Multiple sequence alignment - TraesCS4D01G275500

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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 TraesCS4D01G275500 chr4D 100.000 3797 0 0 1 3797 446427380 446431176 0.000000e+00 7012
1 TraesCS4D01G275500 chr4D 89.474 380 25 8 3430 3797 85665190 85665566 2.070000e-127 466
2 TraesCS4D01G275500 chr4D 84.109 258 26 10 3062 3315 85600593 85600839 6.340000e-58 235
3 TraesCS4D01G275500 chr4D 83.088 136 16 6 3316 3445 85627507 85627641 2.400000e-22 117
4 TraesCS4D01G275500 chr4B 97.630 3797 72 10 13 3797 558577485 558581275 0.000000e+00 6497
5 TraesCS4D01G275500 chr4B 81.852 540 75 16 3264 3783 340553986 340553450 2.100000e-117 433
6 TraesCS4D01G275500 chr4A 94.735 3818 147 23 13 3797 21066300 21062504 0.000000e+00 5888
7 TraesCS4D01G275500 chr4A 91.743 1308 85 10 13 1307 21074689 21073392 0.000000e+00 1796
8 TraesCS4D01G275500 chr4A 98.701 77 1 0 1294 1370 21069349 21069273 1.840000e-28 137


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 TraesCS4D01G275500 chr4D 446427380 446431176 3796 False 7012.0 7012 100.000 1 3797 1 chr4D.!!$F4 3796
1 TraesCS4D01G275500 chr4B 558577485 558581275 3790 False 6497.0 6497 97.630 13 3797 1 chr4B.!!$F1 3784
2 TraesCS4D01G275500 chr4B 340553450 340553986 536 True 433.0 433 81.852 3264 3783 1 chr4B.!!$R1 519
3 TraesCS4D01G275500 chr4A 21062504 21069349 6845 True 3012.5 5888 96.718 13 3797 2 chr4A.!!$R2 3784
4 TraesCS4D01G275500 chr4A 21073392 21074689 1297 True 1796.0 1796 91.743 13 1307 1 chr4A.!!$R1 1294

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
226 3265 1.909302 CCACTGATTAGTCCCCACTGT 59.091 52.381 0.00 0.0 34.07 3.55 F
1149 4202 0.748367 ATCTCGTAGCAGCGTCTGGA 60.748 55.000 8.57 0.0 31.21 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 4307 0.895559 CCCAGCCAAGGACAAGTTCC 60.896 60.000 0.0 0.0 46.33 3.62 R
3147 6201 1.070601 GCTTGGGAAAATGCACCACTT 59.929 47.619 0.0 0.0 33.20 3.16 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
226 3265 1.909302 CCACTGATTAGTCCCCACTGT 59.091 52.381 0.00 0.0 34.07 3.55
442 3482 3.381590 TGAAGGTGGAGACGACATGATAG 59.618 47.826 0.00 0.0 0.00 2.08
756 3808 7.614494 CATTCTTCTTTTGGGGAAATATGTGT 58.386 34.615 0.00 0.0 0.00 3.72
1149 4202 0.748367 ATCTCGTAGCAGCGTCTGGA 60.748 55.000 8.57 0.0 31.21 3.86
1198 4251 1.171308 CCTGGTTGAAGCTGATGGTG 58.829 55.000 2.75 0.0 0.00 4.17
1750 4803 0.322906 AGGGGCAAGCAGTAAGAAGC 60.323 55.000 0.00 0.0 0.00 3.86
1863 4916 0.601558 TAGTCAACACGGGAGCACTC 59.398 55.000 0.00 0.0 0.00 3.51
1878 4931 5.410924 GGAGCACTCCCATTAAAAATGAAC 58.589 41.667 5.30 0.0 43.94 3.18
2074 5127 1.821332 GCTGCACATAGCCCTGGAC 60.821 63.158 0.00 0.0 44.83 4.02
2089 5142 1.280133 CTGGACTGAGCCCATTTCAGA 59.720 52.381 9.06 0.0 43.75 3.27
2093 5146 1.134280 ACTGAGCCCATTTCAGATCCG 60.134 52.381 9.06 0.0 43.75 4.18
2207 5260 1.597742 TTGACTTCACAAGCAGCTCC 58.402 50.000 0.00 0.0 0.00 4.70
2409 5462 5.189736 ACTGAGAGCTGTTGTTCCCAATATA 59.810 40.000 0.00 0.0 32.11 0.86
2766 5819 6.701432 CAAACAAGAGAGAAATTGATTGCC 57.299 37.500 0.00 0.0 34.06 4.52
2831 5884 2.092968 TGCATTAGAGGGCAGATCGTTT 60.093 45.455 0.00 0.0 34.58 3.60
2862 5915 1.899814 TGAACAGGTAGCAGTGGTAGG 59.100 52.381 1.37 0.0 0.00 3.18
3147 6201 2.101415 CCAGTATGCTGAAGGTGATCGA 59.899 50.000 12.93 0.0 45.28 3.59
3173 6227 1.159285 GCATTTTCCCAAGCAAAGCC 58.841 50.000 0.00 0.0 0.00 4.35
3238 6292 0.403271 AGGTGAGTGGCAAGCAAGAT 59.597 50.000 0.00 0.0 0.00 2.40
3323 6377 8.674263 ATCTGGTTATAATGAAAGCTGAAGAG 57.326 34.615 0.00 0.0 36.39 2.85
3373 6435 9.076596 GTCCAATTTTTACTATGTTCATGCTTC 57.923 33.333 0.00 0.0 0.00 3.86
3697 6769 9.529325 CTTAAAGAACCGTGAATAGATATGTGA 57.471 33.333 0.00 0.0 0.00 3.58
3737 6809 2.027745 TCTCATTCTTCAGGACTGGTGC 60.028 50.000 0.00 0.0 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.080772 TGGAAGACGCACGCTGTAG 60.081 57.895 0.00 0.00 0.00 2.74
1 2 1.372499 GTGGAAGACGCACGCTGTA 60.372 57.895 0.00 0.00 0.00 2.74
2 3 2.661866 GTGGAAGACGCACGCTGT 60.662 61.111 0.00 0.00 0.00 4.40
3 4 3.414700 GGTGGAAGACGCACGCTG 61.415 66.667 0.00 0.00 0.00 5.18
226 3265 4.072131 GCACACCTAGAAATTGTGGAGAA 58.928 43.478 12.67 0.00 40.86 2.87
398 3438 6.649155 TCAGTATGAAGCCATTAGCAACTTA 58.351 36.000 0.00 0.00 45.97 2.24
442 3482 7.862372 TCATAAAGTGAATGCAAAAGAACAGTC 59.138 33.333 0.00 0.00 32.78 3.51
573 3615 3.259064 GAAATGCGTCCAGTTGCTAGTA 58.741 45.455 0.00 0.00 27.98 1.82
575 3617 2.076100 TGAAATGCGTCCAGTTGCTAG 58.924 47.619 0.00 0.00 27.98 3.42
756 3808 4.688879 ACGATGTAAAAGCGAAGTTCATGA 59.311 37.500 3.32 0.00 41.20 3.07
1092 4145 5.487488 ACCTCCACCTTTTGTCAGATATGTA 59.513 40.000 0.00 0.00 0.00 2.29
1149 4202 4.071423 GTTTATTTTGCAAGCCCACCAAT 58.929 39.130 0.00 0.00 0.00 3.16
1198 4251 3.852205 GCGTAGTTCCAACAAAGGCTTTC 60.852 47.826 10.08 0.00 0.00 2.62
1254 4307 0.895559 CCCAGCCAAGGACAAGTTCC 60.896 60.000 0.00 0.00 46.33 3.62
1863 4916 6.451393 TGACCTTTCGTTCATTTTTAATGGG 58.549 36.000 0.00 0.00 0.00 4.00
1878 4931 2.810274 CTGCATATCCCATGACCTTTCG 59.190 50.000 0.00 0.00 0.00 3.46
2074 5127 1.590932 CGGATCTGAAATGGGCTCAG 58.409 55.000 0.00 0.00 41.47 3.35
2089 5142 3.389329 AGTATCTGCTGTGAATTCCGGAT 59.611 43.478 4.15 6.06 0.00 4.18
2093 5146 4.331168 GTGTCAGTATCTGCTGTGAATTCC 59.669 45.833 2.27 0.00 37.70 3.01
2207 5260 1.971418 CCATTTTCCCCACCCAACG 59.029 57.895 0.00 0.00 0.00 4.10
2409 5462 6.105397 AGTGATGCTTTGTCCATTTTTGAT 57.895 33.333 0.00 0.00 0.00 2.57
2430 5483 1.771255 GTTATGGCATCTCCCAGGAGT 59.229 52.381 13.36 0.00 42.49 3.85
2766 5819 1.559831 TCATTGCACGAGACATAGCG 58.440 50.000 0.00 0.00 0.00 4.26
2831 5884 5.676552 TGCTACCTGTTCACAACTAGAAAA 58.323 37.500 0.00 0.00 0.00 2.29
2862 5915 3.914426 ATTACATGGACACTGGGAGTC 57.086 47.619 0.00 0.00 35.29 3.36
3147 6201 1.070601 GCTTGGGAAAATGCACCACTT 59.929 47.619 0.00 0.00 33.20 3.16
3323 6377 1.850441 GCAAGCGACATGATTTGATGC 59.150 47.619 0.00 0.00 0.00 3.91
3373 6435 1.078848 CTGAAGCCTCGGTGGAAGG 60.079 63.158 0.00 0.00 38.35 3.46
3697 6769 4.951715 TGAGATGCTTGGTTGCTGATAATT 59.048 37.500 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.