Multiple sequence alignment - TraesCS5A01G382100

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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 TraesCS5A01G382100 chr5A 100.000 2461 0 0 1 2461 580201943 580204403 0.000000e+00 4545
1 TraesCS5A01G382100 chr7A 96.425 1846 58 5 622 2461 47823920 47825763 0.000000e+00 3037
2 TraesCS5A01G382100 chr7A 92.785 1871 99 12 621 2461 332644499 332646363 0.000000e+00 2675
3 TraesCS5A01G382100 chr2D 94.242 1893 59 14 617 2461 645194643 645196533 0.000000e+00 2846
4 TraesCS5A01G382100 chr2D 92.032 1870 93 12 620 2461 21226789 21228630 0.000000e+00 2577
5 TraesCS5A01G382100 chr6D 94.283 1889 53 10 620 2461 100358865 100360745 0.000000e+00 2839
6 TraesCS5A01G382100 chr6D 93.694 1887 63 13 621 2461 17067058 17068934 0.000000e+00 2774
7 TraesCS5A01G382100 chr5D 94.266 1866 68 12 621 2458 543865238 543867092 0.000000e+00 2817
8 TraesCS5A01G382100 chr5D 94.118 136 5 2 488 620 460069683 460069818 1.150000e-48 204
9 TraesCS5A01G382100 chr1A 93.291 1893 67 12 621 2461 567959234 567957350 0.000000e+00 2737
10 TraesCS5A01G382100 chr2B 90.288 1874 109 16 619 2461 28872497 28870666 0.000000e+00 2385
11 TraesCS5A01G382100 chr4A 95.244 1493 46 3 975 2461 436868463 436866990 0.000000e+00 2340
12 TraesCS5A01G382100 chr3A 96.062 1422 49 4 1046 2461 742901718 742900298 0.000000e+00 2309
13 TraesCS5A01G382100 chrUn 82.118 727 63 18 1762 2460 47829412 47828725 5.940000e-156 560
14 TraesCS5A01G382100 chr4B 82.143 728 61 21 1762 2460 669849176 669848489 5.940000e-156 560
15 TraesCS5A01G382100 chr4B 83.908 522 48 13 4 490 2700794 2700274 1.330000e-127 466
16 TraesCS5A01G382100 chr2A 94.915 295 14 1 621 914 111916590 111916296 6.200000e-126 460
17 TraesCS5A01G382100 chr2A 96.029 277 10 1 621 896 12591391 12591667 1.340000e-122 449
18 TraesCS5A01G382100 chr6B 91.923 260 19 1 2203 2460 48430100 48429841 1.800000e-96 363
19 TraesCS5A01G382100 chr5B 92.248 258 17 2 2206 2460 593498701 593498444 1.800000e-96 363
20 TraesCS5A01G382100 chr5B 95.200 125 5 1 497 620 565509698 565509822 1.930000e-46 196
21 TraesCS5A01G382100 chr7B 79.661 413 54 16 81 477 663808391 663807993 1.120000e-68 270


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 TraesCS5A01G382100 chr5A 580201943 580204403 2460 False 4545 4545 100.000 1 2461 1 chr5A.!!$F1 2460
1 TraesCS5A01G382100 chr7A 47823920 47825763 1843 False 3037 3037 96.425 622 2461 1 chr7A.!!$F1 1839
2 TraesCS5A01G382100 chr7A 332644499 332646363 1864 False 2675 2675 92.785 621 2461 1 chr7A.!!$F2 1840
3 TraesCS5A01G382100 chr2D 645194643 645196533 1890 False 2846 2846 94.242 617 2461 1 chr2D.!!$F2 1844
4 TraesCS5A01G382100 chr2D 21226789 21228630 1841 False 2577 2577 92.032 620 2461 1 chr2D.!!$F1 1841
5 TraesCS5A01G382100 chr6D 100358865 100360745 1880 False 2839 2839 94.283 620 2461 1 chr6D.!!$F2 1841
6 TraesCS5A01G382100 chr6D 17067058 17068934 1876 False 2774 2774 93.694 621 2461 1 chr6D.!!$F1 1840
7 TraesCS5A01G382100 chr5D 543865238 543867092 1854 False 2817 2817 94.266 621 2458 1 chr5D.!!$F2 1837
8 TraesCS5A01G382100 chr1A 567957350 567959234 1884 True 2737 2737 93.291 621 2461 1 chr1A.!!$R1 1840
9 TraesCS5A01G382100 chr2B 28870666 28872497 1831 True 2385 2385 90.288 619 2461 1 chr2B.!!$R1 1842
10 TraesCS5A01G382100 chr4A 436866990 436868463 1473 True 2340 2340 95.244 975 2461 1 chr4A.!!$R1 1486
11 TraesCS5A01G382100 chr3A 742900298 742901718 1420 True 2309 2309 96.062 1046 2461 1 chr3A.!!$R1 1415
12 TraesCS5A01G382100 chrUn 47828725 47829412 687 True 560 560 82.118 1762 2460 1 chrUn.!!$R1 698
13 TraesCS5A01G382100 chr4B 669848489 669849176 687 True 560 560 82.143 1762 2460 1 chr4B.!!$R2 698
14 TraesCS5A01G382100 chr4B 2700274 2700794 520 True 466 466 83.908 4 490 1 chr4B.!!$R1 486

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
527 542 0.035056 AAGAAACTCCCATCGCCAGG 60.035 55.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1913 0.039618 TCAGGGCCCATTTTCTCACC 59.96 55.0 27.56 0.0 0.0 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 4.838486 GCTCCTCCGCTCGTCACG 62.838 72.222 0.00 0.00 0.00 4.35
70 71 4.803426 CTCGTCACGGCCTGCCTC 62.803 72.222 6.60 0.00 0.00 4.70
187 202 0.179073 AATCCATCGGCAACTCCTCG 60.179 55.000 0.00 0.00 0.00 4.63
199 214 3.312828 CAACTCCTCGTCAACTCTGAAG 58.687 50.000 0.00 0.00 31.88 3.02
216 231 0.548682 AAGCACCTCTCCCTGTCCAT 60.549 55.000 0.00 0.00 0.00 3.41
221 236 1.630878 ACCTCTCCCTGTCCATGTTTC 59.369 52.381 0.00 0.00 0.00 2.78
230 245 5.602145 TCCCTGTCCATGTTTCAATCTTTTT 59.398 36.000 0.00 0.00 0.00 1.94
239 254 8.891720 CCATGTTTCAATCTTTTTCTTTTGGAA 58.108 29.630 0.00 0.00 0.00 3.53
253 268 7.528996 TTCTTTTGGAACTGATGATGATGTT 57.471 32.000 0.00 0.00 0.00 2.71
255 270 6.716173 TCTTTTGGAACTGATGATGATGTTGA 59.284 34.615 0.00 0.00 0.00 3.18
256 271 5.885230 TTGGAACTGATGATGATGTTGAC 57.115 39.130 0.00 0.00 0.00 3.18
261 276 5.369409 ACTGATGATGATGTTGACCTGAT 57.631 39.130 0.00 0.00 0.00 2.90
264 279 3.353370 TGATGATGTTGACCTGATGCA 57.647 42.857 0.00 0.00 0.00 3.96
265 280 3.893521 TGATGATGTTGACCTGATGCAT 58.106 40.909 0.00 0.00 0.00 3.96
275 290 7.946207 TGTTGACCTGATGCATAGTTTTTAAA 58.054 30.769 0.00 0.00 0.00 1.52
277 292 6.607689 TGACCTGATGCATAGTTTTTAAACG 58.392 36.000 0.00 0.00 43.51 3.60
278 293 6.205853 TGACCTGATGCATAGTTTTTAAACGT 59.794 34.615 0.00 0.00 43.51 3.99
279 294 7.388224 TGACCTGATGCATAGTTTTTAAACGTA 59.612 33.333 0.00 0.00 43.51 3.57
280 295 8.276252 ACCTGATGCATAGTTTTTAAACGTAT 57.724 30.769 0.00 0.00 43.51 3.06
281 296 8.736244 ACCTGATGCATAGTTTTTAAACGTATT 58.264 29.630 0.00 0.00 43.51 1.89
282 297 9.221775 CCTGATGCATAGTTTTTAAACGTATTC 57.778 33.333 0.00 0.00 43.51 1.75
283 298 9.221775 CTGATGCATAGTTTTTAAACGTATTCC 57.778 33.333 0.00 0.00 43.51 3.01
284 299 8.952278 TGATGCATAGTTTTTAAACGTATTCCT 58.048 29.630 0.00 0.00 43.51 3.36
285 300 9.434559 GATGCATAGTTTTTAAACGTATTCCTC 57.565 33.333 0.00 0.00 43.51 3.71
286 301 8.325421 TGCATAGTTTTTAAACGTATTCCTCA 57.675 30.769 0.00 0.00 43.51 3.86
287 302 8.447833 TGCATAGTTTTTAAACGTATTCCTCAG 58.552 33.333 0.00 0.00 43.51 3.35
290 305 7.797038 AGTTTTTAAACGTATTCCTCAGTGT 57.203 32.000 0.00 0.00 43.51 3.55
292 307 8.126700 AGTTTTTAAACGTATTCCTCAGTGTTG 58.873 33.333 0.00 0.00 43.51 3.33
294 309 7.556733 TTTAAACGTATTCCTCAGTGTTGTT 57.443 32.000 0.00 0.00 0.00 2.83
295 310 5.668558 AAACGTATTCCTCAGTGTTGTTC 57.331 39.130 0.00 0.00 0.00 3.18
296 311 3.314553 ACGTATTCCTCAGTGTTGTTCG 58.685 45.455 0.00 0.00 0.00 3.95
297 312 2.666508 CGTATTCCTCAGTGTTGTTCGG 59.333 50.000 0.00 0.00 0.00 4.30
298 313 1.523758 ATTCCTCAGTGTTGTTCGGC 58.476 50.000 0.00 0.00 0.00 5.54
299 314 0.468226 TTCCTCAGTGTTGTTCGGCT 59.532 50.000 0.00 0.00 0.00 5.52
300 315 1.334160 TCCTCAGTGTTGTTCGGCTA 58.666 50.000 0.00 0.00 0.00 3.93
301 316 1.000506 TCCTCAGTGTTGTTCGGCTAC 59.999 52.381 0.00 0.00 0.00 3.58
302 317 1.429463 CTCAGTGTTGTTCGGCTACC 58.571 55.000 0.00 0.00 0.00 3.18
303 318 0.753867 TCAGTGTTGTTCGGCTACCA 59.246 50.000 0.00 0.00 0.00 3.25
304 319 1.346395 TCAGTGTTGTTCGGCTACCAT 59.654 47.619 0.00 0.00 0.00 3.55
305 320 2.563620 TCAGTGTTGTTCGGCTACCATA 59.436 45.455 0.00 0.00 0.00 2.74
306 321 3.196901 TCAGTGTTGTTCGGCTACCATAT 59.803 43.478 0.00 0.00 0.00 1.78
307 322 3.938963 CAGTGTTGTTCGGCTACCATATT 59.061 43.478 0.00 0.00 0.00 1.28
308 323 4.394920 CAGTGTTGTTCGGCTACCATATTT 59.605 41.667 0.00 0.00 0.00 1.40
309 324 5.007682 AGTGTTGTTCGGCTACCATATTTT 58.992 37.500 0.00 0.00 0.00 1.82
310 325 5.475564 AGTGTTGTTCGGCTACCATATTTTT 59.524 36.000 0.00 0.00 0.00 1.94
331 346 7.826260 TTTTTCTCTGCTCGTTTTCAAAAAT 57.174 28.000 0.00 0.00 0.00 1.82
332 347 7.826260 TTTTCTCTGCTCGTTTTCAAAAATT 57.174 28.000 0.00 0.00 0.00 1.82
333 348 7.826260 TTTCTCTGCTCGTTTTCAAAAATTT 57.174 28.000 0.00 0.00 0.00 1.82
334 349 7.449934 TTCTCTGCTCGTTTTCAAAAATTTC 57.550 32.000 0.00 0.00 0.00 2.17
335 350 5.681105 TCTCTGCTCGTTTTCAAAAATTTCG 59.319 36.000 0.00 0.00 0.00 3.46
336 351 4.737765 TCTGCTCGTTTTCAAAAATTTCGG 59.262 37.500 0.00 0.00 0.00 4.30
337 352 4.673441 TGCTCGTTTTCAAAAATTTCGGA 58.327 34.783 0.00 0.00 0.00 4.55
338 353 4.501198 TGCTCGTTTTCAAAAATTTCGGAC 59.499 37.500 0.00 0.00 0.00 4.79
339 354 4.373619 GCTCGTTTTCAAAAATTTCGGACG 60.374 41.667 0.00 0.00 0.00 4.79
340 355 4.906423 TCGTTTTCAAAAATTTCGGACGA 58.094 34.783 0.00 0.20 0.00 4.20
341 356 5.330295 TCGTTTTCAAAAATTTCGGACGAA 58.670 33.333 2.62 2.62 0.00 3.85
342 357 5.972382 TCGTTTTCAAAAATTTCGGACGAAT 59.028 32.000 8.06 0.00 33.79 3.34
343 358 6.472808 TCGTTTTCAAAAATTTCGGACGAATT 59.527 30.769 8.06 2.06 33.79 2.17
344 359 7.009357 TCGTTTTCAAAAATTTCGGACGAATTT 59.991 29.630 8.06 8.20 33.79 1.82
345 360 7.314712 CGTTTTCAAAAATTTCGGACGAATTTC 59.685 33.333 8.06 0.00 33.79 2.17
346 361 7.995463 TTTCAAAAATTTCGGACGAATTTCT 57.005 28.000 8.06 0.00 33.79 2.52
347 362 6.984740 TCAAAAATTTCGGACGAATTTCTG 57.015 33.333 8.06 11.15 33.79 3.02
348 363 5.401079 TCAAAAATTTCGGACGAATTTCTGC 59.599 36.000 8.06 0.00 33.79 4.26
349 364 3.487563 AATTTCGGACGAATTTCTGCC 57.512 42.857 8.06 0.00 33.79 4.85
350 365 1.885560 TTTCGGACGAATTTCTGCCA 58.114 45.000 8.06 0.00 33.79 4.92
351 366 1.885560 TTCGGACGAATTTCTGCCAA 58.114 45.000 2.62 0.00 0.00 4.52
352 367 2.107950 TCGGACGAATTTCTGCCAAT 57.892 45.000 0.00 0.00 0.00 3.16
353 368 2.432444 TCGGACGAATTTCTGCCAATT 58.568 42.857 0.00 0.00 0.00 2.32
354 369 2.817258 TCGGACGAATTTCTGCCAATTT 59.183 40.909 0.00 0.00 0.00 1.82
355 370 3.254657 TCGGACGAATTTCTGCCAATTTT 59.745 39.130 0.00 0.00 0.00 1.82
356 371 3.987220 CGGACGAATTTCTGCCAATTTTT 59.013 39.130 0.00 0.00 0.00 1.94
402 417 9.974750 TTCAAATTTTGGTTTTGTAATTTCGTC 57.025 25.926 9.18 0.00 35.90 4.20
403 418 8.604890 TCAAATTTTGGTTTTGTAATTTCGTCC 58.395 29.630 9.18 0.00 35.90 4.79
404 419 6.757026 ATTTTGGTTTTGTAATTTCGTCCG 57.243 33.333 0.00 0.00 0.00 4.79
405 420 5.496133 TTTGGTTTTGTAATTTCGTCCGA 57.504 34.783 0.00 0.00 0.00 4.55
406 421 4.735662 TGGTTTTGTAATTTCGTCCGAG 57.264 40.909 0.00 0.00 0.00 4.63
407 422 4.378774 TGGTTTTGTAATTTCGTCCGAGA 58.621 39.130 0.00 0.00 0.00 4.04
408 423 4.998672 TGGTTTTGTAATTTCGTCCGAGAT 59.001 37.500 0.00 0.00 0.00 2.75
409 424 5.470777 TGGTTTTGTAATTTCGTCCGAGATT 59.529 36.000 9.87 9.87 34.14 2.40
410 425 6.016943 TGGTTTTGTAATTTCGTCCGAGATTT 60.017 34.615 10.19 0.00 32.36 2.17
411 426 6.859508 GGTTTTGTAATTTCGTCCGAGATTTT 59.140 34.615 10.19 0.00 32.36 1.82
412 427 8.016801 GGTTTTGTAATTTCGTCCGAGATTTTA 58.983 33.333 10.19 0.00 32.36 1.52
413 428 8.834212 GTTTTGTAATTTCGTCCGAGATTTTAC 58.166 33.333 10.19 5.24 32.36 2.01
414 429 6.651755 TGTAATTTCGTCCGAGATTTTACC 57.348 37.500 10.19 0.03 32.36 2.85
415 430 4.852609 AATTTCGTCCGAGATTTTACCG 57.147 40.909 0.16 0.00 0.00 4.02
416 431 3.574284 TTTCGTCCGAGATTTTACCGA 57.426 42.857 0.00 0.00 0.00 4.69
417 432 3.788333 TTCGTCCGAGATTTTACCGAT 57.212 42.857 0.00 0.00 0.00 4.18
418 433 4.898829 TTCGTCCGAGATTTTACCGATA 57.101 40.909 0.00 0.00 0.00 2.92
419 434 5.443185 TTCGTCCGAGATTTTACCGATAT 57.557 39.130 0.00 0.00 0.00 1.63
420 435 5.443185 TCGTCCGAGATTTTACCGATATT 57.557 39.130 0.00 0.00 0.00 1.28
421 436 5.835257 TCGTCCGAGATTTTACCGATATTT 58.165 37.500 0.00 0.00 0.00 1.40
422 437 6.275335 TCGTCCGAGATTTTACCGATATTTT 58.725 36.000 0.00 0.00 0.00 1.82
423 438 6.757947 TCGTCCGAGATTTTACCGATATTTTT 59.242 34.615 0.00 0.00 0.00 1.94
424 439 7.920151 TCGTCCGAGATTTTACCGATATTTTTA 59.080 33.333 0.00 0.00 0.00 1.52
425 440 8.542132 CGTCCGAGATTTTACCGATATTTTTAA 58.458 33.333 0.00 0.00 0.00 1.52
438 453 9.863845 ACCGATATTTTTAAAATGACCGAATTT 57.136 25.926 12.62 0.00 0.00 1.82
443 458 6.546972 TTTTAAAATGACCGAATTTTGGCC 57.453 33.333 0.00 0.00 39.48 5.36
444 459 3.760580 AAAATGACCGAATTTTGGCCA 57.239 38.095 0.00 0.00 38.12 5.36
445 460 3.979101 AAATGACCGAATTTTGGCCAT 57.021 38.095 6.09 0.50 0.00 4.40
446 461 3.525268 AATGACCGAATTTTGGCCATC 57.475 42.857 6.09 0.00 0.00 3.51
447 462 2.214376 TGACCGAATTTTGGCCATCT 57.786 45.000 6.09 0.00 0.00 2.90
448 463 2.091541 TGACCGAATTTTGGCCATCTC 58.908 47.619 6.09 0.00 0.00 2.75
449 464 1.064060 GACCGAATTTTGGCCATCTCG 59.936 52.381 6.09 12.56 0.00 4.04
450 465 1.094785 CCGAATTTTGGCCATCTCGT 58.905 50.000 6.09 0.00 0.00 4.18
451 466 1.472480 CCGAATTTTGGCCATCTCGTT 59.528 47.619 6.09 0.00 0.00 3.85
452 467 2.094752 CCGAATTTTGGCCATCTCGTTT 60.095 45.455 6.09 0.00 0.00 3.60
453 468 3.127895 CCGAATTTTGGCCATCTCGTTTA 59.872 43.478 6.09 0.00 0.00 2.01
454 469 4.342772 CGAATTTTGGCCATCTCGTTTAG 58.657 43.478 6.09 0.00 0.00 1.85
455 470 4.672409 GAATTTTGGCCATCTCGTTTAGG 58.328 43.478 6.09 0.00 0.00 2.69
456 471 3.426787 TTTTGGCCATCTCGTTTAGGA 57.573 42.857 6.09 0.00 0.00 2.94
457 472 2.691409 TTGGCCATCTCGTTTAGGAG 57.309 50.000 6.09 0.00 35.32 3.69
458 473 0.178068 TGGCCATCTCGTTTAGGAGC 59.822 55.000 0.00 0.00 33.98 4.70
459 474 0.876342 GGCCATCTCGTTTAGGAGCG 60.876 60.000 0.00 0.00 33.98 5.03
460 475 0.102481 GCCATCTCGTTTAGGAGCGA 59.898 55.000 0.00 0.00 37.00 4.93
461 476 1.470979 GCCATCTCGTTTAGGAGCGAA 60.471 52.381 0.00 0.00 38.05 4.70
462 477 2.888594 CCATCTCGTTTAGGAGCGAAA 58.111 47.619 0.00 0.00 38.05 3.46
463 478 3.259064 CCATCTCGTTTAGGAGCGAAAA 58.741 45.455 0.00 0.00 38.05 2.29
464 479 3.682858 CCATCTCGTTTAGGAGCGAAAAA 59.317 43.478 0.00 0.00 38.05 1.94
495 510 3.705604 CGAAAGGCAAAACACAACATCT 58.294 40.909 0.00 0.00 0.00 2.90
496 511 4.111916 CGAAAGGCAAAACACAACATCTT 58.888 39.130 0.00 0.00 0.00 2.40
497 512 4.207019 CGAAAGGCAAAACACAACATCTTC 59.793 41.667 0.00 0.00 0.00 2.87
498 513 5.343307 AAAGGCAAAACACAACATCTTCT 57.657 34.783 0.00 0.00 0.00 2.85
499 514 5.343307 AAGGCAAAACACAACATCTTCTT 57.657 34.783 0.00 0.00 0.00 2.52
500 515 4.936891 AGGCAAAACACAACATCTTCTTC 58.063 39.130 0.00 0.00 0.00 2.87
501 516 4.051237 GGCAAAACACAACATCTTCTTCC 58.949 43.478 0.00 0.00 0.00 3.46
502 517 4.051237 GCAAAACACAACATCTTCTTCCC 58.949 43.478 0.00 0.00 0.00 3.97
503 518 4.620982 CAAAACACAACATCTTCTTCCCC 58.379 43.478 0.00 0.00 0.00 4.81
504 519 3.593442 AACACAACATCTTCTTCCCCA 57.407 42.857 0.00 0.00 0.00 4.96
505 520 2.863809 ACACAACATCTTCTTCCCCAC 58.136 47.619 0.00 0.00 0.00 4.61
506 521 1.806542 CACAACATCTTCTTCCCCACG 59.193 52.381 0.00 0.00 0.00 4.94
507 522 1.697432 ACAACATCTTCTTCCCCACGA 59.303 47.619 0.00 0.00 0.00 4.35
508 523 2.105821 ACAACATCTTCTTCCCCACGAA 59.894 45.455 0.00 0.00 0.00 3.85
509 524 3.146066 CAACATCTTCTTCCCCACGAAA 58.854 45.455 0.00 0.00 0.00 3.46
510 525 3.059352 ACATCTTCTTCCCCACGAAAG 57.941 47.619 0.00 0.00 0.00 2.62
511 526 2.637872 ACATCTTCTTCCCCACGAAAGA 59.362 45.455 0.00 0.00 0.00 2.52
512 527 3.072476 ACATCTTCTTCCCCACGAAAGAA 59.928 43.478 0.00 0.00 0.00 2.52
513 528 3.849563 TCTTCTTCCCCACGAAAGAAA 57.150 42.857 0.00 0.00 0.00 2.52
514 529 3.473625 TCTTCTTCCCCACGAAAGAAAC 58.526 45.455 0.00 0.00 0.00 2.78
515 530 3.135895 TCTTCTTCCCCACGAAAGAAACT 59.864 43.478 0.00 0.00 0.00 2.66
516 531 3.121738 TCTTCCCCACGAAAGAAACTC 57.878 47.619 0.00 0.00 0.00 3.01
517 532 2.152016 CTTCCCCACGAAAGAAACTCC 58.848 52.381 0.00 0.00 0.00 3.85
518 533 0.399075 TCCCCACGAAAGAAACTCCC 59.601 55.000 0.00 0.00 0.00 4.30
519 534 0.109723 CCCCACGAAAGAAACTCCCA 59.890 55.000 0.00 0.00 0.00 4.37
520 535 1.271926 CCCCACGAAAGAAACTCCCAT 60.272 52.381 0.00 0.00 0.00 4.00
521 536 2.084546 CCCACGAAAGAAACTCCCATC 58.915 52.381 0.00 0.00 0.00 3.51
522 537 1.732259 CCACGAAAGAAACTCCCATCG 59.268 52.381 0.00 0.00 36.45 3.84
523 538 1.128692 CACGAAAGAAACTCCCATCGC 59.871 52.381 0.00 0.00 33.88 4.58
524 539 0.727398 CGAAAGAAACTCCCATCGCC 59.273 55.000 0.00 0.00 0.00 5.54
525 540 1.821216 GAAAGAAACTCCCATCGCCA 58.179 50.000 0.00 0.00 0.00 5.69
526 541 1.740025 GAAAGAAACTCCCATCGCCAG 59.260 52.381 0.00 0.00 0.00 4.85
527 542 0.035056 AAGAAACTCCCATCGCCAGG 60.035 55.000 0.00 0.00 0.00 4.45
528 543 2.044946 AAACTCCCATCGCCAGGC 60.045 61.111 0.00 0.00 0.00 4.85
529 544 3.645268 AAACTCCCATCGCCAGGCC 62.645 63.158 5.63 0.00 0.00 5.19
531 546 4.559063 CTCCCATCGCCAGGCCTG 62.559 72.222 26.87 26.87 0.00 4.85
535 550 4.889112 CATCGCCAGGCCTGCCAT 62.889 66.667 28.39 14.83 38.92 4.40
536 551 4.889112 ATCGCCAGGCCTGCCATG 62.889 66.667 28.39 14.81 38.92 3.66
545 560 2.361992 CCTGCCATGGCTGCTGAA 60.362 61.111 35.53 14.98 42.51 3.02
546 561 1.980232 CCTGCCATGGCTGCTGAAA 60.980 57.895 35.53 14.21 42.51 2.69
547 562 1.214589 CTGCCATGGCTGCTGAAAC 59.785 57.895 35.53 5.76 42.51 2.78
548 563 2.180017 GCCATGGCTGCTGAAACG 59.820 61.111 29.98 0.00 38.26 3.60
549 564 2.334946 GCCATGGCTGCTGAAACGA 61.335 57.895 29.98 0.00 38.26 3.85
550 565 1.798735 CCATGGCTGCTGAAACGAG 59.201 57.895 0.00 0.00 0.00 4.18
551 566 1.136147 CATGGCTGCTGAAACGAGC 59.864 57.895 0.00 0.00 39.62 5.03
552 567 1.002868 ATGGCTGCTGAAACGAGCT 60.003 52.632 0.00 0.00 39.90 4.09
553 568 1.303799 ATGGCTGCTGAAACGAGCTG 61.304 55.000 0.00 0.00 39.90 4.24
554 569 1.669115 GGCTGCTGAAACGAGCTGA 60.669 57.895 0.00 0.00 39.58 4.26
555 570 1.633852 GGCTGCTGAAACGAGCTGAG 61.634 60.000 0.00 0.00 39.58 3.35
556 571 0.668706 GCTGCTGAAACGAGCTGAGA 60.669 55.000 0.00 0.00 39.58 3.27
557 572 2.006056 GCTGCTGAAACGAGCTGAGAT 61.006 52.381 0.00 0.00 39.58 2.75
558 573 2.344950 CTGCTGAAACGAGCTGAGATT 58.655 47.619 0.00 0.00 39.58 2.40
559 574 2.341257 TGCTGAAACGAGCTGAGATTC 58.659 47.619 0.00 0.00 39.90 2.52
560 575 2.289010 TGCTGAAACGAGCTGAGATTCA 60.289 45.455 0.00 0.80 39.90 2.57
561 576 2.935201 GCTGAAACGAGCTGAGATTCAT 59.065 45.455 10.48 0.00 35.95 2.57
562 577 3.242349 GCTGAAACGAGCTGAGATTCATG 60.242 47.826 10.48 0.00 35.95 3.07
563 578 2.674852 TGAAACGAGCTGAGATTCATGC 59.325 45.455 0.00 0.00 0.00 4.06
564 579 1.661341 AACGAGCTGAGATTCATGCC 58.339 50.000 0.00 0.00 0.00 4.40
565 580 0.179062 ACGAGCTGAGATTCATGCCC 60.179 55.000 0.00 0.00 0.00 5.36
566 581 0.179065 CGAGCTGAGATTCATGCCCA 60.179 55.000 0.00 0.00 0.00 5.36
567 582 1.542767 CGAGCTGAGATTCATGCCCAT 60.543 52.381 0.00 0.00 0.00 4.00
568 583 2.584236 GAGCTGAGATTCATGCCCATT 58.416 47.619 0.00 0.00 0.00 3.16
569 584 2.553172 GAGCTGAGATTCATGCCCATTC 59.447 50.000 0.00 0.00 0.00 2.67
570 585 2.092049 AGCTGAGATTCATGCCCATTCA 60.092 45.455 0.00 0.00 0.00 2.57
571 586 2.691526 GCTGAGATTCATGCCCATTCAA 59.308 45.455 0.00 0.00 0.00 2.69
572 587 3.131577 GCTGAGATTCATGCCCATTCAAA 59.868 43.478 0.00 0.00 0.00 2.69
573 588 4.382254 GCTGAGATTCATGCCCATTCAAAA 60.382 41.667 0.00 0.00 0.00 2.44
574 589 5.333299 TGAGATTCATGCCCATTCAAAAG 57.667 39.130 0.00 0.00 0.00 2.27
575 590 5.018149 TGAGATTCATGCCCATTCAAAAGA 58.982 37.500 0.00 0.00 0.00 2.52
576 591 5.126545 TGAGATTCATGCCCATTCAAAAGAG 59.873 40.000 0.00 0.00 0.00 2.85
577 592 5.266788 AGATTCATGCCCATTCAAAAGAGA 58.733 37.500 0.00 0.00 0.00 3.10
578 593 5.360144 AGATTCATGCCCATTCAAAAGAGAG 59.640 40.000 0.00 0.00 0.00 3.20
579 594 4.305539 TCATGCCCATTCAAAAGAGAGA 57.694 40.909 0.00 0.00 0.00 3.10
580 595 4.665451 TCATGCCCATTCAAAAGAGAGAA 58.335 39.130 0.00 0.00 0.00 2.87
581 596 5.078949 TCATGCCCATTCAAAAGAGAGAAA 58.921 37.500 0.00 0.00 0.00 2.52
582 597 5.539574 TCATGCCCATTCAAAAGAGAGAAAA 59.460 36.000 0.00 0.00 0.00 2.29
583 598 5.867903 TGCCCATTCAAAAGAGAGAAAAA 57.132 34.783 0.00 0.00 0.00 1.94
604 619 6.885952 AAAAGAGAAAAAGAGTAGGAAGGC 57.114 37.500 0.00 0.00 0.00 4.35
605 620 4.195225 AGAGAAAAAGAGTAGGAAGGCG 57.805 45.455 0.00 0.00 0.00 5.52
606 621 3.579151 AGAGAAAAAGAGTAGGAAGGCGT 59.421 43.478 0.00 0.00 0.00 5.68
607 622 4.771054 AGAGAAAAAGAGTAGGAAGGCGTA 59.229 41.667 0.00 0.00 0.00 4.42
608 623 4.818642 AGAAAAAGAGTAGGAAGGCGTAC 58.181 43.478 0.00 0.00 36.01 3.67
609 624 3.606595 AAAAGAGTAGGAAGGCGTACC 57.393 47.619 0.00 0.00 36.33 3.34
610 625 2.226962 AAGAGTAGGAAGGCGTACCA 57.773 50.000 0.00 0.00 39.06 3.25
611 626 1.765230 AGAGTAGGAAGGCGTACCAG 58.235 55.000 0.00 0.00 39.06 4.00
612 627 0.745468 GAGTAGGAAGGCGTACCAGG 59.255 60.000 0.00 0.00 39.06 4.45
613 628 0.333993 AGTAGGAAGGCGTACCAGGA 59.666 55.000 0.00 0.00 39.06 3.86
614 629 1.188863 GTAGGAAGGCGTACCAGGAA 58.811 55.000 0.00 0.00 39.06 3.36
615 630 1.551883 GTAGGAAGGCGTACCAGGAAA 59.448 52.381 0.00 0.00 39.06 3.13
678 694 0.179094 AAGGAGTGCGACGTTGTTGA 60.179 50.000 4.37 0.00 0.00 3.18
696 712 4.281435 TGTTGAAATGAATGGCTGTGATGT 59.719 37.500 0.00 0.00 0.00 3.06
811 827 0.535797 GCGGGACCTAGCAGTTACTT 59.464 55.000 7.46 0.00 0.00 2.24
1017 1043 3.348119 AGTGATGTCTAGCTCGACTTCA 58.652 45.455 24.45 24.45 42.32 3.02
1089 1115 3.067439 AATTGCCCGCGCATGGAA 61.067 55.556 16.62 9.71 46.67 3.53
1128 1154 5.208121 ACTTTTGTGAGGGAAGAAAATGGA 58.792 37.500 0.00 0.00 0.00 3.41
1225 1251 6.749036 ATCTTATGGTCTAATTTCTCCCGT 57.251 37.500 0.00 0.00 0.00 5.28
1571 1600 4.640201 TGGCTAGAGCATTTTATGGTTGTC 59.360 41.667 3.54 0.00 41.77 3.18
1802 1833 5.961272 TGTTTCCTCTGTTTTTGTTCTTCC 58.039 37.500 0.00 0.00 0.00 3.46
1810 1841 6.910995 TCTGTTTTTGTTCTTCCGTTAACAA 58.089 32.000 6.39 0.00 42.27 2.83
1871 1913 1.066002 CTGCCAAATAGATGTTGGGCG 59.934 52.381 5.41 0.00 44.87 6.13
1927 1974 3.334891 ACCAGCCCACCCGCATAA 61.335 61.111 0.00 0.00 0.00 1.90
1933 1980 1.531748 CCCACCCGCATAAGGACAT 59.468 57.895 0.00 0.00 0.00 3.06
2241 2329 2.751688 GGTGTAGAAACCCGGGCA 59.248 61.111 24.08 6.20 33.79 5.36
2242 2330 1.301954 GGTGTAGAAACCCGGGCAT 59.698 57.895 24.08 10.01 33.79 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.309501 CGCACACACATGTCGAGCA 61.310 57.895 12.62 0.00 36.72 4.26
1 2 2.471607 CGCACACACATGTCGAGC 59.528 61.111 0.00 0.00 36.72 5.03
2 3 3.015293 GCCGCACACACATGTCGAG 62.015 63.158 0.00 0.00 36.72 4.04
187 202 2.611722 GGAGAGGTGCTTCAGAGTTGAC 60.612 54.545 0.00 0.00 31.71 3.18
199 214 1.222936 CATGGACAGGGAGAGGTGC 59.777 63.158 0.00 0.00 0.00 5.01
216 231 8.934825 CAGTTCCAAAAGAAAAAGATTGAAACA 58.065 29.630 0.00 0.00 35.85 2.83
221 236 8.876275 TCATCAGTTCCAAAAGAAAAAGATTG 57.124 30.769 0.00 0.00 35.85 2.67
230 245 6.716173 TCAACATCATCATCAGTTCCAAAAGA 59.284 34.615 0.00 0.00 0.00 2.52
239 254 4.831674 TCAGGTCAACATCATCATCAGT 57.168 40.909 0.00 0.00 0.00 3.41
253 268 6.205853 ACGTTTAAAAACTATGCATCAGGTCA 59.794 34.615 0.19 0.00 36.77 4.02
255 270 6.569179 ACGTTTAAAAACTATGCATCAGGT 57.431 33.333 0.19 0.00 36.77 4.00
256 271 9.221775 GAATACGTTTAAAAACTATGCATCAGG 57.778 33.333 0.19 0.00 36.77 3.86
261 276 8.325421 TGAGGAATACGTTTAAAAACTATGCA 57.675 30.769 0.00 0.00 36.77 3.96
264 279 9.498176 ACACTGAGGAATACGTTTAAAAACTAT 57.502 29.630 0.00 0.00 36.77 2.12
265 280 8.891671 ACACTGAGGAATACGTTTAAAAACTA 57.108 30.769 0.00 0.00 36.77 2.24
275 290 3.314553 CGAACAACACTGAGGAATACGT 58.685 45.455 0.00 0.00 0.00 3.57
277 292 2.415512 GCCGAACAACACTGAGGAATAC 59.584 50.000 0.00 0.00 0.00 1.89
278 293 2.301870 AGCCGAACAACACTGAGGAATA 59.698 45.455 0.00 0.00 0.00 1.75
279 294 1.072331 AGCCGAACAACACTGAGGAAT 59.928 47.619 0.00 0.00 0.00 3.01
280 295 0.468226 AGCCGAACAACACTGAGGAA 59.532 50.000 0.00 0.00 0.00 3.36
281 296 1.000506 GTAGCCGAACAACACTGAGGA 59.999 52.381 0.00 0.00 0.00 3.71
282 297 1.429463 GTAGCCGAACAACACTGAGG 58.571 55.000 0.00 0.00 0.00 3.86
283 298 1.270094 TGGTAGCCGAACAACACTGAG 60.270 52.381 0.00 0.00 0.00 3.35
284 299 0.753867 TGGTAGCCGAACAACACTGA 59.246 50.000 0.00 0.00 0.00 3.41
285 300 1.808411 ATGGTAGCCGAACAACACTG 58.192 50.000 0.00 0.00 0.00 3.66
286 301 3.906720 ATATGGTAGCCGAACAACACT 57.093 42.857 0.00 0.00 0.00 3.55
287 302 4.957759 AAATATGGTAGCCGAACAACAC 57.042 40.909 0.00 0.00 0.00 3.32
307 322 7.826260 ATTTTTGAAAACGAGCAGAGAAAAA 57.174 28.000 0.00 0.00 0.00 1.94
308 323 7.826260 AATTTTTGAAAACGAGCAGAGAAAA 57.174 28.000 0.00 0.00 0.00 2.29
309 324 7.253618 CGAAATTTTTGAAAACGAGCAGAGAAA 60.254 33.333 0.00 0.00 0.00 2.52
310 325 6.196353 CGAAATTTTTGAAAACGAGCAGAGAA 59.804 34.615 0.00 0.00 0.00 2.87
311 326 5.681105 CGAAATTTTTGAAAACGAGCAGAGA 59.319 36.000 0.00 0.00 0.00 3.10
312 327 5.108254 CCGAAATTTTTGAAAACGAGCAGAG 60.108 40.000 0.00 0.00 0.00 3.35
313 328 4.737765 CCGAAATTTTTGAAAACGAGCAGA 59.262 37.500 0.00 0.00 0.00 4.26
314 329 4.737765 TCCGAAATTTTTGAAAACGAGCAG 59.262 37.500 0.00 0.00 0.00 4.24
315 330 4.501198 GTCCGAAATTTTTGAAAACGAGCA 59.499 37.500 0.00 0.00 0.00 4.26
316 331 4.373619 CGTCCGAAATTTTTGAAAACGAGC 60.374 41.667 10.73 0.00 0.00 5.03
317 332 4.965158 TCGTCCGAAATTTTTGAAAACGAG 59.035 37.500 13.13 0.00 0.00 4.18
318 333 4.906423 TCGTCCGAAATTTTTGAAAACGA 58.094 34.783 13.13 13.13 0.00 3.85
319 334 5.607858 TTCGTCCGAAATTTTTGAAAACG 57.392 34.783 0.00 5.57 0.00 3.60
320 335 8.325282 AGAAATTCGTCCGAAATTTTTGAAAAC 58.675 29.630 6.19 0.00 37.69 2.43
321 336 8.324567 CAGAAATTCGTCCGAAATTTTTGAAAA 58.675 29.630 6.19 0.00 37.69 2.29
322 337 7.515998 GCAGAAATTCGTCCGAAATTTTTGAAA 60.516 33.333 19.41 0.00 37.69 2.69
323 338 6.074569 GCAGAAATTCGTCCGAAATTTTTGAA 60.075 34.615 19.41 0.00 37.69 2.69
324 339 5.401079 GCAGAAATTCGTCCGAAATTTTTGA 59.599 36.000 19.41 0.00 37.69 2.69
325 340 5.388371 GGCAGAAATTCGTCCGAAATTTTTG 60.388 40.000 6.19 12.32 37.69 2.44
326 341 4.684242 GGCAGAAATTCGTCCGAAATTTTT 59.316 37.500 6.19 3.01 37.69 1.94
327 342 4.234574 GGCAGAAATTCGTCCGAAATTTT 58.765 39.130 6.19 3.70 37.69 1.82
328 343 3.254657 TGGCAGAAATTCGTCCGAAATTT 59.745 39.130 6.19 7.63 37.69 1.82
329 344 2.817258 TGGCAGAAATTCGTCCGAAATT 59.183 40.909 6.19 4.30 37.69 1.82
330 345 2.432444 TGGCAGAAATTCGTCCGAAAT 58.568 42.857 6.19 0.00 37.69 2.17
331 346 1.885560 TGGCAGAAATTCGTCCGAAA 58.114 45.000 6.19 0.00 37.69 3.46
332 347 1.885560 TTGGCAGAAATTCGTCCGAA 58.114 45.000 4.42 4.42 38.59 4.30
333 348 2.107950 ATTGGCAGAAATTCGTCCGA 57.892 45.000 0.00 0.40 0.00 4.55
334 349 2.919666 AATTGGCAGAAATTCGTCCG 57.080 45.000 0.00 0.00 0.00 4.79
376 391 9.974750 GACGAAATTACAAAACCAAAATTTGAA 57.025 25.926 7.37 0.00 39.56 2.69
377 392 8.604890 GGACGAAATTACAAAACCAAAATTTGA 58.395 29.630 7.37 0.00 39.56 2.69
378 393 7.580882 CGGACGAAATTACAAAACCAAAATTTG 59.419 33.333 0.00 0.00 42.18 2.32
379 394 7.491696 TCGGACGAAATTACAAAACCAAAATTT 59.508 29.630 0.00 0.00 34.98 1.82
380 395 6.979238 TCGGACGAAATTACAAAACCAAAATT 59.021 30.769 0.00 0.00 0.00 1.82
381 396 6.505272 TCGGACGAAATTACAAAACCAAAAT 58.495 32.000 0.00 0.00 0.00 1.82
382 397 5.888105 TCGGACGAAATTACAAAACCAAAA 58.112 33.333 0.00 0.00 0.00 2.44
383 398 5.296283 TCTCGGACGAAATTACAAAACCAAA 59.704 36.000 0.00 0.00 0.00 3.28
384 399 4.815308 TCTCGGACGAAATTACAAAACCAA 59.185 37.500 0.00 0.00 0.00 3.67
385 400 4.378774 TCTCGGACGAAATTACAAAACCA 58.621 39.130 0.00 0.00 0.00 3.67
386 401 4.996062 TCTCGGACGAAATTACAAAACC 57.004 40.909 0.00 0.00 0.00 3.27
387 402 7.847166 AAAATCTCGGACGAAATTACAAAAC 57.153 32.000 0.00 0.00 0.00 2.43
388 403 8.016801 GGTAAAATCTCGGACGAAATTACAAAA 58.983 33.333 14.55 0.00 0.00 2.44
389 404 7.520686 GGTAAAATCTCGGACGAAATTACAAA 58.479 34.615 14.55 0.00 0.00 2.83
390 405 6.183360 CGGTAAAATCTCGGACGAAATTACAA 60.183 38.462 14.55 0.00 0.00 2.41
391 406 5.289193 CGGTAAAATCTCGGACGAAATTACA 59.711 40.000 14.55 0.00 0.00 2.41
392 407 5.516339 TCGGTAAAATCTCGGACGAAATTAC 59.484 40.000 0.00 3.67 0.00 1.89
393 408 5.649557 TCGGTAAAATCTCGGACGAAATTA 58.350 37.500 0.00 0.00 0.00 1.40
394 409 4.497300 TCGGTAAAATCTCGGACGAAATT 58.503 39.130 0.00 0.00 0.00 1.82
395 410 4.114058 TCGGTAAAATCTCGGACGAAAT 57.886 40.909 0.00 0.00 0.00 2.17
396 411 3.574284 TCGGTAAAATCTCGGACGAAA 57.426 42.857 0.00 0.00 0.00 3.46
397 412 3.788333 ATCGGTAAAATCTCGGACGAA 57.212 42.857 0.00 0.00 32.39 3.85
398 413 5.443185 AATATCGGTAAAATCTCGGACGA 57.557 39.130 0.00 0.00 0.00 4.20
399 414 6.520792 AAAATATCGGTAAAATCTCGGACG 57.479 37.500 0.00 0.00 0.00 4.79
412 427 9.863845 AAATTCGGTCATTTTAAAAATATCGGT 57.136 25.926 14.75 5.63 0.00 4.69
417 432 8.722394 GGCCAAAATTCGGTCATTTTAAAAATA 58.278 29.630 4.44 0.00 35.09 1.40
418 433 7.229506 TGGCCAAAATTCGGTCATTTTAAAAAT 59.770 29.630 0.61 0.00 35.09 1.82
419 434 6.542370 TGGCCAAAATTCGGTCATTTTAAAAA 59.458 30.769 0.61 0.00 35.09 1.94
420 435 6.055588 TGGCCAAAATTCGGTCATTTTAAAA 58.944 32.000 0.61 2.51 35.09 1.52
421 436 5.611374 TGGCCAAAATTCGGTCATTTTAAA 58.389 33.333 0.61 0.00 35.09 1.52
422 437 5.215252 TGGCCAAAATTCGGTCATTTTAA 57.785 34.783 0.61 0.00 35.09 1.52
423 438 4.873746 TGGCCAAAATTCGGTCATTTTA 57.126 36.364 0.61 0.00 35.09 1.52
424 439 3.760580 TGGCCAAAATTCGGTCATTTT 57.239 38.095 0.61 0.00 36.90 1.82
425 440 3.979101 ATGGCCAAAATTCGGTCATTT 57.021 38.095 10.96 0.00 46.78 2.32
428 443 2.091541 GAGATGGCCAAAATTCGGTCA 58.908 47.619 10.96 3.82 43.65 4.02
429 444 1.064060 CGAGATGGCCAAAATTCGGTC 59.936 52.381 10.96 0.00 0.00 4.79
430 445 1.094785 CGAGATGGCCAAAATTCGGT 58.905 50.000 10.96 0.00 0.00 4.69
431 446 1.094785 ACGAGATGGCCAAAATTCGG 58.905 50.000 25.21 13.50 32.77 4.30
432 447 2.919666 AACGAGATGGCCAAAATTCG 57.080 45.000 22.08 22.08 0.00 3.34
433 448 4.398044 TCCTAAACGAGATGGCCAAAATTC 59.602 41.667 10.96 1.72 0.00 2.17
434 449 4.340617 TCCTAAACGAGATGGCCAAAATT 58.659 39.130 10.96 0.00 0.00 1.82
435 450 3.947834 CTCCTAAACGAGATGGCCAAAAT 59.052 43.478 10.96 0.00 30.97 1.82
436 451 3.343617 CTCCTAAACGAGATGGCCAAAA 58.656 45.455 10.96 0.00 30.97 2.44
437 452 2.939640 GCTCCTAAACGAGATGGCCAAA 60.940 50.000 10.96 0.00 30.97 3.28
438 453 1.406887 GCTCCTAAACGAGATGGCCAA 60.407 52.381 10.96 0.00 30.97 4.52
439 454 0.178068 GCTCCTAAACGAGATGGCCA 59.822 55.000 8.56 8.56 30.97 5.36
440 455 0.876342 CGCTCCTAAACGAGATGGCC 60.876 60.000 0.00 0.00 30.97 5.36
441 456 0.102481 TCGCTCCTAAACGAGATGGC 59.898 55.000 0.00 0.00 33.69 4.40
442 457 2.579207 TTCGCTCCTAAACGAGATGG 57.421 50.000 0.00 0.00 39.81 3.51
443 458 4.921470 TTTTTCGCTCCTAAACGAGATG 57.079 40.909 0.00 0.00 39.81 2.90
462 477 2.911484 TGCCTTTCGGTTTGCATTTTT 58.089 38.095 0.00 0.00 0.00 1.94
463 478 2.611225 TGCCTTTCGGTTTGCATTTT 57.389 40.000 0.00 0.00 0.00 1.82
464 479 2.611225 TTGCCTTTCGGTTTGCATTT 57.389 40.000 0.00 0.00 33.08 2.32
465 480 2.611225 TTTGCCTTTCGGTTTGCATT 57.389 40.000 0.00 0.00 33.08 3.56
466 481 2.209273 GTTTTGCCTTTCGGTTTGCAT 58.791 42.857 0.00 0.00 33.08 3.96
467 482 1.066858 TGTTTTGCCTTTCGGTTTGCA 60.067 42.857 0.00 0.00 0.00 4.08
468 483 1.326245 GTGTTTTGCCTTTCGGTTTGC 59.674 47.619 0.00 0.00 0.00 3.68
469 484 2.611518 TGTGTTTTGCCTTTCGGTTTG 58.388 42.857 0.00 0.00 0.00 2.93
470 485 2.997303 GTTGTGTTTTGCCTTTCGGTTT 59.003 40.909 0.00 0.00 0.00 3.27
471 486 2.028930 TGTTGTGTTTTGCCTTTCGGTT 60.029 40.909 0.00 0.00 0.00 4.44
472 487 1.546476 TGTTGTGTTTTGCCTTTCGGT 59.454 42.857 0.00 0.00 0.00 4.69
473 488 2.285827 TGTTGTGTTTTGCCTTTCGG 57.714 45.000 0.00 0.00 0.00 4.30
474 489 3.705604 AGATGTTGTGTTTTGCCTTTCG 58.294 40.909 0.00 0.00 0.00 3.46
475 490 5.351458 AGAAGATGTTGTGTTTTGCCTTTC 58.649 37.500 0.00 0.00 0.00 2.62
476 491 5.343307 AGAAGATGTTGTGTTTTGCCTTT 57.657 34.783 0.00 0.00 0.00 3.11
477 492 5.343307 AAGAAGATGTTGTGTTTTGCCTT 57.657 34.783 0.00 0.00 0.00 4.35
478 493 4.202151 GGAAGAAGATGTTGTGTTTTGCCT 60.202 41.667 0.00 0.00 0.00 4.75
479 494 4.051237 GGAAGAAGATGTTGTGTTTTGCC 58.949 43.478 0.00 0.00 0.00 4.52
480 495 4.051237 GGGAAGAAGATGTTGTGTTTTGC 58.949 43.478 0.00 0.00 0.00 3.68
481 496 4.099266 TGGGGAAGAAGATGTTGTGTTTTG 59.901 41.667 0.00 0.00 0.00 2.44
482 497 4.099419 GTGGGGAAGAAGATGTTGTGTTTT 59.901 41.667 0.00 0.00 0.00 2.43
483 498 3.636764 GTGGGGAAGAAGATGTTGTGTTT 59.363 43.478 0.00 0.00 0.00 2.83
484 499 3.222603 GTGGGGAAGAAGATGTTGTGTT 58.777 45.455 0.00 0.00 0.00 3.32
485 500 2.810400 CGTGGGGAAGAAGATGTTGTGT 60.810 50.000 0.00 0.00 0.00 3.72
486 501 1.806542 CGTGGGGAAGAAGATGTTGTG 59.193 52.381 0.00 0.00 0.00 3.33
487 502 1.697432 TCGTGGGGAAGAAGATGTTGT 59.303 47.619 0.00 0.00 0.00 3.32
488 503 2.472695 TCGTGGGGAAGAAGATGTTG 57.527 50.000 0.00 0.00 0.00 3.33
489 504 3.072476 TCTTTCGTGGGGAAGAAGATGTT 59.928 43.478 0.00 0.00 35.70 2.71
490 505 2.637872 TCTTTCGTGGGGAAGAAGATGT 59.362 45.455 0.00 0.00 35.70 3.06
491 506 3.334583 TCTTTCGTGGGGAAGAAGATG 57.665 47.619 0.00 0.00 35.70 2.90
492 507 4.072839 GTTTCTTTCGTGGGGAAGAAGAT 58.927 43.478 0.00 0.00 35.70 2.40
493 508 3.135895 AGTTTCTTTCGTGGGGAAGAAGA 59.864 43.478 0.00 0.00 35.70 2.87
494 509 3.477530 AGTTTCTTTCGTGGGGAAGAAG 58.522 45.455 0.00 0.00 35.70 2.85
495 510 3.473625 GAGTTTCTTTCGTGGGGAAGAA 58.526 45.455 0.00 0.00 35.70 2.52
496 511 2.224450 GGAGTTTCTTTCGTGGGGAAGA 60.224 50.000 0.00 0.00 35.70 2.87
497 512 2.152016 GGAGTTTCTTTCGTGGGGAAG 58.848 52.381 0.00 0.00 35.70 3.46
498 513 1.202842 GGGAGTTTCTTTCGTGGGGAA 60.203 52.381 0.00 0.00 0.00 3.97
499 514 0.399075 GGGAGTTTCTTTCGTGGGGA 59.601 55.000 0.00 0.00 0.00 4.81
500 515 0.109723 TGGGAGTTTCTTTCGTGGGG 59.890 55.000 0.00 0.00 0.00 4.96
501 516 2.084546 GATGGGAGTTTCTTTCGTGGG 58.915 52.381 0.00 0.00 0.00 4.61
502 517 1.732259 CGATGGGAGTTTCTTTCGTGG 59.268 52.381 0.00 0.00 0.00 4.94
503 518 1.128692 GCGATGGGAGTTTCTTTCGTG 59.871 52.381 0.00 0.00 0.00 4.35
504 519 1.439679 GCGATGGGAGTTTCTTTCGT 58.560 50.000 0.00 0.00 0.00 3.85
505 520 0.727398 GGCGATGGGAGTTTCTTTCG 59.273 55.000 0.00 0.00 0.00 3.46
506 521 1.740025 CTGGCGATGGGAGTTTCTTTC 59.260 52.381 0.00 0.00 0.00 2.62
507 522 1.614317 CCTGGCGATGGGAGTTTCTTT 60.614 52.381 0.00 0.00 0.00 2.52
508 523 0.035056 CCTGGCGATGGGAGTTTCTT 60.035 55.000 0.00 0.00 0.00 2.52
509 524 1.604378 CCTGGCGATGGGAGTTTCT 59.396 57.895 0.00 0.00 0.00 2.52
510 525 2.115291 GCCTGGCGATGGGAGTTTC 61.115 63.158 1.35 0.00 0.00 2.78
511 526 2.044946 GCCTGGCGATGGGAGTTT 60.045 61.111 1.35 0.00 0.00 2.66
512 527 4.115199 GGCCTGGCGATGGGAGTT 62.115 66.667 13.40 0.00 0.00 3.01
514 529 4.559063 CAGGCCTGGCGATGGGAG 62.559 72.222 26.14 0.00 0.00 4.30
528 543 1.980232 TTTCAGCAGCCATGGCAGG 60.980 57.895 37.18 28.31 44.88 4.85
529 544 1.214589 GTTTCAGCAGCCATGGCAG 59.785 57.895 37.18 30.66 44.88 4.85
530 545 2.628696 CGTTTCAGCAGCCATGGCA 61.629 57.895 37.18 14.94 44.88 4.92
531 546 2.180017 CGTTTCAGCAGCCATGGC 59.820 61.111 30.12 30.12 42.33 4.40
532 547 1.798735 CTCGTTTCAGCAGCCATGG 59.201 57.895 7.63 7.63 0.00 3.66
533 548 1.136147 GCTCGTTTCAGCAGCCATG 59.864 57.895 0.00 0.00 39.43 3.66
534 549 1.002868 AGCTCGTTTCAGCAGCCAT 60.003 52.632 0.00 0.00 42.40 4.40
535 550 1.962822 CAGCTCGTTTCAGCAGCCA 60.963 57.895 0.00 0.00 42.40 4.75
536 551 1.633852 CTCAGCTCGTTTCAGCAGCC 61.634 60.000 0.00 0.00 42.40 4.85
537 552 0.668706 TCTCAGCTCGTTTCAGCAGC 60.669 55.000 0.00 0.00 42.40 5.25
538 553 2.007360 ATCTCAGCTCGTTTCAGCAG 57.993 50.000 0.00 0.00 42.40 4.24
539 554 2.289010 TGAATCTCAGCTCGTTTCAGCA 60.289 45.455 0.00 0.00 42.40 4.41
540 555 2.341257 TGAATCTCAGCTCGTTTCAGC 58.659 47.619 0.00 0.00 39.99 4.26
541 556 3.242349 GCATGAATCTCAGCTCGTTTCAG 60.242 47.826 0.00 5.84 30.56 3.02
542 557 2.674852 GCATGAATCTCAGCTCGTTTCA 59.325 45.455 0.00 7.93 0.00 2.69
543 558 2.031437 GGCATGAATCTCAGCTCGTTTC 59.969 50.000 0.00 0.00 0.00 2.78
544 559 2.012673 GGCATGAATCTCAGCTCGTTT 58.987 47.619 0.00 0.00 0.00 3.60
545 560 1.661341 GGCATGAATCTCAGCTCGTT 58.339 50.000 0.00 0.00 0.00 3.85
546 561 0.179062 GGGCATGAATCTCAGCTCGT 60.179 55.000 0.00 0.00 0.00 4.18
547 562 0.179065 TGGGCATGAATCTCAGCTCG 60.179 55.000 0.00 0.00 0.00 5.03
548 563 2.273538 ATGGGCATGAATCTCAGCTC 57.726 50.000 0.00 0.00 0.00 4.09
549 564 2.092049 TGAATGGGCATGAATCTCAGCT 60.092 45.455 0.00 0.00 0.00 4.24
550 565 2.304092 TGAATGGGCATGAATCTCAGC 58.696 47.619 0.00 0.00 0.00 4.26
551 566 4.994907 TTTGAATGGGCATGAATCTCAG 57.005 40.909 0.00 0.00 0.00 3.35
552 567 5.018149 TCTTTTGAATGGGCATGAATCTCA 58.982 37.500 0.00 0.00 0.00 3.27
553 568 5.359009 TCTCTTTTGAATGGGCATGAATCTC 59.641 40.000 0.00 0.00 0.00 2.75
554 569 5.266788 TCTCTTTTGAATGGGCATGAATCT 58.733 37.500 0.00 0.00 0.00 2.40
555 570 5.359009 TCTCTCTTTTGAATGGGCATGAATC 59.641 40.000 0.00 0.00 0.00 2.52
556 571 5.266788 TCTCTCTTTTGAATGGGCATGAAT 58.733 37.500 0.00 0.00 0.00 2.57
557 572 4.665451 TCTCTCTTTTGAATGGGCATGAA 58.335 39.130 0.00 0.00 0.00 2.57
558 573 4.305539 TCTCTCTTTTGAATGGGCATGA 57.694 40.909 0.00 0.00 0.00 3.07
559 574 5.395682 TTTCTCTCTTTTGAATGGGCATG 57.604 39.130 0.00 0.00 0.00 4.06
560 575 6.423776 TTTTTCTCTCTTTTGAATGGGCAT 57.576 33.333 0.00 0.00 0.00 4.40
561 576 5.867903 TTTTTCTCTCTTTTGAATGGGCA 57.132 34.783 0.00 0.00 0.00 5.36
580 595 6.017026 CGCCTTCCTACTCTTTTTCTCTTTTT 60.017 38.462 0.00 0.00 0.00 1.94
581 596 5.470437 CGCCTTCCTACTCTTTTTCTCTTTT 59.530 40.000 0.00 0.00 0.00 2.27
582 597 4.998033 CGCCTTCCTACTCTTTTTCTCTTT 59.002 41.667 0.00 0.00 0.00 2.52
583 598 4.040584 ACGCCTTCCTACTCTTTTTCTCTT 59.959 41.667 0.00 0.00 0.00 2.85
584 599 3.579151 ACGCCTTCCTACTCTTTTTCTCT 59.421 43.478 0.00 0.00 0.00 3.10
585 600 3.927854 ACGCCTTCCTACTCTTTTTCTC 58.072 45.455 0.00 0.00 0.00 2.87
586 601 4.322574 GGTACGCCTTCCTACTCTTTTTCT 60.323 45.833 0.00 0.00 0.00 2.52
587 602 3.931468 GGTACGCCTTCCTACTCTTTTTC 59.069 47.826 0.00 0.00 0.00 2.29
588 603 3.325716 TGGTACGCCTTCCTACTCTTTTT 59.674 43.478 0.00 0.00 35.27 1.94
589 604 2.901839 TGGTACGCCTTCCTACTCTTTT 59.098 45.455 0.00 0.00 35.27 2.27
590 605 2.496470 CTGGTACGCCTTCCTACTCTTT 59.504 50.000 0.00 0.00 35.27 2.52
591 606 2.100989 CTGGTACGCCTTCCTACTCTT 58.899 52.381 0.00 0.00 35.27 2.85
592 607 1.685491 CCTGGTACGCCTTCCTACTCT 60.685 57.143 0.00 0.00 35.27 3.24
593 608 0.745468 CCTGGTACGCCTTCCTACTC 59.255 60.000 0.00 0.00 35.27 2.59
594 609 0.333993 TCCTGGTACGCCTTCCTACT 59.666 55.000 0.00 0.00 35.27 2.57
595 610 1.188863 TTCCTGGTACGCCTTCCTAC 58.811 55.000 0.00 0.00 35.27 3.18
596 611 1.551883 GTTTCCTGGTACGCCTTCCTA 59.448 52.381 0.00 0.00 35.27 2.94
597 612 0.323957 GTTTCCTGGTACGCCTTCCT 59.676 55.000 0.00 0.00 35.27 3.36
598 613 0.035739 TGTTTCCTGGTACGCCTTCC 59.964 55.000 0.00 0.00 35.27 3.46
599 614 1.154197 GTGTTTCCTGGTACGCCTTC 58.846 55.000 0.00 0.00 35.27 3.46
600 615 0.250597 GGTGTTTCCTGGTACGCCTT 60.251 55.000 19.80 0.00 40.83 4.35
601 616 1.373812 GGTGTTTCCTGGTACGCCT 59.626 57.895 19.80 0.00 40.83 5.52
602 617 2.030958 CGGTGTTTCCTGGTACGCC 61.031 63.158 18.17 18.17 40.66 5.68
603 618 2.030958 CCGGTGTTTCCTGGTACGC 61.031 63.158 0.00 0.26 0.00 4.42
604 619 1.375013 CCCGGTGTTTCCTGGTACG 60.375 63.158 0.00 0.00 36.09 3.67
605 620 4.707791 CCCGGTGTTTCCTGGTAC 57.292 61.111 0.00 0.00 36.09 3.34
608 623 0.251165 ATTGACCCGGTGTTTCCTGG 60.251 55.000 0.00 0.00 44.72 4.45
609 624 2.356135 CTATTGACCCGGTGTTTCCTG 58.644 52.381 0.00 0.00 0.00 3.86
610 625 1.339727 GCTATTGACCCGGTGTTTCCT 60.340 52.381 0.00 0.00 0.00 3.36
611 626 1.092348 GCTATTGACCCGGTGTTTCC 58.908 55.000 0.00 0.00 0.00 3.13
612 627 2.007608 GAGCTATTGACCCGGTGTTTC 58.992 52.381 0.00 0.00 0.00 2.78
613 628 1.339727 GGAGCTATTGACCCGGTGTTT 60.340 52.381 0.00 0.00 0.00 2.83
614 629 0.252197 GGAGCTATTGACCCGGTGTT 59.748 55.000 0.00 0.00 0.00 3.32
615 630 0.617820 AGGAGCTATTGACCCGGTGT 60.618 55.000 0.00 0.00 0.00 4.16
678 694 3.119743 CGTCACATCACAGCCATTCATTT 60.120 43.478 0.00 0.00 0.00 2.32
696 712 6.017440 AGCTATTGTTTGCTTCTAAAACGTCA 60.017 34.615 0.00 0.00 39.81 4.35
1089 1115 2.622064 AAGTCAAACGCTTCAGAGGT 57.378 45.000 0.00 0.00 0.00 3.85
1128 1154 1.822186 AAACTCGCGCCCACAGTTT 60.822 52.632 14.86 14.86 35.88 2.66
1441 1470 0.466372 TCATCGGATCGGCTCTGTCT 60.466 55.000 0.00 0.00 0.00 3.41
1571 1600 9.520204 CAAGTAAAATAAACCCATAGCAATGAG 57.480 33.333 0.00 0.00 34.84 2.90
1802 1833 4.879104 TTGGGTGTGTACTTTGTTAACG 57.121 40.909 0.26 0.00 0.00 3.18
1810 1841 5.891551 AGAAACTGAATTTGGGTGTGTACTT 59.108 36.000 0.00 0.00 0.00 2.24
1856 1898 2.238646 TCTCACCGCCCAACATCTATTT 59.761 45.455 0.00 0.00 0.00 1.40
1871 1913 0.039618 TCAGGGCCCATTTTCTCACC 59.960 55.000 27.56 0.00 0.00 4.02
1924 1971 1.771255 GAGGTGGGCTGATGTCCTTAT 59.229 52.381 0.00 0.00 39.11 1.73
1927 1974 0.339859 TAGAGGTGGGCTGATGTCCT 59.660 55.000 0.00 0.00 39.11 3.85
1933 1980 0.895530 CGAAGTTAGAGGTGGGCTGA 59.104 55.000 0.00 0.00 0.00 4.26
2241 2329 4.821805 GTGTATTGCTATGGGTTGCTACAT 59.178 41.667 0.00 0.00 0.00 2.29
2242 2330 4.196193 GTGTATTGCTATGGGTTGCTACA 58.804 43.478 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.