Multiple sequence alignment - TraesCS1A01G343700

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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 TraesCS1A01G343700 chr1A 100.000 3264 0 0 1 3264 532088394 532091657 0.000000e+00 6028
1 TraesCS1A01G343700 chr1A 95.818 837 35 0 2428 3264 104181073 104180237 0.000000e+00 1352
2 TraesCS1A01G343700 chr1A 95.514 847 35 3 2418 3264 245269760 245270603 0.000000e+00 1351
3 TraesCS1A01G343700 chr1B 87.336 1982 123 58 1 1932 585826455 585828358 0.000000e+00 2152
4 TraesCS1A01G343700 chr1B 91.579 95 5 3 1993 2084 585828388 585828482 9.510000e-26 128
5 TraesCS1A01G343700 chr1D 86.294 1700 79 60 271 1932 433511063 433512646 0.000000e+00 1707
6 TraesCS1A01G343700 chr1D 83.759 431 50 14 2006 2428 433512693 433513111 1.100000e-104 390
7 TraesCS1A01G343700 chr1D 82.627 236 20 11 1 231 433510847 433511066 4.300000e-44 189
8 TraesCS1A01G343700 chr4A 95.986 847 31 3 2418 3264 95837603 95838446 0.000000e+00 1373
9 TraesCS1A01G343700 chr4A 95.637 848 34 3 2418 3264 537054497 537055342 0.000000e+00 1358
10 TraesCS1A01G343700 chr4A 95.818 837 35 0 2428 3264 595758861 595759697 0.000000e+00 1352
11 TraesCS1A01G343700 chr4A 95.514 847 35 3 2418 3264 474971975 474972818 0.000000e+00 1351
12 TraesCS1A01G343700 chr4A 95.813 836 35 0 2429 3264 497825526 497826361 0.000000e+00 1351
13 TraesCS1A01G343700 chr4A 95.699 837 35 1 2428 3264 483136015 483135180 0.000000e+00 1345
14 TraesCS1A01G343700 chr6A 95.579 837 37 0 2428 3264 196848345 196847509 0.000000e+00 1341


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 TraesCS1A01G343700 chr1A 532088394 532091657 3263 False 6028 6028 100.000000 1 3264 1 chr1A.!!$F2 3263
1 TraesCS1A01G343700 chr1A 104180237 104181073 836 True 1352 1352 95.818000 2428 3264 1 chr1A.!!$R1 836
2 TraesCS1A01G343700 chr1A 245269760 245270603 843 False 1351 1351 95.514000 2418 3264 1 chr1A.!!$F1 846
3 TraesCS1A01G343700 chr1B 585826455 585828482 2027 False 1140 2152 89.457500 1 2084 2 chr1B.!!$F1 2083
4 TraesCS1A01G343700 chr1D 433510847 433513111 2264 False 762 1707 84.226667 1 2428 3 chr1D.!!$F1 2427
5 TraesCS1A01G343700 chr4A 95837603 95838446 843 False 1373 1373 95.986000 2418 3264 1 chr4A.!!$F1 846
6 TraesCS1A01G343700 chr4A 537054497 537055342 845 False 1358 1358 95.637000 2418 3264 1 chr4A.!!$F4 846
7 TraesCS1A01G343700 chr4A 595758861 595759697 836 False 1352 1352 95.818000 2428 3264 1 chr4A.!!$F5 836
8 TraesCS1A01G343700 chr4A 474971975 474972818 843 False 1351 1351 95.514000 2418 3264 1 chr4A.!!$F2 846
9 TraesCS1A01G343700 chr4A 497825526 497826361 835 False 1351 1351 95.813000 2429 3264 1 chr4A.!!$F3 835
10 TraesCS1A01G343700 chr4A 483135180 483136015 835 True 1345 1345 95.699000 2428 3264 1 chr4A.!!$R1 836
11 TraesCS1A01G343700 chr6A 196847509 196848345 836 True 1341 1341 95.579000 2428 3264 1 chr6A.!!$R1 836

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
829 876 0.17904 GGTCAAACGGAACCAGACCA 60.179 55.0 0.0 0.0 46.15 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2502 0.038159 CCGACAACTCTGGACTGGAC 60.038 60.0 0.0 0.0 0.0 4.02 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
23 24 0.394565 AGTGAGTGAGAGTTGGTGCC 59.605 55.000 0.00 0.00 0.00 5.01
33 34 2.887152 AGAGTTGGTGCCTTGATTGTTC 59.113 45.455 0.00 0.00 0.00 3.18
34 35 2.622942 GAGTTGGTGCCTTGATTGTTCA 59.377 45.455 0.00 0.00 0.00 3.18
37 38 0.603065 GGTGCCTTGATTGTTCACCC 59.397 55.000 0.00 0.00 40.84 4.61
38 39 1.620822 GTGCCTTGATTGTTCACCCT 58.379 50.000 0.00 0.00 0.00 4.34
39 40 1.963515 GTGCCTTGATTGTTCACCCTT 59.036 47.619 0.00 0.00 0.00 3.95
42 43 2.365293 GCCTTGATTGTTCACCCTTTGT 59.635 45.455 0.00 0.00 0.00 2.83
47 48 5.004922 TGATTGTTCACCCTTTGTTTGTC 57.995 39.130 0.00 0.00 0.00 3.18
48 49 4.464244 TGATTGTTCACCCTTTGTTTGTCA 59.536 37.500 0.00 0.00 0.00 3.58
49 50 5.128499 TGATTGTTCACCCTTTGTTTGTCAT 59.872 36.000 0.00 0.00 0.00 3.06
84 92 1.268032 GCACCGTGCGAAATGAATAGG 60.268 52.381 7.96 0.00 31.71 2.57
85 93 2.276201 CACCGTGCGAAATGAATAGGA 58.724 47.619 0.00 0.00 0.00 2.94
86 94 2.030457 CACCGTGCGAAATGAATAGGAC 59.970 50.000 0.00 0.00 0.00 3.85
125 133 2.059490 AGATCGTCCTAGGCTCCTAGT 58.941 52.381 18.71 3.09 43.22 2.57
126 134 3.008157 CAGATCGTCCTAGGCTCCTAGTA 59.992 52.174 18.71 3.47 43.22 1.82
127 135 2.926778 TCGTCCTAGGCTCCTAGTAC 57.073 55.000 18.71 13.53 43.22 2.73
128 136 2.406559 TCGTCCTAGGCTCCTAGTACT 58.593 52.381 18.71 0.00 43.22 2.73
129 137 3.581101 TCGTCCTAGGCTCCTAGTACTA 58.419 50.000 18.71 1.89 43.22 1.82
130 138 3.577848 TCGTCCTAGGCTCCTAGTACTAG 59.422 52.174 21.11 21.11 43.22 2.57
131 139 3.678289 GTCCTAGGCTCCTAGTACTAGC 58.322 54.545 22.39 14.99 43.22 3.42
132 140 3.328637 GTCCTAGGCTCCTAGTACTAGCT 59.671 52.174 22.39 16.15 43.22 3.32
133 141 4.531732 GTCCTAGGCTCCTAGTACTAGCTA 59.468 50.000 22.39 16.38 43.22 3.32
134 142 4.778958 TCCTAGGCTCCTAGTACTAGCTAG 59.221 50.000 22.39 22.65 43.22 3.42
135 143 3.428413 AGGCTCCTAGTACTAGCTAGC 57.572 52.381 29.63 29.63 38.67 3.42
169 177 2.167684 CGCACAACGCACGTACTG 59.832 61.111 0.00 0.00 42.60 2.74
225 233 2.426023 GACGTGTGCCCCAGTTCT 59.574 61.111 0.00 0.00 0.00 3.01
226 234 1.668151 GACGTGTGCCCCAGTTCTC 60.668 63.158 0.00 0.00 0.00 2.87
227 235 2.377628 GACGTGTGCCCCAGTTCTCA 62.378 60.000 0.00 0.00 0.00 3.27
228 236 1.003355 CGTGTGCCCCAGTTCTCAT 60.003 57.895 0.00 0.00 0.00 2.90
229 237 0.606401 CGTGTGCCCCAGTTCTCATT 60.606 55.000 0.00 0.00 0.00 2.57
230 238 0.883833 GTGTGCCCCAGTTCTCATTG 59.116 55.000 0.00 0.00 0.00 2.82
231 239 0.478072 TGTGCCCCAGTTCTCATTGT 59.522 50.000 0.00 0.00 0.00 2.71
232 240 1.133513 TGTGCCCCAGTTCTCATTGTT 60.134 47.619 0.00 0.00 0.00 2.83
233 241 1.963515 GTGCCCCAGTTCTCATTGTTT 59.036 47.619 0.00 0.00 0.00 2.83
234 242 2.365293 GTGCCCCAGTTCTCATTGTTTT 59.635 45.455 0.00 0.00 0.00 2.43
235 243 3.037549 TGCCCCAGTTCTCATTGTTTTT 58.962 40.909 0.00 0.00 0.00 1.94
258 266 1.817520 CGTGCCACACCTCAACACA 60.818 57.895 0.00 0.00 0.00 3.72
262 270 0.179045 GCCACACCTCAACACACTCT 60.179 55.000 0.00 0.00 0.00 3.24
278 286 3.071602 ACACTCTGCTGGTTATTGACAGT 59.928 43.478 0.00 0.00 37.07 3.55
359 375 4.116238 GTGAGATCGATCCCTTCAAAGAC 58.884 47.826 21.66 4.16 0.00 3.01
360 376 3.133003 TGAGATCGATCCCTTCAAAGACC 59.867 47.826 21.66 0.00 0.00 3.85
365 381 1.354368 GATCCCTTCAAAGACCCACCA 59.646 52.381 0.00 0.00 0.00 4.17
369 385 3.596046 TCCCTTCAAAGACCCACCAATAT 59.404 43.478 0.00 0.00 0.00 1.28
370 386 4.791334 TCCCTTCAAAGACCCACCAATATA 59.209 41.667 0.00 0.00 0.00 0.86
371 387 5.435041 TCCCTTCAAAGACCCACCAATATAT 59.565 40.000 0.00 0.00 0.00 0.86
372 388 6.621931 TCCCTTCAAAGACCCACCAATATATA 59.378 38.462 0.00 0.00 0.00 0.86
373 389 7.297108 TCCCTTCAAAGACCCACCAATATATAT 59.703 37.037 0.00 0.00 0.00 0.86
374 390 7.950124 CCCTTCAAAGACCCACCAATATATATT 59.050 37.037 1.91 1.91 0.00 1.28
375 391 8.796475 CCTTCAAAGACCCACCAATATATATTG 58.204 37.037 23.28 23.28 42.00 1.90
376 392 9.573166 CTTCAAAGACCCACCAATATATATTGA 57.427 33.333 29.23 9.27 44.40 2.57
377 393 9.928618 TTCAAAGACCCACCAATATATATTGAA 57.071 29.630 29.23 13.78 44.40 2.69
378 394 9.928618 TCAAAGACCCACCAATATATATTGAAA 57.071 29.630 29.23 5.11 44.40 2.69
380 396 9.936329 AAAGACCCACCAATATATATTGAAAGT 57.064 29.630 29.23 21.21 44.40 2.66
431 447 0.387622 CCACATGTCCGCAGCAAAAG 60.388 55.000 0.00 0.00 0.00 2.27
432 448 0.311790 CACATGTCCGCAGCAAAAGT 59.688 50.000 0.00 0.00 0.00 2.66
461 477 0.647410 CGACACATTCCATGCGAGTC 59.353 55.000 0.00 0.00 0.00 3.36
535 555 2.672908 CAGCCTCACAGCCCATCA 59.327 61.111 0.00 0.00 0.00 3.07
536 556 1.748122 CAGCCTCACAGCCCATCAC 60.748 63.158 0.00 0.00 0.00 3.06
537 557 2.439156 GCCTCACAGCCCATCACC 60.439 66.667 0.00 0.00 0.00 4.02
569 592 2.510906 CCATCACCCGTCCATCCC 59.489 66.667 0.00 0.00 0.00 3.85
570 593 2.510906 CATCACCCGTCCATCCCC 59.489 66.667 0.00 0.00 0.00 4.81
613 639 4.262617 GAACCCAAAGAGGATAAGACCAC 58.737 47.826 0.00 0.00 41.22 4.16
674 704 1.607801 GGAAAAGCCATGTGGGAGCC 61.608 60.000 0.54 0.00 40.01 4.70
825 872 0.531090 TGTCGGTCAAACGGAACCAG 60.531 55.000 0.00 0.00 0.00 4.00
826 873 0.249573 GTCGGTCAAACGGAACCAGA 60.250 55.000 0.00 0.00 0.00 3.86
827 874 0.249573 TCGGTCAAACGGAACCAGAC 60.250 55.000 0.00 0.00 0.00 3.51
828 875 1.226030 CGGTCAAACGGAACCAGACC 61.226 60.000 0.00 0.00 44.05 3.85
829 876 0.179040 GGTCAAACGGAACCAGACCA 60.179 55.000 0.00 0.00 46.15 4.02
830 877 1.226746 GTCAAACGGAACCAGACCAG 58.773 55.000 0.00 0.00 0.00 4.00
835 882 0.836400 ACGGAACCAGACCAGACCAT 60.836 55.000 0.00 0.00 0.00 3.55
903 950 4.221422 GCCACGCTATCCGCTCCA 62.221 66.667 0.00 0.00 41.76 3.86
904 951 2.028190 CCACGCTATCCGCTCCAG 59.972 66.667 0.00 0.00 41.76 3.86
1082 1138 1.658409 GTTTGAGCAACGGCACAGC 60.658 57.895 0.00 0.00 41.62 4.40
1094 1150 2.415010 CACAGCTCGGGAGATCGG 59.585 66.667 0.00 0.00 38.80 4.18
1111 1167 4.840005 GGCGGCGGAAGAGGGAAG 62.840 72.222 9.78 0.00 0.00 3.46
1113 1169 4.082523 CGGCGGAAGAGGGAAGCA 62.083 66.667 0.00 0.00 0.00 3.91
1175 1241 2.835895 GGCGAGGAGGAGGAGGAC 60.836 72.222 0.00 0.00 0.00 3.85
1367 1433 3.379372 CCGCCAAGTAAGTAGCAGTACTA 59.621 47.826 0.00 0.00 38.66 1.82
1380 1453 5.900865 AGCAGTACTACTCCAACTAACTC 57.099 43.478 0.00 0.00 0.00 3.01
1681 1760 1.017701 GGAACATCCCCGTCAACGAC 61.018 60.000 3.71 0.00 43.02 4.34
1709 1788 2.188817 ACCATCAGTAGGTTCAGGGTC 58.811 52.381 0.00 0.00 35.33 4.46
1720 1800 2.158943 GGTTCAGGGTCTATTTCTCGGG 60.159 54.545 0.00 0.00 0.00 5.14
1744 1824 5.415701 GTCATCAGGCCTCTTAAAATGTTCA 59.584 40.000 0.00 0.00 0.00 3.18
1752 1832 7.121907 AGGCCTCTTAAAATGTTCATCTTCTTC 59.878 37.037 0.00 0.00 0.00 2.87
1753 1833 7.121907 GGCCTCTTAAAATGTTCATCTTCTTCT 59.878 37.037 0.00 0.00 0.00 2.85
1754 1834 8.518702 GCCTCTTAAAATGTTCATCTTCTTCTT 58.481 33.333 0.00 0.00 0.00 2.52
1757 1837 9.014297 TCTTAAAATGTTCATCTTCTTCTTCCC 57.986 33.333 0.00 0.00 0.00 3.97
1758 1838 6.596309 AAAATGTTCATCTTCTTCTTCCCC 57.404 37.500 0.00 0.00 0.00 4.81
1762 1842 4.072839 GTTCATCTTCTTCTTCCCCGTTT 58.927 43.478 0.00 0.00 0.00 3.60
1763 1843 3.939066 TCATCTTCTTCTTCCCCGTTTC 58.061 45.455 0.00 0.00 0.00 2.78
1778 1858 2.028567 CCGTTTCTGCTCTTCTTCTCCT 60.029 50.000 0.00 0.00 0.00 3.69
1779 1859 3.249917 CGTTTCTGCTCTTCTTCTCCTC 58.750 50.000 0.00 0.00 0.00 3.71
1786 1866 2.159296 GCTCTTCTTCTCCTCGTCCTTC 60.159 54.545 0.00 0.00 0.00 3.46
1787 1867 2.425668 CTCTTCTTCTCCTCGTCCTTCC 59.574 54.545 0.00 0.00 0.00 3.46
1837 1917 5.686834 CATTAGTCTGCGAATGATTCATGG 58.313 41.667 5.95 0.00 39.17 3.66
1840 1920 2.945008 GTCTGCGAATGATTCATGGGAA 59.055 45.455 5.95 0.00 37.45 3.97
1853 1933 4.437682 TCATGGGAAGAACTTCTGTGTT 57.562 40.909 13.14 0.00 39.45 3.32
1854 1934 4.389374 TCATGGGAAGAACTTCTGTGTTC 58.611 43.478 13.14 0.00 44.67 3.18
1863 1943 3.107642 ACTTCTGTGTTCGTGTAAGGG 57.892 47.619 0.00 0.00 0.00 3.95
1865 1945 3.118519 ACTTCTGTGTTCGTGTAAGGGTT 60.119 43.478 0.00 0.00 0.00 4.11
1866 1946 2.828877 TCTGTGTTCGTGTAAGGGTTG 58.171 47.619 0.00 0.00 0.00 3.77
1867 1947 2.431419 TCTGTGTTCGTGTAAGGGTTGA 59.569 45.455 0.00 0.00 0.00 3.18
1868 1948 2.800544 CTGTGTTCGTGTAAGGGTTGAG 59.199 50.000 0.00 0.00 0.00 3.02
1869 1949 2.431419 TGTGTTCGTGTAAGGGTTGAGA 59.569 45.455 0.00 0.00 0.00 3.27
1870 1950 3.070446 TGTGTTCGTGTAAGGGTTGAGAT 59.930 43.478 0.00 0.00 0.00 2.75
1871 1951 4.281435 TGTGTTCGTGTAAGGGTTGAGATA 59.719 41.667 0.00 0.00 0.00 1.98
1872 1952 4.863131 GTGTTCGTGTAAGGGTTGAGATAG 59.137 45.833 0.00 0.00 0.00 2.08
1875 1955 5.515797 TCGTGTAAGGGTTGAGATAGATG 57.484 43.478 0.00 0.00 0.00 2.90
1900 1980 7.012515 TGTTGTGATGTAAATACGGAGTTTGTT 59.987 33.333 0.00 0.00 37.78 2.83
1901 1981 7.499321 TGTGATGTAAATACGGAGTTTGTTT 57.501 32.000 0.00 0.00 37.78 2.83
1902 1982 7.356540 TGTGATGTAAATACGGAGTTTGTTTG 58.643 34.615 0.00 0.00 37.78 2.93
1904 1984 8.497554 GTGATGTAAATACGGAGTTTGTTTGTA 58.502 33.333 0.00 0.00 37.78 2.41
1905 1985 9.053840 TGATGTAAATACGGAGTTTGTTTGTAA 57.946 29.630 0.00 0.00 37.78 2.41
1906 1986 9.321590 GATGTAAATACGGAGTTTGTTTGTAAC 57.678 33.333 0.00 0.00 37.78 2.50
1918 1998 5.798015 TTGTTTGTAACTGTACTGCGAAA 57.202 34.783 0.00 0.00 0.00 3.46
1920 2000 5.561993 TGTTTGTAACTGTACTGCGAAAAC 58.438 37.500 0.00 6.78 0.00 2.43
1924 2004 0.601841 ACTGTACTGCGAAAACGGGG 60.602 55.000 0.00 0.00 0.00 5.73
1925 2005 0.320073 CTGTACTGCGAAAACGGGGA 60.320 55.000 0.00 0.00 0.00 4.81
1926 2006 0.320073 TGTACTGCGAAAACGGGGAG 60.320 55.000 0.00 0.00 0.00 4.30
1927 2007 1.375013 TACTGCGAAAACGGGGAGC 60.375 57.895 0.00 0.00 0.00 4.70
1928 2008 2.102109 TACTGCGAAAACGGGGAGCA 62.102 55.000 0.00 0.00 36.34 4.26
1929 2009 2.668212 TGCGAAAACGGGGAGCAG 60.668 61.111 0.00 0.00 33.57 4.24
1930 2010 2.358247 GCGAAAACGGGGAGCAGA 60.358 61.111 0.00 0.00 0.00 4.26
1931 2011 1.745489 GCGAAAACGGGGAGCAGAT 60.745 57.895 0.00 0.00 0.00 2.90
1933 2013 1.287425 CGAAAACGGGGAGCAGATAC 58.713 55.000 0.00 0.00 0.00 2.24
1934 2014 1.287425 GAAAACGGGGAGCAGATACG 58.713 55.000 0.00 0.00 0.00 3.06
1935 2015 0.107848 AAAACGGGGAGCAGATACGG 60.108 55.000 0.00 0.00 0.00 4.02
1936 2016 1.968050 AAACGGGGAGCAGATACGGG 61.968 60.000 0.00 0.00 0.00 5.28
1937 2017 2.520982 CGGGGAGCAGATACGGGA 60.521 66.667 0.00 0.00 0.00 5.14
1938 2018 2.565645 CGGGGAGCAGATACGGGAG 61.566 68.421 0.00 0.00 0.00 4.30
1939 2019 2.210711 GGGGAGCAGATACGGGAGG 61.211 68.421 0.00 0.00 0.00 4.30
1940 2020 1.457831 GGGAGCAGATACGGGAGGT 60.458 63.158 0.00 0.00 0.00 3.85
1941 2021 1.742768 GGAGCAGATACGGGAGGTG 59.257 63.158 0.00 0.00 0.00 4.00
1942 2022 1.068250 GAGCAGATACGGGAGGTGC 59.932 63.158 0.00 0.00 0.00 5.01
1943 2023 2.279517 GCAGATACGGGAGGTGCG 60.280 66.667 0.00 0.00 0.00 5.34
1944 2024 2.279517 CAGATACGGGAGGTGCGC 60.280 66.667 0.00 0.00 0.00 6.09
1945 2025 3.537874 AGATACGGGAGGTGCGCC 61.538 66.667 8.71 8.71 0.00 6.53
1946 2026 4.944372 GATACGGGAGGTGCGCCG 62.944 72.222 11.42 1.64 40.50 6.46
1950 2030 4.524318 CGGGAGGTGCGCCGTATT 62.524 66.667 11.42 0.00 40.50 1.89
1951 2031 2.124860 GGGAGGTGCGCCGTATTT 60.125 61.111 11.42 0.00 40.50 1.40
1952 2032 1.144496 GGGAGGTGCGCCGTATTTA 59.856 57.895 11.42 0.00 40.50 1.40
1953 2033 0.250166 GGGAGGTGCGCCGTATTTAT 60.250 55.000 11.42 0.00 40.50 1.40
1954 2034 1.145803 GGAGGTGCGCCGTATTTATC 58.854 55.000 11.42 0.28 40.50 1.75
1955 2035 1.270147 GGAGGTGCGCCGTATTTATCT 60.270 52.381 11.42 0.00 40.50 1.98
1956 2036 1.792949 GAGGTGCGCCGTATTTATCTG 59.207 52.381 11.42 0.00 40.50 2.90
1957 2037 0.234884 GGTGCGCCGTATTTATCTGC 59.765 55.000 4.18 0.00 0.00 4.26
1958 2038 1.217882 GTGCGCCGTATTTATCTGCT 58.782 50.000 4.18 0.00 0.00 4.24
1959 2039 1.192534 GTGCGCCGTATTTATCTGCTC 59.807 52.381 4.18 0.00 0.00 4.26
1960 2040 0.790814 GCGCCGTATTTATCTGCTCC 59.209 55.000 0.00 0.00 0.00 4.70
1961 2041 1.429463 CGCCGTATTTATCTGCTCCC 58.571 55.000 0.00 0.00 0.00 4.30
1962 2042 1.809684 GCCGTATTTATCTGCTCCCC 58.190 55.000 0.00 0.00 0.00 4.81
1963 2043 1.939838 GCCGTATTTATCTGCTCCCCG 60.940 57.143 0.00 0.00 0.00 5.73
1964 2044 1.343465 CCGTATTTATCTGCTCCCCGT 59.657 52.381 0.00 0.00 0.00 5.28
1965 2045 2.224209 CCGTATTTATCTGCTCCCCGTT 60.224 50.000 0.00 0.00 0.00 4.44
1966 2046 3.463944 CGTATTTATCTGCTCCCCGTTT 58.536 45.455 0.00 0.00 0.00 3.60
1967 2047 3.875134 CGTATTTATCTGCTCCCCGTTTT 59.125 43.478 0.00 0.00 0.00 2.43
1968 2048 4.334481 CGTATTTATCTGCTCCCCGTTTTT 59.666 41.667 0.00 0.00 0.00 1.94
1969 2049 5.524646 CGTATTTATCTGCTCCCCGTTTTTA 59.475 40.000 0.00 0.00 0.00 1.52
1970 2050 6.204108 CGTATTTATCTGCTCCCCGTTTTTAT 59.796 38.462 0.00 0.00 0.00 1.40
1971 2051 6.635030 ATTTATCTGCTCCCCGTTTTTATC 57.365 37.500 0.00 0.00 0.00 1.75
1972 2052 2.413310 TCTGCTCCCCGTTTTTATCC 57.587 50.000 0.00 0.00 0.00 2.59
1973 2053 1.913419 TCTGCTCCCCGTTTTTATCCT 59.087 47.619 0.00 0.00 0.00 3.24
1974 2054 2.017049 CTGCTCCCCGTTTTTATCCTG 58.983 52.381 0.00 0.00 0.00 3.86
1975 2055 1.340600 TGCTCCCCGTTTTTATCCTGG 60.341 52.381 0.00 0.00 0.00 4.45
1976 2056 1.340697 GCTCCCCGTTTTTATCCTGGT 60.341 52.381 0.00 0.00 0.00 4.00
1977 2057 2.092807 GCTCCCCGTTTTTATCCTGGTA 60.093 50.000 0.00 0.00 0.00 3.25
1978 2058 3.622953 GCTCCCCGTTTTTATCCTGGTAA 60.623 47.826 0.00 0.00 0.00 2.85
1979 2059 4.591929 CTCCCCGTTTTTATCCTGGTAAA 58.408 43.478 0.00 0.00 0.00 2.01
1980 2060 5.195848 TCCCCGTTTTTATCCTGGTAAAT 57.804 39.130 0.00 0.00 0.00 1.40
1981 2061 6.324601 TCCCCGTTTTTATCCTGGTAAATA 57.675 37.500 0.00 0.00 0.00 1.40
1982 2062 6.121590 TCCCCGTTTTTATCCTGGTAAATAC 58.878 40.000 0.00 3.63 0.00 1.89
1983 2063 5.007921 CCCCGTTTTTATCCTGGTAAATACG 59.992 44.000 22.08 22.08 42.86 3.06
1985 2065 6.907206 CGTTTTTATCCTGGTAAATACGGA 57.093 37.500 21.72 0.00 41.24 4.69
1989 2069 5.464030 TTATCCTGGTAAATACGGAGCTC 57.536 43.478 4.71 4.71 0.00 4.09
1991 2071 2.957006 TCCTGGTAAATACGGAGCTCTC 59.043 50.000 14.64 2.76 0.00 3.20
2000 2080 2.447244 ACGGAGCTCTCTTTCACTTG 57.553 50.000 14.64 0.00 0.00 3.16
2004 2108 1.003003 GAGCTCTCTTTCACTTGGGCT 59.997 52.381 6.43 0.00 0.00 5.19
2039 2143 0.693049 GGAGGAACTTGGCTGGAGAA 59.307 55.000 0.00 0.00 41.55 2.87
2056 2160 1.003718 AAAGGGCTTTCGTCTCCGG 60.004 57.895 0.00 0.00 33.95 5.14
2077 2182 6.435904 TCCGGTTTCTTTTATGTTGGATGATT 59.564 34.615 0.00 0.00 0.00 2.57
2102 2207 1.710013 TTACAGTGTAGCGCTGCTTC 58.290 50.000 25.90 17.93 44.75 3.86
2103 2208 0.601057 TACAGTGTAGCGCTGCTTCA 59.399 50.000 25.90 13.64 44.75 3.02
2106 2211 1.374758 GTGTAGCGCTGCTTCAGGT 60.375 57.895 25.90 0.00 36.69 4.00
2115 2220 2.288395 CGCTGCTTCAGGTTTGGAATTT 60.288 45.455 0.00 0.00 31.21 1.82
2118 2223 4.553323 CTGCTTCAGGTTTGGAATTTCAG 58.447 43.478 0.00 0.00 0.00 3.02
2138 2243 5.559770 TCAGGTAGATTCTGCAATGTTTCA 58.440 37.500 4.11 0.00 32.63 2.69
2139 2244 5.645067 TCAGGTAGATTCTGCAATGTTTCAG 59.355 40.000 4.11 0.00 32.63 3.02
2146 2251 3.807553 TCTGCAATGTTTCAGTGTCTCA 58.192 40.909 0.00 0.00 31.72 3.27
2148 2253 3.544684 TGCAATGTTTCAGTGTCTCACT 58.455 40.909 0.00 0.00 46.51 3.41
2150 2255 3.363378 GCAATGTTTCAGTGTCTCACTCG 60.363 47.826 0.00 0.00 43.43 4.18
2151 2256 3.735237 ATGTTTCAGTGTCTCACTCGT 57.265 42.857 0.00 0.00 43.43 4.18
2153 2258 4.224715 TGTTTCAGTGTCTCACTCGTAG 57.775 45.455 0.00 0.00 43.43 3.51
2154 2259 2.981140 GTTTCAGTGTCTCACTCGTAGC 59.019 50.000 0.00 0.00 43.43 3.58
2155 2260 2.186532 TCAGTGTCTCACTCGTAGCT 57.813 50.000 0.00 0.00 43.43 3.32
2156 2261 2.077627 TCAGTGTCTCACTCGTAGCTC 58.922 52.381 0.00 0.00 43.43 4.09
2158 2263 1.003812 AGTGTCTCACTCGTAGCTCCT 59.996 52.381 0.00 0.00 41.21 3.69
2159 2264 1.399089 GTGTCTCACTCGTAGCTCCTC 59.601 57.143 0.00 0.00 0.00 3.71
2160 2265 1.003233 TGTCTCACTCGTAGCTCCTCA 59.997 52.381 0.00 0.00 0.00 3.86
2161 2266 1.399089 GTCTCACTCGTAGCTCCTCAC 59.601 57.143 0.00 0.00 0.00 3.51
2163 2268 1.668751 CTCACTCGTAGCTCCTCACTC 59.331 57.143 0.00 0.00 0.00 3.51
2164 2269 1.003233 TCACTCGTAGCTCCTCACTCA 59.997 52.381 0.00 0.00 0.00 3.41
2165 2270 2.020720 CACTCGTAGCTCCTCACTCAT 58.979 52.381 0.00 0.00 0.00 2.90
2166 2271 2.020720 ACTCGTAGCTCCTCACTCATG 58.979 52.381 0.00 0.00 0.00 3.07
2167 2272 2.293170 CTCGTAGCTCCTCACTCATGA 58.707 52.381 0.00 0.00 0.00 3.07
2178 2283 3.119291 CTCACTCATGATAACTCCACGC 58.881 50.000 0.00 0.00 33.22 5.34
2183 2288 0.469917 ATGATAACTCCACGCTGGGG 59.530 55.000 2.76 2.76 45.84 4.96
2281 2386 8.730680 ACACTTCATTCATAGTTTCCATTGTAC 58.269 33.333 0.00 0.00 0.00 2.90
2328 2433 0.977627 ATGAGGTCATCAGTCGGGCA 60.978 55.000 0.00 0.00 42.53 5.36
2329 2434 1.153549 GAGGTCATCAGTCGGGCAC 60.154 63.158 0.00 0.00 0.00 5.01
2331 2436 1.003839 GGTCATCAGTCGGGCACAA 60.004 57.895 0.00 0.00 0.00 3.33
2337 2442 1.450312 CAGTCGGGCACAATCCTCC 60.450 63.158 0.00 0.00 0.00 4.30
2338 2443 1.613630 AGTCGGGCACAATCCTCCT 60.614 57.895 0.00 0.00 0.00 3.69
2339 2444 0.325296 AGTCGGGCACAATCCTCCTA 60.325 55.000 0.00 0.00 0.00 2.94
2349 2454 3.751018 TCCTCCTAGGAGCGGCCA 61.751 66.667 30.56 10.30 40.06 5.36
2354 2459 3.083997 CTAGGAGCGGCCAAGGGT 61.084 66.667 2.24 0.00 40.02 4.34
2370 2475 2.251642 GGTAATGCGGACGGCCATC 61.252 63.158 8.76 0.00 42.61 3.51
2406 2517 0.822532 ACGACGTCCAGTCCAGAGTT 60.823 55.000 10.58 0.00 46.92 3.01
2456 2567 2.165437 TCTTGAGCTTGCGTTGGTTTTT 59.835 40.909 0.00 0.00 0.00 1.94
2592 2703 2.536365 CGATAGCTACTCGCAACCAAA 58.464 47.619 0.00 0.00 42.61 3.28
2630 2742 0.034337 GCCCTTCACGGTCACTTACA 59.966 55.000 0.00 0.00 0.00 2.41
2648 2760 7.581213 ACTTACAAGAGTGAGATCTGATAGG 57.419 40.000 0.00 0.00 35.12 2.57
2760 2872 8.088463 AGATTGATATGATGAGAATAGACCCC 57.912 38.462 0.00 0.00 0.00 4.95
2771 2883 1.746929 ATAGACCCCGGGGCCATAGA 61.747 60.000 40.67 19.20 39.32 1.98
2782 2894 3.576982 CGGGGCCATAGATTTCACTAGTA 59.423 47.826 4.39 0.00 0.00 1.82
2791 2903 8.637986 CCATAGATTTCACTAGTAGCTTCTCTT 58.362 37.037 0.00 0.00 0.00 2.85
2816 2928 7.618019 AAGAGCATAAGTATTCTATGGTGGA 57.382 36.000 0.00 0.00 32.83 4.02
3171 3283 1.065126 GCTAAGCACTTCTCCCATGGT 60.065 52.381 11.73 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.418676 ACAAACAAAGGGTGAACAATCAAG 58.581 37.500 0.00 0.00 37.30 3.02
33 34 1.269448 CCGGATGACAAACAAAGGGTG 59.731 52.381 0.00 0.00 0.00 4.61
34 35 1.144093 TCCGGATGACAAACAAAGGGT 59.856 47.619 0.00 0.00 0.00 4.34
37 38 1.812571 CCCTCCGGATGACAAACAAAG 59.187 52.381 3.57 0.00 0.00 2.77
38 39 1.546773 CCCCTCCGGATGACAAACAAA 60.547 52.381 3.57 0.00 0.00 2.83
39 40 0.037590 CCCCTCCGGATGACAAACAA 59.962 55.000 3.57 0.00 0.00 2.83
42 43 0.546747 ACTCCCCTCCGGATGACAAA 60.547 55.000 3.57 0.00 41.00 2.83
47 48 4.227134 CGCACTCCCCTCCGGATG 62.227 72.222 3.57 0.81 41.00 3.51
97 105 2.413437 CTAGGACGATCTGCCTGCCG 62.413 65.000 12.12 0.00 35.73 5.69
125 133 6.179040 GGCTATTGTACTAGGCTAGCTAGTA 58.821 44.000 21.26 20.75 40.24 1.82
126 134 5.011586 GGCTATTGTACTAGGCTAGCTAGT 58.988 45.833 21.26 22.19 40.24 2.57
127 135 5.010933 TGGCTATTGTACTAGGCTAGCTAG 58.989 45.833 21.26 16.84 42.96 3.42
128 136 4.765856 GTGGCTATTGTACTAGGCTAGCTA 59.234 45.833 21.26 10.06 42.96 3.32
129 137 3.574826 GTGGCTATTGTACTAGGCTAGCT 59.425 47.826 21.26 11.01 42.96 3.32
130 138 3.306156 GGTGGCTATTGTACTAGGCTAGC 60.306 52.174 21.26 6.04 42.96 3.42
131 139 3.057456 CGGTGGCTATTGTACTAGGCTAG 60.057 52.174 19.83 19.83 42.96 3.42
132 140 2.889045 CGGTGGCTATTGTACTAGGCTA 59.111 50.000 14.33 0.00 42.96 3.93
133 141 1.687123 CGGTGGCTATTGTACTAGGCT 59.313 52.381 14.33 0.00 42.96 4.58
134 142 1.872653 GCGGTGGCTATTGTACTAGGC 60.873 57.143 8.33 8.33 42.87 3.93
135 143 1.411246 TGCGGTGGCTATTGTACTAGG 59.589 52.381 0.00 0.00 40.82 3.02
234 242 2.039818 TGAGGTGTGGCACGTAAAAA 57.960 45.000 13.77 0.00 34.83 1.94
235 243 1.671845 GTTGAGGTGTGGCACGTAAAA 59.328 47.619 13.77 0.89 34.83 1.52
236 244 1.301423 GTTGAGGTGTGGCACGTAAA 58.699 50.000 13.77 0.15 34.83 2.01
237 245 0.178301 TGTTGAGGTGTGGCACGTAA 59.822 50.000 13.77 0.67 34.83 3.18
238 246 0.531090 GTGTTGAGGTGTGGCACGTA 60.531 55.000 13.77 0.00 34.83 3.57
239 247 1.817941 GTGTTGAGGTGTGGCACGT 60.818 57.895 13.77 0.00 34.83 4.49
240 248 1.817520 TGTGTTGAGGTGTGGCACG 60.818 57.895 13.77 0.00 34.83 5.34
241 249 0.748005 AGTGTGTTGAGGTGTGGCAC 60.748 55.000 11.55 11.55 0.00 5.01
242 250 0.463654 GAGTGTGTTGAGGTGTGGCA 60.464 55.000 0.00 0.00 0.00 4.92
243 251 0.179045 AGAGTGTGTTGAGGTGTGGC 60.179 55.000 0.00 0.00 0.00 5.01
244 252 1.586422 CAGAGTGTGTTGAGGTGTGG 58.414 55.000 0.00 0.00 0.00 4.17
245 253 0.940126 GCAGAGTGTGTTGAGGTGTG 59.060 55.000 0.00 0.00 0.00 3.82
246 254 0.833287 AGCAGAGTGTGTTGAGGTGT 59.167 50.000 0.00 0.00 0.00 4.16
247 255 1.224075 CAGCAGAGTGTGTTGAGGTG 58.776 55.000 0.00 0.00 39.69 4.00
248 256 0.107456 CCAGCAGAGTGTGTTGAGGT 59.893 55.000 5.65 0.00 39.69 3.85
249 257 0.107456 ACCAGCAGAGTGTGTTGAGG 59.893 55.000 5.65 0.00 39.69 3.86
258 266 4.357918 AACTGTCAATAACCAGCAGAGT 57.642 40.909 0.00 0.00 31.76 3.24
369 385 9.400638 CAGCGTTGGTTTTAAACTTTCAATATA 57.599 29.630 7.79 0.00 0.00 0.86
370 386 7.095816 GCAGCGTTGGTTTTAAACTTTCAATAT 60.096 33.333 7.79 0.00 0.00 1.28
371 387 6.199342 GCAGCGTTGGTTTTAAACTTTCAATA 59.801 34.615 7.79 0.00 0.00 1.90
372 388 5.006261 GCAGCGTTGGTTTTAAACTTTCAAT 59.994 36.000 7.79 0.00 0.00 2.57
373 389 4.327627 GCAGCGTTGGTTTTAAACTTTCAA 59.672 37.500 7.79 1.36 0.00 2.69
374 390 3.860536 GCAGCGTTGGTTTTAAACTTTCA 59.139 39.130 7.79 0.00 0.00 2.69
375 391 4.109766 AGCAGCGTTGGTTTTAAACTTTC 58.890 39.130 7.79 0.00 0.00 2.62
376 392 4.109766 GAGCAGCGTTGGTTTTAAACTTT 58.890 39.130 5.19 0.00 34.61 2.66
377 393 3.490249 GGAGCAGCGTTGGTTTTAAACTT 60.490 43.478 5.19 0.00 34.61 2.66
378 394 2.034179 GGAGCAGCGTTGGTTTTAAACT 59.966 45.455 5.19 0.00 34.61 2.66
379 395 2.034179 AGGAGCAGCGTTGGTTTTAAAC 59.966 45.455 5.19 0.00 34.61 2.01
380 396 2.034053 CAGGAGCAGCGTTGGTTTTAAA 59.966 45.455 5.19 0.00 34.61 1.52
427 443 7.332182 TGGAATGTGTCGCTTTTAAAAACTTTT 59.668 29.630 1.66 0.00 0.00 2.27
431 447 6.580476 CATGGAATGTGTCGCTTTTAAAAAC 58.420 36.000 1.66 0.00 40.20 2.43
432 448 6.761731 CATGGAATGTGTCGCTTTTAAAAA 57.238 33.333 1.66 0.00 40.20 1.94
461 477 0.677731 ATGCCGTGTCCAATGACCAG 60.678 55.000 0.00 0.00 41.01 4.00
557 580 1.385915 ATCATGGGGATGGACGGGT 60.386 57.895 0.00 0.00 34.06 5.28
561 584 2.644299 TGTATGGATCATGGGGATGGAC 59.356 50.000 0.00 0.00 36.00 4.02
569 592 1.139989 GTCGCGTGTATGGATCATGG 58.860 55.000 5.77 0.00 0.00 3.66
570 593 0.778223 CGTCGCGTGTATGGATCATG 59.222 55.000 5.77 0.00 0.00 3.07
674 704 3.431725 GAAAAGCGCCACTCCCCG 61.432 66.667 2.29 0.00 0.00 5.73
825 872 1.518572 CGCGTGGTATGGTCTGGTC 60.519 63.158 0.00 0.00 0.00 4.02
826 873 2.577059 CGCGTGGTATGGTCTGGT 59.423 61.111 0.00 0.00 0.00 4.00
827 874 2.890474 GCGCGTGGTATGGTCTGG 60.890 66.667 8.43 0.00 0.00 3.86
828 875 3.254654 CGCGCGTGGTATGGTCTG 61.255 66.667 24.19 0.00 0.00 3.51
829 876 3.695022 GACGCGCGTGGTATGGTCT 62.695 63.158 42.90 11.87 0.00 3.85
830 877 3.252484 GACGCGCGTGGTATGGTC 61.252 66.667 42.90 19.75 0.00 4.02
957 1013 0.830648 GCGCATATATAGGGCAGGGA 59.169 55.000 0.30 0.00 43.54 4.20
959 1015 1.154205 GCGCGCATATATAGGGCAGG 61.154 60.000 29.10 8.53 44.20 4.85
1078 1134 2.835431 CCCGATCTCCCGAGCTGT 60.835 66.667 0.00 0.00 0.00 4.40
1094 1150 4.840005 CTTCCCTCTTCCGCCGCC 62.840 72.222 0.00 0.00 0.00 6.13
1116 1178 3.966543 AACCAGCTCAACCCCGGG 61.967 66.667 15.80 15.80 0.00 5.73
1293 1359 1.137872 GATGCTGTCCGAGTTCATCCT 59.862 52.381 0.00 0.00 0.00 3.24
1367 1433 2.163815 CGACGGATGAGTTAGTTGGAGT 59.836 50.000 0.00 0.00 0.00 3.85
1369 1435 2.163010 GTCGACGGATGAGTTAGTTGGA 59.837 50.000 0.00 0.00 0.00 3.53
1408 1481 0.179163 GCCACATCGTTAGCCTTTGC 60.179 55.000 0.00 0.00 37.95 3.68
1409 1482 1.131126 CAGCCACATCGTTAGCCTTTG 59.869 52.381 0.00 0.00 0.00 2.77
1681 1760 2.025155 ACCTACTGATGGTAGCAGTCG 58.975 52.381 2.70 0.00 44.85 4.18
1709 1788 2.548920 GGCCTGATGACCCGAGAAATAG 60.549 54.545 0.00 0.00 0.00 1.73
1720 1800 5.415701 TGAACATTTTAAGAGGCCTGATGAC 59.584 40.000 12.00 0.00 0.00 3.06
1744 1824 3.870299 GCAGAAACGGGGAAGAAGAAGAT 60.870 47.826 0.00 0.00 0.00 2.40
1752 1832 1.002544 AGAAGAGCAGAAACGGGGAAG 59.997 52.381 0.00 0.00 0.00 3.46
1753 1833 1.056660 AGAAGAGCAGAAACGGGGAA 58.943 50.000 0.00 0.00 0.00 3.97
1754 1834 1.002087 GAAGAAGAGCAGAAACGGGGA 59.998 52.381 0.00 0.00 0.00 4.81
1755 1835 1.002544 AGAAGAAGAGCAGAAACGGGG 59.997 52.381 0.00 0.00 0.00 5.73
1756 1836 2.342179 GAGAAGAAGAGCAGAAACGGG 58.658 52.381 0.00 0.00 0.00 5.28
1757 1837 2.028567 AGGAGAAGAAGAGCAGAAACGG 60.029 50.000 0.00 0.00 0.00 4.44
1758 1838 3.249917 GAGGAGAAGAAGAGCAGAAACG 58.750 50.000 0.00 0.00 0.00 3.60
1762 1842 2.088423 GACGAGGAGAAGAAGAGCAGA 58.912 52.381 0.00 0.00 0.00 4.26
1763 1843 1.134175 GGACGAGGAGAAGAAGAGCAG 59.866 57.143 0.00 0.00 0.00 4.24
1787 1867 4.749310 ACAAGCAGAGCTCCCGCG 62.749 66.667 17.41 0.00 38.25 6.46
1837 1917 3.195661 ACACGAACACAGAAGTTCTTCC 58.804 45.455 1.56 0.00 44.37 3.46
1840 1920 4.369182 CCTTACACGAACACAGAAGTTCT 58.631 43.478 0.00 0.00 44.37 3.01
1853 1933 4.954202 ACATCTATCTCAACCCTTACACGA 59.046 41.667 0.00 0.00 0.00 4.35
1854 1934 5.263968 ACATCTATCTCAACCCTTACACG 57.736 43.478 0.00 0.00 0.00 4.49
1856 1936 6.212589 TCACAACATCTATCTCAACCCTTACA 59.787 38.462 0.00 0.00 0.00 2.41
1857 1937 6.640518 TCACAACATCTATCTCAACCCTTAC 58.359 40.000 0.00 0.00 0.00 2.34
1858 1938 6.867519 TCACAACATCTATCTCAACCCTTA 57.132 37.500 0.00 0.00 0.00 2.69
1859 1939 5.762179 TCACAACATCTATCTCAACCCTT 57.238 39.130 0.00 0.00 0.00 3.95
1860 1940 5.190528 ACATCACAACATCTATCTCAACCCT 59.809 40.000 0.00 0.00 0.00 4.34
1861 1941 5.431765 ACATCACAACATCTATCTCAACCC 58.568 41.667 0.00 0.00 0.00 4.11
1865 1945 9.463443 CGTATTTACATCACAACATCTATCTCA 57.537 33.333 0.00 0.00 0.00 3.27
1866 1946 8.916654 CCGTATTTACATCACAACATCTATCTC 58.083 37.037 0.00 0.00 0.00 2.75
1867 1947 8.638873 TCCGTATTTACATCACAACATCTATCT 58.361 33.333 0.00 0.00 0.00 1.98
1868 1948 8.812147 TCCGTATTTACATCACAACATCTATC 57.188 34.615 0.00 0.00 0.00 2.08
1869 1949 8.421784 ACTCCGTATTTACATCACAACATCTAT 58.578 33.333 0.00 0.00 0.00 1.98
1870 1950 7.778083 ACTCCGTATTTACATCACAACATCTA 58.222 34.615 0.00 0.00 0.00 1.98
1871 1951 6.640518 ACTCCGTATTTACATCACAACATCT 58.359 36.000 0.00 0.00 0.00 2.90
1872 1952 6.903883 ACTCCGTATTTACATCACAACATC 57.096 37.500 0.00 0.00 0.00 3.06
1875 1955 6.894828 ACAAACTCCGTATTTACATCACAAC 58.105 36.000 0.00 0.00 0.00 3.32
1890 1970 5.734311 CAGTACAGTTACAAACAAACTCCG 58.266 41.667 0.00 0.00 34.99 4.63
1900 1980 3.245754 CCGTTTTCGCAGTACAGTTACAA 59.754 43.478 0.00 0.00 42.58 2.41
1901 1981 2.796031 CCGTTTTCGCAGTACAGTTACA 59.204 45.455 0.00 0.00 42.58 2.41
1902 1982 2.156310 CCCGTTTTCGCAGTACAGTTAC 59.844 50.000 0.00 0.00 42.58 2.50
1904 1984 1.223187 CCCGTTTTCGCAGTACAGTT 58.777 50.000 0.00 0.00 42.58 3.16
1905 1985 0.601841 CCCCGTTTTCGCAGTACAGT 60.602 55.000 0.00 0.00 42.58 3.55
1906 1986 0.320073 TCCCCGTTTTCGCAGTACAG 60.320 55.000 0.00 0.00 42.58 2.74
1918 1998 2.432300 CCCGTATCTGCTCCCCGTT 61.432 63.158 0.00 0.00 0.00 4.44
1920 2000 2.520982 TCCCGTATCTGCTCCCCG 60.521 66.667 0.00 0.00 0.00 5.73
1924 2004 1.068250 GCACCTCCCGTATCTGCTC 59.932 63.158 0.00 0.00 0.00 4.26
1925 2005 2.786495 CGCACCTCCCGTATCTGCT 61.786 63.158 0.00 0.00 0.00 4.24
1926 2006 2.279517 CGCACCTCCCGTATCTGC 60.280 66.667 0.00 0.00 0.00 4.26
1927 2007 2.279517 GCGCACCTCCCGTATCTG 60.280 66.667 0.30 0.00 0.00 2.90
1928 2008 3.537874 GGCGCACCTCCCGTATCT 61.538 66.667 10.83 0.00 0.00 1.98
1929 2009 4.944372 CGGCGCACCTCCCGTATC 62.944 72.222 10.83 0.00 39.67 2.24
1934 2014 0.250166 ATAAATACGGCGCACCTCCC 60.250 55.000 10.83 0.00 0.00 4.30
1935 2015 1.145803 GATAAATACGGCGCACCTCC 58.854 55.000 10.83 0.00 0.00 4.30
1936 2016 1.792949 CAGATAAATACGGCGCACCTC 59.207 52.381 10.83 0.00 0.00 3.85
1937 2017 1.865865 CAGATAAATACGGCGCACCT 58.134 50.000 10.83 0.00 0.00 4.00
1938 2018 0.234884 GCAGATAAATACGGCGCACC 59.765 55.000 10.83 0.00 0.00 5.01
1939 2019 1.192534 GAGCAGATAAATACGGCGCAC 59.807 52.381 10.83 0.00 34.06 5.34
1940 2020 1.497991 GAGCAGATAAATACGGCGCA 58.502 50.000 10.83 0.00 34.06 6.09
1941 2021 0.790814 GGAGCAGATAAATACGGCGC 59.209 55.000 6.90 0.00 34.06 6.53
1942 2022 1.429463 GGGAGCAGATAAATACGGCG 58.571 55.000 4.80 4.80 34.06 6.46
1943 2023 1.809684 GGGGAGCAGATAAATACGGC 58.190 55.000 0.00 0.00 0.00 5.68
1944 2024 1.343465 ACGGGGAGCAGATAAATACGG 59.657 52.381 0.00 0.00 0.00 4.02
1945 2025 2.814280 ACGGGGAGCAGATAAATACG 57.186 50.000 0.00 0.00 0.00 3.06
1946 2026 5.830000 AAAAACGGGGAGCAGATAAATAC 57.170 39.130 0.00 0.00 0.00 1.89
1947 2027 6.713450 GGATAAAAACGGGGAGCAGATAAATA 59.287 38.462 0.00 0.00 0.00 1.40
1948 2028 5.535030 GGATAAAAACGGGGAGCAGATAAAT 59.465 40.000 0.00 0.00 0.00 1.40
1949 2029 4.885325 GGATAAAAACGGGGAGCAGATAAA 59.115 41.667 0.00 0.00 0.00 1.40
1950 2030 4.165372 AGGATAAAAACGGGGAGCAGATAA 59.835 41.667 0.00 0.00 0.00 1.75
1951 2031 3.714798 AGGATAAAAACGGGGAGCAGATA 59.285 43.478 0.00 0.00 0.00 1.98
1952 2032 2.509964 AGGATAAAAACGGGGAGCAGAT 59.490 45.455 0.00 0.00 0.00 2.90
1953 2033 1.913419 AGGATAAAAACGGGGAGCAGA 59.087 47.619 0.00 0.00 0.00 4.26
1954 2034 2.017049 CAGGATAAAAACGGGGAGCAG 58.983 52.381 0.00 0.00 0.00 4.24
1955 2035 1.340600 CCAGGATAAAAACGGGGAGCA 60.341 52.381 0.00 0.00 0.00 4.26
1956 2036 1.340697 ACCAGGATAAAAACGGGGAGC 60.341 52.381 0.00 0.00 0.00 4.70
1957 2037 2.801077 ACCAGGATAAAAACGGGGAG 57.199 50.000 0.00 0.00 0.00 4.30
1958 2038 4.654389 TTTACCAGGATAAAAACGGGGA 57.346 40.909 0.00 0.00 0.00 4.81
1959 2039 5.007921 CGTATTTACCAGGATAAAAACGGGG 59.992 44.000 0.00 0.00 0.00 5.73
1960 2040 5.007921 CCGTATTTACCAGGATAAAAACGGG 59.992 44.000 17.86 0.00 0.00 5.28
1961 2041 5.816777 TCCGTATTTACCAGGATAAAAACGG 59.183 40.000 18.70 18.70 36.05 4.44
1962 2042 6.510638 GCTCCGTATTTACCAGGATAAAAACG 60.511 42.308 0.00 2.15 31.66 3.60
1963 2043 6.541278 AGCTCCGTATTTACCAGGATAAAAAC 59.459 38.462 0.00 0.00 31.66 2.43
1964 2044 6.655930 AGCTCCGTATTTACCAGGATAAAAA 58.344 36.000 0.00 0.00 31.66 1.94
1965 2045 6.099269 AGAGCTCCGTATTTACCAGGATAAAA 59.901 38.462 10.93 0.00 31.66 1.52
1966 2046 5.601313 AGAGCTCCGTATTTACCAGGATAAA 59.399 40.000 10.93 0.00 31.66 1.40
1967 2047 5.145564 AGAGCTCCGTATTTACCAGGATAA 58.854 41.667 10.93 0.00 31.66 1.75
1968 2048 4.737578 AGAGCTCCGTATTTACCAGGATA 58.262 43.478 10.93 0.00 31.66 2.59
1969 2049 3.574826 GAGAGCTCCGTATTTACCAGGAT 59.425 47.826 10.93 0.00 31.66 3.24
1970 2050 2.957006 GAGAGCTCCGTATTTACCAGGA 59.043 50.000 10.93 0.00 0.00 3.86
1971 2051 2.959707 AGAGAGCTCCGTATTTACCAGG 59.040 50.000 10.93 0.00 0.00 4.45
1972 2052 4.657436 AAGAGAGCTCCGTATTTACCAG 57.343 45.455 10.93 0.00 0.00 4.00
1973 2053 4.464951 TGAAAGAGAGCTCCGTATTTACCA 59.535 41.667 10.93 0.00 0.00 3.25
1974 2054 4.804665 GTGAAAGAGAGCTCCGTATTTACC 59.195 45.833 10.93 0.00 0.00 2.85
1975 2055 5.652518 AGTGAAAGAGAGCTCCGTATTTAC 58.347 41.667 10.93 7.86 0.00 2.01
1976 2056 5.916661 AGTGAAAGAGAGCTCCGTATTTA 57.083 39.130 10.93 0.00 0.00 1.40
1977 2057 4.810191 AGTGAAAGAGAGCTCCGTATTT 57.190 40.909 10.93 2.39 0.00 1.40
1978 2058 4.499183 CAAGTGAAAGAGAGCTCCGTATT 58.501 43.478 10.93 0.33 0.00 1.89
1979 2059 3.118956 CCAAGTGAAAGAGAGCTCCGTAT 60.119 47.826 10.93 0.00 0.00 3.06
1980 2060 2.231478 CCAAGTGAAAGAGAGCTCCGTA 59.769 50.000 10.93 0.00 0.00 4.02
1981 2061 1.001406 CCAAGTGAAAGAGAGCTCCGT 59.999 52.381 10.93 0.00 0.00 4.69
1982 2062 1.674221 CCCAAGTGAAAGAGAGCTCCG 60.674 57.143 10.93 0.00 0.00 4.63
1983 2063 1.948144 GCCCAAGTGAAAGAGAGCTCC 60.948 57.143 10.93 1.70 0.00 4.70
1984 2064 1.003003 AGCCCAAGTGAAAGAGAGCTC 59.997 52.381 5.27 5.27 0.00 4.09
1985 2065 1.063183 AGCCCAAGTGAAAGAGAGCT 58.937 50.000 0.00 0.00 0.00 4.09
1989 2069 1.363744 CGCTAGCCCAAGTGAAAGAG 58.636 55.000 9.66 0.00 0.00 2.85
1991 2071 0.955428 TGCGCTAGCCCAAGTGAAAG 60.955 55.000 9.73 0.00 44.33 2.62
2000 2080 1.222115 CGTATCCTTTGCGCTAGCCC 61.222 60.000 9.73 0.00 44.33 5.19
2004 2108 0.387929 CTCCCGTATCCTTTGCGCTA 59.612 55.000 9.73 0.00 31.38 4.26
2077 2182 3.120338 GCAGCGCTACACTGTAAATTTGA 60.120 43.478 10.99 0.00 37.47 2.69
2102 2207 6.660949 AGAATCTACCTGAAATTCCAAACCTG 59.339 38.462 0.00 0.00 31.21 4.00
2103 2208 6.660949 CAGAATCTACCTGAAATTCCAAACCT 59.339 38.462 0.00 0.00 33.65 3.50
2106 2211 6.009589 TGCAGAATCTACCTGAAATTCCAAA 58.990 36.000 0.00 0.00 33.65 3.28
2115 2220 5.559770 TGAAACATTGCAGAATCTACCTGA 58.440 37.500 0.00 0.00 33.65 3.86
2118 2223 5.182001 ACACTGAAACATTGCAGAATCTACC 59.818 40.000 6.61 0.00 36.07 3.18
2139 2244 1.399089 GAGGAGCTACGAGTGAGACAC 59.601 57.143 0.00 0.00 34.10 3.67
2146 2251 2.020720 CATGAGTGAGGAGCTACGAGT 58.979 52.381 0.00 0.00 0.00 4.18
2148 2253 2.420058 TCATGAGTGAGGAGCTACGA 57.580 50.000 0.00 0.00 0.00 3.43
2150 2255 5.278758 GGAGTTATCATGAGTGAGGAGCTAC 60.279 48.000 0.09 0.00 37.87 3.58
2151 2256 4.830046 GGAGTTATCATGAGTGAGGAGCTA 59.170 45.833 0.09 0.00 37.87 3.32
2153 2258 3.386078 TGGAGTTATCATGAGTGAGGAGC 59.614 47.826 0.09 0.00 37.87 4.70
2154 2259 4.498850 CGTGGAGTTATCATGAGTGAGGAG 60.499 50.000 0.09 0.00 37.87 3.69
2155 2260 3.381590 CGTGGAGTTATCATGAGTGAGGA 59.618 47.826 0.09 0.00 37.87 3.71
2156 2261 3.711086 CGTGGAGTTATCATGAGTGAGG 58.289 50.000 0.09 0.00 37.87 3.86
2158 2263 2.760650 AGCGTGGAGTTATCATGAGTGA 59.239 45.455 0.09 0.00 39.04 3.41
2159 2264 2.862536 CAGCGTGGAGTTATCATGAGTG 59.137 50.000 0.09 0.00 0.00 3.51
2160 2265 2.159043 CCAGCGTGGAGTTATCATGAGT 60.159 50.000 0.09 0.00 40.96 3.41
2161 2266 2.477825 CCAGCGTGGAGTTATCATGAG 58.522 52.381 0.09 0.00 40.96 2.90
2163 2268 1.586422 CCCAGCGTGGAGTTATCATG 58.414 55.000 5.71 0.00 40.96 3.07
2164 2269 0.469917 CCCCAGCGTGGAGTTATCAT 59.530 55.000 5.71 0.00 40.96 2.45
2165 2270 0.907704 ACCCCAGCGTGGAGTTATCA 60.908 55.000 5.71 0.00 40.96 2.15
2166 2271 0.179081 GACCCCAGCGTGGAGTTATC 60.179 60.000 5.71 0.00 40.96 1.75
2167 2272 0.907704 TGACCCCAGCGTGGAGTTAT 60.908 55.000 5.71 0.00 40.96 1.89
2178 2283 5.720371 TTTGATAACAATTGTGACCCCAG 57.280 39.130 12.82 0.00 35.85 4.45
2183 2288 7.867445 AACGGAATTTGATAACAATTGTGAC 57.133 32.000 12.82 7.35 35.85 3.67
2184 2289 9.400638 GTAAACGGAATTTGATAACAATTGTGA 57.599 29.630 12.82 4.62 35.85 3.58
2185 2290 9.186323 TGTAAACGGAATTTGATAACAATTGTG 57.814 29.630 12.82 0.00 35.85 3.33
2255 2360 7.765695 ACAATGGAAACTATGAATGAAGTGT 57.234 32.000 0.00 0.00 0.00 3.55
2256 2361 7.904977 CGTACAATGGAAACTATGAATGAAGTG 59.095 37.037 0.00 0.00 0.00 3.16
2261 2366 9.225201 CAATTCGTACAATGGAAACTATGAATG 57.775 33.333 0.00 0.00 28.88 2.67
2262 2367 9.173021 TCAATTCGTACAATGGAAACTATGAAT 57.827 29.630 0.00 0.00 29.26 2.57
2263 2368 8.554835 TCAATTCGTACAATGGAAACTATGAA 57.445 30.769 0.00 0.00 0.00 2.57
2264 2369 8.554835 TTCAATTCGTACAATGGAAACTATGA 57.445 30.769 0.00 0.00 0.00 2.15
2265 2370 9.787532 ATTTCAATTCGTACAATGGAAACTATG 57.212 29.630 16.31 3.41 33.72 2.23
2266 2371 9.787532 CATTTCAATTCGTACAATGGAAACTAT 57.212 29.630 16.31 5.44 33.72 2.12
2297 2402 5.198207 TGATGACCTCATGCTCAATTTCAT 58.802 37.500 0.00 0.00 36.57 2.57
2303 2408 2.417787 CGACTGATGACCTCATGCTCAA 60.418 50.000 0.00 0.00 36.57 3.02
2317 2422 0.179000 GAGGATTGTGCCCGACTGAT 59.821 55.000 0.00 0.00 0.00 2.90
2320 2425 0.325296 TAGGAGGATTGTGCCCGACT 60.325 55.000 0.00 0.00 0.00 4.18
2328 2433 1.403687 GCCGCTCCTAGGAGGATTGT 61.404 60.000 34.75 0.00 44.81 2.71
2329 2434 1.369321 GCCGCTCCTAGGAGGATTG 59.631 63.158 34.75 14.94 44.81 2.67
2331 2436 2.203714 GGCCGCTCCTAGGAGGAT 60.204 66.667 34.75 0.00 44.81 3.24
2337 2442 1.335132 TTACCCTTGGCCGCTCCTAG 61.335 60.000 0.00 0.00 37.43 3.02
2338 2443 0.693092 ATTACCCTTGGCCGCTCCTA 60.693 55.000 0.00 0.00 35.26 2.94
2339 2444 2.001269 ATTACCCTTGGCCGCTCCT 61.001 57.895 0.00 0.00 35.26 3.69
2344 2449 3.209097 CCGCATTACCCTTGGCCG 61.209 66.667 0.00 0.00 0.00 6.13
2345 2450 2.119029 GTCCGCATTACCCTTGGCC 61.119 63.158 0.00 0.00 0.00 5.36
2348 2453 2.469516 GCCGTCCGCATTACCCTTG 61.470 63.158 0.00 0.00 37.47 3.61
2349 2454 2.124860 GCCGTCCGCATTACCCTT 60.125 61.111 0.00 0.00 37.47 3.95
2354 2459 2.110213 GGATGGCCGTCCGCATTA 59.890 61.111 28.22 0.00 40.31 1.90
2392 2502 0.038159 CCGACAACTCTGGACTGGAC 60.038 60.000 0.00 0.00 0.00 4.02
2521 2632 1.762957 GGCTCCTACTGGATTGCTACA 59.237 52.381 0.00 0.00 42.29 2.74
2525 2636 0.464554 GTGGGCTCCTACTGGATTGC 60.465 60.000 0.00 0.00 42.29 3.56
2592 2703 2.092375 GGCTTGACAACCCCTAATAGCT 60.092 50.000 0.00 0.00 0.00 3.32
2760 2872 2.368875 ACTAGTGAAATCTATGGCCCCG 59.631 50.000 0.00 0.00 0.00 5.73
2771 2883 8.194769 GCTCTTAAGAGAAGCTACTAGTGAAAT 58.805 37.037 32.16 0.00 44.74 2.17
2782 2894 8.923270 AGAATACTTATGCTCTTAAGAGAAGCT 58.077 33.333 32.16 18.57 44.74 3.74
2791 2903 8.721133 TCCACCATAGAATACTTATGCTCTTA 57.279 34.615 0.00 0.00 0.00 2.10
2828 2940 6.146601 TCAATTCTGTCAATTGCTCAACAA 57.853 33.333 0.00 0.00 44.01 2.83


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

AutoCloner maintained by Alex Coulton.