Multiple sequence alignment - TraesCS6D01G179800

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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 TraesCS6D01G179800 chr6D 100.000 2411 0 0 1 2411 195491764 195489354 0.000000e+00 4453.0
1 TraesCS6D01G179800 chr6D 95.096 469 21 2 1 468 366214833 366214366 0.000000e+00 737.0
2 TraesCS6D01G179800 chr6B 91.739 1731 133 7 655 2378 384829598 384827871 0.000000e+00 2396.0
3 TraesCS6D01G179800 chr6B 88.776 294 25 5 367 654 571319570 571319861 1.060000e-93 353.0
4 TraesCS6D01G179800 chr6B 97.143 35 0 1 2378 2411 49536774 49536808 9.310000e-05 58.4
5 TraesCS6D01G179800 chr6A 91.287 1228 90 5 1153 2378 260423593 260424805 0.000000e+00 1659.0
6 TraesCS6D01G179800 chr6A 95.316 491 21 1 655 1145 260420426 260420914 0.000000e+00 778.0
7 TraesCS6D01G179800 chr3A 89.024 656 65 5 1 654 106054987 106055637 0.000000e+00 806.0
8 TraesCS6D01G179800 chr3A 94.915 472 23 1 1 471 269561455 269560984 0.000000e+00 737.0
9 TraesCS6D01G179800 chr3A 100.000 30 0 0 2381 2410 587905242 587905213 3.350000e-04 56.5
10 TraesCS6D01G179800 chr3D 95.736 469 19 1 1 468 169665600 169665132 0.000000e+00 754.0
11 TraesCS6D01G179800 chr3D 78.993 457 80 14 192 638 413127750 413127300 5.040000e-77 298.0
12 TraesCS6D01G179800 chr7D 95.522 469 20 1 1 468 317974626 317975094 0.000000e+00 749.0
13 TraesCS6D01G179800 chr7D 94.915 472 23 1 1 471 501634839 501634368 0.000000e+00 737.0
14 TraesCS6D01G179800 chr7D 84.500 200 26 5 2182 2379 506651534 506651338 2.450000e-45 193.0
15 TraesCS6D01G179800 chr7D 84.236 203 25 7 2179 2379 506664985 506664788 8.800000e-45 191.0
16 TraesCS6D01G179800 chr7D 100.000 33 0 0 2379 2411 21768697 21768729 7.200000e-06 62.1
17 TraesCS6D01G179800 chr7D 100.000 31 0 0 2381 2411 549852129 549852159 9.310000e-05 58.4
18 TraesCS6D01G179800 chr7D 100.000 28 0 0 2376 2403 417353547 417353574 4.000000e-03 52.8
19 TraesCS6D01G179800 chr5A 95.289 467 20 2 1 466 27414583 27415048 0.000000e+00 739.0
20 TraesCS6D01G179800 chr4D 95.096 469 22 1 1 468 94745540 94746008 0.000000e+00 737.0
21 TraesCS6D01G179800 chr4D 78.243 478 83 20 189 654 191848818 191849286 1.090000e-73 287.0
22 TraesCS6D01G179800 chr4D 78.070 456 84 14 189 635 216916527 216916975 8.490000e-70 274.0
23 TraesCS6D01G179800 chr4D 100.000 31 0 0 2381 2411 449735617 449735647 9.310000e-05 58.4
24 TraesCS6D01G179800 chr1D 95.096 469 22 1 1 468 104947703 104948171 0.000000e+00 737.0
25 TraesCS6D01G179800 chr1D 80.741 135 24 2 2218 2351 26637951 26638084 1.180000e-18 104.0
26 TraesCS6D01G179800 chr1D 95.122 41 0 2 2372 2411 257429041 257429080 2.000000e-06 63.9
27 TraesCS6D01G179800 chr1B 78.781 443 82 11 201 635 230847489 230847927 1.090000e-73 287.0
28 TraesCS6D01G179800 chr2D 78.125 480 82 22 189 654 268606352 268606822 1.410000e-72 283.0
29 TraesCS6D01G179800 chr2D 77.944 467 81 17 201 654 388892142 388891685 3.050000e-69 272.0
30 TraesCS6D01G179800 chr2D 84.211 76 10 1 1697 1772 398708623 398708550 3.320000e-09 73.1
31 TraesCS6D01G179800 chr2D 84.211 76 10 1 1697 1772 403352450 403352377 3.320000e-09 73.1
32 TraesCS6D01G179800 chr2B 77.974 454 90 9 189 635 348439881 348440331 2.360000e-70 276.0
33 TraesCS6D01G179800 chr2B 100.000 32 0 0 2380 2411 34439698 34439729 2.590000e-05 60.2
34 TraesCS6D01G179800 chr5B 85.930 199 24 4 2181 2377 360766075 360766271 2.430000e-50 209.0
35 TraesCS6D01G179800 chr4B 82.741 197 29 2 2181 2377 366947668 366947477 1.150000e-38 171.0
36 TraesCS6D01G179800 chr4A 81.871 171 17 7 2204 2372 629866434 629866276 5.410000e-27 132.0
37 TraesCS6D01G179800 chr7B 100.000 31 0 0 2381 2411 430844543 430844513 9.310000e-05 58.4
38 TraesCS6D01G179800 chr2A 100.000 31 0 0 2381 2411 46835967 46835937 9.310000e-05 58.4
39 TraesCS6D01G179800 chr1A 100.000 31 0 0 2381 2411 117976293 117976323 9.310000e-05 58.4


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 TraesCS6D01G179800 chr6D 195489354 195491764 2410 True 4453.0 4453 100.0000 1 2411 1 chr6D.!!$R1 2410
1 TraesCS6D01G179800 chr6B 384827871 384829598 1727 True 2396.0 2396 91.7390 655 2378 1 chr6B.!!$R1 1723
2 TraesCS6D01G179800 chr6A 260420426 260424805 4379 False 1218.5 1659 93.3015 655 2378 2 chr6A.!!$F1 1723
3 TraesCS6D01G179800 chr3A 106054987 106055637 650 False 806.0 806 89.0240 1 654 1 chr3A.!!$F1 653

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
508 510 0.026285 CGACCTTATTTTGCCGAGCG 59.974 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 4844 0.457851 TGTTGTTTGTTTCTGGCCCG 59.542 50.0 0.0 0.0 0.0 6.13 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
21 22 0.595825 GTGAAACTTGCTGCTGGTGC 60.596 55.000 0.00 0.00 40.20 5.01
38 39 2.553466 GGTGCAGTTGTGTAATGGGGTA 60.553 50.000 0.00 0.00 0.00 3.69
43 44 2.026262 AGTTGTGTAATGGGGTAGCTGG 60.026 50.000 0.00 0.00 0.00 4.85
70 71 6.925718 TGCTGAAGCTATATCATGTTGTACTC 59.074 38.462 3.61 0.00 42.66 2.59
71 72 7.151308 GCTGAAGCTATATCATGTTGTACTCT 58.849 38.462 0.00 0.00 38.21 3.24
224 225 3.961480 AGCTTGCTAATTGGGTTTTCC 57.039 42.857 0.00 0.00 39.75 3.13
228 229 5.721480 AGCTTGCTAATTGGGTTTTCCTATT 59.279 36.000 0.00 0.00 42.24 1.73
236 237 3.223435 TGGGTTTTCCTATTGCAAACGA 58.777 40.909 1.71 0.00 40.46 3.85
237 238 3.004944 TGGGTTTTCCTATTGCAAACGAC 59.995 43.478 1.71 0.00 40.46 4.34
240 241 5.124936 GGGTTTTCCTATTGCAAACGACTAT 59.875 40.000 1.71 0.00 40.46 2.12
253 254 5.504994 GCAAACGACTATTGAGAAAACACCA 60.505 40.000 0.00 0.00 0.00 4.17
257 258 4.935205 CGACTATTGAGAAAACACCATGGA 59.065 41.667 21.47 0.00 0.00 3.41
280 281 2.591715 ACCTCAGGCAACGCACAC 60.592 61.111 0.00 0.00 46.39 3.82
283 284 1.595109 CTCAGGCAACGCACACAGA 60.595 57.895 0.00 0.00 46.39 3.41
299 300 5.006746 GCACACAGATTCTAGGAATAAACCG 59.993 44.000 0.00 0.00 34.73 4.44
337 338 4.212004 ACAATCACACACGACATTCTCTTG 59.788 41.667 0.00 0.00 0.00 3.02
363 365 0.666374 GTTTGCTTACGCCACCTTGT 59.334 50.000 0.00 0.00 34.43 3.16
365 367 1.791103 TTGCTTACGCCACCTTGTGC 61.791 55.000 0.00 0.00 34.43 4.57
366 368 2.258013 GCTTACGCCACCTTGTGCA 61.258 57.895 0.00 0.00 31.34 4.57
367 369 1.791103 GCTTACGCCACCTTGTGCAA 61.791 55.000 0.00 0.00 31.34 4.08
368 370 0.665835 CTTACGCCACCTTGTGCAAA 59.334 50.000 0.00 0.00 31.34 3.68
369 371 0.382515 TTACGCCACCTTGTGCAAAC 59.617 50.000 0.00 0.00 31.34 2.93
370 372 1.777030 TACGCCACCTTGTGCAAACG 61.777 55.000 0.00 0.00 31.34 3.60
371 373 2.804856 GCCACCTTGTGCAAACGT 59.195 55.556 0.00 0.00 31.34 3.99
372 374 1.140804 GCCACCTTGTGCAAACGTT 59.859 52.632 0.00 0.00 31.34 3.99
373 375 0.459411 GCCACCTTGTGCAAACGTTT 60.459 50.000 7.96 7.96 31.34 3.60
374 376 2.003196 CCACCTTGTGCAAACGTTTT 57.997 45.000 11.66 0.00 31.34 2.43
375 377 1.923864 CCACCTTGTGCAAACGTTTTC 59.076 47.619 11.66 7.34 31.34 2.29
376 378 1.923864 CACCTTGTGCAAACGTTTTCC 59.076 47.619 11.66 6.16 0.00 3.13
377 379 1.822371 ACCTTGTGCAAACGTTTTCCT 59.178 42.857 11.66 0.00 0.00 3.36
378 380 2.232696 ACCTTGTGCAAACGTTTTCCTT 59.767 40.909 11.66 0.00 0.00 3.36
379 381 2.602660 CCTTGTGCAAACGTTTTCCTTG 59.397 45.455 11.66 1.16 0.00 3.61
380 382 2.285827 TGTGCAAACGTTTTCCTTGG 57.714 45.000 11.66 0.00 0.00 3.61
381 383 1.819288 TGTGCAAACGTTTTCCTTGGA 59.181 42.857 11.66 0.00 0.00 3.53
382 384 2.159310 TGTGCAAACGTTTTCCTTGGAG 60.159 45.455 11.66 0.00 0.00 3.86
383 385 2.096248 TGCAAACGTTTTCCTTGGAGT 58.904 42.857 11.66 0.00 0.00 3.85
384 386 2.159310 TGCAAACGTTTTCCTTGGAGTG 60.159 45.455 11.66 0.00 0.00 3.51
385 387 2.098443 GCAAACGTTTTCCTTGGAGTGA 59.902 45.455 11.66 0.00 0.00 3.41
386 388 3.691498 CAAACGTTTTCCTTGGAGTGAC 58.309 45.455 11.66 0.00 0.00 3.67
387 389 3.277142 AACGTTTTCCTTGGAGTGACT 57.723 42.857 0.00 0.00 0.00 3.41
388 390 2.561569 ACGTTTTCCTTGGAGTGACTG 58.438 47.619 0.00 0.00 0.00 3.51
389 391 2.093128 ACGTTTTCCTTGGAGTGACTGT 60.093 45.455 0.00 0.00 0.00 3.55
390 392 2.287915 CGTTTTCCTTGGAGTGACTGTG 59.712 50.000 0.00 0.00 0.00 3.66
391 393 3.279434 GTTTTCCTTGGAGTGACTGTGT 58.721 45.455 0.00 0.00 0.00 3.72
392 394 2.620251 TTCCTTGGAGTGACTGTGTG 57.380 50.000 0.00 0.00 0.00 3.82
393 395 0.758734 TCCTTGGAGTGACTGTGTGG 59.241 55.000 0.00 0.00 0.00 4.17
394 396 0.469917 CCTTGGAGTGACTGTGTGGT 59.530 55.000 0.00 0.00 0.00 4.16
395 397 1.586422 CTTGGAGTGACTGTGTGGTG 58.414 55.000 0.00 0.00 0.00 4.17
396 398 0.908910 TTGGAGTGACTGTGTGGTGT 59.091 50.000 0.00 0.00 0.00 4.16
397 399 0.177836 TGGAGTGACTGTGTGGTGTG 59.822 55.000 0.00 0.00 0.00 3.82
398 400 0.178068 GGAGTGACTGTGTGGTGTGT 59.822 55.000 0.00 0.00 0.00 3.72
399 401 1.411246 GGAGTGACTGTGTGGTGTGTA 59.589 52.381 0.00 0.00 0.00 2.90
400 402 2.037251 GGAGTGACTGTGTGGTGTGTAT 59.963 50.000 0.00 0.00 0.00 2.29
401 403 3.257375 GGAGTGACTGTGTGGTGTGTATA 59.743 47.826 0.00 0.00 0.00 1.47
402 404 4.081642 GGAGTGACTGTGTGGTGTGTATAT 60.082 45.833 0.00 0.00 0.00 0.86
403 405 5.126545 GGAGTGACTGTGTGGTGTGTATATA 59.873 44.000 0.00 0.00 0.00 0.86
404 406 5.962433 AGTGACTGTGTGGTGTGTATATAC 58.038 41.667 5.89 5.89 0.00 1.47
405 407 4.796830 GTGACTGTGTGGTGTGTATATACG 59.203 45.833 8.33 0.00 0.00 3.06
406 408 4.701171 TGACTGTGTGGTGTGTATATACGA 59.299 41.667 8.33 0.00 0.00 3.43
407 409 5.183522 TGACTGTGTGGTGTGTATATACGAA 59.816 40.000 8.33 0.00 0.00 3.85
408 410 5.404946 ACTGTGTGGTGTGTATATACGAAC 58.595 41.667 8.33 8.45 0.00 3.95
409 411 4.413969 TGTGTGGTGTGTATATACGAACG 58.586 43.478 8.33 0.00 0.00 3.95
410 412 3.792956 GTGTGGTGTGTATATACGAACGG 59.207 47.826 8.33 0.00 0.00 4.44
411 413 3.693578 TGTGGTGTGTATATACGAACGGA 59.306 43.478 8.33 0.00 0.00 4.69
412 414 4.157472 TGTGGTGTGTATATACGAACGGAA 59.843 41.667 8.33 0.00 0.00 4.30
413 415 5.101628 GTGGTGTGTATATACGAACGGAAA 58.898 41.667 8.33 0.00 0.00 3.13
414 416 5.004726 GTGGTGTGTATATACGAACGGAAAC 59.995 44.000 8.33 0.00 0.00 2.78
415 417 5.101628 GGTGTGTATATACGAACGGAAACA 58.898 41.667 8.33 1.95 0.00 2.83
416 418 5.750067 GGTGTGTATATACGAACGGAAACAT 59.250 40.000 8.33 0.00 0.00 2.71
417 419 6.256321 GGTGTGTATATACGAACGGAAACATT 59.744 38.462 8.33 0.00 0.00 2.71
418 420 7.201548 GGTGTGTATATACGAACGGAAACATTT 60.202 37.037 8.33 0.00 0.00 2.32
419 421 8.806634 GTGTGTATATACGAACGGAAACATTTA 58.193 33.333 8.33 0.00 0.00 1.40
420 422 9.022915 TGTGTATATACGAACGGAAACATTTAG 57.977 33.333 8.33 0.00 0.00 1.85
421 423 8.000435 GTGTATATACGAACGGAAACATTTAGC 59.000 37.037 8.33 0.00 0.00 3.09
422 424 2.867456 ACGAACGGAAACATTTAGCG 57.133 45.000 0.00 0.00 0.00 4.26
423 425 1.461897 ACGAACGGAAACATTTAGCGG 59.538 47.619 0.00 0.00 0.00 5.52
424 426 1.461897 CGAACGGAAACATTTAGCGGT 59.538 47.619 0.00 0.00 0.00 5.68
425 427 2.723618 CGAACGGAAACATTTAGCGGTG 60.724 50.000 0.00 0.00 0.00 4.94
426 428 2.172851 ACGGAAACATTTAGCGGTGA 57.827 45.000 0.00 0.00 0.00 4.02
427 429 1.802365 ACGGAAACATTTAGCGGTGAC 59.198 47.619 0.00 0.00 0.00 3.67
428 430 2.073816 CGGAAACATTTAGCGGTGACT 58.926 47.619 0.00 0.00 0.00 3.41
429 431 2.159707 CGGAAACATTTAGCGGTGACTG 60.160 50.000 0.00 0.00 0.00 3.51
430 432 3.071479 GGAAACATTTAGCGGTGACTGA 58.929 45.455 3.78 0.00 0.00 3.41
431 433 3.120304 GGAAACATTTAGCGGTGACTGAC 60.120 47.826 3.78 0.00 0.00 3.51
432 434 3.402628 AACATTTAGCGGTGACTGACT 57.597 42.857 3.78 0.00 0.00 3.41
433 435 2.688507 ACATTTAGCGGTGACTGACTG 58.311 47.619 3.78 0.00 0.00 3.51
434 436 2.037251 ACATTTAGCGGTGACTGACTGT 59.963 45.455 3.78 0.00 32.87 3.55
435 437 2.148916 TTTAGCGGTGACTGACTGTG 57.851 50.000 0.00 0.00 32.87 3.66
436 438 1.037493 TTAGCGGTGACTGACTGTGT 58.963 50.000 0.00 0.00 32.87 3.72
437 439 0.313987 TAGCGGTGACTGACTGTGTG 59.686 55.000 0.00 0.00 32.87 3.82
438 440 1.956170 GCGGTGACTGACTGTGTGG 60.956 63.158 0.00 0.00 32.87 4.17
439 441 1.300931 CGGTGACTGACTGTGTGGG 60.301 63.158 0.00 0.00 0.00 4.61
440 442 1.744320 CGGTGACTGACTGTGTGGGA 61.744 60.000 0.00 0.00 0.00 4.37
441 443 0.687354 GGTGACTGACTGTGTGGGAT 59.313 55.000 0.00 0.00 0.00 3.85
442 444 1.609061 GGTGACTGACTGTGTGGGATG 60.609 57.143 0.00 0.00 0.00 3.51
443 445 1.070758 GTGACTGACTGTGTGGGATGT 59.929 52.381 0.00 0.00 0.00 3.06
444 446 2.299013 GTGACTGACTGTGTGGGATGTA 59.701 50.000 0.00 0.00 0.00 2.29
445 447 2.299013 TGACTGACTGTGTGGGATGTAC 59.701 50.000 0.00 0.00 0.00 2.90
446 448 2.563179 GACTGACTGTGTGGGATGTACT 59.437 50.000 0.00 0.00 0.00 2.73
447 449 2.972713 ACTGACTGTGTGGGATGTACTT 59.027 45.455 0.00 0.00 0.00 2.24
448 450 4.157246 ACTGACTGTGTGGGATGTACTTA 58.843 43.478 0.00 0.00 0.00 2.24
449 451 4.021368 ACTGACTGTGTGGGATGTACTTAC 60.021 45.833 0.00 0.00 0.00 2.34
450 452 3.057104 TGACTGTGTGGGATGTACTTACG 60.057 47.826 0.00 0.00 0.00 3.18
451 453 3.159472 ACTGTGTGGGATGTACTTACGA 58.841 45.455 0.00 0.00 0.00 3.43
452 454 3.057033 ACTGTGTGGGATGTACTTACGAC 60.057 47.826 0.00 0.00 0.00 4.34
453 455 2.231964 TGTGTGGGATGTACTTACGACC 59.768 50.000 4.05 0.00 0.00 4.79
454 456 1.473677 TGTGGGATGTACTTACGACCG 59.526 52.381 4.05 0.00 0.00 4.79
455 457 1.745087 GTGGGATGTACTTACGACCGA 59.255 52.381 0.00 0.00 0.00 4.69
456 458 2.164219 GTGGGATGTACTTACGACCGAA 59.836 50.000 0.00 0.00 0.00 4.30
457 459 2.824936 TGGGATGTACTTACGACCGAAA 59.175 45.455 0.00 0.00 0.00 3.46
458 460 3.257873 TGGGATGTACTTACGACCGAAAA 59.742 43.478 0.00 0.00 0.00 2.29
459 461 4.081531 TGGGATGTACTTACGACCGAAAAT 60.082 41.667 0.00 0.00 0.00 1.82
460 462 4.269363 GGGATGTACTTACGACCGAAAATG 59.731 45.833 0.00 0.00 0.00 2.32
461 463 5.104374 GGATGTACTTACGACCGAAAATGA 58.896 41.667 0.00 0.00 0.00 2.57
462 464 5.751990 GGATGTACTTACGACCGAAAATGAT 59.248 40.000 0.00 0.00 0.00 2.45
463 465 6.257193 GGATGTACTTACGACCGAAAATGATT 59.743 38.462 0.00 0.00 0.00 2.57
464 466 7.201582 GGATGTACTTACGACCGAAAATGATTT 60.202 37.037 0.00 0.00 0.00 2.17
465 467 7.052565 TGTACTTACGACCGAAAATGATTTC 57.947 36.000 0.00 0.00 41.27 2.17
475 477 4.574599 GAAAATGATTTCGCATAGGGCT 57.425 40.909 0.00 0.00 41.67 5.19
476 478 4.540824 GAAAATGATTTCGCATAGGGCTC 58.459 43.478 0.00 0.00 41.67 4.70
477 479 1.800805 ATGATTTCGCATAGGGCTCG 58.199 50.000 0.00 0.00 41.67 5.03
478 480 0.880278 TGATTTCGCATAGGGCTCGC 60.880 55.000 0.00 0.00 41.67 5.03
479 481 1.569479 GATTTCGCATAGGGCTCGCC 61.569 60.000 0.00 0.00 41.67 5.54
480 482 4.585526 TTCGCATAGGGCTCGCCG 62.586 66.667 1.24 0.00 41.67 6.46
483 485 4.971125 GCATAGGGCTCGCCGGTC 62.971 72.222 1.90 0.00 40.25 4.79
484 486 4.647615 CATAGGGCTCGCCGGTCG 62.648 72.222 1.90 7.73 36.85 4.79
502 504 1.195900 TCGCACACGACCTTATTTTGC 59.804 47.619 0.00 0.00 45.12 3.68
503 505 1.727857 CGCACACGACCTTATTTTGCC 60.728 52.381 0.00 0.00 43.93 4.52
504 506 1.727857 GCACACGACCTTATTTTGCCG 60.728 52.381 0.00 0.00 0.00 5.69
505 507 1.801771 CACACGACCTTATTTTGCCGA 59.198 47.619 0.00 0.00 0.00 5.54
506 508 2.073816 ACACGACCTTATTTTGCCGAG 58.926 47.619 0.00 0.00 0.00 4.63
507 509 1.084289 ACGACCTTATTTTGCCGAGC 58.916 50.000 0.00 0.00 0.00 5.03
508 510 0.026285 CGACCTTATTTTGCCGAGCG 59.974 55.000 0.00 0.00 0.00 5.03
509 511 1.084289 GACCTTATTTTGCCGAGCGT 58.916 50.000 0.00 0.00 0.00 5.07
510 512 0.802494 ACCTTATTTTGCCGAGCGTG 59.198 50.000 0.00 0.00 0.00 5.34
511 513 0.802494 CCTTATTTTGCCGAGCGTGT 59.198 50.000 0.00 0.00 0.00 4.49
512 514 1.465689 CCTTATTTTGCCGAGCGTGTG 60.466 52.381 0.00 0.00 0.00 3.82
513 515 1.196808 CTTATTTTGCCGAGCGTGTGT 59.803 47.619 0.00 0.00 0.00 3.72
514 516 0.515127 TATTTTGCCGAGCGTGTGTG 59.485 50.000 0.00 0.00 0.00 3.82
515 517 2.731587 ATTTTGCCGAGCGTGTGTGC 62.732 55.000 0.00 0.00 0.00 4.57
518 520 4.374702 GCCGAGCGTGTGTGCAAG 62.375 66.667 0.00 0.00 37.31 4.01
519 521 3.716006 CCGAGCGTGTGTGCAAGG 61.716 66.667 0.00 0.00 37.31 3.61
520 522 2.661537 CGAGCGTGTGTGCAAGGA 60.662 61.111 0.00 0.00 37.31 3.36
521 523 2.661566 CGAGCGTGTGTGCAAGGAG 61.662 63.158 0.00 0.00 37.31 3.69
522 524 2.281070 AGCGTGTGTGCAAGGAGG 60.281 61.111 0.00 0.00 37.31 4.30
523 525 3.357079 GCGTGTGTGCAAGGAGGG 61.357 66.667 0.00 0.00 34.15 4.30
524 526 3.357079 CGTGTGTGCAAGGAGGGC 61.357 66.667 0.00 0.00 0.00 5.19
525 527 2.203337 GTGTGTGCAAGGAGGGCA 60.203 61.111 0.00 0.00 39.32 5.36
526 528 1.604593 GTGTGTGCAAGGAGGGCAT 60.605 57.895 0.00 0.00 44.11 4.40
527 529 0.322456 GTGTGTGCAAGGAGGGCATA 60.322 55.000 0.00 0.00 44.11 3.14
528 530 0.625316 TGTGTGCAAGGAGGGCATAT 59.375 50.000 0.00 0.00 44.11 1.78
529 531 1.312815 GTGTGCAAGGAGGGCATATC 58.687 55.000 0.00 0.00 44.11 1.63
530 532 0.183492 TGTGCAAGGAGGGCATATCC 59.817 55.000 0.00 0.00 44.11 2.59
539 541 2.826702 GGCATATCCCCGACGGTT 59.173 61.111 13.94 0.00 0.00 4.44
540 542 1.147600 GGCATATCCCCGACGGTTT 59.852 57.895 13.94 0.00 0.00 3.27
541 543 0.883370 GGCATATCCCCGACGGTTTC 60.883 60.000 13.94 0.00 0.00 2.78
542 544 0.883370 GCATATCCCCGACGGTTTCC 60.883 60.000 13.94 0.00 0.00 3.13
552 554 3.039588 CGGTTTCCGGGTCGTGTG 61.040 66.667 0.00 0.00 44.15 3.82
553 555 2.667199 GGTTTCCGGGTCGTGTGG 60.667 66.667 0.00 0.00 0.00 4.17
554 556 2.667199 GTTTCCGGGTCGTGTGGG 60.667 66.667 0.00 0.00 0.00 4.61
555 557 2.843411 TTTCCGGGTCGTGTGGGA 60.843 61.111 0.00 0.00 0.00 4.37
556 558 2.441675 TTTCCGGGTCGTGTGGGAA 61.442 57.895 0.00 0.00 36.80 3.97
557 559 2.386064 TTTCCGGGTCGTGTGGGAAG 62.386 60.000 0.00 0.00 39.53 3.46
558 560 4.388499 CCGGGTCGTGTGGGAAGG 62.388 72.222 0.00 0.00 0.00 3.46
559 561 3.307906 CGGGTCGTGTGGGAAGGA 61.308 66.667 0.00 0.00 0.00 3.36
560 562 2.346365 GGGTCGTGTGGGAAGGAC 59.654 66.667 0.00 0.00 34.86 3.85
561 563 2.346365 GGTCGTGTGGGAAGGACC 59.654 66.667 0.78 0.78 45.07 4.46
578 580 2.768344 CCCCCTATCGCCCACACT 60.768 66.667 0.00 0.00 0.00 3.55
579 581 2.808206 CCCCCTATCGCCCACACTC 61.808 68.421 0.00 0.00 0.00 3.51
580 582 2.063979 CCCCTATCGCCCACACTCA 61.064 63.158 0.00 0.00 0.00 3.41
581 583 1.144057 CCCTATCGCCCACACTCAC 59.856 63.158 0.00 0.00 0.00 3.51
582 584 1.330655 CCCTATCGCCCACACTCACT 61.331 60.000 0.00 0.00 0.00 3.41
583 585 1.399714 CCTATCGCCCACACTCACTA 58.600 55.000 0.00 0.00 0.00 2.74
584 586 1.338337 CCTATCGCCCACACTCACTAG 59.662 57.143 0.00 0.00 0.00 2.57
585 587 1.338337 CTATCGCCCACACTCACTAGG 59.662 57.143 0.00 0.00 0.00 3.02
586 588 0.614979 ATCGCCCACACTCACTAGGT 60.615 55.000 0.00 0.00 0.00 3.08
587 589 1.079819 CGCCCACACTCACTAGGTG 60.080 63.158 0.00 0.00 40.19 4.00
588 590 1.532604 CGCCCACACTCACTAGGTGA 61.533 60.000 4.82 0.43 40.50 4.02
589 591 0.037232 GCCCACACTCACTAGGTGAC 60.037 60.000 4.82 0.00 37.67 3.67
590 592 0.243907 CCCACACTCACTAGGTGACG 59.756 60.000 4.82 0.00 37.67 4.35
591 593 0.243907 CCACACTCACTAGGTGACGG 59.756 60.000 4.82 1.88 37.67 4.79
592 594 0.959553 CACACTCACTAGGTGACGGT 59.040 55.000 4.82 0.00 37.67 4.83
593 595 1.340248 CACACTCACTAGGTGACGGTT 59.660 52.381 4.82 0.00 37.67 4.44
594 596 1.612463 ACACTCACTAGGTGACGGTTC 59.388 52.381 4.82 0.00 37.67 3.62
595 597 1.067776 CACTCACTAGGTGACGGTTCC 60.068 57.143 0.00 0.00 37.67 3.62
596 598 0.170561 CTCACTAGGTGACGGTTCCG 59.829 60.000 9.81 9.81 37.67 4.30
597 599 0.250858 TCACTAGGTGACGGTTCCGA 60.251 55.000 18.28 0.00 37.67 4.55
598 600 0.599558 CACTAGGTGACGGTTCCGAA 59.400 55.000 18.28 2.95 35.23 4.30
599 601 0.600057 ACTAGGTGACGGTTCCGAAC 59.400 55.000 18.28 14.10 0.00 3.95
600 602 0.599558 CTAGGTGACGGTTCCGAACA 59.400 55.000 18.28 13.51 0.00 3.18
601 603 0.314935 TAGGTGACGGTTCCGAACAC 59.685 55.000 24.05 24.05 38.38 3.32
602 604 1.957695 GGTGACGGTTCCGAACACC 60.958 63.158 29.61 29.61 44.37 4.16
607 609 3.408851 GGTTCCGAACACCGTCGC 61.409 66.667 13.23 0.00 39.74 5.19
608 610 3.759828 GTTCCGAACACCGTCGCG 61.760 66.667 0.00 0.00 39.74 5.87
619 621 2.262292 CGTCGCGGAAAGGGGTTA 59.738 61.111 6.13 0.00 0.00 2.85
620 622 1.374505 CGTCGCGGAAAGGGGTTAA 60.375 57.895 6.13 0.00 0.00 2.01
621 623 0.950071 CGTCGCGGAAAGGGGTTAAA 60.950 55.000 6.13 0.00 0.00 1.52
622 624 1.237533 GTCGCGGAAAGGGGTTAAAA 58.762 50.000 6.13 0.00 0.00 1.52
623 625 1.608109 GTCGCGGAAAGGGGTTAAAAA 59.392 47.619 6.13 0.00 0.00 1.94
624 626 1.608109 TCGCGGAAAGGGGTTAAAAAC 59.392 47.619 6.13 0.00 0.00 2.43
642 644 9.281075 GTTAAAAACCATTTGTATATCACCGAC 57.719 33.333 0.00 0.00 0.00 4.79
643 645 5.728351 AAACCATTTGTATATCACCGACG 57.272 39.130 0.00 0.00 0.00 5.12
644 646 4.395959 ACCATTTGTATATCACCGACGT 57.604 40.909 0.00 0.00 0.00 4.34
645 647 4.116961 ACCATTTGTATATCACCGACGTG 58.883 43.478 0.00 0.00 41.72 4.49
646 648 4.116961 CCATTTGTATATCACCGACGTGT 58.883 43.478 0.00 0.00 41.09 4.49
647 649 5.163530 ACCATTTGTATATCACCGACGTGTA 60.164 40.000 0.00 0.00 41.09 2.90
648 650 5.174398 CCATTTGTATATCACCGACGTGTAC 59.826 44.000 0.00 0.00 41.09 2.90
649 651 3.969117 TGTATATCACCGACGTGTACC 57.031 47.619 0.00 0.00 41.09 3.34
650 652 3.277715 TGTATATCACCGACGTGTACCA 58.722 45.455 0.00 0.00 41.09 3.25
651 653 3.313249 TGTATATCACCGACGTGTACCAG 59.687 47.826 0.00 0.00 41.09 4.00
652 654 1.825090 TATCACCGACGTGTACCAGT 58.175 50.000 0.00 0.00 41.09 4.00
653 655 0.242825 ATCACCGACGTGTACCAGTG 59.757 55.000 0.00 0.00 41.09 3.66
672 674 5.066375 CCAGTGTTTGTCTGTTCAATTCTGA 59.934 40.000 0.00 0.00 0.00 3.27
686 688 7.445096 TGTTCAATTCTGAGATCTTTACTGCAA 59.555 33.333 0.00 0.00 31.69 4.08
708 710 1.454201 GCAGAGAGCAGGGTAAAACC 58.546 55.000 0.00 0.00 44.79 3.27
783 788 5.974156 TCTCCCCTTTGATGAATATGTGA 57.026 39.130 0.00 0.00 0.00 3.58
1190 3869 3.916989 AGTATTTCCTCTCTTTGGGTGGT 59.083 43.478 0.00 0.00 0.00 4.16
1210 3889 6.295292 GGTGGTTGGAAAAAGATTAGATGCTT 60.295 38.462 0.00 0.00 0.00 3.91
1308 3992 3.190118 GGCTGTCTCTTGAACAGATTTGG 59.810 47.826 7.42 0.00 33.65 3.28
1319 4003 4.024048 TGAACAGATTTGGTCGCTTCTTTC 60.024 41.667 0.00 0.00 44.28 2.62
1363 4047 3.677148 CGTGCTCTACAAGGATCACATGT 60.677 47.826 0.00 0.00 33.54 3.21
1515 4199 3.701454 AGAGCCCCGTCTCTGTTC 58.299 61.111 0.00 0.00 41.57 3.18
1520 4204 1.893786 CCCCGTCTCTGTTCTGGAG 59.106 63.158 0.00 0.00 0.00 3.86
1527 4211 1.429299 TCTCTGTTCTGGAGGTCCTGA 59.571 52.381 0.00 1.62 41.40 3.86
1577 4261 3.714798 AGTGAAAGTGGAAAGTGGTCCTA 59.285 43.478 0.00 0.00 38.62 2.94
1583 4267 6.449830 AAGTGGAAAGTGGTCCTATTAAGT 57.550 37.500 0.00 0.00 38.62 2.24
1598 4282 9.871238 GTCCTATTAAGTTGTCACTTATCTCAA 57.129 33.333 0.00 0.00 43.65 3.02
1652 4337 5.449177 GGTGCCTACTGTTATCAGCATTTTC 60.449 44.000 0.51 0.00 44.77 2.29
1745 4430 6.374417 TTCTTTCTAAGTAATGGAGCCAGT 57.626 37.500 0.00 0.00 0.00 4.00
1757 4442 1.152030 AGCCAGTGAACCCCTCTCA 60.152 57.895 0.00 0.00 0.00 3.27
1828 4513 3.626924 GCGCATATCCGGGTCCCT 61.627 66.667 6.29 0.00 0.00 4.20
1833 4518 1.906574 GCATATCCGGGTCCCTTCATA 59.093 52.381 6.29 0.00 0.00 2.15
1868 4554 3.693085 ACGACGAGCTTTTAGTGGATCTA 59.307 43.478 0.00 0.00 0.00 1.98
1901 4587 4.864704 AAACAGTCAAAACCCGCATATT 57.135 36.364 0.00 0.00 0.00 1.28
1910 4596 5.010112 TCAAAACCCGCATATTGTCTGAAAA 59.990 36.000 0.00 0.00 0.00 2.29
1926 4612 5.181245 GTCTGAAAATTTCCGGACAGATGAA 59.819 40.000 19.56 5.08 36.89 2.57
1949 4635 5.825507 ACTTTTAGCGGATACTAACGGTAG 58.174 41.667 5.79 5.79 42.82 3.18
1982 4668 1.206610 TGAAAAAGCAGCAACTTGCCA 59.793 42.857 10.25 0.00 46.52 4.92
2092 4778 2.223735 GCACCGTTCCTTATCTGATCGA 60.224 50.000 0.00 0.00 0.00 3.59
2118 4804 1.946768 CAGAAGGAAAAACGCAGTCCA 59.053 47.619 0.00 0.00 45.00 4.02
2146 4832 5.391060 GGATCTAAATCCTGTTTTCGACG 57.609 43.478 0.00 0.00 46.97 5.12
2158 4844 2.444700 TTTCGACGAGGGCCAAGGAC 62.445 60.000 6.18 0.00 0.00 3.85
2177 4863 0.457851 CGGGCCAGAAACAAACAACA 59.542 50.000 4.39 0.00 0.00 3.33
2215 4901 3.024547 GGAAGGGGATTGGAAGTTTAGC 58.975 50.000 0.00 0.00 0.00 3.09
2273 4959 5.781818 AGCCATTTTATTCCCAATCCCTATG 59.218 40.000 0.00 0.00 0.00 2.23
2294 4980 6.829229 ATGTGGTGCATGATAGGAATTATG 57.171 37.500 0.00 0.00 36.26 1.90
2354 5040 4.446371 GTTCATGGGAATTGACGAGAGAT 58.554 43.478 0.00 0.00 35.05 2.75
2378 5064 4.911390 AGACCAGGGAAGTGAACATAAAG 58.089 43.478 0.00 0.00 0.00 1.85
2379 5065 4.010349 GACCAGGGAAGTGAACATAAAGG 58.990 47.826 0.00 0.00 0.00 3.11
2380 5066 3.655777 ACCAGGGAAGTGAACATAAAGGA 59.344 43.478 0.00 0.00 0.00 3.36
2381 5067 4.105697 ACCAGGGAAGTGAACATAAAGGAA 59.894 41.667 0.00 0.00 0.00 3.36
2382 5068 5.076873 CCAGGGAAGTGAACATAAAGGAAA 58.923 41.667 0.00 0.00 0.00 3.13
2383 5069 5.538433 CCAGGGAAGTGAACATAAAGGAAAA 59.462 40.000 0.00 0.00 0.00 2.29
2384 5070 6.041523 CCAGGGAAGTGAACATAAAGGAAAAA 59.958 38.462 0.00 0.00 0.00 1.94
2385 5071 6.923508 CAGGGAAGTGAACATAAAGGAAAAAC 59.076 38.462 0.00 0.00 0.00 2.43
2386 5072 6.839134 AGGGAAGTGAACATAAAGGAAAAACT 59.161 34.615 0.00 0.00 0.00 2.66
2387 5073 8.002459 AGGGAAGTGAACATAAAGGAAAAACTA 58.998 33.333 0.00 0.00 0.00 2.24
2388 5074 8.635328 GGGAAGTGAACATAAAGGAAAAACTAA 58.365 33.333 0.00 0.00 0.00 2.24
2389 5075 9.459640 GGAAGTGAACATAAAGGAAAAACTAAC 57.540 33.333 0.00 0.00 0.00 2.34
2390 5076 9.166126 GAAGTGAACATAAAGGAAAAACTAACG 57.834 33.333 0.00 0.00 0.00 3.18
2391 5077 7.136772 AGTGAACATAAAGGAAAAACTAACGC 58.863 34.615 0.00 0.00 0.00 4.84
2392 5078 6.361481 GTGAACATAAAGGAAAAACTAACGCC 59.639 38.462 0.00 0.00 0.00 5.68
2393 5079 5.381174 ACATAAAGGAAAAACTAACGCCC 57.619 39.130 0.00 0.00 0.00 6.13
2394 5080 4.828387 ACATAAAGGAAAAACTAACGCCCA 59.172 37.500 0.00 0.00 0.00 5.36
2395 5081 3.720949 AAAGGAAAAACTAACGCCCAC 57.279 42.857 0.00 0.00 0.00 4.61
2396 5082 2.351706 AGGAAAAACTAACGCCCACA 57.648 45.000 0.00 0.00 0.00 4.17
2397 5083 1.951602 AGGAAAAACTAACGCCCACAC 59.048 47.619 0.00 0.00 0.00 3.82
2398 5084 1.334329 GGAAAAACTAACGCCCACACG 60.334 52.381 0.00 0.00 39.50 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.009723 CAGCTACCCCATTACACAACTG 58.990 50.000 0.00 0.00 0.00 3.16
43 44 4.818546 ACAACATGATATAGCTTCAGCACC 59.181 41.667 0.00 0.00 45.16 5.01
49 50 9.138062 CATCAGAGTACAACATGATATAGCTTC 57.862 37.037 0.00 0.00 31.35 3.86
218 219 7.302524 TCAATAGTCGTTTGCAATAGGAAAAC 58.697 34.615 0.00 0.00 36.80 2.43
222 223 5.972935 TCTCAATAGTCGTTTGCAATAGGA 58.027 37.500 0.00 0.00 0.00 2.94
224 225 8.015087 TGTTTTCTCAATAGTCGTTTGCAATAG 58.985 33.333 0.00 0.00 0.00 1.73
228 229 5.504994 GGTGTTTTCTCAATAGTCGTTTGCA 60.505 40.000 0.00 0.00 0.00 4.08
236 237 4.695455 CGTCCATGGTGTTTTCTCAATAGT 59.305 41.667 12.58 0.00 0.00 2.12
237 238 4.935205 TCGTCCATGGTGTTTTCTCAATAG 59.065 41.667 12.58 0.00 0.00 1.73
240 241 3.201353 TCGTCCATGGTGTTTTCTCAA 57.799 42.857 12.58 0.00 0.00 3.02
253 254 0.977627 TGCCTGAGGTCATCGTCCAT 60.978 55.000 0.00 0.00 0.00 3.41
257 258 1.079819 CGTTGCCTGAGGTCATCGT 60.080 57.895 14.14 0.00 0.00 3.73
280 281 6.037172 CCAACACGGTTTATTCCTAGAATCTG 59.963 42.308 0.00 0.00 0.00 2.90
283 284 6.057321 TCCAACACGGTTTATTCCTAGAAT 57.943 37.500 0.00 0.00 35.57 2.40
299 300 5.630680 GTGTGATTGTTCATTGATCCAACAC 59.369 40.000 15.56 15.56 33.56 3.32
363 365 2.096248 ACTCCAAGGAAAACGTTTGCA 58.904 42.857 20.48 0.00 0.00 4.08
365 367 3.377172 AGTCACTCCAAGGAAAACGTTTG 59.623 43.478 15.46 1.72 0.00 2.93
366 368 3.377172 CAGTCACTCCAAGGAAAACGTTT 59.623 43.478 7.96 7.96 0.00 3.60
367 369 2.943033 CAGTCACTCCAAGGAAAACGTT 59.057 45.455 0.00 0.00 0.00 3.99
368 370 2.093128 ACAGTCACTCCAAGGAAAACGT 60.093 45.455 0.00 0.00 0.00 3.99
369 371 2.287915 CACAGTCACTCCAAGGAAAACG 59.712 50.000 0.00 0.00 0.00 3.60
370 372 3.065371 CACACAGTCACTCCAAGGAAAAC 59.935 47.826 0.00 0.00 0.00 2.43
371 373 3.278574 CACACAGTCACTCCAAGGAAAA 58.721 45.455 0.00 0.00 0.00 2.29
372 374 2.421388 CCACACAGTCACTCCAAGGAAA 60.421 50.000 0.00 0.00 0.00 3.13
373 375 1.140852 CCACACAGTCACTCCAAGGAA 59.859 52.381 0.00 0.00 0.00 3.36
374 376 0.758734 CCACACAGTCACTCCAAGGA 59.241 55.000 0.00 0.00 0.00 3.36
375 377 0.469917 ACCACACAGTCACTCCAAGG 59.530 55.000 0.00 0.00 0.00 3.61
376 378 1.134401 ACACCACACAGTCACTCCAAG 60.134 52.381 0.00 0.00 0.00 3.61
377 379 0.908910 ACACCACACAGTCACTCCAA 59.091 50.000 0.00 0.00 0.00 3.53
378 380 0.177836 CACACCACACAGTCACTCCA 59.822 55.000 0.00 0.00 0.00 3.86
379 381 0.178068 ACACACCACACAGTCACTCC 59.822 55.000 0.00 0.00 0.00 3.85
380 382 2.882927 TACACACCACACAGTCACTC 57.117 50.000 0.00 0.00 0.00 3.51
381 383 5.392703 CGTATATACACACCACACAGTCACT 60.393 44.000 13.22 0.00 0.00 3.41
382 384 4.796830 CGTATATACACACCACACAGTCAC 59.203 45.833 13.22 0.00 0.00 3.67
383 385 4.701171 TCGTATATACACACCACACAGTCA 59.299 41.667 13.22 0.00 0.00 3.41
384 386 5.239359 TCGTATATACACACCACACAGTC 57.761 43.478 13.22 0.00 0.00 3.51
385 387 5.404946 GTTCGTATATACACACCACACAGT 58.595 41.667 13.22 0.00 0.00 3.55
386 388 4.497966 CGTTCGTATATACACACCACACAG 59.502 45.833 13.22 0.00 0.00 3.66
387 389 4.413969 CGTTCGTATATACACACCACACA 58.586 43.478 13.22 0.00 0.00 3.72
388 390 3.792956 CCGTTCGTATATACACACCACAC 59.207 47.826 13.22 0.00 0.00 3.82
389 391 3.693578 TCCGTTCGTATATACACACCACA 59.306 43.478 13.22 0.00 0.00 4.17
390 392 4.291540 TCCGTTCGTATATACACACCAC 57.708 45.455 13.22 1.35 0.00 4.16
391 393 4.979943 TTCCGTTCGTATATACACACCA 57.020 40.909 13.22 0.00 0.00 4.17
392 394 5.101628 TGTTTCCGTTCGTATATACACACC 58.898 41.667 13.22 0.00 0.00 4.16
393 395 6.817270 ATGTTTCCGTTCGTATATACACAC 57.183 37.500 13.22 7.39 0.00 3.82
394 396 7.830940 AAATGTTTCCGTTCGTATATACACA 57.169 32.000 13.22 7.18 0.00 3.72
395 397 8.000435 GCTAAATGTTTCCGTTCGTATATACAC 59.000 37.037 13.22 3.80 0.00 2.90
396 398 7.096518 CGCTAAATGTTTCCGTTCGTATATACA 60.097 37.037 13.22 0.00 0.00 2.29
397 399 7.215844 CGCTAAATGTTTCCGTTCGTATATAC 58.784 38.462 2.53 2.53 0.00 1.47
398 400 6.363088 CCGCTAAATGTTTCCGTTCGTATATA 59.637 38.462 0.00 0.00 0.00 0.86
399 401 5.176223 CCGCTAAATGTTTCCGTTCGTATAT 59.824 40.000 0.00 0.00 0.00 0.86
400 402 4.503734 CCGCTAAATGTTTCCGTTCGTATA 59.496 41.667 0.00 0.00 0.00 1.47
401 403 3.307782 CCGCTAAATGTTTCCGTTCGTAT 59.692 43.478 0.00 0.00 0.00 3.06
402 404 2.667481 CCGCTAAATGTTTCCGTTCGTA 59.333 45.455 0.00 0.00 0.00 3.43
403 405 1.461897 CCGCTAAATGTTTCCGTTCGT 59.538 47.619 0.00 0.00 0.00 3.85
404 406 1.461897 ACCGCTAAATGTTTCCGTTCG 59.538 47.619 0.00 0.00 0.00 3.95
405 407 2.481185 TCACCGCTAAATGTTTCCGTTC 59.519 45.455 0.00 0.00 0.00 3.95
406 408 2.224784 GTCACCGCTAAATGTTTCCGTT 59.775 45.455 0.00 0.00 0.00 4.44
407 409 1.802365 GTCACCGCTAAATGTTTCCGT 59.198 47.619 0.00 0.00 0.00 4.69
408 410 2.073816 AGTCACCGCTAAATGTTTCCG 58.926 47.619 0.00 0.00 0.00 4.30
409 411 3.071479 TCAGTCACCGCTAAATGTTTCC 58.929 45.455 0.00 0.00 0.00 3.13
410 412 3.746492 AGTCAGTCACCGCTAAATGTTTC 59.254 43.478 0.00 0.00 0.00 2.78
411 413 3.498397 CAGTCAGTCACCGCTAAATGTTT 59.502 43.478 0.00 0.00 0.00 2.83
412 414 3.067106 CAGTCAGTCACCGCTAAATGTT 58.933 45.455 0.00 0.00 0.00 2.71
413 415 2.037251 ACAGTCAGTCACCGCTAAATGT 59.963 45.455 0.00 0.00 0.00 2.71
414 416 2.413112 CACAGTCAGTCACCGCTAAATG 59.587 50.000 0.00 0.00 0.00 2.32
415 417 2.037251 ACACAGTCAGTCACCGCTAAAT 59.963 45.455 0.00 0.00 0.00 1.40
416 418 1.411246 ACACAGTCAGTCACCGCTAAA 59.589 47.619 0.00 0.00 0.00 1.85
417 419 1.037493 ACACAGTCAGTCACCGCTAA 58.963 50.000 0.00 0.00 0.00 3.09
418 420 0.313987 CACACAGTCAGTCACCGCTA 59.686 55.000 0.00 0.00 0.00 4.26
419 421 1.068083 CACACAGTCAGTCACCGCT 59.932 57.895 0.00 0.00 0.00 5.52
420 422 1.956170 CCACACAGTCAGTCACCGC 60.956 63.158 0.00 0.00 0.00 5.68
421 423 1.300931 CCCACACAGTCAGTCACCG 60.301 63.158 0.00 0.00 0.00 4.94
422 424 0.687354 ATCCCACACAGTCAGTCACC 59.313 55.000 0.00 0.00 0.00 4.02
423 425 1.070758 ACATCCCACACAGTCAGTCAC 59.929 52.381 0.00 0.00 0.00 3.67
424 426 1.423584 ACATCCCACACAGTCAGTCA 58.576 50.000 0.00 0.00 0.00 3.41
425 427 2.563179 AGTACATCCCACACAGTCAGTC 59.437 50.000 0.00 0.00 0.00 3.51
426 428 2.609747 AGTACATCCCACACAGTCAGT 58.390 47.619 0.00 0.00 0.00 3.41
427 429 3.685139 AAGTACATCCCACACAGTCAG 57.315 47.619 0.00 0.00 0.00 3.51
428 430 3.057104 CGTAAGTACATCCCACACAGTCA 60.057 47.826 0.00 0.00 0.00 3.41
429 431 3.192001 TCGTAAGTACATCCCACACAGTC 59.808 47.826 0.00 0.00 39.48 3.51
430 432 3.057033 GTCGTAAGTACATCCCACACAGT 60.057 47.826 0.00 0.00 39.48 3.55
431 433 3.508762 GTCGTAAGTACATCCCACACAG 58.491 50.000 0.00 0.00 39.48 3.66
432 434 2.231964 GGTCGTAAGTACATCCCACACA 59.768 50.000 0.00 0.00 39.48 3.72
433 435 2.733227 CGGTCGTAAGTACATCCCACAC 60.733 54.545 0.00 0.00 39.48 3.82
434 436 1.473677 CGGTCGTAAGTACATCCCACA 59.526 52.381 0.00 0.00 39.48 4.17
435 437 1.745087 TCGGTCGTAAGTACATCCCAC 59.255 52.381 0.00 0.00 39.48 4.61
436 438 2.127271 TCGGTCGTAAGTACATCCCA 57.873 50.000 0.00 0.00 39.48 4.37
437 439 3.508744 TTTCGGTCGTAAGTACATCCC 57.491 47.619 0.00 0.00 39.48 3.85
438 440 5.104374 TCATTTTCGGTCGTAAGTACATCC 58.896 41.667 0.00 0.00 39.48 3.51
439 441 6.823678 ATCATTTTCGGTCGTAAGTACATC 57.176 37.500 0.00 0.00 39.48 3.06
440 442 7.605410 AAATCATTTTCGGTCGTAAGTACAT 57.395 32.000 0.00 0.00 39.48 2.29
441 443 7.052565 GAAATCATTTTCGGTCGTAAGTACA 57.947 36.000 0.00 0.00 32.49 2.90
466 468 4.971125 GACCGGCGAGCCCTATGC 62.971 72.222 9.30 0.00 41.71 3.14
467 469 4.647615 CGACCGGCGAGCCCTATG 62.648 72.222 9.30 0.00 44.57 2.23
482 484 1.195900 GCAAAATAAGGTCGTGTGCGA 59.804 47.619 0.00 0.00 45.79 5.10
483 485 1.602191 GCAAAATAAGGTCGTGTGCG 58.398 50.000 0.00 0.00 39.92 5.34
484 486 1.727857 CGGCAAAATAAGGTCGTGTGC 60.728 52.381 0.00 0.00 0.00 4.57
485 487 1.801771 TCGGCAAAATAAGGTCGTGTG 59.198 47.619 0.00 0.00 33.14 3.82
486 488 2.073816 CTCGGCAAAATAAGGTCGTGT 58.926 47.619 0.00 0.00 33.14 4.49
487 489 1.202031 GCTCGGCAAAATAAGGTCGTG 60.202 52.381 0.00 0.00 33.14 4.35
488 490 1.084289 GCTCGGCAAAATAAGGTCGT 58.916 50.000 0.00 0.00 33.14 4.34
489 491 0.026285 CGCTCGGCAAAATAAGGTCG 59.974 55.000 0.00 0.00 0.00 4.79
490 492 1.084289 ACGCTCGGCAAAATAAGGTC 58.916 50.000 0.00 0.00 0.00 3.85
491 493 0.802494 CACGCTCGGCAAAATAAGGT 59.198 50.000 0.00 0.00 0.00 3.50
492 494 0.802494 ACACGCTCGGCAAAATAAGG 59.198 50.000 0.00 0.00 0.00 2.69
493 495 1.196808 ACACACGCTCGGCAAAATAAG 59.803 47.619 0.00 0.00 0.00 1.73
494 496 1.069568 CACACACGCTCGGCAAAATAA 60.070 47.619 0.00 0.00 0.00 1.40
495 497 0.515127 CACACACGCTCGGCAAAATA 59.485 50.000 0.00 0.00 0.00 1.40
496 498 1.282570 CACACACGCTCGGCAAAAT 59.717 52.632 0.00 0.00 0.00 1.82
497 499 2.712539 CACACACGCTCGGCAAAA 59.287 55.556 0.00 0.00 0.00 2.44
498 500 3.947841 GCACACACGCTCGGCAAA 61.948 61.111 0.00 0.00 0.00 3.68
501 503 4.374702 CTTGCACACACGCTCGGC 62.375 66.667 0.00 0.00 0.00 5.54
502 504 3.716006 CCTTGCACACACGCTCGG 61.716 66.667 0.00 0.00 0.00 4.63
503 505 2.661537 TCCTTGCACACACGCTCG 60.662 61.111 0.00 0.00 0.00 5.03
504 506 2.320587 CCTCCTTGCACACACGCTC 61.321 63.158 0.00 0.00 0.00 5.03
505 507 2.281070 CCTCCTTGCACACACGCT 60.281 61.111 0.00 0.00 0.00 5.07
506 508 3.357079 CCCTCCTTGCACACACGC 61.357 66.667 0.00 0.00 0.00 5.34
507 509 3.357079 GCCCTCCTTGCACACACG 61.357 66.667 0.00 0.00 0.00 4.49
508 510 0.322456 TATGCCCTCCTTGCACACAC 60.322 55.000 0.00 0.00 42.38 3.82
509 511 0.625316 ATATGCCCTCCTTGCACACA 59.375 50.000 0.00 0.00 42.38 3.72
510 512 1.312815 GATATGCCCTCCTTGCACAC 58.687 55.000 0.00 0.00 42.38 3.82
511 513 0.183492 GGATATGCCCTCCTTGCACA 59.817 55.000 0.00 0.00 42.38 4.57
512 514 3.027419 GGATATGCCCTCCTTGCAC 57.973 57.895 0.00 0.00 42.38 4.57
522 524 0.883370 GAAACCGTCGGGGATATGCC 60.883 60.000 17.28 4.31 39.97 4.40
523 525 0.883370 GGAAACCGTCGGGGATATGC 60.883 60.000 17.28 0.00 39.97 3.14
524 526 0.599204 CGGAAACCGTCGGGGATATG 60.599 60.000 17.28 0.00 42.73 1.78
525 527 1.744014 CGGAAACCGTCGGGGATAT 59.256 57.895 17.28 0.00 42.73 1.63
526 528 2.425569 CCGGAAACCGTCGGGGATA 61.426 63.158 17.28 0.00 46.80 2.59
527 529 3.777910 CCGGAAACCGTCGGGGAT 61.778 66.667 17.28 0.20 46.80 3.85
532 534 4.347453 ACGACCCGGAAACCGTCG 62.347 66.667 23.11 23.11 46.80 5.12
533 535 2.735857 CACGACCCGGAAACCGTC 60.736 66.667 0.73 0.00 46.80 4.79
534 536 3.539791 ACACGACCCGGAAACCGT 61.540 61.111 0.73 3.53 46.80 4.83
536 538 2.667199 CCACACGACCCGGAAACC 60.667 66.667 0.73 0.00 0.00 3.27
537 539 2.663423 TTCCCACACGACCCGGAAAC 62.663 60.000 0.73 0.00 31.47 2.78
538 540 2.386064 CTTCCCACACGACCCGGAAA 62.386 60.000 0.73 0.00 34.07 3.13
539 541 2.843411 TTCCCACACGACCCGGAA 60.843 61.111 0.73 0.00 31.96 4.30
540 542 3.307906 CTTCCCACACGACCCGGA 61.308 66.667 0.73 0.00 0.00 5.14
541 543 4.388499 CCTTCCCACACGACCCGG 62.388 72.222 0.00 0.00 0.00 5.73
542 544 3.307906 TCCTTCCCACACGACCCG 61.308 66.667 0.00 0.00 0.00 5.28
543 545 2.346365 GTCCTTCCCACACGACCC 59.654 66.667 0.00 0.00 0.00 4.46
544 546 2.346365 GGTCCTTCCCACACGACC 59.654 66.667 0.00 0.00 38.18 4.79
561 563 2.768344 AGTGTGGGCGATAGGGGG 60.768 66.667 0.00 0.00 0.00 5.40
562 564 2.063979 TGAGTGTGGGCGATAGGGG 61.064 63.158 0.00 0.00 0.00 4.79
563 565 1.144057 GTGAGTGTGGGCGATAGGG 59.856 63.158 0.00 0.00 0.00 3.53
564 566 1.338337 CTAGTGAGTGTGGGCGATAGG 59.662 57.143 0.00 0.00 0.00 2.57
565 567 1.338337 CCTAGTGAGTGTGGGCGATAG 59.662 57.143 0.00 0.00 0.00 2.08
566 568 1.341679 ACCTAGTGAGTGTGGGCGATA 60.342 52.381 0.00 0.00 0.00 2.92
567 569 0.614979 ACCTAGTGAGTGTGGGCGAT 60.615 55.000 0.00 0.00 0.00 4.58
568 570 1.228769 ACCTAGTGAGTGTGGGCGA 60.229 57.895 0.00 0.00 0.00 5.54
569 571 1.079819 CACCTAGTGAGTGTGGGCG 60.080 63.158 0.00 0.00 35.23 6.13
570 572 0.037232 GTCACCTAGTGAGTGTGGGC 60.037 60.000 0.00 0.00 43.57 5.36
571 573 0.243907 CGTCACCTAGTGAGTGTGGG 59.756 60.000 0.00 0.00 43.57 4.61
572 574 0.243907 CCGTCACCTAGTGAGTGTGG 59.756 60.000 0.00 0.00 43.57 4.17
573 575 0.959553 ACCGTCACCTAGTGAGTGTG 59.040 55.000 0.00 0.00 43.57 3.82
574 576 1.612463 GAACCGTCACCTAGTGAGTGT 59.388 52.381 0.00 0.00 43.57 3.55
575 577 1.067776 GGAACCGTCACCTAGTGAGTG 60.068 57.143 0.00 0.00 43.57 3.51
576 578 1.254954 GGAACCGTCACCTAGTGAGT 58.745 55.000 0.00 0.00 43.57 3.41
577 579 0.170561 CGGAACCGTCACCTAGTGAG 59.829 60.000 4.99 0.00 43.57 3.51
578 580 0.250858 TCGGAACCGTCACCTAGTGA 60.251 55.000 12.93 0.00 37.99 3.41
579 581 0.599558 TTCGGAACCGTCACCTAGTG 59.400 55.000 12.93 0.00 40.74 2.74
580 582 0.600057 GTTCGGAACCGTCACCTAGT 59.400 55.000 9.75 0.00 40.74 2.57
581 583 0.599558 TGTTCGGAACCGTCACCTAG 59.400 55.000 17.62 0.00 40.74 3.02
582 584 0.314935 GTGTTCGGAACCGTCACCTA 59.685 55.000 17.62 0.00 38.34 3.08
583 585 1.068585 GTGTTCGGAACCGTCACCT 59.931 57.895 17.62 0.00 38.34 4.00
584 586 1.957695 GGTGTTCGGAACCGTCACC 60.958 63.158 28.67 28.67 46.75 4.02
585 587 3.633951 GGTGTTCGGAACCGTCAC 58.366 61.111 17.62 23.03 40.80 3.67
590 592 3.408851 GCGACGGTGTTCGGAACC 61.409 66.667 17.62 9.17 44.45 3.62
591 593 3.759828 CGCGACGGTGTTCGGAAC 61.760 66.667 13.86 13.86 44.45 3.62
602 604 0.950071 TTTAACCCCTTTCCGCGACG 60.950 55.000 8.23 0.00 0.00 5.12
603 605 1.237533 TTTTAACCCCTTTCCGCGAC 58.762 50.000 8.23 0.00 0.00 5.19
604 606 1.608109 GTTTTTAACCCCTTTCCGCGA 59.392 47.619 8.23 0.00 0.00 5.87
605 607 1.336148 GGTTTTTAACCCCTTTCCGCG 60.336 52.381 0.00 0.00 46.12 6.46
606 608 2.443887 GGTTTTTAACCCCTTTCCGC 57.556 50.000 0.00 0.00 46.12 5.54
616 618 9.281075 GTCGGTGATATACAAATGGTTTTTAAC 57.719 33.333 0.00 0.00 0.00 2.01
617 619 8.176365 CGTCGGTGATATACAAATGGTTTTTAA 58.824 33.333 0.00 0.00 0.00 1.52
618 620 7.333921 ACGTCGGTGATATACAAATGGTTTTTA 59.666 33.333 0.00 0.00 0.00 1.52
619 621 6.149807 ACGTCGGTGATATACAAATGGTTTTT 59.850 34.615 0.00 0.00 0.00 1.94
620 622 5.644636 ACGTCGGTGATATACAAATGGTTTT 59.355 36.000 0.00 0.00 0.00 2.43
621 623 5.180271 ACGTCGGTGATATACAAATGGTTT 58.820 37.500 0.00 0.00 0.00 3.27
622 624 4.761975 ACGTCGGTGATATACAAATGGTT 58.238 39.130 0.00 0.00 0.00 3.67
623 625 4.395959 ACGTCGGTGATATACAAATGGT 57.604 40.909 0.00 0.00 0.00 3.55
637 639 0.461135 AAACACTGGTACACGTCGGT 59.539 50.000 0.00 0.00 0.00 4.69
638 640 0.856641 CAAACACTGGTACACGTCGG 59.143 55.000 0.00 0.00 0.00 4.79
639 641 1.519758 GACAAACACTGGTACACGTCG 59.480 52.381 0.00 0.00 0.00 5.12
640 642 2.538449 CAGACAAACACTGGTACACGTC 59.462 50.000 0.00 0.00 0.00 4.34
641 643 2.093869 ACAGACAAACACTGGTACACGT 60.094 45.455 0.00 0.00 39.38 4.49
642 644 2.546778 ACAGACAAACACTGGTACACG 58.453 47.619 0.00 0.00 39.38 4.49
643 645 3.936453 TGAACAGACAAACACTGGTACAC 59.064 43.478 0.00 0.00 39.38 2.90
644 646 4.209307 TGAACAGACAAACACTGGTACA 57.791 40.909 0.00 0.00 39.38 2.90
645 647 5.751243 ATTGAACAGACAAACACTGGTAC 57.249 39.130 0.00 0.00 39.38 3.34
646 648 6.038161 CAGAATTGAACAGACAAACACTGGTA 59.962 38.462 0.00 0.00 39.38 3.25
647 649 4.949856 AGAATTGAACAGACAAACACTGGT 59.050 37.500 0.00 0.00 39.38 4.00
648 650 5.066375 TCAGAATTGAACAGACAAACACTGG 59.934 40.000 0.00 0.00 39.38 4.00
649 651 6.037500 TCTCAGAATTGAACAGACAAACACTG 59.962 38.462 0.00 0.00 40.68 3.66
650 652 6.115446 TCTCAGAATTGAACAGACAAACACT 58.885 36.000 0.00 0.00 33.44 3.55
651 653 6.363577 TCTCAGAATTGAACAGACAAACAC 57.636 37.500 0.00 0.00 33.44 3.32
652 654 6.994496 AGATCTCAGAATTGAACAGACAAACA 59.006 34.615 0.00 0.00 33.44 2.83
653 655 7.432350 AGATCTCAGAATTGAACAGACAAAC 57.568 36.000 0.00 0.00 33.44 2.93
708 710 8.932791 ACATTGTTATCTAAAACCTGACTAACG 58.067 33.333 0.00 0.00 0.00 3.18
783 788 3.010584 AGGCCACAACTTCCAGTTCATAT 59.989 43.478 5.01 0.00 36.03 1.78
797 802 4.546829 AAAGTAATACTCGAGGCCACAA 57.453 40.909 18.41 0.00 0.00 3.33
1017 1025 8.021396 ACGAATTTATGTAAGTTCCTTTTCAGC 58.979 33.333 0.00 0.00 30.83 4.26
1149 1157 2.763448 ACTAGTGACAGAATCTCCCAGC 59.237 50.000 0.00 0.00 0.00 4.85
1210 3889 6.318648 AGAGCAACAACAAAGACAGTATTTGA 59.681 34.615 24.24 0.00 39.50 2.69
1308 3992 5.095691 TGATTGTTCTTGAAAGAAGCGAC 57.904 39.130 5.74 0.00 45.01 5.19
1319 4003 4.431986 CGCGCAATTTCTTGATTGTTCTTG 60.432 41.667 8.75 0.00 38.86 3.02
1363 4047 6.375736 AGACAGAACGAGTCTATCATCTTCAA 59.624 38.462 0.00 0.00 44.10 2.69
1515 4199 1.703411 GGAGATCTCAGGACCTCCAG 58.297 60.000 23.85 0.00 43.47 3.86
1520 4204 2.103941 GGATGTTGGAGATCTCAGGACC 59.896 54.545 23.85 14.18 0.00 4.46
1527 4211 2.885388 AGGAGGGATGTTGGAGATCT 57.115 50.000 0.00 0.00 0.00 2.75
1598 4282 5.278957 GGCTGACACCACAAGACAATTAAAT 60.279 40.000 0.00 0.00 0.00 1.40
1692 4377 6.349280 GCAAAAACAGGTCTGCTACATTATGA 60.349 38.462 0.00 0.00 0.00 2.15
1745 4430 2.907892 AGATCAACTGAGAGGGGTTCA 58.092 47.619 0.00 0.00 0.00 3.18
1757 4442 6.603599 GGGCATTTAGGTTTCTTAGATCAACT 59.396 38.462 0.00 0.00 0.00 3.16
1901 4587 4.079980 TCTGTCCGGAAATTTTCAGACA 57.920 40.909 22.53 22.53 40.18 3.41
1910 4596 5.123979 GCTAAAAGTTCATCTGTCCGGAAAT 59.876 40.000 5.23 0.00 0.00 2.17
1926 4612 4.725790 ACCGTTAGTATCCGCTAAAAGT 57.274 40.909 0.00 0.00 33.34 2.66
1982 4668 9.965824 ATGTAGAAAAGAAAATTGACGAAACAT 57.034 25.926 0.00 0.00 0.00 2.71
2058 4744 4.466726 AGGAACGGTGCTTATTAAGAGACT 59.533 41.667 7.63 0.00 0.00 3.24
2092 4778 2.875933 TGCGTTTTTCCTTCTGATCGTT 59.124 40.909 0.00 0.00 0.00 3.85
2137 4823 1.574702 CCTTGGCCCTCGTCGAAAAC 61.575 60.000 0.00 0.00 0.00 2.43
2158 4844 0.457851 TGTTGTTTGTTTCTGGCCCG 59.542 50.000 0.00 0.00 0.00 6.13
2177 4863 4.080413 CCCTTCCCAAATATTGCCAAATGT 60.080 41.667 0.00 0.00 0.00 2.71
2273 4959 5.532406 ACACATAATTCCTATCATGCACCAC 59.468 40.000 0.00 0.00 0.00 4.16
2354 5040 6.442541 TTTATGTTCACTTCCCTGGTCTAA 57.557 37.500 0.00 0.00 0.00 2.10
2378 5064 1.334329 CGTGTGGGCGTTAGTTTTTCC 60.334 52.381 0.00 0.00 0.00 3.13
2379 5065 1.331447 ACGTGTGGGCGTTAGTTTTTC 59.669 47.619 0.00 0.00 43.04 2.29
2380 5066 1.064357 CACGTGTGGGCGTTAGTTTTT 59.936 47.619 7.58 0.00 43.83 1.94
2381 5067 0.658897 CACGTGTGGGCGTTAGTTTT 59.341 50.000 7.58 0.00 43.83 2.43
2382 5068 0.462403 ACACGTGTGGGCGTTAGTTT 60.462 50.000 22.71 0.00 43.83 2.66
2383 5069 1.144496 ACACGTGTGGGCGTTAGTT 59.856 52.632 22.71 0.00 43.83 2.24
2384 5070 1.593209 CACACGTGTGGGCGTTAGT 60.593 57.895 35.65 1.12 43.83 2.24
2385 5071 1.300311 TCACACGTGTGGGCGTTAG 60.300 57.895 39.88 18.65 45.65 2.34
2386 5072 1.592131 GTCACACGTGTGGGCGTTA 60.592 57.895 39.88 22.46 45.65 3.18
2387 5073 2.893404 GTCACACGTGTGGGCGTT 60.893 61.111 39.88 7.83 45.65 4.84
2388 5074 3.454587 ATGTCACACGTGTGGGCGT 62.455 57.895 39.88 30.79 45.65 5.68
2389 5075 2.664851 ATGTCACACGTGTGGGCG 60.665 61.111 39.88 21.10 45.65 6.13
2390 5076 0.884704 AAGATGTCACACGTGTGGGC 60.885 55.000 39.88 32.25 45.65 5.36
2391 5077 0.867746 CAAGATGTCACACGTGTGGG 59.132 55.000 39.88 22.15 45.65 4.61


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

AutoCloner maintained by Alex Coulton.