Multiple sequence alignment - TraesCS2A01G351800

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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 TraesCS2A01G351800 chr2A 100.000 2231 0 0 1 2231 592097436 592095206 0.000000e+00 4120
1 TraesCS2A01G351800 chr2D 92.019 1441 86 13 469 1891 447346791 447345362 0.000000e+00 1997
2 TraesCS2A01G351800 chr2D 93.176 425 16 6 1 423 447347208 447346795 1.460000e-171 612
3 TraesCS2A01G351800 chr2D 84.545 220 23 3 2023 2231 447344809 447344590 8.070000e-50 207
4 TraesCS2A01G351800 chr2B 91.672 1453 94 12 447 1891 527000255 526998822 0.000000e+00 1988
5 TraesCS2A01G351800 chr2B 92.731 454 11 11 1 451 527001033 527000599 8.690000e-179 636
6 TraesCS2A01G351800 chr2B 84.727 275 25 9 1968 2230 526997143 526996874 2.200000e-65 259


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 TraesCS2A01G351800 chr2A 592095206 592097436 2230 True 4120.000000 4120 100.000000 1 2231 1 chr2A.!!$R1 2230
1 TraesCS2A01G351800 chr2D 447344590 447347208 2618 True 938.666667 1997 89.913333 1 2231 3 chr2D.!!$R1 2230
2 TraesCS2A01G351800 chr2B 526996874 527001033 4159 True 961.000000 1988 89.710000 1 2230 3 chr2B.!!$R1 2229


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
285 288 0.107848 CGTCCGTGGGAGGCTTAATT 60.108 55.0 0.0 0.0 30.8 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 2078 0.042431 AGTGAGACAGAGGGCCAGAT 59.958 55.0 6.18 0.0 0.0 2.9 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
239 240 1.871080 CCGGGTATCTAGCTTTGCTG 58.129 55.000 0.00 0.00 40.10 4.41
283 286 2.975536 CGTCCGTGGGAGGCTTAA 59.024 61.111 0.00 0.00 30.80 1.85
285 288 0.107848 CGTCCGTGGGAGGCTTAATT 60.108 55.000 0.00 0.00 30.80 1.40
286 289 1.677820 CGTCCGTGGGAGGCTTAATTT 60.678 52.381 0.00 0.00 30.80 1.82
298 301 6.405176 GGGAGGCTTAATTTGATCAACTCAAG 60.405 42.308 7.89 11.79 44.48 3.02
326 329 5.983540 AGTCAAGCTAGCTAGTATTTGCTT 58.016 37.500 19.70 14.99 40.74 3.91
331 334 5.363939 AGCTAGCTAGTATTTGCTTGAAGG 58.636 41.667 17.69 0.00 40.35 3.46
437 441 4.799564 AGTCTACTCTTTGAAGCTCAGG 57.200 45.455 0.00 0.00 0.00 3.86
554 906 1.139256 TGCCACGTGAACTTTGTCCTA 59.861 47.619 19.30 0.00 0.00 2.94
592 944 3.991242 GCCCTAGCTAGCAACCTAC 57.009 57.895 18.83 0.00 35.50 3.18
630 985 0.532862 GTGATGCATACTGTCCCCCG 60.533 60.000 0.00 0.00 0.00 5.73
668 1023 2.537730 GCGATCTGCCTCGTTTTCATTC 60.538 50.000 0.00 0.00 40.73 2.67
819 1174 2.051638 CGTCTCGTACGTGTGCAAG 58.948 57.895 16.05 4.01 46.72 4.01
825 1180 1.076533 CGTACGTGTGCAAGCTAGGG 61.077 60.000 7.22 0.00 0.00 3.53
833 1188 3.127533 CAAGCTAGGGCGGTGCAC 61.128 66.667 8.80 8.80 44.37 4.57
922 1277 3.120408 ACACGTACACTACTTAGCACGAG 60.120 47.826 10.77 6.94 33.39 4.18
980 1335 1.009389 CGCGTCTTCAACCTCCTCAC 61.009 60.000 0.00 0.00 0.00 3.51
981 1336 0.670854 GCGTCTTCAACCTCCTCACC 60.671 60.000 0.00 0.00 0.00 4.02
982 1337 0.388649 CGTCTTCAACCTCCTCACCG 60.389 60.000 0.00 0.00 0.00 4.94
1413 1779 1.741401 CACACGGCGGTCATGTGAT 60.741 57.895 19.77 0.00 45.34 3.06
1451 1817 0.814010 GCCCGGAGTAATTGCACGAT 60.814 55.000 0.73 0.00 0.00 3.73
1488 1854 6.533012 CGATTGCTTCTCAGTCTAATCTTGAA 59.467 38.462 0.00 0.00 30.09 2.69
1592 1959 1.529226 TGTTTGCCACATTCTACCCG 58.471 50.000 0.00 0.00 0.00 5.28
1613 1980 3.184986 CGACCGTCCGACAAATTTTAACT 59.815 43.478 0.00 0.00 0.00 2.24
1615 1982 5.596268 ACCGTCCGACAAATTTTAACTAC 57.404 39.130 0.00 0.00 0.00 2.73
1645 2013 7.452880 TCTGTTATCAAATTGAAGTCCTTGG 57.547 36.000 0.00 0.00 0.00 3.61
1660 2028 5.990668 AGTCCTTGGTGATATTAGAACCAC 58.009 41.667 0.00 0.00 43.55 4.16
1661 2029 5.487488 AGTCCTTGGTGATATTAGAACCACA 59.513 40.000 0.00 0.00 43.55 4.17
1667 2035 6.591935 TGGTGATATTAGAACCACATTCCTC 58.408 40.000 0.00 0.00 39.05 3.71
1669 2037 6.183361 GGTGATATTAGAACCACATTCCTCCT 60.183 42.308 0.00 0.00 38.16 3.69
1721 2089 2.609534 TTGCTGCATCTGGCCCTCT 61.610 57.895 1.84 0.00 43.89 3.69
1774 2142 1.741145 AGCTTAAACAAATACCGGCCG 59.259 47.619 21.04 21.04 0.00 6.13
1779 2147 3.729862 AAACAAATACCGGCCGAAAAA 57.270 38.095 30.73 9.13 0.00 1.94
1783 2151 0.379316 AATACCGGCCGAAAAATCGC 59.621 50.000 30.73 0.00 0.00 4.58
1784 2152 0.463116 ATACCGGCCGAAAAATCGCT 60.463 50.000 30.73 1.31 0.00 4.93
1796 2164 4.092821 CGAAAAATCGCTGATGTAGACCAA 59.907 41.667 0.00 0.00 0.00 3.67
1807 2179 3.134574 TGTAGACCAAAAGACGCCAAT 57.865 42.857 0.00 0.00 0.00 3.16
1810 2182 2.795329 AGACCAAAAGACGCCAATGAT 58.205 42.857 0.00 0.00 0.00 2.45
1820 2192 3.068165 AGACGCCAATGATAACGATCTGA 59.932 43.478 0.00 0.00 32.79 3.27
1822 2194 3.181475 ACGCCAATGATAACGATCTGAGT 60.181 43.478 0.00 0.00 32.79 3.41
1830 2202 9.004146 CAATGATAACGATCTGAGTATATCACG 57.996 37.037 0.00 0.00 33.89 4.35
1857 2230 2.035632 GGTAGCTAGCACTGAGGATGT 58.964 52.381 18.83 0.00 0.00 3.06
1858 2231 2.223923 GGTAGCTAGCACTGAGGATGTG 60.224 54.545 18.83 0.00 38.36 3.21
1891 2264 6.805016 ATCATAACTCTGGCCATATAGAGG 57.195 41.667 20.43 2.34 43.65 3.69
1907 2454 2.203153 GGCCAAGACACCACACGT 60.203 61.111 0.00 0.00 0.00 4.49
1920 2467 1.404035 CCACACGTCCTCATACGATGA 59.596 52.381 3.10 0.00 45.68 2.92
1951 2498 0.955919 GTTGGAAACGAGGCCAGGAG 60.956 60.000 5.01 0.00 36.92 3.69
2001 4041 2.186903 CATCGCCTTACCACCGCT 59.813 61.111 0.00 0.00 0.00 5.52
2011 4051 3.030652 CCACCGCTGGTCAAACAC 58.969 61.111 0.00 0.00 31.02 3.32
2025 4065 3.678548 GTCAAACACCTAGACTTAAGGCG 59.321 47.826 7.53 0.00 37.67 5.52
2030 4070 3.577415 ACACCTAGACTTAAGGCGAAACT 59.423 43.478 7.53 0.00 37.67 2.66
2052 4092 0.244994 AGCTAGTGCAACCAGAGACG 59.755 55.000 0.00 0.00 42.74 4.18
2064 4104 0.600255 CAGAGACGACACAACCACCC 60.600 60.000 0.00 0.00 0.00 4.61
2071 4111 1.308998 GACACAACCACCCTGAACTG 58.691 55.000 0.00 0.00 0.00 3.16
2091 4131 1.914764 GGTCGTCCCCACCTAACCA 60.915 63.158 0.00 0.00 0.00 3.67
2097 4137 2.355115 CCCACCTAACCAGCACCC 59.645 66.667 0.00 0.00 0.00 4.61
2098 4138 2.046314 CCACCTAACCAGCACCCG 60.046 66.667 0.00 0.00 0.00 5.28
2118 4168 1.888436 AAGGCGATGAGAACTGGCGA 61.888 55.000 0.00 0.00 0.00 5.54
2119 4169 2.167861 GGCGATGAGAACTGGCGAC 61.168 63.158 0.00 0.00 0.00 5.19
2178 4229 1.075050 CCCTAGAGGTGGAGGCGTATA 59.925 57.143 0.00 0.00 0.00 1.47
2183 4234 0.851469 AGGTGGAGGCGTATAGGAGA 59.149 55.000 0.00 0.00 0.00 3.71
2184 4235 1.202952 AGGTGGAGGCGTATAGGAGAG 60.203 57.143 0.00 0.00 0.00 3.20
2194 4245 5.012871 AGGCGTATAGGAGAGTGTCTACATA 59.987 44.000 0.00 0.00 26.62 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
239 240 3.060607 CACATTGTAAAACTTGCGCAACC 60.061 43.478 21.02 3.63 0.00 3.77
314 317 8.055279 TCCAAATTCCTTCAAGCAAATACTAG 57.945 34.615 0.00 0.00 0.00 2.57
316 319 6.721208 TCTCCAAATTCCTTCAAGCAAATACT 59.279 34.615 0.00 0.00 0.00 2.12
317 320 6.924111 TCTCCAAATTCCTTCAAGCAAATAC 58.076 36.000 0.00 0.00 0.00 1.89
318 321 7.015098 TGTTCTCCAAATTCCTTCAAGCAAATA 59.985 33.333 0.00 0.00 0.00 1.40
350 353 2.871096 TGCCGTTTGGTTCCTCTATT 57.129 45.000 0.00 0.00 37.67 1.73
425 429 7.125811 ACCTAGATGTATTACCTGAGCTTCAAA 59.874 37.037 0.00 0.00 0.00 2.69
554 906 2.480419 GCTGTAAGTTCGTTGTGCATCT 59.520 45.455 0.00 0.00 35.30 2.90
592 944 3.192844 TCACTAGGCCTCGAGTTTTAGTG 59.807 47.826 25.85 25.85 39.36 2.74
630 985 1.660607 TCGCTCGACTTTTCATGCATC 59.339 47.619 0.00 0.00 0.00 3.91
668 1023 0.894835 AGTTTGCCCTTAATTGCGGG 59.105 50.000 9.01 9.01 43.60 6.13
922 1277 2.547007 GCAGGGCTAGCTACTAGAAAGC 60.547 54.545 15.72 12.18 36.26 3.51
925 1280 1.319541 CGCAGGGCTAGCTACTAGAA 58.680 55.000 15.72 0.00 36.26 2.10
955 1310 3.335534 GTTGAAGACGCGCACGGT 61.336 61.111 5.73 0.00 46.04 4.83
1221 1576 0.824109 CTCGGTCTCATTAGTGCCCA 59.176 55.000 0.00 0.00 0.00 5.36
1230 1585 0.976641 TTCTTGCACCTCGGTCTCAT 59.023 50.000 0.00 0.00 0.00 2.90
1231 1586 0.756294 TTTCTTGCACCTCGGTCTCA 59.244 50.000 0.00 0.00 0.00 3.27
1413 1779 0.787787 CGACGTTGCGGAAAAGATCA 59.212 50.000 0.00 0.00 0.00 2.92
1438 1804 7.116376 CGACCTTATATTGATCGTGCAATTACT 59.884 37.037 9.93 1.47 39.15 2.24
1451 1817 6.816136 TGAGAAGCAATCGACCTTATATTGA 58.184 36.000 0.00 0.00 33.38 2.57
1592 1959 4.737353 AGTTAAAATTTGTCGGACGGTC 57.263 40.909 3.34 0.00 0.00 4.79
1624 1992 7.214467 TCACCAAGGACTTCAATTTGATAAC 57.786 36.000 0.00 0.00 0.00 1.89
1645 2013 6.708054 CAGGAGGAATGTGGTTCTAATATCAC 59.292 42.308 0.00 0.00 37.01 3.06
1660 2028 0.816825 CGGTGGATGCAGGAGGAATG 60.817 60.000 0.00 0.00 0.00 2.67
1661 2029 1.528824 CGGTGGATGCAGGAGGAAT 59.471 57.895 0.00 0.00 0.00 3.01
1667 2035 4.181010 CCCTCCGGTGGATGCAGG 62.181 72.222 24.22 10.17 0.00 4.85
1710 2078 0.042431 AGTGAGACAGAGGGCCAGAT 59.958 55.000 6.18 0.00 0.00 2.90
1749 2117 5.066764 GGCCGGTATTTGTTTAAGCTTATGA 59.933 40.000 7.08 0.00 0.00 2.15
1753 2121 2.162809 CGGCCGGTATTTGTTTAAGCTT 59.837 45.455 20.10 3.48 0.00 3.74
1765 2133 0.463116 AGCGATTTTTCGGCCGGTAT 60.463 50.000 27.83 13.40 0.00 2.73
1766 2134 1.078988 AGCGATTTTTCGGCCGGTA 60.079 52.632 27.83 11.46 0.00 4.02
1768 2136 1.714899 ATCAGCGATTTTTCGGCCGG 61.715 55.000 27.83 8.29 0.00 6.13
1774 2142 5.545658 TTGGTCTACATCAGCGATTTTTC 57.454 39.130 0.00 0.00 0.00 2.29
1779 2147 4.184629 GTCTTTTGGTCTACATCAGCGAT 58.815 43.478 0.00 0.00 0.00 4.58
1783 2151 2.673368 GGCGTCTTTTGGTCTACATCAG 59.327 50.000 0.00 0.00 0.00 2.90
1784 2152 2.037902 TGGCGTCTTTTGGTCTACATCA 59.962 45.455 0.00 0.00 0.00 3.07
1796 2164 4.271049 CAGATCGTTATCATTGGCGTCTTT 59.729 41.667 0.00 0.00 34.28 2.52
1807 2179 7.148457 GGACGTGATATACTCAGATCGTTATCA 60.148 40.741 0.00 0.00 35.13 2.15
1810 2182 5.410746 GGGACGTGATATACTCAGATCGTTA 59.589 44.000 0.00 0.00 35.13 3.18
1830 2202 2.443390 TGCTAGCTACCCCGGGAC 60.443 66.667 26.32 8.53 0.00 4.46
1857 2230 6.039717 GGCCAGAGTTATGATTATTTTCTGCA 59.960 38.462 0.00 0.00 31.58 4.41
1858 2231 6.039717 TGGCCAGAGTTATGATTATTTTCTGC 59.960 38.462 0.00 0.00 31.58 4.26
1891 2264 2.251642 GGACGTGTGGTGTCTTGGC 61.252 63.158 0.00 0.00 36.58 4.52
1892 2265 0.600255 GAGGACGTGTGGTGTCTTGG 60.600 60.000 0.00 0.00 36.58 3.61
1893 2266 0.104120 TGAGGACGTGTGGTGTCTTG 59.896 55.000 0.00 0.00 36.58 3.02
1894 2267 1.048601 ATGAGGACGTGTGGTGTCTT 58.951 50.000 0.00 0.00 36.58 3.01
1895 2268 1.544691 GTATGAGGACGTGTGGTGTCT 59.455 52.381 0.00 0.00 36.58 3.41
1907 2454 4.888917 TGTTGTTTGTCATCGTATGAGGA 58.111 39.130 0.00 0.00 40.53 3.71
1916 2463 4.481930 TCCAACGATGTTGTTTGTCATC 57.518 40.909 8.68 0.00 37.61 2.92
1933 2480 1.125093 TCTCCTGGCCTCGTTTCCAA 61.125 55.000 3.32 0.00 30.98 3.53
1951 2498 5.238214 GGCACTGAGAAATAAGATCACCATC 59.762 44.000 0.00 0.00 0.00 3.51
2004 4044 3.575256 TCGCCTTAAGTCTAGGTGTTTGA 59.425 43.478 0.97 0.00 42.58 2.69
2011 4051 6.016108 AGCTATAGTTTCGCCTTAAGTCTAGG 60.016 42.308 0.97 0.00 35.80 3.02
2025 4065 5.661458 TCTGGTTGCACTAGCTATAGTTTC 58.339 41.667 0.84 0.00 40.38 2.78
2030 4070 3.315470 CGTCTCTGGTTGCACTAGCTATA 59.685 47.826 0.00 0.00 42.74 1.31
2052 4092 1.308998 CAGTTCAGGGTGGTTGTGTC 58.691 55.000 0.00 0.00 0.00 3.67
2064 4104 1.004918 GGGGACGACCACAGTTCAG 60.005 63.158 6.20 0.00 42.91 3.02
2091 4131 3.376935 CTCATCGCCTTCGGGTGCT 62.377 63.158 0.00 0.00 44.74 4.40
2097 4137 1.424493 GCCAGTTCTCATCGCCTTCG 61.424 60.000 0.00 0.00 0.00 3.79
2098 4138 1.424493 CGCCAGTTCTCATCGCCTTC 61.424 60.000 0.00 0.00 0.00 3.46
2104 4144 1.203928 CATCGTCGCCAGTTCTCATC 58.796 55.000 0.00 0.00 0.00 2.92
2105 4145 0.179100 CCATCGTCGCCAGTTCTCAT 60.179 55.000 0.00 0.00 0.00 2.90
2106 4146 1.215382 CCATCGTCGCCAGTTCTCA 59.785 57.895 0.00 0.00 0.00 3.27
2113 4163 4.467084 GGGCTTCCATCGTCGCCA 62.467 66.667 0.00 0.00 44.23 5.69
2118 4168 0.760945 CCTCCTAGGGCTTCCATCGT 60.761 60.000 9.46 0.00 0.00 3.73
2119 4169 0.470080 TCCTCCTAGGGCTTCCATCG 60.470 60.000 9.46 0.00 35.59 3.84
2178 4229 9.733556 CTGAACTATATATGTAGACACTCTCCT 57.266 37.037 12.95 0.00 0.00 3.69



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

AutoCloner maintained by Alex Coulton.