Multiple sequence alignment - TraesCS5D01G144900

Loading Multiple Alignment...

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 TraesCS5D01G144900 chr5D 100.000 1780 0 0 1 1780 231568235 231570014 0.000000e+00 3288.0
1 TraesCS5D01G144900 chr5D 100.000 259 0 0 2195 2453 231570429 231570687 1.710000e-131 479.0
2 TraesCS5D01G144900 chr5D 81.383 376 42 12 381 740 294610920 294610557 5.160000e-72 281.0
3 TraesCS5D01G144900 chr5D 80.053 376 48 11 381 740 494229852 494229488 1.130000e-63 254.0
4 TraesCS5D01G144900 chr5D 84.722 144 7 6 1 144 294611259 294611131 1.980000e-26 130.0
5 TraesCS5D01G144900 chr5D 83.704 135 7 6 1 135 494230361 494230242 1.990000e-21 113.0
6 TraesCS5D01G144900 chr5B 96.206 817 23 3 743 1554 273889481 273888668 0.000000e+00 1330.0
7 TraesCS5D01G144900 chr5B 86.508 126 12 2 1570 1690 273888685 273888560 1.530000e-27 134.0
8 TraesCS5D01G144900 chr7D 97.071 751 8 6 1 740 595091427 595092174 0.000000e+00 1253.0
9 TraesCS5D01G144900 chr5A 94.411 823 23 8 743 1554 325809344 325808534 0.000000e+00 1243.0
10 TraesCS5D01G144900 chr6A 85.146 754 79 19 1 738 531066610 531067346 0.000000e+00 741.0
11 TraesCS5D01G144900 chr2A 84.412 757 78 23 1 738 358958712 358957977 0.000000e+00 708.0
12 TraesCS5D01G144900 chr4B 81.818 594 83 13 152 737 559123997 559123421 2.210000e-130 475.0
13 TraesCS5D01G144900 chr4B 90.964 166 15 0 1 166 559124180 559124015 8.830000e-55 224.0
14 TraesCS5D01G144900 chr1A 78.982 766 104 35 1 740 228090253 228089519 1.030000e-128 470.0
15 TraesCS5D01G144900 chr1A 82.642 265 17 7 1 236 536850127 536849863 8.890000e-50 207.0
16 TraesCS5D01G144900 chr1B 81.170 393 64 5 357 739 513486634 513486242 8.520000e-80 307.0
17 TraesCS5D01G144900 chr1D 80.053 376 48 11 381 740 442676809 442676445 1.130000e-63 254.0
18 TraesCS5D01G144900 chr1D 82.123 179 11 12 1 176 442677065 442676905 1.530000e-27 134.0
19 TraesCS5D01G144900 chr1D 100.000 40 0 0 197 236 442676914 442676875 9.410000e-10 75.0
20 TraesCS5D01G144900 chr3B 78.780 377 39 13 381 740 417102660 417102308 5.310000e-52 215.0
21 TraesCS5D01G144900 chr3D 80.159 252 16 17 1 236 55782319 55782086 9.080000e-35 158.0
22 TraesCS5D01G144900 chr3A 77.099 262 18 25 1 238 222044737 222044494 1.990000e-21 113.0
23 TraesCS5D01G144900 chr2B 94.231 52 2 1 689 740 174346041 174345991 7.270000e-11 78.7
24 TraesCS5D01G144900 chr4A 100.000 37 0 0 200 236 645712407 645712443 4.380000e-08 69.4


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 TraesCS5D01G144900 chr5D 231568235 231570687 2452 False 1883.5 3288 100.0000 1 2453 2 chr5D.!!$F1 2452
1 TraesCS5D01G144900 chr5D 294610557 294611259 702 True 205.5 281 83.0525 1 740 2 chr5D.!!$R1 739
2 TraesCS5D01G144900 chr5B 273888560 273889481 921 True 732.0 1330 91.3570 743 1690 2 chr5B.!!$R1 947
3 TraesCS5D01G144900 chr7D 595091427 595092174 747 False 1253.0 1253 97.0710 1 740 1 chr7D.!!$F1 739
4 TraesCS5D01G144900 chr5A 325808534 325809344 810 True 1243.0 1243 94.4110 743 1554 1 chr5A.!!$R1 811
5 TraesCS5D01G144900 chr6A 531066610 531067346 736 False 741.0 741 85.1460 1 738 1 chr6A.!!$F1 737
6 TraesCS5D01G144900 chr2A 358957977 358958712 735 True 708.0 708 84.4120 1 738 1 chr2A.!!$R1 737
7 TraesCS5D01G144900 chr4B 559123421 559124180 759 True 349.5 475 86.3910 1 737 2 chr4B.!!$R1 736
8 TraesCS5D01G144900 chr1A 228089519 228090253 734 True 470.0 470 78.9820 1 740 1 chr1A.!!$R1 739

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
253 417 1.071542 TGAGGATTCACAGCCGAACAA 59.928 47.619 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2431 0.251165 CCCAAGCGGAGGAAAGGAAA 60.251 55.0 0.0 0.0 0.0 3.13 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
253 417 1.071542 TGAGGATTCACAGCCGAACAA 59.928 47.619 0.00 0.00 0.00 2.83
740 950 4.557301 GCGCGTGCACTTTTAAGATTTTAT 59.443 37.500 17.66 0.00 42.15 1.40
741 951 5.496969 GCGCGTGCACTTTTAAGATTTTATG 60.497 40.000 17.66 0.00 42.15 1.90
905 1115 4.524714 TCCTTTCCTGATTCTATCGCCTAG 59.475 45.833 0.00 0.00 0.00 3.02
918 1133 3.870538 TCGCCTAGATAACCTACCTCA 57.129 47.619 0.00 0.00 0.00 3.86
919 1134 3.752665 TCGCCTAGATAACCTACCTCAG 58.247 50.000 0.00 0.00 0.00 3.35
1484 1707 7.339976 AGCCTAGAAGTAGAGTCTCGTTTTTAT 59.660 37.037 0.00 0.00 0.00 1.40
1504 1727 2.175202 TCCCACAGTTTTTGTTGCAGT 58.825 42.857 0.00 0.00 38.16 4.40
1560 1783 7.721286 AAGCAAGTATACTGTATTCTGATGC 57.279 36.000 16.79 16.79 0.00 3.91
1561 1784 6.226787 AGCAAGTATACTGTATTCTGATGCC 58.773 40.000 19.09 8.59 0.00 4.40
1562 1785 5.991606 GCAAGTATACTGTATTCTGATGCCA 59.008 40.000 6.06 0.00 0.00 4.92
1563 1786 6.483307 GCAAGTATACTGTATTCTGATGCCAA 59.517 38.462 6.06 0.00 0.00 4.52
1564 1787 7.012327 GCAAGTATACTGTATTCTGATGCCAAA 59.988 37.037 6.06 0.00 0.00 3.28
1565 1788 8.554528 CAAGTATACTGTATTCTGATGCCAAAG 58.445 37.037 6.06 0.00 0.00 2.77
1566 1789 8.023021 AGTATACTGTATTCTGATGCCAAAGA 57.977 34.615 4.10 0.00 0.00 2.52
1567 1790 8.486210 AGTATACTGTATTCTGATGCCAAAGAA 58.514 33.333 4.10 0.00 36.87 2.52
1576 1799 4.099881 TCTGATGCCAAAGAAAAAGCAAGT 59.900 37.500 0.00 0.00 38.99 3.16
1579 1802 7.176515 TCTGATGCCAAAGAAAAAGCAAGTATA 59.823 33.333 0.00 0.00 38.99 1.47
1597 1820 7.708752 GCAAGTATACTGTATTTCTCTGAGCTT 59.291 37.037 6.06 0.00 0.00 3.74
1599 1822 8.526667 AGTATACTGTATTTCTCTGAGCTTGA 57.473 34.615 4.10 0.00 0.00 3.02
1607 1830 5.518848 TTTCTCTGAGCTTGATTTTTGCA 57.481 34.783 0.00 0.00 0.00 4.08
1617 1840 7.874016 TGAGCTTGATTTTTGCAGAATAATTGT 59.126 29.630 0.00 0.00 0.00 2.71
1618 1841 8.025243 AGCTTGATTTTTGCAGAATAATTGTG 57.975 30.769 0.00 0.00 0.00 3.33
1623 1846 4.870123 TTTGCAGAATAATTGTGGCACT 57.130 36.364 19.83 0.54 0.00 4.40
1624 1847 3.853831 TGCAGAATAATTGTGGCACTG 57.146 42.857 19.83 7.03 0.00 3.66
1628 1855 5.651576 TGCAGAATAATTGTGGCACTGATTA 59.348 36.000 19.83 20.51 0.00 1.75
1631 1858 7.707893 GCAGAATAATTGTGGCACTGATTAATT 59.292 33.333 19.83 16.75 0.00 1.40
1644 1871 5.634859 CACTGATTAATTGGGTGCTTGAAAC 59.365 40.000 0.00 0.00 0.00 2.78
1645 1872 4.804108 TGATTAATTGGGTGCTTGAAACG 58.196 39.130 0.00 0.00 0.00 3.60
1646 1873 4.279671 TGATTAATTGGGTGCTTGAAACGT 59.720 37.500 0.00 0.00 0.00 3.99
1675 1903 3.861263 GCCGAATTCGTGGACCGC 61.861 66.667 25.10 16.40 37.74 5.68
1690 1918 0.251916 ACCGCTGGATCAAAATCGGA 59.748 50.000 14.85 0.00 40.04 4.55
1691 1919 0.657840 CCGCTGGATCAAAATCGGAC 59.342 55.000 0.00 0.00 39.23 4.79
1692 1920 0.301687 CGCTGGATCAAAATCGGACG 59.698 55.000 0.00 0.00 32.24 4.79
1693 1921 0.657840 GCTGGATCAAAATCGGACGG 59.342 55.000 0.00 0.00 32.24 4.79
1694 1922 1.742411 GCTGGATCAAAATCGGACGGA 60.742 52.381 0.00 0.00 32.24 4.69
1695 1923 1.933853 CTGGATCAAAATCGGACGGAC 59.066 52.381 0.00 0.00 32.24 4.79
1696 1924 1.296727 GGATCAAAATCGGACGGACC 58.703 55.000 0.00 0.00 32.24 4.46
1697 1925 1.296727 GATCAAAATCGGACGGACCC 58.703 55.000 0.00 0.00 34.64 4.46
1698 1926 0.616371 ATCAAAATCGGACGGACCCA 59.384 50.000 0.00 0.00 34.64 4.51
1699 1927 0.320946 TCAAAATCGGACGGACCCAC 60.321 55.000 0.00 0.00 34.64 4.61
1700 1928 0.321298 CAAAATCGGACGGACCCACT 60.321 55.000 0.00 0.00 34.64 4.00
1701 1929 0.036671 AAAATCGGACGGACCCACTC 60.037 55.000 0.00 0.00 34.64 3.51
1702 1930 2.221906 AAATCGGACGGACCCACTCG 62.222 60.000 0.00 0.00 34.64 4.18
1706 1934 4.131088 GACGGACCCACTCGCCTC 62.131 72.222 0.00 0.00 0.00 4.70
1709 1937 3.003763 GGACCCACTCGCCTCCTT 61.004 66.667 0.00 0.00 0.00 3.36
1710 1938 2.593956 GGACCCACTCGCCTCCTTT 61.594 63.158 0.00 0.00 0.00 3.11
1711 1939 1.376037 GACCCACTCGCCTCCTTTG 60.376 63.158 0.00 0.00 0.00 2.77
1712 1940 2.045926 CCCACTCGCCTCCTTTGG 60.046 66.667 0.00 0.00 0.00 3.28
1713 1941 2.750350 CCACTCGCCTCCTTTGGT 59.250 61.111 0.00 0.00 0.00 3.67
1714 1942 1.376037 CCACTCGCCTCCTTTGGTC 60.376 63.158 0.00 0.00 0.00 4.02
1715 1943 1.738099 CACTCGCCTCCTTTGGTCG 60.738 63.158 0.00 0.00 0.00 4.79
1716 1944 1.906824 ACTCGCCTCCTTTGGTCGA 60.907 57.895 0.00 0.00 35.55 4.20
1717 1945 1.446272 CTCGCCTCCTTTGGTCGAC 60.446 63.158 7.13 7.13 34.13 4.20
1718 1946 2.809601 CGCCTCCTTTGGTCGACG 60.810 66.667 9.92 0.00 0.00 5.12
1719 1947 3.119096 GCCTCCTTTGGTCGACGC 61.119 66.667 9.92 3.20 0.00 5.19
1720 1948 2.657237 CCTCCTTTGGTCGACGCT 59.343 61.111 9.92 0.00 0.00 5.07
1721 1949 1.446272 CCTCCTTTGGTCGACGCTC 60.446 63.158 9.92 0.00 0.00 5.03
1722 1950 1.289066 CTCCTTTGGTCGACGCTCA 59.711 57.895 9.92 0.00 0.00 4.26
1723 1951 0.734253 CTCCTTTGGTCGACGCTCAG 60.734 60.000 9.92 2.72 0.00 3.35
1724 1952 2.383527 CCTTTGGTCGACGCTCAGC 61.384 63.158 9.92 0.00 0.00 4.26
1725 1953 2.357034 TTTGGTCGACGCTCAGCC 60.357 61.111 9.92 0.00 0.00 4.85
1726 1954 3.158537 TTTGGTCGACGCTCAGCCA 62.159 57.895 9.92 0.00 0.00 4.75
1727 1955 3.858868 TTGGTCGACGCTCAGCCAC 62.859 63.158 9.92 0.00 0.00 5.01
1736 1964 4.767255 CTCAGCCACCGCCCTGAC 62.767 72.222 0.00 0.00 34.60 3.51
1746 1974 2.040606 GCCCTGACCACCCCTCTA 59.959 66.667 0.00 0.00 0.00 2.43
1747 1975 1.615424 GCCCTGACCACCCCTCTAA 60.615 63.158 0.00 0.00 0.00 2.10
1748 1976 1.205460 GCCCTGACCACCCCTCTAAA 61.205 60.000 0.00 0.00 0.00 1.85
1749 1977 0.618981 CCCTGACCACCCCTCTAAAC 59.381 60.000 0.00 0.00 0.00 2.01
1750 1978 1.358152 CCTGACCACCCCTCTAAACA 58.642 55.000 0.00 0.00 0.00 2.83
1751 1979 1.916181 CCTGACCACCCCTCTAAACAT 59.084 52.381 0.00 0.00 0.00 2.71
1752 1980 2.356125 CCTGACCACCCCTCTAAACATG 60.356 54.545 0.00 0.00 0.00 3.21
1753 1981 1.004277 TGACCACCCCTCTAAACATGC 59.996 52.381 0.00 0.00 0.00 4.06
1754 1982 1.004277 GACCACCCCTCTAAACATGCA 59.996 52.381 0.00 0.00 0.00 3.96
1755 1983 1.271926 ACCACCCCTCTAAACATGCAC 60.272 52.381 0.00 0.00 0.00 4.57
1756 1984 1.463674 CACCCCTCTAAACATGCACC 58.536 55.000 0.00 0.00 0.00 5.01
1757 1985 0.331616 ACCCCTCTAAACATGCACCC 59.668 55.000 0.00 0.00 0.00 4.61
1758 1986 0.748005 CCCCTCTAAACATGCACCCG 60.748 60.000 0.00 0.00 0.00 5.28
1759 1987 0.251916 CCCTCTAAACATGCACCCGA 59.748 55.000 0.00 0.00 0.00 5.14
1760 1988 1.369625 CCTCTAAACATGCACCCGAC 58.630 55.000 0.00 0.00 0.00 4.79
1761 1989 1.066143 CCTCTAAACATGCACCCGACT 60.066 52.381 0.00 0.00 0.00 4.18
1762 1990 2.167693 CCTCTAAACATGCACCCGACTA 59.832 50.000 0.00 0.00 0.00 2.59
1763 1991 3.448686 CTCTAAACATGCACCCGACTAG 58.551 50.000 0.00 0.00 0.00 2.57
1764 1992 3.093814 TCTAAACATGCACCCGACTAGA 58.906 45.455 0.00 0.00 0.00 2.43
1765 1993 3.704566 TCTAAACATGCACCCGACTAGAT 59.295 43.478 0.00 0.00 0.00 1.98
1766 1994 3.350219 AAACATGCACCCGACTAGATT 57.650 42.857 0.00 0.00 0.00 2.40
1767 1995 3.350219 AACATGCACCCGACTAGATTT 57.650 42.857 0.00 0.00 0.00 2.17
1768 1996 2.906354 ACATGCACCCGACTAGATTTC 58.094 47.619 0.00 0.00 0.00 2.17
1769 1997 2.501723 ACATGCACCCGACTAGATTTCT 59.498 45.455 0.00 0.00 0.00 2.52
1770 1998 2.961526 TGCACCCGACTAGATTTCTC 57.038 50.000 0.00 0.00 0.00 2.87
1771 1999 1.480954 TGCACCCGACTAGATTTCTCC 59.519 52.381 0.00 0.00 0.00 3.71
1772 2000 1.536284 GCACCCGACTAGATTTCTCCG 60.536 57.143 0.00 0.00 0.00 4.63
1773 2001 2.022195 CACCCGACTAGATTTCTCCGA 58.978 52.381 0.00 0.00 0.00 4.55
1774 2002 2.623889 CACCCGACTAGATTTCTCCGAT 59.376 50.000 0.00 0.00 0.00 4.18
1775 2003 2.623889 ACCCGACTAGATTTCTCCGATG 59.376 50.000 0.00 0.00 0.00 3.84
1776 2004 2.885266 CCCGACTAGATTTCTCCGATGA 59.115 50.000 0.00 0.00 0.00 2.92
1777 2005 3.304794 CCCGACTAGATTTCTCCGATGAC 60.305 52.174 0.00 0.00 0.00 3.06
1778 2006 3.546617 CGACTAGATTTCTCCGATGACG 58.453 50.000 0.00 0.00 39.43 4.35
1779 2007 3.002451 CGACTAGATTTCTCCGATGACGT 59.998 47.826 0.00 0.00 37.88 4.34
2216 2444 3.437049 GTCAATCTGTTTCCTTTCCTCCG 59.563 47.826 0.00 0.00 0.00 4.63
2217 2445 2.115343 ATCTGTTTCCTTTCCTCCGC 57.885 50.000 0.00 0.00 0.00 5.54
2218 2446 1.056660 TCTGTTTCCTTTCCTCCGCT 58.943 50.000 0.00 0.00 0.00 5.52
2219 2447 1.420138 TCTGTTTCCTTTCCTCCGCTT 59.580 47.619 0.00 0.00 0.00 4.68
2220 2448 1.537202 CTGTTTCCTTTCCTCCGCTTG 59.463 52.381 0.00 0.00 0.00 4.01
2221 2449 0.881796 GTTTCCTTTCCTCCGCTTGG 59.118 55.000 0.00 0.00 0.00 3.61
2222 2450 0.251165 TTTCCTTTCCTCCGCTTGGG 60.251 55.000 0.00 0.00 37.02 4.12
2223 2451 1.131303 TTCCTTTCCTCCGCTTGGGA 61.131 55.000 0.00 0.00 44.68 4.37
2224 2452 1.377333 CCTTTCCTCCGCTTGGGAC 60.377 63.158 0.00 0.00 40.94 4.46
2225 2453 1.741770 CTTTCCTCCGCTTGGGACG 60.742 63.158 0.00 0.00 40.94 4.79
2226 2454 2.450479 CTTTCCTCCGCTTGGGACGT 62.450 60.000 0.00 0.00 40.94 4.34
2227 2455 2.444700 TTTCCTCCGCTTGGGACGTC 62.445 60.000 7.13 7.13 40.94 4.34
2228 2456 4.796231 CCTCCGCTTGGGACGTCG 62.796 72.222 9.92 0.00 40.94 5.12
2232 2460 3.554692 CGCTTGGGACGTCGCATC 61.555 66.667 32.33 24.67 38.62 3.91
2233 2461 2.125512 GCTTGGGACGTCGCATCT 60.126 61.111 32.33 0.00 38.62 2.90
2234 2462 1.741770 GCTTGGGACGTCGCATCTT 60.742 57.895 32.33 0.00 38.62 2.40
2235 2463 1.970917 GCTTGGGACGTCGCATCTTG 61.971 60.000 32.33 22.57 38.62 3.02
2236 2464 1.970917 CTTGGGACGTCGCATCTTGC 61.971 60.000 32.33 5.90 40.69 4.01
2237 2465 2.125512 GGGACGTCGCATCTTGCT 60.126 61.111 25.93 0.00 42.25 3.91
2238 2466 2.456119 GGGACGTCGCATCTTGCTG 61.456 63.158 25.93 0.00 42.25 4.41
2239 2467 2.397252 GACGTCGCATCTTGCTGC 59.603 61.111 0.00 0.00 42.25 5.25
2240 2468 3.088500 GACGTCGCATCTTGCTGCC 62.089 63.158 0.00 0.00 42.25 4.85
2241 2469 4.214383 CGTCGCATCTTGCTGCCG 62.214 66.667 0.00 0.00 42.25 5.69
2242 2470 4.527157 GTCGCATCTTGCTGCCGC 62.527 66.667 0.00 0.00 42.25 6.53
2243 2471 4.765449 TCGCATCTTGCTGCCGCT 62.765 61.111 0.70 0.00 42.25 5.52
2244 2472 2.891936 CGCATCTTGCTGCCGCTA 60.892 61.111 0.70 0.00 42.25 4.26
2245 2473 2.879070 CGCATCTTGCTGCCGCTAG 61.879 63.158 5.26 5.26 42.25 3.42
2246 2474 3.020627 CATCTTGCTGCCGCTAGC 58.979 61.111 4.06 4.06 43.95 3.42
2255 2483 2.711924 GCCGCTAGCAGCATTGTC 59.288 61.111 18.08 0.00 42.58 3.18
2256 2484 2.828128 GCCGCTAGCAGCATTGTCC 61.828 63.158 18.08 0.00 42.58 4.02
2257 2485 2.182842 CCGCTAGCAGCATTGTCCC 61.183 63.158 16.45 0.00 42.58 4.46
2258 2486 2.182842 CGCTAGCAGCATTGTCCCC 61.183 63.158 16.45 0.00 42.58 4.81
2259 2487 1.077501 GCTAGCAGCATTGTCCCCA 60.078 57.895 10.63 0.00 41.89 4.96
2260 2488 0.466922 GCTAGCAGCATTGTCCCCAT 60.467 55.000 10.63 0.00 41.89 4.00
2261 2489 1.602311 CTAGCAGCATTGTCCCCATC 58.398 55.000 0.00 0.00 0.00 3.51
2262 2490 0.183492 TAGCAGCATTGTCCCCATCC 59.817 55.000 0.00 0.00 0.00 3.51
2263 2491 1.076485 GCAGCATTGTCCCCATCCT 60.076 57.895 0.00 0.00 0.00 3.24
2264 2492 1.389609 GCAGCATTGTCCCCATCCTG 61.390 60.000 0.00 0.00 0.00 3.86
2265 2493 0.754217 CAGCATTGTCCCCATCCTGG 60.754 60.000 0.00 0.00 37.25 4.45
2266 2494 2.129785 GCATTGTCCCCATCCTGGC 61.130 63.158 0.00 0.00 35.79 4.85
2267 2495 1.616921 CATTGTCCCCATCCTGGCT 59.383 57.895 0.00 0.00 35.79 4.75
2268 2496 0.032813 CATTGTCCCCATCCTGGCTT 60.033 55.000 0.00 0.00 35.79 4.35
2269 2497 0.032813 ATTGTCCCCATCCTGGCTTG 60.033 55.000 0.00 0.00 35.79 4.01
2270 2498 2.153898 TTGTCCCCATCCTGGCTTGG 62.154 60.000 8.16 8.16 35.79 3.61
2271 2499 3.743017 TCCCCATCCTGGCTTGGC 61.743 66.667 9.33 0.00 35.79 4.52
2289 2517 2.264794 CTTGCCGGTAAGGACGCT 59.735 61.111 23.29 0.00 45.00 5.07
2290 2518 1.810030 CTTGCCGGTAAGGACGCTC 60.810 63.158 23.29 0.00 45.00 5.03
2291 2519 3.305177 TTGCCGGTAAGGACGCTCC 62.305 63.158 0.00 0.00 45.00 4.70
2292 2520 3.766691 GCCGGTAAGGACGCTCCA 61.767 66.667 1.90 0.00 45.00 3.86
2293 2521 3.090219 GCCGGTAAGGACGCTCCAT 62.090 63.158 1.90 0.00 45.00 3.41
2294 2522 1.227263 CCGGTAAGGACGCTCCATG 60.227 63.158 0.00 0.00 45.00 3.66
2295 2523 1.883084 CGGTAAGGACGCTCCATGC 60.883 63.158 6.78 0.00 39.61 4.06
2296 2524 1.522569 GGTAAGGACGCTCCATGCT 59.477 57.895 6.78 0.00 39.61 3.79
2297 2525 0.107654 GGTAAGGACGCTCCATGCTT 60.108 55.000 6.78 0.00 39.61 3.91
2298 2526 1.291132 GTAAGGACGCTCCATGCTTC 58.709 55.000 6.78 0.00 39.61 3.86
2299 2527 0.179111 TAAGGACGCTCCATGCTTCG 60.179 55.000 6.78 0.00 40.38 3.79
2300 2528 2.125512 GGACGCTCCATGCTTCGT 60.126 61.111 4.46 4.46 40.38 3.85
2301 2529 3.389206 GACGCTCCATGCTTCGTC 58.611 61.111 13.29 13.29 43.23 4.20
2302 2530 2.125512 ACGCTCCATGCTTCGTCC 60.126 61.111 0.00 0.00 40.11 4.79
2303 2531 2.892425 CGCTCCATGCTTCGTCCC 60.892 66.667 0.00 0.00 40.11 4.46
2304 2532 2.892425 GCTCCATGCTTCGTCCCG 60.892 66.667 0.00 0.00 38.95 5.14
2305 2533 2.579201 CTCCATGCTTCGTCCCGT 59.421 61.111 0.00 0.00 0.00 5.28
2306 2534 1.811266 CTCCATGCTTCGTCCCGTG 60.811 63.158 0.00 0.00 0.00 4.94
2307 2535 2.225791 CTCCATGCTTCGTCCCGTGA 62.226 60.000 0.00 0.00 0.00 4.35
2308 2536 2.100631 CCATGCTTCGTCCCGTGAC 61.101 63.158 0.00 0.00 38.18 3.67
2324 2552 3.041701 ACGTCGCACCCGTCTTTA 58.958 55.556 0.00 0.00 31.97 1.85
2325 2553 1.080974 ACGTCGCACCCGTCTTTAG 60.081 57.895 0.00 0.00 31.97 1.85
2326 2554 1.804326 CGTCGCACCCGTCTTTAGG 60.804 63.158 0.00 0.00 35.54 2.69
2327 2555 2.098831 GTCGCACCCGTCTTTAGGC 61.099 63.158 0.00 0.00 35.54 3.93
2328 2556 2.264794 CGCACCCGTCTTTAGGCT 59.735 61.111 0.00 0.00 0.00 4.58
2329 2557 1.810030 CGCACCCGTCTTTAGGCTC 60.810 63.158 0.00 0.00 0.00 4.70
2330 2558 1.810030 GCACCCGTCTTTAGGCTCG 60.810 63.158 0.00 0.00 0.00 5.03
2331 2559 1.810030 CACCCGTCTTTAGGCTCGC 60.810 63.158 0.00 0.00 0.00 5.03
2332 2560 2.202892 CCCGTCTTTAGGCTCGCC 60.203 66.667 0.00 0.00 0.00 5.54
2333 2561 2.577059 CCGTCTTTAGGCTCGCCA 59.423 61.111 11.02 0.00 38.92 5.69
2334 2562 1.810030 CCGTCTTTAGGCTCGCCAC 60.810 63.158 11.02 0.00 38.92 5.01
2335 2563 2.158959 CGTCTTTAGGCTCGCCACG 61.159 63.158 11.02 7.01 38.92 4.94
2336 2564 1.214589 GTCTTTAGGCTCGCCACGA 59.785 57.895 11.02 0.00 38.92 4.35
2337 2565 0.389426 GTCTTTAGGCTCGCCACGAA 60.389 55.000 11.02 0.00 38.92 3.85
2338 2566 0.535335 TCTTTAGGCTCGCCACGAAT 59.465 50.000 11.02 0.00 38.92 3.34
2339 2567 0.652592 CTTTAGGCTCGCCACGAATG 59.347 55.000 11.02 0.65 38.92 2.67
2340 2568 0.248012 TTTAGGCTCGCCACGAATGA 59.752 50.000 11.02 0.00 38.92 2.57
2341 2569 0.464036 TTAGGCTCGCCACGAATGAT 59.536 50.000 11.02 0.00 38.92 2.45
2342 2570 0.464036 TAGGCTCGCCACGAATGATT 59.536 50.000 11.02 0.00 38.92 2.57
2343 2571 0.392998 AGGCTCGCCACGAATGATTT 60.393 50.000 11.02 0.00 38.92 2.17
2344 2572 0.028110 GGCTCGCCACGAATGATTTC 59.972 55.000 2.41 0.00 34.74 2.17
2345 2573 1.009829 GCTCGCCACGAATGATTTCT 58.990 50.000 0.00 0.00 34.74 2.52
2346 2574 1.398390 GCTCGCCACGAATGATTTCTT 59.602 47.619 0.00 0.00 34.74 2.52
2347 2575 2.159517 GCTCGCCACGAATGATTTCTTT 60.160 45.455 0.00 0.00 34.74 2.52
2348 2576 3.670627 GCTCGCCACGAATGATTTCTTTT 60.671 43.478 0.00 0.00 34.74 2.27
2349 2577 3.820689 TCGCCACGAATGATTTCTTTTG 58.179 40.909 0.00 0.00 31.06 2.44
2350 2578 2.342354 CGCCACGAATGATTTCTTTTGC 59.658 45.455 0.00 0.00 0.00 3.68
2351 2579 2.342354 GCCACGAATGATTTCTTTTGCG 59.658 45.455 0.00 0.00 0.00 4.85
2352 2580 3.820689 CCACGAATGATTTCTTTTGCGA 58.179 40.909 0.00 0.00 0.00 5.10
2353 2581 3.848019 CCACGAATGATTTCTTTTGCGAG 59.152 43.478 0.00 0.00 0.00 5.03
2354 2582 4.378356 CCACGAATGATTTCTTTTGCGAGA 60.378 41.667 0.00 0.00 0.00 4.04
2355 2583 5.146460 CACGAATGATTTCTTTTGCGAGAA 58.854 37.500 0.00 0.00 34.00 2.87
2356 2584 5.624900 CACGAATGATTTCTTTTGCGAGAAA 59.375 36.000 10.79 10.79 46.36 2.52
2357 2585 6.142161 CACGAATGATTTCTTTTGCGAGAAAA 59.858 34.615 11.98 0.00 45.68 2.29
2358 2586 6.695278 ACGAATGATTTCTTTTGCGAGAAAAA 59.305 30.769 11.98 6.21 45.68 1.94
2359 2587 7.096477 ACGAATGATTTCTTTTGCGAGAAAAAG 60.096 33.333 9.47 9.47 45.68 2.27
2369 2597 8.743470 CTTTTGCGAGAAAAAGAAAATTCAAG 57.257 30.769 10.07 0.00 45.85 3.02
2370 2598 7.826260 TTTGCGAGAAAAAGAAAATTCAAGT 57.174 28.000 0.00 0.00 0.00 3.16
2371 2599 8.918961 TTTGCGAGAAAAAGAAAATTCAAGTA 57.081 26.923 0.00 0.00 0.00 2.24
2372 2600 7.908193 TGCGAGAAAAAGAAAATTCAAGTAC 57.092 32.000 0.00 0.00 0.00 2.73
2373 2601 7.476667 TGCGAGAAAAAGAAAATTCAAGTACA 58.523 30.769 0.00 0.00 0.00 2.90
2374 2602 8.134895 TGCGAGAAAAAGAAAATTCAAGTACAT 58.865 29.630 0.00 0.00 0.00 2.29
2375 2603 8.420189 GCGAGAAAAAGAAAATTCAAGTACATG 58.580 33.333 0.00 0.00 0.00 3.21
2376 2604 9.663904 CGAGAAAAAGAAAATTCAAGTACATGA 57.336 29.630 0.00 0.00 0.00 3.07
2378 2606 9.468532 AGAAAAAGAAAATTCAAGTACATGAGC 57.531 29.630 0.00 0.00 0.00 4.26
2379 2607 9.468532 GAAAAAGAAAATTCAAGTACATGAGCT 57.531 29.630 0.00 0.00 0.00 4.09
2380 2608 9.822185 AAAAAGAAAATTCAAGTACATGAGCTT 57.178 25.926 0.00 0.00 0.00 3.74
2381 2609 9.822185 AAAAGAAAATTCAAGTACATGAGCTTT 57.178 25.926 0.00 5.29 0.00 3.51
2384 2612 9.899226 AGAAAATTCAAGTACATGAGCTTTAAC 57.101 29.630 0.00 4.83 0.00 2.01
2385 2613 9.677567 GAAAATTCAAGTACATGAGCTTTAACA 57.322 29.630 0.00 0.00 0.00 2.41
2388 2616 9.463443 AATTCAAGTACATGAGCTTTAACAAAC 57.537 29.630 0.00 0.00 0.00 2.93
2389 2617 6.655062 TCAAGTACATGAGCTTTAACAAACG 58.345 36.000 0.00 0.00 0.00 3.60
2390 2618 5.030874 AGTACATGAGCTTTAACAAACGC 57.969 39.130 0.00 0.00 0.00 4.84
2391 2619 4.755123 AGTACATGAGCTTTAACAAACGCT 59.245 37.500 0.00 0.00 35.03 5.07
2392 2620 4.147219 ACATGAGCTTTAACAAACGCTC 57.853 40.909 0.00 9.04 46.74 5.03
2393 2621 3.815401 ACATGAGCTTTAACAAACGCTCT 59.185 39.130 14.97 2.14 46.70 4.09
2394 2622 3.878086 TGAGCTTTAACAAACGCTCTG 57.122 42.857 14.97 0.00 46.70 3.35
2395 2623 3.462982 TGAGCTTTAACAAACGCTCTGA 58.537 40.909 14.97 0.00 46.70 3.27
2396 2624 3.874543 TGAGCTTTAACAAACGCTCTGAA 59.125 39.130 14.97 0.00 46.70 3.02
2397 2625 4.515191 TGAGCTTTAACAAACGCTCTGAAT 59.485 37.500 14.97 0.00 46.70 2.57
2398 2626 5.699001 TGAGCTTTAACAAACGCTCTGAATA 59.301 36.000 14.97 0.00 46.70 1.75
2399 2627 6.203915 TGAGCTTTAACAAACGCTCTGAATAA 59.796 34.615 14.97 0.00 46.70 1.40
2400 2628 7.094805 TGAGCTTTAACAAACGCTCTGAATAAT 60.095 33.333 14.97 0.00 46.70 1.28
2401 2629 8.263940 AGCTTTAACAAACGCTCTGAATAATA 57.736 30.769 0.00 0.00 0.00 0.98
2402 2630 8.726988 AGCTTTAACAAACGCTCTGAATAATAA 58.273 29.630 0.00 0.00 0.00 1.40
2403 2631 9.337091 GCTTTAACAAACGCTCTGAATAATAAA 57.663 29.630 0.00 0.00 0.00 1.40
2427 2655 5.438761 AAAACTAGGTGACATCAAAGCAC 57.561 39.130 0.00 0.00 0.00 4.40
2436 2664 5.343249 GTGACATCAAAGCACCAAATATCC 58.657 41.667 0.00 0.00 0.00 2.59
2437 2665 4.402155 TGACATCAAAGCACCAAATATCCC 59.598 41.667 0.00 0.00 0.00 3.85
2438 2666 3.706086 ACATCAAAGCACCAAATATCCCC 59.294 43.478 0.00 0.00 0.00 4.81
2439 2667 3.464720 TCAAAGCACCAAATATCCCCA 57.535 42.857 0.00 0.00 0.00 4.96
2440 2668 3.096092 TCAAAGCACCAAATATCCCCAC 58.904 45.455 0.00 0.00 0.00 4.61
2441 2669 3.099141 CAAAGCACCAAATATCCCCACT 58.901 45.455 0.00 0.00 0.00 4.00
2442 2670 4.017958 TCAAAGCACCAAATATCCCCACTA 60.018 41.667 0.00 0.00 0.00 2.74
2443 2671 3.577805 AGCACCAAATATCCCCACTAC 57.422 47.619 0.00 0.00 0.00 2.73
2444 2672 3.123273 AGCACCAAATATCCCCACTACT 58.877 45.455 0.00 0.00 0.00 2.57
2445 2673 3.527665 AGCACCAAATATCCCCACTACTT 59.472 43.478 0.00 0.00 0.00 2.24
2446 2674 4.017499 AGCACCAAATATCCCCACTACTTT 60.017 41.667 0.00 0.00 0.00 2.66
2447 2675 4.097892 GCACCAAATATCCCCACTACTTTG 59.902 45.833 0.00 0.00 0.00 2.77
2448 2676 5.261216 CACCAAATATCCCCACTACTTTGT 58.739 41.667 0.00 0.00 0.00 2.83
2449 2677 5.357032 CACCAAATATCCCCACTACTTTGTC 59.643 44.000 0.00 0.00 0.00 3.18
2450 2678 5.253096 ACCAAATATCCCCACTACTTTGTCT 59.747 40.000 0.00 0.00 0.00 3.41
2451 2679 5.823045 CCAAATATCCCCACTACTTTGTCTC 59.177 44.000 0.00 0.00 0.00 3.36
2452 2680 6.353082 CCAAATATCCCCACTACTTTGTCTCT 60.353 42.308 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
697 907 1.306642 ACTGTTCGGCGAGATCGAGT 61.307 55.000 10.46 6.14 43.02 4.18
905 1115 0.750850 TGCGGCTGAGGTAGGTTATC 59.249 55.000 0.00 0.00 0.00 1.75
1415 1638 3.411351 CGTTGTCCTTCCGTGCCG 61.411 66.667 0.00 0.00 0.00 5.69
1484 1707 2.175202 ACTGCAACAAAAACTGTGGGA 58.825 42.857 0.00 0.00 38.67 4.37
1504 1727 5.435686 AGTGTGCCTCAATATAACCTGAA 57.564 39.130 0.00 0.00 0.00 3.02
1547 1770 6.309737 GCTTTTTCTTTGGCATCAGAATACAG 59.690 38.462 9.71 7.76 0.00 2.74
1548 1771 6.158598 GCTTTTTCTTTGGCATCAGAATACA 58.841 36.000 9.71 0.00 0.00 2.29
1549 1772 6.158598 TGCTTTTTCTTTGGCATCAGAATAC 58.841 36.000 9.71 2.89 0.00 1.89
1550 1773 6.343716 TGCTTTTTCTTTGGCATCAGAATA 57.656 33.333 9.71 3.96 0.00 1.75
1551 1774 5.217978 TGCTTTTTCTTTGGCATCAGAAT 57.782 34.783 9.71 0.00 0.00 2.40
1552 1775 4.669206 TGCTTTTTCTTTGGCATCAGAA 57.331 36.364 5.72 5.72 0.00 3.02
1553 1776 4.099881 ACTTGCTTTTTCTTTGGCATCAGA 59.900 37.500 0.00 0.00 34.59 3.27
1554 1777 4.374399 ACTTGCTTTTTCTTTGGCATCAG 58.626 39.130 0.00 0.00 34.59 2.90
1555 1778 4.405116 ACTTGCTTTTTCTTTGGCATCA 57.595 36.364 0.00 0.00 34.59 3.07
1556 1779 7.274250 CAGTATACTTGCTTTTTCTTTGGCATC 59.726 37.037 1.56 0.00 34.59 3.91
1557 1780 7.092716 CAGTATACTTGCTTTTTCTTTGGCAT 58.907 34.615 1.56 0.00 34.59 4.40
1558 1781 6.040391 ACAGTATACTTGCTTTTTCTTTGGCA 59.960 34.615 1.56 0.00 0.00 4.92
1559 1782 6.447162 ACAGTATACTTGCTTTTTCTTTGGC 58.553 36.000 1.56 0.00 0.00 4.52
1567 1790 9.944376 TCAGAGAAATACAGTATACTTGCTTTT 57.056 29.630 1.56 1.52 0.00 2.27
1579 1802 7.992754 AAAATCAAGCTCAGAGAAATACAGT 57.007 32.000 0.00 0.00 0.00 3.55
1597 1820 6.147492 GTGCCACAATTATTCTGCAAAAATCA 59.853 34.615 0.00 0.00 0.00 2.57
1599 1822 6.148150 CAGTGCCACAATTATTCTGCAAAAAT 59.852 34.615 0.00 0.00 0.00 1.82
1607 1830 8.199449 CCAATTAATCAGTGCCACAATTATTCT 58.801 33.333 0.00 0.00 0.00 2.40
1617 1840 1.824230 GCACCCAATTAATCAGTGCCA 59.176 47.619 19.28 0.00 46.25 4.92
1618 1841 2.584492 GCACCCAATTAATCAGTGCC 57.416 50.000 19.28 7.92 46.25 5.01
1623 1846 4.279671 ACGTTTCAAGCACCCAATTAATCA 59.720 37.500 0.00 0.00 0.00 2.57
1624 1847 4.805219 ACGTTTCAAGCACCCAATTAATC 58.195 39.130 0.00 0.00 0.00 1.75
1628 1855 3.535280 AAACGTTTCAAGCACCCAATT 57.465 38.095 7.96 0.00 0.00 2.32
1675 1903 1.933853 GTCCGTCCGATTTTGATCCAG 59.066 52.381 0.00 0.00 0.00 3.86
1692 1920 2.593956 AAAGGAGGCGAGTGGGTCC 61.594 63.158 0.00 0.00 0.00 4.46
1693 1921 1.376037 CAAAGGAGGCGAGTGGGTC 60.376 63.158 0.00 0.00 0.00 4.46
1694 1922 2.750350 CAAAGGAGGCGAGTGGGT 59.250 61.111 0.00 0.00 0.00 4.51
1695 1923 2.045926 CCAAAGGAGGCGAGTGGG 60.046 66.667 0.00 0.00 0.00 4.61
1696 1924 1.376037 GACCAAAGGAGGCGAGTGG 60.376 63.158 0.00 0.00 35.39 4.00
1697 1925 1.738099 CGACCAAAGGAGGCGAGTG 60.738 63.158 0.00 0.00 32.44 3.51
1698 1926 1.906824 TCGACCAAAGGAGGCGAGT 60.907 57.895 0.00 0.00 34.13 4.18
1699 1927 1.446272 GTCGACCAAAGGAGGCGAG 60.446 63.158 3.51 0.00 37.68 5.03
1700 1928 2.654877 GTCGACCAAAGGAGGCGA 59.345 61.111 3.51 0.00 35.77 5.54
1701 1929 2.809601 CGTCGACCAAAGGAGGCG 60.810 66.667 10.58 0.00 0.00 5.52
1702 1930 3.119096 GCGTCGACCAAAGGAGGC 61.119 66.667 10.58 0.58 36.97 4.70
1703 1931 1.446272 GAGCGTCGACCAAAGGAGG 60.446 63.158 10.58 0.00 0.00 4.30
1704 1932 0.734253 CTGAGCGTCGACCAAAGGAG 60.734 60.000 10.58 0.00 0.00 3.69
1705 1933 1.289066 CTGAGCGTCGACCAAAGGA 59.711 57.895 10.58 0.00 0.00 3.36
1706 1934 2.383527 GCTGAGCGTCGACCAAAGG 61.384 63.158 10.58 0.00 0.00 3.11
1707 1935 2.383527 GGCTGAGCGTCGACCAAAG 61.384 63.158 10.58 3.99 0.00 2.77
1708 1936 2.357034 GGCTGAGCGTCGACCAAA 60.357 61.111 10.58 0.00 0.00 3.28
1709 1937 3.611674 TGGCTGAGCGTCGACCAA 61.612 61.111 10.58 0.00 0.00 3.67
1710 1938 4.357947 GTGGCTGAGCGTCGACCA 62.358 66.667 10.58 1.04 0.00 4.02
1719 1947 4.767255 GTCAGGGCGGTGGCTGAG 62.767 72.222 0.00 0.00 39.81 3.35
1728 1956 3.976490 TAGAGGGGTGGTCAGGGCG 62.976 68.421 0.00 0.00 0.00 6.13
1729 1957 1.205460 TTTAGAGGGGTGGTCAGGGC 61.205 60.000 0.00 0.00 0.00 5.19
1730 1958 0.618981 GTTTAGAGGGGTGGTCAGGG 59.381 60.000 0.00 0.00 0.00 4.45
1731 1959 1.358152 TGTTTAGAGGGGTGGTCAGG 58.642 55.000 0.00 0.00 0.00 3.86
1732 1960 2.941415 GCATGTTTAGAGGGGTGGTCAG 60.941 54.545 0.00 0.00 0.00 3.51
1733 1961 1.004277 GCATGTTTAGAGGGGTGGTCA 59.996 52.381 0.00 0.00 0.00 4.02
1734 1962 1.004277 TGCATGTTTAGAGGGGTGGTC 59.996 52.381 0.00 0.00 0.00 4.02
1735 1963 1.072266 TGCATGTTTAGAGGGGTGGT 58.928 50.000 0.00 0.00 0.00 4.16
1736 1964 1.463674 GTGCATGTTTAGAGGGGTGG 58.536 55.000 0.00 0.00 0.00 4.61
1737 1965 1.463674 GGTGCATGTTTAGAGGGGTG 58.536 55.000 0.00 0.00 0.00 4.61
1738 1966 0.331616 GGGTGCATGTTTAGAGGGGT 59.668 55.000 0.00 0.00 0.00 4.95
1739 1967 0.748005 CGGGTGCATGTTTAGAGGGG 60.748 60.000 0.00 0.00 0.00 4.79
1740 1968 0.251916 TCGGGTGCATGTTTAGAGGG 59.748 55.000 0.00 0.00 0.00 4.30
1741 1969 1.066143 AGTCGGGTGCATGTTTAGAGG 60.066 52.381 0.00 0.00 0.00 3.69
1742 1970 2.386661 AGTCGGGTGCATGTTTAGAG 57.613 50.000 0.00 0.00 0.00 2.43
1743 1971 3.093814 TCTAGTCGGGTGCATGTTTAGA 58.906 45.455 0.00 0.00 0.00 2.10
1744 1972 3.520290 TCTAGTCGGGTGCATGTTTAG 57.480 47.619 0.00 0.00 0.00 1.85
1745 1973 4.481368 AATCTAGTCGGGTGCATGTTTA 57.519 40.909 0.00 0.00 0.00 2.01
1746 1974 3.350219 AATCTAGTCGGGTGCATGTTT 57.650 42.857 0.00 0.00 0.00 2.83
1747 1975 3.055094 AGAAATCTAGTCGGGTGCATGTT 60.055 43.478 0.00 0.00 0.00 2.71
1748 1976 2.501723 AGAAATCTAGTCGGGTGCATGT 59.498 45.455 0.00 0.00 0.00 3.21
1749 1977 3.126831 GAGAAATCTAGTCGGGTGCATG 58.873 50.000 0.00 0.00 0.00 4.06
1750 1978 2.103263 GGAGAAATCTAGTCGGGTGCAT 59.897 50.000 0.00 0.00 0.00 3.96
1751 1979 1.480954 GGAGAAATCTAGTCGGGTGCA 59.519 52.381 0.00 0.00 0.00 4.57
1752 1980 1.536284 CGGAGAAATCTAGTCGGGTGC 60.536 57.143 0.00 0.00 0.00 5.01
1753 1981 2.022195 TCGGAGAAATCTAGTCGGGTG 58.978 52.381 0.00 0.00 0.00 4.61
1754 1982 2.431954 TCGGAGAAATCTAGTCGGGT 57.568 50.000 0.00 0.00 0.00 5.28
1755 1983 2.885266 TCATCGGAGAAATCTAGTCGGG 59.115 50.000 0.00 0.00 43.58 5.14
1756 1984 3.607310 CGTCATCGGAGAAATCTAGTCGG 60.607 52.174 0.00 0.00 43.58 4.79
1757 1985 3.002451 ACGTCATCGGAGAAATCTAGTCG 59.998 47.826 0.00 0.00 43.58 4.18
1758 1986 4.555348 ACGTCATCGGAGAAATCTAGTC 57.445 45.455 0.00 0.00 43.58 2.59
2194 2422 3.437049 CGGAGGAAAGGAAACAGATTGAC 59.563 47.826 0.00 0.00 0.00 3.18
2195 2423 3.674997 CGGAGGAAAGGAAACAGATTGA 58.325 45.455 0.00 0.00 0.00 2.57
2196 2424 2.162408 GCGGAGGAAAGGAAACAGATTG 59.838 50.000 0.00 0.00 0.00 2.67
2197 2425 2.040412 AGCGGAGGAAAGGAAACAGATT 59.960 45.455 0.00 0.00 0.00 2.40
2198 2426 1.630878 AGCGGAGGAAAGGAAACAGAT 59.369 47.619 0.00 0.00 0.00 2.90
2199 2427 1.056660 AGCGGAGGAAAGGAAACAGA 58.943 50.000 0.00 0.00 0.00 3.41
2200 2428 1.537202 CAAGCGGAGGAAAGGAAACAG 59.463 52.381 0.00 0.00 0.00 3.16
2201 2429 1.604604 CAAGCGGAGGAAAGGAAACA 58.395 50.000 0.00 0.00 0.00 2.83
2202 2430 0.881796 CCAAGCGGAGGAAAGGAAAC 59.118 55.000 0.00 0.00 0.00 2.78
2203 2431 0.251165 CCCAAGCGGAGGAAAGGAAA 60.251 55.000 0.00 0.00 0.00 3.13
2204 2432 1.131303 TCCCAAGCGGAGGAAAGGAA 61.131 55.000 0.00 0.00 34.86 3.36
2205 2433 1.537889 TCCCAAGCGGAGGAAAGGA 60.538 57.895 0.00 0.00 34.86 3.36
2206 2434 1.377333 GTCCCAAGCGGAGGAAAGG 60.377 63.158 0.00 0.00 43.19 3.11
2207 2435 4.303257 GTCCCAAGCGGAGGAAAG 57.697 61.111 0.00 0.00 43.19 2.62
2215 2443 3.554692 GATGCGACGTCCCAAGCG 61.555 66.667 10.58 0.00 0.00 4.68
2216 2444 1.741770 AAGATGCGACGTCCCAAGC 60.742 57.895 10.58 8.13 0.00 4.01
2217 2445 1.970917 GCAAGATGCGACGTCCCAAG 61.971 60.000 10.58 0.00 31.71 3.61
2218 2446 2.032634 GCAAGATGCGACGTCCCAA 61.033 57.895 10.58 0.00 31.71 4.12
2219 2447 2.434185 GCAAGATGCGACGTCCCA 60.434 61.111 10.58 7.84 31.71 4.37
2238 2466 2.711924 GACAATGCTGCTAGCGGC 59.288 61.111 36.55 36.55 46.26 6.53
2239 2467 2.182842 GGGACAATGCTGCTAGCGG 61.183 63.158 19.74 19.74 46.26 5.52
2240 2468 2.182842 GGGGACAATGCTGCTAGCG 61.183 63.158 10.77 6.22 46.26 4.26
2241 2469 1.077501 TGGGGACAATGCTGCTAGC 60.078 57.895 8.10 8.10 38.76 3.42
2269 2497 2.437895 GTCCTTACCGGCAAGGCC 60.438 66.667 26.48 13.87 44.14 5.19
2270 2498 2.818274 CGTCCTTACCGGCAAGGC 60.818 66.667 26.48 19.78 44.14 4.35
2271 2499 2.818274 GCGTCCTTACCGGCAAGG 60.818 66.667 25.54 25.54 45.59 3.61
2272 2500 1.810030 GAGCGTCCTTACCGGCAAG 60.810 63.158 7.52 7.52 0.00 4.01
2273 2501 2.263540 GAGCGTCCTTACCGGCAA 59.736 61.111 0.00 0.00 0.00 4.52
2274 2502 3.766691 GGAGCGTCCTTACCGGCA 61.767 66.667 0.00 0.00 32.53 5.69
2275 2503 3.090219 ATGGAGCGTCCTTACCGGC 62.090 63.158 0.00 0.00 37.46 6.13
2276 2504 1.227263 CATGGAGCGTCCTTACCGG 60.227 63.158 0.00 0.00 37.46 5.28
2277 2505 1.883084 GCATGGAGCGTCCTTACCG 60.883 63.158 0.00 0.00 37.46 4.02
2278 2506 4.126524 GCATGGAGCGTCCTTACC 57.873 61.111 0.00 0.00 37.46 2.85
2308 2536 1.804326 CCTAAAGACGGGTGCGACG 60.804 63.158 0.00 0.00 37.36 5.12
2309 2537 2.098831 GCCTAAAGACGGGTGCGAC 61.099 63.158 0.00 0.00 0.00 5.19
2310 2538 2.221906 GAGCCTAAAGACGGGTGCGA 62.222 60.000 0.00 0.00 31.26 5.10
2311 2539 1.810030 GAGCCTAAAGACGGGTGCG 60.810 63.158 0.00 0.00 31.26 5.34
2312 2540 1.810030 CGAGCCTAAAGACGGGTGC 60.810 63.158 0.00 0.00 31.26 5.01
2313 2541 1.810030 GCGAGCCTAAAGACGGGTG 60.810 63.158 0.00 0.00 31.26 4.61
2314 2542 2.577593 GCGAGCCTAAAGACGGGT 59.422 61.111 0.00 0.00 34.40 5.28
2315 2543 2.202892 GGCGAGCCTAAAGACGGG 60.203 66.667 6.90 0.00 0.00 5.28
2316 2544 1.810030 GTGGCGAGCCTAAAGACGG 60.810 63.158 15.75 0.00 36.94 4.79
2317 2545 2.158959 CGTGGCGAGCCTAAAGACG 61.159 63.158 15.75 12.04 36.94 4.18
2318 2546 0.389426 TTCGTGGCGAGCCTAAAGAC 60.389 55.000 15.75 3.67 37.14 3.01
2319 2547 0.535335 ATTCGTGGCGAGCCTAAAGA 59.465 50.000 15.75 6.50 37.14 2.52
2320 2548 0.652592 CATTCGTGGCGAGCCTAAAG 59.347 55.000 15.75 4.30 37.14 1.85
2321 2549 0.248012 TCATTCGTGGCGAGCCTAAA 59.752 50.000 15.75 7.19 37.14 1.85
2322 2550 0.464036 ATCATTCGTGGCGAGCCTAA 59.536 50.000 15.75 7.51 37.14 2.69
2323 2551 0.464036 AATCATTCGTGGCGAGCCTA 59.536 50.000 15.75 0.00 37.14 3.93
2324 2552 0.392998 AAATCATTCGTGGCGAGCCT 60.393 50.000 15.75 0.00 37.14 4.58
2325 2553 0.028110 GAAATCATTCGTGGCGAGCC 59.972 55.000 7.26 7.26 37.14 4.70
2326 2554 1.009829 AGAAATCATTCGTGGCGAGC 58.990 50.000 0.00 0.00 40.63 5.03
2327 2555 3.747099 AAAGAAATCATTCGTGGCGAG 57.253 42.857 0.00 0.00 40.63 5.03
2328 2556 3.820689 CAAAAGAAATCATTCGTGGCGA 58.179 40.909 0.00 0.00 40.63 5.54
2329 2557 2.342354 GCAAAAGAAATCATTCGTGGCG 59.658 45.455 0.00 0.00 40.63 5.69
2330 2558 2.342354 CGCAAAAGAAATCATTCGTGGC 59.658 45.455 0.00 0.00 40.63 5.01
2331 2559 3.820689 TCGCAAAAGAAATCATTCGTGG 58.179 40.909 0.00 0.00 40.63 4.94
2332 2560 4.711721 TCTCGCAAAAGAAATCATTCGTG 58.288 39.130 0.00 0.00 40.63 4.35
2333 2561 5.356882 TTCTCGCAAAAGAAATCATTCGT 57.643 34.783 0.00 0.00 40.63 3.85
2334 2562 6.674005 TTTTCTCGCAAAAGAAATCATTCG 57.326 33.333 6.72 0.00 43.02 3.34
2335 2563 8.285776 TCTTTTTCTCGCAAAAGAAATCATTC 57.714 30.769 12.08 0.00 45.58 2.67
2343 2571 8.472683 TTGAATTTTCTTTTTCTCGCAAAAGA 57.527 26.923 10.98 10.98 46.44 2.52
2344 2572 8.382875 ACTTGAATTTTCTTTTTCTCGCAAAAG 58.617 29.630 7.58 7.58 42.77 2.27
2345 2573 8.250538 ACTTGAATTTTCTTTTTCTCGCAAAA 57.749 26.923 0.00 0.00 0.00 2.44
2346 2574 7.826260 ACTTGAATTTTCTTTTTCTCGCAAA 57.174 28.000 0.00 0.00 0.00 3.68
2347 2575 7.971168 TGTACTTGAATTTTCTTTTTCTCGCAA 59.029 29.630 0.00 0.00 0.00 4.85
2348 2576 7.476667 TGTACTTGAATTTTCTTTTTCTCGCA 58.523 30.769 0.00 0.00 0.00 5.10
2349 2577 7.908193 TGTACTTGAATTTTCTTTTTCTCGC 57.092 32.000 0.00 0.00 0.00 5.03
2350 2578 9.663904 TCATGTACTTGAATTTTCTTTTTCTCG 57.336 29.630 8.89 0.00 0.00 4.04
2352 2580 9.468532 GCTCATGTACTTGAATTTTCTTTTTCT 57.531 29.630 12.09 0.00 0.00 2.52
2353 2581 9.468532 AGCTCATGTACTTGAATTTTCTTTTTC 57.531 29.630 12.09 0.00 0.00 2.29
2354 2582 9.822185 AAGCTCATGTACTTGAATTTTCTTTTT 57.178 25.926 12.09 0.00 0.00 1.94
2355 2583 9.822185 AAAGCTCATGTACTTGAATTTTCTTTT 57.178 25.926 12.09 4.02 0.00 2.27
2358 2586 9.899226 GTTAAAGCTCATGTACTTGAATTTTCT 57.101 29.630 18.67 8.18 0.00 2.52
2359 2587 9.677567 TGTTAAAGCTCATGTACTTGAATTTTC 57.322 29.630 18.67 14.66 0.00 2.29
2362 2590 9.463443 GTTTGTTAAAGCTCATGTACTTGAATT 57.537 29.630 12.09 9.88 0.00 2.17
2363 2591 7.803189 CGTTTGTTAAAGCTCATGTACTTGAAT 59.197 33.333 12.09 2.38 0.00 2.57
2364 2592 7.129622 CGTTTGTTAAAGCTCATGTACTTGAA 58.870 34.615 12.09 1.14 0.00 2.69
2365 2593 6.655062 CGTTTGTTAAAGCTCATGTACTTGA 58.345 36.000 10.70 10.70 0.00 3.02
2366 2594 5.339611 GCGTTTGTTAAAGCTCATGTACTTG 59.660 40.000 2.36 2.36 36.09 3.16
2367 2595 5.238650 AGCGTTTGTTAAAGCTCATGTACTT 59.761 36.000 0.00 0.00 44.17 2.24
2368 2596 4.755123 AGCGTTTGTTAAAGCTCATGTACT 59.245 37.500 0.00 0.00 44.17 2.73
2369 2597 5.030874 AGCGTTTGTTAAAGCTCATGTAC 57.969 39.130 0.00 0.00 44.17 2.90
2377 2605 8.889849 TTATTATTCAGAGCGTTTGTTAAAGC 57.110 30.769 0.00 0.00 38.78 3.51
2404 2632 5.221244 GGTGCTTTGATGTCACCTAGTTTTT 60.221 40.000 3.59 0.00 45.04 1.94
2405 2633 4.278419 GGTGCTTTGATGTCACCTAGTTTT 59.722 41.667 3.59 0.00 45.04 2.43
2406 2634 3.821033 GGTGCTTTGATGTCACCTAGTTT 59.179 43.478 3.59 0.00 45.04 2.66
2407 2635 3.412386 GGTGCTTTGATGTCACCTAGTT 58.588 45.455 3.59 0.00 45.04 2.24
2408 2636 3.059352 GGTGCTTTGATGTCACCTAGT 57.941 47.619 3.59 0.00 45.04 2.57
2413 2641 5.343249 GGATATTTGGTGCTTTGATGTCAC 58.657 41.667 0.00 0.00 0.00 3.67
2414 2642 4.402155 GGGATATTTGGTGCTTTGATGTCA 59.598 41.667 0.00 0.00 0.00 3.58
2415 2643 4.202151 GGGGATATTTGGTGCTTTGATGTC 60.202 45.833 0.00 0.00 0.00 3.06
2416 2644 3.706086 GGGGATATTTGGTGCTTTGATGT 59.294 43.478 0.00 0.00 0.00 3.06
2417 2645 3.705579 TGGGGATATTTGGTGCTTTGATG 59.294 43.478 0.00 0.00 0.00 3.07
2418 2646 3.706086 GTGGGGATATTTGGTGCTTTGAT 59.294 43.478 0.00 0.00 0.00 2.57
2419 2647 3.096092 GTGGGGATATTTGGTGCTTTGA 58.904 45.455 0.00 0.00 0.00 2.69
2420 2648 3.099141 AGTGGGGATATTTGGTGCTTTG 58.901 45.455 0.00 0.00 0.00 2.77
2421 2649 3.473113 AGTGGGGATATTTGGTGCTTT 57.527 42.857 0.00 0.00 0.00 3.51
2422 2650 3.527665 AGTAGTGGGGATATTTGGTGCTT 59.472 43.478 0.00 0.00 0.00 3.91
2423 2651 3.123273 AGTAGTGGGGATATTTGGTGCT 58.877 45.455 0.00 0.00 0.00 4.40
2424 2652 3.577805 AGTAGTGGGGATATTTGGTGC 57.422 47.619 0.00 0.00 0.00 5.01
2425 2653 5.261216 ACAAAGTAGTGGGGATATTTGGTG 58.739 41.667 0.00 0.00 33.14 4.17
2426 2654 5.253096 AGACAAAGTAGTGGGGATATTTGGT 59.747 40.000 0.00 0.00 33.14 3.67
2427 2655 5.755849 AGACAAAGTAGTGGGGATATTTGG 58.244 41.667 0.00 0.00 33.14 3.28
2428 2656 6.653989 AGAGACAAAGTAGTGGGGATATTTG 58.346 40.000 0.00 0.00 34.61 2.32
2429 2657 6.893020 AGAGACAAAGTAGTGGGGATATTT 57.107 37.500 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.