Multiple sequence alignment - TraesCS5D01G205400

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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 TraesCS5D01G205400 chr5D 100.000 2625 0 0 1 2625 311352534 311355158 0.000000e+00 4848.0
1 TraesCS5D01G205400 chr5D 96.373 193 6 1 1792 1984 121102665 121102474 1.520000e-82 316.0
2 TraesCS5D01G205400 chr5D 94.554 202 9 2 1792 1993 486861196 486861395 7.050000e-81 311.0
3 TraesCS5D01G205400 chr5B 89.951 1821 100 27 7 1797 357131298 357133065 0.000000e+00 2272.0
4 TraesCS5D01G205400 chr5B 89.124 662 50 11 1980 2625 357133063 357133718 0.000000e+00 804.0
5 TraesCS5D01G205400 chr5A 90.625 1248 68 17 586 1797 404555019 404556253 0.000000e+00 1611.0
6 TraesCS5D01G205400 chr5A 87.234 282 33 3 2021 2302 404556278 404556556 4.220000e-83 318.0
7 TraesCS5D01G205400 chr5A 85.837 233 27 4 2395 2625 404557379 404557607 2.610000e-60 243.0
8 TraesCS5D01G205400 chr5A 89.076 119 6 2 583 700 404554802 404554914 9.800000e-30 141.0
9 TraesCS5D01G205400 chr5A 89.216 102 11 0 2073 2174 608966485 608966586 7.630000e-26 128.0
10 TraesCS5D01G205400 chr5A 93.333 60 4 0 474 533 404554964 404555023 3.600000e-14 89.8
11 TraesCS5D01G205400 chr1D 96.875 192 6 0 1795 1986 93501169 93500978 3.260000e-84 322.0
12 TraesCS5D01G205400 chr7D 97.340 188 5 0 1795 1982 161844388 161844575 1.170000e-83 320.0
13 TraesCS5D01G205400 chr2D 96.859 191 6 0 1795 1985 516410999 516410809 1.170000e-83 320.0
14 TraesCS5D01G205400 chr2D 97.340 188 4 1 1797 1983 35677339 35677152 4.220000e-83 318.0
15 TraesCS5D01G205400 chr2D 88.496 113 13 0 2072 2184 334318866 334318754 1.270000e-28 137.0
16 TraesCS5D01G205400 chr2D 88.889 108 12 0 2072 2179 642216095 642215988 1.640000e-27 134.0
17 TraesCS5D01G205400 chr6D 96.825 189 6 0 1794 1982 394929764 394929952 1.520000e-82 316.0
18 TraesCS5D01G205400 chr6D 94.554 202 8 3 1783 1983 335300564 335300365 2.540000e-80 309.0
19 TraesCS5D01G205400 chr3D 95.897 195 6 1 1792 1986 511346623 511346431 5.450000e-82 315.0
20 TraesCS5D01G205400 chr3D 86.239 109 15 0 2072 2180 452820136 452820244 4.590000e-23 119.0
21 TraesCS5D01G205400 chr2B 92.593 108 8 0 2072 2179 799538006 799538113 3.500000e-34 156.0
22 TraesCS5D01G205400 chr2A 90.566 106 10 0 2072 2177 767024252 767024147 9.800000e-30 141.0
23 TraesCS5D01G205400 chr7B 87.379 103 13 0 2072 2174 676970067 676970169 4.590000e-23 119.0
24 TraesCS5D01G205400 chr6B 85.965 57 6 2 2010 2065 518390085 518390140 2.820000e-05 60.2


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 TraesCS5D01G205400 chr5D 311352534 311355158 2624 False 4848.00 4848 100.0000 1 2625 1 chr5D.!!$F1 2624
1 TraesCS5D01G205400 chr5B 357131298 357133718 2420 False 1538.00 2272 89.5375 7 2625 2 chr5B.!!$F1 2618
2 TraesCS5D01G205400 chr5A 404554802 404557607 2805 False 480.56 1611 89.2210 474 2625 5 chr5A.!!$F2 2151

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
528 541 0.037232 AACGACCTAGACTTGGCAGC 60.037 55.0 2.53 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 2212 0.033504 TCACTCCGCTCCACAACTTC 59.966 55.0 0.0 0.0 0.0 3.01 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
54 55 6.773638 GGACACATCCTACCATCTAATGATT 58.226 40.000 0.00 0.00 42.45 2.57
82 83 2.234143 TCATCATGCGGGTCACAAAAA 58.766 42.857 0.00 0.00 0.00 1.94
107 108 4.447724 TGCACGTTAGTTGATGAGAAAGAC 59.552 41.667 0.00 0.00 0.00 3.01
108 109 4.686554 GCACGTTAGTTGATGAGAAAGACT 59.313 41.667 0.00 0.00 0.00 3.24
114 115 5.317733 AGTTGATGAGAAAGACTAGGTCG 57.682 43.478 0.00 0.00 37.67 4.79
120 121 3.690139 TGAGAAAGACTAGGTCGTGCTAG 59.310 47.826 0.00 0.00 37.67 3.42
177 179 3.319122 GCCAAATGAAGAAGTGACAACCT 59.681 43.478 0.00 0.00 0.00 3.50
184 186 1.352156 GAAGTGACAACCTAGCGGCG 61.352 60.000 0.51 0.51 0.00 6.46
213 215 2.385013 TGCATGTTGTCTCATACGCT 57.615 45.000 0.00 0.00 0.00 5.07
214 216 3.518634 TGCATGTTGTCTCATACGCTA 57.481 42.857 0.00 0.00 0.00 4.26
222 224 2.554462 TGTCTCATACGCTAGAGCATCC 59.446 50.000 1.89 0.00 42.21 3.51
224 226 2.554462 TCTCATACGCTAGAGCATCCAC 59.446 50.000 1.89 0.00 42.21 4.02
252 254 4.919168 ACAATGAAAAACTCATGATGTGCG 59.081 37.500 0.00 0.00 44.43 5.34
295 297 1.933051 TCCTCTCTTCTCCCATCTCCA 59.067 52.381 0.00 0.00 0.00 3.86
299 301 2.175715 TCTCTTCTCCCATCTCCATCGA 59.824 50.000 0.00 0.00 0.00 3.59
308 310 2.326664 CATCTCCATCGAAGCTCATCG 58.673 52.381 1.24 1.24 44.04 3.84
345 348 6.721571 TTGGACTTAAGCATTAGAAAGTCG 57.278 37.500 1.29 0.00 45.61 4.18
368 375 0.323725 ATGCTCAAGTTCGGCCCAAT 60.324 50.000 0.00 0.00 0.00 3.16
371 378 0.523072 CTCAAGTTCGGCCCAATGTG 59.477 55.000 0.00 0.00 0.00 3.21
406 413 0.178068 GTCATTAAGAGCCTCGGCCA 59.822 55.000 2.24 0.00 43.17 5.36
407 414 1.131638 TCATTAAGAGCCTCGGCCAT 58.868 50.000 2.24 0.00 43.17 4.40
408 415 1.202687 TCATTAAGAGCCTCGGCCATG 60.203 52.381 2.24 0.00 43.17 3.66
409 416 1.131638 ATTAAGAGCCTCGGCCATGA 58.868 50.000 2.24 0.00 43.17 3.07
410 417 1.131638 TTAAGAGCCTCGGCCATGAT 58.868 50.000 2.24 0.00 43.17 2.45
411 418 0.394192 TAAGAGCCTCGGCCATGATG 59.606 55.000 2.24 0.00 43.17 3.07
412 419 1.630126 AAGAGCCTCGGCCATGATGT 61.630 55.000 2.24 0.00 43.17 3.06
413 420 1.890979 GAGCCTCGGCCATGATGTG 60.891 63.158 2.24 0.00 43.17 3.21
414 421 3.589881 GCCTCGGCCATGATGTGC 61.590 66.667 2.24 0.00 34.56 4.57
415 422 2.191375 CCTCGGCCATGATGTGCT 59.809 61.111 2.24 0.00 0.00 4.40
416 423 1.452651 CCTCGGCCATGATGTGCTT 60.453 57.895 2.24 0.00 0.00 3.91
417 424 1.442526 CCTCGGCCATGATGTGCTTC 61.443 60.000 2.24 0.00 0.00 3.86
418 425 0.745486 CTCGGCCATGATGTGCTTCA 60.745 55.000 2.24 0.00 0.00 3.02
419 426 0.107066 TCGGCCATGATGTGCTTCAT 60.107 50.000 2.24 0.00 39.77 2.57
433 440 1.340405 GCTTCATCTTGGCCCTTGAGA 60.340 52.381 0.00 0.00 0.00 3.27
466 473 5.303589 TCGAAGAGGTCAGGAAAAACTCTTA 59.696 40.000 3.56 0.00 45.54 2.10
467 474 5.635700 CGAAGAGGTCAGGAAAAACTCTTAG 59.364 44.000 3.56 0.69 45.54 2.18
477 484 4.098501 GGAAAAACTCTTAGGCCATCCATG 59.901 45.833 5.01 0.00 33.74 3.66
528 541 0.037232 AACGACCTAGACTTGGCAGC 60.037 55.000 2.53 0.00 0.00 5.25
536 549 1.059913 AGACTTGGCAGCAACCTAGT 58.940 50.000 10.96 10.96 46.52 2.57
539 552 0.037326 CTTGGCAGCAACCTAGTCGA 60.037 55.000 0.00 0.00 0.00 4.20
541 554 1.805945 GGCAGCAACCTAGTCGACG 60.806 63.158 10.46 0.00 0.00 5.12
542 555 1.080705 GCAGCAACCTAGTCGACGT 60.081 57.895 10.46 0.00 0.00 4.34
543 556 1.071567 GCAGCAACCTAGTCGACGTC 61.072 60.000 10.46 5.18 0.00 4.34
544 557 0.240145 CAGCAACCTAGTCGACGTCA 59.760 55.000 17.16 0.00 0.00 4.35
545 558 0.956633 AGCAACCTAGTCGACGTCAA 59.043 50.000 17.16 0.00 0.00 3.18
546 559 1.068472 AGCAACCTAGTCGACGTCAAG 60.068 52.381 17.16 6.79 0.00 3.02
573 586 1.839994 CCAAGGCTACCAGAGATCCAA 59.160 52.381 0.00 0.00 0.00 3.53
575 588 1.501582 AGGCTACCAGAGATCCAACC 58.498 55.000 0.00 0.00 0.00 3.77
599 613 2.244510 TGAGCCATAACCAACCATCCAT 59.755 45.455 0.00 0.00 0.00 3.41
618 632 3.196463 CATTGCACAAAGACAAAGCCAA 58.804 40.909 0.00 0.00 0.00 4.52
635 652 2.480759 GCCAAGTTAGGATGCATGCAAG 60.481 50.000 26.68 6.04 0.00 4.01
639 656 0.925558 TTAGGATGCATGCAAGGGGA 59.074 50.000 26.68 8.41 0.00 4.81
641 658 0.263765 AGGATGCATGCAAGGGGAAT 59.736 50.000 26.68 5.83 0.00 3.01
643 660 2.091166 AGGATGCATGCAAGGGGAATTA 60.091 45.455 26.68 0.00 0.00 1.40
644 661 2.036346 GGATGCATGCAAGGGGAATTAC 59.964 50.000 26.68 1.64 0.00 1.89
645 662 2.530460 TGCATGCAAGGGGAATTACT 57.470 45.000 20.30 0.00 0.00 2.24
646 663 2.818921 TGCATGCAAGGGGAATTACTT 58.181 42.857 20.30 0.00 0.00 2.24
647 664 2.760092 TGCATGCAAGGGGAATTACTTC 59.240 45.455 20.30 0.00 0.00 3.01
823 848 0.465460 ACAGTGTTGGCCAACGTGAT 60.465 50.000 38.28 26.19 43.94 3.06
884 917 0.319900 ACGCATCCATCCATACGAGC 60.320 55.000 0.00 0.00 0.00 5.03
889 922 0.473694 TCCATCCATACGAGCCCCAT 60.474 55.000 0.00 0.00 0.00 4.00
936 972 0.322456 CGAAGGAAACTGCATCCCCA 60.322 55.000 1.05 0.00 42.68 4.96
946 982 0.918258 TGCATCCCCAGTAATCAGCA 59.082 50.000 0.00 0.00 0.00 4.41
972 1008 7.684670 AGCGCATTTAAACGGATATATACATG 58.315 34.615 11.47 0.00 0.00 3.21
1004 1044 3.314080 GCGGCGCTCTCTATCTATCTATT 59.686 47.826 26.86 0.00 0.00 1.73
1073 1113 4.802051 GCGATGGGGAAGCTGGCA 62.802 66.667 0.00 0.00 0.00 4.92
1082 1122 2.359230 AAGCTGGCAAGGCTCGTC 60.359 61.111 1.36 0.00 39.30 4.20
1355 1395 1.251251 ATCCTTGTGGCAAGCAAGAC 58.749 50.000 16.83 0.00 44.29 3.01
1386 1433 2.214920 GGTCTTGTCTCCCCCGTGT 61.215 63.158 0.00 0.00 0.00 4.49
1387 1434 1.292541 GTCTTGTCTCCCCCGTGTC 59.707 63.158 0.00 0.00 0.00 3.67
1388 1435 2.261671 CTTGTCTCCCCCGTGTCG 59.738 66.667 0.00 0.00 0.00 4.35
1389 1436 2.522436 TTGTCTCCCCCGTGTCGT 60.522 61.111 0.00 0.00 0.00 4.34
1390 1437 2.765250 CTTGTCTCCCCCGTGTCGTG 62.765 65.000 0.00 0.00 0.00 4.35
1603 1664 8.246180 AGATGAACAGTATAAATGGTGCAAAAG 58.754 33.333 0.00 0.00 0.00 2.27
1744 1811 6.134535 ACAACAAAACTGAGGGTATATCCA 57.865 37.500 4.46 0.00 38.11 3.41
1763 1830 3.903090 TCCAGTTTGGATTGCAGGATTTT 59.097 39.130 0.00 0.00 42.67 1.82
1774 1841 6.928492 GGATTGCAGGATTTTTGTTGAAACTA 59.072 34.615 0.00 0.00 0.00 2.24
1800 1867 7.575499 AGGGATATACTCAATTCTTAAGGGG 57.425 40.000 1.85 0.00 0.00 4.79
1801 1868 6.505700 AGGGATATACTCAATTCTTAAGGGGG 59.494 42.308 1.85 0.00 0.00 5.40
1802 1869 6.274908 GGGATATACTCAATTCTTAAGGGGGT 59.725 42.308 1.85 0.00 0.00 4.95
1803 1870 7.168905 GGATATACTCAATTCTTAAGGGGGTG 58.831 42.308 1.85 0.00 0.00 4.61
1804 1871 7.202195 GGATATACTCAATTCTTAAGGGGGTGT 60.202 40.741 1.85 0.00 0.00 4.16
1805 1872 4.741928 ACTCAATTCTTAAGGGGGTGTT 57.258 40.909 1.85 0.00 0.00 3.32
1806 1873 5.074746 ACTCAATTCTTAAGGGGGTGTTT 57.925 39.130 1.85 0.00 0.00 2.83
1807 1874 5.077564 ACTCAATTCTTAAGGGGGTGTTTC 58.922 41.667 1.85 0.00 0.00 2.78
1808 1875 4.076394 TCAATTCTTAAGGGGGTGTTTCG 58.924 43.478 1.85 0.00 0.00 3.46
1809 1876 3.801307 ATTCTTAAGGGGGTGTTTCGT 57.199 42.857 1.85 0.00 0.00 3.85
1810 1877 3.581265 TTCTTAAGGGGGTGTTTCGTT 57.419 42.857 1.85 0.00 0.00 3.85
1811 1878 3.130280 TCTTAAGGGGGTGTTTCGTTC 57.870 47.619 1.85 0.00 0.00 3.95
1812 1879 2.438763 TCTTAAGGGGGTGTTTCGTTCA 59.561 45.455 1.85 0.00 0.00 3.18
1813 1880 2.554370 TAAGGGGGTGTTTCGTTCAG 57.446 50.000 0.00 0.00 0.00 3.02
1814 1881 0.841289 AAGGGGGTGTTTCGTTCAGA 59.159 50.000 0.00 0.00 0.00 3.27
1815 1882 0.841289 AGGGGGTGTTTCGTTCAGAA 59.159 50.000 0.00 0.00 37.01 3.02
1816 1883 1.202770 AGGGGGTGTTTCGTTCAGAAG 60.203 52.381 0.00 0.00 40.40 2.85
1817 1884 1.476291 GGGGGTGTTTCGTTCAGAAGT 60.476 52.381 0.00 0.00 40.40 3.01
1818 1885 1.871676 GGGGTGTTTCGTTCAGAAGTC 59.128 52.381 0.00 0.00 40.40 3.01
1819 1886 1.871676 GGGTGTTTCGTTCAGAAGTCC 59.128 52.381 0.00 0.00 40.40 3.85
1820 1887 2.484947 GGGTGTTTCGTTCAGAAGTCCT 60.485 50.000 0.00 0.00 40.40 3.85
1821 1888 3.243975 GGGTGTTTCGTTCAGAAGTCCTA 60.244 47.826 0.00 0.00 40.40 2.94
1822 1889 3.988517 GGTGTTTCGTTCAGAAGTCCTAG 59.011 47.826 0.00 0.00 40.40 3.02
1823 1890 3.988517 GTGTTTCGTTCAGAAGTCCTAGG 59.011 47.826 0.82 0.82 40.40 3.02
1824 1891 3.893200 TGTTTCGTTCAGAAGTCCTAGGA 59.107 43.478 7.62 7.62 40.40 2.94
1825 1892 4.236147 GTTTCGTTCAGAAGTCCTAGGAC 58.764 47.826 31.29 31.29 44.86 3.85
1885 1952 9.022884 TCTTTAGTAGAGTCTTTTTCTAGTCCC 57.977 37.037 0.00 0.00 33.84 4.46
1886 1953 8.953223 TTTAGTAGAGTCTTTTTCTAGTCCCT 57.047 34.615 0.00 0.00 33.84 4.20
1887 1954 6.844097 AGTAGAGTCTTTTTCTAGTCCCTG 57.156 41.667 0.00 0.00 0.00 4.45
1888 1955 4.545208 AGAGTCTTTTTCTAGTCCCTGC 57.455 45.455 0.00 0.00 0.00 4.85
1889 1956 3.904339 AGAGTCTTTTTCTAGTCCCTGCA 59.096 43.478 0.00 0.00 0.00 4.41
1890 1957 4.020662 AGAGTCTTTTTCTAGTCCCTGCAG 60.021 45.833 6.78 6.78 0.00 4.41
1891 1958 3.904339 AGTCTTTTTCTAGTCCCTGCAGA 59.096 43.478 17.39 0.00 0.00 4.26
1892 1959 4.348168 AGTCTTTTTCTAGTCCCTGCAGAA 59.652 41.667 17.39 0.00 0.00 3.02
1893 1960 5.063880 GTCTTTTTCTAGTCCCTGCAGAAA 58.936 41.667 17.39 2.84 36.70 2.52
1894 1961 5.531287 GTCTTTTTCTAGTCCCTGCAGAAAA 59.469 40.000 17.39 9.41 43.15 2.29
1896 1963 6.391227 TTTTTCTAGTCCCTGCAGAAAAAG 57.609 37.500 17.39 6.02 45.93 2.27
1897 1964 4.706842 TTCTAGTCCCTGCAGAAAAAGT 57.293 40.909 17.39 2.85 0.00 2.66
1898 1965 4.273148 TCTAGTCCCTGCAGAAAAAGTC 57.727 45.455 17.39 0.00 0.00 3.01
1899 1966 2.278332 AGTCCCTGCAGAAAAAGTCC 57.722 50.000 17.39 0.00 0.00 3.85
1900 1967 1.202940 AGTCCCTGCAGAAAAAGTCCC 60.203 52.381 17.39 0.00 0.00 4.46
1901 1968 1.149101 TCCCTGCAGAAAAAGTCCCT 58.851 50.000 17.39 0.00 0.00 4.20
1902 1969 1.073923 TCCCTGCAGAAAAAGTCCCTC 59.926 52.381 17.39 0.00 0.00 4.30
1903 1970 1.539157 CCTGCAGAAAAAGTCCCTCC 58.461 55.000 17.39 0.00 0.00 4.30
1904 1971 1.539157 CTGCAGAAAAAGTCCCTCCC 58.461 55.000 8.42 0.00 0.00 4.30
1905 1972 0.250727 TGCAGAAAAAGTCCCTCCCG 60.251 55.000 0.00 0.00 0.00 5.14
1906 1973 0.250770 GCAGAAAAAGTCCCTCCCGT 60.251 55.000 0.00 0.00 0.00 5.28
1907 1974 1.818131 GCAGAAAAAGTCCCTCCCGTT 60.818 52.381 0.00 0.00 0.00 4.44
1908 1975 2.583143 CAGAAAAAGTCCCTCCCGTTT 58.417 47.619 0.00 0.00 0.00 3.60
1909 1976 2.293399 CAGAAAAAGTCCCTCCCGTTTG 59.707 50.000 0.00 0.00 0.00 2.93
1910 1977 1.611977 GAAAAAGTCCCTCCCGTTTGG 59.388 52.381 0.00 0.00 0.00 3.28
1911 1978 0.554305 AAAAGTCCCTCCCGTTTGGT 59.446 50.000 0.00 0.00 34.77 3.67
1912 1979 0.554305 AAAGTCCCTCCCGTTTGGTT 59.446 50.000 0.00 0.00 34.77 3.67
1913 1980 0.109913 AAGTCCCTCCCGTTTGGTTC 59.890 55.000 0.00 0.00 34.77 3.62
1914 1981 1.303074 GTCCCTCCCGTTTGGTTCC 60.303 63.158 0.00 0.00 34.77 3.62
1915 1982 1.462627 TCCCTCCCGTTTGGTTCCT 60.463 57.895 0.00 0.00 34.77 3.36
1916 1983 0.178897 TCCCTCCCGTTTGGTTCCTA 60.179 55.000 0.00 0.00 34.77 2.94
1917 1984 0.252197 CCCTCCCGTTTGGTTCCTAG 59.748 60.000 0.00 0.00 34.77 3.02
1918 1985 0.252197 CCTCCCGTTTGGTTCCTAGG 59.748 60.000 0.82 0.82 34.77 3.02
1919 1986 0.252197 CTCCCGTTTGGTTCCTAGGG 59.748 60.000 9.46 0.00 40.16 3.53
1920 1987 0.178897 TCCCGTTTGGTTCCTAGGGA 60.179 55.000 9.46 0.00 44.85 4.20
1921 1988 0.035725 CCCGTTTGGTTCCTAGGGAC 60.036 60.000 12.35 12.35 41.26 4.46
1922 1989 0.981943 CCGTTTGGTTCCTAGGGACT 59.018 55.000 20.08 0.00 46.37 3.85
1923 1990 1.350019 CCGTTTGGTTCCTAGGGACTT 59.650 52.381 20.08 0.00 41.75 3.01
1924 1991 2.224695 CCGTTTGGTTCCTAGGGACTTT 60.225 50.000 20.08 0.00 41.75 2.66
1925 1992 3.483421 CGTTTGGTTCCTAGGGACTTTT 58.517 45.455 20.08 0.00 41.75 2.27
1926 1993 3.887110 CGTTTGGTTCCTAGGGACTTTTT 59.113 43.478 20.08 0.00 41.75 1.94
1927 1994 5.065235 CGTTTGGTTCCTAGGGACTTTTTA 58.935 41.667 20.08 0.00 41.75 1.52
1928 1995 5.180680 CGTTTGGTTCCTAGGGACTTTTTAG 59.819 44.000 20.08 4.22 41.75 1.85
1929 1996 4.921644 TGGTTCCTAGGGACTTTTTAGG 57.078 45.455 20.08 0.00 41.75 2.69
1930 1997 3.590182 TGGTTCCTAGGGACTTTTTAGGG 59.410 47.826 20.08 0.00 41.75 3.53
1931 1998 3.848377 GGTTCCTAGGGACTTTTTAGGGA 59.152 47.826 20.08 0.00 41.75 4.20
1932 1999 4.477581 GGTTCCTAGGGACTTTTTAGGGAT 59.522 45.833 20.08 0.00 41.75 3.85
1933 2000 5.044328 GGTTCCTAGGGACTTTTTAGGGATT 60.044 44.000 20.08 0.00 41.75 3.01
1934 2001 6.491383 GTTCCTAGGGACTTTTTAGGGATTT 58.509 40.000 13.55 0.00 41.75 2.17
1935 2002 6.730001 TCCTAGGGACTTTTTAGGGATTTT 57.270 37.500 9.46 0.00 41.75 1.82
1936 2003 7.111136 TCCTAGGGACTTTTTAGGGATTTTT 57.889 36.000 9.46 0.00 41.75 1.94
1972 2039 5.828747 GACTAAAAAGTCCCTGAACCAAAC 58.171 41.667 0.00 0.00 32.97 2.93
1973 2040 5.265989 ACTAAAAAGTCCCTGAACCAAACA 58.734 37.500 0.00 0.00 0.00 2.83
1974 2041 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
1975 2042 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
1976 2043 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
1977 2044 0.185175 GTCCCTGAACCAAACACCCT 59.815 55.000 0.00 0.00 0.00 4.34
1978 2045 0.476771 TCCCTGAACCAAACACCCTC 59.523 55.000 0.00 0.00 0.00 4.30
2058 2126 9.052759 GTCAAACTTTTTCTAGTCCATGAGTTA 57.947 33.333 0.00 0.00 0.00 2.24
2161 2237 0.249911 GTGAAGTTGTGGAGCGGAGT 60.250 55.000 0.00 0.00 0.00 3.85
2188 2264 2.473212 CGAACAGCGCGTAATTAGCAAA 60.473 45.455 8.43 0.00 34.19 3.68
2189 2265 3.484683 GAACAGCGCGTAATTAGCAAAA 58.515 40.909 8.43 0.00 34.19 2.44
2220 2296 7.327214 AGAACTAAAGTTGGCAAACAAATTGA 58.673 30.769 6.76 0.00 45.65 2.57
2229 2305 4.752661 GCAAACAAATTGACATGCCAAT 57.247 36.364 0.80 0.80 41.85 3.16
2231 2307 6.238610 GCAAACAAATTGACATGCCAATAA 57.761 33.333 7.73 0.00 41.85 1.40
2279 2355 3.836949 CAAAATTTGGGTCATGGACGAG 58.163 45.455 0.00 0.00 32.65 4.18
2328 3160 4.651503 ACCATCTAGACATACCCAAGACTG 59.348 45.833 0.00 0.00 0.00 3.51
2345 3180 7.416890 CCCAAGACTGTAGTTATCAAGTCCTAG 60.417 44.444 0.00 0.00 0.00 3.02
2369 3204 4.794067 AGAATACACCCCTTGGACCTTAAT 59.206 41.667 0.00 0.00 34.81 1.40
2376 3211 3.069729 CCCCTTGGACCTTAATCTCGTAG 59.930 52.174 0.00 0.00 0.00 3.51
2489 3326 7.616313 TCTTTTTACTCTCTCCTCATTTCTCC 58.384 38.462 0.00 0.00 0.00 3.71
2502 3339 8.225603 TCCTCATTTCTCCTAAACATATTTGC 57.774 34.615 0.00 0.00 0.00 3.68
2521 3358 1.399727 GCCTTCATTTCGTGTGAACCG 60.400 52.381 0.00 0.00 32.71 4.44
2524 3361 2.519377 TCATTTCGTGTGAACCGTCT 57.481 45.000 0.00 0.00 32.71 4.18
2543 3380 2.300723 TCTAGAAGGCACCGCTACAAAA 59.699 45.455 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.189539 GTGTGGCACCATGGGAAA 57.810 55.556 18.09 0.00 0.00 3.13
22 23 3.127533 GGATGTGTCCTGGCACGC 61.128 66.667 13.83 8.98 41.94 5.34
27 28 8.894248 ATCATTAGATGGTAGGATGTGTCCTGG 61.894 44.444 7.23 0.00 43.25 4.45
42 43 5.840243 TGAAAGCACCAATCATTAGATGG 57.160 39.130 0.00 0.00 33.90 3.51
46 47 5.690409 GCATGATGAAAGCACCAATCATTAG 59.310 40.000 0.00 0.00 30.93 1.73
54 55 1.314534 CCCGCATGATGAAAGCACCA 61.315 55.000 0.00 0.00 30.93 4.17
82 83 3.660501 TCTCATCAACTAACGTGCACT 57.339 42.857 16.19 0.00 0.00 4.40
91 92 5.944599 ACGACCTAGTCTTTCTCATCAACTA 59.055 40.000 0.00 0.00 0.00 2.24
92 93 4.767928 ACGACCTAGTCTTTCTCATCAACT 59.232 41.667 0.00 0.00 0.00 3.16
107 108 1.366679 TGACGACTAGCACGACCTAG 58.633 55.000 15.07 10.94 40.47 3.02
108 109 1.812235 TTGACGACTAGCACGACCTA 58.188 50.000 15.07 3.30 34.70 3.08
114 115 4.789095 TCAAACTTTTGACGACTAGCAC 57.211 40.909 0.07 0.00 41.88 4.40
139 141 1.082756 GGCTTGTGTCGCGAAACAG 60.083 57.895 29.35 23.30 0.00 3.16
144 146 0.882484 TCATTTGGCTTGTGTCGCGA 60.882 50.000 3.71 3.71 0.00 5.87
146 148 1.266718 TCTTCATTTGGCTTGTGTCGC 59.733 47.619 0.00 0.00 0.00 5.19
177 179 3.744719 AACTCTCGTGCGCCGCTA 61.745 61.111 11.67 0.00 36.19 4.26
184 186 0.588252 ACAACATGCAACTCTCGTGC 59.412 50.000 0.00 0.00 0.00 5.34
213 215 7.418337 TTTCATTGTAGTAGTGGATGCTCTA 57.582 36.000 0.00 0.00 0.00 2.43
214 216 5.939764 TTCATTGTAGTAGTGGATGCTCT 57.060 39.130 0.00 0.00 0.00 4.09
222 224 9.764870 CATCATGAGTTTTTCATTGTAGTAGTG 57.235 33.333 0.09 0.00 44.14 2.74
224 226 9.764870 CACATCATGAGTTTTTCATTGTAGTAG 57.235 33.333 0.09 0.00 44.14 2.57
252 254 2.094182 TGGCGTCTACTCATCAAGAACC 60.094 50.000 0.00 0.00 0.00 3.62
295 297 0.757188 AGTCCCCGATGAGCTTCGAT 60.757 55.000 9.37 0.00 41.62 3.59
299 301 1.280457 AAAGAGTCCCCGATGAGCTT 58.720 50.000 0.00 0.00 0.00 3.74
324 327 5.446073 GCACGACTTTCTAATGCTTAAGTCC 60.446 44.000 4.02 0.00 42.04 3.85
336 339 2.741759 TGAGCATGCACGACTTTCTA 57.258 45.000 21.98 0.00 0.00 2.10
338 341 1.532868 ACTTGAGCATGCACGACTTTC 59.467 47.619 21.98 7.20 0.00 2.62
345 348 1.154150 GCCGAACTTGAGCATGCAC 60.154 57.895 21.98 15.08 0.00 4.57
368 375 0.758734 CGGCTATTGGATCTCCCACA 59.241 55.000 0.00 0.00 46.62 4.17
371 378 1.048601 TGACGGCTATTGGATCTCCC 58.951 55.000 0.00 0.00 34.29 4.30
378 385 2.808543 GGCTCTTAATGACGGCTATTGG 59.191 50.000 0.00 0.00 0.00 3.16
409 416 0.333993 AGGGCCAAGATGAAGCACAT 59.666 50.000 6.18 0.00 42.47 3.21
410 417 0.112995 AAGGGCCAAGATGAAGCACA 59.887 50.000 6.18 0.00 30.25 4.57
411 418 0.529378 CAAGGGCCAAGATGAAGCAC 59.471 55.000 6.18 0.00 0.00 4.40
412 419 0.405198 TCAAGGGCCAAGATGAAGCA 59.595 50.000 6.18 0.00 0.00 3.91
413 420 1.101331 CTCAAGGGCCAAGATGAAGC 58.899 55.000 6.18 0.00 0.00 3.86
414 421 2.795231 TCTCAAGGGCCAAGATGAAG 57.205 50.000 6.18 0.00 0.00 3.02
415 422 2.644299 TCTTCTCAAGGGCCAAGATGAA 59.356 45.455 6.18 7.87 0.00 2.57
416 423 2.269023 TCTTCTCAAGGGCCAAGATGA 58.731 47.619 6.18 10.30 0.00 2.92
417 424 2.795231 TCTTCTCAAGGGCCAAGATG 57.205 50.000 6.18 8.10 0.00 2.90
418 425 2.686118 GCATCTTCTCAAGGGCCAAGAT 60.686 50.000 6.18 8.33 36.26 2.40
419 426 1.340405 GCATCTTCTCAAGGGCCAAGA 60.340 52.381 6.18 5.95 0.00 3.02
420 427 1.101331 GCATCTTCTCAAGGGCCAAG 58.899 55.000 6.18 0.00 0.00 3.61
421 428 0.323725 GGCATCTTCTCAAGGGCCAA 60.324 55.000 6.18 0.00 43.95 4.52
422 429 1.210204 AGGCATCTTCTCAAGGGCCA 61.210 55.000 6.18 0.00 45.66 5.36
423 430 0.033699 AAGGCATCTTCTCAAGGGCC 60.034 55.000 0.00 0.00 44.47 5.80
424 431 1.387539 GAAGGCATCTTCTCAAGGGC 58.612 55.000 0.00 0.00 44.43 5.19
425 432 1.208052 TCGAAGGCATCTTCTCAAGGG 59.792 52.381 4.88 0.00 45.36 3.95
426 433 2.680312 TCGAAGGCATCTTCTCAAGG 57.320 50.000 4.88 0.00 45.36 3.61
433 440 1.902508 TGACCTCTTCGAAGGCATCTT 59.097 47.619 24.37 4.07 40.34 2.40
443 450 3.996480 AGAGTTTTTCCTGACCTCTTCG 58.004 45.455 0.00 0.00 0.00 3.79
450 457 3.751518 TGGCCTAAGAGTTTTTCCTGAC 58.248 45.455 3.32 0.00 0.00 3.51
491 498 4.503314 GCTTGAGGCGGCAATGGC 62.503 66.667 13.08 6.50 40.13 4.40
528 541 1.337821 GCTTGACGTCGACTAGGTTG 58.662 55.000 14.70 0.00 0.00 3.77
541 554 2.035442 GCCTTGGAGACGGCTTGAC 61.035 63.158 0.00 0.00 42.98 3.18
542 555 2.347490 GCCTTGGAGACGGCTTGA 59.653 61.111 0.00 0.00 42.98 3.02
546 559 2.187163 GGTAGCCTTGGAGACGGC 59.813 66.667 0.00 0.00 46.65 5.68
563 576 1.407989 GGCTCAAGGGTTGGATCTCTG 60.408 57.143 0.00 0.00 0.00 3.35
573 586 1.272480 GGTTGGTTATGGCTCAAGGGT 60.272 52.381 0.00 0.00 0.00 4.34
575 588 2.214376 TGGTTGGTTATGGCTCAAGG 57.786 50.000 0.00 0.00 0.00 3.61
599 613 2.233431 ACTTGGCTTTGTCTTTGTGCAA 59.767 40.909 0.00 0.00 0.00 4.08
618 632 1.410648 CCCCTTGCATGCATCCTAACT 60.411 52.381 23.37 0.00 0.00 2.24
635 652 9.251440 ACTTTTACCAAATAGAAGTAATTCCCC 57.749 33.333 0.00 0.00 36.65 4.81
643 660 9.495572 CTCTCTCAACTTTTACCAAATAGAAGT 57.504 33.333 0.00 0.00 39.34 3.01
644 661 9.712305 TCTCTCTCAACTTTTACCAAATAGAAG 57.288 33.333 0.00 0.00 32.40 2.85
884 917 4.060667 GGTGGTGGTGGGATGGGG 62.061 72.222 0.00 0.00 0.00 4.96
936 972 4.963276 TTAAATGCGCTTGCTGATTACT 57.037 36.364 9.73 0.00 40.12 2.24
946 982 7.661127 TGTATATATCCGTTTAAATGCGCTT 57.339 32.000 9.73 0.00 0.00 4.68
997 1037 6.326583 GGGGATGACGATGGGATAAATAGATA 59.673 42.308 0.00 0.00 0.00 1.98
1004 1044 0.973632 CGGGGATGACGATGGGATAA 59.026 55.000 0.00 0.00 0.00 1.75
1073 1113 3.701604 GATGCCGTCGACGAGCCTT 62.702 63.158 37.65 25.43 43.02 4.35
1082 1122 1.874019 CCTCGTCTTGATGCCGTCG 60.874 63.158 0.00 0.00 0.00 5.12
1123 1163 2.444895 ACGCCTCCTCCTGATCCC 60.445 66.667 0.00 0.00 0.00 3.85
1386 1433 5.178061 AGCAACTAATGAATCATCACACGA 58.822 37.500 0.00 0.00 38.69 4.35
1387 1434 5.475273 AGCAACTAATGAATCATCACACG 57.525 39.130 0.00 0.00 38.69 4.49
1388 1435 5.291858 TCGAGCAACTAATGAATCATCACAC 59.708 40.000 0.00 0.00 38.69 3.82
1389 1436 5.418676 TCGAGCAACTAATGAATCATCACA 58.581 37.500 0.00 0.00 38.69 3.58
1390 1437 5.973651 TCGAGCAACTAATGAATCATCAC 57.026 39.130 0.00 0.00 38.69 3.06
1495 1546 3.872511 ATGTCAGAGCTCAGAGAACAG 57.127 47.619 17.77 0.00 0.00 3.16
1561 1621 8.474025 ACTGTTCATCTTCCAAAAACAACATAA 58.526 29.630 0.00 0.00 30.16 1.90
1565 1625 9.959749 TTATACTGTTCATCTTCCAAAAACAAC 57.040 29.630 0.00 0.00 30.16 3.32
1623 1684 3.435671 AGCACAGCCTGTACGTTTTATTC 59.564 43.478 0.00 0.00 0.00 1.75
1626 1687 2.139917 CAGCACAGCCTGTACGTTTTA 58.860 47.619 0.00 0.00 0.00 1.52
1669 1730 4.855715 TTGTCAATTTCCGCACCATAAA 57.144 36.364 0.00 0.00 0.00 1.40
1744 1811 5.294734 ACAAAAATCCTGCAATCCAAACT 57.705 34.783 0.00 0.00 0.00 2.66
1774 1841 9.285359 CCCCTTAAGAATTGAGTATATCCCTAT 57.715 37.037 3.36 0.00 28.20 2.57
1794 1861 2.048601 TCTGAACGAAACACCCCCTTA 58.951 47.619 0.00 0.00 0.00 2.69
1795 1862 0.841289 TCTGAACGAAACACCCCCTT 59.159 50.000 0.00 0.00 0.00 3.95
1796 1863 0.841289 TTCTGAACGAAACACCCCCT 59.159 50.000 0.00 0.00 0.00 4.79
1797 1864 1.235724 CTTCTGAACGAAACACCCCC 58.764 55.000 0.00 0.00 0.00 5.40
1798 1865 1.871676 GACTTCTGAACGAAACACCCC 59.128 52.381 0.00 0.00 0.00 4.95
1799 1866 1.871676 GGACTTCTGAACGAAACACCC 59.128 52.381 0.00 0.00 0.00 4.61
1800 1867 2.835027 AGGACTTCTGAACGAAACACC 58.165 47.619 0.00 0.00 0.00 4.16
1801 1868 3.988517 CCTAGGACTTCTGAACGAAACAC 59.011 47.826 1.05 0.00 0.00 3.32
1802 1869 3.893200 TCCTAGGACTTCTGAACGAAACA 59.107 43.478 7.62 0.00 0.00 2.83
1803 1870 4.236147 GTCCTAGGACTTCTGAACGAAAC 58.764 47.826 31.12 3.26 41.57 2.78
1804 1871 4.516365 GTCCTAGGACTTCTGAACGAAA 57.484 45.455 31.12 0.00 41.57 3.46
1859 1926 9.022884 GGGACTAGAAAAAGACTCTACTAAAGA 57.977 37.037 0.00 0.00 0.00 2.52
1860 1927 9.027202 AGGGACTAGAAAAAGACTCTACTAAAG 57.973 37.037 0.00 0.00 36.02 1.85
1861 1928 8.804204 CAGGGACTAGAAAAAGACTCTACTAAA 58.196 37.037 0.00 0.00 36.02 1.85
1862 1929 7.093858 GCAGGGACTAGAAAAAGACTCTACTAA 60.094 40.741 0.00 0.00 36.02 2.24
1863 1930 6.377712 GCAGGGACTAGAAAAAGACTCTACTA 59.622 42.308 0.00 0.00 36.02 1.82
1864 1931 5.186215 GCAGGGACTAGAAAAAGACTCTACT 59.814 44.000 0.00 0.00 36.02 2.57
1865 1932 5.047235 TGCAGGGACTAGAAAAAGACTCTAC 60.047 44.000 0.00 0.00 36.02 2.59
1866 1933 5.084519 TGCAGGGACTAGAAAAAGACTCTA 58.915 41.667 0.00 0.00 36.02 2.43
1867 1934 3.904339 TGCAGGGACTAGAAAAAGACTCT 59.096 43.478 0.00 0.00 36.02 3.24
1868 1935 4.021016 TCTGCAGGGACTAGAAAAAGACTC 60.021 45.833 15.13 0.00 36.02 3.36
1869 1936 3.904339 TCTGCAGGGACTAGAAAAAGACT 59.096 43.478 15.13 0.00 36.02 3.24
1870 1937 4.273148 TCTGCAGGGACTAGAAAAAGAC 57.727 45.455 15.13 0.00 36.02 3.01
1871 1938 4.974645 TTCTGCAGGGACTAGAAAAAGA 57.025 40.909 15.13 0.00 36.02 2.52
1872 1939 6.391227 TTTTTCTGCAGGGACTAGAAAAAG 57.609 37.500 15.13 0.00 46.78 2.27
1874 1941 5.445964 ACTTTTTCTGCAGGGACTAGAAAA 58.554 37.500 15.13 8.67 44.26 2.29
1875 1942 5.048846 ACTTTTTCTGCAGGGACTAGAAA 57.951 39.130 15.13 2.20 38.32 2.52
1876 1943 4.505039 GGACTTTTTCTGCAGGGACTAGAA 60.505 45.833 15.13 0.00 36.02 2.10
1877 1944 3.008049 GGACTTTTTCTGCAGGGACTAGA 59.992 47.826 15.13 0.00 36.02 2.43
1878 1945 3.339141 GGACTTTTTCTGCAGGGACTAG 58.661 50.000 15.13 7.92 36.02 2.57
1879 1946 2.039879 GGGACTTTTTCTGCAGGGACTA 59.960 50.000 15.13 0.00 36.02 2.59
1880 1947 1.202940 GGGACTTTTTCTGCAGGGACT 60.203 52.381 15.13 0.00 43.88 3.85
1881 1948 1.202940 AGGGACTTTTTCTGCAGGGAC 60.203 52.381 15.13 0.00 27.25 4.46
1882 1949 1.073923 GAGGGACTTTTTCTGCAGGGA 59.926 52.381 15.13 0.00 41.55 4.20
1883 1950 1.539157 GAGGGACTTTTTCTGCAGGG 58.461 55.000 15.13 2.19 41.55 4.45
1884 1951 1.539157 GGAGGGACTTTTTCTGCAGG 58.461 55.000 15.13 0.00 41.55 4.85
1885 1952 1.539157 GGGAGGGACTTTTTCTGCAG 58.461 55.000 7.63 7.63 41.55 4.41
1886 1953 0.250727 CGGGAGGGACTTTTTCTGCA 60.251 55.000 0.00 0.00 41.55 4.41
1887 1954 0.250770 ACGGGAGGGACTTTTTCTGC 60.251 55.000 0.00 0.00 41.55 4.26
1888 1955 2.271944 AACGGGAGGGACTTTTTCTG 57.728 50.000 0.00 0.00 41.55 3.02
1889 1956 2.583143 CAAACGGGAGGGACTTTTTCT 58.417 47.619 0.00 0.00 41.55 2.52
1890 1957 1.611977 CCAAACGGGAGGGACTTTTTC 59.388 52.381 0.00 0.00 41.55 2.29
1891 1958 1.063492 ACCAAACGGGAGGGACTTTTT 60.063 47.619 0.00 0.00 41.55 1.94
1892 1959 0.554305 ACCAAACGGGAGGGACTTTT 59.446 50.000 0.00 0.00 41.55 2.27
1893 1960 0.554305 AACCAAACGGGAGGGACTTT 59.446 50.000 0.00 0.00 41.55 2.66
1894 1961 0.109913 GAACCAAACGGGAGGGACTT 59.890 55.000 0.00 0.00 41.55 3.01
1896 1963 1.303074 GGAACCAAACGGGAGGGAC 60.303 63.158 0.00 0.00 41.15 4.46
1897 1964 0.178897 TAGGAACCAAACGGGAGGGA 60.179 55.000 0.00 0.00 41.15 4.20
1898 1965 0.252197 CTAGGAACCAAACGGGAGGG 59.748 60.000 0.00 0.00 41.15 4.30
1899 1966 0.252197 CCTAGGAACCAAACGGGAGG 59.748 60.000 1.05 0.00 41.15 4.30
1900 1967 0.252197 CCCTAGGAACCAAACGGGAG 59.748 60.000 11.48 0.00 41.15 4.30
1901 1968 0.178897 TCCCTAGGAACCAAACGGGA 60.179 55.000 11.48 0.00 41.15 5.14
1902 1969 0.035725 GTCCCTAGGAACCAAACGGG 60.036 60.000 11.48 0.00 44.81 5.28
1903 1970 0.981943 AGTCCCTAGGAACCAAACGG 59.018 55.000 11.48 0.00 31.38 4.44
1904 1971 2.853235 AAGTCCCTAGGAACCAAACG 57.147 50.000 11.48 0.00 31.38 3.60
1905 1972 5.475909 CCTAAAAAGTCCCTAGGAACCAAAC 59.524 44.000 11.48 0.00 35.17 2.93
1906 1973 5.458508 CCCTAAAAAGTCCCTAGGAACCAAA 60.459 44.000 11.48 0.00 35.17 3.28
1907 1974 4.043686 CCCTAAAAAGTCCCTAGGAACCAA 59.956 45.833 11.48 0.00 35.17 3.67
1908 1975 3.590182 CCCTAAAAAGTCCCTAGGAACCA 59.410 47.826 11.48 0.00 35.17 3.67
1909 1976 3.848377 TCCCTAAAAAGTCCCTAGGAACC 59.152 47.826 11.48 0.00 35.17 3.62
1910 1977 5.712084 ATCCCTAAAAAGTCCCTAGGAAC 57.288 43.478 11.48 0.00 35.17 3.62
1911 1978 6.730001 AAATCCCTAAAAAGTCCCTAGGAA 57.270 37.500 11.48 0.00 35.17 3.36
1912 1979 6.730001 AAAATCCCTAAAAAGTCCCTAGGA 57.270 37.500 11.48 0.00 35.17 2.94
1949 2016 5.358725 TGTTTGGTTCAGGGACTTTTTAGTC 59.641 40.000 0.00 0.00 34.60 2.59
1950 2017 5.126545 GTGTTTGGTTCAGGGACTTTTTAGT 59.873 40.000 0.00 0.00 34.60 2.24
1951 2018 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
1952 2019 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
1953 2020 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
1954 2021 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
1955 2022 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
1956 2023 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
1957 2024 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
1958 2025 0.185175 AGGGTGTTTGGTTCAGGGAC 59.815 55.000 0.00 0.00 0.00 4.46
1959 2026 0.476771 GAGGGTGTTTGGTTCAGGGA 59.523 55.000 0.00 0.00 0.00 4.20
1960 2027 0.478507 AGAGGGTGTTTGGTTCAGGG 59.521 55.000 0.00 0.00 0.00 4.45
1961 2028 3.502123 TTAGAGGGTGTTTGGTTCAGG 57.498 47.619 0.00 0.00 0.00 3.86
1962 2029 7.703058 ATTAATTAGAGGGTGTTTGGTTCAG 57.297 36.000 0.00 0.00 0.00 3.02
1963 2030 8.485578 AAATTAATTAGAGGGTGTTTGGTTCA 57.514 30.769 0.01 0.00 0.00 3.18
1964 2031 9.203421 CAAAATTAATTAGAGGGTGTTTGGTTC 57.797 33.333 0.01 0.00 0.00 3.62
1965 2032 7.659799 GCAAAATTAATTAGAGGGTGTTTGGTT 59.340 33.333 0.01 0.00 0.00 3.67
1966 2033 7.158697 GCAAAATTAATTAGAGGGTGTTTGGT 58.841 34.615 0.01 0.00 0.00 3.67
1967 2034 6.593770 GGCAAAATTAATTAGAGGGTGTTTGG 59.406 38.462 0.01 0.00 0.00 3.28
1968 2035 6.593770 GGGCAAAATTAATTAGAGGGTGTTTG 59.406 38.462 0.01 0.64 0.00 2.93
1969 2036 6.296202 GGGGCAAAATTAATTAGAGGGTGTTT 60.296 38.462 0.01 0.00 0.00 2.83
1970 2037 5.188948 GGGGCAAAATTAATTAGAGGGTGTT 59.811 40.000 0.01 0.00 0.00 3.32
1971 2038 4.714802 GGGGCAAAATTAATTAGAGGGTGT 59.285 41.667 0.01 0.00 0.00 4.16
1972 2039 4.714308 TGGGGCAAAATTAATTAGAGGGTG 59.286 41.667 0.01 0.00 0.00 4.61
1973 2040 4.954089 TGGGGCAAAATTAATTAGAGGGT 58.046 39.130 0.01 0.00 0.00 4.34
1974 2041 4.344968 CCTGGGGCAAAATTAATTAGAGGG 59.655 45.833 0.01 0.00 0.00 4.30
1975 2042 5.208121 TCCTGGGGCAAAATTAATTAGAGG 58.792 41.667 0.01 1.44 0.00 3.69
1976 2043 6.983906 ATCCTGGGGCAAAATTAATTAGAG 57.016 37.500 0.01 0.00 0.00 2.43
1977 2044 7.289084 GGTAATCCTGGGGCAAAATTAATTAGA 59.711 37.037 0.01 0.00 0.00 2.10
1978 2045 7.070571 TGGTAATCCTGGGGCAAAATTAATTAG 59.929 37.037 0.01 0.00 34.23 1.73
2136 2204 2.282180 CCACAACTTCACCCCCGG 60.282 66.667 0.00 0.00 0.00 5.73
2141 2209 0.951040 CTCCGCTCCACAACTTCACC 60.951 60.000 0.00 0.00 0.00 4.02
2143 2211 0.249868 CACTCCGCTCCACAACTTCA 60.250 55.000 0.00 0.00 0.00 3.02
2144 2212 0.033504 TCACTCCGCTCCACAACTTC 59.966 55.000 0.00 0.00 0.00 3.01
2145 2213 0.687354 ATCACTCCGCTCCACAACTT 59.313 50.000 0.00 0.00 0.00 2.66
2161 2237 0.388778 TTACGCGCTGTTCGGAATCA 60.389 50.000 5.73 0.00 38.94 2.57
2206 2282 2.492012 GGCATGTCAATTTGTTTGCCA 58.508 42.857 22.94 6.55 46.87 4.92
2229 2305 9.562583 GTTTGTTTCGATATAACTGCCAATTTA 57.437 29.630 0.60 0.00 0.00 1.40
2231 2307 7.540745 GTGTTTGTTTCGATATAACTGCCAATT 59.459 33.333 0.60 0.00 0.00 2.32
2294 2370 1.635487 TCTAGATGGTGGCCAAAGCTT 59.365 47.619 7.24 0.00 36.95 3.74
2345 3180 2.197465 AGGTCCAAGGGGTGTATTCTC 58.803 52.381 0.00 0.00 34.93 2.87
2387 3222 6.232581 AGACTTCCTATGACATTTCCTCTG 57.767 41.667 0.00 0.00 0.00 3.35
2397 3232 6.096987 TGAGGTCATGTTAGACTTCCTATGAC 59.903 42.308 0.00 0.00 42.15 3.06
2400 3235 7.233757 GGTATGAGGTCATGTTAGACTTCCTAT 59.766 40.741 2.56 0.00 42.15 2.57
2489 3326 7.754924 ACACGAAATGAAGGCAAATATGTTTAG 59.245 33.333 0.00 0.00 0.00 1.85
2502 3339 1.871039 ACGGTTCACACGAAATGAAGG 59.129 47.619 0.00 0.00 36.76 3.46
2521 3358 0.815734 TGTAGCGGTGCCTTCTAGAC 59.184 55.000 0.00 0.00 0.00 2.59
2524 3361 2.843401 TTTTGTAGCGGTGCCTTCTA 57.157 45.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.