Multiple sequence alignment - TraesCS5A01G191600

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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 TraesCS5A01G191600 chr5A 100.000 4565 0 0 1 4565 395834828 395839392 0.000000e+00 8431.0
1 TraesCS5A01G191600 chr5A 90.000 340 22 7 4229 4565 395847509 395847839 3.260000e-116 429.0
2 TraesCS5A01G191600 chr5A 83.784 222 17 9 3967 4182 395847311 395847519 4.660000e-45 193.0
3 TraesCS5A01G191600 chr5A 86.928 153 18 2 3306 3456 395846511 395846663 2.180000e-38 171.0
4 TraesCS5A01G191600 chr5D 92.425 1835 79 14 1 1823 302019814 302018028 0.000000e+00 2564.0
5 TraesCS5A01G191600 chr5D 90.367 1173 95 13 1923 3084 302018030 302016865 0.000000e+00 1524.0
6 TraesCS5A01G191600 chr5D 84.738 1068 77 39 3552 4565 302016287 302015252 0.000000e+00 990.0
7 TraesCS5A01G191600 chr5D 95.968 372 13 2 3083 3452 302016704 302016333 1.820000e-168 603.0
8 TraesCS5A01G191600 chr5D 94.516 310 16 1 1 309 328392503 328392812 1.150000e-130 477.0
9 TraesCS5A01G191600 chr5D 87.353 340 31 4 4229 4565 302004503 302004173 3.330000e-101 379.0
10 TraesCS5A01G191600 chr5D 88.028 142 15 1 3315 3456 302011828 302011689 2.820000e-37 167.0
11 TraesCS5A01G191600 chr5B 92.050 1673 111 13 2039 3696 345050774 345049109 0.000000e+00 2333.0
12 TraesCS5A01G191600 chr5B 89.356 1832 108 27 1 1815 345052663 345050902 0.000000e+00 2222.0
13 TraesCS5A01G191600 chr5B 85.780 872 51 29 3761 4565 345048975 345048110 0.000000e+00 856.0
14 TraesCS5A01G191600 chr5B 88.921 343 23 11 4229 4565 344951629 344951296 4.250000e-110 409.0
15 TraesCS5A01G191600 chr5B 82.517 143 23 2 3315 3456 344952633 344952492 1.720000e-24 124.0
16 TraesCS5A01G191600 chr5B 93.103 58 3 1 3948 4004 344951821 344951764 2.930000e-12 84.2
17 TraesCS5A01G191600 chr6A 89.935 308 29 2 3 309 536911985 536911679 3.310000e-106 396.0
18 TraesCS5A01G191600 chr7D 94.545 165 9 0 137 301 55446122 55445958 5.860000e-64 255.0
19 TraesCS5A01G191600 chr3B 97.810 137 3 0 137 273 612294763 612294627 2.120000e-58 237.0


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 TraesCS5A01G191600 chr5A 395834828 395839392 4564 False 8431.000000 8431 100.000000 1 4565 1 chr5A.!!$F1 4564
1 TraesCS5A01G191600 chr5A 395846511 395847839 1328 False 264.333333 429 86.904000 3306 4565 3 chr5A.!!$F2 1259
2 TraesCS5A01G191600 chr5D 302011689 302019814 8125 True 1169.600000 2564 90.305200 1 4565 5 chr5D.!!$R2 4564
3 TraesCS5A01G191600 chr5B 345048110 345052663 4553 True 1803.666667 2333 89.062000 1 4565 3 chr5B.!!$R2 4564
4 TraesCS5A01G191600 chr5B 344951296 344952633 1337 True 205.733333 409 88.180333 3315 4565 3 chr5B.!!$R1 1250

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
988 1004 0.110678 TTAACGGGCCATCAACACCA 59.889 50.0 4.39 0.0 0.00 4.17 F
1833 1882 0.039074 GCTGCGTGCCGAGTCTATAT 60.039 55.0 0.00 0.0 35.15 0.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 2194 0.322008 CTCTGCCCTCACTCCAAACC 60.322 60.0 0.00 0.0 0.00 3.27 R
3706 4305 0.673437 ACCAAATTGGGAGCAACACG 59.327 50.0 17.27 0.0 43.37 4.49 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
122 123 4.867599 GGGAGGTTAGACGGCGCG 62.868 72.222 6.90 0.00 0.00 6.86
215 216 3.046087 TCGAAGTCCGACGCGTCT 61.046 61.111 33.94 17.46 43.23 4.18
443 444 4.016706 CCGCCCTCCCGTGAGTTT 62.017 66.667 0.00 0.00 36.86 2.66
632 633 2.783135 CACTTGCCATTGGTACTGACT 58.217 47.619 4.26 0.00 0.00 3.41
656 657 1.048601 GGAGGTCAGAAGACACCACA 58.951 55.000 0.00 0.00 46.80 4.17
770 783 2.760385 GTCGGAGGAGGGTGAGGG 60.760 72.222 0.00 0.00 0.00 4.30
779 792 4.083862 GGGTGAGGGGACGAGTGC 62.084 72.222 0.00 0.00 0.00 4.40
880 893 3.864686 CCGCCGCCAATTCGTGAG 61.865 66.667 0.00 0.00 0.00 3.51
909 922 2.281276 GGTGGGTGTTGGACGTCC 60.281 66.667 28.17 28.17 0.00 4.79
955 971 1.374252 GCTTTCGGCCTCGTGAAGA 60.374 57.895 0.00 0.00 34.87 2.87
961 977 2.035442 GGCCTCGTGAAGAAGCACC 61.035 63.158 0.00 0.00 38.04 5.01
988 1004 0.110678 TTAACGGGCCATCAACACCA 59.889 50.000 4.39 0.00 0.00 4.17
1037 1057 0.106708 GCCCATATCTCAACGCCTCA 59.893 55.000 0.00 0.00 0.00 3.86
1042 1062 0.179137 TATCTCAACGCCTCAGCACG 60.179 55.000 0.00 0.00 39.83 5.34
1122 1142 2.564458 CGACGATCCACACCACGA 59.436 61.111 0.00 0.00 0.00 4.35
1156 1187 2.125512 GAGGCGATGGCGTTGACT 60.126 61.111 0.61 0.61 41.24 3.41
1162 1193 2.264813 GCGATGGCGTTGACTAACTTA 58.735 47.619 0.00 0.00 40.36 2.24
1324 1355 2.375345 CCCCCTCCCTTGCGTGTAT 61.375 63.158 0.00 0.00 0.00 2.29
1356 1388 0.240945 GTTGAGTCAATTGCGGTGGG 59.759 55.000 9.18 0.00 0.00 4.61
1382 1414 0.390472 GGGATCGGAATCATCGGCTC 60.390 60.000 0.00 0.00 33.21 4.70
1393 1442 2.310538 TCATCGGCTCAGATCTTAGCA 58.689 47.619 26.06 10.64 40.61 3.49
1394 1443 2.035193 TCATCGGCTCAGATCTTAGCAC 59.965 50.000 26.06 16.05 40.61 4.40
1397 1446 1.135915 CGGCTCAGATCTTAGCACTGT 59.864 52.381 26.06 0.00 40.61 3.55
1398 1447 2.797792 CGGCTCAGATCTTAGCACTGTC 60.798 54.545 26.06 10.63 40.61 3.51
1399 1448 2.430332 GGCTCAGATCTTAGCACTGTCT 59.570 50.000 26.06 0.00 40.61 3.41
1400 1449 3.446799 GCTCAGATCTTAGCACTGTCTG 58.553 50.000 21.45 0.00 38.63 3.51
1401 1450 3.737663 GCTCAGATCTTAGCACTGTCTGG 60.738 52.174 21.45 0.00 38.63 3.86
1402 1451 3.435275 TCAGATCTTAGCACTGTCTGGT 58.565 45.455 0.00 0.00 37.49 4.00
1403 1452 3.194329 TCAGATCTTAGCACTGTCTGGTG 59.806 47.826 0.00 0.00 37.49 4.17
1404 1453 3.056250 CAGATCTTAGCACTGTCTGGTGT 60.056 47.826 0.00 0.00 39.21 4.16
1405 1454 3.194542 AGATCTTAGCACTGTCTGGTGTC 59.805 47.826 0.00 0.00 39.21 3.67
1406 1455 2.598565 TCTTAGCACTGTCTGGTGTCT 58.401 47.619 0.00 0.00 39.21 3.41
1407 1456 2.297315 TCTTAGCACTGTCTGGTGTCTG 59.703 50.000 0.00 0.00 39.21 3.51
1408 1457 1.995376 TAGCACTGTCTGGTGTCTGA 58.005 50.000 0.00 0.00 39.21 3.27
1409 1458 1.346062 AGCACTGTCTGGTGTCTGAT 58.654 50.000 0.00 0.00 39.21 2.90
1410 1459 1.696336 AGCACTGTCTGGTGTCTGATT 59.304 47.619 0.00 0.00 39.21 2.57
1411 1460 1.802960 GCACTGTCTGGTGTCTGATTG 59.197 52.381 0.00 0.00 39.21 2.67
1412 1461 1.802960 CACTGTCTGGTGTCTGATTGC 59.197 52.381 0.00 0.00 33.04 3.56
1413 1462 1.696336 ACTGTCTGGTGTCTGATTGCT 59.304 47.619 0.00 0.00 0.00 3.91
1414 1463 2.105477 ACTGTCTGGTGTCTGATTGCTT 59.895 45.455 0.00 0.00 0.00 3.91
1415 1464 3.144506 CTGTCTGGTGTCTGATTGCTTT 58.855 45.455 0.00 0.00 0.00 3.51
1416 1465 2.880268 TGTCTGGTGTCTGATTGCTTTG 59.120 45.455 0.00 0.00 0.00 2.77
1417 1466 1.881973 TCTGGTGTCTGATTGCTTTGC 59.118 47.619 0.00 0.00 0.00 3.68
1418 1467 1.884579 CTGGTGTCTGATTGCTTTGCT 59.115 47.619 0.00 0.00 0.00 3.91
1419 1468 1.881973 TGGTGTCTGATTGCTTTGCTC 59.118 47.619 0.00 0.00 0.00 4.26
1420 1469 2.157738 GGTGTCTGATTGCTTTGCTCT 58.842 47.619 0.00 0.00 0.00 4.09
1424 1473 4.678742 GTGTCTGATTGCTTTGCTCTTTTC 59.321 41.667 0.00 0.00 0.00 2.29
1432 1481 6.592798 TTGCTTTGCTCTTTTCTGAAATTG 57.407 33.333 3.31 0.99 0.00 2.32
1435 1484 5.333111 GCTTTGCTCTTTTCTGAAATTGCAG 60.333 40.000 7.16 7.16 35.69 4.41
1444 1493 8.239314 TCTTTTCTGAAATTGCAGTATGATGTC 58.761 33.333 13.35 0.00 39.69 3.06
1455 1504 7.071069 TGCAGTATGATGTCTTCTTATCCAT 57.929 36.000 0.00 0.00 39.69 3.41
1552 1601 2.992089 AGGTTATTCCTGCATCGCG 58.008 52.632 0.00 0.00 46.19 5.87
1554 1603 0.814010 GGTTATTCCTGCATCGCGGT 60.814 55.000 6.13 0.00 32.22 5.68
1566 1615 2.263077 CATCGCGGTAAGAGATATGGC 58.737 52.381 6.13 0.00 37.27 4.40
1646 1695 7.582435 AATTCTGTATCGTGTTTGTCTAGTG 57.418 36.000 0.00 0.00 0.00 2.74
1662 1711 6.291377 TGTCTAGTGCTGGAAATTATCATCC 58.709 40.000 0.00 0.00 36.21 3.51
1724 1773 2.754648 TGGCGACAAGTAGTTCCCT 58.245 52.632 0.00 0.00 37.44 4.20
1725 1774 0.320374 TGGCGACAAGTAGTTCCCTG 59.680 55.000 0.00 0.00 37.44 4.45
1726 1775 0.606604 GGCGACAAGTAGTTCCCTGA 59.393 55.000 0.00 0.00 0.00 3.86
1783 1832 1.376942 CCTGCTTGGCCAGTCTCAG 60.377 63.158 5.11 11.62 0.00 3.35
1795 1844 4.100189 GGCCAGTCTCAGCTTTTATAGAGA 59.900 45.833 0.00 0.00 34.95 3.10
1815 1864 1.237285 ACCTGAATTCTGCACACGGC 61.237 55.000 7.05 0.00 45.13 5.68
1831 1880 2.105128 GCTGCGTGCCGAGTCTAT 59.895 61.111 0.00 0.00 35.15 1.98
1832 1881 1.359117 GCTGCGTGCCGAGTCTATA 59.641 57.895 0.00 0.00 35.15 1.31
1833 1882 0.039074 GCTGCGTGCCGAGTCTATAT 60.039 55.000 0.00 0.00 35.15 0.86
1834 1883 1.603172 GCTGCGTGCCGAGTCTATATT 60.603 52.381 0.00 0.00 35.15 1.28
1835 1884 2.320367 CTGCGTGCCGAGTCTATATTC 58.680 52.381 0.00 0.00 0.00 1.75
1836 1885 1.954382 TGCGTGCCGAGTCTATATTCT 59.046 47.619 0.00 0.00 0.00 2.40
1837 1886 2.361119 TGCGTGCCGAGTCTATATTCTT 59.639 45.455 0.00 0.00 0.00 2.52
1838 1887 2.981140 GCGTGCCGAGTCTATATTCTTC 59.019 50.000 0.00 0.00 0.00 2.87
1839 1888 3.304794 GCGTGCCGAGTCTATATTCTTCT 60.305 47.826 0.00 0.00 0.00 2.85
1840 1889 4.468643 CGTGCCGAGTCTATATTCTTCTC 58.531 47.826 0.00 0.00 0.00 2.87
1841 1890 4.614078 CGTGCCGAGTCTATATTCTTCTCC 60.614 50.000 0.00 0.00 0.00 3.71
1842 1891 3.827302 TGCCGAGTCTATATTCTTCTCCC 59.173 47.826 0.00 0.00 0.00 4.30
1843 1892 4.083565 GCCGAGTCTATATTCTTCTCCCT 58.916 47.826 0.00 0.00 0.00 4.20
1844 1893 4.525100 GCCGAGTCTATATTCTTCTCCCTT 59.475 45.833 0.00 0.00 0.00 3.95
1845 1894 5.011227 GCCGAGTCTATATTCTTCTCCCTTT 59.989 44.000 0.00 0.00 0.00 3.11
1846 1895 6.683715 CCGAGTCTATATTCTTCTCCCTTTC 58.316 44.000 0.00 0.00 0.00 2.62
1847 1896 6.492087 CCGAGTCTATATTCTTCTCCCTTTCT 59.508 42.308 0.00 0.00 0.00 2.52
1848 1897 7.308951 CCGAGTCTATATTCTTCTCCCTTTCTC 60.309 44.444 0.00 0.00 0.00 2.87
1849 1898 7.308951 CGAGTCTATATTCTTCTCCCTTTCTCC 60.309 44.444 0.00 0.00 0.00 3.71
1850 1899 6.492087 AGTCTATATTCTTCTCCCTTTCTCCG 59.508 42.308 0.00 0.00 0.00 4.63
1851 1900 2.700722 ATTCTTCTCCCTTTCTCCGC 57.299 50.000 0.00 0.00 0.00 5.54
1852 1901 1.348064 TTCTTCTCCCTTTCTCCGCA 58.652 50.000 0.00 0.00 0.00 5.69
1853 1902 1.573108 TCTTCTCCCTTTCTCCGCAT 58.427 50.000 0.00 0.00 0.00 4.73
1854 1903 1.482593 TCTTCTCCCTTTCTCCGCATC 59.517 52.381 0.00 0.00 0.00 3.91
1855 1904 1.208052 CTTCTCCCTTTCTCCGCATCA 59.792 52.381 0.00 0.00 0.00 3.07
1856 1905 1.275666 TCTCCCTTTCTCCGCATCAA 58.724 50.000 0.00 0.00 0.00 2.57
1857 1906 1.839994 TCTCCCTTTCTCCGCATCAAT 59.160 47.619 0.00 0.00 0.00 2.57
1858 1907 3.038280 TCTCCCTTTCTCCGCATCAATA 58.962 45.455 0.00 0.00 0.00 1.90
1859 1908 3.648067 TCTCCCTTTCTCCGCATCAATAT 59.352 43.478 0.00 0.00 0.00 1.28
1860 1909 3.743521 TCCCTTTCTCCGCATCAATATG 58.256 45.455 0.00 0.00 36.09 1.78
1875 1924 7.694388 CATCAATATGCTGTGATTTTCCTTG 57.306 36.000 0.00 0.00 32.06 3.61
1876 1925 7.485810 CATCAATATGCTGTGATTTTCCTTGA 58.514 34.615 0.00 0.00 32.06 3.02
1877 1926 7.465353 TCAATATGCTGTGATTTTCCTTGAA 57.535 32.000 0.00 0.00 0.00 2.69
1878 1927 7.894708 TCAATATGCTGTGATTTTCCTTGAAA 58.105 30.769 0.00 0.00 0.00 2.69
1879 1928 8.366401 TCAATATGCTGTGATTTTCCTTGAAAA 58.634 29.630 4.64 4.64 44.04 2.29
1880 1929 8.653338 CAATATGCTGTGATTTTCCTTGAAAAG 58.347 33.333 7.89 0.00 43.33 2.27
1881 1930 5.596836 TGCTGTGATTTTCCTTGAAAAGT 57.403 34.783 7.89 0.00 44.25 2.66
1882 1931 5.976458 TGCTGTGATTTTCCTTGAAAAGTT 58.024 33.333 7.89 0.00 44.25 2.66
1883 1932 6.042143 TGCTGTGATTTTCCTTGAAAAGTTC 58.958 36.000 7.89 3.05 44.25 3.01
1884 1933 5.173854 GCTGTGATTTTCCTTGAAAAGTTCG 59.826 40.000 7.89 0.00 44.25 3.95
1885 1934 6.202516 TGTGATTTTCCTTGAAAAGTTCGT 57.797 33.333 7.89 0.00 44.25 3.85
1886 1935 6.626302 TGTGATTTTCCTTGAAAAGTTCGTT 58.374 32.000 7.89 0.00 44.25 3.85
1887 1936 6.750039 TGTGATTTTCCTTGAAAAGTTCGTTC 59.250 34.615 7.89 1.30 44.25 3.95
1888 1937 6.750039 GTGATTTTCCTTGAAAAGTTCGTTCA 59.250 34.615 7.89 3.48 44.25 3.18
1889 1938 7.435192 GTGATTTTCCTTGAAAAGTTCGTTCAT 59.565 33.333 7.89 0.00 44.25 2.57
1890 1939 7.434897 TGATTTTCCTTGAAAAGTTCGTTCATG 59.565 33.333 7.89 0.00 44.25 3.07
1891 1940 5.828299 TTCCTTGAAAAGTTCGTTCATGT 57.172 34.783 0.00 0.00 44.25 3.21
1892 1941 5.828299 TCCTTGAAAAGTTCGTTCATGTT 57.172 34.783 0.00 0.00 44.25 2.71
1893 1942 5.816919 TCCTTGAAAAGTTCGTTCATGTTC 58.183 37.500 0.00 0.00 44.25 3.18
1894 1943 5.355630 TCCTTGAAAAGTTCGTTCATGTTCA 59.644 36.000 0.00 0.00 44.25 3.18
1895 1944 6.039270 TCCTTGAAAAGTTCGTTCATGTTCAT 59.961 34.615 0.00 0.00 44.25 2.57
1896 1945 6.697019 CCTTGAAAAGTTCGTTCATGTTCATT 59.303 34.615 0.00 0.00 44.25 2.57
1897 1946 7.860373 CCTTGAAAAGTTCGTTCATGTTCATTA 59.140 33.333 0.00 0.00 44.25 1.90
1898 1947 9.398170 CTTGAAAAGTTCGTTCATGTTCATTAT 57.602 29.630 0.00 0.00 39.70 1.28
1899 1948 8.726650 TGAAAAGTTCGTTCATGTTCATTATG 57.273 30.769 0.00 0.00 30.08 1.90
1900 1949 7.807433 TGAAAAGTTCGTTCATGTTCATTATGG 59.193 33.333 0.00 0.00 30.08 2.74
1901 1950 6.817765 AAGTTCGTTCATGTTCATTATGGT 57.182 33.333 0.00 0.00 0.00 3.55
1902 1951 7.915293 AAGTTCGTTCATGTTCATTATGGTA 57.085 32.000 0.00 0.00 0.00 3.25
1903 1952 8.506168 AAGTTCGTTCATGTTCATTATGGTAT 57.494 30.769 0.00 0.00 0.00 2.73
1904 1953 9.607988 AAGTTCGTTCATGTTCATTATGGTATA 57.392 29.630 0.00 0.00 0.00 1.47
1905 1954 9.607988 AGTTCGTTCATGTTCATTATGGTATAA 57.392 29.630 0.00 0.00 0.00 0.98
1906 1955 9.646336 GTTCGTTCATGTTCATTATGGTATAAC 57.354 33.333 0.00 0.00 0.00 1.89
1907 1956 8.950208 TCGTTCATGTTCATTATGGTATAACA 57.050 30.769 0.00 0.00 34.81 2.41
1908 1957 9.554395 TCGTTCATGTTCATTATGGTATAACAT 57.446 29.630 8.63 8.63 40.44 2.71
1924 1973 8.670135 TGGTATAACATAAACATGTACACTTGC 58.330 33.333 0.00 0.00 33.81 4.01
1947 1996 6.770076 GCAAGTTTGTGCAAAAATTTGACTA 58.230 32.000 30.98 0.00 44.29 2.59
1951 2000 8.130307 AGTTTGTGCAAAAATTTGACTACATC 57.870 30.769 5.11 7.54 40.55 3.06
1985 2034 6.381133 ACAAAAAGGAAAACTGAACCTCTGAT 59.619 34.615 0.00 0.00 33.16 2.90
1986 2035 6.396829 AAAAGGAAAACTGAACCTCTGATG 57.603 37.500 0.00 0.00 33.16 3.07
2031 2094 5.998454 TTTTTGGGTGCAAAACATGTATG 57.002 34.783 0.00 2.70 34.25 2.39
2032 2095 3.674528 TTGGGTGCAAAACATGTATGG 57.325 42.857 0.00 0.00 0.00 2.74
2033 2096 2.603021 TGGGTGCAAAACATGTATGGT 58.397 42.857 0.00 0.00 0.00 3.55
2034 2097 2.560542 TGGGTGCAAAACATGTATGGTC 59.439 45.455 0.00 0.00 0.00 4.02
2035 2098 2.560542 GGGTGCAAAACATGTATGGTCA 59.439 45.455 0.00 0.00 0.00 4.02
2036 2099 3.006323 GGGTGCAAAACATGTATGGTCAA 59.994 43.478 0.00 0.00 0.00 3.18
2037 2100 4.322650 GGGTGCAAAACATGTATGGTCAAT 60.323 41.667 0.00 0.00 0.00 2.57
2055 2118 8.415950 TGGTCAATTGGTCATATTTTTGTACT 57.584 30.769 5.42 0.00 0.00 2.73
2056 2119 8.303156 TGGTCAATTGGTCATATTTTTGTACTG 58.697 33.333 5.42 0.00 0.00 2.74
2130 2194 6.155475 TCTTTAAATCACACCTGTTTTGGG 57.845 37.500 0.00 0.00 0.00 4.12
2143 2207 1.686587 GTTTTGGGGTTTGGAGTGAGG 59.313 52.381 0.00 0.00 0.00 3.86
2162 2226 1.690845 GGGCAGAGGAGAGAGAATGGA 60.691 57.143 0.00 0.00 0.00 3.41
2164 2228 1.688197 GCAGAGGAGAGAGAATGGAGG 59.312 57.143 0.00 0.00 0.00 4.30
2267 2331 6.750963 CAGATTTAGATTTCTGCCTTTCAAGC 59.249 38.462 0.00 0.00 33.56 4.01
2393 2457 7.755591 TCATGATAACAGATTTGAGCTGAAAC 58.244 34.615 0.00 0.00 36.86 2.78
2405 2469 6.916360 TTGAGCTGAAACCCTGAAATATTT 57.084 33.333 0.00 0.00 0.00 1.40
2406 2470 6.916360 TGAGCTGAAACCCTGAAATATTTT 57.084 33.333 1.43 0.00 0.00 1.82
2498 2563 3.898123 CCTCCAGTTTAGATGCTAGCCTA 59.102 47.826 13.29 4.33 0.00 3.93
2539 2604 8.647143 TTCTTTGTGCTTTTATTTCTTCCTTG 57.353 30.769 0.00 0.00 0.00 3.61
2540 2605 8.006298 TCTTTGTGCTTTTATTTCTTCCTTGA 57.994 30.769 0.00 0.00 0.00 3.02
2655 2723 1.884235 AGCCACCTCAACTTTTCGAG 58.116 50.000 0.00 0.00 0.00 4.04
2664 2732 5.526479 ACCTCAACTTTTCGAGACCTAAAAC 59.474 40.000 0.00 0.00 0.00 2.43
2678 2746 4.672899 ACCTAAAACCATGTGCCTATTGT 58.327 39.130 0.00 0.00 0.00 2.71
2757 2825 5.144100 TCATTCCTTCTTTTGTTGCCCTTA 58.856 37.500 0.00 0.00 0.00 2.69
2900 2973 6.861065 TTATGCTGTAACTAGCCTTTATGC 57.139 37.500 0.00 0.00 43.02 3.14
2901 2974 4.214986 TGCTGTAACTAGCCTTTATGCA 57.785 40.909 0.00 0.00 43.02 3.96
2902 2975 3.938963 TGCTGTAACTAGCCTTTATGCAC 59.061 43.478 0.00 0.00 43.02 4.57
2903 2976 3.001330 GCTGTAACTAGCCTTTATGCACG 59.999 47.826 0.00 0.00 37.73 5.34
3000 3075 4.468510 CCTTTGTACTATGTCCCAGTGGTA 59.531 45.833 8.74 0.00 0.00 3.25
3064 3139 7.283329 AGCTCCCTTTCGAAGATAACATTAAT 58.717 34.615 0.00 0.00 35.04 1.40
3116 3353 5.360714 TGATTGCATGGGTTTCTATTTCCTC 59.639 40.000 0.00 0.00 0.00 3.71
3135 3372 3.064545 CCTCTGCTTTATTCAAGGCTTCG 59.935 47.826 0.00 0.00 37.62 3.79
3171 3408 6.392354 AGTCAACACAGCATATTTGATTTGG 58.608 36.000 0.00 0.00 30.96 3.28
3176 3413 4.403432 CACAGCATATTTGATTTGGTCCCT 59.597 41.667 0.00 0.00 0.00 4.20
3177 3414 4.403432 ACAGCATATTTGATTTGGTCCCTG 59.597 41.667 0.00 0.00 0.00 4.45
3183 3421 0.623723 TGATTTGGTCCCTGCCTACC 59.376 55.000 0.00 0.00 36.24 3.18
3224 3462 2.004808 CTGCTGAGCGATCGGTACCA 62.005 60.000 21.30 13.83 0.00 3.25
3233 3471 1.134788 CGATCGGTACCAAAGGAGCTT 60.135 52.381 13.54 0.00 0.00 3.74
3310 3548 9.690434 GATGATTTTACACTGTTTCTATTCGAC 57.310 33.333 0.00 0.00 0.00 4.20
3313 3551 3.299340 ACACTGTTTCTATTCGACGCT 57.701 42.857 0.00 0.00 0.00 5.07
3528 3776 4.100035 ACTCTGCGGTTGAGATCAATCATA 59.900 41.667 6.64 0.00 36.80 2.15
3539 3787 7.916914 TGAGATCAATCATAATGCGATCATT 57.083 32.000 0.00 0.00 44.52 2.57
3581 3829 1.202348 GGCAGTAATTTGTCAGCCACC 59.798 52.381 0.00 0.00 41.63 4.61
3613 3861 3.644966 TGGTACCATTCACCTCCATTC 57.355 47.619 11.60 0.00 36.96 2.67
3619 4089 6.095021 GGTACCATTCACCTCCATTCTTTTAC 59.905 42.308 7.15 0.00 32.98 2.01
3620 4090 5.640147 ACCATTCACCTCCATTCTTTTACA 58.360 37.500 0.00 0.00 0.00 2.41
3622 4092 5.126061 CCATTCACCTCCATTCTTTTACAGG 59.874 44.000 0.00 0.00 0.00 4.00
3625 4095 5.560724 TCACCTCCATTCTTTTACAGGAAG 58.439 41.667 0.00 0.00 0.00 3.46
3627 4097 5.412904 CACCTCCATTCTTTTACAGGAAGTC 59.587 44.000 0.00 0.00 0.00 3.01
3628 4098 4.631813 CCTCCATTCTTTTACAGGAAGTCG 59.368 45.833 0.00 0.00 0.00 4.18
3689 4288 8.528917 AGAAACATGTTTGAAATCATCACATG 57.471 30.769 27.85 22.49 44.83 3.21
3696 4295 7.490840 TGTTTGAAATCATCACATGTCAAGTT 58.509 30.769 0.00 0.00 37.92 2.66
3698 4297 6.880942 TGAAATCATCACATGTCAAGTTGA 57.119 33.333 0.08 0.08 31.50 3.18
3702 4301 6.638096 ATCATCACATGTCAAGTTGAACAA 57.362 33.333 7.25 0.00 0.00 2.83
3703 4302 6.448207 TCATCACATGTCAAGTTGAACAAA 57.552 33.333 7.25 0.00 0.00 2.83
3704 4303 6.264832 TCATCACATGTCAAGTTGAACAAAC 58.735 36.000 7.25 0.00 39.24 2.93
3713 4312 3.131240 AGTTGAACAAACTCGTGTTGC 57.869 42.857 3.24 0.00 46.60 4.17
3715 4314 3.098636 GTTGAACAAACTCGTGTTGCTC 58.901 45.455 3.24 2.28 41.78 4.26
3716 4315 1.668751 TGAACAAACTCGTGTTGCTCC 59.331 47.619 3.24 0.00 41.78 4.70
3717 4316 1.002792 GAACAAACTCGTGTTGCTCCC 60.003 52.381 3.24 0.00 41.78 4.30
3718 4317 0.107410 ACAAACTCGTGTTGCTCCCA 60.107 50.000 3.24 0.00 36.39 4.37
3723 4322 1.608590 ACTCGTGTTGCTCCCAATTTG 59.391 47.619 0.00 0.00 32.75 2.32
3724 4323 0.958091 TCGTGTTGCTCCCAATTTGG 59.042 50.000 8.56 8.56 37.25 3.28
3726 4325 1.883275 CGTGTTGCTCCCAATTTGGTA 59.117 47.619 14.26 0.00 35.17 3.25
3728 4327 2.890945 GTGTTGCTCCCAATTTGGTACT 59.109 45.455 14.26 0.00 35.17 2.73
3730 4329 4.156008 GTGTTGCTCCCAATTTGGTACTAG 59.844 45.833 14.26 7.19 35.17 2.57
3731 4330 4.202524 TGTTGCTCCCAATTTGGTACTAGT 60.203 41.667 14.26 0.00 35.17 2.57
3732 4331 5.013287 TGTTGCTCCCAATTTGGTACTAGTA 59.987 40.000 14.26 0.00 35.17 1.82
3733 4332 5.968676 TGCTCCCAATTTGGTACTAGTAT 57.031 39.130 14.26 0.00 35.17 2.12
3734 4333 6.321821 TGCTCCCAATTTGGTACTAGTATT 57.678 37.500 14.26 0.00 35.17 1.89
3735 4334 6.727394 TGCTCCCAATTTGGTACTAGTATTT 58.273 36.000 14.26 0.00 35.17 1.40
3736 4335 7.179269 TGCTCCCAATTTGGTACTAGTATTTT 58.821 34.615 14.26 0.00 35.17 1.82
3737 4336 7.338449 TGCTCCCAATTTGGTACTAGTATTTTC 59.662 37.037 14.26 0.00 35.17 2.29
3738 4337 7.338449 GCTCCCAATTTGGTACTAGTATTTTCA 59.662 37.037 14.26 0.55 35.17 2.69
3739 4338 9.408648 CTCCCAATTTGGTACTAGTATTTTCAT 57.591 33.333 14.26 0.00 35.17 2.57
3800 4481 8.152898 TGATTGATGACTAATGTAGAATCCCAG 58.847 37.037 0.00 0.00 0.00 4.45
3801 4482 7.437713 TTGATGACTAATGTAGAATCCCAGT 57.562 36.000 0.00 0.00 0.00 4.00
3826 4507 9.537848 GTTTACAACAAATAAATCGACTGTAGG 57.462 33.333 0.00 0.00 0.00 3.18
3842 4523 5.003804 ACTGTAGGCTTTCAAGTTACATGG 58.996 41.667 0.00 1.69 32.18 3.66
3875 4577 5.695851 AGAATGTGCTTACAACAAAGGAG 57.304 39.130 0.00 0.00 0.00 3.69
3942 4644 2.995939 GGAGTGCAAGCCAATAAAAAGC 59.004 45.455 0.00 0.00 0.00 3.51
3945 4647 4.060205 AGTGCAAGCCAATAAAAAGCAAG 58.940 39.130 0.00 0.00 31.78 4.01
3946 4648 3.187022 GTGCAAGCCAATAAAAAGCAAGG 59.813 43.478 0.00 0.00 31.78 3.61
4130 4934 1.889545 AAGTCAAGCCTGAGTTGCTC 58.110 50.000 4.55 0.00 42.51 4.26
4131 4935 0.320247 AGTCAAGCCTGAGTTGCTCG 60.320 55.000 0.00 0.00 38.34 5.03
4132 4936 1.669115 TCAAGCCTGAGTTGCTCGC 60.669 57.895 0.00 0.00 38.34 5.03
4133 4937 1.962822 CAAGCCTGAGTTGCTCGCA 60.963 57.895 0.00 0.00 38.34 5.10
4134 4938 1.670406 AAGCCTGAGTTGCTCGCAG 60.670 57.895 6.33 6.33 42.27 5.18
4135 4939 3.797546 GCCTGAGTTGCTCGCAGC 61.798 66.667 0.00 0.00 41.50 5.25
4146 4965 1.005748 CTCGCAGCTGGTCTGAACA 60.006 57.895 17.12 0.00 45.72 3.18
4179 4998 3.371097 GAGCCAATCACGGAGCGGA 62.371 63.158 0.00 0.00 0.00 5.54
4203 5023 2.426522 ACGATCAGACCAACAACCATG 58.573 47.619 0.00 0.00 0.00 3.66
4226 5050 0.161658 GCGATGCGACGGTATCATTG 59.838 55.000 0.00 0.00 35.26 2.82
4230 5054 0.533032 TGCGACGGTATCATTGTGGA 59.467 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
364 365 0.877743 GAAGAAGAGCAAGGTGGTGC 59.122 55.000 0.00 0.00 45.28 5.01
443 444 1.925455 CCTCCAGGAGGGCCAAGAA 60.925 63.158 26.87 0.00 45.43 2.52
465 466 1.079819 CGGCCTCTCTGAAAAGCGA 60.080 57.895 0.00 0.00 0.00 4.93
628 629 0.471780 TTCTGACCTCCCAGCAGTCA 60.472 55.000 0.00 0.00 38.17 3.41
632 633 0.471780 TGTCTTCTGACCTCCCAGCA 60.472 55.000 0.00 0.00 42.28 4.41
656 657 3.003763 GTGTCTTCCCCTCCGGCT 61.004 66.667 0.00 0.00 0.00 5.52
786 799 2.435586 CTGCCTCCTCCGTGCAAG 60.436 66.667 0.00 0.00 34.06 4.01
868 881 0.438830 GTCACGACTCACGAATTGGC 59.561 55.000 0.00 0.00 45.77 4.52
869 882 1.068474 GGTCACGACTCACGAATTGG 58.932 55.000 0.00 0.00 45.77 3.16
870 883 0.708370 CGGTCACGACTCACGAATTG 59.292 55.000 0.00 0.00 45.77 2.32
871 884 0.388134 CCGGTCACGACTCACGAATT 60.388 55.000 0.00 0.00 45.77 2.17
872 885 1.211969 CCGGTCACGACTCACGAAT 59.788 57.895 0.00 0.00 45.77 3.34
873 886 2.640989 CCGGTCACGACTCACGAA 59.359 61.111 0.00 0.00 45.77 3.85
874 887 4.034258 GCCGGTCACGACTCACGA 62.034 66.667 1.90 0.00 45.77 4.35
909 922 0.323629 TGTTAACTCTTCCCCGCTGG 59.676 55.000 7.22 0.00 0.00 4.85
919 932 1.981495 AGCCCAGCTTCTGTTAACTCT 59.019 47.619 7.22 0.00 33.89 3.24
920 933 2.481289 AGCCCAGCTTCTGTTAACTC 57.519 50.000 7.22 0.00 33.89 3.01
921 934 2.959465 AAGCCCAGCTTCTGTTAACT 57.041 45.000 7.22 0.00 46.77 2.24
943 959 2.035442 GGTGCTTCTTCACGAGGCC 61.035 63.158 0.00 0.00 43.56 5.19
948 964 2.328099 GCCCAGGTGCTTCTTCACG 61.328 63.158 0.00 0.00 37.83 4.35
955 971 0.893727 CGTTAAAGGCCCAGGTGCTT 60.894 55.000 0.00 0.00 0.00 3.91
980 996 0.916086 AAGGTCCTGTGTGGTGTTGA 59.084 50.000 0.00 0.00 37.07 3.18
1008 1028 0.769873 AGATATGGGCTTCCCTGCTG 59.230 55.000 3.27 0.00 45.70 4.41
1037 1057 4.942481 TGTTCGCTGCGTCGTGCT 62.942 61.111 22.48 0.00 46.63 4.40
1042 1062 0.179150 AGAGAGATGTTCGCTGCGTC 60.179 55.000 22.48 16.05 34.39 5.19
1122 1142 2.688515 GCCTCTCTGTAGAACCCTAGCT 60.689 54.545 0.00 0.00 0.00 3.32
1156 1187 3.055675 CCACCACCGTCAGGATTAAGTTA 60.056 47.826 0.00 0.00 41.02 2.24
1162 1193 3.077907 CCCACCACCGTCAGGATT 58.922 61.111 0.00 0.00 41.02 3.01
1319 1350 5.798934 ACTCAACGACAATCGACTAATACAC 59.201 40.000 5.04 0.00 43.74 2.90
1324 1355 4.492791 TGACTCAACGACAATCGACTAA 57.507 40.909 5.04 0.00 43.74 2.24
1356 1388 1.414158 TGATTCCGATCCCTCCAGTC 58.586 55.000 0.00 0.00 0.00 3.51
1382 1414 3.056250 ACACCAGACAGTGCTAAGATCTG 60.056 47.826 0.00 0.00 41.67 2.90
1393 1442 1.696336 AGCAATCAGACACCAGACAGT 59.304 47.619 0.00 0.00 0.00 3.55
1394 1443 2.469274 AGCAATCAGACACCAGACAG 57.531 50.000 0.00 0.00 0.00 3.51
1397 1446 1.881973 GCAAAGCAATCAGACACCAGA 59.118 47.619 0.00 0.00 0.00 3.86
1398 1447 1.884579 AGCAAAGCAATCAGACACCAG 59.115 47.619 0.00 0.00 0.00 4.00
1399 1448 1.881973 GAGCAAAGCAATCAGACACCA 59.118 47.619 0.00 0.00 0.00 4.17
1400 1449 2.157738 AGAGCAAAGCAATCAGACACC 58.842 47.619 0.00 0.00 0.00 4.16
1401 1450 3.911661 AAGAGCAAAGCAATCAGACAC 57.088 42.857 0.00 0.00 0.00 3.67
1402 1451 4.581824 AGAAAAGAGCAAAGCAATCAGACA 59.418 37.500 0.00 0.00 0.00 3.41
1403 1452 4.916249 CAGAAAAGAGCAAAGCAATCAGAC 59.084 41.667 0.00 0.00 0.00 3.51
1404 1453 4.823442 TCAGAAAAGAGCAAAGCAATCAGA 59.177 37.500 0.00 0.00 0.00 3.27
1405 1454 5.117355 TCAGAAAAGAGCAAAGCAATCAG 57.883 39.130 0.00 0.00 0.00 2.90
1406 1455 5.518848 TTCAGAAAAGAGCAAAGCAATCA 57.481 34.783 0.00 0.00 0.00 2.57
1407 1456 7.288672 CAATTTCAGAAAAGAGCAAAGCAATC 58.711 34.615 0.00 0.00 0.00 2.67
1408 1457 6.293244 GCAATTTCAGAAAAGAGCAAAGCAAT 60.293 34.615 0.00 0.00 31.81 3.56
1409 1458 5.006941 GCAATTTCAGAAAAGAGCAAAGCAA 59.993 36.000 0.00 0.00 31.81 3.91
1410 1459 4.508861 GCAATTTCAGAAAAGAGCAAAGCA 59.491 37.500 0.00 0.00 31.81 3.91
1411 1460 4.508861 TGCAATTTCAGAAAAGAGCAAAGC 59.491 37.500 14.39 5.53 36.06 3.51
1412 1461 5.751990 ACTGCAATTTCAGAAAAGAGCAAAG 59.248 36.000 12.25 10.91 37.53 2.77
1413 1462 5.663456 ACTGCAATTTCAGAAAAGAGCAAA 58.337 33.333 12.25 1.79 37.53 3.68
1414 1463 5.266733 ACTGCAATTTCAGAAAAGAGCAA 57.733 34.783 12.25 6.00 37.53 3.91
1415 1464 4.924305 ACTGCAATTTCAGAAAAGAGCA 57.076 36.364 12.25 15.37 36.40 4.26
1416 1465 6.615088 TCATACTGCAATTTCAGAAAAGAGC 58.385 36.000 12.25 5.30 37.51 4.09
1417 1466 8.242053 ACATCATACTGCAATTTCAGAAAAGAG 58.758 33.333 12.25 0.91 37.51 2.85
1418 1467 8.114331 ACATCATACTGCAATTTCAGAAAAGA 57.886 30.769 12.25 4.78 37.51 2.52
1419 1468 8.242053 AGACATCATACTGCAATTTCAGAAAAG 58.758 33.333 12.25 0.00 37.51 2.27
1420 1469 8.114331 AGACATCATACTGCAATTTCAGAAAA 57.886 30.769 12.25 0.00 37.51 2.29
1424 1473 7.317842 AGAAGACATCATACTGCAATTTCAG 57.682 36.000 3.36 3.36 39.86 3.02
1432 1481 6.370994 CCATGGATAAGAAGACATCATACTGC 59.629 42.308 5.56 0.00 0.00 4.40
1435 1484 7.547370 GCTACCATGGATAAGAAGACATCATAC 59.453 40.741 21.47 0.00 0.00 2.39
1444 1493 4.202295 TGCTGAGCTACCATGGATAAGAAG 60.202 45.833 21.47 10.05 0.00 2.85
1455 1504 2.862541 ACAAACAATGCTGAGCTACCA 58.137 42.857 5.83 0.00 0.00 3.25
1552 1601 6.531948 CACTTATAAGCGCCATATCTCTTACC 59.468 42.308 12.54 0.00 0.00 2.85
1554 1603 6.071334 AGCACTTATAAGCGCCATATCTCTTA 60.071 38.462 19.36 0.00 34.73 2.10
1566 1615 7.142306 TCTACACCTATAGCACTTATAAGCG 57.858 40.000 12.54 4.18 35.48 4.68
1628 1677 3.612860 CCAGCACTAGACAAACACGATAC 59.387 47.826 0.00 0.00 0.00 2.24
1646 1695 5.695851 AATCACGGATGATAATTTCCAGC 57.304 39.130 0.00 0.00 45.26 4.85
1662 1711 5.551760 AATTCCAGCACTAGAAAATCACG 57.448 39.130 0.00 0.00 0.00 4.35
1720 1769 2.859404 TCTTCTAGTGAGGGATCAGGGA 59.141 50.000 0.00 0.00 0.00 4.20
1721 1770 3.320610 TCTTCTAGTGAGGGATCAGGG 57.679 52.381 0.00 0.00 0.00 4.45
1722 1771 8.837099 ATTATATCTTCTAGTGAGGGATCAGG 57.163 38.462 0.00 0.00 0.00 3.86
1723 1772 9.699410 AGATTATATCTTCTAGTGAGGGATCAG 57.301 37.037 0.00 0.00 35.76 2.90
1753 1802 2.825205 CCAAGCAGGTGGAAACAAAAG 58.175 47.619 0.00 0.00 46.06 2.27
1783 1832 7.066284 TGCAGAATTCAGGTTCTCTATAAAAGC 59.934 37.037 8.44 0.00 36.33 3.51
1795 1844 1.238439 CCGTGTGCAGAATTCAGGTT 58.762 50.000 8.44 0.00 0.00 3.50
1823 1872 7.308951 GGAGAAAGGGAGAAGAATATAGACTCG 60.309 44.444 0.00 0.00 0.00 4.18
1824 1873 7.308951 CGGAGAAAGGGAGAAGAATATAGACTC 60.309 44.444 0.00 0.00 0.00 3.36
1825 1874 6.492087 CGGAGAAAGGGAGAAGAATATAGACT 59.508 42.308 0.00 0.00 0.00 3.24
1826 1875 6.683715 CGGAGAAAGGGAGAAGAATATAGAC 58.316 44.000 0.00 0.00 0.00 2.59
1827 1876 5.244178 GCGGAGAAAGGGAGAAGAATATAGA 59.756 44.000 0.00 0.00 0.00 1.98
1828 1877 5.011125 TGCGGAGAAAGGGAGAAGAATATAG 59.989 44.000 0.00 0.00 0.00 1.31
1829 1878 4.899457 TGCGGAGAAAGGGAGAAGAATATA 59.101 41.667 0.00 0.00 0.00 0.86
1830 1879 3.711704 TGCGGAGAAAGGGAGAAGAATAT 59.288 43.478 0.00 0.00 0.00 1.28
1831 1880 3.104512 TGCGGAGAAAGGGAGAAGAATA 58.895 45.455 0.00 0.00 0.00 1.75
1832 1881 1.909302 TGCGGAGAAAGGGAGAAGAAT 59.091 47.619 0.00 0.00 0.00 2.40
1833 1882 1.348064 TGCGGAGAAAGGGAGAAGAA 58.652 50.000 0.00 0.00 0.00 2.52
1834 1883 1.482593 GATGCGGAGAAAGGGAGAAGA 59.517 52.381 0.00 0.00 0.00 2.87
1835 1884 1.208052 TGATGCGGAGAAAGGGAGAAG 59.792 52.381 0.00 0.00 0.00 2.85
1836 1885 1.275666 TGATGCGGAGAAAGGGAGAA 58.724 50.000 0.00 0.00 0.00 2.87
1837 1886 1.275666 TTGATGCGGAGAAAGGGAGA 58.724 50.000 0.00 0.00 0.00 3.71
1838 1887 2.338577 ATTGATGCGGAGAAAGGGAG 57.661 50.000 0.00 0.00 0.00 4.30
1839 1888 3.743521 CATATTGATGCGGAGAAAGGGA 58.256 45.455 0.00 0.00 0.00 4.20
1851 1900 7.485810 TCAAGGAAAATCACAGCATATTGATG 58.514 34.615 0.00 0.00 40.09 3.07
1852 1901 7.649533 TCAAGGAAAATCACAGCATATTGAT 57.350 32.000 0.00 0.00 33.74 2.57
1853 1902 7.465353 TTCAAGGAAAATCACAGCATATTGA 57.535 32.000 0.00 0.00 0.00 2.57
1854 1903 8.537049 TTTTCAAGGAAAATCACAGCATATTG 57.463 30.769 0.28 0.00 36.73 1.90
1855 1904 8.370182 ACTTTTCAAGGAAAATCACAGCATATT 58.630 29.630 4.76 0.00 40.14 1.28
1856 1905 7.899973 ACTTTTCAAGGAAAATCACAGCATAT 58.100 30.769 4.76 0.00 40.14 1.78
1857 1906 7.288810 ACTTTTCAAGGAAAATCACAGCATA 57.711 32.000 4.76 0.00 40.14 3.14
1858 1907 6.165700 ACTTTTCAAGGAAAATCACAGCAT 57.834 33.333 4.76 0.00 40.14 3.79
1859 1908 5.596836 ACTTTTCAAGGAAAATCACAGCA 57.403 34.783 4.76 0.00 40.14 4.41
1860 1909 5.173854 CGAACTTTTCAAGGAAAATCACAGC 59.826 40.000 4.76 0.00 40.14 4.40
1861 1910 6.265577 ACGAACTTTTCAAGGAAAATCACAG 58.734 36.000 4.76 0.00 40.14 3.66
1862 1911 6.202516 ACGAACTTTTCAAGGAAAATCACA 57.797 33.333 4.76 0.00 40.14 3.58
1863 1912 6.750039 TGAACGAACTTTTCAAGGAAAATCAC 59.250 34.615 4.76 0.29 40.14 3.06
1864 1913 6.857956 TGAACGAACTTTTCAAGGAAAATCA 58.142 32.000 4.76 2.80 40.14 2.57
1865 1914 7.435192 ACATGAACGAACTTTTCAAGGAAAATC 59.565 33.333 0.00 1.04 40.14 2.17
1866 1915 7.264947 ACATGAACGAACTTTTCAAGGAAAAT 58.735 30.769 0.00 0.00 40.14 1.82
1867 1916 6.626302 ACATGAACGAACTTTTCAAGGAAAA 58.374 32.000 0.00 4.31 38.90 2.29
1868 1917 6.202516 ACATGAACGAACTTTTCAAGGAAA 57.797 33.333 0.00 0.00 36.57 3.13
1869 1918 5.828299 ACATGAACGAACTTTTCAAGGAA 57.172 34.783 0.00 0.00 36.57 3.36
1870 1919 5.355630 TGAACATGAACGAACTTTTCAAGGA 59.644 36.000 0.00 0.00 36.57 3.36
1871 1920 5.577835 TGAACATGAACGAACTTTTCAAGG 58.422 37.500 0.00 0.00 36.57 3.61
1872 1921 7.684062 AATGAACATGAACGAACTTTTCAAG 57.316 32.000 0.00 0.00 36.57 3.02
1873 1922 9.179552 CATAATGAACATGAACGAACTTTTCAA 57.820 29.630 0.00 0.00 36.57 2.69
1874 1923 7.807433 CCATAATGAACATGAACGAACTTTTCA 59.193 33.333 0.00 0.00 37.38 2.69
1875 1924 7.807907 ACCATAATGAACATGAACGAACTTTTC 59.192 33.333 0.00 0.00 0.00 2.29
1876 1925 7.657336 ACCATAATGAACATGAACGAACTTTT 58.343 30.769 0.00 0.00 0.00 2.27
1877 1926 7.214467 ACCATAATGAACATGAACGAACTTT 57.786 32.000 0.00 0.00 0.00 2.66
1878 1927 6.817765 ACCATAATGAACATGAACGAACTT 57.182 33.333 0.00 0.00 0.00 2.66
1879 1928 9.607988 TTATACCATAATGAACATGAACGAACT 57.392 29.630 0.00 0.00 0.00 3.01
1880 1929 9.646336 GTTATACCATAATGAACATGAACGAAC 57.354 33.333 0.00 0.00 0.00 3.95
1881 1930 9.384764 TGTTATACCATAATGAACATGAACGAA 57.615 29.630 0.00 0.00 0.00 3.85
1882 1931 8.950208 TGTTATACCATAATGAACATGAACGA 57.050 30.769 0.00 0.00 0.00 3.85
1898 1947 8.670135 GCAAGTGTACATGTTTATGTTATACCA 58.330 33.333 2.30 0.00 45.01 3.25
1899 1948 8.670135 TGCAAGTGTACATGTTTATGTTATACC 58.330 33.333 2.30 0.00 45.01 2.73
1902 1951 8.792633 ACTTGCAAGTGTACATGTTTATGTTAT 58.207 29.630 30.66 0.00 40.13 1.89
1903 1952 8.160521 ACTTGCAAGTGTACATGTTTATGTTA 57.839 30.769 30.66 0.00 40.13 2.41
1904 1953 7.038154 ACTTGCAAGTGTACATGTTTATGTT 57.962 32.000 30.66 0.00 40.13 2.71
1905 1954 6.633500 ACTTGCAAGTGTACATGTTTATGT 57.367 33.333 30.66 0.92 43.00 2.29
1906 1955 7.434897 ACAAACTTGCAAGTGTACATGTTTATG 59.565 33.333 31.73 13.00 40.24 1.90
1907 1956 7.434897 CACAAACTTGCAAGTGTACATGTTTAT 59.565 33.333 31.73 9.45 40.24 1.40
1908 1957 6.749578 CACAAACTTGCAAGTGTACATGTTTA 59.250 34.615 31.73 0.00 40.24 2.01
1909 1958 5.576384 CACAAACTTGCAAGTGTACATGTTT 59.424 36.000 31.73 16.79 41.85 2.83
1910 1959 5.101628 CACAAACTTGCAAGTGTACATGTT 58.898 37.500 31.73 17.51 39.66 2.71
1911 1960 4.671377 CACAAACTTGCAAGTGTACATGT 58.329 39.130 31.73 24.72 39.66 3.21
1912 1961 3.486841 GCACAAACTTGCAAGTGTACATG 59.513 43.478 31.73 23.32 42.49 3.21
1913 1962 3.705604 GCACAAACTTGCAAGTGTACAT 58.294 40.909 31.73 13.81 42.49 2.29
1914 1963 3.143807 GCACAAACTTGCAAGTGTACA 57.856 42.857 31.73 0.00 42.49 2.90
1923 1972 5.630061 AGTCAAATTTTTGCACAAACTTGC 58.370 33.333 13.21 9.27 43.31 4.01
1924 1973 7.737395 TGTAGTCAAATTTTTGCACAAACTTG 58.263 30.769 12.11 12.11 38.05 3.16
1941 1990 5.447624 TTGTCGAAGTCAGATGTAGTCAA 57.552 39.130 0.00 0.00 0.00 3.18
1947 1996 4.703897 TCCTTTTTGTCGAAGTCAGATGT 58.296 39.130 0.00 0.00 0.00 3.06
1951 2000 5.739161 CAGTTTTCCTTTTTGTCGAAGTCAG 59.261 40.000 0.00 0.00 0.00 3.51
2010 2073 4.141620 ACCATACATGTTTTGCACCCAAAA 60.142 37.500 2.30 0.00 45.83 2.44
2013 2076 2.560542 GACCATACATGTTTTGCACCCA 59.439 45.455 2.30 0.00 0.00 4.51
2017 2080 5.221601 ACCAATTGACCATACATGTTTTGCA 60.222 36.000 2.30 0.00 0.00 4.08
2021 2084 6.855763 ATGACCAATTGACCATACATGTTT 57.144 33.333 2.30 0.00 0.00 2.83
2024 2087 9.820725 AAAAATATGACCAATTGACCATACATG 57.179 29.630 7.12 0.00 0.00 3.21
2030 2093 8.303156 CAGTACAAAAATATGACCAATTGACCA 58.697 33.333 7.12 4.60 0.00 4.02
2031 2094 8.303876 ACAGTACAAAAATATGACCAATTGACC 58.696 33.333 7.12 0.00 0.00 4.02
2104 2167 7.714813 CCCAAAACAGGTGTGATTTAAAGAAAT 59.285 33.333 0.00 0.00 38.00 2.17
2111 2175 3.917300 ACCCCAAAACAGGTGTGATTTA 58.083 40.909 0.00 0.00 34.20 1.40
2122 2186 2.383855 CTCACTCCAAACCCCAAAACA 58.616 47.619 0.00 0.00 0.00 2.83
2123 2187 1.686587 CCTCACTCCAAACCCCAAAAC 59.313 52.381 0.00 0.00 0.00 2.43
2124 2188 1.412361 CCCTCACTCCAAACCCCAAAA 60.412 52.381 0.00 0.00 0.00 2.44
2130 2194 0.322008 CTCTGCCCTCACTCCAAACC 60.322 60.000 0.00 0.00 0.00 3.27
2143 2207 1.688197 CTCCATTCTCTCTCCTCTGCC 59.312 57.143 0.00 0.00 0.00 4.85
2162 2226 3.381908 TGAAATGGTTTTGTGCGTAACCT 59.618 39.130 0.00 0.00 43.36 3.50
2164 2228 4.356289 AGTGAAATGGTTTTGTGCGTAAC 58.644 39.130 0.00 0.00 0.00 2.50
2335 2399 7.774625 TGATGAATATGTTGTCAGCAAAGGATA 59.225 33.333 0.00 0.00 37.23 2.59
2379 2443 4.853924 TTTCAGGGTTTCAGCTCAAATC 57.146 40.909 0.00 0.00 0.00 2.17
2498 2563 8.633561 AGCACAAAGAAAGCTATAAAAGAAACT 58.366 29.630 0.00 0.00 36.73 2.66
2655 2723 4.705023 ACAATAGGCACATGGTTTTAGGTC 59.295 41.667 0.00 0.00 0.00 3.85
2664 2732 3.254166 GCCAATAGACAATAGGCACATGG 59.746 47.826 0.00 0.00 44.59 3.66
2702 2770 2.107726 GGTGGAACTAGGGGACAAGTTT 59.892 50.000 0.00 0.00 36.45 2.66
2757 2825 3.233507 ACCAAGTCACAGCATGGAAAAT 58.766 40.909 0.00 0.00 43.62 1.82
2877 2950 6.260050 GTGCATAAAGGCTAGTTACAGCATAA 59.740 38.462 9.66 0.00 43.67 1.90
2879 2952 4.576463 GTGCATAAAGGCTAGTTACAGCAT 59.424 41.667 9.66 0.00 43.67 3.79
2899 2972 0.937304 TTTCTCAACTCAGTGCGTGC 59.063 50.000 0.00 0.00 0.00 5.34
2900 2973 3.673746 TTTTTCTCAACTCAGTGCGTG 57.326 42.857 0.00 0.00 0.00 5.34
2971 3046 6.134535 TGGGACATAGTACAAAGGTGAAAT 57.865 37.500 0.00 0.00 0.00 2.17
3000 3075 6.282167 TGTCAAACATGATTTGCAGTTTCAT 58.718 32.000 0.00 3.14 32.34 2.57
3073 3148 9.013229 TGCAATCATGGTATTATAGAATGGAAC 57.987 33.333 0.00 0.00 0.00 3.62
3116 3353 4.631813 AGTACGAAGCCTTGAATAAAGCAG 59.368 41.667 0.00 0.00 34.24 4.24
3135 3372 5.929992 TGCTGTGTTGACTTTACCATAGTAC 59.070 40.000 0.00 0.00 0.00 2.73
3171 3408 3.391296 TCAAAGATATGGTAGGCAGGGAC 59.609 47.826 0.00 0.00 0.00 4.46
3176 3413 4.907269 TGGAGATCAAAGATATGGTAGGCA 59.093 41.667 0.00 0.00 0.00 4.75
3177 3414 5.221722 TGTGGAGATCAAAGATATGGTAGGC 60.222 44.000 0.00 0.00 0.00 3.93
3224 3462 0.695347 CCTGGGACTCAAGCTCCTTT 59.305 55.000 0.00 0.00 0.00 3.11
3233 3471 2.853542 TTGGCAGCCTGGGACTCA 60.854 61.111 14.15 0.00 0.00 3.41
3313 3551 3.965379 TGTGAATCTAAACCCGCAGTA 57.035 42.857 0.00 0.00 0.00 2.74
3510 3758 4.470462 GCATTATGATTGATCTCAACCGC 58.530 43.478 0.00 0.00 38.86 5.68
3528 3776 5.220662 CCACGACTTAAAGAATGATCGCATT 60.221 40.000 0.00 0.00 47.00 3.56
3539 3787 5.410439 GCCAGATAAAACCACGACTTAAAGA 59.590 40.000 0.00 0.00 0.00 2.52
3544 3792 3.074412 CTGCCAGATAAAACCACGACTT 58.926 45.455 0.00 0.00 0.00 3.01
3545 3793 2.038557 ACTGCCAGATAAAACCACGACT 59.961 45.455 0.00 0.00 0.00 4.18
3548 3796 5.560966 AATTACTGCCAGATAAAACCACG 57.439 39.130 0.00 0.00 0.00 4.94
3613 3861 5.494632 AAAACACCGACTTCCTGTAAAAG 57.505 39.130 0.00 0.00 0.00 2.27
3681 4280 6.267817 AGTTTGTTCAACTTGACATGTGATG 58.732 36.000 1.15 0.00 43.89 3.07
3689 4288 4.336532 ACACGAGTTTGTTCAACTTGAC 57.663 40.909 8.65 0.00 46.53 3.18
3696 4295 1.668751 GGAGCAACACGAGTTTGTTCA 59.331 47.619 0.00 0.00 37.62 3.18
3698 4297 1.021968 GGGAGCAACACGAGTTTGTT 58.978 50.000 0.00 0.00 40.46 2.83
3702 4301 1.981256 AATTGGGAGCAACACGAGTT 58.019 45.000 0.00 0.00 38.88 3.01
3703 4302 1.608590 CAAATTGGGAGCAACACGAGT 59.391 47.619 0.00 0.00 0.00 4.18
3704 4303 1.068333 CCAAATTGGGAGCAACACGAG 60.068 52.381 3.60 0.00 32.67 4.18
3706 4305 0.673437 ACCAAATTGGGAGCAACACG 59.327 50.000 17.27 0.00 43.37 4.49
3707 4306 2.890945 AGTACCAAATTGGGAGCAACAC 59.109 45.455 17.27 0.00 43.37 3.32
3708 4307 3.237268 AGTACCAAATTGGGAGCAACA 57.763 42.857 17.27 0.00 43.37 3.33
3713 4312 8.801882 TGAAAATACTAGTACCAAATTGGGAG 57.198 34.615 17.27 9.95 43.37 4.30
3715 4314 9.408648 AGATGAAAATACTAGTACCAAATTGGG 57.591 33.333 17.27 0.00 43.37 4.12
3745 4344 6.464834 GCAGACAACATAAGTGCGTTATAAAC 59.535 38.462 0.00 0.00 29.54 2.01
3749 4348 4.000325 TGCAGACAACATAAGTGCGTTAT 59.000 39.130 0.00 0.00 36.92 1.89
3753 4352 3.476295 AATGCAGACAACATAAGTGCG 57.524 42.857 0.00 0.00 36.92 5.34
3801 4482 8.231837 GCCTACAGTCGATTTATTTGTTGTAAA 58.768 33.333 0.00 0.00 0.00 2.01
3817 4498 4.304110 TGTAACTTGAAAGCCTACAGTCG 58.696 43.478 2.89 0.00 0.00 4.18
3826 4507 8.810652 TTATTTGTTCCATGTAACTTGAAAGC 57.189 30.769 2.65 0.00 0.00 3.51
3942 4644 1.394618 TTCGGTTGTGGGTTTCCTTG 58.605 50.000 0.00 0.00 0.00 3.61
3945 4647 0.031585 GCTTTCGGTTGTGGGTTTCC 59.968 55.000 0.00 0.00 0.00 3.13
3946 4648 0.031585 GGCTTTCGGTTGTGGGTTTC 59.968 55.000 0.00 0.00 0.00 2.78
4128 4932 0.390866 ATGTTCAGACCAGCTGCGAG 60.391 55.000 8.66 0.00 44.52 5.03
4129 4933 0.035317 AATGTTCAGACCAGCTGCGA 59.965 50.000 8.66 0.00 44.52 5.10
4130 4934 0.445436 GAATGTTCAGACCAGCTGCG 59.555 55.000 8.66 4.27 44.52 5.18
4131 4935 1.527034 TGAATGTTCAGACCAGCTGC 58.473 50.000 8.66 0.00 44.52 5.25
4132 4936 2.096069 CGTTGAATGTTCAGACCAGCTG 60.096 50.000 6.78 6.78 46.31 4.24
4133 4937 2.146342 CGTTGAATGTTCAGACCAGCT 58.854 47.619 0.00 0.00 38.61 4.24
4134 4938 2.143122 TCGTTGAATGTTCAGACCAGC 58.857 47.619 0.00 0.00 38.61 4.85
4135 4939 3.996363 TGATCGTTGAATGTTCAGACCAG 59.004 43.478 0.00 0.00 38.61 4.00
4179 4998 2.550208 GGTTGTTGGTCTGATCGTTCCT 60.550 50.000 0.00 0.00 0.00 3.36
4203 5023 3.785189 ATACCGTCGCATCGCACCC 62.785 63.158 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.