Multiple sequence alignment - TraesCS7D01G101700

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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 TraesCS7D01G101700 chr7D 100.000 3895 0 0 1866 5760 60693334 60697228 0.000000e+00 7193.0
1 TraesCS7D01G101700 chr7D 100.000 1506 0 0 1 1506 60691469 60692974 0.000000e+00 2782.0
2 TraesCS7D01G101700 chr7D 91.925 322 25 1 325 645 56866496 56866175 3.170000e-122 449.0
3 TraesCS7D01G101700 chr7D 97.500 240 6 0 58 297 56866726 56866487 1.490000e-110 411.0
4 TraesCS7D01G101700 chr7D 96.078 51 2 0 1 51 56866768 56866718 3.700000e-12 84.2
5 TraesCS7D01G101700 chr7B 92.073 1703 103 15 2130 3824 3330138 3331816 0.000000e+00 2368.0
6 TraesCS7D01G101700 chr7B 91.017 1692 91 25 3887 5551 3331949 3333606 0.000000e+00 2226.0
7 TraesCS7D01G101700 chr7B 86.998 623 24 20 872 1482 3176363 3176940 0.000000e+00 649.0
8 TraesCS7D01G101700 chr7B 88.133 573 31 14 872 1432 3329412 3329959 0.000000e+00 647.0
9 TraesCS7D01G101700 chr7B 79.087 526 94 13 3196 3716 3178621 3179135 1.190000e-91 348.0
10 TraesCS7D01G101700 chr7B 88.384 198 19 3 2130 2324 3177174 3177370 9.650000e-58 235.0
11 TraesCS7D01G101700 chr7B 91.538 130 7 3 2009 2137 3329978 3330104 5.930000e-40 176.0
12 TraesCS7D01G101700 chr7B 90.000 110 8 3 732 840 3176149 3176256 7.780000e-29 139.0
13 TraesCS7D01G101700 chr7A 92.934 1387 68 14 2054 3420 64930544 64931920 0.000000e+00 1991.0
14 TraesCS7D01G101700 chr7A 92.169 996 60 13 4126 5116 64935325 64936307 0.000000e+00 1391.0
15 TraesCS7D01G101700 chr7A 95.075 670 28 4 3461 4128 64931915 64932581 0.000000e+00 1050.0
16 TraesCS7D01G101700 chr7A 90.647 695 38 10 828 1496 64929192 64929885 0.000000e+00 898.0
17 TraesCS7D01G101700 chr7A 93.081 607 36 6 5156 5760 64936279 64936881 0.000000e+00 883.0
18 TraesCS7D01G101700 chr7A 87.425 167 14 6 645 809 64928914 64929075 9.860000e-43 185.0
19 TraesCS7D01G101700 chr5B 91.273 825 61 6 2130 2947 345179406 345178586 0.000000e+00 1114.0
20 TraesCS7D01G101700 chr5B 88.764 89 6 2 2050 2137 345179525 345179440 7.890000e-19 106.0
21 TraesCS7D01G101700 chr5B 89.362 47 5 0 677 723 485992861 485992815 6.230000e-05 60.2
22 TraesCS7D01G101700 chr4D 91.525 649 42 3 1 645 281289216 281288577 0.000000e+00 881.0
23 TraesCS7D01G101700 chr4D 97.222 108 2 1 1905 2011 494123003 494122896 1.270000e-41 182.0
24 TraesCS7D01G101700 chr4B 86.047 344 33 10 2 333 195457303 195457643 7.100000e-94 355.0
25 TraesCS7D01G101700 chr3A 93.162 234 15 1 7 239 236543185 236542952 5.530000e-90 342.0
26 TraesCS7D01G101700 chr3A 84.466 103 16 0 1079 1181 507303463 507303361 1.020000e-17 102.0
27 TraesCS7D01G101700 chr1D 87.814 279 23 5 2 271 299886560 299886836 3.350000e-82 316.0
28 TraesCS7D01G101700 chr1D 98.182 110 1 1 1905 2013 465596804 465596913 2.120000e-44 191.0
29 TraesCS7D01G101700 chr2B 91.237 194 16 1 4 197 551445458 551445650 4.430000e-66 263.0
30 TraesCS7D01G101700 chr6B 99.083 109 0 1 1904 2011 506127982 506128090 1.640000e-45 195.0
31 TraesCS7D01G101700 chr6B 97.222 108 2 1 1905 2011 204159137 204159244 1.270000e-41 182.0
32 TraesCS7D01G101700 chr2A 94.400 125 5 2 1898 2020 449280146 449280022 2.120000e-44 191.0
33 TraesCS7D01G101700 chr6D 97.248 109 2 1 1904 2011 318149925 318149817 3.540000e-42 183.0
34 TraesCS7D01G101700 chrUn 97.222 108 2 1 1905 2011 94181871 94181978 1.270000e-41 182.0
35 TraesCS7D01G101700 chr5A 97.222 108 2 1 1905 2011 658993803 658993696 1.270000e-41 182.0
36 TraesCS7D01G101700 chr3B 94.690 113 4 2 1902 2012 771323363 771323475 2.130000e-39 174.0
37 TraesCS7D01G101700 chr3D 85.437 103 15 0 1079 1181 384854755 384854653 2.190000e-19 108.0
38 TraesCS7D01G101700 chr3D 97.143 35 1 0 2749 2783 250458672 250458638 6.230000e-05 60.2
39 TraesCS7D01G101700 chr6A 82.278 79 3 3 2712 2779 29182186 29182108 2.240000e-04 58.4


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 TraesCS7D01G101700 chr7D 60691469 60697228 5759 False 4987.500000 7193 100.000000 1 5760 2 chr7D.!!$F1 5759
1 TraesCS7D01G101700 chr7D 56866175 56866768 593 True 314.733333 449 95.167667 1 645 3 chr7D.!!$R1 644
2 TraesCS7D01G101700 chr7B 3329412 3333606 4194 False 1354.250000 2368 90.690250 872 5551 4 chr7B.!!$F2 4679
3 TraesCS7D01G101700 chr7B 3176149 3179135 2986 False 342.750000 649 86.117250 732 3716 4 chr7B.!!$F1 2984
4 TraesCS7D01G101700 chr7A 64928914 64936881 7967 False 1066.333333 1991 91.888500 645 5760 6 chr7A.!!$F1 5115
5 TraesCS7D01G101700 chr5B 345178586 345179525 939 True 610.000000 1114 90.018500 2050 2947 2 chr5B.!!$R2 897
6 TraesCS7D01G101700 chr4D 281288577 281289216 639 True 881.000000 881 91.525000 1 645 1 chr4D.!!$R1 644

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
249 250 0.379316 ATGTACGTACTCGCGCATCA 59.621 50.000 25.12 3.33 41.18 3.07 F
1221 1376 0.603707 TCGCCTTTCCAGCAGACTTG 60.604 55.000 0.00 0.00 0.00 3.16 F
1222 1377 0.603707 CGCCTTTCCAGCAGACTTGA 60.604 55.000 0.00 0.00 0.00 3.02 F
1966 2153 0.764890 ACAGGGTGCAAAGTAGCTCA 59.235 50.000 0.00 0.00 34.99 4.26 F
1967 2154 1.352352 ACAGGGTGCAAAGTAGCTCAT 59.648 47.619 0.00 0.00 34.99 2.90 F
3262 4600 1.808133 GCATCTCGTGGAAGGATGACC 60.808 57.143 6.38 0.00 39.12 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2181 0.113776 TGGTACTCCCTCCGTTCACT 59.886 55.000 0.00 0.00 0.00 3.41 R
3169 4505 0.680921 AAGTGATGTGGGAATGGCCG 60.681 55.000 0.00 0.00 37.63 6.13 R
3219 4557 5.633182 GCGTTTCCTGATTAAGCATGAAAAA 59.367 36.000 20.76 3.15 0.00 1.94 R
3349 4688 2.029649 AGCTGAATGGTTCACATGTTGC 60.030 45.455 0.00 0.00 40.44 4.17 R
3482 4821 2.569853 TCGGATTCTTACCCTGAAAGCA 59.430 45.455 0.00 0.00 0.00 3.91 R
4899 9074 0.512952 CGGAGCAAGGACAAAACGAG 59.487 55.000 0.00 0.00 0.00 4.18 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
249 250 0.379316 ATGTACGTACTCGCGCATCA 59.621 50.000 25.12 3.33 41.18 3.07
310 314 2.044650 TCTACGACCCAGTCCCCG 60.045 66.667 0.00 0.00 0.00 5.73
311 315 3.145551 CTACGACCCAGTCCCCGG 61.146 72.222 0.00 0.00 0.00 5.73
443 448 2.270874 GATTCCGACCCACAGCCCAT 62.271 60.000 0.00 0.00 0.00 4.00
447 452 2.659063 CGACCCACAGCCCATCTCA 61.659 63.158 0.00 0.00 0.00 3.27
459 464 3.144506 GCCCATCTCATCAATGTCGAAT 58.855 45.455 0.00 0.00 0.00 3.34
519 524 0.801836 CGCGGTCGGGTACGTATTTT 60.802 55.000 0.00 0.00 41.85 1.82
531 536 5.467735 GGGTACGTATTTTTGAACAGTGTCT 59.532 40.000 0.00 0.00 0.00 3.41
592 597 1.375908 ACATCCGCATGCGTCACTT 60.376 52.632 35.55 15.09 37.81 3.16
606 611 3.323243 CGTCACTTAACGTCCAGGATTT 58.677 45.455 0.00 0.00 37.86 2.17
619 624 3.012518 CCAGGATTTCGAGCTCATTTGT 58.987 45.455 15.40 0.00 0.00 2.83
623 628 2.975410 TTTCGAGCTCATTTGTGCTG 57.025 45.000 15.40 5.19 43.90 4.41
659 664 0.669318 CGTCCTGTTTTGCGCCTCTA 60.669 55.000 4.18 0.00 0.00 2.43
719 724 4.041917 TCGTGCCGACACCCGTAC 62.042 66.667 0.00 0.00 44.40 3.67
721 726 4.747529 GTGCCGACACCCGTACCC 62.748 72.222 0.00 0.00 41.21 3.69
723 728 4.006357 GCCGACACCCGTACCCAA 62.006 66.667 0.00 0.00 36.31 4.12
724 729 2.047939 CCGACACCCGTACCCAAC 60.048 66.667 0.00 0.00 36.31 3.77
857 961 1.359130 AGATGGAGGAAAAACAGGGGG 59.641 52.381 0.00 0.00 0.00 5.40
938 1089 0.615261 GAAGACCTTCGACCTCCCCT 60.615 60.000 0.00 0.00 0.00 4.79
949 1100 2.725008 CTCCCCTGCGATCTCGAC 59.275 66.667 3.33 0.00 43.02 4.20
974 1129 2.233605 ATCAATCCGGCCGTCGTTCA 62.234 55.000 26.12 1.96 37.11 3.18
976 1131 3.945304 AATCCGGCCGTCGTTCACC 62.945 63.158 26.12 0.00 37.11 4.02
1113 1268 1.511768 GCTCTTCTACCCGACGCTT 59.488 57.895 0.00 0.00 0.00 4.68
1221 1376 0.603707 TCGCCTTTCCAGCAGACTTG 60.604 55.000 0.00 0.00 0.00 3.16
1222 1377 0.603707 CGCCTTTCCAGCAGACTTGA 60.604 55.000 0.00 0.00 0.00 3.02
1223 1378 1.831580 GCCTTTCCAGCAGACTTGAT 58.168 50.000 0.00 0.00 0.00 2.57
1226 1381 3.269178 CCTTTCCAGCAGACTTGATCTC 58.731 50.000 0.00 0.00 34.41 2.75
1227 1382 3.269178 CTTTCCAGCAGACTTGATCTCC 58.731 50.000 0.00 0.00 34.41 3.71
1228 1383 1.942776 TCCAGCAGACTTGATCTCCA 58.057 50.000 0.00 0.00 34.41 3.86
1267 1438 8.043113 AGTGATTTGTCAGATGAGCAAGTAATA 58.957 33.333 0.00 0.00 0.00 0.98
1302 1473 4.537015 GTGAACTTTTAGATGCAAACGCT 58.463 39.130 0.00 0.00 0.00 5.07
1347 1522 8.749026 TTAAGTATAGTAACCTCTGTCCTGAG 57.251 38.462 0.00 0.00 0.00 3.35
1396 1571 9.288576 AGAAGAAACATTCATCTGAAATGTGTA 57.711 29.630 8.13 0.00 36.47 2.90
1402 1577 9.850628 AACATTCATCTGAAATGTGTAAATCTG 57.149 29.630 8.13 0.00 37.61 2.90
1501 1688 3.338249 GCTTCAGCAGATTGGTAGACAA 58.662 45.455 0.00 0.00 41.53 3.18
1903 2090 7.727331 TTTAAAGCAAACCCAGAATTGAATG 57.273 32.000 0.00 0.00 0.00 2.67
1904 2091 4.961438 AAGCAAACCCAGAATTGAATGT 57.039 36.364 0.00 0.00 0.00 2.71
1905 2092 6.418057 AAAGCAAACCCAGAATTGAATGTA 57.582 33.333 0.00 0.00 0.00 2.29
1906 2093 5.391312 AGCAAACCCAGAATTGAATGTAC 57.609 39.130 0.00 0.00 0.00 2.90
1907 2094 5.079643 AGCAAACCCAGAATTGAATGTACT 58.920 37.500 0.00 0.00 0.00 2.73
1908 2095 5.183904 AGCAAACCCAGAATTGAATGTACTC 59.816 40.000 0.00 0.00 0.00 2.59
1909 2096 5.622233 GCAAACCCAGAATTGAATGTACTCC 60.622 44.000 0.00 0.00 0.00 3.85
1910 2097 4.236527 ACCCAGAATTGAATGTACTCCC 57.763 45.455 0.00 0.00 0.00 4.30
1911 2098 3.852578 ACCCAGAATTGAATGTACTCCCT 59.147 43.478 0.00 0.00 0.00 4.20
1912 2099 4.080299 ACCCAGAATTGAATGTACTCCCTC 60.080 45.833 0.00 0.00 0.00 4.30
1913 2100 4.164988 CCCAGAATTGAATGTACTCCCTCT 59.835 45.833 0.00 0.00 0.00 3.69
1914 2101 5.121811 CCAGAATTGAATGTACTCCCTCTG 58.878 45.833 0.00 0.00 0.00 3.35
1915 2102 5.338708 CCAGAATTGAATGTACTCCCTCTGT 60.339 44.000 0.00 0.00 0.00 3.41
1916 2103 6.176183 CAGAATTGAATGTACTCCCTCTGTT 58.824 40.000 0.00 0.00 0.00 3.16
1917 2104 6.314896 CAGAATTGAATGTACTCCCTCTGTTC 59.685 42.308 0.00 0.00 0.00 3.18
1918 2105 5.762179 ATTGAATGTACTCCCTCTGTTCA 57.238 39.130 0.00 0.00 0.00 3.18
1919 2106 4.537135 TGAATGTACTCCCTCTGTTCAC 57.463 45.455 0.00 0.00 0.00 3.18
1920 2107 4.160329 TGAATGTACTCCCTCTGTTCACT 58.840 43.478 0.00 0.00 0.00 3.41
1921 2108 4.593206 TGAATGTACTCCCTCTGTTCACTT 59.407 41.667 0.00 0.00 0.00 3.16
1922 2109 5.071788 TGAATGTACTCCCTCTGTTCACTTT 59.928 40.000 0.00 0.00 0.00 2.66
1923 2110 5.568620 ATGTACTCCCTCTGTTCACTTTT 57.431 39.130 0.00 0.00 0.00 2.27
1924 2111 6.681729 ATGTACTCCCTCTGTTCACTTTTA 57.318 37.500 0.00 0.00 0.00 1.52
1925 2112 6.681729 TGTACTCCCTCTGTTCACTTTTAT 57.318 37.500 0.00 0.00 0.00 1.40
1926 2113 7.786046 TGTACTCCCTCTGTTCACTTTTATA 57.214 36.000 0.00 0.00 0.00 0.98
1927 2114 8.197592 TGTACTCCCTCTGTTCACTTTTATAA 57.802 34.615 0.00 0.00 0.00 0.98
1928 2115 8.311836 TGTACTCCCTCTGTTCACTTTTATAAG 58.688 37.037 0.00 0.00 37.40 1.73
1929 2116 6.712276 ACTCCCTCTGTTCACTTTTATAAGG 58.288 40.000 0.00 0.00 35.61 2.69
1930 2117 5.497474 TCCCTCTGTTCACTTTTATAAGGC 58.503 41.667 0.00 0.00 35.61 4.35
1931 2118 4.640647 CCCTCTGTTCACTTTTATAAGGCC 59.359 45.833 0.00 0.00 35.61 5.19
1932 2119 5.501156 CCTCTGTTCACTTTTATAAGGCCT 58.499 41.667 0.00 0.00 35.61 5.19
1933 2120 5.946377 CCTCTGTTCACTTTTATAAGGCCTT 59.054 40.000 24.18 24.18 35.61 4.35
1934 2121 6.127897 CCTCTGTTCACTTTTATAAGGCCTTG 60.128 42.308 28.77 12.48 35.61 3.61
1935 2122 6.539173 TCTGTTCACTTTTATAAGGCCTTGA 58.461 36.000 28.77 11.98 35.61 3.02
1936 2123 7.001674 TCTGTTCACTTTTATAAGGCCTTGAA 58.998 34.615 28.77 17.44 35.61 2.69
1937 2124 7.174946 TCTGTTCACTTTTATAAGGCCTTGAAG 59.825 37.037 28.77 24.09 35.61 3.02
1938 2125 7.001674 TGTTCACTTTTATAAGGCCTTGAAGA 58.998 34.615 28.77 15.87 35.61 2.87
1939 2126 7.040686 TGTTCACTTTTATAAGGCCTTGAAGAC 60.041 37.037 28.77 17.56 35.61 3.01
1940 2127 6.539173 TCACTTTTATAAGGCCTTGAAGACA 58.461 36.000 28.77 7.10 35.61 3.41
1941 2128 7.175104 TCACTTTTATAAGGCCTTGAAGACAT 58.825 34.615 28.77 14.50 35.61 3.06
1942 2129 7.669722 TCACTTTTATAAGGCCTTGAAGACATT 59.330 33.333 28.77 0.00 35.61 2.71
1943 2130 8.306761 CACTTTTATAAGGCCTTGAAGACATTT 58.693 33.333 28.77 0.00 35.61 2.32
1944 2131 8.523658 ACTTTTATAAGGCCTTGAAGACATTTC 58.476 33.333 28.77 0.00 35.61 2.17
1945 2132 8.415950 TTTTATAAGGCCTTGAAGACATTTCA 57.584 30.769 28.77 3.15 0.00 2.69
1946 2133 7.630242 TTATAAGGCCTTGAAGACATTTCAG 57.370 36.000 28.77 0.00 0.00 3.02
1947 2134 3.795688 AGGCCTTGAAGACATTTCAGA 57.204 42.857 0.00 0.00 0.00 3.27
1948 2135 3.416156 AGGCCTTGAAGACATTTCAGAC 58.584 45.455 0.00 0.00 0.00 3.51
1949 2136 3.149196 GGCCTTGAAGACATTTCAGACA 58.851 45.455 0.00 0.00 0.00 3.41
1950 2137 3.190118 GGCCTTGAAGACATTTCAGACAG 59.810 47.826 0.00 0.00 0.00 3.51
1951 2138 3.190118 GCCTTGAAGACATTTCAGACAGG 59.810 47.826 0.00 3.03 30.77 4.00
1952 2139 3.755378 CCTTGAAGACATTTCAGACAGGG 59.245 47.826 0.00 0.00 0.00 4.45
1953 2140 4.392940 CTTGAAGACATTTCAGACAGGGT 58.607 43.478 0.00 0.00 0.00 4.34
1954 2141 3.743521 TGAAGACATTTCAGACAGGGTG 58.256 45.455 0.00 0.00 0.00 4.61
1955 2142 2.191128 AGACATTTCAGACAGGGTGC 57.809 50.000 0.00 0.00 0.00 5.01
1956 2143 1.421268 AGACATTTCAGACAGGGTGCA 59.579 47.619 0.00 0.00 0.00 4.57
1957 2144 2.158623 AGACATTTCAGACAGGGTGCAA 60.159 45.455 0.00 0.00 0.00 4.08
1958 2145 2.622942 GACATTTCAGACAGGGTGCAAA 59.377 45.455 0.00 0.00 0.00 3.68
1959 2146 2.624838 ACATTTCAGACAGGGTGCAAAG 59.375 45.455 0.00 0.00 0.00 2.77
1960 2147 2.435372 TTTCAGACAGGGTGCAAAGT 57.565 45.000 0.00 0.00 0.00 2.66
1961 2148 3.569194 TTTCAGACAGGGTGCAAAGTA 57.431 42.857 0.00 0.00 0.00 2.24
1962 2149 2.839486 TCAGACAGGGTGCAAAGTAG 57.161 50.000 0.00 0.00 0.00 2.57
1963 2150 1.160137 CAGACAGGGTGCAAAGTAGC 58.840 55.000 0.00 0.00 0.00 3.58
1964 2151 1.059913 AGACAGGGTGCAAAGTAGCT 58.940 50.000 0.00 0.00 34.99 3.32
1965 2152 1.002544 AGACAGGGTGCAAAGTAGCTC 59.997 52.381 0.00 0.00 34.99 4.09
1966 2153 0.764890 ACAGGGTGCAAAGTAGCTCA 59.235 50.000 0.00 0.00 34.99 4.26
1967 2154 1.352352 ACAGGGTGCAAAGTAGCTCAT 59.648 47.619 0.00 0.00 34.99 2.90
1968 2155 2.224867 ACAGGGTGCAAAGTAGCTCATT 60.225 45.455 0.00 0.00 34.99 2.57
1969 2156 2.821969 CAGGGTGCAAAGTAGCTCATTT 59.178 45.455 0.00 0.00 34.99 2.32
1970 2157 3.256631 CAGGGTGCAAAGTAGCTCATTTT 59.743 43.478 0.00 0.00 34.99 1.82
1971 2158 3.507622 AGGGTGCAAAGTAGCTCATTTTC 59.492 43.478 0.00 0.00 34.99 2.29
1972 2159 3.255642 GGGTGCAAAGTAGCTCATTTTCA 59.744 43.478 0.00 0.00 34.99 2.69
1973 2160 4.479619 GGTGCAAAGTAGCTCATTTTCAG 58.520 43.478 0.00 0.00 34.99 3.02
1974 2161 4.022849 GGTGCAAAGTAGCTCATTTTCAGT 60.023 41.667 0.00 0.00 34.99 3.41
1975 2162 5.507985 GGTGCAAAGTAGCTCATTTTCAGTT 60.508 40.000 0.00 0.00 34.99 3.16
1976 2163 5.400485 GTGCAAAGTAGCTCATTTTCAGTTG 59.600 40.000 0.00 0.00 34.99 3.16
1977 2164 5.067674 TGCAAAGTAGCTCATTTTCAGTTGT 59.932 36.000 0.00 0.00 34.99 3.32
1978 2165 5.626955 GCAAAGTAGCTCATTTTCAGTTGTC 59.373 40.000 0.00 0.00 0.00 3.18
1979 2166 6.514048 GCAAAGTAGCTCATTTTCAGTTGTCT 60.514 38.462 0.00 0.00 0.00 3.41
1980 2167 6.551385 AAGTAGCTCATTTTCAGTTGTCTG 57.449 37.500 0.00 0.00 42.54 3.51
1995 2182 8.294341 TCAGTTGTCTGAACGACTTATAAAAG 57.706 34.615 0.00 0.00 46.14 2.27
1996 2183 7.924412 TCAGTTGTCTGAACGACTTATAAAAGT 59.076 33.333 0.00 0.00 46.14 2.66
1997 2184 8.004344 CAGTTGTCTGAACGACTTATAAAAGTG 58.996 37.037 0.00 0.00 46.14 3.16
1998 2185 7.924412 AGTTGTCTGAACGACTTATAAAAGTGA 59.076 33.333 0.00 0.00 46.14 3.41
1999 2186 8.545420 GTTGTCTGAACGACTTATAAAAGTGAA 58.455 33.333 0.00 0.00 46.09 3.18
2000 2187 8.068893 TGTCTGAACGACTTATAAAAGTGAAC 57.931 34.615 0.00 0.00 46.09 3.18
2001 2188 7.096353 TGTCTGAACGACTTATAAAAGTGAACG 60.096 37.037 0.00 0.00 46.09 3.95
2002 2189 6.364165 TCTGAACGACTTATAAAAGTGAACGG 59.636 38.462 0.00 0.00 46.09 4.44
2003 2190 6.215121 TGAACGACTTATAAAAGTGAACGGA 58.785 36.000 0.00 0.00 46.09 4.69
2004 2191 6.364165 TGAACGACTTATAAAAGTGAACGGAG 59.636 38.462 0.00 0.00 46.09 4.63
2005 2192 5.166398 ACGACTTATAAAAGTGAACGGAGG 58.834 41.667 0.00 0.00 46.09 4.30
2006 2193 4.565564 CGACTTATAAAAGTGAACGGAGGG 59.434 45.833 0.00 0.00 46.09 4.30
2007 2194 5.622914 CGACTTATAAAAGTGAACGGAGGGA 60.623 44.000 0.00 0.00 46.09 4.20
2116 2404 5.043248 GTCTGGTTTGATGTTTTCCAACAG 58.957 41.667 0.00 0.00 46.25 3.16
2117 2405 3.791245 TGGTTTGATGTTTTCCAACAGC 58.209 40.909 0.00 0.00 46.25 4.40
2137 2467 5.180117 ACAGCTTCATAGTGTCATGTTTGTC 59.820 40.000 0.00 0.00 0.00 3.18
2183 2515 4.249638 AGGCCTGCCTGATGTATTTTTA 57.750 40.909 10.51 0.00 46.22 1.52
2350 3543 9.931210 GTATATGGTACTTTTACATTTGCTCAC 57.069 33.333 0.00 0.00 0.00 3.51
2382 3592 9.502091 TGCTGTTTATTATCAGTTTTAGTCACT 57.498 29.630 0.00 0.00 34.57 3.41
2416 3626 4.516698 GTGTCAGTTTCCTCATTCACACAT 59.483 41.667 0.00 0.00 34.36 3.21
2479 3689 3.386768 TGCTGGTTCTGTGTACTTCTC 57.613 47.619 0.00 0.00 0.00 2.87
2545 3868 5.163834 GCCTTTGGTTTTGCATTATGTGATG 60.164 40.000 0.00 0.00 0.00 3.07
2553 3876 7.201548 GGTTTTGCATTATGTGATGGTGAATTC 60.202 37.037 0.00 0.00 0.00 2.17
2561 3884 5.565592 TGTGATGGTGAATTCTAATGCAC 57.434 39.130 7.05 5.38 43.04 4.57
2700 4030 6.560253 TCTCTTTACCAGTTCATTTTGCTC 57.440 37.500 0.00 0.00 0.00 4.26
2797 4127 7.284074 TGAACCATTTGAGACTTTAGTACCAA 58.716 34.615 0.00 0.00 0.00 3.67
2808 4138 9.733219 GAGACTTTAGTACCAACATCAGTATAC 57.267 37.037 0.00 0.00 0.00 1.47
2867 4202 3.124578 TGAACAGCATTGTACAGAGCA 57.875 42.857 19.59 0.00 36.23 4.26
3178 4514 1.947456 GATGAAGTTACCGGCCATTCC 59.053 52.381 0.00 0.00 0.00 3.01
3262 4600 1.808133 GCATCTCGTGGAAGGATGACC 60.808 57.143 6.38 0.00 39.12 4.02
3292 4630 2.034221 AAAGCTGGAAGGGGACGC 59.966 61.111 0.00 0.00 0.00 5.19
3330 4669 6.091441 GTCTTGTGCTATCTGGTAAGTTTCTG 59.909 42.308 0.00 0.00 0.00 3.02
3337 4676 8.103305 TGCTATCTGGTAAGTTTCTGATTCTTT 58.897 33.333 1.44 0.00 0.00 2.52
3361 4700 7.985634 TTTTTAGAGAAAGCAACATGTGAAC 57.014 32.000 0.00 0.00 0.00 3.18
3380 4719 7.422399 TGTGAACCATTCAGCTAAAAACTTAC 58.578 34.615 0.00 0.00 41.01 2.34
3453 4792 6.706270 GGCTATAATCTAAAACAGCTACAGCA 59.294 38.462 3.70 0.00 45.16 4.41
3482 4821 7.968405 GCTATTTACTGAAATCACGGTTTTCAT 59.032 33.333 8.09 3.40 41.03 2.57
3489 4828 4.582701 AATCACGGTTTTCATGCTTTCA 57.417 36.364 0.00 0.00 0.00 2.69
3493 4832 1.613437 CGGTTTTCATGCTTTCAGGGT 59.387 47.619 0.00 0.00 0.00 4.34
3497 4836 4.522789 GGTTTTCATGCTTTCAGGGTAAGA 59.477 41.667 0.00 0.00 0.00 2.10
3499 4838 6.295292 GGTTTTCATGCTTTCAGGGTAAGAAT 60.295 38.462 0.00 0.00 0.00 2.40
3597 4936 5.627499 TTGTATTGTGCTTCAGTGGAATC 57.373 39.130 0.00 0.00 31.34 2.52
3724 5063 4.895889 CAGAGGAAGGTACTGGACATATCA 59.104 45.833 0.00 0.00 40.86 2.15
3831 5170 8.995220 GTGACAAGTTCCATACATTAAGTTACA 58.005 33.333 0.00 0.00 0.00 2.41
3923 5344 7.436673 GTGGTGATAGCTGATAACTAACTGAAG 59.563 40.741 0.00 0.00 0.00 3.02
3957 5378 1.306226 ACTTTAGCGCCCTCTCCCT 60.306 57.895 2.29 0.00 0.00 4.20
3960 5381 1.956629 TTTAGCGCCCTCTCCCTTCG 61.957 60.000 2.29 0.00 0.00 3.79
4034 5456 1.817099 GGAACATCGCTGCCAGGAG 60.817 63.158 0.00 0.00 0.00 3.69
4195 8365 2.742589 GCTACCTGTAAACTGCTTGGAC 59.257 50.000 0.00 0.00 0.00 4.02
4427 8598 5.319043 TGTTGGTCCTTTGGTAGAAGATT 57.681 39.130 0.00 0.00 0.00 2.40
4487 8658 7.278135 ACTCCTACTTAAATATTTTCCCGTCC 58.722 38.462 5.91 0.00 0.00 4.79
4516 8687 2.947652 CTGATAATGGCAGGTGGTTCAG 59.052 50.000 0.00 0.00 0.00 3.02
4606 8777 1.471684 CAAACTGAAGATGGCTCTGGC 59.528 52.381 0.00 0.00 37.82 4.85
4650 8821 1.860484 GCCAGCTTGCCTTCTCACAC 61.860 60.000 0.00 0.00 0.00 3.82
4710 8881 2.269241 CCTGCTTCCTTCCCCGAC 59.731 66.667 0.00 0.00 0.00 4.79
4816 8988 2.202932 ATGTGGAGCCGATGCGAC 60.203 61.111 0.00 0.00 44.33 5.19
4891 9064 1.656594 TGTTCTCACGTTGTTGTGTCG 59.343 47.619 0.00 0.00 40.74 4.35
4893 9066 0.456628 TCTCACGTTGTTGTGTCGGA 59.543 50.000 0.00 0.00 40.74 4.55
4894 9067 1.067974 TCTCACGTTGTTGTGTCGGAT 59.932 47.619 0.00 0.00 40.74 4.18
4895 9068 1.455786 CTCACGTTGTTGTGTCGGATC 59.544 52.381 0.00 0.00 40.74 3.36
4899 9074 1.398451 CGTTGTTGTGTCGGATCAAGC 60.398 52.381 0.00 0.00 0.00 4.01
4906 9081 1.798813 GTGTCGGATCAAGCTCGTTTT 59.201 47.619 0.00 0.00 0.00 2.43
5012 9195 3.519510 CAGGACCAGGACCTCTGATTTTA 59.480 47.826 7.63 0.00 46.18 1.52
5017 9200 7.036863 AGGACCAGGACCTCTGATTTTATTTTA 60.037 37.037 4.34 0.00 46.18 1.52
5109 9292 1.019278 TGCGGAGTTTCGAGATTGGC 61.019 55.000 0.00 0.00 0.00 4.52
5127 9310 2.351418 TGGCGAAATCAGATAAGTTGCG 59.649 45.455 0.00 0.00 0.00 4.85
5132 9315 4.026475 CGAAATCAGATAAGTTGCGGAGTC 60.026 45.833 0.00 0.00 0.00 3.36
5135 9318 3.089284 TCAGATAAGTTGCGGAGTCTCA 58.911 45.455 1.47 0.00 0.00 3.27
5146 9329 1.800655 CGGAGTCTCAAGATTGGCGAG 60.801 57.143 1.47 0.00 0.00 5.03
5150 9333 2.762887 AGTCTCAAGATTGGCGAGATCA 59.237 45.455 0.00 0.00 38.05 2.92
5166 9349 4.295051 GAGATCAGATAAGTTGCGGAGTC 58.705 47.826 0.00 0.00 0.00 3.36
5174 9357 1.178276 AGTTGCGGAGTCTCGAGATT 58.822 50.000 19.90 15.24 0.00 2.40
5194 9377 3.969795 GCGAAATCGACAGTTTCCC 57.030 52.632 7.06 0.00 43.02 3.97
5195 9378 0.094730 GCGAAATCGACAGTTTCCCG 59.905 55.000 7.06 0.00 43.02 5.14
5196 9379 1.425412 CGAAATCGACAGTTTCCCGT 58.575 50.000 0.00 0.00 43.02 5.28
5197 9380 1.389106 CGAAATCGACAGTTTCCCGTC 59.611 52.381 0.00 0.00 43.02 4.79
5281 9465 1.079405 GGGCACCGAATCTCGTTGA 60.079 57.895 0.00 0.00 40.86 3.18
5439 9631 3.701205 AATCCCCAAAGCAAATGGTTC 57.299 42.857 0.00 0.00 36.14 3.62
5484 9676 7.066142 TCTTCTCTGATGATAGCTACCTCTTT 58.934 38.462 0.00 0.00 0.00 2.52
5521 9713 3.999663 CCACTTGTCATGAGAGGTTCTTC 59.000 47.826 4.75 0.00 0.00 2.87
5582 9775 8.480501 AGTAGTATTACATCCGTACCAAAATGT 58.519 33.333 0.00 0.00 36.40 2.71
5588 9781 5.801380 ACATCCGTACCAAAATGTAAGACT 58.199 37.500 0.00 0.00 30.84 3.24
5637 9830 9.691362 ACACAAAACATCTTATATTTTGACACC 57.309 29.630 13.87 0.00 43.07 4.16
5640 9833 9.277565 CAAAACATCTTATATTTTGACACCGAG 57.722 33.333 3.19 0.00 43.07 4.63
5653 9846 5.970317 TGACACCGAGATAGTACTTTTGA 57.030 39.130 0.00 0.00 0.00 2.69
5665 9858 2.172851 ACTTTTGAACCGTCGCCATA 57.827 45.000 0.00 0.00 0.00 2.74
5666 9859 1.802365 ACTTTTGAACCGTCGCCATAC 59.198 47.619 0.00 0.00 0.00 2.39
5750 9943 7.284716 TCTCTAACTCGCCAATGAGAACTATTA 59.715 37.037 0.00 0.00 39.35 0.98
5751 9944 7.778083 TCTAACTCGCCAATGAGAACTATTAA 58.222 34.615 0.00 0.00 39.35 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 4.256180 GCCCCCTATGTCGGCAGG 62.256 72.222 0.00 0.00 42.52 4.85
249 250 1.849975 ATGGAGTTCCTGCTGCAGCT 61.850 55.000 36.61 17.94 40.05 4.24
310 314 2.101700 CGGAGCTCATTTGGAAGCC 58.898 57.895 17.19 0.00 0.00 4.35
342 346 2.554893 GGTGGGTTCACGCAGAAAATTA 59.445 45.455 0.00 0.00 44.50 1.40
443 448 3.447742 CGTCCATTCGACATTGATGAGA 58.552 45.455 0.00 0.00 42.07 3.27
447 452 2.315925 AGCGTCCATTCGACATTGAT 57.684 45.000 0.00 0.00 42.07 2.57
519 524 5.129634 TGCCAGAAAATAGACACTGTTCAA 58.870 37.500 0.00 0.00 0.00 2.69
531 536 0.407528 TGGTGGGCTGCCAGAAAATA 59.592 50.000 22.05 0.00 0.00 1.40
592 597 1.822990 AGCTCGAAATCCTGGACGTTA 59.177 47.619 0.00 0.00 0.00 3.18
606 611 1.300971 GCCAGCACAAATGAGCTCGA 61.301 55.000 9.64 0.00 39.92 4.04
623 628 0.739813 ACGTGGAGTTATTGAGCGCC 60.740 55.000 2.29 0.00 0.00 6.53
687 692 2.812178 CGACACGGCCCGTTTAGG 60.812 66.667 5.76 0.00 38.32 2.69
712 717 2.931649 CTGGGGTTGGGTACGGGT 60.932 66.667 0.00 0.00 0.00 5.28
713 718 3.723922 CCTGGGGTTGGGTACGGG 61.724 72.222 0.00 0.00 0.00 5.28
716 721 0.991893 ATAGCCCTGGGGTTGGGTAC 60.992 60.000 24.43 0.00 46.22 3.34
718 723 1.546460 AATAGCCCTGGGGTTGGGT 60.546 57.895 24.43 4.40 46.22 4.51
720 725 1.076044 CCAATAGCCCTGGGGTTGG 60.076 63.158 24.43 21.07 34.21 3.77
721 726 0.395724 GTCCAATAGCCCTGGGGTTG 60.396 60.000 24.43 15.91 37.65 3.77
722 727 1.580994 GGTCCAATAGCCCTGGGGTT 61.581 60.000 24.43 8.45 37.65 4.11
723 728 2.006991 GGTCCAATAGCCCTGGGGT 61.007 63.158 22.77 22.77 37.65 4.95
724 729 2.927056 GGTCCAATAGCCCTGGGG 59.073 66.667 16.03 4.75 34.46 4.96
766 771 2.436521 GGGTTGAACCAAACCTGGG 58.563 57.895 17.27 0.00 46.75 4.45
838 942 1.357761 TCCCCCTGTTTTTCCTCCATC 59.642 52.381 0.00 0.00 0.00 3.51
841 945 2.391926 TTTCCCCCTGTTTTTCCTCC 57.608 50.000 0.00 0.00 0.00 4.30
904 1055 3.708220 CTTCCGACGAGCTGGCCTC 62.708 68.421 3.32 0.00 37.22 4.70
938 1089 2.954020 GATTGCCCGTCGAGATCGCA 62.954 60.000 0.00 0.00 39.60 5.10
949 1100 3.595758 GGCCGGATTGATTGCCCG 61.596 66.667 5.05 0.00 42.64 6.13
1050 1205 3.724914 CTCCTTCGCCTTCCTCCGC 62.725 68.421 0.00 0.00 0.00 5.54
1113 1268 2.160205 CTCCTCACCACGTTGTAGAGA 58.840 52.381 15.77 3.77 0.00 3.10
1223 1378 0.749818 CTAGGCAGTCTCGCTGGAGA 60.750 60.000 0.00 0.00 46.90 3.71
1226 1381 1.140589 CACTAGGCAGTCTCGCTGG 59.859 63.158 0.00 0.00 45.14 4.85
1228 1383 1.479709 AATCACTAGGCAGTCTCGCT 58.520 50.000 0.00 0.00 30.46 4.93
1237 1408 3.559242 GCTCATCTGACAAATCACTAGGC 59.441 47.826 0.00 0.00 0.00 3.93
1267 1438 1.144057 GTTCACCGCGATGGAGGAT 59.856 57.895 8.23 0.00 42.00 3.24
1326 1497 7.992033 TCTAACTCAGGACAGAGGTTACTATAC 59.008 40.741 0.00 0.00 39.97 1.47
1331 1502 5.979288 TTCTAACTCAGGACAGAGGTTAC 57.021 43.478 0.00 0.00 39.97 2.50
1343 1518 8.127327 CACTCCAAATAATGCATTCTAACTCAG 58.873 37.037 16.86 7.74 0.00 3.35
1347 1522 8.213518 TCTCACTCCAAATAATGCATTCTAAC 57.786 34.615 16.86 0.00 0.00 2.34
1396 1571 0.609131 CAGCCCCACGGAACAGATTT 60.609 55.000 0.00 0.00 0.00 2.17
1402 1577 2.358737 CTGACAGCCCCACGGAAC 60.359 66.667 0.00 0.00 0.00 3.62
1484 1671 2.636830 CCCTTGTCTACCAATCTGCTG 58.363 52.381 0.00 0.00 31.20 4.41
1865 2052 8.752254 GGTTTGCTTTAAAATTACAGAGAACAC 58.248 33.333 0.00 0.00 0.00 3.32
1866 2053 7.923878 GGGTTTGCTTTAAAATTACAGAGAACA 59.076 33.333 0.00 0.00 0.00 3.18
1867 2054 7.923878 TGGGTTTGCTTTAAAATTACAGAGAAC 59.076 33.333 0.00 0.00 0.00 3.01
1868 2055 8.012957 TGGGTTTGCTTTAAAATTACAGAGAA 57.987 30.769 0.00 0.00 0.00 2.87
1869 2056 7.504238 TCTGGGTTTGCTTTAAAATTACAGAGA 59.496 33.333 0.00 0.00 30.00 3.10
1870 2057 7.657336 TCTGGGTTTGCTTTAAAATTACAGAG 58.343 34.615 0.00 0.00 30.00 3.35
1871 2058 7.589958 TCTGGGTTTGCTTTAAAATTACAGA 57.410 32.000 0.00 0.00 0.00 3.41
1872 2059 8.831715 ATTCTGGGTTTGCTTTAAAATTACAG 57.168 30.769 0.00 0.00 0.00 2.74
1873 2060 9.050601 CAATTCTGGGTTTGCTTTAAAATTACA 57.949 29.630 0.00 0.00 0.00 2.41
1874 2061 9.267084 TCAATTCTGGGTTTGCTTTAAAATTAC 57.733 29.630 0.00 0.00 0.00 1.89
1875 2062 9.838339 TTCAATTCTGGGTTTGCTTTAAAATTA 57.162 25.926 0.00 0.00 0.00 1.40
1876 2063 8.744568 TTCAATTCTGGGTTTGCTTTAAAATT 57.255 26.923 0.00 0.00 0.00 1.82
1877 2064 8.785946 CATTCAATTCTGGGTTTGCTTTAAAAT 58.214 29.630 0.00 0.00 0.00 1.82
1878 2065 7.772757 ACATTCAATTCTGGGTTTGCTTTAAAA 59.227 29.630 0.00 0.00 0.00 1.52
1879 2066 7.278875 ACATTCAATTCTGGGTTTGCTTTAAA 58.721 30.769 0.00 0.00 0.00 1.52
1880 2067 6.825610 ACATTCAATTCTGGGTTTGCTTTAA 58.174 32.000 0.00 0.00 0.00 1.52
1881 2068 6.418057 ACATTCAATTCTGGGTTTGCTTTA 57.582 33.333 0.00 0.00 0.00 1.85
1882 2069 5.294734 ACATTCAATTCTGGGTTTGCTTT 57.705 34.783 0.00 0.00 0.00 3.51
1883 2070 4.961438 ACATTCAATTCTGGGTTTGCTT 57.039 36.364 0.00 0.00 0.00 3.91
1884 2071 5.079643 AGTACATTCAATTCTGGGTTTGCT 58.920 37.500 0.00 0.00 0.00 3.91
1890 2077 4.164988 AGAGGGAGTACATTCAATTCTGGG 59.835 45.833 0.00 0.00 0.00 4.45
1903 2090 7.764901 CCTTATAAAAGTGAACAGAGGGAGTAC 59.235 40.741 0.00 0.00 0.00 2.73
1904 2091 7.580882 GCCTTATAAAAGTGAACAGAGGGAGTA 60.581 40.741 0.00 0.00 0.00 2.59
1905 2092 6.712276 CCTTATAAAAGTGAACAGAGGGAGT 58.288 40.000 0.00 0.00 0.00 3.85
1906 2093 5.586643 GCCTTATAAAAGTGAACAGAGGGAG 59.413 44.000 0.00 0.00 0.00 4.30
1907 2094 5.497474 GCCTTATAAAAGTGAACAGAGGGA 58.503 41.667 0.00 0.00 0.00 4.20
1908 2095 4.640647 GGCCTTATAAAAGTGAACAGAGGG 59.359 45.833 0.00 0.00 0.00 4.30
1909 2096 5.501156 AGGCCTTATAAAAGTGAACAGAGG 58.499 41.667 0.00 0.00 0.00 3.69
1910 2097 6.655003 TCAAGGCCTTATAAAAGTGAACAGAG 59.345 38.462 20.00 0.00 0.00 3.35
1911 2098 6.539173 TCAAGGCCTTATAAAAGTGAACAGA 58.461 36.000 20.00 2.74 0.00 3.41
1912 2099 6.817765 TCAAGGCCTTATAAAAGTGAACAG 57.182 37.500 20.00 0.00 0.00 3.16
1913 2100 7.001674 TCTTCAAGGCCTTATAAAAGTGAACA 58.998 34.615 20.00 0.21 0.00 3.18
1914 2101 7.040686 TGTCTTCAAGGCCTTATAAAAGTGAAC 60.041 37.037 20.00 13.04 0.00 3.18
1915 2102 7.001674 TGTCTTCAAGGCCTTATAAAAGTGAA 58.998 34.615 20.00 14.48 0.00 3.18
1916 2103 6.539173 TGTCTTCAAGGCCTTATAAAAGTGA 58.461 36.000 20.00 6.54 0.00 3.41
1917 2104 6.817765 TGTCTTCAAGGCCTTATAAAAGTG 57.182 37.500 20.00 3.72 0.00 3.16
1918 2105 8.422577 AAATGTCTTCAAGGCCTTATAAAAGT 57.577 30.769 20.00 0.00 0.00 2.66
1919 2106 8.522830 TGAAATGTCTTCAAGGCCTTATAAAAG 58.477 33.333 20.00 18.05 0.00 2.27
1920 2107 8.415950 TGAAATGTCTTCAAGGCCTTATAAAA 57.584 30.769 20.00 9.43 0.00 1.52
1921 2108 7.888021 TCTGAAATGTCTTCAAGGCCTTATAAA 59.112 33.333 20.00 11.96 0.00 1.40
1922 2109 7.336931 GTCTGAAATGTCTTCAAGGCCTTATAA 59.663 37.037 20.00 14.54 0.00 0.98
1923 2110 6.823689 GTCTGAAATGTCTTCAAGGCCTTATA 59.176 38.462 20.00 6.65 0.00 0.98
1924 2111 5.649831 GTCTGAAATGTCTTCAAGGCCTTAT 59.350 40.000 20.00 3.68 0.00 1.73
1925 2112 5.003804 GTCTGAAATGTCTTCAAGGCCTTA 58.996 41.667 20.00 2.00 0.00 2.69
1926 2113 3.823304 GTCTGAAATGTCTTCAAGGCCTT 59.177 43.478 13.78 13.78 0.00 4.35
1927 2114 3.181440 TGTCTGAAATGTCTTCAAGGCCT 60.181 43.478 0.00 0.00 0.00 5.19
1928 2115 3.149196 TGTCTGAAATGTCTTCAAGGCC 58.851 45.455 0.00 0.00 0.00 5.19
1929 2116 3.190118 CCTGTCTGAAATGTCTTCAAGGC 59.810 47.826 0.00 0.00 0.00 4.35
1930 2117 3.755378 CCCTGTCTGAAATGTCTTCAAGG 59.245 47.826 0.00 0.00 0.00 3.61
1931 2118 4.214971 CACCCTGTCTGAAATGTCTTCAAG 59.785 45.833 0.00 0.00 0.00 3.02
1932 2119 4.136796 CACCCTGTCTGAAATGTCTTCAA 58.863 43.478 0.00 0.00 0.00 2.69
1933 2120 3.743521 CACCCTGTCTGAAATGTCTTCA 58.256 45.455 0.00 0.00 0.00 3.02
1934 2121 2.485814 GCACCCTGTCTGAAATGTCTTC 59.514 50.000 0.00 0.00 0.00 2.87
1935 2122 2.158623 TGCACCCTGTCTGAAATGTCTT 60.159 45.455 0.00 0.00 0.00 3.01
1936 2123 1.421268 TGCACCCTGTCTGAAATGTCT 59.579 47.619 0.00 0.00 0.00 3.41
1937 2124 1.896220 TGCACCCTGTCTGAAATGTC 58.104 50.000 0.00 0.00 0.00 3.06
1938 2125 2.363306 TTGCACCCTGTCTGAAATGT 57.637 45.000 0.00 0.00 0.00 2.71
1939 2126 2.624838 ACTTTGCACCCTGTCTGAAATG 59.375 45.455 0.00 0.00 0.00 2.32
1940 2127 2.949447 ACTTTGCACCCTGTCTGAAAT 58.051 42.857 0.00 0.00 0.00 2.17
1941 2128 2.435372 ACTTTGCACCCTGTCTGAAA 57.565 45.000 0.00 0.00 0.00 2.69
1942 2129 2.810400 GCTACTTTGCACCCTGTCTGAA 60.810 50.000 0.00 0.00 0.00 3.02
1943 2130 1.270839 GCTACTTTGCACCCTGTCTGA 60.271 52.381 0.00 0.00 0.00 3.27
1944 2131 1.160137 GCTACTTTGCACCCTGTCTG 58.840 55.000 0.00 0.00 0.00 3.51
1945 2132 1.002544 GAGCTACTTTGCACCCTGTCT 59.997 52.381 0.00 0.00 34.99 3.41
1946 2133 1.270839 TGAGCTACTTTGCACCCTGTC 60.271 52.381 0.00 0.00 34.99 3.51
1947 2134 0.764890 TGAGCTACTTTGCACCCTGT 59.235 50.000 0.00 0.00 34.99 4.00
1948 2135 2.119801 ATGAGCTACTTTGCACCCTG 57.880 50.000 0.00 0.00 34.99 4.45
1949 2136 2.887151 AATGAGCTACTTTGCACCCT 57.113 45.000 0.00 0.00 34.99 4.34
1950 2137 3.255642 TGAAAATGAGCTACTTTGCACCC 59.744 43.478 0.00 0.00 34.99 4.61
1951 2138 4.022849 ACTGAAAATGAGCTACTTTGCACC 60.023 41.667 0.00 0.00 34.99 5.01
1952 2139 5.113502 ACTGAAAATGAGCTACTTTGCAC 57.886 39.130 0.00 0.00 34.99 4.57
1953 2140 5.067674 ACAACTGAAAATGAGCTACTTTGCA 59.932 36.000 0.00 0.00 34.99 4.08
1954 2141 5.523369 ACAACTGAAAATGAGCTACTTTGC 58.477 37.500 0.00 0.00 0.00 3.68
1955 2142 6.854892 CAGACAACTGAAAATGAGCTACTTTG 59.145 38.462 0.00 0.00 46.03 2.77
1956 2143 6.963796 CAGACAACTGAAAATGAGCTACTTT 58.036 36.000 0.00 0.00 46.03 2.66
1957 2144 6.551385 CAGACAACTGAAAATGAGCTACTT 57.449 37.500 0.00 0.00 46.03 2.24
1977 2164 6.364165 CCGTTCACTTTTATAAGTCGTTCAGA 59.636 38.462 0.00 0.00 42.67 3.27
1978 2165 6.364165 TCCGTTCACTTTTATAAGTCGTTCAG 59.636 38.462 0.00 0.00 42.67 3.02
1979 2166 6.215121 TCCGTTCACTTTTATAAGTCGTTCA 58.785 36.000 0.00 0.00 42.67 3.18
1980 2167 6.183360 CCTCCGTTCACTTTTATAAGTCGTTC 60.183 42.308 0.00 0.00 42.67 3.95
1981 2168 5.636543 CCTCCGTTCACTTTTATAAGTCGTT 59.363 40.000 0.00 0.00 42.67 3.85
1982 2169 5.166398 CCTCCGTTCACTTTTATAAGTCGT 58.834 41.667 0.00 0.00 42.67 4.34
1983 2170 4.565564 CCCTCCGTTCACTTTTATAAGTCG 59.434 45.833 0.00 0.00 42.67 4.18
1984 2171 5.727434 TCCCTCCGTTCACTTTTATAAGTC 58.273 41.667 0.00 0.00 42.67 3.01
1985 2172 5.247792 ACTCCCTCCGTTCACTTTTATAAGT 59.752 40.000 0.00 0.00 45.40 2.24
1986 2173 5.731591 ACTCCCTCCGTTCACTTTTATAAG 58.268 41.667 0.00 0.00 37.40 1.73
1987 2174 5.750352 ACTCCCTCCGTTCACTTTTATAA 57.250 39.130 0.00 0.00 0.00 0.98
1988 2175 5.127682 GGTACTCCCTCCGTTCACTTTTATA 59.872 44.000 0.00 0.00 0.00 0.98
1989 2176 4.081254 GGTACTCCCTCCGTTCACTTTTAT 60.081 45.833 0.00 0.00 0.00 1.40
1990 2177 3.259123 GGTACTCCCTCCGTTCACTTTTA 59.741 47.826 0.00 0.00 0.00 1.52
1991 2178 2.038164 GGTACTCCCTCCGTTCACTTTT 59.962 50.000 0.00 0.00 0.00 2.27
1992 2179 1.622312 GGTACTCCCTCCGTTCACTTT 59.378 52.381 0.00 0.00 0.00 2.66
1993 2180 1.264295 GGTACTCCCTCCGTTCACTT 58.736 55.000 0.00 0.00 0.00 3.16
1994 2181 0.113776 TGGTACTCCCTCCGTTCACT 59.886 55.000 0.00 0.00 0.00 3.41
1995 2182 1.134788 CATGGTACTCCCTCCGTTCAC 60.135 57.143 0.00 0.00 0.00 3.18
1996 2183 1.191535 CATGGTACTCCCTCCGTTCA 58.808 55.000 0.00 0.00 0.00 3.18
1997 2184 1.192428 ACATGGTACTCCCTCCGTTC 58.808 55.000 0.00 0.00 0.00 3.95
1998 2185 1.652947 AACATGGTACTCCCTCCGTT 58.347 50.000 0.00 0.00 0.00 4.44
1999 2186 1.278127 CAAACATGGTACTCCCTCCGT 59.722 52.381 0.00 0.00 0.00 4.69
2000 2187 1.406887 CCAAACATGGTACTCCCTCCG 60.407 57.143 0.00 0.00 0.00 4.63
2001 2188 1.064685 CCCAAACATGGTACTCCCTCC 60.065 57.143 0.00 0.00 0.00 4.30
2002 2189 1.633945 ACCCAAACATGGTACTCCCTC 59.366 52.381 0.00 0.00 33.26 4.30
2003 2190 1.354368 CACCCAAACATGGTACTCCCT 59.646 52.381 0.00 0.00 33.84 4.20
2004 2191 1.834188 CACCCAAACATGGTACTCCC 58.166 55.000 0.00 0.00 33.84 4.30
2005 2192 1.173913 GCACCCAAACATGGTACTCC 58.826 55.000 0.00 0.00 33.84 3.85
2006 2193 2.084546 GAGCACCCAAACATGGTACTC 58.915 52.381 0.00 0.00 38.69 2.59
2007 2194 1.705186 AGAGCACCCAAACATGGTACT 59.295 47.619 0.00 0.00 33.84 2.73
2116 2404 5.869753 AGACAAACATGACACTATGAAGC 57.130 39.130 0.00 0.00 0.00 3.86
2117 2405 8.759641 GCTATAGACAAACATGACACTATGAAG 58.240 37.037 3.21 0.00 0.00 3.02
2137 2467 2.542618 CGTCTGGTCAGTGCAGCTATAG 60.543 54.545 0.00 0.00 0.00 1.31
2183 2515 5.942236 TCTGCTCATTTGTGCTTTAAGAGAT 59.058 36.000 0.00 0.00 35.73 2.75
2197 2529 7.698506 TCTGAATTCTGATTTCTGCTCATTT 57.301 32.000 10.68 0.00 0.00 2.32
2203 2535 4.157289 TGGCTTCTGAATTCTGATTTCTGC 59.843 41.667 14.89 13.12 0.00 4.26
2267 2599 3.316029 TGCTTGTTTCTCACTTCACCATG 59.684 43.478 0.00 0.00 0.00 3.66
2382 3592 5.680619 AGGAAACTGACACAATGTAGAACA 58.319 37.500 0.00 0.00 41.13 3.18
2416 3626 6.834969 ACCATGGTCATGATCACAATAATCAA 59.165 34.615 13.00 0.00 41.20 2.57
2545 3868 6.150140 ACAGAAAGAGTGCATTAGAATTCACC 59.850 38.462 8.44 0.00 33.82 4.02
2553 3876 6.551385 ACTCAAACAGAAAGAGTGCATTAG 57.449 37.500 0.00 0.00 40.83 1.73
2608 3934 9.685828 GTTAGAATAAGAGCATAGAACCTAGTG 57.314 37.037 0.00 0.00 0.00 2.74
2797 4127 6.594159 GTGTTACTTGCCTTGTATACTGATGT 59.406 38.462 4.17 0.00 0.00 3.06
2808 4138 7.945033 AATTATTTGTGTGTTACTTGCCTTG 57.055 32.000 0.00 0.00 0.00 3.61
2851 4186 5.335127 GGTTAAATGCTCTGTACAATGCTG 58.665 41.667 17.10 0.00 0.00 4.41
2867 4202 7.648039 TCCGTGCAATTATAAAGGGTTAAAT 57.352 32.000 0.00 0.00 0.00 1.40
3154 4490 3.080300 TGGCCGGTAACTTCATCATTT 57.920 42.857 1.90 0.00 0.00 2.32
3155 4491 2.799126 TGGCCGGTAACTTCATCATT 57.201 45.000 1.90 0.00 0.00 2.57
3169 4505 0.680921 AAGTGATGTGGGAATGGCCG 60.681 55.000 0.00 0.00 37.63 6.13
3219 4557 5.633182 GCGTTTCCTGATTAAGCATGAAAAA 59.367 36.000 20.76 3.15 0.00 1.94
3253 4591 5.894298 TGCAGTGAATATAGGTCATCCTT 57.106 39.130 0.00 0.00 42.12 3.36
3262 4600 5.008415 CCTTCCAGCTTTGCAGTGAATATAG 59.992 44.000 0.00 0.00 0.00 1.31
3292 4630 3.494626 AGCACAAGACAATCGTTGTACTG 59.505 43.478 3.83 6.70 45.52 2.74
3337 4676 6.978080 GGTTCACATGTTGCTTTCTCTAAAAA 59.022 34.615 0.00 0.00 0.00 1.94
3349 4688 2.029649 AGCTGAATGGTTCACATGTTGC 60.030 45.455 0.00 0.00 40.44 4.17
3350 4689 3.928727 AGCTGAATGGTTCACATGTTG 57.071 42.857 0.00 0.00 40.44 3.33
3358 4697 6.894828 TCGTAAGTTTTTAGCTGAATGGTTC 58.105 36.000 0.00 0.00 39.48 3.62
3361 4700 7.526608 TGAATCGTAAGTTTTTAGCTGAATGG 58.473 34.615 0.00 0.00 39.48 3.16
3380 4719 4.058817 GGAACCTTGCCTACTATGAATCG 58.941 47.826 0.00 0.00 0.00 3.34
3453 4792 5.978814 ACCGTGATTTCAGTAAATAGCTCT 58.021 37.500 0.00 0.00 35.41 4.09
3462 4801 4.759693 AGCATGAAAACCGTGATTTCAGTA 59.240 37.500 0.00 0.00 46.52 2.74
3482 4821 2.569853 TCGGATTCTTACCCTGAAAGCA 59.430 45.455 0.00 0.00 0.00 3.91
3489 4828 4.409247 AGCAATAGTTCGGATTCTTACCCT 59.591 41.667 0.00 0.00 0.00 4.34
3493 4832 6.406692 AGCTAGCAATAGTTCGGATTCTTA 57.593 37.500 18.83 0.00 0.00 2.10
3497 4836 8.585881 TCTAAATAGCTAGCAATAGTTCGGATT 58.414 33.333 18.83 0.00 0.00 3.01
3499 4838 7.520451 TCTAAATAGCTAGCAATAGTTCGGA 57.480 36.000 18.83 6.59 0.00 4.55
3597 4936 9.859427 TCACCTGATAAAAATCAAGCATAAAAG 57.141 29.630 0.00 0.00 0.00 2.27
3831 5170 6.655848 GTCGATCTGTATAATGTACTCCCTCT 59.344 42.308 0.00 0.00 0.00 3.69
3882 5303 4.753516 TCACCACCTATATGTTGACTGG 57.246 45.455 0.00 0.00 0.00 4.00
3923 5344 5.003778 CGCTAAAGTGCAACATAATTTCTGC 59.996 40.000 0.00 0.00 41.43 4.26
3957 5378 7.136119 CCTTAACAAAGATAAGTGCAAACGAA 58.864 34.615 0.00 0.00 0.00 3.85
3960 5381 6.156519 CCCCTTAACAAAGATAAGTGCAAAC 58.843 40.000 0.00 0.00 0.00 2.93
4034 5456 7.750903 GGTGCAAAGAGTTAGAACAAACATATC 59.249 37.037 0.00 0.00 0.00 1.63
4195 8365 1.808411 AAGTGGCTAACATGTCACGG 58.192 50.000 0.00 0.00 46.09 4.94
4460 8631 9.993454 GACGGGAAAATATTTAAGTAGGAGTAT 57.007 33.333 0.01 0.00 0.00 2.12
4461 8632 8.424133 GGACGGGAAAATATTTAAGTAGGAGTA 58.576 37.037 0.01 0.00 0.00 2.59
4462 8633 7.278135 GGACGGGAAAATATTTAAGTAGGAGT 58.722 38.462 0.01 0.00 0.00 3.85
4463 8634 6.423001 CGGACGGGAAAATATTTAAGTAGGAG 59.577 42.308 0.01 0.00 0.00 3.69
4464 8635 6.282930 CGGACGGGAAAATATTTAAGTAGGA 58.717 40.000 0.01 0.00 0.00 2.94
4465 8636 5.467735 CCGGACGGGAAAATATTTAAGTAGG 59.532 44.000 0.00 3.86 38.47 3.18
4466 8637 6.018507 CACCGGACGGGAAAATATTTAAGTAG 60.019 42.308 9.46 0.00 39.97 2.57
4483 8654 2.040009 ATTATCAGGGCCACCGGACG 62.040 60.000 9.46 0.00 43.86 4.79
4487 8658 1.898574 GCCATTATCAGGGCCACCG 60.899 63.158 6.18 0.00 44.53 4.94
4516 8687 1.925185 GCGACCTTCGTACTGAATTCC 59.075 52.381 2.27 0.00 42.81 3.01
4606 8777 2.620112 CCTGACAACGCCTGGCAAG 61.620 63.158 20.29 9.89 44.75 4.01
4619 8790 1.919600 AAGCTGGCATCCTCCCTGAC 61.920 60.000 0.00 0.00 0.00 3.51
4770 8941 1.293498 CTTGAGACCGGGACCTGTG 59.707 63.158 6.32 0.00 0.00 3.66
4773 8944 1.913762 CCACTTGAGACCGGGACCT 60.914 63.158 6.32 0.00 0.00 3.85
4816 8988 2.900273 TTCCGGCAGAGGAATCGG 59.100 61.111 0.00 0.00 44.66 4.18
4891 9064 2.427506 AGGACAAAACGAGCTTGATCC 58.572 47.619 8.31 6.43 0.00 3.36
4893 9066 2.030805 GCAAGGACAAAACGAGCTTGAT 60.031 45.455 8.31 0.00 0.00 2.57
4894 9067 1.333619 GCAAGGACAAAACGAGCTTGA 59.666 47.619 8.31 0.00 0.00 3.02
4895 9068 1.334869 AGCAAGGACAAAACGAGCTTG 59.665 47.619 0.00 0.00 0.00 4.01
4899 9074 0.512952 CGGAGCAAGGACAAAACGAG 59.487 55.000 0.00 0.00 0.00 4.18
5109 9292 3.865745 ACTCCGCAACTTATCTGATTTCG 59.134 43.478 0.00 0.00 0.00 3.46
5116 9299 3.764434 TCTTGAGACTCCGCAACTTATCT 59.236 43.478 0.00 0.00 0.00 1.98
5127 9310 1.478510 TCTCGCCAATCTTGAGACTCC 59.521 52.381 0.00 0.00 34.00 3.85
5132 9315 3.449528 TCTGATCTCGCCAATCTTGAG 57.550 47.619 0.00 0.00 0.00 3.02
5135 9318 5.543507 ACTTATCTGATCTCGCCAATCTT 57.456 39.130 0.00 0.00 0.00 2.40
5146 9329 4.295051 GAGACTCCGCAACTTATCTGATC 58.705 47.826 0.00 0.00 0.00 2.92
5150 9333 2.356382 CTCGAGACTCCGCAACTTATCT 59.644 50.000 6.58 0.00 0.00 1.98
5166 9349 1.518929 GTCGATTTCGCCAATCTCGAG 59.481 52.381 5.93 5.93 39.50 4.04
5174 9357 1.153353 GGAAACTGTCGATTTCGCCA 58.847 50.000 4.39 0.00 37.00 5.69
5208 9391 5.067023 GCCATCCACAAGAGAATTCTAAAGG 59.933 44.000 8.25 6.74 31.96 3.11
5211 9394 5.178096 TGCCATCCACAAGAGAATTCTAA 57.822 39.130 8.25 0.00 31.96 2.10
5219 9402 2.758089 GCGCTGCCATCCACAAGAG 61.758 63.158 0.00 0.00 0.00 2.85
5276 9460 1.235724 GGGTTCACTTTCCCTCAACG 58.764 55.000 0.00 0.00 40.48 4.10
5277 9461 1.133606 TGGGGTTCACTTTCCCTCAAC 60.134 52.381 0.00 0.00 43.00 3.18
5279 9463 0.771127 CTGGGGTTCACTTTCCCTCA 59.229 55.000 0.00 0.00 43.00 3.86
5281 9465 1.133482 CAACTGGGGTTCACTTTCCCT 60.133 52.381 0.00 0.00 43.00 4.20
5439 9631 5.175090 AGAAGAGAAGAAAAGCAAAACCG 57.825 39.130 0.00 0.00 0.00 4.44
5484 9676 4.182433 TGGCAACAGGGTGTCGCA 62.182 61.111 0.00 0.00 46.17 5.10
5521 9713 1.402968 CCACAAAAGGAGCCATGATCG 59.597 52.381 0.00 0.00 0.00 3.69
5561 9754 9.316730 GTCTTACATTTTGGTACGGATGTAATA 57.683 33.333 15.82 10.24 41.46 0.98
5566 9759 6.737254 AAGTCTTACATTTTGGTACGGATG 57.263 37.500 0.00 0.00 0.00 3.51
5567 9760 7.754851 AAAAGTCTTACATTTTGGTACGGAT 57.245 32.000 0.00 0.00 0.00 4.18
5637 9830 4.494764 CGACGGTTCAAAAGTACTATCTCG 59.505 45.833 0.00 0.00 0.00 4.04
5640 9833 3.305361 GGCGACGGTTCAAAAGTACTATC 59.695 47.826 0.00 0.00 0.00 2.08
5646 9839 1.802365 GTATGGCGACGGTTCAAAAGT 59.198 47.619 0.00 0.00 0.00 2.66
5653 9846 3.746045 AATCTATGTATGGCGACGGTT 57.254 42.857 0.00 0.00 0.00 4.44
5665 9858 5.431765 AGGCGACTGATCAAAAATCTATGT 58.568 37.500 0.00 0.00 41.13 2.29
5666 9859 5.998454 AGGCGACTGATCAAAAATCTATG 57.002 39.130 0.00 0.00 41.13 2.23
5706 9899 9.953697 AGTTAGAGATAAGTGCGATAGTTTTAG 57.046 33.333 0.00 0.00 39.35 1.85


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

AutoCloner maintained by Alex Coulton.