Multiple sequence alignment - TraesCS4A01G079200

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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 TraesCS4A01G079200 chr4A 100.000 4067 0 0 1 4067 80848051 80843985 0.000000e+00 7511.0
1 TraesCS4A01G079200 chr4D 95.922 4071 117 16 4 4066 409148105 409144076 0.000000e+00 6553.0
2 TraesCS4A01G079200 chr4B 93.790 4090 179 33 15 4066 506920203 506924255 0.000000e+00 6076.0
3 TraesCS4A01G079200 chr4B 90.541 74 5 2 1835 1907 237991429 237991501 3.350000e-16 97.1
4 TraesCS4A01G079200 chr4B 100.000 29 0 0 1849 1877 636773293 636773265 2.000000e-03 54.7
5 TraesCS4A01G079200 chr1A 89.011 91 9 1 1021 1111 297845508 297845597 1.190000e-20 111.0
6 TraesCS4A01G079200 chr2D 92.754 69 4 1 1840 1908 588161582 588161649 9.300000e-17 99.0
7 TraesCS4A01G079200 chr6A 97.727 44 0 1 4024 4066 607377002 607376959 1.570000e-09 75.0
8 TraesCS4A01G079200 chr5A 97.561 41 0 1 4027 4066 265046080 265046120 7.290000e-08 69.4
9 TraesCS4A01G079200 chr2B 92.000 50 2 2 4017 4066 13775262 13775309 7.290000e-08 69.4
10 TraesCS4A01G079200 chrUn 97.500 40 0 1 4027 4066 198026640 198026602 2.620000e-07 67.6
11 TraesCS4A01G079200 chrUn 97.500 40 0 1 4027 4066 347055361 347055323 2.620000e-07 67.6
12 TraesCS4A01G079200 chr3D 97.500 40 0 1 4027 4066 303360576 303360538 2.620000e-07 67.6
13 TraesCS4A01G079200 chr1D 97.500 40 0 1 4027 4066 330085777 330085739 2.620000e-07 67.6
14 TraesCS4A01G079200 chr1B 91.837 49 2 2 4018 4066 586766255 586766301 2.620000e-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 TraesCS4A01G079200 chr4A 80843985 80848051 4066 True 7511 7511 100.000 1 4067 1 chr4A.!!$R1 4066
1 TraesCS4A01G079200 chr4D 409144076 409148105 4029 True 6553 6553 95.922 4 4066 1 chr4D.!!$R1 4062
2 TraesCS4A01G079200 chr4B 506920203 506924255 4052 False 6076 6076 93.790 15 4066 1 chr4B.!!$F2 4051

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
188 194 0.962855 GGCTCAAAACTGGCTCTCCC 60.963 60.000 0.00 0.00 0.00 4.30 F
1808 1844 0.319040 CTCGACCCTGTCATATGCGG 60.319 60.000 0.00 0.00 32.09 5.69 F
1830 1866 0.374758 CGGTGATCAAGGTGCATTCG 59.625 55.000 0.00 0.00 0.00 3.34 F
1920 1956 1.001487 CTGGTCGTGTACAACACCGTA 60.001 52.381 16.23 3.26 45.93 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2120 0.179134 GTCCATCACCTCGTCCTTCG 60.179 60.000 0.00 0.0 41.41 3.79 R
2723 2759 0.095935 CTGCACGTTGCTGTAGATGC 59.904 55.000 10.54 0.0 45.31 3.91 R
3057 3093 0.748005 ATTGTGCATCCTACACGGCC 60.748 55.000 0.00 0.0 41.03 6.13 R
3756 3799 1.419387 AGTGGGATGAGGCATCTAAGC 59.581 52.381 0.00 0.0 40.39 3.09 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
113 116 7.668525 ACTGAAGCTTACTTTGTAATGGTAC 57.331 36.000 0.00 0.00 35.82 3.34
188 194 0.962855 GGCTCAAAACTGGCTCTCCC 60.963 60.000 0.00 0.00 0.00 4.30
285 292 1.425428 CCCTGAAATTCAGTCGCGC 59.575 57.895 20.18 0.00 42.80 6.86
443 450 1.000955 TGAGAGAAGACGACTTTGCCC 59.999 52.381 0.83 0.00 36.39 5.36
585 592 3.849953 GACGGCGTGCGTGAATCC 61.850 66.667 21.19 0.00 0.00 3.01
630 637 1.985116 GGTGGGCTCGAGAGGAGTT 60.985 63.158 18.75 0.00 45.03 3.01
631 638 1.513622 GTGGGCTCGAGAGGAGTTC 59.486 63.158 18.75 0.00 45.03 3.01
858 865 4.863925 GCCTCGCCTCGCTCTGAC 62.864 72.222 0.00 0.00 0.00 3.51
859 866 4.544689 CCTCGCCTCGCTCTGACG 62.545 72.222 0.00 0.00 0.00 4.35
879 906 1.524482 GAGGTGTCCCTGGCATCTC 59.476 63.158 0.00 0.00 42.86 2.75
984 1012 2.183811 CCACAGGAGAGCAGAGCG 59.816 66.667 0.00 0.00 0.00 5.03
985 1013 2.183811 CACAGGAGAGCAGAGCGG 59.816 66.667 0.00 0.00 0.00 5.52
986 1014 3.073735 ACAGGAGAGCAGAGCGGG 61.074 66.667 0.00 0.00 0.00 6.13
987 1015 3.847602 CAGGAGAGCAGAGCGGGG 61.848 72.222 0.00 0.00 0.00 5.73
1014 1047 1.403687 GCGAGATGGCTTCCCTACCT 61.404 60.000 0.00 0.00 0.00 3.08
1023 1056 0.969894 CTTCCCTACCTATCTGCCCG 59.030 60.000 0.00 0.00 0.00 6.13
1467 1503 1.218316 GTTCCTGGAGAACGCGGAT 59.782 57.895 12.47 0.00 45.21 4.18
1674 1710 1.298713 CGAGAAGATGCCGGAGTCG 60.299 63.158 5.05 0.00 0.00 4.18
1698 1734 4.794439 TCGCCGGACATGCTCACG 62.794 66.667 5.05 0.00 0.00 4.35
1771 1807 2.356553 GCTTGTACGACCGTGCCA 60.357 61.111 5.20 0.00 0.00 4.92
1808 1844 0.319040 CTCGACCCTGTCATATGCGG 60.319 60.000 0.00 0.00 32.09 5.69
1827 1863 2.858622 CACGGTGATCAAGGTGCAT 58.141 52.632 12.77 0.00 0.00 3.96
1830 1866 0.374758 CGGTGATCAAGGTGCATTCG 59.625 55.000 0.00 0.00 0.00 3.34
1920 1956 1.001487 CTGGTCGTGTACAACACCGTA 60.001 52.381 16.23 3.26 45.93 4.02
1921 1957 1.612950 TGGTCGTGTACAACACCGTAT 59.387 47.619 16.23 0.00 45.93 3.06
1974 2010 2.832129 GGTAGTGAAGACCATCCACAGA 59.168 50.000 0.00 0.00 36.91 3.41
2007 2043 2.203538 AAGGTGCAGCCCAACAGG 60.204 61.111 13.29 0.00 38.26 4.00
2084 2120 2.728922 GATGATCGTGTACCGGAAGAC 58.271 52.381 9.46 3.35 37.11 3.01
2305 2341 2.968574 GAGGCCATACTGAAGGAGATGA 59.031 50.000 5.01 0.00 0.00 2.92
2343 2379 2.648059 CCCAACATCTTCATCCTCACC 58.352 52.381 0.00 0.00 0.00 4.02
2595 2631 4.239991 TCCTTCAAGGAGGCAGCT 57.760 55.556 0.34 0.00 40.06 4.24
2910 2946 2.627217 GGAGGGGAGGAACATGTACTCT 60.627 54.545 22.41 11.36 0.00 3.24
3057 3093 4.152526 CGAAGAAGTCGTCAGAACTAGTG 58.847 47.826 0.00 0.00 45.09 2.74
3066 3102 1.816835 TCAGAACTAGTGGCCGTGTAG 59.183 52.381 0.00 0.85 0.00 2.74
3068 3104 1.180029 GAACTAGTGGCCGTGTAGGA 58.820 55.000 0.00 0.00 45.00 2.94
3090 3126 3.031736 TGCACAATCTAGGAGGAGGTAC 58.968 50.000 0.00 0.00 0.00 3.34
3142 3184 6.072175 GCATAACTTGTGGGTGTTCTGAAATA 60.072 38.462 0.00 0.00 0.00 1.40
3262 3305 4.740695 GCGATGATCTGTTAGAACACCTAC 59.259 45.833 0.00 0.00 29.64 3.18
3306 3349 1.015109 GATGTGTGCTGCCATCTCAG 58.985 55.000 9.28 0.00 35.63 3.35
3340 3383 9.527157 AGACAGTAGTAGCATAGATGATTGTAT 57.473 33.333 0.00 0.00 0.00 2.29
3370 3413 9.758651 AAATAACTGCGTATACATAGATGAACA 57.241 29.630 3.32 0.00 0.00 3.18
3395 3438 2.213499 ACTTGAGCAGTGTACAACAGC 58.787 47.619 0.00 1.89 41.42 4.40
3426 3469 7.917505 AGAAAAACAAGAAGATTTGCAGTGTAG 59.082 33.333 0.00 0.00 0.00 2.74
3518 3561 4.946478 ATATCTTCCAGAGGAACCTTCG 57.054 45.455 0.00 0.00 36.71 3.79
3521 3564 2.761208 TCTTCCAGAGGAACCTTCGATC 59.239 50.000 0.00 0.00 36.71 3.69
3528 3571 0.744771 GGAACCTTCGATCAGGGTGC 60.745 60.000 8.03 2.48 38.42 5.01
3621 3664 4.452795 TGTTCACTCGTCAACTGTTTTCAA 59.547 37.500 0.00 0.00 0.00 2.69
3625 3668 3.306166 ACTCGTCAACTGTTTTCAAGACG 59.694 43.478 18.54 18.54 43.84 4.18
3698 3741 8.519799 AGTTTTTACTGATCAAGAAACTCCAA 57.480 30.769 14.59 1.92 33.46 3.53
3756 3799 8.814235 GCCAAATATTCATCATTGAAGAACTTG 58.186 33.333 6.48 9.88 44.75 3.16
3949 3992 6.599244 GTCAGATGGATGGAAGTATTTTCACA 59.401 38.462 0.00 0.00 0.00 3.58
4014 4065 4.625742 CGAACTTTCCATCAACTATCACGT 59.374 41.667 0.00 0.00 0.00 4.49
4066 4119 7.404104 TCCGTTCCTAGATATAGGGTGTATAGA 59.596 40.741 13.45 0.03 37.81 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.450904 ACTCACAGAAATGGTAGGCCTA 58.549 45.455 8.91 8.91 35.27 3.93
1 2 2.269940 ACTCACAGAAATGGTAGGCCT 58.730 47.619 11.78 11.78 35.27 5.19
2 3 2.789409 ACTCACAGAAATGGTAGGCC 57.211 50.000 0.00 0.00 0.00 5.19
8 9 8.349245 TGTTATGTGTAAAACTCACAGAAATGG 58.651 33.333 7.50 0.00 44.54 3.16
113 116 7.113965 GTCTTGTAGCAAAGATGTTGATGTTTG 59.886 37.037 0.00 0.00 42.87 2.93
188 194 0.389391 CTGCCCAGGTACTATGGACG 59.611 60.000 16.41 4.93 40.51 4.79
285 292 3.179265 CGCAGGTTCTGTACGGCG 61.179 66.667 4.80 4.80 42.14 6.46
443 450 3.493213 GGGCGTGTGATTTACCCG 58.507 61.111 0.00 0.00 33.06 5.28
783 790 1.792949 CTGCCAAAGTACACACGAGAC 59.207 52.381 0.00 0.00 0.00 3.36
784 791 1.411246 ACTGCCAAAGTACACACGAGA 59.589 47.619 0.00 0.00 37.36 4.04
785 792 1.865865 ACTGCCAAAGTACACACGAG 58.134 50.000 0.00 0.00 37.36 4.18
786 793 2.319136 AACTGCCAAAGTACACACGA 57.681 45.000 0.00 0.00 38.56 4.35
851 858 2.505118 GACACCTCGCGTCAGAGC 60.505 66.667 5.77 0.00 36.95 4.09
852 859 2.179517 GGACACCTCGCGTCAGAG 59.820 66.667 5.77 0.00 34.97 3.35
853 860 3.371063 GGGACACCTCGCGTCAGA 61.371 66.667 5.77 0.00 34.97 3.27
854 861 3.374402 AGGGACACCTCGCGTCAG 61.374 66.667 5.77 0.00 46.95 3.51
855 862 3.680786 CAGGGACACCTCGCGTCA 61.681 66.667 5.77 0.00 46.95 4.35
856 863 4.436998 CCAGGGACACCTCGCGTC 62.437 72.222 5.77 0.00 46.95 5.19
859 866 4.101448 ATGCCAGGGACACCTCGC 62.101 66.667 0.00 0.00 46.95 5.03
860 867 2.187946 GATGCCAGGGACACCTCG 59.812 66.667 0.00 0.00 46.95 4.63
861 868 1.524482 GAGATGCCAGGGACACCTC 59.476 63.158 0.00 0.00 46.95 3.85
879 906 1.669115 CTGTCAGCAAGTGGGGTCG 60.669 63.158 0.00 0.00 0.00 4.79
984 1012 3.859414 ATCTCGCTGCTCTGCCCC 61.859 66.667 0.00 0.00 0.00 5.80
985 1013 2.588314 CATCTCGCTGCTCTGCCC 60.588 66.667 0.00 0.00 0.00 5.36
986 1014 2.588314 CCATCTCGCTGCTCTGCC 60.588 66.667 0.00 0.00 0.00 4.85
987 1015 3.270839 GCCATCTCGCTGCTCTGC 61.271 66.667 0.00 0.00 0.00 4.26
988 1016 1.152989 GAAGCCATCTCGCTGCTCTG 61.153 60.000 0.00 0.00 39.64 3.35
1014 1047 2.836360 GGGGACGACGGGCAGATA 60.836 66.667 0.00 0.00 0.00 1.98
1023 1056 1.615165 GGAAGGAGGAAGGGGACGAC 61.615 65.000 0.00 0.00 0.00 4.34
1173 1209 2.034878 GAAATCTTGGGATTCTGGCCC 58.965 52.381 0.00 0.00 46.22 5.80
1182 1218 1.887956 GCAGTGCTGGAAATCTTGGGA 60.888 52.381 8.18 0.00 0.00 4.37
1464 1500 2.045926 ACCTTGCTGCGGACATCC 60.046 61.111 0.00 0.00 0.00 3.51
1467 1503 1.375908 GATGACCTTGCTGCGGACA 60.376 57.895 0.00 1.22 0.00 4.02
1771 1807 0.325484 AGCTGGCATCTCTCAGACCT 60.325 55.000 0.00 0.00 33.11 3.85
1808 1844 2.870372 GCACCTTGATCACCGTGC 59.130 61.111 23.42 23.42 44.17 5.34
1827 1863 1.959226 GAAGTTGCCGCTGGTCGAA 60.959 57.895 0.00 0.00 41.67 3.71
1830 1866 2.357034 TCGAAGTTGCCGCTGGTC 60.357 61.111 0.00 0.00 0.00 4.02
1950 1986 1.906574 TGGATGGTCTTCACTACCCAC 59.093 52.381 0.00 0.00 36.06 4.61
2055 2091 1.064134 CACGATCATCGCGTCCTCA 59.936 57.895 7.05 0.00 45.12 3.86
2084 2120 0.179134 GTCCATCACCTCGTCCTTCG 60.179 60.000 0.00 0.00 41.41 3.79
2305 2341 0.538287 GGCTTGAAACCTGCCTCTGT 60.538 55.000 0.00 0.00 43.05 3.41
2343 2379 1.299468 GTAGCACCGGATGAGCGAG 60.299 63.158 9.46 0.00 0.00 5.03
2379 2415 0.386858 ATGACCTGACAACGTCGTCG 60.387 55.000 1.59 0.00 38.84 5.12
2385 2421 0.948623 TGCCGAATGACCTGACAACG 60.949 55.000 0.00 0.00 0.00 4.10
2595 2631 2.844362 CCGCTCAGGATGCCCCTA 60.844 66.667 0.00 0.00 45.60 3.53
2615 2651 2.579657 ATCTTCACCACGCCACGGA 61.580 57.895 0.00 0.00 0.00 4.69
2723 2759 0.095935 CTGCACGTTGCTGTAGATGC 59.904 55.000 10.54 0.00 45.31 3.91
2796 2832 1.229625 ATGGAGAGTGGTCAGGGCA 60.230 57.895 0.00 0.00 0.00 5.36
2853 2889 3.317571 AGCGGTGGCAGCTCTTCT 61.318 61.111 15.48 3.70 41.83 2.85
2910 2946 2.436109 GAGGCCAGCCCTTTGTCA 59.564 61.111 5.01 0.00 46.60 3.58
3051 3087 1.112113 CATCCTACACGGCCACTAGT 58.888 55.000 2.24 0.00 0.00 2.57
3057 3093 0.748005 ATTGTGCATCCTACACGGCC 60.748 55.000 0.00 0.00 41.03 6.13
3066 3102 2.038295 CCTCCTCCTAGATTGTGCATCC 59.962 54.545 0.00 0.00 31.20 3.51
3068 3104 2.769209 ACCTCCTCCTAGATTGTGCAT 58.231 47.619 0.00 0.00 0.00 3.96
3118 3154 5.766150 TTTCAGAACACCCACAAGTTATG 57.234 39.130 0.00 0.00 38.07 1.90
3124 3160 8.642935 TTATGAATATTTCAGAACACCCACAA 57.357 30.769 0.00 0.00 43.98 3.33
3262 3305 6.422776 ACTAGTCTGCGATAAAAACCATTG 57.577 37.500 0.00 0.00 0.00 2.82
3306 3349 4.785511 TGCTACTACTGTCTTGGTTCTC 57.214 45.455 0.00 0.00 0.00 2.87
3369 3412 2.224042 TGTACACTGCTCAAGTCACCTG 60.224 50.000 0.00 0.00 36.83 4.00
3370 3413 2.039418 TGTACACTGCTCAAGTCACCT 58.961 47.619 0.00 0.00 36.83 4.00
3395 3438 6.757947 TGCAAATCTTCTTGTTTTTCTTCAGG 59.242 34.615 0.00 0.00 0.00 3.86
3426 3469 2.508526 AGCCAACCATTCAGACTGTTC 58.491 47.619 1.59 0.00 0.00 3.18
3518 3561 5.452356 CCTCAAATTTTATGGCACCCTGATC 60.452 44.000 0.00 0.00 0.00 2.92
3521 3564 3.515104 ACCTCAAATTTTATGGCACCCTG 59.485 43.478 0.00 0.00 0.00 4.45
3621 3664 2.035449 TGTCATTCTTCGTTGTCCGTCT 59.965 45.455 0.00 0.00 37.94 4.18
3625 3668 5.107875 GCAATTTTGTCATTCTTCGTTGTCC 60.108 40.000 0.00 0.00 0.00 4.02
3698 3741 1.488812 TGACACCAACTGCTACTGGTT 59.511 47.619 1.93 0.00 43.62 3.67
3756 3799 1.419387 AGTGGGATGAGGCATCTAAGC 59.581 52.381 0.00 0.00 40.39 3.09


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

AutoCloner maintained by Alex Coulton.