Multiple sequence alignment - TraesCS3A01G184200

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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 TraesCS3A01G184200 chr3A 100.000 4098 0 0 1 4098 214291316 214287219 0.000000e+00 7568.0
1 TraesCS3A01G184200 chr3D 97.840 4120 56 14 1 4098 174927311 174923203 0.000000e+00 7084.0
2 TraesCS3A01G184200 chr3D 92.500 40 1 2 3776 3814 607170924 607170962 5.720000e-04 56.5
3 TraesCS3A01G184200 chr3B 95.942 3425 89 21 1 3401 253897592 253894194 0.000000e+00 5509.0
4 TraesCS3A01G184200 chr3B 91.873 283 15 1 3414 3688 253893172 253892890 4.970000e-104 388.0
5 TraesCS3A01G184200 chr3B 83.978 181 16 9 3711 3878 253892906 253892726 1.180000e-35 161.0


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 TraesCS3A01G184200 chr3A 214287219 214291316 4097 True 7568.000000 7568 100.000000 1 4098 1 chr3A.!!$R1 4097
1 TraesCS3A01G184200 chr3D 174923203 174927311 4108 True 7084.000000 7084 97.840000 1 4098 1 chr3D.!!$R1 4097
2 TraesCS3A01G184200 chr3B 253892726 253897592 4866 True 2019.333333 5509 90.597667 1 3878 3 chr3B.!!$R1 3877

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
34 35 1.000486 AGCTAAGCTCGACCTCCCA 60.000 57.895 0.00 0.0 30.62 4.37 F
51 52 1.200519 CCACTCCCGTCCATTCCTAA 58.799 55.000 0.00 0.0 0.00 2.69 F
68 69 1.393539 CTAACACGCACCGGAAATCTG 59.606 52.381 9.46 0.0 0.00 2.90 F
917 933 2.596338 TCGGTCTCTGCACCACGA 60.596 61.111 0.00 0.0 36.01 4.35 F
1602 1626 3.384789 TCTGGTCGAATGCTTAGCTACAT 59.615 43.478 5.60 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1591 1.580059 GACCAGATTACCCCAGTGGA 58.420 55.000 11.95 0.0 38.00 4.02 R
1968 1992 4.141287 AGCTAACTGCATTTGTAACCACA 58.859 39.130 0.00 0.0 45.94 4.17 R
2812 2837 6.907212 GTCAAAGGATTAATAACATGTCAGCG 59.093 38.462 0.00 0.0 0.00 5.18 R
2897 2922 1.963515 CAACTTTGGTCAAGGGAAGGG 59.036 52.381 0.00 0.0 36.72 3.95 R
3996 5069 0.596082 AAAAACTGGATCCGCAACCG 59.404 50.000 7.39 0.0 0.00 4.44 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
34 35 1.000486 AGCTAAGCTCGACCTCCCA 60.000 57.895 0.00 0.00 30.62 4.37
51 52 1.200519 CCACTCCCGTCCATTCCTAA 58.799 55.000 0.00 0.00 0.00 2.69
68 69 1.393539 CTAACACGCACCGGAAATCTG 59.606 52.381 9.46 0.00 0.00 2.90
385 387 3.493176 GGTGAGCAGTTTGGCATTCTTTT 60.493 43.478 0.00 0.00 35.83 2.27
386 388 4.122046 GTGAGCAGTTTGGCATTCTTTTT 58.878 39.130 0.00 0.00 35.83 1.94
769 784 3.755378 GACATGCCATCAGTTCAAGAGTT 59.245 43.478 0.00 0.00 0.00 3.01
797 813 6.607689 TGGTAAACATGCATTTACTCTTTCG 58.392 36.000 17.94 0.00 42.34 3.46
834 850 9.508567 GAATTCTTCTGTTGGTCTTTAATATGC 57.491 33.333 0.00 0.00 0.00 3.14
917 933 2.596338 TCGGTCTCTGCACCACGA 60.596 61.111 0.00 0.00 36.01 4.35
1108 1124 3.556543 AACATTGCCACGCGCCAAG 62.557 57.895 5.73 4.62 36.24 3.61
1602 1626 3.384789 TCTGGTCGAATGCTTAGCTACAT 59.615 43.478 5.60 0.00 0.00 2.29
1668 1692 7.425577 TCAAACAAGATGAGAGTAATGTGTG 57.574 36.000 0.00 0.00 0.00 3.82
1764 1788 5.126061 AGCAAAATCAACTGTCTTGTTCAGT 59.874 36.000 0.00 0.00 46.30 3.41
1968 1992 8.010733 TGGAAACAAAATCAGAATCACTTCTT 57.989 30.769 0.00 0.00 37.17 2.52
2836 2861 6.038161 CCGCTGACATGTTATTAATCCTTTGA 59.962 38.462 0.00 0.00 0.00 2.69
2927 2952 6.208644 CCTTGACCAAAGTTGTTTATCACAG 58.791 40.000 0.00 0.00 32.86 3.66
3101 3126 6.570957 GCAGACAATGGATGAACTTTGATTGA 60.571 38.462 0.00 0.00 0.00 2.57
3102 3127 7.027760 CAGACAATGGATGAACTTTGATTGAG 58.972 38.462 0.00 0.00 0.00 3.02
3103 3128 6.718454 AGACAATGGATGAACTTTGATTGAGT 59.282 34.615 0.00 0.00 0.00 3.41
3104 3129 7.884877 AGACAATGGATGAACTTTGATTGAGTA 59.115 33.333 0.00 0.00 0.00 2.59
3105 3130 7.820648 ACAATGGATGAACTTTGATTGAGTAC 58.179 34.615 0.00 0.00 0.00 2.73
3262 3288 3.007614 ACCTGTAAACTAATGGACAGCGT 59.992 43.478 0.00 0.00 38.37 5.07
3404 4188 3.053831 ACACCCGGATGAACAGTAAAG 57.946 47.619 0.36 0.00 0.00 1.85
3458 4497 6.707440 TGAATGTTCTACTTCCTGCAAAAA 57.293 33.333 0.00 0.00 0.00 1.94
3570 4611 6.695278 GCTGCATGTTTAGTGTTTTTACTCAA 59.305 34.615 0.00 0.00 32.19 3.02
3571 4612 7.221838 GCTGCATGTTTAGTGTTTTTACTCAAA 59.778 33.333 0.00 0.00 32.19 2.69
3760 4819 9.630098 CATAATGCTACTTTTGATGTTGTCTTT 57.370 29.630 0.00 0.00 0.00 2.52
3775 4836 4.931661 TGTCTTTCGTAGTGTTCTCCTT 57.068 40.909 0.00 0.00 0.00 3.36
3883 4956 5.376625 AGCCAAGTCAAGTGAACTATTTGA 58.623 37.500 0.00 0.00 33.23 2.69
4033 5106 0.970640 TTTCCGGATCGAGTTGACCA 59.029 50.000 4.15 0.00 0.00 4.02
4062 5135 6.703607 CCTTGAGCTAGTGAATACTTACATGG 59.296 42.308 0.00 0.00 38.36 3.66
4076 5149 8.896320 ATACTTACATGGCATTTACGTGATTA 57.104 30.769 11.69 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.325082 GCAGATTTCCGGTGCGTGT 61.325 57.895 0.00 0.00 0.00 4.49
75 76 4.123009 TCGTACATGCGCTGCGGA 62.123 61.111 24.61 22.61 0.00 5.54
122 124 0.753262 GCGGCAGATAAGAGGGAAGA 59.247 55.000 0.00 0.00 0.00 2.87
344 346 3.578716 CACCAATATATCGTGAGGACCCT 59.421 47.826 6.96 0.00 0.00 4.34
449 453 1.607251 CGTTACACCCCACAGAACTCC 60.607 57.143 0.00 0.00 0.00 3.85
769 784 8.630054 AAGAGTAAATGCATGTTTACCAGTTA 57.370 30.769 15.92 1.95 42.68 2.24
834 850 9.878599 GTTTGATAATTATAATGGTGAAGGTCG 57.121 33.333 0.00 0.00 0.00 4.79
917 933 2.368439 ACATTCAACAGTGCCGCATAT 58.632 42.857 0.00 0.00 0.00 1.78
1108 1124 1.975680 TGTAGGATCCCGGCTTAATCC 59.024 52.381 8.55 12.85 39.44 3.01
1567 1591 1.580059 GACCAGATTACCCCAGTGGA 58.420 55.000 11.95 0.00 38.00 4.02
1764 1788 6.588756 CACGAGTAATTTTAGCACCTAGAACA 59.411 38.462 0.00 0.00 0.00 3.18
1968 1992 4.141287 AGCTAACTGCATTTGTAACCACA 58.859 39.130 0.00 0.00 45.94 4.17
2812 2837 6.907212 GTCAAAGGATTAATAACATGTCAGCG 59.093 38.462 0.00 0.00 0.00 5.18
2836 2861 2.923121 AGGCAATTGCGTATGATGAGT 58.077 42.857 23.26 0.00 43.26 3.41
2897 2922 1.963515 CAACTTTGGTCAAGGGAAGGG 59.036 52.381 0.00 0.00 36.72 3.95
2927 2952 4.727475 GCTTCCTGCAAAGTAAGAACATC 58.273 43.478 0.36 0.00 42.31 3.06
3101 3126 4.514781 TGTTTGCGTCATCTACTGTACT 57.485 40.909 0.00 0.00 0.00 2.73
3102 3127 6.144080 GGATATGTTTGCGTCATCTACTGTAC 59.856 42.308 0.00 0.00 0.00 2.90
3103 3128 6.040504 AGGATATGTTTGCGTCATCTACTGTA 59.959 38.462 0.00 0.00 0.00 2.74
3104 3129 5.050490 GGATATGTTTGCGTCATCTACTGT 58.950 41.667 0.00 0.00 0.00 3.55
3105 3130 5.176406 CAGGATATGTTTGCGTCATCTACTG 59.824 44.000 0.00 0.00 28.90 2.74
3262 3288 4.381079 GCAACAACTGGTTACACCTTTTCA 60.381 41.667 0.00 0.00 39.58 2.69
3322 3348 8.623310 ACGTTTTGTTTTCGTTTCAATTCTAT 57.377 26.923 0.00 0.00 34.07 1.98
3334 3360 2.781646 GCAGGAGAACGTTTTGTTTTCG 59.218 45.455 0.46 0.00 41.41 3.46
3458 4497 9.345517 CACATCAAATGTTATTTCTTCACGAAT 57.654 29.630 0.00 0.00 42.70 3.34
3570 4611 7.720442 TCATCAAGATATCGTTCATGACTCTT 58.280 34.615 0.00 0.00 0.00 2.85
3571 4612 7.282332 TCATCAAGATATCGTTCATGACTCT 57.718 36.000 0.00 0.00 0.00 3.24
3615 4657 3.030291 TGTGGCAAACATCCTTGAGTTT 58.970 40.909 0.00 0.00 38.40 2.66
3760 4819 6.335471 TCACATAAAAGGAGAACACTACGA 57.665 37.500 0.00 0.00 0.00 3.43
3775 4836 5.670792 ACGGGTCATCTACTTCACATAAA 57.329 39.130 0.00 0.00 0.00 1.40
3862 4935 7.040478 TCCATTCAAATAGTTCACTTGACTTGG 60.040 37.037 0.00 0.00 35.67 3.61
3883 4956 6.661304 AGTTGCTTTTCTTCTTGATCCATT 57.339 33.333 0.00 0.00 0.00 3.16
3968 5041 2.520069 CCCTCCGCACTATAGAGACAT 58.480 52.381 6.78 0.00 0.00 3.06
3996 5069 0.596082 AAAAACTGGATCCGCAACCG 59.404 50.000 7.39 0.00 0.00 4.44
4033 5106 4.615513 AGTATTCACTAGCTCAAGGAGGT 58.384 43.478 0.00 3.28 43.16 3.85
4062 5135 4.495844 GCTCCCACTTAATCACGTAAATGC 60.496 45.833 0.00 0.00 0.00 3.56
4076 5149 1.981256 ATGTTGTTTCGCTCCCACTT 58.019 45.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.