Multiple sequence alignment - TraesCS3D01G400900

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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 TraesCS3D01G400900 chr3D 100.000 2846 0 0 1 2846 515706835 515703990 0.000000e+00 5256
1 TraesCS3D01G400900 chr3D 87.413 286 17 4 2040 2306 6025221 6024936 7.660000e-81 311
2 TraesCS3D01G400900 chr3A 90.080 1875 122 21 1 1845 649953218 649951378 0.000000e+00 2374
3 TraesCS3D01G400900 chr3B 92.385 499 36 2 2134 2631 678178253 678177756 0.000000e+00 710
4 TraesCS3D01G400900 chr3B 88.000 600 42 13 37 626 678204571 678203992 0.000000e+00 682
5 TraesCS3D01G400900 chr3B 92.462 199 14 1 2642 2840 678177660 678177463 1.670000e-72 283
6 TraesCS3D01G400900 chr3B 86.192 239 13 12 674 908 678196719 678196497 1.020000e-59 241
7 TraesCS3D01G400900 chr3B 81.648 267 26 7 2021 2266 409536840 409536576 1.730000e-47 200
8 TraesCS3D01G400900 chr2B 87.015 593 72 4 2040 2632 518512807 518513394 0.000000e+00 664
9 TraesCS3D01G400900 chr2B 84.490 245 19 2 2042 2267 731334361 731334117 1.030000e-54 224
10 TraesCS3D01G400900 chr2B 93.103 87 5 1 2039 2125 647533894 647533979 2.980000e-25 126
11 TraesCS3D01G400900 chr7B 85.784 612 62 8 2040 2629 711737203 711736595 2.410000e-175 625
12 TraesCS3D01G400900 chr5A 85.809 606 65 8 2042 2627 471305594 471306198 8.660000e-175 623
13 TraesCS3D01G400900 chr5A 85.089 617 65 9 2040 2633 471402586 471401974 3.140000e-169 604
14 TraesCS3D01G400900 chr5A 84.943 611 71 7 2040 2630 580409758 580410367 1.460000e-167 599
15 TraesCS3D01G400900 chr5D 85.528 615 66 11 2040 2633 369106181 369105569 3.110000e-174 621
16 TraesCS3D01G400900 chr4D 84.069 634 61 9 2023 2633 307239661 307240277 2.460000e-160 575
17 TraesCS3D01G400900 chr7D 84.298 605 76 8 2044 2633 61232848 61232248 8.840000e-160 573
18 TraesCS3D01G400900 chr7D 83.929 616 73 10 2040 2630 219640166 219639552 1.480000e-157 566
19 TraesCS3D01G400900 chr6B 87.008 508 60 6 2129 2633 681075899 681075395 4.110000e-158 568
20 TraesCS3D01G400900 chr6B 79.116 656 89 23 2024 2633 37765385 37766038 2.640000e-110 409
21 TraesCS3D01G400900 chr6B 78.958 480 65 20 3 457 711694664 711695132 7.710000e-76 294
22 TraesCS3D01G400900 chr6B 85.317 252 37 0 22 273 665131931 665132182 7.820000e-66 261
23 TraesCS3D01G400900 chr2D 81.937 382 59 6 3 378 493882963 493883340 5.920000e-82 315
24 TraesCS3D01G400900 chr2D 80.385 260 41 7 2039 2291 542643734 542643990 3.740000e-44 189
25 TraesCS3D01G400900 chr2A 80.751 426 61 12 3 419 639695096 639694683 2.130000e-81 313
26 TraesCS3D01G400900 chr6D 86.282 277 34 4 3 277 466544381 466544107 5.960000e-77 298
27 TraesCS3D01G400900 chr6D 80.110 362 60 10 3 360 67326410 67326763 2.810000e-65 259
28 TraesCS3D01G400900 chr6A 83.755 277 41 4 3 277 84699477 84699751 2.810000e-65 259


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 TraesCS3D01G400900 chr3D 515703990 515706835 2845 True 5256.0 5256 100.0000 1 2846 1 chr3D.!!$R2 2845
1 TraesCS3D01G400900 chr3A 649951378 649953218 1840 True 2374.0 2374 90.0800 1 1845 1 chr3A.!!$R1 1844
2 TraesCS3D01G400900 chr3B 678203992 678204571 579 True 682.0 682 88.0000 37 626 1 chr3B.!!$R3 589
3 TraesCS3D01G400900 chr3B 678177463 678178253 790 True 496.5 710 92.4235 2134 2840 2 chr3B.!!$R4 706
4 TraesCS3D01G400900 chr2B 518512807 518513394 587 False 664.0 664 87.0150 2040 2632 1 chr2B.!!$F1 592
5 TraesCS3D01G400900 chr7B 711736595 711737203 608 True 625.0 625 85.7840 2040 2629 1 chr7B.!!$R1 589
6 TraesCS3D01G400900 chr5A 471305594 471306198 604 False 623.0 623 85.8090 2042 2627 1 chr5A.!!$F1 585
7 TraesCS3D01G400900 chr5A 471401974 471402586 612 True 604.0 604 85.0890 2040 2633 1 chr5A.!!$R1 593
8 TraesCS3D01G400900 chr5A 580409758 580410367 609 False 599.0 599 84.9430 2040 2630 1 chr5A.!!$F2 590
9 TraesCS3D01G400900 chr5D 369105569 369106181 612 True 621.0 621 85.5280 2040 2633 1 chr5D.!!$R1 593
10 TraesCS3D01G400900 chr4D 307239661 307240277 616 False 575.0 575 84.0690 2023 2633 1 chr4D.!!$F1 610
11 TraesCS3D01G400900 chr7D 61232248 61232848 600 True 573.0 573 84.2980 2044 2633 1 chr7D.!!$R1 589
12 TraesCS3D01G400900 chr7D 219639552 219640166 614 True 566.0 566 83.9290 2040 2630 1 chr7D.!!$R2 590
13 TraesCS3D01G400900 chr6B 681075395 681075899 504 True 568.0 568 87.0080 2129 2633 1 chr6B.!!$R1 504
14 TraesCS3D01G400900 chr6B 37765385 37766038 653 False 409.0 409 79.1160 2024 2633 1 chr6B.!!$F1 609

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
859 880 0.039346 TTGTCGTGGTCGTATCGCAA 60.039 50.0 0.0 0.0 38.33 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 1968 0.030638 CCCCTTATTTCATTGCGCGG 59.969 55.0 8.83 0.0 0.0 6.46 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
19 20 0.321653 GGTGATGGTGATATCCGGGC 60.322 60.000 0.00 0.00 0.00 6.13
57 58 2.939103 GTTATCAGTCACATGAGCCACC 59.061 50.000 0.00 0.00 31.44 4.61
83 84 3.426159 CGGTTGATTTGGAGGAATTCACG 60.426 47.826 7.93 0.00 0.00 4.35
118 119 0.820891 AGCTTTATCATGGCGGCCTG 60.821 55.000 21.46 15.39 0.00 4.85
178 179 1.514553 GGGAGCTTGAGCATTTGCC 59.485 57.895 5.70 0.00 45.16 4.52
273 274 3.056628 CTTGCTAAGCCTGTCTCCG 57.943 57.895 0.00 0.00 0.00 4.63
274 275 0.247736 CTTGCTAAGCCTGTCTCCGT 59.752 55.000 0.00 0.00 0.00 4.69
275 276 0.246635 TTGCTAAGCCTGTCTCCGTC 59.753 55.000 0.00 0.00 0.00 4.79
283 284 0.898320 CCTGTCTCCGTCTCCATTGT 59.102 55.000 0.00 0.00 0.00 2.71
309 319 0.859232 TGCGAGTTTCTTCTTGCGTC 59.141 50.000 0.00 0.00 45.03 5.19
321 331 0.652592 CTTGCGTCGGATTTAGCTGG 59.347 55.000 0.00 0.00 0.00 4.85
322 332 0.248012 TTGCGTCGGATTTAGCTGGA 59.752 50.000 0.00 0.00 0.00 3.86
323 333 0.248012 TGCGTCGGATTTAGCTGGAA 59.752 50.000 0.00 0.00 0.00 3.53
324 334 0.651031 GCGTCGGATTTAGCTGGAAC 59.349 55.000 0.00 0.00 0.00 3.62
398 409 2.886523 TCAATCAGTCAGGCACAAAAGG 59.113 45.455 0.00 0.00 0.00 3.11
414 425 6.237808 GCACAAAAGGAACAACACTTACATTG 60.238 38.462 0.00 0.00 0.00 2.82
506 517 3.306088 GCATAATAGCCGAAGCAGAGGTA 60.306 47.826 0.00 0.00 43.56 3.08
526 537 2.261671 GGCAACGAAGGAGAGCGA 59.738 61.111 0.00 0.00 0.00 4.93
527 538 1.153549 GGCAACGAAGGAGAGCGAT 60.154 57.895 0.00 0.00 0.00 4.58
528 539 1.424493 GGCAACGAAGGAGAGCGATG 61.424 60.000 0.00 0.00 34.10 3.84
529 540 1.424493 GCAACGAAGGAGAGCGATGG 61.424 60.000 0.00 0.00 32.03 3.51
530 541 0.108615 CAACGAAGGAGAGCGATGGT 60.109 55.000 0.00 0.00 0.00 3.55
531 542 0.173708 AACGAAGGAGAGCGATGGTC 59.826 55.000 0.00 0.00 0.00 4.02
690 709 2.770048 AGAAGGGATGGAGGCGGG 60.770 66.667 0.00 0.00 0.00 6.13
727 746 4.824515 CGGAGACCGGGAGAGGCT 62.825 72.222 6.32 0.00 44.15 4.58
791 812 1.776034 GCGAATTCACTGGATCGGCC 61.776 60.000 6.22 0.00 35.91 6.13
797 818 1.762460 CACTGGATCGGCCTAGGGT 60.762 63.158 11.72 0.00 37.63 4.34
840 861 1.613630 ACTGGCCGATCAGTTCCCT 60.614 57.895 0.00 0.00 44.74 4.20
856 877 0.524816 CCCTTGTCGTGGTCGTATCG 60.525 60.000 0.00 0.00 38.33 2.92
857 878 1.138047 CCTTGTCGTGGTCGTATCGC 61.138 60.000 0.00 0.00 38.33 4.58
859 880 0.039346 TTGTCGTGGTCGTATCGCAA 60.039 50.000 0.00 0.00 38.33 4.85
915 940 2.668457 GCACGCCTATATATGACTGCAC 59.332 50.000 0.00 0.00 0.00 4.57
916 941 3.615110 GCACGCCTATATATGACTGCACT 60.615 47.826 0.00 0.00 0.00 4.40
919 944 5.974158 CACGCCTATATATGACTGCACTATC 59.026 44.000 0.00 0.00 0.00 2.08
923 948 7.012421 CGCCTATATATGACTGCACTATCTACA 59.988 40.741 0.00 0.00 0.00 2.74
939 964 4.682778 TCTACAAATCCATAGAACCGGG 57.317 45.455 6.32 0.00 0.00 5.73
998 1023 2.678324 GTCTCGACTTCCAGTTCCAAG 58.322 52.381 0.00 0.00 0.00 3.61
1160 1185 2.089854 GCATAACGCAGTGGGTGAG 58.910 57.895 14.26 7.93 45.00 3.51
1161 1186 1.982073 GCATAACGCAGTGGGTGAGC 61.982 60.000 14.26 13.76 45.00 4.26
1184 1209 4.760047 GGCGAGCAAGCGGGAAGA 62.760 66.667 0.00 0.00 38.18 2.87
1224 1249 2.581354 CCCCTCTGCAAGACCGAG 59.419 66.667 0.00 0.00 38.67 4.63
1237 1262 4.193334 CCGAGAGCGCGTCCATCA 62.193 66.667 8.43 0.00 35.83 3.07
1284 1309 0.810426 AGCAGCATCACATCGAGCAG 60.810 55.000 0.00 0.00 0.00 4.24
1308 1333 4.778143 CACCGCCCGGGGAAGAAG 62.778 72.222 25.28 1.77 42.48 2.85
1310 1335 3.712907 CCGCCCGGGGAAGAAGAA 61.713 66.667 25.28 0.00 0.00 2.52
1311 1336 2.125106 CGCCCGGGGAAGAAGAAG 60.125 66.667 25.28 0.00 0.00 2.85
1312 1337 2.656069 CGCCCGGGGAAGAAGAAGA 61.656 63.158 25.28 0.00 0.00 2.87
1313 1338 1.078356 GCCCGGGGAAGAAGAAGAC 60.078 63.158 25.28 0.00 0.00 3.01
1314 1339 1.218316 CCCGGGGAAGAAGAAGACG 59.782 63.158 14.71 0.00 0.00 4.18
1315 1340 1.255667 CCCGGGGAAGAAGAAGACGA 61.256 60.000 14.71 0.00 0.00 4.20
1316 1341 0.173708 CCGGGGAAGAAGAAGACGAG 59.826 60.000 0.00 0.00 0.00 4.18
1317 1342 1.174783 CGGGGAAGAAGAAGACGAGA 58.825 55.000 0.00 0.00 0.00 4.04
1318 1343 1.135344 CGGGGAAGAAGAAGACGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
1381 1406 1.747367 AGAGAGGTCTCAGGCGACG 60.747 63.158 9.64 0.00 45.21 5.12
1413 1438 1.667724 CAGAAATACTGGAAGCAGCGG 59.332 52.381 0.00 0.00 42.39 5.52
1519 1544 3.740397 TCTACCACGTCCACGGCG 61.740 66.667 4.80 4.80 44.95 6.46
1527 1552 2.579787 GTCCACGGCGTCATCGAG 60.580 66.667 10.85 0.00 39.71 4.04
1529 1554 2.126071 CCACGGCGTCATCGAGTT 60.126 61.111 10.85 0.00 39.71 3.01
1530 1555 1.736645 CCACGGCGTCATCGAGTTT 60.737 57.895 10.85 0.00 39.71 2.66
1534 1559 1.741770 GGCGTCATCGAGTTTGCCT 60.742 57.895 12.67 0.00 39.38 4.75
1535 1560 1.298859 GGCGTCATCGAGTTTGCCTT 61.299 55.000 12.67 0.00 39.38 4.35
1539 1576 2.223144 CGTCATCGAGTTTGCCTTGAAA 59.777 45.455 0.00 0.00 37.14 2.69
1558 1595 3.121030 CGCACGCTTCCAAGGAGG 61.121 66.667 0.00 0.00 39.47 4.30
1599 1636 2.717809 GGAGTTCGTGCGTTCGCTC 61.718 63.158 17.63 13.09 0.00 5.03
1746 1783 2.792290 CGCTTCGCATGTGACGAGG 61.792 63.158 16.22 7.81 41.18 4.63
1812 1849 9.530633 CACTACTTCTACTTGTACTTTTTGAGT 57.469 33.333 0.00 0.00 42.55 3.41
1815 1852 8.421673 ACTTCTACTTGTACTTTTTGAGTGAC 57.578 34.615 0.00 0.00 39.48 3.67
1816 1853 7.222224 ACTTCTACTTGTACTTTTTGAGTGACG 59.778 37.037 0.00 0.00 39.48 4.35
1845 1882 0.108804 ACGTTGGCGGTGAGATGTAG 60.109 55.000 0.00 0.00 43.45 2.74
1846 1883 0.806102 CGTTGGCGGTGAGATGTAGG 60.806 60.000 0.00 0.00 0.00 3.18
1847 1884 0.535335 GTTGGCGGTGAGATGTAGGA 59.465 55.000 0.00 0.00 0.00 2.94
1848 1885 0.535335 TTGGCGGTGAGATGTAGGAC 59.465 55.000 0.00 0.00 0.00 3.85
1849 1886 1.065928 GGCGGTGAGATGTAGGACG 59.934 63.158 0.00 0.00 0.00 4.79
1850 1887 1.664321 GGCGGTGAGATGTAGGACGT 61.664 60.000 0.00 0.00 0.00 4.34
1851 1888 0.525668 GCGGTGAGATGTAGGACGTG 60.526 60.000 0.00 0.00 0.00 4.49
1852 1889 0.809385 CGGTGAGATGTAGGACGTGT 59.191 55.000 0.00 0.00 0.00 4.49
1853 1890 1.201647 CGGTGAGATGTAGGACGTGTT 59.798 52.381 0.00 0.00 0.00 3.32
1854 1891 2.352421 CGGTGAGATGTAGGACGTGTTT 60.352 50.000 0.00 0.00 0.00 2.83
1855 1892 2.993899 GGTGAGATGTAGGACGTGTTTG 59.006 50.000 0.00 0.00 0.00 2.93
1856 1893 3.554337 GGTGAGATGTAGGACGTGTTTGT 60.554 47.826 0.00 0.00 0.00 2.83
1857 1894 4.056050 GTGAGATGTAGGACGTGTTTGTT 58.944 43.478 0.00 0.00 0.00 2.83
1858 1895 4.510340 GTGAGATGTAGGACGTGTTTGTTT 59.490 41.667 0.00 0.00 0.00 2.83
1859 1896 4.748102 TGAGATGTAGGACGTGTTTGTTTC 59.252 41.667 0.00 0.00 0.00 2.78
1860 1897 4.699637 AGATGTAGGACGTGTTTGTTTCA 58.300 39.130 0.00 0.00 0.00 2.69
1861 1898 5.305585 AGATGTAGGACGTGTTTGTTTCAT 58.694 37.500 0.00 0.00 0.00 2.57
1862 1899 4.804608 TGTAGGACGTGTTTGTTTCATG 57.195 40.909 0.00 0.00 0.00 3.07
1863 1900 3.562141 TGTAGGACGTGTTTGTTTCATGG 59.438 43.478 0.00 0.00 0.00 3.66
1864 1901 2.650322 AGGACGTGTTTGTTTCATGGT 58.350 42.857 0.00 0.00 0.00 3.55
1865 1902 3.020984 AGGACGTGTTTGTTTCATGGTT 58.979 40.909 0.00 0.00 0.00 3.67
1866 1903 3.445805 AGGACGTGTTTGTTTCATGGTTT 59.554 39.130 0.00 0.00 0.00 3.27
1867 1904 4.081917 AGGACGTGTTTGTTTCATGGTTTT 60.082 37.500 0.00 0.00 0.00 2.43
1868 1905 4.032331 GGACGTGTTTGTTTCATGGTTTTG 59.968 41.667 0.00 0.00 0.00 2.44
1869 1906 3.369451 ACGTGTTTGTTTCATGGTTTTGC 59.631 39.130 0.00 0.00 0.00 3.68
1870 1907 3.541129 CGTGTTTGTTTCATGGTTTTGCG 60.541 43.478 0.00 0.00 0.00 4.85
1871 1908 2.932614 TGTTTGTTTCATGGTTTTGCGG 59.067 40.909 0.00 0.00 0.00 5.69
1872 1909 1.576356 TTGTTTCATGGTTTTGCGGC 58.424 45.000 0.00 0.00 0.00 6.53
1873 1910 0.249657 TGTTTCATGGTTTTGCGGCC 60.250 50.000 0.00 0.00 0.00 6.13
1874 1911 1.006805 TTTCATGGTTTTGCGGCCG 60.007 52.632 24.05 24.05 0.00 6.13
1875 1912 2.427540 TTTCATGGTTTTGCGGCCGG 62.428 55.000 29.38 8.95 0.00 6.13
1876 1913 3.679738 CATGGTTTTGCGGCCGGT 61.680 61.111 29.38 0.00 0.00 5.28
1877 1914 3.679738 ATGGTTTTGCGGCCGGTG 61.680 61.111 29.38 0.00 0.00 4.94
1879 1916 4.337060 GGTTTTGCGGCCGGTGTC 62.337 66.667 29.38 10.81 0.00 3.67
1880 1917 3.284449 GTTTTGCGGCCGGTGTCT 61.284 61.111 29.38 0.00 0.00 3.41
1881 1918 3.283684 TTTTGCGGCCGGTGTCTG 61.284 61.111 29.38 0.00 0.00 3.51
1882 1919 3.758973 TTTTGCGGCCGGTGTCTGA 62.759 57.895 29.38 0.04 0.00 3.27
1883 1920 3.545124 TTTGCGGCCGGTGTCTGAT 62.545 57.895 29.38 0.00 0.00 2.90
1884 1921 3.950794 TTGCGGCCGGTGTCTGATC 62.951 63.158 29.38 7.00 0.00 2.92
1887 1924 4.451150 GGCCGGTGTCTGATCGCA 62.451 66.667 1.90 0.00 0.00 5.10
1888 1925 2.887568 GCCGGTGTCTGATCGCAG 60.888 66.667 1.90 0.00 43.67 5.18
1889 1926 2.887568 CCGGTGTCTGATCGCAGC 60.888 66.667 0.00 4.52 42.01 5.25
1891 1928 2.887568 GGTGTCTGATCGCAGCGG 60.888 66.667 16.42 0.00 42.01 5.52
1892 1929 3.558411 GTGTCTGATCGCAGCGGC 61.558 66.667 16.42 8.33 42.01 6.53
1893 1930 4.067913 TGTCTGATCGCAGCGGCA 62.068 61.111 16.42 12.74 42.01 5.69
1894 1931 2.587194 GTCTGATCGCAGCGGCAT 60.587 61.111 16.42 0.90 42.01 4.40
1895 1932 2.279717 TCTGATCGCAGCGGCATC 60.280 61.111 16.42 12.16 42.01 3.91
1896 1933 3.344215 CTGATCGCAGCGGCATCC 61.344 66.667 16.42 0.53 41.24 3.51
1907 1944 3.803886 GGCATCCGAACCCGTTAC 58.196 61.111 0.00 0.00 0.00 2.50
1908 1945 1.219935 GGCATCCGAACCCGTTACT 59.780 57.895 0.00 0.00 0.00 2.24
1909 1946 0.808847 GGCATCCGAACCCGTTACTC 60.809 60.000 0.00 0.00 0.00 2.59
1910 1947 0.175073 GCATCCGAACCCGTTACTCT 59.825 55.000 0.00 0.00 0.00 3.24
1911 1948 1.406539 GCATCCGAACCCGTTACTCTA 59.593 52.381 0.00 0.00 0.00 2.43
1912 1949 2.035576 GCATCCGAACCCGTTACTCTAT 59.964 50.000 0.00 0.00 0.00 1.98
1913 1950 3.639538 CATCCGAACCCGTTACTCTATG 58.360 50.000 0.00 0.00 0.00 2.23
1914 1951 2.726821 TCCGAACCCGTTACTCTATGT 58.273 47.619 0.00 0.00 0.00 2.29
1915 1952 3.884895 TCCGAACCCGTTACTCTATGTA 58.115 45.455 0.00 0.00 0.00 2.29
1916 1953 3.627577 TCCGAACCCGTTACTCTATGTAC 59.372 47.826 0.00 0.00 0.00 2.90
1917 1954 3.546815 CCGAACCCGTTACTCTATGTACG 60.547 52.174 0.00 0.00 0.00 3.67
1918 1955 3.309682 CGAACCCGTTACTCTATGTACGA 59.690 47.826 0.00 0.00 31.93 3.43
1919 1956 4.592179 GAACCCGTTACTCTATGTACGAC 58.408 47.826 0.00 0.00 31.93 4.34
1920 1957 2.609459 ACCCGTTACTCTATGTACGACG 59.391 50.000 0.00 0.00 36.00 5.12
1921 1958 2.032549 CCCGTTACTCTATGTACGACGG 60.033 54.545 0.00 10.39 46.79 4.79
1923 1960 4.520743 CGTTACTCTATGTACGACGGAA 57.479 45.455 0.00 0.00 33.91 4.30
1924 1961 4.266945 CGTTACTCTATGTACGACGGAAC 58.733 47.826 0.00 0.00 33.91 3.62
1925 1962 4.033358 CGTTACTCTATGTACGACGGAACT 59.967 45.833 0.00 0.00 33.91 3.01
1926 1963 5.232202 CGTTACTCTATGTACGACGGAACTA 59.768 44.000 0.00 0.00 33.91 2.24
1927 1964 6.237835 CGTTACTCTATGTACGACGGAACTAA 60.238 42.308 0.00 0.00 33.91 2.24
1928 1965 7.464358 GTTACTCTATGTACGACGGAACTAAA 58.536 38.462 0.00 0.00 0.00 1.85
1929 1966 6.690194 ACTCTATGTACGACGGAACTAAAT 57.310 37.500 0.00 0.00 0.00 1.40
1930 1967 7.792374 ACTCTATGTACGACGGAACTAAATA 57.208 36.000 0.00 0.00 0.00 1.40
1931 1968 7.634522 ACTCTATGTACGACGGAACTAAATAC 58.365 38.462 0.00 0.00 0.00 1.89
1932 1969 6.959361 TCTATGTACGACGGAACTAAATACC 58.041 40.000 0.00 0.00 0.00 2.73
1937 1974 2.668203 CGGAACTAAATACCGCGCA 58.332 52.632 8.75 0.00 40.19 6.09
1938 1975 1.000884 CGGAACTAAATACCGCGCAA 58.999 50.000 8.75 0.00 40.19 4.85
1939 1976 1.595794 CGGAACTAAATACCGCGCAAT 59.404 47.619 8.75 0.00 40.19 3.56
1940 1977 2.598907 CGGAACTAAATACCGCGCAATG 60.599 50.000 8.75 0.00 40.19 2.82
1941 1978 2.610374 GGAACTAAATACCGCGCAATGA 59.390 45.455 8.75 0.00 0.00 2.57
1942 1979 3.064271 GGAACTAAATACCGCGCAATGAA 59.936 43.478 8.75 0.00 0.00 2.57
1943 1980 4.437659 GGAACTAAATACCGCGCAATGAAA 60.438 41.667 8.75 0.00 0.00 2.69
1944 1981 4.893424 ACTAAATACCGCGCAATGAAAT 57.107 36.364 8.75 0.00 0.00 2.17
1945 1982 5.994887 ACTAAATACCGCGCAATGAAATA 57.005 34.783 8.75 0.00 0.00 1.40
1946 1983 6.366315 ACTAAATACCGCGCAATGAAATAA 57.634 33.333 8.75 0.00 0.00 1.40
1947 1984 6.427150 ACTAAATACCGCGCAATGAAATAAG 58.573 36.000 8.75 0.00 0.00 1.73
1948 1985 3.896648 ATACCGCGCAATGAAATAAGG 57.103 42.857 8.75 0.00 0.00 2.69
1949 1986 0.738389 ACCGCGCAATGAAATAAGGG 59.262 50.000 8.75 0.00 0.00 3.95
1950 1987 0.030638 CCGCGCAATGAAATAAGGGG 59.969 55.000 8.75 0.00 0.00 4.79
1951 1988 0.594796 CGCGCAATGAAATAAGGGGC 60.595 55.000 8.75 0.00 0.00 5.80
1952 1989 0.746659 GCGCAATGAAATAAGGGGCT 59.253 50.000 0.30 0.00 34.95 5.19
1953 1990 1.536709 GCGCAATGAAATAAGGGGCTG 60.537 52.381 0.30 0.00 34.95 4.85
1954 1991 1.750778 CGCAATGAAATAAGGGGCTGT 59.249 47.619 0.00 0.00 0.00 4.40
1955 1992 2.223572 CGCAATGAAATAAGGGGCTGTC 60.224 50.000 0.00 0.00 0.00 3.51
1956 1993 2.223572 GCAATGAAATAAGGGGCTGTCG 60.224 50.000 0.00 0.00 0.00 4.35
1957 1994 3.278574 CAATGAAATAAGGGGCTGTCGA 58.721 45.455 0.00 0.00 0.00 4.20
1958 1995 2.691409 TGAAATAAGGGGCTGTCGAG 57.309 50.000 0.00 0.00 0.00 4.04
1959 1996 2.184533 TGAAATAAGGGGCTGTCGAGA 58.815 47.619 0.00 0.00 0.00 4.04
1960 1997 2.569853 TGAAATAAGGGGCTGTCGAGAA 59.430 45.455 0.00 0.00 0.00 2.87
1961 1998 2.693267 AATAAGGGGCTGTCGAGAAC 57.307 50.000 0.00 0.00 0.00 3.01
1962 1999 1.568504 ATAAGGGGCTGTCGAGAACA 58.431 50.000 0.00 0.00 36.18 3.18
1963 2000 1.344065 TAAGGGGCTGTCGAGAACAA 58.656 50.000 0.00 0.00 37.45 2.83
1964 2001 0.472471 AAGGGGCTGTCGAGAACAAA 59.528 50.000 0.00 0.00 37.45 2.83
1965 2002 0.250338 AGGGGCTGTCGAGAACAAAC 60.250 55.000 0.00 0.00 37.45 2.93
1966 2003 1.566018 GGGGCTGTCGAGAACAAACG 61.566 60.000 0.00 0.00 37.45 3.60
1967 2004 0.878961 GGGCTGTCGAGAACAAACGT 60.879 55.000 0.00 0.00 37.45 3.99
1968 2005 0.507358 GGCTGTCGAGAACAAACGTC 59.493 55.000 0.00 0.00 37.45 4.34
1969 2006 0.158928 GCTGTCGAGAACAAACGTCG 59.841 55.000 0.00 0.00 37.45 5.12
1970 2007 0.158928 CTGTCGAGAACAAACGTCGC 59.841 55.000 0.00 0.00 37.45 5.19
1971 2008 0.248743 TGTCGAGAACAAACGTCGCT 60.249 50.000 0.00 0.00 34.03 4.93
1972 2009 0.430110 GTCGAGAACAAACGTCGCTC 59.570 55.000 0.00 0.00 33.66 5.03
1973 2010 0.309922 TCGAGAACAAACGTCGCTCT 59.690 50.000 0.00 0.00 33.66 4.09
1974 2011 0.431233 CGAGAACAAACGTCGCTCTG 59.569 55.000 0.00 0.00 0.00 3.35
1975 2012 1.488527 GAGAACAAACGTCGCTCTGT 58.511 50.000 0.00 0.00 0.00 3.41
1976 2013 1.859080 GAGAACAAACGTCGCTCTGTT 59.141 47.619 6.84 6.84 34.78 3.16
1977 2014 1.593006 AGAACAAACGTCGCTCTGTTG 59.407 47.619 10.76 0.00 32.31 3.33
1978 2015 0.655733 AACAAACGTCGCTCTGTTGG 59.344 50.000 6.44 0.00 31.00 3.77
1979 2016 0.461339 ACAAACGTCGCTCTGTTGGT 60.461 50.000 0.00 0.00 0.00 3.67
1980 2017 0.655733 CAAACGTCGCTCTGTTGGTT 59.344 50.000 0.00 0.00 0.00 3.67
1981 2018 1.862201 CAAACGTCGCTCTGTTGGTTA 59.138 47.619 0.00 0.00 0.00 2.85
1982 2019 1.779569 AACGTCGCTCTGTTGGTTAG 58.220 50.000 0.00 0.00 0.00 2.34
1983 2020 0.666577 ACGTCGCTCTGTTGGTTAGC 60.667 55.000 0.00 0.00 0.00 3.09
1984 2021 1.352156 CGTCGCTCTGTTGGTTAGCC 61.352 60.000 0.00 0.00 32.50 3.93
1985 2022 1.019805 GTCGCTCTGTTGGTTAGCCC 61.020 60.000 0.00 0.00 32.50 5.19
1986 2023 1.192146 TCGCTCTGTTGGTTAGCCCT 61.192 55.000 0.00 0.00 32.50 5.19
1987 2024 1.021390 CGCTCTGTTGGTTAGCCCTG 61.021 60.000 0.00 0.00 32.50 4.45
1988 2025 0.036875 GCTCTGTTGGTTAGCCCTGT 59.963 55.000 0.00 0.00 0.00 4.00
1989 2026 1.545651 GCTCTGTTGGTTAGCCCTGTT 60.546 52.381 0.00 0.00 0.00 3.16
1990 2027 2.863809 CTCTGTTGGTTAGCCCTGTTT 58.136 47.619 0.00 0.00 0.00 2.83
1991 2028 3.222603 CTCTGTTGGTTAGCCCTGTTTT 58.777 45.455 0.00 0.00 0.00 2.43
1992 2029 3.636764 CTCTGTTGGTTAGCCCTGTTTTT 59.363 43.478 0.00 0.00 0.00 1.94
2258 2317 2.292521 ACCAAGATCTAGAGGAGCACCA 60.293 50.000 13.89 0.00 38.94 4.17
2283 2343 4.759693 TGCATACAAGGATGTTTTTCGAGT 59.240 37.500 0.00 0.00 41.05 4.18
2413 2494 0.172803 GAAGAAGAGGAACGCCGCTA 59.827 55.000 0.00 0.00 44.17 4.26
2501 2583 1.211449 CGAGAGAGTGTTGAGCGCT 59.789 57.895 11.27 11.27 41.28 5.92
2544 2626 0.721718 CGAATCTGAAGACCGGCAAC 59.278 55.000 0.00 0.00 0.00 4.17
2575 2657 3.573772 CTTGCTCCTCGACGCCACA 62.574 63.158 0.00 0.00 0.00 4.17
2607 2690 1.361993 CCGAGATGGAGGAAGAGCG 59.638 63.158 0.00 0.00 42.00 5.03
2633 2718 1.426041 AATTATTTCGACGCGGCGCT 61.426 50.000 33.29 19.32 0.00 5.92
2634 2719 1.818221 ATTATTTCGACGCGGCGCTC 61.818 55.000 33.29 23.00 0.00 5.03
2635 2720 3.686843 TATTTCGACGCGGCGCTCA 62.687 57.895 33.29 16.69 0.00 4.26
2663 2833 1.519455 CTAAAGCGGCAGACGGAGG 60.519 63.158 1.45 0.00 44.51 4.30
2664 2834 3.659089 TAAAGCGGCAGACGGAGGC 62.659 63.158 1.45 0.00 44.51 4.70
2678 2848 4.779733 AGGCGGACGAGGACCCAT 62.780 66.667 0.00 0.00 0.00 4.00
2740 2910 0.250945 ATATCGCCTCTCTGGAGCGA 60.251 55.000 8.87 8.87 44.80 4.93
2773 2943 3.519930 GGGCGGGTCTCGAGTCTC 61.520 72.222 13.13 5.81 42.43 3.36
2777 2947 2.438795 GGGTCTCGAGTCTCGGCT 60.439 66.667 21.63 0.00 40.88 5.52
2802 2972 4.518970 TGCCACCAGTGTTTAGAGATTTTC 59.481 41.667 0.00 0.00 0.00 2.29
2830 3000 0.868406 GAATATGGGCAGTGCTACGC 59.132 55.000 16.11 0.00 0.00 4.42
2842 3012 3.653009 CTACGCGTCGGGCCGATA 61.653 66.667 33.54 18.92 38.42 2.92
2843 3013 3.185082 CTACGCGTCGGGCCGATAA 62.185 63.158 33.54 14.42 38.42 1.75
2844 3014 2.467946 CTACGCGTCGGGCCGATAAT 62.468 60.000 33.54 19.62 38.42 1.28
2845 3015 2.074230 TACGCGTCGGGCCGATAATT 62.074 55.000 33.54 18.89 38.42 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.814188 TCATGTGACTGATAACATCTTGAGC 59.186 40.000 0.00 0.00 34.81 4.26
57 58 0.391130 TCCTCCAAATCAACCGAGCG 60.391 55.000 0.00 0.00 0.00 5.03
67 68 4.697352 CAGTCTTCGTGAATTCCTCCAAAT 59.303 41.667 2.27 0.00 0.00 2.32
83 84 4.537936 AAAGCTCGTGTTTTCAGTCTTC 57.462 40.909 0.00 0.00 0.00 2.87
118 119 2.026262 TCCTAAGTGCTGGTTCCATTCC 60.026 50.000 0.00 0.00 0.00 3.01
168 169 2.225467 GTCCTATCCAGGCAAATGCTC 58.775 52.381 5.25 0.00 42.30 4.26
178 179 2.423446 GGCCTGCGTCCTATCCAG 59.577 66.667 0.00 0.00 0.00 3.86
210 211 1.185618 TTCTGGAGAGGGTGGACACG 61.186 60.000 0.00 0.00 0.00 4.49
273 274 0.166814 GCAACGCTGACAATGGAGAC 59.833 55.000 0.00 0.00 0.00 3.36
274 275 1.291184 CGCAACGCTGACAATGGAGA 61.291 55.000 0.00 0.00 0.00 3.71
275 276 1.133253 CGCAACGCTGACAATGGAG 59.867 57.895 0.00 0.00 0.00 3.86
283 284 0.859232 GAAGAAACTCGCAACGCTGA 59.141 50.000 0.00 0.00 0.00 4.26
309 319 2.343101 TGTTCGTTCCAGCTAAATCCG 58.657 47.619 0.00 0.00 0.00 4.18
323 333 9.689976 TCAAAATGATGATTATTTGTTGTTCGT 57.310 25.926 0.00 0.00 35.01 3.85
398 409 3.364964 CGGCCTCAATGTAAGTGTTGTTC 60.365 47.826 0.00 0.00 31.21 3.18
414 425 1.314730 TGAAGGACAAAAACGGCCTC 58.685 50.000 0.00 0.00 0.00 4.70
500 511 0.608640 CCTTCGTTGCCACTACCTCT 59.391 55.000 0.00 0.00 0.00 3.69
506 517 1.004440 GCTCTCCTTCGTTGCCACT 60.004 57.895 0.00 0.00 0.00 4.00
526 537 4.820744 GCCGGCCACCATGACCAT 62.821 66.667 18.11 0.00 0.00 3.55
628 639 3.047280 CGCTGCGGCCAACACTAA 61.047 61.111 15.40 0.00 34.44 2.24
654 665 2.111460 TAACACCCCACCACACGC 59.889 61.111 0.00 0.00 0.00 5.34
716 735 4.465446 TCTCCCAGCCTCTCCCGG 62.465 72.222 0.00 0.00 0.00 5.73
727 746 4.626402 AACCCGTCCCGTCTCCCA 62.626 66.667 0.00 0.00 0.00 4.37
791 812 2.224281 TGCCGCTGATAATTCACCCTAG 60.224 50.000 0.00 0.00 0.00 3.02
797 818 2.708216 TCCTTGCCGCTGATAATTCA 57.292 45.000 0.00 0.00 0.00 2.57
837 858 0.524816 CGATACGACCACGACAAGGG 60.525 60.000 0.00 0.00 42.66 3.95
840 861 0.039346 TTGCGATACGACCACGACAA 60.039 50.000 0.00 0.00 42.66 3.18
915 940 6.210784 TCCCGGTTCTATGGATTTGTAGATAG 59.789 42.308 0.00 0.00 0.00 2.08
916 941 6.014840 GTCCCGGTTCTATGGATTTGTAGATA 60.015 42.308 0.00 0.00 0.00 1.98
919 944 4.377897 GTCCCGGTTCTATGGATTTGTAG 58.622 47.826 0.00 0.00 0.00 2.74
923 948 2.102588 CTCGTCCCGGTTCTATGGATTT 59.897 50.000 0.00 0.00 0.00 2.17
939 964 0.591659 GTTTTGGGGCTTGTCTCGTC 59.408 55.000 0.00 0.00 0.00 4.20
945 970 1.324383 CTTACGGTTTTGGGGCTTGT 58.676 50.000 0.00 0.00 0.00 3.16
984 1009 1.915141 CCATGCTTGGAACTGGAAGT 58.085 50.000 13.33 0.00 46.92 3.01
986 1011 1.243342 CGCCATGCTTGGAACTGGAA 61.243 55.000 22.21 0.00 46.92 3.53
1160 1185 4.527157 GCTTGCTCGCCACGATGC 62.527 66.667 0.00 0.00 34.61 3.91
1161 1186 4.214383 CGCTTGCTCGCCACGATG 62.214 66.667 0.00 0.00 34.61 3.84
1179 1204 0.605589 CCGTGGACAAGGGTTCTTCC 60.606 60.000 0.00 0.00 0.00 3.46
1184 1209 3.530910 CTCGCCGTGGACAAGGGTT 62.531 63.158 6.42 0.00 36.12 4.11
1224 1249 2.106938 TGGATGATGGACGCGCTC 59.893 61.111 5.73 2.64 0.00 5.03
1304 1329 3.078837 GAGAGGTGTCTCGTCTTCTTCT 58.921 50.000 0.00 0.00 44.47 2.85
1305 1330 3.481112 GAGAGGTGTCTCGTCTTCTTC 57.519 52.381 0.00 0.00 44.47 2.87
1315 1340 2.983930 GCGCGTCTGAGAGGTGTCT 61.984 63.158 15.89 0.00 34.86 3.41
1316 1341 2.505118 GCGCGTCTGAGAGGTGTC 60.505 66.667 15.89 6.10 31.70 3.67
1317 1342 3.295273 TGCGCGTCTGAGAGGTGT 61.295 61.111 15.89 0.00 31.70 4.16
1318 1343 2.807045 GTGCGCGTCTGAGAGGTG 60.807 66.667 8.43 11.03 0.00 4.00
1381 1406 1.262683 GTATTTCTGCATGCTCGGCTC 59.737 52.381 20.33 0.61 0.00 4.70
1455 1480 2.841988 AGGGCCTGGATCTCTCGC 60.842 66.667 4.50 0.00 0.00 5.03
1458 1483 1.760086 CGTGAGGGCCTGGATCTCT 60.760 63.158 12.95 0.00 0.00 3.10
1500 1525 2.570181 CCGTGGACGTGGTAGACC 59.430 66.667 0.00 0.00 37.74 3.85
1510 1535 2.579787 CTCGATGACGCCGTGGAC 60.580 66.667 0.00 0.00 39.58 4.02
1514 1539 2.380410 GCAAACTCGATGACGCCGT 61.380 57.895 0.00 0.00 39.58 5.68
1519 1544 3.555518 GTTTCAAGGCAAACTCGATGAC 58.444 45.455 0.00 0.00 34.03 3.06
1527 1552 1.206115 CGTGCGGTTTCAAGGCAAAC 61.206 55.000 0.00 0.00 38.58 2.93
1529 1554 2.718731 CGTGCGGTTTCAAGGCAA 59.281 55.556 0.00 0.00 38.58 4.52
1530 1555 3.959975 GCGTGCGGTTTCAAGGCA 61.960 61.111 0.00 0.00 0.00 4.75
1534 1559 1.377366 TTGGAAGCGTGCGGTTTCAA 61.377 50.000 21.50 21.50 45.39 2.69
1535 1560 1.781025 CTTGGAAGCGTGCGGTTTCA 61.781 55.000 12.69 12.69 39.09 2.69
1539 1576 3.883744 CTCCTTGGAAGCGTGCGGT 62.884 63.158 0.00 0.00 0.00 5.68
1570 1607 4.856607 GAACTCCTCCCTCGCGCG 62.857 72.222 26.76 26.76 0.00 6.86
1571 1608 4.856607 CGAACTCCTCCCTCGCGC 62.857 72.222 0.00 0.00 0.00 6.86
1572 1609 3.441290 ACGAACTCCTCCCTCGCG 61.441 66.667 0.00 0.00 36.03 5.87
1575 1612 2.156051 AACGCACGAACTCCTCCCTC 62.156 60.000 0.00 0.00 0.00 4.30
1581 1618 2.717809 GAGCGAACGCACGAACTCC 61.718 63.158 20.66 0.00 44.88 3.85
1670 1707 1.153765 TCGATGTTCAGCTGCGAGG 60.154 57.895 9.47 0.00 0.00 4.63
1711 1748 2.711922 CGGACTCCCTGAACCTCCG 61.712 68.421 0.00 0.00 38.12 4.63
1812 1849 1.403647 CCAACGTAATCTGCCTCGTCA 60.404 52.381 0.00 0.00 35.49 4.35
1815 1852 1.752501 CGCCAACGTAATCTGCCTCG 61.753 60.000 0.00 0.00 33.53 4.63
1816 1853 1.429148 CCGCCAACGTAATCTGCCTC 61.429 60.000 0.00 0.00 37.70 4.70
1845 1882 3.430333 AACCATGAAACAAACACGTCC 57.570 42.857 0.00 0.00 0.00 4.79
1846 1883 4.491763 GCAAAACCATGAAACAAACACGTC 60.492 41.667 0.00 0.00 0.00 4.34
1847 1884 3.369451 GCAAAACCATGAAACAAACACGT 59.631 39.130 0.00 0.00 0.00 4.49
1848 1885 3.541129 CGCAAAACCATGAAACAAACACG 60.541 43.478 0.00 0.00 0.00 4.49
1849 1886 3.242252 CCGCAAAACCATGAAACAAACAC 60.242 43.478 0.00 0.00 0.00 3.32
1850 1887 2.932614 CCGCAAAACCATGAAACAAACA 59.067 40.909 0.00 0.00 0.00 2.83
1851 1888 2.286125 GCCGCAAAACCATGAAACAAAC 60.286 45.455 0.00 0.00 0.00 2.93
1852 1889 1.936547 GCCGCAAAACCATGAAACAAA 59.063 42.857 0.00 0.00 0.00 2.83
1853 1890 1.576356 GCCGCAAAACCATGAAACAA 58.424 45.000 0.00 0.00 0.00 2.83
1854 1891 0.249657 GGCCGCAAAACCATGAAACA 60.250 50.000 0.00 0.00 0.00 2.83
1855 1892 1.281566 CGGCCGCAAAACCATGAAAC 61.282 55.000 14.67 0.00 0.00 2.78
1856 1893 1.006805 CGGCCGCAAAACCATGAAA 60.007 52.632 14.67 0.00 0.00 2.69
1857 1894 2.647875 CGGCCGCAAAACCATGAA 59.352 55.556 14.67 0.00 0.00 2.57
1858 1895 3.369400 CCGGCCGCAAAACCATGA 61.369 61.111 22.85 0.00 0.00 3.07
1859 1896 3.679738 ACCGGCCGCAAAACCATG 61.680 61.111 22.85 4.97 0.00 3.66
1860 1897 3.679738 CACCGGCCGCAAAACCAT 61.680 61.111 22.85 0.00 0.00 3.55
1862 1899 4.337060 GACACCGGCCGCAAAACC 62.337 66.667 22.85 1.84 0.00 3.27
1863 1900 3.284449 AGACACCGGCCGCAAAAC 61.284 61.111 22.85 9.53 0.00 2.43
1864 1901 3.283684 CAGACACCGGCCGCAAAA 61.284 61.111 22.85 0.00 0.00 2.44
1865 1902 3.545124 ATCAGACACCGGCCGCAAA 62.545 57.895 22.85 0.00 0.00 3.68
1866 1903 3.950794 GATCAGACACCGGCCGCAA 62.951 63.158 22.85 0.00 0.00 4.85
1867 1904 4.451150 GATCAGACACCGGCCGCA 62.451 66.667 22.85 0.00 0.00 5.69
1870 1907 4.451150 TGCGATCAGACACCGGCC 62.451 66.667 0.00 0.00 0.00 6.13
1871 1908 2.887568 CTGCGATCAGACACCGGC 60.888 66.667 0.00 0.00 42.95 6.13
1872 1909 2.887568 GCTGCGATCAGACACCGG 60.888 66.667 0.00 0.00 42.95 5.28
1873 1910 3.250323 CGCTGCGATCAGACACCG 61.250 66.667 18.66 0.00 42.95 4.94
1874 1911 2.887568 CCGCTGCGATCAGACACC 60.888 66.667 25.45 0.00 42.95 4.16
1875 1912 3.558411 GCCGCTGCGATCAGACAC 61.558 66.667 25.45 0.00 42.95 3.67
1876 1913 3.375472 ATGCCGCTGCGATCAGACA 62.375 57.895 25.45 11.43 42.95 3.41
1877 1914 2.587194 ATGCCGCTGCGATCAGAC 60.587 61.111 25.45 5.95 42.95 3.51
1878 1915 2.279717 GATGCCGCTGCGATCAGA 60.280 61.111 25.45 2.18 42.95 3.27
1879 1916 3.344215 GGATGCCGCTGCGATCAG 61.344 66.667 25.45 7.71 41.78 2.90
1890 1927 0.808847 GAGTAACGGGTTCGGATGCC 60.809 60.000 0.00 0.00 41.39 4.40
1891 1928 0.175073 AGAGTAACGGGTTCGGATGC 59.825 55.000 0.00 0.00 41.39 3.91
1892 1929 3.067742 ACATAGAGTAACGGGTTCGGATG 59.932 47.826 0.00 0.00 41.39 3.51
1893 1930 3.294214 ACATAGAGTAACGGGTTCGGAT 58.706 45.455 0.00 0.00 41.39 4.18
1894 1931 2.726821 ACATAGAGTAACGGGTTCGGA 58.273 47.619 0.00 0.00 41.39 4.55
1895 1932 3.546815 CGTACATAGAGTAACGGGTTCGG 60.547 52.174 0.00 0.00 41.39 4.30
1896 1933 3.309682 TCGTACATAGAGTAACGGGTTCG 59.690 47.826 0.00 0.00 43.02 3.95
1897 1934 4.592179 GTCGTACATAGAGTAACGGGTTC 58.408 47.826 0.00 0.00 33.72 3.62
1898 1935 3.063997 CGTCGTACATAGAGTAACGGGTT 59.936 47.826 0.00 0.00 34.74 4.11
1899 1936 2.609459 CGTCGTACATAGAGTAACGGGT 59.391 50.000 0.00 0.00 34.74 5.28
1900 1937 2.032549 CCGTCGTACATAGAGTAACGGG 60.033 54.545 9.51 0.00 46.22 5.28
1901 1938 3.244670 CCGTCGTACATAGAGTAACGG 57.755 52.381 4.70 4.70 45.40 4.44
1902 1939 4.033358 AGTTCCGTCGTACATAGAGTAACG 59.967 45.833 0.00 0.00 36.93 3.18
1903 1940 5.476752 AGTTCCGTCGTACATAGAGTAAC 57.523 43.478 0.00 0.00 33.72 2.50
1904 1941 7.609760 TTTAGTTCCGTCGTACATAGAGTAA 57.390 36.000 0.00 0.00 33.72 2.24
1905 1942 7.792374 ATTTAGTTCCGTCGTACATAGAGTA 57.208 36.000 0.00 0.00 0.00 2.59
1906 1943 6.690194 ATTTAGTTCCGTCGTACATAGAGT 57.310 37.500 0.00 0.00 0.00 3.24
1907 1944 7.074502 GGTATTTAGTTCCGTCGTACATAGAG 58.925 42.308 0.00 0.00 0.00 2.43
1908 1945 6.292865 CGGTATTTAGTTCCGTCGTACATAGA 60.293 42.308 0.00 0.00 39.51 1.98
1909 1946 5.848036 CGGTATTTAGTTCCGTCGTACATAG 59.152 44.000 0.00 0.00 39.51 2.23
1910 1947 5.747565 CGGTATTTAGTTCCGTCGTACATA 58.252 41.667 0.00 0.00 39.51 2.29
1911 1948 4.601019 CGGTATTTAGTTCCGTCGTACAT 58.399 43.478 0.00 0.00 39.51 2.29
1912 1949 3.730662 GCGGTATTTAGTTCCGTCGTACA 60.731 47.826 0.00 0.00 45.11 2.90
1913 1950 2.783832 GCGGTATTTAGTTCCGTCGTAC 59.216 50.000 0.00 0.00 45.11 3.67
1914 1951 2.538737 CGCGGTATTTAGTTCCGTCGTA 60.539 50.000 0.00 0.00 45.11 3.43
1915 1952 1.795162 CGCGGTATTTAGTTCCGTCGT 60.795 52.381 0.00 0.00 45.11 4.34
1916 1953 0.841984 CGCGGTATTTAGTTCCGTCG 59.158 55.000 0.00 0.00 45.11 5.12
1917 1954 0.573987 GCGCGGTATTTAGTTCCGTC 59.426 55.000 8.83 0.00 45.11 4.79
1918 1955 0.108709 TGCGCGGTATTTAGTTCCGT 60.109 50.000 8.83 0.00 45.11 4.69
1919 1956 1.000884 TTGCGCGGTATTTAGTTCCG 58.999 50.000 8.83 0.00 45.94 4.30
1920 1957 2.610374 TCATTGCGCGGTATTTAGTTCC 59.390 45.455 8.83 0.00 0.00 3.62
1921 1958 3.936902 TCATTGCGCGGTATTTAGTTC 57.063 42.857 8.83 0.00 0.00 3.01
1922 1959 4.688511 TTTCATTGCGCGGTATTTAGTT 57.311 36.364 8.83 0.00 0.00 2.24
1923 1960 4.893424 ATTTCATTGCGCGGTATTTAGT 57.107 36.364 8.83 0.00 0.00 2.24
1924 1961 5.851177 CCTTATTTCATTGCGCGGTATTTAG 59.149 40.000 8.83 0.00 0.00 1.85
1925 1962 5.278071 CCCTTATTTCATTGCGCGGTATTTA 60.278 40.000 8.83 0.00 0.00 1.40
1926 1963 4.499019 CCCTTATTTCATTGCGCGGTATTT 60.499 41.667 8.83 0.00 0.00 1.40
1927 1964 3.004315 CCCTTATTTCATTGCGCGGTATT 59.996 43.478 8.83 0.00 0.00 1.89
1928 1965 2.552315 CCCTTATTTCATTGCGCGGTAT 59.448 45.455 8.83 0.00 0.00 2.73
1929 1966 1.944024 CCCTTATTTCATTGCGCGGTA 59.056 47.619 8.83 0.00 0.00 4.02
1930 1967 0.738389 CCCTTATTTCATTGCGCGGT 59.262 50.000 8.83 0.00 0.00 5.68
1931 1968 0.030638 CCCCTTATTTCATTGCGCGG 59.969 55.000 8.83 0.00 0.00 6.46
1932 1969 0.594796 GCCCCTTATTTCATTGCGCG 60.595 55.000 0.00 0.00 0.00 6.86
1933 1970 0.746659 AGCCCCTTATTTCATTGCGC 59.253 50.000 0.00 0.00 0.00 6.09
1934 1971 1.750778 ACAGCCCCTTATTTCATTGCG 59.249 47.619 0.00 0.00 0.00 4.85
1935 1972 2.223572 CGACAGCCCCTTATTTCATTGC 60.224 50.000 0.00 0.00 0.00 3.56
1936 1973 3.278574 TCGACAGCCCCTTATTTCATTG 58.721 45.455 0.00 0.00 0.00 2.82
1937 1974 3.199946 TCTCGACAGCCCCTTATTTCATT 59.800 43.478 0.00 0.00 0.00 2.57
1938 1975 2.771943 TCTCGACAGCCCCTTATTTCAT 59.228 45.455 0.00 0.00 0.00 2.57
1939 1976 2.184533 TCTCGACAGCCCCTTATTTCA 58.815 47.619 0.00 0.00 0.00 2.69
1940 1977 2.937149 GTTCTCGACAGCCCCTTATTTC 59.063 50.000 0.00 0.00 0.00 2.17
1941 1978 2.304761 TGTTCTCGACAGCCCCTTATTT 59.695 45.455 0.00 0.00 33.40 1.40
1942 1979 1.906574 TGTTCTCGACAGCCCCTTATT 59.093 47.619 0.00 0.00 33.40 1.40
1943 1980 1.568504 TGTTCTCGACAGCCCCTTAT 58.431 50.000 0.00 0.00 33.40 1.73
1944 1981 1.344065 TTGTTCTCGACAGCCCCTTA 58.656 50.000 0.00 0.00 39.94 2.69
1945 1982 0.472471 TTTGTTCTCGACAGCCCCTT 59.528 50.000 0.00 0.00 39.94 3.95
1946 1983 0.250338 GTTTGTTCTCGACAGCCCCT 60.250 55.000 0.00 0.00 39.94 4.79
1947 1984 1.566018 CGTTTGTTCTCGACAGCCCC 61.566 60.000 0.00 0.00 39.94 5.80
1948 1985 0.878961 ACGTTTGTTCTCGACAGCCC 60.879 55.000 0.00 0.00 39.94 5.19
1949 1986 0.507358 GACGTTTGTTCTCGACAGCC 59.493 55.000 0.00 0.00 39.94 4.85
1950 1987 0.158928 CGACGTTTGTTCTCGACAGC 59.841 55.000 0.00 0.00 39.94 4.40
1951 1988 0.158928 GCGACGTTTGTTCTCGACAG 59.841 55.000 0.00 0.00 39.94 3.51
1952 1989 0.248743 AGCGACGTTTGTTCTCGACA 60.249 50.000 0.00 0.00 36.19 4.35
1953 1990 0.430110 GAGCGACGTTTGTTCTCGAC 59.570 55.000 0.00 0.00 0.00 4.20
1954 1991 0.309922 AGAGCGACGTTTGTTCTCGA 59.690 50.000 0.00 0.00 34.89 4.04
1955 1992 0.431233 CAGAGCGACGTTTGTTCTCG 59.569 55.000 5.36 0.00 34.89 4.04
1956 1993 1.488527 ACAGAGCGACGTTTGTTCTC 58.511 50.000 5.36 0.00 0.00 2.87
1957 1994 1.593006 CAACAGAGCGACGTTTGTTCT 59.407 47.619 9.65 0.00 31.84 3.01
1958 1995 1.332904 CCAACAGAGCGACGTTTGTTC 60.333 52.381 9.65 0.00 31.84 3.18
1959 1996 0.655733 CCAACAGAGCGACGTTTGTT 59.344 50.000 0.00 2.51 34.31 2.83
1960 1997 0.461339 ACCAACAGAGCGACGTTTGT 60.461 50.000 0.00 0.00 0.00 2.83
1961 1998 0.655733 AACCAACAGAGCGACGTTTG 59.344 50.000 0.00 0.00 0.00 2.93
1962 1999 2.132762 CTAACCAACAGAGCGACGTTT 58.867 47.619 0.00 0.00 0.00 3.60
1963 2000 1.779569 CTAACCAACAGAGCGACGTT 58.220 50.000 0.00 0.00 0.00 3.99
1964 2001 0.666577 GCTAACCAACAGAGCGACGT 60.667 55.000 0.00 0.00 0.00 4.34
1965 2002 1.352156 GGCTAACCAACAGAGCGACG 61.352 60.000 0.00 0.00 37.07 5.12
1966 2003 1.019805 GGGCTAACCAACAGAGCGAC 61.020 60.000 0.00 0.00 39.85 5.19
1967 2004 1.192146 AGGGCTAACCAACAGAGCGA 61.192 55.000 0.00 0.00 43.89 4.93
1968 2005 1.021390 CAGGGCTAACCAACAGAGCG 61.021 60.000 0.00 0.00 43.89 5.03
1969 2006 0.036875 ACAGGGCTAACCAACAGAGC 59.963 55.000 0.00 0.00 43.89 4.09
1970 2007 2.568623 AACAGGGCTAACCAACAGAG 57.431 50.000 0.00 0.00 43.89 3.35
1971 2008 3.306472 AAAACAGGGCTAACCAACAGA 57.694 42.857 0.00 0.00 43.89 3.41
2033 2070 8.628882 TGTCTAATGAAACATATGTGTACTCG 57.371 34.615 9.63 0.00 37.67 4.18
2127 2185 6.738114 TCTGCCAAAGTGAAATTCTAGTTTG 58.262 36.000 13.67 13.67 37.11 2.93
2232 2290 5.048083 GTGCTCCTCTAGATCTTGGTATGAG 60.048 48.000 0.00 4.93 0.00 2.90
2258 2317 6.071952 ACTCGAAAAACATCCTTGTATGCAAT 60.072 34.615 0.00 0.00 34.06 3.56
2283 2343 2.125832 GGCGGTCCGTTTCATCGA 60.126 61.111 13.94 0.00 0.00 3.59
2413 2494 4.856801 GCGTGGATGGCGGGATGT 62.857 66.667 0.00 0.00 0.00 3.06
2433 2514 1.102978 GTTTGGTGTCTTGCAGTGGT 58.897 50.000 0.00 0.00 0.00 4.16
2501 2583 3.576078 AGGTTTTGTGTCTGATGGTCA 57.424 42.857 0.00 0.00 0.00 4.02
2518 2600 2.165845 CGGTCTTCAGATTCGGTAAGGT 59.834 50.000 0.00 0.00 0.00 3.50
2544 2626 3.257933 GCAAGTGGCTCGGTCTTG 58.742 61.111 0.00 0.00 40.71 3.02
2575 2657 2.851263 TCTCGGTGGTGCTTTAATGT 57.149 45.000 0.00 0.00 0.00 2.71
2607 2690 3.966218 CCGCGTCGAAATAATTTGATTCC 59.034 43.478 4.92 0.00 31.64 3.01
2633 2718 2.840974 GCTTTAGCGGCTTGAGTGA 58.159 52.632 8.26 0.00 0.00 3.41
2644 2729 2.125673 TCCGTCTGCCGCTTTAGC 60.126 61.111 0.00 0.00 34.38 3.09
2663 2833 4.570663 CGATGGGTCCTCGTCCGC 62.571 72.222 0.00 0.00 0.00 5.54
2664 2834 3.138798 ACGATGGGTCCTCGTCCG 61.139 66.667 0.46 0.00 45.63 4.79
2740 2910 2.584608 CCCGTTCGCTCCTGGAAT 59.415 61.111 0.00 0.00 0.00 3.01
2760 2930 2.438795 AGCCGAGACTCGAGACCC 60.439 66.667 26.11 2.20 43.74 4.46
2777 2947 2.325484 TCTCTAAACACTGGTGGCAGA 58.675 47.619 5.70 4.00 34.19 4.26
2802 2972 6.471146 AGCACTGCCCATATTCTTATAGAAG 58.529 40.000 0.00 0.00 37.69 2.85


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

AutoCloner maintained by Alex Coulton.