Multiple sequence alignment - TraesCS5A01G104100

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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 TraesCS5A01G104100 chr5A 100.000 2291 0 0 1 2291 167118407 167116117 0.000000e+00 4231.0
1 TraesCS5A01G104100 chr5A 99.451 182 1 0 598 779 167116578 167116759 4.720000e-87 331.0
2 TraesCS5A01G104100 chr5A 98.919 185 2 0 1646 1830 167117626 167117810 4.720000e-87 331.0
3 TraesCS5A01G104100 chr5A 100.000 36 0 0 1619 1654 167116547 167116512 1.470000e-07 67.6
4 TraesCS5A01G104100 chr5A 100.000 36 0 0 1861 1896 167116789 167116754 1.470000e-07 67.6
5 TraesCS5A01G104100 chr5B 94.626 1619 64 5 57 1654 173858166 173856550 0.000000e+00 2486.0
6 TraesCS5A01G104100 chr5B 94.090 423 18 3 1874 2291 173856572 173856152 8.930000e-179 636.0
7 TraesCS5A01G104100 chr5B 94.737 190 10 0 1646 1835 173857425 173857614 1.720000e-76 296.0
8 TraesCS5A01G104100 chr5D 94.097 847 34 1 1 831 174827037 174827883 0.000000e+00 1273.0
9 TraesCS5A01G104100 chr5D 93.586 764 23 12 774 1537 174827943 174828680 0.000000e+00 1116.0
10 TraesCS5A01G104100 chr5D 92.689 383 20 4 1908 2288 174828683 174829059 1.550000e-151 545.0
11 TraesCS5A01G104100 chr5D 95.699 186 8 0 1649 1834 174827831 174827646 1.330000e-77 300.0
12 TraesCS5A01G104100 chr5D 91.379 58 5 0 774 831 174827865 174827922 1.890000e-11 80.5
13 TraesCS5A01G104100 chr2A 82.000 150 18 9 432 577 778370277 778370421 4.000000e-23 119.0
14 TraesCS5A01G104100 chr7B 81.208 149 21 5 432 577 718078482 718078338 1.860000e-21 113.0
15 TraesCS5A01G104100 chr6A 81.333 150 19 9 432 577 531100460 531100604 1.860000e-21 113.0


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 TraesCS5A01G104100 chr5A 167116117 167118407 2290 True 1455.400 4231 100.00000 1 2291 3 chr5A.!!$R1 2290
1 TraesCS5A01G104100 chr5A 167116578 167117810 1232 False 331.000 331 99.18500 598 1830 2 chr5A.!!$F1 1232
2 TraesCS5A01G104100 chr5B 173856152 173858166 2014 True 1561.000 2486 94.35800 57 2291 2 chr5B.!!$R1 2234
3 TraesCS5A01G104100 chr5D 174827037 174829059 2022 False 753.625 1273 92.93775 1 2288 4 chr5D.!!$F1 2287

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
370 371 1.001974 TCAACCCTCACCATGAACGAG 59.998 52.381 0.0 0.0 0.0 4.18 F
1147 1282 1.084370 GGTTCATGCGACGGAGAAGG 61.084 60.000 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1362 1.555075 TCTGGAGGGTTCAGTATGCAC 59.445 52.381 0.0 0.0 34.76 4.57 R
2248 3101 5.546621 AAAGGTGTCTTACTTGAGCACTA 57.453 39.130 0.0 0.0 32.01 2.74 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
24 25 3.629087 AGCAATTGAAGGAGGATTCCAG 58.371 45.455 10.34 0.00 46.64 3.86
36 37 4.202305 GGAGGATTCCAGGTCATAGTCAAG 60.202 50.000 5.29 0.00 43.45 3.02
86 87 5.965922 ACCAAATAGCTCCAAACATAAAGC 58.034 37.500 0.00 0.00 34.95 3.51
370 371 1.001974 TCAACCCTCACCATGAACGAG 59.998 52.381 0.00 0.00 0.00 4.18
459 460 3.953612 TCACAAAGTGAACAAGCAGGAAT 59.046 39.130 0.00 0.00 39.78 3.01
470 471 6.436847 TGAACAAGCAGGAATATTCATGGAAA 59.563 34.615 26.44 4.37 39.22 3.13
498 499 6.035843 TCACTTCACAATGAAAACTCAAAGC 58.964 36.000 0.00 0.00 35.73 3.51
499 500 5.806502 CACTTCACAATGAAAACTCAAAGCA 59.193 36.000 0.00 0.00 35.73 3.91
513 514 6.720112 ACTCAAAGCAAATGCCACATATAT 57.280 33.333 0.94 0.00 43.38 0.86
526 527 4.755123 GCCACATATATACCAGACCACAAC 59.245 45.833 0.00 0.00 0.00 3.32
548 549 6.560253 ACCAGTATAACACAAGAAGCAAAG 57.440 37.500 0.00 0.00 0.00 2.77
861 995 2.023888 ACAGACCAGTATCAGGTAGCCT 60.024 50.000 0.00 0.00 40.09 4.58
1147 1282 1.084370 GGTTCATGCGACGGAGAAGG 61.084 60.000 0.00 0.00 0.00 3.46
1177 1312 1.210967 TCAAAGATACGGCGGGGATTT 59.789 47.619 13.24 4.16 0.00 2.17
1216 1351 2.455674 AGTGTCTTGCAGCATTACGA 57.544 45.000 0.00 0.00 0.00 3.43
1227 1362 2.543012 CAGCATTACGAATCCTGCTCAG 59.457 50.000 0.00 0.00 42.79 3.35
1273 1408 1.473965 CGCTTGCACCTCAGTCCATAT 60.474 52.381 0.00 0.00 0.00 1.78
1279 1414 2.826428 CACCTCAGTCCATATTCACCG 58.174 52.381 0.00 0.00 0.00 4.94
1479 1618 1.136828 AGTGCCAGGTACAAAGTGGA 58.863 50.000 10.72 0.00 32.60 4.02
1553 1692 2.878406 ACATTCACAAGTTTCTGGTCGG 59.122 45.455 0.00 0.00 0.00 4.79
1557 1696 3.138304 TCACAAGTTTCTGGTCGGAATG 58.862 45.455 0.00 0.00 0.00 2.67
1832 2684 9.991906 TTGGTAGGTTGTATATCTTGCTAATAC 57.008 33.333 0.00 0.00 0.00 1.89
1833 2685 8.591072 TGGTAGGTTGTATATCTTGCTAATACC 58.409 37.037 0.00 0.00 0.00 2.73
1834 2686 8.813951 GGTAGGTTGTATATCTTGCTAATACCT 58.186 37.037 0.00 0.00 36.36 3.08
1835 2687 9.640963 GTAGGTTGTATATCTTGCTAATACCTG 57.359 37.037 0.00 0.00 34.39 4.00
1836 2688 8.263854 AGGTTGTATATCTTGCTAATACCTGT 57.736 34.615 0.00 0.00 31.48 4.00
1837 2689 8.714906 AGGTTGTATATCTTGCTAATACCTGTT 58.285 33.333 0.00 0.00 31.48 3.16
1838 2690 9.338622 GGTTGTATATCTTGCTAATACCTGTTT 57.661 33.333 0.00 0.00 0.00 2.83
1850 2702 9.674068 TGCTAATACCTGTTTATATGTTGAACA 57.326 29.630 0.00 0.00 0.00 3.18
1857 2709 9.077885 ACCTGTTTATATGTTGAACAAAGATGT 57.922 29.630 0.62 0.00 43.14 3.06
2006 2858 7.418337 TTTCTGTGACTATTCTAGTGGCATA 57.582 36.000 0.00 0.00 39.59 3.14
2007 2859 6.641169 TCTGTGACTATTCTAGTGGCATAG 57.359 41.667 0.00 0.00 39.59 2.23
2066 2919 5.657302 ACCAGTAACAGTAGGAGGTGAATAG 59.343 44.000 0.00 0.00 0.00 1.73
2128 2981 1.490490 TCGGCTGGCCTGATTCTAAAT 59.510 47.619 14.77 0.00 0.00 1.40
2219 3072 1.729472 CGAGACTACCAACTGAGCGTG 60.729 57.143 0.00 0.00 0.00 5.34
2248 3101 5.931146 CAGAGCTGAGAGTAAACAAATGTCT 59.069 40.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.734720 TGTTCTTGACTATGACCTGGAATC 58.265 41.667 0.00 0.00 0.00 2.52
307 308 1.691976 TCACTGACAAGTCCATTCGGT 59.308 47.619 0.00 0.00 32.98 4.69
370 371 0.815615 GGCAGATCGTCAATGTCCCC 60.816 60.000 0.00 0.00 0.00 4.81
490 491 6.720112 ATATATGTGGCATTTGCTTTGAGT 57.280 33.333 2.12 0.00 41.70 3.41
498 499 6.003326 TGGTCTGGTATATATGTGGCATTTG 58.997 40.000 0.00 0.00 0.00 2.32
499 500 6.003950 GTGGTCTGGTATATATGTGGCATTT 58.996 40.000 0.00 0.00 0.00 2.32
513 514 4.839550 TGTTATACTGGTTGTGGTCTGGTA 59.160 41.667 0.00 0.00 0.00 3.25
526 527 6.428159 AGTCTTTGCTTCTTGTGTTATACTGG 59.572 38.462 0.00 0.00 0.00 4.00
861 995 7.569639 TGGTTTGCACTAGTTGTTTAATACA 57.430 32.000 0.00 0.00 34.12 2.29
862 996 9.471084 AAATGGTTTGCACTAGTTGTTTAATAC 57.529 29.630 0.00 0.00 0.00 1.89
1177 1312 3.181451 ACTTGCTCACACTGGATGAGAAA 60.181 43.478 12.89 8.56 45.46 2.52
1227 1362 1.555075 TCTGGAGGGTTCAGTATGCAC 59.445 52.381 0.00 0.00 34.76 4.57
1273 1408 2.367567 AGAACTAAAGCTGGTCGGTGAA 59.632 45.455 0.00 0.00 0.00 3.18
1279 1414 3.338249 TGATGCAGAACTAAAGCTGGTC 58.662 45.455 0.00 0.00 32.83 4.02
1479 1618 3.201930 TGGACATAGTGGCATATGTGGTT 59.798 43.478 20.02 3.70 44.47 3.67
1831 2683 9.077885 ACATCTTTGTTCAACATATAAACAGGT 57.922 29.630 0.00 0.00 34.64 4.00
1832 2684 9.912634 AACATCTTTGTTCAACATATAAACAGG 57.087 29.630 0.00 0.00 42.43 4.00
1841 2693 9.414295 CATGTATTCAACATCTTTGTTCAACAT 57.586 29.630 0.00 0.00 46.15 2.71
1842 2694 7.381948 GCATGTATTCAACATCTTTGTTCAACA 59.618 33.333 0.00 0.00 46.15 3.33
1843 2695 7.381948 TGCATGTATTCAACATCTTTGTTCAAC 59.618 33.333 0.00 0.00 46.15 3.18
1844 2696 7.432059 TGCATGTATTCAACATCTTTGTTCAA 58.568 30.769 0.00 0.00 46.15 2.69
1845 2697 6.979465 TGCATGTATTCAACATCTTTGTTCA 58.021 32.000 0.00 0.00 46.15 3.18
1846 2698 9.740239 ATATGCATGTATTCAACATCTTTGTTC 57.260 29.630 10.16 0.00 46.15 3.18
1855 2707 9.394767 ACAAGAGTTATATGCATGTATTCAACA 57.605 29.630 10.16 0.00 43.86 3.33
2006 2858 9.740710 GGGAGCTTTGAATTTGGTATATATACT 57.259 33.333 19.78 2.55 33.81 2.12
2007 2859 9.515226 TGGGAGCTTTGAATTTGGTATATATAC 57.485 33.333 13.60 13.60 0.00 1.47
2248 3101 5.546621 AAAGGTGTCTTACTTGAGCACTA 57.453 39.130 0.00 0.00 32.01 2.74


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

AutoCloner maintained by Alex Coulton.