Multiple sequence alignment - TraesCS2D01G294000

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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 TraesCS2D01G294000 chr2D 100.000 3740 0 0 1 3740 376352315 376356054 0.000000e+00 6907
1 TraesCS2D01G294000 chr2B 93.412 1943 66 28 1831 3739 447823327 447825241 0.000000e+00 2822
2 TraesCS2D01G294000 chr2B 89.954 1314 77 25 539 1829 447822008 447823289 0.000000e+00 1644
3 TraesCS2D01G294000 chr2B 95.378 238 11 0 3472 3709 233079187 233078950 2.730000e-101 379
4 TraesCS2D01G294000 chr2B 84.282 369 19 11 1 356 447821628 447821970 1.300000e-84 324
5 TraesCS2D01G294000 chr2A 91.472 1923 90 26 642 2556 509577311 509579167 0.000000e+00 2575
6 TraesCS2D01G294000 chr2A 92.588 796 41 11 2558 3342 509579293 509580081 0.000000e+00 1127
7 TraesCS2D01G294000 chr2A 93.151 730 35 11 2621 3338 509990722 509991448 0.000000e+00 1057
8 TraesCS2D01G294000 chr2A 96.602 412 13 1 3326 3737 509580097 509580507 0.000000e+00 682
9 TraesCS2D01G294000 chr2A 93.765 417 13 3 3326 3739 509991468 509991874 6.870000e-172 614
10 TraesCS2D01G294000 chr2A 94.340 159 7 1 5 163 509548820 509548976 3.730000e-60 243
11 TraesCS2D01G294000 chr1A 95.102 245 12 0 3472 3716 36266033 36265789 1.630000e-103 387
12 TraesCS2D01G294000 chr5D 83.004 253 40 1 3490 3739 526410309 526410561 3.760000e-55 226
13 TraesCS2D01G294000 chr5B 82.800 250 40 1 3490 3736 661523996 661524245 1.750000e-53 220
14 TraesCS2D01G294000 chr5B 81.028 253 45 2 3490 3739 661613120 661612868 8.190000e-47 198
15 TraesCS2D01G294000 chr5B 81.646 158 20 6 388 538 23394864 23394709 5.070000e-24 122
16 TraesCS2D01G294000 chr5A 82.400 250 41 2 3490 3736 653474371 653474620 8.140000e-52 215
17 TraesCS2D01G294000 chr3B 81.675 191 22 8 356 534 571313569 571313758 3.010000e-31 147


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 TraesCS2D01G294000 chr2D 376352315 376356054 3739 False 6907.000000 6907 100.000 1 3740 1 chr2D.!!$F1 3739
1 TraesCS2D01G294000 chr2B 447821628 447825241 3613 False 1596.666667 2822 89.216 1 3739 3 chr2B.!!$F1 3738
2 TraesCS2D01G294000 chr2A 509577311 509580507 3196 False 1461.333333 2575 93.554 642 3737 3 chr2A.!!$F2 3095
3 TraesCS2D01G294000 chr2A 509990722 509991874 1152 False 835.500000 1057 93.458 2621 3739 2 chr2A.!!$F3 1118

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
202 203 0.037232 GGTCCTGTTTCGCTAGCAGT 60.037 55.0 16.45 0.0 0.0 4.40 F
791 814 0.179004 TCCTTTCTCCGCAGCCAAAA 60.179 50.0 0.00 0.0 0.0 2.44 F
1599 1637 0.033306 TGCCTGCCTTCAATATGCCA 60.033 50.0 0.00 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1232 0.532573 GTTGATCTGAGACTGGCCGA 59.467 55.000 0.00 0.00 0.00 5.54 R
2354 2436 1.202794 TGACAATGGTTGCTGAGCTCA 60.203 47.619 17.19 17.19 0.00 4.26 R
2800 3007 0.095417 CGGCTTTTCTCTAACAGCGC 59.905 55.000 0.00 0.00 32.68 5.92 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
95 96 3.243035 TGTTGAAACATGCCTCTCGTTTG 60.243 43.478 0.00 0.00 33.18 2.93
106 107 4.461431 TGCCTCTCGTTTGAACTGTAGATA 59.539 41.667 0.00 0.00 0.00 1.98
109 110 6.460399 GCCTCTCGTTTGAACTGTAGATATCT 60.460 42.308 10.73 10.73 0.00 1.98
111 112 6.266323 TCTCGTTTGAACTGTAGATATCTGC 58.734 40.000 15.79 14.54 0.00 4.26
129 130 2.939103 CTGCCACTAGTTGACTATTGCC 59.061 50.000 0.00 0.00 30.50 4.52
136 137 5.122396 CACTAGTTGACTATTGCCCAGTTTC 59.878 44.000 0.00 0.00 0.00 2.78
165 166 3.384467 GGTTGGGATCATTGGGTGTAATG 59.616 47.826 0.00 0.00 38.97 1.90
177 178 9.029368 TCATTGGGTGTAATGATATTTTGAACA 57.971 29.630 0.00 0.00 40.95 3.18
178 179 9.304731 CATTGGGTGTAATGATATTTTGAACAG 57.695 33.333 0.00 0.00 39.79 3.16
179 180 7.403312 TGGGTGTAATGATATTTTGAACAGG 57.597 36.000 0.00 0.00 0.00 4.00
180 181 6.379703 TGGGTGTAATGATATTTTGAACAGGG 59.620 38.462 0.00 0.00 0.00 4.45
181 182 6.379988 GGGTGTAATGATATTTTGAACAGGGT 59.620 38.462 0.00 0.00 0.00 4.34
182 183 7.257722 GGTGTAATGATATTTTGAACAGGGTG 58.742 38.462 0.00 0.00 0.00 4.61
183 184 7.257722 GTGTAATGATATTTTGAACAGGGTGG 58.742 38.462 0.00 0.00 0.00 4.61
184 185 5.937975 AATGATATTTTGAACAGGGTGGG 57.062 39.130 0.00 0.00 0.00 4.61
185 186 4.396357 TGATATTTTGAACAGGGTGGGT 57.604 40.909 0.00 0.00 0.00 4.51
186 187 4.340617 TGATATTTTGAACAGGGTGGGTC 58.659 43.478 0.00 0.00 0.00 4.46
187 188 2.009681 ATTTTGAACAGGGTGGGTCC 57.990 50.000 0.00 0.00 0.00 4.46
188 189 0.930726 TTTTGAACAGGGTGGGTCCT 59.069 50.000 0.00 0.00 37.71 3.85
193 194 4.821935 CAGGGTGGGTCCTGTTTC 57.178 61.111 2.93 0.00 46.89 2.78
194 195 1.302511 CAGGGTGGGTCCTGTTTCG 60.303 63.158 2.93 0.00 46.89 3.46
195 196 2.671963 GGGTGGGTCCTGTTTCGC 60.672 66.667 0.00 0.00 36.25 4.70
196 197 2.430367 GGTGGGTCCTGTTTCGCT 59.570 61.111 0.00 0.00 0.00 4.93
197 198 1.675219 GGTGGGTCCTGTTTCGCTA 59.325 57.895 0.00 0.00 0.00 4.26
198 199 0.391263 GGTGGGTCCTGTTTCGCTAG 60.391 60.000 0.00 0.00 0.00 3.42
199 200 1.019805 GTGGGTCCTGTTTCGCTAGC 61.020 60.000 4.06 4.06 0.00 3.42
200 201 1.295423 GGGTCCTGTTTCGCTAGCA 59.705 57.895 16.45 0.00 0.00 3.49
201 202 0.741221 GGGTCCTGTTTCGCTAGCAG 60.741 60.000 16.45 7.87 0.00 4.24
202 203 0.037232 GGTCCTGTTTCGCTAGCAGT 60.037 55.000 16.45 0.00 0.00 4.40
203 204 1.351153 GTCCTGTTTCGCTAGCAGTC 58.649 55.000 16.45 2.51 0.00 3.51
204 205 0.966179 TCCTGTTTCGCTAGCAGTCA 59.034 50.000 16.45 7.08 0.00 3.41
205 206 1.071605 CCTGTTTCGCTAGCAGTCAC 58.928 55.000 16.45 5.98 0.00 3.67
206 207 1.605457 CCTGTTTCGCTAGCAGTCACA 60.605 52.381 16.45 10.29 0.00 3.58
207 208 1.723542 CTGTTTCGCTAGCAGTCACAG 59.276 52.381 16.45 15.65 0.00 3.66
245 246 1.051812 CCCCCTGCGATGATAGAACT 58.948 55.000 0.00 0.00 0.00 3.01
297 298 3.189702 GCCTTGAAACGGCATTAGTACAA 59.810 43.478 0.00 0.00 46.77 2.41
303 304 1.021968 CGGCATTAGTACAAAGGGCC 58.978 55.000 0.00 0.00 32.68 5.80
304 305 1.408266 CGGCATTAGTACAAAGGGCCT 60.408 52.381 0.00 0.00 37.79 5.19
309 323 5.377478 GCATTAGTACAAAGGGCCTAAGAT 58.623 41.667 6.41 0.00 0.00 2.40
357 371 4.034258 GCGGTGACTGACGTCCGA 62.034 66.667 14.12 0.00 44.86 4.55
359 373 1.728426 CGGTGACTGACGTCCGAAC 60.728 63.158 14.12 10.53 44.86 3.95
388 402 8.842358 TTTTCATGGTAACTTTAGTTCGAGAT 57.158 30.769 0.00 0.00 39.31 2.75
390 404 6.338146 TCATGGTAACTTTAGTTCGAGATGG 58.662 40.000 0.00 0.00 39.31 3.51
391 405 4.501071 TGGTAACTTTAGTTCGAGATGGC 58.499 43.478 0.00 0.00 39.31 4.40
393 407 4.933400 GGTAACTTTAGTTCGAGATGGCAA 59.067 41.667 0.00 0.00 39.31 4.52
395 409 6.093633 GGTAACTTTAGTTCGAGATGGCAAAT 59.906 38.462 0.00 0.00 39.31 2.32
396 410 6.575162 AACTTTAGTTCGAGATGGCAAATT 57.425 33.333 0.00 0.00 31.64 1.82
397 411 6.575162 ACTTTAGTTCGAGATGGCAAATTT 57.425 33.333 0.00 0.00 0.00 1.82
398 412 7.681939 ACTTTAGTTCGAGATGGCAAATTTA 57.318 32.000 0.00 0.00 0.00 1.40
399 413 7.752695 ACTTTAGTTCGAGATGGCAAATTTAG 58.247 34.615 0.00 0.00 0.00 1.85
400 414 7.390718 ACTTTAGTTCGAGATGGCAAATTTAGT 59.609 33.333 0.00 0.00 0.00 2.24
401 415 7.681939 TTAGTTCGAGATGGCAAATTTAGTT 57.318 32.000 0.00 0.00 0.00 2.24
402 416 5.942872 AGTTCGAGATGGCAAATTTAGTTG 58.057 37.500 0.00 0.00 0.00 3.16
403 417 5.473504 AGTTCGAGATGGCAAATTTAGTTGT 59.526 36.000 0.00 0.00 0.00 3.32
404 418 5.545658 TCGAGATGGCAAATTTAGTTGTC 57.454 39.130 0.00 0.00 33.59 3.18
405 419 5.000591 TCGAGATGGCAAATTTAGTTGTCA 58.999 37.500 0.00 0.00 46.45 3.58
406 420 5.471797 TCGAGATGGCAAATTTAGTTGTCAA 59.528 36.000 1.17 0.00 45.60 3.18
407 421 5.796935 CGAGATGGCAAATTTAGTTGTCAAG 59.203 40.000 1.17 0.00 45.60 3.02
408 422 6.348458 CGAGATGGCAAATTTAGTTGTCAAGA 60.348 38.462 1.17 0.00 45.60 3.02
409 423 6.681777 AGATGGCAAATTTAGTTGTCAAGAC 58.318 36.000 1.17 0.00 45.60 3.01
410 424 5.843673 TGGCAAATTTAGTTGTCAAGACA 57.156 34.783 0.00 0.00 40.05 3.41
411 425 5.587289 TGGCAAATTTAGTTGTCAAGACAC 58.413 37.500 1.73 0.00 40.05 3.67
412 426 4.675114 GGCAAATTTAGTTGTCAAGACACG 59.325 41.667 1.73 0.00 41.67 4.49
413 427 4.675114 GCAAATTTAGTTGTCAAGACACGG 59.325 41.667 1.73 0.00 41.67 4.94
414 428 4.483476 AATTTAGTTGTCAAGACACGGC 57.517 40.909 1.73 0.00 41.67 5.68
415 429 2.605837 TTAGTTGTCAAGACACGGCA 57.394 45.000 1.73 0.00 41.67 5.69
416 430 2.605837 TAGTTGTCAAGACACGGCAA 57.394 45.000 1.73 0.00 41.67 4.52
417 431 1.014352 AGTTGTCAAGACACGGCAAC 58.986 50.000 1.73 0.00 41.67 4.17
418 432 1.014352 GTTGTCAAGACACGGCAACT 58.986 50.000 1.73 0.00 41.67 3.16
419 433 1.400494 GTTGTCAAGACACGGCAACTT 59.600 47.619 1.73 0.00 41.67 2.66
420 434 1.745232 TGTCAAGACACGGCAACTTT 58.255 45.000 0.00 0.00 36.21 2.66
421 435 1.400142 TGTCAAGACACGGCAACTTTG 59.600 47.619 0.00 0.00 36.21 2.77
422 436 1.400494 GTCAAGACACGGCAACTTTGT 59.600 47.619 0.00 0.00 33.53 2.83
423 437 1.668751 TCAAGACACGGCAACTTTGTC 59.331 47.619 0.00 0.00 43.84 3.18
424 438 3.780624 AGACACGGCAACTTTGTCT 57.219 47.368 0.00 0.00 46.83 3.41
426 440 1.295792 GACACGGCAACTTTGTCTCA 58.704 50.000 0.00 0.00 41.59 3.27
427 441 1.668751 GACACGGCAACTTTGTCTCAA 59.331 47.619 0.00 0.00 41.59 3.02
428 442 2.290641 GACACGGCAACTTTGTCTCAAT 59.709 45.455 0.00 0.00 41.59 2.57
429 443 2.687935 ACACGGCAACTTTGTCTCAATT 59.312 40.909 0.00 0.00 0.00 2.32
430 444 3.130340 ACACGGCAACTTTGTCTCAATTT 59.870 39.130 0.00 0.00 0.00 1.82
431 445 4.111916 CACGGCAACTTTGTCTCAATTTT 58.888 39.130 0.00 0.00 0.00 1.82
432 446 4.566360 CACGGCAACTTTGTCTCAATTTTT 59.434 37.500 0.00 0.00 0.00 1.94
455 469 8.498054 TTTTTAGAAAATTGCCATGTTTGTCA 57.502 26.923 0.00 0.00 0.00 3.58
456 470 8.498054 TTTTAGAAAATTGCCATGTTTGTCAA 57.502 26.923 0.00 0.00 0.00 3.18
457 471 5.989551 AGAAAATTGCCATGTTTGTCAAC 57.010 34.783 0.00 0.00 0.00 3.18
458 472 4.815846 AGAAAATTGCCATGTTTGTCAACC 59.184 37.500 0.00 0.00 31.02 3.77
459 473 4.420522 AAATTGCCATGTTTGTCAACCT 57.579 36.364 0.00 0.00 31.02 3.50
460 474 3.665745 ATTGCCATGTTTGTCAACCTC 57.334 42.857 0.00 0.00 31.02 3.85
461 475 0.950836 TGCCATGTTTGTCAACCTCG 59.049 50.000 0.00 0.00 31.02 4.63
462 476 0.387239 GCCATGTTTGTCAACCTCGC 60.387 55.000 0.00 0.00 31.02 5.03
463 477 0.950836 CCATGTTTGTCAACCTCGCA 59.049 50.000 0.00 0.00 31.02 5.10
464 478 1.541147 CCATGTTTGTCAACCTCGCAT 59.459 47.619 0.00 0.00 31.02 4.73
465 479 2.587956 CATGTTTGTCAACCTCGCATG 58.412 47.619 0.00 0.00 31.02 4.06
466 480 1.960417 TGTTTGTCAACCTCGCATGA 58.040 45.000 0.00 0.00 31.02 3.07
467 481 2.293170 TGTTTGTCAACCTCGCATGAA 58.707 42.857 0.00 0.00 31.02 2.57
468 482 2.032799 TGTTTGTCAACCTCGCATGAAC 59.967 45.455 0.00 0.00 31.02 3.18
469 483 2.254546 TTGTCAACCTCGCATGAACT 57.745 45.000 0.00 0.00 0.00 3.01
470 484 3.394674 TTGTCAACCTCGCATGAACTA 57.605 42.857 0.00 0.00 0.00 2.24
471 485 3.394674 TGTCAACCTCGCATGAACTAA 57.605 42.857 0.00 0.00 0.00 2.24
472 486 3.734463 TGTCAACCTCGCATGAACTAAA 58.266 40.909 0.00 0.00 0.00 1.85
473 487 4.130857 TGTCAACCTCGCATGAACTAAAA 58.869 39.130 0.00 0.00 0.00 1.52
474 488 4.759693 TGTCAACCTCGCATGAACTAAAAT 59.240 37.500 0.00 0.00 0.00 1.82
475 489 5.240623 TGTCAACCTCGCATGAACTAAAATT 59.759 36.000 0.00 0.00 0.00 1.82
476 490 5.569059 GTCAACCTCGCATGAACTAAAATTG 59.431 40.000 0.00 0.00 0.00 2.32
477 491 4.096732 ACCTCGCATGAACTAAAATTGC 57.903 40.909 0.00 0.00 0.00 3.56
478 492 3.119495 ACCTCGCATGAACTAAAATTGCC 60.119 43.478 0.00 0.00 0.00 4.52
479 493 3.119531 CCTCGCATGAACTAAAATTGCCA 60.120 43.478 0.00 0.00 0.00 4.92
480 494 4.440525 CCTCGCATGAACTAAAATTGCCAT 60.441 41.667 0.00 0.00 0.00 4.40
481 495 4.422840 TCGCATGAACTAAAATTGCCATG 58.577 39.130 0.00 0.00 35.72 3.66
482 496 4.157472 TCGCATGAACTAAAATTGCCATGA 59.843 37.500 0.00 0.00 34.87 3.07
483 497 4.863689 CGCATGAACTAAAATTGCCATGAA 59.136 37.500 0.00 0.00 34.87 2.57
484 498 5.348179 CGCATGAACTAAAATTGCCATGAAA 59.652 36.000 0.00 0.00 34.87 2.69
485 499 6.128607 CGCATGAACTAAAATTGCCATGAAAA 60.129 34.615 0.00 0.00 34.87 2.29
486 500 7.570875 CGCATGAACTAAAATTGCCATGAAAAA 60.571 33.333 0.00 0.00 34.87 1.94
487 501 7.534918 GCATGAACTAAAATTGCCATGAAAAAC 59.465 33.333 0.00 0.00 34.87 2.43
488 502 7.171447 TGAACTAAAATTGCCATGAAAAACG 57.829 32.000 0.00 0.00 0.00 3.60
489 503 6.758886 TGAACTAAAATTGCCATGAAAAACGT 59.241 30.769 0.00 0.00 0.00 3.99
490 504 7.278868 TGAACTAAAATTGCCATGAAAAACGTT 59.721 29.630 0.00 0.00 0.00 3.99
491 505 7.546778 ACTAAAATTGCCATGAAAAACGTTT 57.453 28.000 7.96 7.96 0.00 3.60
492 506 7.405769 ACTAAAATTGCCATGAAAAACGTTTG 58.594 30.769 15.46 1.72 0.00 2.93
493 507 6.428385 AAAATTGCCATGAAAAACGTTTGA 57.572 29.167 15.46 2.09 0.00 2.69
494 508 5.655893 AATTGCCATGAAAAACGTTTGAG 57.344 34.783 15.46 3.14 0.00 3.02
495 509 3.791973 TGCCATGAAAAACGTTTGAGT 57.208 38.095 15.46 2.90 0.00 3.41
496 510 4.116747 TGCCATGAAAAACGTTTGAGTT 57.883 36.364 15.46 5.13 35.59 3.01
497 511 3.862267 TGCCATGAAAAACGTTTGAGTTG 59.138 39.130 15.46 10.27 34.14 3.16
498 512 3.862845 GCCATGAAAAACGTTTGAGTTGT 59.137 39.130 15.46 0.00 34.14 3.32
499 513 4.026886 GCCATGAAAAACGTTTGAGTTGTC 60.027 41.667 15.46 6.27 34.14 3.18
500 514 5.098893 CCATGAAAAACGTTTGAGTTGTCA 58.901 37.500 15.46 11.32 35.12 3.58
501 515 5.748152 CCATGAAAAACGTTTGAGTTGTCAT 59.252 36.000 15.46 12.90 38.83 3.06
502 516 6.291743 CCATGAAAAACGTTTGAGTTGTCATG 60.292 38.462 23.75 23.75 45.34 3.07
503 517 4.560819 TGAAAAACGTTTGAGTTGTCATGC 59.439 37.500 15.46 0.00 34.14 4.06
504 518 4.370364 AAAACGTTTGAGTTGTCATGCT 57.630 36.364 15.46 0.00 34.14 3.79
505 519 4.370364 AAACGTTTGAGTTGTCATGCTT 57.630 36.364 13.81 0.00 34.14 3.91
506 520 5.493133 AAACGTTTGAGTTGTCATGCTTA 57.507 34.783 13.81 0.00 34.14 3.09
507 521 5.493133 AACGTTTGAGTTGTCATGCTTAA 57.507 34.783 0.00 0.00 32.39 1.85
508 522 5.493133 ACGTTTGAGTTGTCATGCTTAAA 57.507 34.783 0.00 0.00 30.85 1.52
509 523 5.885881 ACGTTTGAGTTGTCATGCTTAAAA 58.114 33.333 0.00 0.00 30.85 1.52
510 524 6.503524 ACGTTTGAGTTGTCATGCTTAAAAT 58.496 32.000 0.00 0.00 30.85 1.82
511 525 6.636850 ACGTTTGAGTTGTCATGCTTAAAATC 59.363 34.615 0.00 0.00 30.85 2.17
512 526 6.857964 CGTTTGAGTTGTCATGCTTAAAATCT 59.142 34.615 0.00 0.00 30.85 2.40
513 527 8.015087 CGTTTGAGTTGTCATGCTTAAAATCTA 58.985 33.333 0.00 0.00 30.85 1.98
514 528 9.677567 GTTTGAGTTGTCATGCTTAAAATCTAA 57.322 29.630 0.00 0.00 30.85 2.10
515 529 9.677567 TTTGAGTTGTCATGCTTAAAATCTAAC 57.322 29.630 0.00 0.00 30.85 2.34
516 530 7.816640 TGAGTTGTCATGCTTAAAATCTAACC 58.183 34.615 0.00 0.00 0.00 2.85
517 531 7.446931 TGAGTTGTCATGCTTAAAATCTAACCA 59.553 33.333 0.00 0.00 0.00 3.67
518 532 8.353423 AGTTGTCATGCTTAAAATCTAACCAT 57.647 30.769 0.00 0.00 0.00 3.55
519 533 8.806146 AGTTGTCATGCTTAAAATCTAACCATT 58.194 29.630 0.00 0.00 0.00 3.16
520 534 9.076596 GTTGTCATGCTTAAAATCTAACCATTC 57.923 33.333 0.00 0.00 0.00 2.67
521 535 7.471721 TGTCATGCTTAAAATCTAACCATTCG 58.528 34.615 0.00 0.00 0.00 3.34
522 536 6.912591 GTCATGCTTAAAATCTAACCATTCGG 59.087 38.462 0.00 0.00 38.77 4.30
523 537 5.828299 TGCTTAAAATCTAACCATTCGGG 57.172 39.130 0.00 0.00 44.81 5.14
524 538 5.502079 TGCTTAAAATCTAACCATTCGGGA 58.498 37.500 0.00 0.00 41.15 5.14
525 539 6.126409 TGCTTAAAATCTAACCATTCGGGAT 58.874 36.000 0.00 0.00 41.15 3.85
526 540 6.605594 TGCTTAAAATCTAACCATTCGGGATT 59.394 34.615 0.00 0.00 41.15 3.01
527 541 7.123547 TGCTTAAAATCTAACCATTCGGGATTT 59.876 33.333 0.00 0.00 41.15 2.17
528 542 8.626526 GCTTAAAATCTAACCATTCGGGATTTA 58.373 33.333 0.00 0.00 41.15 1.40
531 545 8.760980 AAAATCTAACCATTCGGGATTTATCA 57.239 30.769 0.00 0.00 41.15 2.15
532 546 8.940397 AAATCTAACCATTCGGGATTTATCAT 57.060 30.769 0.00 0.00 41.15 2.45
533 547 8.940397 AATCTAACCATTCGGGATTTATCATT 57.060 30.769 0.00 0.00 41.15 2.57
534 548 8.940397 ATCTAACCATTCGGGATTTATCATTT 57.060 30.769 0.00 0.00 41.15 2.32
535 549 8.391075 TCTAACCATTCGGGATTTATCATTTC 57.609 34.615 0.00 0.00 41.15 2.17
536 550 6.405278 AACCATTCGGGATTTATCATTTCC 57.595 37.500 0.00 0.00 41.15 3.13
537 551 4.518970 ACCATTCGGGATTTATCATTTCCG 59.481 41.667 0.00 0.00 41.15 4.30
538 552 4.475944 CATTCGGGATTTATCATTTCCGC 58.524 43.478 0.00 0.00 37.65 5.54
539 553 3.201353 TCGGGATTTATCATTTCCGCA 57.799 42.857 0.00 0.00 37.65 5.69
540 554 3.546724 TCGGGATTTATCATTTCCGCAA 58.453 40.909 0.00 0.00 37.65 4.85
541 555 3.948473 TCGGGATTTATCATTTCCGCAAA 59.052 39.130 0.00 0.00 37.65 3.68
542 556 4.036262 TCGGGATTTATCATTTCCGCAAAG 59.964 41.667 0.00 0.00 37.65 2.77
557 571 3.549873 CCGCAAAGTTAGTGTGTTTTTGG 59.450 43.478 0.00 0.00 31.28 3.28
561 575 4.385358 AAGTTAGTGTGTTTTTGGCCTG 57.615 40.909 3.32 0.00 0.00 4.85
562 576 2.100749 AGTTAGTGTGTTTTTGGCCTGC 59.899 45.455 3.32 0.00 0.00 4.85
584 598 2.043752 TCCGTCCGCCTACATCCA 60.044 61.111 0.00 0.00 0.00 3.41
596 611 3.190118 GCCTACATCCATATGAGCAAAGC 59.810 47.826 3.65 0.00 36.54 3.51
787 810 0.179097 CTACTCCTTTCTCCGCAGCC 60.179 60.000 0.00 0.00 0.00 4.85
790 813 0.606401 CTCCTTTCTCCGCAGCCAAA 60.606 55.000 0.00 0.00 0.00 3.28
791 814 0.179004 TCCTTTCTCCGCAGCCAAAA 60.179 50.000 0.00 0.00 0.00 2.44
792 815 0.673437 CCTTTCTCCGCAGCCAAAAA 59.327 50.000 0.00 0.00 0.00 1.94
991 1021 1.075536 TCCCCAAGGAAAGGAAAGAGC 59.924 52.381 0.00 0.00 40.08 4.09
1054 1084 2.284625 TGGCCTCCATCTCCACGT 60.285 61.111 3.32 0.00 0.00 4.49
1149 1179 2.696506 GGAGGTTAAAGTCTTCACCCG 58.303 52.381 9.40 0.00 30.15 5.28
1164 1194 2.431942 CCGTCCACTCCCGTTTCG 60.432 66.667 0.00 0.00 0.00 3.46
1165 1195 2.646719 CGTCCACTCCCGTTTCGA 59.353 61.111 0.00 0.00 0.00 3.71
1166 1196 1.731969 CGTCCACTCCCGTTTCGAC 60.732 63.158 0.00 0.00 0.00 4.20
1194 1232 2.432300 CCCCCTTACGTCGCATCCT 61.432 63.158 0.00 0.00 0.00 3.24
1359 1397 2.218530 GCCTTGTTCGACAAATTGCAAC 59.781 45.455 0.00 0.00 37.69 4.17
1362 1400 3.077229 TGTTCGACAAATTGCAACAGG 57.923 42.857 0.00 0.00 0.00 4.00
1502 1540 1.123928 AGTTTAGGAGATGGAGCCCG 58.876 55.000 0.00 0.00 0.00 6.13
1589 1627 0.251341 ACTCCGAAAATGCCTGCCTT 60.251 50.000 0.00 0.00 0.00 4.35
1591 1629 0.251121 TCCGAAAATGCCTGCCTTCA 60.251 50.000 0.00 0.00 0.00 3.02
1598 1636 1.335145 ATGCCTGCCTTCAATATGCC 58.665 50.000 0.00 0.00 0.00 4.40
1599 1637 0.033306 TGCCTGCCTTCAATATGCCA 60.033 50.000 0.00 0.00 0.00 4.92
1600 1638 1.113788 GCCTGCCTTCAATATGCCAA 58.886 50.000 0.00 0.00 0.00 4.52
1601 1639 1.202452 GCCTGCCTTCAATATGCCAAC 60.202 52.381 0.00 0.00 0.00 3.77
1602 1640 2.101783 CCTGCCTTCAATATGCCAACA 58.898 47.619 0.00 0.00 0.00 3.33
1603 1641 2.100252 CCTGCCTTCAATATGCCAACAG 59.900 50.000 0.00 0.00 0.00 3.16
1604 1642 3.018856 CTGCCTTCAATATGCCAACAGA 58.981 45.455 0.00 0.00 0.00 3.41
1616 1654 2.017049 GCCAACAGACAACAGTGAGTT 58.983 47.619 0.00 0.00 42.42 3.01
1736 1776 7.406031 TGAGTGATCAGGTTACTTAGGTAAG 57.594 40.000 0.00 0.00 38.42 2.34
1740 1780 9.317827 AGTGATCAGGTTACTTAGGTAAGTTTA 57.682 33.333 7.68 0.00 43.57 2.01
1924 2004 3.916776 GCTTTTGTTAGTTGCTGCTGATC 59.083 43.478 0.00 0.00 0.00 2.92
2076 2157 5.415701 TCACTCCATCCAAGCTGAAAATTAC 59.584 40.000 0.00 0.00 0.00 1.89
2328 2410 2.741517 AGTTGTTTTGCTTGTTGTTGCC 59.258 40.909 0.00 0.00 0.00 4.52
2441 2523 2.430610 CCTCCGAGGAAGAGGCCAG 61.431 68.421 9.01 0.00 44.30 4.85
2518 2600 3.159472 TGAAGAACTAGCAGGAACCGTA 58.841 45.455 0.00 0.00 0.00 4.02
2556 2762 7.721286 AGTGCTGTTGCTAGTTCAATATATC 57.279 36.000 0.00 0.00 40.48 1.63
2588 2794 2.437200 TTTTTGCCGCTCCATTTGAG 57.563 45.000 0.00 0.00 44.47 3.02
2589 2795 1.614996 TTTTGCCGCTCCATTTGAGA 58.385 45.000 0.00 0.00 44.42 3.27
2590 2796 1.614996 TTTGCCGCTCCATTTGAGAA 58.385 45.000 0.00 0.00 44.42 2.87
2591 2797 1.614996 TTGCCGCTCCATTTGAGAAA 58.385 45.000 0.00 0.00 44.42 2.52
2634 2840 2.977405 CAAGCTTGCAACAGGTACTC 57.023 50.000 14.65 0.00 34.60 2.59
2767 2974 2.032117 CGTGTTGTGCTGATGCTTGTAA 60.032 45.455 0.00 0.00 40.48 2.41
2775 2982 4.676924 GTGCTGATGCTTGTAACTTCAAAC 59.323 41.667 0.00 0.00 40.48 2.93
2800 3007 8.999431 ACATAATACAAATAAGGTAGATTGCGG 58.001 33.333 0.00 0.00 0.00 5.69
2841 3048 6.360681 GCCGATGTGTAATTATGCTGAATTTC 59.639 38.462 2.38 0.00 31.51 2.17
2955 3162 6.939163 AGCATATCAGATAATGTTCCTGTTCC 59.061 38.462 0.00 0.00 0.00 3.62
3049 3257 1.006337 GCCAATGCTTTGCCGTTCA 60.006 52.632 6.81 0.00 33.53 3.18
3056 3264 1.727880 TGCTTTGCCGTTCATACGTAC 59.272 47.619 0.00 0.00 46.20 3.67
3057 3265 1.997606 GCTTTGCCGTTCATACGTACT 59.002 47.619 0.00 0.00 46.20 2.73
3058 3266 2.414138 GCTTTGCCGTTCATACGTACTT 59.586 45.455 0.00 0.00 46.20 2.24
3059 3267 3.120442 GCTTTGCCGTTCATACGTACTTT 60.120 43.478 0.00 0.00 46.20 2.66
3060 3268 4.091800 GCTTTGCCGTTCATACGTACTTTA 59.908 41.667 0.00 0.00 46.20 1.85
3107 3321 4.960469 TGTAGGTAGGGGAACAGTAGATTG 59.040 45.833 0.00 0.00 0.00 2.67
3119 3333 6.472808 GGAACAGTAGATTGTGATCGTACTTC 59.527 42.308 0.00 0.00 37.37 3.01
3123 3337 4.030134 AGATTGTGATCGTACTTCCGTC 57.970 45.455 0.00 0.00 37.37 4.79
3739 4019 4.351938 CCGTCGGCGTTCTCCACA 62.352 66.667 9.28 0.00 36.15 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 6.642707 ACTAGTGGCAGATATCTACAGTTC 57.357 41.667 17.31 5.42 0.00 3.01
106 107 4.446371 GCAATAGTCAACTAGTGGCAGAT 58.554 43.478 16.64 0.00 42.75 2.90
111 112 3.055094 ACTGGGCAATAGTCAACTAGTGG 60.055 47.826 16.64 0.00 42.75 4.00
129 130 1.283793 CAACCGCAGCTGAAACTGG 59.716 57.895 20.43 12.48 38.16 4.00
136 137 1.033746 AATGATCCCAACCGCAGCTG 61.034 55.000 10.11 10.11 0.00 4.24
165 166 3.699538 GGACCCACCCTGTTCAAAATATC 59.300 47.826 0.00 0.00 0.00 1.63
166 167 3.336694 AGGACCCACCCTGTTCAAAATAT 59.663 43.478 0.00 0.00 40.05 1.28
167 168 2.719705 AGGACCCACCCTGTTCAAAATA 59.280 45.455 0.00 0.00 40.05 1.40
169 170 0.930726 AGGACCCACCCTGTTCAAAA 59.069 50.000 0.00 0.00 40.05 2.44
172 173 3.574952 CAGGACCCACCCTGTTCA 58.425 61.111 0.00 0.00 46.62 3.18
177 178 3.157680 CGAAACAGGACCCACCCT 58.842 61.111 0.00 0.00 40.05 4.34
178 179 1.833787 TAGCGAAACAGGACCCACCC 61.834 60.000 0.00 0.00 40.05 4.61
179 180 0.391263 CTAGCGAAACAGGACCCACC 60.391 60.000 0.00 0.00 39.35 4.61
180 181 1.019805 GCTAGCGAAACAGGACCCAC 61.020 60.000 0.00 0.00 0.00 4.61
181 182 1.295423 GCTAGCGAAACAGGACCCA 59.705 57.895 0.00 0.00 0.00 4.51
182 183 0.741221 CTGCTAGCGAAACAGGACCC 60.741 60.000 10.77 0.00 0.00 4.46
183 184 0.037232 ACTGCTAGCGAAACAGGACC 60.037 55.000 10.77 0.00 35.70 4.46
184 185 1.336887 TGACTGCTAGCGAAACAGGAC 60.337 52.381 10.77 1.55 35.70 3.85
185 186 0.966179 TGACTGCTAGCGAAACAGGA 59.034 50.000 10.77 0.00 35.70 3.86
186 187 1.071605 GTGACTGCTAGCGAAACAGG 58.928 55.000 10.77 0.00 35.70 4.00
187 188 1.723542 CTGTGACTGCTAGCGAAACAG 59.276 52.381 18.98 18.98 37.45 3.16
188 189 1.339929 TCTGTGACTGCTAGCGAAACA 59.660 47.619 10.77 10.70 0.00 2.83
189 190 1.989165 CTCTGTGACTGCTAGCGAAAC 59.011 52.381 10.77 6.48 0.00 2.78
190 191 1.067565 CCTCTGTGACTGCTAGCGAAA 60.068 52.381 10.77 0.00 0.00 3.46
191 192 0.528017 CCTCTGTGACTGCTAGCGAA 59.472 55.000 10.77 0.00 0.00 4.70
192 193 1.938657 GCCTCTGTGACTGCTAGCGA 61.939 60.000 10.77 0.00 0.00 4.93
193 194 1.518133 GCCTCTGTGACTGCTAGCG 60.518 63.158 10.77 7.61 0.00 4.26
194 195 0.177604 ATGCCTCTGTGACTGCTAGC 59.822 55.000 8.10 8.10 0.00 3.42
195 196 2.692557 AGTATGCCTCTGTGACTGCTAG 59.307 50.000 0.00 0.00 0.00 3.42
196 197 2.739943 AGTATGCCTCTGTGACTGCTA 58.260 47.619 0.00 0.00 0.00 3.49
197 198 1.566211 AGTATGCCTCTGTGACTGCT 58.434 50.000 0.00 0.00 0.00 4.24
198 199 2.005451 CAAGTATGCCTCTGTGACTGC 58.995 52.381 0.00 0.00 0.00 4.40
268 269 2.471255 CCGTTTCAAGGCAGCTAGG 58.529 57.895 0.00 0.00 0.00 3.02
294 295 2.919602 TCCTTGATCTTAGGCCCTTTGT 59.080 45.455 0.00 0.00 32.59 2.83
297 298 1.492599 GCTCCTTGATCTTAGGCCCTT 59.507 52.381 0.00 0.00 32.59 3.95
303 304 4.012374 TGCCTTTTGCTCCTTGATCTTAG 58.988 43.478 0.00 0.00 42.00 2.18
304 305 4.032960 TGCCTTTTGCTCCTTGATCTTA 57.967 40.909 0.00 0.00 42.00 2.10
309 323 0.604578 GCATGCCTTTTGCTCCTTGA 59.395 50.000 6.36 0.00 42.00 3.02
363 377 8.717821 CATCTCGAACTAAAGTTACCATGAAAA 58.282 33.333 0.00 0.00 38.56 2.29
364 378 7.333423 CCATCTCGAACTAAAGTTACCATGAAA 59.667 37.037 0.00 0.00 38.56 2.69
365 379 6.816640 CCATCTCGAACTAAAGTTACCATGAA 59.183 38.462 0.00 0.00 38.56 2.57
366 380 6.338146 CCATCTCGAACTAAAGTTACCATGA 58.662 40.000 0.00 0.00 38.56 3.07
367 381 5.006746 GCCATCTCGAACTAAAGTTACCATG 59.993 44.000 0.00 0.00 38.56 3.66
368 382 5.116882 GCCATCTCGAACTAAAGTTACCAT 58.883 41.667 0.00 0.00 38.56 3.55
370 384 4.501071 TGCCATCTCGAACTAAAGTTACC 58.499 43.478 0.00 0.00 38.56 2.85
371 385 6.476243 TTTGCCATCTCGAACTAAAGTTAC 57.524 37.500 0.00 0.00 38.56 2.50
372 386 7.681939 AATTTGCCATCTCGAACTAAAGTTA 57.318 32.000 0.00 0.00 38.56 2.24
373 387 6.575162 AATTTGCCATCTCGAACTAAAGTT 57.425 33.333 0.00 0.00 41.64 2.66
374 388 6.575162 AAATTTGCCATCTCGAACTAAAGT 57.425 33.333 0.00 0.00 0.00 2.66
375 389 7.752695 ACTAAATTTGCCATCTCGAACTAAAG 58.247 34.615 0.00 0.00 0.00 1.85
376 390 7.681939 ACTAAATTTGCCATCTCGAACTAAA 57.318 32.000 0.00 0.00 0.00 1.85
377 391 7.174253 ACAACTAAATTTGCCATCTCGAACTAA 59.826 33.333 0.00 0.00 0.00 2.24
378 392 6.653320 ACAACTAAATTTGCCATCTCGAACTA 59.347 34.615 0.00 0.00 0.00 2.24
380 394 5.699839 ACAACTAAATTTGCCATCTCGAAC 58.300 37.500 0.00 0.00 0.00 3.95
382 396 5.000591 TGACAACTAAATTTGCCATCTCGA 58.999 37.500 0.00 0.00 0.00 4.04
383 397 5.295431 TGACAACTAAATTTGCCATCTCG 57.705 39.130 0.00 0.00 0.00 4.04
384 398 6.803807 GTCTTGACAACTAAATTTGCCATCTC 59.196 38.462 0.00 0.00 0.00 2.75
386 400 6.363357 GTGTCTTGACAACTAAATTTGCCATC 59.637 38.462 4.93 0.00 0.00 3.51
388 402 5.587289 GTGTCTTGACAACTAAATTTGCCA 58.413 37.500 4.93 0.00 0.00 4.92
390 404 4.675114 CCGTGTCTTGACAACTAAATTTGC 59.325 41.667 4.93 0.00 0.00 3.68
391 405 4.675114 GCCGTGTCTTGACAACTAAATTTG 59.325 41.667 4.93 0.00 0.00 2.32
393 407 3.880490 TGCCGTGTCTTGACAACTAAATT 59.120 39.130 4.93 0.00 0.00 1.82
395 409 2.907634 TGCCGTGTCTTGACAACTAAA 58.092 42.857 4.93 0.00 0.00 1.85
396 410 2.605837 TGCCGTGTCTTGACAACTAA 57.394 45.000 4.93 0.00 0.00 2.24
397 411 2.159014 AGTTGCCGTGTCTTGACAACTA 60.159 45.455 4.93 0.00 46.66 2.24
398 412 1.014352 GTTGCCGTGTCTTGACAACT 58.986 50.000 4.93 0.00 38.04 3.16
399 413 1.014352 AGTTGCCGTGTCTTGACAAC 58.986 50.000 4.93 0.00 40.65 3.32
400 414 1.745232 AAGTTGCCGTGTCTTGACAA 58.255 45.000 4.93 0.00 0.00 3.18
401 415 1.400142 CAAAGTTGCCGTGTCTTGACA 59.600 47.619 0.00 0.00 0.00 3.58
402 416 1.400494 ACAAAGTTGCCGTGTCTTGAC 59.600 47.619 0.00 0.00 0.00 3.18
403 417 1.668751 GACAAAGTTGCCGTGTCTTGA 59.331 47.619 0.00 0.00 38.87 3.02
404 418 2.105323 GACAAAGTTGCCGTGTCTTG 57.895 50.000 0.00 0.00 38.87 3.02
406 420 3.780624 AGACAAAGTTGCCGTGTCT 57.219 47.368 2.68 2.68 45.53 3.41
407 421 1.295792 TGAGACAAAGTTGCCGTGTC 58.704 50.000 0.00 0.00 41.62 3.67
408 422 1.745232 TTGAGACAAAGTTGCCGTGT 58.255 45.000 0.00 0.00 0.00 4.49
409 423 3.354089 AATTGAGACAAAGTTGCCGTG 57.646 42.857 0.00 0.00 0.00 4.94
410 424 4.385358 AAAATTGAGACAAAGTTGCCGT 57.615 36.364 0.00 0.00 0.00 5.68
430 444 8.498054 TGACAAACATGGCAATTTTCTAAAAA 57.502 26.923 0.00 0.00 0.00 1.94
431 445 8.394121 GTTGACAAACATGGCAATTTTCTAAAA 58.606 29.630 0.00 0.00 39.24 1.52
432 446 7.011857 GGTTGACAAACATGGCAATTTTCTAAA 59.988 33.333 0.00 0.00 39.24 1.85
433 447 6.481644 GGTTGACAAACATGGCAATTTTCTAA 59.518 34.615 0.00 0.00 39.24 2.10
434 448 5.988561 GGTTGACAAACATGGCAATTTTCTA 59.011 36.000 0.00 0.00 39.24 2.10
435 449 4.815846 GGTTGACAAACATGGCAATTTTCT 59.184 37.500 0.00 0.00 39.24 2.52
436 450 4.815846 AGGTTGACAAACATGGCAATTTTC 59.184 37.500 5.91 0.00 39.24 2.29
437 451 4.779696 AGGTTGACAAACATGGCAATTTT 58.220 34.783 5.91 0.00 39.24 1.82
438 452 4.379652 GAGGTTGACAAACATGGCAATTT 58.620 39.130 5.91 0.00 39.24 1.82
439 453 3.552684 CGAGGTTGACAAACATGGCAATT 60.553 43.478 5.91 0.00 39.24 2.32
440 454 2.030007 CGAGGTTGACAAACATGGCAAT 60.030 45.455 5.91 0.00 39.24 3.56
441 455 1.336440 CGAGGTTGACAAACATGGCAA 59.664 47.619 5.91 0.00 38.10 4.52
442 456 0.950836 CGAGGTTGACAAACATGGCA 59.049 50.000 5.91 0.00 38.10 4.92
443 457 0.387239 GCGAGGTTGACAAACATGGC 60.387 55.000 5.91 1.80 42.91 4.40
444 458 0.950836 TGCGAGGTTGACAAACATGG 59.049 50.000 5.91 0.00 38.10 3.66
445 459 2.226200 TCATGCGAGGTTGACAAACATG 59.774 45.455 5.91 7.76 38.10 3.21
446 460 2.503331 TCATGCGAGGTTGACAAACAT 58.497 42.857 5.91 0.00 38.10 2.71
447 461 1.960417 TCATGCGAGGTTGACAAACA 58.040 45.000 5.91 0.00 38.10 2.83
448 462 2.290641 AGTTCATGCGAGGTTGACAAAC 59.709 45.455 0.00 0.00 35.40 2.93
449 463 2.571212 AGTTCATGCGAGGTTGACAAA 58.429 42.857 0.00 0.00 0.00 2.83
450 464 2.254546 AGTTCATGCGAGGTTGACAA 57.745 45.000 0.00 0.00 0.00 3.18
451 465 3.394674 TTAGTTCATGCGAGGTTGACA 57.605 42.857 0.00 0.00 0.00 3.58
452 466 4.742438 TTTTAGTTCATGCGAGGTTGAC 57.258 40.909 0.00 0.00 0.00 3.18
453 467 5.698832 CAATTTTAGTTCATGCGAGGTTGA 58.301 37.500 0.00 0.00 0.00 3.18
454 468 4.324402 GCAATTTTAGTTCATGCGAGGTTG 59.676 41.667 0.00 0.00 0.00 3.77
455 469 4.485163 GCAATTTTAGTTCATGCGAGGTT 58.515 39.130 0.00 0.00 0.00 3.50
456 470 3.119495 GGCAATTTTAGTTCATGCGAGGT 60.119 43.478 0.00 0.00 37.88 3.85
457 471 3.119531 TGGCAATTTTAGTTCATGCGAGG 60.120 43.478 0.00 0.00 37.88 4.63
458 472 4.095410 TGGCAATTTTAGTTCATGCGAG 57.905 40.909 0.00 0.00 37.88 5.03
459 473 4.157472 TCATGGCAATTTTAGTTCATGCGA 59.843 37.500 0.00 0.00 37.88 5.10
460 474 4.422840 TCATGGCAATTTTAGTTCATGCG 58.577 39.130 0.00 0.00 37.88 4.73
461 475 6.724694 TTTCATGGCAATTTTAGTTCATGC 57.275 33.333 0.00 0.00 33.95 4.06
462 476 7.741216 CGTTTTTCATGGCAATTTTAGTTCATG 59.259 33.333 0.00 0.00 34.89 3.07
463 477 7.440856 ACGTTTTTCATGGCAATTTTAGTTCAT 59.559 29.630 0.00 0.00 0.00 2.57
464 478 6.758886 ACGTTTTTCATGGCAATTTTAGTTCA 59.241 30.769 0.00 0.00 0.00 3.18
465 479 7.172654 ACGTTTTTCATGGCAATTTTAGTTC 57.827 32.000 0.00 0.00 0.00 3.01
466 480 7.546778 AACGTTTTTCATGGCAATTTTAGTT 57.453 28.000 0.00 0.00 0.00 2.24
467 481 7.278868 TCAAACGTTTTTCATGGCAATTTTAGT 59.721 29.630 11.66 0.00 0.00 2.24
468 482 7.625553 TCAAACGTTTTTCATGGCAATTTTAG 58.374 30.769 11.66 0.00 0.00 1.85
469 483 7.278868 ACTCAAACGTTTTTCATGGCAATTTTA 59.721 29.630 11.66 0.00 0.00 1.52
470 484 6.093357 ACTCAAACGTTTTTCATGGCAATTTT 59.907 30.769 11.66 0.00 0.00 1.82
471 485 5.584251 ACTCAAACGTTTTTCATGGCAATTT 59.416 32.000 11.66 0.00 0.00 1.82
472 486 5.115480 ACTCAAACGTTTTTCATGGCAATT 58.885 33.333 11.66 0.00 0.00 2.32
473 487 4.692228 ACTCAAACGTTTTTCATGGCAAT 58.308 34.783 11.66 0.00 0.00 3.56
474 488 4.116747 ACTCAAACGTTTTTCATGGCAA 57.883 36.364 11.66 0.00 0.00 4.52
475 489 3.791973 ACTCAAACGTTTTTCATGGCA 57.208 38.095 11.66 0.00 0.00 4.92
476 490 3.862845 ACAACTCAAACGTTTTTCATGGC 59.137 39.130 11.66 0.00 0.00 4.40
477 491 5.098893 TGACAACTCAAACGTTTTTCATGG 58.901 37.500 11.66 0.00 0.00 3.66
478 492 6.630015 CATGACAACTCAAACGTTTTTCATG 58.370 36.000 11.66 16.22 37.88 3.07
479 493 5.231991 GCATGACAACTCAAACGTTTTTCAT 59.768 36.000 11.66 9.41 31.76 2.57
480 494 4.560819 GCATGACAACTCAAACGTTTTTCA 59.439 37.500 11.66 7.59 0.00 2.69
481 495 4.798387 AGCATGACAACTCAAACGTTTTTC 59.202 37.500 11.66 2.16 0.00 2.29
482 496 4.743493 AGCATGACAACTCAAACGTTTTT 58.257 34.783 11.66 0.12 0.00 1.94
483 497 4.370364 AGCATGACAACTCAAACGTTTT 57.630 36.364 11.66 0.00 0.00 2.43
484 498 4.370364 AAGCATGACAACTCAAACGTTT 57.630 36.364 7.96 7.96 0.00 3.60
485 499 5.493133 TTAAGCATGACAACTCAAACGTT 57.507 34.783 0.00 0.00 0.00 3.99
486 500 5.493133 TTTAAGCATGACAACTCAAACGT 57.507 34.783 0.00 0.00 0.00 3.99
487 501 6.857964 AGATTTTAAGCATGACAACTCAAACG 59.142 34.615 0.00 0.00 0.00 3.60
488 502 9.677567 TTAGATTTTAAGCATGACAACTCAAAC 57.322 29.630 0.00 0.00 0.00 2.93
489 503 9.677567 GTTAGATTTTAAGCATGACAACTCAAA 57.322 29.630 0.00 0.00 0.00 2.69
490 504 8.296713 GGTTAGATTTTAAGCATGACAACTCAA 58.703 33.333 0.00 0.00 0.00 3.02
491 505 7.446931 TGGTTAGATTTTAAGCATGACAACTCA 59.553 33.333 0.00 0.00 31.03 3.41
492 506 7.816640 TGGTTAGATTTTAAGCATGACAACTC 58.183 34.615 0.00 0.00 31.03 3.01
493 507 7.759489 TGGTTAGATTTTAAGCATGACAACT 57.241 32.000 0.00 0.00 31.03 3.16
494 508 8.986477 AATGGTTAGATTTTAAGCATGACAAC 57.014 30.769 11.13 0.00 42.58 3.32
495 509 7.967854 CGAATGGTTAGATTTTAAGCATGACAA 59.032 33.333 11.13 0.00 42.58 3.18
496 510 7.415095 CCGAATGGTTAGATTTTAAGCATGACA 60.415 37.037 11.13 0.00 42.58 3.58
497 511 6.912591 CCGAATGGTTAGATTTTAAGCATGAC 59.087 38.462 11.13 8.50 42.58 3.06
498 512 6.039270 CCCGAATGGTTAGATTTTAAGCATGA 59.961 38.462 11.13 0.00 42.58 3.07
499 513 6.039270 TCCCGAATGGTTAGATTTTAAGCATG 59.961 38.462 11.13 0.00 42.58 4.06
500 514 6.126409 TCCCGAATGGTTAGATTTTAAGCAT 58.874 36.000 5.97 5.97 44.48 3.79
501 515 5.502079 TCCCGAATGGTTAGATTTTAAGCA 58.498 37.500 1.87 1.87 38.94 3.91
502 516 6.635030 ATCCCGAATGGTTAGATTTTAAGC 57.365 37.500 0.00 0.00 34.77 3.09
505 519 9.854668 TGATAAATCCCGAATGGTTAGATTTTA 57.145 29.630 0.00 0.00 36.06 1.52
506 520 8.760980 TGATAAATCCCGAATGGTTAGATTTT 57.239 30.769 0.00 0.00 36.06 1.82
507 521 8.940397 ATGATAAATCCCGAATGGTTAGATTT 57.060 30.769 0.00 0.00 37.40 2.17
508 522 8.940397 AATGATAAATCCCGAATGGTTAGATT 57.060 30.769 0.00 0.00 34.77 2.40
509 523 8.940397 AAATGATAAATCCCGAATGGTTAGAT 57.060 30.769 0.00 0.00 34.77 1.98
510 524 7.447238 GGAAATGATAAATCCCGAATGGTTAGA 59.553 37.037 0.00 0.00 34.77 2.10
511 525 7.573096 CGGAAATGATAAATCCCGAATGGTTAG 60.573 40.741 0.00 0.00 39.31 2.34
512 526 6.205853 CGGAAATGATAAATCCCGAATGGTTA 59.794 38.462 0.00 0.00 39.31 2.85
513 527 5.009610 CGGAAATGATAAATCCCGAATGGTT 59.990 40.000 0.00 0.00 39.31 3.67
514 528 4.518970 CGGAAATGATAAATCCCGAATGGT 59.481 41.667 0.00 0.00 39.31 3.55
515 529 4.615912 GCGGAAATGATAAATCCCGAATGG 60.616 45.833 0.00 0.00 39.31 3.16
516 530 4.023279 TGCGGAAATGATAAATCCCGAATG 60.023 41.667 0.00 0.00 39.31 2.67
517 531 4.141287 TGCGGAAATGATAAATCCCGAAT 58.859 39.130 0.00 0.00 39.31 3.34
518 532 3.546724 TGCGGAAATGATAAATCCCGAA 58.453 40.909 0.00 0.00 39.31 4.30
519 533 3.201353 TGCGGAAATGATAAATCCCGA 57.799 42.857 0.00 0.00 39.31 5.14
520 534 3.980646 TTGCGGAAATGATAAATCCCG 57.019 42.857 0.00 0.00 39.88 5.14
521 535 5.262588 ACTTTGCGGAAATGATAAATCCC 57.737 39.130 1.45 0.00 0.00 3.85
522 536 7.432252 CACTAACTTTGCGGAAATGATAAATCC 59.568 37.037 1.45 0.00 0.00 3.01
523 537 7.968405 ACACTAACTTTGCGGAAATGATAAATC 59.032 33.333 1.45 0.00 0.00 2.17
524 538 7.754924 CACACTAACTTTGCGGAAATGATAAAT 59.245 33.333 1.45 0.00 0.00 1.40
525 539 7.081349 CACACTAACTTTGCGGAAATGATAAA 58.919 34.615 1.45 0.00 0.00 1.40
526 540 6.205853 ACACACTAACTTTGCGGAAATGATAA 59.794 34.615 1.45 0.00 0.00 1.75
527 541 5.703592 ACACACTAACTTTGCGGAAATGATA 59.296 36.000 1.45 0.00 0.00 2.15
528 542 4.518970 ACACACTAACTTTGCGGAAATGAT 59.481 37.500 1.45 0.00 0.00 2.45
529 543 3.880490 ACACACTAACTTTGCGGAAATGA 59.120 39.130 1.45 0.00 0.00 2.57
530 544 4.223320 ACACACTAACTTTGCGGAAATG 57.777 40.909 1.45 0.15 0.00 2.32
531 545 4.911514 AACACACTAACTTTGCGGAAAT 57.088 36.364 1.45 0.00 0.00 2.17
532 546 4.705337 AAACACACTAACTTTGCGGAAA 57.295 36.364 1.05 1.05 0.00 3.13
533 547 4.705337 AAAACACACTAACTTTGCGGAA 57.295 36.364 0.00 0.00 0.00 4.30
534 548 4.416620 CAAAAACACACTAACTTTGCGGA 58.583 39.130 0.00 0.00 0.00 5.54
535 549 3.549873 CCAAAAACACACTAACTTTGCGG 59.450 43.478 0.00 0.00 0.00 5.69
536 550 3.000177 GCCAAAAACACACTAACTTTGCG 60.000 43.478 0.00 0.00 0.00 4.85
537 551 3.308595 GGCCAAAAACACACTAACTTTGC 59.691 43.478 0.00 0.00 0.00 3.68
538 552 4.566360 CAGGCCAAAAACACACTAACTTTG 59.434 41.667 5.01 0.00 0.00 2.77
539 553 4.754322 CAGGCCAAAAACACACTAACTTT 58.246 39.130 5.01 0.00 0.00 2.66
540 554 3.430236 GCAGGCCAAAAACACACTAACTT 60.430 43.478 5.01 0.00 0.00 2.66
541 555 2.100749 GCAGGCCAAAAACACACTAACT 59.899 45.455 5.01 0.00 0.00 2.24
542 556 2.469826 GCAGGCCAAAAACACACTAAC 58.530 47.619 5.01 0.00 0.00 2.34
578 592 4.018490 TGTTGCTTTGCTCATATGGATGT 58.982 39.130 2.13 0.00 34.41 3.06
584 598 7.181143 CAAAGTTTTGTTGCTTTGCTCATAT 57.819 32.000 4.44 0.00 43.02 1.78
792 815 4.137543 ACTCCAATTCGCACTCTCTTTTT 58.862 39.130 0.00 0.00 0.00 1.94
793 816 3.744660 ACTCCAATTCGCACTCTCTTTT 58.255 40.909 0.00 0.00 0.00 2.27
794 817 3.409026 ACTCCAATTCGCACTCTCTTT 57.591 42.857 0.00 0.00 0.00 2.52
795 818 4.744795 ATACTCCAATTCGCACTCTCTT 57.255 40.909 0.00 0.00 0.00 2.85
796 819 4.442192 GGAATACTCCAATTCGCACTCTCT 60.442 45.833 0.00 0.00 41.96 3.10
797 820 3.804873 GGAATACTCCAATTCGCACTCTC 59.195 47.826 0.00 0.00 41.96 3.20
798 821 3.738281 CGGAATACTCCAATTCGCACTCT 60.738 47.826 0.00 0.00 42.58 3.24
799 822 2.540101 CGGAATACTCCAATTCGCACTC 59.460 50.000 0.00 0.00 42.58 3.51
821 847 4.695455 TCAGTTTCTCATGGAAATCGGAAC 59.305 41.667 11.07 1.33 44.46 3.62
852 878 7.519002 CAGAAATCGTACCTCCAGTTTTAAAG 58.481 38.462 0.00 0.00 0.00 1.85
893 922 3.633418 GCTAGGTCTAAGAGAACTGGGA 58.367 50.000 4.25 0.00 43.31 4.37
894 923 2.359531 CGCTAGGTCTAAGAGAACTGGG 59.640 54.545 4.25 0.23 43.31 4.45
895 924 3.065648 GTCGCTAGGTCTAAGAGAACTGG 59.934 52.174 4.25 2.47 43.31 4.00
991 1021 3.592814 CATGGCCATGGCTCTGCG 61.593 66.667 34.31 15.91 41.60 5.18
1149 1179 1.731969 CGTCGAAACGGGAGTGGAC 60.732 63.158 0.00 0.00 46.69 4.02
1194 1232 0.532573 GTTGATCTGAGACTGGCCGA 59.467 55.000 0.00 0.00 0.00 5.54
1290 1328 1.201812 CGTCGAACACTTGCTATGCAC 60.202 52.381 0.00 0.00 38.71 4.57
1322 1360 2.180017 GCATGAAACTGCTGCCCG 59.820 61.111 0.00 0.00 39.12 6.13
1359 1397 2.292267 CTGCACTGGTAAATAGCCCTG 58.708 52.381 0.00 0.00 0.00 4.45
1362 1400 1.672881 CAGCTGCACTGGTAAATAGCC 59.327 52.381 0.00 0.00 43.19 3.93
1507 1545 8.049117 TGACCTGATAAACAAAATCTCTGCTAT 58.951 33.333 0.00 0.00 0.00 2.97
1567 1605 1.401905 GGCAGGCATTTTCGGAGTAAG 59.598 52.381 0.00 0.00 0.00 2.34
1589 1627 4.216042 CACTGTTGTCTGTTGGCATATTGA 59.784 41.667 0.00 0.00 0.00 2.57
1591 1629 4.397420 TCACTGTTGTCTGTTGGCATATT 58.603 39.130 0.00 0.00 0.00 1.28
1689 1729 5.929058 TGTGGCATTTATAATGGAGCAAA 57.071 34.783 0.00 0.00 0.00 3.68
1889 1969 8.638565 CAACTAACAAAAGCTTATATGTTGCAC 58.361 33.333 24.31 0.00 36.71 4.57
1890 1970 8.741101 CAACTAACAAAAGCTTATATGTTGCA 57.259 30.769 24.31 12.10 36.71 4.08
1891 1971 7.666377 GCAACTAACAAAAGCTTATATGTTGC 58.334 34.615 24.31 24.46 45.62 4.17
1924 2004 6.315144 TGTTAACCCATGATCGTTCATTGTAG 59.685 38.462 6.24 0.00 40.70 2.74
2076 2157 9.838339 AAATATGTAGGTTCTTTGATCCAGTAG 57.162 33.333 0.00 0.00 0.00 2.57
2244 2326 4.409718 TCTAATACTTGGCCATAACGCA 57.590 40.909 6.09 0.00 0.00 5.24
2354 2436 1.202794 TGACAATGGTTGCTGAGCTCA 60.203 47.619 17.19 17.19 0.00 4.26
2441 2523 3.247006 TCATCTCTTCCCGTGCTTTAC 57.753 47.619 0.00 0.00 0.00 2.01
2591 2797 5.770417 CATTGCTCAGCTCTTCTTCTTTTT 58.230 37.500 0.00 0.00 0.00 1.94
2634 2840 5.288712 GTCGACATATATAACTCGCCCATTG 59.711 44.000 11.55 0.00 0.00 2.82
2775 2982 7.962918 GCCGCAATCTACCTTATTTGTATTATG 59.037 37.037 0.00 0.00 0.00 1.90
2782 2989 2.602217 GCGCCGCAATCTACCTTATTTG 60.602 50.000 3.15 0.00 0.00 2.32
2800 3007 0.095417 CGGCTTTTCTCTAACAGCGC 59.905 55.000 0.00 0.00 32.68 5.92
2866 3073 7.061441 ACAATATTACGCGTCGATTACATTAGG 59.939 37.037 18.63 3.05 0.00 2.69
2916 3123 1.438651 TATGCTCTTGGACGTGTTGC 58.561 50.000 0.00 0.00 0.00 4.17
2923 3130 7.118971 GGAACATTATCTGATATGCTCTTGGAC 59.881 40.741 0.00 0.00 0.00 4.02
2955 3162 2.094906 TGTCGATGTCCACGAGGTTAAG 60.095 50.000 0.00 0.00 40.37 1.85
3091 3304 3.133003 CGATCACAATCTACTGTTCCCCT 59.867 47.826 0.00 0.00 0.00 4.79
3119 3333 3.925630 ATTGGCAGCCACAGGACGG 62.926 63.158 15.89 0.00 30.78 4.79


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

AutoCloner maintained by Alex Coulton.