Multiple sequence alignment - TraesCS4B01G089200

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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 TraesCS4B01G089200 chr4B 100.000 2972 0 0 1 2972 90507692 90504721 0.000000e+00 5489.0
1 TraesCS4B01G089200 chr4D 94.444 3006 104 24 1 2972 62095220 62098196 0.000000e+00 4567.0
2 TraesCS4B01G089200 chr4A 93.422 2995 124 22 1 2972 535424681 535427625 0.000000e+00 4372.0
3 TraesCS4B01G089200 chr3B 100.000 37 0 0 2178 2214 646007722 646007758 5.320000e-08 69.4


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 TraesCS4B01G089200 chr4B 90504721 90507692 2971 True 5489 5489 100.000 1 2972 1 chr4B.!!$R1 2971
1 TraesCS4B01G089200 chr4D 62095220 62098196 2976 False 4567 4567 94.444 1 2972 1 chr4D.!!$F1 2971
2 TraesCS4B01G089200 chr4A 535424681 535427625 2944 False 4372 4372 93.422 1 2972 1 chr4A.!!$F1 2971

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
679 686 1.414181 ACGGCCAGAAGATACCATCAG 59.586 52.381 2.24 0.0 0.0 2.90 F
1599 1618 3.699894 CCGGACTGCACTGCCTCT 61.700 66.667 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1825 0.034896 ACACTTCCGTCTCGCCATTT 59.965 50.0 0.0 0.0 0.00 2.32 R
2454 2486 1.444836 TGCCCCGTATCTTGAAAACG 58.555 50.0 0.0 0.0 36.42 3.60 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
316 318 7.023197 ACACCACTATTGTAGAAACACAAAC 57.977 36.000 0.00 0.00 41.50 2.93
362 366 4.510038 ACTCAAACATGGTCTTGATTGC 57.490 40.909 0.00 0.00 31.56 3.56
453 457 3.953712 ACACGGTGATAGATGTTGTCA 57.046 42.857 16.29 0.00 0.00 3.58
585 589 3.950397 TGTTGCAAAGGACCTACTATGG 58.050 45.455 0.00 0.00 0.00 2.74
622 626 9.817365 CTCTTCAGTTACTACAACATGATTTTG 57.183 33.333 0.00 0.00 0.00 2.44
633 637 9.494479 CTACAACATGATTTTGCACTATAGTTG 57.506 33.333 1.56 0.00 38.71 3.16
679 686 1.414181 ACGGCCAGAAGATACCATCAG 59.586 52.381 2.24 0.00 0.00 2.90
702 709 4.697514 CTTTTGATGATCTCCTAAGCCGA 58.302 43.478 0.00 0.00 0.00 5.54
747 754 4.112716 TGATTTCATAGTAACGCACGGA 57.887 40.909 0.00 0.00 0.00 4.69
748 755 4.689071 TGATTTCATAGTAACGCACGGAT 58.311 39.130 0.00 0.00 0.00 4.18
772 779 6.808321 ATTGTGCTAGTAATAGTGAAGGGA 57.192 37.500 0.00 0.00 0.00 4.20
773 780 5.854010 TGTGCTAGTAATAGTGAAGGGAG 57.146 43.478 0.00 0.00 0.00 4.30
774 781 5.516044 TGTGCTAGTAATAGTGAAGGGAGA 58.484 41.667 0.00 0.00 0.00 3.71
775 782 5.594725 TGTGCTAGTAATAGTGAAGGGAGAG 59.405 44.000 0.00 0.00 0.00 3.20
1599 1618 3.699894 CCGGACTGCACTGCCTCT 61.700 66.667 0.00 0.00 0.00 3.69
1722 1741 3.740128 GATCATGGTGGACGCGCCT 62.740 63.158 18.14 0.00 37.63 5.52
1725 1744 4.508128 ATGGTGGACGCGCCTACG 62.508 66.667 18.14 0.00 44.07 3.51
1954 1973 0.900182 CCACAGGGAAAAGGAAGGCC 60.900 60.000 0.00 0.00 35.59 5.19
1984 2003 5.835113 TTGCCCTTGAGAGCAAAATATAC 57.165 39.130 0.00 0.00 45.51 1.47
1985 2004 4.854173 TGCCCTTGAGAGCAAAATATACA 58.146 39.130 0.00 0.00 35.69 2.29
1986 2005 5.260424 TGCCCTTGAGAGCAAAATATACAA 58.740 37.500 0.00 0.00 35.69 2.41
1987 2006 5.125417 TGCCCTTGAGAGCAAAATATACAAC 59.875 40.000 0.00 0.00 35.69 3.32
1990 2009 7.467403 GCCCTTGAGAGCAAAATATACAACTAC 60.467 40.741 0.00 0.00 32.73 2.73
1992 2011 8.946085 CCTTGAGAGCAAAATATACAACTACAA 58.054 33.333 0.00 0.00 32.73 2.41
2079 2110 5.128499 TCTTGATTTCTTTTTGTTGCCCTGA 59.872 36.000 0.00 0.00 0.00 3.86
2096 2127 3.056107 CCCTGAGACGGACAAGAATGTTA 60.056 47.826 0.00 0.00 40.74 2.41
2097 2128 3.927142 CCTGAGACGGACAAGAATGTTAC 59.073 47.826 0.00 0.00 40.74 2.50
2103 2134 5.699458 AGACGGACAAGAATGTTACGATTTT 59.301 36.000 11.89 0.00 40.74 1.82
2104 2135 5.923665 ACGGACAAGAATGTTACGATTTTC 58.076 37.500 11.89 0.00 40.74 2.29
2139 2170 9.793252 CATTTTCAGTTATAAACATGGGAAGAG 57.207 33.333 0.00 0.00 0.00 2.85
2454 2486 5.104735 AGGATCAGATCTACAACCACCTTTC 60.105 44.000 10.36 0.00 0.00 2.62
2497 2535 7.278135 CAATGGGGTATATGTCATAGGAGATG 58.722 42.308 0.00 0.00 0.00 2.90
2522 2560 4.639310 AGTCTGATCTGGTCATTGCATTTC 59.361 41.667 0.00 0.00 35.97 2.17
2600 2639 1.460504 CAGCAGCATCATGGTTCAGT 58.539 50.000 0.00 0.00 0.00 3.41
2655 2694 2.233566 TGACTGAGGCAGGCCCAAT 61.234 57.895 6.70 0.00 39.07 3.16
2656 2695 1.000396 GACTGAGGCAGGCCCAATT 60.000 57.895 6.70 0.00 32.43 2.32
2700 2740 1.948834 TGCTTGCATAATCATCCACCG 59.051 47.619 0.00 0.00 0.00 4.94
2702 2742 2.358898 GCTTGCATAATCATCCACCGTT 59.641 45.455 0.00 0.00 0.00 4.44
2707 2747 3.130340 GCATAATCATCCACCGTTGGTTT 59.870 43.478 0.00 0.00 44.35 3.27
2935 2979 0.109723 TCCGCTACAAACCTTGGCTT 59.890 50.000 0.00 0.00 34.12 4.35
2936 2980 0.240945 CCGCTACAAACCTTGGCTTG 59.759 55.000 1.66 1.66 34.12 4.01
2937 2981 0.951558 CGCTACAAACCTTGGCTTGT 59.048 50.000 12.29 12.29 39.13 3.16
2938 2982 2.147958 CGCTACAAACCTTGGCTTGTA 58.852 47.619 13.08 13.08 37.05 2.41
2939 2983 2.095919 CGCTACAAACCTTGGCTTGTAC 60.096 50.000 10.53 7.88 37.05 2.90
2961 3007 4.777896 ACTGTATTTCTTAGACCTCCAGCA 59.222 41.667 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 250 1.138859 TGGGATATCTCGCACCTTGTG 59.861 52.381 2.05 0.00 39.22 3.33
289 291 5.761234 TGTGTTTCTACAATAGTGGTGTTCC 59.239 40.000 0.00 0.00 35.69 3.62
362 366 2.859165 TTGGCTGGGTAGAGAAACTG 57.141 50.000 0.00 0.00 0.00 3.16
399 403 3.857157 TGTTTGCCCCCATCTACTATC 57.143 47.619 0.00 0.00 0.00 2.08
453 457 6.014156 GCACAAGATGGTAGATTAGGTAGGAT 60.014 42.308 0.00 0.00 0.00 3.24
556 560 6.828785 AGTAGGTCCTTTGCAACATTTATAGG 59.171 38.462 0.00 0.98 0.00 2.57
565 569 3.951663 ACCATAGTAGGTCCTTTGCAAC 58.048 45.455 0.00 0.00 37.28 4.17
585 589 6.425577 AGTAACTGAAGAGTATCGAGTGAC 57.574 41.667 0.00 0.00 42.67 3.67
679 686 3.249559 CGGCTTAGGAGATCATCAAAAGC 59.750 47.826 14.94 14.94 42.31 3.51
687 694 2.666317 TGTCATCGGCTTAGGAGATCA 58.334 47.619 0.00 0.00 0.00 2.92
729 736 6.019398 CACAATATCCGTGCGTTACTATGAAA 60.019 38.462 0.00 0.00 0.00 2.69
747 754 8.492415 TCCCTTCACTATTACTAGCACAATAT 57.508 34.615 0.00 0.00 0.00 1.28
748 755 7.783119 TCTCCCTTCACTATTACTAGCACAATA 59.217 37.037 0.00 0.00 0.00 1.90
772 779 3.204158 TGATTGGGAGCTACTCTCTCTCT 59.796 47.826 0.00 0.00 42.94 3.10
773 780 3.561143 TGATTGGGAGCTACTCTCTCTC 58.439 50.000 0.00 0.00 42.94 3.20
774 781 3.678965 TGATTGGGAGCTACTCTCTCT 57.321 47.619 0.00 0.00 42.94 3.10
775 782 4.744795 TTTGATTGGGAGCTACTCTCTC 57.255 45.455 0.00 0.00 42.82 3.20
964 971 0.941542 TGTGTAGCACTTTCGGCAAC 59.058 50.000 0.90 0.00 35.11 4.17
1599 1618 1.692395 TGGATGATCCTTGGGCGGA 60.692 57.895 13.44 0.00 37.46 5.54
1686 1705 2.114625 ACGTCCCACTCCGTCTCA 59.885 61.111 0.00 0.00 30.05 3.27
1722 1741 4.642488 TCTGGCACCCACCCCGTA 62.642 66.667 0.00 0.00 0.00 4.02
1806 1825 0.034896 ACACTTCCGTCTCGCCATTT 59.965 50.000 0.00 0.00 0.00 2.32
1845 1864 1.122019 AGAAGCTGTCCTCCACCGTT 61.122 55.000 0.00 0.00 0.00 4.44
1954 1973 1.203994 CTCTCAAGGGCAAAATGGCAG 59.796 52.381 6.25 0.00 45.76 4.85
1984 2003 9.472361 ACAAACACAGTAGTATAGTTGTAGTTG 57.528 33.333 0.00 0.00 0.00 3.16
1987 2006 9.784680 CCTACAAACACAGTAGTATAGTTGTAG 57.215 37.037 11.46 11.46 37.78 2.74
1990 2009 9.871238 AATCCTACAAACACAGTAGTATAGTTG 57.129 33.333 0.00 0.00 37.78 3.16
2003 2034 7.865889 CCTTTTGGTTCTAAATCCTACAAACAC 59.134 37.037 0.00 0.00 34.07 3.32
2079 2110 3.928727 TCGTAACATTCTTGTCCGTCT 57.071 42.857 0.00 0.00 34.06 4.18
2096 2127 9.533253 ACTGAAAATGAATCAAAAGAAAATCGT 57.467 25.926 0.00 0.00 0.00 3.73
2139 2170 3.146847 AGTTCGAAAACAACAGATCCCC 58.853 45.455 0.00 0.00 37.88 4.81
2190 2221 7.428020 TGAAATTCAGGAAAGAATTCACACAG 58.572 34.615 8.44 0.00 44.96 3.66
2245 2276 2.522836 TGCAACGTGGCATGAATTTT 57.477 40.000 15.19 0.00 39.25 1.82
2246 2277 2.522836 TTGCAACGTGGCATGAATTT 57.477 40.000 20.37 0.00 44.48 1.82
2247 2278 2.339418 CATTGCAACGTGGCATGAATT 58.661 42.857 20.37 0.00 44.48 2.17
2248 2279 1.404449 CCATTGCAACGTGGCATGAAT 60.404 47.619 20.37 6.60 44.48 2.57
2313 2345 1.990060 TGACTCCCTACCTGGCTGC 60.990 63.158 0.00 0.00 0.00 5.25
2454 2486 1.444836 TGCCCCGTATCTTGAAAACG 58.555 50.000 0.00 0.00 36.42 3.60
2497 2535 4.128925 TGCAATGACCAGATCAGACTAC 57.871 45.455 0.00 0.00 41.91 2.73
2522 2560 9.018582 AGTTCAATCTTCCTGAAAAATTAGGAG 57.981 33.333 0.00 0.00 43.54 3.69
2655 2694 7.397892 TGACAACTGAACAAACTCCAAATAA 57.602 32.000 0.00 0.00 0.00 1.40
2656 2695 7.424803 CATGACAACTGAACAAACTCCAAATA 58.575 34.615 0.00 0.00 0.00 1.40
2700 2740 4.082245 CAGTATCCCACCATGAAAACCAAC 60.082 45.833 0.00 0.00 0.00 3.77
2702 2742 3.563261 CCAGTATCCCACCATGAAAACCA 60.563 47.826 0.00 0.00 0.00 3.67
2707 2747 2.845659 AGTCCAGTATCCCACCATGAA 58.154 47.619 0.00 0.00 0.00 2.57
2894 2938 3.773418 TTTTGACGGTTCATGGTCCTA 57.227 42.857 0.00 0.00 32.19 2.94
2935 2979 6.127423 GCTGGAGGTCTAAGAAATACAGTACA 60.127 42.308 0.00 0.00 0.00 2.90
2936 2980 6.127423 TGCTGGAGGTCTAAGAAATACAGTAC 60.127 42.308 0.00 0.00 0.00 2.73
2937 2981 5.955959 TGCTGGAGGTCTAAGAAATACAGTA 59.044 40.000 0.00 0.00 0.00 2.74
2938 2982 4.777896 TGCTGGAGGTCTAAGAAATACAGT 59.222 41.667 0.00 0.00 0.00 3.55
2939 2983 5.112686 GTGCTGGAGGTCTAAGAAATACAG 58.887 45.833 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.