Multiple sequence alignment - TraesCS2D01G288300

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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 TraesCS2D01G288300 chr2D 100.000 2285 0 0 1 2285 369481273 369478989 0 4220
1 TraesCS2D01G288300 chr2B 90.714 2326 119 28 1 2285 439225208 439222939 0 3009
2 TraesCS2D01G288300 chr2A 94.840 1589 66 6 702 2285 500531043 500529466 0 2466
3 TraesCS2D01G288300 chr2A 89.535 688 32 12 1 676 500531695 500531036 0 835


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 TraesCS2D01G288300 chr2D 369478989 369481273 2284 True 4220.0 4220 100.0000 1 2285 1 chr2D.!!$R1 2284
1 TraesCS2D01G288300 chr2B 439222939 439225208 2269 True 3009.0 3009 90.7140 1 2285 1 chr2B.!!$R1 2284
2 TraesCS2D01G288300 chr2A 500529466 500531695 2229 True 1650.5 2466 92.1875 1 2285 2 chr2A.!!$R1 2284

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
974 1007 0.033011 GGAGGCAGGAGTAGTCCAGA 60.033 60.0 19.0 0.0 46.8 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2243 1.000955 TCAAACGGCTGAGACTTCTCC 59.999 52.381 0.0 0.0 42.2 3.71 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
115 121 2.042686 TGCTCCGCTTAATTCTGCAT 57.957 45.000 0.00 0.00 0.00 3.96
118 124 1.672363 CTCCGCTTAATTCTGCATGCA 59.328 47.619 21.29 21.29 0.00 3.96
200 206 2.574006 TGTGATGCCTTTCAGCTCTT 57.426 45.000 0.00 0.00 31.07 2.85
208 214 2.941720 GCCTTTCAGCTCTTATGACCTG 59.058 50.000 0.00 0.00 0.00 4.00
216 222 3.713764 AGCTCTTATGACCTGGCACTATT 59.286 43.478 0.00 0.00 0.00 1.73
233 239 5.278266 GCACTATTTGTGGTGAAGCTTTACA 60.278 40.000 21.43 11.96 46.27 2.41
235 241 4.853924 ATTTGTGGTGAAGCTTTACAGG 57.146 40.909 21.43 0.00 0.00 4.00
331 344 0.740737 GGGATGCATTTGCTTAGCGT 59.259 50.000 0.00 0.00 42.66 5.07
332 345 1.268743 GGGATGCATTTGCTTAGCGTC 60.269 52.381 0.00 0.00 42.14 5.19
333 346 1.672881 GGATGCATTTGCTTAGCGTCT 59.327 47.619 0.00 0.00 42.41 4.18
334 347 2.098117 GGATGCATTTGCTTAGCGTCTT 59.902 45.455 0.00 0.00 42.41 3.01
335 348 3.312421 GGATGCATTTGCTTAGCGTCTTA 59.688 43.478 0.00 0.00 42.41 2.10
336 349 4.521943 GATGCATTTGCTTAGCGTCTTAG 58.478 43.478 0.00 0.00 40.28 2.18
337 350 2.095853 TGCATTTGCTTAGCGTCTTAGC 59.904 45.455 0.00 9.81 42.66 3.09
338 351 2.847254 GCATTTGCTTAGCGTCTTAGCG 60.847 50.000 0.00 0.00 38.73 4.26
527 548 2.414559 CCAATGCACACCACGAATTCTC 60.415 50.000 3.52 0.00 0.00 2.87
594 622 3.655615 ATTCTGACGAGTCTCCTACCT 57.344 47.619 4.78 0.00 0.00 3.08
624 652 6.013379 ACAAGAAGAGACAAGAATGGGTATCA 60.013 38.462 0.00 0.00 0.00 2.15
692 720 0.744771 GCTTTCCCCGTAAGCAGAGG 60.745 60.000 0.00 0.00 45.64 3.69
710 738 3.092403 CTGCGCGCTTATTGCTCA 58.908 55.556 33.29 7.29 40.11 4.26
732 760 3.514309 ACCCAGCTTCGAAGTGTAGTTAT 59.486 43.478 25.24 2.72 0.00 1.89
736 764 6.331061 CCAGCTTCGAAGTGTAGTTATTAGT 58.669 40.000 25.24 0.00 0.00 2.24
828 858 3.976902 GACCAATGGCAGCTTGCGC 62.977 63.158 0.00 0.00 46.21 6.09
902 935 4.675565 CAGACCAGTCGTAGTATAATTGCG 59.324 45.833 0.00 0.00 34.09 4.85
960 993 2.369394 CCATGTTAGGACTTTGGAGGC 58.631 52.381 0.00 0.00 33.95 4.70
974 1007 0.033011 GGAGGCAGGAGTAGTCCAGA 60.033 60.000 19.00 0.00 46.80 3.86
993 1026 4.937620 CCAGAATCGGAGAGAGATAGAGAG 59.062 50.000 0.00 0.00 43.63 3.20
999 1032 2.224426 GGAGAGAGATAGAGAGGCGTCA 60.224 54.545 9.41 0.00 0.00 4.35
1064 1097 0.398381 GTGAGGAGGGAGCAGAGGAT 60.398 60.000 0.00 0.00 0.00 3.24
1070 1103 2.328319 GAGGGAGCAGAGGATGAAGAT 58.672 52.381 0.00 0.00 0.00 2.40
1075 1108 2.102757 GAGCAGAGGATGAAGATGCAGA 59.897 50.000 0.00 0.00 39.34 4.26
1199 1232 1.141881 GCATCTCACCGTCGTCCAT 59.858 57.895 0.00 0.00 0.00 3.41
1201 1234 0.455815 CATCTCACCGTCGTCCATCA 59.544 55.000 0.00 0.00 0.00 3.07
1204 1237 0.455815 CTCACCGTCGTCCATCATCA 59.544 55.000 0.00 0.00 0.00 3.07
1212 1245 0.031314 CGTCCATCATCAGGTCTCCG 59.969 60.000 0.00 0.00 0.00 4.63
1213 1246 1.115467 GTCCATCATCAGGTCTCCGT 58.885 55.000 0.00 0.00 0.00 4.69
1214 1247 1.482593 GTCCATCATCAGGTCTCCGTT 59.517 52.381 0.00 0.00 0.00 4.44
1232 1265 0.106868 TTATCAGGCTCGTCGGAGGA 60.107 55.000 0.00 0.00 40.80 3.71
1274 1310 1.150567 CGCCTCTTCGATTGCCTGAG 61.151 60.000 0.00 0.00 0.00 3.35
1320 1360 9.537848 GTTATGTGTGAGGTTAAAGAATAAACG 57.462 33.333 0.00 0.00 0.00 3.60
1386 1426 4.686091 TGCTCGTATTTCAGCTATGTATGC 59.314 41.667 0.00 0.00 36.53 3.14
1550 1590 7.489113 CCTATTATGGAAGATTTGCAACAACAC 59.511 37.037 0.00 0.00 33.68 3.32
1625 1665 0.883833 CTGCCGCTTCCTTGATTTGT 59.116 50.000 0.00 0.00 0.00 2.83
1637 1677 6.573664 TCCTTGATTTGTTCGATTGTGAAT 57.426 33.333 0.00 0.00 0.00 2.57
1640 1680 6.465781 CCTTGATTTGTTCGATTGTGAATACG 59.534 38.462 0.00 0.00 0.00 3.06
1643 1683 2.689646 TGTTCGATTGTGAATACGCCA 58.310 42.857 0.00 0.00 0.00 5.69
1708 1748 2.863346 CGTCCACGTTCACAGGGGA 61.863 63.158 0.00 0.00 34.11 4.81
1712 1752 1.302431 CACGTTCACAGGGGATGCA 60.302 57.895 0.00 0.00 0.00 3.96
1793 1833 5.279556 GGAAAGTAGCTTCTCTAGTGGTTGT 60.280 44.000 0.00 0.00 31.47 3.32
1799 1839 3.764972 GCTTCTCTAGTGGTTGTCCTACT 59.235 47.826 0.00 0.00 34.23 2.57
1808 1848 3.442977 GTGGTTGTCCTACTATGTCGAGT 59.557 47.826 0.00 0.00 34.23 4.18
1880 1920 6.037610 GCCTCAATACAACACCTGAAAGATAG 59.962 42.308 0.00 0.00 34.07 2.08
1882 1922 7.493971 CCTCAATACAACACCTGAAAGATAGAG 59.506 40.741 0.00 0.00 34.07 2.43
1891 1931 7.787028 ACACCTGAAAGATAGAGGTTAGATTC 58.213 38.462 0.00 0.00 38.07 2.52
2004 2046 2.169769 TCTTACCAGTGAAATAGCCCGG 59.830 50.000 0.00 0.00 0.00 5.73
2107 2149 9.816354 AGCAAACTGTTTATGTTATGTTCTTTT 57.184 25.926 5.31 0.00 0.00 2.27
2156 2198 2.384203 GCTAAGTGCTAGGCAACCG 58.616 57.895 0.00 0.00 41.47 4.44
2157 2199 1.706287 GCTAAGTGCTAGGCAACCGC 61.706 60.000 0.00 0.00 41.47 5.68
2158 2200 0.391130 CTAAGTGCTAGGCAACCGCA 60.391 55.000 0.00 0.00 41.47 5.69
2159 2201 0.035598 TAAGTGCTAGGCAACCGCAA 59.964 50.000 0.00 0.00 43.87 4.85
2175 2217 6.033091 GCAACCGCAACACAATATAACTTAAC 59.967 38.462 0.00 0.00 38.36 2.01
2188 2230 9.820229 CAATATAACTTAACTGCGAAGTTTTCA 57.180 29.630 15.51 0.00 43.03 2.69
2200 2242 5.237561 TGCGAAGTTTTCAACTATACAGCAA 59.762 36.000 0.00 0.00 41.91 3.91
2201 2243 5.790495 GCGAAGTTTTCAACTATACAGCAAG 59.210 40.000 0.00 0.00 41.91 4.01
2202 2244 6.307155 CGAAGTTTTCAACTATACAGCAAGG 58.693 40.000 0.00 0.00 41.91 3.61
2265 2307 4.929146 AGGTTTAACCAGGATAGCAAGT 57.071 40.909 17.10 0.00 41.95 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 33 5.538433 CACCCAAAATTTCCGGGATATACAT 59.462 40.000 25.32 5.17 43.21 2.29
39 43 1.269309 TGTTCGCACCCAAAATTTCCG 60.269 47.619 0.00 0.00 0.00 4.30
216 222 3.118038 AGACCTGTAAAGCTTCACCACAA 60.118 43.478 0.00 0.00 0.00 3.33
233 239 5.648092 CGGTTTCCATTTTATCTTCAGACCT 59.352 40.000 0.00 0.00 0.00 3.85
235 241 5.163652 CCCGGTTTCCATTTTATCTTCAGAC 60.164 44.000 0.00 0.00 0.00 3.51
331 344 1.045407 ACACCTTGTGGTCGCTAAGA 58.955 50.000 0.00 0.00 46.60 2.10
332 345 1.878953 AACACCTTGTGGTCGCTAAG 58.121 50.000 0.00 0.00 46.60 2.18
333 346 3.244284 ACATAACACCTTGTGGTCGCTAA 60.244 43.478 0.00 0.00 46.60 3.09
334 347 2.300723 ACATAACACCTTGTGGTCGCTA 59.699 45.455 0.00 0.00 46.60 4.26
335 348 1.071699 ACATAACACCTTGTGGTCGCT 59.928 47.619 0.00 0.00 46.60 4.93
336 349 1.196808 CACATAACACCTTGTGGTCGC 59.803 52.381 0.00 0.00 46.60 5.19
435 452 1.079503 GCGACAGGGAAGTTGATCAC 58.920 55.000 0.00 0.00 0.00 3.06
473 494 0.106149 ACAACGGTGTCTTCCAGGTC 59.894 55.000 0.00 0.00 29.49 3.85
594 622 6.039717 CCCATTCTTGTCTCTTCTTGTGAAAA 59.960 38.462 0.00 0.00 0.00 2.29
624 652 6.025749 TCTTTCACTCTCGTGTATTGTGAT 57.974 37.500 0.00 0.00 41.89 3.06
651 679 4.442472 GCAATAATCATGCAGGGCTTTTCT 60.442 41.667 0.00 0.00 43.29 2.52
652 680 3.805971 GCAATAATCATGCAGGGCTTTTC 59.194 43.478 0.00 0.00 43.29 2.29
653 681 3.453353 AGCAATAATCATGCAGGGCTTTT 59.547 39.130 0.00 0.00 46.22 2.27
710 738 1.339097 ACTACACTTCGAAGCTGGGT 58.661 50.000 24.86 18.56 0.00 4.51
879 909 4.675565 CGCAATTATACTACGACTGGTCTG 59.324 45.833 0.00 0.00 0.00 3.51
902 935 1.600916 ACAAACGCAGAGGAAGGGC 60.601 57.895 0.00 0.00 0.00 5.19
960 993 2.621055 CTCCGATTCTGGACTACTCCTG 59.379 54.545 0.00 0.00 37.48 3.86
974 1007 3.686016 GCCTCTCTATCTCTCTCCGATT 58.314 50.000 0.00 0.00 0.00 3.34
1183 1216 1.338337 GATGATGGACGACGGTGAGAT 59.662 52.381 0.00 0.00 0.00 2.75
1191 1224 1.067821 GGAGACCTGATGATGGACGAC 59.932 57.143 0.00 0.00 0.00 4.34
1199 1232 2.959030 CCTGATAACGGAGACCTGATGA 59.041 50.000 0.00 0.00 0.00 2.92
1201 1234 1.689273 GCCTGATAACGGAGACCTGAT 59.311 52.381 0.00 0.00 0.00 2.90
1204 1237 1.404843 GAGCCTGATAACGGAGACCT 58.595 55.000 0.00 0.00 0.00 3.85
1212 1245 0.030908 CCTCCGACGAGCCTGATAAC 59.969 60.000 0.00 0.00 34.49 1.89
1213 1246 0.106868 TCCTCCGACGAGCCTGATAA 60.107 55.000 0.00 0.00 34.49 1.75
1214 1247 0.106868 TTCCTCCGACGAGCCTGATA 60.107 55.000 0.00 0.00 34.49 2.15
1320 1360 1.351017 TCACCATCAGAAGAACCCCAC 59.649 52.381 0.00 0.00 0.00 4.61
1386 1426 2.036958 TCATCTTGTAACGGCCCATG 57.963 50.000 0.00 0.00 0.00 3.66
1625 1665 3.997681 TCTTTGGCGTATTCACAATCGAA 59.002 39.130 0.00 0.00 0.00 3.71
1637 1677 2.822306 CGACAGCTTCTTTGGCGTA 58.178 52.632 0.00 0.00 42.01 4.42
1640 1680 2.080286 TAGACGACAGCTTCTTTGGC 57.920 50.000 0.00 0.00 0.00 4.52
1793 1833 5.549347 GAGATACCACTCGACATAGTAGGA 58.451 45.833 0.00 0.00 0.00 2.94
1808 1848 1.878088 GTCGATGGCTACGAGATACCA 59.122 52.381 6.81 0.00 40.37 3.25
1880 1920 9.615295 GTTTATCAGAGTATCGAATCTAACCTC 57.385 37.037 0.00 0.00 42.67 3.85
1882 1922 9.182933 GTGTTTATCAGAGTATCGAATCTAACC 57.817 37.037 0.00 0.00 42.67 2.85
1891 1931 9.463443 TGTTCATATGTGTTTATCAGAGTATCG 57.537 33.333 1.90 0.00 42.67 2.92
1919 1961 8.540507 TCAGGTTAGATCTCTGCTACTTTATT 57.459 34.615 0.00 0.00 0.00 1.40
2004 2046 3.117851 CCTTCCATCCTTTCTCCTTACCC 60.118 52.174 0.00 0.00 0.00 3.69
2122 2164 7.297229 GCACTTAGCTTACTCTTCCTTTTAG 57.703 40.000 0.00 0.00 41.15 1.85
2154 2196 5.737290 GCAGTTAAGTTATATTGTGTTGCGG 59.263 40.000 0.00 0.00 0.00 5.69
2155 2197 5.447846 CGCAGTTAAGTTATATTGTGTTGCG 59.552 40.000 0.00 0.00 42.45 4.85
2156 2198 6.539324 TCGCAGTTAAGTTATATTGTGTTGC 58.461 36.000 0.00 0.00 0.00 4.17
2157 2199 8.227791 ACTTCGCAGTTAAGTTATATTGTGTTG 58.772 33.333 0.00 0.00 33.39 3.33
2158 2200 8.319143 ACTTCGCAGTTAAGTTATATTGTGTT 57.681 30.769 0.00 0.00 33.39 3.32
2159 2201 7.900782 ACTTCGCAGTTAAGTTATATTGTGT 57.099 32.000 0.00 0.00 33.39 3.72
2188 2230 5.717178 TGAGACTTCTCCTTGCTGTATAGTT 59.283 40.000 3.77 0.00 42.20 2.24
2200 2242 1.001406 CAAACGGCTGAGACTTCTCCT 59.999 52.381 0.00 0.00 42.20 3.69
2201 2243 1.000955 TCAAACGGCTGAGACTTCTCC 59.999 52.381 0.00 0.00 42.20 3.71
2202 2244 2.440539 TCAAACGGCTGAGACTTCTC 57.559 50.000 0.00 0.00 43.15 2.87
2241 2283 4.919774 TGCTATCCTGGTTAAACCTTCA 57.080 40.909 0.00 0.00 39.58 3.02


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

AutoCloner maintained by Alex Coulton.