Multiple sequence alignment - TraesCS3D01G084300

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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 TraesCS3D01G084300 chr3D 100.000 3576 0 0 1 3576 42736119 42732544 0.000000e+00 6604.0
1 TraesCS3D01G084300 chr3A 90.167 1556 94 34 2053 3576 54658861 54657333 0.000000e+00 1971.0
2 TraesCS3D01G084300 chr3A 92.281 868 53 2 1100 1955 54659728 54658863 0.000000e+00 1219.0
3 TraesCS3D01G084300 chr3A 93.162 468 14 8 2 451 54662317 54661850 0.000000e+00 671.0
4 TraesCS3D01G084300 chr3A 83.154 279 18 7 827 1091 54660142 54659879 9.990000e-56 228.0
5 TraesCS3D01G084300 chr3A 100.000 28 0 0 675 702 453816918 453816945 6.000000e-03 52.8
6 TraesCS3D01G084300 chr3B 88.258 1269 111 22 2318 3576 66577727 66576487 0.000000e+00 1483.0
7 TraesCS3D01G084300 chr3B 93.490 553 34 2 1404 1955 66578795 66578244 0.000000e+00 821.0
8 TraesCS3D01G084300 chr3B 87.162 592 38 11 2 560 66580271 66579685 3.890000e-179 638.0
9 TraesCS3D01G084300 chr3B 95.175 228 11 0 2045 2272 66578246 66578019 9.440000e-96 361.0
10 TraesCS3D01G084300 chr3B 89.524 105 0 6 1951 2055 620988987 620988894 4.850000e-24 122.0
11 TraesCS3D01G084300 chr2A 92.784 97 3 3 1951 2047 402689379 402689287 1.730000e-28 137.0
12 TraesCS3D01G084300 chr2A 91.262 103 4 4 1950 2051 402689282 402689380 6.230000e-28 135.0
13 TraesCS3D01G084300 chr7D 91.000 100 5 4 1954 2052 618040484 618040388 8.060000e-27 132.0
14 TraesCS3D01G084300 chr4B 91.579 95 5 1 1954 2048 124737579 124737670 1.040000e-25 128.0
15 TraesCS3D01G084300 chr4B 89.524 105 1 4 1944 2048 187091058 187091152 1.350000e-24 124.0
16 TraesCS3D01G084300 chr2D 91.753 97 0 3 1954 2050 115111545 115111457 1.040000e-25 128.0
17 TraesCS3D01G084300 chrUn 90.196 102 1 5 1951 2052 224653396 224653304 1.350000e-24 124.0
18 TraesCS3D01G084300 chr7B 86.842 114 6 7 1953 2065 588501278 588501383 6.270000e-23 119.0
19 TraesCS3D01G084300 chr4A 95.238 42 2 0 675 716 590105073 590105032 2.300000e-07 67.6
20 TraesCS3D01G084300 chr4D 95.122 41 2 0 675 715 12526742 12526782 8.290000e-07 65.8


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 TraesCS3D01G084300 chr3D 42732544 42736119 3575 True 6604.00 6604 100.00000 1 3576 1 chr3D.!!$R1 3575
1 TraesCS3D01G084300 chr3A 54657333 54662317 4984 True 1022.25 1971 89.69100 2 3576 4 chr3A.!!$R1 3574
2 TraesCS3D01G084300 chr3B 66576487 66580271 3784 True 825.75 1483 91.02125 2 3576 4 chr3B.!!$R2 3574

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
556 1736 0.101399 CGTTGCAGTCTATCCGCTCT 59.899 55.0 0.0 0.0 0.00 4.09 F
1952 3607 0.025001 GTACGCACGCAGTAGCAATG 59.975 55.0 0.0 0.0 41.61 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 3907 0.253820 AGGGAGGGGATGGTGTGAAT 60.254 55.0 0.0 0.0 0.00 2.57 R
3300 5213 2.357009 GACATGACCATGCACTGATTCC 59.643 50.0 9.7 0.0 42.39 3.01 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
29 30 3.249091 CTGTCAAGAGGTTGTCATCTCG 58.751 50.000 0.00 0.00 33.38 4.04
122 123 2.711922 CCGCTCCTACGACAAGGCT 61.712 63.158 0.00 0.00 36.51 4.58
223 224 3.817084 CTGACATGGTGAGATTGTTGTGT 59.183 43.478 0.00 0.00 0.00 3.72
370 386 2.730382 TCGGTAGCCAGTCAATCTGTA 58.270 47.619 0.00 0.00 42.19 2.74
381 410 6.072286 GCCAGTCAATCTGTATATGAAATGGG 60.072 42.308 0.00 0.00 42.19 4.00
426 458 0.664224 GGTGGTGGTGGTACAAAACG 59.336 55.000 0.00 0.00 44.16 3.60
435 467 1.868498 TGGTACAAAACGAAGGAAGCG 59.132 47.619 0.00 0.00 31.92 4.68
440 472 1.463444 CAAAACGAAGGAAGCGGTAGG 59.537 52.381 0.00 0.00 0.00 3.18
442 474 1.190178 AACGAAGGAAGCGGTAGGGT 61.190 55.000 0.00 0.00 0.00 4.34
496 1504 4.278419 GCAACTGAAAAGTAGATTGGGTGT 59.722 41.667 0.00 0.00 0.00 4.16
497 1505 5.472137 GCAACTGAAAAGTAGATTGGGTGTA 59.528 40.000 0.00 0.00 0.00 2.90
498 1506 6.016610 GCAACTGAAAAGTAGATTGGGTGTAA 60.017 38.462 0.00 0.00 0.00 2.41
499 1507 7.309194 GCAACTGAAAAGTAGATTGGGTGTAAT 60.309 37.037 0.00 0.00 0.00 1.89
500 1508 8.576442 CAACTGAAAAGTAGATTGGGTGTAATT 58.424 33.333 0.00 0.00 0.00 1.40
501 1509 9.802039 AACTGAAAAGTAGATTGGGTGTAATTA 57.198 29.630 0.00 0.00 0.00 1.40
533 1713 7.213678 TGTTTTAAACCCTTGAATGACCATTC 58.786 34.615 14.09 14.09 45.55 2.67
552 1732 0.578683 CATGCGTTGCAGTCTATCCG 59.421 55.000 0.00 0.00 43.65 4.18
556 1736 0.101399 CGTTGCAGTCTATCCGCTCT 59.899 55.000 0.00 0.00 0.00 4.09
557 1737 1.469940 CGTTGCAGTCTATCCGCTCTT 60.470 52.381 0.00 0.00 0.00 2.85
558 1738 1.929836 GTTGCAGTCTATCCGCTCTTG 59.070 52.381 0.00 0.00 0.00 3.02
559 1739 1.186200 TGCAGTCTATCCGCTCTTGT 58.814 50.000 0.00 0.00 0.00 3.16
560 1740 1.134995 TGCAGTCTATCCGCTCTTGTG 60.135 52.381 0.00 0.00 0.00 3.33
561 1741 1.135139 GCAGTCTATCCGCTCTTGTGA 59.865 52.381 0.00 0.00 0.00 3.58
562 1742 2.797792 GCAGTCTATCCGCTCTTGTGAG 60.798 54.545 0.00 0.00 42.96 3.51
585 1765 2.226912 TGTAATACACAAAAGCCGTGCC 59.773 45.455 0.00 0.00 37.93 5.01
586 1766 1.616159 AATACACAAAAGCCGTGCCT 58.384 45.000 0.00 0.00 37.93 4.75
588 1768 2.257691 TACACAAAAGCCGTGCCTTA 57.742 45.000 0.00 0.00 37.93 2.69
589 1769 1.616159 ACACAAAAGCCGTGCCTTAT 58.384 45.000 0.00 0.00 37.93 1.73
590 1770 1.539827 ACACAAAAGCCGTGCCTTATC 59.460 47.619 0.00 0.00 37.93 1.75
591 1771 1.812571 CACAAAAGCCGTGCCTTATCT 59.187 47.619 0.00 0.00 0.00 1.98
593 1773 3.438781 CACAAAAGCCGTGCCTTATCTTA 59.561 43.478 0.00 0.00 0.00 2.10
634 1823 5.491070 TGTTGAATCCTGGTAGAATGTCAG 58.509 41.667 0.00 0.00 0.00 3.51
649 1838 3.667497 TGTCAGGACTGAATCTGTGAC 57.333 47.619 3.18 0.52 41.85 3.67
650 1839 2.300152 TGTCAGGACTGAATCTGTGACC 59.700 50.000 3.18 0.00 41.85 4.02
651 1840 1.546029 TCAGGACTGAATCTGTGACCG 59.454 52.381 0.00 0.00 36.53 4.79
652 1841 0.898320 AGGACTGAATCTGTGACCGG 59.102 55.000 0.00 0.00 0.00 5.28
653 1842 0.108138 GGACTGAATCTGTGACCGGG 60.108 60.000 6.32 0.00 0.00 5.73
655 1844 1.822990 GACTGAATCTGTGACCGGGTA 59.177 52.381 6.32 0.00 0.00 3.69
656 1845 2.431057 GACTGAATCTGTGACCGGGTAT 59.569 50.000 6.32 0.00 0.00 2.73
658 1847 4.028131 ACTGAATCTGTGACCGGGTATTA 58.972 43.478 6.32 0.00 0.00 0.98
660 1849 5.209818 TGAATCTGTGACCGGGTATTATC 57.790 43.478 6.32 0.00 0.00 1.75
678 1867 8.421002 GGTATTATCATTTTTACCATGGCTTGT 58.579 33.333 13.04 0.00 35.28 3.16
681 1870 8.545229 TTATCATTTTTACCATGGCTTGTTTG 57.455 30.769 13.04 3.77 0.00 2.93
682 1871 5.303971 TCATTTTTACCATGGCTTGTTTGG 58.696 37.500 13.04 0.00 36.56 3.28
684 1873 2.685106 TTACCATGGCTTGTTTGGGA 57.315 45.000 13.04 0.00 34.72 4.37
685 1874 1.917872 TACCATGGCTTGTTTGGGAC 58.082 50.000 13.04 0.00 34.72 4.46
687 1876 0.604578 CCATGGCTTGTTTGGGACTG 59.395 55.000 0.00 0.00 0.00 3.51
689 1878 1.962807 CATGGCTTGTTTGGGACTGAA 59.037 47.619 0.00 0.00 0.00 3.02
690 1879 2.151502 TGGCTTGTTTGGGACTGAAA 57.848 45.000 0.00 0.00 0.00 2.69
691 1880 2.031120 TGGCTTGTTTGGGACTGAAAG 58.969 47.619 0.00 0.00 42.29 2.62
693 1882 1.269778 GCTTGTTTGGGACTGAAAGGC 60.270 52.381 0.00 0.00 46.31 4.35
696 1885 2.745968 TGTTTGGGACTGAAAGGCTTT 58.254 42.857 13.25 13.25 46.21 3.51
703 1892 4.119862 GGGACTGAAAGGCTTTGTTTTTC 58.880 43.478 18.79 1.98 46.21 2.29
705 1894 5.419542 GGACTGAAAGGCTTTGTTTTTCTT 58.580 37.500 18.79 0.00 46.21 2.52
706 1895 5.291858 GGACTGAAAGGCTTTGTTTTTCTTG 59.708 40.000 18.79 2.38 46.21 3.02
708 1897 5.869344 ACTGAAAGGCTTTGTTTTTCTTGTC 59.131 36.000 18.79 0.00 39.30 3.18
709 1898 4.862018 TGAAAGGCTTTGTTTTTCTTGTCG 59.138 37.500 18.79 0.00 33.21 4.35
714 1903 4.387559 GGCTTTGTTTTTCTTGTCGTTGTT 59.612 37.500 0.00 0.00 0.00 2.83
715 1904 5.305036 GCTTTGTTTTTCTTGTCGTTGTTG 58.695 37.500 0.00 0.00 0.00 3.33
716 1905 5.107645 GCTTTGTTTTTCTTGTCGTTGTTGT 60.108 36.000 0.00 0.00 0.00 3.32
717 1906 5.814314 TTGTTTTTCTTGTCGTTGTTGTG 57.186 34.783 0.00 0.00 0.00 3.33
718 1907 4.861210 TGTTTTTCTTGTCGTTGTTGTGT 58.139 34.783 0.00 0.00 0.00 3.72
719 1908 4.912766 TGTTTTTCTTGTCGTTGTTGTGTC 59.087 37.500 0.00 0.00 0.00 3.67
720 1909 5.151389 GTTTTTCTTGTCGTTGTTGTGTCT 58.849 37.500 0.00 0.00 0.00 3.41
722 1911 6.671614 TTTTCTTGTCGTTGTTGTGTCTAT 57.328 33.333 0.00 0.00 0.00 1.98
723 1912 5.651172 TTCTTGTCGTTGTTGTGTCTATG 57.349 39.130 0.00 0.00 0.00 2.23
724 1913 3.493129 TCTTGTCGTTGTTGTGTCTATGC 59.507 43.478 0.00 0.00 0.00 3.14
725 1914 2.139917 TGTCGTTGTTGTGTCTATGCC 58.860 47.619 0.00 0.00 0.00 4.40
726 1915 2.139917 GTCGTTGTTGTGTCTATGCCA 58.860 47.619 0.00 0.00 0.00 4.92
727 1916 2.546368 GTCGTTGTTGTGTCTATGCCAA 59.454 45.455 0.00 0.00 0.00 4.52
728 1917 3.002862 GTCGTTGTTGTGTCTATGCCAAA 59.997 43.478 0.00 0.00 0.00 3.28
729 1918 3.002862 TCGTTGTTGTGTCTATGCCAAAC 59.997 43.478 0.00 0.00 0.00 2.93
730 1919 3.242903 CGTTGTTGTGTCTATGCCAAACA 60.243 43.478 0.00 0.00 0.00 2.83
731 1920 3.980646 TGTTGTGTCTATGCCAAACAC 57.019 42.857 0.00 0.00 42.80 3.32
732 1921 3.550820 TGTTGTGTCTATGCCAAACACT 58.449 40.909 9.01 0.00 42.89 3.55
733 1922 3.314913 TGTTGTGTCTATGCCAAACACTG 59.685 43.478 9.01 0.00 42.89 3.66
734 1923 3.207265 TGTGTCTATGCCAAACACTGT 57.793 42.857 9.01 0.00 42.89 3.55
735 1924 2.877786 TGTGTCTATGCCAAACACTGTG 59.122 45.455 6.19 6.19 42.89 3.66
736 1925 3.138304 GTGTCTATGCCAAACACTGTGA 58.862 45.455 15.86 0.00 40.07 3.58
738 1927 3.752747 TGTCTATGCCAAACACTGTGATG 59.247 43.478 15.86 12.35 0.00 3.07
739 1928 3.127548 GTCTATGCCAAACACTGTGATGG 59.872 47.826 23.58 23.58 33.32 3.51
742 1931 0.318955 GCCAAACACTGTGATGGTGC 60.319 55.000 26.19 15.86 38.14 5.01
743 1932 1.321474 CCAAACACTGTGATGGTGCT 58.679 50.000 15.86 0.00 38.14 4.40
745 1934 2.884012 CCAAACACTGTGATGGTGCTTA 59.116 45.455 15.86 0.00 38.14 3.09
746 1935 3.317711 CCAAACACTGTGATGGTGCTTAA 59.682 43.478 15.86 0.00 38.14 1.85
747 1936 4.022068 CCAAACACTGTGATGGTGCTTAAT 60.022 41.667 15.86 0.00 38.14 1.40
748 1937 5.509501 CCAAACACTGTGATGGTGCTTAATT 60.510 40.000 15.86 0.00 38.14 1.40
750 1939 6.892658 AACACTGTGATGGTGCTTAATTAA 57.107 33.333 15.86 0.00 38.14 1.40
752 1941 7.466746 ACACTGTGATGGTGCTTAATTAATT 57.533 32.000 15.86 5.89 38.14 1.40
753 1942 7.315142 ACACTGTGATGGTGCTTAATTAATTG 58.685 34.615 15.86 0.00 38.14 2.32
755 1944 8.458052 CACTGTGATGGTGCTTAATTAATTGTA 58.542 33.333 11.05 0.00 0.00 2.41
756 1945 8.677300 ACTGTGATGGTGCTTAATTAATTGTAG 58.323 33.333 11.05 8.93 0.00 2.74
758 1947 8.458052 TGTGATGGTGCTTAATTAATTGTAGTG 58.542 33.333 11.05 0.00 0.00 2.74
760 1949 8.673711 TGATGGTGCTTAATTAATTGTAGTGTC 58.326 33.333 11.05 1.36 0.00 3.67
761 1950 7.987750 TGGTGCTTAATTAATTGTAGTGTCA 57.012 32.000 11.05 5.57 0.00 3.58
780 2151 6.660094 AGTGTCAAGTTAGTTTGGTTGGTTTA 59.340 34.615 0.00 0.00 0.00 2.01
791 2162 3.692690 TGGTTGGTTTAGGCCTTGATAC 58.307 45.455 12.58 3.98 0.00 2.24
793 2164 4.083565 GGTTGGTTTAGGCCTTGATACAA 58.916 43.478 12.58 8.06 0.00 2.41
794 2165 4.709886 GGTTGGTTTAGGCCTTGATACAAT 59.290 41.667 12.58 0.00 0.00 2.71
795 2166 5.163550 GGTTGGTTTAGGCCTTGATACAATC 60.164 44.000 12.58 7.48 0.00 2.67
796 2167 4.196193 TGGTTTAGGCCTTGATACAATCG 58.804 43.478 12.58 0.00 0.00 3.34
799 2170 1.668419 AGGCCTTGATACAATCGTGC 58.332 50.000 0.00 0.00 0.00 5.34
800 2171 1.210478 AGGCCTTGATACAATCGTGCT 59.790 47.619 0.00 0.00 0.00 4.40
806 2177 5.566826 GCCTTGATACAATCGTGCTAGGATA 60.567 44.000 0.00 0.00 30.73 2.59
807 2178 6.096036 CCTTGATACAATCGTGCTAGGATAG 58.904 44.000 0.00 0.00 43.09 2.08
821 2192 5.041951 CTAGGATAGCGACAGAGAACATC 57.958 47.826 0.00 0.00 0.00 3.06
822 2193 3.291584 AGGATAGCGACAGAGAACATCA 58.708 45.455 0.00 0.00 0.00 3.07
823 2194 3.894427 AGGATAGCGACAGAGAACATCAT 59.106 43.478 0.00 0.00 0.00 2.45
825 2196 5.182950 AGGATAGCGACAGAGAACATCATAG 59.817 44.000 0.00 0.00 0.00 2.23
839 2220 9.528018 GAGAACATCATAGGTCTAGAAGAAAAG 57.472 37.037 0.00 0.00 0.00 2.27
840 2221 9.261035 AGAACATCATAGGTCTAGAAGAAAAGA 57.739 33.333 0.00 0.00 0.00 2.52
848 2229 9.727859 ATAGGTCTAGAAGAAAAGAAAAAGGAC 57.272 33.333 0.00 0.00 0.00 3.85
883 2326 6.339587 ACAAAAGACAGTGACCAAGAAAAA 57.660 33.333 0.00 0.00 0.00 1.94
888 2331 4.640647 AGACAGTGACCAAGAAAAAGAACC 59.359 41.667 0.00 0.00 0.00 3.62
889 2332 3.699538 ACAGTGACCAAGAAAAAGAACCC 59.300 43.478 0.00 0.00 0.00 4.11
890 2333 3.699038 CAGTGACCAAGAAAAAGAACCCA 59.301 43.478 0.00 0.00 0.00 4.51
891 2334 4.159506 CAGTGACCAAGAAAAAGAACCCAA 59.840 41.667 0.00 0.00 0.00 4.12
892 2335 4.775253 AGTGACCAAGAAAAAGAACCCAAA 59.225 37.500 0.00 0.00 0.00 3.28
893 2336 5.247337 AGTGACCAAGAAAAAGAACCCAAAA 59.753 36.000 0.00 0.00 0.00 2.44
900 2343 9.476202 CCAAGAAAAAGAACCCAAAACTATTAG 57.524 33.333 0.00 0.00 0.00 1.73
932 2389 1.424302 CCATCCATCCAGATCCAAGCT 59.576 52.381 0.00 0.00 0.00 3.74
955 2426 2.877396 GTTAGGGGATAACGACGCG 58.123 57.895 3.53 3.53 34.77 6.01
963 2434 1.628447 GATAACGACGCGGTGCCAAA 61.628 55.000 12.47 0.00 0.00 3.28
973 2448 1.795170 CGGTGCCAAACAGAACCAGG 61.795 60.000 0.00 0.00 32.69 4.45
976 2451 0.178992 TGCCAAACAGAACCAGGAGG 60.179 55.000 0.00 0.00 42.21 4.30
1048 2526 3.716195 CATCCACCGCCTCCACCA 61.716 66.667 0.00 0.00 0.00 4.17
1091 2569 0.914644 TCCTTCCTCCCAGATGCTTG 59.085 55.000 0.00 0.00 0.00 4.01
1093 2571 1.681166 CCTTCCTCCCAGATGCTTGTG 60.681 57.143 0.00 0.00 0.00 3.33
1095 2573 1.067295 TCCTCCCAGATGCTTGTGTT 58.933 50.000 0.00 0.00 0.00 3.32
1096 2574 1.003580 TCCTCCCAGATGCTTGTGTTC 59.996 52.381 0.00 0.00 0.00 3.18
1097 2575 1.271543 CCTCCCAGATGCTTGTGTTCA 60.272 52.381 0.00 0.00 0.00 3.18
1110 2753 2.281484 GTTCACAGCAAGGCGGGA 60.281 61.111 0.00 0.00 0.00 5.14
1174 2817 2.024871 CTCCTCCGTCGCGTCATC 59.975 66.667 5.77 0.00 0.00 2.92
1290 2945 2.647949 CCCCTCCCTCCCTACCACT 61.648 68.421 0.00 0.00 0.00 4.00
1341 2996 8.398665 CCTAAGCTATCACCAAATTAACTGAAC 58.601 37.037 0.00 0.00 0.00 3.18
1343 2998 5.652452 AGCTATCACCAAATTAACTGAACCC 59.348 40.000 0.00 0.00 0.00 4.11
1356 3011 2.633967 ACTGAACCCATTGTACCACGTA 59.366 45.455 0.00 0.00 0.00 3.57
1357 3012 3.262405 ACTGAACCCATTGTACCACGTAT 59.738 43.478 0.00 0.00 0.00 3.06
1358 3013 4.467082 ACTGAACCCATTGTACCACGTATA 59.533 41.667 0.00 0.00 0.00 1.47
1377 3032 7.865889 CACGTATATAGCTGAGTTAATGGTGAA 59.134 37.037 0.00 0.00 0.00 3.18
1378 3033 8.585881 ACGTATATAGCTGAGTTAATGGTGAAT 58.414 33.333 0.00 0.00 0.00 2.57
1381 3036 6.932356 ATAGCTGAGTTAATGGTGAATGTG 57.068 37.500 0.00 0.00 0.00 3.21
1558 3213 3.148279 GATGTCGCCCTCCTCCGT 61.148 66.667 0.00 0.00 0.00 4.69
1568 3223 0.321564 CCTCCTCCGTGCACAAATCA 60.322 55.000 18.64 0.00 0.00 2.57
1579 3234 2.622942 TGCACAAATCAACAAGGACCTC 59.377 45.455 0.00 0.00 0.00 3.85
1619 3274 4.242586 TCCCACTCCCACCGTCCA 62.243 66.667 0.00 0.00 0.00 4.02
1623 3278 4.309950 ACTCCCACCGTCCAACGC 62.310 66.667 0.00 0.00 40.91 4.84
1640 3295 2.347490 CCACCGACCAGGACAAGG 59.653 66.667 0.00 0.00 45.00 3.61
1641 3296 2.516888 CCACCGACCAGGACAAGGT 61.517 63.158 0.00 0.00 45.00 3.50
1684 3339 2.202919 CAGGCCATGATCGACGCA 60.203 61.111 5.01 0.00 0.00 5.24
1772 3427 3.375699 GAGATCAAGGGGGAAGTCTACA 58.624 50.000 0.00 0.00 0.00 2.74
1805 3460 3.062466 CTCTCGCGGAGTGGGACA 61.062 66.667 6.13 0.00 40.94 4.02
1840 3495 1.133761 AGCTACATCTACTCCAGCGGA 60.134 52.381 0.00 0.00 37.32 5.54
1952 3607 0.025001 GTACGCACGCAGTAGCAATG 59.975 55.000 0.00 0.00 41.61 2.82
1953 3608 0.389296 TACGCACGCAGTAGCAATGT 60.389 50.000 0.00 0.00 41.61 2.71
1954 3609 0.389296 ACGCACGCAGTAGCAATGTA 60.389 50.000 0.00 0.00 41.61 2.29
1955 3610 0.025001 CGCACGCAGTAGCAATGTAC 59.975 55.000 0.00 0.00 41.61 2.90
1956 3611 1.359848 GCACGCAGTAGCAATGTACT 58.640 50.000 0.00 0.00 41.61 2.73
1957 3612 1.324736 GCACGCAGTAGCAATGTACTC 59.675 52.381 0.00 0.00 41.61 2.59
1958 3613 1.927174 CACGCAGTAGCAATGTACTCC 59.073 52.381 0.00 0.00 41.61 3.85
1959 3614 1.134788 ACGCAGTAGCAATGTACTCCC 60.135 52.381 0.00 0.00 41.94 4.30
1960 3615 1.137086 CGCAGTAGCAATGTACTCCCT 59.863 52.381 0.00 0.00 42.27 4.20
1961 3616 2.799917 CGCAGTAGCAATGTACTCCCTC 60.800 54.545 0.00 0.00 42.27 4.30
1962 3617 2.483889 GCAGTAGCAATGTACTCCCTCC 60.484 54.545 0.00 0.00 41.58 4.30
1963 3618 2.032620 AGTAGCAATGTACTCCCTCCG 58.967 52.381 0.00 0.00 0.00 4.63
1964 3619 1.755380 GTAGCAATGTACTCCCTCCGT 59.245 52.381 0.00 0.00 0.00 4.69
1965 3620 0.824759 AGCAATGTACTCCCTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
1966 3621 0.179081 GCAATGTACTCCCTCCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
1967 3622 0.464452 CAATGTACTCCCTCCGTCCC 59.536 60.000 0.00 0.00 0.00 4.46
1968 3623 0.042131 AATGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
1969 3624 0.264955 ATGTACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
1970 3625 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
1971 3626 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
1972 3627 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
1973 3628 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
1974 3629 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
1975 3630 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
1976 3631 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
1977 3632 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
1978 3633 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
1979 3634 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
1981 3636 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
1982 3637 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
1983 3638 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
1984 3639 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
1985 3640 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2010 3665 3.543680 ACTGCACTAGTGTCAAAGTGT 57.456 42.857 23.44 12.58 44.03 3.55
2011 3666 3.458189 ACTGCACTAGTGTCAAAGTGTC 58.542 45.455 23.44 4.72 44.03 3.67
2012 3667 3.118775 ACTGCACTAGTGTCAAAGTGTCA 60.119 43.478 23.44 8.96 44.03 3.58
2013 3668 3.867857 TGCACTAGTGTCAAAGTGTCAA 58.132 40.909 23.44 0.00 44.03 3.18
2014 3669 4.257731 TGCACTAGTGTCAAAGTGTCAAA 58.742 39.130 23.44 0.00 44.03 2.69
2015 3670 4.697828 TGCACTAGTGTCAAAGTGTCAAAA 59.302 37.500 23.44 0.00 44.03 2.44
2016 3671 5.182190 TGCACTAGTGTCAAAGTGTCAAAAA 59.818 36.000 23.44 0.00 44.03 1.94
2248 3903 0.537828 TGCAGGTCAGCAGCAATCAA 60.538 50.000 0.00 0.00 40.11 2.57
2252 3907 3.076621 CAGGTCAGCAGCAATCAAACTA 58.923 45.455 0.00 0.00 0.00 2.24
2253 3908 3.693085 CAGGTCAGCAGCAATCAAACTAT 59.307 43.478 0.00 0.00 0.00 2.12
2277 3939 1.638589 CACCATCCCCTCCCTTGTTTA 59.361 52.381 0.00 0.00 0.00 2.01
2279 3941 2.933139 ACCATCCCCTCCCTTGTTTAAT 59.067 45.455 0.00 0.00 0.00 1.40
2282 3944 4.405680 CCATCCCCTCCCTTGTTTAATTTC 59.594 45.833 0.00 0.00 0.00 2.17
2283 3945 4.750833 TCCCCTCCCTTGTTTAATTTCA 57.249 40.909 0.00 0.00 0.00 2.69
2284 3946 4.412843 TCCCCTCCCTTGTTTAATTTCAC 58.587 43.478 0.00 0.00 0.00 3.18
2289 3972 6.267699 CCCTCCCTTGTTTAATTTCACTCTTT 59.732 38.462 0.00 0.00 0.00 2.52
2316 4189 4.989279 AACTGACAGAACACAGCATTTT 57.011 36.364 10.08 0.00 37.61 1.82
2336 4237 7.518211 GCATTTTGTTCAAATAACTTCCACACC 60.518 37.037 0.00 0.00 32.90 4.16
2339 4240 4.582656 TGTTCAAATAACTTCCACACCCAG 59.417 41.667 0.00 0.00 0.00 4.45
2349 4252 1.843851 TCCACACCCAGTCTCAAAAGT 59.156 47.619 0.00 0.00 0.00 2.66
2421 4327 0.306840 TAAGCTGCGTCGTAGATCCG 59.693 55.000 14.97 0.00 40.67 4.18
2445 4351 2.076100 TGCTTGCCTTTCACATACTCG 58.924 47.619 0.00 0.00 0.00 4.18
2450 4356 1.009829 CCTTTCACATACTCGCAGGC 58.990 55.000 0.00 0.00 0.00 4.85
2479 4385 2.436417 TCATCTACTGGTTTTGCAGGC 58.564 47.619 0.00 0.00 0.00 4.85
2483 4389 2.373836 TCTACTGGTTTTGCAGGCCTTA 59.626 45.455 0.00 0.00 0.00 2.69
2491 4397 0.895100 TTGCAGGCCTTAAGGTGCTG 60.895 55.000 27.94 14.54 37.87 4.41
2563 4469 0.439985 CCATCACGTCGTTTGCTCAG 59.560 55.000 0.00 0.00 0.00 3.35
2567 4473 1.269723 TCACGTCGTTTGCTCAGATCT 59.730 47.619 0.00 0.00 0.00 2.75
2583 4489 0.107508 ATCTCCACCTGAATGCCACG 60.108 55.000 0.00 0.00 0.00 4.94
2591 4497 3.127533 GAATGCCACGGCGAGCTT 61.128 61.111 16.62 11.56 45.51 3.74
2593 4499 1.766143 GAATGCCACGGCGAGCTTAG 61.766 60.000 16.62 0.00 45.51 2.18
2613 4521 0.457035 CCCTGCCATATGTGCACAAC 59.543 55.000 25.72 11.52 34.46 3.32
2615 4523 1.545136 CCTGCCATATGTGCACAACAA 59.455 47.619 25.72 12.96 43.61 2.83
2619 4527 4.934515 TGCCATATGTGCACAACAATATG 58.065 39.130 25.72 23.87 43.61 1.78
2620 4528 4.401837 TGCCATATGTGCACAACAATATGT 59.598 37.500 25.72 7.12 43.61 2.29
2622 4530 6.096001 TGCCATATGTGCACAACAATATGTTA 59.904 34.615 25.72 13.76 43.61 2.41
2624 4532 7.652909 GCCATATGTGCACAACAATATGTTATT 59.347 33.333 25.72 4.69 43.61 1.40
2630 4538 9.750125 TGTGCACAACAATATGTTATTTACAAA 57.250 25.926 19.28 0.00 38.77 2.83
2633 4541 8.868916 GCACAACAATATGTTATTTACAAAGGG 58.131 33.333 0.00 0.00 38.77 3.95
2643 4551 6.435904 TGTTATTTACAAAGGGAACCATCTGG 59.564 38.462 0.00 0.00 43.15 3.86
2655 4563 2.035530 CCATCTGGTCTCAAAGCTCC 57.964 55.000 0.00 0.00 0.00 4.70
2658 4566 1.270907 TCTGGTCTCAAAGCTCCCTC 58.729 55.000 0.00 0.00 0.00 4.30
2659 4567 0.251634 CTGGTCTCAAAGCTCCCTCC 59.748 60.000 0.00 0.00 0.00 4.30
2660 4568 0.473694 TGGTCTCAAAGCTCCCTCCA 60.474 55.000 0.00 0.00 0.00 3.86
2664 4572 3.054361 GGTCTCAAAGCTCCCTCCATTTA 60.054 47.826 0.00 0.00 0.00 1.40
2665 4573 4.385754 GGTCTCAAAGCTCCCTCCATTTAT 60.386 45.833 0.00 0.00 0.00 1.40
2666 4574 5.196695 GTCTCAAAGCTCCCTCCATTTATT 58.803 41.667 0.00 0.00 0.00 1.40
2667 4575 5.067023 GTCTCAAAGCTCCCTCCATTTATTG 59.933 44.000 0.00 0.00 0.00 1.90
2668 4576 4.934356 TCAAAGCTCCCTCCATTTATTGT 58.066 39.130 0.00 0.00 0.00 2.71
2669 4577 4.706476 TCAAAGCTCCCTCCATTTATTGTG 59.294 41.667 0.00 0.00 0.00 3.33
2670 4578 4.322057 AAGCTCCCTCCATTTATTGTGT 57.678 40.909 0.00 0.00 0.00 3.72
2671 4579 5.450818 AAGCTCCCTCCATTTATTGTGTA 57.549 39.130 0.00 0.00 0.00 2.90
2672 4580 5.653255 AGCTCCCTCCATTTATTGTGTAT 57.347 39.130 0.00 0.00 0.00 2.29
2673 4581 6.763715 AGCTCCCTCCATTTATTGTGTATA 57.236 37.500 0.00 0.00 0.00 1.47
2674 4582 7.335127 AGCTCCCTCCATTTATTGTGTATAT 57.665 36.000 0.00 0.00 0.00 0.86
2675 4583 7.170965 AGCTCCCTCCATTTATTGTGTATATG 58.829 38.462 0.00 0.00 0.00 1.78
2676 4584 6.127897 GCTCCCTCCATTTATTGTGTATATGC 60.128 42.308 0.00 0.00 0.00 3.14
2677 4585 7.090319 TCCCTCCATTTATTGTGTATATGCT 57.910 36.000 0.00 0.00 0.00 3.79
2678 4586 8.213489 TCCCTCCATTTATTGTGTATATGCTA 57.787 34.615 0.00 0.00 0.00 3.49
2679 4587 8.321353 TCCCTCCATTTATTGTGTATATGCTAG 58.679 37.037 0.00 0.00 0.00 3.42
2680 4588 8.321353 CCCTCCATTTATTGTGTATATGCTAGA 58.679 37.037 0.00 0.00 0.00 2.43
2681 4589 9.376075 CCTCCATTTATTGTGTATATGCTAGAG 57.624 37.037 0.00 0.00 0.00 2.43
2682 4590 8.777865 TCCATTTATTGTGTATATGCTAGAGC 57.222 34.615 0.00 0.00 42.50 4.09
2702 4610 5.864474 AGAGCAGCATAATATACGCTAACAC 59.136 40.000 0.00 0.00 33.82 3.32
2731 4639 3.858247 AGTTATAACCACAAGAGTCGGC 58.142 45.455 12.05 0.00 0.00 5.54
2742 4650 3.130340 ACAAGAGTCGGCACAATTGTTTT 59.870 39.130 8.77 0.00 0.00 2.43
2760 4668 6.282199 TGTTTTAAGCCCTTGTGTAAAACA 57.718 33.333 13.66 13.66 46.37 2.83
2769 4677 4.274950 CCCTTGTGTAAAACAATGACTCGT 59.725 41.667 0.00 0.00 44.97 4.18
2776 4684 7.439955 TGTGTAAAACAATGACTCGTTATCAGT 59.560 33.333 0.00 0.00 35.24 3.41
2839 4750 2.666508 CTGTACTGAAATTCGTCCACGG 59.333 50.000 0.00 0.00 40.29 4.94
2849 4760 0.108520 TCGTCCACGGAACATAAGGC 60.109 55.000 0.00 0.00 40.29 4.35
2873 4784 7.094805 GGCATTGAGTGATTTTACAAGTGTCTA 60.095 37.037 0.00 0.00 0.00 2.59
2923 4834 1.411612 AGACGAACCTTGGTCTCGTTT 59.588 47.619 21.28 16.46 45.25 3.60
2992 4903 1.678101 GCACATGTATTTCCTCAGCCC 59.322 52.381 0.00 0.00 0.00 5.19
3261 5174 4.862018 ACAAAACCTGAACACACAAAATCG 59.138 37.500 0.00 0.00 0.00 3.34
3277 5190 7.601130 ACACAAAATCGACAAGTTAGCTACATA 59.399 33.333 0.00 0.00 0.00 2.29
3376 5289 1.157585 GAGAACGGTTCAGCTTTCCC 58.842 55.000 21.86 0.00 0.00 3.97
3448 5361 3.510388 TCATCTCTTACACTGAAGCGG 57.490 47.619 0.00 0.00 0.00 5.52
3498 5411 2.406024 GCACAAAAAGCACGATCACATG 59.594 45.455 0.00 0.00 0.00 3.21
3508 5421 5.660460 AGCACGATCACATGAGTATGTTTA 58.340 37.500 0.00 0.00 45.01 2.01
3572 5485 4.943705 CACTGTACAGGAAGGCATGTAAAT 59.056 41.667 26.12 0.00 42.21 1.40
3573 5486 4.943705 ACTGTACAGGAAGGCATGTAAATG 59.056 41.667 26.12 0.00 42.21 2.32
3574 5487 5.172687 TGTACAGGAAGGCATGTAAATGA 57.827 39.130 0.00 0.00 42.21 2.57
3575 5488 5.185454 TGTACAGGAAGGCATGTAAATGAG 58.815 41.667 0.00 0.00 42.21 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.062749 TGACAACCTCTTGACAGTAAAGTAT 57.937 36.000 0.00 0.00 30.07 2.12
29 30 1.880340 CGCGAGCTTCATCAGGACC 60.880 63.158 0.00 0.00 0.00 4.46
122 123 4.041917 CCGACCGGGTTCGACGAA 62.042 66.667 15.46 6.10 41.78 3.85
154 155 6.265196 TCACAGGTTCATGCAGAATTAAACTT 59.735 34.615 0.00 0.00 38.76 2.66
223 224 1.547820 TCCTGCAACACACAAGCAAAA 59.452 42.857 0.00 0.00 37.89 2.44
370 386 8.773033 AGCTTCTATTTCAACCCATTTCATAT 57.227 30.769 0.00 0.00 0.00 1.78
381 410 6.372937 ACTCCAAAGCTAGCTTCTATTTCAAC 59.627 38.462 29.42 0.00 34.84 3.18
426 458 0.611714 TCAACCCTACCGCTTCCTTC 59.388 55.000 0.00 0.00 0.00 3.46
435 467 3.163467 ACACACTCTACTCAACCCTACC 58.837 50.000 0.00 0.00 0.00 3.18
440 472 8.847196 TGATGTATATACACACTCTACTCAACC 58.153 37.037 17.69 0.00 39.30 3.77
526 1706 0.523072 ACTGCAACGCATGAATGGTC 59.477 50.000 0.00 0.00 38.13 4.02
533 1713 0.578683 CGGATAGACTGCAACGCATG 59.421 55.000 0.00 0.00 38.13 4.06
552 1732 6.539649 TTGTGTATTACAACTCACAAGAGC 57.460 37.500 0.00 0.00 44.07 4.09
580 1760 5.640732 ACTTGCAAAATAAGATAAGGCACG 58.359 37.500 0.00 0.00 0.00 5.34
634 1823 0.108138 CCCGGTCACAGATTCAGTCC 60.108 60.000 0.00 0.00 0.00 3.85
637 1826 3.543680 AATACCCGGTCACAGATTCAG 57.456 47.619 0.00 0.00 0.00 3.02
649 1838 6.571537 GCCATGGTAAAAATGATAATACCCGG 60.572 42.308 14.67 0.00 37.57 5.73
650 1839 6.208599 AGCCATGGTAAAAATGATAATACCCG 59.791 38.462 14.67 0.00 37.57 5.28
651 1840 7.539034 AGCCATGGTAAAAATGATAATACCC 57.461 36.000 14.67 0.00 37.57 3.69
652 1841 8.421002 ACAAGCCATGGTAAAAATGATAATACC 58.579 33.333 14.67 0.00 38.61 2.73
653 1842 9.816354 AACAAGCCATGGTAAAAATGATAATAC 57.184 29.630 14.67 0.00 0.00 1.89
655 1844 9.165035 CAAACAAGCCATGGTAAAAATGATAAT 57.835 29.630 14.67 0.00 0.00 1.28
656 1845 7.605691 CCAAACAAGCCATGGTAAAAATGATAA 59.394 33.333 14.67 0.00 0.00 1.75
658 1847 5.939296 CCAAACAAGCCATGGTAAAAATGAT 59.061 36.000 14.67 0.00 0.00 2.45
660 1849 4.455190 CCCAAACAAGCCATGGTAAAAATG 59.545 41.667 14.67 6.65 32.13 2.32
678 1867 2.745968 ACAAAGCCTTTCAGTCCCAAA 58.254 42.857 0.00 0.00 0.00 3.28
681 1870 3.819564 AAAACAAAGCCTTTCAGTCCC 57.180 42.857 0.00 0.00 0.00 4.46
682 1871 5.011090 AGAAAAACAAAGCCTTTCAGTCC 57.989 39.130 0.00 0.00 32.59 3.85
684 1873 5.793817 ACAAGAAAAACAAAGCCTTTCAGT 58.206 33.333 0.00 0.00 32.59 3.41
685 1874 5.004726 CGACAAGAAAAACAAAGCCTTTCAG 59.995 40.000 0.00 0.00 32.59 3.02
687 1876 4.862574 ACGACAAGAAAAACAAAGCCTTTC 59.137 37.500 0.00 0.00 0.00 2.62
689 1878 4.450082 ACGACAAGAAAAACAAAGCCTT 57.550 36.364 0.00 0.00 0.00 4.35
690 1879 4.173256 CAACGACAAGAAAAACAAAGCCT 58.827 39.130 0.00 0.00 0.00 4.58
691 1880 3.924073 ACAACGACAAGAAAAACAAAGCC 59.076 39.130 0.00 0.00 0.00 4.35
693 1882 6.074569 ACACAACAACGACAAGAAAAACAAAG 60.075 34.615 0.00 0.00 0.00 2.77
696 1885 4.861210 ACACAACAACGACAAGAAAAACA 58.139 34.783 0.00 0.00 0.00 2.83
703 1892 3.363970 GGCATAGACACAACAACGACAAG 60.364 47.826 0.00 0.00 0.00 3.16
705 1894 2.139917 GGCATAGACACAACAACGACA 58.860 47.619 0.00 0.00 0.00 4.35
706 1895 2.139917 TGGCATAGACACAACAACGAC 58.860 47.619 0.00 0.00 0.00 4.34
708 1897 3.242903 TGTTTGGCATAGACACAACAACG 60.243 43.478 0.00 0.00 0.00 4.10
709 1898 4.041723 GTGTTTGGCATAGACACAACAAC 58.958 43.478 18.50 4.88 42.36 3.32
714 1903 2.877786 CACAGTGTTTGGCATAGACACA 59.122 45.455 22.69 6.13 44.56 3.72
715 1904 3.138304 TCACAGTGTTTGGCATAGACAC 58.862 45.455 16.71 16.71 42.95 3.67
716 1905 3.483808 TCACAGTGTTTGGCATAGACA 57.516 42.857 7.87 1.86 0.00 3.41
717 1906 3.127548 CCATCACAGTGTTTGGCATAGAC 59.872 47.826 8.67 0.00 0.00 2.59
718 1907 3.244875 ACCATCACAGTGTTTGGCATAGA 60.245 43.478 18.05 0.74 32.26 1.98
719 1908 3.084039 ACCATCACAGTGTTTGGCATAG 58.916 45.455 18.05 0.00 32.26 2.23
720 1909 2.819019 CACCATCACAGTGTTTGGCATA 59.181 45.455 18.05 0.00 32.26 3.14
722 1911 1.031235 CACCATCACAGTGTTTGGCA 58.969 50.000 18.05 0.00 32.26 4.92
723 1912 0.318955 GCACCATCACAGTGTTTGGC 60.319 55.000 18.05 7.80 37.56 4.52
724 1913 1.321474 AGCACCATCACAGTGTTTGG 58.679 50.000 16.96 16.96 37.56 3.28
725 1914 4.566545 TTAAGCACCATCACAGTGTTTG 57.433 40.909 0.00 0.06 38.80 2.93
726 1915 5.789643 AATTAAGCACCATCACAGTGTTT 57.210 34.783 0.00 0.00 40.96 2.83
727 1916 6.892658 TTAATTAAGCACCATCACAGTGTT 57.107 33.333 0.00 0.00 37.56 3.32
728 1917 7.039784 ACAATTAATTAAGCACCATCACAGTGT 60.040 33.333 0.00 0.00 37.56 3.55
729 1918 7.315142 ACAATTAATTAAGCACCATCACAGTG 58.685 34.615 0.00 0.00 38.30 3.66
730 1919 7.466746 ACAATTAATTAAGCACCATCACAGT 57.533 32.000 0.00 0.00 0.00 3.55
731 1920 8.677300 ACTACAATTAATTAAGCACCATCACAG 58.323 33.333 0.00 0.00 0.00 3.66
732 1921 8.458052 CACTACAATTAATTAAGCACCATCACA 58.542 33.333 0.00 0.00 0.00 3.58
733 1922 8.458843 ACACTACAATTAATTAAGCACCATCAC 58.541 33.333 0.00 0.00 0.00 3.06
734 1923 8.574251 ACACTACAATTAATTAAGCACCATCA 57.426 30.769 0.00 0.00 0.00 3.07
735 1924 8.673711 TGACACTACAATTAATTAAGCACCATC 58.326 33.333 0.00 0.00 0.00 3.51
736 1925 8.574251 TGACACTACAATTAATTAAGCACCAT 57.426 30.769 0.00 0.00 0.00 3.55
738 1927 8.512138 ACTTGACACTACAATTAATTAAGCACC 58.488 33.333 0.00 0.00 0.00 5.01
739 1928 9.893305 AACTTGACACTACAATTAATTAAGCAC 57.107 29.630 0.00 0.00 0.00 4.40
747 1936 9.398538 ACCAAACTAACTTGACACTACAATTAA 57.601 29.630 0.00 0.00 0.00 1.40
748 1937 8.967664 ACCAAACTAACTTGACACTACAATTA 57.032 30.769 0.00 0.00 0.00 1.40
750 1939 7.201785 CCAACCAAACTAACTTGACACTACAAT 60.202 37.037 0.00 0.00 0.00 2.71
752 1941 5.587043 CCAACCAAACTAACTTGACACTACA 59.413 40.000 0.00 0.00 0.00 2.74
753 1942 5.587443 ACCAACCAAACTAACTTGACACTAC 59.413 40.000 0.00 0.00 0.00 2.73
755 1944 4.595986 ACCAACCAAACTAACTTGACACT 58.404 39.130 0.00 0.00 0.00 3.55
756 1945 4.976224 ACCAACCAAACTAACTTGACAC 57.024 40.909 0.00 0.00 0.00 3.67
758 1947 6.500910 CCTAAACCAACCAAACTAACTTGAC 58.499 40.000 0.00 0.00 0.00 3.18
760 1949 5.286438 GCCTAAACCAACCAAACTAACTTG 58.714 41.667 0.00 0.00 0.00 3.16
761 1950 4.342951 GGCCTAAACCAACCAAACTAACTT 59.657 41.667 0.00 0.00 0.00 2.66
767 2138 2.696187 TCAAGGCCTAAACCAACCAAAC 59.304 45.455 5.16 0.00 0.00 2.93
780 2151 1.210478 AGCACGATTGTATCAAGGCCT 59.790 47.619 0.00 0.00 0.00 5.19
799 2170 4.517075 TGATGTTCTCTGTCGCTATCCTAG 59.483 45.833 0.00 0.00 0.00 3.02
800 2171 4.461198 TGATGTTCTCTGTCGCTATCCTA 58.539 43.478 0.00 0.00 0.00 2.94
806 2177 3.027412 ACCTATGATGTTCTCTGTCGCT 58.973 45.455 0.00 0.00 0.00 4.93
807 2178 3.067461 AGACCTATGATGTTCTCTGTCGC 59.933 47.826 0.00 0.00 0.00 5.19
808 2179 4.909696 AGACCTATGATGTTCTCTGTCG 57.090 45.455 0.00 0.00 0.00 4.35
809 2180 7.500892 TCTTCTAGACCTATGATGTTCTCTGTC 59.499 40.741 0.00 0.00 0.00 3.51
810 2181 7.350382 TCTTCTAGACCTATGATGTTCTCTGT 58.650 38.462 0.00 0.00 0.00 3.41
811 2182 7.815840 TCTTCTAGACCTATGATGTTCTCTG 57.184 40.000 0.00 0.00 0.00 3.35
813 2184 9.528018 CTTTTCTTCTAGACCTATGATGTTCTC 57.472 37.037 0.00 0.00 0.00 2.87
815 2186 9.877178 TTCTTTTCTTCTAGACCTATGATGTTC 57.123 33.333 0.00 0.00 0.00 3.18
820 2191 9.726438 CCTTTTTCTTTTCTTCTAGACCTATGA 57.274 33.333 0.00 0.00 0.00 2.15
821 2192 9.726438 TCCTTTTTCTTTTCTTCTAGACCTATG 57.274 33.333 0.00 0.00 0.00 2.23
822 2193 9.727859 GTCCTTTTTCTTTTCTTCTAGACCTAT 57.272 33.333 0.00 0.00 0.00 2.57
823 2194 8.935741 AGTCCTTTTTCTTTTCTTCTAGACCTA 58.064 33.333 0.00 0.00 0.00 3.08
825 2196 7.715686 TCAGTCCTTTTTCTTTTCTTCTAGACC 59.284 37.037 0.00 0.00 0.00 3.85
848 2229 8.427774 GTCACTGTCTTTTGTTTTCTTTTTCAG 58.572 33.333 0.00 0.00 0.00 3.02
932 2389 3.316308 GCGTCGTTATCCCCTAACTCTTA 59.684 47.826 0.00 0.00 38.05 2.10
955 2426 0.467290 TCCTGGTTCTGTTTGGCACC 60.467 55.000 0.00 0.00 0.00 5.01
963 2434 0.191064 TGAGTCCCTCCTGGTTCTGT 59.809 55.000 0.00 0.00 34.77 3.41
1048 2526 2.716017 CGGAGCCGGAGAAGAAGCT 61.716 63.158 5.05 0.00 38.56 3.74
1082 2560 1.605232 TGCTGTGAACACAAGCATCTG 59.395 47.619 19.51 6.08 41.33 2.90
1091 2569 2.639286 CCGCCTTGCTGTGAACAC 59.361 61.111 0.00 0.00 0.00 3.32
1093 2571 1.244019 AATCCCGCCTTGCTGTGAAC 61.244 55.000 0.00 0.00 0.00 3.18
1095 2573 1.675310 CAATCCCGCCTTGCTGTGA 60.675 57.895 0.00 0.00 0.00 3.58
1096 2574 2.879907 CAATCCCGCCTTGCTGTG 59.120 61.111 0.00 0.00 0.00 3.66
1097 2575 3.064324 GCAATCCCGCCTTGCTGT 61.064 61.111 7.35 0.00 44.36 4.40
1110 2753 2.440539 GACTCGATCCATACCGCAAT 57.559 50.000 0.00 0.00 0.00 3.56
1156 2799 2.750637 ATGACGCGACGGAGGAGT 60.751 61.111 15.93 0.00 0.00 3.85
1169 2812 2.224885 GCTCGTCGGAAGCGATGAC 61.225 63.158 0.00 0.00 38.51 3.06
1238 2893 3.074412 TCTTTTGCTGTTAGGCAGTAGC 58.926 45.455 0.00 0.00 46.64 3.58
1341 2996 5.047590 TCAGCTATATACGTGGTACAATGGG 60.048 44.000 0.00 0.00 44.16 4.00
1343 2998 6.678878 ACTCAGCTATATACGTGGTACAATG 58.321 40.000 0.00 0.00 44.16 2.82
1356 3011 8.213679 ACACATTCACCATTAACTCAGCTATAT 58.786 33.333 0.00 0.00 0.00 0.86
1357 3012 7.495606 CACACATTCACCATTAACTCAGCTATA 59.504 37.037 0.00 0.00 0.00 1.31
1358 3013 6.317140 CACACATTCACCATTAACTCAGCTAT 59.683 38.462 0.00 0.00 0.00 2.97
1377 3032 2.028112 AGGCAGACGAACATACACACAT 60.028 45.455 0.00 0.00 0.00 3.21
1378 3033 1.343142 AGGCAGACGAACATACACACA 59.657 47.619 0.00 0.00 0.00 3.72
1381 3036 2.263077 CAGAGGCAGACGAACATACAC 58.737 52.381 0.00 0.00 0.00 2.90
1558 3213 2.622942 GAGGTCCTTGTTGATTTGTGCA 59.377 45.455 0.00 0.00 0.00 4.57
1568 3223 2.657237 CTCGGCGAGGTCCTTGTT 59.343 61.111 28.52 0.00 0.00 2.83
1616 3271 4.308458 CTGGTCGGTGGCGTTGGA 62.308 66.667 0.00 0.00 0.00 3.53
1619 3274 4.309950 GTCCTGGTCGGTGGCGTT 62.310 66.667 0.00 0.00 0.00 4.84
1623 3278 2.347490 CCTTGTCCTGGTCGGTGG 59.653 66.667 0.00 0.00 0.00 4.61
1640 3295 2.509336 CACCAGGGCGTCGATGAC 60.509 66.667 9.31 5.03 0.00 3.06
1641 3296 3.770040 CCACCAGGGCGTCGATGA 61.770 66.667 9.31 0.00 0.00 2.92
1684 3339 4.070552 GCCGTGAGCTTCCGGTCT 62.071 66.667 21.51 0.00 45.91 3.85
1742 3397 1.142748 CCTTGATCTCGCCGCTCTT 59.857 57.895 0.00 0.00 0.00 2.85
1805 3460 2.028112 TGTAGCTCTTGATGCCTTTCGT 60.028 45.455 0.00 0.00 0.00 3.85
1941 3596 2.483889 GGAGGGAGTACATTGCTACTGC 60.484 54.545 0.00 8.40 35.03 4.40
1943 3598 2.032620 CGGAGGGAGTACATTGCTACT 58.967 52.381 0.00 0.44 0.00 2.57
1952 3607 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
1953 3608 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
1954 3609 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
1955 3610 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
1956 3611 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
1957 3612 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
1958 3613 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
1959 3614 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
1960 3615 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
1990 3645 3.118775 TGACACTTTGACACTAGTGCAGT 60.119 43.478 22.90 15.62 44.34 4.40
1991 3646 3.457234 TGACACTTTGACACTAGTGCAG 58.543 45.455 22.90 15.01 44.34 4.41
1992 3647 3.535280 TGACACTTTGACACTAGTGCA 57.465 42.857 22.90 17.67 44.34 4.57
1993 3648 4.875544 TTTGACACTTTGACACTAGTGC 57.124 40.909 22.90 15.35 44.34 4.40
2014 3669 6.938030 TCTGTCCCATAATGTAAGACGTTTTT 59.062 34.615 0.00 0.00 0.00 1.94
2015 3670 6.469410 TCTGTCCCATAATGTAAGACGTTTT 58.531 36.000 0.00 0.00 0.00 2.43
2016 3671 6.045072 TCTGTCCCATAATGTAAGACGTTT 57.955 37.500 0.00 0.00 0.00 3.60
2017 3672 5.395324 CCTCTGTCCCATAATGTAAGACGTT 60.395 44.000 0.00 0.00 0.00 3.99
2018 3673 4.099573 CCTCTGTCCCATAATGTAAGACGT 59.900 45.833 0.00 0.00 0.00 4.34
2019 3674 4.501571 CCCTCTGTCCCATAATGTAAGACG 60.502 50.000 0.00 0.00 0.00 4.18
2020 3675 4.654262 TCCCTCTGTCCCATAATGTAAGAC 59.346 45.833 0.00 0.00 0.00 3.01
2021 3676 4.890988 TCCCTCTGTCCCATAATGTAAGA 58.109 43.478 0.00 0.00 0.00 2.10
2022 3677 4.656112 ACTCCCTCTGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
2023 3678 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
2024 3679 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
2025 3680 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
2026 3681 4.483950 TCTACTCCCTCTGTCCCATAATG 58.516 47.826 0.00 0.00 0.00 1.90
2027 3682 4.834406 TCTACTCCCTCTGTCCCATAAT 57.166 45.455 0.00 0.00 0.00 1.28
2028 3683 4.834406 ATCTACTCCCTCTGTCCCATAA 57.166 45.455 0.00 0.00 0.00 1.90
2029 3684 5.555941 TGATATCTACTCCCTCTGTCCCATA 59.444 44.000 3.98 0.00 0.00 2.74
2030 3685 4.358310 TGATATCTACTCCCTCTGTCCCAT 59.642 45.833 3.98 0.00 0.00 4.00
2031 3686 3.727391 TGATATCTACTCCCTCTGTCCCA 59.273 47.826 3.98 0.00 0.00 4.37
2032 3687 4.390129 TGATATCTACTCCCTCTGTCCC 57.610 50.000 3.98 0.00 0.00 4.46
2033 3688 5.417580 GTGATGATATCTACTCCCTCTGTCC 59.582 48.000 3.98 0.00 0.00 4.02
2034 3689 6.150976 CAGTGATGATATCTACTCCCTCTGTC 59.849 46.154 3.98 0.00 0.00 3.51
2035 3690 6.009589 CAGTGATGATATCTACTCCCTCTGT 58.990 44.000 3.98 0.00 0.00 3.41
2036 3691 6.009589 ACAGTGATGATATCTACTCCCTCTG 58.990 44.000 3.98 8.99 0.00 3.35
2037 3692 6.212840 ACAGTGATGATATCTACTCCCTCT 57.787 41.667 3.98 0.00 0.00 3.69
2038 3693 6.943146 TGTACAGTGATGATATCTACTCCCTC 59.057 42.308 3.98 0.00 0.00 4.30
2039 3694 6.853490 TGTACAGTGATGATATCTACTCCCT 58.147 40.000 3.98 0.00 0.00 4.20
2040 3695 7.710676 ATGTACAGTGATGATATCTACTCCC 57.289 40.000 0.33 0.00 0.00 4.30
2041 3696 8.247562 GGAATGTACAGTGATGATATCTACTCC 58.752 40.741 0.00 0.00 0.00 3.85
2042 3697 8.797438 TGGAATGTACAGTGATGATATCTACTC 58.203 37.037 0.00 0.00 0.00 2.59
2043 3698 8.712228 TGGAATGTACAGTGATGATATCTACT 57.288 34.615 0.00 3.47 0.00 2.57
2245 3900 3.591527 AGGGGATGGTGTGAATAGTTTGA 59.408 43.478 0.00 0.00 0.00 2.69
2248 3903 2.509964 GGAGGGGATGGTGTGAATAGTT 59.490 50.000 0.00 0.00 0.00 2.24
2252 3907 0.253820 AGGGAGGGGATGGTGTGAAT 60.254 55.000 0.00 0.00 0.00 2.57
2253 3908 0.477597 AAGGGAGGGGATGGTGTGAA 60.478 55.000 0.00 0.00 0.00 3.18
2289 3972 9.448438 AAATGCTGTGTTCTGTCAGTTATATAA 57.552 29.630 0.00 0.00 34.57 0.98
2316 4189 4.537751 TGGGTGTGGAAGTTATTTGAACA 58.462 39.130 0.00 0.00 0.00 3.18
2336 4237 3.409026 ACTGGCTACTTTTGAGACTGG 57.591 47.619 0.00 0.00 0.00 4.00
2339 4240 9.765795 ACATATATTACTGGCTACTTTTGAGAC 57.234 33.333 0.00 0.00 0.00 3.36
2374 4277 1.826385 AGCGCTGCTTGTTTATCCTT 58.174 45.000 10.39 0.00 33.89 3.36
2421 4327 4.003648 AGTATGTGAAAGGCAAGCACTAC 58.996 43.478 0.00 0.00 33.83 2.73
2445 4351 1.099879 AGATGAATCAAGCCGCCTGC 61.100 55.000 0.00 0.00 41.71 4.85
2450 4356 3.185246 ACCAGTAGATGAATCAAGCCG 57.815 47.619 0.00 0.00 0.00 5.52
2479 4385 5.139435 TGATCGATATCAGCACCTTAAGG 57.861 43.478 20.42 20.42 37.20 2.69
2491 4397 4.230657 CGTTTCCAGGTCTGATCGATATC 58.769 47.826 0.00 0.00 0.00 1.63
2563 4469 1.673168 GTGGCATTCAGGTGGAGATC 58.327 55.000 0.00 0.00 0.00 2.75
2567 4473 2.350895 CCGTGGCATTCAGGTGGA 59.649 61.111 0.00 0.00 0.00 4.02
2591 4497 0.179020 GTGCACATATGGCAGGGCTA 60.179 55.000 13.17 0.00 42.85 3.93
2593 4499 1.321805 TTGTGCACATATGGCAGGGC 61.322 55.000 22.39 8.34 42.85 5.19
2615 4523 9.936329 AGATGGTTCCCTTTGTAAATAACATAT 57.064 29.630 0.00 0.00 38.10 1.78
2619 4527 6.863275 CCAGATGGTTCCCTTTGTAAATAAC 58.137 40.000 0.00 0.00 0.00 1.89
2643 4551 2.797177 AATGGAGGGAGCTTTGAGAC 57.203 50.000 0.00 0.00 0.00 3.36
2655 4563 9.376075 CTCTAGCATATACACAATAAATGGAGG 57.624 37.037 0.00 0.00 0.00 4.30
2684 4592 7.596749 AATGAGGTGTTAGCGTATATTATGC 57.403 36.000 0.00 0.00 40.97 3.14
2692 4600 9.520204 GTTATAACTTAATGAGGTGTTAGCGTA 57.480 33.333 8.41 0.00 0.00 4.42
2693 4601 7.493645 GGTTATAACTTAATGAGGTGTTAGCGT 59.506 37.037 15.05 0.00 0.00 5.07
2694 4602 7.493320 TGGTTATAACTTAATGAGGTGTTAGCG 59.507 37.037 15.05 0.00 0.00 4.26
2695 4603 8.610035 GTGGTTATAACTTAATGAGGTGTTAGC 58.390 37.037 15.05 0.00 0.00 3.09
2696 4604 9.661563 TGTGGTTATAACTTAATGAGGTGTTAG 57.338 33.333 15.05 0.00 0.00 2.34
2698 4606 8.927675 TTGTGGTTATAACTTAATGAGGTGTT 57.072 30.769 15.05 0.00 0.00 3.32
2702 4610 9.099454 GACTCTTGTGGTTATAACTTAATGAGG 57.901 37.037 15.05 3.57 0.00 3.86
2714 4622 1.346395 TGTGCCGACTCTTGTGGTTAT 59.654 47.619 0.00 0.00 0.00 1.89
2715 4623 0.753867 TGTGCCGACTCTTGTGGTTA 59.246 50.000 0.00 0.00 0.00 2.85
2731 4639 5.655893 CACAAGGGCTTAAAACAATTGTG 57.344 39.130 12.82 0.00 39.80 3.33
2760 4668 6.154706 AGGAAACCTACTGATAACGAGTCATT 59.845 38.462 0.00 0.00 28.47 2.57
2769 4677 7.822822 GTCTGCTTTTAGGAAACCTACTGATAA 59.177 37.037 0.00 0.00 35.63 1.75
2776 4684 5.298989 TGTGTCTGCTTTTAGGAAACCTA 57.701 39.130 0.00 0.00 34.61 3.08
2839 4750 8.243426 TGTAAAATCACTCAATGCCTTATGTTC 58.757 33.333 0.00 0.00 0.00 3.18
2849 4760 8.993121 ACTAGACACTTGTAAAATCACTCAATG 58.007 33.333 0.00 0.00 0.00 2.82
2873 4784 5.703592 TCTTATTAATGCGTGGTGTTGAACT 59.296 36.000 0.00 0.00 0.00 3.01
2923 4834 7.176515 ACCATGTTATGTTGAAGTAGATGCAAA 59.823 33.333 0.00 0.00 0.00 3.68
2992 4903 5.957798 ACATTTGTAATGGCAGTCATTCAG 58.042 37.500 2.71 0.00 44.32 3.02
3044 4955 5.151297 AGTTGCCCTTTTTCCACAATATG 57.849 39.130 0.00 0.00 0.00 1.78
3046 4957 6.495181 TGATTAGTTGCCCTTTTTCCACAATA 59.505 34.615 0.00 0.00 0.00 1.90
3051 4962 3.258123 GCTGATTAGTTGCCCTTTTTCCA 59.742 43.478 0.00 0.00 0.00 3.53
3052 4963 3.258123 TGCTGATTAGTTGCCCTTTTTCC 59.742 43.478 0.00 0.00 0.00 3.13
3187 5099 2.366916 AGAATTGAGGATCTGGTAGCCG 59.633 50.000 0.00 0.00 39.29 5.52
3261 5174 5.914033 TCCACCATATGTAGCTAACTTGTC 58.086 41.667 0.00 0.00 0.00 3.18
3277 5190 4.706476 CACCAATGTTCTTGTATCCACCAT 59.294 41.667 0.00 0.00 0.00 3.55
3289 5202 2.821969 GCACTGATTCCACCAATGTTCT 59.178 45.455 0.00 0.00 0.00 3.01
3300 5213 2.357009 GACATGACCATGCACTGATTCC 59.643 50.000 9.70 0.00 42.39 3.01
3508 5421 7.615365 TCCCACTTCTGAATATGTTTTAAGCAT 59.385 33.333 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.