Multiple sequence alignment - TraesCS7A01G366100

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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 TraesCS7A01G366100 chr7A 100.000 2582 0 0 1 2582 539853444 539850863 0.000000e+00 4769.0
1 TraesCS7A01G366100 chr7A 84.628 618 78 10 8 608 540756176 540755559 1.320000e-167 599.0
2 TraesCS7A01G366100 chr7A 83.548 620 85 14 8 614 540772063 540771448 4.820000e-157 564.0
3 TraesCS7A01G366100 chr7A 82.871 613 83 14 14 606 540283112 540282502 4.890000e-147 531.0
4 TraesCS7A01G366100 chr7A 83.173 208 22 9 1193 1390 540202097 540201893 7.340000e-41 178.0
5 TraesCS7A01G366100 chr7A 94.030 67 3 1 2317 2382 192736256 192736190 1.630000e-17 100.0
6 TraesCS7A01G366100 chr7A 86.667 60 7 1 1946 2004 383423882 383423823 5.960000e-07 65.8
7 TraesCS7A01G366100 chr7A 86.207 58 4 3 1916 1973 506285550 506285497 2.770000e-05 60.2
8 TraesCS7A01G366100 chr7D 93.357 1144 37 15 612 1733 459746889 459748015 0.000000e+00 1655.0
9 TraesCS7A01G366100 chr7D 94.507 619 32 1 1 617 459746242 459746860 0.000000e+00 953.0
10 TraesCS7A01G366100 chr7D 95.186 457 14 3 1791 2243 459748013 459748465 0.000000e+00 715.0
11 TraesCS7A01G366100 chr7D 89.189 444 48 0 8 451 459432952 459433395 2.900000e-154 555.0
12 TraesCS7A01G366100 chr7D 83.010 618 88 11 8 608 459465781 459466398 6.280000e-151 544.0
13 TraesCS7A01G366100 chr7D 87.302 441 52 4 8 445 459607203 459607642 3.840000e-138 501.0
14 TraesCS7A01G366100 chr7D 88.587 184 8 2 2402 2582 459748505 459748678 7.240000e-51 211.0
15 TraesCS7A01G366100 chr7D 87.619 105 7 4 1191 1295 459450786 459450884 1.620000e-22 117.0
16 TraesCS7A01G366100 chr7D 89.091 55 4 1 1946 2000 447760444 447760496 1.660000e-07 67.6
17 TraesCS7A01G366100 chr7B 83.468 617 83 13 8 606 481617406 481618021 8.070000e-155 556.0
18 TraesCS7A01G366100 chr7B 91.371 197 15 1 1643 1837 481844426 481844622 4.230000e-68 268.0
19 TraesCS7A01G366100 chr7B 85.433 254 20 10 2064 2314 481851733 481851972 5.520000e-62 248.0
20 TraesCS7A01G366100 chr7B 87.435 191 10 10 1193 1374 481814340 481814525 9.360000e-50 207.0
21 TraesCS7A01G366100 chr7B 81.500 200 20 7 612 806 481618090 481618277 5.760000e-32 148.0
22 TraesCS7A01G366100 chr7B 85.926 135 19 0 1412 1546 481844135 481844269 7.450000e-31 145.0
23 TraesCS7A01G366100 chr7B 91.398 93 5 1 1298 1390 481843720 481843809 9.700000e-25 124.0
24 TraesCS7A01G366100 chr7B 92.537 67 4 1 2317 2382 578034384 578034318 7.610000e-16 95.3
25 TraesCS7A01G366100 chr6B 85.280 428 63 0 8 435 6196447 6196020 2.360000e-120 442.0
26 TraesCS7A01G366100 chr6B 88.000 50 4 2 1590 1638 637751088 637751040 9.980000e-05 58.4
27 TraesCS7A01G366100 chr4D 92.537 67 4 1 2317 2382 399081673 399081607 7.610000e-16 95.3
28 TraesCS7A01G366100 chr4D 87.037 54 4 3 1587 1639 337756085 337756136 9.980000e-05 58.4
29 TraesCS7A01G366100 chr3D 92.537 67 4 1 2317 2382 429270862 429270928 7.610000e-16 95.3
30 TraesCS7A01G366100 chr2D 92.537 67 4 1 2317 2382 328596264 328596330 7.610000e-16 95.3
31 TraesCS7A01G366100 chr2D 91.045 67 5 1 2317 2382 643491978 643491912 3.540000e-14 89.8
32 TraesCS7A01G366100 chr2D 88.333 60 4 1 1946 2005 8495912 8495968 4.610000e-08 69.4
33 TraesCS7A01G366100 chr2D 89.583 48 1 4 1926 1973 49200988 49201031 9.980000e-05 58.4
34 TraesCS7A01G366100 chr1D 92.537 67 4 1 2317 2382 69409172 69409238 7.610000e-16 95.3
35 TraesCS7A01G366100 chr3B 91.045 67 5 1 2317 2382 241371165 241371231 3.540000e-14 89.8
36 TraesCS7A01G366100 chr2B 89.552 67 6 1 2317 2382 1095688 1095622 1.650000e-12 84.2
37 TraesCS7A01G366100 chr2A 85.135 74 6 4 1946 2019 601612815 601612883 1.280000e-08 71.3
38 TraesCS7A01G366100 chr6A 87.500 64 2 2 1942 2005 460643428 460643371 4.610000e-08 69.4
39 TraesCS7A01G366100 chr5B 85.075 67 8 2 1936 2000 664376027 664376093 1.660000e-07 67.6
40 TraesCS7A01G366100 chr5B 92.105 38 3 0 1936 1973 692508795 692508832 1.000000e-03 54.7
41 TraesCS7A01G366100 chr5A 86.667 60 5 1 1946 2005 168939906 168939850 2.140000e-06 63.9
42 TraesCS7A01G366100 chr6D 84.058 69 6 3 1946 2009 291149781 291149713 7.710000e-06 62.1
43 TraesCS7A01G366100 chr6D 88.000 50 4 2 1590 1638 422507189 422507141 9.980000e-05 58.4
44 TraesCS7A01G366100 chr4B 89.583 48 1 4 1926 1973 550283399 550283356 9.980000e-05 58.4
45 TraesCS7A01G366100 chr4B 89.583 48 1 4 1926 1973 550317560 550317517 9.980000e-05 58.4
46 TraesCS7A01G366100 chr4B 94.444 36 1 1 1946 1980 515146001 515145966 1.000000e-03 54.7
47 TraesCS7A01G366100 chrUn 100.000 30 0 0 1590 1619 44504532 44504503 3.590000e-04 56.5
48 TraesCS7A01G366100 chr4A 85.455 55 6 2 1924 1978 117943981 117944033 3.590000e-04 56.5


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 TraesCS7A01G366100 chr7A 539850863 539853444 2581 True 4769.0 4769 100.00000 1 2582 1 chr7A.!!$R4 2581
1 TraesCS7A01G366100 chr7A 540755559 540756176 617 True 599.0 599 84.62800 8 608 1 chr7A.!!$R7 600
2 TraesCS7A01G366100 chr7A 540771448 540772063 615 True 564.0 564 83.54800 8 614 1 chr7A.!!$R8 606
3 TraesCS7A01G366100 chr7A 540282502 540283112 610 True 531.0 531 82.87100 14 606 1 chr7A.!!$R6 592
4 TraesCS7A01G366100 chr7D 459746242 459748678 2436 False 883.5 1655 92.90925 1 2582 4 chr7D.!!$F6 2581
5 TraesCS7A01G366100 chr7D 459465781 459466398 617 False 544.0 544 83.01000 8 608 1 chr7D.!!$F4 600
6 TraesCS7A01G366100 chr7B 481617406 481618277 871 False 352.0 556 82.48400 8 806 2 chr7B.!!$F3 798

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
312 313 0.321671 CCGAGAGCCAGGACTTGAAA 59.678 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1773 0.036952 CTGATGACTTGCCGGTGTCT 60.037 55.0 19.47 9.53 34.57 3.41 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
155 156 1.004679 GGTTGGCAATGCAAGGTGG 60.005 57.895 7.79 0.00 0.00 4.61
175 176 1.001860 GTATGGAGCCTGAGATGCCTC 59.998 57.143 0.00 0.00 39.86 4.70
182 183 0.464870 CCTGAGATGCCTCCTGACTG 59.535 60.000 0.00 0.00 38.66 3.51
183 184 0.464870 CTGAGATGCCTCCTGACTGG 59.535 60.000 0.00 0.00 38.66 4.00
217 218 3.299977 CACGACGAGGGGACACCA 61.300 66.667 0.00 0.00 43.89 4.17
312 313 0.321671 CCGAGAGCCAGGACTTGAAA 59.678 55.000 0.00 0.00 0.00 2.69
346 347 6.967199 GGATTGTCTATCATTTTCGGTTTCAC 59.033 38.462 0.00 0.00 34.77 3.18
493 513 8.268850 TCTGATTTGTAAGAGGATGTTTAAGC 57.731 34.615 0.00 0.00 0.00 3.09
543 563 1.276421 GCCCTCTAGACAGCAACTTCA 59.724 52.381 4.68 0.00 0.00 3.02
579 605 1.128200 CGGTGGGAACTGGGATGATA 58.872 55.000 0.00 0.00 0.00 2.15
587 613 3.136443 GGAACTGGGATGATACATGACCA 59.864 47.826 0.00 0.00 0.00 4.02
672 775 5.003804 ACGCTAACAGATTTGACCTTTCAT 58.996 37.500 0.00 0.00 0.00 2.57
886 994 4.318332 TCCTGATATCGGAATGCATGAAC 58.682 43.478 13.42 0.00 0.00 3.18
888 996 4.083643 CCTGATATCGGAATGCATGAACAC 60.084 45.833 13.42 0.00 0.00 3.32
889 997 3.814842 TGATATCGGAATGCATGAACACC 59.185 43.478 0.00 0.00 0.00 4.16
890 998 1.392589 ATCGGAATGCATGAACACCC 58.607 50.000 0.00 0.00 0.00 4.61
919 1036 2.386661 ACTTAGTCAGAACGGCATGG 57.613 50.000 0.00 0.00 0.00 3.66
944 1061 1.270571 TGGCTGAAGTATGAACGCACA 60.271 47.619 0.00 0.00 0.00 4.57
958 1076 1.886542 ACGCACATCTTCCCCTTTTTC 59.113 47.619 0.00 0.00 0.00 2.29
1044 1164 2.202756 CTAGGCGCCTCGTTGACC 60.203 66.667 36.73 0.00 0.00 4.02
1046 1166 1.378911 TAGGCGCCTCGTTGACCTA 60.379 57.895 36.73 9.43 31.79 3.08
1076 1196 8.814235 CATTTCTGATCTCCAAATGCATAAAAC 58.186 33.333 0.00 0.00 32.33 2.43
1077 1197 6.455360 TCTGATCTCCAAATGCATAAAACC 57.545 37.500 0.00 0.00 0.00 3.27
1098 1218 4.617520 TGCAAGCGGCTGGTTCGA 62.618 61.111 7.09 0.00 45.15 3.71
1143 1263 2.063266 TCATTTCGACGCAACCACTAC 58.937 47.619 0.00 0.00 0.00 2.73
1150 1270 1.269998 GACGCAACCACTACAGACTCT 59.730 52.381 0.00 0.00 0.00 3.24
1175 1295 1.467920 GGTCTCCATTCCTTTGCCTG 58.532 55.000 0.00 0.00 0.00 4.85
1181 1301 1.478105 CCATTCCTTTGCCTGGCTAAC 59.522 52.381 21.03 0.00 0.00 2.34
1246 1366 2.045242 CCCTGCTGCTGCTCATGT 60.045 61.111 17.00 0.00 40.48 3.21
1405 1525 7.007725 CGCACTCAATTGTGATTTCTAAACATC 59.992 37.037 14.16 0.00 40.12 3.06
1431 1551 0.320247 CTGTGACTTGCGAGCCTTCT 60.320 55.000 0.00 0.00 0.00 2.85
1435 1555 2.510238 CTTGCGAGCCTTCTCCGG 60.510 66.667 0.00 0.00 35.94 5.14
1486 1606 4.293494 AGATCCTGATCTTGCAGTTCCTA 58.707 43.478 3.80 0.00 45.31 2.94
1499 1619 2.638354 TTCCTAAAGGTCCGCGCGA 61.638 57.895 34.63 15.16 36.34 5.87
1505 1625 0.804933 AAAGGTCCGCGCGAATCTAC 60.805 55.000 34.63 19.45 0.00 2.59
1555 1675 5.886474 CCTGGAACTATGGATATAGACGCTA 59.114 44.000 1.62 0.00 38.88 4.26
1632 1752 2.879103 TCCCACATTCCTCAAGGTTC 57.121 50.000 0.00 0.00 36.34 3.62
1733 1853 1.736645 CCCACCGTACGAACTGCAG 60.737 63.158 18.76 13.48 0.00 4.41
1734 1854 1.287815 CCACCGTACGAACTGCAGA 59.712 57.895 23.35 0.00 0.00 4.26
1735 1855 0.319211 CCACCGTACGAACTGCAGAA 60.319 55.000 23.35 0.00 0.00 3.02
1736 1856 1.060713 CACCGTACGAACTGCAGAAG 58.939 55.000 23.35 13.18 0.00 2.85
1737 1857 0.666577 ACCGTACGAACTGCAGAAGC 60.667 55.000 23.35 7.93 42.57 3.86
1738 1858 1.352156 CCGTACGAACTGCAGAAGCC 61.352 60.000 23.35 5.07 41.13 4.35
1739 1859 1.352156 CGTACGAACTGCAGAAGCCC 61.352 60.000 23.35 2.38 41.13 5.19
1740 1860 0.037232 GTACGAACTGCAGAAGCCCT 60.037 55.000 23.35 0.00 41.13 5.19
1741 1861 0.246635 TACGAACTGCAGAAGCCCTC 59.753 55.000 23.35 5.75 41.13 4.30
1742 1862 1.743252 CGAACTGCAGAAGCCCTCC 60.743 63.158 23.35 0.00 41.13 4.30
1743 1863 1.682257 GAACTGCAGAAGCCCTCCT 59.318 57.895 23.35 0.00 41.13 3.69
1744 1864 0.392327 GAACTGCAGAAGCCCTCCTC 60.392 60.000 23.35 0.00 41.13 3.71
1745 1865 0.839853 AACTGCAGAAGCCCTCCTCT 60.840 55.000 23.35 0.00 41.13 3.69
1746 1866 0.839853 ACTGCAGAAGCCCTCCTCTT 60.840 55.000 23.35 0.00 41.13 2.85
1747 1867 0.107752 CTGCAGAAGCCCTCCTCTTC 60.108 60.000 8.42 0.00 41.13 2.87
1748 1868 1.223211 GCAGAAGCCCTCCTCTTCC 59.777 63.158 0.00 0.00 40.48 3.46
1749 1869 1.519719 CAGAAGCCCTCCTCTTCCG 59.480 63.158 0.00 0.00 40.48 4.30
1750 1870 1.687493 AGAAGCCCTCCTCTTCCGG 60.687 63.158 0.00 0.00 40.48 5.14
1751 1871 1.686110 GAAGCCCTCCTCTTCCGGA 60.686 63.158 0.00 0.00 35.19 5.14
1752 1872 1.229529 AAGCCCTCCTCTTCCGGAA 60.230 57.895 17.73 17.73 31.44 4.30
1753 1873 1.268283 AAGCCCTCCTCTTCCGGAAG 61.268 60.000 34.19 34.19 39.71 3.46
1754 1874 1.686110 GCCCTCCTCTTCCGGAAGA 60.686 63.158 37.80 37.80 44.47 2.87
1755 1875 1.265454 GCCCTCCTCTTCCGGAAGAA 61.265 60.000 38.83 27.61 45.75 2.52
1756 1876 1.501582 CCCTCCTCTTCCGGAAGAAT 58.498 55.000 38.83 0.00 45.75 2.40
1757 1877 2.679082 CCCTCCTCTTCCGGAAGAATA 58.321 52.381 38.83 29.37 45.75 1.75
1758 1878 3.243724 CCCTCCTCTTCCGGAAGAATAT 58.756 50.000 38.83 0.00 45.75 1.28
1759 1879 3.648545 CCCTCCTCTTCCGGAAGAATATT 59.351 47.826 38.83 0.00 45.75 1.28
1760 1880 4.503991 CCCTCCTCTTCCGGAAGAATATTG 60.504 50.000 38.83 28.51 45.75 1.90
1761 1881 4.345257 CCTCCTCTTCCGGAAGAATATTGA 59.655 45.833 38.83 28.02 45.75 2.57
1762 1882 5.163301 CCTCCTCTTCCGGAAGAATATTGAA 60.163 44.000 38.83 20.10 45.75 2.69
1763 1883 6.465035 CCTCCTCTTCCGGAAGAATATTGAAT 60.465 42.308 38.83 0.00 45.75 2.57
1764 1884 6.900194 TCCTCTTCCGGAAGAATATTGAATT 58.100 36.000 38.83 0.00 45.75 2.17
1765 1885 8.029782 TCCTCTTCCGGAAGAATATTGAATTA 57.970 34.615 38.83 18.33 45.75 1.40
1766 1886 8.660435 TCCTCTTCCGGAAGAATATTGAATTAT 58.340 33.333 38.83 0.00 45.75 1.28
1767 1887 9.289782 CCTCTTCCGGAAGAATATTGAATTATT 57.710 33.333 38.83 0.00 45.75 1.40
1769 1889 8.567948 TCTTCCGGAAGAATATTGAATTATTGC 58.432 33.333 38.52 0.00 43.79 3.56
1770 1890 7.214467 TCCGGAAGAATATTGAATTATTGCC 57.786 36.000 0.00 0.00 0.00 4.52
1771 1891 6.775142 TCCGGAAGAATATTGAATTATTGCCA 59.225 34.615 0.00 0.00 0.00 4.92
1772 1892 7.286546 TCCGGAAGAATATTGAATTATTGCCAA 59.713 33.333 0.00 0.00 0.00 4.52
1773 1893 7.382218 CCGGAAGAATATTGAATTATTGCCAAC 59.618 37.037 0.00 0.00 0.00 3.77
1774 1894 8.137437 CGGAAGAATATTGAATTATTGCCAACT 58.863 33.333 0.00 0.00 0.00 3.16
1775 1895 9.252962 GGAAGAATATTGAATTATTGCCAACTG 57.747 33.333 0.00 0.00 0.00 3.16
1776 1896 9.807649 GAAGAATATTGAATTATTGCCAACTGT 57.192 29.630 0.00 0.00 0.00 3.55
1778 1898 9.807649 AGAATATTGAATTATTGCCAACTGTTC 57.192 29.630 0.00 0.00 0.00 3.18
1779 1899 9.585099 GAATATTGAATTATTGCCAACTGTTCA 57.415 29.630 0.00 0.00 0.00 3.18
1780 1900 9.590451 AATATTGAATTATTGCCAACTGTTCAG 57.410 29.630 0.00 0.00 0.00 3.02
1781 1901 5.389859 TGAATTATTGCCAACTGTTCAGG 57.610 39.130 4.82 0.00 0.00 3.86
1782 1902 4.832266 TGAATTATTGCCAACTGTTCAGGT 59.168 37.500 4.82 0.00 0.00 4.00
1783 1903 4.789012 ATTATTGCCAACTGTTCAGGTG 57.211 40.909 10.51 10.51 0.00 4.00
1784 1904 0.675633 ATTGCCAACTGTTCAGGTGC 59.324 50.000 11.84 8.38 0.00 5.01
1785 1905 0.395586 TTGCCAACTGTTCAGGTGCT 60.396 50.000 11.84 0.00 0.00 4.40
1786 1906 0.472044 TGCCAACTGTTCAGGTGCTA 59.528 50.000 11.84 1.10 0.00 3.49
1787 1907 0.875059 GCCAACTGTTCAGGTGCTAC 59.125 55.000 11.84 1.13 0.00 3.58
1788 1908 1.148310 CCAACTGTTCAGGTGCTACG 58.852 55.000 11.84 0.00 0.00 3.51
1789 1909 1.270094 CCAACTGTTCAGGTGCTACGA 60.270 52.381 11.84 0.00 0.00 3.43
1790 1910 2.061773 CAACTGTTCAGGTGCTACGAG 58.938 52.381 4.90 0.00 0.00 4.18
1791 1911 0.038159 ACTGTTCAGGTGCTACGAGC 60.038 55.000 4.82 0.00 42.82 5.03
1826 1946 2.334838 GTTACTGCCGTGTTACCTCTG 58.665 52.381 0.00 0.00 0.00 3.35
1846 1966 3.599343 TGTGGACATGTAATCTCAGTGC 58.401 45.455 0.00 0.00 0.00 4.40
1851 1971 4.498241 GACATGTAATCTCAGTGCTGTCA 58.502 43.478 0.00 0.00 33.66 3.58
1880 2000 4.258543 TGATCTTTGTACCGTTCCAATCC 58.741 43.478 0.00 0.00 0.00 3.01
1932 2052 7.607991 AGATTTTCGTTTTGAGAGGTATGATGT 59.392 33.333 0.00 0.00 0.00 3.06
1933 2053 8.786826 ATTTTCGTTTTGAGAGGTATGATGTA 57.213 30.769 0.00 0.00 0.00 2.29
1934 2054 7.591006 TTTCGTTTTGAGAGGTATGATGTAC 57.409 36.000 0.00 0.00 0.00 2.90
1935 2055 5.337554 TCGTTTTGAGAGGTATGATGTACG 58.662 41.667 0.00 0.00 0.00 3.67
1986 2108 6.935208 AGCGTTTAGATCTTTAGGAAACACTT 59.065 34.615 15.08 1.60 31.73 3.16
2020 2144 7.430211 TCTTTATAGAGTGTGCGTACGTTATTG 59.570 37.037 17.90 0.00 0.00 1.90
2093 2217 4.093556 GGAGGAAAAAGAACATAGACTGCG 59.906 45.833 0.00 0.00 0.00 5.18
2191 2315 7.857885 GGGATTGATACGACTTGAATGAATTTC 59.142 37.037 0.00 0.00 34.72 2.17
2211 2335 1.521450 TTGGAGTCAGTCGTCGGTCC 61.521 60.000 0.00 0.00 0.00 4.46
2234 2358 4.261072 CGATCCACTTGTAGTACGTAGCAT 60.261 45.833 0.00 0.00 0.00 3.79
2243 2367 3.955650 AGTACGTAGCATGTTGTTCCT 57.044 42.857 0.00 0.00 0.00 3.36
2244 2368 4.267349 AGTACGTAGCATGTTGTTCCTT 57.733 40.909 0.00 0.00 0.00 3.36
2245 2369 3.994392 AGTACGTAGCATGTTGTTCCTTG 59.006 43.478 0.00 0.00 0.00 3.61
2246 2370 1.535462 ACGTAGCATGTTGTTCCTTGC 59.465 47.619 0.00 0.00 36.15 4.01
2247 2371 1.806542 CGTAGCATGTTGTTCCTTGCT 59.193 47.619 1.61 1.61 44.89 3.91
2248 2372 3.000041 CGTAGCATGTTGTTCCTTGCTA 59.000 45.455 0.00 0.00 42.16 3.49
2249 2373 3.623060 CGTAGCATGTTGTTCCTTGCTAT 59.377 43.478 6.74 0.00 44.70 2.97
2250 2374 4.494690 CGTAGCATGTTGTTCCTTGCTATG 60.495 45.833 6.74 7.51 44.70 2.23
2251 2375 2.165030 AGCATGTTGTTCCTTGCTATGC 59.835 45.455 0.00 0.00 42.16 3.14
2252 2376 2.165030 GCATGTTGTTCCTTGCTATGCT 59.835 45.455 0.00 0.00 37.17 3.79
2253 2377 3.378112 GCATGTTGTTCCTTGCTATGCTA 59.622 43.478 0.00 0.00 37.17 3.49
2254 2378 4.497006 GCATGTTGTTCCTTGCTATGCTAG 60.497 45.833 0.00 0.00 37.17 3.42
2267 2391 2.935348 TGCTAGGCATGGATGGACT 58.065 52.632 0.00 0.00 31.71 3.85
2268 2392 0.761187 TGCTAGGCATGGATGGACTC 59.239 55.000 0.00 0.00 31.71 3.36
2269 2393 0.320247 GCTAGGCATGGATGGACTCG 60.320 60.000 0.00 0.00 0.00 4.18
2270 2394 1.043816 CTAGGCATGGATGGACTCGT 58.956 55.000 0.00 0.00 0.00 4.18
2271 2395 1.000283 CTAGGCATGGATGGACTCGTC 60.000 57.143 0.00 0.00 0.00 4.20
2287 2411 3.319198 TCCCAACCGAGACTGGCC 61.319 66.667 0.00 0.00 0.00 5.36
2294 2418 0.465705 ACCGAGACTGGCCATACATG 59.534 55.000 5.51 0.00 0.00 3.21
2303 2427 6.259893 AGACTGGCCATACATGTATCTAGAT 58.740 40.000 15.60 10.73 0.00 1.98
2310 2434 6.419116 GCCATACATGTATCTAGATATGCGTG 59.581 42.308 15.60 15.70 35.38 5.34
2311 2435 6.419116 CCATACATGTATCTAGATATGCGTGC 59.581 42.308 15.60 2.69 33.30 5.34
2317 2441 4.797800 ATCTAGATATGCGTGCTGACAT 57.202 40.909 2.53 0.00 0.00 3.06
2318 2442 5.904362 ATCTAGATATGCGTGCTGACATA 57.096 39.130 2.53 0.00 33.52 2.29
2319 2443 5.048153 TCTAGATATGCGTGCTGACATAC 57.952 43.478 0.00 0.00 31.87 2.39
2320 2444 4.762251 TCTAGATATGCGTGCTGACATACT 59.238 41.667 0.00 0.00 31.87 2.12
2321 2445 3.906998 AGATATGCGTGCTGACATACTC 58.093 45.455 0.00 0.00 31.87 2.59
2322 2446 2.509052 TATGCGTGCTGACATACTCC 57.491 50.000 0.00 0.00 0.00 3.85
2323 2447 0.179073 ATGCGTGCTGACATACTCCC 60.179 55.000 0.00 0.00 0.00 4.30
2324 2448 1.521681 GCGTGCTGACATACTCCCC 60.522 63.158 0.00 0.00 0.00 4.81
2325 2449 1.961180 GCGTGCTGACATACTCCCCT 61.961 60.000 0.00 0.00 0.00 4.79
2326 2450 0.179100 CGTGCTGACATACTCCCCTG 60.179 60.000 0.00 0.00 0.00 4.45
2327 2451 0.905357 GTGCTGACATACTCCCCTGT 59.095 55.000 0.00 0.00 0.00 4.00
2328 2452 1.134670 GTGCTGACATACTCCCCTGTC 60.135 57.143 0.00 0.00 41.69 3.51
2329 2453 0.466124 GCTGACATACTCCCCTGTCC 59.534 60.000 0.00 0.00 40.83 4.02
2330 2454 0.747255 CTGACATACTCCCCTGTCCG 59.253 60.000 0.00 0.00 40.83 4.79
2331 2455 0.686441 TGACATACTCCCCTGTCCGG 60.686 60.000 0.00 0.00 40.83 5.14
2332 2456 0.396695 GACATACTCCCCTGTCCGGA 60.397 60.000 0.00 0.00 36.59 5.14
2333 2457 0.042131 ACATACTCCCCTGTCCGGAA 59.958 55.000 5.23 0.00 33.16 4.30
2334 2458 1.200519 CATACTCCCCTGTCCGGAAA 58.799 55.000 5.23 0.00 33.16 3.13
2335 2459 1.768870 CATACTCCCCTGTCCGGAAAT 59.231 52.381 5.23 0.00 33.16 2.17
2336 2460 2.852714 TACTCCCCTGTCCGGAAATA 57.147 50.000 5.23 0.00 33.16 1.40
2337 2461 1.201424 ACTCCCCTGTCCGGAAATAC 58.799 55.000 5.23 0.00 33.16 1.89
2338 2462 1.273666 ACTCCCCTGTCCGGAAATACT 60.274 52.381 5.23 0.00 33.16 2.12
2339 2463 1.838077 CTCCCCTGTCCGGAAATACTT 59.162 52.381 5.23 0.00 33.16 2.24
2340 2464 1.557832 TCCCCTGTCCGGAAATACTTG 59.442 52.381 5.23 0.00 33.16 3.16
2341 2465 1.379527 CCCTGTCCGGAAATACTTGC 58.620 55.000 5.23 0.00 33.16 4.01
2342 2466 1.379527 CCTGTCCGGAAATACTTGCC 58.620 55.000 5.23 0.00 33.16 4.52
2343 2467 1.339631 CCTGTCCGGAAATACTTGCCA 60.340 52.381 5.23 0.00 33.16 4.92
2344 2468 2.643551 CTGTCCGGAAATACTTGCCAT 58.356 47.619 5.23 0.00 0.00 4.40
2345 2469 2.614057 CTGTCCGGAAATACTTGCCATC 59.386 50.000 5.23 0.00 0.00 3.51
2346 2470 2.026729 TGTCCGGAAATACTTGCCATCA 60.027 45.455 5.23 0.00 0.00 3.07
2347 2471 3.013921 GTCCGGAAATACTTGCCATCAA 58.986 45.455 5.23 0.00 0.00 2.57
2348 2472 3.442273 GTCCGGAAATACTTGCCATCAAA 59.558 43.478 5.23 0.00 0.00 2.69
2349 2473 4.082463 GTCCGGAAATACTTGCCATCAAAA 60.082 41.667 5.23 0.00 0.00 2.44
2350 2474 4.709397 TCCGGAAATACTTGCCATCAAAAT 59.291 37.500 0.00 0.00 0.00 1.82
2351 2475 4.805192 CCGGAAATACTTGCCATCAAAATG 59.195 41.667 0.00 0.00 0.00 2.32
2373 2497 9.860898 AAATGGACAAAAGAAAATGTATCTAGC 57.139 29.630 0.00 0.00 0.00 3.42
2374 2498 7.391148 TGGACAAAAGAAAATGTATCTAGCC 57.609 36.000 0.00 0.00 0.00 3.93
2375 2499 6.093495 TGGACAAAAGAAAATGTATCTAGCCG 59.907 38.462 0.00 0.00 0.00 5.52
2376 2500 6.093633 GGACAAAAGAAAATGTATCTAGCCGT 59.906 38.462 0.00 0.00 0.00 5.68
2377 2501 7.279313 GGACAAAAGAAAATGTATCTAGCCGTA 59.721 37.037 0.00 0.00 0.00 4.02
2378 2502 8.732746 ACAAAAGAAAATGTATCTAGCCGTAT 57.267 30.769 0.00 0.00 0.00 3.06
2379 2503 9.174166 ACAAAAGAAAATGTATCTAGCCGTATT 57.826 29.630 0.00 0.00 0.00 1.89
2383 2507 8.073355 AGAAAATGTATCTAGCCGTATTTTCG 57.927 34.615 18.50 0.00 43.70 3.46
2394 2518 2.955614 CGTATTTTCGGACACAGGAGT 58.044 47.619 0.00 0.00 0.00 3.85
2395 2519 4.100707 CGTATTTTCGGACACAGGAGTA 57.899 45.455 0.00 0.00 0.00 2.59
2396 2520 3.855950 CGTATTTTCGGACACAGGAGTAC 59.144 47.826 0.00 0.00 0.00 2.73
2398 2522 1.321474 TTTCGGACACAGGAGTACGT 58.679 50.000 0.00 0.00 45.81 3.57
2399 2523 2.183478 TTCGGACACAGGAGTACGTA 57.817 50.000 1.59 0.00 45.81 3.57
2400 2524 1.442769 TCGGACACAGGAGTACGTAC 58.557 55.000 18.10 18.10 45.81 3.67
2414 2538 8.887717 CAGGAGTACGTACTACTACTTATTTGT 58.112 37.037 34.47 11.13 43.43 2.83
2427 2551 7.215085 ACTACTTATTTGTCACTCGAGGTTTT 58.785 34.615 18.41 0.00 0.00 2.43
2441 2565 1.583495 GGTTTTAGTCCGCCAGTGGC 61.583 60.000 25.07 25.07 46.75 5.01
2450 2574 3.994853 GCCAGTGGCCAAGCAACC 61.995 66.667 24.53 0.00 44.06 3.77
2484 2608 4.121317 TCTTCCGTTTGTAACATTCACGT 58.879 39.130 0.00 0.00 0.00 4.49
2488 2612 4.085158 TCCGTTTGTAACATTCACGTAACG 60.085 41.667 6.06 6.06 36.82 3.18
2489 2613 4.317980 CCGTTTGTAACATTCACGTAACGT 60.318 41.667 10.75 0.00 42.36 3.99
2523 2650 5.376947 CTTTCGCAGCATGTTACTACTAC 57.623 43.478 0.00 0.00 39.31 2.73
2524 2651 4.713824 TTCGCAGCATGTTACTACTACT 57.286 40.909 0.00 0.00 39.31 2.57
2560 2687 2.568956 TGTCTTCAATCCTGAGTCCTGG 59.431 50.000 0.00 0.00 31.69 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 4.093291 AGCTTGGCCTCCTGAGCG 62.093 66.667 3.32 0.00 38.03 5.03
96 97 5.514204 GCTGCAACTGTCAAATAATAGCTTG 59.486 40.000 0.00 0.00 0.00 4.01
155 156 1.055040 AGGCATCTCAGGCTCCATAC 58.945 55.000 0.00 0.00 40.91 2.39
182 183 2.109126 GTGATTGCGCTGGACCTCC 61.109 63.158 9.73 0.00 0.00 4.30
183 184 1.375908 TGTGATTGCGCTGGACCTC 60.376 57.895 9.73 0.00 0.00 3.85
217 218 0.467474 CATGGGATCACCTGCAGCAT 60.467 55.000 8.66 1.18 41.11 3.79
312 313 5.983333 ATGATAGACAATCCCTCCTTTGT 57.017 39.130 0.00 0.00 38.71 2.83
362 363 0.467844 TGCCTTCTTTTGCTGCCTGA 60.468 50.000 0.00 0.00 0.00 3.86
493 513 5.144100 ACTATCCCTCTCCATAGTTGAGTG 58.856 45.833 0.00 0.00 32.84 3.51
543 563 0.028505 CCGTATCGATCGTTGACCGT 59.971 55.000 15.94 0.00 37.94 4.83
587 613 4.503643 CCAAAATCTGGTCCAAAAGCATGT 60.504 41.667 0.00 0.00 40.78 3.21
624 717 5.050634 CCAAATGCATGCACACAATATTAGC 60.051 40.000 25.37 0.00 0.00 3.09
672 775 0.687354 GGCTGTCCCTGTCTGAGAAA 59.313 55.000 0.00 0.00 0.00 2.52
699 802 1.599047 CAGAGGTTGGAGGCATCGT 59.401 57.895 0.00 0.00 0.00 3.73
841 949 2.953648 TGTCAAATCTCGCCGAGGTATA 59.046 45.455 15.08 0.00 0.00 1.47
842 950 1.754803 TGTCAAATCTCGCCGAGGTAT 59.245 47.619 15.08 0.00 0.00 2.73
886 994 3.270877 GACTAAGTTGCCTGTATGGGTG 58.729 50.000 0.00 0.00 36.00 4.61
888 996 3.197766 TCTGACTAAGTTGCCTGTATGGG 59.802 47.826 0.00 0.00 36.00 4.00
889 997 4.471904 TCTGACTAAGTTGCCTGTATGG 57.528 45.455 0.00 0.00 39.35 2.74
890 998 4.327357 CGTTCTGACTAAGTTGCCTGTATG 59.673 45.833 0.00 0.00 0.00 2.39
906 1023 0.108186 CAGCTACCATGCCGTTCTGA 60.108 55.000 0.00 0.00 0.00 3.27
908 1025 1.221840 CCAGCTACCATGCCGTTCT 59.778 57.895 0.00 0.00 0.00 3.01
919 1036 2.860735 CGTTCATACTTCAGCCAGCTAC 59.139 50.000 0.00 0.00 0.00 3.58
944 1061 7.241628 AGTAAATGACAGAAAAAGGGGAAGAT 58.758 34.615 0.00 0.00 0.00 2.40
958 1076 7.979444 TCAAAGGTAGGAAAGTAAATGACAG 57.021 36.000 0.00 0.00 0.00 3.51
1044 1164 6.971184 GCATTTGGAGATCAGAAATGTTGTAG 59.029 38.462 18.06 1.87 38.69 2.74
1046 1166 5.244402 TGCATTTGGAGATCAGAAATGTTGT 59.756 36.000 18.06 0.00 38.69 3.32
1060 1180 3.106827 AGGGGGTTTTATGCATTTGGAG 58.893 45.455 3.54 0.00 0.00 3.86
1084 1204 2.358737 CCTTCGAACCAGCCGCTT 60.359 61.111 0.00 0.00 0.00 4.68
1098 1218 2.549563 CGATCTGTGATATGGCTGCCTT 60.550 50.000 21.03 16.33 0.00 4.35
1143 1263 1.091537 GGAGACCGAGACAGAGTCTG 58.908 60.000 18.83 18.83 43.53 3.51
1150 1270 1.938585 AAGGAATGGAGACCGAGACA 58.061 50.000 0.00 0.00 0.00 3.41
1175 1295 2.154074 ATCCCCATCCCCGTTAGCC 61.154 63.158 0.00 0.00 0.00 3.93
1181 1301 4.586235 GTGCCATCCCCATCCCCG 62.586 72.222 0.00 0.00 0.00 5.73
1246 1366 1.375908 GATGTGGCTTCCTGTGCGA 60.376 57.895 0.00 0.00 0.00 5.10
1322 1442 2.108566 CAGGATCAGCAGCCGGAG 59.891 66.667 5.05 0.00 0.00 4.63
1330 1450 3.805267 CTGAACGGCAGGATCAGC 58.195 61.111 8.49 0.00 41.07 4.26
1405 1525 0.318699 TCGCAAGTCACAGGAACTCG 60.319 55.000 0.00 0.00 35.01 4.18
1431 1551 1.905894 TGATCAGGATGTGTTTCCGGA 59.094 47.619 0.00 0.00 42.89 5.14
1435 1555 6.566197 AACTTTCTGATCAGGATGTGTTTC 57.434 37.500 22.42 0.00 37.40 2.78
1486 1606 0.804933 GTAGATTCGCGCGGACCTTT 60.805 55.000 31.69 5.57 0.00 3.11
1499 1619 1.746517 GGACCATCGCGGGTAGATT 59.253 57.895 6.13 0.00 42.53 2.40
1555 1675 0.250770 GTCTTCTTGCCGGGGTCTTT 60.251 55.000 2.18 0.00 0.00 2.52
1649 1769 1.757682 TGACTTGCCGGTGTCTTTTT 58.242 45.000 19.47 0.00 34.57 1.94
1650 1770 1.880027 GATGACTTGCCGGTGTCTTTT 59.120 47.619 19.47 9.08 34.57 2.27
1651 1771 1.202758 TGATGACTTGCCGGTGTCTTT 60.203 47.619 19.47 10.87 34.57 2.52
1652 1772 0.396435 TGATGACTTGCCGGTGTCTT 59.604 50.000 19.47 15.16 34.57 3.01
1653 1773 0.036952 CTGATGACTTGCCGGTGTCT 60.037 55.000 19.47 9.53 34.57 3.41
1654 1774 0.037326 TCTGATGACTTGCCGGTGTC 60.037 55.000 1.90 10.24 0.00 3.67
1655 1775 0.036952 CTCTGATGACTTGCCGGTGT 60.037 55.000 1.90 0.00 0.00 4.16
1656 1776 0.036952 ACTCTGATGACTTGCCGGTG 60.037 55.000 1.90 0.00 0.00 4.94
1733 1853 1.265454 TTCCGGAAGAGGAGGGCTTC 61.265 60.000 14.35 0.00 41.98 3.86
1734 1854 1.229529 TTCCGGAAGAGGAGGGCTT 60.230 57.895 14.35 0.00 41.98 4.35
1735 1855 1.687493 CTTCCGGAAGAGGAGGGCT 60.687 63.158 36.18 0.00 41.98 5.19
1736 1856 1.265454 TTCTTCCGGAAGAGGAGGGC 61.265 60.000 37.89 0.00 46.80 5.19
1737 1857 1.501582 ATTCTTCCGGAAGAGGAGGG 58.498 55.000 37.89 17.44 46.80 4.30
1738 1858 4.345257 TCAATATTCTTCCGGAAGAGGAGG 59.655 45.833 37.89 27.98 46.80 4.30
1739 1859 5.537300 TCAATATTCTTCCGGAAGAGGAG 57.463 43.478 37.89 27.61 46.80 3.69
1740 1860 5.950544 TTCAATATTCTTCCGGAAGAGGA 57.049 39.130 37.89 30.75 46.80 3.71
1741 1861 8.854614 ATAATTCAATATTCTTCCGGAAGAGG 57.145 34.615 37.89 26.85 46.80 3.69
1743 1863 8.567948 GCAATAATTCAATATTCTTCCGGAAGA 58.432 33.333 37.39 37.39 44.94 2.87
1744 1864 7.809806 GGCAATAATTCAATATTCTTCCGGAAG 59.190 37.037 34.19 34.19 37.36 3.46
1745 1865 7.286546 TGGCAATAATTCAATATTCTTCCGGAA 59.713 33.333 17.73 17.73 38.41 4.30
1746 1866 6.775142 TGGCAATAATTCAATATTCTTCCGGA 59.225 34.615 0.00 0.00 0.00 5.14
1747 1867 6.980593 TGGCAATAATTCAATATTCTTCCGG 58.019 36.000 0.00 0.00 0.00 5.14
1748 1868 8.137437 AGTTGGCAATAATTCAATATTCTTCCG 58.863 33.333 1.92 0.00 0.00 4.30
1749 1869 9.252962 CAGTTGGCAATAATTCAATATTCTTCC 57.747 33.333 1.92 0.00 0.00 3.46
1750 1870 9.807649 ACAGTTGGCAATAATTCAATATTCTTC 57.192 29.630 1.92 0.00 0.00 2.87
1752 1872 9.807649 GAACAGTTGGCAATAATTCAATATTCT 57.192 29.630 1.92 0.00 0.00 2.40
1753 1873 9.585099 TGAACAGTTGGCAATAATTCAATATTC 57.415 29.630 16.02 5.81 0.00 1.75
1754 1874 9.590451 CTGAACAGTTGGCAATAATTCAATATT 57.410 29.630 17.84 0.00 0.00 1.28
1755 1875 8.199449 CCTGAACAGTTGGCAATAATTCAATAT 58.801 33.333 17.84 0.00 0.00 1.28
1756 1876 7.178274 ACCTGAACAGTTGGCAATAATTCAATA 59.822 33.333 17.84 3.24 0.00 1.90
1757 1877 6.014327 ACCTGAACAGTTGGCAATAATTCAAT 60.014 34.615 17.84 10.38 0.00 2.57
1758 1878 5.304101 ACCTGAACAGTTGGCAATAATTCAA 59.696 36.000 17.84 7.68 0.00 2.69
1759 1879 4.832266 ACCTGAACAGTTGGCAATAATTCA 59.168 37.500 16.87 16.87 0.00 2.57
1760 1880 5.163513 CACCTGAACAGTTGGCAATAATTC 58.836 41.667 1.92 8.15 0.00 2.17
1761 1881 4.561326 GCACCTGAACAGTTGGCAATAATT 60.561 41.667 1.92 0.00 0.00 1.40
1762 1882 3.056607 GCACCTGAACAGTTGGCAATAAT 60.057 43.478 1.92 0.00 0.00 1.28
1763 1883 2.295909 GCACCTGAACAGTTGGCAATAA 59.704 45.455 1.92 0.00 0.00 1.40
1764 1884 1.885887 GCACCTGAACAGTTGGCAATA 59.114 47.619 1.92 0.00 0.00 1.90
1765 1885 0.675633 GCACCTGAACAGTTGGCAAT 59.324 50.000 1.92 0.00 0.00 3.56
1766 1886 0.395586 AGCACCTGAACAGTTGGCAA 60.396 50.000 0.00 0.00 0.00 4.52
1767 1887 0.472044 TAGCACCTGAACAGTTGGCA 59.528 50.000 0.00 0.00 0.00 4.92
1768 1888 0.875059 GTAGCACCTGAACAGTTGGC 59.125 55.000 0.00 2.47 0.00 4.52
1769 1889 1.148310 CGTAGCACCTGAACAGTTGG 58.852 55.000 0.00 0.00 0.00 3.77
1770 1890 2.061773 CTCGTAGCACCTGAACAGTTG 58.938 52.381 0.00 0.00 0.00 3.16
1771 1891 1.605712 GCTCGTAGCACCTGAACAGTT 60.606 52.381 1.18 0.00 41.89 3.16
1772 1892 0.038159 GCTCGTAGCACCTGAACAGT 60.038 55.000 1.18 0.00 41.89 3.55
1773 1893 2.743195 GCTCGTAGCACCTGAACAG 58.257 57.895 2.53 0.00 41.89 3.16
1774 1894 4.988065 GCTCGTAGCACCTGAACA 57.012 55.556 2.53 0.00 41.89 3.18
1791 1911 1.068333 AGTAACCGCAGCAAGCATTTG 60.068 47.619 0.00 0.00 46.13 2.32
1792 1912 1.068333 CAGTAACCGCAGCAAGCATTT 60.068 47.619 0.00 0.00 46.13 2.32
1826 1946 3.620374 CAGCACTGAGATTACATGTCCAC 59.380 47.826 0.00 0.00 0.00 4.02
1846 1966 9.261180 ACGGTACAAAGATCAATAATATGACAG 57.739 33.333 0.00 0.00 30.82 3.51
1851 1971 9.621629 TTGGAACGGTACAAAGATCAATAATAT 57.378 29.630 0.00 0.00 0.00 1.28
1880 2000 4.440758 CGCACACCTTTATTTGTTGAAGTG 59.559 41.667 0.00 0.00 0.00 3.16
1990 2112 7.475015 ACGTACGCACACTCTATAAAGAAATA 58.525 34.615 16.72 0.00 0.00 1.40
2000 2122 4.683501 TCAATAACGTACGCACACTCTA 57.316 40.909 16.72 0.00 0.00 2.43
2005 2127 4.434989 GCAAAGATCAATAACGTACGCACA 60.435 41.667 16.72 0.16 0.00 4.57
2020 2144 3.881937 AAGAGCAATTGGGCAAAGATC 57.118 42.857 7.72 0.00 35.83 2.75
2093 2217 2.473609 TCGAAACGTATGTTGACTGCAC 59.526 45.455 0.00 0.00 38.62 4.57
2191 2315 0.109689 GACCGACGACTGACTCCAAG 60.110 60.000 0.00 0.00 0.00 3.61
2211 2335 3.064408 TGCTACGTACTACAAGTGGATCG 59.936 47.826 0.00 0.00 0.00 3.69
2234 2358 3.609853 CCTAGCATAGCAAGGAACAACA 58.390 45.455 0.00 0.00 37.37 3.33
2249 2373 0.761187 GAGTCCATCCATGCCTAGCA 59.239 55.000 0.00 0.00 44.86 3.49
2250 2374 0.320247 CGAGTCCATCCATGCCTAGC 60.320 60.000 0.00 0.00 0.00 3.42
2251 2375 1.000283 GACGAGTCCATCCATGCCTAG 60.000 57.143 0.00 0.00 0.00 3.02
2252 2376 1.040646 GACGAGTCCATCCATGCCTA 58.959 55.000 0.00 0.00 0.00 3.93
2253 2377 1.826024 GACGAGTCCATCCATGCCT 59.174 57.895 0.00 0.00 0.00 4.75
2254 2378 4.445699 GACGAGTCCATCCATGCC 57.554 61.111 0.00 0.00 0.00 4.40
2267 2391 2.273179 CCAGTCTCGGTTGGGACGA 61.273 63.158 0.00 0.00 37.52 4.20
2268 2392 2.261671 CCAGTCTCGGTTGGGACG 59.738 66.667 0.00 0.00 37.52 4.79
2269 2393 2.047179 GCCAGTCTCGGTTGGGAC 60.047 66.667 0.00 0.00 34.96 4.46
2270 2394 3.319198 GGCCAGTCTCGGTTGGGA 61.319 66.667 0.00 0.00 34.96 4.37
2271 2395 1.622607 TATGGCCAGTCTCGGTTGGG 61.623 60.000 13.05 0.00 34.96 4.12
2272 2396 0.462047 GTATGGCCAGTCTCGGTTGG 60.462 60.000 13.05 0.00 37.53 3.77
2273 2397 0.249120 TGTATGGCCAGTCTCGGTTG 59.751 55.000 13.05 0.00 0.00 3.77
2274 2398 1.134401 CATGTATGGCCAGTCTCGGTT 60.134 52.381 13.05 0.00 0.00 4.44
2275 2399 0.465705 CATGTATGGCCAGTCTCGGT 59.534 55.000 13.05 0.00 0.00 4.69
2276 2400 0.465705 ACATGTATGGCCAGTCTCGG 59.534 55.000 13.05 1.17 0.00 4.63
2277 2401 3.256879 AGATACATGTATGGCCAGTCTCG 59.743 47.826 22.93 1.69 0.00 4.04
2287 2411 7.167136 CAGCACGCATATCTAGATACATGTATG 59.833 40.741 22.93 9.61 0.00 2.39
2294 2418 5.048153 TGTCAGCACGCATATCTAGATAC 57.952 43.478 14.71 2.69 0.00 2.24
2303 2427 1.068588 GGGAGTATGTCAGCACGCATA 59.931 52.381 0.00 0.00 0.00 3.14
2310 2434 0.466124 GGACAGGGGAGTATGTCAGC 59.534 60.000 7.54 0.00 46.14 4.26
2311 2435 0.747255 CGGACAGGGGAGTATGTCAG 59.253 60.000 7.54 0.00 46.14 3.51
2317 2441 2.023695 AGTATTTCCGGACAGGGGAGTA 60.024 50.000 1.83 0.00 41.52 2.59
2318 2442 1.201424 GTATTTCCGGACAGGGGAGT 58.799 55.000 1.83 0.00 41.52 3.85
2319 2443 1.497161 AGTATTTCCGGACAGGGGAG 58.503 55.000 1.83 0.00 41.52 4.30
2320 2444 1.557832 CAAGTATTTCCGGACAGGGGA 59.442 52.381 1.83 0.00 41.52 4.81
2321 2445 2.017113 GCAAGTATTTCCGGACAGGGG 61.017 57.143 1.83 0.00 41.52 4.79
2322 2446 1.379527 GCAAGTATTTCCGGACAGGG 58.620 55.000 1.83 0.00 41.52 4.45
2323 2447 1.339631 TGGCAAGTATTTCCGGACAGG 60.340 52.381 1.83 0.00 42.97 4.00
2324 2448 2.107950 TGGCAAGTATTTCCGGACAG 57.892 50.000 1.83 0.00 0.00 3.51
2325 2449 2.026729 TGATGGCAAGTATTTCCGGACA 60.027 45.455 1.83 0.00 0.00 4.02
2326 2450 2.639065 TGATGGCAAGTATTTCCGGAC 58.361 47.619 1.83 0.00 0.00 4.79
2327 2451 3.358111 TTGATGGCAAGTATTTCCGGA 57.642 42.857 0.00 0.00 0.00 5.14
2328 2452 4.448537 TTTTGATGGCAAGTATTTCCGG 57.551 40.909 0.00 0.00 35.04 5.14
2329 2453 4.805192 CCATTTTGATGGCAAGTATTTCCG 59.195 41.667 0.00 0.00 35.04 4.30
2330 2454 5.812127 GTCCATTTTGATGGCAAGTATTTCC 59.188 40.000 0.00 0.00 41.43 3.13
2331 2455 6.397272 TGTCCATTTTGATGGCAAGTATTTC 58.603 36.000 0.00 0.00 41.43 2.17
2332 2456 6.357579 TGTCCATTTTGATGGCAAGTATTT 57.642 33.333 0.00 0.00 41.43 1.40
2333 2457 5.999205 TGTCCATTTTGATGGCAAGTATT 57.001 34.783 0.00 0.00 41.43 1.89
2334 2458 5.999205 TTGTCCATTTTGATGGCAAGTAT 57.001 34.783 0.00 0.00 41.43 2.12
2335 2459 5.798125 TTTGTCCATTTTGATGGCAAGTA 57.202 34.783 0.00 1.86 41.43 2.24
2336 2460 4.686191 TTTGTCCATTTTGATGGCAAGT 57.314 36.364 0.00 0.00 41.43 3.16
2337 2461 5.299148 TCTTTTGTCCATTTTGATGGCAAG 58.701 37.500 0.00 7.32 41.43 4.01
2338 2462 5.287674 TCTTTTGTCCATTTTGATGGCAA 57.712 34.783 0.00 6.03 41.43 4.52
2339 2463 4.952071 TCTTTTGTCCATTTTGATGGCA 57.048 36.364 0.00 0.00 41.43 4.92
2340 2464 6.616774 TTTTCTTTTGTCCATTTTGATGGC 57.383 33.333 0.52 0.00 41.43 4.40
2341 2465 8.156994 ACATTTTCTTTTGTCCATTTTGATGG 57.843 30.769 0.00 0.00 43.01 3.51
2347 2471 9.860898 GCTAGATACATTTTCTTTTGTCCATTT 57.139 29.630 0.00 0.00 0.00 2.32
2348 2472 8.470002 GGCTAGATACATTTTCTTTTGTCCATT 58.530 33.333 0.00 0.00 0.00 3.16
2349 2473 7.201732 CGGCTAGATACATTTTCTTTTGTCCAT 60.202 37.037 0.00 0.00 0.00 3.41
2350 2474 6.093495 CGGCTAGATACATTTTCTTTTGTCCA 59.907 38.462 0.00 0.00 0.00 4.02
2351 2475 6.093633 ACGGCTAGATACATTTTCTTTTGTCC 59.906 38.462 0.00 0.00 0.00 4.02
2352 2476 7.073342 ACGGCTAGATACATTTTCTTTTGTC 57.927 36.000 0.00 0.00 0.00 3.18
2353 2477 8.732746 ATACGGCTAGATACATTTTCTTTTGT 57.267 30.769 0.00 0.00 0.00 2.83
2357 2481 8.548721 CGAAAATACGGCTAGATACATTTTCTT 58.451 33.333 19.58 0.55 38.94 2.52
2358 2482 7.170998 CCGAAAATACGGCTAGATACATTTTCT 59.829 37.037 19.58 0.00 46.20 2.52
2359 2483 7.288672 CCGAAAATACGGCTAGATACATTTTC 58.711 38.462 15.75 15.75 46.20 2.29
2360 2484 7.186021 CCGAAAATACGGCTAGATACATTTT 57.814 36.000 0.00 0.00 46.20 1.82
2361 2485 6.780706 CCGAAAATACGGCTAGATACATTT 57.219 37.500 0.00 0.00 46.20 2.32
2374 2498 2.955614 ACTCCTGTGTCCGAAAATACG 58.044 47.619 0.00 0.00 0.00 3.06
2375 2499 3.855950 CGTACTCCTGTGTCCGAAAATAC 59.144 47.826 0.00 0.00 0.00 1.89
2376 2500 3.507233 ACGTACTCCTGTGTCCGAAAATA 59.493 43.478 0.00 0.00 0.00 1.40
2377 2501 2.298163 ACGTACTCCTGTGTCCGAAAAT 59.702 45.455 0.00 0.00 0.00 1.82
2378 2502 1.682854 ACGTACTCCTGTGTCCGAAAA 59.317 47.619 0.00 0.00 0.00 2.29
2379 2503 1.321474 ACGTACTCCTGTGTCCGAAA 58.679 50.000 0.00 0.00 0.00 3.46
2380 2504 1.806542 GTACGTACTCCTGTGTCCGAA 59.193 52.381 18.47 0.00 0.00 4.30
2381 2505 1.002430 AGTACGTACTCCTGTGTCCGA 59.998 52.381 22.45 0.00 0.00 4.55
2382 2506 1.446907 AGTACGTACTCCTGTGTCCG 58.553 55.000 22.45 0.00 0.00 4.79
2383 2507 3.604582 AGTAGTACGTACTCCTGTGTCC 58.395 50.000 30.53 10.11 37.41 4.02
2384 2508 5.415221 AGTAGTAGTACGTACTCCTGTGTC 58.585 45.833 30.53 15.94 41.42 3.67
2385 2509 5.413309 AGTAGTAGTACGTACTCCTGTGT 57.587 43.478 30.53 11.47 41.42 3.72
2386 2510 8.430801 AATAAGTAGTAGTACGTACTCCTGTG 57.569 38.462 30.53 0.00 41.42 3.66
2387 2511 8.887717 CAAATAAGTAGTAGTACGTACTCCTGT 58.112 37.037 30.53 16.32 41.42 4.00
2388 2512 8.887717 ACAAATAAGTAGTAGTACGTACTCCTG 58.112 37.037 30.53 13.61 41.42 3.86
2389 2513 9.103861 GACAAATAAGTAGTAGTACGTACTCCT 57.896 37.037 30.53 26.09 41.42 3.69
2390 2514 8.883731 TGACAAATAAGTAGTAGTACGTACTCC 58.116 37.037 30.53 20.39 41.42 3.85
2391 2515 9.695884 GTGACAAATAAGTAGTAGTACGTACTC 57.304 37.037 30.53 20.84 41.42 2.59
2392 2516 9.442047 AGTGACAAATAAGTAGTAGTACGTACT 57.558 33.333 29.62 29.62 44.69 2.73
2393 2517 9.695884 GAGTGACAAATAAGTAGTAGTACGTAC 57.304 37.037 18.10 18.10 33.97 3.67
2394 2518 8.595533 CGAGTGACAAATAAGTAGTAGTACGTA 58.404 37.037 5.94 5.94 33.97 3.57
2395 2519 7.331934 TCGAGTGACAAATAAGTAGTAGTACGT 59.668 37.037 2.04 0.00 33.97 3.57
2396 2520 7.679144 TCGAGTGACAAATAAGTAGTAGTACG 58.321 38.462 2.04 0.00 33.97 3.67
2397 2521 8.121708 CCTCGAGTGACAAATAAGTAGTAGTAC 58.878 40.741 12.31 0.00 0.00 2.73
2398 2522 7.826252 ACCTCGAGTGACAAATAAGTAGTAGTA 59.174 37.037 12.31 0.00 0.00 1.82
2399 2523 6.658391 ACCTCGAGTGACAAATAAGTAGTAGT 59.342 38.462 12.31 0.00 0.00 2.73
2400 2524 7.086230 ACCTCGAGTGACAAATAAGTAGTAG 57.914 40.000 12.31 0.00 0.00 2.57
2414 2538 1.068055 GCGGACTAAAACCTCGAGTGA 60.068 52.381 12.31 0.00 0.00 3.41
2450 2574 3.923017 AACGGAAGAAATTTCAGGCTG 57.077 42.857 19.99 8.58 0.00 4.85
2515 2642 7.052873 CAGCAAGAGGGTAGTAAGTAGTAGTA 58.947 42.308 0.00 0.00 0.00 1.82
2516 2643 5.887035 CAGCAAGAGGGTAGTAAGTAGTAGT 59.113 44.000 0.00 0.00 0.00 2.73
2517 2644 5.887035 ACAGCAAGAGGGTAGTAAGTAGTAG 59.113 44.000 0.00 0.00 0.00 2.57
2518 2645 5.824421 ACAGCAAGAGGGTAGTAAGTAGTA 58.176 41.667 0.00 0.00 0.00 1.82
2519 2646 4.675038 ACAGCAAGAGGGTAGTAAGTAGT 58.325 43.478 0.00 0.00 0.00 2.73
2520 2647 4.951094 AGACAGCAAGAGGGTAGTAAGTAG 59.049 45.833 0.00 0.00 0.00 2.57
2521 2648 4.931914 AGACAGCAAGAGGGTAGTAAGTA 58.068 43.478 0.00 0.00 0.00 2.24
2522 2649 3.780626 AGACAGCAAGAGGGTAGTAAGT 58.219 45.455 0.00 0.00 0.00 2.24
2523 2650 4.220821 TGAAGACAGCAAGAGGGTAGTAAG 59.779 45.833 0.00 0.00 0.00 2.34
2524 2651 4.157246 TGAAGACAGCAAGAGGGTAGTAA 58.843 43.478 0.00 0.00 0.00 2.24
2560 2687 0.727398 CTCGAAATCGGGTTCAAGGC 59.273 55.000 2.63 0.00 40.29 4.35


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

AutoCloner maintained by Alex Coulton.