Multiple sequence alignment - TraesCS3A01G092000

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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 TraesCS3A01G092000 chr3A 100.000 3007 0 0 1 3007 57898900 57895894 0.000000e+00 5553
1 TraesCS3A01G092000 chr3D 92.466 1752 86 23 40 1772 46479515 46477791 0.000000e+00 2462
2 TraesCS3A01G092000 chr3D 93.333 885 25 12 2150 3007 46476920 46476043 0.000000e+00 1277
3 TraesCS3A01G092000 chr3B 90.525 1277 75 26 1 1252 72709620 72708365 0.000000e+00 1646
4 TraesCS3A01G092000 chr3B 92.203 885 29 6 2150 3007 72488658 72487787 0.000000e+00 1216
5 TraesCS3A01G092000 chr3B 92.217 424 22 4 1349 1772 72708319 72707907 9.280000e-165 590
6 TraesCS3A01G092000 chr2B 93.108 711 36 2 2256 2954 5489073 5488364 0.000000e+00 1029
7 TraesCS3A01G092000 chr5B 91.586 725 48 9 2242 2954 562419021 562419744 0.000000e+00 989
8 TraesCS3A01G092000 chr1B 88.997 718 66 8 2249 2954 493683691 493682975 0.000000e+00 876
9 TraesCS3A01G092000 chr1B 93.515 293 19 0 2662 2954 8393671 8393379 1.280000e-118 436
10 TraesCS3A01G092000 chr1A 88.187 728 70 2 2242 2969 541158536 541157825 0.000000e+00 854
11 TraesCS3A01G092000 chr4A 88.049 728 74 1 2242 2969 640150234 640149520 0.000000e+00 850
12 TraesCS3A01G092000 chr7B 88.912 487 54 0 2468 2954 432764249 432763763 4.290000e-168 601
13 TraesCS3A01G092000 chr7B 96.250 80 3 0 2257 2336 432764325 432764246 6.760000e-27 132


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 TraesCS3A01G092000 chr3A 57895894 57898900 3006 True 5553.0 5553 100.0000 1 3007 1 chr3A.!!$R1 3006
1 TraesCS3A01G092000 chr3D 46476043 46479515 3472 True 1869.5 2462 92.8995 40 3007 2 chr3D.!!$R1 2967
2 TraesCS3A01G092000 chr3B 72487787 72488658 871 True 1216.0 1216 92.2030 2150 3007 1 chr3B.!!$R1 857
3 TraesCS3A01G092000 chr3B 72707907 72709620 1713 True 1118.0 1646 91.3710 1 1772 2 chr3B.!!$R2 1771
4 TraesCS3A01G092000 chr2B 5488364 5489073 709 True 1029.0 1029 93.1080 2256 2954 1 chr2B.!!$R1 698
5 TraesCS3A01G092000 chr5B 562419021 562419744 723 False 989.0 989 91.5860 2242 2954 1 chr5B.!!$F1 712
6 TraesCS3A01G092000 chr1B 493682975 493683691 716 True 876.0 876 88.9970 2249 2954 1 chr1B.!!$R2 705
7 TraesCS3A01G092000 chr1A 541157825 541158536 711 True 854.0 854 88.1870 2242 2969 1 chr1A.!!$R1 727
8 TraesCS3A01G092000 chr4A 640149520 640150234 714 True 850.0 850 88.0490 2242 2969 1 chr4A.!!$R1 727
9 TraesCS3A01G092000 chr7B 432763763 432764325 562 True 366.5 601 92.5810 2257 2954 2 chr7B.!!$R1 697

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
421 424 0.523072 CCAAACTGCTACGCTGCATT 59.477 50.000 0.00 0.0 42.48 3.56 F
1460 1495 1.080705 GTCACCGGACAAGGAGACG 60.081 63.158 9.46 0.0 43.73 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 1843 0.037303 CACAATCACAGGAGCAGGGT 59.963 55.0 0.0 0.0 0.0 4.34 R
2847 3480 0.039180 TAGCTCGAACACCTCCCAGA 59.961 55.0 0.0 0.0 0.0 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.086765 GTGAACTTACATCAATTTGAGTTGCG 59.913 38.462 5.21 0.00 0.00 4.85
36 37 1.882912 TGAGTTGCGTTTCTCTGCAT 58.117 45.000 0.00 0.00 41.42 3.96
72 73 7.989826 AGAAATAACATGGCACTGAGTTTATC 58.010 34.615 0.00 0.00 0.00 1.75
208 211 4.331968 TGGAAATACATGACACTGGGTTC 58.668 43.478 0.00 0.00 0.00 3.62
210 213 4.764823 GGAAATACATGACACTGGGTTCAA 59.235 41.667 0.00 0.00 0.00 2.69
370 373 8.807948 ATGCTTTTTCTGGTAAAGAATAGCTA 57.192 30.769 16.77 0.00 44.91 3.32
371 374 8.268850 TGCTTTTTCTGGTAAAGAATAGCTAG 57.731 34.615 16.77 0.00 44.91 3.42
372 375 7.148239 TGCTTTTTCTGGTAAAGAATAGCTAGC 60.148 37.037 6.62 6.62 44.91 3.42
373 376 7.066404 GCTTTTTCTGGTAAAGAATAGCTAGCT 59.934 37.037 23.12 23.12 44.46 3.32
421 424 0.523072 CCAAACTGCTACGCTGCATT 59.477 50.000 0.00 0.00 42.48 3.56
422 425 1.466360 CCAAACTGCTACGCTGCATTC 60.466 52.381 0.00 0.00 42.48 2.67
450 455 6.226052 GGATTCCCCATATCAAAATGCTTTC 58.774 40.000 0.00 0.00 34.14 2.62
520 525 2.888834 TCAACCTGGCTTTTCTTTGC 57.111 45.000 0.00 0.00 0.00 3.68
524 529 2.387757 ACCTGGCTTTTCTTTGCTTGA 58.612 42.857 0.00 0.00 0.00 3.02
531 536 4.990426 GGCTTTTCTTTGCTTGATGCTTTA 59.010 37.500 0.00 0.00 43.37 1.85
616 622 3.311596 GCCGCTTTAGTTAACCGATGAAT 59.688 43.478 0.88 0.00 0.00 2.57
717 726 7.843490 CATGAATCTTGATTTTTCATGCCTT 57.157 32.000 10.78 0.00 45.51 4.35
725 734 5.546526 TGATTTTTCATGCCTTTTGTACCC 58.453 37.500 0.00 0.00 0.00 3.69
730 739 4.584638 TCATGCCTTTTGTACCCATAGT 57.415 40.909 0.00 0.00 0.00 2.12
731 740 4.929479 TCATGCCTTTTGTACCCATAGTT 58.071 39.130 0.00 0.00 0.00 2.24
743 752 4.143986 ACCCATAGTTTTCTCTAGCAGC 57.856 45.455 0.00 0.00 0.00 5.25
749 758 3.586892 AGTTTTCTCTAGCAGCGGTAAC 58.413 45.455 0.00 0.00 0.00 2.50
772 781 3.576078 AGTGGAACATGTCTGTTTCCA 57.424 42.857 11.41 11.41 45.57 3.53
773 782 3.480470 AGTGGAACATGTCTGTTTCCAG 58.520 45.455 15.06 0.00 45.57 3.86
826 837 4.320567 GGCAAAGTAACAAGAGGAGAAAGC 60.321 45.833 0.00 0.00 0.00 3.51
831 842 5.486526 AGTAACAAGAGGAGAAAGCTCATG 58.513 41.667 0.00 0.00 43.14 3.07
872 883 6.168389 TCACCCTCTTTCGTTTAGTATTTCC 58.832 40.000 0.00 0.00 0.00 3.13
874 885 6.092259 CACCCTCTTTCGTTTAGTATTTCCAG 59.908 42.308 0.00 0.00 0.00 3.86
884 901 8.472413 TCGTTTAGTATTTCCAGTAATGCTAGT 58.528 33.333 0.00 0.00 35.23 2.57
889 906 7.275920 AGTATTTCCAGTAATGCTAGTTCCTG 58.724 38.462 0.00 0.00 30.12 3.86
893 910 4.530553 TCCAGTAATGCTAGTTCCTGTTGA 59.469 41.667 0.00 0.00 0.00 3.18
915 932 8.979574 GTTGATATCTATTTAAAGACCTGACCG 58.020 37.037 3.98 0.00 0.00 4.79
937 962 2.097825 AGCTGAAACCTCATTGCCATC 58.902 47.619 0.00 0.00 0.00 3.51
972 997 4.099266 TGGTCTGGAAATCAAAAACCTGTG 59.901 41.667 0.00 0.00 0.00 3.66
1122 1149 2.413239 CGTGCTGATCCATGTCAACAAC 60.413 50.000 0.00 0.00 0.00 3.32
1198 1225 1.460689 TCCACCGACAACCCCTCTT 60.461 57.895 0.00 0.00 0.00 2.85
1282 1316 9.265901 TCAAGTTCTATCTATATTTGCTTCTGC 57.734 33.333 0.00 0.00 40.20 4.26
1309 1343 6.984474 AGTTTCGAACTGATGAACAAACTCTA 59.016 34.615 0.00 0.00 41.01 2.43
1312 1346 8.462143 TTCGAACTGATGAACAAACTCTATAC 57.538 34.615 0.00 0.00 0.00 1.47
1315 1349 7.061905 CGAACTGATGAACAAACTCTATACGTT 59.938 37.037 0.00 0.00 0.00 3.99
1316 1350 7.582435 ACTGATGAACAAACTCTATACGTTG 57.418 36.000 0.00 0.00 0.00 4.10
1326 1360 3.128242 ACTCTATACGTTGGTGTTCTCCG 59.872 47.826 0.00 0.00 0.00 4.63
1336 1370 2.289195 TGGTGTTCTCCGTTGTGGTATC 60.289 50.000 0.00 0.00 39.52 2.24
1337 1371 2.289195 GGTGTTCTCCGTTGTGGTATCA 60.289 50.000 0.00 0.00 39.52 2.15
1338 1372 3.395639 GTGTTCTCCGTTGTGGTATCAA 58.604 45.455 0.00 0.00 39.52 2.57
1339 1373 4.000988 GTGTTCTCCGTTGTGGTATCAAT 58.999 43.478 0.00 0.00 39.52 2.57
1340 1374 4.454504 GTGTTCTCCGTTGTGGTATCAATT 59.545 41.667 0.00 0.00 39.52 2.32
1341 1375 5.640357 GTGTTCTCCGTTGTGGTATCAATTA 59.360 40.000 0.00 0.00 39.52 1.40
1342 1376 6.315393 GTGTTCTCCGTTGTGGTATCAATTAT 59.685 38.462 0.00 0.00 39.52 1.28
1343 1377 6.537301 TGTTCTCCGTTGTGGTATCAATTATC 59.463 38.462 0.00 0.00 39.52 1.75
1460 1495 1.080705 GTCACCGGACAAGGAGACG 60.081 63.158 9.46 0.00 43.73 4.18
1535 1575 2.156098 TCCACCCGCAGAATTTTGTAC 58.844 47.619 0.00 0.00 0.00 2.90
1536 1576 1.201414 CCACCCGCAGAATTTTGTACC 59.799 52.381 0.00 0.00 0.00 3.34
1537 1577 1.883275 CACCCGCAGAATTTTGTACCA 59.117 47.619 0.00 0.00 0.00 3.25
1538 1578 2.095263 CACCCGCAGAATTTTGTACCAG 60.095 50.000 0.00 0.00 0.00 4.00
1540 1580 3.244630 ACCCGCAGAATTTTGTACCAGTA 60.245 43.478 0.00 0.00 0.00 2.74
1542 1582 4.398044 CCCGCAGAATTTTGTACCAGTAAT 59.602 41.667 0.00 0.00 0.00 1.89
1543 1583 5.448632 CCCGCAGAATTTTGTACCAGTAATC 60.449 44.000 0.00 0.00 0.00 1.75
1544 1584 5.123186 CCGCAGAATTTTGTACCAGTAATCA 59.877 40.000 0.00 0.00 0.00 2.57
1545 1585 6.183360 CCGCAGAATTTTGTACCAGTAATCAT 60.183 38.462 0.00 0.00 0.00 2.45
1546 1586 7.011950 CCGCAGAATTTTGTACCAGTAATCATA 59.988 37.037 0.00 0.00 0.00 2.15
1586 1626 5.474578 TGTGCTAGATATCATTCCTGTCC 57.525 43.478 5.32 0.00 0.00 4.02
1587 1627 4.021981 TGTGCTAGATATCATTCCTGTCCG 60.022 45.833 5.32 0.00 0.00 4.79
1588 1628 3.056536 TGCTAGATATCATTCCTGTCCGC 60.057 47.826 5.32 0.00 0.00 5.54
1589 1629 3.194542 GCTAGATATCATTCCTGTCCGCT 59.805 47.826 5.32 0.00 0.00 5.52
1590 1630 3.674528 AGATATCATTCCTGTCCGCTG 57.325 47.619 5.32 0.00 0.00 5.18
1591 1631 3.234353 AGATATCATTCCTGTCCGCTGA 58.766 45.455 5.32 0.00 0.00 4.26
1592 1632 3.837146 AGATATCATTCCTGTCCGCTGAT 59.163 43.478 5.32 0.00 0.00 2.90
1626 1666 3.228749 TGTCGTCGAAACTACGTGATTC 58.771 45.455 0.00 0.00 41.08 2.52
1652 1692 4.019231 AGGTTGAGGTCTTTGGGAAGATAC 60.019 45.833 0.00 0.00 43.41 2.24
1732 1772 1.522580 GGTCATCGGAAGCAGAGGC 60.523 63.158 0.00 0.00 41.61 4.70
1779 1819 3.417069 CCCACAGGTTCAGTTGTATGA 57.583 47.619 0.00 0.00 0.00 2.15
1780 1820 3.955471 CCCACAGGTTCAGTTGTATGAT 58.045 45.455 0.00 0.00 0.00 2.45
1781 1821 4.335416 CCCACAGGTTCAGTTGTATGATT 58.665 43.478 0.00 0.00 0.00 2.57
1782 1822 4.396166 CCCACAGGTTCAGTTGTATGATTC 59.604 45.833 0.00 0.00 0.00 2.52
1783 1823 5.248640 CCACAGGTTCAGTTGTATGATTCT 58.751 41.667 0.00 0.00 0.00 2.40
1784 1824 5.707298 CCACAGGTTCAGTTGTATGATTCTT 59.293 40.000 0.00 0.00 0.00 2.52
1785 1825 6.878923 CCACAGGTTCAGTTGTATGATTCTTA 59.121 38.462 0.00 0.00 0.00 2.10
1786 1826 7.390440 CCACAGGTTCAGTTGTATGATTCTTAA 59.610 37.037 0.00 0.00 0.00 1.85
1787 1827 8.950210 CACAGGTTCAGTTGTATGATTCTTAAT 58.050 33.333 0.00 0.00 0.00 1.40
1811 1851 9.542462 AATAAAAGTTAAAGAAAAACCCTGCTC 57.458 29.630 0.00 0.00 0.00 4.26
1812 1852 5.531122 AAGTTAAAGAAAAACCCTGCTCC 57.469 39.130 0.00 0.00 0.00 4.70
1813 1853 4.804597 AGTTAAAGAAAAACCCTGCTCCT 58.195 39.130 0.00 0.00 0.00 3.69
1814 1854 4.584743 AGTTAAAGAAAAACCCTGCTCCTG 59.415 41.667 0.00 0.00 0.00 3.86
1815 1855 2.755952 AAGAAAAACCCTGCTCCTGT 57.244 45.000 0.00 0.00 0.00 4.00
1816 1856 1.986882 AGAAAAACCCTGCTCCTGTG 58.013 50.000 0.00 0.00 0.00 3.66
1817 1857 1.494721 AGAAAAACCCTGCTCCTGTGA 59.505 47.619 0.00 0.00 0.00 3.58
1818 1858 2.108952 AGAAAAACCCTGCTCCTGTGAT 59.891 45.455 0.00 0.00 0.00 3.06
1819 1859 2.683211 AAAACCCTGCTCCTGTGATT 57.317 45.000 0.00 0.00 0.00 2.57
1820 1860 1.915141 AAACCCTGCTCCTGTGATTG 58.085 50.000 0.00 0.00 0.00 2.67
1821 1861 0.773644 AACCCTGCTCCTGTGATTGT 59.226 50.000 0.00 0.00 0.00 2.71
1822 1862 0.037303 ACCCTGCTCCTGTGATTGTG 59.963 55.000 0.00 0.00 0.00 3.33
1823 1863 0.679002 CCCTGCTCCTGTGATTGTGG 60.679 60.000 0.00 0.00 0.00 4.17
1826 1866 0.890542 TGCTCCTGTGATTGTGGCAC 60.891 55.000 11.55 11.55 36.81 5.01
1829 1869 0.602638 TCCTGTGATTGTGGCACGTC 60.603 55.000 13.77 13.84 39.07 4.34
1834 1874 1.964373 GATTGTGGCACGTCCGGTT 60.964 57.895 13.77 0.00 37.80 4.44
1836 1876 2.668185 ATTGTGGCACGTCCGGTTCA 62.668 55.000 13.77 0.00 37.80 3.18
1838 1878 1.079681 GTGGCACGTCCGGTTCATA 60.080 57.895 0.00 0.00 37.80 2.15
1852 1892 3.602483 GGTTCATAGCCGAACTTTACCA 58.398 45.455 10.14 0.00 43.92 3.25
1853 1893 4.196971 GGTTCATAGCCGAACTTTACCAT 58.803 43.478 10.14 0.00 43.92 3.55
1854 1894 4.035208 GGTTCATAGCCGAACTTTACCATG 59.965 45.833 10.14 0.00 43.92 3.66
1866 1907 3.370978 ACTTTACCATGATTTGTCGAGCG 59.629 43.478 0.00 0.00 0.00 5.03
1871 1912 1.014044 ATGATTTGTCGAGCGTGCGT 61.014 50.000 0.00 0.00 0.00 5.24
1872 1913 1.225475 GATTTGTCGAGCGTGCGTG 60.225 57.895 0.00 0.00 0.00 5.34
1879 1920 2.736995 GAGCGTGCGTGCACCTTA 60.737 61.111 18.51 0.00 43.49 2.69
1881 1922 4.445545 GCGTGCGTGCACCTTAGC 62.446 66.667 18.51 12.29 43.49 3.09
1882 1923 2.738521 CGTGCGTGCACCTTAGCT 60.739 61.111 18.51 0.00 43.49 3.32
1883 1924 2.317609 CGTGCGTGCACCTTAGCTT 61.318 57.895 18.51 0.00 43.49 3.74
1884 1925 1.207593 GTGCGTGCACCTTAGCTTG 59.792 57.895 13.90 0.00 40.79 4.01
1885 1926 1.070615 TGCGTGCACCTTAGCTTGA 59.929 52.632 12.15 0.00 34.99 3.02
1886 1927 0.321564 TGCGTGCACCTTAGCTTGAT 60.322 50.000 12.15 0.00 34.99 2.57
1887 1928 0.097674 GCGTGCACCTTAGCTTGATG 59.902 55.000 12.15 0.00 34.99 3.07
1889 1930 1.675714 CGTGCACCTTAGCTTGATGGA 60.676 52.381 12.15 0.00 34.99 3.41
1890 1931 1.740025 GTGCACCTTAGCTTGATGGAC 59.260 52.381 5.22 0.00 34.99 4.02
1892 1933 2.040278 TGCACCTTAGCTTGATGGACTT 59.960 45.455 0.00 0.00 34.99 3.01
1893 1934 2.421424 GCACCTTAGCTTGATGGACTTG 59.579 50.000 0.00 0.00 0.00 3.16
1894 1935 3.869912 GCACCTTAGCTTGATGGACTTGA 60.870 47.826 0.00 0.00 0.00 3.02
1895 1936 4.326826 CACCTTAGCTTGATGGACTTGAA 58.673 43.478 0.00 0.00 0.00 2.69
1896 1937 4.154918 CACCTTAGCTTGATGGACTTGAAC 59.845 45.833 0.00 0.00 0.00 3.18
1897 1938 3.691609 CCTTAGCTTGATGGACTTGAACC 59.308 47.826 0.00 0.00 0.00 3.62
1898 1939 4.566488 CCTTAGCTTGATGGACTTGAACCT 60.566 45.833 0.00 0.00 0.00 3.50
1899 1940 2.787994 AGCTTGATGGACTTGAACCTG 58.212 47.619 0.00 0.00 0.00 4.00
1901 1942 3.327757 AGCTTGATGGACTTGAACCTGTA 59.672 43.478 0.00 0.00 0.00 2.74
1902 1943 3.437049 GCTTGATGGACTTGAACCTGTAC 59.563 47.826 0.00 0.00 0.00 2.90
1903 1944 4.641396 CTTGATGGACTTGAACCTGTACA 58.359 43.478 0.00 0.00 0.00 2.90
1904 1945 4.908601 TGATGGACTTGAACCTGTACAT 57.091 40.909 0.00 0.00 40.13 2.29
1905 1946 4.578871 TGATGGACTTGAACCTGTACATG 58.421 43.478 0.00 0.00 37.81 3.21
1906 1947 4.285775 TGATGGACTTGAACCTGTACATGA 59.714 41.667 0.00 0.00 37.81 3.07
1908 1949 3.244422 TGGACTTGAACCTGTACATGACC 60.244 47.826 0.00 0.00 0.00 4.02
1909 1950 3.244422 GGACTTGAACCTGTACATGACCA 60.244 47.826 0.00 0.00 0.00 4.02
1911 1952 4.326826 ACTTGAACCTGTACATGACCATG 58.673 43.478 0.00 8.34 44.15 3.66
1912 1953 3.348647 TGAACCTGTACATGACCATGG 57.651 47.619 11.19 11.19 42.91 3.66
1913 1954 2.642311 TGAACCTGTACATGACCATGGT 59.358 45.455 19.89 19.89 42.91 3.55
1914 1955 2.787473 ACCTGTACATGACCATGGTG 57.213 50.000 25.52 11.08 42.91 4.17
1915 1956 1.340017 ACCTGTACATGACCATGGTGC 60.340 52.381 25.52 14.46 42.91 5.01
1916 1957 1.382522 CTGTACATGACCATGGTGCC 58.617 55.000 25.52 9.69 42.91 5.01
1917 1958 0.991146 TGTACATGACCATGGTGCCT 59.009 50.000 25.52 3.00 42.91 4.75
1923 1990 1.047002 TGACCATGGTGCCTTTTTGG 58.953 50.000 25.52 0.00 39.35 3.28
1943 2010 4.729918 CTTGGCGGCAGGGCTCTT 62.730 66.667 13.71 0.00 42.84 2.85
1948 2015 4.335647 CGGCAGGGCTCTTGGTGT 62.336 66.667 0.00 0.00 0.00 4.16
1950 2017 2.113986 GCAGGGCTCTTGGTGTGT 59.886 61.111 0.00 0.00 0.00 3.72
1951 2018 1.529244 GCAGGGCTCTTGGTGTGTT 60.529 57.895 0.00 0.00 0.00 3.32
1954 2021 2.617274 GGGCTCTTGGTGTGTTCGC 61.617 63.158 0.00 0.00 0.00 4.70
1955 2022 2.617274 GGCTCTTGGTGTGTTCGCC 61.617 63.158 0.00 0.00 43.87 5.54
1956 2023 2.617274 GCTCTTGGTGTGTTCGCCC 61.617 63.158 0.00 0.00 43.03 6.13
1970 2037 2.740826 GCCCGCGTCTGCTTTGTA 60.741 61.111 4.92 0.00 39.65 2.41
1971 2038 2.106683 GCCCGCGTCTGCTTTGTAT 61.107 57.895 4.92 0.00 39.65 2.29
1972 2039 1.644786 GCCCGCGTCTGCTTTGTATT 61.645 55.000 4.92 0.00 39.65 1.89
1974 2041 1.359848 CCGCGTCTGCTTTGTATTCT 58.640 50.000 4.92 0.00 39.65 2.40
1975 2042 1.324736 CCGCGTCTGCTTTGTATTCTC 59.675 52.381 4.92 0.00 39.65 2.87
1976 2043 1.992667 CGCGTCTGCTTTGTATTCTCA 59.007 47.619 0.00 0.00 39.65 3.27
1977 2044 2.222596 CGCGTCTGCTTTGTATTCTCAC 60.223 50.000 0.00 0.00 39.65 3.51
1978 2045 2.736721 GCGTCTGCTTTGTATTCTCACA 59.263 45.455 0.00 0.00 38.39 3.58
1980 2047 4.237724 CGTCTGCTTTGTATTCTCACAGA 58.762 43.478 0.00 0.00 0.00 3.41
1981 2048 4.867047 CGTCTGCTTTGTATTCTCACAGAT 59.133 41.667 0.00 0.00 35.37 2.90
1982 2049 6.036470 CGTCTGCTTTGTATTCTCACAGATA 58.964 40.000 0.00 0.00 35.37 1.98
1983 2050 6.020281 CGTCTGCTTTGTATTCTCACAGATAC 60.020 42.308 0.00 0.00 35.37 2.24
1984 2051 7.038659 GTCTGCTTTGTATTCTCACAGATACT 58.961 38.462 0.00 0.00 35.37 2.12
2002 2281 9.712305 ACAGATACTATATTTCATAGCAACACC 57.288 33.333 0.00 0.00 0.00 4.16
2003 2282 9.710900 CAGATACTATATTTCATAGCAACACCA 57.289 33.333 0.00 0.00 0.00 4.17
2007 2286 8.383318 ACTATATTTCATAGCAACACCATGAC 57.617 34.615 0.00 0.00 0.00 3.06
2012 2291 4.334552 TCATAGCAACACCATGACATTGT 58.665 39.130 0.00 0.00 0.00 2.71
2017 2296 3.119849 GCAACACCATGACATTGTACTCC 60.120 47.826 0.00 0.00 0.00 3.85
2021 2300 4.000325 CACCATGACATTGTACTCCGAAA 59.000 43.478 0.00 0.00 0.00 3.46
2022 2301 4.635765 CACCATGACATTGTACTCCGAAAT 59.364 41.667 0.00 0.00 0.00 2.17
2024 2303 5.710099 ACCATGACATTGTACTCCGAAATTT 59.290 36.000 0.00 0.00 0.00 1.82
2025 2304 6.882140 ACCATGACATTGTACTCCGAAATTTA 59.118 34.615 0.00 0.00 0.00 1.40
2026 2305 7.148306 ACCATGACATTGTACTCCGAAATTTAC 60.148 37.037 0.00 0.00 0.00 2.01
2027 2306 7.065803 CCATGACATTGTACTCCGAAATTTACT 59.934 37.037 0.00 0.00 0.00 2.24
2028 2307 7.972832 TGACATTGTACTCCGAAATTTACTT 57.027 32.000 0.00 0.00 0.00 2.24
2029 2308 7.802738 TGACATTGTACTCCGAAATTTACTTG 58.197 34.615 0.00 0.00 0.00 3.16
2030 2309 7.094975 TGACATTGTACTCCGAAATTTACTTGG 60.095 37.037 0.00 0.00 0.00 3.61
2031 2310 6.938030 ACATTGTACTCCGAAATTTACTTGGA 59.062 34.615 0.00 0.00 0.00 3.53
2032 2311 7.446013 ACATTGTACTCCGAAATTTACTTGGAA 59.554 33.333 0.00 0.00 0.00 3.53
2033 2312 7.429636 TTGTACTCCGAAATTTACTTGGAAG 57.570 36.000 0.00 0.00 0.00 3.46
2034 2313 5.410439 TGTACTCCGAAATTTACTTGGAAGC 59.590 40.000 0.00 0.00 0.00 3.86
2035 2314 4.652822 ACTCCGAAATTTACTTGGAAGCT 58.347 39.130 0.00 0.00 0.00 3.74
2036 2315 5.801380 ACTCCGAAATTTACTTGGAAGCTA 58.199 37.500 0.00 0.00 0.00 3.32
2037 2316 6.415573 ACTCCGAAATTTACTTGGAAGCTAT 58.584 36.000 0.00 0.00 0.00 2.97
2038 2317 6.316390 ACTCCGAAATTTACTTGGAAGCTATG 59.684 38.462 0.00 0.00 0.00 2.23
2039 2318 6.411376 TCCGAAATTTACTTGGAAGCTATGA 58.589 36.000 0.00 0.00 0.00 2.15
2040 2319 7.054124 TCCGAAATTTACTTGGAAGCTATGAT 58.946 34.615 0.00 0.00 0.00 2.45
2041 2320 7.012327 TCCGAAATTTACTTGGAAGCTATGATG 59.988 37.037 0.00 0.00 0.00 3.07
2049 2328 9.679661 TTACTTGGAAGCTATGATGAAATTACA 57.320 29.630 0.00 0.00 0.00 2.41
2050 2329 8.579850 ACTTGGAAGCTATGATGAAATTACAA 57.420 30.769 0.00 0.00 0.00 2.41
2087 2658 4.832248 TGGAATGTGGAGTGTAGTTCATC 58.168 43.478 0.00 0.00 0.00 2.92
2088 2659 4.285775 TGGAATGTGGAGTGTAGTTCATCA 59.714 41.667 0.00 0.00 0.00 3.07
2089 2660 5.045651 TGGAATGTGGAGTGTAGTTCATCAT 60.046 40.000 0.00 0.00 0.00 2.45
2091 2662 6.703607 GGAATGTGGAGTGTAGTTCATCATAG 59.296 42.308 0.00 0.00 0.00 2.23
2092 2663 5.011090 TGTGGAGTGTAGTTCATCATAGC 57.989 43.478 0.00 0.00 0.00 2.97
2093 2664 4.466015 TGTGGAGTGTAGTTCATCATAGCA 59.534 41.667 0.00 0.00 0.00 3.49
2094 2665 5.046663 TGTGGAGTGTAGTTCATCATAGCAA 60.047 40.000 0.00 0.00 0.00 3.91
2095 2666 5.874810 GTGGAGTGTAGTTCATCATAGCAAA 59.125 40.000 0.00 0.00 0.00 3.68
2096 2667 5.874810 TGGAGTGTAGTTCATCATAGCAAAC 59.125 40.000 0.00 0.00 0.00 2.93
2097 2668 5.874810 GGAGTGTAGTTCATCATAGCAAACA 59.125 40.000 0.00 0.00 0.00 2.83
2098 2669 6.183360 GGAGTGTAGTTCATCATAGCAAACAC 60.183 42.308 0.00 0.00 35.97 3.32
2099 2670 6.467677 AGTGTAGTTCATCATAGCAAACACT 58.532 36.000 0.00 0.00 39.97 3.55
2101 2672 5.643348 TGTAGTTCATCATAGCAAACACTGG 59.357 40.000 0.00 0.00 0.00 4.00
2102 2673 4.012374 AGTTCATCATAGCAAACACTGGG 58.988 43.478 0.00 0.00 0.00 4.45
2104 2675 4.032960 TCATCATAGCAAACACTGGGTT 57.967 40.909 0.00 0.00 42.98 4.11
2112 2683 3.758715 AACACTGGGTTTTTGCAGC 57.241 47.368 0.00 0.00 35.82 5.25
2117 2688 0.881600 CTGGGTTTTTGCAGCTTGCC 60.882 55.000 5.82 0.00 44.23 4.52
2123 2694 1.427592 TTTTGCAGCTTGCCGTTTGC 61.428 50.000 5.82 0.00 44.23 3.68
2131 2702 1.067915 GCTTGCCGTTTGCCATCTTAA 60.068 47.619 0.00 0.00 40.16 1.85
2141 2712 5.007234 CGTTTGCCATCTTAATCGTCCATTA 59.993 40.000 0.00 0.00 0.00 1.90
2142 2713 6.199393 GTTTGCCATCTTAATCGTCCATTAC 58.801 40.000 0.00 0.00 0.00 1.89
2143 2714 5.290493 TGCCATCTTAATCGTCCATTACT 57.710 39.130 0.00 0.00 0.00 2.24
2145 2716 5.527214 TGCCATCTTAATCGTCCATTACTTG 59.473 40.000 0.00 0.00 0.00 3.16
2146 2717 5.758296 GCCATCTTAATCGTCCATTACTTGA 59.242 40.000 0.00 0.00 0.00 3.02
2147 2718 6.428159 GCCATCTTAATCGTCCATTACTTGAT 59.572 38.462 0.00 0.00 0.00 2.57
2148 2719 7.360438 GCCATCTTAATCGTCCATTACTTGATC 60.360 40.741 0.00 0.00 0.00 2.92
2160 2766 1.741401 CTTGATCGGTGCCGCTTCA 60.741 57.895 5.64 8.60 39.59 3.02
2219 2825 1.391577 TTCATTCGATGGCCACATGG 58.608 50.000 8.16 0.00 37.47 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 6.317140 CACAGATAAACTCAGTGCCATGTTAT 59.683 38.462 0.00 0.00 35.02 1.89
72 73 5.919272 AACAGAATGATCGCATATCACAG 57.081 39.130 1.06 0.00 39.69 3.66
208 211 8.405418 ACAGAATGATCTTCATATCCCAATTG 57.595 34.615 0.00 0.00 39.69 2.32
235 238 7.806180 AGAGGCCTTGTTACATCATAAGTAAT 58.194 34.615 6.77 0.00 34.34 1.89
348 351 8.394121 CAGCTAGCTATTCTTTACCAGAAAAAG 58.606 37.037 18.86 0.00 45.06 2.27
421 424 4.991789 TTTGATATGGGGAATCCGATGA 57.008 40.909 0.00 0.00 38.76 2.92
422 425 5.622914 GCATTTTGATATGGGGAATCCGATG 60.623 44.000 0.00 0.00 38.76 3.84
450 455 9.731819 CTTCCAATACAGATGAAATGAAAGATG 57.268 33.333 0.00 0.00 0.00 2.90
520 525 6.981762 ACTGATTCTCACTAAAGCATCAAG 57.018 37.500 0.00 0.00 30.28 3.02
524 529 8.671921 CATGTAAACTGATTCTCACTAAAGCAT 58.328 33.333 0.00 0.00 0.00 3.79
531 536 9.512588 AAATTCTCATGTAAACTGATTCTCACT 57.487 29.630 0.00 0.00 0.00 3.41
550 555 7.066404 GGTATGGACAAGAGGAAAGAAATTCTC 59.934 40.741 0.00 0.00 38.18 2.87
717 726 7.011499 TGCTAGAGAAAACTATGGGTACAAA 57.989 36.000 0.00 0.00 0.00 2.83
725 734 3.786635 ACCGCTGCTAGAGAAAACTATG 58.213 45.455 0.00 0.00 0.00 2.23
730 739 2.300723 TGGTTACCGCTGCTAGAGAAAA 59.699 45.455 0.00 0.00 0.00 2.29
731 740 1.897133 TGGTTACCGCTGCTAGAGAAA 59.103 47.619 0.00 0.00 0.00 2.52
743 752 2.482721 GACATGTTCCACTTGGTTACCG 59.517 50.000 0.00 0.00 36.34 4.02
872 883 8.147058 AGATATCAACAGGAACTAGCATTACTG 58.853 37.037 5.32 4.19 44.89 2.74
889 906 8.979574 CGGTCAGGTCTTTAAATAGATATCAAC 58.020 37.037 5.32 0.00 0.00 3.18
893 910 7.062749 TGCGGTCAGGTCTTTAAATAGATAT 57.937 36.000 0.00 0.00 0.00 1.63
915 932 0.108945 GGCAATGAGGTTTCAGCTGC 60.109 55.000 9.47 0.00 41.74 5.25
937 962 0.732880 CCAGACCAGTGCGTCTAACG 60.733 60.000 12.23 0.00 41.23 3.18
972 997 4.858935 TGCAAAGCTCAGATAAACACAAC 58.141 39.130 0.00 0.00 0.00 3.32
1122 1149 2.768527 TCCTTGCTCATTCTGGTAGGAG 59.231 50.000 0.00 0.00 0.00 3.69
1198 1225 5.553123 ACAGATTCCAATACACGGTAAACA 58.447 37.500 0.00 0.00 0.00 2.83
1273 1307 1.333619 GTTCGAAACTGGCAGAAGCAA 59.666 47.619 23.66 4.10 44.61 3.91
1305 1339 3.128242 ACGGAGAACACCAACGTATAGAG 59.872 47.826 0.00 0.00 35.85 2.43
1309 1343 2.224113 ACAACGGAGAACACCAACGTAT 60.224 45.455 0.00 0.00 36.69 3.06
1312 1346 0.303493 CACAACGGAGAACACCAACG 59.697 55.000 0.00 0.00 0.00 4.10
1315 1349 1.121378 TACCACAACGGAGAACACCA 58.879 50.000 0.00 0.00 38.63 4.17
1316 1350 2.289195 TGATACCACAACGGAGAACACC 60.289 50.000 0.00 0.00 38.63 4.16
1336 1370 9.806203 TTCAGAAGCATGGTAATTTGATAATTG 57.194 29.630 0.00 0.00 35.61 2.32
1339 1373 9.806203 CATTTCAGAAGCATGGTAATTTGATAA 57.194 29.630 0.00 0.00 0.00 1.75
1340 1374 8.415553 CCATTTCAGAAGCATGGTAATTTGATA 58.584 33.333 0.00 0.00 33.90 2.15
1341 1375 7.270047 CCATTTCAGAAGCATGGTAATTTGAT 58.730 34.615 0.00 0.00 33.90 2.57
1342 1376 6.632909 CCATTTCAGAAGCATGGTAATTTGA 58.367 36.000 0.00 0.00 33.90 2.69
1343 1377 5.292589 GCCATTTCAGAAGCATGGTAATTTG 59.707 40.000 13.36 0.00 39.88 2.32
1460 1495 2.621517 CTTGGGCCAGGATCTCCAGC 62.622 65.000 10.68 1.06 38.89 4.85
1519 1559 2.159382 ACTGGTACAAAATTCTGCGGG 58.841 47.619 0.00 0.00 38.70 6.13
1522 1562 9.503427 GTTATGATTACTGGTACAAAATTCTGC 57.497 33.333 0.00 0.00 38.70 4.26
1535 1575 8.915057 ATTTGATCAGGAGTTATGATTACTGG 57.085 34.615 0.00 0.00 37.52 4.00
1537 1577 9.566432 GGAATTTGATCAGGAGTTATGATTACT 57.434 33.333 0.00 0.00 37.52 2.24
1538 1578 9.566432 AGGAATTTGATCAGGAGTTATGATTAC 57.434 33.333 0.00 0.00 37.52 1.89
1540 1580 8.057623 ACAGGAATTTGATCAGGAGTTATGATT 58.942 33.333 0.00 0.00 37.52 2.57
1542 1582 6.825213 CACAGGAATTTGATCAGGAGTTATGA 59.175 38.462 0.00 0.00 0.00 2.15
1543 1583 6.459298 GCACAGGAATTTGATCAGGAGTTATG 60.459 42.308 0.00 0.00 0.00 1.90
1544 1584 5.591877 GCACAGGAATTTGATCAGGAGTTAT 59.408 40.000 0.00 0.00 0.00 1.89
1545 1585 4.943705 GCACAGGAATTTGATCAGGAGTTA 59.056 41.667 0.00 0.00 0.00 2.24
1546 1586 3.760684 GCACAGGAATTTGATCAGGAGTT 59.239 43.478 0.00 0.00 0.00 3.01
1587 1627 3.727079 CGACAAGACAATCAGCAATCAGC 60.727 47.826 0.00 0.00 46.19 4.26
1588 1628 3.434641 ACGACAAGACAATCAGCAATCAG 59.565 43.478 0.00 0.00 0.00 2.90
1589 1629 3.402110 ACGACAAGACAATCAGCAATCA 58.598 40.909 0.00 0.00 0.00 2.57
1590 1630 3.482598 CGACGACAAGACAATCAGCAATC 60.483 47.826 0.00 0.00 0.00 2.67
1591 1631 2.413112 CGACGACAAGACAATCAGCAAT 59.587 45.455 0.00 0.00 0.00 3.56
1592 1632 1.792367 CGACGACAAGACAATCAGCAA 59.208 47.619 0.00 0.00 0.00 3.91
1626 1666 1.237285 CCCAAAGACCTCAACCTGCG 61.237 60.000 0.00 0.00 0.00 5.18
1652 1692 3.885521 GGTCGGGTCGCCGTAGAG 61.886 72.222 1.33 0.00 34.52 2.43
1681 1721 1.816863 GAACCAGGTCGACTGCCTCA 61.817 60.000 16.46 0.00 46.14 3.86
1760 1800 5.248640 AGAATCATACAACTGAACCTGTGG 58.751 41.667 0.00 0.00 0.00 4.17
1785 1825 9.542462 GAGCAGGGTTTTTCTTTAACTTTTATT 57.458 29.630 0.00 0.00 0.00 1.40
1786 1826 8.148351 GGAGCAGGGTTTTTCTTTAACTTTTAT 58.852 33.333 0.00 0.00 0.00 1.40
1787 1827 7.343574 AGGAGCAGGGTTTTTCTTTAACTTTTA 59.656 33.333 0.00 0.00 0.00 1.52
1788 1828 6.156256 AGGAGCAGGGTTTTTCTTTAACTTTT 59.844 34.615 0.00 0.00 0.00 2.27
1789 1829 5.661312 AGGAGCAGGGTTTTTCTTTAACTTT 59.339 36.000 0.00 0.00 0.00 2.66
1790 1830 5.069119 CAGGAGCAGGGTTTTTCTTTAACTT 59.931 40.000 0.00 0.00 0.00 2.66
1791 1831 4.584743 CAGGAGCAGGGTTTTTCTTTAACT 59.415 41.667 0.00 0.00 0.00 2.24
1792 1832 4.341235 ACAGGAGCAGGGTTTTTCTTTAAC 59.659 41.667 0.00 0.00 0.00 2.01
1793 1833 4.340950 CACAGGAGCAGGGTTTTTCTTTAA 59.659 41.667 0.00 0.00 0.00 1.52
1794 1834 3.888930 CACAGGAGCAGGGTTTTTCTTTA 59.111 43.478 0.00 0.00 0.00 1.85
1795 1835 2.695147 CACAGGAGCAGGGTTTTTCTTT 59.305 45.455 0.00 0.00 0.00 2.52
1796 1836 2.091885 TCACAGGAGCAGGGTTTTTCTT 60.092 45.455 0.00 0.00 0.00 2.52
1797 1837 1.494721 TCACAGGAGCAGGGTTTTTCT 59.505 47.619 0.00 0.00 0.00 2.52
1798 1838 1.981256 TCACAGGAGCAGGGTTTTTC 58.019 50.000 0.00 0.00 0.00 2.29
1799 1839 2.629617 CAATCACAGGAGCAGGGTTTTT 59.370 45.455 0.00 0.00 0.00 1.94
1800 1840 2.242043 CAATCACAGGAGCAGGGTTTT 58.758 47.619 0.00 0.00 0.00 2.43
1801 1841 1.145738 ACAATCACAGGAGCAGGGTTT 59.854 47.619 0.00 0.00 0.00 3.27
1802 1842 0.773644 ACAATCACAGGAGCAGGGTT 59.226 50.000 0.00 0.00 0.00 4.11
1803 1843 0.037303 CACAATCACAGGAGCAGGGT 59.963 55.000 0.00 0.00 0.00 4.34
1804 1844 0.679002 CCACAATCACAGGAGCAGGG 60.679 60.000 0.00 0.00 0.00 4.45
1805 1845 1.310933 GCCACAATCACAGGAGCAGG 61.311 60.000 0.00 0.00 0.00 4.85
1806 1846 0.607217 TGCCACAATCACAGGAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
1807 1847 0.890542 GTGCCACAATCACAGGAGCA 60.891 55.000 0.00 0.00 34.73 4.26
1808 1848 1.878775 GTGCCACAATCACAGGAGC 59.121 57.895 0.00 0.00 34.73 4.70
1809 1849 0.603707 ACGTGCCACAATCACAGGAG 60.604 55.000 0.00 0.00 34.27 3.69
1810 1850 0.602638 GACGTGCCACAATCACAGGA 60.603 55.000 0.00 0.00 34.27 3.86
1811 1851 1.577328 GGACGTGCCACAATCACAGG 61.577 60.000 0.00 0.00 36.34 4.00
1812 1852 1.868997 GGACGTGCCACAATCACAG 59.131 57.895 0.00 0.00 36.34 3.66
1813 1853 1.958715 CGGACGTGCCACAATCACA 60.959 57.895 0.00 0.00 35.94 3.58
1814 1854 2.677003 CCGGACGTGCCACAATCAC 61.677 63.158 0.00 0.00 35.94 3.06
1815 1855 2.358125 CCGGACGTGCCACAATCA 60.358 61.111 0.00 0.00 35.94 2.57
1816 1856 1.908066 GAACCGGACGTGCCACAATC 61.908 60.000 9.46 0.00 35.94 2.67
1817 1857 1.964373 GAACCGGACGTGCCACAAT 60.964 57.895 9.46 0.00 35.94 2.71
1818 1858 2.589442 GAACCGGACGTGCCACAA 60.589 61.111 9.46 0.00 35.94 3.33
1819 1859 1.817911 TATGAACCGGACGTGCCACA 61.818 55.000 9.46 0.00 35.94 4.17
1820 1860 1.079681 TATGAACCGGACGTGCCAC 60.080 57.895 9.46 0.00 35.94 5.01
1821 1861 1.216977 CTATGAACCGGACGTGCCA 59.783 57.895 9.46 0.00 35.94 4.92
1822 1862 2.171725 GCTATGAACCGGACGTGCC 61.172 63.158 9.46 0.00 0.00 5.01
1823 1863 2.171725 GGCTATGAACCGGACGTGC 61.172 63.158 9.46 0.00 0.00 5.34
1834 1874 4.746535 TCATGGTAAAGTTCGGCTATGA 57.253 40.909 0.00 0.00 0.00 2.15
1836 1876 5.885912 ACAAATCATGGTAAAGTTCGGCTAT 59.114 36.000 0.00 0.00 0.00 2.97
1838 1878 4.079253 ACAAATCATGGTAAAGTTCGGCT 58.921 39.130 0.00 0.00 0.00 5.52
1852 1892 1.014044 ACGCACGCTCGACAAATCAT 61.014 50.000 3.88 0.00 0.00 2.45
1853 1893 1.663388 ACGCACGCTCGACAAATCA 60.663 52.632 3.88 0.00 0.00 2.57
1854 1894 1.225475 CACGCACGCTCGACAAATC 60.225 57.895 3.88 0.00 0.00 2.17
1866 1907 1.207593 CAAGCTAAGGTGCACGCAC 59.792 57.895 13.78 13.78 45.49 5.34
1871 1912 1.630369 AGTCCATCAAGCTAAGGTGCA 59.370 47.619 0.00 0.00 34.99 4.57
1872 1913 2.409948 AGTCCATCAAGCTAAGGTGC 57.590 50.000 0.00 0.00 0.00 5.01
1874 1915 4.327680 GTTCAAGTCCATCAAGCTAAGGT 58.672 43.478 0.00 0.00 0.00 3.50
1875 1916 3.691609 GGTTCAAGTCCATCAAGCTAAGG 59.308 47.826 0.00 0.00 0.00 2.69
1876 1917 4.394300 CAGGTTCAAGTCCATCAAGCTAAG 59.606 45.833 0.00 0.00 0.00 2.18
1877 1918 4.202461 ACAGGTTCAAGTCCATCAAGCTAA 60.202 41.667 0.00 0.00 0.00 3.09
1878 1919 3.327757 ACAGGTTCAAGTCCATCAAGCTA 59.672 43.478 0.00 0.00 0.00 3.32
1879 1920 2.107204 ACAGGTTCAAGTCCATCAAGCT 59.893 45.455 0.00 0.00 0.00 3.74
1881 1922 4.641396 TGTACAGGTTCAAGTCCATCAAG 58.359 43.478 0.00 0.00 0.00 3.02
1882 1923 4.698201 TGTACAGGTTCAAGTCCATCAA 57.302 40.909 0.00 0.00 0.00 2.57
1883 1924 4.285775 TCATGTACAGGTTCAAGTCCATCA 59.714 41.667 7.49 0.00 0.00 3.07
1884 1925 4.631813 GTCATGTACAGGTTCAAGTCCATC 59.368 45.833 7.49 0.00 0.00 3.51
1885 1926 4.565652 GGTCATGTACAGGTTCAAGTCCAT 60.566 45.833 7.49 0.00 0.00 3.41
1886 1927 3.244422 GGTCATGTACAGGTTCAAGTCCA 60.244 47.826 7.49 0.00 0.00 4.02
1887 1928 3.244422 TGGTCATGTACAGGTTCAAGTCC 60.244 47.826 7.49 1.75 0.00 3.85
1889 1930 4.326826 CATGGTCATGTACAGGTTCAAGT 58.673 43.478 7.49 0.00 34.23 3.16
1890 1931 3.691118 CCATGGTCATGTACAGGTTCAAG 59.309 47.826 7.49 4.63 37.11 3.02
1892 1933 2.642311 ACCATGGTCATGTACAGGTTCA 59.358 45.455 13.00 7.59 37.11 3.18
1893 1934 3.009723 CACCATGGTCATGTACAGGTTC 58.990 50.000 16.53 2.52 37.11 3.62
1894 1935 2.879756 GCACCATGGTCATGTACAGGTT 60.880 50.000 16.53 0.00 37.11 3.50
1895 1936 1.340017 GCACCATGGTCATGTACAGGT 60.340 52.381 16.53 0.96 37.11 4.00
1896 1937 1.382522 GCACCATGGTCATGTACAGG 58.617 55.000 16.53 0.00 37.11 4.00
1897 1938 1.065199 AGGCACCATGGTCATGTACAG 60.065 52.381 16.53 1.82 37.11 2.74
1898 1939 0.991146 AGGCACCATGGTCATGTACA 59.009 50.000 16.53 0.00 37.11 2.90
1899 1940 2.128771 AAGGCACCATGGTCATGTAC 57.871 50.000 16.53 1.61 37.11 2.90
1901 1942 2.014010 AAAAGGCACCATGGTCATGT 57.986 45.000 16.53 0.00 37.11 3.21
1902 1943 2.613474 CCAAAAAGGCACCATGGTCATG 60.613 50.000 16.53 5.29 38.51 3.07
1903 1944 1.624813 CCAAAAAGGCACCATGGTCAT 59.375 47.619 16.53 4.97 0.00 3.06
1904 1945 1.047002 CCAAAAAGGCACCATGGTCA 58.953 50.000 16.53 0.00 0.00 4.02
1905 1946 1.047801 ACCAAAAAGGCACCATGGTC 58.952 50.000 16.53 10.07 40.23 4.02
1906 1947 1.416030 GAACCAAAAAGGCACCATGGT 59.584 47.619 13.00 13.00 45.97 3.55
1908 1949 3.132925 CAAGAACCAAAAAGGCACCATG 58.867 45.455 0.00 0.00 43.14 3.66
1909 1950 2.104622 CCAAGAACCAAAAAGGCACCAT 59.895 45.455 0.00 0.00 43.14 3.55
1911 1952 1.810031 GCCAAGAACCAAAAAGGCACC 60.810 52.381 0.00 0.00 43.14 5.01
1912 1953 1.581934 GCCAAGAACCAAAAAGGCAC 58.418 50.000 0.00 0.00 43.14 5.01
1913 1954 0.103937 CGCCAAGAACCAAAAAGGCA 59.896 50.000 0.00 0.00 42.10 4.75
1914 1955 0.599991 CCGCCAAGAACCAAAAAGGC 60.600 55.000 0.00 0.00 43.14 4.35
1915 1956 0.599991 GCCGCCAAGAACCAAAAAGG 60.600 55.000 0.00 0.00 45.67 3.11
1916 1957 0.103937 TGCCGCCAAGAACCAAAAAG 59.896 50.000 0.00 0.00 0.00 2.27
1917 1958 0.103937 CTGCCGCCAAGAACCAAAAA 59.896 50.000 0.00 0.00 0.00 1.94
1950 2017 4.980805 AAAGCAGACGCGGGCGAA 62.981 61.111 20.98 0.00 45.49 4.70
1954 2021 0.373716 GAATACAAAGCAGACGCGGG 59.626 55.000 12.47 0.00 45.49 6.13
1955 2022 1.324736 GAGAATACAAAGCAGACGCGG 59.675 52.381 12.47 0.00 45.49 6.46
1956 2023 1.992667 TGAGAATACAAAGCAGACGCG 59.007 47.619 3.53 3.53 45.49 6.01
1959 2026 7.038659 AGTATCTGTGAGAATACAAAGCAGAC 58.961 38.462 0.00 0.00 34.87 3.51
1960 2027 7.175347 AGTATCTGTGAGAATACAAAGCAGA 57.825 36.000 0.00 0.00 36.21 4.26
1976 2043 9.712305 GGTGTTGCTATGAAATATAGTATCTGT 57.288 33.333 0.00 0.00 0.00 3.41
1977 2044 9.710900 TGGTGTTGCTATGAAATATAGTATCTG 57.289 33.333 0.00 0.00 0.00 2.90
1981 2048 9.489084 GTCATGGTGTTGCTATGAAATATAGTA 57.511 33.333 0.00 0.00 44.80 1.82
1982 2049 7.992608 TGTCATGGTGTTGCTATGAAATATAGT 59.007 33.333 0.00 0.00 44.80 2.12
1983 2050 8.382030 TGTCATGGTGTTGCTATGAAATATAG 57.618 34.615 0.00 0.00 44.80 1.31
1984 2051 8.922931 ATGTCATGGTGTTGCTATGAAATATA 57.077 30.769 0.00 0.00 44.80 0.86
1988 2267 5.243507 ACAATGTCATGGTGTTGCTATGAAA 59.756 36.000 0.00 0.00 44.80 2.69
1993 2272 4.905429 AGTACAATGTCATGGTGTTGCTA 58.095 39.130 2.83 0.00 0.00 3.49
1995 2274 3.119849 GGAGTACAATGTCATGGTGTTGC 60.120 47.826 2.83 0.00 0.00 4.17
1999 2278 3.245518 TCGGAGTACAATGTCATGGTG 57.754 47.619 2.83 0.00 0.00 4.17
2002 2281 7.974675 AGTAAATTTCGGAGTACAATGTCATG 58.025 34.615 0.00 0.00 0.00 3.07
2003 2282 8.450964 CAAGTAAATTTCGGAGTACAATGTCAT 58.549 33.333 0.00 0.00 0.00 3.06
2005 2284 7.118680 TCCAAGTAAATTTCGGAGTACAATGTC 59.881 37.037 0.00 0.00 0.00 3.06
2006 2285 6.938030 TCCAAGTAAATTTCGGAGTACAATGT 59.062 34.615 0.00 0.00 0.00 2.71
2007 2286 7.372451 TCCAAGTAAATTTCGGAGTACAATG 57.628 36.000 0.00 0.00 0.00 2.82
2012 2291 5.801380 AGCTTCCAAGTAAATTTCGGAGTA 58.199 37.500 0.00 0.00 0.00 2.59
2017 2296 7.919690 TCATCATAGCTTCCAAGTAAATTTCG 58.080 34.615 0.00 0.00 0.00 3.46
2024 2303 9.679661 TTGTAATTTCATCATAGCTTCCAAGTA 57.320 29.630 0.00 0.00 0.00 2.24
2025 2304 8.579850 TTGTAATTTCATCATAGCTTCCAAGT 57.420 30.769 0.00 0.00 0.00 3.16
2026 2305 8.896744 TCTTGTAATTTCATCATAGCTTCCAAG 58.103 33.333 0.00 0.00 0.00 3.61
2027 2306 8.806429 TCTTGTAATTTCATCATAGCTTCCAA 57.194 30.769 0.00 0.00 0.00 3.53
2028 2307 8.806429 TTCTTGTAATTTCATCATAGCTTCCA 57.194 30.769 0.00 0.00 0.00 3.53
2049 2328 7.888021 TCCACATTCCATGTACAGTATTTTCTT 59.112 33.333 0.33 0.00 42.70 2.52
2050 2329 7.402054 TCCACATTCCATGTACAGTATTTTCT 58.598 34.615 0.33 0.00 42.70 2.52
2055 2334 5.189736 ACACTCCACATTCCATGTACAGTAT 59.810 40.000 0.33 0.00 42.70 2.12
2059 2338 4.530553 ACTACACTCCACATTCCATGTACA 59.469 41.667 0.00 0.00 42.70 2.90
2060 2339 5.086104 ACTACACTCCACATTCCATGTAC 57.914 43.478 0.00 0.00 42.70 2.90
2061 2340 5.247337 TGAACTACACTCCACATTCCATGTA 59.753 40.000 0.00 0.00 42.70 2.29
2063 2342 4.578871 TGAACTACACTCCACATTCCATG 58.421 43.478 0.00 0.00 0.00 3.66
2065 2344 4.285775 TGATGAACTACACTCCACATTCCA 59.714 41.667 0.00 0.00 0.00 3.53
2066 2345 4.832248 TGATGAACTACACTCCACATTCC 58.168 43.478 0.00 0.00 0.00 3.01
2068 2347 6.051717 GCTATGATGAACTACACTCCACATT 58.948 40.000 0.00 0.00 0.00 2.71
2069 2348 5.129320 TGCTATGATGAACTACACTCCACAT 59.871 40.000 0.00 0.00 0.00 3.21
2076 2647 6.402550 CCAGTGTTTGCTATGATGAACTACAC 60.403 42.308 0.00 0.00 34.98 2.90
2078 2649 5.065218 CCCAGTGTTTGCTATGATGAACTAC 59.935 44.000 0.00 0.00 0.00 2.73
2079 2650 5.185454 CCCAGTGTTTGCTATGATGAACTA 58.815 41.667 0.00 0.00 0.00 2.24
2092 2663 1.665169 GCTGCAAAAACCCAGTGTTTG 59.335 47.619 6.09 6.09 46.39 2.93
2094 2665 1.194218 AGCTGCAAAAACCCAGTGTT 58.806 45.000 1.02 0.00 39.43 3.32
2095 2666 1.134729 CAAGCTGCAAAAACCCAGTGT 60.135 47.619 1.02 0.00 0.00 3.55
2096 2667 1.574134 CAAGCTGCAAAAACCCAGTG 58.426 50.000 1.02 0.00 0.00 3.66
2097 2668 0.179076 GCAAGCTGCAAAAACCCAGT 60.179 50.000 1.02 0.00 44.26 4.00
2098 2669 2.608640 GCAAGCTGCAAAAACCCAG 58.391 52.632 1.02 0.00 44.26 4.45
2099 2670 4.852962 GCAAGCTGCAAAAACCCA 57.147 50.000 1.02 0.00 44.26 4.51
2109 2680 1.870055 AGATGGCAAACGGCAAGCTG 61.870 55.000 0.00 0.00 41.71 4.24
2110 2681 1.181098 AAGATGGCAAACGGCAAGCT 61.181 50.000 0.00 0.00 46.43 3.74
2117 2688 2.675844 TGGACGATTAAGATGGCAAACG 59.324 45.455 0.00 0.00 0.00 3.60
2123 2694 7.148738 CGATCAAGTAATGGACGATTAAGATGG 60.149 40.741 0.00 3.07 32.72 3.51
2131 2702 3.717707 CACCGATCAAGTAATGGACGAT 58.282 45.455 0.00 0.00 32.72 3.73
2141 2712 1.741770 GAAGCGGCACCGATCAAGT 60.742 57.895 14.43 0.00 42.83 3.16
2142 2713 1.091771 ATGAAGCGGCACCGATCAAG 61.092 55.000 14.43 0.00 42.83 3.02
2143 2714 1.078497 ATGAAGCGGCACCGATCAA 60.078 52.632 14.43 0.00 42.83 2.57
2145 2716 1.521457 TGATGAAGCGGCACCGATC 60.521 57.895 14.43 10.57 42.83 3.69
2146 2717 1.815421 GTGATGAAGCGGCACCGAT 60.815 57.895 14.43 2.72 42.83 4.18
2147 2718 2.434185 GTGATGAAGCGGCACCGA 60.434 61.111 14.43 0.00 42.83 4.69
2148 2719 3.499737 GGTGATGAAGCGGCACCG 61.500 66.667 4.30 4.30 42.20 4.94
2183 2789 3.637926 AAACGCCGCCGAGGTAGAC 62.638 63.158 0.00 0.00 43.70 2.59
2184 2790 3.346631 GAAACGCCGCCGAGGTAGA 62.347 63.158 0.00 0.00 43.70 2.59
2185 2791 2.884207 GAAACGCCGCCGAGGTAG 60.884 66.667 0.00 0.00 43.70 3.18
2186 2792 2.510064 AATGAAACGCCGCCGAGGTA 62.510 55.000 0.00 0.00 43.70 3.08
2187 2793 3.894547 AATGAAACGCCGCCGAGGT 62.895 57.895 0.00 0.00 43.70 3.85
2188 2794 3.095898 GAATGAAACGCCGCCGAGG 62.096 63.158 0.00 0.00 44.97 4.63
2626 3259 2.811317 GCGTCCAGGAAGTGCGAG 60.811 66.667 4.13 0.00 0.00 5.03
2847 3480 0.039180 TAGCTCGAACACCTCCCAGA 59.961 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.