.45
292 301 1.971481 AACCTAAAACCGTCACCCAC 58.029 50.000 0.00 0.00 0.00 4.61
300 309 6.265196 ACCCTAAAACCTAAAACCTAAAACCG 59.735 38.462 0.00 0.00 0.00 4.44
301 310 7.436118 CACCCTAAAACCTAAAACCTAAAACC 58.564 38.462 0.00 0.00 0.00 3.27
302 311 7.436118 CCACCCTAAAACCTAAAACCTAAAAC 58.564 38.462 0.00 0.00 0.00 2.43
303 312 6.554228 CCCACCCTAAAACCTAAAACCTAAAA 59.446 38.462 0.00 0.00 0.00 1.52
304 313 6.076653 CCCACCCTAAAACCTAAAACCTAAA 58.923 40.000 0.00 0.00 0.00 1.85
305 314 5.643176 CCCACCCTAAAACCTAAAACCTAA 58.357 41.667 0.00 0.00 0.00 2.69
306 315 4.508943 GCCCACCCTAAAACCTAAAACCTA 60.509 45.833 0.00 0.00 0.00 3.08
307 316 3.756141 GCCCACCCTAAAACCTAAAACCT 60.756 47.826 0.00 0.00 0.00 3.50
330 339 2.267324 GGGGTGAGAGCAGCAGAC 59.733 66.667 0.00 0.00 44.15 3.51
404 415 3.504863 CAATCTCACGGGCAAAAGATTG 58.495 45.455 11.17 11.17 44.91 2.67
411 422 0.810648 GCATTCAATCTCACGGGCAA 59.189 50.000 0.00 0.00 0.00 4.52
412 423 1.368345 CGCATTCAATCTCACGGGCA 61.368 55.000 0.00 0.00 0.00 5.36
427 438 2.514592 CCCAGTGAATCGCCGCAT 60.515 61.111 0.00 0.00 0.00 4.73
434 445 3.334583 TTACAGCTCACCCAGTGAATC 57.665 47.619 0.00 0.00 42.26 2.52
457 468 1.225704 GTCCCCCAATGAGCCAGAG 59.774 63.158 0.00 0.00 0.00 3.35
460 471 2.204291 AGGTCCCCCAATGAGCCA 60.204 61.111 0.00 0.00 0.00 4.75
472 483 3.375699 TCAATCTCTGGTTAGGAGGTCC 58.624 50.000 0.00 0.00 0.00 4.46
508 519 7.652727 TCCGACATGATTGATAGAAGAAGTAG 58.347 38.462 0.00 0.00 0.00 2.57
516 527 4.279420 CAGTCCTCCGACATGATTGATAGA 59.721 45.833 0.00 0.00 41.87 1.98
572 583 0.239347 CAAAAGACAAGGGCGAGCAG 59.761 55.000 0.00 0.00 0.00 4.24
588 599 0.039617 CCGAAATTCCGCACAGCAAA 60.040 50.000 0.00 0.00 0.00 3.68
697 710 3.259064 TGGAACTAAATGCTCAGCGTAC 58.741 45.455 0.00 0.00 0.00 3.67
700 713 2.744202 ACTTGGAACTAAATGCTCAGCG 59.256 45.455 0.00 0.00 0.00 5.18
705 718 7.349598 AGATATTGGACTTGGAACTAAATGCT 58.650 34.615 0.00 0.00 0.00 3.79
723 736 7.368833 ACCTAACCGACGATTTAGAGATATTG 58.631 38.462 14.39 3.05 0.00 1.90
741 761 5.880887 ACTTAAGCTTAGATGCAACCTAACC 59.119 40.000 6.24 3.24 34.99 2.85
746 766 6.986904 AACTACTTAAGCTTAGATGCAACC 57.013 37.500 6.24 0.00 34.99 3.77
764 785 9.088512 CAGAAGTGGACAAATCATAGTAACTAC 57.911 37.037 0.00 0.00 0.00 2.73
772 793 7.119699 CAGCTAAACAGAAGTGGACAAATCATA 59.880 37.037 0.00 0.00 0.00 2.15
777 798 3.315191 GCAGCTAAACAGAAGTGGACAAA 59.685 43.478 0.00 0.00 0.00 2.83
942 965 5.044550 AGCAAGGGATGGAGAAGAAACTAAT 60.045 40.000 0.00 0.00 0.00 1.73
957 980 4.961730 TGGCACAAAAATATAGCAAGGGAT 59.038 37.500 0.00 0.00 31.92 3.85
989 1012 5.398603 AGACAAACTCATCCTACTGTCAG 57.601 43.478 0.00 0.00 36.49 3.51
1108 1131 2.028020 ACTTGTACCTCTTAGCACCAGC 60.028 50.000 0.00 0.00 42.56 4.85
1179 1202 1.079336 GTCCGCTAGACCCACAACC 60.079 63.158 0.00 0.00 39.84 3.77
1260 1283 1.829533 CTGTGGTGCTGGCTGGTTT 60.830 57.895 0.00 0.00 0.00 3.27
1332 1355 0.392706 TCTCTTCAGACTTTGCGGCA 59.607 50.000 0.00 0.00 0.00 5.69
1368 1391 6.817765 TTCTCCAACTTGACATCAAATACC 57.182 37.500 0.00 0.00 35.15 2.73
1374 1397 6.016024 CCTCAAATTTCTCCAACTTGACATCA 60.016 38.462 0.00 0.00 0.00 3.07
1577 1600 5.246656 TGCAATGTCTGGAATTTGATCCTTT 59.753 36.000 0.00 0.00 40.35 3.11
1591 1614 8.248945 AGAAAGAAATAAGGATTGCAATGTCTG 58.751 33.333 18.59 0.00 0.00 3.51
1592 1615 8.358582 AGAAAGAAATAAGGATTGCAATGTCT 57.641 30.769 18.59 11.19 0.00 3.41
1657 1680 8.560903 ACCATTTCCTCCAAAAGTATAGAGATT 58.439 33.333 0.00 0.00 0.00 2.40
1707 1730 7.148722 GCAACTAAATATCTAGTTCGCATCTCC 60.149 40.741 13.76 0.00 39.57 3.71
1736 1759 5.401531 AGTCTTATTCTAGAACGCCAACA 57.598 39.130 7.48 0.00 0.00 3.33
1897 1923 5.394443 GGCATTTGATCTGTAGCAAAATCCA 60.394 40.000 0.00 0.00 43.64 3.41
1905 1931 6.973229 AAAATTTGGCATTTGATCTGTAGC 57.027 33.333 0.00 0.00 0.00 3.58
1930 1956 2.894763 GCATTCCATTTGCCATGCTA 57.105 45.000 0.00 0.00 39.20 3.49
1949 1975 5.088680 ACAACATAATTTGCCATCTTGGG 57.911 39.130 0.00 0.00 38.19 4.12
1968 1994 4.278170 AGAAAATTGACATCCTCGCAACAA 59.722 37.500 0.00 0.00 0.00 2.83
1972 1998 4.797471 CAAAGAAAATTGACATCCTCGCA 58.203 39.130 0.00 0.00 31.84 5.10
1973 1999 3.609807 GCAAAGAAAATTGACATCCTCGC 59.390 43.478 0.00 0.00 31.84 5.03
1974 2000 4.168760 GGCAAAGAAAATTGACATCCTCG 58.831 43.478 0.00 0.00 38.25 4.63
1982 2008 5.530543 GGGAATGTTTGGCAAAGAAAATTGA 59.469 36.000 13.94 0.00 31.84 2.57
1994 2020 3.525268 AAATGATCGGGAATGTTTGGC 57.475 42.857 0.00 0.00 0.00 4.52
2006 2032 7.008266 CCAAAAGGACGTGATTTAAAATGATCG 59.992 37.037 0.00 0.00 0.00 3.69
2014 2040 5.838531 AACACCAAAAGGACGTGATTTAA 57.161 34.783 0.00 0.00 0.00 1.52
2060 2086 5.944007 ACTTCTAATTACAGGTTCGGCAAAT 59.056 36.000 0.00 0.00 0.00 2.32
2062 2088 4.901868 ACTTCTAATTACAGGTTCGGCAA 58.098 39.130 0.00 0.00 0.00 4.52
2064 2090 6.973229 TTTACTTCTAATTACAGGTTCGGC 57.027 37.500 0.00 0.00 0.00 5.54
2065 2091 8.712285 TCATTTACTTCTAATTACAGGTTCGG 57.288 34.615 0.00 0.00 0.00 4.30
2220 2248 2.706890 ACTTTCATGTACGGGCGAAAT 58.293 42.857 0.00 0.00 0.00 2.17
2312 2340 3.090532 GGGAGAGGCATTCCCGGT 61.091 66.667 10.14 0.00 44.58 5.28
2324 2352 2.683933 GGGTTGGAGAGCGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
2476 2504 3.501040 TGGAAGTTCCGGGGCAACC 62.501 63.158 17.13 0.95 46.67 3.77


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

AutoCloner maintained by Alex Coulton.