Multiple sequence alignment - TraesCS5A01G402900

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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 TraesCS5A01G402900 chr5A 100.000 2282 0 0 1 2282 595407044 595409325 0.000000e+00 4215
1 TraesCS5A01G402900 chr5B 86.972 1681 105 49 1 1609 583471662 583473300 0.000000e+00 1786
2 TraesCS5A01G402900 chr5B 92.342 666 33 6 1620 2282 583473469 583474119 0.000000e+00 931
3 TraesCS5A01G402900 chr3B 86.234 1155 68 30 357 1462 689165727 689166839 0.000000e+00 1168
4 TraesCS5A01G402900 chr5D 87.704 797 50 22 367 1131 476010552 476011332 0.000000e+00 885
5 TraesCS5A01G402900 chr5D 89.736 682 28 20 1620 2282 476011955 476012613 0.000000e+00 833
6 TraesCS5A01G402900 chr5D 89.120 432 37 7 1184 1609 476011340 476011767 1.550000e-146 529
7 TraesCS5A01G402900 chr5D 88.596 228 18 8 1 224 476009980 476010203 1.040000e-68 270


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 TraesCS5A01G402900 chr5A 595407044 595409325 2281 False 4215.00 4215 100.000 1 2282 1 chr5A.!!$F1 2281
1 TraesCS5A01G402900 chr5B 583471662 583474119 2457 False 1358.50 1786 89.657 1 2282 2 chr5B.!!$F1 2281
2 TraesCS5A01G402900 chr3B 689165727 689166839 1112 False 1168.00 1168 86.234 357 1462 1 chr3B.!!$F1 1105
3 TraesCS5A01G402900 chr5D 476009980 476012613 2633 False 629.25 885 88.789 1 2282 4 chr5D.!!$F1 2281

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
831 1098 0.103937 CAGAGCTCCTCGATTGGTCC 59.896 60.0 10.93 0.0 35.36 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1675 2163 0.234884 CCAGAGGTCGAACGTTTTGC 59.765 55.0 0.46 0.0 0.0 3.68 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
23 25 2.890945 ACATACAACCAAGGAACAAGCC 59.109 45.455 0.00 0.00 0.00 4.35
24 26 2.738587 TACAACCAAGGAACAAGCCA 57.261 45.000 0.00 0.00 0.00 4.75
25 27 1.402787 ACAACCAAGGAACAAGCCAG 58.597 50.000 0.00 0.00 0.00 4.85
41 43 5.240844 ACAAGCCAGGTAGTATGTTTTTGAC 59.759 40.000 0.00 0.00 0.00 3.18
42 44 4.332828 AGCCAGGTAGTATGTTTTTGACC 58.667 43.478 0.00 0.00 0.00 4.02
159 163 4.207165 TGGGTGTCTTTTTCTCAAAGGAG 58.793 43.478 0.00 0.00 42.80 3.69
174 178 7.448420 TCTCAAAGGAGAATATATCAGCTTGG 58.552 38.462 0.00 0.00 46.94 3.61
175 179 7.290948 TCTCAAAGGAGAATATATCAGCTTGGA 59.709 37.037 0.00 0.00 46.94 3.53
194 199 7.728981 AGCTTGGATGGATCATAAAAATCTCAT 59.271 33.333 0.00 0.00 0.00 2.90
195 200 8.365647 GCTTGGATGGATCATAAAAATCTCATT 58.634 33.333 0.00 0.00 0.00 2.57
234 244 4.483476 CCAGCTTGTGGTAAGTTTGTAC 57.517 45.455 0.00 0.00 42.17 2.90
251 412 5.736486 TTGTACTACTAGCAGTCGATCAG 57.264 43.478 0.00 0.00 0.00 2.90
263 424 4.504461 GCAGTCGATCAGTACAAATACCAG 59.496 45.833 0.00 0.00 30.88 4.00
285 447 2.035530 AAAGCAGTCATCAGCTAGCC 57.964 50.000 12.13 0.00 40.90 3.93
304 466 2.418197 GCCTGATAAACGTGCTACCAGA 60.418 50.000 1.59 0.00 0.00 3.86
365 580 2.094854 GCTTCAGCTTGGAACATGAAGG 60.095 50.000 13.81 0.00 46.82 3.46
412 629 6.902341 ACAGCATAATTCACACAGTTACAAG 58.098 36.000 0.00 0.00 0.00 3.16
447 666 7.147983 GCCTTGTAGAAAGATTCTAGACAGAGA 60.148 40.741 0.00 0.00 42.56 3.10
448 667 8.405531 CCTTGTAGAAAGATTCTAGACAGAGAG 58.594 40.741 0.00 0.00 42.56 3.20
466 685 1.154469 GTTGGCGTTCGTAAGCAGC 60.154 57.895 2.14 0.00 34.54 5.25
582 834 2.934570 GCGACTCCACCCACGGTAA 61.935 63.158 0.00 0.00 32.11 2.85
638 890 4.678840 GCCCACCATCAATCAATCAGAAAC 60.679 45.833 0.00 0.00 0.00 2.78
827 1094 1.591059 CCGCAGAGCTCCTCGATTG 60.591 63.158 22.06 9.88 35.36 2.67
831 1098 0.103937 CAGAGCTCCTCGATTGGTCC 59.896 60.000 10.93 0.00 35.36 4.46
836 1103 0.747255 CTCCTCGATTGGTCCATCGT 59.253 55.000 17.61 0.00 40.76 3.73
851 1119 5.298276 GGTCCATCGTTGCCTATTTTTATCA 59.702 40.000 0.00 0.00 0.00 2.15
882 1162 2.996621 GCCTCTATAAAATCGCATCGCT 59.003 45.455 0.00 0.00 0.00 4.93
897 1177 3.123620 GCTCTTGCTGCCCACTCG 61.124 66.667 0.00 0.00 36.03 4.18
1089 1370 1.371558 GTTCAGACCCACGGCTTCT 59.628 57.895 0.00 0.00 0.00 2.85
1292 1592 1.927895 GGTCAGTAGATTGCACCGAG 58.072 55.000 0.00 0.00 0.00 4.63
1305 1605 1.301716 ACCGAGCGCTTGAACATGT 60.302 52.632 26.61 11.81 0.00 3.21
1320 1620 2.143122 ACATGTAGCAACACGTTCCTG 58.857 47.619 0.00 0.00 38.78 3.86
1417 1717 4.629200 GCCTTCTGAATGTCTCTGTTACAG 59.371 45.833 5.94 5.94 0.00 2.74
1462 1772 1.745087 CCGTTTTCATGATGGTCCCTG 59.255 52.381 0.00 0.00 0.00 4.45
1465 1775 3.635591 GTTTTCATGATGGTCCCTGGAT 58.364 45.455 0.00 0.00 0.00 3.41
1492 1802 3.950087 AAAGTTCGTTTTCGTGGGTAC 57.050 42.857 0.00 0.00 44.46 3.34
1535 1845 2.610859 GCCAAGTGGGAGGGGAGA 60.611 66.667 0.00 0.00 40.01 3.71
1537 1847 1.918253 CCAAGTGGGAGGGGAGATG 59.082 63.158 0.00 0.00 40.01 2.90
1586 1992 6.294286 GGCTGAAGTAGTAGCGAAATATCTCT 60.294 42.308 0.00 0.00 40.78 3.10
1611 2017 3.687212 TCGCCGAGATATTTTGCTTCAAA 59.313 39.130 0.00 0.00 0.00 2.69
1612 2018 4.155099 TCGCCGAGATATTTTGCTTCAAAA 59.845 37.500 7.11 7.11 45.41 2.44
1658 2146 2.036387 TCTCTGAACCTCAACGTTCCA 58.964 47.619 0.00 0.00 41.24 3.53
1660 2148 1.760613 TCTGAACCTCAACGTTCCAGT 59.239 47.619 0.00 0.00 41.24 4.00
1754 2249 2.254546 TCGATTCCCCGGATCAAATG 57.745 50.000 0.73 0.00 0.00 2.32
1772 2267 4.789075 CTACGTCCGGGTGGTGCG 62.789 72.222 0.00 0.00 39.38 5.34
1784 2287 4.778143 GGTGCGGCGAACCTGGAT 62.778 66.667 29.84 0.00 34.66 3.41
1789 2292 2.825836 GGCGAACCTGGATGGCAG 60.826 66.667 12.62 0.00 40.22 4.85
1923 2429 4.166888 TGGCAGCGGCATCTCTCC 62.167 66.667 11.88 0.00 43.71 3.71
1951 2457 4.943591 CCGCGCGCCGAATCAATG 62.944 66.667 27.36 7.77 40.02 2.82
1970 2476 1.154073 GTACGCGCGAGGATATCCC 60.154 63.158 39.36 8.96 36.42 3.85
1971 2477 2.338015 TACGCGCGAGGATATCCCC 61.338 63.158 39.36 5.55 36.42 4.81
1972 2478 2.759641 TACGCGCGAGGATATCCCCT 62.760 60.000 39.36 12.01 39.77 4.79
2180 2686 4.525949 GGAGGCGCCTACCGTTCC 62.526 72.222 32.97 22.13 39.71 3.62
2213 2719 1.961394 GTTTCCTCCACTTTTCCCACC 59.039 52.381 0.00 0.00 0.00 4.61
2219 2725 1.528309 CACTTTTCCCACCGGCAGT 60.528 57.895 0.00 0.00 0.00 4.40
2220 2726 1.528309 ACTTTTCCCACCGGCAGTG 60.528 57.895 0.00 0.00 46.83 3.66
2248 2757 1.153469 TCGCGAGTGCATGCCAATA 60.153 52.632 16.68 0.00 42.97 1.90
2249 2758 1.153597 TCGCGAGTGCATGCCAATAG 61.154 55.000 16.68 4.41 42.97 1.73
2250 2759 1.009222 GCGAGTGCATGCCAATAGC 60.009 57.895 16.68 10.65 42.15 2.97
2251 2760 1.650912 CGAGTGCATGCCAATAGCC 59.349 57.895 16.68 0.00 42.71 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.073923 ACTACCTGGCTTGTTCCTTGG 59.926 52.381 0.00 0.00 0.00 3.61
14 16 3.629142 ACATACTACCTGGCTTGTTCC 57.371 47.619 0.00 0.00 0.00 3.62
62 64 7.770201 TGAAAAGACAACAAGACATCAAATGA 58.230 30.769 0.00 0.00 0.00 2.57
68 71 7.591426 GGTACAATGAAAAGACAACAAGACATC 59.409 37.037 0.00 0.00 0.00 3.06
159 163 9.842775 TTATGATCCATCCAAGCTGATATATTC 57.157 33.333 0.00 0.00 0.00 1.75
164 168 8.945195 ATTTTTATGATCCATCCAAGCTGATA 57.055 30.769 0.00 0.00 0.00 2.15
167 171 7.013942 TGAGATTTTTATGATCCATCCAAGCTG 59.986 37.037 0.00 0.00 0.00 4.24
168 172 7.064866 TGAGATTTTTATGATCCATCCAAGCT 58.935 34.615 0.00 0.00 0.00 3.74
169 173 7.281040 TGAGATTTTTATGATCCATCCAAGC 57.719 36.000 0.00 0.00 0.00 4.01
170 174 9.909644 GAATGAGATTTTTATGATCCATCCAAG 57.090 33.333 0.00 0.00 0.00 3.61
171 175 9.423964 TGAATGAGATTTTTATGATCCATCCAA 57.576 29.630 0.00 0.00 0.00 3.53
172 176 8.999905 TGAATGAGATTTTTATGATCCATCCA 57.000 30.769 0.00 0.00 0.00 3.41
224 234 7.335171 TGATCGACTGCTAGTAGTACAAACTTA 59.665 37.037 13.91 0.00 37.15 2.24
227 237 5.877031 TGATCGACTGCTAGTAGTACAAAC 58.123 41.667 13.91 5.75 0.00 2.93
228 238 5.646793 ACTGATCGACTGCTAGTAGTACAAA 59.353 40.000 13.91 0.44 0.00 2.83
229 239 5.183969 ACTGATCGACTGCTAGTAGTACAA 58.816 41.667 13.91 2.90 0.00 2.41
230 240 4.767478 ACTGATCGACTGCTAGTAGTACA 58.233 43.478 13.91 10.47 0.00 2.90
231 241 5.752472 TGTACTGATCGACTGCTAGTAGTAC 59.248 44.000 13.91 6.41 39.55 2.73
233 243 4.767478 TGTACTGATCGACTGCTAGTAGT 58.233 43.478 13.82 13.82 0.00 2.73
234 244 5.736486 TTGTACTGATCGACTGCTAGTAG 57.264 43.478 6.26 6.26 0.00 2.57
251 412 6.966021 TGACTGCTTTTTCTGGTATTTGTAC 58.034 36.000 0.00 0.00 0.00 2.90
263 424 3.181502 GGCTAGCTGATGACTGCTTTTTC 60.182 47.826 15.72 0.00 46.30 2.29
285 447 4.111375 AGTCTGGTAGCACGTTTATCAG 57.889 45.455 9.76 9.76 31.84 2.90
304 466 1.432024 AGGTCCTACTGGTGTGGTAGT 59.568 52.381 0.00 0.00 36.02 2.73
364 579 0.108424 TGTGCAGTTTTTGTGGTGCC 60.108 50.000 0.00 0.00 34.91 5.01
365 580 1.135141 TCTGTGCAGTTTTTGTGGTGC 60.135 47.619 0.00 0.00 36.42 5.01
412 629 6.679327 ATCTTTCTACAAGGCGGTAATTTC 57.321 37.500 0.00 0.00 0.00 2.17
447 666 1.566018 GCTGCTTACGAACGCCAACT 61.566 55.000 0.00 0.00 0.00 3.16
448 667 1.154469 GCTGCTTACGAACGCCAAC 60.154 57.895 0.00 0.00 0.00 3.77
466 685 2.071540 TGCTGCTGAAATTGACTCTCG 58.928 47.619 0.00 0.00 0.00 4.04
525 768 0.669619 TGACTGCGACAACTACGGAA 59.330 50.000 0.00 0.00 0.00 4.30
638 890 2.724839 GCCGCTTGAGAATACGTGTTTG 60.725 50.000 0.00 0.00 0.00 2.93
810 1077 1.591059 CCAATCGAGGAGCTCTGCG 60.591 63.158 14.64 16.89 0.00 5.18
827 1094 5.298276 TGATAAAAATAGGCAACGATGGACC 59.702 40.000 0.00 0.00 46.39 4.46
831 1098 5.682862 GTGCTGATAAAAATAGGCAACGATG 59.317 40.000 0.00 0.00 46.39 3.84
836 1103 5.105432 TGCATGTGCTGATAAAAATAGGCAA 60.105 36.000 6.55 0.00 42.66 4.52
851 1119 3.565764 TTTATAGAGGCTGCATGTGCT 57.434 42.857 6.55 0.00 42.66 4.40
882 1162 3.939939 TGCGAGTGGGCAGCAAGA 61.940 61.111 0.00 0.00 38.17 3.02
897 1177 0.755686 ATCGGGGAGATCTTCAGTGC 59.244 55.000 2.72 0.00 33.45 4.40
997 1278 1.332195 TCTATCAGGCTCGACATGGG 58.668 55.000 0.00 0.00 0.00 4.00
1134 1424 2.782615 GTTCCATTTCCGTCGCCG 59.217 61.111 0.00 0.00 0.00 6.46
1135 1425 2.782615 CGTTCCATTTCCGTCGCC 59.217 61.111 0.00 0.00 0.00 5.54
1292 1592 1.069296 TGTTGCTACATGTTCAAGCGC 60.069 47.619 2.30 0.00 39.14 5.92
1301 1601 2.412870 TCAGGAACGTGTTGCTACATG 58.587 47.619 17.35 17.35 45.04 3.21
1305 1605 0.679505 AGCTCAGGAACGTGTTGCTA 59.320 50.000 6.44 0.00 39.28 3.49
1337 1637 3.311596 ACGAAAGACACTTTAGTTGCACC 59.688 43.478 0.00 0.00 0.00 5.01
1338 1638 4.033587 TCACGAAAGACACTTTAGTTGCAC 59.966 41.667 7.13 0.00 0.00 4.57
1417 1717 5.046950 ACCTGACTGGAGAAGAGATTTGTAC 60.047 44.000 5.22 0.00 39.71 2.90
1485 1795 1.290203 TCGATCGTACTCGTACCCAC 58.710 55.000 15.94 0.00 39.62 4.61
1535 1845 5.123227 CCGAGTGGTGGTAATGAATTACAT 58.877 41.667 13.66 0.00 43.33 2.29
1537 1847 3.875134 CCCGAGTGGTGGTAATGAATTAC 59.125 47.826 4.87 4.87 41.38 1.89
1565 1875 7.742963 CGAAGAGAGATATTTCGCTACTACTTC 59.257 40.741 0.00 0.00 37.49 3.01
1586 1992 3.179443 AGCAAAATATCTCGGCGAAGA 57.821 42.857 12.13 11.19 0.00 2.87
1611 2017 4.497300 GTTCAGTATGCATGGCAACAATT 58.503 39.130 10.16 0.00 45.34 2.32
1612 2018 3.427909 CGTTCAGTATGCATGGCAACAAT 60.428 43.478 10.16 0.00 45.34 2.71
1613 2019 2.095314 CGTTCAGTATGCATGGCAACAA 60.095 45.455 10.16 0.00 45.34 2.83
1615 2021 1.468520 ACGTTCAGTATGCATGGCAAC 59.531 47.619 10.16 6.06 43.62 4.17
1616 2022 1.819928 ACGTTCAGTATGCATGGCAA 58.180 45.000 10.16 0.00 43.62 4.52
1617 2023 1.819928 AACGTTCAGTATGCATGGCA 58.180 45.000 10.16 0.00 44.86 4.92
1618 2024 2.919666 AAACGTTCAGTATGCATGGC 57.080 45.000 10.16 1.92 34.76 4.40
1675 2163 0.234884 CCAGAGGTCGAACGTTTTGC 59.765 55.000 0.46 0.00 0.00 3.68
1772 2267 2.819984 TTCTGCCATCCAGGTTCGCC 62.820 60.000 0.00 0.00 42.05 5.54
1872 2375 0.537188 CGGTGACTATTGACTGCCCT 59.463 55.000 0.00 0.00 0.00 5.19
1942 2448 1.084290 CGCGCGTACCATTGATTCG 60.084 57.895 24.19 0.00 0.00 3.34
1951 2457 1.154073 GGATATCCTCGCGCGTACC 60.154 63.158 30.98 17.93 0.00 3.34
2225 2731 4.219846 CATGCACTCGCGAGCTGC 62.220 66.667 35.60 35.60 42.97 5.25
2240 2746 2.519302 GGCACCGGCTATTGGCAT 60.519 61.111 10.97 0.00 44.01 4.40
2241 2747 3.280938 AAGGCACCGGCTATTGGCA 62.281 57.895 17.03 0.00 44.01 4.92
2248 2757 3.249189 TGAAGGAAGGCACCGGCT 61.249 61.111 0.00 0.00 41.24 5.52
2249 2758 3.056328 GTGAAGGAAGGCACCGGC 61.056 66.667 0.00 0.00 40.13 6.13
2250 2759 1.966451 GTGTGAAGGAAGGCACCGG 60.966 63.158 0.00 0.00 34.19 5.28
2251 2760 1.966451 GGTGTGAAGGAAGGCACCG 60.966 63.158 0.00 0.00 41.37 4.94


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

AutoCloner maintained by Alex Coulton.