Multiple sequence alignment - TraesCS5B01G407900

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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 TraesCS5B01G407900 chr5B 100.000 5762 0 0 1 5762 583510385 583516146 0.000000e+00 10641.0
1 TraesCS5B01G407900 chr5B 96.702 667 21 1 2 667 195740428 195739762 0.000000e+00 1109.0
2 TraesCS5B01G407900 chr5B 96.102 667 24 2 2 667 55631628 55630963 0.000000e+00 1086.0
3 TraesCS5B01G407900 chr5B 99.123 114 1 0 1755 1868 145479142 145479255 7.570000e-49 206.0
4 TraesCS5B01G407900 chr5B 99.074 108 1 0 1760 1867 512985321 512985214 1.640000e-45 195.0
5 TraesCS5B01G407900 chr5D 95.675 2636 57 22 2249 4842 476034344 476036964 0.000000e+00 4183.0
6 TraesCS5B01G407900 chr5D 91.560 1019 55 13 748 1742 476033021 476034032 0.000000e+00 1376.0
7 TraesCS5B01G407900 chr5D 94.643 392 18 2 5374 5762 476037694 476038085 6.390000e-169 604.0
8 TraesCS5B01G407900 chr5D 91.844 282 10 6 4839 5107 476037136 476037417 1.170000e-101 381.0
9 TraesCS5B01G407900 chr5D 96.444 225 4 4 5106 5327 476037455 476037678 9.120000e-98 368.0
10 TraesCS5B01G407900 chr5D 93.966 232 13 1 1927 2157 476034112 476034343 3.300000e-92 350.0
11 TraesCS5B01G407900 chr5A 90.072 1108 81 11 3762 4842 595420391 595421496 0.000000e+00 1410.0
12 TraesCS5B01G407900 chr5A 95.958 668 24 3 2 667 18779971 18780637 0.000000e+00 1081.0
13 TraesCS5B01G407900 chr5A 88.166 938 60 19 726 1623 595417774 595418700 0.000000e+00 1070.0
14 TraesCS5B01G407900 chr5A 84.375 832 91 24 1865 2669 595418928 595419747 0.000000e+00 780.0
15 TraesCS5B01G407900 chr5A 82.831 431 41 16 5348 5762 595422261 595422674 7.100000e-94 355.0
16 TraesCS5B01G407900 chr5A 81.994 311 38 7 3030 3323 595420060 595420369 1.240000e-61 248.0
17 TraesCS5B01G407900 chr5A 93.478 92 6 0 2673 2764 595419836 595419927 2.800000e-28 137.0
18 TraesCS5B01G407900 chr6B 96.567 670 22 1 2 670 44070264 44069595 0.000000e+00 1109.0
19 TraesCS5B01G407900 chr6B 96.407 668 23 1 2 668 470631176 470630509 0.000000e+00 1099.0
20 TraesCS5B01G407900 chr6B 95.798 119 5 0 1748 1866 694401056 694401174 5.890000e-45 193.0
21 TraesCS5B01G407900 chr1A 96.413 669 24 0 2 670 464123233 464122565 0.000000e+00 1103.0
22 TraesCS5B01G407900 chr1A 96.263 669 23 2 2 668 11790088 11790756 0.000000e+00 1096.0
23 TraesCS5B01G407900 chr3B 96.547 666 21 2 2 667 739713728 739713065 0.000000e+00 1101.0
24 TraesCS5B01G407900 chr3B 98.276 116 2 0 1759 1874 554097751 554097636 2.720000e-48 204.0
25 TraesCS5B01G407900 chr3B 97.391 115 1 2 1752 1866 22055103 22054991 1.640000e-45 195.0
26 TraesCS5B01G407900 chr3B 99.074 108 1 0 1759 1866 732824767 732824874 1.640000e-45 195.0
27 TraesCS5B01G407900 chr3B 93.750 48 3 0 673 720 2341122 2341169 8.010000e-09 73.1
28 TraesCS5B01G407900 chrUn 96.119 670 24 2 2 670 50607846 50608514 0.000000e+00 1092.0
29 TraesCS5B01G407900 chr2B 98.230 113 1 1 1755 1866 99152088 99152200 4.550000e-46 196.0
30 TraesCS5B01G407900 chr2B 97.345 113 3 0 1755 1867 682917327 682917439 5.890000e-45 193.0
31 TraesCS5B01G407900 chr2B 93.600 125 7 1 1759 1882 701182300 701182176 9.860000e-43 185.0
32 TraesCS5B01G407900 chr2D 91.489 47 4 0 673 719 605714622 605714576 1.340000e-06 65.8


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 TraesCS5B01G407900 chr5B 583510385 583516146 5761 False 10641.000000 10641 100.000000 1 5762 1 chr5B.!!$F2 5761
1 TraesCS5B01G407900 chr5B 195739762 195740428 666 True 1109.000000 1109 96.702000 2 667 1 chr5B.!!$R2 665
2 TraesCS5B01G407900 chr5B 55630963 55631628 665 True 1086.000000 1086 96.102000 2 667 1 chr5B.!!$R1 665
3 TraesCS5B01G407900 chr5D 476033021 476038085 5064 False 1210.333333 4183 94.022000 748 5762 6 chr5D.!!$F1 5014
4 TraesCS5B01G407900 chr5A 18779971 18780637 666 False 1081.000000 1081 95.958000 2 667 1 chr5A.!!$F1 665
5 TraesCS5B01G407900 chr5A 595417774 595422674 4900 False 666.666667 1410 86.819333 726 5762 6 chr5A.!!$F2 5036
6 TraesCS5B01G407900 chr6B 44069595 44070264 669 True 1109.000000 1109 96.567000 2 670 1 chr6B.!!$R1 668
7 TraesCS5B01G407900 chr6B 470630509 470631176 667 True 1099.000000 1099 96.407000 2 668 1 chr6B.!!$R2 666
8 TraesCS5B01G407900 chr1A 464122565 464123233 668 True 1103.000000 1103 96.413000 2 670 1 chr1A.!!$R1 668
9 TraesCS5B01G407900 chr1A 11790088 11790756 668 False 1096.000000 1096 96.263000 2 668 1 chr1A.!!$F1 666
10 TraesCS5B01G407900 chr3B 739713065 739713728 663 True 1101.000000 1101 96.547000 2 667 1 chr3B.!!$R3 665
11 TraesCS5B01G407900 chrUn 50607846 50608514 668 False 1092.000000 1092 96.119000 2 670 1 chrUn.!!$F1 668

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
912 934 0.179161 CTACTCCGCACTGTTCCTCG 60.179 60.0 0.0 0.0 0.00 4.63 F
1585 1686 0.309612 GAAATGTGTTTCGGTGCCGT 59.690 50.0 10.6 0.0 40.74 5.68 F
2982 3237 0.102120 ATGTGTTTTGGTGCCACACG 59.898 50.0 0.0 0.0 43.21 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2216 0.255890 TTCTAAGGTGGCCATGGAGC 59.744 55.000 18.40 5.04 0.00 4.70 R
3498 3773 0.550914 ACTGAAAGAAGCACCACCCA 59.449 50.000 0.00 0.00 37.43 4.51 R
4831 5148 1.226945 GGCGCAACACTGTTTTGCT 60.227 52.632 24.14 0.00 45.99 3.91 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
32 33 2.287970 ACAATCTCACACGACGCAACTA 60.288 45.455 0.00 0.00 0.00 2.24
147 148 7.335673 TCAGTCATCCAAATAGCGTCAAATTTA 59.664 33.333 0.00 0.00 0.00 1.40
361 362 5.975344 CGTATGTGGTCTATGTTACAACGAT 59.025 40.000 0.00 0.00 33.60 3.73
375 376 1.189524 AACGATCGGAGGACCAACCA 61.190 55.000 20.98 0.00 42.04 3.67
388 389 0.817634 CCAACCACTGTTCAAGGCGA 60.818 55.000 0.00 0.00 30.42 5.54
490 491 3.157881 CCTCCTTCGACATAGGCATAGA 58.842 50.000 0.00 0.00 32.59 1.98
618 622 7.201696 CGGGTGTTACTCATAATGCTTTGTATT 60.202 37.037 0.00 0.00 0.00 1.89
627 631 8.861033 TCATAATGCTTTGTATTTGCTTGATC 57.139 30.769 0.00 0.00 0.00 2.92
685 689 5.353394 AAAAGTATCCTATTCACGCAGGA 57.647 39.130 0.00 0.00 44.90 3.86
686 690 4.592485 AAGTATCCTATTCACGCAGGAG 57.408 45.455 0.00 0.00 44.06 3.69
687 691 2.297597 AGTATCCTATTCACGCAGGAGC 59.702 50.000 0.00 0.00 44.06 4.70
710 714 2.746277 CTCCCGGGAGCCAAAACG 60.746 66.667 36.90 12.91 35.31 3.60
715 719 3.292159 GGGAGCCAAAACGCCGTT 61.292 61.111 0.00 0.00 0.00 4.44
716 720 2.254350 GGAGCCAAAACGCCGTTC 59.746 61.111 1.60 0.00 0.00 3.95
717 721 2.258726 GGAGCCAAAACGCCGTTCT 61.259 57.895 1.60 0.00 0.00 3.01
718 722 1.206831 GAGCCAAAACGCCGTTCTC 59.793 57.895 1.60 1.47 0.00 2.87
719 723 2.127383 GCCAAAACGCCGTTCTCG 60.127 61.111 1.60 0.00 0.00 4.04
902 924 2.126071 GCGTTCTGCTACTCCGCA 60.126 61.111 0.00 0.00 43.53 5.69
912 934 0.179161 CTACTCCGCACTGTTCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
934 956 0.658897 CTCTCGTCTCGCTAGTTCCC 59.341 60.000 0.00 0.00 0.00 3.97
1074 1097 2.480073 CGTCATGGTTTGGATGCCAATC 60.480 50.000 0.00 0.00 43.55 2.67
1327 1350 3.112709 GCTCGCGCTCGAAGGTTT 61.113 61.111 5.56 0.00 44.98 3.27
1360 1383 3.473625 TCCCGAAAACTTTGTTCTCCTC 58.526 45.455 0.00 0.00 0.00 3.71
1407 1430 2.051334 TTGTGTTAGTGGTGCTGCTT 57.949 45.000 0.00 0.00 0.00 3.91
1408 1431 2.920724 TGTGTTAGTGGTGCTGCTTA 57.079 45.000 0.00 0.00 0.00 3.09
1433 1474 1.300080 CTTGCACCGTTGGCCTTTG 60.300 57.895 3.32 0.00 0.00 2.77
1437 1478 0.874175 GCACCGTTGGCCTTTGTTTC 60.874 55.000 3.32 0.00 0.00 2.78
1438 1479 0.593773 CACCGTTGGCCTTTGTTTCG 60.594 55.000 3.32 0.00 0.00 3.46
1472 1513 1.336702 TGTTTGATGAAATGCGGTGCC 60.337 47.619 0.00 0.00 0.00 5.01
1494 1537 2.814269 CGTGTACTGTCTGCTATGCAT 58.186 47.619 3.79 3.79 38.13 3.96
1523 1616 6.582295 GCTGTTTGATGAAATGTGTTTACGAT 59.418 34.615 0.00 0.00 0.00 3.73
1548 1641 2.852748 CGTGTGTACTCTGTCTGCTAC 58.147 52.381 0.00 0.00 0.00 3.58
1566 1659 2.882876 GCCTGCCACTGCTTGATG 59.117 61.111 0.00 0.00 38.71 3.07
1569 1662 1.250328 CCTGCCACTGCTTGATGAAA 58.750 50.000 0.00 0.00 38.71 2.69
1572 1665 2.230508 CTGCCACTGCTTGATGAAATGT 59.769 45.455 0.00 0.00 38.71 2.71
1583 1684 2.030363 TGATGAAATGTGTTTCGGTGCC 60.030 45.455 0.00 0.00 45.34 5.01
1585 1686 0.309612 GAAATGTGTTTCGGTGCCGT 59.690 50.000 10.60 0.00 40.74 5.68
1702 1804 6.583562 AGACAACAGCAGTTTAGAACTTACT 58.416 36.000 0.00 0.00 40.46 2.24
1706 1808 5.298347 ACAGCAGTTTAGAACTTACTGACC 58.702 41.667 19.52 4.74 41.96 4.02
1743 1845 2.202440 CGCTGTCGGTCACCTACG 60.202 66.667 0.00 0.00 0.00 3.51
1761 1899 2.673833 ACGCTTGTTGCAGAGTACTAC 58.326 47.619 0.00 0.00 43.06 2.73
1762 1900 2.296471 ACGCTTGTTGCAGAGTACTACT 59.704 45.455 0.00 0.00 43.06 2.57
1763 1901 2.917971 CGCTTGTTGCAGAGTACTACTC 59.082 50.000 8.02 8.02 43.06 2.59
1764 1902 3.254892 GCTTGTTGCAGAGTACTACTCC 58.745 50.000 11.94 0.05 46.18 3.85
1765 1903 3.851098 CTTGTTGCAGAGTACTACTCCC 58.149 50.000 11.94 5.35 46.18 4.30
1766 1904 3.170991 TGTTGCAGAGTACTACTCCCT 57.829 47.619 11.94 0.00 46.18 4.20
1767 1905 3.090037 TGTTGCAGAGTACTACTCCCTC 58.910 50.000 11.94 3.57 46.18 4.30
1768 1906 2.427812 GTTGCAGAGTACTACTCCCTCC 59.572 54.545 11.94 0.79 46.18 4.30
1769 1907 1.310904 GCAGAGTACTACTCCCTCCG 58.689 60.000 11.94 0.00 46.18 4.63
1770 1908 1.408544 GCAGAGTACTACTCCCTCCGT 60.409 57.143 11.94 0.00 46.18 4.69
1771 1909 2.944991 GCAGAGTACTACTCCCTCCGTT 60.945 54.545 11.94 0.00 46.18 4.44
1772 1910 2.944349 CAGAGTACTACTCCCTCCGTTC 59.056 54.545 11.94 0.00 46.18 3.95
1773 1911 2.092484 AGAGTACTACTCCCTCCGTTCC 60.092 54.545 11.94 0.00 46.18 3.62
1774 1912 1.637553 AGTACTACTCCCTCCGTTCCA 59.362 52.381 0.00 0.00 0.00 3.53
1775 1913 2.042162 AGTACTACTCCCTCCGTTCCAA 59.958 50.000 0.00 0.00 0.00 3.53
1776 1914 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1777 1915 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
1778 1916 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
1779 1917 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
1780 1918 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
1781 1919 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
1782 1920 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
1783 1921 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
1784 1922 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
1785 1923 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
1786 1924 3.368116 CCTCCGTTCCAAATTACTCGTCT 60.368 47.826 0.00 0.00 0.00 4.18
1787 1925 3.841643 TCCGTTCCAAATTACTCGTCTC 58.158 45.455 0.00 0.00 0.00 3.36
1788 1926 3.508793 TCCGTTCCAAATTACTCGTCTCT 59.491 43.478 0.00 0.00 0.00 3.10
1789 1927 3.612860 CCGTTCCAAATTACTCGTCTCTG 59.387 47.826 0.00 0.00 0.00 3.35
1790 1928 4.482386 CGTTCCAAATTACTCGTCTCTGA 58.518 43.478 0.00 0.00 0.00 3.27
1791 1929 4.921515 CGTTCCAAATTACTCGTCTCTGAA 59.078 41.667 0.00 0.00 0.00 3.02
1792 1930 5.404366 CGTTCCAAATTACTCGTCTCTGAAA 59.596 40.000 0.00 0.00 0.00 2.69
1793 1931 6.090898 CGTTCCAAATTACTCGTCTCTGAAAT 59.909 38.462 0.00 0.00 0.00 2.17
1794 1932 6.968131 TCCAAATTACTCGTCTCTGAAATG 57.032 37.500 0.00 0.00 0.00 2.32
1795 1933 5.874810 TCCAAATTACTCGTCTCTGAAATGG 59.125 40.000 0.00 0.00 0.00 3.16
1796 1934 5.874810 CCAAATTACTCGTCTCTGAAATGGA 59.125 40.000 0.00 0.00 0.00 3.41
1797 1935 6.540189 CCAAATTACTCGTCTCTGAAATGGAT 59.460 38.462 0.00 0.00 0.00 3.41
1798 1936 7.404985 CAAATTACTCGTCTCTGAAATGGATG 58.595 38.462 0.00 0.00 0.00 3.51
1799 1937 5.661056 TTACTCGTCTCTGAAATGGATGT 57.339 39.130 0.00 0.00 0.00 3.06
1800 1938 6.769134 TTACTCGTCTCTGAAATGGATGTA 57.231 37.500 0.00 0.00 0.00 2.29
1801 1939 5.860941 ACTCGTCTCTGAAATGGATGTAT 57.139 39.130 0.00 0.00 0.00 2.29
1802 1940 5.837437 ACTCGTCTCTGAAATGGATGTATC 58.163 41.667 0.00 0.00 0.00 2.24
1803 1941 5.596361 ACTCGTCTCTGAAATGGATGTATCT 59.404 40.000 0.00 0.00 0.00 1.98
1804 1942 6.773200 ACTCGTCTCTGAAATGGATGTATCTA 59.227 38.462 0.00 0.00 0.00 1.98
1805 1943 7.040755 ACTCGTCTCTGAAATGGATGTATCTAG 60.041 40.741 0.00 0.00 0.00 2.43
1806 1944 6.998673 TCGTCTCTGAAATGGATGTATCTAGA 59.001 38.462 0.00 0.00 0.00 2.43
1807 1945 7.502561 TCGTCTCTGAAATGGATGTATCTAGAA 59.497 37.037 0.00 0.00 0.00 2.10
1808 1946 7.593273 CGTCTCTGAAATGGATGTATCTAGAAC 59.407 40.741 0.00 0.00 0.00 3.01
1809 1947 8.637986 GTCTCTGAAATGGATGTATCTAGAACT 58.362 37.037 0.00 0.00 0.00 3.01
1810 1948 9.868160 TCTCTGAAATGGATGTATCTAGAACTA 57.132 33.333 0.00 0.00 0.00 2.24
1839 1977 6.567959 ACATCTAGATACATCCATATGTGCG 58.432 40.000 4.54 0.00 45.99 5.34
1840 1978 6.378280 ACATCTAGATACATCCATATGTGCGA 59.622 38.462 4.54 0.00 45.99 5.10
1841 1979 6.196079 TCTAGATACATCCATATGTGCGAC 57.804 41.667 1.24 0.00 45.99 5.19
1842 1980 4.871933 AGATACATCCATATGTGCGACA 57.128 40.909 1.24 0.00 45.99 4.35
1843 1981 5.213891 AGATACATCCATATGTGCGACAA 57.786 39.130 1.24 0.00 45.99 3.18
1844 1982 5.233225 AGATACATCCATATGTGCGACAAG 58.767 41.667 1.24 0.00 45.99 3.16
1845 1983 3.266510 ACATCCATATGTGCGACAAGT 57.733 42.857 1.24 0.00 44.79 3.16
1846 1984 4.400529 ACATCCATATGTGCGACAAGTA 57.599 40.909 1.24 0.00 44.79 2.24
1847 1985 4.765273 ACATCCATATGTGCGACAAGTAA 58.235 39.130 1.24 0.00 44.79 2.24
1848 1986 5.368145 ACATCCATATGTGCGACAAGTAAT 58.632 37.500 1.24 0.00 44.79 1.89
1849 1987 5.822519 ACATCCATATGTGCGACAAGTAATT 59.177 36.000 1.24 0.00 44.79 1.40
1850 1988 5.984233 TCCATATGTGCGACAAGTAATTC 57.016 39.130 1.24 0.00 0.00 2.17
1851 1989 4.506288 TCCATATGTGCGACAAGTAATTCG 59.494 41.667 1.24 0.00 38.31 3.34
1852 1990 4.318760 CCATATGTGCGACAAGTAATTCGG 60.319 45.833 1.24 0.00 35.73 4.30
1853 1991 2.442212 TGTGCGACAAGTAATTCGGA 57.558 45.000 0.00 0.00 35.73 4.55
1854 1992 2.756829 TGTGCGACAAGTAATTCGGAA 58.243 42.857 0.00 0.00 37.32 4.30
1855 1993 2.477375 TGTGCGACAAGTAATTCGGAAC 59.523 45.455 0.00 0.00 37.32 3.62
1874 2012 4.080695 GGAACGGAGGGAGTAGGTTTTAAT 60.081 45.833 0.00 0.00 0.00 1.40
1908 2046 5.846203 ACAGAAAAGAACCATCCAAACATG 58.154 37.500 0.00 0.00 0.00 3.21
1918 2067 3.250521 CCATCCAAACATGGTTGCAAAAC 59.749 43.478 18.41 0.00 38.92 2.43
1931 2080 4.436242 TTGCAAAACAACAACTACGGAA 57.564 36.364 0.00 0.00 31.73 4.30
1932 2081 3.760537 TGCAAAACAACAACTACGGAAC 58.239 40.909 0.00 0.00 0.00 3.62
1933 2082 3.440872 TGCAAAACAACAACTACGGAACT 59.559 39.130 0.00 0.00 0.00 3.01
1934 2083 4.634883 TGCAAAACAACAACTACGGAACTA 59.365 37.500 0.00 0.00 0.00 2.24
1935 2084 5.297278 TGCAAAACAACAACTACGGAACTAT 59.703 36.000 0.00 0.00 0.00 2.12
1941 2090 6.518493 ACAACAACTACGGAACTATCAAAGA 58.482 36.000 0.00 0.00 0.00 2.52
1943 2092 7.117812 ACAACAACTACGGAACTATCAAAGATG 59.882 37.037 0.00 0.00 0.00 2.90
2067 2216 2.560542 AGCCTCTGCCTCGATTGTATAG 59.439 50.000 0.00 0.00 38.69 1.31
2152 2301 5.306419 TCTCTGCAATTCAGCCTAGTATGAT 59.694 40.000 0.00 0.00 42.56 2.45
2160 2309 4.152647 TCAGCCTAGTATGATACCCAGTG 58.847 47.826 0.00 0.00 0.00 3.66
2161 2310 4.141018 TCAGCCTAGTATGATACCCAGTGA 60.141 45.833 0.00 0.00 0.00 3.41
2166 2315 6.573289 GCCTAGTATGATACCCAGTGAGAATG 60.573 46.154 0.00 0.00 0.00 2.67
2180 2329 7.011763 CCCAGTGAGAATGTCTGTACAATTATG 59.988 40.741 0.00 0.00 39.58 1.90
2183 2332 8.097038 AGTGAGAATGTCTGTACAATTATGTGT 58.903 33.333 0.00 0.00 40.84 3.72
2187 2336 9.371136 AGAATGTCTGTACAATTATGTGTGTAG 57.629 33.333 0.00 0.00 40.84 2.74
2188 2337 9.366216 GAATGTCTGTACAATTATGTGTGTAGA 57.634 33.333 0.00 0.00 40.84 2.59
2189 2338 9.890629 AATGTCTGTACAATTATGTGTGTAGAT 57.109 29.630 0.00 0.00 40.84 1.98
2190 2339 8.926715 TGTCTGTACAATTATGTGTGTAGATC 57.073 34.615 0.00 0.00 40.84 2.75
2191 2340 8.527810 TGTCTGTACAATTATGTGTGTAGATCA 58.472 33.333 0.00 0.00 40.84 2.92
2192 2341 9.534565 GTCTGTACAATTATGTGTGTAGATCAT 57.465 33.333 0.00 0.00 40.84 2.45
2242 2400 1.726853 AACAGCTACTTTGCCGCTAG 58.273 50.000 0.00 0.00 31.80 3.42
2246 2404 2.603560 CAGCTACTTTGCCGCTAGTTAC 59.396 50.000 4.42 0.00 31.80 2.50
2300 2458 5.904362 GGGAACCGTCTCTTAACTAGTAA 57.096 43.478 0.00 0.00 40.86 2.24
2454 2615 6.142259 TGAACCCACCCTTAATAAAAGCTA 57.858 37.500 0.00 0.00 0.00 3.32
2472 2634 8.494016 AAAAGCTATCTGTACTGGACAATTAC 57.506 34.615 0.00 0.00 37.70 1.89
2504 2666 5.319139 CAACATCTACAGCTTCATTGTTCG 58.681 41.667 0.00 0.00 0.00 3.95
2565 2732 6.693315 ACATAGGTATGTAATTGTTGGTGC 57.307 37.500 0.56 0.00 44.54 5.01
2568 2735 3.761752 AGGTATGTAATTGTTGGTGCCAC 59.238 43.478 0.00 0.00 0.00 5.01
2569 2736 3.508012 GGTATGTAATTGTTGGTGCCACA 59.492 43.478 0.00 0.00 0.00 4.17
2570 2737 4.021894 GGTATGTAATTGTTGGTGCCACAA 60.022 41.667 0.00 8.06 0.00 3.33
2854 3109 3.531538 TGTATTAGTGGTGCTGCTTAGC 58.468 45.455 0.00 0.00 0.00 3.09
2943 3198 3.243877 GTGCGTGTATTCTGTCTGCTATG 59.756 47.826 0.00 0.00 0.00 2.23
2961 3216 2.049888 TGCACACCACTGTTTGATGA 57.950 45.000 0.00 0.00 0.00 2.92
2971 3226 6.313411 CACCACTGTTTGATGAAATGTGTTTT 59.687 34.615 10.77 0.00 31.74 2.43
2982 3237 0.102120 ATGTGTTTTGGTGCCACACG 59.898 50.000 0.00 0.00 43.21 4.49
2999 3254 1.069159 CACGAACTCTGTCTGCTACGT 60.069 52.381 0.00 0.00 0.00 3.57
3001 3256 1.197036 CGAACTCTGTCTGCTACGTCA 59.803 52.381 0.00 0.00 0.00 4.35
3046 3301 3.046390 GCGATGCTGTCTGTACTGTATC 58.954 50.000 0.00 0.00 40.70 2.24
3099 3356 3.826729 GCCCTACATTGTTTCTTCCAAGT 59.173 43.478 0.00 0.00 0.00 3.16
3168 3440 9.315525 GGAATATGTCTCTACCTTAAGTGAAAC 57.684 37.037 0.97 0.00 0.00 2.78
3223 3496 5.334319 TCATTTTTGCATGCAGAATACGAG 58.666 37.500 22.74 13.49 0.00 4.18
3428 3703 6.557253 AGGTACTGCCCATATGAGTTTATGTA 59.443 38.462 3.65 0.00 37.18 2.29
3465 3740 3.054434 TGTGGTGATAAGGGGTCTTCATG 60.054 47.826 0.00 0.00 34.59 3.07
3472 3747 6.828785 GTGATAAGGGGTCTTCATGTATTGTT 59.171 38.462 0.00 0.00 34.59 2.83
3473 3748 6.828273 TGATAAGGGGTCTTCATGTATTGTTG 59.172 38.462 0.00 0.00 34.59 3.33
3479 3754 8.378565 AGGGGTCTTCATGTATTGTTGATATAG 58.621 37.037 0.00 0.00 0.00 1.31
3495 3770 9.618890 TGTTGATATAGCTATTTTGAGAGCTTT 57.381 29.630 12.39 0.00 46.99 3.51
3498 3773 9.618890 TGATATAGCTATTTTGAGAGCTTTGTT 57.381 29.630 12.39 0.00 46.99 2.83
3560 3835 2.762887 TGTGGTTCTTTGCATTGTGGAA 59.237 40.909 0.00 0.00 0.00 3.53
3643 3918 2.482494 AGTGAATCCTAGGGTTCCTGG 58.518 52.381 28.33 0.00 34.61 4.45
3668 3943 7.362142 GGCTAGAGATATGATTGTACGATCACA 60.362 40.741 25.00 16.42 38.75 3.58
3680 3955 7.520119 TTGTACGATCACATGTATCAAAGAC 57.480 36.000 0.00 0.00 0.00 3.01
3752 4027 7.999679 TGTTGTGAAGTTCAATCTGAGAAATT 58.000 30.769 7.25 0.00 36.17 1.82
3790 4065 6.206634 CGGTGAATATAATATGGCCACTTTGT 59.793 38.462 8.16 5.73 0.00 2.83
3862 4137 7.121020 TGTTGCTAATTTCATCAGTAGCATTGA 59.879 33.333 3.91 0.00 46.08 2.57
4090 4380 6.447084 AGGGTGGAAGAAACTTGAGGAATATA 59.553 38.462 0.00 0.00 0.00 0.86
4206 4496 5.047847 GCAAGTGATTACTATGCGACCTTA 58.952 41.667 8.32 0.00 35.69 2.69
4260 4550 8.674263 AGGTATCTGATTTTATTTCAGCTCTG 57.326 34.615 0.00 0.00 40.35 3.35
4437 4729 4.082125 GTCAAGACCCTGAACAATTCCAT 58.918 43.478 0.00 0.00 0.00 3.41
4617 4934 4.844085 TCCTTTAGGAATGTCAGTCCTCAA 59.156 41.667 24.57 18.56 42.02 3.02
4831 5148 8.085296 TCGCTTTCAGCTATTTTTATTCCAAAA 58.915 29.630 0.00 0.00 39.60 2.44
4881 5375 9.638239 ATTTGTAAACATTTTCGCTACATTCAT 57.362 25.926 0.00 0.00 0.00 2.57
4883 5377 7.811653 TGTAAACATTTTCGCTACATTCATGA 58.188 30.769 0.00 0.00 0.00 3.07
5107 5618 1.578206 GAAGCTTGTTCTGCCCGTCC 61.578 60.000 2.10 0.00 0.00 4.79
5108 5619 2.032681 GCTTGTTCTGCCCGTCCT 59.967 61.111 0.00 0.00 0.00 3.85
5131 5699 1.692519 AGTTACCGCTCCACTTCAGTT 59.307 47.619 0.00 0.00 0.00 3.16
5278 5852 5.991606 TGTCTCACTCTAACAAGTTTGATGG 59.008 40.000 0.00 0.00 0.00 3.51
5291 5865 3.010420 GTTTGATGGGCTCTTGGTAGAC 58.990 50.000 0.00 0.00 0.00 2.59
5299 5873 1.270907 CTCTTGGTAGACCCTGTGCT 58.729 55.000 0.00 0.00 34.29 4.40
5345 5919 2.512705 AGGGAAAGAAAGCAAGCTGAG 58.487 47.619 0.00 0.00 0.00 3.35
5365 5979 6.317140 GCTGAGAACCATAAATTGATCACTCA 59.683 38.462 0.00 0.00 0.00 3.41
5382 5996 4.716784 TCACTCAAACCTCATAGTATGCCT 59.283 41.667 5.18 0.00 0.00 4.75
5444 6059 2.949644 CTGACCAAGTTTTCCGTTTCCT 59.050 45.455 0.00 0.00 0.00 3.36
5635 6253 2.228822 CCAACATCAACCACCTAGCAAC 59.771 50.000 0.00 0.00 0.00 4.17
5679 6297 5.865085 GGATTTCTTTAAAGCCCCTGTTTT 58.135 37.500 10.51 0.00 43.93 2.43
5715 6341 1.325355 ACCATTATCAGCTGCCATGC 58.675 50.000 9.47 0.00 0.00 4.06
5746 6375 1.671979 ATTCGCTGTGACCCATGATG 58.328 50.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.465390 TCGTGTGAGATTGTCTTTGGTTAAG 59.535 40.000 0.00 0.00 35.04 1.85
32 33 6.496144 AACAACACTTCTTACTCCCTTACT 57.504 37.500 0.00 0.00 0.00 2.24
147 148 1.750193 CAACAGTTGTGGGCGGATAT 58.250 50.000 4.99 0.00 0.00 1.63
361 362 1.052124 AACAGTGGTTGGTCCTCCGA 61.052 55.000 0.00 0.00 35.46 4.55
375 376 3.525537 CATACAGATCGCCTTGAACAGT 58.474 45.455 0.00 0.00 0.00 3.55
388 389 2.549563 CCTGCTCCAATCGCATACAGAT 60.550 50.000 0.00 0.00 36.70 2.90
429 430 2.560542 GTTATGTTGCCACCCATGTTGA 59.439 45.455 0.00 0.00 0.00 3.18
466 467 1.112113 GCCTATGTCGAAGGAGGTGA 58.888 55.000 5.80 0.00 36.08 4.02
490 491 2.981081 AGTAGAGCCCTATAGACCGACT 59.019 50.000 0.00 0.00 0.00 4.18
618 622 8.985315 ATTATCTCAAATGTAGGATCAAGCAA 57.015 30.769 0.00 0.00 0.00 3.91
627 631 8.237267 GGGCGATTTTATTATCTCAAATGTAGG 58.763 37.037 0.00 0.00 0.00 3.18
693 697 2.746277 CGTTTTGGCTCCCGGGAG 60.746 66.667 41.29 41.29 44.56 4.30
698 702 3.263503 GAACGGCGTTTTGGCTCCC 62.264 63.158 27.48 7.42 42.02 4.30
699 703 2.183858 GAGAACGGCGTTTTGGCTCC 62.184 60.000 27.48 11.90 42.02 4.70
700 704 1.206831 GAGAACGGCGTTTTGGCTC 59.793 57.895 27.48 22.57 42.02 4.70
701 705 2.604174 CGAGAACGGCGTTTTGGCT 61.604 57.895 27.48 18.61 42.02 4.75
702 706 2.127383 CGAGAACGGCGTTTTGGC 60.127 61.111 27.48 13.82 40.44 4.52
712 716 0.179134 CAAGAGCCTACCCGAGAACG 60.179 60.000 0.00 0.00 39.43 3.95
713 717 0.460459 GCAAGAGCCTACCCGAGAAC 60.460 60.000 0.00 0.00 33.58 3.01
714 718 1.898154 GCAAGAGCCTACCCGAGAA 59.102 57.895 0.00 0.00 33.58 2.87
715 719 2.415608 CGCAAGAGCCTACCCGAGA 61.416 63.158 0.00 0.00 43.02 4.04
716 720 1.381928 TACGCAAGAGCCTACCCGAG 61.382 60.000 0.00 0.00 43.62 4.63
717 721 0.754217 ATACGCAAGAGCCTACCCGA 60.754 55.000 0.00 0.00 43.62 5.14
718 722 0.104304 AATACGCAAGAGCCTACCCG 59.896 55.000 0.00 0.00 43.62 5.28
719 723 1.867166 GAATACGCAAGAGCCTACCC 58.133 55.000 0.00 0.00 43.62 3.69
720 724 1.488527 CGAATACGCAAGAGCCTACC 58.511 55.000 0.00 0.00 43.62 3.18
902 924 0.250814 ACGAGAGTCCGAGGAACAGT 60.251 55.000 7.83 0.00 44.19 3.55
934 956 4.404654 GCTTGCGCCGGAAGTTGG 62.405 66.667 19.49 0.00 0.00 3.77
1074 1097 4.446371 ACCAAAGATAGATTTCAGCGGAG 58.554 43.478 0.00 0.00 0.00 4.63
1327 1350 2.043349 TCGGGATTCGAGAGGCCA 60.043 61.111 5.01 0.00 43.74 5.36
1353 1376 1.588597 CGAGCACAGCAGAGGAGAA 59.411 57.895 0.00 0.00 0.00 2.87
1354 1377 2.999485 GCGAGCACAGCAGAGGAGA 61.999 63.158 0.00 0.00 34.19 3.71
1360 1383 2.816958 AATCGGCGAGCACAGCAG 60.817 61.111 17.22 0.00 36.08 4.24
1407 1430 2.080693 CCAACGGTGCAAGCAACTATA 58.919 47.619 8.61 0.00 0.00 1.31
1408 1431 0.881118 CCAACGGTGCAAGCAACTAT 59.119 50.000 8.61 0.00 0.00 2.12
1433 1474 2.742053 ACAGATGGTATGCACACGAAAC 59.258 45.455 0.00 0.00 0.00 2.78
1437 1478 2.741517 TCAAACAGATGGTATGCACACG 59.258 45.455 0.00 0.00 0.00 4.49
1438 1479 4.970662 ATCAAACAGATGGTATGCACAC 57.029 40.909 0.00 0.00 35.06 3.82
1472 1513 1.191944 CATAGCAGACAGTACACGCG 58.808 55.000 3.53 3.53 0.00 6.01
1479 1520 1.664873 CAGCATGCATAGCAGACAGT 58.335 50.000 21.98 0.00 43.65 3.55
1494 1537 3.068448 ACACATTTCATCAAACAGCAGCA 59.932 39.130 0.00 0.00 0.00 4.41
1523 1616 0.318699 GACAGAGTACACACGCAGCA 60.319 55.000 0.00 0.00 0.00 4.41
1548 1641 2.749044 ATCAAGCAGTGGCAGGCG 60.749 61.111 5.53 0.00 44.61 5.52
1560 1653 3.670055 GCACCGAAACACATTTCATCAAG 59.330 43.478 1.13 0.00 43.90 3.02
1566 1659 0.309612 ACGGCACCGAAACACATTTC 59.690 50.000 17.40 0.00 42.83 2.17
1569 1662 1.525077 ACACGGCACCGAAACACAT 60.525 52.632 17.40 0.00 42.83 3.21
1572 1665 1.143401 TACACACGGCACCGAAACA 59.857 52.632 17.40 0.00 42.83 2.83
1585 1686 2.699251 CGTAGCAGACAGTGTACACA 57.301 50.000 27.06 1.38 0.00 3.72
1653 1755 3.878103 TCGGTTTTCTGAAACGGAAATCA 59.122 39.130 1.58 0.00 45.93 2.57
1702 1804 2.110213 GGAGTGTTGCGTGGGTCA 59.890 61.111 0.00 0.00 0.00 4.02
1706 1808 2.111043 ACCTGGAGTGTTGCGTGG 59.889 61.111 0.00 0.00 0.00 4.94
1729 1831 1.287815 CAAGCGTAGGTGACCGACA 59.712 57.895 15.11 0.00 39.47 4.35
1742 1844 2.917971 GAGTAGTACTCTGCAACAAGCG 59.082 50.000 20.95 0.00 41.88 4.68
1743 1845 3.254892 GGAGTAGTACTCTGCAACAAGC 58.745 50.000 25.70 6.07 44.46 4.01
1761 1899 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
1762 1900 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
1763 1901 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1764 1902 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1765 1903 3.846360 AGACGAGTAATTTGGAACGGAG 58.154 45.455 0.00 0.00 0.00 4.63
1766 1904 3.508793 AGAGACGAGTAATTTGGAACGGA 59.491 43.478 0.00 0.00 0.00 4.69
1767 1905 3.612860 CAGAGACGAGTAATTTGGAACGG 59.387 47.826 0.00 0.00 0.00 4.44
1768 1906 4.482386 TCAGAGACGAGTAATTTGGAACG 58.518 43.478 0.00 0.00 0.00 3.95
1769 1907 6.780706 TTTCAGAGACGAGTAATTTGGAAC 57.219 37.500 0.00 0.00 0.00 3.62
1770 1908 6.371548 CCATTTCAGAGACGAGTAATTTGGAA 59.628 38.462 0.00 0.00 0.00 3.53
1771 1909 5.874810 CCATTTCAGAGACGAGTAATTTGGA 59.125 40.000 0.00 0.00 0.00 3.53
1772 1910 5.874810 TCCATTTCAGAGACGAGTAATTTGG 59.125 40.000 0.00 0.00 0.00 3.28
1773 1911 6.968131 TCCATTTCAGAGACGAGTAATTTG 57.032 37.500 0.00 0.00 0.00 2.32
1774 1912 7.106239 ACATCCATTTCAGAGACGAGTAATTT 58.894 34.615 0.00 0.00 0.00 1.82
1775 1913 6.644347 ACATCCATTTCAGAGACGAGTAATT 58.356 36.000 0.00 0.00 0.00 1.40
1776 1914 6.227298 ACATCCATTTCAGAGACGAGTAAT 57.773 37.500 0.00 0.00 0.00 1.89
1777 1915 5.661056 ACATCCATTTCAGAGACGAGTAA 57.339 39.130 0.00 0.00 0.00 2.24
1778 1916 6.773200 AGATACATCCATTTCAGAGACGAGTA 59.227 38.462 0.00 0.00 0.00 2.59
1779 1917 5.596361 AGATACATCCATTTCAGAGACGAGT 59.404 40.000 0.00 0.00 0.00 4.18
1780 1918 6.083098 AGATACATCCATTTCAGAGACGAG 57.917 41.667 0.00 0.00 0.00 4.18
1781 1919 6.998673 TCTAGATACATCCATTTCAGAGACGA 59.001 38.462 0.00 0.00 0.00 4.20
1782 1920 7.208225 TCTAGATACATCCATTTCAGAGACG 57.792 40.000 0.00 0.00 0.00 4.18
1783 1921 8.637986 AGTTCTAGATACATCCATTTCAGAGAC 58.362 37.037 0.00 0.00 0.00 3.36
1784 1922 8.774546 AGTTCTAGATACATCCATTTCAGAGA 57.225 34.615 0.00 0.00 0.00 3.10
1813 1951 8.355913 CGCACATATGGATGTATCTAGATGTAT 58.644 37.037 15.79 9.11 44.68 2.29
1814 1952 7.556275 TCGCACATATGGATGTATCTAGATGTA 59.444 37.037 15.79 4.44 44.68 2.29
1815 1953 6.378280 TCGCACATATGGATGTATCTAGATGT 59.622 38.462 15.79 11.23 46.49 3.06
1816 1954 6.694844 GTCGCACATATGGATGTATCTAGATG 59.305 42.308 15.79 10.16 44.82 2.90
1817 1955 6.378280 TGTCGCACATATGGATGTATCTAGAT 59.622 38.462 10.73 10.73 44.82 1.98
1818 1956 5.710099 TGTCGCACATATGGATGTATCTAGA 59.290 40.000 7.80 0.00 44.82 2.43
1819 1957 5.954335 TGTCGCACATATGGATGTATCTAG 58.046 41.667 7.80 0.00 44.82 2.43
1820 1958 5.975693 TGTCGCACATATGGATGTATCTA 57.024 39.130 7.80 0.00 44.82 1.98
1821 1959 4.871933 TGTCGCACATATGGATGTATCT 57.128 40.909 7.80 0.00 44.82 1.98
1822 1960 4.991056 ACTTGTCGCACATATGGATGTATC 59.009 41.667 7.80 0.00 44.82 2.24
1823 1961 4.960938 ACTTGTCGCACATATGGATGTAT 58.039 39.130 7.80 0.00 44.82 2.29
1824 1962 4.400529 ACTTGTCGCACATATGGATGTA 57.599 40.909 7.80 0.00 44.82 2.29
1826 1964 5.929697 ATTACTTGTCGCACATATGGATG 57.070 39.130 7.80 0.00 39.16 3.51
1827 1965 5.177511 CGAATTACTTGTCGCACATATGGAT 59.822 40.000 7.80 0.00 0.00 3.41
1828 1966 4.506288 CGAATTACTTGTCGCACATATGGA 59.494 41.667 7.80 0.00 0.00 3.41
1829 1967 4.318760 CCGAATTACTTGTCGCACATATGG 60.319 45.833 7.80 0.00 35.93 2.74
1830 1968 4.506288 TCCGAATTACTTGTCGCACATATG 59.494 41.667 0.00 0.00 35.93 1.78
1831 1969 4.689071 TCCGAATTACTTGTCGCACATAT 58.311 39.130 0.00 0.00 35.93 1.78
1832 1970 4.112716 TCCGAATTACTTGTCGCACATA 57.887 40.909 0.00 0.00 35.93 2.29
1833 1971 2.967362 TCCGAATTACTTGTCGCACAT 58.033 42.857 0.00 0.00 35.93 3.21
1834 1972 2.442212 TCCGAATTACTTGTCGCACA 57.558 45.000 0.00 0.00 35.93 4.57
1835 1973 2.471749 CGTTCCGAATTACTTGTCGCAC 60.472 50.000 0.00 0.00 35.93 5.34
1836 1974 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
1837 1975 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
1838 1976 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
1839 1977 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1840 1978 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1841 1979 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1842 1980 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
1843 1981 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
1844 1982 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1845 1983 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1846 1984 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
1847 1985 1.400737 CTACTCCCTCCGTTCCGAAT 58.599 55.000 0.00 0.00 0.00 3.34
1848 1986 0.682209 CCTACTCCCTCCGTTCCGAA 60.682 60.000 0.00 0.00 0.00 4.30
1849 1987 1.077212 CCTACTCCCTCCGTTCCGA 60.077 63.158 0.00 0.00 0.00 4.55
1850 1988 0.969409 AACCTACTCCCTCCGTTCCG 60.969 60.000 0.00 0.00 0.00 4.30
1851 1989 1.273759 AAACCTACTCCCTCCGTTCC 58.726 55.000 0.00 0.00 0.00 3.62
1852 1990 4.541973 TTAAAACCTACTCCCTCCGTTC 57.458 45.455 0.00 0.00 0.00 3.95
1853 1991 5.509832 AATTAAAACCTACTCCCTCCGTT 57.490 39.130 0.00 0.00 0.00 4.44
1854 1992 5.250082 AGAAATTAAAACCTACTCCCTCCGT 59.750 40.000 0.00 0.00 0.00 4.69
1855 1993 5.742063 AGAAATTAAAACCTACTCCCTCCG 58.258 41.667 0.00 0.00 0.00 4.63
1856 1994 6.718294 TGAGAAATTAAAACCTACTCCCTCC 58.282 40.000 0.00 0.00 0.00 4.30
1857 1995 8.101419 TCTTGAGAAATTAAAACCTACTCCCTC 58.899 37.037 0.00 0.00 0.00 4.30
1858 1996 7.985589 TCTTGAGAAATTAAAACCTACTCCCT 58.014 34.615 0.00 0.00 0.00 4.20
1859 1997 8.631480 TTCTTGAGAAATTAAAACCTACTCCC 57.369 34.615 0.00 0.00 0.00 4.30
1860 1998 9.894783 GTTTCTTGAGAAATTAAAACCTACTCC 57.105 33.333 9.20 0.00 44.69 3.85
1874 2012 7.461182 TGGTTCTTTTCTGTTTCTTGAGAAA 57.539 32.000 2.16 2.16 41.29 2.52
1911 2049 3.440872 AGTTCCGTAGTTGTTGTTTTGCA 59.559 39.130 0.00 0.00 0.00 4.08
1918 2067 7.330946 TCATCTTTGATAGTTCCGTAGTTGTTG 59.669 37.037 0.00 0.00 0.00 3.33
1926 2075 6.377429 TCAGTAGTCATCTTTGATAGTTCCGT 59.623 38.462 0.00 0.00 33.56 4.69
1927 2076 6.796426 TCAGTAGTCATCTTTGATAGTTCCG 58.204 40.000 0.00 0.00 33.56 4.30
1928 2077 7.593273 CGATCAGTAGTCATCTTTGATAGTTCC 59.407 40.741 0.00 0.00 33.56 3.62
1929 2078 8.132362 ACGATCAGTAGTCATCTTTGATAGTTC 58.868 37.037 0.00 0.00 33.47 3.01
1930 2079 7.918033 CACGATCAGTAGTCATCTTTGATAGTT 59.082 37.037 0.00 0.00 34.17 2.24
1931 2080 7.067615 ACACGATCAGTAGTCATCTTTGATAGT 59.932 37.037 0.00 0.00 35.33 2.12
1932 2081 7.378194 CACACGATCAGTAGTCATCTTTGATAG 59.622 40.741 0.00 0.00 33.56 2.08
1933 2082 7.067008 TCACACGATCAGTAGTCATCTTTGATA 59.933 37.037 0.00 0.00 33.56 2.15
1934 2083 6.038985 CACACGATCAGTAGTCATCTTTGAT 58.961 40.000 0.00 0.00 33.56 2.57
1935 2084 5.183140 TCACACGATCAGTAGTCATCTTTGA 59.817 40.000 0.00 0.00 0.00 2.69
1941 2090 5.134202 TGTTTCACACGATCAGTAGTCAT 57.866 39.130 0.00 0.00 0.00 3.06
1943 2092 5.515626 GGTATGTTTCACACGATCAGTAGTC 59.484 44.000 0.00 0.00 0.00 2.59
1966 2115 3.255149 GGCCTCATTTTGCAGATCTATGG 59.745 47.826 0.00 0.00 0.00 2.74
2016 2165 2.306805 ACAACTCTCAGGATTGGCATGA 59.693 45.455 0.00 0.00 35.73 3.07
2067 2216 0.255890 TTCTAAGGTGGCCATGGAGC 59.744 55.000 18.40 5.04 0.00 4.70
2152 2301 4.412843 TGTACAGACATTCTCACTGGGTA 58.587 43.478 0.00 0.00 36.17 3.69
2160 2309 8.256611 ACACACATAATTGTACAGACATTCTC 57.743 34.615 0.00 0.00 34.86 2.87
2161 2310 9.371136 CTACACACATAATTGTACAGACATTCT 57.629 33.333 0.00 0.00 34.86 2.40
2166 2315 8.926715 TGATCTACACACATAATTGTACAGAC 57.073 34.615 0.00 0.00 33.76 3.51
2187 2336 8.697507 AGGACCTCCATTTGTAATTAATGATC 57.302 34.615 1.70 0.00 38.89 2.92
2194 2343 9.197306 GGTTAATTAGGACCTCCATTTGTAATT 57.803 33.333 0.00 0.00 38.89 1.40
2203 2354 6.634039 GCTGTTATGGTTAATTAGGACCTCCA 60.634 42.308 0.00 0.00 38.89 3.86
2204 2355 5.763698 GCTGTTATGGTTAATTAGGACCTCC 59.236 44.000 0.00 0.00 36.86 4.30
2454 2615 7.907389 TGAGAAAGTAATTGTCCAGTACAGAT 58.093 34.615 0.00 0.00 39.87 2.90
2472 2634 4.252073 AGCTGTAGATGTTGCTGAGAAAG 58.748 43.478 0.00 0.00 34.19 2.62
2547 2709 3.508012 TGTGGCACCAACAATTACATACC 59.492 43.478 16.26 0.00 0.00 2.73
2548 2710 4.775058 TGTGGCACCAACAATTACATAC 57.225 40.909 16.26 0.00 0.00 2.39
2549 2711 5.127693 GTTGTGGCACCAACAATTACATA 57.872 39.130 16.26 0.00 43.32 2.29
2550 2712 3.988819 GTTGTGGCACCAACAATTACAT 58.011 40.909 16.26 0.00 43.32 2.29
2575 2742 5.590663 GGGGTTTTGACTTTATTGCCAAAAA 59.409 36.000 0.00 0.00 39.32 1.94
2854 3109 4.347453 GGCCAACGGTGCAAGCAG 62.347 66.667 0.00 0.00 0.00 4.24
2943 3198 3.435105 TTTCATCAAACAGTGGTGTGC 57.565 42.857 0.00 0.00 39.59 4.57
2961 3216 2.626840 GTGTGGCACCAAAACACATTT 58.373 42.857 16.26 0.00 45.60 2.32
2971 3226 1.227527 CAGAGTTCGTGTGGCACCA 60.228 57.895 16.26 0.00 0.00 4.17
2982 3237 2.857618 CTGACGTAGCAGACAGAGTTC 58.142 52.381 0.00 0.00 38.14 3.01
2999 3254 3.305539 GCATTTCATCAAACAGTGGCTGA 60.306 43.478 2.91 0.00 35.18 4.26
3001 3256 2.629137 TGCATTTCATCAAACAGTGGCT 59.371 40.909 0.00 0.00 0.00 4.75
3046 3301 3.740631 TGGTGTGCATAGCAGATAGAG 57.259 47.619 11.59 0.00 40.08 2.43
3168 3440 1.153188 TCTGCATGCCGTACCCATG 60.153 57.895 16.68 13.92 42.23 3.66
3428 3703 4.792068 TCACCACAAAAAGAGATTCAGGT 58.208 39.130 0.00 0.00 0.00 4.00
3479 3754 4.021981 ACCCAACAAAGCTCTCAAAATAGC 60.022 41.667 0.00 0.00 39.08 2.97
3495 3770 1.341482 TGAAAGAAGCACCACCCAACA 60.341 47.619 0.00 0.00 0.00 3.33
3498 3773 0.550914 ACTGAAAGAAGCACCACCCA 59.449 50.000 0.00 0.00 37.43 4.51
3534 3809 4.809958 CACAATGCAAAGAACCACATCAAA 59.190 37.500 0.00 0.00 0.00 2.69
3541 3816 4.686191 AATTCCACAATGCAAAGAACCA 57.314 36.364 0.00 0.00 0.00 3.67
3643 3918 7.530863 TGTGATCGTACAATCATATCTCTAGC 58.469 38.462 0.00 0.00 37.93 3.42
3790 4065 7.398618 TCATCCCCTGCATTTGTAATAAGAAAA 59.601 33.333 0.00 0.00 0.00 2.29
3862 4137 7.004086 TGAAAGAATAACAACATGGTCCTTCT 58.996 34.615 0.00 0.00 0.00 2.85
4090 4380 2.567169 TCCACAGTCGTTGAGATGGATT 59.433 45.455 0.00 0.00 32.26 3.01
4206 4496 4.381292 GCAAAGAATAGAGCTGCAAATGGT 60.381 41.667 1.02 0.00 33.19 3.55
4437 4729 6.309389 TCGAGGTGATATAGAGCTATACCA 57.691 41.667 9.46 0.34 31.52 3.25
4640 4957 6.337356 CACTTGTTTACACAGAAAACCCAAT 58.663 36.000 0.00 0.00 36.26 3.16
4831 5148 1.226945 GGCGCAACACTGTTTTGCT 60.227 52.632 24.14 0.00 45.99 3.91
4988 5498 5.003804 AGACCTAGCAACGACAATTTCAAT 58.996 37.500 0.00 0.00 0.00 2.57
4992 5502 4.452455 CAGAAGACCTAGCAACGACAATTT 59.548 41.667 0.00 0.00 0.00 1.82
4996 5506 1.336887 GCAGAAGACCTAGCAACGACA 60.337 52.381 0.00 0.00 0.00 4.35
5107 5618 0.608640 AAGTGGAGCGGTAACTGGAG 59.391 55.000 3.44 0.00 0.00 3.86
5108 5619 0.606604 GAAGTGGAGCGGTAACTGGA 59.393 55.000 3.44 0.00 0.00 3.86
5131 5699 4.992319 CGTATTAACAAAGTCCACCACTGA 59.008 41.667 0.00 0.00 34.56 3.41
5291 5865 5.138276 TGGTAGATACTAGTAAGCACAGGG 58.862 45.833 6.70 0.00 0.00 4.45
5299 5873 3.879295 ACGCGCTTGGTAGATACTAGTAA 59.121 43.478 5.73 0.00 0.00 2.24
5329 5903 3.290710 TGGTTCTCAGCTTGCTTTCTTT 58.709 40.909 0.00 0.00 0.00 2.52
5345 5919 7.830739 AGGTTTGAGTGATCAATTTATGGTTC 58.169 34.615 0.00 0.00 0.00 3.62
5365 5979 7.563924 TGACTAACTAGGCATACTATGAGGTTT 59.436 37.037 0.00 0.00 36.14 3.27
5444 6059 8.138712 ACTTATTCCGTTATGTTTCAGCAAAAA 58.861 29.630 0.00 0.00 0.00 1.94
5635 6253 6.573664 TCCATCAACAAACTGGAGTTATTG 57.426 37.500 8.95 8.95 37.25 1.90
5693 6311 6.511855 AGCATGGCAGCTGATAATGGTACA 62.512 45.833 20.43 1.63 44.66 2.90
5715 6341 1.399440 ACAGCGAATAATGTGCAGCAG 59.601 47.619 0.00 0.00 0.00 4.24
5719 6345 1.737236 GGTCACAGCGAATAATGTGCA 59.263 47.619 0.52 0.00 45.12 4.57
5731 6360 3.505680 TGTTTAACATCATGGGTCACAGC 59.494 43.478 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.