Multiple sequence alignment - TraesCS2D01G272900

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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 TraesCS2D01G272900 chr2D 100.000 2794 0 0 1 2794 338664272 338667065 0.000000e+00 5160
1 TraesCS2D01G272900 chr2A 96.036 2018 61 9 781 2791 448498146 448500151 0.000000e+00 3265
2 TraesCS2D01G272900 chr2A 92.353 340 18 6 463 796 448497793 448498130 7.000000e-131 477
3 TraesCS2D01G272900 chr2A 95.918 98 4 0 365 462 448495047 448495144 2.880000e-35 159
4 TraesCS2D01G272900 chr2B 93.221 1844 96 17 365 2192 405269450 405271280 0.000000e+00 2686
5 TraesCS2D01G272900 chr2B 91.509 212 11 2 2572 2778 405271449 405271658 4.550000e-73 285
6 TraesCS2D01G272900 chr3A 92.298 792 48 10 1414 2192 176148234 176149025 0.000000e+00 1112
7 TraesCS2D01G272900 chr3A 96.186 472 18 0 950 1421 176147534 176148005 0.000000e+00 773
8 TraesCS2D01G272900 chr3A 87.739 261 12 4 410 651 176146345 176146604 1.270000e-73 287
9 TraesCS2D01G272900 chr3A 90.541 148 8 2 2652 2794 176149327 176149473 1.020000e-44 191
10 TraesCS2D01G272900 chr3A 97.468 79 2 0 873 951 176147406 176147484 4.850000e-28 135
11 TraesCS2D01G272900 chr3D 91.847 785 43 9 1414 2192 153506998 153506229 0.000000e+00 1075
12 TraesCS2D01G272900 chr3D 95.763 472 20 0 950 1421 153507699 153507228 0.000000e+00 761
13 TraesCS2D01G272900 chr3D 86.580 231 11 5 409 620 153508602 153508373 1.290000e-58 237
14 TraesCS2D01G272900 chr3D 92.667 150 11 0 728 877 153508165 153508016 1.690000e-52 217
15 TraesCS2D01G272900 chr3D 91.892 148 5 2 2652 2794 153506018 153505873 1.700000e-47 200
16 TraesCS2D01G272900 chr3D 97.468 79 2 0 873 951 153507860 153507782 4.850000e-28 135
17 TraesCS2D01G272900 chr3B 94.205 604 31 4 1414 2013 225173172 225172569 0.000000e+00 918
18 TraesCS2D01G272900 chr3B 94.703 472 22 1 950 1421 225173870 225173402 0.000000e+00 730
19 TraesCS2D01G272900 chr3B 84.685 222 7 6 409 604 225174950 225174730 2.200000e-46 196
20 TraesCS2D01G272900 chr3B 88.961 154 6 3 2652 2794 225172385 225172232 2.210000e-41 180
21 TraesCS2D01G272900 chr3B 96.203 79 3 0 873 951 225174042 225173964 2.260000e-26 130
22 TraesCS2D01G272900 chrUn 96.154 364 14 0 950 1313 480868200 480867837 1.850000e-166 595
23 TraesCS2D01G272900 chrUn 83.648 159 18 7 2258 2410 480163470 480163314 2.900000e-30 143
24 TraesCS2D01G272900 chr4B 80.095 211 31 10 133 340 37872868 37872666 2.240000e-31 147
25 TraesCS2D01G272900 chr1A 84.516 155 14 9 2258 2404 459273383 459273231 8.070000e-31 145
26 TraesCS2D01G272900 chr1A 83.648 159 18 7 2258 2410 486340773 486340617 2.900000e-30 143
27 TraesCS2D01G272900 chr1A 78.571 210 35 9 133 338 34175142 34174939 2.260000e-26 130
28 TraesCS2D01G272900 chr1D 83.648 159 18 7 2258 2410 386432108 386431952 2.900000e-30 143
29 TraesCS2D01G272900 chr1B 83.019 159 19 7 2258 2410 518808039 518807883 1.350000e-28 137
30 TraesCS2D01G272900 chr1B 81.529 157 23 3 2258 2408 130540320 130540164 1.050000e-24 124
31 TraesCS2D01G272900 chr6D 87.069 116 12 3 2295 2408 418157615 418157501 8.120000e-26 128
32 TraesCS2D01G272900 chr5A 81.290 155 21 6 2257 2404 660831251 660831098 4.890000e-23 119


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 TraesCS2D01G272900 chr2D 338664272 338667065 2793 False 5160.000000 5160 100.000000 1 2794 1 chr2D.!!$F1 2793
1 TraesCS2D01G272900 chr2A 448495047 448500151 5104 False 1300.333333 3265 94.769000 365 2791 3 chr2A.!!$F1 2426
2 TraesCS2D01G272900 chr2B 405269450 405271658 2208 False 1485.500000 2686 92.365000 365 2778 2 chr2B.!!$F1 2413
3 TraesCS2D01G272900 chr3A 176146345 176149473 3128 False 499.600000 1112 92.846400 410 2794 5 chr3A.!!$F1 2384
4 TraesCS2D01G272900 chr3D 153505873 153508602 2729 True 437.500000 1075 92.702833 409 2794 6 chr3D.!!$R1 2385
5 TraesCS2D01G272900 chr3B 225172232 225174950 2718 True 430.800000 918 91.751400 409 2794 5 chr3B.!!$R1 2385

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
116 117 0.036952 ATCTCCACCGTGCTGACAAG 60.037 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 5883 0.524862 CGGAGAAAAGCAGCAGCATT 59.475 50.0 3.17 0.0 45.49 3.56 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
17 18 3.771160 GATCGAGGGGTGTGGCGT 61.771 66.667 0.00 0.00 0.00 5.68
18 19 4.082523 ATCGAGGGGTGTGGCGTG 62.083 66.667 0.00 0.00 0.00 5.34
24 25 4.699522 GGGTGTGGCGTGGGAGAC 62.700 72.222 0.00 0.00 0.00 3.36
32 33 4.308458 CGTGGGAGACGGTGGCAA 62.308 66.667 0.00 0.00 44.85 4.52
33 34 2.358737 GTGGGAGACGGTGGCAAG 60.359 66.667 0.00 0.00 0.00 4.01
34 35 4.329545 TGGGAGACGGTGGCAAGC 62.330 66.667 0.00 0.00 0.00 4.01
35 36 4.021925 GGGAGACGGTGGCAAGCT 62.022 66.667 0.00 0.00 0.00 3.74
36 37 2.435059 GGAGACGGTGGCAAGCTC 60.435 66.667 0.00 0.00 0.00 4.09
37 38 2.811317 GAGACGGTGGCAAGCTCG 60.811 66.667 0.00 0.00 0.00 5.03
58 59 2.015736 CGGAGGAGAAACATGTGAGG 57.984 55.000 0.00 0.00 0.00 3.86
59 60 1.550524 CGGAGGAGAAACATGTGAGGA 59.449 52.381 0.00 0.00 0.00 3.71
60 61 2.028112 CGGAGGAGAAACATGTGAGGAA 60.028 50.000 0.00 0.00 0.00 3.36
61 62 3.339141 GGAGGAGAAACATGTGAGGAAC 58.661 50.000 0.00 0.00 0.00 3.62
62 63 2.996621 GAGGAGAAACATGTGAGGAACG 59.003 50.000 0.00 0.00 0.00 3.95
63 64 2.076863 GGAGAAACATGTGAGGAACGG 58.923 52.381 0.00 0.00 0.00 4.44
64 65 2.076863 GAGAAACATGTGAGGAACGGG 58.923 52.381 0.00 0.00 0.00 5.28
65 66 1.697432 AGAAACATGTGAGGAACGGGA 59.303 47.619 0.00 0.00 0.00 5.14
66 67 2.105821 AGAAACATGTGAGGAACGGGAA 59.894 45.455 0.00 0.00 0.00 3.97
67 68 2.185004 AACATGTGAGGAACGGGAAG 57.815 50.000 0.00 0.00 0.00 3.46
68 69 0.324943 ACATGTGAGGAACGGGAAGG 59.675 55.000 0.00 0.00 0.00 3.46
69 70 0.392998 CATGTGAGGAACGGGAAGGG 60.393 60.000 0.00 0.00 0.00 3.95
70 71 1.562672 ATGTGAGGAACGGGAAGGGG 61.563 60.000 0.00 0.00 0.00 4.79
71 72 2.609610 TGAGGAACGGGAAGGGGG 60.610 66.667 0.00 0.00 0.00 5.40
72 73 2.609921 GAGGAACGGGAAGGGGGT 60.610 66.667 0.00 0.00 0.00 4.95
73 74 2.609921 AGGAACGGGAAGGGGGTC 60.610 66.667 0.00 0.00 0.00 4.46
74 75 2.609921 GGAACGGGAAGGGGGTCT 60.610 66.667 0.00 0.00 0.00 3.85
75 76 2.667108 GGAACGGGAAGGGGGTCTC 61.667 68.421 0.00 0.00 0.00 3.36
76 77 2.609921 AACGGGAAGGGGGTCTCC 60.610 66.667 0.00 0.00 0.00 3.71
87 88 2.665603 GGTCTCCCCTGTGCTGAC 59.334 66.667 0.00 0.00 0.00 3.51
88 89 2.262915 GTCTCCCCTGTGCTGACG 59.737 66.667 0.00 0.00 0.00 4.35
89 90 2.997315 TCTCCCCTGTGCTGACGG 60.997 66.667 0.00 0.00 0.00 4.79
95 96 2.046892 CTGTGCTGACGGGAAGGG 60.047 66.667 0.00 0.00 0.00 3.95
96 97 3.612247 CTGTGCTGACGGGAAGGGG 62.612 68.421 0.00 0.00 0.00 4.79
97 98 3.319198 GTGCTGACGGGAAGGGGA 61.319 66.667 0.00 0.00 0.00 4.81
98 99 2.285368 TGCTGACGGGAAGGGGAT 60.285 61.111 0.00 0.00 0.00 3.85
99 100 2.367202 TGCTGACGGGAAGGGGATC 61.367 63.158 0.00 0.00 0.00 3.36
100 101 2.066999 GCTGACGGGAAGGGGATCT 61.067 63.158 0.00 0.00 0.00 2.75
101 102 2.034048 GCTGACGGGAAGGGGATCTC 62.034 65.000 0.00 0.00 0.00 2.75
102 103 1.382695 TGACGGGAAGGGGATCTCC 60.383 63.158 2.22 2.22 0.00 3.71
103 104 1.382695 GACGGGAAGGGGATCTCCA 60.383 63.158 15.83 0.00 37.91 3.86
104 105 1.687297 GACGGGAAGGGGATCTCCAC 61.687 65.000 15.83 7.37 40.63 4.02
105 106 2.444256 CGGGAAGGGGATCTCCACC 61.444 68.421 15.83 16.31 41.50 4.61
106 107 2.444256 GGGAAGGGGATCTCCACCG 61.444 68.421 15.83 0.00 41.50 4.94
107 108 1.689582 GGAAGGGGATCTCCACCGT 60.690 63.158 15.83 0.00 41.50 4.83
108 109 1.522569 GAAGGGGATCTCCACCGTG 59.477 63.158 15.83 0.00 41.50 4.94
109 110 2.595009 GAAGGGGATCTCCACCGTGC 62.595 65.000 15.83 0.00 41.50 5.34
110 111 3.083997 GGGGATCTCCACCGTGCT 61.084 66.667 6.79 0.00 37.91 4.40
111 112 2.187946 GGGATCTCCACCGTGCTG 59.812 66.667 0.00 0.00 37.91 4.41
112 113 2.359169 GGGATCTCCACCGTGCTGA 61.359 63.158 0.00 0.00 37.91 4.26
113 114 1.153549 GGATCTCCACCGTGCTGAC 60.154 63.158 0.00 0.00 35.64 3.51
114 115 1.591703 GATCTCCACCGTGCTGACA 59.408 57.895 0.00 0.00 0.00 3.58
115 116 0.037326 GATCTCCACCGTGCTGACAA 60.037 55.000 0.00 0.00 0.00 3.18
116 117 0.036952 ATCTCCACCGTGCTGACAAG 60.037 55.000 0.00 0.00 0.00 3.16
117 118 1.112916 TCTCCACCGTGCTGACAAGA 61.113 55.000 0.00 0.00 0.00 3.02
118 119 0.249868 CTCCACCGTGCTGACAAGAA 60.250 55.000 0.00 0.00 0.00 2.52
119 120 0.249868 TCCACCGTGCTGACAAGAAG 60.250 55.000 0.00 0.00 0.00 2.85
120 121 1.230635 CCACCGTGCTGACAAGAAGG 61.231 60.000 0.00 0.00 0.00 3.46
121 122 1.071471 ACCGTGCTGACAAGAAGGG 59.929 57.895 0.00 0.00 42.11 3.95
122 123 1.672356 CCGTGCTGACAAGAAGGGG 60.672 63.158 0.00 0.00 33.80 4.79
123 124 1.672356 CGTGCTGACAAGAAGGGGG 60.672 63.158 0.00 0.00 0.00 5.40
140 141 3.131478 GGGGGCGTTTCCATGACG 61.131 66.667 0.00 0.00 43.04 4.35
141 142 3.131478 GGGGCGTTTCCATGACGG 61.131 66.667 7.44 0.00 40.66 4.79
144 145 4.160635 GCGTTTCCATGACGGCCG 62.161 66.667 26.86 26.86 40.66 6.13
145 146 2.433491 CGTTTCCATGACGGCCGA 60.433 61.111 35.90 11.57 36.90 5.54
146 147 2.736682 CGTTTCCATGACGGCCGAC 61.737 63.158 35.90 27.96 36.90 4.79
156 157 4.570663 CGGCCGACGGACCAGATC 62.571 72.222 24.07 0.00 39.42 2.75
157 158 4.222847 GGCCGACGGACCAGATCC 62.223 72.222 20.50 2.99 45.20 3.36
165 166 2.914289 GACCAGATCCAGCAGGGG 59.086 66.667 0.00 0.00 37.22 4.79
166 167 1.690633 GACCAGATCCAGCAGGGGA 60.691 63.158 0.00 0.00 42.21 4.81
167 168 1.692042 ACCAGATCCAGCAGGGGAG 60.692 63.158 0.00 0.00 41.08 4.30
168 169 2.450320 CCAGATCCAGCAGGGGAGG 61.450 68.421 0.00 0.00 41.08 4.30
169 170 2.771762 AGATCCAGCAGGGGAGGC 60.772 66.667 0.00 0.00 41.08 4.70
170 171 2.771762 GATCCAGCAGGGGAGGCT 60.772 66.667 0.00 0.00 41.08 4.58
171 172 2.771762 ATCCAGCAGGGGAGGCTC 60.772 66.667 5.78 5.78 41.08 4.70
184 185 4.087892 GGCTCGCTGGCTTGGAGA 62.088 66.667 3.95 0.00 38.32 3.71
185 186 2.046892 GCTCGCTGGCTTGGAGAA 60.047 61.111 3.95 0.00 0.00 2.87
186 187 1.672356 GCTCGCTGGCTTGGAGAAA 60.672 57.895 3.95 0.00 0.00 2.52
187 188 1.916697 GCTCGCTGGCTTGGAGAAAC 61.917 60.000 3.95 0.00 0.00 2.78
188 189 0.603707 CTCGCTGGCTTGGAGAAACA 60.604 55.000 0.00 0.00 0.00 2.83
189 190 0.603707 TCGCTGGCTTGGAGAAACAG 60.604 55.000 0.00 0.00 0.00 3.16
190 191 1.583477 GCTGGCTTGGAGAAACAGC 59.417 57.895 0.00 0.00 46.24 4.40
191 192 1.871772 CTGGCTTGGAGAAACAGCG 59.128 57.895 0.00 0.00 0.00 5.18
192 193 2.192608 CTGGCTTGGAGAAACAGCGC 62.193 60.000 0.00 0.00 0.00 5.92
193 194 2.174349 GCTTGGAGAAACAGCGCG 59.826 61.111 0.00 0.00 0.00 6.86
194 195 2.317609 GCTTGGAGAAACAGCGCGA 61.318 57.895 12.10 0.00 0.00 5.87
195 196 1.841663 GCTTGGAGAAACAGCGCGAA 61.842 55.000 12.10 0.00 0.00 4.70
196 197 0.798776 CTTGGAGAAACAGCGCGAAT 59.201 50.000 12.10 0.00 0.00 3.34
197 198 0.796312 TTGGAGAAACAGCGCGAATC 59.204 50.000 12.10 0.00 0.00 2.52
198 199 0.037326 TGGAGAAACAGCGCGAATCT 60.037 50.000 12.10 4.62 0.00 2.40
199 200 0.371645 GGAGAAACAGCGCGAATCTG 59.628 55.000 12.10 10.90 37.56 2.90
200 201 0.371645 GAGAAACAGCGCGAATCTGG 59.628 55.000 12.10 0.00 35.94 3.86
201 202 0.320771 AGAAACAGCGCGAATCTGGT 60.321 50.000 12.10 2.88 35.94 4.00
202 203 0.095417 GAAACAGCGCGAATCTGGTC 59.905 55.000 12.10 6.37 35.94 4.02
203 204 0.602638 AAACAGCGCGAATCTGGTCA 60.603 50.000 12.10 0.00 35.94 4.02
204 205 0.602638 AACAGCGCGAATCTGGTCAA 60.603 50.000 12.10 0.00 35.94 3.18
205 206 0.602638 ACAGCGCGAATCTGGTCAAA 60.603 50.000 12.10 0.00 35.94 2.69
206 207 0.095935 CAGCGCGAATCTGGTCAAAG 59.904 55.000 12.10 0.00 0.00 2.77
207 208 0.037326 AGCGCGAATCTGGTCAAAGA 60.037 50.000 12.10 0.00 0.00 2.52
208 209 0.095417 GCGCGAATCTGGTCAAAGAC 59.905 55.000 12.10 0.00 0.00 3.01
209 210 0.366871 CGCGAATCTGGTCAAAGACG 59.633 55.000 0.00 0.00 32.65 4.18
210 211 0.095417 GCGAATCTGGTCAAAGACGC 59.905 55.000 0.00 0.00 35.44 5.19
211 212 1.714794 CGAATCTGGTCAAAGACGCT 58.285 50.000 0.00 0.00 32.65 5.07
212 213 1.656095 CGAATCTGGTCAAAGACGCTC 59.344 52.381 0.00 0.00 32.65 5.03
213 214 1.656095 GAATCTGGTCAAAGACGCTCG 59.344 52.381 0.00 0.00 32.65 5.03
214 215 0.108615 ATCTGGTCAAAGACGCTCGG 60.109 55.000 0.00 0.00 32.65 4.63
215 216 2.357034 TGGTCAAAGACGCTCGGC 60.357 61.111 0.00 0.00 32.65 5.54
248 249 4.783621 GGCTGCAGTCCGCCATGA 62.784 66.667 16.64 0.00 45.59 3.07
249 250 2.747460 GCTGCAGTCCGCCATGAA 60.747 61.111 16.64 0.00 41.33 2.57
250 251 2.117156 GCTGCAGTCCGCCATGAAT 61.117 57.895 16.64 0.00 41.33 2.57
251 252 1.725665 CTGCAGTCCGCCATGAATG 59.274 57.895 5.25 0.00 41.33 2.67
252 253 0.745486 CTGCAGTCCGCCATGAATGA 60.745 55.000 5.25 0.00 41.33 2.57
253 254 0.745486 TGCAGTCCGCCATGAATGAG 60.745 55.000 0.00 0.00 41.33 2.90
254 255 1.442526 GCAGTCCGCCATGAATGAGG 61.443 60.000 0.00 0.00 32.28 3.86
255 256 0.816825 CAGTCCGCCATGAATGAGGG 60.817 60.000 0.00 0.00 32.28 4.30
256 257 0.982852 AGTCCGCCATGAATGAGGGA 60.983 55.000 0.00 0.00 0.00 4.20
257 258 0.109342 GTCCGCCATGAATGAGGGAT 59.891 55.000 0.00 0.00 33.61 3.85
258 259 0.109153 TCCGCCATGAATGAGGGATG 59.891 55.000 0.00 0.00 0.00 3.51
259 260 1.521450 CCGCCATGAATGAGGGATGC 61.521 60.000 0.00 0.00 0.00 3.91
260 261 1.848932 CGCCATGAATGAGGGATGCG 61.849 60.000 0.00 0.00 0.00 4.73
261 262 1.521450 GCCATGAATGAGGGATGCGG 61.521 60.000 0.00 0.00 0.00 5.69
262 263 0.179009 CCATGAATGAGGGATGCGGT 60.179 55.000 0.00 0.00 0.00 5.68
263 264 0.949397 CATGAATGAGGGATGCGGTG 59.051 55.000 0.00 0.00 0.00 4.94
264 265 0.548031 ATGAATGAGGGATGCGGTGT 59.452 50.000 0.00 0.00 0.00 4.16
265 266 0.327924 TGAATGAGGGATGCGGTGTT 59.672 50.000 0.00 0.00 0.00 3.32
266 267 1.271871 TGAATGAGGGATGCGGTGTTT 60.272 47.619 0.00 0.00 0.00 2.83
267 268 1.818674 GAATGAGGGATGCGGTGTTTT 59.181 47.619 0.00 0.00 0.00 2.43
268 269 1.923356 ATGAGGGATGCGGTGTTTTT 58.077 45.000 0.00 0.00 0.00 1.94
295 296 8.854614 TTCAGAATAAAGAAGAAAGGAAGAGG 57.145 34.615 0.00 0.00 0.00 3.69
296 297 7.398024 TCAGAATAAAGAAGAAAGGAAGAGGG 58.602 38.462 0.00 0.00 0.00 4.30
297 298 7.237679 TCAGAATAAAGAAGAAAGGAAGAGGGA 59.762 37.037 0.00 0.00 0.00 4.20
298 299 8.052141 CAGAATAAAGAAGAAAGGAAGAGGGAT 58.948 37.037 0.00 0.00 0.00 3.85
299 300 9.285359 AGAATAAAGAAGAAAGGAAGAGGGATA 57.715 33.333 0.00 0.00 0.00 2.59
300 301 9.332502 GAATAAAGAAGAAAGGAAGAGGGATAC 57.667 37.037 0.00 0.00 0.00 2.24
301 302 6.704056 AAAGAAGAAAGGAAGAGGGATACA 57.296 37.500 0.00 0.00 39.74 2.29
302 303 5.685520 AGAAGAAAGGAAGAGGGATACAC 57.314 43.478 0.00 0.00 39.74 2.90
303 304 4.160626 AGAAGAAAGGAAGAGGGATACACG 59.839 45.833 0.00 0.00 39.74 4.49
304 305 2.168728 AGAAAGGAAGAGGGATACACGC 59.831 50.000 0.00 0.00 39.74 5.34
305 306 0.460311 AAGGAAGAGGGATACACGCG 59.540 55.000 3.53 3.53 39.74 6.01
306 307 1.591863 GGAAGAGGGATACACGCGC 60.592 63.158 5.73 0.00 39.74 6.86
307 308 1.944676 GAAGAGGGATACACGCGCG 60.945 63.158 30.96 30.96 36.49 6.86
308 309 2.609183 GAAGAGGGATACACGCGCGT 62.609 60.000 32.73 32.73 36.49 6.01
317 318 3.853330 CACGCGCGTGGATGAAGG 61.853 66.667 45.91 24.62 42.00 3.46
318 319 4.373116 ACGCGCGTGGATGAAGGT 62.373 61.111 37.37 5.31 0.00 3.50
319 320 3.853330 CGCGCGTGGATGAAGGTG 61.853 66.667 24.19 0.00 0.00 4.00
320 321 2.434185 GCGCGTGGATGAAGGTGA 60.434 61.111 8.43 0.00 0.00 4.02
321 322 2.740714 GCGCGTGGATGAAGGTGAC 61.741 63.158 8.43 0.00 0.00 3.67
322 323 2.100631 CGCGTGGATGAAGGTGACC 61.101 63.158 0.00 0.00 0.00 4.02
323 324 2.100631 GCGTGGATGAAGGTGACCG 61.101 63.158 0.00 0.00 0.00 4.79
324 325 1.447838 CGTGGATGAAGGTGACCGG 60.448 63.158 0.00 0.00 0.00 5.28
325 326 1.745489 GTGGATGAAGGTGACCGGC 60.745 63.158 0.00 0.00 0.00 6.13
326 327 2.124695 GGATGAAGGTGACCGGCC 60.125 66.667 0.00 0.00 0.00 6.13
327 328 2.511600 GATGAAGGTGACCGGCCG 60.512 66.667 21.04 21.04 0.00 6.13
328 329 3.000819 ATGAAGGTGACCGGCCGA 61.001 61.111 30.73 2.89 0.00 5.54
329 330 2.515996 GATGAAGGTGACCGGCCGAA 62.516 60.000 30.73 9.20 0.00 4.30
330 331 2.031465 GAAGGTGACCGGCCGAAA 59.969 61.111 30.73 8.76 0.00 3.46
331 332 2.281276 AAGGTGACCGGCCGAAAC 60.281 61.111 30.73 20.76 0.00 2.78
332 333 2.726822 GAAGGTGACCGGCCGAAACT 62.727 60.000 30.73 17.29 0.00 2.66
333 334 2.281276 GGTGACCGGCCGAAACTT 60.281 61.111 30.73 4.57 0.00 2.66
334 335 2.322830 GGTGACCGGCCGAAACTTC 61.323 63.158 30.73 14.70 0.00 3.01
344 345 4.084888 GAAACTTCGGCCGGCGTG 62.085 66.667 27.83 16.16 0.00 5.34
345 346 4.922026 AAACTTCGGCCGGCGTGT 62.922 61.111 27.83 14.94 0.00 4.49
354 355 4.973055 CCGGCGTGTCGTTCCCAA 62.973 66.667 6.01 0.00 0.00 4.12
355 356 2.968156 CGGCGTGTCGTTCCCAAA 60.968 61.111 0.00 0.00 0.00 3.28
356 357 2.635338 GGCGTGTCGTTCCCAAAC 59.365 61.111 0.00 0.00 0.00 2.93
503 3154 1.837439 ACCAAGGCTACGATCCATTCA 59.163 47.619 0.00 0.00 0.00 2.57
577 3238 4.821589 CCCGTCGCCTCAGCCTTC 62.822 72.222 0.00 0.00 34.57 3.46
755 3848 5.765677 TGTCCAAAATACCATTTCTGTTCGA 59.234 36.000 0.00 0.00 0.00 3.71
773 3866 3.053077 TCGATTAATCCCCCTCACCAAT 58.947 45.455 9.87 0.00 0.00 3.16
807 3931 3.097614 GCAGAACCTAGGTTAGTGGAGA 58.902 50.000 27.16 0.00 38.60 3.71
810 3934 3.077088 AGAACCTAGGTTAGTGGAGACCA 59.923 47.826 27.16 0.00 38.60 4.02
895 4181 4.730949 ATCACCATGGAATGCAGAAAAG 57.269 40.909 21.47 0.00 44.97 2.27
1087 4468 4.772624 ACACTAGCTCAACAGGTAATGAGA 59.227 41.667 6.95 0.00 44.64 3.27
1321 4705 3.769189 TGGTGGAGAGGTACCATCTTA 57.231 47.619 15.94 5.20 41.80 2.10
1489 5350 5.431420 AGTCGCTGTACTCATCTCATTAG 57.569 43.478 0.00 0.00 0.00 1.73
1531 5393 5.883685 ATGATCTCATACTGCTCTCCAAA 57.116 39.130 0.00 0.00 34.26 3.28
1542 5404 4.141711 ACTGCTCTCCAAAGTTTACACTCA 60.142 41.667 0.00 0.00 30.45 3.41
1548 5410 7.803659 GCTCTCCAAAGTTTACACTCATTTTAC 59.196 37.037 0.00 0.00 30.45 2.01
1589 5451 3.547868 CAGGAAACATCATCGTACGACAG 59.452 47.826 22.14 16.27 0.00 3.51
1698 5560 0.107654 ACGGAATAAGCTGACTGGCC 60.108 55.000 0.00 0.00 0.00 5.36
1860 5723 1.260544 GGGATGGCTCTGCTGTTTTT 58.739 50.000 0.00 0.00 0.00 1.94
2040 5914 1.664302 GCTGCTGCTTTTCTCCGAAAC 60.664 52.381 8.53 0.00 36.03 2.78
2138 6014 2.223340 CGGCAAACCATATGAACAGCTC 60.223 50.000 3.65 0.00 34.57 4.09
2139 6015 2.223340 GGCAAACCATATGAACAGCTCG 60.223 50.000 3.65 0.00 35.26 5.03
2140 6016 2.792542 GCAAACCATATGAACAGCTCGC 60.793 50.000 3.65 0.00 0.00 5.03
2141 6017 1.668419 AACCATATGAACAGCTCGCC 58.332 50.000 3.65 0.00 0.00 5.54
2142 6018 0.541392 ACCATATGAACAGCTCGCCA 59.459 50.000 3.65 0.00 0.00 5.69
2143 6019 0.940126 CCATATGAACAGCTCGCCAC 59.060 55.000 3.65 0.00 0.00 5.01
2144 6020 1.655484 CATATGAACAGCTCGCCACA 58.345 50.000 0.00 0.00 0.00 4.17
2145 6021 2.216046 CATATGAACAGCTCGCCACAT 58.784 47.619 0.00 0.00 0.00 3.21
2341 6341 8.617809 TGTTCTAGTGGTTTGTTCACTTATTTC 58.382 33.333 1.99 0.00 42.17 2.17
2342 6342 8.617809 GTTCTAGTGGTTTGTTCACTTATTTCA 58.382 33.333 1.99 0.00 42.17 2.69
2347 6347 5.888724 TGGTTTGTTCACTTATTTCAGTCCA 59.111 36.000 0.00 0.00 0.00 4.02
2434 6434 8.647256 TCTCTAGATCATCATGATGCTTCTTA 57.353 34.615 29.88 21.90 37.20 2.10
2448 6448 7.857456 TGATGCTTCTTAATGGAGTACCTTTA 58.143 34.615 0.88 0.00 35.58 1.85
2464 6464 3.391626 ACCTTTACTCCTATTAGGCAGCC 59.608 47.826 1.84 1.84 34.61 4.85
2486 6486 6.770785 AGCCAAAACTTTCTGTGAACTACATA 59.229 34.615 0.00 0.00 38.92 2.29
2562 6562 2.884827 TCATGAGTTCTCATGTCGCTG 58.115 47.619 29.68 14.40 45.53 5.18
2570 6570 1.616374 TCTCATGTCGCTGGTGTAACA 59.384 47.619 0.00 0.00 39.98 2.41
2631 6631 5.636123 TGGTGTTTGTGGGTGTAGAAATAT 58.364 37.500 0.00 0.00 0.00 1.28
2659 6659 7.830940 TGTGTTAAGACAGTTCGTTTCTAAA 57.169 32.000 0.45 0.00 36.20 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.771160 ACGCCACACCCCTCGATC 61.771 66.667 0.00 0.00 0.00 3.69
1 2 4.082523 CACGCCACACCCCTCGAT 62.083 66.667 0.00 0.00 0.00 3.59
7 8 4.699522 GTCTCCCACGCCACACCC 62.700 72.222 0.00 0.00 0.00 4.61
16 17 2.358737 CTTGCCACCGTCTCCCAC 60.359 66.667 0.00 0.00 0.00 4.61
17 18 4.329545 GCTTGCCACCGTCTCCCA 62.330 66.667 0.00 0.00 0.00 4.37
18 19 3.959991 GAGCTTGCCACCGTCTCCC 62.960 68.421 0.00 0.00 0.00 4.30
19 20 2.435059 GAGCTTGCCACCGTCTCC 60.435 66.667 0.00 0.00 0.00 3.71
20 21 2.811317 CGAGCTTGCCACCGTCTC 60.811 66.667 0.00 0.00 0.00 3.36
30 31 2.507110 TTTCTCCTCCGGCGAGCTTG 62.507 60.000 9.30 0.00 34.49 4.01
31 32 2.283529 TTTCTCCTCCGGCGAGCTT 61.284 57.895 9.30 0.00 34.49 3.74
32 33 2.680352 TTTCTCCTCCGGCGAGCT 60.680 61.111 9.30 0.00 34.49 4.09
33 34 2.509561 GTTTCTCCTCCGGCGAGC 60.510 66.667 9.30 0.00 34.49 5.03
34 35 0.807667 CATGTTTCTCCTCCGGCGAG 60.808 60.000 9.30 11.14 35.72 5.03
35 36 1.218047 CATGTTTCTCCTCCGGCGA 59.782 57.895 9.30 0.00 0.00 5.54
36 37 1.079127 ACATGTTTCTCCTCCGGCG 60.079 57.895 0.00 0.00 0.00 6.46
37 38 0.036388 TCACATGTTTCTCCTCCGGC 60.036 55.000 0.00 0.00 0.00 6.13
38 39 1.406069 CCTCACATGTTTCTCCTCCGG 60.406 57.143 0.00 0.00 0.00 5.14
39 40 1.550524 TCCTCACATGTTTCTCCTCCG 59.449 52.381 0.00 0.00 0.00 4.63
40 41 3.339141 GTTCCTCACATGTTTCTCCTCC 58.661 50.000 0.00 0.00 0.00 4.30
41 42 2.996621 CGTTCCTCACATGTTTCTCCTC 59.003 50.000 0.00 0.00 0.00 3.71
42 43 2.289694 CCGTTCCTCACATGTTTCTCCT 60.290 50.000 0.00 0.00 0.00 3.69
43 44 2.076863 CCGTTCCTCACATGTTTCTCC 58.923 52.381 0.00 0.00 0.00 3.71
44 45 2.076863 CCCGTTCCTCACATGTTTCTC 58.923 52.381 0.00 0.00 0.00 2.87
45 46 1.697432 TCCCGTTCCTCACATGTTTCT 59.303 47.619 0.00 0.00 0.00 2.52
46 47 2.178912 TCCCGTTCCTCACATGTTTC 57.821 50.000 0.00 0.00 0.00 2.78
47 48 2.504367 CTTCCCGTTCCTCACATGTTT 58.496 47.619 0.00 0.00 0.00 2.83
48 49 1.271379 CCTTCCCGTTCCTCACATGTT 60.271 52.381 0.00 0.00 0.00 2.71
49 50 0.324943 CCTTCCCGTTCCTCACATGT 59.675 55.000 0.00 0.00 0.00 3.21
50 51 0.392998 CCCTTCCCGTTCCTCACATG 60.393 60.000 0.00 0.00 0.00 3.21
51 52 1.562672 CCCCTTCCCGTTCCTCACAT 61.563 60.000 0.00 0.00 0.00 3.21
52 53 2.221299 CCCCTTCCCGTTCCTCACA 61.221 63.158 0.00 0.00 0.00 3.58
53 54 2.669240 CCCCTTCCCGTTCCTCAC 59.331 66.667 0.00 0.00 0.00 3.51
54 55 2.609610 CCCCCTTCCCGTTCCTCA 60.610 66.667 0.00 0.00 0.00 3.86
55 56 2.609921 ACCCCCTTCCCGTTCCTC 60.610 66.667 0.00 0.00 0.00 3.71
56 57 2.609921 GACCCCCTTCCCGTTCCT 60.610 66.667 0.00 0.00 0.00 3.36
57 58 2.609921 AGACCCCCTTCCCGTTCC 60.610 66.667 0.00 0.00 0.00 3.62
58 59 2.667108 GGAGACCCCCTTCCCGTTC 61.667 68.421 0.00 0.00 0.00 3.95
59 60 2.609921 GGAGACCCCCTTCCCGTT 60.610 66.667 0.00 0.00 0.00 4.44
71 72 2.262915 CGTCAGCACAGGGGAGAC 59.737 66.667 0.00 0.00 0.00 3.36
72 73 2.997315 CCGTCAGCACAGGGGAGA 60.997 66.667 0.00 0.00 0.00 3.71
73 74 4.087892 CCCGTCAGCACAGGGGAG 62.088 72.222 6.82 0.00 43.31 4.30
74 75 4.631740 TCCCGTCAGCACAGGGGA 62.632 66.667 10.54 10.54 46.35 4.81
75 76 3.612247 CTTCCCGTCAGCACAGGGG 62.612 68.421 6.38 6.38 45.13 4.79
76 77 2.046892 CTTCCCGTCAGCACAGGG 60.047 66.667 0.73 0.73 46.40 4.45
77 78 2.046892 CCTTCCCGTCAGCACAGG 60.047 66.667 0.00 0.00 0.00 4.00
78 79 2.046892 CCCTTCCCGTCAGCACAG 60.047 66.667 0.00 0.00 0.00 3.66
79 80 3.636231 CCCCTTCCCGTCAGCACA 61.636 66.667 0.00 0.00 0.00 4.57
80 81 2.595009 GATCCCCTTCCCGTCAGCAC 62.595 65.000 0.00 0.00 0.00 4.40
81 82 2.285368 ATCCCCTTCCCGTCAGCA 60.285 61.111 0.00 0.00 0.00 4.41
82 83 2.034048 GAGATCCCCTTCCCGTCAGC 62.034 65.000 0.00 0.00 0.00 4.26
83 84 1.403687 GGAGATCCCCTTCCCGTCAG 61.404 65.000 0.00 0.00 0.00 3.51
84 85 1.382695 GGAGATCCCCTTCCCGTCA 60.383 63.158 0.00 0.00 0.00 4.35
85 86 1.382695 TGGAGATCCCCTTCCCGTC 60.383 63.158 0.00 0.00 34.29 4.79
86 87 1.689582 GTGGAGATCCCCTTCCCGT 60.690 63.158 0.00 0.00 34.29 5.28
87 88 2.444256 GGTGGAGATCCCCTTCCCG 61.444 68.421 0.00 0.00 34.29 5.14
88 89 2.444256 CGGTGGAGATCCCCTTCCC 61.444 68.421 0.00 0.00 34.29 3.97
89 90 1.689582 ACGGTGGAGATCCCCTTCC 60.690 63.158 0.00 0.00 34.29 3.46
90 91 1.522569 CACGGTGGAGATCCCCTTC 59.477 63.158 0.00 0.00 34.29 3.46
91 92 2.670148 GCACGGTGGAGATCCCCTT 61.670 63.158 10.60 0.00 34.29 3.95
92 93 3.083997 GCACGGTGGAGATCCCCT 61.084 66.667 10.60 0.00 34.29 4.79
93 94 3.083997 AGCACGGTGGAGATCCCC 61.084 66.667 10.60 0.00 34.29 4.81
94 95 2.187946 CAGCACGGTGGAGATCCC 59.812 66.667 10.60 0.00 34.29 3.85
95 96 1.153549 GTCAGCACGGTGGAGATCC 60.154 63.158 10.60 0.00 0.00 3.36
96 97 0.037326 TTGTCAGCACGGTGGAGATC 60.037 55.000 10.60 0.00 0.00 2.75
97 98 0.036952 CTTGTCAGCACGGTGGAGAT 60.037 55.000 10.60 0.00 0.00 2.75
98 99 1.112916 TCTTGTCAGCACGGTGGAGA 61.113 55.000 10.60 0.00 0.00 3.71
99 100 0.249868 TTCTTGTCAGCACGGTGGAG 60.250 55.000 10.60 0.00 0.00 3.86
100 101 0.249868 CTTCTTGTCAGCACGGTGGA 60.250 55.000 10.60 0.00 0.00 4.02
101 102 1.230635 CCTTCTTGTCAGCACGGTGG 61.231 60.000 10.60 0.00 0.00 4.61
102 103 1.230635 CCCTTCTTGTCAGCACGGTG 61.231 60.000 3.15 3.15 0.00 4.94
103 104 1.071471 CCCTTCTTGTCAGCACGGT 59.929 57.895 0.00 0.00 0.00 4.83
104 105 1.672356 CCCCTTCTTGTCAGCACGG 60.672 63.158 0.00 0.00 0.00 4.94
105 106 1.672356 CCCCCTTCTTGTCAGCACG 60.672 63.158 0.00 0.00 0.00 5.34
106 107 4.404691 CCCCCTTCTTGTCAGCAC 57.595 61.111 0.00 0.00 0.00 4.40
123 124 3.131478 CGTCATGGAAACGCCCCC 61.131 66.667 0.00 0.00 34.97 5.40
124 125 3.131478 CCGTCATGGAAACGCCCC 61.131 66.667 0.14 0.00 42.00 5.80
125 126 3.810896 GCCGTCATGGAAACGCCC 61.811 66.667 0.14 0.00 42.00 6.13
126 127 3.810896 GGCCGTCATGGAAACGCC 61.811 66.667 0.14 2.47 42.00 5.68
127 128 4.160635 CGGCCGTCATGGAAACGC 62.161 66.667 19.50 0.00 42.00 4.84
128 129 2.433491 TCGGCCGTCATGGAAACG 60.433 61.111 27.15 0.00 42.00 3.60
129 130 2.736682 CGTCGGCCGTCATGGAAAC 61.737 63.158 27.15 12.33 42.00 2.78
130 131 2.433491 CGTCGGCCGTCATGGAAA 60.433 61.111 27.15 0.00 42.00 3.13
131 132 4.444838 CCGTCGGCCGTCATGGAA 62.445 66.667 27.15 0.00 42.00 3.53
139 140 4.570663 GATCTGGTCCGTCGGCCG 62.571 72.222 22.12 22.12 0.00 6.13
140 141 4.222847 GGATCTGGTCCGTCGGCC 62.223 72.222 6.34 11.96 37.23 6.13
148 149 1.690633 TCCCCTGCTGGATCTGGTC 60.691 63.158 11.88 0.00 35.39 4.02
149 150 1.692042 CTCCCCTGCTGGATCTGGT 60.692 63.158 11.88 0.00 35.39 4.00
150 151 2.450320 CCTCCCCTGCTGGATCTGG 61.450 68.421 11.88 3.70 35.39 3.86
151 152 3.117452 GCCTCCCCTGCTGGATCTG 62.117 68.421 11.88 0.00 35.39 2.90
152 153 2.771762 GCCTCCCCTGCTGGATCT 60.772 66.667 11.88 0.00 35.39 2.75
153 154 2.771762 AGCCTCCCCTGCTGGATC 60.772 66.667 11.88 0.00 37.76 3.36
154 155 2.771762 GAGCCTCCCCTGCTGGAT 60.772 66.667 11.88 0.00 39.69 3.41
165 166 4.087892 TCCAAGCCAGCGAGCCTC 62.088 66.667 0.00 0.00 0.00 4.70
166 167 4.093291 CTCCAAGCCAGCGAGCCT 62.093 66.667 0.00 0.00 0.00 4.58
167 168 3.612247 TTCTCCAAGCCAGCGAGCC 62.612 63.158 0.00 0.00 0.00 4.70
168 169 1.672356 TTTCTCCAAGCCAGCGAGC 60.672 57.895 0.00 0.00 0.00 5.03
169 170 0.603707 TGTTTCTCCAAGCCAGCGAG 60.604 55.000 0.00 0.00 0.00 5.03
170 171 0.603707 CTGTTTCTCCAAGCCAGCGA 60.604 55.000 0.00 0.00 0.00 4.93
171 172 1.871772 CTGTTTCTCCAAGCCAGCG 59.128 57.895 0.00 0.00 0.00 5.18
172 173 1.583477 GCTGTTTCTCCAAGCCAGC 59.417 57.895 0.00 0.00 41.37 4.85
173 174 1.871772 CGCTGTTTCTCCAAGCCAG 59.128 57.895 0.00 0.00 0.00 4.85
174 175 2.260869 GCGCTGTTTCTCCAAGCCA 61.261 57.895 0.00 0.00 0.00 4.75
175 176 2.563427 GCGCTGTTTCTCCAAGCC 59.437 61.111 0.00 0.00 0.00 4.35
176 177 1.841663 TTCGCGCTGTTTCTCCAAGC 61.842 55.000 5.56 0.00 0.00 4.01
177 178 0.798776 ATTCGCGCTGTTTCTCCAAG 59.201 50.000 5.56 0.00 0.00 3.61
178 179 0.796312 GATTCGCGCTGTTTCTCCAA 59.204 50.000 5.56 0.00 0.00 3.53
179 180 0.037326 AGATTCGCGCTGTTTCTCCA 60.037 50.000 5.56 0.00 0.00 3.86
180 181 0.371645 CAGATTCGCGCTGTTTCTCC 59.628 55.000 5.56 0.00 0.00 3.71
181 182 0.371645 CCAGATTCGCGCTGTTTCTC 59.628 55.000 5.56 0.00 0.00 2.87
182 183 0.320771 ACCAGATTCGCGCTGTTTCT 60.321 50.000 5.56 0.00 0.00 2.52
183 184 0.095417 GACCAGATTCGCGCTGTTTC 59.905 55.000 5.56 0.00 0.00 2.78
184 185 0.602638 TGACCAGATTCGCGCTGTTT 60.603 50.000 5.56 0.00 0.00 2.83
185 186 0.602638 TTGACCAGATTCGCGCTGTT 60.603 50.000 5.56 0.00 0.00 3.16
186 187 0.602638 TTTGACCAGATTCGCGCTGT 60.603 50.000 5.56 0.00 0.00 4.40
187 188 0.095935 CTTTGACCAGATTCGCGCTG 59.904 55.000 5.56 2.72 0.00 5.18
188 189 0.037326 TCTTTGACCAGATTCGCGCT 60.037 50.000 5.56 0.00 0.00 5.92
189 190 0.095417 GTCTTTGACCAGATTCGCGC 59.905 55.000 0.00 0.00 0.00 6.86
190 191 0.366871 CGTCTTTGACCAGATTCGCG 59.633 55.000 0.00 0.00 0.00 5.87
191 192 0.095417 GCGTCTTTGACCAGATTCGC 59.905 55.000 0.00 0.00 32.98 4.70
192 193 1.656095 GAGCGTCTTTGACCAGATTCG 59.344 52.381 0.00 0.00 0.00 3.34
193 194 1.656095 CGAGCGTCTTTGACCAGATTC 59.344 52.381 0.00 0.00 0.00 2.52
194 195 1.673033 CCGAGCGTCTTTGACCAGATT 60.673 52.381 0.00 0.00 0.00 2.40
195 196 0.108615 CCGAGCGTCTTTGACCAGAT 60.109 55.000 0.00 0.00 0.00 2.90
196 197 1.289066 CCGAGCGTCTTTGACCAGA 59.711 57.895 0.00 0.00 0.00 3.86
197 198 2.383527 GCCGAGCGTCTTTGACCAG 61.384 63.158 0.00 0.00 0.00 4.00
198 199 2.357034 GCCGAGCGTCTTTGACCA 60.357 61.111 0.00 0.00 0.00 4.02
223 224 4.704833 GACTGCAGCCTTCGCCCA 62.705 66.667 15.27 0.00 34.57 5.36
235 236 1.442526 CCTCATTCATGGCGGACTGC 61.443 60.000 0.00 0.00 45.38 4.40
236 237 0.816825 CCCTCATTCATGGCGGACTG 60.817 60.000 0.00 0.00 0.00 3.51
237 238 0.982852 TCCCTCATTCATGGCGGACT 60.983 55.000 0.00 0.00 0.00 3.85
238 239 0.109342 ATCCCTCATTCATGGCGGAC 59.891 55.000 0.00 0.00 31.34 4.79
239 240 0.109153 CATCCCTCATTCATGGCGGA 59.891 55.000 0.00 0.02 32.51 5.54
240 241 1.521450 GCATCCCTCATTCATGGCGG 61.521 60.000 0.00 0.00 0.00 6.13
241 242 1.848932 CGCATCCCTCATTCATGGCG 61.849 60.000 0.00 0.00 0.00 5.69
242 243 1.521450 CCGCATCCCTCATTCATGGC 61.521 60.000 0.00 0.00 0.00 4.40
243 244 0.179009 ACCGCATCCCTCATTCATGG 60.179 55.000 0.00 0.00 0.00 3.66
244 245 0.949397 CACCGCATCCCTCATTCATG 59.051 55.000 0.00 0.00 0.00 3.07
245 246 0.548031 ACACCGCATCCCTCATTCAT 59.452 50.000 0.00 0.00 0.00 2.57
246 247 0.327924 AACACCGCATCCCTCATTCA 59.672 50.000 0.00 0.00 0.00 2.57
247 248 1.463674 AAACACCGCATCCCTCATTC 58.536 50.000 0.00 0.00 0.00 2.67
248 249 1.923356 AAAACACCGCATCCCTCATT 58.077 45.000 0.00 0.00 0.00 2.57
249 250 1.923356 AAAAACACCGCATCCCTCAT 58.077 45.000 0.00 0.00 0.00 2.90
250 251 3.430473 AAAAACACCGCATCCCTCA 57.570 47.368 0.00 0.00 0.00 3.86
269 270 9.289782 CCTCTTCCTTTCTTCTTTATTCTGAAA 57.710 33.333 0.00 0.00 0.00 2.69
270 271 7.885399 CCCTCTTCCTTTCTTCTTTATTCTGAA 59.115 37.037 0.00 0.00 0.00 3.02
271 272 7.237679 TCCCTCTTCCTTTCTTCTTTATTCTGA 59.762 37.037 0.00 0.00 0.00 3.27
272 273 7.398024 TCCCTCTTCCTTTCTTCTTTATTCTG 58.602 38.462 0.00 0.00 0.00 3.02
273 274 7.575499 TCCCTCTTCCTTTCTTCTTTATTCT 57.425 36.000 0.00 0.00 0.00 2.40
274 275 9.332502 GTATCCCTCTTCCTTTCTTCTTTATTC 57.667 37.037 0.00 0.00 0.00 1.75
275 276 8.836735 TGTATCCCTCTTCCTTTCTTCTTTATT 58.163 33.333 0.00 0.00 0.00 1.40
276 277 8.268605 GTGTATCCCTCTTCCTTTCTTCTTTAT 58.731 37.037 0.00 0.00 0.00 1.40
277 278 7.578955 CGTGTATCCCTCTTCCTTTCTTCTTTA 60.579 40.741 0.00 0.00 0.00 1.85
278 279 6.477253 GTGTATCCCTCTTCCTTTCTTCTTT 58.523 40.000 0.00 0.00 0.00 2.52
279 280 5.337652 CGTGTATCCCTCTTCCTTTCTTCTT 60.338 44.000 0.00 0.00 0.00 2.52
280 281 4.160626 CGTGTATCCCTCTTCCTTTCTTCT 59.839 45.833 0.00 0.00 0.00 2.85
281 282 4.434520 CGTGTATCCCTCTTCCTTTCTTC 58.565 47.826 0.00 0.00 0.00 2.87
282 283 3.369576 GCGTGTATCCCTCTTCCTTTCTT 60.370 47.826 0.00 0.00 0.00 2.52
283 284 2.168728 GCGTGTATCCCTCTTCCTTTCT 59.831 50.000 0.00 0.00 0.00 2.52
284 285 2.552031 GCGTGTATCCCTCTTCCTTTC 58.448 52.381 0.00 0.00 0.00 2.62
285 286 1.134788 CGCGTGTATCCCTCTTCCTTT 60.135 52.381 0.00 0.00 0.00 3.11
286 287 0.460311 CGCGTGTATCCCTCTTCCTT 59.540 55.000 0.00 0.00 0.00 3.36
287 288 2.017559 GCGCGTGTATCCCTCTTCCT 62.018 60.000 8.43 0.00 0.00 3.36
288 289 1.591863 GCGCGTGTATCCCTCTTCC 60.592 63.158 8.43 0.00 0.00 3.46
289 290 1.944676 CGCGCGTGTATCCCTCTTC 60.945 63.158 24.19 0.00 0.00 2.87
290 291 2.104331 CGCGCGTGTATCCCTCTT 59.896 61.111 24.19 0.00 0.00 2.85
291 292 3.138798 ACGCGCGTGTATCCCTCT 61.139 61.111 37.37 5.31 0.00 3.69
292 293 2.954868 CACGCGCGTGTATCCCTC 60.955 66.667 45.19 0.00 40.91 4.30
300 301 3.853330 CCTTCATCCACGCGCGTG 61.853 66.667 46.27 46.27 45.02 5.34
301 302 4.373116 ACCTTCATCCACGCGCGT 62.373 61.111 32.73 32.73 0.00 6.01
302 303 3.853330 CACCTTCATCCACGCGCG 61.853 66.667 30.96 30.96 0.00 6.86
303 304 2.434185 TCACCTTCATCCACGCGC 60.434 61.111 5.73 0.00 0.00 6.86
304 305 2.100631 GGTCACCTTCATCCACGCG 61.101 63.158 3.53 3.53 0.00 6.01
305 306 2.100631 CGGTCACCTTCATCCACGC 61.101 63.158 0.00 0.00 0.00 5.34
306 307 1.447838 CCGGTCACCTTCATCCACG 60.448 63.158 0.00 0.00 0.00 4.94
307 308 1.745489 GCCGGTCACCTTCATCCAC 60.745 63.158 1.90 0.00 0.00 4.02
308 309 2.668632 GCCGGTCACCTTCATCCA 59.331 61.111 1.90 0.00 0.00 3.41
309 310 2.124695 GGCCGGTCACCTTCATCC 60.125 66.667 0.00 0.00 0.00 3.51
310 311 2.511600 CGGCCGGTCACCTTCATC 60.512 66.667 20.10 0.00 0.00 2.92
311 312 2.119484 TTTCGGCCGGTCACCTTCAT 62.119 55.000 27.83 0.00 0.00 2.57
312 313 2.809307 TTTCGGCCGGTCACCTTCA 61.809 57.895 27.83 0.00 0.00 3.02
313 314 2.031465 TTTCGGCCGGTCACCTTC 59.969 61.111 27.83 0.00 0.00 3.46
314 315 2.281276 GTTTCGGCCGGTCACCTT 60.281 61.111 27.83 0.00 0.00 3.50
315 316 2.726822 GAAGTTTCGGCCGGTCACCT 62.727 60.000 27.83 11.47 0.00 4.00
316 317 2.281276 AAGTTTCGGCCGGTCACC 60.281 61.111 27.83 9.19 0.00 4.02
317 318 2.664436 CGAAGTTTCGGCCGGTCAC 61.664 63.158 27.83 18.97 46.30 3.67
318 319 2.356553 CGAAGTTTCGGCCGGTCA 60.357 61.111 27.83 6.94 46.30 4.02
327 328 4.084888 CACGCCGGCCGAAGTTTC 62.085 66.667 30.73 7.06 41.02 2.78
328 329 4.922026 ACACGCCGGCCGAAGTTT 62.922 61.111 30.73 16.18 41.02 2.66
337 338 4.973055 TTGGGAACGACACGCCGG 62.973 66.667 0.00 0.00 0.00 6.13
338 339 2.968156 TTTGGGAACGACACGCCG 60.968 61.111 0.00 0.00 0.00 6.46
339 340 2.635338 GTTTGGGAACGACACGCC 59.365 61.111 0.00 0.00 0.00 5.68
354 355 6.869695 ACATGTTTTTAGAAAGGGAAACGTT 58.130 32.000 0.00 0.00 40.85 3.99
355 356 6.459670 ACATGTTTTTAGAAAGGGAAACGT 57.540 33.333 0.00 0.00 35.36 3.99
356 357 8.347035 TCTAACATGTTTTTAGAAAGGGAAACG 58.653 33.333 17.78 0.00 33.52 3.60
357 358 9.459640 GTCTAACATGTTTTTAGAAAGGGAAAC 57.540 33.333 17.78 0.00 37.32 2.78
358 359 9.191479 TGTCTAACATGTTTTTAGAAAGGGAAA 57.809 29.630 17.78 0.00 37.32 3.13
359 360 8.754991 TGTCTAACATGTTTTTAGAAAGGGAA 57.245 30.769 17.78 0.00 37.32 3.97
360 361 8.754991 TTGTCTAACATGTTTTTAGAAAGGGA 57.245 30.769 17.78 0.00 37.32 4.20
361 362 9.810545 TTTTGTCTAACATGTTTTTAGAAAGGG 57.189 29.630 17.78 0.00 37.32 3.95
451 453 1.617947 GGACGAGACCTGGGCAATCT 61.618 60.000 0.47 0.00 0.00 2.40
755 3848 7.663501 AATACTATTGGTGAGGGGGATTAAT 57.336 36.000 0.00 0.00 0.00 1.40
773 3866 9.430399 AACCTAGGTTCTGCTATGTTAATACTA 57.570 33.333 21.96 0.00 32.09 1.82
807 3931 7.182060 AGTCAACCTATAAATGTCCAAATGGT 58.818 34.615 0.00 0.00 36.34 3.55
810 3934 8.552296 AGAGAGTCAACCTATAAATGTCCAAAT 58.448 33.333 0.00 0.00 0.00 2.32
854 3978 8.838365 TGGTGATTAGTTTTTACATTACGTTGT 58.162 29.630 0.00 0.00 0.00 3.32
895 4181 5.458041 AATTATACTCATGCATTGTGCCC 57.542 39.130 0.00 0.00 44.23 5.36
1087 4468 3.519510 TCACAGACTGCCTAAAGCCTAAT 59.480 43.478 1.25 0.00 42.71 1.73
1321 4705 5.539955 ACATCAAAACCATAAGGAGCACTTT 59.460 36.000 0.00 0.00 40.64 2.66
1531 5393 9.403583 TCTGGAAAAGTAAAATGAGTGTAAACT 57.596 29.630 0.00 0.00 0.00 2.66
1698 5560 3.242739 GGTTCGACATGAATCCATTTCCG 60.243 47.826 0.00 0.00 39.21 4.30
1768 5630 1.377612 AGCTCCATGTCAGCTGCAA 59.622 52.632 9.47 0.00 45.85 4.08
2015 5881 1.542915 GGAGAAAAGCAGCAGCATTCA 59.457 47.619 17.57 0.00 45.49 2.57
2017 5883 0.524862 CGGAGAAAAGCAGCAGCATT 59.475 50.000 3.17 0.00 45.49 3.56
2139 6015 2.751436 ACCATGTGGCGATGTGGC 60.751 61.111 0.00 0.00 45.12 5.01
2140 6016 3.055080 GCACCATGTGGCGATGTGG 62.055 63.158 0.00 1.63 39.32 4.17
2141 6017 2.486504 GCACCATGTGGCGATGTG 59.513 61.111 0.00 0.00 39.32 3.21
2256 6255 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
2341 6341 6.901081 TCAGTATGGACTACATATGGACTG 57.099 41.667 7.80 0.48 43.55 3.51
2342 6342 7.914427 TTTCAGTATGGACTACATATGGACT 57.086 36.000 7.80 0.00 43.55 3.85
2388 6388 5.513233 AGAAATACTACTACCTCCGTTCCA 58.487 41.667 0.00 0.00 0.00 3.53
2389 6389 5.827267 AGAGAAATACTACTACCTCCGTTCC 59.173 44.000 0.00 0.00 0.00 3.62
2448 6448 3.267031 AGTTTTGGCTGCCTAATAGGAGT 59.733 43.478 21.03 3.63 37.67 3.85
2455 6455 3.068024 CACAGAAAGTTTTGGCTGCCTAA 59.932 43.478 21.03 16.17 31.74 2.69
2464 6464 8.612619 ACACTATGTAGTTCACAGAAAGTTTTG 58.387 33.333 0.00 0.00 41.51 2.44
2486 6486 4.330250 CCTGAAGATTCATCCAACACACT 58.670 43.478 0.00 0.00 36.46 3.55
2562 6562 9.567848 CATAAAACTGGACATTAATGTTACACC 57.432 33.333 21.63 17.52 41.95 4.16
2631 6631 3.864243 ACGAACTGTCTTAACACAACCA 58.136 40.909 0.00 0.00 0.00 3.67
2659 6659 2.419851 GCCTACATTCTCTTGCTGAGCT 60.420 50.000 5.83 0.00 42.38 4.09


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

AutoCloner maintained by Alex Coulton.