Multiple sequence alignment - TraesCS3A01G241900

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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 TraesCS3A01G241900 chr3A 100.000 3162 0 0 1 3162 454170146 454173307 0.000000e+00 5840.0
1 TraesCS3A01G241900 chr3B 92.472 983 61 7 938 1912 434668502 434669479 0.000000e+00 1393.0
2 TraesCS3A01G241900 chr3B 93.407 728 32 6 2446 3159 434670005 434670730 0.000000e+00 1064.0
3 TraesCS3A01G241900 chr3B 95.278 360 15 2 2103 2461 434669634 434669992 1.270000e-158 569.0
4 TraesCS3A01G241900 chr3B 82.881 590 55 21 6 560 434667215 434667793 3.670000e-134 488.0
5 TraesCS3A01G241900 chr3B 98.630 73 1 0 1896 1968 434669492 434669564 2.560000e-26 130.0
6 TraesCS3A01G241900 chr3D 95.380 736 29 3 1896 2627 336832078 336832812 0.000000e+00 1166.0
7 TraesCS3A01G241900 chr3D 92.328 769 40 7 451 1218 336830568 336831318 0.000000e+00 1075.0
8 TraesCS3A01G241900 chr3D 89.163 729 52 13 1209 1912 336831339 336832065 0.000000e+00 883.0
9 TraesCS3A01G241900 chr3D 95.082 549 26 1 2614 3162 336837091 336837638 0.000000e+00 863.0
10 TraesCS3A01G241900 chr3D 91.943 422 17 12 1 417 336829789 336830198 2.740000e-160 575.0
11 TraesCS3A01G241900 chr3D 97.778 45 1 0 403 447 336830226 336830270 9.400000e-11 78.7
12 TraesCS3A01G241900 chr7D 81.911 293 27 10 121 408 22399605 22399876 1.140000e-54 224.0
13 TraesCS3A01G241900 chr7D 81.849 292 27 10 121 408 10740188 10739919 4.100000e-54 222.0
14 TraesCS3A01G241900 chr7D 81.164 292 30 9 121 408 22357392 22357662 8.890000e-51 211.0
15 TraesCS3A01G241900 chr4A 87.821 156 17 1 253 408 728066640 728066793 6.970000e-42 182.0
16 TraesCS3A01G241900 chr6D 87.368 95 12 0 313 407 413794497 413794403 3.330000e-20 110.0
17 TraesCS3A01G241900 chr6D 86.598 97 12 1 312 407 364863740 364863836 4.310000e-19 106.0
18 TraesCS3A01G241900 chr5D 86.458 96 13 0 312 407 327285532 327285437 4.310000e-19 106.0
19 TraesCS3A01G241900 chr1D 86.458 96 13 0 312 407 212091889 212091984 4.310000e-19 106.0
20 TraesCS3A01G241900 chr2D 88.750 80 3 3 121 195 107762641 107762719 3.360000e-15 93.5
21 TraesCS3A01G241900 chr2A 88.750 80 3 3 121 195 207110044 207110122 3.360000e-15 93.5


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 TraesCS3A01G241900 chr3A 454170146 454173307 3161 False 5840.00 5840 100.0000 1 3162 1 chr3A.!!$F1 3161
1 TraesCS3A01G241900 chr3B 434667215 434670730 3515 False 728.80 1393 92.5336 6 3159 5 chr3B.!!$F1 3153
2 TraesCS3A01G241900 chr3D 336837091 336837638 547 False 863.00 863 95.0820 2614 3162 1 chr3D.!!$F1 548
3 TraesCS3A01G241900 chr3D 336829789 336832812 3023 False 755.54 1166 93.3184 1 2627 5 chr3D.!!$F2 2626

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
773 1733 0.328258 ATGCCGCCCTCCCATATAAC 59.672 55.0 0.0 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 3252 0.456142 GCAGAACCGCGATTTTTCCC 60.456 55.0 8.23 0.0 0.0 3.97 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
57 58 7.442364 TGGTAGAGCAATAGCAGTTTATGATTC 59.558 37.037 0.00 0.00 45.49 2.52
86 87 2.222027 CGTGAACCTTGGAGCTTTTCT 58.778 47.619 0.00 0.00 0.00 2.52
125 126 9.601217 AAATAATAACTAGTCGAGTTCTTGCAT 57.399 29.630 0.00 0.00 45.81 3.96
126 127 9.601217 AATAATAACTAGTCGAGTTCTTGCATT 57.399 29.630 0.00 0.00 45.81 3.56
127 128 6.893958 ATAACTAGTCGAGTTCTTGCATTG 57.106 37.500 0.00 0.00 45.81 2.82
128 129 2.996621 ACTAGTCGAGTTCTTGCATTGC 59.003 45.455 0.00 0.46 33.13 3.56
129 130 1.882912 AGTCGAGTTCTTGCATTGCA 58.117 45.000 7.38 7.38 36.47 4.08
297 318 3.754323 CCCAGAAAAATAAGCGGTGTACA 59.246 43.478 0.00 0.00 0.00 2.90
340 361 6.361748 CAGCTTACAACTCTTTCTTGCATTTC 59.638 38.462 0.00 0.00 0.00 2.17
348 381 7.275888 ACTCTTTCTTGCATTTCATGTGTAA 57.724 32.000 0.00 0.00 0.00 2.41
350 383 7.811236 ACTCTTTCTTGCATTTCATGTGTAATG 59.189 33.333 7.68 7.68 36.35 1.90
364 397 6.543100 TCATGTGTAATGCTTATTGAGATGCA 59.457 34.615 0.00 0.00 39.83 3.96
365 398 6.947644 TGTGTAATGCTTATTGAGATGCAT 57.052 33.333 0.00 0.00 46.46 3.96
538 912 7.066404 TGTGTGCTAACTGATTTTGTGTCTAAA 59.934 33.333 0.00 0.00 0.00 1.85
667 1627 7.129109 TCAAATGTTTATTTCTCCGTGTCTC 57.871 36.000 0.00 0.00 34.34 3.36
707 1667 3.569701 ACCTTGCTGTTGACAAACCATAG 59.430 43.478 0.00 0.00 35.25 2.23
710 1670 1.202348 GCTGTTGACAAACCATAGGCC 59.798 52.381 0.00 0.00 35.25 5.19
731 1691 5.261209 CCAACATTTGGTTTTCAGTCAGA 57.739 39.130 0.00 0.00 45.93 3.27
744 1704 6.604735 TTTCAGTCAGAAAAAGTACTGAGC 57.395 37.500 0.00 0.00 46.45 4.26
745 1705 4.632153 TCAGTCAGAAAAAGTACTGAGCC 58.368 43.478 0.00 0.00 42.46 4.70
770 1730 2.759114 CATGCCGCCCTCCCATAT 59.241 61.111 0.00 0.00 0.00 1.78
773 1733 0.328258 ATGCCGCCCTCCCATATAAC 59.672 55.000 0.00 0.00 0.00 1.89
778 1738 3.873910 CCGCCCTCCCATATAACATAAG 58.126 50.000 0.00 0.00 0.00 1.73
779 1739 3.517901 CCGCCCTCCCATATAACATAAGA 59.482 47.826 0.00 0.00 0.00 2.10
797 1757 8.306313 ACATAAGAAATCAGTTTTAATCCCCC 57.694 34.615 0.00 0.00 0.00 5.40
801 1761 7.872061 AGAAATCAGTTTTAATCCCCCTTTT 57.128 32.000 0.00 0.00 0.00 2.27
849 1809 6.862090 GCATAAAGGAAATGAAGCATCTGATC 59.138 38.462 0.00 0.00 0.00 2.92
860 1820 5.129980 TGAAGCATCTGATCTGTATTCTGGT 59.870 40.000 0.00 0.00 0.00 4.00
888 1848 6.744112 TGTTCTGAGAAAACACAAACAACTT 58.256 32.000 0.00 0.00 31.90 2.66
892 1852 7.601856 TCTGAGAAAACACAAACAACTTCATT 58.398 30.769 0.00 0.00 0.00 2.57
896 1856 8.600449 AGAAAACACAAACAACTTCATTGAAA 57.400 26.923 0.01 0.00 41.23 2.69
1072 2049 5.238868 GGAGAAGTTTCTGGTGAAAAGGTAC 59.761 44.000 0.00 0.00 42.94 3.34
1591 2606 3.447040 GCTGCAGCAAGGTGGAAA 58.553 55.556 33.36 0.00 41.59 3.13
1604 2619 3.065462 TGGAAATCCCAACAAGCCC 57.935 52.632 0.00 0.00 43.29 5.19
1646 2661 2.901192 TCGACCAAAACTCCAGGTATCA 59.099 45.455 0.00 0.00 35.36 2.15
1683 2706 5.005740 TCAGATGCAAACTTCAGCTTATGT 58.994 37.500 0.00 0.00 31.56 2.29
1750 2780 9.344309 GTTGAATTATCTACGCTCCTTATACTC 57.656 37.037 0.00 0.00 0.00 2.59
1775 2806 9.383519 TCTAAAATAAGTGGATGTTCTGATCAC 57.616 33.333 0.00 0.00 0.00 3.06
1790 2822 4.864806 TCTGATCACGCAGTTTTAGCTTAG 59.135 41.667 0.00 0.00 41.61 2.18
1816 2848 3.356290 ACAAAGTATGCTGTCCCATTCC 58.644 45.455 0.00 0.00 0.00 3.01
1839 2871 3.865011 TTGCTTGAAGCTTGACAACAA 57.135 38.095 18.94 7.57 42.97 2.83
1888 2922 3.855689 AGTCAACTTGCAATACCATGC 57.144 42.857 0.00 0.00 46.58 4.06
2008 3071 5.130975 ACAATGATGGTACTCCTTATCTGCA 59.869 40.000 0.00 0.00 34.23 4.41
2048 3112 5.126061 ACTCCTTGTATTTGATGGTCAATGC 59.874 40.000 0.00 0.00 36.11 3.56
2328 3393 3.920231 TCTTCCACATTCAGCTATGCT 57.080 42.857 0.00 0.00 40.77 3.79
2443 3509 2.095853 ACACTTTCAAGCAACTGTGACG 59.904 45.455 0.00 0.00 0.00 4.35
2466 3560 5.989168 CGTGTGCTGATTTATACCTAATGGA 59.011 40.000 0.00 0.00 37.04 3.41
2470 3564 6.148480 GTGCTGATTTATACCTAATGGAGCAG 59.852 42.308 0.00 0.00 32.20 4.24
2537 3634 5.722021 ATGTAGAAACCAATTCCCACAAC 57.278 39.130 0.00 0.00 37.17 3.32
2568 3665 1.734388 AAGCCTTCACAAACCGGTGC 61.734 55.000 8.52 4.10 38.66 5.01
2591 3688 5.243426 TCTTTAGCTTTTCACACACAACC 57.757 39.130 0.00 0.00 0.00 3.77
2627 3730 8.674607 GGTGTTGAGACCGAAAAGAATATAAAT 58.325 33.333 0.00 0.00 0.00 1.40
2665 3772 8.948631 ATAATGGACAGTACATTAGTGAACAG 57.051 34.615 20.73 0.00 42.21 3.16
2679 3786 5.083533 AGTGAACAGAGAATAAGCCTCAG 57.916 43.478 0.00 0.00 33.25 3.35
2722 3830 3.188159 TGTGGAGAGGTGTTGTGTTAC 57.812 47.619 0.00 0.00 0.00 2.50
2777 3885 9.959749 CAAAAGACTTAATTGGTTAAGCAACTA 57.040 29.630 21.50 13.04 46.97 2.24
2820 3928 6.233905 TGGCTAGAGTTTACAGCATTATCA 57.766 37.500 0.00 0.00 37.02 2.15
2836 3944 6.842807 AGCATTATCAGGAATTTCTTTGGGAT 59.157 34.615 0.00 0.00 0.00 3.85
2848 3956 6.642733 TTTCTTTGGGATCCTAGAGAATGT 57.357 37.500 25.60 0.00 0.00 2.71
2883 3991 3.125146 CGCTTAAGACAGTATGCAGCAAA 59.875 43.478 6.67 0.00 42.53 3.68
2932 4040 6.441093 ACATATATTGTGCAAGTTGGTGAG 57.559 37.500 4.75 0.00 37.11 3.51
2979 4087 2.167281 AGACAACGGACATCTCTGATGG 59.833 50.000 11.55 0.00 31.29 3.51
3001 4109 1.203441 TGAGGGCTGCTGATCCAGTT 61.203 55.000 0.00 0.00 35.28 3.16
3031 4139 2.816087 AGCGTGAAAGTTGATGCTGAAT 59.184 40.909 0.00 0.00 35.32 2.57
3107 4215 3.851128 GGACTGCGGGGTAGGCTC 61.851 72.222 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.745087 CCAAGGTTCACGGGATCATTG 59.255 52.381 14.57 14.57 35.41 2.82
125 126 1.999648 AAGGGCAAAGTCTCATGCAA 58.000 45.000 11.44 0.00 44.32 4.08
126 127 1.999648 AAAGGGCAAAGTCTCATGCA 58.000 45.000 11.44 0.00 44.32 3.96
127 128 2.560105 AGAAAAGGGCAAAGTCTCATGC 59.440 45.455 2.68 2.68 41.82 4.06
128 129 5.474876 AGTTAGAAAAGGGCAAAGTCTCATG 59.525 40.000 0.00 0.00 0.00 3.07
129 130 5.635120 AGTTAGAAAAGGGCAAAGTCTCAT 58.365 37.500 0.00 0.00 0.00 2.90
253 272 9.871238 CTGGGACAAGCTATATTATTATAACGT 57.129 33.333 0.00 0.00 38.70 3.99
266 285 5.066505 CGCTTATTTTTCTGGGACAAGCTAT 59.933 40.000 0.00 0.00 38.70 2.97
340 361 6.731164 TGCATCTCAATAAGCATTACACATG 58.269 36.000 0.00 0.00 30.46 3.21
364 397 6.331307 ACCAGATTAGGAAAGAAGAGGCATAT 59.669 38.462 0.00 0.00 0.00 1.78
365 398 5.667626 ACCAGATTAGGAAAGAAGAGGCATA 59.332 40.000 0.00 0.00 0.00 3.14
491 865 7.876068 CACACAGGTAAACAGAGAGGTTATTTA 59.124 37.037 0.00 0.00 30.78 1.40
538 912 6.183360 GCAGAGAAGAGTGCCATAAATTTGAT 60.183 38.462 0.00 0.00 33.29 2.57
659 1619 3.868757 TCCACTTAATCAGAGACACGG 57.131 47.619 0.00 0.00 0.00 4.94
667 1627 6.375455 AGCAAGGTTGTTATCCACTTAATCAG 59.625 38.462 0.00 0.00 0.00 2.90
696 1656 4.244862 CAAATGTTGGCCTATGGTTTGTC 58.755 43.478 3.32 0.00 0.00 3.18
710 1670 7.593875 TTTTCTGACTGAAAACCAAATGTTG 57.406 32.000 14.22 0.00 46.20 3.33
725 1685 4.503991 CCTGGCTCAGTACTTTTTCTGACT 60.504 45.833 0.00 0.00 36.04 3.41
731 1691 4.287766 CCTACCTGGCTCAGTACTTTTT 57.712 45.455 0.00 0.00 0.00 1.94
773 1733 8.539117 AGGGGGATTAAAACTGATTTCTTATG 57.461 34.615 0.00 0.00 32.27 1.90
778 1738 7.676004 TGAAAAGGGGGATTAAAACTGATTTC 58.324 34.615 0.00 0.00 32.27 2.17
779 1739 7.625498 TGAAAAGGGGGATTAAAACTGATTT 57.375 32.000 0.00 0.00 34.92 2.17
801 1761 8.235359 TGCCATGTCAATATCAATGTAAATGA 57.765 30.769 0.00 0.00 0.00 2.57
849 1809 6.459066 TCTCAGAACAAGAACCAGAATACAG 58.541 40.000 0.00 0.00 0.00 2.74
860 1820 6.976088 TGTTTGTGTTTTCTCAGAACAAGAA 58.024 32.000 0.00 0.00 38.60 2.52
888 1848 9.044150 GGACAAAACATTTCAGATTTTCAATGA 57.956 29.630 0.00 0.00 32.07 2.57
892 1852 7.123355 AGGGACAAAACATTTCAGATTTTCA 57.877 32.000 0.00 0.00 0.00 2.69
896 1856 7.337938 ACAAAAGGGACAAAACATTTCAGATT 58.662 30.769 0.00 0.00 0.00 2.40
909 1869 8.877864 AGATAACATATGAACAAAAGGGACAA 57.122 30.769 10.38 0.00 0.00 3.18
1072 2049 7.528307 CCTTCATTCTGATCTTGAGTTTCTTG 58.472 38.462 0.00 0.00 0.00 3.02
1154 2131 2.204291 AGGCCAAGATCACCCCCA 60.204 61.111 5.01 0.00 0.00 4.96
1162 2139 1.668826 TACACCCAAGAGGCCAAGAT 58.331 50.000 5.01 0.00 40.58 2.40
1200 2177 1.821216 ACCCATACAAGCTTGGAACG 58.179 50.000 29.18 16.67 34.81 3.95
1263 2270 5.646360 CGATATAAGTGGTGACTTTTTGGGT 59.354 40.000 0.00 0.00 39.56 4.51
1591 2606 0.545071 CCCTTTGGGCTTGTTGGGAT 60.545 55.000 0.00 0.00 35.35 3.85
1604 2619 1.228988 AGCTTCAAGGGGCCCTTTG 60.229 57.895 35.11 35.11 41.69 2.77
1646 2661 7.501559 AGTTTGCATCTGATGAGCATTAGTATT 59.498 33.333 21.30 0.00 38.19 1.89
1736 2766 8.142551 CCACTTATTTTAGAGTATAAGGAGCGT 58.857 37.037 0.00 0.00 38.21 5.07
1737 2767 8.358148 TCCACTTATTTTAGAGTATAAGGAGCG 58.642 37.037 0.00 0.00 38.21 5.03
1750 2780 8.331022 CGTGATCAGAACATCCACTTATTTTAG 58.669 37.037 0.00 0.00 0.00 1.85
1767 2798 3.319137 AGCTAAAACTGCGTGATCAGA 57.681 42.857 0.00 0.00 37.51 3.27
1775 2806 4.174009 TGTAGAGCTAAGCTAAAACTGCG 58.826 43.478 0.00 0.00 39.88 5.18
1780 2811 8.041323 AGCATACTTTGTAGAGCTAAGCTAAAA 58.959 33.333 0.00 0.00 39.88 1.52
1790 2822 3.198872 GGGACAGCATACTTTGTAGAGC 58.801 50.000 0.00 0.00 0.00 4.09
1816 2848 3.054878 GTTGTCAAGCTTCAAGCAATGG 58.945 45.455 13.10 0.00 45.56 3.16
1882 2916 0.467844 TGAACTTGGCACAGCATGGT 60.468 50.000 0.00 0.00 43.62 3.55
1884 2918 1.816835 AGATGAACTTGGCACAGCATG 59.183 47.619 0.00 0.00 42.39 4.06
1888 2922 3.188048 GTGAAGAGATGAACTTGGCACAG 59.812 47.826 0.00 0.00 42.39 3.66
2008 3071 3.177228 AGGAGTTGTCTGCTTAGGATGT 58.823 45.455 0.00 0.00 39.28 3.06
2048 3112 1.138859 TGTTGTGTGAGACTGGGACTG 59.861 52.381 0.00 0.00 0.00 3.51
2084 3148 3.748568 GGCAAACTCAAACTCTCTACAGG 59.251 47.826 0.00 0.00 0.00 4.00
2188 3252 0.456142 GCAGAACCGCGATTTTTCCC 60.456 55.000 8.23 0.00 0.00 3.97
2328 3393 4.365514 TGTTCATTCCTAGCTGGTTCAA 57.634 40.909 0.00 0.00 37.07 2.69
2443 3509 6.073003 GCTCCATTAGGTATAAATCAGCACAC 60.073 42.308 0.00 0.00 35.89 3.82
2512 3609 7.453126 TGTTGTGGGAATTGGTTTCTACATTAT 59.547 33.333 0.00 0.00 34.09 1.28
2537 3634 5.389859 TGTGAAGGCTTTCAATTACCATG 57.610 39.130 13.42 0.00 44.49 3.66
2568 3665 5.066505 AGGTTGTGTGTGAAAAGCTAAAGAG 59.933 40.000 0.00 0.00 30.28 2.85
2591 3688 2.222027 GTCTCAACACCTCCAAACCAG 58.778 52.381 0.00 0.00 0.00 4.00
2665 3772 4.070630 AGCATGACTGAGGCTTATTCTC 57.929 45.455 0.00 0.00 39.11 2.87
2722 3830 1.382522 CAATGTCCCGGTGAGATTGG 58.617 55.000 23.58 12.44 46.05 3.16
2777 3885 3.562176 CCAGGCTAACATGTTTCTCCCTT 60.562 47.826 17.78 0.00 0.00 3.95
2820 3928 5.973124 TCTCTAGGATCCCAAAGAAATTCCT 59.027 40.000 8.55 0.00 37.38 3.36
2836 3944 3.674997 GTTTGGTGCACATTCTCTAGGA 58.325 45.455 20.43 0.00 0.00 2.94
2848 3956 1.463056 CTTAAGCGATCGTTTGGTGCA 59.537 47.619 25.00 3.80 0.00 4.57
2883 3991 2.301870 TCTGATTGTTCACGGCTTAGGT 59.698 45.455 0.00 0.00 0.00 3.08
2917 4025 2.023673 CTTTCCTCACCAACTTGCACA 58.976 47.619 0.00 0.00 0.00 4.57
2932 4040 5.234543 CGTAGCATAGTTTCTTAGGCTTTCC 59.765 44.000 0.00 0.00 40.69 3.13
2945 4053 3.192001 TCCGTTGTCTTCGTAGCATAGTT 59.808 43.478 0.00 0.00 0.00 2.24
2979 4087 1.897615 GGATCAGCAGCCCTCATGC 60.898 63.158 0.00 0.00 44.18 4.06
3001 4109 6.598525 CATCAACTTTCACGCTGTATGTAAA 58.401 36.000 0.00 0.00 0.00 2.01
3031 4139 4.142622 CCAGATGAGCGTCTTTATTTTGCA 60.143 41.667 0.00 0.00 0.00 4.08
3107 4215 3.679389 ACCTGGATGCTCAACTAACAAG 58.321 45.455 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.