Multiple sequence alignment - TraesCS4B01G325600

Loading Multiple Alignment...

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 TraesCS4B01G325600 chr4B 100.000 2927 0 0 1 2927 616737726 616734800 0.000000e+00 5406.0
1 TraesCS4B01G325600 chr4B 89.143 175 13 4 2615 2785 31736088 31735916 2.290000e-51 213.0
2 TraesCS4B01G325600 chr4D 92.991 1869 97 11 775 2622 484495322 484493467 0.000000e+00 2695.0
3 TraesCS4B01G325600 chr4D 92.180 422 29 4 291 709 484495775 484495355 6.980000e-166 593.0
4 TraesCS4B01G325600 chr4D 90.753 292 24 3 5 295 484511426 484511137 1.270000e-103 387.0
5 TraesCS4B01G325600 chr4D 92.857 154 5 3 2779 2927 484493466 484493314 4.910000e-53 219.0
6 TraesCS4B01G325600 chr4D 89.143 175 13 5 2615 2785 26119246 26119074 2.290000e-51 213.0
7 TraesCS4B01G325600 chr5A 90.956 1548 97 18 775 2303 665080278 665078755 0.000000e+00 2043.0
8 TraesCS4B01G325600 chr5A 85.881 687 90 6 5 688 665082172 665081490 0.000000e+00 725.0
9 TraesCS4B01G325600 chr5A 89.701 301 21 5 2326 2622 665078667 665078373 2.750000e-100 375.0
10 TraesCS4B01G325600 chr5A 86.782 174 7 5 2767 2927 665078361 665078191 2.320000e-41 180.0
11 TraesCS4B01G325600 chrUn 87.185 991 82 25 986 1936 270382829 270381844 0.000000e+00 1085.0
12 TraesCS4B01G325600 chrUn 81.431 657 82 23 1115 1757 336370576 336369946 4.350000e-138 501.0
13 TraesCS4B01G325600 chrUn 97.561 41 1 0 708 748 26086814 26086854 1.460000e-08 71.3
14 TraesCS4B01G325600 chrUn 97.561 41 1 0 708 748 322494975 322495015 1.460000e-08 71.3
15 TraesCS4B01G325600 chrUn 97.561 41 1 0 708 748 346765695 346765735 1.460000e-08 71.3
16 TraesCS4B01G325600 chr3A 86.727 987 88 21 986 1933 30996846 30997828 0.000000e+00 1057.0
17 TraesCS4B01G325600 chr3A 81.899 674 82 23 1098 1757 31559372 31560019 1.540000e-147 532.0
18 TraesCS4B01G325600 chr3A 82.105 285 42 8 1121 1405 482184430 482184155 4.880000e-58 235.0
19 TraesCS4B01G325600 chr3A 95.455 44 2 0 708 751 722559978 722559935 1.460000e-08 71.3
20 TraesCS4B01G325600 chr3B 82.526 681 81 20 1090 1757 37970896 37971551 5.480000e-157 564.0
21 TraesCS4B01G325600 chr3B 81.690 639 76 26 1104 1729 38794195 38794805 7.290000e-136 494.0
22 TraesCS4B01G325600 chr3D 82.589 672 81 20 1098 1757 21793221 21793868 7.080000e-156 560.0
23 TraesCS4B01G325600 chr3D 81.860 656 81 22 1115 1757 21888615 21889245 4.320000e-143 518.0
24 TraesCS4B01G325600 chr3D 89.143 175 13 5 2615 2785 176879398 176879570 2.290000e-51 213.0
25 TraesCS4B01G325600 chr7A 89.143 175 13 5 2615 2785 721276364 721276536 2.290000e-51 213.0
26 TraesCS4B01G325600 chr7A 97.727 44 1 0 708 751 133629313 133629270 3.130000e-10 76.8
27 TraesCS4B01G325600 chr6D 89.143 175 13 5 2615 2785 280654812 280654984 2.290000e-51 213.0
28 TraesCS4B01G325600 chr6B 89.143 175 13 5 2615 2785 209474061 209473889 2.290000e-51 213.0
29 TraesCS4B01G325600 chr5B 89.143 175 13 5 2615 2785 150446525 150446697 2.290000e-51 213.0
30 TraesCS4B01G325600 chr5B 89.143 175 13 4 2615 2785 247548604 247548776 2.290000e-51 213.0
31 TraesCS4B01G325600 chr2B 88.764 178 14 5 2615 2788 248248101 248247926 2.290000e-51 213.0
32 TraesCS4B01G325600 chr2B 97.561 41 1 0 708 748 551399975 551400015 1.460000e-08 71.3
33 TraesCS4B01G325600 chr2B 91.667 48 4 0 708 755 763967890 763967843 1.880000e-07 67.6
34 TraesCS4B01G325600 chr1A 80.212 283 47 8 1123 1405 548733572 548733845 1.380000e-48 204.0
35 TraesCS4B01G325600 chr1A 79.298 285 46 10 1123 1405 548789535 548789808 1.380000e-43 187.0
36 TraesCS4B01G325600 chr1D 79.239 289 51 8 1123 1411 454493609 454493330 2.980000e-45 193.0
37 TraesCS4B01G325600 chr1B 78.873 284 47 10 1123 1404 624971035 624971307 2.320000e-41 180.0
38 TraesCS4B01G325600 chr6A 97.561 41 1 0 708 748 27674003 27674043 1.460000e-08 71.3
39 TraesCS4B01G325600 chr2D 97.561 41 1 0 708 748 532552663 532552703 1.460000e-08 71.3


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 TraesCS4B01G325600 chr4B 616734800 616737726 2926 True 5406.00 5406 100.000 1 2927 1 chr4B.!!$R2 2926
1 TraesCS4B01G325600 chr4D 484493314 484495775 2461 True 1169.00 2695 92.676 291 2927 3 chr4D.!!$R3 2636
2 TraesCS4B01G325600 chr5A 665078191 665082172 3981 True 830.75 2043 88.330 5 2927 4 chr5A.!!$R1 2922
3 TraesCS4B01G325600 chrUn 270381844 270382829 985 True 1085.00 1085 87.185 986 1936 1 chrUn.!!$R1 950
4 TraesCS4B01G325600 chrUn 336369946 336370576 630 True 501.00 501 81.431 1115 1757 1 chrUn.!!$R2 642
5 TraesCS4B01G325600 chr3A 30996846 30997828 982 False 1057.00 1057 86.727 986 1933 1 chr3A.!!$F1 947
6 TraesCS4B01G325600 chr3A 31559372 31560019 647 False 532.00 532 81.899 1098 1757 1 chr3A.!!$F2 659
7 TraesCS4B01G325600 chr3B 37970896 37971551 655 False 564.00 564 82.526 1090 1757 1 chr3B.!!$F1 667
8 TraesCS4B01G325600 chr3B 38794195 38794805 610 False 494.00 494 81.690 1104 1729 1 chr3B.!!$F2 625
9 TraesCS4B01G325600 chr3D 21793221 21793868 647 False 560.00 560 82.589 1098 1757 1 chr3D.!!$F1 659
10 TraesCS4B01G325600 chr3D 21888615 21889245 630 False 518.00 518 81.860 1115 1757 1 chr3D.!!$F2 642

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
722 1885 0.038744 AACCTACTCCCTCCGTTCGA 59.961 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 3202 0.329261 TGGGAGAAAGACCATGGCTG 59.671 55.0 13.04 0.0 0.0 4.85 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
61 63 3.639561 ACATTAGTTGTGTGTTTTCCCCC 59.360 43.478 0.00 0.00 37.11 5.40
102 104 4.437682 TCTACCCATTCCATTGACATCC 57.562 45.455 0.00 0.00 0.00 3.51
126 128 3.578282 AGGGATGTGGTTCATTTTCAACC 59.422 43.478 0.00 0.00 43.35 3.77
134 136 3.244078 GGTTCATTTTCAACCTCCAACCC 60.244 47.826 0.00 0.00 40.33 4.11
138 140 4.719273 TCATTTTCAACCTCCAACCCTTTT 59.281 37.500 0.00 0.00 0.00 2.27
144 146 1.856920 ACCTCCAACCCTTTTCTTCCA 59.143 47.619 0.00 0.00 0.00 3.53
187 189 7.302524 CGATTTACCATATAACCAAATTCCCG 58.697 38.462 0.00 0.00 0.00 5.14
194 196 1.826385 AACCAAATTCCCGCTCTCTG 58.174 50.000 0.00 0.00 0.00 3.35
196 198 1.379642 CCAAATTCCCGCTCTCTGCC 61.380 60.000 0.00 0.00 38.78 4.85
204 206 4.219999 GCTCTCTGCCTCGCCTCC 62.220 72.222 0.00 0.00 35.15 4.30
236 238 0.178941 TCCGAGCCCTAACCTATCCC 60.179 60.000 0.00 0.00 0.00 3.85
245 247 2.623889 CCTAACCTATCCCTGTCACGAG 59.376 54.545 0.00 0.00 0.00 4.18
265 267 1.711298 GCTCGACAGCGATCTATTTCG 59.289 52.381 0.00 0.00 46.80 3.46
267 269 3.222361 CTCGACAGCGATCTATTTCGAG 58.778 50.000 14.29 14.29 46.80 4.04
272 274 1.409064 AGCGATCTATTTCGAGTGGCA 59.591 47.619 0.00 0.00 41.62 4.92
275 277 1.789464 GATCTATTTCGAGTGGCAGCG 59.211 52.381 3.51 3.51 0.00 5.18
362 364 2.957402 TTGCATCATCCCCATCTACC 57.043 50.000 0.00 0.00 0.00 3.18
390 392 0.689080 ATCCTGTCTCATGCTCGGGT 60.689 55.000 8.53 0.00 0.00 5.28
395 397 1.375908 TCTCATGCTCGGGTGCAAC 60.376 57.895 0.00 0.00 46.61 4.17
438 440 9.793259 ACTAGTCCAGAAAATAATTTCAGAACA 57.207 29.630 6.07 0.00 46.03 3.18
466 468 4.389576 CTGGCCAACGTTCGCTGC 62.390 66.667 17.37 8.70 0.00 5.25
483 485 2.359354 CGACGGGGTGGCATTTCA 60.359 61.111 0.00 0.00 0.00 2.69
506 508 6.481976 TCAAACGTTTGTCATGACAGTCTTAT 59.518 34.615 33.42 11.98 42.94 1.73
522 524 4.080526 AGTCTTATTTGTGTCGGGGCTAAT 60.081 41.667 0.00 0.00 0.00 1.73
532 534 3.121544 GTCGGGGCTAATAGTTTCTTCG 58.878 50.000 0.00 0.00 0.00 3.79
537 539 3.494573 GGGCTAATAGTTTCTTCGGAGGG 60.495 52.174 0.00 0.00 0.00 4.30
541 543 4.473477 AATAGTTTCTTCGGAGGGACTG 57.527 45.455 9.37 0.00 41.55 3.51
543 545 0.673956 GTTTCTTCGGAGGGACTGGC 60.674 60.000 0.00 0.00 41.55 4.85
545 547 3.382832 CTTCGGAGGGACTGGCGT 61.383 66.667 0.00 0.00 41.55 5.68
579 583 5.067805 GGATGGTAGTTTTAAGCCTTCATGG 59.932 44.000 0.00 0.00 39.35 3.66
601 605 4.337763 GCAGAAAATGTCACGCTATTCTG 58.662 43.478 8.54 8.54 44.00 3.02
667 671 0.967380 CACAAATGCCACCCCTCCTC 60.967 60.000 0.00 0.00 0.00 3.71
709 1872 4.019231 AGGAGGTCCATTTCAGAAACCTAC 60.019 45.833 5.99 5.99 40.39 3.18
711 1874 5.167303 AGGTCCATTTCAGAAACCTACTC 57.833 43.478 2.78 0.00 38.56 2.59
712 1875 4.019231 AGGTCCATTTCAGAAACCTACTCC 60.019 45.833 2.78 0.54 38.56 3.85
713 1876 4.262617 GTCCATTTCAGAAACCTACTCCC 58.737 47.826 0.00 0.00 0.00 4.30
715 1878 4.225267 TCCATTTCAGAAACCTACTCCCTC 59.775 45.833 0.00 0.00 0.00 4.30
716 1879 4.518249 CATTTCAGAAACCTACTCCCTCC 58.482 47.826 0.00 0.00 0.00 4.30
717 1880 1.848652 TCAGAAACCTACTCCCTCCG 58.151 55.000 0.00 0.00 0.00 4.63
718 1881 1.076677 TCAGAAACCTACTCCCTCCGT 59.923 52.381 0.00 0.00 0.00 4.69
719 1882 1.900486 CAGAAACCTACTCCCTCCGTT 59.100 52.381 0.00 0.00 0.00 4.44
720 1883 2.094130 CAGAAACCTACTCCCTCCGTTC 60.094 54.545 0.00 0.00 0.00 3.95
721 1884 0.893447 AAACCTACTCCCTCCGTTCG 59.107 55.000 0.00 0.00 0.00 3.95
722 1885 0.038744 AACCTACTCCCTCCGTTCGA 59.961 55.000 0.00 0.00 0.00 3.71
723 1886 0.038744 ACCTACTCCCTCCGTTCGAA 59.961 55.000 0.00 0.00 0.00 3.71
725 1888 1.755380 CCTACTCCCTCCGTTCGAAAT 59.245 52.381 0.00 0.00 0.00 2.17
726 1889 2.167900 CCTACTCCCTCCGTTCGAAATT 59.832 50.000 0.00 0.00 0.00 1.82
728 1891 4.038883 CCTACTCCCTCCGTTCGAAATTAT 59.961 45.833 0.00 0.00 0.00 1.28
729 1892 4.482952 ACTCCCTCCGTTCGAAATTATT 57.517 40.909 0.00 0.00 0.00 1.40
730 1893 4.840271 ACTCCCTCCGTTCGAAATTATTT 58.160 39.130 0.00 0.00 0.00 1.40
733 1896 4.632688 TCCCTCCGTTCGAAATTATTTGTC 59.367 41.667 0.00 0.00 0.00 3.18
735 1898 5.220605 CCCTCCGTTCGAAATTATTTGTCTC 60.221 44.000 0.00 0.00 0.00 3.36
737 1900 4.327898 TCCGTTCGAAATTATTTGTCTCGG 59.672 41.667 0.00 4.15 33.93 4.63
739 1902 5.163933 CCGTTCGAAATTATTTGTCTCGGAA 60.164 40.000 0.00 0.00 34.20 4.30
740 1903 6.301108 CGTTCGAAATTATTTGTCTCGGAAA 58.699 36.000 0.00 0.00 0.00 3.13
741 1904 6.959311 CGTTCGAAATTATTTGTCTCGGAAAT 59.041 34.615 0.00 0.00 0.00 2.17
742 1905 7.045612 CGTTCGAAATTATTTGTCTCGGAAATG 60.046 37.037 0.00 0.00 0.00 2.32
743 1906 6.781138 TCGAAATTATTTGTCTCGGAAATGG 58.219 36.000 0.00 0.00 0.00 3.16
744 1907 6.596106 TCGAAATTATTTGTCTCGGAAATGGA 59.404 34.615 0.00 0.00 0.00 3.41
745 1908 7.282224 TCGAAATTATTTGTCTCGGAAATGGAT 59.718 33.333 0.00 0.00 0.00 3.41
746 1909 7.376866 CGAAATTATTTGTCTCGGAAATGGATG 59.623 37.037 0.00 0.00 0.00 3.51
747 1910 7.645058 AATTATTTGTCTCGGAAATGGATGT 57.355 32.000 0.00 0.00 0.00 3.06
748 1911 6.677781 TTATTTGTCTCGGAAATGGATGTC 57.322 37.500 0.00 0.00 0.00 3.06
749 1912 3.981071 TTGTCTCGGAAATGGATGTCT 57.019 42.857 0.00 0.00 0.00 3.41
750 1913 3.526931 TGTCTCGGAAATGGATGTCTC 57.473 47.619 0.00 0.00 0.00 3.36
751 1914 2.159240 TGTCTCGGAAATGGATGTCTCG 60.159 50.000 0.00 0.00 0.00 4.04
752 1915 2.099263 GTCTCGGAAATGGATGTCTCGA 59.901 50.000 0.00 0.00 0.00 4.04
753 1916 2.758423 TCTCGGAAATGGATGTCTCGAA 59.242 45.455 0.00 0.00 0.00 3.71
754 1917 3.194755 TCTCGGAAATGGATGTCTCGAAA 59.805 43.478 0.00 0.00 0.00 3.46
755 1918 4.122776 CTCGGAAATGGATGTCTCGAAAT 58.877 43.478 0.00 0.00 0.00 2.17
756 1919 4.513442 TCGGAAATGGATGTCTCGAAATT 58.487 39.130 0.00 0.00 0.00 1.82
757 1920 5.666462 TCGGAAATGGATGTCTCGAAATTA 58.334 37.500 0.00 0.00 0.00 1.40
758 1921 5.522460 TCGGAAATGGATGTCTCGAAATTAC 59.478 40.000 0.00 0.00 0.00 1.89
759 1922 5.523916 CGGAAATGGATGTCTCGAAATTACT 59.476 40.000 0.00 0.00 0.00 2.24
760 1923 6.037172 CGGAAATGGATGTCTCGAAATTACTT 59.963 38.462 0.00 0.00 0.00 2.24
761 1924 7.189512 GGAAATGGATGTCTCGAAATTACTTG 58.810 38.462 0.00 0.00 0.00 3.16
762 1925 7.148239 GGAAATGGATGTCTCGAAATTACTTGT 60.148 37.037 0.00 0.00 0.00 3.16
763 1926 6.910536 ATGGATGTCTCGAAATTACTTGTC 57.089 37.500 0.00 0.00 0.00 3.18
764 1927 6.037786 TGGATGTCTCGAAATTACTTGTCT 57.962 37.500 0.00 0.00 0.00 3.41
765 1928 7.165460 TGGATGTCTCGAAATTACTTGTCTA 57.835 36.000 0.00 0.00 0.00 2.59
766 1929 7.033791 TGGATGTCTCGAAATTACTTGTCTAC 58.966 38.462 0.00 0.00 0.00 2.59
767 1930 7.093902 TGGATGTCTCGAAATTACTTGTCTACT 60.094 37.037 0.00 0.00 0.00 2.57
768 1931 7.432838 GGATGTCTCGAAATTACTTGTCTACTC 59.567 40.741 0.00 0.00 0.00 2.59
769 1932 6.618811 TGTCTCGAAATTACTTGTCTACTCC 58.381 40.000 0.00 0.00 0.00 3.85
770 1933 6.035217 GTCTCGAAATTACTTGTCTACTCCC 58.965 44.000 0.00 0.00 0.00 4.30
771 1934 5.950549 TCTCGAAATTACTTGTCTACTCCCT 59.049 40.000 0.00 0.00 0.00 4.20
772 1935 6.095160 TCTCGAAATTACTTGTCTACTCCCTC 59.905 42.308 0.00 0.00 0.00 4.30
773 1936 5.035443 CGAAATTACTTGTCTACTCCCTCG 58.965 45.833 0.00 0.00 0.00 4.63
787 1950 1.372683 CCTCGGCCTGGATGTATGG 59.627 63.158 0.00 0.00 0.00 2.74
891 2063 8.172484 CACATGAAAAACAAGCATCATATTTGG 58.828 33.333 0.00 0.00 31.59 3.28
943 2115 6.633500 TGTTTTTAACCATTCTGAGGAGTG 57.367 37.500 0.00 0.00 0.00 3.51
1040 2222 3.206150 CAAACCCCGAGATAGACAATGG 58.794 50.000 0.00 0.00 0.00 3.16
1286 2486 1.369692 CCGTCACCAACTACCAGCA 59.630 57.895 0.00 0.00 0.00 4.41
1290 2490 1.057275 TCACCAACTACCAGCACCCA 61.057 55.000 0.00 0.00 0.00 4.51
1332 2547 3.362797 TCGTCCACGAGCGAGCTT 61.363 61.111 0.00 0.00 44.22 3.74
1717 2944 2.204090 TCCGGGAAAAGGGCCTCT 60.204 61.111 6.46 0.00 0.00 3.69
1878 3105 0.320771 ATGTCGCCGTCAAGCTCTTT 60.321 50.000 0.00 0.00 0.00 2.52
1939 3169 3.010420 GGTGGATGAAGAGCAAGGTAAC 58.990 50.000 0.00 0.00 0.00 2.50
1965 3202 0.960364 ACCCATGGTGTGATTGCGAC 60.960 55.000 11.73 0.00 32.98 5.19
2032 3273 1.156736 CAGCGTTTGTAAGTGAGGGG 58.843 55.000 0.00 0.00 0.00 4.79
2047 3288 2.580322 TGAGGGGCAATTCCTTGACATA 59.420 45.455 0.00 0.00 42.67 2.29
2075 3316 8.370493 TCATGTCGATCTTAATTGATTTCTCC 57.630 34.615 0.00 0.00 0.00 3.71
2094 3335 4.042435 TCTCCCTTTTTGAGGTTTATCGGT 59.958 41.667 0.00 0.00 44.71 4.69
2108 3349 0.673333 ATCGGTCAGCGATGTTGCAA 60.673 50.000 11.77 0.00 37.31 4.08
2159 3400 1.935199 CATTGGCAAATCGGGCATTTC 59.065 47.619 3.01 0.00 43.37 2.17
2164 3405 2.159057 GGCAAATCGGGCATTTCTCATT 60.159 45.455 0.00 0.00 31.79 2.57
2177 3418 7.404203 GGCATTTCTCATTGCAAATTATGTTC 58.596 34.615 1.71 0.00 40.66 3.18
2181 3422 5.964758 TCTCATTGCAAATTATGTTCACCC 58.035 37.500 1.71 0.00 0.00 4.61
2198 3439 4.006989 TCACCCGGATGACAAATTTAGTG 58.993 43.478 0.73 0.00 0.00 2.74
2202 3443 4.006989 CCGGATGACAAATTTAGTGGACA 58.993 43.478 0.00 0.00 0.00 4.02
2209 3450 5.138125 ACAAATTTAGTGGACAAGCATGG 57.862 39.130 0.00 0.00 0.00 3.66
2212 3453 6.437162 ACAAATTTAGTGGACAAGCATGGTAT 59.563 34.615 0.00 0.00 0.00 2.73
2259 3501 9.545105 TGTTTTTGTCAGAAAATTATCATGCTT 57.455 25.926 0.00 0.00 31.80 3.91
2291 3533 6.500684 AAATAGCCATAATCGCACCAATAG 57.499 37.500 0.00 0.00 0.00 1.73
2305 3547 4.392754 GCACCAATAGAAATTGCCCAAAAG 59.607 41.667 0.00 0.00 41.06 2.27
2310 3552 6.147656 CCAATAGAAATTGCCCAAAAGAACAC 59.852 38.462 0.00 0.00 41.06 3.32
2313 3555 3.473923 AATTGCCCAAAAGAACACCAG 57.526 42.857 0.00 0.00 0.00 4.00
2316 3558 3.517296 TGCCCAAAAGAACACCAGATA 57.483 42.857 0.00 0.00 0.00 1.98
2319 3561 4.016444 GCCCAAAAGAACACCAGATATGA 58.984 43.478 0.00 0.00 0.00 2.15
2320 3562 4.646492 GCCCAAAAGAACACCAGATATGAT 59.354 41.667 0.00 0.00 0.00 2.45
2321 3563 5.221126 GCCCAAAAGAACACCAGATATGATC 60.221 44.000 0.00 0.00 0.00 2.92
2324 3631 7.227512 CCCAAAAGAACACCAGATATGATCTAC 59.772 40.741 0.00 0.00 37.58 2.59
2379 3687 8.556213 ATATTATTGAATATGCGGTTACCGTT 57.444 30.769 25.13 15.15 38.70 4.44
2391 3701 3.737047 CGGTTACCGTTAGAGCATCATGT 60.737 47.826 16.53 0.00 42.73 3.21
2403 3713 1.536072 GCATCATGTCCAGCAGCATTG 60.536 52.381 0.00 0.00 0.00 2.82
2420 3730 2.937469 TTGTTTGGGCTAATCATGCG 57.063 45.000 0.00 0.00 0.00 4.73
2425 3735 1.882912 TGGGCTAATCATGCGTGATC 58.117 50.000 21.44 9.45 44.20 2.92
2426 3736 1.160137 GGGCTAATCATGCGTGATCC 58.840 55.000 21.44 17.32 44.20 3.36
2427 3737 1.271054 GGGCTAATCATGCGTGATCCT 60.271 52.381 21.44 9.88 44.20 3.24
2432 3742 4.553547 GCTAATCATGCGTGATCCTTTGTC 60.554 45.833 21.44 4.18 44.20 3.18
2618 3931 4.022329 CCATGTTAACCACTTTTGTCTCCC 60.022 45.833 2.48 0.00 0.00 4.30
2622 3935 0.396811 ACCACTTTTGTCTCCCTCCG 59.603 55.000 0.00 0.00 0.00 4.63
2623 3936 0.396811 CCACTTTTGTCTCCCTCCGT 59.603 55.000 0.00 0.00 0.00 4.69
2624 3937 1.202770 CCACTTTTGTCTCCCTCCGTT 60.203 52.381 0.00 0.00 0.00 4.44
2625 3938 2.143925 CACTTTTGTCTCCCTCCGTTC 58.856 52.381 0.00 0.00 0.00 3.95
2626 3939 1.071857 ACTTTTGTCTCCCTCCGTTCC 59.928 52.381 0.00 0.00 0.00 3.62
2627 3940 1.348036 CTTTTGTCTCCCTCCGTTCCT 59.652 52.381 0.00 0.00 0.00 3.36
2628 3941 2.314071 TTTGTCTCCCTCCGTTCCTA 57.686 50.000 0.00 0.00 0.00 2.94
2629 3942 2.314071 TTGTCTCCCTCCGTTCCTAA 57.686 50.000 0.00 0.00 0.00 2.69
2630 3943 2.314071 TGTCTCCCTCCGTTCCTAAA 57.686 50.000 0.00 0.00 0.00 1.85
2631 3944 2.829023 TGTCTCCCTCCGTTCCTAAAT 58.171 47.619 0.00 0.00 0.00 1.40
2632 3945 3.985127 TGTCTCCCTCCGTTCCTAAATA 58.015 45.455 0.00 0.00 0.00 1.40
2633 3946 4.553678 TGTCTCCCTCCGTTCCTAAATAT 58.446 43.478 0.00 0.00 0.00 1.28
2634 3947 5.708544 TGTCTCCCTCCGTTCCTAAATATA 58.291 41.667 0.00 0.00 0.00 0.86
2635 3948 6.138263 TGTCTCCCTCCGTTCCTAAATATAA 58.862 40.000 0.00 0.00 0.00 0.98
2636 3949 6.267014 TGTCTCCCTCCGTTCCTAAATATAAG 59.733 42.308 0.00 0.00 0.00 1.73
2637 3950 6.267242 GTCTCCCTCCGTTCCTAAATATAAGT 59.733 42.308 0.00 0.00 0.00 2.24
2638 3951 6.842807 TCTCCCTCCGTTCCTAAATATAAGTT 59.157 38.462 0.00 0.00 0.00 2.66
2639 3952 6.823497 TCCCTCCGTTCCTAAATATAAGTTG 58.177 40.000 0.00 0.00 0.00 3.16
2640 3953 6.384886 TCCCTCCGTTCCTAAATATAAGTTGT 59.615 38.462 0.00 0.00 0.00 3.32
2641 3954 7.564660 TCCCTCCGTTCCTAAATATAAGTTGTA 59.435 37.037 0.00 0.00 0.00 2.41
2642 3955 7.871463 CCCTCCGTTCCTAAATATAAGTTGTAG 59.129 40.741 0.00 0.00 0.00 2.74
2643 3956 8.636213 CCTCCGTTCCTAAATATAAGTTGTAGA 58.364 37.037 0.00 0.00 0.00 2.59
2644 3957 9.680315 CTCCGTTCCTAAATATAAGTTGTAGAG 57.320 37.037 0.00 0.00 0.00 2.43
2645 3958 9.412460 TCCGTTCCTAAATATAAGTTGTAGAGA 57.588 33.333 0.00 0.00 0.00 3.10
2661 3974 9.509956 AGTTGTAGAGATATCACTATAGACCAC 57.490 37.037 12.27 5.97 0.00 4.16
2662 3975 9.286170 GTTGTAGAGATATCACTATAGACCACA 57.714 37.037 12.27 4.77 0.00 4.17
2706 4019 9.950496 ACATTCTAAGTGTAGATTCACTCATTT 57.050 29.630 0.00 0.00 46.25 2.32
2709 4022 8.256611 TCTAAGTGTAGATTCACTCATTTTGC 57.743 34.615 0.00 0.00 46.25 3.68
2710 4023 8.097038 TCTAAGTGTAGATTCACTCATTTTGCT 58.903 33.333 0.00 0.00 46.25 3.91
2711 4024 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2712 4025 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2713 4026 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2714 4027 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2715 4028 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2716 4029 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2717 4030 6.582636 AGATTCACTCATTTTGCTCCGTATA 58.417 36.000 0.00 0.00 0.00 1.47
2718 4031 7.220030 AGATTCACTCATTTTGCTCCGTATAT 58.780 34.615 0.00 0.00 0.00 0.86
2719 4032 6.603237 TTCACTCATTTTGCTCCGTATATG 57.397 37.500 0.00 0.00 0.00 1.78
2720 4033 5.056480 TCACTCATTTTGCTCCGTATATGG 58.944 41.667 4.41 4.41 0.00 2.74
2721 4034 4.816385 CACTCATTTTGCTCCGTATATGGT 59.184 41.667 10.85 0.00 0.00 3.55
2722 4035 5.050091 CACTCATTTTGCTCCGTATATGGTC 60.050 44.000 10.85 5.19 0.00 4.02
2723 4036 4.385825 TCATTTTGCTCCGTATATGGTCC 58.614 43.478 10.85 4.15 0.00 4.46
2724 4037 3.916359 TTTTGCTCCGTATATGGTCCA 57.084 42.857 10.85 0.00 0.00 4.02
2725 4038 4.431416 TTTTGCTCCGTATATGGTCCAT 57.569 40.909 9.88 9.88 0.00 3.41
2726 4039 5.554437 TTTTGCTCCGTATATGGTCCATA 57.446 39.130 14.08 14.08 0.00 2.74
2727 4040 5.554437 TTTGCTCCGTATATGGTCCATAA 57.446 39.130 15.64 3.08 29.74 1.90
2728 4041 5.755409 TTGCTCCGTATATGGTCCATAAT 57.245 39.130 15.64 7.24 29.74 1.28
2729 4042 5.084818 TGCTCCGTATATGGTCCATAATG 57.915 43.478 15.64 10.00 29.74 1.90
2730 4043 4.775253 TGCTCCGTATATGGTCCATAATGA 59.225 41.667 15.64 8.71 29.74 2.57
2731 4044 5.247337 TGCTCCGTATATGGTCCATAATGAA 59.753 40.000 15.64 0.00 29.74 2.57
2732 4045 6.170506 GCTCCGTATATGGTCCATAATGAAA 58.829 40.000 15.64 1.80 29.74 2.69
2733 4046 6.823689 GCTCCGTATATGGTCCATAATGAAAT 59.176 38.462 15.64 1.91 29.74 2.17
2734 4047 7.011482 GCTCCGTATATGGTCCATAATGAAATC 59.989 40.741 15.64 0.87 29.74 2.17
2735 4048 8.146053 TCCGTATATGGTCCATAATGAAATCT 57.854 34.615 15.64 0.00 29.74 2.40
2736 4049 8.258007 TCCGTATATGGTCCATAATGAAATCTC 58.742 37.037 15.64 0.00 29.74 2.75
2737 4050 8.260818 CCGTATATGGTCCATAATGAAATCTCT 58.739 37.037 15.64 0.00 29.74 3.10
2738 4051 9.658799 CGTATATGGTCCATAATGAAATCTCTT 57.341 33.333 15.64 0.00 29.74 2.85
2742 4055 8.827832 ATGGTCCATAATGAAATCTCTTCAAA 57.172 30.769 1.24 0.00 31.55 2.69
2743 4056 8.284945 TGGTCCATAATGAAATCTCTTCAAAG 57.715 34.615 0.00 0.00 31.55 2.77
2744 4057 8.108999 TGGTCCATAATGAAATCTCTTCAAAGA 58.891 33.333 0.00 0.00 31.55 2.52
2745 4058 8.401709 GGTCCATAATGAAATCTCTTCAAAGAC 58.598 37.037 0.00 0.00 31.55 3.01
2746 4059 9.171877 GTCCATAATGAAATCTCTTCAAAGACT 57.828 33.333 0.00 0.00 31.55 3.24
2747 4060 9.745018 TCCATAATGAAATCTCTTCAAAGACTT 57.255 29.630 0.00 0.00 31.55 3.01
2761 4074 9.595823 TCTTCAAAGACTTATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2762 4075 9.595823 CTTCAAAGACTTATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2763 4076 9.595823 TTCAAAGACTTATATTTAGGAACGGAG 57.404 33.333 0.00 0.00 0.00 4.63
2764 4077 8.202137 TCAAAGACTTATATTTAGGAACGGAGG 58.798 37.037 0.00 0.00 0.00 4.30
2765 4078 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.390718 GGAAAACACACAACTAATGTCTCCTAT 59.609 37.037 0.00 0.00 41.46 2.57
39 41 3.639561 GGGGGAAAACACACAACTAATGT 59.360 43.478 0.00 0.00 45.34 2.71
85 87 2.696707 CCTTGGATGTCAATGGAATGGG 59.303 50.000 0.00 0.00 34.45 4.00
102 104 4.870123 TGAAAATGAACCACATCCCTTG 57.130 40.909 0.00 0.00 38.38 3.61
108 110 4.222336 TGGAGGTTGAAAATGAACCACAT 58.778 39.130 0.00 0.00 44.71 3.21
126 128 2.944129 TGTGGAAGAAAAGGGTTGGAG 58.056 47.619 0.00 0.00 0.00 3.86
134 136 3.187227 CGTGTGAGGATGTGGAAGAAAAG 59.813 47.826 0.00 0.00 0.00 2.27
138 140 0.037326 GCGTGTGAGGATGTGGAAGA 60.037 55.000 0.00 0.00 0.00 2.87
144 146 2.126463 CGTCGCGTGTGAGGATGT 60.126 61.111 5.77 0.00 0.00 3.06
163 165 7.039993 AGCGGGAATTTGGTTATATGGTAAATC 60.040 37.037 0.00 0.00 0.00 2.17
172 174 4.703897 CAGAGAGCGGGAATTTGGTTATA 58.296 43.478 0.00 0.00 0.00 0.98
187 189 4.219999 GGAGGCGAGGCAGAGAGC 62.220 72.222 0.00 0.00 44.65 4.09
210 212 0.967662 GTTAGGGCTCGGATAGGTCC 59.032 60.000 0.00 0.00 41.40 4.46
223 225 1.687123 CGTGACAGGGATAGGTTAGGG 59.313 57.143 0.00 0.00 0.00 3.53
227 229 0.824759 GCTCGTGACAGGGATAGGTT 59.175 55.000 0.00 0.00 0.00 3.50
253 255 1.789464 CTGCCACTCGAAATAGATCGC 59.211 52.381 0.00 0.00 42.44 4.58
265 267 1.785041 TTCACTTTGCGCTGCCACTC 61.785 55.000 9.73 0.00 0.00 3.51
267 269 0.527385 TTTTCACTTTGCGCTGCCAC 60.527 50.000 9.73 0.00 0.00 5.01
272 274 1.541588 GATCCCTTTTCACTTTGCGCT 59.458 47.619 9.73 0.00 0.00 5.92
275 277 1.550524 GGGGATCCCTTTTCACTTTGC 59.449 52.381 30.08 5.10 41.34 3.68
362 364 0.900421 TGAGACAGGATGGAGCTGTG 59.100 55.000 0.00 0.00 43.62 3.66
390 392 2.682352 CGATTCCACATACCATGTTGCA 59.318 45.455 0.00 0.00 42.70 4.08
395 397 5.201713 ACTAGTCGATTCCACATACCATG 57.798 43.478 0.00 0.00 0.00 3.66
438 440 5.619086 CGAACGTTGGCCAGATAAGATTTTT 60.619 40.000 5.00 0.00 0.00 1.94
439 441 4.142687 CGAACGTTGGCCAGATAAGATTTT 60.143 41.667 5.00 0.00 0.00 1.82
466 468 1.519751 TTTGAAATGCCACCCCGTCG 61.520 55.000 0.00 0.00 0.00 5.12
483 485 6.861065 ATAAGACTGTCATGACAAACGTTT 57.139 33.333 27.63 15.33 41.33 3.60
506 508 3.706600 AACTATTAGCCCCGACACAAA 57.293 42.857 0.00 0.00 0.00 2.83
522 524 2.176889 CCAGTCCCTCCGAAGAAACTA 58.823 52.381 0.00 0.00 0.00 2.24
532 534 4.494515 AAAAACGCCAGTCCCTCC 57.505 55.556 0.00 0.00 0.00 4.30
579 583 4.093408 TCAGAATAGCGTGACATTTTCTGC 59.907 41.667 10.83 0.00 39.74 4.26
612 616 5.920273 GTCATTTTTAGTTGTGTGTGGGATG 59.080 40.000 0.00 0.00 0.00 3.51
649 653 1.384191 GAGGAGGGGTGGCATTTGT 59.616 57.895 0.00 0.00 0.00 2.83
671 675 1.576356 CTCCTTAGCTGGCGAATGTC 58.424 55.000 0.00 0.00 0.00 3.06
709 1872 4.634443 ACAAATAATTTCGAACGGAGGGAG 59.366 41.667 0.00 0.00 0.00 4.30
711 1874 4.634443 AGACAAATAATTTCGAACGGAGGG 59.366 41.667 0.00 0.00 0.00 4.30
712 1875 5.500290 CGAGACAAATAATTTCGAACGGAGG 60.500 44.000 0.00 0.00 33.38 4.30
713 1876 5.481472 CGAGACAAATAATTTCGAACGGAG 58.519 41.667 0.00 0.00 33.38 4.63
715 1878 4.327898 TCCGAGACAAATAATTTCGAACGG 59.672 41.667 0.00 3.03 37.37 4.44
716 1879 5.444586 TCCGAGACAAATAATTTCGAACG 57.555 39.130 0.00 0.00 33.38 3.95
717 1880 7.218204 CCATTTCCGAGACAAATAATTTCGAAC 59.782 37.037 0.00 0.00 33.38 3.95
718 1881 7.119992 TCCATTTCCGAGACAAATAATTTCGAA 59.880 33.333 0.00 0.00 33.38 3.71
719 1882 6.596106 TCCATTTCCGAGACAAATAATTTCGA 59.404 34.615 0.00 0.00 33.38 3.71
720 1883 6.781138 TCCATTTCCGAGACAAATAATTTCG 58.219 36.000 0.00 0.00 0.00 3.46
721 1884 8.190784 ACATCCATTTCCGAGACAAATAATTTC 58.809 33.333 0.00 0.00 0.00 2.17
722 1885 8.066612 ACATCCATTTCCGAGACAAATAATTT 57.933 30.769 0.00 0.00 0.00 1.82
723 1886 7.557719 AGACATCCATTTCCGAGACAAATAATT 59.442 33.333 0.00 0.00 0.00 1.40
725 1888 6.414732 AGACATCCATTTCCGAGACAAATAA 58.585 36.000 0.00 0.00 0.00 1.40
726 1889 5.989477 AGACATCCATTTCCGAGACAAATA 58.011 37.500 0.00 0.00 0.00 1.40
728 1891 4.253685 GAGACATCCATTTCCGAGACAAA 58.746 43.478 0.00 0.00 0.00 2.83
729 1892 3.676049 CGAGACATCCATTTCCGAGACAA 60.676 47.826 0.00 0.00 0.00 3.18
730 1893 2.159240 CGAGACATCCATTTCCGAGACA 60.159 50.000 0.00 0.00 0.00 3.41
733 1896 2.871182 TCGAGACATCCATTTCCGAG 57.129 50.000 0.00 0.00 0.00 4.63
735 1898 4.882671 AATTTCGAGACATCCATTTCCG 57.117 40.909 0.00 0.00 0.00 4.30
737 1900 7.752695 ACAAGTAATTTCGAGACATCCATTTC 58.247 34.615 0.00 0.00 0.00 2.17
739 1902 7.106239 AGACAAGTAATTTCGAGACATCCATT 58.894 34.615 0.00 0.00 0.00 3.16
740 1903 6.644347 AGACAAGTAATTTCGAGACATCCAT 58.356 36.000 0.00 0.00 0.00 3.41
741 1904 6.037786 AGACAAGTAATTTCGAGACATCCA 57.962 37.500 0.00 0.00 0.00 3.41
742 1905 7.259161 AGTAGACAAGTAATTTCGAGACATCC 58.741 38.462 0.00 0.00 0.00 3.51
743 1906 7.432838 GGAGTAGACAAGTAATTTCGAGACATC 59.567 40.741 0.00 0.00 0.00 3.06
744 1907 7.259161 GGAGTAGACAAGTAATTTCGAGACAT 58.741 38.462 0.00 0.00 0.00 3.06
745 1908 6.349944 GGGAGTAGACAAGTAATTTCGAGACA 60.350 42.308 0.00 0.00 0.00 3.41
746 1909 6.035217 GGGAGTAGACAAGTAATTTCGAGAC 58.965 44.000 0.00 0.00 0.00 3.36
747 1910 5.950549 AGGGAGTAGACAAGTAATTTCGAGA 59.049 40.000 0.00 0.00 0.00 4.04
748 1911 6.210287 AGGGAGTAGACAAGTAATTTCGAG 57.790 41.667 0.00 0.00 0.00 4.04
749 1912 5.163683 CGAGGGAGTAGACAAGTAATTTCGA 60.164 44.000 0.00 0.00 0.00 3.71
750 1913 5.035443 CGAGGGAGTAGACAAGTAATTTCG 58.965 45.833 0.00 0.00 0.00 3.46
751 1914 5.349809 CCGAGGGAGTAGACAAGTAATTTC 58.650 45.833 0.00 0.00 0.00 2.17
752 1915 4.382793 GCCGAGGGAGTAGACAAGTAATTT 60.383 45.833 0.00 0.00 0.00 1.82
753 1916 3.132467 GCCGAGGGAGTAGACAAGTAATT 59.868 47.826 0.00 0.00 0.00 1.40
754 1917 2.694109 GCCGAGGGAGTAGACAAGTAAT 59.306 50.000 0.00 0.00 0.00 1.89
755 1918 2.097825 GCCGAGGGAGTAGACAAGTAA 58.902 52.381 0.00 0.00 0.00 2.24
756 1919 1.684248 GGCCGAGGGAGTAGACAAGTA 60.684 57.143 0.00 0.00 0.00 2.24
757 1920 0.971447 GGCCGAGGGAGTAGACAAGT 60.971 60.000 0.00 0.00 0.00 3.16
758 1921 0.684805 AGGCCGAGGGAGTAGACAAG 60.685 60.000 0.00 0.00 0.00 3.16
759 1922 0.970937 CAGGCCGAGGGAGTAGACAA 60.971 60.000 0.00 0.00 0.00 3.18
760 1923 1.379977 CAGGCCGAGGGAGTAGACA 60.380 63.158 0.00 0.00 0.00 3.41
761 1924 2.128507 CCAGGCCGAGGGAGTAGAC 61.129 68.421 9.25 0.00 0.00 2.59
762 1925 1.656092 ATCCAGGCCGAGGGAGTAGA 61.656 60.000 17.10 0.00 36.45 2.59
763 1926 1.152440 ATCCAGGCCGAGGGAGTAG 60.152 63.158 17.10 0.00 36.45 2.57
764 1927 1.457643 CATCCAGGCCGAGGGAGTA 60.458 63.158 17.10 0.28 36.45 2.59
765 1928 2.238319 TACATCCAGGCCGAGGGAGT 62.238 60.000 17.10 16.21 36.45 3.85
766 1929 0.833834 ATACATCCAGGCCGAGGGAG 60.834 60.000 17.10 12.19 36.45 4.30
767 1930 1.121407 CATACATCCAGGCCGAGGGA 61.121 60.000 16.09 15.50 37.64 4.20
768 1931 1.372683 CATACATCCAGGCCGAGGG 59.627 63.158 16.09 10.71 0.00 4.30
769 1932 1.372683 CCATACATCCAGGCCGAGG 59.627 63.158 10.74 10.74 0.00 4.63
770 1933 1.372683 CCCATACATCCAGGCCGAG 59.627 63.158 0.00 0.00 0.00 4.63
771 1934 2.818169 GCCCATACATCCAGGCCGA 61.818 63.158 0.00 0.00 39.60 5.54
772 1935 2.281761 GCCCATACATCCAGGCCG 60.282 66.667 0.00 0.00 39.60 6.13
773 1936 0.396974 TTTGCCCATACATCCAGGCC 60.397 55.000 0.00 0.00 45.14 5.19
787 1950 1.587034 GCTGAGTACGACGTATTTGCC 59.413 52.381 11.46 0.00 0.00 4.52
838 2007 7.558444 TGCTTAGTTTTAATGTCCGGGAATATT 59.442 33.333 0.00 5.68 0.00 1.28
856 2025 5.519927 GCTTGTTTTTCATGTGTGCTTAGTT 59.480 36.000 0.00 0.00 0.00 2.24
908 2080 5.983540 TGGTTAAAAACAAGTGCTGGAAAT 58.016 33.333 0.00 0.00 0.00 2.17
957 2129 2.223735 ACTATGGTCGTTGCGTAGATGG 60.224 50.000 0.00 0.00 0.00 3.51
1835 3062 0.883814 GGCCTCATTCTCATCGGCAG 60.884 60.000 0.00 0.00 42.43 4.85
1837 3064 1.958205 CGGCCTCATTCTCATCGGC 60.958 63.158 0.00 0.00 39.98 5.54
1907 3134 4.089839 ATCCACCTGATGACCCCC 57.910 61.111 0.00 0.00 30.54 5.40
1923 3150 5.703130 GTGAAGAAGTTACCTTGCTCTTCAT 59.297 40.000 14.02 0.00 42.27 2.57
1965 3202 0.329261 TGGGAGAAAGACCATGGCTG 59.671 55.000 13.04 0.00 0.00 4.85
2032 3273 6.415867 CGACATGAAATATGTCAAGGAATTGC 59.584 38.462 17.21 0.00 46.38 3.56
2075 3316 7.589526 CGCTGACCGATAAACCTCAAAAAGG 62.590 48.000 0.00 0.00 45.37 3.11
2094 3335 0.874390 GTCCTTTGCAACATCGCTGA 59.126 50.000 0.00 0.00 0.00 4.26
2108 3349 4.624913 TCTGACTGGATATTCAGGTCCTT 58.375 43.478 15.67 0.00 39.86 3.36
2152 3393 6.913873 ACATAATTTGCAATGAGAAATGCC 57.086 33.333 0.00 0.00 41.87 4.40
2159 3400 4.799949 CGGGTGAACATAATTTGCAATGAG 59.200 41.667 0.00 0.00 0.00 2.90
2164 3405 2.796557 TCCGGGTGAACATAATTTGCA 58.203 42.857 0.00 0.00 0.00 4.08
2177 3418 3.128589 CCACTAAATTTGTCATCCGGGTG 59.871 47.826 8.97 8.97 0.00 4.61
2181 3422 5.621197 TTGTCCACTAAATTTGTCATCCG 57.379 39.130 0.00 0.00 0.00 4.18
2219 3460 9.265901 TCTGACAAAAACAAATGAAGTGAAAAA 57.734 25.926 0.00 0.00 0.00 1.94
2220 3461 8.824159 TCTGACAAAAACAAATGAAGTGAAAA 57.176 26.923 0.00 0.00 0.00 2.29
2221 3462 8.824159 TTCTGACAAAAACAAATGAAGTGAAA 57.176 26.923 0.00 0.00 0.00 2.69
2222 3463 8.824159 TTTCTGACAAAAACAAATGAAGTGAA 57.176 26.923 0.00 0.00 0.00 3.18
2234 3476 9.801714 CAAGCATGATAATTTTCTGACAAAAAC 57.198 29.630 0.00 0.00 31.35 2.43
2259 3501 9.672086 GTGCGATTATGGCTATTTTAATTTACA 57.328 29.630 0.34 0.00 0.00 2.41
2265 3507 6.701145 TTGGTGCGATTATGGCTATTTTAA 57.299 33.333 0.34 0.00 0.00 1.52
2270 3512 5.420725 TCTATTGGTGCGATTATGGCTAT 57.579 39.130 0.34 0.00 0.00 2.97
2291 3533 3.802866 TGGTGTTCTTTTGGGCAATTTC 58.197 40.909 0.00 0.00 0.00 2.17
2305 3547 7.772332 AAAACGTAGATCATATCTGGTGTTC 57.228 36.000 0.00 0.00 40.51 3.18
2319 3561 9.410556 ACGTACACAGTAATTTAAAACGTAGAT 57.589 29.630 7.04 0.00 39.05 1.98
2320 3562 8.795786 ACGTACACAGTAATTTAAAACGTAGA 57.204 30.769 7.04 0.00 39.05 2.59
2321 3563 9.503454 GAACGTACACAGTAATTTAAAACGTAG 57.497 33.333 8.75 0.00 39.82 3.51
2324 3631 8.823840 CATGAACGTACACAGTAATTTAAAACG 58.176 33.333 0.00 0.00 0.00 3.60
2336 3643 7.946655 ATAATATCACCATGAACGTACACAG 57.053 36.000 0.00 0.00 0.00 3.66
2379 3687 1.202615 GCTGCTGGACATGATGCTCTA 60.203 52.381 0.00 0.00 0.00 2.43
2391 3701 1.818959 GCCCAAACAATGCTGCTGGA 61.819 55.000 0.00 0.00 32.73 3.86
2403 3713 1.742831 TCACGCATGATTAGCCCAAAC 59.257 47.619 0.00 0.00 0.00 2.93
2420 3730 1.909700 TGGCTTGGACAAAGGATCAC 58.090 50.000 0.00 0.00 36.30 3.06
2445 3755 2.472695 CACCTGCCTGTGTTTAGCTA 57.527 50.000 0.00 0.00 0.00 3.32
2546 3856 7.817641 ACTAGCAGAAAACAGCCTAAAATAAC 58.182 34.615 0.00 0.00 0.00 1.89
2548 3858 9.109393 CATACTAGCAGAAAACAGCCTAAAATA 57.891 33.333 0.00 0.00 0.00 1.40
2618 3931 9.680315 CTCTACAACTTATATTTAGGAACGGAG 57.320 37.037 0.00 0.00 0.00 4.63
2635 3948 9.509956 GTGGTCTATAGTGATATCTCTACAACT 57.490 37.037 15.01 6.53 0.00 3.16
2636 3949 9.286170 TGTGGTCTATAGTGATATCTCTACAAC 57.714 37.037 15.01 10.13 0.00 3.32
2641 3954 9.639563 CCATATGTGGTCTATAGTGATATCTCT 57.360 37.037 11.77 11.77 40.83 3.10
2642 3955 9.634021 TCCATATGTGGTCTATAGTGATATCTC 57.366 37.037 8.51 0.00 46.16 2.75
2645 3958 9.720874 ACATCCATATGTGGTCTATAGTGATAT 57.279 33.333 8.51 0.00 44.79 1.63
2647 3960 9.720874 ATACATCCATATGTGGTCTATAGTGAT 57.279 33.333 8.51 0.00 45.99 3.06
2648 3961 8.971073 CATACATCCATATGTGGTCTATAGTGA 58.029 37.037 8.51 0.00 45.99 3.41
2649 3962 8.753133 ACATACATCCATATGTGGTCTATAGTG 58.247 37.037 8.51 3.59 45.99 2.74
2650 3963 8.901472 ACATACATCCATATGTGGTCTATAGT 57.099 34.615 8.51 0.15 45.99 2.12
2653 3966 9.720874 ATCTACATACATCCATATGTGGTCTAT 57.279 33.333 8.51 0.00 45.99 1.98
2655 3968 8.972127 GTATCTACATACATCCATATGTGGTCT 58.028 37.037 8.51 0.00 45.99 3.85
2656 3969 8.749354 TGTATCTACATACATCCATATGTGGTC 58.251 37.037 8.51 3.30 45.99 4.02
2657 3970 8.664669 TGTATCTACATACATCCATATGTGGT 57.335 34.615 8.51 0.00 45.99 4.16
2689 4002 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2690 4003 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2691 4004 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2692 4005 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2693 4006 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2694 4007 5.741388 ATACGGAGCAAAATGAGTGAATC 57.259 39.130 0.00 0.00 0.00 2.52
2695 4008 6.205464 CCATATACGGAGCAAAATGAGTGAAT 59.795 38.462 0.00 0.00 0.00 2.57
2696 4009 5.527214 CCATATACGGAGCAAAATGAGTGAA 59.473 40.000 0.00 0.00 0.00 3.18
2697 4010 5.056480 CCATATACGGAGCAAAATGAGTGA 58.944 41.667 0.00 0.00 0.00 3.41
2698 4011 4.816385 ACCATATACGGAGCAAAATGAGTG 59.184 41.667 0.00 0.00 0.00 3.51
2699 4012 5.036117 ACCATATACGGAGCAAAATGAGT 57.964 39.130 0.00 0.00 0.00 3.41
2700 4013 4.452455 GGACCATATACGGAGCAAAATGAG 59.548 45.833 0.00 0.00 0.00 2.90
2701 4014 4.141597 TGGACCATATACGGAGCAAAATGA 60.142 41.667 0.00 0.00 0.00 2.57
2702 4015 4.133820 TGGACCATATACGGAGCAAAATG 58.866 43.478 0.00 0.00 0.00 2.32
2703 4016 4.431416 TGGACCATATACGGAGCAAAAT 57.569 40.909 0.00 0.00 0.00 1.82
2704 4017 3.916359 TGGACCATATACGGAGCAAAA 57.084 42.857 0.00 0.00 0.00 2.44
2705 4018 5.554437 TTATGGACCATATACGGAGCAAA 57.446 39.130 15.05 0.00 0.00 3.68
2706 4019 5.247337 TCATTATGGACCATATACGGAGCAA 59.753 40.000 15.05 0.00 0.00 3.91
2707 4020 4.775253 TCATTATGGACCATATACGGAGCA 59.225 41.667 15.05 0.00 0.00 4.26
2708 4021 5.339008 TCATTATGGACCATATACGGAGC 57.661 43.478 15.05 0.00 0.00 4.70
2709 4022 8.260818 AGATTTCATTATGGACCATATACGGAG 58.739 37.037 15.05 2.79 0.00 4.63
2710 4023 8.146053 AGATTTCATTATGGACCATATACGGA 57.854 34.615 15.05 7.69 0.00 4.69
2711 4024 8.260818 AGAGATTTCATTATGGACCATATACGG 58.739 37.037 15.05 5.63 0.00 4.02
2712 4025 9.658799 AAGAGATTTCATTATGGACCATATACG 57.341 33.333 15.05 6.95 0.00 3.06
2716 4029 9.919416 TTTGAAGAGATTTCATTATGGACCATA 57.081 29.630 10.31 10.31 0.00 2.74
2717 4030 8.827832 TTTGAAGAGATTTCATTATGGACCAT 57.172 30.769 12.67 12.67 0.00 3.55
2718 4031 8.108999 TCTTTGAAGAGATTTCATTATGGACCA 58.891 33.333 0.00 0.00 0.00 4.02
2719 4032 8.401709 GTCTTTGAAGAGATTTCATTATGGACC 58.598 37.037 0.00 0.00 35.32 4.46
2720 4033 9.171877 AGTCTTTGAAGAGATTTCATTATGGAC 57.828 33.333 0.00 0.00 35.32 4.02
2721 4034 9.745018 AAGTCTTTGAAGAGATTTCATTATGGA 57.255 29.630 0.00 0.00 35.32 3.41
2735 4048 9.595823 CCGTTCCTAAATATAAGTCTTTGAAGA 57.404 33.333 0.00 0.00 0.00 2.87
2736 4049 9.595823 TCCGTTCCTAAATATAAGTCTTTGAAG 57.404 33.333 0.00 0.00 0.00 3.02
2737 4050 9.595823 CTCCGTTCCTAAATATAAGTCTTTGAA 57.404 33.333 0.00 0.00 0.00 2.69
2738 4051 8.202137 CCTCCGTTCCTAAATATAAGTCTTTGA 58.798 37.037 0.00 0.00 0.00 2.69
2739 4052 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2740 4053 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2741 4054 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2742 4055 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2743 4056 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2744 4057 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2745 4058 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2746 4059 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
2747 4060 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
2748 4061 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
2749 4062 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
2750 4063 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2751 4064 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2752 4065 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
2753 4066 3.461085 AGTATGTACTCCCTCCGTTCCTA 59.539 47.826 0.00 0.00 0.00 2.94
2754 4067 2.244252 AGTATGTACTCCCTCCGTTCCT 59.756 50.000 0.00 0.00 0.00 3.36
2755 4068 2.664015 AGTATGTACTCCCTCCGTTCC 58.336 52.381 0.00 0.00 0.00 3.62
2756 4069 4.459330 ACTAGTATGTACTCCCTCCGTTC 58.541 47.826 0.00 0.00 37.73 3.95
2757 4070 4.516652 ACTAGTATGTACTCCCTCCGTT 57.483 45.455 0.00 0.00 37.73 4.44
2758 4071 4.410228 TGTACTAGTATGTACTCCCTCCGT 59.590 45.833 5.75 0.00 42.22 4.69
2759 4072 4.965814 TGTACTAGTATGTACTCCCTCCG 58.034 47.826 5.75 0.00 42.22 4.63
2760 4073 5.939447 ACTGTACTAGTATGTACTCCCTCC 58.061 45.833 5.75 0.00 42.22 4.30
2761 4074 7.734942 ACTACTGTACTAGTATGTACTCCCTC 58.265 42.308 5.75 0.00 40.94 4.30
2762 4075 7.688918 ACTACTGTACTAGTATGTACTCCCT 57.311 40.000 5.75 0.00 40.94 4.20
2763 4076 7.596995 CGTACTACTGTACTAGTATGTACTCCC 59.403 44.444 21.82 0.00 44.97 4.30
2764 4077 8.138712 ACGTACTACTGTACTAGTATGTACTCC 58.861 40.741 18.62 0.00 43.28 3.85


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

AutoCloner maintained by Alex Coulton.