Multiple sequence alignment - TraesCS6B01G060800

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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 TraesCS6B01G060800 chr6B 100.000 1905 0 0 1 1905 40434330 40432426 0.000000e+00 3518.0
1 TraesCS6B01G060800 chr6B 100.000 162 0 0 2271 2432 40432060 40431899 1.410000e-77 300.0
2 TraesCS6B01G060800 chr6B 76.190 441 68 23 9 424 695847353 695846925 5.300000e-47 198.0
3 TraesCS6B01G060800 chr6D 88.250 783 48 19 857 1619 24595723 24594965 0.000000e+00 896.0
4 TraesCS6B01G060800 chr6D 80.206 778 116 23 818 1576 24580724 24579966 1.270000e-152 549.0
5 TraesCS6B01G060800 chr6D 89.933 149 14 1 1616 1763 24593719 24593571 8.880000e-45 191.0
6 TraesCS6B01G060800 chr6D 92.308 117 9 0 2272 2388 24592982 24592866 1.500000e-37 167.0
7 TraesCS6B01G060800 chr6D 94.792 96 4 1 1776 1870 24593257 24593162 5.420000e-32 148.0
8 TraesCS6B01G060800 chr6D 100.000 45 0 0 2383 2427 24592812 24592768 1.550000e-12 84.2
9 TraesCS6B01G060800 chr6D 94.000 50 2 1 2383 2432 24579013 24578965 9.330000e-10 75.0
10 TraesCS6B01G060800 chr6A 91.416 664 30 13 854 1504 23388724 23389373 0.000000e+00 885.0
11 TraesCS6B01G060800 chr6A 79.016 772 120 27 820 1575 23399864 23400609 7.810000e-135 490.0
12 TraesCS6B01G060800 chr6A 79.545 264 45 7 9 268 37395883 37395625 1.920000e-41 180.0
13 TraesCS6B01G060800 chr6A 76.136 176 24 12 443 610 438027310 438027475 2.590000e-10 76.8
14 TraesCS6B01G060800 chr6A 93.750 48 3 0 1572 1619 23389398 23389445 3.350000e-09 73.1
15 TraesCS6B01G060800 chr5D 79.196 423 68 19 9 424 332445392 332445801 2.380000e-70 276.0
16 TraesCS6B01G060800 chr4D 75.626 439 78 26 2 424 424259988 424259563 8.880000e-45 191.0
17 TraesCS6B01G060800 chr4D 80.247 243 32 10 9 237 506882145 506881905 4.160000e-38 169.0
18 TraesCS6B01G060800 chr4D 79.310 261 34 17 2 253 483205583 483205334 5.380000e-37 165.0
19 TraesCS6B01G060800 chr4D 78.333 180 29 6 441 612 8920874 8921051 9.190000e-20 108.0
20 TraesCS6B01G060800 chr7D 75.120 418 70 25 15 424 25486111 25485720 5.380000e-37 165.0
21 TraesCS6B01G060800 chr7D 77.863 262 48 10 2 258 417934135 417934391 1.160000e-33 154.0
22 TraesCS6B01G060800 chr1A 78.409 264 43 13 9 268 443136869 443136616 2.500000e-35 159.0
23 TraesCS6B01G060800 chr5A 78.571 252 44 7 9 258 641376908 641376665 9.000000e-35 158.0
24 TraesCS6B01G060800 chrUn 80.000 125 16 5 2272 2389 469884542 469884420 1.550000e-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 TraesCS6B01G060800 chr6B 40431899 40434330 2431 True 1909.00 3518 100.0000 1 2432 2 chr6B.!!$R2 2431
1 TraesCS6B01G060800 chr6D 24578965 24580724 1759 True 312.00 549 87.1030 818 2432 2 chr6D.!!$R1 1614
2 TraesCS6B01G060800 chr6D 24592768 24595723 2955 True 297.24 896 93.0566 857 2427 5 chr6D.!!$R2 1570
3 TraesCS6B01G060800 chr6A 23399864 23400609 745 False 490.00 490 79.0160 820 1575 1 chr6A.!!$F1 755
4 TraesCS6B01G060800 chr6A 23388724 23389445 721 False 479.05 885 92.5830 854 1619 2 chr6A.!!$F3 765

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
683 684 0.175073 GATCCTACCAACTCGCCGTT 59.825 55.0 0.0 0.0 35.88 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 2768 0.459585 GGCCGCGAACTTATGTGAGA 60.46 55.0 8.23 0.0 0.0 3.27 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
25 26 8.680039 TTTCATCCTTTTTCAAATGCTTGATT 57.320 26.923 0.00 0.00 41.22 2.57
26 27 9.775854 TTTCATCCTTTTTCAAATGCTTGATTA 57.224 25.926 0.00 0.00 41.22 1.75
27 28 9.775854 TTCATCCTTTTTCAAATGCTTGATTAA 57.224 25.926 0.00 0.00 41.22 1.40
28 29 9.206870 TCATCCTTTTTCAAATGCTTGATTAAC 57.793 29.630 0.00 0.00 41.22 2.01
29 30 8.991026 CATCCTTTTTCAAATGCTTGATTAACA 58.009 29.630 0.00 0.00 41.22 2.41
30 31 9.729281 ATCCTTTTTCAAATGCTTGATTAACAT 57.271 25.926 0.00 0.00 41.22 2.71
31 32 9.558396 TCCTTTTTCAAATGCTTGATTAACATT 57.442 25.926 0.00 0.00 41.22 2.71
124 125 8.905660 AACAAATTTCCAATGATTGATCAACA 57.094 26.923 11.07 11.30 40.69 3.33
125 126 9.509956 AACAAATTTCCAATGATTGATCAACAT 57.490 25.926 11.07 13.03 40.69 2.71
126 127 9.509956 ACAAATTTCCAATGATTGATCAACATT 57.490 25.926 20.89 20.89 40.69 2.71
131 132 9.557061 TTTCCAATGATTGATCAACATTTTTCA 57.443 25.926 22.64 16.89 40.69 2.69
132 133 9.557061 TTCCAATGATTGATCAACATTTTTCAA 57.443 25.926 22.64 14.61 40.69 2.69
133 134 9.557061 TCCAATGATTGATCAACATTTTTCAAA 57.443 25.926 22.64 10.15 40.69 2.69
256 257 8.715191 TTCACATTTAACACTTTTCAAATGCT 57.285 26.923 5.95 0.00 40.43 3.79
257 258 8.715191 TCACATTTAACACTTTTCAAATGCTT 57.285 26.923 5.95 0.00 40.43 3.91
258 259 9.809096 TCACATTTAACACTTTTCAAATGCTTA 57.191 25.926 5.95 0.00 40.43 3.09
260 261 9.816354 ACATTTAACACTTTTCAAATGCTTAGT 57.184 25.926 5.95 0.00 40.43 2.24
262 263 8.865590 TTTAACACTTTTCAAATGCTTAGTCC 57.134 30.769 0.00 0.00 0.00 3.85
263 264 6.463995 AACACTTTTCAAATGCTTAGTCCA 57.536 33.333 0.00 0.00 0.00 4.02
264 265 5.831997 ACACTTTTCAAATGCTTAGTCCAC 58.168 37.500 0.00 0.00 0.00 4.02
265 266 5.359576 ACACTTTTCAAATGCTTAGTCCACA 59.640 36.000 0.00 0.00 0.00 4.17
266 267 6.040842 ACACTTTTCAAATGCTTAGTCCACAT 59.959 34.615 0.00 0.00 0.00 3.21
267 268 6.925165 CACTTTTCAAATGCTTAGTCCACATT 59.075 34.615 0.00 0.00 35.59 2.71
268 269 8.081633 CACTTTTCAAATGCTTAGTCCACATTA 58.918 33.333 0.00 0.00 33.01 1.90
269 270 8.637986 ACTTTTCAAATGCTTAGTCCACATTAA 58.362 29.630 0.00 0.00 33.01 1.40
270 271 9.474920 CTTTTCAAATGCTTAGTCCACATTAAA 57.525 29.630 0.00 0.00 33.01 1.52
271 272 9.823647 TTTTCAAATGCTTAGTCCACATTAAAA 57.176 25.926 0.00 0.00 33.01 1.52
272 273 9.823647 TTTCAAATGCTTAGTCCACATTAAAAA 57.176 25.926 0.00 0.00 33.01 1.94
273 274 9.474920 TTCAAATGCTTAGTCCACATTAAAAAG 57.525 29.630 0.00 0.00 33.01 2.27
274 275 8.855110 TCAAATGCTTAGTCCACATTAAAAAGA 58.145 29.630 0.00 0.00 33.01 2.52
275 276 9.474920 CAAATGCTTAGTCCACATTAAAAAGAA 57.525 29.630 0.00 0.00 33.01 2.52
279 280 9.515226 TGCTTAGTCCACATTAAAAAGAATAGT 57.485 29.630 0.00 0.00 0.00 2.12
390 391 2.278332 AAAAGAGAGGAGGTTGTGGC 57.722 50.000 0.00 0.00 0.00 5.01
391 392 0.402121 AAAGAGAGGAGGTTGTGGCC 59.598 55.000 0.00 0.00 0.00 5.36
392 393 0.474660 AAGAGAGGAGGTTGTGGCCT 60.475 55.000 3.32 0.00 42.53 5.19
404 405 4.392166 TGGCCTCCCACGCTCCTA 62.392 66.667 3.32 0.00 35.79 2.94
405 406 3.541713 GGCCTCCCACGCTCCTAG 61.542 72.222 0.00 0.00 0.00 3.02
406 407 3.541713 GCCTCCCACGCTCCTAGG 61.542 72.222 0.82 0.82 0.00 3.02
407 408 3.541713 CCTCCCACGCTCCTAGGC 61.542 72.222 2.96 0.00 0.00 3.93
408 409 2.443016 CTCCCACGCTCCTAGGCT 60.443 66.667 2.96 0.00 0.00 4.58
409 410 1.152735 CTCCCACGCTCCTAGGCTA 60.153 63.158 2.96 0.00 0.00 3.93
410 411 1.152735 TCCCACGCTCCTAGGCTAG 60.153 63.158 14.77 14.77 0.00 3.42
411 412 2.731374 CCACGCTCCTAGGCTAGC 59.269 66.667 16.26 6.04 35.33 3.42
412 413 2.731374 CACGCTCCTAGGCTAGCC 59.269 66.667 27.19 27.19 35.22 3.93
413 414 2.522193 ACGCTCCTAGGCTAGCCC 60.522 66.667 30.42 12.66 35.22 5.19
414 415 2.521950 CGCTCCTAGGCTAGCCCA 60.522 66.667 30.42 16.83 35.22 5.36
415 416 1.910772 CGCTCCTAGGCTAGCCCAT 60.911 63.158 30.42 15.60 35.22 4.00
416 417 1.882989 CGCTCCTAGGCTAGCCCATC 61.883 65.000 30.42 12.32 35.22 3.51
417 418 0.544120 GCTCCTAGGCTAGCCCATCT 60.544 60.000 30.42 14.41 36.58 2.90
418 419 1.555967 CTCCTAGGCTAGCCCATCTC 58.444 60.000 30.42 4.01 36.58 2.75
419 420 1.077005 CTCCTAGGCTAGCCCATCTCT 59.923 57.143 30.42 13.21 36.58 3.10
420 421 1.203112 TCCTAGGCTAGCCCATCTCTG 60.203 57.143 30.42 11.86 36.58 3.35
421 422 1.482177 CCTAGGCTAGCCCATCTCTGT 60.482 57.143 30.42 11.64 36.58 3.41
422 423 1.892474 CTAGGCTAGCCCATCTCTGTC 59.108 57.143 30.42 0.76 36.58 3.51
423 424 0.264359 AGGCTAGCCCATCTCTGTCT 59.736 55.000 30.42 4.39 36.58 3.41
424 425 1.127343 GGCTAGCCCATCTCTGTCTT 58.873 55.000 24.19 0.00 0.00 3.01
425 426 1.069978 GGCTAGCCCATCTCTGTCTTC 59.930 57.143 24.19 0.00 0.00 2.87
426 427 1.759445 GCTAGCCCATCTCTGTCTTCA 59.241 52.381 2.29 0.00 0.00 3.02
427 428 2.482839 GCTAGCCCATCTCTGTCTTCAC 60.483 54.545 2.29 0.00 0.00 3.18
428 429 1.649321 AGCCCATCTCTGTCTTCACA 58.351 50.000 0.00 0.00 0.00 3.58
441 442 5.330455 TGTCTTCACAGTAGCTAATCTGG 57.670 43.478 14.07 5.37 36.17 3.86
442 443 4.160439 TGTCTTCACAGTAGCTAATCTGGG 59.840 45.833 14.07 10.84 36.54 4.45
443 444 4.402793 GTCTTCACAGTAGCTAATCTGGGA 59.597 45.833 11.30 11.30 41.52 4.37
445 446 5.344743 TTCACAGTAGCTAATCTGGGAAG 57.655 43.478 19.82 6.88 45.33 3.46
446 447 4.610333 TCACAGTAGCTAATCTGGGAAGA 58.390 43.478 12.62 4.63 40.50 2.87
447 448 4.402793 TCACAGTAGCTAATCTGGGAAGAC 59.597 45.833 12.62 0.00 40.50 3.01
448 449 4.160439 CACAGTAGCTAATCTGGGAAGACA 59.840 45.833 14.07 0.00 37.27 3.41
449 450 4.777896 ACAGTAGCTAATCTGGGAAGACAA 59.222 41.667 14.07 0.00 36.17 3.18
450 451 5.112686 CAGTAGCTAATCTGGGAAGACAAC 58.887 45.833 0.00 0.00 0.00 3.32
451 452 3.252974 AGCTAATCTGGGAAGACAACG 57.747 47.619 0.00 0.00 0.00 4.10
452 453 2.832129 AGCTAATCTGGGAAGACAACGA 59.168 45.455 0.00 0.00 0.00 3.85
453 454 3.260884 AGCTAATCTGGGAAGACAACGAA 59.739 43.478 0.00 0.00 0.00 3.85
454 455 4.000988 GCTAATCTGGGAAGACAACGAAA 58.999 43.478 0.00 0.00 0.00 3.46
455 456 4.454504 GCTAATCTGGGAAGACAACGAAAA 59.545 41.667 0.00 0.00 0.00 2.29
456 457 5.123979 GCTAATCTGGGAAGACAACGAAAAT 59.876 40.000 0.00 0.00 0.00 1.82
457 458 6.349363 GCTAATCTGGGAAGACAACGAAAATT 60.349 38.462 0.00 0.00 0.00 1.82
458 459 6.405278 AATCTGGGAAGACAACGAAAATTT 57.595 33.333 0.00 0.00 0.00 1.82
459 460 5.845391 TCTGGGAAGACAACGAAAATTTT 57.155 34.783 2.28 2.28 0.00 1.82
460 461 5.587289 TCTGGGAAGACAACGAAAATTTTG 58.413 37.500 8.47 3.68 0.00 2.44
461 462 5.358442 TCTGGGAAGACAACGAAAATTTTGA 59.642 36.000 8.47 0.00 0.00 2.69
462 463 6.040391 TCTGGGAAGACAACGAAAATTTTGAT 59.960 34.615 8.47 0.00 0.00 2.57
463 464 6.578023 TGGGAAGACAACGAAAATTTTGATT 58.422 32.000 8.47 0.00 0.00 2.57
464 465 6.478344 TGGGAAGACAACGAAAATTTTGATTG 59.522 34.615 8.47 13.82 0.00 2.67
465 466 6.699642 GGGAAGACAACGAAAATTTTGATTGA 59.300 34.615 21.92 0.00 0.00 2.57
466 467 7.096065 GGGAAGACAACGAAAATTTTGATTGAG 60.096 37.037 21.92 6.84 0.00 3.02
467 468 7.435192 GGAAGACAACGAAAATTTTGATTGAGT 59.565 33.333 21.92 9.27 0.00 3.41
468 469 8.702163 AAGACAACGAAAATTTTGATTGAGTT 57.298 26.923 21.92 14.51 0.00 3.01
469 470 8.118893 AGACAACGAAAATTTTGATTGAGTTG 57.881 30.769 21.92 19.52 41.25 3.16
470 471 7.973388 AGACAACGAAAATTTTGATTGAGTTGA 59.027 29.630 21.92 0.00 39.49 3.18
471 472 8.118893 ACAACGAAAATTTTGATTGAGTTGAG 57.881 30.769 21.92 7.30 39.49 3.02
472 473 7.973388 ACAACGAAAATTTTGATTGAGTTGAGA 59.027 29.630 21.92 0.00 39.49 3.27
473 474 8.971321 CAACGAAAATTTTGATTGAGTTGAGAT 58.029 29.630 8.47 0.00 38.80 2.75
474 475 9.533253 AACGAAAATTTTGATTGAGTTGAGATT 57.467 25.926 8.47 0.00 0.00 2.40
475 476 9.533253 ACGAAAATTTTGATTGAGTTGAGATTT 57.467 25.926 8.47 0.00 0.00 2.17
521 522 8.839947 TTATTTGATTGAGTTAATGCATGACG 57.160 30.769 0.00 0.00 0.00 4.35
522 523 5.878332 TTGATTGAGTTAATGCATGACGT 57.122 34.783 0.00 0.00 0.00 4.34
523 524 6.976636 TTGATTGAGTTAATGCATGACGTA 57.023 33.333 0.00 0.00 0.00 3.57
524 525 7.552458 TTGATTGAGTTAATGCATGACGTAT 57.448 32.000 0.00 0.00 0.00 3.06
525 526 7.552458 TGATTGAGTTAATGCATGACGTATT 57.448 32.000 0.00 0.00 34.03 1.89
526 527 7.984391 TGATTGAGTTAATGCATGACGTATTT 58.016 30.769 0.00 0.00 31.71 1.40
527 528 8.458052 TGATTGAGTTAATGCATGACGTATTTT 58.542 29.630 0.00 0.00 31.71 1.82
528 529 8.619146 ATTGAGTTAATGCATGACGTATTTTG 57.381 30.769 0.00 0.00 31.71 2.44
529 530 7.371126 TGAGTTAATGCATGACGTATTTTGA 57.629 32.000 0.00 0.00 31.71 2.69
530 531 7.984391 TGAGTTAATGCATGACGTATTTTGAT 58.016 30.769 0.00 0.00 31.71 2.57
531 532 8.122330 TGAGTTAATGCATGACGTATTTTGATC 58.878 33.333 0.00 0.00 31.71 2.92
532 533 7.984391 AGTTAATGCATGACGTATTTTGATCA 58.016 30.769 0.00 0.00 31.71 2.92
533 534 8.458052 AGTTAATGCATGACGTATTTTGATCAA 58.542 29.630 3.38 3.38 31.71 2.57
534 535 9.236691 GTTAATGCATGACGTATTTTGATCAAT 57.763 29.630 9.40 0.00 31.71 2.57
535 536 9.800433 TTAATGCATGACGTATTTTGATCAATT 57.200 25.926 9.40 2.85 31.71 2.32
536 537 8.706492 AATGCATGACGTATTTTGATCAATTT 57.294 26.923 9.40 2.48 0.00 1.82
537 538 8.706492 ATGCATGACGTATTTTGATCAATTTT 57.294 26.923 9.40 0.00 0.00 1.82
538 539 7.951287 TGCATGACGTATTTTGATCAATTTTG 58.049 30.769 9.40 1.63 0.00 2.44
539 540 7.598118 TGCATGACGTATTTTGATCAATTTTGT 59.402 29.630 9.40 4.88 0.00 2.83
540 541 8.434661 GCATGACGTATTTTGATCAATTTTGTT 58.565 29.630 9.40 0.00 0.00 2.83
573 574 7.549147 TTCAAGTTACTCTATTAGTGGTGGT 57.451 36.000 0.00 0.00 39.39 4.16
574 575 7.549147 TCAAGTTACTCTATTAGTGGTGGTT 57.451 36.000 0.00 0.00 39.39 3.67
575 576 7.970102 TCAAGTTACTCTATTAGTGGTGGTTT 58.030 34.615 0.00 0.00 39.39 3.27
576 577 8.434392 TCAAGTTACTCTATTAGTGGTGGTTTT 58.566 33.333 0.00 0.00 39.39 2.43
577 578 9.715121 CAAGTTACTCTATTAGTGGTGGTTTTA 57.285 33.333 0.00 0.00 39.39 1.52
583 584 9.582648 ACTCTATTAGTGGTGGTTTTATTTTGT 57.417 29.630 0.00 0.00 36.93 2.83
586 587 9.337091 CTATTAGTGGTGGTTTTATTTTGTTCG 57.663 33.333 0.00 0.00 0.00 3.95
587 588 4.939271 AGTGGTGGTTTTATTTTGTTCGG 58.061 39.130 0.00 0.00 0.00 4.30
588 589 3.491639 GTGGTGGTTTTATTTTGTTCGGC 59.508 43.478 0.00 0.00 0.00 5.54
589 590 3.061322 GGTGGTTTTATTTTGTTCGGCC 58.939 45.455 0.00 0.00 0.00 6.13
590 591 3.243941 GGTGGTTTTATTTTGTTCGGCCT 60.244 43.478 0.00 0.00 0.00 5.19
591 592 3.985279 GTGGTTTTATTTTGTTCGGCCTC 59.015 43.478 0.00 0.00 0.00 4.70
592 593 3.637229 TGGTTTTATTTTGTTCGGCCTCA 59.363 39.130 0.00 0.00 0.00 3.86
593 594 4.234574 GGTTTTATTTTGTTCGGCCTCAG 58.765 43.478 0.00 0.00 0.00 3.35
594 595 4.261867 GGTTTTATTTTGTTCGGCCTCAGT 60.262 41.667 0.00 0.00 0.00 3.41
595 596 5.286438 GTTTTATTTTGTTCGGCCTCAGTT 58.714 37.500 0.00 0.00 0.00 3.16
596 597 4.497473 TTATTTTGTTCGGCCTCAGTTG 57.503 40.909 0.00 0.00 0.00 3.16
597 598 2.045561 TTTTGTTCGGCCTCAGTTGA 57.954 45.000 0.00 0.00 0.00 3.18
598 599 1.593196 TTTGTTCGGCCTCAGTTGAG 58.407 50.000 0.00 2.09 41.71 3.02
599 600 0.756294 TTGTTCGGCCTCAGTTGAGA 59.244 50.000 10.64 0.00 44.74 3.27
600 601 0.976641 TGTTCGGCCTCAGTTGAGAT 59.023 50.000 10.64 0.00 44.74 2.75
601 602 2.176045 TGTTCGGCCTCAGTTGAGATA 58.824 47.619 10.64 0.00 44.74 1.98
602 603 2.766263 TGTTCGGCCTCAGTTGAGATAT 59.234 45.455 10.64 0.00 44.74 1.63
603 604 3.958147 TGTTCGGCCTCAGTTGAGATATA 59.042 43.478 10.64 0.00 44.74 0.86
604 605 4.404394 TGTTCGGCCTCAGTTGAGATATAA 59.596 41.667 10.64 0.00 44.74 0.98
605 606 4.585955 TCGGCCTCAGTTGAGATATAAC 57.414 45.455 10.64 0.00 44.74 1.89
606 607 3.958147 TCGGCCTCAGTTGAGATATAACA 59.042 43.478 10.64 0.00 44.74 2.41
607 608 4.404394 TCGGCCTCAGTTGAGATATAACAA 59.596 41.667 10.64 0.00 44.74 2.83
608 609 5.105106 TCGGCCTCAGTTGAGATATAACAAA 60.105 40.000 10.64 0.00 44.74 2.83
609 610 5.584649 CGGCCTCAGTTGAGATATAACAAAA 59.415 40.000 10.64 0.00 44.74 2.44
610 611 6.093495 CGGCCTCAGTTGAGATATAACAAAAA 59.907 38.462 10.64 0.00 44.74 1.94
642 643 2.699938 GGGGGTGGGTGGGATGAT 60.700 66.667 0.00 0.00 0.00 2.45
643 644 1.386772 GGGGGTGGGTGGGATGATA 60.387 63.158 0.00 0.00 0.00 2.15
644 645 0.996762 GGGGGTGGGTGGGATGATAA 60.997 60.000 0.00 0.00 0.00 1.75
645 646 0.930726 GGGGTGGGTGGGATGATAAA 59.069 55.000 0.00 0.00 0.00 1.40
646 647 1.289530 GGGGTGGGTGGGATGATAAAA 59.710 52.381 0.00 0.00 0.00 1.52
647 648 2.384828 GGGTGGGTGGGATGATAAAAC 58.615 52.381 0.00 0.00 0.00 2.43
648 649 2.384828 GGTGGGTGGGATGATAAAACC 58.615 52.381 0.00 0.00 0.00 3.27
649 650 2.291930 GGTGGGTGGGATGATAAAACCA 60.292 50.000 0.00 0.00 32.28 3.67
650 651 3.023832 GTGGGTGGGATGATAAAACCAG 58.976 50.000 0.00 0.00 32.84 4.00
651 652 2.652348 TGGGTGGGATGATAAAACCAGT 59.348 45.455 0.00 0.00 32.84 4.00
652 653 3.023832 GGGTGGGATGATAAAACCAGTG 58.976 50.000 0.00 0.00 32.84 3.66
653 654 3.023832 GGTGGGATGATAAAACCAGTGG 58.976 50.000 7.91 7.91 32.84 4.00
654 655 3.308832 GGTGGGATGATAAAACCAGTGGA 60.309 47.826 18.40 0.00 32.84 4.02
655 656 3.947834 GTGGGATGATAAAACCAGTGGAG 59.052 47.826 18.40 0.00 32.84 3.86
656 657 3.053693 TGGGATGATAAAACCAGTGGAGG 60.054 47.826 18.40 0.00 0.00 4.30
657 658 3.053619 GGGATGATAAAACCAGTGGAGGT 60.054 47.826 18.40 2.12 45.91 3.85
658 659 3.947834 GGATGATAAAACCAGTGGAGGTG 59.052 47.826 18.40 0.00 42.25 4.00
659 660 3.433306 TGATAAAACCAGTGGAGGTGG 57.567 47.619 18.40 0.00 42.25 4.61
660 661 2.041081 TGATAAAACCAGTGGAGGTGGG 59.959 50.000 18.40 0.00 42.25 4.61
661 662 0.774908 TAAAACCAGTGGAGGTGGGG 59.225 55.000 18.40 0.00 42.25 4.96
662 663 2.018884 AAAACCAGTGGAGGTGGGGG 62.019 60.000 18.40 0.00 42.25 5.40
666 667 4.741239 AGTGGAGGTGGGGGCGAT 62.741 66.667 0.00 0.00 0.00 4.58
667 668 4.176752 GTGGAGGTGGGGGCGATC 62.177 72.222 0.00 0.00 0.00 3.69
670 671 2.122989 GAGGTGGGGGCGATCCTA 60.123 66.667 0.00 0.00 35.33 2.94
671 672 2.446036 AGGTGGGGGCGATCCTAC 60.446 66.667 3.06 3.06 37.53 3.18
673 674 2.766651 GTGGGGGCGATCCTACCA 60.767 66.667 0.00 0.00 37.14 3.25
674 675 2.041430 TGGGGGCGATCCTACCAA 59.959 61.111 0.00 0.00 36.76 3.67
675 676 2.372074 TGGGGGCGATCCTACCAAC 61.372 63.158 0.00 0.00 36.76 3.77
676 677 2.070650 GGGGGCGATCCTACCAACT 61.071 63.158 0.00 0.00 35.33 3.16
677 678 1.446366 GGGGCGATCCTACCAACTC 59.554 63.158 0.00 0.00 35.33 3.01
678 679 1.067582 GGGCGATCCTACCAACTCG 59.932 63.158 0.00 0.00 0.00 4.18
680 681 4.732106 CGATCCTACCAACTCGCC 57.268 61.111 0.00 0.00 0.00 5.54
681 682 1.299165 CGATCCTACCAACTCGCCG 60.299 63.158 0.00 0.00 0.00 6.46
682 683 1.814527 GATCCTACCAACTCGCCGT 59.185 57.895 0.00 0.00 0.00 5.68
683 684 0.175073 GATCCTACCAACTCGCCGTT 59.825 55.000 0.00 0.00 35.88 4.44
684 685 1.406539 GATCCTACCAACTCGCCGTTA 59.593 52.381 0.00 0.00 33.63 3.18
685 686 1.255882 TCCTACCAACTCGCCGTTAA 58.744 50.000 0.00 0.00 33.63 2.01
686 687 1.826720 TCCTACCAACTCGCCGTTAAT 59.173 47.619 0.00 0.00 33.63 1.40
687 688 3.023119 TCCTACCAACTCGCCGTTAATA 58.977 45.455 0.00 0.00 33.63 0.98
688 689 3.446873 TCCTACCAACTCGCCGTTAATAA 59.553 43.478 0.00 0.00 33.63 1.40
689 690 4.099881 TCCTACCAACTCGCCGTTAATAAT 59.900 41.667 0.00 0.00 33.63 1.28
690 691 5.301551 TCCTACCAACTCGCCGTTAATAATA 59.698 40.000 0.00 0.00 33.63 0.98
691 692 5.632347 CCTACCAACTCGCCGTTAATAATAG 59.368 44.000 0.00 0.00 33.63 1.73
692 693 5.014808 ACCAACTCGCCGTTAATAATAGT 57.985 39.130 0.00 0.00 33.63 2.12
693 694 5.045872 ACCAACTCGCCGTTAATAATAGTC 58.954 41.667 0.00 0.00 33.63 2.59
694 695 5.045215 CCAACTCGCCGTTAATAATAGTCA 58.955 41.667 0.00 0.00 33.63 3.41
695 696 5.521010 CCAACTCGCCGTTAATAATAGTCAA 59.479 40.000 0.00 0.00 33.63 3.18
696 697 6.292168 CCAACTCGCCGTTAATAATAGTCAAG 60.292 42.308 0.00 0.00 33.63 3.02
697 698 6.140303 ACTCGCCGTTAATAATAGTCAAGA 57.860 37.500 0.00 0.00 0.00 3.02
698 699 6.746120 ACTCGCCGTTAATAATAGTCAAGAT 58.254 36.000 0.00 0.00 0.00 2.40
699 700 7.879070 ACTCGCCGTTAATAATAGTCAAGATA 58.121 34.615 0.00 0.00 0.00 1.98
700 701 8.021973 ACTCGCCGTTAATAATAGTCAAGATAG 58.978 37.037 0.00 0.00 0.00 2.08
701 702 8.102800 TCGCCGTTAATAATAGTCAAGATAGA 57.897 34.615 0.00 0.00 0.00 1.98
702 703 8.235226 TCGCCGTTAATAATAGTCAAGATAGAG 58.765 37.037 0.00 0.00 0.00 2.43
703 704 8.235226 CGCCGTTAATAATAGTCAAGATAGAGA 58.765 37.037 0.00 0.00 0.00 3.10
758 759 9.316730 ACATCATTGATTAATAACAACAATGGC 57.683 29.630 19.06 0.00 44.13 4.40
759 760 9.315525 CATCATTGATTAATAACAACAATGGCA 57.684 29.630 19.06 0.00 44.13 4.92
760 761 9.887629 ATCATTGATTAATAACAACAATGGCAA 57.112 25.926 19.06 7.54 44.13 4.52
761 762 9.887629 TCATTGATTAATAACAACAATGGCAAT 57.112 25.926 19.06 6.09 44.13 3.56
828 829 4.280789 ACAACTACCATCCATCCCTCTA 57.719 45.455 0.00 0.00 0.00 2.43
829 830 4.832492 ACAACTACCATCCATCCCTCTAT 58.168 43.478 0.00 0.00 0.00 1.98
830 831 5.227593 ACAACTACCATCCATCCCTCTATT 58.772 41.667 0.00 0.00 0.00 1.73
831 832 6.390504 ACAACTACCATCCATCCCTCTATTA 58.609 40.000 0.00 0.00 0.00 0.98
832 833 6.498651 ACAACTACCATCCATCCCTCTATTAG 59.501 42.308 0.00 0.00 0.00 1.73
834 835 3.185455 ACCATCCATCCCTCTATTAGCC 58.815 50.000 0.00 0.00 0.00 3.93
835 836 2.169352 CCATCCATCCCTCTATTAGCCG 59.831 54.545 0.00 0.00 0.00 5.52
836 837 1.938585 TCCATCCCTCTATTAGCCGG 58.061 55.000 0.00 0.00 0.00 6.13
837 838 0.250513 CCATCCCTCTATTAGCCGGC 59.749 60.000 21.89 21.89 0.00 6.13
839 840 1.066573 CATCCCTCTATTAGCCGGCAG 60.067 57.143 31.54 17.75 0.00 4.85
840 841 0.187606 TCCCTCTATTAGCCGGCAGA 59.812 55.000 31.54 21.24 0.00 4.26
841 842 1.048601 CCCTCTATTAGCCGGCAGAA 58.951 55.000 31.54 22.57 0.00 3.02
872 873 1.026584 TGGAGTCAAAGTCGTCGTCA 58.973 50.000 0.00 0.00 0.00 4.35
893 900 2.872557 CACCGCTGATGTGCTTGG 59.127 61.111 0.00 0.00 0.00 3.61
894 901 3.058160 ACCGCTGATGTGCTTGGC 61.058 61.111 0.00 0.00 0.00 4.52
896 903 3.425713 CGCTGATGTGCTTGGCGT 61.426 61.111 0.00 0.00 40.78 5.68
897 904 2.956987 GCTGATGTGCTTGGCGTT 59.043 55.556 0.00 0.00 0.00 4.84
898 905 1.443194 GCTGATGTGCTTGGCGTTG 60.443 57.895 0.00 0.00 0.00 4.10
899 906 1.210931 CTGATGTGCTTGGCGTTGG 59.789 57.895 0.00 0.00 0.00 3.77
900 907 2.126346 GATGTGCTTGGCGTTGGC 60.126 61.111 0.00 0.00 38.90 4.52
936 953 4.056050 CACGCTCCACTTTTTGTACTACT 58.944 43.478 0.00 0.00 0.00 2.57
937 954 4.150098 CACGCTCCACTTTTTGTACTACTC 59.850 45.833 0.00 0.00 0.00 2.59
1026 1050 1.677637 ATCCCTCGCCGTTCCTCTTC 61.678 60.000 0.00 0.00 0.00 2.87
1374 1404 2.124695 AGCCTCGCCGATTTTCCC 60.125 61.111 0.00 0.00 0.00 3.97
1507 1589 3.049674 CGTGCATCTTGTGGCGGT 61.050 61.111 0.00 0.00 0.00 5.68
1515 1597 1.698506 TCTTGTGGCGGTCCAATTTT 58.301 45.000 0.00 0.00 45.53 1.82
1539 1625 6.761731 TTTTACTTGGTTTGCGATTGATTG 57.238 33.333 0.00 0.00 0.00 2.67
1542 1628 0.109365 TGGTTTGCGATTGATTGCCG 60.109 50.000 0.93 0.00 36.33 5.69
1577 1677 2.493278 GTTGTGCAGCCCAACATTAGAT 59.507 45.455 15.15 0.00 41.40 1.98
1697 3082 4.474287 GGTAGCTAGGGCCTAGAGTAGATA 59.526 50.000 38.58 18.34 36.26 1.98
1746 3131 0.512518 CCGAGTGTGACGTACGTGTA 59.487 55.000 28.16 11.92 0.00 2.90
1764 3149 4.495019 CGTGTACGAGAAAGGAGATGAGAG 60.495 50.000 0.00 0.00 43.02 3.20
1766 3151 5.010933 TGTACGAGAAAGGAGATGAGAGTT 58.989 41.667 0.00 0.00 0.00 3.01
1767 3152 4.448537 ACGAGAAAGGAGATGAGAGTTG 57.551 45.455 0.00 0.00 0.00 3.16
1768 3153 3.194542 ACGAGAAAGGAGATGAGAGTTGG 59.805 47.826 0.00 0.00 0.00 3.77
1769 3154 3.530535 GAGAAAGGAGATGAGAGTTGGC 58.469 50.000 0.00 0.00 0.00 4.52
1770 3155 3.180507 AGAAAGGAGATGAGAGTTGGCT 58.819 45.455 0.00 0.00 0.00 4.75
1774 3159 5.707066 AAGGAGATGAGAGTTGGCTTAAT 57.293 39.130 0.00 0.00 0.00 1.40
1794 3480 1.619057 TGTCCTCCATGGGCCATGA 60.619 57.895 41.10 26.97 43.81 3.07
1799 3485 1.411930 CCTCCATGGGCCATGATTTGA 60.412 52.381 41.10 28.84 43.81 2.69
1856 3542 2.557056 GTCCTAGTAGCACGATGGCATA 59.443 50.000 0.00 0.00 35.83 3.14
1880 3636 3.107601 CTGGGACCAATAGAAGAGGACA 58.892 50.000 0.00 0.00 0.00 4.02
1885 3649 5.104318 GGGACCAATAGAAGAGGACAAAGAT 60.104 44.000 0.00 0.00 0.00 2.40
1896 3660 8.277918 AGAAGAGGACAAAGATAAATATTGGCT 58.722 33.333 0.00 0.00 32.58 4.75
2295 4059 2.267351 TTGAGCGGTGTTGGGCATG 61.267 57.895 0.00 0.00 0.00 4.06
2378 4142 4.315803 TCGAATGGTTTGAGGAGTTTCTC 58.684 43.478 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.680039 AATCAAGCATTTGAAAAAGGATGAAA 57.320 26.923 0.00 0.00 45.82 2.69
1 2 9.775854 TTAATCAAGCATTTGAAAAAGGATGAA 57.224 25.926 0.00 0.00 45.82 2.57
2 3 9.206870 GTTAATCAAGCATTTGAAAAAGGATGA 57.793 29.630 0.00 0.00 45.82 2.92
3 4 8.991026 TGTTAATCAAGCATTTGAAAAAGGATG 58.009 29.630 0.00 0.00 45.82 3.51
4 5 9.729281 ATGTTAATCAAGCATTTGAAAAAGGAT 57.271 25.926 0.00 0.00 45.82 3.24
5 6 9.558396 AATGTTAATCAAGCATTTGAAAAAGGA 57.442 25.926 0.00 0.00 45.82 3.36
98 99 9.993454 TGTTGATCAATCATTGGAAATTTGTTA 57.007 25.926 12.12 0.00 36.56 2.41
99 100 8.905660 TGTTGATCAATCATTGGAAATTTGTT 57.094 26.923 12.12 0.00 36.56 2.83
100 101 9.509956 AATGTTGATCAATCATTGGAAATTTGT 57.490 25.926 23.59 6.90 36.56 2.83
105 106 9.557061 TGAAAAATGTTGATCAATCATTGGAAA 57.443 25.926 24.31 14.66 36.56 3.13
106 107 9.557061 TTGAAAAATGTTGATCAATCATTGGAA 57.443 25.926 24.31 16.28 36.56 3.53
107 108 9.557061 TTTGAAAAATGTTGATCAATCATTGGA 57.443 25.926 24.31 13.27 36.56 3.53
230 231 9.328845 AGCATTTGAAAAGTGTTAAATGTGAAT 57.671 25.926 0.00 0.00 40.70 2.57
231 232 8.715191 AGCATTTGAAAAGTGTTAAATGTGAA 57.285 26.923 0.00 0.00 40.70 3.18
232 233 8.715191 AAGCATTTGAAAAGTGTTAAATGTGA 57.285 26.923 0.00 0.00 40.70 3.58
234 235 9.816354 ACTAAGCATTTGAAAAGTGTTAAATGT 57.184 25.926 0.00 0.00 40.70 2.71
236 237 9.476202 GGACTAAGCATTTGAAAAGTGTTAAAT 57.524 29.630 0.00 0.00 35.77 1.40
237 238 8.470805 TGGACTAAGCATTTGAAAAGTGTTAAA 58.529 29.630 0.00 0.00 35.77 1.52
238 239 7.918562 GTGGACTAAGCATTTGAAAAGTGTTAA 59.081 33.333 0.00 0.00 35.77 2.01
239 240 7.067615 TGTGGACTAAGCATTTGAAAAGTGTTA 59.932 33.333 0.00 0.00 35.77 2.41
240 241 6.127479 TGTGGACTAAGCATTTGAAAAGTGTT 60.127 34.615 0.00 0.00 35.77 3.32
241 242 5.359576 TGTGGACTAAGCATTTGAAAAGTGT 59.640 36.000 0.00 0.00 35.77 3.55
242 243 5.830912 TGTGGACTAAGCATTTGAAAAGTG 58.169 37.500 0.00 0.00 36.52 3.16
243 244 6.655078 ATGTGGACTAAGCATTTGAAAAGT 57.345 33.333 0.00 0.00 0.00 2.66
244 245 9.474920 TTTAATGTGGACTAAGCATTTGAAAAG 57.525 29.630 0.00 0.00 34.97 2.27
245 246 9.823647 TTTTAATGTGGACTAAGCATTTGAAAA 57.176 25.926 0.00 0.00 34.97 2.29
246 247 9.823647 TTTTTAATGTGGACTAAGCATTTGAAA 57.176 25.926 0.00 0.00 34.97 2.69
247 248 9.474920 CTTTTTAATGTGGACTAAGCATTTGAA 57.525 29.630 0.00 0.00 34.97 2.69
248 249 8.855110 TCTTTTTAATGTGGACTAAGCATTTGA 58.145 29.630 0.00 0.00 34.97 2.69
249 250 9.474920 TTCTTTTTAATGTGGACTAAGCATTTG 57.525 29.630 0.00 0.00 34.97 2.32
253 254 9.515226 ACTATTCTTTTTAATGTGGACTAAGCA 57.485 29.630 0.00 0.00 0.00 3.91
370 371 2.587522 GCCACAACCTCCTCTCTTTTT 58.412 47.619 0.00 0.00 0.00 1.94
371 372 1.202940 GGCCACAACCTCCTCTCTTTT 60.203 52.381 0.00 0.00 0.00 2.27
372 373 0.402121 GGCCACAACCTCCTCTCTTT 59.598 55.000 0.00 0.00 0.00 2.52
373 374 0.474660 AGGCCACAACCTCCTCTCTT 60.475 55.000 5.01 0.00 33.62 2.85
374 375 1.159664 AGGCCACAACCTCCTCTCT 59.840 57.895 5.01 0.00 33.62 3.10
375 376 3.813150 AGGCCACAACCTCCTCTC 58.187 61.111 5.01 0.00 33.62 3.20
381 382 3.953775 CGTGGGAGGCCACAACCT 61.954 66.667 5.01 0.00 45.04 3.50
383 384 4.643387 AGCGTGGGAGGCCACAAC 62.643 66.667 5.01 0.00 40.38 3.32
384 385 4.329545 GAGCGTGGGAGGCCACAA 62.330 66.667 5.01 0.00 40.38 3.33
387 388 4.392166 TAGGAGCGTGGGAGGCCA 62.392 66.667 5.01 0.00 0.00 5.36
388 389 3.541713 CTAGGAGCGTGGGAGGCC 61.542 72.222 0.00 0.00 0.00 5.19
389 390 3.541713 CCTAGGAGCGTGGGAGGC 61.542 72.222 1.05 0.00 0.00 4.70
390 391 2.642183 TAGCCTAGGAGCGTGGGAGG 62.642 65.000 14.75 0.00 38.01 4.30
391 392 1.152735 TAGCCTAGGAGCGTGGGAG 60.153 63.158 14.75 0.00 38.01 4.30
392 393 1.152735 CTAGCCTAGGAGCGTGGGA 60.153 63.158 14.75 0.00 38.01 4.37
393 394 2.862223 GCTAGCCTAGGAGCGTGGG 61.862 68.421 14.75 0.00 38.01 4.61
394 395 2.731374 GCTAGCCTAGGAGCGTGG 59.269 66.667 14.75 0.00 38.01 4.94
395 396 2.731374 GGCTAGCCTAGGAGCGTG 59.269 66.667 27.17 0.00 39.72 5.34
396 397 2.522193 GGGCTAGCCTAGGAGCGT 60.522 66.667 32.18 0.00 39.72 5.07
397 398 1.882989 GATGGGCTAGCCTAGGAGCG 61.883 65.000 32.18 0.00 39.72 5.03
398 399 0.544120 AGATGGGCTAGCCTAGGAGC 60.544 60.000 32.18 13.71 38.00 4.70
399 400 1.077005 AGAGATGGGCTAGCCTAGGAG 59.923 57.143 32.18 2.50 36.10 3.69
400 401 1.162505 AGAGATGGGCTAGCCTAGGA 58.837 55.000 32.18 14.81 36.10 2.94
401 402 1.265236 CAGAGATGGGCTAGCCTAGG 58.735 60.000 32.18 3.67 36.10 3.02
402 403 1.892474 GACAGAGATGGGCTAGCCTAG 59.108 57.143 32.18 16.87 36.10 3.02
403 404 1.501170 AGACAGAGATGGGCTAGCCTA 59.499 52.381 32.18 28.06 36.10 3.93
404 405 0.264359 AGACAGAGATGGGCTAGCCT 59.736 55.000 32.18 14.96 36.10 4.58
405 406 1.069978 GAAGACAGAGATGGGCTAGCC 59.930 57.143 26.55 26.55 0.00 3.93
406 407 1.759445 TGAAGACAGAGATGGGCTAGC 59.241 52.381 6.04 6.04 0.00 3.42
407 408 2.762887 TGTGAAGACAGAGATGGGCTAG 59.237 50.000 0.00 0.00 0.00 3.42
408 409 2.820178 TGTGAAGACAGAGATGGGCTA 58.180 47.619 0.00 0.00 0.00 3.93
409 410 1.649321 TGTGAAGACAGAGATGGGCT 58.351 50.000 0.00 0.00 0.00 5.19
419 420 4.160439 CCCAGATTAGCTACTGTGAAGACA 59.840 45.833 9.51 0.00 32.93 3.41
420 421 4.402793 TCCCAGATTAGCTACTGTGAAGAC 59.597 45.833 9.51 0.00 32.93 3.01
421 422 4.610333 TCCCAGATTAGCTACTGTGAAGA 58.390 43.478 9.51 3.95 32.93 2.87
422 423 5.127845 TCTTCCCAGATTAGCTACTGTGAAG 59.872 44.000 20.90 20.90 44.06 3.02
423 424 5.023452 TCTTCCCAGATTAGCTACTGTGAA 58.977 41.667 9.51 8.85 31.95 3.18
424 425 4.402793 GTCTTCCCAGATTAGCTACTGTGA 59.597 45.833 9.51 1.69 32.93 3.58
425 426 4.160439 TGTCTTCCCAGATTAGCTACTGTG 59.840 45.833 9.74 6.04 32.93 3.66
426 427 4.353777 TGTCTTCCCAGATTAGCTACTGT 58.646 43.478 9.74 0.00 32.93 3.55
427 428 5.112686 GTTGTCTTCCCAGATTAGCTACTG 58.887 45.833 0.00 0.00 0.00 2.74
428 429 4.142138 CGTTGTCTTCCCAGATTAGCTACT 60.142 45.833 0.00 0.00 0.00 2.57
429 430 4.113354 CGTTGTCTTCCCAGATTAGCTAC 58.887 47.826 0.00 0.00 0.00 3.58
430 431 4.021229 TCGTTGTCTTCCCAGATTAGCTA 58.979 43.478 0.00 0.00 0.00 3.32
431 432 2.832129 TCGTTGTCTTCCCAGATTAGCT 59.168 45.455 0.00 0.00 0.00 3.32
432 433 3.247006 TCGTTGTCTTCCCAGATTAGC 57.753 47.619 0.00 0.00 0.00 3.09
433 434 6.743575 ATTTTCGTTGTCTTCCCAGATTAG 57.256 37.500 0.00 0.00 0.00 1.73
434 435 7.519032 AAATTTTCGTTGTCTTCCCAGATTA 57.481 32.000 0.00 0.00 0.00 1.75
435 436 6.405278 AAATTTTCGTTGTCTTCCCAGATT 57.595 33.333 0.00 0.00 0.00 2.40
436 437 6.040391 TCAAAATTTTCGTTGTCTTCCCAGAT 59.960 34.615 0.00 0.00 0.00 2.90
437 438 5.358442 TCAAAATTTTCGTTGTCTTCCCAGA 59.642 36.000 0.00 0.00 0.00 3.86
438 439 5.587289 TCAAAATTTTCGTTGTCTTCCCAG 58.413 37.500 0.00 0.00 0.00 4.45
439 440 5.584253 TCAAAATTTTCGTTGTCTTCCCA 57.416 34.783 0.00 0.00 0.00 4.37
440 441 6.699642 TCAATCAAAATTTTCGTTGTCTTCCC 59.300 34.615 17.65 0.00 0.00 3.97
441 442 7.435192 ACTCAATCAAAATTTTCGTTGTCTTCC 59.565 33.333 17.65 0.00 0.00 3.46
442 443 8.340230 ACTCAATCAAAATTTTCGTTGTCTTC 57.660 30.769 17.65 0.00 0.00 2.87
443 444 8.594687 CAACTCAATCAAAATTTTCGTTGTCTT 58.405 29.630 17.65 11.01 0.00 3.01
444 445 7.973388 TCAACTCAATCAAAATTTTCGTTGTCT 59.027 29.630 17.65 7.41 31.82 3.41
445 446 8.114359 TCAACTCAATCAAAATTTTCGTTGTC 57.886 30.769 17.65 0.00 31.82 3.18
446 447 7.973388 TCTCAACTCAATCAAAATTTTCGTTGT 59.027 29.630 17.65 5.40 31.82 3.32
447 448 8.338985 TCTCAACTCAATCAAAATTTTCGTTG 57.661 30.769 14.38 14.38 31.49 4.10
448 449 9.533253 AATCTCAACTCAATCAAAATTTTCGTT 57.467 25.926 0.00 0.00 0.00 3.85
449 450 9.533253 AAATCTCAACTCAATCAAAATTTTCGT 57.467 25.926 0.00 0.00 0.00 3.85
495 496 9.288124 CGTCATGCATTAACTCAATCAAATAAA 57.712 29.630 0.00 0.00 0.00 1.40
496 497 8.458052 ACGTCATGCATTAACTCAATCAAATAA 58.542 29.630 0.00 0.00 0.00 1.40
497 498 7.984391 ACGTCATGCATTAACTCAATCAAATA 58.016 30.769 0.00 0.00 0.00 1.40
498 499 6.855836 ACGTCATGCATTAACTCAATCAAAT 58.144 32.000 0.00 0.00 0.00 2.32
499 500 6.252967 ACGTCATGCATTAACTCAATCAAA 57.747 33.333 0.00 0.00 0.00 2.69
500 501 5.878332 ACGTCATGCATTAACTCAATCAA 57.122 34.783 0.00 0.00 0.00 2.57
501 502 7.552458 AATACGTCATGCATTAACTCAATCA 57.448 32.000 0.00 0.00 0.00 2.57
502 503 8.736742 CAAAATACGTCATGCATTAACTCAATC 58.263 33.333 0.00 0.00 0.00 2.67
503 504 8.458052 TCAAAATACGTCATGCATTAACTCAAT 58.542 29.630 0.00 0.00 0.00 2.57
504 505 7.811653 TCAAAATACGTCATGCATTAACTCAA 58.188 30.769 0.00 0.00 0.00 3.02
505 506 7.371126 TCAAAATACGTCATGCATTAACTCA 57.629 32.000 0.00 0.00 0.00 3.41
506 507 8.122330 TGATCAAAATACGTCATGCATTAACTC 58.878 33.333 0.00 0.00 0.00 3.01
507 508 7.984391 TGATCAAAATACGTCATGCATTAACT 58.016 30.769 0.00 0.00 0.00 2.24
508 509 8.613613 TTGATCAAAATACGTCATGCATTAAC 57.386 30.769 5.45 0.00 0.00 2.01
509 510 9.800433 AATTGATCAAAATACGTCATGCATTAA 57.200 25.926 13.09 0.00 0.00 1.40
510 511 9.800433 AAATTGATCAAAATACGTCATGCATTA 57.200 25.926 13.09 0.00 0.00 1.90
511 512 8.706492 AAATTGATCAAAATACGTCATGCATT 57.294 26.923 13.09 0.00 0.00 3.56
512 513 8.597227 CAAAATTGATCAAAATACGTCATGCAT 58.403 29.630 13.09 0.00 0.00 3.96
513 514 7.598118 ACAAAATTGATCAAAATACGTCATGCA 59.402 29.630 13.09 0.00 0.00 3.96
514 515 7.952339 ACAAAATTGATCAAAATACGTCATGC 58.048 30.769 13.09 0.00 0.00 4.06
547 548 8.603304 ACCACCACTAATAGAGTAACTTGAAAT 58.397 33.333 0.00 0.00 35.64 2.17
548 549 7.970102 ACCACCACTAATAGAGTAACTTGAAA 58.030 34.615 0.00 0.00 35.64 2.69
549 550 7.549147 ACCACCACTAATAGAGTAACTTGAA 57.451 36.000 0.00 0.00 35.64 2.69
550 551 7.549147 AACCACCACTAATAGAGTAACTTGA 57.451 36.000 0.00 0.00 35.64 3.02
551 552 8.617290 AAAACCACCACTAATAGAGTAACTTG 57.383 34.615 0.00 0.00 35.64 3.16
557 558 9.582648 ACAAAATAAAACCACCACTAATAGAGT 57.417 29.630 0.00 0.00 39.82 3.24
560 561 9.337091 CGAACAAAATAAAACCACCACTAATAG 57.663 33.333 0.00 0.00 0.00 1.73
561 562 8.298140 CCGAACAAAATAAAACCACCACTAATA 58.702 33.333 0.00 0.00 0.00 0.98
562 563 7.149307 CCGAACAAAATAAAACCACCACTAAT 58.851 34.615 0.00 0.00 0.00 1.73
563 564 6.505272 CCGAACAAAATAAAACCACCACTAA 58.495 36.000 0.00 0.00 0.00 2.24
564 565 5.507650 GCCGAACAAAATAAAACCACCACTA 60.508 40.000 0.00 0.00 0.00 2.74
565 566 4.738243 GCCGAACAAAATAAAACCACCACT 60.738 41.667 0.00 0.00 0.00 4.00
566 567 3.491639 GCCGAACAAAATAAAACCACCAC 59.508 43.478 0.00 0.00 0.00 4.16
567 568 3.492829 GGCCGAACAAAATAAAACCACCA 60.493 43.478 0.00 0.00 0.00 4.17
568 569 3.061322 GGCCGAACAAAATAAAACCACC 58.939 45.455 0.00 0.00 0.00 4.61
569 570 3.985008 AGGCCGAACAAAATAAAACCAC 58.015 40.909 0.00 0.00 0.00 4.16
570 571 3.637229 TGAGGCCGAACAAAATAAAACCA 59.363 39.130 0.00 0.00 0.00 3.67
571 572 4.234574 CTGAGGCCGAACAAAATAAAACC 58.765 43.478 0.00 0.00 0.00 3.27
572 573 4.866921 ACTGAGGCCGAACAAAATAAAAC 58.133 39.130 0.00 0.00 0.00 2.43
573 574 5.067936 TCAACTGAGGCCGAACAAAATAAAA 59.932 36.000 0.00 0.00 0.00 1.52
574 575 4.580995 TCAACTGAGGCCGAACAAAATAAA 59.419 37.500 0.00 0.00 0.00 1.40
575 576 4.138290 TCAACTGAGGCCGAACAAAATAA 58.862 39.130 0.00 0.00 0.00 1.40
576 577 3.745799 TCAACTGAGGCCGAACAAAATA 58.254 40.909 0.00 0.00 0.00 1.40
577 578 2.554032 CTCAACTGAGGCCGAACAAAAT 59.446 45.455 0.00 0.00 38.48 1.82
578 579 1.946768 CTCAACTGAGGCCGAACAAAA 59.053 47.619 0.00 0.00 38.48 2.44
579 580 1.140052 TCTCAACTGAGGCCGAACAAA 59.860 47.619 6.87 0.00 42.30 2.83
580 581 0.756294 TCTCAACTGAGGCCGAACAA 59.244 50.000 6.87 0.00 42.30 2.83
581 582 0.976641 ATCTCAACTGAGGCCGAACA 59.023 50.000 6.87 0.00 42.30 3.18
582 583 2.961526 TATCTCAACTGAGGCCGAAC 57.038 50.000 6.87 0.00 42.30 3.95
583 584 4.404394 TGTTATATCTCAACTGAGGCCGAA 59.596 41.667 6.87 0.00 42.30 4.30
584 585 3.958147 TGTTATATCTCAACTGAGGCCGA 59.042 43.478 6.87 0.00 42.30 5.54
585 586 4.322080 TGTTATATCTCAACTGAGGCCG 57.678 45.455 6.87 0.00 42.30 6.13
586 587 7.391148 TTTTTGTTATATCTCAACTGAGGCC 57.609 36.000 6.87 0.00 42.30 5.19
625 626 0.996762 TTATCATCCCACCCACCCCC 60.997 60.000 0.00 0.00 0.00 5.40
626 627 0.930726 TTTATCATCCCACCCACCCC 59.069 55.000 0.00 0.00 0.00 4.95
627 628 2.384828 GTTTTATCATCCCACCCACCC 58.615 52.381 0.00 0.00 0.00 4.61
628 629 2.291930 TGGTTTTATCATCCCACCCACC 60.292 50.000 0.00 0.00 0.00 4.61
629 630 3.023832 CTGGTTTTATCATCCCACCCAC 58.976 50.000 0.00 0.00 0.00 4.61
630 631 2.652348 ACTGGTTTTATCATCCCACCCA 59.348 45.455 0.00 0.00 0.00 4.51
631 632 3.023832 CACTGGTTTTATCATCCCACCC 58.976 50.000 0.00 0.00 0.00 4.61
632 633 3.023832 CCACTGGTTTTATCATCCCACC 58.976 50.000 0.00 0.00 0.00 4.61
633 634 3.947834 CTCCACTGGTTTTATCATCCCAC 59.052 47.826 0.00 0.00 0.00 4.61
634 635 3.053693 CCTCCACTGGTTTTATCATCCCA 60.054 47.826 0.00 0.00 0.00 4.37
635 636 3.053619 ACCTCCACTGGTTTTATCATCCC 60.054 47.826 0.00 0.00 36.89 3.85
636 637 3.947834 CACCTCCACTGGTTTTATCATCC 59.052 47.826 0.00 0.00 38.45 3.51
637 638 3.947834 CCACCTCCACTGGTTTTATCATC 59.052 47.826 0.00 0.00 38.45 2.92
638 639 3.309121 CCCACCTCCACTGGTTTTATCAT 60.309 47.826 0.00 0.00 38.45 2.45
639 640 2.041081 CCCACCTCCACTGGTTTTATCA 59.959 50.000 0.00 0.00 38.45 2.15
640 641 2.620627 CCCCACCTCCACTGGTTTTATC 60.621 54.545 0.00 0.00 38.45 1.75
641 642 1.357761 CCCCACCTCCACTGGTTTTAT 59.642 52.381 0.00 0.00 38.45 1.40
642 643 0.774908 CCCCACCTCCACTGGTTTTA 59.225 55.000 0.00 0.00 38.45 1.52
643 644 1.541672 CCCCACCTCCACTGGTTTT 59.458 57.895 0.00 0.00 38.45 2.43
644 645 2.469765 CCCCCACCTCCACTGGTTT 61.470 63.158 0.00 0.00 38.45 3.27
645 646 2.858974 CCCCCACCTCCACTGGTT 60.859 66.667 0.00 0.00 38.45 3.67
649 650 4.741239 ATCGCCCCCACCTCCACT 62.741 66.667 0.00 0.00 0.00 4.00
650 651 4.176752 GATCGCCCCCACCTCCAC 62.177 72.222 0.00 0.00 0.00 4.02
652 653 3.768833 TAGGATCGCCCCCACCTCC 62.769 68.421 0.00 0.00 34.42 4.30
653 654 2.122989 TAGGATCGCCCCCACCTC 60.123 66.667 0.00 0.00 34.42 3.85
654 655 2.446036 GTAGGATCGCCCCCACCT 60.446 66.667 0.00 0.00 36.65 4.00
655 656 3.557290 GGTAGGATCGCCCCCACC 61.557 72.222 0.00 0.00 34.50 4.61
656 657 2.372074 TTGGTAGGATCGCCCCCAC 61.372 63.158 0.00 0.00 35.92 4.61
657 658 2.041430 TTGGTAGGATCGCCCCCA 59.959 61.111 0.00 0.00 34.75 4.96
658 659 2.041206 GAGTTGGTAGGATCGCCCCC 62.041 65.000 0.00 0.00 34.66 5.40
659 660 1.446366 GAGTTGGTAGGATCGCCCC 59.554 63.158 0.00 0.00 34.66 5.80
660 661 1.067582 CGAGTTGGTAGGATCGCCC 59.932 63.158 0.00 0.00 33.31 6.13
661 662 4.732106 CGAGTTGGTAGGATCGCC 57.268 61.111 0.00 0.00 0.00 5.54
663 664 1.299165 CGGCGAGTTGGTAGGATCG 60.299 63.158 0.00 0.00 38.19 3.69
664 665 0.175073 AACGGCGAGTTGGTAGGATC 59.825 55.000 16.62 0.00 42.39 3.36
665 666 1.477553 TAACGGCGAGTTGGTAGGAT 58.522 50.000 16.62 0.00 44.01 3.24
666 667 1.255882 TTAACGGCGAGTTGGTAGGA 58.744 50.000 16.62 0.00 44.01 2.94
667 668 2.304751 ATTAACGGCGAGTTGGTAGG 57.695 50.000 16.62 0.00 44.01 3.18
668 669 6.211515 ACTATTATTAACGGCGAGTTGGTAG 58.788 40.000 16.62 9.76 44.01 3.18
669 670 6.147864 ACTATTATTAACGGCGAGTTGGTA 57.852 37.500 16.62 0.00 44.01 3.25
670 671 5.014808 ACTATTATTAACGGCGAGTTGGT 57.985 39.130 16.62 0.00 44.01 3.67
671 672 5.045215 TGACTATTATTAACGGCGAGTTGG 58.955 41.667 16.62 0.00 44.01 3.77
672 673 6.474427 TCTTGACTATTATTAACGGCGAGTTG 59.526 38.462 16.62 0.00 44.01 3.16
673 674 6.567050 TCTTGACTATTATTAACGGCGAGTT 58.433 36.000 16.62 0.00 46.36 3.01
674 675 6.140303 TCTTGACTATTATTAACGGCGAGT 57.860 37.500 16.62 3.01 0.00 4.18
675 676 8.235226 TCTATCTTGACTATTATTAACGGCGAG 58.765 37.037 16.62 0.00 0.00 5.03
676 677 8.102800 TCTATCTTGACTATTATTAACGGCGA 57.897 34.615 16.62 0.00 0.00 5.54
677 678 8.235226 TCTCTATCTTGACTATTATTAACGGCG 58.765 37.037 4.80 4.80 0.00 6.46
732 733 9.316730 GCCATTGTTGTTATTAATCAATGATGT 57.683 29.630 20.32 0.00 44.28 3.06
733 734 9.315525 TGCCATTGTTGTTATTAATCAATGATG 57.684 29.630 20.32 13.56 44.28 3.07
734 735 9.887629 TTGCCATTGTTGTTATTAATCAATGAT 57.112 25.926 20.32 0.00 44.28 2.45
735 736 9.887629 ATTGCCATTGTTGTTATTAATCAATGA 57.112 25.926 20.32 8.01 44.28 2.57
794 795 8.875168 TGGATGGTAGTTGTTATTTCCAAATTT 58.125 29.630 0.00 0.00 0.00 1.82
795 796 8.429237 TGGATGGTAGTTGTTATTTCCAAATT 57.571 30.769 0.00 0.00 0.00 1.82
796 797 8.608185 ATGGATGGTAGTTGTTATTTCCAAAT 57.392 30.769 0.00 0.00 35.77 2.32
797 798 7.123547 GGATGGATGGTAGTTGTTATTTCCAAA 59.876 37.037 0.00 0.00 35.77 3.28
798 799 6.605594 GGATGGATGGTAGTTGTTATTTCCAA 59.394 38.462 0.00 0.00 35.77 3.53
799 800 6.126409 GGATGGATGGTAGTTGTTATTTCCA 58.874 40.000 0.00 0.00 36.53 3.53
800 801 5.535030 GGGATGGATGGTAGTTGTTATTTCC 59.465 44.000 0.00 0.00 0.00 3.13
801 802 6.365520 AGGGATGGATGGTAGTTGTTATTTC 58.634 40.000 0.00 0.00 0.00 2.17
802 803 6.160459 AGAGGGATGGATGGTAGTTGTTATTT 59.840 38.462 0.00 0.00 0.00 1.40
803 804 5.672194 AGAGGGATGGATGGTAGTTGTTATT 59.328 40.000 0.00 0.00 0.00 1.40
804 805 5.227593 AGAGGGATGGATGGTAGTTGTTAT 58.772 41.667 0.00 0.00 0.00 1.89
805 806 4.631234 AGAGGGATGGATGGTAGTTGTTA 58.369 43.478 0.00 0.00 0.00 2.41
806 807 3.464828 AGAGGGATGGATGGTAGTTGTT 58.535 45.455 0.00 0.00 0.00 2.83
807 808 3.136641 AGAGGGATGGATGGTAGTTGT 57.863 47.619 0.00 0.00 0.00 3.32
808 809 5.832539 AATAGAGGGATGGATGGTAGTTG 57.167 43.478 0.00 0.00 0.00 3.16
809 810 5.485708 GCTAATAGAGGGATGGATGGTAGTT 59.514 44.000 0.00 0.00 0.00 2.24
810 811 5.026790 GCTAATAGAGGGATGGATGGTAGT 58.973 45.833 0.00 0.00 0.00 2.73
811 812 4.407296 GGCTAATAGAGGGATGGATGGTAG 59.593 50.000 0.00 0.00 0.00 3.18
812 813 4.362677 GGCTAATAGAGGGATGGATGGTA 58.637 47.826 0.00 0.00 0.00 3.25
813 814 3.185455 GGCTAATAGAGGGATGGATGGT 58.815 50.000 0.00 0.00 0.00 3.55
814 815 2.169352 CGGCTAATAGAGGGATGGATGG 59.831 54.545 0.00 0.00 0.00 3.51
815 816 2.169352 CCGGCTAATAGAGGGATGGATG 59.831 54.545 0.00 0.00 0.00 3.51
816 817 2.472029 CCGGCTAATAGAGGGATGGAT 58.528 52.381 0.00 0.00 0.00 3.41
828 829 1.521681 GTCGCTTCTGCCGGCTAAT 60.522 57.895 29.70 0.00 35.36 1.73
829 830 2.125673 GTCGCTTCTGCCGGCTAA 60.126 61.111 29.70 20.27 35.36 3.09
830 831 4.143333 GGTCGCTTCTGCCGGCTA 62.143 66.667 29.70 13.50 35.36 3.93
834 835 4.821589 GGAGGGTCGCTTCTGCCG 62.822 72.222 0.00 0.00 35.36 5.69
835 836 3.036429 ATGGAGGGTCGCTTCTGCC 62.036 63.158 0.00 0.00 35.36 4.85
836 837 1.817099 CATGGAGGGTCGCTTCTGC 60.817 63.158 0.00 0.00 0.00 4.26
837 838 1.153289 CCATGGAGGGTCGCTTCTG 60.153 63.158 5.56 0.00 0.00 3.02
839 840 1.144936 CTCCATGGAGGGTCGCTTC 59.855 63.158 31.14 0.00 38.51 3.86
840 841 1.613630 ACTCCATGGAGGGTCGCTT 60.614 57.895 38.54 18.30 45.88 4.68
841 842 2.039624 ACTCCATGGAGGGTCGCT 59.960 61.111 38.54 19.00 45.88 4.93
896 903 0.616395 TGTGGAGAGGATACGGCCAA 60.616 55.000 2.24 0.00 46.39 4.52
897 904 1.001120 TGTGGAGAGGATACGGCCA 59.999 57.895 2.24 0.00 46.39 5.36
898 905 1.442148 GTGTGGAGAGGATACGGCC 59.558 63.158 0.00 0.00 46.39 6.13
899 906 1.065928 CGTGTGGAGAGGATACGGC 59.934 63.158 0.00 0.00 46.39 5.68
900 907 1.065928 GCGTGTGGAGAGGATACGG 59.934 63.158 0.00 0.00 46.39 4.02
1026 1050 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1317 1344 3.876589 GACGACCGCCTTCTTGCCA 62.877 63.158 0.00 0.00 0.00 4.92
1515 1597 6.292596 GCAATCAATCGCAAACCAAGTAAAAA 60.293 34.615 0.00 0.00 0.00 1.94
1533 1619 0.537143 AAGGTCAGTGCGGCAATCAA 60.537 50.000 3.23 0.00 0.00 2.57
1536 1622 1.228245 ACAAGGTCAGTGCGGCAAT 60.228 52.632 3.23 0.00 0.00 3.56
1539 1625 3.357079 CCACAAGGTCAGTGCGGC 61.357 66.667 0.00 0.00 35.69 6.53
1619 2768 0.459585 GGCCGCGAACTTATGTGAGA 60.460 55.000 8.23 0.00 0.00 3.27
1697 3082 7.148340 GCATCTATCAAACTACTTTTGCAGAGT 60.148 37.037 9.41 9.41 43.90 3.24
1711 3096 3.553511 CACTCGGTGAGCATCTATCAAAC 59.446 47.826 0.00 0.00 35.23 2.93
1741 3126 3.374367 TCTCATCTCCTTTCTCGTACACG 59.626 47.826 0.00 0.00 41.45 4.49
1746 3131 3.194542 CCAACTCTCATCTCCTTTCTCGT 59.805 47.826 0.00 0.00 0.00 4.18
1764 3149 3.350219 TGGAGGACAGATTAAGCCAAC 57.650 47.619 0.00 0.00 0.00 3.77
1766 3151 2.173356 CCATGGAGGACAGATTAAGCCA 59.827 50.000 5.56 0.00 41.22 4.75
1767 3152 2.487986 CCCATGGAGGACAGATTAAGCC 60.488 54.545 15.22 0.00 41.22 4.35
1768 3153 2.856222 CCCATGGAGGACAGATTAAGC 58.144 52.381 15.22 0.00 41.22 3.09
1769 3154 2.487986 GGCCCATGGAGGACAGATTAAG 60.488 54.545 15.22 0.00 41.22 1.85
1770 3155 1.494721 GGCCCATGGAGGACAGATTAA 59.505 52.381 15.22 0.00 41.22 1.40
1774 3159 2.124768 TGGCCCATGGAGGACAGA 59.875 61.111 15.22 0.00 41.26 3.41
1794 3480 3.995199 TCAGTCGAAGAAGTGCTCAAAT 58.005 40.909 0.00 0.00 39.69 2.32
1799 3485 7.721402 AGAATATATTCAGTCGAAGAAGTGCT 58.279 34.615 24.00 0.00 37.53 4.40
1856 3542 2.122768 CTCTTCTATTGGTCCCAGGCT 58.877 52.381 0.00 0.00 0.00 4.58
2270 4034 0.813610 CAACACCGCTCAACACCTCA 60.814 55.000 0.00 0.00 0.00 3.86
2284 4048 2.362889 CTCCCCCATGCCCAACAC 60.363 66.667 0.00 0.00 0.00 3.32
2295 4059 2.612251 CTCTCTCTCCCCTCCCCC 59.388 72.222 0.00 0.00 0.00 5.40
2353 4117 3.771577 ACTCCTCAAACCATTCGAACT 57.228 42.857 0.00 0.00 0.00 3.01
2378 4142 2.023984 AGCCCTTCCCCTAAATTTGAGG 60.024 50.000 0.00 1.07 0.00 3.86


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

AutoCloner maintained by Alex Coulton.