Multiple sequence alignment - TraesCS4A01G012400

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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 TraesCS4A01G012400 chr4A 100.000 2594 0 0 1 2594 7158619 7156026 0.000000e+00 4791
1 TraesCS4A01G012400 chr4B 94.407 894 42 5 867 1754 577012819 577013710 0.000000e+00 1367
2 TraesCS4A01G012400 chr4B 90.583 446 34 2 2149 2594 577014085 577014522 3.720000e-163 584
3 TraesCS4A01G012400 chr4B 86.630 359 28 6 1806 2164 577013730 577014068 1.880000e-101 379
4 TraesCS4A01G012400 chr4B 90.845 142 8 2 459 600 577011504 577011640 4.410000e-43 185
5 TraesCS4A01G012400 chr4B 92.373 118 8 1 764 881 577012686 577012802 1.600000e-37 167
6 TraesCS4A01G012400 chr4B 87.234 141 8 7 469 609 577011879 577012009 4.470000e-33 152
7 TraesCS4A01G012400 chr4D 92.275 945 37 12 681 1599 461557106 461558040 0.000000e+00 1308
8 TraesCS4A01G012400 chr4D 91.873 726 36 8 1598 2323 461559373 461560075 0.000000e+00 992
9 TraesCS4A01G012400 chr4D 91.884 345 20 4 121 458 221285060 221284717 2.340000e-130 475
10 TraesCS4A01G012400 chr4D 91.884 345 20 4 121 458 386936479 386936136 2.340000e-130 475
11 TraesCS4A01G012400 chr4D 91.579 285 16 3 2310 2594 461560186 461560462 1.130000e-103 387
12 TraesCS4A01G012400 chr4D 87.764 237 13 8 459 694 461497509 461497730 1.980000e-66 263
13 TraesCS4A01G012400 chr4D 89.506 162 13 2 714 875 461498048 461498205 4.380000e-48 202
14 TraesCS4A01G012400 chr4D 93.443 122 6 2 1 122 360790273 360790392 2.050000e-41 180
15 TraesCS4A01G012400 chr4D 86.525 141 16 2 459 597 461556447 461556586 4.470000e-33 152
16 TraesCS4A01G012400 chr7B 92.816 348 15 5 121 459 723755896 723756242 1.790000e-136 496
17 TraesCS4A01G012400 chr7B 91.860 344 21 3 121 458 138036351 138036693 8.400000e-130 473
18 TraesCS4A01G012400 chr3D 93.023 344 17 3 121 458 131348719 131349061 1.790000e-136 496
19 TraesCS4A01G012400 chr3D 92.000 350 20 4 121 463 521590918 521591266 3.880000e-133 484
20 TraesCS4A01G012400 chr3D 93.443 122 6 2 1 122 151428090 151427971 2.050000e-41 180
21 TraesCS4A01G012400 chr5B 92.486 346 21 1 121 461 282846858 282846513 8.340000e-135 490
22 TraesCS4A01G012400 chr2B 92.486 346 18 4 121 460 131288333 131287990 3.000000e-134 488
23 TraesCS4A01G012400 chr2B 95.082 122 5 1 1 122 641357296 641357176 9.470000e-45 191
24 TraesCS4A01G012400 chr2D 92.059 340 25 1 121 458 447851408 447851069 6.490000e-131 477
25 TraesCS4A01G012400 chr7D 94.262 122 5 2 1 122 116824874 116824993 4.410000e-43 185
26 TraesCS4A01G012400 chr6B 94.262 122 6 1 1 122 572607382 572607502 4.410000e-43 185
27 TraesCS4A01G012400 chr5A 94.262 122 6 1 1 122 368559934 368560054 4.410000e-43 185
28 TraesCS4A01G012400 chr3B 94.262 122 6 1 1 122 633366248 633366128 4.410000e-43 185
29 TraesCS4A01G012400 chr3A 94.215 121 6 1 2 122 627914866 627914747 1.590000e-42 183
30 TraesCS4A01G012400 chr1B 93.443 122 7 1 1 122 314634754 314634634 2.050000e-41 180


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 TraesCS4A01G012400 chr4A 7156026 7158619 2593 True 4791.000000 4791 100.000000 1 2594 1 chr4A.!!$R1 2593
1 TraesCS4A01G012400 chr4B 577011504 577014522 3018 False 472.333333 1367 90.345333 459 2594 6 chr4B.!!$F1 2135
2 TraesCS4A01G012400 chr4D 461556447 461560462 4015 False 709.750000 1308 90.563000 459 2594 4 chr4D.!!$F3 2135
3 TraesCS4A01G012400 chr4D 461497509 461498205 696 False 232.500000 263 88.635000 459 875 2 chr4D.!!$F2 416

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
424 425 0.036022 AGTTGAGCTGAGCCAACTCC 59.964 55.0 25.34 9.7 42.04 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 5181 0.039618 AATGGTGTTTGATCCGCCCT 59.96 50.0 0.0 0.0 0.0 5.19 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
114 115 9.855021 TTAATTAAGTGCAAAGAAGATTTAGGC 57.145 29.630 0.00 0.00 0.00 3.93
115 116 4.790765 AAGTGCAAAGAAGATTTAGGCC 57.209 40.909 0.00 0.00 0.00 5.19
116 117 4.039603 AGTGCAAAGAAGATTTAGGCCT 57.960 40.909 11.78 11.78 0.00 5.19
117 118 5.179452 AGTGCAAAGAAGATTTAGGCCTA 57.821 39.130 8.91 8.91 0.00 3.93
118 119 5.570320 AGTGCAAAGAAGATTTAGGCCTAA 58.430 37.500 21.68 21.68 0.00 2.69
119 120 6.190587 AGTGCAAAGAAGATTTAGGCCTAAT 58.809 36.000 25.70 15.37 0.00 1.73
120 121 6.665248 AGTGCAAAGAAGATTTAGGCCTAATT 59.335 34.615 25.70 21.47 0.00 1.40
121 122 7.834181 AGTGCAAAGAAGATTTAGGCCTAATTA 59.166 33.333 25.70 12.66 0.00 1.40
122 123 8.466798 GTGCAAAGAAGATTTAGGCCTAATTAA 58.533 33.333 25.70 11.89 0.00 1.40
123 124 9.200817 TGCAAAGAAGATTTAGGCCTAATTAAT 57.799 29.630 25.70 16.26 0.00 1.40
185 186 9.855021 TTAATTAAGTGCAAAGAAGATTTAGGC 57.145 29.630 0.00 0.00 0.00 3.93
186 187 4.790765 AAGTGCAAAGAAGATTTAGGCC 57.209 40.909 0.00 0.00 0.00 5.19
187 188 4.039603 AGTGCAAAGAAGATTTAGGCCT 57.960 40.909 11.78 11.78 0.00 5.19
188 189 5.179452 AGTGCAAAGAAGATTTAGGCCTA 57.821 39.130 8.91 8.91 0.00 3.93
189 190 5.570320 AGTGCAAAGAAGATTTAGGCCTAA 58.430 37.500 21.68 21.68 0.00 2.69
190 191 6.190587 AGTGCAAAGAAGATTTAGGCCTAAT 58.809 36.000 25.70 15.37 0.00 1.73
191 192 6.665248 AGTGCAAAGAAGATTTAGGCCTAATT 59.335 34.615 25.70 21.47 0.00 1.40
192 193 7.834181 AGTGCAAAGAAGATTTAGGCCTAATTA 59.166 33.333 25.70 12.66 0.00 1.40
193 194 8.633561 GTGCAAAGAAGATTTAGGCCTAATTAT 58.366 33.333 25.70 16.99 0.00 1.28
194 195 8.632679 TGCAAAGAAGATTTAGGCCTAATTATG 58.367 33.333 25.70 15.96 0.00 1.90
195 196 8.084684 GCAAAGAAGATTTAGGCCTAATTATGG 58.915 37.037 25.70 11.41 0.00 2.74
211 212 3.758715 TGGCACATGGTCGACTATG 57.241 52.632 32.69 32.69 40.20 2.23
212 213 0.901827 TGGCACATGGTCGACTATGT 59.098 50.000 33.92 33.92 46.84 2.29
217 218 3.953712 ACATGGTCGACTATGTGTTCA 57.046 42.857 37.10 16.48 44.68 3.18
218 219 4.265904 ACATGGTCGACTATGTGTTCAA 57.734 40.909 37.10 0.00 44.68 2.69
219 220 4.832248 ACATGGTCGACTATGTGTTCAAT 58.168 39.130 37.10 17.46 44.68 2.57
220 221 5.972935 ACATGGTCGACTATGTGTTCAATA 58.027 37.500 37.10 0.00 44.68 1.90
221 222 6.582636 ACATGGTCGACTATGTGTTCAATAT 58.417 36.000 37.10 16.17 44.68 1.28
222 223 6.701841 ACATGGTCGACTATGTGTTCAATATC 59.298 38.462 37.10 8.34 44.68 1.63
223 224 5.597806 TGGTCGACTATGTGTTCAATATCC 58.402 41.667 16.46 0.00 0.00 2.59
224 225 5.362717 TGGTCGACTATGTGTTCAATATCCT 59.637 40.000 16.46 0.00 0.00 3.24
225 226 6.548251 TGGTCGACTATGTGTTCAATATCCTA 59.452 38.462 16.46 0.00 0.00 2.94
226 227 7.232737 TGGTCGACTATGTGTTCAATATCCTAT 59.767 37.037 16.46 0.00 0.00 2.57
227 228 8.737175 GGTCGACTATGTGTTCAATATCCTATA 58.263 37.037 16.46 0.00 0.00 1.31
236 237 9.194972 TGTGTTCAATATCCTATATTTTTGGCA 57.805 29.630 0.00 0.00 0.00 4.92
241 242 9.432982 TCAATATCCTATATTTTTGGCAAAGGT 57.567 29.630 13.04 8.39 0.00 3.50
245 246 6.941857 TCCTATATTTTTGGCAAAGGTTTCC 58.058 36.000 13.04 0.00 0.00 3.13
246 247 6.498651 TCCTATATTTTTGGCAAAGGTTTCCA 59.501 34.615 13.04 0.00 0.00 3.53
247 248 7.016661 TCCTATATTTTTGGCAAAGGTTTCCAA 59.983 33.333 13.04 3.19 38.03 3.53
248 249 6.875948 ATATTTTTGGCAAAGGTTTCCAAC 57.124 33.333 13.04 0.00 39.36 3.77
249 250 3.703001 TTTTGGCAAAGGTTTCCAACA 57.297 38.095 13.04 0.00 39.36 3.33
250 251 3.922171 TTTGGCAAAGGTTTCCAACAT 57.078 38.095 8.93 0.00 39.36 2.71
251 252 5.359194 TTTTGGCAAAGGTTTCCAACATA 57.641 34.783 13.04 0.00 39.36 2.29
252 253 5.559148 TTTGGCAAAGGTTTCCAACATAT 57.441 34.783 8.93 0.00 39.36 1.78
253 254 5.559148 TTGGCAAAGGTTTCCAACATATT 57.441 34.783 0.00 0.00 35.17 1.28
254 255 5.146010 TGGCAAAGGTTTCCAACATATTC 57.854 39.130 0.00 0.00 0.00 1.75
255 256 4.590647 TGGCAAAGGTTTCCAACATATTCA 59.409 37.500 0.00 0.00 0.00 2.57
256 257 5.248020 TGGCAAAGGTTTCCAACATATTCAT 59.752 36.000 0.00 0.00 0.00 2.57
257 258 5.812127 GGCAAAGGTTTCCAACATATTCATC 59.188 40.000 0.00 0.00 0.00 2.92
258 259 6.351286 GGCAAAGGTTTCCAACATATTCATCT 60.351 38.462 0.00 0.00 0.00 2.90
259 260 7.099120 GCAAAGGTTTCCAACATATTCATCTT 58.901 34.615 0.00 0.00 0.00 2.40
260 261 8.250332 GCAAAGGTTTCCAACATATTCATCTTA 58.750 33.333 0.00 0.00 0.00 2.10
309 310 8.506168 AATTTTTACCATCTCATTTAGCTCGA 57.494 30.769 0.00 0.00 0.00 4.04
310 311 7.915293 TTTTTACCATCTCATTTAGCTCGAA 57.085 32.000 0.00 0.00 0.00 3.71
311 312 7.915293 TTTTACCATCTCATTTAGCTCGAAA 57.085 32.000 0.00 0.00 0.00 3.46
312 313 6.903883 TTACCATCTCATTTAGCTCGAAAC 57.096 37.500 0.00 0.00 0.00 2.78
313 314 5.091261 ACCATCTCATTTAGCTCGAAACT 57.909 39.130 0.00 0.00 0.00 2.66
314 315 6.222038 ACCATCTCATTTAGCTCGAAACTA 57.778 37.500 0.00 0.00 0.00 2.24
315 316 6.276847 ACCATCTCATTTAGCTCGAAACTAG 58.723 40.000 0.00 0.00 0.00 2.57
316 317 5.176590 CCATCTCATTTAGCTCGAAACTAGC 59.823 44.000 0.00 0.00 40.40 3.42
326 327 2.277969 TCGAAACTAGCTCGAGATCGT 58.722 47.619 18.75 9.77 40.25 3.73
327 328 2.676839 TCGAAACTAGCTCGAGATCGTT 59.323 45.455 18.75 16.10 40.25 3.85
328 329 3.867493 TCGAAACTAGCTCGAGATCGTTA 59.133 43.478 19.23 3.31 40.25 3.18
329 330 3.961240 CGAAACTAGCTCGAGATCGTTAC 59.039 47.826 19.23 4.39 38.61 2.50
330 331 4.493708 CGAAACTAGCTCGAGATCGTTACA 60.494 45.833 19.23 0.00 38.61 2.41
331 332 4.959596 AACTAGCTCGAGATCGTTACAA 57.040 40.909 17.74 0.00 40.80 2.41
332 333 4.539509 ACTAGCTCGAGATCGTTACAAG 57.460 45.455 18.75 4.57 40.80 3.16
333 334 2.196295 AGCTCGAGATCGTTACAAGC 57.804 50.000 18.75 3.65 40.80 4.01
334 335 1.746220 AGCTCGAGATCGTTACAAGCT 59.254 47.619 18.75 8.94 38.93 3.74
335 336 1.849219 GCTCGAGATCGTTACAAGCTG 59.151 52.381 18.75 0.00 40.80 4.24
336 337 2.478031 GCTCGAGATCGTTACAAGCTGA 60.478 50.000 18.75 0.00 40.80 4.26
337 338 3.358775 CTCGAGATCGTTACAAGCTGAG 58.641 50.000 6.58 0.00 40.80 3.35
338 339 1.849219 CGAGATCGTTACAAGCTGAGC 59.151 52.381 0.00 0.00 34.11 4.26
339 340 2.732282 CGAGATCGTTACAAGCTGAGCA 60.732 50.000 7.39 0.00 34.11 4.26
340 341 2.600867 GAGATCGTTACAAGCTGAGCAC 59.399 50.000 7.39 0.00 0.00 4.40
341 342 1.321743 GATCGTTACAAGCTGAGCACG 59.678 52.381 7.39 7.63 0.00 5.34
342 343 0.312729 TCGTTACAAGCTGAGCACGA 59.687 50.000 12.04 12.04 34.45 4.35
343 344 0.710567 CGTTACAAGCTGAGCACGAG 59.289 55.000 7.39 0.00 0.00 4.18
344 345 1.784525 GTTACAAGCTGAGCACGAGT 58.215 50.000 7.39 1.63 0.00 4.18
345 346 1.721926 GTTACAAGCTGAGCACGAGTC 59.278 52.381 7.39 0.00 0.00 3.36
346 347 0.958822 TACAAGCTGAGCACGAGTCA 59.041 50.000 7.39 0.00 0.00 3.41
347 348 0.319728 ACAAGCTGAGCACGAGTCAT 59.680 50.000 7.39 0.00 0.00 3.06
348 349 1.546029 ACAAGCTGAGCACGAGTCATA 59.454 47.619 7.39 0.00 0.00 2.15
349 350 2.167281 ACAAGCTGAGCACGAGTCATAT 59.833 45.455 7.39 0.00 0.00 1.78
350 351 3.193263 CAAGCTGAGCACGAGTCATATT 58.807 45.455 7.39 0.00 0.00 1.28
351 352 3.090952 AGCTGAGCACGAGTCATATTC 57.909 47.619 7.39 0.00 0.00 1.75
352 353 2.692557 AGCTGAGCACGAGTCATATTCT 59.307 45.455 7.39 0.00 0.00 2.40
353 354 3.885901 AGCTGAGCACGAGTCATATTCTA 59.114 43.478 7.39 0.00 0.00 2.10
354 355 3.978217 GCTGAGCACGAGTCATATTCTAC 59.022 47.826 0.00 0.00 0.00 2.59
355 356 4.498177 GCTGAGCACGAGTCATATTCTACA 60.498 45.833 0.00 0.00 0.00 2.74
356 357 5.175090 TGAGCACGAGTCATATTCTACAG 57.825 43.478 0.00 0.00 0.00 2.74
357 358 3.971150 AGCACGAGTCATATTCTACAGC 58.029 45.455 0.00 0.00 0.00 4.40
358 359 3.634448 AGCACGAGTCATATTCTACAGCT 59.366 43.478 0.00 0.00 0.00 4.24
359 360 3.978217 GCACGAGTCATATTCTACAGCTC 59.022 47.826 0.00 0.00 0.00 4.09
360 361 4.215201 CACGAGTCATATTCTACAGCTCG 58.785 47.826 9.10 9.10 46.37 5.03
361 362 4.024809 CACGAGTCATATTCTACAGCTCGA 60.025 45.833 16.19 0.00 44.58 4.04
362 363 4.757657 ACGAGTCATATTCTACAGCTCGAT 59.242 41.667 16.19 0.57 44.58 3.59
363 364 5.106869 ACGAGTCATATTCTACAGCTCGATC 60.107 44.000 16.19 0.00 44.58 3.69
364 365 5.106908 CGAGTCATATTCTACAGCTCGATCA 60.107 44.000 5.28 0.00 44.58 2.92
365 366 6.403092 CGAGTCATATTCTACAGCTCGATCAT 60.403 42.308 5.28 0.00 44.58 2.45
366 367 6.619744 AGTCATATTCTACAGCTCGATCATG 58.380 40.000 0.00 0.00 0.00 3.07
367 368 6.432472 AGTCATATTCTACAGCTCGATCATGA 59.568 38.462 0.00 0.00 0.00 3.07
368 369 6.746822 GTCATATTCTACAGCTCGATCATGAG 59.253 42.308 0.09 0.00 39.05 2.90
392 393 2.357792 CTCAGTTTGAGCTCGCTCG 58.642 57.895 9.64 0.00 45.48 5.03
393 394 0.109551 CTCAGTTTGAGCTCGCTCGA 60.110 55.000 9.64 9.43 45.48 4.04
394 395 0.313987 TCAGTTTGAGCTCGCTCGAA 59.686 50.000 15.72 15.72 45.48 3.71
395 396 1.067565 TCAGTTTGAGCTCGCTCGAAT 60.068 47.619 20.94 10.11 45.11 3.34
396 397 1.728971 CAGTTTGAGCTCGCTCGAATT 59.271 47.619 20.94 15.57 45.11 2.17
397 398 2.158449 CAGTTTGAGCTCGCTCGAATTT 59.842 45.455 20.94 12.01 45.11 1.82
398 399 2.808543 AGTTTGAGCTCGCTCGAATTTT 59.191 40.909 20.94 10.02 45.11 1.82
399 400 3.120511 AGTTTGAGCTCGCTCGAATTTTC 60.121 43.478 20.94 10.68 45.11 2.29
400 401 2.078849 TGAGCTCGCTCGAATTTTCA 57.921 45.000 9.64 0.00 45.48 2.69
401 402 2.621338 TGAGCTCGCTCGAATTTTCAT 58.379 42.857 9.64 0.00 45.48 2.57
402 403 3.780902 TGAGCTCGCTCGAATTTTCATA 58.219 40.909 9.64 0.00 45.48 2.15
403 404 4.371786 TGAGCTCGCTCGAATTTTCATAT 58.628 39.130 9.64 0.00 45.48 1.78
404 405 4.209911 TGAGCTCGCTCGAATTTTCATATG 59.790 41.667 9.64 0.00 45.48 1.78
405 406 4.371786 AGCTCGCTCGAATTTTCATATGA 58.628 39.130 0.00 0.00 0.00 2.15
406 407 4.447054 AGCTCGCTCGAATTTTCATATGAG 59.553 41.667 5.39 0.00 0.00 2.90
407 408 4.210120 GCTCGCTCGAATTTTCATATGAGT 59.790 41.667 5.39 0.00 0.00 3.41
408 409 5.277058 GCTCGCTCGAATTTTCATATGAGTT 60.277 40.000 5.39 2.94 0.00 3.01
409 410 6.036246 TCGCTCGAATTTTCATATGAGTTG 57.964 37.500 5.39 0.00 0.00 3.16
410 411 5.810074 TCGCTCGAATTTTCATATGAGTTGA 59.190 36.000 5.39 2.35 0.00 3.18
411 412 6.019559 TCGCTCGAATTTTCATATGAGTTGAG 60.020 38.462 5.39 11.53 0.00 3.02
412 413 5.906285 GCTCGAATTTTCATATGAGTTGAGC 59.094 40.000 21.72 21.72 37.41 4.26
413 414 6.238320 GCTCGAATTTTCATATGAGTTGAGCT 60.238 38.462 25.08 0.00 40.43 4.09
414 415 7.008440 TCGAATTTTCATATGAGTTGAGCTG 57.992 36.000 5.39 0.00 0.00 4.24
415 416 6.818142 TCGAATTTTCATATGAGTTGAGCTGA 59.182 34.615 5.39 0.00 0.00 4.26
416 417 7.010830 TCGAATTTTCATATGAGTTGAGCTGAG 59.989 37.037 5.39 0.00 0.00 3.35
417 418 5.808042 TTTTCATATGAGTTGAGCTGAGC 57.192 39.130 5.39 0.00 0.00 4.26
418 419 3.465742 TCATATGAGTTGAGCTGAGCC 57.534 47.619 0.00 0.00 0.00 4.70
419 420 2.767960 TCATATGAGTTGAGCTGAGCCA 59.232 45.455 0.00 0.00 0.00 4.75
420 421 3.198417 TCATATGAGTTGAGCTGAGCCAA 59.802 43.478 0.00 2.22 0.00 4.52
421 422 1.818642 ATGAGTTGAGCTGAGCCAAC 58.181 50.000 22.65 22.65 38.78 3.77
422 423 0.761187 TGAGTTGAGCTGAGCCAACT 59.239 50.000 28.74 28.74 45.33 3.16
423 424 3.621953 AGTTGAGCTGAGCCAACTC 57.378 52.632 25.34 9.38 42.04 3.01
424 425 0.036022 AGTTGAGCTGAGCCAACTCC 59.964 55.000 25.34 9.70 42.04 3.85
425 426 0.250467 GTTGAGCTGAGCCAACTCCA 60.250 55.000 22.76 3.29 42.74 3.86
426 427 0.473755 TTGAGCTGAGCCAACTCCAA 59.526 50.000 0.00 0.00 42.74 3.53
427 428 0.250467 TGAGCTGAGCCAACTCCAAC 60.250 55.000 0.00 0.00 42.74 3.77
428 429 0.036022 GAGCTGAGCCAACTCCAACT 59.964 55.000 0.00 0.00 42.74 3.16
429 430 0.036022 AGCTGAGCCAACTCCAACTC 59.964 55.000 0.00 0.00 42.74 3.01
430 431 1.294659 GCTGAGCCAACTCCAACTCG 61.295 60.000 0.00 0.00 42.74 4.18
431 432 1.294659 CTGAGCCAACTCCAACTCGC 61.295 60.000 0.00 0.00 42.74 5.03
432 433 1.004440 GAGCCAACTCCAACTCGCT 60.004 57.895 0.00 0.00 36.90 4.93
433 434 1.004440 AGCCAACTCCAACTCGCTC 60.004 57.895 0.00 0.00 0.00 5.03
434 435 2.383527 GCCAACTCCAACTCGCTCG 61.384 63.158 0.00 0.00 0.00 5.03
435 436 1.289066 CCAACTCCAACTCGCTCGA 59.711 57.895 0.00 0.00 0.00 4.04
436 437 0.734253 CCAACTCCAACTCGCTCGAG 60.734 60.000 16.71 16.71 46.91 4.04
437 438 1.080434 AACTCCAACTCGCTCGAGC 60.080 57.895 27.64 27.64 45.54 5.03
438 439 1.528292 AACTCCAACTCGCTCGAGCT 61.528 55.000 32.88 13.94 45.54 4.09
439 440 1.226547 CTCCAACTCGCTCGAGCTC 60.227 63.158 32.88 2.73 45.54 4.09
440 441 2.578178 CCAACTCGCTCGAGCTCG 60.578 66.667 32.88 30.03 45.54 5.03
441 442 2.481009 CAACTCGCTCGAGCTCGA 59.519 61.111 34.65 34.65 45.54 4.04
442 443 1.865622 CAACTCGCTCGAGCTCGAC 60.866 63.158 33.84 26.44 45.54 4.20
443 444 2.036006 AACTCGCTCGAGCTCGACT 61.036 57.895 33.84 12.70 45.54 4.18
444 445 1.973137 AACTCGCTCGAGCTCGACTC 61.973 60.000 33.84 25.05 45.54 3.36
451 452 4.245054 GAGCTCGACTCGTTTGCA 57.755 55.556 0.00 0.00 35.18 4.08
452 453 2.066000 GAGCTCGACTCGTTTGCAG 58.934 57.895 0.00 0.00 35.18 4.41
453 454 1.950098 GAGCTCGACTCGTTTGCAGC 61.950 60.000 0.00 8.23 35.18 5.25
454 455 3.016474 GCTCGACTCGTTTGCAGCC 62.016 63.158 0.00 0.00 0.00 4.85
455 456 2.357034 TCGACTCGTTTGCAGCCC 60.357 61.111 0.00 0.00 0.00 5.19
456 457 2.357517 CGACTCGTTTGCAGCCCT 60.358 61.111 0.00 0.00 0.00 5.19
457 458 1.080093 CGACTCGTTTGCAGCCCTA 60.080 57.895 0.00 0.00 0.00 3.53
486 489 2.223735 ACAATACGTAGATGGTCTGCCG 60.224 50.000 13.74 0.00 37.67 5.69
488 491 0.394762 TACGTAGATGGTCTGCCGGT 60.395 55.000 1.90 0.00 37.67 5.28
587 590 0.733150 GGTTTAAGTCCCATCGCTGC 59.267 55.000 0.00 0.00 0.00 5.25
628 1509 4.212214 CGCAATAGCACCTTATCTTCTTCC 59.788 45.833 0.00 0.00 42.27 3.46
629 1510 4.517075 GCAATAGCACCTTATCTTCTTCCC 59.483 45.833 0.00 0.00 41.58 3.97
630 1511 5.688766 GCAATAGCACCTTATCTTCTTCCCT 60.689 44.000 0.00 0.00 41.58 4.20
631 1512 6.464465 GCAATAGCACCTTATCTTCTTCCCTA 60.464 42.308 0.00 0.00 41.58 3.53
701 1621 5.292834 CGGCACTGCATATTATTGGATAGAG 59.707 44.000 2.82 0.00 0.00 2.43
719 1899 7.719633 TGGATAGAGTTTTTCCTTACATATGCC 59.280 37.037 1.58 0.00 0.00 4.40
785 2227 8.771920 TCGATGGCTTTATAATTAACGATGAT 57.228 30.769 0.00 0.00 0.00 2.45
795 2237 7.672983 ATAATTAACGATGATCATCACCACC 57.327 36.000 30.13 7.96 37.69 4.61
824 2266 5.163804 TGCCTTTTACTGCACGTACATAATG 60.164 40.000 0.00 0.00 31.31 1.90
841 2283 7.451731 ACATAATGACCATTCCTTTCCTAGA 57.548 36.000 0.00 0.00 32.50 2.43
902 2375 2.495366 TACCAGTTGGCACGGTAGCG 62.495 60.000 13.69 13.69 39.32 4.26
934 2407 5.617308 CGTCCTATATAACTCCTCGCAGTTC 60.617 48.000 0.00 0.00 37.75 3.01
940 2413 0.543174 ACTCCTCGCAGTTCTTCCCT 60.543 55.000 0.00 0.00 0.00 4.20
941 2414 0.610687 CTCCTCGCAGTTCTTCCCTT 59.389 55.000 0.00 0.00 0.00 3.95
942 2415 1.002544 CTCCTCGCAGTTCTTCCCTTT 59.997 52.381 0.00 0.00 0.00 3.11
943 2416 2.233922 CTCCTCGCAGTTCTTCCCTTTA 59.766 50.000 0.00 0.00 0.00 1.85
944 2417 2.635915 TCCTCGCAGTTCTTCCCTTTAA 59.364 45.455 0.00 0.00 0.00 1.52
945 2418 3.003480 CCTCGCAGTTCTTCCCTTTAAG 58.997 50.000 0.00 0.00 0.00 1.85
946 2419 2.416893 CTCGCAGTTCTTCCCTTTAAGC 59.583 50.000 0.00 0.00 0.00 3.09
947 2420 2.151202 CGCAGTTCTTCCCTTTAAGCA 58.849 47.619 0.00 0.00 0.00 3.91
1013 2508 0.527817 GACGTGATGGCTAACTCGGG 60.528 60.000 0.00 0.00 0.00 5.14
1029 2524 1.524849 GGGCGCCTTGATCCTTCTC 60.525 63.158 28.56 0.00 0.00 2.87
1037 2532 4.716794 GCCTTGATCCTTCTCATCTCATT 58.283 43.478 0.00 0.00 0.00 2.57
1052 2547 1.524621 CATTGGTCCTGCTAGCCGG 60.525 63.158 18.50 18.50 0.00 6.13
1053 2548 2.746375 ATTGGTCCTGCTAGCCGGG 61.746 63.158 23.28 19.03 41.74 5.73
1134 2629 0.319900 ACTTCTTCATGCACGACGCT 60.320 50.000 0.00 0.00 43.06 5.07
1586 3081 0.663568 GTGTACGTGCAGCTTCGACT 60.664 55.000 6.58 0.00 0.00 4.18
1650 4479 4.327357 CGTCGAGTGAGCATACTGAATTTT 59.673 41.667 0.00 0.00 0.00 1.82
1656 4485 5.354234 AGTGAGCATACTGAATTTTAACCGG 59.646 40.000 0.00 0.00 0.00 5.28
1727 4556 5.156355 CCTCACAATTTCAAGTATGTGTGC 58.844 41.667 4.86 0.00 42.80 4.57
1891 4720 5.692204 ACTCATCACAAAACGACTTGTAGAG 59.308 40.000 17.90 17.90 37.43 2.43
1914 4743 8.532819 AGAGAGTAAAGTTACCTCGAAAATCAT 58.467 33.333 11.05 0.00 36.71 2.45
1930 4759 7.010183 TCGAAAATCATATTTGTCGTCTTCCTC 59.990 37.037 0.81 0.00 0.00 3.71
1932 4761 5.878406 ATCATATTTGTCGTCTTCCTCCT 57.122 39.130 0.00 0.00 0.00 3.69
1965 4794 4.455606 GCCTACCAGAGCATGAAACTTAT 58.544 43.478 0.00 0.00 0.00 1.73
1966 4795 4.513318 GCCTACCAGAGCATGAAACTTATC 59.487 45.833 0.00 0.00 0.00 1.75
1967 4796 4.747108 CCTACCAGAGCATGAAACTTATCG 59.253 45.833 0.00 0.00 0.00 2.92
1968 4797 4.471904 ACCAGAGCATGAAACTTATCGA 57.528 40.909 0.00 0.00 0.00 3.59
1969 4798 4.832248 ACCAGAGCATGAAACTTATCGAA 58.168 39.130 0.00 0.00 0.00 3.71
1970 4799 4.631813 ACCAGAGCATGAAACTTATCGAAC 59.368 41.667 0.00 0.00 0.00 3.95
1971 4800 4.631377 CCAGAGCATGAAACTTATCGAACA 59.369 41.667 0.00 0.00 0.00 3.18
1972 4801 5.220548 CCAGAGCATGAAACTTATCGAACAG 60.221 44.000 0.00 0.00 0.00 3.16
1973 4802 5.578336 CAGAGCATGAAACTTATCGAACAGA 59.422 40.000 0.00 0.00 0.00 3.41
1974 4803 5.809562 AGAGCATGAAACTTATCGAACAGAG 59.190 40.000 0.00 0.00 0.00 3.35
1975 4804 4.331168 AGCATGAAACTTATCGAACAGAGC 59.669 41.667 0.00 0.00 0.00 4.09
1976 4805 4.093408 GCATGAAACTTATCGAACAGAGCA 59.907 41.667 0.00 0.00 0.00 4.26
1977 4806 5.220739 GCATGAAACTTATCGAACAGAGCAT 60.221 40.000 0.00 0.00 0.00 3.79
1978 4807 5.784750 TGAAACTTATCGAACAGAGCATG 57.215 39.130 0.00 0.00 0.00 4.06
1979 4808 5.478407 TGAAACTTATCGAACAGAGCATGA 58.522 37.500 0.00 0.00 0.00 3.07
1980 4809 5.931724 TGAAACTTATCGAACAGAGCATGAA 59.068 36.000 0.00 0.00 0.00 2.57
1981 4810 6.426633 TGAAACTTATCGAACAGAGCATGAAA 59.573 34.615 0.00 0.00 0.00 2.69
1982 4811 5.786401 ACTTATCGAACAGAGCATGAAAC 57.214 39.130 0.00 0.00 0.00 2.78
1983 4812 5.482908 ACTTATCGAACAGAGCATGAAACT 58.517 37.500 0.00 0.00 0.00 2.66
1984 4813 5.934625 ACTTATCGAACAGAGCATGAAACTT 59.065 36.000 0.00 0.00 0.00 2.66
1985 4814 7.097192 ACTTATCGAACAGAGCATGAAACTTA 58.903 34.615 0.00 0.00 0.00 2.24
2071 4901 2.472695 AGCCACTCACTGCGAATAAA 57.527 45.000 0.00 0.00 0.00 1.40
2087 4917 4.444720 CGAATAAAGAGATCTGGTAACCGC 59.555 45.833 0.00 0.00 0.00 5.68
2127 4957 3.982241 GCACCCCAAGCAGCACAC 61.982 66.667 0.00 0.00 0.00 3.82
2194 5056 1.919918 TTGCCGCTGAACAAAACAAG 58.080 45.000 0.00 0.00 0.00 3.16
2196 5058 1.474478 TGCCGCTGAACAAAACAAGAA 59.526 42.857 0.00 0.00 0.00 2.52
2208 5070 9.197694 TGAACAAAACAAGAAAAGAATTCGAAA 57.802 25.926 0.00 0.00 0.00 3.46
2211 5073 9.364989 ACAAAACAAGAAAAGAATTCGAAATCA 57.635 25.926 15.31 0.00 0.00 2.57
2270 5132 3.189287 GCACACCAACTACCAAGATTCAG 59.811 47.826 0.00 0.00 0.00 3.02
2296 5158 4.133078 GAGCCAATAAATCTAGCAGCACT 58.867 43.478 0.00 0.00 0.00 4.40
2334 5319 1.212751 GCAAGGGCGGATCAAACAC 59.787 57.895 0.00 0.00 0.00 3.32
2396 5381 0.104120 CCATCGTCGCCACCATCTAA 59.896 55.000 0.00 0.00 0.00 2.10
2442 5427 7.373778 AGAACAAAGTTTAAGAGAAACACGT 57.626 32.000 3.26 0.00 32.81 4.49
2467 5452 5.006746 GGACATGCAAGGACTAAAATCTACG 59.993 44.000 0.00 0.00 0.00 3.51
2473 5458 6.148811 TGCAAGGACTAAAATCTACGGAAAAG 59.851 38.462 0.00 0.00 0.00 2.27
2482 5468 2.250031 TCTACGGAAAAGCAGGTACCA 58.750 47.619 15.94 0.00 0.00 3.25
2491 5477 1.201429 AGCAGGTACCAACTCCCCTG 61.201 60.000 15.94 1.60 45.87 4.45
2492 5478 1.198759 GCAGGTACCAACTCCCCTGA 61.199 60.000 15.94 0.00 45.97 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 9.855021 GCCTAAATCTTCTTTGCACTTAATTAA 57.145 29.630 0.00 0.00 0.00 1.40
89 90 8.466798 GGCCTAAATCTTCTTTGCACTTAATTA 58.533 33.333 0.00 0.00 0.00 1.40
90 91 7.179160 AGGCCTAAATCTTCTTTGCACTTAATT 59.821 33.333 1.29 0.00 0.00 1.40
91 92 6.665248 AGGCCTAAATCTTCTTTGCACTTAAT 59.335 34.615 1.29 0.00 0.00 1.40
92 93 6.010219 AGGCCTAAATCTTCTTTGCACTTAA 58.990 36.000 1.29 0.00 0.00 1.85
93 94 5.570320 AGGCCTAAATCTTCTTTGCACTTA 58.430 37.500 1.29 0.00 0.00 2.24
94 95 4.411013 AGGCCTAAATCTTCTTTGCACTT 58.589 39.130 1.29 0.00 0.00 3.16
95 96 4.039603 AGGCCTAAATCTTCTTTGCACT 57.960 40.909 1.29 0.00 0.00 4.40
96 97 5.897377 TTAGGCCTAAATCTTCTTTGCAC 57.103 39.130 23.21 0.00 0.00 4.57
97 98 8.588290 TTAATTAGGCCTAAATCTTCTTTGCA 57.412 30.769 28.50 1.56 0.00 4.08
159 160 9.855021 GCCTAAATCTTCTTTGCACTTAATTAA 57.145 29.630 0.00 0.00 0.00 1.40
160 161 8.466798 GGCCTAAATCTTCTTTGCACTTAATTA 58.533 33.333 0.00 0.00 0.00 1.40
161 162 7.179160 AGGCCTAAATCTTCTTTGCACTTAATT 59.821 33.333 1.29 0.00 0.00 1.40
162 163 6.665248 AGGCCTAAATCTTCTTTGCACTTAAT 59.335 34.615 1.29 0.00 0.00 1.40
163 164 6.010219 AGGCCTAAATCTTCTTTGCACTTAA 58.990 36.000 1.29 0.00 0.00 1.85
164 165 5.570320 AGGCCTAAATCTTCTTTGCACTTA 58.430 37.500 1.29 0.00 0.00 2.24
165 166 4.411013 AGGCCTAAATCTTCTTTGCACTT 58.589 39.130 1.29 0.00 0.00 3.16
166 167 4.039603 AGGCCTAAATCTTCTTTGCACT 57.960 40.909 1.29 0.00 0.00 4.40
167 168 5.897377 TTAGGCCTAAATCTTCTTTGCAC 57.103 39.130 23.21 0.00 0.00 4.57
168 169 8.632679 CATAATTAGGCCTAAATCTTCTTTGCA 58.367 33.333 28.50 2.90 0.00 4.08
169 170 8.084684 CCATAATTAGGCCTAAATCTTCTTTGC 58.915 37.037 28.50 0.00 0.00 3.68
170 171 8.084684 GCCATAATTAGGCCTAAATCTTCTTTG 58.915 37.037 28.50 15.29 46.50 2.77
171 172 8.183104 GCCATAATTAGGCCTAAATCTTCTTT 57.817 34.615 28.50 17.91 46.50 2.52
172 173 7.767250 GCCATAATTAGGCCTAAATCTTCTT 57.233 36.000 28.50 18.58 46.50 2.52
185 186 3.498397 GTCGACCATGTGCCATAATTAGG 59.502 47.826 3.51 0.00 0.00 2.69
186 187 4.380531 AGTCGACCATGTGCCATAATTAG 58.619 43.478 13.01 0.00 0.00 1.73
187 188 4.415881 AGTCGACCATGTGCCATAATTA 57.584 40.909 13.01 0.00 0.00 1.40
188 189 3.281727 AGTCGACCATGTGCCATAATT 57.718 42.857 13.01 0.00 0.00 1.40
189 190 4.202357 ACATAGTCGACCATGTGCCATAAT 60.202 41.667 25.57 1.65 34.15 1.28
190 191 3.133901 ACATAGTCGACCATGTGCCATAA 59.866 43.478 25.57 0.00 34.15 1.90
191 192 2.698274 ACATAGTCGACCATGTGCCATA 59.302 45.455 25.57 3.49 34.15 2.74
192 193 1.486310 ACATAGTCGACCATGTGCCAT 59.514 47.619 25.57 3.74 34.15 4.40
193 194 0.901827 ACATAGTCGACCATGTGCCA 59.098 50.000 25.57 0.00 34.15 4.92
194 195 1.290203 CACATAGTCGACCATGTGCC 58.710 55.000 33.47 0.81 43.86 5.01
197 198 3.953712 TGAACACATAGTCGACCATGT 57.046 42.857 21.67 21.67 35.79 3.21
198 199 6.146184 GGATATTGAACACATAGTCGACCATG 59.854 42.308 20.38 20.38 0.00 3.66
199 200 6.042093 AGGATATTGAACACATAGTCGACCAT 59.958 38.462 13.01 0.00 0.00 3.55
200 201 5.362717 AGGATATTGAACACATAGTCGACCA 59.637 40.000 13.01 0.00 0.00 4.02
201 202 5.844004 AGGATATTGAACACATAGTCGACC 58.156 41.667 13.01 0.00 0.00 4.79
210 211 9.194972 TGCCAAAAATATAGGATATTGAACACA 57.805 29.630 0.00 0.00 0.00 3.72
215 216 9.432982 ACCTTTGCCAAAAATATAGGATATTGA 57.567 29.630 0.00 0.00 0.00 2.57
219 220 8.700973 GGAAACCTTTGCCAAAAATATAGGATA 58.299 33.333 0.00 0.00 0.00 2.59
220 221 7.181845 TGGAAACCTTTGCCAAAAATATAGGAT 59.818 33.333 0.00 0.00 0.00 3.24
221 222 6.498651 TGGAAACCTTTGCCAAAAATATAGGA 59.501 34.615 0.00 0.00 0.00 2.94
222 223 6.706295 TGGAAACCTTTGCCAAAAATATAGG 58.294 36.000 0.00 0.00 0.00 2.57
223 224 8.028540 GTTGGAAACCTTTGCCAAAAATATAG 57.971 34.615 0.00 0.00 42.77 1.31
224 225 7.971183 GTTGGAAACCTTTGCCAAAAATATA 57.029 32.000 0.00 0.00 42.77 0.86
225 226 6.875948 GTTGGAAACCTTTGCCAAAAATAT 57.124 33.333 0.00 0.00 42.77 1.28
283 284 9.607988 TCGAGCTAAATGAGATGGTAAAAATTA 57.392 29.630 0.00 0.00 0.00 1.40
284 285 8.506168 TCGAGCTAAATGAGATGGTAAAAATT 57.494 30.769 0.00 0.00 0.00 1.82
285 286 8.506168 TTCGAGCTAAATGAGATGGTAAAAAT 57.494 30.769 0.00 0.00 0.00 1.82
286 287 7.915293 TTCGAGCTAAATGAGATGGTAAAAA 57.085 32.000 0.00 0.00 0.00 1.94
287 288 7.606456 AGTTTCGAGCTAAATGAGATGGTAAAA 59.394 33.333 0.00 0.00 0.00 1.52
288 289 7.103641 AGTTTCGAGCTAAATGAGATGGTAAA 58.896 34.615 0.00 0.00 0.00 2.01
289 290 6.640518 AGTTTCGAGCTAAATGAGATGGTAA 58.359 36.000 0.00 0.00 0.00 2.85
290 291 6.222038 AGTTTCGAGCTAAATGAGATGGTA 57.778 37.500 0.00 0.00 0.00 3.25
291 292 5.091261 AGTTTCGAGCTAAATGAGATGGT 57.909 39.130 0.00 0.00 0.00 3.55
292 293 5.176590 GCTAGTTTCGAGCTAAATGAGATGG 59.823 44.000 0.00 0.00 36.96 3.51
293 294 6.209129 GCTAGTTTCGAGCTAAATGAGATG 57.791 41.667 0.00 0.00 36.96 2.90
306 307 2.277969 ACGATCTCGAGCTAGTTTCGA 58.722 47.619 7.81 16.82 44.05 3.71
307 308 2.741122 ACGATCTCGAGCTAGTTTCG 57.259 50.000 7.81 11.03 43.02 3.46
308 309 4.906423 TGTAACGATCTCGAGCTAGTTTC 58.094 43.478 17.76 13.84 43.02 2.78
309 310 4.959596 TGTAACGATCTCGAGCTAGTTT 57.040 40.909 17.76 5.89 43.02 2.66
310 311 4.731193 GCTTGTAACGATCTCGAGCTAGTT 60.731 45.833 16.94 16.94 43.02 2.24
311 312 3.242804 GCTTGTAACGATCTCGAGCTAGT 60.243 47.826 7.81 1.12 43.02 2.57
312 313 3.002862 AGCTTGTAACGATCTCGAGCTAG 59.997 47.826 7.81 0.35 40.92 3.42
313 314 2.943690 AGCTTGTAACGATCTCGAGCTA 59.056 45.455 7.81 0.00 40.92 3.32
314 315 1.746220 AGCTTGTAACGATCTCGAGCT 59.254 47.619 7.81 6.75 43.02 4.09
315 316 1.849219 CAGCTTGTAACGATCTCGAGC 59.151 52.381 7.81 4.49 43.02 5.03
316 317 3.358775 CTCAGCTTGTAACGATCTCGAG 58.641 50.000 5.93 5.93 43.02 4.04
317 318 2.478031 GCTCAGCTTGTAACGATCTCGA 60.478 50.000 6.60 0.00 43.02 4.04
318 319 1.849219 GCTCAGCTTGTAACGATCTCG 59.151 52.381 0.00 0.00 46.33 4.04
319 320 2.600867 GTGCTCAGCTTGTAACGATCTC 59.399 50.000 0.00 0.00 0.00 2.75
320 321 2.611518 GTGCTCAGCTTGTAACGATCT 58.388 47.619 0.00 0.00 0.00 2.75
321 322 1.321743 CGTGCTCAGCTTGTAACGATC 59.678 52.381 0.00 0.00 33.03 3.69
322 323 1.067846 TCGTGCTCAGCTTGTAACGAT 60.068 47.619 5.13 0.00 35.35 3.73
323 324 0.312729 TCGTGCTCAGCTTGTAACGA 59.687 50.000 5.13 5.13 37.68 3.85
324 325 0.710567 CTCGTGCTCAGCTTGTAACG 59.289 55.000 0.00 0.00 0.00 3.18
325 326 1.721926 GACTCGTGCTCAGCTTGTAAC 59.278 52.381 0.00 0.00 0.00 2.50
326 327 1.339929 TGACTCGTGCTCAGCTTGTAA 59.660 47.619 0.00 0.00 0.00 2.41
327 328 0.958822 TGACTCGTGCTCAGCTTGTA 59.041 50.000 0.00 0.00 0.00 2.41
328 329 0.319728 ATGACTCGTGCTCAGCTTGT 59.680 50.000 0.00 0.00 0.00 3.16
329 330 2.284263 TATGACTCGTGCTCAGCTTG 57.716 50.000 0.00 0.00 0.00 4.01
330 331 3.131933 AGAATATGACTCGTGCTCAGCTT 59.868 43.478 0.00 0.00 0.00 3.74
331 332 2.692557 AGAATATGACTCGTGCTCAGCT 59.307 45.455 0.00 0.00 0.00 4.24
332 333 3.090952 AGAATATGACTCGTGCTCAGC 57.909 47.619 0.00 0.00 0.00 4.26
333 334 5.175090 TGTAGAATATGACTCGTGCTCAG 57.825 43.478 0.00 0.00 0.00 3.35
334 335 4.498177 GCTGTAGAATATGACTCGTGCTCA 60.498 45.833 0.00 0.00 0.00 4.26
335 336 3.978217 GCTGTAGAATATGACTCGTGCTC 59.022 47.826 0.00 0.00 0.00 4.26
336 337 3.634448 AGCTGTAGAATATGACTCGTGCT 59.366 43.478 0.00 0.00 0.00 4.40
337 338 3.971150 AGCTGTAGAATATGACTCGTGC 58.029 45.455 0.00 0.00 0.00 5.34
338 339 4.024809 TCGAGCTGTAGAATATGACTCGTG 60.025 45.833 9.05 0.00 44.26 4.35
339 340 4.127907 TCGAGCTGTAGAATATGACTCGT 58.872 43.478 9.05 0.00 44.26 4.18
340 341 4.733972 TCGAGCTGTAGAATATGACTCG 57.266 45.455 0.00 0.00 45.02 4.18
341 342 6.247727 TGATCGAGCTGTAGAATATGACTC 57.752 41.667 0.90 0.00 0.00 3.36
342 343 6.432472 TCATGATCGAGCTGTAGAATATGACT 59.568 38.462 0.90 0.00 0.00 3.41
343 344 6.616017 TCATGATCGAGCTGTAGAATATGAC 58.384 40.000 0.90 0.00 0.00 3.06
344 345 6.824305 TCATGATCGAGCTGTAGAATATGA 57.176 37.500 0.90 0.00 0.00 2.15
366 367 2.736192 GAGCTCAAACTGAGTGAAGCTC 59.264 50.000 20.80 20.80 45.94 4.09
367 368 2.765122 GAGCTCAAACTGAGTGAAGCT 58.235 47.619 9.40 14.13 45.94 3.74
368 369 1.458827 CGAGCTCAAACTGAGTGAAGC 59.541 52.381 15.40 6.13 45.94 3.86
369 370 1.458827 GCGAGCTCAAACTGAGTGAAG 59.541 52.381 15.40 0.00 45.94 3.02
370 371 1.069204 AGCGAGCTCAAACTGAGTGAA 59.931 47.619 15.40 0.00 45.94 3.18
371 372 0.676184 AGCGAGCTCAAACTGAGTGA 59.324 50.000 15.40 0.00 45.94 3.41
372 373 1.066914 GAGCGAGCTCAAACTGAGTG 58.933 55.000 19.09 0.00 45.94 3.51
373 374 0.387878 CGAGCGAGCTCAAACTGAGT 60.388 55.000 22.81 0.00 45.94 3.41
374 375 0.109551 TCGAGCGAGCTCAAACTGAG 60.110 55.000 22.81 6.71 46.90 3.35
375 376 0.313987 TTCGAGCGAGCTCAAACTGA 59.686 50.000 22.81 10.07 42.86 3.41
376 377 1.354040 ATTCGAGCGAGCTCAAACTG 58.646 50.000 22.81 8.02 42.86 3.16
377 378 2.086054 AATTCGAGCGAGCTCAAACT 57.914 45.000 22.81 7.61 42.86 2.66
378 379 2.882742 AAATTCGAGCGAGCTCAAAC 57.117 45.000 22.81 2.13 42.86 2.93
379 380 2.805671 TGAAAATTCGAGCGAGCTCAAA 59.194 40.909 22.81 12.96 42.86 2.69
380 381 2.412870 TGAAAATTCGAGCGAGCTCAA 58.587 42.857 22.81 16.09 42.86 3.02
381 382 2.078849 TGAAAATTCGAGCGAGCTCA 57.921 45.000 22.81 6.73 42.86 4.26
382 383 4.445718 TCATATGAAAATTCGAGCGAGCTC 59.554 41.667 14.61 14.61 39.55 4.09
383 384 4.371786 TCATATGAAAATTCGAGCGAGCT 58.628 39.130 1.98 0.00 0.00 4.09
384 385 4.210120 ACTCATATGAAAATTCGAGCGAGC 59.790 41.667 6.90 0.00 0.00 5.03
385 386 5.896922 ACTCATATGAAAATTCGAGCGAG 57.103 39.130 6.90 0.00 0.00 5.03
386 387 5.810074 TCAACTCATATGAAAATTCGAGCGA 59.190 36.000 6.90 0.00 0.00 4.93
387 388 6.036246 TCAACTCATATGAAAATTCGAGCG 57.964 37.500 6.90 0.00 0.00 5.03
388 389 5.906285 GCTCAACTCATATGAAAATTCGAGC 59.094 40.000 6.90 13.24 34.84 5.03
389 390 7.010830 TCAGCTCAACTCATATGAAAATTCGAG 59.989 37.037 6.90 8.03 0.00 4.04
390 391 6.818142 TCAGCTCAACTCATATGAAAATTCGA 59.182 34.615 6.90 0.00 0.00 3.71
391 392 7.008440 TCAGCTCAACTCATATGAAAATTCG 57.992 36.000 6.90 0.00 0.00 3.34
392 393 6.911511 GCTCAGCTCAACTCATATGAAAATTC 59.088 38.462 6.90 0.00 0.00 2.17
393 394 6.183360 GGCTCAGCTCAACTCATATGAAAATT 60.183 38.462 6.90 0.00 0.00 1.82
394 395 5.298777 GGCTCAGCTCAACTCATATGAAAAT 59.701 40.000 6.90 0.00 0.00 1.82
395 396 4.637534 GGCTCAGCTCAACTCATATGAAAA 59.362 41.667 6.90 0.00 0.00 2.29
396 397 4.194640 GGCTCAGCTCAACTCATATGAAA 58.805 43.478 6.90 0.00 0.00 2.69
397 398 3.198417 TGGCTCAGCTCAACTCATATGAA 59.802 43.478 6.90 0.00 0.00 2.57
398 399 2.767960 TGGCTCAGCTCAACTCATATGA 59.232 45.455 5.07 5.07 0.00 2.15
399 400 3.189618 TGGCTCAGCTCAACTCATATG 57.810 47.619 0.00 0.00 0.00 1.78
400 401 3.199508 AGTTGGCTCAGCTCAACTCATAT 59.800 43.478 21.33 6.01 42.04 1.78
401 402 2.568956 AGTTGGCTCAGCTCAACTCATA 59.431 45.455 21.33 0.00 42.04 2.15
402 403 1.350351 AGTTGGCTCAGCTCAACTCAT 59.650 47.619 21.33 6.57 42.04 2.90
403 404 0.761187 AGTTGGCTCAGCTCAACTCA 59.239 50.000 21.33 0.00 42.04 3.41
404 405 3.621953 AGTTGGCTCAGCTCAACTC 57.378 52.632 21.33 4.67 42.04 3.01
405 406 0.036022 GGAGTTGGCTCAGCTCAACT 59.964 55.000 25.01 25.01 45.33 3.16
406 407 0.250467 TGGAGTTGGCTCAGCTCAAC 60.250 55.000 18.30 18.30 42.19 3.18
407 408 0.473755 TTGGAGTTGGCTCAGCTCAA 59.526 50.000 16.61 0.00 42.19 3.02
408 409 0.250467 GTTGGAGTTGGCTCAGCTCA 60.250 55.000 16.61 0.00 42.19 4.26
409 410 0.036022 AGTTGGAGTTGGCTCAGCTC 59.964 55.000 0.00 9.52 43.37 4.09
410 411 0.036022 GAGTTGGAGTTGGCTCAGCT 59.964 55.000 0.00 0.00 43.37 4.24
411 412 1.294659 CGAGTTGGAGTTGGCTCAGC 61.295 60.000 0.00 0.00 43.37 4.26
412 413 1.294659 GCGAGTTGGAGTTGGCTCAG 61.295 60.000 0.00 0.00 43.37 3.35
413 414 1.301716 GCGAGTTGGAGTTGGCTCA 60.302 57.895 0.00 0.00 43.37 4.26
414 415 1.004440 AGCGAGTTGGAGTTGGCTC 60.004 57.895 0.00 0.00 40.93 4.70
415 416 1.004440 GAGCGAGTTGGAGTTGGCT 60.004 57.895 0.00 0.00 0.00 4.75
416 417 2.383527 CGAGCGAGTTGGAGTTGGC 61.384 63.158 0.00 0.00 0.00 4.52
417 418 0.734253 CTCGAGCGAGTTGGAGTTGG 60.734 60.000 11.50 0.00 37.47 3.77
418 419 1.347817 GCTCGAGCGAGTTGGAGTTG 61.348 60.000 23.61 0.00 43.70 3.16
419 420 1.080434 GCTCGAGCGAGTTGGAGTT 60.080 57.895 23.61 0.00 43.70 3.01
420 421 2.569134 GCTCGAGCGAGTTGGAGT 59.431 61.111 23.61 0.00 43.70 3.85
434 435 1.950098 GCTGCAAACGAGTCGAGCTC 61.950 60.000 21.50 2.73 40.77 4.09
435 436 2.024319 GCTGCAAACGAGTCGAGCT 61.024 57.895 21.50 0.00 0.00 4.09
436 437 2.472049 GCTGCAAACGAGTCGAGC 59.528 61.111 21.50 19.17 0.00 5.03
437 438 2.383527 GGGCTGCAAACGAGTCGAG 61.384 63.158 21.50 6.68 0.00 4.04
438 439 1.529152 TAGGGCTGCAAACGAGTCGA 61.529 55.000 21.50 0.00 0.00 4.20
439 440 0.669318 TTAGGGCTGCAAACGAGTCG 60.669 55.000 11.85 11.85 0.00 4.18
440 441 1.739067 ATTAGGGCTGCAAACGAGTC 58.261 50.000 0.50 0.00 0.00 3.36
441 442 1.812571 CAATTAGGGCTGCAAACGAGT 59.187 47.619 0.50 0.00 0.00 4.18
442 443 1.812571 ACAATTAGGGCTGCAAACGAG 59.187 47.619 0.50 0.00 0.00 4.18
443 444 1.539388 CACAATTAGGGCTGCAAACGA 59.461 47.619 0.50 0.00 0.00 3.85
444 445 1.269448 ACACAATTAGGGCTGCAAACG 59.731 47.619 0.50 0.00 0.00 3.60
445 446 3.254657 TGTACACAATTAGGGCTGCAAAC 59.745 43.478 0.50 0.00 0.00 2.93
446 447 3.491342 TGTACACAATTAGGGCTGCAAA 58.509 40.909 0.50 0.00 0.00 3.68
447 448 3.147553 TGTACACAATTAGGGCTGCAA 57.852 42.857 0.50 0.00 0.00 4.08
448 449 2.869101 TGTACACAATTAGGGCTGCA 57.131 45.000 0.50 0.00 0.00 4.41
449 450 4.260620 CGTATTGTACACAATTAGGGCTGC 60.261 45.833 12.50 0.00 43.48 5.25
450 451 4.873827 ACGTATTGTACACAATTAGGGCTG 59.126 41.667 12.50 0.04 43.48 4.85
451 452 5.093849 ACGTATTGTACACAATTAGGGCT 57.906 39.130 12.50 0.00 43.48 5.19
452 453 6.275335 TCTACGTATTGTACACAATTAGGGC 58.725 40.000 12.50 0.00 43.48 5.19
453 454 7.384115 CCATCTACGTATTGTACACAATTAGGG 59.616 40.741 12.50 3.99 43.48 3.53
454 455 7.924412 ACCATCTACGTATTGTACACAATTAGG 59.076 37.037 12.50 5.76 43.48 2.69
455 456 8.867112 ACCATCTACGTATTGTACACAATTAG 57.133 34.615 12.50 8.82 43.48 1.73
456 457 8.689061 AGACCATCTACGTATTGTACACAATTA 58.311 33.333 12.50 0.00 43.48 1.40
457 458 7.491372 CAGACCATCTACGTATTGTACACAATT 59.509 37.037 12.50 0.00 43.48 2.32
486 489 8.825667 TTTTCTTAATTCATGTGGCTAAAACC 57.174 30.769 0.00 0.00 0.00 3.27
524 527 0.323629 AGCTTTAGCCGTAAGTGCCA 59.676 50.000 0.00 0.00 43.38 4.92
587 590 1.201769 GCGTGTGTGCGTGTTACATAG 60.202 52.381 0.00 0.00 0.00 2.23
637 1518 2.988010 AGATGCTATTGTTCCTCGCA 57.012 45.000 0.00 0.00 34.83 5.10
638 1519 4.372656 ACTAAGATGCTATTGTTCCTCGC 58.627 43.478 0.00 0.00 0.00 5.03
679 1561 7.678947 AACTCTATCCAATAATATGCAGTGC 57.321 36.000 8.58 8.58 0.00 4.40
701 1621 5.652994 TGGTGGCATATGTAAGGAAAAAC 57.347 39.130 4.29 0.00 0.00 2.43
719 1899 1.172180 ACCATGGCGTCACTTTGGTG 61.172 55.000 12.80 0.00 44.23 4.17
785 2227 1.073025 GGCAGTGTGGTGGTGATGA 59.927 57.895 0.00 0.00 0.00 2.92
795 2237 1.334059 CGTGCAGTAAAAGGCAGTGTG 60.334 52.381 0.00 0.00 41.35 3.82
824 2266 6.663523 TCCATTTTTCTAGGAAAGGAATGGTC 59.336 38.462 19.00 0.00 39.27 4.02
934 2407 5.707298 TGAGATGAGTTTGCTTAAAGGGAAG 59.293 40.000 0.00 0.00 0.00 3.46
940 2413 7.489435 CGATCTACTGAGATGAGTTTGCTTAAA 59.511 37.037 0.00 0.00 42.80 1.52
941 2414 6.975197 CGATCTACTGAGATGAGTTTGCTTAA 59.025 38.462 0.00 0.00 42.80 1.85
942 2415 6.095580 ACGATCTACTGAGATGAGTTTGCTTA 59.904 38.462 0.00 0.00 42.80 3.09
943 2416 5.105554 ACGATCTACTGAGATGAGTTTGCTT 60.106 40.000 0.00 0.00 42.80 3.91
944 2417 4.400884 ACGATCTACTGAGATGAGTTTGCT 59.599 41.667 0.00 0.00 42.80 3.91
945 2418 4.677584 ACGATCTACTGAGATGAGTTTGC 58.322 43.478 0.00 0.00 42.80 3.68
946 2419 5.453909 CGAACGATCTACTGAGATGAGTTTG 59.546 44.000 0.00 0.39 42.80 2.93
947 2420 5.574082 CGAACGATCTACTGAGATGAGTTT 58.426 41.667 0.00 0.00 42.80 2.66
1013 2508 1.202627 AGATGAGAAGGATCAAGGCGC 60.203 52.381 0.00 0.00 31.76 6.53
1029 2524 2.492012 GCTAGCAGGACCAATGAGATG 58.508 52.381 10.63 0.00 0.00 2.90
1219 2714 4.432741 GGAGGAGGTTGCCTGCCC 62.433 72.222 3.03 1.50 43.25 5.36
1220 2715 3.334054 AGGAGGAGGTTGCCTGCC 61.334 66.667 3.03 0.23 46.52 4.85
1222 2717 2.674220 GGGAGGAGGAGGTTGCCTG 61.674 68.421 0.00 0.00 38.73 4.85
1458 2953 0.997226 CGCCGACGATTATGGACTCG 60.997 60.000 0.00 0.00 43.93 4.18
1544 3039 0.748729 GATCTCCACGACTCCTCCGT 60.749 60.000 0.00 0.00 41.36 4.69
1650 4479 1.268992 CCCCTGGATGTCACCGGTTA 61.269 60.000 2.97 0.00 34.74 2.85
1656 4485 2.286365 TTTTGTCCCCTGGATGTCAC 57.714 50.000 0.00 0.00 32.73 3.67
1700 4529 6.321181 ACACATACTTGAAATTGTGAGGTTGT 59.679 34.615 8.73 0.00 41.50 3.32
1727 4556 6.884096 TTTTTGCAACACATGTGTCTAAAG 57.116 33.333 30.64 18.33 44.13 1.85
1914 4743 6.540438 ACAATAGGAGGAAGACGACAAATA 57.460 37.500 0.00 0.00 0.00 1.40
1930 4759 3.576982 TCTGGTAGGCGGATAACAATAGG 59.423 47.826 0.00 0.00 0.00 2.57
1932 4761 3.006537 GCTCTGGTAGGCGGATAACAATA 59.993 47.826 0.00 0.00 0.00 1.90
1965 4794 4.686091 CAGTAAGTTTCATGCTCTGTTCGA 59.314 41.667 0.00 0.00 0.00 3.71
1966 4795 4.686091 TCAGTAAGTTTCATGCTCTGTTCG 59.314 41.667 0.00 0.00 0.00 3.95
1967 4796 6.017934 TGTTCAGTAAGTTTCATGCTCTGTTC 60.018 38.462 0.00 0.00 0.00 3.18
1968 4797 5.822519 TGTTCAGTAAGTTTCATGCTCTGTT 59.177 36.000 0.00 0.00 0.00 3.16
1969 4798 5.368145 TGTTCAGTAAGTTTCATGCTCTGT 58.632 37.500 0.00 0.00 0.00 3.41
1970 4799 5.929697 TGTTCAGTAAGTTTCATGCTCTG 57.070 39.130 0.00 0.00 0.00 3.35
1971 4800 6.058183 ACTTGTTCAGTAAGTTTCATGCTCT 58.942 36.000 0.00 0.00 34.91 4.09
1972 4801 6.305693 ACTTGTTCAGTAAGTTTCATGCTC 57.694 37.500 0.00 0.00 34.91 4.26
1973 4802 6.073003 GCTACTTGTTCAGTAAGTTTCATGCT 60.073 38.462 0.00 0.00 37.54 3.79
1974 4803 6.080406 GCTACTTGTTCAGTAAGTTTCATGC 58.920 40.000 0.00 0.00 37.54 4.06
1975 4804 7.189693 TGCTACTTGTTCAGTAAGTTTCATG 57.810 36.000 0.00 0.00 37.54 3.07
1976 4805 7.041098 CCTTGCTACTTGTTCAGTAAGTTTCAT 60.041 37.037 0.00 0.00 37.54 2.57
1977 4806 6.260050 CCTTGCTACTTGTTCAGTAAGTTTCA 59.740 38.462 0.00 0.00 37.54 2.69
1978 4807 6.482308 TCCTTGCTACTTGTTCAGTAAGTTTC 59.518 38.462 0.00 0.00 37.54 2.78
1979 4808 6.354130 TCCTTGCTACTTGTTCAGTAAGTTT 58.646 36.000 0.00 0.00 37.54 2.66
1980 4809 5.925509 TCCTTGCTACTTGTTCAGTAAGTT 58.074 37.500 0.00 0.00 37.54 2.66
1981 4810 5.546621 TCCTTGCTACTTGTTCAGTAAGT 57.453 39.130 0.00 0.00 37.54 2.24
1982 4811 6.073003 CCTTTCCTTGCTACTTGTTCAGTAAG 60.073 42.308 0.00 0.00 37.54 2.34
1983 4812 5.763204 CCTTTCCTTGCTACTTGTTCAGTAA 59.237 40.000 0.00 0.00 37.54 2.24
1984 4813 5.305585 CCTTTCCTTGCTACTTGTTCAGTA 58.694 41.667 0.00 0.00 36.88 2.74
1985 4814 4.137543 CCTTTCCTTGCTACTTGTTCAGT 58.862 43.478 0.00 0.00 39.87 3.41
2071 4901 2.145397 TCAGCGGTTACCAGATCTCT 57.855 50.000 1.13 0.00 0.00 3.10
2087 4917 2.069273 GTCCACCTGATGTTCGTTCAG 58.931 52.381 0.00 0.00 40.25 3.02
2102 4932 2.564721 GCTTGGGGTGCTTGTCCAC 61.565 63.158 0.00 0.00 35.00 4.02
2127 4957 2.095110 TGATGGTGAAGAATTGCAAGCG 60.095 45.455 4.94 0.00 0.00 4.68
2174 5036 2.100584 TCTTGTTTTGTTCAGCGGCAAT 59.899 40.909 1.45 0.00 0.00 3.56
2194 5056 5.343325 GGTGCTGTGATTTCGAATTCTTTTC 59.657 40.000 18.06 8.83 0.00 2.29
2196 5058 4.278170 TGGTGCTGTGATTTCGAATTCTTT 59.722 37.500 18.06 0.00 0.00 2.52
2208 5070 1.547372 GCTGGATTTTGGTGCTGTGAT 59.453 47.619 0.00 0.00 0.00 3.06
2211 5073 0.469705 TGGCTGGATTTTGGTGCTGT 60.470 50.000 0.00 0.00 0.00 4.40
2270 5132 6.091986 GTGCTGCTAGATTTATTGGCTCTATC 59.908 42.308 0.00 0.00 0.00 2.08
2288 5150 1.059913 AAGTGAGGGTAAGTGCTGCT 58.940 50.000 0.00 0.00 0.00 4.24
2296 5158 1.203001 CCAAAGGGCAAGTGAGGGTAA 60.203 52.381 0.00 0.00 0.00 2.85
2319 5181 0.039618 AATGGTGTTTGATCCGCCCT 59.960 50.000 0.00 0.00 0.00 5.19
2334 5319 4.513442 TCGGTTTCTTCCTACATCAATGG 58.487 43.478 0.00 0.00 0.00 3.16
2420 5405 6.149807 TCCACGTGTTTCTCTTAAACTTTGTT 59.850 34.615 15.65 0.00 0.00 2.83
2421 5406 5.644636 TCCACGTGTTTCTCTTAAACTTTGT 59.355 36.000 15.65 0.00 0.00 2.83
2422 5407 5.963586 GTCCACGTGTTTCTCTTAAACTTTG 59.036 40.000 15.65 0.00 0.00 2.77
2423 5408 5.644636 TGTCCACGTGTTTCTCTTAAACTTT 59.355 36.000 15.65 0.00 0.00 2.66
2424 5409 5.180271 TGTCCACGTGTTTCTCTTAAACTT 58.820 37.500 15.65 0.00 0.00 2.66
2425 5410 4.761975 TGTCCACGTGTTTCTCTTAAACT 58.238 39.130 15.65 0.00 0.00 2.66
2426 5411 5.440685 CATGTCCACGTGTTTCTCTTAAAC 58.559 41.667 15.65 0.00 0.00 2.01
2442 5427 4.922206 AGATTTTAGTCCTTGCATGTCCA 58.078 39.130 0.00 0.00 0.00 4.02
2467 5452 2.160205 GGAGTTGGTACCTGCTTTTCC 58.840 52.381 14.36 7.90 0.00 3.13
2473 5458 1.299976 CAGGGGAGTTGGTACCTGC 59.700 63.158 14.36 5.81 43.41 4.85
2482 5468 3.705072 CCTCGTTAATAGTCAGGGGAGTT 59.295 47.826 0.00 0.00 0.00 3.01
2491 5477 2.100916 TCTGGCAGCCTCGTTAATAGTC 59.899 50.000 14.15 0.00 0.00 2.59
2492 5478 2.108168 TCTGGCAGCCTCGTTAATAGT 58.892 47.619 14.15 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.