Multiple sequence alignment - TraesCS3A01G149400

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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 TraesCS3A01G149400 chr3A 100.000 3685 0 0 1 3685 134248561 134244877 0.000000e+00 6806.0
1 TraesCS3A01G149400 chr3A 88.103 622 50 16 1 610 493096592 493097201 0.000000e+00 717.0
2 TraesCS3A01G149400 chr3A 100.000 28 0 0 2800 2827 722354138 722354165 7.000000e-03 52.8
3 TraesCS3A01G149400 chr3D 94.015 1203 55 8 648 1843 125497764 125496572 0.000000e+00 1807.0
4 TraesCS3A01G149400 chr3D 94.259 871 34 10 1933 2790 125496478 125495611 0.000000e+00 1317.0
5 TraesCS3A01G149400 chr3D 88.455 615 52 13 1 604 603118624 603119230 0.000000e+00 725.0
6 TraesCS3A01G149400 chr3D 92.475 505 27 5 3186 3685 125494780 125494282 0.000000e+00 712.0
7 TraesCS3A01G149400 chr3D 96.386 83 3 0 2871 2953 125495463 125495381 1.780000e-28 137.0
8 TraesCS3A01G149400 chr3D 95.833 72 1 2 1863 1934 266414598 266414667 8.360000e-22 115.0
9 TraesCS3A01G149400 chr3B 89.040 1177 82 21 739 1887 179381291 179380134 0.000000e+00 1415.0
10 TraesCS3A01G149400 chr3B 89.605 1039 78 20 1933 2952 179380166 179379139 0.000000e+00 1293.0
11 TraesCS3A01G149400 chr3B 90.097 515 28 13 3188 3685 179378795 179378287 0.000000e+00 647.0
12 TraesCS3A01G149400 chr3B 94.872 78 4 0 3027 3104 179379076 179378999 5.000000e-24 122.0
13 TraesCS3A01G149400 chr7D 90.032 622 46 12 1 610 71634028 71634645 0.000000e+00 791.0
14 TraesCS3A01G149400 chr5A 89.320 618 53 9 1 610 12904520 12903908 0.000000e+00 763.0
15 TraesCS3A01G149400 chr5A 86.869 99 9 4 1848 1944 210835077 210835173 1.400000e-19 108.0
16 TraesCS3A01G149400 chr6D 88.350 618 55 11 4 608 22137545 22136932 0.000000e+00 726.0
17 TraesCS3A01G149400 chr6D 87.903 620 49 18 5 610 423361322 423361929 0.000000e+00 706.0
18 TraesCS3A01G149400 chr6A 87.884 619 61 14 5 615 58388325 58387713 0.000000e+00 715.0
19 TraesCS3A01G149400 chr2A 87.640 623 61 11 1 610 768684533 768685152 0.000000e+00 710.0
20 TraesCS3A01G149400 chr1A 87.599 629 57 13 1 615 549883925 549883304 0.000000e+00 710.0
21 TraesCS3A01G149400 chr1A 97.222 72 1 1 1875 1946 347637326 347637256 1.800000e-23 121.0
22 TraesCS3A01G149400 chr1A 89.888 89 3 5 1853 1937 565514123 565514037 3.890000e-20 110.0
23 TraesCS3A01G149400 chr1A 100.000 29 0 0 2800 2828 551134727 551134699 2.000000e-03 54.7
24 TraesCS3A01G149400 chr4A 95.946 74 2 1 1873 1946 499221136 499221064 6.460000e-23 119.0
25 TraesCS3A01G149400 chr4A 98.413 63 1 0 1875 1937 656541109 656541047 1.080000e-20 111.0
26 TraesCS3A01G149400 chr6B 95.890 73 2 1 1874 1946 109783043 109782972 2.330000e-22 117.0
27 TraesCS3A01G149400 chr6B 93.590 78 2 2 1860 1937 80810243 80810169 3.010000e-21 113.0
28 TraesCS3A01G149400 chr2B 94.667 75 3 1 1872 1946 191749233 191749306 8.360000e-22 115.0
29 TraesCS3A01G149400 chr4B 88.462 52 5 1 621 671 167342696 167342747 1.100000e-05 62.1


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 TraesCS3A01G149400 chr3A 134244877 134248561 3684 True 6806.00 6806 100.00000 1 3685 1 chr3A.!!$R1 3684
1 TraesCS3A01G149400 chr3A 493096592 493097201 609 False 717.00 717 88.10300 1 610 1 chr3A.!!$F1 609
2 TraesCS3A01G149400 chr3D 125494282 125497764 3482 True 993.25 1807 94.28375 648 3685 4 chr3D.!!$R1 3037
3 TraesCS3A01G149400 chr3D 603118624 603119230 606 False 725.00 725 88.45500 1 604 1 chr3D.!!$F2 603
4 TraesCS3A01G149400 chr3B 179378287 179381291 3004 True 869.25 1415 90.90350 739 3685 4 chr3B.!!$R1 2946
5 TraesCS3A01G149400 chr7D 71634028 71634645 617 False 791.00 791 90.03200 1 610 1 chr7D.!!$F1 609
6 TraesCS3A01G149400 chr5A 12903908 12904520 612 True 763.00 763 89.32000 1 610 1 chr5A.!!$R1 609
7 TraesCS3A01G149400 chr6D 22136932 22137545 613 True 726.00 726 88.35000 4 608 1 chr6D.!!$R1 604
8 TraesCS3A01G149400 chr6D 423361322 423361929 607 False 706.00 706 87.90300 5 610 1 chr6D.!!$F1 605
9 TraesCS3A01G149400 chr6A 58387713 58388325 612 True 715.00 715 87.88400 5 615 1 chr6A.!!$R1 610
10 TraesCS3A01G149400 chr2A 768684533 768685152 619 False 710.00 710 87.64000 1 610 1 chr2A.!!$F1 609
11 TraesCS3A01G149400 chr1A 549883304 549883925 621 True 710.00 710 87.59900 1 615 1 chr1A.!!$R2 614

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
641 695 0.037975 GTGAGCCAGTTGCCAAATGG 60.038 55.0 19.15 19.15 42.71 3.16 F
1926 2100 0.714180 TTGGGGTAGGCTAGAGGTGA 59.286 55.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2567 2748 0.167470 TGAACGATGACGACGAGGAC 59.833 55.0 0.00 0.0 42.66 3.85 R
3615 4293 0.029167 TCGTAACGCGTCACTTGTCA 59.971 50.0 14.44 0.0 42.13 3.58 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
343 364 1.609072 GCCTCTTGCGGAAGAAAAACT 59.391 47.619 20.33 0.00 37.77 2.66
344 365 2.812011 GCCTCTTGCGGAAGAAAAACTA 59.188 45.455 20.33 0.00 37.77 2.24
354 377 6.206634 TGCGGAAGAAAAACTATGACTTTCAT 59.793 34.615 0.00 0.00 40.72 2.57
433 468 4.771590 TCGAAAAGCTAAGTAAGACGGA 57.228 40.909 0.00 0.00 0.00 4.69
435 470 4.456911 TCGAAAAGCTAAGTAAGACGGAGA 59.543 41.667 0.00 0.00 0.00 3.71
448 484 3.211865 AGACGGAGAGAAAACCAAAACC 58.788 45.455 0.00 0.00 0.00 3.27
449 485 2.292569 GACGGAGAGAAAACCAAAACCC 59.707 50.000 0.00 0.00 0.00 4.11
450 486 2.303175 CGGAGAGAAAACCAAAACCCA 58.697 47.619 0.00 0.00 0.00 4.51
547 598 0.109086 CGTGACGAATGGCTGAGAGT 60.109 55.000 0.00 0.00 0.00 3.24
557 608 0.321671 GGCTGAGAGTGTGCCAAGTA 59.678 55.000 0.00 0.00 45.46 2.24
581 632 1.153549 GATCGTTGCGAGGCTTCCT 60.154 57.895 0.00 0.00 39.91 3.36
612 666 2.557924 TCGTTAACTAGTTGCTCCCGAA 59.442 45.455 18.56 0.00 0.00 4.30
615 669 4.143179 CGTTAACTAGTTGCTCCCGAAAAG 60.143 45.833 18.56 0.66 0.00 2.27
616 670 3.764237 AACTAGTTGCTCCCGAAAAGA 57.236 42.857 7.48 0.00 0.00 2.52
617 671 3.320673 ACTAGTTGCTCCCGAAAAGAG 57.679 47.619 0.00 0.00 0.00 2.85
618 672 2.028020 ACTAGTTGCTCCCGAAAAGAGG 60.028 50.000 0.00 0.00 0.00 3.69
624 678 4.397348 CCCGAAAAGAGGGGTGTG 57.603 61.111 0.00 0.00 45.14 3.82
625 679 1.758592 CCCGAAAAGAGGGGTGTGA 59.241 57.895 0.00 0.00 45.14 3.58
626 680 0.321653 CCCGAAAAGAGGGGTGTGAG 60.322 60.000 0.00 0.00 45.14 3.51
627 681 0.955919 CCGAAAAGAGGGGTGTGAGC 60.956 60.000 0.00 0.00 0.00 4.26
628 682 0.955919 CGAAAAGAGGGGTGTGAGCC 60.956 60.000 0.00 0.00 34.31 4.70
629 683 0.110486 GAAAAGAGGGGTGTGAGCCA 59.890 55.000 0.00 0.00 37.54 4.75
630 684 0.111253 AAAAGAGGGGTGTGAGCCAG 59.889 55.000 0.00 0.00 37.54 4.85
631 685 1.062488 AAAGAGGGGTGTGAGCCAGT 61.062 55.000 0.00 0.00 37.54 4.00
632 686 1.062488 AAGAGGGGTGTGAGCCAGTT 61.062 55.000 0.00 0.00 37.54 3.16
633 687 1.302832 GAGGGGTGTGAGCCAGTTG 60.303 63.158 0.00 0.00 37.54 3.16
634 688 2.985847 GGGGTGTGAGCCAGTTGC 60.986 66.667 0.00 0.00 37.54 4.17
635 689 2.985847 GGGTGTGAGCCAGTTGCC 60.986 66.667 0.00 0.00 42.71 4.52
636 690 2.203337 GGTGTGAGCCAGTTGCCA 60.203 61.111 0.00 0.00 42.71 4.92
637 691 1.827789 GGTGTGAGCCAGTTGCCAA 60.828 57.895 0.00 0.00 42.71 4.52
638 692 1.391157 GGTGTGAGCCAGTTGCCAAA 61.391 55.000 0.00 0.00 42.71 3.28
639 693 0.675633 GTGTGAGCCAGTTGCCAAAT 59.324 50.000 0.00 0.00 42.71 2.32
640 694 0.675083 TGTGAGCCAGTTGCCAAATG 59.325 50.000 0.00 0.00 42.71 2.32
641 695 0.037975 GTGAGCCAGTTGCCAAATGG 60.038 55.000 19.15 19.15 42.71 3.16
737 791 4.599047 TGTTTCTTGGGCCAGTTTAATG 57.401 40.909 6.23 0.00 0.00 1.90
785 839 1.479709 CCCAACTCACCACAACCAAA 58.520 50.000 0.00 0.00 0.00 3.28
787 841 1.202405 CCAACTCACCACAACCAAAGC 60.202 52.381 0.00 0.00 0.00 3.51
878 943 2.867855 AACGACGCTCAAGGCTCCA 61.868 57.895 0.00 0.00 39.13 3.86
1007 1072 2.503356 AGCTGGGTAAGAAGATGGTGAG 59.497 50.000 0.00 0.00 0.00 3.51
1207 1277 5.183713 TCATCAGTTCCTAATTTTGTGCTGG 59.816 40.000 0.00 0.00 0.00 4.85
1351 1421 7.482654 TGAGCTTTTCGGTAATTATCTCATG 57.517 36.000 0.00 0.00 0.00 3.07
1369 1441 2.499205 CTGCATCCTCGGGCGTTA 59.501 61.111 0.00 0.00 0.00 3.18
1387 1459 4.146443 GCGTTATGAACTGTTTTGTTCTGC 59.854 41.667 8.52 0.00 44.63 4.26
1396 1468 8.031864 TGAACTGTTTTGTTCTGCTTATTTCAA 58.968 29.630 8.52 0.00 44.63 2.69
1438 1519 4.152647 TGTGCCATAGCTGCTAGTATACT 58.847 43.478 15.41 10.87 40.80 2.12
1620 1701 9.462606 ACAGTAATATTACTCTTTCCCCAAAAG 57.537 33.333 22.60 10.92 41.82 2.27
1647 1729 5.247110 AGTGAAGTTCTTTCTGGAGCATCTA 59.753 40.000 4.17 0.00 36.71 1.98
1681 1771 3.753272 ACGCAGTTGAAAGCATTATGTCT 59.247 39.130 0.00 0.00 37.78 3.41
1682 1772 4.216257 ACGCAGTTGAAAGCATTATGTCTT 59.784 37.500 0.00 0.00 37.78 3.01
1683 1773 4.790140 CGCAGTTGAAAGCATTATGTCTTC 59.210 41.667 0.00 0.00 0.00 2.87
1684 1774 5.617529 CGCAGTTGAAAGCATTATGTCTTCA 60.618 40.000 6.90 6.90 0.00 3.02
1685 1775 6.151691 GCAGTTGAAAGCATTATGTCTTCAA 58.848 36.000 15.00 15.00 0.00 2.69
1686 1776 6.642131 GCAGTTGAAAGCATTATGTCTTCAAA 59.358 34.615 18.35 8.10 0.00 2.69
1687 1777 7.148853 GCAGTTGAAAGCATTATGTCTTCAAAG 60.149 37.037 18.35 15.76 0.00 2.77
1769 1860 3.125316 CACCCAGCGAAAAGAACTACATC 59.875 47.826 0.00 0.00 0.00 3.06
1786 1877 4.045636 ACATCCTCAAACAAAAGCACAC 57.954 40.909 0.00 0.00 0.00 3.82
1792 1883 4.268405 CCTCAAACAAAAGCACACATCAAC 59.732 41.667 0.00 0.00 0.00 3.18
1793 1884 5.070770 TCAAACAAAAGCACACATCAACT 57.929 34.783 0.00 0.00 0.00 3.16
1799 1890 4.734398 AAAGCACACATCAACTTTTCCA 57.266 36.364 0.00 0.00 0.00 3.53
1800 1891 4.734398 AAGCACACATCAACTTTTCCAA 57.266 36.364 0.00 0.00 0.00 3.53
1807 1898 6.254157 CACACATCAACTTTTCCAAAACAGAG 59.746 38.462 0.00 0.00 0.00 3.35
1857 2031 5.803020 AGCGAGCTGTTAAAAAGGATTAG 57.197 39.130 0.00 0.00 0.00 1.73
1885 2059 4.433186 GCATAGGCATACAACAACAACA 57.567 40.909 0.00 0.00 40.72 3.33
1886 2060 4.804108 GCATAGGCATACAACAACAACAA 58.196 39.130 0.00 0.00 40.72 2.83
1887 2061 5.226396 GCATAGGCATACAACAACAACAAA 58.774 37.500 0.00 0.00 40.72 2.83
1888 2062 5.345741 GCATAGGCATACAACAACAACAAAG 59.654 40.000 0.00 0.00 40.72 2.77
1889 2063 3.716601 AGGCATACAACAACAACAAAGC 58.283 40.909 0.00 0.00 0.00 3.51
1890 2064 2.799978 GGCATACAACAACAACAAAGCC 59.200 45.455 0.00 0.00 0.00 4.35
1891 2065 3.492482 GGCATACAACAACAACAAAGCCT 60.492 43.478 0.00 0.00 35.63 4.58
1892 2066 4.119136 GCATACAACAACAACAAAGCCTT 58.881 39.130 0.00 0.00 0.00 4.35
1893 2067 4.570369 GCATACAACAACAACAAAGCCTTT 59.430 37.500 0.00 0.00 0.00 3.11
1894 2068 5.751028 GCATACAACAACAACAAAGCCTTTA 59.249 36.000 0.00 0.00 0.00 1.85
1895 2069 6.074356 GCATACAACAACAACAAAGCCTTTAG 60.074 38.462 0.00 0.00 0.00 1.85
1896 2070 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
1897 2071 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
1898 2072 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
1899 2073 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
1900 2074 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
1901 2075 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
1902 2076 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
1903 2077 4.142026 ACAACAAAGCCTTTAGTCCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
1904 2078 3.637769 ACAAAGCCTTTAGTCCCAAACA 58.362 40.909 0.00 0.00 0.00 2.83
1905 2079 4.027437 ACAAAGCCTTTAGTCCCAAACAA 58.973 39.130 0.00 0.00 0.00 2.83
1906 2080 4.099419 ACAAAGCCTTTAGTCCCAAACAAG 59.901 41.667 0.00 0.00 0.00 3.16
1907 2081 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16
1908 2082 3.910989 AGCCTTTAGTCCCAAACAAGTT 58.089 40.909 0.00 0.00 0.00 2.66
1909 2083 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
1918 2092 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
1919 2093 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
1920 2094 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
1921 2095 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
1922 2096 2.188817 ACAAGTTGGGGTAGGCTAGAG 58.811 52.381 7.96 0.00 0.00 2.43
1923 2097 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.00 0.00 3.69
1924 2098 0.717196 AGTTGGGGTAGGCTAGAGGT 59.283 55.000 0.00 0.00 0.00 3.85
1925 2099 0.831307 GTTGGGGTAGGCTAGAGGTG 59.169 60.000 0.00 0.00 0.00 4.00
1926 2100 0.714180 TTGGGGTAGGCTAGAGGTGA 59.286 55.000 0.00 0.00 0.00 4.02
1927 2101 0.714180 TGGGGTAGGCTAGAGGTGAA 59.286 55.000 0.00 0.00 0.00 3.18
1928 2102 1.079825 TGGGGTAGGCTAGAGGTGAAA 59.920 52.381 0.00 0.00 0.00 2.69
1929 2103 1.485480 GGGGTAGGCTAGAGGTGAAAC 59.515 57.143 0.00 0.00 0.00 2.78
1944 2118 4.926860 GTGAAACCCATTAGCATTTTGC 57.073 40.909 0.00 0.00 45.46 3.68
1963 2137 3.971032 GCATAGGCATACAACAGAACC 57.029 47.619 0.00 0.00 40.72 3.62
1974 2148 7.319646 GCATACAACAGAACCATTTCCAATTA 58.680 34.615 0.00 0.00 31.28 1.40
2011 2188 8.622157 TGCTTACTCTTACACAGACTATATGTC 58.378 37.037 0.00 0.00 45.67 3.06
2241 2420 7.229306 TGACTTGAAACTTTGCACTATCTCAAT 59.771 33.333 0.00 0.00 0.00 2.57
2287 2466 2.823924 TTAAGAAGCAGCGTACACCA 57.176 45.000 0.00 0.00 0.00 4.17
2347 2526 9.448294 CAGAAAAGAGAACAAAAGAAGATTGAG 57.552 33.333 0.00 0.00 0.00 3.02
2363 2542 6.232581 AGATTGAGGAGGTATGTTTCTCAG 57.767 41.667 0.00 0.00 36.11 3.35
2415 2596 3.549471 GTGAGTGACGCATGATAACTCTG 59.451 47.826 13.43 0.00 38.44 3.35
2459 2640 9.337396 GGGATTTTTAGGAAACAAAACAAGAAT 57.663 29.630 0.00 0.00 0.00 2.40
2712 2893 3.696051 CACCTGCCTATTGTGCTTTGTAT 59.304 43.478 0.00 0.00 0.00 2.29
2713 2894 4.881273 CACCTGCCTATTGTGCTTTGTATA 59.119 41.667 0.00 0.00 0.00 1.47
2782 2963 5.200454 CCGTTTTTGCATCGAGATATCTTG 58.800 41.667 13.18 13.18 0.00 3.02
2792 2973 7.614192 TGCATCGAGATATCTTGGGTTATACTA 59.386 37.037 18.23 0.00 0.00 1.82
2793 2974 8.467598 GCATCGAGATATCTTGGGTTATACTAA 58.532 37.037 18.23 0.00 0.00 2.24
2821 3028 9.559732 TCAAAGACATTTATTTTGAGACAGAGA 57.440 29.630 0.00 0.00 36.28 3.10
2828 3035 9.868277 CATTTATTTTGAGACAGAGAGAGTACT 57.132 33.333 0.00 0.00 0.00 2.73
2876 3129 6.548251 TCGAAGTGACCATCCTATGTTACATA 59.452 38.462 4.89 4.89 0.00 2.29
2928 3181 6.725834 TCAGCTTCCCAGAATTCCTTTATTTT 59.274 34.615 0.65 0.00 0.00 1.82
2957 3210 1.146041 TGCTTGTGCACTTCGACCT 59.854 52.632 19.41 0.00 45.31 3.85
2958 3211 0.391228 TGCTTGTGCACTTCGACCTA 59.609 50.000 19.41 0.00 45.31 3.08
2959 3212 1.001974 TGCTTGTGCACTTCGACCTAT 59.998 47.619 19.41 0.00 45.31 2.57
2960 3213 1.661112 GCTTGTGCACTTCGACCTATC 59.339 52.381 19.41 0.00 39.41 2.08
2961 3214 2.930887 GCTTGTGCACTTCGACCTATCA 60.931 50.000 19.41 0.00 39.41 2.15
2962 3215 3.525537 CTTGTGCACTTCGACCTATCAT 58.474 45.455 19.41 0.00 0.00 2.45
2963 3216 3.165058 TGTGCACTTCGACCTATCATC 57.835 47.619 19.41 0.00 0.00 2.92
2964 3217 2.495669 TGTGCACTTCGACCTATCATCA 59.504 45.455 19.41 0.00 0.00 3.07
2965 3218 3.056179 TGTGCACTTCGACCTATCATCAA 60.056 43.478 19.41 0.00 0.00 2.57
2966 3219 3.932710 GTGCACTTCGACCTATCATCAAA 59.067 43.478 10.32 0.00 0.00 2.69
2967 3220 4.391830 GTGCACTTCGACCTATCATCAAAA 59.608 41.667 10.32 0.00 0.00 2.44
2968 3221 4.631377 TGCACTTCGACCTATCATCAAAAG 59.369 41.667 0.00 0.00 0.00 2.27
2969 3222 4.870426 GCACTTCGACCTATCATCAAAAGA 59.130 41.667 0.00 0.00 0.00 2.52
2970 3223 5.220491 GCACTTCGACCTATCATCAAAAGAC 60.220 44.000 0.00 0.00 0.00 3.01
2971 3224 5.869344 CACTTCGACCTATCATCAAAAGACA 59.131 40.000 0.00 0.00 0.00 3.41
2972 3225 6.536582 CACTTCGACCTATCATCAAAAGACAT 59.463 38.462 0.00 0.00 0.00 3.06
2973 3226 7.065085 CACTTCGACCTATCATCAAAAGACATT 59.935 37.037 0.00 0.00 0.00 2.71
2974 3227 8.258007 ACTTCGACCTATCATCAAAAGACATTA 58.742 33.333 0.00 0.00 0.00 1.90
2975 3228 9.098355 CTTCGACCTATCATCAAAAGACATTAA 57.902 33.333 0.00 0.00 0.00 1.40
2976 3229 9.613428 TTCGACCTATCATCAAAAGACATTAAT 57.387 29.630 0.00 0.00 0.00 1.40
2977 3230 9.613428 TCGACCTATCATCAAAAGACATTAATT 57.387 29.630 0.00 0.00 0.00 1.40
2990 3243 9.435688 AAAAGACATTAATTTATTTCCCTGTGC 57.564 29.630 0.00 0.00 0.00 4.57
2991 3244 7.961326 AGACATTAATTTATTTCCCTGTGCT 57.039 32.000 0.00 0.00 0.00 4.40
2992 3245 8.366359 AGACATTAATTTATTTCCCTGTGCTT 57.634 30.769 0.00 0.00 0.00 3.91
2993 3246 8.253113 AGACATTAATTTATTTCCCTGTGCTTG 58.747 33.333 0.00 0.00 0.00 4.01
2994 3247 7.906327 ACATTAATTTATTTCCCTGTGCTTGT 58.094 30.769 0.00 0.00 0.00 3.16
2995 3248 7.818930 ACATTAATTTATTTCCCTGTGCTTGTG 59.181 33.333 0.00 0.00 0.00 3.33
2996 3249 3.658757 TTTATTTCCCTGTGCTTGTGC 57.341 42.857 0.00 0.00 40.20 4.57
3013 3266 0.390340 TGCACTTCGACCTGATCAGC 60.390 55.000 17.76 3.70 0.00 4.26
3015 3268 1.638133 CACTTCGACCTGATCAGCAG 58.362 55.000 17.76 10.18 44.49 4.24
3088 3369 2.496899 AAAACCTGATCCTGCGATGT 57.503 45.000 0.00 0.00 0.00 3.06
3104 3646 4.051922 GCGATGTCAACTTCGGAGATAAT 58.948 43.478 16.88 0.00 41.82 1.28
3106 3648 5.690409 GCGATGTCAACTTCGGAGATAATAA 59.310 40.000 16.88 0.00 41.82 1.40
3107 3649 6.345882 GCGATGTCAACTTCGGAGATAATAAC 60.346 42.308 16.88 0.00 41.82 1.89
3108 3650 6.695713 CGATGTCAACTTCGGAGATAATAACA 59.304 38.462 0.00 0.00 39.09 2.41
3112 3729 6.817140 GTCAACTTCGGAGATAATAACAGGTT 59.183 38.462 0.00 0.00 35.04 3.50
3135 3752 0.693049 AGGAGCCAACAGTTACAGGG 59.307 55.000 0.00 0.00 0.00 4.45
3151 3768 1.067582 GGGCGGATCGTGTAAGGAG 59.932 63.158 0.00 0.00 32.39 3.69
3180 3797 6.899393 ATTTTAATTGTCTGTTGCCTCTGA 57.101 33.333 0.00 0.00 0.00 3.27
3181 3798 6.707440 TTTTAATTGTCTGTTGCCTCTGAA 57.293 33.333 0.00 0.00 0.00 3.02
3182 3799 5.947228 TTAATTGTCTGTTGCCTCTGAAG 57.053 39.130 0.00 0.00 0.00 3.02
3214 3881 5.562113 CGGTTTTTGAACCCATCACTCTAAC 60.562 44.000 2.94 0.00 39.68 2.34
3225 3892 3.081710 TCACTCTAACCCTGATCGTGA 57.918 47.619 0.00 0.00 0.00 4.35
3226 3893 3.632333 TCACTCTAACCCTGATCGTGAT 58.368 45.455 0.00 0.00 0.00 3.06
3227 3894 3.632604 TCACTCTAACCCTGATCGTGATC 59.367 47.826 2.86 2.86 38.29 2.92
3228 3895 2.619177 ACTCTAACCCTGATCGTGATCG 59.381 50.000 5.46 1.14 40.63 3.69
3229 3896 2.619177 CTCTAACCCTGATCGTGATCGT 59.381 50.000 5.46 0.00 40.63 3.73
3230 3897 2.357952 TCTAACCCTGATCGTGATCGTG 59.642 50.000 5.46 1.49 40.63 4.35
3272 3939 7.412346 GCAGAATCTCACAAATACACAGTACTG 60.412 40.741 21.44 21.44 0.00 2.74
3349 4024 8.556213 TTATTATTACACAGACACTCAAACCC 57.444 34.615 0.00 0.00 0.00 4.11
3391 4066 2.030363 TGCAATGTAAACCGGCTTTCAG 60.030 45.455 0.00 0.00 0.00 3.02
3441 4117 0.521735 GTCCGCTGTTGGTTTGATCC 59.478 55.000 0.00 0.00 0.00 3.36
3512 4190 4.552355 CATGTTTTCTGTGCATGATGTGT 58.448 39.130 0.00 0.00 41.62 3.72
3530 4208 5.398176 TGTGTTTGACAACTTCATACGAC 57.602 39.130 0.00 0.00 38.62 4.34
3533 4211 4.804665 TGTTTGACAACTTCATACGACGAA 59.195 37.500 0.00 0.00 38.62 3.85
3536 4214 4.361420 TGACAACTTCATACGACGAAACA 58.639 39.130 0.00 0.00 0.00 2.83
3548 4226 0.387565 ACGAAACAACAATGCCCACC 59.612 50.000 0.00 0.00 0.00 4.61
3615 4293 3.873910 CCGTTGATACCTTCATTCCTGT 58.126 45.455 0.00 0.00 33.34 4.00
3628 4306 0.874175 TTCCTGTGACAAGTGACGCG 60.874 55.000 3.53 3.53 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 196 0.737715 GCTTTCGCGAGAGTCATGGT 60.738 55.000 25.34 0.00 43.69 3.55
190 199 2.860735 GTTATGCTTTCGCGAGAGTCAT 59.139 45.455 26.73 26.73 43.69 3.06
208 217 2.144833 TTTCGCGAGAGGCACGGTTA 62.145 55.000 9.59 0.00 43.84 2.85
294 315 2.568956 TGCTTTAGTGAGAGTCATGGCT 59.431 45.455 0.00 0.00 0.00 4.75
425 459 4.818005 GGTTTTGGTTTTCTCTCCGTCTTA 59.182 41.667 0.00 0.00 0.00 2.10
464 501 1.201343 GCACGCGTTTTTGGCTTTTA 58.799 45.000 10.22 0.00 0.00 1.52
496 547 1.810755 GGACGCTTCCTTCGGATTTTT 59.189 47.619 1.07 0.00 39.13 1.94
532 583 0.671781 GCACACTCTCAGCCATTCGT 60.672 55.000 0.00 0.00 0.00 3.85
547 598 0.740868 GATCAGCGCTACTTGGCACA 60.741 55.000 10.99 0.00 0.00 4.57
581 632 3.012518 ACTAGTTAACGAGCGCTCCTTA 58.987 45.455 30.66 25.00 0.00 2.69
612 666 1.062488 ACTGGCTCACACCCCTCTTT 61.062 55.000 0.00 0.00 0.00 2.52
615 669 1.302832 CAACTGGCTCACACCCCTC 60.303 63.158 0.00 0.00 0.00 4.30
616 670 2.839098 CAACTGGCTCACACCCCT 59.161 61.111 0.00 0.00 0.00 4.79
617 671 2.985847 GCAACTGGCTCACACCCC 60.986 66.667 0.00 0.00 40.25 4.95
618 672 2.985847 GGCAACTGGCTCACACCC 60.986 66.667 0.00 0.00 44.01 4.61
619 673 1.391157 TTTGGCAACTGGCTCACACC 61.391 55.000 0.00 0.00 44.01 4.16
620 674 0.675633 ATTTGGCAACTGGCTCACAC 59.324 50.000 0.00 0.00 44.01 3.82
621 675 0.675083 CATTTGGCAACTGGCTCACA 59.325 50.000 9.52 0.00 44.01 3.58
622 676 0.037975 CCATTTGGCAACTGGCTCAC 60.038 55.000 21.64 0.00 44.01 3.51
623 677 2.353858 CCATTTGGCAACTGGCTCA 58.646 52.632 21.64 0.00 44.01 4.26
643 697 2.475200 GCCTTAAGCGCCAGTTATTG 57.525 50.000 2.29 0.00 0.00 1.90
671 725 1.542547 GGCCTCCTCTTCGTCAAAACA 60.543 52.381 0.00 0.00 0.00 2.83
737 791 3.308530 GCTTTGTTGTGGTTAGCATGTC 58.691 45.455 0.00 0.00 0.00 3.06
878 943 1.141053 GGTGGACAAAGCGGAGGATAT 59.859 52.381 0.00 0.00 0.00 1.63
989 1054 2.196595 CCCTCACCATCTTCTTACCCA 58.803 52.381 0.00 0.00 0.00 4.51
1168 1238 1.764723 TGATGATGGCTCGGAACAGAT 59.235 47.619 0.00 0.00 0.00 2.90
1207 1277 1.487142 GACCCCTAGAGGAGAAAAGGC 59.513 57.143 0.00 0.00 38.24 4.35
1351 1421 2.996168 ATAACGCCCGAGGATGCAGC 62.996 60.000 0.00 0.00 0.00 5.25
1396 1468 5.409214 GCACATGCTGAAATTTAAACCACAT 59.591 36.000 0.00 0.00 38.21 3.21
1438 1519 2.736721 GCACGAGCTGTTCTTTGACATA 59.263 45.455 0.00 0.00 37.91 2.29
1620 1701 3.500299 GCTCCAGAAAGAACTTCACTTCC 59.500 47.826 0.00 0.00 36.40 3.46
1647 1729 3.990092 TCAACTGCGTCTATGTTTCTGT 58.010 40.909 0.00 0.00 0.00 3.41
1685 1775 9.762381 TCCATATTATAGTTTGGGTTTGAACTT 57.238 29.630 5.16 0.00 37.32 2.66
1686 1776 9.762381 TTCCATATTATAGTTTGGGTTTGAACT 57.238 29.630 5.16 0.00 39.32 3.01
1687 1777 9.797556 GTTCCATATTATAGTTTGGGTTTGAAC 57.202 33.333 5.16 0.00 0.00 3.18
1749 1839 2.678336 GGATGTAGTTCTTTTCGCTGGG 59.322 50.000 0.00 0.00 0.00 4.45
1769 1860 4.044336 TGATGTGTGCTTTTGTTTGAGG 57.956 40.909 0.00 0.00 0.00 3.86
1786 1877 5.594926 AGCTCTGTTTTGGAAAAGTTGATG 58.405 37.500 0.00 0.00 0.00 3.07
1792 1883 3.885297 TCTGGAGCTCTGTTTTGGAAAAG 59.115 43.478 14.64 0.00 0.00 2.27
1793 1884 3.897239 TCTGGAGCTCTGTTTTGGAAAA 58.103 40.909 14.64 0.00 0.00 2.29
1799 1890 3.586618 AGGATCTTCTGGAGCTCTGTTTT 59.413 43.478 14.64 0.00 0.00 2.43
1800 1891 3.055240 CAGGATCTTCTGGAGCTCTGTTT 60.055 47.826 14.64 0.00 30.05 2.83
1807 1898 3.492482 GCTAAGACAGGATCTTCTGGAGC 60.492 52.174 4.31 7.18 44.99 4.70
1878 2052 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
1880 2054 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
1881 2055 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
1882 2056 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
1884 2058 4.099419 ACTTGTTTGGGACTAAAGGCTTTG 59.901 41.667 22.32 13.97 0.00 2.77
1885 2059 4.286707 ACTTGTTTGGGACTAAAGGCTTT 58.713 39.130 17.76 17.76 0.00 3.51
1886 2060 3.910989 ACTTGTTTGGGACTAAAGGCTT 58.089 40.909 0.00 0.00 0.00 4.35
1887 2061 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
1888 2062 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
1899 2073 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
1900 2074 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
1901 2075 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
1902 2076 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
1903 2077 1.486726 CCTCTAGCCTACCCCAACTTG 59.513 57.143 0.00 0.00 0.00 3.16
1904 2078 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.00 0.00 2.66
1905 2079 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.00 0.00 3.16
1906 2080 0.831307 CACCTCTAGCCTACCCCAAC 59.169 60.000 0.00 0.00 0.00 3.77
1907 2081 0.714180 TCACCTCTAGCCTACCCCAA 59.286 55.000 0.00 0.00 0.00 4.12
1908 2082 0.714180 TTCACCTCTAGCCTACCCCA 59.286 55.000 0.00 0.00 0.00 4.96
1909 2083 1.485480 GTTTCACCTCTAGCCTACCCC 59.515 57.143 0.00 0.00 0.00 4.95
1910 2084 1.485480 GGTTTCACCTCTAGCCTACCC 59.515 57.143 0.00 0.00 34.73 3.69
1911 2085 1.485480 GGGTTTCACCTCTAGCCTACC 59.515 57.143 0.00 0.00 38.64 3.18
1912 2086 2.185387 TGGGTTTCACCTCTAGCCTAC 58.815 52.381 0.00 0.00 38.64 3.18
1913 2087 2.634639 TGGGTTTCACCTCTAGCCTA 57.365 50.000 0.00 0.00 38.64 3.93
1914 2088 1.972588 ATGGGTTTCACCTCTAGCCT 58.027 50.000 0.00 0.00 38.64 4.58
1915 2089 2.808906 AATGGGTTTCACCTCTAGCC 57.191 50.000 0.00 0.00 38.64 3.93
1916 2090 3.206964 GCTAATGGGTTTCACCTCTAGC 58.793 50.000 0.00 0.00 38.64 3.42
1917 2091 4.487714 TGCTAATGGGTTTCACCTCTAG 57.512 45.455 0.00 0.00 38.64 2.43
1918 2092 5.450818 AATGCTAATGGGTTTCACCTCTA 57.549 39.130 0.00 0.00 38.64 2.43
1919 2093 4.322057 AATGCTAATGGGTTTCACCTCT 57.678 40.909 0.00 0.00 38.64 3.69
1920 2094 5.170748 CAAAATGCTAATGGGTTTCACCTC 58.829 41.667 0.00 0.00 38.64 3.85
1921 2095 4.563374 GCAAAATGCTAATGGGTTTCACCT 60.563 41.667 0.00 0.00 40.96 4.00
1922 2096 3.684305 GCAAAATGCTAATGGGTTTCACC 59.316 43.478 0.00 0.00 40.96 4.02
1923 2097 4.314121 TGCAAAATGCTAATGGGTTTCAC 58.686 39.130 3.78 0.00 45.31 3.18
1924 2098 4.613925 TGCAAAATGCTAATGGGTTTCA 57.386 36.364 3.78 0.00 45.31 2.69
1925 2099 5.754890 CCTATGCAAAATGCTAATGGGTTTC 59.245 40.000 3.78 0.00 45.31 2.78
1926 2100 5.673514 CCTATGCAAAATGCTAATGGGTTT 58.326 37.500 3.78 0.00 45.31 3.27
1927 2101 4.443315 GCCTATGCAAAATGCTAATGGGTT 60.443 41.667 3.78 0.00 45.31 4.11
1928 2102 3.070015 GCCTATGCAAAATGCTAATGGGT 59.930 43.478 3.78 0.00 45.31 4.51
1929 2103 3.069872 TGCCTATGCAAAATGCTAATGGG 59.930 43.478 3.78 2.79 46.66 4.00
1930 2104 4.325028 TGCCTATGCAAAATGCTAATGG 57.675 40.909 3.78 2.66 46.66 3.16
1943 2117 3.278574 TGGTTCTGTTGTATGCCTATGC 58.721 45.455 0.00 0.00 38.26 3.14
1944 2118 6.455360 AAATGGTTCTGTTGTATGCCTATG 57.545 37.500 0.00 0.00 0.00 2.23
1945 2119 5.594317 GGAAATGGTTCTGTTGTATGCCTAT 59.406 40.000 0.00 0.00 33.92 2.57
1946 2120 4.947388 GGAAATGGTTCTGTTGTATGCCTA 59.053 41.667 0.00 0.00 33.92 3.93
1947 2121 3.763897 GGAAATGGTTCTGTTGTATGCCT 59.236 43.478 0.00 0.00 33.92 4.75
1948 2122 3.509575 TGGAAATGGTTCTGTTGTATGCC 59.490 43.478 0.00 0.00 33.92 4.40
1949 2123 4.782019 TGGAAATGGTTCTGTTGTATGC 57.218 40.909 0.00 0.00 33.92 3.14
1950 2124 9.874205 AATAATTGGAAATGGTTCTGTTGTATG 57.126 29.630 0.00 0.00 33.92 2.39
1952 2126 9.921637 GAAATAATTGGAAATGGTTCTGTTGTA 57.078 29.630 0.00 0.00 33.92 2.41
1953 2127 8.428063 TGAAATAATTGGAAATGGTTCTGTTGT 58.572 29.630 0.00 0.00 33.92 3.32
1954 2128 8.830201 TGAAATAATTGGAAATGGTTCTGTTG 57.170 30.769 0.00 0.00 33.92 3.33
1955 2129 8.869109 TCTGAAATAATTGGAAATGGTTCTGTT 58.131 29.630 0.00 0.00 33.92 3.16
1956 2130 8.421249 TCTGAAATAATTGGAAATGGTTCTGT 57.579 30.769 0.00 0.00 33.92 3.41
1974 2148 9.066892 TGTGTAAGAGTAAGCAAAATCTGAAAT 57.933 29.630 0.00 0.00 0.00 2.17
2011 2188 7.308782 AGTCTGTTTAGTTGAAGAAACACTG 57.691 36.000 2.22 0.00 39.88 3.66
2241 2420 6.350110 GGCCTATTGCAGACAAATGAAAACTA 60.350 38.462 0.00 0.00 43.89 2.24
2287 2466 2.176364 AGCTGGGATTGCCACAGATAAT 59.824 45.455 0.00 0.00 35.63 1.28
2347 2526 6.532988 AGAGTAACTGAGAAACATACCTCC 57.467 41.667 0.00 0.00 0.00 4.30
2363 2542 5.121454 CAGAGCAAACCAGAATCAGAGTAAC 59.879 44.000 0.00 0.00 0.00 2.50
2415 2596 2.038557 TCCCAAGCAGTCTTTCCTGTAC 59.961 50.000 0.00 0.00 34.84 2.90
2459 2640 8.375506 TCTGGTCTAAGCTTCTCAAATTTCTTA 58.624 33.333 0.00 0.00 0.00 2.10
2564 2745 1.583967 CGATGACGACGAGGACTGC 60.584 63.158 0.00 0.00 42.66 4.40
2566 2747 0.447011 GAACGATGACGACGAGGACT 59.553 55.000 0.00 0.00 42.66 3.85
2567 2748 0.167470 TGAACGATGACGACGAGGAC 59.833 55.000 0.00 0.00 42.66 3.85
2712 2893 5.425217 TCTTCTTCCTGCATGTATCTTGGTA 59.575 40.000 0.00 0.00 0.00 3.25
2713 2894 4.225942 TCTTCTTCCTGCATGTATCTTGGT 59.774 41.667 0.00 0.00 0.00 3.67
2747 2928 2.446282 CAAAAACGGTTCAAGGTGTCG 58.554 47.619 0.00 0.00 0.00 4.35
2795 2976 9.559732 TCTCTGTCTCAAAATAAATGTCTTTGA 57.440 29.630 0.00 0.00 36.87 2.69
2797 2978 9.784531 TCTCTCTGTCTCAAAATAAATGTCTTT 57.215 29.630 0.00 0.00 0.00 2.52
2798 2979 9.434420 CTCTCTCTGTCTCAAAATAAATGTCTT 57.566 33.333 0.00 0.00 0.00 3.01
2799 2980 8.592809 ACTCTCTCTGTCTCAAAATAAATGTCT 58.407 33.333 0.00 0.00 0.00 3.41
2801 2982 9.646427 GTACTCTCTCTGTCTCAAAATAAATGT 57.354 33.333 0.00 0.00 0.00 2.71
2804 2985 9.698309 CAAGTACTCTCTCTGTCTCAAAATAAA 57.302 33.333 0.00 0.00 0.00 1.40
2805 2986 8.861086 ACAAGTACTCTCTCTGTCTCAAAATAA 58.139 33.333 0.00 0.00 0.00 1.40
2806 2987 8.410673 ACAAGTACTCTCTCTGTCTCAAAATA 57.589 34.615 0.00 0.00 0.00 1.40
2813 3020 9.391006 CTTAAGATACAAGTACTCTCTCTGTCT 57.609 37.037 0.00 0.00 0.00 3.41
2828 3035 9.392259 TCGACTGAGAGATTACTTAAGATACAA 57.608 33.333 10.09 0.00 0.00 2.41
2846 3053 1.821753 AGGATGGTCACTTCGACTGAG 59.178 52.381 0.00 0.00 44.70 3.35
2851 3058 4.707934 TGTAACATAGGATGGTCACTTCGA 59.292 41.667 0.00 0.00 33.60 3.71
2876 3129 2.494471 TCATCGGGTAACATCAGACGTT 59.506 45.455 0.00 0.00 39.74 3.99
2928 3181 1.529010 CACAAGCACCCCAGAAGCA 60.529 57.895 0.00 0.00 0.00 3.91
2964 3217 9.435688 GCACAGGGAAATAAATTAATGTCTTTT 57.564 29.630 0.00 0.00 0.00 2.27
2965 3218 8.815912 AGCACAGGGAAATAAATTAATGTCTTT 58.184 29.630 0.00 0.00 0.00 2.52
2966 3219 8.366359 AGCACAGGGAAATAAATTAATGTCTT 57.634 30.769 0.00 0.00 0.00 3.01
2967 3220 7.961326 AGCACAGGGAAATAAATTAATGTCT 57.039 32.000 0.00 0.00 0.00 3.41
2968 3221 8.034804 ACAAGCACAGGGAAATAAATTAATGTC 58.965 33.333 0.00 0.00 0.00 3.06
2969 3222 7.818930 CACAAGCACAGGGAAATAAATTAATGT 59.181 33.333 0.00 0.00 0.00 2.71
2970 3223 7.201548 GCACAAGCACAGGGAAATAAATTAATG 60.202 37.037 0.00 0.00 41.58 1.90
2971 3224 6.818142 GCACAAGCACAGGGAAATAAATTAAT 59.182 34.615 0.00 0.00 41.58 1.40
2972 3225 6.162777 GCACAAGCACAGGGAAATAAATTAA 58.837 36.000 0.00 0.00 41.58 1.40
2973 3226 5.719173 GCACAAGCACAGGGAAATAAATTA 58.281 37.500 0.00 0.00 41.58 1.40
2974 3227 4.568956 GCACAAGCACAGGGAAATAAATT 58.431 39.130 0.00 0.00 41.58 1.82
2975 3228 4.192429 GCACAAGCACAGGGAAATAAAT 57.808 40.909 0.00 0.00 41.58 1.40
2976 3229 3.658757 GCACAAGCACAGGGAAATAAA 57.341 42.857 0.00 0.00 41.58 1.40
2989 3242 0.880278 TCAGGTCGAAGTGCACAAGC 60.880 55.000 21.04 10.77 42.57 4.01
2990 3243 1.728971 GATCAGGTCGAAGTGCACAAG 59.271 52.381 21.04 9.73 0.00 3.16
2991 3244 1.069978 TGATCAGGTCGAAGTGCACAA 59.930 47.619 21.04 0.00 0.00 3.33
2992 3245 0.678950 TGATCAGGTCGAAGTGCACA 59.321 50.000 21.04 0.00 0.00 4.57
2993 3246 1.354040 CTGATCAGGTCGAAGTGCAC 58.646 55.000 15.38 9.40 0.00 4.57
2994 3247 0.390340 GCTGATCAGGTCGAAGTGCA 60.390 55.000 23.89 0.00 0.00 4.57
2995 3248 0.390340 TGCTGATCAGGTCGAAGTGC 60.390 55.000 23.89 7.79 0.00 4.40
2996 3249 1.203287 TCTGCTGATCAGGTCGAAGTG 59.797 52.381 23.89 0.00 43.06 3.16
2997 3250 1.550327 TCTGCTGATCAGGTCGAAGT 58.450 50.000 23.89 0.00 43.06 3.01
2998 3251 2.165234 TCTTCTGCTGATCAGGTCGAAG 59.835 50.000 23.89 20.06 43.06 3.79
3001 3254 1.203287 TGTCTTCTGCTGATCAGGTCG 59.797 52.381 23.89 0.00 43.06 4.79
3088 3369 6.540438 ACCTGTTATTATCTCCGAAGTTGA 57.460 37.500 0.00 0.00 0.00 3.18
3104 3646 4.794334 TGTTGGCTCCTTTAAACCTGTTA 58.206 39.130 0.00 0.00 0.00 2.41
3106 3648 3.222603 CTGTTGGCTCCTTTAAACCTGT 58.777 45.455 0.00 0.00 0.00 4.00
3107 3649 3.222603 ACTGTTGGCTCCTTTAAACCTG 58.777 45.455 0.00 0.00 0.00 4.00
3108 3650 3.595190 ACTGTTGGCTCCTTTAAACCT 57.405 42.857 0.00 0.00 0.00 3.50
3112 3729 4.394729 CCTGTAACTGTTGGCTCCTTTAA 58.605 43.478 2.69 0.00 0.00 1.52
3135 3752 0.739561 AGACTCCTTACACGATCCGC 59.260 55.000 0.00 0.00 0.00 5.54
3151 3768 9.129209 GAGGCAACAGACAATTAAAATTTAGAC 57.871 33.333 0.00 0.00 41.41 2.59
3166 3783 2.161211 GCAATCTTCAGAGGCAACAGAC 59.839 50.000 0.00 0.00 41.41 3.51
3180 3797 4.866921 GGTTCAAAAACCGTAGCAATCTT 58.133 39.130 0.00 0.00 45.33 2.40
3181 3798 4.499037 GGTTCAAAAACCGTAGCAATCT 57.501 40.909 0.00 0.00 45.33 2.40
3214 3881 0.873312 CAGCACGATCACGATCAGGG 60.873 60.000 7.75 3.01 42.66 4.45
3225 3892 2.680913 GGCGTTTGAGCAGCACGAT 61.681 57.895 7.16 0.00 39.27 3.73
3226 3893 2.428960 TAGGCGTTTGAGCAGCACGA 62.429 55.000 7.16 0.00 39.27 4.35
3227 3894 1.959899 CTAGGCGTTTGAGCAGCACG 61.960 60.000 0.00 0.00 39.27 5.34
3228 3895 1.790387 CTAGGCGTTTGAGCAGCAC 59.210 57.895 0.00 0.00 39.27 4.40
3229 3896 2.034879 GCTAGGCGTTTGAGCAGCA 61.035 57.895 0.00 0.00 36.53 4.41
3230 3897 2.034879 TGCTAGGCGTTTGAGCAGC 61.035 57.895 0.00 0.00 41.18 5.25
3272 3939 2.098443 TCGTTGCAAGAAGTTTTGGGTC 59.902 45.455 0.00 0.00 0.00 4.46
3349 4024 2.408565 TGCCTACCTTATCAGAAGGGG 58.591 52.381 2.40 0.00 41.71 4.79
3391 4066 3.093717 TCAAACGTGACTTCACTCTCC 57.906 47.619 7.74 0.00 44.34 3.71
3409 4084 0.324738 AGCGGACCTCCTTCTGATCA 60.325 55.000 0.00 0.00 0.00 2.92
3512 4190 5.291371 TGTTTCGTCGTATGAAGTTGTCAAA 59.709 36.000 0.00 0.00 40.50 2.69
3530 4208 0.662970 CGGTGGGCATTGTTGTTTCG 60.663 55.000 0.00 0.00 0.00 3.46
3533 4211 0.673437 CTTCGGTGGGCATTGTTGTT 59.327 50.000 0.00 0.00 0.00 2.83
3536 4214 4.095590 CCTTCGGTGGGCATTGTT 57.904 55.556 0.00 0.00 0.00 2.83
3578 4256 1.006805 CGGCCTATTCAGAGGAGCG 60.007 63.158 0.00 0.00 39.15 5.03
3581 4259 1.860641 TCAACGGCCTATTCAGAGGA 58.139 50.000 0.00 0.00 39.15 3.71
3584 4262 3.305720 AGGTATCAACGGCCTATTCAGA 58.694 45.455 0.00 0.00 0.00 3.27
3615 4293 0.029167 TCGTAACGCGTCACTTGTCA 59.971 50.000 14.44 0.00 42.13 3.58
3628 4306 6.043327 TGCAATGCATATAACACTCGTAAC 57.957 37.500 2.72 0.00 31.71 2.50


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

AutoCloner maintained by Alex Coulton.