Multiple sequence alignment - TraesCS6A01G028600

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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 TraesCS6A01G028600 chr6A 100.000 2720 0 0 1 2720 14570486 14567767 0.000000e+00 5024.0
1 TraesCS6A01G028600 chr6A 93.976 83 5 0 1667 1749 615180518 615180436 2.840000e-25 126.0
2 TraesCS6A01G028600 chr5A 97.316 1751 42 3 1 1747 277340254 277342003 0.000000e+00 2968.0
3 TraesCS6A01G028600 chr5A 89.073 1748 183 6 5 1747 602904182 602905926 0.000000e+00 2163.0
4 TraesCS6A01G028600 chr7A 95.836 1753 68 3 1 1748 30885387 30887139 0.000000e+00 2828.0
5 TraesCS6A01G028600 chr7A 96.504 801 25 3 950 1749 414145152 414144354 0.000000e+00 1321.0
6 TraesCS6A01G028600 chr7A 80.000 220 36 8 1995 2208 666582723 666582940 3.630000e-34 156.0
7 TraesCS6A01G028600 chr2B 86.554 766 83 3 983 1747 768037738 768036992 0.000000e+00 826.0
8 TraesCS6A01G028600 chr2B 88.172 465 36 7 1995 2442 441605689 441605227 1.110000e-148 536.0
9 TraesCS6A01G028600 chr2B 81.739 115 15 5 1854 1964 131824398 131824510 1.040000e-14 91.6
10 TraesCS6A01G028600 chr2B 83.951 81 8 5 2540 2619 317083253 317083329 3.760000e-09 73.1
11 TraesCS6A01G028600 chr2B 94.595 37 2 0 2618 2654 317083308 317083344 1.050000e-04 58.4
12 TraesCS6A01G028600 chr2A 82.548 785 126 7 972 1749 662598833 662599613 0.000000e+00 680.0
13 TraesCS6A01G028600 chr2A 89.418 378 24 6 2079 2440 170945270 170945647 1.910000e-126 462.0
14 TraesCS6A01G028600 chr2A 90.602 266 25 0 2455 2720 170945815 170946080 1.200000e-93 353.0
15 TraesCS6A01G028600 chr5B 88.651 467 34 8 1995 2444 524456745 524457209 3.960000e-153 551.0
16 TraesCS6A01G028600 chr5B 83.417 398 46 11 2000 2380 586530268 586529874 4.310000e-93 351.0
17 TraesCS6A01G028600 chr5B 84.150 347 39 6 2085 2415 181485688 181485342 3.380000e-84 322.0
18 TraesCS6A01G028600 chr5B 91.333 150 13 0 2456 2605 524457368 524457517 3.550000e-49 206.0
19 TraesCS6A01G028600 chr5B 88.889 81 9 0 2549 2629 181485319 181485239 1.720000e-17 100.0
20 TraesCS6A01G028600 chr5B 100.000 29 0 0 1936 1964 21729865 21729893 1.000000e-03 54.7
21 TraesCS6A01G028600 chr5B 100.000 29 0 0 2416 2444 181485366 181485338 1.000000e-03 54.7
22 TraesCS6A01G028600 chr4B 88.132 455 36 8 1997 2433 581896328 581895874 2.400000e-145 525.0
23 TraesCS6A01G028600 chr7B 81.093 439 64 10 1995 2415 748178163 748177726 1.560000e-87 333.0
24 TraesCS6A01G028600 chr7B 81.007 437 60 12 1995 2411 748169331 748168898 2.610000e-85 326.0
25 TraesCS6A01G028600 chr7B 88.889 81 9 0 2549 2629 748173777 748173697 1.720000e-17 100.0
26 TraesCS6A01G028600 chr7B 88.889 81 9 0 2549 2629 748177694 748177614 1.720000e-17 100.0
27 TraesCS6A01G028600 chr7B 86.420 81 11 0 2549 2629 748168862 748168782 3.730000e-14 89.8
28 TraesCS6A01G028600 chr1B 84.790 309 40 7 1995 2299 649700105 649699800 1.220000e-78 303.0
29 TraesCS6A01G028600 chr7D 80.717 223 34 9 1997 2214 619229322 619229104 6.030000e-37 165.0
30 TraesCS6A01G028600 chr7D 90.000 80 8 0 2369 2448 619228916 619228837 1.330000e-18 104.0
31 TraesCS6A01G028600 chr7D 100.000 29 0 0 1936 1964 43074182 43074154 1.000000e-03 54.7
32 TraesCS6A01G028600 chr3D 80.269 223 37 7 1997 2214 364518742 364518522 7.790000e-36 161.0
33 TraesCS6A01G028600 chr5D 89.655 116 8 4 2540 2654 206093456 206093344 7.850000e-31 145.0
34 TraesCS6A01G028600 chr5D 100.000 32 0 0 2413 2444 49305064 49305095 2.920000e-05 60.2
35 TraesCS6A01G028600 chr6D 85.088 114 15 1 1853 1964 381019851 381019964 6.150000e-22 115.0
36 TraesCS6A01G028600 chr6D 87.500 80 10 0 2365 2444 344311077 344311156 2.880000e-15 93.5
37 TraesCS6A01G028600 chr2D 95.918 49 2 0 2536 2584 531341249 531341297 2.250000e-11 80.5
38 TraesCS6A01G028600 chr3B 100.000 29 0 0 1936 1964 507795823 507795851 1.000000e-03 54.7
39 TraesCS6A01G028600 chr3A 100.000 29 0 0 1936 1964 235768 235740 1.000000e-03 54.7


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 TraesCS6A01G028600 chr6A 14567767 14570486 2719 True 5024.0 5024 100.0000 1 2720 1 chr6A.!!$R1 2719
1 TraesCS6A01G028600 chr5A 277340254 277342003 1749 False 2968.0 2968 97.3160 1 1747 1 chr5A.!!$F1 1746
2 TraesCS6A01G028600 chr5A 602904182 602905926 1744 False 2163.0 2163 89.0730 5 1747 1 chr5A.!!$F2 1742
3 TraesCS6A01G028600 chr7A 30885387 30887139 1752 False 2828.0 2828 95.8360 1 1748 1 chr7A.!!$F1 1747
4 TraesCS6A01G028600 chr7A 414144354 414145152 798 True 1321.0 1321 96.5040 950 1749 1 chr7A.!!$R1 799
5 TraesCS6A01G028600 chr2B 768036992 768037738 746 True 826.0 826 86.5540 983 1747 1 chr2B.!!$R2 764
6 TraesCS6A01G028600 chr2A 662598833 662599613 780 False 680.0 680 82.5480 972 1749 1 chr2A.!!$F1 777
7 TraesCS6A01G028600 chr2A 170945270 170946080 810 False 407.5 462 90.0100 2079 2720 2 chr2A.!!$F2 641
8 TraesCS6A01G028600 chr5B 524456745 524457517 772 False 378.5 551 89.9920 1995 2605 2 chr5B.!!$F2 610
9 TraesCS6A01G028600 chr7B 748168782 748169331 549 True 207.9 326 83.7135 1995 2629 2 chr7B.!!$R1 634

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
487 491 1.384525 TTCCTGACAACCAAACGGTG 58.615 50.0 0.0 0.0 36.67 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 1969 0.034337 GAAACGTGTGCTACCCCTGA 59.966 55.0 0.0 0.0 0.0 3.86 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
49 50 2.027385 GCTTTCAGATTCCCATGGGAC 58.973 52.381 34.00 22.49 45.11 4.46
108 109 3.114606 GTGGGGAATGGAAAATGGGAAT 58.885 45.455 0.00 0.00 0.00 3.01
139 140 2.369983 TTGGAGATCATGGGATTGGC 57.630 50.000 0.00 0.00 32.67 4.52
398 402 1.610886 GGAGAGTTGGGAACGGAAAGG 60.611 57.143 0.00 0.00 36.23 3.11
470 474 8.801913 GCACTTTAAATACTTCTCATGCATTTC 58.198 33.333 0.00 0.00 0.00 2.17
487 491 1.384525 TTCCTGACAACCAAACGGTG 58.615 50.000 0.00 0.00 36.67 4.94
762 766 7.154191 TGGAGATAGCCTGGAAGAAATTATT 57.846 36.000 0.00 0.00 34.07 1.40
1138 1143 1.303236 CATCCCCTGCGTGTTTCCA 60.303 57.895 0.00 0.00 0.00 3.53
1151 1156 4.378459 GCGTGTTTCCAGACAGATTAAAGG 60.378 45.833 0.00 0.00 0.00 3.11
1246 1251 0.394352 GAAATGGACTCCGCCACCAT 60.394 55.000 0.00 0.00 44.87 3.55
1321 1326 3.459598 AGCTGGGTATGGTGTTATCATGT 59.540 43.478 0.00 0.00 0.00 3.21
1491 1502 9.587772 GATTGTCTCTCACTTGTTAATAAGCTA 57.412 33.333 11.49 0.17 0.00 3.32
1512 1523 0.621571 AACAGCAGGGGCAGGATAGA 60.622 55.000 0.00 0.00 44.61 1.98
1621 1633 1.001641 GAGGCAGCCCATGTTCTGT 60.002 57.895 8.22 0.00 33.09 3.41
1727 1739 5.698741 TTAAGGAATGAATGAGAGGCTGA 57.301 39.130 0.00 0.00 0.00 4.26
1766 1778 5.397142 AAAAATTCTGGATGTTCTGCTCC 57.603 39.130 0.00 0.00 0.00 4.70
1767 1779 2.725221 ATTCTGGATGTTCTGCTCCC 57.275 50.000 0.00 0.00 0.00 4.30
1768 1780 1.361204 TTCTGGATGTTCTGCTCCCA 58.639 50.000 0.00 0.00 0.00 4.37
1769 1781 1.588239 TCTGGATGTTCTGCTCCCAT 58.412 50.000 0.00 0.00 0.00 4.00
1770 1782 1.487976 TCTGGATGTTCTGCTCCCATC 59.512 52.381 0.00 0.00 35.37 3.51
1771 1783 0.178767 TGGATGTTCTGCTCCCATCG 59.821 55.000 0.00 0.00 36.65 3.84
1772 1784 0.533755 GGATGTTCTGCTCCCATCGG 60.534 60.000 0.00 0.00 36.65 4.18
1773 1785 0.179000 GATGTTCTGCTCCCATCGGT 59.821 55.000 0.00 0.00 0.00 4.69
1774 1786 1.412710 GATGTTCTGCTCCCATCGGTA 59.587 52.381 0.00 0.00 0.00 4.02
1775 1787 1.496060 TGTTCTGCTCCCATCGGTAT 58.504 50.000 0.00 0.00 0.00 2.73
1776 1788 2.673258 TGTTCTGCTCCCATCGGTATA 58.327 47.619 0.00 0.00 0.00 1.47
1777 1789 2.628178 TGTTCTGCTCCCATCGGTATAG 59.372 50.000 0.00 0.00 0.00 1.31
1778 1790 1.924731 TCTGCTCCCATCGGTATAGG 58.075 55.000 0.00 0.00 0.00 2.57
1779 1791 1.147191 TCTGCTCCCATCGGTATAGGT 59.853 52.381 0.00 0.00 0.00 3.08
1780 1792 1.273606 CTGCTCCCATCGGTATAGGTG 59.726 57.143 0.00 0.00 0.00 4.00
1781 1793 1.133294 TGCTCCCATCGGTATAGGTGA 60.133 52.381 0.00 0.00 0.00 4.02
1782 1794 1.546476 GCTCCCATCGGTATAGGTGAG 59.454 57.143 0.00 0.00 0.00 3.51
1783 1795 1.546476 CTCCCATCGGTATAGGTGAGC 59.454 57.143 0.00 0.00 0.00 4.26
1784 1796 0.608640 CCCATCGGTATAGGTGAGCC 59.391 60.000 0.00 0.00 0.00 4.70
1786 1798 1.273606 CCATCGGTATAGGTGAGCCTG 59.726 57.143 0.00 0.00 46.47 4.85
1787 1799 2.239400 CATCGGTATAGGTGAGCCTGA 58.761 52.381 0.00 0.00 46.47 3.86
1788 1800 1.982660 TCGGTATAGGTGAGCCTGAG 58.017 55.000 0.00 0.00 46.47 3.35
1789 1801 0.315568 CGGTATAGGTGAGCCTGAGC 59.684 60.000 0.00 0.00 46.47 4.26
1790 1802 0.682292 GGTATAGGTGAGCCTGAGCC 59.318 60.000 0.00 0.00 46.47 4.70
1791 1803 1.414158 GTATAGGTGAGCCTGAGCCA 58.586 55.000 0.00 0.00 46.47 4.75
1792 1804 1.342819 GTATAGGTGAGCCTGAGCCAG 59.657 57.143 0.00 0.00 46.47 4.85
1793 1805 1.694133 ATAGGTGAGCCTGAGCCAGC 61.694 60.000 0.00 0.00 46.47 4.85
1797 1809 3.859414 GAGCCTGAGCCAGCGGAT 61.859 66.667 0.00 0.00 41.25 4.18
1798 1810 4.172512 AGCCTGAGCCAGCGGATG 62.173 66.667 0.00 0.00 41.25 3.51
1799 1811 4.479993 GCCTGAGCCAGCGGATGT 62.480 66.667 0.00 0.00 0.00 3.06
1800 1812 2.513204 CCTGAGCCAGCGGATGTG 60.513 66.667 0.00 0.00 0.00 3.21
1801 1813 2.513204 CTGAGCCAGCGGATGTGG 60.513 66.667 0.00 0.00 38.21 4.17
1802 1814 3.320879 CTGAGCCAGCGGATGTGGT 62.321 63.158 0.00 0.00 37.40 4.16
1803 1815 2.821366 GAGCCAGCGGATGTGGTG 60.821 66.667 0.00 0.00 37.40 4.17
1806 1818 2.821366 CCAGCGGATGTGGTGCTC 60.821 66.667 0.00 0.00 36.69 4.26
1807 1819 2.046988 CAGCGGATGTGGTGCTCA 60.047 61.111 0.00 0.00 36.69 4.26
1808 1820 1.672030 CAGCGGATGTGGTGCTCAA 60.672 57.895 0.00 0.00 36.69 3.02
1809 1821 1.672356 AGCGGATGTGGTGCTCAAC 60.672 57.895 0.00 0.00 32.44 3.18
1810 1822 3.027170 GCGGATGTGGTGCTCAACG 62.027 63.158 0.00 0.00 0.00 4.10
1811 1823 2.870372 GGATGTGGTGCTCAACGC 59.130 61.111 0.00 0.00 39.77 4.84
1812 1824 2.476051 GATGTGGTGCTCAACGCG 59.524 61.111 3.53 3.53 43.27 6.01
1813 1825 3.027170 GATGTGGTGCTCAACGCGG 62.027 63.158 12.47 0.00 43.27 6.46
1814 1826 3.529341 ATGTGGTGCTCAACGCGGA 62.529 57.895 12.47 0.00 43.27 5.54
1815 1827 3.712881 GTGGTGCTCAACGCGGAC 61.713 66.667 12.47 0.00 43.27 4.79
1816 1828 4.228567 TGGTGCTCAACGCGGACA 62.229 61.111 12.47 0.00 43.27 4.02
1817 1829 3.414700 GGTGCTCAACGCGGACAG 61.415 66.667 12.47 3.27 43.27 3.51
1818 1830 4.077188 GTGCTCAACGCGGACAGC 62.077 66.667 12.47 14.67 43.27 4.40
1819 1831 4.299547 TGCTCAACGCGGACAGCT 62.300 61.111 21.24 0.00 45.59 4.24
1820 1832 3.482783 GCTCAACGCGGACAGCTC 61.483 66.667 12.47 0.00 45.59 4.09
1821 1833 2.049156 CTCAACGCGGACAGCTCA 60.049 61.111 12.47 0.00 45.59 4.26
1822 1834 1.446792 CTCAACGCGGACAGCTCAT 60.447 57.895 12.47 0.00 45.59 2.90
1823 1835 1.690283 CTCAACGCGGACAGCTCATG 61.690 60.000 12.47 0.00 45.59 3.07
1824 1836 1.737735 CAACGCGGACAGCTCATGA 60.738 57.895 12.47 0.00 45.59 3.07
1825 1837 1.005037 AACGCGGACAGCTCATGAA 60.005 52.632 12.47 0.00 45.59 2.57
1826 1838 1.016130 AACGCGGACAGCTCATGAAG 61.016 55.000 12.47 0.00 45.59 3.02
1827 1839 2.169789 CGCGGACAGCTCATGAAGG 61.170 63.158 0.00 0.00 45.59 3.46
1828 1840 1.219124 GCGGACAGCTCATGAAGGA 59.781 57.895 0.00 0.00 44.04 3.36
1829 1841 1.086634 GCGGACAGCTCATGAAGGAC 61.087 60.000 0.00 0.00 44.04 3.85
1830 1842 0.803768 CGGACAGCTCATGAAGGACG 60.804 60.000 0.00 0.00 0.00 4.79
1831 1843 0.247736 GGACAGCTCATGAAGGACGT 59.752 55.000 0.00 0.00 0.00 4.34
1832 1844 1.354040 GACAGCTCATGAAGGACGTG 58.646 55.000 0.00 0.00 36.90 4.49
1833 1845 0.036952 ACAGCTCATGAAGGACGTGG 60.037 55.000 0.00 0.00 36.29 4.94
1834 1846 0.036952 CAGCTCATGAAGGACGTGGT 60.037 55.000 0.00 0.00 36.29 4.16
1835 1847 0.036952 AGCTCATGAAGGACGTGGTG 60.037 55.000 0.00 0.00 36.29 4.17
1836 1848 1.639298 GCTCATGAAGGACGTGGTGC 61.639 60.000 0.00 0.00 36.29 5.01
1838 1850 2.742372 ATGAAGGACGTGGTGCGC 60.742 61.111 0.00 0.00 46.11 6.09
1839 1851 3.529341 ATGAAGGACGTGGTGCGCA 62.529 57.895 5.66 5.66 46.11 6.09
1840 1852 2.970324 GAAGGACGTGGTGCGCAA 60.970 61.111 14.00 0.00 46.11 4.85
1841 1853 3.236618 GAAGGACGTGGTGCGCAAC 62.237 63.158 21.09 21.09 46.11 4.17
1854 1866 2.097160 GCAACGCGCATGACTGAG 59.903 61.111 15.79 0.00 41.79 3.35
1855 1867 2.097160 CAACGCGCATGACTGAGC 59.903 61.111 5.73 0.00 43.86 4.26
1859 1871 4.684265 GCGCATGACTGAGCAATG 57.316 55.556 0.30 0.00 46.23 2.82
1860 1872 1.585521 GCGCATGACTGAGCAATGC 60.586 57.895 0.30 9.25 46.23 3.56
1861 1873 1.989966 GCGCATGACTGAGCAATGCT 61.990 55.000 7.79 7.79 46.23 3.79
1862 1874 1.292992 CGCATGACTGAGCAATGCTA 58.707 50.000 8.12 0.00 39.88 3.49
1863 1875 1.260825 CGCATGACTGAGCAATGCTAG 59.739 52.381 8.12 8.81 39.88 3.42
1864 1876 2.558378 GCATGACTGAGCAATGCTAGA 58.442 47.619 8.12 0.00 39.88 2.43
1865 1877 2.287373 GCATGACTGAGCAATGCTAGAC 59.713 50.000 8.12 7.38 39.88 2.59
1866 1878 3.794717 CATGACTGAGCAATGCTAGACT 58.205 45.455 8.12 0.00 39.88 3.24
1867 1879 3.516981 TGACTGAGCAATGCTAGACTC 57.483 47.619 8.12 1.22 39.88 3.36
1868 1880 2.827921 TGACTGAGCAATGCTAGACTCA 59.172 45.455 8.12 4.03 39.88 3.41
1869 1881 3.186119 GACTGAGCAATGCTAGACTCAC 58.814 50.000 8.12 0.00 39.88 3.51
1870 1882 2.564504 ACTGAGCAATGCTAGACTCACA 59.435 45.455 8.12 0.00 39.88 3.58
1871 1883 3.188492 CTGAGCAATGCTAGACTCACAG 58.812 50.000 8.12 5.56 39.88 3.66
1872 1884 2.093816 TGAGCAATGCTAGACTCACAGG 60.094 50.000 8.12 0.00 39.88 4.00
1873 1885 1.209019 AGCAATGCTAGACTCACAGGG 59.791 52.381 5.69 0.00 36.99 4.45
1874 1886 1.065854 GCAATGCTAGACTCACAGGGT 60.066 52.381 0.00 0.00 0.00 4.34
1875 1887 2.898705 CAATGCTAGACTCACAGGGTC 58.101 52.381 0.00 0.00 0.00 4.46
1876 1888 2.499289 CAATGCTAGACTCACAGGGTCT 59.501 50.000 4.78 4.78 44.83 3.85
1877 1889 2.310779 TGCTAGACTCACAGGGTCTT 57.689 50.000 4.69 0.00 42.96 3.01
1878 1890 2.609747 TGCTAGACTCACAGGGTCTTT 58.390 47.619 4.69 0.00 42.96 2.52
1879 1891 2.972713 TGCTAGACTCACAGGGTCTTTT 59.027 45.455 4.69 0.00 42.96 2.27
1880 1892 3.391296 TGCTAGACTCACAGGGTCTTTTT 59.609 43.478 4.69 0.00 42.96 1.94
1881 1893 4.591498 TGCTAGACTCACAGGGTCTTTTTA 59.409 41.667 4.69 0.00 42.96 1.52
1882 1894 4.930405 GCTAGACTCACAGGGTCTTTTTAC 59.070 45.833 4.69 0.00 42.96 2.01
1883 1895 5.510861 GCTAGACTCACAGGGTCTTTTTACA 60.511 44.000 4.69 0.00 42.96 2.41
1884 1896 4.962155 AGACTCACAGGGTCTTTTTACAG 58.038 43.478 0.00 0.00 40.65 2.74
1885 1897 4.065789 GACTCACAGGGTCTTTTTACAGG 58.934 47.826 0.00 0.00 0.00 4.00
1886 1898 3.458487 ACTCACAGGGTCTTTTTACAGGT 59.542 43.478 0.00 0.00 0.00 4.00
1887 1899 4.079958 ACTCACAGGGTCTTTTTACAGGTT 60.080 41.667 0.00 0.00 0.00 3.50
1888 1900 4.862371 TCACAGGGTCTTTTTACAGGTTT 58.138 39.130 0.00 0.00 0.00 3.27
1889 1901 5.265989 TCACAGGGTCTTTTTACAGGTTTT 58.734 37.500 0.00 0.00 0.00 2.43
1890 1902 6.424883 TCACAGGGTCTTTTTACAGGTTTTA 58.575 36.000 0.00 0.00 0.00 1.52
1891 1903 6.319405 TCACAGGGTCTTTTTACAGGTTTTAC 59.681 38.462 0.00 0.00 0.00 2.01
1892 1904 5.297527 ACAGGGTCTTTTTACAGGTTTTACG 59.702 40.000 0.00 0.00 0.00 3.18
1893 1905 4.823442 AGGGTCTTTTTACAGGTTTTACGG 59.177 41.667 0.00 0.00 0.00 4.02
1894 1906 4.821260 GGGTCTTTTTACAGGTTTTACGGA 59.179 41.667 0.00 0.00 0.00 4.69
1895 1907 5.049198 GGGTCTTTTTACAGGTTTTACGGAG 60.049 44.000 0.00 0.00 0.00 4.63
1896 1908 5.049198 GGTCTTTTTACAGGTTTTACGGAGG 60.049 44.000 0.00 0.00 0.00 4.30
1897 1909 5.528690 GTCTTTTTACAGGTTTTACGGAGGT 59.471 40.000 0.00 0.00 0.00 3.85
1898 1910 5.528320 TCTTTTTACAGGTTTTACGGAGGTG 59.472 40.000 0.00 0.00 0.00 4.00
1899 1911 2.460757 TACAGGTTTTACGGAGGTGC 57.539 50.000 0.00 0.00 0.00 5.01
1900 1912 0.763035 ACAGGTTTTACGGAGGTGCT 59.237 50.000 0.00 0.00 0.00 4.40
1901 1913 1.972795 ACAGGTTTTACGGAGGTGCTA 59.027 47.619 0.00 0.00 0.00 3.49
1902 1914 2.369532 ACAGGTTTTACGGAGGTGCTAA 59.630 45.455 0.00 0.00 0.00 3.09
1903 1915 2.740447 CAGGTTTTACGGAGGTGCTAAC 59.260 50.000 0.00 0.00 0.00 2.34
1904 1916 1.728425 GGTTTTACGGAGGTGCTAACG 59.272 52.381 0.00 0.00 0.00 3.18
1905 1917 2.407090 GTTTTACGGAGGTGCTAACGT 58.593 47.619 0.00 0.00 42.71 3.99
1906 1918 3.574614 GTTTTACGGAGGTGCTAACGTA 58.425 45.455 0.00 0.00 40.38 3.57
1907 1919 3.492421 TTTACGGAGGTGCTAACGTAG 57.508 47.619 0.00 0.00 41.93 3.51
1908 1920 1.382522 TACGGAGGTGCTAACGTAGG 58.617 55.000 0.00 0.00 40.38 3.18
1909 1921 0.610232 ACGGAGGTGCTAACGTAGGT 60.610 55.000 0.00 0.00 37.85 3.08
1910 1922 0.100146 CGGAGGTGCTAACGTAGGTC 59.900 60.000 0.00 0.00 0.00 3.85
1911 1923 1.472188 GGAGGTGCTAACGTAGGTCT 58.528 55.000 0.00 0.00 0.00 3.85
1912 1924 1.823610 GGAGGTGCTAACGTAGGTCTT 59.176 52.381 0.00 0.00 0.00 3.01
1913 1925 2.233186 GGAGGTGCTAACGTAGGTCTTT 59.767 50.000 0.00 0.00 0.00 2.52
1914 1926 3.251571 GAGGTGCTAACGTAGGTCTTTG 58.748 50.000 0.00 0.00 0.00 2.77
1915 1927 2.895404 AGGTGCTAACGTAGGTCTTTGA 59.105 45.455 0.00 0.00 0.00 2.69
1916 1928 3.056749 AGGTGCTAACGTAGGTCTTTGAG 60.057 47.826 0.00 0.00 0.00 3.02
1917 1929 3.057033 GGTGCTAACGTAGGTCTTTGAGA 60.057 47.826 0.00 0.00 0.00 3.27
1918 1930 4.381718 GGTGCTAACGTAGGTCTTTGAGAT 60.382 45.833 0.00 0.00 0.00 2.75
1919 1931 5.169295 GTGCTAACGTAGGTCTTTGAGATT 58.831 41.667 0.00 0.00 0.00 2.40
1920 1932 5.062308 GTGCTAACGTAGGTCTTTGAGATTG 59.938 44.000 0.00 0.00 0.00 2.67
1921 1933 4.567159 GCTAACGTAGGTCTTTGAGATTGG 59.433 45.833 0.00 0.00 0.00 3.16
1922 1934 4.884668 AACGTAGGTCTTTGAGATTGGA 57.115 40.909 0.00 0.00 0.00 3.53
1923 1935 5.422214 AACGTAGGTCTTTGAGATTGGAT 57.578 39.130 0.00 0.00 0.00 3.41
1924 1936 5.422214 ACGTAGGTCTTTGAGATTGGATT 57.578 39.130 0.00 0.00 0.00 3.01
1925 1937 6.540438 ACGTAGGTCTTTGAGATTGGATTA 57.460 37.500 0.00 0.00 0.00 1.75
1926 1938 6.942976 ACGTAGGTCTTTGAGATTGGATTAA 58.057 36.000 0.00 0.00 0.00 1.40
1927 1939 7.391620 ACGTAGGTCTTTGAGATTGGATTAAA 58.608 34.615 0.00 0.00 0.00 1.52
1928 1940 8.047310 ACGTAGGTCTTTGAGATTGGATTAAAT 58.953 33.333 0.00 0.00 0.00 1.40
1929 1941 8.338259 CGTAGGTCTTTGAGATTGGATTAAATG 58.662 37.037 0.00 0.00 0.00 2.32
1930 1942 9.396022 GTAGGTCTTTGAGATTGGATTAAATGA 57.604 33.333 0.00 0.00 0.00 2.57
1931 1943 8.517062 AGGTCTTTGAGATTGGATTAAATGAG 57.483 34.615 0.00 0.00 0.00 2.90
1932 1944 8.112183 AGGTCTTTGAGATTGGATTAAATGAGT 58.888 33.333 0.00 0.00 0.00 3.41
1933 1945 8.186821 GGTCTTTGAGATTGGATTAAATGAGTG 58.813 37.037 0.00 0.00 0.00 3.51
1934 1946 8.950210 GTCTTTGAGATTGGATTAAATGAGTGA 58.050 33.333 0.00 0.00 0.00 3.41
1935 1947 9.170734 TCTTTGAGATTGGATTAAATGAGTGAG 57.829 33.333 0.00 0.00 0.00 3.51
1936 1948 9.170734 CTTTGAGATTGGATTAAATGAGTGAGA 57.829 33.333 0.00 0.00 0.00 3.27
1937 1949 9.519191 TTTGAGATTGGATTAAATGAGTGAGAA 57.481 29.630 0.00 0.00 0.00 2.87
1938 1950 8.728337 TGAGATTGGATTAAATGAGTGAGAAG 57.272 34.615 0.00 0.00 0.00 2.85
1939 1951 7.772292 TGAGATTGGATTAAATGAGTGAGAAGG 59.228 37.037 0.00 0.00 0.00 3.46
1940 1952 7.059156 AGATTGGATTAAATGAGTGAGAAGGG 58.941 38.462 0.00 0.00 0.00 3.95
1941 1953 5.116084 TGGATTAAATGAGTGAGAAGGGG 57.884 43.478 0.00 0.00 0.00 4.79
1942 1954 3.885901 GGATTAAATGAGTGAGAAGGGGC 59.114 47.826 0.00 0.00 0.00 5.80
1943 1955 3.366052 TTAAATGAGTGAGAAGGGGCC 57.634 47.619 0.00 0.00 0.00 5.80
1944 1956 0.332972 AAATGAGTGAGAAGGGGCCC 59.667 55.000 17.12 17.12 0.00 5.80
1945 1957 0.846427 AATGAGTGAGAAGGGGCCCA 60.846 55.000 27.72 0.00 0.00 5.36
1946 1958 1.566298 ATGAGTGAGAAGGGGCCCAC 61.566 60.000 27.72 18.41 0.00 4.61
1947 1959 2.936032 AGTGAGAAGGGGCCCACC 60.936 66.667 27.72 15.98 39.11 4.61
1957 1969 2.449777 GGCCCACCCCCTGAAAAT 59.550 61.111 0.00 0.00 0.00 1.82
1958 1970 1.685765 GGCCCACCCCCTGAAAATC 60.686 63.158 0.00 0.00 0.00 2.17
1959 1971 1.078347 GCCCACCCCCTGAAAATCA 59.922 57.895 0.00 0.00 0.00 2.57
1960 1972 0.972471 GCCCACCCCCTGAAAATCAG 60.972 60.000 0.32 0.32 43.91 2.90
1970 1982 3.071874 CTGAAAATCAGGGGTAGCACA 57.928 47.619 0.00 0.00 40.71 4.57
1971 1983 2.749621 CTGAAAATCAGGGGTAGCACAC 59.250 50.000 0.00 0.00 40.71 3.82
1972 1984 1.737793 GAAAATCAGGGGTAGCACACG 59.262 52.381 0.00 0.00 0.00 4.49
1973 1985 0.690762 AAATCAGGGGTAGCACACGT 59.309 50.000 0.00 0.00 0.00 4.49
1974 1986 0.690762 AATCAGGGGTAGCACACGTT 59.309 50.000 0.00 0.00 0.00 3.99
1975 1987 0.690762 ATCAGGGGTAGCACACGTTT 59.309 50.000 0.00 0.00 0.00 3.60
1976 1988 0.034337 TCAGGGGTAGCACACGTTTC 59.966 55.000 0.00 0.00 0.00 2.78
1977 1989 0.250124 CAGGGGTAGCACACGTTTCA 60.250 55.000 0.00 0.00 0.00 2.69
1978 1990 0.250166 AGGGGTAGCACACGTTTCAC 60.250 55.000 0.00 0.00 0.00 3.18
1979 1991 0.533308 GGGGTAGCACACGTTTCACA 60.533 55.000 0.00 0.00 0.00 3.58
1980 1992 1.519408 GGGTAGCACACGTTTCACAT 58.481 50.000 0.00 0.00 0.00 3.21
1981 1993 1.463444 GGGTAGCACACGTTTCACATC 59.537 52.381 0.00 0.00 0.00 3.06
1982 1994 2.139917 GGTAGCACACGTTTCACATCA 58.860 47.619 0.00 0.00 0.00 3.07
1983 1995 2.096417 GGTAGCACACGTTTCACATCAC 60.096 50.000 0.00 0.00 0.00 3.06
1984 1996 1.662517 AGCACACGTTTCACATCACA 58.337 45.000 0.00 0.00 0.00 3.58
1985 1997 2.221169 AGCACACGTTTCACATCACAT 58.779 42.857 0.00 0.00 0.00 3.21
1986 1998 2.618241 AGCACACGTTTCACATCACATT 59.382 40.909 0.00 0.00 0.00 2.71
1987 1999 2.973224 GCACACGTTTCACATCACATTC 59.027 45.455 0.00 0.00 0.00 2.67
1988 2000 3.217608 CACACGTTTCACATCACATTCG 58.782 45.455 0.00 0.00 0.00 3.34
1989 2001 3.059935 CACACGTTTCACATCACATTCGA 60.060 43.478 0.00 0.00 0.00 3.71
1990 2002 3.059868 ACACGTTTCACATCACATTCGAC 60.060 43.478 0.00 0.00 0.00 4.20
1991 2003 3.059935 CACGTTTCACATCACATTCGACA 60.060 43.478 0.00 0.00 0.00 4.35
1992 2004 3.558006 ACGTTTCACATCACATTCGACAA 59.442 39.130 0.00 0.00 0.00 3.18
1993 2005 4.143835 CGTTTCACATCACATTCGACAAG 58.856 43.478 0.00 0.00 0.00 3.16
1998 2010 5.778862 TCACATCACATTCGACAAGTAAGA 58.221 37.500 0.00 0.00 0.00 2.10
2045 2059 2.250924 CCACAGGAGGCCTTTTTCATT 58.749 47.619 6.77 0.00 0.00 2.57
2077 2092 3.561120 TTTCGCCCAATCACGCCCT 62.561 57.895 0.00 0.00 0.00 5.19
2120 2135 2.987413 TTAGCGAAAGTTACGTCCGA 57.013 45.000 0.00 0.00 0.00 4.55
2208 2226 1.763770 CCCCACAAGTCAGCCTCTT 59.236 57.895 0.00 0.00 0.00 2.85
2210 2228 1.479389 CCCCACAAGTCAGCCTCTTTT 60.479 52.381 0.00 0.00 0.00 2.27
2253 2284 1.395045 CGTGCATGGCCTCTCTCCTA 61.395 60.000 3.32 0.00 0.00 2.94
2498 2682 0.456221 CTCCCATGTAAGAGCGACGT 59.544 55.000 0.00 0.00 0.00 4.34
2605 2789 4.498520 CGACGCCGATGCTCCACT 62.499 66.667 0.00 0.00 38.22 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 3.492011 GGCTTCTTCAATTTGTTGCACAG 59.508 43.478 0.00 0.00 0.00 3.66
108 109 6.359804 CCATGATCTCCAATGAACCTTCTTA 58.640 40.000 0.00 0.00 0.00 2.10
282 283 1.153429 CGACCAGAAATCCCCGTCC 60.153 63.158 0.00 0.00 0.00 4.79
362 366 4.290093 ACTCTCCACATGATACCTTGCTA 58.710 43.478 0.00 0.00 0.00 3.49
398 402 7.391833 CCAGGTATCTCTAAGGATTTTAATGGC 59.608 40.741 0.00 0.00 0.00 4.40
443 447 7.636150 ATGCATGAGAAGTATTTAAAGTGCT 57.364 32.000 0.00 0.00 0.00 4.40
487 491 5.002516 CCATTCTCCTCCATTAGAGCATTC 58.997 45.833 0.00 0.00 41.74 2.67
918 922 7.757624 TCCAAATTTCTTTAACATATTCGCACC 59.242 33.333 0.00 0.00 0.00 5.01
1204 1209 1.131638 ACTGACTTCAAGGCCTCACA 58.868 50.000 5.23 0.00 0.00 3.58
1246 1251 5.670792 ACGTTGATCAACATTAGTCCCTA 57.329 39.130 32.06 0.00 41.20 3.53
1321 1326 5.013079 CCTGCATAACCCCTAGATGATTACA 59.987 44.000 0.00 0.00 0.00 2.41
1491 1502 1.207488 TATCCTGCCCCTGCTGTTGT 61.207 55.000 0.00 0.00 38.71 3.32
1512 1523 1.238439 CAATGGCACCTGTCGAAGTT 58.762 50.000 0.00 0.00 0.00 2.66
1621 1633 1.191489 TCATGTTCTGCCGACCTGGA 61.191 55.000 0.00 0.00 42.00 3.86
1749 1761 1.361204 TGGGAGCAGAACATCCAGAA 58.639 50.000 0.00 0.00 37.33 3.02
1750 1762 1.487976 GATGGGAGCAGAACATCCAGA 59.512 52.381 0.00 0.00 37.33 3.86
1751 1763 1.809271 CGATGGGAGCAGAACATCCAG 60.809 57.143 0.00 0.00 38.15 3.86
1752 1764 0.178767 CGATGGGAGCAGAACATCCA 59.821 55.000 0.00 0.00 38.15 3.41
1753 1765 0.533755 CCGATGGGAGCAGAACATCC 60.534 60.000 0.00 0.00 38.15 3.51
1754 1766 0.179000 ACCGATGGGAGCAGAACATC 59.821 55.000 0.00 0.00 38.06 3.06
1755 1767 1.496060 TACCGATGGGAGCAGAACAT 58.504 50.000 0.00 0.00 36.97 2.71
1756 1768 1.496060 ATACCGATGGGAGCAGAACA 58.504 50.000 0.00 0.00 36.97 3.18
1757 1769 2.028930 CCTATACCGATGGGAGCAGAAC 60.029 54.545 0.00 0.00 35.71 3.01
1758 1770 2.248248 CCTATACCGATGGGAGCAGAA 58.752 52.381 0.00 0.00 35.71 3.02
1759 1771 1.147191 ACCTATACCGATGGGAGCAGA 59.853 52.381 0.00 0.00 37.16 4.26
1760 1772 1.273606 CACCTATACCGATGGGAGCAG 59.726 57.143 0.00 0.00 37.16 4.24
1761 1773 1.133294 TCACCTATACCGATGGGAGCA 60.133 52.381 0.00 0.00 37.16 4.26
1762 1774 1.546476 CTCACCTATACCGATGGGAGC 59.454 57.143 0.00 0.00 37.16 4.70
1763 1775 1.546476 GCTCACCTATACCGATGGGAG 59.454 57.143 0.00 0.00 37.16 4.30
1764 1776 1.629043 GCTCACCTATACCGATGGGA 58.371 55.000 0.00 0.00 37.16 4.37
1765 1777 0.608640 GGCTCACCTATACCGATGGG 59.391 60.000 0.00 0.00 39.60 4.00
1780 1792 3.859414 ATCCGCTGGCTCAGGCTC 61.859 66.667 0.00 0.00 38.73 4.70
1781 1793 4.172512 CATCCGCTGGCTCAGGCT 62.173 66.667 0.00 0.00 38.73 4.58
1782 1794 4.479993 ACATCCGCTGGCTCAGGC 62.480 66.667 0.00 0.00 37.82 4.85
1783 1795 2.513204 CACATCCGCTGGCTCAGG 60.513 66.667 4.65 0.00 31.21 3.86
1784 1796 2.513204 CCACATCCGCTGGCTCAG 60.513 66.667 0.00 0.00 34.12 3.35
1785 1797 3.321648 ACCACATCCGCTGGCTCA 61.322 61.111 0.00 0.00 31.13 4.26
1786 1798 2.821366 CACCACATCCGCTGGCTC 60.821 66.667 0.00 0.00 31.13 4.70
1789 1801 2.821366 GAGCACCACATCCGCTGG 60.821 66.667 0.00 0.00 35.75 4.85
1790 1802 1.672030 TTGAGCACCACATCCGCTG 60.672 57.895 0.00 0.00 35.75 5.18
1791 1803 1.672356 GTTGAGCACCACATCCGCT 60.672 57.895 0.00 0.00 39.12 5.52
1792 1804 2.870372 GTTGAGCACCACATCCGC 59.130 61.111 0.00 0.00 0.00 5.54
1793 1805 3.168271 CGTTGAGCACCACATCCG 58.832 61.111 0.00 0.00 0.00 4.18
1803 1815 3.482783 GAGCTGTCCGCGTTGAGC 61.483 66.667 4.92 8.92 45.59 4.26
1804 1816 1.446792 ATGAGCTGTCCGCGTTGAG 60.447 57.895 4.92 0.00 45.59 3.02
1805 1817 1.737735 CATGAGCTGTCCGCGTTGA 60.738 57.895 4.92 0.00 45.59 3.18
1806 1818 1.291184 TTCATGAGCTGTCCGCGTTG 61.291 55.000 4.92 0.00 45.59 4.10
1807 1819 1.005037 TTCATGAGCTGTCCGCGTT 60.005 52.632 4.92 0.00 45.59 4.84
1808 1820 1.446792 CTTCATGAGCTGTCCGCGT 60.447 57.895 4.92 0.00 45.59 6.01
1809 1821 2.169789 CCTTCATGAGCTGTCCGCG 61.170 63.158 0.00 0.00 45.59 6.46
1810 1822 1.086634 GTCCTTCATGAGCTGTCCGC 61.087 60.000 0.00 0.00 39.57 5.54
1811 1823 0.803768 CGTCCTTCATGAGCTGTCCG 60.804 60.000 0.00 0.00 0.00 4.79
1812 1824 0.247736 ACGTCCTTCATGAGCTGTCC 59.752 55.000 0.00 0.00 0.00 4.02
1813 1825 1.354040 CACGTCCTTCATGAGCTGTC 58.646 55.000 0.00 0.00 0.00 3.51
1814 1826 0.036952 CCACGTCCTTCATGAGCTGT 60.037 55.000 0.00 0.00 0.00 4.40
1815 1827 0.036952 ACCACGTCCTTCATGAGCTG 60.037 55.000 0.00 0.00 0.00 4.24
1816 1828 0.036952 CACCACGTCCTTCATGAGCT 60.037 55.000 0.00 0.00 0.00 4.09
1817 1829 1.639298 GCACCACGTCCTTCATGAGC 61.639 60.000 0.00 0.00 0.00 4.26
1818 1830 1.354337 CGCACCACGTCCTTCATGAG 61.354 60.000 0.00 0.00 36.87 2.90
1819 1831 1.374125 CGCACCACGTCCTTCATGA 60.374 57.895 0.00 0.00 36.87 3.07
1820 1832 3.027170 GCGCACCACGTCCTTCATG 62.027 63.158 0.30 0.00 46.11 3.07
1821 1833 2.742372 GCGCACCACGTCCTTCAT 60.742 61.111 0.30 0.00 46.11 2.57
1822 1834 3.741830 TTGCGCACCACGTCCTTCA 62.742 57.895 11.12 0.00 46.11 3.02
1823 1835 2.970324 TTGCGCACCACGTCCTTC 60.970 61.111 11.12 0.00 46.11 3.46
1824 1836 3.276846 GTTGCGCACCACGTCCTT 61.277 61.111 11.12 0.00 46.11 3.36
1837 1849 2.097160 CTCAGTCATGCGCGTTGC 59.903 61.111 8.43 0.00 46.70 4.17
1838 1850 2.097160 GCTCAGTCATGCGCGTTG 59.903 61.111 8.43 6.40 0.00 4.10
1839 1851 1.300971 ATTGCTCAGTCATGCGCGTT 61.301 50.000 8.43 0.00 40.10 4.84
1840 1852 1.742880 ATTGCTCAGTCATGCGCGT 60.743 52.632 8.43 0.00 40.10 6.01
1841 1853 1.297378 CATTGCTCAGTCATGCGCG 60.297 57.895 0.00 0.00 40.10 6.86
1842 1854 1.585521 GCATTGCTCAGTCATGCGC 60.586 57.895 0.00 0.00 37.67 6.09
1843 1855 1.260825 CTAGCATTGCTCAGTCATGCG 59.739 52.381 15.81 0.00 42.51 4.73
1844 1856 2.287373 GTCTAGCATTGCTCAGTCATGC 59.713 50.000 15.81 0.00 40.44 4.06
1845 1857 3.794717 AGTCTAGCATTGCTCAGTCATG 58.205 45.455 15.81 0.00 40.44 3.07
1846 1858 3.450096 TGAGTCTAGCATTGCTCAGTCAT 59.550 43.478 15.81 0.00 40.44 3.06
1847 1859 2.827921 TGAGTCTAGCATTGCTCAGTCA 59.172 45.455 15.81 17.18 40.44 3.41
1848 1860 3.186119 GTGAGTCTAGCATTGCTCAGTC 58.814 50.000 15.81 14.93 40.44 3.51
1849 1861 2.564504 TGTGAGTCTAGCATTGCTCAGT 59.435 45.455 15.81 6.00 40.44 3.41
1850 1862 3.188492 CTGTGAGTCTAGCATTGCTCAG 58.812 50.000 15.81 10.38 40.44 3.35
1851 1863 2.093816 CCTGTGAGTCTAGCATTGCTCA 60.094 50.000 15.81 3.80 40.44 4.26
1852 1864 2.548875 CCTGTGAGTCTAGCATTGCTC 58.451 52.381 15.81 0.57 40.44 4.26
1853 1865 1.209019 CCCTGTGAGTCTAGCATTGCT 59.791 52.381 16.63 16.63 43.41 3.91
1854 1866 1.065854 ACCCTGTGAGTCTAGCATTGC 60.066 52.381 0.00 0.00 0.00 3.56
1855 1867 2.499289 AGACCCTGTGAGTCTAGCATTG 59.501 50.000 0.00 0.00 42.76 2.82
1856 1868 2.826488 AGACCCTGTGAGTCTAGCATT 58.174 47.619 0.00 0.00 42.76 3.56
1857 1869 2.541233 AGACCCTGTGAGTCTAGCAT 57.459 50.000 0.00 0.00 42.76 3.79
1858 1870 2.310779 AAGACCCTGTGAGTCTAGCA 57.689 50.000 0.00 0.00 43.77 3.49
1859 1871 3.686916 AAAAGACCCTGTGAGTCTAGC 57.313 47.619 0.00 0.00 43.77 3.42
1860 1872 6.097915 TGTAAAAAGACCCTGTGAGTCTAG 57.902 41.667 0.00 0.00 43.77 2.43
1861 1873 5.011738 CCTGTAAAAAGACCCTGTGAGTCTA 59.988 44.000 0.00 0.00 43.77 2.59
1862 1874 4.202367 CCTGTAAAAAGACCCTGTGAGTCT 60.202 45.833 0.00 0.00 46.50 3.24
1863 1875 4.065789 CCTGTAAAAAGACCCTGTGAGTC 58.934 47.826 0.00 0.00 34.31 3.36
1864 1876 3.458487 ACCTGTAAAAAGACCCTGTGAGT 59.542 43.478 0.00 0.00 0.00 3.41
1865 1877 4.086706 ACCTGTAAAAAGACCCTGTGAG 57.913 45.455 0.00 0.00 0.00 3.51
1866 1878 4.513406 AACCTGTAAAAAGACCCTGTGA 57.487 40.909 0.00 0.00 0.00 3.58
1867 1879 5.592104 AAAACCTGTAAAAAGACCCTGTG 57.408 39.130 0.00 0.00 0.00 3.66
1868 1880 5.297527 CGTAAAACCTGTAAAAAGACCCTGT 59.702 40.000 0.00 0.00 0.00 4.00
1869 1881 5.278120 CCGTAAAACCTGTAAAAAGACCCTG 60.278 44.000 0.00 0.00 0.00 4.45
1870 1882 4.823442 CCGTAAAACCTGTAAAAAGACCCT 59.177 41.667 0.00 0.00 0.00 4.34
1871 1883 4.821260 TCCGTAAAACCTGTAAAAAGACCC 59.179 41.667 0.00 0.00 0.00 4.46
1872 1884 5.049198 CCTCCGTAAAACCTGTAAAAAGACC 60.049 44.000 0.00 0.00 0.00 3.85
1873 1885 5.528690 ACCTCCGTAAAACCTGTAAAAAGAC 59.471 40.000 0.00 0.00 0.00 3.01
1874 1886 5.528320 CACCTCCGTAAAACCTGTAAAAAGA 59.472 40.000 0.00 0.00 0.00 2.52
1875 1887 5.754778 CACCTCCGTAAAACCTGTAAAAAG 58.245 41.667 0.00 0.00 0.00 2.27
1876 1888 4.036616 GCACCTCCGTAAAACCTGTAAAAA 59.963 41.667 0.00 0.00 0.00 1.94
1877 1889 3.565063 GCACCTCCGTAAAACCTGTAAAA 59.435 43.478 0.00 0.00 0.00 1.52
1878 1890 3.140623 GCACCTCCGTAAAACCTGTAAA 58.859 45.455 0.00 0.00 0.00 2.01
1879 1891 2.369532 AGCACCTCCGTAAAACCTGTAA 59.630 45.455 0.00 0.00 0.00 2.41
1880 1892 1.972795 AGCACCTCCGTAAAACCTGTA 59.027 47.619 0.00 0.00 0.00 2.74
1881 1893 0.763035 AGCACCTCCGTAAAACCTGT 59.237 50.000 0.00 0.00 0.00 4.00
1882 1894 2.740447 GTTAGCACCTCCGTAAAACCTG 59.260 50.000 0.00 0.00 0.00 4.00
1883 1895 2.611224 CGTTAGCACCTCCGTAAAACCT 60.611 50.000 0.00 0.00 0.00 3.50
1884 1896 1.728425 CGTTAGCACCTCCGTAAAACC 59.272 52.381 0.00 0.00 0.00 3.27
1885 1897 2.407090 ACGTTAGCACCTCCGTAAAAC 58.593 47.619 0.00 0.00 0.00 2.43
1886 1898 2.818130 ACGTTAGCACCTCCGTAAAA 57.182 45.000 0.00 0.00 0.00 1.52
1887 1899 2.164219 CCTACGTTAGCACCTCCGTAAA 59.836 50.000 0.00 0.00 35.62 2.01
1888 1900 1.745087 CCTACGTTAGCACCTCCGTAA 59.255 52.381 0.00 0.00 35.62 3.18
1889 1901 1.340017 ACCTACGTTAGCACCTCCGTA 60.340 52.381 0.00 0.00 34.95 4.02
1890 1902 0.610232 ACCTACGTTAGCACCTCCGT 60.610 55.000 0.00 0.00 37.33 4.69
1891 1903 0.100146 GACCTACGTTAGCACCTCCG 59.900 60.000 0.00 0.00 0.00 4.63
1892 1904 1.472188 AGACCTACGTTAGCACCTCC 58.528 55.000 0.00 0.00 0.00 4.30
1893 1905 3.057033 TCAAAGACCTACGTTAGCACCTC 60.057 47.826 0.00 0.00 0.00 3.85
1894 1906 2.895404 TCAAAGACCTACGTTAGCACCT 59.105 45.455 0.00 0.00 0.00 4.00
1895 1907 3.057033 TCTCAAAGACCTACGTTAGCACC 60.057 47.826 0.00 0.00 0.00 5.01
1896 1908 4.170292 TCTCAAAGACCTACGTTAGCAC 57.830 45.455 0.00 0.00 0.00 4.40
1897 1909 5.168569 CAATCTCAAAGACCTACGTTAGCA 58.831 41.667 0.00 0.00 0.00 3.49
1898 1910 4.567159 CCAATCTCAAAGACCTACGTTAGC 59.433 45.833 0.00 0.00 0.00 3.09
1899 1911 5.962433 TCCAATCTCAAAGACCTACGTTAG 58.038 41.667 0.00 0.00 0.00 2.34
1900 1912 5.988310 TCCAATCTCAAAGACCTACGTTA 57.012 39.130 0.00 0.00 0.00 3.18
1901 1913 4.884668 TCCAATCTCAAAGACCTACGTT 57.115 40.909 0.00 0.00 0.00 3.99
1902 1914 5.422214 AATCCAATCTCAAAGACCTACGT 57.578 39.130 0.00 0.00 0.00 3.57
1903 1915 7.843490 TTTAATCCAATCTCAAAGACCTACG 57.157 36.000 0.00 0.00 0.00 3.51
1904 1916 9.396022 TCATTTAATCCAATCTCAAAGACCTAC 57.604 33.333 0.00 0.00 0.00 3.18
1905 1917 9.618890 CTCATTTAATCCAATCTCAAAGACCTA 57.381 33.333 0.00 0.00 0.00 3.08
1906 1918 8.112183 ACTCATTTAATCCAATCTCAAAGACCT 58.888 33.333 0.00 0.00 0.00 3.85
1907 1919 8.186821 CACTCATTTAATCCAATCTCAAAGACC 58.813 37.037 0.00 0.00 0.00 3.85
1908 1920 8.950210 TCACTCATTTAATCCAATCTCAAAGAC 58.050 33.333 0.00 0.00 0.00 3.01
1909 1921 9.170734 CTCACTCATTTAATCCAATCTCAAAGA 57.829 33.333 0.00 0.00 0.00 2.52
1910 1922 9.170734 TCTCACTCATTTAATCCAATCTCAAAG 57.829 33.333 0.00 0.00 0.00 2.77
1911 1923 9.519191 TTCTCACTCATTTAATCCAATCTCAAA 57.481 29.630 0.00 0.00 0.00 2.69
1912 1924 9.170734 CTTCTCACTCATTTAATCCAATCTCAA 57.829 33.333 0.00 0.00 0.00 3.02
1913 1925 7.772292 CCTTCTCACTCATTTAATCCAATCTCA 59.228 37.037 0.00 0.00 0.00 3.27
1914 1926 7.228308 CCCTTCTCACTCATTTAATCCAATCTC 59.772 40.741 0.00 0.00 0.00 2.75
1915 1927 7.059156 CCCTTCTCACTCATTTAATCCAATCT 58.941 38.462 0.00 0.00 0.00 2.40
1916 1928 6.264067 CCCCTTCTCACTCATTTAATCCAATC 59.736 42.308 0.00 0.00 0.00 2.67
1917 1929 6.131961 CCCCTTCTCACTCATTTAATCCAAT 58.868 40.000 0.00 0.00 0.00 3.16
1918 1930 5.509498 CCCCTTCTCACTCATTTAATCCAA 58.491 41.667 0.00 0.00 0.00 3.53
1919 1931 4.628715 GCCCCTTCTCACTCATTTAATCCA 60.629 45.833 0.00 0.00 0.00 3.41
1920 1932 3.885901 GCCCCTTCTCACTCATTTAATCC 59.114 47.826 0.00 0.00 0.00 3.01
1921 1933 3.885901 GGCCCCTTCTCACTCATTTAATC 59.114 47.826 0.00 0.00 0.00 1.75
1922 1934 3.373110 GGGCCCCTTCTCACTCATTTAAT 60.373 47.826 12.23 0.00 0.00 1.40
1923 1935 2.025321 GGGCCCCTTCTCACTCATTTAA 60.025 50.000 12.23 0.00 0.00 1.52
1924 1936 1.564348 GGGCCCCTTCTCACTCATTTA 59.436 52.381 12.23 0.00 0.00 1.40
1925 1937 0.332972 GGGCCCCTTCTCACTCATTT 59.667 55.000 12.23 0.00 0.00 2.32
1926 1938 0.846427 TGGGCCCCTTCTCACTCATT 60.846 55.000 22.27 0.00 0.00 2.57
1927 1939 1.229951 TGGGCCCCTTCTCACTCAT 60.230 57.895 22.27 0.00 0.00 2.90
1928 1940 2.206900 TGGGCCCCTTCTCACTCA 59.793 61.111 22.27 0.00 0.00 3.41
1929 1941 2.671682 GTGGGCCCCTTCTCACTC 59.328 66.667 22.27 0.00 0.00 3.51
1930 1942 2.936032 GGTGGGCCCCTTCTCACT 60.936 66.667 22.27 0.00 0.00 3.41
1940 1952 1.685765 GATTTTCAGGGGGTGGGCC 60.686 63.158 0.00 0.00 0.00 5.80
1941 1953 0.972471 CTGATTTTCAGGGGGTGGGC 60.972 60.000 0.00 0.00 40.71 5.36
1942 1954 3.288099 CTGATTTTCAGGGGGTGGG 57.712 57.895 0.00 0.00 40.71 4.61
1950 1962 2.749621 GTGTGCTACCCCTGATTTTCAG 59.250 50.000 0.00 0.00 43.91 3.02
1951 1963 2.790433 GTGTGCTACCCCTGATTTTCA 58.210 47.619 0.00 0.00 0.00 2.69
1952 1964 1.737793 CGTGTGCTACCCCTGATTTTC 59.262 52.381 0.00 0.00 0.00 2.29
1953 1965 1.073284 ACGTGTGCTACCCCTGATTTT 59.927 47.619 0.00 0.00 0.00 1.82
1954 1966 0.690762 ACGTGTGCTACCCCTGATTT 59.309 50.000 0.00 0.00 0.00 2.17
1955 1967 0.690762 AACGTGTGCTACCCCTGATT 59.309 50.000 0.00 0.00 0.00 2.57
1956 1968 0.690762 AAACGTGTGCTACCCCTGAT 59.309 50.000 0.00 0.00 0.00 2.90
1957 1969 0.034337 GAAACGTGTGCTACCCCTGA 59.966 55.000 0.00 0.00 0.00 3.86
1958 1970 0.250124 TGAAACGTGTGCTACCCCTG 60.250 55.000 0.00 0.00 0.00 4.45
1959 1971 0.250166 GTGAAACGTGTGCTACCCCT 60.250 55.000 0.00 0.00 0.00 4.79
1960 1972 0.533308 TGTGAAACGTGTGCTACCCC 60.533 55.000 0.00 0.00 42.39 4.95
1961 1973 1.463444 GATGTGAAACGTGTGCTACCC 59.537 52.381 0.00 0.00 42.39 3.69
1962 1974 2.096417 GTGATGTGAAACGTGTGCTACC 60.096 50.000 0.00 0.00 42.39 3.18
1963 1975 2.542178 TGTGATGTGAAACGTGTGCTAC 59.458 45.455 0.00 0.00 42.39 3.58
1964 1976 2.827652 TGTGATGTGAAACGTGTGCTA 58.172 42.857 0.00 0.00 42.39 3.49
1965 1977 1.662517 TGTGATGTGAAACGTGTGCT 58.337 45.000 0.00 0.00 42.39 4.40
1966 1978 2.686558 ATGTGATGTGAAACGTGTGC 57.313 45.000 0.00 0.00 42.39 4.57
1967 1979 3.059935 TCGAATGTGATGTGAAACGTGTG 60.060 43.478 0.00 0.00 42.39 3.82
1968 1980 3.059868 GTCGAATGTGATGTGAAACGTGT 60.060 43.478 0.00 0.00 42.39 4.49
1969 1981 3.059935 TGTCGAATGTGATGTGAAACGTG 60.060 43.478 0.00 0.00 42.39 4.49
1970 1982 3.127589 TGTCGAATGTGATGTGAAACGT 58.872 40.909 0.00 0.00 42.39 3.99
1971 1983 3.786657 TGTCGAATGTGATGTGAAACG 57.213 42.857 0.00 0.00 42.39 3.60
1972 1984 5.095691 ACTTGTCGAATGTGATGTGAAAC 57.904 39.130 0.00 0.00 37.35 2.78
1973 1985 6.704050 TCTTACTTGTCGAATGTGATGTGAAA 59.296 34.615 0.00 0.00 0.00 2.69
1974 1986 6.220201 TCTTACTTGTCGAATGTGATGTGAA 58.780 36.000 0.00 0.00 0.00 3.18
1975 1987 5.778862 TCTTACTTGTCGAATGTGATGTGA 58.221 37.500 0.00 0.00 0.00 3.58
1976 1988 5.445142 GCTCTTACTTGTCGAATGTGATGTG 60.445 44.000 0.00 0.00 0.00 3.21
1977 1989 4.627467 GCTCTTACTTGTCGAATGTGATGT 59.373 41.667 0.00 0.00 0.00 3.06
1978 1990 4.627035 TGCTCTTACTTGTCGAATGTGATG 59.373 41.667 0.00 0.00 0.00 3.07
1979 1991 4.820897 TGCTCTTACTTGTCGAATGTGAT 58.179 39.130 0.00 0.00 0.00 3.06
1980 1992 4.251543 TGCTCTTACTTGTCGAATGTGA 57.748 40.909 0.00 0.00 0.00 3.58
1981 1993 4.867047 AGATGCTCTTACTTGTCGAATGTG 59.133 41.667 0.00 0.00 0.00 3.21
1982 1994 5.078411 AGATGCTCTTACTTGTCGAATGT 57.922 39.130 0.00 0.00 0.00 2.71
1983 1995 4.505922 GGAGATGCTCTTACTTGTCGAATG 59.494 45.833 0.00 0.00 0.00 2.67
1984 1996 4.160439 TGGAGATGCTCTTACTTGTCGAAT 59.840 41.667 0.00 0.00 0.00 3.34
1985 1997 3.509967 TGGAGATGCTCTTACTTGTCGAA 59.490 43.478 0.00 0.00 0.00 3.71
1986 1998 3.089284 TGGAGATGCTCTTACTTGTCGA 58.911 45.455 0.00 0.00 0.00 4.20
1987 1999 3.443037 CTGGAGATGCTCTTACTTGTCG 58.557 50.000 0.00 0.00 0.00 4.35
1988 2000 3.194062 GCTGGAGATGCTCTTACTTGTC 58.806 50.000 0.00 0.00 0.00 3.18
1989 2001 2.093235 GGCTGGAGATGCTCTTACTTGT 60.093 50.000 0.00 0.00 0.00 3.16
1990 2002 2.559440 GGCTGGAGATGCTCTTACTTG 58.441 52.381 0.00 0.00 0.00 3.16
1991 2003 1.137872 CGGCTGGAGATGCTCTTACTT 59.862 52.381 0.00 0.00 0.00 2.24
1992 2004 0.749649 CGGCTGGAGATGCTCTTACT 59.250 55.000 0.00 0.00 0.00 2.24
1993 2005 0.878086 GCGGCTGGAGATGCTCTTAC 60.878 60.000 0.00 0.00 0.00 2.34
2012 2024 2.037367 TGTGGTCTCTCGAGGGGG 59.963 66.667 13.54 3.59 0.00 5.40
2017 2029 1.679305 GCCTCCTGTGGTCTCTCGA 60.679 63.158 0.00 0.00 0.00 4.04
2024 2036 0.555769 TGAAAAAGGCCTCCTGTGGT 59.444 50.000 5.23 0.00 32.13 4.16
2027 2039 1.620323 GCAATGAAAAAGGCCTCCTGT 59.380 47.619 5.23 0.00 32.13 4.00
2045 2059 1.498166 CGAAAAATACGTGCCGGCA 59.502 52.632 29.03 29.03 0.00 5.69
2106 2121 2.242564 GTACCGTCGGACGTAACTTTC 58.757 52.381 26.72 8.17 40.58 2.62
2120 2135 1.151221 GGGTTTGGGTTGGTACCGT 59.849 57.895 7.57 0.00 46.04 4.83
2208 2226 1.075536 GGCCTGGGAGGAAAAGAGAAA 59.924 52.381 0.00 0.00 37.67 2.52
2210 2228 1.208165 GGGCCTGGGAGGAAAAGAGA 61.208 60.000 0.84 0.00 37.67 3.10
2321 2352 4.400109 GCACTCCTCGTCGACGCA 62.400 66.667 32.19 19.50 39.60 5.24
2444 2475 4.228567 TGCTCCACGCGTCACCAA 62.229 61.111 9.86 0.00 43.27 3.67
2445 2476 4.662961 CTGCTCCACGCGTCACCA 62.663 66.667 9.86 3.30 43.27 4.17
2448 2479 2.355837 GAACTGCTCCACGCGTCA 60.356 61.111 9.86 2.86 43.27 4.35
2461 2645 3.459969 GGGAGAAATACCCATCAGGAACT 59.540 47.826 0.00 0.00 46.05 3.01
2596 2780 2.435586 GCGCACAGAGTGGAGCAT 60.436 61.111 0.30 0.00 33.64 3.79


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

AutoCloner maintained by Alex Coulton.