Multiple sequence alignment - TraesCS1D01G017500

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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 TraesCS1D01G017500 chr1D 100.000 2725 0 0 1 2725 7832513 7835237 0.000000e+00 5033.0
1 TraesCS1D01G017500 chr1D 90.372 1911 110 29 1 1865 7035938 7034056 0.000000e+00 2442.0
2 TraesCS1D01G017500 chr1D 87.500 600 60 6 167 751 22188373 22187774 0.000000e+00 678.0
3 TraesCS1D01G017500 chr1D 85.475 179 6 6 2048 2213 7034054 7033883 4.670000e-38 169.0
4 TraesCS1D01G017500 chr1A 93.389 1195 50 11 440 1626 9475590 9476763 0.000000e+00 1742.0
5 TraesCS1D01G017500 chr1A 91.198 409 24 3 1 397 9475184 9475592 1.850000e-151 545.0
6 TraesCS1D01G017500 chr1A 79.727 513 86 12 2225 2723 20971449 20970941 3.340000e-94 355.0
7 TraesCS1D01G017500 chr1A 85.542 83 8 3 1 80 8627009 8626928 1.740000e-12 84.2
8 TraesCS1D01G017500 chr3B 91.440 514 35 4 1100 1604 13920284 13920797 0.000000e+00 697.0
9 TraesCS1D01G017500 chr3B 88.017 242 19 4 167 398 810926008 810925767 7.430000e-71 278.0
10 TraesCS1D01G017500 chr5D 87.648 591 65 6 167 751 120392851 120392263 0.000000e+00 680.0
11 TraesCS1D01G017500 chr5D 81.225 506 79 13 2229 2723 91344218 91343718 7.070000e-106 394.0
12 TraesCS1D01G017500 chr5D 80.538 483 74 15 2252 2723 217286899 217287372 1.200000e-93 353.0
13 TraesCS1D01G017500 chr5D 79.493 434 82 6 1106 1537 406462460 406462032 4.410000e-78 302.0
14 TraesCS1D01G017500 chr1B 87.315 607 61 8 160 751 608840677 608840072 0.000000e+00 680.0
15 TraesCS1D01G017500 chr1B 87.416 596 57 9 167 747 673502907 673502315 0.000000e+00 669.0
16 TraesCS1D01G017500 chr5A 87.396 603 60 8 164 751 395878852 395879453 0.000000e+00 678.0
17 TraesCS1D01G017500 chr5A 80.102 392 68 8 1084 1472 512067600 512067216 1.600000e-72 283.0
18 TraesCS1D01G017500 chr4B 86.409 596 69 9 166 751 648841098 648840505 2.290000e-180 641.0
19 TraesCS1D01G017500 chr7B 85.476 599 76 10 160 751 654864183 654863589 4.990000e-172 614.0
20 TraesCS1D01G017500 chr7B 83.071 508 70 10 2226 2721 559677197 559677700 5.350000e-122 448.0
21 TraesCS1D01G017500 chr7B 82.573 241 32 6 164 394 64168406 64168646 1.280000e-48 204.0
22 TraesCS1D01G017500 chr3A 82.592 517 64 16 2225 2723 584952717 584952209 1.500000e-117 433.0
23 TraesCS1D01G017500 chr3A 89.593 221 20 3 1386 1604 11173810 11173591 7.430000e-71 278.0
24 TraesCS1D01G017500 chr5B 81.373 510 81 9 2227 2723 546834187 546834695 1.180000e-108 403.0
25 TraesCS1D01G017500 chr5B 78.788 429 83 6 1111 1537 487471576 487471154 5.740000e-72 281.0
26 TraesCS1D01G017500 chr5B 78.462 195 36 6 1346 1537 487487327 487487136 3.680000e-24 122.0
27 TraesCS1D01G017500 chr2B 82.189 466 72 6 2219 2675 390812625 390813088 9.150000e-105 390.0
28 TraesCS1D01G017500 chrUn 91.429 280 18 3 1099 1372 478017727 478017448 1.980000e-101 379.0
29 TraesCS1D01G017500 chrUn 88.172 186 19 1 1443 1625 271418421 271418236 4.570000e-53 219.0
30 TraesCS1D01G017500 chr6B 80.469 512 73 16 2225 2723 143521433 143521930 1.540000e-97 366.0
31 TraesCS1D01G017500 chr6B 82.500 240 29 6 164 393 1117583 1117819 5.950000e-47 198.0
32 TraesCS1D01G017500 chr4A 80.354 509 78 14 2226 2722 91596515 91597013 1.540000e-97 366.0
33 TraesCS1D01G017500 chr2A 79.505 444 84 6 1107 1548 120671756 120671318 2.640000e-80 309.0
34 TraesCS1D01G017500 chr2D 79.091 440 85 6 1111 1548 118805173 118804739 2.050000e-76 296.0
35 TraesCS1D01G017500 chr2D 86.555 238 22 6 167 394 83098240 83098003 1.250000e-63 254.0


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 TraesCS1D01G017500 chr1D 7832513 7835237 2724 False 5033.0 5033 100.0000 1 2725 1 chr1D.!!$F1 2724
1 TraesCS1D01G017500 chr1D 7033883 7035938 2055 True 1305.5 2442 87.9235 1 2213 2 chr1D.!!$R2 2212
2 TraesCS1D01G017500 chr1D 22187774 22188373 599 True 678.0 678 87.5000 167 751 1 chr1D.!!$R1 584
3 TraesCS1D01G017500 chr1A 9475184 9476763 1579 False 1143.5 1742 92.2935 1 1626 2 chr1A.!!$F1 1625
4 TraesCS1D01G017500 chr1A 20970941 20971449 508 True 355.0 355 79.7270 2225 2723 1 chr1A.!!$R2 498
5 TraesCS1D01G017500 chr3B 13920284 13920797 513 False 697.0 697 91.4400 1100 1604 1 chr3B.!!$F1 504
6 TraesCS1D01G017500 chr5D 120392263 120392851 588 True 680.0 680 87.6480 167 751 1 chr5D.!!$R2 584
7 TraesCS1D01G017500 chr5D 91343718 91344218 500 True 394.0 394 81.2250 2229 2723 1 chr5D.!!$R1 494
8 TraesCS1D01G017500 chr1B 608840072 608840677 605 True 680.0 680 87.3150 160 751 1 chr1B.!!$R1 591
9 TraesCS1D01G017500 chr1B 673502315 673502907 592 True 669.0 669 87.4160 167 747 1 chr1B.!!$R2 580
10 TraesCS1D01G017500 chr5A 395878852 395879453 601 False 678.0 678 87.3960 164 751 1 chr5A.!!$F1 587
11 TraesCS1D01G017500 chr4B 648840505 648841098 593 True 641.0 641 86.4090 166 751 1 chr4B.!!$R1 585
12 TraesCS1D01G017500 chr7B 654863589 654864183 594 True 614.0 614 85.4760 160 751 1 chr7B.!!$R1 591
13 TraesCS1D01G017500 chr7B 559677197 559677700 503 False 448.0 448 83.0710 2226 2721 1 chr7B.!!$F2 495
14 TraesCS1D01G017500 chr3A 584952209 584952717 508 True 433.0 433 82.5920 2225 2723 1 chr3A.!!$R2 498
15 TraesCS1D01G017500 chr5B 546834187 546834695 508 False 403.0 403 81.3730 2227 2723 1 chr5B.!!$F1 496

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
115 118 1.610554 GCCTTCATGCAACCATGGCT 61.611 55.0 13.04 0.0 47.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 2077 0.036765 TCATTCGACAAACCGGGGAG 60.037 55.0 6.32 0.0 0.0 4.3 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
26 27 7.615365 TGTTCCTACTAAATCCTTCCTACGTTA 59.385 37.037 0.00 0.00 0.00 3.18
115 118 1.610554 GCCTTCATGCAACCATGGCT 61.611 55.000 13.04 0.00 47.00 4.75
189 192 4.074799 TCTGGAAAACCAGATCCTAGGA 57.925 45.455 15.46 15.46 41.27 2.94
255 258 3.685058 GATGCCTTCATCAAAGTAACGC 58.315 45.455 0.81 0.00 46.44 4.84
301 328 2.851263 TTCACCGGCAACTATGTCTT 57.149 45.000 0.00 0.00 0.00 3.01
357 396 2.427540 GATCCGATCACCCAGCCTCG 62.428 65.000 3.33 0.00 0.00 4.63
492 532 2.995574 ACGTAACGGCAGCCTCCT 60.996 61.111 10.54 0.00 0.00 3.69
640 686 1.623311 TCGCAAGGAGATCCAAGTCAA 59.377 47.619 0.92 0.00 38.89 3.18
790 839 9.378504 AGTCTTATCTCAATATCTTGATGAGGT 57.621 33.333 2.53 0.00 40.52 3.85
920 973 5.708230 GTGGTGGTTGGAATGTCTAACAATA 59.292 40.000 6.79 0.00 39.27 1.90
1018 1071 0.249489 CGAGCCCCTACATACACAGC 60.249 60.000 0.00 0.00 0.00 4.40
1050 1103 1.137675 TCTGATCGCCATGACTTCCTG 59.862 52.381 0.00 0.00 0.00 3.86
1234 1293 2.792599 GTCGGAGTGCTCGACGAT 59.207 61.111 0.00 0.00 45.53 3.73
1274 1333 0.173481 CCCGAGAAACTCATCGCTGA 59.827 55.000 0.00 0.00 37.61 4.26
1632 1694 6.877611 ACTGTTAATTGTTACTGGGAACTG 57.122 37.500 0.00 0.00 0.00 3.16
1643 1709 4.993705 ACTGGGAACTGGATTAAACTGA 57.006 40.909 0.00 0.00 0.00 3.41
1655 1721 9.520515 ACTGGATTAAACTGAACTTATGTGATT 57.479 29.630 0.00 0.00 0.00 2.57
1662 1728 7.986085 AACTGAACTTATGTGATTAAGCACT 57.014 32.000 23.17 12.06 39.49 4.40
1678 1744 1.849823 ACTGGAGCTGGAGGCCTTT 60.850 57.895 6.77 0.00 43.05 3.11
1682 1748 1.682257 GAGCTGGAGGCCTTTCTGT 59.318 57.895 6.77 0.00 43.05 3.41
1687 1753 1.301293 GGAGGCCTTTCTGTCCCAG 59.699 63.158 6.77 0.00 0.00 4.45
1688 1754 1.201429 GGAGGCCTTTCTGTCCCAGA 61.201 60.000 6.77 0.00 38.87 3.86
1689 1755 0.251634 GAGGCCTTTCTGTCCCAGAG 59.748 60.000 6.77 0.00 41.75 3.35
1690 1756 1.377856 GGCCTTTCTGTCCCAGAGC 60.378 63.158 0.00 0.00 41.75 4.09
1691 1757 1.682257 GCCTTTCTGTCCCAGAGCT 59.318 57.895 0.00 0.00 41.75 4.09
1692 1758 0.676151 GCCTTTCTGTCCCAGAGCTG 60.676 60.000 0.00 0.00 41.75 4.24
1702 1768 3.274393 CCAGAGCTGGCGTATGTAC 57.726 57.895 3.18 0.00 44.73 2.90
1703 1769 0.747255 CCAGAGCTGGCGTATGTACT 59.253 55.000 3.18 0.00 44.73 2.73
1704 1770 1.269309 CCAGAGCTGGCGTATGTACTC 60.269 57.143 3.18 0.00 44.73 2.59
1705 1771 1.405463 CAGAGCTGGCGTATGTACTCA 59.595 52.381 0.00 0.00 0.00 3.41
1707 1773 2.695666 AGAGCTGGCGTATGTACTCAAT 59.304 45.455 0.00 0.00 0.00 2.57
1710 1776 3.889538 AGCTGGCGTATGTACTCAATAGA 59.110 43.478 0.00 0.00 0.00 1.98
1723 1793 4.848357 ACTCAATAGACATTGTTCCCTGG 58.152 43.478 0.00 0.00 41.96 4.45
1725 1795 5.014123 ACTCAATAGACATTGTTCCCTGGAA 59.986 40.000 0.00 0.00 41.96 3.53
1726 1796 6.078456 TCAATAGACATTGTTCCCTGGAAT 57.922 37.500 1.26 0.00 41.96 3.01
1728 1798 7.638444 TCAATAGACATTGTTCCCTGGAATAA 58.362 34.615 10.05 10.05 41.96 1.40
1729 1799 7.775093 TCAATAGACATTGTTCCCTGGAATAAG 59.225 37.037 12.68 8.14 41.96 1.73
1730 1800 4.273318 AGACATTGTTCCCTGGAATAAGC 58.727 43.478 12.68 6.11 38.31 3.09
1731 1801 4.018050 AGACATTGTTCCCTGGAATAAGCT 60.018 41.667 12.68 7.84 38.31 3.74
1732 1802 4.273318 ACATTGTTCCCTGGAATAAGCTC 58.727 43.478 12.68 0.00 38.31 4.09
1734 1804 1.300481 GTTCCCTGGAATAAGCTCGC 58.700 55.000 1.26 0.00 36.45 5.03
1735 1805 1.134371 GTTCCCTGGAATAAGCTCGCT 60.134 52.381 1.26 0.00 36.45 4.93
1736 1806 0.465705 TCCCTGGAATAAGCTCGCTG 59.534 55.000 0.00 0.00 0.00 5.18
1737 1807 1.162800 CCCTGGAATAAGCTCGCTGC 61.163 60.000 0.00 0.00 43.29 5.25
1746 1816 2.185350 GCTCGCTGCTCCTGCTAA 59.815 61.111 0.00 0.00 40.48 3.09
1747 1817 2.170434 GCTCGCTGCTCCTGCTAAC 61.170 63.158 0.00 0.00 40.48 2.34
1748 1818 1.520342 CTCGCTGCTCCTGCTAACC 60.520 63.158 0.00 0.00 40.48 2.85
1749 1819 1.954362 CTCGCTGCTCCTGCTAACCT 61.954 60.000 0.00 0.00 40.48 3.50
1750 1820 1.078848 CGCTGCTCCTGCTAACCTT 60.079 57.895 0.00 0.00 40.48 3.50
1751 1821 1.086634 CGCTGCTCCTGCTAACCTTC 61.087 60.000 0.00 0.00 40.48 3.46
1752 1822 0.251634 GCTGCTCCTGCTAACCTTCT 59.748 55.000 0.00 0.00 40.48 2.85
1753 1823 1.339535 GCTGCTCCTGCTAACCTTCTT 60.340 52.381 0.00 0.00 40.48 2.52
1760 1830 5.596845 CTCCTGCTAACCTTCTTGATCTAC 58.403 45.833 0.00 0.00 0.00 2.59
1768 1838 7.604545 GCTAACCTTCTTGATCTACTCAGTTTT 59.395 37.037 0.00 0.00 34.68 2.43
1844 1919 9.672086 CATACGTTCCAAAGAGATTTGTTTTTA 57.328 29.630 0.00 0.00 0.00 1.52
1867 1942 6.727824 ATGTATCACTACTTGAAGTTGTGC 57.272 37.500 27.17 17.42 46.51 4.57
1868 1943 4.684242 TGTATCACTACTTGAAGTTGTGCG 59.316 41.667 27.17 11.56 46.51 5.34
1869 1944 3.446310 TCACTACTTGAAGTTGTGCGA 57.554 42.857 27.17 13.88 46.51 5.10
1870 1945 3.381045 TCACTACTTGAAGTTGTGCGAG 58.619 45.455 27.17 11.08 46.51 5.03
1871 1946 2.476619 CACTACTTGAAGTTGTGCGAGG 59.523 50.000 22.66 3.90 42.85 4.63
1872 1947 2.102588 ACTACTTGAAGTTGTGCGAGGT 59.897 45.455 11.42 0.00 33.15 3.85
1873 1948 2.902705 ACTTGAAGTTGTGCGAGGTA 57.097 45.000 0.00 0.00 0.00 3.08
1874 1949 3.402628 ACTTGAAGTTGTGCGAGGTAT 57.597 42.857 0.00 0.00 0.00 2.73
1875 1950 3.067106 ACTTGAAGTTGTGCGAGGTATG 58.933 45.455 0.00 0.00 0.00 2.39
1876 1951 2.093306 TGAAGTTGTGCGAGGTATGG 57.907 50.000 0.00 0.00 0.00 2.74
1877 1952 0.727398 GAAGTTGTGCGAGGTATGGC 59.273 55.000 0.00 0.00 0.00 4.40
1878 1953 0.036164 AAGTTGTGCGAGGTATGGCA 59.964 50.000 0.00 0.00 37.88 4.92
1879 1954 0.391661 AGTTGTGCGAGGTATGGCAG 60.392 55.000 0.00 0.00 41.16 4.85
1880 1955 0.673644 GTTGTGCGAGGTATGGCAGT 60.674 55.000 0.00 0.00 41.16 4.40
1881 1956 0.899019 TTGTGCGAGGTATGGCAGTA 59.101 50.000 0.00 0.00 41.16 2.74
1882 1957 0.899019 TGTGCGAGGTATGGCAGTAA 59.101 50.000 0.00 0.00 41.16 2.24
1883 1958 1.287425 GTGCGAGGTATGGCAGTAAC 58.713 55.000 0.00 0.00 41.16 2.50
1884 1959 0.899019 TGCGAGGTATGGCAGTAACA 59.101 50.000 0.00 0.00 34.97 2.41
1885 1960 1.484653 TGCGAGGTATGGCAGTAACAT 59.515 47.619 0.00 0.00 34.97 2.71
1886 1961 1.867233 GCGAGGTATGGCAGTAACATG 59.133 52.381 0.00 0.00 0.00 3.21
1887 1962 1.867233 CGAGGTATGGCAGTAACATGC 59.133 52.381 0.00 0.00 45.74 4.06
1888 1963 2.483714 CGAGGTATGGCAGTAACATGCT 60.484 50.000 0.00 0.00 45.75 3.79
1889 1964 3.545703 GAGGTATGGCAGTAACATGCTT 58.454 45.455 0.00 0.00 45.75 3.91
1890 1965 3.545703 AGGTATGGCAGTAACATGCTTC 58.454 45.455 0.00 0.00 45.75 3.86
1891 1966 3.054434 AGGTATGGCAGTAACATGCTTCA 60.054 43.478 0.00 0.00 45.75 3.02
1892 1967 3.885297 GGTATGGCAGTAACATGCTTCAT 59.115 43.478 0.00 0.00 45.75 2.57
1893 1968 4.339247 GGTATGGCAGTAACATGCTTCATT 59.661 41.667 0.00 0.00 45.75 2.57
1894 1969 5.163519 GGTATGGCAGTAACATGCTTCATTT 60.164 40.000 0.00 0.00 45.75 2.32
1895 1970 4.870123 TGGCAGTAACATGCTTCATTTT 57.130 36.364 0.00 0.00 45.75 1.82
1896 1971 4.808558 TGGCAGTAACATGCTTCATTTTC 58.191 39.130 0.00 0.00 45.75 2.29
1897 1972 4.523943 TGGCAGTAACATGCTTCATTTTCT 59.476 37.500 0.00 0.00 45.75 2.52
1898 1973 5.010922 TGGCAGTAACATGCTTCATTTTCTT 59.989 36.000 0.00 0.00 45.75 2.52
1899 1974 5.574443 GGCAGTAACATGCTTCATTTTCTTC 59.426 40.000 0.00 0.00 45.75 2.87
1900 1975 6.151691 GCAGTAACATGCTTCATTTTCTTCA 58.848 36.000 0.00 0.00 43.07 3.02
1901 1976 6.810182 GCAGTAACATGCTTCATTTTCTTCAT 59.190 34.615 0.00 0.00 43.07 2.57
1902 1977 7.008992 GCAGTAACATGCTTCATTTTCTTCATC 59.991 37.037 0.00 0.00 43.07 2.92
1903 1978 8.242053 CAGTAACATGCTTCATTTTCTTCATCT 58.758 33.333 0.00 0.00 0.00 2.90
1904 1979 8.800332 AGTAACATGCTTCATTTTCTTCATCTT 58.200 29.630 0.00 0.00 0.00 2.40
1905 1980 9.415544 GTAACATGCTTCATTTTCTTCATCTTT 57.584 29.630 0.00 0.00 0.00 2.52
1906 1981 8.897872 AACATGCTTCATTTTCTTCATCTTTT 57.102 26.923 0.00 0.00 0.00 2.27
1907 1982 8.897872 ACATGCTTCATTTTCTTCATCTTTTT 57.102 26.923 0.00 0.00 0.00 1.94
1934 2009 3.913855 TTCCTGGGAACACTGCAAA 57.086 47.368 0.00 0.00 35.60 3.68
1935 2010 2.380064 TTCCTGGGAACACTGCAAAT 57.620 45.000 0.00 0.00 35.60 2.32
1936 2011 1.619654 TCCTGGGAACACTGCAAATG 58.380 50.000 0.00 0.00 35.60 2.32
1937 2012 1.144708 TCCTGGGAACACTGCAAATGA 59.855 47.619 4.68 0.00 35.60 2.57
1938 2013 1.270550 CCTGGGAACACTGCAAATGAC 59.729 52.381 4.68 0.00 35.60 3.06
1939 2014 1.270550 CTGGGAACACTGCAAATGACC 59.729 52.381 4.68 7.17 35.60 4.02
1940 2015 0.603065 GGGAACACTGCAAATGACCC 59.397 55.000 15.72 15.72 33.12 4.46
1941 2016 1.327303 GGAACACTGCAAATGACCCA 58.673 50.000 4.68 0.00 0.00 4.51
1942 2017 1.895131 GGAACACTGCAAATGACCCAT 59.105 47.619 4.68 0.00 0.00 4.00
1943 2018 2.299867 GGAACACTGCAAATGACCCATT 59.700 45.455 4.68 0.00 35.39 3.16
1944 2019 3.509575 GGAACACTGCAAATGACCCATTA 59.490 43.478 4.68 0.00 32.43 1.90
1945 2020 4.160252 GGAACACTGCAAATGACCCATTAT 59.840 41.667 4.68 0.00 32.43 1.28
1946 2021 5.359576 GGAACACTGCAAATGACCCATTATA 59.640 40.000 4.68 0.00 32.43 0.98
1947 2022 6.455360 AACACTGCAAATGACCCATTATAG 57.545 37.500 4.68 0.00 32.43 1.31
1948 2023 5.754782 ACACTGCAAATGACCCATTATAGA 58.245 37.500 4.68 0.00 32.43 1.98
1949 2024 6.367983 ACACTGCAAATGACCCATTATAGAT 58.632 36.000 4.68 0.00 32.43 1.98
1950 2025 6.488006 ACACTGCAAATGACCCATTATAGATC 59.512 38.462 4.68 0.00 32.43 2.75
1951 2026 6.006449 ACTGCAAATGACCCATTATAGATCC 58.994 40.000 0.00 0.00 32.43 3.36
1952 2027 6.183361 ACTGCAAATGACCCATTATAGATCCT 60.183 38.462 0.00 0.00 32.43 3.24
1953 2028 6.240894 TGCAAATGACCCATTATAGATCCTC 58.759 40.000 0.00 0.00 32.43 3.71
1954 2029 5.352569 GCAAATGACCCATTATAGATCCTCG 59.647 44.000 0.00 0.00 32.43 4.63
1955 2030 6.467677 CAAATGACCCATTATAGATCCTCGT 58.532 40.000 0.00 0.00 32.43 4.18
1956 2031 7.611770 CAAATGACCCATTATAGATCCTCGTA 58.388 38.462 0.00 0.00 32.43 3.43
1957 2032 7.979786 AATGACCCATTATAGATCCTCGTAT 57.020 36.000 0.00 0.00 31.77 3.06
1958 2033 7.979786 ATGACCCATTATAGATCCTCGTATT 57.020 36.000 0.00 0.00 0.00 1.89
1959 2034 7.406031 TGACCCATTATAGATCCTCGTATTC 57.594 40.000 0.00 0.00 0.00 1.75
1960 2035 6.951778 TGACCCATTATAGATCCTCGTATTCA 59.048 38.462 0.00 0.00 0.00 2.57
1961 2036 7.453439 TGACCCATTATAGATCCTCGTATTCAA 59.547 37.037 0.00 0.00 0.00 2.69
1962 2037 7.841956 ACCCATTATAGATCCTCGTATTCAAG 58.158 38.462 0.00 0.00 0.00 3.02
1963 2038 7.674348 ACCCATTATAGATCCTCGTATTCAAGA 59.326 37.037 0.00 0.00 0.00 3.02
1964 2039 8.194104 CCCATTATAGATCCTCGTATTCAAGAG 58.806 40.741 0.00 0.00 0.00 2.85
1970 2045 1.841450 CTCGTATTCAAGAGGGCGAC 58.159 55.000 0.00 0.00 0.00 5.19
1971 2046 1.405821 CTCGTATTCAAGAGGGCGACT 59.594 52.381 0.00 0.00 0.00 4.18
1972 2047 1.404391 TCGTATTCAAGAGGGCGACTC 59.596 52.381 0.00 0.00 46.98 3.36
1981 2056 2.011540 GAGGGCGACTCTAAACTTGG 57.988 55.000 0.00 0.00 43.14 3.61
1982 2057 1.275573 GAGGGCGACTCTAAACTTGGT 59.724 52.381 0.00 0.00 43.14 3.67
1983 2058 1.002087 AGGGCGACTCTAAACTTGGTG 59.998 52.381 0.00 0.00 0.00 4.17
1984 2059 0.796927 GGCGACTCTAAACTTGGTGC 59.203 55.000 0.00 0.00 0.00 5.01
1985 2060 1.608283 GGCGACTCTAAACTTGGTGCT 60.608 52.381 0.00 0.00 0.00 4.40
1986 2061 1.461127 GCGACTCTAAACTTGGTGCTG 59.539 52.381 0.00 0.00 0.00 4.41
1987 2062 2.069273 CGACTCTAAACTTGGTGCTGG 58.931 52.381 0.00 0.00 0.00 4.85
1988 2063 2.427506 GACTCTAAACTTGGTGCTGGG 58.572 52.381 0.00 0.00 0.00 4.45
1989 2064 2.038557 GACTCTAAACTTGGTGCTGGGA 59.961 50.000 0.00 0.00 0.00 4.37
1990 2065 2.644798 ACTCTAAACTTGGTGCTGGGAT 59.355 45.455 0.00 0.00 0.00 3.85
1991 2066 3.074538 ACTCTAAACTTGGTGCTGGGATT 59.925 43.478 0.00 0.00 0.00 3.01
1992 2067 3.420893 TCTAAACTTGGTGCTGGGATTG 58.579 45.455 0.00 0.00 0.00 2.67
1993 2068 2.086610 AAACTTGGTGCTGGGATTGT 57.913 45.000 0.00 0.00 0.00 2.71
1994 2069 2.969821 AACTTGGTGCTGGGATTGTA 57.030 45.000 0.00 0.00 0.00 2.41
1995 2070 2.200373 ACTTGGTGCTGGGATTGTAC 57.800 50.000 0.00 0.00 0.00 2.90
1996 2071 1.423541 ACTTGGTGCTGGGATTGTACA 59.576 47.619 0.00 0.00 0.00 2.90
1997 2072 2.041620 ACTTGGTGCTGGGATTGTACAT 59.958 45.455 0.00 0.00 0.00 2.29
1998 2073 2.418368 TGGTGCTGGGATTGTACATC 57.582 50.000 0.00 0.00 0.00 3.06
1999 2074 1.064758 TGGTGCTGGGATTGTACATCC 60.065 52.381 13.11 13.11 37.47 3.51
2000 2075 1.212935 GGTGCTGGGATTGTACATCCT 59.787 52.381 18.10 0.00 38.26 3.24
2001 2076 2.438021 GGTGCTGGGATTGTACATCCTA 59.562 50.000 18.10 13.71 38.26 2.94
2002 2077 3.467803 GTGCTGGGATTGTACATCCTAC 58.532 50.000 18.10 11.41 38.26 3.18
2003 2078 3.134804 GTGCTGGGATTGTACATCCTACT 59.865 47.826 18.10 0.00 38.26 2.57
2004 2079 3.388024 TGCTGGGATTGTACATCCTACTC 59.612 47.826 18.10 9.45 38.26 2.59
2005 2080 3.244249 GCTGGGATTGTACATCCTACTCC 60.244 52.174 18.10 9.20 38.26 3.85
2006 2081 3.314693 TGGGATTGTACATCCTACTCCC 58.685 50.000 18.10 15.60 41.07 4.30
2007 2082 2.638363 GGGATTGTACATCCTACTCCCC 59.362 54.545 18.10 8.23 38.26 4.81
2008 2083 2.299297 GGATTGTACATCCTACTCCCCG 59.701 54.545 13.85 0.00 35.36 5.73
2009 2084 1.784358 TTGTACATCCTACTCCCCGG 58.216 55.000 0.00 0.00 0.00 5.73
2010 2085 0.632835 TGTACATCCTACTCCCCGGT 59.367 55.000 0.00 0.00 0.00 5.28
2011 2086 1.007479 TGTACATCCTACTCCCCGGTT 59.993 52.381 0.00 0.00 0.00 4.44
2012 2087 2.113807 GTACATCCTACTCCCCGGTTT 58.886 52.381 0.00 0.00 0.00 3.27
2013 2088 0.909623 ACATCCTACTCCCCGGTTTG 59.090 55.000 0.00 0.00 0.00 2.93
2014 2089 0.909623 CATCCTACTCCCCGGTTTGT 59.090 55.000 0.00 0.00 0.00 2.83
2015 2090 1.134491 CATCCTACTCCCCGGTTTGTC 60.134 57.143 0.00 0.00 0.00 3.18
2016 2091 1.217244 CCTACTCCCCGGTTTGTCG 59.783 63.158 0.00 0.00 0.00 4.35
2017 2092 1.252904 CCTACTCCCCGGTTTGTCGA 61.253 60.000 0.00 0.00 0.00 4.20
2018 2093 0.604578 CTACTCCCCGGTTTGTCGAA 59.395 55.000 0.00 0.00 0.00 3.71
2019 2094 1.206371 CTACTCCCCGGTTTGTCGAAT 59.794 52.381 0.00 0.00 0.00 3.34
2020 2095 0.321298 ACTCCCCGGTTTGTCGAATG 60.321 55.000 0.00 0.00 0.00 2.67
2021 2096 0.036765 CTCCCCGGTTTGTCGAATGA 60.037 55.000 0.00 0.00 0.00 2.57
2022 2097 0.036765 TCCCCGGTTTGTCGAATGAG 60.037 55.000 0.00 0.00 0.00 2.90
2023 2098 1.644786 CCCCGGTTTGTCGAATGAGC 61.645 60.000 0.00 0.00 0.00 4.26
2024 2099 0.673644 CCCGGTTTGTCGAATGAGCT 60.674 55.000 0.00 0.00 0.00 4.09
2025 2100 1.404986 CCCGGTTTGTCGAATGAGCTA 60.405 52.381 0.00 0.00 0.00 3.32
2026 2101 1.927174 CCGGTTTGTCGAATGAGCTAG 59.073 52.381 0.00 0.00 0.00 3.42
2027 2102 2.607187 CGGTTTGTCGAATGAGCTAGT 58.393 47.619 0.00 0.00 0.00 2.57
2028 2103 2.599082 CGGTTTGTCGAATGAGCTAGTC 59.401 50.000 0.00 0.00 0.00 2.59
2029 2104 3.673594 CGGTTTGTCGAATGAGCTAGTCT 60.674 47.826 0.00 0.00 0.00 3.24
2030 2105 3.860536 GGTTTGTCGAATGAGCTAGTCTC 59.139 47.826 7.10 7.10 42.23 3.36
2031 2106 4.381079 GGTTTGTCGAATGAGCTAGTCTCT 60.381 45.833 13.14 0.00 42.38 3.10
2032 2107 5.164954 GTTTGTCGAATGAGCTAGTCTCTT 58.835 41.667 13.14 6.34 42.38 2.85
2033 2108 6.323266 GTTTGTCGAATGAGCTAGTCTCTTA 58.677 40.000 13.14 0.00 42.38 2.10
2034 2109 6.510879 TTGTCGAATGAGCTAGTCTCTTAA 57.489 37.500 13.14 0.00 42.38 1.85
2035 2110 6.701145 TGTCGAATGAGCTAGTCTCTTAAT 57.299 37.500 13.14 0.02 42.38 1.40
2036 2111 7.101652 TGTCGAATGAGCTAGTCTCTTAATT 57.898 36.000 13.14 6.76 42.38 1.40
2037 2112 8.221965 TGTCGAATGAGCTAGTCTCTTAATTA 57.778 34.615 13.14 0.00 42.38 1.40
2038 2113 8.346300 TGTCGAATGAGCTAGTCTCTTAATTAG 58.654 37.037 13.14 7.25 42.38 1.73
2039 2114 8.347035 GTCGAATGAGCTAGTCTCTTAATTAGT 58.653 37.037 13.14 0.00 42.38 2.24
2040 2115 8.561212 TCGAATGAGCTAGTCTCTTAATTAGTC 58.439 37.037 13.14 3.14 42.38 2.59
2041 2116 7.806014 CGAATGAGCTAGTCTCTTAATTAGTCC 59.194 40.741 13.14 0.00 42.38 3.85
2042 2117 6.621316 TGAGCTAGTCTCTTAATTAGTCCG 57.379 41.667 13.14 0.00 42.38 4.79
2043 2118 6.354938 TGAGCTAGTCTCTTAATTAGTCCGA 58.645 40.000 13.14 0.00 42.38 4.55
2044 2119 6.999272 TGAGCTAGTCTCTTAATTAGTCCGAT 59.001 38.462 13.14 0.00 42.38 4.18
2045 2120 7.041030 TGAGCTAGTCTCTTAATTAGTCCGATG 60.041 40.741 13.14 0.00 42.38 3.84
2046 2121 6.207810 AGCTAGTCTCTTAATTAGTCCGATGG 59.792 42.308 0.00 0.00 0.00 3.51
2080 2155 1.651987 ATGTTCAGGTCAATACGGCG 58.348 50.000 4.80 4.80 0.00 6.46
2081 2156 0.390603 TGTTCAGGTCAATACGGCGG 60.391 55.000 13.24 0.00 0.00 6.13
2082 2157 1.448893 TTCAGGTCAATACGGCGGC 60.449 57.895 13.24 0.00 0.00 6.53
2098 2173 1.519751 CGGCCGGGTTGATTTTCACA 61.520 55.000 20.10 0.00 0.00 3.58
2101 2176 1.200020 GCCGGGTTGATTTTCACAGAG 59.800 52.381 2.18 0.00 0.00 3.35
2120 2195 8.296713 TCACAGAGTTAAATAAATGTTTGAGCC 58.703 33.333 0.00 0.00 0.00 4.70
2136 2224 2.736531 CCCAACCTGCAACAAGGC 59.263 61.111 0.00 0.00 41.46 4.35
2190 2278 4.826556 TCTTTGAAAGGAGAAGAGCTAGC 58.173 43.478 6.62 6.62 0.00 3.42
2199 2287 0.460311 GAAGAGCTAGCCCGCTGTAA 59.540 55.000 12.13 0.00 41.08 2.41
2213 2301 3.059884 CGCTGTAAATATGGCATCGTCT 58.940 45.455 1.65 0.00 0.00 4.18
2214 2302 3.120889 CGCTGTAAATATGGCATCGTCTG 60.121 47.826 1.65 0.00 0.00 3.51
2215 2303 3.187227 GCTGTAAATATGGCATCGTCTGG 59.813 47.826 1.65 0.00 0.00 3.86
2232 2320 5.126222 TCGTCTGGCATTCATATATCCTCTC 59.874 44.000 0.00 0.00 0.00 3.20
2260 2348 8.312896 ACACTAAGCTTCTTAGTTTTAAGAGC 57.687 34.615 14.54 9.03 44.46 4.09
2269 2357 8.691661 TTCTTAGTTTTAAGAGCCTCACATTT 57.308 30.769 0.00 0.00 44.46 2.32
2291 2379 7.466746 TTTAATTGAGGTCTCCCATTGAAAG 57.533 36.000 0.00 0.00 0.00 2.62
2292 2380 2.496899 TGAGGTCTCCCATTGAAAGC 57.503 50.000 0.00 0.00 0.00 3.51
2294 2382 0.984230 AGGTCTCCCATTGAAAGCGA 59.016 50.000 0.00 0.00 0.00 4.93
2312 2400 1.337823 CGAGTCACCCGATTTTGACCT 60.338 52.381 0.00 0.00 42.73 3.85
2395 2483 8.522830 TCTTAATTTTGAAGGCCTCACAATTAG 58.477 33.333 22.01 18.52 42.99 1.73
2424 2513 6.314784 GTCTTCAATTTAGAATTGGGTCACG 58.685 40.000 12.06 0.00 0.00 4.35
2456 2545 4.705023 ACCGGGTCAATAATTTCTCAAAGG 59.295 41.667 6.32 0.00 0.00 3.11
2463 2552 6.601217 GTCAATAATTTCTCAAAGGGCTCTCT 59.399 38.462 0.00 0.00 0.00 3.10
2470 2559 3.197333 TCTCAAAGGGCTCTCTCATTCAG 59.803 47.826 0.00 0.00 0.00 3.02
2473 2562 4.077822 CAAAGGGCTCTCTCATTCAGTTT 58.922 43.478 0.00 0.00 0.00 2.66
2541 2631 9.492973 CAGTTGAGGTATTCAATTTTGGATTTT 57.507 29.630 0.00 0.00 46.85 1.82
2700 2804 1.296056 ACCGACGCAGAAATTTCCCG 61.296 55.000 20.68 20.68 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.010552 CAGAACAGATGAAATAACGTAGGAAGG 59.989 40.741 0.00 0.00 0.00 3.46
26 27 2.086869 CGGCCACAGAACAGATGAAAT 58.913 47.619 2.24 0.00 0.00 2.17
115 118 5.690865 ACAGATACAACAAAAGGTTCCTGA 58.309 37.500 0.00 0.00 37.72 3.86
151 154 9.003658 GTTTTCCAGATCAGAGTGAAAGAATAA 57.996 33.333 0.00 0.00 0.00 1.40
189 192 3.338250 TGCTGCTCCGGGGGAAAT 61.338 61.111 1.90 0.00 0.00 2.17
362 401 0.107508 CTCCTACGTCGGAGGTGGTA 60.108 60.000 24.80 2.78 45.53 3.25
383 422 0.818040 GATAATGGCGGTGGTGGTCC 60.818 60.000 0.00 0.00 0.00 4.46
417 456 1.216710 CTGAAGCACTCCGGGTCTC 59.783 63.158 0.00 0.00 0.00 3.36
616 661 0.606096 TTGGATCTCCTTGCGACGAA 59.394 50.000 0.00 0.00 36.82 3.85
735 781 3.077556 AACCGCGCATCTCCCTCT 61.078 61.111 8.75 0.00 0.00 3.69
790 839 9.787435 AATTAGTTGTACTGGAAAAGTATGTGA 57.213 29.630 0.00 0.00 43.30 3.58
821 870 2.826725 AGTACAAAAGCTAGCTCGGTCT 59.173 45.455 19.65 12.02 0.00 3.85
1018 1071 1.781555 GATCAGACCAACGTGTGCG 59.218 57.895 0.00 0.00 44.93 5.34
1050 1103 0.813821 GAGGGAAAGCAACATCCAGC 59.186 55.000 0.00 0.00 37.46 4.85
1274 1333 3.782443 GGACTGGAACCGGCCGAT 61.782 66.667 30.73 16.01 0.00 4.18
1380 1439 3.572447 CTGCCCACCATGACCAGCA 62.572 63.158 0.00 0.00 0.00 4.41
1554 1613 0.749454 ATCCATCTTCGCCAACAGGC 60.749 55.000 0.00 0.00 45.19 4.85
1564 1623 1.672881 CGTTTCCAGGCATCCATCTTC 59.327 52.381 0.00 0.00 0.00 2.87
1643 1709 5.355350 GCTCCAGTGCTTAATCACATAAGTT 59.645 40.000 11.73 0.00 39.35 2.66
1655 1721 1.903877 GCCTCCAGCTCCAGTGCTTA 61.904 60.000 0.00 0.00 41.98 3.09
1658 1724 4.792804 GGCCTCCAGCTCCAGTGC 62.793 72.222 0.00 0.00 43.05 4.40
1660 1726 1.846712 GAAAGGCCTCCAGCTCCAGT 61.847 60.000 5.23 0.00 43.05 4.00
1662 1728 1.539869 AGAAAGGCCTCCAGCTCCA 60.540 57.895 5.23 0.00 43.05 3.86
1687 1753 2.579207 TTGAGTACATACGCCAGCTC 57.421 50.000 0.00 0.00 0.00 4.09
1688 1754 3.889538 TCTATTGAGTACATACGCCAGCT 59.110 43.478 0.00 0.00 0.00 4.24
1689 1755 3.982058 GTCTATTGAGTACATACGCCAGC 59.018 47.826 0.00 0.00 0.00 4.85
1690 1756 5.183014 TGTCTATTGAGTACATACGCCAG 57.817 43.478 0.00 0.00 0.00 4.85
1691 1757 5.784578 ATGTCTATTGAGTACATACGCCA 57.215 39.130 0.00 0.00 32.21 5.69
1692 1758 5.983720 ACAATGTCTATTGAGTACATACGCC 59.016 40.000 6.98 0.00 45.21 5.68
1694 1760 7.169308 GGGAACAATGTCTATTGAGTACATACG 59.831 40.741 6.98 0.00 45.21 3.06
1695 1761 8.204836 AGGGAACAATGTCTATTGAGTACATAC 58.795 37.037 6.98 0.00 45.21 2.39
1696 1762 8.204160 CAGGGAACAATGTCTATTGAGTACATA 58.796 37.037 6.98 0.00 45.21 2.29
1697 1763 7.050377 CAGGGAACAATGTCTATTGAGTACAT 58.950 38.462 6.98 0.00 45.21 2.29
1698 1764 6.406370 CAGGGAACAATGTCTATTGAGTACA 58.594 40.000 6.98 0.00 45.21 2.90
1699 1765 5.817816 CCAGGGAACAATGTCTATTGAGTAC 59.182 44.000 6.98 0.00 45.21 2.73
1700 1766 5.724370 TCCAGGGAACAATGTCTATTGAGTA 59.276 40.000 6.98 0.00 45.21 2.59
1701 1767 4.536090 TCCAGGGAACAATGTCTATTGAGT 59.464 41.667 6.98 0.00 45.21 3.41
1702 1768 5.102953 TCCAGGGAACAATGTCTATTGAG 57.897 43.478 6.98 0.00 45.21 3.02
1703 1769 5.512942 TTCCAGGGAACAATGTCTATTGA 57.487 39.130 6.98 0.00 45.21 2.57
1705 1771 6.547510 GCTTATTCCAGGGAACAATGTCTATT 59.452 38.462 2.23 0.00 36.91 1.73
1707 1773 5.191722 AGCTTATTCCAGGGAACAATGTCTA 59.808 40.000 2.23 0.00 36.91 2.59
1710 1776 4.273318 GAGCTTATTCCAGGGAACAATGT 58.727 43.478 2.23 0.00 36.91 2.71
1729 1799 2.170434 GTTAGCAGGAGCAGCGAGC 61.170 63.158 0.00 0.00 45.49 5.03
1730 1800 1.520342 GGTTAGCAGGAGCAGCGAG 60.520 63.158 0.00 0.00 45.49 5.03
1731 1801 1.544825 AAGGTTAGCAGGAGCAGCGA 61.545 55.000 0.00 0.00 45.49 4.93
1732 1802 1.078848 AAGGTTAGCAGGAGCAGCG 60.079 57.895 0.00 0.00 45.49 5.18
1734 1804 2.027745 TCAAGAAGGTTAGCAGGAGCAG 60.028 50.000 0.00 0.00 45.49 4.24
1735 1805 1.977854 TCAAGAAGGTTAGCAGGAGCA 59.022 47.619 0.00 0.00 45.49 4.26
1736 1806 2.770164 TCAAGAAGGTTAGCAGGAGC 57.230 50.000 0.00 0.00 42.56 4.70
1737 1807 4.751767 AGATCAAGAAGGTTAGCAGGAG 57.248 45.455 0.00 0.00 0.00 3.69
1738 1808 5.273208 AGTAGATCAAGAAGGTTAGCAGGA 58.727 41.667 0.00 0.00 0.00 3.86
1739 1809 5.127845 TGAGTAGATCAAGAAGGTTAGCAGG 59.872 44.000 0.00 0.00 34.02 4.85
1740 1810 6.127479 ACTGAGTAGATCAAGAAGGTTAGCAG 60.127 42.308 0.00 0.00 37.52 4.24
1741 1811 5.717178 ACTGAGTAGATCAAGAAGGTTAGCA 59.283 40.000 0.00 0.00 37.52 3.49
1742 1812 6.215495 ACTGAGTAGATCAAGAAGGTTAGC 57.785 41.667 0.00 0.00 37.52 3.09
1744 1814 9.924650 GTAAAACTGAGTAGATCAAGAAGGTTA 57.075 33.333 0.00 0.00 37.52 2.85
1745 1815 8.429641 TGTAAAACTGAGTAGATCAAGAAGGTT 58.570 33.333 0.00 0.00 37.52 3.50
1746 1816 7.963532 TGTAAAACTGAGTAGATCAAGAAGGT 58.036 34.615 0.00 0.00 37.52 3.50
1747 1817 9.442047 AATGTAAAACTGAGTAGATCAAGAAGG 57.558 33.333 0.00 0.00 37.52 3.46
1822 1896 8.574196 ACATAAAAACAAATCTCTTTGGAACG 57.426 30.769 3.42 0.00 44.97 3.95
1844 1919 5.348724 CGCACAACTTCAAGTAGTGATACAT 59.651 40.000 0.00 0.00 35.70 2.29
1858 1933 0.727398 GCCATACCTCGCACAACTTC 59.273 55.000 0.00 0.00 0.00 3.01
1865 1940 0.899019 TGTTACTGCCATACCTCGCA 59.101 50.000 0.00 0.00 0.00 5.10
1866 1941 1.867233 CATGTTACTGCCATACCTCGC 59.133 52.381 0.00 0.00 0.00 5.03
1867 1942 1.867233 GCATGTTACTGCCATACCTCG 59.133 52.381 0.00 0.00 36.10 4.63
1868 1943 3.199880 AGCATGTTACTGCCATACCTC 57.800 47.619 0.00 0.00 43.33 3.85
1869 1944 3.054434 TGAAGCATGTTACTGCCATACCT 60.054 43.478 0.00 0.00 43.33 3.08
1870 1945 3.278574 TGAAGCATGTTACTGCCATACC 58.721 45.455 0.00 0.00 43.33 2.73
1871 1946 5.505173 AATGAAGCATGTTACTGCCATAC 57.495 39.130 0.00 0.00 43.33 2.39
1872 1947 6.377996 AGAAAATGAAGCATGTTACTGCCATA 59.622 34.615 0.00 0.00 43.33 2.74
1873 1948 5.186409 AGAAAATGAAGCATGTTACTGCCAT 59.814 36.000 0.00 0.27 43.33 4.40
1874 1949 4.523943 AGAAAATGAAGCATGTTACTGCCA 59.476 37.500 0.00 0.00 43.33 4.92
1875 1950 5.064441 AGAAAATGAAGCATGTTACTGCC 57.936 39.130 0.00 0.00 43.33 4.85
1876 1951 6.151691 TGAAGAAAATGAAGCATGTTACTGC 58.848 36.000 0.00 0.00 42.62 4.40
1877 1952 8.242053 AGATGAAGAAAATGAAGCATGTTACTG 58.758 33.333 0.00 0.00 0.00 2.74
1878 1953 8.345724 AGATGAAGAAAATGAAGCATGTTACT 57.654 30.769 0.00 0.00 0.00 2.24
1879 1954 8.976986 AAGATGAAGAAAATGAAGCATGTTAC 57.023 30.769 0.00 0.00 0.00 2.50
1880 1955 9.985730 AAAAGATGAAGAAAATGAAGCATGTTA 57.014 25.926 0.00 0.00 0.00 2.41
1881 1956 8.897872 AAAAGATGAAGAAAATGAAGCATGTT 57.102 26.923 0.00 0.00 0.00 2.71
1882 1957 8.897872 AAAAAGATGAAGAAAATGAAGCATGT 57.102 26.923 0.00 0.00 0.00 3.21
1916 1991 1.962807 CATTTGCAGTGTTCCCAGGAA 59.037 47.619 0.00 0.00 0.00 3.36
1917 1992 1.144708 TCATTTGCAGTGTTCCCAGGA 59.855 47.619 0.00 0.00 0.00 3.86
1918 1993 1.270550 GTCATTTGCAGTGTTCCCAGG 59.729 52.381 0.00 0.00 0.00 4.45
1919 1994 1.270550 GGTCATTTGCAGTGTTCCCAG 59.729 52.381 0.00 0.00 0.00 4.45
1920 1995 1.327303 GGTCATTTGCAGTGTTCCCA 58.673 50.000 0.00 0.00 0.00 4.37
1921 1996 0.603065 GGGTCATTTGCAGTGTTCCC 59.397 55.000 15.12 15.12 0.00 3.97
1922 1997 1.327303 TGGGTCATTTGCAGTGTTCC 58.673 50.000 0.00 0.00 0.00 3.62
1923 1998 3.665745 AATGGGTCATTTGCAGTGTTC 57.334 42.857 0.00 0.00 28.76 3.18
1924 1999 6.186957 TCTATAATGGGTCATTTGCAGTGTT 58.813 36.000 0.00 0.00 35.54 3.32
1925 2000 5.754782 TCTATAATGGGTCATTTGCAGTGT 58.245 37.500 0.00 0.00 35.54 3.55
1926 2001 6.072286 GGATCTATAATGGGTCATTTGCAGTG 60.072 42.308 0.00 0.00 35.54 3.66
1927 2002 6.006449 GGATCTATAATGGGTCATTTGCAGT 58.994 40.000 0.00 0.00 35.54 4.40
1928 2003 6.243900 AGGATCTATAATGGGTCATTTGCAG 58.756 40.000 0.00 0.00 35.54 4.41
1929 2004 6.204852 AGGATCTATAATGGGTCATTTGCA 57.795 37.500 0.00 0.00 35.54 4.08
1930 2005 5.352569 CGAGGATCTATAATGGGTCATTTGC 59.647 44.000 0.00 0.00 35.54 3.68
1931 2006 6.467677 ACGAGGATCTATAATGGGTCATTTG 58.532 40.000 0.00 0.00 35.54 2.32
1932 2007 6.688073 ACGAGGATCTATAATGGGTCATTT 57.312 37.500 0.00 0.00 35.54 2.32
1933 2008 7.979786 ATACGAGGATCTATAATGGGTCATT 57.020 36.000 0.00 0.00 37.80 2.57
1934 2009 7.619698 TGAATACGAGGATCTATAATGGGTCAT 59.380 37.037 0.00 0.00 0.00 3.06
1935 2010 6.951778 TGAATACGAGGATCTATAATGGGTCA 59.048 38.462 0.00 0.00 0.00 4.02
1936 2011 7.406031 TGAATACGAGGATCTATAATGGGTC 57.594 40.000 0.00 0.00 0.00 4.46
1937 2012 7.674348 TCTTGAATACGAGGATCTATAATGGGT 59.326 37.037 0.00 0.00 0.00 4.51
1938 2013 8.067751 TCTTGAATACGAGGATCTATAATGGG 57.932 38.462 0.00 0.00 0.00 4.00
1950 2025 0.744874 TCGCCCTCTTGAATACGAGG 59.255 55.000 0.00 0.00 45.10 4.63
1951 2026 1.405821 AGTCGCCCTCTTGAATACGAG 59.594 52.381 0.00 0.00 0.00 4.18
1952 2027 1.404391 GAGTCGCCCTCTTGAATACGA 59.596 52.381 0.00 0.00 37.22 3.43
1953 2028 1.841450 GAGTCGCCCTCTTGAATACG 58.159 55.000 0.00 0.00 37.22 3.06
1962 2037 1.275573 ACCAAGTTTAGAGTCGCCCTC 59.724 52.381 0.00 0.00 40.80 4.30
1963 2038 1.002087 CACCAAGTTTAGAGTCGCCCT 59.998 52.381 0.00 0.00 0.00 5.19
1964 2039 1.439679 CACCAAGTTTAGAGTCGCCC 58.560 55.000 0.00 0.00 0.00 6.13
1965 2040 0.796927 GCACCAAGTTTAGAGTCGCC 59.203 55.000 0.00 0.00 0.00 5.54
1966 2041 1.461127 CAGCACCAAGTTTAGAGTCGC 59.539 52.381 0.00 0.00 0.00 5.19
1967 2042 2.069273 CCAGCACCAAGTTTAGAGTCG 58.931 52.381 0.00 0.00 0.00 4.18
1968 2043 2.038557 TCCCAGCACCAAGTTTAGAGTC 59.961 50.000 0.00 0.00 0.00 3.36
1969 2044 2.054799 TCCCAGCACCAAGTTTAGAGT 58.945 47.619 0.00 0.00 0.00 3.24
1970 2045 2.859165 TCCCAGCACCAAGTTTAGAG 57.141 50.000 0.00 0.00 0.00 2.43
1971 2046 3.181434 ACAATCCCAGCACCAAGTTTAGA 60.181 43.478 0.00 0.00 0.00 2.10
1972 2047 3.157087 ACAATCCCAGCACCAAGTTTAG 58.843 45.455 0.00 0.00 0.00 1.85
1973 2048 3.237268 ACAATCCCAGCACCAAGTTTA 57.763 42.857 0.00 0.00 0.00 2.01
1974 2049 2.086610 ACAATCCCAGCACCAAGTTT 57.913 45.000 0.00 0.00 0.00 2.66
1975 2050 2.158534 TGTACAATCCCAGCACCAAGTT 60.159 45.455 0.00 0.00 0.00 2.66
1976 2051 1.423541 TGTACAATCCCAGCACCAAGT 59.576 47.619 0.00 0.00 0.00 3.16
1977 2052 2.198827 TGTACAATCCCAGCACCAAG 57.801 50.000 0.00 0.00 0.00 3.61
1978 2053 2.620367 GGATGTACAATCCCAGCACCAA 60.620 50.000 0.00 0.00 32.09 3.67
1979 2054 1.064758 GGATGTACAATCCCAGCACCA 60.065 52.381 0.00 0.00 32.09 4.17
1980 2055 1.212935 AGGATGTACAATCCCAGCACC 59.787 52.381 16.22 0.00 38.98 5.01
1981 2056 2.717639 AGGATGTACAATCCCAGCAC 57.282 50.000 16.22 0.00 38.98 4.40
1982 2057 3.384168 AGTAGGATGTACAATCCCAGCA 58.616 45.455 16.22 2.88 38.98 4.41
1983 2058 3.244249 GGAGTAGGATGTACAATCCCAGC 60.244 52.174 16.22 9.68 38.98 4.85
1984 2059 3.325135 GGGAGTAGGATGTACAATCCCAG 59.675 52.174 17.71 0.00 43.67 4.45
1985 2060 3.314693 GGGAGTAGGATGTACAATCCCA 58.685 50.000 17.71 6.57 43.67 4.37
1986 2061 2.638363 GGGGAGTAGGATGTACAATCCC 59.362 54.545 16.22 15.97 43.52 3.85
1987 2062 2.299297 CGGGGAGTAGGATGTACAATCC 59.701 54.545 0.00 7.88 38.47 3.01
1988 2063 2.299297 CCGGGGAGTAGGATGTACAATC 59.701 54.545 0.00 0.00 0.00 2.67
1989 2064 2.326428 CCGGGGAGTAGGATGTACAAT 58.674 52.381 0.00 0.00 0.00 2.71
1990 2065 1.007479 ACCGGGGAGTAGGATGTACAA 59.993 52.381 6.32 0.00 0.00 2.41
1991 2066 0.632835 ACCGGGGAGTAGGATGTACA 59.367 55.000 6.32 0.00 0.00 2.90
1992 2067 1.785647 AACCGGGGAGTAGGATGTAC 58.214 55.000 6.32 0.00 0.00 2.90
1993 2068 2.112998 CAAACCGGGGAGTAGGATGTA 58.887 52.381 6.32 0.00 0.00 2.29
1994 2069 0.909623 CAAACCGGGGAGTAGGATGT 59.090 55.000 6.32 0.00 0.00 3.06
1995 2070 0.909623 ACAAACCGGGGAGTAGGATG 59.090 55.000 6.32 0.00 0.00 3.51
1996 2071 1.201424 GACAAACCGGGGAGTAGGAT 58.799 55.000 6.32 0.00 0.00 3.24
1997 2072 1.252904 CGACAAACCGGGGAGTAGGA 61.253 60.000 6.32 0.00 0.00 2.94
1998 2073 1.217244 CGACAAACCGGGGAGTAGG 59.783 63.158 6.32 0.00 0.00 3.18
1999 2074 0.604578 TTCGACAAACCGGGGAGTAG 59.395 55.000 6.32 1.00 0.00 2.57
2000 2075 1.066716 CATTCGACAAACCGGGGAGTA 60.067 52.381 6.32 0.00 0.00 2.59
2001 2076 0.321298 CATTCGACAAACCGGGGAGT 60.321 55.000 6.32 0.00 0.00 3.85
2002 2077 0.036765 TCATTCGACAAACCGGGGAG 60.037 55.000 6.32 0.00 0.00 4.30
2003 2078 0.036765 CTCATTCGACAAACCGGGGA 60.037 55.000 6.32 0.00 0.00 4.81
2004 2079 1.644786 GCTCATTCGACAAACCGGGG 61.645 60.000 6.32 0.00 0.00 5.73
2005 2080 0.673644 AGCTCATTCGACAAACCGGG 60.674 55.000 6.32 0.00 0.00 5.73
2006 2081 1.927174 CTAGCTCATTCGACAAACCGG 59.073 52.381 0.00 0.00 0.00 5.28
2007 2082 2.599082 GACTAGCTCATTCGACAAACCG 59.401 50.000 0.00 0.00 0.00 4.44
2008 2083 3.851098 AGACTAGCTCATTCGACAAACC 58.149 45.455 0.00 0.00 0.00 3.27
2009 2084 4.739195 AGAGACTAGCTCATTCGACAAAC 58.261 43.478 14.12 0.00 46.45 2.93
2010 2085 5.392767 AAGAGACTAGCTCATTCGACAAA 57.607 39.130 14.12 0.00 46.45 2.83
2011 2086 6.510879 TTAAGAGACTAGCTCATTCGACAA 57.489 37.500 14.12 0.00 46.45 3.18
2012 2087 6.701145 ATTAAGAGACTAGCTCATTCGACA 57.299 37.500 14.12 0.00 46.45 4.35
2013 2088 8.347035 ACTAATTAAGAGACTAGCTCATTCGAC 58.653 37.037 14.12 0.00 46.45 4.20
2014 2089 8.453238 ACTAATTAAGAGACTAGCTCATTCGA 57.547 34.615 14.12 0.00 46.45 3.71
2015 2090 7.806014 GGACTAATTAAGAGACTAGCTCATTCG 59.194 40.741 14.12 6.43 46.45 3.34
2016 2091 7.806014 CGGACTAATTAAGAGACTAGCTCATTC 59.194 40.741 14.12 0.00 46.45 2.67
2017 2092 7.502895 TCGGACTAATTAAGAGACTAGCTCATT 59.497 37.037 14.12 8.97 46.45 2.57
2018 2093 6.999272 TCGGACTAATTAAGAGACTAGCTCAT 59.001 38.462 14.12 6.94 46.45 2.90
2019 2094 6.354938 TCGGACTAATTAAGAGACTAGCTCA 58.645 40.000 14.12 0.00 46.45 4.26
2020 2095 6.864360 TCGGACTAATTAAGAGACTAGCTC 57.136 41.667 0.00 6.17 44.29 4.09
2021 2096 6.207810 CCATCGGACTAATTAAGAGACTAGCT 59.792 42.308 0.00 0.00 0.00 3.32
2022 2097 6.016108 ACCATCGGACTAATTAAGAGACTAGC 60.016 42.308 0.00 0.00 0.00 3.42
2023 2098 7.513371 ACCATCGGACTAATTAAGAGACTAG 57.487 40.000 0.00 0.00 0.00 2.57
2024 2099 9.011095 CATACCATCGGACTAATTAAGAGACTA 57.989 37.037 0.00 0.00 0.00 2.59
2025 2100 7.506261 ACATACCATCGGACTAATTAAGAGACT 59.494 37.037 0.00 0.00 0.00 3.24
2026 2101 7.659186 ACATACCATCGGACTAATTAAGAGAC 58.341 38.462 0.00 0.00 0.00 3.36
2027 2102 7.834881 ACATACCATCGGACTAATTAAGAGA 57.165 36.000 0.00 0.00 0.00 3.10
2028 2103 9.627395 CTAACATACCATCGGACTAATTAAGAG 57.373 37.037 0.00 0.00 0.00 2.85
2029 2104 8.582437 CCTAACATACCATCGGACTAATTAAGA 58.418 37.037 0.00 0.00 0.00 2.10
2030 2105 8.365647 ACCTAACATACCATCGGACTAATTAAG 58.634 37.037 0.00 0.00 0.00 1.85
2031 2106 8.253867 ACCTAACATACCATCGGACTAATTAA 57.746 34.615 0.00 0.00 0.00 1.40
2032 2107 7.844493 ACCTAACATACCATCGGACTAATTA 57.156 36.000 0.00 0.00 0.00 1.40
2033 2108 6.742559 ACCTAACATACCATCGGACTAATT 57.257 37.500 0.00 0.00 0.00 1.40
2034 2109 6.325545 TCAACCTAACATACCATCGGACTAAT 59.674 38.462 0.00 0.00 0.00 1.73
2035 2110 5.657745 TCAACCTAACATACCATCGGACTAA 59.342 40.000 0.00 0.00 0.00 2.24
2036 2111 5.202765 TCAACCTAACATACCATCGGACTA 58.797 41.667 0.00 0.00 0.00 2.59
2037 2112 4.028131 TCAACCTAACATACCATCGGACT 58.972 43.478 0.00 0.00 0.00 3.85
2038 2113 4.395959 TCAACCTAACATACCATCGGAC 57.604 45.455 0.00 0.00 0.00 4.79
2039 2114 5.423704 TTTCAACCTAACATACCATCGGA 57.576 39.130 0.00 0.00 0.00 4.55
2040 2115 5.588648 ACATTTCAACCTAACATACCATCGG 59.411 40.000 0.00 0.00 0.00 4.18
2041 2116 6.677781 ACATTTCAACCTAACATACCATCG 57.322 37.500 0.00 0.00 0.00 3.84
2042 2117 8.050778 TGAACATTTCAACCTAACATACCATC 57.949 34.615 0.00 0.00 36.59 3.51
2043 2118 7.122650 CCTGAACATTTCAACCTAACATACCAT 59.877 37.037 0.00 0.00 39.58 3.55
2044 2119 6.432783 CCTGAACATTTCAACCTAACATACCA 59.567 38.462 0.00 0.00 39.58 3.25
2045 2120 6.433093 ACCTGAACATTTCAACCTAACATACC 59.567 38.462 0.00 0.00 39.58 2.73
2046 2121 7.174253 TGACCTGAACATTTCAACCTAACATAC 59.826 37.037 0.00 0.00 39.58 2.39
2080 2155 0.243636 CTGTGAAAATCAACCCGGCC 59.756 55.000 0.00 0.00 0.00 6.13
2081 2156 1.200020 CTCTGTGAAAATCAACCCGGC 59.800 52.381 0.00 0.00 0.00 6.13
2082 2157 2.504367 ACTCTGTGAAAATCAACCCGG 58.496 47.619 0.00 0.00 0.00 5.73
2098 2173 7.775053 TGGGCTCAAACATTTATTTAACTCT 57.225 32.000 0.00 0.00 0.00 3.24
2101 2176 7.117667 CAGGTTGGGCTCAAACATTTATTTAAC 59.882 37.037 18.52 0.00 42.79 2.01
2120 2195 0.032540 GAAGCCTTGTTGCAGGTTGG 59.967 55.000 0.00 0.00 36.15 3.77
2151 2239 8.986477 TTTCAAAGAAGGCTTTATATTCAAGC 57.014 30.769 0.00 9.77 42.27 4.01
2187 2275 1.418264 TGCCATATTTACAGCGGGCTA 59.582 47.619 0.00 0.00 41.86 3.93
2188 2276 0.182537 TGCCATATTTACAGCGGGCT 59.817 50.000 0.00 0.00 41.86 5.19
2189 2277 1.200020 GATGCCATATTTACAGCGGGC 59.800 52.381 0.00 0.00 41.70 6.13
2190 2278 1.464608 CGATGCCATATTTACAGCGGG 59.535 52.381 0.00 0.00 39.36 6.13
2199 2287 2.574006 ATGCCAGACGATGCCATATT 57.426 45.000 0.00 0.00 0.00 1.28
2213 2301 7.455953 AGTGTTAGAGAGGATATATGAATGCCA 59.544 37.037 0.00 0.00 0.00 4.92
2214 2302 7.846066 AGTGTTAGAGAGGATATATGAATGCC 58.154 38.462 0.00 0.00 0.00 4.40
2218 2306 9.815306 AGCTTAGTGTTAGAGAGGATATATGAA 57.185 33.333 0.00 0.00 0.00 2.57
2219 2307 9.815306 AAGCTTAGTGTTAGAGAGGATATATGA 57.185 33.333 0.00 0.00 0.00 2.15
2222 2310 9.869667 AAGAAGCTTAGTGTTAGAGAGGATATA 57.130 33.333 0.00 0.00 0.00 0.86
2223 2311 8.776061 AAGAAGCTTAGTGTTAGAGAGGATAT 57.224 34.615 0.00 0.00 0.00 1.63
2283 2371 0.443869 CGGGTGACTCGCTTTCAATG 59.556 55.000 0.00 0.00 0.00 2.82
2291 2379 0.442699 GTCAAAATCGGGTGACTCGC 59.557 55.000 0.00 0.00 40.82 5.03
2292 2380 1.076332 GGTCAAAATCGGGTGACTCG 58.924 55.000 0.00 0.00 43.06 4.18
2294 2382 1.271379 CCAGGTCAAAATCGGGTGACT 60.271 52.381 4.02 0.00 43.06 3.41
2312 2400 5.869579 AGAGCTTTGAGAAATAGTTGACCA 58.130 37.500 0.00 0.00 0.00 4.02
2320 2408 9.458727 AATTGAATGAGAGAGCTTTGAGAAATA 57.541 29.630 0.00 0.00 0.00 1.40
2371 2459 8.189119 ACTAATTGTGAGGCCTTCAAAATTAA 57.811 30.769 25.07 16.42 46.96 1.40
2379 2467 2.755103 CCCAACTAATTGTGAGGCCTTC 59.245 50.000 6.77 4.06 33.60 3.46
2395 2483 6.014584 ACCCAATTCTAAATTGAAGACCCAAC 60.015 38.462 12.73 0.00 0.00 3.77
2424 2513 3.975246 TGACCCGGTCAAAATCGC 58.025 55.556 18.34 0.00 39.78 4.58
2501 2591 9.905713 AATACCTCAACTGAATGAAATAGCTTA 57.094 29.630 0.00 0.00 0.00 3.09
2541 2631 2.129607 GCTCGGTCAAAGTCGTAAACA 58.870 47.619 0.00 0.00 0.00 2.83
2550 2640 3.855689 AAATCATTGGCTCGGTCAAAG 57.144 42.857 0.00 0.00 28.60 2.77
2573 2664 0.657312 CGCCGATTGCTGCTGATTTA 59.343 50.000 0.00 0.00 38.05 1.40
2592 2687 8.675888 GTGCGCGGAATTATTAAGTTTTTATAC 58.324 33.333 8.83 0.00 0.00 1.47
2602 2697 2.215196 GAGGGTGCGCGGAATTATTAA 58.785 47.619 8.83 0.00 0.00 1.40
2605 2700 1.227853 GGAGGGTGCGCGGAATTAT 60.228 57.895 8.83 0.00 0.00 1.28
2675 2779 1.234615 ATTTCTGCGTCGGTGGTTGG 61.235 55.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.