Multiple sequence alignment - TraesCS4B01G182900

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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 TraesCS4B01G182900 chr4B 100.000 2504 0 0 1 2504 401880412 401882915 0.000000e+00 4625.0
1 TraesCS4B01G182900 chr4D 95.836 1777 30 8 2 1752 319703234 319701476 0.000000e+00 2832.0
2 TraesCS4B01G182900 chr4A 97.094 1411 33 6 350 1754 153778902 153780310 0.000000e+00 2372.0
3 TraesCS4B01G182900 chr4A 92.977 598 29 7 1913 2504 631641168 631640578 0.000000e+00 859.0
4 TraesCS4B01G182900 chr4A 93.865 326 14 4 5 328 153775961 153776282 1.040000e-133 486.0
5 TraesCS4B01G182900 chr4A 87.805 164 17 3 1754 1916 87418687 87418848 3.290000e-44 189.0
6 TraesCS4B01G182900 chr4A 100.000 30 0 0 320 349 153778850 153778879 3.480000e-04 56.5
7 TraesCS4B01G182900 chr6B 93.813 598 30 2 1913 2504 45530324 45530920 0.000000e+00 893.0
8 TraesCS4B01G182900 chr7B 93.581 592 34 2 1913 2504 478465856 478465269 0.000000e+00 880.0
9 TraesCS4B01G182900 chr7B 91.304 161 13 1 1751 1911 743704228 743704387 4.190000e-53 219.0
10 TraesCS4B01G182900 chr7B 87.195 164 20 1 1754 1916 631318519 631318356 4.250000e-43 185.0
11 TraesCS4B01G182900 chr3A 93.243 592 40 0 1913 2504 749478300 749477709 0.000000e+00 872.0
12 TraesCS4B01G182900 chr3B 93.121 596 29 6 1913 2504 41012298 41012885 0.000000e+00 863.0
13 TraesCS4B01G182900 chr3B 90.741 162 12 3 1754 1914 55006787 55006628 1.950000e-51 213.0
14 TraesCS4B01G182900 chr5B 92.809 598 35 5 1913 2504 454685217 454685812 0.000000e+00 859.0
15 TraesCS4B01G182900 chr2B 92.736 592 41 1 1913 2504 19386232 19386821 0.000000e+00 854.0
16 TraesCS4B01G182900 chr2B 92.736 592 37 5 1913 2504 235076535 235077120 0.000000e+00 850.0
17 TraesCS4B01G182900 chr6D 92.487 599 38 4 1913 2504 144603480 144604078 0.000000e+00 850.0
18 TraesCS4B01G182900 chr6D 85.802 162 20 3 1751 1911 82231796 82231637 4.280000e-38 169.0
19 TraesCS4B01G182900 chr1D 84.840 686 64 22 1751 2398 346025855 346026538 0.000000e+00 654.0
20 TraesCS4B01G182900 chr2A 88.024 167 18 2 1751 1916 617663438 617663603 1.960000e-46 196.0
21 TraesCS4B01G182900 chr2A 87.952 166 16 4 1752 1916 411113262 411113424 2.540000e-45 193.0
22 TraesCS4B01G182900 chr1B 81.707 164 28 2 1747 1910 146790360 146790199 4.340000e-28 135.0


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 TraesCS4B01G182900 chr4B 401880412 401882915 2503 False 4625.0 4625 100.000000 1 2504 1 chr4B.!!$F1 2503
1 TraesCS4B01G182900 chr4D 319701476 319703234 1758 True 2832.0 2832 95.836000 2 1752 1 chr4D.!!$R1 1750
2 TraesCS4B01G182900 chr4A 153775961 153780310 4349 False 971.5 2372 96.986333 5 1754 3 chr4A.!!$F2 1749
3 TraesCS4B01G182900 chr4A 631640578 631641168 590 True 859.0 859 92.977000 1913 2504 1 chr4A.!!$R1 591
4 TraesCS4B01G182900 chr6B 45530324 45530920 596 False 893.0 893 93.813000 1913 2504 1 chr6B.!!$F1 591
5 TraesCS4B01G182900 chr7B 478465269 478465856 587 True 880.0 880 93.581000 1913 2504 1 chr7B.!!$R1 591
6 TraesCS4B01G182900 chr3A 749477709 749478300 591 True 872.0 872 93.243000 1913 2504 1 chr3A.!!$R1 591
7 TraesCS4B01G182900 chr3B 41012298 41012885 587 False 863.0 863 93.121000 1913 2504 1 chr3B.!!$F1 591
8 TraesCS4B01G182900 chr5B 454685217 454685812 595 False 859.0 859 92.809000 1913 2504 1 chr5B.!!$F1 591
9 TraesCS4B01G182900 chr2B 19386232 19386821 589 False 854.0 854 92.736000 1913 2504 1 chr2B.!!$F1 591
10 TraesCS4B01G182900 chr2B 235076535 235077120 585 False 850.0 850 92.736000 1913 2504 1 chr2B.!!$F2 591
11 TraesCS4B01G182900 chr6D 144603480 144604078 598 False 850.0 850 92.487000 1913 2504 1 chr6D.!!$F1 591
12 TraesCS4B01G182900 chr1D 346025855 346026538 683 False 654.0 654 84.840000 1751 2398 1 chr1D.!!$F1 647

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
399 3004 1.001633 GCTCAGGAACGTAAGGTGGAA 59.998 52.381 0.0 0.0 37.5 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 4385 0.040781 ACAAAATCGCCGTCCGTTTG 60.041 50.0 0.0 0.0 38.28 2.93 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
35 36 2.044946 GGCTGTTGGCGGATTCCT 60.045 61.111 0.30 0.00 42.94 3.36
51 52 1.538047 TCCTCATGGTTGAAAGCTGC 58.462 50.000 0.00 0.00 34.23 5.25
161 162 2.165319 AGAAAGAACGTTTCGGGAGG 57.835 50.000 0.46 0.00 33.86 4.30
219 221 2.885644 CTCGACGCCGATGGGTTG 60.886 66.667 0.00 0.00 44.62 3.77
371 2976 1.783365 ACAGCCTTCCTTCCTTTCCTT 59.217 47.619 0.00 0.00 0.00 3.36
399 3004 1.001633 GCTCAGGAACGTAAGGTGGAA 59.998 52.381 0.00 0.00 37.50 3.53
818 3425 1.700955 GTCCACGAATAGCCCTCCTA 58.299 55.000 0.00 0.00 0.00 2.94
901 3508 2.687909 ATAGCCTCCCAGCCCTCTCC 62.688 65.000 0.00 0.00 0.00 3.71
914 3521 1.522569 CTCTCCGCCTCCCGAAAAT 59.477 57.895 0.00 0.00 40.02 1.82
1580 4188 3.243724 CCCCCTAAAATTTGGTTGGTGA 58.756 45.455 0.00 0.00 0.00 4.02
1754 4363 4.211125 TCTACTCTCCTGCAGGTCATAAG 58.789 47.826 31.58 20.95 36.34 1.73
1767 4376 2.673368 GGTCATAAGAGCAACTCCAACG 59.327 50.000 0.00 0.00 41.81 4.10
1770 4379 0.321298 TAAGAGCAACTCCAACGGGC 60.321 55.000 0.00 0.00 0.00 6.13
1789 4398 4.668118 GACCCAAACGGACGGCGA 62.668 66.667 16.62 0.00 34.64 5.54
1790 4399 3.945304 GACCCAAACGGACGGCGAT 62.945 63.158 16.62 0.00 34.64 4.58
1814 4423 2.247637 GTCCGCTTTTTATCCGTTTGC 58.752 47.619 0.00 0.00 0.00 3.68
1838 4447 3.636043 CAGGCGAACGTGCGTGTT 61.636 61.111 18.93 0.02 43.69 3.32
1873 4482 1.375396 TCGGCTTGACCATCCAACG 60.375 57.895 0.00 0.00 39.03 4.10
1874 4483 1.375396 CGGCTTGACCATCCAACGA 60.375 57.895 0.00 0.00 39.03 3.85
1876 4485 1.026718 GGCTTGACCATCCAACGAGG 61.027 60.000 0.00 0.00 38.86 4.63
1902 4511 0.466543 ACCTAAATATGCCGGCGTGA 59.533 50.000 31.45 14.60 0.00 4.35
2023 4670 2.203684 CCTTGCCCTTGCCCTTGT 60.204 61.111 0.00 0.00 36.33 3.16
2028 4675 3.170362 CCCTTGCCCTTGTCCTCA 58.830 61.111 0.00 0.00 0.00 3.86
2035 4682 2.030562 CCTTGTCCTCAACGCCGT 59.969 61.111 0.00 0.00 0.00 5.68
2055 4702 1.004595 CGTCGTCAGTGAGGTCGATA 58.995 55.000 22.18 0.00 32.80 2.92
2276 4926 2.989639 CCGGTGCTCCTTCCATCA 59.010 61.111 2.85 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.266718 GCCAAGACGATGCTGACAAAA 59.733 47.619 0.00 0.00 0.00 2.44
35 36 4.405116 AAAAAGCAGCTTTCAACCATGA 57.595 36.364 20.85 0.00 31.99 3.07
51 52 0.437295 CTCGTGCCGACGGTAAAAAG 59.563 55.000 16.73 5.49 46.11 2.27
219 221 1.570967 GGTGACAAACGCGGTTACC 59.429 57.895 10.12 10.83 37.68 2.85
371 2976 2.355837 GTTCCTGAGCGCGTGTGA 60.356 61.111 8.43 0.00 0.00 3.58
399 3004 4.918129 ACGCGCGTGACTGTTCGT 62.918 61.111 37.37 12.76 0.00 3.85
586 3193 1.456705 GTGGGGCCACAGGTTTTCA 60.457 57.895 8.77 0.00 45.53 2.69
818 3425 3.181446 GGAATAGAATTCTCCAGCTGGCT 60.181 47.826 28.91 19.50 34.44 4.75
901 3508 1.807742 TGTTTGTATTTTCGGGAGGCG 59.192 47.619 0.00 0.00 0.00 5.52
914 3521 2.156891 GCGCGATCTCTGTTTGTTTGTA 59.843 45.455 12.10 0.00 0.00 2.41
1694 4303 5.801531 TCCAAGGATACACGCATAGTATT 57.198 39.130 0.00 0.00 41.41 1.89
1754 4363 3.056328 GGCCCGTTGGAGTTGCTC 61.056 66.667 0.00 0.00 0.00 4.26
1776 4385 0.040781 ACAAAATCGCCGTCCGTTTG 60.041 50.000 0.00 0.00 38.28 2.93
1787 4396 3.783943 CGGATAAAAAGCGGACAAAATCG 59.216 43.478 0.00 0.00 0.00 3.34
1788 4397 4.729595 ACGGATAAAAAGCGGACAAAATC 58.270 39.130 0.00 0.00 0.00 2.17
1789 4398 4.776795 ACGGATAAAAAGCGGACAAAAT 57.223 36.364 0.00 0.00 0.00 1.82
1790 4399 4.571372 AACGGATAAAAAGCGGACAAAA 57.429 36.364 0.00 0.00 0.00 2.44
1835 4444 4.230657 CGACCCATTTTAAAATGCGAACA 58.769 39.130 28.17 0.00 43.38 3.18
1838 4447 2.416162 GCCGACCCATTTTAAAATGCGA 60.416 45.455 28.17 0.00 43.38 5.10
1867 4476 2.747686 GTTGGCCTCCTCGTTGGA 59.252 61.111 3.32 0.58 43.86 3.53
1873 4482 3.149981 GCATATTTAGGTTGGCCTCCTC 58.850 50.000 20.27 4.43 45.64 3.71
1874 4483 2.158460 GGCATATTTAGGTTGGCCTCCT 60.158 50.000 20.44 20.44 45.64 3.69
1876 4485 1.880027 CGGCATATTTAGGTTGGCCTC 59.120 52.381 3.32 0.00 45.64 4.70
1882 4491 1.134340 TCACGCCGGCATATTTAGGTT 60.134 47.619 28.98 0.00 0.00 3.50
2035 4682 0.672711 ATCGACCTCACTGACGACGA 60.673 55.000 0.00 5.44 37.58 4.20
2055 4702 2.134630 CTGGCCCTGCTCCAGTCTTT 62.135 60.000 0.00 0.00 44.62 2.52
2261 4911 0.460987 CGAGTGATGGAAGGAGCACC 60.461 60.000 0.00 0.00 31.85 5.01
2456 5121 1.472662 CCACTCCCCACTCTTCGTGT 61.473 60.000 0.00 0.00 42.20 4.49


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

AutoCloner maintained by Alex Coulton.