Multiple sequence alignment - TraesCS4A01G202600

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 TraesCS4A01G202600 chr4A 100.000 5399 0 0 1 5399 492535557 492530159 0.000000e+00 9971
1 TraesCS4A01G202600 chr4A 87.964 2127 178 40 2357 4430 36413869 36411768 0.000000e+00 2438
2 TraesCS4A01G202600 chr4A 89.623 424 37 3 851 1267 36414917 36414494 2.860000e-147 532
3 TraesCS4A01G202600 chr4A 81.633 637 75 28 4466 5083 36411763 36411150 1.750000e-134 490
4 TraesCS4A01G202600 chr4A 87.931 116 11 2 2105 2220 36414446 36414334 3.390000e-27 134
5 TraesCS4A01G202600 chr4D 96.713 2282 55 7 3126 5399 82293361 82291092 0.000000e+00 3781
6 TraesCS4A01G202600 chr4D 87.242 2281 201 52 2218 4435 435064869 435062616 0.000000e+00 2518
7 TraesCS4A01G202600 chr4D 94.103 1221 35 12 1934 3130 82294637 82293430 0.000000e+00 1821
8 TraesCS4A01G202600 chr4D 92.152 892 42 15 782 1657 82295589 82294710 0.000000e+00 1234
9 TraesCS4A01G202600 chr4D 86.510 934 82 21 4466 5368 435062616 435061696 0.000000e+00 987
10 TraesCS4A01G202600 chr4D 87.891 479 48 6 798 1267 435065857 435065380 6.110000e-154 555
11 TraesCS4A01G202600 chr4D 86.036 222 23 3 2006 2220 435065384 435065164 1.170000e-56 231
12 TraesCS4A01G202600 chr4B 96.893 1577 42 4 3126 4698 116214314 116212741 0.000000e+00 2634
13 TraesCS4A01G202600 chr4B 92.758 1229 43 12 1935 3129 116215609 116214393 0.000000e+00 1735
14 TraesCS4A01G202600 chr4B 88.816 1368 110 20 2367 3700 535249283 535247925 0.000000e+00 1639
15 TraesCS4A01G202600 chr4B 85.485 1495 145 41 3699 5149 535247770 535246304 0.000000e+00 1493
16 TraesCS4A01G202600 chr4B 97.190 783 21 1 1 782 545150313 545151095 0.000000e+00 1323
17 TraesCS4A01G202600 chr4B 90.207 919 39 26 782 1657 116216595 116215685 0.000000e+00 1151
18 TraesCS4A01G202600 chr4B 94.221 571 22 7 4826 5392 116212745 116212182 0.000000e+00 861
19 TraesCS4A01G202600 chr4B 89.756 410 40 2 851 1258 535251590 535251181 1.720000e-144 523
20 TraesCS4A01G202600 chr4B 98.406 251 3 1 1686 1936 36970493 36970244 1.780000e-119 440
21 TraesCS4A01G202600 chr4B 81.471 340 27 11 4799 5114 535237229 535236902 4.180000e-61 246
22 TraesCS4A01G202600 chr4B 91.892 74 6 0 2218 2291 535249481 535249408 2.660000e-18 104
23 TraesCS4A01G202600 chr1B 97.959 784 15 1 1 783 305298636 305299419 0.000000e+00 1358
24 TraesCS4A01G202600 chr1B 98.819 254 1 1 1684 1937 37633244 37633495 8.250000e-123 451
25 TraesCS4A01G202600 chr1B 98.810 252 2 1 1691 1941 687177489 687177740 1.070000e-121 448
26 TraesCS4A01G202600 chr1B 99.190 247 2 0 1689 1935 91965432 91965678 3.840000e-121 446
27 TraesCS4A01G202600 chr2A 97.179 780 20 2 1 778 651275779 651276558 0.000000e+00 1317
28 TraesCS4A01G202600 chr2A 99.197 249 1 1 1688 1936 553492522 553492275 1.070000e-121 448
29 TraesCS4A01G202600 chr3B 96.447 788 26 2 1 787 719914764 719915550 0.000000e+00 1299
30 TraesCS4A01G202600 chr3B 97.115 520 14 1 265 783 779681026 779681545 0.000000e+00 876
31 TraesCS4A01G202600 chr7B 96.036 782 26 2 3 783 749318620 749317843 0.000000e+00 1267
32 TraesCS4A01G202600 chr5D 94.584 794 34 2 1 785 352451659 352452452 0.000000e+00 1219
33 TraesCS4A01G202600 chr5D 94.177 790 35 3 1 780 276932221 276933009 0.000000e+00 1194
34 TraesCS4A01G202600 chr1A 93.459 795 37 8 1 784 206801720 206802510 0.000000e+00 1166
35 TraesCS4A01G202600 chr1A 99.197 249 1 1 1688 1936 580495309 580495062 1.070000e-121 448
36 TraesCS4A01G202600 chr3D 93.229 576 31 1 1 568 609616643 609616068 0.000000e+00 841
37 TraesCS4A01G202600 chr5A 82.912 831 78 28 1 780 280713308 280712491 0.000000e+00 689
38 TraesCS4A01G202600 chr2B 99.190 247 2 0 1689 1935 449930598 449930352 3.840000e-121 446
39 TraesCS4A01G202600 chrUn 98.790 248 3 0 1692 1939 181264299 181264052 4.960000e-120 442
40 TraesCS4A01G202600 chr6A 97.318 261 5 2 1677 1935 64535812 64536072 4.960000e-120 442


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 TraesCS4A01G202600 chr4A 492530159 492535557 5398 True 9971.000000 9971 100.000000 1 5399 1 chr4A.!!$R1 5398
1 TraesCS4A01G202600 chr4A 36411150 36414917 3767 True 898.500000 2438 86.787750 851 5083 4 chr4A.!!$R2 4232
2 TraesCS4A01G202600 chr4D 82291092 82295589 4497 True 2278.666667 3781 94.322667 782 5399 3 chr4D.!!$R1 4617
3 TraesCS4A01G202600 chr4D 435061696 435065857 4161 True 1072.750000 2518 86.919750 798 5368 4 chr4D.!!$R2 4570
4 TraesCS4A01G202600 chr4B 116212182 116216595 4413 True 1595.250000 2634 93.519750 782 5392 4 chr4B.!!$R3 4610
5 TraesCS4A01G202600 chr4B 545150313 545151095 782 False 1323.000000 1323 97.190000 1 782 1 chr4B.!!$F1 781
6 TraesCS4A01G202600 chr4B 535246304 535251590 5286 True 939.750000 1639 88.987250 851 5149 4 chr4B.!!$R4 4298
7 TraesCS4A01G202600 chr1B 305298636 305299419 783 False 1358.000000 1358 97.959000 1 783 1 chr1B.!!$F3 782
8 TraesCS4A01G202600 chr2A 651275779 651276558 779 False 1317.000000 1317 97.179000 1 778 1 chr2A.!!$F1 777
9 TraesCS4A01G202600 chr3B 719914764 719915550 786 False 1299.000000 1299 96.447000 1 787 1 chr3B.!!$F1 786
10 TraesCS4A01G202600 chr3B 779681026 779681545 519 False 876.000000 876 97.115000 265 783 1 chr3B.!!$F2 518
11 TraesCS4A01G202600 chr7B 749317843 749318620 777 True 1267.000000 1267 96.036000 3 783 1 chr7B.!!$R1 780
12 TraesCS4A01G202600 chr5D 352451659 352452452 793 False 1219.000000 1219 94.584000 1 785 1 chr5D.!!$F2 784
13 TraesCS4A01G202600 chr5D 276932221 276933009 788 False 1194.000000 1194 94.177000 1 780 1 chr5D.!!$F1 779
14 TraesCS4A01G202600 chr1A 206801720 206802510 790 False 1166.000000 1166 93.459000 1 784 1 chr1A.!!$F1 783
15 TraesCS4A01G202600 chr3D 609616068 609616643 575 True 841.000000 841 93.229000 1 568 1 chr3D.!!$R1 567
16 TraesCS4A01G202600 chr5A 280712491 280713308 817 True 689.000000 689 82.912000 1 780 1 chr5A.!!$R1 779

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
960 1065 0.105913 CTCCCCCTCCTACCTCACTC 60.106 65.0 0.00 0.0 0.00 3.51 F
1726 1891 0.040425 CCAAAATATAGCGCGCCCAC 60.040 55.0 30.33 0.0 0.00 4.61 F
1906 2071 0.105224 TGAAGCACGAAAACCGAGGA 59.895 50.0 0.00 0.0 41.76 3.71 F
1915 2080 0.457035 AAAACCGAGGACGCGCTATA 59.543 50.0 5.73 0.0 38.29 1.31 F
1916 2081 0.672342 AAACCGAGGACGCGCTATAT 59.328 50.0 5.73 0.0 38.29 0.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 2084 0.042131 ACCATACTCCCTCCGTTCCA 59.958 55.000 0.00 0.0 0.00 3.53 R
3519 5433 1.880027 GGTCACCTAGGTTGCACAAAG 59.120 52.381 13.15 0.0 0.00 2.77 R
3999 6082 3.181515 CGCCGCTGTAATGTAATTCACAA 60.182 43.478 0.00 0.0 41.55 3.33 R
4010 6094 1.137086 AGTCTTGATCGCCGCTGTAAT 59.863 47.619 0.00 0.0 0.00 1.89 R
4542 6661 7.992754 AATCCTGATAAAGATCATACTTGCC 57.007 36.000 0.00 0.0 41.33 4.52 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
77 78 1.414181 CTGATCATGGTAACCTCCGCT 59.586 52.381 0.00 0.00 0.00 5.52
117 119 2.937799 ACAAAGCCAAAAGACGTCGTTA 59.062 40.909 17.05 0.00 0.00 3.18
172 174 1.133976 GCAATGCTCCACCTAGACCAT 60.134 52.381 0.00 0.00 0.00 3.55
788 861 5.318630 TGTATCCAAACAACCCCTTAACTC 58.681 41.667 0.00 0.00 0.00 3.01
960 1065 0.105913 CTCCCCCTCCTACCTCACTC 60.106 65.000 0.00 0.00 0.00 3.51
1050 1155 0.386731 CGGTGGCGATGGTTTGTTTC 60.387 55.000 0.00 0.00 0.00 2.78
1282 1401 1.135333 CTACTGCTTCCTCGTCTTCCC 59.865 57.143 0.00 0.00 0.00 3.97
1384 1503 2.980233 AGTTTGCCCAGCAGCGTC 60.980 61.111 0.00 0.00 40.61 5.19
1445 1578 2.604914 TCGCATCTGAATTTTCTCGCTC 59.395 45.455 0.00 0.00 0.00 5.03
1499 1633 7.147811 TGCCTTAGTTTGGTAGAAAATGTGTTT 60.148 33.333 0.00 0.00 0.00 2.83
1537 1671 0.370273 GTGCACGGTTGATTAGCTCG 59.630 55.000 0.00 0.00 0.00 5.03
1540 1674 1.518572 ACGGTTGATTAGCTCGCGG 60.519 57.895 6.13 0.00 0.00 6.46
1578 1712 0.391263 AGGACGACGCAGGAATTTCC 60.391 55.000 7.39 7.39 36.58 3.13
1605 1739 6.426980 TGATCTGCATTTCATCTTACACAC 57.573 37.500 0.00 0.00 0.00 3.82
1606 1740 6.175471 TGATCTGCATTTCATCTTACACACT 58.825 36.000 0.00 0.00 0.00 3.55
1708 1873 4.750021 AAAATACTACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
1709 1874 3.393426 AATACTACTCCCTCCGTTCCA 57.607 47.619 0.00 0.00 0.00 3.53
1710 1875 2.905415 TACTACTCCCTCCGTTCCAA 57.095 50.000 0.00 0.00 0.00 3.53
1711 1876 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1712 1877 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
1713 1878 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
1714 1879 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
1715 1880 4.720273 ACTACTCCCTCCGTTCCAAAATAT 59.280 41.667 0.00 0.00 0.00 1.28
1716 1881 5.901276 ACTACTCCCTCCGTTCCAAAATATA 59.099 40.000 0.00 0.00 0.00 0.86
1717 1882 5.291905 ACTCCCTCCGTTCCAAAATATAG 57.708 43.478 0.00 0.00 0.00 1.31
1718 1883 4.065789 CTCCCTCCGTTCCAAAATATAGC 58.934 47.826 0.00 0.00 0.00 2.97
1719 1884 2.806244 CCCTCCGTTCCAAAATATAGCG 59.194 50.000 0.00 0.00 0.00 4.26
1720 1885 2.223377 CCTCCGTTCCAAAATATAGCGC 59.777 50.000 0.00 0.00 0.00 5.92
1721 1886 1.862201 TCCGTTCCAAAATATAGCGCG 59.138 47.619 0.00 0.00 0.00 6.86
1722 1887 1.658968 CGTTCCAAAATATAGCGCGC 58.341 50.000 26.66 26.66 0.00 6.86
1723 1888 1.659211 CGTTCCAAAATATAGCGCGCC 60.659 52.381 30.33 10.31 0.00 6.53
1724 1889 0.948678 TTCCAAAATATAGCGCGCCC 59.051 50.000 30.33 0.16 0.00 6.13
1725 1890 0.179043 TCCAAAATATAGCGCGCCCA 60.179 50.000 30.33 17.44 0.00 5.36
1726 1891 0.040425 CCAAAATATAGCGCGCCCAC 60.040 55.000 30.33 0.00 0.00 4.61
1727 1892 0.384230 CAAAATATAGCGCGCCCACG 60.384 55.000 30.33 4.40 44.07 4.94
1737 1902 3.788766 CGCCCACGCTTTTCGAGG 61.789 66.667 0.00 0.00 46.50 4.63
1738 1903 2.668550 GCCCACGCTTTTCGAGGT 60.669 61.111 0.71 0.00 45.67 3.85
1739 1904 2.258726 GCCCACGCTTTTCGAGGTT 61.259 57.895 0.71 0.00 45.67 3.50
1740 1905 1.866925 CCCACGCTTTTCGAGGTTC 59.133 57.895 0.71 0.00 45.67 3.62
1741 1906 0.882927 CCCACGCTTTTCGAGGTTCA 60.883 55.000 0.71 0.00 45.67 3.18
1742 1907 0.941542 CCACGCTTTTCGAGGTTCAA 59.058 50.000 0.00 0.00 42.79 2.69
1743 1908 1.333791 CCACGCTTTTCGAGGTTCAAC 60.334 52.381 0.00 0.00 42.79 3.18
1744 1909 1.597663 CACGCTTTTCGAGGTTCAACT 59.402 47.619 0.00 0.00 41.67 3.16
1745 1910 2.031683 CACGCTTTTCGAGGTTCAACTT 59.968 45.455 0.00 0.00 41.67 2.66
1746 1911 2.681344 ACGCTTTTCGAGGTTCAACTTT 59.319 40.909 0.00 0.00 41.67 2.66
1747 1912 3.035942 CGCTTTTCGAGGTTCAACTTTG 58.964 45.455 0.00 0.00 41.67 2.77
1748 1913 3.242608 CGCTTTTCGAGGTTCAACTTTGA 60.243 43.478 0.00 0.00 41.67 2.69
1749 1914 4.035684 GCTTTTCGAGGTTCAACTTTGAC 58.964 43.478 0.00 0.00 36.83 3.18
1750 1915 4.598062 CTTTTCGAGGTTCAACTTTGACC 58.402 43.478 0.00 0.00 36.83 4.02
1751 1916 2.992124 TCGAGGTTCAACTTTGACCA 57.008 45.000 11.01 0.00 36.83 4.02
1752 1917 3.485463 TCGAGGTTCAACTTTGACCAT 57.515 42.857 11.01 0.00 36.83 3.55
1753 1918 4.610605 TCGAGGTTCAACTTTGACCATA 57.389 40.909 11.01 0.00 36.83 2.74
1754 1919 4.963373 TCGAGGTTCAACTTTGACCATAA 58.037 39.130 11.01 0.00 36.83 1.90
1755 1920 5.369833 TCGAGGTTCAACTTTGACCATAAA 58.630 37.500 11.01 0.00 36.83 1.40
1756 1921 6.001460 TCGAGGTTCAACTTTGACCATAAAT 58.999 36.000 11.01 0.00 36.83 1.40
1757 1922 6.488683 TCGAGGTTCAACTTTGACCATAAATT 59.511 34.615 11.01 0.00 36.83 1.82
1758 1923 7.013846 TCGAGGTTCAACTTTGACCATAAATTT 59.986 33.333 0.00 0.00 36.83 1.82
1759 1924 8.293867 CGAGGTTCAACTTTGACCATAAATTTA 58.706 33.333 0.00 0.00 36.83 1.40
1760 1925 9.974980 GAGGTTCAACTTTGACCATAAATTTAA 57.025 29.630 1.21 0.00 36.83 1.52
1761 1926 9.758651 AGGTTCAACTTTGACCATAAATTTAAC 57.241 29.630 1.21 0.00 36.83 2.01
1762 1927 8.984764 GGTTCAACTTTGACCATAAATTTAACC 58.015 33.333 1.21 0.00 36.83 2.85
1763 1928 8.984764 GTTCAACTTTGACCATAAATTTAACCC 58.015 33.333 1.21 0.00 36.83 4.11
1764 1929 8.251383 TCAACTTTGACCATAAATTTAACCCA 57.749 30.769 1.21 0.00 31.01 4.51
1765 1930 8.145122 TCAACTTTGACCATAAATTTAACCCAC 58.855 33.333 1.21 0.00 31.01 4.61
1766 1931 6.683715 ACTTTGACCATAAATTTAACCCACG 58.316 36.000 1.21 0.00 0.00 4.94
1767 1932 6.490721 ACTTTGACCATAAATTTAACCCACGA 59.509 34.615 1.21 0.00 0.00 4.35
1768 1933 6.503589 TTGACCATAAATTTAACCCACGAG 57.496 37.500 1.21 0.00 0.00 4.18
1769 1934 5.806818 TGACCATAAATTTAACCCACGAGA 58.193 37.500 1.21 0.00 0.00 4.04
1770 1935 5.644636 TGACCATAAATTTAACCCACGAGAC 59.355 40.000 1.21 0.00 0.00 3.36
1771 1936 4.945543 ACCATAAATTTAACCCACGAGACC 59.054 41.667 1.21 0.00 0.00 3.85
1772 1937 4.034742 CCATAAATTTAACCCACGAGACCG 59.965 45.833 1.21 0.00 42.50 4.79
1773 1938 3.405823 AAATTTAACCCACGAGACCGA 57.594 42.857 0.00 0.00 39.50 4.69
1774 1939 2.375173 ATTTAACCCACGAGACCGAC 57.625 50.000 0.00 0.00 39.50 4.79
1775 1940 1.331214 TTTAACCCACGAGACCGACT 58.669 50.000 0.00 0.00 39.50 4.18
1776 1941 0.599558 TTAACCCACGAGACCGACTG 59.400 55.000 0.00 0.00 39.50 3.51
1777 1942 1.870055 TAACCCACGAGACCGACTGC 61.870 60.000 0.00 0.00 39.50 4.40
1778 1943 4.778415 CCCACGAGACCGACTGCG 62.778 72.222 0.00 0.00 39.50 5.18
1788 1953 4.812476 CGACTGCGGCGGGATCAA 62.812 66.667 14.26 0.00 0.00 2.57
1789 1954 2.435938 GACTGCGGCGGGATCAAA 60.436 61.111 14.26 0.00 0.00 2.69
1790 1955 2.033448 ACTGCGGCGGGATCAAAA 59.967 55.556 14.26 0.00 0.00 2.44
1791 1956 1.582610 GACTGCGGCGGGATCAAAAA 61.583 55.000 14.26 0.00 0.00 1.94
1792 1957 0.965363 ACTGCGGCGGGATCAAAAAT 60.965 50.000 14.26 0.00 0.00 1.82
1793 1958 0.173255 CTGCGGCGGGATCAAAAATT 59.827 50.000 9.78 0.00 0.00 1.82
1794 1959 1.403679 CTGCGGCGGGATCAAAAATTA 59.596 47.619 9.78 0.00 0.00 1.40
1795 1960 2.028130 TGCGGCGGGATCAAAAATTAT 58.972 42.857 9.78 0.00 0.00 1.28
1796 1961 3.215151 TGCGGCGGGATCAAAAATTATA 58.785 40.909 9.78 0.00 0.00 0.98
1797 1962 3.823873 TGCGGCGGGATCAAAAATTATAT 59.176 39.130 9.78 0.00 0.00 0.86
1798 1963 5.004448 TGCGGCGGGATCAAAAATTATATA 58.996 37.500 9.78 0.00 0.00 0.86
1799 1964 5.473846 TGCGGCGGGATCAAAAATTATATAA 59.526 36.000 9.78 0.00 0.00 0.98
1800 1965 6.151985 TGCGGCGGGATCAAAAATTATATAAT 59.848 34.615 9.78 1.91 0.00 1.28
1801 1966 7.033185 GCGGCGGGATCAAAAATTATATAATT 58.967 34.615 13.85 13.85 37.49 1.40
1802 1967 8.185505 GCGGCGGGATCAAAAATTATATAATTA 58.814 33.333 18.75 6.09 35.00 1.40
1867 2032 4.336581 CGCAGTCGGTCTTGTTGA 57.663 55.556 0.00 0.00 0.00 3.18
1868 2033 2.827604 CGCAGTCGGTCTTGTTGAT 58.172 52.632 0.00 0.00 0.00 2.57
1869 2034 1.148310 CGCAGTCGGTCTTGTTGATT 58.852 50.000 0.00 0.00 0.00 2.57
1870 2035 2.333926 CGCAGTCGGTCTTGTTGATTA 58.666 47.619 0.00 0.00 0.00 1.75
1871 2036 2.734606 CGCAGTCGGTCTTGTTGATTAA 59.265 45.455 0.00 0.00 0.00 1.40
1872 2037 3.185594 CGCAGTCGGTCTTGTTGATTAAA 59.814 43.478 0.00 0.00 0.00 1.52
1873 2038 4.142902 CGCAGTCGGTCTTGTTGATTAAAT 60.143 41.667 0.00 0.00 0.00 1.40
1874 2039 5.616866 CGCAGTCGGTCTTGTTGATTAAATT 60.617 40.000 0.00 0.00 0.00 1.82
1875 2040 6.401688 CGCAGTCGGTCTTGTTGATTAAATTA 60.402 38.462 0.00 0.00 0.00 1.40
1876 2041 7.302524 GCAGTCGGTCTTGTTGATTAAATTAA 58.697 34.615 0.00 0.00 0.00 1.40
1877 2042 7.968405 GCAGTCGGTCTTGTTGATTAAATTAAT 59.032 33.333 0.00 0.00 0.00 1.40
1878 2043 9.277565 CAGTCGGTCTTGTTGATTAAATTAATG 57.722 33.333 2.58 0.00 0.00 1.90
1879 2044 8.458843 AGTCGGTCTTGTTGATTAAATTAATGG 58.541 33.333 2.58 0.00 0.00 3.16
1880 2045 8.241367 GTCGGTCTTGTTGATTAAATTAATGGT 58.759 33.333 2.58 0.00 0.00 3.55
1881 2046 8.455682 TCGGTCTTGTTGATTAAATTAATGGTC 58.544 33.333 2.58 0.00 0.00 4.02
1882 2047 8.240682 CGGTCTTGTTGATTAAATTAATGGTCA 58.759 33.333 2.58 0.00 0.00 4.02
1883 2048 9.921637 GGTCTTGTTGATTAAATTAATGGTCAA 57.078 29.630 2.58 0.04 0.00 3.18
1893 2058 9.995003 ATTAAATTAATGGTCAAAGTTGAAGCA 57.005 25.926 0.00 0.00 39.21 3.91
1894 2059 7.713764 AAATTAATGGTCAAAGTTGAAGCAC 57.286 32.000 0.00 0.00 39.21 4.40
1895 2060 3.354089 AATGGTCAAAGTTGAAGCACG 57.646 42.857 0.00 0.00 39.21 5.34
1896 2061 2.031258 TGGTCAAAGTTGAAGCACGA 57.969 45.000 0.00 0.00 39.21 4.35
1897 2062 2.360844 TGGTCAAAGTTGAAGCACGAA 58.639 42.857 0.00 0.00 39.21 3.85
1898 2063 2.750166 TGGTCAAAGTTGAAGCACGAAA 59.250 40.909 0.00 0.00 39.21 3.46
1899 2064 3.191581 TGGTCAAAGTTGAAGCACGAAAA 59.808 39.130 0.00 0.00 39.21 2.29
1900 2065 3.546271 GGTCAAAGTTGAAGCACGAAAAC 59.454 43.478 0.00 0.00 39.21 2.43
1901 2066 3.546271 GTCAAAGTTGAAGCACGAAAACC 59.454 43.478 0.00 0.00 39.21 3.27
1902 2067 2.468532 AAGTTGAAGCACGAAAACCG 57.531 45.000 0.00 0.00 45.44 4.44
1903 2068 1.658994 AGTTGAAGCACGAAAACCGA 58.341 45.000 0.00 0.00 41.76 4.69
1904 2069 1.597663 AGTTGAAGCACGAAAACCGAG 59.402 47.619 0.00 0.00 41.76 4.63
1905 2070 0.941542 TTGAAGCACGAAAACCGAGG 59.058 50.000 0.00 0.00 41.76 4.63
1906 2071 0.105224 TGAAGCACGAAAACCGAGGA 59.895 50.000 0.00 0.00 41.76 3.71
1907 2072 0.511653 GAAGCACGAAAACCGAGGAC 59.488 55.000 0.00 0.00 41.76 3.85
1908 2073 1.219522 AAGCACGAAAACCGAGGACG 61.220 55.000 0.00 0.00 41.76 4.79
1909 2074 2.851104 CACGAAAACCGAGGACGC 59.149 61.111 0.00 0.00 41.76 5.19
1910 2075 2.732094 ACGAAAACCGAGGACGCG 60.732 61.111 3.53 3.53 41.76 6.01
1911 2076 4.130281 CGAAAACCGAGGACGCGC 62.130 66.667 5.73 0.00 41.76 6.86
1912 2077 2.737376 GAAAACCGAGGACGCGCT 60.737 61.111 5.73 0.00 38.29 5.92
1913 2078 1.444895 GAAAACCGAGGACGCGCTA 60.445 57.895 5.73 0.00 38.29 4.26
1914 2079 0.804933 GAAAACCGAGGACGCGCTAT 60.805 55.000 5.73 0.00 38.29 2.97
1915 2080 0.457035 AAAACCGAGGACGCGCTATA 59.543 50.000 5.73 0.00 38.29 1.31
1916 2081 0.672342 AAACCGAGGACGCGCTATAT 59.328 50.000 5.73 0.00 38.29 0.86
1917 2082 0.672342 AACCGAGGACGCGCTATATT 59.328 50.000 5.73 0.00 38.29 1.28
1918 2083 0.672342 ACCGAGGACGCGCTATATTT 59.328 50.000 5.73 0.00 38.29 1.40
1919 2084 1.068127 ACCGAGGACGCGCTATATTTT 59.932 47.619 5.73 0.00 38.29 1.82
1920 2085 1.455786 CCGAGGACGCGCTATATTTTG 59.544 52.381 5.73 0.00 38.29 2.44
1921 2086 1.455786 CGAGGACGCGCTATATTTTGG 59.544 52.381 5.73 0.00 0.00 3.28
1922 2087 2.750948 GAGGACGCGCTATATTTTGGA 58.249 47.619 5.73 0.00 0.00 3.53
1923 2088 3.128349 GAGGACGCGCTATATTTTGGAA 58.872 45.455 5.73 0.00 0.00 3.53
1924 2089 2.870411 AGGACGCGCTATATTTTGGAAC 59.130 45.455 5.73 0.00 0.00 3.62
1925 2090 2.348218 GGACGCGCTATATTTTGGAACG 60.348 50.000 5.73 0.00 0.00 3.95
1926 2091 1.595794 ACGCGCTATATTTTGGAACGG 59.404 47.619 5.73 0.00 0.00 4.44
1927 2092 1.862201 CGCGCTATATTTTGGAACGGA 59.138 47.619 5.56 0.00 0.00 4.69
1928 2093 2.096909 CGCGCTATATTTTGGAACGGAG 60.097 50.000 5.56 0.00 0.00 4.63
1929 2094 2.223377 GCGCTATATTTTGGAACGGAGG 59.777 50.000 0.00 0.00 0.00 4.30
1930 2095 2.806244 CGCTATATTTTGGAACGGAGGG 59.194 50.000 0.00 0.00 0.00 4.30
1931 2096 3.493699 CGCTATATTTTGGAACGGAGGGA 60.494 47.826 0.00 0.00 0.00 4.20
1932 2097 4.065789 GCTATATTTTGGAACGGAGGGAG 58.934 47.826 0.00 0.00 0.00 4.30
1948 2113 4.569865 GGAGGGAGTATGGTGTTGGAATTT 60.570 45.833 0.00 0.00 0.00 1.82
1992 2157 2.771372 TGCATTAGTGGCCTGATGAGTA 59.229 45.455 3.32 0.00 36.95 2.59
2108 2298 2.079925 GATGACAGGCAGTGTTTCCTC 58.920 52.381 0.00 0.00 40.56 3.71
2130 2320 5.226396 TCAACTGGAAACACAAACAACTTG 58.774 37.500 0.00 0.00 41.19 3.16
2360 4116 4.015084 ACCTTGCTACACTACGATGTACT 58.985 43.478 0.00 0.00 33.85 2.73
2361 4117 5.188434 ACCTTGCTACACTACGATGTACTA 58.812 41.667 0.00 0.00 33.85 1.82
2773 4562 1.537562 GGATACCGGTTAGCCTGAACG 60.538 57.143 15.04 0.00 32.93 3.95
2953 4754 1.295792 TATGCGTTTCGATTGCCTCC 58.704 50.000 0.00 0.00 0.00 4.30
2966 4767 1.069935 GCCTCCCTTCTATGGCGAC 59.930 63.158 0.00 0.00 35.79 5.19
3017 4818 2.503920 ATATACCGCAACTCACCGAC 57.496 50.000 0.00 0.00 0.00 4.79
3105 4913 1.945394 GTCAAGCATAGCCTGGTCATG 59.055 52.381 0.00 0.40 33.48 3.07
3145 5054 8.807667 TGTTCTACTTACTACTACTGTTTTGC 57.192 34.615 0.00 0.00 0.00 3.68
3456 5365 3.303329 CGACTGCGCAAATATGTATGCTT 60.303 43.478 13.05 0.00 40.39 3.91
3457 5366 3.956233 ACTGCGCAAATATGTATGCTTG 58.044 40.909 13.05 0.00 40.39 4.01
3460 5369 4.742417 TGCGCAAATATGTATGCTTGTTT 58.258 34.783 8.16 0.00 40.39 2.83
3519 5433 5.673337 TTGATTGCTGTTGTGACTAGTTC 57.327 39.130 0.00 0.00 0.00 3.01
3951 6029 4.884961 ACTCCCATATACCAGTCTGAGTT 58.115 43.478 0.00 0.00 0.00 3.01
3984 6067 2.766970 ATTTGTTTCGTTCCGTGTGG 57.233 45.000 0.00 0.00 0.00 4.17
3999 6082 5.007034 TCCGTGTGGAATTTGTTATGACAT 58.993 37.500 0.00 0.00 42.85 3.06
4181 6265 7.092716 ACAAGTTGAATTACAGATGCCAAATC 58.907 34.615 10.54 0.00 0.00 2.17
4408 6497 4.202223 CCATTGGCGACTAAGTGTACCTAT 60.202 45.833 0.00 0.00 0.00 2.57
4542 6661 5.657474 AGAATGGAAAAGTAATGCATGCTG 58.343 37.500 20.33 0.00 33.64 4.41
4650 6776 9.801873 ATTATGTCAATGTAGTTAATTTGGTGC 57.198 29.630 0.00 0.00 0.00 5.01
4727 6861 8.347035 TGAATGTTAAAAAGGTTCGTTAAGAGG 58.653 33.333 0.00 0.00 0.00 3.69
4878 7045 8.826710 TCAAGACAATGTAACAAACTTCTACTG 58.173 33.333 0.00 0.00 0.00 2.74
4990 7159 3.554934 ACAAATTCTGCTTGACCAGTGA 58.445 40.909 0.00 0.00 34.47 3.41
5338 7522 8.383374 AGTAGGGTAACAAAGTATGACCATTA 57.617 34.615 0.00 0.00 39.74 1.90
5392 7576 9.231297 CAATAAGAGTTGTATCTTCCTTTGGAA 57.769 33.333 0.00 0.00 40.08 3.53
5393 7577 9.807921 AATAAGAGTTGTATCTTCCTTTGGAAA 57.192 29.630 0.53 0.00 41.54 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
354 381 3.208594 CATGATTGATTCTCAAGCCGGA 58.791 45.455 5.05 0.00 41.68 5.14
960 1065 0.538118 TAACGGGAATTGGGAGGACG 59.462 55.000 0.00 0.00 0.00 4.79
996 1101 4.809496 CAGGAGCCCGCCATTGCT 62.809 66.667 0.00 0.00 41.42 3.91
1282 1401 1.150567 CGCGGAGAAGAGAAGGCATG 61.151 60.000 0.00 0.00 0.00 4.06
1306 1425 1.744741 GACAGCCCAAGAGCAGAGC 60.745 63.158 0.00 0.00 34.23 4.09
1351 1470 0.765510 AACTGGCCGAAGAAACTCCT 59.234 50.000 0.00 0.00 0.00 3.69
1384 1503 4.636435 AACAAGGACCACGGGCCG 62.636 66.667 27.06 27.06 0.00 6.13
1445 1578 0.994995 CACTGTTGCCTCTCGAATCG 59.005 55.000 0.00 0.00 0.00 3.34
1508 1642 2.143122 CAACCGTGCACATAGAAGTGT 58.857 47.619 18.64 0.00 41.52 3.55
1509 1643 2.412870 TCAACCGTGCACATAGAAGTG 58.587 47.619 18.64 4.63 42.37 3.16
1537 1671 3.810896 CCCAACCGCTAAAGCCGC 61.811 66.667 0.00 0.00 37.91 6.53
1540 1674 2.007608 CTAACTCCCAACCGCTAAAGC 58.992 52.381 0.00 0.00 37.78 3.51
1578 1712 5.587443 TGTAAGATGAAATGCAGATCAGGTG 59.413 40.000 9.71 0.00 0.00 4.00
1584 1718 6.175471 TGAGTGTGTAAGATGAAATGCAGAT 58.825 36.000 0.00 0.00 0.00 2.90
1605 1739 0.320247 AAGTCGCTGTGAAGGCTGAG 60.320 55.000 0.00 0.00 0.00 3.35
1606 1740 0.106708 AAAGTCGCTGTGAAGGCTGA 59.893 50.000 0.00 0.00 0.00 4.26
1636 1770 3.020274 TCAGAAACTCTCGAGATCCAGG 58.980 50.000 17.03 6.32 0.00 4.45
1693 1858 3.629142 ATTTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
1696 1861 4.065789 GCTATATTTTGGAACGGAGGGAG 58.934 47.826 0.00 0.00 0.00 4.30
1698 1863 2.806244 CGCTATATTTTGGAACGGAGGG 59.194 50.000 0.00 0.00 0.00 4.30
1701 1866 1.862201 CGCGCTATATTTTGGAACGGA 59.138 47.619 5.56 0.00 0.00 4.69
1702 1867 1.659211 GCGCGCTATATTTTGGAACGG 60.659 52.381 26.67 0.00 0.00 4.44
1703 1868 1.658968 GCGCGCTATATTTTGGAACG 58.341 50.000 26.67 0.00 0.00 3.95
1704 1869 1.334689 GGGCGCGCTATATTTTGGAAC 60.335 52.381 32.29 8.93 0.00 3.62
1705 1870 0.948678 GGGCGCGCTATATTTTGGAA 59.051 50.000 32.29 0.00 0.00 3.53
1706 1871 0.179043 TGGGCGCGCTATATTTTGGA 60.179 50.000 32.29 0.00 0.00 3.53
1707 1872 0.040425 GTGGGCGCGCTATATTTTGG 60.040 55.000 32.29 0.00 0.00 3.28
1708 1873 0.384230 CGTGGGCGCGCTATATTTTG 60.384 55.000 32.29 9.06 0.00 2.44
1709 1874 1.938861 CGTGGGCGCGCTATATTTT 59.061 52.632 32.29 0.00 0.00 1.82
1710 1875 3.637714 CGTGGGCGCGCTATATTT 58.362 55.556 32.29 0.00 0.00 1.40
1720 1885 3.788766 CCTCGAAAAGCGTGGGCG 61.789 66.667 0.00 0.00 46.89 6.13
1724 1889 1.597663 AGTTGAACCTCGAAAAGCGTG 59.402 47.619 0.00 0.00 41.80 5.34
1725 1890 1.949465 AGTTGAACCTCGAAAAGCGT 58.051 45.000 0.00 0.00 41.80 5.07
1726 1891 3.035942 CAAAGTTGAACCTCGAAAAGCG 58.964 45.455 0.00 0.00 42.69 4.68
1727 1892 4.035684 GTCAAAGTTGAACCTCGAAAAGC 58.964 43.478 0.00 0.00 39.21 3.51
1728 1893 4.095782 TGGTCAAAGTTGAACCTCGAAAAG 59.904 41.667 6.62 0.00 44.20 2.27
1729 1894 4.011023 TGGTCAAAGTTGAACCTCGAAAA 58.989 39.130 6.62 0.00 44.20 2.29
1730 1895 3.611970 TGGTCAAAGTTGAACCTCGAAA 58.388 40.909 6.62 0.00 44.20 3.46
1731 1896 3.269538 TGGTCAAAGTTGAACCTCGAA 57.730 42.857 6.62 0.00 44.20 3.71
1732 1897 2.992124 TGGTCAAAGTTGAACCTCGA 57.008 45.000 6.62 0.00 44.20 4.04
1733 1898 5.682943 TTTATGGTCAAAGTTGAACCTCG 57.317 39.130 6.62 0.00 44.20 4.63
1734 1899 9.974980 TTAAATTTATGGTCAAAGTTGAACCTC 57.025 29.630 6.62 0.00 44.20 3.85
1735 1900 9.758651 GTTAAATTTATGGTCAAAGTTGAACCT 57.241 29.630 6.62 0.00 44.20 3.50
1736 1901 8.984764 GGTTAAATTTATGGTCAAAGTTGAACC 58.015 33.333 6.62 6.25 44.20 3.62
1737 1902 8.984764 GGGTTAAATTTATGGTCAAAGTTGAAC 58.015 33.333 1.98 1.98 45.04 3.18
1738 1903 8.705594 TGGGTTAAATTTATGGTCAAAGTTGAA 58.294 29.630 0.00 0.00 39.21 2.69
1739 1904 8.145122 GTGGGTTAAATTTATGGTCAAAGTTGA 58.855 33.333 0.00 0.00 34.20 3.18
1740 1905 7.115663 CGTGGGTTAAATTTATGGTCAAAGTTG 59.884 37.037 0.00 0.00 29.44 3.16
1741 1906 7.014422 TCGTGGGTTAAATTTATGGTCAAAGTT 59.986 33.333 0.00 0.00 31.36 2.66
1742 1907 6.490721 TCGTGGGTTAAATTTATGGTCAAAGT 59.509 34.615 0.00 0.00 0.00 2.66
1743 1908 6.915349 TCGTGGGTTAAATTTATGGTCAAAG 58.085 36.000 0.00 0.00 0.00 2.77
1744 1909 6.715718 TCTCGTGGGTTAAATTTATGGTCAAA 59.284 34.615 0.00 0.00 0.00 2.69
1745 1910 6.149807 GTCTCGTGGGTTAAATTTATGGTCAA 59.850 38.462 0.00 0.00 0.00 3.18
1746 1911 5.644636 GTCTCGTGGGTTAAATTTATGGTCA 59.355 40.000 0.00 0.00 0.00 4.02
1747 1912 5.065602 GGTCTCGTGGGTTAAATTTATGGTC 59.934 44.000 0.00 0.00 0.00 4.02
1748 1913 4.945543 GGTCTCGTGGGTTAAATTTATGGT 59.054 41.667 0.00 0.00 0.00 3.55
1749 1914 4.034742 CGGTCTCGTGGGTTAAATTTATGG 59.965 45.833 0.00 0.00 0.00 2.74
1750 1915 4.871557 TCGGTCTCGTGGGTTAAATTTATG 59.128 41.667 0.00 0.00 37.69 1.90
1751 1916 4.872124 GTCGGTCTCGTGGGTTAAATTTAT 59.128 41.667 0.00 0.00 37.69 1.40
1752 1917 4.021192 AGTCGGTCTCGTGGGTTAAATTTA 60.021 41.667 0.00 0.00 37.69 1.40
1753 1918 3.069289 GTCGGTCTCGTGGGTTAAATTT 58.931 45.455 0.00 0.00 37.69 1.82
1754 1919 2.301009 AGTCGGTCTCGTGGGTTAAATT 59.699 45.455 0.00 0.00 37.69 1.82
1755 1920 1.897802 AGTCGGTCTCGTGGGTTAAAT 59.102 47.619 0.00 0.00 37.69 1.40
1756 1921 1.000060 CAGTCGGTCTCGTGGGTTAAA 60.000 52.381 0.00 0.00 37.69 1.52
1757 1922 0.599558 CAGTCGGTCTCGTGGGTTAA 59.400 55.000 0.00 0.00 37.69 2.01
1758 1923 1.870055 GCAGTCGGTCTCGTGGGTTA 61.870 60.000 0.00 0.00 37.69 2.85
1759 1924 3.048602 CAGTCGGTCTCGTGGGTT 58.951 61.111 0.00 0.00 37.69 4.11
1760 1925 3.681835 GCAGTCGGTCTCGTGGGT 61.682 66.667 0.00 0.00 37.69 4.51
1761 1926 4.778415 CGCAGTCGGTCTCGTGGG 62.778 72.222 0.00 0.00 37.69 4.61
1771 1936 4.812476 TTGATCCCGCCGCAGTCG 62.812 66.667 0.00 0.00 0.00 4.18
1772 1937 1.582610 TTTTTGATCCCGCCGCAGTC 61.583 55.000 0.00 0.00 0.00 3.51
1773 1938 0.965363 ATTTTTGATCCCGCCGCAGT 60.965 50.000 0.00 0.00 0.00 4.40
1774 1939 0.173255 AATTTTTGATCCCGCCGCAG 59.827 50.000 0.00 0.00 0.00 5.18
1775 1940 1.464734 TAATTTTTGATCCCGCCGCA 58.535 45.000 0.00 0.00 0.00 5.69
1776 1941 2.793278 ATAATTTTTGATCCCGCCGC 57.207 45.000 0.00 0.00 0.00 6.53
1850 2015 1.148310 AATCAACAAGACCGACTGCG 58.852 50.000 0.00 0.00 37.24 5.18
1851 2016 4.742438 TTTAATCAACAAGACCGACTGC 57.258 40.909 0.00 0.00 0.00 4.40
1852 2017 9.277565 CATTAATTTAATCAACAAGACCGACTG 57.722 33.333 0.00 0.00 0.00 3.51
1853 2018 8.458843 CCATTAATTTAATCAACAAGACCGACT 58.541 33.333 0.00 0.00 0.00 4.18
1854 2019 8.241367 ACCATTAATTTAATCAACAAGACCGAC 58.759 33.333 0.00 0.00 0.00 4.79
1855 2020 8.343168 ACCATTAATTTAATCAACAAGACCGA 57.657 30.769 0.00 0.00 0.00 4.69
1856 2021 8.240682 TGACCATTAATTTAATCAACAAGACCG 58.759 33.333 0.00 0.00 0.00 4.79
1857 2022 9.921637 TTGACCATTAATTTAATCAACAAGACC 57.078 29.630 0.00 0.00 0.00 3.85
1867 2032 9.995003 TGCTTCAACTTTGACCATTAATTTAAT 57.005 25.926 0.00 0.00 36.83 1.40
1868 2033 9.255304 GTGCTTCAACTTTGACCATTAATTTAA 57.745 29.630 0.00 0.00 36.83 1.52
1869 2034 7.593273 CGTGCTTCAACTTTGACCATTAATTTA 59.407 33.333 0.00 0.00 36.83 1.40
1870 2035 6.420604 CGTGCTTCAACTTTGACCATTAATTT 59.579 34.615 0.00 0.00 36.83 1.82
1871 2036 5.920273 CGTGCTTCAACTTTGACCATTAATT 59.080 36.000 0.00 0.00 36.83 1.40
1872 2037 5.240623 TCGTGCTTCAACTTTGACCATTAAT 59.759 36.000 0.00 0.00 36.83 1.40
1873 2038 4.576873 TCGTGCTTCAACTTTGACCATTAA 59.423 37.500 0.00 0.00 36.83 1.40
1874 2039 4.130857 TCGTGCTTCAACTTTGACCATTA 58.869 39.130 0.00 0.00 36.83 1.90
1875 2040 2.948979 TCGTGCTTCAACTTTGACCATT 59.051 40.909 0.00 0.00 36.83 3.16
1876 2041 2.571212 TCGTGCTTCAACTTTGACCAT 58.429 42.857 0.00 0.00 36.83 3.55
1877 2042 2.031258 TCGTGCTTCAACTTTGACCA 57.969 45.000 0.00 0.00 36.83 4.02
1878 2043 3.414549 TTTCGTGCTTCAACTTTGACC 57.585 42.857 0.00 0.00 36.83 4.02
1879 2044 3.546271 GGTTTTCGTGCTTCAACTTTGAC 59.454 43.478 0.00 0.00 36.83 3.18
1880 2045 3.729462 CGGTTTTCGTGCTTCAACTTTGA 60.729 43.478 0.00 0.00 34.92 2.69
1881 2046 2.529894 CGGTTTTCGTGCTTCAACTTTG 59.470 45.455 0.00 0.00 0.00 2.77
1882 2047 2.420722 TCGGTTTTCGTGCTTCAACTTT 59.579 40.909 0.00 0.00 40.32 2.66
1883 2048 2.011222 TCGGTTTTCGTGCTTCAACTT 58.989 42.857 0.00 0.00 40.32 2.66
1884 2049 1.597663 CTCGGTTTTCGTGCTTCAACT 59.402 47.619 0.00 0.00 40.32 3.16
1885 2050 1.333791 CCTCGGTTTTCGTGCTTCAAC 60.334 52.381 0.00 0.00 40.32 3.18
1886 2051 0.941542 CCTCGGTTTTCGTGCTTCAA 59.058 50.000 0.00 0.00 40.32 2.69
1887 2052 0.105224 TCCTCGGTTTTCGTGCTTCA 59.895 50.000 0.00 0.00 40.32 3.02
1888 2053 0.511653 GTCCTCGGTTTTCGTGCTTC 59.488 55.000 0.00 0.00 40.32 3.86
1889 2054 1.219522 CGTCCTCGGTTTTCGTGCTT 61.220 55.000 0.00 0.00 40.32 3.91
1890 2055 1.663702 CGTCCTCGGTTTTCGTGCT 60.664 57.895 0.00 0.00 40.32 4.40
1891 2056 2.851104 CGTCCTCGGTTTTCGTGC 59.149 61.111 0.00 0.00 40.32 5.34
1892 2057 2.851104 GCGTCCTCGGTTTTCGTG 59.149 61.111 0.00 0.00 40.32 4.35
1893 2058 2.732094 CGCGTCCTCGGTTTTCGT 60.732 61.111 0.00 0.00 40.32 3.85
1894 2059 4.130281 GCGCGTCCTCGGTTTTCG 62.130 66.667 8.43 0.00 40.90 3.46
1895 2060 0.804933 ATAGCGCGTCCTCGGTTTTC 60.805 55.000 8.43 0.00 40.82 2.29
1896 2061 0.457035 TATAGCGCGTCCTCGGTTTT 59.543 50.000 8.43 0.00 40.82 2.43
1897 2062 0.672342 ATATAGCGCGTCCTCGGTTT 59.328 50.000 8.43 0.00 40.82 3.27
1898 2063 0.672342 AATATAGCGCGTCCTCGGTT 59.328 50.000 8.43 0.00 40.82 4.44
1899 2064 0.672342 AAATATAGCGCGTCCTCGGT 59.328 50.000 8.43 0.00 43.07 4.69
1900 2065 1.455786 CAAAATATAGCGCGTCCTCGG 59.544 52.381 8.43 0.00 37.56 4.63
1901 2066 1.455786 CCAAAATATAGCGCGTCCTCG 59.544 52.381 8.43 0.00 40.37 4.63
1902 2067 2.750948 TCCAAAATATAGCGCGTCCTC 58.249 47.619 8.43 0.00 0.00 3.71
1903 2068 2.870411 GTTCCAAAATATAGCGCGTCCT 59.130 45.455 8.43 0.00 0.00 3.85
1904 2069 2.348218 CGTTCCAAAATATAGCGCGTCC 60.348 50.000 8.43 0.00 0.00 4.79
1905 2070 2.348218 CCGTTCCAAAATATAGCGCGTC 60.348 50.000 8.43 0.00 0.00 5.19
1906 2071 1.595794 CCGTTCCAAAATATAGCGCGT 59.404 47.619 8.43 0.00 0.00 6.01
1907 2072 1.862201 TCCGTTCCAAAATATAGCGCG 59.138 47.619 0.00 0.00 0.00 6.86
1908 2073 2.223377 CCTCCGTTCCAAAATATAGCGC 59.777 50.000 0.00 0.00 0.00 5.92
1909 2074 2.806244 CCCTCCGTTCCAAAATATAGCG 59.194 50.000 0.00 0.00 0.00 4.26
1910 2075 4.065789 CTCCCTCCGTTCCAAAATATAGC 58.934 47.826 0.00 0.00 0.00 2.97
1911 2076 5.291905 ACTCCCTCCGTTCCAAAATATAG 57.708 43.478 0.00 0.00 0.00 1.31
1912 2077 6.239772 CCATACTCCCTCCGTTCCAAAATATA 60.240 42.308 0.00 0.00 0.00 0.86
1913 2078 5.456186 CCATACTCCCTCCGTTCCAAAATAT 60.456 44.000 0.00 0.00 0.00 1.28
1914 2079 4.141574 CCATACTCCCTCCGTTCCAAAATA 60.142 45.833 0.00 0.00 0.00 1.40
1915 2080 3.371595 CCATACTCCCTCCGTTCCAAAAT 60.372 47.826 0.00 0.00 0.00 1.82
1916 2081 2.026636 CCATACTCCCTCCGTTCCAAAA 60.027 50.000 0.00 0.00 0.00 2.44
1917 2082 1.557832 CCATACTCCCTCCGTTCCAAA 59.442 52.381 0.00 0.00 0.00 3.28
1918 2083 1.200519 CCATACTCCCTCCGTTCCAA 58.799 55.000 0.00 0.00 0.00 3.53
1919 2084 0.042131 ACCATACTCCCTCCGTTCCA 59.958 55.000 0.00 0.00 0.00 3.53
1920 2085 0.464452 CACCATACTCCCTCCGTTCC 59.536 60.000 0.00 0.00 0.00 3.62
1921 2086 1.192428 ACACCATACTCCCTCCGTTC 58.808 55.000 0.00 0.00 0.00 3.95
1922 2087 1.278127 CAACACCATACTCCCTCCGTT 59.722 52.381 0.00 0.00 0.00 4.44
1923 2088 0.902531 CAACACCATACTCCCTCCGT 59.097 55.000 0.00 0.00 0.00 4.69
1924 2089 0.178068 CCAACACCATACTCCCTCCG 59.822 60.000 0.00 0.00 0.00 4.63
1925 2090 1.580059 TCCAACACCATACTCCCTCC 58.420 55.000 0.00 0.00 0.00 4.30
1926 2091 3.933861 ATTCCAACACCATACTCCCTC 57.066 47.619 0.00 0.00 0.00 4.30
1927 2092 4.675063 AAATTCCAACACCATACTCCCT 57.325 40.909 0.00 0.00 0.00 4.20
1928 2093 4.770010 TGAAAATTCCAACACCATACTCCC 59.230 41.667 0.00 0.00 0.00 4.30
1929 2094 5.975693 TGAAAATTCCAACACCATACTCC 57.024 39.130 0.00 0.00 0.00 3.85
1930 2095 6.332630 CCATGAAAATTCCAACACCATACTC 58.667 40.000 0.00 0.00 0.00 2.59
1931 2096 5.337491 GCCATGAAAATTCCAACACCATACT 60.337 40.000 0.00 0.00 0.00 2.12
1932 2097 4.869861 GCCATGAAAATTCCAACACCATAC 59.130 41.667 0.00 0.00 0.00 2.39
1992 2157 8.770010 AGGTATTGACTAGTTTAGTATGCTCT 57.230 34.615 0.00 0.00 39.59 4.09
2014 2196 2.643304 GAGGAGGAAAAGGTACCAAGGT 59.357 50.000 15.94 0.00 0.00 3.50
2108 2298 4.143137 GCAAGTTGTTTGTGTTTCCAGTTG 60.143 41.667 4.48 0.00 39.08 3.16
2130 2320 1.140816 GACGATTAGCGAATGGGAGC 58.859 55.000 0.00 0.00 44.57 4.70
2773 4562 6.604735 AGAAACATACGGTTAGATTGATGC 57.395 37.500 0.00 0.00 39.29 3.91
2953 4754 3.388308 CAGAATCAGTCGCCATAGAAGG 58.612 50.000 0.00 0.00 0.00 3.46
2966 4767 5.106830 TGCATTATCATTAGCGCAGAATCAG 60.107 40.000 11.47 0.00 0.00 2.90
3017 4818 2.733552 CTCATTGTGTGTGAGAAGGACG 59.266 50.000 0.00 0.00 44.57 4.79
3139 5048 5.241662 AGGTAATCTCAGAGTCAGCAAAAC 58.758 41.667 0.00 0.00 0.00 2.43
3145 5054 5.913137 ACTCAAGGTAATCTCAGAGTCAG 57.087 43.478 0.00 0.00 36.61 3.51
3519 5433 1.880027 GGTCACCTAGGTTGCACAAAG 59.120 52.381 13.15 0.00 0.00 2.77
3999 6082 3.181515 CGCCGCTGTAATGTAATTCACAA 60.182 43.478 0.00 0.00 41.55 3.33
4010 6094 1.137086 AGTCTTGATCGCCGCTGTAAT 59.863 47.619 0.00 0.00 0.00 1.89
4542 6661 7.992754 AATCCTGATAAAGATCATACTTGCC 57.007 36.000 0.00 0.00 41.33 4.52
4650 6776 3.228749 CAGAGTTACATTTGCAAGTGCG 58.771 45.455 20.63 3.65 45.83 5.34
4727 6861 4.455533 TGTCACTTCACTGCCAACATTATC 59.544 41.667 0.00 0.00 0.00 1.75
4878 7045 3.619979 ACAGCATGGTAGCAGGTAACTTC 60.620 47.826 8.51 0.00 45.44 3.01
4905 7072 1.215647 CACAGTCGGTAGGTGAGCC 59.784 63.158 0.00 0.00 34.52 4.70
5136 7314 1.882623 CTTTGGGGAGCAAAGAGACAC 59.117 52.381 0.00 0.00 40.91 3.67
5206 7390 1.846175 GACTGCGCAAGAACAACAAAC 59.154 47.619 13.05 0.00 43.02 2.93
5220 7404 0.109597 GACAGCAATTTGGGACTGCG 60.110 55.000 0.00 0.00 41.05 5.18
5338 7522 9.883142 TTCCATTCAAGTTAAACATTGTTCTTT 57.117 25.926 1.83 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.