Multiple sequence alignment - TraesCS3A01G487100

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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 TraesCS3A01G487100 chr3A 100.000 3955 0 0 1 3955 714938068 714942022 0.000000e+00 7304.0
1 TraesCS3A01G487100 chr3A 99.644 843 2 1 1 842 610433071 610433913 0.000000e+00 1539.0
2 TraesCS3A01G487100 chr3A 99.409 846 3 2 1 844 24303468 24302623 0.000000e+00 1533.0
3 TraesCS3A01G487100 chr3A 91.498 988 74 7 1001 1986 679915893 679916872 0.000000e+00 1351.0
4 TraesCS3A01G487100 chr3A 91.597 714 53 7 2592 3301 679923340 679924050 0.000000e+00 979.0
5 TraesCS3A01G487100 chr3A 92.830 530 35 3 1983 2510 679922820 679923348 0.000000e+00 765.0
6 TraesCS3A01G487100 chr3A 92.593 189 9 1 3466 3654 679924448 679924631 2.340000e-67 267.0
7 TraesCS3A01G487100 chr3A 96.000 75 3 0 910 984 679915833 679915907 5.370000e-24 122.0
8 TraesCS3A01G487100 chr3A 98.333 60 1 0 3658 3717 679924665 679924724 5.410000e-19 106.0
9 TraesCS3A01G487100 chr3A 93.846 65 4 0 3891 3955 679924735 679924799 9.040000e-17 99.0
10 TraesCS3A01G487100 chr3B 93.220 2640 127 22 1001 3609 774456544 774459162 0.000000e+00 3836.0
11 TraesCS3A01G487100 chr3B 92.982 171 11 1 3720 3890 685076700 685076869 8.490000e-62 248.0
12 TraesCS3A01G487100 chr3B 100.000 30 0 0 1551 1580 752972960 752972931 5.520000e-04 56.5
13 TraesCS3A01G487100 chr3D 93.952 1951 84 20 1001 2934 579697377 579699310 0.000000e+00 2918.0
14 TraesCS3A01G487100 chr3D 81.219 804 109 23 1235 2002 2991695 2990898 9.400000e-171 610.0
15 TraesCS3A01G487100 chr3D 84.134 479 70 5 1911 2385 2920449 2919973 3.600000e-125 459.0
16 TraesCS3A01G487100 chr3D 93.248 311 15 4 3305 3611 579699318 579699626 1.680000e-123 453.0
17 TraesCS3A01G487100 chr3D 75.461 542 92 29 1906 2434 2932390 2932903 3.980000e-55 226.0
18 TraesCS3A01G487100 chr3D 89.583 48 5 0 2568 2615 417504558 417504511 1.190000e-05 62.1
19 TraesCS3A01G487100 chr3D 100.000 30 0 0 3725 3754 85449521 85449492 5.520000e-04 56.5
20 TraesCS3A01G487100 chr3D 100.000 30 0 0 1551 1580 565535853 565535882 5.520000e-04 56.5
21 TraesCS3A01G487100 chr3D 96.970 33 0 1 3726 3758 35898324 35898293 2.000000e-03 54.7
22 TraesCS3A01G487100 chr3D 96.875 32 1 0 3726 3757 482599406 482599375 2.000000e-03 54.7
23 TraesCS3A01G487100 chr7B 90.018 1713 107 25 1067 2766 7199606 7201267 0.000000e+00 2158.0
24 TraesCS3A01G487100 chr7B 99.644 843 2 1 1 842 563641258 563642100 0.000000e+00 1539.0
25 TraesCS3A01G487100 chr7B 92.000 600 37 9 2710 3301 7203390 7203986 0.000000e+00 832.0
26 TraesCS3A01G487100 chr7B 88.482 191 17 1 3466 3656 7204343 7204528 3.980000e-55 226.0
27 TraesCS3A01G487100 chr7B 95.385 65 3 0 3891 3955 7185255 7185191 1.940000e-18 104.0
28 TraesCS3A01G487100 chr7B 94.643 56 3 0 3891 3946 7204819 7204874 1.960000e-13 87.9
29 TraesCS3A01G487100 chr5A 99.644 843 2 1 1 842 38619534 38618692 0.000000e+00 1539.0
30 TraesCS3A01G487100 chr5A 95.732 164 7 0 3728 3891 570380387 570380224 8.430000e-67 265.0
31 TraesCS3A01G487100 chr5A 92.857 42 1 2 3724 3764 665776315 665776275 4.270000e-05 60.2
32 TraesCS3A01G487100 chr2B 99.644 843 2 1 1 842 165300968 165301810 0.000000e+00 1539.0
33 TraesCS3A01G487100 chr2B 91.122 811 58 8 1001 1809 755344660 755345458 0.000000e+00 1086.0
34 TraesCS3A01G487100 chr2B 97.333 75 2 0 910 984 755344600 755344674 1.150000e-25 128.0
35 TraesCS3A01G487100 chr2B 92.157 51 4 0 2567 2617 444847785 444847835 5.480000e-09 73.1
36 TraesCS3A01G487100 chr2B 87.755 49 2 4 3727 3772 408095971 408095924 2.000000e-03 54.7
37 TraesCS3A01G487100 chr1A 99.644 842 3 0 1 842 515216293 515217134 0.000000e+00 1539.0
38 TraesCS3A01G487100 chr1A 91.837 49 4 0 2567 2615 108071426 108071474 7.090000e-08 69.4
39 TraesCS3A01G487100 chr1A 92.308 39 3 0 3726 3764 117188300 117188262 5.520000e-04 56.5
40 TraesCS3A01G487100 chr1A 94.286 35 2 0 3723 3757 100269973 100270007 2.000000e-03 54.7
41 TraesCS3A01G487100 chr1A 96.875 32 1 0 3723 3754 556112616 556112647 2.000000e-03 54.7
42 TraesCS3A01G487100 chr4A 99.526 844 3 1 1 843 45399250 45400093 0.000000e+00 1535.0
43 TraesCS3A01G487100 chr4A 99.063 854 4 4 1 850 35598145 35597292 0.000000e+00 1530.0
44 TraesCS3A01G487100 chr4A 90.672 1072 85 9 2585 3653 9681330 9682389 0.000000e+00 1411.0
45 TraesCS3A01G487100 chr4A 92.028 853 62 6 996 1844 9670700 9671550 0.000000e+00 1194.0
46 TraesCS3A01G487100 chr4A 91.703 687 53 3 1840 2524 9680672 9681356 0.000000e+00 950.0
47 TraesCS3A01G487100 chr4A 90.789 76 6 1 909 984 9670647 9670721 2.510000e-17 100.0
48 TraesCS3A01G487100 chr4A 91.837 49 4 0 2567 2615 191062915 191062963 7.090000e-08 69.4
49 TraesCS3A01G487100 chr2A 99.526 844 2 2 1 842 714271402 714272245 0.000000e+00 1535.0
50 TraesCS3A01G487100 chr2A 94.972 179 8 1 3716 3893 662605603 662605425 3.010000e-71 279.0
51 TraesCS3A01G487100 chr2A 95.181 166 8 0 3725 3890 686832698 686832533 3.030000e-66 263.0
52 TraesCS3A01G487100 chrUn 79.783 920 135 32 1235 2113 32127046 32126137 4.340000e-174 621.0
53 TraesCS3A01G487100 chrUn 86.538 52 7 0 2567 2618 61037106 61037157 1.540000e-04 58.4
54 TraesCS3A01G487100 chrUn 88.000 50 4 2 2567 2615 178199871 178199823 1.540000e-04 58.4
55 TraesCS3A01G487100 chrUn 88.000 50 4 2 2567 2615 265597658 265597610 1.540000e-04 58.4
56 TraesCS3A01G487100 chrUn 88.000 50 4 2 2567 2615 276141543 276141591 1.540000e-04 58.4
57 TraesCS3A01G487100 chrUn 88.000 50 4 2 2567 2615 290791175 290791127 1.540000e-04 58.4
58 TraesCS3A01G487100 chr7A 94.545 165 9 0 3726 3890 63872859 63873023 5.070000e-64 255.0
59 TraesCS3A01G487100 chr6A 93.939 165 10 0 3726 3890 30446041 30446205 2.360000e-62 250.0
60 TraesCS3A01G487100 chr6A 92.500 40 3 0 3725 3764 263887018 263886979 1.540000e-04 58.4
61 TraesCS3A01G487100 chr4B 91.667 48 4 0 2567 2614 642778109 642778062 2.550000e-07 67.6
62 TraesCS3A01G487100 chr4B 89.091 55 3 3 2567 2620 92657093 92657145 9.170000e-07 65.8
63 TraesCS3A01G487100 chr4B 92.500 40 3 0 3725 3764 413830723 413830762 1.540000e-04 58.4
64 TraesCS3A01G487100 chr1D 88.889 54 6 0 2571 2624 205500246 205500299 2.550000e-07 67.6
65 TraesCS3A01G487100 chr1D 89.796 49 5 0 2567 2615 403331730 403331682 3.300000e-06 63.9
66 TraesCS3A01G487100 chr1D 96.970 33 1 0 3725 3757 418194250 418194218 5.520000e-04 56.5
67 TraesCS3A01G487100 chr1D 90.244 41 4 0 2575 2615 453059956 453059916 2.000000e-03 54.7
68 TraesCS3A01G487100 chr1D 100.000 29 0 0 3726 3754 492643877 492643905 2.000000e-03 54.7
69 TraesCS3A01G487100 chr1D 96.774 31 1 0 2588 2618 205490317 205490287 7.000000e-03 52.8
70 TraesCS3A01G487100 chr1D 96.774 31 1 0 2588 2618 222028452 222028422 7.000000e-03 52.8
71 TraesCS3A01G487100 chr1D 100.000 28 0 0 2588 2615 401169158 401169131 7.000000e-03 52.8
72 TraesCS3A01G487100 chr1D 94.286 35 1 1 3719 3753 486120094 486120061 7.000000e-03 52.8
73 TraesCS3A01G487100 chr6D 88.889 54 5 1 2564 2616 218447280 218447333 9.170000e-07 65.8
74 TraesCS3A01G487100 chr6B 88.889 54 5 1 2564 2616 342988753 342988700 9.170000e-07 65.8
75 TraesCS3A01G487100 chr5D 88.889 54 5 1 2564 2616 197149710 197149763 9.170000e-07 65.8
76 TraesCS3A01G487100 chr5D 89.796 49 5 0 2567 2615 18085062 18085014 3.300000e-06 63.9
77 TraesCS3A01G487100 chr5D 83.871 62 8 2 2564 2623 257162729 257162668 1.540000e-04 58.4
78 TraesCS3A01G487100 chr5D 96.875 32 1 0 3726 3757 138470370 138470339 2.000000e-03 54.7
79 TraesCS3A01G487100 chr4D 90.196 51 3 2 2567 2616 39410723 39410674 9.170000e-07 65.8
80 TraesCS3A01G487100 chr4D 92.308 39 3 0 3726 3764 335774284 335774322 5.520000e-04 56.5
81 TraesCS3A01G487100 chr2D 88.679 53 5 1 2564 2615 607675808 607675860 3.300000e-06 63.9
82 TraesCS3A01G487100 chr1B 89.583 48 3 1 3717 3764 52571349 52571394 4.270000e-05 60.2
83 TraesCS3A01G487100 chr1B 89.583 48 3 1 3717 3764 52641758 52641803 4.270000e-05 60.2
84 TraesCS3A01G487100 chr7D 89.130 46 5 0 3719 3764 463262402 463262357 1.540000e-04 58.4
85 TraesCS3A01G487100 chr5B 92.105 38 3 0 3726 3763 243421534 243421497 2.000000e-03 54.7


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 TraesCS3A01G487100 chr3A 714938068 714942022 3954 False 7304.000 7304 100.00000 1 3955 1 chr3A.!!$F2 3954
1 TraesCS3A01G487100 chr3A 610433071 610433913 842 False 1539.000 1539 99.64400 1 842 1 chr3A.!!$F1 841
2 TraesCS3A01G487100 chr3A 24302623 24303468 845 True 1533.000 1533 99.40900 1 844 1 chr3A.!!$R1 843
3 TraesCS3A01G487100 chr3A 679915833 679916872 1039 False 736.500 1351 93.74900 910 1986 2 chr3A.!!$F3 1076
4 TraesCS3A01G487100 chr3A 679922820 679924799 1979 False 443.200 979 93.83980 1983 3955 5 chr3A.!!$F4 1972
5 TraesCS3A01G487100 chr3B 774456544 774459162 2618 False 3836.000 3836 93.22000 1001 3609 1 chr3B.!!$F2 2608
6 TraesCS3A01G487100 chr3D 579697377 579699626 2249 False 1685.500 2918 93.60000 1001 3611 2 chr3D.!!$F3 2610
7 TraesCS3A01G487100 chr3D 2990898 2991695 797 True 610.000 610 81.21900 1235 2002 1 chr3D.!!$R2 767
8 TraesCS3A01G487100 chr3D 2932390 2932903 513 False 226.000 226 75.46100 1906 2434 1 chr3D.!!$F1 528
9 TraesCS3A01G487100 chr7B 563641258 563642100 842 False 1539.000 1539 99.64400 1 842 1 chr7B.!!$F1 841
10 TraesCS3A01G487100 chr7B 7199606 7204874 5268 False 825.975 2158 91.28575 1067 3946 4 chr7B.!!$F2 2879
11 TraesCS3A01G487100 chr5A 38618692 38619534 842 True 1539.000 1539 99.64400 1 842 1 chr5A.!!$R1 841
12 TraesCS3A01G487100 chr2B 165300968 165301810 842 False 1539.000 1539 99.64400 1 842 1 chr2B.!!$F1 841
13 TraesCS3A01G487100 chr2B 755344600 755345458 858 False 607.000 1086 94.22750 910 1809 2 chr2B.!!$F3 899
14 TraesCS3A01G487100 chr1A 515216293 515217134 841 False 1539.000 1539 99.64400 1 842 1 chr1A.!!$F3 841
15 TraesCS3A01G487100 chr4A 45399250 45400093 843 False 1535.000 1535 99.52600 1 843 1 chr4A.!!$F1 842
16 TraesCS3A01G487100 chr4A 35597292 35598145 853 True 1530.000 1530 99.06300 1 850 1 chr4A.!!$R1 849
17 TraesCS3A01G487100 chr4A 9680672 9682389 1717 False 1180.500 1411 91.18750 1840 3653 2 chr4A.!!$F4 1813
18 TraesCS3A01G487100 chr4A 9670647 9671550 903 False 647.000 1194 91.40850 909 1844 2 chr4A.!!$F3 935
19 TraesCS3A01G487100 chr2A 714271402 714272245 843 False 1535.000 1535 99.52600 1 842 1 chr2A.!!$F1 841
20 TraesCS3A01G487100 chrUn 32126137 32127046 909 True 621.000 621 79.78300 1235 2113 1 chrUn.!!$R1 878

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
864 870 0.110104 TGCATGGTGATGTGTGGTGA 59.890 50.0 0.0 0.0 31.50 4.02 F
897 903 0.170339 GCGCGCAAAGGGTTAGAAAT 59.830 50.0 29.1 0.0 34.93 2.17 F
1760 1768 0.038599 TGCCTACTACGTCCTCACCA 59.961 55.0 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 1768 0.904865 TGTCCCTGGAACGAGCTGAT 60.905 55.000 0.00 0.0 0.00 2.90 R
2013 2054 1.006102 GCGGTATCTATGCAGCCGT 60.006 57.895 11.92 0.0 43.78 5.68 R
3052 5447 0.679960 GGGCACTTTTAGCGGTGGAT 60.680 55.000 0.00 0.0 34.41 3.41 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
844 850 8.618702 TGAAATTACTACGAAACCCAACAATA 57.381 30.769 0.00 0.00 0.00 1.90
845 851 9.233649 TGAAATTACTACGAAACCCAACAATAT 57.766 29.630 0.00 0.00 0.00 1.28
846 852 9.498307 GAAATTACTACGAAACCCAACAATATG 57.502 33.333 0.00 0.00 0.00 1.78
847 853 4.957759 ACTACGAAACCCAACAATATGC 57.042 40.909 0.00 0.00 0.00 3.14
848 854 4.328536 ACTACGAAACCCAACAATATGCA 58.671 39.130 0.00 0.00 0.00 3.96
849 855 4.947388 ACTACGAAACCCAACAATATGCAT 59.053 37.500 3.79 3.79 0.00 3.96
850 856 4.108699 ACGAAACCCAACAATATGCATG 57.891 40.909 10.16 0.00 0.00 4.06
851 857 3.119173 ACGAAACCCAACAATATGCATGG 60.119 43.478 10.16 1.47 0.00 3.66
852 858 3.119173 CGAAACCCAACAATATGCATGGT 60.119 43.478 10.16 2.78 0.00 3.55
853 859 3.891422 AACCCAACAATATGCATGGTG 57.109 42.857 10.16 9.62 35.23 4.17
854 860 3.098774 ACCCAACAATATGCATGGTGA 57.901 42.857 10.16 0.00 37.71 4.02
855 861 3.645434 ACCCAACAATATGCATGGTGAT 58.355 40.909 10.16 0.00 37.71 3.06
856 862 3.385433 ACCCAACAATATGCATGGTGATG 59.615 43.478 10.16 11.44 37.71 3.07
857 863 3.385433 CCCAACAATATGCATGGTGATGT 59.615 43.478 10.16 4.27 37.71 3.06
858 864 4.364860 CCAACAATATGCATGGTGATGTG 58.635 43.478 10.16 8.10 37.71 3.21
859 865 4.142116 CCAACAATATGCATGGTGATGTGT 60.142 41.667 10.16 0.00 37.71 3.72
860 866 4.642445 ACAATATGCATGGTGATGTGTG 57.358 40.909 10.16 0.00 31.50 3.82
861 867 3.382227 ACAATATGCATGGTGATGTGTGG 59.618 43.478 10.16 0.00 31.50 4.17
862 868 2.804986 TATGCATGGTGATGTGTGGT 57.195 45.000 10.16 0.00 31.50 4.16
863 869 1.179152 ATGCATGGTGATGTGTGGTG 58.821 50.000 0.00 0.00 31.50 4.17
864 870 0.110104 TGCATGGTGATGTGTGGTGA 59.890 50.000 0.00 0.00 31.50 4.02
865 871 1.246649 GCATGGTGATGTGTGGTGAA 58.753 50.000 0.00 0.00 31.50 3.18
866 872 1.200716 GCATGGTGATGTGTGGTGAAG 59.799 52.381 0.00 0.00 31.50 3.02
867 873 2.781923 CATGGTGATGTGTGGTGAAGA 58.218 47.619 0.00 0.00 0.00 2.87
868 874 3.349927 CATGGTGATGTGTGGTGAAGAT 58.650 45.455 0.00 0.00 0.00 2.40
869 875 3.507162 TGGTGATGTGTGGTGAAGATT 57.493 42.857 0.00 0.00 0.00 2.40
870 876 3.148412 TGGTGATGTGTGGTGAAGATTG 58.852 45.455 0.00 0.00 0.00 2.67
871 877 3.181446 TGGTGATGTGTGGTGAAGATTGA 60.181 43.478 0.00 0.00 0.00 2.57
872 878 3.820467 GGTGATGTGTGGTGAAGATTGAA 59.180 43.478 0.00 0.00 0.00 2.69
873 879 4.083110 GGTGATGTGTGGTGAAGATTGAAG 60.083 45.833 0.00 0.00 0.00 3.02
874 880 4.516698 GTGATGTGTGGTGAAGATTGAAGT 59.483 41.667 0.00 0.00 0.00 3.01
875 881 5.009010 GTGATGTGTGGTGAAGATTGAAGTT 59.991 40.000 0.00 0.00 0.00 2.66
876 882 4.898829 TGTGTGGTGAAGATTGAAGTTG 57.101 40.909 0.00 0.00 0.00 3.16
877 883 4.269183 TGTGTGGTGAAGATTGAAGTTGT 58.731 39.130 0.00 0.00 0.00 3.32
878 884 4.096231 TGTGTGGTGAAGATTGAAGTTGTG 59.904 41.667 0.00 0.00 0.00 3.33
879 885 3.066621 TGTGGTGAAGATTGAAGTTGTGC 59.933 43.478 0.00 0.00 0.00 4.57
880 886 2.290367 TGGTGAAGATTGAAGTTGTGCG 59.710 45.455 0.00 0.00 0.00 5.34
881 887 2.310577 GTGAAGATTGAAGTTGTGCGC 58.689 47.619 0.00 0.00 0.00 6.09
882 888 1.069973 TGAAGATTGAAGTTGTGCGCG 60.070 47.619 0.00 0.00 0.00 6.86
883 889 0.385974 AAGATTGAAGTTGTGCGCGC 60.386 50.000 27.26 27.26 0.00 6.86
884 890 1.082169 GATTGAAGTTGTGCGCGCA 60.082 52.632 33.09 33.09 0.00 6.09
885 891 0.660005 GATTGAAGTTGTGCGCGCAA 60.660 50.000 38.24 31.06 0.00 4.85
886 892 0.248825 ATTGAAGTTGTGCGCGCAAA 60.249 45.000 38.24 30.71 0.00 3.68
887 893 0.865218 TTGAAGTTGTGCGCGCAAAG 60.865 50.000 38.24 0.00 0.00 2.77
888 894 2.010817 GAAGTTGTGCGCGCAAAGG 61.011 57.895 38.24 0.00 0.00 3.11
889 895 3.483235 AAGTTGTGCGCGCAAAGGG 62.483 57.895 38.24 0.00 0.00 3.95
890 896 4.264638 GTTGTGCGCGCAAAGGGT 62.265 61.111 38.24 0.00 34.93 4.34
891 897 3.522731 TTGTGCGCGCAAAGGGTT 61.523 55.556 38.24 0.00 34.93 4.11
892 898 2.187493 TTGTGCGCGCAAAGGGTTA 61.187 52.632 38.24 12.78 34.93 2.85
893 899 2.123988 TTGTGCGCGCAAAGGGTTAG 62.124 55.000 38.24 0.00 34.93 2.34
894 900 2.031314 TGCGCGCAAAGGGTTAGA 59.969 55.556 34.66 3.17 34.93 2.10
895 901 1.598407 TGCGCGCAAAGGGTTAGAA 60.598 52.632 34.66 2.51 34.93 2.10
896 902 1.167155 TGCGCGCAAAGGGTTAGAAA 61.167 50.000 34.66 2.25 34.93 2.52
897 903 0.170339 GCGCGCAAAGGGTTAGAAAT 59.830 50.000 29.10 0.00 34.93 2.17
898 904 1.399089 GCGCGCAAAGGGTTAGAAATA 59.601 47.619 29.10 0.00 34.93 1.40
899 905 2.538939 GCGCGCAAAGGGTTAGAAATAG 60.539 50.000 29.10 0.00 34.93 1.73
900 906 2.538939 CGCGCAAAGGGTTAGAAATAGC 60.539 50.000 8.75 0.00 0.00 2.97
901 907 2.223502 GCGCAAAGGGTTAGAAATAGCC 60.224 50.000 0.30 0.00 0.00 3.93
902 908 3.013921 CGCAAAGGGTTAGAAATAGCCA 58.986 45.455 0.00 0.00 35.62 4.75
903 909 3.632145 CGCAAAGGGTTAGAAATAGCCAT 59.368 43.478 0.00 0.00 35.62 4.40
904 910 4.819630 CGCAAAGGGTTAGAAATAGCCATA 59.180 41.667 0.00 0.00 35.62 2.74
905 911 5.473504 CGCAAAGGGTTAGAAATAGCCATAT 59.526 40.000 0.00 0.00 35.62 1.78
906 912 6.016276 CGCAAAGGGTTAGAAATAGCCATATT 60.016 38.462 0.00 0.00 35.62 1.28
907 913 7.371159 GCAAAGGGTTAGAAATAGCCATATTC 58.629 38.462 0.00 0.00 35.62 1.75
908 914 7.584987 CAAAGGGTTAGAAATAGCCATATTCG 58.415 38.462 0.00 0.00 35.62 3.34
977 983 9.796120 CCTTTACGGCTGATGAATAAATAAAAA 57.204 29.630 0.00 0.00 0.00 1.94
982 988 9.783256 ACGGCTGATGAATAAATAAAAAGTAAC 57.217 29.630 0.00 0.00 0.00 2.50
990 996 9.303116 TGAATAAATAAAAAGTAACTCCCTGCA 57.697 29.630 0.00 0.00 0.00 4.41
1069 1075 0.820074 CCACCGTTGGTTGGCACTTA 60.820 55.000 0.00 0.00 38.23 2.24
1293 1301 0.613260 CAGTGGGAAATCCTCGTCCA 59.387 55.000 0.00 0.00 35.44 4.02
1467 1475 2.342650 CCGTGGTTGATGCCTTGGG 61.343 63.158 0.00 0.00 0.00 4.12
1530 1538 4.492791 TCGACGACTACAACAAATCTCA 57.507 40.909 0.00 0.00 0.00 3.27
1687 1695 4.682334 TACCCTCACCGCCCGTCA 62.682 66.667 0.00 0.00 0.00 4.35
1760 1768 0.038599 TGCCTACTACGTCCTCACCA 59.961 55.000 0.00 0.00 0.00 4.17
1945 1983 0.108585 ACACGGTGGCAGAGTCATTT 59.891 50.000 13.48 0.00 0.00 2.32
2013 2054 0.473755 ATGGATGGTATGCTCGGCAA 59.526 50.000 2.68 0.00 43.62 4.52
2039 2080 1.081892 CATAGATACCGCTGCCATGC 58.918 55.000 0.00 0.00 0.00 4.06
2048 2089 3.746889 CTGCCATGCCCGCGAAAA 61.747 61.111 8.23 0.00 0.00 2.29
2244 2290 0.532862 ACTGTGACAACAAGGCGAGG 60.533 55.000 0.00 0.00 35.37 4.63
2290 2336 3.942829 ACATTGATCCAAAGCTTCTCGA 58.057 40.909 0.00 0.00 0.00 4.04
2348 2394 1.561643 TCGAGAGGAAAGATGGCAGT 58.438 50.000 0.00 0.00 0.00 4.40
2438 2486 3.066900 TCTCCTTGCTTACTATCGCTGTC 59.933 47.826 0.00 0.00 0.00 3.51
2487 2535 8.440833 CCTTTGTGACCTAAAACGTCTTATAAG 58.559 37.037 6.11 6.11 0.00 1.73
2532 2662 1.437547 AGTAGGAGGGAGGTTGGACTT 59.562 52.381 0.00 0.00 0.00 3.01
2617 2753 0.754217 CCGGACGGAGGGAGTATGAA 60.754 60.000 4.40 0.00 37.50 2.57
2633 2769 6.751888 GGAGTATGAACCAAATGTTAATGCAC 59.248 38.462 0.00 0.00 37.29 4.57
2656 2865 1.338973 CTGCACTCACCATGCTTGTTT 59.661 47.619 0.00 0.00 43.77 2.83
2728 2937 7.001674 TGTGTATAAAACCTTGTGGAAGATGT 58.998 34.615 0.00 0.00 37.04 3.06
2835 5223 6.777782 TGCAAGATGGGGAAAAATGTTTTAT 58.222 32.000 0.00 0.00 0.00 1.40
2837 5225 7.821846 TGCAAGATGGGGAAAAATGTTTTATAC 59.178 33.333 0.00 0.00 0.00 1.47
2888 5279 7.142306 ACTGATGATATGCTTGCATGAATAC 57.858 36.000 17.26 7.42 0.00 1.89
2989 5384 5.760253 TGGAGTTTTGCTTCTTGAGACTTAG 59.240 40.000 0.00 0.00 0.00 2.18
3011 5406 0.598065 GGTGTGCATTGGACCACTTC 59.402 55.000 5.81 0.00 33.26 3.01
3023 5418 4.871933 GGACCACTTCCATCAAAATGTT 57.128 40.909 0.00 0.00 45.10 2.71
3025 5420 6.339587 GGACCACTTCCATCAAAATGTTAA 57.660 37.500 0.00 0.00 45.10 2.01
3052 5447 5.893500 ACCTATCTACTGCTTCAGCCTATA 58.106 41.667 0.00 0.00 41.18 1.31
3054 5449 6.605594 ACCTATCTACTGCTTCAGCCTATATC 59.394 42.308 0.00 0.00 41.18 1.63
3055 5450 5.930837 ATCTACTGCTTCAGCCTATATCC 57.069 43.478 0.00 0.00 41.18 2.59
3079 5474 2.423538 CGCTAAAAGTGCCCAGCTATTT 59.576 45.455 0.00 0.00 31.74 1.40
3126 5521 3.404224 TCGGCACATGTTTGGTTAGTA 57.596 42.857 0.00 0.00 0.00 1.82
3127 5522 3.741249 TCGGCACATGTTTGGTTAGTAA 58.259 40.909 0.00 0.00 0.00 2.24
3131 5526 5.447279 CGGCACATGTTTGGTTAGTAATCTC 60.447 44.000 0.00 0.00 0.00 2.75
3173 5568 7.367285 GTTTGCTTGTATTGGTAGAATCACAA 58.633 34.615 0.00 0.00 0.00 3.33
3232 5627 0.182775 AACCCTGCAAGTTCCTTCGT 59.817 50.000 0.00 0.00 0.00 3.85
3301 5697 5.069648 TCCTGGACTTGCAGTAATGATCTAG 59.930 44.000 0.00 0.00 0.00 2.43
3390 5914 1.605710 CTTGTGTCCACTTCCAGCTTG 59.394 52.381 0.00 0.00 0.00 4.01
3471 6181 5.105635 TCAGAAACATCATCATTTGGCTTCC 60.106 40.000 0.00 0.00 0.00 3.46
3493 6203 4.234574 CGTTTATCCTGGTTGCCTTTTTC 58.765 43.478 0.00 0.00 0.00 2.29
3582 6292 6.018469 TCTCCACATTTGAATTTCCCATTCT 58.982 36.000 0.00 0.00 0.00 2.40
3708 6672 5.712152 ACATTCAGTTTGAGGACATTTCC 57.288 39.130 0.00 0.00 43.22 3.13
3726 6690 9.781834 GACATTTCCGAAACACAAAATATGATA 57.218 29.630 0.00 0.00 0.00 2.15
3727 6691 9.567848 ACATTTCCGAAACACAAAATATGATAC 57.432 29.630 0.00 0.00 0.00 2.24
3728 6692 9.787532 CATTTCCGAAACACAAAATATGATACT 57.212 29.630 0.00 0.00 0.00 2.12
3730 6694 7.548196 TCCGAAACACAAAATATGATACTCC 57.452 36.000 0.00 0.00 0.00 3.85
3731 6695 6.540914 TCCGAAACACAAAATATGATACTCCC 59.459 38.462 0.00 0.00 0.00 4.30
3732 6696 6.542370 CCGAAACACAAAATATGATACTCCCT 59.458 38.462 0.00 0.00 0.00 4.20
3733 6697 7.254795 CCGAAACACAAAATATGATACTCCCTC 60.255 40.741 0.00 0.00 0.00 4.30
3734 6698 7.254795 CGAAACACAAAATATGATACTCCCTCC 60.255 40.741 0.00 0.00 0.00 4.30
3735 6699 5.611374 ACACAAAATATGATACTCCCTCCG 58.389 41.667 0.00 0.00 0.00 4.63
3736 6700 5.130477 ACACAAAATATGATACTCCCTCCGT 59.870 40.000 0.00 0.00 0.00 4.69
3737 6701 6.055588 CACAAAATATGATACTCCCTCCGTT 58.944 40.000 0.00 0.00 0.00 4.44
3738 6702 6.202954 CACAAAATATGATACTCCCTCCGTTC 59.797 42.308 0.00 0.00 0.00 3.95
3739 6703 6.126883 ACAAAATATGATACTCCCTCCGTTCA 60.127 38.462 0.00 0.00 0.00 3.18
3740 6704 6.688073 AAATATGATACTCCCTCCGTTCAT 57.312 37.500 0.00 0.00 0.00 2.57
3741 6705 7.792364 AAATATGATACTCCCTCCGTTCATA 57.208 36.000 0.00 0.00 32.43 2.15
3742 6706 7.792364 AATATGATACTCCCTCCGTTCATAA 57.208 36.000 0.00 0.00 31.86 1.90
3743 6707 7.792364 ATATGATACTCCCTCCGTTCATAAA 57.208 36.000 0.00 0.00 31.86 1.40
3744 6708 6.688073 ATGATACTCCCTCCGTTCATAAAT 57.312 37.500 0.00 0.00 0.00 1.40
3745 6709 7.792364 ATGATACTCCCTCCGTTCATAAATA 57.208 36.000 0.00 0.00 0.00 1.40
3746 6710 7.792364 TGATACTCCCTCCGTTCATAAATAT 57.208 36.000 0.00 0.00 0.00 1.28
3747 6711 8.888836 TGATACTCCCTCCGTTCATAAATATA 57.111 34.615 0.00 0.00 0.00 0.86
3748 6712 9.316594 TGATACTCCCTCCGTTCATAAATATAA 57.683 33.333 0.00 0.00 0.00 0.98
3749 6713 9.804758 GATACTCCCTCCGTTCATAAATATAAG 57.195 37.037 0.00 0.00 0.00 1.73
3750 6714 7.850935 ACTCCCTCCGTTCATAAATATAAGA 57.149 36.000 0.00 0.00 0.00 2.10
3751 6715 8.437274 ACTCCCTCCGTTCATAAATATAAGAT 57.563 34.615 0.00 0.00 0.00 2.40
3752 6716 8.314751 ACTCCCTCCGTTCATAAATATAAGATG 58.685 37.037 0.00 0.00 0.00 2.90
3753 6717 8.202461 TCCCTCCGTTCATAAATATAAGATGT 57.798 34.615 0.00 0.00 0.00 3.06
3754 6718 9.316594 TCCCTCCGTTCATAAATATAAGATGTA 57.683 33.333 0.00 0.00 0.00 2.29
3768 6732 9.586732 AATATAAGATGTATTAGCTTTTGGCCA 57.413 29.630 0.00 0.00 43.05 5.36
3769 6733 5.582689 AAGATGTATTAGCTTTTGGCCAC 57.417 39.130 3.88 0.00 43.05 5.01
3770 6734 4.599041 AGATGTATTAGCTTTTGGCCACA 58.401 39.130 3.88 0.00 43.05 4.17
3771 6735 5.203528 AGATGTATTAGCTTTTGGCCACAT 58.796 37.500 3.88 0.34 43.05 3.21
3772 6736 5.658190 AGATGTATTAGCTTTTGGCCACATT 59.342 36.000 3.88 0.00 43.05 2.71
3773 6737 5.323371 TGTATTAGCTTTTGGCCACATTC 57.677 39.130 3.88 0.00 43.05 2.67
3774 6738 5.016173 TGTATTAGCTTTTGGCCACATTCT 58.984 37.500 3.88 3.17 43.05 2.40
3775 6739 6.184068 TGTATTAGCTTTTGGCCACATTCTA 58.816 36.000 3.88 2.05 43.05 2.10
3776 6740 5.582689 ATTAGCTTTTGGCCACATTCTAC 57.417 39.130 3.88 0.00 43.05 2.59
3777 6741 2.875296 AGCTTTTGGCCACATTCTACA 58.125 42.857 3.88 0.00 43.05 2.74
3778 6742 2.558359 AGCTTTTGGCCACATTCTACAC 59.442 45.455 3.88 0.00 43.05 2.90
3779 6743 2.668279 GCTTTTGGCCACATTCTACACG 60.668 50.000 3.88 0.00 34.27 4.49
3780 6744 2.264005 TTTGGCCACATTCTACACGT 57.736 45.000 3.88 0.00 0.00 4.49
3781 6745 3.404224 TTTGGCCACATTCTACACGTA 57.596 42.857 3.88 0.00 0.00 3.57
3782 6746 3.620427 TTGGCCACATTCTACACGTAT 57.380 42.857 3.88 0.00 0.00 3.06
3783 6747 3.173668 TGGCCACATTCTACACGTATC 57.826 47.619 0.00 0.00 0.00 2.24
3784 6748 2.498078 TGGCCACATTCTACACGTATCA 59.502 45.455 0.00 0.00 0.00 2.15
3785 6749 3.055747 TGGCCACATTCTACACGTATCAA 60.056 43.478 0.00 0.00 0.00 2.57
3786 6750 3.936453 GGCCACATTCTACACGTATCAAA 59.064 43.478 0.00 0.00 0.00 2.69
3787 6751 4.574828 GGCCACATTCTACACGTATCAAAT 59.425 41.667 0.00 0.00 0.00 2.32
3788 6752 5.501715 GCCACATTCTACACGTATCAAATG 58.498 41.667 9.88 9.88 0.00 2.32
3789 6753 5.064707 GCCACATTCTACACGTATCAAATGT 59.935 40.000 10.84 10.84 37.71 2.71
3790 6754 6.256975 GCCACATTCTACACGTATCAAATGTA 59.743 38.462 14.38 0.38 36.02 2.29
3791 6755 7.042051 GCCACATTCTACACGTATCAAATGTAT 60.042 37.037 14.38 0.00 36.02 2.29
3792 6756 8.487970 CCACATTCTACACGTATCAAATGTATC 58.512 37.037 14.38 0.00 36.02 2.24
3793 6757 9.249457 CACATTCTACACGTATCAAATGTATCT 57.751 33.333 14.38 0.00 36.02 1.98
3798 6762 9.333724 TCTACACGTATCAAATGTATCTAGACA 57.666 33.333 0.00 0.00 0.00 3.41
3800 6764 8.803201 ACACGTATCAAATGTATCTAGACATG 57.197 34.615 0.00 0.00 39.99 3.21
3801 6765 8.414003 ACACGTATCAAATGTATCTAGACATGT 58.586 33.333 0.00 0.00 39.99 3.21
3802 6766 9.249457 CACGTATCAAATGTATCTAGACATGTT 57.751 33.333 0.00 0.00 39.99 2.71
3803 6767 9.464714 ACGTATCAAATGTATCTAGACATGTTC 57.535 33.333 0.00 0.00 39.99 3.18
3804 6768 9.684448 CGTATCAAATGTATCTAGACATGTTCT 57.316 33.333 0.00 1.27 39.99 3.01
3817 6781 8.621921 CTAGACATGTTCTAGTGTGTACATTC 57.378 38.462 17.40 0.00 46.38 2.67
3818 6782 6.993079 AGACATGTTCTAGTGTGTACATTCA 58.007 36.000 0.00 0.00 30.17 2.57
3819 6783 7.615403 AGACATGTTCTAGTGTGTACATTCAT 58.385 34.615 0.00 0.00 30.17 2.57
3820 6784 8.097038 AGACATGTTCTAGTGTGTACATTCATT 58.903 33.333 0.00 0.00 30.17 2.57
3821 6785 8.256611 ACATGTTCTAGTGTGTACATTCATTC 57.743 34.615 0.00 0.00 0.00 2.67
3822 6786 8.097038 ACATGTTCTAGTGTGTACATTCATTCT 58.903 33.333 0.00 0.00 0.00 2.40
3823 6787 8.939929 CATGTTCTAGTGTGTACATTCATTCTT 58.060 33.333 0.00 0.00 0.00 2.52
3824 6788 8.902540 TGTTCTAGTGTGTACATTCATTCTTT 57.097 30.769 0.00 0.00 0.00 2.52
3825 6789 9.337396 TGTTCTAGTGTGTACATTCATTCTTTT 57.663 29.630 0.00 0.00 0.00 2.27
3854 6818 9.803315 GTATGAATCTAGACAACATGTAGAACA 57.197 33.333 0.00 3.85 36.80 3.18
3855 6819 8.709386 ATGAATCTAGACAACATGTAGAACAC 57.291 34.615 0.00 0.00 36.80 3.32
3856 6820 7.097192 TGAATCTAGACAACATGTAGAACACC 58.903 38.462 0.00 0.00 36.80 4.16
3857 6821 6.859112 ATCTAGACAACATGTAGAACACCT 57.141 37.500 0.00 0.00 36.80 4.00
3858 6822 7.956328 ATCTAGACAACATGTAGAACACCTA 57.044 36.000 0.00 0.00 36.80 3.08
3859 6823 7.770366 TCTAGACAACATGTAGAACACCTAA 57.230 36.000 0.00 0.00 30.39 2.69
3860 6824 8.185506 TCTAGACAACATGTAGAACACCTAAA 57.814 34.615 0.00 0.00 30.39 1.85
3861 6825 8.644216 TCTAGACAACATGTAGAACACCTAAAA 58.356 33.333 0.00 0.00 30.39 1.52
3862 6826 7.492352 AGACAACATGTAGAACACCTAAAAC 57.508 36.000 0.00 0.00 0.00 2.43
3863 6827 7.051623 AGACAACATGTAGAACACCTAAAACA 58.948 34.615 0.00 0.00 0.00 2.83
3864 6828 7.719633 AGACAACATGTAGAACACCTAAAACAT 59.280 33.333 0.00 0.00 0.00 2.71
3865 6829 7.871853 ACAACATGTAGAACACCTAAAACATC 58.128 34.615 0.00 0.00 0.00 3.06
3866 6830 7.719633 ACAACATGTAGAACACCTAAAACATCT 59.280 33.333 0.00 0.00 0.00 2.90
3867 6831 8.567948 CAACATGTAGAACACCTAAAACATCTT 58.432 33.333 0.00 0.00 0.00 2.40
3868 6832 9.787435 AACATGTAGAACACCTAAAACATCTTA 57.213 29.630 0.00 0.00 0.00 2.10
3869 6833 9.959721 ACATGTAGAACACCTAAAACATCTTAT 57.040 29.630 0.00 0.00 0.00 1.73
3885 6849 8.974060 AACATCTTATATTAAAAAGCGGAGGA 57.026 30.769 0.00 0.00 0.00 3.71
3886 6850 8.974060 ACATCTTATATTAAAAAGCGGAGGAA 57.026 30.769 0.00 0.00 0.00 3.36
3887 6851 9.057089 ACATCTTATATTAAAAAGCGGAGGAAG 57.943 33.333 0.00 0.00 0.00 3.46
3888 6852 9.057089 CATCTTATATTAAAAAGCGGAGGAAGT 57.943 33.333 0.00 0.00 0.00 3.01
3912 6876 5.585820 TTTCCTTATTTACGGGGCATTTC 57.414 39.130 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
844 850 1.179152 CACCACACATCACCATGCAT 58.821 50.000 0.00 0.00 32.57 3.96
845 851 0.110104 TCACCACACATCACCATGCA 59.890 50.000 0.00 0.00 32.57 3.96
846 852 1.200716 CTTCACCACACATCACCATGC 59.799 52.381 0.00 0.00 32.57 4.06
847 853 2.781923 TCTTCACCACACATCACCATG 58.218 47.619 0.00 0.00 35.92 3.66
848 854 3.726557 ATCTTCACCACACATCACCAT 57.273 42.857 0.00 0.00 0.00 3.55
849 855 3.148412 CAATCTTCACCACACATCACCA 58.852 45.455 0.00 0.00 0.00 4.17
850 856 3.411446 TCAATCTTCACCACACATCACC 58.589 45.455 0.00 0.00 0.00 4.02
851 857 4.516698 ACTTCAATCTTCACCACACATCAC 59.483 41.667 0.00 0.00 0.00 3.06
852 858 4.717877 ACTTCAATCTTCACCACACATCA 58.282 39.130 0.00 0.00 0.00 3.07
853 859 5.009010 ACAACTTCAATCTTCACCACACATC 59.991 40.000 0.00 0.00 0.00 3.06
854 860 4.889409 ACAACTTCAATCTTCACCACACAT 59.111 37.500 0.00 0.00 0.00 3.21
855 861 4.096231 CACAACTTCAATCTTCACCACACA 59.904 41.667 0.00 0.00 0.00 3.72
856 862 4.601019 CACAACTTCAATCTTCACCACAC 58.399 43.478 0.00 0.00 0.00 3.82
857 863 3.066621 GCACAACTTCAATCTTCACCACA 59.933 43.478 0.00 0.00 0.00 4.17
858 864 3.632189 GCACAACTTCAATCTTCACCAC 58.368 45.455 0.00 0.00 0.00 4.16
859 865 2.290367 CGCACAACTTCAATCTTCACCA 59.710 45.455 0.00 0.00 0.00 4.17
860 866 2.918131 GCGCACAACTTCAATCTTCACC 60.918 50.000 0.30 0.00 0.00 4.02
861 867 2.310577 GCGCACAACTTCAATCTTCAC 58.689 47.619 0.30 0.00 0.00 3.18
862 868 1.069973 CGCGCACAACTTCAATCTTCA 60.070 47.619 8.75 0.00 0.00 3.02
863 869 1.595609 CGCGCACAACTTCAATCTTC 58.404 50.000 8.75 0.00 0.00 2.87
864 870 0.385974 GCGCGCACAACTTCAATCTT 60.386 50.000 29.10 0.00 0.00 2.40
865 871 1.207593 GCGCGCACAACTTCAATCT 59.792 52.632 29.10 0.00 0.00 2.40
866 872 0.660005 TTGCGCGCACAACTTCAATC 60.660 50.000 36.72 0.00 0.00 2.67
867 873 0.248825 TTTGCGCGCACAACTTCAAT 60.249 45.000 36.72 0.00 0.00 2.57
868 874 0.865218 CTTTGCGCGCACAACTTCAA 60.865 50.000 36.72 22.22 0.00 2.69
869 875 1.298264 CTTTGCGCGCACAACTTCA 60.298 52.632 36.72 15.39 0.00 3.02
870 876 2.010817 CCTTTGCGCGCACAACTTC 61.011 57.895 36.72 0.01 0.00 3.01
871 877 2.026014 CCTTTGCGCGCACAACTT 59.974 55.556 36.72 0.00 0.00 2.66
872 878 3.964875 CCCTTTGCGCGCACAACT 61.965 61.111 36.72 0.00 0.00 3.16
873 879 2.395367 TAACCCTTTGCGCGCACAAC 62.395 55.000 36.72 2.77 0.00 3.32
874 880 2.123988 CTAACCCTTTGCGCGCACAA 62.124 55.000 36.72 27.16 0.00 3.33
875 881 2.592001 TAACCCTTTGCGCGCACA 60.592 55.556 36.72 27.96 0.00 4.57
876 882 1.847890 TTCTAACCCTTTGCGCGCAC 61.848 55.000 36.72 4.65 0.00 5.34
877 883 1.167155 TTTCTAACCCTTTGCGCGCA 61.167 50.000 33.09 33.09 0.00 6.09
878 884 0.170339 ATTTCTAACCCTTTGCGCGC 59.830 50.000 27.26 27.26 0.00 6.86
879 885 2.538939 GCTATTTCTAACCCTTTGCGCG 60.539 50.000 0.00 0.00 0.00 6.86
880 886 2.223502 GGCTATTTCTAACCCTTTGCGC 60.224 50.000 0.00 0.00 0.00 6.09
881 887 3.013921 TGGCTATTTCTAACCCTTTGCG 58.986 45.455 0.00 0.00 0.00 4.85
882 888 6.901081 ATATGGCTATTTCTAACCCTTTGC 57.099 37.500 0.00 0.00 0.00 3.68
883 889 7.444183 TCGAATATGGCTATTTCTAACCCTTTG 59.556 37.037 0.00 0.00 0.00 2.77
884 890 7.514721 TCGAATATGGCTATTTCTAACCCTTT 58.485 34.615 0.00 0.00 0.00 3.11
885 891 7.074653 TCGAATATGGCTATTTCTAACCCTT 57.925 36.000 0.00 0.00 0.00 3.95
886 892 6.681729 TCGAATATGGCTATTTCTAACCCT 57.318 37.500 0.00 0.00 0.00 4.34
887 893 7.606456 TCATTCGAATATGGCTATTTCTAACCC 59.394 37.037 10.97 0.00 0.00 4.11
888 894 8.547967 TCATTCGAATATGGCTATTTCTAACC 57.452 34.615 10.97 0.00 0.00 2.85
892 898 8.887717 GCTTATCATTCGAATATGGCTATTTCT 58.112 33.333 10.97 0.00 0.00 2.52
893 899 8.668353 TGCTTATCATTCGAATATGGCTATTTC 58.332 33.333 10.97 0.00 0.00 2.17
894 900 8.565896 TGCTTATCATTCGAATATGGCTATTT 57.434 30.769 10.97 0.00 0.00 1.40
895 901 8.565896 TTGCTTATCATTCGAATATGGCTATT 57.434 30.769 10.97 0.00 0.00 1.73
896 902 8.743085 ATTGCTTATCATTCGAATATGGCTAT 57.257 30.769 10.97 10.12 0.00 2.97
897 903 7.823799 TGATTGCTTATCATTCGAATATGGCTA 59.176 33.333 10.97 8.43 38.35 3.93
898 904 6.656270 TGATTGCTTATCATTCGAATATGGCT 59.344 34.615 10.97 0.00 38.35 4.75
899 905 6.845302 TGATTGCTTATCATTCGAATATGGC 58.155 36.000 10.97 11.15 38.35 4.40
1009 1015 9.382244 CAACTTACTTGATGCAGTTTTAGTTAC 57.618 33.333 0.00 0.00 30.42 2.50
1019 1025 4.391216 CCTCTCACAACTTACTTGATGCAG 59.609 45.833 0.00 0.00 33.59 4.41
1069 1075 5.345741 GCAAACATGACTTGCACGAATATTT 59.654 36.000 23.42 0.00 46.78 1.40
1530 1538 1.202417 CGTGGATGGTGAAGCTACGAT 60.202 52.381 0.00 0.00 32.36 3.73
1630 1638 2.107953 GTCAGATCCGGGAGCTGC 59.892 66.667 32.13 23.84 44.52 5.25
1687 1695 2.035312 AGGACACGGTAGTCGCCT 59.965 61.111 0.00 0.00 43.89 5.52
1760 1768 0.904865 TGTCCCTGGAACGAGCTGAT 60.905 55.000 0.00 0.00 0.00 2.90
1945 1983 1.915228 GGGAGATTGCACCCAGCTA 59.085 57.895 5.25 0.00 43.72 3.32
2013 2054 1.006102 GCGGTATCTATGCAGCCGT 60.006 57.895 11.92 0.00 43.78 5.68
2039 2080 2.265182 ACACCCATGTTTTCGCGGG 61.265 57.895 6.13 0.00 44.88 6.13
2048 2089 1.628846 GTAGTCCTCCAACACCCATGT 59.371 52.381 0.00 0.00 42.46 3.21
2244 2290 5.072329 TCTCCCATAGGAATTTCTGGATCAC 59.928 44.000 0.00 0.00 43.40 3.06
2320 2366 5.423015 CATCTTTCCTCTCGAAGAATGGAA 58.577 41.667 0.00 0.00 42.95 3.53
2438 2486 8.644374 AGGGAGTATTTTCTAGCTAGATACTG 57.356 38.462 28.25 4.95 30.13 2.74
2487 2535 9.549078 CTTAGGAATTACTCCCTCTGTAAATTC 57.451 37.037 0.00 0.00 46.81 2.17
2571 2707 9.911788 AATTACTTGTCTCTCCAATGAATGTAT 57.088 29.630 0.00 0.00 0.00 2.29
2577 2713 5.419542 CGGAATTACTTGTCTCTCCAATGA 58.580 41.667 0.00 0.00 0.00 2.57
2581 2717 3.194968 GTCCGGAATTACTTGTCTCTCCA 59.805 47.826 5.23 0.00 0.00 3.86
2617 2753 1.892474 AGGCGTGCATTAACATTTGGT 59.108 42.857 0.00 0.00 0.00 3.67
2633 2769 3.807538 GCATGGTGAGTGCAGGCG 61.808 66.667 0.00 0.00 42.08 5.52
2728 2937 9.832445 GGTTAAAATAGATCAGTGTCATCCTTA 57.168 33.333 0.00 0.00 0.00 2.69
2835 5223 9.582648 TGTTATCTGTAAGCTACCATATCTGTA 57.417 33.333 0.00 0.00 0.00 2.74
2837 5225 9.764363 TTTGTTATCTGTAAGCTACCATATCTG 57.236 33.333 0.00 0.00 0.00 2.90
2842 5230 8.100791 TCAGTTTTGTTATCTGTAAGCTACCAT 58.899 33.333 0.00 0.00 0.00 3.55
2907 5302 5.192927 CCACCTGGTATTCTGCTATTTCAA 58.807 41.667 0.00 0.00 0.00 2.69
2935 5330 8.957466 GTTTTAATGCTTATCAAGAACCTACCT 58.043 33.333 0.00 0.00 0.00 3.08
2973 5368 1.909302 CCCCCTAAGTCTCAAGAAGCA 59.091 52.381 0.00 0.00 0.00 3.91
2974 5369 1.909986 ACCCCCTAAGTCTCAAGAAGC 59.090 52.381 0.00 0.00 0.00 3.86
2989 5384 2.679996 GGTCCAATGCACACCCCC 60.680 66.667 0.00 0.00 0.00 5.40
3023 5418 6.015350 GGCTGAAGCAGTAGATAGGTACATTA 60.015 42.308 4.43 0.00 44.36 1.90
3025 5420 4.282195 GGCTGAAGCAGTAGATAGGTACAT 59.718 45.833 4.43 0.00 44.36 2.29
3052 5447 0.679960 GGGCACTTTTAGCGGTGGAT 60.680 55.000 0.00 0.00 34.41 3.41
3054 5449 1.586154 CTGGGCACTTTTAGCGGTGG 61.586 60.000 0.00 0.00 34.41 4.61
3055 5450 1.875963 CTGGGCACTTTTAGCGGTG 59.124 57.895 0.00 0.00 36.62 4.94
3079 5474 6.496218 AGCACTCCACAGATAGATAATCATCA 59.504 38.462 0.00 0.00 37.03 3.07
3113 5508 3.308866 GCGCGAGATTACTAACCAAACAT 59.691 43.478 12.10 0.00 0.00 2.71
3116 5511 2.273557 GGCGCGAGATTACTAACCAAA 58.726 47.619 12.10 0.00 0.00 3.28
3126 5521 1.967319 AATATGTTGGGCGCGAGATT 58.033 45.000 12.10 0.00 0.00 2.40
3127 5522 2.612972 CCTAATATGTTGGGCGCGAGAT 60.613 50.000 12.10 5.92 0.00 2.75
3131 5526 1.305201 AACCTAATATGTTGGGCGCG 58.695 50.000 0.00 0.00 39.44 6.86
3173 5568 5.356751 TCAAACTGTCACTGCAAACTGTAAT 59.643 36.000 6.53 0.00 0.00 1.89
3232 5627 8.260818 CCAATTTGAGAAAGTATCAGACCTCTA 58.739 37.037 0.00 0.00 0.00 2.43
3301 5697 7.164803 ACTTCCTTGCTGGATTATATCTAAGC 58.835 38.462 0.09 0.00 45.68 3.09
3390 5914 1.544314 GGTCAGCCCCATTCTAGCATC 60.544 57.143 0.00 0.00 0.00 3.91
3471 6181 3.934457 AAAAGGCAACCAGGATAAACG 57.066 42.857 0.00 0.00 37.17 3.60
3582 6292 5.972935 TGAAGTCTGCAGGAATTTCGTATA 58.027 37.500 15.13 0.00 32.03 1.47
3656 6366 1.343465 GAAGAAACGGACAGTGAGGGA 59.657 52.381 0.00 0.00 0.00 4.20
3708 6672 7.254795 GGAGGGAGTATCATATTTTGTGTTTCG 60.255 40.741 0.00 0.00 36.25 3.46
3717 6681 6.688073 ATGAACGGAGGGAGTATCATATTT 57.312 37.500 0.00 0.00 36.25 1.40
3718 6682 7.792364 TTATGAACGGAGGGAGTATCATATT 57.208 36.000 0.00 0.00 36.25 1.28
3721 6685 6.688073 ATTTATGAACGGAGGGAGTATCAT 57.312 37.500 0.00 0.00 36.25 2.45
3726 6690 7.850935 TCTTATATTTATGAACGGAGGGAGT 57.149 36.000 0.00 0.00 0.00 3.85
3727 6691 8.314751 ACATCTTATATTTATGAACGGAGGGAG 58.685 37.037 0.00 0.00 0.00 4.30
3728 6692 8.202461 ACATCTTATATTTATGAACGGAGGGA 57.798 34.615 0.00 0.00 0.00 4.20
3742 6706 9.586732 TGGCCAAAAGCTAATACATCTTATATT 57.413 29.630 0.61 0.00 43.05 1.28
3743 6707 9.014297 GTGGCCAAAAGCTAATACATCTTATAT 57.986 33.333 7.24 0.00 43.05 0.86
3744 6708 7.996066 TGTGGCCAAAAGCTAATACATCTTATA 59.004 33.333 7.24 0.00 43.05 0.98
3745 6709 6.833416 TGTGGCCAAAAGCTAATACATCTTAT 59.167 34.615 7.24 0.00 43.05 1.73
3746 6710 6.184068 TGTGGCCAAAAGCTAATACATCTTA 58.816 36.000 7.24 0.00 43.05 2.10
3747 6711 5.016173 TGTGGCCAAAAGCTAATACATCTT 58.984 37.500 7.24 0.00 43.05 2.40
3748 6712 4.599041 TGTGGCCAAAAGCTAATACATCT 58.401 39.130 7.24 0.00 43.05 2.90
3749 6713 4.981806 TGTGGCCAAAAGCTAATACATC 57.018 40.909 7.24 0.00 43.05 3.06
3750 6714 5.658190 AGAATGTGGCCAAAAGCTAATACAT 59.342 36.000 7.24 0.00 43.05 2.29
3751 6715 5.016173 AGAATGTGGCCAAAAGCTAATACA 58.984 37.500 7.24 0.00 43.05 2.29
3752 6716 5.582689 AGAATGTGGCCAAAAGCTAATAC 57.417 39.130 7.24 0.00 43.05 1.89
3753 6717 6.094881 GTGTAGAATGTGGCCAAAAGCTAATA 59.905 38.462 7.24 0.00 43.05 0.98
3754 6718 5.016173 TGTAGAATGTGGCCAAAAGCTAAT 58.984 37.500 7.24 0.00 43.05 1.73
3755 6719 4.217550 GTGTAGAATGTGGCCAAAAGCTAA 59.782 41.667 7.24 0.00 43.05 3.09
3756 6720 3.756434 GTGTAGAATGTGGCCAAAAGCTA 59.244 43.478 7.24 5.41 43.05 3.32
3757 6721 2.558359 GTGTAGAATGTGGCCAAAAGCT 59.442 45.455 7.24 6.57 43.05 3.74
3758 6722 2.668279 CGTGTAGAATGTGGCCAAAAGC 60.668 50.000 7.24 0.00 42.60 3.51
3759 6723 2.552315 ACGTGTAGAATGTGGCCAAAAG 59.448 45.455 7.24 0.00 0.00 2.27
3760 6724 2.577700 ACGTGTAGAATGTGGCCAAAA 58.422 42.857 7.24 0.00 0.00 2.44
3761 6725 2.264005 ACGTGTAGAATGTGGCCAAA 57.736 45.000 7.24 0.15 0.00 3.28
3762 6726 3.055747 TGATACGTGTAGAATGTGGCCAA 60.056 43.478 7.24 0.00 0.00 4.52
3763 6727 2.498078 TGATACGTGTAGAATGTGGCCA 59.502 45.455 0.00 0.00 0.00 5.36
3764 6728 3.173668 TGATACGTGTAGAATGTGGCC 57.826 47.619 0.00 0.00 0.00 5.36
3765 6729 5.064707 ACATTTGATACGTGTAGAATGTGGC 59.935 40.000 18.48 0.00 36.63 5.01
3766 6730 6.662414 ACATTTGATACGTGTAGAATGTGG 57.338 37.500 18.48 1.83 36.63 4.17
3767 6731 9.249457 AGATACATTTGATACGTGTAGAATGTG 57.751 33.333 23.75 9.92 37.99 3.21
3772 6736 9.333724 TGTCTAGATACATTTGATACGTGTAGA 57.666 33.333 0.00 0.00 32.45 2.59
3774 6738 9.893305 CATGTCTAGATACATTTGATACGTGTA 57.107 33.333 0.00 0.00 38.01 2.90
3775 6739 8.414003 ACATGTCTAGATACATTTGATACGTGT 58.586 33.333 0.00 0.00 38.01 4.49
3776 6740 8.803201 ACATGTCTAGATACATTTGATACGTG 57.197 34.615 0.00 0.00 38.01 4.49
3777 6741 9.464714 GAACATGTCTAGATACATTTGATACGT 57.535 33.333 0.00 0.00 38.01 3.57
3778 6742 9.684448 AGAACATGTCTAGATACATTTGATACG 57.316 33.333 0.00 0.00 38.01 3.06
3793 6757 8.117813 TGAATGTACACACTAGAACATGTCTA 57.882 34.615 0.00 1.94 37.84 2.59
3794 6758 6.993079 TGAATGTACACACTAGAACATGTCT 58.007 36.000 0.00 0.69 40.71 3.41
3795 6759 7.834068 ATGAATGTACACACTAGAACATGTC 57.166 36.000 0.00 0.00 33.04 3.06
3796 6760 8.097038 AGAATGAATGTACACACTAGAACATGT 58.903 33.333 0.00 0.00 33.04 3.21
3797 6761 8.484641 AGAATGAATGTACACACTAGAACATG 57.515 34.615 0.00 0.00 33.04 3.21
3798 6762 9.507329 AAAGAATGAATGTACACACTAGAACAT 57.493 29.630 0.00 0.00 34.11 2.71
3799 6763 8.902540 AAAGAATGAATGTACACACTAGAACA 57.097 30.769 0.00 0.00 0.00 3.18
3828 6792 9.803315 TGTTCTACATGTTGTCTAGATTCATAC 57.197 33.333 2.30 0.00 0.00 2.39
3829 6793 9.803315 GTGTTCTACATGTTGTCTAGATTCATA 57.197 33.333 2.30 0.00 0.00 2.15
3830 6794 7.766278 GGTGTTCTACATGTTGTCTAGATTCAT 59.234 37.037 2.30 0.00 0.00 2.57
3831 6795 7.039011 AGGTGTTCTACATGTTGTCTAGATTCA 60.039 37.037 2.30 0.78 0.00 2.57
3832 6796 7.324178 AGGTGTTCTACATGTTGTCTAGATTC 58.676 38.462 2.30 0.00 0.00 2.52
3833 6797 7.246171 AGGTGTTCTACATGTTGTCTAGATT 57.754 36.000 2.30 0.00 0.00 2.40
3834 6798 6.859112 AGGTGTTCTACATGTTGTCTAGAT 57.141 37.500 2.30 0.00 0.00 1.98
3835 6799 7.770366 TTAGGTGTTCTACATGTTGTCTAGA 57.230 36.000 2.30 0.00 0.00 2.43
3836 6800 8.709646 GTTTTAGGTGTTCTACATGTTGTCTAG 58.290 37.037 2.30 0.00 0.00 2.43
3837 6801 8.205512 TGTTTTAGGTGTTCTACATGTTGTCTA 58.794 33.333 2.30 0.00 0.00 2.59
3838 6802 7.051623 TGTTTTAGGTGTTCTACATGTTGTCT 58.948 34.615 2.30 0.22 0.00 3.41
3839 6803 7.254227 TGTTTTAGGTGTTCTACATGTTGTC 57.746 36.000 2.30 1.18 0.00 3.18
3840 6804 7.719633 AGATGTTTTAGGTGTTCTACATGTTGT 59.280 33.333 2.30 0.00 0.00 3.32
3841 6805 8.099364 AGATGTTTTAGGTGTTCTACATGTTG 57.901 34.615 2.30 1.19 0.00 3.33
3842 6806 8.691661 AAGATGTTTTAGGTGTTCTACATGTT 57.308 30.769 2.30 0.00 0.00 2.71
3843 6807 9.959721 ATAAGATGTTTTAGGTGTTCTACATGT 57.040 29.630 2.69 2.69 0.00 3.21
3859 6823 9.403583 TCCTCCGCTTTTTAATATAAGATGTTT 57.596 29.630 0.00 0.00 0.00 2.83
3860 6824 8.974060 TCCTCCGCTTTTTAATATAAGATGTT 57.026 30.769 0.00 0.00 0.00 2.71
3861 6825 8.974060 TTCCTCCGCTTTTTAATATAAGATGT 57.026 30.769 0.00 0.00 0.00 3.06
3862 6826 9.057089 ACTTCCTCCGCTTTTTAATATAAGATG 57.943 33.333 0.00 0.00 0.00 2.90
3868 6832 8.847196 GGAAATACTTCCTCCGCTTTTTAATAT 58.153 33.333 0.00 0.00 46.80 1.28
3869 6833 8.217131 GGAAATACTTCCTCCGCTTTTTAATA 57.783 34.615 0.00 0.00 46.80 0.98
3870 6834 7.096884 GGAAATACTTCCTCCGCTTTTTAAT 57.903 36.000 0.00 0.00 46.80 1.40
3871 6835 6.505044 GGAAATACTTCCTCCGCTTTTTAA 57.495 37.500 0.00 0.00 46.80 1.52
3884 6848 5.824097 TGCCCCGTAAATAAGGAAATACTTC 59.176 40.000 0.00 0.00 32.02 3.01
3885 6849 5.757988 TGCCCCGTAAATAAGGAAATACTT 58.242 37.500 0.00 0.00 34.52 2.24
3886 6850 5.376756 TGCCCCGTAAATAAGGAAATACT 57.623 39.130 0.00 0.00 0.00 2.12
3887 6851 6.644248 AATGCCCCGTAAATAAGGAAATAC 57.356 37.500 0.00 0.00 0.00 1.89
3888 6852 7.013846 CAGAAATGCCCCGTAAATAAGGAAATA 59.986 37.037 0.00 0.00 0.00 1.40
3889 6853 5.897250 AGAAATGCCCCGTAAATAAGGAAAT 59.103 36.000 0.00 0.00 0.00 2.17
3893 6857 4.204012 TCAGAAATGCCCCGTAAATAAGG 58.796 43.478 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.