Multiple sequence alignment - TraesCS5D01G125300

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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 TraesCS5D01G125300 chr5D 100.000 3538 0 0 3570 7107 191902120 191905657 0.000000e+00 6534.0
1 TraesCS5D01G125300 chr5D 100.000 3196 0 0 1 3196 191898551 191901746 0.000000e+00 5903.0
2 TraesCS5D01G125300 chr5D 94.258 1254 65 7 1910 3159 16150270 16149020 0.000000e+00 1910.0
3 TraesCS5D01G125300 chr5D 89.189 74 8 0 406 479 191899029 191898956 7.590000e-15 93.5
4 TraesCS5D01G125300 chr5D 94.643 56 3 0 506 561 191899000 191899055 3.530000e-13 87.9
5 TraesCS5D01G125300 chr5D 94.643 56 3 0 450 505 191899056 191899111 3.530000e-13 87.9
6 TraesCS5D01G125300 chr5D 100.000 36 0 0 407 442 409522042 409522007 4.600000e-07 67.6
7 TraesCS5D01G125300 chr5B 94.169 3001 114 18 3932 6917 196236947 196239901 0.000000e+00 4516.0
8 TraesCS5D01G125300 chr5B 94.050 1210 43 5 731 1912 196232846 196234054 0.000000e+00 1808.0
9 TraesCS5D01G125300 chr5B 96.990 299 9 0 3582 3880 196234046 196234344 2.960000e-138 503.0
10 TraesCS5D01G125300 chr5B 87.745 408 29 4 2 409 196232330 196232716 2.340000e-124 457.0
11 TraesCS5D01G125300 chr5B 97.949 195 2 2 6915 7107 196239941 196240135 3.180000e-88 337.0
12 TraesCS5D01G125300 chr5B 97.222 36 1 0 548 583 652635011 652635046 2.140000e-05 62.1
13 TraesCS5D01G125300 chr5B 94.595 37 2 0 443 479 56826931 56826967 2.770000e-04 58.4
14 TraesCS5D01G125300 chr5B 100.000 31 0 0 3907 3937 196235479 196235509 2.770000e-04 58.4
15 TraesCS5D01G125300 chr5A 95.078 2316 84 13 4621 6917 229926150 229923846 0.000000e+00 3618.0
16 TraesCS5D01G125300 chr5A 91.708 1218 44 11 731 1912 229928258 229927062 0.000000e+00 1637.0
17 TraesCS5D01G125300 chr5A 96.030 932 27 3 3581 4512 229927071 229926150 0.000000e+00 1507.0
18 TraesCS5D01G125300 chr5A 89.231 390 28 2 2 391 229935313 229934938 6.450000e-130 475.0
19 TraesCS5D01G125300 chr5A 95.876 194 5 3 6916 7107 229923803 229923611 1.930000e-80 311.0
20 TraesCS5D01G125300 chr5A 92.857 42 1 2 446 485 589300566 589300525 7.700000e-05 60.2
21 TraesCS5D01G125300 chr6D 94.904 1256 58 6 1908 3160 58225324 58224072 0.000000e+00 1960.0
22 TraesCS5D01G125300 chr6D 91.164 1143 92 8 1910 3048 348672831 348671694 0.000000e+00 1543.0
23 TraesCS5D01G125300 chr2D 94.835 1239 60 4 1924 3160 364829756 364828520 0.000000e+00 1930.0
24 TraesCS5D01G125300 chr2D 94.387 1247 66 4 1916 3160 364672291 364671047 0.000000e+00 1912.0
25 TraesCS5D01G125300 chr3D 94.547 1247 64 4 1916 3160 419653928 419655172 0.000000e+00 1923.0
26 TraesCS5D01G125300 chr3D 87.934 663 44 12 6230 6882 447632229 447632865 0.000000e+00 749.0
27 TraesCS5D01G125300 chr3D 88.614 202 9 4 6919 7107 447632980 447633180 4.290000e-57 233.0
28 TraesCS5D01G125300 chr3D 96.970 33 1 0 447 479 236291801 236291769 1.000000e-03 56.5
29 TraesCS5D01G125300 chr4D 89.887 1236 110 13 1910 3135 85614088 85615318 0.000000e+00 1576.0
30 TraesCS5D01G125300 chr7B 88.818 1252 133 7 1913 3161 684373065 684371818 0.000000e+00 1530.0
31 TraesCS5D01G125300 chr7D 88.615 1256 134 8 1910 3158 107807615 107806362 0.000000e+00 1519.0
32 TraesCS5D01G125300 chr7D 95.745 47 2 0 396 442 125897437 125897391 7.640000e-10 76.8
33 TraesCS5D01G125300 chr7D 100.000 30 0 0 510 539 263515547 263515518 1.000000e-03 56.5
34 TraesCS5D01G125300 chr7D 100.000 29 0 0 4738 4766 32944316 32944344 4.000000e-03 54.7
35 TraesCS5D01G125300 chr3A 89.099 688 50 8 6251 6917 589373291 589373974 0.000000e+00 832.0
36 TraesCS5D01G125300 chr3A 84.541 207 7 6 6915 7107 589374016 589374211 1.570000e-41 182.0
37 TraesCS5D01G125300 chr3B 87.822 427 27 11 6494 6917 586862220 586862624 1.790000e-130 477.0
38 TraesCS5D01G125300 chr3B 88.835 206 9 5 6915 7107 586862666 586862870 2.560000e-59 241.0
39 TraesCS5D01G125300 chr2B 90.038 261 26 0 2 262 129396584 129396324 8.830000e-89 339.0
40 TraesCS5D01G125300 chr2B 97.436 39 1 0 402 440 731610542 731610580 4.600000e-07 67.6
41 TraesCS5D01G125300 chr2B 97.368 38 0 1 447 483 567166622 567166659 5.950000e-06 63.9
42 TraesCS5D01G125300 chr6A 83.908 87 10 3 7 89 27078125 27078211 5.910000e-11 80.5
43 TraesCS5D01G125300 chr6B 83.908 87 3 2 406 481 278127893 278127807 9.890000e-09 73.1
44 TraesCS5D01G125300 chr6B 82.022 89 6 4 405 483 704858674 704858762 4.600000e-07 67.6
45 TraesCS5D01G125300 chr4B 82.955 88 4 1 406 482 249778649 249778562 1.280000e-07 69.4
46 TraesCS5D01G125300 chr1A 82.105 95 4 3 397 479 48977156 48977249 1.280000e-07 69.4
47 TraesCS5D01G125300 chr1A 91.489 47 3 1 437 483 132133477 132133522 5.950000e-06 63.9
48 TraesCS5D01G125300 chrUn 97.368 38 1 0 405 442 252429505 252429468 1.650000e-06 65.8
49 TraesCS5D01G125300 chrUn 97.368 38 1 0 405 442 396604937 396604900 1.650000e-06 65.8
50 TraesCS5D01G125300 chr2A 92.500 40 1 2 443 481 733413855 733413893 1.000000e-03 56.5
51 TraesCS5D01G125300 chr7A 100.000 29 0 0 4738 4766 33191354 33191382 4.000000e-03 54.7


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 TraesCS5D01G125300 chr5D 191898551 191905657 7106 False 3153.20 6534 97.3215 1 7107 4 chr5D.!!$F1 7106
1 TraesCS5D01G125300 chr5D 16149020 16150270 1250 True 1910.00 1910 94.2580 1910 3159 1 chr5D.!!$R1 1249
2 TraesCS5D01G125300 chr5B 196232330 196240135 7805 False 1279.90 4516 95.1505 2 7107 6 chr5B.!!$F3 7105
3 TraesCS5D01G125300 chr5A 229923611 229928258 4647 True 1768.25 3618 94.6730 731 7107 4 chr5A.!!$R3 6376
4 TraesCS5D01G125300 chr6D 58224072 58225324 1252 True 1960.00 1960 94.9040 1908 3160 1 chr6D.!!$R1 1252
5 TraesCS5D01G125300 chr6D 348671694 348672831 1137 True 1543.00 1543 91.1640 1910 3048 1 chr6D.!!$R2 1138
6 TraesCS5D01G125300 chr2D 364828520 364829756 1236 True 1930.00 1930 94.8350 1924 3160 1 chr2D.!!$R2 1236
7 TraesCS5D01G125300 chr2D 364671047 364672291 1244 True 1912.00 1912 94.3870 1916 3160 1 chr2D.!!$R1 1244
8 TraesCS5D01G125300 chr3D 419653928 419655172 1244 False 1923.00 1923 94.5470 1916 3160 1 chr3D.!!$F1 1244
9 TraesCS5D01G125300 chr3D 447632229 447633180 951 False 491.00 749 88.2740 6230 7107 2 chr3D.!!$F2 877
10 TraesCS5D01G125300 chr4D 85614088 85615318 1230 False 1576.00 1576 89.8870 1910 3135 1 chr4D.!!$F1 1225
11 TraesCS5D01G125300 chr7B 684371818 684373065 1247 True 1530.00 1530 88.8180 1913 3161 1 chr7B.!!$R1 1248
12 TraesCS5D01G125300 chr7D 107806362 107807615 1253 True 1519.00 1519 88.6150 1910 3158 1 chr7D.!!$R1 1248
13 TraesCS5D01G125300 chr3A 589373291 589374211 920 False 507.00 832 86.8200 6251 7107 2 chr3A.!!$F1 856
14 TraesCS5D01G125300 chr3B 586862220 586862870 650 False 359.00 477 88.3285 6494 7107 2 chr3B.!!$F1 613

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
625 626 0.035458 ACAAAGAACCTCCTCAGGCG 59.965 55.000 0.00 0.00 45.05 5.52 F
842 843 0.182299 GGATGGCTTCCTAGCTGCTT 59.818 55.000 7.79 0.00 46.90 3.91 F
2119 2156 0.528924 AAGCTACATACGACGCACCA 59.471 50.000 0.00 0.00 0.00 4.17 F
3778 3827 0.108662 TGTCAATGTCGATGAGCGCT 60.109 50.000 11.27 11.27 40.61 5.92 F
4242 6851 0.038801 TGAGCTCTGCTGACGTTGAG 60.039 55.000 16.19 0.00 39.88 3.02 F
4607 7216 0.867746 GTTGATCAGACGTTGCTGCA 59.132 50.000 0.00 0.00 35.86 4.41 F
5336 7954 1.080974 GCTGCTCACAACACATGGC 60.081 57.895 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1667 0.522626 CACCAGAATGTGATGCGCAA 59.477 50.000 17.11 0.0 38.55 4.85 R
2302 2339 0.655733 GTGGCGGTGAATATTGGTCG 59.344 55.000 0.00 0.0 0.00 4.79 R
4012 6621 1.196200 GCTCTGTCGAATCGCTTCTC 58.804 55.000 0.00 0.0 0.00 2.87 R
4607 7216 0.622665 CTTTCTCCTCCCCTGCACAT 59.377 55.000 0.00 0.0 0.00 3.21 R
5449 8067 0.657840 GCCGCGCTGTCATAATCTTT 59.342 50.000 5.56 0.0 0.00 2.52 R
5474 8092 1.608025 GGATGTCGTTCTTGTCAGGCA 60.608 52.381 0.00 0.0 0.00 4.75 R
6917 9618 0.888619 CGTCAGTGCTTAGGAGGTGA 59.111 55.000 0.00 0.0 0.00 4.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 5.671493 GGTAACTTCCTGCTATACACATGT 58.329 41.667 0.00 0.00 0.00 3.21
43 44 6.753180 ACTTCCTGCTATACACATGTCATAG 58.247 40.000 15.35 15.35 0.00 2.23
64 65 8.246871 TCATAGTCTCATTGAGTACAAGACTTG 58.753 37.037 13.77 13.77 39.06 3.16
117 118 3.853475 CCTTGGAATGCTTTGATTGACC 58.147 45.455 0.00 0.00 0.00 4.02
124 125 1.872952 TGCTTTGATTGACCACAGTCG 59.127 47.619 0.00 0.00 46.74 4.18
202 203 2.618709 GCTAGTGGCACCCAATATGAAC 59.381 50.000 15.27 0.00 41.35 3.18
214 215 7.414098 GCACCCAATATGAACTGTGTAGTAAAG 60.414 40.741 0.00 0.00 35.69 1.85
215 216 7.065803 CACCCAATATGAACTGTGTAGTAAAGG 59.934 40.741 0.00 0.00 35.69 3.11
245 246 6.783892 TTTTATCAGGAGCACAAAATTTGC 57.216 33.333 5.52 0.00 40.52 3.68
259 260 8.006027 GCACAAAATTTGCAAAGTAGAGATTTC 58.994 33.333 18.19 0.00 39.93 2.17
274 275 8.798402 AGTAGAGATTTCTGTAAGATAATCCGG 58.202 37.037 0.00 0.00 46.36 5.14
277 278 4.395959 TTTCTGTAAGATAATCCGGCGT 57.604 40.909 6.01 0.00 46.36 5.68
291 292 1.091537 CGGCGTTGTTATCATTGGGT 58.908 50.000 0.00 0.00 0.00 4.51
295 296 3.880490 GGCGTTGTTATCATTGGGTATCA 59.120 43.478 0.00 0.00 0.00 2.15
296 297 4.518970 GGCGTTGTTATCATTGGGTATCAT 59.481 41.667 0.00 0.00 0.00 2.45
300 301 7.571244 GCGTTGTTATCATTGGGTATCATACTG 60.571 40.741 0.00 0.00 0.00 2.74
308 309 8.262601 TCATTGGGTATCATACTGAGTTATGT 57.737 34.615 0.00 0.00 0.00 2.29
309 310 8.150296 TCATTGGGTATCATACTGAGTTATGTG 58.850 37.037 0.00 0.00 0.00 3.21
310 311 7.432148 TTGGGTATCATACTGAGTTATGTGT 57.568 36.000 0.00 0.00 0.00 3.72
311 312 7.432148 TGGGTATCATACTGAGTTATGTGTT 57.568 36.000 0.00 0.00 0.00 3.32
312 313 8.541899 TGGGTATCATACTGAGTTATGTGTTA 57.458 34.615 0.00 0.00 0.00 2.41
313 314 8.638873 TGGGTATCATACTGAGTTATGTGTTAG 58.361 37.037 0.00 0.00 0.00 2.34
314 315 7.599245 GGGTATCATACTGAGTTATGTGTTAGC 59.401 40.741 0.00 0.00 0.00 3.09
315 316 8.361139 GGTATCATACTGAGTTATGTGTTAGCT 58.639 37.037 0.00 0.00 0.00 3.32
318 319 9.920133 ATCATACTGAGTTATGTGTTAGCTATG 57.080 33.333 0.00 0.00 0.00 2.23
319 320 9.131791 TCATACTGAGTTATGTGTTAGCTATGA 57.868 33.333 0.00 0.00 0.00 2.15
332 333 5.709631 TGTTAGCTATGATTGCCAACTTTCA 59.290 36.000 10.64 0.00 34.19 2.69
336 337 4.640201 GCTATGATTGCCAACTTTCAGGTA 59.360 41.667 0.00 0.00 0.00 3.08
337 338 5.220931 GCTATGATTGCCAACTTTCAGGTAG 60.221 44.000 0.00 0.00 0.00 3.18
342 343 2.706723 TGCCAACTTTCAGGTAGTACCA 59.293 45.455 21.49 0.00 41.95 3.25
343 344 3.136809 TGCCAACTTTCAGGTAGTACCAA 59.863 43.478 21.49 5.07 41.95 3.67
344 345 4.202524 TGCCAACTTTCAGGTAGTACCAAT 60.203 41.667 21.49 0.00 41.95 3.16
345 346 5.013287 TGCCAACTTTCAGGTAGTACCAATA 59.987 40.000 21.49 3.26 41.95 1.90
346 347 5.941647 GCCAACTTTCAGGTAGTACCAATAA 59.058 40.000 21.49 9.18 41.95 1.40
347 348 6.602009 GCCAACTTTCAGGTAGTACCAATAAT 59.398 38.462 21.49 0.00 41.95 1.28
348 349 7.415206 GCCAACTTTCAGGTAGTACCAATAATG 60.415 40.741 21.49 10.30 41.95 1.90
366 367 7.993183 CCAATAATGGTAGAACCTAGTGATTGT 59.007 37.037 0.00 0.00 42.18 2.71
387 388 9.846248 GATTGTTGTTGCTTAAGTAATTCAGAT 57.154 29.630 9.31 2.50 0.00 2.90
409 410 9.891828 CAGATATCTCAGTGTTGTATTCTACTC 57.108 37.037 1.03 0.00 0.00 2.59
410 411 9.073475 AGATATCTCAGTGTTGTATTCTACTCC 57.927 37.037 0.00 0.00 0.00 3.85
412 413 5.580998 TCTCAGTGTTGTATTCTACTCCCT 58.419 41.667 0.00 0.00 0.00 4.20
413 414 5.652891 TCTCAGTGTTGTATTCTACTCCCTC 59.347 44.000 0.00 0.00 0.00 4.30
414 415 4.710375 TCAGTGTTGTATTCTACTCCCTCC 59.290 45.833 0.00 0.00 0.00 4.30
415 416 3.700038 AGTGTTGTATTCTACTCCCTCCG 59.300 47.826 0.00 0.00 0.00 4.63
416 417 3.446516 GTGTTGTATTCTACTCCCTCCGT 59.553 47.826 0.00 0.00 0.00 4.69
417 418 3.698040 TGTTGTATTCTACTCCCTCCGTC 59.302 47.826 0.00 0.00 0.00 4.79
418 419 2.941480 TGTATTCTACTCCCTCCGTCC 58.059 52.381 0.00 0.00 0.00 4.79
419 420 2.237643 GTATTCTACTCCCTCCGTCCC 58.762 57.143 0.00 0.00 0.00 4.46
423 424 1.424302 TCTACTCCCTCCGTCCCATAG 59.576 57.143 0.00 0.00 0.00 2.23
425 426 0.397254 ACTCCCTCCGTCCCATAGTG 60.397 60.000 0.00 0.00 0.00 2.74
426 427 0.397254 CTCCCTCCGTCCCATAGTGT 60.397 60.000 0.00 0.00 0.00 3.55
427 428 0.928505 TCCCTCCGTCCCATAGTGTA 59.071 55.000 0.00 0.00 0.00 2.90
428 429 1.288633 TCCCTCCGTCCCATAGTGTAA 59.711 52.381 0.00 0.00 0.00 2.41
429 430 1.687123 CCCTCCGTCCCATAGTGTAAG 59.313 57.143 0.00 0.00 0.00 2.34
430 431 2.662866 CCTCCGTCCCATAGTGTAAGA 58.337 52.381 0.00 0.00 0.00 2.10
431 432 2.361438 CCTCCGTCCCATAGTGTAAGAC 59.639 54.545 0.00 0.00 0.00 3.01
433 434 1.747355 CCGTCCCATAGTGTAAGACGT 59.253 52.381 9.63 0.00 46.62 4.34
434 435 2.165030 CCGTCCCATAGTGTAAGACGTT 59.835 50.000 9.63 0.00 46.62 3.99
435 436 3.367703 CCGTCCCATAGTGTAAGACGTTT 60.368 47.826 9.63 0.00 46.62 3.60
436 437 4.240096 CGTCCCATAGTGTAAGACGTTTT 58.760 43.478 0.00 0.00 43.89 2.43
437 438 4.687483 CGTCCCATAGTGTAAGACGTTTTT 59.313 41.667 0.00 0.00 43.89 1.94
484 485 4.399483 TGGAACAGAGGGAGTACTAACT 57.601 45.455 0.00 0.00 39.21 2.24
485 486 4.748701 TGGAACAGAGGGAGTACTAACTT 58.251 43.478 0.00 0.00 35.56 2.66
486 487 5.152934 TGGAACAGAGGGAGTACTAACTTT 58.847 41.667 0.00 0.00 35.56 2.66
487 488 5.245526 TGGAACAGAGGGAGTACTAACTTTC 59.754 44.000 0.00 0.00 35.56 2.62
488 489 5.245526 GGAACAGAGGGAGTACTAACTTTCA 59.754 44.000 0.00 0.00 35.56 2.69
489 490 6.239515 GGAACAGAGGGAGTACTAACTTTCAA 60.240 42.308 0.00 0.00 35.56 2.69
490 491 6.742559 ACAGAGGGAGTACTAACTTTCAAA 57.257 37.500 0.00 0.00 35.56 2.69
491 492 6.760291 ACAGAGGGAGTACTAACTTTCAAAG 58.240 40.000 0.00 0.00 35.56 2.77
492 493 6.326843 ACAGAGGGAGTACTAACTTTCAAAGT 59.673 38.462 0.00 0.00 45.46 2.66
493 494 7.508296 ACAGAGGGAGTACTAACTTTCAAAGTA 59.492 37.037 2.38 0.00 41.91 2.24
494 495 7.813627 CAGAGGGAGTACTAACTTTCAAAGTAC 59.186 40.741 2.38 0.00 43.79 2.73
509 510 5.968387 CAAAGTACTCTCTTTGTCAACGT 57.032 39.130 0.00 0.00 45.08 3.99
510 511 5.964070 CAAAGTACTCTCTTTGTCAACGTC 58.036 41.667 0.00 0.00 45.08 4.34
511 512 5.517322 AAGTACTCTCTTTGTCAACGTCT 57.483 39.130 0.00 0.00 0.00 4.18
512 513 5.517322 AGTACTCTCTTTGTCAACGTCTT 57.483 39.130 0.00 0.00 0.00 3.01
513 514 6.630444 AGTACTCTCTTTGTCAACGTCTTA 57.370 37.500 0.00 0.00 0.00 2.10
514 515 7.216973 AGTACTCTCTTTGTCAACGTCTTAT 57.783 36.000 0.00 0.00 0.00 1.73
515 516 8.332996 AGTACTCTCTTTGTCAACGTCTTATA 57.667 34.615 0.00 0.00 0.00 0.98
516 517 8.958506 AGTACTCTCTTTGTCAACGTCTTATAT 58.041 33.333 0.00 0.00 0.00 0.86
517 518 9.570488 GTACTCTCTTTGTCAACGTCTTATATT 57.430 33.333 0.00 0.00 0.00 1.28
526 527 9.961265 TTGTCAACGTCTTATATTATAGGACAG 57.039 33.333 19.89 15.68 32.73 3.51
527 528 9.346005 TGTCAACGTCTTATATTATAGGACAGA 57.654 33.333 19.89 13.56 0.00 3.41
528 529 9.828852 GTCAACGTCTTATATTATAGGACAGAG 57.171 37.037 19.89 11.60 0.00 3.35
529 530 9.788889 TCAACGTCTTATATTATAGGACAGAGA 57.211 33.333 19.89 13.07 0.00 3.10
532 533 9.661563 ACGTCTTATATTATAGGACAGAGAGAG 57.338 37.037 19.89 8.83 0.00 3.20
533 534 9.661563 CGTCTTATATTATAGGACAGAGAGAGT 57.338 37.037 19.89 0.00 0.00 3.24
543 544 8.741603 ATAGGACAGAGAGAGTACTAACTTTC 57.258 38.462 0.00 0.00 36.10 2.62
544 545 6.544650 AGGACAGAGAGAGTACTAACTTTCA 58.455 40.000 0.00 0.00 38.91 2.69
545 546 7.005296 AGGACAGAGAGAGTACTAACTTTCAA 58.995 38.462 0.00 0.00 38.91 2.69
546 547 7.506261 AGGACAGAGAGAGTACTAACTTTCAAA 59.494 37.037 0.00 0.00 38.91 2.69
547 548 7.810759 GGACAGAGAGAGTACTAACTTTCAAAG 59.189 40.741 0.00 0.00 38.91 2.77
548 549 8.240267 ACAGAGAGAGTACTAACTTTCAAAGT 57.760 34.615 0.00 0.00 45.46 2.66
549 550 9.352191 ACAGAGAGAGTACTAACTTTCAAAGTA 57.648 33.333 2.38 0.00 41.91 2.24
550 551 9.615295 CAGAGAGAGTACTAACTTTCAAAGTAC 57.385 37.037 2.38 0.00 43.79 2.73
568 569 7.978982 CAAAGTACTCTCTTTGTCCCATAATG 58.021 38.462 0.00 0.00 45.08 1.90
574 575 8.095452 ACTCTCTTTGTCCCATAATGTAAGAT 57.905 34.615 0.00 0.00 0.00 2.40
601 602 8.699749 GTTTTACATTGTTTTGTAGCTGGAATC 58.300 33.333 0.00 0.00 33.81 2.52
602 603 5.046910 ACATTGTTTTGTAGCTGGAATCG 57.953 39.130 0.00 0.00 0.00 3.34
612 613 1.902508 AGCTGGAATCGAGGACAAAGA 59.097 47.619 0.00 0.00 0.00 2.52
620 621 1.893801 TCGAGGACAAAGAACCTCCTC 59.106 52.381 0.00 3.24 46.87 3.71
625 626 0.035458 ACAAAGAACCTCCTCAGGCG 59.965 55.000 0.00 0.00 45.05 5.52
646 647 4.832608 CGCCCCAACCGCTAGTCC 62.833 72.222 0.00 0.00 0.00 3.85
649 650 2.029307 GCCCCAACCGCTAGTCCTAG 62.029 65.000 0.00 0.00 36.29 3.02
650 651 0.686769 CCCCAACCGCTAGTCCTAGT 60.687 60.000 3.45 0.00 35.65 2.57
651 652 0.745468 CCCAACCGCTAGTCCTAGTC 59.255 60.000 3.45 0.00 35.65 2.59
652 653 0.745468 CCAACCGCTAGTCCTAGTCC 59.255 60.000 3.45 0.00 35.65 3.85
653 654 1.471119 CAACCGCTAGTCCTAGTCCA 58.529 55.000 3.45 0.00 35.65 4.02
654 655 1.405821 CAACCGCTAGTCCTAGTCCAG 59.594 57.143 3.45 0.00 35.65 3.86
655 656 0.624785 ACCGCTAGTCCTAGTCCAGT 59.375 55.000 3.45 0.00 35.65 4.00
656 657 1.310904 CCGCTAGTCCTAGTCCAGTC 58.689 60.000 3.45 0.00 35.65 3.51
657 658 1.408405 CCGCTAGTCCTAGTCCAGTCA 60.408 57.143 3.45 0.00 35.65 3.41
658 659 2.366533 CGCTAGTCCTAGTCCAGTCAA 58.633 52.381 3.45 0.00 35.65 3.18
659 660 2.097791 CGCTAGTCCTAGTCCAGTCAAC 59.902 54.545 3.45 0.00 35.65 3.18
660 661 3.090037 GCTAGTCCTAGTCCAGTCAACA 58.910 50.000 3.45 0.00 35.65 3.33
661 662 3.702045 GCTAGTCCTAGTCCAGTCAACAT 59.298 47.826 3.45 0.00 35.65 2.71
662 663 4.202070 GCTAGTCCTAGTCCAGTCAACATC 60.202 50.000 3.45 0.00 35.65 3.06
663 664 2.755655 AGTCCTAGTCCAGTCAACATCG 59.244 50.000 0.00 0.00 0.00 3.84
664 665 2.492484 GTCCTAGTCCAGTCAACATCGT 59.508 50.000 0.00 0.00 0.00 3.73
665 666 2.492088 TCCTAGTCCAGTCAACATCGTG 59.508 50.000 0.00 0.00 0.00 4.35
666 667 2.231478 CCTAGTCCAGTCAACATCGTGT 59.769 50.000 0.00 0.00 0.00 4.49
667 668 2.910688 AGTCCAGTCAACATCGTGTT 57.089 45.000 0.00 0.00 42.08 3.32
668 669 2.755650 AGTCCAGTCAACATCGTGTTC 58.244 47.619 1.17 0.00 38.77 3.18
669 670 1.798813 GTCCAGTCAACATCGTGTTCC 59.201 52.381 1.17 0.00 38.77 3.62
670 671 1.156736 CCAGTCAACATCGTGTTCCC 58.843 55.000 1.17 0.00 38.77 3.97
671 672 1.156736 CAGTCAACATCGTGTTCCCC 58.843 55.000 1.17 0.00 38.77 4.81
672 673 0.762418 AGTCAACATCGTGTTCCCCA 59.238 50.000 1.17 0.00 38.77 4.96
673 674 1.142060 AGTCAACATCGTGTTCCCCAA 59.858 47.619 1.17 0.00 38.77 4.12
674 675 1.950909 GTCAACATCGTGTTCCCCAAA 59.049 47.619 1.17 0.00 38.77 3.28
675 676 2.359531 GTCAACATCGTGTTCCCCAAAA 59.640 45.455 1.17 0.00 38.77 2.44
676 677 3.024547 TCAACATCGTGTTCCCCAAAAA 58.975 40.909 1.17 0.00 38.77 1.94
697 698 1.990799 TAAATCTCGTCAGCACCGTG 58.009 50.000 0.00 0.00 0.00 4.94
706 707 4.082523 AGCACCGTGGCGCATAGT 62.083 61.111 10.83 0.00 39.27 2.12
707 708 2.202824 GCACCGTGGCGCATAGTA 60.203 61.111 10.83 0.00 0.00 1.82
708 709 2.237751 GCACCGTGGCGCATAGTAG 61.238 63.158 10.83 0.00 0.00 2.57
709 710 1.141019 CACCGTGGCGCATAGTAGT 59.859 57.895 10.83 0.00 0.00 2.73
710 711 0.382873 CACCGTGGCGCATAGTAGTA 59.617 55.000 10.83 0.00 0.00 1.82
711 712 1.000607 CACCGTGGCGCATAGTAGTAT 60.001 52.381 10.83 0.00 0.00 2.12
712 713 2.227149 CACCGTGGCGCATAGTAGTATA 59.773 50.000 10.83 0.00 0.00 1.47
713 714 2.486982 ACCGTGGCGCATAGTAGTATAG 59.513 50.000 10.83 0.00 0.00 1.31
714 715 2.745821 CCGTGGCGCATAGTAGTATAGA 59.254 50.000 10.83 0.00 0.00 1.98
715 716 3.189910 CCGTGGCGCATAGTAGTATAGAA 59.810 47.826 10.83 0.00 0.00 2.10
716 717 4.142447 CCGTGGCGCATAGTAGTATAGAAT 60.142 45.833 10.83 0.00 0.00 2.40
717 718 5.399858 CGTGGCGCATAGTAGTATAGAATT 58.600 41.667 10.83 0.00 0.00 2.17
718 719 5.862323 CGTGGCGCATAGTAGTATAGAATTT 59.138 40.000 10.83 0.00 0.00 1.82
719 720 6.365247 CGTGGCGCATAGTAGTATAGAATTTT 59.635 38.462 10.83 0.00 0.00 1.82
720 721 7.095774 CGTGGCGCATAGTAGTATAGAATTTTT 60.096 37.037 10.83 0.00 0.00 1.94
721 722 8.221766 GTGGCGCATAGTAGTATAGAATTTTTC 58.778 37.037 10.83 0.00 0.00 2.29
722 723 7.115805 TGGCGCATAGTAGTATAGAATTTTTCG 59.884 37.037 10.83 0.00 34.02 3.46
723 724 6.948777 GCGCATAGTAGTATAGAATTTTTCGC 59.051 38.462 0.30 0.00 34.02 4.70
724 725 7.358931 GCGCATAGTAGTATAGAATTTTTCGCA 60.359 37.037 0.30 0.00 34.84 5.10
725 726 8.484799 CGCATAGTAGTATAGAATTTTTCGCAA 58.515 33.333 0.00 0.00 34.02 4.85
765 766 1.137086 GGTAGAAGAGAATGGCTGCGA 59.863 52.381 0.00 0.00 0.00 5.10
769 770 1.806542 GAAGAGAATGGCTGCGAACAA 59.193 47.619 0.00 0.00 0.00 2.83
838 839 1.690219 CCACGGATGGCTTCCTAGCT 61.690 60.000 16.47 0.00 46.90 3.32
839 840 0.531532 CACGGATGGCTTCCTAGCTG 60.532 60.000 16.47 4.15 46.90 4.24
840 841 1.596477 CGGATGGCTTCCTAGCTGC 60.596 63.158 16.47 0.00 46.90 5.25
841 842 1.835693 GGATGGCTTCCTAGCTGCT 59.164 57.895 7.57 7.57 46.90 4.24
842 843 0.182299 GGATGGCTTCCTAGCTGCTT 59.818 55.000 7.79 0.00 46.90 3.91
843 844 1.409381 GGATGGCTTCCTAGCTGCTTT 60.409 52.381 7.79 0.00 46.90 3.51
844 845 1.674962 GATGGCTTCCTAGCTGCTTTG 59.325 52.381 7.79 1.06 46.90 2.77
845 846 0.962356 TGGCTTCCTAGCTGCTTTGC 60.962 55.000 7.79 5.54 46.90 3.68
847 848 1.172175 GCTTCCTAGCTGCTTTGCTT 58.828 50.000 7.79 0.00 44.27 3.91
848 849 1.135460 GCTTCCTAGCTGCTTTGCTTG 60.135 52.381 7.79 3.73 44.27 4.01
849 850 0.883833 TTCCTAGCTGCTTTGCTTGC 59.116 50.000 7.79 0.00 43.74 4.01
850 851 0.962356 TCCTAGCTGCTTTGCTTGCC 60.962 55.000 7.79 0.00 43.74 4.52
851 852 0.964358 CCTAGCTGCTTTGCTTGCCT 60.964 55.000 7.79 0.00 43.74 4.75
852 853 0.886563 CTAGCTGCTTTGCTTGCCTT 59.113 50.000 7.79 0.00 43.74 4.35
881 884 7.921214 TCACTGTTAGTAAAACTCAAGTCTCTG 59.079 37.037 0.00 0.00 0.00 3.35
1020 1049 2.029649 CCATCCAACAAACTGAAGCAGG 60.030 50.000 0.00 0.00 35.51 4.85
1069 1098 2.700773 GGGCAATTCGGTGACCTGC 61.701 63.158 5.11 5.11 44.17 4.85
1297 1326 2.668550 GTTGCCCTCCACGTCACC 60.669 66.667 0.00 0.00 0.00 4.02
1398 1427 1.005340 GACGGCTTCTGCAATCTCAG 58.995 55.000 0.00 0.00 41.91 3.35
1400 1429 1.712977 CGGCTTCTGCAATCTCAGCC 61.713 60.000 10.02 10.02 45.73 4.85
1667 1698 4.019174 ACATTCTGGTGTTTCATCCATCC 58.981 43.478 0.00 0.00 33.01 3.51
1710 1744 8.843733 CAAGTGACATTGTTTTCTTATTCATCG 58.156 33.333 0.00 0.00 0.00 3.84
1760 1794 1.078759 CAAGTACTGCGCGAAGAGGG 61.079 60.000 24.02 1.12 0.00 4.30
1762 1796 1.080025 GTACTGCGCGAAGAGGGTT 60.080 57.895 24.02 0.00 34.93 4.11
1865 1899 2.289631 TGCTGCACTACAAGTATGCTGT 60.290 45.455 0.00 0.00 40.13 4.40
1900 1936 4.382788 CGCCTTTTTGGGGTACGA 57.617 55.556 0.00 0.00 43.08 3.43
1903 1939 1.542472 CGCCTTTTTGGGGTACGAAAT 59.458 47.619 0.00 0.00 43.08 2.17
1904 1940 2.029739 CGCCTTTTTGGGGTACGAAATT 60.030 45.455 0.00 0.00 43.08 1.82
1905 1941 3.553302 CGCCTTTTTGGGGTACGAAATTT 60.553 43.478 0.00 0.00 43.08 1.82
1906 1942 3.991773 GCCTTTTTGGGGTACGAAATTTC 59.008 43.478 8.20 8.20 32.60 2.17
1910 1946 6.708502 CCTTTTTGGGGTACGAAATTTCAAAT 59.291 34.615 17.99 5.55 32.60 2.32
1913 1949 8.590719 TTTTGGGGTACGAAATTTCAAATTAC 57.409 30.769 17.99 11.77 0.00 1.89
1944 1980 9.582648 AAGGTTTTCGCCCTGTTTTATATATAT 57.417 29.630 0.00 0.00 30.99 0.86
1993 2030 1.068194 CACACCCACAAAAACACACGT 60.068 47.619 0.00 0.00 0.00 4.49
2019 2056 3.060479 TCCAAGGCAGGATACATAGGT 57.940 47.619 0.00 0.00 41.41 3.08
2119 2156 0.528924 AAGCTACATACGACGCACCA 59.471 50.000 0.00 0.00 0.00 4.17
2233 2270 4.724602 GCAGCGAGAGTCGTGGCA 62.725 66.667 8.71 0.00 42.81 4.92
2302 2339 2.963599 TAGAACAGGTTTTCACCCCC 57.036 50.000 0.00 0.00 45.63 5.40
2323 2360 0.329931 ACCAATATTCACCGCCACCA 59.670 50.000 0.00 0.00 0.00 4.17
2500 2539 4.338879 ACCTCAACCAAAGAGATGAATGG 58.661 43.478 0.00 0.00 38.91 3.16
2616 2655 4.536316 GAGACGAGCTCGGTCCTA 57.464 61.111 36.93 0.00 44.95 2.94
2707 2747 3.374402 CGAGTCCGGTCCTGCTGT 61.374 66.667 0.00 0.00 0.00 4.40
3066 3108 1.696314 AACCACCACCTCCACCACT 60.696 57.895 0.00 0.00 0.00 4.00
3165 3214 2.174334 CCAGATGTGGCAGAAACGG 58.826 57.895 0.00 0.00 36.89 4.44
3166 3215 1.308069 CCAGATGTGGCAGAAACGGG 61.308 60.000 0.00 0.00 36.89 5.28
3167 3216 1.675641 AGATGTGGCAGAAACGGGC 60.676 57.895 0.00 0.00 0.00 6.13
3168 3217 1.971167 GATGTGGCAGAAACGGGCA 60.971 57.895 0.00 0.00 38.62 5.36
3174 3223 4.025401 CAGAAACGGGCACGCCAC 62.025 66.667 9.12 0.00 46.04 5.01
3737 3786 0.839277 TGACTCATCCATCGGCCATT 59.161 50.000 2.24 0.00 0.00 3.16
3778 3827 0.108662 TGTCAATGTCGATGAGCGCT 60.109 50.000 11.27 11.27 40.61 5.92
4012 6621 1.227089 CCAGGCGACCTCTCAATCG 60.227 63.158 0.00 0.00 41.32 3.34
4162 6771 2.932184 TCTCCCCAGGTACATACACA 57.068 50.000 0.00 0.00 0.00 3.72
4242 6851 0.038801 TGAGCTCTGCTGACGTTGAG 60.039 55.000 16.19 0.00 39.88 3.02
4307 6916 1.243902 CCATGTTTACAGTGGCCGTT 58.756 50.000 0.00 0.00 0.00 4.44
4354 6963 4.074970 TGAAGGTCTTGAAATCTTCAGCC 58.925 43.478 0.00 0.00 40.13 4.85
4391 7000 3.295273 TCGGGGAGATCGGCATCG 61.295 66.667 0.00 0.00 33.75 3.84
4405 7014 1.297967 CATCGTCAGCTCCGTCGAG 60.298 63.158 0.00 0.00 39.33 4.04
4558 7167 2.511600 CTGGATGTTCCCGTCGCC 60.512 66.667 0.00 0.00 35.03 5.54
4576 7185 2.416701 CGCCATGGATGTTTACAAACCC 60.417 50.000 18.40 0.00 38.11 4.11
4577 7186 2.564947 GCCATGGATGTTTACAAACCCA 59.435 45.455 18.40 4.26 38.11 4.51
4578 7187 3.007398 GCCATGGATGTTTACAAACCCAA 59.993 43.478 18.40 0.00 38.11 4.12
4579 7188 4.323409 GCCATGGATGTTTACAAACCCAAT 60.323 41.667 18.40 0.00 38.11 3.16
4580 7189 5.802821 GCCATGGATGTTTACAAACCCAATT 60.803 40.000 18.40 0.00 38.11 2.32
4581 7190 6.575254 GCCATGGATGTTTACAAACCCAATTA 60.575 38.462 18.40 0.00 38.11 1.40
4586 7195 8.310382 TGGATGTTTACAAACCCAATTATGAAG 58.690 33.333 2.55 0.00 38.11 3.02
4595 7204 7.015098 ACAAACCCAATTATGAAGTGTTGATCA 59.985 33.333 0.00 0.00 0.00 2.92
4605 7214 2.138320 AGTGTTGATCAGACGTTGCTG 58.862 47.619 0.00 0.00 37.24 4.41
4607 7216 0.867746 GTTGATCAGACGTTGCTGCA 59.132 50.000 0.00 0.00 35.86 4.41
4982 7591 2.604686 AGGAAGCCGGTGAGCTCA 60.605 61.111 13.74 13.74 44.11 4.26
5102 7716 6.073331 TGGTGCTTTAATTTAATTTGTGCTGC 60.073 34.615 0.00 0.00 0.00 5.25
5199 7813 1.248486 CCGGCGAGATGGAGAGAATA 58.752 55.000 9.30 0.00 0.00 1.75
5238 7852 4.796231 ATCCGTCGAGCACCGCAC 62.796 66.667 0.00 0.00 38.37 5.34
5270 7884 5.835113 AGCATGGCAAACGTAAGATTTAT 57.165 34.783 0.00 0.00 43.62 1.40
5277 7891 5.558888 GGCAAACGTAAGATTTATTATCGCG 59.441 40.000 0.00 0.00 43.62 5.87
5310 7928 2.035449 ACTTGGTCGTCTTGTTCGATCA 59.965 45.455 0.00 0.00 44.78 2.92
5336 7954 1.080974 GCTGCTCACAACACATGGC 60.081 57.895 0.00 0.00 0.00 4.40
5449 8067 4.210093 ACGACAACCACGGCGACA 62.210 61.111 16.62 0.00 34.93 4.35
5458 8076 2.006888 ACCACGGCGACAAAGATTATG 58.993 47.619 16.62 0.00 0.00 1.90
5682 8300 4.758251 CATGGCGGGAGTGCACGA 62.758 66.667 12.01 0.00 45.89 4.35
5683 8301 4.457496 ATGGCGGGAGTGCACGAG 62.457 66.667 12.01 5.40 45.89 4.18
5704 8322 6.932400 ACGAGTTTTTGTGTAGATACCATCAA 59.068 34.615 0.00 0.00 0.00 2.57
5711 8329 6.902224 TGTGTAGATACCATCAACAATTCG 57.098 37.500 0.00 0.00 0.00 3.34
5726 8344 6.413526 TCAACAATTCGTTTGATTCTTTCGTG 59.586 34.615 7.65 0.00 38.76 4.35
6031 8671 8.915871 AATTTGAAATGAACACATAAGATCCG 57.084 30.769 0.00 0.00 0.00 4.18
6061 8701 3.168035 ACTGCCCATCCAAACAATACA 57.832 42.857 0.00 0.00 0.00 2.29
6190 8830 8.531146 TGATGTGTATGTCTCTGATTGAACTAA 58.469 33.333 0.00 0.00 0.00 2.24
6207 8847 7.493743 TGAACTAACCAGTTTAAACGCATAA 57.506 32.000 12.54 0.00 45.18 1.90
6308 8952 1.086696 CACGGAATTCGCAGGTCAAT 58.913 50.000 0.00 0.00 43.89 2.57
6502 9149 3.132289 CACTATAGGTCAACACCGATGGT 59.868 47.826 4.43 0.00 46.30 3.55
6575 9222 6.573664 TGGATGACAATTCAAGTTAACAGG 57.426 37.500 8.61 0.00 34.61 4.00
6590 9237 5.820947 AGTTAACAGGAGTCACGAACAAATT 59.179 36.000 8.61 0.00 0.00 1.82
6591 9238 4.552166 AACAGGAGTCACGAACAAATTG 57.448 40.909 0.00 0.00 0.00 2.32
6635 9282 5.644206 TGTGCTCAAAACCGCAATAGTTATA 59.356 36.000 0.00 0.00 37.97 0.98
6822 9490 0.592637 CATGTTCAACGCTTGGAGCA 59.407 50.000 0.50 0.00 42.58 4.26
6917 9618 4.389374 CATGGTCACACTAACAGTCCTTT 58.611 43.478 0.00 0.00 0.00 3.11
7048 9813 3.300009 GGCTGAAAATGAACAAGTGTCG 58.700 45.455 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.488308 AGGAAGTTACCTGAGTTTTCTAGTTA 57.512 34.615 0.00 0.00 39.01 2.24
28 29 9.136323 ACTCAATGAGACTATGACATGTGTATA 57.864 33.333 18.20 0.97 33.32 1.47
38 39 7.946381 AGTCTTGTACTCAATGAGACTATGA 57.054 36.000 18.20 6.60 35.96 2.15
43 44 4.390297 GGCAAGTCTTGTACTCAATGAGAC 59.610 45.833 18.20 10.98 37.50 3.36
64 65 5.189180 AGTCAAAATATCAGAACCTCAGGC 58.811 41.667 0.00 0.00 0.00 4.85
117 118 1.192534 GGCGAAGAAGTTTCGACTGTG 59.807 52.381 12.88 0.00 45.80 3.66
124 125 1.982612 GCCAATGGCGAAGAAGTTTC 58.017 50.000 9.14 0.00 39.62 2.78
156 157 0.240411 GCAGAAGGCAGAGCACTTTG 59.760 55.000 0.00 0.00 43.97 2.77
182 183 3.879295 CAGTTCATATTGGGTGCCACTAG 59.121 47.826 0.00 0.00 30.78 2.57
185 186 2.164219 CACAGTTCATATTGGGTGCCAC 59.836 50.000 0.00 0.00 30.78 5.01
194 195 7.048512 GCCTCCTTTACTACACAGTTCATATT 58.951 38.462 0.00 0.00 36.14 1.28
202 203 6.575162 AAAATTGCCTCCTTTACTACACAG 57.425 37.500 0.00 0.00 0.00 3.66
214 215 3.067320 GTGCTCCTGATAAAATTGCCTCC 59.933 47.826 0.00 0.00 0.00 4.30
215 216 3.696051 TGTGCTCCTGATAAAATTGCCTC 59.304 43.478 0.00 0.00 0.00 4.70
259 260 3.454375 ACAACGCCGGATTATCTTACAG 58.546 45.455 5.05 0.00 0.00 2.74
273 274 3.880490 TGATACCCAATGATAACAACGCC 59.120 43.478 0.00 0.00 0.00 5.68
274 275 5.689383 ATGATACCCAATGATAACAACGC 57.311 39.130 0.00 0.00 0.00 4.84
296 297 9.750125 CAATCATAGCTAACACATAACTCAGTA 57.250 33.333 0.00 0.00 0.00 2.74
300 301 6.483307 TGGCAATCATAGCTAACACATAACTC 59.517 38.462 0.00 0.00 0.00 3.01
310 311 5.357878 CCTGAAAGTTGGCAATCATAGCTAA 59.642 40.000 1.92 0.00 0.00 3.09
311 312 4.883585 CCTGAAAGTTGGCAATCATAGCTA 59.116 41.667 1.92 0.00 0.00 3.32
312 313 3.698040 CCTGAAAGTTGGCAATCATAGCT 59.302 43.478 1.92 0.00 0.00 3.32
313 314 3.445096 ACCTGAAAGTTGGCAATCATAGC 59.555 43.478 1.92 0.00 0.00 2.97
314 315 5.882557 ACTACCTGAAAGTTGGCAATCATAG 59.117 40.000 1.92 5.90 0.00 2.23
315 316 5.815581 ACTACCTGAAAGTTGGCAATCATA 58.184 37.500 1.92 0.00 0.00 2.15
316 317 4.666512 ACTACCTGAAAGTTGGCAATCAT 58.333 39.130 1.92 0.00 0.00 2.45
317 318 4.098914 ACTACCTGAAAGTTGGCAATCA 57.901 40.909 1.92 2.19 0.00 2.57
318 319 4.395231 GGTACTACCTGAAAGTTGGCAATC 59.605 45.833 1.92 0.00 34.73 2.67
319 320 4.202524 TGGTACTACCTGAAAGTTGGCAAT 60.203 41.667 1.92 0.00 39.58 3.56
342 343 9.396022 CAACAATCACTAGGTTCTACCATTATT 57.604 33.333 0.00 0.00 41.95 1.40
343 344 8.548877 ACAACAATCACTAGGTTCTACCATTAT 58.451 33.333 0.00 0.00 41.95 1.28
344 345 7.913789 ACAACAATCACTAGGTTCTACCATTA 58.086 34.615 0.00 0.00 41.95 1.90
345 346 6.779860 ACAACAATCACTAGGTTCTACCATT 58.220 36.000 0.00 0.00 41.95 3.16
346 347 6.374417 ACAACAATCACTAGGTTCTACCAT 57.626 37.500 0.00 0.00 41.95 3.55
347 348 5.818678 ACAACAATCACTAGGTTCTACCA 57.181 39.130 0.00 0.00 41.95 3.25
348 349 5.106673 GCAACAACAATCACTAGGTTCTACC 60.107 44.000 0.00 0.00 38.99 3.18
349 350 5.701290 AGCAACAACAATCACTAGGTTCTAC 59.299 40.000 0.00 0.00 0.00 2.59
350 351 5.865085 AGCAACAACAATCACTAGGTTCTA 58.135 37.500 0.00 0.00 0.00 2.10
387 388 7.355101 AGGGAGTAGAATACAACACTGAGATA 58.645 38.462 0.00 0.00 46.26 1.98
391 392 4.710375 GGAGGGAGTAGAATACAACACTGA 59.290 45.833 0.00 0.00 46.26 3.41
400 401 1.854939 TGGGACGGAGGGAGTAGAATA 59.145 52.381 0.00 0.00 0.00 1.75
409 410 1.687123 CTTACACTATGGGACGGAGGG 59.313 57.143 0.00 0.00 0.00 4.30
410 411 2.361438 GTCTTACACTATGGGACGGAGG 59.639 54.545 0.00 0.00 0.00 4.30
412 413 2.019249 CGTCTTACACTATGGGACGGA 58.981 52.381 0.00 0.00 43.69 4.69
413 414 2.486951 CGTCTTACACTATGGGACGG 57.513 55.000 0.00 0.00 43.69 4.79
447 448 9.326413 CCTCTGTTCCATAATATAAGACGTTTT 57.674 33.333 0.00 0.00 0.00 2.43
448 449 7.931948 CCCTCTGTTCCATAATATAAGACGTTT 59.068 37.037 0.00 0.00 0.00 3.60
449 450 7.289317 TCCCTCTGTTCCATAATATAAGACGTT 59.711 37.037 0.00 0.00 0.00 3.99
450 451 6.781014 TCCCTCTGTTCCATAATATAAGACGT 59.219 38.462 0.00 0.00 0.00 4.34
451 452 7.039644 ACTCCCTCTGTTCCATAATATAAGACG 60.040 40.741 0.00 0.00 0.00 4.18
452 453 8.196378 ACTCCCTCTGTTCCATAATATAAGAC 57.804 38.462 0.00 0.00 0.00 3.01
453 454 9.310449 GTACTCCCTCTGTTCCATAATATAAGA 57.690 37.037 0.00 0.00 0.00 2.10
454 455 9.315363 AGTACTCCCTCTGTTCCATAATATAAG 57.685 37.037 0.00 0.00 0.00 1.73
457 458 9.091220 GTTAGTACTCCCTCTGTTCCATAATAT 57.909 37.037 0.00 0.00 0.00 1.28
458 459 8.287350 AGTTAGTACTCCCTCTGTTCCATAATA 58.713 37.037 0.00 0.00 0.00 0.98
459 460 7.133483 AGTTAGTACTCCCTCTGTTCCATAAT 58.867 38.462 0.00 0.00 0.00 1.28
460 461 6.500336 AGTTAGTACTCCCTCTGTTCCATAA 58.500 40.000 0.00 0.00 0.00 1.90
461 462 6.088541 AGTTAGTACTCCCTCTGTTCCATA 57.911 41.667 0.00 0.00 0.00 2.74
462 463 4.949121 AGTTAGTACTCCCTCTGTTCCAT 58.051 43.478 0.00 0.00 0.00 3.41
463 464 4.399483 AGTTAGTACTCCCTCTGTTCCA 57.601 45.455 0.00 0.00 0.00 3.53
464 465 5.245526 TGAAAGTTAGTACTCCCTCTGTTCC 59.754 44.000 0.00 0.00 31.99 3.62
465 466 6.342338 TGAAAGTTAGTACTCCCTCTGTTC 57.658 41.667 0.00 0.00 31.99 3.18
466 467 6.742559 TTGAAAGTTAGTACTCCCTCTGTT 57.257 37.500 0.00 0.00 31.99 3.16
467 468 6.326843 ACTTTGAAAGTTAGTACTCCCTCTGT 59.673 38.462 4.45 0.00 39.04 3.41
468 469 6.760291 ACTTTGAAAGTTAGTACTCCCTCTG 58.240 40.000 4.45 0.00 39.04 3.35
469 470 6.997942 ACTTTGAAAGTTAGTACTCCCTCT 57.002 37.500 4.45 0.00 39.04 3.69
488 489 5.903810 AGACGTTGACAAAGAGAGTACTTT 58.096 37.500 8.17 0.00 40.16 2.66
489 490 5.517322 AGACGTTGACAAAGAGAGTACTT 57.483 39.130 8.17 0.00 0.00 2.24
490 491 5.517322 AAGACGTTGACAAAGAGAGTACT 57.483 39.130 8.17 0.00 0.00 2.73
491 492 9.570488 AATATAAGACGTTGACAAAGAGAGTAC 57.430 33.333 8.17 0.00 0.00 2.73
500 501 9.961265 CTGTCCTATAATATAAGACGTTGACAA 57.039 33.333 5.00 0.00 0.00 3.18
501 502 9.346005 TCTGTCCTATAATATAAGACGTTGACA 57.654 33.333 5.00 0.00 0.00 3.58
502 503 9.828852 CTCTGTCCTATAATATAAGACGTTGAC 57.171 37.037 5.00 0.00 0.00 3.18
503 504 9.788889 TCTCTGTCCTATAATATAAGACGTTGA 57.211 33.333 5.00 3.33 0.00 3.18
506 507 9.661563 CTCTCTCTGTCCTATAATATAAGACGT 57.338 37.037 5.00 0.00 0.00 4.34
507 508 9.661563 ACTCTCTCTGTCCTATAATATAAGACG 57.338 37.037 5.00 1.56 0.00 4.18
517 518 9.835389 GAAAGTTAGTACTCTCTCTGTCCTATA 57.165 37.037 0.00 0.00 31.99 1.31
518 519 8.330247 TGAAAGTTAGTACTCTCTCTGTCCTAT 58.670 37.037 0.00 0.00 31.99 2.57
519 520 7.687388 TGAAAGTTAGTACTCTCTCTGTCCTA 58.313 38.462 0.00 0.00 31.99 2.94
520 521 6.544650 TGAAAGTTAGTACTCTCTCTGTCCT 58.455 40.000 0.00 0.00 31.99 3.85
521 522 6.821031 TGAAAGTTAGTACTCTCTCTGTCC 57.179 41.667 0.00 0.00 31.99 4.02
522 523 8.354426 ACTTTGAAAGTTAGTACTCTCTCTGTC 58.646 37.037 4.45 0.00 39.04 3.51
523 524 8.240267 ACTTTGAAAGTTAGTACTCTCTCTGT 57.760 34.615 4.45 0.00 39.04 3.41
524 525 9.615295 GTACTTTGAAAGTTAGTACTCTCTCTG 57.385 37.037 16.49 0.00 42.81 3.35
556 557 9.521841 TGTAAAACATCTTACATTATGGGACAA 57.478 29.630 0.00 0.00 38.20 3.18
557 558 9.693739 ATGTAAAACATCTTACATTATGGGACA 57.306 29.630 3.68 0.00 45.83 4.02
574 575 7.101652 TCCAGCTACAAAACAATGTAAAACA 57.898 32.000 0.00 0.00 35.48 2.83
592 593 1.902508 TCTTTGTCCTCGATTCCAGCT 59.097 47.619 0.00 0.00 0.00 4.24
637 638 1.310904 GACTGGACTAGGACTAGCGG 58.689 60.000 6.28 0.00 36.66 5.52
646 647 3.577649 ACACGATGTTGACTGGACTAG 57.422 47.619 0.00 0.00 0.00 2.57
649 650 1.798813 GGAACACGATGTTGACTGGAC 59.201 52.381 7.89 0.00 41.28 4.02
650 651 1.270625 GGGAACACGATGTTGACTGGA 60.271 52.381 7.89 0.00 41.28 3.86
651 652 1.156736 GGGAACACGATGTTGACTGG 58.843 55.000 7.89 0.00 41.28 4.00
652 653 1.156736 GGGGAACACGATGTTGACTG 58.843 55.000 7.89 0.00 41.28 3.51
653 654 0.762418 TGGGGAACACGATGTTGACT 59.238 50.000 7.89 0.00 41.28 3.41
654 655 1.600023 TTGGGGAACACGATGTTGAC 58.400 50.000 7.89 2.31 41.28 3.18
655 656 2.350057 TTTGGGGAACACGATGTTGA 57.650 45.000 7.89 0.00 41.28 3.18
656 657 3.444703 TTTTTGGGGAACACGATGTTG 57.555 42.857 7.89 0.00 41.28 3.33
673 674 4.454504 ACGGTGCTGACGAGATTTATTTTT 59.545 37.500 0.00 0.00 34.93 1.94
674 675 4.000988 ACGGTGCTGACGAGATTTATTTT 58.999 39.130 0.00 0.00 34.93 1.82
675 676 3.370978 CACGGTGCTGACGAGATTTATTT 59.629 43.478 0.00 0.00 34.93 1.40
676 677 2.930040 CACGGTGCTGACGAGATTTATT 59.070 45.455 0.00 0.00 34.93 1.40
677 678 2.540515 CACGGTGCTGACGAGATTTAT 58.459 47.619 0.00 0.00 34.93 1.40
678 679 1.403647 CCACGGTGCTGACGAGATTTA 60.404 52.381 1.68 0.00 34.93 1.40
679 680 0.670546 CCACGGTGCTGACGAGATTT 60.671 55.000 1.68 0.00 34.93 2.17
680 681 1.079819 CCACGGTGCTGACGAGATT 60.080 57.895 1.68 0.00 34.93 2.40
681 682 2.573869 CCACGGTGCTGACGAGAT 59.426 61.111 1.68 0.00 34.93 2.75
682 683 4.357947 GCCACGGTGCTGACGAGA 62.358 66.667 1.68 0.00 34.93 4.04
697 698 7.445836 CGAAAAATTCTATACTACTATGCGCC 58.554 38.462 4.18 0.00 0.00 6.53
765 766 4.251268 GCCGTGGATTTACTAGTCTTGTT 58.749 43.478 0.00 0.00 0.00 2.83
769 770 1.407979 CCGCCGTGGATTTACTAGTCT 59.592 52.381 0.00 0.00 42.00 3.24
831 832 0.962356 GGCAAGCAAAGCAGCTAGGA 60.962 55.000 0.00 0.00 45.89 2.94
834 835 0.883833 GAAGGCAAGCAAAGCAGCTA 59.116 50.000 0.00 0.00 45.89 3.32
837 838 0.386478 GACGAAGGCAAGCAAAGCAG 60.386 55.000 0.00 0.00 0.00 4.24
838 839 1.100463 TGACGAAGGCAAGCAAAGCA 61.100 50.000 0.00 0.00 0.00 3.91
839 840 0.661483 GTGACGAAGGCAAGCAAAGC 60.661 55.000 0.00 0.00 0.00 3.51
840 841 0.947244 AGTGACGAAGGCAAGCAAAG 59.053 50.000 0.00 0.00 0.00 2.77
841 842 0.662619 CAGTGACGAAGGCAAGCAAA 59.337 50.000 0.00 0.00 0.00 3.68
842 843 0.463654 ACAGTGACGAAGGCAAGCAA 60.464 50.000 0.00 0.00 0.00 3.91
843 844 0.463654 AACAGTGACGAAGGCAAGCA 60.464 50.000 0.00 0.00 0.00 3.91
844 845 1.461127 CTAACAGTGACGAAGGCAAGC 59.539 52.381 0.00 0.00 0.00 4.01
845 846 2.755650 ACTAACAGTGACGAAGGCAAG 58.244 47.619 0.00 0.00 0.00 4.01
847 848 4.325028 TTTACTAACAGTGACGAAGGCA 57.675 40.909 0.00 0.00 0.00 4.75
848 849 4.748600 AGTTTTACTAACAGTGACGAAGGC 59.251 41.667 0.00 0.00 0.00 4.35
849 850 5.981315 TGAGTTTTACTAACAGTGACGAAGG 59.019 40.000 0.00 0.00 0.00 3.46
850 851 7.222224 ACTTGAGTTTTACTAACAGTGACGAAG 59.778 37.037 0.00 0.00 0.00 3.79
851 852 7.037438 ACTTGAGTTTTACTAACAGTGACGAA 58.963 34.615 0.00 0.00 0.00 3.85
852 853 6.567050 ACTTGAGTTTTACTAACAGTGACGA 58.433 36.000 0.00 0.00 0.00 4.20
1069 1098 2.584970 ACGCCACACAGACACACG 60.585 61.111 0.00 0.00 0.00 4.49
1330 1359 4.567385 GCGGCTCTGCTCCTCTCG 62.567 72.222 0.00 0.00 0.00 4.04
1636 1667 0.522626 CACCAGAATGTGATGCGCAA 59.477 50.000 17.11 0.00 38.55 4.85
1865 1899 2.747446 GGCGCAGAAGAAACTTTATGGA 59.253 45.455 10.83 0.00 0.00 3.41
1913 1949 1.138069 ACAGGGCGAAAACCTTTTTGG 59.862 47.619 0.00 0.00 35.78 3.28
1922 1958 9.727859 TGCTATATATATAAAACAGGGCGAAAA 57.272 29.630 4.06 0.00 0.00 2.29
1944 1980 4.661222 TGGATTGTTGGTGATCTTTGCTA 58.339 39.130 0.00 0.00 0.00 3.49
1993 2030 3.111484 TGTATCCTGCCTTGGATGTGTA 58.889 45.455 11.71 0.00 45.58 2.90
2091 2128 4.201930 CGTCGTATGTAGCTTCTTCTCCTT 60.202 45.833 0.00 0.00 0.00 3.36
2119 2156 4.431131 CACCGCCTTGGAGCCCAT 62.431 66.667 0.00 0.00 42.00 4.00
2233 2270 1.607251 CGTACCCTTCTTGAAGGCGTT 60.607 52.381 20.71 11.21 38.63 4.84
2302 2339 0.655733 GTGGCGGTGAATATTGGTCG 59.344 55.000 0.00 0.00 0.00 4.79
2399 2437 3.276846 GTGGTGTCGCGGTGCTTT 61.277 61.111 6.13 0.00 0.00 3.51
2441 2479 1.229082 AGGTGGCGTCAAGGTCCTA 60.229 57.895 0.00 0.00 0.00 2.94
2481 2519 5.477984 CCTTTCCATTCATCTCTTTGGTTGA 59.522 40.000 0.00 0.00 0.00 3.18
2851 2892 1.446272 CTGGACTTCTTCGGCGTCC 60.446 63.158 6.85 5.84 45.76 4.79
2955 2997 2.754375 GTGGTGATGGTTCGGGGT 59.246 61.111 0.00 0.00 0.00 4.95
3121 3170 4.070552 GCGGGCTCGGACTCTGTT 62.071 66.667 8.71 0.00 36.79 3.16
3569 3618 5.983118 AGCCAATTTGAAAACGTCCTAAAAG 59.017 36.000 0.00 0.00 0.00 2.27
3570 3619 5.751028 CAGCCAATTTGAAAACGTCCTAAAA 59.249 36.000 0.00 0.00 0.00 1.52
3571 3620 5.067936 TCAGCCAATTTGAAAACGTCCTAAA 59.932 36.000 0.00 0.00 0.00 1.85
3572 3621 4.580995 TCAGCCAATTTGAAAACGTCCTAA 59.419 37.500 0.00 0.00 0.00 2.69
3573 3622 4.138290 TCAGCCAATTTGAAAACGTCCTA 58.862 39.130 0.00 0.00 0.00 2.94
3574 3623 2.955660 TCAGCCAATTTGAAAACGTCCT 59.044 40.909 0.00 0.00 0.00 3.85
3575 3624 3.363341 TCAGCCAATTTGAAAACGTCC 57.637 42.857 0.00 0.00 0.00 4.79
3576 3625 4.382754 GTCATCAGCCAATTTGAAAACGTC 59.617 41.667 0.00 0.00 0.00 4.34
3577 3626 4.298332 GTCATCAGCCAATTTGAAAACGT 58.702 39.130 0.00 0.00 0.00 3.99
3578 3627 3.361644 CGTCATCAGCCAATTTGAAAACG 59.638 43.478 0.00 3.34 33.43 3.60
3579 3628 4.298332 ACGTCATCAGCCAATTTGAAAAC 58.702 39.130 0.00 0.00 0.00 2.43
3658 3707 2.865343 TCTTCCGGTAGATTCTTCGC 57.135 50.000 6.70 0.00 0.00 4.70
3778 3827 1.601419 CTACCTTTGGCGAGACGGGA 61.601 60.000 0.00 0.00 0.00 5.14
4012 6621 1.196200 GCTCTGTCGAATCGCTTCTC 58.804 55.000 0.00 0.00 0.00 2.87
4162 6771 6.422701 CAGAACTGACAATGAAATGTTGCATT 59.577 34.615 0.00 0.00 35.24 3.56
4220 6829 1.128136 CAACGTCAGCAGAGCTCATTG 59.872 52.381 17.77 10.88 36.40 2.82
4307 6916 2.048222 CTCCTTGCCGTCTTCGCA 60.048 61.111 0.00 0.00 35.54 5.10
4354 6963 1.202582 ACGAACTCCTTCATCACCTCG 59.797 52.381 0.00 0.00 0.00 4.63
4377 6986 1.006805 CTGACGATGCCGATCTCCC 60.007 63.158 0.00 0.00 39.50 4.30
4405 7014 2.126346 GCCATGGCGTTCTTGTGC 60.126 61.111 23.48 0.00 0.00 4.57
4548 7157 2.189257 CATCCATGGCGACGGGAA 59.811 61.111 6.96 0.00 39.50 3.97
4558 7167 8.256605 TCATAATTGGGTTTGTAAACATCCATG 58.743 33.333 9.44 4.57 40.63 3.66
4576 7185 7.065216 ACGTCTGATCAACACTTCATAATTG 57.935 36.000 0.00 0.00 0.00 2.32
4577 7186 7.521529 CAACGTCTGATCAACACTTCATAATT 58.478 34.615 0.00 0.00 0.00 1.40
4578 7187 6.402550 GCAACGTCTGATCAACACTTCATAAT 60.403 38.462 0.00 0.00 0.00 1.28
4579 7188 5.107104 GCAACGTCTGATCAACACTTCATAA 60.107 40.000 0.00 0.00 0.00 1.90
4580 7189 4.388773 GCAACGTCTGATCAACACTTCATA 59.611 41.667 0.00 0.00 0.00 2.15
4581 7190 3.187227 GCAACGTCTGATCAACACTTCAT 59.813 43.478 0.00 0.00 0.00 2.57
4586 7195 1.398960 GCAGCAACGTCTGATCAACAC 60.399 52.381 8.35 0.00 36.19 3.32
4595 7204 2.949106 GCACATGCAGCAACGTCT 59.051 55.556 0.00 0.00 41.59 4.18
4605 7214 2.124403 CTCCTCCCCTGCACATGC 60.124 66.667 0.00 0.00 42.50 4.06
4607 7216 0.622665 CTTTCTCCTCCCCTGCACAT 59.377 55.000 0.00 0.00 0.00 3.21
4616 7225 2.373224 CCCTTGCATTCTTTCTCCTCC 58.627 52.381 0.00 0.00 0.00 4.30
4617 7226 1.747924 GCCCTTGCATTCTTTCTCCTC 59.252 52.381 0.00 0.00 37.47 3.71
4618 7227 1.357079 AGCCCTTGCATTCTTTCTCCT 59.643 47.619 0.00 0.00 41.13 3.69
4619 7228 1.747924 GAGCCCTTGCATTCTTTCTCC 59.252 52.381 0.00 0.00 41.13 3.71
4725 7334 0.834261 TCCCTGTGAATCACCGGACA 60.834 55.000 22.79 8.12 40.41 4.02
5064 7678 4.320608 AAAGCACCATTCACGATTGTTT 57.679 36.364 0.00 0.00 0.00 2.83
5102 7716 3.913573 CGACGGAATTCGCCTGCG 61.914 66.667 4.92 4.92 43.89 5.18
5270 7884 5.465390 CCAAGTAAAATGGAGATCGCGATAA 59.535 40.000 23.76 8.65 40.56 1.75
5277 7891 5.420409 AGACGACCAAGTAAAATGGAGATC 58.580 41.667 0.00 0.00 40.56 2.75
5310 7928 2.480419 GTGTTGTGAGCAGCTAACGATT 59.520 45.455 2.80 0.00 0.00 3.34
5449 8067 0.657840 GCCGCGCTGTCATAATCTTT 59.342 50.000 5.56 0.00 0.00 2.52
5474 8092 1.608025 GGATGTCGTTCTTGTCAGGCA 60.608 52.381 0.00 0.00 0.00 4.75
5478 8096 3.026630 GACTGGATGTCGTTCTTGTCA 57.973 47.619 0.00 0.00 35.81 3.58
5682 8300 8.458573 TTGTTGATGGTATCTACACAAAAACT 57.541 30.769 5.76 0.00 42.93 2.66
5683 8301 9.691362 AATTGTTGATGGTATCTACACAAAAAC 57.309 29.630 5.76 0.00 42.93 2.43
5704 8322 5.816919 ACACGAAAGAATCAAACGAATTGT 58.183 33.333 0.00 0.00 40.11 2.71
5941 8566 3.129287 GGGTTGTTTGCATGAGGAGTATG 59.871 47.826 0.00 0.00 0.00 2.39
6031 8671 5.659440 TTGGATGGGCAGTATTTTTCTTC 57.341 39.130 0.00 0.00 0.00 2.87
6061 8701 4.163078 AGAACCAGAATTCTCCATCGATGT 59.837 41.667 23.27 4.09 33.50 3.06
6190 8830 7.675962 TTCTGTATTATGCGTTTAAACTGGT 57.324 32.000 16.01 4.48 0.00 4.00
6225 8865 7.189512 AGCACGATCATGAAGTTTTATTTAGC 58.810 34.615 0.00 0.89 0.00 3.09
6308 8952 3.588842 ACAATCCACCTCTCTCATTTCCA 59.411 43.478 0.00 0.00 0.00 3.53
6502 9149 7.230510 GGTAATCATATTGCAAGGGTGTCATTA 59.769 37.037 4.94 2.77 0.00 1.90
6575 9222 4.149922 TCATCGACAATTTGTTCGTGACTC 59.850 41.667 3.08 0.00 0.00 3.36
6641 9288 7.649057 TGATGACATCGACGTATCTAAAATCT 58.351 34.615 10.79 0.00 0.00 2.40
6654 9302 5.697473 TCTATTCCTCTGATGACATCGAC 57.303 43.478 10.79 0.00 0.00 4.20
6660 9308 8.099364 TGTTTGTTTTCTATTCCTCTGATGAC 57.901 34.615 0.00 0.00 0.00 3.06
6822 9490 9.023962 TGCATTCTCCAGTTTCAAACTTATTAT 57.976 29.630 0.00 0.00 40.46 1.28
6917 9618 0.888619 CGTCAGTGCTTAGGAGGTGA 59.111 55.000 0.00 0.00 0.00 4.02
7048 9813 6.423905 GCTTCCTTTGTTATTCTTTTGGAACC 59.576 38.462 0.00 0.00 36.70 3.62


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

AutoCloner maintained by Alex Coulton.