Multiple sequence alignment - TraesCS6D01G270000

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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 TraesCS6D01G270000 chr6D 100.000 2821 0 0 1 2821 379725390 379722570 0.000000e+00 5210.0
1 TraesCS6D01G270000 chr6D 92.273 220 17 0 89 308 427337296 427337077 2.110000e-81 313.0
2 TraesCS6D01G270000 chr6A 85.314 1641 107 55 306 1867 520868846 520870431 0.000000e+00 1572.0
3 TraesCS6D01G270000 chr6A 91.371 394 19 10 2429 2821 520870960 520871339 2.490000e-145 525.0
4 TraesCS6D01G270000 chr6A 85.347 505 39 21 1976 2473 520870480 520870956 9.080000e-135 490.0
5 TraesCS6D01G270000 chr6A 86.590 261 32 1 2561 2821 90034061 90033804 4.600000e-73 285.0
6 TraesCS6D01G270000 chr6B 91.126 924 44 11 936 1836 566535052 566535960 0.000000e+00 1218.0
7 TraesCS6D01G270000 chr6B 92.488 639 41 5 2184 2821 566536174 566536806 0.000000e+00 907.0
8 TraesCS6D01G270000 chr6B 86.137 642 38 21 306 936 566534405 566535006 0.000000e+00 645.0
9 TraesCS6D01G270000 chr7D 94.570 221 11 1 89 309 102943432 102943651 9.680000e-90 340.0
10 TraesCS6D01G270000 chr7D 93.578 218 14 0 89 306 565390470 565390687 2.710000e-85 326.0
11 TraesCS6D01G270000 chr7D 91.928 223 17 1 89 311 493774560 493774781 7.590000e-81 311.0
12 TraesCS6D01G270000 chr7D 88.235 153 17 1 1376 1528 136253350 136253199 6.210000e-42 182.0
13 TraesCS6D01G270000 chr4D 93.119 218 15 0 89 306 6027125 6026908 1.260000e-83 320.0
14 TraesCS6D01G270000 chr3D 92.000 225 18 0 89 313 501043800 501044024 1.630000e-82 316.0
15 TraesCS6D01G270000 chr3D 92.694 219 15 1 89 306 542377310 542377528 5.870000e-82 315.0
16 TraesCS6D01G270000 chr5D 92.661 218 16 0 89 306 541577769 541577986 5.870000e-82 315.0
17 TraesCS6D01G270000 chr5D 92.273 220 17 0 89 308 476712116 476711897 2.110000e-81 313.0
18 TraesCS6D01G270000 chr5D 84.416 77 10 2 1404 1479 113391589 113391514 1.080000e-09 75.0
19 TraesCS6D01G270000 chr7B 88.235 153 17 1 1376 1528 99130796 99130645 6.210000e-42 182.0
20 TraesCS6D01G270000 chr7B 100.000 35 0 0 1918 1952 11836923 11836957 6.520000e-07 65.8
21 TraesCS6D01G270000 chr5B 84.146 82 11 2 1404 1484 123760773 123760693 8.380000e-11 78.7
22 TraesCS6D01G270000 chr5A 84.146 82 11 2 1404 1484 118670814 118670734 8.380000e-11 78.7
23 TraesCS6D01G270000 chr7A 97.500 40 1 0 1918 1957 75159197 75159236 5.040000e-08 69.4


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 TraesCS6D01G270000 chr6D 379722570 379725390 2820 True 5210.000000 5210 100.000 1 2821 1 chr6D.!!$R1 2820
1 TraesCS6D01G270000 chr6A 520868846 520871339 2493 False 862.333333 1572 87.344 306 2821 3 chr6A.!!$F1 2515
2 TraesCS6D01G270000 chr6B 566534405 566536806 2401 False 923.333333 1218 89.917 306 2821 3 chr6B.!!$F1 2515

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
289 290 0.033601 TTTGGCCACTTATGCGGGAT 60.034 50.0 3.88 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2092 0.178873 TGCTCTCCTTTGTACCCCCT 60.179 55.0 0.0 0.0 0.0 4.79 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
105 106 4.573162 CTCCGTCGAGGTTTGACC 57.427 61.111 4.18 0.00 41.99 4.02
106 107 1.443872 CTCCGTCGAGGTTTGACCG 60.444 63.158 4.18 0.00 44.90 4.79
107 108 2.431942 CCGTCGAGGTTTGACCGG 60.432 66.667 0.00 0.00 44.90 5.28
108 109 2.337532 CGTCGAGGTTTGACCGGT 59.662 61.111 6.92 6.92 44.90 5.28
109 110 1.580942 CGTCGAGGTTTGACCGGTA 59.419 57.895 7.34 0.00 44.90 4.02
110 111 0.171903 CGTCGAGGTTTGACCGGTAT 59.828 55.000 7.34 0.00 44.90 2.73
111 112 1.401552 CGTCGAGGTTTGACCGGTATA 59.598 52.381 7.34 0.00 44.90 1.47
112 113 2.792542 CGTCGAGGTTTGACCGGTATAC 60.793 54.545 7.34 5.81 44.90 1.47
113 114 1.401552 TCGAGGTTTGACCGGTATACG 59.598 52.381 7.34 7.25 44.90 3.06
122 123 4.948080 CGGTATACGGGGCCCCCT 62.948 72.222 36.13 26.48 42.67 4.79
123 124 2.532906 GGTATACGGGGCCCCCTA 59.467 66.667 36.13 27.85 42.67 3.53
124 125 1.081648 GGTATACGGGGCCCCCTAT 59.918 63.158 36.13 31.90 42.67 2.57
125 126 0.339510 GGTATACGGGGCCCCCTATA 59.660 60.000 36.13 30.83 42.67 1.31
126 127 1.061889 GGTATACGGGGCCCCCTATAT 60.062 57.143 36.13 28.73 42.67 0.86
127 128 2.630452 GGTATACGGGGCCCCCTATATT 60.630 54.545 36.13 15.30 42.67 1.28
128 129 1.889174 ATACGGGGCCCCCTATATTC 58.111 55.000 36.13 7.91 42.67 1.75
129 130 0.615544 TACGGGGCCCCCTATATTCG 60.616 60.000 36.13 22.49 42.67 3.34
130 131 2.666098 CGGGGCCCCCTATATTCGG 61.666 68.421 36.13 14.10 42.67 4.30
131 132 2.675371 GGGCCCCCTATATTCGGC 59.325 66.667 12.23 0.00 40.85 5.54
133 134 3.821886 GCCCCCTATATTCGGCCT 58.178 61.111 0.00 0.00 35.23 5.19
134 135 2.075837 GCCCCCTATATTCGGCCTT 58.924 57.895 0.00 0.00 35.23 4.35
135 136 0.035343 GCCCCCTATATTCGGCCTTC 60.035 60.000 0.00 0.00 35.23 3.46
136 137 0.618981 CCCCCTATATTCGGCCTTCC 59.381 60.000 0.00 0.00 0.00 3.46
137 138 1.358152 CCCCTATATTCGGCCTTCCA 58.642 55.000 0.00 0.00 0.00 3.53
138 139 1.702957 CCCCTATATTCGGCCTTCCAA 59.297 52.381 0.00 0.00 0.00 3.53
139 140 2.552373 CCCCTATATTCGGCCTTCCAAC 60.552 54.545 0.00 0.00 0.00 3.77
140 141 2.552373 CCCTATATTCGGCCTTCCAACC 60.552 54.545 0.00 0.00 0.00 3.77
141 142 2.372172 CCTATATTCGGCCTTCCAACCT 59.628 50.000 0.00 0.00 0.00 3.50
142 143 2.640316 ATATTCGGCCTTCCAACCTC 57.360 50.000 0.00 0.00 0.00 3.85
143 144 0.544697 TATTCGGCCTTCCAACCTCC 59.455 55.000 0.00 0.00 0.00 4.30
144 145 1.497309 ATTCGGCCTTCCAACCTCCA 61.497 55.000 0.00 0.00 0.00 3.86
145 146 1.710996 TTCGGCCTTCCAACCTCCAA 61.711 55.000 0.00 0.00 0.00 3.53
146 147 1.228429 CGGCCTTCCAACCTCCAAA 60.228 57.895 0.00 0.00 0.00 3.28
147 148 1.244019 CGGCCTTCCAACCTCCAAAG 61.244 60.000 0.00 0.00 0.00 2.77
148 149 0.112412 GGCCTTCCAACCTCCAAAGA 59.888 55.000 0.00 0.00 0.00 2.52
149 150 1.272704 GGCCTTCCAACCTCCAAAGAT 60.273 52.381 0.00 0.00 0.00 2.40
150 151 2.025321 GGCCTTCCAACCTCCAAAGATA 60.025 50.000 0.00 0.00 0.00 1.98
151 152 3.563479 GGCCTTCCAACCTCCAAAGATAA 60.563 47.826 0.00 0.00 0.00 1.75
152 153 3.696548 GCCTTCCAACCTCCAAAGATAAG 59.303 47.826 0.00 0.00 0.00 1.73
153 154 4.567747 GCCTTCCAACCTCCAAAGATAAGA 60.568 45.833 0.00 0.00 0.00 2.10
154 155 5.189180 CCTTCCAACCTCCAAAGATAAGAG 58.811 45.833 0.00 0.00 0.00 2.85
155 156 5.280727 CCTTCCAACCTCCAAAGATAAGAGT 60.281 44.000 0.00 0.00 0.00 3.24
156 157 5.843019 TCCAACCTCCAAAGATAAGAGTT 57.157 39.130 0.00 0.00 0.00 3.01
157 158 6.200878 TCCAACCTCCAAAGATAAGAGTTT 57.799 37.500 0.00 0.00 0.00 2.66
158 159 6.238648 TCCAACCTCCAAAGATAAGAGTTTC 58.761 40.000 0.00 0.00 0.00 2.78
159 160 5.122396 CCAACCTCCAAAGATAAGAGTTTCG 59.878 44.000 0.00 0.00 0.00 3.46
160 161 4.833390 ACCTCCAAAGATAAGAGTTTCGG 58.167 43.478 0.00 0.00 0.00 4.30
161 162 4.192317 CCTCCAAAGATAAGAGTTTCGGG 58.808 47.826 0.00 0.00 0.00 5.14
162 163 4.323562 CCTCCAAAGATAAGAGTTTCGGGT 60.324 45.833 0.00 0.00 0.00 5.28
163 164 4.575885 TCCAAAGATAAGAGTTTCGGGTG 58.424 43.478 0.00 0.00 0.00 4.61
164 165 4.041198 TCCAAAGATAAGAGTTTCGGGTGT 59.959 41.667 0.00 0.00 0.00 4.16
165 166 5.246656 TCCAAAGATAAGAGTTTCGGGTGTA 59.753 40.000 0.00 0.00 0.00 2.90
166 167 5.350640 CCAAAGATAAGAGTTTCGGGTGTAC 59.649 44.000 0.00 0.00 0.00 2.90
167 168 5.733620 AAGATAAGAGTTTCGGGTGTACA 57.266 39.130 0.00 0.00 0.00 2.90
168 169 5.934402 AGATAAGAGTTTCGGGTGTACAT 57.066 39.130 0.00 0.00 0.00 2.29
169 170 6.295719 AGATAAGAGTTTCGGGTGTACATT 57.704 37.500 0.00 0.00 0.00 2.71
170 171 6.708285 AGATAAGAGTTTCGGGTGTACATTT 58.292 36.000 0.00 0.00 0.00 2.32
171 172 6.594159 AGATAAGAGTTTCGGGTGTACATTTG 59.406 38.462 0.00 0.00 0.00 2.32
172 173 2.812011 AGAGTTTCGGGTGTACATTTGC 59.188 45.455 0.00 0.00 0.00 3.68
173 174 1.533731 AGTTTCGGGTGTACATTTGCG 59.466 47.619 0.00 0.00 0.00 4.85
174 175 0.875728 TTTCGGGTGTACATTTGCGG 59.124 50.000 0.00 0.00 0.00 5.69
175 176 0.250381 TTCGGGTGTACATTTGCGGT 60.250 50.000 0.00 0.00 0.00 5.68
176 177 0.951525 TCGGGTGTACATTTGCGGTG 60.952 55.000 0.00 0.00 0.00 4.94
177 178 1.880186 GGGTGTACATTTGCGGTGG 59.120 57.895 0.00 0.00 0.00 4.61
178 179 1.211709 GGTGTACATTTGCGGTGGC 59.788 57.895 0.00 0.00 40.52 5.01
179 180 1.211709 GTGTACATTTGCGGTGGCC 59.788 57.895 0.00 0.00 38.85 5.36
180 181 1.974343 TGTACATTTGCGGTGGCCC 60.974 57.895 0.00 0.00 38.85 5.80
181 182 1.677633 GTACATTTGCGGTGGCCCT 60.678 57.895 0.00 0.00 38.85 5.19
182 183 1.075836 TACATTTGCGGTGGCCCTT 59.924 52.632 0.00 0.00 38.85 3.95
183 184 0.328592 TACATTTGCGGTGGCCCTTA 59.671 50.000 0.00 0.00 38.85 2.69
184 185 0.540830 ACATTTGCGGTGGCCCTTAA 60.541 50.000 0.00 0.00 38.85 1.85
185 186 0.605589 CATTTGCGGTGGCCCTTAAA 59.394 50.000 0.00 0.00 38.85 1.52
186 187 1.001406 CATTTGCGGTGGCCCTTAAAA 59.999 47.619 0.00 0.00 38.85 1.52
187 188 1.120530 TTTGCGGTGGCCCTTAAAAA 58.879 45.000 0.00 0.00 38.85 1.94
208 209 7.908827 AAAAATTTACGGTTTTGACCACTTT 57.091 28.000 0.00 0.00 0.00 2.66
209 210 7.908827 AAAATTTACGGTTTTGACCACTTTT 57.091 28.000 0.00 0.00 0.00 2.27
210 211 8.999220 AAAATTTACGGTTTTGACCACTTTTA 57.001 26.923 0.00 0.00 0.00 1.52
211 212 7.990541 AATTTACGGTTTTGACCACTTTTAC 57.009 32.000 0.00 0.00 0.00 2.01
212 213 3.678915 ACGGTTTTGACCACTTTTACG 57.321 42.857 0.00 0.00 0.00 3.18
213 214 2.355444 ACGGTTTTGACCACTTTTACGG 59.645 45.455 0.00 0.00 0.00 4.02
214 215 2.355444 CGGTTTTGACCACTTTTACGGT 59.645 45.455 0.00 0.00 38.56 4.83
215 216 3.181498 CGGTTTTGACCACTTTTACGGTT 60.181 43.478 0.00 0.00 34.99 4.44
216 217 4.674885 CGGTTTTGACCACTTTTACGGTTT 60.675 41.667 0.00 0.00 34.99 3.27
217 218 4.799949 GGTTTTGACCACTTTTACGGTTTC 59.200 41.667 0.00 0.00 34.99 2.78
218 219 5.393352 GGTTTTGACCACTTTTACGGTTTCT 60.393 40.000 0.00 0.00 34.99 2.52
219 220 4.886247 TTGACCACTTTTACGGTTTCTG 57.114 40.909 0.00 0.00 34.99 3.02
220 221 3.876341 TGACCACTTTTACGGTTTCTGT 58.124 40.909 0.00 0.00 34.99 3.41
221 222 4.263435 TGACCACTTTTACGGTTTCTGTT 58.737 39.130 0.00 0.00 34.99 3.16
222 223 4.333372 TGACCACTTTTACGGTTTCTGTTC 59.667 41.667 0.00 0.00 34.99 3.18
223 224 4.520179 ACCACTTTTACGGTTTCTGTTCT 58.480 39.130 0.00 0.00 28.43 3.01
224 225 4.334481 ACCACTTTTACGGTTTCTGTTCTG 59.666 41.667 0.00 0.00 28.43 3.02
225 226 4.261031 CCACTTTTACGGTTTCTGTTCTGG 60.261 45.833 0.00 0.00 0.00 3.86
226 227 3.314357 ACTTTTACGGTTTCTGTTCTGGC 59.686 43.478 0.00 0.00 0.00 4.85
227 228 2.623878 TTACGGTTTCTGTTCTGGCA 57.376 45.000 0.00 0.00 0.00 4.92
228 229 2.623878 TACGGTTTCTGTTCTGGCAA 57.376 45.000 0.00 0.00 0.00 4.52
229 230 1.021968 ACGGTTTCTGTTCTGGCAAC 58.978 50.000 0.00 0.00 0.00 4.17
230 231 1.308998 CGGTTTCTGTTCTGGCAACT 58.691 50.000 0.00 0.00 37.61 3.16
231 232 1.676006 CGGTTTCTGTTCTGGCAACTT 59.324 47.619 0.00 0.00 37.61 2.66
232 233 2.099098 CGGTTTCTGTTCTGGCAACTTT 59.901 45.455 0.00 0.00 37.61 2.66
233 234 3.428862 CGGTTTCTGTTCTGGCAACTTTT 60.429 43.478 0.00 0.00 37.61 2.27
234 235 4.503910 GGTTTCTGTTCTGGCAACTTTTT 58.496 39.130 0.00 0.00 37.61 1.94
254 255 5.532025 TTTTTGCCCAAAACTGTAAAACG 57.468 34.783 5.73 0.00 39.70 3.60
255 256 2.211353 TGCCCAAAACTGTAAAACGC 57.789 45.000 0.00 0.00 0.00 4.84
256 257 1.476891 TGCCCAAAACTGTAAAACGCA 59.523 42.857 0.00 0.00 0.00 5.24
257 258 2.094182 TGCCCAAAACTGTAAAACGCAA 60.094 40.909 0.00 0.00 0.00 4.85
258 259 2.930682 GCCCAAAACTGTAAAACGCAAA 59.069 40.909 0.00 0.00 0.00 3.68
259 260 3.371285 GCCCAAAACTGTAAAACGCAAAA 59.629 39.130 0.00 0.00 0.00 2.44
260 261 4.142881 GCCCAAAACTGTAAAACGCAAAAA 60.143 37.500 0.00 0.00 0.00 1.94
279 280 4.991789 AAAATTTATGGGTTTGGCCACT 57.008 36.364 3.88 0.00 39.65 4.00
280 281 4.991789 AAATTTATGGGTTTGGCCACTT 57.008 36.364 3.88 0.00 39.65 3.16
281 282 6.441088 AAAATTTATGGGTTTGGCCACTTA 57.559 33.333 3.88 0.00 39.65 2.24
282 283 6.634889 AAATTTATGGGTTTGGCCACTTAT 57.365 33.333 3.88 0.00 39.65 1.73
283 284 5.612725 ATTTATGGGTTTGGCCACTTATG 57.387 39.130 3.88 0.00 39.65 1.90
284 285 1.194218 ATGGGTTTGGCCACTTATGC 58.806 50.000 3.88 0.00 39.65 3.14
285 286 1.247419 TGGGTTTGGCCACTTATGCG 61.247 55.000 3.88 0.00 39.65 4.73
286 287 1.510844 GGTTTGGCCACTTATGCGG 59.489 57.895 3.88 0.00 37.17 5.69
287 288 1.510844 GTTTGGCCACTTATGCGGG 59.489 57.895 3.88 0.00 0.00 6.13
288 289 0.963355 GTTTGGCCACTTATGCGGGA 60.963 55.000 3.88 0.00 0.00 5.14
289 290 0.033601 TTTGGCCACTTATGCGGGAT 60.034 50.000 3.88 0.00 0.00 3.85
290 291 0.465460 TTGGCCACTTATGCGGGATC 60.465 55.000 3.88 0.00 0.00 3.36
291 292 1.344953 TGGCCACTTATGCGGGATCT 61.345 55.000 0.00 0.00 0.00 2.75
292 293 0.886490 GGCCACTTATGCGGGATCTG 60.886 60.000 0.00 0.00 0.00 2.90
293 294 1.510480 GCCACTTATGCGGGATCTGC 61.510 60.000 3.88 3.88 0.00 4.26
294 295 0.107456 CCACTTATGCGGGATCTGCT 59.893 55.000 10.94 1.54 0.00 4.24
295 296 1.344438 CCACTTATGCGGGATCTGCTA 59.656 52.381 10.94 0.36 0.00 3.49
296 297 2.611473 CCACTTATGCGGGATCTGCTAG 60.611 54.545 10.94 8.36 0.00 3.42
297 298 2.297315 CACTTATGCGGGATCTGCTAGA 59.703 50.000 10.94 0.00 0.00 2.43
298 299 2.560542 ACTTATGCGGGATCTGCTAGAG 59.439 50.000 10.94 8.25 0.00 2.43
299 300 2.586648 TATGCGGGATCTGCTAGAGA 57.413 50.000 10.94 0.00 34.25 3.10
300 301 1.935799 ATGCGGGATCTGCTAGAGAT 58.064 50.000 10.94 0.00 44.78 2.75
301 302 0.964700 TGCGGGATCTGCTAGAGATG 59.035 55.000 10.94 0.00 41.91 2.90
302 303 0.965439 GCGGGATCTGCTAGAGATGT 59.035 55.000 8.78 0.00 41.91 3.06
303 304 1.342819 GCGGGATCTGCTAGAGATGTT 59.657 52.381 8.78 0.00 41.91 2.71
304 305 2.609244 GCGGGATCTGCTAGAGATGTTC 60.609 54.545 8.78 0.00 41.91 3.18
384 385 1.382629 GGGCCACAGTAACACCCAT 59.617 57.895 4.39 0.00 40.52 4.00
385 386 0.251608 GGGCCACAGTAACACCCATT 60.252 55.000 4.39 0.00 40.52 3.16
390 391 3.343617 CCACAGTAACACCCATTACAGG 58.656 50.000 0.00 0.00 37.49 4.00
470 472 4.923415 AGAAATTTCTGGTAGGAACCCTG 58.077 43.478 19.86 0.00 46.16 4.45
484 486 1.149101 ACCCTGGAAGAAGGCAAGAA 58.851 50.000 0.00 0.00 35.85 2.52
485 487 1.074566 ACCCTGGAAGAAGGCAAGAAG 59.925 52.381 0.00 0.00 35.85 2.85
490 492 3.480470 TGGAAGAAGGCAAGAAGAACTG 58.520 45.455 0.00 0.00 0.00 3.16
493 495 3.567478 AGAAGGCAAGAAGAACTGTGT 57.433 42.857 0.00 0.00 0.00 3.72
507 509 2.828877 ACTGTGTCCGAAAACGATGAA 58.171 42.857 0.00 0.00 0.00 2.57
538 551 5.945310 TGTATCATACCCGGTAGAGTAACT 58.055 41.667 0.00 0.00 0.00 2.24
541 554 1.767759 TACCCGGTAGAGTAACTGGC 58.232 55.000 0.00 0.00 43.53 4.85
552 565 2.676342 GAGTAACTGGCCCATGTTTACG 59.324 50.000 0.00 0.00 0.00 3.18
618 631 3.578282 ACCCCTTTGACAATTCATTCACC 59.422 43.478 0.00 0.00 0.00 4.02
620 633 3.367292 CCCTTTGACAATTCATTCACCCG 60.367 47.826 0.00 0.00 0.00 5.28
621 634 3.367292 CCTTTGACAATTCATTCACCCGG 60.367 47.826 0.00 0.00 0.00 5.73
622 635 2.869101 TGACAATTCATTCACCCGGA 57.131 45.000 0.73 0.00 0.00 5.14
624 637 2.224646 TGACAATTCATTCACCCGGACA 60.225 45.455 0.73 0.00 0.00 4.02
625 638 3.016736 GACAATTCATTCACCCGGACAT 58.983 45.455 0.73 0.00 0.00 3.06
659 672 0.107268 GTTACCCAACCACCGTGTCT 59.893 55.000 0.00 0.00 0.00 3.41
677 690 0.747283 CTCTGAATGGCCTCAGCACC 60.747 60.000 15.57 0.00 42.25 5.01
706 719 2.223144 GTGCGAGTGATGTGCTACAAAA 59.777 45.455 0.00 0.00 0.00 2.44
707 720 2.480037 TGCGAGTGATGTGCTACAAAAG 59.520 45.455 0.00 0.00 0.00 2.27
716 729 2.877691 CTACAAAAGCTGCCCGGC 59.122 61.111 1.04 1.04 0.00 6.13
717 730 2.675075 TACAAAAGCTGCCCGGCC 60.675 61.111 7.03 0.00 0.00 6.13
732 745 2.825836 GCCCTGCACCTCATTCCG 60.826 66.667 0.00 0.00 0.00 4.30
764 778 1.701545 GATCGCGGCGAACAAATGGA 61.702 55.000 29.93 2.72 39.99 3.41
766 780 2.202298 GCGGCGAACAAATGGACG 60.202 61.111 12.98 0.00 41.87 4.79
805 819 2.170187 ACATTTTCCAAAAGCTGGCACA 59.830 40.909 0.00 0.00 45.98 4.57
821 837 5.667644 GCTGGCACAAATAATAAAACAACGC 60.668 40.000 0.00 0.00 38.70 4.84
852 868 2.487986 CCCATCAAGACCCCTGCTAATC 60.488 54.545 0.00 0.00 0.00 1.75
853 869 2.487986 CCATCAAGACCCCTGCTAATCC 60.488 54.545 0.00 0.00 0.00 3.01
871 895 1.680522 CCCTGATCCCAGTCTCGGTG 61.681 65.000 0.00 0.00 38.74 4.94
894 919 4.703897 CCAATCCCATGTCGTTATGTAGT 58.296 43.478 0.00 0.00 0.00 2.73
896 921 5.694910 CCAATCCCATGTCGTTATGTAGTAC 59.305 44.000 0.00 0.00 0.00 2.73
900 925 6.359804 TCCCATGTCGTTATGTAGTACTAGT 58.640 40.000 1.87 0.00 0.00 2.57
901 926 7.508687 TCCCATGTCGTTATGTAGTACTAGTA 58.491 38.462 1.87 0.00 0.00 1.82
902 927 7.442364 TCCCATGTCGTTATGTAGTACTAGTAC 59.558 40.741 23.03 23.03 36.35 2.73
903 928 7.286508 CCATGTCGTTATGTAGTACTAGTACG 58.713 42.308 23.87 14.36 40.80 3.67
904 929 6.828502 TGTCGTTATGTAGTACTAGTACGG 57.171 41.667 23.87 9.62 40.80 4.02
905 930 6.569780 TGTCGTTATGTAGTACTAGTACGGA 58.430 40.000 23.87 15.09 40.80 4.69
906 931 6.697455 TGTCGTTATGTAGTACTAGTACGGAG 59.303 42.308 23.87 12.42 40.80 4.63
929 954 6.640518 AGTAGTATGTGCAAGCTAAGCTAAA 58.359 36.000 11.76 0.00 38.25 1.85
1117 1208 3.138798 TACCTCTCGGCTGCGACC 61.139 66.667 0.00 0.00 0.00 4.79
1561 1661 2.863153 GTGCTGCGCGACAATTCT 59.137 55.556 12.10 0.00 0.00 2.40
1562 1662 1.207593 GTGCTGCGCGACAATTCTT 59.792 52.632 12.10 0.00 0.00 2.52
1563 1663 0.790866 GTGCTGCGCGACAATTCTTC 60.791 55.000 12.10 0.00 0.00 2.87
1567 1667 1.298157 TGCGCGACAATTCTTCCCTG 61.298 55.000 12.10 0.00 0.00 4.45
1616 1725 3.708220 CTCGAGAAGCTCCCGGTGC 62.708 68.421 6.58 4.38 0.00 5.01
1618 1727 4.821589 GAGAAGCTCCCGGTGCCG 62.822 72.222 12.27 3.25 39.44 5.69
1650 1759 1.605451 TGGAGGACGCGGAAGAAGA 60.605 57.895 12.47 0.00 0.00 2.87
1651 1760 1.183030 TGGAGGACGCGGAAGAAGAA 61.183 55.000 12.47 0.00 0.00 2.52
1655 1764 0.458716 GGACGCGGAAGAAGAAGAGG 60.459 60.000 12.47 0.00 0.00 3.69
1656 1765 0.458716 GACGCGGAAGAAGAAGAGGG 60.459 60.000 12.47 0.00 0.00 4.30
1684 1803 6.426327 GGTGATATGATCGACTAGATGATCG 58.574 44.000 17.81 8.68 43.10 3.69
1685 1804 6.426327 GTGATATGATCGACTAGATGATCGG 58.574 44.000 17.81 0.00 43.10 4.18
1703 1828 8.689251 ATGATCGGTGTTATTATATGAGAACG 57.311 34.615 1.20 0.00 0.00 3.95
1730 1855 5.957842 TTACCATTTTTGTACCTCTGCTG 57.042 39.130 0.00 0.00 0.00 4.41
1740 1868 1.857965 ACCTCTGCTGTGCTCTATGA 58.142 50.000 0.00 0.00 0.00 2.15
1803 1931 4.433615 CCAGTGTTGGCATGTACTACTAG 58.566 47.826 0.00 0.00 37.73 2.57
1874 2018 9.755804 TTCATAATCTTCTGTCATCATGTACTC 57.244 33.333 0.00 0.00 0.00 2.59
1875 2019 8.363390 TCATAATCTTCTGTCATCATGTACTCC 58.637 37.037 0.00 0.00 0.00 3.85
1876 2020 5.543507 ATCTTCTGTCATCATGTACTCCC 57.456 43.478 0.00 0.00 0.00 4.30
1877 2021 4.614475 TCTTCTGTCATCATGTACTCCCT 58.386 43.478 0.00 0.00 0.00 4.20
1879 2023 4.256983 TCTGTCATCATGTACTCCCTCT 57.743 45.455 0.00 0.00 0.00 3.69
1881 2025 5.958321 TCTGTCATCATGTACTCCCTCTAT 58.042 41.667 0.00 0.00 0.00 1.98
1882 2026 6.007076 TCTGTCATCATGTACTCCCTCTATC 58.993 44.000 0.00 0.00 0.00 2.08
1883 2027 5.705400 TGTCATCATGTACTCCCTCTATCA 58.295 41.667 0.00 0.00 0.00 2.15
1884 2028 6.136155 TGTCATCATGTACTCCCTCTATCAA 58.864 40.000 0.00 0.00 0.00 2.57
1885 2029 6.266330 TGTCATCATGTACTCCCTCTATCAAG 59.734 42.308 0.00 0.00 0.00 3.02
1886 2030 6.491745 GTCATCATGTACTCCCTCTATCAAGA 59.508 42.308 0.00 0.00 0.00 3.02
1887 2031 7.014711 GTCATCATGTACTCCCTCTATCAAGAA 59.985 40.741 0.00 0.00 0.00 2.52
1888 2032 7.732140 TCATCATGTACTCCCTCTATCAAGAAT 59.268 37.037 0.00 0.00 0.00 2.40
1889 2033 9.029368 CATCATGTACTCCCTCTATCAAGAATA 57.971 37.037 0.00 0.00 0.00 1.75
1890 2034 9.781425 ATCATGTACTCCCTCTATCAAGAATAT 57.219 33.333 0.00 0.00 0.00 1.28
1917 2061 9.606631 AAGATCTTTTAGAGCACTATACTTTGG 57.393 33.333 0.88 0.00 31.99 3.28
1918 2062 8.763601 AGATCTTTTAGAGCACTATACTTTGGT 58.236 33.333 0.00 0.00 31.99 3.67
1919 2063 8.723942 ATCTTTTAGAGCACTATACTTTGGTG 57.276 34.615 0.00 0.00 0.00 4.17
1920 2064 7.903145 TCTTTTAGAGCACTATACTTTGGTGA 58.097 34.615 0.00 0.00 33.32 4.02
1921 2065 8.540388 TCTTTTAGAGCACTATACTTTGGTGAT 58.460 33.333 0.00 0.00 33.32 3.06
1922 2066 8.718102 TTTTAGAGCACTATACTTTGGTGATC 57.282 34.615 0.00 0.00 43.78 2.92
1927 2071 8.132604 GAGCACTATACTTTGGTGATCTAAAC 57.867 38.462 0.00 0.00 41.35 2.01
1928 2072 6.757010 AGCACTATACTTTGGTGATCTAAACG 59.243 38.462 0.00 0.00 33.32 3.60
1929 2073 6.755141 GCACTATACTTTGGTGATCTAAACGA 59.245 38.462 0.00 0.00 33.32 3.85
1930 2074 7.438459 GCACTATACTTTGGTGATCTAAACGAT 59.562 37.037 0.00 0.00 33.32 3.73
1951 2095 7.897864 ACGATCTTATATTTCCTAACAGAGGG 58.102 38.462 0.00 0.00 46.70 4.30
1952 2096 7.038941 ACGATCTTATATTTCCTAACAGAGGGG 60.039 40.741 0.00 0.00 46.70 4.79
1974 2118 4.327680 GGTACAAAGGAGAGCATGAAGTT 58.672 43.478 0.00 0.00 0.00 2.66
1997 2159 2.488937 CAAGGGCCATGGCAAAAATTTC 59.511 45.455 36.56 17.20 44.11 2.17
1998 2160 1.704070 AGGGCCATGGCAAAAATTTCA 59.296 42.857 36.56 0.00 44.11 2.69
2028 2191 9.277783 GCTATATATCTCCACAAATCACAACTT 57.722 33.333 0.00 0.00 0.00 2.66
2064 2227 9.675464 TTTAAGTTTAAAAACCTCTCTCTCACA 57.325 29.630 2.02 0.00 39.71 3.58
2072 2235 2.890311 ACCTCTCTCTCACACACAGAAG 59.110 50.000 0.00 0.00 0.00 2.85
2146 2310 8.789762 CCAATCAACATTAGCTGATATCATCAA 58.210 33.333 5.72 1.32 39.11 2.57
2147 2311 9.608617 CAATCAACATTAGCTGATATCATCAAC 57.391 33.333 5.72 0.00 39.11 3.18
2148 2312 9.570468 AATCAACATTAGCTGATATCATCAACT 57.430 29.630 5.72 4.62 39.11 3.16
2150 2314 9.481340 TCAACATTAGCTGATATCATCAACTAC 57.519 33.333 5.72 0.00 37.60 2.73
2151 2315 9.486497 CAACATTAGCTGATATCATCAACTACT 57.514 33.333 5.72 0.00 37.60 2.57
2152 2316 9.703892 AACATTAGCTGATATCATCAACTACTC 57.296 33.333 5.72 0.00 37.60 2.59
2166 2330 4.948621 TCAACTACTCCTACTTGACTAGGC 59.051 45.833 0.00 0.00 34.25 3.93
2169 2333 3.741245 ACTCCTACTTGACTAGGCTGA 57.259 47.619 0.00 0.00 34.25 4.26
2178 2342 5.211973 ACTTGACTAGGCTGAATAGATCCA 58.788 41.667 0.00 0.00 0.00 3.41
2216 2380 7.222000 TGTAACTGGAAAATCAACATTACCC 57.778 36.000 0.00 0.00 0.00 3.69
2227 2391 5.607939 TCAACATTACCCGTCTCATGTAT 57.392 39.130 0.00 0.00 0.00 2.29
2228 2392 6.718522 TCAACATTACCCGTCTCATGTATA 57.281 37.500 0.00 0.00 0.00 1.47
2259 2423 6.950619 AGATTTCTGGATAAGCAAAAGGTTCT 59.049 34.615 0.00 0.00 0.00 3.01
2276 2440 5.688807 AGGTTCTAGCATGCAACTCAATAT 58.311 37.500 21.98 0.00 0.00 1.28
2279 2443 5.200368 TCTAGCATGCAACTCAATATCGA 57.800 39.130 21.98 0.00 0.00 3.59
2324 2491 8.583810 GCAAATCTGTGCAAACATCATATAAT 57.416 30.769 0.00 0.00 44.29 1.28
2330 2497 8.508875 TCTGTGCAAACATCATATAATAGCATG 58.491 33.333 0.00 0.00 0.00 4.06
2336 2503 9.603298 CAAACATCATATAATAGCATGTCACAC 57.397 33.333 0.00 0.00 0.00 3.82
2403 2570 1.604593 AGGCACACCAGATGCAACC 60.605 57.895 0.00 0.00 45.27 3.77
2415 2582 1.933853 GATGCAACCGACCAGACATAC 59.066 52.381 0.00 0.00 0.00 2.39
2417 2584 2.172679 TGCAACCGACCAGACATACTA 58.827 47.619 0.00 0.00 0.00 1.82
2419 2586 3.955551 TGCAACCGACCAGACATACTATA 59.044 43.478 0.00 0.00 0.00 1.31
2467 2637 7.710475 CAGAAATAACCAAAAACTCAATGGTGT 59.290 33.333 0.00 0.00 46.46 4.16
2492 2707 4.606961 ACAACAGGCAAATACGAAAAGTG 58.393 39.130 0.00 0.00 0.00 3.16
2502 2717 6.474102 GCAAATACGAAAAGTGGAAAGACAAA 59.526 34.615 0.00 0.00 0.00 2.83
2517 2732 7.872993 TGGAAAGACAAAGACTGACACTTATAG 59.127 37.037 0.00 0.00 0.00 1.31
2582 2797 1.356059 AGTACTGCCTCTCACTCCTCA 59.644 52.381 0.00 0.00 0.00 3.86
2783 2998 1.302033 CTTGCCACAGAACGCCTCT 60.302 57.895 0.00 0.00 33.23 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 1.443872 CGGTCAAACCTCGACGGAG 60.444 63.158 7.76 0.00 40.14 4.63
89 90 2.646719 CGGTCAAACCTCGACGGA 59.353 61.111 7.76 0.00 35.66 4.69
90 91 1.865788 TACCGGTCAAACCTCGACGG 61.866 60.000 12.40 5.41 35.66 4.79
91 92 0.171903 ATACCGGTCAAACCTCGACG 59.828 55.000 12.40 0.00 35.66 5.12
92 93 2.792542 CGTATACCGGTCAAACCTCGAC 60.793 54.545 12.40 0.00 35.66 4.20
93 94 1.401552 CGTATACCGGTCAAACCTCGA 59.598 52.381 12.40 0.00 35.66 4.04
94 95 1.831343 CGTATACCGGTCAAACCTCG 58.169 55.000 12.40 4.05 35.66 4.63
113 114 2.980177 GCCGAATATAGGGGGCCCC 61.980 68.421 35.78 35.78 45.90 5.80
114 115 2.675371 GCCGAATATAGGGGGCCC 59.325 66.667 15.76 15.76 39.67 5.80
116 117 0.035343 GAAGGCCGAATATAGGGGGC 60.035 60.000 0.00 5.36 46.00 5.80
117 118 0.618981 GGAAGGCCGAATATAGGGGG 59.381 60.000 0.00 0.00 0.00 5.40
118 119 1.358152 TGGAAGGCCGAATATAGGGG 58.642 55.000 0.00 0.00 36.79 4.79
119 120 2.552373 GGTTGGAAGGCCGAATATAGGG 60.552 54.545 0.00 0.00 36.79 3.53
120 121 2.372172 AGGTTGGAAGGCCGAATATAGG 59.628 50.000 0.00 0.00 36.79 2.57
121 122 3.557264 GGAGGTTGGAAGGCCGAATATAG 60.557 52.174 0.00 0.00 36.79 1.31
122 123 2.370849 GGAGGTTGGAAGGCCGAATATA 59.629 50.000 0.00 0.00 36.79 0.86
123 124 1.143073 GGAGGTTGGAAGGCCGAATAT 59.857 52.381 0.00 0.00 36.79 1.28
124 125 0.544697 GGAGGTTGGAAGGCCGAATA 59.455 55.000 0.00 0.00 36.79 1.75
125 126 1.303282 GGAGGTTGGAAGGCCGAAT 59.697 57.895 0.00 0.00 36.79 3.34
126 127 1.710996 TTGGAGGTTGGAAGGCCGAA 61.711 55.000 0.00 0.00 36.79 4.30
127 128 1.710996 TTTGGAGGTTGGAAGGCCGA 61.711 55.000 0.00 0.00 36.79 5.54
128 129 1.228429 TTTGGAGGTTGGAAGGCCG 60.228 57.895 0.00 0.00 36.79 6.13
129 130 0.112412 TCTTTGGAGGTTGGAAGGCC 59.888 55.000 0.00 0.00 0.00 5.19
130 131 2.222227 ATCTTTGGAGGTTGGAAGGC 57.778 50.000 0.00 0.00 0.00 4.35
131 132 5.179452 TCTTATCTTTGGAGGTTGGAAGG 57.821 43.478 0.00 0.00 0.00 3.46
132 133 5.810095 ACTCTTATCTTTGGAGGTTGGAAG 58.190 41.667 0.00 0.00 0.00 3.46
133 134 5.843019 ACTCTTATCTTTGGAGGTTGGAA 57.157 39.130 0.00 0.00 0.00 3.53
134 135 5.843019 AACTCTTATCTTTGGAGGTTGGA 57.157 39.130 0.00 0.00 0.00 3.53
135 136 5.122396 CGAAACTCTTATCTTTGGAGGTTGG 59.878 44.000 0.00 0.00 37.17 3.77
136 137 5.122396 CCGAAACTCTTATCTTTGGAGGTTG 59.878 44.000 0.00 0.00 37.17 3.77
137 138 5.246307 CCGAAACTCTTATCTTTGGAGGTT 58.754 41.667 0.00 0.00 39.36 3.50
138 139 4.323562 CCCGAAACTCTTATCTTTGGAGGT 60.324 45.833 0.00 0.00 0.00 3.85
139 140 4.192317 CCCGAAACTCTTATCTTTGGAGG 58.808 47.826 0.00 0.00 0.00 4.30
140 141 4.631813 CACCCGAAACTCTTATCTTTGGAG 59.368 45.833 0.00 0.00 0.00 3.86
141 142 4.041198 ACACCCGAAACTCTTATCTTTGGA 59.959 41.667 0.00 0.00 0.00 3.53
142 143 4.324267 ACACCCGAAACTCTTATCTTTGG 58.676 43.478 0.00 0.00 0.00 3.28
143 144 5.929992 TGTACACCCGAAACTCTTATCTTTG 59.070 40.000 0.00 0.00 0.00 2.77
144 145 6.105397 TGTACACCCGAAACTCTTATCTTT 57.895 37.500 0.00 0.00 0.00 2.52
145 146 5.733620 TGTACACCCGAAACTCTTATCTT 57.266 39.130 0.00 0.00 0.00 2.40
146 147 5.934402 ATGTACACCCGAAACTCTTATCT 57.066 39.130 0.00 0.00 0.00 1.98
147 148 6.674760 GCAAATGTACACCCGAAACTCTTATC 60.675 42.308 0.00 0.00 0.00 1.75
148 149 5.123344 GCAAATGTACACCCGAAACTCTTAT 59.877 40.000 0.00 0.00 0.00 1.73
149 150 4.453136 GCAAATGTACACCCGAAACTCTTA 59.547 41.667 0.00 0.00 0.00 2.10
150 151 3.252458 GCAAATGTACACCCGAAACTCTT 59.748 43.478 0.00 0.00 0.00 2.85
151 152 2.812011 GCAAATGTACACCCGAAACTCT 59.188 45.455 0.00 0.00 0.00 3.24
152 153 2.412325 CGCAAATGTACACCCGAAACTC 60.412 50.000 0.00 0.00 0.00 3.01
153 154 1.533731 CGCAAATGTACACCCGAAACT 59.466 47.619 0.00 0.00 0.00 2.66
154 155 1.400500 CCGCAAATGTACACCCGAAAC 60.400 52.381 0.00 0.00 0.00 2.78
155 156 0.875728 CCGCAAATGTACACCCGAAA 59.124 50.000 0.00 0.00 0.00 3.46
156 157 0.250381 ACCGCAAATGTACACCCGAA 60.250 50.000 0.00 0.00 0.00 4.30
157 158 0.951525 CACCGCAAATGTACACCCGA 60.952 55.000 0.00 0.00 0.00 5.14
158 159 1.499949 CACCGCAAATGTACACCCG 59.500 57.895 0.00 0.00 0.00 5.28
159 160 1.880186 CCACCGCAAATGTACACCC 59.120 57.895 0.00 0.00 0.00 4.61
160 161 1.211709 GCCACCGCAAATGTACACC 59.788 57.895 0.00 0.00 34.03 4.16
161 162 1.211709 GGCCACCGCAAATGTACAC 59.788 57.895 0.00 0.00 36.38 2.90
162 163 1.974343 GGGCCACCGCAAATGTACA 60.974 57.895 4.39 0.00 36.38 2.90
163 164 1.248101 AAGGGCCACCGCAAATGTAC 61.248 55.000 6.18 0.00 43.47 2.90
164 165 0.328592 TAAGGGCCACCGCAAATGTA 59.671 50.000 6.18 0.00 43.47 2.29
165 166 0.540830 TTAAGGGCCACCGCAAATGT 60.541 50.000 6.18 0.00 43.47 2.71
166 167 0.605589 TTTAAGGGCCACCGCAAATG 59.394 50.000 6.18 0.00 43.47 2.32
167 168 1.343069 TTTTAAGGGCCACCGCAAAT 58.657 45.000 6.18 0.00 43.47 2.32
168 169 1.120530 TTTTTAAGGGCCACCGCAAA 58.879 45.000 6.18 0.00 43.47 3.68
169 170 2.822215 TTTTTAAGGGCCACCGCAA 58.178 47.368 6.18 0.00 43.47 4.85
170 171 4.601042 TTTTTAAGGGCCACCGCA 57.399 50.000 6.18 0.00 43.47 5.69
194 195 4.374843 AACCGTAAAAGTGGTCAAAACC 57.625 40.909 0.00 0.00 46.66 3.27
195 196 5.513849 CAGAAACCGTAAAAGTGGTCAAAAC 59.486 40.000 0.00 0.00 37.54 2.43
196 197 5.183522 ACAGAAACCGTAAAAGTGGTCAAAA 59.816 36.000 0.00 0.00 37.54 2.44
197 198 4.701171 ACAGAAACCGTAAAAGTGGTCAAA 59.299 37.500 0.00 0.00 37.54 2.69
198 199 4.263435 ACAGAAACCGTAAAAGTGGTCAA 58.737 39.130 0.00 0.00 37.54 3.18
199 200 3.876341 ACAGAAACCGTAAAAGTGGTCA 58.124 40.909 0.00 0.00 37.54 4.02
200 201 4.573607 AGAACAGAAACCGTAAAAGTGGTC 59.426 41.667 0.00 0.00 37.54 4.02
201 202 4.334481 CAGAACAGAAACCGTAAAAGTGGT 59.666 41.667 0.00 0.00 41.20 4.16
202 203 4.261031 CCAGAACAGAAACCGTAAAAGTGG 60.261 45.833 0.00 0.00 0.00 4.00
203 204 4.788521 GCCAGAACAGAAACCGTAAAAGTG 60.789 45.833 0.00 0.00 0.00 3.16
204 205 3.314357 GCCAGAACAGAAACCGTAAAAGT 59.686 43.478 0.00 0.00 0.00 2.66
205 206 3.314080 TGCCAGAACAGAAACCGTAAAAG 59.686 43.478 0.00 0.00 0.00 2.27
206 207 3.280295 TGCCAGAACAGAAACCGTAAAA 58.720 40.909 0.00 0.00 0.00 1.52
207 208 2.920524 TGCCAGAACAGAAACCGTAAA 58.079 42.857 0.00 0.00 0.00 2.01
208 209 2.614983 GTTGCCAGAACAGAAACCGTAA 59.385 45.455 0.00 0.00 0.00 3.18
209 210 2.158871 AGTTGCCAGAACAGAAACCGTA 60.159 45.455 0.00 0.00 0.00 4.02
210 211 1.021968 GTTGCCAGAACAGAAACCGT 58.978 50.000 0.00 0.00 0.00 4.83
211 212 1.308998 AGTTGCCAGAACAGAAACCG 58.691 50.000 0.00 0.00 0.00 4.44
212 213 3.801114 AAAGTTGCCAGAACAGAAACC 57.199 42.857 0.00 0.00 0.00 3.27
232 233 4.142881 GCGTTTTACAGTTTTGGGCAAAAA 60.143 37.500 0.00 0.00 41.37 1.94
233 234 3.371285 GCGTTTTACAGTTTTGGGCAAAA 59.629 39.130 0.00 0.00 37.90 2.44
234 235 2.930682 GCGTTTTACAGTTTTGGGCAAA 59.069 40.909 0.00 0.00 0.00 3.68
235 236 2.094182 TGCGTTTTACAGTTTTGGGCAA 60.094 40.909 0.00 0.00 0.00 4.52
236 237 1.476891 TGCGTTTTACAGTTTTGGGCA 59.523 42.857 0.00 0.00 0.00 5.36
237 238 2.211353 TGCGTTTTACAGTTTTGGGC 57.789 45.000 0.00 0.00 0.00 5.36
238 239 5.532025 TTTTTGCGTTTTACAGTTTTGGG 57.468 34.783 0.00 0.00 0.00 4.12
257 258 5.317600 AGTGGCCAAACCCATAAATTTTT 57.682 34.783 7.24 0.00 37.20 1.94
258 259 4.991789 AGTGGCCAAACCCATAAATTTT 57.008 36.364 7.24 0.00 37.20 1.82
259 260 4.991789 AAGTGGCCAAACCCATAAATTT 57.008 36.364 7.24 0.00 37.20 1.82
260 261 5.628899 GCATAAGTGGCCAAACCCATAAATT 60.629 40.000 7.24 0.00 37.20 1.82
261 262 4.141733 GCATAAGTGGCCAAACCCATAAAT 60.142 41.667 7.24 0.00 37.20 1.40
262 263 3.196685 GCATAAGTGGCCAAACCCATAAA 59.803 43.478 7.24 0.00 37.20 1.40
263 264 2.763448 GCATAAGTGGCCAAACCCATAA 59.237 45.455 7.24 0.00 37.20 1.90
264 265 2.383855 GCATAAGTGGCCAAACCCATA 58.616 47.619 7.24 0.00 37.20 2.74
265 266 1.194218 GCATAAGTGGCCAAACCCAT 58.806 50.000 7.24 0.00 37.20 4.00
266 267 1.247419 CGCATAAGTGGCCAAACCCA 61.247 55.000 7.24 0.00 37.83 4.51
267 268 1.510844 CGCATAAGTGGCCAAACCC 59.489 57.895 7.24 0.00 37.83 4.11
268 269 1.510844 CCGCATAAGTGGCCAAACC 59.489 57.895 7.24 0.00 38.83 3.27
269 270 0.963355 TCCCGCATAAGTGGCCAAAC 60.963 55.000 7.24 0.00 44.28 2.93
270 271 0.033601 ATCCCGCATAAGTGGCCAAA 60.034 50.000 7.24 0.00 44.28 3.28
271 272 0.465460 GATCCCGCATAAGTGGCCAA 60.465 55.000 7.24 0.00 44.28 4.52
272 273 1.148273 GATCCCGCATAAGTGGCCA 59.852 57.895 0.00 0.00 44.28 5.36
273 274 0.886490 CAGATCCCGCATAAGTGGCC 60.886 60.000 0.00 0.00 44.28 5.36
274 275 1.510480 GCAGATCCCGCATAAGTGGC 61.510 60.000 0.00 0.00 44.28 5.01
275 276 0.107456 AGCAGATCCCGCATAAGTGG 59.893 55.000 7.42 0.00 45.25 4.00
276 277 2.297315 TCTAGCAGATCCCGCATAAGTG 59.703 50.000 7.42 0.00 0.00 3.16
277 278 2.560542 CTCTAGCAGATCCCGCATAAGT 59.439 50.000 7.42 0.00 0.00 2.24
278 279 2.822561 TCTCTAGCAGATCCCGCATAAG 59.177 50.000 7.42 2.51 0.00 1.73
279 280 2.876581 TCTCTAGCAGATCCCGCATAA 58.123 47.619 7.42 0.00 0.00 1.90
280 281 2.586648 TCTCTAGCAGATCCCGCATA 57.413 50.000 7.42 0.00 0.00 3.14
281 282 1.549620 CATCTCTAGCAGATCCCGCAT 59.450 52.381 7.42 0.00 40.20 4.73
282 283 0.964700 CATCTCTAGCAGATCCCGCA 59.035 55.000 7.42 0.00 40.20 5.69
283 284 0.965439 ACATCTCTAGCAGATCCCGC 59.035 55.000 0.00 0.00 40.20 6.13
284 285 2.890311 AGAACATCTCTAGCAGATCCCG 59.110 50.000 0.00 0.00 40.20 5.14
285 286 4.953940 AAGAACATCTCTAGCAGATCCC 57.046 45.455 0.00 0.00 40.20 3.85
286 287 6.446318 CACTAAGAACATCTCTAGCAGATCC 58.554 44.000 0.00 0.00 40.20 3.36
287 288 6.446318 CCACTAAGAACATCTCTAGCAGATC 58.554 44.000 2.74 0.00 40.20 2.75
288 289 5.221422 GCCACTAAGAACATCTCTAGCAGAT 60.221 44.000 0.00 0.44 43.33 2.90
289 290 4.098654 GCCACTAAGAACATCTCTAGCAGA 59.901 45.833 0.00 0.00 32.46 4.26
290 291 4.142071 TGCCACTAAGAACATCTCTAGCAG 60.142 45.833 0.00 0.00 32.46 4.24
291 292 3.769300 TGCCACTAAGAACATCTCTAGCA 59.231 43.478 0.00 0.00 32.46 3.49
292 293 4.392921 TGCCACTAAGAACATCTCTAGC 57.607 45.455 0.00 0.00 32.46 3.42
293 294 5.971763 ACTTGCCACTAAGAACATCTCTAG 58.028 41.667 0.00 0.00 32.46 2.43
294 295 6.166279 CAACTTGCCACTAAGAACATCTCTA 58.834 40.000 0.00 0.00 32.46 2.43
295 296 4.899352 ACTTGCCACTAAGAACATCTCT 57.101 40.909 0.00 0.00 35.13 3.10
296 297 4.378874 GCAACTTGCCACTAAGAACATCTC 60.379 45.833 1.95 0.00 37.42 2.75
297 298 3.503748 GCAACTTGCCACTAAGAACATCT 59.496 43.478 1.95 0.00 37.42 2.90
298 299 3.826466 GCAACTTGCCACTAAGAACATC 58.174 45.455 1.95 0.00 37.42 3.06
299 300 3.923017 GCAACTTGCCACTAAGAACAT 57.077 42.857 1.95 0.00 37.42 2.71
384 385 2.916934 AGGTGATTAGGTTGGCCTGTAA 59.083 45.455 3.32 0.00 46.47 2.41
385 386 2.557869 AGGTGATTAGGTTGGCCTGTA 58.442 47.619 3.32 0.00 46.47 2.74
390 391 2.239907 AGAGGAAGGTGATTAGGTTGGC 59.760 50.000 0.00 0.00 0.00 4.52
470 472 3.251972 CACAGTTCTTCTTGCCTTCTTCC 59.748 47.826 0.00 0.00 0.00 3.46
484 486 2.589798 TCGTTTTCGGACACAGTTCT 57.410 45.000 0.00 0.00 44.25 3.01
485 487 2.798283 TCATCGTTTTCGGACACAGTTC 59.202 45.455 0.00 0.00 44.25 3.01
490 492 2.798283 TCAGTTCATCGTTTTCGGACAC 59.202 45.455 0.00 0.00 44.25 3.67
493 495 3.920446 TGATCAGTTCATCGTTTTCGGA 58.080 40.909 0.00 0.00 44.25 4.55
518 520 4.150359 CCAGTTACTCTACCGGGTATGAT 58.850 47.826 6.32 0.00 0.00 2.45
525 527 0.974010 TGGGCCAGTTACTCTACCGG 60.974 60.000 0.00 0.00 0.00 5.28
538 551 2.370349 CAATACCGTAAACATGGGCCA 58.630 47.619 9.61 9.61 0.00 5.36
541 554 3.541632 AGAGCAATACCGTAAACATGGG 58.458 45.455 0.00 0.00 0.00 4.00
552 565 2.819608 TGTGGCTTGAAAGAGCAATACC 59.180 45.455 0.00 0.00 44.49 2.73
581 594 5.601313 TCAAAGGGGTGTACATCTATACTCC 59.399 44.000 6.00 0.00 35.29 3.85
582 595 6.097839 TGTCAAAGGGGTGTACATCTATACTC 59.902 42.308 6.00 0.00 0.00 2.59
618 631 0.177836 TGACAGCCATGTATGTCCGG 59.822 55.000 19.33 0.00 44.19 5.14
620 633 2.283298 CAGTGACAGCCATGTATGTCC 58.717 52.381 19.33 13.00 44.19 4.02
621 634 2.977914 ACAGTGACAGCCATGTATGTC 58.022 47.619 16.67 16.67 44.88 3.06
622 635 3.423539 AACAGTGACAGCCATGTATGT 57.576 42.857 0.00 0.00 40.68 2.29
624 637 3.370527 GGGTAACAGTGACAGCCATGTAT 60.371 47.826 0.00 0.00 38.06 2.29
625 638 2.027561 GGGTAACAGTGACAGCCATGTA 60.028 50.000 0.00 0.00 38.06 2.29
659 672 1.203441 AGGTGCTGAGGCCATTCAGA 61.203 55.000 22.77 7.81 45.95 3.27
712 725 4.431131 AATGAGGTGCAGGGCCGG 62.431 66.667 0.00 0.00 0.00 6.13
713 726 2.825836 GAATGAGGTGCAGGGCCG 60.826 66.667 0.00 0.00 0.00 6.13
714 727 2.440980 GGAATGAGGTGCAGGGCC 60.441 66.667 0.00 0.00 0.00 5.80
715 728 2.825836 CGGAATGAGGTGCAGGGC 60.826 66.667 0.00 0.00 0.00 5.19
716 729 2.825836 GCGGAATGAGGTGCAGGG 60.826 66.667 0.00 0.00 0.00 4.45
717 730 2.825836 GGCGGAATGAGGTGCAGG 60.826 66.667 0.00 0.00 0.00 4.85
718 731 0.962356 AAAGGCGGAATGAGGTGCAG 60.962 55.000 0.00 0.00 0.00 4.41
719 732 0.539438 AAAAGGCGGAATGAGGTGCA 60.539 50.000 0.00 0.00 0.00 4.57
722 735 2.514458 ATGAAAAGGCGGAATGAGGT 57.486 45.000 0.00 0.00 0.00 3.85
732 745 1.919918 CCGCGATCAAAATGAAAAGGC 59.080 47.619 8.23 0.00 0.00 4.35
766 780 2.285024 TGCATGCCTCCAAAAGGGC 61.285 57.895 16.68 0.00 46.32 5.19
767 781 1.186917 TGTGCATGCCTCCAAAAGGG 61.187 55.000 16.68 0.00 46.32 3.95
805 819 7.464444 GCATCATGCAGCGTTGTTTTATTATTT 60.464 33.333 4.20 0.00 44.26 1.40
852 868 1.381872 ACCGAGACTGGGATCAGGG 60.382 63.158 10.93 0.00 44.99 4.45
853 869 1.819229 CACCGAGACTGGGATCAGG 59.181 63.158 10.93 0.00 44.99 3.86
871 895 2.297701 ACATAACGACATGGGATTGGC 58.702 47.619 0.00 0.00 0.00 4.52
894 919 5.917462 TGCACATACTACTCCGTACTAGTA 58.083 41.667 0.00 0.00 31.54 1.82
896 921 5.746307 TTGCACATACTACTCCGTACTAG 57.254 43.478 0.00 0.00 0.00 2.57
900 925 3.021695 AGCTTGCACATACTACTCCGTA 58.978 45.455 0.00 0.00 0.00 4.02
901 926 1.825474 AGCTTGCACATACTACTCCGT 59.175 47.619 0.00 0.00 0.00 4.69
902 927 2.586258 AGCTTGCACATACTACTCCG 57.414 50.000 0.00 0.00 0.00 4.63
903 928 3.804873 GCTTAGCTTGCACATACTACTCC 59.195 47.826 0.00 0.00 0.00 3.85
904 929 4.688021 AGCTTAGCTTGCACATACTACTC 58.312 43.478 0.00 0.00 33.89 2.59
905 930 4.744795 AGCTTAGCTTGCACATACTACT 57.255 40.909 0.00 0.00 33.89 2.57
906 931 6.510317 GCTTTAGCTTAGCTTGCACATACTAC 60.510 42.308 13.44 0.00 40.44 2.73
929 954 2.597805 ACCCACGTCGTCAGAGCT 60.598 61.111 0.00 0.00 0.00 4.09
1138 1229 1.153168 CGGAGCCACCTGGTAATGG 60.153 63.158 0.00 0.00 39.16 3.16
1211 1302 4.787280 CGAGGAGCAGGGGGAGGT 62.787 72.222 0.00 0.00 0.00 3.85
1214 1305 2.043248 GTACGAGGAGCAGGGGGA 60.043 66.667 0.00 0.00 0.00 4.81
1390 1490 3.066190 TTCGAGACCATCCGCCGT 61.066 61.111 0.00 0.00 0.00 5.68
1507 1607 3.858868 GACGCGGTTGAGCTGGTCA 62.859 63.158 12.47 5.28 34.40 4.02
1644 1753 3.562108 TCACCCTACCCTCTTCTTCTT 57.438 47.619 0.00 0.00 0.00 2.52
1650 1759 4.090090 CGATCATATCACCCTACCCTCTT 58.910 47.826 0.00 0.00 0.00 2.85
1651 1760 3.333980 TCGATCATATCACCCTACCCTCT 59.666 47.826 0.00 0.00 0.00 3.69
1655 1764 5.498393 TCTAGTCGATCATATCACCCTACC 58.502 45.833 0.00 0.00 0.00 3.18
1656 1765 6.824196 TCATCTAGTCGATCATATCACCCTAC 59.176 42.308 0.00 0.00 0.00 3.18
1703 1828 6.806739 GCAGAGGTACAAAAATGGTAATTCAC 59.193 38.462 0.00 0.00 0.00 3.18
1730 1855 1.068250 GGCGTCCCTCATAGAGCAC 59.932 63.158 0.00 0.00 0.00 4.40
1740 1868 0.255890 ATGCTAACAATGGCGTCCCT 59.744 50.000 0.00 0.00 35.46 4.20
1891 2035 9.606631 CCAAAGTATAGTGCTCTAAAAGATCTT 57.393 33.333 0.88 0.88 0.00 2.40
1892 2036 8.763601 ACCAAAGTATAGTGCTCTAAAAGATCT 58.236 33.333 0.00 0.00 0.00 2.75
1893 2037 8.821894 CACCAAAGTATAGTGCTCTAAAAGATC 58.178 37.037 0.00 0.00 0.00 2.75
1894 2038 8.540388 TCACCAAAGTATAGTGCTCTAAAAGAT 58.460 33.333 0.00 0.00 0.00 2.40
1895 2039 7.903145 TCACCAAAGTATAGTGCTCTAAAAGA 58.097 34.615 0.00 0.00 0.00 2.52
1896 2040 8.723942 ATCACCAAAGTATAGTGCTCTAAAAG 57.276 34.615 0.00 0.00 0.00 2.27
1897 2041 8.540388 AGATCACCAAAGTATAGTGCTCTAAAA 58.460 33.333 0.00 0.00 35.76 1.52
1898 2042 8.079211 AGATCACCAAAGTATAGTGCTCTAAA 57.921 34.615 0.00 0.00 35.76 1.85
1899 2043 7.661536 AGATCACCAAAGTATAGTGCTCTAA 57.338 36.000 0.00 0.00 35.76 2.10
1900 2044 8.762481 TTAGATCACCAAAGTATAGTGCTCTA 57.238 34.615 0.00 0.00 37.89 2.43
1901 2045 7.661536 TTAGATCACCAAAGTATAGTGCTCT 57.338 36.000 0.00 0.00 39.54 4.09
1902 2046 7.043325 CGTTTAGATCACCAAAGTATAGTGCTC 60.043 40.741 0.00 0.00 0.00 4.26
1903 2047 6.757010 CGTTTAGATCACCAAAGTATAGTGCT 59.243 38.462 0.00 0.00 0.00 4.40
1904 2048 6.755141 TCGTTTAGATCACCAAAGTATAGTGC 59.245 38.462 0.00 0.00 0.00 4.40
1905 2049 8.873215 ATCGTTTAGATCACCAAAGTATAGTG 57.127 34.615 0.00 0.00 33.45 2.74
1940 2084 2.238898 CCTTTGTACCCCCTCTGTTAGG 59.761 54.545 0.00 0.00 46.09 2.69
1941 2085 3.178865 TCCTTTGTACCCCCTCTGTTAG 58.821 50.000 0.00 0.00 0.00 2.34
1942 2086 3.178865 CTCCTTTGTACCCCCTCTGTTA 58.821 50.000 0.00 0.00 0.00 2.41
1943 2087 1.985895 CTCCTTTGTACCCCCTCTGTT 59.014 52.381 0.00 0.00 0.00 3.16
1944 2088 1.151413 TCTCCTTTGTACCCCCTCTGT 59.849 52.381 0.00 0.00 0.00 3.41
1945 2089 1.834263 CTCTCCTTTGTACCCCCTCTG 59.166 57.143 0.00 0.00 0.00 3.35
1946 2090 1.902141 GCTCTCCTTTGTACCCCCTCT 60.902 57.143 0.00 0.00 0.00 3.69
1947 2091 0.542333 GCTCTCCTTTGTACCCCCTC 59.458 60.000 0.00 0.00 0.00 4.30
1948 2092 0.178873 TGCTCTCCTTTGTACCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
1949 2093 0.919710 ATGCTCTCCTTTGTACCCCC 59.080 55.000 0.00 0.00 0.00 5.40
1950 2094 1.559682 TCATGCTCTCCTTTGTACCCC 59.440 52.381 0.00 0.00 0.00 4.95
1951 2095 3.274288 CTTCATGCTCTCCTTTGTACCC 58.726 50.000 0.00 0.00 0.00 3.69
1952 2096 3.944087 ACTTCATGCTCTCCTTTGTACC 58.056 45.455 0.00 0.00 0.00 3.34
1974 2118 0.765903 TTTTTGCCATGGCCCTTGGA 60.766 50.000 33.44 11.50 41.09 3.53
1997 2159 8.715998 GTGATTTGTGGAGATATATAGCACTTG 58.284 37.037 0.07 0.00 0.00 3.16
1998 2160 8.432013 TGTGATTTGTGGAGATATATAGCACTT 58.568 33.333 0.07 0.00 0.00 3.16
2060 2223 8.367911 AGATTATCTTTGTACTTCTGTGTGTGA 58.632 33.333 0.00 0.00 0.00 3.58
2061 2224 8.539770 AGATTATCTTTGTACTTCTGTGTGTG 57.460 34.615 0.00 0.00 0.00 3.82
2146 2310 4.227754 TCAGCCTAGTCAAGTAGGAGTAGT 59.772 45.833 13.98 0.00 42.18 2.73
2147 2311 4.783055 TCAGCCTAGTCAAGTAGGAGTAG 58.217 47.826 13.98 0.00 42.18 2.57
2148 2312 4.857130 TCAGCCTAGTCAAGTAGGAGTA 57.143 45.455 13.98 0.00 42.18 2.59
2149 2313 3.741245 TCAGCCTAGTCAAGTAGGAGT 57.259 47.619 13.98 0.00 42.18 3.85
2150 2314 6.065374 TCTATTCAGCCTAGTCAAGTAGGAG 58.935 44.000 13.98 6.34 42.18 3.69
2151 2315 6.014771 TCTATTCAGCCTAGTCAAGTAGGA 57.985 41.667 13.98 0.00 42.18 2.94
2152 2316 6.071616 GGATCTATTCAGCCTAGTCAAGTAGG 60.072 46.154 6.55 6.55 42.45 3.18
2166 2330 4.316645 CTGCCTGATGTGGATCTATTCAG 58.683 47.826 12.34 12.34 0.00 3.02
2169 2333 2.709934 AGCTGCCTGATGTGGATCTATT 59.290 45.455 0.00 0.00 0.00 1.73
2178 2342 3.432749 CCAGTTACATAGCTGCCTGATGT 60.433 47.826 14.39 14.39 37.55 3.06
2227 2391 6.499106 TGCTTATCCAGAAATCTCATGGTA 57.501 37.500 0.00 0.00 35.51 3.25
2228 2392 5.378230 TGCTTATCCAGAAATCTCATGGT 57.622 39.130 0.00 0.00 35.51 3.55
2259 2423 4.948847 ACTCGATATTGAGTTGCATGCTA 58.051 39.130 20.33 8.83 46.85 3.49
2308 2472 8.291740 GTGACATGCTATTATATGATGTTTGCA 58.708 33.333 0.00 0.00 0.00 4.08
2324 2491 8.785329 TTGAATACATTAAGTGTGACATGCTA 57.215 30.769 0.00 0.00 42.24 3.49
2330 2497 8.706035 ACTACGTTTGAATACATTAAGTGTGAC 58.294 33.333 0.00 0.00 42.24 3.67
2403 2570 5.670149 ACGAACTATAGTATGTCTGGTCG 57.330 43.478 5.65 11.27 0.00 4.79
2467 2637 6.693545 CACTTTTCGTATTTGCCTGTTGTTTA 59.306 34.615 0.00 0.00 0.00 2.01
2492 2707 8.088981 TCTATAAGTGTCAGTCTTTGTCTTTCC 58.911 37.037 0.00 0.00 0.00 3.13
2502 2717 7.394641 TGATGAGTGTTCTATAAGTGTCAGTCT 59.605 37.037 0.00 0.00 0.00 3.24
2517 2732 3.430218 CCGAGTGTCTTTGATGAGTGTTC 59.570 47.826 0.00 0.00 0.00 3.18
2579 2794 1.543941 GCGCCGAATCTGACGATGAG 61.544 60.000 0.00 0.00 0.00 2.90
2582 2797 1.299468 GAGCGCCGAATCTGACGAT 60.299 57.895 2.29 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.