Multiple sequence alignment - TraesCS1D01G104600

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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 TraesCS1D01G104600 chr1D 100.000 4142 0 0 1 4142 96037578 96033437 0.000000e+00 7649
1 TraesCS1D01G104600 chr1D 96.860 4108 97 17 1 4084 64334440 64338539 0.000000e+00 6842
2 TraesCS1D01G104600 chr1D 95.078 2174 70 19 1991 4142 439404020 439406178 0.000000e+00 3387
3 TraesCS1D01G104600 chr1D 94.527 1480 59 9 150 1623 439402107 439403570 0.000000e+00 2265
4 TraesCS1D01G104600 chr4A 93.016 4138 181 45 29 4142 557665562 557661509 0.000000e+00 5941
5 TraesCS1D01G104600 chr4A 92.365 4139 184 56 26 4142 554696783 554700811 0.000000e+00 5771
6 TraesCS1D01G104600 chr7D 94.255 3673 143 28 486 4140 600061961 600065583 0.000000e+00 5552
7 TraesCS1D01G104600 chr7D 91.054 503 14 5 1 488 600061435 600061921 0.000000e+00 651
8 TraesCS1D01G104600 chr7B 93.357 3447 167 21 713 4142 6997819 7001220 0.000000e+00 5040
9 TraesCS1D01G104600 chr6A 93.475 2958 136 24 1203 4142 121725818 121722900 0.000000e+00 4340
10 TraesCS1D01G104600 chr3B 94.118 2346 89 23 1808 4142 734914114 734911807 0.000000e+00 3522
11 TraesCS1D01G104600 chr3B 90.692 2342 149 33 1835 4142 774402758 774405064 0.000000e+00 3053
12 TraesCS1D01G104600 chr3B 94.846 1300 57 5 486 1777 774216736 774218033 0.000000e+00 2021
13 TraesCS1D01G104600 chr3B 90.448 1518 88 17 2583 4072 774218732 774220220 0.000000e+00 1947
14 TraesCS1D01G104600 chr3B 91.502 506 21 7 1 488 734914928 734914427 0.000000e+00 676
15 TraesCS1D01G104600 chr3B 91.054 503 22 4 1 488 774400955 774401449 0.000000e+00 658
16 TraesCS1D01G104600 chr3B 93.814 291 15 2 1640 1930 774402735 774403022 6.360000e-118 435
17 TraesCS1D01G104600 chr3B 84.173 278 36 3 1664 1936 734914087 734913813 3.180000e-66 263
18 TraesCS1D01G104600 chr4D 96.860 1815 48 5 1296 3106 42333705 42335514 0.000000e+00 3027
19 TraesCS1D01G104600 chr4D 93.774 1285 54 18 26 1303 42331644 42332909 0.000000e+00 1906
20 TraesCS1D01G104600 chr3A 91.814 2211 123 22 1951 4142 714788240 714790411 0.000000e+00 3027
21 TraesCS1D01G104600 chr3A 92.719 1813 80 18 2347 4142 607845896 607847673 0.000000e+00 2569
22 TraesCS1D01G104600 chr3D 94.606 1372 42 7 2323 3678 579688196 579689551 0.000000e+00 2095
23 TraesCS1D01G104600 chr3D 93.793 1305 53 10 486 1767 579686711 579688010 0.000000e+00 1936
24 TraesCS1D01G104600 chr3D 91.913 507 22 5 1 488 579686165 579686671 0.000000e+00 691
25 TraesCS1D01G104600 chr3D 92.045 440 26 3 3712 4142 579689548 579689987 9.840000e-171 610
26 TraesCS1D01G104600 chr2B 84.901 2126 219 56 1045 3131 760892561 760890499 0.000000e+00 2054
27 TraesCS1D01G104600 chr2B 95.112 941 41 5 486 1424 755328532 755329469 0.000000e+00 1478
28 TraesCS1D01G104600 chr2B 90.824 425 29 4 3728 4142 755331619 755332043 1.010000e-155 560
29 TraesCS1D01G104600 chr2D 89.601 1154 103 14 1985 3131 620512053 620510910 0.000000e+00 1450
30 TraesCS1D01G104600 chr6B 91.951 733 38 18 26 750 144005962 144006681 0.000000e+00 1007
31 TraesCS1D01G104600 chr6D 91.440 736 39 17 25 750 68973066 68973787 0.000000e+00 989


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 TraesCS1D01G104600 chr1D 96033437 96037578 4141 True 7649.0 7649 100.000000 1 4142 1 chr1D.!!$R1 4141
1 TraesCS1D01G104600 chr1D 64334440 64338539 4099 False 6842.0 6842 96.860000 1 4084 1 chr1D.!!$F1 4083
2 TraesCS1D01G104600 chr1D 439402107 439406178 4071 False 2826.0 3387 94.802500 150 4142 2 chr1D.!!$F2 3992
3 TraesCS1D01G104600 chr4A 557661509 557665562 4053 True 5941.0 5941 93.016000 29 4142 1 chr4A.!!$R1 4113
4 TraesCS1D01G104600 chr4A 554696783 554700811 4028 False 5771.0 5771 92.365000 26 4142 1 chr4A.!!$F1 4116
5 TraesCS1D01G104600 chr7D 600061435 600065583 4148 False 3101.5 5552 92.654500 1 4140 2 chr7D.!!$F1 4139
6 TraesCS1D01G104600 chr7B 6997819 7001220 3401 False 5040.0 5040 93.357000 713 4142 1 chr7B.!!$F1 3429
7 TraesCS1D01G104600 chr6A 121722900 121725818 2918 True 4340.0 4340 93.475000 1203 4142 1 chr6A.!!$R1 2939
8 TraesCS1D01G104600 chr3B 774216736 774220220 3484 False 1984.0 2021 92.647000 486 4072 2 chr3B.!!$F1 3586
9 TraesCS1D01G104600 chr3B 734911807 734914928 3121 True 1487.0 3522 89.931000 1 4142 3 chr3B.!!$R1 4141
10 TraesCS1D01G104600 chr3B 774400955 774405064 4109 False 1382.0 3053 91.853333 1 4142 3 chr3B.!!$F2 4141
11 TraesCS1D01G104600 chr4D 42331644 42335514 3870 False 2466.5 3027 95.317000 26 3106 2 chr4D.!!$F1 3080
12 TraesCS1D01G104600 chr3A 714788240 714790411 2171 False 3027.0 3027 91.814000 1951 4142 1 chr3A.!!$F2 2191
13 TraesCS1D01G104600 chr3A 607845896 607847673 1777 False 2569.0 2569 92.719000 2347 4142 1 chr3A.!!$F1 1795
14 TraesCS1D01G104600 chr3D 579686165 579689987 3822 False 1333.0 2095 93.089250 1 4142 4 chr3D.!!$F1 4141
15 TraesCS1D01G104600 chr2B 760890499 760892561 2062 True 2054.0 2054 84.901000 1045 3131 1 chr2B.!!$R1 2086
16 TraesCS1D01G104600 chr2B 755328532 755332043 3511 False 1019.0 1478 92.968000 486 4142 2 chr2B.!!$F1 3656
17 TraesCS1D01G104600 chr2D 620510910 620512053 1143 True 1450.0 1450 89.601000 1985 3131 1 chr2D.!!$R1 1146
18 TraesCS1D01G104600 chr6B 144005962 144006681 719 False 1007.0 1007 91.951000 26 750 1 chr6B.!!$F1 724
19 TraesCS1D01G104600 chr6D 68973066 68973787 721 False 989.0 989 91.440000 25 750 1 chr6D.!!$F1 725

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
913 1020 1.109323 GGTTTGGCACTGCACTCCTT 61.109 55.0 2.82 0.00 0.0 3.36 F
1687 2941 0.798776 GCAATGGTCACCTGTCTTCG 59.201 55.0 0.00 0.00 0.0 3.79 F
1853 3107 1.180029 AGGTTGCAATGATCACCTGC 58.820 50.0 19.96 19.96 36.6 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2567 3884 0.542805 CGGAAATTACCTTCGGGGGA 59.457 55.000 1.80 0.0 40.03 4.81 R
3118 4496 1.525995 CATCCACCCATGGCGTACC 60.526 63.158 6.09 0.0 46.80 3.34 R
3765 5281 0.670546 CGAATTGCCTCACCAGACGT 60.671 55.000 0.00 0.0 0.00 4.34 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
36 37 3.159213 TGCCTTGAGATGGATTGTTGT 57.841 42.857 0.00 0.00 0.00 3.32
43 48 4.619973 TGAGATGGATTGTTGTTTGTTGC 58.380 39.130 0.00 0.00 0.00 4.17
56 61 4.695396 TGTTTGTTGCTTGATTGATTGCT 58.305 34.783 0.00 0.00 0.00 3.91
383 422 9.793252 GACATATCACATTTGCTCTTTATTGTT 57.207 29.630 0.00 0.00 0.00 2.83
691 795 6.668645 TGGTAATGGTAACCTTATGAATGCT 58.331 36.000 0.00 0.00 37.91 3.79
781 887 2.096496 GTGGTGAGCTGACATATTGTGC 59.904 50.000 5.47 0.00 0.00 4.57
913 1020 1.109323 GGTTTGGCACTGCACTCCTT 61.109 55.000 2.82 0.00 0.00 3.36
1217 1337 4.951715 GGGGGTTAGGTTGTCGATTATTTT 59.048 41.667 0.00 0.00 0.00 1.82
1347 2275 6.154203 TGTATCTTCTGAGCAGGTCATTAG 57.846 41.667 1.94 3.98 33.51 1.73
1646 2805 8.964772 CAATAGGGAGAATTTTTGAGAGTGAAT 58.035 33.333 0.00 0.00 0.00 2.57
1687 2941 0.798776 GCAATGGTCACCTGTCTTCG 59.201 55.000 0.00 0.00 0.00 3.79
1747 3001 7.817418 TTACTGAAGCAACTTTATCTTTGGT 57.183 32.000 0.00 0.00 34.97 3.67
1748 3002 8.911918 TTACTGAAGCAACTTTATCTTTGGTA 57.088 30.769 0.00 0.00 33.19 3.25
1749 3003 7.817418 ACTGAAGCAACTTTATCTTTGGTAA 57.183 32.000 0.00 0.00 33.19 2.85
1750 3004 8.409358 ACTGAAGCAACTTTATCTTTGGTAAT 57.591 30.769 0.00 0.00 33.19 1.89
1753 3007 8.637986 TGAAGCAACTTTATCTTTGGTAATGTT 58.362 29.630 0.00 0.00 33.19 2.71
1754 3008 8.816640 AAGCAACTTTATCTTTGGTAATGTTG 57.183 30.769 17.49 17.49 43.17 3.33
1756 3010 8.421002 AGCAACTTTATCTTTGGTAATGTTGTT 58.579 29.630 20.28 15.66 42.76 2.83
1778 3032 8.781067 TGTTTAAATCTGATTTGAGAAACACG 57.219 30.769 24.68 0.00 35.22 4.49
1779 3033 8.616942 TGTTTAAATCTGATTTGAGAAACACGA 58.383 29.630 24.68 12.47 35.22 4.35
1781 3035 9.445786 TTTAAATCTGATTTGAGAAACACGAAC 57.554 29.630 22.47 0.00 33.82 3.95
1784 3038 5.116180 TCTGATTTGAGAAACACGAACAGT 58.884 37.500 0.00 0.00 0.00 3.55
1786 3040 6.200286 TCTGATTTGAGAAACACGAACAGTAC 59.800 38.462 0.00 0.00 0.00 2.73
1787 3041 6.046593 TGATTTGAGAAACACGAACAGTACT 58.953 36.000 0.00 0.00 0.00 2.73
1788 3042 7.204604 TGATTTGAGAAACACGAACAGTACTA 58.795 34.615 0.00 0.00 0.00 1.82
1789 3043 7.381408 TGATTTGAGAAACACGAACAGTACTAG 59.619 37.037 0.00 0.00 0.00 2.57
1790 3044 4.543692 TGAGAAACACGAACAGTACTAGC 58.456 43.478 0.00 0.00 0.00 3.42
1791 3045 3.910648 AGAAACACGAACAGTACTAGCC 58.089 45.455 0.00 0.00 0.00 3.93
1792 3046 3.573110 AGAAACACGAACAGTACTAGCCT 59.427 43.478 0.00 0.00 0.00 4.58
1793 3047 3.299340 AACACGAACAGTACTAGCCTG 57.701 47.619 0.00 8.15 36.01 4.85
1794 3048 2.511659 ACACGAACAGTACTAGCCTGA 58.488 47.619 15.00 0.00 34.04 3.86
1795 3049 3.090037 ACACGAACAGTACTAGCCTGAT 58.910 45.455 15.00 5.02 34.04 2.90
1796 3050 3.128938 ACACGAACAGTACTAGCCTGATC 59.871 47.826 15.00 11.85 34.04 2.92
1797 3051 3.128764 CACGAACAGTACTAGCCTGATCA 59.871 47.826 15.00 0.00 32.91 2.92
1798 3052 3.762288 ACGAACAGTACTAGCCTGATCAA 59.238 43.478 15.00 0.00 32.91 2.57
1799 3053 4.402793 ACGAACAGTACTAGCCTGATCAAT 59.597 41.667 15.00 3.65 32.91 2.57
1801 3055 6.146216 CGAACAGTACTAGCCTGATCAATAG 58.854 44.000 15.00 2.49 32.91 1.73
1807 3061 7.446931 CAGTACTAGCCTGATCAATAGAGAGAA 59.553 40.741 13.46 0.00 31.38 2.87
1808 3062 8.170061 AGTACTAGCCTGATCAATAGAGAGAAT 58.830 37.037 13.46 0.00 0.00 2.40
1810 3064 7.669427 ACTAGCCTGATCAATAGAGAGAATTG 58.331 38.462 13.46 0.00 35.98 2.32
1812 3066 6.523840 AGCCTGATCAATAGAGAGAATTGTC 58.476 40.000 0.00 0.00 36.07 3.18
1813 3067 6.099413 AGCCTGATCAATAGAGAGAATTGTCA 59.901 38.462 5.28 0.00 36.07 3.58
1814 3068 6.765036 GCCTGATCAATAGAGAGAATTGTCAA 59.235 38.462 5.28 0.00 36.07 3.18
1818 3072 9.730705 TGATCAATAGAGAGAATTGTCAAAAGT 57.269 29.630 5.28 0.00 36.07 2.66
1820 3074 8.327941 TCAATAGAGAGAATTGTCAAAAGTGG 57.672 34.615 5.28 0.00 36.07 4.00
1821 3075 6.749923 ATAGAGAGAATTGTCAAAAGTGGC 57.250 37.500 5.28 0.00 0.00 5.01
1822 3076 3.823304 AGAGAGAATTGTCAAAAGTGGCC 59.177 43.478 5.28 0.00 0.00 5.36
1823 3077 3.823304 GAGAGAATTGTCAAAAGTGGCCT 59.177 43.478 3.32 0.00 0.00 5.19
1826 3080 3.571401 AGAATTGTCAAAAGTGGCCTCTG 59.429 43.478 8.37 0.00 0.00 3.35
1828 3082 2.435372 TGTCAAAAGTGGCCTCTGTT 57.565 45.000 8.37 6.21 0.00 3.16
1831 3085 4.274147 TGTCAAAAGTGGCCTCTGTTTTA 58.726 39.130 8.37 0.00 0.00 1.52
1832 3086 4.338118 TGTCAAAAGTGGCCTCTGTTTTAG 59.662 41.667 8.37 0.00 0.00 1.85
1833 3087 4.338400 GTCAAAAGTGGCCTCTGTTTTAGT 59.662 41.667 8.37 0.00 0.00 2.24
1834 3088 5.529800 GTCAAAAGTGGCCTCTGTTTTAGTA 59.470 40.000 8.37 0.00 0.00 1.82
1835 3089 5.763204 TCAAAAGTGGCCTCTGTTTTAGTAG 59.237 40.000 8.37 0.00 0.00 2.57
1836 3090 3.983044 AGTGGCCTCTGTTTTAGTAGG 57.017 47.619 6.51 0.00 0.00 3.18
1837 3091 3.248888 AGTGGCCTCTGTTTTAGTAGGT 58.751 45.455 6.51 0.00 0.00 3.08
1838 3092 3.651423 AGTGGCCTCTGTTTTAGTAGGTT 59.349 43.478 6.51 0.00 0.00 3.50
1839 3093 3.751698 GTGGCCTCTGTTTTAGTAGGTTG 59.248 47.826 3.32 0.00 0.00 3.77
1840 3094 2.747989 GGCCTCTGTTTTAGTAGGTTGC 59.252 50.000 0.00 0.00 0.00 4.17
1841 3095 3.408634 GCCTCTGTTTTAGTAGGTTGCA 58.591 45.455 0.00 0.00 0.00 4.08
1842 3096 3.818773 GCCTCTGTTTTAGTAGGTTGCAA 59.181 43.478 0.00 0.00 0.00 4.08
1843 3097 4.459337 GCCTCTGTTTTAGTAGGTTGCAAT 59.541 41.667 0.59 0.00 0.00 3.56
1844 3098 5.619981 GCCTCTGTTTTAGTAGGTTGCAATG 60.620 44.000 0.59 0.00 0.00 2.82
1845 3099 5.705441 CCTCTGTTTTAGTAGGTTGCAATGA 59.295 40.000 0.59 0.00 0.00 2.57
1846 3100 6.375455 CCTCTGTTTTAGTAGGTTGCAATGAT 59.625 38.462 0.59 0.00 0.00 2.45
1847 3101 7.377766 TCTGTTTTAGTAGGTTGCAATGATC 57.622 36.000 0.59 0.00 0.00 2.92
1848 3102 6.939730 TCTGTTTTAGTAGGTTGCAATGATCA 59.060 34.615 0.59 0.00 0.00 2.92
1850 3104 6.072175 TGTTTTAGTAGGTTGCAATGATCACC 60.072 38.462 0.59 0.00 0.00 4.02
1851 3105 5.435686 TTAGTAGGTTGCAATGATCACCT 57.564 39.130 10.27 10.27 0.00 4.00
1852 3106 3.614092 AGTAGGTTGCAATGATCACCTG 58.386 45.455 14.50 6.44 0.00 4.00
1853 3107 1.180029 AGGTTGCAATGATCACCTGC 58.820 50.000 19.96 19.96 36.60 4.85
1854 3108 1.180029 GGTTGCAATGATCACCTGCT 58.820 50.000 24.56 0.00 37.00 4.24
1857 3111 3.248266 GTTGCAATGATCACCTGCTTTC 58.752 45.455 24.56 14.66 37.00 2.62
1858 3112 1.820519 TGCAATGATCACCTGCTTTCC 59.179 47.619 24.56 4.47 37.00 3.13
1859 3113 2.097825 GCAATGATCACCTGCTTTCCT 58.902 47.619 19.63 0.00 33.20 3.36
1860 3114 2.494870 GCAATGATCACCTGCTTTCCTT 59.505 45.455 19.63 0.00 33.20 3.36
1861 3115 3.675228 GCAATGATCACCTGCTTTCCTTG 60.675 47.826 19.63 8.63 33.20 3.61
1862 3116 2.205022 TGATCACCTGCTTTCCTTGG 57.795 50.000 0.00 0.00 0.00 3.61
1863 3117 1.425066 TGATCACCTGCTTTCCTTGGT 59.575 47.619 0.00 0.00 0.00 3.67
1864 3118 2.158475 TGATCACCTGCTTTCCTTGGTT 60.158 45.455 0.00 0.00 0.00 3.67
1866 3120 3.586470 TCACCTGCTTTCCTTGGTTTA 57.414 42.857 0.00 0.00 0.00 2.01
1868 3122 4.079253 TCACCTGCTTTCCTTGGTTTATC 58.921 43.478 0.00 0.00 0.00 1.75
1869 3123 3.826157 CACCTGCTTTCCTTGGTTTATCA 59.174 43.478 0.00 0.00 0.00 2.15
1870 3124 4.280677 CACCTGCTTTCCTTGGTTTATCAA 59.719 41.667 0.00 0.00 0.00 2.57
1871 3125 5.047092 CACCTGCTTTCCTTGGTTTATCAAT 60.047 40.000 0.00 0.00 0.00 2.57
1873 3127 4.819769 TGCTTTCCTTGGTTTATCAATGC 58.180 39.130 0.00 0.00 0.00 3.56
1875 3129 5.046448 TGCTTTCCTTGGTTTATCAATGCAT 60.046 36.000 0.00 0.00 0.00 3.96
1877 3131 6.476706 GCTTTCCTTGGTTTATCAATGCATAC 59.523 38.462 0.00 0.00 0.00 2.39
1878 3132 7.631377 GCTTTCCTTGGTTTATCAATGCATACT 60.631 37.037 0.00 0.00 0.00 2.12
1879 3133 6.698008 TCCTTGGTTTATCAATGCATACTG 57.302 37.500 0.00 0.00 0.00 2.74
1880 3134 5.593909 TCCTTGGTTTATCAATGCATACTGG 59.406 40.000 0.00 0.00 0.00 4.00
1881 3135 5.593909 CCTTGGTTTATCAATGCATACTGGA 59.406 40.000 0.00 0.00 0.00 3.86
1882 3136 6.096705 CCTTGGTTTATCAATGCATACTGGAA 59.903 38.462 0.00 0.00 0.00 3.53
1885 3139 6.889177 TGGTTTATCAATGCATACTGGAAGAA 59.111 34.615 0.00 0.00 37.43 2.52
1887 3141 8.416329 GGTTTATCAATGCATACTGGAAGAAAT 58.584 33.333 0.00 0.00 37.43 2.17
1914 3168 9.793252 ATAATTACTGAAGCAACTTTAGCATTG 57.207 29.630 0.00 0.00 31.48 2.82
1917 3171 6.633500 ACTGAAGCAACTTTAGCATTGTAA 57.367 33.333 0.00 0.00 31.48 2.41
1919 3173 7.661040 ACTGAAGCAACTTTAGCATTGTAAAT 58.339 30.769 0.00 0.00 31.48 1.40
1920 3174 7.596248 ACTGAAGCAACTTTAGCATTGTAAATG 59.404 33.333 0.00 0.00 31.48 2.32
1922 3176 7.925483 TGAAGCAACTTTAGCATTGTAAATGTT 59.075 29.630 2.23 0.00 0.00 2.71
1923 3177 7.642071 AGCAACTTTAGCATTGTAAATGTTG 57.358 32.000 17.65 17.65 36.04 3.33
1927 3181 9.457110 CAACTTTAGCATTGTAAATGTTGTGTA 57.543 29.630 15.68 0.00 32.90 2.90
1933 3187 8.746922 AGCATTGTAAATGTTGTGTAAATCTG 57.253 30.769 2.23 0.00 0.00 2.90
1934 3188 8.575589 AGCATTGTAAATGTTGTGTAAATCTGA 58.424 29.630 2.23 0.00 0.00 3.27
1935 3189 9.357652 GCATTGTAAATGTTGTGTAAATCTGAT 57.642 29.630 2.23 0.00 0.00 2.90
1944 3198 9.683069 ATGTTGTGTAAATCTGATTTGAGAAAC 57.317 29.630 22.47 19.41 33.82 2.78
1946 3200 9.515020 GTTGTGTAAATCTGATTTGAGAAACAA 57.485 29.630 22.47 17.03 36.65 2.83
1947 3201 9.734620 TTGTGTAAATCTGATTTGAGAAACAAG 57.265 29.630 22.47 0.00 39.77 3.16
1949 3203 9.950680 GTGTAAATCTGATTTGAGAAACAAGAA 57.049 29.630 22.47 0.00 39.77 2.52
1950 3204 9.950680 TGTAAATCTGATTTGAGAAACAAGAAC 57.049 29.630 22.47 10.43 39.77 3.01
1954 3208 8.908786 ATCTGATTTGAGAAACAAGAACAGTA 57.091 30.769 0.00 0.00 39.77 2.74
2109 3371 7.433131 GCATTCATAATGTGTGTAAACCTGATG 59.567 37.037 1.94 0.00 41.01 3.07
2111 3373 7.994425 TCATAATGTGTGTAAACCTGATGTT 57.006 32.000 0.00 0.00 39.43 2.71
2113 3375 8.855110 TCATAATGTGTGTAAACCTGATGTTTT 58.145 29.630 0.00 0.00 44.80 2.43
2114 3376 8.914654 CATAATGTGTGTAAACCTGATGTTTTG 58.085 33.333 0.00 0.00 44.80 2.44
2556 3873 3.303351 ACATCCATTTCCCACTGGATC 57.697 47.619 0.00 0.00 46.95 3.36
2567 3884 2.176364 CCCACTGGATCATCCCTTCAAT 59.824 50.000 0.00 0.00 35.03 2.57
2941 4317 5.123027 GGTTCCTTCAGCAACTTAATCTCAG 59.877 44.000 0.00 0.00 0.00 3.35
3242 4653 6.088085 GGATGTTTGCTAATTTCGAAACACAG 59.912 38.462 13.81 11.25 40.19 3.66
3354 4766 6.126796 TGGAGTTGCAGGACTATAAATCATCA 60.127 38.462 0.00 0.00 0.00 3.07
3395 4807 8.647143 TTCAAATGGTCAGAGTTTGAATTTTC 57.353 30.769 11.53 0.00 43.17 2.29
3670 5101 7.509141 TTTAAGTTGCTCATGTCATTTCAGA 57.491 32.000 0.00 0.00 0.00 3.27
3705 5136 2.972021 TGGAACTGATGAGAGACAACCA 59.028 45.455 0.00 0.00 0.00 3.67
3765 5281 1.063567 GGCTTACCTCTCCTCCTCTCA 60.064 57.143 0.00 0.00 0.00 3.27
3942 5473 2.852748 CTCGTTCTCGATTCGTCTGTT 58.147 47.619 5.89 0.00 45.21 3.16
4117 5649 0.822121 GTGTTCTTGGGGCCGTTTCT 60.822 55.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.816258 TCAAAGCAATCAATCAAGCAACAAA 59.184 32.000 0.00 0.00 0.00 2.83
43 48 6.203808 TCCATCTCAAAGCAATCAATCAAG 57.796 37.500 0.00 0.00 0.00 3.02
56 61 7.053316 ACAACAATCAACAATCCATCTCAAA 57.947 32.000 0.00 0.00 0.00 2.69
383 422 2.375174 ACCCATCAGTGTCCTTAGCAAA 59.625 45.455 0.00 0.00 0.00 3.68
1347 2275 6.112734 ACAGAACAAAATCCAAGGGTTTTTC 58.887 36.000 7.34 4.58 33.82 2.29
1568 2667 7.380423 AAATAGTCTAGTCCATGCCTAACAT 57.620 36.000 0.00 0.00 40.66 2.71
1646 2805 4.566907 GCCACCTCACCTCCTAAAACATAA 60.567 45.833 0.00 0.00 0.00 1.90
1687 2941 9.903682 TTCCAGTATGCGTTAATATAGACTAAC 57.096 33.333 0.00 0.00 31.97 2.34
1753 3007 8.616942 TCGTGTTTCTCAAATCAGATTTAAACA 58.383 29.630 21.41 21.41 36.58 2.83
1754 3008 9.445786 TTCGTGTTTCTCAAATCAGATTTAAAC 57.554 29.630 18.25 18.25 32.72 2.01
1756 3010 8.616942 TGTTCGTGTTTCTCAAATCAGATTTAA 58.383 29.630 8.12 0.00 0.00 1.52
1758 3012 7.026631 TGTTCGTGTTTCTCAAATCAGATTT 57.973 32.000 2.20 2.20 0.00 2.17
1759 3013 6.260936 ACTGTTCGTGTTTCTCAAATCAGATT 59.739 34.615 0.00 0.00 0.00 2.40
1761 3015 5.116180 ACTGTTCGTGTTTCTCAAATCAGA 58.884 37.500 0.00 0.00 0.00 3.27
1762 3016 5.409643 ACTGTTCGTGTTTCTCAAATCAG 57.590 39.130 0.00 0.00 0.00 2.90
1764 3018 6.526566 AGTACTGTTCGTGTTTCTCAAATC 57.473 37.500 0.00 0.00 0.00 2.17
1765 3019 6.145696 GCTAGTACTGTTCGTGTTTCTCAAAT 59.854 38.462 5.39 0.00 0.00 2.32
1766 3020 5.461078 GCTAGTACTGTTCGTGTTTCTCAAA 59.539 40.000 5.39 0.00 0.00 2.69
1767 3021 4.980434 GCTAGTACTGTTCGTGTTTCTCAA 59.020 41.667 5.39 0.00 0.00 3.02
1769 3023 3.919197 GGCTAGTACTGTTCGTGTTTCTC 59.081 47.826 5.39 0.00 0.00 2.87
1770 3024 3.573110 AGGCTAGTACTGTTCGTGTTTCT 59.427 43.478 5.39 0.00 0.00 2.52
1773 3027 2.889045 TCAGGCTAGTACTGTTCGTGTT 59.111 45.455 5.39 0.00 37.25 3.32
1775 3029 3.128764 TGATCAGGCTAGTACTGTTCGTG 59.871 47.826 5.39 6.45 37.44 4.35
1778 3032 7.229707 TCTCTATTGATCAGGCTAGTACTGTTC 59.770 40.741 5.39 14.54 37.25 3.18
1779 3033 7.063593 TCTCTATTGATCAGGCTAGTACTGTT 58.936 38.462 5.39 7.78 37.25 3.16
1781 3035 6.939730 TCTCTCTATTGATCAGGCTAGTACTG 59.060 42.308 5.39 9.49 37.30 2.74
1784 3038 8.801299 CAATTCTCTCTATTGATCAGGCTAGTA 58.199 37.037 0.00 0.00 35.49 1.82
1786 3040 7.669427 ACAATTCTCTCTATTGATCAGGCTAG 58.331 38.462 0.00 0.00 36.67 3.42
1787 3041 7.288621 TGACAATTCTCTCTATTGATCAGGCTA 59.711 37.037 0.00 0.00 36.67 3.93
1788 3042 6.099413 TGACAATTCTCTCTATTGATCAGGCT 59.901 38.462 0.00 0.00 36.67 4.58
1789 3043 6.286758 TGACAATTCTCTCTATTGATCAGGC 58.713 40.000 0.00 0.00 36.67 4.85
1790 3044 8.728337 TTTGACAATTCTCTCTATTGATCAGG 57.272 34.615 0.00 0.00 36.67 3.86
1792 3046 9.730705 ACTTTTGACAATTCTCTCTATTGATCA 57.269 29.630 0.00 0.00 36.67 2.92
1793 3047 9.985318 CACTTTTGACAATTCTCTCTATTGATC 57.015 33.333 0.00 0.00 36.67 2.92
1794 3048 8.954350 CCACTTTTGACAATTCTCTCTATTGAT 58.046 33.333 0.00 0.00 36.67 2.57
1795 3049 7.094634 GCCACTTTTGACAATTCTCTCTATTGA 60.095 37.037 0.00 0.00 36.67 2.57
1796 3050 7.025963 GCCACTTTTGACAATTCTCTCTATTG 58.974 38.462 0.00 0.00 38.61 1.90
1797 3051 6.151817 GGCCACTTTTGACAATTCTCTCTATT 59.848 38.462 0.00 0.00 0.00 1.73
1798 3052 5.649831 GGCCACTTTTGACAATTCTCTCTAT 59.350 40.000 0.00 0.00 0.00 1.98
1799 3053 5.003804 GGCCACTTTTGACAATTCTCTCTA 58.996 41.667 0.00 0.00 0.00 2.43
1801 3055 3.823304 AGGCCACTTTTGACAATTCTCTC 59.177 43.478 5.01 0.00 0.00 3.20
1807 3061 2.949447 ACAGAGGCCACTTTTGACAAT 58.051 42.857 5.01 0.00 0.00 2.71
1808 3062 2.435372 ACAGAGGCCACTTTTGACAA 57.565 45.000 5.01 0.00 0.00 3.18
1810 3064 3.801114 AAAACAGAGGCCACTTTTGAC 57.199 42.857 5.01 0.00 0.00 3.18
1812 3066 4.918810 ACTAAAACAGAGGCCACTTTTG 57.081 40.909 5.01 0.00 0.00 2.44
1813 3067 5.070685 CCTACTAAAACAGAGGCCACTTTT 58.929 41.667 5.01 5.25 0.00 2.27
1814 3068 4.104261 ACCTACTAAAACAGAGGCCACTTT 59.896 41.667 5.01 0.00 31.81 2.66
1818 3072 3.809324 GCAACCTACTAAAACAGAGGCCA 60.809 47.826 5.01 0.00 31.81 5.36
1820 3074 3.408634 TGCAACCTACTAAAACAGAGGC 58.591 45.455 0.00 0.00 31.81 4.70
1821 3075 5.705441 TCATTGCAACCTACTAAAACAGAGG 59.295 40.000 0.00 0.00 35.05 3.69
1822 3076 6.801539 TCATTGCAACCTACTAAAACAGAG 57.198 37.500 0.00 0.00 0.00 3.35
1823 3077 6.939730 TGATCATTGCAACCTACTAAAACAGA 59.060 34.615 0.00 0.00 0.00 3.41
1826 3080 6.151144 AGGTGATCATTGCAACCTACTAAAAC 59.849 38.462 0.00 0.00 0.00 2.43
1828 3082 5.647658 CAGGTGATCATTGCAACCTACTAAA 59.352 40.000 0.00 0.00 0.00 1.85
1831 3085 3.614092 CAGGTGATCATTGCAACCTACT 58.386 45.455 0.00 0.00 0.00 2.57
1832 3086 2.098117 GCAGGTGATCATTGCAACCTAC 59.902 50.000 22.79 6.34 37.75 3.18
1833 3087 2.025981 AGCAGGTGATCATTGCAACCTA 60.026 45.455 26.85 0.00 40.22 3.08
1834 3088 1.180029 GCAGGTGATCATTGCAACCT 58.820 50.000 22.79 11.29 37.75 3.50
1835 3089 1.180029 AGCAGGTGATCATTGCAACC 58.820 50.000 26.85 12.35 40.22 3.77
1836 3090 3.248266 GAAAGCAGGTGATCATTGCAAC 58.752 45.455 26.85 17.36 40.22 4.17
1837 3091 2.231964 GGAAAGCAGGTGATCATTGCAA 59.768 45.455 26.85 0.00 40.22 4.08
1838 3092 1.820519 GGAAAGCAGGTGATCATTGCA 59.179 47.619 26.85 0.00 40.22 4.08
1839 3093 2.097825 AGGAAAGCAGGTGATCATTGC 58.902 47.619 21.13 21.13 38.09 3.56
1840 3094 3.119245 CCAAGGAAAGCAGGTGATCATTG 60.119 47.826 0.00 2.04 34.40 2.82
1841 3095 3.094572 CCAAGGAAAGCAGGTGATCATT 58.905 45.455 0.00 0.00 0.00 2.57
1842 3096 2.042162 ACCAAGGAAAGCAGGTGATCAT 59.958 45.455 0.00 0.00 32.04 2.45
1843 3097 1.425066 ACCAAGGAAAGCAGGTGATCA 59.575 47.619 0.00 0.00 32.04 2.92
1844 3098 2.206576 ACCAAGGAAAGCAGGTGATC 57.793 50.000 0.00 0.00 32.04 2.92
1845 3099 2.683211 AACCAAGGAAAGCAGGTGAT 57.317 45.000 0.00 0.00 33.93 3.06
1846 3100 2.452600 AAACCAAGGAAAGCAGGTGA 57.547 45.000 0.00 0.00 33.93 4.02
1847 3101 3.826157 TGATAAACCAAGGAAAGCAGGTG 59.174 43.478 0.00 0.00 33.93 4.00
1848 3102 4.112634 TGATAAACCAAGGAAAGCAGGT 57.887 40.909 0.00 0.00 35.47 4.00
1850 3104 4.866486 GCATTGATAAACCAAGGAAAGCAG 59.134 41.667 0.00 0.00 30.19 4.24
1851 3105 4.282957 TGCATTGATAAACCAAGGAAAGCA 59.717 37.500 0.00 0.00 30.19 3.91
1852 3106 4.819769 TGCATTGATAAACCAAGGAAAGC 58.180 39.130 0.00 0.00 30.19 3.51
1853 3107 7.703621 CAGTATGCATTGATAAACCAAGGAAAG 59.296 37.037 3.54 0.00 30.19 2.62
1854 3108 7.363705 CCAGTATGCATTGATAAACCAAGGAAA 60.364 37.037 3.54 0.00 30.19 3.13
1857 3111 5.593909 TCCAGTATGCATTGATAAACCAAGG 59.406 40.000 3.54 0.00 31.97 3.61
1858 3112 6.698008 TCCAGTATGCATTGATAAACCAAG 57.302 37.500 3.54 0.00 31.97 3.61
1859 3113 6.889177 TCTTCCAGTATGCATTGATAAACCAA 59.111 34.615 3.54 0.00 31.97 3.67
1860 3114 6.422333 TCTTCCAGTATGCATTGATAAACCA 58.578 36.000 3.54 0.00 31.97 3.67
1861 3115 6.942532 TCTTCCAGTATGCATTGATAAACC 57.057 37.500 3.54 0.00 31.97 3.27
1891 3145 7.219484 ACAATGCTAAAGTTGCTTCAGTAAT 57.781 32.000 0.00 0.00 0.00 1.89
1892 3146 6.633500 ACAATGCTAAAGTTGCTTCAGTAA 57.367 33.333 0.00 0.00 0.00 2.24
1893 3147 7.737972 TTACAATGCTAAAGTTGCTTCAGTA 57.262 32.000 0.00 0.00 0.00 2.74
1894 3148 6.633500 TTACAATGCTAAAGTTGCTTCAGT 57.367 33.333 0.00 0.00 0.00 3.41
1895 3149 7.596248 ACATTTACAATGCTAAAGTTGCTTCAG 59.404 33.333 0.00 0.00 0.00 3.02
1896 3150 7.432869 ACATTTACAATGCTAAAGTTGCTTCA 58.567 30.769 0.00 0.00 0.00 3.02
1897 3151 7.873739 ACATTTACAATGCTAAAGTTGCTTC 57.126 32.000 0.00 0.00 0.00 3.86
1898 3152 7.710475 ACAACATTTACAATGCTAAAGTTGCTT 59.290 29.630 12.61 0.00 33.56 3.91
1901 3155 8.351495 ACACAACATTTACAATGCTAAAGTTG 57.649 30.769 11.67 11.67 34.73 3.16
1908 3162 8.575589 TCAGATTTACACAACATTTACAATGCT 58.424 29.630 0.00 0.00 0.00 3.79
1909 3163 8.741101 TCAGATTTACACAACATTTACAATGC 57.259 30.769 0.00 0.00 0.00 3.56
1919 3173 8.681806 TGTTTCTCAAATCAGATTTACACAACA 58.318 29.630 8.12 11.72 0.00 3.33
1920 3174 9.515020 TTGTTTCTCAAATCAGATTTACACAAC 57.485 29.630 8.12 9.66 32.64 3.32
1922 3176 9.119418 TCTTGTTTCTCAAATCAGATTTACACA 57.881 29.630 8.12 0.77 35.48 3.72
1923 3177 9.950680 TTCTTGTTTCTCAAATCAGATTTACAC 57.049 29.630 8.12 0.00 35.48 2.90
1927 3181 8.689972 ACTGTTCTTGTTTCTCAAATCAGATTT 58.310 29.630 2.20 2.20 35.48 2.17
1928 3182 8.230472 ACTGTTCTTGTTTCTCAAATCAGATT 57.770 30.769 0.00 0.00 35.48 2.40
1930 3184 7.226720 GGTACTGTTCTTGTTTCTCAAATCAGA 59.773 37.037 0.00 0.00 35.48 3.27
1931 3185 7.012327 TGGTACTGTTCTTGTTTCTCAAATCAG 59.988 37.037 0.00 0.00 35.48 2.90
1933 3187 7.259290 TGGTACTGTTCTTGTTTCTCAAATC 57.741 36.000 0.00 0.00 35.48 2.17
1934 3188 7.040409 GGATGGTACTGTTCTTGTTTCTCAAAT 60.040 37.037 0.00 0.00 35.48 2.32
1935 3189 6.262273 GGATGGTACTGTTCTTGTTTCTCAAA 59.738 38.462 0.00 0.00 35.48 2.69
1936 3190 5.763204 GGATGGTACTGTTCTTGTTTCTCAA 59.237 40.000 0.00 0.00 34.61 3.02
1938 3192 5.552178 AGGATGGTACTGTTCTTGTTTCTC 58.448 41.667 0.00 0.00 0.00 2.87
1939 3193 5.568620 AGGATGGTACTGTTCTTGTTTCT 57.431 39.130 0.00 0.00 0.00 2.52
1942 3196 5.072600 TGGTTAGGATGGTACTGTTCTTGTT 59.927 40.000 0.00 0.00 0.00 2.83
1944 3198 5.160607 TGGTTAGGATGGTACTGTTCTTG 57.839 43.478 0.00 0.00 0.00 3.02
1946 3200 6.901300 TCTATTGGTTAGGATGGTACTGTTCT 59.099 38.462 0.00 0.00 0.00 3.01
1947 3201 7.069578 TCTCTATTGGTTAGGATGGTACTGTTC 59.930 40.741 0.00 0.00 0.00 3.18
1949 3203 6.441222 TCTCTATTGGTTAGGATGGTACTGT 58.559 40.000 0.00 0.00 0.00 3.55
1950 3204 6.778069 TCTCTCTATTGGTTAGGATGGTACTG 59.222 42.308 0.00 0.00 0.00 2.74
1952 3206 7.598759 TTCTCTCTATTGGTTAGGATGGTAC 57.401 40.000 0.00 0.00 0.00 3.34
1954 3208 6.846505 TGATTCTCTCTATTGGTTAGGATGGT 59.153 38.462 0.00 0.00 0.00 3.55
2109 3371 7.010091 CCACTTATTCTCCACAAAACACAAAAC 59.990 37.037 0.00 0.00 0.00 2.43
2111 3373 6.568869 CCACTTATTCTCCACAAAACACAAA 58.431 36.000 0.00 0.00 0.00 2.83
2112 3374 5.451242 GCCACTTATTCTCCACAAAACACAA 60.451 40.000 0.00 0.00 0.00 3.33
2113 3375 4.037446 GCCACTTATTCTCCACAAAACACA 59.963 41.667 0.00 0.00 0.00 3.72
2114 3376 4.278419 AGCCACTTATTCTCCACAAAACAC 59.722 41.667 0.00 0.00 0.00 3.32
2556 3873 0.550914 TTCGGGGGATTGAAGGGATG 59.449 55.000 0.00 0.00 0.00 3.51
2567 3884 0.542805 CGGAAATTACCTTCGGGGGA 59.457 55.000 1.80 0.00 40.03 4.81
3118 4496 1.525995 CATCCACCCATGGCGTACC 60.526 63.158 6.09 0.00 46.80 3.34
3242 4653 6.485648 AGAAGTACACAAATGGAAGTAACCAC 59.514 38.462 0.00 0.00 43.03 4.16
3354 4766 8.409358 ACCATTTGAAAGCATAGAAACTTACT 57.591 30.769 0.00 0.00 0.00 2.24
3740 5256 2.022527 AGGAGGAGAGGTAAGCCATTCT 60.023 50.000 0.00 0.00 37.19 2.40
3765 5281 0.670546 CGAATTGCCTCACCAGACGT 60.671 55.000 0.00 0.00 0.00 4.34
3897 5428 4.685169 AATGACAAATCAGACGCGATTT 57.315 36.364 15.93 5.23 44.52 2.17
3942 5473 1.870402 TCAAATCAGACGCGCTTCAAA 59.130 42.857 16.85 3.68 0.00 2.69


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

AutoCloner maintained by Alex Coulton.