Multiple sequence alignment - TraesCS1B01G424300

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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 TraesCS1B01G424300 chr1B 100.000 2663 0 0 1 2663 648030795 648033457 0.000000e+00 4918.0
1 TraesCS1B01G424300 chr1D 89.476 1929 88 44 1 1889 468720331 468722184 0.000000e+00 2331.0
2 TraesCS1B01G424300 chr1A 92.195 1435 52 21 467 1889 561496342 561497728 0.000000e+00 1975.0
3 TraesCS1B01G424300 chr1A 95.833 192 3 5 274 464 561496028 561496215 3.330000e-79 305.0
4 TraesCS1B01G424300 chr1A 80.928 388 58 13 2284 2663 23017570 23017949 2.590000e-75 292.0
5 TraesCS1B01G424300 chr1A 84.456 193 15 8 1 191 561495828 561496007 2.720000e-40 176.0
6 TraesCS1B01G424300 chr3B 84.075 427 42 20 2112 2531 785683094 785682687 3.210000e-104 388.0
7 TraesCS1B01G424300 chr3B 85.417 96 12 2 1921 2014 785683283 785683188 6.070000e-17 99.0
8 TraesCS1B01G424300 chr3B 100.000 28 0 0 1950 1977 646718084 646718057 5.000000e-03 52.8
9 TraesCS1B01G424300 chr7A 84.054 370 45 13 2293 2656 275710269 275709908 7.060000e-91 344.0
10 TraesCS1B01G424300 chr7A 81.395 387 58 12 2284 2663 100550212 100550591 1.200000e-78 303.0
11 TraesCS1B01G424300 chr7D 83.033 389 49 12 2284 2663 265266014 265266394 1.180000e-88 337.0
12 TraesCS1B01G424300 chr6D 82.880 368 46 13 2287 2645 143660462 143660103 5.530000e-82 315.0
13 TraesCS1B01G424300 chr6D 91.111 90 8 0 4 93 12458509 12458420 3.600000e-24 122.0
14 TraesCS1B01G424300 chr6D 80.519 77 13 2 1922 1998 36770061 36770135 1.030000e-04 58.4
15 TraesCS1B01G424300 chr4D 82.078 385 53 10 2287 2663 506608658 506608282 5.530000e-82 315.0
16 TraesCS1B01G424300 chr5A 81.347 386 55 14 2287 2663 239403590 239403213 5.570000e-77 298.0
17 TraesCS1B01G424300 chr5A 91.139 79 7 0 5 83 51477556 51477478 1.010000e-19 108.0
18 TraesCS1B01G424300 chr3D 81.432 377 53 12 2284 2651 507767292 507767660 2.590000e-75 292.0


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 TraesCS1B01G424300 chr1B 648030795 648033457 2662 False 4918.000000 4918 100.000 1 2663 1 chr1B.!!$F1 2662
1 TraesCS1B01G424300 chr1D 468720331 468722184 1853 False 2331.000000 2331 89.476 1 1889 1 chr1D.!!$F1 1888
2 TraesCS1B01G424300 chr1A 561495828 561497728 1900 False 818.666667 1975 90.828 1 1889 3 chr1A.!!$F2 1888
3 TraesCS1B01G424300 chr3B 785682687 785683283 596 True 243.500000 388 84.746 1921 2531 2 chr3B.!!$R2 610

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
110 111 0.249398 AGCGTTCCGGCTAAATCTGT 59.751 50.0 0.0 0.0 42.62 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2196 0.389166 GACTTGGTCAGAGTGGCGAG 60.389 60.0 0.0 0.0 32.09 5.03 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
109 110 0.931005 GAGCGTTCCGGCTAAATCTG 59.069 55.000 0.00 0.00 44.93 2.90
110 111 0.249398 AGCGTTCCGGCTAAATCTGT 59.751 50.000 0.00 0.00 42.62 3.41
111 112 1.084289 GCGTTCCGGCTAAATCTGTT 58.916 50.000 0.00 0.00 0.00 3.16
112 113 1.062148 GCGTTCCGGCTAAATCTGTTC 59.938 52.381 0.00 0.00 0.00 3.18
113 114 1.664151 CGTTCCGGCTAAATCTGTTCC 59.336 52.381 0.00 0.00 0.00 3.62
114 115 1.664151 GTTCCGGCTAAATCTGTTCCG 59.336 52.381 0.00 0.00 39.79 4.30
136 137 1.959899 GAAGCGCTCATGACACCGTG 61.960 60.000 12.06 0.00 0.00 4.94
184 196 1.503818 TTTCGCTTGCCGTCCAGTTC 61.504 55.000 0.00 0.00 38.35 3.01
185 197 2.357517 CGCTTGCCGTCCAGTTCT 60.358 61.111 0.00 0.00 0.00 3.01
186 198 1.080093 CGCTTGCCGTCCAGTTCTA 60.080 57.895 0.00 0.00 0.00 2.10
187 199 1.078759 CGCTTGCCGTCCAGTTCTAG 61.079 60.000 0.00 0.00 0.00 2.43
188 200 0.741221 GCTTGCCGTCCAGTTCTAGG 60.741 60.000 0.00 0.00 0.00 3.02
189 201 0.895530 CTTGCCGTCCAGTTCTAGGA 59.104 55.000 0.00 0.00 0.00 2.94
190 202 1.482593 CTTGCCGTCCAGTTCTAGGAT 59.517 52.381 0.00 0.00 37.52 3.24
191 203 1.112113 TGCCGTCCAGTTCTAGGATC 58.888 55.000 0.00 0.00 37.52 3.36
192 204 1.342076 TGCCGTCCAGTTCTAGGATCT 60.342 52.381 0.00 0.00 37.52 2.75
198 210 4.211920 GTCCAGTTCTAGGATCTGCTAGT 58.788 47.826 5.76 0.00 37.52 2.57
207 219 2.892852 AGGATCTGCTAGTGATGCTCTC 59.107 50.000 13.18 0.00 37.98 3.20
208 220 2.627221 GGATCTGCTAGTGATGCTCTCA 59.373 50.000 10.43 0.00 31.05 3.27
231 243 4.505191 ACACCCGAAATCGTATAAACATCG 59.495 41.667 1.79 0.00 37.74 3.84
241 253 5.623335 TCGTATAAACATCGTTGCCAAAAG 58.377 37.500 0.00 0.00 0.00 2.27
245 257 7.113684 CGTATAAACATCGTTGCCAAAAGAAAA 59.886 33.333 0.00 0.00 0.00 2.29
247 259 5.463499 AACATCGTTGCCAAAAGAAAAAC 57.537 34.783 0.00 0.00 0.00 2.43
248 260 4.499183 ACATCGTTGCCAAAAGAAAAACA 58.501 34.783 0.00 0.00 0.00 2.83
250 262 5.409826 ACATCGTTGCCAAAAGAAAAACAAA 59.590 32.000 0.00 0.00 0.00 2.83
251 263 5.270812 TCGTTGCCAAAAGAAAAACAAAC 57.729 34.783 0.00 0.00 0.00 2.93
252 264 4.152580 TCGTTGCCAAAAGAAAAACAAACC 59.847 37.500 0.00 0.00 0.00 3.27
253 265 4.153296 CGTTGCCAAAAGAAAAACAAACCT 59.847 37.500 0.00 0.00 0.00 3.50
270 282 9.772973 AAACAAACCTTATAAACAATTCCCTTC 57.227 29.630 0.00 0.00 0.00 3.46
313 325 1.674322 GTAGTGGGCCGCACACATT 60.674 57.895 27.10 10.54 41.21 2.71
345 357 4.487412 CGGACGCACGTCTACCCC 62.487 72.222 21.19 5.55 44.04 4.95
369 381 4.672801 GCTCAAAGTCTTTGCCTAAATCCG 60.673 45.833 18.80 0.00 40.43 4.18
402 414 0.465460 TCGTGCCAAAGCCTTTCACT 60.465 50.000 7.25 0.00 38.69 3.41
424 436 0.375454 CACAAAAACGCACTGGACGA 59.625 50.000 0.00 0.00 0.00 4.20
426 438 0.653323 CAAAAACGCACTGGACGACG 60.653 55.000 0.00 0.00 0.00 5.12
427 439 2.369477 AAAAACGCACTGGACGACGC 62.369 55.000 0.00 0.00 0.00 5.19
504 670 1.737838 CCATCGTGCACAGTAATGGT 58.262 50.000 18.64 0.00 33.66 3.55
514 680 6.417044 CGTGCACAGTAATGGTTATCTACTAC 59.583 42.308 18.64 0.00 0.00 2.73
515 681 7.490000 GTGCACAGTAATGGTTATCTACTACT 58.510 38.462 13.17 0.00 0.00 2.57
516 682 8.627403 GTGCACAGTAATGGTTATCTACTACTA 58.373 37.037 13.17 0.00 0.00 1.82
517 683 9.363401 TGCACAGTAATGGTTATCTACTACTAT 57.637 33.333 0.00 0.00 0.00 2.12
639 805 2.597217 CGGAAGCAACCCAAGGCA 60.597 61.111 0.00 0.00 0.00 4.75
911 1080 0.798159 GCTGTCACACATCATTCGCA 59.202 50.000 0.00 0.00 0.00 5.10
917 1086 2.019249 CACACATCATTCGCATTCCCT 58.981 47.619 0.00 0.00 0.00 4.20
922 1091 1.037030 TCATTCGCATTCCCTTGCCC 61.037 55.000 0.00 0.00 39.52 5.36
938 1107 0.257905 GCCCCTCCTTCCGGTTTATT 59.742 55.000 0.00 0.00 0.00 1.40
939 1108 1.749635 GCCCCTCCTTCCGGTTTATTC 60.750 57.143 0.00 0.00 0.00 1.75
940 1109 1.562475 CCCCTCCTTCCGGTTTATTCA 59.438 52.381 0.00 0.00 0.00 2.57
963 1132 6.426025 TCATCATCATAGGCAAGATTCTTTCG 59.574 38.462 0.00 0.00 0.00 3.46
966 1135 5.084818 TCATAGGCAAGATTCTTTCGTCA 57.915 39.130 0.00 0.00 0.00 4.35
971 1140 3.126000 GGCAAGATTCTTTCGTCAAGAGG 59.874 47.826 0.00 0.00 42.76 3.69
980 1149 4.770531 TCTTTCGTCAAGAGGGTAGATTGA 59.229 41.667 0.00 0.00 36.51 2.57
991 1160 1.404391 GGTAGATTGAAGCGAGTCCGA 59.596 52.381 0.00 0.00 38.22 4.55
1584 1762 3.142838 GTGCTGCCCATCGCCATT 61.143 61.111 0.00 0.00 36.24 3.16
1620 1798 1.079057 GCTCTTCGTCACCTTCCCC 60.079 63.158 0.00 0.00 0.00 4.81
1674 1852 2.287427 GCAGCATTGATTGATTCCCGAG 60.287 50.000 0.00 0.00 0.00 4.63
1697 1875 2.300437 GCTGCCCTTCCTACTATTCGAT 59.700 50.000 0.00 0.00 0.00 3.59
1698 1876 3.615351 GCTGCCCTTCCTACTATTCGATC 60.615 52.174 0.00 0.00 0.00 3.69
1699 1877 2.897969 TGCCCTTCCTACTATTCGATCC 59.102 50.000 0.00 0.00 0.00 3.36
1700 1878 2.897969 GCCCTTCCTACTATTCGATCCA 59.102 50.000 0.00 0.00 0.00 3.41
1723 1901 7.976734 TCCACGATTATTTCTTCTTCTCTCTTC 59.023 37.037 0.00 0.00 0.00 2.87
1725 1903 9.019764 CACGATTATTTCTTCTTCTCTCTTCTC 57.980 37.037 0.00 0.00 0.00 2.87
1727 1905 9.801873 CGATTATTTCTTCTTCTCTCTTCTCTT 57.198 33.333 0.00 0.00 0.00 2.85
1730 1908 9.703892 TTATTTCTTCTTCTCTCTTCTCTTGTG 57.296 33.333 0.00 0.00 0.00 3.33
1731 1909 5.720371 TCTTCTTCTCTCTTCTCTTGTGG 57.280 43.478 0.00 0.00 0.00 4.17
1732 1910 5.389520 TCTTCTTCTCTCTTCTCTTGTGGA 58.610 41.667 0.00 0.00 0.00 4.02
1733 1911 5.476599 TCTTCTTCTCTCTTCTCTTGTGGAG 59.523 44.000 0.00 0.00 43.12 3.86
1734 1912 4.735369 TCTTCTCTCTTCTCTTGTGGAGT 58.265 43.478 0.00 0.00 42.40 3.85
1735 1913 5.882040 TCTTCTCTCTTCTCTTGTGGAGTA 58.118 41.667 0.00 0.00 42.40 2.59
1736 1914 6.489603 TCTTCTCTCTTCTCTTGTGGAGTAT 58.510 40.000 0.00 0.00 42.40 2.12
1737 1915 7.634718 TCTTCTCTCTTCTCTTGTGGAGTATA 58.365 38.462 0.00 0.00 42.40 1.47
1738 1916 8.110271 TCTTCTCTCTTCTCTTGTGGAGTATAA 58.890 37.037 0.00 0.00 42.40 0.98
1739 1917 8.651589 TTCTCTCTTCTCTTGTGGAGTATAAA 57.348 34.615 0.00 0.00 42.40 1.40
1740 1918 8.287439 TCTCTCTTCTCTTGTGGAGTATAAAG 57.713 38.462 0.00 0.00 42.40 1.85
1741 1919 8.110271 TCTCTCTTCTCTTGTGGAGTATAAAGA 58.890 37.037 0.00 0.00 42.40 2.52
1742 1920 8.651589 TCTCTTCTCTTGTGGAGTATAAAGAA 57.348 34.615 0.00 0.00 42.40 2.52
1743 1921 9.090103 TCTCTTCTCTTGTGGAGTATAAAGAAA 57.910 33.333 0.00 0.00 42.40 2.52
1744 1922 9.712305 CTCTTCTCTTGTGGAGTATAAAGAAAA 57.288 33.333 0.00 0.00 42.40 2.29
1745 1923 9.712305 TCTTCTCTTGTGGAGTATAAAGAAAAG 57.288 33.333 0.00 0.00 42.40 2.27
1752 1930 9.691362 TTGTGGAGTATAAAGAAAAGAAAATGC 57.309 29.630 0.00 0.00 0.00 3.56
1792 1970 3.129502 CCGCGACGAGGGAGTACA 61.130 66.667 8.23 0.00 34.27 2.90
1798 1976 1.538512 CGACGAGGGAGTACAAAGTGA 59.461 52.381 0.00 0.00 0.00 3.41
1821 1999 7.168804 GTGACAGGCGGTAAAGAGTAAATATAC 59.831 40.741 0.00 0.00 0.00 1.47
1822 2000 6.519382 ACAGGCGGTAAAGAGTAAATATACC 58.481 40.000 0.00 0.00 34.09 2.73
1861 2043 2.225467 GTCCCTCATATTTGCCTCAGC 58.775 52.381 0.00 0.00 40.48 4.26
1865 2047 3.434739 CCCTCATATTTGCCTCAGCTTCT 60.435 47.826 0.00 0.00 40.80 2.85
1889 2071 3.084786 CTGAAAGACCCTCATCCCAAAC 58.915 50.000 0.00 0.00 34.07 2.93
1890 2072 2.084546 GAAAGACCCTCATCCCAAACG 58.915 52.381 0.00 0.00 0.00 3.60
1891 2073 0.322546 AAGACCCTCATCCCAAACGC 60.323 55.000 0.00 0.00 0.00 4.84
1892 2074 1.002624 GACCCTCATCCCAAACGCA 60.003 57.895 0.00 0.00 0.00 5.24
1893 2075 1.002134 ACCCTCATCCCAAACGCAG 60.002 57.895 0.00 0.00 0.00 5.18
1894 2076 2.409870 CCCTCATCCCAAACGCAGC 61.410 63.158 0.00 0.00 0.00 5.25
1895 2077 2.753966 CCTCATCCCAAACGCAGCG 61.754 63.158 14.82 14.82 0.00 5.18
1896 2078 1.741401 CTCATCCCAAACGCAGCGA 60.741 57.895 24.65 0.00 0.00 4.93
1897 2079 1.970917 CTCATCCCAAACGCAGCGAC 61.971 60.000 24.65 0.00 0.00 5.19
1898 2080 2.034879 CATCCCAAACGCAGCGACT 61.035 57.895 24.65 4.88 0.00 4.18
1899 2081 0.739462 CATCCCAAACGCAGCGACTA 60.739 55.000 24.65 0.40 0.00 2.59
1900 2082 0.178068 ATCCCAAACGCAGCGACTAT 59.822 50.000 24.65 1.15 0.00 2.12
1901 2083 0.036765 TCCCAAACGCAGCGACTATT 60.037 50.000 24.65 7.92 0.00 1.73
1902 2084 0.802494 CCCAAACGCAGCGACTATTT 59.198 50.000 24.65 8.68 0.00 1.40
1903 2085 2.004017 CCCAAACGCAGCGACTATTTA 58.996 47.619 24.65 0.00 0.00 1.40
1904 2086 2.612212 CCCAAACGCAGCGACTATTTAT 59.388 45.455 24.65 0.00 0.00 1.40
1905 2087 3.303132 CCCAAACGCAGCGACTATTTATC 60.303 47.826 24.65 0.00 0.00 1.75
1906 2088 3.522362 CAAACGCAGCGACTATTTATCG 58.478 45.455 24.65 0.00 42.55 2.92
1949 2132 1.394917 CTGAAGCGGTTGGAGAAATCG 59.605 52.381 3.70 0.00 45.55 3.34
1953 2136 1.078426 CGGTTGGAGAAATCGGGCT 60.078 57.895 0.00 0.00 38.79 5.19
1984 2167 5.744345 TGTTCGCGCAGAAAAAGAAAAATAA 59.256 32.000 8.75 0.00 41.10 1.40
1985 2168 6.419413 TGTTCGCGCAGAAAAAGAAAAATAAT 59.581 30.769 8.75 0.00 41.10 1.28
1989 2172 9.944663 TCGCGCAGAAAAAGAAAAATAATATAT 57.055 25.926 8.75 0.00 0.00 0.86
2008 2191 1.227292 GGGAGAAGCGGGATTCGAC 60.227 63.158 0.00 0.00 42.43 4.20
2016 2199 2.107141 GGGATTCGACCCTGCTCG 59.893 66.667 3.83 0.00 45.90 5.03
2017 2200 2.586357 GGATTCGACCCTGCTCGC 60.586 66.667 0.00 0.00 33.47 5.03
2018 2201 2.586357 GATTCGACCCTGCTCGCC 60.586 66.667 0.00 0.00 33.47 5.54
2022 2231 4.803426 CGACCCTGCTCGCCACTC 62.803 72.222 0.00 0.00 0.00 3.51
2023 2232 3.386237 GACCCTGCTCGCCACTCT 61.386 66.667 0.00 0.00 0.00 3.24
2025 2234 3.385384 CCCTGCTCGCCACTCTGA 61.385 66.667 0.00 0.00 0.00 3.27
2027 2236 2.125753 CTGCTCGCCACTCTGACC 60.126 66.667 0.00 0.00 0.00 4.02
2029 2238 2.343758 GCTCGCCACTCTGACCAA 59.656 61.111 0.00 0.00 0.00 3.67
2033 2242 0.827925 TCGCCACTCTGACCAAGTCT 60.828 55.000 0.00 0.00 33.15 3.24
2034 2243 0.389166 CGCCACTCTGACCAAGTCTC 60.389 60.000 0.00 0.00 33.15 3.36
2038 2247 1.000283 CACTCTGACCAAGTCTCGCTT 60.000 52.381 0.00 0.00 38.08 4.68
2054 2263 5.683743 GTCTCGCTTGTGATAAGTATGAGAC 59.316 44.000 17.54 17.54 41.82 3.36
2056 2265 3.180584 CGCTTGTGATAAGTATGAGACGC 59.819 47.826 0.00 0.00 0.00 5.19
2057 2266 3.491267 GCTTGTGATAAGTATGAGACGCC 59.509 47.826 0.00 0.00 0.00 5.68
2059 2268 5.339008 TTGTGATAAGTATGAGACGCCTT 57.661 39.130 0.00 0.00 0.00 4.35
2060 2269 5.339008 TGTGATAAGTATGAGACGCCTTT 57.661 39.130 0.00 0.00 0.00 3.11
2062 2271 6.170506 TGTGATAAGTATGAGACGCCTTTTT 58.829 36.000 0.00 0.00 0.00 1.94
2082 2291 3.434940 TTTTAGAAGAACAGGGAGGCC 57.565 47.619 0.00 0.00 0.00 5.19
2083 2292 2.038863 TTAGAAGAACAGGGAGGCCA 57.961 50.000 5.01 0.00 0.00 5.36
2084 2293 2.270434 TAGAAGAACAGGGAGGCCAT 57.730 50.000 5.01 0.00 0.00 4.40
2085 2294 1.376649 AGAAGAACAGGGAGGCCATT 58.623 50.000 5.01 0.00 0.00 3.16
2086 2295 1.713078 AGAAGAACAGGGAGGCCATTT 59.287 47.619 5.01 0.00 0.00 2.32
2087 2296 1.821136 GAAGAACAGGGAGGCCATTTG 59.179 52.381 5.01 0.00 0.00 2.32
2088 2297 0.779997 AGAACAGGGAGGCCATTTGT 59.220 50.000 5.01 0.24 0.00 2.83
2089 2298 1.147817 AGAACAGGGAGGCCATTTGTT 59.852 47.619 5.01 10.10 34.91 2.83
2090 2299 1.970640 GAACAGGGAGGCCATTTGTTT 59.029 47.619 5.01 0.00 32.58 2.83
2091 2300 2.101640 ACAGGGAGGCCATTTGTTTT 57.898 45.000 5.01 0.00 0.00 2.43
2092 2301 1.970640 ACAGGGAGGCCATTTGTTTTC 59.029 47.619 5.01 0.00 0.00 2.29
2093 2302 1.276138 CAGGGAGGCCATTTGTTTTCC 59.724 52.381 5.01 0.00 0.00 3.13
2094 2303 1.132881 AGGGAGGCCATTTGTTTTCCA 60.133 47.619 5.01 0.00 0.00 3.53
2095 2304 1.001974 GGGAGGCCATTTGTTTTCCAC 59.998 52.381 5.01 0.00 0.00 4.02
2096 2305 1.970640 GGAGGCCATTTGTTTTCCACT 59.029 47.619 5.01 0.00 0.00 4.00
2097 2306 2.029020 GGAGGCCATTTGTTTTCCACTC 60.029 50.000 5.01 0.00 0.00 3.51
2098 2307 1.970640 AGGCCATTTGTTTTCCACTCC 59.029 47.619 5.01 0.00 0.00 3.85
2099 2308 1.336795 GGCCATTTGTTTTCCACTCCG 60.337 52.381 0.00 0.00 0.00 4.63
2100 2309 1.611491 GCCATTTGTTTTCCACTCCGA 59.389 47.619 0.00 0.00 0.00 4.55
2101 2310 2.035321 GCCATTTGTTTTCCACTCCGAA 59.965 45.455 0.00 0.00 0.00 4.30
2102 2311 3.638484 CCATTTGTTTTCCACTCCGAAC 58.362 45.455 0.00 0.00 0.00 3.95
2103 2312 3.067461 CCATTTGTTTTCCACTCCGAACA 59.933 43.478 0.00 0.00 0.00 3.18
2104 2313 4.440802 CCATTTGTTTTCCACTCCGAACAA 60.441 41.667 0.00 0.00 39.44 2.83
2105 2314 4.785511 TTTGTTTTCCACTCCGAACAAA 57.214 36.364 8.62 8.62 44.81 2.83
2106 2315 4.785511 TTGTTTTCCACTCCGAACAAAA 57.214 36.364 0.00 0.00 38.58 2.44
2107 2316 4.785511 TGTTTTCCACTCCGAACAAAAA 57.214 36.364 0.00 0.00 0.00 1.94
2132 2341 5.752955 AGTCGGTTTTCCATTTGTTTTCATG 59.247 36.000 0.00 0.00 40.70 3.07
2133 2342 5.522097 GTCGGTTTTCCATTTGTTTTCATGT 59.478 36.000 0.00 0.00 40.70 3.21
2135 2344 6.595716 TCGGTTTTCCATTTGTTTTCATGTTT 59.404 30.769 0.00 0.00 40.70 2.83
2216 2429 9.214957 CACTTTTTGTTTAGTTTTCCTTTTCCT 57.785 29.630 0.00 0.00 0.00 3.36
2221 2434 8.780846 TTGTTTAGTTTTCCTTTTCCTTTTCC 57.219 30.769 0.00 0.00 0.00 3.13
2222 2435 7.908453 TGTTTAGTTTTCCTTTTCCTTTTCCA 58.092 30.769 0.00 0.00 0.00 3.53
2264 2477 0.461339 TTTCTTCTCCGGGCGTATGC 60.461 55.000 0.00 0.00 41.71 3.14
2280 2493 4.384547 GCGTATGCTTCATTTTCGGTTTTT 59.615 37.500 0.00 0.00 38.39 1.94
2282 2495 5.060446 CGTATGCTTCATTTTCGGTTTTTCC 59.940 40.000 0.00 0.00 0.00 3.13
2284 2497 5.017294 TGCTTCATTTTCGGTTTTTCCTT 57.983 34.783 0.00 0.00 0.00 3.36
2288 2501 7.549488 TGCTTCATTTTCGGTTTTTCCTTAAAA 59.451 29.630 0.00 0.00 35.10 1.52
2289 2502 8.556194 GCTTCATTTTCGGTTTTTCCTTAAAAT 58.444 29.630 0.00 0.00 38.64 1.82
2290 2503 9.862585 CTTCATTTTCGGTTTTTCCTTAAAATG 57.137 29.630 17.87 17.87 45.66 2.32
2291 2504 7.856556 TCATTTTCGGTTTTTCCTTAAAATGC 58.143 30.769 18.50 0.00 44.98 3.56
2292 2505 7.713073 TCATTTTCGGTTTTTCCTTAAAATGCT 59.287 29.630 18.50 0.00 44.98 3.79
2293 2506 7.851387 TTTTCGGTTTTTCCTTAAAATGCTT 57.149 28.000 0.00 0.00 37.98 3.91
2294 2507 6.836577 TTCGGTTTTTCCTTAAAATGCTTG 57.163 33.333 0.00 0.00 37.98 4.01
2295 2508 5.908341 TCGGTTTTTCCTTAAAATGCTTGT 58.092 33.333 0.00 0.00 37.98 3.16
2296 2509 6.342111 TCGGTTTTTCCTTAAAATGCTTGTT 58.658 32.000 0.00 0.00 37.98 2.83
2297 2510 6.819146 TCGGTTTTTCCTTAAAATGCTTGTTT 59.181 30.769 0.00 0.00 37.98 2.83
2298 2511 7.980099 TCGGTTTTTCCTTAAAATGCTTGTTTA 59.020 29.630 0.00 0.00 37.98 2.01
2299 2512 8.604890 CGGTTTTTCCTTAAAATGCTTGTTTAA 58.395 29.630 0.00 0.00 37.98 1.52
2300 2513 9.710979 GGTTTTTCCTTAAAATGCTTGTTTAAC 57.289 29.630 0.00 0.00 37.98 2.01
2341 2554 9.515020 TGTTCAACATTTTCTCAAATACTTGTC 57.485 29.630 0.00 0.00 33.94 3.18
2353 2566 8.681806 TCTCAAATACTTGTCAACATTTTGTCA 58.318 29.630 0.00 0.00 34.02 3.58
2364 2577 9.429359 TGTCAACATTTTGTCAAAATACTTGTT 57.571 25.926 20.44 18.28 38.97 2.83
2556 2792 8.655651 TTTCAAATACCTGTTCAACATTTTCC 57.344 30.769 0.00 0.00 0.00 3.13
2557 2793 7.353414 TCAAATACCTGTTCAACATTTTCCA 57.647 32.000 0.00 0.00 0.00 3.53
2558 2794 7.786030 TCAAATACCTGTTCAACATTTTCCAA 58.214 30.769 0.00 0.00 0.00 3.53
2559 2795 8.260818 TCAAATACCTGTTCAACATTTTCCAAA 58.739 29.630 0.00 0.00 0.00 3.28
2560 2796 9.054922 CAAATACCTGTTCAACATTTTCCAAAT 57.945 29.630 0.00 0.00 0.00 2.32
2561 2797 8.606040 AATACCTGTTCAACATTTTCCAAATG 57.394 30.769 7.52 7.52 0.00 2.32
2562 2798 4.815846 ACCTGTTCAACATTTTCCAAATGC 59.184 37.500 8.77 0.00 0.00 3.56
2563 2799 5.058490 CCTGTTCAACATTTTCCAAATGCT 58.942 37.500 8.77 0.00 0.00 3.79
2564 2800 5.528320 CCTGTTCAACATTTTCCAAATGCTT 59.472 36.000 8.77 1.68 0.00 3.91
2565 2801 6.360844 TGTTCAACATTTTCCAAATGCTTG 57.639 33.333 8.77 11.36 0.00 4.01
2574 2810 2.507339 CCAAATGCTTGGTCAACGTT 57.493 45.000 0.00 0.00 46.25 3.99
2575 2811 2.393764 CCAAATGCTTGGTCAACGTTC 58.606 47.619 0.00 0.00 46.25 3.95
2576 2812 2.223688 CCAAATGCTTGGTCAACGTTCA 60.224 45.455 0.00 0.00 46.25 3.18
2577 2813 3.552684 CCAAATGCTTGGTCAACGTTCAT 60.553 43.478 0.00 0.00 46.25 2.57
2578 2814 4.320861 CCAAATGCTTGGTCAACGTTCATA 60.321 41.667 0.00 0.00 46.25 2.15
2579 2815 5.218885 CAAATGCTTGGTCAACGTTCATAA 58.781 37.500 0.00 0.00 0.00 1.90
2580 2816 5.446143 AATGCTTGGTCAACGTTCATAAA 57.554 34.783 0.00 0.00 0.00 1.40
2581 2817 5.643379 ATGCTTGGTCAACGTTCATAAAT 57.357 34.783 0.00 0.00 0.00 1.40
2582 2818 6.751514 ATGCTTGGTCAACGTTCATAAATA 57.248 33.333 0.00 0.00 0.00 1.40
2583 2819 5.933790 TGCTTGGTCAACGTTCATAAATAC 58.066 37.500 0.00 0.00 0.00 1.89
2584 2820 5.703592 TGCTTGGTCAACGTTCATAAATACT 59.296 36.000 0.00 0.00 0.00 2.12
2585 2821 6.874664 TGCTTGGTCAACGTTCATAAATACTA 59.125 34.615 0.00 0.00 0.00 1.82
2586 2822 7.064134 TGCTTGGTCAACGTTCATAAATACTAG 59.936 37.037 0.00 0.00 0.00 2.57
2587 2823 7.064253 GCTTGGTCAACGTTCATAAATACTAGT 59.936 37.037 0.00 0.00 0.00 2.57
2588 2824 8.836268 TTGGTCAACGTTCATAAATACTAGTT 57.164 30.769 0.00 0.00 0.00 2.24
2589 2825 9.926158 TTGGTCAACGTTCATAAATACTAGTTA 57.074 29.630 0.00 0.00 0.00 2.24
2590 2826 9.926158 TGGTCAACGTTCATAAATACTAGTTAA 57.074 29.630 0.00 0.00 0.00 2.01
2652 2888 9.985730 ATGATCAACATTTGTTCAAATACTTGT 57.014 25.926 0.00 4.04 41.25 3.16
2656 2892 9.509855 TCAACATTTGTTCAAATACTTGTACAC 57.490 29.630 9.91 0.00 41.04 2.90
2657 2893 8.751335 CAACATTTGTTCAAATACTTGTACACC 58.249 33.333 9.91 0.00 41.04 4.16
2658 2894 8.001881 ACATTTGTTCAAATACTTGTACACCA 57.998 30.769 9.91 0.00 41.04 4.17
2659 2895 8.637986 ACATTTGTTCAAATACTTGTACACCAT 58.362 29.630 9.91 0.00 41.04 3.55
2660 2896 9.474920 CATTTGTTCAAATACTTGTACACCATT 57.525 29.630 9.91 0.00 41.04 3.16
2662 2898 9.877178 TTTGTTCAAATACTTGTACACCATTTT 57.123 25.926 0.00 0.00 41.04 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.589111 CACATTTCAATGATATGAACCAAATGA 57.411 29.630 18.13 0.00 38.95 2.57
27 28 9.373603 ACACATTTCAATGATATGAACCAAATG 57.626 29.630 18.13 8.38 38.95 2.32
100 101 1.327764 CTTCGGCGGAACAGATTTAGC 59.672 52.381 7.21 0.00 0.00 3.09
102 103 1.365699 GCTTCGGCGGAACAGATTTA 58.634 50.000 7.21 0.00 0.00 1.40
114 115 2.815211 TGTCATGAGCGCTTCGGC 60.815 61.111 13.26 5.20 37.65 5.54
184 196 4.081406 AGAGCATCACTAGCAGATCCTAG 58.919 47.826 4.89 4.89 40.47 3.02
185 197 4.078537 GAGAGCATCACTAGCAGATCCTA 58.921 47.826 0.00 0.00 37.82 2.94
186 198 2.892852 GAGAGCATCACTAGCAGATCCT 59.107 50.000 0.00 0.00 37.82 3.24
187 199 2.627221 TGAGAGCATCACTAGCAGATCC 59.373 50.000 0.00 0.00 37.82 3.36
198 210 0.684535 TTTCGGGTGTGAGAGCATCA 59.315 50.000 0.00 0.00 37.82 3.07
207 219 5.555631 CGATGTTTATACGATTTCGGGTGTG 60.556 44.000 4.84 0.00 44.95 3.82
208 220 4.505191 CGATGTTTATACGATTTCGGGTGT 59.495 41.667 4.84 0.00 44.95 4.16
209 221 4.505191 ACGATGTTTATACGATTTCGGGTG 59.495 41.667 4.84 0.00 44.95 4.61
231 243 5.621197 AGGTTTGTTTTTCTTTTGGCAAC 57.379 34.783 0.00 0.00 0.00 4.17
245 257 8.372459 GGAAGGGAATTGTTTATAAGGTTTGTT 58.628 33.333 0.00 0.00 0.00 2.83
247 259 7.033185 CGGAAGGGAATTGTTTATAAGGTTTG 58.967 38.462 0.00 0.00 0.00 2.93
248 260 6.949463 TCGGAAGGGAATTGTTTATAAGGTTT 59.051 34.615 0.00 0.00 0.00 3.27
250 262 6.069705 TCGGAAGGGAATTGTTTATAAGGT 57.930 37.500 0.00 0.00 0.00 3.50
251 263 6.260271 GTCTCGGAAGGGAATTGTTTATAAGG 59.740 42.308 0.00 0.00 46.15 2.69
252 264 7.048512 AGTCTCGGAAGGGAATTGTTTATAAG 58.951 38.462 0.00 0.00 46.15 1.73
253 265 6.954232 AGTCTCGGAAGGGAATTGTTTATAA 58.046 36.000 0.00 0.00 46.15 0.98
270 282 0.387367 CACAAGGACACGAGTCTCGG 60.387 60.000 25.25 16.27 45.59 4.63
313 325 4.662961 CCGTGTCGTGCCAGCTGA 62.663 66.667 17.39 0.00 0.00 4.26
345 357 3.896648 TTTAGGCAAAGACTTTGAGCG 57.103 42.857 28.15 5.47 43.26 5.03
369 381 3.571571 TGGCACGATGCGTATTACTATC 58.428 45.455 0.00 0.00 46.21 2.08
402 414 1.131504 GTCCAGTGCGTTTTTGTGTGA 59.868 47.619 0.00 0.00 0.00 3.58
426 438 0.595567 TTATCCGTACCGTGCATCGC 60.596 55.000 0.00 0.00 38.35 4.58
427 439 1.719246 CATTATCCGTACCGTGCATCG 59.281 52.381 0.00 0.00 39.52 3.84
428 440 3.021269 TCATTATCCGTACCGTGCATC 57.979 47.619 0.00 0.00 0.00 3.91
514 680 7.533222 CCAACACGCGTAGTTATAGACTAATAG 59.467 40.741 13.44 0.00 42.31 1.73
515 681 7.355017 CCAACACGCGTAGTTATAGACTAATA 58.645 38.462 13.44 0.00 42.31 0.98
516 682 6.204359 CCAACACGCGTAGTTATAGACTAAT 58.796 40.000 13.44 0.00 42.31 1.73
517 683 5.572211 CCAACACGCGTAGTTATAGACTAA 58.428 41.667 13.44 0.00 42.31 2.24
519 685 3.733077 GCCAACACGCGTAGTTATAGACT 60.733 47.826 13.44 0.00 42.55 3.24
520 686 2.533129 GCCAACACGCGTAGTTATAGAC 59.467 50.000 13.44 4.06 0.00 2.59
521 687 2.801063 GCCAACACGCGTAGTTATAGA 58.199 47.619 13.44 0.00 0.00 1.98
555 721 1.226746 GCAGTTGAGTAACGCAAGGT 58.773 50.000 0.00 0.00 41.71 3.50
639 805 1.338020 CCGCTTCAAGTCAAAGCCTTT 59.662 47.619 2.54 0.00 45.00 3.11
719 888 0.320421 CGACACAAATCGGTGGAGGT 60.320 55.000 0.00 0.00 43.08 3.85
911 1080 1.584717 GGAAGGAGGGGCAAGGGAAT 61.585 60.000 0.00 0.00 0.00 3.01
938 1107 6.426025 CGAAAGAATCTTGCCTATGATGATGA 59.574 38.462 0.00 0.00 0.00 2.92
939 1108 6.204301 ACGAAAGAATCTTGCCTATGATGATG 59.796 38.462 0.00 0.00 0.00 3.07
940 1109 6.294473 ACGAAAGAATCTTGCCTATGATGAT 58.706 36.000 0.00 0.00 0.00 2.45
963 1132 3.119101 TCGCTTCAATCTACCCTCTTGAC 60.119 47.826 0.00 0.00 0.00 3.18
966 1135 3.100671 ACTCGCTTCAATCTACCCTCTT 58.899 45.455 0.00 0.00 0.00 2.85
971 1140 1.404391 TCGGACTCGCTTCAATCTACC 59.596 52.381 0.00 0.00 36.13 3.18
1013 1182 2.425592 CCACCACCTCGTTCTGCA 59.574 61.111 0.00 0.00 0.00 4.41
1140 1318 1.478510 CTCTGGTACGTCTGGCTGATT 59.521 52.381 0.00 0.00 0.00 2.57
1503 1681 3.400590 GACACGACGTTGCGGTCC 61.401 66.667 14.34 1.31 33.30 4.46
1508 1686 2.159272 GAAGCAGGACACGACGTTGC 62.159 60.000 13.18 13.18 0.00 4.17
1661 1839 0.659957 GCAGCACTCGGGAATCAATC 59.340 55.000 0.00 0.00 0.00 2.67
1662 1840 0.749454 GGCAGCACTCGGGAATCAAT 60.749 55.000 0.00 0.00 0.00 2.57
1663 1841 1.377202 GGCAGCACTCGGGAATCAA 60.377 57.895 0.00 0.00 0.00 2.57
1664 1842 2.268920 GGCAGCACTCGGGAATCA 59.731 61.111 0.00 0.00 0.00 2.57
1674 1852 2.803492 CGAATAGTAGGAAGGGCAGCAC 60.803 54.545 0.00 0.00 0.00 4.40
1697 1875 7.411486 AGAGAGAAGAAGAAATAATCGTGGA 57.589 36.000 0.00 0.00 0.00 4.02
1698 1876 7.978975 AGAAGAGAGAAGAAGAAATAATCGTGG 59.021 37.037 0.00 0.00 0.00 4.94
1699 1877 8.925161 AGAAGAGAGAAGAAGAAATAATCGTG 57.075 34.615 0.00 0.00 0.00 4.35
1700 1878 8.966868 AGAGAAGAGAGAAGAAGAAATAATCGT 58.033 33.333 0.00 0.00 0.00 3.73
1707 1885 6.325028 TCCACAAGAGAAGAGAGAAGAAGAAA 59.675 38.462 0.00 0.00 0.00 2.52
1727 1905 9.077885 AGCATTTTCTTTTCTTTATACTCCACA 57.922 29.630 0.00 0.00 0.00 4.17
1736 1914 8.926710 CGAGAGAGTAGCATTTTCTTTTCTTTA 58.073 33.333 0.00 0.00 0.00 1.85
1737 1915 7.095017 CCGAGAGAGTAGCATTTTCTTTTCTTT 60.095 37.037 0.00 0.00 0.00 2.52
1738 1916 6.370166 CCGAGAGAGTAGCATTTTCTTTTCTT 59.630 38.462 0.00 0.00 0.00 2.52
1739 1917 5.872070 CCGAGAGAGTAGCATTTTCTTTTCT 59.128 40.000 0.00 0.00 0.00 2.52
1740 1918 5.446607 GCCGAGAGAGTAGCATTTTCTTTTC 60.447 44.000 0.00 0.00 0.00 2.29
1741 1919 4.393371 GCCGAGAGAGTAGCATTTTCTTTT 59.607 41.667 0.00 0.00 0.00 2.27
1742 1920 3.935828 GCCGAGAGAGTAGCATTTTCTTT 59.064 43.478 0.00 0.00 0.00 2.52
1743 1921 3.526534 GCCGAGAGAGTAGCATTTTCTT 58.473 45.455 0.00 0.00 0.00 2.52
1744 1922 2.159028 GGCCGAGAGAGTAGCATTTTCT 60.159 50.000 0.00 0.00 0.00 2.52
1745 1923 2.205911 GGCCGAGAGAGTAGCATTTTC 58.794 52.381 0.00 0.00 0.00 2.29
1752 1930 2.409651 GCACGGCCGAGAGAGTAG 59.590 66.667 35.90 11.31 0.00 2.57
1775 1953 2.203972 TTTGTACTCCCTCGTCGCGG 62.204 60.000 6.13 0.00 0.00 6.46
1776 1954 0.797249 CTTTGTACTCCCTCGTCGCG 60.797 60.000 0.00 0.00 0.00 5.87
1781 1959 2.352814 CCTGTCACTTTGTACTCCCTCG 60.353 54.545 0.00 0.00 0.00 4.63
1792 1970 2.104281 ACTCTTTACCGCCTGTCACTTT 59.896 45.455 0.00 0.00 0.00 2.66
1798 1976 6.098695 TGGTATATTTACTCTTTACCGCCTGT 59.901 38.462 0.00 0.00 36.02 4.00
1821 1999 6.486320 AGGGACATTTTGTTTAAAAAGCATGG 59.514 34.615 0.00 0.00 39.09 3.66
1822 2000 7.226325 TGAGGGACATTTTGTTTAAAAAGCATG 59.774 33.333 0.00 0.00 39.09 4.06
1835 2016 5.127519 TGAGGCAAATATGAGGGACATTTTG 59.872 40.000 0.00 0.00 40.07 2.44
1861 2043 4.502962 GATGAGGGTCTTTCAGACAGAAG 58.497 47.826 6.25 0.00 46.79 2.85
1865 2047 1.909302 GGGATGAGGGTCTTTCAGACA 59.091 52.381 6.25 0.00 46.79 3.41
1879 2061 2.032634 GTCGCTGCGTTTGGGATGA 61.033 57.895 22.48 0.00 0.00 2.92
1901 2083 9.935682 GAGACATCTTTTCAAATAATGCGATAA 57.064 29.630 0.00 0.00 0.00 1.75
1902 2084 8.275632 CGAGACATCTTTTCAAATAATGCGATA 58.724 33.333 0.00 0.00 0.00 2.92
1903 2085 7.128331 CGAGACATCTTTTCAAATAATGCGAT 58.872 34.615 0.00 0.00 0.00 4.58
1904 2086 6.477742 CGAGACATCTTTTCAAATAATGCGA 58.522 36.000 0.00 0.00 0.00 5.10
1905 2087 5.170270 GCGAGACATCTTTTCAAATAATGCG 59.830 40.000 0.00 0.00 0.00 4.73
1906 2088 6.195983 CAGCGAGACATCTTTTCAAATAATGC 59.804 38.462 0.00 0.00 0.00 3.56
1907 2089 7.466805 TCAGCGAGACATCTTTTCAAATAATG 58.533 34.615 0.00 0.00 0.00 1.90
1908 2090 7.615582 TCAGCGAGACATCTTTTCAAATAAT 57.384 32.000 0.00 0.00 0.00 1.28
1909 2091 7.433708 TTCAGCGAGACATCTTTTCAAATAA 57.566 32.000 0.00 0.00 0.00 1.40
1910 2092 6.402550 GCTTCAGCGAGACATCTTTTCAAATA 60.403 38.462 0.00 0.00 0.00 1.40
1911 2093 5.618640 GCTTCAGCGAGACATCTTTTCAAAT 60.619 40.000 0.00 0.00 0.00 2.32
1912 2094 4.319766 GCTTCAGCGAGACATCTTTTCAAA 60.320 41.667 0.00 0.00 0.00 2.69
1913 2095 3.187227 GCTTCAGCGAGACATCTTTTCAA 59.813 43.478 0.00 0.00 0.00 2.69
1914 2096 2.738846 GCTTCAGCGAGACATCTTTTCA 59.261 45.455 0.00 0.00 0.00 2.69
1915 2097 3.382015 GCTTCAGCGAGACATCTTTTC 57.618 47.619 0.00 0.00 0.00 2.29
1937 2119 1.657751 GCCAGCCCGATTTCTCCAAC 61.658 60.000 0.00 0.00 0.00 3.77
1940 2122 2.517166 GGCCAGCCCGATTTCTCC 60.517 66.667 0.00 0.00 0.00 3.71
1984 2167 3.133003 CGAATCCCGCTTCTCCCATATAT 59.867 47.826 0.00 0.00 0.00 0.86
1985 2168 2.496070 CGAATCCCGCTTCTCCCATATA 59.504 50.000 0.00 0.00 0.00 0.86
1989 2172 1.684391 TCGAATCCCGCTTCTCCCA 60.684 57.895 0.00 0.00 38.37 4.37
2008 2191 3.385384 TCAGAGTGGCGAGCAGGG 61.385 66.667 0.00 0.00 0.00 4.45
2011 2194 2.440385 CTTGGTCAGAGTGGCGAGCA 62.440 60.000 0.00 0.00 37.84 4.26
2013 2196 0.389166 GACTTGGTCAGAGTGGCGAG 60.389 60.000 0.00 0.00 32.09 5.03
2014 2197 0.827925 AGACTTGGTCAGAGTGGCGA 60.828 55.000 0.52 0.00 34.60 5.54
2016 2199 0.389166 CGAGACTTGGTCAGAGTGGC 60.389 60.000 0.52 0.00 34.60 5.01
2017 2200 0.389166 GCGAGACTTGGTCAGAGTGG 60.389 60.000 0.52 0.00 34.60 4.00
2018 2201 0.600557 AGCGAGACTTGGTCAGAGTG 59.399 55.000 0.52 0.00 34.60 3.51
2029 2238 5.590663 TCTCATACTTATCACAAGCGAGACT 59.409 40.000 0.00 0.00 0.00 3.24
2033 2242 4.598062 CGTCTCATACTTATCACAAGCGA 58.402 43.478 0.00 0.00 0.00 4.93
2034 2243 3.180584 GCGTCTCATACTTATCACAAGCG 59.819 47.826 0.00 0.00 0.00 4.68
2038 2247 5.339008 AAAGGCGTCTCATACTTATCACA 57.661 39.130 0.00 0.00 0.00 3.58
2039 2248 6.663944 AAAAAGGCGTCTCATACTTATCAC 57.336 37.500 0.00 0.00 0.00 3.06
2062 2271 2.714250 TGGCCTCCCTGTTCTTCTAAAA 59.286 45.455 3.32 0.00 0.00 1.52
2064 2273 2.038863 TGGCCTCCCTGTTCTTCTAA 57.961 50.000 3.32 0.00 0.00 2.10
2065 2274 2.270434 ATGGCCTCCCTGTTCTTCTA 57.730 50.000 3.32 0.00 0.00 2.10
2066 2275 1.376649 AATGGCCTCCCTGTTCTTCT 58.623 50.000 3.32 0.00 0.00 2.85
2067 2276 1.821136 CAAATGGCCTCCCTGTTCTTC 59.179 52.381 3.32 0.00 0.00 2.87
2068 2277 1.147817 ACAAATGGCCTCCCTGTTCTT 59.852 47.619 3.32 0.00 0.00 2.52
2071 2280 2.101640 AAACAAATGGCCTCCCTGTT 57.898 45.000 3.32 5.78 0.00 3.16
2072 2281 1.970640 GAAAACAAATGGCCTCCCTGT 59.029 47.619 3.32 0.00 0.00 4.00
2073 2282 1.276138 GGAAAACAAATGGCCTCCCTG 59.724 52.381 3.32 0.00 0.00 4.45
2076 2285 1.970640 AGTGGAAAACAAATGGCCTCC 59.029 47.619 3.32 0.00 0.00 4.30
2079 2288 1.336795 CGGAGTGGAAAACAAATGGCC 60.337 52.381 0.00 0.00 0.00 5.36
2080 2289 1.611491 TCGGAGTGGAAAACAAATGGC 59.389 47.619 0.00 0.00 0.00 4.40
2082 2291 4.300189 TGTTCGGAGTGGAAAACAAATG 57.700 40.909 0.00 0.00 0.00 2.32
2083 2292 4.993029 TTGTTCGGAGTGGAAAACAAAT 57.007 36.364 0.00 0.00 38.33 2.32
2084 2293 4.785511 TTTGTTCGGAGTGGAAAACAAA 57.214 36.364 7.86 7.86 44.73 2.83
2085 2294 4.785511 TTTTGTTCGGAGTGGAAAACAA 57.214 36.364 0.00 0.00 39.21 2.83
2086 2295 4.785511 TTTTTGTTCGGAGTGGAAAACA 57.214 36.364 0.00 0.00 0.00 2.83
2104 2313 7.173390 TGAAAACAAATGGAAAACCGACTTTTT 59.827 29.630 0.00 0.00 31.81 1.94
2105 2314 6.651225 TGAAAACAAATGGAAAACCGACTTTT 59.349 30.769 0.00 0.00 34.56 2.27
2106 2315 6.166982 TGAAAACAAATGGAAAACCGACTTT 58.833 32.000 0.00 0.00 0.00 2.66
2107 2316 5.725362 TGAAAACAAATGGAAAACCGACTT 58.275 33.333 0.00 0.00 0.00 3.01
2108 2317 5.331876 TGAAAACAAATGGAAAACCGACT 57.668 34.783 0.00 0.00 0.00 4.18
2109 2318 5.522097 ACATGAAAACAAATGGAAAACCGAC 59.478 36.000 0.00 0.00 0.00 4.79
2110 2319 5.665459 ACATGAAAACAAATGGAAAACCGA 58.335 33.333 0.00 0.00 0.00 4.69
2171 2380 7.718334 AAAGTGGAGAAGAGAAAAGGAAAAA 57.282 32.000 0.00 0.00 0.00 1.94
2177 2386 9.508567 CTAAACAAAAAGTGGAGAAGAGAAAAG 57.491 33.333 0.00 0.00 0.00 2.27
2184 2393 8.251026 AGGAAAACTAAACAAAAAGTGGAGAAG 58.749 33.333 0.00 0.00 0.00 2.85
2187 2396 8.771920 AAAGGAAAACTAAACAAAAAGTGGAG 57.228 30.769 0.00 0.00 0.00 3.86
2190 2399 9.214957 AGGAAAAGGAAAACTAAACAAAAAGTG 57.785 29.630 0.00 0.00 0.00 3.16
2191 2400 9.787435 AAGGAAAAGGAAAACTAAACAAAAAGT 57.213 25.926 0.00 0.00 0.00 2.66
2243 2456 2.352388 CATACGCCCGGAGAAGAAAAA 58.648 47.619 0.73 0.00 0.00 1.94
2244 2457 2.010043 GCATACGCCCGGAGAAGAAAA 61.010 52.381 0.73 0.00 0.00 2.29
2245 2458 0.461339 GCATACGCCCGGAGAAGAAA 60.461 55.000 0.73 0.00 0.00 2.52
2246 2459 1.143183 GCATACGCCCGGAGAAGAA 59.857 57.895 0.73 0.00 0.00 2.52
2247 2460 1.327690 AAGCATACGCCCGGAGAAGA 61.328 55.000 0.73 0.00 39.83 2.87
2248 2461 0.876342 GAAGCATACGCCCGGAGAAG 60.876 60.000 0.73 0.00 39.83 2.85
2255 2468 1.268539 CCGAAAATGAAGCATACGCCC 60.269 52.381 0.00 0.00 39.83 6.13
2258 2471 5.060446 GGAAAAACCGAAAATGAAGCATACG 59.940 40.000 0.00 0.00 0.00 3.06
2259 2472 6.156519 AGGAAAAACCGAAAATGAAGCATAC 58.843 36.000 0.00 0.00 44.74 2.39
2261 2474 5.213891 AGGAAAAACCGAAAATGAAGCAT 57.786 34.783 0.00 0.00 44.74 3.79
2339 2552 9.900264 GAACAAGTATTTTGACAAAATGTTGAC 57.100 29.630 32.11 24.02 41.01 3.18
2449 2685 6.981762 AGCATTTGAAAAATGTTGAACACA 57.018 29.167 0.00 0.00 40.71 3.72
2450 2686 7.242783 ACAAGCATTTGAAAAATGTTGAACAC 58.757 30.769 21.35 0.00 37.73 3.32
2453 2689 8.037382 TGAACAAGCATTTGAAAAATGTTGAA 57.963 26.923 21.35 11.77 37.73 2.69
2530 2766 9.103861 GGAAAATGTTGAACAGGTATTTGAAAA 57.896 29.630 3.74 0.00 0.00 2.29
2531 2767 8.260818 TGGAAAATGTTGAACAGGTATTTGAAA 58.739 29.630 3.74 0.00 0.00 2.69
2532 2768 7.786030 TGGAAAATGTTGAACAGGTATTTGAA 58.214 30.769 3.74 0.00 0.00 2.69
2533 2769 7.353414 TGGAAAATGTTGAACAGGTATTTGA 57.647 32.000 3.74 0.00 0.00 2.69
2534 2770 8.430801 TTTGGAAAATGTTGAACAGGTATTTG 57.569 30.769 3.74 0.00 0.00 2.32
2535 2771 9.054922 CATTTGGAAAATGTTGAACAGGTATTT 57.945 29.630 3.74 2.87 0.00 1.40
2536 2772 7.173047 GCATTTGGAAAATGTTGAACAGGTATT 59.827 33.333 3.74 0.00 0.00 1.89
2537 2773 6.650390 GCATTTGGAAAATGTTGAACAGGTAT 59.350 34.615 3.74 0.00 0.00 2.73
2538 2774 5.988561 GCATTTGGAAAATGTTGAACAGGTA 59.011 36.000 3.74 0.00 0.00 3.08
2539 2775 4.815846 GCATTTGGAAAATGTTGAACAGGT 59.184 37.500 3.74 0.00 0.00 4.00
2540 2776 5.058490 AGCATTTGGAAAATGTTGAACAGG 58.942 37.500 3.74 0.00 0.00 4.00
2541 2777 6.423862 CAAGCATTTGGAAAATGTTGAACAG 58.576 36.000 3.74 0.00 0.00 3.16
2542 2778 6.360844 CAAGCATTTGGAAAATGTTGAACA 57.639 33.333 0.00 0.00 0.00 3.18
2556 2792 3.077229 TGAACGTTGACCAAGCATTTG 57.923 42.857 5.00 0.00 0.00 2.32
2557 2793 5.446143 TTATGAACGTTGACCAAGCATTT 57.554 34.783 5.00 0.00 0.00 2.32
2558 2794 5.446143 TTTATGAACGTTGACCAAGCATT 57.554 34.783 5.00 0.00 0.00 3.56
2559 2795 5.643379 ATTTATGAACGTTGACCAAGCAT 57.357 34.783 5.00 3.40 0.00 3.79
2560 2796 5.703592 AGTATTTATGAACGTTGACCAAGCA 59.296 36.000 5.00 0.00 0.00 3.91
2561 2797 6.178239 AGTATTTATGAACGTTGACCAAGC 57.822 37.500 5.00 0.00 0.00 4.01
2562 2798 8.475331 ACTAGTATTTATGAACGTTGACCAAG 57.525 34.615 5.00 0.00 0.00 3.61
2563 2799 8.836268 AACTAGTATTTATGAACGTTGACCAA 57.164 30.769 5.00 0.00 0.00 3.67
2564 2800 9.926158 TTAACTAGTATTTATGAACGTTGACCA 57.074 29.630 5.00 0.00 0.00 4.02
2626 2862 9.985730 ACAAGTATTTGAACAAATGTTGATCAT 57.014 25.926 25.77 12.84 41.24 2.45
2630 2866 9.509855 GTGTACAAGTATTTGAACAAATGTTGA 57.490 29.630 25.77 15.68 40.83 3.18
2631 2867 8.751335 GGTGTACAAGTATTTGAACAAATGTTG 58.249 33.333 19.00 20.58 40.83 3.33
2632 2868 8.470805 TGGTGTACAAGTATTTGAACAAATGTT 58.529 29.630 19.00 11.41 40.83 2.71
2633 2869 8.001881 TGGTGTACAAGTATTTGAACAAATGT 57.998 30.769 19.00 13.47 40.83 2.71
2634 2870 9.474920 AATGGTGTACAAGTATTTGAACAAATG 57.525 29.630 19.00 9.20 40.83 2.32
2636 2872 9.877178 AAAATGGTGTACAAGTATTTGAACAAA 57.123 25.926 4.81 2.48 37.73 2.83


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

AutoCloner maintained by Alex Coulton.