Multiple sequence alignment - TraesCS5D01G392800

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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 TraesCS5D01G392800 chr5D 100.000 2264 0 0 1 2264 460941810 460944073 0.000000e+00 4181
1 TraesCS5D01G392800 chr5A 94.288 2276 83 20 1 2262 581139936 581137694 0.000000e+00 3439
2 TraesCS5D01G392800 chr5B 93.657 2286 95 22 1 2262 567020813 567018554 0.000000e+00 3373
3 TraesCS5D01G392800 chr7D 80.878 319 59 2 4 321 531083962 531084279 1.340000e-62 250
4 TraesCS5D01G392800 chr7A 80.564 319 60 2 4 321 611496421 611496738 6.250000e-61 244
5 TraesCS5D01G392800 chr7B 80.921 304 56 2 4 306 571575737 571576039 2.910000e-59 239


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 TraesCS5D01G392800 chr5D 460941810 460944073 2263 False 4181 4181 100.000 1 2264 1 chr5D.!!$F1 2263
1 TraesCS5D01G392800 chr5A 581137694 581139936 2242 True 3439 3439 94.288 1 2262 1 chr5A.!!$R1 2261
2 TraesCS5D01G392800 chr5B 567018554 567020813 2259 True 3373 3373 93.657 1 2262 1 chr5B.!!$R1 2261

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
772 783 0.179121 ATGGATTTCGACTGCGCGTA 60.179 50.0 8.43 0.71 37.46 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 2193 0.036952 ACGCATCAGTCAAGGTCCTG 60.037 55.0 0.0 0.0 0.0 3.86 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
525 529 0.867753 CGATCGAGACGCCTTTCAGG 60.868 60.000 10.26 0.00 38.80 3.86
727 738 1.815421 CGGGAAGGATGCGGAACTG 60.815 63.158 0.00 0.00 0.00 3.16
772 783 0.179121 ATGGATTTCGACTGCGCGTA 60.179 50.000 8.43 0.71 37.46 4.42
895 909 2.361610 CAATGCCGCCCAAGAGGT 60.362 61.111 0.00 0.00 38.26 3.85
896 910 2.361610 AATGCCGCCCAAGAGGTG 60.362 61.111 0.00 0.00 46.61 4.00
897 911 3.210012 AATGCCGCCCAAGAGGTGT 62.210 57.895 0.00 0.00 45.49 4.16
898 912 3.925630 ATGCCGCCCAAGAGGTGTG 62.926 63.158 0.00 0.00 45.49 3.82
901 915 4.641645 CGCCCAAGAGGTGTGGCA 62.642 66.667 0.00 0.00 41.29 4.92
902 916 2.203480 GCCCAAGAGGTGTGGCAA 60.203 61.111 0.00 0.00 41.05 4.52
903 917 1.607467 GCCCAAGAGGTGTGGCAAT 60.607 57.895 0.00 0.00 41.05 3.56
904 918 0.323360 GCCCAAGAGGTGTGGCAATA 60.323 55.000 0.00 0.00 41.05 1.90
905 919 1.755179 CCCAAGAGGTGTGGCAATAG 58.245 55.000 0.00 0.00 34.56 1.73
906 920 1.281867 CCCAAGAGGTGTGGCAATAGA 59.718 52.381 0.00 0.00 34.56 1.98
907 921 2.359900 CCAAGAGGTGTGGCAATAGAC 58.640 52.381 0.00 0.00 0.00 2.59
908 922 2.290260 CCAAGAGGTGTGGCAATAGACA 60.290 50.000 0.00 0.00 0.00 3.41
909 923 3.005554 CAAGAGGTGTGGCAATAGACAG 58.994 50.000 0.00 0.00 29.33 3.51
910 924 2.260822 AGAGGTGTGGCAATAGACAGT 58.739 47.619 0.00 0.00 29.33 3.55
911 925 2.027745 AGAGGTGTGGCAATAGACAGTG 60.028 50.000 0.00 0.00 29.33 3.66
912 926 1.003580 AGGTGTGGCAATAGACAGTGG 59.996 52.381 0.00 0.00 29.33 4.00
913 927 1.003118 GGTGTGGCAATAGACAGTGGA 59.997 52.381 0.00 0.00 29.33 4.02
914 928 2.076863 GTGTGGCAATAGACAGTGGAC 58.923 52.381 0.00 0.00 29.33 4.02
915 929 1.696884 TGTGGCAATAGACAGTGGACA 59.303 47.619 0.00 0.00 29.33 4.02
916 930 2.076863 GTGGCAATAGACAGTGGACAC 58.923 52.381 0.00 0.00 29.33 3.67
938 952 6.016024 ACACACACGTACCAGTAAAGAAGATA 60.016 38.462 0.00 0.00 0.00 1.98
957 971 1.818642 AGCTCATCTGAACCTTGTGC 58.181 50.000 0.00 0.00 0.00 4.57
1267 1281 4.860261 CGGCCGGCGTGTAGTACC 62.860 72.222 22.54 1.28 0.00 3.34
1365 1379 2.182030 GTGGAGTTCTCGGCGAGG 59.818 66.667 33.93 17.24 0.00 4.63
1389 1403 0.172578 TTGTCCTCACGGCGATGTAG 59.827 55.000 16.62 4.69 0.00 2.74
1417 1431 1.827344 CACAGTAGGCTCAGATCACCA 59.173 52.381 0.00 0.00 0.00 4.17
1419 1433 1.107114 AGTAGGCTCAGATCACCACG 58.893 55.000 0.00 0.00 0.00 4.94
1424 1438 1.137872 GGCTCAGATCACCACGAGAAT 59.862 52.381 0.00 0.00 0.00 2.40
1442 1456 1.896220 ATGTCGCTGCCTTCAAGAAA 58.104 45.000 0.00 0.00 0.00 2.52
1464 1482 6.959639 AAGAGAAGGAACATTGCAGTTTTA 57.040 33.333 0.00 0.00 0.00 1.52
1551 1569 2.363018 CCGGTGAGGCTCCTCTCA 60.363 66.667 12.86 0.37 43.12 3.27
1761 1779 7.254852 TCACACTTTGTGTTAGGAAAATTCAC 58.745 34.615 6.22 0.00 45.08 3.18
1765 1783 8.755018 CACTTTGTGTTAGGAAAATTCACATTC 58.245 33.333 0.00 0.00 38.50 2.67
1779 1802 5.739752 TTCACATTCATTCCATCGATCAC 57.260 39.130 0.00 0.00 0.00 3.06
1798 1821 4.817517 TCACGGAAAGTAACTGAGGATTC 58.182 43.478 0.00 0.00 0.00 2.52
1799 1822 4.527038 TCACGGAAAGTAACTGAGGATTCT 59.473 41.667 0.00 0.00 0.00 2.40
1800 1823 5.011738 TCACGGAAAGTAACTGAGGATTCTT 59.988 40.000 0.00 0.00 0.00 2.52
1901 1929 1.226717 CTCCGCGTAGTCCTTGAGC 60.227 63.158 4.92 0.00 0.00 4.26
1904 1932 2.126071 GCGTAGTCCTTGAGCGCA 60.126 61.111 11.47 0.00 46.23 6.09
1907 1935 1.352156 CGTAGTCCTTGAGCGCAACC 61.352 60.000 11.47 0.00 0.00 3.77
2174 2202 2.359975 GCCCCGTTCAGGACCTTG 60.360 66.667 0.00 0.00 45.00 3.61
2210 2238 0.310854 GTCCGGACAAGGCAACAAAG 59.689 55.000 29.75 0.00 41.41 2.77
2262 2294 5.582953 TCATGGAGATTTTGGGTTCAGATT 58.417 37.500 0.00 0.00 0.00 2.40
2263 2295 6.730447 TCATGGAGATTTTGGGTTCAGATTA 58.270 36.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 0.038618 CGTCAACATGGTGTCCTCGA 60.039 55.000 11.27 0.00 0.00 4.04
119 120 3.298958 TGTCCAGCGACATCCTCC 58.701 61.111 0.00 0.00 44.20 4.30
464 468 2.595463 TCGTCGGGGTGTTCTCGT 60.595 61.111 0.00 0.00 0.00 4.18
543 547 6.136541 AGGAAAACTTTCTTACTTGCAGTG 57.863 37.500 2.41 0.00 37.35 3.66
560 564 8.236585 TGATCAATGAAGTTTGAGAAGGAAAA 57.763 30.769 0.00 0.00 38.90 2.29
564 568 6.091437 GCTTGATCAATGAAGTTTGAGAAGG 58.909 40.000 8.96 0.00 38.90 3.46
677 688 1.776662 ATGGAGAGATCGACGGGAAA 58.223 50.000 0.00 0.00 0.00 3.13
875 889 1.508088 CTCTTGGGCGGCATTGAAC 59.492 57.895 12.47 0.00 0.00 3.18
895 909 1.696884 TGTCCACTGTCTATTGCCACA 59.303 47.619 0.00 0.00 0.00 4.17
896 910 2.076863 GTGTCCACTGTCTATTGCCAC 58.923 52.381 0.00 0.00 0.00 5.01
897 911 1.696884 TGTGTCCACTGTCTATTGCCA 59.303 47.619 0.00 0.00 0.00 4.92
898 912 2.076863 GTGTGTCCACTGTCTATTGCC 58.923 52.381 0.00 0.00 38.61 4.52
899 913 2.480419 GTGTGTGTCCACTGTCTATTGC 59.520 50.000 0.00 0.00 42.34 3.56
900 914 2.731451 CGTGTGTGTCCACTGTCTATTG 59.269 50.000 0.00 0.00 42.34 1.90
901 915 2.364324 ACGTGTGTGTCCACTGTCTATT 59.636 45.455 0.00 0.00 42.34 1.73
902 916 1.961394 ACGTGTGTGTCCACTGTCTAT 59.039 47.619 0.00 0.00 42.34 1.98
903 917 1.395635 ACGTGTGTGTCCACTGTCTA 58.604 50.000 0.00 0.00 42.34 2.59
904 918 1.066605 GTACGTGTGTGTCCACTGTCT 59.933 52.381 0.00 0.00 42.34 3.41
905 919 1.484356 GTACGTGTGTGTCCACTGTC 58.516 55.000 0.00 0.00 42.34 3.51
906 920 0.103572 GGTACGTGTGTGTCCACTGT 59.896 55.000 0.00 0.00 42.34 3.55
907 921 0.103390 TGGTACGTGTGTGTCCACTG 59.897 55.000 0.00 0.00 42.34 3.66
908 922 0.387929 CTGGTACGTGTGTGTCCACT 59.612 55.000 0.00 0.00 42.34 4.00
909 923 0.103572 ACTGGTACGTGTGTGTCCAC 59.896 55.000 0.00 0.00 42.19 4.02
910 924 1.689984 TACTGGTACGTGTGTGTCCA 58.310 50.000 0.00 0.00 34.14 4.02
911 925 2.798976 TTACTGGTACGTGTGTGTCC 57.201 50.000 0.00 0.00 0.00 4.02
912 926 3.968649 TCTTTACTGGTACGTGTGTGTC 58.031 45.455 0.00 0.00 0.00 3.67
913 927 4.098349 TCTTCTTTACTGGTACGTGTGTGT 59.902 41.667 0.00 0.00 0.00 3.72
914 928 4.613944 TCTTCTTTACTGGTACGTGTGTG 58.386 43.478 0.00 0.00 0.00 3.82
915 929 4.924305 TCTTCTTTACTGGTACGTGTGT 57.076 40.909 0.00 0.00 0.00 3.72
916 930 5.515626 GCTATCTTCTTTACTGGTACGTGTG 59.484 44.000 0.00 0.00 0.00 3.82
921 935 7.865385 CAGATGAGCTATCTTCTTTACTGGTAC 59.135 40.741 0.00 0.00 43.68 3.34
938 952 1.612726 GGCACAAGGTTCAGATGAGCT 60.613 52.381 0.00 0.00 32.33 4.09
957 971 1.468520 GACATGTTCGATGTGGTTGGG 59.531 52.381 0.00 0.00 31.52 4.12
982 996 1.209019 CATCACCAGAGGGGAGTTCAG 59.791 57.143 0.00 0.00 39.13 3.02
1267 1281 2.279120 GATCGACTCCTGCGCCAG 60.279 66.667 4.18 1.92 0.00 4.85
1397 1411 1.827344 TGGTGATCTGAGCCTACTGTG 59.173 52.381 0.00 0.00 0.00 3.66
1417 1431 0.737715 GAAGGCAGCGACATTCTCGT 60.738 55.000 0.00 0.00 44.92 4.18
1419 1433 1.396301 CTTGAAGGCAGCGACATTCTC 59.604 52.381 7.69 0.00 31.79 2.87
1424 1438 1.202639 TCTTTCTTGAAGGCAGCGACA 60.203 47.619 0.00 0.00 35.98 4.35
1442 1456 6.064717 ACTAAAACTGCAATGTTCCTTCTCT 58.935 36.000 0.00 0.00 0.00 3.10
1449 1463 5.352643 ACGGTACTAAAACTGCAATGTTC 57.647 39.130 0.00 0.00 0.00 3.18
1454 1468 3.472283 TGGACGGTACTAAAACTGCAA 57.528 42.857 0.00 0.00 0.00 4.08
1456 1474 3.396560 ACTTGGACGGTACTAAAACTGC 58.603 45.455 0.00 0.00 0.00 4.40
1464 1482 0.038526 CGCTCAACTTGGACGGTACT 60.039 55.000 0.00 0.00 0.00 2.73
1551 1569 2.418910 CGGGCAGAGTGAGGTCGAT 61.419 63.158 0.00 0.00 0.00 3.59
1584 1602 2.746375 GGAGATGGTGCCGGTGGAT 61.746 63.158 1.90 0.00 0.00 3.41
1605 1623 2.583593 GTCATCGCGGTCAGAGCC 60.584 66.667 6.13 0.00 0.00 4.70
1635 1653 2.430146 CGTCAACGTGCGCGACATA 61.430 57.895 28.73 5.64 42.00 2.29
1761 1779 3.392882 TCCGTGATCGATGGAATGAATG 58.607 45.455 0.54 0.00 36.75 2.67
1779 1802 5.348997 GTGAAGAATCCTCAGTTACTTTCCG 59.651 44.000 0.00 0.00 0.00 4.30
1798 1821 7.117812 CCAAGGTACTACAATTACAGTGTGAAG 59.882 40.741 5.88 0.00 38.49 3.02
1799 1822 6.932400 CCAAGGTACTACAATTACAGTGTGAA 59.068 38.462 5.88 0.00 38.49 3.18
1800 1823 6.042322 ACCAAGGTACTACAATTACAGTGTGA 59.958 38.462 5.88 0.00 38.49 3.58
1888 1916 1.352156 GGTTGCGCTCAAGGACTACG 61.352 60.000 9.73 0.00 31.93 3.51
2165 2193 0.036952 ACGCATCAGTCAAGGTCCTG 60.037 55.000 0.00 0.00 0.00 3.86
2210 2238 3.301116 GCTTACAAGTCGATCTCAACGTC 59.699 47.826 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.