Multiple sequence alignment - TraesCS3D01G524700

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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 TraesCS3D01G524700 chr3D 100.000 2447 0 0 1 2447 604446843 604449289 0.000000e+00 4519.0
1 TraesCS3D01G524700 chr3A 90.151 1523 86 28 171 1645 734151061 734152567 0.000000e+00 1923.0
2 TraesCS3D01G524700 chr3A 77.239 268 49 5 347 612 722227026 722226769 1.960000e-31 147.0
3 TraesCS3D01G524700 chr3A 80.184 217 23 10 2000 2198 734166980 734167194 7.050000e-31 145.0
4 TraesCS3D01G524700 chr3B 86.574 1661 142 44 4 1612 811495663 811497294 0.000000e+00 1757.0
5 TraesCS3D01G524700 chr3B 85.894 1191 105 40 1 1159 811471087 811472246 0.000000e+00 1210.0
6 TraesCS3D01G524700 chr3B 82.897 573 36 25 1912 2447 811497719 811498266 2.220000e-125 459.0
7 TraesCS3D01G524700 chr3B 80.198 101 19 1 393 492 650661023 650661123 9.380000e-10 75.0
8 TraesCS3D01G524700 chr2B 88.409 440 49 2 1006 1444 769378609 769378171 1.670000e-146 529.0
9 TraesCS3D01G524700 chr2B 88.155 439 52 0 1006 1444 769428918 769428480 7.750000e-145 523.0
10 TraesCS3D01G524700 chr2B 88.564 411 47 0 1034 1444 769478557 769478147 1.310000e-137 499.0
11 TraesCS3D01G524700 chr2B 86.301 438 54 2 1007 1444 769491311 769490880 2.850000e-129 472.0
12 TraesCS3D01G524700 chr2B 81.443 291 50 4 1 288 615589178 615589467 4.070000e-58 235.0
13 TraesCS3D01G524700 chr2B 85.149 101 13 2 378 477 167473023 167472924 4.300000e-18 102.0
14 TraesCS3D01G524700 chr2B 82.353 119 17 3 348 463 545432124 545432241 1.550000e-17 100.0
15 TraesCS3D01G524700 chr2D 87.699 439 48 2 1006 1444 627361692 627361260 7.810000e-140 507.0
16 TraesCS3D01G524700 chr2A 87.016 439 57 0 1006 1444 758056063 758055625 1.690000e-136 496.0
17 TraesCS3D01G524700 chrUn 82.916 439 52 7 1006 1444 316524967 316524552 8.260000e-100 374.0
18 TraesCS3D01G524700 chr6D 84.694 294 39 4 1 288 59784308 59784015 3.080000e-74 289.0
19 TraesCS3D01G524700 chr6D 97.727 44 1 0 390 433 408659782 408659825 2.610000e-10 76.8
20 TraesCS3D01G524700 chr1D 84.211 285 37 5 1 279 460601554 460601836 1.120000e-68 270.0
21 TraesCS3D01G524700 chr1D 83.275 287 37 8 1 278 233506637 233506921 1.120000e-63 254.0
22 TraesCS3D01G524700 chr1D 82.394 284 43 4 1 278 396309858 396310140 8.740000e-60 241.0
23 TraesCS3D01G524700 chr1D 92.308 52 1 1 1767 1815 18399171 18399222 1.210000e-08 71.3
24 TraesCS3D01G524700 chr1A 83.333 294 44 2 1 289 489168356 489168063 1.440000e-67 267.0
25 TraesCS3D01G524700 chr5B 82.594 293 41 8 1 288 709581051 709580764 1.450000e-62 250.0
26 TraesCS3D01G524700 chr1B 79.887 353 60 6 1 346 523235585 523235237 5.230000e-62 248.0
27 TraesCS3D01G524700 chr1B 87.861 173 19 2 1273 1444 597456549 597456378 4.130000e-48 202.0


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 TraesCS3D01G524700 chr3D 604446843 604449289 2446 False 4519 4519 100.0000 1 2447 1 chr3D.!!$F1 2446
1 TraesCS3D01G524700 chr3A 734151061 734152567 1506 False 1923 1923 90.1510 171 1645 1 chr3A.!!$F1 1474
2 TraesCS3D01G524700 chr3B 811471087 811472246 1159 False 1210 1210 85.8940 1 1159 1 chr3B.!!$F2 1158
3 TraesCS3D01G524700 chr3B 811495663 811498266 2603 False 1108 1757 84.7355 4 2447 2 chr3B.!!$F3 2443

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
148 154 0.469518 AGGCACCGGGGTATCTAGAC 60.47 60.0 5.12 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2263 0.036388 CCGGCTGCCTCTGTTTCTTA 60.036 55.0 17.92 0.0 0.0 2.1 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
82 87 7.216973 ACCTCGAGATCGTATAAATAAGCTT 57.783 36.000 15.71 3.48 40.80 3.74
99 104 9.692749 AAATAAGCTTTAGTCTAAAAACCTTGC 57.307 29.630 3.20 10.94 0.00 4.01
105 110 7.361031 GCTTTAGTCTAAAAACCTTGCCTCTAC 60.361 40.741 6.51 0.00 0.00 2.59
108 113 5.307196 AGTCTAAAAACCTTGCCTCTACAGA 59.693 40.000 0.00 0.00 0.00 3.41
147 153 1.151760 TAGGCACCGGGGTATCTAGA 58.848 55.000 5.12 0.00 0.00 2.43
148 154 0.469518 AGGCACCGGGGTATCTAGAC 60.470 60.000 5.12 0.00 0.00 2.59
160 166 6.489361 CGGGGTATCTAGACTTACAAGTATGT 59.511 42.308 0.00 0.00 39.88 2.29
162 168 7.504911 GGGGTATCTAGACTTACAAGTATGTCA 59.495 40.741 21.11 10.96 40.56 3.58
185 191 6.156256 TCAACTACAACTAGGGATAACATGCT 59.844 38.462 0.00 0.00 0.00 3.79
215 221 1.636988 ATACGCCTTGAAGTGTACGC 58.363 50.000 0.00 0.00 35.67 4.42
225 231 2.101750 TGAAGTGTACGCCAAGTCTTCA 59.898 45.455 1.98 2.75 38.25 3.02
226 232 3.244078 TGAAGTGTACGCCAAGTCTTCAT 60.244 43.478 1.98 0.00 36.74 2.57
229 235 2.603560 GTGTACGCCAAGTCTTCATAGC 59.396 50.000 0.00 0.00 0.00 2.97
233 239 4.137116 ACGCCAAGTCTTCATAGCATTA 57.863 40.909 0.00 0.00 0.00 1.90
312 329 4.114997 CAACAATGGCGGGCCGAC 62.115 66.667 33.44 31.09 39.42 4.79
379 400 4.098654 CAGATCTATGAGGAGTTCAACGGT 59.901 45.833 0.00 0.00 39.77 4.83
388 409 4.906618 AGGAGTTCAACGGTGATAATTGT 58.093 39.130 2.76 0.00 32.48 2.71
417 438 1.826024 CGCTGGTCCTTAGAGGCAT 59.174 57.895 0.00 0.00 34.61 4.40
433 454 1.001378 GGCATGTGCACGAAGACTTTT 60.001 47.619 13.13 0.00 44.36 2.27
442 464 2.864343 CACGAAGACTTTTCGGTTGTCT 59.136 45.455 13.06 0.00 45.34 3.41
446 468 4.877323 AAGACTTTTCGGTTGTCTTCAC 57.123 40.909 0.00 0.00 44.65 3.18
480 502 4.541648 AGGTAGGGGAGCGGCGAT 62.542 66.667 12.98 2.76 0.00 4.58
532 554 4.379813 GCAATAGTGGTTGTTGATGGTCTG 60.380 45.833 0.00 0.00 30.08 3.51
585 608 9.958234 TTTGAGATGTTTTGTATTTTCGATGAA 57.042 25.926 0.00 0.00 0.00 2.57
620 645 2.093658 TCGGATCCTTTTCTTTCCCGAG 60.094 50.000 10.75 0.00 39.43 4.63
667 695 8.589338 GCAGGAGATATTTCTCTTCTACCATTA 58.411 37.037 12.20 0.00 46.46 1.90
683 715 4.085733 ACCATTAATGTGGCTTGCAACTA 58.914 39.130 14.25 0.00 43.27 2.24
746 778 0.535797 AAGCTAGGTGGCGGAACTAC 59.464 55.000 0.00 0.00 37.29 2.73
749 781 1.739371 GCTAGGTGGCGGAACTACTTG 60.739 57.143 0.00 0.00 0.00 3.16
753 785 2.039879 AGGTGGCGGAACTACTTGAATT 59.960 45.455 0.00 0.00 0.00 2.17
850 883 5.755849 TCCACAAGGAAGAGAAGAAAAGTT 58.244 37.500 0.00 0.00 42.23 2.66
964 1011 1.202475 TCAGCTAGCAACACGTCACAA 60.202 47.619 18.83 0.00 0.00 3.33
980 1027 4.269123 CGTCACAAACACACAAACTAGCTA 59.731 41.667 0.00 0.00 0.00 3.32
1001 1048 4.767578 ATAGCAGGTTGTCACTGATCAT 57.232 40.909 0.00 0.00 38.20 2.45
1451 1523 1.069159 CGACTGCCGCGACTAGATTAT 60.069 52.381 8.23 0.00 0.00 1.28
1454 1526 2.882761 ACTGCCGCGACTAGATTATGTA 59.117 45.455 8.23 0.00 0.00 2.29
1467 1545 8.107399 ACTAGATTATGTATCCGTCGATCAAA 57.893 34.615 0.00 0.00 33.45 2.69
1476 1554 1.471676 CCGTCGATCAAAGGCTAGCTT 60.472 52.381 15.72 3.40 0.00 3.74
1493 1571 8.040132 AGGCTAGCTTGCTATGATAAGAATAAG 58.960 37.037 19.45 0.00 0.00 1.73
1526 1616 1.400142 CTACGAGTGAGCTCAGACTGG 59.600 57.143 18.89 15.15 41.71 4.00
1529 1619 0.170116 GAGTGAGCTCAGACTGGTCG 59.830 60.000 18.89 0.00 41.29 4.79
1596 1693 7.862741 CGTGTATACAATACGTACATGGAAT 57.137 36.000 7.25 9.16 37.86 3.01
1628 1725 6.419791 AGTGGATCAAATCAAACGGGTTATA 58.580 36.000 0.00 0.00 0.00 0.98
1654 1751 6.961359 TTCATGTGTGGATTTTACTACGAG 57.039 37.500 0.00 0.00 0.00 4.18
1691 1821 8.761689 ACCAGTTCATATTTTGGATTTGCTAAT 58.238 29.630 0.00 0.00 34.76 1.73
1738 1872 9.962809 ACAGTCTCATTTAACTACTACTAGTCT 57.037 33.333 0.00 0.00 31.42 3.24
1747 1881 9.447157 TTTAACTACTACTAGTCTCTCTGTTCC 57.553 37.037 0.00 0.00 31.42 3.62
1748 1882 6.623979 ACTACTACTAGTCTCTCTGTTCCA 57.376 41.667 0.00 0.00 0.00 3.53
1749 1883 7.202972 ACTACTACTAGTCTCTCTGTTCCAT 57.797 40.000 0.00 0.00 0.00 3.41
1750 1884 8.321621 ACTACTACTAGTCTCTCTGTTCCATA 57.678 38.462 0.00 0.00 0.00 2.74
1751 1885 8.770322 ACTACTACTAGTCTCTCTGTTCCATAA 58.230 37.037 0.00 0.00 0.00 1.90
1752 1886 9.787435 CTACTACTAGTCTCTCTGTTCCATAAT 57.213 37.037 0.00 0.00 0.00 1.28
1754 1888 9.482175 ACTACTAGTCTCTCTGTTCCATAATTT 57.518 33.333 0.00 0.00 0.00 1.82
1757 1891 9.442047 ACTAGTCTCTCTGTTCCATAATTTTTG 57.558 33.333 0.00 0.00 0.00 2.44
1758 1892 9.442047 CTAGTCTCTCTGTTCCATAATTTTTGT 57.558 33.333 0.00 0.00 0.00 2.83
1759 1893 8.329203 AGTCTCTCTGTTCCATAATTTTTGTC 57.671 34.615 0.00 0.00 0.00 3.18
1760 1894 7.118390 AGTCTCTCTGTTCCATAATTTTTGTCG 59.882 37.037 0.00 0.00 0.00 4.35
1761 1895 6.934645 TCTCTCTGTTCCATAATTTTTGTCGT 59.065 34.615 0.00 0.00 0.00 4.34
1762 1896 6.898041 TCTCTGTTCCATAATTTTTGTCGTG 58.102 36.000 0.00 0.00 0.00 4.35
1763 1897 6.007936 TCTGTTCCATAATTTTTGTCGTGG 57.992 37.500 0.00 0.00 0.00 4.94
1764 1898 5.533154 TCTGTTCCATAATTTTTGTCGTGGT 59.467 36.000 0.00 0.00 0.00 4.16
1765 1899 5.524284 TGTTCCATAATTTTTGTCGTGGTG 58.476 37.500 0.00 0.00 0.00 4.17
1766 1900 4.167554 TCCATAATTTTTGTCGTGGTGC 57.832 40.909 0.00 0.00 0.00 5.01
1767 1901 3.057174 TCCATAATTTTTGTCGTGGTGCC 60.057 43.478 0.00 0.00 0.00 5.01
1768 1902 3.305676 CCATAATTTTTGTCGTGGTGCCA 60.306 43.478 0.00 0.00 0.00 4.92
1769 1903 4.493547 CATAATTTTTGTCGTGGTGCCAT 58.506 39.130 0.00 0.00 0.00 4.40
1770 1904 5.393569 CCATAATTTTTGTCGTGGTGCCATA 60.394 40.000 0.00 0.00 0.00 2.74
1771 1905 4.592485 AATTTTTGTCGTGGTGCCATAA 57.408 36.364 0.00 0.00 0.00 1.90
1772 1906 4.799564 ATTTTTGTCGTGGTGCCATAAT 57.200 36.364 0.00 0.00 0.00 1.28
1773 1907 4.592485 TTTTTGTCGTGGTGCCATAATT 57.408 36.364 0.00 0.00 0.00 1.40
1774 1908 3.567576 TTTGTCGTGGTGCCATAATTG 57.432 42.857 0.00 0.00 0.00 2.32
1775 1909 2.192664 TGTCGTGGTGCCATAATTGT 57.807 45.000 0.00 0.00 0.00 2.71
1776 1910 2.509569 TGTCGTGGTGCCATAATTGTT 58.490 42.857 0.00 0.00 0.00 2.83
1777 1911 2.227626 TGTCGTGGTGCCATAATTGTTG 59.772 45.455 0.00 0.00 0.00 3.33
1778 1912 2.227865 GTCGTGGTGCCATAATTGTTGT 59.772 45.455 0.00 0.00 0.00 3.32
1779 1913 2.486203 TCGTGGTGCCATAATTGTTGTC 59.514 45.455 0.00 0.00 0.00 3.18
1780 1914 2.727607 CGTGGTGCCATAATTGTTGTCG 60.728 50.000 0.00 0.00 0.00 4.35
1781 1915 2.227865 GTGGTGCCATAATTGTTGTCGT 59.772 45.455 0.00 0.00 0.00 4.34
1782 1916 2.887783 TGGTGCCATAATTGTTGTCGTT 59.112 40.909 0.00 0.00 0.00 3.85
1783 1917 4.072839 TGGTGCCATAATTGTTGTCGTTA 58.927 39.130 0.00 0.00 0.00 3.18
1784 1918 4.519350 TGGTGCCATAATTGTTGTCGTTAA 59.481 37.500 0.00 0.00 0.00 2.01
1785 1919 5.009710 TGGTGCCATAATTGTTGTCGTTAAA 59.990 36.000 0.00 0.00 0.00 1.52
1796 1930 5.558307 TGTTGTCGTTAAACTAAAACCACG 58.442 37.500 0.00 0.00 0.00 4.94
1798 1932 6.036953 TGTTGTCGTTAAACTAAAACCACGAT 59.963 34.615 0.00 0.00 38.76 3.73
1800 1934 7.706281 TGTCGTTAAACTAAAACCACGATAA 57.294 32.000 0.00 0.00 38.76 1.75
1815 1949 5.526111 ACCACGATAAGAATTATGAAACGGG 59.474 40.000 0.00 0.00 42.35 5.28
1819 1955 5.107065 CGATAAGAATTATGAAACGGGGAGC 60.107 44.000 0.00 0.00 42.35 4.70
1836 1973 5.319453 GGGGAGCAGATCATTTGATTATCA 58.681 41.667 0.00 0.00 34.37 2.15
1850 1987 5.651387 TGATTATCAAACGAAAATGGGCA 57.349 34.783 0.00 0.00 0.00 5.36
1858 1995 3.124578 ACGAAAATGGGCAAGCATTTT 57.875 38.095 11.19 11.19 41.83 1.82
1860 1997 2.416202 CGAAAATGGGCAAGCATTTTCC 59.584 45.455 23.04 12.76 46.66 3.13
1861 1998 2.495155 AAATGGGCAAGCATTTTCCC 57.505 45.000 0.00 0.00 38.44 3.97
1862 1999 0.620030 AATGGGCAAGCATTTTCCCC 59.380 50.000 0.00 0.00 37.47 4.81
1863 2000 1.152161 TGGGCAAGCATTTTCCCCA 60.152 52.632 0.00 0.00 43.19 4.96
1864 2001 0.547229 TGGGCAAGCATTTTCCCCAT 60.547 50.000 0.00 0.00 40.67 4.00
1870 2007 3.370672 GCAAGCATTTTCCCCATAAAACG 59.629 43.478 0.00 0.00 31.50 3.60
1877 2014 5.810080 TTTTCCCCATAAAACGAAATGGT 57.190 34.783 0.00 0.00 40.97 3.55
1880 2017 4.919793 TCCCCATAAAACGAAATGGTGTA 58.080 39.130 0.00 0.00 40.97 2.90
1899 2036 5.538433 GGTGTAGGAGCTAGATGAGAATTCT 59.462 44.000 7.95 7.95 0.00 2.40
1900 2037 6.041523 GGTGTAGGAGCTAGATGAGAATTCTT 59.958 42.308 9.87 0.00 0.00 2.52
1901 2038 7.418483 GGTGTAGGAGCTAGATGAGAATTCTTT 60.418 40.741 9.87 0.15 0.00 2.52
1906 2043 9.158097 AGGAGCTAGATGAGAATTCTTTAATCT 57.842 33.333 22.47 22.47 0.00 2.40
1907 2044 9.423061 GGAGCTAGATGAGAATTCTTTAATCTC 57.577 37.037 22.50 16.26 0.00 2.75
1908 2045 9.128107 GAGCTAGATGAGAATTCTTTAATCTCG 57.872 37.037 22.50 19.14 0.00 4.04
1910 2047 8.911662 GCTAGATGAGAATTCTTTAATCTCGTC 58.088 37.037 22.50 13.78 41.32 4.20
1915 2052 9.959749 ATGAGAATTCTTTAATCTCGTCTAGAC 57.040 33.333 13.18 13.18 36.93 2.59
1930 2231 3.314080 GTCTAGACGAGAGCTAGCAACAT 59.686 47.826 18.83 0.00 37.58 2.71
1938 2239 5.212934 CGAGAGCTAGCAACATCGTTAATA 58.787 41.667 18.83 0.00 0.00 0.98
1944 2245 8.077836 AGCTAGCAACATCGTTAATATTTCTC 57.922 34.615 18.83 0.00 0.00 2.87
1956 2257 7.220300 TCGTTAATATTTCTCGTCTTTCTCTGC 59.780 37.037 0.00 0.00 0.00 4.26
1957 2258 5.957910 AATATTTCTCGTCTTTCTCTGCG 57.042 39.130 0.00 0.00 0.00 5.18
1958 2259 1.419374 TTTCTCGTCTTTCTCTGCGC 58.581 50.000 0.00 0.00 0.00 6.09
1959 2260 0.598562 TTCTCGTCTTTCTCTGCGCT 59.401 50.000 9.73 0.00 0.00 5.92
1960 2261 0.169230 TCTCGTCTTTCTCTGCGCTC 59.831 55.000 9.73 0.00 0.00 5.03
1961 2262 0.800300 CTCGTCTTTCTCTGCGCTCC 60.800 60.000 9.73 0.00 0.00 4.70
1962 2263 1.214062 CGTCTTTCTCTGCGCTCCT 59.786 57.895 9.73 0.00 0.00 3.69
1963 2264 0.452184 CGTCTTTCTCTGCGCTCCTA 59.548 55.000 9.73 0.00 0.00 2.94
1964 2265 1.135373 CGTCTTTCTCTGCGCTCCTAA 60.135 52.381 9.73 0.00 0.00 2.69
1972 2274 1.893137 TCTGCGCTCCTAAGAAACAGA 59.107 47.619 9.73 0.00 0.00 3.41
1982 2284 2.747855 GAAACAGAGGCAGCCGGG 60.748 66.667 5.55 1.80 0.00 5.73
2007 2309 4.530710 AAGCAGTAGTACGTCCAAATCA 57.469 40.909 0.00 0.00 0.00 2.57
2008 2310 3.846360 AGCAGTAGTACGTCCAAATCAC 58.154 45.455 0.00 0.00 0.00 3.06
2009 2311 2.597305 GCAGTAGTACGTCCAAATCACG 59.403 50.000 0.00 0.00 43.13 4.35
2047 2349 4.213482 GCACGACTAGTTGGTCAAATTTCT 59.787 41.667 14.75 0.00 36.12 2.52
2048 2350 5.679906 CACGACTAGTTGGTCAAATTTCTG 58.320 41.667 14.75 0.00 36.12 3.02
2049 2351 5.465390 CACGACTAGTTGGTCAAATTTCTGA 59.535 40.000 14.75 0.00 36.12 3.27
2050 2352 6.018262 CACGACTAGTTGGTCAAATTTCTGAA 60.018 38.462 14.75 0.00 36.12 3.02
2051 2353 6.202954 ACGACTAGTTGGTCAAATTTCTGAAG 59.797 38.462 14.75 0.00 36.12 3.02
2052 2354 6.319141 ACTAGTTGGTCAAATTTCTGAAGC 57.681 37.500 0.00 0.00 0.00 3.86
2053 2355 6.064717 ACTAGTTGGTCAAATTTCTGAAGCT 58.935 36.000 0.00 0.00 0.00 3.74
2054 2356 5.859205 AGTTGGTCAAATTTCTGAAGCTT 57.141 34.783 0.00 0.00 0.00 3.74
2055 2357 6.959639 AGTTGGTCAAATTTCTGAAGCTTA 57.040 33.333 0.00 0.00 0.00 3.09
2056 2358 6.739112 AGTTGGTCAAATTTCTGAAGCTTAC 58.261 36.000 0.00 0.00 0.00 2.34
2057 2359 5.356882 TGGTCAAATTTCTGAAGCTTACG 57.643 39.130 0.00 0.00 0.00 3.18
2058 2360 4.159120 GGTCAAATTTCTGAAGCTTACGC 58.841 43.478 0.00 0.00 0.00 4.42
2059 2361 4.320202 GGTCAAATTTCTGAAGCTTACGCA 60.320 41.667 0.00 0.00 39.10 5.24
2060 2362 4.848299 GTCAAATTTCTGAAGCTTACGCAG 59.152 41.667 0.00 2.76 39.10 5.18
2061 2363 4.754618 TCAAATTTCTGAAGCTTACGCAGA 59.245 37.500 11.27 11.27 39.10 4.26
2062 2364 5.238432 TCAAATTTCTGAAGCTTACGCAGAA 59.762 36.000 19.70 19.70 44.33 3.02
2063 2365 5.886960 AATTTCTGAAGCTTACGCAGAAT 57.113 34.783 22.59 11.33 45.06 2.40
2064 2366 5.886960 ATTTCTGAAGCTTACGCAGAATT 57.113 34.783 22.59 17.97 45.06 2.17
2065 2367 4.928661 TTCTGAAGCTTACGCAGAATTC 57.071 40.909 19.70 0.00 42.03 2.17
2066 2368 3.925379 TCTGAAGCTTACGCAGAATTCA 58.075 40.909 12.57 0.00 35.87 2.57
2067 2369 4.314961 TCTGAAGCTTACGCAGAATTCAA 58.685 39.130 12.57 0.00 35.87 2.69
2068 2370 4.389992 TCTGAAGCTTACGCAGAATTCAAG 59.610 41.667 12.57 3.28 35.87 3.02
2069 2371 4.065088 TGAAGCTTACGCAGAATTCAAGT 58.935 39.130 8.44 6.93 39.10 3.16
2185 2499 4.749245 AACAAACTAATCCTGAAGCGTG 57.251 40.909 0.00 0.00 0.00 5.34
2197 2511 0.389948 GAAGCGTGGAATCGTCAGGT 60.390 55.000 0.00 0.00 0.00 4.00
2203 2517 0.323087 TGGAATCGTCAGGTCCGAGA 60.323 55.000 0.00 0.00 37.81 4.04
2225 2539 3.922364 GGCTTGGGGTTGGGGGAA 61.922 66.667 0.00 0.00 0.00 3.97
2231 2545 2.445155 GGGTTGGGGGAATGCACT 59.555 61.111 0.00 0.00 0.00 4.40
2233 2547 0.395724 GGGTTGGGGGAATGCACTAG 60.396 60.000 0.00 0.00 0.00 2.57
2234 2548 0.623723 GGTTGGGGGAATGCACTAGA 59.376 55.000 0.00 0.00 0.00 2.43
2235 2549 1.682087 GGTTGGGGGAATGCACTAGAC 60.682 57.143 0.00 0.00 0.00 2.59
2237 2551 1.279025 TGGGGGAATGCACTAGACCC 61.279 60.000 0.00 8.04 39.79 4.46
2238 2552 1.146263 GGGGAATGCACTAGACCCG 59.854 63.158 0.00 0.00 41.25 5.28
2239 2553 1.623542 GGGGAATGCACTAGACCCGT 61.624 60.000 0.00 0.00 41.25 5.28
2240 2554 1.117150 GGGAATGCACTAGACCCGTA 58.883 55.000 0.00 0.00 0.00 4.02
2263 2604 3.247886 CGTCATCTTCTTCTGGATGCATG 59.752 47.826 2.46 0.00 39.14 4.06
2268 2609 1.288188 TCTTCTGGATGCATGTGGGA 58.712 50.000 2.46 0.00 0.00 4.37
2277 2618 2.040544 GCATGTGGGACGGGTCAAG 61.041 63.158 0.75 0.00 0.00 3.02
2282 2623 1.072505 TGGGACGGGTCAAGCTTTC 59.927 57.895 0.00 0.00 0.00 2.62
2314 2655 1.197812 ATCCAAGCCAAAATCCAGCC 58.802 50.000 0.00 0.00 0.00 4.85
2317 2658 0.819582 CAAGCCAAAATCCAGCCGAT 59.180 50.000 0.00 0.00 0.00 4.18
2318 2659 2.023673 CAAGCCAAAATCCAGCCGATA 58.976 47.619 0.00 0.00 0.00 2.92
2321 2662 3.299503 AGCCAAAATCCAGCCGATATTT 58.700 40.909 0.00 0.00 0.00 1.40
2345 2686 1.939934 TGGATGCTACTGCGTATTTGC 59.060 47.619 0.00 0.00 43.34 3.68
2391 2732 5.389859 TCAAAAATCTTGGCGTGATTGAT 57.610 34.783 5.72 0.00 34.74 2.57
2394 2735 1.027357 ATCTTGGCGTGATTGATGGC 58.973 50.000 0.00 0.00 36.65 4.40
2413 2754 2.747686 CCAGGCGTGTAAGGGTGT 59.252 61.111 5.57 0.00 0.00 4.16
2416 2757 0.036388 CAGGCGTGTAAGGGTGTCAT 60.036 55.000 0.00 0.00 0.00 3.06
2424 2765 2.027192 TGTAAGGGTGTCATCCTGCTTC 60.027 50.000 5.09 0.00 34.34 3.86
2442 2783 3.316308 GCTTCAAGATATTGCGGTGGAAT 59.684 43.478 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.933463 CCCACAATCAATACAAAACAAGCAT 59.067 36.000 0.00 0.00 0.00 3.79
42 47 4.390264 TCGAGGTAGATCATCCTGTACTG 58.610 47.826 12.41 0.00 33.83 2.74
82 87 7.015877 TCTGTAGAGGCAAGGTTTTTAGACTAA 59.984 37.037 0.00 0.00 0.00 2.24
89 94 4.439253 AGTCTGTAGAGGCAAGGTTTTT 57.561 40.909 0.00 0.00 0.00 1.94
99 104 2.688958 CGAGGGGTTTAGTCTGTAGAGG 59.311 54.545 0.00 0.00 0.00 3.69
105 110 0.613777 AAGCCGAGGGGTTTAGTCTG 59.386 55.000 0.00 0.00 40.84 3.51
108 113 2.193993 ACATAAGCCGAGGGGTTTAGT 58.806 47.619 4.25 1.70 40.84 2.24
147 153 9.909644 CTAGTTGTAGTTGACATACTTGTAAGT 57.090 33.333 2.51 2.51 38.07 2.24
148 154 9.355215 CCTAGTTGTAGTTGACATACTTGTAAG 57.645 37.037 0.00 0.00 38.07 2.34
160 166 6.156256 AGCATGTTATCCCTAGTTGTAGTTGA 59.844 38.462 0.00 0.00 0.00 3.18
162 168 6.156256 TCAGCATGTTATCCCTAGTTGTAGTT 59.844 38.462 0.00 0.00 37.40 2.24
185 191 7.120579 ACACTTCAAGGCGTATTTAAATGATCA 59.879 33.333 11.05 0.00 0.00 2.92
215 221 7.496920 TCAAGATGTAATGCTATGAAGACTTGG 59.503 37.037 0.00 0.00 33.29 3.61
225 231 5.923114 CAGCGTACTCAAGATGTAATGCTAT 59.077 40.000 0.00 0.00 34.39 2.97
226 232 5.281727 CAGCGTACTCAAGATGTAATGCTA 58.718 41.667 0.00 0.00 34.39 3.49
229 235 3.060940 CGCAGCGTACTCAAGATGTAATG 60.061 47.826 6.65 0.00 0.00 1.90
233 239 0.458543 CCGCAGCGTACTCAAGATGT 60.459 55.000 15.05 0.00 0.00 3.06
333 350 1.182667 CACCTGATGACGGTGTCCTA 58.817 55.000 1.16 0.00 45.36 2.94
379 400 2.733956 GCCCTGGAACCACAATTATCA 58.266 47.619 0.00 0.00 0.00 2.15
417 438 0.934496 CCGAAAAGTCTTCGTGCACA 59.066 50.000 18.64 0.81 40.04 4.57
433 454 1.483004 TGACCTTGTGAAGACAACCGA 59.517 47.619 0.00 0.00 37.15 4.69
442 464 0.183492 AGCTGGCTTGACCTTGTGAA 59.817 50.000 0.00 0.00 40.22 3.18
446 468 0.959372 CCTGAGCTGGCTTGACCTTG 60.959 60.000 0.00 0.00 40.22 3.61
592 616 7.416326 CGGGAAAGAAAAGGATCCGATTTATTT 60.416 37.037 25.49 25.49 38.42 1.40
620 645 3.814945 CGTGGAGCAAGTTCTCATTTTC 58.185 45.455 0.00 0.00 34.84 2.29
667 695 2.035832 GGTTGTAGTTGCAAGCCACATT 59.964 45.455 0.00 0.00 39.96 2.71
850 883 4.570369 CGTCTCACATGTTATGTTGGCATA 59.430 41.667 0.00 0.00 42.70 3.14
892 925 6.598064 TCGCGGATGATGAGTTTATATAGAGA 59.402 38.462 6.13 0.00 0.00 3.10
964 1011 5.178797 CCTGCTATAGCTAGTTTGTGTGTT 58.821 41.667 24.61 0.00 42.66 3.32
980 1027 4.162888 TCATGATCAGTGACAACCTGCTAT 59.837 41.667 0.09 0.00 0.00 2.97
1451 1523 1.754803 AGCCTTTGATCGACGGATACA 59.245 47.619 9.69 0.00 31.51 2.29
1454 1526 1.269831 GCTAGCCTTTGATCGACGGAT 60.270 52.381 9.69 5.56 34.96 4.18
1467 1545 5.815233 TTCTTATCATAGCAAGCTAGCCT 57.185 39.130 12.13 3.98 34.23 4.58
1476 1554 7.398618 AGCTAGCCTCTTATTCTTATCATAGCA 59.601 37.037 12.13 0.00 34.61 3.49
1519 1609 1.073964 CAACAGCATCGACCAGTCTG 58.926 55.000 0.00 0.00 0.00 3.51
1526 1616 4.974591 AGCTTTTATTCAACAGCATCGAC 58.025 39.130 0.00 0.00 34.49 4.20
1529 1619 5.741040 GTGCTAGCTTTTATTCAACAGCATC 59.259 40.000 17.23 0.00 39.69 3.91
1582 1679 8.836413 CCACTTTATTTCATTCCATGTACGTAT 58.164 33.333 0.00 0.00 0.00 3.06
1596 1693 7.812191 CCGTTTGATTTGATCCACTTTATTTCA 59.188 33.333 0.00 0.00 0.00 2.69
1613 1710 9.349713 ACACATGAATATATAACCCGTTTGATT 57.650 29.630 0.00 0.00 0.00 2.57
1615 1712 7.227711 CCACACATGAATATATAACCCGTTTGA 59.772 37.037 0.00 0.00 0.00 2.69
1628 1725 9.261180 CTCGTAGTAAAATCCACACATGAATAT 57.739 33.333 0.00 0.00 0.00 1.28
1721 1855 9.447157 GGAACAGAGAGACTAGTAGTAGTTAAA 57.553 37.037 11.56 0.00 39.78 1.52
1722 1856 8.600668 TGGAACAGAGAGACTAGTAGTAGTTAA 58.399 37.037 11.56 0.00 39.78 2.01
1724 1858 7.018487 TGGAACAGAGAGACTAGTAGTAGTT 57.982 40.000 11.56 2.50 39.78 2.24
1725 1859 6.623979 TGGAACAGAGAGACTAGTAGTAGT 57.376 41.667 10.09 10.09 42.59 2.73
1743 1877 4.384547 GCACCACGACAAAAATTATGGAAC 59.615 41.667 0.00 0.00 0.00 3.62
1744 1878 4.551388 GCACCACGACAAAAATTATGGAA 58.449 39.130 0.00 0.00 0.00 3.53
1745 1879 3.057174 GGCACCACGACAAAAATTATGGA 60.057 43.478 0.00 0.00 0.00 3.41
1746 1880 3.249917 GGCACCACGACAAAAATTATGG 58.750 45.455 0.00 0.00 0.00 2.74
1747 1881 3.906998 TGGCACCACGACAAAAATTATG 58.093 40.909 0.00 0.00 0.00 1.90
1748 1882 4.799564 ATGGCACCACGACAAAAATTAT 57.200 36.364 0.00 0.00 0.00 1.28
1749 1883 5.707242 TTATGGCACCACGACAAAAATTA 57.293 34.783 0.00 0.00 0.00 1.40
1750 1884 4.592485 TTATGGCACCACGACAAAAATT 57.408 36.364 0.00 0.00 0.00 1.82
1751 1885 4.799564 ATTATGGCACCACGACAAAAAT 57.200 36.364 0.00 0.00 0.00 1.82
1752 1886 4.202161 ACAATTATGGCACCACGACAAAAA 60.202 37.500 0.00 0.00 0.00 1.94
1753 1887 3.319405 ACAATTATGGCACCACGACAAAA 59.681 39.130 0.00 0.00 0.00 2.44
1754 1888 2.887783 ACAATTATGGCACCACGACAAA 59.112 40.909 0.00 0.00 0.00 2.83
1755 1889 2.509569 ACAATTATGGCACCACGACAA 58.490 42.857 0.00 0.00 0.00 3.18
1756 1890 2.192664 ACAATTATGGCACCACGACA 57.807 45.000 0.00 0.00 0.00 4.35
1757 1891 2.227865 ACAACAATTATGGCACCACGAC 59.772 45.455 0.00 0.00 0.00 4.34
1758 1892 2.486203 GACAACAATTATGGCACCACGA 59.514 45.455 0.00 0.00 0.00 4.35
1759 1893 2.727607 CGACAACAATTATGGCACCACG 60.728 50.000 0.00 0.00 0.00 4.94
1760 1894 2.227865 ACGACAACAATTATGGCACCAC 59.772 45.455 0.00 0.00 0.00 4.16
1761 1895 2.509569 ACGACAACAATTATGGCACCA 58.490 42.857 0.00 0.00 0.00 4.17
1762 1896 3.569250 AACGACAACAATTATGGCACC 57.431 42.857 0.00 0.00 0.00 5.01
1763 1897 6.146898 AGTTTAACGACAACAATTATGGCAC 58.853 36.000 0.00 0.00 0.00 5.01
1764 1898 6.320494 AGTTTAACGACAACAATTATGGCA 57.680 33.333 0.00 0.00 0.00 4.92
1765 1899 8.730970 TTTAGTTTAACGACAACAATTATGGC 57.269 30.769 0.00 0.00 0.00 4.40
1769 1903 9.500864 GTGGTTTTAGTTTAACGACAACAATTA 57.499 29.630 8.86 0.00 35.24 1.40
1770 1904 7.218583 CGTGGTTTTAGTTTAACGACAACAATT 59.781 33.333 8.86 0.00 34.96 2.32
1771 1905 6.687958 CGTGGTTTTAGTTTAACGACAACAAT 59.312 34.615 8.86 0.00 34.96 2.71
1772 1906 6.020372 CGTGGTTTTAGTTTAACGACAACAA 58.980 36.000 8.86 0.00 34.96 2.83
1773 1907 5.349817 TCGTGGTTTTAGTTTAACGACAACA 59.650 36.000 8.86 0.00 34.96 3.33
1774 1908 5.794720 TCGTGGTTTTAGTTTAACGACAAC 58.205 37.500 0.00 0.00 34.96 3.32
1775 1909 6.601741 ATCGTGGTTTTAGTTTAACGACAA 57.398 33.333 0.00 0.00 42.13 3.18
1776 1910 7.651304 TCTTATCGTGGTTTTAGTTTAACGACA 59.349 33.333 0.00 0.00 42.13 4.35
1777 1911 8.006741 TCTTATCGTGGTTTTAGTTTAACGAC 57.993 34.615 0.00 0.00 42.13 4.34
1778 1912 8.586570 TTCTTATCGTGGTTTTAGTTTAACGA 57.413 30.769 0.00 0.00 43.29 3.85
1779 1913 9.815936 AATTCTTATCGTGGTTTTAGTTTAACG 57.184 29.630 0.00 0.00 0.00 3.18
1796 1930 5.763204 TGCTCCCCGTTTCATAATTCTTATC 59.237 40.000 0.00 0.00 0.00 1.75
1798 1932 5.104693 TCTGCTCCCCGTTTCATAATTCTTA 60.105 40.000 0.00 0.00 0.00 2.10
1800 1934 3.199946 TCTGCTCCCCGTTTCATAATTCT 59.800 43.478 0.00 0.00 0.00 2.40
1808 1942 2.044123 AATGATCTGCTCCCCGTTTC 57.956 50.000 0.00 0.00 0.00 2.78
1836 1973 2.837532 ATGCTTGCCCATTTTCGTTT 57.162 40.000 0.00 0.00 0.00 3.60
1847 1984 3.625649 TTTATGGGGAAAATGCTTGCC 57.374 42.857 0.00 0.00 0.00 4.52
1850 1987 5.476091 TTCGTTTTATGGGGAAAATGCTT 57.524 34.783 0.00 0.00 35.94 3.91
1858 1995 3.768878 ACACCATTTCGTTTTATGGGGA 58.231 40.909 10.16 0.00 46.25 4.81
1860 1997 4.944930 TCCTACACCATTTCGTTTTATGGG 59.055 41.667 0.00 0.00 44.53 4.00
1861 1998 5.448632 GCTCCTACACCATTTCGTTTTATGG 60.449 44.000 0.00 0.00 45.49 2.74
1862 1999 5.354234 AGCTCCTACACCATTTCGTTTTATG 59.646 40.000 0.00 0.00 0.00 1.90
1863 2000 5.497474 AGCTCCTACACCATTTCGTTTTAT 58.503 37.500 0.00 0.00 0.00 1.40
1864 2001 4.901868 AGCTCCTACACCATTTCGTTTTA 58.098 39.130 0.00 0.00 0.00 1.52
1870 2007 5.303078 TCTCATCTAGCTCCTACACCATTTC 59.697 44.000 0.00 0.00 0.00 2.17
1877 2014 7.667575 AAAGAATTCTCATCTAGCTCCTACA 57.332 36.000 8.78 0.00 0.00 2.74
1880 2017 9.158097 AGATTAAAGAATTCTCATCTAGCTCCT 57.842 33.333 17.29 2.24 0.00 3.69
1908 2045 2.678836 TGTTGCTAGCTCTCGTCTAGAC 59.321 50.000 17.23 13.18 36.50 2.59
1910 2047 3.605922 CGATGTTGCTAGCTCTCGTCTAG 60.606 52.174 17.23 2.63 37.25 2.43
1911 2048 2.288186 CGATGTTGCTAGCTCTCGTCTA 59.712 50.000 17.23 0.00 0.00 2.59
1912 2049 1.064803 CGATGTTGCTAGCTCTCGTCT 59.935 52.381 17.23 0.00 0.00 4.18
1913 2050 1.202200 ACGATGTTGCTAGCTCTCGTC 60.202 52.381 17.23 14.46 34.58 4.20
1914 2051 0.811915 ACGATGTTGCTAGCTCTCGT 59.188 50.000 17.23 19.37 34.80 4.18
1915 2052 1.914634 AACGATGTTGCTAGCTCTCG 58.085 50.000 17.23 18.78 0.00 4.04
1925 2226 9.409949 GAAAGACGAGAAATATTAACGATGTTG 57.590 33.333 13.10 0.00 0.00 3.33
1930 2231 7.220300 GCAGAGAAAGACGAGAAATATTAACGA 59.780 37.037 13.10 0.00 0.00 3.85
1938 2239 1.996191 GCGCAGAGAAAGACGAGAAAT 59.004 47.619 0.30 0.00 0.00 2.17
1944 2245 0.452184 TAGGAGCGCAGAGAAAGACG 59.548 55.000 11.47 0.00 0.00 4.18
1956 2257 1.066858 TGCCTCTGTTTCTTAGGAGCG 60.067 52.381 0.00 0.00 31.64 5.03
1957 2258 2.626840 CTGCCTCTGTTTCTTAGGAGC 58.373 52.381 0.00 0.00 31.64 4.70
1958 2259 2.626840 GCTGCCTCTGTTTCTTAGGAG 58.373 52.381 0.00 0.00 31.64 3.69
1959 2260 1.279271 GGCTGCCTCTGTTTCTTAGGA 59.721 52.381 12.43 0.00 31.64 2.94
1960 2261 1.743996 GGCTGCCTCTGTTTCTTAGG 58.256 55.000 12.43 0.00 0.00 2.69
1961 2262 1.363744 CGGCTGCCTCTGTTTCTTAG 58.636 55.000 17.92 0.00 0.00 2.18
1962 2263 0.036388 CCGGCTGCCTCTGTTTCTTA 60.036 55.000 17.92 0.00 0.00 2.10
1963 2264 1.302832 CCGGCTGCCTCTGTTTCTT 60.303 57.895 17.92 0.00 0.00 2.52
1964 2265 2.348998 CCGGCTGCCTCTGTTTCT 59.651 61.111 17.92 0.00 0.00 2.52
1972 2274 2.361230 GCTTTTACCCGGCTGCCT 60.361 61.111 17.92 0.00 0.00 4.75
1982 2284 6.366877 TGATTTGGACGTACTACTGCTTTTAC 59.633 38.462 0.00 0.00 0.00 2.01
2007 2309 3.850923 CAATCGGTGCACGTACGT 58.149 55.556 16.72 16.72 44.69 3.57
2032 2334 5.859205 AAGCTTCAGAAATTTGACCAACT 57.141 34.783 0.00 0.00 0.00 3.16
2052 2354 8.796278 GTTACTACTACTTGAATTCTGCGTAAG 58.204 37.037 7.05 4.11 43.44 2.34
2053 2355 8.298854 TGTTACTACTACTTGAATTCTGCGTAA 58.701 33.333 7.05 1.51 0.00 3.18
2054 2356 7.819644 TGTTACTACTACTTGAATTCTGCGTA 58.180 34.615 7.05 4.76 0.00 4.42
2055 2357 6.684686 TGTTACTACTACTTGAATTCTGCGT 58.315 36.000 7.05 3.84 0.00 5.24
2056 2358 7.445836 GTTGTTACTACTACTTGAATTCTGCG 58.554 38.462 7.05 0.00 0.00 5.18
2057 2359 7.411588 CCGTTGTTACTACTACTTGAATTCTGC 60.412 40.741 7.05 0.00 0.00 4.26
2058 2360 7.811236 TCCGTTGTTACTACTACTTGAATTCTG 59.189 37.037 7.05 2.42 0.00 3.02
2059 2361 7.889469 TCCGTTGTTACTACTACTTGAATTCT 58.111 34.615 7.05 0.00 0.00 2.40
2060 2362 8.524870 TTCCGTTGTTACTACTACTTGAATTC 57.475 34.615 0.00 0.00 0.00 2.17
2061 2363 8.768019 GTTTCCGTTGTTACTACTACTTGAATT 58.232 33.333 0.00 0.00 0.00 2.17
2062 2364 7.927629 TGTTTCCGTTGTTACTACTACTTGAAT 59.072 33.333 0.00 0.00 0.00 2.57
2063 2365 7.264221 TGTTTCCGTTGTTACTACTACTTGAA 58.736 34.615 0.00 0.00 0.00 2.69
2064 2366 6.804677 TGTTTCCGTTGTTACTACTACTTGA 58.195 36.000 0.00 0.00 0.00 3.02
2065 2367 6.346359 GCTGTTTCCGTTGTTACTACTACTTG 60.346 42.308 0.00 0.00 0.00 3.16
2066 2368 5.693555 GCTGTTTCCGTTGTTACTACTACTT 59.306 40.000 0.00 0.00 0.00 2.24
2067 2369 5.225642 GCTGTTTCCGTTGTTACTACTACT 58.774 41.667 0.00 0.00 0.00 2.57
2068 2370 4.386954 GGCTGTTTCCGTTGTTACTACTAC 59.613 45.833 0.00 0.00 0.00 2.73
2069 2371 4.039004 TGGCTGTTTCCGTTGTTACTACTA 59.961 41.667 0.00 0.00 0.00 1.82
2141 2454 0.899720 AAAGGAATCGGCGGTCTGTA 59.100 50.000 7.21 0.00 0.00 2.74
2143 2456 0.391130 TGAAAGGAATCGGCGGTCTG 60.391 55.000 7.21 0.00 0.00 3.51
2185 2499 0.815734 TTCTCGGACCTGACGATTCC 59.184 55.000 0.00 0.00 39.89 3.01
2203 2517 4.994756 CCAACCCCAAGCCGGCTT 62.995 66.667 35.84 35.84 36.60 4.35
2209 2523 1.989508 CATTCCCCCAACCCCAAGC 60.990 63.158 0.00 0.00 0.00 4.01
2225 2539 0.737219 GACGTACGGGTCTAGTGCAT 59.263 55.000 21.06 0.00 34.09 3.96
2231 2545 3.272574 AGAAGATGACGTACGGGTCTA 57.727 47.619 21.06 0.91 37.81 2.59
2233 2547 2.422832 AGAAGAAGATGACGTACGGGTC 59.577 50.000 21.06 13.68 37.45 4.46
2234 2548 2.163815 CAGAAGAAGATGACGTACGGGT 59.836 50.000 21.06 4.51 0.00 5.28
2235 2549 2.479730 CCAGAAGAAGATGACGTACGGG 60.480 54.545 21.06 1.97 0.00 5.28
2237 2551 3.759527 TCCAGAAGAAGATGACGTACG 57.240 47.619 15.01 15.01 0.00 3.67
2238 2552 3.799420 GCATCCAGAAGAAGATGACGTAC 59.201 47.826 4.25 0.00 42.04 3.67
2239 2553 3.447229 TGCATCCAGAAGAAGATGACGTA 59.553 43.478 4.25 0.00 42.04 3.57
2240 2554 2.234661 TGCATCCAGAAGAAGATGACGT 59.765 45.455 4.25 0.00 42.04 4.34
2263 2604 1.228154 AAAGCTTGACCCGTCCCAC 60.228 57.895 0.00 0.00 0.00 4.61
2268 2609 2.032071 CCGGAAAGCTTGACCCGT 59.968 61.111 24.28 0.64 40.30 5.28
2277 2618 2.029307 ATAGAGACGGGCCGGAAAGC 62.029 60.000 31.78 14.21 0.00 3.51
2282 2623 2.088674 CTTGGATAGAGACGGGCCGG 62.089 65.000 31.78 12.53 0.00 6.13
2314 2655 5.613360 CGCAGTAGCATCCAGAAAAATATCG 60.613 44.000 0.00 0.00 42.27 2.92
2317 2658 4.513442 ACGCAGTAGCATCCAGAAAAATA 58.487 39.130 0.00 0.00 41.94 1.40
2318 2659 3.347216 ACGCAGTAGCATCCAGAAAAAT 58.653 40.909 0.00 0.00 41.94 1.82
2363 2704 1.669795 CGCCAAGATTTTTGAGGCCAC 60.670 52.381 5.01 0.00 42.28 5.01
2372 2713 3.676873 GCCATCAATCACGCCAAGATTTT 60.677 43.478 0.00 0.00 33.64 1.82
2394 2735 3.327404 ACCCTTACACGCCTGGGG 61.327 66.667 9.49 9.49 43.72 4.96
2405 2746 2.265367 TGAAGCAGGATGACACCCTTA 58.735 47.619 0.00 0.00 39.69 2.69
2408 2749 1.003580 TCTTGAAGCAGGATGACACCC 59.996 52.381 0.00 0.00 39.69 4.61
2413 2754 3.811497 CGCAATATCTTGAAGCAGGATGA 59.189 43.478 2.73 0.00 33.78 2.92
2416 2757 2.092968 ACCGCAATATCTTGAAGCAGGA 60.093 45.455 0.00 0.00 34.04 3.86
2424 2765 5.954434 CAAAATTCCACCGCAATATCTTG 57.046 39.130 0.00 0.00 35.36 3.02


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

AutoCloner maintained by Alex Coulton.