Multiple sequence alignment - TraesCS3D01G343600

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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 TraesCS3D01G343600 chr3D 100.000 2240 0 0 1 2240 455863674 455865913 0.000000e+00 4137.0
1 TraesCS3D01G343600 chr3A 95.752 2001 55 11 268 2240 598548819 598550817 0.000000e+00 3197.0
2 TraesCS3D01G343600 chr3A 89.868 227 19 3 1 226 598548593 598548816 2.810000e-74 289.0
3 TraesCS3D01G343600 chr3A 96.000 50 1 1 218 266 475279705 475279754 1.840000e-11 80.5
4 TraesCS3D01G343600 chr3B 95.896 1876 55 8 384 2240 602302406 602304278 0.000000e+00 3018.0
5 TraesCS3D01G343600 chr3B 96.053 228 9 0 1 228 602302052 602302279 2.720000e-99 372.0
6 TraesCS3D01G343600 chr3B 95.652 46 2 0 262 307 602302275 602302320 8.580000e-10 75.0
7 TraesCS3D01G343600 chr7B 96.000 50 0 2 225 272 684939919 684939968 1.840000e-11 80.5
8 TraesCS3D01G343600 chr7B 92.593 54 1 3 215 266 829838 829786 8.580000e-10 75.0
9 TraesCS3D01G343600 chr5D 94.231 52 2 1 216 266 528980780 528980831 6.630000e-11 78.7
10 TraesCS3D01G343600 chr2A 97.826 46 0 1 223 267 689711913 689711958 6.630000e-11 78.7
11 TraesCS3D01G343600 chr1A 95.918 49 0 2 219 266 241320012 241319965 6.630000e-11 78.7
12 TraesCS3D01G343600 chr2B 95.833 48 1 1 218 264 417500758 417500805 2.390000e-10 76.8
13 TraesCS3D01G343600 chr4B 94.118 51 0 3 224 272 34029045 34029094 8.580000e-10 75.0
14 TraesCS3D01G343600 chr4B 94.000 50 1 2 221 269 612271491 612271443 8.580000e-10 75.0
15 TraesCS3D01G343600 chr7A 100.000 32 0 0 344 375 673029591 673029622 2.400000e-05 60.2


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 TraesCS3D01G343600 chr3D 455863674 455865913 2239 False 4137 4137 100.000 1 2240 1 chr3D.!!$F1 2239
1 TraesCS3D01G343600 chr3A 598548593 598550817 2224 False 1743 3197 92.810 1 2240 2 chr3A.!!$F2 2239
2 TraesCS3D01G343600 chr3B 602302052 602304278 2226 False 1155 3018 95.867 1 2240 3 chr3B.!!$F1 2239

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
239 240 0.116342 TTGCTACTCCCTCTGTCCCA 59.884 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2107 0.039165 GTGCCTGGGAAGCTTTTTCG 60.039 55.0 0.0 0.0 0.0 3.46 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
36 37 0.475906 AAAAGCTCCAGTGTCAGGCT 59.524 50.000 0.00 0.0 34.52 4.58
102 103 3.943671 TCAGGGTTCTTTGGTTTCTCA 57.056 42.857 0.00 0.0 0.00 3.27
142 143 9.087424 GTTTTGAAAAAGCTATCTGTTTCTTGT 57.913 29.630 9.94 0.0 43.69 3.16
173 174 1.469703 TCAAATGCACATGAAGCCTCG 59.530 47.619 0.00 0.0 0.00 4.63
179 180 2.279741 GCACATGAAGCCTCGTTGATA 58.720 47.619 0.00 0.0 0.00 2.15
228 229 3.386768 TGGTCACTCTGTTTGCTACTC 57.613 47.619 0.00 0.0 0.00 2.59
229 230 2.037251 TGGTCACTCTGTTTGCTACTCC 59.963 50.000 0.00 0.0 0.00 3.85
230 231 2.613223 GGTCACTCTGTTTGCTACTCCC 60.613 54.545 0.00 0.0 0.00 4.30
231 232 2.300437 GTCACTCTGTTTGCTACTCCCT 59.700 50.000 0.00 0.0 0.00 4.20
232 233 2.563179 TCACTCTGTTTGCTACTCCCTC 59.437 50.000 0.00 0.0 0.00 4.30
233 234 2.564947 CACTCTGTTTGCTACTCCCTCT 59.435 50.000 0.00 0.0 0.00 3.69
234 235 2.564947 ACTCTGTTTGCTACTCCCTCTG 59.435 50.000 0.00 0.0 0.00 3.35
235 236 2.564947 CTCTGTTTGCTACTCCCTCTGT 59.435 50.000 0.00 0.0 0.00 3.41
236 237 2.563179 TCTGTTTGCTACTCCCTCTGTC 59.437 50.000 0.00 0.0 0.00 3.51
237 238 1.623811 TGTTTGCTACTCCCTCTGTCC 59.376 52.381 0.00 0.0 0.00 4.02
238 239 1.066071 GTTTGCTACTCCCTCTGTCCC 60.066 57.143 0.00 0.0 0.00 4.46
239 240 0.116342 TTGCTACTCCCTCTGTCCCA 59.884 55.000 0.00 0.0 0.00 4.37
240 241 0.339859 TGCTACTCCCTCTGTCCCAT 59.660 55.000 0.00 0.0 0.00 4.00
241 242 1.573857 TGCTACTCCCTCTGTCCCATA 59.426 52.381 0.00 0.0 0.00 2.74
242 243 2.023404 TGCTACTCCCTCTGTCCCATAA 60.023 50.000 0.00 0.0 0.00 1.90
243 244 3.243724 GCTACTCCCTCTGTCCCATAAT 58.756 50.000 0.00 0.0 0.00 1.28
244 245 4.140782 TGCTACTCCCTCTGTCCCATAATA 60.141 45.833 0.00 0.0 0.00 0.98
245 246 5.026790 GCTACTCCCTCTGTCCCATAATAT 58.973 45.833 0.00 0.0 0.00 1.28
246 247 6.195700 GCTACTCCCTCTGTCCCATAATATA 58.804 44.000 0.00 0.0 0.00 0.86
247 248 6.668283 GCTACTCCCTCTGTCCCATAATATAA 59.332 42.308 0.00 0.0 0.00 0.98
248 249 7.147811 GCTACTCCCTCTGTCCCATAATATAAG 60.148 44.444 0.00 0.0 0.00 1.73
249 250 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.0 0.00 2.10
250 251 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.0 0.00 2.85
251 252 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.0 0.00 4.09
252 253 5.394663 CCCTCTGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.0 0.00 5.03
253 254 5.186021 CCTCTGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.0 0.00 5.07
254 255 6.295349 CCTCTGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.0 0.00 4.84
255 256 7.062749 TCTGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.0 0.00 3.60
256 257 7.506114 TCTGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.0 0.00 2.43
257 258 7.990886 TCTGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.0 0.00 1.94
312 314 5.118990 GCACTACATAGTTGATCATGTGGT 58.881 41.667 9.60 9.6 44.64 4.16
320 322 4.655963 AGTTGATCATGTGGTAAACTGCT 58.344 39.130 0.00 0.0 0.00 4.24
327 329 2.503331 TGTGGTAAACTGCTGACATGG 58.497 47.619 0.00 0.0 0.00 3.66
329 331 2.484264 GTGGTAAACTGCTGACATGGTC 59.516 50.000 0.00 0.0 0.00 4.02
363 365 6.429692 TGTTCATTCTACATCAAACGACCAAT 59.570 34.615 0.00 0.0 0.00 3.16
795 850 4.308458 TTGTAGTGCACCGCCGCT 62.308 61.111 14.63 0.0 0.00 5.52
1630 1685 3.356267 GTGCGTGCATGTGCTCCA 61.356 61.111 7.93 0.0 42.66 3.86
1635 1690 2.358615 TGCATGTGCTCCACGTCC 60.359 61.111 6.55 0.0 42.66 4.79
1690 1745 2.176546 CCGTTGATGCCACGCAAG 59.823 61.111 0.00 0.0 43.62 4.01
1859 1914 4.690748 CGTTCAAATTGAGGTAGAAGCTGA 59.309 41.667 0.00 0.0 0.00 4.26
1861 1916 6.374578 GTTCAAATTGAGGTAGAAGCTGAAC 58.625 40.000 0.00 0.0 35.04 3.18
1872 1931 0.870393 AAGCTGAACGCATCACACAG 59.130 50.000 0.00 0.0 42.61 3.66
1901 1960 7.652524 AGTAGCTTTCACTGATCATCTCTAA 57.347 36.000 0.00 0.0 0.00 2.10
1921 1980 4.618920 AACAAGTAGTTCTCGGTTGGAT 57.381 40.909 0.00 0.0 34.74 3.41
1937 1996 4.496341 GGTTGGATTGCGACATGTAGAATG 60.496 45.833 10.44 0.0 0.00 2.67
2164 2237 1.185618 TGCTACCGGAGTTGAGCAGT 61.186 55.000 9.46 0.0 39.93 4.40
2180 2253 3.526931 GCAGTAGCTAGGTTGATGTGA 57.473 47.619 0.00 0.0 37.91 3.58
2181 2254 4.065321 GCAGTAGCTAGGTTGATGTGAT 57.935 45.455 0.00 0.0 37.91 3.06
2199 2275 5.109210 TGTGATTGATTTAGTAGCTCCGTG 58.891 41.667 0.00 0.0 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 7.436673 GCTTTTTCAAAACAAAACAAAAACCCT 59.563 29.630 0.00 0.0 0.00 4.34
142 143 0.825425 TGCATTTGAGGTGCGGGAAA 60.825 50.000 0.00 0.0 45.37 3.13
173 174 8.288208 GTGGATCAGATGAATCAACATATCAAC 58.712 37.037 0.00 0.0 0.00 3.18
179 180 6.940867 CCATAGTGGATCAGATGAATCAACAT 59.059 38.462 0.00 0.0 40.96 2.71
264 265 9.550811 GCAAATGTACAATACAAACCTAACTAC 57.449 33.333 0.00 0.0 42.76 2.73
265 266 9.286170 TGCAAATGTACAATACAAACCTAACTA 57.714 29.630 0.00 0.0 42.76 2.24
272 273 8.964420 ATGTAGTGCAAATGTACAATACAAAC 57.036 30.769 0.00 0.0 46.48 2.93
312 314 3.394674 TTCGACCATGTCAGCAGTTTA 57.605 42.857 0.00 0.0 32.09 2.01
320 322 3.469008 ACAGACTTTTCGACCATGTCA 57.531 42.857 10.71 0.0 32.09 3.58
327 329 6.764877 TGTAGAATGAACAGACTTTTCGAC 57.235 37.500 0.00 0.0 0.00 4.20
329 331 7.351414 TGATGTAGAATGAACAGACTTTTCG 57.649 36.000 0.00 0.0 0.00 3.46
507 562 2.435059 GCCAGGGAGCAGAACGAC 60.435 66.667 0.00 0.0 0.00 4.34
1630 1685 1.508632 CGACCAACAGATTTGGACGT 58.491 50.000 16.36 0.0 46.81 4.34
1635 1690 5.180117 AGTTTCTGATCGACCAACAGATTTG 59.820 40.000 12.00 0.0 39.78 2.32
1690 1745 1.227497 CGATCTCCAGGAAGGCAGC 60.227 63.158 0.00 0.0 37.29 5.25
1859 1914 0.308684 CTTGTGCTGTGTGATGCGTT 59.691 50.000 0.00 0.0 0.00 4.84
1861 1916 1.127397 CTACTTGTGCTGTGTGATGCG 59.873 52.381 0.00 0.0 0.00 4.73
1872 1931 3.748048 TGATCAGTGAAAGCTACTTGTGC 59.252 43.478 0.00 0.0 0.00 4.57
1901 1960 4.315803 CAATCCAACCGAGAACTACTTGT 58.684 43.478 0.00 0.0 0.00 3.16
1921 1980 3.118445 TCCATCCATTCTACATGTCGCAA 60.118 43.478 0.00 0.0 0.00 4.85
1937 1996 3.868754 GCGGGTAACTTATCCATCCATCC 60.869 52.174 0.00 0.0 0.00 3.51
1971 2034 0.975887 TTCCCTTCATTTGGGCTTGC 59.024 50.000 0.00 0.0 44.23 4.01
1973 2036 2.999185 TCTTCCCTTCATTTGGGCTT 57.001 45.000 0.00 0.0 44.23 4.35
2044 2107 0.039165 GTGCCTGGGAAGCTTTTTCG 60.039 55.000 0.00 0.0 0.00 3.46
2164 2237 8.486210 ACTAAATCAATCACATCAACCTAGCTA 58.514 33.333 0.00 0.0 0.00 3.32
2174 2247 5.986135 ACGGAGCTACTAAATCAATCACATC 59.014 40.000 0.00 0.0 0.00 3.06
2176 2249 5.109210 CACGGAGCTACTAAATCAATCACA 58.891 41.667 0.00 0.0 0.00 3.58
2179 2252 3.182572 CGCACGGAGCTACTAAATCAATC 59.817 47.826 0.00 0.0 42.61 2.67
2180 2253 3.123804 CGCACGGAGCTACTAAATCAAT 58.876 45.455 0.00 0.0 42.61 2.57
2181 2254 2.094390 ACGCACGGAGCTACTAAATCAA 60.094 45.455 0.00 0.0 42.61 2.57
2199 2275 0.317770 TGCAAGCAAAGTAAGCACGC 60.318 50.000 0.00 0.0 33.63 5.34


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

AutoCloner maintained by Alex Coulton.