Multiple sequence alignment - TraesCS5D01G345100

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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 TraesCS5D01G345100 chr5D 100.000 2372 0 0 1 2372 432335799 432338170 0 4381
1 TraesCS5D01G345100 chr5D 96.547 2375 78 4 1 2372 503245467 503247840 0 3928
2 TraesCS5D01G345100 chr5D 96.546 2374 78 4 2 2372 503264580 503262208 0 3927
3 TraesCS5D01G345100 chr3A 96.716 2375 74 4 1 2372 66004938 66002565 0 3951
4 TraesCS5D01G345100 chr6D 96.547 2375 78 4 1 2372 389245627 389243254 0 3928
5 TraesCS5D01G345100 chr2A 96.505 2375 79 4 1 2372 726906260 726903887 0 3923
6 TraesCS5D01G345100 chr2D 96.463 2375 80 4 1 2372 591984804 591987177 0 3917
7 TraesCS5D01G345100 chr3D 96.463 2375 79 5 1 2372 589263331 589260959 0 3916
8 TraesCS5D01G345100 chr7B 96.168 2375 87 4 1 2372 663099230 663096857 0 3879


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 TraesCS5D01G345100 chr5D 432335799 432338170 2371 False 4381 4381 100.000 1 2372 1 chr5D.!!$F1 2371
1 TraesCS5D01G345100 chr5D 503245467 503247840 2373 False 3928 3928 96.547 1 2372 1 chr5D.!!$F2 2371
2 TraesCS5D01G345100 chr5D 503262208 503264580 2372 True 3927 3927 96.546 2 2372 1 chr5D.!!$R1 2370
3 TraesCS5D01G345100 chr3A 66002565 66004938 2373 True 3951 3951 96.716 1 2372 1 chr3A.!!$R1 2371
4 TraesCS5D01G345100 chr6D 389243254 389245627 2373 True 3928 3928 96.547 1 2372 1 chr6D.!!$R1 2371
5 TraesCS5D01G345100 chr2A 726903887 726906260 2373 True 3923 3923 96.505 1 2372 1 chr2A.!!$R1 2371
6 TraesCS5D01G345100 chr2D 591984804 591987177 2373 False 3917 3917 96.463 1 2372 1 chr2D.!!$F1 2371
7 TraesCS5D01G345100 chr3D 589260959 589263331 2372 True 3916 3916 96.463 1 2372 1 chr3D.!!$R1 2371
8 TraesCS5D01G345100 chr7B 663096857 663099230 2373 True 3879 3879 96.168 1 2372 1 chr7B.!!$R1 2371

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
379 381 0.331616 GGTAGGATGGGCACTTGGTT 59.668 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 1596 0.03601 AGGTGGTCCTTGCTGATTCG 60.036 55.0 0.0 0.0 42.12 3.34 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
67 68 1.001764 TTCACGGGCGAGGTCTCTA 60.002 57.895 0.00 0.00 0.00 2.43
198 200 1.626321 TCCGCTCTTACAATTGGGTCA 59.374 47.619 10.83 0.00 0.00 4.02
249 251 3.442625 TCCAGGCGGTAATGATAGTATCG 59.557 47.826 5.68 0.00 0.00 2.92
261 263 7.584122 AATGATAGTATCGTGTACCTGAACT 57.416 36.000 5.62 0.00 0.00 3.01
270 272 0.389948 GTACCTGAACTGGTGGCTCG 60.390 60.000 12.44 0.00 41.05 5.03
281 283 2.552315 CTGGTGGCTCGCTTTTTCTAAA 59.448 45.455 0.00 0.00 0.00 1.85
373 375 0.399233 AGAGGAGGTAGGATGGGCAC 60.399 60.000 0.00 0.00 0.00 5.01
379 381 0.331616 GGTAGGATGGGCACTTGGTT 59.668 55.000 0.00 0.00 0.00 3.67
405 407 7.575414 GATCTAGTATGGATCGTACATGGAT 57.425 40.000 0.00 8.34 43.25 3.41
418 420 5.362717 TCGTACATGGATGATAGTTGGAGTT 59.637 40.000 0.00 0.00 0.00 3.01
445 447 1.575788 TCTCCTAGGCTTCCCTCATCA 59.424 52.381 2.96 0.00 41.75 3.07
569 571 1.265454 GGACCGACCCCATTGTCTCT 61.265 60.000 0.00 0.00 32.97 3.10
574 576 1.880941 GACCCCATTGTCTCTACCCT 58.119 55.000 0.00 0.00 32.39 4.34
602 604 2.320781 CTACGAGATCACCCCAAGGAT 58.679 52.381 0.00 0.00 36.73 3.24
740 743 8.879759 CGTTCTTAAACCAGCATTCTTAAGATA 58.120 33.333 5.89 0.00 39.11 1.98
765 769 2.033602 CGGCGGAAAAAGGGGAGT 59.966 61.111 0.00 0.00 0.00 3.85
916 920 5.277297 CGATGAAAGTTGTAAGCTGTGTTCA 60.277 40.000 0.00 0.00 0.00 3.18
922 926 0.960861 GTAAGCTGTGTTCAGGGGGC 60.961 60.000 0.00 0.00 41.57 5.80
944 948 3.551046 CGAGTTATTGTCTATCGCTGGCT 60.551 47.826 0.00 0.00 0.00 4.75
1007 1011 2.665000 CCTGTGGCGGATGTCAGT 59.335 61.111 0.00 0.00 0.00 3.41
1078 1082 1.730176 CGATAGCACCGAATTTTGCG 58.270 50.000 0.00 0.00 43.87 4.85
1107 1111 4.084849 GGCAGTTCGATCTATGATTTCACG 60.085 45.833 0.00 0.00 0.00 4.35
1161 1165 2.694397 AGCACCTTAGGATGGCATAGA 58.306 47.619 4.77 0.00 0.00 1.98
1226 1230 2.493687 GGATACCTAGGCACCCAGAGAT 60.494 54.545 9.30 0.00 0.00 2.75
1258 1262 0.457853 AGCGAGCGACGAAATGCTTA 60.458 50.000 0.00 0.00 42.60 3.09
1299 1303 3.778954 AGATCCGGAGATTCCCAAATC 57.221 47.619 11.34 0.00 41.43 2.17
1376 1380 4.865365 GCGAACTGAAACATCTTAGTAGCT 59.135 41.667 0.00 0.00 0.00 3.32
1397 1401 9.004717 GTAGCTAGAGGAAAAGAAATCAAAAGT 57.995 33.333 0.00 0.00 0.00 2.66
1447 1451 1.464997 GAGCAGCCTAAACCGTGAAAG 59.535 52.381 0.00 0.00 0.00 2.62
1448 1452 1.202770 AGCAGCCTAAACCGTGAAAGT 60.203 47.619 0.00 0.00 0.00 2.66
1588 1592 2.308722 ATGGGGCACGTGGAATCCT 61.309 57.895 18.88 0.00 0.00 3.24
1592 1596 2.870372 GCACGTGGAATCCTGTGC 59.130 61.111 25.69 25.69 44.24 4.57
1637 1641 3.460825 AGGCTAAATACTCCTGGGTGAA 58.539 45.455 0.00 0.00 0.00 3.18
1655 1659 4.034975 GGTGAACGATAGCGAAGTAGTACT 59.965 45.833 7.69 0.00 41.64 2.73
1667 1671 4.217983 CGAAGTAGTACTGTGAGGGAAAGT 59.782 45.833 5.39 0.00 0.00 2.66
1687 1691 0.469144 TGAAAAGAACCCCCAGTGGC 60.469 55.000 2.61 0.00 0.00 5.01
1702 1706 4.323485 CCCAGTGGCTAGTGAAATAGAACA 60.323 45.833 6.45 0.00 0.00 3.18
1707 1711 6.595716 AGTGGCTAGTGAAATAGAACATGAAC 59.404 38.462 0.00 0.00 0.00 3.18
1720 1724 0.957395 CATGAACCCGTGCTGAGCTT 60.957 55.000 5.83 0.00 0.00 3.74
1781 1785 1.745115 TTGAAGAATGAGCCGGCGG 60.745 57.895 24.35 24.35 0.00 6.13
1796 1800 2.903357 CGGCTCATAGGCAGTGGT 59.097 61.111 1.24 0.00 41.44 4.16
1812 1816 2.173143 AGTGGTTTGGTTAAGGGAACGA 59.827 45.455 0.00 0.00 39.12 3.85
1863 1867 6.474140 TTCTTAATAGGGCGATTGTCACTA 57.526 37.500 0.00 0.00 0.00 2.74
1976 1980 2.037902 TCAGCGGATGAGTTGTGGTTAA 59.962 45.455 0.00 0.00 32.77 2.01
2154 2158 2.713828 AAATAACAGGGGCCAAGGTT 57.286 45.000 4.39 8.91 0.00 3.50
2183 2187 2.897969 GAGACGATGGGGGATAAGCTTA 59.102 50.000 8.99 8.99 0.00 3.09
2187 2191 3.910627 ACGATGGGGGATAAGCTTAATCT 59.089 43.478 10.85 0.00 0.00 2.40
2271 2275 2.116125 GGGGGTGCAAAGACAGCT 59.884 61.111 0.00 0.00 38.14 4.24
2357 2361 1.218047 CGCTGAAGATGAACGGGGA 59.782 57.895 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.037441 TCGCCCCTACGATCCAAA 57.963 55.556 0.00 0.00 37.09 3.28
67 68 0.329596 GGCCATCCTGGACTTGAACT 59.670 55.000 0.00 0.00 44.12 3.01
187 189 3.181501 CGTAATCGCAATGACCCAATTGT 60.182 43.478 4.43 0.00 39.33 2.71
198 200 0.393808 AGCCAACCCGTAATCGCAAT 60.394 50.000 0.00 0.00 35.54 3.56
249 251 0.396811 AGCCACCAGTTCAGGTACAC 59.603 55.000 0.00 0.00 40.77 2.90
261 263 2.264005 TTAGAAAAAGCGAGCCACCA 57.736 45.000 0.00 0.00 0.00 4.17
270 272 7.342026 TCCTCTTCCCCATTATTTAGAAAAAGC 59.658 37.037 0.00 0.00 0.00 3.51
281 283 4.540099 TGTTTCAGTCCTCTTCCCCATTAT 59.460 41.667 0.00 0.00 0.00 1.28
373 375 7.455641 ACGATCCATACTAGATCTAACCAAG 57.544 40.000 3.57 0.00 38.39 3.61
379 381 7.858498 TCCATGTACGATCCATACTAGATCTA 58.142 38.462 1.69 1.69 38.39 1.98
405 407 0.392461 GCCGCCAACTCCAACTATCA 60.392 55.000 0.00 0.00 0.00 2.15
418 420 3.984186 AAGCCTAGGAGAGCCGCCA 62.984 63.158 14.75 0.00 39.96 5.69
445 447 1.319799 CTCTTCCCCTGGGATCCCT 59.680 63.158 31.05 0.00 44.74 4.20
454 456 1.918957 CCAACTTGATCCTCTTCCCCT 59.081 52.381 0.00 0.00 0.00 4.79
569 571 4.164796 TGATCTCGTAGTTCCTACAGGGTA 59.835 45.833 0.00 0.00 36.83 3.69
574 576 3.285484 GGGTGATCTCGTAGTTCCTACA 58.715 50.000 0.00 0.00 36.83 2.74
668 670 3.470888 CCCAACCGGAGAGCGGAT 61.471 66.667 9.46 0.00 0.00 4.18
740 743 1.607148 CCTTTTTCCGCCGACTCTTTT 59.393 47.619 0.00 0.00 0.00 2.27
881 885 2.960819 ACTTTCATCGTACTGTGCTCC 58.039 47.619 0.00 0.00 0.00 4.70
916 920 2.170012 TAGACAATAACTCGCCCCCT 57.830 50.000 0.00 0.00 0.00 4.79
922 926 2.726760 GCCAGCGATAGACAATAACTCG 59.273 50.000 0.00 0.00 39.76 4.18
944 948 2.026641 CCGACGGGTTCTACCATAGAA 58.973 52.381 5.81 0.00 41.02 2.10
1007 1011 1.404391 GAGATAAGCGGACTCGAACCA 59.596 52.381 8.65 0.00 39.00 3.67
1078 1082 4.299155 TCATAGATCGAACTGCCGAATTC 58.701 43.478 5.31 0.00 42.22 2.17
1107 1111 5.360591 AGGATCTTATCAACGTCCATGAAC 58.639 41.667 0.00 0.00 0.00 3.18
1161 1165 3.323751 ACCTCGCCATTAACGTTAAGT 57.676 42.857 23.78 12.66 0.00 2.24
1226 1230 2.361992 TCGCTACGCCCTTCCTCA 60.362 61.111 0.00 0.00 0.00 3.86
1242 1246 0.931005 CCCTAAGCATTTCGTCGCTC 59.069 55.000 0.00 0.00 37.54 5.03
1258 1262 6.327386 TCTATGCTTATTTTCAACTCCCCT 57.673 37.500 0.00 0.00 0.00 4.79
1299 1303 2.621526 AGGCAGTTTAAAAGGTTGACCG 59.378 45.455 0.00 0.00 42.08 4.79
1390 1394 4.501071 GCTACTACGGGAATCACTTTTGA 58.499 43.478 0.00 0.00 35.73 2.69
1447 1451 2.034221 GCTCTCCCACAACCCCAC 59.966 66.667 0.00 0.00 0.00 4.61
1448 1452 1.434513 ATTGCTCTCCCACAACCCCA 61.435 55.000 0.00 0.00 0.00 4.96
1556 1560 1.622607 CCCCATGCTACTCGGGTCAA 61.623 60.000 0.00 0.00 38.40 3.18
1588 1592 0.955428 GGTCCTTGCTGATTCGCACA 60.955 55.000 3.27 0.00 40.09 4.57
1592 1596 0.036010 AGGTGGTCCTTGCTGATTCG 60.036 55.000 0.00 0.00 42.12 3.34
1637 1641 4.186926 TCACAGTACTACTTCGCTATCGT 58.813 43.478 0.00 0.00 36.96 3.73
1655 1659 4.401202 GGTTCTTTTCAACTTTCCCTCACA 59.599 41.667 0.00 0.00 0.00 3.58
1667 1671 2.032151 GCCACTGGGGGTTCTTTTCAA 61.032 52.381 0.00 0.00 37.04 2.69
1687 1691 6.036083 CACGGGTTCATGTTCTATTTCACTAG 59.964 42.308 0.00 0.00 0.00 2.57
1702 1706 0.674895 GAAGCTCAGCACGGGTTCAT 60.675 55.000 0.00 0.00 39.05 2.57
1707 1711 2.032528 TTGGAAGCTCAGCACGGG 59.967 61.111 0.00 0.00 0.00 5.28
1736 1740 1.135257 CGCGGTCAGAGATCACTTTCT 60.135 52.381 0.00 0.00 0.00 2.52
1781 1785 1.098050 CCAAACCACTGCCTATGAGC 58.902 55.000 0.00 0.00 0.00 4.26
1796 1800 2.957680 GGGTTTCGTTCCCTTAACCAAA 59.042 45.455 0.00 0.00 41.39 3.28
1812 1816 2.924101 TACGGCTCCGGTGGGTTT 60.924 61.111 13.31 0.00 44.69 3.27
1840 1844 5.353394 AGTGACAATCGCCCTATTAAGAA 57.647 39.130 0.00 0.00 0.00 2.52
1863 1867 0.909623 CCAGGTTCGGGTCCATAAGT 59.090 55.000 0.00 0.00 0.00 2.24
1976 1980 0.400213 TTCGAGTGGCATTTCACCCT 59.600 50.000 0.00 0.00 38.34 4.34
2036 2040 2.419297 CCTAGATGTCCAGTCAACTGCC 60.419 54.545 4.58 0.00 42.47 4.85
2086 2090 0.179145 CTCGATTTGGTACCGCTCGT 60.179 55.000 22.24 3.33 0.00 4.18
2154 2158 2.710902 CCCATCGTCTCACTCGCCA 61.711 63.158 0.00 0.00 0.00 5.69
2158 2162 1.996798 TATCCCCCATCGTCTCACTC 58.003 55.000 0.00 0.00 0.00 3.51
2183 2187 2.355209 GGCTGTTTCCCTCTCGAAGATT 60.355 50.000 0.00 0.00 33.89 2.40
2187 2191 1.677552 GGGCTGTTTCCCTCTCGAA 59.322 57.895 0.00 0.00 43.13 3.71
2271 2275 2.501723 CTGCTTCTAGGCAAACCTCCTA 59.498 50.000 0.00 0.00 46.34 2.94


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

AutoCloner maintained by Alex Coulton.