Multiple sequence alignment - TraesCS3D01G176300

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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 TraesCS3D01G176300 chr3D 100.000 2684 0 0 1 2684 157749013 157751696 0.000000e+00 4957.0
1 TraesCS3D01G176300 chr3D 81.804 654 74 20 1058 1677 157659684 157660326 8.570000e-140 507.0
2 TraesCS3D01G176300 chr3D 84.375 96 14 1 68 162 312862686 312862591 2.850000e-15 93.5
3 TraesCS3D01G176300 chr6D 92.778 1897 72 13 183 2068 438517708 438519550 0.000000e+00 2684.0
4 TraesCS3D01G176300 chr6D 93.210 486 25 3 2161 2646 438523200 438523677 0.000000e+00 708.0
5 TraesCS3D01G176300 chr6D 94.462 325 14 3 2360 2684 438532905 438532585 5.160000e-137 497.0
6 TraesCS3D01G176300 chr6D 100.000 29 0 0 187 215 262434351 262434323 1.000000e-03 54.7
7 TraesCS3D01G176300 chr3B 91.562 1920 87 17 186 2065 229005427 229007311 0.000000e+00 2579.0
8 TraesCS3D01G176300 chr3B 92.605 622 25 8 2069 2684 229007368 229007974 0.000000e+00 874.0
9 TraesCS3D01G176300 chr3B 81.750 663 75 27 1058 1677 228983028 228983687 1.840000e-141 512.0
10 TraesCS3D01G176300 chr3A 92.347 1764 77 21 333 2068 170391771 170390038 0.000000e+00 2457.0
11 TraesCS3D01G176300 chr3A 94.851 505 20 4 2186 2684 170389930 170389426 0.000000e+00 784.0
12 TraesCS3D01G176300 chr3A 81.424 646 79 22 1071 1677 170486463 170485820 8.630000e-135 490.0
13 TraesCS3D01G176300 chr3A 89.203 389 11 14 1519 1899 170310545 170310910 8.760000e-125 457.0
14 TraesCS3D01G176300 chrUn 89.203 389 11 14 1519 1899 293324346 293324711 8.760000e-125 457.0
15 TraesCS3D01G176300 chrUn 89.203 389 11 14 1519 1899 389790917 389791282 8.760000e-125 457.0
16 TraesCS3D01G176300 chrUn 88.325 394 15 14 1519 1904 287217075 287216705 6.820000e-121 444.0
17 TraesCS3D01G176300 chrUn 88.325 394 15 14 1519 1904 300435793 300436163 6.820000e-121 444.0
18 TraesCS3D01G176300 chr7B 82.340 453 40 21 1049 1465 750391069 750390621 9.140000e-95 357.0
19 TraesCS3D01G176300 chr7B 82.184 348 52 8 213 558 750391782 750391443 9.400000e-75 291.0
20 TraesCS3D01G176300 chr7B 91.667 84 5 2 1857 1938 750378902 750378819 6.070000e-22 115.0
21 TraesCS3D01G176300 chr7B 95.455 66 3 0 847 912 750391282 750391217 3.650000e-19 106.0
22 TraesCS3D01G176300 chr7A 82.086 441 47 21 1051 1459 732842251 732842691 5.500000e-92 348.0
23 TraesCS3D01G176300 chr7A 87.500 144 11 6 415 558 732841740 732841876 2.770000e-35 159.0
24 TraesCS3D01G176300 chr7A 75.138 181 19 12 872 1042 732842051 732842215 8.020000e-06 62.1
25 TraesCS3D01G176300 chr7D 81.250 448 53 20 1049 1465 633695431 633694984 1.540000e-87 333.0
26 TraesCS3D01G176300 chr7D 82.400 250 26 10 458 697 633696036 633695795 4.530000e-48 202.0
27 TraesCS3D01G176300 chr7D 78.140 215 22 18 847 1049 633695661 633695460 2.180000e-21 113.0
28 TraesCS3D01G176300 chr2A 82.353 119 17 3 21 137 709691621 709691505 1.700000e-17 100.0
29 TraesCS3D01G176300 chr6B 97.143 35 0 1 186 220 348089271 348089304 1.040000e-04 58.4
30 TraesCS3D01G176300 chr6A 97.059 34 1 0 186 219 523337848 523337815 1.040000e-04 58.4
31 TraesCS3D01G176300 chr5B 96.774 31 1 0 183 213 351145663 351145693 5.000000e-03 52.8
32 TraesCS3D01G176300 chr1B 96.774 31 1 0 186 216 354243761 354243731 5.000000e-03 52.8


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 TraesCS3D01G176300 chr3D 157749013 157751696 2683 False 4957.000000 4957 100.000000 1 2684 1 chr3D.!!$F2 2683
1 TraesCS3D01G176300 chr3D 157659684 157660326 642 False 507.000000 507 81.804000 1058 1677 1 chr3D.!!$F1 619
2 TraesCS3D01G176300 chr6D 438517708 438523677 5969 False 1696.000000 2684 92.994000 183 2646 2 chr6D.!!$F1 2463
3 TraesCS3D01G176300 chr3B 229005427 229007974 2547 False 1726.500000 2579 92.083500 186 2684 2 chr3B.!!$F2 2498
4 TraesCS3D01G176300 chr3B 228983028 228983687 659 False 512.000000 512 81.750000 1058 1677 1 chr3B.!!$F1 619
5 TraesCS3D01G176300 chr3A 170389426 170391771 2345 True 1620.500000 2457 93.599000 333 2684 2 chr3A.!!$R2 2351
6 TraesCS3D01G176300 chr3A 170485820 170486463 643 True 490.000000 490 81.424000 1071 1677 1 chr3A.!!$R1 606
7 TraesCS3D01G176300 chr7B 750390621 750391782 1161 True 251.333333 357 86.659667 213 1465 3 chr7B.!!$R2 1252
8 TraesCS3D01G176300 chr7D 633694984 633696036 1052 True 216.000000 333 80.596667 458 1465 3 chr7D.!!$R1 1007

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
177 178 0.095935 GCTGCAGCAGAACACGTATG 59.904 55.0 33.36 0.0 41.59 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 5974 0.373716 GGCCTGCAAGTCGTAATTCG 59.626 55.0 0.0 0.0 41.41 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
33 34 4.609018 CCTGTATGGCGGCCGGAG 62.609 72.222 29.38 6.95 0.00 4.63
34 35 3.536917 CTGTATGGCGGCCGGAGA 61.537 66.667 29.38 1.91 0.00 3.71
35 36 3.506059 CTGTATGGCGGCCGGAGAG 62.506 68.421 29.38 8.58 0.00 3.20
36 37 4.301027 GTATGGCGGCCGGAGAGG 62.301 72.222 29.38 0.00 44.97 3.69
37 38 4.853142 TATGGCGGCCGGAGAGGT 62.853 66.667 29.38 0.00 43.70 3.85
38 39 3.440162 TATGGCGGCCGGAGAGGTA 62.440 63.158 29.38 0.00 43.70 3.08
41 42 3.145551 GCGGCCGGAGAGGTAGAA 61.146 66.667 29.38 0.00 43.70 2.10
42 43 2.806237 CGGCCGGAGAGGTAGAAC 59.194 66.667 20.10 0.00 43.70 3.01
43 44 2.806237 GGCCGGAGAGGTAGAACG 59.194 66.667 5.05 0.00 43.70 3.95
44 45 2.783288 GGCCGGAGAGGTAGAACGG 61.783 68.421 5.05 0.00 46.78 4.44
45 46 2.806237 CCGGAGAGGTAGAACGGC 59.194 66.667 0.00 0.00 37.93 5.68
46 47 2.408022 CGGAGAGGTAGAACGGCG 59.592 66.667 4.80 4.80 0.00 6.46
47 48 2.806237 GGAGAGGTAGAACGGCGG 59.194 66.667 13.24 0.00 0.00 6.13
48 49 2.104530 GAGAGGTAGAACGGCGGC 59.895 66.667 13.24 0.00 0.00 6.53
49 50 2.678934 AGAGGTAGAACGGCGGCA 60.679 61.111 13.24 0.00 0.00 5.69
50 51 2.221906 GAGAGGTAGAACGGCGGCAA 62.222 60.000 13.24 0.00 0.00 4.52
51 52 2.047560 AGGTAGAACGGCGGCAAC 60.048 61.111 13.24 3.49 0.00 4.17
52 53 2.357760 GGTAGAACGGCGGCAACA 60.358 61.111 13.24 0.00 0.00 3.33
53 54 2.388232 GGTAGAACGGCGGCAACAG 61.388 63.158 13.24 0.00 0.00 3.16
54 55 1.373748 GTAGAACGGCGGCAACAGA 60.374 57.895 13.24 0.00 0.00 3.41
55 56 1.080093 TAGAACGGCGGCAACAGAG 60.080 57.895 13.24 0.00 0.00 3.35
56 57 2.501223 TAGAACGGCGGCAACAGAGG 62.501 60.000 13.24 0.00 0.00 3.69
57 58 3.876589 GAACGGCGGCAACAGAGGA 62.877 63.158 13.24 0.00 0.00 3.71
58 59 3.883744 AACGGCGGCAACAGAGGAG 62.884 63.158 13.24 0.00 0.00 3.69
60 61 3.706373 GGCGGCAACAGAGGAGGA 61.706 66.667 3.07 0.00 0.00 3.71
61 62 2.125350 GCGGCAACAGAGGAGGAG 60.125 66.667 0.00 0.00 0.00 3.69
62 63 2.650116 GCGGCAACAGAGGAGGAGA 61.650 63.158 0.00 0.00 0.00 3.71
63 64 1.515020 CGGCAACAGAGGAGGAGAG 59.485 63.158 0.00 0.00 0.00 3.20
64 65 1.254284 CGGCAACAGAGGAGGAGAGT 61.254 60.000 0.00 0.00 0.00 3.24
65 66 0.248843 GGCAACAGAGGAGGAGAGTG 59.751 60.000 0.00 0.00 0.00 3.51
66 67 1.261480 GCAACAGAGGAGGAGAGTGA 58.739 55.000 0.00 0.00 0.00 3.41
67 68 1.204467 GCAACAGAGGAGGAGAGTGAG 59.796 57.143 0.00 0.00 0.00 3.51
68 69 1.824230 CAACAGAGGAGGAGAGTGAGG 59.176 57.143 0.00 0.00 0.00 3.86
69 70 1.377690 ACAGAGGAGGAGAGTGAGGA 58.622 55.000 0.00 0.00 0.00 3.71
70 71 1.929494 ACAGAGGAGGAGAGTGAGGAT 59.071 52.381 0.00 0.00 0.00 3.24
71 72 2.309613 CAGAGGAGGAGAGTGAGGATG 58.690 57.143 0.00 0.00 0.00 3.51
72 73 1.039856 GAGGAGGAGAGTGAGGATGC 58.960 60.000 0.00 0.00 0.00 3.91
73 74 0.337773 AGGAGGAGAGTGAGGATGCA 59.662 55.000 0.00 0.00 0.00 3.96
74 75 1.198713 GGAGGAGAGTGAGGATGCAA 58.801 55.000 0.00 0.00 0.00 4.08
75 76 1.556911 GGAGGAGAGTGAGGATGCAAA 59.443 52.381 0.00 0.00 0.00 3.68
76 77 2.419851 GGAGGAGAGTGAGGATGCAAAG 60.420 54.545 0.00 0.00 0.00 2.77
77 78 2.235898 GAGGAGAGTGAGGATGCAAAGT 59.764 50.000 0.00 0.00 0.00 2.66
78 79 3.445008 AGGAGAGTGAGGATGCAAAGTA 58.555 45.455 0.00 0.00 0.00 2.24
79 80 3.840666 AGGAGAGTGAGGATGCAAAGTAA 59.159 43.478 0.00 0.00 0.00 2.24
80 81 4.081198 AGGAGAGTGAGGATGCAAAGTAAG 60.081 45.833 0.00 0.00 0.00 2.34
81 82 4.187694 GAGAGTGAGGATGCAAAGTAAGG 58.812 47.826 0.00 0.00 0.00 2.69
82 83 3.054802 AGAGTGAGGATGCAAAGTAAGGG 60.055 47.826 0.00 0.00 0.00 3.95
83 84 2.912956 AGTGAGGATGCAAAGTAAGGGA 59.087 45.455 0.00 0.00 0.00 4.20
84 85 3.330701 AGTGAGGATGCAAAGTAAGGGAA 59.669 43.478 0.00 0.00 0.00 3.97
85 86 3.691609 GTGAGGATGCAAAGTAAGGGAAG 59.308 47.826 0.00 0.00 0.00 3.46
86 87 3.587061 TGAGGATGCAAAGTAAGGGAAGA 59.413 43.478 0.00 0.00 0.00 2.87
87 88 4.042809 TGAGGATGCAAAGTAAGGGAAGAA 59.957 41.667 0.00 0.00 0.00 2.52
88 89 4.593956 AGGATGCAAAGTAAGGGAAGAAG 58.406 43.478 0.00 0.00 0.00 2.85
89 90 3.696548 GGATGCAAAGTAAGGGAAGAAGG 59.303 47.826 0.00 0.00 0.00 3.46
90 91 3.154827 TGCAAAGTAAGGGAAGAAGGG 57.845 47.619 0.00 0.00 0.00 3.95
91 92 2.445525 TGCAAAGTAAGGGAAGAAGGGT 59.554 45.455 0.00 0.00 0.00 4.34
92 93 3.082548 GCAAAGTAAGGGAAGAAGGGTC 58.917 50.000 0.00 0.00 0.00 4.46
93 94 3.335579 CAAAGTAAGGGAAGAAGGGTCG 58.664 50.000 0.00 0.00 0.00 4.79
94 95 1.569653 AGTAAGGGAAGAAGGGTCGG 58.430 55.000 0.00 0.00 0.00 4.79
95 96 1.078324 AGTAAGGGAAGAAGGGTCGGA 59.922 52.381 0.00 0.00 0.00 4.55
96 97 2.117051 GTAAGGGAAGAAGGGTCGGAT 58.883 52.381 0.00 0.00 0.00 4.18
97 98 2.563039 AAGGGAAGAAGGGTCGGATA 57.437 50.000 0.00 0.00 0.00 2.59
98 99 2.089600 AGGGAAGAAGGGTCGGATAG 57.910 55.000 0.00 0.00 0.00 2.08
99 100 1.049402 GGGAAGAAGGGTCGGATAGG 58.951 60.000 0.00 0.00 0.00 2.57
100 101 1.412649 GGGAAGAAGGGTCGGATAGGA 60.413 57.143 0.00 0.00 0.00 2.94
101 102 2.395619 GGAAGAAGGGTCGGATAGGAA 58.604 52.381 0.00 0.00 0.00 3.36
102 103 2.365941 GGAAGAAGGGTCGGATAGGAAG 59.634 54.545 0.00 0.00 0.00 3.46
103 104 3.297736 GAAGAAGGGTCGGATAGGAAGA 58.702 50.000 0.00 0.00 0.00 2.87
104 105 3.399952 AGAAGGGTCGGATAGGAAGAA 57.600 47.619 0.00 0.00 0.00 2.52
105 106 3.721021 AGAAGGGTCGGATAGGAAGAAA 58.279 45.455 0.00 0.00 0.00 2.52
106 107 4.101856 AGAAGGGTCGGATAGGAAGAAAA 58.898 43.478 0.00 0.00 0.00 2.29
107 108 4.722279 AGAAGGGTCGGATAGGAAGAAAAT 59.278 41.667 0.00 0.00 0.00 1.82
108 109 4.423625 AGGGTCGGATAGGAAGAAAATG 57.576 45.455 0.00 0.00 0.00 2.32
109 110 3.136626 AGGGTCGGATAGGAAGAAAATGG 59.863 47.826 0.00 0.00 0.00 3.16
110 111 3.477530 GGTCGGATAGGAAGAAAATGGG 58.522 50.000 0.00 0.00 0.00 4.00
111 112 3.135895 GGTCGGATAGGAAGAAAATGGGA 59.864 47.826 0.00 0.00 0.00 4.37
112 113 4.127907 GTCGGATAGGAAGAAAATGGGAC 58.872 47.826 0.00 0.00 0.00 4.46
113 114 3.135895 TCGGATAGGAAGAAAATGGGACC 59.864 47.826 0.00 0.00 0.00 4.46
114 115 3.477530 GGATAGGAAGAAAATGGGACCG 58.522 50.000 0.00 0.00 0.00 4.79
115 116 3.477530 GATAGGAAGAAAATGGGACCGG 58.522 50.000 0.00 0.00 0.00 5.28
116 117 0.331616 AGGAAGAAAATGGGACCGGG 59.668 55.000 6.32 0.00 0.00 5.73
117 118 0.330267 GGAAGAAAATGGGACCGGGA 59.670 55.000 6.32 0.00 0.00 5.14
118 119 1.682087 GGAAGAAAATGGGACCGGGAG 60.682 57.143 6.32 0.00 0.00 4.30
119 120 1.280998 GAAGAAAATGGGACCGGGAGA 59.719 52.381 6.32 0.00 0.00 3.71
120 121 0.912486 AGAAAATGGGACCGGGAGAG 59.088 55.000 6.32 0.00 0.00 3.20
121 122 0.107165 GAAAATGGGACCGGGAGAGG 60.107 60.000 6.32 0.00 37.30 3.69
122 123 1.571773 AAAATGGGACCGGGAGAGGG 61.572 60.000 6.32 0.00 35.02 4.30
123 124 4.499116 ATGGGACCGGGAGAGGGG 62.499 72.222 6.32 0.00 35.02 4.79
125 126 4.173701 GGGACCGGGAGAGGGGAT 62.174 72.222 6.32 0.00 35.02 3.85
126 127 2.040779 GGACCGGGAGAGGGGATT 60.041 66.667 6.32 0.00 35.02 3.01
127 128 2.141448 GGACCGGGAGAGGGGATTC 61.141 68.421 6.32 0.00 35.02 2.52
128 129 1.382695 GACCGGGAGAGGGGATTCA 60.383 63.158 6.32 0.00 35.02 2.57
129 130 1.383248 ACCGGGAGAGGGGATTCAG 60.383 63.158 6.32 0.00 35.02 3.02
130 131 1.383248 CCGGGAGAGGGGATTCAGT 60.383 63.158 0.00 0.00 0.00 3.41
131 132 1.690219 CCGGGAGAGGGGATTCAGTG 61.690 65.000 0.00 0.00 0.00 3.66
132 133 1.690219 CGGGAGAGGGGATTCAGTGG 61.690 65.000 0.00 0.00 0.00 4.00
133 134 1.348775 GGGAGAGGGGATTCAGTGGG 61.349 65.000 0.00 0.00 0.00 4.61
134 135 1.529309 GAGAGGGGATTCAGTGGGC 59.471 63.158 0.00 0.00 0.00 5.36
135 136 1.988982 GAGAGGGGATTCAGTGGGCC 61.989 65.000 0.00 0.00 0.00 5.80
136 137 2.003548 GAGGGGATTCAGTGGGCCT 61.004 63.158 4.53 0.00 0.00 5.19
137 138 2.276309 GAGGGGATTCAGTGGGCCTG 62.276 65.000 4.53 0.00 42.97 4.85
138 139 2.276740 GGGATTCAGTGGGCCTGG 59.723 66.667 4.53 0.00 41.83 4.45
139 140 2.276740 GGATTCAGTGGGCCTGGG 59.723 66.667 4.53 0.00 41.83 4.45
140 141 2.276740 GATTCAGTGGGCCTGGGG 59.723 66.667 4.53 0.00 41.83 4.96
141 142 2.535317 ATTCAGTGGGCCTGGGGT 60.535 61.111 4.53 0.00 41.83 4.95
142 143 2.843912 GATTCAGTGGGCCTGGGGTG 62.844 65.000 4.53 0.00 41.83 4.61
143 144 4.918360 TCAGTGGGCCTGGGGTGT 62.918 66.667 4.53 0.00 41.83 4.16
144 145 4.351054 CAGTGGGCCTGGGGTGTC 62.351 72.222 4.53 0.00 37.54 3.67
150 151 3.637273 GCCTGGGGTGTCGGAGTT 61.637 66.667 0.00 0.00 0.00 3.01
151 152 2.663196 CCTGGGGTGTCGGAGTTC 59.337 66.667 0.00 0.00 0.00 3.01
152 153 1.913762 CCTGGGGTGTCGGAGTTCT 60.914 63.158 0.00 0.00 0.00 3.01
153 154 0.613853 CCTGGGGTGTCGGAGTTCTA 60.614 60.000 0.00 0.00 0.00 2.10
154 155 0.531200 CTGGGGTGTCGGAGTTCTAC 59.469 60.000 0.00 0.00 0.00 2.59
155 156 1.246056 TGGGGTGTCGGAGTTCTACG 61.246 60.000 0.00 0.00 0.00 3.51
156 157 1.246737 GGGGTGTCGGAGTTCTACGT 61.247 60.000 4.34 0.00 0.00 3.57
157 158 0.109412 GGGTGTCGGAGTTCTACGTG 60.109 60.000 0.00 0.00 0.00 4.49
158 159 0.109412 GGTGTCGGAGTTCTACGTGG 60.109 60.000 0.00 0.00 0.00 4.94
159 160 0.731855 GTGTCGGAGTTCTACGTGGC 60.732 60.000 0.00 0.00 0.00 5.01
160 161 0.892358 TGTCGGAGTTCTACGTGGCT 60.892 55.000 0.00 0.00 0.00 4.75
161 162 0.456312 GTCGGAGTTCTACGTGGCTG 60.456 60.000 0.00 0.00 0.00 4.85
162 163 1.805945 CGGAGTTCTACGTGGCTGC 60.806 63.158 0.00 0.00 0.00 5.25
163 164 1.292223 GGAGTTCTACGTGGCTGCA 59.708 57.895 0.00 0.00 0.00 4.41
164 165 0.737715 GGAGTTCTACGTGGCTGCAG 60.738 60.000 10.11 10.11 0.00 4.41
165 166 1.355066 GAGTTCTACGTGGCTGCAGC 61.355 60.000 30.88 30.88 41.14 5.25
166 167 1.667830 GTTCTACGTGGCTGCAGCA 60.668 57.895 37.63 22.06 44.36 4.41
167 168 1.374631 TTCTACGTGGCTGCAGCAG 60.375 57.895 37.63 28.65 44.36 4.24
168 169 1.815817 TTCTACGTGGCTGCAGCAGA 61.816 55.000 37.63 27.69 44.36 4.26
169 170 1.374631 CTACGTGGCTGCAGCAGAA 60.375 57.895 37.63 21.15 44.36 3.02
170 171 1.630244 CTACGTGGCTGCAGCAGAAC 61.630 60.000 37.63 28.77 44.36 3.01
171 172 2.376228 TACGTGGCTGCAGCAGAACA 62.376 55.000 37.63 24.22 44.36 3.18
172 173 2.641559 GTGGCTGCAGCAGAACAC 59.358 61.111 37.63 30.01 44.36 3.32
173 174 2.974148 TGGCTGCAGCAGAACACG 60.974 61.111 37.63 0.00 44.36 4.49
174 175 2.974698 GGCTGCAGCAGAACACGT 60.975 61.111 37.63 0.00 44.36 4.49
175 176 1.667830 GGCTGCAGCAGAACACGTA 60.668 57.895 37.63 0.00 44.36 3.57
176 177 1.021390 GGCTGCAGCAGAACACGTAT 61.021 55.000 37.63 0.00 44.36 3.06
177 178 0.095935 GCTGCAGCAGAACACGTATG 59.904 55.000 33.36 0.00 41.59 2.39
178 179 0.723414 CTGCAGCAGAACACGTATGG 59.277 55.000 18.42 0.00 32.44 2.74
179 180 0.320050 TGCAGCAGAACACGTATGGA 59.680 50.000 0.00 0.00 0.00 3.41
180 181 0.721718 GCAGCAGAACACGTATGGAC 59.278 55.000 0.00 0.00 0.00 4.02
181 182 1.359848 CAGCAGAACACGTATGGACC 58.640 55.000 0.00 0.00 0.00 4.46
184 185 0.389296 CAGAACACGTATGGACCGCA 60.389 55.000 0.00 0.00 0.00 5.69
195 196 1.228154 GGACCGCAGTTTGAGGGTT 60.228 57.895 3.93 0.00 41.96 4.11
222 223 1.423161 GGAGATGCCCTTAGCTTCCAT 59.577 52.381 0.00 0.00 44.73 3.41
227 228 4.600983 AGATGCCCTTAGCTTCCATATTCT 59.399 41.667 0.00 0.00 44.73 2.40
256 257 8.369462 CGATAGTTTAAATTTGAAGAGTGTGC 57.631 34.615 0.00 0.00 0.00 4.57
277 279 8.003784 GTGTGCATTAAATTTGTTAAGCTGAAC 58.996 33.333 7.04 7.04 0.00 3.18
322 324 6.696583 TGATATGCATTTGGTTTTGCTATTCG 59.303 34.615 3.54 0.00 39.60 3.34
324 326 3.256879 TGCATTTGGTTTTGCTATTCGGA 59.743 39.130 0.00 0.00 39.60 4.55
343 345 5.183228 TCGGAAGAACTGAGTTTTTCTTGT 58.817 37.500 22.61 0.00 41.21 3.16
358 360 9.946165 AGTTTTTCTTGTTAGTTATGCACTTAC 57.054 29.630 0.00 0.00 36.88 2.34
370 372 6.757010 AGTTATGCACTTACGAACTTATCCAG 59.243 38.462 0.00 0.00 27.32 3.86
525 528 4.585581 TGGCATATGAGTGGATTTGATTGG 59.414 41.667 6.97 0.00 0.00 3.16
544 547 1.954146 TTCTCGTCGTTGCCACTGC 60.954 57.895 0.00 0.00 38.26 4.40
701 715 2.110578 AGCACAAAGAAACAAAGGGCT 58.889 42.857 0.00 0.00 0.00 5.19
1221 1363 4.286297 TCCAACCCACACTATCTTCTTG 57.714 45.455 0.00 0.00 0.00 3.02
1359 1507 2.582226 TGCTTCGCCGCGACTATG 60.582 61.111 16.57 7.38 34.89 2.23
1488 1669 3.741476 GCTTGCAAGGAGCCGTGG 61.741 66.667 27.10 0.14 44.83 4.94
1709 1943 1.141234 GGTTCATCGTCGTCCCTCC 59.859 63.158 0.00 0.00 0.00 4.30
1747 1981 0.251354 CTGCAGGAGTGTGTATGGCT 59.749 55.000 5.57 0.00 0.00 4.75
1846 2091 6.685527 TGCTTCAGTCTGTCTATACTACTG 57.314 41.667 0.00 0.00 39.59 2.74
1938 2186 7.816995 TGTGAATTTATATTGGTGGTTCAAAGC 59.183 33.333 0.00 0.00 0.00 3.51
1939 2187 7.816995 GTGAATTTATATTGGTGGTTCAAAGCA 59.183 33.333 0.00 0.00 0.00 3.91
1947 2195 0.107410 TGGTTCAAAGCACACTCCGT 60.107 50.000 0.00 0.00 0.00 4.69
1953 2201 2.299013 TCAAAGCACACTCCGTCTATGT 59.701 45.455 0.00 0.00 0.00 2.29
2038 2292 1.194772 GCAGTCTGTCAACGGCTTAAC 59.805 52.381 0.93 0.00 37.37 2.01
2050 2304 2.556622 ACGGCTTAACCCAAACAGAATG 59.443 45.455 0.00 0.00 37.33 2.67
2086 2393 2.728839 GACTGAAGGATCATCGATTCGC 59.271 50.000 0.00 0.00 34.37 4.70
2113 2423 3.743521 TCCAGGCAGCACATGTATTATC 58.256 45.455 0.00 0.00 0.00 1.75
2115 2425 4.077108 CCAGGCAGCACATGTATTATCAT 58.923 43.478 0.00 0.00 0.00 2.45
2142 2452 8.190784 TGTTTTCAATTTCCTTTCTCTTCTCAC 58.809 33.333 0.00 0.00 0.00 3.51
2149 2459 9.853177 AATTTCCTTTCTCTTCTCACTCTTTTA 57.147 29.630 0.00 0.00 0.00 1.52
2229 6040 7.012327 CCCTTCACTGCATTTCTCGAATTATAA 59.988 37.037 0.00 0.00 0.00 0.98
2470 6289 8.437575 ACTCTTTAGAGAAAAATGTTACCTCCA 58.562 33.333 13.47 0.00 44.74 3.86
2495 6315 5.295431 TCGGAGATTTTTACAGCACAATG 57.705 39.130 0.00 0.00 0.00 2.82
2499 6319 6.446318 GGAGATTTTTACAGCACAATGTGAA 58.554 36.000 18.66 0.45 35.23 3.18
2501 6321 5.922544 AGATTTTTACAGCACAATGTGAAGC 59.077 36.000 18.66 1.28 35.23 3.86
2510 6330 4.458654 GCACAATGTGAAGCAATCAGCTG 61.459 47.826 18.66 7.63 44.05 4.24
2648 6468 3.385384 CGAGGGCTCAGTCCAGCA 61.385 66.667 0.00 0.00 41.65 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.609018 CTCCGGCCGCCATACAGG 62.609 72.222 22.85 2.99 41.84 4.00
17 18 3.506059 CTCTCCGGCCGCCATACAG 62.506 68.421 22.85 3.88 0.00 2.74
18 19 3.536917 CTCTCCGGCCGCCATACA 61.537 66.667 22.85 0.00 0.00 2.29
19 20 4.301027 CCTCTCCGGCCGCCATAC 62.301 72.222 22.85 0.00 0.00 2.39
20 21 3.440162 TACCTCTCCGGCCGCCATA 62.440 63.158 22.85 3.31 35.61 2.74
21 22 4.853142 TACCTCTCCGGCCGCCAT 62.853 66.667 22.85 3.55 35.61 4.40
24 25 3.145551 TTCTACCTCTCCGGCCGC 61.146 66.667 22.85 0.00 35.61 6.53
25 26 2.806237 GTTCTACCTCTCCGGCCG 59.194 66.667 21.04 21.04 35.61 6.13
26 27 2.783288 CCGTTCTACCTCTCCGGCC 61.783 68.421 0.00 0.00 35.61 6.13
27 28 2.806237 CCGTTCTACCTCTCCGGC 59.194 66.667 0.00 0.00 35.61 6.13
28 29 2.806237 GCCGTTCTACCTCTCCGG 59.194 66.667 0.00 0.00 41.50 5.14
29 30 2.408022 CGCCGTTCTACCTCTCCG 59.592 66.667 0.00 0.00 0.00 4.63
30 31 2.806237 CCGCCGTTCTACCTCTCC 59.194 66.667 0.00 0.00 0.00 3.71
31 32 2.104530 GCCGCCGTTCTACCTCTC 59.895 66.667 0.00 0.00 0.00 3.20
32 33 2.280552 TTGCCGCCGTTCTACCTCT 61.281 57.895 0.00 0.00 0.00 3.69
33 34 2.098831 GTTGCCGCCGTTCTACCTC 61.099 63.158 0.00 0.00 0.00 3.85
34 35 2.047560 GTTGCCGCCGTTCTACCT 60.048 61.111 0.00 0.00 0.00 3.08
35 36 2.357760 TGTTGCCGCCGTTCTACC 60.358 61.111 0.00 0.00 0.00 3.18
36 37 1.352156 CTCTGTTGCCGCCGTTCTAC 61.352 60.000 0.00 0.00 0.00 2.59
37 38 1.080093 CTCTGTTGCCGCCGTTCTA 60.080 57.895 0.00 0.00 0.00 2.10
38 39 2.357517 CTCTGTTGCCGCCGTTCT 60.358 61.111 0.00 0.00 0.00 3.01
39 40 3.423154 CCTCTGTTGCCGCCGTTC 61.423 66.667 0.00 0.00 0.00 3.95
40 41 3.883744 CTCCTCTGTTGCCGCCGTT 62.884 63.158 0.00 0.00 0.00 4.44
41 42 4.379243 CTCCTCTGTTGCCGCCGT 62.379 66.667 0.00 0.00 0.00 5.68
43 44 3.672295 CTCCTCCTCTGTTGCCGCC 62.672 68.421 0.00 0.00 0.00 6.13
44 45 2.125350 CTCCTCCTCTGTTGCCGC 60.125 66.667 0.00 0.00 0.00 6.53
45 46 1.254284 ACTCTCCTCCTCTGTTGCCG 61.254 60.000 0.00 0.00 0.00 5.69
46 47 0.248843 CACTCTCCTCCTCTGTTGCC 59.751 60.000 0.00 0.00 0.00 4.52
47 48 1.204467 CTCACTCTCCTCCTCTGTTGC 59.796 57.143 0.00 0.00 0.00 4.17
48 49 1.824230 CCTCACTCTCCTCCTCTGTTG 59.176 57.143 0.00 0.00 0.00 3.33
49 50 1.713647 TCCTCACTCTCCTCCTCTGTT 59.286 52.381 0.00 0.00 0.00 3.16
50 51 1.377690 TCCTCACTCTCCTCCTCTGT 58.622 55.000 0.00 0.00 0.00 3.41
51 52 2.309613 CATCCTCACTCTCCTCCTCTG 58.690 57.143 0.00 0.00 0.00 3.35
52 53 1.411501 GCATCCTCACTCTCCTCCTCT 60.412 57.143 0.00 0.00 0.00 3.69
53 54 1.039856 GCATCCTCACTCTCCTCCTC 58.960 60.000 0.00 0.00 0.00 3.71
54 55 0.337773 TGCATCCTCACTCTCCTCCT 59.662 55.000 0.00 0.00 0.00 3.69
55 56 1.198713 TTGCATCCTCACTCTCCTCC 58.801 55.000 0.00 0.00 0.00 4.30
56 57 2.235898 ACTTTGCATCCTCACTCTCCTC 59.764 50.000 0.00 0.00 0.00 3.71
57 58 2.264455 ACTTTGCATCCTCACTCTCCT 58.736 47.619 0.00 0.00 0.00 3.69
58 59 2.777832 ACTTTGCATCCTCACTCTCC 57.222 50.000 0.00 0.00 0.00 3.71
59 60 4.187694 CCTTACTTTGCATCCTCACTCTC 58.812 47.826 0.00 0.00 0.00 3.20
60 61 3.054802 CCCTTACTTTGCATCCTCACTCT 60.055 47.826 0.00 0.00 0.00 3.24
61 62 3.055094 TCCCTTACTTTGCATCCTCACTC 60.055 47.826 0.00 0.00 0.00 3.51
62 63 2.912956 TCCCTTACTTTGCATCCTCACT 59.087 45.455 0.00 0.00 0.00 3.41
63 64 3.350219 TCCCTTACTTTGCATCCTCAC 57.650 47.619 0.00 0.00 0.00 3.51
64 65 3.587061 TCTTCCCTTACTTTGCATCCTCA 59.413 43.478 0.00 0.00 0.00 3.86
65 66 4.222124 TCTTCCCTTACTTTGCATCCTC 57.778 45.455 0.00 0.00 0.00 3.71
66 67 4.568592 CCTTCTTCCCTTACTTTGCATCCT 60.569 45.833 0.00 0.00 0.00 3.24
67 68 3.696548 CCTTCTTCCCTTACTTTGCATCC 59.303 47.826 0.00 0.00 0.00 3.51
68 69 3.696548 CCCTTCTTCCCTTACTTTGCATC 59.303 47.826 0.00 0.00 0.00 3.91
69 70 3.076032 ACCCTTCTTCCCTTACTTTGCAT 59.924 43.478 0.00 0.00 0.00 3.96
70 71 2.445525 ACCCTTCTTCCCTTACTTTGCA 59.554 45.455 0.00 0.00 0.00 4.08
71 72 3.082548 GACCCTTCTTCCCTTACTTTGC 58.917 50.000 0.00 0.00 0.00 3.68
72 73 3.335579 CGACCCTTCTTCCCTTACTTTG 58.664 50.000 0.00 0.00 0.00 2.77
73 74 2.305052 CCGACCCTTCTTCCCTTACTTT 59.695 50.000 0.00 0.00 0.00 2.66
74 75 1.907255 CCGACCCTTCTTCCCTTACTT 59.093 52.381 0.00 0.00 0.00 2.24
75 76 1.078324 TCCGACCCTTCTTCCCTTACT 59.922 52.381 0.00 0.00 0.00 2.24
76 77 1.565067 TCCGACCCTTCTTCCCTTAC 58.435 55.000 0.00 0.00 0.00 2.34
77 78 2.563039 ATCCGACCCTTCTTCCCTTA 57.437 50.000 0.00 0.00 0.00 2.69
78 79 2.399580 CTATCCGACCCTTCTTCCCTT 58.600 52.381 0.00 0.00 0.00 3.95
79 80 1.413227 CCTATCCGACCCTTCTTCCCT 60.413 57.143 0.00 0.00 0.00 4.20
80 81 1.049402 CCTATCCGACCCTTCTTCCC 58.951 60.000 0.00 0.00 0.00 3.97
81 82 2.083628 TCCTATCCGACCCTTCTTCC 57.916 55.000 0.00 0.00 0.00 3.46
82 83 3.297736 TCTTCCTATCCGACCCTTCTTC 58.702 50.000 0.00 0.00 0.00 2.87
83 84 3.399952 TCTTCCTATCCGACCCTTCTT 57.600 47.619 0.00 0.00 0.00 2.52
84 85 3.399952 TTCTTCCTATCCGACCCTTCT 57.600 47.619 0.00 0.00 0.00 2.85
85 86 4.482952 TTTTCTTCCTATCCGACCCTTC 57.517 45.455 0.00 0.00 0.00 3.46
86 87 4.385310 CCATTTTCTTCCTATCCGACCCTT 60.385 45.833 0.00 0.00 0.00 3.95
87 88 3.136626 CCATTTTCTTCCTATCCGACCCT 59.863 47.826 0.00 0.00 0.00 4.34
88 89 3.477530 CCATTTTCTTCCTATCCGACCC 58.522 50.000 0.00 0.00 0.00 4.46
89 90 3.135895 TCCCATTTTCTTCCTATCCGACC 59.864 47.826 0.00 0.00 0.00 4.79
90 91 4.127907 GTCCCATTTTCTTCCTATCCGAC 58.872 47.826 0.00 0.00 0.00 4.79
91 92 3.135895 GGTCCCATTTTCTTCCTATCCGA 59.864 47.826 0.00 0.00 0.00 4.55
92 93 3.477530 GGTCCCATTTTCTTCCTATCCG 58.522 50.000 0.00 0.00 0.00 4.18
93 94 3.477530 CGGTCCCATTTTCTTCCTATCC 58.522 50.000 0.00 0.00 0.00 2.59
94 95 3.477530 CCGGTCCCATTTTCTTCCTATC 58.522 50.000 0.00 0.00 0.00 2.08
95 96 2.174854 CCCGGTCCCATTTTCTTCCTAT 59.825 50.000 0.00 0.00 0.00 2.57
96 97 1.562475 CCCGGTCCCATTTTCTTCCTA 59.438 52.381 0.00 0.00 0.00 2.94
97 98 0.331616 CCCGGTCCCATTTTCTTCCT 59.668 55.000 0.00 0.00 0.00 3.36
98 99 0.330267 TCCCGGTCCCATTTTCTTCC 59.670 55.000 0.00 0.00 0.00 3.46
99 100 1.280998 TCTCCCGGTCCCATTTTCTTC 59.719 52.381 0.00 0.00 0.00 2.87
100 101 1.282157 CTCTCCCGGTCCCATTTTCTT 59.718 52.381 0.00 0.00 0.00 2.52
101 102 0.912486 CTCTCCCGGTCCCATTTTCT 59.088 55.000 0.00 0.00 0.00 2.52
102 103 0.107165 CCTCTCCCGGTCCCATTTTC 60.107 60.000 0.00 0.00 0.00 2.29
103 104 1.571773 CCCTCTCCCGGTCCCATTTT 61.572 60.000 0.00 0.00 0.00 1.82
104 105 2.001269 CCCTCTCCCGGTCCCATTT 61.001 63.158 0.00 0.00 0.00 2.32
105 106 2.366972 CCCTCTCCCGGTCCCATT 60.367 66.667 0.00 0.00 0.00 3.16
106 107 4.499116 CCCCTCTCCCGGTCCCAT 62.499 72.222 0.00 0.00 0.00 4.00
108 109 3.715848 AATCCCCTCTCCCGGTCCC 62.716 68.421 0.00 0.00 0.00 4.46
109 110 2.040779 AATCCCCTCTCCCGGTCC 60.041 66.667 0.00 0.00 0.00 4.46
110 111 1.382695 TGAATCCCCTCTCCCGGTC 60.383 63.158 0.00 0.00 0.00 4.79
111 112 1.383248 CTGAATCCCCTCTCCCGGT 60.383 63.158 0.00 0.00 0.00 5.28
112 113 1.383248 ACTGAATCCCCTCTCCCGG 60.383 63.158 0.00 0.00 0.00 5.73
113 114 1.690219 CCACTGAATCCCCTCTCCCG 61.690 65.000 0.00 0.00 0.00 5.14
114 115 1.348775 CCCACTGAATCCCCTCTCCC 61.349 65.000 0.00 0.00 0.00 4.30
115 116 1.988982 GCCCACTGAATCCCCTCTCC 61.989 65.000 0.00 0.00 0.00 3.71
116 117 1.529309 GCCCACTGAATCCCCTCTC 59.471 63.158 0.00 0.00 0.00 3.20
117 118 2.003548 GGCCCACTGAATCCCCTCT 61.004 63.158 0.00 0.00 0.00 3.69
118 119 2.003548 AGGCCCACTGAATCCCCTC 61.004 63.158 0.00 0.00 0.00 4.30
119 120 2.128226 AGGCCCACTGAATCCCCT 59.872 61.111 0.00 0.00 0.00 4.79
133 134 3.607370 GAACTCCGACACCCCAGGC 62.607 68.421 0.00 0.00 0.00 4.85
134 135 0.613853 TAGAACTCCGACACCCCAGG 60.614 60.000 0.00 0.00 0.00 4.45
135 136 0.531200 GTAGAACTCCGACACCCCAG 59.469 60.000 0.00 0.00 0.00 4.45
136 137 1.246056 CGTAGAACTCCGACACCCCA 61.246 60.000 0.00 0.00 0.00 4.96
137 138 1.246737 ACGTAGAACTCCGACACCCC 61.247 60.000 0.00 0.00 0.00 4.95
138 139 0.109412 CACGTAGAACTCCGACACCC 60.109 60.000 0.00 0.00 0.00 4.61
139 140 0.109412 CCACGTAGAACTCCGACACC 60.109 60.000 0.00 0.00 0.00 4.16
140 141 0.731855 GCCACGTAGAACTCCGACAC 60.732 60.000 0.00 0.00 0.00 3.67
141 142 0.892358 AGCCACGTAGAACTCCGACA 60.892 55.000 0.00 0.00 0.00 4.35
142 143 0.456312 CAGCCACGTAGAACTCCGAC 60.456 60.000 0.00 0.00 0.00 4.79
143 144 1.880894 CAGCCACGTAGAACTCCGA 59.119 57.895 0.00 0.00 0.00 4.55
144 145 1.805945 GCAGCCACGTAGAACTCCG 60.806 63.158 0.00 0.00 0.00 4.63
145 146 0.737715 CTGCAGCCACGTAGAACTCC 60.738 60.000 0.00 0.00 0.00 3.85
146 147 1.355066 GCTGCAGCCACGTAGAACTC 61.355 60.000 28.76 0.00 34.31 3.01
147 148 1.374758 GCTGCAGCCACGTAGAACT 60.375 57.895 28.76 0.00 34.31 3.01
148 149 1.630244 CTGCTGCAGCCACGTAGAAC 61.630 60.000 34.64 4.94 41.18 3.01
149 150 1.374631 CTGCTGCAGCCACGTAGAA 60.375 57.895 34.64 13.45 41.18 2.10
150 151 1.815817 TTCTGCTGCAGCCACGTAGA 61.816 55.000 34.64 26.08 41.18 2.59
151 152 1.374631 TTCTGCTGCAGCCACGTAG 60.375 57.895 34.64 24.26 41.18 3.51
152 153 1.667830 GTTCTGCTGCAGCCACGTA 60.668 57.895 34.64 15.76 41.18 3.57
153 154 2.974698 GTTCTGCTGCAGCCACGT 60.975 61.111 34.64 0.00 41.18 4.49
154 155 2.974148 TGTTCTGCTGCAGCCACG 60.974 61.111 34.64 22.41 41.18 4.94
155 156 2.641559 GTGTTCTGCTGCAGCCAC 59.358 61.111 34.64 28.53 41.18 5.01
156 157 2.376228 TACGTGTTCTGCTGCAGCCA 62.376 55.000 34.64 22.44 41.18 4.75
157 158 1.021390 ATACGTGTTCTGCTGCAGCC 61.021 55.000 34.64 20.02 41.18 4.85
158 159 0.095935 CATACGTGTTCTGCTGCAGC 59.904 55.000 31.89 31.89 42.50 5.25
159 160 0.723414 CCATACGTGTTCTGCTGCAG 59.277 55.000 23.31 23.31 0.00 4.41
160 161 0.320050 TCCATACGTGTTCTGCTGCA 59.680 50.000 0.88 0.88 0.00 4.41
161 162 0.721718 GTCCATACGTGTTCTGCTGC 59.278 55.000 0.00 0.00 0.00 5.25
162 163 1.359848 GGTCCATACGTGTTCTGCTG 58.640 55.000 0.00 0.00 0.00 4.41
163 164 0.108804 CGGTCCATACGTGTTCTGCT 60.109 55.000 0.00 0.00 0.00 4.24
164 165 1.693083 GCGGTCCATACGTGTTCTGC 61.693 60.000 0.00 0.00 0.00 4.26
165 166 0.389296 TGCGGTCCATACGTGTTCTG 60.389 55.000 0.00 0.00 0.00 3.02
166 167 0.108804 CTGCGGTCCATACGTGTTCT 60.109 55.000 0.00 0.00 0.00 3.01
167 168 0.389426 ACTGCGGTCCATACGTGTTC 60.389 55.000 0.00 0.00 0.00 3.18
168 169 0.034337 AACTGCGGTCCATACGTGTT 59.966 50.000 0.00 0.00 0.00 3.32
169 170 0.034337 AAACTGCGGTCCATACGTGT 59.966 50.000 0.00 0.00 0.00 4.49
170 171 0.442310 CAAACTGCGGTCCATACGTG 59.558 55.000 0.00 0.00 0.00 4.49
171 172 0.319083 TCAAACTGCGGTCCATACGT 59.681 50.000 0.00 0.00 0.00 3.57
172 173 0.999406 CTCAAACTGCGGTCCATACG 59.001 55.000 0.00 0.00 0.00 3.06
173 174 1.369625 CCTCAAACTGCGGTCCATAC 58.630 55.000 0.00 0.00 0.00 2.39
174 175 0.251916 CCCTCAAACTGCGGTCCATA 59.748 55.000 0.00 0.00 0.00 2.74
175 176 1.002134 CCCTCAAACTGCGGTCCAT 60.002 57.895 0.00 0.00 0.00 3.41
176 177 1.990160 AACCCTCAAACTGCGGTCCA 61.990 55.000 0.00 0.00 0.00 4.02
177 178 1.228154 AACCCTCAAACTGCGGTCC 60.228 57.895 0.00 0.00 0.00 4.46
178 179 1.515521 CCAACCCTCAAACTGCGGTC 61.516 60.000 0.00 0.00 0.00 4.79
179 180 1.528309 CCAACCCTCAAACTGCGGT 60.528 57.895 0.00 0.00 0.00 5.68
180 181 2.919494 GCCAACCCTCAAACTGCGG 61.919 63.158 0.00 0.00 0.00 5.69
181 182 1.526575 ATGCCAACCCTCAAACTGCG 61.527 55.000 0.00 0.00 0.00 5.18
184 185 1.133199 TCCAATGCCAACCCTCAAACT 60.133 47.619 0.00 0.00 0.00 2.66
322 324 7.986562 ACTAACAAGAAAAACTCAGTTCTTCC 58.013 34.615 0.00 0.00 41.12 3.46
343 345 8.252417 TGGATAAGTTCGTAAGTGCATAACTAA 58.748 33.333 0.00 0.00 38.56 2.24
370 372 0.941542 TGTTACTCTGCACCAAACGC 59.058 50.000 0.00 0.00 0.00 4.84
514 517 3.000727 ACGACGAGAACCAATCAAATCC 58.999 45.455 0.00 0.00 0.00 3.01
525 528 1.853319 CAGTGGCAACGACGAGAAC 59.147 57.895 0.00 0.00 42.51 3.01
544 547 1.762419 GATGCTGCAAGTTGTGTGTG 58.238 50.000 6.36 0.00 35.30 3.82
545 548 0.308684 CGATGCTGCAAGTTGTGTGT 59.691 50.000 6.36 0.00 35.30 3.72
665 678 1.017177 TGCTTCATCCGTACGTTGGC 61.017 55.000 15.21 11.11 0.00 4.52
701 715 4.979204 CGGTTCCTAGAACGCACA 57.021 55.556 0.00 0.00 0.00 4.57
1493 1674 3.760035 TCCCCTTCTCGCAGTCGC 61.760 66.667 0.00 0.00 35.26 5.19
1709 1943 3.870419 GCAGAATCTTACTCCTCTTGCAG 59.130 47.826 0.00 0.00 0.00 4.41
1747 1981 3.536956 AAAGAGAACTCCAACGACACA 57.463 42.857 0.00 0.00 0.00 3.72
1947 2195 5.185635 CCTTTTGATTGCCCTTTCACATAGA 59.814 40.000 0.00 0.00 0.00 1.98
1953 2201 3.966665 AGTTCCTTTTGATTGCCCTTTCA 59.033 39.130 0.00 0.00 0.00 2.69
1986 2240 5.244626 ACACTGCCTTATTTCAGCTCATTTT 59.755 36.000 0.00 0.00 33.80 1.82
1987 2241 4.768968 ACACTGCCTTATTTCAGCTCATTT 59.231 37.500 0.00 0.00 33.80 2.32
1988 2242 4.157289 CACACTGCCTTATTTCAGCTCATT 59.843 41.667 0.00 0.00 33.80 2.57
2013 2267 1.559814 CGTTGACAGACTGCACACG 59.440 57.895 1.25 4.51 0.00 4.49
2038 2292 3.891366 AGTTTGAGTCCATTCTGTTTGGG 59.109 43.478 0.00 0.00 34.85 4.12
2050 2304 3.685139 TCAGTCATCCAGTTTGAGTCC 57.315 47.619 0.00 0.00 0.00 3.85
2086 2393 3.357079 GTGCTGCCTGGAACACGG 61.357 66.667 0.00 0.00 0.00 4.94
2113 2423 9.538508 AGAAGAGAAAGGAAATTGAAAACAATG 57.461 29.630 0.00 0.00 0.00 2.82
2115 2425 8.748412 TGAGAAGAGAAAGGAAATTGAAAACAA 58.252 29.630 0.00 0.00 0.00 2.83
2163 5974 0.373716 GGCCTGCAAGTCGTAATTCG 59.626 55.000 0.00 0.00 41.41 3.34
2367 6185 4.536765 AGTTGGTGGTGTTCTTCTCATTT 58.463 39.130 0.00 0.00 0.00 2.32
2470 6289 5.957842 TGTGCTGTAAAAATCTCCGATTT 57.042 34.783 0.00 0.00 0.00 2.17
2480 6299 5.003692 TGCTTCACATTGTGCTGTAAAAA 57.996 34.783 12.04 0.00 32.98 1.94
2510 6330 4.264460 ACAAGAACTCAGGTCATCAGAC 57.736 45.455 0.00 0.00 44.21 3.51
2648 6468 4.660938 GGCGCTGGTCTTGGGGTT 62.661 66.667 7.64 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.