Multiple sequence alignment - TraesCS2D01G492300

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 TraesCS2D01G492300 chr2D 100.000 1645 0 0 689 2333 590155268 590156912 0.000000e+00 3038.0
1 TraesCS2D01G492300 chr2D 100.000 420 0 0 1 420 590154580 590154999 0.000000e+00 776.0
2 TraesCS2D01G492300 chr2D 90.419 167 15 1 186 352 342099633 342099798 3.900000e-53 219.0
3 TraesCS2D01G492300 chr2A 87.169 943 57 25 1421 2325 724523366 724524282 0.000000e+00 1013.0
4 TraesCS2D01G492300 chr2A 90.370 675 52 5 719 1385 724522699 724523368 0.000000e+00 874.0
5 TraesCS2D01G492300 chr2A 88.764 178 13 5 181 352 155590899 155591075 6.530000e-51 211.0
6 TraesCS2D01G492300 chr2A 89.222 167 17 1 186 352 451810376 451810541 8.450000e-50 207.0
7 TraesCS2D01G492300 chr2A 95.000 60 3 0 12 71 724522233 724522292 6.860000e-16 95.3
8 TraesCS2D01G492300 chr2B 84.900 1000 73 33 1390 2321 714785542 714786531 0.000000e+00 939.0
9 TraesCS2D01G492300 chr2B 90.801 674 44 9 689 1347 714784879 714785549 0.000000e+00 885.0
10 TraesCS2D01G492300 chr2B 88.889 171 16 3 186 355 206754545 206754377 8.450000e-50 207.0
11 TraesCS2D01G492300 chr2B 89.222 167 17 1 186 352 407236176 407236341 8.450000e-50 207.0
12 TraesCS2D01G492300 chr2B 94.000 50 3 0 12 61 714784152 714784201 2.490000e-10 76.8
13 TraesCS2D01G492300 chr7A 90.751 346 31 1 987 1331 556102889 556102544 5.870000e-126 460.0
14 TraesCS2D01G492300 chr7D 90.145 345 34 0 987 1331 488609372 488609028 1.270000e-122 449.0
15 TraesCS2D01G492300 chr7D 88.304 171 18 2 186 355 312467082 312466913 1.090000e-48 204.0
16 TraesCS2D01G492300 chr7B 89.855 345 35 0 987 1331 516931633 516931289 5.920000e-121 444.0
17 TraesCS2D01G492300 chr1D 90.476 168 15 1 185 352 250738442 250738608 1.090000e-53 220.0
18 TraesCS2D01G492300 chr4A 88.889 171 15 3 187 355 580299045 580298877 8.450000e-50 207.0
19 TraesCS2D01G492300 chr1A 89.091 165 17 1 185 349 320892568 320892731 1.090000e-48 204.0


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 TraesCS2D01G492300 chr2D 590154580 590156912 2332 False 1907.000000 3038 100.000000 1 2333 2 chr2D.!!$F2 2332
1 TraesCS2D01G492300 chr2A 724522233 724524282 2049 False 660.766667 1013 90.846333 12 2325 3 chr2A.!!$F3 2313
2 TraesCS2D01G492300 chr2B 714784152 714786531 2379 False 633.600000 939 89.900333 12 2321 3 chr2B.!!$F2 2309

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
303 421 0.03582 TTGGCTATTCGGTGACCCAC 60.036 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1843 0.110238 CCACATTTCAAGTCACGGCG 60.11 55.0 4.8 4.8 0.0 6.46 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
61 62 1.466558 GTGGCTTCTGTAGAAAGCAGC 59.533 52.381 9.76 6.58 33.17 5.25
67 74 4.531332 CTTCTGTAGAAAGCAGCAAACAC 58.469 43.478 0.00 0.00 33.07 3.32
88 182 3.244044 ACACAATTTGCAACCATACCCAC 60.244 43.478 0.00 0.00 0.00 4.61
92 186 3.510531 TTTGCAACCATACCCACTGTA 57.489 42.857 0.00 0.00 0.00 2.74
93 187 3.730215 TTGCAACCATACCCACTGTAT 57.270 42.857 0.00 0.00 40.91 2.29
94 188 3.275617 TGCAACCATACCCACTGTATC 57.724 47.619 0.00 0.00 38.10 2.24
95 189 2.843730 TGCAACCATACCCACTGTATCT 59.156 45.455 0.00 0.00 38.10 1.98
96 190 3.206150 GCAACCATACCCACTGTATCTG 58.794 50.000 0.00 0.00 38.10 2.90
97 191 3.370527 GCAACCATACCCACTGTATCTGT 60.371 47.826 0.00 0.00 38.10 3.41
101 195 6.630203 ACCATACCCACTGTATCTGTTTTA 57.370 37.500 0.00 0.00 38.10 1.52
102 196 7.023171 ACCATACCCACTGTATCTGTTTTAA 57.977 36.000 0.00 0.00 38.10 1.52
104 198 8.113462 ACCATACCCACTGTATCTGTTTTAATT 58.887 33.333 0.00 0.00 38.10 1.40
108 202 8.747538 ACCCACTGTATCTGTTTTAATTATCC 57.252 34.615 0.00 0.00 0.00 2.59
115 232 9.928618 TGTATCTGTTTTAATTATCCCATGGAA 57.071 29.630 15.22 0.00 34.34 3.53
136 253 5.355350 GGAACCTGATGACAGTAAATGAAGG 59.645 44.000 0.00 0.00 42.05 3.46
138 255 3.310774 CCTGATGACAGTAAATGAAGGCG 59.689 47.826 0.00 0.00 42.05 5.52
143 260 3.071479 GACAGTAAATGAAGGCGTTGGA 58.929 45.455 0.00 0.00 0.00 3.53
145 262 4.079253 ACAGTAAATGAAGGCGTTGGAAT 58.921 39.130 0.00 0.00 0.00 3.01
174 292 7.035612 GGGGTTGAATTTGAAATCATACTGTC 58.964 38.462 0.00 0.00 0.00 3.51
175 293 7.309744 GGGGTTGAATTTGAAATCATACTGTCA 60.310 37.037 0.00 0.00 0.00 3.58
177 295 9.079833 GGTTGAATTTGAAATCATACTGTCATG 57.920 33.333 0.00 0.00 0.00 3.07
178 296 9.079833 GTTGAATTTGAAATCATACTGTCATGG 57.920 33.333 0.00 0.00 0.00 3.66
180 298 8.805175 TGAATTTGAAATCATACTGTCATGGTT 58.195 29.630 0.00 0.00 30.38 3.67
181 299 8.991243 AATTTGAAATCATACTGTCATGGTTG 57.009 30.769 0.00 0.00 29.65 3.77
182 300 7.757941 TTTGAAATCATACTGTCATGGTTGA 57.242 32.000 0.00 0.00 29.65 3.18
183 301 7.757941 TTGAAATCATACTGTCATGGTTGAA 57.242 32.000 0.00 0.00 29.65 2.69
192 310 6.017400 ACTGTCATGGTTGAATCAATGTTC 57.983 37.500 0.00 0.00 32.48 3.18
195 313 5.047872 TGTCATGGTTGAATCAATGTTCAGG 60.048 40.000 0.00 0.00 39.13 3.86
196 314 5.183713 GTCATGGTTGAATCAATGTTCAGGA 59.816 40.000 0.00 1.10 39.13 3.86
197 315 5.953548 TCATGGTTGAATCAATGTTCAGGAT 59.046 36.000 0.00 0.00 39.13 3.24
198 316 7.067372 GTCATGGTTGAATCAATGTTCAGGATA 59.933 37.037 0.00 0.00 39.13 2.59
199 317 7.781219 TCATGGTTGAATCAATGTTCAGGATAT 59.219 33.333 0.00 0.00 39.13 1.63
200 318 7.572523 TGGTTGAATCAATGTTCAGGATATC 57.427 36.000 0.00 0.00 39.13 1.63
201 319 6.260714 TGGTTGAATCAATGTTCAGGATATCG 59.739 38.462 0.00 0.00 39.13 2.92
202 320 6.293626 GGTTGAATCAATGTTCAGGATATCGG 60.294 42.308 0.00 0.00 39.13 4.18
203 321 5.928976 TGAATCAATGTTCAGGATATCGGT 58.071 37.500 0.00 0.00 33.41 4.69
204 322 7.061566 TGAATCAATGTTCAGGATATCGGTA 57.938 36.000 0.00 0.00 33.41 4.02
205 323 7.505258 TGAATCAATGTTCAGGATATCGGTAA 58.495 34.615 0.00 0.00 33.41 2.85
206 324 7.441157 TGAATCAATGTTCAGGATATCGGTAAC 59.559 37.037 0.00 1.75 33.41 2.50
207 325 6.479972 TCAATGTTCAGGATATCGGTAACT 57.520 37.500 11.58 0.00 0.00 2.24
208 326 6.280643 TCAATGTTCAGGATATCGGTAACTG 58.719 40.000 4.80 4.80 0.00 3.16
209 327 4.665833 TGTTCAGGATATCGGTAACTGG 57.334 45.455 9.93 0.00 0.00 4.00
210 328 4.028131 TGTTCAGGATATCGGTAACTGGT 58.972 43.478 9.93 0.00 0.00 4.00
211 329 5.202765 TGTTCAGGATATCGGTAACTGGTA 58.797 41.667 9.93 0.00 0.00 3.25
212 330 5.068198 TGTTCAGGATATCGGTAACTGGTAC 59.932 44.000 9.93 0.00 0.00 3.34
213 331 5.057843 TCAGGATATCGGTAACTGGTACT 57.942 43.478 2.46 0.00 32.80 2.73
214 332 6.191657 TCAGGATATCGGTAACTGGTACTA 57.808 41.667 2.46 0.00 32.80 1.82
215 333 6.787170 TCAGGATATCGGTAACTGGTACTAT 58.213 40.000 2.46 0.31 32.80 2.12
216 334 7.921304 TCAGGATATCGGTAACTGGTACTATA 58.079 38.462 2.46 2.47 32.80 1.31
217 335 8.554870 TCAGGATATCGGTAACTGGTACTATAT 58.445 37.037 2.46 6.85 32.80 0.86
218 336 8.838365 CAGGATATCGGTAACTGGTACTATATC 58.162 40.741 19.47 19.47 37.34 1.63
219 337 8.554870 AGGATATCGGTAACTGGTACTATATCA 58.445 37.037 24.06 4.23 38.35 2.15
220 338 8.838365 GGATATCGGTAACTGGTACTATATCAG 58.162 40.741 24.06 0.00 42.62 2.90
226 344 4.450305 ACTGGTACTATATCAGTCGGGT 57.550 45.455 0.00 0.00 46.78 5.28
227 345 4.142790 ACTGGTACTATATCAGTCGGGTG 58.857 47.826 0.00 0.00 46.78 4.61
228 346 2.889045 TGGTACTATATCAGTCGGGTGC 59.111 50.000 0.00 0.00 38.80 5.01
229 347 3.155501 GGTACTATATCAGTCGGGTGCT 58.844 50.000 0.00 0.00 38.80 4.40
230 348 3.057456 GGTACTATATCAGTCGGGTGCTG 60.057 52.174 0.00 0.00 38.80 4.41
231 349 2.945456 ACTATATCAGTCGGGTGCTGA 58.055 47.619 0.00 0.00 45.59 4.26
232 350 2.887783 ACTATATCAGTCGGGTGCTGAG 59.112 50.000 0.00 0.00 44.86 3.35
233 351 1.781786 ATATCAGTCGGGTGCTGAGT 58.218 50.000 0.00 0.00 44.86 3.41
234 352 2.430248 TATCAGTCGGGTGCTGAGTA 57.570 50.000 0.00 0.00 44.86 2.59
235 353 1.107114 ATCAGTCGGGTGCTGAGTAG 58.893 55.000 0.00 0.00 44.86 2.57
236 354 0.965866 TCAGTCGGGTGCTGAGTAGG 60.966 60.000 0.00 0.00 37.98 3.18
237 355 1.682684 AGTCGGGTGCTGAGTAGGG 60.683 63.158 0.00 0.00 0.00 3.53
238 356 2.363795 TCGGGTGCTGAGTAGGGG 60.364 66.667 0.00 0.00 0.00 4.79
239 357 2.363795 CGGGTGCTGAGTAGGGGA 60.364 66.667 0.00 0.00 0.00 4.81
240 358 1.762460 CGGGTGCTGAGTAGGGGAT 60.762 63.158 0.00 0.00 0.00 3.85
241 359 0.469331 CGGGTGCTGAGTAGGGGATA 60.469 60.000 0.00 0.00 0.00 2.59
242 360 1.802553 GGGTGCTGAGTAGGGGATAA 58.197 55.000 0.00 0.00 0.00 1.75
243 361 2.124411 GGGTGCTGAGTAGGGGATAAA 58.876 52.381 0.00 0.00 0.00 1.40
244 362 2.711547 GGGTGCTGAGTAGGGGATAAAT 59.288 50.000 0.00 0.00 0.00 1.40
245 363 3.496870 GGGTGCTGAGTAGGGGATAAATG 60.497 52.174 0.00 0.00 0.00 2.32
246 364 3.496870 GGTGCTGAGTAGGGGATAAATGG 60.497 52.174 0.00 0.00 0.00 3.16
247 365 2.711009 TGCTGAGTAGGGGATAAATGGG 59.289 50.000 0.00 0.00 0.00 4.00
248 366 2.553247 GCTGAGTAGGGGATAAATGGGC 60.553 54.545 0.00 0.00 0.00 5.36
249 367 1.697432 TGAGTAGGGGATAAATGGGCG 59.303 52.381 0.00 0.00 0.00 6.13
250 368 1.975680 GAGTAGGGGATAAATGGGCGA 59.024 52.381 0.00 0.00 0.00 5.54
251 369 2.370849 GAGTAGGGGATAAATGGGCGAA 59.629 50.000 0.00 0.00 0.00 4.70
252 370 2.986728 AGTAGGGGATAAATGGGCGAAT 59.013 45.455 0.00 0.00 0.00 3.34
253 371 3.397955 AGTAGGGGATAAATGGGCGAATT 59.602 43.478 0.00 0.00 0.00 2.17
254 372 2.597455 AGGGGATAAATGGGCGAATTG 58.403 47.619 0.00 0.00 0.00 2.32
255 373 2.091333 AGGGGATAAATGGGCGAATTGT 60.091 45.455 0.00 0.00 0.00 2.71
256 374 2.035832 GGGGATAAATGGGCGAATTGTG 59.964 50.000 0.00 0.00 0.00 3.33
257 375 2.545742 GGGATAAATGGGCGAATTGTGC 60.546 50.000 0.00 0.00 0.00 4.57
258 376 2.100584 GGATAAATGGGCGAATTGTGCA 59.899 45.455 2.08 0.00 0.00 4.57
259 377 2.937469 TAAATGGGCGAATTGTGCAG 57.063 45.000 0.00 0.00 0.00 4.41
260 378 0.968405 AAATGGGCGAATTGTGCAGT 59.032 45.000 0.00 0.00 0.00 4.40
261 379 0.968405 AATGGGCGAATTGTGCAGTT 59.032 45.000 0.00 0.00 0.00 3.16
262 380 1.832883 ATGGGCGAATTGTGCAGTTA 58.167 45.000 0.00 0.00 0.00 2.24
263 381 1.610363 TGGGCGAATTGTGCAGTTAA 58.390 45.000 0.00 0.00 0.00 2.01
264 382 2.166829 TGGGCGAATTGTGCAGTTAAT 58.833 42.857 0.00 0.00 0.00 1.40
265 383 2.163412 TGGGCGAATTGTGCAGTTAATC 59.837 45.455 0.00 0.00 0.00 1.75
266 384 2.163412 GGGCGAATTGTGCAGTTAATCA 59.837 45.455 0.00 0.00 0.00 2.57
267 385 3.429085 GGCGAATTGTGCAGTTAATCAG 58.571 45.455 0.00 0.00 0.00 2.90
268 386 3.126858 GGCGAATTGTGCAGTTAATCAGA 59.873 43.478 0.00 0.00 0.00 3.27
269 387 4.091424 GCGAATTGTGCAGTTAATCAGAC 58.909 43.478 0.00 0.00 0.00 3.51
270 388 4.326205 CGAATTGTGCAGTTAATCAGACG 58.674 43.478 0.00 0.00 0.00 4.18
271 389 4.091365 CGAATTGTGCAGTTAATCAGACGA 59.909 41.667 0.00 0.00 0.00 4.20
272 390 5.220472 CGAATTGTGCAGTTAATCAGACGAT 60.220 40.000 0.00 0.00 0.00 3.73
273 391 6.019881 CGAATTGTGCAGTTAATCAGACGATA 60.020 38.462 0.00 0.00 0.00 2.92
274 392 7.464045 CGAATTGTGCAGTTAATCAGACGATAA 60.464 37.037 0.00 0.00 0.00 1.75
275 393 7.609760 ATTGTGCAGTTAATCAGACGATAAA 57.390 32.000 0.00 0.00 0.00 1.40
276 394 7.609760 TTGTGCAGTTAATCAGACGATAAAT 57.390 32.000 0.00 0.00 0.00 1.40
277 395 7.234187 TGTGCAGTTAATCAGACGATAAATC 57.766 36.000 0.00 0.00 0.00 2.17
278 396 6.816140 TGTGCAGTTAATCAGACGATAAATCA 59.184 34.615 0.00 0.00 0.00 2.57
279 397 7.010460 TGTGCAGTTAATCAGACGATAAATCAG 59.990 37.037 0.00 0.00 0.00 2.90
280 398 7.010552 GTGCAGTTAATCAGACGATAAATCAGT 59.989 37.037 0.00 0.00 0.00 3.41
281 399 7.549134 TGCAGTTAATCAGACGATAAATCAGTT 59.451 33.333 0.00 0.00 0.00 3.16
282 400 9.031360 GCAGTTAATCAGACGATAAATCAGTTA 57.969 33.333 0.00 0.00 0.00 2.24
288 406 7.246674 TCAGACGATAAATCAGTTAATTGGC 57.753 36.000 0.00 0.00 0.00 4.52
289 407 7.047891 TCAGACGATAAATCAGTTAATTGGCT 58.952 34.615 0.00 0.00 0.00 4.75
290 408 8.201464 TCAGACGATAAATCAGTTAATTGGCTA 58.799 33.333 0.00 0.00 0.00 3.93
291 409 8.993121 CAGACGATAAATCAGTTAATTGGCTAT 58.007 33.333 0.00 0.00 0.00 2.97
292 410 9.561069 AGACGATAAATCAGTTAATTGGCTATT 57.439 29.630 0.00 0.00 0.00 1.73
293 411 9.813080 GACGATAAATCAGTTAATTGGCTATTC 57.187 33.333 0.00 0.00 0.00 1.75
294 412 8.495949 ACGATAAATCAGTTAATTGGCTATTCG 58.504 33.333 0.00 5.39 0.00 3.34
295 413 7.957484 CGATAAATCAGTTAATTGGCTATTCGG 59.043 37.037 0.00 0.00 0.00 4.30
296 414 8.691661 ATAAATCAGTTAATTGGCTATTCGGT 57.308 30.769 0.00 0.00 0.00 4.69
297 415 6.377327 AATCAGTTAATTGGCTATTCGGTG 57.623 37.500 0.00 0.00 0.00 4.94
298 416 5.092554 TCAGTTAATTGGCTATTCGGTGA 57.907 39.130 0.00 0.00 0.00 4.02
299 417 4.873827 TCAGTTAATTGGCTATTCGGTGAC 59.126 41.667 0.00 0.00 0.00 3.67
300 418 4.035208 CAGTTAATTGGCTATTCGGTGACC 59.965 45.833 0.00 0.00 0.00 4.02
301 419 2.052782 AATTGGCTATTCGGTGACCC 57.947 50.000 0.00 0.00 0.00 4.46
302 420 0.916086 ATTGGCTATTCGGTGACCCA 59.084 50.000 0.00 0.00 0.00 4.51
303 421 0.035820 TTGGCTATTCGGTGACCCAC 60.036 55.000 0.00 0.00 0.00 4.61
311 429 4.534401 GGTGACCCACCGAATAGC 57.466 61.111 0.00 0.00 44.95 2.97
312 430 1.520787 GGTGACCCACCGAATAGCG 60.521 63.158 0.00 0.00 44.95 4.26
313 431 1.514087 GTGACCCACCGAATAGCGA 59.486 57.895 0.00 0.00 44.57 4.93
314 432 0.104304 GTGACCCACCGAATAGCGAT 59.896 55.000 0.00 0.00 44.57 4.58
315 433 0.828022 TGACCCACCGAATAGCGATT 59.172 50.000 0.00 0.00 44.57 3.34
316 434 1.202486 TGACCCACCGAATAGCGATTC 60.202 52.381 9.31 9.31 44.57 2.52
317 435 0.828022 ACCCACCGAATAGCGATTCA 59.172 50.000 18.05 0.00 41.48 2.57
318 436 1.217882 CCCACCGAATAGCGATTCAC 58.782 55.000 18.05 0.00 41.48 3.18
319 437 1.202533 CCCACCGAATAGCGATTCACT 60.203 52.381 18.05 0.99 41.48 3.41
320 438 1.860950 CCACCGAATAGCGATTCACTG 59.139 52.381 18.05 11.79 41.48 3.66
321 439 2.481276 CCACCGAATAGCGATTCACTGA 60.481 50.000 18.05 0.00 41.48 3.41
322 440 2.535984 CACCGAATAGCGATTCACTGAC 59.464 50.000 18.05 0.00 41.48 3.51
323 441 2.128035 CCGAATAGCGATTCACTGACC 58.872 52.381 18.05 0.00 41.48 4.02
324 442 1.781429 CGAATAGCGATTCACTGACCG 59.219 52.381 18.05 0.97 41.48 4.79
325 443 2.540973 CGAATAGCGATTCACTGACCGA 60.541 50.000 18.05 0.00 41.48 4.69
326 444 2.783828 ATAGCGATTCACTGACCGAG 57.216 50.000 4.65 0.00 0.00 4.63
327 445 1.746470 TAGCGATTCACTGACCGAGA 58.254 50.000 4.65 0.00 0.00 4.04
328 446 1.107114 AGCGATTCACTGACCGAGAT 58.893 50.000 4.65 0.00 0.00 2.75
329 447 1.202348 AGCGATTCACTGACCGAGATG 60.202 52.381 4.65 0.00 0.00 2.90
330 448 1.203928 CGATTCACTGACCGAGATGC 58.796 55.000 0.00 0.00 0.00 3.91
331 449 1.576356 GATTCACTGACCGAGATGCC 58.424 55.000 0.00 0.00 0.00 4.40
332 450 0.179100 ATTCACTGACCGAGATGCCG 60.179 55.000 0.00 0.00 0.00 5.69
333 451 1.248101 TTCACTGACCGAGATGCCGA 61.248 55.000 0.00 0.00 0.00 5.54
334 452 1.037579 TCACTGACCGAGATGCCGAT 61.038 55.000 0.00 0.00 0.00 4.18
335 453 0.179100 CACTGACCGAGATGCCGATT 60.179 55.000 0.00 0.00 0.00 3.34
336 454 1.067060 CACTGACCGAGATGCCGATTA 59.933 52.381 0.00 0.00 0.00 1.75
337 455 1.754803 ACTGACCGAGATGCCGATTAA 59.245 47.619 0.00 0.00 0.00 1.40
338 456 2.128035 CTGACCGAGATGCCGATTAAC 58.872 52.381 0.00 0.00 0.00 2.01
339 457 1.754803 TGACCGAGATGCCGATTAACT 59.245 47.619 0.00 0.00 0.00 2.24
340 458 2.128035 GACCGAGATGCCGATTAACTG 58.872 52.381 0.00 0.00 0.00 3.16
341 459 1.202533 ACCGAGATGCCGATTAACTGG 60.203 52.381 0.00 0.00 0.00 4.00
346 464 4.456806 GCCGATTAACTGGCCGAT 57.543 55.556 8.31 0.00 45.73 4.18
347 465 3.599412 GCCGATTAACTGGCCGATA 57.401 52.632 8.31 0.00 45.73 2.92
348 466 2.094762 GCCGATTAACTGGCCGATAT 57.905 50.000 8.31 0.00 45.73 1.63
349 467 2.423577 GCCGATTAACTGGCCGATATT 58.576 47.619 8.31 0.00 45.73 1.28
350 468 2.812011 GCCGATTAACTGGCCGATATTT 59.188 45.455 8.31 0.00 45.73 1.40
351 469 3.364964 GCCGATTAACTGGCCGATATTTG 60.365 47.826 8.31 0.00 45.73 2.32
352 470 4.062293 CCGATTAACTGGCCGATATTTGA 58.938 43.478 0.00 0.00 0.00 2.69
353 471 4.513692 CCGATTAACTGGCCGATATTTGAA 59.486 41.667 0.00 0.00 0.00 2.69
354 472 5.008217 CCGATTAACTGGCCGATATTTGAAA 59.992 40.000 0.00 0.00 0.00 2.69
355 473 6.293955 CCGATTAACTGGCCGATATTTGAAAT 60.294 38.462 0.00 0.00 0.00 2.17
356 474 7.138736 CGATTAACTGGCCGATATTTGAAATT 58.861 34.615 0.00 0.00 0.00 1.82
357 475 7.113404 CGATTAACTGGCCGATATTTGAAATTG 59.887 37.037 0.00 0.00 0.00 2.32
358 476 5.659440 AACTGGCCGATATTTGAAATTGT 57.341 34.783 0.00 0.00 0.00 2.71
359 477 5.659440 ACTGGCCGATATTTGAAATTGTT 57.341 34.783 0.00 0.00 0.00 2.83
360 478 5.410067 ACTGGCCGATATTTGAAATTGTTG 58.590 37.500 0.00 0.00 0.00 3.33
361 479 5.184864 ACTGGCCGATATTTGAAATTGTTGA 59.815 36.000 0.00 0.00 0.00 3.18
362 480 6.127366 ACTGGCCGATATTTGAAATTGTTGAT 60.127 34.615 0.00 0.00 0.00 2.57
363 481 6.638610 TGGCCGATATTTGAAATTGTTGATT 58.361 32.000 0.00 0.00 0.00 2.57
364 482 7.776107 TGGCCGATATTTGAAATTGTTGATTA 58.224 30.769 0.00 0.00 0.00 1.75
365 483 8.420222 TGGCCGATATTTGAAATTGTTGATTAT 58.580 29.630 0.00 0.00 0.00 1.28
366 484 8.702438 GGCCGATATTTGAAATTGTTGATTATG 58.298 33.333 0.00 0.00 0.00 1.90
367 485 9.462174 GCCGATATTTGAAATTGTTGATTATGA 57.538 29.630 0.00 0.00 0.00 2.15
395 513 8.522542 TCTAGTGGTATACTTCCTTTTCTCTC 57.477 38.462 2.25 0.00 40.89 3.20
398 521 6.954684 AGTGGTATACTTCCTTTTCTCTCAGA 59.045 38.462 2.25 0.00 35.67 3.27
416 539 4.665281 CAGAGCAATCTGTTCTGTTCTG 57.335 45.455 11.16 2.25 46.36 3.02
417 540 4.063689 CAGAGCAATCTGTTCTGTTCTGT 58.936 43.478 11.16 0.00 46.36 3.41
419 542 4.754114 AGAGCAATCTGTTCTGTTCTGTTC 59.246 41.667 0.00 0.00 36.56 3.18
720 957 6.019640 CACTGGTTGCAAGTTCAACAAATAAG 60.020 38.462 0.00 9.39 45.98 1.73
723 970 7.271511 TGGTTGCAAGTTCAACAAATAAGAAT 58.728 30.769 0.00 0.00 45.98 2.40
746 993 2.380660 GCTTCTTCTCGAGATGCTACG 58.619 52.381 17.44 8.40 46.57 3.51
761 1008 1.714794 CTACGTCCAAAGCTCCAGTG 58.285 55.000 0.00 0.00 0.00 3.66
765 1012 0.108585 GTCCAAAGCTCCAGTGACCA 59.891 55.000 0.00 0.00 0.00 4.02
769 1016 3.073798 TCCAAAGCTCCAGTGACCAAATA 59.926 43.478 0.00 0.00 0.00 1.40
778 1025 7.232534 AGCTCCAGTGACCAAATAAACAATTTA 59.767 33.333 0.00 0.00 35.54 1.40
797 1044 7.872483 ACAATTTACCTTTTGATTCGATGCTTT 59.128 29.630 0.00 0.00 0.00 3.51
802 1049 5.418840 ACCTTTTGATTCGATGCTTTACCAT 59.581 36.000 0.00 0.00 0.00 3.55
805 1052 7.331687 CCTTTTGATTCGATGCTTTACCATTTT 59.668 33.333 0.00 0.00 0.00 1.82
806 1053 9.352784 CTTTTGATTCGATGCTTTACCATTTTA 57.647 29.630 0.00 0.00 0.00 1.52
807 1054 8.682128 TTTGATTCGATGCTTTACCATTTTAC 57.318 30.769 0.00 0.00 0.00 2.01
808 1055 7.384439 TGATTCGATGCTTTACCATTTTACA 57.616 32.000 0.00 0.00 0.00 2.41
809 1056 7.471721 TGATTCGATGCTTTACCATTTTACAG 58.528 34.615 0.00 0.00 0.00 2.74
869 1124 1.460504 ACATCCAATGCTGCAGTCAG 58.539 50.000 16.64 3.15 43.16 3.51
931 1186 7.713764 ACCATTTAATTTCTTTTGCTGACAC 57.286 32.000 0.00 0.00 0.00 3.67
960 1216 6.887013 AGATGACTAGATTCTGACAAGCAAT 58.113 36.000 0.00 0.00 0.00 3.56
1342 1598 1.331138 AGAAGCGATAGACGAACGAGG 59.669 52.381 0.14 0.00 45.77 4.63
1344 1600 1.096386 AGCGATAGACGAACGAGGCT 61.096 55.000 0.14 0.00 45.77 4.58
1346 1602 0.317103 CGATAGACGAACGAGGCTGG 60.317 60.000 0.00 0.00 45.77 4.85
1355 1611 2.125912 CGAGGCTGGTTCGTCAGG 60.126 66.667 0.00 0.00 35.43 3.86
1360 1616 2.750350 CTGGTTCGTCAGGCCCTT 59.250 61.111 0.00 0.00 0.00 3.95
1361 1617 1.073199 CTGGTTCGTCAGGCCCTTT 59.927 57.895 0.00 0.00 0.00 3.11
1362 1618 1.228124 TGGTTCGTCAGGCCCTTTG 60.228 57.895 0.00 0.00 0.00 2.77
1363 1619 1.971695 GGTTCGTCAGGCCCTTTGG 60.972 63.158 0.00 0.00 0.00 3.28
1383 1639 1.187567 GGGGCCTCATTTTGTGCTGT 61.188 55.000 0.84 0.00 0.00 4.40
1384 1640 0.681175 GGGCCTCATTTTGTGCTGTT 59.319 50.000 0.84 0.00 0.00 3.16
1385 1641 1.606224 GGGCCTCATTTTGTGCTGTTG 60.606 52.381 0.84 0.00 0.00 3.33
1386 1642 1.069049 GGCCTCATTTTGTGCTGTTGT 59.931 47.619 0.00 0.00 0.00 3.32
1387 1643 2.129607 GCCTCATTTTGTGCTGTTGTG 58.870 47.619 0.00 0.00 0.00 3.33
1388 1644 2.746269 CCTCATTTTGTGCTGTTGTGG 58.254 47.619 0.00 0.00 0.00 4.17
1389 1645 2.129607 CTCATTTTGTGCTGTTGTGGC 58.870 47.619 0.00 0.00 0.00 5.01
1405 1661 3.284197 GGCATGCTGGCATTTGATC 57.716 52.632 18.92 0.00 43.14 2.92
1447 1706 1.724623 GAACGAACAGCGCTGTATTCA 59.275 47.619 40.76 0.00 44.13 2.57
1450 1709 1.004610 CGAACAGCGCTGTATTCATGG 60.005 52.381 40.76 23.09 44.13 3.66
1484 1751 6.015265 GGTACTGATAGGAGAATACAACCCTC 60.015 46.154 0.00 0.00 0.00 4.30
1581 1872 3.422303 GCATGCGCCGTGACTTGA 61.422 61.111 4.18 0.00 0.00 3.02
1689 1980 1.885163 AATGAAGCAAGCTGGCAGCC 61.885 55.000 34.33 20.06 43.77 4.85
1795 2095 1.328680 CACTTGTAGCGCTTAGGCATG 59.671 52.381 18.68 14.04 38.60 4.06
1827 2127 2.995939 TGTATCGCAGCTTTCAGAACTG 59.004 45.455 0.00 0.00 34.48 3.16
1840 2140 3.320626 TCAGAACTGTGAAGATGCTTCG 58.679 45.455 0.00 0.00 0.00 3.79
1848 2148 2.152013 GAAGATGCTTCGCGGCGATC 62.152 60.000 26.95 19.74 35.23 3.69
1933 2234 0.798776 CCTCTGTTACCAGCAAAGCG 59.201 55.000 0.00 0.00 38.66 4.68
1946 2247 2.096819 AGCAAAGCGTTCGAAAGTTGAA 59.903 40.909 15.25 0.00 0.00 2.69
1947 2248 3.042887 GCAAAGCGTTCGAAAGTTGAAT 58.957 40.909 15.25 0.00 0.00 2.57
1948 2249 3.121696 GCAAAGCGTTCGAAAGTTGAATG 60.122 43.478 15.25 9.99 35.83 2.67
1950 2251 4.545823 AAGCGTTCGAAAGTTGAATGAA 57.454 36.364 12.65 0.00 34.92 2.57
1951 2252 4.545823 AGCGTTCGAAAGTTGAATGAAA 57.454 36.364 12.65 0.00 34.92 2.69
1952 2253 4.527564 AGCGTTCGAAAGTTGAATGAAAG 58.472 39.130 12.65 0.00 34.92 2.62
1953 2254 3.664025 GCGTTCGAAAGTTGAATGAAAGG 59.336 43.478 12.65 0.00 34.92 3.11
2013 2315 2.975851 GCACAAAGTCAGCGAATCAAAG 59.024 45.455 0.00 0.00 0.00 2.77
2016 2318 3.876914 ACAAAGTCAGCGAATCAAAGTCA 59.123 39.130 0.00 0.00 0.00 3.41
2017 2319 4.024556 ACAAAGTCAGCGAATCAAAGTCAG 60.025 41.667 0.00 0.00 0.00 3.51
2018 2320 2.693069 AGTCAGCGAATCAAAGTCAGG 58.307 47.619 0.00 0.00 0.00 3.86
2019 2321 1.734465 GTCAGCGAATCAAAGTCAGGG 59.266 52.381 0.00 0.00 0.00 4.45
2020 2322 1.089920 CAGCGAATCAAAGTCAGGGG 58.910 55.000 0.00 0.00 0.00 4.79
2060 2366 0.179200 GAAAATACAGTGCCGCCACG 60.179 55.000 0.00 0.00 46.62 4.94
2093 2399 1.000993 AACCCACCCAAACTGTGCA 59.999 52.632 0.00 0.00 32.30 4.57
2098 2404 1.202405 CCACCCAAACTGTGCACTTTC 60.202 52.381 19.41 0.00 32.30 2.62
2099 2405 1.476085 CACCCAAACTGTGCACTTTCA 59.524 47.619 19.41 0.00 0.00 2.69
2100 2406 2.101249 CACCCAAACTGTGCACTTTCAT 59.899 45.455 19.41 0.00 0.00 2.57
2101 2407 2.362077 ACCCAAACTGTGCACTTTCATC 59.638 45.455 19.41 0.00 0.00 2.92
2183 2501 2.643933 AACGCTAACCTCCGACTAAC 57.356 50.000 0.00 0.00 0.00 2.34
2209 2527 5.897050 GCTTCTGTCAAGCAGTATAGTACT 58.103 41.667 0.00 0.00 45.23 2.73
2225 2543 3.015327 AGTACTGTACGTCTCATGGACC 58.985 50.000 11.97 0.00 41.64 4.46
2248 2566 4.551702 TGCTCAATCTGCTAACCAACTA 57.448 40.909 0.00 0.00 0.00 2.24
2250 2568 4.877823 TGCTCAATCTGCTAACCAACTATG 59.122 41.667 0.00 0.00 0.00 2.23
2268 2603 0.720590 TGGTAAAATTACGCGCCGTC 59.279 50.000 5.73 0.00 41.54 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.550524 CACCAACTAGCAGTGGAGCTA 59.449 52.381 13.24 0.00 44.50 3.32
5 6 0.321671 TCACCAACTAGCAGTGGAGC 59.678 55.000 13.24 0.00 32.29 4.70
6 7 2.839486 TTCACCAACTAGCAGTGGAG 57.161 50.000 13.24 6.73 32.29 3.86
7 8 3.569194 TTTTCACCAACTAGCAGTGGA 57.431 42.857 13.24 0.16 32.29 4.02
8 9 3.569701 ACATTTTCACCAACTAGCAGTGG 59.430 43.478 6.23 6.23 32.29 4.00
9 10 4.036734 ACACATTTTCACCAACTAGCAGTG 59.963 41.667 0.00 0.00 0.00 3.66
10 11 4.036734 CACACATTTTCACCAACTAGCAGT 59.963 41.667 0.00 0.00 0.00 4.40
11 12 4.539870 CACACATTTTCACCAACTAGCAG 58.460 43.478 0.00 0.00 0.00 4.24
12 13 3.243367 GCACACATTTTCACCAACTAGCA 60.243 43.478 0.00 0.00 0.00 3.49
13 14 3.004734 AGCACACATTTTCACCAACTAGC 59.995 43.478 0.00 0.00 0.00 3.42
61 62 4.879104 ATGGTTGCAAATTGTGTGTTTG 57.121 36.364 0.00 0.00 39.08 2.93
67 74 3.006752 AGTGGGTATGGTTGCAAATTGTG 59.993 43.478 0.00 0.00 0.00 3.33
78 172 5.514500 AAAACAGATACAGTGGGTATGGT 57.486 39.130 0.00 0.00 42.76 3.55
79 173 8.519799 AATTAAAACAGATACAGTGGGTATGG 57.480 34.615 0.00 0.00 42.76 2.74
88 182 9.573166 TCCATGGGATAATTAAAACAGATACAG 57.427 33.333 13.02 0.00 0.00 2.74
92 186 8.067488 AGGTTCCATGGGATAATTAAAACAGAT 58.933 33.333 13.02 0.00 0.00 2.90
93 187 7.341769 CAGGTTCCATGGGATAATTAAAACAGA 59.658 37.037 13.02 0.00 0.00 3.41
94 188 7.341769 TCAGGTTCCATGGGATAATTAAAACAG 59.658 37.037 13.02 2.75 0.00 3.16
95 189 7.185565 TCAGGTTCCATGGGATAATTAAAACA 58.814 34.615 13.02 0.00 0.00 2.83
96 190 7.654022 TCAGGTTCCATGGGATAATTAAAAC 57.346 36.000 13.02 5.26 0.00 2.43
97 191 8.064389 TCATCAGGTTCCATGGGATAATTAAAA 58.936 33.333 13.02 0.00 0.00 1.52
101 195 5.103558 TGTCATCAGGTTCCATGGGATAATT 60.104 40.000 13.02 0.00 0.00 1.40
102 196 4.416513 TGTCATCAGGTTCCATGGGATAAT 59.583 41.667 13.02 0.00 0.00 1.28
104 198 3.392285 CTGTCATCAGGTTCCATGGGATA 59.608 47.826 13.02 0.00 37.97 2.59
106 200 1.561076 CTGTCATCAGGTTCCATGGGA 59.439 52.381 13.02 0.00 37.97 4.37
107 201 1.283029 ACTGTCATCAGGTTCCATGGG 59.717 52.381 13.02 0.00 45.14 4.00
108 202 2.795231 ACTGTCATCAGGTTCCATGG 57.205 50.000 4.97 4.97 45.14 3.66
115 232 4.265073 GCCTTCATTTACTGTCATCAGGT 58.735 43.478 0.47 0.00 45.14 4.00
136 253 0.173255 CAACCCCATCATTCCAACGC 59.827 55.000 0.00 0.00 0.00 4.84
138 255 4.824479 AATTCAACCCCATCATTCCAAC 57.176 40.909 0.00 0.00 0.00 3.77
143 260 7.018487 TGATTTCAAATTCAACCCCATCATT 57.982 32.000 0.00 0.00 0.00 2.57
145 262 6.623979 ATGATTTCAAATTCAACCCCATCA 57.376 33.333 0.00 0.00 0.00 3.07
174 292 5.648178 TCCTGAACATTGATTCAACCATG 57.352 39.130 0.15 0.00 38.12 3.66
175 293 7.040892 CGATATCCTGAACATTGATTCAACCAT 60.041 37.037 0.15 0.00 38.12 3.55
177 295 6.293626 CCGATATCCTGAACATTGATTCAACC 60.294 42.308 0.15 0.00 38.12 3.77
178 296 6.260936 ACCGATATCCTGAACATTGATTCAAC 59.739 38.462 0.15 0.00 38.12 3.18
180 298 5.928976 ACCGATATCCTGAACATTGATTCA 58.071 37.500 0.00 0.00 37.08 2.57
181 299 7.657761 AGTTACCGATATCCTGAACATTGATTC 59.342 37.037 0.00 0.00 0.00 2.52
182 300 7.442364 CAGTTACCGATATCCTGAACATTGATT 59.558 37.037 0.00 0.00 0.00 2.57
183 301 6.931281 CAGTTACCGATATCCTGAACATTGAT 59.069 38.462 0.00 0.00 0.00 2.57
192 310 8.749026 ATATAGTACCAGTTACCGATATCCTG 57.251 38.462 0.00 0.00 0.00 3.86
195 313 9.393512 ACTGATATAGTACCAGTTACCGATATC 57.606 37.037 0.00 0.00 37.86 1.63
196 314 9.393512 GACTGATATAGTACCAGTTACCGATAT 57.606 37.037 3.65 0.00 40.80 1.63
197 315 7.547019 CGACTGATATAGTACCAGTTACCGATA 59.453 40.741 3.65 0.00 40.80 2.92
198 316 6.370994 CGACTGATATAGTACCAGTTACCGAT 59.629 42.308 3.65 0.00 40.80 4.18
199 317 5.698089 CGACTGATATAGTACCAGTTACCGA 59.302 44.000 3.65 0.00 40.80 4.69
200 318 5.106791 CCGACTGATATAGTACCAGTTACCG 60.107 48.000 3.65 3.53 40.80 4.02
201 319 5.182760 CCCGACTGATATAGTACCAGTTACC 59.817 48.000 3.65 0.00 40.80 2.85
202 320 5.767168 ACCCGACTGATATAGTACCAGTTAC 59.233 44.000 3.65 0.00 40.80 2.50
203 321 5.766670 CACCCGACTGATATAGTACCAGTTA 59.233 44.000 3.65 0.00 40.80 2.24
204 322 4.583489 CACCCGACTGATATAGTACCAGTT 59.417 45.833 3.65 0.00 40.80 3.16
205 323 4.142790 CACCCGACTGATATAGTACCAGT 58.857 47.826 1.87 1.87 43.11 4.00
206 324 3.057456 GCACCCGACTGATATAGTACCAG 60.057 52.174 0.00 0.00 40.53 4.00
207 325 2.889045 GCACCCGACTGATATAGTACCA 59.111 50.000 0.00 0.00 40.53 3.25
208 326 3.057456 CAGCACCCGACTGATATAGTACC 60.057 52.174 0.00 0.00 40.53 3.34
209 327 3.819337 TCAGCACCCGACTGATATAGTAC 59.181 47.826 0.00 0.00 40.53 2.73
210 328 4.072839 CTCAGCACCCGACTGATATAGTA 58.927 47.826 0.00 0.00 42.99 1.82
211 329 2.887783 CTCAGCACCCGACTGATATAGT 59.112 50.000 0.00 0.00 42.99 2.12
212 330 2.887783 ACTCAGCACCCGACTGATATAG 59.112 50.000 0.00 0.00 42.99 1.31
213 331 2.945456 ACTCAGCACCCGACTGATATA 58.055 47.619 0.00 0.00 42.99 0.86
214 332 1.781786 ACTCAGCACCCGACTGATAT 58.218 50.000 0.00 0.00 42.99 1.63
215 333 2.298610 CTACTCAGCACCCGACTGATA 58.701 52.381 0.00 0.00 42.99 2.15
216 334 1.107114 CTACTCAGCACCCGACTGAT 58.893 55.000 0.00 0.00 42.99 2.90
217 335 0.965866 CCTACTCAGCACCCGACTGA 60.966 60.000 0.00 0.00 41.78 3.41
218 336 1.513158 CCTACTCAGCACCCGACTG 59.487 63.158 0.00 0.00 36.44 3.51
219 337 1.682684 CCCTACTCAGCACCCGACT 60.683 63.158 0.00 0.00 0.00 4.18
220 338 2.722201 CCCCTACTCAGCACCCGAC 61.722 68.421 0.00 0.00 0.00 4.79
221 339 2.238319 ATCCCCTACTCAGCACCCGA 62.238 60.000 0.00 0.00 0.00 5.14
222 340 0.469331 TATCCCCTACTCAGCACCCG 60.469 60.000 0.00 0.00 0.00 5.28
223 341 1.802553 TTATCCCCTACTCAGCACCC 58.197 55.000 0.00 0.00 0.00 4.61
224 342 3.496870 CCATTTATCCCCTACTCAGCACC 60.497 52.174 0.00 0.00 0.00 5.01
225 343 3.496870 CCCATTTATCCCCTACTCAGCAC 60.497 52.174 0.00 0.00 0.00 4.40
226 344 2.711009 CCCATTTATCCCCTACTCAGCA 59.289 50.000 0.00 0.00 0.00 4.41
227 345 2.553247 GCCCATTTATCCCCTACTCAGC 60.553 54.545 0.00 0.00 0.00 4.26
228 346 2.289694 CGCCCATTTATCCCCTACTCAG 60.290 54.545 0.00 0.00 0.00 3.35
229 347 1.697432 CGCCCATTTATCCCCTACTCA 59.303 52.381 0.00 0.00 0.00 3.41
230 348 1.975680 TCGCCCATTTATCCCCTACTC 59.024 52.381 0.00 0.00 0.00 2.59
231 349 2.112279 TCGCCCATTTATCCCCTACT 57.888 50.000 0.00 0.00 0.00 2.57
232 350 2.943036 TTCGCCCATTTATCCCCTAC 57.057 50.000 0.00 0.00 0.00 3.18
233 351 3.139397 ACAATTCGCCCATTTATCCCCTA 59.861 43.478 0.00 0.00 0.00 3.53
234 352 2.091333 ACAATTCGCCCATTTATCCCCT 60.091 45.455 0.00 0.00 0.00 4.79
235 353 2.035832 CACAATTCGCCCATTTATCCCC 59.964 50.000 0.00 0.00 0.00 4.81
236 354 2.545742 GCACAATTCGCCCATTTATCCC 60.546 50.000 0.00 0.00 0.00 3.85
237 355 2.100584 TGCACAATTCGCCCATTTATCC 59.899 45.455 0.00 0.00 0.00 2.59
238 356 3.181487 ACTGCACAATTCGCCCATTTATC 60.181 43.478 0.00 0.00 0.00 1.75
239 357 2.760092 ACTGCACAATTCGCCCATTTAT 59.240 40.909 0.00 0.00 0.00 1.40
240 358 2.166829 ACTGCACAATTCGCCCATTTA 58.833 42.857 0.00 0.00 0.00 1.40
241 359 0.968405 ACTGCACAATTCGCCCATTT 59.032 45.000 0.00 0.00 0.00 2.32
242 360 0.968405 AACTGCACAATTCGCCCATT 59.032 45.000 0.00 0.00 0.00 3.16
243 361 1.832883 TAACTGCACAATTCGCCCAT 58.167 45.000 0.00 0.00 0.00 4.00
244 362 1.610363 TTAACTGCACAATTCGCCCA 58.390 45.000 0.00 0.00 0.00 5.36
245 363 2.163412 TGATTAACTGCACAATTCGCCC 59.837 45.455 0.00 0.00 0.00 6.13
246 364 3.126858 TCTGATTAACTGCACAATTCGCC 59.873 43.478 0.00 0.00 0.00 5.54
247 365 4.091424 GTCTGATTAACTGCACAATTCGC 58.909 43.478 0.00 0.00 0.00 4.70
248 366 4.091365 TCGTCTGATTAACTGCACAATTCG 59.909 41.667 0.00 0.00 0.00 3.34
249 367 5.530519 TCGTCTGATTAACTGCACAATTC 57.469 39.130 0.00 0.00 0.00 2.17
250 368 7.609760 TTATCGTCTGATTAACTGCACAATT 57.390 32.000 0.00 0.00 35.99 2.32
251 369 7.609760 TTTATCGTCTGATTAACTGCACAAT 57.390 32.000 0.00 0.00 35.99 2.71
252 370 7.333174 TGATTTATCGTCTGATTAACTGCACAA 59.667 33.333 0.00 0.00 35.99 3.33
253 371 6.816140 TGATTTATCGTCTGATTAACTGCACA 59.184 34.615 0.00 0.00 35.99 4.57
254 372 7.010552 ACTGATTTATCGTCTGATTAACTGCAC 59.989 37.037 0.00 0.00 35.99 4.57
255 373 7.041721 ACTGATTTATCGTCTGATTAACTGCA 58.958 34.615 0.00 0.00 35.99 4.41
256 374 7.470289 ACTGATTTATCGTCTGATTAACTGC 57.530 36.000 0.00 0.00 35.99 4.40
262 380 8.345565 GCCAATTAACTGATTTATCGTCTGATT 58.654 33.333 0.00 0.00 35.99 2.57
263 381 7.716998 AGCCAATTAACTGATTTATCGTCTGAT 59.283 33.333 0.00 0.00 38.67 2.90
264 382 7.047891 AGCCAATTAACTGATTTATCGTCTGA 58.952 34.615 0.00 0.00 0.00 3.27
265 383 7.251704 AGCCAATTAACTGATTTATCGTCTG 57.748 36.000 0.00 0.00 0.00 3.51
266 384 9.561069 AATAGCCAATTAACTGATTTATCGTCT 57.439 29.630 0.00 0.00 0.00 4.18
267 385 9.813080 GAATAGCCAATTAACTGATTTATCGTC 57.187 33.333 0.00 0.00 0.00 4.20
268 386 8.495949 CGAATAGCCAATTAACTGATTTATCGT 58.504 33.333 0.00 0.00 0.00 3.73
269 387 7.957484 CCGAATAGCCAATTAACTGATTTATCG 59.043 37.037 0.00 0.00 0.00 2.92
270 388 8.784043 ACCGAATAGCCAATTAACTGATTTATC 58.216 33.333 0.00 0.00 0.00 1.75
271 389 8.567948 CACCGAATAGCCAATTAACTGATTTAT 58.432 33.333 0.00 0.00 0.00 1.40
272 390 7.771361 TCACCGAATAGCCAATTAACTGATTTA 59.229 33.333 0.00 0.00 0.00 1.40
273 391 6.601613 TCACCGAATAGCCAATTAACTGATTT 59.398 34.615 0.00 0.00 0.00 2.17
274 392 6.038271 GTCACCGAATAGCCAATTAACTGATT 59.962 38.462 0.00 0.00 0.00 2.57
275 393 5.527582 GTCACCGAATAGCCAATTAACTGAT 59.472 40.000 0.00 0.00 0.00 2.90
276 394 4.873827 GTCACCGAATAGCCAATTAACTGA 59.126 41.667 0.00 0.00 0.00 3.41
277 395 4.035208 GGTCACCGAATAGCCAATTAACTG 59.965 45.833 0.00 0.00 0.00 3.16
278 396 4.196971 GGTCACCGAATAGCCAATTAACT 58.803 43.478 0.00 0.00 0.00 2.24
279 397 3.314357 GGGTCACCGAATAGCCAATTAAC 59.686 47.826 0.00 0.00 33.37 2.01
280 398 3.054287 TGGGTCACCGAATAGCCAATTAA 60.054 43.478 0.00 0.00 40.18 1.40
281 399 2.506231 TGGGTCACCGAATAGCCAATTA 59.494 45.455 0.00 0.00 40.18 1.40
282 400 1.283613 TGGGTCACCGAATAGCCAATT 59.716 47.619 0.00 0.00 40.18 2.32
283 401 0.916086 TGGGTCACCGAATAGCCAAT 59.084 50.000 0.00 0.00 40.18 3.16
284 402 0.035820 GTGGGTCACCGAATAGCCAA 60.036 55.000 3.80 0.00 44.36 4.52
285 403 1.600107 GTGGGTCACCGAATAGCCA 59.400 57.895 0.00 0.00 40.82 4.75
286 404 1.153229 GGTGGGTCACCGAATAGCC 60.153 63.158 1.01 0.00 44.95 3.93
287 405 4.534401 GGTGGGTCACCGAATAGC 57.466 61.111 1.01 0.00 44.95 2.97
295 413 0.104304 ATCGCTATTCGGTGGGTCAC 59.896 55.000 0.00 0.00 39.05 3.67
296 414 0.828022 AATCGCTATTCGGTGGGTCA 59.172 50.000 0.00 0.00 39.05 4.02
297 415 1.202486 TGAATCGCTATTCGGTGGGTC 60.202 52.381 6.49 0.00 43.84 4.46
298 416 0.828022 TGAATCGCTATTCGGTGGGT 59.172 50.000 6.49 0.00 43.84 4.51
299 417 1.202533 AGTGAATCGCTATTCGGTGGG 60.203 52.381 6.49 0.00 43.84 4.61
300 418 1.860950 CAGTGAATCGCTATTCGGTGG 59.139 52.381 6.49 0.00 43.84 4.61
301 419 2.535984 GTCAGTGAATCGCTATTCGGTG 59.464 50.000 6.49 6.32 43.84 4.94
302 420 2.481449 GGTCAGTGAATCGCTATTCGGT 60.481 50.000 6.49 0.00 43.84 4.69
303 421 2.128035 GGTCAGTGAATCGCTATTCGG 58.872 52.381 6.49 0.00 43.84 4.30
304 422 1.781429 CGGTCAGTGAATCGCTATTCG 59.219 52.381 6.49 0.00 43.84 3.34
305 423 3.046390 CTCGGTCAGTGAATCGCTATTC 58.954 50.000 11.04 4.06 41.69 1.75
306 424 2.688446 TCTCGGTCAGTGAATCGCTATT 59.312 45.455 11.04 0.00 0.00 1.73
307 425 2.298610 TCTCGGTCAGTGAATCGCTAT 58.701 47.619 11.04 0.00 0.00 2.97
308 426 1.746470 TCTCGGTCAGTGAATCGCTA 58.254 50.000 11.04 1.40 0.00 4.26
309 427 1.107114 ATCTCGGTCAGTGAATCGCT 58.893 50.000 11.04 0.00 0.00 4.93
310 428 1.203928 CATCTCGGTCAGTGAATCGC 58.796 55.000 11.04 0.00 0.00 4.58
311 429 1.203928 GCATCTCGGTCAGTGAATCG 58.796 55.000 9.95 9.95 0.00 3.34
312 430 1.576356 GGCATCTCGGTCAGTGAATC 58.424 55.000 0.00 0.00 0.00 2.52
313 431 0.179100 CGGCATCTCGGTCAGTGAAT 60.179 55.000 0.00 0.00 0.00 2.57
314 432 1.215382 CGGCATCTCGGTCAGTGAA 59.785 57.895 0.00 0.00 0.00 3.18
315 433 1.037579 ATCGGCATCTCGGTCAGTGA 61.038 55.000 0.00 0.00 0.00 3.41
316 434 0.179100 AATCGGCATCTCGGTCAGTG 60.179 55.000 0.00 0.00 0.00 3.66
317 435 1.399714 TAATCGGCATCTCGGTCAGT 58.600 50.000 0.00 0.00 0.00 3.41
318 436 2.128035 GTTAATCGGCATCTCGGTCAG 58.872 52.381 0.00 0.00 0.00 3.51
319 437 1.754803 AGTTAATCGGCATCTCGGTCA 59.245 47.619 0.00 0.00 0.00 4.02
320 438 2.128035 CAGTTAATCGGCATCTCGGTC 58.872 52.381 0.00 0.00 0.00 4.79
321 439 1.202533 CCAGTTAATCGGCATCTCGGT 60.203 52.381 0.00 0.00 0.00 4.69
322 440 1.502231 CCAGTTAATCGGCATCTCGG 58.498 55.000 0.00 0.00 0.00 4.63
330 448 4.062293 TCAAATATCGGCCAGTTAATCGG 58.938 43.478 2.24 0.00 0.00 4.18
331 449 5.666969 TTCAAATATCGGCCAGTTAATCG 57.333 39.130 2.24 0.00 0.00 3.34
332 450 7.920682 ACAATTTCAAATATCGGCCAGTTAATC 59.079 33.333 2.24 0.00 0.00 1.75
333 451 7.781056 ACAATTTCAAATATCGGCCAGTTAAT 58.219 30.769 2.24 0.00 0.00 1.40
334 452 7.164230 ACAATTTCAAATATCGGCCAGTTAA 57.836 32.000 2.24 0.00 0.00 2.01
335 453 6.767524 ACAATTTCAAATATCGGCCAGTTA 57.232 33.333 2.24 0.00 0.00 2.24
336 454 5.659440 ACAATTTCAAATATCGGCCAGTT 57.341 34.783 2.24 0.00 0.00 3.16
337 455 5.184864 TCAACAATTTCAAATATCGGCCAGT 59.815 36.000 2.24 0.00 0.00 4.00
338 456 5.649557 TCAACAATTTCAAATATCGGCCAG 58.350 37.500 2.24 0.00 0.00 4.85
339 457 5.651387 TCAACAATTTCAAATATCGGCCA 57.349 34.783 2.24 0.00 0.00 5.36
340 458 8.702438 CATAATCAACAATTTCAAATATCGGCC 58.298 33.333 0.00 0.00 0.00 6.13
341 459 9.462174 TCATAATCAACAATTTCAAATATCGGC 57.538 29.630 0.00 0.00 0.00 5.54
365 483 9.886132 GAAAAGGAAGTATACCACTAGAATTCA 57.114 33.333 8.44 0.00 36.04 2.57
697 934 6.272318 TCTTATTTGTTGAACTTGCAACCAG 58.728 36.000 0.00 0.00 45.75 4.00
720 957 4.586334 GCATCTCGAGAAGAAGCAAATTC 58.414 43.478 20.91 0.00 45.83 2.17
732 979 1.746470 TTGGACGTAGCATCTCGAGA 58.254 50.000 19.19 19.19 0.00 4.04
746 993 0.108585 TGGTCACTGGAGCTTTGGAC 59.891 55.000 0.00 0.00 42.05 4.02
769 1016 7.872483 AGCATCGAATCAAAAGGTAAATTGTTT 59.128 29.630 0.00 0.00 0.00 2.83
778 1025 4.764823 TGGTAAAGCATCGAATCAAAAGGT 59.235 37.500 0.00 0.00 0.00 3.50
786 1033 7.391148 ACTGTAAAATGGTAAAGCATCGAAT 57.609 32.000 0.00 0.00 0.00 3.34
788 1035 8.500753 AATACTGTAAAATGGTAAAGCATCGA 57.499 30.769 0.00 0.00 0.00 3.59
789 1036 9.221775 GAAATACTGTAAAATGGTAAAGCATCG 57.778 33.333 0.00 0.00 0.00 3.84
797 1044 7.539366 GCGCAAAAGAAATACTGTAAAATGGTA 59.461 33.333 0.30 0.00 0.00 3.25
802 1049 7.938563 AATGCGCAAAAGAAATACTGTAAAA 57.061 28.000 17.11 0.00 0.00 1.52
805 1052 6.128145 TGCTAATGCGCAAAAGAAATACTGTA 60.128 34.615 17.11 0.00 43.34 2.74
806 1053 5.095490 GCTAATGCGCAAAAGAAATACTGT 58.905 37.500 17.11 0.00 0.00 3.55
807 1054 5.094812 TGCTAATGCGCAAAAGAAATACTG 58.905 37.500 17.11 0.00 43.34 2.74
808 1055 5.309323 TGCTAATGCGCAAAAGAAATACT 57.691 34.783 17.11 0.00 43.34 2.12
831 1086 4.226427 TGTAGCATCAGGAGAAGCAAAT 57.774 40.909 0.00 0.00 40.78 2.32
841 1096 2.552743 CAGCATTGGATGTAGCATCAGG 59.447 50.000 10.71 0.00 0.00 3.86
842 1097 2.031069 GCAGCATTGGATGTAGCATCAG 60.031 50.000 10.71 0.34 34.09 2.90
843 1098 1.951602 GCAGCATTGGATGTAGCATCA 59.048 47.619 10.71 0.00 34.09 3.07
874 1129 6.815142 TCCCTAAGAGAAATAAACGTGCTAAC 59.185 38.462 0.00 0.00 0.00 2.34
878 1133 5.504173 GCATCCCTAAGAGAAATAAACGTGC 60.504 44.000 0.00 0.00 0.00 5.34
880 1135 5.990668 AGCATCCCTAAGAGAAATAAACGT 58.009 37.500 0.00 0.00 0.00 3.99
881 1136 6.927294 AAGCATCCCTAAGAGAAATAAACG 57.073 37.500 0.00 0.00 0.00 3.60
884 1139 8.333235 TGGTAAAAGCATCCCTAAGAGAAATAA 58.667 33.333 0.00 0.00 0.00 1.40
886 1141 6.731467 TGGTAAAAGCATCCCTAAGAGAAAT 58.269 36.000 0.00 0.00 0.00 2.17
931 1186 6.968263 TGTCAGAATCTAGTCATCTTAGGG 57.032 41.667 0.00 0.00 0.00 3.53
960 1216 1.679139 CTGTGAAAACCAGGAGCACA 58.321 50.000 0.00 0.00 37.81 4.57
981 1237 1.593750 GGCTGTCGGATGCTGCTAG 60.594 63.158 0.00 0.00 0.00 3.42
1342 1598 3.553095 AAGGGCCTGACGAACCAGC 62.553 63.158 6.92 0.00 32.97 4.85
1344 1600 1.228124 CAAAGGGCCTGACGAACCA 60.228 57.895 6.92 0.00 0.00 3.67
1346 1602 1.971695 CCCAAAGGGCCTGACGAAC 60.972 63.158 6.92 0.00 35.35 3.95
1363 1619 1.610379 AGCACAAAATGAGGCCCCC 60.610 57.895 0.00 0.00 0.00 5.40
1364 1620 1.187567 ACAGCACAAAATGAGGCCCC 61.188 55.000 0.00 0.00 0.00 5.80
1369 1625 2.129607 GCCACAACAGCACAAAATGAG 58.870 47.619 0.00 0.00 0.00 2.90
1377 1633 1.372499 CAGCATGCCACAACAGCAC 60.372 57.895 15.66 0.00 44.40 4.40
1383 1639 0.320858 CAAATGCCAGCATGCCACAA 60.321 50.000 15.66 0.00 36.68 3.33
1384 1640 1.186267 TCAAATGCCAGCATGCCACA 61.186 50.000 15.66 10.84 36.68 4.17
1385 1641 0.177141 ATCAAATGCCAGCATGCCAC 59.823 50.000 15.66 4.51 36.68 5.01
1386 1642 0.462375 GATCAAATGCCAGCATGCCA 59.538 50.000 15.66 5.74 36.68 4.92
1387 1643 0.596600 CGATCAAATGCCAGCATGCC 60.597 55.000 15.66 0.00 36.68 4.40
1388 1644 0.382873 TCGATCAAATGCCAGCATGC 59.617 50.000 10.51 10.51 36.68 4.06
1389 1645 3.365666 GGTATCGATCAAATGCCAGCATG 60.366 47.826 5.78 0.00 36.68 4.06
1399 1655 6.540438 AACCTACTCTTGGTATCGATCAAA 57.460 37.500 0.00 0.00 36.69 2.69
1400 1656 6.338146 CAAACCTACTCTTGGTATCGATCAA 58.662 40.000 0.00 0.00 36.69 2.57
1401 1657 5.681437 GCAAACCTACTCTTGGTATCGATCA 60.681 44.000 0.00 0.00 36.69 2.92
1402 1658 4.745620 GCAAACCTACTCTTGGTATCGATC 59.254 45.833 0.00 0.00 36.69 3.69
1403 1659 4.443034 GGCAAACCTACTCTTGGTATCGAT 60.443 45.833 2.16 2.16 36.69 3.59
1405 1661 3.195661 GGCAAACCTACTCTTGGTATCG 58.804 50.000 0.00 0.00 36.69 2.92
1447 1706 5.908831 TCCTATCAGTACCAAACCATACCAT 59.091 40.000 0.00 0.00 0.00 3.55
1450 1709 6.726490 TCTCCTATCAGTACCAAACCATAC 57.274 41.667 0.00 0.00 0.00 2.39
1565 1839 0.168788 ATTTCAAGTCACGGCGCATG 59.831 50.000 10.83 7.22 0.00 4.06
1566 1840 0.168788 CATTTCAAGTCACGGCGCAT 59.831 50.000 10.83 0.00 0.00 4.73
1567 1841 1.163420 ACATTTCAAGTCACGGCGCA 61.163 50.000 10.83 0.00 0.00 6.09
1568 1842 0.725784 CACATTTCAAGTCACGGCGC 60.726 55.000 6.90 0.00 0.00 6.53
1569 1843 0.110238 CCACATTTCAAGTCACGGCG 60.110 55.000 4.80 4.80 0.00 6.46
1570 1844 1.234821 TCCACATTTCAAGTCACGGC 58.765 50.000 0.00 0.00 0.00 5.68
1571 1845 2.094258 CGATCCACATTTCAAGTCACGG 59.906 50.000 0.00 0.00 0.00 4.94
1581 1872 3.801698 CCAGTCATCTCGATCCACATTT 58.198 45.455 0.00 0.00 0.00 2.32
1643 1934 1.214367 AACAACCATGTCACGTCGTC 58.786 50.000 0.00 0.00 39.40 4.20
1644 1935 2.512485 TAACAACCATGTCACGTCGT 57.488 45.000 0.00 0.00 39.40 4.34
1689 1980 3.264897 GCACACTAGGCGCCATCG 61.265 66.667 31.54 18.43 39.07 3.84
1713 2007 1.744741 GCACTTCCAGCTGGCTCTC 60.745 63.158 28.91 11.57 34.44 3.20
1779 2079 0.179084 GGACATGCCTAAGCGCTACA 60.179 55.000 12.05 7.66 44.31 2.74
1795 2095 2.748605 CTGCGATACAGGATTCTGGAC 58.251 52.381 5.84 0.00 44.99 4.02
1933 2234 4.912187 GCTCCTTTCATTCAACTTTCGAAC 59.088 41.667 0.00 0.00 0.00 3.95
1946 2247 2.685999 GCCTGGGGCTCCTTTCAT 59.314 61.111 3.07 0.00 46.69 2.57
2038 2344 0.179163 GGCGGCACTGTATTTTCAGC 60.179 55.000 3.07 0.00 38.84 4.26
2060 2366 0.753111 GGGTTCCTGCCATCATCACC 60.753 60.000 0.00 0.00 0.00 4.02
2093 2399 7.308649 GCTGCTTATGATGATGATGATGAAAGT 60.309 37.037 0.00 0.00 0.00 2.66
2098 2404 5.163713 CCTGCTGCTTATGATGATGATGATG 60.164 44.000 0.00 0.00 0.00 3.07
2099 2405 4.944317 CCTGCTGCTTATGATGATGATGAT 59.056 41.667 0.00 0.00 0.00 2.45
2100 2406 4.202430 ACCTGCTGCTTATGATGATGATGA 60.202 41.667 0.00 0.00 0.00 2.92
2101 2407 4.072839 ACCTGCTGCTTATGATGATGATG 58.927 43.478 0.00 0.00 0.00 3.07
2225 2543 3.755378 AGTTGGTTAGCAGATTGAGCAAG 59.245 43.478 0.00 0.00 31.11 4.01
2248 2566 1.328374 GACGGCGCGTAATTTTACCAT 59.672 47.619 6.90 0.00 41.37 3.55
2250 2568 1.001624 AGACGGCGCGTAATTTTACC 58.998 50.000 6.90 0.00 41.37 2.85
2262 2597 1.153647 TAGGTCATGCAAGACGGCG 60.154 57.895 15.31 4.80 39.42 6.46


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

AutoCloner maintained by Alex Coulton.