Multiple sequence alignment - TraesCS2B01G182400

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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 TraesCS2B01G182400 chr2B 100.000 2119 0 0 266 2384 157313675 157315793 0.000000e+00 3914.0
1 TraesCS2B01G182400 chr2B 96.454 141 5 0 266 406 199744171 199744311 1.420000e-57 233.0
2 TraesCS2B01G182400 chr2B 94.595 148 6 2 266 411 199739340 199739487 6.630000e-56 228.0
3 TraesCS2B01G182400 chr2B 100.000 31 0 0 1 31 157313410 157313440 9.200000e-05 58.4
4 TraesCS2B01G182400 chr2B 88.000 50 5 1 2106 2154 790743790 790743839 9.200000e-05 58.4
5 TraesCS2B01G182400 chr2A 89.114 1975 124 44 431 2384 103363681 103365585 0.000000e+00 2372.0
6 TraesCS2B01G182400 chr2D 94.753 1315 35 13 589 1882 107000091 107001392 0.000000e+00 2015.0
7 TraesCS2B01G182400 chr2D 90.559 519 16 7 1877 2384 107010551 107011047 0.000000e+00 656.0
8 TraesCS2B01G182400 chr3B 83.534 747 72 20 748 1459 152878522 152877792 0.000000e+00 651.0
9 TraesCS2B01G182400 chr3B 77.660 282 44 11 1537 1803 790758886 790759163 1.140000e-33 154.0
10 TraesCS2B01G182400 chr3D 85.669 628 72 10 840 1464 101861132 101860520 0.000000e+00 645.0
11 TraesCS2B01G182400 chr3D 97.183 142 4 0 266 407 300146041 300145900 8.520000e-60 241.0
12 TraesCS2B01G182400 chr3A 85.538 567 63 11 837 1401 554017891 554018440 2.060000e-160 575.0
13 TraesCS2B01G182400 chr6B 97.857 140 3 0 266 405 281506362 281506223 2.370000e-60 243.0
14 TraesCS2B01G182400 chr6B 95.918 147 4 2 266 410 281511780 281511634 1.100000e-58 237.0
15 TraesCS2B01G182400 chr7D 95.973 149 4 2 266 412 111351453 111351601 8.520000e-60 241.0
16 TraesCS2B01G182400 chr7A 97.163 141 3 1 266 406 15299852 15299991 1.100000e-58 237.0
17 TraesCS2B01G182400 chr1A 91.329 173 15 0 1218 1390 536930769 536930597 1.100000e-58 237.0
18 TraesCS2B01G182400 chr1D 94.667 150 4 4 266 412 339329334 339329482 1.840000e-56 230.0
19 TraesCS2B01G182400 chr5A 93.506 154 8 2 266 418 706508365 706508517 6.630000e-56 228.0
20 TraesCS2B01G182400 chr5A 77.778 135 25 4 2017 2149 635491232 635491101 7.070000e-11 78.7
21 TraesCS2B01G182400 chr1B 88.083 193 22 1 1210 1401 598925999 598926191 6.630000e-56 228.0
22 TraesCS2B01G182400 chr5B 76.161 323 51 17 2075 2384 639157449 639157758 1.910000e-31 147.0
23 TraesCS2B01G182400 chr4D 74.932 367 62 17 2031 2379 366222221 366222575 8.880000e-30 141.0
24 TraesCS2B01G182400 chr4D 72.800 375 77 17 2029 2384 509802481 509802113 1.170000e-18 104.0
25 TraesCS2B01G182400 chr4B 74.044 366 75 15 2029 2378 115942285 115941924 5.350000e-27 132.0
26 TraesCS2B01G182400 chr5D 74.892 231 45 6 2041 2260 507878173 507877945 2.520000e-15 93.5
27 TraesCS2B01G182400 chr5D 75.000 184 36 2 2068 2242 507870780 507870598 2.540000e-10 76.8
28 TraesCS2B01G182400 chrUn 100.000 28 0 0 1500 1527 299525734 299525707 4.000000e-03 52.8


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 TraesCS2B01G182400 chr2B 157313410 157315793 2383 False 1986.2 3914 100.000 1 2384 2 chr2B.!!$F4 2383
1 TraesCS2B01G182400 chr2A 103363681 103365585 1904 False 2372.0 2372 89.114 431 2384 1 chr2A.!!$F1 1953
2 TraesCS2B01G182400 chr2D 107000091 107001392 1301 False 2015.0 2015 94.753 589 1882 1 chr2D.!!$F1 1293
3 TraesCS2B01G182400 chr3B 152877792 152878522 730 True 651.0 651 83.534 748 1459 1 chr3B.!!$R1 711
4 TraesCS2B01G182400 chr3D 101860520 101861132 612 True 645.0 645 85.669 840 1464 1 chr3D.!!$R1 624
5 TraesCS2B01G182400 chr3A 554017891 554018440 549 False 575.0 575 85.538 837 1401 1 chr3A.!!$F1 564

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
298 299 0.11694 ATTGGATTTGTGGCCCACCT 59.883 50.0 12.25 0.0 36.63 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1553 0.102481 ATGCACGGGCGTTCTACTAG 59.898 55.0 4.58 0.0 45.35 2.57 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
287 288 5.888691 TGTATTGCACGTGTATTGGATTT 57.111 34.783 18.38 0.00 0.00 2.17
288 289 5.635866 TGTATTGCACGTGTATTGGATTTG 58.364 37.500 18.38 0.00 0.00 2.32
289 290 4.782019 ATTGCACGTGTATTGGATTTGT 57.218 36.364 18.38 0.00 0.00 2.83
290 291 3.550950 TGCACGTGTATTGGATTTGTG 57.449 42.857 18.38 0.00 0.00 3.33
291 292 2.227626 TGCACGTGTATTGGATTTGTGG 59.772 45.455 18.38 0.00 0.00 4.17
292 293 2.862512 CACGTGTATTGGATTTGTGGC 58.137 47.619 7.58 0.00 0.00 5.01
293 294 1.816224 ACGTGTATTGGATTTGTGGCC 59.184 47.619 0.00 0.00 0.00 5.36
294 295 1.134175 CGTGTATTGGATTTGTGGCCC 59.866 52.381 0.00 0.00 0.00 5.80
295 296 2.175202 GTGTATTGGATTTGTGGCCCA 58.825 47.619 0.00 0.00 0.00 5.36
296 297 2.094234 GTGTATTGGATTTGTGGCCCAC 60.094 50.000 7.01 7.01 34.56 4.61
297 298 1.480545 GTATTGGATTTGTGGCCCACC 59.519 52.381 12.25 0.00 32.73 4.61
298 299 0.116940 ATTGGATTTGTGGCCCACCT 59.883 50.000 12.25 0.00 36.63 4.00
299 300 0.541764 TTGGATTTGTGGCCCACCTC 60.542 55.000 12.25 5.56 36.63 3.85
300 301 1.682344 GGATTTGTGGCCCACCTCC 60.682 63.158 12.25 11.14 36.63 4.30
301 302 1.384191 GATTTGTGGCCCACCTCCT 59.616 57.895 12.25 0.00 36.63 3.69
302 303 0.623723 GATTTGTGGCCCACCTCCTA 59.376 55.000 12.25 0.00 36.63 2.94
303 304 1.215423 GATTTGTGGCCCACCTCCTAT 59.785 52.381 12.25 0.00 36.63 2.57
304 305 1.080638 TTTGTGGCCCACCTCCTATT 58.919 50.000 12.25 0.00 36.63 1.73
305 306 0.623723 TTGTGGCCCACCTCCTATTC 59.376 55.000 12.25 0.00 36.63 1.75
306 307 0.253160 TGTGGCCCACCTCCTATTCT 60.253 55.000 12.25 0.00 36.63 2.40
307 308 0.919710 GTGGCCCACCTCCTATTCTT 59.080 55.000 1.17 0.00 36.63 2.52
308 309 0.918983 TGGCCCACCTCCTATTCTTG 59.081 55.000 0.00 0.00 36.63 3.02
309 310 0.919710 GGCCCACCTCCTATTCTTGT 59.080 55.000 0.00 0.00 0.00 3.16
310 311 2.124411 GGCCCACCTCCTATTCTTGTA 58.876 52.381 0.00 0.00 0.00 2.41
311 312 2.711547 GGCCCACCTCCTATTCTTGTAT 59.288 50.000 0.00 0.00 0.00 2.29
312 313 3.908103 GGCCCACCTCCTATTCTTGTATA 59.092 47.826 0.00 0.00 0.00 1.47
313 314 4.020128 GGCCCACCTCCTATTCTTGTATAG 60.020 50.000 0.00 0.00 0.00 1.31
314 315 4.593634 GCCCACCTCCTATTCTTGTATAGT 59.406 45.833 0.00 0.00 0.00 2.12
315 316 5.071923 GCCCACCTCCTATTCTTGTATAGTT 59.928 44.000 0.00 0.00 0.00 2.24
316 317 6.525629 CCCACCTCCTATTCTTGTATAGTTG 58.474 44.000 0.00 0.00 0.00 3.16
317 318 6.326583 CCCACCTCCTATTCTTGTATAGTTGA 59.673 42.308 0.00 0.00 0.00 3.18
318 319 7.437748 CCACCTCCTATTCTTGTATAGTTGAG 58.562 42.308 0.00 0.00 0.00 3.02
319 320 7.437748 CACCTCCTATTCTTGTATAGTTGAGG 58.562 42.308 12.98 12.98 39.71 3.86
320 321 7.070074 CACCTCCTATTCTTGTATAGTTGAGGT 59.930 40.741 13.78 13.78 43.31 3.85
321 322 8.287350 ACCTCCTATTCTTGTATAGTTGAGGTA 58.713 37.037 16.01 0.00 42.14 3.08
322 323 8.798402 CCTCCTATTCTTGTATAGTTGAGGTAG 58.202 40.741 0.00 0.00 34.81 3.18
323 324 9.575868 CTCCTATTCTTGTATAGTTGAGGTAGA 57.424 37.037 0.00 0.00 0.00 2.59
324 325 9.575868 TCCTATTCTTGTATAGTTGAGGTAGAG 57.424 37.037 0.00 0.00 0.00 2.43
325 326 8.798402 CCTATTCTTGTATAGTTGAGGTAGAGG 58.202 40.741 0.00 0.00 0.00 3.69
326 327 6.466885 TTCTTGTATAGTTGAGGTAGAGGC 57.533 41.667 0.00 0.00 0.00 4.70
327 328 4.894114 TCTTGTATAGTTGAGGTAGAGGCC 59.106 45.833 0.00 0.00 0.00 5.19
328 329 4.537945 TGTATAGTTGAGGTAGAGGCCT 57.462 45.455 3.86 3.86 42.53 5.19
329 330 4.880164 TGTATAGTTGAGGTAGAGGCCTT 58.120 43.478 6.77 0.00 39.34 4.35
330 331 4.894114 TGTATAGTTGAGGTAGAGGCCTTC 59.106 45.833 6.77 0.00 39.34 3.46
331 332 1.574263 AGTTGAGGTAGAGGCCTTCC 58.426 55.000 6.77 10.69 39.34 3.46
332 333 0.542333 GTTGAGGTAGAGGCCTTCCC 59.458 60.000 6.77 7.52 39.34 3.97
334 335 0.417841 TGAGGTAGAGGCCTTCCCTT 59.582 55.000 6.77 0.00 46.60 3.95
335 336 0.833949 GAGGTAGAGGCCTTCCCTTG 59.166 60.000 6.77 0.00 46.60 3.61
336 337 0.119358 AGGTAGAGGCCTTCCCTTGT 59.881 55.000 6.77 0.00 46.60 3.16
337 338 1.365028 AGGTAGAGGCCTTCCCTTGTA 59.635 52.381 6.77 0.00 46.60 2.41
338 339 2.021936 AGGTAGAGGCCTTCCCTTGTAT 60.022 50.000 6.77 0.00 46.60 2.29
339 340 2.778270 GGTAGAGGCCTTCCCTTGTATT 59.222 50.000 6.77 0.00 46.60 1.89
340 341 3.971971 GGTAGAGGCCTTCCCTTGTATTA 59.028 47.826 6.77 0.00 46.60 0.98
341 342 4.597940 GGTAGAGGCCTTCCCTTGTATTAT 59.402 45.833 6.77 0.00 46.60 1.28
342 343 5.783875 GGTAGAGGCCTTCCCTTGTATTATA 59.216 44.000 6.77 0.00 46.60 0.98
343 344 6.444171 GGTAGAGGCCTTCCCTTGTATTATAT 59.556 42.308 6.77 0.00 46.60 0.86
344 345 7.622479 GGTAGAGGCCTTCCCTTGTATTATATA 59.378 40.741 6.77 0.00 46.60 0.86
345 346 9.214962 GTAGAGGCCTTCCCTTGTATTATATAT 57.785 37.037 6.77 0.00 46.60 0.86
347 348 9.214962 AGAGGCCTTCCCTTGTATTATATATAC 57.785 37.037 6.77 0.00 46.60 1.47
348 349 8.019656 AGGCCTTCCCTTGTATTATATATACG 57.980 38.462 0.00 0.00 43.06 3.06
349 350 7.622479 AGGCCTTCCCTTGTATTATATATACGT 59.378 37.037 0.00 0.00 43.06 3.57
350 351 7.709613 GGCCTTCCCTTGTATTATATATACGTG 59.290 40.741 0.00 0.00 0.00 4.49
351 352 7.224167 GCCTTCCCTTGTATTATATATACGTGC 59.776 40.741 0.00 0.00 0.00 5.34
352 353 8.255206 CCTTCCCTTGTATTATATATACGTGCA 58.745 37.037 0.00 0.00 0.00 4.57
353 354 8.991243 TTCCCTTGTATTATATATACGTGCAC 57.009 34.615 6.82 6.82 0.00 4.57
354 355 7.549839 TCCCTTGTATTATATATACGTGCACC 58.450 38.462 12.15 0.00 0.00 5.01
355 356 7.178805 TCCCTTGTATTATATATACGTGCACCA 59.821 37.037 12.15 0.00 0.00 4.17
356 357 7.491372 CCCTTGTATTATATATACGTGCACCAG 59.509 40.741 12.15 0.00 0.00 4.00
357 358 7.010183 CCTTGTATTATATATACGTGCACCAGC 59.990 40.741 12.15 0.00 42.57 4.85
367 368 2.283101 GCACCAGCACCCCATCAA 60.283 61.111 0.00 0.00 41.58 2.57
368 369 1.683365 GCACCAGCACCCCATCAAT 60.683 57.895 0.00 0.00 41.58 2.57
369 370 0.395586 GCACCAGCACCCCATCAATA 60.396 55.000 0.00 0.00 41.58 1.90
370 371 1.392589 CACCAGCACCCCATCAATAC 58.607 55.000 0.00 0.00 0.00 1.89
371 372 0.998928 ACCAGCACCCCATCAATACA 59.001 50.000 0.00 0.00 0.00 2.29
372 373 1.357420 ACCAGCACCCCATCAATACAA 59.643 47.619 0.00 0.00 0.00 2.41
373 374 1.750778 CCAGCACCCCATCAATACAAC 59.249 52.381 0.00 0.00 0.00 3.32
374 375 2.445427 CAGCACCCCATCAATACAACA 58.555 47.619 0.00 0.00 0.00 3.33
375 376 3.025978 CAGCACCCCATCAATACAACAT 58.974 45.455 0.00 0.00 0.00 2.71
376 377 3.067180 CAGCACCCCATCAATACAACATC 59.933 47.826 0.00 0.00 0.00 3.06
377 378 3.053395 AGCACCCCATCAATACAACATCT 60.053 43.478 0.00 0.00 0.00 2.90
378 379 4.165950 AGCACCCCATCAATACAACATCTA 59.834 41.667 0.00 0.00 0.00 1.98
379 380 5.072741 GCACCCCATCAATACAACATCTAT 58.927 41.667 0.00 0.00 0.00 1.98
380 381 5.536161 GCACCCCATCAATACAACATCTATT 59.464 40.000 0.00 0.00 0.00 1.73
381 382 6.515531 GCACCCCATCAATACAACATCTATTG 60.516 42.308 0.00 0.00 34.24 1.90
382 383 6.547141 CACCCCATCAATACAACATCTATTGT 59.453 38.462 0.00 0.00 44.87 2.71
383 384 7.719193 CACCCCATCAATACAACATCTATTGTA 59.281 37.037 1.16 1.16 46.33 2.41
395 396 9.762933 ACAACATCTATTGTATTGCAAACTTTT 57.237 25.926 1.71 0.00 41.04 2.27
397 398 8.986477 ACATCTATTGTATTGCAAACTTTTCC 57.014 30.769 1.71 0.00 40.91 3.13
398 399 7.754924 ACATCTATTGTATTGCAAACTTTTCCG 59.245 33.333 1.71 0.00 40.91 4.30
399 400 7.209471 TCTATTGTATTGCAAACTTTTCCGT 57.791 32.000 1.71 0.00 40.91 4.69
400 401 7.302524 TCTATTGTATTGCAAACTTTTCCGTC 58.697 34.615 1.71 0.00 40.91 4.79
401 402 5.508200 TTGTATTGCAAACTTTTCCGTCT 57.492 34.783 1.71 0.00 33.53 4.18
402 403 6.621316 TTGTATTGCAAACTTTTCCGTCTA 57.379 33.333 1.71 0.00 33.53 2.59
403 404 5.992729 TGTATTGCAAACTTTTCCGTCTAC 58.007 37.500 1.71 0.00 0.00 2.59
404 405 5.527951 TGTATTGCAAACTTTTCCGTCTACA 59.472 36.000 1.71 0.00 0.00 2.74
405 406 4.545823 TTGCAAACTTTTCCGTCTACAG 57.454 40.909 0.00 0.00 0.00 2.74
406 407 3.537580 TGCAAACTTTTCCGTCTACAGT 58.462 40.909 0.00 0.00 0.00 3.55
407 408 4.695396 TGCAAACTTTTCCGTCTACAGTA 58.305 39.130 0.00 0.00 0.00 2.74
408 409 5.302360 TGCAAACTTTTCCGTCTACAGTAT 58.698 37.500 0.00 0.00 0.00 2.12
409 410 5.407387 TGCAAACTTTTCCGTCTACAGTATC 59.593 40.000 0.00 0.00 0.00 2.24
410 411 5.407387 GCAAACTTTTCCGTCTACAGTATCA 59.593 40.000 0.00 0.00 0.00 2.15
411 412 6.092259 GCAAACTTTTCCGTCTACAGTATCAT 59.908 38.462 0.00 0.00 0.00 2.45
412 413 7.456253 CAAACTTTTCCGTCTACAGTATCATG 58.544 38.462 0.00 0.00 0.00 3.07
413 414 6.282199 ACTTTTCCGTCTACAGTATCATGT 57.718 37.500 0.00 0.00 37.19 3.21
414 415 6.100004 ACTTTTCCGTCTACAGTATCATGTG 58.900 40.000 0.00 0.00 34.56 3.21
415 416 5.654603 TTTCCGTCTACAGTATCATGTGT 57.345 39.130 0.00 0.00 34.56 3.72
416 417 6.762702 TTTCCGTCTACAGTATCATGTGTA 57.237 37.500 0.00 0.00 34.56 2.90
417 418 6.373186 TTCCGTCTACAGTATCATGTGTAG 57.627 41.667 12.71 12.71 45.11 2.74
418 419 4.275196 TCCGTCTACAGTATCATGTGTAGC 59.725 45.833 13.68 9.45 43.94 3.58
419 420 4.537965 CGTCTACAGTATCATGTGTAGCC 58.462 47.826 13.68 4.79 43.94 3.93
420 421 4.276183 CGTCTACAGTATCATGTGTAGCCT 59.724 45.833 13.68 0.00 43.94 4.58
421 422 5.561145 CGTCTACAGTATCATGTGTAGCCTC 60.561 48.000 13.68 7.85 43.94 4.70
422 423 5.533154 GTCTACAGTATCATGTGTAGCCTCT 59.467 44.000 13.68 0.00 43.94 3.69
423 424 6.039941 GTCTACAGTATCATGTGTAGCCTCTT 59.960 42.308 13.68 0.00 43.94 2.85
424 425 5.269505 ACAGTATCATGTGTAGCCTCTTC 57.730 43.478 0.00 0.00 30.46 2.87
425 426 4.959210 ACAGTATCATGTGTAGCCTCTTCT 59.041 41.667 0.00 0.00 30.46 2.85
426 427 6.129874 ACAGTATCATGTGTAGCCTCTTCTA 58.870 40.000 0.00 0.00 30.46 2.10
427 428 6.039941 ACAGTATCATGTGTAGCCTCTTCTAC 59.960 42.308 0.00 0.00 39.40 2.59
428 429 6.039829 CAGTATCATGTGTAGCCTCTTCTACA 59.960 42.308 0.00 0.00 44.61 2.74
429 430 4.991153 TCATGTGTAGCCTCTTCTACAG 57.009 45.455 4.09 0.00 46.59 2.74
430 431 4.344978 TCATGTGTAGCCTCTTCTACAGT 58.655 43.478 4.09 0.00 46.59 3.55
431 432 5.506708 TCATGTGTAGCCTCTTCTACAGTA 58.493 41.667 4.09 0.00 46.59 2.74
432 433 6.129874 TCATGTGTAGCCTCTTCTACAGTAT 58.870 40.000 4.09 0.89 46.59 2.12
433 434 6.263392 TCATGTGTAGCCTCTTCTACAGTATC 59.737 42.308 4.09 0.00 46.59 2.24
434 435 5.506708 TGTGTAGCCTCTTCTACAGTATCA 58.493 41.667 4.09 0.00 46.59 2.15
435 436 6.129874 TGTGTAGCCTCTTCTACAGTATCAT 58.870 40.000 4.09 0.00 46.59 2.45
436 437 6.039829 TGTGTAGCCTCTTCTACAGTATCATG 59.960 42.308 4.09 0.00 46.59 3.07
437 438 6.039941 GTGTAGCCTCTTCTACAGTATCATGT 59.960 42.308 4.09 0.00 46.59 3.21
438 439 5.528043 AGCCTCTTCTACAGTATCATGTG 57.472 43.478 0.00 0.00 34.56 3.21
439 440 4.959210 AGCCTCTTCTACAGTATCATGTGT 59.041 41.667 0.00 0.00 34.56 3.72
450 451 2.879002 ATCATGTGTAGCCTCGTCTG 57.121 50.000 0.00 0.00 0.00 3.51
458 459 2.626266 TGTAGCCTCGTCTGTTTCTTCA 59.374 45.455 0.00 0.00 0.00 3.02
467 468 1.939934 TCTGTTTCTTCAACGGCTGTG 59.060 47.619 0.00 0.00 41.13 3.66
470 471 1.002792 GTTTCTTCAACGGCTGTGTCC 60.003 52.381 0.00 0.00 0.00 4.02
558 559 2.105128 GTCTGATGGAGGCGGACG 59.895 66.667 0.00 0.00 32.56 4.79
566 567 3.839432 GAGGCGGACGGAGGGAAG 61.839 72.222 0.00 0.00 0.00 3.46
579 580 4.481112 GGAAGCCGCGCCACAATG 62.481 66.667 0.00 0.00 0.00 2.82
580 581 4.481112 GAAGCCGCGCCACAATGG 62.481 66.667 0.00 0.00 41.55 3.16
619 620 4.247380 GCTGGGAGATGGCCTCGG 62.247 72.222 3.32 0.00 42.89 4.63
758 760 1.990799 TAGCACATATGGCGCGTATC 58.009 50.000 8.43 0.00 36.08 2.24
860 883 1.140134 CCCTCTCCAAACCCCCTTCA 61.140 60.000 0.00 0.00 0.00 3.02
936 962 2.008242 CAGGGAGAGATCCACCTAGG 57.992 60.000 7.41 7.41 39.47 3.02
941 967 2.324541 GAGAGATCCACCTAGGTGCAT 58.675 52.381 32.98 26.46 44.16 3.96
981 1009 1.744320 AAACCCGCAAGAAACCAGCC 61.744 55.000 0.00 0.00 43.02 4.85
989 1017 3.047877 GAAACCAGCCACCGGACG 61.048 66.667 9.46 0.00 0.00 4.79
1341 1381 4.692475 GCCAACCCCTACACGCGT 62.692 66.667 5.58 5.58 0.00 6.01
1394 1435 1.927174 CATGAACTGATTCGTCGTCCC 59.073 52.381 0.00 0.00 37.69 4.46
1466 1520 3.991051 CGGCGAGGAGGTGTGTGT 61.991 66.667 0.00 0.00 0.00 3.72
1467 1521 2.357517 GGCGAGGAGGTGTGTGTG 60.358 66.667 0.00 0.00 0.00 3.82
1485 1539 3.488090 GCCGTGCGAGCACCTAAC 61.488 66.667 20.79 5.79 43.49 2.34
1492 1546 3.177487 GTGCGAGCACCTAACTACTAAC 58.823 50.000 16.66 0.00 40.79 2.34
1496 1550 4.413087 CGAGCACCTAACTACTAACTGTG 58.587 47.826 0.00 0.00 0.00 3.66
1498 1552 5.135508 AGCACCTAACTACTAACTGTGTG 57.864 43.478 0.00 0.00 0.00 3.82
1499 1553 3.678548 GCACCTAACTACTAACTGTGTGC 59.321 47.826 0.00 0.00 39.61 4.57
1500 1554 4.560919 GCACCTAACTACTAACTGTGTGCT 60.561 45.833 0.00 0.00 42.31 4.40
1501 1555 5.336213 GCACCTAACTACTAACTGTGTGCTA 60.336 44.000 0.00 0.00 42.31 3.49
1528 1582 1.097547 GCCCGTGCATTGCTACAGAT 61.098 55.000 10.49 0.00 37.47 2.90
1644 1701 4.980573 ACACTTAGCTTCACATTAACCCA 58.019 39.130 0.00 0.00 0.00 4.51
1688 1757 5.847514 CTTGATAACAATTGCGTGGAGCTTT 60.848 40.000 5.05 0.00 39.98 3.51
1716 1785 6.110707 AGTCGTGGACTTTAAAGAAGACAAA 58.889 36.000 21.92 3.56 40.28 2.83
1834 1905 4.766007 CGTTTGTGCTGCTATACATCATC 58.234 43.478 0.00 0.00 0.00 2.92
1843 1914 4.820897 TGCTATACATCATCGATCCAACC 58.179 43.478 0.00 0.00 0.00 3.77
1862 1933 6.207810 TCCAACCAATTTAACGACTGCTATTT 59.792 34.615 0.00 0.00 0.00 1.40
1900 1976 4.342378 TGAGTAGCTTCTATGTGTCCATCC 59.658 45.833 0.00 0.00 32.29 3.51
1906 1982 4.446371 CTTCTATGTGTCCATCCTGTTCC 58.554 47.826 0.00 0.00 32.29 3.62
1912 1988 2.171448 GTGTCCATCCTGTTCCTGCTAT 59.829 50.000 0.00 0.00 0.00 2.97
1941 2017 5.802465 TGCATGGCAATTTATTCCTTTTGA 58.198 33.333 0.00 0.00 34.76 2.69
1969 2045 7.805071 ACTTGTCTTCATATTTGAAAAAGAGCG 59.195 33.333 15.93 0.00 41.22 5.03
1972 2048 6.743172 GTCTTCATATTTGAAAAAGAGCGGAC 59.257 38.462 0.20 0.00 41.22 4.79
1987 2063 4.083484 AGAGCGGACTTTTATTTTTGGACG 60.083 41.667 0.00 0.00 0.00 4.79
1991 2067 3.985279 GGACTTTTATTTTTGGACGTGGC 59.015 43.478 0.00 0.00 0.00 5.01
2007 2083 4.908877 GCTAGCGAGCGTCCGTCC 62.909 72.222 2.13 0.00 39.39 4.79
2015 2091 1.240256 GAGCGTCCGTCCTCTCATAT 58.760 55.000 0.00 0.00 0.00 1.78
2016 2092 2.424557 GAGCGTCCGTCCTCTCATATA 58.575 52.381 0.00 0.00 0.00 0.86
2017 2093 3.011119 GAGCGTCCGTCCTCTCATATAT 58.989 50.000 0.00 0.00 0.00 0.86
2018 2094 4.190001 GAGCGTCCGTCCTCTCATATATA 58.810 47.826 0.00 0.00 0.00 0.86
2020 2096 5.008331 AGCGTCCGTCCTCTCATATATAAA 58.992 41.667 0.00 0.00 0.00 1.40
2021 2097 5.652891 AGCGTCCGTCCTCTCATATATAAAT 59.347 40.000 0.00 0.00 0.00 1.40
2024 2100 7.124471 CGTCCGTCCTCTCATATATAAATACG 58.876 42.308 0.00 0.00 0.00 3.06
2025 2101 6.911511 GTCCGTCCTCTCATATATAAATACGC 59.088 42.308 0.00 0.00 0.00 4.42
2026 2102 6.039047 TCCGTCCTCTCATATATAAATACGCC 59.961 42.308 0.00 0.00 0.00 5.68
2027 2103 6.183360 CCGTCCTCTCATATATAAATACGCCA 60.183 42.308 0.00 0.00 0.00 5.69
2028 2104 7.426410 CGTCCTCTCATATATAAATACGCCAT 58.574 38.462 0.00 0.00 0.00 4.40
2029 2105 8.565416 CGTCCTCTCATATATAAATACGCCATA 58.435 37.037 0.00 0.00 0.00 2.74
2033 2109 9.920133 CTCTCATATATAAATACGCCATATGCT 57.080 33.333 0.00 0.00 38.05 3.79
2036 2112 9.191995 TCATATATAAATACGCCATATGCTTCG 57.808 33.333 0.00 3.13 38.05 3.79
2037 2113 8.978539 CATATATAAATACGCCATATGCTTCGT 58.021 33.333 16.20 16.20 38.05 3.85
2039 2115 6.887376 ATAAATACGCCATATGCTTCGTAG 57.113 37.500 19.88 0.62 40.14 3.51
2040 2116 3.936372 ATACGCCATATGCTTCGTAGT 57.064 42.857 19.88 11.03 40.14 2.73
2041 2117 2.596904 ACGCCATATGCTTCGTAGTT 57.403 45.000 12.16 0.00 38.05 2.24
2042 2118 2.901249 ACGCCATATGCTTCGTAGTTT 58.099 42.857 12.16 0.00 38.05 2.66
2043 2119 3.267483 ACGCCATATGCTTCGTAGTTTT 58.733 40.909 12.16 0.00 38.05 2.43
2044 2120 4.435425 ACGCCATATGCTTCGTAGTTTTA 58.565 39.130 12.16 0.00 38.05 1.52
2045 2121 4.871557 ACGCCATATGCTTCGTAGTTTTAA 59.128 37.500 12.16 0.00 38.05 1.52
2046 2122 5.006358 ACGCCATATGCTTCGTAGTTTTAAG 59.994 40.000 12.16 0.00 38.05 1.85
2047 2123 5.233476 CGCCATATGCTTCGTAGTTTTAAGA 59.767 40.000 0.00 0.00 38.05 2.10
2125 2201 5.946942 TCAACAATATCTCAAGGAGCTCT 57.053 39.130 14.64 0.00 0.00 4.09
2170 2255 7.624549 TCATTAGTTTTGGAGCTCTTCTGTAT 58.375 34.615 14.64 0.00 0.00 2.29
2175 2260 3.998099 TGGAGCTCTTCTGTATGATCG 57.002 47.619 14.64 0.00 0.00 3.69
2210 2295 9.471084 AATTTTAGATTTGGTTAACGACTTTGG 57.529 29.630 0.00 0.00 0.00 3.28
2212 2297 3.886505 AGATTTGGTTAACGACTTTGGCA 59.113 39.130 0.00 0.00 0.00 4.92
2236 2321 8.787884 GCAAAGTCAACAATTTTTGAAATCAAC 58.212 29.630 8.56 0.00 37.24 3.18
2237 2322 9.276397 CAAAGTCAACAATTTTTGAAATCAACC 57.724 29.630 8.56 0.00 37.24 3.77
2243 2328 5.007528 ACAATTTTTGAAATCAACCGGCAAG 59.992 36.000 0.00 0.00 35.28 4.01
2247 2332 1.611491 TGAAATCAACCGGCAAGAACC 59.389 47.619 0.00 0.00 0.00 3.62
2269 2354 5.357032 ACCGGCCTATAAAAAGAGTGAATTG 59.643 40.000 0.00 0.00 0.00 2.32
2288 2373 1.272807 GTGCACCCTCTAACCACCTA 58.727 55.000 5.22 0.00 0.00 3.08
2289 2374 1.207329 GTGCACCCTCTAACCACCTAG 59.793 57.143 5.22 0.00 0.00 3.02
2322 2408 2.096762 CGCCAACATGTGATATGTAGCG 60.097 50.000 19.33 19.33 43.35 4.26
2331 2417 4.306600 TGTGATATGTAGCGCCAACATAG 58.693 43.478 27.22 0.00 41.71 2.23
2338 2424 1.299541 AGCGCCAACATAGTACATGC 58.700 50.000 2.29 0.00 0.00 4.06
2354 2440 4.937201 ACATGCTATCACCGACATAGAA 57.063 40.909 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.046604 TCGAAGCGTCTCCGGAGA 60.047 61.111 30.49 30.49 34.56 3.71
10 11 3.437795 GGTCGAAGCGTCTCCGGA 61.438 66.667 2.93 2.93 33.68 5.14
11 12 4.831307 CGGTCGAAGCGTCTCCGG 62.831 72.222 19.11 0.00 35.13 5.14
265 266 5.182190 ACAAATCCAATACACGTGCAATACA 59.818 36.000 17.22 0.00 0.00 2.29
266 267 5.511377 CACAAATCCAATACACGTGCAATAC 59.489 40.000 17.22 0.00 0.00 1.89
267 268 5.392487 CCACAAATCCAATACACGTGCAATA 60.392 40.000 17.22 0.36 0.00 1.90
268 269 4.484236 CACAAATCCAATACACGTGCAAT 58.516 39.130 17.22 6.83 0.00 3.56
269 270 3.304996 CCACAAATCCAATACACGTGCAA 60.305 43.478 17.22 4.26 0.00 4.08
270 271 2.227626 CCACAAATCCAATACACGTGCA 59.772 45.455 17.22 2.06 0.00 4.57
271 272 2.862512 CCACAAATCCAATACACGTGC 58.137 47.619 17.22 0.00 0.00 5.34
272 273 2.415357 GGCCACAAATCCAATACACGTG 60.415 50.000 15.48 15.48 0.00 4.49
273 274 1.816224 GGCCACAAATCCAATACACGT 59.184 47.619 0.00 0.00 0.00 4.49
274 275 1.134175 GGGCCACAAATCCAATACACG 59.866 52.381 4.39 0.00 0.00 4.49
275 276 2.094234 GTGGGCCACAAATCCAATACAC 60.094 50.000 31.26 0.00 34.08 2.90
276 277 2.175202 GTGGGCCACAAATCCAATACA 58.825 47.619 31.26 0.00 34.08 2.29
277 278 1.480545 GGTGGGCCACAAATCCAATAC 59.519 52.381 35.69 12.40 35.86 1.89
278 279 1.360852 AGGTGGGCCACAAATCCAATA 59.639 47.619 35.69 0.00 35.86 1.90
279 280 0.116940 AGGTGGGCCACAAATCCAAT 59.883 50.000 35.69 9.63 35.86 3.16
280 281 0.541764 GAGGTGGGCCACAAATCCAA 60.542 55.000 35.69 0.00 35.86 3.53
281 282 1.076549 GAGGTGGGCCACAAATCCA 59.923 57.895 35.69 0.00 35.86 3.41
282 283 1.682344 GGAGGTGGGCCACAAATCC 60.682 63.158 35.69 31.40 35.86 3.01
283 284 0.623723 TAGGAGGTGGGCCACAAATC 59.376 55.000 35.69 27.53 35.86 2.17
284 285 1.308877 ATAGGAGGTGGGCCACAAAT 58.691 50.000 35.69 21.94 35.86 2.32
285 286 1.005450 GAATAGGAGGTGGGCCACAAA 59.995 52.381 35.69 17.03 35.86 2.83
286 287 0.623723 GAATAGGAGGTGGGCCACAA 59.376 55.000 35.69 16.69 35.86 3.33
287 288 0.253160 AGAATAGGAGGTGGGCCACA 60.253 55.000 35.69 17.34 35.86 4.17
288 289 0.919710 AAGAATAGGAGGTGGGCCAC 59.080 55.000 28.69 28.69 37.19 5.01
289 290 0.918983 CAAGAATAGGAGGTGGGCCA 59.081 55.000 0.00 0.00 37.19 5.36
290 291 0.919710 ACAAGAATAGGAGGTGGGCC 59.080 55.000 0.00 0.00 0.00 5.80
291 292 4.593634 ACTATACAAGAATAGGAGGTGGGC 59.406 45.833 0.00 0.00 34.34 5.36
292 293 6.326583 TCAACTATACAAGAATAGGAGGTGGG 59.673 42.308 0.00 0.00 34.34 4.61
293 294 7.361457 TCAACTATACAAGAATAGGAGGTGG 57.639 40.000 0.00 0.00 34.34 4.61
294 295 7.070074 ACCTCAACTATACAAGAATAGGAGGTG 59.930 40.741 15.31 0.00 42.91 4.00
295 296 7.133483 ACCTCAACTATACAAGAATAGGAGGT 58.867 38.462 12.39 12.39 41.46 3.85
296 297 7.604657 ACCTCAACTATACAAGAATAGGAGG 57.395 40.000 0.00 0.00 40.36 4.30
297 298 9.575868 TCTACCTCAACTATACAAGAATAGGAG 57.424 37.037 0.00 0.00 34.34 3.69
298 299 9.575868 CTCTACCTCAACTATACAAGAATAGGA 57.424 37.037 0.00 0.00 34.34 2.94
299 300 8.798402 CCTCTACCTCAACTATACAAGAATAGG 58.202 40.741 0.00 0.00 34.34 2.57
300 301 8.301002 GCCTCTACCTCAACTATACAAGAATAG 58.699 40.741 0.00 0.00 35.86 1.73
301 302 7.232941 GGCCTCTACCTCAACTATACAAGAATA 59.767 40.741 0.00 0.00 0.00 1.75
302 303 6.042208 GGCCTCTACCTCAACTATACAAGAAT 59.958 42.308 0.00 0.00 0.00 2.40
303 304 5.363005 GGCCTCTACCTCAACTATACAAGAA 59.637 44.000 0.00 0.00 0.00 2.52
304 305 4.894114 GGCCTCTACCTCAACTATACAAGA 59.106 45.833 0.00 0.00 0.00 3.02
305 306 4.896482 AGGCCTCTACCTCAACTATACAAG 59.104 45.833 0.00 0.00 33.62 3.16
306 307 4.880164 AGGCCTCTACCTCAACTATACAA 58.120 43.478 0.00 0.00 33.62 2.41
307 308 4.537945 AGGCCTCTACCTCAACTATACA 57.462 45.455 0.00 0.00 33.62 2.29
308 309 4.281435 GGAAGGCCTCTACCTCAACTATAC 59.719 50.000 5.23 0.00 39.93 1.47
309 310 4.481072 GGAAGGCCTCTACCTCAACTATA 58.519 47.826 5.23 0.00 39.93 1.31
310 311 3.310193 GGAAGGCCTCTACCTCAACTAT 58.690 50.000 5.23 0.00 39.93 2.12
311 312 2.626149 GGGAAGGCCTCTACCTCAACTA 60.626 54.545 5.23 0.00 39.93 2.24
312 313 1.574263 GGAAGGCCTCTACCTCAACT 58.426 55.000 5.23 0.00 39.93 3.16
313 314 0.542333 GGGAAGGCCTCTACCTCAAC 59.458 60.000 5.23 0.00 39.93 3.18
314 315 0.417841 AGGGAAGGCCTCTACCTCAA 59.582 55.000 5.23 0.00 39.93 3.02
315 316 0.417841 AAGGGAAGGCCTCTACCTCA 59.582 55.000 19.66 0.00 39.93 3.86
316 317 0.833949 CAAGGGAAGGCCTCTACCTC 59.166 60.000 19.66 7.95 39.93 3.85
317 318 0.119358 ACAAGGGAAGGCCTCTACCT 59.881 55.000 5.23 11.73 43.91 3.08
318 319 1.875488 TACAAGGGAAGGCCTCTACC 58.125 55.000 5.23 9.20 0.00 3.18
319 320 5.827326 ATAATACAAGGGAAGGCCTCTAC 57.173 43.478 5.23 0.03 0.00 2.59
321 322 9.214962 GTATATATAATACAAGGGAAGGCCTCT 57.785 37.037 5.23 0.00 0.00 3.69
322 323 8.142551 CGTATATATAATACAAGGGAAGGCCTC 58.857 40.741 5.23 0.00 0.00 4.70
323 324 7.622479 ACGTATATATAATACAAGGGAAGGCCT 59.378 37.037 0.00 0.00 0.00 5.19
324 325 7.709613 CACGTATATATAATACAAGGGAAGGCC 59.290 40.741 0.00 0.00 0.00 5.19
325 326 7.224167 GCACGTATATATAATACAAGGGAAGGC 59.776 40.741 0.00 0.00 0.00 4.35
326 327 8.255206 TGCACGTATATATAATACAAGGGAAGG 58.745 37.037 0.00 0.00 0.00 3.46
327 328 9.084164 GTGCACGTATATATAATACAAGGGAAG 57.916 37.037 0.00 0.00 0.00 3.46
328 329 8.036575 GGTGCACGTATATATAATACAAGGGAA 58.963 37.037 11.45 0.00 0.00 3.97
329 330 7.178805 TGGTGCACGTATATATAATACAAGGGA 59.821 37.037 11.45 0.00 0.00 4.20
330 331 7.324935 TGGTGCACGTATATATAATACAAGGG 58.675 38.462 11.45 0.00 0.00 3.95
331 332 7.010183 GCTGGTGCACGTATATATAATACAAGG 59.990 40.741 11.45 0.00 39.41 3.61
332 333 7.544217 TGCTGGTGCACGTATATATAATACAAG 59.456 37.037 11.45 0.00 45.31 3.16
333 334 7.379750 TGCTGGTGCACGTATATATAATACAA 58.620 34.615 11.45 0.00 45.31 2.41
334 335 6.926313 TGCTGGTGCACGTATATATAATACA 58.074 36.000 11.45 0.00 45.31 2.29
350 351 0.395586 TATTGATGGGGTGCTGGTGC 60.396 55.000 0.00 0.00 40.20 5.01
351 352 1.340893 TGTATTGATGGGGTGCTGGTG 60.341 52.381 0.00 0.00 0.00 4.17
352 353 0.998928 TGTATTGATGGGGTGCTGGT 59.001 50.000 0.00 0.00 0.00 4.00
353 354 1.750778 GTTGTATTGATGGGGTGCTGG 59.249 52.381 0.00 0.00 0.00 4.85
354 355 2.445427 TGTTGTATTGATGGGGTGCTG 58.555 47.619 0.00 0.00 0.00 4.41
355 356 2.897271 TGTTGTATTGATGGGGTGCT 57.103 45.000 0.00 0.00 0.00 4.40
356 357 3.290710 AGATGTTGTATTGATGGGGTGC 58.709 45.455 0.00 0.00 0.00 5.01
357 358 6.547141 ACAATAGATGTTGTATTGATGGGGTG 59.453 38.462 10.34 0.00 40.06 4.61
358 359 6.672593 ACAATAGATGTTGTATTGATGGGGT 58.327 36.000 10.34 0.00 40.06 4.95
369 370 9.762933 AAAAGTTTGCAATACAATAGATGTTGT 57.237 25.926 0.00 0.60 43.63 3.32
371 372 9.423061 GGAAAAGTTTGCAATACAATAGATGTT 57.577 29.630 0.00 0.00 43.63 2.71
372 373 7.754924 CGGAAAAGTTTGCAATACAATAGATGT 59.245 33.333 0.00 0.00 46.36 3.06
373 374 7.754924 ACGGAAAAGTTTGCAATACAATAGATG 59.245 33.333 0.00 0.00 38.31 2.90
374 375 7.826690 ACGGAAAAGTTTGCAATACAATAGAT 58.173 30.769 0.00 0.00 38.31 1.98
375 376 7.174253 AGACGGAAAAGTTTGCAATACAATAGA 59.826 33.333 0.00 0.00 38.31 1.98
376 377 7.305474 AGACGGAAAAGTTTGCAATACAATAG 58.695 34.615 0.00 0.00 38.31 1.73
377 378 7.209471 AGACGGAAAAGTTTGCAATACAATA 57.791 32.000 0.00 0.00 38.31 1.90
378 379 6.084326 AGACGGAAAAGTTTGCAATACAAT 57.916 33.333 0.00 0.00 38.31 2.71
379 380 5.508200 AGACGGAAAAGTTTGCAATACAA 57.492 34.783 0.00 0.00 36.13 2.41
380 381 5.527951 TGTAGACGGAAAAGTTTGCAATACA 59.472 36.000 0.00 0.00 0.00 2.29
381 382 5.992729 TGTAGACGGAAAAGTTTGCAATAC 58.007 37.500 0.00 1.64 0.00 1.89
382 383 5.761234 ACTGTAGACGGAAAAGTTTGCAATA 59.239 36.000 0.00 0.00 0.00 1.90
383 384 4.578928 ACTGTAGACGGAAAAGTTTGCAAT 59.421 37.500 0.00 0.00 0.00 3.56
384 385 3.942748 ACTGTAGACGGAAAAGTTTGCAA 59.057 39.130 0.00 0.00 0.00 4.08
385 386 3.537580 ACTGTAGACGGAAAAGTTTGCA 58.462 40.909 0.00 0.00 0.00 4.08
386 387 5.407387 TGATACTGTAGACGGAAAAGTTTGC 59.593 40.000 0.00 0.00 0.00 3.68
387 388 7.117812 ACATGATACTGTAGACGGAAAAGTTTG 59.882 37.037 0.00 0.00 0.00 2.93
388 389 7.117812 CACATGATACTGTAGACGGAAAAGTTT 59.882 37.037 0.00 0.00 0.00 2.66
389 390 6.590292 CACATGATACTGTAGACGGAAAAGTT 59.410 38.462 0.00 0.00 0.00 2.66
390 391 6.100004 CACATGATACTGTAGACGGAAAAGT 58.900 40.000 0.00 0.00 0.00 2.66
391 392 6.100004 ACACATGATACTGTAGACGGAAAAG 58.900 40.000 0.00 0.00 0.00 2.27
392 393 6.032956 ACACATGATACTGTAGACGGAAAA 57.967 37.500 0.00 0.00 0.00 2.29
393 394 5.654603 ACACATGATACTGTAGACGGAAA 57.345 39.130 0.00 0.00 0.00 3.13
394 395 5.220989 GCTACACATGATACTGTAGACGGAA 60.221 44.000 19.90 0.00 41.65 4.30
395 396 4.275196 GCTACACATGATACTGTAGACGGA 59.725 45.833 19.90 0.00 41.65 4.69
396 397 4.537965 GCTACACATGATACTGTAGACGG 58.462 47.826 19.90 1.31 41.65 4.79
397 398 4.537965 GGCTACACATGATACTGTAGACG 58.462 47.826 19.90 1.59 41.65 4.18
398 399 5.533154 AGAGGCTACACATGATACTGTAGAC 59.467 44.000 19.90 17.94 45.86 2.59
399 400 5.696030 AGAGGCTACACATGATACTGTAGA 58.304 41.667 19.90 0.00 41.65 2.59
400 401 6.264292 AGAAGAGGCTACACATGATACTGTAG 59.736 42.308 14.02 14.02 41.91 2.74
401 402 6.129874 AGAAGAGGCTACACATGATACTGTA 58.870 40.000 0.00 0.00 0.00 2.74
402 403 4.959210 AGAAGAGGCTACACATGATACTGT 59.041 41.667 0.00 0.00 0.00 3.55
403 404 5.528043 AGAAGAGGCTACACATGATACTG 57.472 43.478 0.00 0.00 0.00 2.74
404 405 6.129874 TGTAGAAGAGGCTACACATGATACT 58.870 40.000 0.00 0.00 44.15 2.12
405 406 6.039941 ACTGTAGAAGAGGCTACACATGATAC 59.960 42.308 0.00 0.00 44.15 2.24
406 407 6.129874 ACTGTAGAAGAGGCTACACATGATA 58.870 40.000 0.00 0.00 44.15 2.15
407 408 4.959210 ACTGTAGAAGAGGCTACACATGAT 59.041 41.667 0.00 0.00 44.15 2.45
408 409 4.344978 ACTGTAGAAGAGGCTACACATGA 58.655 43.478 0.00 0.00 44.15 3.07
409 410 4.727507 ACTGTAGAAGAGGCTACACATG 57.272 45.455 0.00 0.00 44.15 3.21
410 411 6.129874 TGATACTGTAGAAGAGGCTACACAT 58.870 40.000 0.00 0.00 44.15 3.21
411 412 5.506708 TGATACTGTAGAAGAGGCTACACA 58.493 41.667 0.00 0.00 44.15 3.72
412 413 6.039941 ACATGATACTGTAGAAGAGGCTACAC 59.960 42.308 0.00 0.00 44.15 2.90
413 414 6.039829 CACATGATACTGTAGAAGAGGCTACA 59.960 42.308 0.00 0.00 46.14 2.74
414 415 6.039941 ACACATGATACTGTAGAAGAGGCTAC 59.960 42.308 0.00 0.00 40.85 3.58
415 416 6.129874 ACACATGATACTGTAGAAGAGGCTA 58.870 40.000 0.00 0.00 0.00 3.93
416 417 4.959210 ACACATGATACTGTAGAAGAGGCT 59.041 41.667 0.00 0.00 0.00 4.58
417 418 5.269505 ACACATGATACTGTAGAAGAGGC 57.730 43.478 0.00 0.00 0.00 4.70
418 419 6.442952 GCTACACATGATACTGTAGAAGAGG 58.557 44.000 19.90 0.46 41.65 3.69
419 420 6.264292 AGGCTACACATGATACTGTAGAAGAG 59.736 42.308 19.90 2.25 41.65 2.85
420 421 6.129874 AGGCTACACATGATACTGTAGAAGA 58.870 40.000 19.90 0.00 41.65 2.87
421 422 6.398234 AGGCTACACATGATACTGTAGAAG 57.602 41.667 19.90 2.84 41.65 2.85
422 423 5.008712 CGAGGCTACACATGATACTGTAGAA 59.991 44.000 19.90 0.00 41.65 2.10
423 424 4.515567 CGAGGCTACACATGATACTGTAGA 59.484 45.833 19.90 0.00 41.65 2.59
424 425 4.276183 ACGAGGCTACACATGATACTGTAG 59.724 45.833 14.02 14.02 41.91 2.74
425 426 4.204799 ACGAGGCTACACATGATACTGTA 58.795 43.478 0.00 0.00 0.00 2.74
426 427 3.024547 ACGAGGCTACACATGATACTGT 58.975 45.455 0.00 0.00 0.00 3.55
427 428 3.316588 AGACGAGGCTACACATGATACTG 59.683 47.826 0.00 0.00 0.00 2.74
428 429 3.316588 CAGACGAGGCTACACATGATACT 59.683 47.826 0.00 0.00 0.00 2.12
429 430 3.066900 ACAGACGAGGCTACACATGATAC 59.933 47.826 0.00 0.00 0.00 2.24
430 431 3.288092 ACAGACGAGGCTACACATGATA 58.712 45.455 0.00 0.00 0.00 2.15
431 432 2.103373 ACAGACGAGGCTACACATGAT 58.897 47.619 0.00 0.00 0.00 2.45
432 433 1.545841 ACAGACGAGGCTACACATGA 58.454 50.000 0.00 0.00 0.00 3.07
433 434 2.370281 AACAGACGAGGCTACACATG 57.630 50.000 0.00 0.00 0.00 3.21
434 435 2.563179 AGAAACAGACGAGGCTACACAT 59.437 45.455 0.00 0.00 0.00 3.21
435 436 1.961394 AGAAACAGACGAGGCTACACA 59.039 47.619 0.00 0.00 0.00 3.72
436 437 2.726832 AGAAACAGACGAGGCTACAC 57.273 50.000 0.00 0.00 0.00 2.90
437 438 2.626266 TGAAGAAACAGACGAGGCTACA 59.374 45.455 0.00 0.00 0.00 2.74
438 439 3.299340 TGAAGAAACAGACGAGGCTAC 57.701 47.619 0.00 0.00 0.00 3.58
439 440 3.650139 GTTGAAGAAACAGACGAGGCTA 58.350 45.455 0.00 0.00 38.75 3.93
450 451 1.002792 GGACACAGCCGTTGAAGAAAC 60.003 52.381 0.00 0.00 35.25 2.78
458 459 0.532862 CAACTGAGGACACAGCCGTT 60.533 55.000 0.00 0.00 41.06 4.44
572 573 2.751436 CTCACCCCGCCATTGTGG 60.751 66.667 0.00 0.00 41.55 4.17
573 574 3.443045 GCTCACCCCGCCATTGTG 61.443 66.667 0.00 0.00 0.00 3.33
758 760 1.402968 CCCAGCAAGATCGAAACCATG 59.597 52.381 0.00 0.00 0.00 3.66
860 883 1.074926 ATGGAGAGGAGATGCGGGT 60.075 57.895 0.00 0.00 0.00 5.28
936 962 0.441145 GTCGGTTTGTCGGTATGCAC 59.559 55.000 0.00 0.00 0.00 4.57
941 967 1.172180 AGTCGGTCGGTTTGTCGGTA 61.172 55.000 0.00 0.00 0.00 4.02
981 1009 1.080705 GTCAGTCTTCCGTCCGGTG 60.081 63.158 0.00 0.00 36.47 4.94
989 1017 1.457346 CCTTGCCATGTCAGTCTTCC 58.543 55.000 0.00 0.00 0.00 3.46
1394 1435 0.179034 GCAAGATCCACCAGGCCTAG 60.179 60.000 3.98 0.00 33.74 3.02
1492 1546 1.630148 GGCGTTCTACTAGCACACAG 58.370 55.000 0.00 0.00 0.00 3.66
1496 1550 0.801067 CACGGGCGTTCTACTAGCAC 60.801 60.000 0.00 0.00 0.00 4.40
1498 1552 1.877165 GCACGGGCGTTCTACTAGC 60.877 63.158 0.00 0.00 0.00 3.42
1499 1553 0.102481 ATGCACGGGCGTTCTACTAG 59.898 55.000 4.58 0.00 45.35 2.57
1500 1554 0.533491 AATGCACGGGCGTTCTACTA 59.467 50.000 12.34 0.00 46.01 1.82
1501 1555 1.019278 CAATGCACGGGCGTTCTACT 61.019 55.000 15.71 0.00 46.01 2.57
1688 1757 2.886523 TCTTTAAAGTCCACGACTCCGA 59.113 45.455 14.74 0.00 42.59 4.55
1690 1759 4.685165 GTCTTCTTTAAAGTCCACGACTCC 59.315 45.833 14.74 0.00 42.59 3.85
1716 1785 4.401519 CCTTTCCATCAATGCTCATGTTCT 59.598 41.667 0.00 0.00 0.00 3.01
1834 1905 4.647964 CAGTCGTTAAATTGGTTGGATCG 58.352 43.478 0.00 0.00 0.00 3.69
1884 1957 4.163078 AGGAACAGGATGGACACATAGAAG 59.837 45.833 0.00 0.00 43.62 2.85
1900 1976 1.066605 GCATGGCAATAGCAGGAACAG 59.933 52.381 0.00 0.00 44.61 3.16
1906 1982 3.886044 CCATGCATGGCAATAGCAG 57.114 52.632 31.95 6.10 43.62 4.24
1969 2045 3.985279 GCCACGTCCAAAAATAAAAGTCC 59.015 43.478 0.00 0.00 0.00 3.85
1972 2048 4.857037 GCTAGCCACGTCCAAAAATAAAAG 59.143 41.667 2.29 0.00 0.00 2.27
1991 2067 3.170810 GAGGACGGACGCTCGCTAG 62.171 68.421 0.00 0.00 0.00 3.42
2024 2100 6.258068 AGTCTTAAAACTACGAAGCATATGGC 59.742 38.462 4.56 0.00 45.30 4.40
2025 2101 7.491372 TGAGTCTTAAAACTACGAAGCATATGG 59.509 37.037 4.56 0.00 0.00 2.74
2026 2102 8.321716 GTGAGTCTTAAAACTACGAAGCATATG 58.678 37.037 0.00 0.00 0.00 1.78
2027 2103 8.033038 TGTGAGTCTTAAAACTACGAAGCATAT 58.967 33.333 0.00 0.00 0.00 1.78
2028 2104 7.372714 TGTGAGTCTTAAAACTACGAAGCATA 58.627 34.615 0.00 0.00 0.00 3.14
2029 2105 6.220930 TGTGAGTCTTAAAACTACGAAGCAT 58.779 36.000 0.00 0.00 0.00 3.79
2030 2106 5.593968 TGTGAGTCTTAAAACTACGAAGCA 58.406 37.500 0.00 0.00 0.00 3.91
2080 2156 9.992910 TTGATCTGATTAAAATTGAATGACTCG 57.007 29.630 0.00 0.00 0.00 4.18
2096 2172 7.444792 GCTCCTTGAGATATTGTTGATCTGATT 59.555 37.037 0.00 0.00 33.71 2.57
2100 2176 6.327104 AGAGCTCCTTGAGATATTGTTGATCT 59.673 38.462 10.93 0.00 36.33 2.75
2113 2189 7.274447 AGAATTAAATGAGAGAGCTCCTTGAG 58.726 38.462 10.93 0.00 40.55 3.02
2115 2191 7.862512 AAGAATTAAATGAGAGAGCTCCTTG 57.137 36.000 10.93 0.00 40.55 3.61
2148 2224 7.004555 TCATACAGAAGAGCTCCAAAACTAA 57.995 36.000 10.93 0.00 0.00 2.24
2151 2227 5.006165 CGATCATACAGAAGAGCTCCAAAAC 59.994 44.000 10.93 0.00 0.00 2.43
2190 2275 3.886505 TGCCAAAGTCGTTAACCAAATCT 59.113 39.130 0.00 0.00 0.00 2.40
2191 2276 4.231718 TGCCAAAGTCGTTAACCAAATC 57.768 40.909 0.00 0.00 0.00 2.17
2209 2294 7.470900 TGATTTCAAAAATTGTTGACTTTGCC 58.529 30.769 10.70 0.00 37.24 4.52
2210 2295 8.787884 GTTGATTTCAAAAATTGTTGACTTTGC 58.212 29.630 10.70 0.77 37.24 3.68
2212 2297 8.174422 CGGTTGATTTCAAAAATTGTTGACTTT 58.826 29.630 10.70 0.00 37.24 2.66
2243 2328 4.510571 TCACTCTTTTTATAGGCCGGTTC 58.489 43.478 1.90 0.00 0.00 3.62
2247 2332 6.258160 CACAATTCACTCTTTTTATAGGCCG 58.742 40.000 0.00 0.00 0.00 6.13
2252 2337 6.719370 AGGGTGCACAATTCACTCTTTTTATA 59.281 34.615 20.43 0.00 42.21 0.98
2269 2354 1.207329 CTAGGTGGTTAGAGGGTGCAC 59.793 57.143 8.80 8.80 0.00 4.57
2322 2408 4.452455 GGTGATAGCATGTACTATGTTGGC 59.548 45.833 0.00 0.00 32.95 4.52
2331 2417 5.372547 TCTATGTCGGTGATAGCATGTAC 57.627 43.478 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.