Multiple sequence alignment - TraesCS7B01G499300

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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 TraesCS7B01G499300 chr7B 100.000 2616 0 0 1 2616 749558302 749560917 0.000000e+00 4831.0
1 TraesCS7B01G499300 chr7D 92.746 1089 56 12 555 1634 633538416 633539490 0.000000e+00 1552.0
2 TraesCS7B01G499300 chr7D 95.979 746 28 2 1873 2616 423335869 423335124 0.000000e+00 1210.0
3 TraesCS7B01G499300 chr7D 94.966 298 14 1 62 359 633538134 633538430 1.420000e-127 466.0
4 TraesCS7B01G499300 chr7D 96.429 112 3 1 1903 2013 423335980 423335869 1.600000e-42 183.0
5 TraesCS7B01G499300 chr7D 89.831 118 3 1 1733 1850 633539739 633539847 2.710000e-30 143.0
6 TraesCS7B01G499300 chr7D 98.649 74 0 1 483 556 169416538 169416466 2.110000e-26 130.0
7 TraesCS7B01G499300 chr7A 87.783 884 88 9 865 1738 733514121 733513248 0.000000e+00 1016.0
8 TraesCS7B01G499300 chr7A 90.601 383 33 1 2235 2614 727280187 727279805 3.000000e-139 505.0
9 TraesCS7B01G499300 chr7A 90.601 383 33 1 2235 2614 727306106 727305724 3.000000e-139 505.0
10 TraesCS7B01G499300 chr7A 88.783 419 29 4 2198 2616 100620124 100620524 5.030000e-137 497.0
11 TraesCS7B01G499300 chr7A 89.728 331 30 4 1871 2199 727280509 727280181 1.120000e-113 420.0
12 TraesCS7B01G499300 chr7A 89.728 331 29 5 1871 2199 727306427 727306100 4.030000e-113 418.0
13 TraesCS7B01G499300 chr7A 87.252 353 34 6 12 361 733520836 733520492 2.440000e-105 392.0
14 TraesCS7B01G499300 chr7A 88.136 118 2 2 1733 1850 733511875 733511770 2.110000e-26 130.0
15 TraesCS7B01G499300 chr2D 90.000 680 62 4 1940 2616 33299785 33299109 0.000000e+00 874.0
16 TraesCS7B01G499300 chr2D 76.791 642 122 19 990 1625 556071898 556071278 4.170000e-88 335.0
17 TraesCS7B01G499300 chr1D 96.767 433 14 0 2184 2616 332212227 332211795 0.000000e+00 723.0
18 TraesCS7B01G499300 chr5B 89.628 511 51 2 2107 2616 550522747 550523256 0.000000e+00 649.0
19 TraesCS7B01G499300 chr5A 91.810 464 29 6 2155 2616 625733833 625734289 2.840000e-179 638.0
20 TraesCS7B01G499300 chr5A 94.444 54 1 2 502 555 569164392 569164341 6.000000e-12 82.4
21 TraesCS7B01G499300 chr2A 91.102 472 36 3 2145 2616 27320743 27321208 3.670000e-178 634.0
22 TraesCS7B01G499300 chr2A 77.093 633 117 18 999 1625 695523882 695523272 8.970000e-90 340.0
23 TraesCS7B01G499300 chr6A 79.502 844 125 22 804 1635 404460837 404461644 8.180000e-155 556.0
24 TraesCS7B01G499300 chr6D 81.638 354 49 13 1181 1521 283809017 283808667 1.980000e-71 279.0
25 TraesCS7B01G499300 chr6D 91.667 60 5 0 1018 1077 283809772 283809713 1.670000e-12 84.2


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 TraesCS7B01G499300 chr7B 749558302 749560917 2615 False 4831.000000 4831 100.000000 1 2616 1 chr7B.!!$F1 2615
1 TraesCS7B01G499300 chr7D 633538134 633539847 1713 False 720.333333 1552 92.514333 62 1850 3 chr7D.!!$F1 1788
2 TraesCS7B01G499300 chr7D 423335124 423335980 856 True 696.500000 1210 96.204000 1873 2616 2 chr7D.!!$R2 743
3 TraesCS7B01G499300 chr7A 733511770 733514121 2351 True 573.000000 1016 87.959500 865 1850 2 chr7A.!!$R4 985
4 TraesCS7B01G499300 chr7A 727279805 727280509 704 True 462.500000 505 90.164500 1871 2614 2 chr7A.!!$R2 743
5 TraesCS7B01G499300 chr7A 727305724 727306427 703 True 461.500000 505 90.164500 1871 2614 2 chr7A.!!$R3 743
6 TraesCS7B01G499300 chr2D 33299109 33299785 676 True 874.000000 874 90.000000 1940 2616 1 chr2D.!!$R1 676
7 TraesCS7B01G499300 chr2D 556071278 556071898 620 True 335.000000 335 76.791000 990 1625 1 chr2D.!!$R2 635
8 TraesCS7B01G499300 chr5B 550522747 550523256 509 False 649.000000 649 89.628000 2107 2616 1 chr5B.!!$F1 509
9 TraesCS7B01G499300 chr2A 695523272 695523882 610 True 340.000000 340 77.093000 999 1625 1 chr2A.!!$R1 626
10 TraesCS7B01G499300 chr6A 404460837 404461644 807 False 556.000000 556 79.502000 804 1635 1 chr6A.!!$F1 831

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
387 388 0.036732 AAGACAATGGGCTGAAGCGA 59.963 50.0 0.0 0.0 43.26 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2281 3685 0.318107 CGAAACAAGTGCTTGCCCAG 60.318 55.0 11.43 0.0 44.03 4.45 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
30 31 8.764524 AGGATCTAATTAATCAACTCATACGC 57.235 34.615 0.00 0.00 0.00 4.42
31 32 8.589338 AGGATCTAATTAATCAACTCATACGCT 58.411 33.333 0.00 0.00 0.00 5.07
32 33 9.209175 GGATCTAATTAATCAACTCATACGCTT 57.791 33.333 0.00 0.00 0.00 4.68
36 37 9.197694 CTAATTAATCAACTCATACGCTTAGCT 57.802 33.333 1.76 0.00 0.00 3.32
38 39 9.542462 AATTAATCAACTCATACGCTTAGCTAA 57.458 29.630 5.94 5.94 0.00 3.09
39 40 8.936070 TTAATCAACTCATACGCTTAGCTAAA 57.064 30.769 7.74 0.00 0.00 1.85
40 41 7.470289 AATCAACTCATACGCTTAGCTAAAG 57.530 36.000 7.74 7.30 38.32 1.85
41 42 5.962433 TCAACTCATACGCTTAGCTAAAGT 58.038 37.500 7.74 12.58 37.53 2.66
42 43 7.092137 TCAACTCATACGCTTAGCTAAAGTA 57.908 36.000 18.15 18.15 37.53 2.24
43 44 7.541162 TCAACTCATACGCTTAGCTAAAGTAA 58.459 34.615 19.16 8.37 37.53 2.24
44 45 7.701078 TCAACTCATACGCTTAGCTAAAGTAAG 59.299 37.037 19.16 16.22 37.53 2.34
47 48 7.092137 TCATACGCTTAGCTAAAGTAAGACA 57.908 36.000 19.16 5.17 37.53 3.41
49 50 7.861372 TCATACGCTTAGCTAAAGTAAGACATC 59.139 37.037 19.16 0.00 37.53 3.06
52 53 6.320672 ACGCTTAGCTAAAGTAAGACATCCTA 59.679 38.462 7.74 0.00 37.53 2.94
54 55 7.468906 CGCTTAGCTAAAGTAAGACATCCTACT 60.469 40.741 7.74 0.00 37.53 2.57
55 56 7.863877 GCTTAGCTAAAGTAAGACATCCTACTC 59.136 40.741 7.74 0.00 37.53 2.59
56 57 9.127277 CTTAGCTAAAGTAAGACATCCTACTCT 57.873 37.037 7.74 0.00 30.21 3.24
57 58 7.964666 AGCTAAAGTAAGACATCCTACTCTT 57.035 36.000 0.00 0.00 0.00 2.85
60 61 7.147880 GCTAAAGTAAGACATCCTACTCTTCCA 60.148 40.741 0.00 0.00 0.00 3.53
95 96 7.013942 ACCAATTAAGAAAAGTACACTCAACCC 59.986 37.037 0.00 0.00 0.00 4.11
147 148 1.614317 CCCAGCCTTTAGAACCAGTGG 60.614 57.143 7.91 7.91 0.00 4.00
156 157 1.525077 GAACCAGTGGACCGTGCAA 60.525 57.895 18.40 0.00 0.00 4.08
162 163 1.522806 GTGGACCGTGCAAGTCACA 60.523 57.895 17.33 11.10 45.92 3.58
209 210 3.938112 GCCACGGCGATAGTGATC 58.062 61.111 16.62 0.00 41.83 2.92
212 213 1.806623 GCCACGGCGATAGTGATCTTT 60.807 52.381 16.62 0.00 41.83 2.52
216 217 2.427453 ACGGCGATAGTGATCTTTCTGT 59.573 45.455 16.62 0.00 39.35 3.41
290 291 0.664166 CCAAACTGATGTTGCACGCC 60.664 55.000 0.00 0.00 36.39 5.68
305 306 2.429739 GCCGTGCAAAAGAGCTGC 60.430 61.111 0.00 0.00 40.35 5.25
348 349 3.415457 AGAAAGAGAGCAAGACAAGGG 57.585 47.619 0.00 0.00 0.00 3.95
350 351 3.586618 AGAAAGAGAGCAAGACAAGGGAT 59.413 43.478 0.00 0.00 0.00 3.85
359 360 4.892934 AGCAAGACAAGGGATAAACACAAA 59.107 37.500 0.00 0.00 0.00 2.83
360 361 5.010012 AGCAAGACAAGGGATAAACACAAAG 59.990 40.000 0.00 0.00 0.00 2.77
361 362 5.222631 CAAGACAAGGGATAAACACAAAGC 58.777 41.667 0.00 0.00 0.00 3.51
362 363 4.729868 AGACAAGGGATAAACACAAAGCT 58.270 39.130 0.00 0.00 0.00 3.74
363 364 4.520492 AGACAAGGGATAAACACAAAGCTG 59.480 41.667 0.00 0.00 0.00 4.24
364 365 4.469657 ACAAGGGATAAACACAAAGCTGA 58.530 39.130 0.00 0.00 0.00 4.26
365 366 5.079643 ACAAGGGATAAACACAAAGCTGAT 58.920 37.500 0.00 0.00 0.00 2.90
366 367 5.047802 ACAAGGGATAAACACAAAGCTGATG 60.048 40.000 0.00 0.00 0.00 3.07
367 368 3.445096 AGGGATAAACACAAAGCTGATGC 59.555 43.478 0.00 0.00 40.05 3.91
368 369 3.193267 GGGATAAACACAAAGCTGATGCA 59.807 43.478 0.00 0.00 42.74 3.96
369 370 4.321899 GGGATAAACACAAAGCTGATGCAA 60.322 41.667 0.00 0.00 42.74 4.08
370 371 4.860907 GGATAAACACAAAGCTGATGCAAG 59.139 41.667 0.00 0.00 42.74 4.01
371 372 5.335897 GGATAAACACAAAGCTGATGCAAGA 60.336 40.000 0.00 0.00 42.74 3.02
372 373 3.360249 AACACAAAGCTGATGCAAGAC 57.640 42.857 0.00 0.00 42.74 3.01
373 374 2.300433 ACACAAAGCTGATGCAAGACA 58.700 42.857 0.00 0.00 42.74 3.41
374 375 2.689471 ACACAAAGCTGATGCAAGACAA 59.311 40.909 0.00 0.00 42.74 3.18
375 376 3.319972 ACACAAAGCTGATGCAAGACAAT 59.680 39.130 0.00 0.00 42.74 2.71
376 377 3.673338 CACAAAGCTGATGCAAGACAATG 59.327 43.478 0.00 0.00 42.74 2.82
377 378 3.250744 CAAAGCTGATGCAAGACAATGG 58.749 45.455 0.00 0.00 42.74 3.16
378 379 1.471119 AGCTGATGCAAGACAATGGG 58.529 50.000 0.00 0.00 42.74 4.00
379 380 0.179119 GCTGATGCAAGACAATGGGC 60.179 55.000 0.00 0.00 39.41 5.36
380 381 1.471119 CTGATGCAAGACAATGGGCT 58.529 50.000 0.00 0.00 0.00 5.19
381 382 1.134367 CTGATGCAAGACAATGGGCTG 59.866 52.381 0.00 0.00 0.00 4.85
382 383 1.272037 TGATGCAAGACAATGGGCTGA 60.272 47.619 0.00 0.00 0.00 4.26
383 384 1.820519 GATGCAAGACAATGGGCTGAA 59.179 47.619 0.00 0.00 0.00 3.02
384 385 1.250328 TGCAAGACAATGGGCTGAAG 58.750 50.000 0.00 0.00 0.00 3.02
385 386 0.108945 GCAAGACAATGGGCTGAAGC 60.109 55.000 0.00 0.00 41.14 3.86
386 387 0.169672 CAAGACAATGGGCTGAAGCG 59.830 55.000 0.00 0.00 43.26 4.68
387 388 0.036732 AAGACAATGGGCTGAAGCGA 59.963 50.000 0.00 0.00 43.26 4.93
388 389 0.392193 AGACAATGGGCTGAAGCGAG 60.392 55.000 0.00 0.00 43.26 5.03
389 390 0.674895 GACAATGGGCTGAAGCGAGT 60.675 55.000 0.00 0.00 43.26 4.18
390 391 0.250901 ACAATGGGCTGAAGCGAGTT 60.251 50.000 0.00 0.00 43.26 3.01
391 392 0.883833 CAATGGGCTGAAGCGAGTTT 59.116 50.000 0.00 0.00 43.26 2.66
392 393 0.883833 AATGGGCTGAAGCGAGTTTG 59.116 50.000 0.00 0.00 43.26 2.93
393 394 0.962356 ATGGGCTGAAGCGAGTTTGG 60.962 55.000 0.00 0.00 43.26 3.28
394 395 2.335712 GGGCTGAAGCGAGTTTGGG 61.336 63.158 0.00 0.00 43.26 4.12
395 396 1.600916 GGCTGAAGCGAGTTTGGGT 60.601 57.895 0.00 0.00 43.26 4.51
396 397 1.578206 GGCTGAAGCGAGTTTGGGTC 61.578 60.000 0.00 0.00 43.26 4.46
397 398 1.901650 GCTGAAGCGAGTTTGGGTCG 61.902 60.000 0.00 0.00 40.50 4.79
398 399 0.600255 CTGAAGCGAGTTTGGGTCGT 60.600 55.000 0.00 0.00 39.69 4.34
399 400 0.179067 TGAAGCGAGTTTGGGTCGTT 60.179 50.000 0.00 0.00 39.69 3.85
400 401 0.942252 GAAGCGAGTTTGGGTCGTTT 59.058 50.000 0.00 0.00 42.57 3.60
401 402 1.332686 GAAGCGAGTTTGGGTCGTTTT 59.667 47.619 0.00 0.00 40.38 2.43
402 403 2.243602 AGCGAGTTTGGGTCGTTTTA 57.756 45.000 0.00 0.00 39.69 1.52
403 404 2.140717 AGCGAGTTTGGGTCGTTTTAG 58.859 47.619 0.00 0.00 39.69 1.85
404 405 1.869132 GCGAGTTTGGGTCGTTTTAGT 59.131 47.619 0.00 0.00 39.69 2.24
405 406 2.288729 GCGAGTTTGGGTCGTTTTAGTT 59.711 45.455 0.00 0.00 39.69 2.24
406 407 3.242837 GCGAGTTTGGGTCGTTTTAGTTT 60.243 43.478 0.00 0.00 39.69 2.66
407 408 4.024977 GCGAGTTTGGGTCGTTTTAGTTTA 60.025 41.667 0.00 0.00 39.69 2.01
408 409 5.673029 CGAGTTTGGGTCGTTTTAGTTTAG 58.327 41.667 0.00 0.00 32.62 1.85
409 410 5.463061 CGAGTTTGGGTCGTTTTAGTTTAGA 59.537 40.000 0.00 0.00 32.62 2.10
410 411 6.346359 CGAGTTTGGGTCGTTTTAGTTTAGAG 60.346 42.308 0.00 0.00 32.62 2.43
411 412 6.351711 AGTTTGGGTCGTTTTAGTTTAGAGT 58.648 36.000 0.00 0.00 0.00 3.24
412 413 7.500141 AGTTTGGGTCGTTTTAGTTTAGAGTA 58.500 34.615 0.00 0.00 0.00 2.59
413 414 7.986889 AGTTTGGGTCGTTTTAGTTTAGAGTAA 59.013 33.333 0.00 0.00 0.00 2.24
414 415 8.777413 GTTTGGGTCGTTTTAGTTTAGAGTAAT 58.223 33.333 0.00 0.00 0.00 1.89
415 416 8.907222 TTGGGTCGTTTTAGTTTAGAGTAATT 57.093 30.769 0.00 0.00 0.00 1.40
416 417 8.314143 TGGGTCGTTTTAGTTTAGAGTAATTG 57.686 34.615 0.00 0.00 0.00 2.32
417 418 7.933033 TGGGTCGTTTTAGTTTAGAGTAATTGT 59.067 33.333 0.00 0.00 0.00 2.71
418 419 8.225777 GGGTCGTTTTAGTTTAGAGTAATTGTG 58.774 37.037 0.00 0.00 0.00 3.33
419 420 8.225777 GGTCGTTTTAGTTTAGAGTAATTGTGG 58.774 37.037 0.00 0.00 0.00 4.17
420 421 8.981647 GTCGTTTTAGTTTAGAGTAATTGTGGA 58.018 33.333 0.00 0.00 0.00 4.02
421 422 9.715121 TCGTTTTAGTTTAGAGTAATTGTGGAT 57.285 29.630 0.00 0.00 0.00 3.41
422 423 9.755064 CGTTTTAGTTTAGAGTAATTGTGGATG 57.245 33.333 0.00 0.00 0.00 3.51
432 433 8.110860 AGAGTAATTGTGGATGTACTTTTTGG 57.889 34.615 0.00 0.00 0.00 3.28
433 434 7.942341 AGAGTAATTGTGGATGTACTTTTTGGA 59.058 33.333 0.00 0.00 0.00 3.53
434 435 8.110860 AGTAATTGTGGATGTACTTTTTGGAG 57.889 34.615 0.00 0.00 0.00 3.86
435 436 5.982890 ATTGTGGATGTACTTTTTGGAGG 57.017 39.130 0.00 0.00 0.00 4.30
436 437 3.761897 TGTGGATGTACTTTTTGGAGGG 58.238 45.455 0.00 0.00 0.00 4.30
437 438 3.139397 TGTGGATGTACTTTTTGGAGGGT 59.861 43.478 0.00 0.00 0.00 4.34
438 439 3.756963 GTGGATGTACTTTTTGGAGGGTC 59.243 47.826 0.00 0.00 0.00 4.46
439 440 3.655777 TGGATGTACTTTTTGGAGGGTCT 59.344 43.478 0.00 0.00 0.00 3.85
440 441 4.262617 GGATGTACTTTTTGGAGGGTCTC 58.737 47.826 0.00 0.00 0.00 3.36
441 442 4.019231 GGATGTACTTTTTGGAGGGTCTCT 60.019 45.833 0.00 0.00 0.00 3.10
442 443 5.515008 GGATGTACTTTTTGGAGGGTCTCTT 60.515 44.000 0.00 0.00 0.00 2.85
443 444 4.969484 TGTACTTTTTGGAGGGTCTCTTC 58.031 43.478 0.00 0.00 0.00 2.87
444 445 4.658901 TGTACTTTTTGGAGGGTCTCTTCT 59.341 41.667 0.00 0.00 0.00 2.85
445 446 5.842328 TGTACTTTTTGGAGGGTCTCTTCTA 59.158 40.000 0.00 0.00 0.00 2.10
446 447 5.491323 ACTTTTTGGAGGGTCTCTTCTAG 57.509 43.478 0.00 0.00 0.00 2.43
447 448 4.908481 ACTTTTTGGAGGGTCTCTTCTAGT 59.092 41.667 0.00 0.00 0.00 2.57
448 449 4.891992 TTTTGGAGGGTCTCTTCTAGTG 57.108 45.455 0.00 0.00 0.00 2.74
449 450 3.544698 TTGGAGGGTCTCTTCTAGTGT 57.455 47.619 0.00 0.00 0.00 3.55
450 451 3.088789 TGGAGGGTCTCTTCTAGTGTC 57.911 52.381 0.00 0.00 0.00 3.67
451 452 2.018515 GGAGGGTCTCTTCTAGTGTCG 58.981 57.143 0.00 0.00 0.00 4.35
452 453 1.402613 GAGGGTCTCTTCTAGTGTCGC 59.597 57.143 0.00 0.00 0.00 5.19
453 454 1.004979 AGGGTCTCTTCTAGTGTCGCT 59.995 52.381 0.00 0.00 0.00 4.93
454 455 1.133407 GGGTCTCTTCTAGTGTCGCTG 59.867 57.143 0.00 0.00 0.00 5.18
455 456 2.085320 GGTCTCTTCTAGTGTCGCTGA 58.915 52.381 0.00 0.00 0.00 4.26
456 457 2.685897 GGTCTCTTCTAGTGTCGCTGAT 59.314 50.000 0.00 0.00 0.00 2.90
457 458 3.129638 GGTCTCTTCTAGTGTCGCTGATT 59.870 47.826 0.00 0.00 0.00 2.57
458 459 4.381079 GGTCTCTTCTAGTGTCGCTGATTT 60.381 45.833 0.00 0.00 0.00 2.17
459 460 5.164954 GTCTCTTCTAGTGTCGCTGATTTT 58.835 41.667 0.00 0.00 0.00 1.82
460 461 5.287513 GTCTCTTCTAGTGTCGCTGATTTTC 59.712 44.000 0.00 0.00 0.00 2.29
461 462 4.166523 TCTTCTAGTGTCGCTGATTTTCG 58.833 43.478 0.00 0.00 0.00 3.46
462 463 2.259618 TCTAGTGTCGCTGATTTTCGC 58.740 47.619 0.00 0.00 0.00 4.70
463 464 2.094700 TCTAGTGTCGCTGATTTTCGCT 60.095 45.455 0.00 0.00 0.00 4.93
464 465 0.792640 AGTGTCGCTGATTTTCGCTG 59.207 50.000 0.00 0.00 0.00 5.18
465 466 0.512952 GTGTCGCTGATTTTCGCTGT 59.487 50.000 0.00 0.00 0.00 4.40
466 467 0.512518 TGTCGCTGATTTTCGCTGTG 59.487 50.000 0.00 0.00 0.00 3.66
467 468 0.512952 GTCGCTGATTTTCGCTGTGT 59.487 50.000 0.00 0.00 0.00 3.72
468 469 1.069906 GTCGCTGATTTTCGCTGTGTT 60.070 47.619 0.00 0.00 0.00 3.32
469 470 1.601903 TCGCTGATTTTCGCTGTGTTT 59.398 42.857 0.00 0.00 0.00 2.83
470 471 2.032799 TCGCTGATTTTCGCTGTGTTTT 59.967 40.909 0.00 0.00 0.00 2.43
471 472 2.788786 CGCTGATTTTCGCTGTGTTTTT 59.211 40.909 0.00 0.00 0.00 1.94
472 473 3.360956 CGCTGATTTTCGCTGTGTTTTTG 60.361 43.478 0.00 0.00 0.00 2.44
473 474 3.060339 GCTGATTTTCGCTGTGTTTTTGG 60.060 43.478 0.00 0.00 0.00 3.28
474 475 3.452474 TGATTTTCGCTGTGTTTTTGGG 58.548 40.909 0.00 0.00 0.00 4.12
475 476 2.301577 TTTTCGCTGTGTTTTTGGGG 57.698 45.000 0.00 0.00 0.00 4.96
476 477 0.179097 TTTCGCTGTGTTTTTGGGGC 60.179 50.000 0.00 0.00 0.00 5.80
477 478 1.040339 TTCGCTGTGTTTTTGGGGCT 61.040 50.000 0.00 0.00 0.00 5.19
478 479 1.300080 CGCTGTGTTTTTGGGGCTG 60.300 57.895 0.00 0.00 0.00 4.85
479 480 1.822615 GCTGTGTTTTTGGGGCTGT 59.177 52.632 0.00 0.00 0.00 4.40
480 481 0.177836 GCTGTGTTTTTGGGGCTGTT 59.822 50.000 0.00 0.00 0.00 3.16
481 482 1.406751 GCTGTGTTTTTGGGGCTGTTT 60.407 47.619 0.00 0.00 0.00 2.83
482 483 2.278854 CTGTGTTTTTGGGGCTGTTTG 58.721 47.619 0.00 0.00 0.00 2.93
483 484 1.625818 TGTGTTTTTGGGGCTGTTTGT 59.374 42.857 0.00 0.00 0.00 2.83
484 485 2.039084 TGTGTTTTTGGGGCTGTTTGTT 59.961 40.909 0.00 0.00 0.00 2.83
485 486 3.078097 GTGTTTTTGGGGCTGTTTGTTT 58.922 40.909 0.00 0.00 0.00 2.83
486 487 3.504134 GTGTTTTTGGGGCTGTTTGTTTT 59.496 39.130 0.00 0.00 0.00 2.43
487 488 3.503748 TGTTTTTGGGGCTGTTTGTTTTG 59.496 39.130 0.00 0.00 0.00 2.44
488 489 2.409948 TTTGGGGCTGTTTGTTTTGG 57.590 45.000 0.00 0.00 0.00 3.28
489 490 1.280457 TTGGGGCTGTTTGTTTTGGT 58.720 45.000 0.00 0.00 0.00 3.67
490 491 0.827368 TGGGGCTGTTTGTTTTGGTC 59.173 50.000 0.00 0.00 0.00 4.02
491 492 0.249280 GGGGCTGTTTGTTTTGGTCG 60.249 55.000 0.00 0.00 0.00 4.79
492 493 0.458260 GGGCTGTTTGTTTTGGTCGT 59.542 50.000 0.00 0.00 0.00 4.34
493 494 1.134936 GGGCTGTTTGTTTTGGTCGTT 60.135 47.619 0.00 0.00 0.00 3.85
494 495 2.612604 GGCTGTTTGTTTTGGTCGTTT 58.387 42.857 0.00 0.00 0.00 3.60
495 496 2.347150 GGCTGTTTGTTTTGGTCGTTTG 59.653 45.455 0.00 0.00 0.00 2.93
496 497 2.990514 GCTGTTTGTTTTGGTCGTTTGT 59.009 40.909 0.00 0.00 0.00 2.83
497 498 4.167268 GCTGTTTGTTTTGGTCGTTTGTA 58.833 39.130 0.00 0.00 0.00 2.41
498 499 4.030865 GCTGTTTGTTTTGGTCGTTTGTAC 59.969 41.667 0.00 0.00 0.00 2.90
499 500 5.373981 TGTTTGTTTTGGTCGTTTGTACT 57.626 34.783 0.00 0.00 0.00 2.73
500 501 5.392286 TGTTTGTTTTGGTCGTTTGTACTC 58.608 37.500 0.00 0.00 0.00 2.59
501 502 4.619437 TTGTTTTGGTCGTTTGTACTCC 57.381 40.909 0.00 0.00 0.00 3.85
502 503 2.944349 TGTTTTGGTCGTTTGTACTCCC 59.056 45.455 0.00 0.00 0.00 4.30
503 504 3.208594 GTTTTGGTCGTTTGTACTCCCT 58.791 45.455 0.00 0.00 0.00 4.20
504 505 2.825861 TTGGTCGTTTGTACTCCCTC 57.174 50.000 0.00 0.00 0.00 4.30
505 506 2.005370 TGGTCGTTTGTACTCCCTCT 57.995 50.000 0.00 0.00 0.00 3.69
506 507 1.891150 TGGTCGTTTGTACTCCCTCTC 59.109 52.381 0.00 0.00 0.00 3.20
507 508 2.169330 GGTCGTTTGTACTCCCTCTCT 58.831 52.381 0.00 0.00 0.00 3.10
508 509 2.561858 GGTCGTTTGTACTCCCTCTCTT 59.438 50.000 0.00 0.00 0.00 2.85
509 510 3.760684 GGTCGTTTGTACTCCCTCTCTTA 59.239 47.826 0.00 0.00 0.00 2.10
510 511 4.401837 GGTCGTTTGTACTCCCTCTCTTAT 59.598 45.833 0.00 0.00 0.00 1.73
511 512 5.450274 GGTCGTTTGTACTCCCTCTCTTATC 60.450 48.000 0.00 0.00 0.00 1.75
512 513 5.357596 GTCGTTTGTACTCCCTCTCTTATCT 59.642 44.000 0.00 0.00 0.00 1.98
513 514 5.950549 TCGTTTGTACTCCCTCTCTTATCTT 59.049 40.000 0.00 0.00 0.00 2.40
514 515 6.436532 TCGTTTGTACTCCCTCTCTTATCTTT 59.563 38.462 0.00 0.00 0.00 2.52
515 516 7.613022 TCGTTTGTACTCCCTCTCTTATCTTTA 59.387 37.037 0.00 0.00 0.00 1.85
516 517 8.248945 CGTTTGTACTCCCTCTCTTATCTTTAA 58.751 37.037 0.00 0.00 0.00 1.52
547 548 1.081892 CAGTTCTCCTGCATGGTTCG 58.918 55.000 0.00 0.00 33.59 3.95
548 549 0.976641 AGTTCTCCTGCATGGTTCGA 59.023 50.000 0.00 0.00 37.07 3.71
549 550 1.347707 AGTTCTCCTGCATGGTTCGAA 59.652 47.619 0.00 0.00 37.07 3.71
550 551 2.151202 GTTCTCCTGCATGGTTCGAAA 58.849 47.619 0.00 0.00 37.07 3.46
551 552 2.552315 GTTCTCCTGCATGGTTCGAAAA 59.448 45.455 0.00 0.00 37.07 2.29
552 553 2.857483 TCTCCTGCATGGTTCGAAAAA 58.143 42.857 0.00 0.00 37.07 1.94
575 576 4.635699 AAGGGATAAACACGAAAGGAGT 57.364 40.909 0.00 0.00 0.00 3.85
609 610 8.742554 AGCCGTTGAAAATTATTTTGAACTAG 57.257 30.769 22.84 17.13 42.20 2.57
654 655 5.645624 CAACGCATAACCCACATTTTGATA 58.354 37.500 0.00 0.00 0.00 2.15
670 671 8.428063 ACATTTTGATAATCAAACCTGGTCAAA 58.572 29.630 0.00 0.74 45.03 2.69
683 684 4.202461 ACCTGGTCAAAGCTGAATGTAGAA 60.202 41.667 0.00 0.00 31.88 2.10
706 707 1.072391 CGTGCGCACCATGTAAGTAA 58.928 50.000 33.23 0.00 0.00 2.24
710 711 1.664151 GCGCACCATGTAAGTAAGGAC 59.336 52.381 0.30 0.00 0.00 3.85
711 712 2.933492 GCGCACCATGTAAGTAAGGACA 60.933 50.000 0.30 0.00 0.00 4.02
712 713 2.930040 CGCACCATGTAAGTAAGGACAG 59.070 50.000 0.00 0.00 0.00 3.51
713 714 3.368013 CGCACCATGTAAGTAAGGACAGA 60.368 47.826 0.00 0.00 0.00 3.41
714 715 4.184629 GCACCATGTAAGTAAGGACAGAG 58.815 47.826 0.00 0.00 0.00 3.35
715 716 4.759782 CACCATGTAAGTAAGGACAGAGG 58.240 47.826 0.00 0.00 33.28 3.69
722 723 2.009165 AGTAAGGACAGAGGGGGTAGT 58.991 52.381 0.00 0.00 0.00 2.73
791 793 8.483307 AATAAAAACAAGATTGATGGTGATGC 57.517 30.769 0.00 0.00 0.00 3.91
792 794 4.460948 AAACAAGATTGATGGTGATGCC 57.539 40.909 0.00 0.00 37.90 4.40
796 798 0.740149 GATTGATGGTGATGCCGCAA 59.260 50.000 0.00 0.00 41.21 4.85
884 887 4.199310 ACATCCCAACCAACATATTCTCG 58.801 43.478 0.00 0.00 0.00 4.04
885 888 4.080582 ACATCCCAACCAACATATTCTCGA 60.081 41.667 0.00 0.00 0.00 4.04
891 894 2.347452 ACCAACATATTCTCGAAACGCG 59.653 45.455 3.53 3.53 42.69 6.01
939 943 8.932945 ATGAAATCTATATATGTACACTGGCG 57.067 34.615 0.00 0.00 0.00 5.69
940 944 6.811665 TGAAATCTATATATGTACACTGGCGC 59.188 38.462 0.00 0.00 0.00 6.53
941 945 5.914898 ATCTATATATGTACACTGGCGCA 57.085 39.130 10.83 0.00 0.00 6.09
942 946 5.055642 TCTATATATGTACACTGGCGCAC 57.944 43.478 10.83 0.00 0.00 5.34
1107 1111 2.042686 TGATCCCTCAATTGCTTCCG 57.957 50.000 0.00 0.00 0.00 4.30
1120 1124 1.153939 CTTCCGGACGTGCTCTCAG 60.154 63.158 1.83 0.00 0.00 3.35
1199 1203 3.777522 CCTCCTGGTTAGAATCTGAACCT 59.222 47.826 16.69 0.00 44.63 3.50
1236 1241 5.006386 CAGCAAGGTCTATTTTCCTCTTGT 58.994 41.667 0.00 0.00 35.43 3.16
1372 1385 2.357637 TGAAAACTTTGTCAAGGAGGCG 59.642 45.455 1.07 0.00 33.82 5.52
1373 1386 2.341846 AAACTTTGTCAAGGAGGCGA 57.658 45.000 1.07 0.00 33.82 5.54
1387 1400 4.345854 AGGAGGCGATAGTAATAGAAGGG 58.654 47.826 0.00 0.00 39.35 3.95
1402 1415 1.488393 GAAGGGGGTCTCCTCAATCTG 59.512 57.143 0.00 0.00 35.43 2.90
1442 1458 3.119388 CGTACGGTTTGAGATTGTAGGGA 60.119 47.826 7.57 0.00 0.00 4.20
1471 1487 8.642885 GCAGATAACACATCTACAATAAGATCG 58.357 37.037 0.00 0.00 33.87 3.69
1601 1618 2.272146 GCGATGAGAAAGGCCCCA 59.728 61.111 0.00 0.00 0.00 4.96
1625 1647 5.273944 AGCAAACTTTGTAAGAAGAAAGCG 58.726 37.500 3.48 0.00 39.09 4.68
1635 1657 1.578206 GAAGAAAGCGTCCCACCAGC 61.578 60.000 0.00 0.00 0.00 4.85
1636 1658 2.032681 GAAAGCGTCCCACCAGCT 59.967 61.111 0.00 0.00 43.90 4.24
1637 1659 2.281761 AAAGCGTCCCACCAGCTG 60.282 61.111 6.78 6.78 41.53 4.24
1638 1660 3.850098 AAAGCGTCCCACCAGCTGG 62.850 63.158 31.60 31.60 41.53 4.85
1662 1684 5.960105 GTCGATGCACAAAATAAGTTAGAGC 59.040 40.000 0.00 0.00 0.00 4.09
1663 1685 5.641636 TCGATGCACAAAATAAGTTAGAGCA 59.358 36.000 0.00 0.00 0.00 4.26
1681 1703 4.082895 AGAGCAACTTCATGTTTGATCTGC 60.083 41.667 18.08 9.01 36.63 4.26
1685 1707 5.118203 GCAACTTCATGTTTGATCTGCTTTC 59.882 40.000 8.15 0.00 36.63 2.62
1686 1708 6.444633 CAACTTCATGTTTGATCTGCTTTCT 58.555 36.000 0.00 0.00 36.63 2.52
1692 1714 6.207221 TCATGTTTGATCTGCTTTCTTGCTTA 59.793 34.615 0.00 0.00 0.00 3.09
1715 1737 5.636837 ACATTTGTCGTATGTTTACATGCC 58.363 37.500 5.64 0.00 35.88 4.40
1767 3167 4.602006 GCTTATGCTTAGCTAAGTTTGGC 58.398 43.478 29.42 22.56 35.74 4.52
1850 3250 6.071447 CCCAAGTCATCTCATATCTAGGTCAG 60.071 46.154 0.00 0.00 0.00 3.51
1851 3251 6.718912 CCAAGTCATCTCATATCTAGGTCAGA 59.281 42.308 0.00 0.00 37.79 3.27
1852 3252 7.232330 CCAAGTCATCTCATATCTAGGTCAGAA 59.768 40.741 0.00 0.00 36.67 3.02
1853 3253 8.637099 CAAGTCATCTCATATCTAGGTCAGAAA 58.363 37.037 0.00 0.00 36.67 2.52
1854 3254 8.408043 AGTCATCTCATATCTAGGTCAGAAAG 57.592 38.462 0.00 0.00 36.67 2.62
1855 3255 7.451255 AGTCATCTCATATCTAGGTCAGAAAGG 59.549 40.741 0.00 0.00 36.67 3.11
1856 3256 6.210385 TCATCTCATATCTAGGTCAGAAAGGC 59.790 42.308 0.00 0.00 36.67 4.35
1857 3257 5.458595 TCTCATATCTAGGTCAGAAAGGCA 58.541 41.667 0.00 0.00 36.67 4.75
1858 3258 5.538053 TCTCATATCTAGGTCAGAAAGGCAG 59.462 44.000 0.00 0.00 36.67 4.85
1859 3259 4.590647 TCATATCTAGGTCAGAAAGGCAGG 59.409 45.833 0.00 0.00 36.67 4.85
1860 3260 0.905357 TCTAGGTCAGAAAGGCAGGC 59.095 55.000 0.00 0.00 0.00 4.85
1861 3261 0.908198 CTAGGTCAGAAAGGCAGGCT 59.092 55.000 0.00 0.00 0.00 4.58
1862 3262 0.905357 TAGGTCAGAAAGGCAGGCTC 59.095 55.000 0.00 0.00 0.00 4.70
1863 3263 0.839853 AGGTCAGAAAGGCAGGCTCT 60.840 55.000 0.00 0.00 0.00 4.09
1864 3264 0.676151 GGTCAGAAAGGCAGGCTCTG 60.676 60.000 0.00 1.56 38.34 3.35
1865 3265 0.322975 GTCAGAAAGGCAGGCTCTGA 59.677 55.000 10.87 10.87 42.49 3.27
1866 3266 0.612229 TCAGAAAGGCAGGCTCTGAG 59.388 55.000 10.87 0.00 40.44 3.35
1867 3267 1.025647 CAGAAAGGCAGGCTCTGAGC 61.026 60.000 21.17 21.17 39.15 4.26
1868 3268 2.046507 AAAGGCAGGCTCTGAGCG 60.047 61.111 22.25 11.42 43.62 5.03
1869 3269 4.774503 AAGGCAGGCTCTGAGCGC 62.775 66.667 22.25 19.79 43.62 5.92
1875 3275 4.828925 GGCTCTGAGCGCCAGACC 62.829 72.222 22.25 20.25 46.38 3.85
1876 3276 4.828925 GCTCTGAGCGCCAGACCC 62.829 72.222 20.28 12.64 46.38 4.46
1914 3314 4.410400 GGCTCGGGTGTCCCTTGG 62.410 72.222 3.25 0.00 42.67 3.61
2051 3454 3.408229 CCAGATCTGGTGGGCACT 58.592 61.111 30.55 0.00 45.53 4.40
2182 3586 1.603455 ACGCACAAACCTGGATGGG 60.603 57.895 0.00 0.93 41.11 4.00
2260 3664 2.344741 GTGGAATTGTTCGAGAGCGTAC 59.655 50.000 0.00 0.00 38.15 3.67
2410 3817 0.246635 GTAGCTTTGACCTCCTGCGA 59.753 55.000 0.00 0.00 0.00 5.10
2495 3902 3.496130 CCGGTGATGAGATGCAAACTATC 59.504 47.826 0.00 0.00 0.00 2.08
2517 3924 3.885521 GCGGCTTGATGCAGAGGC 61.886 66.667 10.02 10.02 45.15 4.70
2599 4007 1.321743 GCGACGTCACATGAATGACTC 59.678 52.381 17.16 9.14 45.73 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.856488 GCGTATGAGTTGATTAATTAGATCCTA 57.144 33.333 0.00 0.00 0.00 2.94
5 6 8.589338 AGCGTATGAGTTGATTAATTAGATCCT 58.411 33.333 0.00 0.00 0.00 3.24
6 7 8.764524 AGCGTATGAGTTGATTAATTAGATCC 57.235 34.615 0.00 0.00 0.00 3.36
10 11 9.197694 AGCTAAGCGTATGAGTTGATTAATTAG 57.802 33.333 0.00 0.00 0.00 1.73
12 13 9.542462 TTAGCTAAGCGTATGAGTTGATTAATT 57.458 29.630 0.86 0.00 0.00 1.40
13 14 9.542462 TTTAGCTAAGCGTATGAGTTGATTAAT 57.458 29.630 6.24 0.00 0.00 1.40
14 15 8.936070 TTTAGCTAAGCGTATGAGTTGATTAA 57.064 30.769 6.24 0.00 0.00 1.40
15 16 8.195436 ACTTTAGCTAAGCGTATGAGTTGATTA 58.805 33.333 6.24 0.00 37.37 1.75
17 18 6.574350 ACTTTAGCTAAGCGTATGAGTTGAT 58.426 36.000 6.24 0.00 37.37 2.57
18 19 5.962433 ACTTTAGCTAAGCGTATGAGTTGA 58.038 37.500 6.24 0.00 37.37 3.18
20 21 7.701501 GTCTTACTTTAGCTAAGCGTATGAGTT 59.298 37.037 21.12 6.62 37.37 3.01
22 23 7.194278 TGTCTTACTTTAGCTAAGCGTATGAG 58.806 38.462 21.12 15.19 37.37 2.90
23 24 7.092137 TGTCTTACTTTAGCTAAGCGTATGA 57.908 36.000 18.92 18.92 37.37 2.15
24 25 7.115095 GGATGTCTTACTTTAGCTAAGCGTATG 59.885 40.741 6.24 13.09 37.37 2.39
25 26 7.014422 AGGATGTCTTACTTTAGCTAAGCGTAT 59.986 37.037 6.24 0.00 37.37 3.06
26 27 6.320672 AGGATGTCTTACTTTAGCTAAGCGTA 59.679 38.462 6.24 9.46 37.37 4.42
27 28 5.127356 AGGATGTCTTACTTTAGCTAAGCGT 59.873 40.000 6.24 10.40 37.37 5.07
29 30 7.718525 AGTAGGATGTCTTACTTTAGCTAAGC 58.281 38.462 6.24 0.00 35.57 3.09
30 31 9.127277 AGAGTAGGATGTCTTACTTTAGCTAAG 57.873 37.037 6.24 4.07 38.63 2.18
31 32 9.476928 AAGAGTAGGATGTCTTACTTTAGCTAA 57.523 33.333 0.86 0.86 38.63 3.09
32 33 9.122779 GAAGAGTAGGATGTCTTACTTTAGCTA 57.877 37.037 6.31 0.00 38.63 3.32
33 34 7.068962 GGAAGAGTAGGATGTCTTACTTTAGCT 59.931 40.741 6.31 0.00 38.63 3.32
34 35 7.147880 TGGAAGAGTAGGATGTCTTACTTTAGC 60.148 40.741 6.31 0.00 38.63 3.09
36 37 8.660295 TTGGAAGAGTAGGATGTCTTACTTTA 57.340 34.615 6.31 0.00 38.63 1.85
37 38 7.554959 TTGGAAGAGTAGGATGTCTTACTTT 57.445 36.000 6.31 0.00 38.63 2.66
38 39 7.554959 TTTGGAAGAGTAGGATGTCTTACTT 57.445 36.000 6.31 0.00 38.63 2.24
39 40 7.400339 TGATTTGGAAGAGTAGGATGTCTTACT 59.600 37.037 4.69 4.69 40.79 2.24
40 41 7.556844 TGATTTGGAAGAGTAGGATGTCTTAC 58.443 38.462 0.00 0.00 34.60 2.34
41 42 7.733773 TGATTTGGAAGAGTAGGATGTCTTA 57.266 36.000 0.00 0.00 33.04 2.10
42 43 6.627087 TGATTTGGAAGAGTAGGATGTCTT 57.373 37.500 0.00 0.00 35.67 3.01
43 44 6.627087 TTGATTTGGAAGAGTAGGATGTCT 57.373 37.500 0.00 0.00 0.00 3.41
44 45 7.872113 AATTGATTTGGAAGAGTAGGATGTC 57.128 36.000 0.00 0.00 0.00 3.06
47 48 7.872138 TGGTAATTGATTTGGAAGAGTAGGAT 58.128 34.615 0.00 0.00 0.00 3.24
49 50 7.938140 TTGGTAATTGATTTGGAAGAGTAGG 57.062 36.000 0.00 0.00 0.00 3.18
77 78 3.974642 AGAGGGGTTGAGTGTACTTTTCT 59.025 43.478 0.00 0.00 0.00 2.52
95 96 9.667107 TGACTGTCTGGTTTTATAATTAAGAGG 57.333 33.333 9.51 0.00 0.00 3.69
156 157 4.273480 CGAAAACAATCTTGGAGTGTGACT 59.727 41.667 1.50 0.00 39.99 3.41
162 163 7.660208 ACTGTTATACGAAAACAATCTTGGAGT 59.340 33.333 0.00 0.00 36.46 3.85
209 210 5.830912 TGTTGGATTGCAACTTACAGAAAG 58.169 37.500 19.80 0.00 41.33 2.62
212 213 5.048782 GTGATGTTGGATTGCAACTTACAGA 60.049 40.000 19.80 1.38 33.97 3.41
216 217 5.981088 ATGTGATGTTGGATTGCAACTTA 57.019 34.783 19.80 3.41 33.97 2.24
290 291 2.686558 TTAAGCAGCTCTTTTGCACG 57.313 45.000 0.00 0.00 43.92 5.34
296 297 6.462067 GGGATATGCAAATTAAGCAGCTCTTT 60.462 38.462 10.69 0.00 46.36 2.52
305 306 2.095263 CGCCCGGGATATGCAAATTAAG 60.095 50.000 29.31 0.00 0.00 1.85
348 349 5.570589 GTCTTGCATCAGCTTTGTGTTTATC 59.429 40.000 0.00 0.00 42.74 1.75
350 351 4.337836 TGTCTTGCATCAGCTTTGTGTTTA 59.662 37.500 0.00 0.00 42.74 2.01
359 360 1.471119 CCCATTGTCTTGCATCAGCT 58.529 50.000 0.00 0.00 42.74 4.24
360 361 0.179119 GCCCATTGTCTTGCATCAGC 60.179 55.000 0.00 0.00 42.57 4.26
361 362 1.134367 CAGCCCATTGTCTTGCATCAG 59.866 52.381 0.00 0.00 0.00 2.90
362 363 1.179152 CAGCCCATTGTCTTGCATCA 58.821 50.000 0.00 0.00 0.00 3.07
363 364 1.466856 TCAGCCCATTGTCTTGCATC 58.533 50.000 0.00 0.00 0.00 3.91
364 365 1.822990 CTTCAGCCCATTGTCTTGCAT 59.177 47.619 0.00 0.00 0.00 3.96
365 366 1.250328 CTTCAGCCCATTGTCTTGCA 58.750 50.000 0.00 0.00 0.00 4.08
366 367 0.108945 GCTTCAGCCCATTGTCTTGC 60.109 55.000 0.00 0.00 34.31 4.01
367 368 0.169672 CGCTTCAGCCCATTGTCTTG 59.830 55.000 0.00 0.00 37.91 3.02
368 369 0.036732 TCGCTTCAGCCCATTGTCTT 59.963 50.000 0.00 0.00 37.91 3.01
369 370 0.392193 CTCGCTTCAGCCCATTGTCT 60.392 55.000 0.00 0.00 37.91 3.41
370 371 0.674895 ACTCGCTTCAGCCCATTGTC 60.675 55.000 0.00 0.00 37.91 3.18
371 372 0.250901 AACTCGCTTCAGCCCATTGT 60.251 50.000 0.00 0.00 37.91 2.71
372 373 0.883833 AAACTCGCTTCAGCCCATTG 59.116 50.000 0.00 0.00 37.91 2.82
373 374 0.883833 CAAACTCGCTTCAGCCCATT 59.116 50.000 0.00 0.00 37.91 3.16
374 375 0.962356 CCAAACTCGCTTCAGCCCAT 60.962 55.000 0.00 0.00 37.91 4.00
375 376 1.600636 CCAAACTCGCTTCAGCCCA 60.601 57.895 0.00 0.00 37.91 5.36
376 377 2.335712 CCCAAACTCGCTTCAGCCC 61.336 63.158 0.00 0.00 37.91 5.19
377 378 1.578206 GACCCAAACTCGCTTCAGCC 61.578 60.000 0.00 0.00 37.91 4.85
378 379 1.869690 GACCCAAACTCGCTTCAGC 59.130 57.895 0.00 0.00 37.78 4.26
379 380 0.600255 ACGACCCAAACTCGCTTCAG 60.600 55.000 0.00 0.00 34.34 3.02
380 381 0.179067 AACGACCCAAACTCGCTTCA 60.179 50.000 0.00 0.00 34.34 3.02
381 382 0.942252 AAACGACCCAAACTCGCTTC 59.058 50.000 0.00 0.00 34.34 3.86
382 383 1.385528 AAAACGACCCAAACTCGCTT 58.614 45.000 0.00 0.00 34.34 4.68
383 384 2.140717 CTAAAACGACCCAAACTCGCT 58.859 47.619 0.00 0.00 34.34 4.93
384 385 1.869132 ACTAAAACGACCCAAACTCGC 59.131 47.619 0.00 0.00 34.34 5.03
385 386 4.541085 AAACTAAAACGACCCAAACTCG 57.459 40.909 0.00 0.00 37.17 4.18
386 387 6.481313 ACTCTAAACTAAAACGACCCAAACTC 59.519 38.462 0.00 0.00 0.00 3.01
387 388 6.351711 ACTCTAAACTAAAACGACCCAAACT 58.648 36.000 0.00 0.00 0.00 2.66
388 389 6.609237 ACTCTAAACTAAAACGACCCAAAC 57.391 37.500 0.00 0.00 0.00 2.93
389 390 8.907222 ATTACTCTAAACTAAAACGACCCAAA 57.093 30.769 0.00 0.00 0.00 3.28
390 391 8.776470 CAATTACTCTAAACTAAAACGACCCAA 58.224 33.333 0.00 0.00 0.00 4.12
391 392 7.933033 ACAATTACTCTAAACTAAAACGACCCA 59.067 33.333 0.00 0.00 0.00 4.51
392 393 8.225777 CACAATTACTCTAAACTAAAACGACCC 58.774 37.037 0.00 0.00 0.00 4.46
393 394 8.225777 CCACAATTACTCTAAACTAAAACGACC 58.774 37.037 0.00 0.00 0.00 4.79
394 395 8.981647 TCCACAATTACTCTAAACTAAAACGAC 58.018 33.333 0.00 0.00 0.00 4.34
395 396 9.715121 ATCCACAATTACTCTAAACTAAAACGA 57.285 29.630 0.00 0.00 0.00 3.85
396 397 9.755064 CATCCACAATTACTCTAAACTAAAACG 57.245 33.333 0.00 0.00 0.00 3.60
406 407 9.226606 CCAAAAAGTACATCCACAATTACTCTA 57.773 33.333 0.00 0.00 0.00 2.43
407 408 7.942341 TCCAAAAAGTACATCCACAATTACTCT 59.058 33.333 0.00 0.00 0.00 3.24
408 409 8.106247 TCCAAAAAGTACATCCACAATTACTC 57.894 34.615 0.00 0.00 0.00 2.59
409 410 7.176690 CCTCCAAAAAGTACATCCACAATTACT 59.823 37.037 0.00 0.00 0.00 2.24
410 411 7.312899 CCTCCAAAAAGTACATCCACAATTAC 58.687 38.462 0.00 0.00 0.00 1.89
411 412 6.435904 CCCTCCAAAAAGTACATCCACAATTA 59.564 38.462 0.00 0.00 0.00 1.40
412 413 5.245977 CCCTCCAAAAAGTACATCCACAATT 59.754 40.000 0.00 0.00 0.00 2.32
413 414 4.772100 CCCTCCAAAAAGTACATCCACAAT 59.228 41.667 0.00 0.00 0.00 2.71
414 415 4.148838 CCCTCCAAAAAGTACATCCACAA 58.851 43.478 0.00 0.00 0.00 3.33
415 416 3.139397 ACCCTCCAAAAAGTACATCCACA 59.861 43.478 0.00 0.00 0.00 4.17
416 417 3.756963 GACCCTCCAAAAAGTACATCCAC 59.243 47.826 0.00 0.00 0.00 4.02
417 418 3.655777 AGACCCTCCAAAAAGTACATCCA 59.344 43.478 0.00 0.00 0.00 3.41
418 419 4.019231 AGAGACCCTCCAAAAAGTACATCC 60.019 45.833 0.00 0.00 0.00 3.51
419 420 5.167303 AGAGACCCTCCAAAAAGTACATC 57.833 43.478 0.00 0.00 0.00 3.06
420 421 5.310857 AGAAGAGACCCTCCAAAAAGTACAT 59.689 40.000 0.00 0.00 0.00 2.29
421 422 4.658901 AGAAGAGACCCTCCAAAAAGTACA 59.341 41.667 0.00 0.00 0.00 2.90
422 423 5.230323 AGAAGAGACCCTCCAAAAAGTAC 57.770 43.478 0.00 0.00 0.00 2.73
423 424 6.014499 CACTAGAAGAGACCCTCCAAAAAGTA 60.014 42.308 0.00 0.00 0.00 2.24
424 425 4.908481 ACTAGAAGAGACCCTCCAAAAAGT 59.092 41.667 0.00 0.00 0.00 2.66
425 426 5.221742 ACACTAGAAGAGACCCTCCAAAAAG 60.222 44.000 0.00 0.00 0.00 2.27
426 427 4.658901 ACACTAGAAGAGACCCTCCAAAAA 59.341 41.667 0.00 0.00 0.00 1.94
427 428 4.232091 ACACTAGAAGAGACCCTCCAAAA 58.768 43.478 0.00 0.00 0.00 2.44
428 429 3.833070 GACACTAGAAGAGACCCTCCAAA 59.167 47.826 0.00 0.00 0.00 3.28
429 430 3.432378 GACACTAGAAGAGACCCTCCAA 58.568 50.000 0.00 0.00 0.00 3.53
430 431 2.618302 CGACACTAGAAGAGACCCTCCA 60.618 54.545 0.00 0.00 0.00 3.86
431 432 2.018515 CGACACTAGAAGAGACCCTCC 58.981 57.143 0.00 0.00 0.00 4.30
432 433 1.402613 GCGACACTAGAAGAGACCCTC 59.597 57.143 0.00 0.00 0.00 4.30
433 434 1.004979 AGCGACACTAGAAGAGACCCT 59.995 52.381 0.00 0.00 0.00 4.34
434 435 1.133407 CAGCGACACTAGAAGAGACCC 59.867 57.143 0.00 0.00 0.00 4.46
435 436 2.085320 TCAGCGACACTAGAAGAGACC 58.915 52.381 0.00 0.00 0.00 3.85
436 437 4.364415 AATCAGCGACACTAGAAGAGAC 57.636 45.455 0.00 0.00 0.00 3.36
437 438 5.392767 AAAATCAGCGACACTAGAAGAGA 57.607 39.130 0.00 0.00 0.00 3.10
438 439 4.264145 CGAAAATCAGCGACACTAGAAGAG 59.736 45.833 0.00 0.00 0.00 2.85
439 440 4.166523 CGAAAATCAGCGACACTAGAAGA 58.833 43.478 0.00 0.00 0.00 2.87
440 441 3.241804 GCGAAAATCAGCGACACTAGAAG 60.242 47.826 0.00 0.00 0.00 2.85
441 442 2.666508 GCGAAAATCAGCGACACTAGAA 59.333 45.455 0.00 0.00 0.00 2.10
442 443 2.094700 AGCGAAAATCAGCGACACTAGA 60.095 45.455 0.00 0.00 38.61 2.43
443 444 2.028523 CAGCGAAAATCAGCGACACTAG 59.971 50.000 0.00 0.00 38.61 2.57
444 445 1.992667 CAGCGAAAATCAGCGACACTA 59.007 47.619 0.00 0.00 38.61 2.74
445 446 0.792640 CAGCGAAAATCAGCGACACT 59.207 50.000 0.00 0.00 38.61 3.55
446 447 0.512952 ACAGCGAAAATCAGCGACAC 59.487 50.000 0.00 0.00 38.61 3.67
447 448 0.512518 CACAGCGAAAATCAGCGACA 59.487 50.000 0.00 0.00 38.61 4.35
448 449 0.512952 ACACAGCGAAAATCAGCGAC 59.487 50.000 0.00 0.00 38.61 5.19
449 450 1.225855 AACACAGCGAAAATCAGCGA 58.774 45.000 0.00 0.00 38.61 4.93
450 451 2.036556 AAACACAGCGAAAATCAGCG 57.963 45.000 0.00 0.00 38.61 5.18
451 452 3.060339 CCAAAAACACAGCGAAAATCAGC 60.060 43.478 0.00 0.00 0.00 4.26
452 453 3.490526 CCCAAAAACACAGCGAAAATCAG 59.509 43.478 0.00 0.00 0.00 2.90
453 454 3.452474 CCCAAAAACACAGCGAAAATCA 58.548 40.909 0.00 0.00 0.00 2.57
454 455 2.799978 CCCCAAAAACACAGCGAAAATC 59.200 45.455 0.00 0.00 0.00 2.17
455 456 2.832563 CCCCAAAAACACAGCGAAAAT 58.167 42.857 0.00 0.00 0.00 1.82
456 457 1.740718 GCCCCAAAAACACAGCGAAAA 60.741 47.619 0.00 0.00 0.00 2.29
457 458 0.179097 GCCCCAAAAACACAGCGAAA 60.179 50.000 0.00 0.00 0.00 3.46
458 459 1.040339 AGCCCCAAAAACACAGCGAA 61.040 50.000 0.00 0.00 0.00 4.70
459 460 1.454847 AGCCCCAAAAACACAGCGA 60.455 52.632 0.00 0.00 0.00 4.93
460 461 1.300080 CAGCCCCAAAAACACAGCG 60.300 57.895 0.00 0.00 0.00 5.18
461 462 0.177836 AACAGCCCCAAAAACACAGC 59.822 50.000 0.00 0.00 0.00 4.40
462 463 2.278854 CAAACAGCCCCAAAAACACAG 58.721 47.619 0.00 0.00 0.00 3.66
463 464 1.625818 ACAAACAGCCCCAAAAACACA 59.374 42.857 0.00 0.00 0.00 3.72
464 465 2.394930 ACAAACAGCCCCAAAAACAC 57.605 45.000 0.00 0.00 0.00 3.32
465 466 3.425162 AAACAAACAGCCCCAAAAACA 57.575 38.095 0.00 0.00 0.00 2.83
466 467 3.119673 CCAAAACAAACAGCCCCAAAAAC 60.120 43.478 0.00 0.00 0.00 2.43
467 468 3.084786 CCAAAACAAACAGCCCCAAAAA 58.915 40.909 0.00 0.00 0.00 1.94
468 469 2.040412 ACCAAAACAAACAGCCCCAAAA 59.960 40.909 0.00 0.00 0.00 2.44
469 470 1.630878 ACCAAAACAAACAGCCCCAAA 59.369 42.857 0.00 0.00 0.00 3.28
470 471 1.208293 GACCAAAACAAACAGCCCCAA 59.792 47.619 0.00 0.00 0.00 4.12
471 472 0.827368 GACCAAAACAAACAGCCCCA 59.173 50.000 0.00 0.00 0.00 4.96
472 473 0.249280 CGACCAAAACAAACAGCCCC 60.249 55.000 0.00 0.00 0.00 5.80
473 474 0.458260 ACGACCAAAACAAACAGCCC 59.542 50.000 0.00 0.00 0.00 5.19
474 475 2.287393 AACGACCAAAACAAACAGCC 57.713 45.000 0.00 0.00 0.00 4.85
475 476 2.990514 ACAAACGACCAAAACAAACAGC 59.009 40.909 0.00 0.00 0.00 4.40
476 477 5.395642 AGTACAAACGACCAAAACAAACAG 58.604 37.500 0.00 0.00 0.00 3.16
477 478 5.373981 AGTACAAACGACCAAAACAAACA 57.626 34.783 0.00 0.00 0.00 2.83
478 479 4.794762 GGAGTACAAACGACCAAAACAAAC 59.205 41.667 0.00 0.00 0.00 2.93
479 480 4.142425 GGGAGTACAAACGACCAAAACAAA 60.142 41.667 0.00 0.00 0.00 2.83
480 481 3.377798 GGGAGTACAAACGACCAAAACAA 59.622 43.478 0.00 0.00 0.00 2.83
481 482 2.944349 GGGAGTACAAACGACCAAAACA 59.056 45.455 0.00 0.00 0.00 2.83
482 483 3.208594 AGGGAGTACAAACGACCAAAAC 58.791 45.455 0.00 0.00 0.00 2.43
483 484 3.135167 AGAGGGAGTACAAACGACCAAAA 59.865 43.478 0.00 0.00 0.00 2.44
484 485 2.701951 AGAGGGAGTACAAACGACCAAA 59.298 45.455 0.00 0.00 0.00 3.28
485 486 2.298163 GAGAGGGAGTACAAACGACCAA 59.702 50.000 0.00 0.00 0.00 3.67
486 487 1.891150 GAGAGGGAGTACAAACGACCA 59.109 52.381 0.00 0.00 0.00 4.02
487 488 2.169330 AGAGAGGGAGTACAAACGACC 58.831 52.381 0.00 0.00 0.00 4.79
488 489 3.938289 AAGAGAGGGAGTACAAACGAC 57.062 47.619 0.00 0.00 0.00 4.34
489 490 5.507637 AGATAAGAGAGGGAGTACAAACGA 58.492 41.667 0.00 0.00 0.00 3.85
490 491 5.838531 AGATAAGAGAGGGAGTACAAACG 57.161 43.478 0.00 0.00 0.00 3.60
529 530 0.976641 TCGAACCATGCAGGAGAACT 59.023 50.000 0.00 0.00 41.22 3.01
530 531 1.808411 TTCGAACCATGCAGGAGAAC 58.192 50.000 0.00 0.00 41.22 3.01
531 532 2.559698 TTTCGAACCATGCAGGAGAA 57.440 45.000 0.00 4.57 41.22 2.87
532 533 2.559698 TTTTCGAACCATGCAGGAGA 57.440 45.000 0.00 0.00 41.22 3.71
551 552 5.831525 ACTCCTTTCGTGTTTATCCCTTTTT 59.168 36.000 0.00 0.00 0.00 1.94
552 553 5.382616 ACTCCTTTCGTGTTTATCCCTTTT 58.617 37.500 0.00 0.00 0.00 2.27
553 554 4.981812 ACTCCTTTCGTGTTTATCCCTTT 58.018 39.130 0.00 0.00 0.00 3.11
554 555 4.635699 ACTCCTTTCGTGTTTATCCCTT 57.364 40.909 0.00 0.00 0.00 3.95
555 556 5.482878 TCTTACTCCTTTCGTGTTTATCCCT 59.517 40.000 0.00 0.00 0.00 4.20
556 557 5.727434 TCTTACTCCTTTCGTGTTTATCCC 58.273 41.667 0.00 0.00 0.00 3.85
557 558 7.845066 ATTCTTACTCCTTTCGTGTTTATCC 57.155 36.000 0.00 0.00 0.00 2.59
560 561 8.715088 GCTTAATTCTTACTCCTTTCGTGTTTA 58.285 33.333 0.00 0.00 0.00 2.01
561 562 7.308408 GGCTTAATTCTTACTCCTTTCGTGTTT 60.308 37.037 0.00 0.00 0.00 2.83
562 563 6.148976 GGCTTAATTCTTACTCCTTTCGTGTT 59.851 38.462 0.00 0.00 0.00 3.32
563 564 5.642491 GGCTTAATTCTTACTCCTTTCGTGT 59.358 40.000 0.00 0.00 0.00 4.49
564 565 5.220416 CGGCTTAATTCTTACTCCTTTCGTG 60.220 44.000 0.00 0.00 0.00 4.35
565 566 4.868734 CGGCTTAATTCTTACTCCTTTCGT 59.131 41.667 0.00 0.00 0.00 3.85
566 567 4.868734 ACGGCTTAATTCTTACTCCTTTCG 59.131 41.667 0.00 0.00 0.00 3.46
567 568 6.370718 TCAACGGCTTAATTCTTACTCCTTTC 59.629 38.462 0.00 0.00 0.00 2.62
568 569 6.235664 TCAACGGCTTAATTCTTACTCCTTT 58.764 36.000 0.00 0.00 0.00 3.11
569 570 5.801380 TCAACGGCTTAATTCTTACTCCTT 58.199 37.500 0.00 0.00 0.00 3.36
654 655 3.565307 TCAGCTTTGACCAGGTTTGATT 58.435 40.909 0.00 0.00 0.00 2.57
670 671 3.551890 CGCACGTATTTCTACATTCAGCT 59.448 43.478 0.00 0.00 0.00 4.24
683 684 1.663643 CTTACATGGTGCGCACGTATT 59.336 47.619 32.35 19.43 0.00 1.89
706 707 0.635555 GGTACTACCCCCTCTGTCCT 59.364 60.000 0.00 0.00 30.04 3.85
796 798 9.831737 GTTTATACGATATAGTCAACCATACGT 57.168 33.333 0.00 0.00 35.71 3.57
833 835 2.000429 GCATCACATTGTGCTTTCCC 58.000 50.000 12.04 0.00 38.30 3.97
842 844 5.361135 TGTCAACACTAAGCATCACATTG 57.639 39.130 0.00 0.00 0.00 2.82
846 848 3.375299 GGGATGTCAACACTAAGCATCAC 59.625 47.826 0.00 0.00 38.06 3.06
891 894 3.430929 TTTGTGTGCAATTGTTGGGTACC 60.431 43.478 2.17 2.17 41.51 3.34
939 943 1.951181 TTATCAACGAGTGCGCGTGC 61.951 55.000 15.48 15.48 44.86 5.34
940 944 0.023732 CTTATCAACGAGTGCGCGTG 59.976 55.000 8.43 0.00 44.86 5.34
942 946 0.294887 GACTTATCAACGAGTGCGCG 59.705 55.000 0.00 0.00 42.48 6.86
1107 1111 0.455295 CGAACTCTGAGAGCACGTCC 60.455 60.000 12.44 0.00 32.04 4.79
1120 1124 1.202604 TCCAACCACAACCTCGAACTC 60.203 52.381 0.00 0.00 0.00 3.01
1224 1228 6.194235 TGGGTGCATATTACAAGAGGAAAAT 58.806 36.000 0.00 0.00 0.00 1.82
1236 1241 7.838079 AGCTATGAATTTTGGGTGCATATTA 57.162 32.000 0.00 0.00 0.00 0.98
1294 1307 2.038295 CAGTCCAGGGATTCCTAGCATC 59.962 54.545 2.01 0.00 42.67 3.91
1372 1385 5.906254 AGGAGACCCCCTTCTATTACTATC 58.094 45.833 0.00 0.00 30.99 2.08
1373 1386 5.378985 TGAGGAGACCCCCTTCTATTACTAT 59.621 44.000 0.00 0.00 36.49 2.12
1387 1400 1.813102 ATCCCAGATTGAGGAGACCC 58.187 55.000 0.00 0.00 35.08 4.46
1402 1415 6.128200 ACCGTACGAAATACTTCAAAAATCCC 60.128 38.462 18.76 0.00 0.00 3.85
1442 1458 9.836864 TCTTATTGTAGATGTGTTATCTGCATT 57.163 29.630 8.19 7.69 39.74 3.56
1471 1487 5.582665 GTCCTCAACTTCATATTCCACAGTC 59.417 44.000 0.00 0.00 0.00 3.51
1601 1618 5.743872 CGCTTTCTTCTTACAAAGTTTGCTT 59.256 36.000 15.59 0.00 36.30 3.91
1635 1657 4.685169 ACTTATTTTGTGCATCGACCAG 57.315 40.909 0.00 0.00 0.00 4.00
1636 1658 5.935206 TCTAACTTATTTTGTGCATCGACCA 59.065 36.000 0.00 0.00 0.00 4.02
1637 1659 6.417191 TCTAACTTATTTTGTGCATCGACC 57.583 37.500 0.00 0.00 0.00 4.79
1638 1660 5.960105 GCTCTAACTTATTTTGTGCATCGAC 59.040 40.000 0.00 0.00 32.03 4.20
1639 1661 5.641636 TGCTCTAACTTATTTTGTGCATCGA 59.358 36.000 0.00 0.00 35.46 3.59
1662 1684 6.444633 AGAAAGCAGATCAAACATGAAGTTG 58.555 36.000 0.00 0.78 41.19 3.16
1663 1685 6.645790 AGAAAGCAGATCAAACATGAAGTT 57.354 33.333 0.00 0.00 43.89 2.66
1670 1692 4.924305 AAGCAAGAAAGCAGATCAAACA 57.076 36.364 0.00 0.00 36.85 2.83
1673 1695 6.579666 AATGTAAGCAAGAAAGCAGATCAA 57.420 33.333 0.00 0.00 36.85 2.57
1675 1697 6.385033 ACAAATGTAAGCAAGAAAGCAGATC 58.615 36.000 0.00 0.00 36.85 2.75
1681 1703 7.298122 ACATACGACAAATGTAAGCAAGAAAG 58.702 34.615 0.00 0.00 35.82 2.62
1685 1707 8.012809 TGTAAACATACGACAAATGTAAGCAAG 58.987 33.333 0.00 0.00 36.56 4.01
1686 1708 7.862648 TGTAAACATACGACAAATGTAAGCAA 58.137 30.769 0.00 0.00 36.56 3.91
1692 1714 5.636837 GGCATGTAAACATACGACAAATGT 58.363 37.500 0.00 0.00 39.22 2.71
1715 1737 7.030165 AGAAGACTTCACTATACATGACAACG 58.970 38.462 17.34 0.00 0.00 4.10
1767 3167 5.415701 AGTGACATAACCTTGGCTGTATTTG 59.584 40.000 0.00 0.00 0.00 2.32
1850 3250 2.105466 CGCTCAGAGCCTGCCTTTC 61.105 63.158 17.16 0.00 38.18 2.62
1851 3251 2.046507 CGCTCAGAGCCTGCCTTT 60.047 61.111 17.16 0.00 38.18 3.11
1852 3252 4.774503 GCGCTCAGAGCCTGCCTT 62.775 66.667 17.16 0.00 38.18 4.35
1905 3305 1.152567 CTGGGTTTGCCAAGGGACA 60.153 57.895 0.00 0.00 31.92 4.02
2164 3568 1.603455 CCCATCCAGGTTTGTGCGT 60.603 57.895 0.00 0.00 34.66 5.24
2281 3685 0.318107 CGAAACAAGTGCTTGCCCAG 60.318 55.000 11.43 0.00 44.03 4.45
2410 3817 2.034066 CCACAACCGCCATGGAGT 59.966 61.111 18.40 9.23 42.00 3.85
2495 3902 3.177272 CTGCATCAAGCCGCCATCG 62.177 63.158 0.00 0.00 44.83 3.84
2517 3924 3.620300 CTGCCGCTGCACAACCATG 62.620 63.158 0.00 0.00 44.23 3.66


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

AutoCloner maintained by Alex Coulton.