Multiple sequence alignment - TraesCS5A01G246400

Loading Multiple Alignment...

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 TraesCS5A01G246400 chr5A 100.000 2549 0 0 1 2549 459744309 459746857 0.000000e+00 4708.0
1 TraesCS5A01G246400 chr6B 98.938 1978 18 3 573 2549 660437743 660435768 0.000000e+00 3533.0
2 TraesCS5A01G246400 chr7A 98.788 1980 23 1 571 2549 701581939 701583918 0.000000e+00 3522.0
3 TraesCS5A01G246400 chr7A 87.671 146 15 2 222 367 701689064 701689206 1.570000e-37 167.0
4 TraesCS5A01G246400 chr7A 92.035 113 8 1 222 333 116896471 116896359 9.440000e-35 158.0
5 TraesCS5A01G246400 chr7A 90.000 40 4 0 500 539 330424539 330424500 5.000000e-03 52.8
6 TraesCS5A01G246400 chr6A 98.932 1967 21 0 573 2539 617222869 617220903 0.000000e+00 3517.0
7 TraesCS5A01G246400 chr7B 98.636 1980 25 1 572 2549 552932144 552930165 0.000000e+00 3506.0
8 TraesCS5A01G246400 chr7B 98.534 1978 26 2 571 2547 692881450 692883425 0.000000e+00 3489.0
9 TraesCS5A01G246400 chr3B 98.686 1978 23 2 573 2549 379294093 379296068 0.000000e+00 3506.0
10 TraesCS5A01G246400 chr4A 98.781 1969 23 1 572 2539 36562912 36564880 0.000000e+00 3502.0
11 TraesCS5A01G246400 chr4A 86.000 150 20 1 219 368 496075371 496075223 2.620000e-35 159.0
12 TraesCS5A01G246400 chr1A 98.440 1987 27 4 563 2549 22791521 22793503 0.000000e+00 3494.0
13 TraesCS5A01G246400 chr5B 98.535 1979 27 2 572 2549 206051426 206049449 0.000000e+00 3493.0
14 TraesCS5A01G246400 chr3D 88.356 146 9 2 222 367 451640846 451640983 4.360000e-38 169.0
15 TraesCS5A01G246400 chr3D 92.241 116 8 1 221 336 275836617 275836503 2.030000e-36 163.0
16 TraesCS5A01G246400 chr3D 92.857 112 7 1 221 331 577483484 577483373 7.300000e-36 161.0
17 TraesCS5A01G246400 chr5D 86.667 150 17 3 221 370 127274491 127274345 2.030000e-36 163.0
18 TraesCS5A01G246400 chr6D 91.964 112 8 1 221 331 34038209 34038320 3.400000e-34 156.0
19 TraesCS5A01G246400 chr2B 90.598 117 9 2 222 337 666488152 666488037 1.220000e-33 154.0


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 TraesCS5A01G246400 chr5A 459744309 459746857 2548 False 4708 4708 100.000 1 2549 1 chr5A.!!$F1 2548
1 TraesCS5A01G246400 chr6B 660435768 660437743 1975 True 3533 3533 98.938 573 2549 1 chr6B.!!$R1 1976
2 TraesCS5A01G246400 chr7A 701581939 701583918 1979 False 3522 3522 98.788 571 2549 1 chr7A.!!$F1 1978
3 TraesCS5A01G246400 chr6A 617220903 617222869 1966 True 3517 3517 98.932 573 2539 1 chr6A.!!$R1 1966
4 TraesCS5A01G246400 chr7B 552930165 552932144 1979 True 3506 3506 98.636 572 2549 1 chr7B.!!$R1 1977
5 TraesCS5A01G246400 chr7B 692881450 692883425 1975 False 3489 3489 98.534 571 2547 1 chr7B.!!$F1 1976
6 TraesCS5A01G246400 chr3B 379294093 379296068 1975 False 3506 3506 98.686 573 2549 1 chr3B.!!$F1 1976
7 TraesCS5A01G246400 chr4A 36562912 36564880 1968 False 3502 3502 98.781 572 2539 1 chr4A.!!$F1 1967
8 TraesCS5A01G246400 chr1A 22791521 22793503 1982 False 3494 3494 98.440 563 2549 1 chr1A.!!$F1 1986
9 TraesCS5A01G246400 chr5B 206049449 206051426 1977 True 3493 3493 98.535 572 2549 1 chr5B.!!$R1 1977

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
219 220 0.114364 TGCCTAGACACAGGAGGTCA 59.886 55.0 0.0 0.0 38.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2053 1.297364 GGCACCTGGCGTAAACCTA 59.703 57.895 0.0 0.0 46.16 3.08 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
96 97 9.943163 AAAAACAATACACCAAACATTATTTGC 57.057 25.926 0.00 0.00 0.00 3.68
97 98 8.668510 AAACAATACACCAAACATTATTTGCA 57.331 26.923 0.00 0.00 0.00 4.08
98 99 8.845413 AACAATACACCAAACATTATTTGCAT 57.155 26.923 0.00 0.00 0.00 3.96
99 100 8.845413 ACAATACACCAAACATTATTTGCATT 57.155 26.923 0.00 0.00 0.00 3.56
100 101 9.282569 ACAATACACCAAACATTATTTGCATTT 57.717 25.926 0.00 0.00 0.00 2.32
127 128 8.848474 TTAAAAAGTTGTTCACCATTTTTCCA 57.152 26.923 0.00 0.00 35.39 3.53
128 129 7.751768 AAAAAGTTGTTCACCATTTTTCCAA 57.248 28.000 0.00 0.00 29.54 3.53
129 130 6.735678 AAAGTTGTTCACCATTTTTCCAAC 57.264 33.333 0.00 0.00 0.00 3.77
130 131 5.413309 AGTTGTTCACCATTTTTCCAACA 57.587 34.783 0.00 0.00 34.62 3.33
131 132 5.799213 AGTTGTTCACCATTTTTCCAACAA 58.201 33.333 0.00 0.00 34.62 2.83
132 133 6.234177 AGTTGTTCACCATTTTTCCAACAAA 58.766 32.000 0.00 0.00 35.96 2.83
133 134 6.883756 AGTTGTTCACCATTTTTCCAACAAAT 59.116 30.769 0.00 0.00 35.96 2.32
134 135 6.674694 TGTTCACCATTTTTCCAACAAATG 57.325 33.333 0.00 0.00 40.11 2.32
164 165 6.645700 TTTTGTTTTCTAAAACTGCTGCTG 57.354 33.333 16.79 4.89 46.37 4.41
165 166 3.705604 TGTTTTCTAAAACTGCTGCTGC 58.294 40.909 16.79 8.89 46.37 5.25
166 167 3.130164 TGTTTTCTAAAACTGCTGCTGCA 59.870 39.130 17.88 17.88 46.37 4.41
179 180 5.703978 TGCTGCTGCATTTAGTTCTTAAA 57.296 34.783 14.93 0.00 45.31 1.52
180 181 6.271488 TGCTGCTGCATTTAGTTCTTAAAT 57.729 33.333 14.93 0.00 45.31 1.40
181 182 6.690530 TGCTGCTGCATTTAGTTCTTAAATT 58.309 32.000 14.93 0.00 45.31 1.82
182 183 7.153985 TGCTGCTGCATTTAGTTCTTAAATTT 58.846 30.769 14.93 0.00 45.31 1.82
183 184 7.656948 TGCTGCTGCATTTAGTTCTTAAATTTT 59.343 29.630 14.93 0.00 45.31 1.82
184 185 8.164790 GCTGCTGCATTTAGTTCTTAAATTTTC 58.835 33.333 11.11 0.00 39.41 2.29
185 186 8.226543 TGCTGCATTTAGTTCTTAAATTTTCG 57.773 30.769 0.00 0.00 39.41 3.46
186 187 7.148820 TGCTGCATTTAGTTCTTAAATTTTCGC 60.149 33.333 0.00 0.00 39.41 4.70
187 188 7.062255 GCTGCATTTAGTTCTTAAATTTTCGCT 59.938 33.333 0.00 0.00 39.41 4.93
188 189 8.810652 TGCATTTAGTTCTTAAATTTTCGCTT 57.189 26.923 0.00 0.00 39.41 4.68
189 190 9.255304 TGCATTTAGTTCTTAAATTTTCGCTTT 57.745 25.926 0.00 0.00 39.41 3.51
190 191 9.516091 GCATTTAGTTCTTAAATTTTCGCTTTG 57.484 29.630 0.00 0.00 39.41 2.77
191 192 9.516091 CATTTAGTTCTTAAATTTTCGCTTTGC 57.484 29.630 0.00 0.00 39.41 3.68
192 193 7.631915 TTAGTTCTTAAATTTTCGCTTTGCC 57.368 32.000 0.00 0.00 0.00 4.52
193 194 5.842907 AGTTCTTAAATTTTCGCTTTGCCT 58.157 33.333 0.00 0.00 0.00 4.75
194 195 6.977213 AGTTCTTAAATTTTCGCTTTGCCTA 58.023 32.000 0.00 0.00 0.00 3.93
195 196 7.430441 AGTTCTTAAATTTTCGCTTTGCCTAA 58.570 30.769 0.00 0.00 0.00 2.69
196 197 7.923878 AGTTCTTAAATTTTCGCTTTGCCTAAA 59.076 29.630 0.00 0.00 0.00 1.85
197 198 8.544597 GTTCTTAAATTTTCGCTTTGCCTAAAA 58.455 29.630 0.00 0.00 0.00 1.52
198 199 8.067780 TCTTAAATTTTCGCTTTGCCTAAAAC 57.932 30.769 0.00 0.00 0.00 2.43
199 200 7.923878 TCTTAAATTTTCGCTTTGCCTAAAACT 59.076 29.630 0.00 0.00 0.00 2.66
200 201 6.918892 AAATTTTCGCTTTGCCTAAAACTT 57.081 29.167 0.00 0.00 0.00 2.66
201 202 5.905480 ATTTTCGCTTTGCCTAAAACTTG 57.095 34.783 0.00 0.00 0.00 3.16
202 203 2.415697 TCGCTTTGCCTAAAACTTGC 57.584 45.000 0.00 0.00 0.00 4.01
203 204 1.000717 TCGCTTTGCCTAAAACTTGCC 60.001 47.619 0.00 0.00 0.00 4.52
204 205 1.000274 CGCTTTGCCTAAAACTTGCCT 60.000 47.619 0.00 0.00 0.00 4.75
205 206 2.227865 CGCTTTGCCTAAAACTTGCCTA 59.772 45.455 0.00 0.00 0.00 3.93
206 207 3.670627 CGCTTTGCCTAAAACTTGCCTAG 60.671 47.826 0.00 0.00 0.00 3.02
207 208 3.506067 GCTTTGCCTAAAACTTGCCTAGA 59.494 43.478 0.00 0.00 0.00 2.43
208 209 4.616143 GCTTTGCCTAAAACTTGCCTAGAC 60.616 45.833 0.00 0.00 0.00 2.59
209 210 3.780804 TGCCTAAAACTTGCCTAGACA 57.219 42.857 0.00 0.00 0.00 3.41
210 211 3.408634 TGCCTAAAACTTGCCTAGACAC 58.591 45.455 0.00 0.00 0.00 3.67
211 212 3.181449 TGCCTAAAACTTGCCTAGACACA 60.181 43.478 0.00 0.00 0.00 3.72
212 213 3.437049 GCCTAAAACTTGCCTAGACACAG 59.563 47.826 0.00 0.00 0.00 3.66
213 214 4.003648 CCTAAAACTTGCCTAGACACAGG 58.996 47.826 0.00 0.00 38.86 4.00
214 215 3.857157 AAAACTTGCCTAGACACAGGA 57.143 42.857 0.00 0.00 38.00 3.86
215 216 3.409026 AAACTTGCCTAGACACAGGAG 57.591 47.619 0.00 0.00 38.00 3.69
216 217 1.270907 ACTTGCCTAGACACAGGAGG 58.729 55.000 0.00 0.00 38.00 4.30
217 218 1.270907 CTTGCCTAGACACAGGAGGT 58.729 55.000 0.00 0.00 38.00 3.85
218 219 1.205893 CTTGCCTAGACACAGGAGGTC 59.794 57.143 0.00 0.00 38.00 3.85
219 220 0.114364 TGCCTAGACACAGGAGGTCA 59.886 55.000 0.00 0.00 38.00 4.02
220 221 1.267121 GCCTAGACACAGGAGGTCAA 58.733 55.000 0.00 0.00 38.00 3.18
221 222 1.623811 GCCTAGACACAGGAGGTCAAA 59.376 52.381 0.00 0.00 38.00 2.69
222 223 2.237392 GCCTAGACACAGGAGGTCAAAT 59.763 50.000 0.00 0.00 38.00 2.32
223 224 3.451178 GCCTAGACACAGGAGGTCAAATA 59.549 47.826 0.00 0.00 38.00 1.40
224 225 4.101741 GCCTAGACACAGGAGGTCAAATAT 59.898 45.833 0.00 0.00 38.00 1.28
225 226 5.740513 GCCTAGACACAGGAGGTCAAATATC 60.741 48.000 0.00 0.00 38.00 1.63
226 227 4.392921 AGACACAGGAGGTCAAATATCG 57.607 45.455 0.00 0.00 37.74 2.92
227 228 3.133003 AGACACAGGAGGTCAAATATCGG 59.867 47.826 0.00 0.00 37.74 4.18
228 229 2.213499 CACAGGAGGTCAAATATCGGC 58.787 52.381 0.00 0.00 0.00 5.54
229 230 1.202533 ACAGGAGGTCAAATATCGGCG 60.203 52.381 0.00 0.00 0.00 6.46
230 231 0.249911 AGGAGGTCAAATATCGGCGC 60.250 55.000 0.00 0.00 0.00 6.53
231 232 1.228657 GGAGGTCAAATATCGGCGCC 61.229 60.000 19.07 19.07 0.00 6.53
232 233 0.249911 GAGGTCAAATATCGGCGCCT 60.250 55.000 26.68 9.55 0.00 5.52
233 234 0.532862 AGGTCAAATATCGGCGCCTG 60.533 55.000 26.68 18.23 0.00 4.85
234 235 1.507141 GGTCAAATATCGGCGCCTGG 61.507 60.000 26.68 10.37 0.00 4.45
235 236 1.227823 TCAAATATCGGCGCCTGGG 60.228 57.895 26.68 9.50 0.00 4.45
236 237 2.113139 AAATATCGGCGCCTGGGG 59.887 61.111 26.68 9.07 0.00 4.96
237 238 2.448582 AAATATCGGCGCCTGGGGA 61.449 57.895 26.68 15.03 0.00 4.81
238 239 2.676163 AAATATCGGCGCCTGGGGAC 62.676 60.000 26.68 11.31 0.00 4.46
248 249 3.077556 CTGGGGACGACCTGGAGG 61.078 72.222 0.00 0.00 40.03 4.30
252 253 4.131088 GGACGACCTGGAGGCGAC 62.131 72.222 13.97 9.04 39.32 5.19
253 254 4.477975 GACGACCTGGAGGCGACG 62.478 72.222 13.97 10.04 39.32 5.12
261 262 4.899239 GGAGGCGACGGCTGGATG 62.899 72.222 30.01 0.00 38.98 3.51
287 288 3.546543 CCCCCAGCGCCGATTCTA 61.547 66.667 2.29 0.00 0.00 2.10
288 289 2.280186 CCCCAGCGCCGATTCTAC 60.280 66.667 2.29 0.00 0.00 2.59
289 290 2.280186 CCCAGCGCCGATTCTACC 60.280 66.667 2.29 0.00 0.00 3.18
290 291 2.658593 CCAGCGCCGATTCTACCG 60.659 66.667 2.29 0.00 0.00 4.02
291 292 3.330853 CAGCGCCGATTCTACCGC 61.331 66.667 2.29 0.00 46.14 5.68
292 293 4.587189 AGCGCCGATTCTACCGCC 62.587 66.667 2.29 0.00 46.90 6.13
296 297 3.912907 CCGATTCTACCGCCGGCT 61.913 66.667 26.68 9.55 35.29 5.52
297 298 2.558286 CCGATTCTACCGCCGGCTA 61.558 63.158 26.68 10.32 35.29 3.93
298 299 1.081376 CGATTCTACCGCCGGCTAG 60.081 63.158 26.68 20.08 0.00 3.42
299 300 1.373121 GATTCTACCGCCGGCTAGC 60.373 63.158 26.68 6.04 0.00 3.42
300 301 2.766875 GATTCTACCGCCGGCTAGCC 62.767 65.000 26.68 24.75 0.00 3.93
316 317 3.002583 CCCCCAGGCGGCAATTTT 61.003 61.111 13.08 0.00 0.00 1.82
317 318 2.592032 CCCCCAGGCGGCAATTTTT 61.592 57.895 13.08 0.00 0.00 1.94
318 319 1.261238 CCCCCAGGCGGCAATTTTTA 61.261 55.000 13.08 0.00 0.00 1.52
319 320 0.829990 CCCCAGGCGGCAATTTTTAT 59.170 50.000 13.08 0.00 0.00 1.40
320 321 1.473080 CCCCAGGCGGCAATTTTTATG 60.473 52.381 13.08 0.00 0.00 1.90
321 322 1.289276 CCAGGCGGCAATTTTTATGC 58.711 50.000 13.08 0.00 43.08 3.14
328 329 2.223537 GCAATTTTTATGCCTCCGGG 57.776 50.000 0.00 0.00 37.85 5.73
329 330 1.202521 GCAATTTTTATGCCTCCGGGG 60.203 52.381 0.00 0.00 37.85 5.73
330 331 1.412343 CAATTTTTATGCCTCCGGGGG 59.588 52.381 19.17 19.17 35.12 5.40
331 332 0.930726 ATTTTTATGCCTCCGGGGGA 59.069 50.000 29.58 15.91 40.52 4.81
358 359 3.743017 GGGGGCAATGGCTGGAGA 61.743 66.667 6.78 0.00 40.87 3.71
359 360 2.605299 GGGGCAATGGCTGGAGAT 59.395 61.111 6.78 0.00 40.87 2.75
360 361 1.719063 GGGGGCAATGGCTGGAGATA 61.719 60.000 6.78 0.00 40.87 1.98
361 362 0.538287 GGGGCAATGGCTGGAGATAC 60.538 60.000 6.78 0.00 40.87 2.24
362 363 0.475906 GGGCAATGGCTGGAGATACT 59.524 55.000 6.78 0.00 40.87 2.12
363 364 1.544314 GGGCAATGGCTGGAGATACTC 60.544 57.143 6.78 0.00 40.87 2.59
364 365 1.419387 GGCAATGGCTGGAGATACTCT 59.581 52.381 0.00 0.00 40.87 3.24
365 366 2.634940 GGCAATGGCTGGAGATACTCTA 59.365 50.000 0.00 0.00 40.87 2.43
366 367 3.071602 GGCAATGGCTGGAGATACTCTAA 59.928 47.826 0.00 0.00 40.87 2.10
367 368 4.314121 GCAATGGCTGGAGATACTCTAAG 58.686 47.826 0.00 0.00 36.96 2.18
368 369 4.802248 GCAATGGCTGGAGATACTCTAAGG 60.802 50.000 0.00 0.00 36.96 2.69
369 370 3.973472 TGGCTGGAGATACTCTAAGGA 57.027 47.619 0.00 0.00 0.00 3.36
370 371 4.265856 TGGCTGGAGATACTCTAAGGAA 57.734 45.455 0.00 0.00 0.00 3.36
371 372 3.961408 TGGCTGGAGATACTCTAAGGAAC 59.039 47.826 0.00 0.00 0.00 3.62
372 373 3.961408 GGCTGGAGATACTCTAAGGAACA 59.039 47.826 0.00 0.00 0.00 3.18
373 374 4.202172 GGCTGGAGATACTCTAAGGAACAC 60.202 50.000 0.00 0.00 0.00 3.32
374 375 4.202172 GCTGGAGATACTCTAAGGAACACC 60.202 50.000 0.00 0.00 0.00 4.16
375 376 3.952323 TGGAGATACTCTAAGGAACACCG 59.048 47.826 0.00 0.00 0.00 4.94
376 377 3.318557 GGAGATACTCTAAGGAACACCGG 59.681 52.174 0.00 0.00 0.00 5.28
377 378 3.297736 AGATACTCTAAGGAACACCGGG 58.702 50.000 6.32 0.00 0.00 5.73
378 379 1.188863 TACTCTAAGGAACACCGGGC 58.811 55.000 6.32 0.00 0.00 6.13
379 380 0.544595 ACTCTAAGGAACACCGGGCT 60.545 55.000 6.32 0.00 0.00 5.19
380 381 0.613777 CTCTAAGGAACACCGGGCTT 59.386 55.000 6.32 0.00 0.00 4.35
381 382 0.611714 TCTAAGGAACACCGGGCTTC 59.388 55.000 6.32 5.54 0.00 3.86
382 383 0.323629 CTAAGGAACACCGGGCTTCA 59.676 55.000 6.32 0.00 0.00 3.02
383 384 0.323629 TAAGGAACACCGGGCTTCAG 59.676 55.000 6.32 0.00 0.00 3.02
384 385 3.056328 GGAACACCGGGCTTCAGC 61.056 66.667 6.32 0.00 41.14 4.26
385 386 3.423154 GAACACCGGGCTTCAGCG 61.423 66.667 6.32 0.00 43.26 5.18
386 387 4.250305 AACACCGGGCTTCAGCGT 62.250 61.111 6.32 0.00 43.26 5.07
387 388 4.988598 ACACCGGGCTTCAGCGTG 62.989 66.667 6.32 4.36 43.26 5.34
388 389 4.988598 CACCGGGCTTCAGCGTGT 62.989 66.667 6.32 0.00 43.26 4.49
389 390 4.988598 ACCGGGCTTCAGCGTGTG 62.989 66.667 6.32 0.00 43.26 3.82
391 392 4.988598 CGGGCTTCAGCGTGTGGT 62.989 66.667 0.00 0.00 43.26 4.16
392 393 2.594592 GGGCTTCAGCGTGTGGTT 60.595 61.111 0.00 0.00 43.26 3.67
393 394 2.639286 GGCTTCAGCGTGTGGTTG 59.361 61.111 0.00 0.00 43.26 3.77
394 395 2.050985 GCTTCAGCGTGTGGTTGC 60.051 61.111 0.00 0.00 0.00 4.17
395 396 2.249309 CTTCAGCGTGTGGTTGCG 59.751 61.111 0.00 0.00 35.87 4.85
396 397 2.202946 TTCAGCGTGTGGTTGCGA 60.203 55.556 0.00 0.00 35.87 5.10
397 398 2.162921 CTTCAGCGTGTGGTTGCGAG 62.163 60.000 0.00 0.00 35.87 5.03
398 399 2.916502 TTCAGCGTGTGGTTGCGAGT 62.917 55.000 0.00 0.00 35.87 4.18
399 400 2.203015 AGCGTGTGGTTGCGAGTT 60.203 55.556 0.00 0.00 35.87 3.01
400 401 1.817941 AGCGTGTGGTTGCGAGTTT 60.818 52.632 0.00 0.00 35.87 2.66
401 402 1.654137 GCGTGTGGTTGCGAGTTTG 60.654 57.895 0.00 0.00 0.00 2.93
402 403 2.010670 CGTGTGGTTGCGAGTTTGA 58.989 52.632 0.00 0.00 0.00 2.69
403 404 0.586319 CGTGTGGTTGCGAGTTTGAT 59.414 50.000 0.00 0.00 0.00 2.57
404 405 1.002900 CGTGTGGTTGCGAGTTTGATT 60.003 47.619 0.00 0.00 0.00 2.57
405 406 2.650608 GTGTGGTTGCGAGTTTGATTC 58.349 47.619 0.00 0.00 0.00 2.52
406 407 1.606668 TGTGGTTGCGAGTTTGATTCC 59.393 47.619 0.00 0.00 0.00 3.01
407 408 1.880027 GTGGTTGCGAGTTTGATTCCT 59.120 47.619 0.00 0.00 0.00 3.36
408 409 3.071479 GTGGTTGCGAGTTTGATTCCTA 58.929 45.455 0.00 0.00 0.00 2.94
409 410 3.125316 GTGGTTGCGAGTTTGATTCCTAG 59.875 47.826 0.00 0.00 0.00 3.02
410 411 3.244422 TGGTTGCGAGTTTGATTCCTAGT 60.244 43.478 0.00 0.00 0.00 2.57
411 412 4.020928 TGGTTGCGAGTTTGATTCCTAGTA 60.021 41.667 0.00 0.00 0.00 1.82
412 413 4.933400 GGTTGCGAGTTTGATTCCTAGTAA 59.067 41.667 0.00 0.00 0.00 2.24
413 414 5.410439 GGTTGCGAGTTTGATTCCTAGTAAA 59.590 40.000 0.00 0.00 0.00 2.01
414 415 6.402226 GGTTGCGAGTTTGATTCCTAGTAAAG 60.402 42.308 0.00 0.00 0.00 1.85
415 416 4.630069 TGCGAGTTTGATTCCTAGTAAAGC 59.370 41.667 0.00 0.00 0.00 3.51
416 417 4.034163 GCGAGTTTGATTCCTAGTAAAGCC 59.966 45.833 0.00 0.00 0.00 4.35
417 418 4.571176 CGAGTTTGATTCCTAGTAAAGCCC 59.429 45.833 0.00 0.00 0.00 5.19
418 419 5.497474 GAGTTTGATTCCTAGTAAAGCCCA 58.503 41.667 0.00 0.00 0.00 5.36
419 420 6.079712 AGTTTGATTCCTAGTAAAGCCCAT 57.920 37.500 0.00 0.00 0.00 4.00
420 421 6.494059 AGTTTGATTCCTAGTAAAGCCCATT 58.506 36.000 0.00 0.00 0.00 3.16
421 422 6.954102 AGTTTGATTCCTAGTAAAGCCCATTT 59.046 34.615 0.00 0.00 34.72 2.32
422 423 7.454694 AGTTTGATTCCTAGTAAAGCCCATTTT 59.545 33.333 0.00 0.00 32.01 1.82
423 424 7.404671 TTGATTCCTAGTAAAGCCCATTTTC 57.595 36.000 0.00 0.00 32.01 2.29
424 425 5.588648 TGATTCCTAGTAAAGCCCATTTTCG 59.411 40.000 0.00 0.00 32.01 3.46
425 426 3.881220 TCCTAGTAAAGCCCATTTTCGG 58.119 45.455 0.00 0.00 32.01 4.30
433 434 3.199290 CCCATTTTCGGGCCATACA 57.801 52.632 4.39 0.00 40.07 2.29
434 435 1.703411 CCCATTTTCGGGCCATACAT 58.297 50.000 4.39 0.00 40.07 2.29
435 436 2.038659 CCCATTTTCGGGCCATACATT 58.961 47.619 4.39 0.00 40.07 2.71
436 437 2.224018 CCCATTTTCGGGCCATACATTG 60.224 50.000 4.39 0.00 40.07 2.82
437 438 2.472816 CATTTTCGGGCCATACATTGC 58.527 47.619 4.39 0.00 0.00 3.56
438 439 1.846007 TTTTCGGGCCATACATTGCT 58.154 45.000 4.39 0.00 0.00 3.91
439 440 2.719531 TTTCGGGCCATACATTGCTA 57.280 45.000 4.39 0.00 0.00 3.49
440 441 2.719531 TTCGGGCCATACATTGCTAA 57.280 45.000 4.39 0.00 0.00 3.09
441 442 1.961793 TCGGGCCATACATTGCTAAC 58.038 50.000 4.39 0.00 0.00 2.34
442 443 0.586319 CGGGCCATACATTGCTAACG 59.414 55.000 4.39 0.00 0.00 3.18
443 444 0.951558 GGGCCATACATTGCTAACGG 59.048 55.000 4.39 0.00 0.00 4.44
444 445 1.675552 GGCCATACATTGCTAACGGT 58.324 50.000 0.00 0.00 0.00 4.83
445 446 2.485835 GGGCCATACATTGCTAACGGTA 60.486 50.000 4.39 0.00 0.00 4.02
446 447 2.546789 GGCCATACATTGCTAACGGTAC 59.453 50.000 0.00 0.00 0.00 3.34
447 448 3.463944 GCCATACATTGCTAACGGTACT 58.536 45.455 0.00 0.00 0.00 2.73
448 449 4.501915 GGCCATACATTGCTAACGGTACTA 60.502 45.833 0.00 0.00 0.00 1.82
449 450 4.684703 GCCATACATTGCTAACGGTACTAG 59.315 45.833 0.00 0.00 0.00 2.57
450 451 4.684703 CCATACATTGCTAACGGTACTAGC 59.315 45.833 5.82 5.82 41.83 3.42
451 452 5.509163 CCATACATTGCTAACGGTACTAGCT 60.509 44.000 12.32 0.00 41.96 3.32
452 453 4.467198 ACATTGCTAACGGTACTAGCTT 57.533 40.909 12.32 0.47 41.96 3.74
453 454 5.587388 ACATTGCTAACGGTACTAGCTTA 57.413 39.130 12.32 3.47 41.96 3.09
454 455 5.346522 ACATTGCTAACGGTACTAGCTTAC 58.653 41.667 12.32 0.00 41.96 2.34
455 456 5.126707 ACATTGCTAACGGTACTAGCTTACT 59.873 40.000 12.32 0.00 41.96 2.24
456 457 4.889832 TGCTAACGGTACTAGCTTACTC 57.110 45.455 12.32 0.00 41.96 2.59
457 458 4.521146 TGCTAACGGTACTAGCTTACTCT 58.479 43.478 12.32 0.00 41.96 3.24
458 459 5.674525 TGCTAACGGTACTAGCTTACTCTA 58.325 41.667 12.32 0.00 41.96 2.43
459 460 6.115446 TGCTAACGGTACTAGCTTACTCTAA 58.885 40.000 12.32 0.00 41.96 2.10
460 461 6.769822 TGCTAACGGTACTAGCTTACTCTAAT 59.230 38.462 12.32 0.00 41.96 1.73
461 462 7.284034 TGCTAACGGTACTAGCTTACTCTAATT 59.716 37.037 12.32 0.00 41.96 1.40
462 463 7.590689 GCTAACGGTACTAGCTTACTCTAATTG 59.409 40.741 0.00 0.00 38.99 2.32
463 464 7.401955 AACGGTACTAGCTTACTCTAATTGT 57.598 36.000 0.00 0.00 0.00 2.71
464 465 7.401955 ACGGTACTAGCTTACTCTAATTGTT 57.598 36.000 0.00 0.00 0.00 2.83
465 466 8.511604 ACGGTACTAGCTTACTCTAATTGTTA 57.488 34.615 0.00 0.00 0.00 2.41
466 467 9.129532 ACGGTACTAGCTTACTCTAATTGTTAT 57.870 33.333 0.00 0.00 0.00 1.89
471 472 9.984190 ACTAGCTTACTCTAATTGTTATAAGGC 57.016 33.333 0.00 0.00 0.00 4.35
502 503 4.818546 AGCATGGTACAAATGTAGATGCTC 59.181 41.667 22.54 7.52 45.43 4.26
503 504 5.629834 AGCATGGTACAAATGTAGATGCTCA 60.630 40.000 22.54 6.64 45.43 4.26
504 505 6.914478 AGCATGGTACAAATGTAGATGCTCAT 60.914 38.462 22.54 10.50 45.43 2.90
505 506 7.690054 AGCATGGTACAAATGTAGATGCTCATA 60.690 37.037 22.54 0.00 45.43 2.15
509 510 8.646900 TGGTACAAATGTAGATGCTCATATACA 58.353 33.333 16.57 16.57 41.68 2.29
522 523 6.400579 GCTCATATACATGTGCATACACTC 57.599 41.667 9.11 0.00 46.27 3.51
523 524 5.928264 GCTCATATACATGTGCATACACTCA 59.072 40.000 9.11 0.00 46.27 3.41
524 525 6.592994 GCTCATATACATGTGCATACACTCAT 59.407 38.462 9.11 0.00 46.27 2.90
525 526 7.118825 GCTCATATACATGTGCATACACTCATT 59.881 37.037 9.11 0.00 46.27 2.57
535 536 7.133891 GTGCATACACTCATTCTTGTAAACT 57.866 36.000 0.00 0.00 43.85 2.66
536 537 7.237173 GTGCATACACTCATTCTTGTAAACTC 58.763 38.462 0.00 0.00 43.85 3.01
537 538 6.934083 TGCATACACTCATTCTTGTAAACTCA 59.066 34.615 0.00 0.00 32.07 3.41
538 539 7.095229 TGCATACACTCATTCTTGTAAACTCAC 60.095 37.037 0.00 0.00 32.07 3.51
539 540 7.118390 GCATACACTCATTCTTGTAAACTCACT 59.882 37.037 0.00 0.00 32.07 3.41
540 541 8.651588 CATACACTCATTCTTGTAAACTCACTC 58.348 37.037 0.00 0.00 32.07 3.51
541 542 6.582636 ACACTCATTCTTGTAAACTCACTCA 58.417 36.000 0.00 0.00 0.00 3.41
542 543 6.480320 ACACTCATTCTTGTAAACTCACTCAC 59.520 38.462 0.00 0.00 0.00 3.51
543 544 6.479990 CACTCATTCTTGTAAACTCACTCACA 59.520 38.462 0.00 0.00 0.00 3.58
544 545 7.011389 CACTCATTCTTGTAAACTCACTCACAA 59.989 37.037 0.00 0.00 0.00 3.33
545 546 7.011482 ACTCATTCTTGTAAACTCACTCACAAC 59.989 37.037 0.00 0.00 0.00 3.32
546 547 7.047891 TCATTCTTGTAAACTCACTCACAACT 58.952 34.615 0.00 0.00 0.00 3.16
547 548 7.552687 TCATTCTTGTAAACTCACTCACAACTT 59.447 33.333 0.00 0.00 0.00 2.66
548 549 8.826710 CATTCTTGTAAACTCACTCACAACTTA 58.173 33.333 0.00 0.00 0.00 2.24
549 550 7.766219 TCTTGTAAACTCACTCACAACTTAC 57.234 36.000 0.00 0.00 0.00 2.34
550 551 6.759827 TCTTGTAAACTCACTCACAACTTACC 59.240 38.462 0.00 0.00 0.00 2.85
551 552 5.362263 TGTAAACTCACTCACAACTTACCC 58.638 41.667 0.00 0.00 0.00 3.69
552 553 4.772886 AAACTCACTCACAACTTACCCT 57.227 40.909 0.00 0.00 0.00 4.34
553 554 5.881923 AAACTCACTCACAACTTACCCTA 57.118 39.130 0.00 0.00 0.00 3.53
554 555 5.470047 AACTCACTCACAACTTACCCTAG 57.530 43.478 0.00 0.00 0.00 3.02
555 556 3.833070 ACTCACTCACAACTTACCCTAGG 59.167 47.826 0.06 0.06 0.00 3.02
556 557 4.087182 CTCACTCACAACTTACCCTAGGA 58.913 47.826 11.48 0.00 0.00 2.94
557 558 4.087182 TCACTCACAACTTACCCTAGGAG 58.913 47.826 11.48 1.80 0.00 3.69
558 559 2.832733 ACTCACAACTTACCCTAGGAGC 59.167 50.000 11.48 0.00 0.00 4.70
559 560 2.832129 CTCACAACTTACCCTAGGAGCA 59.168 50.000 11.48 0.00 0.00 4.26
560 561 2.565834 TCACAACTTACCCTAGGAGCAC 59.434 50.000 11.48 0.00 0.00 4.40
561 562 1.907255 ACAACTTACCCTAGGAGCACC 59.093 52.381 11.48 0.00 0.00 5.01
563 564 2.572104 CAACTTACCCTAGGAGCACCTT 59.428 50.000 11.48 0.00 45.36 3.50
564 565 2.917205 ACTTACCCTAGGAGCACCTTT 58.083 47.619 11.48 0.00 45.36 3.11
565 566 2.572104 ACTTACCCTAGGAGCACCTTTG 59.428 50.000 11.48 1.91 45.36 2.77
566 567 2.634639 TACCCTAGGAGCACCTTTGA 57.365 50.000 11.48 0.00 45.36 2.69
567 568 1.280457 ACCCTAGGAGCACCTTTGAG 58.720 55.000 11.48 0.00 45.36 3.02
568 569 1.203313 ACCCTAGGAGCACCTTTGAGA 60.203 52.381 11.48 0.00 45.36 3.27
569 570 1.484240 CCCTAGGAGCACCTTTGAGAG 59.516 57.143 11.48 0.00 45.36 3.20
869 870 4.856801 GGCGGTGACCATGGCGAT 62.857 66.667 13.04 0.00 0.00 4.58
962 963 1.153269 GGAAGCTAGCAGTGGAGGC 60.153 63.158 18.83 0.00 0.00 4.70
1043 1044 4.519437 CTCGCGGATGCAGAGCCA 62.519 66.667 6.13 0.00 42.97 4.75
1175 1176 1.493446 GAATGGGGTAAGAATCGGGGT 59.507 52.381 0.00 0.00 0.00 4.95
1414 1415 4.531854 TGACAGAGAGCTAGCTATTGAGT 58.468 43.478 19.38 14.06 0.00 3.41
2036 2039 5.927819 ACCAAAATGTCATGGAAAATGTGT 58.072 33.333 0.00 0.00 39.12 3.72
2050 2053 4.833478 AAATGTGTCTCAGCTCTGGTAT 57.167 40.909 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 9.943163 GCAAATAATGTTTGGTGTATTGTTTTT 57.057 25.926 4.70 0.00 0.00 1.94
71 72 9.113838 TGCAAATAATGTTTGGTGTATTGTTTT 57.886 25.926 4.70 0.00 0.00 2.43
72 73 8.668510 TGCAAATAATGTTTGGTGTATTGTTT 57.331 26.923 4.70 0.00 0.00 2.83
73 74 8.845413 ATGCAAATAATGTTTGGTGTATTGTT 57.155 26.923 4.70 0.00 0.00 2.83
74 75 8.845413 AATGCAAATAATGTTTGGTGTATTGT 57.155 26.923 4.70 0.00 0.00 2.71
101 102 9.284968 TGGAAAAATGGTGAACAACTTTTTAAA 57.715 25.926 13.83 0.00 31.88 1.52
102 103 8.848474 TGGAAAAATGGTGAACAACTTTTTAA 57.152 26.923 13.83 4.44 31.88 1.52
103 104 8.722394 GTTGGAAAAATGGTGAACAACTTTTTA 58.278 29.630 13.83 0.99 35.24 1.52
104 105 7.229506 TGTTGGAAAAATGGTGAACAACTTTTT 59.770 29.630 9.55 9.55 37.99 1.94
105 106 6.712547 TGTTGGAAAAATGGTGAACAACTTTT 59.287 30.769 0.00 0.00 37.99 2.27
106 107 6.234177 TGTTGGAAAAATGGTGAACAACTTT 58.766 32.000 0.00 0.00 37.99 2.66
107 108 5.799213 TGTTGGAAAAATGGTGAACAACTT 58.201 33.333 0.00 0.00 37.99 2.66
108 109 5.413309 TGTTGGAAAAATGGTGAACAACT 57.587 34.783 0.00 0.00 37.99 3.16
109 110 6.487689 TTTGTTGGAAAAATGGTGAACAAC 57.512 33.333 0.00 0.00 34.08 3.32
110 111 7.081526 CATTTGTTGGAAAAATGGTGAACAA 57.918 32.000 0.00 0.00 40.02 2.83
111 112 6.674694 CATTTGTTGGAAAAATGGTGAACA 57.325 33.333 1.77 0.00 40.02 3.18
158 159 7.586714 AAATTTAAGAACTAAATGCAGCAGC 57.413 32.000 0.00 0.00 38.94 5.25
159 160 8.368126 CGAAAATTTAAGAACTAAATGCAGCAG 58.632 33.333 0.00 0.00 38.94 4.24
160 161 7.148820 GCGAAAATTTAAGAACTAAATGCAGCA 60.149 33.333 0.00 0.00 38.94 4.41
161 162 7.062255 AGCGAAAATTTAAGAACTAAATGCAGC 59.938 33.333 0.00 0.00 38.94 5.25
162 163 8.452989 AGCGAAAATTTAAGAACTAAATGCAG 57.547 30.769 0.00 0.00 38.94 4.41
163 164 8.810652 AAGCGAAAATTTAAGAACTAAATGCA 57.189 26.923 0.00 0.00 38.94 3.96
164 165 9.516091 CAAAGCGAAAATTTAAGAACTAAATGC 57.484 29.630 0.00 0.00 38.94 3.56
165 166 9.516091 GCAAAGCGAAAATTTAAGAACTAAATG 57.484 29.630 0.00 0.00 38.94 2.32
166 167 8.708742 GGCAAAGCGAAAATTTAAGAACTAAAT 58.291 29.630 0.00 0.00 41.16 1.40
167 168 7.923878 AGGCAAAGCGAAAATTTAAGAACTAAA 59.076 29.630 0.00 0.00 34.00 1.85
168 169 7.430441 AGGCAAAGCGAAAATTTAAGAACTAA 58.570 30.769 0.00 0.00 0.00 2.24
169 170 6.977213 AGGCAAAGCGAAAATTTAAGAACTA 58.023 32.000 0.00 0.00 0.00 2.24
170 171 5.842907 AGGCAAAGCGAAAATTTAAGAACT 58.157 33.333 0.00 0.00 0.00 3.01
171 172 7.631915 TTAGGCAAAGCGAAAATTTAAGAAC 57.368 32.000 0.00 0.00 0.00 3.01
172 173 8.544597 GTTTTAGGCAAAGCGAAAATTTAAGAA 58.455 29.630 0.00 0.00 30.78 2.52
173 174 7.923878 AGTTTTAGGCAAAGCGAAAATTTAAGA 59.076 29.630 0.00 0.00 30.78 2.10
174 175 8.072238 AGTTTTAGGCAAAGCGAAAATTTAAG 57.928 30.769 0.00 0.00 30.78 1.85
175 176 8.331742 CAAGTTTTAGGCAAAGCGAAAATTTAA 58.668 29.630 0.00 0.00 29.92 1.52
176 177 7.517575 GCAAGTTTTAGGCAAAGCGAAAATTTA 60.518 33.333 0.00 0.00 29.92 1.40
177 178 6.714492 CAAGTTTTAGGCAAAGCGAAAATTT 58.286 32.000 0.00 0.00 30.52 1.82
178 179 5.277297 GCAAGTTTTAGGCAAAGCGAAAATT 60.277 36.000 0.00 0.00 30.78 1.82
179 180 4.211164 GCAAGTTTTAGGCAAAGCGAAAAT 59.789 37.500 0.00 0.00 30.78 1.82
180 181 3.553917 GCAAGTTTTAGGCAAAGCGAAAA 59.446 39.130 0.00 0.00 30.79 2.29
181 182 3.120041 GCAAGTTTTAGGCAAAGCGAAA 58.880 40.909 0.00 0.00 30.79 3.46
182 183 2.544903 GGCAAGTTTTAGGCAAAGCGAA 60.545 45.455 0.00 0.00 30.79 4.70
183 184 1.000717 GGCAAGTTTTAGGCAAAGCGA 60.001 47.619 0.00 0.00 30.79 4.93
184 185 1.000274 AGGCAAGTTTTAGGCAAAGCG 60.000 47.619 0.00 0.00 30.79 4.68
185 186 2.820059 AGGCAAGTTTTAGGCAAAGC 57.180 45.000 0.00 0.00 0.00 3.51
186 187 4.518970 TGTCTAGGCAAGTTTTAGGCAAAG 59.481 41.667 0.00 0.00 0.00 2.77
187 188 4.277423 GTGTCTAGGCAAGTTTTAGGCAAA 59.723 41.667 0.00 0.00 31.52 3.68
188 189 3.818773 GTGTCTAGGCAAGTTTTAGGCAA 59.181 43.478 0.00 0.00 31.52 4.52
189 190 3.181449 TGTGTCTAGGCAAGTTTTAGGCA 60.181 43.478 0.00 0.00 0.00 4.75
190 191 3.408634 TGTGTCTAGGCAAGTTTTAGGC 58.591 45.455 0.00 0.00 0.00 3.93
191 192 4.003648 CCTGTGTCTAGGCAAGTTTTAGG 58.996 47.826 0.00 0.00 0.00 2.69
192 193 4.894784 TCCTGTGTCTAGGCAAGTTTTAG 58.105 43.478 0.00 0.00 37.76 1.85
193 194 4.262894 CCTCCTGTGTCTAGGCAAGTTTTA 60.263 45.833 0.00 0.00 37.76 1.52
194 195 3.496870 CCTCCTGTGTCTAGGCAAGTTTT 60.497 47.826 0.00 0.00 37.76 2.43
195 196 2.039084 CCTCCTGTGTCTAGGCAAGTTT 59.961 50.000 0.00 0.00 37.76 2.66
196 197 1.625818 CCTCCTGTGTCTAGGCAAGTT 59.374 52.381 0.00 0.00 37.76 2.66
197 198 1.270907 CCTCCTGTGTCTAGGCAAGT 58.729 55.000 0.00 0.00 37.76 3.16
198 199 1.205893 GACCTCCTGTGTCTAGGCAAG 59.794 57.143 0.00 0.00 37.76 4.01
199 200 1.267121 GACCTCCTGTGTCTAGGCAA 58.733 55.000 0.00 0.00 37.76 4.52
200 201 0.114364 TGACCTCCTGTGTCTAGGCA 59.886 55.000 0.00 0.00 37.76 4.75
201 202 1.267121 TTGACCTCCTGTGTCTAGGC 58.733 55.000 0.00 0.00 37.76 3.93
202 203 5.508153 CGATATTTGACCTCCTGTGTCTAGG 60.508 48.000 0.00 0.00 39.29 3.02
203 204 5.508153 CCGATATTTGACCTCCTGTGTCTAG 60.508 48.000 0.00 0.00 33.83 2.43
204 205 4.341235 CCGATATTTGACCTCCTGTGTCTA 59.659 45.833 0.00 0.00 33.83 2.59
205 206 3.133003 CCGATATTTGACCTCCTGTGTCT 59.867 47.826 0.00 0.00 33.83 3.41
206 207 3.458189 CCGATATTTGACCTCCTGTGTC 58.542 50.000 0.00 0.00 0.00 3.67
207 208 2.420129 GCCGATATTTGACCTCCTGTGT 60.420 50.000 0.00 0.00 0.00 3.72
208 209 2.213499 GCCGATATTTGACCTCCTGTG 58.787 52.381 0.00 0.00 0.00 3.66
209 210 1.202533 CGCCGATATTTGACCTCCTGT 60.203 52.381 0.00 0.00 0.00 4.00
210 211 1.502231 CGCCGATATTTGACCTCCTG 58.498 55.000 0.00 0.00 0.00 3.86
211 212 0.249911 GCGCCGATATTTGACCTCCT 60.250 55.000 0.00 0.00 0.00 3.69
212 213 1.228657 GGCGCCGATATTTGACCTCC 61.229 60.000 12.58 0.00 0.00 4.30
213 214 0.249911 AGGCGCCGATATTTGACCTC 60.250 55.000 23.20 0.00 0.00 3.85
214 215 0.532862 CAGGCGCCGATATTTGACCT 60.533 55.000 23.20 0.00 0.00 3.85
215 216 1.507141 CCAGGCGCCGATATTTGACC 61.507 60.000 23.20 0.00 0.00 4.02
216 217 1.507141 CCCAGGCGCCGATATTTGAC 61.507 60.000 23.20 0.00 0.00 3.18
217 218 1.227823 CCCAGGCGCCGATATTTGA 60.228 57.895 23.20 0.00 0.00 2.69
218 219 2.260869 CCCCAGGCGCCGATATTTG 61.261 63.158 23.20 12.82 0.00 2.32
219 220 2.113139 CCCCAGGCGCCGATATTT 59.887 61.111 23.20 0.00 0.00 1.40
220 221 2.847234 TCCCCAGGCGCCGATATT 60.847 61.111 23.20 0.00 0.00 1.28
221 222 3.626924 GTCCCCAGGCGCCGATAT 61.627 66.667 23.20 0.00 0.00 1.63
230 231 3.077556 CTCCAGGTCGTCCCCAGG 61.078 72.222 0.00 0.00 0.00 4.45
231 232 3.077556 CCTCCAGGTCGTCCCCAG 61.078 72.222 0.00 0.00 0.00 4.45
235 236 4.131088 GTCGCCTCCAGGTCGTCC 62.131 72.222 8.62 0.00 36.56 4.79
236 237 4.477975 CGTCGCCTCCAGGTCGTC 62.478 72.222 8.62 3.98 36.56 4.20
244 245 4.899239 CATCCAGCCGTCGCCTCC 62.899 72.222 0.00 0.00 34.57 4.30
270 271 3.546543 TAGAATCGGCGCTGGGGG 61.547 66.667 17.88 0.00 0.00 5.40
271 272 2.280186 GTAGAATCGGCGCTGGGG 60.280 66.667 17.88 0.00 0.00 4.96
272 273 2.280186 GGTAGAATCGGCGCTGGG 60.280 66.667 17.88 1.40 0.00 4.45
273 274 2.658593 CGGTAGAATCGGCGCTGG 60.659 66.667 17.88 4.31 0.00 4.85
274 275 3.330853 GCGGTAGAATCGGCGCTG 61.331 66.667 10.86 10.86 0.00 5.18
275 276 4.587189 GGCGGTAGAATCGGCGCT 62.587 66.667 7.64 0.00 42.80 5.92
279 280 2.473664 CTAGCCGGCGGTAGAATCGG 62.474 65.000 28.82 5.66 41.72 4.18
280 281 1.081376 CTAGCCGGCGGTAGAATCG 60.081 63.158 28.82 5.49 41.72 3.34
281 282 1.373121 GCTAGCCGGCGGTAGAATC 60.373 63.158 28.82 9.53 41.72 2.52
282 283 2.735237 GCTAGCCGGCGGTAGAAT 59.265 61.111 28.82 11.08 41.72 2.40
283 284 3.534056 GGCTAGCCGGCGGTAGAA 61.534 66.667 28.82 9.55 41.72 2.10
299 300 1.261238 TAAAAATTGCCGCCTGGGGG 61.261 55.000 24.52 24.52 38.76 5.40
300 301 0.829990 ATAAAAATTGCCGCCTGGGG 59.170 50.000 3.33 3.33 35.78 4.96
301 302 1.938625 CATAAAAATTGCCGCCTGGG 58.061 50.000 0.00 0.00 39.58 4.45
302 303 1.289276 GCATAAAAATTGCCGCCTGG 58.711 50.000 0.00 0.00 33.95 4.45
341 342 1.719063 TATCTCCAGCCATTGCCCCC 61.719 60.000 0.00 0.00 38.69 5.40
342 343 0.538287 GTATCTCCAGCCATTGCCCC 60.538 60.000 0.00 0.00 38.69 5.80
343 344 0.475906 AGTATCTCCAGCCATTGCCC 59.524 55.000 0.00 0.00 38.69 5.36
344 345 1.889545 GAGTATCTCCAGCCATTGCC 58.110 55.000 0.00 0.00 38.69 4.52
357 358 2.223994 GCCCGGTGTTCCTTAGAGTATC 60.224 54.545 0.00 0.00 0.00 2.24
358 359 1.761198 GCCCGGTGTTCCTTAGAGTAT 59.239 52.381 0.00 0.00 0.00 2.12
359 360 1.188863 GCCCGGTGTTCCTTAGAGTA 58.811 55.000 0.00 0.00 0.00 2.59
360 361 0.544595 AGCCCGGTGTTCCTTAGAGT 60.545 55.000 0.00 0.00 0.00 3.24
361 362 0.613777 AAGCCCGGTGTTCCTTAGAG 59.386 55.000 0.00 0.00 0.00 2.43
362 363 0.611714 GAAGCCCGGTGTTCCTTAGA 59.388 55.000 0.00 0.00 0.00 2.10
363 364 0.323629 TGAAGCCCGGTGTTCCTTAG 59.676 55.000 0.00 0.00 0.00 2.18
364 365 0.323629 CTGAAGCCCGGTGTTCCTTA 59.676 55.000 0.00 0.00 0.00 2.69
365 366 1.073199 CTGAAGCCCGGTGTTCCTT 59.927 57.895 0.00 0.00 0.00 3.36
366 367 2.750350 CTGAAGCCCGGTGTTCCT 59.250 61.111 0.00 0.00 0.00 3.36
367 368 3.056328 GCTGAAGCCCGGTGTTCC 61.056 66.667 0.00 0.00 34.31 3.62
368 369 3.423154 CGCTGAAGCCCGGTGTTC 61.423 66.667 0.00 3.13 37.91 3.18
369 370 4.250305 ACGCTGAAGCCCGGTGTT 62.250 61.111 0.00 0.00 41.85 3.32
370 371 4.988598 CACGCTGAAGCCCGGTGT 62.989 66.667 0.00 0.00 45.20 4.16
371 372 4.988598 ACACGCTGAAGCCCGGTG 62.989 66.667 0.00 7.12 37.91 4.94
372 373 4.988598 CACACGCTGAAGCCCGGT 62.989 66.667 0.00 0.00 37.91 5.28
374 375 4.988598 ACCACACGCTGAAGCCCG 62.989 66.667 0.00 0.00 37.91 6.13
375 376 2.594592 AACCACACGCTGAAGCCC 60.595 61.111 0.00 0.00 37.91 5.19
376 377 2.639286 CAACCACACGCTGAAGCC 59.361 61.111 0.00 0.00 37.91 4.35
377 378 2.050985 GCAACCACACGCTGAAGC 60.051 61.111 0.00 0.00 37.78 3.86
378 379 2.162921 CTCGCAACCACACGCTGAAG 62.163 60.000 0.00 0.00 0.00 3.02
379 380 2.202946 TCGCAACCACACGCTGAA 60.203 55.556 0.00 0.00 0.00 3.02
380 381 2.661537 CTCGCAACCACACGCTGA 60.662 61.111 0.00 0.00 0.00 4.26
381 382 2.047151 AAACTCGCAACCACACGCTG 62.047 55.000 0.00 0.00 0.00 5.18
382 383 1.817941 AAACTCGCAACCACACGCT 60.818 52.632 0.00 0.00 0.00 5.07
383 384 1.654137 CAAACTCGCAACCACACGC 60.654 57.895 0.00 0.00 0.00 5.34
384 385 0.586319 ATCAAACTCGCAACCACACG 59.414 50.000 0.00 0.00 0.00 4.49
385 386 2.604614 GGAATCAAACTCGCAACCACAC 60.605 50.000 0.00 0.00 0.00 3.82
386 387 1.606668 GGAATCAAACTCGCAACCACA 59.393 47.619 0.00 0.00 0.00 4.17
387 388 1.880027 AGGAATCAAACTCGCAACCAC 59.120 47.619 0.00 0.00 0.00 4.16
388 389 2.270352 AGGAATCAAACTCGCAACCA 57.730 45.000 0.00 0.00 0.00 3.67
389 390 3.335579 ACTAGGAATCAAACTCGCAACC 58.664 45.455 0.00 0.00 0.00 3.77
390 391 6.476243 TTTACTAGGAATCAAACTCGCAAC 57.524 37.500 0.00 0.00 0.00 4.17
391 392 5.121768 GCTTTACTAGGAATCAAACTCGCAA 59.878 40.000 0.00 0.00 0.00 4.85
392 393 4.630069 GCTTTACTAGGAATCAAACTCGCA 59.370 41.667 0.00 0.00 0.00 5.10
393 394 4.034163 GGCTTTACTAGGAATCAAACTCGC 59.966 45.833 0.00 0.00 0.00 5.03
394 395 4.571176 GGGCTTTACTAGGAATCAAACTCG 59.429 45.833 0.00 0.00 0.00 4.18
395 396 5.497474 TGGGCTTTACTAGGAATCAAACTC 58.503 41.667 0.00 0.00 0.00 3.01
396 397 5.514500 TGGGCTTTACTAGGAATCAAACT 57.486 39.130 0.00 0.00 0.00 2.66
397 398 6.775594 AATGGGCTTTACTAGGAATCAAAC 57.224 37.500 0.00 0.00 0.00 2.93
398 399 7.362574 CGAAAATGGGCTTTACTAGGAATCAAA 60.363 37.037 0.00 0.00 0.00 2.69
399 400 6.094881 CGAAAATGGGCTTTACTAGGAATCAA 59.905 38.462 0.00 0.00 0.00 2.57
400 401 5.588648 CGAAAATGGGCTTTACTAGGAATCA 59.411 40.000 0.00 0.00 0.00 2.57
401 402 5.008712 CCGAAAATGGGCTTTACTAGGAATC 59.991 44.000 0.00 0.00 0.00 2.52
402 403 4.887655 CCGAAAATGGGCTTTACTAGGAAT 59.112 41.667 0.00 0.00 0.00 3.01
403 404 4.266714 CCGAAAATGGGCTTTACTAGGAA 58.733 43.478 0.00 0.00 0.00 3.36
404 405 3.371166 CCCGAAAATGGGCTTTACTAGGA 60.371 47.826 0.00 0.00 43.70 2.94
405 406 2.949644 CCCGAAAATGGGCTTTACTAGG 59.050 50.000 0.00 0.00 43.70 3.02
416 417 2.802774 GCAATGTATGGCCCGAAAATGG 60.803 50.000 0.00 0.00 0.00 3.16
417 418 2.101249 AGCAATGTATGGCCCGAAAATG 59.899 45.455 0.00 0.00 0.00 2.32
418 419 2.387757 AGCAATGTATGGCCCGAAAAT 58.612 42.857 0.00 0.00 0.00 1.82
419 420 1.846007 AGCAATGTATGGCCCGAAAA 58.154 45.000 0.00 0.00 0.00 2.29
420 421 2.685897 GTTAGCAATGTATGGCCCGAAA 59.314 45.455 0.00 0.00 0.00 3.46
421 422 2.294074 GTTAGCAATGTATGGCCCGAA 58.706 47.619 0.00 0.00 0.00 4.30
422 423 1.808512 CGTTAGCAATGTATGGCCCGA 60.809 52.381 0.00 0.00 0.00 5.14
423 424 0.586319 CGTTAGCAATGTATGGCCCG 59.414 55.000 0.00 0.00 0.00 6.13
424 425 0.951558 CCGTTAGCAATGTATGGCCC 59.048 55.000 0.00 0.00 0.00 5.80
425 426 1.675552 ACCGTTAGCAATGTATGGCC 58.324 50.000 0.00 0.00 0.00 5.36
426 427 3.463944 AGTACCGTTAGCAATGTATGGC 58.536 45.455 0.00 0.00 0.00 4.40
427 428 4.684703 GCTAGTACCGTTAGCAATGTATGG 59.315 45.833 7.54 0.00 42.38 2.74
428 429 5.529791 AGCTAGTACCGTTAGCAATGTATG 58.470 41.667 13.34 0.00 44.65 2.39
429 430 5.786264 AGCTAGTACCGTTAGCAATGTAT 57.214 39.130 13.34 0.00 44.65 2.29
430 431 5.587388 AAGCTAGTACCGTTAGCAATGTA 57.413 39.130 13.34 0.00 44.65 2.29
431 432 4.467198 AAGCTAGTACCGTTAGCAATGT 57.533 40.909 13.34 0.00 44.65 2.71
432 433 5.589192 AGTAAGCTAGTACCGTTAGCAATG 58.411 41.667 13.34 0.00 44.65 2.82
433 434 5.593502 AGAGTAAGCTAGTACCGTTAGCAAT 59.406 40.000 13.34 6.01 44.65 3.56
434 435 4.946157 AGAGTAAGCTAGTACCGTTAGCAA 59.054 41.667 13.34 1.07 44.65 3.91
435 436 4.521146 AGAGTAAGCTAGTACCGTTAGCA 58.479 43.478 13.34 0.00 44.65 3.49
436 437 6.610741 TTAGAGTAAGCTAGTACCGTTAGC 57.389 41.667 4.81 4.81 42.99 3.09
437 438 8.619546 ACAATTAGAGTAAGCTAGTACCGTTAG 58.380 37.037 0.00 0.00 0.00 2.34
438 439 8.511604 ACAATTAGAGTAAGCTAGTACCGTTA 57.488 34.615 0.00 0.00 0.00 3.18
439 440 7.401955 ACAATTAGAGTAAGCTAGTACCGTT 57.598 36.000 0.00 0.00 0.00 4.44
440 441 7.401955 AACAATTAGAGTAAGCTAGTACCGT 57.598 36.000 0.00 0.00 0.00 4.83
445 446 9.984190 GCCTTATAACAATTAGAGTAAGCTAGT 57.016 33.333 0.00 0.00 0.00 2.57
474 475 8.137437 GCATCTACATTTGTACCATGCTTTTAT 58.863 33.333 16.06 0.00 38.01 1.40
475 476 7.339212 AGCATCTACATTTGTACCATGCTTTTA 59.661 33.333 18.40 0.00 43.07 1.52
476 477 6.153340 AGCATCTACATTTGTACCATGCTTTT 59.847 34.615 18.40 5.89 43.07 2.27
477 478 5.653769 AGCATCTACATTTGTACCATGCTTT 59.346 36.000 18.40 6.36 43.07 3.51
478 479 5.195940 AGCATCTACATTTGTACCATGCTT 58.804 37.500 18.40 9.30 43.07 3.91
479 480 4.785301 AGCATCTACATTTGTACCATGCT 58.215 39.130 18.40 18.40 42.02 3.79
480 481 4.576053 TGAGCATCTACATTTGTACCATGC 59.424 41.667 15.78 15.78 39.60 4.06
481 482 6.872628 ATGAGCATCTACATTTGTACCATG 57.127 37.500 0.00 0.00 34.92 3.66
482 483 9.658799 GTATATGAGCATCTACATTTGTACCAT 57.341 33.333 0.00 0.00 34.92 3.55
483 484 8.646900 TGTATATGAGCATCTACATTTGTACCA 58.353 33.333 5.04 0.00 34.92 3.25
484 485 9.658799 ATGTATATGAGCATCTACATTTGTACC 57.341 33.333 12.86 0.00 37.64 3.34
487 488 8.996271 CACATGTATATGAGCATCTACATTTGT 58.004 33.333 17.82 13.33 38.34 2.83
488 489 7.961283 GCACATGTATATGAGCATCTACATTTG 59.039 37.037 19.85 19.85 46.18 2.32
489 490 8.037382 GCACATGTATATGAGCATCTACATTT 57.963 34.615 15.17 9.14 46.18 2.32
490 491 7.606858 GCACATGTATATGAGCATCTACATT 57.393 36.000 15.17 7.67 46.18 2.71
511 512 7.095229 TGAGTTTACAAGAATGAGTGTATGCAC 60.095 37.037 5.71 5.71 45.57 4.57
512 513 6.934083 TGAGTTTACAAGAATGAGTGTATGCA 59.066 34.615 0.00 0.00 30.59 3.96
513 514 7.118390 AGTGAGTTTACAAGAATGAGTGTATGC 59.882 37.037 0.00 0.00 30.59 3.14
514 515 8.539770 AGTGAGTTTACAAGAATGAGTGTATG 57.460 34.615 0.00 0.00 30.59 2.39
515 516 8.367911 TGAGTGAGTTTACAAGAATGAGTGTAT 58.632 33.333 0.00 0.00 30.59 2.29
516 517 7.652105 GTGAGTGAGTTTACAAGAATGAGTGTA 59.348 37.037 0.00 0.00 0.00 2.90
517 518 6.480320 GTGAGTGAGTTTACAAGAATGAGTGT 59.520 38.462 0.00 0.00 0.00 3.55
518 519 6.479990 TGTGAGTGAGTTTACAAGAATGAGTG 59.520 38.462 0.00 0.00 0.00 3.51
519 520 6.582636 TGTGAGTGAGTTTACAAGAATGAGT 58.417 36.000 0.00 0.00 0.00 3.41
520 521 7.225538 AGTTGTGAGTGAGTTTACAAGAATGAG 59.774 37.037 0.00 0.00 34.11 2.90
521 522 7.047891 AGTTGTGAGTGAGTTTACAAGAATGA 58.952 34.615 0.00 0.00 34.11 2.57
522 523 7.251704 AGTTGTGAGTGAGTTTACAAGAATG 57.748 36.000 0.00 0.00 34.11 2.67
523 524 7.865706 AAGTTGTGAGTGAGTTTACAAGAAT 57.134 32.000 0.00 0.00 34.11 2.40
524 525 7.279313 GGTAAGTTGTGAGTGAGTTTACAAGAA 59.721 37.037 0.00 0.00 34.11 2.52
525 526 6.759827 GGTAAGTTGTGAGTGAGTTTACAAGA 59.240 38.462 0.00 0.00 34.11 3.02
526 527 6.018180 GGGTAAGTTGTGAGTGAGTTTACAAG 60.018 42.308 0.00 0.00 34.11 3.16
527 528 5.818857 GGGTAAGTTGTGAGTGAGTTTACAA 59.181 40.000 0.00 0.00 0.00 2.41
528 529 5.129815 AGGGTAAGTTGTGAGTGAGTTTACA 59.870 40.000 0.00 0.00 0.00 2.41
529 530 5.608449 AGGGTAAGTTGTGAGTGAGTTTAC 58.392 41.667 0.00 0.00 0.00 2.01
530 531 5.881923 AGGGTAAGTTGTGAGTGAGTTTA 57.118 39.130 0.00 0.00 0.00 2.01
531 532 4.772886 AGGGTAAGTTGTGAGTGAGTTT 57.227 40.909 0.00 0.00 0.00 2.66
532 533 4.283722 CCTAGGGTAAGTTGTGAGTGAGTT 59.716 45.833 0.00 0.00 0.00 3.01
533 534 3.833070 CCTAGGGTAAGTTGTGAGTGAGT 59.167 47.826 0.00 0.00 0.00 3.41
534 535 4.087182 TCCTAGGGTAAGTTGTGAGTGAG 58.913 47.826 9.46 0.00 0.00 3.51
535 536 4.087182 CTCCTAGGGTAAGTTGTGAGTGA 58.913 47.826 9.46 0.00 0.00 3.41
536 537 3.368531 GCTCCTAGGGTAAGTTGTGAGTG 60.369 52.174 9.46 0.00 0.00 3.51
537 538 2.832733 GCTCCTAGGGTAAGTTGTGAGT 59.167 50.000 9.46 0.00 0.00 3.41
538 539 2.832129 TGCTCCTAGGGTAAGTTGTGAG 59.168 50.000 9.46 0.00 0.00 3.51
539 540 2.565834 GTGCTCCTAGGGTAAGTTGTGA 59.434 50.000 9.46 0.00 0.00 3.58
540 541 2.354805 GGTGCTCCTAGGGTAAGTTGTG 60.355 54.545 9.46 0.00 0.00 3.33
541 542 1.907255 GGTGCTCCTAGGGTAAGTTGT 59.093 52.381 9.46 0.00 0.00 3.32
542 543 2.188817 AGGTGCTCCTAGGGTAAGTTG 58.811 52.381 9.46 0.00 43.12 3.16
543 544 2.644060 AGGTGCTCCTAGGGTAAGTT 57.356 50.000 9.46 0.00 43.12 2.66
544 545 2.572104 CAAAGGTGCTCCTAGGGTAAGT 59.428 50.000 9.46 0.00 44.35 2.24
545 546 2.838202 TCAAAGGTGCTCCTAGGGTAAG 59.162 50.000 9.46 0.00 44.35 2.34
546 547 2.838202 CTCAAAGGTGCTCCTAGGGTAA 59.162 50.000 9.46 0.00 44.35 2.85
547 548 2.043939 TCTCAAAGGTGCTCCTAGGGTA 59.956 50.000 9.46 0.00 44.35 3.69
548 549 1.203313 TCTCAAAGGTGCTCCTAGGGT 60.203 52.381 9.46 0.00 44.35 4.34
549 550 1.484240 CTCTCAAAGGTGCTCCTAGGG 59.516 57.143 9.46 4.27 44.35 3.53
550 551 2.183679 ACTCTCAAAGGTGCTCCTAGG 58.816 52.381 7.96 0.82 44.35 3.02
551 552 3.383185 CCTACTCTCAAAGGTGCTCCTAG 59.617 52.174 7.96 3.89 44.35 3.02
552 553 3.366396 CCTACTCTCAAAGGTGCTCCTA 58.634 50.000 7.96 0.00 44.35 2.94
554 555 1.208293 CCCTACTCTCAAAGGTGCTCC 59.792 57.143 0.00 0.00 0.00 4.70
555 556 1.903183 ACCCTACTCTCAAAGGTGCTC 59.097 52.381 0.00 0.00 0.00 4.26
556 557 2.031495 ACCCTACTCTCAAAGGTGCT 57.969 50.000 0.00 0.00 0.00 4.40
557 558 2.861147 AACCCTACTCTCAAAGGTGC 57.139 50.000 0.00 0.00 0.00 5.01
558 559 7.715686 GGATAATTAACCCTACTCTCAAAGGTG 59.284 40.741 0.24 0.00 0.00 4.00
559 560 7.628101 AGGATAATTAACCCTACTCTCAAAGGT 59.372 37.037 8.09 0.00 0.00 3.50
560 561 8.035448 AGGATAATTAACCCTACTCTCAAAGG 57.965 38.462 8.09 0.00 0.00 3.11
561 562 9.907229 AAAGGATAATTAACCCTACTCTCAAAG 57.093 33.333 8.09 0.00 0.00 2.77
563 564 9.681062 CAAAAGGATAATTAACCCTACTCTCAA 57.319 33.333 8.09 0.00 0.00 3.02
564 565 7.773690 GCAAAAGGATAATTAACCCTACTCTCA 59.226 37.037 8.09 0.00 0.00 3.27
565 566 7.228906 GGCAAAAGGATAATTAACCCTACTCTC 59.771 40.741 8.09 0.00 0.00 3.20
566 567 7.061054 GGCAAAAGGATAATTAACCCTACTCT 58.939 38.462 8.09 0.00 0.00 3.24
567 568 6.264744 GGGCAAAAGGATAATTAACCCTACTC 59.735 42.308 8.09 0.00 31.84 2.59
568 569 6.068438 AGGGCAAAAGGATAATTAACCCTACT 60.068 38.462 8.09 0.00 43.36 2.57
569 570 6.134055 AGGGCAAAAGGATAATTAACCCTAC 58.866 40.000 8.09 1.34 43.36 3.18
869 870 2.360726 TCACCGCCGTGCTCTCTA 60.361 61.111 0.00 0.00 40.04 2.43
1175 1176 3.423776 CGACGACGAAAATGGTGCAATTA 60.424 43.478 0.00 0.00 42.66 1.40
1414 1415 7.883311 CCTAACCTTCTTCTTCAACATCCTAAA 59.117 37.037 0.00 0.00 0.00 1.85
2036 2039 4.579340 CGTAAACCTATACCAGAGCTGAGA 59.421 45.833 0.00 0.00 0.00 3.27
2050 2053 1.297364 GGCACCTGGCGTAAACCTA 59.703 57.895 0.00 0.00 46.16 3.08


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

AutoCloner maintained by Alex Coulton.