Multiple sequence alignment - TraesCS6D01G343800

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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 TraesCS6D01G343800 chr6D 100.000 2639 0 0 1 2639 443742352 443739714 0.000000e+00 4874.0
1 TraesCS6D01G343800 chr6D 84.516 465 42 23 998 1447 443754011 443753562 1.450000e-117 433.0
2 TraesCS6D01G343800 chr6D 95.588 68 3 0 1571 1638 443753487 443753420 2.780000e-20 110.0
3 TraesCS6D01G343800 chr6D 87.671 73 1 2 808 879 443754201 443754136 7.830000e-11 78.7
4 TraesCS6D01G343800 chr6A 90.898 1681 83 32 552 2216 591381641 591380015 0.000000e+00 2193.0
5 TraesCS6D01G343800 chr6A 89.083 229 4 8 23 240 591382140 591381922 5.600000e-67 265.0
6 TraesCS6D01G343800 chr6A 90.370 135 12 1 2350 2483 591379904 591379770 2.700000e-40 176.0
7 TraesCS6D01G343800 chr6B 87.785 1318 75 42 502 1791 668030521 668029262 0.000000e+00 1463.0
8 TraesCS6D01G343800 chr6B 82.195 747 63 36 1912 2619 668029218 668028503 1.760000e-161 579.0
9 TraesCS6D01G343800 chr6B 88.294 299 21 8 14 299 668030948 668030651 1.940000e-91 346.0
10 TraesCS6D01G343800 chr6B 84.932 73 3 4 808 879 668137071 668137006 1.700000e-07 67.6
11 TraesCS6D01G343800 chr4D 90.964 166 12 3 292 455 51076185 51076349 1.230000e-53 220.0
12 TraesCS6D01G343800 chr3B 91.613 155 11 2 292 445 36421507 36421660 2.060000e-51 213.0
13 TraesCS6D01G343800 chr3B 89.677 155 14 2 292 445 493121789 493121636 2.070000e-46 196.0
14 TraesCS6D01G343800 chr3B 88.387 155 16 2 292 445 229307716 229307869 4.490000e-43 185.0
15 TraesCS6D01G343800 chr5D 90.062 161 12 4 292 451 494083091 494082934 3.440000e-49 206.0
16 TraesCS6D01G343800 chr3A 89.873 158 14 2 292 448 501225795 501225639 4.450000e-48 202.0
17 TraesCS6D01G343800 chr3D 89.542 153 13 2 292 443 554769070 554769220 9.640000e-45 191.0
18 TraesCS6D01G343800 chr1B 88.889 153 15 2 293 444 670782794 670782945 1.250000e-43 187.0
19 TraesCS6D01G343800 chr2B 88.816 152 15 2 292 441 785273426 785273577 4.490000e-43 185.0
20 TraesCS6D01G343800 chr2B 91.736 121 8 2 1199 1318 726546001 726546120 1.620000e-37 167.0
21 TraesCS6D01G343800 chr2B 87.179 78 10 0 1012 1089 726135854 726135931 3.620000e-14 89.8
22 TraesCS6D01G343800 chr2B 87.179 78 10 0 1012 1089 726545801 726545878 3.620000e-14 89.8
23 TraesCS6D01G343800 chr2D 92.562 121 7 2 1199 1318 598712894 598713013 3.490000e-39 172.0
24 TraesCS6D01G343800 chr7D 93.103 116 8 0 1204 1319 93949218 93949103 1.260000e-38 171.0
25 TraesCS6D01G343800 chr7D 90.076 131 12 1 1204 1334 94005718 94005847 4.520000e-38 169.0
26 TraesCS6D01G343800 chr7D 95.604 91 4 0 999 1089 93949387 93949297 2.120000e-31 147.0
27 TraesCS6D01G343800 chr7D 95.556 90 4 0 1000 1089 94005549 94005638 7.610000e-31 145.0
28 TraesCS6D01G343800 chr7D 84.211 114 12 6 495 607 359084056 359084164 3.590000e-19 106.0
29 TraesCS6D01G343800 chr7A 85.714 161 19 4 1204 1362 97267112 97267270 1.620000e-37 167.0
30 TraesCS6D01G343800 chr7A 94.444 90 5 0 1000 1089 97266936 97267025 3.540000e-29 139.0
31 TraesCS6D01G343800 chr2A 90.909 121 9 2 1199 1318 732580516 732580635 7.560000e-36 161.0
32 TraesCS6D01G343800 chr7B 90.517 116 11 0 1204 1319 47737435 47737550 1.260000e-33 154.0
33 TraesCS6D01G343800 chr7B 95.604 91 4 0 999 1089 47737265 47737355 2.120000e-31 147.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G343800 chr6D 443739714 443742352 2638 True 4874.000000 4874 100.000000 1 2639 1 chr6D.!!$R1 2638
1 TraesCS6D01G343800 chr6D 443753420 443754201 781 True 207.233333 433 89.258333 808 1638 3 chr6D.!!$R2 830
2 TraesCS6D01G343800 chr6A 591379770 591382140 2370 True 878.000000 2193 90.117000 23 2483 3 chr6A.!!$R1 2460
3 TraesCS6D01G343800 chr6B 668028503 668030948 2445 True 796.000000 1463 86.091333 14 2619 3 chr6B.!!$R2 2605

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
370 453 0.096976 CTATGTTTGCCAACCTCGCG 59.903 55.0 0.0 0.0 31.02 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2422 0.107897 TAGCACGCCATTGATCGGTT 60.108 50.0 0.0 0.0 0.0 4.44 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
137 149 1.085091 CAGTCTTTAGCAGCAGCAGG 58.915 55.000 3.17 0.00 45.49 4.85
139 151 1.377725 TCTTTAGCAGCAGCAGGGC 60.378 57.895 3.17 0.00 45.49 5.19
140 152 1.676635 CTTTAGCAGCAGCAGGGCA 60.677 57.895 3.17 0.00 45.49 5.36
195 207 3.181482 CCCGTGCATGGCTATCTATCTAG 60.181 52.174 20.27 0.00 0.00 2.43
196 208 3.181482 CCGTGCATGGCTATCTATCTAGG 60.181 52.174 13.11 0.00 0.00 3.02
197 209 3.696548 CGTGCATGGCTATCTATCTAGGA 59.303 47.826 0.00 0.00 0.00 2.94
198 210 4.202000 CGTGCATGGCTATCTATCTAGGAG 60.202 50.000 0.00 0.00 0.00 3.69
279 361 6.697641 AAAGTCTCCCTCCATACTTAACAA 57.302 37.500 0.00 0.00 32.09 2.83
281 363 6.893020 AGTCTCCCTCCATACTTAACAATT 57.107 37.500 0.00 0.00 0.00 2.32
299 382 2.600470 TTGCCTTGGCTCAACTTTTG 57.400 45.000 13.18 0.00 0.00 2.44
300 383 0.104671 TGCCTTGGCTCAACTTTTGC 59.895 50.000 13.18 0.00 0.00 3.68
301 384 0.390492 GCCTTGGCTCAACTTTTGCT 59.610 50.000 4.11 0.00 0.00 3.91
302 385 1.870993 GCCTTGGCTCAACTTTTGCTG 60.871 52.381 4.11 0.00 0.00 4.41
303 386 1.410153 CCTTGGCTCAACTTTTGCTGT 59.590 47.619 0.00 0.00 0.00 4.40
304 387 2.159057 CCTTGGCTCAACTTTTGCTGTT 60.159 45.455 0.00 0.00 0.00 3.16
305 388 3.068024 CCTTGGCTCAACTTTTGCTGTTA 59.932 43.478 0.00 0.00 0.00 2.41
306 389 4.441356 CCTTGGCTCAACTTTTGCTGTTAA 60.441 41.667 0.00 0.00 0.00 2.01
307 390 4.727507 TGGCTCAACTTTTGCTGTTAAA 57.272 36.364 0.00 0.00 0.00 1.52
308 391 4.429108 TGGCTCAACTTTTGCTGTTAAAC 58.571 39.130 0.00 0.00 0.00 2.01
309 392 4.081972 TGGCTCAACTTTTGCTGTTAAACA 60.082 37.500 0.00 0.00 0.00 2.83
310 393 5.049828 GGCTCAACTTTTGCTGTTAAACAT 58.950 37.500 0.00 0.00 0.00 2.71
311 394 5.050837 GGCTCAACTTTTGCTGTTAAACATG 60.051 40.000 0.00 0.00 0.00 3.21
312 395 5.050837 GCTCAACTTTTGCTGTTAAACATGG 60.051 40.000 0.00 0.00 0.00 3.66
313 396 4.808364 TCAACTTTTGCTGTTAAACATGGC 59.192 37.500 0.00 0.00 0.00 4.40
314 397 4.399004 ACTTTTGCTGTTAAACATGGCA 57.601 36.364 0.00 0.00 29.08 4.92
315 398 4.764172 ACTTTTGCTGTTAAACATGGCAA 58.236 34.783 0.00 0.00 37.45 4.52
316 399 4.570369 ACTTTTGCTGTTAAACATGGCAAC 59.430 37.500 0.00 0.00 38.45 4.17
317 400 4.399004 TTTGCTGTTAAACATGGCAACT 57.601 36.364 0.00 0.00 38.45 3.16
318 401 4.399004 TTGCTGTTAAACATGGCAACTT 57.601 36.364 0.00 0.00 35.33 2.66
319 402 4.399004 TGCTGTTAAACATGGCAACTTT 57.601 36.364 0.00 0.00 28.22 2.66
320 403 4.118410 TGCTGTTAAACATGGCAACTTTG 58.882 39.130 0.00 0.00 28.22 2.77
321 404 4.119136 GCTGTTAAACATGGCAACTTTGT 58.881 39.130 0.00 0.00 35.56 2.83
322 405 4.209080 GCTGTTAAACATGGCAACTTTGTC 59.791 41.667 0.00 0.00 33.40 3.18
323 406 4.688021 TGTTAAACATGGCAACTTTGTCC 58.312 39.130 0.00 0.00 33.40 4.02
324 407 2.908688 AAACATGGCAACTTTGTCCC 57.091 45.000 0.00 0.00 33.40 4.46
325 408 1.786937 AACATGGCAACTTTGTCCCA 58.213 45.000 0.00 0.00 33.40 4.37
326 409 1.331214 ACATGGCAACTTTGTCCCAG 58.669 50.000 0.00 0.00 37.61 4.45
327 410 1.331214 CATGGCAACTTTGTCCCAGT 58.669 50.000 0.00 0.00 37.61 4.00
328 411 1.688197 CATGGCAACTTTGTCCCAGTT 59.312 47.619 0.00 0.00 34.67 3.16
329 412 1.398692 TGGCAACTTTGTCCCAGTTC 58.601 50.000 0.00 0.00 31.83 3.01
330 413 0.310854 GGCAACTTTGTCCCAGTTCG 59.689 55.000 0.00 0.00 31.83 3.95
331 414 1.021968 GCAACTTTGTCCCAGTTCGT 58.978 50.000 0.00 0.00 31.83 3.85
332 415 1.404035 GCAACTTTGTCCCAGTTCGTT 59.596 47.619 0.00 0.00 31.83 3.85
333 416 2.159296 GCAACTTTGTCCCAGTTCGTTT 60.159 45.455 0.00 0.00 31.83 3.60
334 417 3.674955 GCAACTTTGTCCCAGTTCGTTTT 60.675 43.478 0.00 0.00 31.83 2.43
335 418 4.490743 CAACTTTGTCCCAGTTCGTTTTT 58.509 39.130 0.00 0.00 31.83 1.94
336 419 4.365899 ACTTTGTCCCAGTTCGTTTTTC 57.634 40.909 0.00 0.00 0.00 2.29
337 420 4.014406 ACTTTGTCCCAGTTCGTTTTTCT 58.986 39.130 0.00 0.00 0.00 2.52
338 421 4.461431 ACTTTGTCCCAGTTCGTTTTTCTT 59.539 37.500 0.00 0.00 0.00 2.52
339 422 4.364415 TTGTCCCAGTTCGTTTTTCTTG 57.636 40.909 0.00 0.00 0.00 3.02
340 423 3.349022 TGTCCCAGTTCGTTTTTCTTGT 58.651 40.909 0.00 0.00 0.00 3.16
341 424 3.375922 TGTCCCAGTTCGTTTTTCTTGTC 59.624 43.478 0.00 0.00 0.00 3.18
342 425 3.375922 GTCCCAGTTCGTTTTTCTTGTCA 59.624 43.478 0.00 0.00 0.00 3.58
343 426 3.625764 TCCCAGTTCGTTTTTCTTGTCAG 59.374 43.478 0.00 0.00 0.00 3.51
344 427 3.625764 CCCAGTTCGTTTTTCTTGTCAGA 59.374 43.478 0.00 0.00 0.00 3.27
345 428 4.095782 CCCAGTTCGTTTTTCTTGTCAGAA 59.904 41.667 0.00 0.00 37.24 3.02
346 429 5.392595 CCCAGTTCGTTTTTCTTGTCAGAAA 60.393 40.000 0.00 0.00 45.63 2.52
359 442 8.578308 TTCTTGTCAGAAAATTGCTATGTTTG 57.422 30.769 0.00 0.00 35.99 2.93
360 443 6.642131 TCTTGTCAGAAAATTGCTATGTTTGC 59.358 34.615 0.00 0.00 0.00 3.68
361 444 5.229423 TGTCAGAAAATTGCTATGTTTGCC 58.771 37.500 0.00 0.00 0.00 4.52
362 445 5.221402 TGTCAGAAAATTGCTATGTTTGCCA 60.221 36.000 0.00 0.00 0.00 4.92
363 446 5.695816 GTCAGAAAATTGCTATGTTTGCCAA 59.304 36.000 0.00 0.00 0.00 4.52
364 447 5.695816 TCAGAAAATTGCTATGTTTGCCAAC 59.304 36.000 0.00 0.00 0.00 3.77
365 448 4.996758 AGAAAATTGCTATGTTTGCCAACC 59.003 37.500 0.00 0.00 31.02 3.77
366 449 4.622260 AAATTGCTATGTTTGCCAACCT 57.378 36.364 0.00 0.00 31.02 3.50
367 450 3.874392 ATTGCTATGTTTGCCAACCTC 57.126 42.857 0.00 0.00 31.02 3.85
368 451 1.164411 TGCTATGTTTGCCAACCTCG 58.836 50.000 0.00 0.00 31.02 4.63
369 452 0.179163 GCTATGTTTGCCAACCTCGC 60.179 55.000 0.00 0.00 31.02 5.03
370 453 0.096976 CTATGTTTGCCAACCTCGCG 59.903 55.000 0.00 0.00 31.02 5.87
371 454 0.604243 TATGTTTGCCAACCTCGCGT 60.604 50.000 5.77 0.00 31.02 6.01
372 455 2.051345 GTTTGCCAACCTCGCGTG 60.051 61.111 5.77 2.75 0.00 5.34
373 456 2.203084 TTTGCCAACCTCGCGTGA 60.203 55.556 10.21 0.00 0.00 4.35
374 457 1.820056 TTTGCCAACCTCGCGTGAA 60.820 52.632 10.21 0.00 0.00 3.18
375 458 2.054140 TTTGCCAACCTCGCGTGAAC 62.054 55.000 10.21 0.00 0.00 3.18
376 459 2.665185 GCCAACCTCGCGTGAACT 60.665 61.111 10.21 0.00 0.00 3.01
377 460 1.373748 GCCAACCTCGCGTGAACTA 60.374 57.895 10.21 0.00 0.00 2.24
378 461 0.947180 GCCAACCTCGCGTGAACTAA 60.947 55.000 10.21 0.00 0.00 2.24
379 462 1.504359 CCAACCTCGCGTGAACTAAA 58.496 50.000 10.21 0.00 0.00 1.85
380 463 1.868498 CCAACCTCGCGTGAACTAAAA 59.132 47.619 10.21 0.00 0.00 1.52
381 464 2.482721 CCAACCTCGCGTGAACTAAAAT 59.517 45.455 10.21 0.00 0.00 1.82
382 465 3.058501 CCAACCTCGCGTGAACTAAAATT 60.059 43.478 10.21 0.00 0.00 1.82
383 466 3.806316 ACCTCGCGTGAACTAAAATTG 57.194 42.857 10.21 0.00 0.00 2.32
384 467 3.135994 ACCTCGCGTGAACTAAAATTGT 58.864 40.909 10.21 0.00 0.00 2.71
385 468 3.185797 ACCTCGCGTGAACTAAAATTGTC 59.814 43.478 10.21 0.00 0.00 3.18
386 469 3.185594 CCTCGCGTGAACTAAAATTGTCA 59.814 43.478 10.21 0.00 0.00 3.58
387 470 4.142902 CCTCGCGTGAACTAAAATTGTCAT 60.143 41.667 10.21 0.00 0.00 3.06
388 471 4.707563 TCGCGTGAACTAAAATTGTCATG 58.292 39.130 5.77 0.00 0.00 3.07
389 472 4.449405 TCGCGTGAACTAAAATTGTCATGA 59.551 37.500 5.77 0.00 0.00 3.07
390 473 5.050023 TCGCGTGAACTAAAATTGTCATGAA 60.050 36.000 5.77 0.00 0.00 2.57
391 474 5.623264 CGCGTGAACTAAAATTGTCATGAAA 59.377 36.000 0.00 0.00 0.00 2.69
392 475 6.141527 CGCGTGAACTAAAATTGTCATGAAAA 59.858 34.615 0.00 0.00 0.00 2.29
393 476 7.305705 CGCGTGAACTAAAATTGTCATGAAAAA 60.306 33.333 1.55 0.00 0.00 1.94
394 477 8.487176 GCGTGAACTAAAATTGTCATGAAAAAT 58.513 29.630 1.55 0.70 0.00 1.82
405 488 7.754069 TTGTCATGAAAAATATTCGGATTGC 57.246 32.000 0.00 0.00 0.00 3.56
406 489 6.272318 TGTCATGAAAAATATTCGGATTGCC 58.728 36.000 0.00 0.00 0.00 4.52
407 490 6.127507 TGTCATGAAAAATATTCGGATTGCCA 60.128 34.615 0.00 0.00 0.00 4.92
408 491 6.925165 GTCATGAAAAATATTCGGATTGCCAT 59.075 34.615 0.00 0.00 0.00 4.40
409 492 6.924612 TCATGAAAAATATTCGGATTGCCATG 59.075 34.615 0.00 0.00 0.00 3.66
410 493 5.049167 TGAAAAATATTCGGATTGCCATGC 58.951 37.500 0.00 0.00 0.00 4.06
411 494 4.942761 AAAATATTCGGATTGCCATGCT 57.057 36.364 0.00 0.00 0.00 3.79
412 495 4.942761 AAATATTCGGATTGCCATGCTT 57.057 36.364 0.00 0.00 0.00 3.91
413 496 6.403866 AAAATATTCGGATTGCCATGCTTA 57.596 33.333 0.00 0.00 0.00 3.09
414 497 6.403866 AAATATTCGGATTGCCATGCTTAA 57.596 33.333 0.00 0.00 0.00 1.85
415 498 6.403866 AATATTCGGATTGCCATGCTTAAA 57.596 33.333 0.00 0.00 0.00 1.52
416 499 4.734398 ATTCGGATTGCCATGCTTAAAA 57.266 36.364 0.00 0.00 0.00 1.52
417 500 4.734398 TTCGGATTGCCATGCTTAAAAT 57.266 36.364 0.00 0.00 0.00 1.82
418 501 4.305989 TCGGATTGCCATGCTTAAAATC 57.694 40.909 0.00 0.00 0.00 2.17
419 502 3.068024 TCGGATTGCCATGCTTAAAATCC 59.932 43.478 10.61 10.61 41.84 3.01
420 503 3.383761 GGATTGCCATGCTTAAAATCCG 58.616 45.455 0.00 0.00 37.58 4.18
421 504 3.068024 GGATTGCCATGCTTAAAATCCGA 59.932 43.478 0.00 0.00 37.58 4.55
422 505 4.441356 GGATTGCCATGCTTAAAATCCGAA 60.441 41.667 0.00 0.00 37.58 4.30
423 506 3.502191 TGCCATGCTTAAAATCCGAAC 57.498 42.857 0.00 0.00 0.00 3.95
424 507 2.159448 TGCCATGCTTAAAATCCGAACG 60.159 45.455 0.00 0.00 0.00 3.95
425 508 2.159435 GCCATGCTTAAAATCCGAACGT 60.159 45.455 0.00 0.00 0.00 3.99
426 509 3.672241 GCCATGCTTAAAATCCGAACGTT 60.672 43.478 0.00 0.00 0.00 3.99
427 510 4.481463 CCATGCTTAAAATCCGAACGTTT 58.519 39.130 0.46 0.00 0.00 3.60
428 511 4.323336 CCATGCTTAAAATCCGAACGTTTG 59.677 41.667 8.68 8.68 0.00 2.93
429 512 3.891324 TGCTTAAAATCCGAACGTTTGG 58.109 40.909 26.25 26.25 0.00 3.28
430 513 3.239254 GCTTAAAATCCGAACGTTTGGG 58.761 45.455 30.12 20.92 32.26 4.12
431 514 3.058085 GCTTAAAATCCGAACGTTTGGGA 60.058 43.478 30.12 24.87 41.96 4.37
438 521 3.940319 TCCGAACGTTTGGGATTTATCA 58.060 40.909 30.12 9.22 32.17 2.15
439 522 4.519213 TCCGAACGTTTGGGATTTATCAT 58.481 39.130 30.12 0.00 32.17 2.45
440 523 4.944930 TCCGAACGTTTGGGATTTATCATT 59.055 37.500 30.12 0.00 32.17 2.57
441 524 5.416326 TCCGAACGTTTGGGATTTATCATTT 59.584 36.000 30.12 0.00 32.17 2.32
442 525 5.741982 CCGAACGTTTGGGATTTATCATTTC 59.258 40.000 24.79 0.00 0.00 2.17
443 526 5.741982 CGAACGTTTGGGATTTATCATTTCC 59.258 40.000 7.72 0.00 0.00 3.13
444 527 5.243426 ACGTTTGGGATTTATCATTTCCG 57.757 39.130 0.00 0.00 0.00 4.30
445 528 4.041723 CGTTTGGGATTTATCATTTCCGC 58.958 43.478 0.00 0.00 0.00 5.54
446 529 4.439426 CGTTTGGGATTTATCATTTCCGCA 60.439 41.667 0.00 0.00 0.00 5.69
447 530 5.415221 GTTTGGGATTTATCATTTCCGCAA 58.585 37.500 0.00 0.00 0.00 4.85
448 531 4.647424 TGGGATTTATCATTTCCGCAAC 57.353 40.909 0.00 0.00 0.00 4.17
449 532 4.277476 TGGGATTTATCATTTCCGCAACT 58.723 39.130 0.00 0.00 0.00 3.16
450 533 4.709397 TGGGATTTATCATTTCCGCAACTT 59.291 37.500 0.00 0.00 0.00 2.66
451 534 5.186797 TGGGATTTATCATTTCCGCAACTTT 59.813 36.000 0.00 0.00 0.00 2.66
452 535 6.106003 GGGATTTATCATTTCCGCAACTTTT 58.894 36.000 0.00 0.00 0.00 2.27
477 560 5.641783 TCTCTCAAGAGACATGTCAGAAG 57.358 43.478 27.02 15.69 45.48 2.85
487 570 4.282957 AGACATGTCAGAAGAAAGCTGAGA 59.717 41.667 27.02 0.00 42.57 3.27
513 681 7.935804 AAAAATTGCGCAATATGAAATTTCG 57.064 28.000 34.05 1.54 31.13 3.46
515 683 6.884096 AATTGCGCAATATGAAATTTCGAA 57.116 29.167 34.05 2.49 0.00 3.71
522 690 7.576602 GCGCAATATGAAATTTCGAATTTCAAG 59.423 33.333 25.44 19.44 46.84 3.02
529 697 7.786114 TGAAATTTCGAATTTCAAGCATGAAC 58.214 30.769 22.30 0.00 45.01 3.18
530 698 5.997732 ATTTCGAATTTCAAGCATGAACG 57.002 34.783 3.39 5.42 45.01 3.95
531 699 4.740741 TTCGAATTTCAAGCATGAACGA 57.259 36.364 3.39 7.74 45.01 3.85
532 700 4.740741 TCGAATTTCAAGCATGAACGAA 57.259 36.364 11.80 0.00 45.01 3.85
533 701 4.463209 TCGAATTTCAAGCATGAACGAAC 58.537 39.130 11.80 1.87 45.01 3.95
534 702 3.295397 CGAATTTCAAGCATGAACGAACG 59.705 43.478 3.39 4.89 45.01 3.95
555 723 2.280524 TCGAACCCAAGCCACACG 60.281 61.111 0.00 0.00 0.00 4.49
655 824 3.732048 AAACAAAGATATCGGGTGGGT 57.268 42.857 0.00 0.00 0.00 4.51
671 840 3.756727 GTCCGACGGTGTCCTCCC 61.757 72.222 14.79 0.00 0.00 4.30
760 943 1.299648 CCGCAGATTCCCACTTCCA 59.700 57.895 0.00 0.00 0.00 3.53
781 964 0.743345 AGTCCCGCCGCACTTTAATC 60.743 55.000 0.00 0.00 0.00 1.75
857 1052 2.743928 GCAGAACGCACTCCCCTG 60.744 66.667 0.00 0.00 41.79 4.45
1112 1354 1.595382 CCTACCTAGCCATGCACGC 60.595 63.158 0.00 0.00 0.00 5.34
1137 1383 3.313274 GACTTCGTCGATCTCTCTGAC 57.687 52.381 0.00 0.00 0.00 3.51
1163 1412 0.670546 ACGGTGATTCTTGGTCGCTG 60.671 55.000 0.00 0.00 38.21 5.18
1180 1429 2.662596 GGTGGCTCACCGTGATCA 59.337 61.111 0.62 0.00 44.95 2.92
1181 1430 1.448540 GGTGGCTCACCGTGATCAG 60.449 63.158 0.62 0.00 44.95 2.90
1182 1431 1.448540 GTGGCTCACCGTGATCAGG 60.449 63.158 8.47 8.47 39.70 3.86
1183 1432 1.609210 TGGCTCACCGTGATCAGGA 60.609 57.895 16.84 1.92 39.70 3.86
1184 1433 1.153549 GGCTCACCGTGATCAGGAC 60.154 63.158 16.84 0.00 0.00 3.85
1185 1434 1.608717 GGCTCACCGTGATCAGGACT 61.609 60.000 16.84 0.00 0.00 3.85
1186 1435 0.459237 GCTCACCGTGATCAGGACTG 60.459 60.000 16.84 10.97 0.00 3.51
1221 1483 1.447838 TTGCAGGAAGACGCGGATC 60.448 57.895 12.47 5.18 0.00 3.36
1322 1587 4.636435 CACCAACTTCCCCGCCGT 62.636 66.667 0.00 0.00 0.00 5.68
1653 1939 1.397390 ATTAGCCAAGCCAGCCATGC 61.397 55.000 0.00 0.00 0.00 4.06
1689 1981 3.071206 TGCCTCTGCTCGACTCCC 61.071 66.667 0.00 0.00 38.71 4.30
1694 1986 0.107214 CTCTGCTCGACTCCCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
1798 2090 4.221482 AGTCAGTGAGCTATGTGATGTGAA 59.779 41.667 0.00 0.00 0.00 3.18
1821 2113 3.253677 CACCGGAGAAGAGCTCGTATTAT 59.746 47.826 9.46 0.00 44.91 1.28
1823 2115 5.048921 CACCGGAGAAGAGCTCGTATTATTA 60.049 44.000 9.46 0.00 44.91 0.98
1824 2116 5.181622 ACCGGAGAAGAGCTCGTATTATTAG 59.818 44.000 9.46 0.00 44.91 1.73
1825 2117 5.181622 CCGGAGAAGAGCTCGTATTATTAGT 59.818 44.000 8.37 0.00 44.91 2.24
1826 2118 6.294065 CCGGAGAAGAGCTCGTATTATTAGTT 60.294 42.308 8.37 0.00 44.91 2.24
1828 2120 7.520131 CGGAGAAGAGCTCGTATTATTAGTTCA 60.520 40.741 8.37 0.00 44.91 3.18
1829 2121 7.806014 GGAGAAGAGCTCGTATTATTAGTTCAG 59.194 40.741 8.37 0.00 44.91 3.02
1830 2122 8.228035 AGAAGAGCTCGTATTATTAGTTCAGT 57.772 34.615 8.37 0.00 0.00 3.41
1944 2236 4.725790 ATACACCCTACGGTAACAAGTC 57.274 45.455 0.00 0.00 42.04 3.01
1964 2256 8.652290 ACAAGTCTAATCCTCTCTGTTTTTACT 58.348 33.333 0.00 0.00 0.00 2.24
2052 2350 2.110627 AGCCATCTGATCTGCCGC 59.889 61.111 5.35 0.00 0.00 6.53
2072 2370 2.095461 CCCTCGAGAGTCAAGACATCA 58.905 52.381 15.71 0.00 0.00 3.07
2073 2371 2.493675 CCCTCGAGAGTCAAGACATCAA 59.506 50.000 15.71 0.00 0.00 2.57
2074 2372 3.056536 CCCTCGAGAGTCAAGACATCAAA 60.057 47.826 15.71 0.00 0.00 2.69
2075 2373 4.382470 CCCTCGAGAGTCAAGACATCAAAT 60.382 45.833 15.71 0.00 0.00 2.32
2076 2374 4.803088 CCTCGAGAGTCAAGACATCAAATC 59.197 45.833 15.71 0.00 0.00 2.17
2120 2418 1.726791 ACGTGCGATGCTTAACTGAAG 59.273 47.619 0.00 0.00 38.30 3.02
2210 2516 4.641396 CCGGATAATAAATCAGCCAGACA 58.359 43.478 0.00 0.00 0.00 3.41
2216 2522 0.613260 AAATCAGCCAGACACGCCTA 59.387 50.000 0.00 0.00 0.00 3.93
2217 2523 0.108138 AATCAGCCAGACACGCCTAC 60.108 55.000 0.00 0.00 0.00 3.18
2219 2525 2.675423 AGCCAGACACGCCTACGA 60.675 61.111 0.00 0.00 43.93 3.43
2275 2602 1.303091 TGGCTCGATCGTCGACAGAA 61.303 55.000 17.16 0.05 44.82 3.02
2277 2604 1.534175 GGCTCGATCGTCGACAGAATT 60.534 52.381 17.16 0.03 44.82 2.17
2278 2605 2.286831 GGCTCGATCGTCGACAGAATTA 60.287 50.000 17.16 3.30 44.82 1.40
2279 2606 3.556513 GCTCGATCGTCGACAGAATTAT 58.443 45.455 17.16 0.00 44.82 1.28
2312 2639 3.705051 ACATGCCATGGACTGAATTTCT 58.295 40.909 18.40 0.00 33.60 2.52
2320 2647 3.653344 TGGACTGAATTTCTCTGTGTCG 58.347 45.455 0.00 0.00 36.43 4.35
2321 2648 3.069586 TGGACTGAATTTCTCTGTGTCGT 59.930 43.478 0.00 0.00 36.43 4.34
2322 2649 4.058817 GGACTGAATTTCTCTGTGTCGTT 58.941 43.478 0.00 0.00 36.43 3.85
2323 2650 5.221362 TGGACTGAATTTCTCTGTGTCGTTA 60.221 40.000 0.00 0.00 36.43 3.18
2332 2659 1.000506 TCTGTGTCGTTAGTTGGCTCC 59.999 52.381 0.00 0.00 0.00 4.70
2336 2663 1.899814 TGTCGTTAGTTGGCTCCTCAT 59.100 47.619 0.00 0.00 0.00 2.90
2340 2667 2.436417 GTTAGTTGGCTCCTCATTGCA 58.564 47.619 0.00 0.00 0.00 4.08
2342 2669 0.403271 AGTTGGCTCCTCATTGCAGT 59.597 50.000 0.00 0.00 0.00 4.40
2345 2672 1.001641 GGCTCCTCATTGCAGTGGT 60.002 57.895 9.56 0.00 0.00 4.16
2346 2673 1.310933 GGCTCCTCATTGCAGTGGTG 61.311 60.000 9.56 3.06 0.00 4.17
2388 2716 3.242381 GCATTTCTTTGTGGTGTGTTTGC 60.242 43.478 0.00 0.00 0.00 3.68
2389 2717 2.270275 TTCTTTGTGGTGTGTTTGCG 57.730 45.000 0.00 0.00 0.00 4.85
2417 2746 3.756933 TGTGCTGATGCTGCATATCTA 57.243 42.857 16.23 0.05 40.15 1.98
2420 2749 3.927758 GTGCTGATGCTGCATATCTAGAG 59.072 47.826 16.23 6.09 40.15 2.43
2421 2750 3.830755 TGCTGATGCTGCATATCTAGAGA 59.169 43.478 16.23 0.00 40.48 3.10
2462 2791 0.395586 GCCACATGACCCTGCCAATA 60.396 55.000 0.00 0.00 0.00 1.90
2475 2804 2.045438 CAATACCGGGCAGCACCA 60.045 61.111 6.32 0.00 42.05 4.17
2476 2805 2.045340 AATACCGGGCAGCACCAC 60.045 61.111 6.32 0.00 42.05 4.16
2483 2812 4.284550 GGCAGCACCACCCCTGAA 62.285 66.667 0.00 0.00 38.86 3.02
2485 2814 2.034687 CAGCACCACCCCTGAAGG 59.965 66.667 0.00 0.00 0.00 3.46
2498 2827 3.815717 TGAAGGGACATCAGGGAGT 57.184 52.632 0.00 0.00 30.39 3.85
2526 2856 1.299620 CGTGTGTCCGTCGAAACCT 60.300 57.895 0.00 0.00 0.00 3.50
2530 2860 0.249155 GTGTCCGTCGAAACCTCACA 60.249 55.000 0.00 0.00 0.00 3.58
2531 2861 0.249155 TGTCCGTCGAAACCTCACAC 60.249 55.000 0.00 0.00 0.00 3.82
2545 2875 1.898574 CACACCCACCACCTTCAGC 60.899 63.158 0.00 0.00 0.00 4.26
2553 2883 0.773644 ACCACCTTCAGCTTGGATGT 59.226 50.000 8.39 0.67 34.24 3.06
2582 2923 1.019673 CACCGAGGAATGGCTGATTG 58.980 55.000 0.00 0.00 0.00 2.67
2588 2929 0.176449 GGAATGGCTGATTGGTTGGC 59.824 55.000 0.00 0.00 0.00 4.52
2620 2961 3.947173 CGGAGGAGATGAGCTGGT 58.053 61.111 0.00 0.00 0.00 4.00
2621 2962 1.440893 CGGAGGAGATGAGCTGGTG 59.559 63.158 0.00 0.00 0.00 4.17
2622 2963 1.326213 CGGAGGAGATGAGCTGGTGT 61.326 60.000 0.00 0.00 0.00 4.16
2623 2964 0.463620 GGAGGAGATGAGCTGGTGTC 59.536 60.000 0.00 0.00 0.00 3.67
2624 2965 0.463620 GAGGAGATGAGCTGGTGTCC 59.536 60.000 0.00 0.00 0.00 4.02
2625 2966 0.980231 AGGAGATGAGCTGGTGTCCC 60.980 60.000 0.00 0.00 0.00 4.46
2626 2967 1.267574 GGAGATGAGCTGGTGTCCCA 61.268 60.000 0.00 0.00 38.87 4.37
2635 2976 2.004120 TGGTGTCCCAGTTGGTGGT 61.004 57.895 0.00 0.00 46.37 4.16
2636 2977 1.228154 GGTGTCCCAGTTGGTGGTC 60.228 63.158 0.00 0.00 46.37 4.02
2637 2978 1.705997 GGTGTCCCAGTTGGTGGTCT 61.706 60.000 0.00 0.00 46.37 3.85
2638 2979 0.535102 GTGTCCCAGTTGGTGGTCTG 60.535 60.000 0.00 0.00 46.37 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.728427 GATCCAGCCGGCGTAGTACG 62.728 65.000 23.20 18.37 45.88 3.67
8 9 1.007618 GATCCAGCCGGCGTAGTAC 60.008 63.158 23.20 8.79 0.00 2.73
9 10 2.198287 GGATCCAGCCGGCGTAGTA 61.198 63.158 23.20 6.63 0.00 1.82
10 11 3.537874 GGATCCAGCCGGCGTAGT 61.538 66.667 23.20 9.17 0.00 2.73
21 22 2.045708 GTGCATGCAACCGGATCCA 61.046 57.895 24.58 0.00 0.00 3.41
85 88 2.251818 TCTGTGGCCATAGCTAGGATC 58.748 52.381 23.86 0.00 39.73 3.36
139 151 1.596603 TTCCCGTCTATGCATGCATG 58.403 50.000 37.43 27.00 37.82 4.06
140 152 2.346766 TTTCCCGTCTATGCATGCAT 57.653 45.000 33.92 33.92 40.19 3.96
247 320 8.706521 AGTATGGAGGGAGACTTTTTCTTATAC 58.293 37.037 0.00 0.00 33.22 1.47
279 361 2.807837 GCAAAAGTTGAGCCAAGGCAAT 60.808 45.455 14.40 0.00 44.88 3.56
281 363 0.104671 GCAAAAGTTGAGCCAAGGCA 59.895 50.000 14.40 0.00 44.88 4.75
299 382 4.119136 ACAAAGTTGCCATGTTTAACAGC 58.881 39.130 3.63 3.21 0.00 4.40
300 383 4.744631 GGACAAAGTTGCCATGTTTAACAG 59.255 41.667 3.63 0.00 0.00 3.16
301 384 4.442192 GGGACAAAGTTGCCATGTTTAACA 60.442 41.667 0.00 0.00 0.00 2.41
302 385 4.055360 GGGACAAAGTTGCCATGTTTAAC 58.945 43.478 0.00 0.00 0.00 2.01
303 386 3.706594 TGGGACAAAGTTGCCATGTTTAA 59.293 39.130 0.00 0.00 31.92 1.52
304 387 3.300388 TGGGACAAAGTTGCCATGTTTA 58.700 40.909 0.00 0.00 31.92 2.01
305 388 2.102925 CTGGGACAAAGTTGCCATGTTT 59.897 45.455 0.00 0.00 38.70 2.83
306 389 1.688197 CTGGGACAAAGTTGCCATGTT 59.312 47.619 0.00 0.00 38.70 2.71
307 390 1.331214 CTGGGACAAAGTTGCCATGT 58.669 50.000 0.00 0.00 38.70 3.21
308 391 1.331214 ACTGGGACAAAGTTGCCATG 58.669 50.000 6.77 0.00 38.70 3.66
309 392 1.963515 GAACTGGGACAAAGTTGCCAT 59.036 47.619 0.00 0.00 37.98 4.40
310 393 1.398692 GAACTGGGACAAAGTTGCCA 58.601 50.000 0.00 0.00 37.98 4.92
311 394 0.310854 CGAACTGGGACAAAGTTGCC 59.689 55.000 0.00 0.00 37.98 4.52
312 395 1.021968 ACGAACTGGGACAAAGTTGC 58.978 50.000 0.00 0.00 37.98 4.17
313 396 3.775661 AAACGAACTGGGACAAAGTTG 57.224 42.857 0.00 0.00 37.98 3.16
314 397 4.461431 AGAAAAACGAACTGGGACAAAGTT 59.539 37.500 0.00 0.00 40.54 2.66
315 398 4.014406 AGAAAAACGAACTGGGACAAAGT 58.986 39.130 0.00 0.00 38.70 2.66
316 399 4.632538 AGAAAAACGAACTGGGACAAAG 57.367 40.909 0.00 0.00 38.70 2.77
317 400 4.218852 ACAAGAAAAACGAACTGGGACAAA 59.781 37.500 0.00 0.00 38.70 2.83
318 401 3.759618 ACAAGAAAAACGAACTGGGACAA 59.240 39.130 0.00 0.00 38.70 3.18
319 402 3.349022 ACAAGAAAAACGAACTGGGACA 58.651 40.909 0.00 0.00 0.00 4.02
320 403 3.375922 TGACAAGAAAAACGAACTGGGAC 59.624 43.478 0.00 0.00 0.00 4.46
321 404 3.611970 TGACAAGAAAAACGAACTGGGA 58.388 40.909 0.00 0.00 0.00 4.37
322 405 3.625764 TCTGACAAGAAAAACGAACTGGG 59.374 43.478 0.00 0.00 0.00 4.45
323 406 4.875544 TCTGACAAGAAAAACGAACTGG 57.124 40.909 0.00 0.00 0.00 4.00
334 417 7.169645 GCAAACATAGCAATTTTCTGACAAGAA 59.830 33.333 0.00 0.00 40.76 2.52
335 418 6.642131 GCAAACATAGCAATTTTCTGACAAGA 59.358 34.615 0.00 0.00 0.00 3.02
336 419 6.128742 GGCAAACATAGCAATTTTCTGACAAG 60.129 38.462 0.00 0.00 0.00 3.16
337 420 5.695816 GGCAAACATAGCAATTTTCTGACAA 59.304 36.000 0.00 0.00 0.00 3.18
338 421 5.221402 TGGCAAACATAGCAATTTTCTGACA 60.221 36.000 0.00 0.00 0.00 3.58
339 422 5.229423 TGGCAAACATAGCAATTTTCTGAC 58.771 37.500 0.00 0.00 0.00 3.51
340 423 5.465532 TGGCAAACATAGCAATTTTCTGA 57.534 34.783 0.00 0.00 0.00 3.27
341 424 5.106987 GGTTGGCAAACATAGCAATTTTCTG 60.107 40.000 11.10 0.00 38.10 3.02
342 425 4.996758 GGTTGGCAAACATAGCAATTTTCT 59.003 37.500 11.10 0.00 38.10 2.52
343 426 4.996758 AGGTTGGCAAACATAGCAATTTTC 59.003 37.500 18.93 0.00 38.10 2.29
344 427 4.971939 AGGTTGGCAAACATAGCAATTTT 58.028 34.783 18.93 0.00 38.10 1.82
345 428 4.568956 GAGGTTGGCAAACATAGCAATTT 58.431 39.130 18.93 0.00 38.10 1.82
346 429 3.367292 CGAGGTTGGCAAACATAGCAATT 60.367 43.478 18.93 0.00 38.10 2.32
347 430 2.164219 CGAGGTTGGCAAACATAGCAAT 59.836 45.455 18.93 0.00 38.10 3.56
348 431 1.539388 CGAGGTTGGCAAACATAGCAA 59.461 47.619 18.93 0.00 38.10 3.91
349 432 1.164411 CGAGGTTGGCAAACATAGCA 58.836 50.000 18.93 0.00 38.10 3.49
350 433 0.179163 GCGAGGTTGGCAAACATAGC 60.179 55.000 18.93 15.15 40.52 2.97
351 434 0.096976 CGCGAGGTTGGCAAACATAG 59.903 55.000 18.93 9.05 38.10 2.23
352 435 0.604243 ACGCGAGGTTGGCAAACATA 60.604 50.000 18.93 0.00 38.10 2.29
353 436 1.896660 ACGCGAGGTTGGCAAACAT 60.897 52.632 18.93 0.00 38.10 2.71
354 437 2.515057 ACGCGAGGTTGGCAAACA 60.515 55.556 18.93 0.00 38.10 2.83
355 438 2.051345 CACGCGAGGTTGGCAAAC 60.051 61.111 15.93 7.31 35.40 2.93
356 439 1.820056 TTCACGCGAGGTTGGCAAA 60.820 52.632 15.93 0.00 0.00 3.68
357 440 2.203084 TTCACGCGAGGTTGGCAA 60.203 55.556 15.93 0.00 0.00 4.52
358 441 2.089887 TAGTTCACGCGAGGTTGGCA 62.090 55.000 15.93 0.00 0.00 4.92
359 442 0.947180 TTAGTTCACGCGAGGTTGGC 60.947 55.000 15.93 0.00 0.00 4.52
360 443 1.504359 TTTAGTTCACGCGAGGTTGG 58.496 50.000 15.93 0.00 0.00 3.77
361 444 3.806316 ATTTTAGTTCACGCGAGGTTG 57.194 42.857 15.93 0.00 0.00 3.77
362 445 3.562557 ACAATTTTAGTTCACGCGAGGTT 59.437 39.130 15.93 0.00 0.00 3.50
363 446 3.135994 ACAATTTTAGTTCACGCGAGGT 58.864 40.909 15.93 0.00 0.00 3.85
364 447 3.185594 TGACAATTTTAGTTCACGCGAGG 59.814 43.478 15.93 4.29 0.00 4.63
365 448 4.383774 TGACAATTTTAGTTCACGCGAG 57.616 40.909 15.93 4.59 0.00 5.03
366 449 4.449405 TCATGACAATTTTAGTTCACGCGA 59.551 37.500 15.93 0.00 0.00 5.87
367 450 4.707563 TCATGACAATTTTAGTTCACGCG 58.292 39.130 3.53 3.53 0.00 6.01
368 451 6.984740 TTTCATGACAATTTTAGTTCACGC 57.015 33.333 0.00 0.00 0.00 5.34
379 462 8.819974 GCAATCCGAATATTTTTCATGACAATT 58.180 29.630 0.00 0.00 0.00 2.32
380 463 7.439056 GGCAATCCGAATATTTTTCATGACAAT 59.561 33.333 0.00 0.00 0.00 2.71
381 464 6.756074 GGCAATCCGAATATTTTTCATGACAA 59.244 34.615 0.00 0.00 0.00 3.18
382 465 6.127507 TGGCAATCCGAATATTTTTCATGACA 60.128 34.615 0.00 0.00 34.14 3.58
383 466 6.272318 TGGCAATCCGAATATTTTTCATGAC 58.728 36.000 0.00 0.00 34.14 3.06
384 467 6.462552 TGGCAATCCGAATATTTTTCATGA 57.537 33.333 0.00 0.00 34.14 3.07
385 468 6.347079 GCATGGCAATCCGAATATTTTTCATG 60.347 38.462 0.00 0.00 34.14 3.07
386 469 5.697633 GCATGGCAATCCGAATATTTTTCAT 59.302 36.000 0.00 0.00 34.14 2.57
387 470 5.049167 GCATGGCAATCCGAATATTTTTCA 58.951 37.500 0.00 0.00 34.14 2.69
388 471 5.291971 AGCATGGCAATCCGAATATTTTTC 58.708 37.500 0.00 0.00 34.14 2.29
389 472 5.280654 AGCATGGCAATCCGAATATTTTT 57.719 34.783 0.00 0.00 34.14 1.94
390 473 4.942761 AGCATGGCAATCCGAATATTTT 57.057 36.364 0.00 0.00 34.14 1.82
391 474 4.942761 AAGCATGGCAATCCGAATATTT 57.057 36.364 0.00 0.00 34.14 1.40
392 475 6.403866 TTTAAGCATGGCAATCCGAATATT 57.596 33.333 0.00 0.00 34.14 1.28
393 476 6.403866 TTTTAAGCATGGCAATCCGAATAT 57.596 33.333 0.00 0.00 34.14 1.28
394 477 5.843673 TTTTAAGCATGGCAATCCGAATA 57.156 34.783 0.00 0.00 34.14 1.75
395 478 4.734398 TTTTAAGCATGGCAATCCGAAT 57.266 36.364 0.00 0.00 34.14 3.34
396 479 4.441356 GGATTTTAAGCATGGCAATCCGAA 60.441 41.667 0.00 0.00 34.98 4.30
397 480 3.068024 GGATTTTAAGCATGGCAATCCGA 59.932 43.478 0.00 0.00 34.98 4.55
398 481 3.383761 GGATTTTAAGCATGGCAATCCG 58.616 45.455 0.00 0.00 34.98 4.18
399 482 3.068024 TCGGATTTTAAGCATGGCAATCC 59.932 43.478 0.00 7.57 39.66 3.01
400 483 4.305989 TCGGATTTTAAGCATGGCAATC 57.694 40.909 0.00 0.00 0.00 2.67
401 484 4.432712 GTTCGGATTTTAAGCATGGCAAT 58.567 39.130 0.00 0.00 0.00 3.56
402 485 3.671971 CGTTCGGATTTTAAGCATGGCAA 60.672 43.478 0.00 0.00 0.00 4.52
403 486 2.159448 CGTTCGGATTTTAAGCATGGCA 60.159 45.455 0.00 0.00 0.00 4.92
404 487 2.159435 ACGTTCGGATTTTAAGCATGGC 60.159 45.455 0.00 0.00 0.00 4.40
405 488 3.757745 ACGTTCGGATTTTAAGCATGG 57.242 42.857 0.00 0.00 0.00 3.66
406 489 4.323336 CCAAACGTTCGGATTTTAAGCATG 59.677 41.667 0.00 0.00 0.00 4.06
407 490 4.481463 CCAAACGTTCGGATTTTAAGCAT 58.519 39.130 0.00 0.00 0.00 3.79
408 491 3.304794 CCCAAACGTTCGGATTTTAAGCA 60.305 43.478 6.90 0.00 0.00 3.91
409 492 3.058085 TCCCAAACGTTCGGATTTTAAGC 60.058 43.478 6.90 0.00 0.00 3.09
410 493 4.752661 TCCCAAACGTTCGGATTTTAAG 57.247 40.909 6.90 0.00 0.00 1.85
411 494 5.708877 AATCCCAAACGTTCGGATTTTAA 57.291 34.783 25.82 5.57 42.48 1.52
415 498 4.944930 TGATAAATCCCAAACGTTCGGATT 59.055 37.500 25.82 25.82 46.12 3.01
416 499 4.519213 TGATAAATCCCAAACGTTCGGAT 58.481 39.130 19.27 19.27 38.04 4.18
417 500 3.940319 TGATAAATCCCAAACGTTCGGA 58.060 40.909 16.84 16.84 0.00 4.55
418 501 4.893424 ATGATAAATCCCAAACGTTCGG 57.107 40.909 0.00 0.00 0.00 4.30
419 502 5.741982 GGAAATGATAAATCCCAAACGTTCG 59.258 40.000 0.00 0.00 0.00 3.95
420 503 5.741982 CGGAAATGATAAATCCCAAACGTTC 59.258 40.000 0.00 0.00 0.00 3.95
421 504 5.646606 CGGAAATGATAAATCCCAAACGTT 58.353 37.500 0.00 0.00 0.00 3.99
422 505 4.439563 GCGGAAATGATAAATCCCAAACGT 60.440 41.667 0.00 0.00 0.00 3.99
423 506 4.041723 GCGGAAATGATAAATCCCAAACG 58.958 43.478 0.00 0.00 0.00 3.60
424 507 5.004922 TGCGGAAATGATAAATCCCAAAC 57.995 39.130 0.00 0.00 0.00 2.93
425 508 5.186797 AGTTGCGGAAATGATAAATCCCAAA 59.813 36.000 0.00 0.00 30.52 3.28
426 509 4.709397 AGTTGCGGAAATGATAAATCCCAA 59.291 37.500 0.00 0.00 0.00 4.12
427 510 4.277476 AGTTGCGGAAATGATAAATCCCA 58.723 39.130 0.00 0.00 0.00 4.37
428 511 4.918810 AGTTGCGGAAATGATAAATCCC 57.081 40.909 0.00 0.00 0.00 3.85
429 512 7.595311 AAAAAGTTGCGGAAATGATAAATCC 57.405 32.000 0.00 0.00 0.00 3.01
466 549 4.613925 TCTCAGCTTTCTTCTGACATGT 57.386 40.909 0.00 0.00 35.81 3.21
497 580 7.576602 GCTTGAAATTCGAAATTTCATATTGCG 59.423 33.333 23.77 3.13 44.45 4.85
513 681 4.463209 TCGTTCGTTCATGCTTGAAATTC 58.537 39.130 15.87 4.33 43.29 2.17
515 683 4.083324 ACATCGTTCGTTCATGCTTGAAAT 60.083 37.500 15.87 3.32 43.29 2.17
522 690 0.989164 TCGACATCGTTCGTTCATGC 59.011 50.000 0.54 0.00 40.07 4.06
529 697 0.713883 CTTGGGTTCGACATCGTTCG 59.286 55.000 0.54 0.00 40.80 3.95
530 698 0.442699 GCTTGGGTTCGACATCGTTC 59.557 55.000 0.54 0.00 40.80 3.95
531 699 0.953960 GGCTTGGGTTCGACATCGTT 60.954 55.000 0.54 0.00 40.80 3.85
532 700 1.375523 GGCTTGGGTTCGACATCGT 60.376 57.895 0.54 0.00 40.80 3.73
533 701 1.375396 TGGCTTGGGTTCGACATCG 60.375 57.895 0.00 0.00 41.45 3.84
534 702 0.605319 TGTGGCTTGGGTTCGACATC 60.605 55.000 0.00 0.00 0.00 3.06
555 723 5.688621 GGTTATCCTTTTGTTCCAACGAAAC 59.311 40.000 1.33 0.00 37.37 2.78
620 789 3.619233 TTGTTTAGCTCGTTTTGGCTC 57.381 42.857 0.00 0.00 39.65 4.70
727 910 3.068064 CGGGGTGTTTGGATGGGC 61.068 66.667 0.00 0.00 0.00 5.36
760 943 2.386064 TTAAAGTGCGGCGGGACTGT 62.386 55.000 18.87 15.88 44.87 3.55
781 964 4.020485 CGGGAGGTATAAATAACAGGGGAG 60.020 50.000 0.00 0.00 0.00 4.30
847 1042 4.792804 GGAGCAGCAGGGGAGTGC 62.793 72.222 0.00 0.00 44.35 4.40
848 1043 4.106925 GGGAGCAGCAGGGGAGTG 62.107 72.222 0.00 0.00 0.00 3.51
892 1116 2.263021 TGCTGCTGTGCATGGACAC 61.263 57.895 16.89 13.45 38.13 3.67
1077 1316 0.683504 AGGTAGGTACGCACAGGAGG 60.684 60.000 0.00 0.00 0.00 4.30
1123 1365 1.652930 GCGCGTCAGAGAGATCGAC 60.653 63.158 8.43 0.00 0.00 4.20
1126 1368 1.749153 GTAAGCGCGTCAGAGAGATC 58.251 55.000 8.43 0.00 0.00 2.75
1131 1373 2.152699 CACCGTAAGCGCGTCAGAG 61.153 63.158 8.43 0.00 36.67 3.35
1137 1383 0.025001 CAAGAATCACCGTAAGCGCG 59.975 55.000 0.00 0.00 36.67 6.86
1173 1422 0.456824 CACCGTCAGTCCTGATCACG 60.457 60.000 0.00 0.58 42.18 4.35
1178 1427 0.888619 GTCATCACCGTCAGTCCTGA 59.111 55.000 0.00 0.00 37.24 3.86
1179 1428 0.456824 CGTCATCACCGTCAGTCCTG 60.457 60.000 0.00 0.00 0.00 3.86
1180 1429 1.595993 CCGTCATCACCGTCAGTCCT 61.596 60.000 0.00 0.00 0.00 3.85
1181 1430 1.153823 CCGTCATCACCGTCAGTCC 60.154 63.158 0.00 0.00 0.00 3.85
1182 1431 0.732880 CACCGTCATCACCGTCAGTC 60.733 60.000 0.00 0.00 0.00 3.51
1183 1432 1.289066 CACCGTCATCACCGTCAGT 59.711 57.895 0.00 0.00 0.00 3.41
1184 1433 1.446099 CCACCGTCATCACCGTCAG 60.446 63.158 0.00 0.00 0.00 3.51
1185 1434 1.750341 AACCACCGTCATCACCGTCA 61.750 55.000 0.00 0.00 0.00 4.35
1186 1435 1.005394 AACCACCGTCATCACCGTC 60.005 57.895 0.00 0.00 0.00 4.79
1221 1483 3.965539 CTCGAAGGTGCCCAGCCAG 62.966 68.421 0.00 0.00 0.00 4.85
1653 1939 2.047465 AGGAAGCAGAGCACGCTG 60.047 61.111 0.00 0.00 40.35 5.18
1689 1981 0.667487 TCGCGCCAAGAAACAGAGAG 60.667 55.000 0.00 0.00 0.00 3.20
1694 1986 1.225376 ATCGTTCGCGCCAAGAAACA 61.225 50.000 0.00 0.00 41.05 2.83
1734 2026 1.582937 CGCTACGCTACACTGGACG 60.583 63.158 0.00 0.00 0.00 4.79
1738 2030 1.129998 ACACTACGCTACGCTACACTG 59.870 52.381 0.00 0.00 0.00 3.66
1798 2090 0.322277 TACGAGCTCTTCTCCGGTGT 60.322 55.000 12.85 1.18 38.62 4.16
1821 2113 7.361127 CGTAGAAGAACTCTTGACTGAACTAA 58.639 38.462 0.00 0.00 36.11 2.24
1823 2115 5.764131 CGTAGAAGAACTCTTGACTGAACT 58.236 41.667 0.00 0.00 36.11 3.01
1824 2116 4.383351 GCGTAGAAGAACTCTTGACTGAAC 59.617 45.833 0.00 0.00 36.11 3.18
1825 2117 4.278669 AGCGTAGAAGAACTCTTGACTGAA 59.721 41.667 0.00 0.00 36.11 3.02
1826 2118 3.821600 AGCGTAGAAGAACTCTTGACTGA 59.178 43.478 0.00 0.00 36.11 3.41
1828 2120 5.005094 ACTAGCGTAGAAGAACTCTTGACT 58.995 41.667 0.00 0.00 36.11 3.41
1829 2121 5.090083 CACTAGCGTAGAAGAACTCTTGAC 58.910 45.833 0.00 0.00 36.11 3.18
1830 2122 5.001874 TCACTAGCGTAGAAGAACTCTTGA 58.998 41.667 0.00 0.00 36.11 3.02
1964 2256 2.164219 CCGAGCACCGTAAAAGGTACTA 59.836 50.000 0.00 0.00 43.89 1.82
1965 2257 1.067354 CCGAGCACCGTAAAAGGTACT 60.067 52.381 0.00 0.00 43.89 2.73
1966 2258 1.353076 CCGAGCACCGTAAAAGGTAC 58.647 55.000 0.00 0.00 43.89 3.34
2052 2350 2.095461 TGATGTCTTGACTCTCGAGGG 58.905 52.381 11.78 11.78 0.00 4.30
2072 2370 9.777297 ACCTTGTGCTATTTTTATGTTTGATTT 57.223 25.926 0.00 0.00 0.00 2.17
2075 2373 9.685828 GTTACCTTGTGCTATTTTTATGTTTGA 57.314 29.630 0.00 0.00 0.00 2.69
2076 2374 8.635124 CGTTACCTTGTGCTATTTTTATGTTTG 58.365 33.333 0.00 0.00 0.00 2.93
2120 2418 1.297598 CGCCATTGATCGGTTTCGC 60.298 57.895 0.00 0.00 36.13 4.70
2124 2422 0.107897 TAGCACGCCATTGATCGGTT 60.108 50.000 0.00 0.00 0.00 4.44
2210 2516 1.480954 AGATGGTTCATTCGTAGGCGT 59.519 47.619 0.00 0.00 39.49 5.68
2216 2522 2.698855 CCAGGAGATGGTTCATTCGT 57.301 50.000 0.00 0.00 44.91 3.85
2275 2602 4.543744 TGGCATGTATGGTATGGGGATAAT 59.456 41.667 0.00 0.00 0.00 1.28
2277 2604 3.536287 TGGCATGTATGGTATGGGGATA 58.464 45.455 0.00 0.00 0.00 2.59
2278 2605 2.357274 TGGCATGTATGGTATGGGGAT 58.643 47.619 0.00 0.00 0.00 3.85
2279 2606 1.826447 TGGCATGTATGGTATGGGGA 58.174 50.000 0.00 0.00 0.00 4.81
2312 2639 1.000506 GGAGCCAACTAACGACACAGA 59.999 52.381 0.00 0.00 0.00 3.41
2320 2647 2.421424 CTGCAATGAGGAGCCAACTAAC 59.579 50.000 0.00 0.00 0.00 2.34
2321 2648 2.040278 ACTGCAATGAGGAGCCAACTAA 59.960 45.455 0.00 0.00 39.69 2.24
2322 2649 1.630369 ACTGCAATGAGGAGCCAACTA 59.370 47.619 0.00 0.00 39.69 2.24
2323 2650 0.403271 ACTGCAATGAGGAGCCAACT 59.597 50.000 0.00 0.00 39.69 3.16
2332 2659 2.612672 CTGATAGCACCACTGCAATGAG 59.387 50.000 0.00 0.00 46.97 2.90
2336 2663 3.452264 ACTATCTGATAGCACCACTGCAA 59.548 43.478 21.58 0.00 46.97 4.08
2340 2667 2.968574 CCCACTATCTGATAGCACCACT 59.031 50.000 21.58 1.61 36.30 4.00
2342 2669 1.694150 GCCCACTATCTGATAGCACCA 59.306 52.381 21.58 0.00 36.30 4.17
2345 2672 0.318441 GCGCCCACTATCTGATAGCA 59.682 55.000 21.58 0.00 36.30 3.49
2346 2673 0.318441 TGCGCCCACTATCTGATAGC 59.682 55.000 21.58 10.19 36.30 2.97
2347 2674 1.671261 GCTGCGCCCACTATCTGATAG 60.671 57.143 20.37 20.37 38.81 2.08
2348 2675 0.318441 GCTGCGCCCACTATCTGATA 59.682 55.000 4.18 0.00 0.00 2.15
2356 2684 1.181098 AAAGAAATGCTGCGCCCACT 61.181 50.000 4.18 0.00 0.00 4.00
2388 2716 1.669265 AGCATCAGCACAATCATGTCG 59.331 47.619 0.00 0.00 45.49 4.35
2389 2717 2.794981 GCAGCATCAGCACAATCATGTC 60.795 50.000 0.00 0.00 45.49 3.06
2417 2746 2.803285 TGATGGGGCTAATCCTCTCT 57.197 50.000 0.00 0.00 35.85 3.10
2420 2749 2.503895 CCATGATGGGGCTAATCCTC 57.496 55.000 2.79 0.00 32.67 3.71
2483 2812 2.427002 CCTGATACTCCCTGATGTCCCT 60.427 54.545 0.00 0.00 0.00 4.20
2485 2814 1.346068 GCCTGATACTCCCTGATGTCC 59.654 57.143 0.00 0.00 0.00 4.02
2486 2815 1.000283 CGCCTGATACTCCCTGATGTC 60.000 57.143 0.00 0.00 0.00 3.06
2487 2816 1.043816 CGCCTGATACTCCCTGATGT 58.956 55.000 0.00 0.00 0.00 3.06
2488 2817 1.000283 GACGCCTGATACTCCCTGATG 60.000 57.143 0.00 0.00 0.00 3.07
2489 2818 1.333177 GACGCCTGATACTCCCTGAT 58.667 55.000 0.00 0.00 0.00 2.90
2490 2819 1.101635 CGACGCCTGATACTCCCTGA 61.102 60.000 0.00 0.00 0.00 3.86
2491 2820 1.360551 CGACGCCTGATACTCCCTG 59.639 63.158 0.00 0.00 0.00 4.45
2492 2821 1.076923 ACGACGCCTGATACTCCCT 60.077 57.895 0.00 0.00 0.00 4.20
2493 2822 1.065928 CACGACGCCTGATACTCCC 59.934 63.158 0.00 0.00 0.00 4.30
2494 2823 0.525668 CACACGACGCCTGATACTCC 60.526 60.000 0.00 0.00 0.00 3.85
2495 2824 0.170561 ACACACGACGCCTGATACTC 59.829 55.000 0.00 0.00 0.00 2.59
2496 2825 0.170561 GACACACGACGCCTGATACT 59.829 55.000 0.00 0.00 0.00 2.12
2497 2826 0.801067 GGACACACGACGCCTGATAC 60.801 60.000 0.00 0.00 0.00 2.24
2498 2827 1.509463 GGACACACGACGCCTGATA 59.491 57.895 0.00 0.00 0.00 2.15
2526 2856 1.836391 CTGAAGGTGGTGGGTGTGA 59.164 57.895 0.00 0.00 0.00 3.58
2530 2860 1.151450 CAAGCTGAAGGTGGTGGGT 59.849 57.895 0.00 0.00 0.00 4.51
2531 2861 1.604593 CCAAGCTGAAGGTGGTGGG 60.605 63.158 0.00 0.00 0.00 4.61
2545 2875 2.154462 GTGGACCTGAACACATCCAAG 58.846 52.381 0.00 0.00 42.79 3.61
2553 2883 0.761323 TTCCTCGGTGGACCTGAACA 60.761 55.000 0.00 0.00 46.14 3.18
2603 2944 1.326213 ACACCAGCTCATCTCCTCCG 61.326 60.000 0.00 0.00 0.00 4.63
2619 2960 0.535102 CAGACCACCAACTGGGACAC 60.535 60.000 0.00 0.00 45.78 3.67
2620 2961 1.836391 CAGACCACCAACTGGGACA 59.164 57.895 0.00 0.00 45.78 4.02
2621 2962 4.800554 CAGACCACCAACTGGGAC 57.199 61.111 0.00 0.00 45.78 4.46


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

AutoCloner maintained by Alex Coulton.