Multiple sequence alignment - TraesCS5A01G105300

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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 TraesCS5A01G105300 chr5A 100.000 2499 0 0 1 2499 169625505 169623007 0 4615
1 TraesCS5A01G105300 chr5D 96.348 1917 54 5 586 2499 135521265 135523168 0 3138
2 TraesCS5A01G105300 chr5D 92.424 594 33 3 1 582 135520633 135521226 0 837
3 TraesCS5A01G105300 chr5B 94.367 1935 70 6 586 2499 147156485 147158401 0 2933
4 TraesCS5A01G105300 chr5B 94.108 594 21 5 1 582 147155857 147156448 0 891


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 TraesCS5A01G105300 chr5A 169623007 169625505 2498 True 4615.0 4615 100.0000 1 2499 1 chr5A.!!$R1 2498
1 TraesCS5A01G105300 chr5D 135520633 135523168 2535 False 1987.5 3138 94.3860 1 2499 2 chr5D.!!$F1 2498
2 TraesCS5A01G105300 chr5B 147155857 147158401 2544 False 1912.0 2933 94.2375 1 2499 2 chr5B.!!$F1 2498

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
463 479 1.258982 CGGTTGCTTCTCATGCGTATC 59.741 52.381 0.00 0.00 0.00 2.24 F
852 904 2.044946 GACCCTGACCATGGTGGC 60.045 66.667 25.52 9.69 42.67 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1327 1.329171 TGCTTTTGTTGGCTGCACCT 61.329 50.000 0.50 0.0 40.22 4.00 R
1728 1780 3.944087 ACTGTTAGCTCAGAATGTTCCC 58.056 45.455 9.28 0.0 38.63 3.97 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
192 197 2.484558 TGCACCACAGCTATGCATG 58.515 52.632 10.16 0.00 44.17 4.06
214 221 5.128205 TGCTTCAAAGTATCAGATCCCATG 58.872 41.667 0.00 0.00 0.00 3.66
351 367 2.023673 GCAGGCAGGCAAACACATATA 58.976 47.619 0.00 0.00 0.00 0.86
364 380 7.095313 GGCAAACACATATATCTCATGAGAGTG 60.095 40.741 27.64 27.64 42.66 3.51
463 479 1.258982 CGGTTGCTTCTCATGCGTATC 59.741 52.381 0.00 0.00 0.00 2.24
495 511 7.048629 TCAAAATAAGTTCATGGCAGACAAA 57.951 32.000 0.00 0.00 0.00 2.83
582 598 3.245984 TGTGTTCCCATCTCTTCTCCCTA 60.246 47.826 0.00 0.00 0.00 3.53
583 599 3.133183 GTGTTCCCATCTCTTCTCCCTAC 59.867 52.174 0.00 0.00 0.00 3.18
584 600 3.012959 TGTTCCCATCTCTTCTCCCTACT 59.987 47.826 0.00 0.00 0.00 2.57
631 682 6.462768 GCTGTCTCATGATTCTCCAAGTAGAT 60.463 42.308 0.00 0.00 0.00 1.98
634 685 7.081349 GTCTCATGATTCTCCAAGTAGATACG 58.919 42.308 0.00 0.00 0.00 3.06
760 812 3.367087 GCTCAAGTAGAAGCCAACGACTA 60.367 47.826 0.00 0.00 0.00 2.59
787 839 4.889832 AAAATCGTTCATGATCCTCTGC 57.110 40.909 0.00 0.00 0.00 4.26
816 868 9.228949 GAGCTTGTCAAATCATTCATATCCTAT 57.771 33.333 0.00 0.00 0.00 2.57
852 904 2.044946 GACCCTGACCATGGTGGC 60.045 66.667 25.52 9.69 42.67 5.01
855 907 2.605607 CCCTGACCATGGTGGCAGA 61.606 63.158 27.26 6.17 42.67 4.26
873 925 4.452795 GGCAGAGTTCCAACTAGAAAACTC 59.547 45.833 16.38 16.38 45.04 3.01
980 1032 8.451908 AAGAACAAACAGTAGCAGATTTTAGT 57.548 30.769 0.00 0.00 0.00 2.24
1077 1129 3.565902 GCATCCCTCTAAACCTGCAATAC 59.434 47.826 0.00 0.00 0.00 1.89
1131 1183 6.256539 ACGATGACATTCAAGCATTACTGTAG 59.743 38.462 0.00 0.00 0.00 2.74
1134 1186 5.874810 TGACATTCAAGCATTACTGTAGTCC 59.125 40.000 0.00 0.00 0.00 3.85
1219 1271 6.830912 TGATATGCTCCATAAAGTAACTGCT 58.169 36.000 0.00 0.00 29.74 4.24
1227 1279 5.125417 TCCATAAAGTAACTGCTTGGATTGC 59.875 40.000 0.00 0.00 0.00 3.56
1228 1280 3.942130 AAAGTAACTGCTTGGATTGCC 57.058 42.857 0.00 0.00 0.00 4.52
1300 1352 1.136695 CAGCCAACAAAAGCAAGGTCA 59.863 47.619 0.00 0.00 0.00 4.02
1450 1502 1.667191 CGCAGACACAGCAAGCTCT 60.667 57.895 0.00 0.00 0.00 4.09
1666 1718 7.689812 CAGTGTTAAACTCTGCATTAATCTTCG 59.310 37.037 0.00 0.00 36.83 3.79
1728 1780 3.565482 AGCCGCACCTGATTGTAATATTG 59.435 43.478 0.00 0.00 0.00 1.90
1831 1883 3.420839 ACAGCCTTCAGTTTTGTTTCG 57.579 42.857 0.00 0.00 0.00 3.46
1878 1930 3.181465 GGGAGTCAAGAGTTCACAACAGA 60.181 47.826 0.00 0.00 0.00 3.41
1890 1942 4.556942 TCACAACAGAGCTCAATGTTTG 57.443 40.909 17.77 16.76 37.54 2.93
1911 1963 8.306038 TGTTTGTATGCATTTTCTATTTCAGCT 58.694 29.630 3.54 0.00 0.00 4.24
2036 2088 7.781324 ACCAAGAGAATGTTAATGGACAATT 57.219 32.000 0.00 0.00 32.47 2.32
2093 2145 6.204882 GGAAAAAGTACCATGGATTATCCTCG 59.795 42.308 21.47 3.36 37.46 4.63
2143 2195 8.339714 AGTTCATCAAAACATCAAAATGCTTTG 58.660 29.630 7.59 7.59 44.66 2.77
2181 2233 6.595716 AGGTAGACAATTGACTACAATCAAGC 59.404 38.462 33.53 21.34 44.67 4.01
2184 2236 4.323417 ACAATTGACTACAATCAAGCGGA 58.677 39.130 13.59 0.00 44.67 5.54
2463 2536 9.967346 TGATGTATATAGTAACTGACAAGCTTC 57.033 33.333 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 110 3.833070 GAGTGGAGAGTAAGTTCTTCCCA 59.167 47.826 0.00 0.00 0.00 4.37
192 197 4.023365 GCATGGGATCTGATACTTTGAAGC 60.023 45.833 0.00 0.00 0.00 3.86
351 367 2.168106 GAGCCACACACTCTCATGAGAT 59.832 50.000 25.30 12.92 42.73 2.75
364 380 0.874390 TTGCTGATTTCGAGCCACAC 59.126 50.000 0.00 0.00 35.43 3.82
416 432 1.974236 GGACCCCAGTGATAGATGGAG 59.026 57.143 0.00 0.00 39.02 3.86
463 479 6.587608 GCCATGAACTTATTTTGAACTCCTTG 59.412 38.462 0.00 0.00 0.00 3.61
495 511 2.036346 GCTTGTCTGGTTGCAAAGGATT 59.964 45.455 0.00 0.00 0.00 3.01
631 682 2.304092 CTGTCCTATGGCAGTACCGTA 58.696 52.381 0.00 0.00 43.94 4.02
760 812 8.781196 CAGAGGATCATGAACGATTTTATTCAT 58.219 33.333 0.00 0.00 44.52 2.57
787 839 5.578005 ATGAATGATTTGACAAGCTCCTG 57.422 39.130 0.00 0.00 0.00 3.86
816 868 0.319813 CACACGGACTGCACATCTGA 60.320 55.000 8.71 0.00 0.00 3.27
873 925 5.602978 CCCCAACCCTGGTATATATAGCTAG 59.397 48.000 19.79 15.08 41.72 3.42
874 926 5.259252 TCCCCAACCCTGGTATATATAGCTA 59.741 44.000 19.79 0.00 41.72 3.32
900 952 2.907042 CCTCTTGGTTGGTACCTCTCTT 59.093 50.000 14.36 0.00 45.27 2.85
980 1032 2.777960 AACAAAGGCTGGGGAGGCA 61.778 57.895 0.00 0.00 36.76 4.75
1077 1129 7.031975 GGAATCTACCAAATTGAAAGCTTCAG 58.968 38.462 0.00 0.00 41.38 3.02
1131 1183 7.987458 TCACTAGGATATGAACAATCTTTGGAC 59.013 37.037 0.00 0.00 34.12 4.02
1134 1186 9.605275 TCTTCACTAGGATATGAACAATCTTTG 57.395 33.333 0.00 0.00 31.62 2.77
1227 1279 5.192927 TGTTCTTAACTTCCCTGCATATGG 58.807 41.667 4.56 0.00 0.00 2.74
1228 1280 5.297776 CCTGTTCTTAACTTCCCTGCATATG 59.702 44.000 0.00 0.00 0.00 1.78
1275 1327 1.329171 TGCTTTTGTTGGCTGCACCT 61.329 50.000 0.50 0.00 40.22 4.00
1300 1352 1.370437 CCACAGTGCTGTCTCTGCT 59.630 57.895 1.31 0.00 42.83 4.24
1332 1384 2.178106 CTGGGGTAGTAGATCCCTGTCT 59.822 54.545 0.00 0.00 43.00 3.41
1438 1490 2.031516 CGTGGGAGAGCTTGCTGTG 61.032 63.158 0.00 0.00 0.00 3.66
1666 1718 6.558009 TCAGTGAAAATGAGAATGCAATAGC 58.442 36.000 0.00 0.00 35.16 2.97
1728 1780 3.944087 ACTGTTAGCTCAGAATGTTCCC 58.056 45.455 9.28 0.00 38.63 3.97
1831 1883 4.644685 TGCATAATTTCTTCCCTACAAGGC 59.355 41.667 0.00 0.00 32.73 4.35
1878 1930 6.694447 AGAAAATGCATACAAACATTGAGCT 58.306 32.000 0.00 0.00 36.64 4.09
1906 1958 9.944376 GGATATGGTTAATTACAATCTAGCTGA 57.056 33.333 0.00 0.00 0.00 4.26
1909 1961 9.944376 TCTGGATATGGTTAATTACAATCTAGC 57.056 33.333 0.00 0.00 0.00 3.42
2069 2121 6.766467 ACGAGGATAATCCATGGTACTTTTTC 59.234 38.462 12.58 6.53 39.61 2.29
2093 2145 8.715088 ACTTGGACGTTTTCATAGTAACATAAC 58.285 33.333 0.00 0.00 0.00 1.89
2143 2195 6.635030 ATTGTCTACCTGGAAAGTTGTTTC 57.365 37.500 0.00 0.00 41.35 2.78


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

AutoCloner maintained by Alex Coulton.