Multiple sequence alignment - TraesCS4A01G161400

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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 TraesCS4A01G161400 chr4A 100.000 2309 0 0 1 2309 350239804 350237496 0 4265
1 TraesCS4A01G161400 chr7D 96.416 2316 75 6 1 2309 382089827 382087513 0 3810
2 TraesCS4A01G161400 chr7D 96.076 2319 77 8 1 2309 626711167 626713481 0 3766
3 TraesCS4A01G161400 chr6B 96.167 2322 74 9 1 2309 596601830 596604149 0 3781
4 TraesCS4A01G161400 chr7A 96.124 2322 76 7 1 2309 638507636 638509956 0 3777
5 TraesCS4A01G161400 chr7A 95.910 2323 78 11 1 2309 708245653 708243334 0 3747
6 TraesCS4A01G161400 chr4D 96.159 2317 79 7 1 2309 123401547 123399233 0 3777
7 TraesCS4A01G161400 chrUn 95.993 2321 80 8 1 2309 171008314 171005995 0 3759
8 TraesCS4A01G161400 chr1B 95.815 2318 84 9 3 2309 672541248 672538933 0 3731


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 TraesCS4A01G161400 chr4A 350237496 350239804 2308 True 4265 4265 100.000 1 2309 1 chr4A.!!$R1 2308
1 TraesCS4A01G161400 chr7D 382087513 382089827 2314 True 3810 3810 96.416 1 2309 1 chr7D.!!$R1 2308
2 TraesCS4A01G161400 chr7D 626711167 626713481 2314 False 3766 3766 96.076 1 2309 1 chr7D.!!$F1 2308
3 TraesCS4A01G161400 chr6B 596601830 596604149 2319 False 3781 3781 96.167 1 2309 1 chr6B.!!$F1 2308
4 TraesCS4A01G161400 chr7A 638507636 638509956 2320 False 3777 3777 96.124 1 2309 1 chr7A.!!$F1 2308
5 TraesCS4A01G161400 chr7A 708243334 708245653 2319 True 3747 3747 95.910 1 2309 1 chr7A.!!$R1 2308
6 TraesCS4A01G161400 chr4D 123399233 123401547 2314 True 3777 3777 96.159 1 2309 1 chr4D.!!$R1 2308
7 TraesCS4A01G161400 chrUn 171005995 171008314 2319 True 3759 3759 95.993 1 2309 1 chrUn.!!$R1 2308
8 TraesCS4A01G161400 chr1B 672538933 672541248 2315 True 3731 3731 95.815 3 2309 1 chr1B.!!$R1 2306

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
587 593 0.40404 GGAATGATTATCCCCGCCCA 59.596 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 1937 0.173481 CTGGATGACGACGTCACCAT 59.827 55.0 32.85 21.69 45.65 3.55 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
47 48 4.454678 AGCAAGAAGACACATTCAAGTCA 58.545 39.130 0.00 0.00 37.23 3.41
62 63 9.295825 ACATTCAAGTCAATCTATTACAACCAA 57.704 29.630 0.00 0.00 0.00 3.67
88 89 6.302313 CGTGGTTGTTCGTATTTCATTTTCTC 59.698 38.462 0.00 0.00 0.00 2.87
159 160 7.222000 ACTTACTGAATCTCGTCTTTCTCTT 57.778 36.000 0.00 0.00 0.00 2.85
353 359 7.447510 CCCCCTTTACCTTCTCTTTCTATTA 57.552 40.000 0.00 0.00 0.00 0.98
382 388 2.029828 CGGCGAACATCTAATCTAGGCT 60.030 50.000 0.00 0.00 0.00 4.58
409 415 2.632377 CCTTTCTATGAAGGCGAGCAA 58.368 47.619 0.00 0.00 39.75 3.91
440 446 7.500141 CCCCCTTGTTGAAATTTGGATATTAG 58.500 38.462 0.00 0.00 0.00 1.73
507 513 2.668550 GCCTCCTGCGGTCGTTTT 60.669 61.111 0.00 0.00 0.00 2.43
521 527 4.464112 GGTCGTTTTAGTGACTCAATTGC 58.536 43.478 0.00 0.00 35.45 3.56
550 556 0.964700 CTCAGCTCAGACTGGTGTCA 59.035 55.000 1.81 0.00 45.20 3.58
587 593 0.404040 GGAATGATTATCCCCGCCCA 59.596 55.000 0.00 0.00 0.00 5.36
605 611 3.141398 CCCAATGGGTCTACATTCATCG 58.859 50.000 10.91 0.00 38.94 3.84
665 671 4.525487 TCTTGTAACCGTCACCTGTAATCT 59.475 41.667 0.00 0.00 0.00 2.40
679 685 0.608130 TAATCTGCGCAGGTGTGTCT 59.392 50.000 35.36 17.07 0.00 3.41
773 780 3.950397 TCACTTTCCCGTATGAGCATTT 58.050 40.909 0.00 0.00 0.00 2.32
775 782 3.689161 CACTTTCCCGTATGAGCATTTGA 59.311 43.478 0.00 0.00 0.00 2.69
875 882 2.666862 TTCGCCGCGGTTCATTGT 60.667 55.556 28.70 0.00 0.00 2.71
882 889 0.725784 CGCGGTTCATTGTTGTGCTC 60.726 55.000 0.00 0.00 0.00 4.26
991 1001 2.529312 GGGCTCCCGTAGAGGAAAT 58.471 57.895 2.29 0.00 45.00 2.17
1019 1029 0.040058 ATGTCAGATGCAAAGCCCCA 59.960 50.000 0.00 0.00 0.00 4.96
1057 1067 9.160496 GATCATATTGGCATACTCTCCTAAAAG 57.840 37.037 0.00 0.00 0.00 2.27
1065 1078 5.522097 GCATACTCTCCTAAAAGAAGAGCAC 59.478 44.000 0.00 0.00 0.00 4.40
1210 1223 7.177878 AGAAGTCATGGAAGTGTGGATAAATT 58.822 34.615 0.00 0.00 0.00 1.82
1312 1326 3.490933 CCTCGAGATCGCATTTTAGGTCA 60.491 47.826 15.71 0.00 39.60 4.02
1342 1356 1.280457 CTAGGGAGTCTGTGGGCTTT 58.720 55.000 0.00 0.00 0.00 3.51
1357 1371 2.416747 GGCTTTCCTTGGCATTTCAAC 58.583 47.619 0.00 0.00 0.00 3.18
1377 1391 4.222124 ACATGGCCTCTATCGTCTTTTT 57.778 40.909 3.32 0.00 0.00 1.94
1439 1453 2.107204 AGAGACAAAAGCAGTCCCACAT 59.893 45.455 0.00 0.00 36.68 3.21
1523 1537 2.633657 CGAACGCTTGCAGTTGCT 59.366 55.556 5.62 0.00 42.66 3.91
1699 1713 1.694696 GGATGGATCGAGGTTTAGGCT 59.305 52.381 0.00 0.00 0.00 4.58
1721 1740 0.331616 GGGGCTTGCTCCCTTTCTTA 59.668 55.000 0.00 0.00 45.80 2.10
1724 1743 2.621668 GGGCTTGCTCCCTTTCTTATGT 60.622 50.000 2.57 0.00 43.13 2.29
1762 1781 1.480789 GGGTGGCATTTCCGGTAAAT 58.519 50.000 0.00 3.63 38.36 1.40
1780 1799 2.594536 ATGGGGAATCTCAAGGAGGA 57.405 50.000 0.00 0.00 0.00 3.71
1829 1848 1.964373 GGGTTGGCGTTGTGTCGAT 60.964 57.895 0.00 0.00 0.00 3.59
1844 1863 2.914289 GATGACCCCCTCTGGCTG 59.086 66.667 0.00 0.00 0.00 4.85
1871 1890 6.459923 GGCTAGAGGTAATTTCGATGATCTT 58.540 40.000 0.00 0.00 0.00 2.40
1899 1918 2.549992 CCTTTGTTCCTCGTCACCATCA 60.550 50.000 0.00 0.00 0.00 3.07
1918 1937 7.336679 CACCATCACAATAACAATAAGGAGACA 59.663 37.037 0.00 0.00 0.00 3.41
1919 1938 8.055181 ACCATCACAATAACAATAAGGAGACAT 58.945 33.333 0.00 0.00 0.00 3.06
2133 2154 2.962859 AGGAACTGGCCAATTCACTTT 58.037 42.857 26.87 7.82 37.18 2.66
2191 2212 5.634859 GGTGGCATTTGACATCTAAAGTTTG 59.365 40.000 0.00 0.00 34.33 2.93
2196 2217 7.092716 GCATTTGACATCTAAAGTTTGACCAT 58.907 34.615 0.00 0.00 0.00 3.55
2210 2231 1.291033 TGACCATCCCTACTACTGCCT 59.709 52.381 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 5.427036 AAATGAAATACGAACAACCACGT 57.573 34.783 0.00 0.00 44.72 4.49
176 177 1.092348 CTGATCGACCCAGACACGTA 58.908 55.000 10.25 0.00 33.65 3.57
184 185 1.320344 CCGAACCTCTGATCGACCCA 61.320 60.000 1.01 0.00 41.43 4.51
353 359 9.355215 CTAGATTAGATGTTCGCCGTTTTATAT 57.645 33.333 0.00 0.00 0.00 0.86
361 367 2.029828 AGCCTAGATTAGATGTTCGCCG 60.030 50.000 0.00 0.00 0.00 6.46
382 388 1.136305 CCTTCATAGAAAGGCGACCGA 59.864 52.381 0.00 0.00 39.47 4.69
409 415 1.955458 TTTCAACAAGGGGGCTGGGT 61.955 55.000 0.00 0.00 0.00 4.51
440 446 1.021968 ATTGCGAAATACGGCTTCCC 58.978 50.000 0.00 0.00 42.83 3.97
507 513 1.630369 AGCCAGGCAATTGAGTCACTA 59.370 47.619 15.80 0.00 0.00 2.74
521 527 2.254737 CTGAGCTGAGGGAAGCCAGG 62.255 65.000 0.00 0.00 44.68 4.45
550 556 2.122954 GGTCCTGGGAGAGGTGGT 59.877 66.667 0.00 0.00 43.37 4.16
587 593 3.134623 TCAGCGATGAATGTAGACCCATT 59.865 43.478 0.00 0.00 37.74 3.16
605 611 2.000447 GAGTACCCAACGACATTCAGC 59.000 52.381 0.00 0.00 0.00 4.26
617 623 1.652947 GGGGAAGTGAAGAGTACCCA 58.347 55.000 0.00 0.00 39.10 4.51
679 685 1.612442 GTCCACTCTAGGGGGTGCA 60.612 63.158 0.00 0.00 32.68 4.57
851 858 4.747529 ACCGCGGCGAACCCTTAC 62.748 66.667 28.58 0.00 0.00 2.34
882 889 1.757699 GGAGAAGGGTAGCCTAGTGTG 59.242 57.143 15.26 0.00 0.00 3.82
991 1001 1.003003 TGCATCTGACATTCGTTGGGA 59.997 47.619 0.00 0.00 0.00 4.37
1019 1029 6.604171 TGCCAATATGATCTTAATGAGGTGT 58.396 36.000 5.47 0.00 0.00 4.16
1057 1067 1.815003 CTTCAATGGGGTGTGCTCTTC 59.185 52.381 0.00 0.00 0.00 2.87
1232 1245 3.023832 AGGATGGTTAGGGCGATTTTTG 58.976 45.455 0.00 0.00 0.00 2.44
1285 1298 1.043116 AATGCGATCTCGAGGACCCA 61.043 55.000 13.56 6.13 43.02 4.51
1312 1326 2.506644 AGACTCCCTAGCGTCTCTACTT 59.493 50.000 2.78 0.00 35.72 2.24
1342 1356 1.275856 GCCATGTTGAAATGCCAAGGA 59.724 47.619 0.00 0.00 0.00 3.36
1357 1371 4.191544 TCAAAAAGACGATAGAGGCCATG 58.808 43.478 5.01 0.00 41.38 3.66
1377 1391 2.347490 GCAAACGGGAGGCTCTCA 59.653 61.111 15.97 0.00 31.08 3.27
1668 1682 1.722034 GATCCATCCCAGAGTAGCCA 58.278 55.000 0.00 0.00 0.00 4.75
1721 1740 2.436173 GCAGGTCCTTCCTTAGCTACAT 59.564 50.000 0.00 0.00 45.67 2.29
1724 1743 1.112113 CGCAGGTCCTTCCTTAGCTA 58.888 55.000 0.00 0.00 45.67 3.32
1750 1769 4.079443 TGAGATTCCCCATTTACCGGAAAT 60.079 41.667 9.46 7.28 39.07 2.17
1762 1781 2.021639 AGATCCTCCTTGAGATTCCCCA 60.022 50.000 0.00 0.00 0.00 4.96
1780 1799 1.205893 GCACTTCGAAGGTCTGGAGAT 59.794 52.381 27.86 1.65 0.00 2.75
1844 1863 1.068127 TCGAAATTACCTCTAGCCCGC 59.932 52.381 0.00 0.00 0.00 6.13
1871 1890 2.856988 AGGAACAAAGGGCCGGGA 60.857 61.111 2.18 0.00 0.00 5.14
1899 1918 7.336931 GTCACCATGTCTCCTTATTGTTATTGT 59.663 37.037 0.00 0.00 0.00 2.71
1918 1937 0.173481 CTGGATGACGACGTCACCAT 59.827 55.000 32.85 21.69 45.65 3.55
1919 1938 0.891904 TCTGGATGACGACGTCACCA 60.892 55.000 31.69 31.69 45.65 4.17
2110 2131 2.893489 AGTGAATTGGCCAGTTCCTTTC 59.107 45.455 31.33 20.45 0.00 2.62
2191 2212 1.689273 CAGGCAGTAGTAGGGATGGTC 59.311 57.143 0.00 0.00 0.00 4.02
2196 2217 3.039011 GGATTTCAGGCAGTAGTAGGGA 58.961 50.000 0.00 0.00 0.00 4.20
2210 2231 1.888512 GCTCACCAAAGCAGGATTTCA 59.111 47.619 0.00 0.00 42.05 2.69


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

AutoCloner maintained by Alex Coulton.