Multiple sequence alignment - TraesCS5D01G342300

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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 TraesCS5D01G342300 chr5D 100.000 3305 0 0 1 3305 430444545 430447849 0.000000e+00 6104.0
1 TraesCS5D01G342300 chr5D 92.091 1454 106 6 997 2449 430164059 430165504 0.000000e+00 2039.0
2 TraesCS5D01G342300 chr5D 90.199 1561 115 17 790 2322 430511419 430512969 0.000000e+00 2001.0
3 TraesCS5D01G342300 chr5A 92.860 2311 126 11 998 3300 546146219 546148498 0.000000e+00 3317.0
4 TraesCS5D01G342300 chr5A 89.580 1881 144 26 917 2786 545984533 545986372 0.000000e+00 2340.0
5 TraesCS5D01G342300 chr5A 92.022 1454 107 6 997 2449 545870668 545872113 0.000000e+00 2034.0
6 TraesCS5D01G342300 chr5A 93.007 143 4 3 692 828 545984382 545984524 1.550000e-48 204.0
7 TraesCS5D01G342300 chr5A 88.235 119 8 4 578 690 545983923 545984041 1.600000e-28 137.0
8 TraesCS5D01G342300 chr5A 77.885 208 15 13 790 980 546145970 546146163 2.100000e-17 100.0
9 TraesCS5D01G342300 chr5B 93.404 1789 87 7 688 2449 519660711 519662495 0.000000e+00 2621.0
10 TraesCS5D01G342300 chr5B 89.176 2014 152 46 790 2779 520036592 520038563 0.000000e+00 2451.0
11 TraesCS5D01G342300 chr5B 90.108 1567 117 16 790 2322 520046282 520047844 0.000000e+00 2001.0
12 TraesCS5D01G342300 chr5B 91.472 1454 114 6 997 2449 519451328 519452772 0.000000e+00 1989.0
13 TraesCS5D01G342300 chr5B 95.897 390 14 2 301 690 519645617 519646004 6.020000e-177 630.0
14 TraesCS5D01G342300 chr5B 93.548 310 11 2 1 304 519644746 519645052 1.400000e-123 453.0
15 TraesCS5D01G342300 chr5B 82.390 477 56 19 2266 2733 519895340 519895797 1.110000e-104 390.0
16 TraesCS5D01G342300 chr2D 93.258 89 4 2 2785 2873 318557817 318557731 2.680000e-26 130.0
17 TraesCS5D01G342300 chr4B 97.561 41 0 1 2834 2873 427498502 427498462 5.920000e-08 69.4
18 TraesCS5D01G342300 chr2B 90.476 42 4 0 2788 2829 143818171 143818212 4.610000e-04 56.5


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 TraesCS5D01G342300 chr5D 430444545 430447849 3304 False 6104.000000 6104 100.0000 1 3305 1 chr5D.!!$F2 3304
1 TraesCS5D01G342300 chr5D 430164059 430165504 1445 False 2039.000000 2039 92.0910 997 2449 1 chr5D.!!$F1 1452
2 TraesCS5D01G342300 chr5D 430511419 430512969 1550 False 2001.000000 2001 90.1990 790 2322 1 chr5D.!!$F3 1532
3 TraesCS5D01G342300 chr5A 545870668 545872113 1445 False 2034.000000 2034 92.0220 997 2449 1 chr5A.!!$F1 1452
4 TraesCS5D01G342300 chr5A 546145970 546148498 2528 False 1708.500000 3317 85.3725 790 3300 2 chr5A.!!$F3 2510
5 TraesCS5D01G342300 chr5A 545983923 545986372 2449 False 893.666667 2340 90.2740 578 2786 3 chr5A.!!$F2 2208
6 TraesCS5D01G342300 chr5B 519660711 519662495 1784 False 2621.000000 2621 93.4040 688 2449 1 chr5B.!!$F2 1761
7 TraesCS5D01G342300 chr5B 520036592 520038563 1971 False 2451.000000 2451 89.1760 790 2779 1 chr5B.!!$F4 1989
8 TraesCS5D01G342300 chr5B 520046282 520047844 1562 False 2001.000000 2001 90.1080 790 2322 1 chr5B.!!$F5 1532
9 TraesCS5D01G342300 chr5B 519451328 519452772 1444 False 1989.000000 1989 91.4720 997 2449 1 chr5B.!!$F1 1452
10 TraesCS5D01G342300 chr5B 519644746 519646004 1258 False 541.500000 630 94.7225 1 690 2 chr5B.!!$F6 689

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
484 491 0.109153 TGTCCACTGCTCAACATGCT 59.891 50.0 0.00 0.00 0.0 3.79 F
2181 2675 0.328258 ACTTCATGCCGGCCTACTTT 59.672 50.0 26.77 0.54 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 2819 1.272807 TCACAGTTAGGCCACCTACC 58.727 55.0 5.01 0.0 35.63 3.18 R
3015 3572 1.365699 AATGTTCCGCGTGTACATCC 58.634 50.0 15.95 0.0 31.63 3.51 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
62 63 5.714806 TCAAACATCCATAGTTCTTTTCCCC 59.285 40.000 0.00 0.00 0.00 4.81
64 65 2.413310 TCCATAGTTCTTTTCCCCGC 57.587 50.000 0.00 0.00 0.00 6.13
83 84 1.779157 GCTTTTCTGCGTTTTTCGTCC 59.221 47.619 0.00 0.00 42.13 4.79
84 85 2.381589 CTTTTCTGCGTTTTTCGTCCC 58.618 47.619 0.00 0.00 42.13 4.46
141 142 2.674754 GGCCATTCCCCTCGTCAA 59.325 61.111 0.00 0.00 0.00 3.18
142 143 1.001393 GGCCATTCCCCTCGTCAAA 60.001 57.895 0.00 0.00 0.00 2.69
276 277 7.494625 TCTCGTTCTATTGCGAAAGGATTATTT 59.505 33.333 0.00 0.00 36.65 1.40
282 283 5.403897 TTGCGAAAGGATTATTTCTAGCG 57.596 39.130 0.00 0.00 37.10 4.26
304 311 5.345702 CGGTAAGTGAAATATTGAGTCGGA 58.654 41.667 0.00 0.00 0.00 4.55
305 312 5.231568 CGGTAAGTGAAATATTGAGTCGGAC 59.768 44.000 0.00 0.00 0.00 4.79
308 315 4.184629 AGTGAAATATTGAGTCGGACTGC 58.815 43.478 16.72 7.91 0.00 4.40
309 316 4.081420 AGTGAAATATTGAGTCGGACTGCT 60.081 41.667 16.72 2.29 0.00 4.24
311 318 5.986135 GTGAAATATTGAGTCGGACTGCTAT 59.014 40.000 16.72 11.39 0.00 2.97
313 320 7.652105 GTGAAATATTGAGTCGGACTGCTATTA 59.348 37.037 16.72 3.60 0.00 0.98
314 321 8.201464 TGAAATATTGAGTCGGACTGCTATTAA 58.799 33.333 16.72 5.60 0.00 1.40
318 325 6.710597 TTGAGTCGGACTGCTATTAATACT 57.289 37.500 16.72 0.00 0.00 2.12
319 326 6.710597 TGAGTCGGACTGCTATTAATACTT 57.289 37.500 16.72 0.00 0.00 2.24
320 327 6.504398 TGAGTCGGACTGCTATTAATACTTG 58.496 40.000 16.72 0.00 0.00 3.16
321 328 6.320418 TGAGTCGGACTGCTATTAATACTTGA 59.680 38.462 16.72 0.00 0.00 3.02
322 329 6.505272 AGTCGGACTGCTATTAATACTTGAC 58.495 40.000 10.41 0.00 0.00 3.18
323 330 6.321690 AGTCGGACTGCTATTAATACTTGACT 59.678 38.462 10.41 0.00 0.00 3.41
324 331 7.501559 AGTCGGACTGCTATTAATACTTGACTA 59.498 37.037 10.41 0.00 0.00 2.59
325 332 8.133627 GTCGGACTGCTATTAATACTTGACTAA 58.866 37.037 0.00 0.00 0.00 2.24
326 333 8.350722 TCGGACTGCTATTAATACTTGACTAAG 58.649 37.037 0.00 0.00 39.86 2.18
327 334 8.350722 CGGACTGCTATTAATACTTGACTAAGA 58.649 37.037 0.00 0.00 37.36 2.10
373 380 9.996554 AATGTTTAATTTCGAAAGGGAAAAGAT 57.003 25.926 16.80 13.09 39.19 2.40
375 382 9.902196 TGTTTAATTTCGAAAGGGAAAAGATAC 57.098 29.630 16.80 5.65 39.19 2.24
376 383 9.350357 GTTTAATTTCGAAAGGGAAAAGATACC 57.650 33.333 16.80 0.94 39.19 2.73
377 384 8.873186 TTAATTTCGAAAGGGAAAAGATACCT 57.127 30.769 16.80 0.00 39.19 3.08
379 386 5.492855 TTCGAAAGGGAAAAGATACCTGA 57.507 39.130 0.00 0.00 34.17 3.86
381 388 5.871834 TCGAAAGGGAAAAGATACCTGAAA 58.128 37.500 0.00 0.00 34.17 2.69
384 391 4.903045 AGGGAAAAGATACCTGAAACGA 57.097 40.909 0.00 0.00 32.26 3.85
386 393 5.246307 AGGGAAAAGATACCTGAAACGAAG 58.754 41.667 0.00 0.00 32.26 3.79
387 394 5.012768 AGGGAAAAGATACCTGAAACGAAGA 59.987 40.000 0.00 0.00 32.26 2.87
390 397 6.371825 GGAAAAGATACCTGAAACGAAGACAT 59.628 38.462 0.00 0.00 0.00 3.06
398 405 4.508124 CCTGAAACGAAGACATATAGGCAC 59.492 45.833 0.00 0.00 0.00 5.01
400 407 3.795623 AACGAAGACATATAGGCACGT 57.204 42.857 0.00 0.00 40.96 4.49
401 408 3.079960 ACGAAGACATATAGGCACGTG 57.920 47.619 12.28 12.28 38.63 4.49
402 409 2.223735 ACGAAGACATATAGGCACGTGG 60.224 50.000 18.88 0.44 38.63 4.94
403 410 2.135933 GAAGACATATAGGCACGTGGC 58.864 52.381 32.77 32.77 43.74 5.01
413 420 2.813100 GCACGTGGCAAGGAAATTG 58.187 52.632 18.88 0.00 43.97 2.32
414 421 0.667184 GCACGTGGCAAGGAAATTGG 60.667 55.000 18.88 0.00 43.97 3.16
422 429 3.391506 GCAAGGAAATTGGCTTTCAGT 57.608 42.857 2.23 0.00 44.29 3.41
423 430 3.320626 GCAAGGAAATTGGCTTTCAGTC 58.679 45.455 2.23 0.00 44.29 3.51
424 431 3.006217 GCAAGGAAATTGGCTTTCAGTCT 59.994 43.478 2.23 0.00 44.29 3.24
425 432 4.502087 GCAAGGAAATTGGCTTTCAGTCTT 60.502 41.667 2.23 0.00 44.29 3.01
426 433 5.604565 CAAGGAAATTGGCTTTCAGTCTTT 58.395 37.500 2.23 0.00 44.29 2.52
427 434 5.205759 AGGAAATTGGCTTTCAGTCTTTG 57.794 39.130 2.23 0.00 44.29 2.77
428 435 4.651045 AGGAAATTGGCTTTCAGTCTTTGT 59.349 37.500 2.23 0.00 44.29 2.83
429 436 4.984785 GGAAATTGGCTTTCAGTCTTTGTC 59.015 41.667 2.23 0.00 44.29 3.18
430 437 3.904136 ATTGGCTTTCAGTCTTTGTCG 57.096 42.857 0.00 0.00 0.00 4.35
431 438 2.325583 TGGCTTTCAGTCTTTGTCGT 57.674 45.000 0.00 0.00 0.00 4.34
432 439 1.939934 TGGCTTTCAGTCTTTGTCGTG 59.060 47.619 0.00 0.00 0.00 4.35
433 440 1.334149 GGCTTTCAGTCTTTGTCGTGC 60.334 52.381 0.00 0.00 0.00 5.34
434 441 1.657538 GCTTTCAGTCTTTGTCGTGCG 60.658 52.381 0.00 0.00 0.00 5.34
435 442 1.593006 CTTTCAGTCTTTGTCGTGCGT 59.407 47.619 0.00 0.00 0.00 5.24
436 443 2.495409 TTCAGTCTTTGTCGTGCGTA 57.505 45.000 0.00 0.00 0.00 4.42
437 444 2.495409 TCAGTCTTTGTCGTGCGTAA 57.505 45.000 0.00 0.00 0.00 3.18
438 445 2.811855 TCAGTCTTTGTCGTGCGTAAA 58.188 42.857 0.00 0.00 0.00 2.01
439 446 3.386486 TCAGTCTTTGTCGTGCGTAAAT 58.614 40.909 0.00 0.00 0.00 1.40
440 447 3.805422 TCAGTCTTTGTCGTGCGTAAATT 59.195 39.130 0.00 0.00 0.00 1.82
441 448 3.900116 CAGTCTTTGTCGTGCGTAAATTG 59.100 43.478 0.00 0.00 0.00 2.32
442 449 3.805422 AGTCTTTGTCGTGCGTAAATTGA 59.195 39.130 0.00 0.00 0.00 2.57
443 450 4.084537 AGTCTTTGTCGTGCGTAAATTGAG 60.085 41.667 0.00 0.00 0.00 3.02
444 451 3.805422 TCTTTGTCGTGCGTAAATTGAGT 59.195 39.130 0.00 0.00 0.00 3.41
445 452 3.513462 TTGTCGTGCGTAAATTGAGTG 57.487 42.857 0.00 0.00 0.00 3.51
446 453 2.745102 TGTCGTGCGTAAATTGAGTGA 58.255 42.857 0.00 0.00 0.00 3.41
447 454 3.322369 TGTCGTGCGTAAATTGAGTGAT 58.678 40.909 0.00 0.00 0.00 3.06
448 455 4.487019 TGTCGTGCGTAAATTGAGTGATA 58.513 39.130 0.00 0.00 0.00 2.15
449 456 5.106442 TGTCGTGCGTAAATTGAGTGATAT 58.894 37.500 0.00 0.00 0.00 1.63
450 457 5.231357 TGTCGTGCGTAAATTGAGTGATATC 59.769 40.000 0.00 0.00 0.00 1.63
451 458 5.231357 GTCGTGCGTAAATTGAGTGATATCA 59.769 40.000 0.00 0.00 0.00 2.15
452 459 5.983118 TCGTGCGTAAATTGAGTGATATCAT 59.017 36.000 9.02 0.00 0.00 2.45
453 460 6.478673 TCGTGCGTAAATTGAGTGATATCATT 59.521 34.615 9.02 4.24 0.00 2.57
454 461 6.571154 CGTGCGTAAATTGAGTGATATCATTG 59.429 38.462 9.02 0.00 0.00 2.82
455 462 7.409697 GTGCGTAAATTGAGTGATATCATTGT 58.590 34.615 9.02 0.00 0.00 2.71
456 463 7.374228 GTGCGTAAATTGAGTGATATCATTGTG 59.626 37.037 9.02 0.00 0.00 3.33
457 464 6.852853 GCGTAAATTGAGTGATATCATTGTGG 59.147 38.462 9.02 0.00 0.00 4.17
458 465 7.254761 GCGTAAATTGAGTGATATCATTGTGGA 60.255 37.037 9.02 0.00 0.00 4.02
459 466 8.611757 CGTAAATTGAGTGATATCATTGTGGAA 58.388 33.333 9.02 0.00 0.00 3.53
460 467 9.722056 GTAAATTGAGTGATATCATTGTGGAAC 57.278 33.333 9.02 0.00 37.35 3.62
461 468 8.585471 AAATTGAGTGATATCATTGTGGAACT 57.415 30.769 9.02 0.00 38.04 3.01
462 469 7.798596 ATTGAGTGATATCATTGTGGAACTC 57.201 36.000 9.02 8.49 38.04 3.01
463 470 6.298441 TGAGTGATATCATTGTGGAACTCA 57.702 37.500 9.02 10.91 40.19 3.41
464 471 6.892485 TGAGTGATATCATTGTGGAACTCAT 58.108 36.000 9.02 0.00 38.23 2.90
465 472 7.341030 TGAGTGATATCATTGTGGAACTCATT 58.659 34.615 9.02 0.00 38.23 2.57
466 473 7.281549 TGAGTGATATCATTGTGGAACTCATTG 59.718 37.037 9.02 0.00 38.23 2.82
467 474 7.114754 AGTGATATCATTGTGGAACTCATTGT 58.885 34.615 9.02 0.00 38.04 2.71
468 475 7.281774 AGTGATATCATTGTGGAACTCATTGTC 59.718 37.037 9.02 0.00 38.04 3.18
469 476 6.543465 TGATATCATTGTGGAACTCATTGTCC 59.457 38.462 0.00 0.00 38.04 4.02
470 477 4.097551 TCATTGTGGAACTCATTGTCCA 57.902 40.909 0.00 0.00 38.04 4.02
474 481 1.537202 GTGGAACTCATTGTCCACTGC 59.463 52.381 14.20 0.00 46.53 4.40
475 482 1.421268 TGGAACTCATTGTCCACTGCT 59.579 47.619 0.00 0.00 0.00 4.24
476 483 2.079925 GGAACTCATTGTCCACTGCTC 58.920 52.381 0.00 0.00 0.00 4.26
477 484 2.550855 GGAACTCATTGTCCACTGCTCA 60.551 50.000 0.00 0.00 0.00 4.26
478 485 2.936919 ACTCATTGTCCACTGCTCAA 57.063 45.000 0.00 0.00 0.00 3.02
479 486 2.498167 ACTCATTGTCCACTGCTCAAC 58.502 47.619 0.00 0.00 0.00 3.18
480 487 2.158769 ACTCATTGTCCACTGCTCAACA 60.159 45.455 0.00 0.00 0.00 3.33
481 488 3.079578 CTCATTGTCCACTGCTCAACAT 58.920 45.455 0.00 0.00 0.00 2.71
482 489 2.815503 TCATTGTCCACTGCTCAACATG 59.184 45.455 0.00 0.00 0.00 3.21
483 490 0.953727 TTGTCCACTGCTCAACATGC 59.046 50.000 0.00 0.00 0.00 4.06
484 491 0.109153 TGTCCACTGCTCAACATGCT 59.891 50.000 0.00 0.00 0.00 3.79
485 492 1.242076 GTCCACTGCTCAACATGCTT 58.758 50.000 0.00 0.00 0.00 3.91
486 493 1.610522 GTCCACTGCTCAACATGCTTT 59.389 47.619 0.00 0.00 0.00 3.51
487 494 2.035066 GTCCACTGCTCAACATGCTTTT 59.965 45.455 0.00 0.00 0.00 2.27
488 495 3.253188 GTCCACTGCTCAACATGCTTTTA 59.747 43.478 0.00 0.00 0.00 1.52
489 496 4.081406 TCCACTGCTCAACATGCTTTTAT 58.919 39.130 0.00 0.00 0.00 1.40
490 497 4.523943 TCCACTGCTCAACATGCTTTTATT 59.476 37.500 0.00 0.00 0.00 1.40
491 498 4.624024 CCACTGCTCAACATGCTTTTATTG 59.376 41.667 0.00 0.00 0.00 1.90
492 499 4.624024 CACTGCTCAACATGCTTTTATTGG 59.376 41.667 0.00 0.00 0.00 3.16
493 500 4.523943 ACTGCTCAACATGCTTTTATTGGA 59.476 37.500 0.00 0.00 0.00 3.53
494 501 5.063180 TGCTCAACATGCTTTTATTGGAG 57.937 39.130 0.00 0.00 0.00 3.86
495 502 4.766373 TGCTCAACATGCTTTTATTGGAGA 59.234 37.500 0.00 0.00 0.00 3.71
496 503 5.098211 GCTCAACATGCTTTTATTGGAGAC 58.902 41.667 0.00 0.00 0.00 3.36
497 504 5.335897 GCTCAACATGCTTTTATTGGAGACA 60.336 40.000 0.00 0.00 39.83 3.41
512 519 4.199310 TGGAGACAAACTCTTGAAACAGG 58.801 43.478 0.00 0.00 44.37 4.00
513 520 3.003793 GGAGACAAACTCTTGAAACAGGC 59.996 47.826 0.00 0.00 44.37 4.85
514 521 3.879892 GAGACAAACTCTTGAAACAGGCT 59.120 43.478 0.00 0.00 41.94 4.58
515 522 4.273318 AGACAAACTCTTGAAACAGGCTT 58.727 39.130 0.00 0.00 36.33 4.35
516 523 4.096984 AGACAAACTCTTGAAACAGGCTTG 59.903 41.667 0.00 0.00 36.33 4.01
517 524 3.763897 ACAAACTCTTGAAACAGGCTTGT 59.236 39.130 0.00 0.00 36.29 3.16
518 525 4.220602 ACAAACTCTTGAAACAGGCTTGTT 59.779 37.500 8.63 8.63 41.30 2.83
519 526 5.417580 ACAAACTCTTGAAACAGGCTTGTTA 59.582 36.000 15.22 0.00 39.99 2.41
520 527 6.096846 ACAAACTCTTGAAACAGGCTTGTTAT 59.903 34.615 15.22 5.44 39.99 1.89
521 528 6.715347 AACTCTTGAAACAGGCTTGTTATT 57.285 33.333 15.22 0.00 46.54 1.40
522 529 6.715347 ACTCTTGAAACAGGCTTGTTATTT 57.285 33.333 15.22 0.00 46.54 1.40
523 530 6.739112 ACTCTTGAAACAGGCTTGTTATTTC 58.261 36.000 15.22 9.56 46.54 2.17
524 531 6.084326 TCTTGAAACAGGCTTGTTATTTCC 57.916 37.500 15.22 3.34 46.54 3.13
525 532 4.864704 TGAAACAGGCTTGTTATTTCCC 57.135 40.909 15.22 1.71 46.54 3.97
526 533 4.219115 TGAAACAGGCTTGTTATTTCCCA 58.781 39.130 15.22 4.12 46.54 4.37
527 534 4.280677 TGAAACAGGCTTGTTATTTCCCAG 59.719 41.667 15.22 0.00 46.54 4.45
528 535 3.806949 ACAGGCTTGTTATTTCCCAGA 57.193 42.857 0.00 0.00 32.28 3.86
529 536 3.421844 ACAGGCTTGTTATTTCCCAGAC 58.578 45.455 0.00 0.00 32.28 3.51
530 537 3.074538 ACAGGCTTGTTATTTCCCAGACT 59.925 43.478 0.00 0.00 32.28 3.24
531 538 4.082125 CAGGCTTGTTATTTCCCAGACTT 58.918 43.478 0.00 0.00 0.00 3.01
532 539 4.524328 CAGGCTTGTTATTTCCCAGACTTT 59.476 41.667 0.00 0.00 0.00 2.66
533 540 5.011023 CAGGCTTGTTATTTCCCAGACTTTT 59.989 40.000 0.00 0.00 0.00 2.27
534 541 5.011023 AGGCTTGTTATTTCCCAGACTTTTG 59.989 40.000 0.00 0.00 0.00 2.44
535 542 5.221441 GGCTTGTTATTTCCCAGACTTTTGT 60.221 40.000 0.00 0.00 0.00 2.83
536 543 6.280643 GCTTGTTATTTCCCAGACTTTTGTT 58.719 36.000 0.00 0.00 0.00 2.83
537 544 7.430441 GCTTGTTATTTCCCAGACTTTTGTTA 58.570 34.615 0.00 0.00 0.00 2.41
538 545 8.088365 GCTTGTTATTTCCCAGACTTTTGTTAT 58.912 33.333 0.00 0.00 0.00 1.89
539 546 9.981114 CTTGTTATTTCCCAGACTTTTGTTATT 57.019 29.630 0.00 0.00 0.00 1.40
541 548 9.974980 TGTTATTTCCCAGACTTTTGTTATTTC 57.025 29.630 0.00 0.00 0.00 2.17
542 549 9.419297 GTTATTTCCCAGACTTTTGTTATTTCC 57.581 33.333 0.00 0.00 0.00 3.13
543 550 7.855784 ATTTCCCAGACTTTTGTTATTTCCT 57.144 32.000 0.00 0.00 0.00 3.36
544 551 8.950007 ATTTCCCAGACTTTTGTTATTTCCTA 57.050 30.769 0.00 0.00 0.00 2.94
545 552 7.996098 TTCCCAGACTTTTGTTATTTCCTAG 57.004 36.000 0.00 0.00 0.00 3.02
546 553 7.324388 TCCCAGACTTTTGTTATTTCCTAGA 57.676 36.000 0.00 0.00 0.00 2.43
547 554 7.166167 TCCCAGACTTTTGTTATTTCCTAGAC 58.834 38.462 0.00 0.00 0.00 2.59
548 555 7.017254 TCCCAGACTTTTGTTATTTCCTAGACT 59.983 37.037 0.00 0.00 0.00 3.24
549 556 8.319146 CCCAGACTTTTGTTATTTCCTAGACTA 58.681 37.037 0.00 0.00 0.00 2.59
550 557 9.372369 CCAGACTTTTGTTATTTCCTAGACTAG 57.628 37.037 2.18 2.18 0.00 2.57
551 558 9.930693 CAGACTTTTGTTATTTCCTAGACTAGT 57.069 33.333 8.68 0.00 0.00 2.57
552 559 9.930693 AGACTTTTGTTATTTCCTAGACTAGTG 57.069 33.333 0.00 0.85 0.00 2.74
553 560 9.708092 GACTTTTGTTATTTCCTAGACTAGTGT 57.292 33.333 0.00 0.00 0.00 3.55
559 566 9.841295 TGTTATTTCCTAGACTAGTGTTTTTGT 57.159 29.630 0.00 0.00 0.00 2.83
632 645 7.624549 ACATATATTGAGTCGGATGGCTATTT 58.375 34.615 0.00 0.00 0.00 1.40
644 657 8.086522 GTCGGATGGCTATTTATACTTGACTAA 58.913 37.037 0.00 0.00 0.00 2.24
758 1116 2.371841 ACAAGCATGGATTATAGGCGGA 59.628 45.455 0.00 0.00 0.00 5.54
993 1402 1.896660 GAAACTGCTGCCCCGACAA 60.897 57.895 0.00 0.00 0.00 3.18
1376 1823 3.625632 ATCCTGACCTGGAGGCGGT 62.626 63.158 0.00 0.00 39.78 5.68
1557 2036 1.152756 GCACCACCACAAGGACCTT 60.153 57.895 0.00 0.00 38.69 3.50
2181 2675 0.328258 ACTTCATGCCGGCCTACTTT 59.672 50.000 26.77 0.54 0.00 2.66
2300 2819 3.287867 AGAATGTTGCTACTCCATGGG 57.712 47.619 13.02 5.22 0.00 4.00
2336 2862 7.548196 AACTGTGAATTAGTCGAAGAAACAA 57.452 32.000 0.00 0.00 39.69 2.83
2556 3101 6.903479 CCGACTTGAACACTAAACTACAAAAC 59.097 38.462 0.00 0.00 0.00 2.43
2563 3108 7.554835 TGAACACTAAACTACAAAACCACTGAT 59.445 33.333 0.00 0.00 0.00 2.90
2667 3214 2.703416 CAGCAGGACTCTGTTGCATAA 58.297 47.619 0.00 0.00 43.34 1.90
2668 3215 3.276857 CAGCAGGACTCTGTTGCATAAT 58.723 45.455 0.00 0.00 43.34 1.28
2794 3347 8.622157 GCAAAAAGAAACTAAGAAACTACTCCT 58.378 33.333 0.00 0.00 0.00 3.69
2808 3361 5.832539 ACTACTCCTTCCATCCCATAATG 57.167 43.478 0.00 0.00 0.00 1.90
2809 3362 5.227593 ACTACTCCTTCCATCCCATAATGT 58.772 41.667 0.00 0.00 0.00 2.71
2810 3363 6.390504 ACTACTCCTTCCATCCCATAATGTA 58.609 40.000 0.00 0.00 0.00 2.29
2812 3365 4.599241 ACTCCTTCCATCCCATAATGTAGG 59.401 45.833 0.00 0.00 32.15 3.18
2813 3366 4.838403 TCCTTCCATCCCATAATGTAGGA 58.162 43.478 0.00 0.00 35.16 2.94
2814 3367 4.597507 TCCTTCCATCCCATAATGTAGGAC 59.402 45.833 0.00 0.00 33.81 3.85
2815 3368 4.563580 CCTTCCATCCCATAATGTAGGACG 60.564 50.000 0.00 0.00 32.40 4.79
2816 3369 3.583228 TCCATCCCATAATGTAGGACGT 58.417 45.455 0.00 0.00 30.97 4.34
2817 3370 3.971305 TCCATCCCATAATGTAGGACGTT 59.029 43.478 0.00 0.00 30.97 3.99
2818 3371 4.065088 CCATCCCATAATGTAGGACGTTG 58.935 47.826 0.00 0.00 30.97 4.10
2819 3372 4.444306 CCATCCCATAATGTAGGACGTTGT 60.444 45.833 0.00 0.00 30.97 3.32
2820 3373 4.829872 TCCCATAATGTAGGACGTTGTT 57.170 40.909 0.00 0.00 0.00 2.83
2821 3374 5.168647 TCCCATAATGTAGGACGTTGTTT 57.831 39.130 0.00 0.00 0.00 2.83
2822 3375 4.938832 TCCCATAATGTAGGACGTTGTTTG 59.061 41.667 0.00 0.00 0.00 2.93
2823 3376 4.938832 CCCATAATGTAGGACGTTGTTTGA 59.061 41.667 0.00 0.00 0.00 2.69
2824 3377 5.163794 CCCATAATGTAGGACGTTGTTTGAC 60.164 44.000 0.00 0.00 0.00 3.18
2825 3378 5.410132 CCATAATGTAGGACGTTGTTTGACA 59.590 40.000 0.00 0.00 0.00 3.58
2826 3379 4.806342 AATGTAGGACGTTGTTTGACAC 57.194 40.909 0.00 0.00 0.00 3.67
2827 3380 3.530265 TGTAGGACGTTGTTTGACACT 57.470 42.857 0.00 0.00 0.00 3.55
2828 3381 4.652421 TGTAGGACGTTGTTTGACACTA 57.348 40.909 0.00 0.00 0.00 2.74
2829 3382 5.204409 TGTAGGACGTTGTTTGACACTAT 57.796 39.130 0.00 0.00 0.00 2.12
2830 3383 4.986034 TGTAGGACGTTGTTTGACACTATG 59.014 41.667 0.00 0.00 0.00 2.23
2831 3384 4.067972 AGGACGTTGTTTGACACTATGT 57.932 40.909 0.00 0.00 33.57 2.29
2832 3385 3.807622 AGGACGTTGTTTGACACTATGTG 59.192 43.478 0.00 0.00 39.75 3.21
2885 3442 5.895534 ACGGAGGGAGTAACAAAGATACATA 59.104 40.000 0.00 0.00 0.00 2.29
2912 3469 0.467844 AGAACAACACCATGGCAGCA 60.468 50.000 13.04 0.00 0.00 4.41
2926 3483 1.604378 CAGCACCCGGGAAGATCTT 59.396 57.895 32.02 7.95 0.00 2.40
2954 3511 2.290577 ACTGAGCCCAATCTTGAAGGAC 60.291 50.000 0.00 0.00 0.00 3.85
2956 3513 2.108075 TGAGCCCAATCTTGAAGGACAA 59.892 45.455 0.00 0.00 36.97 3.18
3015 3572 3.752412 TGTGACTACGTAGAATGTCGG 57.248 47.619 28.74 0.88 32.64 4.79
3023 3580 3.018856 ACGTAGAATGTCGGGATGTACA 58.981 45.455 0.00 0.00 0.00 2.90
3026 3583 0.928229 GAATGTCGGGATGTACACGC 59.072 55.000 0.00 0.00 45.95 5.34
3028 3585 2.581409 GTCGGGATGTACACGCGG 60.581 66.667 23.74 1.27 45.95 6.46
3045 3602 3.004315 ACGCGGAACATTTTGTCAGAATT 59.996 39.130 12.47 0.00 0.00 2.17
3047 3604 4.088496 CGCGGAACATTTTGTCAGAATTTC 59.912 41.667 0.00 0.00 0.00 2.17
3115 3672 0.605589 ACGCTCCTGGGTGCTAAAAC 60.606 55.000 11.15 0.00 37.97 2.43
3135 3692 0.683504 GCCCCTCTCGTCCACTAGAA 60.684 60.000 0.00 0.00 0.00 2.10
3138 3695 1.477295 CCCTCTCGTCCACTAGAAACC 59.523 57.143 0.00 0.00 0.00 3.27
3213 3770 7.454260 AAGCACTAAATCTTGTAGGAAAAGG 57.546 36.000 0.00 0.00 0.00 3.11
3247 3804 7.404671 TGGAAATCCTCATAAGCCTTTTTAC 57.595 36.000 0.44 0.00 36.82 2.01
3300 3857 8.466798 GTGCCTTACAAAAGTATTGGTTATGAT 58.533 33.333 0.00 0.00 0.00 2.45
3301 3858 9.030452 TGCCTTACAAAAGTATTGGTTATGATT 57.970 29.630 0.00 0.00 0.00 2.57
3302 3859 9.869757 GCCTTACAAAAGTATTGGTTATGATTT 57.130 29.630 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.879458 ACTATGGATGTTTGAGTTAGTGGTTC 59.121 38.462 0.00 0.00 0.00 3.62
64 65 2.032924 AGGGACGAAAAACGCAGAAAAG 59.967 45.455 0.00 0.00 46.94 2.27
73 74 2.946990 TCACCAAGAAGGGACGAAAAAC 59.053 45.455 0.00 0.00 43.89 2.43
83 84 3.146104 ACCATGAGTTCACCAAGAAGG 57.854 47.619 0.00 0.00 45.67 3.46
84 85 4.022849 GGAAACCATGAGTTCACCAAGAAG 60.023 45.833 0.00 0.00 37.88 2.85
239 240 7.742963 TCGCAATAGAACGAGAAATAACAAAAC 59.257 33.333 0.00 0.00 33.69 2.43
249 250 4.182693 TCCTTTCGCAATAGAACGAGAA 57.817 40.909 0.00 0.00 39.81 2.87
276 277 7.108841 ACTCAATATTTCACTTACCGCTAGA 57.891 36.000 0.00 0.00 0.00 2.43
282 283 6.255887 CAGTCCGACTCAATATTTCACTTACC 59.744 42.308 0.00 0.00 0.00 2.85
347 354 9.996554 ATCTTTTCCCTTTCGAAATTAAACATT 57.003 25.926 11.70 0.00 32.00 2.71
349 356 9.902196 GTATCTTTTCCCTTTCGAAATTAAACA 57.098 29.630 11.70 2.95 32.00 2.83
350 357 9.350357 GGTATCTTTTCCCTTTCGAAATTAAAC 57.650 33.333 11.70 1.71 32.00 2.01
351 358 9.304335 AGGTATCTTTTCCCTTTCGAAATTAAA 57.696 29.630 11.70 9.28 32.00 1.52
352 359 8.736244 CAGGTATCTTTTCCCTTTCGAAATTAA 58.264 33.333 11.70 3.50 32.00 1.40
353 360 8.104566 TCAGGTATCTTTTCCCTTTCGAAATTA 58.895 33.333 11.70 0.00 32.00 1.40
354 361 6.946009 TCAGGTATCTTTTCCCTTTCGAAATT 59.054 34.615 11.70 0.00 32.00 1.82
355 362 6.481643 TCAGGTATCTTTTCCCTTTCGAAAT 58.518 36.000 11.70 0.00 32.00 2.17
356 363 5.871834 TCAGGTATCTTTTCCCTTTCGAAA 58.128 37.500 10.71 10.71 0.00 3.46
357 364 5.492855 TCAGGTATCTTTTCCCTTTCGAA 57.507 39.130 0.00 0.00 0.00 3.71
358 365 5.492855 TTCAGGTATCTTTTCCCTTTCGA 57.507 39.130 0.00 0.00 0.00 3.71
359 366 5.390567 CGTTTCAGGTATCTTTTCCCTTTCG 60.391 44.000 0.00 0.00 0.00 3.46
360 367 5.704053 TCGTTTCAGGTATCTTTTCCCTTTC 59.296 40.000 0.00 0.00 0.00 2.62
361 368 5.627135 TCGTTTCAGGTATCTTTTCCCTTT 58.373 37.500 0.00 0.00 0.00 3.11
362 369 5.237236 TCGTTTCAGGTATCTTTTCCCTT 57.763 39.130 0.00 0.00 0.00 3.95
363 370 4.903045 TCGTTTCAGGTATCTTTTCCCT 57.097 40.909 0.00 0.00 0.00 4.20
364 371 5.121925 GTCTTCGTTTCAGGTATCTTTTCCC 59.878 44.000 0.00 0.00 0.00 3.97
365 372 5.699458 TGTCTTCGTTTCAGGTATCTTTTCC 59.301 40.000 0.00 0.00 0.00 3.13
366 373 6.780706 TGTCTTCGTTTCAGGTATCTTTTC 57.219 37.500 0.00 0.00 0.00 2.29
368 375 9.751542 CTATATGTCTTCGTTTCAGGTATCTTT 57.248 33.333 0.00 0.00 0.00 2.52
369 376 8.361139 CCTATATGTCTTCGTTTCAGGTATCTT 58.639 37.037 0.00 0.00 0.00 2.40
370 377 7.524038 GCCTATATGTCTTCGTTTCAGGTATCT 60.524 40.741 0.00 0.00 0.00 1.98
371 378 6.586844 GCCTATATGTCTTCGTTTCAGGTATC 59.413 42.308 0.00 0.00 0.00 2.24
372 379 6.041637 TGCCTATATGTCTTCGTTTCAGGTAT 59.958 38.462 0.00 0.00 0.00 2.73
373 380 5.361571 TGCCTATATGTCTTCGTTTCAGGTA 59.638 40.000 0.00 0.00 0.00 3.08
374 381 4.161565 TGCCTATATGTCTTCGTTTCAGGT 59.838 41.667 0.00 0.00 0.00 4.00
375 382 4.508124 GTGCCTATATGTCTTCGTTTCAGG 59.492 45.833 0.00 0.00 0.00 3.86
376 383 4.207224 CGTGCCTATATGTCTTCGTTTCAG 59.793 45.833 0.00 0.00 0.00 3.02
377 384 4.109766 CGTGCCTATATGTCTTCGTTTCA 58.890 43.478 0.00 0.00 0.00 2.69
379 386 3.863424 CACGTGCCTATATGTCTTCGTTT 59.137 43.478 0.82 0.00 0.00 3.60
381 388 2.223735 CCACGTGCCTATATGTCTTCGT 60.224 50.000 10.91 0.00 0.00 3.85
384 391 1.484653 TGCCACGTGCCTATATGTCTT 59.515 47.619 10.91 0.00 40.16 3.01
386 393 1.867233 CTTGCCACGTGCCTATATGTC 59.133 52.381 10.91 0.00 40.16 3.06
387 394 1.475034 CCTTGCCACGTGCCTATATGT 60.475 52.381 10.91 0.00 40.16 2.29
390 397 0.906066 TTCCTTGCCACGTGCCTATA 59.094 50.000 10.91 0.00 40.16 1.31
398 405 0.318120 AAGCCAATTTCCTTGCCACG 59.682 50.000 0.00 0.00 33.20 4.94
400 407 2.037511 CTGAAAGCCAATTTCCTTGCCA 59.962 45.455 0.00 0.00 45.74 4.92
401 408 2.037641 ACTGAAAGCCAATTTCCTTGCC 59.962 45.455 0.00 0.00 45.74 4.52
402 409 3.006217 AGACTGAAAGCCAATTTCCTTGC 59.994 43.478 0.00 0.00 45.74 4.01
403 410 4.861102 AGACTGAAAGCCAATTTCCTTG 57.139 40.909 0.00 0.00 45.74 3.61
404 411 5.129320 ACAAAGACTGAAAGCCAATTTCCTT 59.871 36.000 0.00 0.00 45.74 3.36
405 412 4.651045 ACAAAGACTGAAAGCCAATTTCCT 59.349 37.500 0.00 0.00 45.74 3.36
406 413 4.948847 ACAAAGACTGAAAGCCAATTTCC 58.051 39.130 0.00 0.00 45.74 3.13
407 414 4.676924 CGACAAAGACTGAAAGCCAATTTC 59.323 41.667 0.00 0.00 46.37 2.17
408 415 4.097892 ACGACAAAGACTGAAAGCCAATTT 59.902 37.500 0.00 0.00 37.60 1.82
409 416 3.632145 ACGACAAAGACTGAAAGCCAATT 59.368 39.130 0.00 0.00 37.60 2.32
410 417 3.003689 CACGACAAAGACTGAAAGCCAAT 59.996 43.478 0.00 0.00 37.60 3.16
411 418 2.354510 CACGACAAAGACTGAAAGCCAA 59.645 45.455 0.00 0.00 37.60 4.52
412 419 1.939934 CACGACAAAGACTGAAAGCCA 59.060 47.619 0.00 0.00 37.60 4.75
413 420 1.334149 GCACGACAAAGACTGAAAGCC 60.334 52.381 0.00 0.00 37.60 4.35
414 421 1.657538 CGCACGACAAAGACTGAAAGC 60.658 52.381 0.00 0.00 37.60 3.51
415 422 1.593006 ACGCACGACAAAGACTGAAAG 59.407 47.619 0.00 0.00 42.29 2.62
416 423 1.647346 ACGCACGACAAAGACTGAAA 58.353 45.000 0.00 0.00 0.00 2.69
417 424 2.495409 TACGCACGACAAAGACTGAA 57.505 45.000 0.00 0.00 0.00 3.02
418 425 2.495409 TTACGCACGACAAAGACTGA 57.505 45.000 0.00 0.00 0.00 3.41
419 426 3.788434 ATTTACGCACGACAAAGACTG 57.212 42.857 0.00 0.00 0.00 3.51
420 427 3.805422 TCAATTTACGCACGACAAAGACT 59.195 39.130 0.00 0.00 0.00 3.24
421 428 4.123276 TCAATTTACGCACGACAAAGAC 57.877 40.909 0.00 0.00 0.00 3.01
422 429 3.805422 ACTCAATTTACGCACGACAAAGA 59.195 39.130 0.00 0.00 0.00 2.52
423 430 3.900116 CACTCAATTTACGCACGACAAAG 59.100 43.478 0.00 0.00 0.00 2.77
424 431 3.556365 TCACTCAATTTACGCACGACAAA 59.444 39.130 0.00 0.00 0.00 2.83
425 432 3.124560 TCACTCAATTTACGCACGACAA 58.875 40.909 0.00 0.00 0.00 3.18
426 433 2.745102 TCACTCAATTTACGCACGACA 58.255 42.857 0.00 0.00 0.00 4.35
427 434 3.991605 ATCACTCAATTTACGCACGAC 57.008 42.857 0.00 0.00 0.00 4.34
428 435 5.344884 TGATATCACTCAATTTACGCACGA 58.655 37.500 0.00 0.00 0.00 4.35
429 436 5.635549 TGATATCACTCAATTTACGCACG 57.364 39.130 0.00 0.00 0.00 5.34
430 437 7.374228 CACAATGATATCACTCAATTTACGCAC 59.626 37.037 7.78 0.00 0.00 5.34
431 438 7.408910 CACAATGATATCACTCAATTTACGCA 58.591 34.615 7.78 0.00 0.00 5.24
432 439 6.852853 CCACAATGATATCACTCAATTTACGC 59.147 38.462 7.78 0.00 0.00 4.42
433 440 8.141835 TCCACAATGATATCACTCAATTTACG 57.858 34.615 7.78 0.00 0.00 3.18
434 441 9.722056 GTTCCACAATGATATCACTCAATTTAC 57.278 33.333 7.78 0.00 0.00 2.01
435 442 9.685276 AGTTCCACAATGATATCACTCAATTTA 57.315 29.630 7.78 0.00 0.00 1.40
436 443 8.585471 AGTTCCACAATGATATCACTCAATTT 57.415 30.769 7.78 0.00 0.00 1.82
437 444 7.830697 TGAGTTCCACAATGATATCACTCAATT 59.169 33.333 7.78 0.00 37.15 2.32
438 445 7.341030 TGAGTTCCACAATGATATCACTCAAT 58.659 34.615 7.78 0.00 37.15 2.57
439 446 6.710278 TGAGTTCCACAATGATATCACTCAA 58.290 36.000 7.78 0.00 37.15 3.02
440 447 6.298441 TGAGTTCCACAATGATATCACTCA 57.702 37.500 7.78 10.49 37.63 3.41
441 448 7.281774 ACAATGAGTTCCACAATGATATCACTC 59.718 37.037 7.78 8.02 0.00 3.51
442 449 7.114754 ACAATGAGTTCCACAATGATATCACT 58.885 34.615 7.78 0.00 0.00 3.41
443 450 7.325660 ACAATGAGTTCCACAATGATATCAC 57.674 36.000 7.78 0.00 0.00 3.06
444 451 6.543465 GGACAATGAGTTCCACAATGATATCA 59.457 38.462 8.10 8.10 0.00 2.15
445 452 6.543465 TGGACAATGAGTTCCACAATGATATC 59.457 38.462 0.00 0.00 0.00 1.63
446 453 6.319658 GTGGACAATGAGTTCCACAATGATAT 59.680 38.462 14.34 0.00 42.75 1.63
447 454 5.647658 GTGGACAATGAGTTCCACAATGATA 59.352 40.000 14.34 0.00 42.75 2.15
448 455 4.460382 GTGGACAATGAGTTCCACAATGAT 59.540 41.667 14.34 0.00 42.75 2.45
449 456 3.820467 GTGGACAATGAGTTCCACAATGA 59.180 43.478 14.34 0.00 42.75 2.57
450 457 3.822735 AGTGGACAATGAGTTCCACAATG 59.177 43.478 19.40 0.00 44.22 2.82
451 458 3.822735 CAGTGGACAATGAGTTCCACAAT 59.177 43.478 19.40 2.03 44.22 2.71
452 459 3.213506 CAGTGGACAATGAGTTCCACAA 58.786 45.455 19.40 0.00 44.22 3.33
453 460 2.849942 CAGTGGACAATGAGTTCCACA 58.150 47.619 19.40 0.00 44.22 4.17
454 461 1.537202 GCAGTGGACAATGAGTTCCAC 59.463 52.381 12.08 12.08 43.16 4.02
455 462 1.421268 AGCAGTGGACAATGAGTTCCA 59.579 47.619 3.70 0.00 0.00 3.53
456 463 2.079925 GAGCAGTGGACAATGAGTTCC 58.920 52.381 3.70 0.00 0.00 3.62
457 464 2.771089 TGAGCAGTGGACAATGAGTTC 58.229 47.619 3.70 0.00 0.00 3.01
458 465 2.880890 GTTGAGCAGTGGACAATGAGTT 59.119 45.455 3.70 0.00 0.00 3.01
459 466 2.158769 TGTTGAGCAGTGGACAATGAGT 60.159 45.455 3.70 0.00 0.00 3.41
460 467 2.497138 TGTTGAGCAGTGGACAATGAG 58.503 47.619 3.70 0.00 0.00 2.90
461 468 2.636647 TGTTGAGCAGTGGACAATGA 57.363 45.000 3.70 0.00 0.00 2.57
462 469 2.670229 GCATGTTGAGCAGTGGACAATG 60.670 50.000 0.00 0.00 0.00 2.82
463 470 1.542915 GCATGTTGAGCAGTGGACAAT 59.457 47.619 0.00 0.00 0.00 2.71
464 471 0.953727 GCATGTTGAGCAGTGGACAA 59.046 50.000 0.00 0.00 0.00 3.18
465 472 0.109153 AGCATGTTGAGCAGTGGACA 59.891 50.000 0.00 0.00 0.00 4.02
466 473 1.242076 AAGCATGTTGAGCAGTGGAC 58.758 50.000 0.00 0.00 0.00 4.02
467 474 1.985473 AAAGCATGTTGAGCAGTGGA 58.015 45.000 0.00 0.00 0.00 4.02
468 475 2.806608 AAAAGCATGTTGAGCAGTGG 57.193 45.000 0.00 0.00 0.00 4.00
469 476 4.624024 CCAATAAAAGCATGTTGAGCAGTG 59.376 41.667 0.00 0.00 0.00 3.66
470 477 4.523943 TCCAATAAAAGCATGTTGAGCAGT 59.476 37.500 0.00 0.00 0.00 4.40
471 478 5.063180 TCCAATAAAAGCATGTTGAGCAG 57.937 39.130 0.00 0.00 0.00 4.24
472 479 4.766373 TCTCCAATAAAAGCATGTTGAGCA 59.234 37.500 0.00 0.00 0.00 4.26
473 480 5.098211 GTCTCCAATAAAAGCATGTTGAGC 58.902 41.667 0.00 0.00 0.00 4.26
474 481 6.258230 TGTCTCCAATAAAAGCATGTTGAG 57.742 37.500 0.00 0.00 0.00 3.02
475 482 6.647334 TTGTCTCCAATAAAAGCATGTTGA 57.353 33.333 0.00 0.00 0.00 3.18
476 483 6.925165 AGTTTGTCTCCAATAAAAGCATGTTG 59.075 34.615 0.00 0.00 0.00 3.33
477 484 7.014615 AGAGTTTGTCTCCAATAAAAGCATGTT 59.985 33.333 0.00 0.00 43.71 2.71
478 485 6.491403 AGAGTTTGTCTCCAATAAAAGCATGT 59.509 34.615 0.00 0.00 43.71 3.21
479 486 6.917533 AGAGTTTGTCTCCAATAAAAGCATG 58.082 36.000 0.00 0.00 43.71 4.06
480 487 7.231317 TCAAGAGTTTGTCTCCAATAAAAGCAT 59.769 33.333 0.00 0.00 43.71 3.79
481 488 6.545666 TCAAGAGTTTGTCTCCAATAAAAGCA 59.454 34.615 0.00 0.00 43.71 3.91
482 489 6.970484 TCAAGAGTTTGTCTCCAATAAAAGC 58.030 36.000 0.00 0.00 43.71 3.51
483 490 9.237846 GTTTCAAGAGTTTGTCTCCAATAAAAG 57.762 33.333 0.00 0.00 43.71 2.27
484 491 8.744652 TGTTTCAAGAGTTTGTCTCCAATAAAA 58.255 29.630 0.00 0.00 43.71 1.52
485 492 8.287439 TGTTTCAAGAGTTTGTCTCCAATAAA 57.713 30.769 0.00 0.00 43.71 1.40
486 493 7.013274 CCTGTTTCAAGAGTTTGTCTCCAATAA 59.987 37.037 0.00 0.00 43.71 1.40
487 494 6.486657 CCTGTTTCAAGAGTTTGTCTCCAATA 59.513 38.462 0.00 0.00 43.71 1.90
488 495 5.300286 CCTGTTTCAAGAGTTTGTCTCCAAT 59.700 40.000 0.00 0.00 43.71 3.16
489 496 4.640201 CCTGTTTCAAGAGTTTGTCTCCAA 59.360 41.667 0.00 0.00 43.71 3.53
490 497 4.199310 CCTGTTTCAAGAGTTTGTCTCCA 58.801 43.478 0.00 0.00 43.71 3.86
491 498 3.003793 GCCTGTTTCAAGAGTTTGTCTCC 59.996 47.826 0.00 0.00 43.71 3.71
492 499 3.879892 AGCCTGTTTCAAGAGTTTGTCTC 59.120 43.478 0.00 0.00 43.05 3.36
493 500 3.891049 AGCCTGTTTCAAGAGTTTGTCT 58.109 40.909 0.00 0.00 36.94 3.41
494 501 4.142381 ACAAGCCTGTTTCAAGAGTTTGTC 60.142 41.667 0.00 0.00 31.78 3.18
495 502 3.763897 ACAAGCCTGTTTCAAGAGTTTGT 59.236 39.130 0.00 0.00 31.78 2.83
496 503 4.376340 ACAAGCCTGTTTCAAGAGTTTG 57.624 40.909 0.00 0.00 31.32 2.93
497 504 6.715347 ATAACAAGCCTGTTTCAAGAGTTT 57.285 33.333 5.92 0.00 43.45 2.66
498 505 6.715347 AATAACAAGCCTGTTTCAAGAGTT 57.285 33.333 5.92 0.00 43.45 3.01
499 506 6.239036 GGAAATAACAAGCCTGTTTCAAGAGT 60.239 38.462 5.92 0.00 43.45 3.24
500 507 6.152379 GGAAATAACAAGCCTGTTTCAAGAG 58.848 40.000 5.92 0.00 43.45 2.85
501 508 5.010617 GGGAAATAACAAGCCTGTTTCAAGA 59.989 40.000 5.92 0.00 43.45 3.02
502 509 5.221422 TGGGAAATAACAAGCCTGTTTCAAG 60.221 40.000 5.92 0.00 43.45 3.02
503 510 4.651503 TGGGAAATAACAAGCCTGTTTCAA 59.348 37.500 5.92 0.00 43.45 2.69
504 511 4.219115 TGGGAAATAACAAGCCTGTTTCA 58.781 39.130 5.92 0.00 43.45 2.69
505 512 4.522789 TCTGGGAAATAACAAGCCTGTTTC 59.477 41.667 5.92 0.00 43.45 2.78
506 513 4.280929 GTCTGGGAAATAACAAGCCTGTTT 59.719 41.667 5.92 0.00 43.45 2.83
508 515 3.074538 AGTCTGGGAAATAACAAGCCTGT 59.925 43.478 0.00 0.00 37.39 4.00
509 516 3.690460 AGTCTGGGAAATAACAAGCCTG 58.310 45.455 0.00 0.00 0.00 4.85
510 517 4.388577 AAGTCTGGGAAATAACAAGCCT 57.611 40.909 0.00 0.00 0.00 4.58
511 518 5.221441 ACAAAAGTCTGGGAAATAACAAGCC 60.221 40.000 0.00 0.00 0.00 4.35
512 519 5.842907 ACAAAAGTCTGGGAAATAACAAGC 58.157 37.500 0.00 0.00 0.00 4.01
513 520 9.981114 AATAACAAAAGTCTGGGAAATAACAAG 57.019 29.630 0.00 0.00 0.00 3.16
515 522 9.974980 GAAATAACAAAAGTCTGGGAAATAACA 57.025 29.630 0.00 0.00 0.00 2.41
516 523 9.419297 GGAAATAACAAAAGTCTGGGAAATAAC 57.581 33.333 0.00 0.00 0.00 1.89
517 524 9.374711 AGGAAATAACAAAAGTCTGGGAAATAA 57.625 29.630 0.00 0.00 0.00 1.40
518 525 8.950007 AGGAAATAACAAAAGTCTGGGAAATA 57.050 30.769 0.00 0.00 0.00 1.40
519 526 7.855784 AGGAAATAACAAAAGTCTGGGAAAT 57.144 32.000 0.00 0.00 0.00 2.17
520 527 8.221944 TCTAGGAAATAACAAAAGTCTGGGAAA 58.778 33.333 0.00 0.00 0.00 3.13
521 528 7.664318 GTCTAGGAAATAACAAAAGTCTGGGAA 59.336 37.037 0.00 0.00 0.00 3.97
522 529 7.017254 AGTCTAGGAAATAACAAAAGTCTGGGA 59.983 37.037 0.00 0.00 0.00 4.37
523 530 7.168905 AGTCTAGGAAATAACAAAAGTCTGGG 58.831 38.462 0.00 0.00 0.00 4.45
524 531 9.372369 CTAGTCTAGGAAATAACAAAAGTCTGG 57.628 37.037 0.00 0.00 0.00 3.86
525 532 9.930693 ACTAGTCTAGGAAATAACAAAAGTCTG 57.069 33.333 11.61 0.00 0.00 3.51
526 533 9.930693 CACTAGTCTAGGAAATAACAAAAGTCT 57.069 33.333 11.61 0.00 0.00 3.24
527 534 9.708092 ACACTAGTCTAGGAAATAACAAAAGTC 57.292 33.333 11.61 0.00 0.00 3.01
533 540 9.841295 ACAAAAACACTAGTCTAGGAAATAACA 57.159 29.630 11.61 0.00 0.00 2.41
758 1116 3.069729 GTGTAGTTGAGACTTGACCTGGT 59.930 47.826 0.00 0.00 37.33 4.00
993 1402 1.145738 ACCTTGACCTCCATTGCTGTT 59.854 47.619 0.00 0.00 0.00 3.16
1191 1638 2.955881 GCGGTACTGGGCAAGGACT 61.956 63.158 3.78 0.00 40.01 3.85
1258 1705 2.737376 GCCACGGTCGTTGAGGAC 60.737 66.667 3.08 0.00 36.18 3.85
1434 1881 2.109387 TGGTTGGACGTGAACCCG 59.891 61.111 18.93 0.00 42.05 5.28
1557 2036 1.952133 CGACGACCGTGGCTTGAAA 60.952 57.895 0.00 0.00 0.00 2.69
2300 2819 1.272807 TCACAGTTAGGCCACCTACC 58.727 55.000 5.01 0.00 35.63 3.18
2336 2862 4.033709 ACTAATGTATGTGCCTCACTCCT 58.966 43.478 0.00 0.00 35.11 3.69
2510 3055 7.231722 AGTCGGATCAAACAGTAGCTAAGATAT 59.768 37.037 0.00 0.00 0.00 1.63
2790 3343 4.846367 TCCTACATTATGGGATGGAAGGAG 59.154 45.833 0.00 0.00 37.90 3.69
2794 3347 3.971305 ACGTCCTACATTATGGGATGGAA 59.029 43.478 12.21 0.00 46.88 3.53
2808 3361 4.986659 ACATAGTGTCAAACAACGTCCTAC 59.013 41.667 0.00 0.00 0.00 3.18
2809 3362 4.986034 CACATAGTGTCAAACAACGTCCTA 59.014 41.667 0.00 0.00 0.00 2.94
2810 3363 3.807622 CACATAGTGTCAAACAACGTCCT 59.192 43.478 0.00 0.00 0.00 3.85
2812 3365 4.789095 ACACATAGTGTCAAACAACGTC 57.211 40.909 0.00 0.00 43.92 4.34
2813 3366 5.353938 ACTACACATAGTGTCAAACAACGT 58.646 37.500 6.00 0.00 43.92 3.99
2814 3367 5.900339 ACTACACATAGTGTCAAACAACG 57.100 39.130 6.00 0.00 43.92 4.10
2825 3378 5.464389 GGACGTTTTTGACACTACACATAGT 59.536 40.000 0.00 0.00 42.74 2.12
2826 3379 5.694910 AGGACGTTTTTGACACTACACATAG 59.305 40.000 0.00 0.00 34.25 2.23
2827 3380 5.603596 AGGACGTTTTTGACACTACACATA 58.396 37.500 0.00 0.00 0.00 2.29
2828 3381 4.448210 AGGACGTTTTTGACACTACACAT 58.552 39.130 0.00 0.00 0.00 3.21
2829 3382 3.864243 AGGACGTTTTTGACACTACACA 58.136 40.909 0.00 0.00 0.00 3.72
2830 3383 4.085415 CGTAGGACGTTTTTGACACTACAC 60.085 45.833 0.00 0.00 36.74 2.90
2831 3384 4.043750 CGTAGGACGTTTTTGACACTACA 58.956 43.478 0.00 0.00 36.74 2.74
2832 3385 4.619931 CGTAGGACGTTTTTGACACTAC 57.380 45.455 0.00 0.00 36.74 2.73
2853 3406 2.077687 TACTCCCTCCGTCCCATAAC 57.922 55.000 0.00 0.00 0.00 1.89
2862 3415 4.730949 TGTATCTTTGTTACTCCCTCCG 57.269 45.455 0.00 0.00 0.00 4.63
2864 3417 9.099454 CTGTTTATGTATCTTTGTTACTCCCTC 57.901 37.037 0.00 0.00 0.00 4.30
2885 3442 4.202111 GCCATGGTGTTGTTCTTACTGTTT 60.202 41.667 14.67 0.00 0.00 2.83
2912 3469 0.618981 GAACCAAGATCTTCCCGGGT 59.381 55.000 22.86 7.19 0.00 5.28
2926 3483 0.038166 GATTGGGCTCAGTGGAACCA 59.962 55.000 0.00 0.00 37.80 3.67
2954 3511 7.885297 TGGACCAACTCTTTCAGATAATTTTG 58.115 34.615 0.00 0.00 0.00 2.44
2956 3513 7.363268 GCATGGACCAACTCTTTCAGATAATTT 60.363 37.037 0.00 0.00 0.00 1.82
2991 3548 5.152097 CGACATTCTACGTAGTCACAAAGT 58.848 41.667 21.53 11.58 43.93 2.66
3015 3572 1.365699 AATGTTCCGCGTGTACATCC 58.634 50.000 15.95 0.00 31.63 3.51
3023 3580 1.588674 TCTGACAAAATGTTCCGCGT 58.411 45.000 4.92 0.00 0.00 6.01
3026 3583 5.115472 CACGAAATTCTGACAAAATGTTCCG 59.885 40.000 0.00 0.00 0.00 4.30
3028 3585 6.690957 TGTCACGAAATTCTGACAAAATGTTC 59.309 34.615 18.74 0.00 42.98 3.18
3075 3632 7.346208 GCGTATGCTCCTTGTTTTTAAAATT 57.654 32.000 0.55 0.00 38.39 1.82
3097 3654 1.635663 CGTTTTAGCACCCAGGAGCG 61.636 60.000 0.23 0.00 36.83 5.03
3115 3672 2.439701 TAGTGGACGAGAGGGGCG 60.440 66.667 0.00 0.00 0.00 6.13
3135 3692 6.295916 CCTCGGGAGCAAATCTATATAAGGTT 60.296 42.308 0.00 0.00 0.00 3.50
3138 3695 5.665459 CCCTCGGGAGCAAATCTATATAAG 58.335 45.833 0.00 0.00 37.50 1.73
3213 3770 7.329471 GCTTATGAGGATTTCCAAACTTTGAAC 59.671 37.037 2.87 0.00 38.89 3.18
3247 3804 3.018149 ACGCTTTCTACCTACCTCTCTG 58.982 50.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.