Multiple sequence alignment - TraesCS2A01G156500

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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 TraesCS2A01G156500 chr2A 100.000 2399 0 0 1 2399 103215269 103217667 0 4431
1 TraesCS2A01G156500 chr2A 95.458 2400 105 4 1 2398 746319240 746316843 0 3825
2 TraesCS2A01G156500 chr2A 95.417 2400 106 4 1 2398 537943050 537940653 0 3819
3 TraesCS2A01G156500 chr6A 96.114 2393 88 5 1 2391 298157863 298155474 0 3899
4 TraesCS2A01G156500 chr5A 95.797 2403 95 4 1 2398 453463417 453465818 0 3873
5 TraesCS2A01G156500 chr3A 95.630 2403 98 5 1 2398 624551968 624554368 0 3849
6 TraesCS2A01G156500 chr3A 95.210 2401 107 6 1 2395 491667261 491669659 0 3790
7 TraesCS2A01G156500 chr7A 95.375 2400 108 3 1 2398 246505120 246507518 0 3814
8 TraesCS2A01G156500 chr7A 95.292 2400 107 4 1 2398 161872834 161875229 0 3801
9 TraesCS2A01G156500 chr4A 95.303 2406 103 9 1 2398 3626352 3628755 0 3808


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 TraesCS2A01G156500 chr2A 103215269 103217667 2398 False 4431 4431 100.000 1 2399 1 chr2A.!!$F1 2398
1 TraesCS2A01G156500 chr2A 746316843 746319240 2397 True 3825 3825 95.458 1 2398 1 chr2A.!!$R2 2397
2 TraesCS2A01G156500 chr2A 537940653 537943050 2397 True 3819 3819 95.417 1 2398 1 chr2A.!!$R1 2397
3 TraesCS2A01G156500 chr6A 298155474 298157863 2389 True 3899 3899 96.114 1 2391 1 chr6A.!!$R1 2390
4 TraesCS2A01G156500 chr5A 453463417 453465818 2401 False 3873 3873 95.797 1 2398 1 chr5A.!!$F1 2397
5 TraesCS2A01G156500 chr3A 624551968 624554368 2400 False 3849 3849 95.630 1 2398 1 chr3A.!!$F2 2397
6 TraesCS2A01G156500 chr3A 491667261 491669659 2398 False 3790 3790 95.210 1 2395 1 chr3A.!!$F1 2394
7 TraesCS2A01G156500 chr7A 246505120 246507518 2398 False 3814 3814 95.375 1 2398 1 chr7A.!!$F2 2397
8 TraesCS2A01G156500 chr7A 161872834 161875229 2395 False 3801 3801 95.292 1 2398 1 chr7A.!!$F1 2397
9 TraesCS2A01G156500 chr4A 3626352 3628755 2403 False 3808 3808 95.303 1 2398 1 chr4A.!!$F1 2397

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
918 927 0.82346 TGACAGCTCACATCGCCATA 59.177 50.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 1955 0.526739 CCACGTGACAGTGTCGACAA 60.527 55.0 21.95 0.23 40.33 3.18 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
170 175 6.094048 CCACCAGCCAAATATGCATATAGTAC 59.906 42.308 19.39 9.98 0.00 2.73
196 201 8.557864 CAGCTGTTTCATTCCATTATTCTCTAG 58.442 37.037 5.25 0.00 0.00 2.43
225 230 2.440517 TGCCAGCATATTCCATGTGT 57.559 45.000 0.00 0.00 0.00 3.72
237 243 1.134068 TCCATGTGTTGACCCGTTTCA 60.134 47.619 0.00 0.00 0.00 2.69
280 286 6.595326 TGCAGACTTTTCAGACGATGATTAAT 59.405 34.615 0.00 0.00 37.89 1.40
300 306 7.571080 TTAATGAGTTTTTAGGTCGTGGTTT 57.429 32.000 0.00 0.00 0.00 3.27
350 356 3.582647 TGGACTCACTTATCTTCCAAGCA 59.417 43.478 0.00 0.00 33.31 3.91
381 388 7.011669 GCTGTTAACGTTATAGATGGCCTTAAA 59.988 37.037 18.79 0.00 0.00 1.52
485 492 3.423539 ACTGTGTGGTGTCAGCATTAT 57.576 42.857 8.18 0.00 35.37 1.28
612 620 6.797454 AGCTAAAGACCTAGAACACTATTCG 58.203 40.000 0.00 0.00 0.00 3.34
669 677 0.836606 TTAGGATGGCGGATGCAAGA 59.163 50.000 0.00 0.00 45.35 3.02
771 779 1.676014 CCAAGCTTCACCGGAACCTAG 60.676 57.143 9.46 0.00 0.00 3.02
849 858 1.002430 ACGTTCATGCCAGTCACTGAT 59.998 47.619 6.30 0.00 32.44 2.90
901 910 3.713003 TGGAGTCTAGGAAAGAGCATGA 58.287 45.455 0.00 0.00 33.88 3.07
918 927 0.823460 TGACAGCTCACATCGCCATA 59.177 50.000 0.00 0.00 0.00 2.74
940 949 2.166664 GGACGCATTGGAGAAGTCTACT 59.833 50.000 0.00 0.00 32.86 2.57
978 987 7.540474 GGATACTATCTACCAGATTTGTGGA 57.460 40.000 0.02 0.00 40.44 4.02
1068 1078 2.157834 TAAACCAGCACATTCGACGT 57.842 45.000 0.00 0.00 0.00 4.34
1080 1090 1.034356 TTCGACGTCAGGAGAACCAA 58.966 50.000 17.16 0.00 38.94 3.67
1133 1143 4.396478 GGCTAAGACAAGAATCAAGGAACC 59.604 45.833 0.00 0.00 0.00 3.62
1423 1433 6.075949 AGACCACCTCATCAGTAGTAGTAA 57.924 41.667 0.00 0.00 0.00 2.24
1565 1576 7.018249 TGTTTTCTCTTTAGACCCCCTCTATTT 59.982 37.037 0.00 0.00 31.11 1.40
1633 1645 2.158871 CCCGGATTTACCTTTCCATCGA 60.159 50.000 0.73 0.00 36.31 3.59
1707 1719 5.198965 CAGAATCAGAATCAGGGGAACAAT 58.801 41.667 0.00 0.00 0.00 2.71
1757 1772 3.410631 TGATCACTTAGCCCGTTTTCA 57.589 42.857 0.00 0.00 0.00 2.69
1890 1905 1.068333 GTGAAGTTTGCCGCACATCAT 60.068 47.619 0.00 0.00 0.00 2.45
1940 1955 3.823304 GAGAATTTCACAGCCACTTTCCT 59.177 43.478 0.00 0.00 0.00 3.36
2268 2283 5.973565 GCAGCAGCAAATTAAGAATCGTAAT 59.026 36.000 0.00 0.00 41.58 1.89
2270 2285 7.805071 GCAGCAGCAAATTAAGAATCGTAATAT 59.195 33.333 2.09 0.00 41.58 1.28
2391 2406 0.241749 CGCACAATCACAATGGCACT 59.758 50.000 0.00 0.00 0.00 4.40
2398 2413 5.589855 CACAATCACAATGGCACTAGGAATA 59.410 40.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 175 7.330900 AGAGAATAATGGAATGAAACAGCTG 57.669 36.000 13.48 13.48 0.00 4.24
196 201 2.122783 TATGCTGGCAAGGTAACACC 57.877 50.000 0.00 0.00 38.99 4.16
225 230 1.896660 GCAGCCTGAAACGGGTCAA 60.897 57.895 0.00 0.00 31.09 3.18
237 243 2.704725 CAACATTAACGTTGCAGCCT 57.295 45.000 11.99 0.00 39.82 4.58
280 286 7.933033 AGTATAAAACCACGACCTAAAAACTCA 59.067 33.333 0.00 0.00 0.00 3.41
300 306 3.449377 TCCAACGGCATCACTGAGTATAA 59.551 43.478 0.00 0.00 0.00 0.98
350 356 5.694910 CCATCTATAACGTTAACAGCGGAAT 59.305 40.000 12.81 0.00 0.00 3.01
362 368 5.362105 TGGTTTAAGGCCATCTATAACGT 57.638 39.130 5.01 0.00 0.00 3.99
419 426 8.792830 AGTAGCAATCACACACTTATTACATT 57.207 30.769 0.00 0.00 0.00 2.71
485 492 0.541392 CGGTGTCATCCCTGGATCAA 59.459 55.000 0.00 0.00 31.62 2.57
612 620 2.831526 AGAAGTCAGAAGAGAAGAGGGC 59.168 50.000 0.00 0.00 0.00 5.19
669 677 2.496111 TCCGGTTGCGTGAACTTATTT 58.504 42.857 0.00 0.00 34.66 1.40
771 779 2.762745 TCTTCAGGTAAAGTGGCGTTC 58.237 47.619 0.00 0.00 0.00 3.95
849 858 6.009589 TGCATCAAAAGAAAACTCTATGGGA 58.990 36.000 0.00 0.00 0.00 4.37
901 910 0.105593 CCTATGGCGATGTGAGCTGT 59.894 55.000 0.00 0.00 34.52 4.40
918 927 1.270907 AGACTTCTCCAATGCGTCCT 58.729 50.000 0.00 0.00 0.00 3.85
940 949 7.550597 AGATAGTATCCTTGAGATCATTGCA 57.449 36.000 6.53 0.00 36.33 4.08
978 987 0.036952 CCCAGTGTTCATCTCAGCGT 60.037 55.000 0.00 0.00 0.00 5.07
1068 1078 1.522668 CGCACATTTGGTTCTCCTGA 58.477 50.000 0.00 0.00 34.23 3.86
1080 1090 1.202521 TCTATCATGTCGGCGCACATT 60.203 47.619 17.96 10.40 34.60 2.71
1133 1143 1.897560 AGCCTTGAGTTTTTCCTCCG 58.102 50.000 0.00 0.00 0.00 4.63
1423 1433 7.672660 TCGGACTACTATATTTACATGGTGGAT 59.327 37.037 0.00 0.00 0.00 3.41
1465 1475 4.887748 ACAAGGGCATACAATCGATCTAG 58.112 43.478 0.00 0.00 0.00 2.43
1565 1576 9.449719 GAGGGTTTAGAAAAGATGAGATGTAAA 57.550 33.333 0.00 0.00 0.00 2.01
1633 1645 1.004044 CTGGATCAACTGGGTGAGCTT 59.996 52.381 3.93 0.00 34.32 3.74
1707 1719 1.685491 GGTGGTGGTGGGTTGTTGTTA 60.685 52.381 0.00 0.00 0.00 2.41
1773 1788 1.414919 TCGGTGCTACTGGAAAACACT 59.585 47.619 0.00 0.00 0.00 3.55
1890 1905 0.911769 ATGATGCGGGTCCTTCAAGA 59.088 50.000 0.00 0.00 0.00 3.02
1940 1955 0.526739 CCACGTGACAGTGTCGACAA 60.527 55.000 21.95 0.23 40.33 3.18
2016 2031 3.316308 AGTTGCGAAACTCATGCTTCTTT 59.684 39.130 1.82 0.00 0.00 2.52
2268 2283 8.141298 TGTACTTTCCTTGTCCATACTTCATA 57.859 34.615 0.00 0.00 0.00 2.15
2270 2285 6.428083 TGTACTTTCCTTGTCCATACTTCA 57.572 37.500 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.