Multiple sequence alignment - TraesCS2B01G443900

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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 TraesCS2B01G443900 chr2B 100.000 2426 0 0 1 2426 636777429 636775004 0.000000e+00 4481
1 TraesCS2B01G443900 chr2A 88.573 1864 129 39 1 1814 678673005 678671176 0.000000e+00 2185
2 TraesCS2B01G443900 chr2A 93.983 349 16 4 2061 2409 678671180 678670837 7.690000e-145 523
3 TraesCS2B01G443900 chr2A 79.178 365 42 15 2064 2424 678670074 678669740 3.140000e-54 222
4 TraesCS2B01G443900 chr2D 87.191 1538 117 40 1 1496 535573361 535571862 0.000000e+00 1676
5 TraesCS2B01G443900 chr2D 94.851 369 11 5 2061 2426 535571583 535571220 9.730000e-159 569
6 TraesCS2B01G443900 chr2D 92.414 290 17 3 1527 1814 535571865 535571579 2.250000e-110 409
7 TraesCS2B01G443900 chr2D 80.055 361 39 14 2064 2424 535570470 535570143 1.120000e-58 237
8 TraesCS2B01G443900 chr4D 92.946 241 13 4 1815 2052 51076340 51076101 4.960000e-92 348
9 TraesCS2B01G443900 chr4D 89.695 262 25 2 1802 2061 331710060 331709799 1.390000e-87 333
10 TraesCS2B01G443900 chr4B 92.181 243 17 2 1815 2056 447455463 447455222 2.310000e-90 342
11 TraesCS2B01G443900 chr6B 92.050 239 19 0 1815 2053 352091544 352091782 1.070000e-88 337
12 TraesCS2B01G443900 chr3B 92.050 239 16 3 1815 2053 519399319 519399084 1.390000e-87 333
13 TraesCS2B01G443900 chr4A 90.400 250 24 0 1806 2055 674523385 674523634 1.800000e-86 329
14 TraesCS2B01G443900 chr1B 90.574 244 21 2 1811 2053 589055662 589055904 3.010000e-84 322
15 TraesCS2B01G443900 chr1B 89.328 253 24 3 1809 2061 553450277 553450028 5.040000e-82 315
16 TraesCS2B01G443900 chr3A 89.723 253 21 4 1810 2061 501225636 501225884 3.890000e-83 318


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 TraesCS2B01G443900 chr2B 636775004 636777429 2425 True 4481.000000 4481 100.000000 1 2426 1 chr2B.!!$R1 2425
1 TraesCS2B01G443900 chr2A 678669740 678673005 3265 True 976.666667 2185 87.244667 1 2424 3 chr2A.!!$R1 2423
2 TraesCS2B01G443900 chr2D 535570143 535573361 3218 True 722.750000 1676 88.627750 1 2426 4 chr2D.!!$R1 2425

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
391 436 0.234884 GAACGTCCTGTTTGCTTCGG 59.765 55.0 0.0 0.0 42.09 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1931 0.031449 AAAACGTTCGGGTTGCCATG 59.969 50.0 0.0 0.0 0.0 3.66 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
37 38 1.268589 CGTGTCTATCCATTCGACGCT 60.269 52.381 0.00 0.00 36.36 5.07
221 231 2.018544 CCCAAACGTCAACGAGCAA 58.981 52.632 9.88 0.00 43.02 3.91
222 232 0.316689 CCCAAACGTCAACGAGCAAC 60.317 55.000 9.88 0.00 43.02 4.17
223 233 0.375454 CCAAACGTCAACGAGCAACA 59.625 50.000 9.88 0.00 43.02 3.33
224 234 1.452717 CAAACGTCAACGAGCAACAC 58.547 50.000 9.88 0.00 43.02 3.32
257 279 2.586648 AAATCTCGAGCCCAAAAGGT 57.413 45.000 7.81 0.00 38.26 3.50
273 295 1.563616 AGGTATCATCCCCCTCCTCT 58.436 55.000 0.00 0.00 0.00 3.69
279 301 2.416923 ATCCCCCTCCTCTCTCCCC 61.417 68.421 0.00 0.00 0.00 4.81
295 317 3.130160 CCTGGCTTCTTCGCTGCC 61.130 66.667 0.00 0.00 46.26 4.85
302 324 0.532573 CTTCTTCGCTGCCACTCCTA 59.467 55.000 0.00 0.00 0.00 2.94
303 328 1.137872 CTTCTTCGCTGCCACTCCTAT 59.862 52.381 0.00 0.00 0.00 2.57
305 330 0.249657 CTTCGCTGCCACTCCTATCC 60.250 60.000 0.00 0.00 0.00 2.59
306 331 2.016393 TTCGCTGCCACTCCTATCCG 62.016 60.000 0.00 0.00 0.00 4.18
310 335 2.093537 CTGCCACTCCTATCCGCCTC 62.094 65.000 0.00 0.00 0.00 4.70
346 391 4.452733 CCGACCCGCCTCCAGAAC 62.453 72.222 0.00 0.00 0.00 3.01
347 392 4.452733 CGACCCGCCTCCAGAACC 62.453 72.222 0.00 0.00 0.00 3.62
348 393 3.319198 GACCCGCCTCCAGAACCA 61.319 66.667 0.00 0.00 0.00 3.67
349 394 3.316573 GACCCGCCTCCAGAACCAG 62.317 68.421 0.00 0.00 0.00 4.00
350 395 3.322466 CCCGCCTCCAGAACCAGT 61.322 66.667 0.00 0.00 0.00 4.00
351 396 2.266055 CCGCCTCCAGAACCAGTC 59.734 66.667 0.00 0.00 0.00 3.51
352 397 2.125912 CGCCTCCAGAACCAGTCG 60.126 66.667 0.00 0.00 0.00 4.18
353 398 2.435059 GCCTCCAGAACCAGTCGC 60.435 66.667 0.00 0.00 0.00 5.19
354 399 2.266055 CCTCCAGAACCAGTCGCC 59.734 66.667 0.00 0.00 0.00 5.54
355 400 2.286523 CCTCCAGAACCAGTCGCCT 61.287 63.158 0.00 0.00 0.00 5.52
356 401 1.216710 CTCCAGAACCAGTCGCCTC 59.783 63.158 0.00 0.00 0.00 4.70
357 402 2.232298 CTCCAGAACCAGTCGCCTCC 62.232 65.000 0.00 0.00 0.00 4.30
358 403 2.583441 CCAGAACCAGTCGCCTCCA 61.583 63.158 0.00 0.00 0.00 3.86
359 404 1.079543 CAGAACCAGTCGCCTCCAG 60.080 63.158 0.00 0.00 0.00 3.86
360 405 1.228894 AGAACCAGTCGCCTCCAGA 60.229 57.895 0.00 0.00 0.00 3.86
369 414 4.148825 GCCTCCAGATCGGTGCGT 62.149 66.667 3.97 0.00 35.57 5.24
370 415 2.105128 CCTCCAGATCGGTGCGTC 59.895 66.667 3.97 0.00 35.57 5.19
374 419 2.180769 CAGATCGGTGCGTCGGAA 59.819 61.111 0.00 0.00 0.00 4.30
391 436 0.234884 GAACGTCCTGTTTGCTTCGG 59.765 55.000 0.00 0.00 42.09 4.30
453 498 1.315981 TTGGTGTTGTTTGGCGAGCA 61.316 50.000 0.00 0.00 0.00 4.26
485 530 3.359194 CTTCTCCACCGAGATGCAG 57.641 57.895 0.00 0.00 44.68 4.41
490 535 1.751351 CTCCACCGAGATGCAGTTAGA 59.249 52.381 0.00 0.00 38.52 2.10
515 560 8.329203 ACTCTGTTTTTCTAGGTTGATTGATC 57.671 34.615 0.00 0.00 0.00 2.92
524 569 2.432510 AGGTTGATTGATCCGAGTCCTC 59.567 50.000 0.00 0.00 0.00 3.71
539 584 5.461032 GAGTCCTCGATTAGATGATTGGT 57.539 43.478 0.00 0.00 0.00 3.67
540 585 6.576662 GAGTCCTCGATTAGATGATTGGTA 57.423 41.667 0.00 0.00 0.00 3.25
541 586 6.582677 AGTCCTCGATTAGATGATTGGTAG 57.417 41.667 0.00 0.00 0.00 3.18
542 587 6.071984 AGTCCTCGATTAGATGATTGGTAGT 58.928 40.000 0.00 0.00 0.00 2.73
543 588 7.232188 AGTCCTCGATTAGATGATTGGTAGTA 58.768 38.462 0.00 0.00 0.00 1.82
544 589 7.392113 AGTCCTCGATTAGATGATTGGTAGTAG 59.608 40.741 0.00 0.00 0.00 2.57
545 590 7.175293 GTCCTCGATTAGATGATTGGTAGTAGT 59.825 40.741 0.00 0.00 0.00 2.73
546 591 8.380867 TCCTCGATTAGATGATTGGTAGTAGTA 58.619 37.037 0.00 0.00 0.00 1.82
547 592 8.670135 CCTCGATTAGATGATTGGTAGTAGTAG 58.330 40.741 0.00 0.00 0.00 2.57
573 618 7.849322 AGTAGTAGTAGTAGTAGTCCTACCC 57.151 44.000 10.17 0.00 46.15 3.69
574 619 6.785466 AGTAGTAGTAGTAGTAGTCCTACCCC 59.215 46.154 10.17 0.00 46.15 4.95
576 621 3.658725 AGTAGTAGTAGTCCTACCCCGA 58.341 50.000 0.89 0.00 46.15 5.14
581 626 1.064832 AGTAGTCCTACCCCGACTGTC 60.065 57.143 0.00 0.00 40.75 3.51
585 630 1.345415 GTCCTACCCCGACTGTCAAAA 59.655 52.381 8.73 0.00 0.00 2.44
586 631 1.345415 TCCTACCCCGACTGTCAAAAC 59.655 52.381 8.73 0.00 0.00 2.43
604 649 5.067283 TCAAAACTTGGTAGCTTCAACCTTC 59.933 40.000 5.75 0.00 37.91 3.46
625 670 0.322906 GGAAGGGGTTGGAGAGCTTG 60.323 60.000 0.00 0.00 0.00 4.01
626 671 0.962855 GAAGGGGTTGGAGAGCTTGC 60.963 60.000 0.00 0.00 0.00 4.01
628 673 2.747855 GGGTTGGAGAGCTTGCCG 60.748 66.667 0.00 0.00 0.00 5.69
643 701 2.280524 CCGGTGGTTTGACGCTCA 60.281 61.111 0.00 0.00 0.00 4.26
659 717 5.178623 TGACGCTCAATTTCGTTCAGTAATT 59.821 36.000 0.00 0.00 39.22 1.40
664 722 5.617609 TCAATTTCGTTCAGTAATTGCTCG 58.382 37.500 0.00 0.00 43.16 5.03
687 745 1.066858 CCGTGCCTGTGAATCAGTACT 60.067 52.381 0.00 0.00 42.19 2.73
688 746 2.165641 CCGTGCCTGTGAATCAGTACTA 59.834 50.000 0.00 0.00 42.19 1.82
698 756 3.696051 TGAATCAGTACTACCGTGGGTAC 59.304 47.826 0.00 7.93 37.09 3.34
715 773 2.277084 GTACTGGGCGTTTATCCTGTG 58.723 52.381 0.00 0.00 36.73 3.66
716 774 0.690762 ACTGGGCGTTTATCCTGTGT 59.309 50.000 0.00 0.00 34.60 3.72
730 795 0.675837 CTGTGTGATGTGCTCTGGGG 60.676 60.000 0.00 0.00 0.00 4.96
747 812 0.618981 GGGGGAAAGTGGACTGTAGG 59.381 60.000 0.00 0.00 0.00 3.18
748 813 0.618981 GGGGAAAGTGGACTGTAGGG 59.381 60.000 0.00 0.00 0.00 3.53
754 819 2.528673 AGTGGACTGTAGGGGTAGAC 57.471 55.000 0.00 0.00 0.00 2.59
764 829 4.950361 TGTAGGGGTAGACAAGTATGGAA 58.050 43.478 0.00 0.00 0.00 3.53
770 835 5.308237 GGGGTAGACAAGTATGGAATCTCAT 59.692 44.000 0.00 0.00 0.00 2.90
804 875 4.739793 TGAAATTCTGAGTTTGGGTGGAT 58.260 39.130 2.68 0.00 0.00 3.41
806 877 6.493166 TGAAATTCTGAGTTTGGGTGGATAT 58.507 36.000 2.68 0.00 0.00 1.63
816 887 3.699025 TGGGTGGATATGTAGGTCAGA 57.301 47.619 0.00 0.00 0.00 3.27
895 966 3.747099 AAGATGTTTACTGCGCACATC 57.253 42.857 23.22 23.22 44.88 3.06
913 984 5.471116 GCACATCTAATATCTGCAACCATGA 59.529 40.000 0.00 0.00 0.00 3.07
937 1008 8.353684 TGATAGTTCTGTCTAGCTTATAACTGC 58.646 37.037 0.00 0.00 0.00 4.40
938 1009 6.531503 AGTTCTGTCTAGCTTATAACTGCA 57.468 37.500 0.00 0.00 0.00 4.41
950 1021 5.008415 GCTTATAACTGCACATTGAGCTCAT 59.992 40.000 19.04 4.99 0.00 2.90
952 1023 2.195741 ACTGCACATTGAGCTCATGT 57.804 45.000 19.04 19.44 0.00 3.21
962 1033 1.201414 TGAGCTCATGTTGCATGCTTG 59.799 47.619 20.33 11.19 33.83 4.01
973 1044 1.296056 GCATGCTTGCCTTGCCTTTG 61.296 55.000 11.37 0.00 43.38 2.77
974 1045 1.004200 ATGCTTGCCTTGCCTTTGC 60.004 52.632 0.00 0.00 38.26 3.68
1129 1205 8.437360 TGTTGCTCCTTCTACATTATGTTATG 57.563 34.615 2.23 0.00 0.00 1.90
1133 1209 7.227314 TGCTCCTTCTACATTATGTTATGCTTG 59.773 37.037 2.23 0.00 0.00 4.01
1186 1265 6.538894 CGTTCATACGGAAATGATGTTTTG 57.461 37.500 0.00 0.00 43.94 2.44
1187 1266 6.083630 CGTTCATACGGAAATGATGTTTTGT 58.916 36.000 0.00 0.00 43.94 2.83
1323 1402 0.252881 AGACTCCCCATCAAGAGCCA 60.253 55.000 0.00 0.00 33.18 4.75
1365 1444 0.785979 CAAACGCCAAAGCAAGCATC 59.214 50.000 0.00 0.00 39.83 3.91
1383 1462 1.593196 TCAACCAGCCAACTTCTTCG 58.407 50.000 0.00 0.00 0.00 3.79
1549 1628 3.882888 TGTAGTTGCTGGAAACTTTCAGG 59.117 43.478 0.00 0.00 40.77 3.86
1552 1631 1.691196 TGCTGGAAACTTTCAGGGTG 58.309 50.000 3.93 0.00 0.00 4.61
1578 1657 9.935241 GTTGGAAGCTATATGAAGATGAATCTA 57.065 33.333 0.00 0.00 35.76 1.98
1769 1851 9.368674 CAGTATGCCATATTTGATCAAAAACAA 57.631 29.630 23.91 10.87 33.56 2.83
1816 1898 9.908152 AGTTTGATTTAGTCCTTAATTTTTCGG 57.092 29.630 0.00 0.00 0.00 4.30
1817 1899 9.902196 GTTTGATTTAGTCCTTAATTTTTCGGA 57.098 29.630 0.00 0.00 0.00 4.55
1831 1913 9.522804 TTAATTTTTCGGAAATGATAAATCCCG 57.477 29.630 3.67 0.00 38.41 5.14
1832 1914 6.761099 TTTTTCGGAAATGATAAATCCCGA 57.239 33.333 3.67 0.00 43.36 5.14
1835 1917 5.940192 TCGGAAATGATAAATCCCGAATG 57.060 39.130 0.00 0.00 42.31 2.67
1836 1918 5.373222 TCGGAAATGATAAATCCCGAATGT 58.627 37.500 0.00 0.00 42.31 2.71
1837 1919 5.825679 TCGGAAATGATAAATCCCGAATGTT 59.174 36.000 0.00 0.00 42.31 2.71
1838 1920 6.017440 TCGGAAATGATAAATCCCGAATGTTC 60.017 38.462 0.00 0.00 42.31 3.18
1852 1934 5.854835 CGAATGTTCGGATTTTAAGCATG 57.145 39.130 7.24 0.00 46.30 4.06
1853 1935 4.734854 CGAATGTTCGGATTTTAAGCATGG 59.265 41.667 7.24 0.00 46.30 3.66
1854 1936 3.502191 TGTTCGGATTTTAAGCATGGC 57.498 42.857 0.00 0.00 0.00 4.40
1855 1937 2.822561 TGTTCGGATTTTAAGCATGGCA 59.177 40.909 0.00 0.00 0.00 4.92
1856 1938 3.256879 TGTTCGGATTTTAAGCATGGCAA 59.743 39.130 0.00 0.00 0.00 4.52
1857 1939 3.502191 TCGGATTTTAAGCATGGCAAC 57.498 42.857 0.00 0.00 0.00 4.17
1858 1940 2.165437 TCGGATTTTAAGCATGGCAACC 59.835 45.455 0.00 0.00 0.00 3.77
1859 1941 2.738321 CGGATTTTAAGCATGGCAACCC 60.738 50.000 0.00 0.00 0.00 4.11
1860 1942 2.539476 GATTTTAAGCATGGCAACCCG 58.461 47.619 0.00 0.00 0.00 5.28
1861 1943 1.621992 TTTTAAGCATGGCAACCCGA 58.378 45.000 0.00 0.00 0.00 5.14
1862 1944 1.621992 TTTAAGCATGGCAACCCGAA 58.378 45.000 0.00 0.00 0.00 4.30
1863 1945 0.885196 TTAAGCATGGCAACCCGAAC 59.115 50.000 0.00 0.00 0.00 3.95
1864 1946 1.302383 TAAGCATGGCAACCCGAACG 61.302 55.000 0.00 0.00 0.00 3.95
1865 1947 3.361977 GCATGGCAACCCGAACGT 61.362 61.111 0.00 0.00 0.00 3.99
1866 1948 2.914908 GCATGGCAACCCGAACGTT 61.915 57.895 0.00 0.00 0.00 3.99
1867 1949 1.657556 CATGGCAACCCGAACGTTT 59.342 52.632 0.46 0.00 0.00 3.60
1868 1950 0.031449 CATGGCAACCCGAACGTTTT 59.969 50.000 0.46 0.00 0.00 2.43
1869 1951 0.747852 ATGGCAACCCGAACGTTTTT 59.252 45.000 0.46 0.00 0.00 1.94
1870 1952 0.100861 TGGCAACCCGAACGTTTTTC 59.899 50.000 0.46 0.00 0.00 2.29
1871 1953 0.100861 GGCAACCCGAACGTTTTTCA 59.899 50.000 0.46 0.00 0.00 2.69
1872 1954 1.269361 GGCAACCCGAACGTTTTTCAT 60.269 47.619 0.46 0.00 0.00 2.57
1873 1955 1.784283 GCAACCCGAACGTTTTTCATG 59.216 47.619 0.46 1.11 0.00 3.07
1874 1956 2.389998 CAACCCGAACGTTTTTCATGG 58.610 47.619 0.46 0.00 0.00 3.66
1875 1957 0.312729 ACCCGAACGTTTTTCATGGC 59.687 50.000 0.46 0.00 0.00 4.40
1876 1958 0.312416 CCCGAACGTTTTTCATGGCA 59.688 50.000 0.46 0.00 0.00 4.92
1877 1959 1.269309 CCCGAACGTTTTTCATGGCAA 60.269 47.619 0.46 0.00 0.00 4.52
1878 1960 1.784283 CCGAACGTTTTTCATGGCAAC 59.216 47.619 0.46 0.00 0.00 4.17
1879 1961 2.542824 CCGAACGTTTTTCATGGCAACT 60.543 45.455 0.46 0.00 37.61 3.16
1880 1962 3.112580 CGAACGTTTTTCATGGCAACTT 58.887 40.909 0.46 0.00 37.61 2.66
1881 1963 3.549873 CGAACGTTTTTCATGGCAACTTT 59.450 39.130 0.46 0.00 37.61 2.66
1882 1964 4.735822 CGAACGTTTTTCATGGCAACTTTA 59.264 37.500 0.46 0.00 37.61 1.85
1883 1965 5.108405 CGAACGTTTTTCATGGCAACTTTAG 60.108 40.000 0.46 0.00 37.61 1.85
1884 1966 5.257082 ACGTTTTTCATGGCAACTTTAGT 57.743 34.783 0.00 0.00 37.61 2.24
1885 1967 5.656480 ACGTTTTTCATGGCAACTTTAGTT 58.344 33.333 0.00 0.00 39.12 2.24
1886 1968 5.746721 ACGTTTTTCATGGCAACTTTAGTTC 59.253 36.000 0.00 0.00 35.83 3.01
1887 1969 5.746245 CGTTTTTCATGGCAACTTTAGTTCA 59.254 36.000 0.00 0.00 35.83 3.18
1888 1970 6.291585 CGTTTTTCATGGCAACTTTAGTTCAC 60.292 38.462 0.00 0.00 35.83 3.18
1889 1971 4.481930 TTCATGGCAACTTTAGTTCACG 57.518 40.909 0.00 0.00 35.83 4.35
1890 1972 3.472652 TCATGGCAACTTTAGTTCACGT 58.527 40.909 0.00 0.00 35.83 4.49
1891 1973 3.249799 TCATGGCAACTTTAGTTCACGTG 59.750 43.478 9.94 9.94 35.83 4.49
1892 1974 2.907634 TGGCAACTTTAGTTCACGTGA 58.092 42.857 15.76 15.76 35.83 4.35
1893 1975 2.869801 TGGCAACTTTAGTTCACGTGAG 59.130 45.455 19.11 8.51 35.83 3.51
1894 1976 2.223377 GGCAACTTTAGTTCACGTGAGG 59.777 50.000 19.11 8.43 35.83 3.86
1895 1977 2.870411 GCAACTTTAGTTCACGTGAGGT 59.130 45.455 19.11 12.29 35.83 3.85
1896 1978 3.311596 GCAACTTTAGTTCACGTGAGGTT 59.688 43.478 19.11 13.81 35.83 3.50
1897 1979 4.785341 GCAACTTTAGTTCACGTGAGGTTG 60.785 45.833 19.11 22.76 35.83 3.77
1898 1980 3.463944 ACTTTAGTTCACGTGAGGTTGG 58.536 45.455 19.11 10.90 0.00 3.77
1899 1981 1.873698 TTAGTTCACGTGAGGTTGGC 58.126 50.000 19.11 6.32 0.00 4.52
1900 1982 0.753867 TAGTTCACGTGAGGTTGGCA 59.246 50.000 19.11 0.00 0.00 4.92
1901 1983 0.107410 AGTTCACGTGAGGTTGGCAA 60.107 50.000 19.11 0.00 0.00 4.52
1902 1984 0.736053 GTTCACGTGAGGTTGGCAAA 59.264 50.000 19.11 0.00 0.00 3.68
1903 1985 0.736053 TTCACGTGAGGTTGGCAAAC 59.264 50.000 19.11 7.31 35.40 2.93
1904 1986 0.393132 TCACGTGAGGTTGGCAAACA 60.393 50.000 18.93 8.37 38.10 2.83
1905 1987 0.667993 CACGTGAGGTTGGCAAACAT 59.332 50.000 18.93 0.00 38.10 2.71
1906 1988 0.667993 ACGTGAGGTTGGCAAACATG 59.332 50.000 18.93 16.93 38.10 3.21
1907 1989 0.039256 CGTGAGGTTGGCAAACATGG 60.039 55.000 18.93 0.00 38.10 3.66
1908 1990 0.319813 GTGAGGTTGGCAAACATGGC 60.320 55.000 18.93 4.36 38.10 4.40
1909 1991 0.758310 TGAGGTTGGCAAACATGGCA 60.758 50.000 18.93 7.03 42.75 4.92
1916 1998 3.488778 TGGCAAACATGGCAATTTTCT 57.511 38.095 2.31 0.00 41.49 2.52
1917 1999 3.139850 TGGCAAACATGGCAATTTTCTG 58.860 40.909 2.31 0.00 41.49 3.02
1918 2000 3.181457 TGGCAAACATGGCAATTTTCTGA 60.181 39.130 2.31 0.00 41.49 3.27
1919 2001 3.187022 GGCAAACATGGCAATTTTCTGAC 59.813 43.478 0.00 0.00 0.00 3.51
1920 2002 3.808726 GCAAACATGGCAATTTTCTGACA 59.191 39.130 0.00 0.00 39.14 3.58
1921 2003 4.272991 GCAAACATGGCAATTTTCTGACAA 59.727 37.500 0.00 0.00 38.03 3.18
1922 2004 5.220815 GCAAACATGGCAATTTTCTGACAAA 60.221 36.000 0.00 0.00 38.03 2.83
1923 2005 6.677431 GCAAACATGGCAATTTTCTGACAAAA 60.677 34.615 0.00 0.00 38.03 2.44
1924 2006 6.998968 AACATGGCAATTTTCTGACAAAAA 57.001 29.167 0.00 0.00 38.03 1.94
1942 2024 2.863401 AAAACGAACTGGGACAAAGC 57.137 45.000 0.00 0.00 38.70 3.51
1943 2025 2.052782 AAACGAACTGGGACAAAGCT 57.947 45.000 0.00 0.00 38.70 3.74
1944 2026 1.308998 AACGAACTGGGACAAAGCTG 58.691 50.000 0.00 0.00 38.70 4.24
1945 2027 1.166531 ACGAACTGGGACAAAGCTGC 61.167 55.000 0.00 0.00 38.70 5.25
1946 2028 1.856265 CGAACTGGGACAAAGCTGCC 61.856 60.000 0.00 0.00 38.70 4.85
1947 2029 0.823356 GAACTGGGACAAAGCTGCCA 60.823 55.000 0.00 0.00 38.70 4.92
1948 2030 0.178953 AACTGGGACAAAGCTGCCAT 60.179 50.000 0.00 0.00 38.70 4.40
1949 2031 0.896940 ACTGGGACAAAGCTGCCATG 60.897 55.000 0.00 0.00 38.70 3.66
1950 2032 0.896940 CTGGGACAAAGCTGCCATGT 60.897 55.000 7.53 7.53 38.70 3.21
1951 2033 1.180456 TGGGACAAAGCTGCCATGTG 61.180 55.000 11.97 0.92 31.92 3.21
1952 2034 1.181098 GGGACAAAGCTGCCATGTGT 61.181 55.000 11.97 4.03 0.00 3.72
1953 2035 0.675633 GGACAAAGCTGCCATGTGTT 59.324 50.000 11.97 0.00 0.00 3.32
1954 2036 1.885887 GGACAAAGCTGCCATGTGTTA 59.114 47.619 11.97 0.00 0.00 2.41
1955 2037 2.295909 GGACAAAGCTGCCATGTGTTAA 59.704 45.455 11.97 0.00 0.00 2.01
1956 2038 3.308530 GACAAAGCTGCCATGTGTTAAC 58.691 45.455 11.97 0.00 0.00 2.01
1957 2039 2.692557 ACAAAGCTGCCATGTGTTAACA 59.307 40.909 3.59 3.59 41.58 2.41
1958 2040 3.131933 ACAAAGCTGCCATGTGTTAACAA 59.868 39.130 10.51 1.41 40.46 2.83
1959 2041 3.369546 AAGCTGCCATGTGTTAACAAC 57.630 42.857 10.51 5.61 40.46 3.32
1960 2042 2.586425 AGCTGCCATGTGTTAACAACT 58.414 42.857 10.51 0.00 40.46 3.16
1961 2043 3.750371 AGCTGCCATGTGTTAACAACTA 58.250 40.909 10.51 0.22 40.46 2.24
1962 2044 4.141287 AGCTGCCATGTGTTAACAACTAA 58.859 39.130 10.51 0.00 40.46 2.24
1963 2045 4.582656 AGCTGCCATGTGTTAACAACTAAA 59.417 37.500 10.51 0.00 40.46 1.85
1964 2046 4.917415 GCTGCCATGTGTTAACAACTAAAG 59.083 41.667 10.51 5.60 40.46 1.85
1965 2047 5.507315 GCTGCCATGTGTTAACAACTAAAGT 60.507 40.000 10.51 0.00 40.46 2.66
1966 2048 6.458232 TGCCATGTGTTAACAACTAAAGTT 57.542 33.333 10.51 0.00 40.46 2.66
1976 2058 1.235724 AACTAAAGTTGCCACCTCGC 58.764 50.000 0.00 0.00 36.80 5.03
1977 2059 0.107831 ACTAAAGTTGCCACCTCGCA 59.892 50.000 0.00 0.00 36.85 5.10
1978 2060 1.271379 ACTAAAGTTGCCACCTCGCAT 60.271 47.619 0.00 0.00 38.87 4.73
1979 2061 1.398390 CTAAAGTTGCCACCTCGCATC 59.602 52.381 0.00 0.00 38.87 3.91
1980 2062 0.537143 AAAGTTGCCACCTCGCATCA 60.537 50.000 0.00 0.00 38.87 3.07
1981 2063 0.537143 AAGTTGCCACCTCGCATCAA 60.537 50.000 0.00 0.00 38.87 2.57
1982 2064 1.210155 GTTGCCACCTCGCATCAAC 59.790 57.895 0.00 0.00 38.87 3.18
1983 2065 1.073025 TTGCCACCTCGCATCAACT 59.927 52.632 0.00 0.00 38.87 3.16
1984 2066 0.323302 TTGCCACCTCGCATCAACTA 59.677 50.000 0.00 0.00 38.87 2.24
1985 2067 0.323302 TGCCACCTCGCATCAACTAA 59.677 50.000 0.00 0.00 32.62 2.24
1986 2068 1.271108 TGCCACCTCGCATCAACTAAA 60.271 47.619 0.00 0.00 32.62 1.85
1987 2069 1.810151 GCCACCTCGCATCAACTAAAA 59.190 47.619 0.00 0.00 0.00 1.52
1988 2070 2.423538 GCCACCTCGCATCAACTAAAAT 59.576 45.455 0.00 0.00 0.00 1.82
1989 2071 3.119495 GCCACCTCGCATCAACTAAAATT 60.119 43.478 0.00 0.00 0.00 1.82
1990 2072 4.414852 CCACCTCGCATCAACTAAAATTG 58.585 43.478 0.00 0.00 0.00 2.32
1991 2073 3.853671 CACCTCGCATCAACTAAAATTGC 59.146 43.478 0.00 0.00 0.00 3.56
1992 2074 3.119495 ACCTCGCATCAACTAAAATTGCC 60.119 43.478 0.00 0.00 0.00 4.52
1993 2075 3.119531 CCTCGCATCAACTAAAATTGCCA 60.120 43.478 0.00 0.00 0.00 4.92
1994 2076 4.440525 CCTCGCATCAACTAAAATTGCCAT 60.441 41.667 0.00 0.00 0.00 4.40
1995 2077 4.422840 TCGCATCAACTAAAATTGCCATG 58.577 39.130 0.00 0.00 0.00 3.66
1996 2078 4.157472 TCGCATCAACTAAAATTGCCATGA 59.843 37.500 0.00 0.00 0.00 3.07
1997 2079 4.863689 CGCATCAACTAAAATTGCCATGAA 59.136 37.500 0.00 0.00 0.00 2.57
1998 2080 5.348179 CGCATCAACTAAAATTGCCATGAAA 59.652 36.000 0.00 0.00 0.00 2.69
1999 2081 6.128607 CGCATCAACTAAAATTGCCATGAAAA 60.129 34.615 0.00 0.00 0.00 2.29
2000 2082 7.570875 CGCATCAACTAAAATTGCCATGAAAAA 60.571 33.333 0.00 0.00 0.00 1.94
2018 2100 1.375551 AAACGTTCGGGGTGATATGC 58.624 50.000 0.00 0.00 0.00 3.14
2019 2101 0.539986 AACGTTCGGGGTGATATGCT 59.460 50.000 0.00 0.00 0.00 3.79
2020 2102 0.539986 ACGTTCGGGGTGATATGCTT 59.460 50.000 0.00 0.00 0.00 3.91
2021 2103 1.758280 ACGTTCGGGGTGATATGCTTA 59.242 47.619 0.00 0.00 0.00 3.09
2022 2104 2.168936 ACGTTCGGGGTGATATGCTTAA 59.831 45.455 0.00 0.00 0.00 1.85
2023 2105 3.199677 CGTTCGGGGTGATATGCTTAAA 58.800 45.455 0.00 0.00 0.00 1.52
2024 2106 3.623960 CGTTCGGGGTGATATGCTTAAAA 59.376 43.478 0.00 0.00 0.00 1.52
2025 2107 4.274950 CGTTCGGGGTGATATGCTTAAAAT 59.725 41.667 0.00 0.00 0.00 1.82
2026 2108 5.560183 CGTTCGGGGTGATATGCTTAAAATC 60.560 44.000 0.00 0.00 0.00 2.17
2027 2109 4.394729 TCGGGGTGATATGCTTAAAATCC 58.605 43.478 0.00 0.00 0.00 3.01
2028 2110 3.188460 CGGGGTGATATGCTTAAAATCCG 59.812 47.826 0.00 0.00 0.00 4.18
2029 2111 4.394729 GGGGTGATATGCTTAAAATCCGA 58.605 43.478 0.00 0.00 0.00 4.55
2030 2112 4.825085 GGGGTGATATGCTTAAAATCCGAA 59.175 41.667 0.00 0.00 0.00 4.30
2031 2113 5.278315 GGGGTGATATGCTTAAAATCCGAAC 60.278 44.000 0.00 0.00 0.00 3.95
2032 2114 5.440685 GGTGATATGCTTAAAATCCGAACG 58.559 41.667 0.00 0.00 0.00 3.95
2033 2115 4.904154 GTGATATGCTTAAAATCCGAACGC 59.096 41.667 0.00 0.00 0.00 4.84
2034 2116 4.814234 TGATATGCTTAAAATCCGAACGCT 59.186 37.500 0.00 0.00 0.00 5.07
2035 2117 3.675467 ATGCTTAAAATCCGAACGCTC 57.325 42.857 0.00 0.00 0.00 5.03
2036 2118 1.392168 TGCTTAAAATCCGAACGCTCG 59.608 47.619 0.15 0.15 45.02 5.03
2046 2128 2.135664 CGAACGCTCGGGATTTATCT 57.864 50.000 0.00 0.00 41.57 1.98
2047 2129 1.787155 CGAACGCTCGGGATTTATCTG 59.213 52.381 0.00 0.00 41.57 2.90
2048 2130 2.135933 GAACGCTCGGGATTTATCTGG 58.864 52.381 0.00 0.00 0.00 3.86
2049 2131 0.393077 ACGCTCGGGATTTATCTGGG 59.607 55.000 0.00 0.00 0.00 4.45
2050 2132 0.393077 CGCTCGGGATTTATCTGGGT 59.607 55.000 0.00 0.00 0.00 4.51
2051 2133 1.605712 CGCTCGGGATTTATCTGGGTC 60.606 57.143 0.00 0.00 0.00 4.46
2052 2134 1.270893 GCTCGGGATTTATCTGGGTCC 60.271 57.143 0.00 0.00 0.00 4.46
2053 2135 2.330216 CTCGGGATTTATCTGGGTCCT 58.670 52.381 0.00 0.00 0.00 3.85
2054 2136 3.507411 CTCGGGATTTATCTGGGTCCTA 58.493 50.000 0.00 0.00 0.00 2.94
2055 2137 4.097418 CTCGGGATTTATCTGGGTCCTAT 58.903 47.826 0.00 0.00 0.00 2.57
2056 2138 4.499472 TCGGGATTTATCTGGGTCCTATT 58.501 43.478 0.00 0.00 0.00 1.73
2057 2139 4.911522 TCGGGATTTATCTGGGTCCTATTT 59.088 41.667 0.00 0.00 0.00 1.40
2058 2140 5.371472 TCGGGATTTATCTGGGTCCTATTTT 59.629 40.000 0.00 0.00 0.00 1.82
2059 2141 6.068670 CGGGATTTATCTGGGTCCTATTTTT 58.931 40.000 0.00 0.00 0.00 1.94
2383 2468 5.534207 AATTTCACCAAGAAGTGATTGCA 57.466 34.783 0.00 0.00 45.80 4.08
2411 3584 2.971330 CAGTGGAGCTGGATAGAAGGAT 59.029 50.000 0.00 0.00 41.42 3.24
2414 3587 4.591072 AGTGGAGCTGGATAGAAGGATAAC 59.409 45.833 0.00 0.00 0.00 1.89
2419 3592 3.681897 GCTGGATAGAAGGATAACATGCG 59.318 47.826 0.00 0.00 0.00 4.73
2424 3597 5.992217 GGATAGAAGGATAACATGCGTCTTT 59.008 40.000 1.96 0.00 39.74 2.52
2425 3598 6.073548 GGATAGAAGGATAACATGCGTCTTTG 60.074 42.308 1.96 0.00 39.74 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 4.346049 CCGAGAAGGGCTGAGAGA 57.654 61.111 0.00 0.00 35.97 3.10
221 231 0.981183 TTTAGATGGCTCGGTGGTGT 59.019 50.000 0.00 0.00 0.00 4.16
222 232 2.158900 AGATTTAGATGGCTCGGTGGTG 60.159 50.000 0.00 0.00 0.00 4.17
223 233 2.103263 GAGATTTAGATGGCTCGGTGGT 59.897 50.000 0.00 0.00 0.00 4.16
224 234 2.760374 GAGATTTAGATGGCTCGGTGG 58.240 52.381 0.00 0.00 0.00 4.61
257 279 1.719378 GGAGAGAGGAGGGGGATGATA 59.281 57.143 0.00 0.00 0.00 2.15
273 295 2.660064 GCGAAGAAGCCAGGGGAGA 61.660 63.158 0.00 0.00 0.00 3.71
295 317 3.043419 CGGAGGCGGATAGGAGTG 58.957 66.667 0.00 0.00 0.00 3.51
345 390 2.418910 CGATCTGGAGGCGACTGGT 61.419 63.158 0.00 0.00 44.43 4.00
346 391 2.415010 CGATCTGGAGGCGACTGG 59.585 66.667 0.00 0.00 44.43 4.00
347 392 2.415010 CCGATCTGGAGGCGACTG 59.585 66.667 0.00 0.00 44.43 3.51
349 394 2.105128 CACCGATCTGGAGGCGAC 59.895 66.667 10.05 0.00 42.00 5.19
350 395 3.838271 GCACCGATCTGGAGGCGA 61.838 66.667 10.05 0.00 42.00 5.54
352 397 4.148825 ACGCACCGATCTGGAGGC 62.149 66.667 10.05 10.97 42.00 4.70
353 398 2.105128 GACGCACCGATCTGGAGG 59.895 66.667 10.05 0.00 42.00 4.30
354 399 2.278206 CGACGCACCGATCTGGAG 60.278 66.667 10.05 4.11 42.00 3.86
355 400 3.822192 CCGACGCACCGATCTGGA 61.822 66.667 10.05 0.00 42.00 3.86
356 401 3.350909 TTCCGACGCACCGATCTGG 62.351 63.158 2.55 2.55 46.41 3.86
357 402 2.158959 GTTCCGACGCACCGATCTG 61.159 63.158 0.00 0.00 0.00 2.90
358 403 2.181021 GTTCCGACGCACCGATCT 59.819 61.111 0.00 0.00 0.00 2.75
359 404 3.245315 CGTTCCGACGCACCGATC 61.245 66.667 0.00 0.00 43.03 3.69
369 414 0.179067 AAGCAAACAGGACGTTCCGA 60.179 50.000 0.00 0.00 42.75 4.55
370 415 0.234884 GAAGCAAACAGGACGTTCCG 59.765 55.000 0.00 0.00 42.75 4.30
374 419 1.597027 CCCGAAGCAAACAGGACGT 60.597 57.895 0.00 0.00 0.00 4.34
377 422 2.282180 GCCCCGAAGCAAACAGGA 60.282 61.111 0.00 0.00 0.00 3.86
391 436 1.065126 AGCTTACTTGATCTGGTGCCC 60.065 52.381 0.00 0.00 0.00 5.36
483 528 7.926555 TCAACCTAGAAAAACAGAGTCTAACTG 59.073 37.037 0.00 0.00 40.68 3.16
485 530 8.834749 ATCAACCTAGAAAAACAGAGTCTAAC 57.165 34.615 0.00 0.00 0.00 2.34
490 535 7.391833 GGATCAATCAACCTAGAAAAACAGAGT 59.608 37.037 0.00 0.00 0.00 3.24
570 615 1.675552 CAAGTTTTGACAGTCGGGGT 58.324 50.000 0.00 0.00 0.00 4.95
573 618 2.223377 GCTACCAAGTTTTGACAGTCGG 59.777 50.000 0.00 0.00 0.00 4.79
574 619 3.131396 AGCTACCAAGTTTTGACAGTCG 58.869 45.455 0.00 0.00 0.00 4.18
576 621 4.523083 TGAAGCTACCAAGTTTTGACAGT 58.477 39.130 0.00 0.00 0.00 3.55
581 626 4.918810 AGGTTGAAGCTACCAAGTTTTG 57.081 40.909 6.91 0.00 38.16 2.44
585 630 2.767505 CGAAGGTTGAAGCTACCAAGT 58.232 47.619 6.91 0.00 38.16 3.16
604 649 2.990479 CTCTCCAACCCCTTCCCG 59.010 66.667 0.00 0.00 0.00 5.14
613 658 2.032681 ACCGGCAAGCTCTCCAAC 59.967 61.111 0.00 0.00 0.00 3.77
625 670 3.723348 GAGCGTCAAACCACCGGC 61.723 66.667 0.00 0.00 0.00 6.13
626 671 1.234615 ATTGAGCGTCAAACCACCGG 61.235 55.000 0.00 0.00 40.12 5.28
628 673 2.661594 GAAATTGAGCGTCAAACCACC 58.338 47.619 4.87 0.00 40.12 4.61
643 701 4.403453 GCGAGCAATTACTGAACGAAATT 58.597 39.130 0.00 0.00 0.00 1.82
664 722 3.134127 GATTCACAGGCACGGGGC 61.134 66.667 1.25 1.25 43.74 5.80
675 733 2.494870 ACCCACGGTAGTACTGATTCAC 59.505 50.000 16.20 0.00 32.11 3.18
687 745 3.069946 CGCCCAGTACCCACGGTA 61.070 66.667 0.00 0.00 37.09 4.02
698 756 1.086696 CACACAGGATAAACGCCCAG 58.913 55.000 0.00 0.00 0.00 4.45
730 795 0.618981 CCCCTACAGTCCACTTTCCC 59.381 60.000 0.00 0.00 0.00 3.97
734 799 2.111255 TGTCTACCCCTACAGTCCACTT 59.889 50.000 0.00 0.00 0.00 3.16
735 800 1.714787 TGTCTACCCCTACAGTCCACT 59.285 52.381 0.00 0.00 0.00 4.00
747 812 5.871396 TGAGATTCCATACTTGTCTACCC 57.129 43.478 0.00 0.00 0.00 3.69
754 819 8.093307 AGTGCAGTATATGAGATTCCATACTTG 58.907 37.037 0.00 0.00 33.08 3.16
764 829 8.649591 AGAATTTCAGAGTGCAGTATATGAGAT 58.350 33.333 0.00 0.00 0.00 2.75
770 835 7.175347 ACTCAGAATTTCAGAGTGCAGTATA 57.825 36.000 19.92 0.00 40.94 1.47
775 846 4.276678 CCAAACTCAGAATTTCAGAGTGCA 59.723 41.667 20.93 0.00 41.50 4.57
804 875 5.467738 ACCCAATCTGATCTGACCTACATA 58.532 41.667 4.21 0.00 0.00 2.29
806 877 3.724478 ACCCAATCTGATCTGACCTACA 58.276 45.455 4.21 0.00 0.00 2.74
816 887 2.766263 TGACTTCGCTACCCAATCTGAT 59.234 45.455 0.00 0.00 0.00 2.90
895 966 8.933807 CAGAACTATCATGGTTGCAGATATTAG 58.066 37.037 0.00 0.00 0.00 1.73
913 984 8.138712 GTGCAGTTATAAGCTAGACAGAACTAT 58.861 37.037 0.00 0.00 0.00 2.12
937 1008 3.179048 CATGCAACATGAGCTCAATGTG 58.821 45.455 22.50 17.12 0.00 3.21
938 1009 2.416836 GCATGCAACATGAGCTCAATGT 60.417 45.455 22.50 20.73 0.00 2.71
973 1044 0.959553 CCTGATGGGAATGCTGATGC 59.040 55.000 0.00 0.00 37.23 3.91
974 1045 2.105993 TCTCCTGATGGGAATGCTGATG 59.894 50.000 0.00 0.00 44.58 3.07
1138 1217 7.224753 CGTATGTGCTTCAGTACCATAGAAAAT 59.775 37.037 0.00 0.00 0.00 1.82
1141 1220 5.126545 ACGTATGTGCTTCAGTACCATAGAA 59.873 40.000 0.00 0.00 0.00 2.10
1142 1221 4.643334 ACGTATGTGCTTCAGTACCATAGA 59.357 41.667 0.00 0.00 0.00 1.98
1143 1222 4.933330 ACGTATGTGCTTCAGTACCATAG 58.067 43.478 0.00 0.00 0.00 2.23
1230 1309 1.410083 GCAAGGAATCCACTGGCCATA 60.410 52.381 5.51 0.00 0.00 2.74
1323 1402 1.707427 AGAAAGGTTGGATCAGGCTGT 59.293 47.619 15.27 1.47 0.00 4.40
1365 1444 0.040067 GCGAAGAAGTTGGCTGGTTG 60.040 55.000 0.00 0.00 34.71 3.77
1383 1462 2.715046 TGGGAATCATCACTCACTTGC 58.285 47.619 0.00 0.00 0.00 4.01
1549 1628 6.291377 TCATCTTCATATAGCTTCCAACACC 58.709 40.000 0.00 0.00 0.00 4.16
1552 1631 8.845413 AGATTCATCTTCATATAGCTTCCAAC 57.155 34.615 0.00 0.00 31.97 3.77
1673 1753 8.803235 TGCTAAAGAAGTCTGACAGAATTAGTA 58.197 33.333 17.50 8.62 32.11 1.82
1761 1843 7.761249 AGGACAAAAAGAGACTCATTGTTTTTG 59.239 33.333 24.58 24.58 46.39 2.44
1769 1851 8.624776 CAAACTAAAGGACAAAAAGAGACTCAT 58.375 33.333 5.02 0.00 0.00 2.90
1813 1895 5.373222 ACATTCGGGATTTATCATTTCCGA 58.627 37.500 0.00 0.00 43.73 4.55
1814 1896 5.689383 ACATTCGGGATTTATCATTTCCG 57.311 39.130 0.00 0.00 38.92 4.30
1815 1897 6.142817 CGAACATTCGGGATTTATCATTTCC 58.857 40.000 6.11 0.00 46.30 3.13
1831 1913 4.504097 GCCATGCTTAAAATCCGAACATTC 59.496 41.667 0.00 0.00 0.00 2.67
1832 1914 4.081752 TGCCATGCTTAAAATCCGAACATT 60.082 37.500 0.00 0.00 0.00 2.71
1833 1915 3.446873 TGCCATGCTTAAAATCCGAACAT 59.553 39.130 0.00 0.00 0.00 2.71
1834 1916 2.822561 TGCCATGCTTAAAATCCGAACA 59.177 40.909 0.00 0.00 0.00 3.18
1835 1917 3.502191 TGCCATGCTTAAAATCCGAAC 57.498 42.857 0.00 0.00 0.00 3.95
1836 1918 3.367910 GGTTGCCATGCTTAAAATCCGAA 60.368 43.478 0.00 0.00 0.00 4.30
1837 1919 2.165437 GGTTGCCATGCTTAAAATCCGA 59.835 45.455 0.00 0.00 0.00 4.55
1838 1920 2.539476 GGTTGCCATGCTTAAAATCCG 58.461 47.619 0.00 0.00 0.00 4.18
1839 1921 2.738321 CGGGTTGCCATGCTTAAAATCC 60.738 50.000 0.00 0.00 0.00 3.01
1840 1922 2.165437 TCGGGTTGCCATGCTTAAAATC 59.835 45.455 0.00 0.00 0.00 2.17
1841 1923 2.175202 TCGGGTTGCCATGCTTAAAAT 58.825 42.857 0.00 0.00 0.00 1.82
1842 1924 1.621992 TCGGGTTGCCATGCTTAAAA 58.378 45.000 0.00 0.00 0.00 1.52
1843 1925 1.271102 GTTCGGGTTGCCATGCTTAAA 59.729 47.619 0.00 0.00 0.00 1.52
1844 1926 0.885196 GTTCGGGTTGCCATGCTTAA 59.115 50.000 0.00 0.00 0.00 1.85
1845 1927 1.302383 CGTTCGGGTTGCCATGCTTA 61.302 55.000 0.00 0.00 0.00 3.09
1846 1928 2.625823 CGTTCGGGTTGCCATGCTT 61.626 57.895 0.00 0.00 0.00 3.91
1847 1929 3.055719 CGTTCGGGTTGCCATGCT 61.056 61.111 0.00 0.00 0.00 3.79
1848 1930 2.414840 AAACGTTCGGGTTGCCATGC 62.415 55.000 0.00 0.00 0.00 4.06
1849 1931 0.031449 AAAACGTTCGGGTTGCCATG 59.969 50.000 0.00 0.00 0.00 3.66
1850 1932 0.747852 AAAAACGTTCGGGTTGCCAT 59.252 45.000 0.00 0.00 0.00 4.40
1851 1933 0.100861 GAAAAACGTTCGGGTTGCCA 59.899 50.000 0.00 0.00 0.00 4.92
1852 1934 0.100861 TGAAAAACGTTCGGGTTGCC 59.899 50.000 0.00 0.00 0.00 4.52
1853 1935 1.784283 CATGAAAAACGTTCGGGTTGC 59.216 47.619 0.00 0.00 0.00 4.17
1854 1936 2.389998 CCATGAAAAACGTTCGGGTTG 58.610 47.619 0.00 0.00 0.00 3.77
1855 1937 1.269361 GCCATGAAAAACGTTCGGGTT 60.269 47.619 0.00 0.00 0.00 4.11
1856 1938 0.312729 GCCATGAAAAACGTTCGGGT 59.687 50.000 0.00 0.00 0.00 5.28
1857 1939 0.312416 TGCCATGAAAAACGTTCGGG 59.688 50.000 0.00 0.00 0.00 5.14
1858 1940 1.784283 GTTGCCATGAAAAACGTTCGG 59.216 47.619 0.00 0.00 0.00 4.30
1859 1941 2.726633 AGTTGCCATGAAAAACGTTCG 58.273 42.857 0.00 0.00 0.00 3.95
1860 1942 5.746721 ACTAAAGTTGCCATGAAAAACGTTC 59.253 36.000 0.00 0.00 30.16 3.95
1861 1943 5.656480 ACTAAAGTTGCCATGAAAAACGTT 58.344 33.333 0.00 0.00 31.87 3.99
1862 1944 5.257082 ACTAAAGTTGCCATGAAAAACGT 57.743 34.783 0.00 0.00 0.00 3.99
1863 1945 5.746245 TGAACTAAAGTTGCCATGAAAAACG 59.254 36.000 0.00 0.00 38.56 3.60
1864 1946 6.291585 CGTGAACTAAAGTTGCCATGAAAAAC 60.292 38.462 0.00 0.00 38.56 2.43
1865 1947 5.746245 CGTGAACTAAAGTTGCCATGAAAAA 59.254 36.000 0.00 0.00 38.56 1.94
1866 1948 5.163602 ACGTGAACTAAAGTTGCCATGAAAA 60.164 36.000 0.00 0.00 38.56 2.29
1867 1949 4.336993 ACGTGAACTAAAGTTGCCATGAAA 59.663 37.500 0.00 0.00 38.56 2.69
1868 1950 3.880490 ACGTGAACTAAAGTTGCCATGAA 59.120 39.130 0.00 0.00 38.56 2.57
1869 1951 3.249799 CACGTGAACTAAAGTTGCCATGA 59.750 43.478 10.90 0.00 38.56 3.07
1870 1952 3.249799 TCACGTGAACTAAAGTTGCCATG 59.750 43.478 17.62 1.74 38.56 3.66
1871 1953 3.472652 TCACGTGAACTAAAGTTGCCAT 58.527 40.909 17.62 0.00 38.56 4.40
1872 1954 2.869801 CTCACGTGAACTAAAGTTGCCA 59.130 45.455 20.49 0.00 38.56 4.92
1873 1955 2.223377 CCTCACGTGAACTAAAGTTGCC 59.777 50.000 20.49 0.00 38.56 4.52
1874 1956 2.870411 ACCTCACGTGAACTAAAGTTGC 59.130 45.455 20.49 0.00 38.56 4.17
1875 1957 4.260620 CCAACCTCACGTGAACTAAAGTTG 60.261 45.833 20.49 21.28 38.56 3.16
1876 1958 3.875134 CCAACCTCACGTGAACTAAAGTT 59.125 43.478 20.49 12.58 41.64 2.66
1877 1959 3.463944 CCAACCTCACGTGAACTAAAGT 58.536 45.455 20.49 7.36 0.00 2.66
1878 1960 2.223377 GCCAACCTCACGTGAACTAAAG 59.777 50.000 20.49 6.48 0.00 1.85
1879 1961 2.215196 GCCAACCTCACGTGAACTAAA 58.785 47.619 20.49 0.00 0.00 1.85
1880 1962 1.139256 TGCCAACCTCACGTGAACTAA 59.861 47.619 20.49 0.00 0.00 2.24
1881 1963 0.753867 TGCCAACCTCACGTGAACTA 59.246 50.000 20.49 0.00 0.00 2.24
1882 1964 0.107410 TTGCCAACCTCACGTGAACT 60.107 50.000 20.49 4.15 0.00 3.01
1883 1965 0.736053 TTTGCCAACCTCACGTGAAC 59.264 50.000 20.49 5.66 0.00 3.18
1884 1966 0.736053 GTTTGCCAACCTCACGTGAA 59.264 50.000 20.49 0.00 0.00 3.18
1885 1967 0.393132 TGTTTGCCAACCTCACGTGA 60.393 50.000 18.88 18.88 31.02 4.35
1886 1968 0.667993 ATGTTTGCCAACCTCACGTG 59.332 50.000 9.94 9.94 31.02 4.49
1887 1969 0.667993 CATGTTTGCCAACCTCACGT 59.332 50.000 0.00 0.00 31.02 4.49
1888 1970 0.039256 CCATGTTTGCCAACCTCACG 60.039 55.000 0.00 0.00 31.02 4.35
1889 1971 0.319813 GCCATGTTTGCCAACCTCAC 60.320 55.000 0.00 0.00 31.02 3.51
1890 1972 0.758310 TGCCATGTTTGCCAACCTCA 60.758 50.000 0.00 0.00 31.02 3.86
1891 1973 0.392336 TTGCCATGTTTGCCAACCTC 59.608 50.000 0.00 0.00 31.02 3.85
1892 1974 1.058284 ATTGCCATGTTTGCCAACCT 58.942 45.000 0.00 0.00 31.02 3.50
1893 1975 1.894881 AATTGCCATGTTTGCCAACC 58.105 45.000 0.00 0.00 31.02 3.77
1894 1976 3.565063 AGAAAATTGCCATGTTTGCCAAC 59.435 39.130 0.00 0.00 0.00 3.77
1895 1977 3.564644 CAGAAAATTGCCATGTTTGCCAA 59.435 39.130 0.00 0.00 0.00 4.52
1896 1978 3.139850 CAGAAAATTGCCATGTTTGCCA 58.860 40.909 0.00 0.00 0.00 4.92
1897 1979 3.187022 GTCAGAAAATTGCCATGTTTGCC 59.813 43.478 0.00 0.00 0.00 4.52
1898 1980 3.808726 TGTCAGAAAATTGCCATGTTTGC 59.191 39.130 0.00 0.00 0.00 3.68
1899 1981 5.987777 TTGTCAGAAAATTGCCATGTTTG 57.012 34.783 0.00 0.00 0.00 2.93
1900 1982 6.998968 TTTTGTCAGAAAATTGCCATGTTT 57.001 29.167 0.00 0.00 0.00 2.83
1901 1983 6.998968 TTTTTGTCAGAAAATTGCCATGTT 57.001 29.167 0.00 0.00 0.00 2.71
1922 2004 2.758423 AGCTTTGTCCCAGTTCGTTTTT 59.242 40.909 0.00 0.00 0.00 1.94
1923 2005 2.099098 CAGCTTTGTCCCAGTTCGTTTT 59.901 45.455 0.00 0.00 0.00 2.43
1924 2006 1.676006 CAGCTTTGTCCCAGTTCGTTT 59.324 47.619 0.00 0.00 0.00 3.60
1925 2007 1.308998 CAGCTTTGTCCCAGTTCGTT 58.691 50.000 0.00 0.00 0.00 3.85
1926 2008 1.166531 GCAGCTTTGTCCCAGTTCGT 61.167 55.000 0.00 0.00 0.00 3.85
1927 2009 1.576421 GCAGCTTTGTCCCAGTTCG 59.424 57.895 0.00 0.00 0.00 3.95
1928 2010 0.823356 TGGCAGCTTTGTCCCAGTTC 60.823 55.000 0.00 0.00 0.00 3.01
1929 2011 0.178953 ATGGCAGCTTTGTCCCAGTT 60.179 50.000 0.00 0.00 0.00 3.16
1930 2012 0.896940 CATGGCAGCTTTGTCCCAGT 60.897 55.000 0.00 0.00 0.00 4.00
1931 2013 0.896940 ACATGGCAGCTTTGTCCCAG 60.897 55.000 0.00 0.00 0.00 4.45
1932 2014 1.153524 ACATGGCAGCTTTGTCCCA 59.846 52.632 0.00 0.00 0.00 4.37
1933 2015 1.181098 ACACATGGCAGCTTTGTCCC 61.181 55.000 0.00 0.00 0.00 4.46
1934 2016 0.675633 AACACATGGCAGCTTTGTCC 59.324 50.000 0.00 0.00 0.00 4.02
1935 2017 3.243367 TGTTAACACATGGCAGCTTTGTC 60.243 43.478 3.59 0.00 0.00 3.18
1936 2018 2.692557 TGTTAACACATGGCAGCTTTGT 59.307 40.909 3.59 0.00 0.00 2.83
1937 2019 3.367992 TGTTAACACATGGCAGCTTTG 57.632 42.857 3.59 0.00 0.00 2.77
1938 2020 3.384467 AGTTGTTAACACATGGCAGCTTT 59.616 39.130 8.07 0.00 31.06 3.51
1939 2021 2.958355 AGTTGTTAACACATGGCAGCTT 59.042 40.909 8.07 0.00 31.06 3.74
1940 2022 2.586425 AGTTGTTAACACATGGCAGCT 58.414 42.857 8.07 0.00 31.06 4.24
1941 2023 4.497473 TTAGTTGTTAACACATGGCAGC 57.503 40.909 8.07 0.00 31.06 5.25
1942 2024 6.072112 ACTTTAGTTGTTAACACATGGCAG 57.928 37.500 8.07 3.35 31.06 4.85
1943 2025 6.458232 AACTTTAGTTGTTAACACATGGCA 57.542 33.333 8.07 0.00 36.80 4.92
1957 2039 1.235724 GCGAGGTGGCAACTTTAGTT 58.764 50.000 6.46 0.00 39.12 2.24
1958 2040 0.107831 TGCGAGGTGGCAACTTTAGT 59.892 50.000 6.46 0.00 40.59 2.24
1959 2041 2.927004 TGCGAGGTGGCAACTTTAG 58.073 52.632 6.46 2.61 40.59 1.85
1967 2049 1.448985 TTTAGTTGATGCGAGGTGGC 58.551 50.000 0.00 0.00 0.00 5.01
1968 2050 4.414852 CAATTTTAGTTGATGCGAGGTGG 58.585 43.478 0.00 0.00 0.00 4.61
1969 2051 3.853671 GCAATTTTAGTTGATGCGAGGTG 59.146 43.478 0.00 0.00 0.00 4.00
1970 2052 3.119495 GGCAATTTTAGTTGATGCGAGGT 60.119 43.478 0.00 0.00 37.88 3.85
1971 2053 3.119531 TGGCAATTTTAGTTGATGCGAGG 60.120 43.478 0.00 0.00 37.88 4.63
1972 2054 4.095410 TGGCAATTTTAGTTGATGCGAG 57.905 40.909 0.00 0.00 37.88 5.03
1973 2055 4.157472 TCATGGCAATTTTAGTTGATGCGA 59.843 37.500 0.00 0.00 37.88 5.10
1974 2056 4.422840 TCATGGCAATTTTAGTTGATGCG 58.577 39.130 0.00 0.00 37.88 4.73
1975 2057 6.724694 TTTCATGGCAATTTTAGTTGATGC 57.275 33.333 0.00 0.00 36.31 3.91
1997 2079 2.162809 GCATATCACCCCGAACGTTTTT 59.837 45.455 0.46 0.00 0.00 1.94
1998 2080 1.741145 GCATATCACCCCGAACGTTTT 59.259 47.619 0.46 0.00 0.00 2.43
1999 2081 1.065709 AGCATATCACCCCGAACGTTT 60.066 47.619 0.46 0.00 0.00 3.60
2000 2082 0.539986 AGCATATCACCCCGAACGTT 59.460 50.000 0.00 0.00 0.00 3.99
2001 2083 0.539986 AAGCATATCACCCCGAACGT 59.460 50.000 0.00 0.00 0.00 3.99
2002 2084 2.519377 TAAGCATATCACCCCGAACG 57.481 50.000 0.00 0.00 0.00 3.95
2003 2085 5.278315 GGATTTTAAGCATATCACCCCGAAC 60.278 44.000 0.00 0.00 0.00 3.95
2004 2086 4.825085 GGATTTTAAGCATATCACCCCGAA 59.175 41.667 0.00 0.00 0.00 4.30
2005 2087 4.394729 GGATTTTAAGCATATCACCCCGA 58.605 43.478 0.00 0.00 0.00 5.14
2006 2088 3.188460 CGGATTTTAAGCATATCACCCCG 59.812 47.826 0.00 0.00 0.00 5.73
2007 2089 4.394729 TCGGATTTTAAGCATATCACCCC 58.605 43.478 0.00 0.00 0.00 4.95
2008 2090 5.560183 CGTTCGGATTTTAAGCATATCACCC 60.560 44.000 0.00 0.00 0.00 4.61
2009 2091 5.440685 CGTTCGGATTTTAAGCATATCACC 58.559 41.667 0.00 0.00 0.00 4.02
2010 2092 4.904154 GCGTTCGGATTTTAAGCATATCAC 59.096 41.667 0.00 0.00 0.00 3.06
2011 2093 4.814234 AGCGTTCGGATTTTAAGCATATCA 59.186 37.500 0.00 0.00 0.00 2.15
2012 2094 5.344207 AGCGTTCGGATTTTAAGCATATC 57.656 39.130 0.00 0.00 0.00 1.63
2013 2095 4.084537 CGAGCGTTCGGATTTTAAGCATAT 60.085 41.667 14.37 0.00 43.05 1.78
2014 2096 3.244345 CGAGCGTTCGGATTTTAAGCATA 59.756 43.478 14.37 0.00 43.05 3.14
2015 2097 2.030457 CGAGCGTTCGGATTTTAAGCAT 59.970 45.455 14.37 0.00 43.05 3.79
2016 2098 1.392168 CGAGCGTTCGGATTTTAAGCA 59.608 47.619 14.37 0.00 43.05 3.91
2017 2099 2.072990 CGAGCGTTCGGATTTTAAGC 57.927 50.000 14.37 0.00 43.05 3.09
2027 2109 1.787155 CAGATAAATCCCGAGCGTTCG 59.213 52.381 15.26 15.26 46.29 3.95
2028 2110 2.135933 CCAGATAAATCCCGAGCGTTC 58.864 52.381 0.00 0.00 0.00 3.95
2029 2111 1.202651 CCCAGATAAATCCCGAGCGTT 60.203 52.381 0.00 0.00 0.00 4.84
2030 2112 0.393077 CCCAGATAAATCCCGAGCGT 59.607 55.000 0.00 0.00 0.00 5.07
2031 2113 0.393077 ACCCAGATAAATCCCGAGCG 59.607 55.000 0.00 0.00 0.00 5.03
2032 2114 1.270893 GGACCCAGATAAATCCCGAGC 60.271 57.143 0.00 0.00 0.00 5.03
2033 2115 2.330216 AGGACCCAGATAAATCCCGAG 58.670 52.381 0.00 0.00 30.99 4.63
2034 2116 2.489528 AGGACCCAGATAAATCCCGA 57.510 50.000 0.00 0.00 30.99 5.14
2035 2117 4.910458 AATAGGACCCAGATAAATCCCG 57.090 45.455 0.00 0.00 30.99 5.14
2259 2344 8.693120 TTATGACATACAAACCAACCAAGTTA 57.307 30.769 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.