Multiple sequence alignment - TraesCS4B01G209000

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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 TraesCS4B01G209000 chr4B 100.000 2568 0 0 1 2568 446334380 446336947 0.000000e+00 4743.0
1 TraesCS4B01G209000 chr4D 90.107 1769 95 35 37 1750 360953814 360952071 0.000000e+00 2224.0
2 TraesCS4B01G209000 chr4D 87.900 281 31 2 2291 2568 360951523 360951243 6.850000e-86 327.0
3 TraesCS4B01G209000 chr4D 89.516 248 23 2 2275 2519 360951771 360951524 6.900000e-81 311.0
4 TraesCS4B01G209000 chr4D 82.555 321 29 5 1893 2192 360952090 360951776 9.120000e-65 257.0
5 TraesCS4B01G209000 chr4A 92.638 1372 49 13 1 1349 103726337 103727679 0.000000e+00 1927.0
6 TraesCS4B01G209000 chr4A 89.286 420 33 8 1339 1747 103729647 103730065 1.360000e-142 516.0
7 TraesCS4B01G209000 chr4A 86.532 297 37 2 2275 2568 103730370 103730666 8.860000e-85 324.0
8 TraesCS4B01G209000 chr4A 88.406 207 22 2 1893 2098 103730049 103730254 5.490000e-62 248.0
9 TraesCS4B01G209000 chr4A 91.667 132 7 4 1761 1889 216809766 216809636 2.030000e-41 180.0
10 TraesCS4B01G209000 chr4A 89.412 85 5 2 2191 2275 477033331 477033251 1.260000e-18 104.0
11 TraesCS4B01G209000 chr1D 95.000 120 5 1 1771 1889 211684811 211684930 1.210000e-43 187.0
12 TraesCS4B01G209000 chr1D 94.215 121 6 1 1771 1890 341039711 341039591 1.570000e-42 183.0
13 TraesCS4B01G209000 chr1B 94.262 122 6 1 1771 1891 402109964 402109843 4.360000e-43 185.0
14 TraesCS4B01G209000 chr7A 92.248 129 9 1 1771 1898 117020639 117020511 5.640000e-42 182.0
15 TraesCS4B01G209000 chr7A 86.316 95 8 3 2181 2275 70709348 70709437 5.850000e-17 99.0
16 TraesCS4B01G209000 chr7B 92.800 125 7 2 1771 1893 489828500 489828624 2.030000e-41 180.0
17 TraesCS4B01G209000 chr7B 92.623 122 8 1 1771 1891 40353997 40354118 9.450000e-40 174.0
18 TraesCS4B01G209000 chr1A 93.443 122 7 1 1771 1891 554284243 554284364 2.030000e-41 180.0
19 TraesCS4B01G209000 chr1A 88.194 144 13 4 1771 1913 47208183 47208043 4.390000e-38 169.0
20 TraesCS4B01G209000 chr6D 97.059 68 1 1 2191 2257 413075622 413075555 2.090000e-21 113.0
21 TraesCS4B01G209000 chr6D 89.362 94 2 6 2184 2275 8138020 8137933 7.510000e-21 111.0
22 TraesCS4B01G209000 chr7D 89.412 85 5 2 2191 2275 93783199 93783279 1.260000e-18 104.0
23 TraesCS4B01G209000 chr3D 88.889 90 3 4 2189 2275 383544163 383544078 1.260000e-18 104.0
24 TraesCS4B01G209000 chr3D 86.458 96 4 6 2191 2284 593120405 593120493 2.100000e-16 97.1
25 TraesCS4B01G209000 chr2A 89.412 85 2 3 2191 2275 445715002 445714925 1.630000e-17 100.0
26 TraesCS4B01G209000 chr2D 85.263 95 10 2 2182 2276 128111966 128112056 7.560000e-16 95.3


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G209000 chr4B 446334380 446336947 2567 False 4743.00 4743 100.0000 1 2568 1 chr4B.!!$F1 2567
1 TraesCS4B01G209000 chr4D 360951243 360953814 2571 True 779.75 2224 87.5195 37 2568 4 chr4D.!!$R1 2531
2 TraesCS4B01G209000 chr4A 103726337 103730666 4329 False 753.75 1927 89.2155 1 2568 4 chr4A.!!$F1 2567

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
600 638 0.46187 CCGCTCCCGAATCACAATCA 60.462 55.0 0.0 0.0 36.29 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 3947 0.033109 ATTCCAGTTAAGGGCAGCCC 60.033 55.0 24.9 24.9 45.9 5.19 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
34 35 6.905544 TTACGAATACCAATCGCAATGTTA 57.094 33.333 0.00 0.00 43.88 2.41
122 127 5.061853 CAGAACCATCCATATTCCAGTCTG 58.938 45.833 0.00 0.00 0.00 3.51
146 151 2.632512 CAAGGGTGGGCAAATTGTTAGT 59.367 45.455 0.00 0.00 0.00 2.24
154 159 4.038162 TGGGCAAATTGTTAGTACCACAAC 59.962 41.667 9.78 3.59 36.97 3.32
227 234 1.345415 ACTACCAATCGACCACCGTTT 59.655 47.619 0.00 0.00 39.75 3.60
231 238 1.591158 CCAATCGACCACCGTTTATCG 59.409 52.381 0.00 0.00 39.75 2.92
403 434 1.375268 GCTCCTCCTCACTGCACAC 60.375 63.158 0.00 0.00 0.00 3.82
404 435 2.052779 CTCCTCCTCACTGCACACA 58.947 57.895 0.00 0.00 0.00 3.72
414 445 2.124942 TGCACACAGAACGCCACA 60.125 55.556 0.00 0.00 0.00 4.17
415 446 2.327940 GCACACAGAACGCCACAC 59.672 61.111 0.00 0.00 0.00 3.82
439 473 3.741476 CTCAGCCGCAGCCCAAAC 61.741 66.667 0.00 0.00 41.25 2.93
600 638 0.461870 CCGCTCCCGAATCACAATCA 60.462 55.000 0.00 0.00 36.29 2.57
661 699 4.430765 CGGTGTCGCGGTTAGCCT 62.431 66.667 6.13 0.00 44.76 4.58
662 700 2.813908 GGTGTCGCGGTTAGCCTG 60.814 66.667 6.13 0.00 44.76 4.85
663 701 2.048503 GTGTCGCGGTTAGCCTGT 60.049 61.111 6.13 0.00 44.76 4.00
664 702 2.048597 TGTCGCGGTTAGCCTGTG 60.049 61.111 6.13 0.00 44.76 3.66
665 703 3.488090 GTCGCGGTTAGCCTGTGC 61.488 66.667 6.13 0.00 44.76 4.57
704 742 2.717809 GGTGAGCGCTCGTTCGTTC 61.718 63.158 30.75 14.53 39.59 3.95
1209 1271 2.184830 CATGATGAGGGTGGCTGCG 61.185 63.158 0.00 0.00 0.00 5.18
1284 1346 2.766229 GGCCTCTCCCTCCTCACC 60.766 72.222 0.00 0.00 0.00 4.02
1311 1373 2.893886 GCGTGACGCGTTTGTTATC 58.106 52.632 16.19 0.00 44.55 1.75
1315 1377 2.470140 CGTGACGCGTTTGTTATCTGTC 60.470 50.000 15.53 0.00 35.54 3.51
1323 1391 4.034048 GCGTTTGTTATCTGTCCGAATCAT 59.966 41.667 0.00 0.00 0.00 2.45
1336 1404 2.063541 GAATCATTTCGCCCCGCCTG 62.064 60.000 0.00 0.00 0.00 4.85
1337 1405 2.837031 AATCATTTCGCCCCGCCTGT 62.837 55.000 0.00 0.00 0.00 4.00
1339 1407 1.525995 CATTTCGCCCCGCCTGTAT 60.526 57.895 0.00 0.00 0.00 2.29
1340 1408 0.250124 CATTTCGCCCCGCCTGTATA 60.250 55.000 0.00 0.00 0.00 1.47
1342 1410 0.470766 TTTCGCCCCGCCTGTATAAT 59.529 50.000 0.00 0.00 0.00 1.28
1343 1411 0.250124 TTCGCCCCGCCTGTATAATG 60.250 55.000 0.00 0.00 0.00 1.90
1373 3423 3.646611 TTGCATTGATGGACAGTGTTG 57.353 42.857 0.00 0.00 38.28 3.33
1378 3428 4.445385 GCATTGATGGACAGTGTTGTTTTC 59.555 41.667 0.00 0.00 37.76 2.29
1383 3433 2.616376 TGGACAGTGTTGTTTTCGGATG 59.384 45.455 0.00 0.00 37.76 3.51
1384 3434 2.031157 GGACAGTGTTGTTTTCGGATGG 60.031 50.000 0.00 0.00 37.76 3.51
1385 3435 2.616842 GACAGTGTTGTTTTCGGATGGT 59.383 45.455 0.00 0.00 37.76 3.55
1386 3436 2.616842 ACAGTGTTGTTTTCGGATGGTC 59.383 45.455 0.00 0.00 32.28 4.02
1387 3437 1.871039 AGTGTTGTTTTCGGATGGTCG 59.129 47.619 0.00 0.00 0.00 4.79
1388 3438 1.069500 GTGTTGTTTTCGGATGGTCGG 60.069 52.381 0.00 0.00 0.00 4.79
1389 3439 1.232119 GTTGTTTTCGGATGGTCGGT 58.768 50.000 0.00 0.00 0.00 4.69
1390 3440 1.069500 GTTGTTTTCGGATGGTCGGTG 60.069 52.381 0.00 0.00 0.00 4.94
1391 3441 0.604243 TGTTTTCGGATGGTCGGTGG 60.604 55.000 0.00 0.00 0.00 4.61
1392 3442 1.673009 TTTTCGGATGGTCGGTGGC 60.673 57.895 0.00 0.00 0.00 5.01
1406 3456 3.241530 TGGCTCGGTGCTGACCTT 61.242 61.111 1.77 0.00 40.58 3.50
1408 3458 3.426568 GCTCGGTGCTGACCTTGC 61.427 66.667 0.00 0.00 40.58 4.01
1409 3459 2.345244 CTCGGTGCTGACCTTGCT 59.655 61.111 0.00 0.00 40.58 3.91
1495 3561 2.563179 CGAGAAGTTTGAGAGGGAGGAA 59.437 50.000 0.00 0.00 0.00 3.36
1540 3606 2.694760 GCAGAAGAGGGCCAAAGCG 61.695 63.158 6.18 0.00 41.24 4.68
1622 3688 2.224523 TGGCTGGTTCTTCTGTAACCTG 60.225 50.000 6.56 6.97 45.53 4.00
1629 3695 2.972348 TCTTCTGTAACCTGGGTGAGT 58.028 47.619 0.00 0.00 0.00 3.41
1664 3731 4.032960 TCTGCCTTTGCTTCTTGGAATA 57.967 40.909 0.00 0.00 38.71 1.75
1714 3781 9.601217 ACATATTTAGTATGAGTGAGTTTGTCC 57.399 33.333 1.75 0.00 42.34 4.02
1721 3788 4.916983 TGAGTGAGTTTGTCCCATTTTG 57.083 40.909 0.00 0.00 0.00 2.44
1729 3796 5.205056 AGTTTGTCCCATTTTGTACCAAGA 58.795 37.500 0.00 0.00 0.00 3.02
1746 3813 8.630917 TGTACCAAGAACTAGAATATGACTAGC 58.369 37.037 13.67 3.49 40.40 3.42
1747 3814 6.740110 ACCAAGAACTAGAATATGACTAGCG 58.260 40.000 13.67 0.00 40.40 4.26
1748 3815 6.546403 ACCAAGAACTAGAATATGACTAGCGA 59.454 38.462 13.67 0.00 40.40 4.93
1749 3816 7.068348 ACCAAGAACTAGAATATGACTAGCGAA 59.932 37.037 13.67 0.00 40.40 4.70
1750 3817 7.593273 CCAAGAACTAGAATATGACTAGCGAAG 59.407 40.741 13.67 0.00 40.40 3.79
1751 3818 7.209471 AGAACTAGAATATGACTAGCGAAGG 57.791 40.000 13.67 0.00 40.40 3.46
1752 3819 5.968528 ACTAGAATATGACTAGCGAAGGG 57.031 43.478 13.67 0.00 40.40 3.95
1753 3820 4.767928 ACTAGAATATGACTAGCGAAGGGG 59.232 45.833 13.67 0.00 40.40 4.79
1754 3821 3.845860 AGAATATGACTAGCGAAGGGGA 58.154 45.455 0.00 0.00 0.00 4.81
1755 3822 3.829601 AGAATATGACTAGCGAAGGGGAG 59.170 47.826 0.00 0.00 0.00 4.30
1756 3823 1.329256 TATGACTAGCGAAGGGGAGC 58.671 55.000 0.00 0.00 0.00 4.70
1757 3824 1.403687 ATGACTAGCGAAGGGGAGCC 61.404 60.000 0.00 0.00 0.00 4.70
1758 3825 1.758906 GACTAGCGAAGGGGAGCCT 60.759 63.158 0.00 0.00 0.00 4.58
1759 3826 1.306226 ACTAGCGAAGGGGAGCCTT 60.306 57.895 0.00 0.00 0.00 4.35
1760 3827 1.144936 CTAGCGAAGGGGAGCCTTG 59.855 63.158 0.00 0.00 0.00 3.61
1761 3828 2.317149 CTAGCGAAGGGGAGCCTTGG 62.317 65.000 0.00 0.00 0.00 3.61
1762 3829 4.035102 GCGAAGGGGAGCCTTGGT 62.035 66.667 0.00 0.00 0.00 3.67
1763 3830 2.045926 CGAAGGGGAGCCTTGGTG 60.046 66.667 0.00 0.00 0.00 4.17
1764 3831 2.361737 GAAGGGGAGCCTTGGTGC 60.362 66.667 0.00 0.00 0.00 5.01
1765 3832 3.185203 AAGGGGAGCCTTGGTGCA 61.185 61.111 0.00 0.00 0.00 4.57
1766 3833 3.215587 AAGGGGAGCCTTGGTGCAG 62.216 63.158 0.00 0.00 0.00 4.41
1767 3834 3.971702 GGGGAGCCTTGGTGCAGT 61.972 66.667 0.00 0.00 0.00 4.40
1768 3835 2.674380 GGGAGCCTTGGTGCAGTG 60.674 66.667 0.00 0.00 0.00 3.66
1769 3836 2.674380 GGAGCCTTGGTGCAGTGG 60.674 66.667 0.00 0.00 0.00 4.00
1770 3837 2.113986 GAGCCTTGGTGCAGTGGT 59.886 61.111 0.00 0.00 0.00 4.16
1771 3838 1.968540 GAGCCTTGGTGCAGTGGTC 60.969 63.158 0.00 0.00 0.00 4.02
1772 3839 2.203337 GCCTTGGTGCAGTGGTCA 60.203 61.111 0.00 0.00 0.00 4.02
1773 3840 1.827789 GCCTTGGTGCAGTGGTCAA 60.828 57.895 0.00 0.00 0.00 3.18
1774 3841 1.799258 GCCTTGGTGCAGTGGTCAAG 61.799 60.000 0.00 0.00 37.09 3.02
1775 3842 0.466189 CCTTGGTGCAGTGGTCAAGT 60.466 55.000 0.00 0.00 35.98 3.16
1776 3843 0.947244 CTTGGTGCAGTGGTCAAGTC 59.053 55.000 0.00 0.00 33.85 3.01
1777 3844 0.465460 TTGGTGCAGTGGTCAAGTCC 60.465 55.000 0.00 0.00 0.00 3.85
1778 3845 1.344953 TGGTGCAGTGGTCAAGTCCT 61.345 55.000 0.00 0.00 0.00 3.85
1779 3846 0.886490 GGTGCAGTGGTCAAGTCCTG 60.886 60.000 0.00 0.00 0.00 3.86
1780 3847 0.886490 GTGCAGTGGTCAAGTCCTGG 60.886 60.000 0.00 0.00 0.00 4.45
1781 3848 1.053835 TGCAGTGGTCAAGTCCTGGA 61.054 55.000 0.00 0.00 0.00 3.86
1782 3849 0.108585 GCAGTGGTCAAGTCCTGGAA 59.891 55.000 0.00 0.00 0.00 3.53
1783 3850 1.476833 GCAGTGGTCAAGTCCTGGAAA 60.477 52.381 0.00 0.00 0.00 3.13
1784 3851 2.222027 CAGTGGTCAAGTCCTGGAAAC 58.778 52.381 0.00 0.00 0.00 2.78
1785 3852 1.843851 AGTGGTCAAGTCCTGGAAACA 59.156 47.619 0.00 0.00 39.59 2.83
1799 3866 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
1800 3867 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
1801 3868 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
1802 3869 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
1803 3870 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
1804 3871 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
1805 3872 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
1806 3873 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
1807 3874 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
1808 3875 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
1809 3876 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
1810 3877 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
1811 3878 6.576442 GCCTCTTACAGAAATGTAGGGAAAGA 60.576 42.308 0.00 0.00 0.00 2.52
1812 3879 6.819146 CCTCTTACAGAAATGTAGGGAAAGAC 59.181 42.308 0.00 0.00 0.00 3.01
1813 3880 7.310734 CCTCTTACAGAAATGTAGGGAAAGACT 60.311 40.741 0.00 0.00 0.00 3.24
1814 3881 7.386851 TCTTACAGAAATGTAGGGAAAGACTG 58.613 38.462 0.00 0.00 0.00 3.51
1815 3882 4.327680 ACAGAAATGTAGGGAAAGACTGC 58.672 43.478 0.00 0.00 0.00 4.40
1816 3883 3.372206 CAGAAATGTAGGGAAAGACTGCG 59.628 47.826 0.00 0.00 0.00 5.18
1817 3884 3.008049 AGAAATGTAGGGAAAGACTGCGT 59.992 43.478 0.00 0.00 0.00 5.24
1818 3885 4.222145 AGAAATGTAGGGAAAGACTGCGTA 59.778 41.667 0.00 0.00 0.00 4.42
1819 3886 3.521947 ATGTAGGGAAAGACTGCGTAC 57.478 47.619 0.00 0.00 37.28 3.67
1820 3887 2.241160 TGTAGGGAAAGACTGCGTACA 58.759 47.619 0.00 0.00 42.31 2.90
1821 3888 3.119101 ATGTAGGGAAAGACTGCGTACAG 60.119 47.826 5.34 0.00 45.87 2.74
1831 3898 2.736144 CTGCGTACAGTAGACCCAAA 57.264 50.000 0.00 0.00 39.22 3.28
1832 3899 2.607187 CTGCGTACAGTAGACCCAAAG 58.393 52.381 0.00 0.00 39.22 2.77
1833 3900 1.965643 TGCGTACAGTAGACCCAAAGT 59.034 47.619 0.00 0.00 0.00 2.66
1834 3901 2.288579 TGCGTACAGTAGACCCAAAGTG 60.289 50.000 0.00 0.00 0.00 3.16
1835 3902 2.929592 GCGTACAGTAGACCCAAAGTGG 60.930 54.545 0.00 0.00 37.25 4.00
1836 3903 2.298163 CGTACAGTAGACCCAAAGTGGT 59.702 50.000 0.00 0.00 42.79 4.16
1843 3910 2.945718 ACCCAAAGTGGTCAGACCT 58.054 52.632 20.82 0.00 39.58 3.85
1844 3911 1.222567 ACCCAAAGTGGTCAGACCTT 58.777 50.000 20.82 4.67 39.58 3.50
1845 3912 1.569072 ACCCAAAGTGGTCAGACCTTT 59.431 47.619 20.82 10.75 39.58 3.11
1846 3913 2.230660 CCCAAAGTGGTCAGACCTTTC 58.769 52.381 20.82 10.83 39.58 2.62
1847 3914 2.230660 CCAAAGTGGTCAGACCTTTCC 58.769 52.381 20.82 6.14 39.58 3.13
1848 3915 2.230660 CAAAGTGGTCAGACCTTTCCC 58.769 52.381 20.82 3.78 39.58 3.97
1849 3916 1.821088 AAGTGGTCAGACCTTTCCCT 58.179 50.000 20.82 5.92 39.58 4.20
1850 3917 1.059913 AGTGGTCAGACCTTTCCCTG 58.940 55.000 20.82 0.00 39.58 4.45
1851 3918 0.036875 GTGGTCAGACCTTTCCCTGG 59.963 60.000 20.82 0.00 39.58 4.45
1852 3919 0.104672 TGGTCAGACCTTTCCCTGGA 60.105 55.000 20.82 0.00 39.58 3.86
1853 3920 0.325272 GGTCAGACCTTTCCCTGGAC 59.675 60.000 12.94 0.00 34.73 4.02
1854 3921 0.325272 GTCAGACCTTTCCCTGGACC 59.675 60.000 0.00 0.00 0.00 4.46
1855 3922 0.193574 TCAGACCTTTCCCTGGACCT 59.806 55.000 0.00 0.00 0.00 3.85
1856 3923 0.326264 CAGACCTTTCCCTGGACCTG 59.674 60.000 0.00 0.00 0.00 4.00
1857 3924 1.002011 GACCTTTCCCTGGACCTGC 60.002 63.158 0.00 0.00 0.00 4.85
1858 3925 2.356667 CCTTTCCCTGGACCTGCC 59.643 66.667 0.00 0.00 37.10 4.85
1859 3926 2.356667 CTTTCCCTGGACCTGCCC 59.643 66.667 0.00 0.00 34.97 5.36
1860 3927 2.451493 TTTCCCTGGACCTGCCCA 60.451 61.111 0.00 0.00 34.97 5.36
1861 3928 2.080336 CTTTCCCTGGACCTGCCCAA 62.080 60.000 0.00 0.00 35.47 4.12
1862 3929 2.080336 TTTCCCTGGACCTGCCCAAG 62.080 60.000 0.00 0.00 35.47 3.61
1863 3930 4.748144 CCCTGGACCTGCCCAAGC 62.748 72.222 0.00 0.00 35.47 4.01
1880 3947 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
1881 3948 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
1882 3949 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
1883 3950 1.821332 GGAGCTACATGCACTGGGC 60.821 63.158 0.00 0.00 45.94 5.36
1884 3951 1.222936 GAGCTACATGCACTGGGCT 59.777 57.895 2.50 13.76 45.94 5.19
1885 3952 1.077930 AGCTACATGCACTGGGCTG 60.078 57.895 2.50 1.44 45.94 4.85
1886 3953 2.768492 GCTACATGCACTGGGCTGC 61.768 63.158 2.50 0.00 45.15 5.25
1887 3954 2.045045 TACATGCACTGGGCTGCC 60.045 61.111 11.05 11.05 45.15 4.85
1888 3955 3.643595 TACATGCACTGGGCTGCCC 62.644 63.158 30.97 30.97 45.71 5.36
1889 3956 4.753662 CATGCACTGGGCTGCCCT 62.754 66.667 35.80 16.65 45.70 5.19
1890 3957 3.988678 ATGCACTGGGCTGCCCTT 61.989 61.111 35.80 21.48 45.70 3.95
1891 3958 2.615465 ATGCACTGGGCTGCCCTTA 61.615 57.895 35.80 18.01 45.70 2.69
1892 3959 2.035626 GCACTGGGCTGCCCTTAA 59.964 61.111 35.80 17.25 45.70 1.85
1893 3960 2.343426 GCACTGGGCTGCCCTTAAC 61.343 63.158 35.80 20.18 45.70 2.01
1894 3961 1.380302 CACTGGGCTGCCCTTAACT 59.620 57.895 35.80 12.60 45.70 2.24
1895 3962 0.962356 CACTGGGCTGCCCTTAACTG 60.962 60.000 35.80 19.56 45.70 3.16
1896 3963 1.379044 CTGGGCTGCCCTTAACTGG 60.379 63.158 35.80 14.36 45.70 4.00
1897 3964 1.850289 TGGGCTGCCCTTAACTGGA 60.850 57.895 35.80 12.68 45.70 3.86
1898 3965 1.382629 GGGCTGCCCTTAACTGGAA 59.617 57.895 30.42 0.00 41.34 3.53
1899 3966 0.033109 GGGCTGCCCTTAACTGGAAT 60.033 55.000 30.42 0.00 41.34 3.01
1900 3967 1.214424 GGGCTGCCCTTAACTGGAATA 59.786 52.381 30.42 0.00 41.34 1.75
1901 3968 2.158460 GGGCTGCCCTTAACTGGAATAT 60.158 50.000 30.42 0.00 41.34 1.28
1902 3969 2.887152 GGCTGCCCTTAACTGGAATATG 59.113 50.000 7.66 0.00 0.00 1.78
1903 3970 3.435026 GGCTGCCCTTAACTGGAATATGA 60.435 47.826 7.66 0.00 0.00 2.15
1904 3971 3.565902 GCTGCCCTTAACTGGAATATGAC 59.434 47.826 0.00 0.00 0.00 3.06
1910 3977 6.226787 CCCTTAACTGGAATATGACTAGCAG 58.773 44.000 0.00 0.00 0.00 4.24
1913 3980 7.655328 CCTTAACTGGAATATGACTAGCAGAAG 59.345 40.741 0.00 0.00 0.00 2.85
1935 4002 5.892348 AGTATTCAACCAGACCTTCCAAAT 58.108 37.500 0.00 0.00 0.00 2.32
1950 4018 6.954102 ACCTTCCAAATAAACTTATTCAGCCT 59.046 34.615 0.00 0.00 32.46 4.58
1983 4051 7.325599 GCTACAAGCAGAATTTTGTACTTTG 57.674 36.000 0.00 1.74 41.89 2.77
1987 4055 3.640967 AGCAGAATTTTGTACTTTGGCCA 59.359 39.130 0.00 0.00 0.00 5.36
1988 4056 4.284234 AGCAGAATTTTGTACTTTGGCCAT 59.716 37.500 6.09 0.00 0.00 4.40
1989 4057 4.389687 GCAGAATTTTGTACTTTGGCCATG 59.610 41.667 6.09 5.34 0.00 3.66
2000 4068 2.334006 TTGGCCATGGGGTAAAATGT 57.666 45.000 15.13 0.00 36.17 2.71
2014 4082 5.221009 GGGTAAAATGTTTACGGTGTGACAA 60.221 40.000 5.13 0.00 0.00 3.18
2022 4090 5.155643 GTTTACGGTGTGACAACAAAACTT 58.844 37.500 16.72 0.00 38.27 2.66
2061 4129 6.779049 ACCATTAGATGCATTGTCATATTGGT 59.221 34.615 0.00 8.59 0.00 3.67
2062 4130 7.288389 ACCATTAGATGCATTGTCATATTGGTT 59.712 33.333 0.00 0.00 0.00 3.67
2079 4147 4.811555 TGGTTCAAAGAAACATCTCACG 57.188 40.909 0.00 0.00 0.00 4.35
2087 4155 4.456280 AGAAACATCTCACGCTCACATA 57.544 40.909 0.00 0.00 0.00 2.29
2098 4166 4.154015 TCACGCTCACATATGGAAGTTTTG 59.846 41.667 7.80 3.60 0.00 2.44
2113 4202 8.696410 TGGAAGTTTTGAACATGTTTTTAGAC 57.304 30.769 13.36 8.44 0.00 2.59
2114 4203 8.307483 TGGAAGTTTTGAACATGTTTTTAGACA 58.693 29.630 13.36 1.71 0.00 3.41
2119 4208 8.807581 GTTTTGAACATGTTTTTAGACAGAAGG 58.192 33.333 13.36 0.00 32.19 3.46
2120 4209 7.639113 TTGAACATGTTTTTAGACAGAAGGT 57.361 32.000 13.36 0.00 32.19 3.50
2123 4212 4.887071 ACATGTTTTTAGACAGAAGGTGCA 59.113 37.500 0.00 0.00 32.19 4.57
2135 4224 4.821935 GGTGCACCCAGCTTTACT 57.178 55.556 26.31 0.00 45.94 2.24
2136 4225 3.036431 GGTGCACCCAGCTTTACTT 57.964 52.632 26.31 0.00 45.94 2.24
2137 4226 2.194201 GGTGCACCCAGCTTTACTTA 57.806 50.000 26.31 0.00 45.94 2.24
2138 4227 1.810755 GGTGCACCCAGCTTTACTTAC 59.189 52.381 26.31 0.00 45.94 2.34
2139 4228 2.552373 GGTGCACCCAGCTTTACTTACT 60.552 50.000 26.31 0.00 45.94 2.24
2140 4229 3.307199 GGTGCACCCAGCTTTACTTACTA 60.307 47.826 26.31 0.00 45.94 1.82
2188 4277 8.044060 TCAAGATAGCAAAACAGGATAAACTG 57.956 34.615 0.00 0.00 44.03 3.16
2192 4281 9.331282 AGATAGCAAAACAGGATAAACTGATAC 57.669 33.333 0.00 0.00 40.97 2.24
2194 4283 7.617041 AGCAAAACAGGATAAACTGATACTC 57.383 36.000 0.00 0.00 40.97 2.59
2196 4285 6.183360 GCAAAACAGGATAAACTGATACTCCC 60.183 42.308 0.00 0.00 40.97 4.30
2197 4286 6.893020 AAACAGGATAAACTGATACTCCCT 57.107 37.500 0.00 0.00 40.97 4.20
2198 4287 6.487299 AACAGGATAAACTGATACTCCCTC 57.513 41.667 0.00 0.00 40.97 4.30
2199 4288 4.902448 ACAGGATAAACTGATACTCCCTCC 59.098 45.833 0.00 0.00 40.97 4.30
2200 4289 4.021894 CAGGATAAACTGATACTCCCTCCG 60.022 50.000 0.00 0.00 40.97 4.63
2201 4290 4.140994 AGGATAAACTGATACTCCCTCCGA 60.141 45.833 0.00 0.00 0.00 4.55
2202 4291 4.773149 GGATAAACTGATACTCCCTCCGAT 59.227 45.833 0.00 0.00 0.00 4.18
2203 4292 5.105675 GGATAAACTGATACTCCCTCCGATC 60.106 48.000 0.00 0.00 0.00 3.69
2204 4293 2.296073 ACTGATACTCCCTCCGATCC 57.704 55.000 0.00 0.00 0.00 3.36
2205 4294 1.499438 ACTGATACTCCCTCCGATCCA 59.501 52.381 0.00 0.00 0.00 3.41
2206 4295 2.110899 ACTGATACTCCCTCCGATCCAT 59.889 50.000 0.00 0.00 0.00 3.41
2207 4296 3.333980 ACTGATACTCCCTCCGATCCATA 59.666 47.826 0.00 0.00 0.00 2.74
2208 4297 4.017037 ACTGATACTCCCTCCGATCCATAT 60.017 45.833 0.00 0.00 0.00 1.78
2209 4298 4.947883 TGATACTCCCTCCGATCCATATT 58.052 43.478 0.00 0.00 0.00 1.28
2210 4299 6.087276 TGATACTCCCTCCGATCCATATTA 57.913 41.667 0.00 0.00 0.00 0.98
2211 4300 6.683537 TGATACTCCCTCCGATCCATATTAT 58.316 40.000 0.00 0.00 0.00 1.28
2212 4301 7.132805 TGATACTCCCTCCGATCCATATTATT 58.867 38.462 0.00 0.00 0.00 1.40
2213 4302 7.623677 TGATACTCCCTCCGATCCATATTATTT 59.376 37.037 0.00 0.00 0.00 1.40
2214 4303 6.054860 ACTCCCTCCGATCCATATTATTTG 57.945 41.667 0.00 0.00 0.00 2.32
2215 4304 5.548056 ACTCCCTCCGATCCATATTATTTGT 59.452 40.000 0.00 0.00 0.00 2.83
2216 4305 6.049955 TCCCTCCGATCCATATTATTTGTC 57.950 41.667 0.00 0.00 0.00 3.18
2217 4306 5.785423 TCCCTCCGATCCATATTATTTGTCT 59.215 40.000 0.00 0.00 0.00 3.41
2218 4307 6.272324 TCCCTCCGATCCATATTATTTGTCTT 59.728 38.462 0.00 0.00 0.00 3.01
2219 4308 7.456585 TCCCTCCGATCCATATTATTTGTCTTA 59.543 37.037 0.00 0.00 0.00 2.10
2220 4309 7.766278 CCCTCCGATCCATATTATTTGTCTTAG 59.234 40.741 0.00 0.00 0.00 2.18
2221 4310 8.531982 CCTCCGATCCATATTATTTGTCTTAGA 58.468 37.037 0.00 0.00 0.00 2.10
2236 4325 9.751542 ATTTGTCTTAGATTTGTCTAGATACGG 57.248 33.333 0.00 0.00 0.00 4.02
2237 4326 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
2238 4327 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
2239 4328 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
2240 4329 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
2241 4330 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
2256 4345 6.199937 ACGGATGTATCTAACACTAAACGT 57.800 37.500 0.00 0.00 42.09 3.99
2257 4346 6.624423 ACGGATGTATCTAACACTAAACGTT 58.376 36.000 0.00 0.00 42.09 3.99
2258 4347 7.092716 ACGGATGTATCTAACACTAAACGTTT 58.907 34.615 18.90 18.90 42.09 3.60
2259 4348 7.599998 ACGGATGTATCTAACACTAAACGTTTT 59.400 33.333 20.19 2.88 42.09 2.43
2260 4349 9.075519 CGGATGTATCTAACACTAAACGTTTTA 57.924 33.333 20.19 4.02 42.09 1.52
2316 4405 9.897744 CATCAATTTTACAAGAAAGTGCTAGAA 57.102 29.630 0.00 0.00 35.30 2.10
2355 4447 7.743520 AAACTAACACACCAAATTTTGTACG 57.256 32.000 8.26 0.00 0.00 3.67
2364 4456 6.127842 ACACCAAATTTTGTACGATGGATACC 60.128 38.462 7.36 0.00 0.00 2.73
2375 4467 4.658063 ACGATGGATACCAAAGAACCAAA 58.342 39.130 0.00 0.00 36.95 3.28
2382 4474 5.300792 GGATACCAAAGAACCAAAACACTCA 59.699 40.000 0.00 0.00 0.00 3.41
2430 4522 7.562088 ACCTTAAGAAAAAGTATTCAACCACCA 59.438 33.333 3.36 0.00 0.00 4.17
2442 4534 8.097038 AGTATTCAACCACCATATATGCTACTG 58.903 37.037 7.24 1.32 0.00 2.74
2449 4541 6.270927 ACCACCATATATGCTACTGTCAGAAT 59.729 38.462 6.91 0.00 0.00 2.40
2466 4558 4.761739 TCAGAATTTTGTACTTCAGCCAGG 59.238 41.667 0.00 0.00 0.00 4.45
2472 4564 0.324943 GTACTTCAGCCAGGGAGCAA 59.675 55.000 0.00 0.00 34.23 3.91
2526 4850 5.510520 GGTTCAGCTGGTCCATATCTCTAAG 60.511 48.000 15.13 0.00 0.00 2.18
2533 4857 4.202535 TGGTCCATATCTCTAAGCCGTAGA 60.203 45.833 0.00 0.00 37.30 2.59
2538 4862 3.669251 ATCTCTAAGCCGTAGAATGCC 57.331 47.619 0.00 0.00 38.41 4.40
2539 4863 2.667470 TCTCTAAGCCGTAGAATGCCT 58.333 47.619 0.00 0.00 38.41 4.75
2544 4868 5.539048 TCTAAGCCGTAGAATGCCTATTTC 58.461 41.667 0.00 0.00 35.81 2.17
2557 4881 3.252701 TGCCTATTTCGGTATCTCGAGAC 59.747 47.826 19.30 6.49 40.42 3.36
2559 4883 4.073549 CCTATTTCGGTATCTCGAGACCT 58.926 47.826 19.30 5.40 40.40 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.554528 CAGCATTCTGAATATTCTGTAATTCGT 58.445 33.333 16.24 3.56 42.95 3.85
122 127 1.416030 ACAATTTGCCCACCCTTGAAC 59.584 47.619 0.00 0.00 0.00 3.18
146 151 2.050918 TGGATGTGTGGAGTTGTGGTA 58.949 47.619 0.00 0.00 0.00 3.25
154 159 3.572632 AAGGATGATGGATGTGTGGAG 57.427 47.619 0.00 0.00 0.00 3.86
231 238 0.027324 GGTACGGATCAGTCGTCGAC 59.973 60.000 17.70 17.70 41.38 4.20
384 415 1.838396 TGTGCAGTGAGGAGGAGCA 60.838 57.895 0.00 0.00 0.00 4.26
403 434 2.908073 GCAAGGGTGTGGCGTTCTG 61.908 63.158 0.00 0.00 0.00 3.02
404 435 2.594592 GCAAGGGTGTGGCGTTCT 60.595 61.111 0.00 0.00 0.00 3.01
405 436 3.670377 GGCAAGGGTGTGGCGTTC 61.670 66.667 0.00 0.00 34.03 3.95
409 440 2.674380 CTGAGGCAAGGGTGTGGC 60.674 66.667 0.00 0.00 44.15 5.01
410 441 2.674380 GCTGAGGCAAGGGTGTGG 60.674 66.667 0.00 0.00 38.54 4.17
439 473 4.201763 GGCTTATCTCTTCTGCTGTTTTCG 60.202 45.833 0.00 0.00 0.00 3.46
659 697 3.062466 TCGAGACCCGAGCACAGG 61.062 66.667 0.00 0.00 43.23 4.00
667 705 4.778415 CACCGCACTCGAGACCCG 62.778 72.222 21.68 16.91 38.10 5.28
704 742 1.388431 GCACTCGAAGAAGAGAAAGCG 59.612 52.381 0.62 0.00 40.57 4.68
788 832 0.239347 TCGAGACGAAGGAAACCGAC 59.761 55.000 0.00 0.00 31.06 4.79
1209 1271 0.660595 CGGTGATGCTATCGTCGTCC 60.661 60.000 0.00 0.00 0.00 4.79
1218 1280 3.387091 ACGGTGGCGGTGATGCTA 61.387 61.111 0.00 0.00 34.52 3.49
1269 1331 1.112315 CGATGGTGAGGAGGGAGAGG 61.112 65.000 0.00 0.00 0.00 3.69
1323 1391 0.470766 ATTATACAGGCGGGGCGAAA 59.529 50.000 0.00 0.00 0.00 3.46
1329 1397 1.812571 GCCATTCATTATACAGGCGGG 59.187 52.381 0.00 0.00 31.88 6.13
1332 1400 5.156355 CAATTCGCCATTCATTATACAGGC 58.844 41.667 0.00 0.00 38.73 4.85
1336 1404 6.862608 TCAATGCAATTCGCCATTCATTATAC 59.137 34.615 0.00 0.00 41.33 1.47
1337 1405 6.979465 TCAATGCAATTCGCCATTCATTATA 58.021 32.000 0.00 0.00 41.33 0.98
1339 1407 5.259832 TCAATGCAATTCGCCATTCATTA 57.740 34.783 0.00 0.00 41.33 1.90
1340 1408 4.126208 TCAATGCAATTCGCCATTCATT 57.874 36.364 0.00 0.00 41.33 2.57
1342 1410 3.449632 CATCAATGCAATTCGCCATTCA 58.550 40.909 0.00 0.00 41.33 2.57
1343 1411 2.798283 CCATCAATGCAATTCGCCATTC 59.202 45.455 0.00 0.00 41.33 2.67
1357 3407 4.261572 CCGAAAACAACACTGTCCATCAAT 60.262 41.667 0.00 0.00 33.45 2.57
1373 3423 1.918868 GCCACCGACCATCCGAAAAC 61.919 60.000 0.00 0.00 0.00 2.43
1378 3428 4.873129 CGAGCCACCGACCATCCG 62.873 72.222 0.00 0.00 0.00 4.18
1403 3453 0.891373 TCGAGAGAAGACCAGCAAGG 59.109 55.000 0.00 0.00 39.92 3.61
1404 3454 2.732412 TTCGAGAGAAGACCAGCAAG 57.268 50.000 0.00 0.00 46.92 4.01
1416 3466 3.176552 AGATCACCTGCATTTCGAGAG 57.823 47.619 0.00 0.00 0.00 3.20
1420 3470 3.744942 CCAGATAGATCACCTGCATTTCG 59.255 47.826 0.00 0.00 0.00 3.46
1495 3561 3.091545 CTCCTCTTTCTGTCTCTCAGCT 58.908 50.000 0.00 0.00 43.32 4.24
1537 3603 2.951229 TTCTTTTCTTTCCCCTCGCT 57.049 45.000 0.00 0.00 0.00 4.93
1540 3606 4.142881 CGTCGATTTCTTTTCTTTCCCCTC 60.143 45.833 0.00 0.00 0.00 4.30
1622 3688 6.403746 GCAGAAAAGCTAAGAATTACTCACCC 60.404 42.308 0.00 0.00 0.00 4.61
1629 3695 6.209391 AGCAAAGGCAGAAAAGCTAAGAATTA 59.791 34.615 0.00 0.00 44.61 1.40
1691 3758 8.141298 TGGGACAAACTCACTCATACTAAATA 57.859 34.615 0.00 0.00 31.92 1.40
1701 3768 7.632636 TGGTACAAAATGGGACAAACTCACTC 61.633 42.308 0.00 0.00 37.35 3.51
1702 3769 5.867151 TGGTACAAAATGGGACAAACTCACT 60.867 40.000 0.00 0.00 37.35 3.41
1721 3788 7.804129 CGCTAGTCATATTCTAGTTCTTGGTAC 59.196 40.741 11.18 0.00 37.69 3.34
1729 3796 5.244178 CCCCTTCGCTAGTCATATTCTAGTT 59.756 44.000 11.18 0.00 37.69 2.24
1749 3816 3.655211 CTGCACCAAGGCTCCCCT 61.655 66.667 0.00 0.00 45.77 4.79
1750 3817 3.971702 ACTGCACCAAGGCTCCCC 61.972 66.667 0.00 0.00 34.04 4.81
1751 3818 2.674380 CACTGCACCAAGGCTCCC 60.674 66.667 0.00 0.00 34.04 4.30
1752 3819 2.674380 CCACTGCACCAAGGCTCC 60.674 66.667 0.00 0.00 34.04 4.70
1753 3820 1.968540 GACCACTGCACCAAGGCTC 60.969 63.158 0.00 0.00 34.04 4.70
1754 3821 2.113986 GACCACTGCACCAAGGCT 59.886 61.111 0.00 0.00 34.04 4.58
1755 3822 1.799258 CTTGACCACTGCACCAAGGC 61.799 60.000 0.00 0.00 34.11 4.35
1756 3823 0.466189 ACTTGACCACTGCACCAAGG 60.466 55.000 0.00 0.00 40.02 3.61
1757 3824 0.947244 GACTTGACCACTGCACCAAG 59.053 55.000 0.00 0.00 41.12 3.61
1758 3825 0.465460 GGACTTGACCACTGCACCAA 60.465 55.000 0.00 0.00 0.00 3.67
1759 3826 1.148273 GGACTTGACCACTGCACCA 59.852 57.895 0.00 0.00 0.00 4.17
1760 3827 0.886490 CAGGACTTGACCACTGCACC 60.886 60.000 0.00 0.00 0.00 5.01
1761 3828 0.886490 CCAGGACTTGACCACTGCAC 60.886 60.000 0.00 0.00 0.00 4.57
1762 3829 1.053835 TCCAGGACTTGACCACTGCA 61.054 55.000 0.00 0.00 0.00 4.41
1763 3830 0.108585 TTCCAGGACTTGACCACTGC 59.891 55.000 0.00 0.00 0.00 4.40
1764 3831 2.222027 GTTTCCAGGACTTGACCACTG 58.778 52.381 0.00 0.00 0.00 3.66
1765 3832 1.843851 TGTTTCCAGGACTTGACCACT 59.156 47.619 0.00 0.00 0.00 4.00
1766 3833 2.222027 CTGTTTCCAGGACTTGACCAC 58.778 52.381 0.00 0.00 34.90 4.16
1767 3834 1.476833 GCTGTTTCCAGGACTTGACCA 60.477 52.381 0.00 0.00 39.22 4.02
1768 3835 1.239347 GCTGTTTCCAGGACTTGACC 58.761 55.000 0.00 0.00 39.22 4.02
1769 3836 1.202818 AGGCTGTTTCCAGGACTTGAC 60.203 52.381 0.00 0.00 39.22 3.18
1770 3837 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
1771 3838 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
1772 3839 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
1773 3840 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
1774 3841 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
1775 3842 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
1776 3843 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
1777 3844 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
1789 3856 7.386851 CAGTCTTTCCCTACATTTCTGTAAGA 58.613 38.462 0.00 0.00 44.68 2.10
1790 3857 6.092807 GCAGTCTTTCCCTACATTTCTGTAAG 59.907 42.308 0.00 0.00 37.41 2.34
1791 3858 5.938125 GCAGTCTTTCCCTACATTTCTGTAA 59.062 40.000 0.00 0.00 37.41 2.41
1792 3859 5.488341 GCAGTCTTTCCCTACATTTCTGTA 58.512 41.667 0.00 0.00 36.79 2.74
1793 3860 4.327680 GCAGTCTTTCCCTACATTTCTGT 58.672 43.478 0.00 0.00 39.49 3.41
1794 3861 3.372206 CGCAGTCTTTCCCTACATTTCTG 59.628 47.826 0.00 0.00 0.00 3.02
1795 3862 3.008049 ACGCAGTCTTTCCCTACATTTCT 59.992 43.478 0.00 0.00 29.74 2.52
1796 3863 3.335579 ACGCAGTCTTTCCCTACATTTC 58.664 45.455 0.00 0.00 29.74 2.17
1797 3864 3.418684 ACGCAGTCTTTCCCTACATTT 57.581 42.857 0.00 0.00 29.74 2.32
1798 3865 3.259876 TGTACGCAGTCTTTCCCTACATT 59.740 43.478 0.00 0.00 43.93 2.71
1799 3866 2.829720 TGTACGCAGTCTTTCCCTACAT 59.170 45.455 0.00 0.00 43.93 2.29
1800 3867 2.230508 CTGTACGCAGTCTTTCCCTACA 59.769 50.000 0.00 0.00 43.93 2.74
1801 3868 2.877335 CTGTACGCAGTCTTTCCCTAC 58.123 52.381 0.00 0.00 43.93 3.18
1813 3880 1.965643 ACTTTGGGTCTACTGTACGCA 59.034 47.619 0.00 0.00 37.94 5.24
1814 3881 2.334838 CACTTTGGGTCTACTGTACGC 58.665 52.381 0.00 0.00 0.00 4.42
1815 3882 2.298163 ACCACTTTGGGTCTACTGTACG 59.702 50.000 0.00 0.00 43.37 3.67
1825 3892 1.222567 AAGGTCTGACCACTTTGGGT 58.777 50.000 27.48 2.32 43.37 4.51
1826 3893 2.230660 GAAAGGTCTGACCACTTTGGG 58.769 52.381 27.48 0.00 43.37 4.12
1827 3894 2.230660 GGAAAGGTCTGACCACTTTGG 58.769 52.381 27.48 0.00 41.95 3.28
1828 3895 2.158608 AGGGAAAGGTCTGACCACTTTG 60.159 50.000 27.48 0.00 41.95 2.77
1829 3896 2.136026 AGGGAAAGGTCTGACCACTTT 58.864 47.619 27.48 19.45 41.95 2.66
1830 3897 1.421646 CAGGGAAAGGTCTGACCACTT 59.578 52.381 27.48 19.47 41.95 3.16
1831 3898 1.059913 CAGGGAAAGGTCTGACCACT 58.940 55.000 27.48 14.37 41.95 4.00
1832 3899 0.036875 CCAGGGAAAGGTCTGACCAC 59.963 60.000 27.48 17.34 41.95 4.16
1833 3900 0.104672 TCCAGGGAAAGGTCTGACCA 60.105 55.000 27.48 1.56 41.95 4.02
1834 3901 0.325272 GTCCAGGGAAAGGTCTGACC 59.675 60.000 19.20 19.20 38.99 4.02
1835 3902 0.325272 GGTCCAGGGAAAGGTCTGAC 59.675 60.000 0.00 0.00 33.11 3.51
1836 3903 0.193574 AGGTCCAGGGAAAGGTCTGA 59.806 55.000 0.00 0.00 33.11 3.27
1837 3904 0.326264 CAGGTCCAGGGAAAGGTCTG 59.674 60.000 0.00 0.00 0.00 3.51
1838 3905 1.492993 GCAGGTCCAGGGAAAGGTCT 61.493 60.000 0.00 0.00 0.00 3.85
1839 3906 1.002011 GCAGGTCCAGGGAAAGGTC 60.002 63.158 0.00 0.00 0.00 3.85
1840 3907 2.539081 GGCAGGTCCAGGGAAAGGT 61.539 63.158 0.00 0.00 34.01 3.50
1841 3908 2.356667 GGCAGGTCCAGGGAAAGG 59.643 66.667 0.00 0.00 34.01 3.11
1842 3909 2.080336 TTGGGCAGGTCCAGGGAAAG 62.080 60.000 0.00 0.00 38.17 2.62
1843 3910 2.080336 CTTGGGCAGGTCCAGGGAAA 62.080 60.000 0.00 0.00 38.17 3.13
1844 3911 2.451493 TTGGGCAGGTCCAGGGAA 60.451 61.111 0.00 0.00 38.17 3.97
1845 3912 2.935481 CTTGGGCAGGTCCAGGGA 60.935 66.667 0.00 0.00 38.17 4.20
1846 3913 4.748144 GCTTGGGCAGGTCCAGGG 62.748 72.222 4.13 0.00 38.17 4.45
1858 3925 2.182842 GCATGTAGCTCCCGCTTGG 61.183 63.158 0.00 0.00 46.47 3.61
1859 3926 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
1860 3927 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
1862 3929 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
1863 3930 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
1864 3931 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
1865 3932 1.821332 GCCCAGTGCATGTAGCTCC 60.821 63.158 0.00 0.00 45.94 4.70
1866 3933 1.094073 CAGCCCAGTGCATGTAGCTC 61.094 60.000 0.00 0.00 45.94 4.09
1867 3934 1.077930 CAGCCCAGTGCATGTAGCT 60.078 57.895 0.00 0.00 45.94 3.32
1868 3935 2.768492 GCAGCCCAGTGCATGTAGC 61.768 63.158 0.00 0.00 43.41 3.58
1869 3936 2.117156 GGCAGCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 45.93 2.74
1870 3937 2.045045 GGCAGCCCAGTGCATGTA 60.045 61.111 0.00 0.00 45.93 2.29
1880 3947 0.033109 ATTCCAGTTAAGGGCAGCCC 60.033 55.000 24.90 24.90 45.90 5.19
1881 3948 2.729028 TATTCCAGTTAAGGGCAGCC 57.271 50.000 1.26 1.26 0.00 4.85
1882 3949 3.565902 GTCATATTCCAGTTAAGGGCAGC 59.434 47.826 0.00 0.00 0.00 5.25
1883 3950 5.041191 AGTCATATTCCAGTTAAGGGCAG 57.959 43.478 0.00 0.00 0.00 4.85
1884 3951 5.454755 GCTAGTCATATTCCAGTTAAGGGCA 60.455 44.000 0.00 0.00 0.00 5.36
1885 3952 4.998033 GCTAGTCATATTCCAGTTAAGGGC 59.002 45.833 0.00 0.00 0.00 5.19
1886 3953 6.042093 TCTGCTAGTCATATTCCAGTTAAGGG 59.958 42.308 0.00 0.00 0.00 3.95
1887 3954 7.055667 TCTGCTAGTCATATTCCAGTTAAGG 57.944 40.000 0.00 0.00 0.00 2.69
1888 3955 8.200792 ACTTCTGCTAGTCATATTCCAGTTAAG 58.799 37.037 0.00 0.00 0.00 1.85
1889 3956 8.079211 ACTTCTGCTAGTCATATTCCAGTTAA 57.921 34.615 0.00 0.00 0.00 2.01
1890 3957 7.661536 ACTTCTGCTAGTCATATTCCAGTTA 57.338 36.000 0.00 0.00 0.00 2.24
1891 3958 6.552445 ACTTCTGCTAGTCATATTCCAGTT 57.448 37.500 0.00 0.00 0.00 3.16
1892 3959 7.847711 ATACTTCTGCTAGTCATATTCCAGT 57.152 36.000 0.00 0.00 0.00 4.00
1893 3960 8.363390 TGAATACTTCTGCTAGTCATATTCCAG 58.637 37.037 11.48 0.00 0.00 3.86
1894 3961 8.250143 TGAATACTTCTGCTAGTCATATTCCA 57.750 34.615 11.48 0.00 0.00 3.53
1895 3962 8.983724 GTTGAATACTTCTGCTAGTCATATTCC 58.016 37.037 11.48 0.00 0.00 3.01
1896 3963 8.983724 GGTTGAATACTTCTGCTAGTCATATTC 58.016 37.037 0.00 2.48 0.00 1.75
1897 3964 8.486210 TGGTTGAATACTTCTGCTAGTCATATT 58.514 33.333 0.00 0.00 0.00 1.28
1898 3965 8.023021 TGGTTGAATACTTCTGCTAGTCATAT 57.977 34.615 0.00 0.00 0.00 1.78
1899 3966 7.342026 TCTGGTTGAATACTTCTGCTAGTCATA 59.658 37.037 0.00 0.00 0.00 2.15
1900 3967 6.155221 TCTGGTTGAATACTTCTGCTAGTCAT 59.845 38.462 0.00 0.00 0.00 3.06
1901 3968 5.480422 TCTGGTTGAATACTTCTGCTAGTCA 59.520 40.000 0.00 0.00 0.00 3.41
1902 3969 5.808030 GTCTGGTTGAATACTTCTGCTAGTC 59.192 44.000 0.00 0.00 0.00 2.59
1903 3970 5.337652 GGTCTGGTTGAATACTTCTGCTAGT 60.338 44.000 0.00 0.00 0.00 2.57
1904 3971 5.105146 AGGTCTGGTTGAATACTTCTGCTAG 60.105 44.000 0.00 0.00 0.00 3.42
1910 3977 4.906618 TGGAAGGTCTGGTTGAATACTTC 58.093 43.478 0.00 0.00 34.37 3.01
1913 3980 7.696992 TTATTTGGAAGGTCTGGTTGAATAC 57.303 36.000 0.00 0.00 0.00 1.89
1919 3986 8.721133 AATAAGTTTATTTGGAAGGTCTGGTT 57.279 30.769 0.00 0.00 29.40 3.67
1929 3996 5.588648 CGGAGGCTGAATAAGTTTATTTGGA 59.411 40.000 0.00 0.00 33.72 3.53
1935 4002 6.872020 GCATATACGGAGGCTGAATAAGTTTA 59.128 38.462 0.00 0.00 0.00 2.01
1983 4051 3.429684 CGTAAACATTTTACCCCATGGCC 60.430 47.826 6.09 0.00 33.59 5.36
1987 4055 4.218852 CACACCGTAAACATTTTACCCCAT 59.781 41.667 3.76 0.00 0.00 4.00
1988 4056 3.568853 CACACCGTAAACATTTTACCCCA 59.431 43.478 3.76 0.00 0.00 4.96
1989 4057 3.819902 TCACACCGTAAACATTTTACCCC 59.180 43.478 3.76 0.00 0.00 4.95
2000 4068 5.373981 AAGTTTTGTTGTCACACCGTAAA 57.626 34.783 0.00 0.00 30.32 2.01
2041 4109 7.878547 TTGAACCAATATGACAATGCATCTA 57.121 32.000 0.00 0.00 0.00 1.98
2057 4125 4.497340 GCGTGAGATGTTTCTTTGAACCAA 60.497 41.667 0.00 0.00 30.30 3.67
2061 4129 4.024893 GTGAGCGTGAGATGTTTCTTTGAA 60.025 41.667 0.00 0.00 30.30 2.69
2062 4130 3.494626 GTGAGCGTGAGATGTTTCTTTGA 59.505 43.478 0.00 0.00 30.30 2.69
2079 4147 6.012658 TGTTCAAAACTTCCATATGTGAGC 57.987 37.500 1.24 0.10 0.00 4.26
2087 4155 9.313118 GTCTAAAAACATGTTCAAAACTTCCAT 57.687 29.630 12.39 0.00 0.00 3.41
2098 4166 5.915196 GCACCTTCTGTCTAAAAACATGTTC 59.085 40.000 12.39 0.00 0.00 3.18
2113 4202 0.825010 AAAGCTGGGTGCACCTTCTG 60.825 55.000 33.91 22.15 45.94 3.02
2114 4203 0.771127 TAAAGCTGGGTGCACCTTCT 59.229 50.000 33.91 23.75 45.94 2.85
2119 4208 2.779506 AGTAAGTAAAGCTGGGTGCAC 58.220 47.619 8.80 8.80 45.94 4.57
2120 4209 4.627284 TTAGTAAGTAAAGCTGGGTGCA 57.373 40.909 0.00 0.00 45.94 4.57
2152 4241 1.604278 GCTATCTTGATGGCCGGTTTC 59.396 52.381 1.90 0.00 0.00 2.78
2188 4277 7.604657 AATAATATGGATCGGAGGGAGTATC 57.395 40.000 0.00 0.00 0.00 2.24
2192 4281 6.054860 ACAAATAATATGGATCGGAGGGAG 57.945 41.667 0.00 0.00 0.00 4.30
2194 4283 6.054860 AGACAAATAATATGGATCGGAGGG 57.945 41.667 0.00 0.00 0.00 4.30
2210 4299 9.751542 CCGTATCTAGACAAATCTAAGACAAAT 57.248 33.333 0.00 0.00 36.98 2.32
2211 4300 8.963725 TCCGTATCTAGACAAATCTAAGACAAA 58.036 33.333 0.00 0.00 36.98 2.83
2212 4301 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2213 4302 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
2214 4303 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
2215 4304 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
2231 4320 7.934457 ACGTTTAGTGTTAGATACATCCGTAT 58.066 34.615 0.00 0.00 41.16 3.06
2232 4321 7.320443 ACGTTTAGTGTTAGATACATCCGTA 57.680 36.000 0.00 0.00 39.39 4.02
2233 4322 6.199937 ACGTTTAGTGTTAGATACATCCGT 57.800 37.500 0.00 0.00 39.39 4.69
2234 4323 7.515957 AAACGTTTAGTGTTAGATACATCCG 57.484 36.000 12.83 0.00 39.39 4.18
2253 4342 9.431887 ACATTGATGTATCTAACACTAAAACGT 57.568 29.630 0.00 0.00 42.09 3.99
2285 4374 9.034544 GCACTTTCTTGTAAAATTGATGAACTT 57.965 29.630 0.00 0.00 0.00 2.66
2329 4418 8.648968 CGTACAAAATTTGGTGTGTTAGTTTTT 58.351 29.630 8.56 0.00 34.12 1.94
2334 4423 6.580791 CCATCGTACAAAATTTGGTGTGTTAG 59.419 38.462 8.56 0.00 34.12 2.34
2335 4424 6.262496 TCCATCGTACAAAATTTGGTGTGTTA 59.738 34.615 8.56 0.00 34.12 2.41
2342 4434 6.443934 TGGTATCCATCGTACAAAATTTGG 57.556 37.500 10.71 0.00 34.12 3.28
2344 4436 8.343168 TCTTTGGTATCCATCGTACAAAATTT 57.657 30.769 0.00 0.00 31.53 1.82
2355 4447 6.015434 AGTGTTTTGGTTCTTTGGTATCCATC 60.015 38.462 0.00 0.00 31.53 3.51
2364 4456 6.642131 CCATATGTGAGTGTTTTGGTTCTTTG 59.358 38.462 1.24 0.00 0.00 2.77
2375 4467 9.113838 GAATGAATACTTCCATATGTGAGTGTT 57.886 33.333 14.96 14.32 0.00 3.32
2382 4474 7.577303 AGGTGTGAATGAATACTTCCATATGT 58.423 34.615 1.24 0.00 0.00 2.29
2400 4492 8.626526 GGTTGAATACTTTTTCTTAAGGTGTGA 58.373 33.333 1.85 0.00 0.00 3.58
2411 4503 9.463443 GCATATATGGTGGTTGAATACTTTTTC 57.537 33.333 14.51 0.00 0.00 2.29
2415 4507 8.660435 AGTAGCATATATGGTGGTTGAATACTT 58.340 33.333 24.30 3.15 39.14 2.24
2442 4534 5.335191 CCTGGCTGAAGTACAAAATTCTGAC 60.335 44.000 0.00 0.00 34.10 3.51
2449 4541 2.814097 GCTCCCTGGCTGAAGTACAAAA 60.814 50.000 0.00 0.00 0.00 2.44
2481 4573 0.620556 TGGGTCAGCAAATCCTCTCC 59.379 55.000 0.00 0.00 0.00 3.71
2526 4850 1.798813 CCGAAATAGGCATTCTACGGC 59.201 52.381 0.00 0.00 32.70 5.68
2533 4857 4.523173 TCTCGAGATACCGAAATAGGCATT 59.477 41.667 12.08 0.00 38.17 3.56
2538 4862 6.988622 ATAGGTCTCGAGATACCGAAATAG 57.011 41.667 19.90 0.00 40.88 1.73
2539 4863 7.389232 TGTATAGGTCTCGAGATACCGAAATA 58.611 38.462 19.90 13.29 40.88 1.40
2544 4868 3.371591 GCTGTATAGGTCTCGAGATACCG 59.628 52.174 19.90 13.56 40.88 4.02


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

AutoCloner maintained by Alex Coulton.