Multiple sequence alignment - TraesCS2A01G523000

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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 TraesCS2A01G523000 chr2A 100.000 2126 0 0 1 2126 744978658 744980783 0 3927
1 TraesCS2A01G523000 chr2B 92.784 2148 115 22 1 2126 748699766 748701895 0 3072
2 TraesCS2A01G523000 chr2D 87.757 1315 102 25 1 1273 613321097 613322394 0 1482
3 TraesCS2A01G523000 chr2D 92.958 852 60 0 1275 2126 613322459 613323310 0 1242


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 TraesCS2A01G523000 chr2A 744978658 744980783 2125 False 3927 3927 100.0000 1 2126 1 chr2A.!!$F1 2125
1 TraesCS2A01G523000 chr2B 748699766 748701895 2129 False 3072 3072 92.7840 1 2126 1 chr2B.!!$F1 2125
2 TraesCS2A01G523000 chr2D 613321097 613323310 2213 False 1362 1482 90.3575 1 2126 2 chr2D.!!$F1 2125

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
995 1032 0.038166 TTGGGACCAGCAAGCCTAAG 59.962 55.0 0.0 0.0 0.0 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1997 1.269448 CTTGGAACACCCATTGAACCG 59.731 52.381 0.0 0.0 46.1 4.44 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
50 51 7.497909 GGATTTGGATCAAATTTGCATTCTGAT 59.502 33.333 13.54 0.00 43.05 2.90
64 66 8.579850 TTGCATTCTGATATAGGTTGTTTCTT 57.420 30.769 0.00 0.00 0.00 2.52
71 73 9.177608 TCTGATATAGGTTGTTTCTTGGATTTG 57.822 33.333 0.00 0.00 0.00 2.32
77 79 1.344114 TGTTTCTTGGATTTGGCTGCC 59.656 47.619 12.87 12.87 0.00 4.85
82 84 2.676471 GGATTTGGCTGCCGGTGT 60.676 61.111 14.98 0.00 0.00 4.16
109 111 5.603596 ACACATGATGCTTGTCATTTTTGT 58.396 33.333 0.00 0.00 36.72 2.83
114 116 6.395426 TGATGCTTGTCATTTTTGTCTCTT 57.605 33.333 0.00 0.00 35.05 2.85
125 127 3.851976 TTTGTCTCTTAGAGTCGGCTC 57.148 47.619 9.58 9.58 41.94 4.70
132 137 5.289917 GTCTCTTAGAGTCGGCTCATTTTTC 59.710 44.000 20.97 0.18 44.00 2.29
136 141 6.710744 TCTTAGAGTCGGCTCATTTTTCTTTT 59.289 34.615 20.97 0.00 44.00 2.27
138 143 4.821805 AGAGTCGGCTCATTTTTCTTTTCA 59.178 37.500 20.97 0.00 44.00 2.69
140 145 5.464168 AGTCGGCTCATTTTTCTTTTCATG 58.536 37.500 0.00 0.00 0.00 3.07
141 146 5.010012 AGTCGGCTCATTTTTCTTTTCATGT 59.990 36.000 0.00 0.00 0.00 3.21
143 148 4.386652 CGGCTCATTTTTCTTTTCATGTGG 59.613 41.667 0.00 0.00 0.00 4.17
144 149 5.299949 GGCTCATTTTTCTTTTCATGTGGT 58.700 37.500 0.00 0.00 0.00 4.16
165 170 6.436218 GTGGTCCCCTTCATTAGTATTTTTGT 59.564 38.462 0.00 0.00 0.00 2.83
225 230 7.092623 TGGACATAACTACCAACTTATCACCAT 60.093 37.037 0.00 0.00 0.00 3.55
226 231 7.226720 GGACATAACTACCAACTTATCACCATG 59.773 40.741 0.00 0.00 0.00 3.66
227 232 6.542370 ACATAACTACCAACTTATCACCATGC 59.458 38.462 0.00 0.00 0.00 4.06
228 233 4.568072 ACTACCAACTTATCACCATGCA 57.432 40.909 0.00 0.00 0.00 3.96
311 321 1.743958 TCCCTAAGAAGTCGAAGCTCG 59.256 52.381 0.00 0.00 42.10 5.03
328 338 5.083533 AGCTCGAGATGTTGAGAAAAGAT 57.916 39.130 18.75 0.00 36.37 2.40
445 466 7.961283 GCTGTATTGGTTTTAAAGTAGCACTAC 59.039 37.037 10.39 10.39 36.35 2.73
493 519 3.423539 TCTCAAGCAAACACCATAGCT 57.576 42.857 0.00 0.00 39.37 3.32
557 594 2.919666 ACTGAAAATACATGCACCGC 57.080 45.000 0.00 0.00 0.00 5.68
657 694 7.918076 TCATACTTCTGGATTTCCTTACAAGT 58.082 34.615 0.00 3.93 36.82 3.16
695 732 3.733443 ATTTTCACCTGTGGTTCTTGC 57.267 42.857 0.00 0.00 31.02 4.01
745 782 5.897250 TGTGGATGAGTAGGCTTGATACTTA 59.103 40.000 0.00 0.00 33.64 2.24
806 843 6.691508 AGCTTCTGTCAGTTGTTTTCTTTTT 58.308 32.000 0.00 0.00 0.00 1.94
873 910 1.747924 TCTTGCAGATCTCAGAGGACG 59.252 52.381 0.00 0.00 0.00 4.79
883 920 4.265904 TCTCAGAGGACGTTTAATTGCA 57.734 40.909 0.00 0.00 0.00 4.08
909 946 6.599244 TGATATGAAGTCTGTTTGTGGATTCC 59.401 38.462 0.00 0.00 0.00 3.01
910 947 3.486383 TGAAGTCTGTTTGTGGATTCCC 58.514 45.455 0.00 0.00 0.00 3.97
966 1003 0.093535 CGTAGTGCTGCAACATCACG 59.906 55.000 2.77 10.66 35.90 4.35
967 1004 1.428448 GTAGTGCTGCAACATCACGA 58.572 50.000 2.77 0.00 35.90 4.35
974 1011 2.160219 GCTGCAACATCACGATTTCTCA 59.840 45.455 0.00 0.00 0.00 3.27
975 1012 3.740590 CTGCAACATCACGATTTCTCAC 58.259 45.455 0.00 0.00 0.00 3.51
986 1023 2.087646 GATTTCTCACTTGGGACCAGC 58.912 52.381 0.00 0.00 0.00 4.85
995 1032 0.038166 TTGGGACCAGCAAGCCTAAG 59.962 55.000 0.00 0.00 0.00 2.18
1042 1079 0.738975 CTTCATCGGTAGTGGCTCGA 59.261 55.000 0.00 0.00 37.33 4.04
1053 1090 2.440409 AGTGGCTCGAATTGCAAGAAT 58.560 42.857 4.94 0.00 0.00 2.40
1128 1165 7.663043 AGTTGTTAAACTGGGGTTTTGATTA 57.337 32.000 0.00 0.00 45.12 1.75
1168 1218 4.272504 CGCTCTAGTCTTTCTCTGTCCTAG 59.727 50.000 0.00 0.00 0.00 3.02
1175 1225 5.014333 AGTCTTTCTCTGTCCTAGTCCTACA 59.986 44.000 0.00 0.00 0.00 2.74
1183 1233 7.937942 TCTCTGTCCTAGTCCTACATTATACAC 59.062 40.741 0.00 0.00 0.00 2.90
1394 1507 4.202151 GGACCAATGCCAAATCTGTATTCC 60.202 45.833 0.00 0.00 0.00 3.01
1403 1516 4.153117 CCAAATCTGTATTCCGCTGATAGC 59.847 45.833 0.00 0.00 38.02 2.97
1489 1602 0.546598 GATCCTGGGTTACTGGTGGG 59.453 60.000 0.00 0.00 39.12 4.61
1530 1643 4.045636 AGAAATTTGCAGTCCACAACAC 57.954 40.909 0.00 0.00 0.00 3.32
1632 1745 5.163612 GCCAAAAGGAAGTCAGGTGATTATC 60.164 44.000 0.00 0.00 0.00 1.75
1771 1884 2.803155 GATCAGCACGGGGTTGAGCA 62.803 60.000 7.49 0.00 41.99 4.26
1772 1885 3.357079 CAGCACGGGGTTGAGCAC 61.357 66.667 0.00 0.00 0.00 4.40
1787 1900 3.710722 CACAGCCCCGAGCCTTCT 61.711 66.667 0.00 0.00 45.47 2.85
1799 1912 1.006922 GCCTTCTGCAACAACTGGC 60.007 57.895 0.00 0.00 40.77 4.85
1827 1940 5.299028 TCTTTTGCTGCAACTTCAGATACAA 59.701 36.000 15.72 1.71 36.19 2.41
1884 1997 0.723981 GCGCCATCTCAAGAAGTGTC 59.276 55.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.241941 TCCATGCCAAGCTGAATCCTAA 59.758 45.455 0.00 0.00 0.00 2.69
8 9 1.700955 ATCCATGCCAAGCTGAATCC 58.299 50.000 0.00 0.00 0.00 3.01
16 17 4.475051 TTTGATCCAAATCCATGCCAAG 57.525 40.909 0.00 0.00 0.00 3.61
50 51 6.152661 CAGCCAAATCCAAGAAACAACCTATA 59.847 38.462 0.00 0.00 0.00 1.31
64 66 2.676121 CACCGGCAGCCAAATCCA 60.676 61.111 13.30 0.00 0.00 3.41
71 73 2.281208 TGTACAACACCGGCAGCC 60.281 61.111 0.00 0.00 0.00 4.85
82 84 5.963176 AATGACAAGCATCATGTGTACAA 57.037 34.783 0.00 0.00 39.32 2.41
109 111 5.186021 AGAAAAATGAGCCGACTCTAAGAGA 59.814 40.000 0.00 0.00 43.85 3.10
114 116 5.995282 TGAAAAGAAAAATGAGCCGACTCTA 59.005 36.000 0.00 0.00 43.85 2.43
143 148 7.462571 ACACAAAAATACTAATGAAGGGGAC 57.537 36.000 0.00 0.00 0.00 4.46
144 149 6.373216 CGACACAAAAATACTAATGAAGGGGA 59.627 38.462 0.00 0.00 0.00 4.81
165 170 7.991460 TCTTCTCATACTAGGATTTACTCGACA 59.009 37.037 0.00 0.00 0.00 4.35
328 338 3.888930 GTGGGACAAGTGGAAGAAATTGA 59.111 43.478 0.00 0.00 44.16 2.57
416 437 8.175716 GTGCTACTTTAAAACCAATACAGCTAG 58.824 37.037 0.00 0.00 0.00 3.42
417 438 7.881232 AGTGCTACTTTAAAACCAATACAGCTA 59.119 33.333 0.00 0.00 0.00 3.32
445 466 6.153067 ACATGAATTAGCGCTTAGTAGCTAG 58.847 40.000 18.68 0.99 45.31 3.42
745 782 9.579932 AAATATGAAGGAGAACTCAAAAGACTT 57.420 29.630 4.23 0.00 0.00 3.01
838 875 4.071961 TGCAAGAAAGTCAAGTAGCAGA 57.928 40.909 0.00 0.00 0.00 4.26
873 910 9.793252 AACAGACTTCATATCATGCAATTAAAC 57.207 29.630 0.00 0.00 0.00 2.01
883 920 7.284034 GGAATCCACAAACAGACTTCATATCAT 59.716 37.037 0.00 0.00 0.00 2.45
966 1003 2.087646 GCTGGTCCCAAGTGAGAAATC 58.912 52.381 0.00 0.00 0.00 2.17
967 1004 1.425066 TGCTGGTCCCAAGTGAGAAAT 59.575 47.619 0.00 0.00 0.00 2.17
974 1011 1.133809 TAGGCTTGCTGGTCCCAAGT 61.134 55.000 8.99 0.00 41.27 3.16
975 1012 0.038166 TTAGGCTTGCTGGTCCCAAG 59.962 55.000 0.00 4.04 41.93 3.61
1026 1063 1.860950 CAATTCGAGCCACTACCGATG 59.139 52.381 0.00 0.00 32.07 3.84
1027 1064 1.806623 GCAATTCGAGCCACTACCGAT 60.807 52.381 0.00 0.00 32.07 4.18
1042 1079 7.377766 AGTACACGTCAATATTCTTGCAATT 57.622 32.000 0.00 0.00 0.00 2.32
1053 1090 6.483974 ACACAAAATGGAAGTACACGTCAATA 59.516 34.615 0.00 0.00 0.00 1.90
1095 1132 3.697045 CCAGTTTAACAACTTCACCACCA 59.303 43.478 0.00 0.00 40.66 4.17
1128 1165 2.045926 GCTGTCCAGTGGCCGAAT 60.046 61.111 3.51 0.00 0.00 3.34
1289 1402 6.457528 GCCCAAATGATTTTCTAGAAGTCTCG 60.458 42.308 16.32 6.55 0.00 4.04
1403 1516 0.964860 TGTTGCCACCGGATGATTGG 60.965 55.000 9.46 5.95 0.00 3.16
1489 1602 0.322975 TGAGCTGCCTCTTGAAGTCC 59.677 55.000 0.00 0.00 38.93 3.85
1632 1745 2.935201 GAGCAAACAGAGGTGATAGCTG 59.065 50.000 0.00 0.00 35.81 4.24
1637 1750 2.373169 TCTTGGAGCAAACAGAGGTGAT 59.627 45.455 0.00 0.00 0.00 3.06
1787 1900 1.473258 AAGAACAGCCAGTTGTTGCA 58.527 45.000 4.51 0.00 41.62 4.08
1799 1912 3.772932 TGAAGTTGCAGCAAAAGAACAG 58.227 40.909 10.11 0.00 0.00 3.16
1827 1940 5.130145 GCTCCCCATTATCAGTGCTATCTAT 59.870 44.000 0.00 0.00 0.00 1.98
1884 1997 1.269448 CTTGGAACACCCATTGAACCG 59.731 52.381 0.00 0.00 46.10 4.44
2012 2125 2.815647 CGCTTTCCTCCTCCGTGC 60.816 66.667 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.