Multiple sequence alignment - TraesCS3A01G063400

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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 TraesCS3A01G063400 chr3A 100.000 2071 0 0 1 2071 37970065 37972135 0.000000e+00 3825.0
1 TraesCS3A01G063400 chr3A 97.396 2074 51 2 1 2071 24109697 24107624 0.000000e+00 3528.0
2 TraesCS3A01G063400 chr3A 100.000 722 0 0 2333 3054 37972397 37973118 0.000000e+00 1334.0
3 TraesCS3A01G063400 chr3A 97.510 723 17 1 2333 3054 24107578 24106856 0.000000e+00 1234.0
4 TraesCS3A01G063400 chr7B 96.575 2073 58 2 1 2071 252388836 252386775 0.000000e+00 3422.0
5 TraesCS3A01G063400 chr7B 96.819 723 21 2 2333 3054 252386729 252386008 0.000000e+00 1206.0
6 TraesCS3A01G063400 chr3D 96.257 2004 63 4 1 2001 604384004 604382010 0.000000e+00 3275.0
7 TraesCS3A01G063400 chr3D 95.577 2035 79 3 1 2034 77343711 77345735 0.000000e+00 3249.0
8 TraesCS3A01G063400 chr3D 97.077 650 18 1 2406 3054 604381672 604381023 0.000000e+00 1094.0
9 TraesCS3A01G063400 chr3D 85.714 70 4 2 2348 2411 597050793 597050724 5.460000e-08 69.4
10 TraesCS3A01G063400 chr7D 93.522 2084 108 19 1 2071 540632547 540634616 0.000000e+00 3075.0
11 TraesCS3A01G063400 chr6D 95.905 1636 62 4 1 1633 458416609 458414976 0.000000e+00 2645.0
12 TraesCS3A01G063400 chr6D 95.782 1636 64 4 1 1633 458426350 458424717 0.000000e+00 2634.0
13 TraesCS3A01G063400 chr6D 96.952 689 20 1 2367 3054 458414531 458413843 0.000000e+00 1155.0
14 TraesCS3A01G063400 chr6D 96.486 370 12 1 1702 2071 458424717 458424349 7.240000e-171 610.0
15 TraesCS3A01G063400 chr6D 95.687 371 15 1 1702 2071 458414976 458414606 2.030000e-166 595.0
16 TraesCS3A01G063400 chr2B 93.863 1222 55 4 851 2071 742548288 742547086 0.000000e+00 1823.0
17 TraesCS3A01G063400 chr2B 95.566 857 35 2 1 855 742553913 742553058 0.000000e+00 1369.0
18 TraesCS3A01G063400 chr2B 95.961 718 23 3 2333 3045 742547039 742546323 0.000000e+00 1160.0
19 TraesCS3A01G063400 chr2D 87.405 921 80 13 1176 2071 615213990 615214899 0.000000e+00 1026.0
20 TraesCS3A01G063400 chr2D 88.105 723 56 14 40 745 615213296 615214005 0.000000e+00 832.0
21 TraesCS3A01G063400 chr2D 90.657 578 44 3 2469 3045 615215477 615216045 0.000000e+00 760.0
22 TraesCS3A01G063400 chr4B 90.830 578 44 3 2469 3045 133361787 133362356 0.000000e+00 765.0
23 TraesCS3A01G063400 chr4B 87.397 484 51 7 1593 2071 133360847 133361325 5.760000e-152 547.0
24 TraesCS3A01G063400 chr4B 92.063 63 5 0 2348 2410 133361413 133361475 4.190000e-14 89.8
25 TraesCS3A01G063400 chr6A 84.511 807 78 20 1225 2009 113071035 113071816 0.000000e+00 754.0
26 TraesCS3A01G063400 chr6A 87.692 585 55 9 2469 3046 113308774 113309348 0.000000e+00 665.0
27 TraesCS3A01G063400 chr6A 86.792 583 60 7 2469 3044 113085659 113086231 4.300000e-178 634.0
28 TraesCS3A01G063400 chr6A 91.176 68 6 0 2344 2411 113085357 113085424 3.240000e-15 93.5
29 TraesCS3A01G063400 chr7A 86.250 320 36 5 745 1063 109848464 109848152 1.050000e-89 340.0
30 TraesCS3A01G063400 chr7A 85.016 307 39 3 758 1063 732709946 732710246 3.830000e-79 305.0
31 TraesCS3A01G063400 chr1D 87.097 62 4 2 2345 2402 125788203 125788264 1.970000e-07 67.6


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 TraesCS3A01G063400 chr3A 37970065 37973118 3053 False 2579.500000 3825 100.000000 1 3054 2 chr3A.!!$F1 3053
1 TraesCS3A01G063400 chr3A 24106856 24109697 2841 True 2381.000000 3528 97.453000 1 3054 2 chr3A.!!$R1 3053
2 TraesCS3A01G063400 chr7B 252386008 252388836 2828 True 2314.000000 3422 96.697000 1 3054 2 chr7B.!!$R1 3053
3 TraesCS3A01G063400 chr3D 77343711 77345735 2024 False 3249.000000 3249 95.577000 1 2034 1 chr3D.!!$F1 2033
4 TraesCS3A01G063400 chr3D 604381023 604384004 2981 True 2184.500000 3275 96.667000 1 3054 2 chr3D.!!$R2 3053
5 TraesCS3A01G063400 chr7D 540632547 540634616 2069 False 3075.000000 3075 93.522000 1 2071 1 chr7D.!!$F1 2070
6 TraesCS3A01G063400 chr6D 458424349 458426350 2001 True 1622.000000 2634 96.134000 1 2071 2 chr6D.!!$R2 2070
7 TraesCS3A01G063400 chr6D 458413843 458416609 2766 True 1465.000000 2645 96.181333 1 3054 3 chr6D.!!$R1 3053
8 TraesCS3A01G063400 chr2B 742546323 742548288 1965 True 1491.500000 1823 94.912000 851 3045 2 chr2B.!!$R2 2194
9 TraesCS3A01G063400 chr2B 742553058 742553913 855 True 1369.000000 1369 95.566000 1 855 1 chr2B.!!$R1 854
10 TraesCS3A01G063400 chr2D 615213296 615216045 2749 False 872.666667 1026 88.722333 40 3045 3 chr2D.!!$F1 3005
11 TraesCS3A01G063400 chr4B 133360847 133362356 1509 False 467.266667 765 90.096667 1593 3045 3 chr4B.!!$F1 1452
12 TraesCS3A01G063400 chr6A 113071035 113071816 781 False 754.000000 754 84.511000 1225 2009 1 chr6A.!!$F1 784
13 TraesCS3A01G063400 chr6A 113308774 113309348 574 False 665.000000 665 87.692000 2469 3046 1 chr6A.!!$F2 577
14 TraesCS3A01G063400 chr6A 113085357 113086231 874 False 363.750000 634 88.984000 2344 3044 2 chr6A.!!$F3 700

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
865 887 0.251474 TGGTGTACAGGCGTAGGAGT 60.251 55.0 0.00 0.00 0.00 3.85 F
927 949 0.533308 AAACTGGAAACTACGCGCCA 60.533 50.0 5.73 2.82 0.00 5.69 F
1041 1063 0.807275 CTCCGTCGAAGATGCATGCA 60.807 55.0 25.04 25.04 43.31 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1925 1.735926 TGGGGACATGTACCACAAGA 58.264 50.000 28.58 3.75 37.93 3.02 R
2011 2094 5.128919 ACCTTGAAGGAATGCATGATCTAC 58.871 41.667 19.83 0.00 37.67 2.59 R
2931 3438 3.327757 AGGAGAGTAACAGCCAACATTCA 59.672 43.478 0.00 0.00 0.00 2.57 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
358 375 5.996669 AAGACTAAACAGTTTAACGTGGG 57.003 39.130 7.18 0.00 0.00 4.61
468 485 3.441572 AGGAAGAAAGGATTGTCAATGCG 59.558 43.478 10.97 0.00 34.03 4.73
514 531 7.444183 CGGGCCATATTTGTCTAGAAAAGAATA 59.556 37.037 4.39 0.00 35.47 1.75
549 567 5.957771 ACAGGACCTAGCAAATATTGAGA 57.042 39.130 0.00 0.00 0.00 3.27
772 794 1.736612 TCATGAATACGCAAGCTGCA 58.263 45.000 1.02 0.00 45.36 4.41
776 798 4.516321 TCATGAATACGCAAGCTGCATATT 59.484 37.500 1.02 8.51 43.33 1.28
865 887 0.251474 TGGTGTACAGGCGTAGGAGT 60.251 55.000 0.00 0.00 0.00 3.85
927 949 0.533308 AAACTGGAAACTACGCGCCA 60.533 50.000 5.73 2.82 0.00 5.69
1041 1063 0.807275 CTCCGTCGAAGATGCATGCA 60.807 55.000 25.04 25.04 43.31 3.96
1069 1123 0.954449 CTTCCAGAGCCACTGTGCAG 60.954 60.000 1.29 0.00 44.40 4.41
1095 1149 4.735132 CGGCGTGTGGTCGTGGAT 62.735 66.667 0.00 0.00 39.39 3.41
1132 1186 1.534697 GAAGGGTGTGTTGGGGTCA 59.465 57.895 0.00 0.00 0.00 4.02
1267 1321 2.174363 TGTGCACAGATGAGTCCTTG 57.826 50.000 17.42 0.00 0.00 3.61
1844 1925 3.370315 GGCTCAACACATCTGAATCTCCT 60.370 47.826 0.00 0.00 0.00 3.69
1985 2068 5.285607 CCGTGATGTCTTCTCGTTTACTAAC 59.714 44.000 8.72 0.00 39.17 2.34
2011 2094 4.753233 AGCATGCTCTTGTCTGTACTAAG 58.247 43.478 16.30 0.00 0.00 2.18
2564 3062 9.624697 TCTGCAATGTTGTTTAATAAACTCATC 57.375 29.630 15.80 10.08 41.90 2.92
2624 3122 5.861251 GCCGCACATCTATATCTATATCAGC 59.139 44.000 0.00 0.00 0.00 4.26
2931 3438 9.768662 AGAAAGCAATGATCAAAAGTATTTGTT 57.231 25.926 0.00 0.00 45.02 2.83
2972 3479 2.548057 CCTTTTCTGCGTACAAAGCTGA 59.452 45.455 0.00 0.00 40.05 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 169 5.165961 TCTCTATGTATAATGCAAGCCCC 57.834 43.478 0.00 0.00 0.00 5.80
253 270 7.329588 ACACACTTTTAAAAGAAATCCTCGT 57.670 32.000 29.97 13.87 39.31 4.18
358 375 8.920509 AACACACATAAAAAGGTTTCAGTAAC 57.079 30.769 0.00 0.00 35.94 2.50
468 485 2.745102 GCTAGCTGACTTATCCGAACC 58.255 52.381 7.70 0.00 0.00 3.62
514 531 2.644798 AGGTCCTGTTACATTTCTGCCT 59.355 45.455 0.00 0.00 0.00 4.75
792 814 3.618507 GCAACCTCATGCTTGTACTCTCT 60.619 47.826 0.00 0.00 43.06 3.10
865 887 7.578458 AAATTAACCCCCTTGTTCTAGTCTA 57.422 36.000 0.00 0.00 0.00 2.59
915 937 1.449601 CATCCCTGGCGCGTAGTTT 60.450 57.895 8.43 0.00 0.00 2.66
927 949 4.396357 TGGGTTACAAAACATCATCCCT 57.604 40.909 0.00 0.00 37.34 4.20
1041 1063 4.308526 CTCTGGAAGCACCGCAAT 57.691 55.556 0.00 0.00 42.61 3.56
1083 1137 1.103803 GAGCTCTATCCACGACCACA 58.896 55.000 6.43 0.00 0.00 4.17
1094 1148 4.528076 TCCAGACTTGGTAGAGCTCTAT 57.472 45.455 25.74 10.09 45.26 1.98
1095 1149 4.274147 CTTCCAGACTTGGTAGAGCTCTA 58.726 47.826 19.72 19.72 42.72 2.43
1267 1321 3.746492 AGAACTGTGACAACGAAATAGGC 59.254 43.478 0.00 0.00 0.00 3.93
1481 1536 5.006386 AGAACTGCTCCCAAACTAAGATTG 58.994 41.667 0.00 0.00 0.00 2.67
1844 1925 1.735926 TGGGGACATGTACCACAAGA 58.264 50.000 28.58 3.75 37.93 3.02
2011 2094 5.128919 ACCTTGAAGGAATGCATGATCTAC 58.871 41.667 19.83 0.00 37.67 2.59
2564 3062 8.822652 AATCTAAAGGCAAGAACATTTTCAAG 57.177 30.769 0.00 0.00 33.72 3.02
2603 3101 7.870826 AGACGCTGATATAGATATAGATGTGC 58.129 38.462 0.00 0.00 0.00 4.57
2931 3438 3.327757 AGGAGAGTAACAGCCAACATTCA 59.672 43.478 0.00 0.00 0.00 2.57
2972 3479 6.379133 ACAGAAGTTGAATGCCATGACATTAT 59.621 34.615 7.27 0.00 40.31 1.28


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

AutoCloner maintained by Alex Coulton.