Multiple sequence alignment - TraesCS5B01G386800

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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 TraesCS5B01G386800 chr5B 100.000 4599 0 0 1 4599 565932563 565927965 0.000000e+00 8493.0
1 TraesCS5B01G386800 chr5B 87.870 338 28 5 3026 3360 565897386 565897713 7.220000e-103 385.0
2 TraesCS5B01G386800 chr5B 90.566 265 16 3 3104 3360 565880099 565880362 4.410000e-90 342.0
3 TraesCS5B01G386800 chr5B 95.146 103 5 0 4104 4206 166379079 166379181 3.680000e-36 163.0
4 TraesCS5B01G386800 chr5B 90.991 111 10 0 2683 2793 64266318 64266208 2.870000e-32 150.0
5 TraesCS5B01G386800 chr5B 82.883 111 19 0 2683 2793 559992112 559992222 2.930000e-17 100.0
6 TraesCS5B01G386800 chr5D 95.611 3828 93 30 415 4213 460396805 460393024 0.000000e+00 6069.0
7 TraesCS5B01G386800 chr5D 95.908 391 9 3 4215 4599 460392859 460392470 1.090000e-175 627.0
8 TraesCS5B01G386800 chr5D 92.053 302 21 2 3034 3332 460225444 460225745 5.500000e-114 422.0
9 TraesCS5B01G386800 chr5D 87.912 182 13 6 1 177 460396986 460396809 6.030000e-49 206.0
10 TraesCS5B01G386800 chr5D 95.833 96 4 0 4111 4206 139441012 139440917 6.160000e-34 156.0
11 TraesCS5B01G386800 chr5D 90.351 114 11 0 2680 2793 66755390 66755503 2.870000e-32 150.0
12 TraesCS5B01G386800 chr5D 82.883 111 19 0 2683 2793 457777065 457777175 2.930000e-17 100.0
13 TraesCS5B01G386800 chr5D 100.000 35 0 0 320 354 460396822 460396788 1.070000e-06 65.8
14 TraesCS5B01G386800 chr5A 94.244 3127 109 34 1519 4599 580467121 580464020 0.000000e+00 4711.0
15 TraesCS5B01G386800 chr5A 94.112 1087 24 17 415 1492 580468176 580467121 0.000000e+00 1616.0
16 TraesCS5B01G386800 chr5A 84.918 305 26 9 3034 3333 580449588 580449877 1.620000e-74 291.0
17 TraesCS5B01G386800 chr5A 92.697 178 10 3 1 177 580468355 580468180 2.120000e-63 254.0
18 TraesCS5B01G386800 chr5A 90.991 111 10 0 2683 2793 57376725 57376615 2.870000e-32 150.0
19 TraesCS5B01G386800 chr5A 95.699 93 4 0 4111 4203 174594025 174594117 2.870000e-32 150.0
20 TraesCS5B01G386800 chr5A 97.727 44 1 0 2683 2726 575658477 575658520 4.930000e-10 76.8
21 TraesCS5B01G386800 chr7B 94.792 96 5 0 4111 4206 162120908 162120813 2.870000e-32 150.0
22 TraesCS5B01G386800 chr6D 93.137 102 7 0 4109 4210 94768128 94768027 2.870000e-32 150.0
23 TraesCS5B01G386800 chr3A 93.204 103 5 2 4106 4206 470095675 470095777 2.870000e-32 150.0
24 TraesCS5B01G386800 chr3A 96.429 56 2 0 2980 3035 147791563 147791618 4.900000e-15 93.5
25 TraesCS5B01G386800 chr1B 92.233 103 8 0 4104 4206 587275914 587275812 3.710000e-31 147.0
26 TraesCS5B01G386800 chr3D 96.429 56 2 0 2980 3035 134083624 134083679 4.900000e-15 93.5
27 TraesCS5B01G386800 chr3B 96.429 56 2 0 2980 3035 190470961 190471016 4.900000e-15 93.5


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 TraesCS5B01G386800 chr5B 565927965 565932563 4598 True 8493.000000 8493 100.000000 1 4599 1 chr5B.!!$R2 4598
1 TraesCS5B01G386800 chr5D 460392470 460396986 4516 True 1741.950000 6069 94.857750 1 4599 4 chr5D.!!$R2 4598
2 TraesCS5B01G386800 chr5A 580464020 580468355 4335 True 2193.666667 4711 93.684333 1 4599 3 chr5A.!!$R2 4598

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
372 379 0.034337 GGTGCCTTGTACTTCCGTGA 59.966 55.000 0.00 0.0 0.0 4.35 F
1799 1825 0.458669 CATGTGCAGGCCTTCAATCC 59.541 55.000 6.68 0.0 0.0 3.01 F
2089 2115 1.070134 TGTCAGAGAGGAAAACCGGTG 59.930 52.381 8.52 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 1939 0.396139 TGCCATGGGATCTCCTTTGC 60.396 55.000 15.13 0.0 36.2 3.68 R
3115 3176 1.865340 AGCCGACGAAAGAAACTGAAC 59.135 47.619 0.00 0.0 0.0 3.18 R
3752 3815 8.363390 TCAATAACTCAATGACAGATAGGCTAG 58.637 37.037 0.00 0.0 0.0 3.42 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
177 184 9.526713 AGAAACAATATATATGATAGAGCTGCG 57.473 33.333 0.00 0.00 0.00 5.18
178 185 7.706281 AACAATATATATGATAGAGCTGCGC 57.294 36.000 0.00 0.00 0.00 6.09
179 186 7.048629 ACAATATATATGATAGAGCTGCGCT 57.951 36.000 9.73 11.39 43.88 5.92
180 187 8.171164 ACAATATATATGATAGAGCTGCGCTA 57.829 34.615 15.33 15.33 39.88 4.26
181 188 8.801299 ACAATATATATGATAGAGCTGCGCTAT 58.199 33.333 23.05 23.05 39.88 2.97
184 191 7.751768 ATATATGATAGAGCTGCGCTATACA 57.248 36.000 22.92 20.69 39.88 2.29
185 192 3.560902 TGATAGAGCTGCGCTATACAC 57.439 47.619 22.92 13.05 39.88 2.90
186 193 2.884639 TGATAGAGCTGCGCTATACACA 59.115 45.455 22.92 15.17 39.88 3.72
187 194 2.776312 TAGAGCTGCGCTATACACAC 57.224 50.000 9.73 0.00 39.88 3.82
188 195 0.248661 AGAGCTGCGCTATACACACG 60.249 55.000 9.73 0.00 39.88 4.49
189 196 0.248498 GAGCTGCGCTATACACACGA 60.248 55.000 9.73 0.00 39.88 4.35
190 197 0.385751 AGCTGCGCTATACACACGAT 59.614 50.000 9.73 0.00 36.99 3.73
191 198 1.607148 AGCTGCGCTATACACACGATA 59.393 47.619 9.73 0.00 36.99 2.92
192 199 2.034179 AGCTGCGCTATACACACGATAA 59.966 45.455 9.73 0.00 36.99 1.75
193 200 2.792674 GCTGCGCTATACACACGATAAA 59.207 45.455 9.73 0.00 0.00 1.40
194 201 3.244345 GCTGCGCTATACACACGATAAAA 59.756 43.478 9.73 0.00 0.00 1.52
195 202 4.084537 GCTGCGCTATACACACGATAAAAT 60.085 41.667 9.73 0.00 0.00 1.82
196 203 5.118050 GCTGCGCTATACACACGATAAAATA 59.882 40.000 9.73 0.00 0.00 1.40
197 204 6.183360 GCTGCGCTATACACACGATAAAATAT 60.183 38.462 9.73 0.00 0.00 1.28
198 205 7.044589 TGCGCTATACACACGATAAAATATG 57.955 36.000 9.73 0.00 0.00 1.78
199 206 6.864165 TGCGCTATACACACGATAAAATATGA 59.136 34.615 9.73 0.00 0.00 2.15
200 207 7.382759 TGCGCTATACACACGATAAAATATGAA 59.617 33.333 9.73 0.00 0.00 2.57
201 208 7.682865 GCGCTATACACACGATAAAATATGAAC 59.317 37.037 0.00 0.00 0.00 3.18
202 209 7.886212 CGCTATACACACGATAAAATATGAACG 59.114 37.037 0.00 0.00 0.00 3.95
203 210 8.908678 GCTATACACACGATAAAATATGAACGA 58.091 33.333 0.00 0.00 0.00 3.85
205 212 8.867112 ATACACACGATAAAATATGAACGACT 57.133 30.769 0.00 0.00 0.00 4.18
206 213 7.218145 ACACACGATAAAATATGAACGACTC 57.782 36.000 0.00 0.00 0.00 3.36
207 214 6.809689 ACACACGATAAAATATGAACGACTCA 59.190 34.615 0.00 0.00 38.81 3.41
208 215 7.491372 ACACACGATAAAATATGAACGACTCAT 59.509 33.333 9.21 9.21 46.86 2.90
226 233 9.930693 ACGACTCATAGAGGATATTTAAAATCC 57.069 33.333 15.84 15.84 42.85 3.01
227 234 9.077674 CGACTCATAGAGGATATTTAAAATCCG 57.922 37.037 16.82 8.22 46.37 4.18
228 235 9.372369 GACTCATAGAGGATATTTAAAATCCGG 57.628 37.037 16.82 0.00 46.37 5.14
229 236 7.824779 ACTCATAGAGGATATTTAAAATCCGGC 59.175 37.037 16.82 14.32 46.37 6.13
230 237 7.110155 TCATAGAGGATATTTAAAATCCGGCC 58.890 38.462 16.82 0.00 46.37 6.13
231 238 5.319043 AGAGGATATTTAAAATCCGGCCA 57.681 39.130 2.24 0.00 46.37 5.36
232 239 5.070685 AGAGGATATTTAAAATCCGGCCAC 58.929 41.667 2.24 10.88 46.37 5.01
233 240 4.798882 AGGATATTTAAAATCCGGCCACA 58.201 39.130 2.24 0.00 46.37 4.17
234 241 4.583073 AGGATATTTAAAATCCGGCCACAC 59.417 41.667 2.24 0.00 46.37 3.82
235 242 4.339814 GGATATTTAAAATCCGGCCACACA 59.660 41.667 2.24 0.00 33.95 3.72
236 243 5.010617 GGATATTTAAAATCCGGCCACACAT 59.989 40.000 2.24 0.00 33.95 3.21
237 244 6.207810 GGATATTTAAAATCCGGCCACACATA 59.792 38.462 2.24 0.00 33.95 2.29
238 245 7.093945 GGATATTTAAAATCCGGCCACACATAT 60.094 37.037 2.24 0.00 33.95 1.78
239 246 4.909696 TTAAAATCCGGCCACACATATG 57.090 40.909 2.24 0.00 0.00 1.78
240 247 2.435372 AAATCCGGCCACACATATGT 57.565 45.000 2.24 1.41 40.80 2.29
253 260 3.904571 CACATATGTGCATACATTGGGC 58.095 45.455 22.27 0.00 45.01 5.36
254 261 3.318557 CACATATGTGCATACATTGGGCA 59.681 43.478 22.27 0.00 45.01 5.36
258 265 3.668147 TGCATACATTGGGCACTGT 57.332 47.368 0.00 0.00 31.58 3.55
259 266 1.462616 TGCATACATTGGGCACTGTC 58.537 50.000 0.00 0.00 31.58 3.51
260 267 0.740737 GCATACATTGGGCACTGTCC 59.259 55.000 0.00 0.00 0.00 4.02
261 268 1.016627 CATACATTGGGCACTGTCCG 58.983 55.000 0.00 0.00 0.00 4.79
262 269 0.748005 ATACATTGGGCACTGTCCGC 60.748 55.000 0.00 0.00 0.00 5.54
263 270 1.836999 TACATTGGGCACTGTCCGCT 61.837 55.000 0.00 0.00 0.00 5.52
264 271 2.360350 ATTGGGCACTGTCCGCTG 60.360 61.111 0.00 0.00 0.00 5.18
265 272 3.925630 ATTGGGCACTGTCCGCTGG 62.926 63.158 0.00 0.00 0.00 4.85
267 274 4.101448 GGGCACTGTCCGCTGGAT 62.101 66.667 0.67 0.00 32.73 3.41
268 275 2.731571 GGGCACTGTCCGCTGGATA 61.732 63.158 0.67 0.00 32.73 2.59
269 276 1.447643 GGCACTGTCCGCTGGATAT 59.552 57.895 0.67 0.00 32.73 1.63
270 277 0.601311 GGCACTGTCCGCTGGATATC 60.601 60.000 0.00 0.00 32.73 1.63
271 278 0.941463 GCACTGTCCGCTGGATATCG 60.941 60.000 0.00 0.00 32.73 2.92
272 279 0.668535 CACTGTCCGCTGGATATCGA 59.331 55.000 0.00 0.00 32.73 3.59
273 280 1.270826 CACTGTCCGCTGGATATCGAT 59.729 52.381 2.16 2.16 32.73 3.59
274 281 1.270826 ACTGTCCGCTGGATATCGATG 59.729 52.381 8.54 0.00 32.73 3.84
275 282 1.270826 CTGTCCGCTGGATATCGATGT 59.729 52.381 8.54 0.00 32.73 3.06
276 283 1.269723 TGTCCGCTGGATATCGATGTC 59.730 52.381 13.31 13.31 32.73 3.06
277 284 0.521735 TCCGCTGGATATCGATGTCG 59.478 55.000 14.97 5.22 41.45 4.35
278 285 0.241213 CCGCTGGATATCGATGTCGT 59.759 55.000 14.97 0.00 40.80 4.34
279 286 1.331241 CGCTGGATATCGATGTCGTG 58.669 55.000 14.97 11.16 40.80 4.35
280 287 1.063806 GCTGGATATCGATGTCGTGC 58.936 55.000 14.97 16.18 40.80 5.34
281 288 1.602920 GCTGGATATCGATGTCGTGCA 60.603 52.381 22.86 13.22 40.80 4.57
282 289 2.928301 GCTGGATATCGATGTCGTGCAT 60.928 50.000 22.86 4.22 41.24 3.96
283 290 2.665052 CTGGATATCGATGTCGTGCATG 59.335 50.000 14.97 0.00 38.06 4.06
284 291 1.391485 GGATATCGATGTCGTGCATGC 59.609 52.381 11.82 11.82 38.06 4.06
285 292 2.061028 GATATCGATGTCGTGCATGCA 58.939 47.619 18.46 18.46 38.06 3.96
286 293 2.153366 TATCGATGTCGTGCATGCAT 57.847 45.000 25.64 7.13 38.06 3.96
287 294 0.863799 ATCGATGTCGTGCATGCATC 59.136 50.000 25.64 22.77 38.06 3.91
288 295 4.886982 GATGTCGTGCATGCATCG 57.113 55.556 25.64 26.06 38.06 3.84
289 296 1.277739 GATGTCGTGCATGCATCGG 59.722 57.895 29.20 20.51 38.06 4.18
290 297 2.109538 GATGTCGTGCATGCATCGGG 62.110 60.000 29.20 18.55 38.06 5.14
291 298 4.241999 GTCGTGCATGCATCGGGC 62.242 66.667 29.20 21.95 45.13 6.13
300 307 3.512516 GCATCGGGCAGCAGGAAC 61.513 66.667 0.00 0.00 43.97 3.62
301 308 3.197790 CATCGGGCAGCAGGAACG 61.198 66.667 0.00 0.00 0.00 3.95
302 309 3.706373 ATCGGGCAGCAGGAACGT 61.706 61.111 0.00 0.00 0.00 3.99
303 310 3.958147 ATCGGGCAGCAGGAACGTG 62.958 63.158 0.00 0.00 0.00 4.49
306 313 3.058160 GGCAGCAGGAACGTGCAT 61.058 61.111 18.93 0.00 46.60 3.96
307 314 2.177531 GCAGCAGGAACGTGCATG 59.822 61.111 18.93 3.14 46.60 4.06
308 315 2.327343 GCAGCAGGAACGTGCATGA 61.327 57.895 13.50 0.00 46.60 3.07
309 316 1.855213 GCAGCAGGAACGTGCATGAA 61.855 55.000 13.50 0.00 46.60 2.57
310 317 0.167470 CAGCAGGAACGTGCATGAAG 59.833 55.000 13.50 0.00 46.60 3.02
311 318 1.154150 GCAGGAACGTGCATGAAGC 60.154 57.895 13.50 5.10 43.41 3.86
354 361 8.246180 ACTGCAACAACTCATATTAATTTGAGG 58.754 33.333 28.46 18.85 42.93 3.86
355 362 8.121305 TGCAACAACTCATATTAATTTGAGGT 57.879 30.769 28.46 23.64 42.93 3.85
360 367 7.961326 AACTCATATTAATTTGAGGTGCCTT 57.039 32.000 28.46 16.56 42.93 4.35
361 368 7.338800 ACTCATATTAATTTGAGGTGCCTTG 57.661 36.000 28.46 11.29 42.93 3.61
362 369 6.891908 ACTCATATTAATTTGAGGTGCCTTGT 59.108 34.615 28.46 11.77 42.93 3.16
363 370 8.052748 ACTCATATTAATTTGAGGTGCCTTGTA 58.947 33.333 28.46 0.16 42.93 2.41
364 371 8.220755 TCATATTAATTTGAGGTGCCTTGTAC 57.779 34.615 4.67 0.00 0.00 2.90
365 372 8.052748 TCATATTAATTTGAGGTGCCTTGTACT 58.947 33.333 4.67 0.00 0.00 2.73
366 373 8.686334 CATATTAATTTGAGGTGCCTTGTACTT 58.314 33.333 0.00 0.00 0.00 2.24
367 374 6.569179 TTAATTTGAGGTGCCTTGTACTTC 57.431 37.500 0.00 0.00 0.00 3.01
368 375 2.561478 TTGAGGTGCCTTGTACTTCC 57.439 50.000 0.00 0.00 0.00 3.46
369 376 0.320374 TGAGGTGCCTTGTACTTCCG 59.680 55.000 0.00 0.00 0.00 4.30
370 377 0.320697 GAGGTGCCTTGTACTTCCGT 59.679 55.000 0.00 0.00 0.00 4.69
371 378 0.034896 AGGTGCCTTGTACTTCCGTG 59.965 55.000 0.00 0.00 0.00 4.94
372 379 0.034337 GGTGCCTTGTACTTCCGTGA 59.966 55.000 0.00 0.00 0.00 4.35
373 380 1.541670 GGTGCCTTGTACTTCCGTGAA 60.542 52.381 0.00 0.00 0.00 3.18
374 381 1.529865 GTGCCTTGTACTTCCGTGAAC 59.470 52.381 0.00 0.00 0.00 3.18
375 382 1.414919 TGCCTTGTACTTCCGTGAACT 59.585 47.619 0.00 0.00 0.00 3.01
376 383 2.158871 TGCCTTGTACTTCCGTGAACTT 60.159 45.455 0.00 0.00 0.00 2.66
377 384 2.876550 GCCTTGTACTTCCGTGAACTTT 59.123 45.455 0.00 0.00 0.00 2.66
378 385 3.303791 GCCTTGTACTTCCGTGAACTTTG 60.304 47.826 0.00 0.00 0.00 2.77
379 386 4.124238 CCTTGTACTTCCGTGAACTTTGA 58.876 43.478 0.00 0.00 0.00 2.69
380 387 4.755123 CCTTGTACTTCCGTGAACTTTGAT 59.245 41.667 0.00 0.00 0.00 2.57
381 388 5.929992 CCTTGTACTTCCGTGAACTTTGATA 59.070 40.000 0.00 0.00 0.00 2.15
382 389 6.425721 CCTTGTACTTCCGTGAACTTTGATAA 59.574 38.462 0.00 0.00 0.00 1.75
383 390 7.119262 CCTTGTACTTCCGTGAACTTTGATAAT 59.881 37.037 0.00 0.00 0.00 1.28
384 391 9.146984 CTTGTACTTCCGTGAACTTTGATAATA 57.853 33.333 0.00 0.00 0.00 0.98
385 392 9.491675 TTGTACTTCCGTGAACTTTGATAATAA 57.508 29.630 0.00 0.00 0.00 1.40
386 393 9.491675 TGTACTTCCGTGAACTTTGATAATAAA 57.508 29.630 0.00 0.00 0.00 1.40
389 396 9.449719 ACTTCCGTGAACTTTGATAATAAATCT 57.550 29.630 0.00 0.00 0.00 2.40
390 397 9.708222 CTTCCGTGAACTTTGATAATAAATCTG 57.292 33.333 0.00 0.00 0.00 2.90
391 398 9.443323 TTCCGTGAACTTTGATAATAAATCTGA 57.557 29.630 0.00 0.00 0.00 3.27
392 399 9.098355 TCCGTGAACTTTGATAATAAATCTGAG 57.902 33.333 0.00 0.00 0.00 3.35
393 400 8.883731 CCGTGAACTTTGATAATAAATCTGAGT 58.116 33.333 0.00 0.00 0.00 3.41
402 409 8.786826 TGATAATAAATCTGAGTTGTTTCCGT 57.213 30.769 5.23 0.00 0.00 4.69
403 410 9.878667 TGATAATAAATCTGAGTTGTTTCCGTA 57.121 29.630 5.23 0.00 0.00 4.02
406 413 8.842358 AATAAATCTGAGTTGTTTCCGTAAGA 57.158 30.769 0.00 0.00 43.02 2.10
407 414 8.842358 ATAAATCTGAGTTGTTTCCGTAAGAA 57.158 30.769 0.00 0.00 43.02 2.52
408 415 7.562454 AAATCTGAGTTGTTTCCGTAAGAAA 57.438 32.000 0.00 0.00 42.28 2.52
409 416 7.562454 AATCTGAGTTGTTTCCGTAAGAAAA 57.438 32.000 0.00 0.00 45.93 2.29
410 417 6.988622 TCTGAGTTGTTTCCGTAAGAAAAA 57.011 33.333 0.00 0.00 45.93 1.94
411 418 7.011828 TCTGAGTTGTTTCCGTAAGAAAAAG 57.988 36.000 0.00 0.00 45.93 2.27
412 419 6.819649 TCTGAGTTGTTTCCGTAAGAAAAAGA 59.180 34.615 0.00 0.00 45.93 2.52
413 420 7.334921 TCTGAGTTGTTTCCGTAAGAAAAAGAA 59.665 33.333 0.00 0.00 45.93 2.52
414 421 7.818642 TGAGTTGTTTCCGTAAGAAAAAGAAA 58.181 30.769 0.00 0.00 45.93 2.52
415 422 8.298140 TGAGTTGTTTCCGTAAGAAAAAGAAAA 58.702 29.630 0.00 0.00 45.93 2.29
416 423 8.456904 AGTTGTTTCCGTAAGAAAAAGAAAAC 57.543 30.769 0.00 0.00 45.93 2.43
417 424 8.301720 AGTTGTTTCCGTAAGAAAAAGAAAACT 58.698 29.630 0.00 0.00 45.93 2.66
418 425 8.581263 GTTGTTTCCGTAAGAAAAAGAAAACTC 58.419 33.333 0.00 0.00 45.93 3.01
419 426 7.818642 TGTTTCCGTAAGAAAAAGAAAACTCA 58.181 30.769 0.00 0.00 45.93 3.41
420 427 8.463607 TGTTTCCGTAAGAAAAAGAAAACTCAT 58.536 29.630 0.00 0.00 45.93 2.90
421 428 9.940166 GTTTCCGTAAGAAAAAGAAAACTCATA 57.060 29.630 0.00 0.00 45.93 2.15
488 496 5.902613 TGCTATTGATCTTGGACCAAAAG 57.097 39.130 8.59 0.00 0.00 2.27
662 673 2.880890 AGCAAGTAGAGCAAACCACTTG 59.119 45.455 8.56 8.56 46.78 3.16
702 716 5.957842 TTCACCCTGTTGACATTTCATAC 57.042 39.130 0.00 0.00 0.00 2.39
713 727 4.137543 GACATTTCATACCACTGGATCCC 58.862 47.826 9.90 0.00 0.00 3.85
889 903 2.565834 TGTTCTAGTAACCCCACAGCTC 59.434 50.000 0.00 0.00 0.00 4.09
937 957 1.573108 TCACCACTTCATCTCCCTCC 58.427 55.000 0.00 0.00 0.00 4.30
938 958 1.079490 TCACCACTTCATCTCCCTCCT 59.921 52.381 0.00 0.00 0.00 3.69
1152 1172 2.028337 GCTAGCTAGCCGACCAGC 59.972 66.667 31.67 9.83 43.39 4.85
1493 1513 5.074584 TGGTAGGTTGTTGGTTTTGTTTC 57.925 39.130 0.00 0.00 0.00 2.78
1508 1528 7.502895 TGGTTTTGTTTCCTAACTAACATAGCA 59.497 33.333 0.00 0.00 34.52 3.49
1509 1529 8.520351 GGTTTTGTTTCCTAACTAACATAGCAT 58.480 33.333 0.00 0.00 34.52 3.79
1510 1530 9.556030 GTTTTGTTTCCTAACTAACATAGCATC 57.444 33.333 0.00 0.00 34.52 3.91
1511 1531 7.534085 TTGTTTCCTAACTAACATAGCATCG 57.466 36.000 0.00 0.00 34.52 3.84
1522 1542 7.244898 ACTAACATAGCATCGATCGAGTAATC 58.755 38.462 23.84 9.86 0.00 1.75
1652 1675 3.544684 AGAGTTTGAACATGTGTGCTCA 58.455 40.909 0.00 0.00 0.00 4.26
1723 1749 6.391227 TCCTTCTTTTCATTCTGGTTGTTC 57.609 37.500 0.00 0.00 0.00 3.18
1727 1753 4.644234 TCTTTTCATTCTGGTTGTTCAGCA 59.356 37.500 0.00 0.00 34.91 4.41
1799 1825 0.458669 CATGTGCAGGCCTTCAATCC 59.541 55.000 6.68 0.00 0.00 3.01
1818 1844 7.822658 TCAATCCTTTTTCCCGTTATAAACTG 58.177 34.615 0.00 0.00 0.00 3.16
1844 1870 6.403333 TTTCTCGAGTTTGGATTCGTTATG 57.597 37.500 13.13 0.00 36.51 1.90
1847 1873 6.802608 TCTCGAGTTTGGATTCGTTATGTAT 58.197 36.000 13.13 0.00 36.51 2.29
1872 1898 7.795482 TTATAGGACGTTGAATAAACCATGG 57.205 36.000 11.19 11.19 35.13 3.66
1913 1939 5.560183 CGCTTTAAGTAGGGCAAAATATCCG 60.560 44.000 0.00 0.00 0.00 4.18
2013 2039 4.281525 GCGAATTATTAACGCCTTTCCA 57.718 40.909 0.00 0.00 45.35 3.53
2080 2106 3.883489 CGGTACATACATGTCAGAGAGGA 59.117 47.826 0.00 0.00 41.97 3.71
2081 2107 4.338400 CGGTACATACATGTCAGAGAGGAA 59.662 45.833 0.00 0.00 41.97 3.36
2084 2110 6.535508 GGTACATACATGTCAGAGAGGAAAAC 59.464 42.308 0.00 0.00 41.97 2.43
2085 2111 5.491982 ACATACATGTCAGAGAGGAAAACC 58.508 41.667 0.00 0.00 35.87 3.27
2086 2112 3.045601 ACATGTCAGAGAGGAAAACCG 57.954 47.619 0.00 0.00 0.00 4.44
2087 2113 2.289694 ACATGTCAGAGAGGAAAACCGG 60.290 50.000 0.00 0.00 0.00 5.28
2088 2114 1.420430 TGTCAGAGAGGAAAACCGGT 58.580 50.000 0.00 0.00 0.00 5.28
2089 2115 1.070134 TGTCAGAGAGGAAAACCGGTG 59.930 52.381 8.52 0.00 0.00 4.94
2090 2116 1.343465 GTCAGAGAGGAAAACCGGTGA 59.657 52.381 8.52 0.00 0.00 4.02
2091 2117 2.028020 GTCAGAGAGGAAAACCGGTGAT 60.028 50.000 8.52 0.00 0.00 3.06
2092 2118 2.028112 TCAGAGAGGAAAACCGGTGATG 60.028 50.000 8.52 0.00 0.00 3.07
2093 2119 1.978580 AGAGAGGAAAACCGGTGATGT 59.021 47.619 8.52 0.00 0.00 3.06
2096 2122 4.041198 AGAGAGGAAAACCGGTGATGTTTA 59.959 41.667 8.52 0.00 34.97 2.01
2097 2123 4.918588 AGAGGAAAACCGGTGATGTTTAT 58.081 39.130 8.52 0.00 34.97 1.40
2113 2143 9.125026 GTGATGTTTATACTTTCCATCCATCTT 57.875 33.333 0.00 0.00 32.78 2.40
2245 2285 2.480224 CCATGATTCATGTGGCGTTC 57.520 50.000 21.95 0.00 39.94 3.95
2300 2341 6.014499 ACCATAATGATAGTGGTACTGCTACC 60.014 42.308 0.38 0.00 44.08 3.18
2310 2354 3.841845 TGGTACTGCTACCACCATAAAGT 59.158 43.478 0.78 0.00 46.53 2.66
2316 2360 2.159435 GCTACCACCATAAAGTTTGCCG 60.159 50.000 0.00 0.00 0.00 5.69
2471 2515 7.365295 GGGTTGGACTTGGAACTAGATTATGTA 60.365 40.741 0.00 0.00 0.00 2.29
2519 2564 5.773575 TGTAAATTTGTGGCTAATTTCGCA 58.226 33.333 0.00 7.14 36.75 5.10
2523 2568 3.485947 TTGTGGCTAATTTCGCATGTC 57.514 42.857 0.00 0.00 0.00 3.06
3115 3176 1.006832 CAATTAAGCGAGGTCCACGG 58.993 55.000 10.84 0.00 0.00 4.94
4132 4201 7.888514 AATACTCCCTCCAATCCATAATACA 57.111 36.000 0.00 0.00 0.00 2.29
4206 4275 4.227527 ACTTATTTTGGATCGGAGGGAGTT 59.772 41.667 0.00 0.00 0.00 3.01
4213 4445 0.755686 ATCGGAGGGAGTTGCATCTC 59.244 55.000 15.21 15.21 0.00 2.75
4303 4535 9.450807 GATTTACTGCATATCAAATGTAACCAC 57.549 33.333 0.00 0.00 0.00 4.16
4322 4554 1.153745 AGGCATCTCAACGCTCGTC 60.154 57.895 0.00 0.00 0.00 4.20
4395 4627 3.338249 GCTTACATCAAACTGGAGCTGA 58.662 45.455 0.00 0.00 31.01 4.26
4501 4739 5.187186 ACGTAACTAATTCCACATGGACTCT 59.813 40.000 0.00 0.00 45.39 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.006323 TGTTGGTTGTGTGCTTGAACTTT 59.994 39.130 0.00 0.00 0.00 2.66
82 88 9.676861 ACTTGTTTCTTTAAGGTACTGTTTACT 57.323 29.630 0.00 0.00 40.86 2.24
87 93 8.570068 TTGAACTTGTTTCTTTAAGGTACTGT 57.430 30.769 0.00 0.00 34.81 3.55
100 107 4.864247 TCTTGCTTTGCTTGAACTTGTTTC 59.136 37.500 0.00 0.00 34.41 2.78
173 180 5.576337 ATTTTATCGTGTGTATAGCGCAG 57.424 39.130 11.47 0.00 38.41 5.18
174 181 6.864165 TCATATTTTATCGTGTGTATAGCGCA 59.136 34.615 11.47 0.00 34.86 6.09
175 182 7.273188 TCATATTTTATCGTGTGTATAGCGC 57.727 36.000 0.00 0.00 0.00 5.92
176 183 7.886212 CGTTCATATTTTATCGTGTGTATAGCG 59.114 37.037 0.00 0.00 0.00 4.26
177 184 8.908678 TCGTTCATATTTTATCGTGTGTATAGC 58.091 33.333 0.00 0.00 0.00 2.97
179 186 9.955208 AGTCGTTCATATTTTATCGTGTGTATA 57.045 29.630 0.00 0.00 0.00 1.47
180 187 8.867112 AGTCGTTCATATTTTATCGTGTGTAT 57.133 30.769 0.00 0.00 0.00 2.29
181 188 7.969508 TGAGTCGTTCATATTTTATCGTGTGTA 59.030 33.333 0.00 0.00 0.00 2.90
182 189 6.809689 TGAGTCGTTCATATTTTATCGTGTGT 59.190 34.615 0.00 0.00 0.00 3.72
183 190 7.216920 TGAGTCGTTCATATTTTATCGTGTG 57.783 36.000 0.00 0.00 0.00 3.82
184 191 9.181805 CTATGAGTCGTTCATATTTTATCGTGT 57.818 33.333 11.06 0.00 45.36 4.49
185 192 9.394477 TCTATGAGTCGTTCATATTTTATCGTG 57.606 33.333 11.06 0.89 45.36 4.35
186 193 9.613957 CTCTATGAGTCGTTCATATTTTATCGT 57.386 33.333 11.06 0.00 45.36 3.73
187 194 9.066939 CCTCTATGAGTCGTTCATATTTTATCG 57.933 37.037 11.06 0.00 45.36 2.92
200 207 9.930693 GGATTTTAAATATCCTCTATGAGTCGT 57.069 33.333 16.12 0.00 38.81 4.34
201 208 9.077674 CGGATTTTAAATATCCTCTATGAGTCG 57.922 37.037 18.85 6.19 39.55 4.18
202 209 9.372369 CCGGATTTTAAATATCCTCTATGAGTC 57.628 37.037 18.85 0.00 39.55 3.36
203 210 7.824779 GCCGGATTTTAAATATCCTCTATGAGT 59.175 37.037 5.05 0.00 39.55 3.41
204 211 7.281100 GGCCGGATTTTAAATATCCTCTATGAG 59.719 40.741 5.05 8.30 39.55 2.90
205 212 7.110155 GGCCGGATTTTAAATATCCTCTATGA 58.890 38.462 5.05 0.00 39.55 2.15
206 213 6.884295 TGGCCGGATTTTAAATATCCTCTATG 59.116 38.462 5.05 9.19 39.55 2.23
207 214 6.884836 GTGGCCGGATTTTAAATATCCTCTAT 59.115 38.462 5.05 0.00 39.55 1.98
208 215 6.183361 TGTGGCCGGATTTTAAATATCCTCTA 60.183 38.462 5.05 10.84 39.55 2.43
209 216 5.070685 GTGGCCGGATTTTAAATATCCTCT 58.929 41.667 5.05 0.00 39.55 3.69
210 217 4.825085 TGTGGCCGGATTTTAAATATCCTC 59.175 41.667 5.05 13.37 39.55 3.71
211 218 4.583073 GTGTGGCCGGATTTTAAATATCCT 59.417 41.667 5.05 0.00 39.55 3.24
212 219 4.339814 TGTGTGGCCGGATTTTAAATATCC 59.660 41.667 5.05 14.52 38.55 2.59
213 220 5.508200 TGTGTGGCCGGATTTTAAATATC 57.492 39.130 5.05 0.00 0.00 1.63
214 221 7.232534 ACATATGTGTGGCCGGATTTTAAATAT 59.767 33.333 5.05 0.00 37.14 1.28
215 222 6.547880 ACATATGTGTGGCCGGATTTTAAATA 59.452 34.615 5.05 0.00 37.14 1.40
216 223 5.362430 ACATATGTGTGGCCGGATTTTAAAT 59.638 36.000 5.05 0.00 37.14 1.40
217 224 4.707448 ACATATGTGTGGCCGGATTTTAAA 59.293 37.500 5.05 0.00 37.14 1.52
218 225 4.274147 ACATATGTGTGGCCGGATTTTAA 58.726 39.130 5.05 0.00 37.14 1.52
219 226 3.892284 ACATATGTGTGGCCGGATTTTA 58.108 40.909 5.05 0.00 37.14 1.52
220 227 2.733956 ACATATGTGTGGCCGGATTTT 58.266 42.857 5.05 0.00 37.14 1.82
221 228 2.435372 ACATATGTGTGGCCGGATTT 57.565 45.000 5.05 0.00 37.14 2.17
231 238 3.318839 GCCCAATGTATGCACATATGTGT 59.681 43.478 31.10 18.33 44.83 3.72
232 239 3.318557 TGCCCAATGTATGCACATATGTG 59.681 43.478 28.07 28.07 44.83 3.21
233 240 3.564264 TGCCCAATGTATGCACATATGT 58.436 40.909 1.41 1.41 44.83 2.29
240 247 1.462616 GACAGTGCCCAATGTATGCA 58.537 50.000 0.99 0.00 39.96 3.96
241 248 0.740737 GGACAGTGCCCAATGTATGC 59.259 55.000 0.99 0.00 39.96 3.14
242 249 1.016627 CGGACAGTGCCCAATGTATG 58.983 55.000 0.99 0.00 39.96 2.39
243 250 0.748005 GCGGACAGTGCCCAATGTAT 60.748 55.000 0.99 0.00 39.96 2.29
244 251 1.376683 GCGGACAGTGCCCAATGTA 60.377 57.895 0.99 0.00 39.96 2.29
245 252 2.672996 GCGGACAGTGCCCAATGT 60.673 61.111 0.53 0.53 42.81 2.71
246 253 2.360350 AGCGGACAGTGCCCAATG 60.360 61.111 0.00 0.00 0.00 2.82
247 254 2.360350 CAGCGGACAGTGCCCAAT 60.360 61.111 0.00 0.00 0.00 3.16
248 255 4.641645 CCAGCGGACAGTGCCCAA 62.642 66.667 0.00 0.00 0.00 4.12
250 257 2.044806 ATATCCAGCGGACAGTGCCC 62.045 60.000 0.00 0.00 32.98 5.36
251 258 0.601311 GATATCCAGCGGACAGTGCC 60.601 60.000 0.00 0.00 32.98 5.01
252 259 0.941463 CGATATCCAGCGGACAGTGC 60.941 60.000 0.00 0.00 32.98 4.40
253 260 0.668535 TCGATATCCAGCGGACAGTG 59.331 55.000 0.00 0.00 32.98 3.66
254 261 1.270826 CATCGATATCCAGCGGACAGT 59.729 52.381 0.00 0.00 32.98 3.55
255 262 1.270826 ACATCGATATCCAGCGGACAG 59.729 52.381 0.00 0.00 32.98 3.51
256 263 1.269723 GACATCGATATCCAGCGGACA 59.730 52.381 0.00 0.00 32.98 4.02
257 264 1.729472 CGACATCGATATCCAGCGGAC 60.729 57.143 0.00 0.00 43.02 4.79
258 265 0.521735 CGACATCGATATCCAGCGGA 59.478 55.000 0.00 0.00 43.02 5.54
259 266 0.241213 ACGACATCGATATCCAGCGG 59.759 55.000 8.54 0.00 43.02 5.52
260 267 1.331241 CACGACATCGATATCCAGCG 58.669 55.000 8.54 0.00 43.02 5.18
261 268 1.063806 GCACGACATCGATATCCAGC 58.936 55.000 8.54 0.00 43.02 4.85
262 269 2.422276 TGCACGACATCGATATCCAG 57.578 50.000 8.54 0.00 43.02 3.86
263 270 2.676076 CATGCACGACATCGATATCCA 58.324 47.619 8.54 0.00 43.02 3.41
264 271 1.391485 GCATGCACGACATCGATATCC 59.609 52.381 14.21 0.00 43.02 2.59
265 272 2.061028 TGCATGCACGACATCGATATC 58.939 47.619 18.46 0.00 43.02 1.63
266 273 2.153366 TGCATGCACGACATCGATAT 57.847 45.000 18.46 0.00 43.02 1.63
267 274 2.061028 GATGCATGCACGACATCGATA 58.939 47.619 25.37 0.00 43.02 2.92
268 275 0.863799 GATGCATGCACGACATCGAT 59.136 50.000 25.37 2.84 43.02 3.59
269 276 2.300533 GATGCATGCACGACATCGA 58.699 52.632 25.37 0.00 43.02 3.59
270 277 4.886982 GATGCATGCACGACATCG 57.113 55.556 25.37 0.00 46.33 3.84
271 278 1.277739 CCGATGCATGCACGACATC 59.722 57.895 30.80 21.10 36.64 3.06
272 279 2.182181 CCCGATGCATGCACGACAT 61.182 57.895 30.80 15.69 40.66 3.06
273 280 2.819154 CCCGATGCATGCACGACA 60.819 61.111 30.80 10.19 0.00 4.35
274 281 4.241999 GCCCGATGCATGCACGAC 62.242 66.667 30.80 22.28 40.77 4.34
283 290 3.512516 GTTCCTGCTGCCCGATGC 61.513 66.667 0.00 0.00 41.77 3.91
284 291 3.197790 CGTTCCTGCTGCCCGATG 61.198 66.667 0.00 0.00 0.00 3.84
285 292 3.706373 ACGTTCCTGCTGCCCGAT 61.706 61.111 0.00 0.00 0.00 4.18
286 293 4.680237 CACGTTCCTGCTGCCCGA 62.680 66.667 0.00 0.00 0.00 5.14
289 296 3.058160 ATGCACGTTCCTGCTGCC 61.058 61.111 0.00 0.00 38.07 4.85
290 297 1.855213 TTCATGCACGTTCCTGCTGC 61.855 55.000 0.00 0.00 38.07 5.25
291 298 0.167470 CTTCATGCACGTTCCTGCTG 59.833 55.000 0.00 0.00 38.07 4.41
292 299 1.580845 GCTTCATGCACGTTCCTGCT 61.581 55.000 0.00 0.00 42.31 4.24
293 300 1.154150 GCTTCATGCACGTTCCTGC 60.154 57.895 0.00 0.00 42.31 4.85
303 310 3.125146 TCACATACGAAACTGCTTCATGC 59.875 43.478 0.00 0.00 43.25 4.06
304 311 4.926860 TCACATACGAAACTGCTTCATG 57.073 40.909 0.00 0.00 33.17 3.07
305 312 6.818644 AGTTATCACATACGAAACTGCTTCAT 59.181 34.615 0.00 0.00 33.17 2.57
306 313 6.090763 CAGTTATCACATACGAAACTGCTTCA 59.909 38.462 0.00 0.00 40.20 3.02
307 314 6.470160 CAGTTATCACATACGAAACTGCTTC 58.530 40.000 0.00 0.00 40.20 3.86
308 315 6.408858 CAGTTATCACATACGAAACTGCTT 57.591 37.500 0.00 0.00 40.20 3.91
311 318 5.778161 TGCAGTTATCACATACGAAACTG 57.222 39.130 8.72 8.72 46.18 3.16
312 319 5.699001 TGTTGCAGTTATCACATACGAAACT 59.301 36.000 0.00 0.00 0.00 2.66
313 320 5.922546 TGTTGCAGTTATCACATACGAAAC 58.077 37.500 0.00 0.00 0.00 2.78
314 321 6.203915 AGTTGTTGCAGTTATCACATACGAAA 59.796 34.615 0.00 0.00 0.00 3.46
315 322 5.699001 AGTTGTTGCAGTTATCACATACGAA 59.301 36.000 0.00 0.00 0.00 3.85
316 323 5.234752 AGTTGTTGCAGTTATCACATACGA 58.765 37.500 0.00 0.00 0.00 3.43
317 324 5.120053 TGAGTTGTTGCAGTTATCACATACG 59.880 40.000 0.00 0.00 0.00 3.06
318 325 6.480524 TGAGTTGTTGCAGTTATCACATAC 57.519 37.500 0.00 0.00 0.00 2.39
364 371 9.708222 CAGATTTATTATCAAAGTTCACGGAAG 57.292 33.333 0.00 0.00 0.00 3.46
365 372 9.443323 TCAGATTTATTATCAAAGTTCACGGAA 57.557 29.630 0.00 0.00 0.00 4.30
366 373 9.098355 CTCAGATTTATTATCAAAGTTCACGGA 57.902 33.333 0.00 0.00 0.00 4.69
367 374 8.883731 ACTCAGATTTATTATCAAAGTTCACGG 58.116 33.333 0.00 0.00 0.00 4.94
376 383 9.226606 ACGGAAACAACTCAGATTTATTATCAA 57.773 29.630 0.00 0.00 0.00 2.57
377 384 8.786826 ACGGAAACAACTCAGATTTATTATCA 57.213 30.769 0.00 0.00 0.00 2.15
380 387 9.932207 TCTTACGGAAACAACTCAGATTTATTA 57.068 29.630 0.00 0.00 0.00 0.98
381 388 8.842358 TCTTACGGAAACAACTCAGATTTATT 57.158 30.769 0.00 0.00 0.00 1.40
382 389 8.842358 TTCTTACGGAAACAACTCAGATTTAT 57.158 30.769 0.00 0.00 0.00 1.40
383 390 8.665643 TTTCTTACGGAAACAACTCAGATTTA 57.334 30.769 0.00 0.00 38.81 1.40
384 391 7.562454 TTTCTTACGGAAACAACTCAGATTT 57.438 32.000 0.00 0.00 38.81 2.17
385 392 7.562454 TTTTCTTACGGAAACAACTCAGATT 57.438 32.000 0.00 0.00 42.80 2.40
386 393 7.497909 TCTTTTTCTTACGGAAACAACTCAGAT 59.502 33.333 0.00 0.00 42.80 2.90
387 394 6.819649 TCTTTTTCTTACGGAAACAACTCAGA 59.180 34.615 0.00 0.00 42.80 3.27
388 395 7.011828 TCTTTTTCTTACGGAAACAACTCAG 57.988 36.000 0.00 0.00 42.80 3.35
389 396 6.988622 TCTTTTTCTTACGGAAACAACTCA 57.011 33.333 0.00 0.00 42.80 3.41
390 397 8.581263 GTTTTCTTTTTCTTACGGAAACAACTC 58.419 33.333 0.00 0.00 42.80 3.01
391 398 8.301720 AGTTTTCTTTTTCTTACGGAAACAACT 58.698 29.630 0.00 0.00 42.80 3.16
392 399 8.456904 AGTTTTCTTTTTCTTACGGAAACAAC 57.543 30.769 0.00 0.00 42.80 3.32
393 400 8.298140 TGAGTTTTCTTTTTCTTACGGAAACAA 58.702 29.630 0.00 0.00 42.80 2.83
394 401 7.818642 TGAGTTTTCTTTTTCTTACGGAAACA 58.181 30.769 0.00 0.00 42.80 2.83
395 402 8.851960 ATGAGTTTTCTTTTTCTTACGGAAAC 57.148 30.769 0.00 0.00 42.80 2.78
427 434 4.654915 TGTCTCATGATTTGAAGGCTCAA 58.345 39.130 0.00 0.00 39.87 3.02
428 435 4.290711 TGTCTCATGATTTGAAGGCTCA 57.709 40.909 0.00 0.00 32.78 4.26
429 436 4.880120 TCATGTCTCATGATTTGAAGGCTC 59.120 41.667 8.14 0.00 32.78 4.70
430 437 4.851843 TCATGTCTCATGATTTGAAGGCT 58.148 39.130 8.14 0.00 32.78 4.58
431 438 5.125097 AGTTCATGTCTCATGATTTGAAGGC 59.875 40.000 12.22 0.00 32.78 4.35
488 496 9.434559 GTTTTAGTCGATGCATTTAAGGATTAC 57.565 33.333 0.00 0.00 0.00 1.89
597 605 8.086522 GGTCGAAATATAATTAGTCACCAGCTA 58.913 37.037 0.00 0.00 0.00 3.32
631 639 9.760077 GGTTTGCTCTACTTGCTAGTATAATTA 57.240 33.333 8.49 0.00 36.32 1.40
702 716 0.405585 ACCAACTTGGGATCCAGTGG 59.594 55.000 15.23 14.34 43.37 4.00
713 727 0.400213 TGTGGAGGCCTACCAACTTG 59.600 55.000 21.19 0.00 39.22 3.16
889 903 2.938838 CTGGTAGGGTGGTAGAGAGAG 58.061 57.143 0.00 0.00 0.00 3.20
937 957 5.365021 AGAGAAAGAGAGAGGAGAGAGAG 57.635 47.826 0.00 0.00 0.00 3.20
938 958 5.339200 GGAAGAGAAAGAGAGAGGAGAGAGA 60.339 48.000 0.00 0.00 0.00 3.10
1307 1327 1.817099 CGGAGTCTTCCTGCATGCC 60.817 63.158 16.68 0.00 41.67 4.40
1308 1328 2.467826 GCGGAGTCTTCCTGCATGC 61.468 63.158 11.82 11.82 41.67 4.06
1309 1329 1.817099 GGCGGAGTCTTCCTGCATG 60.817 63.158 10.76 0.00 41.62 4.06
1466 1486 6.754193 ACAAAACCAACAACCTACCATAATG 58.246 36.000 0.00 0.00 0.00 1.90
1493 1513 5.939457 TCGATCGATGCTATGTTAGTTAGG 58.061 41.667 15.15 0.00 0.00 2.69
1508 1528 9.619316 CTAGAAAAATCAGATTACTCGATCGAT 57.381 33.333 19.78 11.36 0.00 3.59
1509 1529 7.591795 GCTAGAAAAATCAGATTACTCGATCGA 59.408 37.037 18.32 18.32 0.00 3.59
1510 1530 7.593273 AGCTAGAAAAATCAGATTACTCGATCG 59.407 37.037 9.36 9.36 0.00 3.69
1511 1531 8.810652 AGCTAGAAAAATCAGATTACTCGATC 57.189 34.615 0.00 0.00 0.00 3.69
1522 1542 7.989741 TCCATTCCTAGAAGCTAGAAAAATCAG 59.010 37.037 0.00 0.00 0.00 2.90
1541 1561 5.574970 AGGAGATAATCAGGTTCCATTCC 57.425 43.478 0.00 0.00 0.00 3.01
1581 1601 6.610075 ATGGATCTTTTGCTAAACAACCAT 57.390 33.333 5.26 5.26 38.23 3.55
1723 1749 4.756642 TGTGTACTTCTGGATCTTTTGCTG 59.243 41.667 0.00 0.00 0.00 4.41
1727 1753 8.784043 GTTTATGTGTGTACTTCTGGATCTTTT 58.216 33.333 0.00 0.00 0.00 2.27
1777 1803 1.529152 TTGAAGGCCTGCACATGCTG 61.529 55.000 15.07 4.56 42.66 4.41
1818 1844 3.497262 ACGAATCCAAACTCGAGAAAACC 59.503 43.478 21.68 0.00 38.43 3.27
1847 1873 7.201750 GCCATGGTTTATTCAACGTCCTATAAA 60.202 37.037 14.67 0.00 36.05 1.40
1856 1882 2.859538 GCATGCCATGGTTTATTCAACG 59.140 45.455 14.67 0.00 36.05 4.10
1872 1898 1.789116 CGTTTGCCCATTTGCATGC 59.211 52.632 11.82 11.82 41.70 4.06
1913 1939 0.396139 TGCCATGGGATCTCCTTTGC 60.396 55.000 15.13 0.00 36.20 3.68
1940 1966 2.359850 GGATGGTGTCGCCTTGCA 60.360 61.111 3.62 0.00 38.35 4.08
2013 2039 4.981806 AGTGCGCATATGTTTATGGTTT 57.018 36.364 15.91 0.00 36.49 3.27
2080 2106 6.490721 TGGAAAGTATAAACATCACCGGTTTT 59.509 34.615 2.97 5.68 39.12 2.43
2081 2107 6.005198 TGGAAAGTATAAACATCACCGGTTT 58.995 36.000 2.97 0.00 41.11 3.27
2084 2110 5.238650 GGATGGAAAGTATAAACATCACCGG 59.761 44.000 0.00 0.00 39.63 5.28
2085 2111 5.820423 TGGATGGAAAGTATAAACATCACCG 59.180 40.000 0.00 0.00 39.63 4.94
2086 2112 7.721399 AGATGGATGGAAAGTATAAACATCACC 59.279 37.037 0.00 0.00 39.63 4.02
2087 2113 8.682936 AGATGGATGGAAAGTATAAACATCAC 57.317 34.615 0.00 0.00 39.63 3.06
2088 2114 9.699410 AAAGATGGATGGAAAGTATAAACATCA 57.301 29.630 0.00 0.00 39.63 3.07
2194 2234 1.891933 TCCACAGCCCCAATCATCTA 58.108 50.000 0.00 0.00 0.00 1.98
2195 2235 1.229131 ATCCACAGCCCCAATCATCT 58.771 50.000 0.00 0.00 0.00 2.90
2196 2236 2.957402 TATCCACAGCCCCAATCATC 57.043 50.000 0.00 0.00 0.00 2.92
2300 2341 1.402720 CCTGCGGCAAACTTTATGGTG 60.403 52.381 3.44 0.00 0.00 4.17
2316 2360 6.345565 CGTTTAACTAATCTATGTACGCCTGC 60.346 42.308 0.00 0.00 0.00 4.85
2402 2446 9.158233 CAAATAAGATTCTCCATTGCAATTGTT 57.842 29.630 9.83 1.69 0.00 2.83
2471 2515 2.687935 ACCACTTGCAAATCAGTTCGTT 59.312 40.909 0.00 0.00 0.00 3.85
2519 2564 1.153568 CCTGGTCGACGCATGACAT 60.154 57.895 9.92 0.00 38.10 3.06
2523 2568 4.758251 TGCCCTGGTCGACGCATG 62.758 66.667 9.92 5.98 0.00 4.06
3115 3176 1.865340 AGCCGACGAAAGAAACTGAAC 59.135 47.619 0.00 0.00 0.00 3.18
3752 3815 8.363390 TCAATAACTCAATGACAGATAGGCTAG 58.637 37.037 0.00 0.00 0.00 3.42
4003 4066 8.408601 ACATAACATCTGCATATTCCTTTTGAC 58.591 33.333 0.00 0.00 0.00 3.18
4131 4200 4.024048 ACCTTAGTTCAAAACTGCGACATG 60.024 41.667 2.65 0.00 42.84 3.21
4132 4201 4.134563 ACCTTAGTTCAAAACTGCGACAT 58.865 39.130 2.65 0.00 42.84 3.06
4165 4234 4.795970 AAGTGTCGCAGTTTTGAACTAG 57.204 40.909 0.00 0.00 40.46 2.57
4179 4248 3.555956 CCTCCGATCCAAAATAAGTGTCG 59.444 47.826 0.00 0.00 0.00 4.35
4206 4275 4.471904 AAGGAGTTAATGTCGAGATGCA 57.528 40.909 0.00 0.00 0.00 3.96
4213 4445 9.146984 TGACACTATTTTAAGGAGTTAATGTCG 57.853 33.333 0.00 0.00 36.64 4.35
4303 4535 1.416813 GACGAGCGTTGAGATGCCTG 61.417 60.000 0.00 0.00 38.61 4.85
4322 4554 6.996282 ACTGATGTTATTAATCTTTACCCCCG 59.004 38.462 0.00 0.00 0.00 5.73
4359 4591 8.644374 TTGATGTAAGCCAGTTACCTTTTAAT 57.356 30.769 0.00 0.00 40.49 1.40
4395 4627 6.899393 TCTCCTTGATTTGTACATTTGCTT 57.101 33.333 0.00 0.00 0.00 3.91
4463 4701 6.630444 TTAGTTACGTGTTATTTTTGGCCA 57.370 33.333 0.00 0.00 0.00 5.36
4469 4707 9.834628 CATGTGGAATTAGTTACGTGTTATTTT 57.165 29.630 0.00 0.00 0.00 1.82
4501 4739 3.788227 AACTGGCTGTACAGGATGAAA 57.212 42.857 23.95 0.00 42.75 2.69


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

AutoCloner maintained by Alex Coulton.