Multiple sequence alignment - TraesCS6D01G280600

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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 TraesCS6D01G280600 chr6D 100.000 1688 0 0 835 2522 388137562 388135875 0.000000e+00 3118
1 TraesCS6D01G280600 chr6D 100.000 366 0 0 1 366 388138396 388138031 0.000000e+00 676
2 TraesCS6D01G280600 chr6B 90.726 992 45 20 835 1816 579550733 579549779 0.000000e+00 1279
3 TraesCS6D01G280600 chr6B 82.511 709 82 19 1815 2522 579549539 579548872 3.620000e-163 584
4 TraesCS6D01G280600 chr6B 85.124 121 3 4 1 106 579551180 579551060 2.650000e-20 110
5 TraesCS6D01G280600 chr6A 91.145 926 39 17 835 1752 534747830 534746940 0.000000e+00 1216
6 TraesCS6D01G280600 chr6A 88.181 753 74 11 1777 2522 534746947 534746203 0.000000e+00 883
7 TraesCS6D01G280600 chr6A 89.238 669 65 5 1856 2522 534712288 534711625 0.000000e+00 830
8 TraesCS6D01G280600 chr6A 91.829 514 32 5 1377 1888 533466931 533466426 0.000000e+00 708
9 TraesCS6D01G280600 chr6A 85.198 581 77 3 1949 2522 533464595 533464017 2.790000e-164 588
10 TraesCS6D01G280600 chr6A 88.212 509 15 18 835 1311 533467423 533466928 1.310000e-157 566
11 TraesCS6D01G280600 chr6A 91.089 202 16 2 2322 2522 534715767 534715567 3.200000e-69 272
12 TraesCS6D01G280600 chr6A 81.868 182 16 7 1 169 534748469 534748292 1.220000e-28 137


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 TraesCS6D01G280600 chr6D 388135875 388138396 2521 True 1897.000000 3118 100.000000 1 2522 2 chr6D.!!$R1 2521
1 TraesCS6D01G280600 chr6B 579548872 579551180 2308 True 657.666667 1279 86.120333 1 2522 3 chr6B.!!$R1 2521
2 TraesCS6D01G280600 chr6A 534746203 534748469 2266 True 745.333333 1216 87.064667 1 2522 3 chr6A.!!$R3 2521
3 TraesCS6D01G280600 chr6A 533464017 533467423 3406 True 620.666667 708 88.413000 835 2522 3 chr6A.!!$R1 1687
4 TraesCS6D01G280600 chr6A 534711625 534715767 4142 True 551.000000 830 90.163500 1856 2522 2 chr6A.!!$R2 666

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
138 154 0.322816 TGGCCAGCCTGTTCTGAATC 60.323 55.0 0.0 0.0 36.19 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 4798 0.112218 TTGTGCCACTTGTAGCCCAT 59.888 50.0 0.0 0.0 0.0 4.0 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
93 108 3.747976 GCCCCATTTCGCAACGCT 61.748 61.111 0.00 0.00 0.00 5.07
101 117 0.531974 TTTCGCAACGCTCCTCAACT 60.532 50.000 0.00 0.00 0.00 3.16
112 128 2.746362 GCTCCTCAACTGTTTGATCTGG 59.254 50.000 0.00 0.00 41.05 3.86
114 130 1.815003 CCTCAACTGTTTGATCTGGCC 59.185 52.381 0.00 0.00 41.05 5.36
116 132 0.523072 CAACTGTTTGATCTGGCCGG 59.477 55.000 4.71 4.71 34.24 6.13
118 134 2.361104 TGTTTGATCTGGCCGGCC 60.361 61.111 39.40 39.40 0.00 6.13
119 135 2.044946 GTTTGATCTGGCCGGCCT 60.045 61.111 43.34 26.79 36.94 5.19
120 136 2.045045 TTTGATCTGGCCGGCCTG 60.045 61.111 43.34 40.98 36.94 4.85
133 149 4.357279 GCCTGGCCAGCCTGTTCT 62.357 66.667 28.39 0.00 36.94 3.01
134 150 2.360852 CCTGGCCAGCCTGTTCTG 60.361 66.667 28.39 7.14 36.94 3.02
135 151 2.752358 CTGGCCAGCCTGTTCTGA 59.248 61.111 22.33 0.00 36.19 3.27
137 153 0.323178 CTGGCCAGCCTGTTCTGAAT 60.323 55.000 22.33 0.00 36.19 2.57
138 154 0.322816 TGGCCAGCCTGTTCTGAATC 60.323 55.000 0.00 0.00 36.19 2.52
141 157 1.093159 CCAGCCTGTTCTGAATCAGC 58.907 55.000 5.18 7.20 36.19 4.26
151 167 1.152989 CTGAATCAGCTCAGCTCGGC 61.153 60.000 0.00 0.00 36.40 5.54
152 168 2.202851 AATCAGCTCAGCTCGGCG 60.203 61.111 0.00 0.00 36.40 6.46
171 187 1.294138 CCTTCGGAGGCAAACGGTA 59.706 57.895 0.00 0.00 35.94 4.02
172 188 0.739813 CCTTCGGAGGCAAACGGTAG 60.740 60.000 0.00 0.00 35.94 3.18
176 192 1.078637 GGAGGCAAACGGTAGGTCC 60.079 63.158 0.00 0.00 0.00 4.46
177 193 1.551019 GGAGGCAAACGGTAGGTCCT 61.551 60.000 0.00 0.00 0.00 3.85
187 203 1.533338 CGGTAGGTCCTGAAACGATCG 60.533 57.143 14.88 14.88 0.00 3.69
298 386 6.237306 CCGAAAAGATAACGTAGGTTAACGAC 60.237 42.308 11.72 0.00 45.68 4.34
343 431 0.597637 AGAACAACCACGACTCTGCG 60.598 55.000 0.00 0.00 37.29 5.18
1063 1174 3.333189 CGCGCATCATGGAGTCCG 61.333 66.667 8.75 0.00 0.00 4.79
1171 1291 4.400961 GCGCCAGGAGGAAGCACT 62.401 66.667 0.00 0.00 39.11 4.40
1172 1292 2.125350 CGCCAGGAGGAAGCACTC 60.125 66.667 0.00 0.00 36.89 3.51
1173 1293 2.125350 GCCAGGAGGAAGCACTCG 60.125 66.667 0.00 0.00 38.39 4.18
1174 1294 2.581354 CCAGGAGGAAGCACTCGG 59.419 66.667 0.00 0.00 38.39 4.63
1175 1295 2.581354 CAGGAGGAAGCACTCGGG 59.419 66.667 0.00 0.00 38.39 5.14
1176 1296 2.685380 AGGAGGAAGCACTCGGGG 60.685 66.667 0.00 0.00 38.39 5.73
1620 1745 3.115554 CGTTTGGCAAAGTCCTTTTCAG 58.884 45.455 13.94 0.00 0.00 3.02
1714 1842 5.368145 TCATCAGAAGAAATACATTCCGGG 58.632 41.667 0.00 0.00 38.94 5.73
1726 1854 7.648039 AATACATTCCGGGTTTTTGCTATAA 57.352 32.000 0.00 0.00 0.00 0.98
1775 1903 7.461182 TGAAAGACTCAAACCAAGAAAAGAA 57.539 32.000 0.00 0.00 0.00 2.52
1831 2201 4.216411 TCTTCTTATAGCCAACCCACAC 57.784 45.455 0.00 0.00 0.00 3.82
1850 2221 1.712977 CGAGAACCCCGTCTACCTCG 61.713 65.000 0.00 0.00 37.72 4.63
1858 2229 3.138798 GTCTACCTCGCCGCCAGA 61.139 66.667 0.00 0.00 0.00 3.86
1859 2230 2.829003 TCTACCTCGCCGCCAGAG 60.829 66.667 0.00 0.00 35.60 3.35
1861 2232 2.123854 TACCTCGCCGCCAGAGAT 60.124 61.111 0.00 0.00 37.93 2.75
1888 3513 0.603707 TCAGAAAGGAGCGGTTGCAG 60.604 55.000 0.00 0.00 46.23 4.41
1905 4774 3.642705 TGCAGAGACCGAATCATAATCG 58.357 45.455 0.00 0.00 39.92 3.34
1928 4797 6.483974 TCGTAGAAACAACACACACCATTATT 59.516 34.615 0.00 0.00 0.00 1.40
1929 4798 7.656542 TCGTAGAAACAACACACACCATTATTA 59.343 33.333 0.00 0.00 0.00 0.98
1930 4799 8.447833 CGTAGAAACAACACACACCATTATTAT 58.552 33.333 0.00 0.00 0.00 1.28
1968 5365 1.243902 TAAAAACCTGCCGCAAGAGG 58.756 50.000 0.00 0.00 43.02 3.69
1981 5378 3.198068 CGCAAGAGGCAGTACATAACAT 58.802 45.455 0.00 0.00 45.17 2.71
1997 5394 5.407387 ACATAACATACGCTTGAAGAACGTT 59.593 36.000 0.00 0.00 40.99 3.99
2094 5498 4.079970 TGAGGCTTAACGAAGAGAGAAGA 58.920 43.478 0.00 0.00 34.25 2.87
2095 5499 4.523173 TGAGGCTTAACGAAGAGAGAAGAA 59.477 41.667 0.00 0.00 34.25 2.52
2101 5505 6.651975 TTAACGAAGAGAGAAGAAACTCCT 57.348 37.500 0.00 0.00 37.60 3.69
2145 5549 8.812513 TCAAGATTCAACATCAGGTTTGATAT 57.187 30.769 0.00 0.00 42.12 1.63
2162 5566 0.108709 TATTTTGTACGTCGCCGGCT 60.109 50.000 26.68 8.22 38.78 5.52
2226 5630 2.337879 GACCACACCCTCACAAGCCA 62.338 60.000 0.00 0.00 0.00 4.75
2316 5720 1.669760 TTGTCGTCGCCCAACATCC 60.670 57.895 0.00 0.00 0.00 3.51
2344 5749 6.912203 TGAGACACGTGAACAAAAATCTAA 57.088 33.333 25.01 1.70 0.00 2.10
2345 5750 6.943981 TGAGACACGTGAACAAAAATCTAAG 58.056 36.000 25.01 0.00 0.00 2.18
2378 5783 1.142060 ACACATTGGTCGGAGAAACCA 59.858 47.619 0.00 0.00 44.98 3.67
2422 5827 0.409484 AAGATGGTGGGAACAAGGGG 59.591 55.000 0.00 0.00 46.06 4.79
2429 5834 2.283821 GGAACAAGGGGCATGCCA 60.284 61.111 36.56 0.00 37.98 4.92
2505 5910 8.719648 CGAGACCTCGTATGTTCTATACTATTT 58.280 37.037 10.96 0.00 46.99 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 84 4.160635 CGAAATGGGGCGTGCGAC 62.161 66.667 0.00 0.00 0.00 5.19
93 108 2.553028 GGCCAGATCAAACAGTTGAGGA 60.553 50.000 0.00 0.00 46.75 3.71
101 117 2.361104 GGCCGGCCAGATCAAACA 60.361 61.111 40.73 0.00 35.81 2.83
118 134 0.323178 ATTCAGAACAGGCTGGCCAG 60.323 55.000 29.34 29.34 38.92 4.85
119 135 0.322816 GATTCAGAACAGGCTGGCCA 60.323 55.000 20.34 4.71 38.92 5.36
120 136 0.322816 TGATTCAGAACAGGCTGGCC 60.323 55.000 20.34 9.82 36.55 5.36
122 138 1.093159 GCTGATTCAGAACAGGCTGG 58.907 55.000 20.34 0.21 36.55 4.85
124 140 1.627329 TGAGCTGATTCAGAACAGGCT 59.373 47.619 17.87 6.70 35.05 4.58
125 141 2.008329 CTGAGCTGATTCAGAACAGGC 58.992 52.381 17.87 1.54 45.95 4.85
127 143 2.931325 GAGCTGAGCTGATTCAGAACAG 59.069 50.000 13.71 23.64 45.95 3.16
129 145 1.925847 CGAGCTGAGCTGATTCAGAAC 59.074 52.381 13.71 10.11 45.95 3.01
130 146 1.134877 CCGAGCTGAGCTGATTCAGAA 60.135 52.381 13.71 1.34 45.95 3.02
132 148 1.152989 GCCGAGCTGAGCTGATTCAG 61.153 60.000 13.71 9.40 45.85 3.02
133 149 1.153489 GCCGAGCTGAGCTGATTCA 60.153 57.895 13.71 0.00 39.88 2.57
134 150 2.236382 CGCCGAGCTGAGCTGATTC 61.236 63.158 13.71 0.00 39.88 2.52
135 151 2.202851 CGCCGAGCTGAGCTGATT 60.203 61.111 13.71 0.00 39.88 2.57
169 185 1.475682 ACCGATCGTTTCAGGACCTAC 59.524 52.381 15.09 0.00 0.00 3.18
171 187 0.974383 AACCGATCGTTTCAGGACCT 59.026 50.000 15.09 0.00 0.00 3.85
172 188 1.804601 AAACCGATCGTTTCAGGACC 58.195 50.000 15.09 0.00 40.86 4.46
199 215 8.041323 GGTGATACAGATAGAGTTTTTCCTTCA 58.959 37.037 0.00 0.00 0.00 3.02
201 217 8.152023 AGGTGATACAGATAGAGTTTTTCCTT 57.848 34.615 0.00 0.00 0.00 3.36
203 219 8.915036 TCTAGGTGATACAGATAGAGTTTTTCC 58.085 37.037 0.00 0.00 0.00 3.13
255 337 1.655099 CGGCGGCATTTGATTTTCTTG 59.345 47.619 10.53 0.00 0.00 3.02
262 344 1.173043 TCTTTTCGGCGGCATTTGAT 58.827 45.000 10.53 0.00 0.00 2.57
263 345 1.173043 ATCTTTTCGGCGGCATTTGA 58.827 45.000 10.53 0.20 0.00 2.69
841 929 3.503748 ACTTCATTTTCTAGCACCAGCAC 59.496 43.478 0.00 0.00 45.49 4.40
1050 1161 2.969238 GCGCCGGACTCCATGATG 60.969 66.667 5.05 0.00 0.00 3.07
1063 1174 3.995506 ATGGCTGGTACTTGGCGCC 62.996 63.158 22.73 22.73 41.06 6.53
1384 1507 3.733960 GAAGTTTCCGGCGGTGGC 61.734 66.667 27.32 16.19 38.90 5.01
1620 1745 7.096065 GCTGTACAAATGACATCCTTTTGTTTC 60.096 37.037 9.51 5.69 45.26 2.78
1632 1757 3.944650 ACTTGTGTGCTGTACAAATGACA 59.055 39.130 8.56 0.00 41.89 3.58
1714 1842 9.624697 TGATGTTTGTCAGATTATAGCAAAAAC 57.375 29.630 0.00 0.00 31.99 2.43
1741 1869 9.527157 TTGGTTTGAGTCTTTCAATATATTCCA 57.473 29.630 0.00 0.00 44.90 3.53
1748 1876 9.184523 TCTTTTCTTGGTTTGAGTCTTTCAATA 57.815 29.630 0.00 0.00 44.90 1.90
1775 1903 4.578928 GCCTTTGGATACCACGATGTATTT 59.421 41.667 0.00 0.00 31.67 1.40
1831 2201 1.712977 CGAGGTAGACGGGGTTCTCG 61.713 65.000 0.00 0.00 38.17 4.04
1850 2221 2.035961 TGACTACAATATCTCTGGCGGC 59.964 50.000 0.00 0.00 0.00 6.53
1856 2227 6.238897 CGCTCCTTTCTGACTACAATATCTCT 60.239 42.308 0.00 0.00 0.00 3.10
1858 2229 5.221342 CCGCTCCTTTCTGACTACAATATCT 60.221 44.000 0.00 0.00 0.00 1.98
1859 2230 4.985409 CCGCTCCTTTCTGACTACAATATC 59.015 45.833 0.00 0.00 0.00 1.63
1861 2232 3.767673 ACCGCTCCTTTCTGACTACAATA 59.232 43.478 0.00 0.00 0.00 1.90
1888 3513 6.916387 TGTTTCTACGATTATGATTCGGTCTC 59.084 38.462 0.00 0.00 40.83 3.36
1905 4774 9.554724 CATAATAATGGTGTGTGTTGTTTCTAC 57.445 33.333 0.00 0.00 0.00 2.59
1928 4797 0.988063 TGTGCCACTTGTAGCCCATA 59.012 50.000 0.00 0.00 0.00 2.74
1929 4798 0.112218 TTGTGCCACTTGTAGCCCAT 59.888 50.000 0.00 0.00 0.00 4.00
1930 4799 0.112218 ATTGTGCCACTTGTAGCCCA 59.888 50.000 0.00 0.00 0.00 5.36
1939 4808 3.385193 GCAGGTTTTTATTGTGCCACT 57.615 42.857 0.00 0.00 0.00 4.00
1968 5365 5.518847 TCTTCAAGCGTATGTTATGTACTGC 59.481 40.000 0.00 0.00 0.00 4.40
1972 5369 6.094719 ACGTTCTTCAAGCGTATGTTATGTA 58.905 36.000 0.00 0.00 37.07 2.29
1981 5378 2.129607 GGTCAACGTTCTTCAAGCGTA 58.870 47.619 0.00 0.00 37.92 4.42
2013 5410 4.341806 ACAAATCTTTGCAACCTGATCACA 59.658 37.500 0.00 0.00 41.79 3.58
2054 5451 0.400594 CAGACGGGGGTTCTTCCTTT 59.599 55.000 0.00 0.00 36.25 3.11
2094 5498 4.411212 AGTGTTAAGGTGGTACAGGAGTTT 59.589 41.667 0.00 0.00 41.80 2.66
2095 5499 3.971971 AGTGTTAAGGTGGTACAGGAGTT 59.028 43.478 0.00 0.00 41.80 3.01
2101 5505 7.305813 TCTTGATAAGTGTTAAGGTGGTACA 57.694 36.000 0.00 0.00 0.00 2.90
2162 5566 2.438254 GGGCGATGTGATGGTGCA 60.438 61.111 0.00 0.00 0.00 4.57
2226 5630 2.686816 CGCTCCAAAATCGGCGGTT 61.687 57.895 7.21 1.94 43.25 4.44
2286 5690 4.422506 CGACAACATCGCAACAGC 57.577 55.556 0.00 0.00 45.52 4.40
2304 5708 3.642503 AACGGGGATGTTGGGCGA 61.643 61.111 0.00 0.00 0.00 5.54
2344 5749 6.220726 ACCAATGTGTACTTTCTTTTTGCT 57.779 33.333 0.00 0.00 0.00 3.91
2345 5750 5.173131 CGACCAATGTGTACTTTCTTTTTGC 59.827 40.000 0.00 0.00 0.00 3.68
2378 5783 1.199425 GGGGAGACGAAGGGGAACTT 61.199 60.000 0.00 0.00 43.65 2.66
2422 5827 0.034670 AACCCTCTTCTCTGGCATGC 60.035 55.000 9.90 9.90 0.00 4.06


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

AutoCloner maintained by Alex Coulton.