Multiple sequence alignment - TraesCS3A01G424600

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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 TraesCS3A01G424600 chr3A 100.000 2459 0 0 1 2459 667219385 667221843 0.000000e+00 4542
1 TraesCS3A01G424600 chr3A 96.472 1644 52 3 127 1770 667278210 667279847 0.000000e+00 2710
2 TraesCS3A01G424600 chr3A 94.444 126 7 0 1 126 667262454 667262579 6.940000e-46 195
3 TraesCS3A01G424600 chr3B 94.124 1770 93 6 1 1770 704135217 704136975 0.000000e+00 2682
4 TraesCS3A01G424600 chr3B 94.667 975 46 3 796 1770 704042513 704043481 0.000000e+00 1507
5 TraesCS3A01G424600 chr3B 94.929 631 32 0 1 631 704040445 704041075 0.000000e+00 989
6 TraesCS3A01G424600 chr3B 93.852 244 14 1 2214 2457 704044651 704044893 1.390000e-97 366
7 TraesCS3A01G424600 chr3B 93.724 239 14 1 2214 2452 704158425 704158662 8.360000e-95 357
8 TraesCS3A01G424600 chr3D 89.869 306 23 4 1769 2067 472881876 472882180 1.070000e-103 387
9 TraesCS3A01G424600 chr1A 89.644 309 24 5 1765 2067 285590023 285590329 1.070000e-103 387
10 TraesCS3A01G424600 chr6B 89.610 308 24 4 1769 2069 18721166 18721472 3.840000e-103 385
11 TraesCS3A01G424600 chr6B 89.542 306 24 4 1769 2067 39363054 39362750 4.960000e-102 381
12 TraesCS3A01G424600 chr6B 89.542 306 24 4 1769 2067 460488777 460488473 4.960000e-102 381
13 TraesCS3A01G424600 chr5D 89.836 305 24 3 1769 2067 347680359 347680056 3.840000e-103 385
14 TraesCS3A01G424600 chr7D 89.172 314 25 5 1769 2075 568468326 568468015 1.380000e-102 383
15 TraesCS3A01G424600 chr1D 89.577 307 24 4 1769 2068 411904893 411905198 1.380000e-102 383
16 TraesCS3A01G424600 chr2A 89.251 307 24 5 1769 2067 223718610 223718915 2.310000e-100 375


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 TraesCS3A01G424600 chr3A 667219385 667221843 2458 False 4542 4542 100.000000 1 2459 1 chr3A.!!$F1 2458
1 TraesCS3A01G424600 chr3A 667278210 667279847 1637 False 2710 2710 96.472000 127 1770 1 chr3A.!!$F3 1643
2 TraesCS3A01G424600 chr3B 704135217 704136975 1758 False 2682 2682 94.124000 1 1770 1 chr3B.!!$F1 1769
3 TraesCS3A01G424600 chr3B 704040445 704044893 4448 False 954 1507 94.482667 1 2457 3 chr3B.!!$F3 2456

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
892 2172 0.033011 AGAGTGGGCTATGTCGGAGT 60.033 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 3055 0.250858 TACACTCTTCACCGGACGGA 60.251 55.0 18.8 0.0 38.96 4.69 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
40 41 1.224965 GGCGCCAGATGAAGAAGATC 58.775 55.000 24.80 0.00 0.00 2.75
70 71 0.819259 AGCTTCTCAACGCCAAGCAA 60.819 50.000 5.73 0.00 44.24 3.91
79 80 2.896801 CGCCAAGCAAGTGAAGCGT 61.897 57.895 0.00 0.00 38.81 5.07
82 83 0.040958 CCAAGCAAGTGAAGCGTGTC 60.041 55.000 0.00 0.00 39.36 3.67
300 301 0.836400 TTCCCGCTGGACTTCTTCCT 60.836 55.000 0.00 0.00 46.10 3.36
511 512 1.227263 CCCGGAGACTATTGGTGCG 60.227 63.158 0.73 0.00 0.00 5.34
577 578 7.162082 CGTAGAAGAATAATTTGGCCTCCTAT 58.838 38.462 3.32 0.00 0.00 2.57
892 2172 0.033011 AGAGTGGGCTATGTCGGAGT 60.033 55.000 0.00 0.00 0.00 3.85
922 2202 1.276622 ACCCGAGACTATGGCAAAGT 58.723 50.000 0.00 0.00 0.00 2.66
958 2238 3.056107 TCAAAGCGTTCTAGGTGCACTAT 60.056 43.478 17.98 8.58 0.00 2.12
971 2251 3.432749 GGTGCACTATGAGGTGTCATCAT 60.433 47.826 17.98 2.70 42.80 2.45
983 2263 4.407621 AGGTGTCATCATTAATACCGACCA 59.592 41.667 0.00 0.00 33.55 4.02
1009 2289 2.030946 GGACTGAACTACATGCGAATGC 59.969 50.000 2.30 0.00 43.20 3.56
1103 2383 6.891361 TGTGAAATCATGGGTTATCACATTCT 59.109 34.615 13.09 0.00 41.39 2.40
1291 2571 1.531149 CGATTCTGTTTGGCACGTCTT 59.469 47.619 0.00 0.00 0.00 3.01
1359 2639 3.520721 TGCTTCCTGATGGAGAGAATTCA 59.479 43.478 8.44 0.00 44.24 2.57
1441 2721 6.682746 CATTTGAGAGCTACTCCGTATGTAT 58.317 40.000 9.71 0.00 44.34 2.29
1513 2793 3.432749 CCCTCGTCATCATGTTCTTCCAT 60.433 47.826 0.00 0.00 0.00 3.41
1515 2795 5.359756 CCTCGTCATCATGTTCTTCCATTA 58.640 41.667 0.00 0.00 0.00 1.90
1516 2796 5.817296 CCTCGTCATCATGTTCTTCCATTAA 59.183 40.000 0.00 0.00 0.00 1.40
1517 2797 6.484643 CCTCGTCATCATGTTCTTCCATTAAT 59.515 38.462 0.00 0.00 0.00 1.40
1518 2798 7.012704 CCTCGTCATCATGTTCTTCCATTAATT 59.987 37.037 0.00 0.00 0.00 1.40
1519 2799 7.696755 TCGTCATCATGTTCTTCCATTAATTG 58.303 34.615 0.00 0.00 0.00 2.32
1520 2800 7.336679 TCGTCATCATGTTCTTCCATTAATTGT 59.663 33.333 0.00 0.00 0.00 2.71
1521 2801 8.611757 CGTCATCATGTTCTTCCATTAATTGTA 58.388 33.333 0.00 0.00 0.00 2.41
1522 2802 9.722056 GTCATCATGTTCTTCCATTAATTGTAC 57.278 33.333 0.00 0.00 0.00 2.90
1556 2836 8.380099 ACTTCATAATAAGAGTGGGTGTTTACA 58.620 33.333 0.00 0.00 0.00 2.41
1627 2907 6.626095 GGTCGCGTTGAATGTTGTAATAATAC 59.374 38.462 5.77 0.00 0.00 1.89
1712 2992 7.958088 TCCATCAAGTAAATATATGGACACGA 58.042 34.615 0.00 0.00 40.84 4.35
1774 3054 9.944376 TGTTGATATATGCTCTAAATTACTCCC 57.056 33.333 0.00 0.00 0.00 4.30
1777 3057 8.982723 TGATATATGCTCTAAATTACTCCCTCC 58.017 37.037 0.00 0.00 0.00 4.30
1778 3058 4.608948 ATGCTCTAAATTACTCCCTCCG 57.391 45.455 0.00 0.00 0.00 4.63
1779 3059 3.371965 TGCTCTAAATTACTCCCTCCGT 58.628 45.455 0.00 0.00 0.00 4.69
1780 3060 3.383825 TGCTCTAAATTACTCCCTCCGTC 59.616 47.826 0.00 0.00 0.00 4.79
1781 3061 3.243805 GCTCTAAATTACTCCCTCCGTCC 60.244 52.174 0.00 0.00 0.00 4.79
1782 3062 2.954318 TCTAAATTACTCCCTCCGTCCG 59.046 50.000 0.00 0.00 0.00 4.79
1783 3063 0.828677 AAATTACTCCCTCCGTCCGG 59.171 55.000 0.00 0.00 0.00 5.14
1784 3064 0.325016 AATTACTCCCTCCGTCCGGT 60.325 55.000 0.00 0.00 36.47 5.28
1785 3065 1.041447 ATTACTCCCTCCGTCCGGTG 61.041 60.000 0.00 3.10 36.47 4.94
1786 3066 2.141011 TTACTCCCTCCGTCCGGTGA 62.141 60.000 0.00 0.00 36.47 4.02
1787 3067 2.141011 TACTCCCTCCGTCCGGTGAA 62.141 60.000 0.00 0.00 36.47 3.18
1788 3068 2.678934 TCCCTCCGTCCGGTGAAG 60.679 66.667 0.00 0.00 36.47 3.02
1789 3069 2.678934 CCCTCCGTCCGGTGAAGA 60.679 66.667 0.00 0.00 36.47 2.87
1790 3070 2.711922 CCCTCCGTCCGGTGAAGAG 61.712 68.421 0.00 3.95 36.47 2.85
1791 3071 1.977544 CCTCCGTCCGGTGAAGAGT 60.978 63.158 0.00 0.00 36.47 3.24
1792 3072 1.213013 CTCCGTCCGGTGAAGAGTG 59.787 63.158 0.00 0.00 36.47 3.51
1793 3073 1.524863 CTCCGTCCGGTGAAGAGTGT 61.525 60.000 0.00 0.00 36.47 3.55
1794 3074 0.250858 TCCGTCCGGTGAAGAGTGTA 60.251 55.000 0.00 0.00 36.47 2.90
1795 3075 0.815734 CCGTCCGGTGAAGAGTGTAT 59.184 55.000 0.00 0.00 0.00 2.29
1796 3076 1.469251 CCGTCCGGTGAAGAGTGTATG 60.469 57.143 0.00 0.00 0.00 2.39
1797 3077 1.201647 CGTCCGGTGAAGAGTGTATGT 59.798 52.381 0.00 0.00 0.00 2.29
1798 3078 2.352421 CGTCCGGTGAAGAGTGTATGTT 60.352 50.000 0.00 0.00 0.00 2.71
1799 3079 3.660865 GTCCGGTGAAGAGTGTATGTTT 58.339 45.455 0.00 0.00 0.00 2.83
1800 3080 3.432252 GTCCGGTGAAGAGTGTATGTTTG 59.568 47.826 0.00 0.00 0.00 2.93
1801 3081 2.742053 CCGGTGAAGAGTGTATGTTTGG 59.258 50.000 0.00 0.00 0.00 3.28
1802 3082 2.159627 CGGTGAAGAGTGTATGTTTGGC 59.840 50.000 0.00 0.00 0.00 4.52
1803 3083 3.412386 GGTGAAGAGTGTATGTTTGGCT 58.588 45.455 0.00 0.00 0.00 4.75
1804 3084 3.821033 GGTGAAGAGTGTATGTTTGGCTT 59.179 43.478 0.00 0.00 0.00 4.35
1805 3085 4.083271 GGTGAAGAGTGTATGTTTGGCTTC 60.083 45.833 0.00 0.00 0.00 3.86
1806 3086 4.515191 GTGAAGAGTGTATGTTTGGCTTCA 59.485 41.667 0.00 0.00 38.23 3.02
1807 3087 5.008613 GTGAAGAGTGTATGTTTGGCTTCAA 59.991 40.000 0.00 0.00 41.02 2.69
1808 3088 5.592282 TGAAGAGTGTATGTTTGGCTTCAAA 59.408 36.000 0.00 0.00 37.79 2.69
1809 3089 6.096141 TGAAGAGTGTATGTTTGGCTTCAAAA 59.904 34.615 0.00 0.00 41.43 2.44
1810 3090 6.655078 AGAGTGTATGTTTGGCTTCAAAAT 57.345 33.333 0.00 0.00 41.43 1.82
1811 3091 7.054491 AGAGTGTATGTTTGGCTTCAAAATT 57.946 32.000 0.00 0.00 41.43 1.82
1812 3092 7.500141 AGAGTGTATGTTTGGCTTCAAAATTT 58.500 30.769 0.00 0.00 41.43 1.82
1813 3093 8.637986 AGAGTGTATGTTTGGCTTCAAAATTTA 58.362 29.630 0.00 0.00 41.43 1.40
1814 3094 9.423061 GAGTGTATGTTTGGCTTCAAAATTTAT 57.577 29.630 0.00 0.00 41.43 1.40
1815 3095 9.423061 AGTGTATGTTTGGCTTCAAAATTTATC 57.577 29.630 0.00 0.00 41.43 1.75
1816 3096 8.655970 GTGTATGTTTGGCTTCAAAATTTATCC 58.344 33.333 0.00 0.00 41.43 2.59
1817 3097 8.370940 TGTATGTTTGGCTTCAAAATTTATCCA 58.629 29.630 0.00 0.00 41.43 3.41
1818 3098 9.382275 GTATGTTTGGCTTCAAAATTTATCCAT 57.618 29.630 0.00 0.00 41.43 3.41
1820 3100 9.956640 ATGTTTGGCTTCAAAATTTATCCATAA 57.043 25.926 0.00 0.00 41.43 1.90
1821 3101 9.784531 TGTTTGGCTTCAAAATTTATCCATAAA 57.215 25.926 0.00 0.00 41.43 1.40
1825 3105 9.874205 TGGCTTCAAAATTTATCCATAAAAGAG 57.126 29.630 0.00 0.00 36.02 2.85
1826 3106 9.875691 GGCTTCAAAATTTATCCATAAAAGAGT 57.124 29.630 0.00 0.00 36.02 3.24
1845 3125 9.981460 AAAAGAGTGTAATTCTATCTTCCCAAT 57.019 29.630 0.00 0.00 28.25 3.16
1846 3126 8.970859 AAGAGTGTAATTCTATCTTCCCAATG 57.029 34.615 0.00 0.00 28.25 2.82
1847 3127 6.995091 AGAGTGTAATTCTATCTTCCCAATGC 59.005 38.462 0.00 0.00 27.58 3.56
1848 3128 6.662755 AGTGTAATTCTATCTTCCCAATGCA 58.337 36.000 0.00 0.00 0.00 3.96
1849 3129 6.543831 AGTGTAATTCTATCTTCCCAATGCAC 59.456 38.462 0.00 0.00 0.00 4.57
1850 3130 6.543831 GTGTAATTCTATCTTCCCAATGCACT 59.456 38.462 0.00 0.00 0.00 4.40
1851 3131 7.067494 GTGTAATTCTATCTTCCCAATGCACTT 59.933 37.037 0.00 0.00 0.00 3.16
1852 3132 7.615365 TGTAATTCTATCTTCCCAATGCACTTT 59.385 33.333 0.00 0.00 0.00 2.66
1853 3133 9.120538 GTAATTCTATCTTCCCAATGCACTTTA 57.879 33.333 0.00 0.00 0.00 1.85
1854 3134 8.593945 AATTCTATCTTCCCAATGCACTTTAA 57.406 30.769 0.00 0.00 0.00 1.52
1855 3135 8.593945 ATTCTATCTTCCCAATGCACTTTAAA 57.406 30.769 0.00 0.00 0.00 1.52
1856 3136 7.630242 TCTATCTTCCCAATGCACTTTAAAG 57.370 36.000 13.76 13.76 0.00 1.85
1857 3137 7.175104 TCTATCTTCCCAATGCACTTTAAAGT 58.825 34.615 15.22 15.22 40.60 2.66
1858 3138 8.325787 TCTATCTTCCCAATGCACTTTAAAGTA 58.674 33.333 20.15 6.90 37.08 2.24
1859 3139 7.775053 ATCTTCCCAATGCACTTTAAAGTAA 57.225 32.000 20.15 12.20 37.08 2.24
1860 3140 7.589958 TCTTCCCAATGCACTTTAAAGTAAA 57.410 32.000 20.15 11.85 37.08 2.01
1861 3141 8.012957 TCTTCCCAATGCACTTTAAAGTAAAA 57.987 30.769 20.15 9.48 37.08 1.52
1862 3142 8.478877 TCTTCCCAATGCACTTTAAAGTAAAAA 58.521 29.630 20.15 7.14 37.08 1.94
1886 3166 5.869753 AAAATTTCTCTCTCATCACACGG 57.130 39.130 0.00 0.00 0.00 4.94
1887 3167 4.543590 AATTTCTCTCTCATCACACGGT 57.456 40.909 0.00 0.00 0.00 4.83
1888 3168 5.661056 AATTTCTCTCTCATCACACGGTA 57.339 39.130 0.00 0.00 0.00 4.02
1889 3169 5.661056 ATTTCTCTCTCATCACACGGTAA 57.339 39.130 0.00 0.00 0.00 2.85
1890 3170 5.661056 TTTCTCTCTCATCACACGGTAAT 57.339 39.130 0.00 0.00 0.00 1.89
1891 3171 4.902443 TCTCTCTCATCACACGGTAATC 57.098 45.455 0.00 0.00 0.00 1.75
1892 3172 4.270008 TCTCTCTCATCACACGGTAATCA 58.730 43.478 0.00 0.00 0.00 2.57
1893 3173 4.705023 TCTCTCTCATCACACGGTAATCAA 59.295 41.667 0.00 0.00 0.00 2.57
1894 3174 4.998788 TCTCTCATCACACGGTAATCAAG 58.001 43.478 0.00 0.00 0.00 3.02
1895 3175 4.705023 TCTCTCATCACACGGTAATCAAGA 59.295 41.667 0.00 0.00 0.00 3.02
1896 3176 4.744570 TCTCATCACACGGTAATCAAGAC 58.255 43.478 0.00 0.00 0.00 3.01
1897 3177 3.857052 TCATCACACGGTAATCAAGACC 58.143 45.455 0.00 0.00 0.00 3.85
1898 3178 3.259625 TCATCACACGGTAATCAAGACCA 59.740 43.478 0.00 0.00 36.72 4.02
1899 3179 3.755112 TCACACGGTAATCAAGACCAA 57.245 42.857 0.00 0.00 36.72 3.67
1900 3180 4.280436 TCACACGGTAATCAAGACCAAT 57.720 40.909 0.00 0.00 36.72 3.16
1901 3181 5.408880 TCACACGGTAATCAAGACCAATA 57.591 39.130 0.00 0.00 36.72 1.90
1902 3182 5.416083 TCACACGGTAATCAAGACCAATAG 58.584 41.667 0.00 0.00 36.72 1.73
1903 3183 4.034048 CACACGGTAATCAAGACCAATAGC 59.966 45.833 0.00 0.00 36.72 2.97
1904 3184 4.188462 CACGGTAATCAAGACCAATAGCA 58.812 43.478 0.00 0.00 36.72 3.49
1905 3185 4.634004 CACGGTAATCAAGACCAATAGCAA 59.366 41.667 0.00 0.00 36.72 3.91
1906 3186 5.296780 CACGGTAATCAAGACCAATAGCAAT 59.703 40.000 0.00 0.00 36.72 3.56
1907 3187 5.296780 ACGGTAATCAAGACCAATAGCAATG 59.703 40.000 0.00 0.00 36.72 2.82
1908 3188 5.296780 CGGTAATCAAGACCAATAGCAATGT 59.703 40.000 0.00 0.00 36.72 2.71
1909 3189 6.481976 CGGTAATCAAGACCAATAGCAATGTA 59.518 38.462 0.00 0.00 36.72 2.29
1910 3190 7.518370 CGGTAATCAAGACCAATAGCAATGTAC 60.518 40.741 0.00 0.00 36.72 2.90
1911 3191 7.282224 GGTAATCAAGACCAATAGCAATGTACA 59.718 37.037 0.00 0.00 36.91 2.90
1912 3192 6.683974 ATCAAGACCAATAGCAATGTACAC 57.316 37.500 0.00 0.00 0.00 2.90
1913 3193 5.555966 TCAAGACCAATAGCAATGTACACA 58.444 37.500 0.00 0.00 0.00 3.72
1914 3194 6.179756 TCAAGACCAATAGCAATGTACACAT 58.820 36.000 0.00 0.00 38.41 3.21
1915 3195 6.093909 TCAAGACCAATAGCAATGTACACATG 59.906 38.462 0.00 1.44 36.56 3.21
1916 3196 4.883585 AGACCAATAGCAATGTACACATGG 59.116 41.667 0.00 1.99 36.56 3.66
1917 3197 4.599041 ACCAATAGCAATGTACACATGGT 58.401 39.130 16.53 16.53 36.56 3.55
1918 3198 4.640201 ACCAATAGCAATGTACACATGGTC 59.360 41.667 15.97 0.70 36.56 4.02
1919 3199 4.883585 CCAATAGCAATGTACACATGGTCT 59.116 41.667 15.97 6.61 36.56 3.85
1920 3200 5.357878 CCAATAGCAATGTACACATGGTCTT 59.642 40.000 15.97 11.26 36.56 3.01
1921 3201 6.458751 CCAATAGCAATGTACACATGGTCTTC 60.459 42.308 15.97 0.00 36.56 2.87
1922 3202 4.292186 AGCAATGTACACATGGTCTTCT 57.708 40.909 0.00 0.00 36.56 2.85
1923 3203 4.655963 AGCAATGTACACATGGTCTTCTT 58.344 39.130 0.00 0.00 36.56 2.52
1924 3204 5.804639 AGCAATGTACACATGGTCTTCTTA 58.195 37.500 0.00 0.00 36.56 2.10
1925 3205 6.237901 AGCAATGTACACATGGTCTTCTTAA 58.762 36.000 0.00 0.00 36.56 1.85
1926 3206 6.886459 AGCAATGTACACATGGTCTTCTTAAT 59.114 34.615 0.00 0.00 36.56 1.40
1927 3207 7.394359 AGCAATGTACACATGGTCTTCTTAATT 59.606 33.333 0.00 0.00 36.56 1.40
1928 3208 8.028938 GCAATGTACACATGGTCTTCTTAATTT 58.971 33.333 0.00 0.00 36.56 1.82
1929 3209 9.559958 CAATGTACACATGGTCTTCTTAATTTC 57.440 33.333 0.00 0.00 36.56 2.17
1930 3210 9.520515 AATGTACACATGGTCTTCTTAATTTCT 57.479 29.630 0.00 0.00 36.56 2.52
1932 3212 9.431887 TGTACACATGGTCTTCTTAATTTCTAC 57.568 33.333 0.00 0.00 0.00 2.59
1933 3213 9.431887 GTACACATGGTCTTCTTAATTTCTACA 57.568 33.333 0.00 0.00 0.00 2.74
1935 3215 8.950210 ACACATGGTCTTCTTAATTTCTACATG 58.050 33.333 0.00 0.00 38.27 3.21
1936 3216 7.912250 CACATGGTCTTCTTAATTTCTACATGC 59.088 37.037 0.00 0.00 36.40 4.06
1937 3217 7.611467 ACATGGTCTTCTTAATTTCTACATGCA 59.389 33.333 0.00 0.00 36.40 3.96
1938 3218 7.377766 TGGTCTTCTTAATTTCTACATGCAC 57.622 36.000 0.00 0.00 0.00 4.57
1939 3219 7.168219 TGGTCTTCTTAATTTCTACATGCACT 58.832 34.615 0.00 0.00 0.00 4.40
1940 3220 7.334421 TGGTCTTCTTAATTTCTACATGCACTC 59.666 37.037 0.00 0.00 0.00 3.51
1941 3221 7.334421 GGTCTTCTTAATTTCTACATGCACTCA 59.666 37.037 0.00 0.00 0.00 3.41
1942 3222 8.887717 GTCTTCTTAATTTCTACATGCACTCAT 58.112 33.333 0.00 0.00 0.00 2.90
1943 3223 9.453572 TCTTCTTAATTTCTACATGCACTCATT 57.546 29.630 0.00 0.00 0.00 2.57
1944 3224 9.499585 CTTCTTAATTTCTACATGCACTCATTG 57.500 33.333 0.00 0.00 0.00 2.82
1945 3225 8.791327 TCTTAATTTCTACATGCACTCATTGA 57.209 30.769 0.00 0.00 0.00 2.57
1946 3226 8.886719 TCTTAATTTCTACATGCACTCATTGAG 58.113 33.333 12.17 12.17 35.52 3.02
1947 3227 6.446781 AATTTCTACATGCACTCATTGAGG 57.553 37.500 17.66 7.98 33.35 3.86
1948 3228 4.824479 TTCTACATGCACTCATTGAGGA 57.176 40.909 17.66 2.10 33.35 3.71
1949 3229 5.363562 TTCTACATGCACTCATTGAGGAT 57.636 39.130 17.66 4.29 33.35 3.24
1950 3230 5.363562 TCTACATGCACTCATTGAGGATT 57.636 39.130 17.66 0.00 33.35 3.01
1951 3231 5.121105 TCTACATGCACTCATTGAGGATTG 58.879 41.667 17.66 8.28 33.35 2.67
1952 3232 3.021695 ACATGCACTCATTGAGGATTGG 58.978 45.455 17.66 6.93 33.35 3.16
1953 3233 2.133281 TGCACTCATTGAGGATTGGG 57.867 50.000 17.66 1.93 33.35 4.12
1954 3234 1.355381 TGCACTCATTGAGGATTGGGT 59.645 47.619 17.66 0.00 33.35 4.51
1955 3235 2.575735 TGCACTCATTGAGGATTGGGTA 59.424 45.455 17.66 0.00 33.35 3.69
1956 3236 3.010027 TGCACTCATTGAGGATTGGGTAA 59.990 43.478 17.66 0.00 33.35 2.85
1957 3237 4.210331 GCACTCATTGAGGATTGGGTAAT 58.790 43.478 17.66 0.00 33.35 1.89
1958 3238 4.646492 GCACTCATTGAGGATTGGGTAATT 59.354 41.667 17.66 0.00 33.35 1.40
1959 3239 5.827797 GCACTCATTGAGGATTGGGTAATTA 59.172 40.000 17.66 0.00 33.35 1.40
1960 3240 6.321181 GCACTCATTGAGGATTGGGTAATTAA 59.679 38.462 17.66 0.00 33.35 1.40
1961 3241 7.147915 GCACTCATTGAGGATTGGGTAATTAAA 60.148 37.037 17.66 0.00 33.35 1.52
1962 3242 8.748412 CACTCATTGAGGATTGGGTAATTAAAA 58.252 33.333 17.66 0.00 33.35 1.52
1963 3243 8.971073 ACTCATTGAGGATTGGGTAATTAAAAG 58.029 33.333 17.66 0.00 33.35 2.27
1964 3244 8.305046 TCATTGAGGATTGGGTAATTAAAAGG 57.695 34.615 0.00 0.00 0.00 3.11
1965 3245 8.119246 TCATTGAGGATTGGGTAATTAAAAGGA 58.881 33.333 0.00 0.00 0.00 3.36
1966 3246 7.954666 TTGAGGATTGGGTAATTAAAAGGAG 57.045 36.000 0.00 0.00 0.00 3.69
1967 3247 7.278724 TGAGGATTGGGTAATTAAAAGGAGA 57.721 36.000 0.00 0.00 0.00 3.71
1968 3248 7.346471 TGAGGATTGGGTAATTAAAAGGAGAG 58.654 38.462 0.00 0.00 0.00 3.20
1969 3249 7.183839 TGAGGATTGGGTAATTAAAAGGAGAGA 59.816 37.037 0.00 0.00 0.00 3.10
1970 3250 7.578203 AGGATTGGGTAATTAAAAGGAGAGAG 58.422 38.462 0.00 0.00 0.00 3.20
1971 3251 7.406151 AGGATTGGGTAATTAAAAGGAGAGAGA 59.594 37.037 0.00 0.00 0.00 3.10
1972 3252 8.221251 GGATTGGGTAATTAAAAGGAGAGAGAT 58.779 37.037 0.00 0.00 0.00 2.75
1973 3253 8.986929 ATTGGGTAATTAAAAGGAGAGAGATG 57.013 34.615 0.00 0.00 0.00 2.90
1974 3254 7.749377 TGGGTAATTAAAAGGAGAGAGATGA 57.251 36.000 0.00 0.00 0.00 2.92
1975 3255 8.337118 TGGGTAATTAAAAGGAGAGAGATGAT 57.663 34.615 0.00 0.00 0.00 2.45
1976 3256 8.213679 TGGGTAATTAAAAGGAGAGAGATGATG 58.786 37.037 0.00 0.00 0.00 3.07
1977 3257 7.663493 GGGTAATTAAAAGGAGAGAGATGATGG 59.337 40.741 0.00 0.00 0.00 3.51
1978 3258 7.174080 GGTAATTAAAAGGAGAGAGATGATGGC 59.826 40.741 0.00 0.00 0.00 4.40
1979 3259 5.965033 TTAAAAGGAGAGAGATGATGGCT 57.035 39.130 0.00 0.00 0.00 4.75
1980 3260 4.858965 AAAAGGAGAGAGATGATGGCTT 57.141 40.909 0.00 0.00 0.00 4.35
1981 3261 3.842007 AAGGAGAGAGATGATGGCTTG 57.158 47.619 0.00 0.00 0.00 4.01
1982 3262 1.417145 AGGAGAGAGATGATGGCTTGC 59.583 52.381 0.00 0.00 0.00 4.01
1983 3263 1.140452 GGAGAGAGATGATGGCTTGCA 59.860 52.381 0.00 0.00 0.00 4.08
1984 3264 2.211806 GAGAGAGATGATGGCTTGCAC 58.788 52.381 0.00 0.00 0.00 4.57
1985 3265 1.134159 AGAGAGATGATGGCTTGCACC 60.134 52.381 0.00 0.00 0.00 5.01
1986 3266 0.917533 AGAGATGATGGCTTGCACCT 59.082 50.000 0.00 0.00 0.00 4.00
1987 3267 1.284198 AGAGATGATGGCTTGCACCTT 59.716 47.619 0.00 0.00 0.00 3.50
1988 3268 2.097825 GAGATGATGGCTTGCACCTTT 58.902 47.619 0.00 0.00 0.00 3.11
1989 3269 2.494870 GAGATGATGGCTTGCACCTTTT 59.505 45.455 0.00 0.00 0.00 2.27
1990 3270 2.494870 AGATGATGGCTTGCACCTTTTC 59.505 45.455 0.00 0.00 0.00 2.29
1991 3271 1.702182 TGATGGCTTGCACCTTTTCA 58.298 45.000 0.00 0.00 0.00 2.69
1992 3272 2.037901 TGATGGCTTGCACCTTTTCAA 58.962 42.857 0.00 0.00 0.00 2.69
1993 3273 2.633967 TGATGGCTTGCACCTTTTCAAT 59.366 40.909 0.00 0.00 0.00 2.57
1994 3274 2.529780 TGGCTTGCACCTTTTCAATG 57.470 45.000 0.00 0.00 0.00 2.82
1995 3275 1.150827 GGCTTGCACCTTTTCAATGC 58.849 50.000 0.00 0.00 39.88 3.56
2002 3282 5.831702 TGCACCTTTTCAATGCAATTTTT 57.168 30.435 0.00 0.00 45.96 1.94
2053 3333 8.994429 AATTTCTAGATGTACACTCTTCACTG 57.006 34.615 0.00 0.00 0.00 3.66
2054 3334 6.516739 TTCTAGATGTACACTCTTCACTGG 57.483 41.667 0.00 0.00 0.00 4.00
2055 3335 5.816682 TCTAGATGTACACTCTTCACTGGA 58.183 41.667 0.00 0.00 0.00 3.86
2056 3336 6.427441 TCTAGATGTACACTCTTCACTGGAT 58.573 40.000 0.00 0.00 0.00 3.41
2057 3337 5.336150 AGATGTACACTCTTCACTGGATG 57.664 43.478 0.00 0.00 0.00 3.51
2058 3338 3.961480 TGTACACTCTTCACTGGATGG 57.039 47.619 0.00 0.00 0.00 3.51
2059 3339 3.506398 TGTACACTCTTCACTGGATGGA 58.494 45.455 0.00 0.00 0.00 3.41
2060 3340 3.511540 TGTACACTCTTCACTGGATGGAG 59.488 47.826 0.00 0.00 34.80 3.86
2061 3341 2.894731 ACACTCTTCACTGGATGGAGA 58.105 47.619 0.00 0.00 41.05 3.71
2065 3345 3.464720 TCTTCACTGGATGGAGAGAGT 57.535 47.619 0.00 0.00 38.11 3.24
2066 3346 4.592997 TCTTCACTGGATGGAGAGAGTA 57.407 45.455 0.00 0.00 38.11 2.59
2070 3350 5.654901 TCACTGGATGGAGAGAGTATACT 57.345 43.478 4.68 4.68 0.00 2.12
2083 3363 9.577222 GGAGAGAGTATACTGTTAGGTCTAAAT 57.423 37.037 10.90 0.00 0.00 1.40
2111 3391 0.907486 TCATTGGAGAGGACAGGCTG 59.093 55.000 14.16 14.16 0.00 4.85
2123 3403 4.104831 AGGACAGGCTGGAGTAACTTATT 58.895 43.478 20.34 0.00 0.00 1.40
2132 3412 5.160607 TGGAGTAACTTATTCACCACCTG 57.839 43.478 0.00 0.00 0.00 4.00
2139 3419 4.332828 ACTTATTCACCACCTGTTAAGCC 58.667 43.478 0.00 0.00 0.00 4.35
2143 3423 0.953960 CACCACCTGTTAAGCCGGAC 60.954 60.000 5.05 0.00 0.00 4.79
2156 3436 0.463116 GCCGGACGGGTGATATTTGT 60.463 55.000 5.05 0.00 38.44 2.83
2164 3444 3.945285 ACGGGTGATATTTGTTGACATCC 59.055 43.478 0.00 0.00 0.00 3.51
2169 3449 6.461509 GGGTGATATTTGTTGACATCCAATCC 60.462 42.308 0.00 0.00 37.08 3.01
2171 3451 5.598005 TGATATTTGTTGACATCCAATCCCC 59.402 40.000 0.00 0.00 37.08 4.81
2172 3452 1.832883 TTGTTGACATCCAATCCCCG 58.167 50.000 0.00 0.00 37.08 5.73
2173 3453 0.034574 TGTTGACATCCAATCCCCGG 60.035 55.000 0.00 0.00 37.08 5.73
2192 3472 4.812626 CCCGGGTATGTGTAAACACTTATC 59.187 45.833 14.18 11.62 46.55 1.75
2227 4531 2.961768 GGGTCACCATGCCAAACG 59.038 61.111 0.00 0.00 36.50 3.60
2241 4545 2.543430 GCCAAACGATGCATTGTTGTTT 59.457 40.909 28.86 19.46 34.71 2.83
2307 4611 5.186215 TCAATCGTAGTTGGAGGTTGTGATA 59.814 40.000 0.00 0.00 0.00 2.15
2318 4622 6.015918 TGGAGGTTGTGATATGAACCAAATT 58.984 36.000 0.00 0.00 43.63 1.82
2319 4623 7.178573 TGGAGGTTGTGATATGAACCAAATTA 58.821 34.615 0.00 0.00 43.63 1.40
2433 4737 4.038522 TCTTCCATAGAAGCTCATTCTCCG 59.961 45.833 0.00 0.00 45.50 4.63
2437 4741 2.663826 AGAAGCTCATTCTCCGACAC 57.336 50.000 0.00 0.00 45.50 3.67
2450 4754 1.270550 TCCGACACGAACCTTTAGGAC 59.729 52.381 2.06 0.00 38.94 3.85
2452 4756 2.325761 CGACACGAACCTTTAGGACAG 58.674 52.381 2.06 0.00 38.94 3.51
2457 4761 3.875134 CACGAACCTTTAGGACAGTTGTT 59.125 43.478 2.06 0.00 38.94 2.83
2458 4762 4.025145 CACGAACCTTTAGGACAGTTGTTC 60.025 45.833 2.06 0.00 38.94 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.327200 TGAGAAGCTCCATGATGCAG 57.673 50.000 11.40 0.00 0.00 4.41
70 71 1.286260 GGACTCGACACGCTTCACT 59.714 57.895 0.00 0.00 0.00 3.41
79 80 1.672854 CGGCCCTTATGGACTCGACA 61.673 60.000 0.00 0.00 41.74 4.35
82 83 1.364171 CTCGGCCCTTATGGACTCG 59.636 63.158 0.00 0.00 41.74 4.18
110 111 1.746991 CAAAGGAGCGGAAGAGGCC 60.747 63.158 0.00 0.00 0.00 5.19
300 301 2.400798 GTACGATCCGCGACGACA 59.599 61.111 21.82 9.93 44.57 4.35
349 350 0.183492 GGATGCAGCCATAACTCCCA 59.817 55.000 18.08 0.00 0.00 4.37
511 512 5.582665 GGAAGGAGTACTCACAAACATGATC 59.417 44.000 23.91 2.50 0.00 2.92
577 578 9.890629 AAGACTACTTGAATCACATTAATAGCA 57.109 29.630 0.00 0.00 34.80 3.49
922 2202 3.181469 ACGCTTTGAACCTCTAGTTGTGA 60.181 43.478 0.00 0.00 39.40 3.58
958 2238 5.452776 GGTCGGTATTAATGATGACACCTCA 60.453 44.000 14.01 0.00 0.00 3.86
971 2251 3.109151 AGTCCACCATGGTCGGTATTAA 58.891 45.455 24.15 9.32 37.07 1.40
983 2263 2.677902 CGCATGTAGTTCAGTCCACCAT 60.678 50.000 0.00 0.00 0.00 3.55
1009 2289 7.848128 TGTAACCTAAGAACCTCCTTGATAAG 58.152 38.462 0.00 0.00 0.00 1.73
1103 2383 7.517614 TTAACATGTATCTTTGTGCCTTTGA 57.482 32.000 0.00 0.00 0.00 2.69
1291 2571 1.031571 GCCAATGCAATCTCCACGGA 61.032 55.000 0.00 0.00 37.47 4.69
1377 2657 1.279271 ACTCCCATCCCAAAAGTCTCG 59.721 52.381 0.00 0.00 0.00 4.04
1556 2836 6.959639 ATCAAACTAACTTGACATGTTGGT 57.040 33.333 14.87 14.87 40.05 3.67
1590 2870 1.667830 CGCGACCACATCAACCACT 60.668 57.895 0.00 0.00 0.00 4.00
1627 2907 6.627243 AGAATTCACACAATCATCACAATGG 58.373 36.000 8.44 0.00 33.42 3.16
1739 3019 9.529325 TTAGAGCATATATCAACACACTTGTAC 57.471 33.333 0.00 0.00 33.55 2.90
1770 3050 2.678934 TTCACCGGACGGAGGGAG 60.679 66.667 18.80 2.08 38.96 4.30
1771 3051 2.678934 CTTCACCGGACGGAGGGA 60.679 66.667 18.80 8.89 38.96 4.20
1772 3052 2.678934 TCTTCACCGGACGGAGGG 60.679 66.667 18.80 6.62 38.96 4.30
1773 3053 1.977544 ACTCTTCACCGGACGGAGG 60.978 63.158 18.80 9.15 38.96 4.30
1774 3054 1.213013 CACTCTTCACCGGACGGAG 59.787 63.158 18.80 10.03 38.96 4.63
1775 3055 0.250858 TACACTCTTCACCGGACGGA 60.251 55.000 18.80 0.00 38.96 4.69
1776 3056 0.815734 ATACACTCTTCACCGGACGG 59.184 55.000 9.46 9.56 42.03 4.79
1777 3057 1.201647 ACATACACTCTTCACCGGACG 59.798 52.381 9.46 0.00 0.00 4.79
1778 3058 3.314541 AACATACACTCTTCACCGGAC 57.685 47.619 9.46 0.00 0.00 4.79
1779 3059 3.556213 CCAAACATACACTCTTCACCGGA 60.556 47.826 9.46 0.00 0.00 5.14
1780 3060 2.742053 CCAAACATACACTCTTCACCGG 59.258 50.000 0.00 0.00 0.00 5.28
1781 3061 2.159627 GCCAAACATACACTCTTCACCG 59.840 50.000 0.00 0.00 0.00 4.94
1782 3062 3.412386 AGCCAAACATACACTCTTCACC 58.588 45.455 0.00 0.00 0.00 4.02
1783 3063 4.515191 TGAAGCCAAACATACACTCTTCAC 59.485 41.667 0.00 0.00 35.12 3.18
1784 3064 4.713553 TGAAGCCAAACATACACTCTTCA 58.286 39.130 0.00 0.00 36.93 3.02
1785 3065 5.689383 TTGAAGCCAAACATACACTCTTC 57.311 39.130 0.00 0.00 0.00 2.87
1786 3066 6.463995 TTTTGAAGCCAAACATACACTCTT 57.536 33.333 0.00 0.00 41.54 2.85
1787 3067 6.655078 ATTTTGAAGCCAAACATACACTCT 57.345 33.333 0.00 0.00 41.54 3.24
1788 3068 7.713764 AAATTTTGAAGCCAAACATACACTC 57.286 32.000 0.00 0.00 41.54 3.51
1789 3069 9.423061 GATAAATTTTGAAGCCAAACATACACT 57.577 29.630 0.00 0.00 41.54 3.55
1790 3070 8.655970 GGATAAATTTTGAAGCCAAACATACAC 58.344 33.333 0.00 0.00 41.54 2.90
1791 3071 8.370940 TGGATAAATTTTGAAGCCAAACATACA 58.629 29.630 0.00 0.00 41.54 2.29
1792 3072 8.770438 TGGATAAATTTTGAAGCCAAACATAC 57.230 30.769 0.00 0.00 41.54 2.39
1794 3074 9.956640 TTATGGATAAATTTTGAAGCCAAACAT 57.043 25.926 0.79 0.00 41.54 2.71
1795 3075 9.784531 TTTATGGATAAATTTTGAAGCCAAACA 57.215 25.926 0.79 0.00 41.54 2.83
1799 3079 9.874205 CTCTTTTATGGATAAATTTTGAAGCCA 57.126 29.630 0.00 0.00 32.78 4.75
1800 3080 9.875691 ACTCTTTTATGGATAAATTTTGAAGCC 57.124 29.630 0.00 0.00 32.78 4.35
1819 3099 9.981460 ATTGGGAAGATAGAATTACACTCTTTT 57.019 29.630 0.00 0.00 0.00 2.27
1820 3100 9.401058 CATTGGGAAGATAGAATTACACTCTTT 57.599 33.333 0.00 0.00 0.00 2.52
1821 3101 7.500559 GCATTGGGAAGATAGAATTACACTCTT 59.499 37.037 0.00 0.00 0.00 2.85
1822 3102 6.995091 GCATTGGGAAGATAGAATTACACTCT 59.005 38.462 0.00 0.00 0.00 3.24
1823 3103 6.767902 TGCATTGGGAAGATAGAATTACACTC 59.232 38.462 0.00 0.00 0.00 3.51
1824 3104 6.543831 GTGCATTGGGAAGATAGAATTACACT 59.456 38.462 0.00 0.00 0.00 3.55
1825 3105 6.543831 AGTGCATTGGGAAGATAGAATTACAC 59.456 38.462 0.00 0.00 0.00 2.90
1826 3106 6.662755 AGTGCATTGGGAAGATAGAATTACA 58.337 36.000 0.00 0.00 0.00 2.41
1827 3107 7.573968 AAGTGCATTGGGAAGATAGAATTAC 57.426 36.000 0.00 0.00 0.00 1.89
1828 3108 9.693739 TTAAAGTGCATTGGGAAGATAGAATTA 57.306 29.630 0.00 0.00 0.00 1.40
1829 3109 8.593945 TTAAAGTGCATTGGGAAGATAGAATT 57.406 30.769 0.00 0.00 0.00 2.17
1830 3110 8.593945 TTTAAAGTGCATTGGGAAGATAGAAT 57.406 30.769 0.00 0.00 0.00 2.40
1831 3111 7.669722 ACTTTAAAGTGCATTGGGAAGATAGAA 59.330 33.333 19.94 0.00 37.98 2.10
1832 3112 7.175104 ACTTTAAAGTGCATTGGGAAGATAGA 58.825 34.615 19.94 0.00 37.98 1.98
1833 3113 7.396540 ACTTTAAAGTGCATTGGGAAGATAG 57.603 36.000 19.94 0.00 37.98 2.08
1834 3114 8.871629 TTACTTTAAAGTGCATTGGGAAGATA 57.128 30.769 27.40 2.69 40.07 1.98
1835 3115 7.775053 TTACTTTAAAGTGCATTGGGAAGAT 57.225 32.000 27.40 1.31 40.07 2.40
1836 3116 7.589958 TTTACTTTAAAGTGCATTGGGAAGA 57.410 32.000 27.40 3.30 40.07 2.87
1837 3117 8.655651 TTTTTACTTTAAAGTGCATTGGGAAG 57.344 30.769 27.40 0.00 40.07 3.46
1863 3143 5.765182 ACCGTGTGATGAGAGAGAAATTTTT 59.235 36.000 0.00 0.00 0.00 1.94
1864 3144 5.308825 ACCGTGTGATGAGAGAGAAATTTT 58.691 37.500 0.00 0.00 0.00 1.82
1865 3145 4.899502 ACCGTGTGATGAGAGAGAAATTT 58.100 39.130 0.00 0.00 0.00 1.82
1866 3146 4.543590 ACCGTGTGATGAGAGAGAAATT 57.456 40.909 0.00 0.00 0.00 1.82
1867 3147 5.661056 TTACCGTGTGATGAGAGAGAAAT 57.339 39.130 0.00 0.00 0.00 2.17
1868 3148 5.185056 TGATTACCGTGTGATGAGAGAGAAA 59.815 40.000 0.00 0.00 0.00 2.52
1869 3149 4.705023 TGATTACCGTGTGATGAGAGAGAA 59.295 41.667 0.00 0.00 0.00 2.87
1870 3150 4.270008 TGATTACCGTGTGATGAGAGAGA 58.730 43.478 0.00 0.00 0.00 3.10
1871 3151 4.639135 TGATTACCGTGTGATGAGAGAG 57.361 45.455 0.00 0.00 0.00 3.20
1872 3152 4.705023 TCTTGATTACCGTGTGATGAGAGA 59.295 41.667 0.00 0.00 0.00 3.10
1873 3153 4.800993 GTCTTGATTACCGTGTGATGAGAG 59.199 45.833 0.00 0.00 0.00 3.20
1874 3154 4.381612 GGTCTTGATTACCGTGTGATGAGA 60.382 45.833 0.00 0.00 0.00 3.27
1875 3155 3.865745 GGTCTTGATTACCGTGTGATGAG 59.134 47.826 0.00 0.00 0.00 2.90
1876 3156 3.259625 TGGTCTTGATTACCGTGTGATGA 59.740 43.478 0.00 0.00 40.08 2.92
1877 3157 3.595173 TGGTCTTGATTACCGTGTGATG 58.405 45.455 0.00 0.00 40.08 3.07
1878 3158 3.973206 TGGTCTTGATTACCGTGTGAT 57.027 42.857 0.00 0.00 40.08 3.06
1879 3159 3.755112 TTGGTCTTGATTACCGTGTGA 57.245 42.857 0.00 0.00 40.08 3.58
1880 3160 4.034048 GCTATTGGTCTTGATTACCGTGTG 59.966 45.833 0.00 0.00 40.08 3.82
1881 3161 4.189231 GCTATTGGTCTTGATTACCGTGT 58.811 43.478 0.00 0.00 40.08 4.49
1882 3162 4.188462 TGCTATTGGTCTTGATTACCGTG 58.812 43.478 0.00 0.00 40.08 4.94
1883 3163 4.481368 TGCTATTGGTCTTGATTACCGT 57.519 40.909 0.00 0.00 40.08 4.83
1884 3164 5.296780 ACATTGCTATTGGTCTTGATTACCG 59.703 40.000 0.00 0.00 40.08 4.02
1885 3165 6.699575 ACATTGCTATTGGTCTTGATTACC 57.300 37.500 0.00 0.00 37.53 2.85
1886 3166 8.122952 GTGTACATTGCTATTGGTCTTGATTAC 58.877 37.037 0.00 0.00 0.00 1.89
1887 3167 7.826744 TGTGTACATTGCTATTGGTCTTGATTA 59.173 33.333 0.00 0.00 0.00 1.75
1888 3168 6.658816 TGTGTACATTGCTATTGGTCTTGATT 59.341 34.615 0.00 0.00 0.00 2.57
1889 3169 6.179756 TGTGTACATTGCTATTGGTCTTGAT 58.820 36.000 0.00 0.00 0.00 2.57
1890 3170 5.555966 TGTGTACATTGCTATTGGTCTTGA 58.444 37.500 0.00 0.00 0.00 3.02
1891 3171 5.878332 TGTGTACATTGCTATTGGTCTTG 57.122 39.130 0.00 0.00 0.00 3.02
1892 3172 5.357878 CCATGTGTACATTGCTATTGGTCTT 59.642 40.000 0.00 0.00 33.61 3.01
1893 3173 4.883585 CCATGTGTACATTGCTATTGGTCT 59.116 41.667 0.00 0.00 33.61 3.85
1894 3174 4.640201 ACCATGTGTACATTGCTATTGGTC 59.360 41.667 0.00 0.00 33.61 4.02
1895 3175 4.599041 ACCATGTGTACATTGCTATTGGT 58.401 39.130 0.00 2.51 33.61 3.67
1896 3176 4.883585 AGACCATGTGTACATTGCTATTGG 59.116 41.667 0.00 1.89 33.61 3.16
1897 3177 6.317140 AGAAGACCATGTGTACATTGCTATTG 59.683 38.462 0.00 0.00 33.61 1.90
1898 3178 6.418101 AGAAGACCATGTGTACATTGCTATT 58.582 36.000 0.00 0.00 33.61 1.73
1899 3179 5.994250 AGAAGACCATGTGTACATTGCTAT 58.006 37.500 0.00 0.00 33.61 2.97
1900 3180 5.420725 AGAAGACCATGTGTACATTGCTA 57.579 39.130 0.00 0.00 33.61 3.49
1901 3181 4.292186 AGAAGACCATGTGTACATTGCT 57.708 40.909 0.00 0.00 33.61 3.91
1902 3182 6.494893 TTAAGAAGACCATGTGTACATTGC 57.505 37.500 0.00 0.00 33.61 3.56
1903 3183 9.559958 GAAATTAAGAAGACCATGTGTACATTG 57.440 33.333 0.00 0.00 33.61 2.82
1904 3184 9.520515 AGAAATTAAGAAGACCATGTGTACATT 57.479 29.630 0.00 0.00 33.61 2.71
1906 3186 9.431887 GTAGAAATTAAGAAGACCATGTGTACA 57.568 33.333 0.00 0.00 0.00 2.90
1907 3187 9.431887 TGTAGAAATTAAGAAGACCATGTGTAC 57.568 33.333 0.00 0.00 0.00 2.90
1909 3189 8.950210 CATGTAGAAATTAAGAAGACCATGTGT 58.050 33.333 0.00 0.00 0.00 3.72
1910 3190 7.912250 GCATGTAGAAATTAAGAAGACCATGTG 59.088 37.037 0.00 0.00 0.00 3.21
1911 3191 7.611467 TGCATGTAGAAATTAAGAAGACCATGT 59.389 33.333 0.00 0.00 0.00 3.21
1912 3192 7.912250 GTGCATGTAGAAATTAAGAAGACCATG 59.088 37.037 0.00 0.00 0.00 3.66
1913 3193 7.831193 AGTGCATGTAGAAATTAAGAAGACCAT 59.169 33.333 0.00 0.00 0.00 3.55
1914 3194 7.168219 AGTGCATGTAGAAATTAAGAAGACCA 58.832 34.615 0.00 0.00 0.00 4.02
1915 3195 7.334421 TGAGTGCATGTAGAAATTAAGAAGACC 59.666 37.037 0.00 0.00 0.00 3.85
1916 3196 8.256611 TGAGTGCATGTAGAAATTAAGAAGAC 57.743 34.615 0.00 0.00 0.00 3.01
1917 3197 9.453572 AATGAGTGCATGTAGAAATTAAGAAGA 57.546 29.630 0.00 0.00 34.26 2.87
1918 3198 9.499585 CAATGAGTGCATGTAGAAATTAAGAAG 57.500 33.333 0.00 0.00 34.26 2.85
1919 3199 9.230122 TCAATGAGTGCATGTAGAAATTAAGAA 57.770 29.630 0.00 0.00 34.26 2.52
1920 3200 8.791327 TCAATGAGTGCATGTAGAAATTAAGA 57.209 30.769 0.00 0.00 34.26 2.10
1921 3201 8.127327 CCTCAATGAGTGCATGTAGAAATTAAG 58.873 37.037 9.63 0.00 34.26 1.85
1922 3202 7.828717 TCCTCAATGAGTGCATGTAGAAATTAA 59.171 33.333 9.63 0.00 34.26 1.40
1923 3203 7.337938 TCCTCAATGAGTGCATGTAGAAATTA 58.662 34.615 9.63 0.00 34.26 1.40
1924 3204 6.182627 TCCTCAATGAGTGCATGTAGAAATT 58.817 36.000 9.63 0.00 34.26 1.82
1925 3205 5.748402 TCCTCAATGAGTGCATGTAGAAAT 58.252 37.500 9.63 0.00 34.26 2.17
1926 3206 5.164620 TCCTCAATGAGTGCATGTAGAAA 57.835 39.130 9.63 0.00 34.26 2.52
1927 3207 4.824479 TCCTCAATGAGTGCATGTAGAA 57.176 40.909 9.63 0.00 34.26 2.10
1928 3208 5.121105 CAATCCTCAATGAGTGCATGTAGA 58.879 41.667 9.63 0.00 34.26 2.59
1929 3209 4.275196 CCAATCCTCAATGAGTGCATGTAG 59.725 45.833 9.63 0.00 34.26 2.74
1930 3210 4.201657 CCAATCCTCAATGAGTGCATGTA 58.798 43.478 9.63 0.00 34.26 2.29
1931 3211 3.021695 CCAATCCTCAATGAGTGCATGT 58.978 45.455 9.63 0.00 34.26 3.21
1932 3212 2.361119 CCCAATCCTCAATGAGTGCATG 59.639 50.000 9.63 3.05 34.26 4.06
1933 3213 2.024655 ACCCAATCCTCAATGAGTGCAT 60.025 45.455 9.63 0.00 35.92 3.96
1934 3214 1.355381 ACCCAATCCTCAATGAGTGCA 59.645 47.619 9.63 0.00 0.00 4.57
1935 3215 2.134789 ACCCAATCCTCAATGAGTGC 57.865 50.000 9.63 0.00 0.00 4.40
1936 3216 7.880160 TTAATTACCCAATCCTCAATGAGTG 57.120 36.000 9.63 1.04 0.00 3.51
1937 3217 8.893563 TTTTAATTACCCAATCCTCAATGAGT 57.106 30.769 9.63 0.00 0.00 3.41
1938 3218 8.416329 CCTTTTAATTACCCAATCCTCAATGAG 58.584 37.037 2.68 2.68 0.00 2.90
1939 3219 8.119246 TCCTTTTAATTACCCAATCCTCAATGA 58.881 33.333 0.00 0.00 0.00 2.57
1940 3220 8.305046 TCCTTTTAATTACCCAATCCTCAATG 57.695 34.615 0.00 0.00 0.00 2.82
1941 3221 8.343787 TCTCCTTTTAATTACCCAATCCTCAAT 58.656 33.333 0.00 0.00 0.00 2.57
1942 3222 7.704727 TCTCCTTTTAATTACCCAATCCTCAA 58.295 34.615 0.00 0.00 0.00 3.02
1943 3223 7.183839 TCTCTCCTTTTAATTACCCAATCCTCA 59.816 37.037 0.00 0.00 0.00 3.86
1944 3224 7.574607 TCTCTCCTTTTAATTACCCAATCCTC 58.425 38.462 0.00 0.00 0.00 3.71
1945 3225 7.406151 TCTCTCTCCTTTTAATTACCCAATCCT 59.594 37.037 0.00 0.00 0.00 3.24
1946 3226 7.574607 TCTCTCTCCTTTTAATTACCCAATCC 58.425 38.462 0.00 0.00 0.00 3.01
1947 3227 9.061435 CATCTCTCTCCTTTTAATTACCCAATC 57.939 37.037 0.00 0.00 0.00 2.67
1948 3228 8.781951 TCATCTCTCTCCTTTTAATTACCCAAT 58.218 33.333 0.00 0.00 0.00 3.16
1949 3229 8.158025 TCATCTCTCTCCTTTTAATTACCCAA 57.842 34.615 0.00 0.00 0.00 4.12
1950 3230 7.749377 TCATCTCTCTCCTTTTAATTACCCA 57.251 36.000 0.00 0.00 0.00 4.51
1951 3231 7.663493 CCATCATCTCTCTCCTTTTAATTACCC 59.337 40.741 0.00 0.00 0.00 3.69
1952 3232 7.174080 GCCATCATCTCTCTCCTTTTAATTACC 59.826 40.741 0.00 0.00 0.00 2.85
1953 3233 7.936301 AGCCATCATCTCTCTCCTTTTAATTAC 59.064 37.037 0.00 0.00 0.00 1.89
1954 3234 8.038862 AGCCATCATCTCTCTCCTTTTAATTA 57.961 34.615 0.00 0.00 0.00 1.40
1955 3235 6.909076 AGCCATCATCTCTCTCCTTTTAATT 58.091 36.000 0.00 0.00 0.00 1.40
1956 3236 6.512514 AGCCATCATCTCTCTCCTTTTAAT 57.487 37.500 0.00 0.00 0.00 1.40
1957 3237 5.965033 AGCCATCATCTCTCTCCTTTTAA 57.035 39.130 0.00 0.00 0.00 1.52
1958 3238 5.678583 CAAGCCATCATCTCTCTCCTTTTA 58.321 41.667 0.00 0.00 0.00 1.52
1959 3239 4.525024 CAAGCCATCATCTCTCTCCTTTT 58.475 43.478 0.00 0.00 0.00 2.27
1960 3240 3.684981 GCAAGCCATCATCTCTCTCCTTT 60.685 47.826 0.00 0.00 0.00 3.11
1961 3241 2.158784 GCAAGCCATCATCTCTCTCCTT 60.159 50.000 0.00 0.00 0.00 3.36
1962 3242 1.417145 GCAAGCCATCATCTCTCTCCT 59.583 52.381 0.00 0.00 0.00 3.69
1963 3243 1.140452 TGCAAGCCATCATCTCTCTCC 59.860 52.381 0.00 0.00 0.00 3.71
1964 3244 2.211806 GTGCAAGCCATCATCTCTCTC 58.788 52.381 0.00 0.00 0.00 3.20
1965 3245 1.134159 GGTGCAAGCCATCATCTCTCT 60.134 52.381 0.00 0.00 0.00 3.10
1966 3246 1.134159 AGGTGCAAGCCATCATCTCTC 60.134 52.381 0.00 0.00 32.25 3.20
1967 3247 0.917533 AGGTGCAAGCCATCATCTCT 59.082 50.000 0.00 0.00 32.25 3.10
1968 3248 1.760192 AAGGTGCAAGCCATCATCTC 58.240 50.000 0.00 0.00 32.25 2.75
1969 3249 2.226962 AAAGGTGCAAGCCATCATCT 57.773 45.000 0.00 0.00 32.25 2.90
1970 3250 2.231964 TGAAAAGGTGCAAGCCATCATC 59.768 45.455 0.00 0.00 32.25 2.92
1971 3251 2.250031 TGAAAAGGTGCAAGCCATCAT 58.750 42.857 0.00 0.00 32.25 2.45
1972 3252 1.702182 TGAAAAGGTGCAAGCCATCA 58.298 45.000 0.00 0.00 32.25 3.07
1973 3253 2.818130 TTGAAAAGGTGCAAGCCATC 57.182 45.000 0.00 0.00 32.25 3.51
1974 3254 2.872842 GCATTGAAAAGGTGCAAGCCAT 60.873 45.455 0.00 0.00 38.68 4.40
1975 3255 1.540797 GCATTGAAAAGGTGCAAGCCA 60.541 47.619 0.00 0.00 38.68 4.75
1976 3256 1.150827 GCATTGAAAAGGTGCAAGCC 58.849 50.000 0.00 0.00 38.68 4.35
1977 3257 1.868469 TGCATTGAAAAGGTGCAAGC 58.132 45.000 0.00 0.00 44.99 4.01
1980 3260 5.831702 AAAAATTGCATTGAAAAGGTGCA 57.168 30.435 0.00 0.00 46.15 4.57
2027 3307 9.429359 CAGTGAAGAGTGTACATCTAGAAATTT 57.571 33.333 0.00 0.00 0.00 1.82
2028 3308 8.037758 CCAGTGAAGAGTGTACATCTAGAAATT 58.962 37.037 0.00 0.00 0.00 1.82
2029 3309 7.397476 TCCAGTGAAGAGTGTACATCTAGAAAT 59.603 37.037 0.00 0.00 0.00 2.17
2030 3310 6.719829 TCCAGTGAAGAGTGTACATCTAGAAA 59.280 38.462 0.00 0.00 0.00 2.52
2031 3311 6.246163 TCCAGTGAAGAGTGTACATCTAGAA 58.754 40.000 0.00 0.00 0.00 2.10
2032 3312 5.816682 TCCAGTGAAGAGTGTACATCTAGA 58.183 41.667 0.00 0.00 0.00 2.43
2033 3313 6.460814 CCATCCAGTGAAGAGTGTACATCTAG 60.461 46.154 0.00 0.00 0.00 2.43
2034 3314 5.360999 CCATCCAGTGAAGAGTGTACATCTA 59.639 44.000 0.00 0.00 0.00 1.98
2035 3315 4.161189 CCATCCAGTGAAGAGTGTACATCT 59.839 45.833 0.00 0.27 0.00 2.90
2036 3316 4.160439 TCCATCCAGTGAAGAGTGTACATC 59.840 45.833 0.00 0.00 0.00 3.06
2037 3317 4.096681 TCCATCCAGTGAAGAGTGTACAT 58.903 43.478 0.00 0.00 0.00 2.29
2038 3318 3.506398 TCCATCCAGTGAAGAGTGTACA 58.494 45.455 0.00 0.00 0.00 2.90
2039 3319 3.764434 TCTCCATCCAGTGAAGAGTGTAC 59.236 47.826 0.00 0.00 0.00 2.90
2040 3320 4.019858 CTCTCCATCCAGTGAAGAGTGTA 58.980 47.826 0.00 0.00 31.02 2.90
2041 3321 2.830923 CTCTCCATCCAGTGAAGAGTGT 59.169 50.000 0.00 0.00 31.02 3.55
2042 3322 3.095332 TCTCTCCATCCAGTGAAGAGTG 58.905 50.000 0.00 0.00 35.91 3.51
2043 3323 3.245586 ACTCTCTCCATCCAGTGAAGAGT 60.246 47.826 0.00 0.00 37.28 3.24
2044 3324 3.364549 ACTCTCTCCATCCAGTGAAGAG 58.635 50.000 0.00 0.00 36.10 2.85
2045 3325 3.464720 ACTCTCTCCATCCAGTGAAGA 57.535 47.619 0.00 0.00 0.00 2.87
2046 3326 6.016360 CAGTATACTCTCTCCATCCAGTGAAG 60.016 46.154 1.26 0.00 0.00 3.02
2047 3327 5.830457 CAGTATACTCTCTCCATCCAGTGAA 59.170 44.000 1.26 0.00 0.00 3.18
2048 3328 5.103898 ACAGTATACTCTCTCCATCCAGTGA 60.104 44.000 1.26 0.00 0.00 3.41
2049 3329 5.136828 ACAGTATACTCTCTCCATCCAGTG 58.863 45.833 1.26 0.00 0.00 3.66
2050 3330 5.396057 ACAGTATACTCTCTCCATCCAGT 57.604 43.478 1.26 0.00 0.00 4.00
2051 3331 6.432783 CCTAACAGTATACTCTCTCCATCCAG 59.567 46.154 1.26 0.00 0.00 3.86
2052 3332 6.126156 ACCTAACAGTATACTCTCTCCATCCA 60.126 42.308 1.26 0.00 0.00 3.41
2053 3333 6.308566 ACCTAACAGTATACTCTCTCCATCC 58.691 44.000 1.26 0.00 0.00 3.51
2054 3334 7.228590 AGACCTAACAGTATACTCTCTCCATC 58.771 42.308 1.26 0.00 0.00 3.51
2055 3335 7.156694 AGACCTAACAGTATACTCTCTCCAT 57.843 40.000 1.26 0.00 0.00 3.41
2056 3336 6.578313 AGACCTAACAGTATACTCTCTCCA 57.422 41.667 1.26 0.00 0.00 3.86
2057 3337 8.977267 TTTAGACCTAACAGTATACTCTCTCC 57.023 38.462 1.26 0.00 0.00 3.71
2083 3363 6.183361 CCTGTCCTCTCCAATGACACATAATA 60.183 42.308 0.00 0.00 35.34 0.98
2087 3367 2.238144 CCTGTCCTCTCCAATGACACAT 59.762 50.000 0.00 0.00 35.34 3.21
2107 3387 3.939592 GTGGTGAATAAGTTACTCCAGCC 59.060 47.826 0.00 1.00 0.00 4.85
2111 3391 5.161943 ACAGGTGGTGAATAAGTTACTCC 57.838 43.478 0.00 0.00 0.00 3.85
2123 3403 1.122632 TCCGGCTTAACAGGTGGTGA 61.123 55.000 0.00 0.00 34.76 4.02
2132 3412 0.461135 TATCACCCGTCCGGCTTAAC 59.539 55.000 0.00 0.00 33.26 2.01
2139 3419 2.350498 GTCAACAAATATCACCCGTCCG 59.650 50.000 0.00 0.00 0.00 4.79
2143 3423 3.944650 TGGATGTCAACAAATATCACCCG 59.055 43.478 0.00 0.00 0.00 5.28
2156 3436 1.211567 ACCCGGGGATTGGATGTCAA 61.212 55.000 27.92 0.00 40.01 3.18
2164 3444 2.946990 GTTTACACATACCCGGGGATTG 59.053 50.000 27.92 23.19 0.00 2.67
2192 3472 1.125711 CCGGTTCCCTATACCCCCAG 61.126 65.000 0.00 0.00 31.75 4.45
2227 4531 3.618150 GCCCATGTAAACAACAATGCATC 59.382 43.478 0.00 0.00 42.70 3.91
2276 4580 4.814771 CCTCCAACTACGATTGAAATACCC 59.185 45.833 0.00 0.00 0.00 3.69
2307 4611 8.156165 ACAACCATCACATTTAATTTGGTTCAT 58.844 29.630 4.33 0.00 43.62 2.57
2433 4737 3.382048 ACTGTCCTAAAGGTTCGTGTC 57.618 47.619 0.00 0.00 36.34 3.67
2437 4741 4.727235 GAACAACTGTCCTAAAGGTTCG 57.273 45.455 0.00 0.00 36.34 3.95


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

AutoCloner maintained by Alex Coulton.