Multiple sequence alignment - TraesCS5D01G036500

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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 TraesCS5D01G036500 chr5D 100.000 2459 0 0 1 2459 35559974 35562432 0.000000e+00 4542.0
1 TraesCS5D01G036500 chr5D 94.460 722 32 3 54 767 438209590 438210311 0.000000e+00 1105.0
2 TraesCS5D01G036500 chr5D 81.798 890 105 41 942 1804 35223660 35222801 0.000000e+00 693.0
3 TraesCS5D01G036500 chr5D 88.219 365 23 3 1904 2248 509681655 509681291 3.780000e-113 418.0
4 TraesCS5D01G036500 chr5D 77.181 447 64 31 1016 1433 35534216 35534653 2.460000e-55 226.0
5 TraesCS5D01G036500 chr5D 100.000 68 0 0 1 68 438209480 438209547 2.570000e-25 126.0
6 TraesCS5D01G036500 chr5D 82.090 134 18 4 2261 2388 35220105 35219972 2.590000e-20 110.0
7 TraesCS5D01G036500 chr6D 96.062 711 27 1 54 763 160965908 160966618 0.000000e+00 1157.0
8 TraesCS5D01G036500 chr6D 88.424 717 70 12 54 763 24903559 24904269 0.000000e+00 852.0
9 TraesCS5D01G036500 chr1D 96.056 710 28 0 59 768 488637209 488636500 0.000000e+00 1157.0
10 TraesCS5D01G036500 chr1D 83.448 145 16 5 1 137 108827322 108827466 7.140000e-26 128.0
11 TraesCS5D01G036500 chr3D 95.628 709 31 0 59 767 278814456 278813748 0.000000e+00 1138.0
12 TraesCS5D01G036500 chr3D 95.115 696 34 0 72 767 574629405 574628710 0.000000e+00 1098.0
13 TraesCS5D01G036500 chr3D 89.607 356 21 9 1909 2248 417156821 417156466 2.900000e-119 438.0
14 TraesCS5D01G036500 chr3D 87.463 335 40 2 1906 2239 430388399 430388732 3.840000e-103 385.0
15 TraesCS5D01G036500 chr3D 100.000 68 0 0 1 68 278814572 278814505 2.570000e-25 126.0
16 TraesCS5D01G036500 chr5A 88.337 926 68 19 768 1692 24188554 24189440 0.000000e+00 1075.0
17 TraesCS5D01G036500 chr5A 86.277 838 76 14 803 1607 23915800 23914969 0.000000e+00 874.0
18 TraesCS5D01G036500 chr5A 78.241 432 73 16 1017 1433 24161359 24161784 8.720000e-65 257.0
19 TraesCS5D01G036500 chr5A 81.595 163 24 5 2261 2419 23914552 23914392 1.980000e-26 130.0
20 TraesCS5D01G036500 chr7D 95.960 594 22 2 54 646 212816087 212816679 0.000000e+00 963.0
21 TraesCS5D01G036500 chr7D 89.694 359 22 3 1904 2248 91748700 91749057 6.240000e-121 444.0
22 TraesCS5D01G036500 chrUn 85.865 948 76 33 766 1690 313467080 313467992 0.000000e+00 955.0
23 TraesCS5D01G036500 chrUn 86.289 795 68 14 790 1570 293019800 293019033 0.000000e+00 826.0
24 TraesCS5D01G036500 chrUn 86.289 795 68 14 790 1570 326320983 326320216 0.000000e+00 826.0
25 TraesCS5D01G036500 chrUn 89.751 361 21 2 1904 2248 223002006 223002366 4.820000e-122 448.0
26 TraesCS5D01G036500 chrUn 89.444 360 23 1 1904 2248 92407127 92406768 8.070000e-120 440.0
27 TraesCS5D01G036500 chrUn 89.831 354 21 1 1904 2242 380756443 380756796 8.070000e-120 440.0
28 TraesCS5D01G036500 chrUn 81.350 311 29 23 1611 1899 318490560 318490257 2.460000e-55 226.0
29 TraesCS5D01G036500 chrUn 88.265 196 14 9 2269 2459 344039263 344039072 2.460000e-55 226.0
30 TraesCS5D01G036500 chr5B 85.404 829 72 26 790 1605 26606473 26605681 0.000000e+00 815.0
31 TraesCS5D01G036500 chr5B 91.111 90 8 0 1606 1695 26604135 26604046 3.320000e-24 122.0
32 TraesCS5D01G036500 chr2D 84.353 703 101 7 61 756 606191155 606191855 0.000000e+00 680.0
33 TraesCS5D01G036500 chr2D 87.500 360 30 2 1904 2248 451377857 451378216 3.810000e-108 401.0
34 TraesCS5D01G036500 chr2B 83.903 702 96 14 54 749 664360999 664361689 0.000000e+00 654.0
35 TraesCS5D01G036500 chr2B 86.559 372 30 5 1909 2264 49080291 49080658 2.290000e-105 392.0
36 TraesCS5D01G036500 chr2B 100.000 28 0 0 739 766 747098238 747098211 4.000000e-03 52.8
37 TraesCS5D01G036500 chr4A 88.669 353 33 7 1904 2252 688390712 688391061 8.130000e-115 424.0
38 TraesCS5D01G036500 chr3A 86.982 338 41 3 1905 2241 568527751 568528086 6.420000e-101 377.0
39 TraesCS5D01G036500 chr3A 83.448 145 16 4 1 137 430520643 430520787 7.140000e-26 128.0
40 TraesCS5D01G036500 chr1B 84.866 337 32 5 1904 2222 48479641 48479976 3.050000e-84 322.0
41 TraesCS5D01G036500 chr7B 85.246 244 19 5 1904 2130 640507740 640507497 4.090000e-58 235.0
42 TraesCS5D01G036500 chr7B 94.000 50 2 1 2270 2318 540787558 540787509 9.430000e-10 75.0
43 TraesCS5D01G036500 chr6A 84.138 145 15 5 1 137 63868881 63869025 1.530000e-27 134.0
44 TraesCS5D01G036500 chr6A 98.529 68 1 0 1 68 77787280 77787347 1.190000e-23 121.0
45 TraesCS5D01G036500 chr7A 100.000 68 0 0 1 68 308633750 308633683 2.570000e-25 126.0
46 TraesCS5D01G036500 chr4B 82.759 145 17 5 1 137 53862222 53862366 3.320000e-24 122.0
47 TraesCS5D01G036500 chr4D 98.529 68 1 0 1 68 208557081 208557014 1.190000e-23 121.0
48 TraesCS5D01G036500 chr2A 78.000 200 28 12 2260 2455 687257931 687258118 7.190000e-21 111.0
49 TraesCS5D01G036500 chr2A 78.613 173 24 10 2260 2421 687256091 687256261 4.330000e-18 102.0
50 TraesCS5D01G036500 chr2A 76.847 203 25 18 2260 2456 687258492 687258678 7.240000e-16 95.3
51 TraesCS5D01G036500 chr2A 76.500 200 30 13 2260 2456 687256725 687256910 2.600000e-15 93.5
52 TraesCS5D01G036500 chr2A 77.586 174 24 12 2260 2421 687257340 687257510 9.360000e-15 91.6


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 TraesCS5D01G036500 chr5D 35559974 35562432 2458 False 4542.0 4542 100.0000 1 2459 1 chr5D.!!$F2 2458
1 TraesCS5D01G036500 chr5D 438209480 438210311 831 False 615.5 1105 97.2300 1 767 2 chr5D.!!$F3 766
2 TraesCS5D01G036500 chr5D 35219972 35223660 3688 True 401.5 693 81.9440 942 2388 2 chr5D.!!$R2 1446
3 TraesCS5D01G036500 chr6D 160965908 160966618 710 False 1157.0 1157 96.0620 54 763 1 chr6D.!!$F2 709
4 TraesCS5D01G036500 chr6D 24903559 24904269 710 False 852.0 852 88.4240 54 763 1 chr6D.!!$F1 709
5 TraesCS5D01G036500 chr1D 488636500 488637209 709 True 1157.0 1157 96.0560 59 768 1 chr1D.!!$R1 709
6 TraesCS5D01G036500 chr3D 574628710 574629405 695 True 1098.0 1098 95.1150 72 767 1 chr3D.!!$R2 695
7 TraesCS5D01G036500 chr3D 278813748 278814572 824 True 632.0 1138 97.8140 1 767 2 chr3D.!!$R3 766
8 TraesCS5D01G036500 chr5A 24188554 24189440 886 False 1075.0 1075 88.3370 768 1692 1 chr5A.!!$F2 924
9 TraesCS5D01G036500 chr5A 23914392 23915800 1408 True 502.0 874 83.9360 803 2419 2 chr5A.!!$R1 1616
10 TraesCS5D01G036500 chr7D 212816087 212816679 592 False 963.0 963 95.9600 54 646 1 chr7D.!!$F2 592
11 TraesCS5D01G036500 chrUn 313467080 313467992 912 False 955.0 955 85.8650 766 1690 1 chrUn.!!$F2 924
12 TraesCS5D01G036500 chrUn 293019033 293019800 767 True 826.0 826 86.2890 790 1570 1 chrUn.!!$R2 780
13 TraesCS5D01G036500 chrUn 326320216 326320983 767 True 826.0 826 86.2890 790 1570 1 chrUn.!!$R4 780
14 TraesCS5D01G036500 chr5B 26604046 26606473 2427 True 468.5 815 88.2575 790 1695 2 chr5B.!!$R1 905
15 TraesCS5D01G036500 chr2D 606191155 606191855 700 False 680.0 680 84.3530 61 756 1 chr2D.!!$F2 695
16 TraesCS5D01G036500 chr2B 664360999 664361689 690 False 654.0 654 83.9030 54 749 1 chr2B.!!$F2 695

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
602 675 0.735978 ACGCGCGATGTTGAGATGAA 60.736 50.0 39.36 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1718 0.107654 GGCTGCTGTTCCCTACGATT 60.108 55.0 0.0 0.0 0.0 3.34 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
79 138 2.629137 TGTGTGGGCGAACTAGTTTCTA 59.371 45.455 10.02 0.00 31.20 2.10
189 248 3.236322 CGCGAACGTGGCAACTAA 58.764 55.556 0.00 0.00 37.61 2.24
190 249 1.565591 CGCGAACGTGGCAACTAAA 59.434 52.632 0.00 0.00 37.61 1.85
530 603 2.276201 CAACTAAATCGTCATCCCGCA 58.724 47.619 0.00 0.00 0.00 5.69
602 675 0.735978 ACGCGCGATGTTGAGATGAA 60.736 50.000 39.36 0.00 0.00 2.57
672 745 1.331214 CAATTCTAATGCCCGCCCAT 58.669 50.000 0.00 0.00 0.00 4.00
674 747 2.890311 CAATTCTAATGCCCGCCCATAA 59.110 45.455 0.00 0.00 0.00 1.90
705 778 2.186826 GGTTGCCTTGTGCTCACGT 61.187 57.895 0.00 0.00 42.00 4.49
781 854 3.211045 CGTTCTTCAGAAAAAGGTCCCA 58.789 45.455 0.00 0.00 35.58 4.37
872 949 1.282875 GGCAAGAAGACGTGTTGGC 59.717 57.895 1.19 8.80 46.65 4.52
900 982 4.127907 TGGTCATTGGCGCGTTAATTATA 58.872 39.130 8.43 0.00 0.00 0.98
956 1057 7.484007 CACGCGGGTAAAAGTAGACTATATATG 59.516 40.741 12.47 0.00 0.00 1.78
965 1066 7.540474 AAGTAGACTATATATGTGTGGTGGG 57.460 40.000 0.00 0.00 0.00 4.61
975 1082 4.699522 GTGGTGGGACGGTCAGGC 62.700 72.222 10.76 0.00 0.00 4.85
1122 1247 4.124351 TCATCGTCGTCGCACCCC 62.124 66.667 0.00 0.00 36.96 4.95
1176 1310 3.620785 GCGGGGATCGATGAGGCT 61.621 66.667 0.54 0.00 42.43 4.58
1274 1411 2.483745 GACCGACGACAGCGATCA 59.516 61.111 0.00 0.00 41.64 2.92
1470 1607 0.991920 ATTCCTGAACCACGGGTCAT 59.008 50.000 3.82 0.00 44.89 3.06
1480 1622 4.201679 CGGGTCATAGCGTCGGCA 62.202 66.667 0.00 0.00 43.41 5.69
1560 1707 3.499737 CCGGCGGCAACAGATGAC 61.500 66.667 15.42 0.00 0.00 3.06
1571 1718 3.496884 GCAACAGATGACGTTTCCTGTTA 59.503 43.478 21.48 0.00 44.97 2.41
1578 1725 6.020599 CAGATGACGTTTCCTGTTAATCGTAG 60.021 42.308 0.00 0.00 35.54 3.51
1582 1735 4.021192 ACGTTTCCTGTTAATCGTAGGGAA 60.021 41.667 0.00 0.00 34.10 3.97
1584 1737 5.240121 GTTTCCTGTTAATCGTAGGGAACA 58.760 41.667 8.44 0.00 45.47 3.18
1608 1761 1.519234 CGCCGTGCAGAGATAGCAA 60.519 57.895 0.00 0.00 44.64 3.91
1643 3341 1.766494 TGGCCATGTGACCATTCATC 58.234 50.000 0.00 0.00 33.11 2.92
1676 3384 6.749118 CCATGCAAAGACAAAGCTAAAGATAC 59.251 38.462 0.00 0.00 0.00 2.24
1692 3400 7.254898 GCTAAAGATACAGCTTGCACATTCATA 60.255 37.037 0.00 0.00 34.86 2.15
1697 3436 7.770433 AGATACAGCTTGCACATTCATACTTTA 59.230 33.333 0.00 0.00 0.00 1.85
1707 3446 6.074782 GCACATTCATACTTTAGCTACGTCTC 60.075 42.308 0.00 0.00 0.00 3.36
1708 3447 7.197017 CACATTCATACTTTAGCTACGTCTCT 58.803 38.462 0.00 0.00 0.00 3.10
1712 3451 7.154435 TCATACTTTAGCTACGTCTCTTGTT 57.846 36.000 0.00 0.00 0.00 2.83
1718 3457 7.707893 ACTTTAGCTACGTCTCTTGTTGTTTTA 59.292 33.333 0.00 0.00 0.00 1.52
1732 3571 6.287589 TGTTGTTTTACCTTGTCCAAACAT 57.712 33.333 0.00 0.00 38.56 2.71
1782 3622 0.859232 CGGACGCATTTCCTATTCGG 59.141 55.000 0.00 0.00 32.88 4.30
1785 3625 1.082756 CGCATTTCCTATTCGGCGC 60.083 57.895 0.00 0.00 37.96 6.53
1791 3631 0.179084 TTCCTATTCGGCGCCTTCAG 60.179 55.000 26.68 15.34 0.00 3.02
1804 3675 0.440371 CCTTCAGCGCTCGTTTCTTC 59.560 55.000 7.13 0.00 0.00 2.87
1812 3686 2.219674 GCGCTCGTTTCTTCCATATCTG 59.780 50.000 0.00 0.00 0.00 2.90
1818 3692 5.000591 TCGTTTCTTCCATATCTGCAAACA 58.999 37.500 0.00 0.00 0.00 2.83
1822 3696 2.804986 TCCATATCTGCAAACAGGCA 57.195 45.000 0.00 0.00 44.59 4.75
1828 3702 0.679321 TCTGCAAACAGGCACACACA 60.679 50.000 0.00 0.00 44.59 3.72
1865 3741 6.071896 GGCCAGCCCATCTTATATACTTTTTC 60.072 42.308 0.00 0.00 0.00 2.29
1922 3798 7.110179 CGTAAGGTGCAGATATAGTGATTTG 57.890 40.000 0.00 0.00 0.00 2.32
1924 3800 7.096023 CGTAAGGTGCAGATATAGTGATTTGAC 60.096 40.741 0.00 0.00 0.00 3.18
1925 3801 5.292765 AGGTGCAGATATAGTGATTTGACG 58.707 41.667 0.00 0.00 0.00 4.35
1926 3802 4.449068 GGTGCAGATATAGTGATTTGACGG 59.551 45.833 0.00 0.00 0.00 4.79
1927 3803 4.058124 TGCAGATATAGTGATTTGACGGC 58.942 43.478 0.00 0.00 0.00 5.68
1928 3804 3.433615 GCAGATATAGTGATTTGACGGCC 59.566 47.826 0.00 0.00 0.00 6.13
1929 3805 4.800914 GCAGATATAGTGATTTGACGGCCT 60.801 45.833 0.00 0.00 0.00 5.19
1932 3808 5.538813 AGATATAGTGATTTGACGGCCTACA 59.461 40.000 0.00 0.00 0.00 2.74
1934 3810 1.623811 AGTGATTTGACGGCCTACACT 59.376 47.619 0.00 3.04 33.29 3.55
1935 3811 2.038557 AGTGATTTGACGGCCTACACTT 59.961 45.455 0.00 0.00 34.21 3.16
1936 3812 2.812011 GTGATTTGACGGCCTACACTTT 59.188 45.455 0.00 0.00 0.00 2.66
1937 3813 3.252458 GTGATTTGACGGCCTACACTTTT 59.748 43.478 0.00 0.00 0.00 2.27
1938 3814 4.453136 GTGATTTGACGGCCTACACTTTTA 59.547 41.667 0.00 0.00 0.00 1.52
1939 3815 4.693566 TGATTTGACGGCCTACACTTTTAG 59.306 41.667 0.00 0.00 0.00 1.85
1940 3816 2.754946 TGACGGCCTACACTTTTAGG 57.245 50.000 0.00 0.00 41.65 2.69
1941 3817 1.276989 TGACGGCCTACACTTTTAGGG 59.723 52.381 0.00 0.00 39.39 3.53
1942 3818 0.616891 ACGGCCTACACTTTTAGGGG 59.383 55.000 0.00 0.00 39.39 4.79
1943 3819 0.906775 CGGCCTACACTTTTAGGGGA 59.093 55.000 0.00 0.00 39.39 4.81
1944 3820 1.489230 CGGCCTACACTTTTAGGGGAT 59.511 52.381 0.00 0.00 39.39 3.85
1945 3821 2.484947 CGGCCTACACTTTTAGGGGATC 60.485 54.545 0.00 0.00 39.39 3.36
1946 3822 2.508300 GGCCTACACTTTTAGGGGATCA 59.492 50.000 0.00 0.00 39.39 2.92
1947 3823 3.138468 GGCCTACACTTTTAGGGGATCAT 59.862 47.826 0.00 0.00 39.39 2.45
1949 3825 4.747009 GCCTACACTTTTAGGGGATCATCC 60.747 50.000 0.00 0.00 39.39 3.51
1958 3834 2.113986 GGATCATCCCGGCCCAAG 59.886 66.667 0.00 0.00 0.00 3.61
1959 3835 2.757124 GGATCATCCCGGCCCAAGT 61.757 63.158 0.00 0.00 0.00 3.16
1960 3836 1.415672 GGATCATCCCGGCCCAAGTA 61.416 60.000 0.00 0.00 0.00 2.24
1961 3837 0.250338 GATCATCCCGGCCCAAGTAC 60.250 60.000 0.00 0.00 0.00 2.73
1962 3838 2.040009 ATCATCCCGGCCCAAGTACG 62.040 60.000 0.00 0.00 0.00 3.67
1963 3839 2.686106 ATCCCGGCCCAAGTACGT 60.686 61.111 0.00 0.00 0.00 3.57
1965 3841 2.248086 ATCCCGGCCCAAGTACGTTC 62.248 60.000 0.00 0.00 0.00 3.95
1966 3842 2.344500 CCGGCCCAAGTACGTTCA 59.656 61.111 0.00 0.00 0.00 3.18
1967 3843 1.078708 CCGGCCCAAGTACGTTCAT 60.079 57.895 0.00 0.00 0.00 2.57
1968 3844 1.087771 CCGGCCCAAGTACGTTCATC 61.088 60.000 0.00 0.00 0.00 2.92
1969 3845 1.418342 CGGCCCAAGTACGTTCATCG 61.418 60.000 0.00 0.00 46.00 3.84
1970 3846 0.108520 GGCCCAAGTACGTTCATCGA 60.109 55.000 0.00 0.00 42.86 3.59
1971 3847 1.472728 GGCCCAAGTACGTTCATCGAT 60.473 52.381 0.00 0.00 42.86 3.59
1972 3848 1.859080 GCCCAAGTACGTTCATCGATC 59.141 52.381 0.00 0.00 42.86 3.69
1973 3849 2.737359 GCCCAAGTACGTTCATCGATCA 60.737 50.000 0.00 0.00 42.86 2.92
1974 3850 3.517602 CCCAAGTACGTTCATCGATCAA 58.482 45.455 0.00 0.00 42.86 2.57
1975 3851 3.551890 CCCAAGTACGTTCATCGATCAAG 59.448 47.826 0.00 0.00 42.86 3.02
1976 3852 4.421058 CCAAGTACGTTCATCGATCAAGA 58.579 43.478 0.00 0.00 42.86 3.02
1979 3855 6.036083 CCAAGTACGTTCATCGATCAAGATTT 59.964 38.462 0.00 0.00 42.86 2.17
1980 3856 6.814076 AGTACGTTCATCGATCAAGATTTC 57.186 37.500 0.00 0.00 42.86 2.17
1982 3858 3.871594 ACGTTCATCGATCAAGATTTCCC 59.128 43.478 0.00 0.00 42.86 3.97
1983 3859 3.871006 CGTTCATCGATCAAGATTTCCCA 59.129 43.478 0.00 0.00 42.86 4.37
1984 3860 4.512944 CGTTCATCGATCAAGATTTCCCAT 59.487 41.667 0.00 0.00 42.86 4.00
1985 3861 5.333645 CGTTCATCGATCAAGATTTCCCATC 60.334 44.000 0.00 0.00 42.86 3.51
1986 3862 5.557576 TCATCGATCAAGATTTCCCATCT 57.442 39.130 0.00 0.00 0.00 2.90
1987 3863 5.933617 TCATCGATCAAGATTTCCCATCTT 58.066 37.500 0.00 0.00 38.78 2.40
1989 3865 6.830324 TCATCGATCAAGATTTCCCATCTTTT 59.170 34.615 0.00 0.00 36.32 2.27
1990 3866 7.340232 TCATCGATCAAGATTTCCCATCTTTTT 59.660 33.333 0.00 0.00 36.32 1.94
1992 3868 6.038356 CGATCAAGATTTCCCATCTTTTTGG 58.962 40.000 0.00 0.00 36.32 3.28
1993 3869 6.127647 CGATCAAGATTTCCCATCTTTTTGGA 60.128 38.462 0.00 0.00 39.25 3.53
1995 6145 6.938507 TCAAGATTTCCCATCTTTTTGGATG 58.061 36.000 0.00 0.00 41.77 3.51
2004 6154 2.956132 TCTTTTTGGATGGGCAACTCA 58.044 42.857 0.00 0.00 0.00 3.41
2007 6157 1.631405 TTTGGATGGGCAACTCAAGG 58.369 50.000 0.00 0.00 0.00 3.61
2008 6158 0.899717 TTGGATGGGCAACTCAAGGC 60.900 55.000 0.00 0.00 0.00 4.35
2010 6160 3.056313 GATGGGCAACTCAAGGCGC 62.056 63.158 0.00 0.00 42.61 6.53
2015 6165 1.654220 GCAACTCAAGGCGCTTTCA 59.346 52.632 7.64 0.00 0.00 2.69
2023 6173 2.102252 TCAAGGCGCTTTCAAAAACCAT 59.898 40.909 7.64 0.00 0.00 3.55
2026 6176 4.535526 AGGCGCTTTCAAAAACCATTAT 57.464 36.364 7.64 0.00 0.00 1.28
2027 6177 4.893608 AGGCGCTTTCAAAAACCATTATT 58.106 34.783 7.64 0.00 0.00 1.40
2028 6178 4.690280 AGGCGCTTTCAAAAACCATTATTG 59.310 37.500 7.64 0.00 0.00 1.90
2043 6193 6.573664 CCATTATTGGTGAAAGAGTGACAA 57.426 37.500 0.00 0.00 38.30 3.18
2045 6195 6.016360 CCATTATTGGTGAAAGAGTGACAACA 60.016 38.462 0.00 0.00 38.30 3.33
2047 6197 5.695851 ATTGGTGAAAGAGTGACAACATC 57.304 39.130 0.00 0.00 31.31 3.06
2049 6199 3.131396 GGTGAAAGAGTGACAACATCGT 58.869 45.455 0.00 0.00 0.00 3.73
2050 6200 3.560068 GGTGAAAGAGTGACAACATCGTT 59.440 43.478 0.00 0.00 0.00 3.85
2052 6202 3.002246 TGAAAGAGTGACAACATCGTTGC 59.998 43.478 6.77 1.43 0.00 4.17
2054 6204 2.408050 AGAGTGACAACATCGTTGCTC 58.592 47.619 6.77 5.96 0.00 4.26
2056 6206 1.202639 AGTGACAACATCGTTGCTCCA 60.203 47.619 6.77 0.89 0.00 3.86
2057 6207 1.195448 GTGACAACATCGTTGCTCCAG 59.805 52.381 6.77 0.00 0.00 3.86
2058 6208 1.202639 TGACAACATCGTTGCTCCAGT 60.203 47.619 6.77 0.00 0.00 4.00
2059 6209 1.461127 GACAACATCGTTGCTCCAGTC 59.539 52.381 6.77 0.00 0.00 3.51
2060 6210 0.798776 CAACATCGTTGCTCCAGTCC 59.201 55.000 0.00 0.00 0.00 3.85
2062 6212 0.396435 ACATCGTTGCTCCAGTCCAA 59.604 50.000 0.00 0.00 0.00 3.53
2063 6213 1.003580 ACATCGTTGCTCCAGTCCAAT 59.996 47.619 0.00 0.00 0.00 3.16
2064 6214 2.086869 CATCGTTGCTCCAGTCCAATT 58.913 47.619 0.00 0.00 0.00 2.32
2066 6216 0.109597 CGTTGCTCCAGTCCAATTGC 60.110 55.000 0.00 0.00 0.00 3.56
2067 6217 0.961019 GTTGCTCCAGTCCAATTGCA 59.039 50.000 0.00 0.00 0.00 4.08
2068 6218 1.068055 GTTGCTCCAGTCCAATTGCAG 60.068 52.381 0.00 0.00 0.00 4.41
2070 6220 1.941999 GCTCCAGTCCAATTGCAGCC 61.942 60.000 0.00 0.00 0.00 4.85
2071 6221 0.323178 CTCCAGTCCAATTGCAGCCT 60.323 55.000 0.00 0.00 0.00 4.58
2072 6222 0.322816 TCCAGTCCAATTGCAGCCTC 60.323 55.000 0.00 0.00 0.00 4.70
2073 6223 0.323178 CCAGTCCAATTGCAGCCTCT 60.323 55.000 0.00 0.00 0.00 3.69
2074 6224 1.542492 CAGTCCAATTGCAGCCTCTT 58.458 50.000 0.00 0.00 0.00 2.85
2075 6225 1.891150 CAGTCCAATTGCAGCCTCTTT 59.109 47.619 0.00 0.00 0.00 2.52
2078 6228 2.164422 GTCCAATTGCAGCCTCTTTACC 59.836 50.000 0.00 0.00 0.00 2.85
2079 6229 1.133025 CCAATTGCAGCCTCTTTACCG 59.867 52.381 0.00 0.00 0.00 4.02
2080 6230 2.083774 CAATTGCAGCCTCTTTACCGA 58.916 47.619 0.00 0.00 0.00 4.69
2081 6231 2.487762 CAATTGCAGCCTCTTTACCGAA 59.512 45.455 0.00 0.00 0.00 4.30
2083 6233 0.685097 TGCAGCCTCTTTACCGAAGT 59.315 50.000 0.00 0.00 36.70 3.01
2084 6234 1.337823 TGCAGCCTCTTTACCGAAGTC 60.338 52.381 0.00 0.00 36.70 3.01
2085 6235 1.066787 GCAGCCTCTTTACCGAAGTCT 60.067 52.381 0.00 0.00 36.70 3.24
2086 6236 2.613223 GCAGCCTCTTTACCGAAGTCTT 60.613 50.000 0.00 0.00 36.70 3.01
2087 6237 3.665190 CAGCCTCTTTACCGAAGTCTTT 58.335 45.455 0.00 0.00 36.70 2.52
2089 6239 2.742589 GCCTCTTTACCGAAGTCTTTGG 59.257 50.000 16.37 16.37 40.28 3.28
2090 6240 3.556423 GCCTCTTTACCGAAGTCTTTGGA 60.556 47.826 23.64 6.42 37.65 3.53
2092 6242 4.262506 CCTCTTTACCGAAGTCTTTGGAGT 60.263 45.833 23.64 6.55 37.65 3.85
2093 6243 5.047519 CCTCTTTACCGAAGTCTTTGGAGTA 60.048 44.000 23.64 5.60 37.65 2.59
2094 6244 6.351117 CCTCTTTACCGAAGTCTTTGGAGTAT 60.351 42.308 23.64 5.53 37.65 2.12
2095 6245 7.001099 TCTTTACCGAAGTCTTTGGAGTATT 57.999 36.000 23.64 5.18 37.65 1.89
2096 6246 7.447594 TCTTTACCGAAGTCTTTGGAGTATTT 58.552 34.615 23.64 4.50 37.65 1.40
2097 6247 7.601508 TCTTTACCGAAGTCTTTGGAGTATTTC 59.398 37.037 23.64 0.00 37.65 2.17
2098 6248 5.485209 ACCGAAGTCTTTGGAGTATTTCT 57.515 39.130 23.64 0.00 37.65 2.52
2099 6249 5.866207 ACCGAAGTCTTTGGAGTATTTCTT 58.134 37.500 23.64 0.00 37.65 2.52
2100 6250 5.932883 ACCGAAGTCTTTGGAGTATTTCTTC 59.067 40.000 23.64 0.00 37.65 2.87
2101 6251 5.062308 CCGAAGTCTTTGGAGTATTTCTTCG 59.938 44.000 13.11 14.24 46.52 3.79
2103 6253 7.284518 GAAGTCTTTGGAGTATTTCTTCGAG 57.715 40.000 0.00 0.00 0.00 4.04
2104 6254 5.172205 AGTCTTTGGAGTATTTCTTCGAGC 58.828 41.667 0.00 0.00 0.00 5.03
2105 6255 4.929808 GTCTTTGGAGTATTTCTTCGAGCA 59.070 41.667 0.00 0.00 0.00 4.26
2106 6256 5.062809 GTCTTTGGAGTATTTCTTCGAGCAG 59.937 44.000 0.00 0.00 0.00 4.24
2107 6257 4.801330 TTGGAGTATTTCTTCGAGCAGA 57.199 40.909 0.00 0.00 0.00 4.26
2110 6260 4.220821 TGGAGTATTTCTTCGAGCAGAGTT 59.779 41.667 0.00 0.00 0.00 3.01
2111 6261 5.172205 GGAGTATTTCTTCGAGCAGAGTTT 58.828 41.667 0.00 0.00 0.00 2.66
2112 6262 5.062809 GGAGTATTTCTTCGAGCAGAGTTTG 59.937 44.000 0.00 0.00 0.00 2.93
2113 6263 5.784177 AGTATTTCTTCGAGCAGAGTTTGA 58.216 37.500 0.00 0.00 0.00 2.69
2114 6264 4.999751 ATTTCTTCGAGCAGAGTTTGAC 57.000 40.909 0.00 0.00 0.00 3.18
2115 6265 3.452755 TTCTTCGAGCAGAGTTTGACA 57.547 42.857 0.00 0.00 0.00 3.58
2116 6266 2.743938 TCTTCGAGCAGAGTTTGACAC 58.256 47.619 0.00 0.00 0.00 3.67
2117 6267 1.795286 CTTCGAGCAGAGTTTGACACC 59.205 52.381 0.00 0.00 0.00 4.16
2118 6268 0.318699 TCGAGCAGAGTTTGACACCG 60.319 55.000 0.00 0.00 0.00 4.94
2119 6269 0.597637 CGAGCAGAGTTTGACACCGT 60.598 55.000 0.00 0.00 0.00 4.83
2120 6270 0.861837 GAGCAGAGTTTGACACCGTG 59.138 55.000 0.00 0.00 0.00 4.94
2121 6271 0.464036 AGCAGAGTTTGACACCGTGA 59.536 50.000 5.28 0.00 0.00 4.35
2122 6272 1.134521 AGCAGAGTTTGACACCGTGAA 60.135 47.619 5.28 0.00 0.00 3.18
2123 6273 1.261619 GCAGAGTTTGACACCGTGAAG 59.738 52.381 5.28 0.00 0.00 3.02
2124 6274 2.821546 CAGAGTTTGACACCGTGAAGA 58.178 47.619 5.28 0.00 0.00 2.87
2125 6275 3.194861 CAGAGTTTGACACCGTGAAGAA 58.805 45.455 5.28 0.00 0.00 2.52
2127 6277 2.544267 GAGTTTGACACCGTGAAGAAGG 59.456 50.000 5.28 0.00 0.00 3.46
2128 6278 2.093128 AGTTTGACACCGTGAAGAAGGT 60.093 45.455 5.28 0.00 42.34 3.50
2136 6286 3.349022 ACCGTGAAGAAGGTGTTTTCAA 58.651 40.909 0.00 0.00 39.66 2.69
2137 6287 3.377172 ACCGTGAAGAAGGTGTTTTCAAG 59.623 43.478 0.00 0.00 39.66 3.02
2139 6289 4.260784 CCGTGAAGAAGGTGTTTTCAAGAG 60.261 45.833 1.88 0.00 33.89 2.85
2140 6290 4.570772 CGTGAAGAAGGTGTTTTCAAGAGA 59.429 41.667 0.00 0.00 33.89 3.10
2142 6292 6.238484 CGTGAAGAAGGTGTTTTCAAGAGATT 60.238 38.462 0.00 0.00 33.89 2.40
2143 6293 7.484140 GTGAAGAAGGTGTTTTCAAGAGATTT 58.516 34.615 0.00 0.00 33.10 2.17
2145 6295 7.339212 TGAAGAAGGTGTTTTCAAGAGATTTCA 59.661 33.333 0.00 0.00 0.00 2.69
2146 6296 7.830099 AGAAGGTGTTTTCAAGAGATTTCAT 57.170 32.000 0.00 0.00 0.00 2.57
2147 6297 8.242729 AGAAGGTGTTTTCAAGAGATTTCATT 57.757 30.769 0.00 0.00 0.00 2.57
2148 6298 8.139989 AGAAGGTGTTTTCAAGAGATTTCATTG 58.860 33.333 0.00 0.00 0.00 2.82
2149 6299 7.352079 AGGTGTTTTCAAGAGATTTCATTGT 57.648 32.000 0.00 0.00 0.00 2.71
2150 6300 8.463930 AGGTGTTTTCAAGAGATTTCATTGTA 57.536 30.769 0.00 0.00 0.00 2.41
2152 6302 9.696917 GGTGTTTTCAAGAGATTTCATTGTAAT 57.303 29.630 0.00 0.00 0.00 1.89
2190 6340 9.793259 TGAGTTACTTTGTATTTTCTTGGATCT 57.207 29.630 0.00 0.00 0.00 2.75
2196 6346 9.232473 ACTTTGTATTTTCTTGGATCTTAGGTC 57.768 33.333 0.00 0.00 0.00 3.85
2197 6347 8.575649 TTTGTATTTTCTTGGATCTTAGGTCC 57.424 34.615 4.22 4.22 36.26 4.46
2206 6356 5.102953 TGGATCTTAGGTCCAAATCAGTG 57.897 43.478 12.45 0.00 42.56 3.66
2207 6357 4.536090 TGGATCTTAGGTCCAAATCAGTGT 59.464 41.667 12.45 0.00 42.56 3.55
2208 6358 5.724370 TGGATCTTAGGTCCAAATCAGTGTA 59.276 40.000 12.45 0.00 42.56 2.90
2209 6359 6.049790 GGATCTTAGGTCCAAATCAGTGTAC 58.950 44.000 6.66 0.00 35.76 2.90
2210 6360 5.416271 TCTTAGGTCCAAATCAGTGTACC 57.584 43.478 0.00 0.00 0.00 3.34
2211 6361 5.091552 TCTTAGGTCCAAATCAGTGTACCT 58.908 41.667 0.00 0.00 40.38 3.08
2212 6362 6.258354 TCTTAGGTCCAAATCAGTGTACCTA 58.742 40.000 0.00 0.00 38.31 3.08
2213 6363 6.901300 TCTTAGGTCCAAATCAGTGTACCTAT 59.099 38.462 0.00 0.00 38.88 2.57
2214 6364 8.063153 TCTTAGGTCCAAATCAGTGTACCTATA 58.937 37.037 0.00 0.00 38.88 1.31
2215 6365 8.612486 TTAGGTCCAAATCAGTGTACCTATAA 57.388 34.615 0.00 0.00 38.88 0.98
2216 6366 7.691993 AGGTCCAAATCAGTGTACCTATAAT 57.308 36.000 0.00 0.00 35.61 1.28
2217 6367 8.102484 AGGTCCAAATCAGTGTACCTATAATT 57.898 34.615 0.00 0.00 35.61 1.40
2218 6368 7.993183 AGGTCCAAATCAGTGTACCTATAATTG 59.007 37.037 0.00 0.00 35.61 2.32
2219 6369 7.773690 GGTCCAAATCAGTGTACCTATAATTGT 59.226 37.037 0.00 0.00 0.00 2.71
2220 6370 9.174166 GTCCAAATCAGTGTACCTATAATTGTT 57.826 33.333 0.00 0.00 0.00 2.83
2225 6375 9.793259 AATCAGTGTACCTATAATTGTTATGGG 57.207 33.333 9.68 9.68 46.40 4.00
2243 6393 9.621629 TGTTATGGGTATGAATAAAGTTACAGG 57.378 33.333 0.00 0.00 0.00 4.00
2244 6394 9.623000 GTTATGGGTATGAATAAAGTTACAGGT 57.377 33.333 0.00 0.00 0.00 4.00
2245 6395 9.621629 TTATGGGTATGAATAAAGTTACAGGTG 57.378 33.333 0.00 0.00 0.00 4.00
2246 6396 7.023171 TGGGTATGAATAAAGTTACAGGTGT 57.977 36.000 0.00 0.00 0.00 4.16
2247 6397 7.463431 TGGGTATGAATAAAGTTACAGGTGTT 58.537 34.615 0.00 0.00 0.00 3.32
2248 6398 7.608761 TGGGTATGAATAAAGTTACAGGTGTTC 59.391 37.037 0.00 0.00 0.00 3.18
2249 6399 7.827729 GGGTATGAATAAAGTTACAGGTGTTCT 59.172 37.037 0.00 0.00 0.00 3.01
2250 6400 9.227777 GGTATGAATAAAGTTACAGGTGTTCTT 57.772 33.333 0.00 0.00 0.00 2.52
2328 6478 6.428799 TCTTCAAATAAACAACGTAAACCCG 58.571 36.000 0.00 0.00 0.00 5.28
2339 6489 4.018649 ACGTAAACCCGTTTGTTTTCTG 57.981 40.909 3.07 0.00 37.96 3.02
2340 6490 3.439825 ACGTAAACCCGTTTGTTTTCTGT 59.560 39.130 3.07 0.00 37.96 3.41
2341 6491 4.082841 ACGTAAACCCGTTTGTTTTCTGTT 60.083 37.500 3.07 0.00 37.96 3.16
2344 6494 5.599359 AAACCCGTTTGTTTTCTGTTTTG 57.401 34.783 0.00 0.00 34.92 2.44
2345 6495 3.591023 ACCCGTTTGTTTTCTGTTTTGG 58.409 40.909 0.00 0.00 0.00 3.28
2347 6497 2.350192 CCGTTTGTTTTCTGTTTTGGCC 59.650 45.455 0.00 0.00 0.00 5.36
2348 6498 2.028643 CGTTTGTTTTCTGTTTTGGCCG 59.971 45.455 0.00 0.00 0.00 6.13
2349 6499 2.301577 TTGTTTTCTGTTTTGGCCGG 57.698 45.000 0.00 0.00 0.00 6.13
2354 6511 3.336138 TTTCTGTTTTGGCCGGTTTTT 57.664 38.095 1.90 0.00 0.00 1.94
2355 6512 2.588027 TCTGTTTTGGCCGGTTTTTC 57.412 45.000 1.90 0.00 0.00 2.29
2358 6515 2.863740 CTGTTTTGGCCGGTTTTTCTTC 59.136 45.455 1.90 0.00 0.00 2.87
2360 6530 3.700038 TGTTTTGGCCGGTTTTTCTTCTA 59.300 39.130 1.90 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 138 4.204028 GGTGGTGGCTGTGTGGGT 62.204 66.667 0.00 0.00 0.00 4.51
189 248 9.801873 GAATTATAGTTGCCATGTGTGTTTATT 57.198 29.630 0.00 0.00 0.00 1.40
190 249 8.128582 CGAATTATAGTTGCCATGTGTGTTTAT 58.871 33.333 0.00 0.00 0.00 1.40
221 282 1.005294 GCAATTGCAGTTGCCGTCAG 61.005 55.000 30.49 2.50 46.69 3.51
591 664 6.878923 CCCAACAAGTACTATTCATCTCAACA 59.121 38.462 0.00 0.00 0.00 3.33
594 667 5.428253 GCCCAACAAGTACTATTCATCTCA 58.572 41.667 0.00 0.00 0.00 3.27
602 675 2.614481 CCACACGCCCAACAAGTACTAT 60.614 50.000 0.00 0.00 0.00 2.12
689 762 1.436195 GTGACGTGAGCACAAGGCAA 61.436 55.000 7.24 0.00 44.20 4.52
721 794 4.157289 CGTGTGGTATATTAGGTATCCGCT 59.843 45.833 0.00 0.00 0.00 5.52
756 829 1.663161 CCTTTTTCTGAAGAACGCCGC 60.663 52.381 0.00 0.00 33.13 6.53
763 836 3.053077 TCCTGGGACCTTTTTCTGAAGA 58.947 45.455 0.00 0.00 0.00 2.87
809 882 2.352960 GCCTTCTGCTTGAACTATTCCG 59.647 50.000 0.00 0.00 36.87 4.30
838 911 0.745128 TGCCGTTTCTTGGTCAACGT 60.745 50.000 3.98 0.00 43.43 3.99
839 912 0.378962 TTGCCGTTTCTTGGTCAACG 59.621 50.000 0.00 0.00 44.34 4.10
872 949 0.523968 CGCGCCAATGACCAAATCTG 60.524 55.000 0.00 0.00 0.00 2.90
900 982 2.817844 GTCAACGAATTAGCCCCAAACT 59.182 45.455 0.00 0.00 0.00 2.66
956 1057 2.030562 CTGACCGTCCCACCACAC 59.969 66.667 0.00 0.00 0.00 3.82
989 1096 4.677584 GTCTCTAGACATGGTGATCACAC 58.322 47.826 26.47 16.16 44.18 3.82
1176 1310 4.221422 GGATACGCGGCCAGCTCA 62.221 66.667 12.47 5.50 45.59 4.26
1374 1511 3.749064 AGCCACTCGTCGACGCAT 61.749 61.111 32.19 19.57 39.60 4.73
1443 1580 1.468914 GTGGTTCAGGAATTCTTCGCC 59.531 52.381 5.23 3.01 0.00 5.54
1480 1622 0.622136 TCTCCATGTCTTGGCTGCAT 59.378 50.000 0.50 0.00 46.01 3.96
1492 1634 5.500234 ACTATCTAGCTAGCTCTCTCCATG 58.500 45.833 23.26 7.79 0.00 3.66
1560 1707 4.114058 TCCCTACGATTAACAGGAAACG 57.886 45.455 0.00 0.00 0.00 3.60
1571 1718 0.107654 GGCTGCTGTTCCCTACGATT 60.108 55.000 0.00 0.00 0.00 3.34
1601 1754 6.456988 CCAAAACGATGTACTCCTTTGCTATC 60.457 42.308 0.00 0.00 0.00 2.08
1608 1761 2.224670 TGGCCAAAACGATGTACTCCTT 60.225 45.455 0.61 0.00 0.00 3.36
1676 3384 5.032863 GCTAAAGTATGAATGTGCAAGCTG 58.967 41.667 0.00 0.00 0.00 4.24
1692 3400 5.197682 ACAACAAGAGACGTAGCTAAAGT 57.802 39.130 0.00 0.00 0.00 2.66
1697 3436 4.748600 GGTAAAACAACAAGAGACGTAGCT 59.251 41.667 0.00 0.00 0.00 3.32
1707 3446 6.159988 TGTTTGGACAAGGTAAAACAACAAG 58.840 36.000 7.14 0.00 39.02 3.16
1708 3447 6.097915 TGTTTGGACAAGGTAAAACAACAA 57.902 33.333 7.14 0.00 39.02 2.83
1712 3451 6.287589 ACAATGTTTGGACAAGGTAAAACA 57.712 33.333 10.42 10.42 44.15 2.83
1718 3457 8.912988 CCATTATATACAATGTTTGGACAAGGT 58.087 33.333 3.17 0.00 39.66 3.50
1758 3598 4.555313 CGAATAGGAAATGCGTCCGTACTA 60.555 45.833 0.00 0.00 43.03 1.82
1759 3599 3.714391 GAATAGGAAATGCGTCCGTACT 58.286 45.455 0.00 0.00 43.03 2.73
1764 3604 0.586802 GCCGAATAGGAAATGCGTCC 59.413 55.000 0.00 0.00 45.00 4.79
1766 3606 1.772063 GCGCCGAATAGGAAATGCGT 61.772 55.000 0.00 0.00 45.00 5.24
1785 3625 0.440371 GAAGAAACGAGCGCTGAAGG 59.560 55.000 18.48 3.33 0.00 3.46
1791 3631 2.219674 CAGATATGGAAGAAACGAGCGC 59.780 50.000 0.00 0.00 0.00 5.92
1795 3635 5.000591 TGTTTGCAGATATGGAAGAAACGA 58.999 37.500 0.00 0.00 0.00 3.85
1796 3636 5.295431 TGTTTGCAGATATGGAAGAAACG 57.705 39.130 0.00 0.00 0.00 3.60
1800 3671 3.282021 GCCTGTTTGCAGATATGGAAGA 58.718 45.455 0.00 0.00 45.28 2.87
1804 3675 2.093890 TGTGCCTGTTTGCAGATATGG 58.906 47.619 0.00 0.00 45.28 2.74
1812 3686 1.226945 GGTGTGTGTGCCTGTTTGC 60.227 57.895 0.00 0.00 0.00 3.68
1818 3692 2.129555 GATGGAGGGTGTGTGTGCCT 62.130 60.000 0.00 0.00 0.00 4.75
1822 3696 1.492133 CCCAGATGGAGGGTGTGTGT 61.492 60.000 0.00 0.00 41.61 3.72
1858 3733 9.803315 GAAGGTTTTACAGAATGAAGAAAAAGT 57.197 29.630 0.00 0.00 39.69 2.66
1888 3764 1.003118 TGCACCTTACGGAGCTCATTT 59.997 47.619 17.19 0.79 45.79 2.32
1890 3766 0.176680 CTGCACCTTACGGAGCTCAT 59.823 55.000 17.19 5.44 45.79 2.90
1891 3767 0.898326 TCTGCACCTTACGGAGCTCA 60.898 55.000 17.19 0.00 45.79 4.26
1892 3768 0.461961 ATCTGCACCTTACGGAGCTC 59.538 55.000 4.71 4.71 45.79 4.09
1893 3769 1.776662 TATCTGCACCTTACGGAGCT 58.223 50.000 9.03 0.00 45.79 4.09
1894 3770 2.821991 ATATCTGCACCTTACGGAGC 57.178 50.000 0.44 0.44 45.80 4.70
1895 3771 4.519350 TCACTATATCTGCACCTTACGGAG 59.481 45.833 0.00 0.00 0.00 4.63
1896 3772 4.466827 TCACTATATCTGCACCTTACGGA 58.533 43.478 0.00 0.00 0.00 4.69
1897 3773 4.848562 TCACTATATCTGCACCTTACGG 57.151 45.455 0.00 0.00 0.00 4.02
1899 3775 7.096023 CGTCAAATCACTATATCTGCACCTTAC 60.096 40.741 0.00 0.00 0.00 2.34
1900 3776 6.923508 CGTCAAATCACTATATCTGCACCTTA 59.076 38.462 0.00 0.00 0.00 2.69
1901 3777 5.755375 CGTCAAATCACTATATCTGCACCTT 59.245 40.000 0.00 0.00 0.00 3.50
1904 3780 4.084328 GCCGTCAAATCACTATATCTGCAC 60.084 45.833 0.00 0.00 0.00 4.57
1905 3781 4.058124 GCCGTCAAATCACTATATCTGCA 58.942 43.478 0.00 0.00 0.00 4.41
1907 3783 4.887748 AGGCCGTCAAATCACTATATCTG 58.112 43.478 0.00 0.00 0.00 2.90
1911 3787 4.647853 AGTGTAGGCCGTCAAATCACTATA 59.352 41.667 0.00 0.00 33.78 1.31
1912 3788 3.451178 AGTGTAGGCCGTCAAATCACTAT 59.549 43.478 0.00 0.00 33.78 2.12
1913 3789 2.829720 AGTGTAGGCCGTCAAATCACTA 59.170 45.455 0.00 0.00 33.78 2.74
1914 3790 1.623811 AGTGTAGGCCGTCAAATCACT 59.376 47.619 0.00 3.05 0.00 3.41
1915 3791 2.094762 AGTGTAGGCCGTCAAATCAC 57.905 50.000 0.00 0.64 0.00 3.06
1916 3792 2.851263 AAGTGTAGGCCGTCAAATCA 57.149 45.000 0.00 0.00 0.00 2.57
1918 3794 4.007659 CCTAAAAGTGTAGGCCGTCAAAT 58.992 43.478 0.00 0.00 34.50 2.32
1920 3796 2.289819 CCCTAAAAGTGTAGGCCGTCAA 60.290 50.000 0.00 0.00 39.60 3.18
1921 3797 1.276989 CCCTAAAAGTGTAGGCCGTCA 59.723 52.381 0.00 0.00 39.60 4.35
1922 3798 1.406477 CCCCTAAAAGTGTAGGCCGTC 60.406 57.143 0.00 0.00 39.60 4.79
1924 3800 0.906775 TCCCCTAAAAGTGTAGGCCG 59.093 55.000 0.00 0.00 39.60 6.13
1925 3801 2.508300 TGATCCCCTAAAAGTGTAGGCC 59.492 50.000 0.00 0.00 39.60 5.19
1926 3802 3.926058 TGATCCCCTAAAAGTGTAGGC 57.074 47.619 0.00 0.00 39.60 3.93
1927 3803 4.974399 GGATGATCCCCTAAAAGTGTAGG 58.026 47.826 0.00 0.00 40.48 3.18
1941 3817 1.415672 TACTTGGGCCGGGATGATCC 61.416 60.000 2.18 1.94 35.23 3.36
1942 3818 0.250338 GTACTTGGGCCGGGATGATC 60.250 60.000 2.18 0.00 0.00 2.92
1943 3819 1.837090 GTACTTGGGCCGGGATGAT 59.163 57.895 2.18 0.00 0.00 2.45
1944 3820 2.727392 CGTACTTGGGCCGGGATGA 61.727 63.158 2.18 0.00 0.00 2.92
1945 3821 2.203015 CGTACTTGGGCCGGGATG 60.203 66.667 2.18 0.00 0.00 3.51
1946 3822 2.248086 GAACGTACTTGGGCCGGGAT 62.248 60.000 2.18 0.00 0.00 3.85
1947 3823 2.924101 AACGTACTTGGGCCGGGA 60.924 61.111 2.18 0.00 0.00 5.14
1949 3825 1.078708 ATGAACGTACTTGGGCCGG 60.079 57.895 0.00 0.00 0.00 6.13
1950 3826 1.418342 CGATGAACGTACTTGGGCCG 61.418 60.000 0.00 0.00 37.22 6.13
1951 3827 0.108520 TCGATGAACGTACTTGGGCC 60.109 55.000 0.00 0.00 43.13 5.80
1952 3828 1.859080 GATCGATGAACGTACTTGGGC 59.141 52.381 0.54 0.00 43.13 5.36
1953 3829 3.159353 TGATCGATGAACGTACTTGGG 57.841 47.619 0.54 0.00 43.13 4.12
1954 3830 4.421058 TCTTGATCGATGAACGTACTTGG 58.579 43.478 0.54 0.00 43.13 3.61
1955 3831 6.575083 AATCTTGATCGATGAACGTACTTG 57.425 37.500 0.54 0.00 43.13 3.16
1956 3832 6.255887 GGAAATCTTGATCGATGAACGTACTT 59.744 38.462 0.54 0.00 43.13 2.24
1957 3833 5.749109 GGAAATCTTGATCGATGAACGTACT 59.251 40.000 0.54 0.00 43.13 2.73
1958 3834 5.050972 GGGAAATCTTGATCGATGAACGTAC 60.051 44.000 0.54 0.00 43.13 3.67
1959 3835 5.047847 GGGAAATCTTGATCGATGAACGTA 58.952 41.667 0.54 0.00 43.13 3.57
1960 3836 3.871594 GGGAAATCTTGATCGATGAACGT 59.128 43.478 0.54 0.00 43.13 3.99
1961 3837 3.871006 TGGGAAATCTTGATCGATGAACG 59.129 43.478 0.54 0.00 44.09 3.95
1962 3838 5.762218 AGATGGGAAATCTTGATCGATGAAC 59.238 40.000 0.54 0.00 0.00 3.18
1963 3839 5.933617 AGATGGGAAATCTTGATCGATGAA 58.066 37.500 0.54 0.00 0.00 2.57
1965 3841 6.630444 AAAGATGGGAAATCTTGATCGATG 57.370 37.500 0.54 0.00 38.29 3.84
1966 3842 7.417116 CCAAAAAGATGGGAAATCTTGATCGAT 60.417 37.037 0.00 0.00 38.29 3.59
1967 3843 6.127647 CCAAAAAGATGGGAAATCTTGATCGA 60.128 38.462 1.54 0.00 38.29 3.59
1968 3844 6.038356 CCAAAAAGATGGGAAATCTTGATCG 58.962 40.000 1.54 0.00 38.29 3.69
1969 3845 7.174107 TCCAAAAAGATGGGAAATCTTGATC 57.826 36.000 1.54 0.00 41.05 2.92
1970 3846 7.562135 CATCCAAAAAGATGGGAAATCTTGAT 58.438 34.615 1.54 0.00 40.03 2.57
1971 3847 6.938507 CATCCAAAAAGATGGGAAATCTTGA 58.061 36.000 1.54 0.00 40.03 3.02
1982 3858 3.258872 TGAGTTGCCCATCCAAAAAGATG 59.741 43.478 0.00 0.00 42.79 2.90
1983 3859 3.509442 TGAGTTGCCCATCCAAAAAGAT 58.491 40.909 0.00 0.00 0.00 2.40
1984 3860 2.956132 TGAGTTGCCCATCCAAAAAGA 58.044 42.857 0.00 0.00 0.00 2.52
1985 3861 3.555586 CCTTGAGTTGCCCATCCAAAAAG 60.556 47.826 0.00 0.00 0.00 2.27
1986 3862 2.368221 CCTTGAGTTGCCCATCCAAAAA 59.632 45.455 0.00 0.00 0.00 1.94
1987 3863 1.969923 CCTTGAGTTGCCCATCCAAAA 59.030 47.619 0.00 0.00 0.00 2.44
1989 3865 0.899717 GCCTTGAGTTGCCCATCCAA 60.900 55.000 0.00 0.00 0.00 3.53
1990 3866 1.304381 GCCTTGAGTTGCCCATCCA 60.304 57.895 0.00 0.00 0.00 3.41
1992 3868 3.056313 GCGCCTTGAGTTGCCCATC 62.056 63.158 0.00 0.00 0.00 3.51
1993 3869 3.064324 GCGCCTTGAGTTGCCCAT 61.064 61.111 0.00 0.00 0.00 4.00
1995 6145 2.477972 GAAAGCGCCTTGAGTTGCCC 62.478 60.000 2.29 0.00 0.00 5.36
1998 6148 2.490328 TTTGAAAGCGCCTTGAGTTG 57.510 45.000 2.29 0.00 0.00 3.16
2000 6150 2.481276 GGTTTTTGAAAGCGCCTTGAGT 60.481 45.455 2.29 0.00 0.00 3.41
2004 6154 2.908688 ATGGTTTTTGAAAGCGCCTT 57.091 40.000 2.29 0.00 0.00 4.35
2007 6157 4.956793 CCAATAATGGTTTTTGAAAGCGC 58.043 39.130 0.00 0.00 42.18 5.92
2023 6173 6.073276 CGATGTTGTCACTCTTTCACCAATAA 60.073 38.462 0.00 0.00 0.00 1.40
2026 6176 3.559655 CGATGTTGTCACTCTTTCACCAA 59.440 43.478 0.00 0.00 0.00 3.67
2027 6177 3.130633 CGATGTTGTCACTCTTTCACCA 58.869 45.455 0.00 0.00 0.00 4.17
2028 6178 3.131396 ACGATGTTGTCACTCTTTCACC 58.869 45.455 0.00 0.00 0.00 4.02
2029 6179 4.518217 CAACGATGTTGTCACTCTTTCAC 58.482 43.478 1.59 0.00 0.00 3.18
2030 6180 3.002246 GCAACGATGTTGTCACTCTTTCA 59.998 43.478 10.96 0.00 0.00 2.69
2031 6181 3.248602 AGCAACGATGTTGTCACTCTTTC 59.751 43.478 10.96 0.00 0.00 2.62
2032 6182 3.206150 AGCAACGATGTTGTCACTCTTT 58.794 40.909 10.96 0.00 0.00 2.52
2033 6183 2.802816 GAGCAACGATGTTGTCACTCTT 59.197 45.455 10.96 0.00 0.00 2.85
2034 6184 2.408050 GAGCAACGATGTTGTCACTCT 58.592 47.619 10.96 0.00 0.00 3.24
2035 6185 1.461127 GGAGCAACGATGTTGTCACTC 59.539 52.381 10.96 8.75 0.00 3.51
2036 6186 1.202639 TGGAGCAACGATGTTGTCACT 60.203 47.619 10.96 0.57 0.00 3.41
2038 6188 1.202639 ACTGGAGCAACGATGTTGTCA 60.203 47.619 10.96 6.85 0.00 3.58
2039 6189 1.461127 GACTGGAGCAACGATGTTGTC 59.539 52.381 10.96 7.38 0.00 3.18
2042 6192 0.396435 TGGACTGGAGCAACGATGTT 59.604 50.000 0.00 0.00 0.00 2.71
2043 6193 0.396435 TTGGACTGGAGCAACGATGT 59.604 50.000 0.00 0.00 0.00 3.06
2045 6195 2.086869 CAATTGGACTGGAGCAACGAT 58.913 47.619 0.00 0.00 0.00 3.73
2047 6197 0.109597 GCAATTGGACTGGAGCAACG 60.110 55.000 7.72 0.00 0.00 4.10
2049 6199 1.250328 CTGCAATTGGACTGGAGCAA 58.750 50.000 7.72 0.00 0.00 3.91
2050 6200 2.951269 CTGCAATTGGACTGGAGCA 58.049 52.632 7.72 0.00 0.00 4.26
2052 6202 0.323178 AGGCTGCAATTGGACTGGAG 60.323 55.000 7.72 0.00 35.51 3.86
2054 6204 0.323178 AGAGGCTGCAATTGGACTGG 60.323 55.000 7.72 0.00 0.00 4.00
2056 6206 2.299326 AAAGAGGCTGCAATTGGACT 57.701 45.000 7.72 0.00 0.00 3.85
2057 6207 2.164422 GGTAAAGAGGCTGCAATTGGAC 59.836 50.000 7.72 0.00 0.00 4.02
2058 6208 2.446435 GGTAAAGAGGCTGCAATTGGA 58.554 47.619 7.72 2.96 0.00 3.53
2059 6209 1.133025 CGGTAAAGAGGCTGCAATTGG 59.867 52.381 7.72 0.00 0.00 3.16
2060 6210 2.083774 TCGGTAAAGAGGCTGCAATTG 58.916 47.619 0.00 0.00 0.00 2.32
2062 6212 2.290323 ACTTCGGTAAAGAGGCTGCAAT 60.290 45.455 0.50 0.00 38.44 3.56
2063 6213 1.071699 ACTTCGGTAAAGAGGCTGCAA 59.928 47.619 0.50 0.00 38.44 4.08
2064 6214 0.685097 ACTTCGGTAAAGAGGCTGCA 59.315 50.000 0.50 0.00 38.44 4.41
2066 6216 3.320673 AAGACTTCGGTAAAGAGGCTG 57.679 47.619 0.00 0.00 38.44 4.85
2067 6217 3.557264 CCAAAGACTTCGGTAAAGAGGCT 60.557 47.826 0.00 0.00 38.44 4.58
2068 6218 2.742589 CCAAAGACTTCGGTAAAGAGGC 59.257 50.000 0.00 0.00 38.44 4.70
2070 6220 4.884247 ACTCCAAAGACTTCGGTAAAGAG 58.116 43.478 0.00 0.00 38.44 2.85
2071 6221 4.950205 ACTCCAAAGACTTCGGTAAAGA 57.050 40.909 0.00 0.00 38.44 2.52
2072 6222 7.603024 AGAAATACTCCAAAGACTTCGGTAAAG 59.397 37.037 0.00 0.00 41.08 1.85
2073 6223 7.447594 AGAAATACTCCAAAGACTTCGGTAAA 58.552 34.615 0.00 0.00 0.00 2.01
2074 6224 7.001099 AGAAATACTCCAAAGACTTCGGTAA 57.999 36.000 0.00 0.00 0.00 2.85
2075 6225 6.600882 AGAAATACTCCAAAGACTTCGGTA 57.399 37.500 0.00 0.00 0.00 4.02
2078 6228 6.083925 CGAAGAAATACTCCAAAGACTTCG 57.916 41.667 0.00 0.00 45.11 3.79
2079 6229 6.183360 GCTCGAAGAAATACTCCAAAGACTTC 60.183 42.308 0.00 0.00 34.09 3.01
2080 6230 5.639931 GCTCGAAGAAATACTCCAAAGACTT 59.360 40.000 0.00 0.00 34.09 3.01
2081 6231 5.172205 GCTCGAAGAAATACTCCAAAGACT 58.828 41.667 0.00 0.00 34.09 3.24
2083 6233 5.047306 TCTGCTCGAAGAAATACTCCAAAGA 60.047 40.000 0.00 0.00 34.09 2.52
2084 6234 5.171476 TCTGCTCGAAGAAATACTCCAAAG 58.829 41.667 0.00 0.00 34.09 2.77
2085 6235 5.147330 TCTGCTCGAAGAAATACTCCAAA 57.853 39.130 0.00 0.00 34.09 3.28
2086 6236 4.220821 ACTCTGCTCGAAGAAATACTCCAA 59.779 41.667 0.00 0.00 34.09 3.53
2087 6237 3.764434 ACTCTGCTCGAAGAAATACTCCA 59.236 43.478 0.00 0.00 34.09 3.86
2089 6239 5.864474 TCAAACTCTGCTCGAAGAAATACTC 59.136 40.000 0.00 0.00 34.09 2.59
2090 6240 5.635700 GTCAAACTCTGCTCGAAGAAATACT 59.364 40.000 0.00 0.00 34.09 2.12
2092 6242 5.405571 GTGTCAAACTCTGCTCGAAGAAATA 59.594 40.000 0.00 0.00 34.09 1.40
2093 6243 4.212214 GTGTCAAACTCTGCTCGAAGAAAT 59.788 41.667 0.00 0.00 34.09 2.17
2094 6244 3.555956 GTGTCAAACTCTGCTCGAAGAAA 59.444 43.478 0.00 0.00 34.09 2.52
2095 6245 3.123804 GTGTCAAACTCTGCTCGAAGAA 58.876 45.455 0.00 0.00 34.09 2.52
2096 6246 2.545952 GGTGTCAAACTCTGCTCGAAGA 60.546 50.000 0.00 0.00 0.00 2.87
2097 6247 1.795286 GGTGTCAAACTCTGCTCGAAG 59.205 52.381 0.00 0.00 0.00 3.79
2098 6248 1.865865 GGTGTCAAACTCTGCTCGAA 58.134 50.000 0.00 0.00 0.00 3.71
2099 6249 0.318699 CGGTGTCAAACTCTGCTCGA 60.319 55.000 0.00 0.00 0.00 4.04
2100 6250 0.597637 ACGGTGTCAAACTCTGCTCG 60.598 55.000 0.00 0.00 0.00 5.03
2101 6251 0.861837 CACGGTGTCAAACTCTGCTC 59.138 55.000 0.00 0.00 0.00 4.26
2103 6253 1.261619 CTTCACGGTGTCAAACTCTGC 59.738 52.381 8.17 0.00 0.00 4.26
2104 6254 2.821546 TCTTCACGGTGTCAAACTCTG 58.178 47.619 8.17 0.00 0.00 3.35
2105 6255 3.458189 CTTCTTCACGGTGTCAAACTCT 58.542 45.455 8.17 0.00 0.00 3.24
2106 6256 2.544267 CCTTCTTCACGGTGTCAAACTC 59.456 50.000 8.17 0.00 0.00 3.01
2107 6257 2.093128 ACCTTCTTCACGGTGTCAAACT 60.093 45.455 8.17 0.00 30.90 2.66
2110 6260 1.948104 CACCTTCTTCACGGTGTCAA 58.052 50.000 8.17 0.00 44.38 3.18
2111 6261 3.678921 CACCTTCTTCACGGTGTCA 57.321 52.632 8.17 0.00 44.38 3.58
2115 6265 2.993937 TGAAAACACCTTCTTCACGGT 58.006 42.857 0.00 0.00 0.00 4.83
2116 6266 3.625764 TCTTGAAAACACCTTCTTCACGG 59.374 43.478 0.00 0.00 0.00 4.94
2117 6267 4.570772 TCTCTTGAAAACACCTTCTTCACG 59.429 41.667 0.00 0.00 0.00 4.35
2118 6268 6.625873 ATCTCTTGAAAACACCTTCTTCAC 57.374 37.500 0.00 0.00 0.00 3.18
2119 6269 7.339212 TGAAATCTCTTGAAAACACCTTCTTCA 59.661 33.333 0.00 0.00 0.00 3.02
2120 6270 7.707104 TGAAATCTCTTGAAAACACCTTCTTC 58.293 34.615 0.00 0.00 0.00 2.87
2121 6271 7.645058 TGAAATCTCTTGAAAACACCTTCTT 57.355 32.000 0.00 0.00 0.00 2.52
2122 6272 7.830099 ATGAAATCTCTTGAAAACACCTTCT 57.170 32.000 0.00 0.00 0.00 2.85
2123 6273 7.922811 ACAATGAAATCTCTTGAAAACACCTTC 59.077 33.333 0.00 0.00 0.00 3.46
2124 6274 7.785033 ACAATGAAATCTCTTGAAAACACCTT 58.215 30.769 0.00 0.00 0.00 3.50
2125 6275 7.352079 ACAATGAAATCTCTTGAAAACACCT 57.648 32.000 0.00 0.00 0.00 4.00
2164 6314 9.793259 AGATCCAAGAAAATACAAAGTAACTCA 57.207 29.630 0.00 0.00 0.00 3.41
2170 6320 9.232473 GACCTAAGATCCAAGAAAATACAAAGT 57.768 33.333 0.00 0.00 0.00 2.66
2172 6322 8.167392 TGGACCTAAGATCCAAGAAAATACAAA 58.833 33.333 0.00 0.00 43.43 2.83
2174 6324 7.265599 TGGACCTAAGATCCAAGAAAATACA 57.734 36.000 0.00 0.00 43.43 2.29
2186 6336 6.049790 GGTACACTGATTTGGACCTAAGATC 58.950 44.000 0.00 0.00 46.07 2.75
2188 6338 5.416271 GGTACACTGATTTGGACCTAAGA 57.584 43.478 0.00 0.00 46.07 2.10
2194 6344 8.732746 ACAATTATAGGTACACTGATTTGGAC 57.267 34.615 0.00 0.00 0.00 4.02
2200 6350 8.945193 ACCCATAACAATTATAGGTACACTGAT 58.055 33.333 0.00 0.00 36.13 2.90
2201 6351 8.326765 ACCCATAACAATTATAGGTACACTGA 57.673 34.615 0.00 0.00 36.13 3.41
2217 6367 9.621629 CCTGTAACTTTATTCATACCCATAACA 57.378 33.333 0.00 0.00 0.00 2.41
2218 6368 9.623000 ACCTGTAACTTTATTCATACCCATAAC 57.377 33.333 0.00 0.00 0.00 1.89
2219 6369 9.621629 CACCTGTAACTTTATTCATACCCATAA 57.378 33.333 0.00 0.00 0.00 1.90
2220 6370 8.774183 ACACCTGTAACTTTATTCATACCCATA 58.226 33.333 0.00 0.00 0.00 2.74
2221 6371 7.639378 ACACCTGTAACTTTATTCATACCCAT 58.361 34.615 0.00 0.00 0.00 4.00
2222 6372 7.023171 ACACCTGTAACTTTATTCATACCCA 57.977 36.000 0.00 0.00 0.00 4.51
2223 6373 7.827729 AGAACACCTGTAACTTTATTCATACCC 59.172 37.037 0.00 0.00 0.00 3.69
2224 6374 8.788325 AGAACACCTGTAACTTTATTCATACC 57.212 34.615 0.00 0.00 0.00 2.73
2257 6407 8.708742 GCACAACAAGAAAGTTTTCTAGTTTTT 58.291 29.630 7.49 0.00 46.22 1.94
2258 6408 7.330946 GGCACAACAAGAAAGTTTTCTAGTTTT 59.669 33.333 7.49 0.00 46.22 2.43
2259 6409 6.811665 GGCACAACAAGAAAGTTTTCTAGTTT 59.188 34.615 7.49 0.01 46.22 2.66
2266 6416 5.914898 ACTAGGCACAACAAGAAAGTTTT 57.085 34.783 0.00 0.00 0.00 2.43
2328 6478 2.350192 CCGGCCAAAACAGAAAACAAAC 59.650 45.455 2.24 0.00 0.00 2.93
2332 6482 2.303163 AACCGGCCAAAACAGAAAAC 57.697 45.000 0.00 0.00 0.00 2.43
2336 6486 2.104170 AGAAAAACCGGCCAAAACAGA 58.896 42.857 0.00 0.00 0.00 3.41
2337 6487 2.595124 AGAAAAACCGGCCAAAACAG 57.405 45.000 0.00 0.00 0.00 3.16
2339 6489 3.173668 AGAAGAAAAACCGGCCAAAAC 57.826 42.857 0.00 0.00 0.00 2.43
2340 6490 5.538849 AATAGAAGAAAAACCGGCCAAAA 57.461 34.783 0.00 0.00 0.00 2.44
2341 6491 5.538849 AAATAGAAGAAAAACCGGCCAAA 57.461 34.783 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.