Multiple sequence alignment - TraesCS4B01G054600

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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 TraesCS4B01G054600 chr4B 100.000 2591 0 0 1 2591 43182671 43180081 0.000000e+00 4785.0
1 TraesCS4B01G054600 chr4D 89.082 1264 75 29 567 1786 30310435 30309191 0.000000e+00 1511.0
2 TraesCS4B01G054600 chr4D 86.655 592 45 14 2005 2590 30297415 30296852 2.190000e-175 625.0
3 TraesCS4B01G054600 chr4D 94.872 39 2 0 1799 1837 30300524 30300486 7.740000e-06 62.1
4 TraesCS4B01G054600 chr4A 87.102 1256 72 43 608 1837 572649132 572650323 0.000000e+00 1339.0
5 TraesCS4B01G054600 chr2B 94.728 569 29 1 1 568 114409110 114408542 0.000000e+00 883.0
6 TraesCS4B01G054600 chr2B 83.784 111 10 6 2246 2351 23088903 23089010 5.900000e-17 99.0
7 TraesCS4B01G054600 chr6A 95.135 555 22 5 10 560 10984856 10984303 0.000000e+00 870.0
8 TraesCS4B01G054600 chr5A 94.404 554 28 3 10 560 7707802 7707249 0.000000e+00 848.0
9 TraesCS4B01G054600 chr5A 81.899 337 51 7 2005 2339 7117600 7117272 2.540000e-70 276.0
10 TraesCS4B01G054600 chr1A 92.894 577 35 6 10 582 460601518 460600944 0.000000e+00 833.0
11 TraesCS4B01G054600 chr1A 91.404 570 38 10 13 572 388848262 388847694 0.000000e+00 771.0
12 TraesCS4B01G054600 chr3D 92.212 565 28 12 10 559 24208415 24207852 0.000000e+00 785.0
13 TraesCS4B01G054600 chr1D 92.115 558 34 6 10 559 29834694 29835249 0.000000e+00 778.0
14 TraesCS4B01G054600 chr1D 83.588 262 39 3 2092 2350 62779582 62779842 2.580000e-60 243.0
15 TraesCS4B01G054600 chr7D 91.741 557 37 5 10 559 530412729 530413283 0.000000e+00 765.0
16 TraesCS4B01G054600 chr7D 77.515 338 49 12 2005 2339 88380163 88380476 7.370000e-41 178.0
17 TraesCS4B01G054600 chr5D 90.734 572 40 8 10 568 520085816 520085245 0.000000e+00 750.0
18 TraesCS4B01G054600 chr7A 81.429 350 52 7 2005 2350 57798026 57797686 9.130000e-70 274.0
19 TraesCS4B01G054600 chr6D 82.838 303 48 4 2050 2350 48145114 48144814 4.250000e-68 268.0
20 TraesCS4B01G054600 chr3A 85.465 172 23 2 2169 2339 118589822 118589652 7.370000e-41 178.0


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 TraesCS4B01G054600 chr4B 43180081 43182671 2590 True 4785.00 4785 100.0000 1 2591 1 chr4B.!!$R1 2590
1 TraesCS4B01G054600 chr4D 30309191 30310435 1244 True 1511.00 1511 89.0820 567 1786 1 chr4D.!!$R1 1219
2 TraesCS4B01G054600 chr4D 30296852 30300524 3672 True 343.55 625 90.7635 1799 2590 2 chr4D.!!$R2 791
3 TraesCS4B01G054600 chr4A 572649132 572650323 1191 False 1339.00 1339 87.1020 608 1837 1 chr4A.!!$F1 1229
4 TraesCS4B01G054600 chr2B 114408542 114409110 568 True 883.00 883 94.7280 1 568 1 chr2B.!!$R1 567
5 TraesCS4B01G054600 chr6A 10984303 10984856 553 True 870.00 870 95.1350 10 560 1 chr6A.!!$R1 550
6 TraesCS4B01G054600 chr5A 7707249 7707802 553 True 848.00 848 94.4040 10 560 1 chr5A.!!$R2 550
7 TraesCS4B01G054600 chr1A 460600944 460601518 574 True 833.00 833 92.8940 10 582 1 chr1A.!!$R2 572
8 TraesCS4B01G054600 chr1A 388847694 388848262 568 True 771.00 771 91.4040 13 572 1 chr1A.!!$R1 559
9 TraesCS4B01G054600 chr3D 24207852 24208415 563 True 785.00 785 92.2120 10 559 1 chr3D.!!$R1 549
10 TraesCS4B01G054600 chr1D 29834694 29835249 555 False 778.00 778 92.1150 10 559 1 chr1D.!!$F1 549
11 TraesCS4B01G054600 chr7D 530412729 530413283 554 False 765.00 765 91.7410 10 559 1 chr7D.!!$F2 549
12 TraesCS4B01G054600 chr5D 520085245 520085816 571 True 750.00 750 90.7340 10 568 1 chr5D.!!$R1 558

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
929 980 0.096281 GCGCGAGATCGAGATAGAGG 59.904 60.0 12.1 0.0 41.67 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 3189 0.040425 GTTGACGGCGTGCTTTCAAT 60.04 50.0 21.19 0.0 30.96 2.57 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
86 99 3.326588 TGGCAACTGTCCAGTGTTAGTAT 59.673 43.478 0.00 0.00 41.58 2.12
198 218 2.224744 TGACCTAAGATGGCAACTGCAA 60.225 45.455 0.00 0.00 44.36 4.08
262 282 2.862541 ACTTCAGCAACATGGCAACTA 58.137 42.857 0.00 0.00 35.83 2.24
525 556 3.049674 CAGGACGTGCGGCACAAT 61.050 61.111 30.23 18.96 33.40 2.71
536 567 0.179084 CGGCACAATCACCCGATACT 60.179 55.000 0.00 0.00 44.55 2.12
568 599 3.449737 TGACAAGTATCGGGACCCTAAAG 59.550 47.826 9.41 0.00 0.00 1.85
569 600 3.703052 GACAAGTATCGGGACCCTAAAGA 59.297 47.826 9.41 0.00 0.00 2.52
570 601 4.098894 ACAAGTATCGGGACCCTAAAGAA 58.901 43.478 9.41 0.00 0.00 2.52
577 608 2.683362 CGGGACCCTAAAGAAATTGAGC 59.317 50.000 9.41 0.00 0.00 4.26
852 903 2.895680 CCCGCTAGCTCTGCTTCA 59.104 61.111 13.93 0.00 40.44 3.02
859 910 2.768698 CTAGCTCTGCTTCATCCCATG 58.231 52.381 0.00 0.00 40.44 3.66
864 915 1.137675 TCTGCTTCATCCCATGTCGAG 59.862 52.381 0.00 0.00 0.00 4.04
865 916 0.178767 TGCTTCATCCCATGTCGAGG 59.821 55.000 0.00 0.00 0.00 4.63
867 918 0.467384 CTTCATCCCATGTCGAGGCT 59.533 55.000 0.00 0.00 0.00 4.58
877 928 1.227674 GTCGAGGCTTGCCCATAGG 60.228 63.158 8.17 0.00 35.39 2.57
929 980 0.096281 GCGCGAGATCGAGATAGAGG 59.904 60.000 12.10 0.00 41.67 3.69
938 991 1.982226 TCGAGATAGAGGGAGAGAGGG 59.018 57.143 0.00 0.00 0.00 4.30
939 992 1.982226 CGAGATAGAGGGAGAGAGGGA 59.018 57.143 0.00 0.00 0.00 4.20
940 993 2.027192 CGAGATAGAGGGAGAGAGGGAG 60.027 59.091 0.00 0.00 0.00 4.30
1027 1086 1.112315 CCTGGATCACTCGGAGGAGG 61.112 65.000 10.23 0.00 44.93 4.30
1028 1087 0.106469 CTGGATCACTCGGAGGAGGA 60.106 60.000 10.23 4.48 44.93 3.71
1029 1088 0.106469 TGGATCACTCGGAGGAGGAG 60.106 60.000 10.23 0.00 44.93 3.69
1067 1132 4.451150 CTACGGCAGCGGAGGCAA 62.451 66.667 7.02 0.00 43.41 4.52
1073 1138 2.435586 CAGCGGAGGCAAGAGGTG 60.436 66.667 0.00 0.00 43.41 4.00
1368 1445 2.202440 CTCCAGTACGTGCGGTCG 60.202 66.667 0.00 0.00 0.00 4.79
1386 1463 1.375908 GATGCACAGGTCTTCGGCA 60.376 57.895 0.00 0.00 39.03 5.69
1510 1608 1.604915 GAGGGGAGGAAGGACAAGC 59.395 63.158 0.00 0.00 0.00 4.01
1511 1609 1.151810 AGGGGAGGAAGGACAAGCA 60.152 57.895 0.00 0.00 0.00 3.91
1512 1610 1.204113 AGGGGAGGAAGGACAAGCAG 61.204 60.000 0.00 0.00 0.00 4.24
1513 1611 1.377856 GGGAGGAAGGACAAGCAGC 60.378 63.158 0.00 0.00 0.00 5.25
1514 1612 1.743252 GGAGGAAGGACAAGCAGCG 60.743 63.158 0.00 0.00 0.00 5.18
1515 1613 1.743252 GAGGAAGGACAAGCAGCGG 60.743 63.158 0.00 0.00 0.00 5.52
1516 1614 3.435186 GGAAGGACAAGCAGCGGC 61.435 66.667 0.00 0.00 41.61 6.53
1536 1634 0.673022 AGCAGCAGAAGAAGAAGCGG 60.673 55.000 0.00 0.00 0.00 5.52
1539 1637 0.389166 AGCAGAAGAAGAAGCGGTCG 60.389 55.000 0.00 0.00 0.00 4.79
1638 1741 3.737266 TGTCGTCGCGTTTAATTCTCTTT 59.263 39.130 5.77 0.00 0.00 2.52
1655 1768 5.597806 TCTCTTTGTTGATCGTACTGTGTT 58.402 37.500 0.00 0.00 0.00 3.32
1703 1818 1.215647 CGTGTCACCTACTCTGGGC 59.784 63.158 0.00 0.00 0.00 5.36
1745 1860 4.163458 GGTTTGTTTCCTTTCCCTTTCCTT 59.837 41.667 0.00 0.00 0.00 3.36
1775 1890 3.514417 TCGATGACGAGGAGCAGG 58.486 61.111 0.00 0.00 43.81 4.85
1783 1898 2.070028 GACGAGGAGCAGGAAAAAGAC 58.930 52.381 0.00 0.00 0.00 3.01
1790 1905 4.082136 AGGAGCAGGAAAAAGACTACTACG 60.082 45.833 0.00 0.00 0.00 3.51
1791 1906 4.082354 GGAGCAGGAAAAAGACTACTACGA 60.082 45.833 0.00 0.00 0.00 3.43
1793 1908 3.925299 GCAGGAAAAAGACTACTACGACC 59.075 47.826 0.00 0.00 0.00 4.79
1794 1909 4.560108 GCAGGAAAAAGACTACTACGACCA 60.560 45.833 0.00 0.00 0.00 4.02
1795 1910 4.922103 CAGGAAAAAGACTACTACGACCAC 59.078 45.833 0.00 0.00 0.00 4.16
1796 1911 4.831710 AGGAAAAAGACTACTACGACCACT 59.168 41.667 0.00 0.00 0.00 4.00
1797 1912 4.922103 GGAAAAAGACTACTACGACCACTG 59.078 45.833 0.00 0.00 0.00 3.66
1837 1952 4.391830 TCTGAGTTGTGACACTTGTGTTTC 59.608 41.667 7.20 5.36 0.00 2.78
1838 1953 3.124466 TGAGTTGTGACACTTGTGTTTCG 59.876 43.478 7.20 0.00 0.00 3.46
1840 1955 1.443802 TGTGACACTTGTGTTTCGCA 58.556 45.000 7.20 6.34 39.94 5.10
1841 1956 1.807142 TGTGACACTTGTGTTTCGCAA 59.193 42.857 7.20 0.00 39.49 4.85
1842 1957 2.421775 TGTGACACTTGTGTTTCGCAAT 59.578 40.909 7.20 0.00 39.49 3.56
1843 1958 3.623510 TGTGACACTTGTGTTTCGCAATA 59.376 39.130 7.20 0.00 39.49 1.90
1844 1959 4.095036 TGTGACACTTGTGTTTCGCAATAA 59.905 37.500 7.20 0.00 39.49 1.40
1845 1960 5.212194 GTGACACTTGTGTTTCGCAATAAT 58.788 37.500 7.87 0.00 34.56 1.28
1846 1961 6.017852 TGTGACACTTGTGTTTCGCAATAATA 60.018 34.615 7.20 0.00 39.49 0.98
1847 1962 7.021196 GTGACACTTGTGTTTCGCAATAATAT 58.979 34.615 7.87 0.00 34.56 1.28
1848 1963 7.537306 GTGACACTTGTGTTTCGCAATAATATT 59.463 33.333 7.87 0.00 34.56 1.28
1849 1964 7.536964 TGACACTTGTGTTTCGCAATAATATTG 59.463 33.333 8.55 8.55 33.31 1.90
1850 1965 6.307800 ACACTTGTGTTTCGCAATAATATTGC 59.692 34.615 23.85 23.85 41.71 3.56
1851 1966 6.307558 CACTTGTGTTTCGCAATAATATTGCA 59.692 34.615 30.01 18.06 45.14 4.08
1852 1967 6.527722 ACTTGTGTTTCGCAATAATATTGCAG 59.472 34.615 30.01 23.25 45.14 4.41
1855 1970 7.702386 TGTGTTTCGCAATAATATTGCAGTAT 58.298 30.769 30.01 0.00 45.14 2.12
1857 1972 7.855409 GTGTTTCGCAATAATATTGCAGTATGA 59.145 33.333 30.01 19.01 45.14 2.15
1861 1976 6.705825 TCGCAATAATATTGCAGTATGAGTGT 59.294 34.615 30.01 0.00 45.14 3.55
1865 3105 9.049523 CAATAATATTGCAGTATGAGTGTGACT 57.950 33.333 2.06 0.00 39.69 3.41
1874 3114 7.065923 TGCAGTATGAGTGTGACTTAGTACTAG 59.934 40.741 2.23 0.74 39.69 2.57
1878 3118 6.010294 TGAGTGTGACTTAGTACTAGCAAC 57.990 41.667 2.23 2.10 0.00 4.17
1882 3122 5.981315 GTGTGACTTAGTACTAGCAACAACA 59.019 40.000 2.23 2.59 0.00 3.33
1883 3123 5.981315 TGTGACTTAGTACTAGCAACAACAC 59.019 40.000 2.23 8.47 0.00 3.32
1884 3124 5.981315 GTGACTTAGTACTAGCAACAACACA 59.019 40.000 2.23 0.00 0.00 3.72
1885 3125 5.981315 TGACTTAGTACTAGCAACAACACAC 59.019 40.000 2.23 0.00 0.00 3.82
1886 3126 5.909477 ACTTAGTACTAGCAACAACACACA 58.091 37.500 2.23 0.00 0.00 3.72
1887 3127 5.983720 ACTTAGTACTAGCAACAACACACAG 59.016 40.000 2.23 0.00 0.00 3.66
1889 3129 4.119862 AGTACTAGCAACAACACACAGTG 58.880 43.478 0.00 0.00 39.75 3.66
1891 3131 1.603802 CTAGCAACAACACACAGTGGG 59.396 52.381 0.00 0.00 37.94 4.61
1892 3132 0.034574 AGCAACAACACACAGTGGGA 60.035 50.000 10.68 0.00 37.94 4.37
1893 3133 0.814457 GCAACAACACACAGTGGGAA 59.186 50.000 10.68 0.00 37.94 3.97
1894 3134 1.469079 GCAACAACACACAGTGGGAAC 60.469 52.381 10.68 0.00 37.94 3.62
1895 3135 1.815613 CAACAACACACAGTGGGAACA 59.184 47.619 10.68 0.00 37.94 3.18
1909 3161 4.105754 TGGGAACACACCATACAATTGA 57.894 40.909 13.59 0.00 33.40 2.57
1914 3166 5.240623 GGAACACACCATACAATTGAGACAA 59.759 40.000 13.59 0.00 0.00 3.18
1920 3172 6.716628 ACACCATACAATTGAGACAATGAGTT 59.283 34.615 13.59 0.00 0.00 3.01
1921 3173 7.025365 CACCATACAATTGAGACAATGAGTTG 58.975 38.462 13.59 0.00 41.20 3.16
1922 3174 6.942005 ACCATACAATTGAGACAATGAGTTGA 59.058 34.615 13.59 0.00 38.71 3.18
1923 3175 7.448161 ACCATACAATTGAGACAATGAGTTGAA 59.552 33.333 13.59 0.00 38.71 2.69
1924 3176 8.298854 CCATACAATTGAGACAATGAGTTGAAA 58.701 33.333 13.59 0.00 38.71 2.69
1925 3177 9.121517 CATACAATTGAGACAATGAGTTGAAAC 57.878 33.333 13.59 0.00 38.71 2.78
1926 3178 7.099266 ACAATTGAGACAATGAGTTGAAACA 57.901 32.000 13.59 0.00 38.71 2.83
1928 3180 4.794248 TGAGACAATGAGTTGAAACACG 57.206 40.909 0.00 0.00 38.71 4.49
1929 3181 4.188462 TGAGACAATGAGTTGAAACACGT 58.812 39.130 0.00 0.00 38.71 4.49
1932 3184 4.816385 AGACAATGAGTTGAAACACGTGAT 59.184 37.500 25.01 7.78 38.71 3.06
1933 3185 4.847633 ACAATGAGTTGAAACACGTGATG 58.152 39.130 25.01 0.00 38.71 3.07
1934 3186 3.542712 ATGAGTTGAAACACGTGATGC 57.457 42.857 25.01 10.25 0.00 3.91
1935 3187 2.284190 TGAGTTGAAACACGTGATGCA 58.716 42.857 25.01 13.43 0.00 3.96
1936 3188 2.287644 TGAGTTGAAACACGTGATGCAG 59.712 45.455 25.01 0.00 0.00 4.41
1937 3189 2.543848 GAGTTGAAACACGTGATGCAGA 59.456 45.455 25.01 3.60 0.00 4.26
1938 3190 3.141398 AGTTGAAACACGTGATGCAGAT 58.859 40.909 25.01 4.73 0.00 2.90
1941 3193 3.137533 TGAAACACGTGATGCAGATTGA 58.862 40.909 25.01 0.00 0.00 2.57
1942 3194 3.563390 TGAAACACGTGATGCAGATTGAA 59.437 39.130 25.01 0.00 0.00 2.69
1943 3195 4.036144 TGAAACACGTGATGCAGATTGAAA 59.964 37.500 25.01 0.00 0.00 2.69
1944 3196 3.818961 ACACGTGATGCAGATTGAAAG 57.181 42.857 25.01 0.00 0.00 2.62
1946 3198 2.095617 CACGTGATGCAGATTGAAAGCA 60.096 45.455 10.90 0.00 43.14 3.91
1948 3200 2.512885 GTGATGCAGATTGAAAGCACG 58.487 47.619 0.00 0.00 41.60 5.34
1949 3201 1.135603 TGATGCAGATTGAAAGCACGC 60.136 47.619 0.00 0.00 41.60 5.34
1950 3202 0.171903 ATGCAGATTGAAAGCACGCC 59.828 50.000 0.00 0.00 41.60 5.68
1951 3203 1.512734 GCAGATTGAAAGCACGCCG 60.513 57.895 0.00 0.00 0.00 6.46
1952 3204 1.868997 CAGATTGAAAGCACGCCGT 59.131 52.632 0.00 0.00 0.00 5.68
1955 3207 0.237235 GATTGAAAGCACGCCGTCAA 59.763 50.000 7.26 7.26 34.68 3.18
1956 3208 0.040425 ATTGAAAGCACGCCGTCAAC 60.040 50.000 7.03 0.00 33.09 3.18
1957 3209 2.054140 TTGAAAGCACGCCGTCAACC 62.054 55.000 0.00 0.00 0.00 3.77
1959 3211 2.711185 GAAAGCACGCCGTCAACCAC 62.711 60.000 0.00 0.00 0.00 4.16
1962 3214 2.903547 GCACGCCGTCAACCACATT 61.904 57.895 0.00 0.00 0.00 2.71
1963 3215 1.082169 CACGCCGTCAACCACATTG 60.082 57.895 0.00 0.00 39.94 2.82
1964 3216 1.525077 ACGCCGTCAACCACATTGT 60.525 52.632 0.00 0.00 39.54 2.71
1965 3217 1.098712 ACGCCGTCAACCACATTGTT 61.099 50.000 0.00 0.00 39.54 2.83
1967 3219 1.466950 CGCCGTCAACCACATTGTTAT 59.533 47.619 0.00 0.00 39.54 1.89
1968 3220 2.475519 CGCCGTCAACCACATTGTTATC 60.476 50.000 0.00 0.00 39.54 1.75
1971 3223 4.380444 GCCGTCAACCACATTGTTATCAAT 60.380 41.667 0.00 0.00 44.02 2.57
1972 3224 5.331902 CCGTCAACCACATTGTTATCAATC 58.668 41.667 0.00 0.00 41.66 2.67
1973 3225 5.021389 CGTCAACCACATTGTTATCAATCG 58.979 41.667 0.00 0.00 41.66 3.34
1974 3226 4.793216 GTCAACCACATTGTTATCAATCGC 59.207 41.667 0.00 0.00 41.66 4.58
1986 4229 7.087409 TGTTATCAATCGCATCATGTTCTTT 57.913 32.000 0.00 0.00 0.00 2.52
1988 4231 7.697710 TGTTATCAATCGCATCATGTTCTTTTC 59.302 33.333 0.00 0.00 0.00 2.29
1991 4234 5.412286 TCAATCGCATCATGTTCTTTTCTGA 59.588 36.000 0.00 0.00 0.00 3.27
1992 4235 4.934075 TCGCATCATGTTCTTTTCTGAG 57.066 40.909 0.00 0.00 0.00 3.35
1993 4236 3.125829 TCGCATCATGTTCTTTTCTGAGC 59.874 43.478 0.00 0.00 0.00 4.26
1994 4237 3.120095 CGCATCATGTTCTTTTCTGAGCA 60.120 43.478 0.00 0.00 0.00 4.26
1995 4238 4.164294 GCATCATGTTCTTTTCTGAGCAC 58.836 43.478 0.00 0.00 30.43 4.40
1996 4239 4.730657 CATCATGTTCTTTTCTGAGCACC 58.269 43.478 0.00 0.00 30.43 5.01
1997 4240 3.819368 TCATGTTCTTTTCTGAGCACCA 58.181 40.909 0.00 0.00 30.43 4.17
1998 4241 4.206375 TCATGTTCTTTTCTGAGCACCAA 58.794 39.130 0.00 0.00 30.43 3.67
2000 4243 5.302568 TCATGTTCTTTTCTGAGCACCAAAT 59.697 36.000 0.00 0.00 30.43 2.32
2003 5021 6.042143 TGTTCTTTTCTGAGCACCAAATTTC 58.958 36.000 0.00 0.00 0.00 2.17
2014 5032 3.160269 CACCAAATTTCAAGGGCTCTCT 58.840 45.455 0.00 0.00 0.00 3.10
2032 5050 3.119101 TCTCTTTGGCACTAGAACGATCC 60.119 47.826 0.00 0.00 0.00 3.36
2033 5051 2.832129 TCTTTGGCACTAGAACGATCCT 59.168 45.455 0.00 0.00 0.00 3.24
2034 5052 2.672961 TTGGCACTAGAACGATCCTG 57.327 50.000 0.00 0.00 0.00 3.86
2037 5055 3.093814 TGGCACTAGAACGATCCTGTTA 58.906 45.455 0.00 0.00 30.75 2.41
2040 5058 4.381718 GGCACTAGAACGATCCTGTTAACT 60.382 45.833 7.22 0.00 30.75 2.24
2041 5059 5.169295 GCACTAGAACGATCCTGTTAACTT 58.831 41.667 7.22 0.00 30.75 2.66
2042 5060 5.638234 GCACTAGAACGATCCTGTTAACTTT 59.362 40.000 7.22 0.00 30.75 2.66
2043 5061 6.810182 GCACTAGAACGATCCTGTTAACTTTA 59.190 38.462 7.22 0.00 30.75 1.85
2044 5062 7.201418 GCACTAGAACGATCCTGTTAACTTTAC 60.201 40.741 7.22 0.00 30.75 2.01
2045 5063 7.275123 CACTAGAACGATCCTGTTAACTTTACC 59.725 40.741 7.22 0.00 30.75 2.85
2046 5064 6.356186 AGAACGATCCTGTTAACTTTACCT 57.644 37.500 7.22 0.00 30.75 3.08
2047 5065 7.472334 AGAACGATCCTGTTAACTTTACCTA 57.528 36.000 7.22 0.00 30.75 3.08
2070 5088 0.035317 ACAGCTTCAGTCCGATTGCA 59.965 50.000 0.00 0.00 0.00 4.08
2072 5090 1.016130 AGCTTCAGTCCGATTGCACG 61.016 55.000 0.00 0.00 0.00 5.34
2102 5120 1.949465 AGGCGTTCACGGATAATTCC 58.051 50.000 0.81 0.00 40.23 3.01
2103 5121 0.942252 GGCGTTCACGGATAATTCCC 59.058 55.000 0.81 0.00 39.01 3.97
2111 5129 3.838317 TCACGGATAATTCCCTGGATAGG 59.162 47.826 0.00 0.00 44.18 2.57
2113 5131 4.775780 CACGGATAATTCCCTGGATAGGTA 59.224 45.833 0.00 0.00 42.96 3.08
2114 5132 5.024118 ACGGATAATTCCCTGGATAGGTAG 58.976 45.833 0.00 0.00 42.96 3.18
2116 5134 5.351405 GGATAATTCCCTGGATAGGTAGGT 58.649 45.833 0.00 0.00 42.96 3.08
2117 5135 6.509386 GGATAATTCCCTGGATAGGTAGGTA 58.491 44.000 0.00 0.00 42.96 3.08
2124 5142 5.043582 TCCCTGGATAGGTAGGTATATGGAC 60.044 48.000 0.00 0.00 42.96 4.02
2162 5180 3.069586 TCAAACGCTCCATGGATACTAGG 59.930 47.826 16.63 3.17 37.61 3.02
2174 5192 3.956199 TGGATACTAGGGTAGTTGTTCCG 59.044 47.826 0.00 0.00 40.14 4.30
2175 5193 3.320256 GGATACTAGGGTAGTTGTTCCGG 59.680 52.174 0.00 0.00 40.14 5.14
2193 5211 6.600427 TGTTCCGGTAAAAATTTATCCCTCTC 59.400 38.462 0.00 0.00 0.00 3.20
2217 5235 9.620660 CTCAAAATAGGGTTACACATTGTTTAC 57.379 33.333 0.00 0.00 0.00 2.01
2218 5236 9.132923 TCAAAATAGGGTTACACATTGTTTACA 57.867 29.630 0.00 0.00 0.00 2.41
2263 5282 5.271355 ACACTGCGTGTTGGTTAAACCAC 62.271 47.826 8.25 0.00 45.08 4.16
2337 5356 8.114301 ACCTTGGAATAAATACCCTATGACTT 57.886 34.615 0.00 0.00 0.00 3.01
2353 5375 4.027572 TGACTTCCGCAAAGAAAAACTG 57.972 40.909 3.02 0.00 38.44 3.16
2375 5397 0.326595 TCTCGGCAATTGCACCCTTA 59.673 50.000 30.32 8.82 44.36 2.69
2409 5431 9.923143 CAATTCCAATATTGCATCATGTAGAAT 57.077 29.630 10.11 7.30 0.00 2.40
2421 5443 5.723492 TCATGTAGAATGATGAAGTTGCG 57.277 39.130 0.00 0.00 0.00 4.85
2431 5453 2.254546 TGAAGTTGCGGAGTTCATGT 57.745 45.000 6.17 0.00 41.60 3.21
2449 5471 7.643764 AGTTCATGTTTGTTCGTAGAAACAATG 59.356 33.333 18.72 16.24 46.53 2.82
2453 5475 5.513495 TGTTTGTTCGTAGAAACAATGCAAC 59.487 36.000 13.79 4.61 42.48 4.17
2455 5477 4.843147 TGTTCGTAGAAACAATGCAACTG 58.157 39.130 0.00 0.00 45.90 3.16
2460 5482 5.295787 TCGTAGAAACAATGCAACTGAAACT 59.704 36.000 6.19 4.76 0.00 2.66
2461 5483 5.396362 CGTAGAAACAATGCAACTGAAACTG 59.604 40.000 6.19 0.00 0.00 3.16
2462 5484 4.685924 AGAAACAATGCAACTGAAACTGG 58.314 39.130 6.19 0.00 0.00 4.00
2464 5486 4.734398 AACAATGCAACTGAAACTGGAA 57.266 36.364 6.19 0.00 0.00 3.53
2465 5487 4.045636 ACAATGCAACTGAAACTGGAAC 57.954 40.909 6.19 0.00 0.00 3.62
2466 5488 3.181476 ACAATGCAACTGAAACTGGAACC 60.181 43.478 6.19 0.00 0.00 3.62
2467 5489 2.136298 TGCAACTGAAACTGGAACCA 57.864 45.000 0.00 0.00 0.00 3.67
2468 5490 2.665165 TGCAACTGAAACTGGAACCAT 58.335 42.857 0.00 0.00 0.00 3.55
2469 5491 3.030291 TGCAACTGAAACTGGAACCATT 58.970 40.909 0.00 0.00 0.00 3.16
2470 5492 3.450457 TGCAACTGAAACTGGAACCATTT 59.550 39.130 0.00 0.00 0.00 2.32
2471 5493 4.646945 TGCAACTGAAACTGGAACCATTTA 59.353 37.500 0.00 0.00 0.00 1.40
2472 5494 5.304101 TGCAACTGAAACTGGAACCATTTAT 59.696 36.000 0.00 0.00 0.00 1.40
2473 5495 6.183360 TGCAACTGAAACTGGAACCATTTATT 60.183 34.615 0.00 0.00 0.00 1.40
2474 5496 6.366061 GCAACTGAAACTGGAACCATTTATTC 59.634 38.462 0.00 0.00 0.00 1.75
2475 5497 7.432869 CAACTGAAACTGGAACCATTTATTCA 58.567 34.615 0.00 3.12 0.00 2.57
2476 5498 7.595819 ACTGAAACTGGAACCATTTATTCAA 57.404 32.000 0.00 0.00 0.00 2.69
2477 5499 8.017418 ACTGAAACTGGAACCATTTATTCAAA 57.983 30.769 0.00 0.00 0.00 2.69
2478 5500 7.926018 ACTGAAACTGGAACCATTTATTCAAAC 59.074 33.333 0.00 0.00 0.00 2.93
2479 5501 7.213678 TGAAACTGGAACCATTTATTCAAACC 58.786 34.615 0.00 0.00 0.00 3.27
2480 5502 6.994421 AACTGGAACCATTTATTCAAACCT 57.006 33.333 0.00 0.00 0.00 3.50
2481 5503 6.994421 ACTGGAACCATTTATTCAAACCTT 57.006 33.333 0.00 0.00 0.00 3.50
2482 5504 8.485578 AACTGGAACCATTTATTCAAACCTTA 57.514 30.769 0.00 0.00 0.00 2.69
2483 5505 7.892609 ACTGGAACCATTTATTCAAACCTTAC 58.107 34.615 0.00 0.00 0.00 2.34
2484 5506 7.507616 ACTGGAACCATTTATTCAAACCTTACA 59.492 33.333 0.00 0.00 0.00 2.41
2556 5578 3.270027 CGTGTAAGGGCATCTTGAATGA 58.730 45.455 2.32 0.00 36.93 2.57
2585 5607 9.793259 TCCTCTAAAATGGACATGGTATTTATC 57.207 33.333 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 218 1.274167 CAGTTGCCATGGTTGCTCAAT 59.726 47.619 14.67 0.00 0.00 2.57
243 263 2.553602 TGTAGTTGCCATGTTGCTGAAG 59.446 45.455 0.00 0.00 0.00 3.02
262 282 1.067516 GTTGCCATGTTGCTGAACTGT 59.932 47.619 0.00 0.00 32.79 3.55
525 556 0.609957 ACGTGTGGAGTATCGGGTGA 60.610 55.000 0.00 0.00 34.37 4.02
536 567 2.606065 CGATACTTGTCACACGTGTGGA 60.606 50.000 39.88 27.32 45.65 4.02
548 579 3.716431 TCTTTAGGGTCCCGATACTTGT 58.284 45.455 0.99 0.00 0.00 3.16
551 582 5.427481 TCAATTTCTTTAGGGTCCCGATACT 59.573 40.000 0.99 0.00 0.00 2.12
552 583 5.677567 TCAATTTCTTTAGGGTCCCGATAC 58.322 41.667 0.99 0.00 0.00 2.24
568 599 6.020837 GCATCTTTCATTCTTCGCTCAATTTC 60.021 38.462 0.00 0.00 0.00 2.17
569 600 5.803967 GCATCTTTCATTCTTCGCTCAATTT 59.196 36.000 0.00 0.00 0.00 1.82
570 601 5.338365 GCATCTTTCATTCTTCGCTCAATT 58.662 37.500 0.00 0.00 0.00 2.32
577 608 1.667724 AGGCGCATCTTTCATTCTTCG 59.332 47.619 10.83 0.00 0.00 3.79
663 702 3.834726 CTCGCTCGAGGATGAGGT 58.165 61.111 15.58 0.00 38.51 3.85
729 772 5.072193 AGGGAATTGGGAATGGAATTATTGC 59.928 40.000 0.00 0.00 36.07 3.56
775 818 2.154854 TTGACAAGAGTTGCTCGAGG 57.845 50.000 15.58 0.00 35.36 4.63
852 903 1.153086 GCAAGCCTCGACATGGGAT 60.153 57.895 0.00 0.00 0.00 3.85
859 910 1.227674 CCTATGGGCAAGCCTCGAC 60.228 63.158 11.40 0.00 36.10 4.20
929 980 2.766229 GCACCCCTCCCTCTCTCC 60.766 72.222 0.00 0.00 0.00 3.71
1027 1086 2.015726 TCCCCTCCTCCTCCTCCTC 61.016 68.421 0.00 0.00 0.00 3.71
1028 1087 2.018086 CTCCCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1029 1088 2.612251 CTCCCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1057 1116 2.925170 ACACCTCTTGCCTCCGCT 60.925 61.111 0.00 0.00 35.36 5.52
1101 1166 1.673665 CAGCTGGTGGTGGCTCTTC 60.674 63.158 5.57 0.00 37.97 2.87
1206 1271 2.992689 TGGGACAGCCGCTCGTAA 60.993 61.111 0.00 0.00 33.83 3.18
1315 1386 3.041627 GCTTCTGCTGCTGCTGCTC 62.042 63.158 27.67 8.99 40.48 4.26
1316 1387 3.056938 GCTTCTGCTGCTGCTGCT 61.057 61.111 27.67 0.00 40.48 4.24
1317 1388 4.117661 GGCTTCTGCTGCTGCTGC 62.118 66.667 22.51 22.51 40.48 5.25
1318 1389 3.800863 CGGCTTCTGCTGCTGCTG 61.801 66.667 17.00 15.94 38.88 4.41
1368 1445 1.364626 CTGCCGAAGACCTGTGCATC 61.365 60.000 0.00 0.00 0.00 3.91
1486 1584 1.383803 CCTTCCTCCCCTCCTCAGG 60.384 68.421 0.00 0.00 39.98 3.86
1487 1585 0.689412 GTCCTTCCTCCCCTCCTCAG 60.689 65.000 0.00 0.00 0.00 3.35
1510 1608 3.800863 CTTCTGCTGCTGCCGCTG 61.801 66.667 16.81 15.82 38.71 5.18
1511 1609 3.541950 TTCTTCTGCTGCTGCCGCT 62.542 57.895 16.81 0.00 38.71 5.52
1512 1610 3.036783 CTTCTTCTGCTGCTGCCGC 62.037 63.158 13.47 9.23 38.71 6.53
1513 1611 0.952497 TTCTTCTTCTGCTGCTGCCG 60.952 55.000 13.47 6.90 38.71 5.69
1514 1612 0.803740 CTTCTTCTTCTGCTGCTGCC 59.196 55.000 13.47 0.00 38.71 4.85
1515 1613 0.168568 GCTTCTTCTTCTGCTGCTGC 59.831 55.000 8.89 8.89 40.20 5.25
1516 1614 0.443088 CGCTTCTTCTTCTGCTGCTG 59.557 55.000 0.00 0.00 0.00 4.41
1523 1621 0.109689 CGACGACCGCTTCTTCTTCT 60.110 55.000 0.00 0.00 0.00 2.85
1638 1741 4.441744 CACGTAAACACAGTACGATCAACA 59.558 41.667 10.64 0.00 45.63 3.33
1703 1818 1.999051 CGAACAAGATCGGCGAAGG 59.001 57.895 15.93 6.29 39.12 3.46
1710 1825 3.551551 GAAACAAACCCGAACAAGATCG 58.448 45.455 0.00 0.00 42.37 3.69
1768 1883 4.082354 TCGTAGTAGTCTTTTTCCTGCTCC 60.082 45.833 0.00 0.00 0.00 4.70
1775 1890 4.922103 CCAGTGGTCGTAGTAGTCTTTTTC 59.078 45.833 0.00 0.00 0.00 2.29
1783 1898 4.440250 CCAATTCTCCAGTGGTCGTAGTAG 60.440 50.000 9.54 0.00 0.00 2.57
1790 1905 2.206576 AAGCCAATTCTCCAGTGGTC 57.793 50.000 9.54 0.00 34.71 4.02
1791 1906 2.519013 GAAAGCCAATTCTCCAGTGGT 58.481 47.619 9.54 0.00 34.71 4.16
1793 1908 2.800250 AGGAAAGCCAATTCTCCAGTG 58.200 47.619 0.00 0.00 36.29 3.66
1794 1909 3.075134 AGAAGGAAAGCCAATTCTCCAGT 59.925 43.478 0.00 0.00 36.29 4.00
1795 1910 3.442977 CAGAAGGAAAGCCAATTCTCCAG 59.557 47.826 0.00 0.00 36.29 3.86
1796 1911 3.074390 TCAGAAGGAAAGCCAATTCTCCA 59.926 43.478 0.00 0.00 36.29 3.86
1797 1912 3.690460 TCAGAAGGAAAGCCAATTCTCC 58.310 45.455 0.00 0.00 36.29 3.71
1838 1953 7.800380 GTCACACTCATACTGCAATATTATTGC 59.200 37.037 27.11 27.11 45.11 3.56
1840 1955 9.618890 AAGTCACACTCATACTGCAATATTATT 57.381 29.630 0.00 0.00 0.00 1.40
1842 1957 9.750125 CTAAGTCACACTCATACTGCAATATTA 57.250 33.333 0.00 0.00 0.00 0.98
1843 1958 8.260818 ACTAAGTCACACTCATACTGCAATATT 58.739 33.333 0.00 0.00 0.00 1.28
1844 1959 7.786030 ACTAAGTCACACTCATACTGCAATAT 58.214 34.615 0.00 0.00 0.00 1.28
1845 1960 7.170393 ACTAAGTCACACTCATACTGCAATA 57.830 36.000 0.00 0.00 0.00 1.90
1846 1961 6.042638 ACTAAGTCACACTCATACTGCAAT 57.957 37.500 0.00 0.00 0.00 3.56
1847 1962 5.468540 ACTAAGTCACACTCATACTGCAA 57.531 39.130 0.00 0.00 0.00 4.08
1848 1963 5.710567 AGTACTAAGTCACACTCATACTGCA 59.289 40.000 0.00 0.00 0.00 4.41
1849 1964 6.197364 AGTACTAAGTCACACTCATACTGC 57.803 41.667 0.00 0.00 0.00 4.40
1850 1965 7.065923 TGCTAGTACTAAGTCACACTCATACTG 59.934 40.741 3.76 0.00 28.99 2.74
1851 1966 7.110810 TGCTAGTACTAAGTCACACTCATACT 58.889 38.462 3.76 0.00 30.30 2.12
1852 1967 7.317842 TGCTAGTACTAAGTCACACTCATAC 57.682 40.000 3.76 0.00 0.00 2.39
1855 1970 5.533528 TGTTGCTAGTACTAAGTCACACTCA 59.466 40.000 3.76 0.00 0.00 3.41
1857 1972 6.183360 TGTTGTTGCTAGTACTAAGTCACACT 60.183 38.462 3.76 0.00 0.00 3.55
1861 1976 5.981315 GTGTGTTGTTGCTAGTACTAAGTCA 59.019 40.000 3.76 0.02 0.00 3.41
1865 3105 5.751509 CACTGTGTGTTGTTGCTAGTACTAA 59.248 40.000 3.76 0.00 0.00 2.24
1867 3107 4.119862 CACTGTGTGTTGTTGCTAGTACT 58.880 43.478 0.00 0.00 0.00 2.73
1874 3114 0.814457 TTCCCACTGTGTGTTGTTGC 59.186 50.000 7.08 0.00 0.00 4.17
1878 3118 1.132262 GTGTGTTCCCACTGTGTGTTG 59.868 52.381 7.08 0.00 42.34 3.33
1882 3122 0.550914 ATGGTGTGTTCCCACTGTGT 59.449 50.000 7.08 0.00 42.34 3.72
1883 3123 2.151202 GTATGGTGTGTTCCCACTGTG 58.849 52.381 0.00 0.00 42.34 3.66
1884 3124 1.771854 TGTATGGTGTGTTCCCACTGT 59.228 47.619 0.00 0.00 42.34 3.55
1885 3125 2.559698 TGTATGGTGTGTTCCCACTG 57.440 50.000 0.00 0.00 42.34 3.66
1886 3126 3.806949 ATTGTATGGTGTGTTCCCACT 57.193 42.857 0.00 0.00 42.34 4.00
1887 3127 3.823873 TCAATTGTATGGTGTGTTCCCAC 59.176 43.478 5.13 0.00 42.19 4.61
1889 3129 4.156008 GTCTCAATTGTATGGTGTGTTCCC 59.844 45.833 5.13 0.00 0.00 3.97
1891 3131 5.940192 TGTCTCAATTGTATGGTGTGTTC 57.060 39.130 5.13 0.00 0.00 3.18
1892 3132 6.489700 TCATTGTCTCAATTGTATGGTGTGTT 59.510 34.615 5.13 0.00 0.00 3.32
1893 3133 6.003326 TCATTGTCTCAATTGTATGGTGTGT 58.997 36.000 5.13 0.00 0.00 3.72
1894 3134 6.149973 ACTCATTGTCTCAATTGTATGGTGTG 59.850 38.462 5.13 3.44 0.00 3.82
1895 3135 6.240894 ACTCATTGTCTCAATTGTATGGTGT 58.759 36.000 5.13 4.17 0.00 4.16
1898 3138 7.381766 TCAACTCATTGTCTCAATTGTATGG 57.618 36.000 5.13 0.00 37.11 2.74
1899 3139 9.121517 GTTTCAACTCATTGTCTCAATTGTATG 57.878 33.333 5.13 3.71 37.11 2.39
1900 3140 8.849168 TGTTTCAACTCATTGTCTCAATTGTAT 58.151 29.630 5.13 0.00 37.11 2.29
1902 3142 6.974622 GTGTTTCAACTCATTGTCTCAATTGT 59.025 34.615 5.13 0.00 37.11 2.71
1903 3143 6.141211 CGTGTTTCAACTCATTGTCTCAATTG 59.859 38.462 0.00 0.00 37.11 2.32
1904 3144 6.183360 ACGTGTTTCAACTCATTGTCTCAATT 60.183 34.615 0.00 0.00 37.11 2.32
1909 3161 4.188462 TCACGTGTTTCAACTCATTGTCT 58.812 39.130 16.51 0.00 37.11 3.41
1914 3166 2.877786 TGCATCACGTGTTTCAACTCAT 59.122 40.909 16.51 0.00 0.00 2.90
1920 3172 3.137533 TCAATCTGCATCACGTGTTTCA 58.862 40.909 16.51 7.13 0.00 2.69
1921 3173 3.811722 TCAATCTGCATCACGTGTTTC 57.188 42.857 16.51 1.96 0.00 2.78
1922 3174 4.539870 CTTTCAATCTGCATCACGTGTTT 58.460 39.130 16.51 1.32 0.00 2.83
1923 3175 3.610114 GCTTTCAATCTGCATCACGTGTT 60.610 43.478 16.51 3.97 0.00 3.32
1924 3176 2.095567 GCTTTCAATCTGCATCACGTGT 60.096 45.455 16.51 0.00 0.00 4.49
1925 3177 2.095617 TGCTTTCAATCTGCATCACGTG 60.096 45.455 9.94 9.94 0.00 4.49
1926 3178 2.095567 GTGCTTTCAATCTGCATCACGT 60.096 45.455 0.00 0.00 39.00 4.49
1928 3180 2.512885 CGTGCTTTCAATCTGCATCAC 58.487 47.619 0.00 0.00 39.00 3.06
1929 3181 1.135603 GCGTGCTTTCAATCTGCATCA 60.136 47.619 0.00 0.00 39.00 3.07
1932 3184 1.580942 GGCGTGCTTTCAATCTGCA 59.419 52.632 0.00 0.00 0.00 4.41
1933 3185 1.512734 CGGCGTGCTTTCAATCTGC 60.513 57.895 0.00 0.00 0.00 4.26
1934 3186 0.179215 GACGGCGTGCTTTCAATCTG 60.179 55.000 21.19 0.00 0.00 2.90
1935 3187 0.602638 TGACGGCGTGCTTTCAATCT 60.603 50.000 21.19 0.00 0.00 2.40
1936 3188 0.237235 TTGACGGCGTGCTTTCAATC 59.763 50.000 21.19 0.00 0.00 2.67
1937 3189 0.040425 GTTGACGGCGTGCTTTCAAT 60.040 50.000 21.19 0.00 30.96 2.57
1938 3190 1.353804 GTTGACGGCGTGCTTTCAA 59.646 52.632 21.19 12.59 0.00 2.69
1941 3193 2.515057 TGGTTGACGGCGTGCTTT 60.515 55.556 21.19 0.00 0.00 3.51
1942 3194 3.276846 GTGGTTGACGGCGTGCTT 61.277 61.111 21.19 0.00 0.00 3.91
1943 3195 3.825160 ATGTGGTTGACGGCGTGCT 62.825 57.895 21.19 0.00 0.00 4.40
1944 3196 2.903547 AATGTGGTTGACGGCGTGC 61.904 57.895 21.19 10.08 0.00 5.34
1946 3198 1.098712 AACAATGTGGTTGACGGCGT 61.099 50.000 14.65 14.65 40.37 5.68
1948 3200 2.486203 TGATAACAATGTGGTTGACGGC 59.514 45.455 0.00 0.00 40.37 5.68
1949 3201 4.757799 TTGATAACAATGTGGTTGACGG 57.242 40.909 0.00 0.00 40.37 4.79
1950 3202 5.021389 CGATTGATAACAATGTGGTTGACG 58.979 41.667 2.55 0.00 45.30 4.35
1951 3203 4.793216 GCGATTGATAACAATGTGGTTGAC 59.207 41.667 2.55 0.00 45.30 3.18
1952 3204 4.457257 TGCGATTGATAACAATGTGGTTGA 59.543 37.500 2.55 0.00 45.30 3.18
1955 3207 4.639755 TGATGCGATTGATAACAATGTGGT 59.360 37.500 2.55 0.00 45.30 4.16
1956 3208 5.172460 TGATGCGATTGATAACAATGTGG 57.828 39.130 2.55 0.00 45.30 4.17
1957 3209 6.203647 ACATGATGCGATTGATAACAATGTG 58.796 36.000 2.55 0.00 45.30 3.21
1959 3211 7.136772 AGAACATGATGCGATTGATAACAATG 58.863 34.615 2.55 0.00 45.30 2.82
1962 3214 6.682423 AAGAACATGATGCGATTGATAACA 57.318 33.333 0.00 0.00 0.00 2.41
1963 3215 7.912250 AGAAAAGAACATGATGCGATTGATAAC 59.088 33.333 0.00 0.00 0.00 1.89
1964 3216 7.911727 CAGAAAAGAACATGATGCGATTGATAA 59.088 33.333 0.00 0.00 0.00 1.75
1965 3217 7.280652 TCAGAAAAGAACATGATGCGATTGATA 59.719 33.333 0.00 0.00 0.00 2.15
1967 3219 5.412286 TCAGAAAAGAACATGATGCGATTGA 59.588 36.000 0.00 0.00 0.00 2.57
1968 3220 5.633927 TCAGAAAAGAACATGATGCGATTG 58.366 37.500 0.00 0.00 0.00 2.67
1971 3223 3.125829 GCTCAGAAAAGAACATGATGCGA 59.874 43.478 0.00 0.00 0.00 5.10
1972 3224 3.120095 TGCTCAGAAAAGAACATGATGCG 60.120 43.478 0.00 0.00 0.00 4.73
1973 3225 4.164294 GTGCTCAGAAAAGAACATGATGC 58.836 43.478 0.00 0.00 0.00 3.91
1974 3226 4.216902 TGGTGCTCAGAAAAGAACATGATG 59.783 41.667 0.00 0.00 0.00 3.07
1986 4229 3.321682 CCCTTGAAATTTGGTGCTCAGAA 59.678 43.478 0.00 0.00 0.00 3.02
1988 4231 2.611224 GCCCTTGAAATTTGGTGCTCAG 60.611 50.000 0.00 0.00 0.00 3.35
1991 4234 1.620323 GAGCCCTTGAAATTTGGTGCT 59.380 47.619 0.00 2.36 32.75 4.40
1992 4235 1.620323 AGAGCCCTTGAAATTTGGTGC 59.380 47.619 0.00 0.00 0.00 5.01
1993 4236 3.160269 AGAGAGCCCTTGAAATTTGGTG 58.840 45.455 0.00 0.00 0.00 4.17
1994 4237 3.532641 AGAGAGCCCTTGAAATTTGGT 57.467 42.857 0.00 0.00 0.00 3.67
1995 4238 4.562143 CCAAAGAGAGCCCTTGAAATTTGG 60.562 45.833 0.00 0.00 39.41 3.28
1996 4239 4.563061 CCAAAGAGAGCCCTTGAAATTTG 58.437 43.478 0.00 0.00 0.00 2.32
1997 4240 3.007290 GCCAAAGAGAGCCCTTGAAATTT 59.993 43.478 0.00 0.00 0.00 1.82
1998 4241 2.564504 GCCAAAGAGAGCCCTTGAAATT 59.435 45.455 0.00 0.00 0.00 1.82
2000 4243 1.133513 TGCCAAAGAGAGCCCTTGAAA 60.134 47.619 0.00 0.00 0.00 2.69
2003 5021 0.251077 AGTGCCAAAGAGAGCCCTTG 60.251 55.000 0.00 0.00 0.00 3.61
2014 5032 2.301870 ACAGGATCGTTCTAGTGCCAAA 59.698 45.455 0.00 0.00 0.00 3.28
2037 5055 8.422566 GGACTGAAGCTGTATATAGGTAAAGTT 58.577 37.037 13.69 0.00 29.48 2.66
2040 5058 6.774170 TCGGACTGAAGCTGTATATAGGTAAA 59.226 38.462 1.31 0.00 0.00 2.01
2041 5059 6.301486 TCGGACTGAAGCTGTATATAGGTAA 58.699 40.000 1.31 0.00 0.00 2.85
2042 5060 5.872963 TCGGACTGAAGCTGTATATAGGTA 58.127 41.667 1.31 0.00 0.00 3.08
2043 5061 4.726583 TCGGACTGAAGCTGTATATAGGT 58.273 43.478 0.00 0.00 0.00 3.08
2044 5062 5.906113 ATCGGACTGAAGCTGTATATAGG 57.094 43.478 0.00 0.00 0.00 2.57
2045 5063 5.574830 GCAATCGGACTGAAGCTGTATATAG 59.425 44.000 0.00 0.00 0.00 1.31
2046 5064 5.010617 TGCAATCGGACTGAAGCTGTATATA 59.989 40.000 11.84 0.00 34.04 0.86
2047 5065 4.202253 TGCAATCGGACTGAAGCTGTATAT 60.202 41.667 11.84 0.00 34.04 0.86
2078 5096 0.459585 TATCCGTGAACGCCTTGAGC 60.460 55.000 0.00 0.00 38.18 4.26
2083 5101 1.949465 GGAATTATCCGTGAACGCCT 58.051 50.000 0.00 0.00 35.59 5.52
2103 5121 7.286546 CAGATGTCCATATACCTACCTATCCAG 59.713 44.444 0.00 0.00 0.00 3.86
2111 5129 7.036220 CCGAAATCAGATGTCCATATACCTAC 58.964 42.308 0.00 0.00 0.00 3.18
2113 5131 5.780282 TCCGAAATCAGATGTCCATATACCT 59.220 40.000 0.00 0.00 0.00 3.08
2114 5132 6.037786 TCCGAAATCAGATGTCCATATACC 57.962 41.667 0.00 0.00 0.00 2.73
2116 5134 7.397192 TGATCTCCGAAATCAGATGTCCATATA 59.603 37.037 0.00 0.00 29.01 0.86
2117 5135 6.212187 TGATCTCCGAAATCAGATGTCCATAT 59.788 38.462 0.00 0.00 29.01 1.78
2124 5142 4.551603 GCGTTTGATCTCCGAAATCAGATG 60.552 45.833 0.00 0.00 34.76 2.90
2162 5180 7.970061 GGATAAATTTTTACCGGAACAACTACC 59.030 37.037 9.46 0.00 0.00 3.18
2193 5211 9.751542 TTGTAAACAATGTGTAACCCTATTTTG 57.248 29.630 0.00 0.00 34.36 2.44
2268 5287 0.457443 TAGCTCACTGATGCACGGAG 59.543 55.000 0.00 0.00 0.00 4.63
2271 5290 1.554392 GACTAGCTCACTGATGCACG 58.446 55.000 0.00 0.00 0.00 5.34
2272 5291 1.554392 CGACTAGCTCACTGATGCAC 58.446 55.000 0.00 0.00 0.00 4.57
2273 5292 0.179127 GCGACTAGCTCACTGATGCA 60.179 55.000 0.00 0.00 44.04 3.96
2274 5293 2.587574 GCGACTAGCTCACTGATGC 58.412 57.895 0.00 0.00 44.04 3.91
2320 5339 5.818678 TGCGGAAGTCATAGGGTATTTAT 57.181 39.130 0.00 0.00 0.00 1.40
2335 5354 2.808244 TGCAGTTTTTCTTTGCGGAAG 58.192 42.857 0.00 0.00 40.62 3.46
2337 5356 2.622942 AGATGCAGTTTTTCTTTGCGGA 59.377 40.909 0.00 0.00 40.62 5.54
2353 5375 1.226773 GGTGCAATTGCCGAGATGC 60.227 57.895 26.94 0.93 41.18 3.91
2375 5397 4.776837 TGCAATATTGGAATTGACAAGGGT 59.223 37.500 17.02 0.00 38.84 4.34
2409 5431 2.542020 TGAACTCCGCAACTTCATCA 57.458 45.000 0.00 0.00 0.00 3.07
2420 5442 3.985279 TCTACGAACAAACATGAACTCCG 59.015 43.478 0.00 0.00 0.00 4.63
2421 5443 5.917541 TTCTACGAACAAACATGAACTCC 57.082 39.130 0.00 0.00 0.00 3.85
2449 5471 3.733443 AATGGTTCCAGTTTCAGTTGC 57.267 42.857 0.00 0.00 0.00 4.17
2453 5475 7.384932 GGTTTGAATAAATGGTTCCAGTTTCAG 59.615 37.037 9.72 0.00 0.00 3.02
2455 5477 7.441836 AGGTTTGAATAAATGGTTCCAGTTTC 58.558 34.615 9.72 3.79 0.00 2.78
2460 5482 7.841282 TGTAAGGTTTGAATAAATGGTTCCA 57.159 32.000 0.00 0.00 0.00 3.53
2461 5483 8.581578 TCTTGTAAGGTTTGAATAAATGGTTCC 58.418 33.333 0.00 0.00 0.00 3.62
2471 5493 8.637986 TGCTTGTTTATCTTGTAAGGTTTGAAT 58.362 29.630 0.00 0.00 0.00 2.57
2472 5494 7.918562 GTGCTTGTTTATCTTGTAAGGTTTGAA 59.081 33.333 0.00 0.00 0.00 2.69
2473 5495 7.284489 AGTGCTTGTTTATCTTGTAAGGTTTGA 59.716 33.333 0.00 0.00 0.00 2.69
2474 5496 7.425606 AGTGCTTGTTTATCTTGTAAGGTTTG 58.574 34.615 0.00 0.00 0.00 2.93
2475 5497 7.519970 CGAGTGCTTGTTTATCTTGTAAGGTTT 60.520 37.037 0.00 0.00 0.00 3.27
2476 5498 6.073222 CGAGTGCTTGTTTATCTTGTAAGGTT 60.073 38.462 0.00 0.00 0.00 3.50
2477 5499 5.408604 CGAGTGCTTGTTTATCTTGTAAGGT 59.591 40.000 0.00 0.00 0.00 3.50
2478 5500 5.408604 ACGAGTGCTTGTTTATCTTGTAAGG 59.591 40.000 0.00 0.00 0.00 2.69
2479 5501 6.467723 ACGAGTGCTTGTTTATCTTGTAAG 57.532 37.500 0.00 0.00 0.00 2.34
2480 5502 6.293190 CCAACGAGTGCTTGTTTATCTTGTAA 60.293 38.462 2.26 0.00 35.11 2.41
2481 5503 5.178623 CCAACGAGTGCTTGTTTATCTTGTA 59.821 40.000 2.26 0.00 35.11 2.41
2482 5504 4.024048 CCAACGAGTGCTTGTTTATCTTGT 60.024 41.667 2.26 0.00 35.11 3.16
2483 5505 4.466828 CCAACGAGTGCTTGTTTATCTTG 58.533 43.478 2.26 0.00 35.11 3.02
2484 5506 3.058224 GCCAACGAGTGCTTGTTTATCTT 60.058 43.478 2.26 0.00 35.11 2.40
2494 5516 1.032014 ATGTTTTGCCAACGAGTGCT 58.968 45.000 0.00 0.00 0.00 4.40
2522 5544 3.408634 CCTTACACGGTTTTGGAGATGT 58.591 45.455 0.00 0.00 0.00 3.06
2523 5545 2.747446 CCCTTACACGGTTTTGGAGATG 59.253 50.000 0.00 0.00 0.00 2.90
2524 5546 2.878526 GCCCTTACACGGTTTTGGAGAT 60.879 50.000 0.00 0.00 0.00 2.75
2525 5547 1.543871 GCCCTTACACGGTTTTGGAGA 60.544 52.381 0.00 0.00 0.00 3.71
2526 5548 0.879090 GCCCTTACACGGTTTTGGAG 59.121 55.000 0.00 0.00 0.00 3.86
2527 5549 0.183014 TGCCCTTACACGGTTTTGGA 59.817 50.000 0.00 0.00 0.00 3.53
2529 5551 2.159382 AGATGCCCTTACACGGTTTTG 58.841 47.619 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.