Multiple sequence alignment - TraesCS7D01G530200

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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 TraesCS7D01G530200 chr7D 100.000 2648 0 0 1 2648 625188649 625191296 0.000000e+00 4891
1 TraesCS7D01G530200 chr7D 94.900 549 25 2 1 548 139846597 139847143 0.000000e+00 856
2 TraesCS7D01G530200 chr7D 86.915 726 95 0 934 1659 625207342 625208067 0.000000e+00 815
3 TraesCS7D01G530200 chr7D 78.468 757 158 4 907 1659 625145938 625146693 8.520000e-135 490
4 TraesCS7D01G530200 chr7D 98.578 211 3 0 379 589 625183110 625183320 8.950000e-100 374
5 TraesCS7D01G530200 chr7B 89.784 1204 114 9 589 1789 723934697 723933500 0.000000e+00 1533
6 TraesCS7D01G530200 chr7B 85.118 719 107 0 934 1652 723956083 723955365 0.000000e+00 736
7 TraesCS7D01G530200 chr7A 91.897 1049 83 2 607 1654 720934614 720933567 0.000000e+00 1465
8 TraesCS7D01G530200 chr7A 86.431 737 100 0 926 1662 720913129 720912393 0.000000e+00 808
9 TraesCS7D01G530200 chr7A 94.313 211 12 0 378 588 693386726 693386516 9.140000e-85 324
10 TraesCS7D01G530200 chr5D 98.810 588 7 0 1 588 60123977 60123390 0.000000e+00 1048
11 TraesCS7D01G530200 chr5D 98.585 212 3 0 378 589 60138177 60137966 2.490000e-100 375
12 TraesCS7D01G530200 chr1A 94.946 554 22 3 1 548 488659852 488660405 0.000000e+00 863
13 TraesCS7D01G530200 chr1A 93.040 546 35 3 1 544 561145902 561146446 0.000000e+00 795
14 TraesCS7D01G530200 chr2A 94.718 549 27 2 1 548 240861207 240860660 0.000000e+00 852
15 TraesCS7D01G530200 chr5A 93.273 550 33 4 1 548 425558779 425559326 0.000000e+00 808
16 TraesCS7D01G530200 chr6A 94.990 479 23 1 1 478 520720979 520720501 0.000000e+00 750
17 TraesCS7D01G530200 chr6A 82.243 428 61 7 1884 2309 617743033 617743447 3.240000e-94 355
18 TraesCS7D01G530200 chr6A 83.158 285 35 10 2306 2583 617743516 617743794 5.660000e-62 248
19 TraesCS7D01G530200 chr2D 92.191 397 25 5 1 395 623362732 623363124 8.280000e-155 556
20 TraesCS7D01G530200 chr2D 83.942 274 31 10 2314 2583 586950040 586949776 1.570000e-62 250
21 TraesCS7D01G530200 chr3A 88.764 445 35 11 1 436 26574387 26574825 5.020000e-147 531
22 TraesCS7D01G530200 chr3D 83.534 249 36 3 2335 2583 610597101 610597344 7.370000e-56 228


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 TraesCS7D01G530200 chr7D 625188649 625191296 2647 False 4891.0 4891 100.0000 1 2648 1 chr7D.!!$F4 2647
1 TraesCS7D01G530200 chr7D 139846597 139847143 546 False 856.0 856 94.9000 1 548 1 chr7D.!!$F1 547
2 TraesCS7D01G530200 chr7D 625207342 625208067 725 False 815.0 815 86.9150 934 1659 1 chr7D.!!$F5 725
3 TraesCS7D01G530200 chr7D 625145938 625146693 755 False 490.0 490 78.4680 907 1659 1 chr7D.!!$F2 752
4 TraesCS7D01G530200 chr7B 723933500 723934697 1197 True 1533.0 1533 89.7840 589 1789 1 chr7B.!!$R1 1200
5 TraesCS7D01G530200 chr7B 723955365 723956083 718 True 736.0 736 85.1180 934 1652 1 chr7B.!!$R2 718
6 TraesCS7D01G530200 chr7A 720933567 720934614 1047 True 1465.0 1465 91.8970 607 1654 1 chr7A.!!$R3 1047
7 TraesCS7D01G530200 chr7A 720912393 720913129 736 True 808.0 808 86.4310 926 1662 1 chr7A.!!$R2 736
8 TraesCS7D01G530200 chr5D 60123390 60123977 587 True 1048.0 1048 98.8100 1 588 1 chr5D.!!$R1 587
9 TraesCS7D01G530200 chr1A 488659852 488660405 553 False 863.0 863 94.9460 1 548 1 chr1A.!!$F1 547
10 TraesCS7D01G530200 chr1A 561145902 561146446 544 False 795.0 795 93.0400 1 544 1 chr1A.!!$F2 543
11 TraesCS7D01G530200 chr2A 240860660 240861207 547 True 852.0 852 94.7180 1 548 1 chr2A.!!$R1 547
12 TraesCS7D01G530200 chr5A 425558779 425559326 547 False 808.0 808 93.2730 1 548 1 chr5A.!!$F1 547
13 TraesCS7D01G530200 chr6A 617743033 617743794 761 False 301.5 355 82.7005 1884 2583 2 chr6A.!!$F1 699

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
692 701 0.923358 TTGTTGTGGAGTGTCCCCTT 59.077 50.0 0.0 0.0 35.03 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 1842 0.181824 AGTTTGTGTTAGTGGGCGGT 59.818 50.0 0.0 0.0 0.0 5.68 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
559 568 8.089115 AGAGATCAACAGTTTTGCTTTACTAC 57.911 34.615 0.00 0.00 0.00 2.73
561 570 8.089115 AGATCAACAGTTTTGCTTTACTACTC 57.911 34.615 0.00 0.00 0.00 2.59
567 576 8.396272 ACAGTTTTGCTTTACTACTCATTCAT 57.604 30.769 0.00 0.00 0.00 2.57
615 624 3.662247 AACCGAGTCCTAGTTTGACAG 57.338 47.619 1.24 0.00 35.15 3.51
636 645 3.587797 CCATATGCTTGAATGATGGCC 57.412 47.619 0.00 0.00 31.24 5.36
692 701 0.923358 TTGTTGTGGAGTGTCCCCTT 59.077 50.000 0.00 0.00 35.03 3.95
708 717 6.007703 TGTCCCCTTTGGTTTCTAATACAAG 58.992 40.000 0.00 0.00 34.77 3.16
864 873 9.569122 AATGTACTGTTACTAATCAACCACTTT 57.431 29.630 0.00 0.00 0.00 2.66
865 874 8.967664 TGTACTGTTACTAATCAACCACTTTT 57.032 30.769 0.00 0.00 0.00 2.27
1018 1028 3.567579 ATGGAGGTTGTGTGGGGCG 62.568 63.158 0.00 0.00 0.00 6.13
1020 1030 4.265056 GAGGTTGTGTGGGGCGGT 62.265 66.667 0.00 0.00 0.00 5.68
1119 1129 0.111061 AGTCCCAAGCTGATGTTGCA 59.889 50.000 0.00 0.00 0.00 4.08
1139 1149 1.738099 CGCTATATGCCACCCTCGC 60.738 63.158 0.00 0.00 38.78 5.03
1190 1200 1.707427 GTATGGGATGGGAGCAAGGAT 59.293 52.381 0.00 0.00 0.00 3.24
1209 1219 5.579047 AGGATGTTTGGGATCATTAACACA 58.421 37.500 7.60 0.00 33.77 3.72
1291 1301 2.449031 AATGAACCGTCTCGCTGCCA 62.449 55.000 0.00 0.00 0.00 4.92
1416 1426 1.228124 CTTCGACAACCCCCAAGCA 60.228 57.895 0.00 0.00 0.00 3.91
1485 1495 1.440060 CGCGGAGGGTAAGTGCATA 59.560 57.895 0.00 0.00 34.98 3.14
1539 1549 4.917415 GCATATGCTTTCTTTGACAACGTT 59.083 37.500 20.64 0.00 38.21 3.99
1575 1585 2.012554 GCTGCTGAGATGAGTGCACAT 61.013 52.381 21.04 4.26 0.00 3.21
1654 1664 4.511527 AGCACACGAGAGATGATTGATTT 58.488 39.130 0.00 0.00 0.00 2.17
1699 1709 5.240713 ACGGAGTATTAGTTTACAGACGG 57.759 43.478 0.00 0.00 41.94 4.79
1720 1730 6.349300 ACGGAGTATAAGACATGCTTGATTT 58.651 36.000 6.60 3.07 41.94 2.17
1732 1742 9.768662 AGACATGCTTGATTTTCTTAAATTTGT 57.231 25.926 6.60 0.00 34.16 2.83
1755 1765 9.495572 TTGTGTGATCTTGTATGTTGTTGTATA 57.504 29.630 0.00 0.00 0.00 1.47
1759 1769 9.438291 GTGATCTTGTATGTTGTTGTATATTGC 57.562 33.333 0.00 0.00 0.00 3.56
1786 1796 5.199723 TGAAAGCTCCATATATTGCCAACA 58.800 37.500 0.00 0.00 0.00 3.33
1789 1799 6.736110 AAGCTCCATATATTGCCAACAAAT 57.264 33.333 0.00 0.00 39.77 2.32
1790 1800 6.092955 AGCTCCATATATTGCCAACAAATG 57.907 37.500 0.00 0.00 39.77 2.32
1791 1801 5.599656 AGCTCCATATATTGCCAACAAATGT 59.400 36.000 0.00 0.00 39.77 2.71
1792 1802 6.098695 AGCTCCATATATTGCCAACAAATGTT 59.901 34.615 0.00 0.00 39.77 2.71
1793 1803 6.421801 GCTCCATATATTGCCAACAAATGTTC 59.578 38.462 0.00 0.00 39.77 3.18
1794 1804 7.415592 TCCATATATTGCCAACAAATGTTCA 57.584 32.000 0.00 0.00 39.77 3.18
1795 1805 8.020777 TCCATATATTGCCAACAAATGTTCAT 57.979 30.769 0.00 0.00 39.77 2.57
1796 1806 7.927092 TCCATATATTGCCAACAAATGTTCATG 59.073 33.333 0.00 0.00 39.77 3.07
1797 1807 7.307514 CCATATATTGCCAACAAATGTTCATGC 60.308 37.037 0.00 1.10 39.77 4.06
1798 1808 2.904697 TGCCAACAAATGTTCATGCA 57.095 40.000 9.37 9.37 35.83 3.96
1799 1809 3.189618 TGCCAACAAATGTTCATGCAA 57.810 38.095 10.48 0.00 35.83 4.08
1800 1810 2.871022 TGCCAACAAATGTTCATGCAAC 59.129 40.909 10.48 0.00 35.83 4.17
1801 1811 2.223845 GCCAACAAATGTTCATGCAACC 59.776 45.455 0.00 0.00 35.83 3.77
1802 1812 3.464907 CCAACAAATGTTCATGCAACCA 58.535 40.909 0.00 0.00 35.83 3.67
1803 1813 3.495377 CCAACAAATGTTCATGCAACCAG 59.505 43.478 0.00 0.00 35.83 4.00
1804 1814 4.370049 CAACAAATGTTCATGCAACCAGA 58.630 39.130 0.00 0.00 35.83 3.86
1805 1815 4.247267 ACAAATGTTCATGCAACCAGAG 57.753 40.909 0.00 0.00 33.51 3.35
1806 1816 3.638160 ACAAATGTTCATGCAACCAGAGT 59.362 39.130 0.00 0.00 33.51 3.24
1807 1817 4.232221 CAAATGTTCATGCAACCAGAGTC 58.768 43.478 0.00 0.00 33.51 3.36
1808 1818 2.636647 TGTTCATGCAACCAGAGTCA 57.363 45.000 0.00 0.00 33.51 3.41
1809 1819 2.929641 TGTTCATGCAACCAGAGTCAA 58.070 42.857 0.00 0.00 33.51 3.18
1810 1820 2.618241 TGTTCATGCAACCAGAGTCAAC 59.382 45.455 0.00 0.00 33.51 3.18
1811 1821 2.618241 GTTCATGCAACCAGAGTCAACA 59.382 45.455 0.00 0.00 0.00 3.33
1812 1822 2.221169 TCATGCAACCAGAGTCAACAC 58.779 47.619 0.00 0.00 0.00 3.32
1813 1823 1.069703 CATGCAACCAGAGTCAACACG 60.070 52.381 0.00 0.00 0.00 4.49
1814 1824 1.279840 GCAACCAGAGTCAACACGC 59.720 57.895 0.00 0.00 0.00 5.34
1815 1825 1.564622 CAACCAGAGTCAACACGCG 59.435 57.895 3.53 3.53 0.00 6.01
1816 1826 1.143183 AACCAGAGTCAACACGCGT 59.857 52.632 5.58 5.58 0.00 6.01
1817 1827 0.874607 AACCAGAGTCAACACGCGTC 60.875 55.000 9.86 0.00 0.00 5.19
1818 1828 1.299850 CCAGAGTCAACACGCGTCA 60.300 57.895 9.86 0.00 0.00 4.35
1819 1829 0.667487 CCAGAGTCAACACGCGTCAT 60.667 55.000 9.86 0.00 0.00 3.06
1820 1830 0.436150 CAGAGTCAACACGCGTCATG 59.564 55.000 9.86 12.01 0.00 3.07
1821 1831 1.130613 GAGTCAACACGCGTCATGC 59.869 57.895 9.86 7.84 41.47 4.06
1822 1832 1.556591 GAGTCAACACGCGTCATGCA 61.557 55.000 9.86 0.00 46.97 3.96
1823 1833 1.154599 GTCAACACGCGTCATGCAG 60.155 57.895 9.86 0.00 46.97 4.41
1824 1834 2.174107 CAACACGCGTCATGCAGG 59.826 61.111 9.86 0.00 46.97 4.85
1825 1835 2.030412 AACACGCGTCATGCAGGA 59.970 55.556 9.86 0.00 46.97 3.86
1826 1836 1.375908 AACACGCGTCATGCAGGAT 60.376 52.632 9.86 0.00 46.97 3.24
1827 1837 1.638388 AACACGCGTCATGCAGGATG 61.638 55.000 16.08 16.08 46.97 3.51
1828 1838 2.512286 ACGCGTCATGCAGGATGG 60.512 61.111 21.13 13.60 46.97 3.51
1829 1839 3.945434 CGCGTCATGCAGGATGGC 61.945 66.667 21.13 17.76 46.97 4.40
1836 1846 2.203195 TGCAGGATGGCATACCGC 60.203 61.111 11.09 11.09 39.25 5.68
1845 1855 4.946038 GCATACCGCCCACTAACA 57.054 55.556 0.00 0.00 32.94 2.41
1846 1856 2.390427 GCATACCGCCCACTAACAC 58.610 57.895 0.00 0.00 32.94 3.32
1847 1857 0.391927 GCATACCGCCCACTAACACA 60.392 55.000 0.00 0.00 32.94 3.72
1848 1858 1.946747 GCATACCGCCCACTAACACAA 60.947 52.381 0.00 0.00 32.94 3.33
1849 1859 2.428491 CATACCGCCCACTAACACAAA 58.572 47.619 0.00 0.00 0.00 2.83
1850 1860 1.881591 TACCGCCCACTAACACAAAC 58.118 50.000 0.00 0.00 0.00 2.93
1851 1861 0.181824 ACCGCCCACTAACACAAACT 59.818 50.000 0.00 0.00 0.00 2.66
1852 1862 1.314730 CCGCCCACTAACACAAACTT 58.685 50.000 0.00 0.00 0.00 2.66
1853 1863 2.158784 ACCGCCCACTAACACAAACTTA 60.159 45.455 0.00 0.00 0.00 2.24
1854 1864 2.879646 CCGCCCACTAACACAAACTTAA 59.120 45.455 0.00 0.00 0.00 1.85
1855 1865 3.304190 CCGCCCACTAACACAAACTTAAC 60.304 47.826 0.00 0.00 0.00 2.01
1856 1866 3.312973 CGCCCACTAACACAAACTTAACA 59.687 43.478 0.00 0.00 0.00 2.41
1857 1867 4.603985 GCCCACTAACACAAACTTAACAC 58.396 43.478 0.00 0.00 0.00 3.32
1858 1868 4.337274 GCCCACTAACACAAACTTAACACT 59.663 41.667 0.00 0.00 0.00 3.55
1859 1869 5.528320 GCCCACTAACACAAACTTAACACTA 59.472 40.000 0.00 0.00 0.00 2.74
1860 1870 6.038492 GCCCACTAACACAAACTTAACACTAA 59.962 38.462 0.00 0.00 0.00 2.24
1861 1871 7.415429 GCCCACTAACACAAACTTAACACTAAA 60.415 37.037 0.00 0.00 0.00 1.85
1862 1872 8.126700 CCCACTAACACAAACTTAACACTAAAG 58.873 37.037 0.00 0.00 0.00 1.85
1863 1873 7.642586 CCACTAACACAAACTTAACACTAAAGC 59.357 37.037 0.00 0.00 0.00 3.51
1864 1874 8.178964 CACTAACACAAACTTAACACTAAAGCA 58.821 33.333 0.00 0.00 0.00 3.91
1865 1875 8.732531 ACTAACACAAACTTAACACTAAAGCAA 58.267 29.630 0.00 0.00 0.00 3.91
1866 1876 9.562583 CTAACACAAACTTAACACTAAAGCAAA 57.437 29.630 0.00 0.00 0.00 3.68
1867 1877 8.819643 AACACAAACTTAACACTAAAGCAAAA 57.180 26.923 0.00 0.00 0.00 2.44
1868 1878 8.819643 ACACAAACTTAACACTAAAGCAAAAA 57.180 26.923 0.00 0.00 0.00 1.94
1869 1879 8.921670 ACACAAACTTAACACTAAAGCAAAAAG 58.078 29.630 0.00 0.00 0.00 2.27
1870 1880 7.897800 CACAAACTTAACACTAAAGCAAAAAGC 59.102 33.333 0.00 0.00 46.19 3.51
1895 1905 3.736126 GCTATCTCATGCAAGGTTTTGGC 60.736 47.826 0.00 0.00 34.79 4.52
1897 1907 1.614903 TCTCATGCAAGGTTTTGGCTG 59.385 47.619 0.00 0.00 34.79 4.85
1909 1919 2.570442 TTTGGCTGTCGTTTTTGGTC 57.430 45.000 0.00 0.00 0.00 4.02
1912 1922 1.403679 TGGCTGTCGTTTTTGGTCTTG 59.596 47.619 0.00 0.00 0.00 3.02
1916 1926 3.311596 GCTGTCGTTTTTGGTCTTGTACT 59.688 43.478 0.00 0.00 0.00 2.73
1930 1941 0.322322 TGTACTGGGCCGAACGAAAT 59.678 50.000 0.00 0.00 0.00 2.17
1932 1943 0.322322 TACTGGGCCGAACGAAATGT 59.678 50.000 0.00 0.00 0.00 2.71
1935 1946 2.622011 GGGCCGAACGAAATGTGCA 61.622 57.895 0.00 0.00 0.00 4.57
1945 1956 2.814919 ACGAAATGTGCAAAATCCGGTA 59.185 40.909 0.00 0.00 0.00 4.02
1950 1961 5.398603 AATGTGCAAAATCCGGTATTTCA 57.601 34.783 0.00 1.75 36.76 2.69
1951 1962 4.433186 TGTGCAAAATCCGGTATTTCAG 57.567 40.909 0.00 4.73 36.76 3.02
1952 1963 3.192422 TGTGCAAAATCCGGTATTTCAGG 59.808 43.478 0.00 2.17 36.76 3.86
1981 1992 3.056891 TGGGAAAAACTCGGATGAAATGC 60.057 43.478 0.00 0.00 0.00 3.56
2019 2030 9.587772 TTTGAAATTTAGAACGAAAATTGTCCA 57.412 25.926 0.00 0.00 36.81 4.02
2030 2041 7.602517 ACGAAAATTGTCCAAAATTTGAACA 57.397 28.000 7.37 0.00 39.20 3.18
2038 2049 9.786105 ATTGTCCAAAATTTGAACAAAAATGAC 57.214 25.926 14.10 6.78 33.92 3.06
2039 2050 8.558973 TGTCCAAAATTTGAACAAAAATGACT 57.441 26.923 7.37 0.00 33.56 3.41
2041 2052 7.909641 GTCCAAAATTTGAACAAAAATGACTGG 59.090 33.333 7.37 6.14 33.56 4.00
2050 2061 8.010733 TGAACAAAAATGACTGGAATTTCTCT 57.989 30.769 0.00 0.00 0.00 3.10
2058 2069 8.712228 AATGACTGGAATTTCTCTAAAAGGTT 57.288 30.769 0.00 0.00 0.00 3.50
2059 2070 7.745620 TGACTGGAATTTCTCTAAAAGGTTC 57.254 36.000 0.00 0.00 0.00 3.62
2062 2073 7.168905 ACTGGAATTTCTCTAAAAGGTTCGAT 58.831 34.615 0.00 0.00 0.00 3.59
2064 2075 6.598064 TGGAATTTCTCTAAAAGGTTCGATCC 59.402 38.462 4.21 4.21 0.00 3.36
2068 2079 5.995565 TCTCTAAAAGGTTCGATCCAAGA 57.004 39.130 14.83 9.99 0.00 3.02
2070 2081 6.765403 TCTCTAAAAGGTTCGATCCAAGAAA 58.235 36.000 14.83 0.00 0.00 2.52
2073 2084 7.645402 TCTAAAAGGTTCGATCCAAGAAAAAC 58.355 34.615 14.83 0.00 0.00 2.43
2074 2085 4.848562 AAGGTTCGATCCAAGAAAAACC 57.151 40.909 14.83 1.40 37.10 3.27
2079 2090 5.989168 GGTTCGATCCAAGAAAAACCAAAAT 59.011 36.000 7.68 0.00 36.89 1.82
2080 2091 6.073819 GGTTCGATCCAAGAAAAACCAAAATG 60.074 38.462 7.68 0.00 36.89 2.32
2081 2092 6.155475 TCGATCCAAGAAAAACCAAAATGT 57.845 33.333 0.00 0.00 0.00 2.71
2086 2097 8.980143 ATCCAAGAAAAACCAAAATGTATACG 57.020 30.769 0.00 0.00 0.00 3.06
2092 2103 2.927028 ACCAAAATGTATACGGGGAGC 58.073 47.619 0.00 0.00 0.00 4.70
2098 2109 5.362105 AAATGTATACGGGGAGCAAACTA 57.638 39.130 0.00 0.00 0.00 2.24
2103 2114 0.953960 ACGGGGAGCAAACTAAAGCG 60.954 55.000 0.00 0.00 35.48 4.68
2111 2122 4.617223 GGAGCAAACTAAAGCGAAATCAAC 59.383 41.667 0.00 0.00 35.48 3.18
2120 2131 4.701956 AAGCGAAATCAACGAATTCCAT 57.298 36.364 0.00 0.00 0.00 3.41
2183 2194 4.494350 TTGTCATCAAGCTCAAAGAAGC 57.506 40.909 0.00 0.00 42.82 3.86
2184 2195 2.816087 TGTCATCAAGCTCAAAGAAGCC 59.184 45.455 0.00 0.00 43.56 4.35
2191 2202 4.826733 TCAAGCTCAAAGAAGCCATACAAA 59.173 37.500 0.00 0.00 43.56 2.83
2201 2212 6.966534 AGAAGCCATACAAATGATAAAGGG 57.033 37.500 0.00 0.00 34.84 3.95
2210 2221 4.286808 ACAAATGATAAAGGGCTGGCTTTT 59.713 37.500 15.24 15.24 0.00 2.27
2211 2222 4.743057 AATGATAAAGGGCTGGCTTTTC 57.257 40.909 14.39 2.98 0.00 2.29
2212 2223 2.456577 TGATAAAGGGCTGGCTTTTCC 58.543 47.619 14.39 8.87 0.00 3.13
2213 2224 1.757118 GATAAAGGGCTGGCTTTTCCC 59.243 52.381 14.39 4.89 40.36 3.97
2214 2225 0.485099 TAAAGGGCTGGCTTTTCCCA 59.515 50.000 14.39 0.00 42.52 4.37
2215 2226 0.399806 AAAGGGCTGGCTTTTCCCAA 60.400 50.000 5.47 0.00 42.52 4.12
2216 2227 0.833409 AAGGGCTGGCTTTTCCCAAG 60.833 55.000 0.00 0.00 42.52 3.61
2217 2228 2.659016 GGCTGGCTTTTCCCAAGC 59.341 61.111 0.00 0.00 42.30 4.01
2218 2229 2.209315 GGCTGGCTTTTCCCAAGCA 61.209 57.895 8.74 0.00 44.71 3.91
2219 2230 1.005748 GCTGGCTTTTCCCAAGCAC 60.006 57.895 8.74 0.00 44.71 4.40
2220 2231 1.286880 CTGGCTTTTCCCAAGCACG 59.713 57.895 8.74 0.00 44.71 5.34
2221 2232 2.146073 CTGGCTTTTCCCAAGCACGG 62.146 60.000 8.74 0.39 44.71 4.94
2253 2264 1.134907 TCCAACGCCGGACTTTATCTC 60.135 52.381 5.05 0.00 0.00 2.75
2258 2269 1.202268 CGCCGGACTTTATCTCGTTCT 60.202 52.381 5.05 0.00 0.00 3.01
2260 2271 2.159282 GCCGGACTTTATCTCGTTCTCA 60.159 50.000 5.05 0.00 0.00 3.27
2263 2274 4.380655 CCGGACTTTATCTCGTTCTCAAGT 60.381 45.833 0.00 0.00 0.00 3.16
2268 2279 4.521130 TTATCTCGTTCTCAAGTGCTGT 57.479 40.909 0.00 0.00 0.00 4.40
2269 2280 2.423926 TCTCGTTCTCAAGTGCTGTC 57.576 50.000 0.00 0.00 0.00 3.51
2285 2296 2.294233 GCTGTCTGAGCCAAACATTTGA 59.706 45.455 5.91 0.00 42.54 2.69
2286 2297 3.611057 GCTGTCTGAGCCAAACATTTGAG 60.611 47.826 5.91 0.00 42.54 3.02
2287 2298 3.554934 TGTCTGAGCCAAACATTTGAGT 58.445 40.909 5.91 0.00 40.55 3.41
2299 2352 7.412853 CCAAACATTTGAGTATGAGTAGATGC 58.587 38.462 5.91 0.00 40.55 3.91
2307 2360 6.289064 TGAGTATGAGTAGATGCGAAGTAGA 58.711 40.000 0.00 0.00 0.00 2.59
2323 2376 2.691011 AGTAGAAGAACGAGGAGGATGC 59.309 50.000 0.00 0.00 0.00 3.91
2332 2385 3.474570 GGAGGATGCGGACTGCCT 61.475 66.667 3.22 0.00 45.60 4.75
2333 2386 2.586792 GAGGATGCGGACTGCCTT 59.413 61.111 3.22 0.00 45.60 4.35
2334 2387 1.817099 GAGGATGCGGACTGCCTTG 60.817 63.158 3.22 0.00 45.60 3.61
2335 2388 3.512516 GGATGCGGACTGCCTTGC 61.513 66.667 3.22 0.00 45.60 4.01
2387 2473 0.438830 CCGCGCTGTAAACAGAAGTC 59.561 55.000 14.21 0.00 46.59 3.01
2391 2477 1.387084 CGCTGTAAACAGAAGTCGAGC 59.613 52.381 14.21 0.00 46.59 5.03
2393 2479 2.155924 GCTGTAAACAGAAGTCGAGCAC 59.844 50.000 14.21 0.00 46.59 4.40
2417 2503 6.144078 CGAAAGGATAAAATTAGGGTTGGG 57.856 41.667 0.00 0.00 0.00 4.12
2420 2506 6.417503 AAGGATAAAATTAGGGTTGGGAGT 57.582 37.500 0.00 0.00 0.00 3.85
2421 2507 6.014771 AGGATAAAATTAGGGTTGGGAGTC 57.985 41.667 0.00 0.00 0.00 3.36
2425 2511 5.333566 AAAATTAGGGTTGGGAGTCTTCA 57.666 39.130 0.00 0.00 0.00 3.02
2427 2513 2.715763 TAGGGTTGGGAGTCTTCAGT 57.284 50.000 0.00 0.00 0.00 3.41
2432 2518 2.838202 GGTTGGGAGTCTTCAGTATGGA 59.162 50.000 0.00 0.00 36.16 3.41
2437 2523 4.223032 TGGGAGTCTTCAGTATGGACTTTC 59.777 45.833 0.00 0.00 37.67 2.62
2445 2531 8.421784 GTCTTCAGTATGGACTTTCATACCATA 58.578 37.037 10.30 0.00 46.36 2.74
2447 2533 8.547481 TTCAGTATGGACTTTCATACCATAGA 57.453 34.615 0.00 0.00 46.36 1.98
2449 2535 6.870965 CAGTATGGACTTTCATACCATAGAGC 59.129 42.308 0.00 0.00 46.36 4.09
2458 2544 3.007290 TCATACCATAGAGCACATCAGCC 59.993 47.826 0.00 0.00 34.23 4.85
2465 2551 0.807667 GAGCACATCAGCCACCTACG 60.808 60.000 0.00 0.00 34.23 3.51
2478 2564 0.031515 ACCTACGGTGGATCCATGGA 60.032 55.000 19.62 18.88 32.98 3.41
2480 2566 0.032130 CTACGGTGGATCCATGGACG 59.968 60.000 18.99 20.90 35.57 4.79
2482 2568 2.203209 GGTGGATCCATGGACGGC 60.203 66.667 18.99 9.60 35.97 5.68
2490 2576 2.745884 CATGGACGGCGCCAGAAA 60.746 61.111 28.98 9.51 42.15 2.52
2494 2580 2.761195 GGACGGCGCCAGAAATTCC 61.761 63.158 28.98 16.78 0.00 3.01
2499 2585 1.713597 GGCGCCAGAAATTCCAAAAG 58.286 50.000 24.80 0.00 0.00 2.27
2500 2586 1.672737 GGCGCCAGAAATTCCAAAAGG 60.673 52.381 24.80 0.00 0.00 3.11
2502 2588 1.672737 CGCCAGAAATTCCAAAAGGGC 60.673 52.381 0.00 0.00 36.21 5.19
2504 2590 1.066929 CCAGAAATTCCAAAAGGGCCG 60.067 52.381 0.00 0.00 36.21 6.13
2505 2591 1.892474 CAGAAATTCCAAAAGGGCCGA 59.108 47.619 0.00 0.00 36.21 5.54
2507 2593 2.969262 AGAAATTCCAAAAGGGCCGAAA 59.031 40.909 0.00 0.00 36.21 3.46
2509 2595 3.333029 AATTCCAAAAGGGCCGAAATG 57.667 42.857 0.00 0.00 36.21 2.32
2520 2607 1.966762 CCGAAATGTTTGGCCAGCT 59.033 52.632 5.11 0.00 0.00 4.24
2521 2608 0.318120 CCGAAATGTTTGGCCAGCTT 59.682 50.000 5.11 0.00 0.00 3.74
2553 2640 2.091541 GGGCCTTGACGAAATTGATGA 58.908 47.619 0.84 0.00 0.00 2.92
2558 2645 6.329496 GGCCTTGACGAAATTGATGAATTTA 58.671 36.000 2.67 0.00 41.06 1.40
2583 2670 3.933332 ACGAAAATCAGAAATCTCGGACC 59.067 43.478 0.00 0.00 0.00 4.46
2584 2671 3.932710 CGAAAATCAGAAATCTCGGACCA 59.067 43.478 0.00 0.00 0.00 4.02
2585 2672 4.201724 CGAAAATCAGAAATCTCGGACCAC 60.202 45.833 0.00 0.00 0.00 4.16
2586 2673 4.559862 AAATCAGAAATCTCGGACCACT 57.440 40.909 0.00 0.00 0.00 4.00
2587 2674 4.559862 AATCAGAAATCTCGGACCACTT 57.440 40.909 0.00 0.00 0.00 3.16
2588 2675 3.319137 TCAGAAATCTCGGACCACTTG 57.681 47.619 0.00 0.00 0.00 3.16
2589 2676 2.897326 TCAGAAATCTCGGACCACTTGA 59.103 45.455 0.00 0.00 0.00 3.02
2590 2677 3.515502 TCAGAAATCTCGGACCACTTGAT 59.484 43.478 0.00 0.00 0.00 2.57
2591 2678 3.620374 CAGAAATCTCGGACCACTTGATG 59.380 47.826 0.00 0.00 0.00 3.07
2592 2679 3.515502 AGAAATCTCGGACCACTTGATGA 59.484 43.478 0.00 0.00 0.00 2.92
2593 2680 4.163078 AGAAATCTCGGACCACTTGATGAT 59.837 41.667 0.00 0.00 0.00 2.45
2594 2681 3.742433 ATCTCGGACCACTTGATGATC 57.258 47.619 0.00 0.00 0.00 2.92
2595 2682 2.739943 TCTCGGACCACTTGATGATCT 58.260 47.619 0.00 0.00 0.00 2.75
2596 2683 2.690497 TCTCGGACCACTTGATGATCTC 59.310 50.000 0.00 0.00 0.00 2.75
2597 2684 1.405463 TCGGACCACTTGATGATCTCG 59.595 52.381 0.00 0.00 0.00 4.04
2598 2685 1.135139 CGGACCACTTGATGATCTCGT 59.865 52.381 0.00 0.00 0.00 4.18
2599 2686 2.417379 CGGACCACTTGATGATCTCGTT 60.417 50.000 0.00 0.00 0.00 3.85
2600 2687 3.181490 CGGACCACTTGATGATCTCGTTA 60.181 47.826 0.00 0.00 0.00 3.18
2601 2688 4.499865 CGGACCACTTGATGATCTCGTTAT 60.500 45.833 0.00 0.00 0.00 1.89
2602 2689 4.747108 GGACCACTTGATGATCTCGTTATG 59.253 45.833 0.00 0.00 0.00 1.90
2603 2690 5.451937 GGACCACTTGATGATCTCGTTATGA 60.452 44.000 0.00 0.00 0.00 2.15
2604 2691 6.166984 ACCACTTGATGATCTCGTTATGAT 57.833 37.500 0.00 0.00 0.00 2.45
2605 2692 6.586344 ACCACTTGATGATCTCGTTATGATT 58.414 36.000 0.00 0.00 0.00 2.57
2606 2693 7.050377 ACCACTTGATGATCTCGTTATGATTT 58.950 34.615 0.00 0.00 0.00 2.17
2607 2694 7.225538 ACCACTTGATGATCTCGTTATGATTTC 59.774 37.037 0.00 0.00 0.00 2.17
2608 2695 7.279342 CACTTGATGATCTCGTTATGATTTCG 58.721 38.462 0.00 0.00 0.00 3.46
2609 2696 6.980978 ACTTGATGATCTCGTTATGATTTCGT 59.019 34.615 0.00 0.00 0.00 3.85
2610 2697 8.135529 ACTTGATGATCTCGTTATGATTTCGTA 58.864 33.333 0.00 0.00 0.00 3.43
2611 2698 8.865590 TTGATGATCTCGTTATGATTTCGTAA 57.134 30.769 0.00 0.00 0.00 3.18
2612 2699 8.865590 TGATGATCTCGTTATGATTTCGTAAA 57.134 30.769 0.00 0.00 0.00 2.01
2613 2700 9.476202 TGATGATCTCGTTATGATTTCGTAAAT 57.524 29.630 0.00 0.00 0.00 1.40
2647 2734 7.966246 TTTTTCAAAAAGTCATCCATGATGG 57.034 32.000 4.74 4.74 40.15 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
559 568 6.271566 TGAGATTGAACGAGAGATGAATGAG 58.728 40.000 0.00 0.00 0.00 2.90
561 570 6.898912 TTGAGATTGAACGAGAGATGAATG 57.101 37.500 0.00 0.00 0.00 2.67
567 576 4.944048 TGTGTTTGAGATTGAACGAGAGA 58.056 39.130 0.00 0.00 0.00 3.10
636 645 4.188462 TGAGAATTGTGGCTTGTATACGG 58.812 43.478 0.00 0.00 0.00 4.02
1018 1028 2.029290 TGAGCTTGGAGACTTTACGACC 60.029 50.000 0.00 0.00 0.00 4.79
1020 1030 3.427638 CGATGAGCTTGGAGACTTTACGA 60.428 47.826 0.00 0.00 0.00 3.43
1122 1132 1.376037 GGCGAGGGTGGCATATAGC 60.376 63.158 0.00 0.00 44.65 2.97
1139 1149 0.741221 GGCGGCAGAGTAGTTTGAGG 60.741 60.000 3.07 0.00 0.00 3.86
1190 1200 4.735369 ACCTGTGTTAATGATCCCAAACA 58.265 39.130 0.00 0.00 0.00 2.83
1209 1219 1.481056 GCACACACCCTACTGGACCT 61.481 60.000 0.00 0.00 38.00 3.85
1240 1250 3.708734 CCCCGTCGCGTTCAACAC 61.709 66.667 5.77 0.00 0.00 3.32
1416 1426 3.284449 GCGTTCACAAACCCGGCT 61.284 61.111 0.00 0.00 31.27 5.52
1485 1495 2.244651 GCACAGTGTCGCGTTCCTT 61.245 57.895 5.77 0.00 0.00 3.36
1557 1567 1.734163 CATGTGCACTCATCTCAGCA 58.266 50.000 19.41 0.00 34.10 4.41
1564 1574 3.494378 GAGCGCATGTGCACTCAT 58.506 55.556 31.29 11.86 46.35 2.90
1575 1585 4.717629 CCGTCCACGAAGAGCGCA 62.718 66.667 11.47 0.00 46.04 6.09
1603 1613 3.127533 GCTGATGGGTGCGGTGAC 61.128 66.667 0.00 0.00 0.00 3.67
1635 1645 8.899427 ATGAATAAATCAATCATCTCTCGTGT 57.101 30.769 0.00 0.00 42.54 4.49
1672 1682 9.591404 CGTCTGTAAACTAATACTCCGTATAAG 57.409 37.037 0.00 0.00 0.00 1.73
1673 1683 8.559536 CCGTCTGTAAACTAATACTCCGTATAA 58.440 37.037 0.00 0.00 0.00 0.98
1675 1685 6.767902 TCCGTCTGTAAACTAATACTCCGTAT 59.232 38.462 0.00 0.00 0.00 3.06
1676 1686 6.112734 TCCGTCTGTAAACTAATACTCCGTA 58.887 40.000 0.00 0.00 0.00 4.02
1677 1687 4.943705 TCCGTCTGTAAACTAATACTCCGT 59.056 41.667 0.00 0.00 0.00 4.69
1678 1688 5.065731 ACTCCGTCTGTAAACTAATACTCCG 59.934 44.000 0.00 0.00 0.00 4.63
1687 1697 7.481642 CATGTCTTATACTCCGTCTGTAAACT 58.518 38.462 0.00 0.00 0.00 2.66
1688 1698 6.198591 GCATGTCTTATACTCCGTCTGTAAAC 59.801 42.308 0.00 0.00 0.00 2.01
1691 1701 5.131067 AGCATGTCTTATACTCCGTCTGTA 58.869 41.667 0.00 0.00 0.00 2.74
1693 1703 4.576216 AGCATGTCTTATACTCCGTCTG 57.424 45.455 0.00 0.00 0.00 3.51
1695 1705 4.933330 TCAAGCATGTCTTATACTCCGTC 58.067 43.478 0.00 0.00 32.74 4.79
1696 1706 5.537300 ATCAAGCATGTCTTATACTCCGT 57.463 39.130 0.00 0.00 32.74 4.69
1697 1707 6.851222 AAATCAAGCATGTCTTATACTCCG 57.149 37.500 0.00 0.00 32.74 4.63
1698 1708 8.443953 AGAAAATCAAGCATGTCTTATACTCC 57.556 34.615 0.00 0.00 32.74 3.85
1725 1735 9.033481 CAACAACATACAAGATCACACAAATTT 57.967 29.630 0.00 0.00 0.00 1.82
1727 1737 7.715657 ACAACAACATACAAGATCACACAAAT 58.284 30.769 0.00 0.00 0.00 2.32
1759 1769 6.808829 TGGCAATATATGGAGCTTTCAAAAG 58.191 36.000 0.00 0.00 39.03 2.27
1764 1774 5.772825 TGTTGGCAATATATGGAGCTTTC 57.227 39.130 1.92 0.00 0.00 2.62
1768 1778 5.846203 ACATTTGTTGGCAATATATGGAGC 58.154 37.500 23.53 2.82 34.18 4.70
1786 1796 3.890756 TGACTCTGGTTGCATGAACATTT 59.109 39.130 0.00 0.00 36.12 2.32
1789 1799 2.618241 GTTGACTCTGGTTGCATGAACA 59.382 45.455 0.00 0.00 36.12 3.18
1790 1800 2.618241 TGTTGACTCTGGTTGCATGAAC 59.382 45.455 0.00 0.00 0.00 3.18
1791 1801 2.618241 GTGTTGACTCTGGTTGCATGAA 59.382 45.455 0.00 0.00 0.00 2.57
1792 1802 2.221169 GTGTTGACTCTGGTTGCATGA 58.779 47.619 0.00 0.00 0.00 3.07
1793 1803 1.069703 CGTGTTGACTCTGGTTGCATG 60.070 52.381 0.00 0.00 0.00 4.06
1794 1804 1.229428 CGTGTTGACTCTGGTTGCAT 58.771 50.000 0.00 0.00 0.00 3.96
1795 1805 1.436195 GCGTGTTGACTCTGGTTGCA 61.436 55.000 0.00 0.00 0.00 4.08
1796 1806 1.279840 GCGTGTTGACTCTGGTTGC 59.720 57.895 0.00 0.00 0.00 4.17
1797 1807 1.151777 ACGCGTGTTGACTCTGGTTG 61.152 55.000 12.93 0.00 0.00 3.77
1798 1808 0.874607 GACGCGTGTTGACTCTGGTT 60.875 55.000 20.70 0.00 0.00 3.67
1799 1809 1.299926 GACGCGTGTTGACTCTGGT 60.300 57.895 20.70 0.00 0.00 4.00
1800 1810 0.667487 ATGACGCGTGTTGACTCTGG 60.667 55.000 20.70 0.00 0.00 3.86
1801 1811 0.436150 CATGACGCGTGTTGACTCTG 59.564 55.000 20.70 0.00 0.00 3.35
1802 1812 1.284982 GCATGACGCGTGTTGACTCT 61.285 55.000 20.70 0.00 0.00 3.24
1803 1813 1.130613 GCATGACGCGTGTTGACTC 59.869 57.895 20.70 0.00 0.00 3.36
1804 1814 1.560004 CTGCATGACGCGTGTTGACT 61.560 55.000 20.70 0.00 46.97 3.41
1805 1815 1.154599 CTGCATGACGCGTGTTGAC 60.155 57.895 20.70 10.53 46.97 3.18
1806 1816 2.316867 CCTGCATGACGCGTGTTGA 61.317 57.895 20.70 0.00 46.97 3.18
1807 1817 1.638388 ATCCTGCATGACGCGTGTTG 61.638 55.000 20.70 15.45 46.97 3.33
1808 1818 1.375908 ATCCTGCATGACGCGTGTT 60.376 52.632 20.70 0.00 46.97 3.32
1809 1819 2.102438 CATCCTGCATGACGCGTGT 61.102 57.895 20.70 0.00 46.97 4.49
1810 1820 2.705220 CATCCTGCATGACGCGTG 59.295 61.111 20.70 2.85 46.97 5.34
1811 1821 2.512286 CCATCCTGCATGACGCGT 60.512 61.111 13.85 13.85 46.97 6.01
1812 1822 3.945434 GCCATCCTGCATGACGCG 61.945 66.667 3.53 3.53 46.97 6.01
1813 1823 2.825387 TGCCATCCTGCATGACGC 60.825 61.111 0.00 0.00 42.89 5.19
1819 1829 2.203195 GCGGTATGCCATCCTGCA 60.203 61.111 0.00 0.00 46.94 4.41
1828 1838 0.391927 TGTGTTAGTGGGCGGTATGC 60.392 55.000 0.00 0.00 45.38 3.14
1829 1839 2.102070 TTGTGTTAGTGGGCGGTATG 57.898 50.000 0.00 0.00 0.00 2.39
1830 1840 2.039348 AGTTTGTGTTAGTGGGCGGTAT 59.961 45.455 0.00 0.00 0.00 2.73
1831 1841 1.417145 AGTTTGTGTTAGTGGGCGGTA 59.583 47.619 0.00 0.00 0.00 4.02
1832 1842 0.181824 AGTTTGTGTTAGTGGGCGGT 59.818 50.000 0.00 0.00 0.00 5.68
1833 1843 1.314730 AAGTTTGTGTTAGTGGGCGG 58.685 50.000 0.00 0.00 0.00 6.13
1834 1844 3.312973 TGTTAAGTTTGTGTTAGTGGGCG 59.687 43.478 0.00 0.00 0.00 6.13
1835 1845 4.337274 AGTGTTAAGTTTGTGTTAGTGGGC 59.663 41.667 0.00 0.00 0.00 5.36
1836 1846 7.556733 TTAGTGTTAAGTTTGTGTTAGTGGG 57.443 36.000 0.00 0.00 0.00 4.61
1837 1847 7.642586 GCTTTAGTGTTAAGTTTGTGTTAGTGG 59.357 37.037 0.00 0.00 0.00 4.00
1838 1848 8.178964 TGCTTTAGTGTTAAGTTTGTGTTAGTG 58.821 33.333 0.00 0.00 0.00 2.74
1839 1849 8.271312 TGCTTTAGTGTTAAGTTTGTGTTAGT 57.729 30.769 0.00 0.00 0.00 2.24
1840 1850 9.562583 TTTGCTTTAGTGTTAAGTTTGTGTTAG 57.437 29.630 0.00 0.00 0.00 2.34
1841 1851 9.909644 TTTTGCTTTAGTGTTAAGTTTGTGTTA 57.090 25.926 0.00 0.00 0.00 2.41
1842 1852 8.819643 TTTTGCTTTAGTGTTAAGTTTGTGTT 57.180 26.923 0.00 0.00 0.00 3.32
1843 1853 8.819643 TTTTTGCTTTAGTGTTAAGTTTGTGT 57.180 26.923 0.00 0.00 0.00 3.72
1844 1854 7.897800 GCTTTTTGCTTTAGTGTTAAGTTTGTG 59.102 33.333 0.00 0.00 38.95 3.33
1845 1855 7.959733 GCTTTTTGCTTTAGTGTTAAGTTTGT 58.040 30.769 0.00 0.00 38.95 2.83
1862 1872 3.550678 GCATGAGATAGCAAGCTTTTTGC 59.449 43.478 0.00 0.00 45.22 3.68
1863 1873 4.740268 TGCATGAGATAGCAAGCTTTTTG 58.260 39.130 0.00 0.00 37.90 2.44
1864 1874 5.395682 TTGCATGAGATAGCAAGCTTTTT 57.604 34.783 0.00 0.00 44.98 1.94
1872 1882 3.444742 CCAAAACCTTGCATGAGATAGCA 59.555 43.478 0.00 0.00 39.32 3.49
1873 1883 3.736126 GCCAAAACCTTGCATGAGATAGC 60.736 47.826 0.00 0.00 0.00 2.97
1874 1884 3.698040 AGCCAAAACCTTGCATGAGATAG 59.302 43.478 0.00 0.00 0.00 2.08
1875 1885 3.444742 CAGCCAAAACCTTGCATGAGATA 59.555 43.478 0.00 0.00 0.00 1.98
1876 1886 2.232941 CAGCCAAAACCTTGCATGAGAT 59.767 45.455 0.00 0.00 0.00 2.75
1877 1887 1.614903 CAGCCAAAACCTTGCATGAGA 59.385 47.619 0.00 0.00 0.00 3.27
1878 1888 1.342174 ACAGCCAAAACCTTGCATGAG 59.658 47.619 0.00 0.00 0.00 2.90
1879 1889 1.340889 GACAGCCAAAACCTTGCATGA 59.659 47.619 0.00 0.00 0.00 3.07
1880 1890 1.787012 GACAGCCAAAACCTTGCATG 58.213 50.000 0.00 0.00 0.00 4.06
1881 1891 0.314935 CGACAGCCAAAACCTTGCAT 59.685 50.000 0.00 0.00 0.00 3.96
1882 1892 1.034838 ACGACAGCCAAAACCTTGCA 61.035 50.000 0.00 0.00 0.00 4.08
1888 1898 2.601314 GACCAAAAACGACAGCCAAAAC 59.399 45.455 0.00 0.00 0.00 2.43
1895 1905 4.260620 CCAGTACAAGACCAAAAACGACAG 60.261 45.833 0.00 0.00 0.00 3.51
1897 1907 3.002965 CCCAGTACAAGACCAAAAACGAC 59.997 47.826 0.00 0.00 0.00 4.34
1909 1919 0.320073 TTCGTTCGGCCCAGTACAAG 60.320 55.000 0.00 0.00 0.00 3.16
1912 1922 0.725117 CATTTCGTTCGGCCCAGTAC 59.275 55.000 0.00 0.00 0.00 2.73
1916 1926 2.622011 GCACATTTCGTTCGGCCCA 61.622 57.895 0.00 0.00 0.00 5.36
1930 1941 3.192422 CCTGAAATACCGGATTTTGCACA 59.808 43.478 9.46 3.76 37.90 4.57
1932 1943 3.691575 TCCTGAAATACCGGATTTTGCA 58.308 40.909 9.46 2.10 37.90 4.08
1960 1971 3.511699 GCATTTCATCCGAGTTTTTCCC 58.488 45.455 0.00 0.00 0.00 3.97
1974 1985 6.834959 TCAAATTTTAGTTTGCGCATTTCA 57.165 29.167 12.75 0.00 38.61 2.69
1993 2004 9.587772 TGGACAATTTTCGTTCTAAATTTCAAA 57.412 25.926 0.00 0.00 34.01 2.69
2016 2027 7.826252 TCCAGTCATTTTTGTTCAAATTTTGGA 59.174 29.630 9.18 0.00 31.33 3.53
2030 2041 9.987272 CCTTTTAGAGAAATTCCAGTCATTTTT 57.013 29.630 0.00 0.00 0.00 1.94
2038 2049 7.201652 GGATCGAACCTTTTAGAGAAATTCCAG 60.202 40.741 4.14 0.00 0.00 3.86
2039 2050 6.598064 GGATCGAACCTTTTAGAGAAATTCCA 59.402 38.462 4.14 0.00 0.00 3.53
2041 2052 7.611213 TGGATCGAACCTTTTAGAGAAATTC 57.389 36.000 13.40 0.00 0.00 2.17
2050 2061 6.321690 TGGTTTTTCTTGGATCGAACCTTTTA 59.678 34.615 13.40 0.00 37.87 1.52
2058 2069 6.155475 ACATTTTGGTTTTTCTTGGATCGA 57.845 33.333 0.00 0.00 0.00 3.59
2059 2070 9.072294 GTATACATTTTGGTTTTTCTTGGATCG 57.928 33.333 0.00 0.00 0.00 3.69
2062 2073 7.371936 CCGTATACATTTTGGTTTTTCTTGGA 58.628 34.615 3.32 0.00 0.00 3.53
2064 2075 6.588373 CCCCGTATACATTTTGGTTTTTCTTG 59.412 38.462 3.32 0.00 0.00 3.02
2068 2079 5.336929 GCTCCCCGTATACATTTTGGTTTTT 60.337 40.000 3.32 0.00 0.00 1.94
2070 2081 3.697542 GCTCCCCGTATACATTTTGGTTT 59.302 43.478 3.32 0.00 0.00 3.27
2073 2084 2.925724 TGCTCCCCGTATACATTTTGG 58.074 47.619 3.32 0.00 0.00 3.28
2074 2085 4.398044 AGTTTGCTCCCCGTATACATTTTG 59.602 41.667 3.32 0.00 0.00 2.44
2079 2090 4.761975 CTTTAGTTTGCTCCCCGTATACA 58.238 43.478 3.32 0.00 0.00 2.29
2080 2091 3.558829 GCTTTAGTTTGCTCCCCGTATAC 59.441 47.826 0.00 0.00 0.00 1.47
2081 2092 3.738899 CGCTTTAGTTTGCTCCCCGTATA 60.739 47.826 0.00 0.00 0.00 1.47
2086 2097 1.530323 TTCGCTTTAGTTTGCTCCCC 58.470 50.000 0.00 0.00 0.00 4.81
2092 2103 6.911484 ATTCGTTGATTTCGCTTTAGTTTG 57.089 33.333 0.00 0.00 0.00 2.93
2098 2109 4.497473 TGGAATTCGTTGATTTCGCTTT 57.503 36.364 0.00 0.00 0.00 3.51
2120 2131 9.677567 GTTCACTGCTTTTCAGATTGTTAATTA 57.322 29.630 0.00 0.00 45.72 1.40
2139 2150 0.886490 AAGGCCGAGCTTGTTCACTG 60.886 55.000 0.00 0.00 0.00 3.66
2183 2194 4.262164 GCCAGCCCTTTATCATTTGTATGG 60.262 45.833 0.00 0.00 32.40 2.74
2184 2195 4.586001 AGCCAGCCCTTTATCATTTGTATG 59.414 41.667 0.00 0.00 0.00 2.39
2191 2202 3.033909 GGAAAAGCCAGCCCTTTATCAT 58.966 45.455 0.00 0.00 34.12 2.45
2201 2212 1.005748 GTGCTTGGGAAAAGCCAGC 60.006 57.895 7.55 0.00 42.36 4.85
2244 2255 4.926238 CAGCACTTGAGAACGAGATAAAGT 59.074 41.667 0.00 0.00 0.00 2.66
2245 2256 4.926238 ACAGCACTTGAGAACGAGATAAAG 59.074 41.667 0.00 0.00 0.00 1.85
2253 2264 2.057316 CTCAGACAGCACTTGAGAACG 58.943 52.381 2.49 0.00 0.00 3.95
2268 2279 5.559770 TCATACTCAAATGTTTGGCTCAGA 58.440 37.500 5.71 0.00 38.66 3.27
2269 2280 5.413833 ACTCATACTCAAATGTTTGGCTCAG 59.586 40.000 5.71 0.00 38.66 3.35
2274 2285 7.412853 GCATCTACTCATACTCAAATGTTTGG 58.587 38.462 5.71 0.30 38.66 3.28
2277 2288 6.573434 TCGCATCTACTCATACTCAAATGTT 58.427 36.000 0.00 0.00 0.00 2.71
2285 2296 6.993308 TCTTCTACTTCGCATCTACTCATACT 59.007 38.462 0.00 0.00 0.00 2.12
2286 2297 7.192148 TCTTCTACTTCGCATCTACTCATAC 57.808 40.000 0.00 0.00 0.00 2.39
2287 2298 7.518529 CGTTCTTCTACTTCGCATCTACTCATA 60.519 40.741 0.00 0.00 0.00 2.15
2299 2352 3.008330 TCCTCCTCGTTCTTCTACTTCG 58.992 50.000 0.00 0.00 0.00 3.79
2307 2360 0.970937 TCCGCATCCTCCTCGTTCTT 60.971 55.000 0.00 0.00 0.00 2.52
2339 2425 2.534903 GGCTATTGGCGACGGAAGC 61.535 63.158 0.00 0.16 42.94 3.86
2364 2450 4.973055 TGTTTACAGCGCGGCGGT 62.973 61.111 22.54 22.54 40.45 5.68
2387 2473 4.616181 AATTTTATCCTTTCGGTGCTCG 57.384 40.909 0.00 0.00 40.90 5.03
2391 2477 6.405397 CCAACCCTAATTTTATCCTTTCGGTG 60.405 42.308 0.00 0.00 0.00 4.94
2393 2479 5.068591 CCCAACCCTAATTTTATCCTTTCGG 59.931 44.000 0.00 0.00 0.00 4.30
2415 2501 4.223032 TGAAAGTCCATACTGAAGACTCCC 59.777 45.833 0.00 0.00 39.92 4.30
2417 2503 6.981559 GGTATGAAAGTCCATACTGAAGACTC 59.018 42.308 12.10 0.00 44.98 3.36
2420 2506 6.867519 TGGTATGAAAGTCCATACTGAAGA 57.132 37.500 12.10 0.00 44.98 2.87
2421 2507 8.642432 TCTATGGTATGAAAGTCCATACTGAAG 58.358 37.037 12.10 8.07 44.98 3.02
2425 2511 6.554982 TGCTCTATGGTATGAAAGTCCATACT 59.445 38.462 12.10 0.00 44.98 2.12
2427 2513 6.326323 TGTGCTCTATGGTATGAAAGTCCATA 59.674 38.462 0.00 0.00 41.45 2.74
2432 2518 6.239217 TGATGTGCTCTATGGTATGAAAGT 57.761 37.500 0.00 0.00 0.00 2.66
2437 2523 3.244318 TGGCTGATGTGCTCTATGGTATG 60.244 47.826 0.00 0.00 0.00 2.39
2445 2531 0.539051 GTAGGTGGCTGATGTGCTCT 59.461 55.000 0.00 0.00 0.00 4.09
2447 2533 1.219124 CGTAGGTGGCTGATGTGCT 59.781 57.895 0.00 0.00 0.00 4.40
2465 2551 2.203209 GCCGTCCATGGATCCACC 60.203 66.667 18.99 3.17 39.54 4.61
2478 2564 1.175983 TTTGGAATTTCTGGCGCCGT 61.176 50.000 23.90 1.63 0.00 5.68
2480 2566 1.672737 CCTTTTGGAATTTCTGGCGCC 60.673 52.381 22.73 22.73 44.07 6.53
2482 2568 1.672737 GCCCTTTTGGAATTTCTGGCG 60.673 52.381 0.00 0.00 44.07 5.69
2490 2576 2.256306 ACATTTCGGCCCTTTTGGAAT 58.744 42.857 0.00 0.00 44.07 3.01
2494 2580 2.142319 CCAAACATTTCGGCCCTTTTG 58.858 47.619 0.00 0.00 0.00 2.44
2502 2588 0.318120 AAGCTGGCCAAACATTTCGG 59.682 50.000 7.01 0.00 0.00 4.30
2505 2591 9.981114 GTATAAATATAAGCTGGCCAAACATTT 57.019 29.630 7.01 9.36 0.00 2.32
2507 2593 7.094377 CGGTATAAATATAAGCTGGCCAAACAT 60.094 37.037 7.01 0.09 0.00 2.71
2509 2595 6.349033 CCGGTATAAATATAAGCTGGCCAAAC 60.349 42.308 7.01 1.16 0.00 2.93
2517 2604 5.249852 TCAAGGCCCGGTATAAATATAAGCT 59.750 40.000 0.00 0.00 0.00 3.74
2520 2607 5.245751 TCGTCAAGGCCCGGTATAAATATAA 59.754 40.000 0.00 0.00 0.00 0.98
2521 2608 4.771577 TCGTCAAGGCCCGGTATAAATATA 59.228 41.667 0.00 0.00 0.00 0.86
2553 2640 8.391106 CGAGATTTCTGATTTTCGTCCTAAATT 58.609 33.333 0.00 0.00 0.00 1.82
2558 2645 4.081642 TCCGAGATTTCTGATTTTCGTCCT 60.082 41.667 0.00 0.00 0.00 3.85
2570 2657 3.515502 TCATCAAGTGGTCCGAGATTTCT 59.484 43.478 0.00 0.00 0.00 2.52
2583 2670 7.043125 ACGAAATCATAACGAGATCATCAAGTG 60.043 37.037 0.00 0.00 0.00 3.16
2584 2671 6.980978 ACGAAATCATAACGAGATCATCAAGT 59.019 34.615 0.00 0.00 0.00 3.16
2585 2672 7.400158 ACGAAATCATAACGAGATCATCAAG 57.600 36.000 0.00 0.00 0.00 3.02
2586 2673 8.865590 TTACGAAATCATAACGAGATCATCAA 57.134 30.769 0.00 0.00 0.00 2.57
2587 2674 8.865590 TTTACGAAATCATAACGAGATCATCA 57.134 30.769 0.00 0.00 0.00 3.07
2623 2710 7.966246 CCATCATGGATGACTTTTTGAAAAA 57.034 32.000 0.00 2.83 42.09 1.94


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

AutoCloner maintained by Alex Coulton.