Multiple sequence alignment - TraesCS4A01G080400

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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 TraesCS4A01G080400 chr4A 100.000 2396 0 0 1 2396 83313484 83311089 0.000000e+00 4425.0
1 TraesCS4A01G080400 chr4B 90.646 1208 67 26 508 1686 468000806 468001996 0.000000e+00 1563.0
2 TraesCS4A01G080400 chr4B 91.509 530 27 8 1872 2396 468002104 468002620 0.000000e+00 713.0
3 TraesCS4A01G080400 chr4B 90.079 252 24 1 10 260 468000557 468000808 2.300000e-85 326.0
4 TraesCS4A01G080400 chr4B 96.429 56 2 0 1783 1838 468002052 468002107 2.540000e-15 93.5
5 TraesCS4A01G080400 chr4D 89.272 1277 55 42 508 1757 380531434 380532655 0.000000e+00 1524.0
6 TraesCS4A01G080400 chr4D 89.968 628 37 18 1784 2396 380532660 380533276 0.000000e+00 787.0
7 TraesCS4A01G080400 chr4D 90.270 185 13 3 1 183 380531214 380531395 1.110000e-58 237.0
8 TraesCS4A01G080400 chr7A 89.542 153 16 0 257 409 348087503 348087351 6.760000e-46 195.0
9 TraesCS4A01G080400 chr6D 88.312 154 17 1 257 409 62112907 62112754 1.460000e-42 183.0
10 TraesCS4A01G080400 chr1B 87.117 163 18 3 253 414 66929112 66928952 5.260000e-42 182.0
11 TraesCS4A01G080400 chr5A 88.235 153 15 3 258 410 463596460 463596609 1.890000e-41 180.0
12 TraesCS4A01G080400 chr5B 87.582 153 19 0 257 409 478753099 478753251 6.810000e-41 178.0
13 TraesCS4A01G080400 chr2B 87.919 149 18 0 260 408 230216432 230216580 2.450000e-40 176.0
14 TraesCS4A01G080400 chr2B 87.333 150 19 0 260 409 465655112 465655261 3.170000e-39 172.0
15 TraesCS4A01G080400 chr7B 86.928 153 20 0 257 409 60241494 60241646 3.170000e-39 172.0
16 TraesCS4A01G080400 chr6B 86.842 152 18 2 258 409 57239838 57239987 4.100000e-38 169.0
17 TraesCS4A01G080400 chr3D 88.333 60 3 3 421 478 613599639 613599696 4.270000e-08 69.4


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 TraesCS4A01G080400 chr4A 83311089 83313484 2395 True 4425.000000 4425 100.000000 1 2396 1 chr4A.!!$R1 2395
1 TraesCS4A01G080400 chr4B 468000557 468002620 2063 False 673.875000 1563 92.165750 10 2396 4 chr4B.!!$F1 2386
2 TraesCS4A01G080400 chr4D 380531214 380533276 2062 False 849.333333 1524 89.836667 1 2396 3 chr4D.!!$F1 2395

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
849 876 0.032678 CCAATCCATCCGTCTCCTCG 59.967 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 2272 0.036671 CCCGAGTACAGTTTCCCACC 60.037 60.0 0.0 0.0 0.0 4.61 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
20 21 2.200373 ACACAATCTGGGCTACAACC 57.800 50.000 0.00 0.00 0.00 3.77
65 66 2.541556 GGCGGTCAGTCTAATCACTTC 58.458 52.381 0.00 0.00 0.00 3.01
125 128 3.243501 CCTGAATTATTGGCCGTGGAATG 60.244 47.826 0.00 0.00 0.00 2.67
128 131 4.278170 TGAATTATTGGCCGTGGAATGATC 59.722 41.667 0.00 0.00 0.00 2.92
186 189 8.571461 TCACTTTTAGATTCCGACTAGACTAA 57.429 34.615 0.00 0.00 0.00 2.24
222 225 4.142004 ACCATTCTATGTACCGTCACCTTC 60.142 45.833 0.00 0.00 0.00 3.46
225 228 3.959293 TCTATGTACCGTCACCTTCTCA 58.041 45.455 0.00 0.00 0.00 3.27
228 231 2.313317 TGTACCGTCACCTTCTCACTT 58.687 47.619 0.00 0.00 0.00 3.16
234 237 2.483013 CGTCACCTTCTCACTTCACCAA 60.483 50.000 0.00 0.00 0.00 3.67
237 240 3.964688 TCACCTTCTCACTTCACCAAGTA 59.035 43.478 0.00 0.00 41.24 2.24
248 251 3.719268 TCACCAAGTATGTGGCTTCAT 57.281 42.857 0.00 0.00 43.00 2.57
257 260 5.938279 AGTATGTGGCTTCATCTCATCAAT 58.062 37.500 0.00 0.00 0.00 2.57
258 261 6.363065 AGTATGTGGCTTCATCTCATCAATT 58.637 36.000 0.00 0.00 0.00 2.32
259 262 7.512130 AGTATGTGGCTTCATCTCATCAATTA 58.488 34.615 0.00 0.00 0.00 1.40
260 263 6.879276 ATGTGGCTTCATCTCATCAATTAG 57.121 37.500 0.00 0.00 0.00 1.73
261 264 5.128205 TGTGGCTTCATCTCATCAATTAGG 58.872 41.667 0.00 0.00 0.00 2.69
262 265 4.518211 GTGGCTTCATCTCATCAATTAGGG 59.482 45.833 0.00 0.00 0.00 3.53
263 266 3.505293 GGCTTCATCTCATCAATTAGGGC 59.495 47.826 0.00 0.00 0.00 5.19
264 267 4.139786 GCTTCATCTCATCAATTAGGGCA 58.860 43.478 0.00 0.00 0.00 5.36
265 268 4.765856 GCTTCATCTCATCAATTAGGGCAT 59.234 41.667 0.00 0.00 0.00 4.40
266 269 5.335740 GCTTCATCTCATCAATTAGGGCATG 60.336 44.000 0.00 0.00 0.00 4.06
267 270 5.314718 TCATCTCATCAATTAGGGCATGT 57.685 39.130 0.00 0.00 0.00 3.21
268 271 6.438186 TCATCTCATCAATTAGGGCATGTA 57.562 37.500 0.00 0.00 0.00 2.29
269 272 6.233434 TCATCTCATCAATTAGGGCATGTAC 58.767 40.000 0.00 0.00 0.00 2.90
270 273 5.628797 TCTCATCAATTAGGGCATGTACA 57.371 39.130 0.00 0.00 0.00 2.90
271 274 6.000246 TCTCATCAATTAGGGCATGTACAA 58.000 37.500 0.00 0.00 0.00 2.41
272 275 6.604171 TCTCATCAATTAGGGCATGTACAAT 58.396 36.000 0.00 0.00 0.00 2.71
273 276 7.744733 TCTCATCAATTAGGGCATGTACAATA 58.255 34.615 0.00 0.00 0.00 1.90
274 277 7.879677 TCTCATCAATTAGGGCATGTACAATAG 59.120 37.037 0.00 0.00 0.00 1.73
275 278 7.517320 TCATCAATTAGGGCATGTACAATAGT 58.483 34.615 0.00 0.00 0.00 2.12
276 279 7.445096 TCATCAATTAGGGCATGTACAATAGTG 59.555 37.037 0.00 0.00 0.00 2.74
277 280 6.894682 TCAATTAGGGCATGTACAATAGTGA 58.105 36.000 0.00 0.00 0.00 3.41
278 281 6.765989 TCAATTAGGGCATGTACAATAGTGAC 59.234 38.462 0.00 0.00 0.00 3.67
279 282 5.685520 TTAGGGCATGTACAATAGTGACA 57.314 39.130 0.00 0.00 0.00 3.58
280 283 4.778213 AGGGCATGTACAATAGTGACAT 57.222 40.909 0.00 0.00 34.11 3.06
281 284 5.887214 AGGGCATGTACAATAGTGACATA 57.113 39.130 0.00 0.00 32.58 2.29
282 285 6.439636 AGGGCATGTACAATAGTGACATAT 57.560 37.500 0.00 0.00 32.58 1.78
283 286 6.233434 AGGGCATGTACAATAGTGACATATG 58.767 40.000 0.00 0.00 32.58 1.78
284 287 6.043127 AGGGCATGTACAATAGTGACATATGA 59.957 38.462 10.38 0.00 32.58 2.15
285 288 6.710295 GGGCATGTACAATAGTGACATATGAA 59.290 38.462 10.38 0.00 32.58 2.57
286 289 7.391554 GGGCATGTACAATAGTGACATATGAAT 59.608 37.037 10.38 0.00 32.58 2.57
287 290 9.435688 GGCATGTACAATAGTGACATATGAATA 57.564 33.333 10.38 0.00 32.58 1.75
294 297 8.777413 ACAATAGTGACATATGAATACACATGC 58.223 33.333 10.38 0.00 34.66 4.06
295 298 7.912056 ATAGTGACATATGAATACACATGCC 57.088 36.000 10.38 0.00 34.66 4.40
296 299 5.933617 AGTGACATATGAATACACATGCCT 58.066 37.500 10.38 0.00 34.66 4.75
297 300 5.994054 AGTGACATATGAATACACATGCCTC 59.006 40.000 10.38 0.00 34.66 4.70
298 301 5.759763 GTGACATATGAATACACATGCCTCA 59.240 40.000 10.38 0.00 34.66 3.86
299 302 6.429078 GTGACATATGAATACACATGCCTCAT 59.571 38.462 10.38 0.00 34.66 2.90
300 303 7.603784 GTGACATATGAATACACATGCCTCATA 59.396 37.037 10.38 0.00 34.66 2.15
301 304 8.156165 TGACATATGAATACACATGCCTCATAA 58.844 33.333 10.38 0.00 34.66 1.90
302 305 8.327941 ACATATGAATACACATGCCTCATAAC 57.672 34.615 10.38 0.00 34.66 1.89
303 306 7.938490 ACATATGAATACACATGCCTCATAACA 59.062 33.333 10.38 0.00 34.66 2.41
304 307 8.785946 CATATGAATACACATGCCTCATAACAA 58.214 33.333 0.00 0.00 33.83 2.83
305 308 7.643569 ATGAATACACATGCCTCATAACAAA 57.356 32.000 0.00 0.00 0.00 2.83
306 309 7.459795 TGAATACACATGCCTCATAACAAAA 57.540 32.000 0.00 0.00 0.00 2.44
307 310 7.890515 TGAATACACATGCCTCATAACAAAAA 58.109 30.769 0.00 0.00 0.00 1.94
355 358 5.824904 TTTTCTCCTCAATGCAAGCTATC 57.175 39.130 0.00 0.00 0.00 2.08
356 359 4.492494 TTCTCCTCAATGCAAGCTATCA 57.508 40.909 0.00 0.00 0.00 2.15
357 360 4.701651 TCTCCTCAATGCAAGCTATCAT 57.298 40.909 0.00 0.00 0.00 2.45
358 361 5.045012 TCTCCTCAATGCAAGCTATCATT 57.955 39.130 7.35 7.35 33.56 2.57
359 362 6.178607 TCTCCTCAATGCAAGCTATCATTA 57.821 37.500 11.56 0.00 32.22 1.90
360 363 6.228995 TCTCCTCAATGCAAGCTATCATTAG 58.771 40.000 11.56 7.26 32.22 1.73
361 364 5.933617 TCCTCAATGCAAGCTATCATTAGT 58.066 37.500 11.56 0.00 32.22 2.24
362 365 5.761726 TCCTCAATGCAAGCTATCATTAGTG 59.238 40.000 11.56 3.54 32.22 2.74
363 366 5.048921 CCTCAATGCAAGCTATCATTAGTGG 60.049 44.000 11.56 11.71 32.22 4.00
364 367 4.823442 TCAATGCAAGCTATCATTAGTGGG 59.177 41.667 11.56 2.45 32.22 4.61
365 368 2.575532 TGCAAGCTATCATTAGTGGGC 58.424 47.619 0.00 0.00 0.00 5.36
366 369 1.882623 GCAAGCTATCATTAGTGGGCC 59.117 52.381 0.00 0.00 0.00 5.80
367 370 2.487986 GCAAGCTATCATTAGTGGGCCT 60.488 50.000 4.53 0.00 0.00 5.19
368 371 3.406764 CAAGCTATCATTAGTGGGCCTC 58.593 50.000 4.53 0.00 0.00 4.70
369 372 2.694397 AGCTATCATTAGTGGGCCTCA 58.306 47.619 4.53 0.00 0.00 3.86
370 373 3.254960 AGCTATCATTAGTGGGCCTCAT 58.745 45.455 4.53 0.00 0.00 2.90
371 374 3.262915 AGCTATCATTAGTGGGCCTCATC 59.737 47.826 4.53 0.00 0.00 2.92
372 375 3.008375 GCTATCATTAGTGGGCCTCATCA 59.992 47.826 4.53 0.00 0.00 3.07
373 376 4.505566 GCTATCATTAGTGGGCCTCATCAA 60.506 45.833 4.53 0.00 0.00 2.57
374 377 4.736611 ATCATTAGTGGGCCTCATCAAT 57.263 40.909 4.53 0.00 0.00 2.57
375 378 5.848286 ATCATTAGTGGGCCTCATCAATA 57.152 39.130 4.53 0.00 0.00 1.90
376 379 5.645056 TCATTAGTGGGCCTCATCAATAA 57.355 39.130 4.53 2.07 0.00 1.40
377 380 6.012337 TCATTAGTGGGCCTCATCAATAAA 57.988 37.500 4.53 0.00 29.38 1.40
378 381 6.613699 TCATTAGTGGGCCTCATCAATAAAT 58.386 36.000 4.53 0.00 29.38 1.40
379 382 7.754624 TCATTAGTGGGCCTCATCAATAAATA 58.245 34.615 4.53 0.00 29.38 1.40
380 383 7.884877 TCATTAGTGGGCCTCATCAATAAATAG 59.115 37.037 4.53 0.00 29.38 1.73
381 384 5.912149 AGTGGGCCTCATCAATAAATAGA 57.088 39.130 4.53 0.00 0.00 1.98
382 385 6.266131 AGTGGGCCTCATCAATAAATAGAA 57.734 37.500 4.53 0.00 0.00 2.10
383 386 6.672593 AGTGGGCCTCATCAATAAATAGAAA 58.327 36.000 4.53 0.00 0.00 2.52
384 387 7.125391 AGTGGGCCTCATCAATAAATAGAAAA 58.875 34.615 4.53 0.00 0.00 2.29
385 388 7.786464 AGTGGGCCTCATCAATAAATAGAAAAT 59.214 33.333 4.53 0.00 0.00 1.82
386 389 9.077885 GTGGGCCTCATCAATAAATAGAAAATA 57.922 33.333 4.53 0.00 0.00 1.40
387 390 9.653516 TGGGCCTCATCAATAAATAGAAAATAA 57.346 29.630 4.53 0.00 0.00 1.40
410 413 5.888691 AGACTCTAGTACATATGCATCCG 57.111 43.478 0.19 0.00 0.00 4.18
411 414 5.317808 AGACTCTAGTACATATGCATCCGT 58.682 41.667 0.19 4.08 0.00 4.69
412 415 5.413213 AGACTCTAGTACATATGCATCCGTC 59.587 44.000 0.19 1.88 0.00 4.79
413 416 5.317808 ACTCTAGTACATATGCATCCGTCT 58.682 41.667 0.19 4.38 0.00 4.18
414 417 5.413213 ACTCTAGTACATATGCATCCGTCTC 59.587 44.000 0.19 0.00 0.00 3.36
415 418 3.944055 AGTACATATGCATCCGTCTCC 57.056 47.619 0.19 0.00 0.00 3.71
416 419 2.563179 AGTACATATGCATCCGTCTCCC 59.437 50.000 0.19 0.00 0.00 4.30
417 420 0.318441 ACATATGCATCCGTCTCCCG 59.682 55.000 0.19 0.00 0.00 5.14
418 421 1.016130 CATATGCATCCGTCTCCCGC 61.016 60.000 0.19 0.00 34.38 6.13
419 422 1.188219 ATATGCATCCGTCTCCCGCT 61.188 55.000 0.19 0.00 34.38 5.52
420 423 2.087462 TATGCATCCGTCTCCCGCTG 62.087 60.000 0.19 0.00 34.38 5.18
421 424 3.838271 GCATCCGTCTCCCGCTGA 61.838 66.667 0.00 0.00 34.38 4.26
422 425 2.415010 CATCCGTCTCCCGCTGAG 59.585 66.667 0.00 0.00 42.90 3.35
423 426 2.835431 ATCCGTCTCCCGCTGAGG 60.835 66.667 0.00 0.00 41.76 3.86
424 427 3.360423 ATCCGTCTCCCGCTGAGGA 62.360 63.158 0.00 0.00 45.00 3.71
425 428 2.648613 ATCCGTCTCCCGCTGAGGAT 62.649 60.000 0.00 0.00 45.00 3.24
426 429 2.725008 CGTCTCCCGCTGAGGATC 59.275 66.667 0.00 0.00 45.00 3.36
427 430 2.851071 CGTCTCCCGCTGAGGATCC 61.851 68.421 2.48 2.48 45.00 3.36
428 431 2.123251 TCTCCCGCTGAGGATCCC 60.123 66.667 8.55 0.11 45.00 3.85
429 432 3.610669 CTCCCGCTGAGGATCCCG 61.611 72.222 8.55 4.49 45.00 5.14
432 435 3.854669 CCGCTGAGGATCCCGCTT 61.855 66.667 8.55 0.00 45.00 4.68
433 436 2.279784 CGCTGAGGATCCCGCTTC 60.280 66.667 8.55 0.00 0.00 3.86
434 437 2.790791 CGCTGAGGATCCCGCTTCT 61.791 63.158 8.55 0.00 0.00 2.85
435 438 1.456196 CGCTGAGGATCCCGCTTCTA 61.456 60.000 8.55 0.00 0.00 2.10
436 439 0.972883 GCTGAGGATCCCGCTTCTAT 59.027 55.000 8.55 0.00 0.00 1.98
437 440 1.337635 GCTGAGGATCCCGCTTCTATG 60.338 57.143 8.55 0.00 0.00 2.23
438 441 1.967066 CTGAGGATCCCGCTTCTATGT 59.033 52.381 8.55 0.00 0.00 2.29
439 442 1.964223 TGAGGATCCCGCTTCTATGTC 59.036 52.381 8.55 0.00 0.00 3.06
440 443 1.273886 GAGGATCCCGCTTCTATGTCC 59.726 57.143 8.55 0.00 0.00 4.02
441 444 1.048601 GGATCCCGCTTCTATGTCCA 58.951 55.000 0.00 0.00 0.00 4.02
442 445 1.416401 GGATCCCGCTTCTATGTCCAA 59.584 52.381 0.00 0.00 0.00 3.53
443 446 2.158813 GGATCCCGCTTCTATGTCCAAA 60.159 50.000 0.00 0.00 0.00 3.28
444 447 2.396590 TCCCGCTTCTATGTCCAAAC 57.603 50.000 0.00 0.00 0.00 2.93
445 448 1.065709 TCCCGCTTCTATGTCCAAACC 60.066 52.381 0.00 0.00 0.00 3.27
446 449 1.379527 CCGCTTCTATGTCCAAACCC 58.620 55.000 0.00 0.00 0.00 4.11
447 450 1.339631 CCGCTTCTATGTCCAAACCCA 60.340 52.381 0.00 0.00 0.00 4.51
448 451 1.737793 CGCTTCTATGTCCAAACCCAC 59.262 52.381 0.00 0.00 0.00 4.61
449 452 2.615493 CGCTTCTATGTCCAAACCCACT 60.615 50.000 0.00 0.00 0.00 4.00
450 453 3.421844 GCTTCTATGTCCAAACCCACTT 58.578 45.455 0.00 0.00 0.00 3.16
451 454 3.826729 GCTTCTATGTCCAAACCCACTTT 59.173 43.478 0.00 0.00 0.00 2.66
452 455 5.007682 GCTTCTATGTCCAAACCCACTTTA 58.992 41.667 0.00 0.00 0.00 1.85
453 456 5.652452 GCTTCTATGTCCAAACCCACTTTAT 59.348 40.000 0.00 0.00 0.00 1.40
454 457 6.152831 GCTTCTATGTCCAAACCCACTTTATT 59.847 38.462 0.00 0.00 0.00 1.40
455 458 7.309805 GCTTCTATGTCCAAACCCACTTTATTT 60.310 37.037 0.00 0.00 0.00 1.40
456 459 7.461182 TCTATGTCCAAACCCACTTTATTTG 57.539 36.000 0.00 0.00 33.90 2.32
457 460 7.235079 TCTATGTCCAAACCCACTTTATTTGA 58.765 34.615 0.00 0.00 35.73 2.69
458 461 6.933514 ATGTCCAAACCCACTTTATTTGAT 57.066 33.333 0.00 0.00 35.73 2.57
459 462 9.184523 CTATGTCCAAACCCACTTTATTTGATA 57.815 33.333 0.00 0.00 35.73 2.15
460 463 8.608185 ATGTCCAAACCCACTTTATTTGATAT 57.392 30.769 0.00 0.00 35.73 1.63
461 464 8.062065 TGTCCAAACCCACTTTATTTGATATC 57.938 34.615 0.00 0.00 35.73 1.63
462 465 7.123547 TGTCCAAACCCACTTTATTTGATATCC 59.876 37.037 0.00 0.00 35.73 2.59
463 466 6.320164 TCCAAACCCACTTTATTTGATATCCG 59.680 38.462 0.00 0.00 35.73 4.18
464 467 6.320164 CCAAACCCACTTTATTTGATATCCGA 59.680 38.462 0.00 0.00 35.73 4.55
465 468 7.014230 CCAAACCCACTTTATTTGATATCCGAT 59.986 37.037 0.00 0.00 35.73 4.18
466 469 7.745620 AACCCACTTTATTTGATATCCGATC 57.254 36.000 0.00 0.00 0.00 3.69
467 470 6.238648 ACCCACTTTATTTGATATCCGATCC 58.761 40.000 0.00 0.00 0.00 3.36
468 471 6.044404 ACCCACTTTATTTGATATCCGATCCT 59.956 38.462 0.00 0.00 0.00 3.24
469 472 7.236847 ACCCACTTTATTTGATATCCGATCCTA 59.763 37.037 0.00 0.00 0.00 2.94
470 473 7.549488 CCCACTTTATTTGATATCCGATCCTAC 59.451 40.741 0.00 0.00 0.00 3.18
471 474 8.094548 CCACTTTATTTGATATCCGATCCTACA 58.905 37.037 0.00 0.00 0.00 2.74
472 475 9.658799 CACTTTATTTGATATCCGATCCTACAT 57.341 33.333 0.00 0.00 0.00 2.29
473 476 9.658799 ACTTTATTTGATATCCGATCCTACATG 57.341 33.333 0.00 0.00 0.00 3.21
474 477 9.102757 CTTTATTTGATATCCGATCCTACATGG 57.897 37.037 0.00 0.00 37.10 3.66
475 478 4.471904 TTGATATCCGATCCTACATGGC 57.528 45.455 0.00 0.00 35.26 4.40
476 479 3.440127 TGATATCCGATCCTACATGGCA 58.560 45.455 0.00 0.00 35.26 4.92
477 480 4.033009 TGATATCCGATCCTACATGGCAT 58.967 43.478 0.00 0.00 35.26 4.40
478 481 4.100035 TGATATCCGATCCTACATGGCATC 59.900 45.833 0.00 0.00 35.26 3.91
479 482 1.715785 TCCGATCCTACATGGCATCA 58.284 50.000 0.00 0.00 35.26 3.07
480 483 1.344438 TCCGATCCTACATGGCATCAC 59.656 52.381 0.00 0.00 35.26 3.06
481 484 1.609061 CCGATCCTACATGGCATCACC 60.609 57.143 0.00 0.00 39.84 4.02
482 485 1.609061 CGATCCTACATGGCATCACCC 60.609 57.143 0.00 0.00 37.83 4.61
483 486 1.701847 GATCCTACATGGCATCACCCT 59.298 52.381 0.00 0.00 37.83 4.34
484 487 2.487746 TCCTACATGGCATCACCCTA 57.512 50.000 0.00 0.00 37.83 3.53
485 488 2.770447 TCCTACATGGCATCACCCTAA 58.230 47.619 0.00 0.00 37.83 2.69
486 489 2.705658 TCCTACATGGCATCACCCTAAG 59.294 50.000 0.00 0.00 37.83 2.18
487 490 2.705658 CCTACATGGCATCACCCTAAGA 59.294 50.000 0.00 0.00 37.83 2.10
488 491 3.328931 CCTACATGGCATCACCCTAAGAT 59.671 47.826 0.00 0.00 37.83 2.40
489 492 3.959495 ACATGGCATCACCCTAAGATT 57.041 42.857 0.00 0.00 37.83 2.40
490 493 5.013079 CCTACATGGCATCACCCTAAGATTA 59.987 44.000 0.00 0.00 37.83 1.75
491 494 5.589367 ACATGGCATCACCCTAAGATTAT 57.411 39.130 0.00 0.00 37.83 1.28
492 495 5.319453 ACATGGCATCACCCTAAGATTATG 58.681 41.667 0.00 0.00 37.83 1.90
493 496 4.371624 TGGCATCACCCTAAGATTATGG 57.628 45.455 0.00 0.00 37.83 2.74
494 497 3.074390 TGGCATCACCCTAAGATTATGGG 59.926 47.826 0.00 0.00 46.07 4.00
500 503 2.876581 CCCTAAGATTATGGGTTGGCC 58.123 52.381 0.00 0.00 36.32 5.36
501 504 2.176798 CCCTAAGATTATGGGTTGGCCA 59.823 50.000 0.00 0.00 36.32 5.36
502 505 3.181418 CCCTAAGATTATGGGTTGGCCAT 60.181 47.826 6.09 0.00 36.32 4.40
503 506 3.828451 CCTAAGATTATGGGTTGGCCATG 59.172 47.826 6.09 0.00 36.17 3.66
504 507 1.708341 AGATTATGGGTTGGCCATGC 58.292 50.000 6.09 2.08 36.17 4.06
587 591 4.423732 GTGTTCCCAAACATACATCATGC 58.576 43.478 0.00 0.00 46.58 4.06
713 717 4.131088 GACGTCCACCGGGAGCTC 62.131 72.222 6.32 4.71 46.12 4.09
714 718 4.988716 ACGTCCACCGGGAGCTCA 62.989 66.667 17.19 0.00 46.12 4.26
715 719 3.461773 CGTCCACCGGGAGCTCAT 61.462 66.667 17.19 0.00 46.12 2.90
716 720 2.501610 GTCCACCGGGAGCTCATC 59.498 66.667 17.19 6.14 46.12 2.92
717 721 3.147595 TCCACCGGGAGCTCATCG 61.148 66.667 17.19 17.70 38.64 3.84
755 759 2.758089 GCAGACAGCGCCAATCCTG 61.758 63.158 2.29 6.15 35.26 3.86
756 760 2.110967 CAGACAGCGCCAATCCTGG 61.111 63.158 2.29 0.00 46.65 4.45
757 761 2.825836 GACAGCGCCAATCCTGGG 60.826 66.667 2.29 0.00 43.74 4.45
759 763 3.136123 CAGCGCCAATCCTGGGTG 61.136 66.667 2.29 0.00 43.74 4.61
762 766 3.136123 CGCCAATCCTGGGTGCTG 61.136 66.667 0.00 0.00 43.74 4.41
763 767 2.757099 GCCAATCCTGGGTGCTGG 60.757 66.667 0.00 0.00 43.74 4.85
764 768 2.043652 CCAATCCTGGGTGCTGGG 60.044 66.667 0.00 0.00 39.30 4.45
765 769 2.765969 CAATCCTGGGTGCTGGGT 59.234 61.111 0.00 0.00 0.00 4.51
766 770 1.379044 CAATCCTGGGTGCTGGGTC 60.379 63.158 0.00 0.00 0.00 4.46
767 771 1.542375 AATCCTGGGTGCTGGGTCT 60.542 57.895 0.00 0.00 0.00 3.85
768 772 0.253160 AATCCTGGGTGCTGGGTCTA 60.253 55.000 0.00 0.00 0.00 2.59
769 773 0.692419 ATCCTGGGTGCTGGGTCTAG 60.692 60.000 0.00 0.00 0.00 2.43
770 774 2.370445 CCTGGGTGCTGGGTCTAGG 61.370 68.421 0.00 0.00 0.00 3.02
789 807 3.982576 GGTGAATAATTTAGCCACCGG 57.017 47.619 0.00 0.00 38.03 5.28
808 826 0.890996 GAAGTCCACAAGCCCACAGG 60.891 60.000 0.00 0.00 0.00 4.00
849 876 0.032678 CCAATCCATCCGTCTCCTCG 59.967 60.000 0.00 0.00 0.00 4.63
850 877 0.598680 CAATCCATCCGTCTCCTCGC 60.599 60.000 0.00 0.00 0.00 5.03
851 878 1.749334 AATCCATCCGTCTCCTCGCC 61.749 60.000 0.00 0.00 0.00 5.54
852 879 2.928988 ATCCATCCGTCTCCTCGCCA 62.929 60.000 0.00 0.00 0.00 5.69
853 880 2.105128 CATCCGTCTCCTCGCCAC 59.895 66.667 0.00 0.00 0.00 5.01
854 881 3.518998 ATCCGTCTCCTCGCCACG 61.519 66.667 0.00 0.00 0.00 4.94
882 909 4.374702 CACAGCCGCAACACGCTC 62.375 66.667 0.00 0.00 41.76 5.03
963 999 3.964875 AGGCCAAGCAAACGCACG 61.965 61.111 5.01 0.00 0.00 5.34
1251 1296 1.227002 CTTCGAGGGCTACTTCGGC 60.227 63.158 0.00 0.00 0.00 5.54
1409 1454 2.092212 AGGCTTGATGGAATGATCGGTT 60.092 45.455 0.00 0.00 0.00 4.44
1429 1474 2.775890 TCTCCGATCCATACCTCGTAC 58.224 52.381 0.00 0.00 33.11 3.67
1459 1514 5.752955 TGTGTATGTATGTGATTCCATCGTG 59.247 40.000 0.00 0.00 0.00 4.35
1474 1529 3.532950 CATCGTGTCGATCTGTAGTACG 58.467 50.000 1.58 0.00 45.19 3.67
1564 1622 6.853490 TCCTCCTGTACTGTACATAGATGAT 58.147 40.000 19.99 0.00 38.15 2.45
1565 1623 6.717084 TCCTCCTGTACTGTACATAGATGATG 59.283 42.308 19.99 6.82 41.79 3.07
1566 1624 6.071672 CCTCCTGTACTGTACATAGATGATGG 60.072 46.154 19.99 14.70 40.18 3.51
1584 1642 7.677745 AGATGATGGAGGTTATATTCTGCTAGT 59.322 37.037 0.00 0.00 0.00 2.57
1585 1643 8.901472 ATGATGGAGGTTATATTCTGCTAGTA 57.099 34.615 0.00 0.00 0.00 1.82
1587 1645 6.591750 TGGAGGTTATATTCTGCTAGTAGC 57.408 41.667 15.56 15.56 42.82 3.58
1588 1646 6.315714 TGGAGGTTATATTCTGCTAGTAGCT 58.684 40.000 22.34 5.33 42.97 3.32
1611 1669 8.097662 AGCTAAAAACTATAGAGCTTGAGTGTT 58.902 33.333 6.78 0.00 40.55 3.32
1614 1672 8.549338 AAAAACTATAGAGCTTGAGTGTTACC 57.451 34.615 6.78 0.00 0.00 2.85
1641 1699 4.439057 TGTACTGGTTCTTGTTCTGTGTC 58.561 43.478 0.00 0.00 0.00 3.67
1646 1704 5.104900 ACTGGTTCTTGTTCTGTGTCTTACT 60.105 40.000 0.00 0.00 0.00 2.24
1647 1705 5.116180 TGGTTCTTGTTCTGTGTCTTACTG 58.884 41.667 0.00 0.00 0.00 2.74
1648 1706 5.105106 TGGTTCTTGTTCTGTGTCTTACTGA 60.105 40.000 0.00 0.00 35.72 3.41
1649 1707 5.815740 GGTTCTTGTTCTGTGTCTTACTGAA 59.184 40.000 0.00 0.00 42.63 3.02
1658 1716 8.725148 GTTCTGTGTCTTACTGAATGAATCAAT 58.275 33.333 0.00 0.00 45.21 2.57
1669 1727 8.641498 ACTGAATGAATCAATAGGTTTCTGTT 57.359 30.769 0.00 0.00 37.67 3.16
1685 1743 9.588096 AGGTTTCTGTTGGAAAATTTACTCTAT 57.412 29.630 0.00 0.00 44.34 1.98
1686 1744 9.841880 GGTTTCTGTTGGAAAATTTACTCTATC 57.158 33.333 0.00 0.00 44.34 2.08
1687 1745 9.841880 GTTTCTGTTGGAAAATTTACTCTATCC 57.158 33.333 0.00 0.00 44.34 2.59
1688 1746 9.581289 TTTCTGTTGGAAAATTTACTCTATCCA 57.419 29.630 3.40 3.40 40.51 3.41
1689 1747 8.561738 TCTGTTGGAAAATTTACTCTATCCAC 57.438 34.615 6.54 4.20 36.73 4.02
1690 1748 8.383175 TCTGTTGGAAAATTTACTCTATCCACT 58.617 33.333 6.54 0.00 36.73 4.00
1691 1749 8.335532 TGTTGGAAAATTTACTCTATCCACTG 57.664 34.615 6.54 0.00 36.73 3.66
1692 1750 7.094377 TGTTGGAAAATTTACTCTATCCACTGC 60.094 37.037 6.54 2.65 36.73 4.40
1693 1751 6.480763 TGGAAAATTTACTCTATCCACTGCA 58.519 36.000 3.40 0.00 32.28 4.41
1694 1752 6.374333 TGGAAAATTTACTCTATCCACTGCAC 59.626 38.462 3.40 0.00 32.28 4.57
1695 1753 6.183360 GGAAAATTTACTCTATCCACTGCACC 60.183 42.308 0.00 0.00 0.00 5.01
1696 1754 5.700402 AATTTACTCTATCCACTGCACCT 57.300 39.130 0.00 0.00 0.00 4.00
1697 1755 5.700402 ATTTACTCTATCCACTGCACCTT 57.300 39.130 0.00 0.00 0.00 3.50
1698 1756 6.808321 ATTTACTCTATCCACTGCACCTTA 57.192 37.500 0.00 0.00 0.00 2.69
1699 1757 6.808321 TTTACTCTATCCACTGCACCTTAT 57.192 37.500 0.00 0.00 0.00 1.73
1700 1758 7.907841 TTTACTCTATCCACTGCACCTTATA 57.092 36.000 0.00 0.00 0.00 0.98
1701 1759 7.907841 TTACTCTATCCACTGCACCTTATAA 57.092 36.000 0.00 0.00 0.00 0.98
1702 1760 8.492415 TTACTCTATCCACTGCACCTTATAAT 57.508 34.615 0.00 0.00 0.00 1.28
1703 1761 6.998802 ACTCTATCCACTGCACCTTATAATC 58.001 40.000 0.00 0.00 0.00 1.75
1704 1762 6.554982 ACTCTATCCACTGCACCTTATAATCA 59.445 38.462 0.00 0.00 0.00 2.57
1705 1763 7.071196 ACTCTATCCACTGCACCTTATAATCAA 59.929 37.037 0.00 0.00 0.00 2.57
1706 1764 7.977818 TCTATCCACTGCACCTTATAATCAAT 58.022 34.615 0.00 0.00 0.00 2.57
1707 1765 8.097038 TCTATCCACTGCACCTTATAATCAATC 58.903 37.037 0.00 0.00 0.00 2.67
1708 1766 6.000246 TCCACTGCACCTTATAATCAATCA 58.000 37.500 0.00 0.00 0.00 2.57
1715 1773 8.523915 TGCACCTTATAATCAATCATTCTGTT 57.476 30.769 0.00 0.00 0.00 3.16
1845 1929 3.001736 GCACAAAGGAAGATACGATCAGC 59.998 47.826 0.00 0.00 0.00 4.26
1894 1978 3.237268 AGTAGGAGCATAGACTGGAGG 57.763 52.381 0.00 0.00 0.00 4.30
1951 2036 4.764050 TCTGGTATTATCCCTTTGCGAA 57.236 40.909 0.00 0.00 0.00 4.70
1954 2039 2.546789 GGTATTATCCCTTTGCGAACGG 59.453 50.000 0.00 0.00 0.00 4.44
1967 2052 1.595382 GAACGGATCTCGGCCCATG 60.595 63.158 0.00 0.00 44.45 3.66
2016 2106 2.042831 GCTTGCTGGTGGTGCTAGG 61.043 63.158 0.00 0.00 34.72 3.02
2017 2107 1.679311 CTTGCTGGTGGTGCTAGGA 59.321 57.895 0.00 0.00 31.54 2.94
2018 2108 0.674895 CTTGCTGGTGGTGCTAGGAC 60.675 60.000 5.70 5.70 31.54 3.85
2019 2109 2.125512 GCTGGTGGTGCTAGGACG 60.126 66.667 8.41 0.00 0.00 4.79
2020 2110 2.579201 CTGGTGGTGCTAGGACGG 59.421 66.667 8.41 0.00 0.00 4.79
2021 2111 1.982395 CTGGTGGTGCTAGGACGGA 60.982 63.158 8.41 0.00 0.00 4.69
2022 2112 1.534476 TGGTGGTGCTAGGACGGAA 60.534 57.895 8.41 0.00 0.00 4.30
2023 2113 1.218316 GGTGGTGCTAGGACGGAAG 59.782 63.158 8.41 0.00 0.00 3.46
2084 2174 1.840635 AGATAGGGAGAGGTTGTTGGC 59.159 52.381 0.00 0.00 0.00 4.52
2109 2199 5.815222 CCGTCAATGGATATCACTTTGTACA 59.185 40.000 4.83 0.00 0.00 2.90
2146 2236 5.357878 TGCATGATCCACAGAAACCTTATTC 59.642 40.000 0.00 0.00 0.00 1.75
2203 2293 0.971386 TGGGAAACTGTACTCGGGTC 59.029 55.000 0.00 0.00 0.00 4.46
2207 2297 0.316204 AAACTGTACTCGGGTCGTGG 59.684 55.000 0.00 0.00 0.00 4.94
2211 2301 0.394762 TGTACTCGGGTCGTGGCTAT 60.395 55.000 0.00 0.00 0.00 2.97
2215 2305 1.287425 CTCGGGTCGTGGCTATTTTC 58.713 55.000 0.00 0.00 0.00 2.29
2218 2308 1.093496 GGGTCGTGGCTATTTTCCCG 61.093 60.000 0.00 0.00 0.00 5.14
2263 2364 3.878160 TTAATTAAGGCGGGCTTTTGG 57.122 42.857 22.38 0.00 0.00 3.28
2288 2389 4.299485 AGGGGGAGAAAATTACTCGATCT 58.701 43.478 0.00 0.00 35.49 2.75
2317 2420 1.561250 GGTTGTTGTTCCGACGACG 59.439 57.895 0.00 0.00 42.16 5.12
2340 2443 2.762360 CGGCCACGAAGATAGCAAA 58.238 52.632 2.24 0.00 44.60 3.68
2387 2493 0.745845 CCCGGAAGTGCATCCTCTTG 60.746 60.000 0.73 0.00 37.34 3.02
2389 2495 1.372087 CGGAAGTGCATCCTCTTGGC 61.372 60.000 4.86 0.00 37.34 4.52
2390 2496 0.322816 GGAAGTGCATCCTCTTGGCA 60.323 55.000 0.00 0.00 36.50 4.92
2392 2498 1.471684 GAAGTGCATCCTCTTGGCAAG 59.528 52.381 21.17 21.17 39.57 4.01
2394 2500 0.322816 GTGCATCCTCTTGGCAAGGA 60.323 55.000 25.92 18.23 46.68 3.36
2395 2501 0.322816 TGCATCCTCTTGGCAAGGAC 60.323 55.000 25.92 7.97 45.50 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.348666 CCGGATCTTCTAAAGCAACACG 59.651 50.000 0.00 0.00 0.00 4.49
65 66 3.202151 TGATTTAGGCCTAAAGTGAGGGG 59.798 47.826 34.75 0.00 38.30 4.79
125 128 3.619038 GTCCATTCAAGTCGACAAGGATC 59.381 47.826 19.50 6.57 0.00 3.36
128 131 2.738846 CTGTCCATTCAAGTCGACAAGG 59.261 50.000 19.50 9.65 34.98 3.61
161 164 8.571461 TTAGTCTAGTCGGAATCTAAAAGTGA 57.429 34.615 0.00 0.00 0.00 3.41
202 205 4.954202 TGAGAAGGTGACGGTACATAGAAT 59.046 41.667 0.00 0.00 0.00 2.40
208 211 1.991121 AGTGAGAAGGTGACGGTACA 58.009 50.000 0.00 0.00 0.00 2.90
213 216 1.068588 TGGTGAAGTGAGAAGGTGACG 59.931 52.381 0.00 0.00 0.00 4.35
222 225 2.744202 GCCACATACTTGGTGAAGTGAG 59.256 50.000 0.00 0.00 42.66 3.51
225 228 3.181445 TGAAGCCACATACTTGGTGAAGT 60.181 43.478 0.00 0.00 44.90 3.01
228 231 3.264193 AGATGAAGCCACATACTTGGTGA 59.736 43.478 0.00 0.00 39.09 4.02
234 237 5.363562 TTGATGAGATGAAGCCACATACT 57.636 39.130 0.00 0.00 0.00 2.12
237 240 5.768662 CCTAATTGATGAGATGAAGCCACAT 59.231 40.000 0.00 0.00 0.00 3.21
248 251 5.628797 TGTACATGCCCTAATTGATGAGA 57.371 39.130 0.00 0.00 0.00 3.27
257 260 5.685520 TGTCACTATTGTACATGCCCTAA 57.314 39.130 0.00 0.00 0.00 2.69
258 261 5.887214 ATGTCACTATTGTACATGCCCTA 57.113 39.130 0.00 0.00 32.74 3.53
259 262 4.778213 ATGTCACTATTGTACATGCCCT 57.222 40.909 0.00 0.00 32.74 5.19
260 263 6.230472 TCATATGTCACTATTGTACATGCCC 58.770 40.000 1.90 0.00 35.54 5.36
261 264 7.728847 TTCATATGTCACTATTGTACATGCC 57.271 36.000 1.90 0.00 35.54 4.40
268 271 8.777413 GCATGTGTATTCATATGTCACTATTGT 58.223 33.333 10.06 0.00 42.49 2.71
269 272 8.232513 GGCATGTGTATTCATATGTCACTATTG 58.767 37.037 8.45 8.69 43.75 1.90
270 273 8.159447 AGGCATGTGTATTCATATGTCACTATT 58.841 33.333 14.36 0.00 45.67 1.73
271 274 7.683578 AGGCATGTGTATTCATATGTCACTAT 58.316 34.615 14.36 0.00 45.67 2.12
272 275 7.066307 AGGCATGTGTATTCATATGTCACTA 57.934 36.000 14.36 1.83 45.67 2.74
273 276 5.933617 AGGCATGTGTATTCATATGTCACT 58.066 37.500 14.36 6.78 45.67 3.41
274 277 5.759763 TGAGGCATGTGTATTCATATGTCAC 59.240 40.000 14.36 9.50 45.67 3.67
275 278 5.927819 TGAGGCATGTGTATTCATATGTCA 58.072 37.500 14.36 7.17 45.67 3.58
276 279 8.446273 GTTATGAGGCATGTGTATTCATATGTC 58.554 37.037 5.68 5.68 44.33 3.06
277 280 7.938490 TGTTATGAGGCATGTGTATTCATATGT 59.062 33.333 10.06 0.00 42.49 2.29
278 281 8.326680 TGTTATGAGGCATGTGTATTCATATG 57.673 34.615 4.93 4.93 43.08 1.78
279 282 8.922931 TTGTTATGAGGCATGTGTATTCATAT 57.077 30.769 0.00 0.00 32.56 1.78
280 283 8.744568 TTTGTTATGAGGCATGTGTATTCATA 57.255 30.769 0.00 0.00 31.49 2.15
281 284 7.643569 TTTGTTATGAGGCATGTGTATTCAT 57.356 32.000 0.00 0.32 33.44 2.57
282 285 7.459795 TTTTGTTATGAGGCATGTGTATTCA 57.540 32.000 0.00 0.00 0.00 2.57
332 335 5.711506 TGATAGCTTGCATTGAGGAGAAAAA 59.288 36.000 0.00 0.00 0.00 1.94
333 336 5.255687 TGATAGCTTGCATTGAGGAGAAAA 58.744 37.500 0.00 0.00 0.00 2.29
334 337 4.847198 TGATAGCTTGCATTGAGGAGAAA 58.153 39.130 0.00 0.00 0.00 2.52
335 338 4.492494 TGATAGCTTGCATTGAGGAGAA 57.508 40.909 0.00 0.00 0.00 2.87
336 339 4.701651 ATGATAGCTTGCATTGAGGAGA 57.298 40.909 0.00 0.00 0.00 3.71
337 340 5.996513 ACTAATGATAGCTTGCATTGAGGAG 59.003 40.000 18.58 12.47 36.27 3.69
338 341 5.761726 CACTAATGATAGCTTGCATTGAGGA 59.238 40.000 18.58 3.75 36.27 3.71
339 342 5.048921 CCACTAATGATAGCTTGCATTGAGG 60.049 44.000 18.58 14.27 36.27 3.86
340 343 5.048921 CCCACTAATGATAGCTTGCATTGAG 60.049 44.000 18.58 14.56 36.27 3.02
341 344 4.823442 CCCACTAATGATAGCTTGCATTGA 59.177 41.667 18.58 6.93 36.27 2.57
342 345 4.558095 GCCCACTAATGATAGCTTGCATTG 60.558 45.833 18.58 12.80 36.27 2.82
343 346 3.571401 GCCCACTAATGATAGCTTGCATT 59.429 43.478 15.30 15.30 38.24 3.56
344 347 3.152341 GCCCACTAATGATAGCTTGCAT 58.848 45.455 0.00 0.00 31.96 3.96
345 348 2.575532 GCCCACTAATGATAGCTTGCA 58.424 47.619 0.00 0.00 31.96 4.08
346 349 1.882623 GGCCCACTAATGATAGCTTGC 59.117 52.381 0.00 0.00 31.96 4.01
347 350 3.181451 TGAGGCCCACTAATGATAGCTTG 60.181 47.826 0.00 0.00 31.96 4.01
348 351 3.048600 TGAGGCCCACTAATGATAGCTT 58.951 45.455 0.00 0.00 31.96 3.74
349 352 2.694397 TGAGGCCCACTAATGATAGCT 58.306 47.619 0.00 0.00 31.96 3.32
350 353 3.008375 TGATGAGGCCCACTAATGATAGC 59.992 47.826 0.00 0.00 31.96 2.97
351 354 4.897509 TGATGAGGCCCACTAATGATAG 57.102 45.455 0.00 0.00 35.14 2.08
352 355 5.848286 ATTGATGAGGCCCACTAATGATA 57.152 39.130 0.00 0.00 0.00 2.15
353 356 4.736611 ATTGATGAGGCCCACTAATGAT 57.263 40.909 0.00 0.00 0.00 2.45
354 357 5.645056 TTATTGATGAGGCCCACTAATGA 57.355 39.130 0.00 0.00 0.00 2.57
355 358 6.906157 ATTTATTGATGAGGCCCACTAATG 57.094 37.500 0.00 0.00 0.00 1.90
356 359 7.988937 TCTATTTATTGATGAGGCCCACTAAT 58.011 34.615 0.00 4.80 0.00 1.73
357 360 7.387265 TCTATTTATTGATGAGGCCCACTAA 57.613 36.000 0.00 0.00 0.00 2.24
358 361 7.387265 TTCTATTTATTGATGAGGCCCACTA 57.613 36.000 0.00 0.00 0.00 2.74
359 362 5.912149 TCTATTTATTGATGAGGCCCACT 57.088 39.130 0.00 0.00 0.00 4.00
360 363 6.959639 TTTCTATTTATTGATGAGGCCCAC 57.040 37.500 0.00 0.00 0.00 4.61
361 364 9.653516 TTATTTTCTATTTATTGATGAGGCCCA 57.346 29.630 0.00 0.00 0.00 5.36
384 387 8.462811 CGGATGCATATGTACTAGAGTCTTTAT 58.537 37.037 0.00 0.00 0.00 1.40
385 388 7.447545 ACGGATGCATATGTACTAGAGTCTTTA 59.552 37.037 0.00 0.00 0.00 1.85
386 389 6.265649 ACGGATGCATATGTACTAGAGTCTTT 59.734 38.462 0.00 0.00 0.00 2.52
387 390 5.770663 ACGGATGCATATGTACTAGAGTCTT 59.229 40.000 0.00 0.00 0.00 3.01
388 391 5.317808 ACGGATGCATATGTACTAGAGTCT 58.682 41.667 0.00 0.00 0.00 3.24
389 392 5.413213 AGACGGATGCATATGTACTAGAGTC 59.587 44.000 0.00 6.60 0.00 3.36
390 393 5.317808 AGACGGATGCATATGTACTAGAGT 58.682 41.667 0.00 0.00 0.00 3.24
391 394 5.163703 GGAGACGGATGCATATGTACTAGAG 60.164 48.000 0.00 0.00 0.00 2.43
392 395 4.700692 GGAGACGGATGCATATGTACTAGA 59.299 45.833 0.00 0.00 0.00 2.43
393 396 4.142359 GGGAGACGGATGCATATGTACTAG 60.142 50.000 0.00 0.00 0.00 2.57
394 397 3.762288 GGGAGACGGATGCATATGTACTA 59.238 47.826 0.00 0.00 0.00 1.82
395 398 2.563179 GGGAGACGGATGCATATGTACT 59.437 50.000 0.00 1.24 0.00 2.73
396 399 2.671351 CGGGAGACGGATGCATATGTAC 60.671 54.545 0.00 0.00 39.42 2.90
397 400 1.544246 CGGGAGACGGATGCATATGTA 59.456 52.381 0.00 0.00 39.42 2.29
398 401 0.318441 CGGGAGACGGATGCATATGT 59.682 55.000 0.00 0.01 39.42 2.29
399 402 1.016130 GCGGGAGACGGATGCATATG 61.016 60.000 0.00 0.00 44.51 1.78
400 403 1.188219 AGCGGGAGACGGATGCATAT 61.188 55.000 0.00 0.00 44.51 1.78
401 404 1.832608 AGCGGGAGACGGATGCATA 60.833 57.895 0.00 0.00 44.51 3.14
402 405 3.157252 AGCGGGAGACGGATGCAT 61.157 61.111 0.00 0.00 44.51 3.96
403 406 4.147449 CAGCGGGAGACGGATGCA 62.147 66.667 0.00 0.00 40.21 3.96
404 407 3.838271 TCAGCGGGAGACGGATGC 61.838 66.667 0.00 0.00 45.49 3.91
412 415 3.610669 CGGGATCCTCAGCGGGAG 61.611 72.222 12.58 1.85 43.65 4.30
415 418 3.798954 GAAGCGGGATCCTCAGCGG 62.799 68.421 12.58 0.00 34.34 5.52
416 419 1.456196 TAGAAGCGGGATCCTCAGCG 61.456 60.000 12.58 7.77 34.34 5.18
417 420 0.972883 ATAGAAGCGGGATCCTCAGC 59.027 55.000 12.58 14.71 0.00 4.26
418 421 1.967066 ACATAGAAGCGGGATCCTCAG 59.033 52.381 12.58 4.90 0.00 3.35
419 422 1.964223 GACATAGAAGCGGGATCCTCA 59.036 52.381 12.58 0.00 0.00 3.86
420 423 1.273886 GGACATAGAAGCGGGATCCTC 59.726 57.143 12.58 0.56 0.00 3.71
421 424 1.343069 GGACATAGAAGCGGGATCCT 58.657 55.000 12.58 0.00 0.00 3.24
422 425 1.048601 TGGACATAGAAGCGGGATCC 58.951 55.000 1.92 1.92 0.00 3.36
423 426 2.872858 GTTTGGACATAGAAGCGGGATC 59.127 50.000 0.00 0.00 0.00 3.36
424 427 2.421529 GGTTTGGACATAGAAGCGGGAT 60.422 50.000 0.00 0.00 0.00 3.85
425 428 1.065709 GGTTTGGACATAGAAGCGGGA 60.066 52.381 0.00 0.00 0.00 5.14
426 429 1.379527 GGTTTGGACATAGAAGCGGG 58.620 55.000 0.00 0.00 0.00 6.13
427 430 1.339631 TGGGTTTGGACATAGAAGCGG 60.340 52.381 0.00 0.00 0.00 5.52
428 431 1.737793 GTGGGTTTGGACATAGAAGCG 59.262 52.381 0.00 0.00 0.00 4.68
429 432 3.073274 AGTGGGTTTGGACATAGAAGC 57.927 47.619 0.00 0.00 0.00 3.86
430 433 7.703058 AATAAAGTGGGTTTGGACATAGAAG 57.297 36.000 0.00 0.00 0.00 2.85
431 434 7.726291 TCAAATAAAGTGGGTTTGGACATAGAA 59.274 33.333 0.00 0.00 34.48 2.10
432 435 7.235079 TCAAATAAAGTGGGTTTGGACATAGA 58.765 34.615 0.00 0.00 34.48 1.98
433 436 7.461182 TCAAATAAAGTGGGTTTGGACATAG 57.539 36.000 0.00 0.00 34.48 2.23
434 437 9.707957 ATATCAAATAAAGTGGGTTTGGACATA 57.292 29.630 0.00 0.00 34.48 2.29
435 438 6.933514 ATCAAATAAAGTGGGTTTGGACAT 57.066 33.333 0.00 0.00 34.48 3.06
436 439 7.123547 GGATATCAAATAAAGTGGGTTTGGACA 59.876 37.037 4.83 0.00 34.48 4.02
437 440 7.489160 GGATATCAAATAAAGTGGGTTTGGAC 58.511 38.462 4.83 0.00 34.48 4.02
438 441 6.320164 CGGATATCAAATAAAGTGGGTTTGGA 59.680 38.462 4.83 0.00 34.48 3.53
439 442 6.320164 TCGGATATCAAATAAAGTGGGTTTGG 59.680 38.462 4.83 0.00 34.48 3.28
440 443 7.328277 TCGGATATCAAATAAAGTGGGTTTG 57.672 36.000 4.83 0.00 34.90 2.93
441 444 7.230712 GGATCGGATATCAAATAAAGTGGGTTT 59.769 37.037 4.83 0.00 0.00 3.27
442 445 6.715264 GGATCGGATATCAAATAAAGTGGGTT 59.285 38.462 4.83 0.00 0.00 4.11
443 446 6.044404 AGGATCGGATATCAAATAAAGTGGGT 59.956 38.462 4.83 0.00 0.00 4.51
444 447 6.476378 AGGATCGGATATCAAATAAAGTGGG 58.524 40.000 4.83 0.00 0.00 4.61
445 448 8.094548 TGTAGGATCGGATATCAAATAAAGTGG 58.905 37.037 4.83 0.00 0.00 4.00
446 449 9.658799 ATGTAGGATCGGATATCAAATAAAGTG 57.341 33.333 4.83 0.00 0.00 3.16
447 450 9.658799 CATGTAGGATCGGATATCAAATAAAGT 57.341 33.333 4.83 0.00 0.00 2.66
448 451 9.102757 CCATGTAGGATCGGATATCAAATAAAG 57.897 37.037 4.83 0.00 41.22 1.85
449 452 7.552687 GCCATGTAGGATCGGATATCAAATAAA 59.447 37.037 4.83 0.00 41.22 1.40
450 453 7.047891 GCCATGTAGGATCGGATATCAAATAA 58.952 38.462 4.83 0.00 41.22 1.40
451 454 6.156083 TGCCATGTAGGATCGGATATCAAATA 59.844 38.462 4.83 0.00 41.22 1.40
452 455 5.045651 TGCCATGTAGGATCGGATATCAAAT 60.046 40.000 4.83 0.00 41.22 2.32
453 456 4.285775 TGCCATGTAGGATCGGATATCAAA 59.714 41.667 4.83 0.00 41.22 2.69
454 457 3.837731 TGCCATGTAGGATCGGATATCAA 59.162 43.478 4.83 0.00 41.22 2.57
455 458 3.440127 TGCCATGTAGGATCGGATATCA 58.560 45.455 4.83 0.00 41.22 2.15
456 459 4.100035 TGATGCCATGTAGGATCGGATATC 59.900 45.833 0.00 0.00 41.22 1.63
457 460 4.033009 TGATGCCATGTAGGATCGGATAT 58.967 43.478 0.00 0.00 41.22 1.63
458 461 3.195610 GTGATGCCATGTAGGATCGGATA 59.804 47.826 0.00 0.00 41.22 2.59
459 462 2.027745 GTGATGCCATGTAGGATCGGAT 60.028 50.000 0.00 0.00 41.22 4.18
460 463 1.344438 GTGATGCCATGTAGGATCGGA 59.656 52.381 0.00 0.00 41.22 4.55
461 464 1.609061 GGTGATGCCATGTAGGATCGG 60.609 57.143 0.00 0.00 41.22 4.18
462 465 1.609061 GGGTGATGCCATGTAGGATCG 60.609 57.143 0.00 0.00 41.22 3.69
463 466 1.701847 AGGGTGATGCCATGTAGGATC 59.298 52.381 0.00 0.00 41.22 3.36
464 467 1.825105 AGGGTGATGCCATGTAGGAT 58.175 50.000 0.00 0.00 41.22 3.24
465 468 2.487746 TAGGGTGATGCCATGTAGGA 57.512 50.000 0.00 0.00 41.22 2.94
466 469 2.705658 TCTTAGGGTGATGCCATGTAGG 59.294 50.000 0.00 0.00 39.65 3.18
467 470 4.630644 ATCTTAGGGTGATGCCATGTAG 57.369 45.455 0.00 0.00 39.65 2.74
468 471 6.475504 CATAATCTTAGGGTGATGCCATGTA 58.524 40.000 0.00 0.00 39.65 2.29
469 472 3.959495 AATCTTAGGGTGATGCCATGT 57.041 42.857 0.00 0.00 39.65 3.21
470 473 4.703575 CCATAATCTTAGGGTGATGCCATG 59.296 45.833 0.00 0.00 39.65 3.66
471 474 4.264083 CCCATAATCTTAGGGTGATGCCAT 60.264 45.833 0.50 0.00 39.65 4.40
472 475 3.074390 CCCATAATCTTAGGGTGATGCCA 59.926 47.826 0.50 0.00 39.65 4.92
473 476 3.690460 CCCATAATCTTAGGGTGATGCC 58.310 50.000 0.50 0.00 37.81 4.40
481 484 3.593442 TGGCCAACCCATAATCTTAGG 57.407 47.619 0.61 0.00 39.18 2.69
498 501 1.943340 GCAGAGTAGTAAAGGCATGGC 59.057 52.381 12.14 12.14 0.00 4.40
499 502 2.939103 GTGCAGAGTAGTAAAGGCATGG 59.061 50.000 0.00 0.00 33.43 3.66
500 503 3.599343 TGTGCAGAGTAGTAAAGGCATG 58.401 45.455 0.00 0.00 33.43 4.06
501 504 3.981071 TGTGCAGAGTAGTAAAGGCAT 57.019 42.857 0.00 0.00 33.43 4.40
502 505 3.981071 ATGTGCAGAGTAGTAAAGGCA 57.019 42.857 0.00 0.00 0.00 4.75
503 506 5.601662 TGATATGTGCAGAGTAGTAAAGGC 58.398 41.667 0.00 0.00 0.00 4.35
504 507 5.694006 GCTGATATGTGCAGAGTAGTAAAGG 59.306 44.000 0.00 0.00 35.39 3.11
505 508 6.276091 TGCTGATATGTGCAGAGTAGTAAAG 58.724 40.000 0.00 0.00 35.39 1.85
506 509 6.220726 TGCTGATATGTGCAGAGTAGTAAA 57.779 37.500 0.00 0.00 35.39 2.01
587 591 7.943952 GCTATCATCATTAGCTTTACGTGTAG 58.056 38.462 0.00 0.00 39.18 2.74
673 677 1.024271 GTCAGCAAAACAGCACCTCA 58.976 50.000 0.00 0.00 36.85 3.86
675 679 1.447317 CCGTCAGCAAAACAGCACCT 61.447 55.000 0.00 0.00 36.85 4.00
705 709 1.372748 GCTGATCGATGAGCTCCCG 60.373 63.158 26.87 14.80 34.05 5.14
713 717 3.657015 AGGTATCACAGCTGATCGATG 57.343 47.619 23.35 7.93 38.21 3.84
747 751 2.043652 CCCAGCACCCAGGATTGG 60.044 66.667 0.00 0.00 44.60 3.16
755 759 1.198759 TTCACCTAGACCCAGCACCC 61.199 60.000 0.00 0.00 0.00 4.61
756 760 0.912486 ATTCACCTAGACCCAGCACC 59.088 55.000 0.00 0.00 0.00 5.01
757 761 3.906720 TTATTCACCTAGACCCAGCAC 57.093 47.619 0.00 0.00 0.00 4.40
759 763 5.470437 GCTAAATTATTCACCTAGACCCAGC 59.530 44.000 0.00 0.00 0.00 4.85
760 764 5.998363 GGCTAAATTATTCACCTAGACCCAG 59.002 44.000 0.00 0.00 0.00 4.45
762 766 5.763698 GTGGCTAAATTATTCACCTAGACCC 59.236 44.000 0.00 0.00 0.00 4.46
763 767 5.763698 GGTGGCTAAATTATTCACCTAGACC 59.236 44.000 13.82 0.00 43.14 3.85
764 768 5.465724 CGGTGGCTAAATTATTCACCTAGAC 59.534 44.000 16.85 0.00 43.98 2.59
765 769 5.454187 CCGGTGGCTAAATTATTCACCTAGA 60.454 44.000 16.85 0.00 43.98 2.43
766 770 4.755123 CCGGTGGCTAAATTATTCACCTAG 59.245 45.833 16.85 8.90 43.98 3.02
767 771 4.409574 TCCGGTGGCTAAATTATTCACCTA 59.590 41.667 16.85 7.49 43.98 3.08
768 772 3.201266 TCCGGTGGCTAAATTATTCACCT 59.799 43.478 16.85 0.00 43.98 4.00
769 773 3.547746 TCCGGTGGCTAAATTATTCACC 58.452 45.455 0.00 12.07 43.06 4.02
770 774 4.638865 ACTTCCGGTGGCTAAATTATTCAC 59.361 41.667 0.00 0.00 0.00 3.18
788 806 0.890996 CTGTGGGCTTGTGGACTTCC 60.891 60.000 0.00 0.00 0.00 3.46
789 807 0.890996 CCTGTGGGCTTGTGGACTTC 60.891 60.000 0.00 0.00 0.00 3.01
808 826 3.858868 TTCGTGCGTGGAGTGGAGC 62.859 63.158 0.00 0.00 0.00 4.70
884 911 2.601741 GGCGCGTAACTGCTAGTAGTAG 60.602 54.545 14.28 13.18 33.91 2.57
885 912 1.331756 GGCGCGTAACTGCTAGTAGTA 59.668 52.381 14.28 0.43 0.00 1.82
886 913 0.100146 GGCGCGTAACTGCTAGTAGT 59.900 55.000 7.78 7.78 0.00 2.73
923 959 1.076727 GGTGGGGAAAGTGGAAGGG 59.923 63.158 0.00 0.00 0.00 3.95
976 1012 1.208614 CCTCGCTGCTTCTTTGTGC 59.791 57.895 0.00 0.00 0.00 4.57
978 1014 1.227943 TGCCTCGCTGCTTCTTTGT 60.228 52.632 0.00 0.00 0.00 2.83
1251 1296 1.677637 GGCTCTCGGTGGGGTAGAAG 61.678 65.000 0.00 0.00 0.00 2.85
1336 1381 1.525077 CGAGGACGAGGAGGAGGAG 60.525 68.421 0.00 0.00 42.66 3.69
1409 1454 2.775890 GTACGAGGTATGGATCGGAGA 58.224 52.381 0.00 0.00 43.12 3.71
1429 1474 6.699642 TGGAATCACATACATACACACATACG 59.300 38.462 0.00 0.00 0.00 3.06
1459 1514 3.744942 TCATAGGCGTACTACAGATCGAC 59.255 47.826 0.00 0.00 33.70 4.20
1474 1529 5.839621 AGCAACAATCAATCATTCATAGGC 58.160 37.500 0.00 0.00 0.00 3.93
1528 1586 1.203100 ACAGGAGGAAAAGCAAGGCAT 60.203 47.619 0.00 0.00 0.00 4.40
1564 1622 6.315714 AGCTACTAGCAGAATATAACCTCCA 58.684 40.000 10.73 0.00 45.56 3.86
1565 1623 6.844097 AGCTACTAGCAGAATATAACCTCC 57.156 41.667 10.73 0.00 45.56 4.30
1584 1642 8.750298 ACACTCAAGCTCTATAGTTTTTAGCTA 58.250 33.333 11.99 0.00 42.49 3.32
1585 1643 7.616313 ACACTCAAGCTCTATAGTTTTTAGCT 58.384 34.615 7.00 7.00 45.12 3.32
1588 1646 9.649167 GGTAACACTCAAGCTCTATAGTTTTTA 57.351 33.333 0.00 0.00 0.00 1.52
1611 1669 3.170717 CAAGAACCAGTACAGAGGGGTA 58.829 50.000 0.00 0.00 32.21 3.69
1614 1672 3.325135 AGAACAAGAACCAGTACAGAGGG 59.675 47.826 0.00 0.00 0.00 4.30
1646 1704 7.669304 TCCAACAGAAACCTATTGATTCATTCA 59.331 33.333 0.00 0.00 0.00 2.57
1647 1705 8.055279 TCCAACAGAAACCTATTGATTCATTC 57.945 34.615 0.00 0.00 0.00 2.67
1648 1706 8.421249 TTCCAACAGAAACCTATTGATTCATT 57.579 30.769 0.00 0.00 0.00 2.57
1649 1707 8.421249 TTTCCAACAGAAACCTATTGATTCAT 57.579 30.769 0.00 0.00 39.60 2.57
1658 1716 8.990163 AGAGTAAATTTTCCAACAGAAACCTA 57.010 30.769 0.00 0.00 44.20 3.08
1669 1727 6.374333 GTGCAGTGGATAGAGTAAATTTTCCA 59.626 38.462 0.00 0.00 0.00 3.53
1685 1743 6.000246 TGATTGATTATAAGGTGCAGTGGA 58.000 37.500 0.00 0.00 0.00 4.02
1686 1744 6.889301 ATGATTGATTATAAGGTGCAGTGG 57.111 37.500 0.00 0.00 0.00 4.00
1687 1745 8.074370 CAGAATGATTGATTATAAGGTGCAGTG 58.926 37.037 0.00 0.00 39.69 3.66
1688 1746 7.776969 ACAGAATGATTGATTATAAGGTGCAGT 59.223 33.333 0.00 0.00 39.69 4.40
1689 1747 8.162878 ACAGAATGATTGATTATAAGGTGCAG 57.837 34.615 0.00 0.00 39.69 4.41
1690 1748 8.407832 CAACAGAATGATTGATTATAAGGTGCA 58.592 33.333 0.00 0.00 39.69 4.57
1691 1749 8.623903 TCAACAGAATGATTGATTATAAGGTGC 58.376 33.333 0.00 0.00 39.69 5.01
1706 1764 9.246670 AGGACATCAAATATTTCAACAGAATGA 57.753 29.630 0.00 0.00 39.69 2.57
1707 1765 9.865321 AAGGACATCAAATATTTCAACAGAATG 57.135 29.630 0.00 0.00 46.00 2.67
1715 1773 7.921786 AGAACGAAGGACATCAAATATTTCA 57.078 32.000 0.00 0.00 0.00 2.69
1773 1857 4.122143 CTGCAACCCAGTTTCAGAAAAA 57.878 40.909 0.00 0.00 38.64 1.94
1774 1858 3.799281 CTGCAACCCAGTTTCAGAAAA 57.201 42.857 0.00 0.00 38.64 2.29
1845 1929 2.423898 ATCTACCCGCTGTGTCCCG 61.424 63.158 0.00 0.00 0.00 5.14
1951 2036 3.550431 CCATGGGCCGAGATCCGT 61.550 66.667 2.85 0.00 36.31 4.69
1967 2052 1.472376 CGAGAGGACAAGATTCTGGCC 60.472 57.143 0.00 0.00 45.99 5.36
2016 2106 2.010497 GCAATCTTCCTTCCTTCCGTC 58.990 52.381 0.00 0.00 0.00 4.79
2017 2107 1.340114 GGCAATCTTCCTTCCTTCCGT 60.340 52.381 0.00 0.00 0.00 4.69
2018 2108 1.383523 GGCAATCTTCCTTCCTTCCG 58.616 55.000 0.00 0.00 0.00 4.30
2019 2109 1.065418 TCGGCAATCTTCCTTCCTTCC 60.065 52.381 0.00 0.00 0.00 3.46
2020 2110 2.010497 GTCGGCAATCTTCCTTCCTTC 58.990 52.381 0.00 0.00 0.00 3.46
2021 2111 1.676014 CGTCGGCAATCTTCCTTCCTT 60.676 52.381 0.00 0.00 0.00 3.36
2022 2112 0.108138 CGTCGGCAATCTTCCTTCCT 60.108 55.000 0.00 0.00 0.00 3.36
2023 2113 1.706287 GCGTCGGCAATCTTCCTTCC 61.706 60.000 0.00 0.00 39.62 3.46
2084 2174 4.199310 ACAAAGTGATATCCATTGACGGG 58.801 43.478 15.20 0.00 0.00 5.28
2146 2236 1.103803 TCGGGATCTTTCTCCTGTCG 58.896 55.000 0.00 0.00 41.67 4.35
2182 2272 0.036671 CCCGAGTACAGTTTCCCACC 60.037 60.000 0.00 0.00 0.00 4.61
2190 2280 2.633509 GCCACGACCCGAGTACAGT 61.634 63.158 0.00 0.00 0.00 3.55
2203 2293 1.597663 GATGACGGGAAAATAGCCACG 59.402 52.381 0.00 0.00 0.00 4.94
2207 2297 3.454375 TCGAAGATGACGGGAAAATAGC 58.546 45.455 0.00 0.00 0.00 2.97
2211 2301 2.063266 CGTTCGAAGATGACGGGAAAA 58.937 47.619 0.00 0.00 35.04 2.29
2215 2305 2.165301 GCCGTTCGAAGATGACGGG 61.165 63.158 23.03 8.63 43.41 5.28
2218 2308 1.805945 AGCGCCGTTCGAAGATGAC 60.806 57.895 2.29 0.00 41.67 3.06
2263 2364 3.705072 TCGAGTAATTTTCTCCCCCTCTC 59.295 47.826 0.00 0.00 0.00 3.20
2344 2447 6.706716 GGGCTAGAGATTCGCTTACTTTAATT 59.293 38.462 0.00 0.00 0.00 1.40
2345 2448 6.224584 GGGCTAGAGATTCGCTTACTTTAAT 58.775 40.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.