Multiple sequence alignment - TraesCS2A01G532400

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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 TraesCS2A01G532400 chr2A 100.000 2273 0 0 1 2273 748775021 748777293 0.000000e+00 4198
1 TraesCS2A01G532400 chr2A 82.971 552 69 14 723 1273 748697862 748698389 2.040000e-130 475
2 TraesCS2A01G532400 chr2A 78.617 622 93 23 882 1491 748559894 748560487 2.130000e-100 375
3 TraesCS2A01G532400 chr2A 83.243 370 45 13 908 1269 748822877 748823237 7.830000e-85 324
4 TraesCS2A01G532400 chr2A 81.006 179 26 8 281 453 748822180 748822356 3.940000e-28 135
5 TraesCS2A01G532400 chr2B 88.880 1214 92 20 907 2108 754342716 754343898 0.000000e+00 1454
6 TraesCS2A01G532400 chr2B 92.323 495 27 7 282 776 754342194 754342677 0.000000e+00 693
7 TraesCS2A01G532400 chr2B 76.279 919 138 51 732 1603 754010689 754011574 1.260000e-112 416
8 TraesCS2A01G532400 chr2B 82.368 380 48 12 888 1263 754015872 754016236 1.700000e-81 313
9 TraesCS2A01G532400 chr2B 96.667 60 2 0 1 60 754342094 754342153 1.440000e-17 100
10 TraesCS2A01G532400 chr2D 91.165 1030 52 15 282 1285 618101582 618102598 0.000000e+00 1362
11 TraesCS2A01G532400 chr2D 86.234 385 27 8 1304 1687 606092592 606092951 5.880000e-106 394
12 TraesCS2A01G532400 chr2D 83.416 404 48 13 878 1273 618003987 618004379 7.720000e-95 357
13 TraesCS2A01G532400 chr2D 89.091 275 29 1 995 1269 618132563 618132836 7.780000e-90 340
14 TraesCS2A01G532400 chr2D 86.552 290 37 2 984 1271 617941868 617942157 3.640000e-83 318
15 TraesCS2A01G532400 chr2D 88.489 139 11 2 2083 2217 606093049 606093186 1.810000e-36 163
16 TraesCS2A01G532400 chr2D 81.538 195 30 6 281 471 618131881 618132073 3.020000e-34 156
17 TraesCS2A01G532400 chr2D 91.509 106 9 0 840 945 606092460 606092565 1.820000e-31 147
18 TraesCS2A01G532400 chr2D 84.906 106 10 3 1286 1385 618102730 618102835 3.990000e-18 102
19 TraesCS2A01G532400 chr2D 98.246 57 1 0 1 57 618101480 618101536 1.440000e-17 100
20 TraesCS2A01G532400 chr3B 89.247 93 7 2 2127 2217 43689913 43690004 1.850000e-21 113


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 TraesCS2A01G532400 chr2A 748775021 748777293 2272 False 4198.000000 4198 100.000000 1 2273 1 chr2A.!!$F3 2272
1 TraesCS2A01G532400 chr2A 748697862 748698389 527 False 475.000000 475 82.971000 723 1273 1 chr2A.!!$F2 550
2 TraesCS2A01G532400 chr2A 748559894 748560487 593 False 375.000000 375 78.617000 882 1491 1 chr2A.!!$F1 609
3 TraesCS2A01G532400 chr2A 748822180 748823237 1057 False 229.500000 324 82.124500 281 1269 2 chr2A.!!$F4 988
4 TraesCS2A01G532400 chr2B 754342094 754343898 1804 False 749.000000 1454 92.623333 1 2108 3 chr2B.!!$F3 2107
5 TraesCS2A01G532400 chr2B 754010689 754011574 885 False 416.000000 416 76.279000 732 1603 1 chr2B.!!$F1 871
6 TraesCS2A01G532400 chr2D 618101480 618102835 1355 False 521.333333 1362 91.439000 1 1385 3 chr2D.!!$F4 1384
7 TraesCS2A01G532400 chr2D 618131881 618132836 955 False 248.000000 340 85.314500 281 1269 2 chr2D.!!$F5 988
8 TraesCS2A01G532400 chr2D 606092460 606093186 726 False 234.666667 394 88.744000 840 2217 3 chr2D.!!$F3 1377

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
253 264 0.107643 GCATCCTACTCCCAAGCCTC 59.892 60.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 1784 0.178876 TGGATGGACAAGGAGGGTGA 60.179 55.0 0.0 0.0 0.0 4.02 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
106 117 2.978824 GGAACGGCAGGTGCTCTA 59.021 61.111 1.26 0.00 41.70 2.43
107 118 1.522569 GGAACGGCAGGTGCTCTAT 59.477 57.895 1.26 0.00 41.70 1.98
108 119 0.530870 GGAACGGCAGGTGCTCTATC 60.531 60.000 1.26 0.00 41.70 2.08
109 120 0.461961 GAACGGCAGGTGCTCTATCT 59.538 55.000 1.26 0.00 41.70 1.98
110 121 0.905357 AACGGCAGGTGCTCTATCTT 59.095 50.000 1.26 0.00 41.70 2.40
111 122 0.905357 ACGGCAGGTGCTCTATCTTT 59.095 50.000 1.26 0.00 41.70 2.52
112 123 1.279271 ACGGCAGGTGCTCTATCTTTT 59.721 47.619 1.26 0.00 41.70 2.27
113 124 1.936547 CGGCAGGTGCTCTATCTTTTC 59.063 52.381 1.26 0.00 41.70 2.29
114 125 2.677902 CGGCAGGTGCTCTATCTTTTCA 60.678 50.000 1.26 0.00 41.70 2.69
115 126 3.549794 GGCAGGTGCTCTATCTTTTCAT 58.450 45.455 1.26 0.00 41.70 2.57
116 127 3.950395 GGCAGGTGCTCTATCTTTTCATT 59.050 43.478 1.26 0.00 41.70 2.57
117 128 5.126067 GGCAGGTGCTCTATCTTTTCATTA 58.874 41.667 1.26 0.00 41.70 1.90
118 129 5.767168 GGCAGGTGCTCTATCTTTTCATTAT 59.233 40.000 1.26 0.00 41.70 1.28
119 130 6.936900 GGCAGGTGCTCTATCTTTTCATTATA 59.063 38.462 1.26 0.00 41.70 0.98
120 131 7.118971 GGCAGGTGCTCTATCTTTTCATTATAG 59.881 40.741 1.26 0.00 41.70 1.31
121 132 7.875041 GCAGGTGCTCTATCTTTTCATTATAGA 59.125 37.037 0.00 0.00 38.21 1.98
122 133 9.770097 CAGGTGCTCTATCTTTTCATTATAGAA 57.230 33.333 0.00 0.00 33.12 2.10
123 134 9.995003 AGGTGCTCTATCTTTTCATTATAGAAG 57.005 33.333 0.00 0.00 33.12 2.85
124 135 9.213799 GGTGCTCTATCTTTTCATTATAGAAGG 57.786 37.037 0.00 0.00 33.12 3.46
125 136 9.213799 GTGCTCTATCTTTTCATTATAGAAGGG 57.786 37.037 0.00 0.00 33.12 3.95
126 137 8.378565 TGCTCTATCTTTTCATTATAGAAGGGG 58.621 37.037 0.00 0.00 33.12 4.79
127 138 8.598041 GCTCTATCTTTTCATTATAGAAGGGGA 58.402 37.037 0.00 0.00 33.12 4.81
133 144 9.822727 TCTTTTCATTATAGAAGGGGAAAAACT 57.177 29.630 0.00 0.00 34.86 2.66
134 145 9.860898 CTTTTCATTATAGAAGGGGAAAAACTG 57.139 33.333 0.00 0.00 34.86 3.16
135 146 8.950007 TTTCATTATAGAAGGGGAAAAACTGT 57.050 30.769 0.00 0.00 0.00 3.55
137 148 9.457436 TTCATTATAGAAGGGGAAAAACTGTAC 57.543 33.333 0.00 0.00 0.00 2.90
138 149 8.607713 TCATTATAGAAGGGGAAAAACTGTACA 58.392 33.333 0.00 0.00 0.00 2.90
139 150 9.238368 CATTATAGAAGGGGAAAAACTGTACAA 57.762 33.333 0.00 0.00 0.00 2.41
140 151 9.816787 ATTATAGAAGGGGAAAAACTGTACAAA 57.183 29.630 0.00 0.00 0.00 2.83
141 152 7.761038 ATAGAAGGGGAAAAACTGTACAAAG 57.239 36.000 0.00 0.00 0.00 2.77
142 153 4.893524 AGAAGGGGAAAAACTGTACAAAGG 59.106 41.667 0.00 0.00 0.00 3.11
143 154 2.963101 AGGGGAAAAACTGTACAAAGGC 59.037 45.455 0.00 0.00 0.00 4.35
144 155 2.036733 GGGGAAAAACTGTACAAAGGCC 59.963 50.000 0.00 0.00 0.00 5.19
145 156 2.696187 GGGAAAAACTGTACAAAGGCCA 59.304 45.455 5.01 0.00 0.00 5.36
146 157 3.133183 GGGAAAAACTGTACAAAGGCCAA 59.867 43.478 5.01 0.00 0.00 4.52
147 158 4.383226 GGGAAAAACTGTACAAAGGCCAAA 60.383 41.667 5.01 0.00 0.00 3.28
148 159 4.808895 GGAAAAACTGTACAAAGGCCAAAG 59.191 41.667 5.01 0.00 0.00 2.77
149 160 5.414789 AAAAACTGTACAAAGGCCAAAGT 57.585 34.783 5.01 1.77 0.00 2.66
150 161 6.406065 GGAAAAACTGTACAAAGGCCAAAGTA 60.406 38.462 5.01 0.62 0.00 2.24
151 162 5.767816 AAACTGTACAAAGGCCAAAGTAG 57.232 39.130 5.01 0.00 0.00 2.57
152 163 3.146847 ACTGTACAAAGGCCAAAGTAGC 58.853 45.455 5.01 0.58 0.00 3.58
159 170 1.382629 GGCCAAAGTAGCCTTGGGA 59.617 57.895 0.00 0.00 43.67 4.37
160 171 0.681243 GGCCAAAGTAGCCTTGGGAG 60.681 60.000 0.00 0.00 43.67 4.30
161 172 0.681243 GCCAAAGTAGCCTTGGGAGG 60.681 60.000 0.53 0.00 43.67 4.30
162 173 0.991920 CCAAAGTAGCCTTGGGAGGA 59.008 55.000 0.00 0.00 43.67 3.71
163 174 1.354368 CCAAAGTAGCCTTGGGAGGAA 59.646 52.381 0.00 0.00 43.67 3.36
164 175 2.225017 CCAAAGTAGCCTTGGGAGGAAA 60.225 50.000 0.00 0.00 43.67 3.13
165 176 3.084786 CAAAGTAGCCTTGGGAGGAAAG 58.915 50.000 0.00 0.00 46.74 2.62
166 177 2.344093 AGTAGCCTTGGGAGGAAAGA 57.656 50.000 0.00 0.00 46.74 2.52
167 178 2.632537 AGTAGCCTTGGGAGGAAAGAA 58.367 47.619 0.00 0.00 46.74 2.52
168 179 2.306219 AGTAGCCTTGGGAGGAAAGAAC 59.694 50.000 0.00 0.00 46.74 3.01
169 180 1.149101 AGCCTTGGGAGGAAAGAACA 58.851 50.000 0.00 0.00 46.74 3.18
170 181 1.499007 AGCCTTGGGAGGAAAGAACAA 59.501 47.619 0.00 0.00 46.74 2.83
171 182 1.889170 GCCTTGGGAGGAAAGAACAAG 59.111 52.381 0.00 0.00 46.74 3.16
172 183 2.489073 GCCTTGGGAGGAAAGAACAAGA 60.489 50.000 0.00 0.00 46.74 3.02
173 184 3.416156 CCTTGGGAGGAAAGAACAAGAG 58.584 50.000 0.00 0.00 46.74 2.85
174 185 3.073062 CCTTGGGAGGAAAGAACAAGAGA 59.927 47.826 0.00 0.00 46.74 3.10
175 186 4.322567 CTTGGGAGGAAAGAACAAGAGAG 58.677 47.826 0.00 0.00 40.60 3.20
176 187 3.587498 TGGGAGGAAAGAACAAGAGAGA 58.413 45.455 0.00 0.00 0.00 3.10
177 188 3.973973 TGGGAGGAAAGAACAAGAGAGAA 59.026 43.478 0.00 0.00 0.00 2.87
178 189 4.412199 TGGGAGGAAAGAACAAGAGAGAAA 59.588 41.667 0.00 0.00 0.00 2.52
179 190 5.104109 TGGGAGGAAAGAACAAGAGAGAAAA 60.104 40.000 0.00 0.00 0.00 2.29
180 191 5.239744 GGGAGGAAAGAACAAGAGAGAAAAC 59.760 44.000 0.00 0.00 0.00 2.43
181 192 5.239744 GGAGGAAAGAACAAGAGAGAAAACC 59.760 44.000 0.00 0.00 0.00 3.27
182 193 5.755849 AGGAAAGAACAAGAGAGAAAACCA 58.244 37.500 0.00 0.00 0.00 3.67
183 194 5.825151 AGGAAAGAACAAGAGAGAAAACCAG 59.175 40.000 0.00 0.00 0.00 4.00
184 195 5.823045 GGAAAGAACAAGAGAGAAAACCAGA 59.177 40.000 0.00 0.00 0.00 3.86
185 196 6.318900 GGAAAGAACAAGAGAGAAAACCAGAA 59.681 38.462 0.00 0.00 0.00 3.02
186 197 7.148069 GGAAAGAACAAGAGAGAAAACCAGAAA 60.148 37.037 0.00 0.00 0.00 2.52
187 198 7.703058 AAGAACAAGAGAGAAAACCAGAAAA 57.297 32.000 0.00 0.00 0.00 2.29
188 199 7.703058 AGAACAAGAGAGAAAACCAGAAAAA 57.297 32.000 0.00 0.00 0.00 1.94
189 200 7.766283 AGAACAAGAGAGAAAACCAGAAAAAG 58.234 34.615 0.00 0.00 0.00 2.27
190 201 7.611855 AGAACAAGAGAGAAAACCAGAAAAAGA 59.388 33.333 0.00 0.00 0.00 2.52
191 202 7.326968 ACAAGAGAGAAAACCAGAAAAAGAG 57.673 36.000 0.00 0.00 0.00 2.85
192 203 6.319911 ACAAGAGAGAAAACCAGAAAAAGAGG 59.680 38.462 0.00 0.00 0.00 3.69
193 204 4.824537 AGAGAGAAAACCAGAAAAAGAGGC 59.175 41.667 0.00 0.00 0.00 4.70
194 205 3.891977 AGAGAAAACCAGAAAAAGAGGCC 59.108 43.478 0.00 0.00 0.00 5.19
195 206 3.891977 GAGAAAACCAGAAAAAGAGGCCT 59.108 43.478 3.86 3.86 0.00 5.19
196 207 3.638627 AGAAAACCAGAAAAAGAGGCCTG 59.361 43.478 12.00 0.00 0.00 4.85
197 208 3.312736 AAACCAGAAAAAGAGGCCTGA 57.687 42.857 12.00 0.00 0.00 3.86
198 209 2.575805 ACCAGAAAAAGAGGCCTGAG 57.424 50.000 12.00 0.00 0.00 3.35
199 210 2.057922 ACCAGAAAAAGAGGCCTGAGA 58.942 47.619 12.00 0.00 0.00 3.27
200 211 2.224646 ACCAGAAAAAGAGGCCTGAGAC 60.225 50.000 12.00 0.00 0.00 3.36
201 212 2.039613 CCAGAAAAAGAGGCCTGAGACT 59.960 50.000 12.00 0.00 0.00 3.24
202 213 3.072944 CAGAAAAAGAGGCCTGAGACTG 58.927 50.000 12.00 8.41 0.00 3.51
203 214 2.039613 AGAAAAAGAGGCCTGAGACTGG 59.960 50.000 12.00 0.00 0.00 4.00
204 215 0.695347 AAAAGAGGCCTGAGACTGGG 59.305 55.000 12.00 0.00 0.00 4.45
205 216 0.178891 AAAGAGGCCTGAGACTGGGA 60.179 55.000 12.00 0.00 0.00 4.37
206 217 0.907230 AAGAGGCCTGAGACTGGGAC 60.907 60.000 12.00 0.00 0.00 4.46
207 218 2.681778 AGGCCTGAGACTGGGACG 60.682 66.667 3.11 0.00 35.38 4.79
208 219 2.680352 GGCCTGAGACTGGGACGA 60.680 66.667 0.00 0.00 0.00 4.20
209 220 2.716017 GGCCTGAGACTGGGACGAG 61.716 68.421 0.00 0.00 0.00 4.18
210 221 2.888863 CCTGAGACTGGGACGAGC 59.111 66.667 0.00 0.00 0.00 5.03
211 222 2.716017 CCTGAGACTGGGACGAGCC 61.716 68.421 0.00 0.00 0.00 4.70
212 223 1.979155 CTGAGACTGGGACGAGCCA 60.979 63.158 0.00 0.00 38.95 4.75
213 224 1.943116 CTGAGACTGGGACGAGCCAG 61.943 65.000 0.00 0.00 38.95 4.85
214 225 3.363844 GAGACTGGGACGAGCCAGC 62.364 68.421 0.00 0.00 38.95 4.85
215 226 4.459089 GACTGGGACGAGCCAGCC 62.459 72.222 0.00 0.00 38.95 4.85
221 232 3.461773 GACGAGCCAGCCCAGCTA 61.462 66.667 0.00 0.00 41.75 3.32
222 233 2.765807 ACGAGCCAGCCCAGCTAT 60.766 61.111 0.00 0.00 41.75 2.97
223 234 1.457643 ACGAGCCAGCCCAGCTATA 60.458 57.895 0.00 0.00 41.75 1.31
224 235 1.005630 CGAGCCAGCCCAGCTATAC 60.006 63.158 0.00 0.00 41.75 1.47
225 236 1.748329 CGAGCCAGCCCAGCTATACA 61.748 60.000 0.00 0.00 41.75 2.29
226 237 0.689623 GAGCCAGCCCAGCTATACAT 59.310 55.000 0.00 0.00 41.75 2.29
227 238 0.399454 AGCCAGCCCAGCTATACATG 59.601 55.000 0.00 0.00 39.29 3.21
228 239 0.109342 GCCAGCCCAGCTATACATGT 59.891 55.000 2.69 2.69 36.40 3.21
229 240 1.879796 GCCAGCCCAGCTATACATGTC 60.880 57.143 0.00 0.00 36.40 3.06
230 241 1.271054 CCAGCCCAGCTATACATGTCC 60.271 57.143 0.00 0.00 36.40 4.02
231 242 1.417517 CAGCCCAGCTATACATGTCCA 59.582 52.381 0.00 0.00 36.40 4.02
232 243 1.417890 AGCCCAGCTATACATGTCCAC 59.582 52.381 0.00 0.00 36.99 4.02
233 244 1.873903 GCCCAGCTATACATGTCCACG 60.874 57.143 0.00 0.00 0.00 4.94
234 245 1.270305 CCCAGCTATACATGTCCACGG 60.270 57.143 0.00 0.00 0.00 4.94
235 246 1.502231 CAGCTATACATGTCCACGGC 58.498 55.000 0.00 1.27 0.00 5.68
236 247 1.119684 AGCTATACATGTCCACGGCA 58.880 50.000 0.00 0.00 0.00 5.69
237 248 1.694150 AGCTATACATGTCCACGGCAT 59.306 47.619 0.00 0.00 0.00 4.40
238 249 2.069273 GCTATACATGTCCACGGCATC 58.931 52.381 0.00 0.00 0.00 3.91
239 250 2.688507 CTATACATGTCCACGGCATCC 58.311 52.381 0.00 0.00 0.00 3.51
240 251 1.131638 ATACATGTCCACGGCATCCT 58.868 50.000 0.00 0.00 0.00 3.24
241 252 1.783071 TACATGTCCACGGCATCCTA 58.217 50.000 0.00 0.00 0.00 2.94
242 253 0.178068 ACATGTCCACGGCATCCTAC 59.822 55.000 0.00 0.00 0.00 3.18
243 254 0.465705 CATGTCCACGGCATCCTACT 59.534 55.000 0.00 0.00 0.00 2.57
244 255 0.753262 ATGTCCACGGCATCCTACTC 59.247 55.000 0.00 0.00 0.00 2.59
245 256 1.327690 TGTCCACGGCATCCTACTCC 61.328 60.000 0.00 0.00 0.00 3.85
246 257 1.760875 TCCACGGCATCCTACTCCC 60.761 63.158 0.00 0.00 0.00 4.30
247 258 2.063979 CCACGGCATCCTACTCCCA 61.064 63.158 0.00 0.00 0.00 4.37
248 259 1.622607 CCACGGCATCCTACTCCCAA 61.623 60.000 0.00 0.00 0.00 4.12
249 260 0.179073 CACGGCATCCTACTCCCAAG 60.179 60.000 0.00 0.00 0.00 3.61
250 261 1.227674 CGGCATCCTACTCCCAAGC 60.228 63.158 0.00 0.00 0.00 4.01
251 262 1.149401 GGCATCCTACTCCCAAGCC 59.851 63.158 0.00 0.00 0.00 4.35
252 263 1.348775 GGCATCCTACTCCCAAGCCT 61.349 60.000 0.00 0.00 37.67 4.58
253 264 0.107643 GCATCCTACTCCCAAGCCTC 59.892 60.000 0.00 0.00 0.00 4.70
254 265 0.761802 CATCCTACTCCCAAGCCTCC 59.238 60.000 0.00 0.00 0.00 4.30
255 266 0.400670 ATCCTACTCCCAAGCCTCCC 60.401 60.000 0.00 0.00 0.00 4.30
256 267 1.003573 CCTACTCCCAAGCCTCCCT 59.996 63.158 0.00 0.00 0.00 4.20
257 268 1.341156 CCTACTCCCAAGCCTCCCTG 61.341 65.000 0.00 0.00 0.00 4.45
258 269 1.306997 TACTCCCAAGCCTCCCTGG 60.307 63.158 0.00 0.00 39.35 4.45
259 270 1.821966 TACTCCCAAGCCTCCCTGGA 61.822 60.000 0.00 0.00 38.35 3.86
260 271 2.285668 TCCCAAGCCTCCCTGGAG 60.286 66.667 6.20 6.20 41.63 3.86
270 281 3.560226 TCCCTGGAGGAGGCTAATC 57.440 57.895 0.00 0.00 40.93 1.75
271 282 0.944999 TCCCTGGAGGAGGCTAATCT 59.055 55.000 0.00 0.00 40.93 2.40
272 283 1.133009 TCCCTGGAGGAGGCTAATCTC 60.133 57.143 0.00 0.00 40.93 2.75
273 284 1.413662 CCCTGGAGGAGGCTAATCTCA 60.414 57.143 12.11 3.26 41.19 3.27
274 285 2.618794 CCTGGAGGAGGCTAATCTCAT 58.381 52.381 12.11 0.00 34.01 2.90
275 286 2.566724 CCTGGAGGAGGCTAATCTCATC 59.433 54.545 12.11 0.00 42.02 2.92
276 287 3.509442 CTGGAGGAGGCTAATCTCATCT 58.491 50.000 12.11 0.00 42.28 2.90
277 288 3.505386 TGGAGGAGGCTAATCTCATCTC 58.495 50.000 12.11 0.00 42.28 2.75
278 289 3.141838 TGGAGGAGGCTAATCTCATCTCT 59.858 47.826 12.11 0.00 42.28 3.10
279 290 4.355287 TGGAGGAGGCTAATCTCATCTCTA 59.645 45.833 12.11 0.00 42.28 2.43
316 328 4.808414 TCCTCGAAATTGACATGAGAGT 57.192 40.909 0.00 0.00 0.00 3.24
518 636 7.042051 GGAAAAAGAGCCACTAAAATGAAAACC 60.042 37.037 0.00 0.00 0.00 3.27
780 918 2.513897 GATCCGAAAGCACCCGGG 60.514 66.667 22.25 22.25 45.36 5.73
797 935 0.178961 GGGTTCCTGGAAAACCAGCT 60.179 55.000 20.60 0.00 46.60 4.24
822 960 4.404654 CCGCCTGTTTTGCTCCGC 62.405 66.667 0.00 0.00 0.00 5.54
972 1162 1.067000 CAGTCTCCACTCTCCAGCAAG 60.067 57.143 0.00 0.00 0.00 4.01
979 1169 0.252479 ACTCTCCAGCAAGGCATCAG 59.748 55.000 0.00 0.00 37.29 2.90
1289 1644 7.232127 ACCCAATTAGTATTAGCGCTTAGTAGA 59.768 37.037 18.68 0.00 0.00 2.59
1296 1651 8.393671 AGTATTAGCGCTTAGTAGAATGTAGT 57.606 34.615 18.68 0.00 0.00 2.73
1380 1757 6.962686 TGATGATGATGAAAATTTCGGCTAG 58.037 36.000 0.97 0.00 0.00 3.42
1394 1778 6.726490 TTTCGGCTAGGAGTTTATATCACT 57.274 37.500 0.00 0.00 0.00 3.41
1395 1779 5.961396 TCGGCTAGGAGTTTATATCACTC 57.039 43.478 6.47 6.47 40.12 3.51
1396 1780 5.382616 TCGGCTAGGAGTTTATATCACTCA 58.617 41.667 14.15 0.00 42.28 3.41
1397 1781 5.831525 TCGGCTAGGAGTTTATATCACTCAA 59.168 40.000 14.15 4.25 42.28 3.02
1398 1782 6.493802 TCGGCTAGGAGTTTATATCACTCAAT 59.506 38.462 14.15 7.04 42.28 2.57
1399 1783 7.668469 TCGGCTAGGAGTTTATATCACTCAATA 59.332 37.037 14.15 7.61 42.28 1.90
1400 1784 8.470805 CGGCTAGGAGTTTATATCACTCAATAT 58.529 37.037 14.15 3.45 42.28 1.28
1401 1785 9.810545 GGCTAGGAGTTTATATCACTCAATATC 57.189 37.037 14.15 5.28 42.28 1.63
1422 1806 0.466922 CCCTCCTTGTCCATCCATGC 60.467 60.000 0.00 0.00 0.00 4.06
1451 1835 4.278170 TGTGACTATTGTTTGAAAGGCCAG 59.722 41.667 5.01 0.00 0.00 4.85
1497 1882 0.524862 GCGTTCAGAGTTAGACGGGA 59.475 55.000 0.00 0.00 0.00 5.14
1507 1892 3.813724 GAGTTAGACGGGAAAAGCAACTT 59.186 43.478 0.00 0.00 0.00 2.66
1525 1910 0.030773 TTAGCAGAGCGAGGCATACG 59.969 55.000 0.00 0.00 0.00 3.06
1590 1976 0.315251 GCCCAACTCTGAACAAAGGC 59.685 55.000 0.00 0.00 0.00 4.35
1709 2095 6.299141 ACCTGTTCTGAATTTCTTTGCTCTA 58.701 36.000 0.00 0.00 0.00 2.43
1715 2101 5.934625 TCTGAATTTCTTTGCTCTACACTCC 59.065 40.000 0.00 0.00 0.00 3.85
1716 2102 4.690748 TGAATTTCTTTGCTCTACACTCCG 59.309 41.667 0.00 0.00 0.00 4.63
1722 2108 0.243907 TGCTCTACACTCCGCTGAAC 59.756 55.000 0.00 0.00 0.00 3.18
1723 2109 0.458716 GCTCTACACTCCGCTGAACC 60.459 60.000 0.00 0.00 0.00 3.62
1729 2115 3.382832 CTCCGCTGAACCCCGACT 61.383 66.667 0.00 0.00 0.00 4.18
1731 2117 4.003788 CCGCTGAACCCCGACTGT 62.004 66.667 0.00 0.00 0.00 3.55
1733 2119 1.515954 CGCTGAACCCCGACTGTAT 59.484 57.895 0.00 0.00 0.00 2.29
1745 2131 4.369182 CCCGACTGTATGATACCAAGTTC 58.631 47.826 0.00 0.00 0.00 3.01
1768 2162 5.122869 TCAACTAAAAGCATGATCAGAGTGC 59.877 40.000 11.10 11.10 39.10 4.40
1785 2179 8.893219 TCAGAGTGCTGATGTTATTAATAAGG 57.107 34.615 8.18 0.00 45.88 2.69
1820 2214 4.098044 AGTTAGTGATGACATAGTGGGACG 59.902 45.833 0.00 0.00 0.00 4.79
1823 2217 1.134818 TGATGACATAGTGGGACGCAC 60.135 52.381 14.45 14.45 44.14 5.34
1884 2278 6.455360 TCAGAGTGAATTTATGGGAATTGC 57.545 37.500 0.00 0.00 29.75 3.56
1899 2293 0.815734 ATTGCTGAATGCCTGCTGAC 59.184 50.000 0.00 0.00 42.00 3.51
1935 2329 5.420725 TGCTGCTCCTAAGAACTGAATTA 57.579 39.130 0.00 0.00 0.00 1.40
2002 2396 8.398665 GTGCTACTGATTTGATTTTTACTAGGG 58.601 37.037 0.00 0.00 0.00 3.53
2024 2418 5.221244 GGGTCTTGAACTAAATGTTGCAAGT 60.221 40.000 0.00 0.00 40.48 3.16
2054 2448 7.467557 TTGAGAAAAATGAAATGTGAGTTGC 57.532 32.000 0.00 0.00 0.00 4.17
2109 2503 6.654793 AGAGCGATTCTTCTTTGTGTTATC 57.345 37.500 0.00 0.00 29.61 1.75
2131 2525 1.196354 CCTTGCGCTCAACTGAAGAAG 59.804 52.381 9.73 0.00 0.00 2.85
2145 2539 7.180229 TCAACTGAAGAAGACCTTACATGGATA 59.820 37.037 0.00 0.00 34.68 2.59
2209 2607 2.897326 TGTGGTAGCAGCTTCAGACTTA 59.103 45.455 0.00 0.00 0.00 2.24
2217 2615 4.646945 AGCAGCTTCAGACTTACTAGCATA 59.353 41.667 0.00 0.00 33.90 3.14
2218 2616 5.304101 AGCAGCTTCAGACTTACTAGCATAT 59.696 40.000 0.00 0.00 33.90 1.78
2219 2617 5.988561 GCAGCTTCAGACTTACTAGCATATT 59.011 40.000 0.00 0.00 33.90 1.28
2220 2618 7.014711 AGCAGCTTCAGACTTACTAGCATATTA 59.985 37.037 0.00 0.00 33.90 0.98
2221 2619 7.328249 GCAGCTTCAGACTTACTAGCATATTAG 59.672 40.741 0.00 0.00 33.90 1.73
2222 2620 7.812191 CAGCTTCAGACTTACTAGCATATTAGG 59.188 40.741 0.00 0.00 33.90 2.69
2223 2621 7.039363 AGCTTCAGACTTACTAGCATATTAGGG 60.039 40.741 0.00 0.00 33.90 3.53
2224 2622 6.591750 TCAGACTTACTAGCATATTAGGGC 57.408 41.667 0.00 0.00 0.00 5.19
2225 2623 6.075315 TCAGACTTACTAGCATATTAGGGCA 58.925 40.000 0.00 0.00 0.00 5.36
2226 2624 6.553476 TCAGACTTACTAGCATATTAGGGCAA 59.447 38.462 0.00 0.00 0.00 4.52
2227 2625 6.647067 CAGACTTACTAGCATATTAGGGCAAC 59.353 42.308 0.00 0.00 0.00 4.17
2228 2626 6.326583 AGACTTACTAGCATATTAGGGCAACA 59.673 38.462 0.00 0.00 39.74 3.33
2229 2627 6.525629 ACTTACTAGCATATTAGGGCAACAG 58.474 40.000 0.00 0.00 39.74 3.16
2230 2628 3.744660 ACTAGCATATTAGGGCAACAGC 58.255 45.455 0.00 0.00 39.74 4.40
2244 2642 4.729918 CAGCCCCACTGCCTCCAC 62.730 72.222 0.00 0.00 40.19 4.02
2245 2643 4.990910 AGCCCCACTGCCTCCACT 62.991 66.667 0.00 0.00 0.00 4.00
2246 2644 3.971702 GCCCCACTGCCTCCACTT 61.972 66.667 0.00 0.00 0.00 3.16
2247 2645 2.846532 CCCCACTGCCTCCACTTT 59.153 61.111 0.00 0.00 0.00 2.66
2248 2646 2.074967 CCCCACTGCCTCCACTTTA 58.925 57.895 0.00 0.00 0.00 1.85
2249 2647 0.625849 CCCCACTGCCTCCACTTTAT 59.374 55.000 0.00 0.00 0.00 1.40
2250 2648 1.005924 CCCCACTGCCTCCACTTTATT 59.994 52.381 0.00 0.00 0.00 1.40
2251 2649 2.094675 CCCACTGCCTCCACTTTATTG 58.905 52.381 0.00 0.00 0.00 1.90
2252 2650 2.290896 CCCACTGCCTCCACTTTATTGA 60.291 50.000 0.00 0.00 0.00 2.57
2253 2651 3.012518 CCACTGCCTCCACTTTATTGAG 58.987 50.000 0.00 0.00 0.00 3.02
2254 2652 3.307691 CCACTGCCTCCACTTTATTGAGA 60.308 47.826 0.00 0.00 0.00 3.27
2255 2653 4.326826 CACTGCCTCCACTTTATTGAGAA 58.673 43.478 0.00 0.00 0.00 2.87
2256 2654 4.154918 CACTGCCTCCACTTTATTGAGAAC 59.845 45.833 0.00 0.00 0.00 3.01
2257 2655 4.202461 ACTGCCTCCACTTTATTGAGAACA 60.202 41.667 0.00 0.00 0.00 3.18
2258 2656 4.724399 TGCCTCCACTTTATTGAGAACAA 58.276 39.130 0.00 0.00 40.42 2.83
2259 2657 5.136828 TGCCTCCACTTTATTGAGAACAAA 58.863 37.500 0.00 0.00 39.54 2.83
2260 2658 5.596361 TGCCTCCACTTTATTGAGAACAAAA 59.404 36.000 0.00 0.00 39.54 2.44
2261 2659 6.152379 GCCTCCACTTTATTGAGAACAAAAG 58.848 40.000 0.00 0.00 39.54 2.27
2262 2660 6.016276 GCCTCCACTTTATTGAGAACAAAAGA 60.016 38.462 0.00 0.00 39.54 2.52
2263 2661 7.309438 GCCTCCACTTTATTGAGAACAAAAGAT 60.309 37.037 0.00 0.00 39.54 2.40
2264 2662 9.231297 CCTCCACTTTATTGAGAACAAAAGATA 57.769 33.333 0.00 0.00 39.54 1.98
2266 2664 9.793259 TCCACTTTATTGAGAACAAAAGATACT 57.207 29.630 0.00 0.00 39.54 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 99 2.298158 ATAGAGCACCTGCCGTTCCG 62.298 60.000 0.00 0.00 43.38 4.30
89 100 0.530870 GATAGAGCACCTGCCGTTCC 60.531 60.000 0.00 0.00 43.38 3.62
90 101 0.461961 AGATAGAGCACCTGCCGTTC 59.538 55.000 0.00 0.00 43.38 3.95
91 102 0.905357 AAGATAGAGCACCTGCCGTT 59.095 50.000 0.00 0.00 43.38 4.44
92 103 0.905357 AAAGATAGAGCACCTGCCGT 59.095 50.000 0.00 0.00 43.38 5.68
93 104 1.936547 GAAAAGATAGAGCACCTGCCG 59.063 52.381 0.00 0.00 43.38 5.69
94 105 2.991250 TGAAAAGATAGAGCACCTGCC 58.009 47.619 0.00 0.00 43.38 4.85
95 106 6.874288 ATAATGAAAAGATAGAGCACCTGC 57.126 37.500 0.00 0.00 42.49 4.85
96 107 9.770097 TTCTATAATGAAAAGATAGAGCACCTG 57.230 33.333 0.00 0.00 34.51 4.00
97 108 9.995003 CTTCTATAATGAAAAGATAGAGCACCT 57.005 33.333 0.00 0.00 34.51 4.00
98 109 9.213799 CCTTCTATAATGAAAAGATAGAGCACC 57.786 37.037 0.00 0.00 34.51 5.01
99 110 9.213799 CCCTTCTATAATGAAAAGATAGAGCAC 57.786 37.037 0.00 0.00 34.51 4.40
100 111 8.378565 CCCCTTCTATAATGAAAAGATAGAGCA 58.621 37.037 0.00 0.00 34.51 4.26
101 112 8.598041 TCCCCTTCTATAATGAAAAGATAGAGC 58.402 37.037 0.00 0.00 34.51 4.09
107 118 9.822727 AGTTTTTCCCCTTCTATAATGAAAAGA 57.177 29.630 0.00 0.00 34.39 2.52
108 119 9.860898 CAGTTTTTCCCCTTCTATAATGAAAAG 57.139 33.333 0.00 0.00 34.39 2.27
109 120 9.374711 ACAGTTTTTCCCCTTCTATAATGAAAA 57.625 29.630 0.00 0.00 31.87 2.29
110 121 8.950007 ACAGTTTTTCCCCTTCTATAATGAAA 57.050 30.769 0.00 0.00 0.00 2.69
111 122 9.457436 GTACAGTTTTTCCCCTTCTATAATGAA 57.543 33.333 0.00 0.00 0.00 2.57
112 123 8.607713 TGTACAGTTTTTCCCCTTCTATAATGA 58.392 33.333 0.00 0.00 0.00 2.57
113 124 8.801882 TGTACAGTTTTTCCCCTTCTATAATG 57.198 34.615 0.00 0.00 0.00 1.90
114 125 9.816787 TTTGTACAGTTTTTCCCCTTCTATAAT 57.183 29.630 0.00 0.00 0.00 1.28
115 126 9.292195 CTTTGTACAGTTTTTCCCCTTCTATAA 57.708 33.333 0.00 0.00 0.00 0.98
116 127 7.886446 CCTTTGTACAGTTTTTCCCCTTCTATA 59.114 37.037 0.00 0.00 0.00 1.31
117 128 6.719829 CCTTTGTACAGTTTTTCCCCTTCTAT 59.280 38.462 0.00 0.00 0.00 1.98
118 129 6.066032 CCTTTGTACAGTTTTTCCCCTTCTA 58.934 40.000 0.00 0.00 0.00 2.10
119 130 4.893524 CCTTTGTACAGTTTTTCCCCTTCT 59.106 41.667 0.00 0.00 0.00 2.85
120 131 4.500887 GCCTTTGTACAGTTTTTCCCCTTC 60.501 45.833 0.00 0.00 0.00 3.46
121 132 3.386726 GCCTTTGTACAGTTTTTCCCCTT 59.613 43.478 0.00 0.00 0.00 3.95
122 133 2.963101 GCCTTTGTACAGTTTTTCCCCT 59.037 45.455 0.00 0.00 0.00 4.79
123 134 2.036733 GGCCTTTGTACAGTTTTTCCCC 59.963 50.000 0.00 0.00 0.00 4.81
124 135 2.696187 TGGCCTTTGTACAGTTTTTCCC 59.304 45.455 3.32 0.00 0.00 3.97
125 136 4.394439 TTGGCCTTTGTACAGTTTTTCC 57.606 40.909 3.32 0.00 0.00 3.13
126 137 5.416083 ACTTTGGCCTTTGTACAGTTTTTC 58.584 37.500 3.32 0.00 0.00 2.29
127 138 5.414789 ACTTTGGCCTTTGTACAGTTTTT 57.585 34.783 3.32 0.00 0.00 1.94
128 139 5.451381 GCTACTTTGGCCTTTGTACAGTTTT 60.451 40.000 3.32 0.00 0.00 2.43
129 140 4.037565 GCTACTTTGGCCTTTGTACAGTTT 59.962 41.667 3.32 0.00 0.00 2.66
130 141 3.568430 GCTACTTTGGCCTTTGTACAGTT 59.432 43.478 3.32 0.00 0.00 3.16
131 142 3.146847 GCTACTTTGGCCTTTGTACAGT 58.853 45.455 3.32 0.00 0.00 3.55
132 143 2.488153 GGCTACTTTGGCCTTTGTACAG 59.512 50.000 3.32 0.00 45.57 2.74
133 144 2.510613 GGCTACTTTGGCCTTTGTACA 58.489 47.619 3.32 0.00 45.57 2.90
142 153 0.681243 CCTCCCAAGGCTACTTTGGC 60.681 60.000 3.10 0.00 38.93 4.52
143 154 0.991920 TCCTCCCAAGGCTACTTTGG 59.008 55.000 1.69 1.69 43.02 3.28
144 155 2.879103 TTCCTCCCAAGGCTACTTTG 57.121 50.000 0.00 0.00 43.02 2.77
145 156 2.986728 TCTTTCCTCCCAAGGCTACTTT 59.013 45.455 0.00 0.00 43.02 2.66
146 157 2.632537 TCTTTCCTCCCAAGGCTACTT 58.367 47.619 0.00 0.00 43.02 2.24
147 158 2.306219 GTTCTTTCCTCCCAAGGCTACT 59.694 50.000 0.00 0.00 43.02 2.57
148 159 2.039879 TGTTCTTTCCTCCCAAGGCTAC 59.960 50.000 0.00 0.00 43.02 3.58
149 160 2.344592 TGTTCTTTCCTCCCAAGGCTA 58.655 47.619 0.00 0.00 43.02 3.93
150 161 1.149101 TGTTCTTTCCTCCCAAGGCT 58.851 50.000 0.00 0.00 43.02 4.58
151 162 1.889170 CTTGTTCTTTCCTCCCAAGGC 59.111 52.381 0.00 0.00 43.02 4.35
152 163 3.073062 TCTCTTGTTCTTTCCTCCCAAGG 59.927 47.826 0.00 0.00 44.89 3.61
153 164 4.040952 TCTCTCTTGTTCTTTCCTCCCAAG 59.959 45.833 0.00 0.00 35.09 3.61
154 165 3.973973 TCTCTCTTGTTCTTTCCTCCCAA 59.026 43.478 0.00 0.00 0.00 4.12
155 166 3.587498 TCTCTCTTGTTCTTTCCTCCCA 58.413 45.455 0.00 0.00 0.00 4.37
156 167 4.625607 TTCTCTCTTGTTCTTTCCTCCC 57.374 45.455 0.00 0.00 0.00 4.30
157 168 5.239744 GGTTTTCTCTCTTGTTCTTTCCTCC 59.760 44.000 0.00 0.00 0.00 4.30
158 169 5.823045 TGGTTTTCTCTCTTGTTCTTTCCTC 59.177 40.000 0.00 0.00 0.00 3.71
159 170 5.755849 TGGTTTTCTCTCTTGTTCTTTCCT 58.244 37.500 0.00 0.00 0.00 3.36
160 171 5.823045 TCTGGTTTTCTCTCTTGTTCTTTCC 59.177 40.000 0.00 0.00 0.00 3.13
161 172 6.927294 TCTGGTTTTCTCTCTTGTTCTTTC 57.073 37.500 0.00 0.00 0.00 2.62
162 173 7.703058 TTTCTGGTTTTCTCTCTTGTTCTTT 57.297 32.000 0.00 0.00 0.00 2.52
163 174 7.703058 TTTTCTGGTTTTCTCTCTTGTTCTT 57.297 32.000 0.00 0.00 0.00 2.52
164 175 7.611855 TCTTTTTCTGGTTTTCTCTCTTGTTCT 59.388 33.333 0.00 0.00 0.00 3.01
165 176 7.762382 TCTTTTTCTGGTTTTCTCTCTTGTTC 58.238 34.615 0.00 0.00 0.00 3.18
166 177 7.148000 CCTCTTTTTCTGGTTTTCTCTCTTGTT 60.148 37.037 0.00 0.00 0.00 2.83
167 178 6.319911 CCTCTTTTTCTGGTTTTCTCTCTTGT 59.680 38.462 0.00 0.00 0.00 3.16
168 179 6.733145 CCTCTTTTTCTGGTTTTCTCTCTTG 58.267 40.000 0.00 0.00 0.00 3.02
169 180 5.300539 GCCTCTTTTTCTGGTTTTCTCTCTT 59.699 40.000 0.00 0.00 0.00 2.85
170 181 4.824537 GCCTCTTTTTCTGGTTTTCTCTCT 59.175 41.667 0.00 0.00 0.00 3.10
171 182 4.022762 GGCCTCTTTTTCTGGTTTTCTCTC 60.023 45.833 0.00 0.00 0.00 3.20
172 183 3.891977 GGCCTCTTTTTCTGGTTTTCTCT 59.108 43.478 0.00 0.00 0.00 3.10
173 184 3.891977 AGGCCTCTTTTTCTGGTTTTCTC 59.108 43.478 0.00 0.00 0.00 2.87
174 185 3.638627 CAGGCCTCTTTTTCTGGTTTTCT 59.361 43.478 0.00 0.00 0.00 2.52
175 186 3.636764 TCAGGCCTCTTTTTCTGGTTTTC 59.363 43.478 0.00 0.00 0.00 2.29
176 187 3.638627 CTCAGGCCTCTTTTTCTGGTTTT 59.361 43.478 0.00 0.00 0.00 2.43
177 188 3.117512 TCTCAGGCCTCTTTTTCTGGTTT 60.118 43.478 0.00 0.00 0.00 3.27
178 189 2.443255 TCTCAGGCCTCTTTTTCTGGTT 59.557 45.455 0.00 0.00 0.00 3.67
179 190 2.057922 TCTCAGGCCTCTTTTTCTGGT 58.942 47.619 0.00 0.00 0.00 4.00
180 191 2.039613 AGTCTCAGGCCTCTTTTTCTGG 59.960 50.000 0.00 0.00 0.00 3.86
181 192 3.072944 CAGTCTCAGGCCTCTTTTTCTG 58.927 50.000 0.00 3.49 0.00 3.02
182 193 2.039613 CCAGTCTCAGGCCTCTTTTTCT 59.960 50.000 0.00 0.00 0.00 2.52
183 194 2.431454 CCAGTCTCAGGCCTCTTTTTC 58.569 52.381 0.00 0.00 0.00 2.29
184 195 1.074566 CCCAGTCTCAGGCCTCTTTTT 59.925 52.381 0.00 0.00 0.00 1.94
185 196 0.695347 CCCAGTCTCAGGCCTCTTTT 59.305 55.000 0.00 0.00 0.00 2.27
186 197 0.178891 TCCCAGTCTCAGGCCTCTTT 60.179 55.000 0.00 0.00 0.00 2.52
187 198 0.907230 GTCCCAGTCTCAGGCCTCTT 60.907 60.000 0.00 0.00 0.00 2.85
188 199 1.305718 GTCCCAGTCTCAGGCCTCT 60.306 63.158 0.00 0.00 0.00 3.69
189 200 2.716017 CGTCCCAGTCTCAGGCCTC 61.716 68.421 0.00 0.00 0.00 4.70
190 201 2.681778 CGTCCCAGTCTCAGGCCT 60.682 66.667 0.00 0.00 0.00 5.19
191 202 2.680352 TCGTCCCAGTCTCAGGCC 60.680 66.667 0.00 0.00 0.00 5.19
192 203 2.888863 CTCGTCCCAGTCTCAGGC 59.111 66.667 0.00 0.00 0.00 4.85
193 204 2.716017 GGCTCGTCCCAGTCTCAGG 61.716 68.421 0.00 0.00 0.00 3.86
194 205 1.943116 CTGGCTCGTCCCAGTCTCAG 61.943 65.000 13.60 0.00 45.87 3.35
195 206 1.979155 CTGGCTCGTCCCAGTCTCA 60.979 63.158 13.60 0.00 45.87 3.27
196 207 2.888863 CTGGCTCGTCCCAGTCTC 59.111 66.667 13.60 0.00 45.87 3.36
204 215 1.464376 TATAGCTGGGCTGGCTCGTC 61.464 60.000 0.00 0.00 40.10 4.20
205 216 1.457643 TATAGCTGGGCTGGCTCGT 60.458 57.895 0.00 2.79 40.10 4.18
206 217 1.005630 GTATAGCTGGGCTGGCTCG 60.006 63.158 0.00 0.00 40.10 5.03
207 218 0.689623 ATGTATAGCTGGGCTGGCTC 59.310 55.000 0.00 0.00 40.10 4.70
208 219 0.399454 CATGTATAGCTGGGCTGGCT 59.601 55.000 0.00 9.33 40.10 4.75
209 220 0.109342 ACATGTATAGCTGGGCTGGC 59.891 55.000 0.00 0.00 40.10 4.85
210 221 1.271054 GGACATGTATAGCTGGGCTGG 60.271 57.143 0.00 0.00 40.10 4.85
211 222 1.417517 TGGACATGTATAGCTGGGCTG 59.582 52.381 0.00 0.00 40.10 4.85
212 223 1.417890 GTGGACATGTATAGCTGGGCT 59.582 52.381 0.00 0.00 43.41 5.19
213 224 1.873903 CGTGGACATGTATAGCTGGGC 60.874 57.143 0.00 0.00 0.00 5.36
214 225 1.270305 CCGTGGACATGTATAGCTGGG 60.270 57.143 0.00 0.00 0.00 4.45
215 226 1.873903 GCCGTGGACATGTATAGCTGG 60.874 57.143 0.00 0.00 0.00 4.85
216 227 1.202521 TGCCGTGGACATGTATAGCTG 60.203 52.381 0.00 0.00 0.00 4.24
217 228 1.119684 TGCCGTGGACATGTATAGCT 58.880 50.000 0.00 0.00 0.00 3.32
218 229 2.069273 GATGCCGTGGACATGTATAGC 58.931 52.381 0.00 0.00 0.00 2.97
219 230 2.300152 AGGATGCCGTGGACATGTATAG 59.700 50.000 0.00 0.00 0.00 1.31
220 231 2.325484 AGGATGCCGTGGACATGTATA 58.675 47.619 0.00 0.00 0.00 1.47
221 232 1.131638 AGGATGCCGTGGACATGTAT 58.868 50.000 0.00 0.00 0.00 2.29
222 233 1.411246 GTAGGATGCCGTGGACATGTA 59.589 52.381 0.00 0.00 0.00 2.29
223 234 0.178068 GTAGGATGCCGTGGACATGT 59.822 55.000 0.00 0.00 0.00 3.21
224 235 0.465705 AGTAGGATGCCGTGGACATG 59.534 55.000 0.00 0.00 0.00 3.21
225 236 0.753262 GAGTAGGATGCCGTGGACAT 59.247 55.000 0.00 0.00 0.00 3.06
226 237 1.327690 GGAGTAGGATGCCGTGGACA 61.328 60.000 0.00 0.00 0.00 4.02
227 238 1.442148 GGAGTAGGATGCCGTGGAC 59.558 63.158 0.00 0.00 0.00 4.02
228 239 1.760875 GGGAGTAGGATGCCGTGGA 60.761 63.158 0.00 0.00 0.00 4.02
229 240 1.622607 TTGGGAGTAGGATGCCGTGG 61.623 60.000 0.00 0.00 32.30 4.94
230 241 0.179073 CTTGGGAGTAGGATGCCGTG 60.179 60.000 0.00 0.00 32.30 4.94
231 242 1.972660 GCTTGGGAGTAGGATGCCGT 61.973 60.000 0.00 0.00 32.30 5.68
232 243 1.227674 GCTTGGGAGTAGGATGCCG 60.228 63.158 0.00 0.00 32.30 5.69
233 244 1.149401 GGCTTGGGAGTAGGATGCC 59.851 63.158 0.00 0.00 0.00 4.40
234 245 0.107643 GAGGCTTGGGAGTAGGATGC 59.892 60.000 0.00 0.00 0.00 3.91
235 246 0.761802 GGAGGCTTGGGAGTAGGATG 59.238 60.000 0.00 0.00 0.00 3.51
236 247 0.400670 GGGAGGCTTGGGAGTAGGAT 60.401 60.000 0.00 0.00 0.00 3.24
237 248 1.003051 GGGAGGCTTGGGAGTAGGA 59.997 63.158 0.00 0.00 0.00 2.94
238 249 1.003573 AGGGAGGCTTGGGAGTAGG 59.996 63.158 0.00 0.00 0.00 3.18
239 250 1.341156 CCAGGGAGGCTTGGGAGTAG 61.341 65.000 0.00 0.00 0.00 2.57
240 251 1.306997 CCAGGGAGGCTTGGGAGTA 60.307 63.158 0.00 0.00 0.00 2.59
241 252 2.612115 CCAGGGAGGCTTGGGAGT 60.612 66.667 0.00 0.00 0.00 3.85
242 253 2.285668 TCCAGGGAGGCTTGGGAG 60.286 66.667 3.95 0.00 37.29 4.30
243 254 2.285668 CTCCAGGGAGGCTTGGGA 60.286 66.667 7.48 1.23 38.51 4.37
252 263 0.944999 AGATTAGCCTCCTCCAGGGA 59.055 55.000 0.00 0.00 43.70 4.20
253 264 1.347062 GAGATTAGCCTCCTCCAGGG 58.653 60.000 0.00 0.00 43.70 4.45
254 265 2.094100 TGAGATTAGCCTCCTCCAGG 57.906 55.000 0.00 0.00 46.82 4.45
255 266 3.509442 AGATGAGATTAGCCTCCTCCAG 58.491 50.000 0.00 0.00 31.02 3.86
256 267 3.141838 AGAGATGAGATTAGCCTCCTCCA 59.858 47.826 0.00 0.00 31.02 3.86
257 268 3.778265 AGAGATGAGATTAGCCTCCTCC 58.222 50.000 0.00 0.00 31.02 4.30
258 269 8.588290 TTATTAGAGATGAGATTAGCCTCCTC 57.412 38.462 0.00 0.00 32.32 3.71
259 270 8.397957 TCTTATTAGAGATGAGATTAGCCTCCT 58.602 37.037 0.00 0.00 32.32 3.69
260 271 8.588290 TCTTATTAGAGATGAGATTAGCCTCC 57.412 38.462 0.00 0.00 32.32 4.30
261 272 9.855021 GTTCTTATTAGAGATGAGATTAGCCTC 57.145 37.037 0.00 0.00 0.00 4.70
262 273 9.600432 AGTTCTTATTAGAGATGAGATTAGCCT 57.400 33.333 0.00 0.00 0.00 4.58
274 285 8.625651 CGAGGAATCTGAAGTTCTTATTAGAGA 58.374 37.037 4.17 0.00 0.00 3.10
275 286 8.625651 TCGAGGAATCTGAAGTTCTTATTAGAG 58.374 37.037 4.17 0.00 0.00 2.43
276 287 8.521170 TCGAGGAATCTGAAGTTCTTATTAGA 57.479 34.615 4.17 0.00 0.00 2.10
277 288 9.587772 TTTCGAGGAATCTGAAGTTCTTATTAG 57.412 33.333 4.17 0.00 0.00 1.73
279 290 9.454859 AATTTCGAGGAATCTGAAGTTCTTATT 57.545 29.630 4.17 3.92 0.00 1.40
316 328 3.273434 GCATGTCTAAATCTCTGCCACA 58.727 45.455 0.00 0.00 0.00 4.17
371 386 6.187727 TCTGTAGATTTTCCAACAAGAGGT 57.812 37.500 0.00 0.00 0.00 3.85
518 636 9.956720 ATCAAGAAAGAAACACAATAGTTCTTG 57.043 29.630 14.18 14.18 45.99 3.02
696 830 3.702048 GGTAGCTGCCCACCACGA 61.702 66.667 10.19 0.00 34.77 4.35
737 871 4.842091 CTTGCTTGCGCCGCATCC 62.842 66.667 14.63 7.65 38.76 3.51
822 960 2.097825 CGGGGTTATATACGGGAGAGG 58.902 57.143 0.00 0.00 0.00 3.69
972 1162 2.026822 TCTTCTTCTTGGTCCTGATGCC 60.027 50.000 0.00 0.00 0.00 4.40
979 1169 5.418676 CATCTCTTCTCTTCTTCTTGGTCC 58.581 45.833 0.00 0.00 0.00 4.46
1221 1445 3.844090 GTCCTCAGCGCCTCCTCC 61.844 72.222 2.29 0.00 0.00 4.30
1279 1503 4.681942 GCCATGACTACATTCTACTAAGCG 59.318 45.833 0.00 0.00 34.15 4.68
1289 1644 3.713248 TGATCTGAGGCCATGACTACATT 59.287 43.478 5.01 0.00 34.15 2.71
1293 1648 3.319031 TCTGATCTGAGGCCATGACTA 57.681 47.619 5.01 0.00 0.00 2.59
1296 1651 3.434596 CCAAATCTGATCTGAGGCCATGA 60.435 47.826 5.01 0.00 0.00 3.07
1380 1757 8.598041 AGGGTGATATTGAGTGATATAAACTCC 58.402 37.037 13.05 1.87 42.85 3.85
1394 1778 3.459828 TGGACAAGGAGGGTGATATTGA 58.540 45.455 0.00 0.00 0.00 2.57
1395 1779 3.931907 TGGACAAGGAGGGTGATATTG 57.068 47.619 0.00 0.00 0.00 1.90
1396 1780 3.395941 GGATGGACAAGGAGGGTGATATT 59.604 47.826 0.00 0.00 0.00 1.28
1397 1781 2.982488 GGATGGACAAGGAGGGTGATAT 59.018 50.000 0.00 0.00 0.00 1.63
1398 1782 2.293519 TGGATGGACAAGGAGGGTGATA 60.294 50.000 0.00 0.00 0.00 2.15
1399 1783 1.216990 GGATGGACAAGGAGGGTGAT 58.783 55.000 0.00 0.00 0.00 3.06
1400 1784 0.178876 TGGATGGACAAGGAGGGTGA 60.179 55.000 0.00 0.00 0.00 4.02
1401 1785 0.921896 ATGGATGGACAAGGAGGGTG 59.078 55.000 0.00 0.00 0.00 4.61
1402 1786 0.921896 CATGGATGGACAAGGAGGGT 59.078 55.000 0.00 0.00 0.00 4.34
1403 1787 0.466922 GCATGGATGGACAAGGAGGG 60.467 60.000 0.00 0.00 0.00 4.30
1422 1806 4.990543 TCAAACAATAGTCACAGAAGCG 57.009 40.909 0.00 0.00 0.00 4.68
1451 1835 2.805099 CTCTCTTGACAAACACAGCCTC 59.195 50.000 0.00 0.00 0.00 4.70
1497 1882 2.481952 CTCGCTCTGCTAAGTTGCTTTT 59.518 45.455 0.00 0.00 0.00 2.27
1507 1892 1.654774 CGTATGCCTCGCTCTGCTA 59.345 57.895 0.00 0.00 0.00 3.49
1525 1910 5.532779 ACTGAATGAAGTTCCTCTGTTTTCC 59.467 40.000 0.00 0.00 35.91 3.13
1551 1937 1.327460 CTGTTCGGTAATCGGCACATG 59.673 52.381 0.00 0.00 39.77 3.21
1552 1938 1.651987 CTGTTCGGTAATCGGCACAT 58.348 50.000 0.00 0.00 39.77 3.21
1556 1942 2.178235 GGGCTGTTCGGTAATCGGC 61.178 63.158 0.00 0.00 39.77 5.54
1557 1943 0.391927 TTGGGCTGTTCGGTAATCGG 60.392 55.000 0.00 0.00 39.77 4.18
1590 1976 3.412237 TCTCTTTCCCCCTGTTTTACG 57.588 47.619 0.00 0.00 0.00 3.18
1679 2065 7.255277 GCAAAGAAATTCAGAACAGGTTAGTCT 60.255 37.037 0.00 0.00 0.00 3.24
1709 2095 4.003788 CGGGGTTCAGCGGAGTGT 62.004 66.667 0.00 0.00 0.00 3.55
1715 2101 0.806102 CATACAGTCGGGGTTCAGCG 60.806 60.000 0.00 0.00 0.00 5.18
1716 2102 0.535335 TCATACAGTCGGGGTTCAGC 59.465 55.000 0.00 0.00 0.00 4.26
1722 2108 2.698797 ACTTGGTATCATACAGTCGGGG 59.301 50.000 0.00 0.00 0.00 5.73
1723 2109 4.142026 TGAACTTGGTATCATACAGTCGGG 60.142 45.833 0.00 0.00 0.00 5.14
1729 2115 8.726988 GCTTTTAGTTGAACTTGGTATCATACA 58.273 33.333 1.97 0.00 0.00 2.29
1731 2117 8.856153 TGCTTTTAGTTGAACTTGGTATCATA 57.144 30.769 1.97 0.00 0.00 2.15
1733 2119 7.446931 TCATGCTTTTAGTTGAACTTGGTATCA 59.553 33.333 1.97 0.00 0.00 2.15
1745 2131 5.330295 GCACTCTGATCATGCTTTTAGTTG 58.670 41.667 11.67 0.00 36.40 3.16
1820 2214 2.568090 CAAATGGGACTGCGGTGC 59.432 61.111 8.99 8.99 0.00 5.01
1823 2217 1.080569 GTTGCAAATGGGACTGCGG 60.081 57.895 0.00 0.00 41.63 5.69
1884 2278 2.789917 GCGTCAGCAGGCATTCAG 59.210 61.111 0.00 0.00 44.35 3.02
1921 2315 6.647212 TGCGTCACATAATTCAGTTCTTAG 57.353 37.500 0.00 0.00 0.00 2.18
1935 2329 5.237815 TCTAAATCTCTGTTTGCGTCACAT 58.762 37.500 0.00 0.00 0.00 3.21
2002 2396 6.751888 ACAACTTGCAACATTTAGTTCAAGAC 59.248 34.615 18.14 0.00 42.02 3.01
2046 2440 3.058224 GGTACAAATGGACAGCAACTCAC 60.058 47.826 0.00 0.00 0.00 3.51
2047 2441 3.146066 GGTACAAATGGACAGCAACTCA 58.854 45.455 0.00 0.00 0.00 3.41
2094 2488 3.188460 GCAAGGCGATAACACAAAGAAGA 59.812 43.478 0.00 0.00 0.00 2.87
2117 2511 4.632153 TGTAAGGTCTTCTTCAGTTGAGC 58.368 43.478 0.00 0.00 36.93 4.26
2118 2512 5.641209 CCATGTAAGGTCTTCTTCAGTTGAG 59.359 44.000 0.00 0.00 36.93 3.02
2131 2525 5.872070 GCATAGAAGCTATCCATGTAAGGTC 59.128 44.000 0.00 0.00 30.73 3.85
2145 2539 2.756760 CCACCAAATGTGCATAGAAGCT 59.243 45.455 0.00 0.00 44.01 3.74
2170 2568 2.620115 CACAGCCACAAGACAAGACAAT 59.380 45.455 0.00 0.00 0.00 2.71
2171 2569 2.016318 CACAGCCACAAGACAAGACAA 58.984 47.619 0.00 0.00 0.00 3.18
2172 2570 1.667236 CACAGCCACAAGACAAGACA 58.333 50.000 0.00 0.00 0.00 3.41
2209 2607 3.744660 GCTGTTGCCCTAATATGCTAGT 58.255 45.455 0.00 0.00 0.00 2.57
2229 2627 2.137177 TAAAGTGGAGGCAGTGGGGC 62.137 60.000 0.00 0.00 43.80 5.80
2230 2628 0.625849 ATAAAGTGGAGGCAGTGGGG 59.374 55.000 0.00 0.00 0.00 4.96
2231 2629 2.094675 CAATAAAGTGGAGGCAGTGGG 58.905 52.381 0.00 0.00 0.00 4.61
2232 2630 3.012518 CTCAATAAAGTGGAGGCAGTGG 58.987 50.000 0.00 0.00 0.00 4.00
2233 2631 3.942829 TCTCAATAAAGTGGAGGCAGTG 58.057 45.455 0.00 0.00 0.00 3.66
2234 2632 4.202461 TGTTCTCAATAAAGTGGAGGCAGT 60.202 41.667 0.00 0.00 0.00 4.40
2235 2633 4.326826 TGTTCTCAATAAAGTGGAGGCAG 58.673 43.478 0.00 0.00 0.00 4.85
2236 2634 4.365514 TGTTCTCAATAAAGTGGAGGCA 57.634 40.909 0.00 0.00 0.00 4.75
2237 2635 5.705609 TTTGTTCTCAATAAAGTGGAGGC 57.294 39.130 0.00 0.00 33.32 4.70
2238 2636 7.510549 TCTTTTGTTCTCAATAAAGTGGAGG 57.489 36.000 0.00 0.00 33.32 4.30
2240 2638 9.793259 AGTATCTTTTGTTCTCAATAAAGTGGA 57.207 29.630 0.00 0.00 33.32 4.02


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

AutoCloner maintained by Alex Coulton.