Multiple sequence alignment - TraesCS3A01G182100

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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 TraesCS3A01G182100 chr3A 100.000 2582 0 0 1 2582 211189997 211187416 0.000000e+00 4769.0
1 TraesCS3A01G182100 chr3A 97.321 336 6 3 1740 2073 436452010 436452344 3.730000e-158 568.0
2 TraesCS3A01G182100 chr3A 95.954 346 12 2 1742 2085 213242586 213242241 6.240000e-156 560.0
3 TraesCS3A01G182100 chr3D 95.346 924 34 3 825 1740 173394440 173395362 0.000000e+00 1459.0
4 TraesCS3A01G182100 chr3D 88.098 731 78 9 68 791 604796426 604795698 0.000000e+00 859.0
5 TraesCS3A01G182100 chr3D 93.819 453 20 5 2129 2578 173395353 173395800 0.000000e+00 675.0
6 TraesCS3A01G182100 chr3B 94.054 925 31 4 825 1740 251782023 251782932 0.000000e+00 1382.0
7 TraesCS3A01G182100 chr3B 94.066 455 22 4 2129 2582 251782923 251783373 0.000000e+00 686.0
8 TraesCS3A01G182100 chr3B 93.750 48 3 0 1 48 251781922 251781969 3.560000e-09 73.1
9 TraesCS3A01G182100 chr4D 88.363 739 74 12 66 796 329141752 329142486 0.000000e+00 878.0
10 TraesCS3A01G182100 chr4D 87.891 735 75 12 66 791 318591758 318592487 0.000000e+00 852.0
11 TraesCS3A01G182100 chr4D 87.551 731 80 11 66 789 396364437 396365163 0.000000e+00 835.0
12 TraesCS3A01G182100 chr7D 87.722 733 81 8 70 796 384815990 384816719 0.000000e+00 846.0
13 TraesCS3A01G182100 chr1D 87.895 727 75 13 66 783 110921946 110922668 0.000000e+00 843.0
14 TraesCS3A01G182100 chr1D 86.420 405 37 9 1742 2129 488823854 488824257 6.600000e-116 427.0
15 TraesCS3A01G182100 chr6D 87.432 740 79 12 66 796 17972279 17973013 0.000000e+00 839.0
16 TraesCS3A01G182100 chr2A 87.741 726 79 8 66 784 652769089 652769811 0.000000e+00 839.0
17 TraesCS3A01G182100 chr2A 92.944 411 6 8 1741 2128 442513400 442513810 6.200000e-161 577.0
18 TraesCS3A01G182100 chr2A 91.435 432 13 5 1734 2142 109327001 109327431 2.880000e-159 571.0
19 TraesCS3A01G182100 chr6B 87.364 736 85 8 66 795 523507243 523507976 0.000000e+00 837.0
20 TraesCS3A01G182100 chr7A 92.892 408 7 2 1744 2129 567710372 567709965 8.010000e-160 573.0
21 TraesCS3A01G182100 chr1A 92.718 412 7 3 1742 2130 419037632 419038043 8.010000e-160 573.0
22 TraesCS3A01G182100 chr1A 92.402 408 9 3 1742 2128 499392940 499392534 1.730000e-156 562.0
23 TraesCS3A01G182100 chr5A 92.402 408 7 5 1744 2128 229498442 229498848 6.240000e-156 560.0
24 TraesCS3A01G182100 chr4A 97.161 317 7 2 1742 2057 177619798 177620113 3.780000e-148 534.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G182100 chr3A 211187416 211189997 2581 True 4769.0 4769 100.000000 1 2582 1 chr3A.!!$R1 2581
1 TraesCS3A01G182100 chr3D 173394440 173395800 1360 False 1067.0 1459 94.582500 825 2578 2 chr3D.!!$F1 1753
2 TraesCS3A01G182100 chr3D 604795698 604796426 728 True 859.0 859 88.098000 68 791 1 chr3D.!!$R1 723
3 TraesCS3A01G182100 chr3B 251781922 251783373 1451 False 713.7 1382 93.956667 1 2582 3 chr3B.!!$F1 2581
4 TraesCS3A01G182100 chr4D 329141752 329142486 734 False 878.0 878 88.363000 66 796 1 chr4D.!!$F2 730
5 TraesCS3A01G182100 chr4D 318591758 318592487 729 False 852.0 852 87.891000 66 791 1 chr4D.!!$F1 725
6 TraesCS3A01G182100 chr4D 396364437 396365163 726 False 835.0 835 87.551000 66 789 1 chr4D.!!$F3 723
7 TraesCS3A01G182100 chr7D 384815990 384816719 729 False 846.0 846 87.722000 70 796 1 chr7D.!!$F1 726
8 TraesCS3A01G182100 chr1D 110921946 110922668 722 False 843.0 843 87.895000 66 783 1 chr1D.!!$F1 717
9 TraesCS3A01G182100 chr6D 17972279 17973013 734 False 839.0 839 87.432000 66 796 1 chr6D.!!$F1 730
10 TraesCS3A01G182100 chr2A 652769089 652769811 722 False 839.0 839 87.741000 66 784 1 chr2A.!!$F3 718
11 TraesCS3A01G182100 chr6B 523507243 523507976 733 False 837.0 837 87.364000 66 795 1 chr6B.!!$F1 729

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
802 821 0.392998 ACGGCGCAATCTGGAGATTT 60.393 50.0 10.83 0.0 42.41 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1799 0.031449 GCTATGTGGAGCTCGGTCTC 59.969 60.0 7.83 0.0 39.5 3.36 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
41 42 3.686241 TCGTTTCTAGATCGACGGAGAAA 59.314 43.478 18.00 11.46 36.27 2.52
42 43 4.154737 TCGTTTCTAGATCGACGGAGAAAA 59.845 41.667 18.00 3.34 37.22 2.29
43 44 5.035443 CGTTTCTAGATCGACGGAGAAAAT 58.965 41.667 15.29 0.00 37.22 1.82
44 45 5.515626 CGTTTCTAGATCGACGGAGAAAATT 59.484 40.000 15.29 0.00 37.22 1.82
45 46 6.034683 CGTTTCTAGATCGACGGAGAAAATTT 59.965 38.462 15.29 0.00 37.22 1.82
46 47 7.411588 CGTTTCTAGATCGACGGAGAAAATTTT 60.412 37.037 15.29 2.28 37.22 1.82
47 48 8.866956 GTTTCTAGATCGACGGAGAAAATTTTA 58.133 33.333 15.29 0.00 37.22 1.52
48 49 7.982371 TCTAGATCGACGGAGAAAATTTTAC 57.018 36.000 2.75 1.49 0.00 2.01
49 50 5.697848 AGATCGACGGAGAAAATTTTACG 57.302 39.130 16.02 16.02 0.00 3.18
50 51 5.404946 AGATCGACGGAGAAAATTTTACGA 58.595 37.500 21.45 16.34 0.00 3.43
51 52 5.865552 AGATCGACGGAGAAAATTTTACGAA 59.134 36.000 21.45 11.25 0.00 3.85
52 53 5.903764 TCGACGGAGAAAATTTTACGAAA 57.096 34.783 21.45 9.04 0.00 3.46
53 54 6.284475 TCGACGGAGAAAATTTTACGAAAA 57.716 33.333 21.45 8.79 34.41 2.29
54 55 6.713520 TCGACGGAGAAAATTTTACGAAAAA 58.286 32.000 21.45 7.58 38.87 1.94
105 106 7.065085 CGTCTCCTTTATCACTCATTTTGTCAT 59.935 37.037 0.00 0.00 0.00 3.06
163 165 9.760077 TTGGTTTCGGCTTAAAAATGTTTTATA 57.240 25.926 0.00 0.00 0.00 0.98
216 221 7.907045 CAGTTTTCATCATTAAATCTGTCTCGG 59.093 37.037 0.00 0.00 32.63 4.63
248 254 7.824289 TCTTCAAAACTAGACCCATGTTGATAG 59.176 37.037 0.00 0.00 0.00 2.08
298 308 9.169468 CAAAAGTTGTCATGATGTTTACACTAC 57.831 33.333 0.00 0.00 0.00 2.73
300 310 7.421530 AGTTGTCATGATGTTTACACTACAC 57.578 36.000 0.00 0.00 0.00 2.90
304 314 9.719355 TTGTCATGATGTTTACACTACACTTAT 57.281 29.630 0.00 0.00 0.00 1.73
332 342 5.339611 CGTGCTTAAACTAAAGTTGTCATGC 59.660 40.000 0.00 1.05 38.44 4.06
353 363 4.217334 TGCGGCAATTTCAATTTGTAGAGA 59.783 37.500 0.00 0.00 0.00 3.10
402 412 4.220602 GGCAACTCCAGTATTTTGACCATT 59.779 41.667 0.00 0.00 34.01 3.16
474 484 9.814899 CATGGCAATTTTAGTTTATGGTTCATA 57.185 29.630 0.00 0.00 0.00 2.15
497 507 6.628644 AGCAGGTCTAGTTTCTTAATTCCT 57.371 37.500 0.00 0.00 0.00 3.36
555 567 9.826574 TGTAGAAGAAAATAGCGGTAACATATT 57.173 29.630 0.00 0.00 31.38 1.28
599 611 5.340439 TCATGGCAATTCATGTGCAATAA 57.660 34.783 8.81 0.00 44.07 1.40
784 803 2.276868 GCATGCGTGCGATGACAC 60.277 61.111 16.43 0.00 42.28 3.67
796 815 2.040213 GATGACACGGCGCAATCTGG 62.040 60.000 10.83 0.00 0.00 3.86
797 816 2.434185 GACACGGCGCAATCTGGA 60.434 61.111 10.83 0.00 0.00 3.86
798 817 2.434884 ACACGGCGCAATCTGGAG 60.435 61.111 10.83 0.00 0.00 3.86
799 818 2.125552 CACGGCGCAATCTGGAGA 60.126 61.111 10.83 0.00 0.00 3.71
800 819 1.522355 CACGGCGCAATCTGGAGAT 60.522 57.895 10.83 0.00 36.07 2.75
801 820 1.091771 CACGGCGCAATCTGGAGATT 61.092 55.000 10.83 0.00 44.93 2.40
802 821 0.392998 ACGGCGCAATCTGGAGATTT 60.393 50.000 10.83 0.00 42.41 2.17
803 822 0.734889 CGGCGCAATCTGGAGATTTT 59.265 50.000 10.83 0.00 42.41 1.82
804 823 1.268234 CGGCGCAATCTGGAGATTTTC 60.268 52.381 10.83 0.00 42.41 2.29
805 824 1.745087 GGCGCAATCTGGAGATTTTCA 59.255 47.619 10.83 0.00 42.41 2.69
806 825 2.478539 GGCGCAATCTGGAGATTTTCAC 60.479 50.000 10.83 0.00 42.41 3.18
807 826 2.478539 GCGCAATCTGGAGATTTTCACC 60.479 50.000 0.30 0.00 42.41 4.02
808 827 2.749076 CGCAATCTGGAGATTTTCACCA 59.251 45.455 0.00 0.00 42.41 4.17
815 834 4.868172 TGGAGATTTTCACCAGATCCAT 57.132 40.909 0.00 0.00 32.13 3.41
816 835 4.529897 TGGAGATTTTCACCAGATCCATG 58.470 43.478 0.00 0.00 32.13 3.66
817 836 3.317430 GGAGATTTTCACCAGATCCATGC 59.683 47.826 0.00 0.00 0.00 4.06
818 837 3.949754 GAGATTTTCACCAGATCCATGCA 59.050 43.478 0.00 0.00 0.00 3.96
819 838 4.543689 AGATTTTCACCAGATCCATGCAT 58.456 39.130 0.00 0.00 0.00 3.96
820 839 4.341235 AGATTTTCACCAGATCCATGCATG 59.659 41.667 20.19 20.19 0.00 4.06
821 840 1.395635 TTCACCAGATCCATGCATGC 58.604 50.000 21.69 11.82 0.00 4.06
822 841 0.549469 TCACCAGATCCATGCATGCT 59.451 50.000 21.69 10.26 0.00 3.79
823 842 1.770061 TCACCAGATCCATGCATGCTA 59.230 47.619 21.69 11.61 0.00 3.49
830 849 0.402887 TCCATGCATGCTATCCTGGG 59.597 55.000 21.69 4.32 0.00 4.45
930 949 3.290710 ACCTGAGCACACTTGTCATTTT 58.709 40.909 0.00 0.00 0.00 1.82
967 986 2.731691 AAAGAAGCTTCGCTCCGCCA 62.732 55.000 20.43 0.00 38.25 5.69
984 1018 1.567504 CCACCCGCGTATAAGACAAG 58.432 55.000 4.92 0.00 0.00 3.16
985 1019 1.135527 CCACCCGCGTATAAGACAAGA 59.864 52.381 4.92 0.00 0.00 3.02
986 1020 2.417651 CCACCCGCGTATAAGACAAGAA 60.418 50.000 4.92 0.00 0.00 2.52
987 1021 2.601763 CACCCGCGTATAAGACAAGAAC 59.398 50.000 4.92 0.00 0.00 3.01
988 1022 2.199236 CCCGCGTATAAGACAAGAACC 58.801 52.381 4.92 0.00 0.00 3.62
989 1023 2.199236 CCGCGTATAAGACAAGAACCC 58.801 52.381 4.92 0.00 0.00 4.11
990 1024 2.417651 CCGCGTATAAGACAAGAACCCA 60.418 50.000 4.92 0.00 0.00 4.51
991 1025 3.255725 CGCGTATAAGACAAGAACCCAA 58.744 45.455 0.00 0.00 0.00 4.12
992 1026 3.306166 CGCGTATAAGACAAGAACCCAAG 59.694 47.826 0.00 0.00 0.00 3.61
993 1027 4.501071 GCGTATAAGACAAGAACCCAAGA 58.499 43.478 0.00 0.00 0.00 3.02
994 1028 4.933400 GCGTATAAGACAAGAACCCAAGAA 59.067 41.667 0.00 0.00 0.00 2.52
995 1029 5.063564 GCGTATAAGACAAGAACCCAAGAAG 59.936 44.000 0.00 0.00 0.00 2.85
996 1030 5.063564 CGTATAAGACAAGAACCCAAGAAGC 59.936 44.000 0.00 0.00 0.00 3.86
997 1031 3.297134 AAGACAAGAACCCAAGAAGCA 57.703 42.857 0.00 0.00 0.00 3.91
998 1032 3.297134 AGACAAGAACCCAAGAAGCAA 57.703 42.857 0.00 0.00 0.00 3.91
1254 1288 4.208686 CTGCCGGCCGAGTACCTC 62.209 72.222 30.73 6.72 0.00 3.85
1269 1303 4.180946 CTCGACCTCCTCGCCGTG 62.181 72.222 0.00 0.00 42.62 4.94
1413 1447 2.363147 GACTCCTGGCTCCTCCGT 60.363 66.667 0.00 0.00 37.80 4.69
1521 1555 1.296001 CTACGTCGACGAGCACGAG 60.296 63.158 41.52 22.77 43.02 4.18
1583 1617 0.248215 GCGCTGTGGCACATGTAATC 60.248 55.000 22.35 5.56 44.52 1.75
1588 1622 1.818060 TGTGGCACATGTAATCAAGCC 59.182 47.619 17.96 14.13 44.52 4.35
1605 1644 1.135699 GCCAGCAAACGATCAATGCG 61.136 55.000 8.25 0.00 44.60 4.73
1730 1773 4.214119 TGAAATCTCTCGCTGAAAAAGGTG 59.786 41.667 0.00 0.00 0.00 4.00
1731 1774 3.685139 ATCTCTCGCTGAAAAAGGTGA 57.315 42.857 0.00 0.00 0.00 4.02
1732 1775 3.685139 TCTCTCGCTGAAAAAGGTGAT 57.315 42.857 0.00 0.00 0.00 3.06
1733 1776 3.329386 TCTCTCGCTGAAAAAGGTGATG 58.671 45.455 0.00 0.00 0.00 3.07
1734 1777 3.070018 CTCTCGCTGAAAAAGGTGATGT 58.930 45.455 0.00 0.00 0.00 3.06
1735 1778 4.021456 TCTCTCGCTGAAAAAGGTGATGTA 60.021 41.667 0.00 0.00 0.00 2.29
1736 1779 4.832248 TCTCGCTGAAAAAGGTGATGTAT 58.168 39.130 0.00 0.00 0.00 2.29
1737 1780 5.972935 TCTCGCTGAAAAAGGTGATGTATA 58.027 37.500 0.00 0.00 0.00 1.47
1738 1781 6.042777 TCTCGCTGAAAAAGGTGATGTATAG 58.957 40.000 0.00 0.00 0.00 1.31
1739 1782 5.116180 TCGCTGAAAAAGGTGATGTATAGG 58.884 41.667 0.00 0.00 0.00 2.57
1740 1783 4.273480 CGCTGAAAAAGGTGATGTATAGGG 59.727 45.833 0.00 0.00 0.00 3.53
1741 1784 4.036852 GCTGAAAAAGGTGATGTATAGGGC 59.963 45.833 0.00 0.00 0.00 5.19
1742 1785 4.196193 TGAAAAAGGTGATGTATAGGGCG 58.804 43.478 0.00 0.00 0.00 6.13
1743 1786 4.080807 TGAAAAAGGTGATGTATAGGGCGA 60.081 41.667 0.00 0.00 0.00 5.54
1744 1787 4.497291 AAAAGGTGATGTATAGGGCGAA 57.503 40.909 0.00 0.00 0.00 4.70
1745 1788 4.497291 AAAGGTGATGTATAGGGCGAAA 57.503 40.909 0.00 0.00 0.00 3.46
1746 1789 4.497291 AAGGTGATGTATAGGGCGAAAA 57.503 40.909 0.00 0.00 0.00 2.29
1747 1790 4.497291 AGGTGATGTATAGGGCGAAAAA 57.503 40.909 0.00 0.00 0.00 1.94
1748 1791 4.451900 AGGTGATGTATAGGGCGAAAAAG 58.548 43.478 0.00 0.00 0.00 2.27
1749 1792 3.003378 GGTGATGTATAGGGCGAAAAAGC 59.997 47.826 0.00 0.00 0.00 3.51
1750 1793 3.625764 GTGATGTATAGGGCGAAAAAGCA 59.374 43.478 0.00 0.00 39.27 3.91
1751 1794 4.275936 GTGATGTATAGGGCGAAAAAGCAT 59.724 41.667 0.00 0.00 39.27 3.79
1752 1795 4.887071 TGATGTATAGGGCGAAAAAGCATT 59.113 37.500 0.00 0.00 39.27 3.56
1753 1796 4.630894 TGTATAGGGCGAAAAAGCATTG 57.369 40.909 0.00 0.00 39.27 2.82
1754 1797 2.584492 ATAGGGCGAAAAAGCATTGC 57.416 45.000 0.00 0.00 39.27 3.56
1755 1798 1.252175 TAGGGCGAAAAAGCATTGCA 58.748 45.000 11.91 0.00 39.27 4.08
1756 1799 0.037975 AGGGCGAAAAAGCATTGCAG 60.038 50.000 11.91 0.00 39.27 4.41
1757 1800 0.038343 GGGCGAAAAAGCATTGCAGA 60.038 50.000 11.91 0.00 39.27 4.26
1758 1801 1.343506 GGCGAAAAAGCATTGCAGAG 58.656 50.000 11.91 0.00 39.27 3.35
1759 1802 1.068333 GGCGAAAAAGCATTGCAGAGA 60.068 47.619 11.91 0.00 39.27 3.10
1760 1803 1.981533 GCGAAAAAGCATTGCAGAGAC 59.018 47.619 11.91 0.00 37.05 3.36
1761 1804 2.589014 CGAAAAAGCATTGCAGAGACC 58.411 47.619 11.91 0.00 0.00 3.85
1762 1805 2.589014 GAAAAAGCATTGCAGAGACCG 58.411 47.619 11.91 0.00 0.00 4.79
1763 1806 1.896220 AAAAGCATTGCAGAGACCGA 58.104 45.000 11.91 0.00 0.00 4.69
1764 1807 1.446907 AAAGCATTGCAGAGACCGAG 58.553 50.000 11.91 0.00 0.00 4.63
1765 1808 1.023513 AAGCATTGCAGAGACCGAGC 61.024 55.000 11.91 0.00 0.00 5.03
1766 1809 1.449246 GCATTGCAGAGACCGAGCT 60.449 57.895 3.15 0.00 0.00 4.09
1767 1810 1.427592 GCATTGCAGAGACCGAGCTC 61.428 60.000 2.73 2.73 35.11 4.09
1768 1811 0.809241 CATTGCAGAGACCGAGCTCC 60.809 60.000 8.47 0.00 35.49 4.70
1769 1812 1.260538 ATTGCAGAGACCGAGCTCCA 61.261 55.000 8.47 0.00 35.49 3.86
1770 1813 2.159819 TTGCAGAGACCGAGCTCCAC 62.160 60.000 8.47 0.00 35.49 4.02
1771 1814 2.640302 GCAGAGACCGAGCTCCACA 61.640 63.158 8.47 0.00 35.49 4.17
1772 1815 1.954362 GCAGAGACCGAGCTCCACAT 61.954 60.000 8.47 0.00 35.49 3.21
1773 1816 1.393603 CAGAGACCGAGCTCCACATA 58.606 55.000 8.47 0.00 35.49 2.29
1774 1817 1.336440 CAGAGACCGAGCTCCACATAG 59.664 57.143 8.47 0.00 35.49 2.23
1775 1818 0.031449 GAGACCGAGCTCCACATAGC 59.969 60.000 8.47 0.00 43.11 2.97
1810 1853 9.737427 TTTTTCAGCGAAAATACTATTTTCACA 57.263 25.926 24.42 9.58 40.50 3.58
1811 1854 8.722342 TTTCAGCGAAAATACTATTTTCACAC 57.278 30.769 24.42 16.60 38.07 3.82
1812 1855 7.428282 TCAGCGAAAATACTATTTTCACACA 57.572 32.000 24.42 10.13 38.07 3.72
1813 1856 8.039603 TCAGCGAAAATACTATTTTCACACAT 57.960 30.769 24.42 9.69 38.07 3.21
1814 1857 8.511321 TCAGCGAAAATACTATTTTCACACATT 58.489 29.630 24.42 5.86 38.07 2.71
1815 1858 9.767684 CAGCGAAAATACTATTTTCACACATTA 57.232 29.630 24.42 0.00 38.07 1.90
1999 2042 3.804518 TGTGTAGCACGCAAATAACTG 57.195 42.857 0.89 0.00 35.42 3.16
2000 2043 3.394719 TGTGTAGCACGCAAATAACTGA 58.605 40.909 0.89 0.00 35.42 3.41
2001 2044 3.810386 TGTGTAGCACGCAAATAACTGAA 59.190 39.130 0.89 0.00 35.42 3.02
2002 2045 4.454161 TGTGTAGCACGCAAATAACTGAAT 59.546 37.500 0.89 0.00 35.42 2.57
2003 2046 5.049060 TGTGTAGCACGCAAATAACTGAATT 60.049 36.000 0.89 0.00 35.42 2.17
2004 2047 6.147985 TGTGTAGCACGCAAATAACTGAATTA 59.852 34.615 0.89 0.00 35.42 1.40
2005 2048 6.464834 GTGTAGCACGCAAATAACTGAATTAC 59.535 38.462 0.00 0.00 0.00 1.89
2006 2049 5.621197 AGCACGCAAATAACTGAATTACA 57.379 34.783 0.00 0.00 0.00 2.41
2007 2050 6.194796 AGCACGCAAATAACTGAATTACAT 57.805 33.333 0.00 0.00 0.00 2.29
2008 2051 6.029607 AGCACGCAAATAACTGAATTACATG 58.970 36.000 0.00 0.00 0.00 3.21
2009 2052 6.027131 GCACGCAAATAACTGAATTACATGA 58.973 36.000 0.00 0.00 0.00 3.07
2010 2053 6.692681 GCACGCAAATAACTGAATTACATGAT 59.307 34.615 0.00 0.00 0.00 2.45
2011 2054 7.305590 GCACGCAAATAACTGAATTACATGATG 60.306 37.037 0.00 0.00 0.00 3.07
2012 2055 7.909641 CACGCAAATAACTGAATTACATGATGA 59.090 33.333 0.00 0.00 0.00 2.92
2013 2056 8.458052 ACGCAAATAACTGAATTACATGATGAA 58.542 29.630 0.00 0.00 0.00 2.57
2014 2057 9.288124 CGCAAATAACTGAATTACATGATGAAA 57.712 29.630 0.00 0.00 0.00 2.69
2030 2073 9.349713 ACATGATGAAACTTTTTACCTACTTGA 57.650 29.630 0.00 0.00 0.00 3.02
2031 2074 9.612620 CATGATGAAACTTTTTACCTACTTGAC 57.387 33.333 0.00 0.00 0.00 3.18
2032 2075 8.740123 TGATGAAACTTTTTACCTACTTGACA 57.260 30.769 0.00 0.00 0.00 3.58
2033 2076 9.179909 TGATGAAACTTTTTACCTACTTGACAA 57.820 29.630 0.00 0.00 0.00 3.18
2035 2078 9.797556 ATGAAACTTTTTACCTACTTGACAAAC 57.202 29.630 0.00 0.00 0.00 2.93
2036 2079 8.794553 TGAAACTTTTTACCTACTTGACAAACA 58.205 29.630 0.00 0.00 0.00 2.83
2037 2080 9.797556 GAAACTTTTTACCTACTTGACAAACAT 57.202 29.630 0.00 0.00 0.00 2.71
2038 2081 9.581099 AAACTTTTTACCTACTTGACAAACATG 57.419 29.630 0.00 0.00 0.00 3.21
2039 2082 7.200455 ACTTTTTACCTACTTGACAAACATGC 58.800 34.615 0.00 0.00 0.00 4.06
2040 2083 6.701145 TTTTACCTACTTGACAAACATGCA 57.299 33.333 0.00 0.00 0.00 3.96
2041 2084 6.892658 TTTACCTACTTGACAAACATGCAT 57.107 33.333 0.00 0.00 0.00 3.96
2042 2085 7.987750 TTTACCTACTTGACAAACATGCATA 57.012 32.000 0.00 0.00 0.00 3.14
2043 2086 8.574251 TTTACCTACTTGACAAACATGCATAT 57.426 30.769 0.00 0.00 0.00 1.78
2044 2087 6.441093 ACCTACTTGACAAACATGCATATG 57.559 37.500 0.00 0.00 40.24 1.78
2046 2089 7.109501 ACCTACTTGACAAACATGCATATGTA 58.890 34.615 0.00 0.00 46.54 2.29
2047 2090 7.775093 ACCTACTTGACAAACATGCATATGTAT 59.225 33.333 0.00 1.99 46.54 2.29
2048 2091 8.623903 CCTACTTGACAAACATGCATATGTATT 58.376 33.333 3.23 0.00 46.54 1.89
2050 2093 8.692110 ACTTGACAAACATGCATATGTATTTG 57.308 30.769 14.58 14.58 46.54 2.32
2051 2094 8.306038 ACTTGACAAACATGCATATGTATTTGT 58.694 29.630 19.23 19.23 46.54 2.83
2052 2095 9.786105 CTTGACAAACATGCATATGTATTTGTA 57.214 29.630 19.19 9.11 46.54 2.41
2098 2141 3.802948 TTTTTAGCAAAACGGGCTCAA 57.197 38.095 0.00 0.00 42.62 3.02
2099 2142 4.329462 TTTTTAGCAAAACGGGCTCAAT 57.671 36.364 0.00 0.00 42.62 2.57
2100 2143 5.455056 TTTTTAGCAAAACGGGCTCAATA 57.545 34.783 0.00 0.00 42.62 1.90
2101 2144 4.695217 TTTAGCAAAACGGGCTCAATAG 57.305 40.909 0.00 0.00 42.62 1.73
2102 2145 2.489938 AGCAAAACGGGCTCAATAGA 57.510 45.000 0.00 0.00 36.81 1.98
2103 2146 2.359900 AGCAAAACGGGCTCAATAGAG 58.640 47.619 0.00 0.00 44.96 2.43
2111 2154 3.555967 CTCAATAGAGCCCGGCCT 58.444 61.111 5.55 5.71 34.61 5.19
2112 2155 1.369321 CTCAATAGAGCCCGGCCTC 59.631 63.158 3.71 3.71 34.61 4.70
2113 2156 1.075226 TCAATAGAGCCCGGCCTCT 60.075 57.895 20.24 20.24 44.12 3.69
2114 2157 1.070445 CAATAGAGCCCGGCCTCTG 59.930 63.158 24.72 5.47 42.01 3.35
2115 2158 2.812619 AATAGAGCCCGGCCTCTGC 61.813 63.158 24.72 8.47 42.01 4.26
2116 2159 4.777854 TAGAGCCCGGCCTCTGCA 62.778 66.667 24.72 2.66 42.01 4.41
2127 2170 3.782244 CTCTGCAACGCCGCACTC 61.782 66.667 0.00 0.00 36.86 3.51
2145 2188 2.289072 ACTCGATGTATAGGTGCATGGC 60.289 50.000 0.00 0.00 30.30 4.40
2196 2239 3.193267 GTCTTGGTAAATGATGCTTGGCA 59.807 43.478 0.00 0.00 44.86 4.92
2333 2377 9.716556 TTCTAGAAGGTTAAAGTATCCATCTCT 57.283 33.333 0.00 0.00 32.67 3.10
2466 2513 2.357075 ACTCAATGAGCAGTGCATCTG 58.643 47.619 19.20 8.89 46.12 2.90
2528 2577 1.857217 CTTGCGATCGATGAGTTGGAG 59.143 52.381 21.57 0.00 0.00 3.86
2532 2581 2.057316 CGATCGATGAGTTGGAGATGC 58.943 52.381 10.26 0.00 0.00 3.91
2533 2582 2.057316 GATCGATGAGTTGGAGATGCG 58.943 52.381 0.54 0.00 0.00 4.73
2534 2583 0.817654 TCGATGAGTTGGAGATGCGT 59.182 50.000 0.00 0.00 0.00 5.24
2535 2584 1.204704 TCGATGAGTTGGAGATGCGTT 59.795 47.619 0.00 0.00 0.00 4.84
2558 2607 2.414559 CGGCTTGCCAACTCTAACATTG 60.415 50.000 12.45 0.00 0.00 2.82
2563 2612 1.810151 GCCAACTCTAACATTGCGGAA 59.190 47.619 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.197468 GTCGATCTAGAAACGAAGGATCTTTG 59.803 42.308 21.00 0.00 37.77 2.77
11 12 5.504337 CGTCGATCTAGAAACGAAGGATCTT 60.504 44.000 21.00 0.00 37.31 2.40
51 52 2.525055 GATGTGCGTGTGTGTGTTTTT 58.475 42.857 0.00 0.00 0.00 1.94
52 53 1.530852 CGATGTGCGTGTGTGTGTTTT 60.531 47.619 0.00 0.00 34.64 2.43
53 54 0.027455 CGATGTGCGTGTGTGTGTTT 59.973 50.000 0.00 0.00 34.64 2.83
54 55 1.641140 CGATGTGCGTGTGTGTGTT 59.359 52.632 0.00 0.00 34.64 3.32
55 56 2.881266 GCGATGTGCGTGTGTGTGT 61.881 57.895 0.00 0.00 43.41 3.72
56 57 2.127646 GCGATGTGCGTGTGTGTG 60.128 61.111 0.00 0.00 43.41 3.82
105 106 8.620116 TTCTGTTGATTTCATCTGTTCACATA 57.380 30.769 0.00 0.00 0.00 2.29
125 126 4.099419 AGCCGAAACCAAAAAGATTTCTGT 59.901 37.500 0.00 0.00 31.47 3.41
199 204 3.380320 TCTCGCCGAGACAGATTTAATGA 59.620 43.478 13.77 0.00 33.35 2.57
216 221 3.866327 GGGTCTAGTTTTGAAGATCTCGC 59.134 47.826 0.00 0.00 0.00 5.03
298 308 8.656849 ACTTTAGTTTAAGCACGATGATAAGTG 58.343 33.333 0.00 0.00 41.01 3.16
300 310 9.478019 CAACTTTAGTTTAAGCACGATGATAAG 57.522 33.333 0.00 0.00 35.83 1.73
304 314 6.480651 TGACAACTTTAGTTTAAGCACGATGA 59.519 34.615 0.00 0.00 35.83 2.92
308 318 5.339611 GCATGACAACTTTAGTTTAAGCACG 59.660 40.000 0.00 0.00 35.83 5.34
332 342 7.008628 GTCATTCTCTACAAATTGAAATTGCCG 59.991 37.037 0.00 0.00 0.00 5.69
365 375 4.009675 GGAGTTGCCATCATCAAACACTA 58.990 43.478 0.00 0.00 36.34 2.74
367 377 2.557924 TGGAGTTGCCATCATCAAACAC 59.442 45.455 0.00 0.00 43.33 3.32
474 484 6.628398 CGAGGAATTAAGAAACTAGACCTGCT 60.628 42.308 0.00 0.00 0.00 4.24
526 538 9.826574 ATGTTACCGCTATTTTCTTCTACATTA 57.173 29.630 0.00 0.00 0.00 1.90
545 557 8.413229 ACATTGAAGTTGCCATAATATGTTACC 58.587 33.333 0.00 0.00 0.00 2.85
555 567 7.459795 TGATGTTTACATTGAAGTTGCCATA 57.540 32.000 0.00 0.00 36.57 2.74
672 689 6.907741 TGTTTTCATCATTAAATCACTCGCA 58.092 32.000 0.00 0.00 0.00 5.10
784 803 0.734889 AAAATCTCCAGATTGCGCCG 59.265 50.000 4.18 0.00 43.41 6.46
796 815 3.949754 TGCATGGATCTGGTGAAAATCTC 59.050 43.478 0.00 0.00 0.00 2.75
797 816 3.972133 TGCATGGATCTGGTGAAAATCT 58.028 40.909 0.00 0.00 0.00 2.40
798 817 4.617959 CATGCATGGATCTGGTGAAAATC 58.382 43.478 19.40 0.00 0.00 2.17
799 818 3.181469 GCATGCATGGATCTGGTGAAAAT 60.181 43.478 27.34 0.00 0.00 1.82
800 819 2.166870 GCATGCATGGATCTGGTGAAAA 59.833 45.455 27.34 0.00 0.00 2.29
801 820 1.752498 GCATGCATGGATCTGGTGAAA 59.248 47.619 27.34 0.00 0.00 2.69
802 821 1.064240 AGCATGCATGGATCTGGTGAA 60.064 47.619 27.34 0.00 0.00 3.18
803 822 0.549469 AGCATGCATGGATCTGGTGA 59.451 50.000 27.34 0.00 0.00 4.02
804 823 2.265589 TAGCATGCATGGATCTGGTG 57.734 50.000 27.34 0.94 0.00 4.17
805 824 2.290768 GGATAGCATGCATGGATCTGGT 60.291 50.000 27.34 10.61 0.00 4.00
806 825 2.026169 AGGATAGCATGCATGGATCTGG 60.026 50.000 27.34 0.91 0.00 3.86
807 826 3.010420 CAGGATAGCATGCATGGATCTG 58.990 50.000 27.34 14.57 0.00 2.90
808 827 2.026169 CCAGGATAGCATGCATGGATCT 60.026 50.000 27.34 17.91 0.00 2.75
809 828 2.366533 CCAGGATAGCATGCATGGATC 58.633 52.381 27.34 15.52 0.00 3.36
810 829 1.005569 CCCAGGATAGCATGCATGGAT 59.994 52.381 27.34 10.15 0.00 3.41
811 830 0.402887 CCCAGGATAGCATGCATGGA 59.597 55.000 27.34 1.93 0.00 3.41
812 831 0.611062 CCCCAGGATAGCATGCATGG 60.611 60.000 27.34 17.71 0.00 3.66
813 832 0.111832 ACCCCAGGATAGCATGCATG 59.888 55.000 22.70 22.70 0.00 4.06
814 833 0.403271 GACCCCAGGATAGCATGCAT 59.597 55.000 21.98 11.35 0.00 3.96
815 834 0.987613 TGACCCCAGGATAGCATGCA 60.988 55.000 21.98 6.36 0.00 3.96
816 835 0.536006 GTGACCCCAGGATAGCATGC 60.536 60.000 10.51 10.51 0.00 4.06
817 836 0.250038 CGTGACCCCAGGATAGCATG 60.250 60.000 0.00 0.00 0.00 4.06
818 837 0.691078 ACGTGACCCCAGGATAGCAT 60.691 55.000 0.00 0.00 32.83 3.79
819 838 0.032912 TACGTGACCCCAGGATAGCA 60.033 55.000 0.00 0.00 32.83 3.49
820 839 0.388294 GTACGTGACCCCAGGATAGC 59.612 60.000 0.00 0.00 32.83 2.97
821 840 0.666913 CGTACGTGACCCCAGGATAG 59.333 60.000 7.22 0.00 32.83 2.08
822 841 0.752743 CCGTACGTGACCCCAGGATA 60.753 60.000 15.21 0.00 32.83 2.59
823 842 2.056223 CCGTACGTGACCCCAGGAT 61.056 63.158 15.21 0.00 32.83 3.24
856 875 3.238497 CGGGTGGTGGACTGGTGA 61.238 66.667 0.00 0.00 0.00 4.02
863 882 1.306654 AGGATAAGCGGGTGGTGGA 60.307 57.895 0.00 0.00 0.00 4.02
967 986 2.417787 GGTTCTTGTCTTATACGCGGGT 60.418 50.000 12.47 10.91 0.00 5.28
984 1018 3.306294 CCTCCATTTTGCTTCTTGGGTTC 60.306 47.826 0.00 0.00 0.00 3.62
985 1019 2.634453 CCTCCATTTTGCTTCTTGGGTT 59.366 45.455 0.00 0.00 0.00 4.11
986 1020 2.250924 CCTCCATTTTGCTTCTTGGGT 58.749 47.619 0.00 0.00 0.00 4.51
987 1021 2.028748 CACCTCCATTTTGCTTCTTGGG 60.029 50.000 0.00 0.00 0.00 4.12
988 1022 2.028748 CCACCTCCATTTTGCTTCTTGG 60.029 50.000 0.00 0.00 0.00 3.61
989 1023 2.611224 GCCACCTCCATTTTGCTTCTTG 60.611 50.000 0.00 0.00 0.00 3.02
990 1024 1.620323 GCCACCTCCATTTTGCTTCTT 59.380 47.619 0.00 0.00 0.00 2.52
991 1025 1.260544 GCCACCTCCATTTTGCTTCT 58.739 50.000 0.00 0.00 0.00 2.85
992 1026 0.247460 GGCCACCTCCATTTTGCTTC 59.753 55.000 0.00 0.00 0.00 3.86
993 1027 1.535204 CGGCCACCTCCATTTTGCTT 61.535 55.000 2.24 0.00 0.00 3.91
994 1028 1.978617 CGGCCACCTCCATTTTGCT 60.979 57.895 2.24 0.00 0.00 3.91
995 1029 2.573340 CGGCCACCTCCATTTTGC 59.427 61.111 2.24 0.00 0.00 3.68
996 1030 3.005540 GCCGGCCACCTCCATTTTG 62.006 63.158 18.11 0.00 0.00 2.44
997 1031 2.679996 GCCGGCCACCTCCATTTT 60.680 61.111 18.11 0.00 0.00 1.82
1053 1087 2.604686 ACGAGCAGGAGGAGGCAA 60.605 61.111 0.00 0.00 0.00 4.52
1181 1215 3.399181 TGGCGGCGGAGGAGAAAT 61.399 61.111 9.78 0.00 0.00 2.17
1182 1216 4.388499 GTGGCGGCGGAGGAGAAA 62.388 66.667 9.78 0.00 0.00 2.52
1489 1523 1.830633 GACGTAGATTTCGTCGTCGTG 59.169 52.381 1.33 0.00 45.64 4.35
1533 1567 0.547553 AGTAGGACGAGGAGGAGGAC 59.452 60.000 0.00 0.00 0.00 3.85
1534 1568 0.838608 GAGTAGGACGAGGAGGAGGA 59.161 60.000 0.00 0.00 0.00 3.71
1583 1617 2.256174 CATTGATCGTTTGCTGGCTTG 58.744 47.619 0.00 0.00 0.00 4.01
1588 1622 0.523968 CCCGCATTGATCGTTTGCTG 60.524 55.000 11.16 5.99 34.23 4.41
1641 1680 0.249953 TGCCTCTCGCGTGGTAAAAA 60.250 50.000 5.77 0.00 42.08 1.94
1730 1773 5.215160 CAATGCTTTTTCGCCCTATACATC 58.785 41.667 0.00 0.00 0.00 3.06
1731 1774 4.499696 GCAATGCTTTTTCGCCCTATACAT 60.500 41.667 0.00 0.00 0.00 2.29
1732 1775 3.181491 GCAATGCTTTTTCGCCCTATACA 60.181 43.478 0.00 0.00 0.00 2.29
1733 1776 3.181491 TGCAATGCTTTTTCGCCCTATAC 60.181 43.478 6.82 0.00 0.00 1.47
1734 1777 3.020274 TGCAATGCTTTTTCGCCCTATA 58.980 40.909 6.82 0.00 0.00 1.31
1735 1778 1.824230 TGCAATGCTTTTTCGCCCTAT 59.176 42.857 6.82 0.00 0.00 2.57
1736 1779 1.202114 CTGCAATGCTTTTTCGCCCTA 59.798 47.619 6.82 0.00 0.00 3.53
1737 1780 0.037975 CTGCAATGCTTTTTCGCCCT 60.038 50.000 6.82 0.00 0.00 5.19
1738 1781 0.038343 TCTGCAATGCTTTTTCGCCC 60.038 50.000 6.82 0.00 0.00 6.13
1739 1782 1.068333 TCTCTGCAATGCTTTTTCGCC 60.068 47.619 6.82 0.00 0.00 5.54
1740 1783 1.981533 GTCTCTGCAATGCTTTTTCGC 59.018 47.619 6.82 0.00 0.00 4.70
1741 1784 2.589014 GGTCTCTGCAATGCTTTTTCG 58.411 47.619 6.82 0.00 0.00 3.46
1742 1785 2.226437 TCGGTCTCTGCAATGCTTTTTC 59.774 45.455 6.82 0.00 0.00 2.29
1743 1786 2.227388 CTCGGTCTCTGCAATGCTTTTT 59.773 45.455 6.82 0.00 0.00 1.94
1744 1787 1.808945 CTCGGTCTCTGCAATGCTTTT 59.191 47.619 6.82 0.00 0.00 2.27
1745 1788 1.446907 CTCGGTCTCTGCAATGCTTT 58.553 50.000 6.82 0.00 0.00 3.51
1746 1789 1.023513 GCTCGGTCTCTGCAATGCTT 61.024 55.000 6.82 0.00 0.00 3.91
1747 1790 1.449246 GCTCGGTCTCTGCAATGCT 60.449 57.895 6.82 0.00 0.00 3.79
1748 1791 1.427592 GAGCTCGGTCTCTGCAATGC 61.428 60.000 0.00 0.00 0.00 3.56
1749 1792 0.809241 GGAGCTCGGTCTCTGCAATG 60.809 60.000 7.83 0.00 33.70 2.82
1750 1793 1.260538 TGGAGCTCGGTCTCTGCAAT 61.261 55.000 7.83 0.00 33.70 3.56
1751 1794 1.908299 TGGAGCTCGGTCTCTGCAA 60.908 57.895 7.83 0.00 33.70 4.08
1752 1795 2.283173 TGGAGCTCGGTCTCTGCA 60.283 61.111 7.83 0.00 33.70 4.41
1753 1796 1.954362 ATGTGGAGCTCGGTCTCTGC 61.954 60.000 7.83 0.00 33.70 4.26
1754 1797 1.336440 CTATGTGGAGCTCGGTCTCTG 59.664 57.143 7.83 0.00 33.70 3.35
1755 1798 1.686355 CTATGTGGAGCTCGGTCTCT 58.314 55.000 7.83 0.00 33.70 3.10
1756 1799 0.031449 GCTATGTGGAGCTCGGTCTC 59.969 60.000 7.83 0.00 39.50 3.36
1757 1800 2.119886 GCTATGTGGAGCTCGGTCT 58.880 57.895 7.83 0.00 39.50 3.85
1758 1801 4.740235 GCTATGTGGAGCTCGGTC 57.260 61.111 7.83 1.06 39.50 4.79
1784 1827 9.737427 TGTGAAAATAGTATTTTCGCTGAAAAA 57.263 25.926 37.29 25.04 43.32 1.94
1785 1828 9.176181 GTGTGAAAATAGTATTTTCGCTGAAAA 57.824 29.630 37.29 25.51 44.63 2.29
1786 1829 8.346300 TGTGTGAAAATAGTATTTTCGCTGAAA 58.654 29.630 37.29 25.75 44.63 2.69
1787 1830 7.866729 TGTGTGAAAATAGTATTTTCGCTGAA 58.133 30.769 37.29 27.55 44.63 3.02
1788 1831 7.428282 TGTGTGAAAATAGTATTTTCGCTGA 57.572 32.000 37.29 28.27 44.63 4.26
1789 1832 8.673626 AATGTGTGAAAATAGTATTTTCGCTG 57.326 30.769 37.29 0.00 44.63 5.18
1975 2018 5.457148 CAGTTATTTGCGTGCTACACAAAAA 59.543 36.000 6.57 0.00 34.36 1.94
1976 2019 4.973051 CAGTTATTTGCGTGCTACACAAAA 59.027 37.500 6.57 0.00 34.36 2.44
1977 2020 4.273724 TCAGTTATTTGCGTGCTACACAAA 59.726 37.500 0.00 5.40 35.04 2.83
1978 2021 3.810386 TCAGTTATTTGCGTGCTACACAA 59.190 39.130 0.00 0.00 33.40 3.33
1979 2022 3.394719 TCAGTTATTTGCGTGCTACACA 58.605 40.909 0.00 0.00 33.40 3.72
1980 2023 4.398549 TTCAGTTATTTGCGTGCTACAC 57.601 40.909 0.00 0.00 0.00 2.90
1981 2024 5.621197 AATTCAGTTATTTGCGTGCTACA 57.379 34.783 0.00 0.00 0.00 2.74
1982 2025 6.539324 TGTAATTCAGTTATTTGCGTGCTAC 58.461 36.000 0.00 0.00 0.00 3.58
1983 2026 6.729391 TGTAATTCAGTTATTTGCGTGCTA 57.271 33.333 0.00 0.00 0.00 3.49
1984 2027 5.621197 TGTAATTCAGTTATTTGCGTGCT 57.379 34.783 0.00 0.00 0.00 4.40
1985 2028 6.027131 TCATGTAATTCAGTTATTTGCGTGC 58.973 36.000 0.00 0.00 0.00 5.34
1986 2029 7.909641 TCATCATGTAATTCAGTTATTTGCGTG 59.090 33.333 0.00 0.00 0.00 5.34
1987 2030 7.984391 TCATCATGTAATTCAGTTATTTGCGT 58.016 30.769 0.00 0.00 0.00 5.24
1988 2031 8.839947 TTCATCATGTAATTCAGTTATTTGCG 57.160 30.769 0.00 0.00 0.00 4.85
2004 2047 9.349713 TCAAGTAGGTAAAAAGTTTCATCATGT 57.650 29.630 0.00 0.00 0.00 3.21
2005 2048 9.612620 GTCAAGTAGGTAAAAAGTTTCATCATG 57.387 33.333 0.00 0.00 0.00 3.07
2006 2049 9.349713 TGTCAAGTAGGTAAAAAGTTTCATCAT 57.650 29.630 0.00 0.00 0.00 2.45
2007 2050 8.740123 TGTCAAGTAGGTAAAAAGTTTCATCA 57.260 30.769 0.00 0.00 0.00 3.07
2009 2052 9.797556 GTTTGTCAAGTAGGTAAAAAGTTTCAT 57.202 29.630 0.00 0.00 0.00 2.57
2010 2053 8.794553 TGTTTGTCAAGTAGGTAAAAAGTTTCA 58.205 29.630 0.00 0.00 0.00 2.69
2011 2054 9.797556 ATGTTTGTCAAGTAGGTAAAAAGTTTC 57.202 29.630 0.00 0.00 0.00 2.78
2012 2055 9.581099 CATGTTTGTCAAGTAGGTAAAAAGTTT 57.419 29.630 0.00 0.00 0.00 2.66
2013 2056 7.704899 GCATGTTTGTCAAGTAGGTAAAAAGTT 59.295 33.333 0.00 0.00 0.00 2.66
2014 2057 7.147983 TGCATGTTTGTCAAGTAGGTAAAAAGT 60.148 33.333 0.00 0.00 0.00 2.66
2015 2058 7.199766 TGCATGTTTGTCAAGTAGGTAAAAAG 58.800 34.615 0.00 0.00 0.00 2.27
2016 2059 7.101652 TGCATGTTTGTCAAGTAGGTAAAAA 57.898 32.000 0.00 0.00 0.00 1.94
2017 2060 6.701145 TGCATGTTTGTCAAGTAGGTAAAA 57.299 33.333 0.00 0.00 0.00 1.52
2018 2061 6.892658 ATGCATGTTTGTCAAGTAGGTAAA 57.107 33.333 0.00 0.00 0.00 2.01
2019 2062 7.609918 ACATATGCATGTTTGTCAAGTAGGTAA 59.390 33.333 10.16 0.00 42.98 2.85
2020 2063 7.109501 ACATATGCATGTTTGTCAAGTAGGTA 58.890 34.615 10.16 0.00 42.98 3.08
2021 2064 5.945784 ACATATGCATGTTTGTCAAGTAGGT 59.054 36.000 10.16 0.00 42.98 3.08
2022 2065 6.441093 ACATATGCATGTTTGTCAAGTAGG 57.559 37.500 10.16 0.00 42.98 3.18
2024 2067 9.786105 CAAATACATATGCATGTTTGTCAAGTA 57.214 29.630 10.16 0.00 42.98 2.24
2025 2068 8.306038 ACAAATACATATGCATGTTTGTCAAGT 58.694 29.630 10.16 0.00 42.98 3.16
2026 2069 8.692110 ACAAATACATATGCATGTTTGTCAAG 57.308 30.769 10.16 4.88 42.98 3.02
2078 2121 3.802948 TTGAGCCCGTTTTGCTAAAAA 57.197 38.095 0.00 0.00 39.69 1.94
2079 2122 4.762765 TCTATTGAGCCCGTTTTGCTAAAA 59.237 37.500 0.00 0.00 39.69 1.52
2080 2123 4.328536 TCTATTGAGCCCGTTTTGCTAAA 58.671 39.130 0.00 0.00 39.69 1.85
2081 2124 3.938963 CTCTATTGAGCCCGTTTTGCTAA 59.061 43.478 0.00 0.00 39.69 3.09
2082 2125 3.531538 CTCTATTGAGCCCGTTTTGCTA 58.468 45.455 0.00 0.00 39.69 3.49
2083 2126 2.359900 CTCTATTGAGCCCGTTTTGCT 58.640 47.619 0.00 0.00 43.03 3.91
2084 2127 2.832672 CTCTATTGAGCCCGTTTTGC 57.167 50.000 0.00 0.00 33.12 3.68
2094 2137 1.369321 GAGGCCGGGCTCTATTGAG 59.631 63.158 42.01 0.00 42.96 3.02
2095 2138 3.550974 GAGGCCGGGCTCTATTGA 58.449 61.111 42.01 0.00 0.00 2.57
2114 2157 4.505217 CATCGAGTGCGGCGTTGC 62.505 66.667 9.37 0.00 38.28 4.17
2115 2158 1.145759 ATACATCGAGTGCGGCGTTG 61.146 55.000 9.37 0.00 38.28 4.10
2116 2159 0.382873 TATACATCGAGTGCGGCGTT 59.617 50.000 9.37 0.00 38.28 4.84
2117 2160 0.040336 CTATACATCGAGTGCGGCGT 60.040 55.000 9.37 0.00 38.28 5.68
2118 2161 0.729478 CCTATACATCGAGTGCGGCG 60.729 60.000 0.51 0.51 38.28 6.46
2119 2162 0.314302 ACCTATACATCGAGTGCGGC 59.686 55.000 0.00 0.00 38.28 6.53
2120 2163 1.930817 GCACCTATACATCGAGTGCGG 60.931 57.143 7.77 0.00 43.70 5.69
2121 2164 1.409412 GCACCTATACATCGAGTGCG 58.591 55.000 7.77 0.00 43.70 5.34
2123 2166 3.320626 CCATGCACCTATACATCGAGTG 58.679 50.000 0.00 0.00 0.00 3.51
2124 2167 2.289072 GCCATGCACCTATACATCGAGT 60.289 50.000 0.00 0.00 0.00 4.18
2125 2168 2.028658 AGCCATGCACCTATACATCGAG 60.029 50.000 0.00 0.00 0.00 4.04
2126 2169 1.970640 AGCCATGCACCTATACATCGA 59.029 47.619 0.00 0.00 0.00 3.59
2127 2170 2.071540 CAGCCATGCACCTATACATCG 58.928 52.381 0.00 0.00 0.00 3.84
2196 2239 6.294176 GCCATCGTTATCCATAAAAGCAATCT 60.294 38.462 0.00 0.00 0.00 2.40
2257 2300 8.971321 GTACAATTGAATCACAATATTGCCATC 58.029 33.333 15.48 9.24 46.90 3.51
2303 2347 8.660295 TGGATACTTTAACCTTCTAGAAGACA 57.340 34.615 30.17 13.79 37.90 3.41
2466 2513 1.940613 GTCTGGTCGATTATGGTTGGC 59.059 52.381 0.00 0.00 0.00 4.52
2533 2582 0.321298 TAGAGTTGGCAAGCCGGAAC 60.321 55.000 5.05 6.41 39.42 3.62
2534 2583 0.398696 TTAGAGTTGGCAAGCCGGAA 59.601 50.000 5.05 0.00 39.42 4.30
2535 2584 0.321298 GTTAGAGTTGGCAAGCCGGA 60.321 55.000 5.05 0.00 39.42 5.14
2558 2607 3.932710 TCTGTGTGATGTATTTCTTCCGC 59.067 43.478 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.