Multiple sequence alignment - TraesCS3D01G354100

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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 TraesCS3D01G354100 chr3D 100.000 3656 0 0 802 4457 464800338 464803993 0.000000e+00 6752.0
1 TraesCS3D01G354100 chr3D 100.000 428 0 0 1 428 464799537 464799964 0.000000e+00 791.0
2 TraesCS3D01G354100 chr3D 87.719 57 3 4 4283 4336 19768370 19768315 3.720000e-06 63.9
3 TraesCS3D01G354100 chr3A 94.602 3668 152 33 802 4457 608189040 608192673 0.000000e+00 5635.0
4 TraesCS3D01G354100 chr3A 89.087 449 14 12 1 428 608188508 608188942 3.950000e-145 525.0
5 TraesCS3D01G354100 chr3B 93.820 3495 130 34 812 4276 618148510 618151948 0.000000e+00 5179.0
6 TraesCS3D01G354100 chr3B 86.885 183 10 9 12 185 618147928 618148105 4.550000e-45 193.0
7 TraesCS3D01G354100 chr2A 97.619 42 1 0 4295 4336 2479753 2479794 6.180000e-09 73.1
8 TraesCS3D01G354100 chr1A 95.556 45 1 1 4296 4339 6898876 6898832 2.220000e-08 71.3
9 TraesCS3D01G354100 chr1A 93.617 47 1 2 4294 4339 551582253 551582298 8.000000e-08 69.4
10 TraesCS3D01G354100 chr1A 86.885 61 3 4 4296 4355 321396833 321396777 3.720000e-06 63.9
11 TraesCS3D01G354100 chr7D 93.617 47 2 1 4289 4334 568464300 568464254 8.000000e-08 69.4
12 TraesCS3D01G354100 chr7A 92.000 50 1 3 4293 4340 383423898 383423850 2.880000e-07 67.6
13 TraesCS3D01G354100 chr4D 87.500 56 6 1 4300 4354 7650911 7650966 3.720000e-06 63.9


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 TraesCS3D01G354100 chr3D 464799537 464803993 4456 False 3771.5 6752 100.0000 1 4457 2 chr3D.!!$F1 4456
1 TraesCS3D01G354100 chr3A 608188508 608192673 4165 False 3080.0 5635 91.8445 1 4457 2 chr3A.!!$F1 4456
2 TraesCS3D01G354100 chr3B 618147928 618151948 4020 False 2686.0 5179 90.3525 12 4276 2 chr3B.!!$F1 4264

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
927 1021 0.465642 TCCGCGCTGATCTCCTTCTA 60.466 55.0 5.56 0.0 0.0 2.1 F
1848 1954 0.322277 CTGTGCCTTCTGATGCTGGT 60.322 55.0 2.10 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1989 0.036732 AAATCCTCGGCTGAACTGCA 59.963 50.0 0.0 0.0 34.04 4.41 R
3810 3920 0.601558 GACCGTTACTGGCTGAGACA 59.398 55.0 0.0 0.0 0.00 3.41 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
47 48 3.614870 GCAACCAGGAAATTCATGTGTCC 60.615 47.826 6.89 0.00 0.00 4.02
265 325 2.581409 CACCACGTACGCCCGATC 60.581 66.667 16.72 0.00 0.00 3.69
266 326 3.830192 ACCACGTACGCCCGATCC 61.830 66.667 16.72 0.00 0.00 3.36
267 327 4.580551 CCACGTACGCCCGATCCC 62.581 72.222 16.72 0.00 0.00 3.85
818 898 2.432456 CGCAACGCAGCTCAGGTA 60.432 61.111 0.00 0.00 0.00 3.08
819 899 2.730672 CGCAACGCAGCTCAGGTAC 61.731 63.158 0.00 0.00 0.00 3.34
820 900 2.730672 GCAACGCAGCTCAGGTACG 61.731 63.158 0.00 0.00 0.00 3.67
860 940 1.327690 GCCAGCCCCCGATATCGATA 61.328 60.000 26.32 7.75 43.02 2.92
864 944 3.487372 CAGCCCCCGATATCGATATCTA 58.513 50.000 32.23 5.99 43.02 1.98
870 950 5.645929 CCCCCGATATCGATATCTATCTCTG 59.354 48.000 32.23 19.70 43.02 3.35
882 962 1.675483 CTATCTCTGCTCGTCAGTGCT 59.325 52.381 7.18 1.09 43.32 4.40
927 1021 0.465642 TCCGCGCTGATCTCCTTCTA 60.466 55.000 5.56 0.00 0.00 2.10
959 1053 1.225704 GCCAGGTGGGAGATTGGAG 59.774 63.158 0.00 0.00 40.01 3.86
962 1056 1.486726 CCAGGTGGGAGATTGGAGTAC 59.513 57.143 0.00 0.00 40.01 2.73
963 1057 1.137086 CAGGTGGGAGATTGGAGTACG 59.863 57.143 0.00 0.00 0.00 3.67
964 1058 1.006758 AGGTGGGAGATTGGAGTACGA 59.993 52.381 0.00 0.00 0.00 3.43
967 1061 3.285484 GTGGGAGATTGGAGTACGAGTA 58.715 50.000 0.00 0.00 0.00 2.59
969 1063 4.023021 GTGGGAGATTGGAGTACGAGTATC 60.023 50.000 0.00 0.00 0.00 2.24
970 1064 4.141228 TGGGAGATTGGAGTACGAGTATCT 60.141 45.833 0.00 4.11 0.00 1.98
971 1065 5.072736 TGGGAGATTGGAGTACGAGTATCTA 59.927 44.000 0.00 0.00 0.00 1.98
972 1066 6.181908 GGGAGATTGGAGTACGAGTATCTAT 58.818 44.000 0.00 0.00 0.00 1.98
973 1067 6.316890 GGGAGATTGGAGTACGAGTATCTATC 59.683 46.154 0.00 0.00 0.00 2.08
974 1068 6.316890 GGAGATTGGAGTACGAGTATCTATCC 59.683 46.154 0.00 0.00 0.00 2.59
975 1069 6.780901 AGATTGGAGTACGAGTATCTATCCA 58.219 40.000 0.00 0.00 33.68 3.41
976 1070 7.406916 AGATTGGAGTACGAGTATCTATCCAT 58.593 38.462 0.00 3.22 35.42 3.41
977 1071 7.554835 AGATTGGAGTACGAGTATCTATCCATC 59.445 40.741 0.00 8.81 35.42 3.51
978 1072 5.498393 TGGAGTACGAGTATCTATCCATCC 58.502 45.833 0.00 0.00 30.63 3.51
979 1073 5.013808 TGGAGTACGAGTATCTATCCATCCA 59.986 44.000 0.00 0.00 30.63 3.41
980 1074 6.123651 GGAGTACGAGTATCTATCCATCCAT 58.876 44.000 0.00 0.00 0.00 3.41
996 1090 1.607612 CATCTTAACCGCCACCCCT 59.392 57.895 0.00 0.00 0.00 4.79
1526 1629 3.046087 CAGCAGCGTCACCACCAG 61.046 66.667 0.00 0.00 0.00 4.00
1619 1722 1.515020 CTGCTCTCGAGTTCCCCAG 59.485 63.158 13.13 8.84 0.00 4.45
1620 1723 2.185608 GCTCTCGAGTTCCCCAGC 59.814 66.667 13.13 9.07 0.00 4.85
1738 1844 3.591254 AACCCTCTTCCTGACGCGC 62.591 63.158 5.73 0.00 0.00 6.86
1848 1954 0.322277 CTGTGCCTTCTGATGCTGGT 60.322 55.000 2.10 0.00 0.00 4.00
1858 1964 1.329906 CTGATGCTGGTTTGAGCGATC 59.670 52.381 0.00 0.00 42.32 3.69
1883 1989 2.672307 GCAGAGCCAGCAAGCAGT 60.672 61.111 0.55 0.00 34.23 4.40
1951 2057 2.810274 GAGAGCAAGCTTGTGATTGACA 59.190 45.455 26.55 0.00 41.64 3.58
1959 2065 2.475187 GCTTGTGATTGACATCGACAGC 60.475 50.000 0.00 0.00 33.40 4.40
1972 2078 1.068748 TCGACAGCTTACCGTCAGTTC 60.069 52.381 3.18 0.00 32.24 3.01
2271 2377 1.077265 CAAAGGGTCTGGCCATGGT 59.923 57.895 14.67 0.00 39.65 3.55
2292 2398 2.494530 GGGCCGTGGCAAGAAACAA 61.495 57.895 13.76 0.00 44.11 2.83
2301 2407 3.859386 GTGGCAAGAAACAAGTCAAACAG 59.141 43.478 0.00 0.00 0.00 3.16
2349 2455 3.518705 AGACTCTCCTCATTCATTGTGCT 59.481 43.478 0.00 0.00 0.00 4.40
2355 2461 3.262660 TCCTCATTCATTGTGCTCAGTCT 59.737 43.478 0.00 0.00 0.00 3.24
2358 2464 3.749609 TCATTCATTGTGCTCAGTCTGTG 59.250 43.478 0.00 0.00 0.00 3.66
2502 2608 4.574674 TGCTGGTAATGGAAGTCAGATT 57.425 40.909 0.00 0.00 0.00 2.40
2514 2620 7.724305 TGGAAGTCAGATTTACAAGTTACAC 57.276 36.000 0.00 0.00 0.00 2.90
2566 2672 3.007614 TCTGAAAGCCTACCAACTGTACC 59.992 47.826 0.00 0.00 0.00 3.34
2885 2991 3.192001 GCATCTCAATTTGAGGCTGTTCA 59.808 43.478 22.86 5.54 44.39 3.18
3120 3226 3.118261 TGTTCCAGTTCTCTGCTCACTTT 60.118 43.478 0.00 0.00 40.09 2.66
3450 3556 0.183731 GGAAGGCGAATCCCCAATCT 59.816 55.000 0.00 0.00 34.51 2.40
3457 3563 2.368875 GCGAATCCCCAATCTTCCTAGA 59.631 50.000 0.00 0.00 34.21 2.43
3567 3676 1.134936 ACCGGCACCAAAGAAACAAAC 60.135 47.619 0.00 0.00 0.00 2.93
3703 3812 5.592282 TCACAGGAACAGTTAGCATTTTTGA 59.408 36.000 0.00 0.00 0.00 2.69
3760 3870 2.084610 TCTTCTTGCATGGTCAGTCG 57.915 50.000 0.00 0.00 0.00 4.18
3807 3917 9.877178 AGAGTACTATTCAGTAATGTTTCAAGG 57.123 33.333 0.00 0.00 38.98 3.61
3825 3935 3.618690 AGGAATGTCTCAGCCAGTAAC 57.381 47.619 0.00 0.00 0.00 2.50
3884 3995 2.795329 ACGCCTTGTCTTGATTTCCAT 58.205 42.857 0.00 0.00 0.00 3.41
4081 4192 1.274447 ACTCTGCCGTTGTACCTAACC 59.726 52.381 0.00 0.00 0.00 2.85
4137 4249 0.673985 TCCCAGTCTGTTGAGTGACG 59.326 55.000 0.00 0.00 44.27 4.35
4195 4309 4.635765 TCTGGTGTGAAAATGCTATAGTGC 59.364 41.667 0.84 0.00 0.00 4.40
4210 4324 6.153510 TGCTATAGTGCTGGTTCCTATGATAG 59.846 42.308 0.84 0.00 0.00 2.08
4319 4434 7.343833 AGTTGATACTCCCTCCGTAAAGAAATA 59.656 37.037 0.00 0.00 0.00 1.40
4332 4447 9.754382 TCCGTAAAGAAATATAAGAGCGTTTAT 57.246 29.630 2.15 2.15 0.00 1.40
4381 4496 1.322442 AACTGGGTTGCTGAGCTTTC 58.678 50.000 5.83 0.00 0.00 2.62
4413 4528 2.103432 TCGTTTTCCAGTCTGCCTTGTA 59.897 45.455 0.00 0.00 0.00 2.41
4450 4565 4.074970 GTCCAGTGTCCACATTCAGAAAT 58.925 43.478 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.233507 ACACATGAATTTCCTGGTTGCT 58.766 40.909 0.00 0.00 0.00 3.91
25 26 3.578688 GACACATGAATTTCCTGGTTGC 58.421 45.455 0.00 0.00 0.00 4.17
26 27 3.366273 CGGACACATGAATTTCCTGGTTG 60.366 47.826 0.00 0.31 0.00 3.77
47 48 1.065102 TCCGCGACTCTTTCTAATCCG 59.935 52.381 8.23 0.00 0.00 4.18
75 82 1.204312 GACTGCCGTTTGACTTCGC 59.796 57.895 0.00 0.00 0.00 4.70
801 881 2.432456 TACCTGAGCTGCGTTGCG 60.432 61.111 0.00 0.00 38.13 4.85
802 882 2.730672 CGTACCTGAGCTGCGTTGC 61.731 63.158 0.00 0.00 0.00 4.17
803 883 2.730672 GCGTACCTGAGCTGCGTTG 61.731 63.158 0.00 0.00 0.00 4.10
804 884 2.432628 GCGTACCTGAGCTGCGTT 60.433 61.111 0.00 0.00 0.00 4.84
805 885 4.778415 CGCGTACCTGAGCTGCGT 62.778 66.667 0.00 0.00 43.50 5.24
844 924 2.757894 AGATATCGATATCGGGGGCT 57.242 50.000 30.32 15.55 43.01 5.19
850 930 6.364976 ACGAGCAGAGATAGATATCGATATCG 59.635 42.308 30.32 19.14 43.01 2.92
851 931 7.383843 TGACGAGCAGAGATAGATATCGATATC 59.616 40.741 30.03 30.03 39.50 1.63
852 932 7.213678 TGACGAGCAGAGATAGATATCGATAT 58.786 38.462 17.77 17.77 37.76 1.63
854 934 5.423886 TGACGAGCAGAGATAGATATCGAT 58.576 41.667 2.16 2.16 37.76 3.59
870 950 1.799519 CGACTCAGCACTGACGAGC 60.800 63.158 5.07 0.00 35.46 5.03
882 962 1.136774 CGACGGCTGATTCGACTCA 59.863 57.895 5.28 5.28 37.43 3.41
927 1021 0.108520 CCTGGCAGATGCGCAAAAAT 60.109 50.000 17.11 0.00 43.26 1.82
959 1053 7.633193 AAGATGGATGGATAGATACTCGTAC 57.367 40.000 0.00 0.00 0.00 3.67
962 1056 7.484975 GGTTAAGATGGATGGATAGATACTCG 58.515 42.308 0.00 0.00 0.00 4.18
963 1057 7.484975 CGGTTAAGATGGATGGATAGATACTC 58.515 42.308 0.00 0.00 0.00 2.59
964 1058 6.127310 GCGGTTAAGATGGATGGATAGATACT 60.127 42.308 0.00 0.00 0.00 2.12
967 1061 4.080863 GGCGGTTAAGATGGATGGATAGAT 60.081 45.833 0.00 0.00 0.00 1.98
969 1063 3.007940 TGGCGGTTAAGATGGATGGATAG 59.992 47.826 0.00 0.00 0.00 2.08
970 1064 2.976185 TGGCGGTTAAGATGGATGGATA 59.024 45.455 0.00 0.00 0.00 2.59
971 1065 1.774254 TGGCGGTTAAGATGGATGGAT 59.226 47.619 0.00 0.00 0.00 3.41
972 1066 1.134220 GTGGCGGTTAAGATGGATGGA 60.134 52.381 0.00 0.00 0.00 3.41
973 1067 1.308998 GTGGCGGTTAAGATGGATGG 58.691 55.000 0.00 0.00 0.00 3.51
974 1068 1.308998 GGTGGCGGTTAAGATGGATG 58.691 55.000 0.00 0.00 0.00 3.51
975 1069 0.182775 GGGTGGCGGTTAAGATGGAT 59.817 55.000 0.00 0.00 0.00 3.41
976 1070 1.605453 GGGTGGCGGTTAAGATGGA 59.395 57.895 0.00 0.00 0.00 3.41
977 1071 1.453197 GGGGTGGCGGTTAAGATGG 60.453 63.158 0.00 0.00 0.00 3.51
978 1072 0.034477 AAGGGGTGGCGGTTAAGATG 60.034 55.000 0.00 0.00 0.00 2.90
979 1073 0.034477 CAAGGGGTGGCGGTTAAGAT 60.034 55.000 0.00 0.00 0.00 2.40
980 1074 1.377229 CAAGGGGTGGCGGTTAAGA 59.623 57.895 0.00 0.00 0.00 2.10
1020 1123 1.883084 GGCGTCCATGACCATCGAC 60.883 63.158 0.00 0.00 0.00 4.20
1526 1629 2.328099 CCGTGGCTGTTGAAGGAGC 61.328 63.158 0.00 0.00 34.23 4.70
1602 1705 2.650116 GCTGGGGAACTCGAGAGCA 61.650 63.158 21.68 0.00 0.00 4.26
1707 1813 1.358787 AGAGGGTTGAATTCCATGGCA 59.641 47.619 6.96 0.00 0.00 4.92
1826 1932 0.677098 AGCATCAGAAGGCACAGCAG 60.677 55.000 0.76 0.00 33.71 4.24
1836 1942 1.159285 CGCTCAAACCAGCATCAGAA 58.841 50.000 0.00 0.00 39.62 3.02
1837 1943 0.321346 TCGCTCAAACCAGCATCAGA 59.679 50.000 0.00 0.00 39.62 3.27
1838 1944 1.329906 GATCGCTCAAACCAGCATCAG 59.670 52.381 0.00 0.00 39.62 2.90
1848 1954 2.481568 CTGCAGAACAAGATCGCTCAAA 59.518 45.455 8.42 0.00 0.00 2.69
1858 1964 0.887836 TGCTGGCTCTGCAGAACAAG 60.888 55.000 18.85 17.28 33.63 3.16
1883 1989 0.036732 AAATCCTCGGCTGAACTGCA 59.963 50.000 0.00 0.00 34.04 4.41
1972 2078 6.653740 ACAACCTTCTTATCTTCTTTAACCCG 59.346 38.462 0.00 0.00 0.00 5.28
2271 2377 0.891904 GTTTCTTGCCACGGCCCTTA 60.892 55.000 5.42 0.00 41.09 2.69
2292 2398 1.494721 TCCTTCTTGGGCTGTTTGACT 59.505 47.619 0.00 0.00 36.20 3.41
2301 2407 1.002011 GACCACCTCCTTCTTGGGC 60.002 63.158 0.00 0.00 34.41 5.36
2349 2455 3.306989 GGTCATCAATGGACACAGACTGA 60.307 47.826 10.08 0.00 37.00 3.41
2355 2461 0.676466 GCCGGTCATCAATGGACACA 60.676 55.000 1.90 0.00 37.00 3.72
2358 2464 2.180204 CCGCCGGTCATCAATGGAC 61.180 63.158 1.90 0.00 34.52 4.02
2394 2500 0.382158 CATGCTGCCTGATCTGCTTG 59.618 55.000 0.00 0.00 32.79 4.01
2502 2608 5.870433 CCGTGATATGGTGTGTAACTTGTAA 59.130 40.000 0.00 0.00 38.04 2.41
2514 2620 2.795681 GCATGCAAACCGTGATATGGTG 60.796 50.000 14.21 0.00 37.61 4.17
2566 2672 1.404391 CTTGAATGGGCAAGCTGCTAG 59.596 52.381 0.90 0.00 44.28 3.42
2885 2991 4.078922 TCTCAATGTGGAGATCCTCTACCT 60.079 45.833 7.78 0.00 40.50 3.08
3120 3226 3.719268 ATGTTAGCCTCCAACATGTCA 57.281 42.857 0.00 0.00 43.27 3.58
3450 3556 6.443849 AGGTCACCATTTACAGAATCTAGGAA 59.556 38.462 0.00 0.00 0.00 3.36
3457 3563 5.630121 TGAACAGGTCACCATTTACAGAAT 58.370 37.500 0.00 0.00 0.00 2.40
3567 3676 1.673400 TGTCACCGGTGAACAAATGTG 59.327 47.619 37.75 6.97 41.85 3.21
3581 3690 4.692228 ACAAACAAATGAACCATGTCACC 58.308 39.130 0.00 0.00 0.00 4.02
3703 3812 4.901849 TCTAACATAAGTAGCCTGCTCCAT 59.098 41.667 0.00 0.00 0.00 3.41
3807 3917 2.271800 CCGTTACTGGCTGAGACATTC 58.728 52.381 0.00 0.00 0.00 2.67
3810 3920 0.601558 GACCGTTACTGGCTGAGACA 59.398 55.000 0.00 0.00 0.00 3.41
3825 3935 2.061028 GCAAATGAAAAAGGCTGACCG 58.939 47.619 0.00 0.00 42.76 4.79
3866 3977 6.212888 ACATAATGGAAATCAAGACAAGGC 57.787 37.500 0.00 0.00 0.00 4.35
3915 4026 5.674052 AGAGGGATATATGAGTGCATGAC 57.326 43.478 0.00 0.00 35.94 3.06
4068 4179 7.808672 TCAAACATTATTGGTTAGGTACAACG 58.191 34.615 0.00 0.00 29.51 4.10
4169 4282 7.412853 CACTATAGCATTTTCACACCAGAATC 58.587 38.462 0.00 0.00 0.00 2.52
4173 4286 4.637534 AGCACTATAGCATTTTCACACCAG 59.362 41.667 0.00 0.00 36.85 4.00
4195 4309 6.234177 GGTCCAAATCTATCATAGGAACCAG 58.766 44.000 0.00 0.00 0.00 4.00
4210 4324 3.066760 GTCATTTGATCGGGGTCCAAATC 59.933 47.826 0.00 0.00 38.13 2.17
4276 4391 3.052036 CAACTTGCCATTCGAAAACAGG 58.948 45.455 0.00 4.02 0.00 4.00
4277 4392 3.963665 TCAACTTGCCATTCGAAAACAG 58.036 40.909 0.00 0.00 0.00 3.16
4332 4447 7.050377 GGCCTATATGAGCTTGCAATAAGATA 58.950 38.462 0.00 0.00 0.00 1.98
4342 4457 2.556144 TGCTGGCCTATATGAGCTTG 57.444 50.000 3.32 0.00 32.41 4.01
4381 4496 2.480419 CTGGAAAACGAGTTGTGGCTAG 59.520 50.000 0.00 0.00 0.00 3.42
4394 4509 5.453567 AAATACAAGGCAGACTGGAAAAC 57.546 39.130 4.26 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.