Multiple sequence alignment - TraesCS3D01G439900

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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 TraesCS3D01G439900 chr3D 100.000 2573 0 0 1 2573 550268998 550271570 0.000000e+00 4752.0
1 TraesCS3D01G439900 chr3D 83.832 835 116 18 1750 2572 537593066 537593893 0.000000e+00 776.0
2 TraesCS3D01G439900 chr3D 82.908 901 111 27 29 914 362865929 362865057 0.000000e+00 771.0
3 TraesCS3D01G439900 chr3D 81.081 111 17 4 809 916 15913968 15913859 4.560000e-13 86.1
4 TraesCS3D01G439900 chr3A 95.350 1441 48 9 736 2170 687103047 687104474 0.000000e+00 2272.0
5 TraesCS3D01G439900 chr3A 96.901 710 18 4 1 707 687102345 687103053 0.000000e+00 1186.0
6 TraesCS3D01G439900 chr3B 91.725 1281 97 8 343 1615 729723746 729725025 0.000000e+00 1770.0
7 TraesCS3D01G439900 chr3B 92.291 947 51 15 1636 2573 729725074 729726007 0.000000e+00 1325.0
8 TraesCS3D01G439900 chr5B 86.553 818 98 11 29 839 167295538 167296350 0.000000e+00 891.0
9 TraesCS3D01G439900 chr5A 83.516 910 123 16 29 916 189012168 189013072 0.000000e+00 824.0
10 TraesCS3D01G439900 chr5A 84.013 638 92 8 25 655 693493381 693494015 2.830000e-169 604.0
11 TraesCS3D01G439900 chr4D 86.104 770 92 11 100 860 483204553 483203790 0.000000e+00 815.0
12 TraesCS3D01G439900 chr2D 84.689 836 98 24 1750 2573 398645218 398646035 0.000000e+00 808.0
13 TraesCS3D01G439900 chr2D 82.754 835 118 21 1750 2571 521409893 521409072 0.000000e+00 721.0
14 TraesCS3D01G439900 chr6A 84.810 790 101 14 29 806 454544397 454543615 0.000000e+00 776.0
15 TraesCS3D01G439900 chr2A 83.914 833 109 20 1750 2573 535833839 535834655 0.000000e+00 773.0
16 TraesCS3D01G439900 chr5D 82.068 909 119 24 29 914 178459600 178458713 0.000000e+00 736.0
17 TraesCS3D01G439900 chr6B 84.375 736 99 13 1750 2477 471005280 471004553 0.000000e+00 708.0
18 TraesCS3D01G439900 chr4A 82.233 833 128 18 1750 2571 133846279 133845456 0.000000e+00 701.0
19 TraesCS3D01G439900 chr4A 77.477 111 21 4 810 917 20639557 20639448 2.140000e-06 63.9
20 TraesCS3D01G439900 chr2B 82.382 806 114 24 1780 2571 614504861 614505652 0.000000e+00 676.0
21 TraesCS3D01G439900 chr7B 84.362 697 98 10 34 721 333355507 333354813 0.000000e+00 673.0
22 TraesCS3D01G439900 chr7A 82.976 699 100 17 34 721 195201569 195202259 4.710000e-172 614.0
23 TraesCS3D01G439900 chr1D 79.091 110 19 4 810 916 340669030 340669138 3.550000e-09 73.1
24 TraesCS3D01G439900 chr1B 78.182 110 19 5 810 916 29500417 29500524 5.940000e-07 65.8


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 TraesCS3D01G439900 chr3D 550268998 550271570 2572 False 4752.0 4752 100.0000 1 2573 1 chr3D.!!$F2 2572
1 TraesCS3D01G439900 chr3D 537593066 537593893 827 False 776.0 776 83.8320 1750 2572 1 chr3D.!!$F1 822
2 TraesCS3D01G439900 chr3D 362865057 362865929 872 True 771.0 771 82.9080 29 914 1 chr3D.!!$R2 885
3 TraesCS3D01G439900 chr3A 687102345 687104474 2129 False 1729.0 2272 96.1255 1 2170 2 chr3A.!!$F1 2169
4 TraesCS3D01G439900 chr3B 729723746 729726007 2261 False 1547.5 1770 92.0080 343 2573 2 chr3B.!!$F1 2230
5 TraesCS3D01G439900 chr5B 167295538 167296350 812 False 891.0 891 86.5530 29 839 1 chr5B.!!$F1 810
6 TraesCS3D01G439900 chr5A 189012168 189013072 904 False 824.0 824 83.5160 29 916 1 chr5A.!!$F1 887
7 TraesCS3D01G439900 chr5A 693493381 693494015 634 False 604.0 604 84.0130 25 655 1 chr5A.!!$F2 630
8 TraesCS3D01G439900 chr4D 483203790 483204553 763 True 815.0 815 86.1040 100 860 1 chr4D.!!$R1 760
9 TraesCS3D01G439900 chr2D 398645218 398646035 817 False 808.0 808 84.6890 1750 2573 1 chr2D.!!$F1 823
10 TraesCS3D01G439900 chr2D 521409072 521409893 821 True 721.0 721 82.7540 1750 2571 1 chr2D.!!$R1 821
11 TraesCS3D01G439900 chr6A 454543615 454544397 782 True 776.0 776 84.8100 29 806 1 chr6A.!!$R1 777
12 TraesCS3D01G439900 chr2A 535833839 535834655 816 False 773.0 773 83.9140 1750 2573 1 chr2A.!!$F1 823
13 TraesCS3D01G439900 chr5D 178458713 178459600 887 True 736.0 736 82.0680 29 914 1 chr5D.!!$R1 885
14 TraesCS3D01G439900 chr6B 471004553 471005280 727 True 708.0 708 84.3750 1750 2477 1 chr6B.!!$R1 727
15 TraesCS3D01G439900 chr4A 133845456 133846279 823 True 701.0 701 82.2330 1750 2571 1 chr4A.!!$R2 821
16 TraesCS3D01G439900 chr2B 614504861 614505652 791 False 676.0 676 82.3820 1780 2571 1 chr2B.!!$F1 791
17 TraesCS3D01G439900 chr7B 333354813 333355507 694 True 673.0 673 84.3620 34 721 1 chr7B.!!$R1 687
18 TraesCS3D01G439900 chr7A 195201569 195202259 690 False 614.0 614 82.9760 34 721 1 chr7A.!!$F1 687

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
853 905 0.602638 TACAACAAGCTGCAGGGACG 60.603 55.0 17.12 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1870 2.290705 TGAGTGGTCTCAGATGTACCGA 60.291 50.0 0.0 0.0 44.58 4.69 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
21 22 4.543590 CTTCATGTACTTCCAGTGTCCT 57.456 45.455 0.00 0.00 0.00 3.85
22 23 5.661056 CTTCATGTACTTCCAGTGTCCTA 57.339 43.478 0.00 0.00 0.00 2.94
25 26 6.620877 TCATGTACTTCCAGTGTCCTAAAT 57.379 37.500 0.00 0.00 0.00 1.40
26 27 6.640518 TCATGTACTTCCAGTGTCCTAAATC 58.359 40.000 0.00 0.00 0.00 2.17
27 28 6.440647 TCATGTACTTCCAGTGTCCTAAATCT 59.559 38.462 0.00 0.00 0.00 2.40
29 30 7.786046 TGTACTTCCAGTGTCCTAAATCTTA 57.214 36.000 0.00 0.00 0.00 2.10
30 31 8.375493 TGTACTTCCAGTGTCCTAAATCTTAT 57.625 34.615 0.00 0.00 0.00 1.73
31 32 9.483489 TGTACTTCCAGTGTCCTAAATCTTATA 57.517 33.333 0.00 0.00 0.00 0.98
359 368 5.753721 AAGAGAGAAGCTGGTGAAAGTAT 57.246 39.130 0.00 0.00 0.00 2.12
391 403 7.255104 GCCTACGGATTGTGATTTATTCATTGA 60.255 37.037 0.00 0.00 36.54 2.57
828 880 3.443681 CCAACTTAAAGATGGATTGCGGT 59.556 43.478 0.00 0.00 40.25 5.68
835 887 5.913137 AAAGATGGATTGCGGTTTGATTA 57.087 34.783 0.00 0.00 0.00 1.75
853 905 0.602638 TACAACAAGCTGCAGGGACG 60.603 55.000 17.12 0.00 0.00 4.79
889 950 3.119743 ACGACGAACGATCAGAAATGGTA 60.120 43.478 0.00 0.00 45.77 3.25
925 987 2.761208 AGGTAGAGATATGGGCGTATGC 59.239 50.000 0.00 0.00 41.71 3.14
927 989 3.133003 GGTAGAGATATGGGCGTATGCAT 59.867 47.826 9.59 3.79 45.35 3.96
928 990 3.257469 AGAGATATGGGCGTATGCATG 57.743 47.619 10.16 0.00 45.35 4.06
930 992 2.932614 GAGATATGGGCGTATGCATGTC 59.067 50.000 10.16 2.81 45.35 3.06
1156 1218 3.473647 TCCTCTCAGCATGCCCGG 61.474 66.667 15.66 7.99 34.76 5.73
1167 1229 1.227853 ATGCCCGGCGAGTAAATCC 60.228 57.895 9.30 0.00 0.00 3.01
1470 1532 2.082231 CTCTCGAAAGACGGTGACCTA 58.918 52.381 0.00 0.00 42.82 3.08
1576 1638 2.557924 ACACCGTCCACGTATTAGAACA 59.442 45.455 0.00 0.00 37.74 3.18
1626 1688 8.432359 GCGCCACTAATAATATAAATTTTTGGC 58.568 33.333 16.35 16.35 0.00 4.52
1778 1870 2.169146 GCGCGGTTGCCTTACGTAT 61.169 57.895 8.83 0.00 38.08 3.06
1806 1899 4.244066 CATCTGAGACCACTCACTTCTTG 58.756 47.826 0.00 0.00 46.55 3.02
2560 2678 7.370383 ACTATGCAAAGTGAAATGTAGGTTTG 58.630 34.615 0.00 0.00 0.00 2.93
2561 2679 5.843673 TGCAAAGTGAAATGTAGGTTTGA 57.156 34.783 0.00 0.00 0.00 2.69
2564 2682 6.756074 TGCAAAGTGAAATGTAGGTTTGAAAG 59.244 34.615 0.00 0.00 0.00 2.62
2565 2683 6.756542 GCAAAGTGAAATGTAGGTTTGAAAGT 59.243 34.615 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
391 403 3.054802 AGGAGCGAGTCAGGAAATGATTT 60.055 43.478 0.00 0.00 40.92 2.17
828 880 3.005684 CCCTGCAGCTTGTTGTAATCAAA 59.994 43.478 8.66 0.00 35.20 2.69
835 887 1.893808 CGTCCCTGCAGCTTGTTGT 60.894 57.895 8.66 0.00 0.00 3.32
873 933 2.671396 GCACGTACCATTTCTGATCGTT 59.329 45.455 0.00 0.00 0.00 3.85
923 985 2.822758 GCGCTATTGCCGACATGCA 61.823 57.895 0.00 0.00 40.07 3.96
925 987 2.633657 GGCGCTATTGCCGACATG 59.366 61.111 7.64 0.00 46.75 3.21
1116 1178 2.097825 GTGACACAGTACTCCGGGTAT 58.902 52.381 0.00 0.00 32.56 2.73
1157 1219 2.574222 GCGTCCGCGGATTTACTCG 61.574 63.158 33.58 28.09 38.78 4.18
1248 1310 1.710244 TCCTTGATGCCCTTTTCCTCA 59.290 47.619 0.00 0.00 0.00 3.86
1470 1532 1.489481 TGACGCCCATGATCTTCTCT 58.511 50.000 0.00 0.00 0.00 3.10
1778 1870 2.290705 TGAGTGGTCTCAGATGTACCGA 60.291 50.000 0.00 0.00 44.58 4.69
1806 1899 5.988561 GGTCATACATTCTCAGGAATCTCAC 59.011 44.000 0.00 0.00 39.87 3.51
1815 1909 4.895889 TCTAGGTGGGTCATACATTCTCAG 59.104 45.833 0.00 0.00 0.00 3.35
1872 1967 5.760253 ACTGACACTGATTTGACTAACAAGG 59.240 40.000 0.00 0.00 39.77 3.61
2332 2441 9.621629 ATCACATCCATTTCAATTGCATATTTT 57.378 25.926 0.00 0.00 0.00 1.82
2337 2446 7.931578 AAAATCACATCCATTTCAATTGCAT 57.068 28.000 0.00 0.00 0.00 3.96
2538 2656 6.403866 TCAAACCTACATTTCACTTTGCAT 57.596 33.333 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.