Multiple sequence alignment - TraesCS5B01G032300

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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 TraesCS5B01G032300 chr5B 100.000 2531 0 0 1 2531 35531648 35534178 0.000000e+00 4674.0
1 TraesCS5B01G032300 chr5A 91.371 1773 83 21 87 1807 29683246 29685000 0.000000e+00 2362.0
2 TraesCS5B01G032300 chr5A 91.667 300 23 2 2230 2528 29685802 29686100 5.040000e-112 414.0
3 TraesCS5B01G032300 chr5A 89.048 210 19 4 2031 2238 29685572 29685779 8.980000e-65 257.0
4 TraesCS5B01G032300 chr5D 91.808 1587 99 22 171 1735 41408051 41409628 0.000000e+00 2182.0
5 TraesCS5B01G032300 chr5D 90.881 318 24 2 2219 2531 41430409 41430726 3.010000e-114 422.0
6 TraesCS5B01G032300 chr5D 89.820 167 15 2 2073 2238 41430217 41430382 1.970000e-51 213.0
7 TraesCS5B01G032300 chr2B 93.162 117 8 0 1807 1923 18932865 18932981 3.350000e-39 172.0
8 TraesCS5B01G032300 chr2B 92.105 114 9 0 1813 1926 335389115 335389002 7.250000e-36 161.0
9 TraesCS5B01G032300 chr4D 92.373 118 9 0 1806 1923 472662258 472662375 4.330000e-38 169.0
10 TraesCS5B01G032300 chr7B 93.694 111 7 0 1813 1923 668028079 668027969 1.560000e-37 167.0
11 TraesCS5B01G032300 chr3B 92.857 112 8 0 1813 1924 34000275 34000164 2.010000e-36 163.0
12 TraesCS5B01G032300 chr2A 92.857 112 8 0 1813 1924 62286355 62286244 2.010000e-36 163.0
13 TraesCS5B01G032300 chrUn 91.453 117 10 0 1810 1926 48888598 48888714 7.250000e-36 161.0
14 TraesCS5B01G032300 chr4A 91.453 117 10 0 1807 1923 692965467 692965583 7.250000e-36 161.0
15 TraesCS5B01G032300 chr7D 90.244 123 11 1 1803 1924 256189321 256189443 2.610000e-35 159.0
16 TraesCS5B01G032300 chr2D 83.908 87 10 2 1 84 474927712 474927627 2.090000e-11 80.5


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 TraesCS5B01G032300 chr5B 35531648 35534178 2530 False 4674.0 4674 100.000000 1 2531 1 chr5B.!!$F1 2530
1 TraesCS5B01G032300 chr5A 29683246 29686100 2854 False 1011.0 2362 90.695333 87 2528 3 chr5A.!!$F1 2441
2 TraesCS5B01G032300 chr5D 41408051 41409628 1577 False 2182.0 2182 91.808000 171 1735 1 chr5D.!!$F1 1564
3 TraesCS5B01G032300 chr5D 41430217 41430726 509 False 317.5 422 90.350500 2073 2531 2 chr5D.!!$F2 458

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
51 52 0.037326 TCGGTGACCAACTCATGAGC 60.037 55.0 22.83 6.49 0.0 4.26 F
52 53 0.320683 CGGTGACCAACTCATGAGCA 60.321 55.0 22.83 9.17 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1092 1131 0.172578 TGTACTCGATGTTGCTCCCG 59.827 55.0 0.00 0.0 0.0 5.14 R
1781 1844 0.305922 GATTTTCAGCGGCCATCTCG 59.694 55.0 2.24 0.0 0.0 4.04 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
25 26 6.951062 TGATGAGTTTGTCCAAATACAACA 57.049 33.333 0.00 2.92 39.02 3.33
26 27 7.340122 TGATGAGTTTGTCCAAATACAACAA 57.660 32.000 0.00 0.00 39.02 2.83
27 28 7.199766 TGATGAGTTTGTCCAAATACAACAAC 58.800 34.615 0.00 0.00 39.02 3.32
28 29 6.516739 TGAGTTTGTCCAAATACAACAACA 57.483 33.333 0.00 0.00 39.02 3.33
29 30 6.925211 TGAGTTTGTCCAAATACAACAACAA 58.075 32.000 0.00 0.00 39.02 2.83
30 31 7.378966 TGAGTTTGTCCAAATACAACAACAAA 58.621 30.769 0.00 0.00 39.02 2.83
31 32 8.037758 TGAGTTTGTCCAAATACAACAACAAAT 58.962 29.630 0.00 0.00 39.02 2.32
32 33 8.785329 AGTTTGTCCAAATACAACAACAAATT 57.215 26.923 0.00 0.00 39.02 1.82
33 34 8.878769 AGTTTGTCCAAATACAACAACAAATTC 58.121 29.630 0.00 0.00 39.02 2.17
34 35 7.456684 TTGTCCAAATACAACAACAAATTCG 57.543 32.000 0.00 0.00 34.50 3.34
35 36 5.980116 TGTCCAAATACAACAACAAATTCGG 59.020 36.000 0.00 0.00 0.00 4.30
36 37 5.980715 GTCCAAATACAACAACAAATTCGGT 59.019 36.000 0.00 0.00 0.00 4.69
37 38 5.980116 TCCAAATACAACAACAAATTCGGTG 59.020 36.000 0.00 0.00 0.00 4.94
38 39 5.980116 CCAAATACAACAACAAATTCGGTGA 59.020 36.000 0.00 0.00 0.00 4.02
39 40 6.074569 CCAAATACAACAACAAATTCGGTGAC 60.075 38.462 0.00 0.00 0.00 3.67
40 41 3.430333 ACAACAACAAATTCGGTGACC 57.570 42.857 0.00 0.00 0.00 4.02
41 42 2.755655 ACAACAACAAATTCGGTGACCA 59.244 40.909 1.11 0.00 0.00 4.02
42 43 3.193691 ACAACAACAAATTCGGTGACCAA 59.806 39.130 1.11 0.00 0.00 3.67
43 44 3.430333 ACAACAAATTCGGTGACCAAC 57.570 42.857 1.11 0.00 0.00 3.77
44 45 3.020984 ACAACAAATTCGGTGACCAACT 58.979 40.909 1.11 0.00 0.00 3.16
45 46 3.066203 ACAACAAATTCGGTGACCAACTC 59.934 43.478 1.11 0.00 0.00 3.01
46 47 2.925724 ACAAATTCGGTGACCAACTCA 58.074 42.857 1.11 0.00 0.00 3.41
47 48 3.486383 ACAAATTCGGTGACCAACTCAT 58.514 40.909 1.11 0.00 0.00 2.90
48 49 3.253188 ACAAATTCGGTGACCAACTCATG 59.747 43.478 1.11 0.00 0.00 3.07
49 50 3.417069 AATTCGGTGACCAACTCATGA 57.583 42.857 1.11 0.00 0.00 3.07
50 51 2.455674 TTCGGTGACCAACTCATGAG 57.544 50.000 21.37 21.37 0.00 2.90
51 52 0.037326 TCGGTGACCAACTCATGAGC 60.037 55.000 22.83 6.49 0.00 4.26
52 53 0.320683 CGGTGACCAACTCATGAGCA 60.321 55.000 22.83 9.17 0.00 4.26
53 54 1.446907 GGTGACCAACTCATGAGCAG 58.553 55.000 22.83 14.57 0.00 4.24
54 55 0.801251 GTGACCAACTCATGAGCAGC 59.199 55.000 22.83 8.44 0.00 5.25
55 56 0.689055 TGACCAACTCATGAGCAGCT 59.311 50.000 22.83 0.00 0.00 4.24
56 57 1.072806 TGACCAACTCATGAGCAGCTT 59.927 47.619 22.83 6.55 0.00 3.74
57 58 2.302733 TGACCAACTCATGAGCAGCTTA 59.697 45.455 22.83 3.03 0.00 3.09
58 59 3.244526 TGACCAACTCATGAGCAGCTTAA 60.245 43.478 22.83 0.63 0.00 1.85
59 60 3.341823 ACCAACTCATGAGCAGCTTAAG 58.658 45.455 22.83 6.97 0.00 1.85
60 61 3.008375 ACCAACTCATGAGCAGCTTAAGA 59.992 43.478 22.83 0.00 0.00 2.10
61 62 4.005650 CCAACTCATGAGCAGCTTAAGAA 58.994 43.478 22.83 0.00 0.00 2.52
62 63 4.456911 CCAACTCATGAGCAGCTTAAGAAA 59.543 41.667 22.83 0.00 0.00 2.52
63 64 5.125097 CCAACTCATGAGCAGCTTAAGAAAT 59.875 40.000 22.83 0.00 0.00 2.17
64 65 6.317140 CCAACTCATGAGCAGCTTAAGAAATA 59.683 38.462 22.83 0.00 0.00 1.40
65 66 7.013083 CCAACTCATGAGCAGCTTAAGAAATAT 59.987 37.037 22.83 0.00 0.00 1.28
66 67 7.727331 ACTCATGAGCAGCTTAAGAAATATC 57.273 36.000 22.83 0.00 0.00 1.63
67 68 7.507829 ACTCATGAGCAGCTTAAGAAATATCT 58.492 34.615 22.83 0.00 37.57 1.98
68 69 7.441760 ACTCATGAGCAGCTTAAGAAATATCTG 59.558 37.037 22.83 3.98 35.59 2.90
69 70 7.503549 TCATGAGCAGCTTAAGAAATATCTGA 58.496 34.615 6.67 0.00 35.59 3.27
70 71 8.155510 TCATGAGCAGCTTAAGAAATATCTGAT 58.844 33.333 6.67 1.10 35.59 2.90
71 72 8.784994 CATGAGCAGCTTAAGAAATATCTGATT 58.215 33.333 6.67 0.00 35.59 2.57
72 73 8.151141 TGAGCAGCTTAAGAAATATCTGATTG 57.849 34.615 6.67 0.00 35.59 2.67
73 74 7.989170 TGAGCAGCTTAAGAAATATCTGATTGA 59.011 33.333 6.67 0.00 35.59 2.57
74 75 8.380743 AGCAGCTTAAGAAATATCTGATTGAG 57.619 34.615 6.67 0.00 35.59 3.02
75 76 7.041235 AGCAGCTTAAGAAATATCTGATTGAGC 60.041 37.037 6.67 0.00 35.59 4.26
76 77 7.255035 GCAGCTTAAGAAATATCTGATTGAGCA 60.255 37.037 6.67 0.00 35.59 4.26
77 78 8.784994 CAGCTTAAGAAATATCTGATTGAGCAT 58.215 33.333 6.67 0.00 35.59 3.79
83 84 8.563123 AGAAATATCTGATTGAGCATATGTGG 57.437 34.615 4.29 0.00 33.59 4.17
84 85 7.610692 AGAAATATCTGATTGAGCATATGTGGG 59.389 37.037 4.29 0.00 33.59 4.61
85 86 4.719026 ATCTGATTGAGCATATGTGGGT 57.281 40.909 4.29 0.00 0.00 4.51
100 101 2.988636 TGGGTTGTCCATCCATTTCA 57.011 45.000 0.00 0.00 41.46 2.69
106 107 2.023673 TGTCCATCCATTTCAATCGGC 58.976 47.619 0.00 0.00 0.00 5.54
140 141 4.862371 TGACTAAAAGAACCCCAACTGTT 58.138 39.130 0.00 0.00 0.00 3.16
166 167 4.478317 AGATATCCCCAACACCTTGAATCA 59.522 41.667 0.00 0.00 0.00 2.57
168 169 3.085952 TCCCCAACACCTTGAATCATC 57.914 47.619 0.00 0.00 0.00 2.92
169 170 2.102578 CCCCAACACCTTGAATCATCC 58.897 52.381 0.00 0.00 0.00 3.51
184 199 8.798975 TTGAATCATCCTTTATAGAGTAGGGT 57.201 34.615 0.00 0.00 0.00 4.34
215 232 8.568794 GCCTGTTTTAAGAGAGTAAGACAATTT 58.431 33.333 0.00 0.00 30.32 1.82
227 244 4.630894 AAGACAATTTGACGACAAAGCA 57.369 36.364 17.37 0.00 46.84 3.91
249 274 5.124457 GCAATAGTCACCATGAACAACAGAT 59.876 40.000 0.00 0.00 0.00 2.90
325 350 6.134730 CGAAGAAGCATATGAAGATCTTTGC 58.865 40.000 18.17 18.17 0.00 3.68
374 399 5.035784 TCATCGTGCTTAGTCATATCTCG 57.964 43.478 0.00 0.00 0.00 4.04
407 432 6.246919 TCCCTGGAACGGAACAAAAATATTA 58.753 36.000 0.00 0.00 36.31 0.98
438 463 3.629398 GTCATTTCCAAGATTGCTCCGAT 59.371 43.478 0.00 0.00 0.00 4.18
517 542 6.604171 TGTTATTGGATGGATGCACTCTAAT 58.396 36.000 0.00 10.83 0.00 1.73
873 912 5.132312 GGCTTTTCCCTCCTATAACTAAGGT 59.868 44.000 0.00 0.00 35.48 3.50
879 918 7.183298 TCCCTCCTATAACTAAGGTTATCCA 57.817 40.000 4.91 0.00 44.57 3.41
895 934 6.006449 GGTTATCCATTGGAGTATGCATCTT 58.994 40.000 11.78 0.00 35.22 2.40
978 1017 4.248058 CAAGACAAGAATTTGATTGGGGC 58.752 43.478 0.00 0.00 37.73 5.80
979 1018 2.833943 AGACAAGAATTTGATTGGGGCC 59.166 45.455 0.00 0.00 37.73 5.80
1006 1045 1.226686 GCGCTCTGGTGCTATGGATG 61.227 60.000 0.00 0.00 44.66 3.51
1053 1092 1.080025 GCGGTTGAAGCCTACGAGT 60.080 57.895 0.00 0.00 0.00 4.18
1067 1106 1.032657 ACGAGTCGGAGCAGTAGCAT 61.033 55.000 18.30 0.00 45.49 3.79
1311 1350 2.703798 GGCGTACCTACAGTCGGCA 61.704 63.158 0.00 0.00 41.13 5.69
1467 1506 3.148279 GACCCCGCCGAGATCTGT 61.148 66.667 0.00 0.00 0.00 3.41
1477 1516 1.424493 CGAGATCTGTGCCGCTTTCC 61.424 60.000 0.00 0.00 0.00 3.13
1595 1649 7.148755 GCTTCCATCATTATTGTTGTTGTTGTC 60.149 37.037 0.00 0.00 0.00 3.18
1638 1692 2.710471 TGAGATATATGTTGGCCTGGCA 59.290 45.455 22.05 1.21 0.00 4.92
1669 1729 6.237901 TGCCATGTTTGTTTAGTCAGATAGT 58.762 36.000 0.00 0.00 0.00 2.12
1670 1730 7.390823 TGCCATGTTTGTTTAGTCAGATAGTA 58.609 34.615 0.00 0.00 0.00 1.82
1671 1731 7.549134 TGCCATGTTTGTTTAGTCAGATAGTAG 59.451 37.037 0.00 0.00 0.00 2.57
1712 1772 2.223665 GCAAGCATATCCTTGGAGTTGC 60.224 50.000 8.47 14.84 41.88 4.17
1713 1773 3.018856 CAAGCATATCCTTGGAGTTGCA 58.981 45.455 20.98 0.00 38.78 4.08
1750 1810 0.323629 TTTGAGGAACGGGTAGCAGG 59.676 55.000 0.00 0.00 0.00 4.85
1781 1844 8.020819 TGTTGTTGAATACTAGTTGCATAAAGC 58.979 33.333 0.00 0.00 45.96 3.51
1791 1854 1.571460 GCATAAAGCGAGATGGCCG 59.429 57.895 0.00 0.00 0.00 6.13
1807 1870 2.288666 GGCCGCTGAAAATCTCACATA 58.711 47.619 0.00 0.00 0.00 2.29
1808 1871 2.880890 GGCCGCTGAAAATCTCACATAT 59.119 45.455 0.00 0.00 0.00 1.78
1810 1873 4.531332 GCCGCTGAAAATCTCACATATTC 58.469 43.478 0.00 0.00 0.00 1.75
1811 1874 4.274459 GCCGCTGAAAATCTCACATATTCT 59.726 41.667 0.00 0.00 0.00 2.40
1812 1875 5.559799 GCCGCTGAAAATCTCACATATTCTC 60.560 44.000 0.00 0.00 0.00 2.87
1814 1877 6.073873 CCGCTGAAAATCTCACATATTCTCTC 60.074 42.308 0.00 0.00 0.00 3.20
1818 1881 6.980978 TGAAAATCTCACATATTCTCTCCGTC 59.019 38.462 0.00 0.00 0.00 4.79
1820 1883 2.879026 TCTCACATATTCTCTCCGTCCG 59.121 50.000 0.00 0.00 0.00 4.79
1821 1884 2.879026 CTCACATATTCTCTCCGTCCGA 59.121 50.000 0.00 0.00 0.00 4.55
1823 1886 3.697542 TCACATATTCTCTCCGTCCGAAA 59.302 43.478 0.00 0.00 0.00 3.46
1824 1887 4.158949 TCACATATTCTCTCCGTCCGAAAA 59.841 41.667 0.00 0.00 0.00 2.29
1825 1888 5.050490 CACATATTCTCTCCGTCCGAAAAT 58.950 41.667 0.00 0.00 0.00 1.82
1826 1889 6.040054 TCACATATTCTCTCCGTCCGAAAATA 59.960 38.462 0.00 0.00 0.00 1.40
1828 1891 7.385205 CACATATTCTCTCCGTCCGAAAATAAT 59.615 37.037 0.00 0.00 0.00 1.28
1829 1892 7.931948 ACATATTCTCTCCGTCCGAAAATAATT 59.068 33.333 0.00 0.00 0.00 1.40
1830 1893 6.604735 ATTCTCTCCGTCCGAAAATAATTG 57.395 37.500 0.00 0.00 0.00 2.32
1831 1894 5.080969 TCTCTCCGTCCGAAAATAATTGT 57.919 39.130 0.00 0.00 0.00 2.71
1832 1895 5.107133 TCTCTCCGTCCGAAAATAATTGTC 58.893 41.667 0.00 0.00 0.00 3.18
1833 1896 3.861113 TCTCCGTCCGAAAATAATTGTCG 59.139 43.478 0.00 0.00 34.58 4.35
1843 1906 7.241663 CGAAAATAATTGTCGGAGTAATGGA 57.758 36.000 0.00 0.00 0.00 3.41
1844 1907 7.861630 CGAAAATAATTGTCGGAGTAATGGAT 58.138 34.615 0.00 0.00 0.00 3.41
1845 1908 7.798516 CGAAAATAATTGTCGGAGTAATGGATG 59.201 37.037 0.00 0.00 0.00 3.51
1846 1909 8.519799 AAAATAATTGTCGGAGTAATGGATGT 57.480 30.769 0.00 0.00 0.00 3.06
1847 1910 9.621629 AAAATAATTGTCGGAGTAATGGATGTA 57.378 29.630 0.00 0.00 0.00 2.29
1848 1911 9.793259 AAATAATTGTCGGAGTAATGGATGTAT 57.207 29.630 0.00 0.00 0.00 2.29
1849 1912 9.436957 AATAATTGTCGGAGTAATGGATGTATC 57.563 33.333 0.00 0.00 0.00 2.24
1850 1913 6.672266 ATTGTCGGAGTAATGGATGTATCT 57.328 37.500 0.00 0.00 0.00 1.98
1851 1914 7.776618 ATTGTCGGAGTAATGGATGTATCTA 57.223 36.000 0.00 0.00 0.00 1.98
1852 1915 6.819397 TGTCGGAGTAATGGATGTATCTAG 57.181 41.667 0.00 0.00 0.00 2.43
1853 1916 6.304624 TGTCGGAGTAATGGATGTATCTAGT 58.695 40.000 0.00 0.00 0.00 2.57
1854 1917 6.776116 TGTCGGAGTAATGGATGTATCTAGTT 59.224 38.462 0.00 0.00 0.00 2.24
1855 1918 7.085116 GTCGGAGTAATGGATGTATCTAGTTG 58.915 42.308 0.00 0.00 0.00 3.16
1856 1919 6.776116 TCGGAGTAATGGATGTATCTAGTTGT 59.224 38.462 0.00 0.00 0.00 3.32
1857 1920 7.940688 TCGGAGTAATGGATGTATCTAGTTGTA 59.059 37.037 0.00 0.00 0.00 2.41
1858 1921 8.740906 CGGAGTAATGGATGTATCTAGTTGTAT 58.259 37.037 0.00 0.00 0.00 2.29
1887 1950 7.555965 AGTTTTAGATGCATCCATTTTTACCC 58.444 34.615 23.06 1.70 0.00 3.69
1888 1951 7.180051 AGTTTTAGATGCATCCATTTTTACCCA 59.820 33.333 23.06 0.00 0.00 4.51
1889 1952 7.673641 TTTAGATGCATCCATTTTTACCCAT 57.326 32.000 23.06 2.35 0.00 4.00
1890 1953 7.673641 TTAGATGCATCCATTTTTACCCATT 57.326 32.000 23.06 1.91 0.00 3.16
1891 1954 6.564557 AGATGCATCCATTTTTACCCATTT 57.435 33.333 23.06 0.00 0.00 2.32
1892 1955 6.961042 AGATGCATCCATTTTTACCCATTTT 58.039 32.000 23.06 0.00 0.00 1.82
1893 1956 7.049754 AGATGCATCCATTTTTACCCATTTTC 58.950 34.615 23.06 0.00 0.00 2.29
1894 1957 5.174395 TGCATCCATTTTTACCCATTTTCG 58.826 37.500 0.00 0.00 0.00 3.46
1895 1958 4.033932 GCATCCATTTTTACCCATTTTCGC 59.966 41.667 0.00 0.00 0.00 4.70
1896 1959 3.839293 TCCATTTTTACCCATTTTCGCG 58.161 40.909 0.00 0.00 0.00 5.87
1897 1960 3.506455 TCCATTTTTACCCATTTTCGCGA 59.494 39.130 3.71 3.71 0.00 5.87
1898 1961 3.610677 CCATTTTTACCCATTTTCGCGAC 59.389 43.478 9.15 0.00 0.00 5.19
1899 1962 3.984508 TTTTTACCCATTTTCGCGACA 57.015 38.095 9.15 0.00 0.00 4.35
1900 1963 3.984508 TTTTACCCATTTTCGCGACAA 57.015 38.095 9.15 9.93 0.00 3.18
1901 1964 3.546002 TTTACCCATTTTCGCGACAAG 57.454 42.857 9.15 0.00 0.00 3.16
1902 1965 2.172851 TACCCATTTTCGCGACAAGT 57.827 45.000 9.15 5.93 0.00 3.16
1903 1966 2.172851 ACCCATTTTCGCGACAAGTA 57.827 45.000 9.15 0.00 0.00 2.24
1904 1967 2.706890 ACCCATTTTCGCGACAAGTAT 58.293 42.857 9.15 0.00 0.00 2.12
1905 1968 3.078837 ACCCATTTTCGCGACAAGTATT 58.921 40.909 9.15 0.00 0.00 1.89
1906 1969 3.504520 ACCCATTTTCGCGACAAGTATTT 59.495 39.130 9.15 0.00 0.00 1.40
1907 1970 4.095610 CCCATTTTCGCGACAAGTATTTC 58.904 43.478 9.15 0.00 0.00 2.17
1908 1971 4.142687 CCCATTTTCGCGACAAGTATTTCT 60.143 41.667 9.15 0.00 0.00 2.52
1909 1972 4.788100 CCATTTTCGCGACAAGTATTTCTG 59.212 41.667 9.15 1.59 0.00 3.02
1910 1973 4.398549 TTTTCGCGACAAGTATTTCTGG 57.601 40.909 9.15 0.00 0.00 3.86
1911 1974 3.306917 TTCGCGACAAGTATTTCTGGA 57.693 42.857 9.15 0.00 0.00 3.86
1912 1975 2.602878 TCGCGACAAGTATTTCTGGAC 58.397 47.619 3.71 0.00 0.00 4.02
1913 1976 1.320555 CGCGACAAGTATTTCTGGACG 59.679 52.381 0.00 0.00 38.06 4.79
1914 1977 1.659098 GCGACAAGTATTTCTGGACGG 59.341 52.381 0.00 0.00 36.20 4.79
1915 1978 2.673043 GCGACAAGTATTTCTGGACGGA 60.673 50.000 0.00 0.00 36.20 4.69
1916 1979 3.179830 CGACAAGTATTTCTGGACGGAG 58.820 50.000 0.00 0.00 33.12 4.63
1917 1980 3.522553 GACAAGTATTTCTGGACGGAGG 58.477 50.000 0.00 0.00 0.00 4.30
1918 1981 2.236395 ACAAGTATTTCTGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
1919 1982 2.500098 CAAGTATTTCTGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
1920 1983 2.389715 AGTATTTCTGGACGGAGGGAG 58.610 52.381 0.00 0.00 0.00 4.30
1921 1984 2.108970 GTATTTCTGGACGGAGGGAGT 58.891 52.381 0.00 0.00 0.00 3.85
1922 1985 2.544844 ATTTCTGGACGGAGGGAGTA 57.455 50.000 0.00 0.00 0.00 2.59
1923 1986 1.553706 TTTCTGGACGGAGGGAGTAC 58.446 55.000 0.00 0.00 0.00 2.73
1924 1987 0.702902 TTCTGGACGGAGGGAGTACT 59.297 55.000 0.00 0.00 0.00 2.73
1925 1988 0.702902 TCTGGACGGAGGGAGTACTT 59.297 55.000 0.00 0.00 0.00 2.24
1949 2012 6.485830 TGGAGGGAACATGTAGAAATAGAG 57.514 41.667 0.00 0.00 0.00 2.43
1970 2033 3.629398 AGAAGTTTCTCTTGGCAACACTG 59.371 43.478 0.00 0.00 39.13 3.66
1978 2041 1.948508 TGGCAACACTGTTCATCGC 59.051 52.632 0.00 0.00 46.17 4.58
1980 2043 1.270571 TGGCAACACTGTTCATCGCTA 60.271 47.619 0.00 0.00 46.17 4.26
1989 2052 8.604035 CAACACTGTTCATCGCTATAATTTACT 58.396 33.333 0.00 0.00 0.00 2.24
2004 2067 5.777526 AATTTACTGGAATGGGGCAAAAT 57.222 34.783 0.00 0.00 0.00 1.82
2005 2068 6.882768 AATTTACTGGAATGGGGCAAAATA 57.117 33.333 0.00 0.00 0.00 1.40
2053 2559 8.779354 ATCTTAGTATCAAAGGAGAAACACAC 57.221 34.615 0.00 0.00 0.00 3.82
2054 2560 7.732025 TCTTAGTATCAAAGGAGAAACACACA 58.268 34.615 0.00 0.00 0.00 3.72
2056 2562 8.918202 TTAGTATCAAAGGAGAAACACACAAT 57.082 30.769 0.00 0.00 0.00 2.71
2057 2563 7.823745 AGTATCAAAGGAGAAACACACAATT 57.176 32.000 0.00 0.00 0.00 2.32
2058 2564 8.237811 AGTATCAAAGGAGAAACACACAATTT 57.762 30.769 0.00 0.00 0.00 1.82
2059 2565 8.695456 AGTATCAAAGGAGAAACACACAATTTT 58.305 29.630 0.00 0.00 0.00 1.82
2060 2566 9.313118 GTATCAAAGGAGAAACACACAATTTTT 57.687 29.630 0.00 0.00 0.00 1.94
2084 2590 1.519455 CAACTCATCCGACCGCCTC 60.519 63.158 0.00 0.00 0.00 4.70
2096 2602 2.799917 CGACCGCCTCTTAGATTTCCTG 60.800 54.545 0.00 0.00 0.00 3.86
2105 2611 5.884792 CCTCTTAGATTTCCTGCACAAGAAT 59.115 40.000 0.00 0.00 0.00 2.40
2120 2626 3.834231 ACAAGAATGGAAATGGGGTCTTG 59.166 43.478 9.13 9.13 44.74 3.02
2182 2688 9.585099 TTAATGTGGATTTTAACTTGATCATGC 57.415 29.630 8.45 0.00 0.00 4.06
2216 2722 4.998672 TCCGGTGTTTTTCTGTTACTATGG 59.001 41.667 0.00 0.00 0.00 2.74
2229 2736 9.918630 TTCTGTTACTATGGACTAAACACTTAC 57.081 33.333 0.00 0.00 0.00 2.34
2324 2882 8.754991 TCCTATTCCTCTGTTTTTAAAACACA 57.245 30.769 17.93 8.54 0.00 3.72
2347 2905 6.929606 ACAGTGAACTAAAGAGTCGCTTAATT 59.070 34.615 0.00 0.00 35.24 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.776107 TGTTGTATTTGGACAAACTCATCAAA 58.224 30.769 0.00 0.00 40.88 2.69
1 2 7.340122 TGTTGTATTTGGACAAACTCATCAA 57.660 32.000 0.00 0.30 40.88 2.57
2 3 6.951062 TGTTGTATTTGGACAAACTCATCA 57.049 33.333 0.00 5.50 40.88 3.07
3 4 7.199766 TGTTGTTGTATTTGGACAAACTCATC 58.800 34.615 0.00 3.36 40.88 2.92
4 5 7.106439 TGTTGTTGTATTTGGACAAACTCAT 57.894 32.000 0.00 0.00 40.88 2.90
5 6 6.516739 TGTTGTTGTATTTGGACAAACTCA 57.483 33.333 0.00 0.41 40.88 3.41
6 7 7.820044 TTTGTTGTTGTATTTGGACAAACTC 57.180 32.000 0.00 0.00 40.88 3.01
7 8 8.785329 AATTTGTTGTTGTATTTGGACAAACT 57.215 26.923 0.00 0.00 40.88 2.66
8 9 7.843686 CGAATTTGTTGTTGTATTTGGACAAAC 59.156 33.333 0.00 0.00 40.88 2.93
9 10 7.010552 CCGAATTTGTTGTTGTATTTGGACAAA 59.989 33.333 0.00 0.00 40.88 2.83
10 11 6.477033 CCGAATTTGTTGTTGTATTTGGACAA 59.523 34.615 0.00 0.00 34.70 3.18
11 12 5.980116 CCGAATTTGTTGTTGTATTTGGACA 59.020 36.000 0.00 0.00 34.70 4.02
12 13 5.980715 ACCGAATTTGTTGTTGTATTTGGAC 59.019 36.000 0.00 0.00 35.81 4.02
13 14 5.980116 CACCGAATTTGTTGTTGTATTTGGA 59.020 36.000 0.00 0.00 35.81 3.53
14 15 5.980116 TCACCGAATTTGTTGTTGTATTTGG 59.020 36.000 0.00 0.00 37.49 3.28
15 16 6.074569 GGTCACCGAATTTGTTGTTGTATTTG 60.075 38.462 0.00 0.00 0.00 2.32
16 17 5.980715 GGTCACCGAATTTGTTGTTGTATTT 59.019 36.000 0.00 0.00 0.00 1.40
17 18 5.067936 TGGTCACCGAATTTGTTGTTGTATT 59.932 36.000 0.00 0.00 0.00 1.89
18 19 4.580995 TGGTCACCGAATTTGTTGTTGTAT 59.419 37.500 0.00 0.00 0.00 2.29
19 20 3.945921 TGGTCACCGAATTTGTTGTTGTA 59.054 39.130 0.00 0.00 0.00 2.41
20 21 2.755655 TGGTCACCGAATTTGTTGTTGT 59.244 40.909 0.00 0.00 0.00 3.32
21 22 3.428746 TGGTCACCGAATTTGTTGTTG 57.571 42.857 0.00 0.00 0.00 3.33
22 23 3.445805 AGTTGGTCACCGAATTTGTTGTT 59.554 39.130 0.00 0.00 0.00 2.83
23 24 3.020984 AGTTGGTCACCGAATTTGTTGT 58.979 40.909 0.00 0.00 0.00 3.32
24 25 3.066064 TGAGTTGGTCACCGAATTTGTTG 59.934 43.478 0.00 0.00 0.00 3.33
25 26 3.283751 TGAGTTGGTCACCGAATTTGTT 58.716 40.909 0.00 0.00 0.00 2.83
26 27 2.925724 TGAGTTGGTCACCGAATTTGT 58.074 42.857 0.00 0.00 0.00 2.83
27 28 3.501828 TCATGAGTTGGTCACCGAATTTG 59.498 43.478 0.00 0.00 38.28 2.32
28 29 3.750371 TCATGAGTTGGTCACCGAATTT 58.250 40.909 0.00 0.00 38.28 1.82
29 30 3.338249 CTCATGAGTTGGTCACCGAATT 58.662 45.455 14.95 0.00 38.28 2.17
30 31 2.936993 GCTCATGAGTTGGTCACCGAAT 60.937 50.000 23.38 0.00 38.28 3.34
31 32 1.608025 GCTCATGAGTTGGTCACCGAA 60.608 52.381 23.38 0.00 38.28 4.30
32 33 0.037326 GCTCATGAGTTGGTCACCGA 60.037 55.000 23.38 0.00 38.28 4.69
33 34 0.320683 TGCTCATGAGTTGGTCACCG 60.321 55.000 23.38 0.00 38.28 4.94
34 35 1.446907 CTGCTCATGAGTTGGTCACC 58.553 55.000 23.38 5.27 38.28 4.02
35 36 0.801251 GCTGCTCATGAGTTGGTCAC 59.199 55.000 23.38 5.99 38.28 3.67
36 37 0.689055 AGCTGCTCATGAGTTGGTCA 59.311 50.000 23.38 11.55 40.38 4.02
37 38 1.818642 AAGCTGCTCATGAGTTGGTC 58.181 50.000 23.38 7.41 0.00 4.02
38 39 3.008375 TCTTAAGCTGCTCATGAGTTGGT 59.992 43.478 23.38 17.73 0.00 3.67
39 40 3.603532 TCTTAAGCTGCTCATGAGTTGG 58.396 45.455 23.38 14.25 0.00 3.77
40 41 5.618056 TTTCTTAAGCTGCTCATGAGTTG 57.382 39.130 23.38 16.59 0.00 3.16
41 42 7.992033 AGATATTTCTTAAGCTGCTCATGAGTT 59.008 33.333 23.38 12.34 0.00 3.01
42 43 7.441760 CAGATATTTCTTAAGCTGCTCATGAGT 59.558 37.037 23.38 6.31 0.00 3.41
43 44 7.656542 TCAGATATTTCTTAAGCTGCTCATGAG 59.343 37.037 18.84 18.84 0.00 2.90
44 45 7.503549 TCAGATATTTCTTAAGCTGCTCATGA 58.496 34.615 1.00 0.00 0.00 3.07
45 46 7.725818 TCAGATATTTCTTAAGCTGCTCATG 57.274 36.000 1.00 0.00 0.00 3.07
46 47 8.784994 CAATCAGATATTTCTTAAGCTGCTCAT 58.215 33.333 1.00 0.00 0.00 2.90
47 48 7.989170 TCAATCAGATATTTCTTAAGCTGCTCA 59.011 33.333 1.00 0.00 0.00 4.26
48 49 8.375608 TCAATCAGATATTTCTTAAGCTGCTC 57.624 34.615 1.00 0.00 0.00 4.26
49 50 7.041235 GCTCAATCAGATATTTCTTAAGCTGCT 60.041 37.037 0.00 0.00 0.00 4.24
50 51 7.076983 GCTCAATCAGATATTTCTTAAGCTGC 58.923 38.462 0.00 0.00 0.00 5.25
51 52 8.151141 TGCTCAATCAGATATTTCTTAAGCTG 57.849 34.615 0.00 0.00 0.00 4.24
52 53 8.921353 ATGCTCAATCAGATATTTCTTAAGCT 57.079 30.769 0.00 0.00 0.00 3.74
57 58 9.011095 CCACATATGCTCAATCAGATATTTCTT 57.989 33.333 1.58 0.00 0.00 2.52
58 59 7.610692 CCCACATATGCTCAATCAGATATTTCT 59.389 37.037 1.58 0.00 0.00 2.52
59 60 7.392673 ACCCACATATGCTCAATCAGATATTTC 59.607 37.037 1.58 0.00 0.00 2.17
60 61 7.236529 ACCCACATATGCTCAATCAGATATTT 58.763 34.615 1.58 0.00 0.00 1.40
61 62 6.787170 ACCCACATATGCTCAATCAGATATT 58.213 36.000 1.58 0.00 0.00 1.28
62 63 6.384342 ACCCACATATGCTCAATCAGATAT 57.616 37.500 1.58 0.00 0.00 1.63
63 64 5.830799 ACCCACATATGCTCAATCAGATA 57.169 39.130 1.58 0.00 0.00 1.98
64 65 4.719026 ACCCACATATGCTCAATCAGAT 57.281 40.909 1.58 0.00 0.00 2.90
65 66 4.201657 CAACCCACATATGCTCAATCAGA 58.798 43.478 1.58 0.00 0.00 3.27
66 67 3.949754 ACAACCCACATATGCTCAATCAG 59.050 43.478 1.58 0.00 0.00 2.90
67 68 3.947196 GACAACCCACATATGCTCAATCA 59.053 43.478 1.58 0.00 0.00 2.57
68 69 3.316308 GGACAACCCACATATGCTCAATC 59.684 47.826 1.58 0.00 34.14 2.67
69 70 3.290710 GGACAACCCACATATGCTCAAT 58.709 45.455 1.58 0.00 34.14 2.57
70 71 2.040947 TGGACAACCCACATATGCTCAA 59.959 45.455 1.58 0.00 40.82 3.02
71 72 1.632920 TGGACAACCCACATATGCTCA 59.367 47.619 1.58 0.00 40.82 4.26
72 73 2.418368 TGGACAACCCACATATGCTC 57.582 50.000 1.58 0.00 40.82 4.26
82 83 3.181487 CGATTGAAATGGATGGACAACCC 60.181 47.826 0.00 0.00 34.81 4.11
83 84 3.181487 CCGATTGAAATGGATGGACAACC 60.181 47.826 0.00 0.00 0.00 3.77
84 85 3.734902 GCCGATTGAAATGGATGGACAAC 60.735 47.826 0.00 0.00 0.00 3.32
85 86 2.426738 GCCGATTGAAATGGATGGACAA 59.573 45.455 0.00 0.00 0.00 3.18
106 107 1.550130 TTTAGTCAGAGGGTGGCCGG 61.550 60.000 0.00 0.00 0.00 6.13
140 141 3.849574 TCAAGGTGTTGGGGATATCTTCA 59.150 43.478 2.05 0.00 34.09 3.02
166 167 6.043358 GGCTTTCACCCTACTCTATAAAGGAT 59.957 42.308 0.00 0.00 31.64 3.24
168 169 5.367060 AGGCTTTCACCCTACTCTATAAAGG 59.633 44.000 0.00 0.00 0.00 3.11
169 170 6.127026 ACAGGCTTTCACCCTACTCTATAAAG 60.127 42.308 0.00 0.00 0.00 1.85
184 199 7.441458 GTCTTACTCTCTTAAAACAGGCTTTCA 59.559 37.037 0.00 0.00 0.00 2.69
202 217 5.846473 GCTTTGTCGTCAAATTGTCTTACTC 59.154 40.000 8.25 0.00 41.77 2.59
215 232 3.064207 GGTGACTATTGCTTTGTCGTCA 58.936 45.455 0.00 0.00 33.81 4.35
218 235 3.684305 TCATGGTGACTATTGCTTTGTCG 59.316 43.478 0.00 0.00 33.81 4.35
227 244 5.124457 GCATCTGTTGTTCATGGTGACTATT 59.876 40.000 0.00 0.00 0.00 1.73
249 274 1.883732 GAGTGCTAGTCAGACCGCA 59.116 57.895 10.30 10.30 0.00 5.69
325 350 0.311790 AACAATGTGCTCAGCCAACG 59.688 50.000 0.00 0.00 0.00 4.10
357 382 5.914085 AATTGCGAGATATGACTAAGCAC 57.086 39.130 0.00 0.00 34.94 4.40
374 399 3.020984 TCCGTTCCAGGGAAATAATTGC 58.979 45.455 1.58 0.00 35.75 3.56
407 432 6.694447 CAATCTTGGAAATGACAAATGACCT 58.306 36.000 0.00 0.00 0.00 3.85
517 542 3.905968 TGTCGGGGTACATATTCTCTGA 58.094 45.455 0.00 0.00 0.00 3.27
564 591 4.615949 TCCATTCCAACAAAACATTCACG 58.384 39.130 0.00 0.00 0.00 4.35
763 802 2.246993 TTCAATGCGGTTAAGGCGCG 62.247 55.000 0.00 0.00 0.00 6.86
873 912 6.604171 ACAAGATGCATACTCCAATGGATAA 58.396 36.000 0.87 0.00 37.95 1.75
879 918 6.421485 AGAGAAACAAGATGCATACTCCAAT 58.579 36.000 0.00 0.00 0.00 3.16
889 928 4.199432 TGAGAGGAGAGAAACAAGATGC 57.801 45.455 0.00 0.00 0.00 3.91
895 934 3.617531 GCGGAAATGAGAGGAGAGAAACA 60.618 47.826 0.00 0.00 0.00 2.83
1040 1079 1.654954 GCTCCGACTCGTAGGCTTCA 61.655 60.000 0.00 0.00 0.00 3.02
1047 1086 0.392060 TGCTACTGCTCCGACTCGTA 60.392 55.000 0.00 0.00 40.48 3.43
1050 1089 0.317436 CGATGCTACTGCTCCGACTC 60.317 60.000 0.00 0.00 40.48 3.36
1053 1092 2.490148 CCCGATGCTACTGCTCCGA 61.490 63.158 0.00 0.00 40.48 4.55
1092 1131 0.172578 TGTACTCGATGTTGCTCCCG 59.827 55.000 0.00 0.00 0.00 5.14
1311 1350 3.889692 CTGCCACCCACCACCACT 61.890 66.667 0.00 0.00 0.00 4.00
1467 1506 3.551496 CTGGGTGAGGAAAGCGGCA 62.551 63.158 1.45 0.00 0.00 5.69
1581 1635 4.551388 ACAACAACGACAACAACAACAAT 58.449 34.783 0.00 0.00 0.00 2.71
1595 1649 9.083080 TCTCACAATATAGATACAACAACAACG 57.917 33.333 0.00 0.00 0.00 4.10
1638 1692 6.265196 TGACTAAACAAACATGGCAAGAGAAT 59.735 34.615 0.00 0.00 0.00 2.40
1691 1751 2.223665 GCAACTCCAAGGATATGCTTGC 60.224 50.000 26.63 14.52 34.72 4.01
1750 1810 6.640499 TGCAACTAGTATTCAACAACAAATGC 59.360 34.615 0.00 0.00 0.00 3.56
1781 1844 0.305922 GATTTTCAGCGGCCATCTCG 59.694 55.000 2.24 0.00 0.00 4.04
1791 1854 6.073873 CGGAGAGAATATGTGAGATTTTCAGC 60.074 42.308 0.00 0.00 36.21 4.26
1807 1870 6.113411 ACAATTATTTTCGGACGGAGAGAAT 58.887 36.000 0.00 0.00 0.00 2.40
1808 1871 5.484715 ACAATTATTTTCGGACGGAGAGAA 58.515 37.500 0.00 0.00 0.00 2.87
1810 1873 4.026804 CGACAATTATTTTCGGACGGAGAG 60.027 45.833 5.68 0.00 0.00 3.20
1811 1874 3.861113 CGACAATTATTTTCGGACGGAGA 59.139 43.478 5.68 0.00 0.00 3.71
1812 1875 4.178156 CGACAATTATTTTCGGACGGAG 57.822 45.455 5.68 0.00 0.00 4.63
1820 1883 8.621286 ACATCCATTACTCCGACAATTATTTTC 58.379 33.333 0.00 0.00 0.00 2.29
1821 1884 8.519799 ACATCCATTACTCCGACAATTATTTT 57.480 30.769 0.00 0.00 0.00 1.82
1823 1886 9.436957 GATACATCCATTACTCCGACAATTATT 57.563 33.333 0.00 0.00 0.00 1.40
1824 1887 8.816894 AGATACATCCATTACTCCGACAATTAT 58.183 33.333 0.00 0.00 0.00 1.28
1825 1888 8.190326 AGATACATCCATTACTCCGACAATTA 57.810 34.615 0.00 0.00 0.00 1.40
1826 1889 7.067496 AGATACATCCATTACTCCGACAATT 57.933 36.000 0.00 0.00 0.00 2.32
1828 1891 6.776116 ACTAGATACATCCATTACTCCGACAA 59.224 38.462 0.00 0.00 0.00 3.18
1829 1892 6.304624 ACTAGATACATCCATTACTCCGACA 58.695 40.000 0.00 0.00 0.00 4.35
1830 1893 6.821031 ACTAGATACATCCATTACTCCGAC 57.179 41.667 0.00 0.00 0.00 4.79
1831 1894 6.776116 ACAACTAGATACATCCATTACTCCGA 59.224 38.462 0.00 0.00 0.00 4.55
1832 1895 6.982852 ACAACTAGATACATCCATTACTCCG 58.017 40.000 0.00 0.00 0.00 4.63
1861 1924 8.691797 GGGTAAAAATGGATGCATCTAAAACTA 58.308 33.333 25.28 8.56 0.00 2.24
1862 1925 7.180051 TGGGTAAAAATGGATGCATCTAAAACT 59.820 33.333 25.28 9.47 0.00 2.66
1863 1926 7.327214 TGGGTAAAAATGGATGCATCTAAAAC 58.673 34.615 25.28 13.78 0.00 2.43
1864 1927 7.487822 TGGGTAAAAATGGATGCATCTAAAA 57.512 32.000 25.28 10.04 0.00 1.52
1865 1928 7.673641 ATGGGTAAAAATGGATGCATCTAAA 57.326 32.000 25.28 12.43 0.00 1.85
1866 1929 7.673641 AATGGGTAAAAATGGATGCATCTAA 57.326 32.000 25.28 14.87 0.00 2.10
1867 1930 7.673641 AAATGGGTAAAAATGGATGCATCTA 57.326 32.000 25.28 20.79 0.00 1.98
1868 1931 6.564557 AAATGGGTAAAAATGGATGCATCT 57.435 33.333 25.28 7.83 0.00 2.90
1869 1932 6.018832 CGAAAATGGGTAAAAATGGATGCATC 60.019 38.462 18.81 18.81 0.00 3.91
1870 1933 5.816777 CGAAAATGGGTAAAAATGGATGCAT 59.183 36.000 0.00 0.00 0.00 3.96
1871 1934 5.174395 CGAAAATGGGTAAAAATGGATGCA 58.826 37.500 0.00 0.00 0.00 3.96
1872 1935 4.033932 GCGAAAATGGGTAAAAATGGATGC 59.966 41.667 0.00 0.00 0.00 3.91
1873 1936 4.267452 CGCGAAAATGGGTAAAAATGGATG 59.733 41.667 0.00 0.00 0.00 3.51
1874 1937 4.158764 TCGCGAAAATGGGTAAAAATGGAT 59.841 37.500 6.20 0.00 0.00 3.41
1875 1938 3.506455 TCGCGAAAATGGGTAAAAATGGA 59.494 39.130 6.20 0.00 0.00 3.41
1876 1939 3.610677 GTCGCGAAAATGGGTAAAAATGG 59.389 43.478 12.06 0.00 0.00 3.16
1877 1940 4.230657 TGTCGCGAAAATGGGTAAAAATG 58.769 39.130 12.06 0.00 0.00 2.32
1878 1941 4.506886 TGTCGCGAAAATGGGTAAAAAT 57.493 36.364 12.06 0.00 0.00 1.82
1879 1942 3.984508 TGTCGCGAAAATGGGTAAAAA 57.015 38.095 12.06 0.00 0.00 1.94
1880 1943 3.315749 ACTTGTCGCGAAAATGGGTAAAA 59.684 39.130 13.05 0.00 0.00 1.52
1881 1944 2.879646 ACTTGTCGCGAAAATGGGTAAA 59.120 40.909 13.05 0.00 0.00 2.01
1882 1945 2.496111 ACTTGTCGCGAAAATGGGTAA 58.504 42.857 13.05 0.00 0.00 2.85
1883 1946 2.172851 ACTTGTCGCGAAAATGGGTA 57.827 45.000 13.05 0.00 0.00 3.69
1884 1947 2.172851 TACTTGTCGCGAAAATGGGT 57.827 45.000 13.05 9.79 0.00 4.51
1885 1948 3.757745 AATACTTGTCGCGAAAATGGG 57.242 42.857 13.05 3.56 0.00 4.00
1886 1949 4.788100 CAGAAATACTTGTCGCGAAAATGG 59.212 41.667 13.05 4.35 0.00 3.16
1887 1950 4.788100 CCAGAAATACTTGTCGCGAAAATG 59.212 41.667 13.05 9.32 0.00 2.32
1888 1951 4.693566 TCCAGAAATACTTGTCGCGAAAAT 59.306 37.500 13.05 5.74 0.00 1.82
1889 1952 4.059511 TCCAGAAATACTTGTCGCGAAAA 58.940 39.130 12.06 12.01 0.00 2.29
1890 1953 3.430895 GTCCAGAAATACTTGTCGCGAAA 59.569 43.478 12.06 0.54 0.00 3.46
1891 1954 2.991190 GTCCAGAAATACTTGTCGCGAA 59.009 45.455 12.06 0.00 0.00 4.70
1892 1955 2.602878 GTCCAGAAATACTTGTCGCGA 58.397 47.619 3.71 3.71 0.00 5.87
1893 1956 1.320555 CGTCCAGAAATACTTGTCGCG 59.679 52.381 0.00 0.00 0.00 5.87
1894 1957 1.659098 CCGTCCAGAAATACTTGTCGC 59.341 52.381 0.00 0.00 0.00 5.19
1895 1958 3.179830 CTCCGTCCAGAAATACTTGTCG 58.820 50.000 0.00 0.00 0.00 4.35
1896 1959 3.522553 CCTCCGTCCAGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
1897 1960 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
1898 1961 2.500098 TCCCTCCGTCCAGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
1899 1962 2.766828 CTCCCTCCGTCCAGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
1900 1963 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
1901 1964 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
1902 1965 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
1903 1966 2.108970 GTACTCCCTCCGTCCAGAAAT 58.891 52.381 0.00 0.00 0.00 2.17
1904 1967 1.076677 AGTACTCCCTCCGTCCAGAAA 59.923 52.381 0.00 0.00 0.00 2.52
1905 1968 0.702902 AGTACTCCCTCCGTCCAGAA 59.297 55.000 0.00 0.00 0.00 3.02
1906 1969 0.702902 AAGTACTCCCTCCGTCCAGA 59.297 55.000 0.00 0.00 0.00 3.86
1907 1970 1.204941 CAAAGTACTCCCTCCGTCCAG 59.795 57.143 0.00 0.00 0.00 3.86
1908 1971 1.263356 CAAAGTACTCCCTCCGTCCA 58.737 55.000 0.00 0.00 0.00 4.02
1909 1972 0.535797 CCAAAGTACTCCCTCCGTCC 59.464 60.000 0.00 0.00 0.00 4.79
1910 1973 1.477295 CTCCAAAGTACTCCCTCCGTC 59.523 57.143 0.00 0.00 0.00 4.79
1911 1974 1.558233 CTCCAAAGTACTCCCTCCGT 58.442 55.000 0.00 0.00 0.00 4.69
1912 1975 0.824759 CCTCCAAAGTACTCCCTCCG 59.175 60.000 0.00 0.00 0.00 4.63
1913 1976 1.205055 CCCTCCAAAGTACTCCCTCC 58.795 60.000 0.00 0.00 0.00 4.30
1914 1977 2.236644 GTTCCCTCCAAAGTACTCCCTC 59.763 54.545 0.00 0.00 0.00 4.30
1915 1978 2.267192 GTTCCCTCCAAAGTACTCCCT 58.733 52.381 0.00 0.00 0.00 4.20
1916 1979 1.982958 TGTTCCCTCCAAAGTACTCCC 59.017 52.381 0.00 0.00 0.00 4.30
1917 1980 3.009143 ACATGTTCCCTCCAAAGTACTCC 59.991 47.826 0.00 0.00 0.00 3.85
1918 1981 4.287766 ACATGTTCCCTCCAAAGTACTC 57.712 45.455 0.00 0.00 0.00 2.59
1919 1982 5.091552 TCTACATGTTCCCTCCAAAGTACT 58.908 41.667 2.30 0.00 0.00 2.73
1920 1983 5.416271 TCTACATGTTCCCTCCAAAGTAC 57.584 43.478 2.30 0.00 0.00 2.73
1921 1984 6.442541 TTTCTACATGTTCCCTCCAAAGTA 57.557 37.500 2.30 0.00 0.00 2.24
1922 1985 4.993705 TTCTACATGTTCCCTCCAAAGT 57.006 40.909 2.30 0.00 0.00 2.66
1923 1986 7.338710 TCTATTTCTACATGTTCCCTCCAAAG 58.661 38.462 2.30 0.00 0.00 2.77
1924 1987 7.182026 TCTCTATTTCTACATGTTCCCTCCAAA 59.818 37.037 2.30 0.00 0.00 3.28
1925 1988 6.672218 TCTCTATTTCTACATGTTCCCTCCAA 59.328 38.462 2.30 0.00 0.00 3.53
1949 2012 3.378427 ACAGTGTTGCCAAGAGAAACTTC 59.622 43.478 0.00 0.00 36.61 3.01
1958 2021 1.664016 GCGATGAACAGTGTTGCCAAG 60.664 52.381 14.57 6.26 0.00 3.61
1968 2031 7.946655 TCCAGTAAATTATAGCGATGAACAG 57.053 36.000 0.00 0.00 0.00 3.16
1970 2033 8.230486 CCATTCCAGTAAATTATAGCGATGAAC 58.770 37.037 0.00 0.00 0.00 3.18
1978 2041 7.595819 TTTGCCCCATTCCAGTAAATTATAG 57.404 36.000 0.00 0.00 0.00 1.31
1980 2043 6.882768 TTTTGCCCCATTCCAGTAAATTAT 57.117 33.333 0.00 0.00 0.00 1.28
2019 2082 9.658799 CTCCTTTGATACTAAGATCAAACAGAA 57.341 33.333 7.33 0.00 46.12 3.02
2020 2083 9.035890 TCTCCTTTGATACTAAGATCAAACAGA 57.964 33.333 7.33 8.67 46.12 3.41
2021 2084 9.658799 TTCTCCTTTGATACTAAGATCAAACAG 57.341 33.333 7.33 6.96 46.12 3.16
2025 2088 9.436957 GTGTTTCTCCTTTGATACTAAGATCAA 57.563 33.333 0.00 0.00 42.68 2.57
2027 2090 8.874816 GTGTGTTTCTCCTTTGATACTAAGATC 58.125 37.037 0.00 0.00 0.00 2.75
2028 2091 8.375506 TGTGTGTTTCTCCTTTGATACTAAGAT 58.624 33.333 0.00 0.00 0.00 2.40
2029 2092 7.732025 TGTGTGTTTCTCCTTTGATACTAAGA 58.268 34.615 0.00 0.00 0.00 2.10
2058 2564 4.330620 GCGGTCGGATGAGTTGTATAAAAA 59.669 41.667 0.00 0.00 0.00 1.94
2059 2565 3.866910 GCGGTCGGATGAGTTGTATAAAA 59.133 43.478 0.00 0.00 0.00 1.52
2060 2566 3.450578 GCGGTCGGATGAGTTGTATAAA 58.549 45.455 0.00 0.00 0.00 1.40
2061 2567 2.223876 GGCGGTCGGATGAGTTGTATAA 60.224 50.000 0.00 0.00 0.00 0.98
2062 2568 1.338973 GGCGGTCGGATGAGTTGTATA 59.661 52.381 0.00 0.00 0.00 1.47
2063 2569 0.104304 GGCGGTCGGATGAGTTGTAT 59.896 55.000 0.00 0.00 0.00 2.29
2080 2586 2.991250 TGTGCAGGAAATCTAAGAGGC 58.009 47.619 0.00 0.00 0.00 4.70
2084 2590 5.649395 TCCATTCTTGTGCAGGAAATCTAAG 59.351 40.000 1.01 0.00 30.11 2.18
2096 2602 1.901833 ACCCCATTTCCATTCTTGTGC 59.098 47.619 0.00 0.00 0.00 4.57
2105 2611 1.422024 TCGTTCAAGACCCCATTTCCA 59.578 47.619 0.00 0.00 0.00 3.53
2157 2663 8.970020 AGCATGATCAAGTTAAAATCCACATTA 58.030 29.630 0.00 0.00 0.00 1.90
2158 2664 7.844009 AGCATGATCAAGTTAAAATCCACATT 58.156 30.769 0.00 0.00 0.00 2.71
2182 2688 7.120726 ACAGAAAAACACCGGAATCCTAATAAG 59.879 37.037 9.46 0.00 0.00 1.73
2229 2736 6.081049 TGGTACGCATAGAAAATTGAAAACG 58.919 36.000 0.00 0.00 0.00 3.60
2321 2879 3.643763 AGCGACTCTTTAGTTCACTGTG 58.356 45.455 0.17 0.17 35.56 3.66
2361 2919 7.341256 TGTGGAGTAGAGTTTTACGATCCTATT 59.659 37.037 0.00 0.00 0.00 1.73
2378 2936 5.063204 TCCTTTGTTGTTCATGTGGAGTAG 58.937 41.667 0.00 0.00 0.00 2.57
2440 2998 6.017605 CGCATAGTTTTGCAAGATTAGGATCT 60.018 38.462 8.10 0.00 42.91 2.75
2484 3042 1.620819 ACCTCCGCATCCATAGTCATC 59.379 52.381 0.00 0.00 0.00 2.92
2486 3044 0.752658 CACCTCCGCATCCATAGTCA 59.247 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.