Multiple sequence alignment - TraesCS5A01G098800

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 TraesCS5A01G098800 chr5A 100.000 6077 0 0 1 6077 140596505 140590429 0.000000e+00 11223.0
1 TraesCS5A01G098800 chr5A 97.521 242 5 1 1648 1888 140594619 140594378 4.380000e-111 412.0
2 TraesCS5A01G098800 chr5A 97.521 242 5 1 1887 2128 140594858 140594618 4.380000e-111 412.0
3 TraesCS5A01G098800 chr5A 87.255 102 12 1 2540 2641 140594131 140594031 1.380000e-21 115.0
4 TraesCS5A01G098800 chr5A 92.982 57 4 0 2484 2540 9843191 9843135 3.900000e-12 84.2
5 TraesCS5A01G098800 chr5B 97.197 3996 102 9 1884 5877 137994221 137998208 0.000000e+00 6750.0
6 TraesCS5A01G098800 chr5B 95.901 1488 40 9 415 1888 137992985 137994465 0.000000e+00 2390.0
7 TraesCS5A01G098800 chr5B 89.889 722 40 20 5360 6077 138000556 138001248 0.000000e+00 898.0
8 TraesCS5A01G098800 chr5B 90.717 474 20 8 1 463 137992444 137992904 1.450000e-170 610.0
9 TraesCS5A01G098800 chr5B 87.821 156 17 1 2280 2433 170586175 170586020 1.350000e-41 182.0
10 TraesCS5A01G098800 chr5B 91.228 57 5 0 2484 2540 12846961 12846905 1.820000e-10 78.7
11 TraesCS5A01G098800 chr5D 96.943 3958 106 8 1884 5834 125506648 125510597 0.000000e+00 6625.0
12 TraesCS5A01G098800 chr5D 96.416 1479 44 6 415 1888 125505418 125506892 0.000000e+00 2429.0
13 TraesCS5A01G098800 chr5D 92.160 574 35 8 5507 6077 125560236 125560802 0.000000e+00 802.0
14 TraesCS5A01G098800 chr5D 92.373 472 17 3 1 463 125504915 125505376 0.000000e+00 654.0
15 TraesCS5A01G098800 chr5D 95.732 164 7 0 5360 5523 125560060 125560223 1.300000e-66 265.0
16 TraesCS5A01G098800 chr5D 85.276 163 20 4 2275 2434 251307870 251307709 1.360000e-36 165.0
17 TraesCS5A01G098800 chr5D 85.294 102 12 2 2540 2641 125507139 125507237 1.080000e-17 102.0
18 TraesCS5A01G098800 chr5D 93.548 62 4 0 2540 2601 125808296 125808235 6.490000e-15 93.5
19 TraesCS5A01G098800 chr4D 90.000 180 14 1 726 905 64390635 64390460 4.740000e-56 230.0
20 TraesCS5A01G098800 chr4D 86.335 161 20 2 2276 2435 190482459 190482618 2.250000e-39 174.0
21 TraesCS5A01G098800 chr4D 82.353 85 12 3 2454 2538 121406497 121406578 3.040000e-08 71.3
22 TraesCS5A01G098800 chr4D 89.286 56 5 1 2463 2517 9438885 9438940 1.090000e-07 69.4
23 TraesCS5A01G098800 chr4B 90.751 173 12 1 729 901 406389457 406389289 1.700000e-55 228.0
24 TraesCS5A01G098800 chr2D 90.698 172 12 1 728 899 169037731 169037564 6.130000e-55 226.0
25 TraesCS5A01G098800 chr2D 89.888 178 13 2 720 896 299891725 299891552 2.200000e-54 224.0
26 TraesCS5A01G098800 chr2D 89.385 179 13 3 729 906 413879607 413879780 2.850000e-53 220.0
27 TraesCS5A01G098800 chr2D 87.261 157 19 1 2280 2435 256675284 256675128 1.740000e-40 178.0
28 TraesCS5A01G098800 chr2D 83.721 129 16 3 2279 2402 600978529 600978657 3.850000e-22 117.0
29 TraesCS5A01G098800 chr6D 88.830 188 14 4 718 904 438321724 438321905 2.200000e-54 224.0
30 TraesCS5A01G098800 chr6D 87.821 156 18 1 2280 2434 365846887 365847042 1.350000e-41 182.0
31 TraesCS5A01G098800 chr6D 96.721 61 2 0 2540 2600 365846982 365847042 1.080000e-17 102.0
32 TraesCS5A01G098800 chr2A 90.116 172 13 1 728 899 180983840 180984007 2.850000e-53 220.0
33 TraesCS5A01G098800 chr2A 87.261 157 18 2 2280 2435 252088383 252088538 1.740000e-40 178.0
34 TraesCS5A01G098800 chr2B 89.032 155 16 1 2280 2433 166470895 166470741 2.240000e-44 191.0
35 TraesCS5A01G098800 chr2B 87.898 157 18 1 2280 2435 288943719 288943563 3.740000e-42 183.0
36 TraesCS5A01G098800 chr2B 95.161 62 3 0 2540 2601 288943624 288943563 1.390000e-16 99.0
37 TraesCS5A01G098800 chr3B 88.312 154 18 0 2280 2433 71401859 71401706 1.040000e-42 185.0
38 TraesCS5A01G098800 chr3B 85.802 162 19 3 2276 2434 180277639 180277479 1.050000e-37 169.0
39 TraesCS5A01G098800 chr3B 96.721 61 2 0 2540 2600 694031519 694031459 1.080000e-17 102.0
40 TraesCS5A01G098800 chr3D 83.333 162 24 2 2276 2434 126219677 126219516 4.910000e-31 147.0
41 TraesCS5A01G098800 chr3D 82.143 84 12 3 2454 2537 156296001 156296081 1.090000e-07 69.4
42 TraesCS5A01G098800 chr4A 83.766 154 24 1 2282 2434 1518950 1518797 1.770000e-30 145.0
43 TraesCS5A01G098800 chr3A 85.965 114 16 0 2276 2389 135971581 135971468 8.270000e-24 122.0
44 TraesCS5A01G098800 chr3A 80.220 91 14 3 2443 2530 198175346 198175257 1.410000e-06 65.8
45 TraesCS5A01G098800 chr1B 95.161 62 3 0 2540 2601 217286372 217286311 1.390000e-16 99.0
46 TraesCS5A01G098800 chr1A 95.161 62 3 0 2540 2601 189713096 189713035 1.390000e-16 99.0
47 TraesCS5A01G098800 chr7D 93.548 62 4 0 2540 2601 236827479 236827540 6.490000e-15 93.5


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 TraesCS5A01G098800 chr5A 140590429 140596505 6076 True 3040.5 11223 95.57425 1 6077 4 chr5A.!!$R2 6076
1 TraesCS5A01G098800 chr5B 137992444 138001248 8804 False 2662.0 6750 93.42600 1 6077 4 chr5B.!!$F1 6076
2 TraesCS5A01G098800 chr5D 125504915 125510597 5682 False 2452.5 6625 92.75650 1 5834 4 chr5D.!!$F1 5833
3 TraesCS5A01G098800 chr5D 125560060 125560802 742 False 533.5 802 93.94600 5360 6077 2 chr5D.!!$F2 717

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
133 135 1.680314 CCCAGCCCTTCCTTTCTGC 60.680 63.158 0.00 0.0 0.00 4.26 F
169 172 1.937546 GCTTTCTGGATTGCCACCGG 61.938 60.000 0.00 0.0 39.92 5.28 F
1819 1974 2.107378 TCCCTTTGTACTGTTCCATGCA 59.893 45.455 0.00 0.0 0.00 3.96 F
1870 2025 0.526662 AACTCTGCGTTCTCCCTACG 59.473 55.000 0.00 0.0 41.71 3.51 F
3539 3694 0.178981 AAGCAGCTTGAAGGAGGCAA 60.179 50.000 6.93 0.0 0.00 4.52 F
3851 4006 1.964223 AGAAGAGTCGCAAGTCCTTGA 59.036 47.619 11.12 0.0 42.93 3.02 F
4500 4655 0.393537 CTGAAGCGAAGGCCCTTGAT 60.394 55.000 0.00 0.0 41.24 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1778 2.098117 GCTGACAATTCGAAATGGGAGG 59.902 50.000 17.14 5.93 0.00 4.30 R
1852 2007 2.181584 CGTAGGGAGAACGCAGAGT 58.818 57.895 0.00 0.00 33.04 3.24 R
3539 3694 1.004918 CGAACAGCTTCCTTCGGGT 60.005 57.895 9.21 0.00 36.46 5.28 R
3786 3941 3.304257 CCTTCATGTGCATAAGCGATTCC 60.304 47.826 0.00 0.00 46.23 3.01 R
4431 4586 0.804989 CTGATTGCAACCGTTCCTCC 59.195 55.000 0.00 0.00 0.00 4.30 R
5030 5185 1.194218 TCATGGAGAACTGCCATCGA 58.806 50.000 0.00 0.00 44.08 3.59 R
5975 9022 0.247460 TCAATCGTCAGTGAGGCAGG 59.753 55.000 7.98 0.36 0.00 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
67 68 3.159347 ATCGGACCGCCTAACCCC 61.159 66.667 9.66 0.00 0.00 4.95
68 69 3.988050 ATCGGACCGCCTAACCCCA 62.988 63.158 9.66 0.00 0.00 4.96
69 70 3.708544 CGGACCGCCTAACCCCAA 61.709 66.667 0.00 0.00 0.00 4.12
70 71 2.045634 GGACCGCCTAACCCCAAC 60.046 66.667 0.00 0.00 0.00 3.77
71 72 2.045634 GACCGCCTAACCCCAACC 60.046 66.667 0.00 0.00 0.00 3.77
72 73 3.633609 GACCGCCTAACCCCAACCC 62.634 68.421 0.00 0.00 0.00 4.11
73 74 4.435970 CCGCCTAACCCCAACCCC 62.436 72.222 0.00 0.00 0.00 4.95
74 75 3.653078 CGCCTAACCCCAACCCCA 61.653 66.667 0.00 0.00 0.00 4.96
75 76 2.855597 GCCTAACCCCAACCCCAA 59.144 61.111 0.00 0.00 0.00 4.12
82 83 2.123077 CCCAACCCCAACAAGCCA 60.123 61.111 0.00 0.00 0.00 4.75
133 135 1.680314 CCCAGCCCTTCCTTTCTGC 60.680 63.158 0.00 0.00 0.00 4.26
134 136 1.680314 CCAGCCCTTCCTTTCTGCC 60.680 63.158 0.00 0.00 0.00 4.85
169 172 1.937546 GCTTTCTGGATTGCCACCGG 61.938 60.000 0.00 0.00 39.92 5.28
201 204 2.158740 ACCTCTCTCTGCGCATCTACTA 60.159 50.000 12.24 0.00 0.00 1.82
281 284 8.960591 TGTCTGGATTGATTTCCTTATTTTCTC 58.039 33.333 0.00 0.00 36.68 2.87
282 285 8.409371 GTCTGGATTGATTTCCTTATTTTCTCC 58.591 37.037 0.00 0.00 36.68 3.71
355 358 3.424829 CCGTTGTGATGTGCTTATGTGAC 60.425 47.826 0.00 0.00 0.00 3.67
366 369 4.576463 GTGCTTATGTGACTATTCAAGGGG 59.424 45.833 0.00 0.00 31.90 4.79
452 595 6.211515 AGAATGAATTAGAAATGCGGAATGC 58.788 36.000 0.00 0.00 46.70 3.56
512 655 3.446873 CAGCAGGGCATTTTACCATGTTA 59.553 43.478 0.00 0.00 41.03 2.41
517 660 6.183360 GCAGGGCATTTTACCATGTTATTTTG 60.183 38.462 0.00 0.00 41.03 2.44
632 778 5.413833 ACGATCCCATGAATCTTCAATATGC 59.586 40.000 0.00 0.00 41.13 3.14
638 784 6.418819 CCCATGAATCTTCAATATGCGTTTTC 59.581 38.462 0.00 0.00 41.13 2.29
737 883 7.443302 TCAAATTGATCATTCTACTCCCTCT 57.557 36.000 0.00 0.00 0.00 3.69
766 912 8.865090 TCCTAAATATGAGTCTTTCTGGAGATC 58.135 37.037 0.00 0.00 0.00 2.75
797 943 5.730550 AGACTACATACGGAGCAAAATGAA 58.269 37.500 0.00 0.00 0.00 2.57
912 1065 9.160412 AGGGAGTAGTATATATTGCAGAAAGTT 57.840 33.333 0.00 0.00 0.00 2.66
930 1083 6.998673 AGAAAGTTGTGTACCATTAGCTTTCT 59.001 34.615 15.25 15.25 43.13 2.52
1312 1467 4.430407 TTTTGAAAAAGAAACGCATCGC 57.570 36.364 0.00 0.00 0.00 4.58
1335 1490 3.312421 GTGTTGTGAAAACTGCTAGCTCA 59.688 43.478 17.23 7.93 0.00 4.26
1465 1620 8.537728 TGAAATGTCTAATTATTTCCCATGCT 57.462 30.769 8.31 0.00 40.73 3.79
1623 1778 4.736896 GGTGACGGCGAGGGTGTC 62.737 72.222 16.62 0.00 0.00 3.67
1707 1862 9.632807 TGGATTGTTTTTAAATTTACATCCTCG 57.367 29.630 0.00 0.00 0.00 4.63
1708 1863 9.634163 GGATTGTTTTTAAATTTACATCCTCGT 57.366 29.630 0.00 0.00 0.00 4.18
1710 1865 9.974980 ATTGTTTTTAAATTTACATCCTCGTGT 57.025 25.926 0.00 0.00 36.13 4.49
1711 1866 9.804758 TTGTTTTTAAATTTACATCCTCGTGTT 57.195 25.926 0.00 0.00 33.62 3.32
1717 1872 9.661563 TTAAATTTACATCCTCGTGTTATGAGT 57.338 29.630 0.00 0.00 33.62 3.41
1718 1873 7.772332 AATTTACATCCTCGTGTTATGAGTC 57.228 36.000 4.62 0.00 33.62 3.36
1719 1874 6.525578 TTTACATCCTCGTGTTATGAGTCT 57.474 37.500 0.00 0.00 33.62 3.24
1720 1875 6.525578 TTACATCCTCGTGTTATGAGTCTT 57.474 37.500 0.00 0.00 33.62 3.01
1721 1876 7.634671 TTACATCCTCGTGTTATGAGTCTTA 57.365 36.000 0.00 0.00 33.62 2.10
1722 1877 6.525578 ACATCCTCGTGTTATGAGTCTTAA 57.474 37.500 0.00 0.00 29.27 1.85
1723 1878 6.565234 ACATCCTCGTGTTATGAGTCTTAAG 58.435 40.000 0.00 0.00 29.27 1.85
1724 1879 6.377429 ACATCCTCGTGTTATGAGTCTTAAGA 59.623 38.462 0.00 0.00 29.27 2.10
1725 1880 7.068839 ACATCCTCGTGTTATGAGTCTTAAGAT 59.931 37.037 8.75 0.00 29.27 2.40
1726 1881 6.796426 TCCTCGTGTTATGAGTCTTAAGATG 58.204 40.000 8.75 8.19 29.27 2.90
1727 1882 6.602009 TCCTCGTGTTATGAGTCTTAAGATGA 59.398 38.462 8.75 13.78 29.27 2.92
1728 1883 7.285629 TCCTCGTGTTATGAGTCTTAAGATGAT 59.714 37.037 8.75 4.04 29.27 2.45
1729 1884 7.593273 CCTCGTGTTATGAGTCTTAAGATGATC 59.407 40.741 8.75 8.19 29.27 2.92
1730 1885 7.426410 TCGTGTTATGAGTCTTAAGATGATCC 58.574 38.462 8.75 0.00 0.00 3.36
1731 1886 6.642950 CGTGTTATGAGTCTTAAGATGATCCC 59.357 42.308 8.75 0.00 0.00 3.85
1732 1887 7.470702 CGTGTTATGAGTCTTAAGATGATCCCT 60.471 40.741 8.75 0.00 0.00 4.20
1733 1888 8.861086 GTGTTATGAGTCTTAAGATGATCCCTA 58.139 37.037 8.75 0.94 0.00 3.53
1734 1889 9.607333 TGTTATGAGTCTTAAGATGATCCCTAT 57.393 33.333 8.75 1.38 0.00 2.57
1735 1890 9.868277 GTTATGAGTCTTAAGATGATCCCTATG 57.132 37.037 8.75 0.00 0.00 2.23
1736 1891 9.828691 TTATGAGTCTTAAGATGATCCCTATGA 57.171 33.333 8.75 0.00 0.00 2.15
1737 1892 8.733092 ATGAGTCTTAAGATGATCCCTATGAA 57.267 34.615 8.75 0.00 0.00 2.57
1738 1893 8.733092 TGAGTCTTAAGATGATCCCTATGAAT 57.267 34.615 8.75 0.00 0.00 2.57
1739 1894 9.163894 TGAGTCTTAAGATGATCCCTATGAATT 57.836 33.333 8.75 0.00 0.00 2.17
1740 1895 9.434420 GAGTCTTAAGATGATCCCTATGAATTG 57.566 37.037 8.75 0.00 0.00 2.32
1741 1896 8.943085 AGTCTTAAGATGATCCCTATGAATTGT 58.057 33.333 8.75 0.00 0.00 2.71
1747 1902 7.334090 AGATGATCCCTATGAATTGTAATCCG 58.666 38.462 0.00 0.00 0.00 4.18
1748 1903 6.433847 TGATCCCTATGAATTGTAATCCGT 57.566 37.500 0.00 0.00 0.00 4.69
1749 1904 6.230472 TGATCCCTATGAATTGTAATCCGTG 58.770 40.000 0.00 0.00 0.00 4.94
1750 1905 5.623956 TCCCTATGAATTGTAATCCGTGT 57.376 39.130 0.00 0.00 0.00 4.49
1751 1906 5.607477 TCCCTATGAATTGTAATCCGTGTC 58.393 41.667 0.00 0.00 0.00 3.67
1752 1907 5.129650 TCCCTATGAATTGTAATCCGTGTCA 59.870 40.000 0.00 0.00 0.00 3.58
1753 1908 5.997746 CCCTATGAATTGTAATCCGTGTCAT 59.002 40.000 0.00 0.00 0.00 3.06
1754 1909 6.073058 CCCTATGAATTGTAATCCGTGTCATG 60.073 42.308 0.00 0.00 0.00 3.07
1755 1910 6.483307 CCTATGAATTGTAATCCGTGTCATGT 59.517 38.462 0.00 0.00 0.00 3.21
1756 1911 6.757897 ATGAATTGTAATCCGTGTCATGTT 57.242 33.333 0.00 0.00 0.00 2.71
1757 1912 6.567687 TGAATTGTAATCCGTGTCATGTTT 57.432 33.333 0.00 0.00 0.00 2.83
1758 1913 6.976088 TGAATTGTAATCCGTGTCATGTTTT 58.024 32.000 0.00 0.00 0.00 2.43
1759 1914 7.429633 TGAATTGTAATCCGTGTCATGTTTTT 58.570 30.769 0.00 0.00 0.00 1.94
1760 1915 7.593273 TGAATTGTAATCCGTGTCATGTTTTTC 59.407 33.333 0.00 0.00 0.00 2.29
1761 1916 6.627395 TTGTAATCCGTGTCATGTTTTTCT 57.373 33.333 0.00 0.00 0.00 2.52
1762 1917 7.731882 TTGTAATCCGTGTCATGTTTTTCTA 57.268 32.000 0.00 0.00 0.00 2.10
1763 1918 7.915293 TGTAATCCGTGTCATGTTTTTCTAT 57.085 32.000 0.00 0.00 0.00 1.98
1764 1919 7.970384 TGTAATCCGTGTCATGTTTTTCTATC 58.030 34.615 0.00 0.00 0.00 2.08
1765 1920 7.822334 TGTAATCCGTGTCATGTTTTTCTATCT 59.178 33.333 0.00 0.00 0.00 1.98
1766 1921 9.309516 GTAATCCGTGTCATGTTTTTCTATCTA 57.690 33.333 0.00 0.00 0.00 1.98
1767 1922 8.425577 AATCCGTGTCATGTTTTTCTATCTAG 57.574 34.615 0.00 0.00 0.00 2.43
1768 1923 6.338146 TCCGTGTCATGTTTTTCTATCTAGG 58.662 40.000 0.00 0.00 0.00 3.02
1769 1924 5.006746 CCGTGTCATGTTTTTCTATCTAGGC 59.993 44.000 0.00 0.00 0.00 3.93
1770 1925 5.812642 CGTGTCATGTTTTTCTATCTAGGCT 59.187 40.000 0.00 0.00 0.00 4.58
1771 1926 6.978659 CGTGTCATGTTTTTCTATCTAGGCTA 59.021 38.462 0.00 0.00 0.00 3.93
1772 1927 7.043325 CGTGTCATGTTTTTCTATCTAGGCTAC 60.043 40.741 0.00 0.00 0.00 3.58
1773 1928 7.982354 GTGTCATGTTTTTCTATCTAGGCTACT 59.018 37.037 0.00 0.00 0.00 2.57
1774 1929 8.540388 TGTCATGTTTTTCTATCTAGGCTACTT 58.460 33.333 0.00 0.00 0.00 2.24
1792 1947 9.573133 AGGCTACTTAATTTTGATTGAAATTCG 57.427 29.630 0.00 0.00 39.32 3.34
1793 1948 9.353999 GGCTACTTAATTTTGATTGAAATTCGT 57.646 29.630 0.00 2.50 39.32 3.85
1801 1956 6.693315 TTTGATTGAAATTCGTAGGATCCC 57.307 37.500 8.55 0.00 0.00 3.85
1802 1957 5.630415 TGATTGAAATTCGTAGGATCCCT 57.370 39.130 8.55 0.00 37.71 4.20
1803 1958 6.001449 TGATTGAAATTCGTAGGATCCCTT 57.999 37.500 8.55 0.00 34.61 3.95
1804 1959 6.423182 TGATTGAAATTCGTAGGATCCCTTT 58.577 36.000 8.55 0.00 34.61 3.11
1805 1960 6.318648 TGATTGAAATTCGTAGGATCCCTTTG 59.681 38.462 8.55 0.00 34.61 2.77
1806 1961 5.174037 TGAAATTCGTAGGATCCCTTTGT 57.826 39.130 8.55 0.00 34.61 2.83
1807 1962 6.302535 TGAAATTCGTAGGATCCCTTTGTA 57.697 37.500 8.55 0.00 34.61 2.41
1808 1963 6.110707 TGAAATTCGTAGGATCCCTTTGTAC 58.889 40.000 8.55 2.97 34.61 2.90
1809 1964 5.952347 AATTCGTAGGATCCCTTTGTACT 57.048 39.130 8.55 0.00 34.61 2.73
1810 1965 4.730949 TTCGTAGGATCCCTTTGTACTG 57.269 45.455 8.55 1.56 34.61 2.74
1811 1966 3.705051 TCGTAGGATCCCTTTGTACTGT 58.295 45.455 8.55 0.00 34.61 3.55
1812 1967 4.091549 TCGTAGGATCCCTTTGTACTGTT 58.908 43.478 8.55 0.00 34.61 3.16
1813 1968 4.159135 TCGTAGGATCCCTTTGTACTGTTC 59.841 45.833 8.55 0.00 34.61 3.18
1814 1969 4.679905 CGTAGGATCCCTTTGTACTGTTCC 60.680 50.000 8.55 0.00 34.61 3.62
1815 1970 3.256704 AGGATCCCTTTGTACTGTTCCA 58.743 45.455 8.55 0.00 0.00 3.53
1816 1971 3.852578 AGGATCCCTTTGTACTGTTCCAT 59.147 43.478 8.55 0.00 0.00 3.41
1817 1972 3.947834 GGATCCCTTTGTACTGTTCCATG 59.052 47.826 0.00 0.00 0.00 3.66
1818 1973 2.790433 TCCCTTTGTACTGTTCCATGC 58.210 47.619 0.00 0.00 0.00 4.06
1819 1974 2.107378 TCCCTTTGTACTGTTCCATGCA 59.893 45.455 0.00 0.00 0.00 3.96
1820 1975 2.890311 CCCTTTGTACTGTTCCATGCAA 59.110 45.455 0.00 0.00 0.00 4.08
1821 1976 3.320541 CCCTTTGTACTGTTCCATGCAAA 59.679 43.478 0.00 0.00 0.00 3.68
1822 1977 4.202202 CCCTTTGTACTGTTCCATGCAAAA 60.202 41.667 0.00 0.00 0.00 2.44
1823 1978 5.355596 CCTTTGTACTGTTCCATGCAAAAA 58.644 37.500 0.00 0.00 0.00 1.94
1824 1979 5.990996 CCTTTGTACTGTTCCATGCAAAAAT 59.009 36.000 0.00 0.00 0.00 1.82
1825 1980 6.482973 CCTTTGTACTGTTCCATGCAAAAATT 59.517 34.615 0.00 0.00 0.00 1.82
1826 1981 7.307337 CCTTTGTACTGTTCCATGCAAAAATTC 60.307 37.037 0.00 0.00 0.00 2.17
1827 1982 5.537188 TGTACTGTTCCATGCAAAAATTCC 58.463 37.500 0.00 0.00 0.00 3.01
1828 1983 4.006780 ACTGTTCCATGCAAAAATTCCC 57.993 40.909 0.00 0.00 0.00 3.97
1829 1984 3.390639 ACTGTTCCATGCAAAAATTCCCA 59.609 39.130 0.00 0.00 0.00 4.37
1830 1985 4.041938 ACTGTTCCATGCAAAAATTCCCAT 59.958 37.500 0.00 0.00 0.00 4.00
1831 1986 4.983053 TGTTCCATGCAAAAATTCCCATT 58.017 34.783 0.00 0.00 0.00 3.16
1832 1987 5.002516 TGTTCCATGCAAAAATTCCCATTC 58.997 37.500 0.00 0.00 0.00 2.67
1833 1988 4.904895 TCCATGCAAAAATTCCCATTCA 57.095 36.364 0.00 0.00 0.00 2.57
1834 1989 5.438698 TCCATGCAAAAATTCCCATTCAT 57.561 34.783 0.00 0.00 0.00 2.57
1835 1990 6.556974 TCCATGCAAAAATTCCCATTCATA 57.443 33.333 0.00 0.00 0.00 2.15
1836 1991 6.347696 TCCATGCAAAAATTCCCATTCATAC 58.652 36.000 0.00 0.00 0.00 2.39
1837 1992 6.070366 TCCATGCAAAAATTCCCATTCATACA 60.070 34.615 0.00 0.00 0.00 2.29
1838 1993 6.598457 CCATGCAAAAATTCCCATTCATACAA 59.402 34.615 0.00 0.00 0.00 2.41
1839 1994 7.120873 CCATGCAAAAATTCCCATTCATACAAA 59.879 33.333 0.00 0.00 0.00 2.83
1840 1995 8.679100 CATGCAAAAATTCCCATTCATACAAAT 58.321 29.630 0.00 0.00 0.00 2.32
1841 1996 8.041829 TGCAAAAATTCCCATTCATACAAATG 57.958 30.769 0.00 0.00 36.57 2.32
1842 1997 7.664731 TGCAAAAATTCCCATTCATACAAATGT 59.335 29.630 0.00 0.00 35.31 2.71
1843 1998 8.177013 GCAAAAATTCCCATTCATACAAATGTC 58.823 33.333 0.00 0.00 35.31 3.06
1844 1999 9.439500 CAAAAATTCCCATTCATACAAATGTCT 57.561 29.630 0.00 0.00 35.31 3.41
1846 2001 9.439500 AAAATTCCCATTCATACAAATGTCTTG 57.561 29.630 0.00 0.00 35.31 3.02
1847 2002 7.722949 ATTCCCATTCATACAAATGTCTTGT 57.277 32.000 0.00 0.00 35.31 3.16
1848 2003 8.821686 ATTCCCATTCATACAAATGTCTTGTA 57.178 30.769 0.18 0.18 38.99 2.41
1849 2004 8.642935 TTCCCATTCATACAAATGTCTTGTAA 57.357 30.769 1.76 0.00 38.26 2.41
1850 2005 8.279970 TCCCATTCATACAAATGTCTTGTAAG 57.720 34.615 1.76 0.00 38.26 2.34
1851 2006 8.106462 TCCCATTCATACAAATGTCTTGTAAGA 58.894 33.333 1.76 0.78 38.26 2.10
1852 2007 8.739039 CCCATTCATACAAATGTCTTGTAAGAA 58.261 33.333 14.18 14.18 42.71 2.52
1853 2008 9.559958 CCATTCATACAAATGTCTTGTAAGAAC 57.440 33.333 14.13 0.00 41.93 3.01
1856 2011 9.778741 TTCATACAAATGTCTTGTAAGAACTCT 57.221 29.630 9.87 0.00 37.54 3.24
1857 2012 9.208022 TCATACAAATGTCTTGTAAGAACTCTG 57.792 33.333 1.76 0.00 38.26 3.35
1858 2013 6.305693 ACAAATGTCTTGTAAGAACTCTGC 57.694 37.500 0.00 0.00 36.68 4.26
1859 2014 5.050091 ACAAATGTCTTGTAAGAACTCTGCG 60.050 40.000 0.00 0.00 36.68 5.18
1860 2015 3.728076 TGTCTTGTAAGAACTCTGCGT 57.272 42.857 0.00 0.00 36.68 5.24
1861 2016 4.054780 TGTCTTGTAAGAACTCTGCGTT 57.945 40.909 0.00 0.00 36.68 4.84
1869 2024 2.281140 GAACTCTGCGTTCTCCCTAC 57.719 55.000 3.39 0.00 46.74 3.18
1870 2025 0.526662 AACTCTGCGTTCTCCCTACG 59.473 55.000 0.00 0.00 41.71 3.51
1871 2026 1.313812 ACTCTGCGTTCTCCCTACGG 61.314 60.000 0.00 0.00 39.31 4.02
1872 2027 1.303888 TCTGCGTTCTCCCTACGGT 60.304 57.895 0.00 0.00 39.31 4.83
1873 2028 1.153823 CTGCGTTCTCCCTACGGTG 60.154 63.158 0.00 0.00 39.31 4.94
1874 2029 1.874345 CTGCGTTCTCCCTACGGTGT 61.874 60.000 0.00 0.00 39.31 4.16
1875 2030 0.608856 TGCGTTCTCCCTACGGTGTA 60.609 55.000 0.00 0.00 39.31 2.90
1876 2031 0.743097 GCGTTCTCCCTACGGTGTAT 59.257 55.000 0.00 0.00 39.31 2.29
1877 2032 1.268948 GCGTTCTCCCTACGGTGTATC 60.269 57.143 0.00 0.00 39.31 2.24
1878 2033 2.019249 CGTTCTCCCTACGGTGTATCA 58.981 52.381 0.00 0.00 35.47 2.15
1879 2034 2.033049 CGTTCTCCCTACGGTGTATCAG 59.967 54.545 0.00 0.00 35.47 2.90
1880 2035 3.285484 GTTCTCCCTACGGTGTATCAGA 58.715 50.000 0.00 0.00 0.00 3.27
1881 2036 2.928334 TCTCCCTACGGTGTATCAGAC 58.072 52.381 0.00 0.00 0.00 3.51
1882 2037 2.240414 TCTCCCTACGGTGTATCAGACA 59.760 50.000 0.00 0.00 34.94 3.41
1896 2051 7.834881 TGTATCAGACACCCTTACCTTATAG 57.165 40.000 0.00 0.00 31.20 1.31
1897 2052 7.589081 TGTATCAGACACCCTTACCTTATAGA 58.411 38.462 0.00 0.00 31.20 1.98
1898 2053 8.063153 TGTATCAGACACCCTTACCTTATAGAA 58.937 37.037 0.00 0.00 31.20 2.10
1899 2054 7.989947 ATCAGACACCCTTACCTTATAGAAA 57.010 36.000 0.00 0.00 0.00 2.52
1900 2055 7.989947 TCAGACACCCTTACCTTATAGAAAT 57.010 36.000 0.00 0.00 0.00 2.17
1901 2056 9.670442 ATCAGACACCCTTACCTTATAGAAATA 57.330 33.333 0.00 0.00 0.00 1.40
1902 2057 9.496710 TCAGACACCCTTACCTTATAGAAATAA 57.503 33.333 0.00 0.00 0.00 1.40
1962 2117 6.137794 ACATCCTCGTGTTATGAGTCTTAG 57.862 41.667 0.00 0.00 29.27 2.18
1990 2145 6.660521 TGATCCCTATGAATTGTAATCCATGC 59.339 38.462 0.00 0.00 0.00 4.06
2046 2201 5.687166 TGTAATTCGTAGGATCCCTTTGT 57.313 39.130 8.55 0.00 34.61 2.83
2108 2263 3.129792 GAACTCTGCGTTCTCCCTG 57.870 57.895 3.39 0.00 46.74 4.45
2332 2487 4.440826 TGGGGTAAGCTACAGTTGAAAA 57.559 40.909 0.00 0.00 0.00 2.29
2368 2523 2.885135 TCAAGTCATGGTTCTGGCAT 57.115 45.000 0.00 0.00 0.00 4.40
2371 2526 3.008923 TCAAGTCATGGTTCTGGCATGTA 59.991 43.478 0.00 0.00 0.00 2.29
2524 2679 6.768381 GGTAAGCTAGAGTTGAAAGCCATAAT 59.232 38.462 0.00 0.00 36.92 1.28
2530 2685 9.883142 GCTAGAGTTGAAAGCCATAATATATCT 57.117 33.333 0.00 0.00 0.00 1.98
2612 2767 3.341823 GTCCTTCAGACTTGACATGCAT 58.658 45.455 0.00 0.00 42.69 3.96
2650 2805 1.494721 CATACCATACCCACCTTGCCT 59.505 52.381 0.00 0.00 0.00 4.75
2963 3118 5.237344 AGGCAGATAGTCGAACATAATTTGC 59.763 40.000 0.00 0.00 0.00 3.68
3077 3232 5.932303 TCTTTCCAGTTATTTCACCTCTTCG 59.068 40.000 0.00 0.00 0.00 3.79
3280 3435 8.871629 ATTATCCGAATATACTCTGACTCTGT 57.128 34.615 0.00 0.00 0.00 3.41
3539 3694 0.178981 AAGCAGCTTGAAGGAGGCAA 60.179 50.000 6.93 0.00 0.00 4.52
3772 3927 2.996621 GCTGCTCAACTTCGTAATGAGT 59.003 45.455 4.19 0.00 42.00 3.41
3786 3941 7.525688 TCGTAATGAGTCTAAAGCAATTCAG 57.474 36.000 0.00 0.00 0.00 3.02
3851 4006 1.964223 AGAAGAGTCGCAAGTCCTTGA 59.036 47.619 11.12 0.00 42.93 3.02
3898 4053 6.127647 TGCATATAAACAGGCTTTGGAAGAAG 60.128 38.462 0.00 0.00 0.00 2.85
4118 4273 3.470709 CTGAAGAGGAAAGCACACTTCA 58.529 45.455 0.00 0.00 42.59 3.02
4157 4312 3.495543 GCTGGAGTTAGCAGCTGC 58.504 61.111 31.53 31.53 43.17 5.25
4353 4508 2.158682 TGAGTCTAAAACTGCCCTGCAA 60.159 45.455 0.00 0.00 38.74 4.08
4500 4655 0.393537 CTGAAGCGAAGGCCCTTGAT 60.394 55.000 0.00 0.00 41.24 2.57
4512 4667 3.053395 AGGCCCTTGATCAGATTAAGCAA 60.053 43.478 9.07 0.00 0.00 3.91
4609 4764 6.038997 AGTTTGAATCTCTTAGCCGTAAGT 57.961 37.500 0.00 0.00 37.50 2.24
4677 4832 0.798776 CGCAAGTGGAAGCTGTTAGG 59.201 55.000 0.00 0.00 0.00 2.69
4893 5048 1.714899 AAGCACACGCAACCACACTC 61.715 55.000 0.00 0.00 42.27 3.51
4958 5113 2.449464 TGATGGGCATCAAAGGAACAG 58.551 47.619 0.00 0.00 44.14 3.16
5030 5185 4.591321 TTCATAAGAAGAAGGGCCATGT 57.409 40.909 6.18 0.00 0.00 3.21
5048 5203 1.293924 GTCGATGGCAGTTCTCCATG 58.706 55.000 0.00 0.00 43.90 3.66
5084 5239 8.447200 TGGGGAAAAATCTGTATGATATCATCA 58.553 33.333 21.42 16.68 44.55 3.07
5141 5296 7.724305 TCTAGTTCATGTTTCCACTTTGTAC 57.276 36.000 0.00 0.00 0.00 2.90
5156 5311 7.282224 TCCACTTTGTACAATATAGATGGTTGC 59.718 37.037 9.56 0.00 0.00 4.17
5168 5324 3.368248 AGATGGTTGCATGCCATACTTT 58.632 40.909 16.68 2.70 45.87 2.66
5266 5422 8.454570 TGTTTATTTTCTAACTCCTTTTCGGT 57.545 30.769 0.00 0.00 0.00 4.69
5561 5747 7.158021 TGGGTATTTCAAAACCATTTGTGATC 58.842 34.615 1.69 0.00 45.02 2.92
5605 5795 4.932200 TCAAAACCAATCCACAACAACAAC 59.068 37.500 0.00 0.00 0.00 3.32
5728 5918 9.430623 GCTTAGTTTTGGCTGGAAATAATTTTA 57.569 29.630 0.00 0.00 0.00 1.52
5751 5941 8.630054 TTACTATGTCCAGCACACTTATTTTT 57.370 30.769 0.00 0.00 38.04 1.94
5763 5953 9.593134 AGCACACTTATTTTTGTTTATTGTGAA 57.407 25.926 0.00 0.00 34.99 3.18
5890 8936 3.308688 CCAGTCCATGACCCATTTCTCTT 60.309 47.826 0.00 0.00 32.18 2.85
5896 8942 5.044624 TCCATGACCCATTTCTCTTCATCTT 60.045 40.000 0.00 0.00 0.00 2.40
5975 9022 2.158081 ACATCCTCCCTATCTCCCTTCC 60.158 54.545 0.00 0.00 0.00 3.46
5976 9023 0.868186 TCCTCCCTATCTCCCTTCCC 59.132 60.000 0.00 0.00 0.00 3.97
5979 9026 0.104934 TCCCTATCTCCCTTCCCTGC 60.105 60.000 0.00 0.00 0.00 4.85
6018 9065 1.072965 CTACCCAAGGCATCATCCTCC 59.927 57.143 0.00 0.00 34.82 4.30
6019 9066 0.625683 ACCCAAGGCATCATCCTCCT 60.626 55.000 0.00 0.00 34.82 3.69
6020 9067 0.110104 CCCAAGGCATCATCCTCCTC 59.890 60.000 0.00 0.00 34.82 3.71
6029 9076 0.687757 TCATCCTCCTCCTCCGGTTG 60.688 60.000 0.00 0.00 0.00 3.77
6034 9081 1.306141 TCCTCCTCCGGTTGCTGAT 60.306 57.895 0.00 0.00 0.00 2.90
6053 9100 4.915704 TGATGTCAACCAACGAGAAAAAC 58.084 39.130 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 2.506957 GGGTGGCTTGTTGGGGTTG 61.507 63.158 0.00 0.00 0.00 3.77
68 69 2.123033 GGGTGGCTTGTTGGGGTT 60.123 61.111 0.00 0.00 0.00 4.11
69 70 2.945178 CTTGGGTGGCTTGTTGGGGT 62.945 60.000 0.00 0.00 0.00 4.95
70 71 2.123077 TTGGGTGGCTTGTTGGGG 60.123 61.111 0.00 0.00 0.00 4.96
71 72 2.871253 GCTTGGGTGGCTTGTTGGG 61.871 63.158 0.00 0.00 0.00 4.12
72 73 2.736531 GCTTGGGTGGCTTGTTGG 59.263 61.111 0.00 0.00 0.00 3.77
73 74 2.736531 GGCTTGGGTGGCTTGTTG 59.263 61.111 0.00 0.00 0.00 3.33
74 75 2.524148 GGGCTTGGGTGGCTTGTT 60.524 61.111 0.00 0.00 0.00 2.83
75 76 4.621087 GGGGCTTGGGTGGCTTGT 62.621 66.667 0.00 0.00 0.00 3.16
169 172 2.250741 GAGAGAGGTGAGGCCCAAGC 62.251 65.000 0.00 0.00 38.26 4.01
201 204 0.034896 ATGTCAGGCCGAAACGAACT 59.965 50.000 0.00 0.00 0.00 3.01
229 232 2.247699 TCTAGGGCTTAGCAGGAACA 57.752 50.000 6.53 0.00 0.00 3.18
309 312 2.447244 AGCGTCTCTCAAAGGACAAG 57.553 50.000 0.00 0.00 33.19 3.16
355 358 2.700371 GCCCCAAAATCCCCTTGAATAG 59.300 50.000 0.00 0.00 0.00 1.73
401 404 0.190069 AAACCCTTCCAACCCCCTTC 59.810 55.000 0.00 0.00 0.00 3.46
402 405 0.105194 CAAACCCTTCCAACCCCCTT 60.105 55.000 0.00 0.00 0.00 3.95
403 406 1.546738 CAAACCCTTCCAACCCCCT 59.453 57.895 0.00 0.00 0.00 4.79
476 619 3.788937 CCCTGCTGCTCCAAAATTTATG 58.211 45.455 0.00 0.00 0.00 1.90
517 660 7.410728 GCATGCATGACACTGTAATTTTTGTAC 60.411 37.037 30.64 1.38 0.00 2.90
606 752 7.281774 GCATATTGAAGATTCATGGGATCGTAT 59.718 37.037 0.00 0.00 37.00 3.06
737 883 8.146053 TCCAGAAAGACTCATATTTAGGAACA 57.854 34.615 0.00 0.00 0.00 3.18
766 912 5.417894 TGCTCCGTATGTAGTCTATATTGGG 59.582 44.000 0.00 0.00 0.00 4.12
816 962 9.457436 ACATACGGATGTATACAGACATACATA 57.543 33.333 12.79 0.00 46.96 2.29
818 964 7.754851 ACATACGGATGTATACAGACATACA 57.245 36.000 12.79 0.00 44.77 2.29
819 965 8.944029 ACTACATACGGATGTATACAGACATAC 58.056 37.037 20.64 0.00 45.42 2.39
879 1032 6.377712 GCAATATATACTACTCCCTCCGTTCT 59.622 42.308 0.00 0.00 0.00 3.01
912 1065 4.393834 TGCAAGAAAGCTAATGGTACACA 58.606 39.130 0.00 0.00 36.77 3.72
930 1083 5.068987 AGGAGTTACAGAAAAGCATTTGCAA 59.931 36.000 5.20 0.00 45.16 4.08
1042 1195 7.348274 TCTTGTATCTATTTCTCCAACCTCCAT 59.652 37.037 0.00 0.00 0.00 3.41
1164 1317 3.053831 TGCAAAGTAACTACCTCTGCC 57.946 47.619 0.00 0.00 0.00 4.85
1312 1467 2.287915 AGCTAGCAGTTTTCACAACACG 59.712 45.455 18.83 0.00 0.00 4.49
1465 1620 7.011857 GGGTAAATTTCTCAACAACAAAATGCA 59.988 33.333 0.00 0.00 0.00 3.96
1623 1778 2.098117 GCTGACAATTCGAAATGGGAGG 59.902 50.000 17.14 5.93 0.00 4.30
1681 1836 9.632807 CGAGGATGTAAATTTAAAAACAATCCA 57.367 29.630 16.33 0.00 0.00 3.41
1682 1837 9.634163 ACGAGGATGTAAATTTAAAAACAATCC 57.366 29.630 0.00 6.39 0.00 3.01
1684 1839 9.974980 ACACGAGGATGTAAATTTAAAAACAAT 57.025 25.926 0.00 0.00 0.00 2.71
1685 1840 9.804758 AACACGAGGATGTAAATTTAAAAACAA 57.195 25.926 0.00 0.00 30.75 2.83
1691 1846 9.661563 ACTCATAACACGAGGATGTAAATTTAA 57.338 29.630 0.00 0.00 34.66 1.52
1692 1847 9.309516 GACTCATAACACGAGGATGTAAATTTA 57.690 33.333 0.00 0.00 34.66 1.40
1693 1848 8.041323 AGACTCATAACACGAGGATGTAAATTT 58.959 33.333 0.00 0.00 34.66 1.82
1694 1849 7.556844 AGACTCATAACACGAGGATGTAAATT 58.443 34.615 0.00 0.00 34.66 1.82
1695 1850 7.113658 AGACTCATAACACGAGGATGTAAAT 57.886 36.000 0.00 0.00 34.66 1.40
1696 1851 6.525578 AGACTCATAACACGAGGATGTAAA 57.474 37.500 0.00 0.00 34.66 2.01
1697 1852 6.525578 AAGACTCATAACACGAGGATGTAA 57.474 37.500 0.00 0.00 34.66 2.41
1698 1853 7.555195 TCTTAAGACTCATAACACGAGGATGTA 59.445 37.037 0.00 0.00 34.66 2.29
1699 1854 6.377429 TCTTAAGACTCATAACACGAGGATGT 59.623 38.462 0.00 0.00 34.66 3.06
1700 1855 6.796426 TCTTAAGACTCATAACACGAGGATG 58.204 40.000 0.00 0.00 34.66 3.51
1701 1856 7.285629 TCATCTTAAGACTCATAACACGAGGAT 59.714 37.037 7.48 0.00 34.66 3.24
1702 1857 6.602009 TCATCTTAAGACTCATAACACGAGGA 59.398 38.462 7.48 0.00 34.66 3.71
1703 1858 6.796426 TCATCTTAAGACTCATAACACGAGG 58.204 40.000 7.48 0.00 34.66 4.63
1704 1859 7.593273 GGATCATCTTAAGACTCATAACACGAG 59.407 40.741 7.48 0.00 36.53 4.18
1705 1860 7.426410 GGATCATCTTAAGACTCATAACACGA 58.574 38.462 7.48 0.00 0.00 4.35
1706 1861 6.642950 GGGATCATCTTAAGACTCATAACACG 59.357 42.308 7.48 0.00 0.00 4.49
1707 1862 7.731054 AGGGATCATCTTAAGACTCATAACAC 58.269 38.462 7.48 0.00 0.00 3.32
1708 1863 7.921041 AGGGATCATCTTAAGACTCATAACA 57.079 36.000 7.48 0.00 0.00 2.41
1709 1864 9.868277 CATAGGGATCATCTTAAGACTCATAAC 57.132 37.037 7.48 0.00 0.00 1.89
1710 1865 9.828691 TCATAGGGATCATCTTAAGACTCATAA 57.171 33.333 7.48 0.00 0.00 1.90
1711 1866 9.828691 TTCATAGGGATCATCTTAAGACTCATA 57.171 33.333 7.48 3.49 0.00 2.15
1712 1867 8.733092 TTCATAGGGATCATCTTAAGACTCAT 57.267 34.615 7.48 0.00 0.00 2.90
1713 1868 8.733092 ATTCATAGGGATCATCTTAAGACTCA 57.267 34.615 7.48 0.00 0.00 3.41
1714 1869 9.434420 CAATTCATAGGGATCATCTTAAGACTC 57.566 37.037 7.48 5.25 0.00 3.36
1715 1870 8.943085 ACAATTCATAGGGATCATCTTAAGACT 58.057 33.333 7.48 1.78 0.00 3.24
1721 1876 7.826252 CGGATTACAATTCATAGGGATCATCTT 59.174 37.037 0.00 0.00 0.00 2.40
1722 1877 7.038017 ACGGATTACAATTCATAGGGATCATCT 60.038 37.037 0.00 0.00 0.00 2.90
1723 1878 7.065085 CACGGATTACAATTCATAGGGATCATC 59.935 40.741 0.00 0.00 0.00 2.92
1724 1879 6.881065 CACGGATTACAATTCATAGGGATCAT 59.119 38.462 0.00 0.00 0.00 2.45
1725 1880 6.183361 ACACGGATTACAATTCATAGGGATCA 60.183 38.462 0.00 0.00 0.00 2.92
1726 1881 6.231211 ACACGGATTACAATTCATAGGGATC 58.769 40.000 0.00 0.00 0.00 3.36
1727 1882 6.183361 TGACACGGATTACAATTCATAGGGAT 60.183 38.462 0.00 0.00 0.00 3.85
1728 1883 5.129650 TGACACGGATTACAATTCATAGGGA 59.870 40.000 0.00 0.00 0.00 4.20
1729 1884 5.364778 TGACACGGATTACAATTCATAGGG 58.635 41.667 0.00 0.00 0.00 3.53
1730 1885 6.483307 ACATGACACGGATTACAATTCATAGG 59.517 38.462 0.00 0.00 0.00 2.57
1731 1886 7.482654 ACATGACACGGATTACAATTCATAG 57.517 36.000 0.00 0.00 0.00 2.23
1732 1887 7.857734 AACATGACACGGATTACAATTCATA 57.142 32.000 0.00 0.00 0.00 2.15
1733 1888 6.757897 AACATGACACGGATTACAATTCAT 57.242 33.333 0.00 0.00 0.00 2.57
1734 1889 6.567687 AAACATGACACGGATTACAATTCA 57.432 33.333 0.00 0.00 0.00 2.57
1735 1890 7.807907 AGAAAAACATGACACGGATTACAATTC 59.192 33.333 0.00 0.00 0.00 2.17
1736 1891 7.657336 AGAAAAACATGACACGGATTACAATT 58.343 30.769 0.00 0.00 0.00 2.32
1737 1892 7.214467 AGAAAAACATGACACGGATTACAAT 57.786 32.000 0.00 0.00 0.00 2.71
1738 1893 6.627395 AGAAAAACATGACACGGATTACAA 57.373 33.333 0.00 0.00 0.00 2.41
1739 1894 7.822334 AGATAGAAAAACATGACACGGATTACA 59.178 33.333 0.00 0.00 0.00 2.41
1740 1895 8.197988 AGATAGAAAAACATGACACGGATTAC 57.802 34.615 0.00 0.00 0.00 1.89
1741 1896 9.529325 CTAGATAGAAAAACATGACACGGATTA 57.471 33.333 0.00 0.00 0.00 1.75
1742 1897 7.495934 CCTAGATAGAAAAACATGACACGGATT 59.504 37.037 0.00 0.00 0.00 3.01
1743 1898 6.986817 CCTAGATAGAAAAACATGACACGGAT 59.013 38.462 0.00 0.00 0.00 4.18
1744 1899 6.338146 CCTAGATAGAAAAACATGACACGGA 58.662 40.000 0.00 0.00 0.00 4.69
1745 1900 5.006746 GCCTAGATAGAAAAACATGACACGG 59.993 44.000 0.00 0.00 0.00 4.94
1746 1901 5.812642 AGCCTAGATAGAAAAACATGACACG 59.187 40.000 0.00 0.00 0.00 4.49
1747 1902 7.982354 AGTAGCCTAGATAGAAAAACATGACAC 59.018 37.037 0.00 0.00 0.00 3.67
1748 1903 8.079211 AGTAGCCTAGATAGAAAAACATGACA 57.921 34.615 0.00 0.00 0.00 3.58
1749 1904 8.950208 AAGTAGCCTAGATAGAAAAACATGAC 57.050 34.615 0.00 0.00 0.00 3.06
1766 1921 9.573133 CGAATTTCAATCAAAATTAAGTAGCCT 57.427 29.630 0.00 0.00 38.59 4.58
1767 1922 9.353999 ACGAATTTCAATCAAAATTAAGTAGCC 57.646 29.630 0.00 0.00 38.59 3.93
1775 1930 8.197439 GGGATCCTACGAATTTCAATCAAAATT 58.803 33.333 12.58 0.00 40.60 1.82
1776 1931 7.561356 AGGGATCCTACGAATTTCAATCAAAAT 59.439 33.333 12.58 0.00 28.47 1.82
1777 1932 6.889722 AGGGATCCTACGAATTTCAATCAAAA 59.110 34.615 12.58 0.00 28.47 2.44
1778 1933 6.423182 AGGGATCCTACGAATTTCAATCAAA 58.577 36.000 12.58 0.00 28.47 2.69
1779 1934 6.001449 AGGGATCCTACGAATTTCAATCAA 57.999 37.500 12.58 0.00 28.47 2.57
1780 1935 5.630415 AGGGATCCTACGAATTTCAATCA 57.370 39.130 12.58 0.00 28.47 2.57
1781 1936 6.318900 ACAAAGGGATCCTACGAATTTCAATC 59.681 38.462 12.58 0.00 31.13 2.67
1782 1937 6.187682 ACAAAGGGATCCTACGAATTTCAAT 58.812 36.000 12.58 0.00 31.13 2.57
1783 1938 5.566469 ACAAAGGGATCCTACGAATTTCAA 58.434 37.500 12.58 0.00 31.13 2.69
1784 1939 5.174037 ACAAAGGGATCCTACGAATTTCA 57.826 39.130 12.58 0.00 31.13 2.69
1785 1940 6.258068 CAGTACAAAGGGATCCTACGAATTTC 59.742 42.308 12.58 0.00 31.13 2.17
1786 1941 6.113411 CAGTACAAAGGGATCCTACGAATTT 58.887 40.000 12.58 1.27 31.13 1.82
1787 1942 5.189145 ACAGTACAAAGGGATCCTACGAATT 59.811 40.000 12.58 0.00 31.13 2.17
1788 1943 4.715297 ACAGTACAAAGGGATCCTACGAAT 59.285 41.667 12.58 0.00 31.13 3.34
1789 1944 4.091549 ACAGTACAAAGGGATCCTACGAA 58.908 43.478 12.58 0.00 31.13 3.85
1790 1945 3.705051 ACAGTACAAAGGGATCCTACGA 58.295 45.455 12.58 0.00 31.13 3.43
1791 1946 4.430908 GAACAGTACAAAGGGATCCTACG 58.569 47.826 12.58 5.31 31.13 3.51
1792 1947 4.224370 TGGAACAGTACAAAGGGATCCTAC 59.776 45.833 12.58 5.85 31.13 3.18
1793 1948 4.431378 TGGAACAGTACAAAGGGATCCTA 58.569 43.478 12.58 0.00 31.13 2.94
1794 1949 3.256704 TGGAACAGTACAAAGGGATCCT 58.743 45.455 12.58 0.00 33.87 3.24
1795 1950 3.713826 TGGAACAGTACAAAGGGATCC 57.286 47.619 1.92 1.92 0.00 3.36
1810 1965 5.002516 TGAATGGGAATTTTTGCATGGAAC 58.997 37.500 0.00 0.00 0.00 3.62
1811 1966 5.238624 TGAATGGGAATTTTTGCATGGAA 57.761 34.783 0.00 0.00 0.00 3.53
1812 1967 4.904895 TGAATGGGAATTTTTGCATGGA 57.095 36.364 0.00 0.00 0.00 3.41
1813 1968 6.114089 TGTATGAATGGGAATTTTTGCATGG 58.886 36.000 0.00 0.00 0.00 3.66
1814 1969 7.612668 TTGTATGAATGGGAATTTTTGCATG 57.387 32.000 0.00 0.00 0.00 4.06
1815 1970 8.679100 CATTTGTATGAATGGGAATTTTTGCAT 58.321 29.630 0.00 0.00 34.20 3.96
1816 1971 7.664731 ACATTTGTATGAATGGGAATTTTTGCA 59.335 29.630 3.06 0.00 40.50 4.08
1817 1972 8.042944 ACATTTGTATGAATGGGAATTTTTGC 57.957 30.769 3.06 0.00 40.50 3.68
1818 1973 9.439500 AGACATTTGTATGAATGGGAATTTTTG 57.561 29.630 3.06 0.00 40.50 2.44
1820 1975 9.439500 CAAGACATTTGTATGAATGGGAATTTT 57.561 29.630 3.06 0.00 40.50 1.82
1821 1976 8.596293 ACAAGACATTTGTATGAATGGGAATTT 58.404 29.630 3.06 0.00 40.50 1.82
1822 1977 8.137745 ACAAGACATTTGTATGAATGGGAATT 57.862 30.769 3.06 0.00 40.50 2.17
1823 1978 7.722949 ACAAGACATTTGTATGAATGGGAAT 57.277 32.000 3.06 0.00 40.50 3.01
1824 1979 8.642935 TTACAAGACATTTGTATGAATGGGAA 57.357 30.769 1.09 0.00 40.50 3.97
1825 1980 8.106462 TCTTACAAGACATTTGTATGAATGGGA 58.894 33.333 11.08 0.00 40.50 4.37
1826 1981 8.279970 TCTTACAAGACATTTGTATGAATGGG 57.720 34.615 11.08 0.00 40.50 4.00
1827 1982 9.559958 GTTCTTACAAGACATTTGTATGAATGG 57.440 33.333 21.06 0.00 43.93 3.16
1830 1985 9.778741 AGAGTTCTTACAAGACATTTGTATGAA 57.221 29.630 17.29 17.29 42.01 2.57
1831 1986 9.208022 CAGAGTTCTTACAAGACATTTGTATGA 57.792 33.333 9.99 9.99 37.31 2.15
1832 1987 7.959651 GCAGAGTTCTTACAAGACATTTGTATG 59.040 37.037 1.09 4.21 35.15 2.39
1833 1988 7.148573 CGCAGAGTTCTTACAAGACATTTGTAT 60.149 37.037 1.09 0.00 35.15 2.29
1834 1989 6.145534 CGCAGAGTTCTTACAAGACATTTGTA 59.854 38.462 0.00 0.00 34.13 2.41
1835 1990 5.050091 CGCAGAGTTCTTACAAGACATTTGT 60.050 40.000 0.00 0.00 34.13 2.83
1836 1991 5.050091 ACGCAGAGTTCTTACAAGACATTTG 60.050 40.000 0.00 0.00 34.13 2.32
1837 1992 5.057149 ACGCAGAGTTCTTACAAGACATTT 58.943 37.500 0.00 0.00 34.13 2.32
1838 1993 4.632153 ACGCAGAGTTCTTACAAGACATT 58.368 39.130 0.00 0.00 34.13 2.71
1839 1994 4.258702 ACGCAGAGTTCTTACAAGACAT 57.741 40.909 0.00 0.00 34.13 3.06
1840 1995 3.728076 ACGCAGAGTTCTTACAAGACA 57.272 42.857 0.00 0.00 34.13 3.41
1852 2007 2.181584 CGTAGGGAGAACGCAGAGT 58.818 57.895 0.00 0.00 33.04 3.24
1872 2027 7.589081 TCTATAAGGTAAGGGTGTCTGATACA 58.411 38.462 6.87 0.00 35.06 2.29
1873 2028 8.474710 TTCTATAAGGTAAGGGTGTCTGATAC 57.525 38.462 0.00 0.00 0.00 2.24
1874 2029 9.670442 ATTTCTATAAGGTAAGGGTGTCTGATA 57.330 33.333 0.00 0.00 0.00 2.15
1875 2030 7.989947 TTTCTATAAGGTAAGGGTGTCTGAT 57.010 36.000 0.00 0.00 0.00 2.90
1876 2031 7.989947 ATTTCTATAAGGTAAGGGTGTCTGA 57.010 36.000 0.00 0.00 0.00 3.27
1962 2117 7.405292 TGGATTACAATTCATAGGGATCATCC 58.595 38.462 0.00 0.00 35.23 3.51
1990 2145 9.832445 TTAAGTAGCCTAGATAGAAAAACATGG 57.168 33.333 0.00 0.00 0.00 3.66
2219 2374 9.822185 ATTGCAAATTTAAGGGTATCTTTGATC 57.178 29.630 1.71 0.00 36.93 2.92
2271 2426 3.129287 AGGCTTTGCTGTTGTACATATGC 59.871 43.478 1.58 1.91 0.00 3.14
2332 2487 8.906867 CATGACTTGATTTTGGTATCTTATGGT 58.093 33.333 0.00 0.00 0.00 3.55
2345 2500 3.896888 TGCCAGAACCATGACTTGATTTT 59.103 39.130 0.00 0.00 0.00 1.82
2368 2523 7.016858 AGGGTTTGTGGAACTTAACTATCTACA 59.983 37.037 0.00 0.00 38.35 2.74
2371 2526 6.238648 CAGGGTTTGTGGAACTTAACTATCT 58.761 40.000 0.00 0.00 38.35 1.98
2524 2679 9.517868 GGAAGTTAGCTACTTGGTCTAGATATA 57.482 37.037 11.68 0.00 47.00 0.86
2530 2685 4.157289 CGTGGAAGTTAGCTACTTGGTCTA 59.843 45.833 11.68 0.00 47.00 2.59
2532 2687 3.251571 CGTGGAAGTTAGCTACTTGGTC 58.748 50.000 11.68 1.12 47.00 4.02
2650 2805 4.360964 GTGGCCGCTGCATTGCAA 62.361 61.111 13.18 0.00 38.41 4.08
2737 2892 3.760684 GACACAATTCTCTGGCCAAAGAT 59.239 43.478 10.24 0.00 0.00 2.40
3077 3232 8.897752 AGTAATATCAGAAGTCATGAAAAAGGC 58.102 33.333 0.00 0.00 0.00 4.35
3539 3694 1.004918 CGAACAGCTTCCTTCGGGT 60.005 57.895 9.21 0.00 36.46 5.28
3657 3812 8.796475 TCTAATGAGGTTTCAAAATCCTTCTTG 58.204 33.333 0.00 0.00 36.78 3.02
3786 3941 3.304257 CCTTCATGTGCATAAGCGATTCC 60.304 47.826 0.00 0.00 46.23 3.01
3851 4006 5.374921 CATTCCTAGCAACATCCTTCTCAT 58.625 41.667 0.00 0.00 0.00 2.90
3898 4053 8.671921 TCTCAAATATGACAATTTCTTCTCAGC 58.328 33.333 0.00 0.00 0.00 4.26
4118 4273 7.319646 CAGCTTCAGTGATTCTACTAAGTTCT 58.680 38.462 0.00 0.00 0.00 3.01
4157 4312 1.334869 GTTGACTGTGGTCCTGCTTTG 59.665 52.381 0.00 0.00 41.47 2.77
4353 4508 4.586884 TCTTCTGCATCATTTCAGCTTCT 58.413 39.130 0.00 0.00 0.00 2.85
4431 4586 0.804989 CTGATTGCAACCGTTCCTCC 59.195 55.000 0.00 0.00 0.00 4.30
4500 4655 7.410120 TCTGTCTGATAGTTGCTTAATCTGA 57.590 36.000 1.23 0.00 0.00 3.27
4512 4667 3.244033 GCACTTGCTCTGTCTGATAGT 57.756 47.619 1.23 0.00 38.21 2.12
4609 4764 6.323996 TCACTCAACTTCTCTGACTCCTTTAA 59.676 38.462 0.00 0.00 0.00 1.52
4677 4832 2.899339 GCCTCATTCTCGCTGGCC 60.899 66.667 0.00 0.00 37.81 5.36
4683 4838 5.801350 TTTTCTGTATTGCCTCATTCTCG 57.199 39.130 0.00 0.00 0.00 4.04
4893 5048 2.499289 AGGAGCCTTGTGTACAGATGAG 59.501 50.000 7.40 0.00 0.00 2.90
4958 5113 1.471684 CCTTCCTCAACAGCATTCTGC 59.528 52.381 0.00 0.00 44.10 4.26
5030 5185 1.194218 TCATGGAGAACTGCCATCGA 58.806 50.000 0.00 0.00 44.08 3.59
5048 5203 4.889995 CAGATTTTTCCCCAGGAAGGTATC 59.110 45.833 0.00 2.31 43.06 2.24
5120 5275 6.767524 TTGTACAAAGTGGAAACATGAACT 57.232 33.333 5.64 0.00 46.14 3.01
5141 5296 5.654603 ATGGCATGCAACCATCTATATTG 57.345 39.130 21.36 0.00 44.85 1.90
5334 5490 8.731275 ATATGAAATCAAACGTGGTTCTATCA 57.269 30.769 0.00 0.00 0.00 2.15
5524 5709 5.954153 TGAAATACCCAAATGCAATGGAT 57.046 34.783 20.35 8.55 40.56 3.41
5678 5868 9.869757 AGCTCGGTAAATAATTTTTATTTTGCT 57.130 25.926 9.73 9.21 0.00 3.91
5699 5889 1.808411 TCCAGCCAAAACTAAGCTCG 58.192 50.000 0.00 0.00 33.70 5.03
5700 5890 4.790765 ATTTCCAGCCAAAACTAAGCTC 57.209 40.909 0.00 0.00 33.70 4.09
5728 5918 6.490040 ACAAAAATAAGTGTGCTGGACATAGT 59.510 34.615 5.02 0.00 36.78 2.12
5732 5922 5.590530 AACAAAAATAAGTGTGCTGGACA 57.409 34.783 0.00 0.00 0.00 4.02
5890 8936 0.670239 TTGCTCTTGCGCGAAGATGA 60.670 50.000 12.10 0.00 40.06 2.92
5896 8942 1.594021 TGAAGTTGCTCTTGCGCGA 60.594 52.632 12.10 0.00 43.34 5.87
5951 8998 2.732507 AGGGAGATAGGGAGGATGTCAT 59.267 50.000 0.00 0.00 0.00 3.06
5952 8999 2.156425 AGGGAGATAGGGAGGATGTCA 58.844 52.381 0.00 0.00 0.00 3.58
5975 9022 0.247460 TCAATCGTCAGTGAGGCAGG 59.753 55.000 7.98 0.36 0.00 4.85
5976 9023 1.638133 CTCAATCGTCAGTGAGGCAG 58.362 55.000 7.98 1.06 38.08 4.85
5979 9026 0.460987 GGGCTCAATCGTCAGTGAGG 60.461 60.000 6.49 6.49 41.36 3.86
6029 9076 1.795768 TCTCGTTGGTTGACATCAGC 58.204 50.000 0.00 0.00 0.00 4.26
6034 9081 3.001414 TCGTTTTTCTCGTTGGTTGACA 58.999 40.909 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.