Multiple sequence alignment - TraesCS4B01G179100

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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 TraesCS4B01G179100 chr4B 100.000 6036 0 0 1 6036 392112965 392106930 0.000000e+00 11147.0
1 TraesCS4B01G179100 chr4D 96.814 6058 125 30 1 6036 314407035 314401024 0.000000e+00 10056.0
2 TraesCS4B01G179100 chr4A 95.630 3295 108 16 1 3284 162072625 162075894 0.000000e+00 5254.0
3 TraesCS4B01G179100 chr4A 94.905 2532 97 15 3290 5796 162077735 162080259 0.000000e+00 3932.0
4 TraesCS4B01G179100 chr4A 90.909 121 10 1 5796 5916 162082930 162083049 1.740000e-35 161.0
5 TraesCS4B01G179100 chr4A 81.538 130 11 3 5907 6036 162083439 162083555 1.790000e-15 95.3
6 TraesCS4B01G179100 chrUn 100.000 394 0 0 3920 4313 479501494 479501887 0.000000e+00 728.0
7 TraesCS4B01G179100 chr7A 90.385 52 2 3 5718 5766 671806333 671806384 1.400000e-06 65.8
8 TraesCS4B01G179100 chr5B 87.931 58 4 3 5483 5539 430325796 430325851 1.400000e-06 65.8
9 TraesCS4B01G179100 chr7B 94.872 39 0 2 5718 5754 646613292 646613330 6.530000e-05 60.2


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 TraesCS4B01G179100 chr4B 392106930 392112965 6035 True 11147.000 11147 100.0000 1 6036 1 chr4B.!!$R1 6035
1 TraesCS4B01G179100 chr4D 314401024 314407035 6011 True 10056.000 10056 96.8140 1 6036 1 chr4D.!!$R1 6035
2 TraesCS4B01G179100 chr4A 162072625 162083555 10930 False 2360.575 5254 90.7455 1 6036 4 chr4A.!!$F1 6035

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
797 806 0.320374 TGGCTAACCTGTCGAACTGG 59.680 55.000 8.61 8.61 42.22 4.00 F
976 986 2.092914 GTGATTCTGATCCGGAAAGGGT 60.093 50.000 9.01 1.80 41.52 4.34 F
2782 2794 4.950205 TCGAAGGACCAGTCTTACTTTT 57.050 40.909 0.00 0.00 0.00 2.27 F
3012 3024 0.615850 GAGGCCAGGCACTAGTTCTT 59.384 55.000 15.19 0.00 36.02 2.52 F
4801 6663 0.463654 GCGGTGCATCTGGGATTACA 60.464 55.000 0.00 0.00 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2412 2423 2.017049 GGTGCAACTCTTCAACTGTGT 58.983 47.619 0.00 0.00 36.74 3.72 R
2803 2815 0.469144 AATGGTTTTGGCTCCGTGGT 60.469 50.000 0.00 0.00 0.00 4.16 R
4357 6216 0.320771 CAGAAGGTTCACCCTCCACG 60.321 60.000 0.00 0.00 45.47 4.94 R
4978 6840 0.392729 CTGCTCCCTTCAGCTCAAGG 60.393 60.000 9.89 9.89 42.57 3.61 R
5845 10396 1.003116 CATACCCTTCTACGGTCGTCG 60.003 57.143 0.00 0.00 45.88 5.12 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
30 31 8.988064 TTCTTGTAAAAAGTGCATGTTTTGTA 57.012 26.923 16.40 4.52 0.00 2.41
58 59 4.574674 TTCTCAACTGGCTGGATTACAT 57.425 40.909 0.00 0.00 0.00 2.29
95 96 0.453390 TGTTGCATTGACGTGTTGCA 59.547 45.000 11.40 11.40 44.12 4.08
97 98 3.248626 TGCATTGACGTGTTGCAAC 57.751 47.368 22.83 22.83 42.95 4.17
716 725 0.469144 GTGTTTGGGACATGGGTGGT 60.469 55.000 0.00 0.00 41.10 4.16
797 806 0.320374 TGGCTAACCTGTCGAACTGG 59.680 55.000 8.61 8.61 42.22 4.00
871 880 8.380644 GGCTTTACTTTCAGTTTGTTTTTCTTC 58.619 33.333 0.00 0.00 0.00 2.87
976 986 2.092914 GTGATTCTGATCCGGAAAGGGT 60.093 50.000 9.01 1.80 41.52 4.34
1412 1422 4.970662 TGCATGGCAGAACTATCTTTTC 57.029 40.909 0.00 0.00 32.03 2.29
2456 2467 6.126507 CCTTATGCCCCCAAAAGGAAAATATT 60.127 38.462 0.00 0.00 40.85 1.28
2554 2565 6.543465 TGGTGCTGAGAATAATTGTATTCCTG 59.457 38.462 3.43 2.15 44.66 3.86
2748 2760 7.446769 TGCTAGACTACAAAAGAACCACATTA 58.553 34.615 0.00 0.00 0.00 1.90
2749 2761 7.934665 TGCTAGACTACAAAAGAACCACATTAA 59.065 33.333 0.00 0.00 0.00 1.40
2782 2794 4.950205 TCGAAGGACCAGTCTTACTTTT 57.050 40.909 0.00 0.00 0.00 2.27
2803 2815 9.553064 ACTTTTCAAAATGGTGCAATAAACATA 57.447 25.926 0.00 0.00 0.00 2.29
2815 2827 3.637911 ATAAACATACCACGGAGCCAA 57.362 42.857 0.00 0.00 0.00 4.52
2924 2936 2.698797 ACTTATATGCCACGTAGCCAGT 59.301 45.455 2.86 0.00 0.00 4.00
3009 3021 2.982130 CGAGGCCAGGCACTAGTT 59.018 61.111 15.19 0.00 36.02 2.24
3012 3024 0.615850 GAGGCCAGGCACTAGTTCTT 59.384 55.000 15.19 0.00 36.02 2.52
3046 3060 1.187974 CCTCCATGCCAGCAAAATGA 58.812 50.000 0.00 0.00 0.00 2.57
3080 3094 2.362736 TGTATCTCGGCGTAGTGACTT 58.637 47.619 6.85 0.00 0.00 3.01
3399 5255 6.721571 AGTATTATGTGTCCAAAACTGTCG 57.278 37.500 0.00 0.00 0.00 4.35
3822 5681 9.522804 GGTGAGTTTTGATGTGTTATTGTTTTA 57.477 29.630 0.00 0.00 0.00 1.52
4313 6172 2.158726 AGTTTGGGCAGAAGTTTCGGTA 60.159 45.455 0.00 0.00 0.00 4.02
4357 6216 4.893424 TGTTGCTAAAAGGAGTGTTGTC 57.107 40.909 0.00 0.00 0.00 3.18
4525 6384 3.264193 AGGATGCAGTATCACCTGTTGAA 59.736 43.478 0.49 0.00 37.92 2.69
4566 6425 3.062763 CAGAACGGCATAGCTTAGATGG 58.937 50.000 0.00 0.00 0.00 3.51
4715 6577 4.250464 TGTTATAAGCTCAACTGAACCCG 58.750 43.478 0.00 0.00 0.00 5.28
4761 6623 0.884704 CAGGAGTTTGGTGGTCACGG 60.885 60.000 0.00 0.00 0.00 4.94
4774 6636 2.058001 TCACGGCCCATCAGATCGT 61.058 57.895 0.00 0.00 34.19 3.73
4798 6660 2.124151 GGCGGTGCATCTGGGATT 60.124 61.111 0.00 0.00 0.00 3.01
4801 6663 0.463654 GCGGTGCATCTGGGATTACA 60.464 55.000 0.00 0.00 0.00 2.41
4808 6670 5.376625 GTGCATCTGGGATTACAAAGGATA 58.623 41.667 0.00 0.00 0.00 2.59
4923 6785 1.669760 TTAAGGTTGGCTCGGTGCG 60.670 57.895 0.00 0.00 44.05 5.34
4978 6840 6.459923 GTCTGAGATTATAGGTGATGGTTCC 58.540 44.000 0.00 0.00 0.00 3.62
4999 6861 0.612229 TTGAGCTGAAGGGAGCAGAG 59.388 55.000 0.00 0.00 41.83 3.35
5004 6866 1.809651 GCTGAAGGGAGCAGAGCATAC 60.810 57.143 0.00 0.00 38.95 2.39
5018 6880 0.888285 GCATACTGAGCAGGGCATCC 60.888 60.000 2.20 0.00 0.00 3.51
5037 6899 5.009610 GCATCCCAACAAAACTGAGTTAAGA 59.990 40.000 0.00 0.00 0.00 2.10
5038 6900 6.672147 CATCCCAACAAAACTGAGTTAAGAG 58.328 40.000 0.00 0.00 0.00 2.85
5109 6971 0.307760 CTCTGTTTGTGTTGGTCGGC 59.692 55.000 0.00 0.00 0.00 5.54
5143 7005 2.290260 TGCTTATGGCTACTGCAGTTGT 60.290 45.455 27.06 9.84 42.39 3.32
5167 7029 0.315251 TCAGCTTGACGACTGACAGG 59.685 55.000 7.51 0.00 37.99 4.00
5270 7138 3.146847 GGTGAGGGAAAATCGTTTCTGT 58.853 45.455 0.00 0.00 42.45 3.41
5271 7139 3.568430 GGTGAGGGAAAATCGTTTCTGTT 59.432 43.478 0.00 0.00 42.45 3.16
5272 7140 4.037565 GGTGAGGGAAAATCGTTTCTGTTT 59.962 41.667 0.00 0.00 42.45 2.83
5273 7141 4.976116 GTGAGGGAAAATCGTTTCTGTTTG 59.024 41.667 0.00 0.00 42.45 2.93
5336 7208 7.230510 GGCACTATTGGGTGAAATGTAATCATA 59.769 37.037 0.00 0.00 39.34 2.15
5337 7209 8.796475 GCACTATTGGGTGAAATGTAATCATAT 58.204 33.333 0.00 0.00 39.34 1.78
5409 7283 3.603857 CGGCAACTGTGTTCTCTTTTACG 60.604 47.826 0.00 0.00 0.00 3.18
5452 7326 2.493030 GCGCATGCTTGCCATCTT 59.507 55.556 17.13 0.00 46.57 2.40
5458 7332 1.136305 CATGCTTGCCATCTTCCCTTG 59.864 52.381 0.00 0.00 29.71 3.61
5467 7341 3.372458 GCCATCTTCCCTTGGAGATTTCT 60.372 47.826 0.00 0.00 34.81 2.52
5522 7399 5.298026 GCTCCCTCTCTGATTTCCATTAAAC 59.702 44.000 0.00 0.00 0.00 2.01
5530 7407 7.393234 TCTCTGATTTCCATTAAACGAAACCAT 59.607 33.333 0.00 0.00 31.15 3.55
5559 7436 2.024273 TCCTAACAGGCTACCAGCTACT 60.024 50.000 0.00 0.00 41.99 2.57
5615 7494 1.972660 AACGCAGTCAGGCTATCCCC 61.973 60.000 0.00 0.00 45.00 4.81
5642 7521 0.698238 CATCCCAACCACAGGAAGGA 59.302 55.000 0.00 0.00 35.30 3.36
5658 7537 9.539825 CACAGGAAGGATATATCAGCATATAAC 57.460 37.037 14.60 0.00 32.25 1.89
5659 7538 9.271921 ACAGGAAGGATATATCAGCATATAACA 57.728 33.333 14.60 0.00 32.25 2.41
5661 7540 8.709308 AGGAAGGATATATCAGCATATAACACC 58.291 37.037 14.60 2.75 32.25 4.16
5845 10396 1.660333 GCAAAAGTCACGCACTAGCAC 60.660 52.381 0.00 0.00 42.27 4.40
5936 10885 0.900647 AGGAAGGAGGGACACTGTCG 60.901 60.000 3.04 0.00 32.65 4.35
6003 10961 3.250762 TGAAGACTTTTCACCAGCGATTG 59.749 43.478 0.00 0.00 0.00 2.67
6009 10967 0.035152 TTCACCAGCGATTGCCTCAT 60.035 50.000 0.00 0.00 44.31 2.90
6010 10968 0.035152 TCACCAGCGATTGCCTCATT 60.035 50.000 0.00 0.00 44.31 2.57
6011 10969 0.813184 CACCAGCGATTGCCTCATTT 59.187 50.000 0.00 0.00 44.31 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.629617 CCAGCCAGTTGAGAAACCAAAT 59.370 45.455 0.00 0.00 0.00 2.32
58 59 6.517605 TGCAACACACACTTAGTATTACTCA 58.482 36.000 0.00 0.00 0.00 3.41
72 73 1.090728 ACACGTCAATGCAACACACA 58.909 45.000 0.00 0.00 0.00 3.72
95 96 6.316390 CAGAGTGAAAACAGGTGACTTTAGTT 59.684 38.462 0.00 0.00 40.21 2.24
97 98 5.277538 GCAGAGTGAAAACAGGTGACTTTAG 60.278 44.000 0.00 0.00 40.21 1.85
760 769 4.985538 AGCCAACTGATCTGAGGTAAAAA 58.014 39.130 6.60 0.00 0.00 1.94
797 806 2.093235 AGAGGACAGAGGTGCTTTATGC 60.093 50.000 0.00 0.00 46.62 3.14
871 880 6.266558 AGGGATGCAGTCTCAGTATTAACTAG 59.733 42.308 0.00 0.00 33.48 2.57
976 986 6.217294 TGTATGTCTGTAATTCACACGTTCA 58.783 36.000 0.00 0.00 32.33 3.18
1062 1072 7.658525 AAATATATGACTCATGGCCAAAACA 57.341 32.000 10.96 6.73 0.00 2.83
1239 1249 1.098869 TTTCTGTGCTCCAAAACGCA 58.901 45.000 0.00 0.00 0.00 5.24
1412 1422 1.586154 AAGGCACGGGAATTTCAGCG 61.586 55.000 0.00 0.00 0.00 5.18
1519 1529 1.893801 GAAGGGAGAGACGAAGAACCA 59.106 52.381 0.00 0.00 0.00 3.67
1684 1695 4.158394 AGTTATGCATGATGACCACCAAAC 59.842 41.667 10.16 0.80 0.00 2.93
1909 1920 6.883756 TGCAATACACATAAGGAAGATTGTCA 59.116 34.615 0.00 0.00 0.00 3.58
2412 2423 2.017049 GGTGCAACTCTTCAACTGTGT 58.983 47.619 0.00 0.00 36.74 3.72
2413 2424 2.292267 AGGTGCAACTCTTCAACTGTG 58.708 47.619 0.00 0.00 36.74 3.66
2554 2565 9.787532 AACTGTGCAATATGAACATTAACATAC 57.212 29.630 0.00 0.00 34.92 2.39
2748 2760 6.127451 ACTGGTCCTTCGAAAATGTTTCTTTT 60.127 34.615 0.00 0.00 0.00 2.27
2749 2761 5.359860 ACTGGTCCTTCGAAAATGTTTCTTT 59.640 36.000 0.00 0.00 0.00 2.52
2782 2794 6.870965 GTGGTATGTTTATTGCACCATTTTGA 59.129 34.615 0.00 0.00 41.12 2.69
2803 2815 0.469144 AATGGTTTTGGCTCCGTGGT 60.469 50.000 0.00 0.00 0.00 4.16
2924 2936 1.694150 ACTGCTTTGGTCTGCACTCTA 59.306 47.619 0.00 0.00 35.20 2.43
3046 3060 2.436173 GAGATACAACCCTTGCTAGCCT 59.564 50.000 13.29 0.00 0.00 4.58
3080 3094 3.572642 TCAGTTTCCAGTAGACCTCACA 58.427 45.455 0.00 0.00 0.00 3.58
3399 5255 5.359009 TCTTCATCAGATTTTCATCCTTGGC 59.641 40.000 0.00 0.00 0.00 4.52
3449 5308 1.207791 CTCCCCATACCTGAAGCAGT 58.792 55.000 0.00 0.00 0.00 4.40
4313 6172 5.746990 AGTGCTGGAACATAAGTAAGTCT 57.253 39.130 0.00 0.00 38.20 3.24
4357 6216 0.320771 CAGAAGGTTCACCCTCCACG 60.321 60.000 0.00 0.00 45.47 4.94
4525 6384 4.887071 TCTGTTTTTACATGCTCAGGTTGT 59.113 37.500 0.00 0.00 0.00 3.32
4566 6425 5.008415 CAGCCCTCATTCTGTTGATGAATAC 59.992 44.000 0.00 0.00 33.38 1.89
4715 6577 5.074584 AGACCTTTTCGTCCAGAACTATC 57.925 43.478 0.00 0.00 38.83 2.08
4761 6623 2.128035 CTTTCGTACGATCTGATGGGC 58.872 52.381 20.27 0.00 0.00 5.36
4774 6636 0.739462 CAGATGCACCGCCTTTCGTA 60.739 55.000 0.00 0.00 36.19 3.43
4798 6660 6.486657 GCAATGTAGCCTTCATATCCTTTGTA 59.513 38.462 0.00 0.00 0.00 2.41
4801 6663 5.699143 AGCAATGTAGCCTTCATATCCTTT 58.301 37.500 0.00 0.00 34.23 3.11
4808 6670 4.226427 TCTTGAGCAATGTAGCCTTCAT 57.774 40.909 0.00 0.00 34.23 2.57
4855 6717 1.406341 CCTTTTGCTTGCCCATCCATG 60.406 52.381 0.00 0.00 0.00 3.66
4923 6785 2.529151 CCGCCACATTTAGTTTGATGC 58.471 47.619 0.00 0.00 0.00 3.91
4954 6816 6.459923 GGAACCATCACCTATAATCTCAGAC 58.540 44.000 0.00 0.00 0.00 3.51
4978 6840 0.392729 CTGCTCCCTTCAGCTCAAGG 60.393 60.000 9.89 9.89 42.57 3.61
4999 6861 0.888285 GGATGCCCTGCTCAGTATGC 60.888 60.000 0.00 0.00 34.76 3.14
5004 6866 1.751927 GTTGGGATGCCCTGCTCAG 60.752 63.158 0.00 0.00 45.70 3.35
5018 6880 4.338118 TGCCTCTTAACTCAGTTTTGTTGG 59.662 41.667 0.00 0.00 0.00 3.77
5109 6971 3.861689 GCCATAAGCAAAAGCAGCTAAAG 59.138 43.478 0.00 0.00 42.53 1.85
5167 7029 3.069443 ACCAAACCAACCATGATGTCAAC 59.931 43.478 0.00 0.00 0.00 3.18
5270 7138 3.157881 TGAGGACCAACACAACAACAAA 58.842 40.909 0.00 0.00 0.00 2.83
5271 7139 2.796557 TGAGGACCAACACAACAACAA 58.203 42.857 0.00 0.00 0.00 2.83
5272 7140 2.498644 TGAGGACCAACACAACAACA 57.501 45.000 0.00 0.00 0.00 3.33
5273 7141 2.948979 TGATGAGGACCAACACAACAAC 59.051 45.455 0.00 0.00 0.00 3.32
5385 7259 0.180406 AAGAGAACACAGTTGCCGGT 59.820 50.000 1.90 0.00 0.00 5.28
5425 7299 2.249337 CAAGCATGCGCGACATAAAAA 58.751 42.857 12.10 0.00 45.49 1.94
5480 7357 4.203226 GGAGCTCTCTTTATCCCAAAAGG 58.797 47.826 14.64 0.00 37.13 3.11
5522 7399 6.037172 CCTGTTAGGAAGACATTATGGTTTCG 59.963 42.308 0.00 0.00 37.67 3.46
5530 7407 5.027460 TGGTAGCCTGTTAGGAAGACATTA 58.973 41.667 0.00 0.00 37.67 1.90
5559 7436 1.663445 CGCCGGTTTATGTTTTTCGCA 60.663 47.619 1.90 0.00 0.00 5.10
5642 7521 9.982651 GGTTATCGGTGTTATATGCTGATATAT 57.017 33.333 0.00 0.00 32.53 0.86
5658 7537 8.419442 ACCTTAAGTTTATCTAGGTTATCGGTG 58.581 37.037 0.97 0.00 32.83 4.94
5659 7538 8.544687 ACCTTAAGTTTATCTAGGTTATCGGT 57.455 34.615 0.97 0.00 32.83 4.69
5712 7592 3.645212 TCCCAGGATGATGATTCTCTGAC 59.355 47.826 0.00 0.00 39.69 3.51
5808 10359 2.032680 TGCAAGAATTACCGGTAGCC 57.967 50.000 15.20 8.03 0.00 3.93
5845 10396 1.003116 CATACCCTTCTACGGTCGTCG 60.003 57.143 0.00 0.00 45.88 5.12
5936 10885 2.094182 TCGCTTAGGATCACTGTTGGAC 60.094 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.