Multiple sequence alignment - TraesCS6D01G262400

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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 TraesCS6D01G262400 chr6D 100.000 2348 0 0 1 2348 370695599 370693252 0.000000e+00 4337.0
1 TraesCS6D01G262400 chr6D 94.203 345 14 4 4 343 370730585 370730242 2.670000e-144 521.0
2 TraesCS6D01G262400 chr6D 89.130 46 5 0 1150 1195 128101405 128101360 9.060000e-05 58.4
3 TraesCS6D01G262400 chr6A 94.202 1190 41 13 675 1842 511540884 511539701 0.000000e+00 1790.0
4 TraesCS6D01G262400 chr6A 89.130 46 5 0 1150 1195 150226828 150226873 9.060000e-05 58.4
5 TraesCS6D01G262400 chr6B 86.000 700 52 22 333 1010 555810820 555810145 0.000000e+00 708.0
6 TraesCS6D01G262400 chr6B 94.811 424 21 1 1545 1967 555810150 555809727 0.000000e+00 660.0
7 TraesCS6D01G262400 chr6B 93.452 168 9 1 1991 2156 555809739 555809572 5.010000e-62 248.0
8 TraesCS6D01G262400 chr6B 89.130 46 5 0 1150 1195 226872501 226872456 9.060000e-05 58.4
9 TraesCS6D01G262400 chr3B 93.195 338 17 4 1 334 411807379 411807714 2.100000e-135 492.0
10 TraesCS6D01G262400 chr3D 92.197 346 23 3 1 343 63454978 63454634 9.750000e-134 486.0
11 TraesCS6D01G262400 chr3D 92.285 337 20 4 1 333 63417227 63416893 7.590000e-130 473.0
12 TraesCS6D01G262400 chr3D 92.285 337 20 4 1 333 63418770 63418436 7.590000e-130 473.0
13 TraesCS6D01G262400 chr3D 92.285 337 20 4 1 333 63420313 63419979 7.590000e-130 473.0
14 TraesCS6D01G262400 chr2D 93.114 334 18 3 4 333 346164218 346163886 3.510000e-133 484.0
15 TraesCS6D01G262400 chr2A 92.515 334 20 3 5 334 610040867 610041199 7.590000e-130 473.0
16 TraesCS6D01G262400 chr5D 92.239 335 23 2 1 333 179519990 179520323 2.730000e-129 472.0


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 TraesCS6D01G262400 chr6D 370693252 370695599 2347 True 4337.000000 4337 100.000 1 2348 1 chr6D.!!$R2 2347
1 TraesCS6D01G262400 chr6A 511539701 511540884 1183 True 1790.000000 1790 94.202 675 1842 1 chr6A.!!$R1 1167
2 TraesCS6D01G262400 chr6B 555809572 555810820 1248 True 538.666667 708 91.421 333 2156 3 chr6B.!!$R2 1823
3 TraesCS6D01G262400 chr3D 63416893 63420313 3420 True 473.000000 473 92.285 1 333 3 chr3D.!!$R2 332

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
260 264 0.028242 CGTAAACCTTGCGTGCACAA 59.972 50.0 18.64 3.4 33.98 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 4038 0.09473 GTGAAGCACCGAACGTATGC 59.905 55.0 11.03 11.03 39.74 3.14 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
47 48 2.102757 TCATTATAGCGGGCGTTACCAA 59.897 45.455 0.00 0.00 42.05 3.67
95 98 0.036010 CCTGTGTAACTGAGGCCTGG 60.036 60.000 12.00 5.16 38.12 4.45
99 102 0.984230 TGTAACTGAGGCCTGGGAAG 59.016 55.000 12.00 4.71 0.00 3.46
149 152 1.455849 CCTCTGGCACAAGGGTTCA 59.544 57.895 3.66 0.00 38.70 3.18
151 154 0.890996 CTCTGGCACAAGGGTTCACC 60.891 60.000 0.00 0.00 38.70 4.02
213 217 2.117156 GCACCGAGACGTAGGGCTA 61.117 63.158 8.73 0.00 0.00 3.93
219 223 2.883386 CCGAGACGTAGGGCTATTACTT 59.117 50.000 0.00 0.00 0.00 2.24
220 224 3.058363 CCGAGACGTAGGGCTATTACTTC 60.058 52.174 0.00 0.00 0.00 3.01
221 225 3.058363 CGAGACGTAGGGCTATTACTTCC 60.058 52.174 0.00 0.00 0.00 3.46
222 226 4.143543 GAGACGTAGGGCTATTACTTCCT 58.856 47.826 0.00 0.00 0.00 3.36
223 227 4.143543 AGACGTAGGGCTATTACTTCCTC 58.856 47.826 0.00 0.00 0.00 3.71
224 228 3.229293 ACGTAGGGCTATTACTTCCTCC 58.771 50.000 0.00 0.00 0.00 4.30
225 229 2.228343 CGTAGGGCTATTACTTCCTCCG 59.772 54.545 0.00 0.00 0.00 4.63
226 230 2.769602 AGGGCTATTACTTCCTCCGA 57.230 50.000 0.00 0.00 0.00 4.55
227 231 2.599677 AGGGCTATTACTTCCTCCGAG 58.400 52.381 0.00 0.00 0.00 4.63
228 232 2.177233 AGGGCTATTACTTCCTCCGAGA 59.823 50.000 0.00 0.00 0.00 4.04
229 233 2.963782 GGGCTATTACTTCCTCCGAGAA 59.036 50.000 0.00 0.00 0.00 2.87
231 235 3.006003 GGCTATTACTTCCTCCGAGAAGG 59.994 52.174 12.46 4.01 46.24 3.46
232 236 3.890147 GCTATTACTTCCTCCGAGAAGGA 59.110 47.826 12.46 6.05 46.24 3.36
233 237 4.261698 GCTATTACTTCCTCCGAGAAGGAC 60.262 50.000 12.46 0.00 45.20 3.85
234 238 2.140839 TACTTCCTCCGAGAAGGACC 57.859 55.000 12.46 0.00 45.20 4.46
235 239 0.410270 ACTTCCTCCGAGAAGGACCT 59.590 55.000 12.46 0.00 45.20 3.85
236 240 0.820871 CTTCCTCCGAGAAGGACCTG 59.179 60.000 0.00 0.00 45.20 4.00
237 241 0.408309 TTCCTCCGAGAAGGACCTGA 59.592 55.000 0.00 0.00 45.20 3.86
238 242 0.408309 TCCTCCGAGAAGGACCTGAA 59.592 55.000 0.00 0.00 45.98 3.02
239 243 0.533032 CCTCCGAGAAGGACCTGAAC 59.467 60.000 0.00 0.00 45.98 3.18
240 244 1.551452 CTCCGAGAAGGACCTGAACT 58.449 55.000 0.00 0.00 45.98 3.01
241 245 1.474879 CTCCGAGAAGGACCTGAACTC 59.525 57.143 0.00 4.24 45.98 3.01
242 246 0.171455 CCGAGAAGGACCTGAACTCG 59.829 60.000 25.67 25.67 46.20 4.18
243 247 0.882474 CGAGAAGGACCTGAACTCGT 59.118 55.000 24.92 0.00 43.19 4.18
244 248 2.082231 CGAGAAGGACCTGAACTCGTA 58.918 52.381 24.92 0.00 43.19 3.43
245 249 2.486982 CGAGAAGGACCTGAACTCGTAA 59.513 50.000 24.92 0.00 43.19 3.18
246 250 3.057736 CGAGAAGGACCTGAACTCGTAAA 60.058 47.826 24.92 0.00 43.19 2.01
247 251 4.236147 GAGAAGGACCTGAACTCGTAAAC 58.764 47.826 0.00 0.00 0.00 2.01
248 252 3.006644 AGAAGGACCTGAACTCGTAAACC 59.993 47.826 0.00 0.00 0.00 3.27
249 253 2.606378 AGGACCTGAACTCGTAAACCT 58.394 47.619 0.00 0.00 0.00 3.50
250 254 2.970640 AGGACCTGAACTCGTAAACCTT 59.029 45.455 0.00 0.00 0.00 3.50
251 255 3.064931 GGACCTGAACTCGTAAACCTTG 58.935 50.000 0.00 0.00 0.00 3.61
252 256 2.479275 GACCTGAACTCGTAAACCTTGC 59.521 50.000 0.00 0.00 0.00 4.01
253 257 1.459592 CCTGAACTCGTAAACCTTGCG 59.540 52.381 0.00 0.00 40.22 4.85
254 258 2.132762 CTGAACTCGTAAACCTTGCGT 58.867 47.619 0.00 0.00 39.81 5.24
255 259 1.862201 TGAACTCGTAAACCTTGCGTG 59.138 47.619 0.00 0.00 39.81 5.34
256 260 0.584876 AACTCGTAAACCTTGCGTGC 59.415 50.000 0.00 0.00 39.81 5.34
257 261 0.531090 ACTCGTAAACCTTGCGTGCA 60.531 50.000 0.00 0.00 39.81 4.57
258 262 0.110823 CTCGTAAACCTTGCGTGCAC 60.111 55.000 6.82 6.82 39.81 4.57
259 263 0.810426 TCGTAAACCTTGCGTGCACA 60.810 50.000 18.64 0.00 39.81 4.57
260 264 0.028242 CGTAAACCTTGCGTGCACAA 59.972 50.000 18.64 3.40 33.98 3.33
261 265 1.472990 GTAAACCTTGCGTGCACAAC 58.527 50.000 18.64 8.87 0.00 3.32
262 266 0.382515 TAAACCTTGCGTGCACAACC 59.617 50.000 18.64 4.90 0.00 3.77
263 267 1.319614 AAACCTTGCGTGCACAACCT 61.320 50.000 18.64 0.00 0.00 3.50
264 268 1.724582 AACCTTGCGTGCACAACCTC 61.725 55.000 18.64 0.48 0.00 3.85
265 269 2.186160 CCTTGCGTGCACAACCTCA 61.186 57.895 18.64 3.24 0.00 3.86
266 270 1.009675 CTTGCGTGCACAACCTCAC 60.010 57.895 18.64 0.00 0.00 3.51
267 271 2.392613 CTTGCGTGCACAACCTCACC 62.393 60.000 18.64 0.00 0.00 4.02
268 272 4.012895 GCGTGCACAACCTCACCG 62.013 66.667 18.64 0.00 0.00 4.94
269 273 2.587753 CGTGCACAACCTCACCGT 60.588 61.111 18.64 0.00 0.00 4.83
270 274 1.300311 CGTGCACAACCTCACCGTA 60.300 57.895 18.64 0.00 0.00 4.02
271 275 1.282248 CGTGCACAACCTCACCGTAG 61.282 60.000 18.64 0.00 0.00 3.51
272 276 1.301401 TGCACAACCTCACCGTAGC 60.301 57.895 0.00 0.00 0.00 3.58
273 277 1.004918 GCACAACCTCACCGTAGCT 60.005 57.895 0.00 0.00 0.00 3.32
274 278 0.245539 GCACAACCTCACCGTAGCTA 59.754 55.000 0.00 0.00 0.00 3.32
275 279 1.736032 GCACAACCTCACCGTAGCTAG 60.736 57.143 0.00 0.00 0.00 3.42
276 280 1.135083 CACAACCTCACCGTAGCTAGG 60.135 57.143 6.46 6.46 35.14 3.02
277 281 0.460311 CAACCTCACCGTAGCTAGGG 59.540 60.000 27.08 27.08 37.27 3.53
278 282 1.328430 AACCTCACCGTAGCTAGGGC 61.328 60.000 28.29 1.01 34.69 5.19
279 283 2.499827 CCTCACCGTAGCTAGGGCC 61.500 68.421 28.29 0.00 39.73 5.80
280 284 1.455959 CTCACCGTAGCTAGGGCCT 60.456 63.158 28.29 12.58 39.73 5.19
281 285 1.001248 TCACCGTAGCTAGGGCCTT 59.999 57.895 28.29 9.98 39.73 4.35
282 286 0.259647 TCACCGTAGCTAGGGCCTTA 59.740 55.000 28.29 11.44 39.73 2.69
283 287 0.388294 CACCGTAGCTAGGGCCTTAC 59.612 60.000 28.29 7.68 39.73 2.34
284 288 0.758310 ACCGTAGCTAGGGCCTTACC 60.758 60.000 28.29 0.00 39.73 2.85
285 289 0.469518 CCGTAGCTAGGGCCTTACCT 60.470 60.000 18.99 8.49 44.75 3.08
286 290 0.960286 CGTAGCTAGGGCCTTACCTC 59.040 60.000 13.45 0.00 42.09 3.85
287 291 1.340088 GTAGCTAGGGCCTTACCTCC 58.660 60.000 13.45 0.00 42.09 4.30
288 292 1.133104 GTAGCTAGGGCCTTACCTCCT 60.133 57.143 13.45 1.94 42.09 3.69
289 293 0.105401 AGCTAGGGCCTTACCTCCTC 60.105 60.000 13.45 0.00 42.09 3.71
290 294 1.122632 GCTAGGGCCTTACCTCCTCC 61.123 65.000 13.45 0.00 42.09 4.30
291 295 0.563672 CTAGGGCCTTACCTCCTCCT 59.436 60.000 13.45 0.00 42.09 3.69
292 296 1.787676 CTAGGGCCTTACCTCCTCCTA 59.212 57.143 13.45 0.00 42.09 2.94
293 297 0.265254 AGGGCCTTACCTCCTCCTAC 59.735 60.000 0.00 0.00 35.43 3.18
294 298 1.114119 GGGCCTTACCTCCTCCTACG 61.114 65.000 0.84 0.00 39.10 3.51
295 299 0.396835 GGCCTTACCTCCTCCTACGT 60.397 60.000 0.00 0.00 34.51 3.57
296 300 1.133668 GGCCTTACCTCCTCCTACGTA 60.134 57.143 0.00 0.00 34.51 3.57
297 301 1.952990 GCCTTACCTCCTCCTACGTAC 59.047 57.143 0.00 0.00 0.00 3.67
298 302 2.580962 CCTTACCTCCTCCTACGTACC 58.419 57.143 0.00 0.00 0.00 3.34
299 303 2.580962 CTTACCTCCTCCTACGTACCC 58.419 57.143 0.00 0.00 0.00 3.69
300 304 0.846693 TACCTCCTCCTACGTACCCC 59.153 60.000 0.00 0.00 0.00 4.95
301 305 1.152589 CCTCCTCCTACGTACCCCC 60.153 68.421 0.00 0.00 0.00 5.40
302 306 1.653161 CCTCCTCCTACGTACCCCCT 61.653 65.000 0.00 0.00 0.00 4.79
303 307 1.143813 CTCCTCCTACGTACCCCCTA 58.856 60.000 0.00 0.00 0.00 3.53
304 308 1.709679 CTCCTCCTACGTACCCCCTAT 59.290 57.143 0.00 0.00 0.00 2.57
305 309 2.109657 CTCCTCCTACGTACCCCCTATT 59.890 54.545 0.00 0.00 0.00 1.73
306 310 2.108952 TCCTCCTACGTACCCCCTATTC 59.891 54.545 0.00 0.00 0.00 1.75
307 311 2.109657 CCTCCTACGTACCCCCTATTCT 59.890 54.545 0.00 0.00 0.00 2.40
308 312 3.437637 CCTCCTACGTACCCCCTATTCTT 60.438 52.174 0.00 0.00 0.00 2.52
309 313 4.202609 CCTCCTACGTACCCCCTATTCTTA 60.203 50.000 0.00 0.00 0.00 2.10
310 314 4.729868 TCCTACGTACCCCCTATTCTTAC 58.270 47.826 0.00 0.00 0.00 2.34
311 315 4.416848 TCCTACGTACCCCCTATTCTTACT 59.583 45.833 0.00 0.00 0.00 2.24
312 316 4.522022 CCTACGTACCCCCTATTCTTACTG 59.478 50.000 0.00 0.00 0.00 2.74
313 317 3.986435 ACGTACCCCCTATTCTTACTGT 58.014 45.455 0.00 0.00 0.00 3.55
314 318 3.956848 ACGTACCCCCTATTCTTACTGTC 59.043 47.826 0.00 0.00 0.00 3.51
315 319 3.956199 CGTACCCCCTATTCTTACTGTCA 59.044 47.826 0.00 0.00 0.00 3.58
316 320 4.587684 CGTACCCCCTATTCTTACTGTCAT 59.412 45.833 0.00 0.00 0.00 3.06
317 321 5.771666 CGTACCCCCTATTCTTACTGTCATA 59.228 44.000 0.00 0.00 0.00 2.15
318 322 6.294397 CGTACCCCCTATTCTTACTGTCATAC 60.294 46.154 0.00 0.00 0.00 2.39
319 323 5.789535 ACCCCCTATTCTTACTGTCATACT 58.210 41.667 0.00 0.00 0.00 2.12
320 324 6.210522 ACCCCCTATTCTTACTGTCATACTT 58.789 40.000 0.00 0.00 0.00 2.24
321 325 7.367828 ACCCCCTATTCTTACTGTCATACTTA 58.632 38.462 0.00 0.00 0.00 2.24
322 326 7.289549 ACCCCCTATTCTTACTGTCATACTTAC 59.710 40.741 0.00 0.00 0.00 2.34
323 327 7.509659 CCCCCTATTCTTACTGTCATACTTACT 59.490 40.741 0.00 0.00 0.00 2.24
324 328 8.578151 CCCCTATTCTTACTGTCATACTTACTC 58.422 40.741 0.00 0.00 0.00 2.59
325 329 8.578151 CCCTATTCTTACTGTCATACTTACTCC 58.422 40.741 0.00 0.00 0.00 3.85
326 330 8.578151 CCTATTCTTACTGTCATACTTACTCCC 58.422 40.741 0.00 0.00 0.00 4.30
327 331 7.973048 ATTCTTACTGTCATACTTACTCCCA 57.027 36.000 0.00 0.00 0.00 4.37
328 332 6.770746 TCTTACTGTCATACTTACTCCCAC 57.229 41.667 0.00 0.00 0.00 4.61
329 333 5.356190 TCTTACTGTCATACTTACTCCCACG 59.644 44.000 0.00 0.00 0.00 4.94
330 334 3.693807 ACTGTCATACTTACTCCCACGA 58.306 45.455 0.00 0.00 0.00 4.35
331 335 3.442977 ACTGTCATACTTACTCCCACGAC 59.557 47.826 0.00 0.00 0.00 4.34
351 355 1.889573 GCGGCTCCCAGAATGCTAC 60.890 63.158 0.00 0.00 31.97 3.58
355 359 0.530870 GCTCCCAGAATGCTACGTCC 60.531 60.000 0.00 0.00 31.97 4.79
359 363 2.104331 AGAATGCTACGTCCGCGG 59.896 61.111 22.12 22.12 43.45 6.46
389 393 1.555075 GCTGGAACCATGGTCACTAGA 59.445 52.381 27.11 8.50 0.00 2.43
405 409 0.812549 TAGATGCTACAACGGCGTCA 59.187 50.000 15.17 6.96 45.13 4.35
431 435 1.020861 TGCTGCATCCACGACATCAC 61.021 55.000 0.00 0.00 0.00 3.06
440 444 1.365999 ACGACATCACGTGCTGGAA 59.634 52.632 22.18 0.00 44.84 3.53
460 464 3.053896 GTTGCCACCGGGTGCTAC 61.054 66.667 21.88 18.01 36.17 3.58
461 465 4.338710 TTGCCACCGGGTGCTACC 62.339 66.667 21.88 9.58 37.60 3.18
464 468 3.632080 CCACCGGGTGCTACCACA 61.632 66.667 21.88 0.00 43.88 4.17
465 469 2.428187 CACCGGGTGCTACCACAA 59.572 61.111 15.29 0.00 43.88 3.33
466 470 1.964373 CACCGGGTGCTACCACAAC 60.964 63.158 15.29 0.00 43.88 3.32
467 471 2.740826 CCGGGTGCTACCACAACG 60.741 66.667 0.00 0.00 43.88 4.10
468 472 2.340809 CGGGTGCTACCACAACGA 59.659 61.111 7.49 0.00 43.88 3.85
469 473 2.025418 CGGGTGCTACCACAACGAC 61.025 63.158 7.49 0.00 43.88 4.34
470 474 1.370064 GGGTGCTACCACAACGACT 59.630 57.895 7.49 0.00 43.88 4.18
471 475 0.949105 GGGTGCTACCACAACGACTG 60.949 60.000 7.49 0.00 43.88 3.51
472 476 0.949105 GGTGCTACCACAACGACTGG 60.949 60.000 0.00 0.00 43.88 4.00
480 484 1.447838 ACAACGACTGGCCATAGCG 60.448 57.895 5.51 13.33 41.24 4.26
504 508 4.367450 TGGCTTACATCAAAAGTTGCAAC 58.633 39.130 22.17 22.17 0.00 4.17
505 509 3.740832 GGCTTACATCAAAAGTTGCAACC 59.259 43.478 25.62 8.37 0.00 3.77
507 511 4.791411 GCTTACATCAAAAGTTGCAACCGA 60.791 41.667 25.62 16.83 0.00 4.69
508 512 3.078594 ACATCAAAAGTTGCAACCGAC 57.921 42.857 25.62 1.42 0.00 4.79
520 544 1.486439 CAACCGACACCACATTTTGC 58.514 50.000 0.00 0.00 0.00 3.68
589 617 4.824166 GCGGCAACTGCGAGCATG 62.824 66.667 13.55 0.00 42.23 4.06
590 618 4.824166 CGGCAACTGCGAGCATGC 62.824 66.667 10.51 10.51 43.26 4.06
592 620 3.740397 GCAACTGCGAGCATGCCA 61.740 61.111 15.66 4.33 32.73 4.92
593 621 2.177531 CAACTGCGAGCATGCCAC 59.822 61.111 15.66 8.29 0.00 5.01
612 640 4.332637 GCCACCGTGCTGCAAGTG 62.333 66.667 21.09 21.09 35.30 3.16
613 641 2.591429 CCACCGTGCTGCAAGTGA 60.591 61.111 26.67 0.00 35.30 3.41
614 642 2.610694 CCACCGTGCTGCAAGTGAG 61.611 63.158 26.67 16.67 35.30 3.51
615 643 2.281070 ACCGTGCTGCAAGTGAGG 60.281 61.111 14.22 10.45 35.30 3.86
616 644 2.281070 CCGTGCTGCAAGTGAGGT 60.281 61.111 14.22 0.00 35.30 3.85
617 645 2.610694 CCGTGCTGCAAGTGAGGTG 61.611 63.158 14.22 0.00 35.30 4.00
618 646 2.610694 CGTGCTGCAAGTGAGGTGG 61.611 63.158 2.77 0.00 35.30 4.61
619 647 1.526917 GTGCTGCAAGTGAGGTGGT 60.527 57.895 2.77 0.00 35.30 4.16
629 657 1.385347 TGAGGTGGTGGGAGGTGTT 60.385 57.895 0.00 0.00 0.00 3.32
630 658 0.104882 TGAGGTGGTGGGAGGTGTTA 60.105 55.000 0.00 0.00 0.00 2.41
633 661 1.131928 GGTGGTGGGAGGTGTTAGGT 61.132 60.000 0.00 0.00 0.00 3.08
634 662 0.036306 GTGGTGGGAGGTGTTAGGTG 59.964 60.000 0.00 0.00 0.00 4.00
636 664 1.489560 GGTGGGAGGTGTTAGGTGCT 61.490 60.000 0.00 0.00 0.00 4.40
637 665 0.321653 GTGGGAGGTGTTAGGTGCTG 60.322 60.000 0.00 0.00 0.00 4.41
659 687 4.845580 CGAGCAATGCGAGGGGCT 62.846 66.667 0.00 0.00 44.05 5.19
660 688 3.207669 GAGCAATGCGAGGGGCTG 61.208 66.667 0.00 0.00 44.05 4.85
669 697 2.614013 GAGGGGCTGGAAAGGGGA 60.614 66.667 0.00 0.00 0.00 4.81
671 699 2.280079 GGGGCTGGAAAGGGGATG 59.720 66.667 0.00 0.00 0.00 3.51
672 700 2.626467 GGGGCTGGAAAGGGGATGT 61.626 63.158 0.00 0.00 0.00 3.06
784 817 4.164252 CGTAGCGTTCGCCTTCTT 57.836 55.556 13.54 0.00 0.00 2.52
785 818 2.442084 CGTAGCGTTCGCCTTCTTT 58.558 52.632 13.54 0.00 0.00 2.52
1553 3069 0.462937 CCATTTGCACCGGTCCGATA 60.463 55.000 14.39 0.00 0.00 2.92
1741 3782 2.911102 GGCAGTACGTTACTTGTACGAC 59.089 50.000 0.00 0.00 45.31 4.34
1870 3912 4.566759 ACGAATGTTTGGTGAGTGATATCG 59.433 41.667 0.00 0.00 0.00 2.92
1887 3929 7.009631 AGTGATATCGTCGTGAAATTCTCAAAG 59.990 37.037 0.00 0.00 35.22 2.77
1898 3940 7.009540 CGTGAAATTCTCAAAGGGATTTAATGC 59.990 37.037 0.00 0.00 35.22 3.56
1917 3959 2.708861 TGCCTACTTGGAACAGAAGGAA 59.291 45.455 0.00 0.00 42.39 3.36
1927 3969 7.288621 ACTTGGAACAGAAGGAAGAAAAATGAT 59.711 33.333 0.00 0.00 42.39 2.45
1932 3974 9.533253 GAACAGAAGGAAGAAAAATGATGAAAA 57.467 29.630 0.00 0.00 0.00 2.29
1974 4017 8.895932 ATAAAAACATGCATACGTTCTTCTTC 57.104 30.769 0.00 0.00 0.00 2.87
1975 4018 6.560253 AAAACATGCATACGTTCTTCTTCT 57.440 33.333 0.00 0.00 0.00 2.85
1976 4019 6.560253 AAACATGCATACGTTCTTCTTCTT 57.440 33.333 0.00 0.00 0.00 2.52
1977 4020 6.560253 AACATGCATACGTTCTTCTTCTTT 57.440 33.333 0.00 0.00 0.00 2.52
1978 4021 6.560253 ACATGCATACGTTCTTCTTCTTTT 57.440 33.333 0.00 0.00 0.00 2.27
1979 4022 6.970484 ACATGCATACGTTCTTCTTCTTTTT 58.030 32.000 0.00 0.00 0.00 1.94
2006 4049 3.218721 GCAACATGCATACGTTCGG 57.781 52.632 0.00 0.00 44.26 4.30
2028 4071 1.493772 CTTCACACGGCGAAACTACA 58.506 50.000 16.62 0.00 0.00 2.74
2031 4074 1.271379 TCACACGGCGAAACTACAGAT 59.729 47.619 16.62 0.00 0.00 2.90
2043 4086 7.180748 GCGAAACTACAGATAAATTTCTGGAC 58.819 38.462 11.02 0.00 46.04 4.02
2072 4117 2.239907 TCTCTCCGAGAGATCACCTCAA 59.760 50.000 22.00 0.00 45.77 3.02
2138 4183 5.757886 CTTCTTCCGTACAAAAATGCTTGA 58.242 37.500 0.00 0.00 0.00 3.02
2156 4201 9.692325 AATGCTTGAAAGATTAGATTCCTACTT 57.308 29.630 0.00 0.00 0.00 2.24
2157 4202 9.692325 ATGCTTGAAAGATTAGATTCCTACTTT 57.308 29.630 0.00 0.00 29.27 2.66
2158 4203 9.520515 TGCTTGAAAGATTAGATTCCTACTTTT 57.479 29.630 0.00 0.00 27.77 2.27
2182 4227 4.724279 TTTAGGGGGATTAGATTCCTGC 57.276 45.455 0.00 0.00 35.97 4.85
2183 4228 2.522013 AGGGGGATTAGATTCCTGCT 57.478 50.000 0.00 0.00 35.97 4.24
2184 4229 2.061061 AGGGGGATTAGATTCCTGCTG 58.939 52.381 0.00 0.00 35.97 4.41
2185 4230 1.074566 GGGGGATTAGATTCCTGCTGG 59.925 57.143 2.58 2.58 35.97 4.85
2186 4231 1.777272 GGGGATTAGATTCCTGCTGGT 59.223 52.381 9.73 0.00 35.97 4.00
2187 4232 2.175715 GGGGATTAGATTCCTGCTGGTT 59.824 50.000 9.73 0.00 35.97 3.67
2188 4233 3.217626 GGGATTAGATTCCTGCTGGTTG 58.782 50.000 9.73 0.00 35.97 3.77
2189 4234 3.217626 GGATTAGATTCCTGCTGGTTGG 58.782 50.000 9.73 0.00 32.68 3.77
2190 4235 3.372025 GGATTAGATTCCTGCTGGTTGGT 60.372 47.826 9.73 0.00 32.68 3.67
2191 4236 4.141482 GGATTAGATTCCTGCTGGTTGGTA 60.141 45.833 9.73 0.00 32.68 3.25
2192 4237 5.456763 GGATTAGATTCCTGCTGGTTGGTAT 60.457 44.000 9.73 0.00 32.68 2.73
2193 4238 6.239887 GGATTAGATTCCTGCTGGTTGGTATA 60.240 42.308 9.73 0.00 32.68 1.47
2194 4239 6.763715 TTAGATTCCTGCTGGTTGGTATAT 57.236 37.500 9.73 0.00 34.23 0.86
2195 4240 5.653255 AGATTCCTGCTGGTTGGTATATT 57.347 39.130 9.73 0.00 34.23 1.28
2196 4241 6.018433 AGATTCCTGCTGGTTGGTATATTT 57.982 37.500 9.73 0.00 34.23 1.40
2197 4242 7.149202 AGATTCCTGCTGGTTGGTATATTTA 57.851 36.000 9.73 0.00 34.23 1.40
2198 4243 7.227156 AGATTCCTGCTGGTTGGTATATTTAG 58.773 38.462 9.73 0.00 34.23 1.85
2199 4244 6.569127 TTCCTGCTGGTTGGTATATTTAGA 57.431 37.500 9.73 0.00 34.23 2.10
2200 4245 6.174720 TCCTGCTGGTTGGTATATTTAGAG 57.825 41.667 9.73 0.00 34.23 2.43
2201 4246 4.757149 CCTGCTGGTTGGTATATTTAGAGC 59.243 45.833 0.51 0.00 0.00 4.09
2202 4247 5.366482 TGCTGGTTGGTATATTTAGAGCA 57.634 39.130 0.00 0.00 0.00 4.26
2203 4248 5.750524 TGCTGGTTGGTATATTTAGAGCAA 58.249 37.500 0.00 0.00 33.20 3.91
2204 4249 6.364701 TGCTGGTTGGTATATTTAGAGCAAT 58.635 36.000 0.00 0.00 37.27 3.56
2205 4250 6.833416 TGCTGGTTGGTATATTTAGAGCAATT 59.167 34.615 0.00 0.00 37.27 2.32
2206 4251 7.013274 TGCTGGTTGGTATATTTAGAGCAATTC 59.987 37.037 0.00 0.00 37.27 2.17
2207 4252 7.013274 GCTGGTTGGTATATTTAGAGCAATTCA 59.987 37.037 0.83 2.98 37.27 2.57
2208 4253 8.995027 TGGTTGGTATATTTAGAGCAATTCAT 57.005 30.769 0.83 0.00 37.27 2.57
2209 4254 9.420118 TGGTTGGTATATTTAGAGCAATTCATT 57.580 29.630 0.83 0.00 37.27 2.57
2217 4262 9.807649 ATATTTAGAGCAATTCATTTGTTCCAC 57.192 29.630 0.00 0.00 44.20 4.02
2218 4263 6.647334 TTAGAGCAATTCATTTGTTCCACA 57.353 33.333 0.00 0.00 44.20 4.17
2219 4264 5.733620 AGAGCAATTCATTTGTTCCACAT 57.266 34.783 0.00 0.00 44.20 3.21
2220 4265 6.105397 AGAGCAATTCATTTGTTCCACATT 57.895 33.333 0.00 0.00 44.20 2.71
2221 4266 5.929992 AGAGCAATTCATTTGTTCCACATTG 59.070 36.000 0.00 0.00 44.20 2.82
2222 4267 4.453136 AGCAATTCATTTGTTCCACATTGC 59.547 37.500 5.95 5.95 37.06 3.56
2223 4268 4.213694 GCAATTCATTTGTTCCACATTGCA 59.786 37.500 8.68 0.00 36.90 4.08
2224 4269 5.277876 GCAATTCATTTGTTCCACATTGCAA 60.278 36.000 0.00 0.00 36.90 4.08
2225 4270 6.568844 GCAATTCATTTGTTCCACATTGCAAT 60.569 34.615 5.99 5.99 36.90 3.56
2226 4271 7.364200 CAATTCATTTGTTCCACATTGCAATT 58.636 30.769 9.83 0.00 0.00 2.32
2227 4272 6.939132 TTCATTTGTTCCACATTGCAATTT 57.061 29.167 9.83 0.00 0.00 1.82
2228 4273 6.542574 TCATTTGTTCCACATTGCAATTTC 57.457 33.333 9.83 0.00 0.00 2.17
2229 4274 6.289834 TCATTTGTTCCACATTGCAATTTCT 58.710 32.000 9.83 0.00 0.00 2.52
2230 4275 6.766944 TCATTTGTTCCACATTGCAATTTCTT 59.233 30.769 9.83 0.00 0.00 2.52
2231 4276 6.998968 TTTGTTCCACATTGCAATTTCTTT 57.001 29.167 9.83 0.00 0.00 2.52
2232 4277 6.998968 TTGTTCCACATTGCAATTTCTTTT 57.001 29.167 9.83 0.00 0.00 2.27
2233 4278 6.601741 TGTTCCACATTGCAATTTCTTTTC 57.398 33.333 9.83 0.00 0.00 2.29
2234 4279 6.347696 TGTTCCACATTGCAATTTCTTTTCT 58.652 32.000 9.83 0.00 0.00 2.52
2235 4280 6.822676 TGTTCCACATTGCAATTTCTTTTCTT 59.177 30.769 9.83 0.00 0.00 2.52
2236 4281 7.336427 TGTTCCACATTGCAATTTCTTTTCTTT 59.664 29.630 9.83 0.00 0.00 2.52
2237 4282 7.862512 TCCACATTGCAATTTCTTTTCTTTT 57.137 28.000 9.83 0.00 0.00 2.27
2238 4283 8.278729 TCCACATTGCAATTTCTTTTCTTTTT 57.721 26.923 9.83 0.00 0.00 1.94
2264 4309 6.942163 TTCAAATGGGGAATTGGTATGAAA 57.058 33.333 0.00 0.00 0.00 2.69
2268 4313 7.828223 TCAAATGGGGAATTGGTATGAAATTTG 59.172 33.333 0.00 0.00 34.29 2.32
2271 4316 4.875536 GGGGAATTGGTATGAAATTTGTGC 59.124 41.667 0.00 0.00 0.00 4.57
2272 4317 5.338300 GGGGAATTGGTATGAAATTTGTGCT 60.338 40.000 0.00 0.00 0.00 4.40
2280 4325 8.770438 TGGTATGAAATTTGTGCTTAAAATCC 57.230 30.769 0.00 0.00 0.00 3.01
2283 4328 9.087424 GTATGAAATTTGTGCTTAAAATCCTCC 57.913 33.333 0.00 0.00 0.00 4.30
2284 4329 7.060383 TGAAATTTGTGCTTAAAATCCTCCA 57.940 32.000 0.00 0.00 0.00 3.86
2285 4330 7.504403 TGAAATTTGTGCTTAAAATCCTCCAA 58.496 30.769 0.00 0.00 0.00 3.53
2287 4332 8.744568 AAATTTGTGCTTAAAATCCTCCAAAA 57.255 26.923 0.00 0.00 0.00 2.44
2291 4336 6.222389 TGTGCTTAAAATCCTCCAAAATGTG 58.778 36.000 0.00 0.00 0.00 3.21
2307 4352 6.809869 CAAAATGTGGAGGAAAGAGAAGTTT 58.190 36.000 0.00 0.00 0.00 2.66
2308 4353 6.641169 AAATGTGGAGGAAAGAGAAGTTTC 57.359 37.500 0.00 0.00 35.95 2.78
2323 4368 6.890979 AGAAGTTTCTCTTTGGAATCCTTG 57.109 37.500 0.00 0.00 36.40 3.61
2325 4370 4.734266 AGTTTCTCTTTGGAATCCTTGCT 58.266 39.130 0.00 0.00 0.00 3.91
2326 4371 4.764308 AGTTTCTCTTTGGAATCCTTGCTC 59.236 41.667 0.00 0.00 0.00 4.26
2327 4372 3.356529 TCTCTTTGGAATCCTTGCTCC 57.643 47.619 0.00 0.00 0.00 4.70
2328 4373 2.644299 TCTCTTTGGAATCCTTGCTCCA 59.356 45.455 0.00 0.00 40.03 3.86
2329 4374 3.267812 TCTCTTTGGAATCCTTGCTCCAT 59.732 43.478 0.00 0.00 41.36 3.41
2330 4375 3.624777 TCTTTGGAATCCTTGCTCCATC 58.375 45.455 0.00 0.00 41.36 3.51
2331 4376 2.442236 TTGGAATCCTTGCTCCATCC 57.558 50.000 0.00 0.00 41.36 3.51
2332 4377 0.552848 TGGAATCCTTGCTCCATCCC 59.447 55.000 0.00 0.00 36.79 3.85
2333 4378 0.849417 GGAATCCTTGCTCCATCCCT 59.151 55.000 0.00 0.00 0.00 4.20
2335 4380 2.224646 GGAATCCTTGCTCCATCCCTAC 60.225 54.545 0.00 0.00 0.00 3.18
2337 4382 2.196742 TCCTTGCTCCATCCCTACAT 57.803 50.000 0.00 0.00 0.00 2.29
2339 4384 2.852449 TCCTTGCTCCATCCCTACATTT 59.148 45.455 0.00 0.00 0.00 2.32
2340 4385 3.117888 TCCTTGCTCCATCCCTACATTTC 60.118 47.826 0.00 0.00 0.00 2.17
2341 4386 3.371917 CCTTGCTCCATCCCTACATTTCA 60.372 47.826 0.00 0.00 0.00 2.69
2342 4387 4.272489 CTTGCTCCATCCCTACATTTCAA 58.728 43.478 0.00 0.00 0.00 2.69
2343 4388 4.314522 TGCTCCATCCCTACATTTCAAA 57.685 40.909 0.00 0.00 0.00 2.69
2344 4389 4.272489 TGCTCCATCCCTACATTTCAAAG 58.728 43.478 0.00 0.00 0.00 2.77
2345 4390 4.263905 TGCTCCATCCCTACATTTCAAAGT 60.264 41.667 0.00 0.00 0.00 2.66
2346 4391 4.336713 GCTCCATCCCTACATTTCAAAGTC 59.663 45.833 0.00 0.00 0.00 3.01
2347 4392 4.855340 TCCATCCCTACATTTCAAAGTCC 58.145 43.478 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.040247 CGCCCGCTATAATGACTATTAATGA 58.960 40.000 0.00 0.00 32.80 2.57
32 33 1.938625 GTTATTGGTAACGCCCGCTA 58.061 50.000 0.00 0.00 42.51 4.26
73 76 1.489560 GGCCTCAGTTACACAGGGGT 61.490 60.000 0.00 0.00 0.00 4.95
74 77 1.201429 AGGCCTCAGTTACACAGGGG 61.201 60.000 0.00 0.00 0.00 4.79
99 102 1.263356 TATATAGAGTGCGCCACCCC 58.737 55.000 4.18 0.00 34.49 4.95
151 154 2.890371 CGTGAGAGTTACCCGGGG 59.110 66.667 27.92 12.73 0.00 5.73
155 158 3.181469 TGGATTATGCGTGAGAGTTACCC 60.181 47.826 0.00 0.00 0.00 3.69
156 159 4.054780 TGGATTATGCGTGAGAGTTACC 57.945 45.455 0.00 0.00 0.00 2.85
213 217 3.032459 GGTCCTTCTCGGAGGAAGTAAT 58.968 50.000 4.96 0.00 46.95 1.89
219 223 0.408309 TTCAGGTCCTTCTCGGAGGA 59.592 55.000 4.96 0.00 44.20 3.71
220 224 0.533032 GTTCAGGTCCTTCTCGGAGG 59.467 60.000 4.96 0.00 44.20 4.30
221 225 1.474879 GAGTTCAGGTCCTTCTCGGAG 59.525 57.143 0.00 0.00 44.20 4.63
222 226 1.546961 GAGTTCAGGTCCTTCTCGGA 58.453 55.000 0.00 0.00 40.30 4.55
223 227 0.171455 CGAGTTCAGGTCCTTCTCGG 59.829 60.000 20.98 9.58 42.45 4.63
224 228 3.704381 CGAGTTCAGGTCCTTCTCG 57.296 57.895 17.63 17.63 41.02 4.04
225 229 4.236147 GTTTACGAGTTCAGGTCCTTCTC 58.764 47.826 0.00 0.00 0.00 2.87
226 230 3.006644 GGTTTACGAGTTCAGGTCCTTCT 59.993 47.826 0.00 0.00 0.00 2.85
227 231 3.006644 AGGTTTACGAGTTCAGGTCCTTC 59.993 47.826 0.00 0.00 0.00 3.46
228 232 2.970640 AGGTTTACGAGTTCAGGTCCTT 59.029 45.455 0.00 0.00 0.00 3.36
229 233 2.606378 AGGTTTACGAGTTCAGGTCCT 58.394 47.619 0.00 0.00 0.00 3.85
230 234 3.064931 CAAGGTTTACGAGTTCAGGTCC 58.935 50.000 0.00 0.00 0.00 4.46
231 235 2.479275 GCAAGGTTTACGAGTTCAGGTC 59.521 50.000 0.00 0.00 0.00 3.85
232 236 2.490991 GCAAGGTTTACGAGTTCAGGT 58.509 47.619 0.00 0.00 0.00 4.00
233 237 1.459592 CGCAAGGTTTACGAGTTCAGG 59.540 52.381 0.00 0.00 0.00 3.86
234 238 2.096909 CACGCAAGGTTTACGAGTTCAG 60.097 50.000 0.00 0.00 46.39 3.02
235 239 1.862201 CACGCAAGGTTTACGAGTTCA 59.138 47.619 0.00 0.00 46.39 3.18
236 240 1.398071 GCACGCAAGGTTTACGAGTTC 60.398 52.381 0.00 0.00 46.39 3.01
237 241 0.584876 GCACGCAAGGTTTACGAGTT 59.415 50.000 0.00 0.00 46.39 3.01
238 242 0.531090 TGCACGCAAGGTTTACGAGT 60.531 50.000 0.00 0.00 46.39 4.18
239 243 0.110823 GTGCACGCAAGGTTTACGAG 60.111 55.000 0.00 0.00 46.39 4.18
240 244 0.810426 TGTGCACGCAAGGTTTACGA 60.810 50.000 13.13 0.00 46.39 3.43
241 245 0.028242 TTGTGCACGCAAGGTTTACG 59.972 50.000 13.13 0.00 46.39 3.18
242 246 1.472990 GTTGTGCACGCAAGGTTTAC 58.527 50.000 13.13 0.00 46.39 2.01
243 247 0.382515 GGTTGTGCACGCAAGGTTTA 59.617 50.000 13.13 0.00 46.39 2.01
244 248 1.140804 GGTTGTGCACGCAAGGTTT 59.859 52.632 13.13 0.00 46.39 3.27
245 249 1.724582 GAGGTTGTGCACGCAAGGTT 61.725 55.000 13.13 0.00 46.39 3.50
246 250 2.124320 AGGTTGTGCACGCAAGGT 60.124 55.556 13.13 0.00 46.39 3.50
247 251 2.186160 TGAGGTTGTGCACGCAAGG 61.186 57.895 13.13 0.00 46.39 3.61
249 253 2.477176 GGTGAGGTTGTGCACGCAA 61.477 57.895 13.13 0.00 35.91 4.85
250 254 2.899838 GGTGAGGTTGTGCACGCA 60.900 61.111 13.13 0.00 35.91 5.24
251 255 4.012895 CGGTGAGGTTGTGCACGC 62.013 66.667 13.13 7.53 35.91 5.34
252 256 1.282248 CTACGGTGAGGTTGTGCACG 61.282 60.000 13.13 0.00 35.91 5.34
253 257 1.566018 GCTACGGTGAGGTTGTGCAC 61.566 60.000 10.75 10.75 0.00 4.57
254 258 1.301401 GCTACGGTGAGGTTGTGCA 60.301 57.895 0.00 0.00 0.00 4.57
255 259 0.245539 TAGCTACGGTGAGGTTGTGC 59.754 55.000 0.00 0.00 0.00 4.57
256 260 1.135083 CCTAGCTACGGTGAGGTTGTG 60.135 57.143 0.00 0.00 0.00 3.33
257 261 1.183549 CCTAGCTACGGTGAGGTTGT 58.816 55.000 0.00 0.00 0.00 3.32
258 262 0.460311 CCCTAGCTACGGTGAGGTTG 59.540 60.000 0.86 0.00 0.00 3.77
259 263 1.328430 GCCCTAGCTACGGTGAGGTT 61.328 60.000 10.08 0.00 35.50 3.50
260 264 1.757340 GCCCTAGCTACGGTGAGGT 60.757 63.158 10.08 0.00 35.50 3.85
261 265 2.499827 GGCCCTAGCTACGGTGAGG 61.500 68.421 10.08 1.03 39.73 3.86
262 266 1.043673 AAGGCCCTAGCTACGGTGAG 61.044 60.000 0.00 0.00 39.73 3.51
263 267 0.259647 TAAGGCCCTAGCTACGGTGA 59.740 55.000 0.00 0.00 39.73 4.02
264 268 0.388294 GTAAGGCCCTAGCTACGGTG 59.612 60.000 0.00 3.17 39.73 4.94
265 269 0.758310 GGTAAGGCCCTAGCTACGGT 60.758 60.000 0.00 0.00 39.73 4.83
266 270 0.469518 AGGTAAGGCCCTAGCTACGG 60.470 60.000 11.46 4.51 39.73 4.02
267 271 0.960286 GAGGTAAGGCCCTAGCTACG 59.040 60.000 13.07 0.00 39.73 3.51
268 272 1.133104 AGGAGGTAAGGCCCTAGCTAC 60.133 57.143 14.12 14.12 39.73 3.58
269 273 1.147399 GAGGAGGTAAGGCCCTAGCTA 59.853 57.143 13.07 0.00 39.73 3.32
270 274 0.105401 GAGGAGGTAAGGCCCTAGCT 60.105 60.000 12.96 12.96 39.73 3.32
271 275 1.122632 GGAGGAGGTAAGGCCCTAGC 61.123 65.000 0.00 0.00 38.26 3.42
272 276 0.563672 AGGAGGAGGTAAGGCCCTAG 59.436 60.000 0.00 0.00 38.26 3.02
273 277 1.502474 GTAGGAGGAGGTAAGGCCCTA 59.498 57.143 0.00 0.00 38.26 3.53
274 278 0.265254 GTAGGAGGAGGTAAGGCCCT 59.735 60.000 0.00 0.00 38.26 5.19
275 279 1.114119 CGTAGGAGGAGGTAAGGCCC 61.114 65.000 0.00 0.00 38.26 5.80
276 280 0.396835 ACGTAGGAGGAGGTAAGGCC 60.397 60.000 0.00 0.00 37.58 5.19
277 281 1.952990 GTACGTAGGAGGAGGTAAGGC 59.047 57.143 0.00 0.00 0.00 4.35
278 282 2.580962 GGTACGTAGGAGGAGGTAAGG 58.419 57.143 0.00 0.00 0.00 2.69
279 283 2.580962 GGGTACGTAGGAGGAGGTAAG 58.419 57.143 0.00 0.00 0.00 2.34
280 284 1.215423 GGGGTACGTAGGAGGAGGTAA 59.785 57.143 0.00 0.00 0.00 2.85
281 285 0.846693 GGGGTACGTAGGAGGAGGTA 59.153 60.000 0.00 0.00 0.00 3.08
282 286 1.617475 GGGGTACGTAGGAGGAGGT 59.383 63.158 0.00 0.00 0.00 3.85
283 287 1.152589 GGGGGTACGTAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
284 288 1.143813 TAGGGGGTACGTAGGAGGAG 58.856 60.000 0.00 0.00 0.00 3.69
285 289 1.838611 ATAGGGGGTACGTAGGAGGA 58.161 55.000 0.00 0.00 0.00 3.71
286 290 2.109657 AGAATAGGGGGTACGTAGGAGG 59.890 54.545 0.00 0.00 0.00 4.30
287 291 3.522392 AGAATAGGGGGTACGTAGGAG 57.478 52.381 0.00 0.00 0.00 3.69
288 292 3.979501 AAGAATAGGGGGTACGTAGGA 57.020 47.619 0.00 0.00 0.00 2.94
289 293 4.522022 CAGTAAGAATAGGGGGTACGTAGG 59.478 50.000 0.00 0.00 0.00 3.18
290 294 5.136105 ACAGTAAGAATAGGGGGTACGTAG 58.864 45.833 0.00 0.00 0.00 3.51
291 295 5.129368 ACAGTAAGAATAGGGGGTACGTA 57.871 43.478 0.00 0.00 0.00 3.57
292 296 3.956848 GACAGTAAGAATAGGGGGTACGT 59.043 47.826 0.00 0.00 0.00 3.57
293 297 3.956199 TGACAGTAAGAATAGGGGGTACG 59.044 47.826 0.00 0.00 0.00 3.67
294 298 6.781507 AGTATGACAGTAAGAATAGGGGGTAC 59.218 42.308 0.00 0.00 0.00 3.34
295 299 6.930475 AGTATGACAGTAAGAATAGGGGGTA 58.070 40.000 0.00 0.00 0.00 3.69
296 300 5.789535 AGTATGACAGTAAGAATAGGGGGT 58.210 41.667 0.00 0.00 0.00 4.95
297 301 6.749036 AAGTATGACAGTAAGAATAGGGGG 57.251 41.667 0.00 0.00 0.00 5.40
298 302 8.480133 AGTAAGTATGACAGTAAGAATAGGGG 57.520 38.462 0.00 0.00 0.00 4.79
299 303 8.578151 GGAGTAAGTATGACAGTAAGAATAGGG 58.422 40.741 0.00 0.00 0.00 3.53
300 304 8.578151 GGGAGTAAGTATGACAGTAAGAATAGG 58.422 40.741 0.00 0.00 0.00 2.57
301 305 9.132923 TGGGAGTAAGTATGACAGTAAGAATAG 57.867 37.037 0.00 0.00 0.00 1.73
302 306 8.910944 GTGGGAGTAAGTATGACAGTAAGAATA 58.089 37.037 0.00 0.00 0.00 1.75
303 307 7.416438 CGTGGGAGTAAGTATGACAGTAAGAAT 60.416 40.741 0.00 0.00 0.00 2.40
304 308 6.127814 CGTGGGAGTAAGTATGACAGTAAGAA 60.128 42.308 0.00 0.00 0.00 2.52
305 309 5.356190 CGTGGGAGTAAGTATGACAGTAAGA 59.644 44.000 0.00 0.00 0.00 2.10
306 310 5.356190 TCGTGGGAGTAAGTATGACAGTAAG 59.644 44.000 0.00 0.00 0.00 2.34
307 311 5.124457 GTCGTGGGAGTAAGTATGACAGTAA 59.876 44.000 0.00 0.00 0.00 2.24
308 312 4.637534 GTCGTGGGAGTAAGTATGACAGTA 59.362 45.833 0.00 0.00 0.00 2.74
309 313 3.442977 GTCGTGGGAGTAAGTATGACAGT 59.557 47.826 0.00 0.00 0.00 3.55
310 314 3.442625 TGTCGTGGGAGTAAGTATGACAG 59.557 47.826 0.00 0.00 34.99 3.51
311 315 3.423749 TGTCGTGGGAGTAAGTATGACA 58.576 45.455 0.00 0.00 36.89 3.58
312 316 3.734293 GCTGTCGTGGGAGTAAGTATGAC 60.734 52.174 0.00 0.00 0.00 3.06
313 317 2.426024 GCTGTCGTGGGAGTAAGTATGA 59.574 50.000 0.00 0.00 0.00 2.15
314 318 2.794981 CGCTGTCGTGGGAGTAAGTATG 60.795 54.545 0.00 0.00 0.00 2.39
315 319 1.404391 CGCTGTCGTGGGAGTAAGTAT 59.596 52.381 0.00 0.00 0.00 2.12
316 320 0.806868 CGCTGTCGTGGGAGTAAGTA 59.193 55.000 0.00 0.00 0.00 2.24
317 321 1.585006 CGCTGTCGTGGGAGTAAGT 59.415 57.895 0.00 0.00 0.00 2.24
318 322 1.153823 CCGCTGTCGTGGGAGTAAG 60.154 63.158 0.00 0.00 37.15 2.34
319 323 2.967397 CCGCTGTCGTGGGAGTAA 59.033 61.111 0.00 0.00 37.15 2.24
320 324 3.755628 GCCGCTGTCGTGGGAGTA 61.756 66.667 0.00 0.00 41.23 2.59
322 326 4.803426 GAGCCGCTGTCGTGGGAG 62.803 72.222 0.00 0.00 41.23 4.30
328 332 3.376935 ATTCTGGGAGCCGCTGTCG 62.377 63.158 0.00 0.00 0.00 4.35
329 333 1.817099 CATTCTGGGAGCCGCTGTC 60.817 63.158 0.00 0.00 0.00 3.51
330 334 2.270205 CATTCTGGGAGCCGCTGT 59.730 61.111 0.00 0.00 0.00 4.40
331 335 2.315781 TAGCATTCTGGGAGCCGCTG 62.316 60.000 0.00 0.00 0.00 5.18
366 370 0.537143 GTGACCATGGTTCCAGCACA 60.537 55.000 20.85 7.51 0.00 4.57
378 382 3.181475 CCGTTGTAGCATCTAGTGACCAT 60.181 47.826 0.00 0.00 0.00 3.55
389 393 0.736325 GAGTGACGCCGTTGTAGCAT 60.736 55.000 0.00 0.00 0.00 3.79
431 435 4.025401 GGCAACCGTTCCAGCACG 62.025 66.667 0.00 0.00 40.02 5.34
454 458 1.566018 GCCAGTCGTTGTGGTAGCAC 61.566 60.000 18.10 18.10 37.40 4.40
456 460 2.033194 GGCCAGTCGTTGTGGTAGC 61.033 63.158 0.00 0.00 37.40 3.58
460 464 1.369091 GCTATGGCCAGTCGTTGTGG 61.369 60.000 13.05 0.00 38.21 4.17
461 465 1.695893 CGCTATGGCCAGTCGTTGTG 61.696 60.000 13.05 0.00 34.44 3.33
462 466 1.447838 CGCTATGGCCAGTCGTTGT 60.448 57.895 13.05 0.00 34.44 3.32
463 467 0.530650 ATCGCTATGGCCAGTCGTTG 60.531 55.000 13.05 0.00 34.44 4.10
464 468 0.530650 CATCGCTATGGCCAGTCGTT 60.531 55.000 13.05 6.70 34.44 3.85
465 469 1.068083 CATCGCTATGGCCAGTCGT 59.932 57.895 13.05 0.00 34.44 4.34
466 470 1.665916 CCATCGCTATGGCCAGTCG 60.666 63.158 13.05 14.48 46.17 4.18
467 471 4.368391 CCATCGCTATGGCCAGTC 57.632 61.111 13.05 1.09 46.17 3.51
485 489 4.675114 GTCGGTTGCAACTTTTGATGTAAG 59.325 41.667 27.64 6.48 28.86 2.34
488 492 2.425312 TGTCGGTTGCAACTTTTGATGT 59.575 40.909 27.64 0.00 0.00 3.06
491 495 1.133407 GGTGTCGGTTGCAACTTTTGA 59.867 47.619 27.64 17.37 0.00 2.69
520 544 4.514577 CTGGTCCGCCCTACGCAG 62.515 72.222 0.00 0.00 41.76 5.18
549 573 1.820906 ATGCGCTGTCGGATGCAAT 60.821 52.632 9.73 0.00 45.07 3.56
573 601 4.824166 GCATGCTCGCAGTTGCCG 62.824 66.667 11.37 0.00 37.91 5.69
611 639 0.104882 TAACACCTCCCACCACCTCA 60.105 55.000 0.00 0.00 0.00 3.86
612 640 0.613777 CTAACACCTCCCACCACCTC 59.386 60.000 0.00 0.00 0.00 3.85
613 641 0.840722 CCTAACACCTCCCACCACCT 60.841 60.000 0.00 0.00 0.00 4.00
614 642 1.131928 ACCTAACACCTCCCACCACC 61.132 60.000 0.00 0.00 0.00 4.61
615 643 0.036306 CACCTAACACCTCCCACCAC 59.964 60.000 0.00 0.00 0.00 4.16
616 644 1.774894 GCACCTAACACCTCCCACCA 61.775 60.000 0.00 0.00 0.00 4.17
617 645 1.002502 GCACCTAACACCTCCCACC 60.003 63.158 0.00 0.00 0.00 4.61
618 646 0.321653 CAGCACCTAACACCTCCCAC 60.322 60.000 0.00 0.00 0.00 4.61
619 647 0.766674 ACAGCACCTAACACCTCCCA 60.767 55.000 0.00 0.00 0.00 4.37
647 675 1.379044 CTTTCCAGCCCCTCGCATT 60.379 57.895 0.00 0.00 41.38 3.56
687 719 0.816825 GCATGTGCCGTCAGATCCAT 60.817 55.000 0.00 0.00 34.31 3.41
737 769 2.036006 CGACCGGCCCAATTTTCGA 61.036 57.895 0.00 0.00 0.00 3.71
795 828 1.948104 TGCCCGTTCTGTGCATATAC 58.052 50.000 0.00 0.00 0.00 1.47
797 830 1.472480 GTTTGCCCGTTCTGTGCATAT 59.528 47.619 0.00 0.00 34.51 1.78
840 878 1.223187 AATTTGAACGCGTCGTCCTT 58.777 45.000 14.44 0.83 39.99 3.36
841 879 1.223187 AAATTTGAACGCGTCGTCCT 58.777 45.000 14.44 0.00 39.99 3.85
842 880 2.859870 TAAATTTGAACGCGTCGTCC 57.140 45.000 14.44 2.82 39.99 4.79
932 982 2.202222 GTTCACGTGCATGCGAGC 60.202 61.111 14.09 0.00 35.59 5.03
1553 3069 7.394359 ACAGAACAATAATAAAGCACCAGATGT 59.606 33.333 0.00 0.00 0.00 3.06
1655 3692 4.801147 ATTCACGATGTGATTGAATCCG 57.199 40.909 2.26 1.58 42.40 4.18
1741 3782 0.297525 CATACACACACGCGAATCGG 59.702 55.000 15.93 1.08 43.86 4.18
1857 3899 3.416119 TTCACGACGATATCACTCACC 57.584 47.619 0.00 0.00 0.00 4.02
1870 3912 5.629079 AATCCCTTTGAGAATTTCACGAC 57.371 39.130 0.00 0.00 34.94 4.34
1887 3929 4.953579 TGTTCCAAGTAGGCATTAAATCCC 59.046 41.667 0.00 0.00 37.29 3.85
1898 3940 4.891992 TCTTCCTTCTGTTCCAAGTAGG 57.108 45.455 0.00 0.00 36.37 3.18
1940 3983 9.825972 ACGTATGCATGTTTTTATAATATGCTC 57.174 29.630 10.16 7.54 43.29 4.26
1988 4031 0.446222 ACCGAACGTATGCATGTTGC 59.554 50.000 10.16 0.26 45.29 4.17
1989 4032 1.790123 GCACCGAACGTATGCATGTTG 60.790 52.381 10.16 0.98 39.23 3.33
1990 4033 0.446222 GCACCGAACGTATGCATGTT 59.554 50.000 10.16 5.71 39.23 2.71
1991 4034 0.391130 AGCACCGAACGTATGCATGT 60.391 50.000 10.16 0.00 41.97 3.21
1992 4035 0.726827 AAGCACCGAACGTATGCATG 59.273 50.000 10.16 0.00 41.97 4.06
1993 4036 1.006832 GAAGCACCGAACGTATGCAT 58.993 50.000 17.92 3.79 41.97 3.96
1994 4037 0.319986 TGAAGCACCGAACGTATGCA 60.320 50.000 17.92 0.00 41.97 3.96
1995 4038 0.094730 GTGAAGCACCGAACGTATGC 59.905 55.000 11.03 11.03 39.74 3.14
1996 4039 1.126113 GTGTGAAGCACCGAACGTATG 59.874 52.381 0.00 0.00 42.10 2.39
1997 4040 1.425412 GTGTGAAGCACCGAACGTAT 58.575 50.000 0.00 0.00 42.10 3.06
1998 4041 0.935831 CGTGTGAAGCACCGAACGTA 60.936 55.000 0.00 0.00 44.97 3.57
1999 4042 2.235016 CGTGTGAAGCACCGAACGT 61.235 57.895 0.00 0.00 44.97 3.99
2000 4043 2.544359 CGTGTGAAGCACCGAACG 59.456 61.111 0.00 0.00 44.97 3.95
2001 4044 2.935955 CCGTGTGAAGCACCGAAC 59.064 61.111 0.00 0.00 44.97 3.95
2002 4045 2.970324 GCCGTGTGAAGCACCGAA 60.970 61.111 0.00 0.00 44.97 4.30
2005 4048 2.539338 TTTCGCCGTGTGAAGCACC 61.539 57.895 0.00 0.00 44.97 5.01
2006 4049 1.368850 GTTTCGCCGTGTGAAGCAC 60.369 57.895 8.41 0.00 44.36 4.40
2159 4204 5.195756 AGCAGGAATCTAATCCCCCTAAAAA 59.804 40.000 0.00 0.00 40.59 1.94
2160 4205 4.731929 AGCAGGAATCTAATCCCCCTAAAA 59.268 41.667 0.00 0.00 40.59 1.52
2161 4206 4.104738 CAGCAGGAATCTAATCCCCCTAAA 59.895 45.833 0.00 0.00 40.59 1.85
2162 4207 3.652869 CAGCAGGAATCTAATCCCCCTAA 59.347 47.826 0.00 0.00 40.59 2.69
2163 4208 3.251484 CAGCAGGAATCTAATCCCCCTA 58.749 50.000 0.00 0.00 40.59 3.53
2164 4209 2.061061 CAGCAGGAATCTAATCCCCCT 58.939 52.381 0.00 0.00 40.59 4.79
2165 4210 1.074566 CCAGCAGGAATCTAATCCCCC 59.925 57.143 0.00 0.00 40.59 5.40
2166 4211 1.777272 ACCAGCAGGAATCTAATCCCC 59.223 52.381 0.35 0.00 40.59 4.81
2167 4212 3.217626 CAACCAGCAGGAATCTAATCCC 58.782 50.000 0.35 0.00 40.59 3.85
2168 4213 3.217626 CCAACCAGCAGGAATCTAATCC 58.782 50.000 0.35 0.00 39.96 3.01
2169 4214 3.891049 ACCAACCAGCAGGAATCTAATC 58.109 45.455 0.35 0.00 38.69 1.75
2170 4215 5.653255 ATACCAACCAGCAGGAATCTAAT 57.347 39.130 0.35 0.00 38.69 1.73
2171 4216 6.763715 ATATACCAACCAGCAGGAATCTAA 57.236 37.500 0.35 0.00 38.69 2.10
2172 4217 6.763715 AATATACCAACCAGCAGGAATCTA 57.236 37.500 0.35 0.00 38.69 1.98
2173 4218 5.653255 AATATACCAACCAGCAGGAATCT 57.347 39.130 0.35 0.00 38.69 2.40
2174 4219 7.224297 TCTAAATATACCAACCAGCAGGAATC 58.776 38.462 0.35 0.00 38.69 2.52
2175 4220 7.149202 TCTAAATATACCAACCAGCAGGAAT 57.851 36.000 0.35 0.00 38.69 3.01
2176 4221 6.569127 TCTAAATATACCAACCAGCAGGAA 57.431 37.500 0.35 0.00 38.69 3.36
2177 4222 5.454755 GCTCTAAATATACCAACCAGCAGGA 60.455 44.000 0.35 0.00 38.69 3.86
2178 4223 4.757149 GCTCTAAATATACCAACCAGCAGG 59.243 45.833 0.00 0.00 42.21 4.85
2179 4224 5.368145 TGCTCTAAATATACCAACCAGCAG 58.632 41.667 0.00 0.00 30.98 4.24
2180 4225 5.366482 TGCTCTAAATATACCAACCAGCA 57.634 39.130 0.00 0.00 32.06 4.41
2181 4226 6.884280 ATTGCTCTAAATATACCAACCAGC 57.116 37.500 0.00 0.00 0.00 4.85
2182 4227 8.450578 TGAATTGCTCTAAATATACCAACCAG 57.549 34.615 0.00 0.00 0.00 4.00
2183 4228 8.995027 ATGAATTGCTCTAAATATACCAACCA 57.005 30.769 0.00 0.00 0.00 3.67
2191 4236 9.807649 GTGGAACAAATGAATTGCTCTAAATAT 57.192 29.630 0.00 0.00 44.16 1.28
2211 4256 6.849588 AGAAAAGAAATTGCAATGTGGAAC 57.150 33.333 13.82 2.96 28.29 3.62
2212 4257 7.862512 AAAGAAAAGAAATTGCAATGTGGAA 57.137 28.000 13.82 0.00 30.73 3.53
2213 4258 7.862512 AAAAGAAAAGAAATTGCAATGTGGA 57.137 28.000 13.82 0.00 0.00 4.02
2238 4283 7.321717 TCATACCAATTCCCCATTTGAAAAA 57.678 32.000 0.00 0.00 0.00 1.94
2239 4284 6.942163 TCATACCAATTCCCCATTTGAAAA 57.058 33.333 0.00 0.00 0.00 2.29
2240 4285 6.942163 TTCATACCAATTCCCCATTTGAAA 57.058 33.333 0.00 0.00 0.00 2.69
2241 4286 6.942163 TTTCATACCAATTCCCCATTTGAA 57.058 33.333 0.00 0.00 0.00 2.69
2242 4287 7.507797 AATTTCATACCAATTCCCCATTTGA 57.492 32.000 0.00 0.00 0.00 2.69
2243 4288 7.611079 ACAAATTTCATACCAATTCCCCATTTG 59.389 33.333 0.00 0.00 35.15 2.32
2244 4289 7.611079 CACAAATTTCATACCAATTCCCCATTT 59.389 33.333 0.00 0.00 0.00 2.32
2245 4290 7.111466 CACAAATTTCATACCAATTCCCCATT 58.889 34.615 0.00 0.00 0.00 3.16
2246 4291 6.652053 CACAAATTTCATACCAATTCCCCAT 58.348 36.000 0.00 0.00 0.00 4.00
2247 4292 5.570439 GCACAAATTTCATACCAATTCCCCA 60.570 40.000 0.00 0.00 0.00 4.96
2248 4293 4.875536 GCACAAATTTCATACCAATTCCCC 59.124 41.667 0.00 0.00 0.00 4.81
2249 4294 5.733676 AGCACAAATTTCATACCAATTCCC 58.266 37.500 0.00 0.00 0.00 3.97
2250 4295 8.770438 TTAAGCACAAATTTCATACCAATTCC 57.230 30.769 0.00 0.00 0.00 3.01
2254 4299 9.213799 GGATTTTAAGCACAAATTTCATACCAA 57.786 29.630 0.00 0.00 0.00 3.67
2255 4300 8.592809 AGGATTTTAAGCACAAATTTCATACCA 58.407 29.630 0.00 0.00 0.00 3.25
2256 4301 9.087424 GAGGATTTTAAGCACAAATTTCATACC 57.913 33.333 0.00 0.00 0.00 2.73
2257 4302 9.087424 GGAGGATTTTAAGCACAAATTTCATAC 57.913 33.333 0.00 0.00 0.00 2.39
2258 4303 8.811017 TGGAGGATTTTAAGCACAAATTTCATA 58.189 29.630 0.00 0.00 0.00 2.15
2264 4309 7.938490 ACATTTTGGAGGATTTTAAGCACAAAT 59.062 29.630 0.00 0.00 0.00 2.32
2268 4313 6.710692 CACATTTTGGAGGATTTTAAGCAC 57.289 37.500 0.00 0.00 0.00 4.40
2283 4328 6.396829 AACTTCTCTTTCCTCCACATTTTG 57.603 37.500 0.00 0.00 0.00 2.44
2284 4329 6.836007 AGAAACTTCTCTTTCCTCCACATTTT 59.164 34.615 0.00 0.00 29.94 1.82
2285 4330 6.368805 AGAAACTTCTCTTTCCTCCACATTT 58.631 36.000 0.00 0.00 29.94 2.32
2287 4332 5.574970 AGAAACTTCTCTTTCCTCCACAT 57.425 39.130 0.00 0.00 29.94 3.21
2300 4345 5.242615 GCAAGGATTCCAAAGAGAAACTTCT 59.757 40.000 5.29 0.00 41.00 2.85
2303 4348 4.734266 AGCAAGGATTCCAAAGAGAAACT 58.266 39.130 5.29 0.00 0.00 2.66
2304 4349 4.082517 GGAGCAAGGATTCCAAAGAGAAAC 60.083 45.833 5.29 0.00 33.55 2.78
2305 4350 4.082125 GGAGCAAGGATTCCAAAGAGAAA 58.918 43.478 5.29 0.00 33.55 2.52
2307 4352 2.644299 TGGAGCAAGGATTCCAAAGAGA 59.356 45.455 5.29 0.00 40.41 3.10
2308 4353 3.077484 TGGAGCAAGGATTCCAAAGAG 57.923 47.619 5.29 0.00 40.41 2.85
2310 4355 2.692041 GGATGGAGCAAGGATTCCAAAG 59.308 50.000 5.29 0.00 45.94 2.77
2311 4356 2.624029 GGGATGGAGCAAGGATTCCAAA 60.624 50.000 5.29 0.00 45.94 3.28
2312 4357 1.063717 GGGATGGAGCAAGGATTCCAA 60.064 52.381 5.29 0.00 45.94 3.53
2313 4358 0.552848 GGGATGGAGCAAGGATTCCA 59.447 55.000 5.29 0.00 46.79 3.53
2314 4359 0.849417 AGGGATGGAGCAAGGATTCC 59.151 55.000 0.00 0.00 0.00 3.01
2316 4361 2.492025 TGTAGGGATGGAGCAAGGATT 58.508 47.619 0.00 0.00 0.00 3.01
2317 4362 2.196742 TGTAGGGATGGAGCAAGGAT 57.803 50.000 0.00 0.00 0.00 3.24
2319 4364 3.217626 GAAATGTAGGGATGGAGCAAGG 58.782 50.000 0.00 0.00 0.00 3.61
2321 4366 4.314522 TTGAAATGTAGGGATGGAGCAA 57.685 40.909 0.00 0.00 0.00 3.91
2322 4367 4.263905 ACTTTGAAATGTAGGGATGGAGCA 60.264 41.667 0.00 0.00 0.00 4.26
2323 4368 4.273318 ACTTTGAAATGTAGGGATGGAGC 58.727 43.478 0.00 0.00 0.00 4.70
2325 4370 4.855340 GGACTTTGAAATGTAGGGATGGA 58.145 43.478 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.