Multiple sequence alignment - TraesCS5A01G194700

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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 TraesCS5A01G194700 chr5A 100.000 2757 0 0 1 2757 398268345 398271101 0.000000e+00 5092
1 TraesCS5A01G194700 chr5D 94.442 1979 76 13 783 2757 301101221 301103169 0.000000e+00 3014
2 TraesCS5A01G194700 chr5D 89.809 471 17 15 17 459 300936578 300936111 2.380000e-160 575
3 TraesCS5A01G194700 chr5D 86.392 485 27 18 17 472 301099334 301099808 6.860000e-136 494
4 TraesCS5A01G194700 chr5B 93.168 1127 60 11 1633 2757 344298003 344299114 0.000000e+00 1639
5 TraesCS5A01G194700 chr5B 92.254 865 28 8 771 1635 344297114 344297939 0.000000e+00 1190
6 TraesCS5A01G194700 chr5B 86.151 491 36 14 17 477 344296053 344296541 4.100000e-138 501
7 TraesCS5A01G194700 chr5B 88.889 216 8 6 575 781 344296885 344297093 4.560000e-63 252
8 TraesCS5A01G194700 chr5B 90.000 120 8 1 467 582 344296744 344296863 4.760000e-33 152


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 TraesCS5A01G194700 chr5A 398268345 398271101 2756 False 5092.0 5092 100.0000 1 2757 1 chr5A.!!$F1 2756
1 TraesCS5A01G194700 chr5D 301099334 301103169 3835 False 1754.0 3014 90.4170 17 2757 2 chr5D.!!$F1 2740
2 TraesCS5A01G194700 chr5B 344296053 344299114 3061 False 746.8 1639 90.0924 17 2757 5 chr5B.!!$F1 2740

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
528 781 0.036294 AAGCGGGGTAAGAGCTGTTC 60.036 55.0 0.0 0.0 41.53 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 3371 0.398318 AAAGTCTCAGGAGGCACACC 59.602 55.0 3.47 0.0 40.21 4.16 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
147 149 2.006062 CGACGATGAGGACGATGCG 61.006 63.158 0.00 0.00 34.70 4.73
199 201 3.252215 TGTGGCAGTTTTAACCGATGAAG 59.748 43.478 0.00 0.00 0.00 3.02
234 262 3.561120 TTCCCTCGCGTGGCCAATT 62.561 57.895 21.51 0.00 0.00 2.32
241 269 1.582610 CGCGTGGCCAATTGGTAAGT 61.583 55.000 25.19 0.00 37.57 2.24
246 274 1.072489 TGGCCAATTGGTAAGTCGACA 59.928 47.619 25.19 3.12 37.57 4.35
253 282 0.973632 TGGTAAGTCGACACATGCCT 59.026 50.000 19.50 0.00 28.14 4.75
266 295 0.518636 CATGCCTGTGTGGTTTCGAG 59.481 55.000 0.00 0.00 38.35 4.04
274 303 0.250124 TGTGGTTTCGAGTTCGGCAT 60.250 50.000 1.26 0.00 40.29 4.40
282 311 1.134818 TCGAGTTCGGCATTGCTACAT 60.135 47.619 8.82 0.00 40.29 2.29
300 329 4.607293 ACATCACACCGATAGCATGTAT 57.393 40.909 0.00 0.00 33.28 2.29
310 339 4.177026 CGATAGCATGTATGTAGCCTTCC 58.823 47.826 0.00 0.00 0.00 3.46
347 376 4.821805 CCAGTATGTGGTTCATATGGTTCC 59.178 45.833 2.13 4.10 42.17 3.62
396 425 2.085320 GGCATCATTTTGCATTTGCCA 58.915 42.857 13.74 0.00 46.87 4.92
426 455 1.624813 CCATGCCCCTTGTCAAAATGT 59.375 47.619 0.00 0.00 0.00 2.71
435 464 5.534654 CCCCTTGTCAAAATGTAGACTCAAA 59.465 40.000 0.00 0.00 35.81 2.69
436 465 6.438763 CCCTTGTCAAAATGTAGACTCAAAC 58.561 40.000 0.00 0.00 35.81 2.93
437 466 6.039270 CCCTTGTCAAAATGTAGACTCAAACA 59.961 38.462 0.00 0.00 35.81 2.83
444 473 7.973388 TCAAAATGTAGACTCAAACAAGGTTTG 59.027 33.333 14.05 14.05 32.67 2.93
478 727 0.934496 CAAGCTGGTGTTTCGTTCGA 59.066 50.000 0.00 0.00 0.00 3.71
483 732 1.146957 TGGTGTTTCGTTCGACCGTG 61.147 55.000 1.29 0.00 0.00 4.94
518 771 5.163281 TGTTTTATCTGTAAAGCGGGGTA 57.837 39.130 0.00 0.00 34.77 3.69
528 781 0.036294 AAGCGGGGTAAGAGCTGTTC 60.036 55.000 0.00 0.00 41.53 3.18
531 784 1.601419 CGGGGTAAGAGCTGTTCCGA 61.601 60.000 14.80 0.00 38.42 4.55
535 788 2.093106 GGTAAGAGCTGTTCCGAGAGA 58.907 52.381 0.00 0.00 0.00 3.10
620 907 5.869579 ACCTATCTATGGATTGCAACGAAT 58.130 37.500 0.00 0.00 33.71 3.34
649 936 2.009774 AGATCAAAAATCTCACGCGGG 58.990 47.619 12.47 6.51 0.00 6.13
650 937 1.064060 GATCAAAAATCTCACGCGGGG 59.936 52.381 9.32 0.00 0.00 5.73
655 945 2.188062 AAATCTCACGCGGGGTTTTA 57.812 45.000 9.32 0.00 0.00 1.52
712 1009 7.446931 ACATACATCAACTCAATGTACCACAAA 59.553 33.333 0.00 0.00 41.15 2.83
715 1012 6.017109 ACATCAACTCAATGTACCACAAAGTC 60.017 38.462 0.00 0.00 35.62 3.01
727 1024 4.761975 ACCACAAAGTCTTACGTTTCTCA 58.238 39.130 0.00 0.00 0.00 3.27
807 2139 1.805428 GCCTGAACAATGGCCGTGTT 61.805 55.000 21.19 21.19 43.11 3.32
812 2144 2.088423 GAACAATGGCCGTGTTATCCA 58.912 47.619 21.11 0.00 39.29 3.41
838 2170 2.157834 TGGCACAAAATACGTCTCGT 57.842 45.000 0.00 0.00 38.88 4.18
891 2228 1.077005 TGCTTTACCATTTCAGCCCCT 59.923 47.619 0.00 0.00 0.00 4.79
913 2250 0.603975 GCTTCCCTCGCTTTGTGAGT 60.604 55.000 7.26 0.00 38.37 3.41
921 2258 2.210116 TCGCTTTGTGAGTGAGTTTCC 58.790 47.619 0.00 0.00 39.89 3.13
922 2259 1.264288 CGCTTTGTGAGTGAGTTTCCC 59.736 52.381 0.00 0.00 38.15 3.97
923 2260 2.576615 GCTTTGTGAGTGAGTTTCCCT 58.423 47.619 0.00 0.00 0.00 4.20
924 2261 2.550180 GCTTTGTGAGTGAGTTTCCCTC 59.450 50.000 0.00 0.00 40.89 4.30
930 2267 0.547954 AGTGAGTTTCCCTCCCCTCC 60.548 60.000 0.00 0.00 39.65 4.30
931 2268 1.229853 TGAGTTTCCCTCCCCTCCC 60.230 63.158 0.00 0.00 39.65 4.30
1364 2701 2.248835 CGTTCGTGAACCCACCCAC 61.249 63.158 7.13 0.00 40.12 4.61
1489 2826 1.874562 CTGAACAAGCTGGCTCTGC 59.125 57.895 0.00 0.00 0.00 4.26
1516 2853 1.403814 CGAGGGCTGAATGAGTAGGA 58.596 55.000 0.00 0.00 0.00 2.94
1646 3049 0.816825 AGCAGGTAGGATGCAATGCG 60.817 55.000 0.00 0.00 46.31 4.73
1753 3156 8.458843 CAGTTTATTTCGGGTGATAAAATGTCT 58.541 33.333 7.65 0.00 38.23 3.41
1851 3254 1.418908 AAGTCAGGGGAGTGTGTGGG 61.419 60.000 0.00 0.00 0.00 4.61
1958 3362 7.287810 TCTAGTATAGATAGACTTGTGTGCCA 58.712 38.462 0.00 0.00 44.15 4.92
1966 3370 3.424703 AGACTTGTGTGCCAAATATGCT 58.575 40.909 0.00 0.00 31.20 3.79
1967 3371 3.192001 AGACTTGTGTGCCAAATATGCTG 59.808 43.478 0.00 0.00 31.20 4.41
1991 3395 2.235898 GTGCCTCCTGAGACTTTCTGAT 59.764 50.000 0.00 0.00 0.00 2.90
2004 3408 4.848757 ACTTTCTGATTTCTTGTTGCGAC 58.151 39.130 0.00 0.00 0.00 5.19
2043 3448 5.068636 AGAGAACATTTTCTGTGCTGTCAT 58.931 37.500 0.00 0.00 44.41 3.06
2229 3634 5.617528 TGTAGGTGGACTTGAAGTTACAA 57.382 39.130 0.00 0.00 0.00 2.41
2279 3684 4.927425 CCTCATTTGTCTCAGCAATTTTGG 59.073 41.667 0.00 0.00 0.00 3.28
2282 3687 3.648339 TTGTCTCAGCAATTTTGGAGC 57.352 42.857 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
1 2 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
2 3 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
3 4 0.477204 ATCATACTCCCTCCGTCCGA 59.523 55.000 0.00 0.00 0.00 4.55
4 5 1.329256 AATCATACTCCCTCCGTCCG 58.671 55.000 0.00 0.00 0.00 4.79
5 6 3.840124 AAAATCATACTCCCTCCGTCC 57.160 47.619 0.00 0.00 0.00 4.79
6 7 5.532664 ACTAAAATCATACTCCCTCCGTC 57.467 43.478 0.00 0.00 0.00 4.79
7 8 6.610425 ACTTACTAAAATCATACTCCCTCCGT 59.390 38.462 0.00 0.00 0.00 4.69
8 9 7.052142 ACTTACTAAAATCATACTCCCTCCG 57.948 40.000 0.00 0.00 0.00 4.63
9 10 7.226918 GCAACTTACTAAAATCATACTCCCTCC 59.773 40.741 0.00 0.00 0.00 4.30
10 11 7.988028 AGCAACTTACTAAAATCATACTCCCTC 59.012 37.037 0.00 0.00 0.00 4.30
11 12 7.862675 AGCAACTTACTAAAATCATACTCCCT 58.137 34.615 0.00 0.00 0.00 4.20
12 13 8.398665 CAAGCAACTTACTAAAATCATACTCCC 58.601 37.037 0.00 0.00 0.00 4.30
13 14 8.398665 CCAAGCAACTTACTAAAATCATACTCC 58.601 37.037 0.00 0.00 0.00 3.85
14 15 8.398665 CCCAAGCAACTTACTAAAATCATACTC 58.601 37.037 0.00 0.00 0.00 2.59
15 16 7.148069 GCCCAAGCAACTTACTAAAATCATACT 60.148 37.037 0.00 0.00 39.53 2.12
147 149 7.064371 CAGAGATATTCATTGGAATCATCGTCC 59.936 40.741 0.00 0.00 42.66 4.79
199 201 0.957888 GAAGAACACTGGCCTGGAGC 60.958 60.000 14.82 0.61 42.60 4.70
234 262 0.973632 AGGCATGTGTCGACTTACCA 59.026 50.000 17.92 8.53 0.00 3.25
246 274 0.179032 TCGAAACCACACAGGCATGT 60.179 50.000 0.00 0.00 43.14 3.21
253 282 1.155424 GCCGAACTCGAAACCACACA 61.155 55.000 0.00 0.00 43.02 3.72
266 295 1.737236 TGTGATGTAGCAATGCCGAAC 59.263 47.619 0.00 0.00 0.00 3.95
274 303 2.167487 TGCTATCGGTGTGATGTAGCAA 59.833 45.455 3.17 0.00 42.77 3.91
282 311 4.558697 GCTACATACATGCTATCGGTGTGA 60.559 45.833 0.00 0.00 0.00 3.58
344 373 3.591527 ACATCCTCATTGGTGGTAAGGAA 59.408 43.478 0.00 0.00 39.47 3.36
346 375 3.652057 ACATCCTCATTGGTGGTAAGG 57.348 47.619 0.00 0.00 37.07 2.69
347 376 5.745227 AGTTACATCCTCATTGGTGGTAAG 58.255 41.667 0.00 0.00 36.70 2.34
401 430 1.379044 GACAAGGGGCATGGAGGTG 60.379 63.158 0.00 0.00 0.00 4.00
426 455 5.036117 AGAGCAAACCTTGTTTGAGTCTA 57.964 39.130 20.53 0.00 0.00 2.59
435 464 4.399303 GCCATATGTTAGAGCAAACCTTGT 59.601 41.667 1.24 0.00 0.00 3.16
436 465 4.202050 GGCCATATGTTAGAGCAAACCTTG 60.202 45.833 0.00 0.00 0.00 3.61
437 466 3.954258 GGCCATATGTTAGAGCAAACCTT 59.046 43.478 0.00 0.00 0.00 3.50
444 473 2.551459 CAGCTTGGCCATATGTTAGAGC 59.449 50.000 6.09 10.38 0.00 4.09
478 727 3.202829 ACATGAACCAAAGTACACGGT 57.797 42.857 0.00 0.00 33.32 4.83
518 771 0.892063 GGTCTCTCGGAACAGCTCTT 59.108 55.000 0.00 0.00 0.00 2.85
528 781 9.982651 TTCTAAGATATTTTTATGGTCTCTCGG 57.017 33.333 0.00 0.00 0.00 4.63
569 822 7.175816 TCCTTACAATTTGCTTGCACTACATTA 59.824 33.333 0.00 0.00 38.50 1.90
620 907 7.287950 CGTGAGATTTTTGATCTGTCGTTTTA 58.712 34.615 0.00 0.00 0.00 1.52
727 1024 3.236618 GAGCGCGCCTTTCAAACGT 62.237 57.895 30.33 4.23 0.00 3.99
807 2139 6.038161 CGTATTTTGTGCCAAAGAGATGGATA 59.962 38.462 0.00 0.00 43.54 2.59
812 2144 5.003804 AGACGTATTTTGTGCCAAAGAGAT 58.996 37.500 0.00 0.00 0.00 2.75
853 2188 1.028868 CACTAAAGCTCAGCCCAGCC 61.029 60.000 0.00 0.00 40.65 4.85
854 2189 1.652167 GCACTAAAGCTCAGCCCAGC 61.652 60.000 0.00 0.00 39.99 4.85
855 2190 0.035630 AGCACTAAAGCTCAGCCCAG 60.036 55.000 0.00 0.00 42.18 4.45
856 2191 0.401738 AAGCACTAAAGCTCAGCCCA 59.598 50.000 0.00 0.00 45.89 5.36
857 2192 1.539157 AAAGCACTAAAGCTCAGCCC 58.461 50.000 0.00 0.00 45.89 5.19
858 2193 2.420372 GGTAAAGCACTAAAGCTCAGCC 59.580 50.000 0.00 0.00 45.89 4.85
859 2194 3.074412 TGGTAAAGCACTAAAGCTCAGC 58.926 45.455 0.00 0.00 45.89 4.26
860 2195 5.886960 AATGGTAAAGCACTAAAGCTCAG 57.113 39.130 0.00 0.00 45.89 3.35
861 2196 5.767665 TGAAATGGTAAAGCACTAAAGCTCA 59.232 36.000 0.00 0.00 45.89 4.26
862 2197 6.254281 TGAAATGGTAAAGCACTAAAGCTC 57.746 37.500 0.00 0.00 45.89 4.09
891 2228 0.603707 CACAAAGCGAGGGAAGCAGA 60.604 55.000 0.00 0.00 37.01 4.26
919 2256 2.543637 AAGAGGGGAGGGGAGGGA 60.544 66.667 0.00 0.00 0.00 4.20
920 2257 2.040359 GAAGAGGGGAGGGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
921 2258 1.074850 GAGAAGAGGGGAGGGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
922 2259 1.074850 GGAGAAGAGGGGAGGGGAG 60.075 68.421 0.00 0.00 0.00 4.30
923 2260 2.647949 GGGAGAAGAGGGGAGGGGA 61.648 68.421 0.00 0.00 0.00 4.81
924 2261 2.040359 GGGAGAAGAGGGGAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
930 2267 2.122167 CGAGACGGGGAGAAGAGGG 61.122 68.421 0.00 0.00 0.00 4.30
931 2268 0.680280 TTCGAGACGGGGAGAAGAGG 60.680 60.000 0.00 0.00 0.00 3.69
1508 2845 2.472695 ACAAAAGCGCATCCTACTCA 57.527 45.000 11.47 0.00 0.00 3.41
1509 2846 3.492313 CAAACAAAAGCGCATCCTACTC 58.508 45.455 11.47 0.00 0.00 2.59
1516 2853 1.067516 ACTCTGCAAACAAAAGCGCAT 59.932 42.857 11.47 0.00 33.15 4.73
1646 3049 6.690194 ATGGAAAACACTTATCAGAGATGC 57.310 37.500 0.00 0.00 0.00 3.91
1684 3087 3.635373 TGGTTACTAACTAGCATCTCCGG 59.365 47.826 0.00 0.00 0.00 5.14
1753 3156 9.689976 AACATTTTAATTCACACGATGATTCAA 57.310 25.926 0.00 0.00 37.11 2.69
1951 3355 1.545582 ACACCAGCATATTTGGCACAC 59.454 47.619 3.41 0.00 39.29 3.82
1958 3362 1.285962 AGGAGGCACACCAGCATATTT 59.714 47.619 0.00 0.00 43.22 1.40
1966 3370 0.764369 AAGTCTCAGGAGGCACACCA 60.764 55.000 3.47 0.00 43.22 4.17
1967 3371 0.398318 AAAGTCTCAGGAGGCACACC 59.602 55.000 3.47 0.00 40.21 4.16
1991 3395 9.607285 GATTTTTCTATAAGTCGCAACAAGAAA 57.393 29.630 0.00 0.00 31.58 2.52
2034 3439 3.254166 ACACATCCTTTCAATGACAGCAC 59.746 43.478 0.00 0.00 0.00 4.40
2043 3448 5.068855 TCAATGCAGAAACACATCCTTTCAA 59.931 36.000 0.00 0.00 31.12 2.69
2229 3634 6.499699 TCTCACTATGATATGCTGGAAGGATT 59.500 38.462 0.00 0.00 45.52 3.01
2279 3684 7.426929 TCTGATTTACTCTTGTCAAAAGCTC 57.573 36.000 0.00 0.00 0.00 4.09
2282 3687 7.080724 GGCTTCTGATTTACTCTTGTCAAAAG 58.919 38.462 0.00 0.00 0.00 2.27
2488 3893 6.006449 ACTTCTACAAAAGGATGCACATTCT 58.994 36.000 0.00 0.00 0.00 2.40
2622 4027 3.745975 TGTCCATTAAGAACTGAGCGTTG 59.254 43.478 0.00 0.00 35.56 4.10


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

AutoCloner maintained by Alex Coulton.