Multiple sequence alignment - TraesCS2B01G568300

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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 TraesCS2B01G568300 chr2B 100.000 2678 0 0 361 3038 759177205 759174528 0.000000e+00 4946.0
1 TraesCS2B01G568300 chr2B 92.692 1122 74 5 987 2104 758921597 758922714 0.000000e+00 1611.0
2 TraesCS2B01G568300 chr2B 75.031 797 187 8 1168 1958 35320290 35321080 2.880000e-95 359.0
3 TraesCS2B01G568300 chr2B 83.010 206 23 6 2255 2458 758924951 758925146 3.110000e-40 176.0
4 TraesCS2B01G568300 chr2B 100.000 47 0 0 1 47 759177565 759177519 1.500000e-13 87.9
5 TraesCS2B01G568300 chr2D 91.213 2037 148 15 1001 3037 619605825 619603820 0.000000e+00 2741.0
6 TraesCS2B01G568300 chr2D 88.253 332 18 9 584 899 619606374 619606048 7.950000e-101 377.0
7 TraesCS2B01G568300 chr2D 84.638 345 30 14 558 891 619601013 619600681 3.780000e-84 322.0
8 TraesCS2B01G568300 chr2D 84.337 332 24 11 558 872 619607891 619607571 1.770000e-77 300.0
9 TraesCS2B01G568300 chr2D 90.244 82 8 0 361 442 78800916 78800835 1.150000e-19 108.0
10 TraesCS2B01G568300 chr2D 88.095 84 6 4 361 442 288601825 288601906 2.490000e-16 97.1
11 TraesCS2B01G568300 chr2D 100.000 49 0 0 851 899 619606040 619605992 1.160000e-14 91.6
12 TraesCS2B01G568300 chr2A 89.918 1954 142 27 990 2929 751097085 751095173 0.000000e+00 2466.0
13 TraesCS2B01G568300 chr2A 78.757 885 174 11 1181 2059 24002389 24003265 5.650000e-162 580.0
14 TraesCS2B01G568300 chr2A 84.615 273 20 13 590 847 751097420 751097155 5.030000e-63 252.0
15 TraesCS2B01G568300 chr1B 78.907 915 161 20 1118 2007 664611533 664610626 2.610000e-165 592.0
16 TraesCS2B01G568300 chr7A 79.726 804 148 12 1210 2007 46910996 46911790 4.400000e-158 568.0
17 TraesCS2B01G568300 chr7D 77.551 882 174 20 1166 2038 163010616 163011482 7.510000e-141 510.0
18 TraesCS2B01G568300 chr7B 77.556 851 167 20 1166 2007 125064770 125065605 2.720000e-135 492.0
19 TraesCS2B01G568300 chr7B 89.157 83 7 2 361 442 517096656 517096575 5.360000e-18 102.0
20 TraesCS2B01G568300 chr6D 85.366 123 17 1 2529 2651 27211564 27211443 3.180000e-25 126.0
21 TraesCS2B01G568300 chr6D 87.952 83 8 2 361 442 3062168 3062249 2.490000e-16 97.1
22 TraesCS2B01G568300 chr3B 86.207 116 16 0 2536 2651 373130458 373130343 3.180000e-25 126.0
23 TraesCS2B01G568300 chr1A 83.740 123 19 1 2529 2651 389251773 389251652 6.880000e-22 115.0
24 TraesCS2B01G568300 chr3D 90.000 80 6 2 361 440 578901044 578901121 5.360000e-18 102.0
25 TraesCS2B01G568300 chr3D 90.541 74 6 1 362 435 403673866 403673938 2.490000e-16 97.1
26 TraesCS2B01G568300 chr5A 87.952 83 8 2 361 442 340819744 340819663 2.490000e-16 97.1
27 TraesCS2B01G568300 chr4A 91.549 71 5 1 361 430 672520269 672520339 2.490000e-16 97.1
28 TraesCS2B01G568300 chr6B 90.000 70 7 0 361 430 240842592 240842661 1.160000e-14 91.6
29 TraesCS2B01G568300 chr5D 92.593 54 3 1 2301 2353 556158023 556158076 3.250000e-10 76.8


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 TraesCS2B01G568300 chr2B 759174528 759177565 3037 True 2516.95 4946 100.0000 1 3038 2 chr2B.!!$R1 3037
1 TraesCS2B01G568300 chr2B 758921597 758925146 3549 False 893.50 1611 87.8510 987 2458 2 chr2B.!!$F2 1471
2 TraesCS2B01G568300 chr2B 35320290 35321080 790 False 359.00 359 75.0310 1168 1958 1 chr2B.!!$F1 790
3 TraesCS2B01G568300 chr2D 619600681 619607891 7210 True 766.32 2741 89.6882 558 3037 5 chr2D.!!$R2 2479
4 TraesCS2B01G568300 chr2A 751095173 751097420 2247 True 1359.00 2466 87.2665 590 2929 2 chr2A.!!$R1 2339
5 TraesCS2B01G568300 chr2A 24002389 24003265 876 False 580.00 580 78.7570 1181 2059 1 chr2A.!!$F1 878
6 TraesCS2B01G568300 chr1B 664610626 664611533 907 True 592.00 592 78.9070 1118 2007 1 chr1B.!!$R1 889
7 TraesCS2B01G568300 chr7A 46910996 46911790 794 False 568.00 568 79.7260 1210 2007 1 chr7A.!!$F1 797
8 TraesCS2B01G568300 chr7D 163010616 163011482 866 False 510.00 510 77.5510 1166 2038 1 chr7D.!!$F1 872
9 TraesCS2B01G568300 chr7B 125064770 125065605 835 False 492.00 492 77.5560 1166 2007 1 chr7B.!!$F1 841

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
44 45 0.034896 GGAGGCAAAGACTTCACCGA 59.965 55.0 0.00 0.0 0.0 4.69 F
46 47 0.035458 AGGCAAAGACTTCACCGAGG 59.965 55.0 0.00 0.0 0.0 4.63 F
513 514 0.249911 AGGCGCGACTGAGTCTTTTT 60.250 50.0 17.28 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1084 2765 1.299014 GATGCTGCGACGAGGAGAG 60.299 63.158 0.0 0.0 41.23 3.20 R
1716 3434 2.045242 AGCTCCTCGTACCGCAGA 60.045 61.111 0.0 0.0 0.00 4.26 R
2509 6345 1.618487 GTGGGGGTATAGAGACTCGG 58.382 60.000 0.0 0.0 0.00 4.63 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
17 18 3.213402 GAGAGAGAGGGGCGTCGG 61.213 72.222 0.00 0.00 0.00 4.79
35 36 4.082523 CGGCGAGGGAGGCAAAGA 62.083 66.667 0.00 0.00 36.37 2.52
36 37 2.436824 GGCGAGGGAGGCAAAGAC 60.437 66.667 0.00 0.00 36.61 3.01
37 38 2.665603 GCGAGGGAGGCAAAGACT 59.334 61.111 0.00 0.00 0.00 3.24
38 39 1.003233 GCGAGGGAGGCAAAGACTT 60.003 57.895 0.00 0.00 0.00 3.01
39 40 1.021920 GCGAGGGAGGCAAAGACTTC 61.022 60.000 0.00 0.00 0.00 3.01
40 41 0.321671 CGAGGGAGGCAAAGACTTCA 59.678 55.000 0.00 0.00 0.00 3.02
41 42 1.814793 GAGGGAGGCAAAGACTTCAC 58.185 55.000 0.00 0.00 0.00 3.18
42 43 0.402121 AGGGAGGCAAAGACTTCACC 59.598 55.000 0.00 0.00 0.00 4.02
43 44 0.955919 GGGAGGCAAAGACTTCACCG 60.956 60.000 0.00 0.00 0.00 4.94
44 45 0.034896 GGAGGCAAAGACTTCACCGA 59.965 55.000 0.00 0.00 0.00 4.69
45 46 1.433534 GAGGCAAAGACTTCACCGAG 58.566 55.000 0.00 0.00 0.00 4.63
46 47 0.035458 AGGCAAAGACTTCACCGAGG 59.965 55.000 0.00 0.00 0.00 4.63
377 378 2.044946 AATGGAAGGCTGACCGGC 60.045 61.111 0.00 0.00 42.76 6.13
378 379 3.976701 AATGGAAGGCTGACCGGCG 62.977 63.158 0.00 0.00 44.22 6.46
386 387 4.379243 CTGACCGGCGGCTGTCTT 62.379 66.667 28.71 4.60 32.67 3.01
387 388 4.680237 TGACCGGCGGCTGTCTTG 62.680 66.667 28.71 0.00 32.67 3.02
392 393 3.064324 GGCGGCTGTCTTGGCATT 61.064 61.111 0.00 0.00 0.00 3.56
393 394 2.180017 GCGGCTGTCTTGGCATTG 59.820 61.111 0.00 0.00 0.00 2.82
394 395 2.334946 GCGGCTGTCTTGGCATTGA 61.335 57.895 0.00 0.00 0.00 2.57
395 396 1.660560 GCGGCTGTCTTGGCATTGAT 61.661 55.000 0.00 0.00 0.00 2.57
396 397 0.813184 CGGCTGTCTTGGCATTGATT 59.187 50.000 0.00 0.00 0.00 2.57
397 398 1.202222 CGGCTGTCTTGGCATTGATTC 60.202 52.381 0.00 0.00 0.00 2.52
398 399 1.135721 GGCTGTCTTGGCATTGATTCC 59.864 52.381 0.00 0.00 0.00 3.01
399 400 1.135721 GCTGTCTTGGCATTGATTCCC 59.864 52.381 0.00 0.00 0.00 3.97
400 401 1.753073 CTGTCTTGGCATTGATTCCCC 59.247 52.381 0.00 0.00 0.00 4.81
401 402 0.740737 GTCTTGGCATTGATTCCCCG 59.259 55.000 0.00 0.00 0.00 5.73
402 403 1.037030 TCTTGGCATTGATTCCCCGC 61.037 55.000 0.00 0.00 0.00 6.13
403 404 2.340453 CTTGGCATTGATTCCCCGCG 62.340 60.000 0.00 0.00 0.00 6.46
404 405 3.595758 GGCATTGATTCCCCGCGG 61.596 66.667 21.04 21.04 0.00 6.46
405 406 3.595758 GCATTGATTCCCCGCGGG 61.596 66.667 37.99 37.99 46.11 6.13
427 428 4.570663 CGAGGCGACGGGGATGAC 62.571 72.222 0.00 0.00 0.00 3.06
428 429 3.458163 GAGGCGACGGGGATGACA 61.458 66.667 0.00 0.00 0.00 3.58
429 430 3.000819 AGGCGACGGGGATGACAA 61.001 61.111 0.00 0.00 0.00 3.18
430 431 2.046700 GGCGACGGGGATGACAAA 60.047 61.111 0.00 0.00 0.00 2.83
431 432 1.451387 GGCGACGGGGATGACAAAT 60.451 57.895 0.00 0.00 0.00 2.32
432 433 1.714899 GGCGACGGGGATGACAAATG 61.715 60.000 0.00 0.00 0.00 2.32
433 434 1.721487 CGACGGGGATGACAAATGC 59.279 57.895 0.00 0.00 0.00 3.56
434 435 1.721487 GACGGGGATGACAAATGCG 59.279 57.895 0.00 0.00 0.00 4.73
435 436 1.714899 GACGGGGATGACAAATGCGG 61.715 60.000 0.00 0.00 0.00 5.69
436 437 2.807622 GGGGATGACAAATGCGGC 59.192 61.111 0.00 0.00 0.00 6.53
437 438 2.408835 GGGATGACAAATGCGGCG 59.591 61.111 0.51 0.51 0.00 6.46
438 439 2.408835 GGATGACAAATGCGGCGG 59.591 61.111 9.78 0.00 0.00 6.13
439 440 2.408835 GATGACAAATGCGGCGGG 59.591 61.111 9.78 0.00 0.00 6.13
440 441 2.361104 ATGACAAATGCGGCGGGT 60.361 55.556 9.78 0.00 0.00 5.28
441 442 2.322999 GATGACAAATGCGGCGGGTC 62.323 60.000 9.78 1.00 0.00 4.46
442 443 3.810896 GACAAATGCGGCGGGTCC 61.811 66.667 9.78 0.00 0.00 4.46
443 444 4.652131 ACAAATGCGGCGGGTCCA 62.652 61.111 9.78 0.00 34.01 4.02
444 445 4.114997 CAAATGCGGCGGGTCCAC 62.115 66.667 9.78 0.00 34.01 4.02
452 453 4.660938 GCGGGTCCACCAGGCTTT 62.661 66.667 0.00 0.00 40.22 3.51
453 454 2.359975 CGGGTCCACCAGGCTTTC 60.360 66.667 0.00 0.00 40.22 2.62
454 455 2.359975 GGGTCCACCAGGCTTTCG 60.360 66.667 0.00 0.00 39.85 3.46
455 456 3.056328 GGTCCACCAGGCTTTCGC 61.056 66.667 0.00 0.00 35.64 4.70
456 457 3.423154 GTCCACCAGGCTTTCGCG 61.423 66.667 0.00 0.00 36.88 5.87
457 458 3.936203 TCCACCAGGCTTTCGCGT 61.936 61.111 5.77 0.00 36.88 6.01
458 459 2.978010 CCACCAGGCTTTCGCGTT 60.978 61.111 5.77 0.00 36.88 4.84
459 460 1.669760 CCACCAGGCTTTCGCGTTA 60.670 57.895 5.77 0.00 36.88 3.18
460 461 1.231958 CCACCAGGCTTTCGCGTTAA 61.232 55.000 5.77 0.66 36.88 2.01
461 462 0.589223 CACCAGGCTTTCGCGTTAAA 59.411 50.000 5.77 0.00 36.88 1.52
462 463 1.199097 CACCAGGCTTTCGCGTTAAAT 59.801 47.619 5.77 0.00 36.88 1.40
463 464 1.883926 ACCAGGCTTTCGCGTTAAATT 59.116 42.857 5.77 0.00 36.88 1.82
464 465 2.095415 ACCAGGCTTTCGCGTTAAATTC 60.095 45.455 5.77 0.00 36.88 2.17
465 466 2.166007 CAGGCTTTCGCGTTAAATTCG 58.834 47.619 5.77 0.00 36.88 3.34
466 467 1.129811 AGGCTTTCGCGTTAAATTCGG 59.870 47.619 5.77 0.00 36.88 4.30
467 468 0.905175 GCTTTCGCGTTAAATTCGGC 59.095 50.000 5.77 0.00 0.00 5.54
468 469 1.465187 GCTTTCGCGTTAAATTCGGCT 60.465 47.619 5.77 0.00 0.00 5.52
469 470 2.428114 CTTTCGCGTTAAATTCGGCTC 58.572 47.619 5.77 0.00 0.00 4.70
470 471 1.717194 TTCGCGTTAAATTCGGCTCT 58.283 45.000 5.77 0.00 0.00 4.09
471 472 2.565210 TCGCGTTAAATTCGGCTCTA 57.435 45.000 5.77 0.00 0.00 2.43
472 473 2.878580 TCGCGTTAAATTCGGCTCTAA 58.121 42.857 5.77 0.00 0.00 2.10
473 474 3.450578 TCGCGTTAAATTCGGCTCTAAT 58.549 40.909 5.77 0.00 0.00 1.73
474 475 3.866910 TCGCGTTAAATTCGGCTCTAATT 59.133 39.130 5.77 0.00 0.00 1.40
475 476 5.042593 TCGCGTTAAATTCGGCTCTAATTA 58.957 37.500 5.77 0.00 0.00 1.40
476 477 5.174398 TCGCGTTAAATTCGGCTCTAATTAG 59.826 40.000 5.77 6.11 0.00 1.73
477 478 5.138095 GCGTTAAATTCGGCTCTAATTAGC 58.862 41.667 7.67 0.00 41.99 3.09
478 479 5.277154 GCGTTAAATTCGGCTCTAATTAGCA 60.277 40.000 7.67 0.00 44.64 3.49
479 480 6.711579 CGTTAAATTCGGCTCTAATTAGCAA 58.288 36.000 7.67 0.00 44.64 3.91
480 481 7.184106 CGTTAAATTCGGCTCTAATTAGCAAA 58.816 34.615 7.67 0.00 44.64 3.68
481 482 7.694784 CGTTAAATTCGGCTCTAATTAGCAAAA 59.305 33.333 7.67 0.00 44.64 2.44
482 483 9.349145 GTTAAATTCGGCTCTAATTAGCAAAAA 57.651 29.630 7.67 0.00 44.64 1.94
483 484 9.567848 TTAAATTCGGCTCTAATTAGCAAAAAG 57.432 29.630 7.67 1.01 44.64 2.27
484 485 6.759497 ATTCGGCTCTAATTAGCAAAAAGT 57.241 33.333 7.67 0.00 44.64 2.66
485 486 5.545658 TCGGCTCTAATTAGCAAAAAGTG 57.454 39.130 7.67 0.00 44.64 3.16
486 487 4.394920 TCGGCTCTAATTAGCAAAAAGTGG 59.605 41.667 7.67 0.00 44.64 4.00
487 488 4.156008 CGGCTCTAATTAGCAAAAAGTGGT 59.844 41.667 7.67 0.00 44.64 4.16
488 489 5.335661 CGGCTCTAATTAGCAAAAAGTGGTT 60.336 40.000 7.67 0.00 44.64 3.67
489 490 6.455647 GGCTCTAATTAGCAAAAAGTGGTTT 58.544 36.000 7.67 0.00 44.64 3.27
490 491 6.586463 GGCTCTAATTAGCAAAAAGTGGTTTC 59.414 38.462 7.67 0.00 44.64 2.78
491 492 7.145323 GCTCTAATTAGCAAAAAGTGGTTTCA 58.855 34.615 7.67 0.00 42.30 2.69
492 493 7.327032 GCTCTAATTAGCAAAAAGTGGTTTCAG 59.673 37.037 7.67 0.00 42.30 3.02
493 494 7.657336 TCTAATTAGCAAAAAGTGGTTTCAGG 58.343 34.615 7.67 0.00 39.22 3.86
494 495 6.478512 AATTAGCAAAAAGTGGTTTCAGGA 57.521 33.333 0.00 0.00 39.22 3.86
495 496 5.514274 TTAGCAAAAAGTGGTTTCAGGAG 57.486 39.130 0.00 0.00 39.22 3.69
496 497 2.695147 AGCAAAAAGTGGTTTCAGGAGG 59.305 45.455 0.00 0.00 32.77 4.30
497 498 2.803133 GCAAAAAGTGGTTTCAGGAGGC 60.803 50.000 0.00 0.00 0.00 4.70
498 499 1.318576 AAAAGTGGTTTCAGGAGGCG 58.681 50.000 0.00 0.00 0.00 5.52
499 500 1.172812 AAAGTGGTTTCAGGAGGCGC 61.173 55.000 0.00 0.00 0.00 6.53
500 501 3.423154 GTGGTTTCAGGAGGCGCG 61.423 66.667 0.00 0.00 0.00 6.86
501 502 3.621805 TGGTTTCAGGAGGCGCGA 61.622 61.111 12.10 0.00 0.00 5.87
502 503 3.119096 GGTTTCAGGAGGCGCGAC 61.119 66.667 12.10 7.34 0.00 5.19
503 504 2.048127 GTTTCAGGAGGCGCGACT 60.048 61.111 18.34 18.34 0.00 4.18
504 505 2.048222 TTTCAGGAGGCGCGACTG 60.048 61.111 25.24 16.71 0.00 3.51
505 506 2.570284 TTTCAGGAGGCGCGACTGA 61.570 57.895 25.24 18.91 39.31 3.41
506 507 2.492449 TTTCAGGAGGCGCGACTGAG 62.492 60.000 25.24 9.29 41.71 3.35
507 508 3.753434 CAGGAGGCGCGACTGAGT 61.753 66.667 25.24 0.00 34.21 3.41
508 509 3.444805 AGGAGGCGCGACTGAGTC 61.445 66.667 25.24 4.19 0.00 3.36
509 510 3.444805 GGAGGCGCGACTGAGTCT 61.445 66.667 25.24 0.00 30.16 3.24
510 511 2.569134 GAGGCGCGACTGAGTCTT 59.431 61.111 25.24 0.00 26.42 3.01
511 512 1.080434 GAGGCGCGACTGAGTCTTT 60.080 57.895 25.24 0.00 26.42 2.52
512 513 0.667792 GAGGCGCGACTGAGTCTTTT 60.668 55.000 25.24 0.00 26.42 2.27
513 514 0.249911 AGGCGCGACTGAGTCTTTTT 60.250 50.000 17.28 0.00 0.00 1.94
553 554 2.604382 CCTTGGGGGCTTGTTGGG 60.604 66.667 0.00 0.00 0.00 4.12
554 555 2.604382 CTTGGGGGCTTGTTGGGG 60.604 66.667 0.00 0.00 0.00 4.96
555 556 4.247130 TTGGGGGCTTGTTGGGGG 62.247 66.667 0.00 0.00 0.00 5.40
571 572 1.640917 GGGGGCATATAGAAGTCGGA 58.359 55.000 0.00 0.00 0.00 4.55
574 575 2.567615 GGGGCATATAGAAGTCGGATGT 59.432 50.000 0.00 0.00 0.00 3.06
576 577 4.381718 GGGGCATATAGAAGTCGGATGTAC 60.382 50.000 0.00 0.00 0.00 2.90
578 579 4.082895 GGCATATAGAAGTCGGATGTACGT 60.083 45.833 0.00 0.00 34.94 3.57
588 2080 4.860907 AGTCGGATGTACGTTTATTGTGTC 59.139 41.667 0.00 0.00 34.94 3.67
593 2085 6.237384 CGGATGTACGTTTATTGTGTCTGTAC 60.237 42.308 0.00 0.00 33.23 2.90
605 2097 4.157246 TGTGTCTGTACCACCTATTCACT 58.843 43.478 0.00 0.00 31.71 3.41
608 2100 5.638234 GTGTCTGTACCACCTATTCACTTTC 59.362 44.000 0.00 0.00 0.00 2.62
616 2108 7.645058 ACCACCTATTCACTTTCATTAATGG 57.355 36.000 15.36 2.35 0.00 3.16
660 2152 8.834749 TTTACCAAAAATAAAAATTCCCCTCG 57.165 30.769 0.00 0.00 0.00 4.63
691 2183 4.143473 CGCAGTGAATTGAAAAATGCTGAC 60.143 41.667 0.00 0.00 0.00 3.51
694 2186 6.238157 GCAGTGAATTGAAAAATGCTGACAAA 60.238 34.615 0.00 0.00 0.00 2.83
704 2196 0.609957 TGCTGACAAATGGGAGCTGG 60.610 55.000 0.00 0.00 32.41 4.85
766 2274 4.227982 TGGATATACATATGTGGGCTGCAT 59.772 41.667 18.81 4.55 0.00 3.96
768 2276 2.275134 TACATATGTGGGCTGCATGG 57.725 50.000 18.81 1.18 0.00 3.66
769 2277 0.259647 ACATATGTGGGCTGCATGGT 59.740 50.000 7.78 1.67 0.00 3.55
770 2278 0.671796 CATATGTGGGCTGCATGGTG 59.328 55.000 0.50 1.60 0.00 4.17
771 2279 0.259647 ATATGTGGGCTGCATGGTGT 59.740 50.000 0.50 0.00 0.00 4.16
772 2280 0.915364 TATGTGGGCTGCATGGTGTA 59.085 50.000 0.50 0.00 0.00 2.90
773 2281 0.259647 ATGTGGGCTGCATGGTGTAT 59.740 50.000 0.50 0.00 0.00 2.29
840 2354 2.510906 GAGGGGCGTGCATGGTAT 59.489 61.111 8.27 0.00 0.00 2.73
903 2509 4.964897 TGATCTCTCTCTCTCTCTCAGACT 59.035 45.833 0.00 0.00 0.00 3.24
940 2584 2.600867 CGCTCTCCTTTCAACGAATCTC 59.399 50.000 0.00 0.00 0.00 2.75
945 2589 2.236395 TCCTTTCAACGAATCTCCCCTC 59.764 50.000 0.00 0.00 0.00 4.30
953 2597 3.642741 AATCTCCCCTCCCCTGCGT 62.643 63.158 0.00 0.00 0.00 5.24
959 2603 2.685380 CCTCCCCTGCGTCCTTCT 60.685 66.667 0.00 0.00 0.00 2.85
962 2606 0.970937 CTCCCCTGCGTCCTTCTACA 60.971 60.000 0.00 0.00 0.00 2.74
964 2608 1.258445 CCCCTGCGTCCTTCTACAGT 61.258 60.000 0.00 0.00 0.00 3.55
965 2609 0.608640 CCCTGCGTCCTTCTACAGTT 59.391 55.000 0.00 0.00 0.00 3.16
966 2610 1.404315 CCCTGCGTCCTTCTACAGTTC 60.404 57.143 0.00 0.00 0.00 3.01
967 2611 1.404315 CCTGCGTCCTTCTACAGTTCC 60.404 57.143 0.00 0.00 0.00 3.62
968 2612 1.272490 CTGCGTCCTTCTACAGTTCCA 59.728 52.381 0.00 0.00 0.00 3.53
969 2613 1.000506 TGCGTCCTTCTACAGTTCCAC 59.999 52.381 0.00 0.00 0.00 4.02
970 2614 1.272769 GCGTCCTTCTACAGTTCCACT 59.727 52.381 0.00 0.00 0.00 4.00
971 2615 2.671632 GCGTCCTTCTACAGTTCCACTC 60.672 54.545 0.00 0.00 0.00 3.51
973 2617 2.897969 GTCCTTCTACAGTTCCACTCCA 59.102 50.000 0.00 0.00 0.00 3.86
974 2618 2.897969 TCCTTCTACAGTTCCACTCCAC 59.102 50.000 0.00 0.00 0.00 4.02
976 2620 1.254026 TCTACAGTTCCACTCCACCG 58.746 55.000 0.00 0.00 0.00 4.94
977 2621 0.389948 CTACAGTTCCACTCCACCGC 60.390 60.000 0.00 0.00 0.00 5.68
978 2622 1.116536 TACAGTTCCACTCCACCGCA 61.117 55.000 0.00 0.00 0.00 5.69
980 2624 2.140792 AGTTCCACTCCACCGCAGT 61.141 57.895 0.00 0.00 0.00 4.40
981 2625 0.830444 AGTTCCACTCCACCGCAGTA 60.830 55.000 0.00 0.00 0.00 2.74
982 2626 0.389948 GTTCCACTCCACCGCAGTAG 60.390 60.000 0.00 0.00 0.00 2.57
984 2628 1.215647 CCACTCCACCGCAGTAGTC 59.784 63.158 0.00 0.00 0.00 2.59
985 2629 1.532604 CCACTCCACCGCAGTAGTCA 61.533 60.000 0.00 0.00 0.00 3.41
999 2674 5.106475 CGCAGTAGTCAAGTAGAAGAAGAGT 60.106 44.000 0.00 0.00 0.00 3.24
1084 2765 4.076394 TGTTGTTATAGGCACAAACCTCC 58.924 43.478 0.00 0.00 41.50 4.30
1093 2774 0.969894 CACAAACCTCCTCTCCTCGT 59.030 55.000 0.00 0.00 0.00 4.18
1101 2782 2.780094 CCTCTCCTCGTCGCAGCAT 61.780 63.158 0.00 0.00 0.00 3.79
1243 2925 2.897350 CCCTCCAGCGGCGATTTC 60.897 66.667 12.98 0.00 0.00 2.17
1497 3194 4.838152 CCGCTCCCGATGGTGGTG 62.838 72.222 0.00 0.00 36.29 4.17
1716 3434 1.600916 GCCGGACAAGGTGCTCTTT 60.601 57.895 5.05 0.00 32.41 2.52
1794 3512 1.600058 TCCTGGGAATGCCATTCTCT 58.400 50.000 17.76 0.00 40.46 3.10
1806 3524 0.107993 CATTCTCTGCAGCGGAGGAA 60.108 55.000 27.88 20.50 37.46 3.36
1851 3569 2.202851 CGGCTCTGCAGCTTCGAT 60.203 61.111 9.47 0.00 46.03 3.59
1880 3598 1.665442 GCCTGGACGCCAACAAAAT 59.335 52.632 0.00 0.00 30.80 1.82
1991 3712 4.803426 GGCGAGCCGTCTGGACAG 62.803 72.222 0.00 0.00 37.49 3.51
2048 3769 4.568152 ATTTTCGGTGACTTTTGACCTG 57.432 40.909 0.00 0.00 0.00 4.00
2055 3776 2.676342 GTGACTTTTGACCTGTTCACGT 59.324 45.455 0.00 0.00 32.26 4.49
2056 3777 3.866910 GTGACTTTTGACCTGTTCACGTA 59.133 43.478 0.00 0.00 32.26 3.57
2137 3894 9.995003 TGCCAACATTTTCTTTTAATCAGTATT 57.005 25.926 0.00 0.00 0.00 1.89
2208 3969 6.091986 GTCAAACCTTGCAAATTTTGACAAGA 59.908 34.615 34.46 16.96 46.91 3.02
2257 6084 2.632377 AGAGCATTCACGGTACCAATG 58.368 47.619 13.54 14.89 0.00 2.82
2268 6095 4.035091 CACGGTACCAATGAATACCATGTG 59.965 45.833 13.54 3.10 40.90 3.21
2269 6096 4.196193 CGGTACCAATGAATACCATGTGT 58.804 43.478 13.54 0.00 40.90 3.72
2280 6107 2.099141 ACCATGTGTCCGTCATGAAG 57.901 50.000 0.00 0.00 43.47 3.02
2392 6225 6.327386 AGACCAACCAAATATGTGGAGTAT 57.673 37.500 19.42 7.29 41.65 2.12
2393 6226 6.731467 AGACCAACCAAATATGTGGAGTATT 58.269 36.000 19.42 0.00 41.65 1.89
2394 6227 7.182060 AGACCAACCAAATATGTGGAGTATTT 58.818 34.615 19.42 0.00 41.65 1.40
2395 6228 7.339466 AGACCAACCAAATATGTGGAGTATTTC 59.661 37.037 19.42 6.87 41.65 2.17
2396 6229 7.182060 ACCAACCAAATATGTGGAGTATTTCT 58.818 34.615 19.42 0.00 41.65 2.52
2397 6230 7.673926 ACCAACCAAATATGTGGAGTATTTCTT 59.326 33.333 19.42 0.00 41.65 2.52
2399 6232 9.927668 CAACCAAATATGTGGAGTATTTCTTTT 57.072 29.630 19.42 0.00 41.65 2.27
2477 6313 8.040727 AGTATCACACAAAATGTAGCACATCTA 58.959 33.333 2.85 0.00 40.64 1.98
2485 6321 8.531982 ACAAAATGTAGCACATCTACTAAGAGA 58.468 33.333 2.85 0.00 46.15 3.10
2523 6359 8.763356 CATATACGTAATCCGAGTCTCTATACC 58.237 40.741 0.00 0.00 40.70 2.73
2532 6368 1.133544 AGTCTCTATACCCCCACGGAC 60.134 57.143 0.00 0.00 34.64 4.79
2534 6370 0.466922 CTCTATACCCCCACGGACGT 60.467 60.000 0.00 0.00 34.64 4.34
2554 6394 4.373116 CCGTGGACACTGACCGGG 62.373 72.222 6.32 0.00 35.11 5.73
2571 6411 2.285083 CGGGCGGATATCAAAACTTGA 58.715 47.619 4.83 0.00 45.01 3.02
2577 6417 5.516339 GGCGGATATCAAAACTTGACATTTG 59.484 40.000 4.83 0.00 43.48 2.32
2632 6472 1.573026 TACGAACACATGCACGTTGT 58.427 45.000 3.02 0.00 39.59 3.32
2642 6482 3.181482 ACATGCACGTTGTTCATTTTGGA 60.181 39.130 0.00 0.00 0.00 3.53
2643 6483 2.803451 TGCACGTTGTTCATTTTGGAC 58.197 42.857 0.00 0.00 0.00 4.02
2644 6484 2.164422 TGCACGTTGTTCATTTTGGACA 59.836 40.909 0.00 0.00 0.00 4.02
2649 6489 5.290643 CACGTTGTTCATTTTGGACAAACAT 59.709 36.000 3.01 0.00 35.31 2.71
2672 6512 2.248280 TAGCTTTGGTTGCGAAGTGA 57.752 45.000 0.00 0.00 35.28 3.41
2685 6525 1.460743 CGAAGTGATTCGAAGCTGCAA 59.539 47.619 15.31 0.00 46.52 4.08
2751 6591 3.064682 CGGTGAAGTGATGTTTGTTGACA 59.935 43.478 0.00 0.00 0.00 3.58
2758 6598 7.435784 TGAAGTGATGTTTGTTGACAATGATTG 59.564 33.333 3.16 3.16 35.55 2.67
2784 6624 0.608640 AGAGCGGTCGAAGGAAACAT 59.391 50.000 9.28 0.00 0.00 2.71
2803 6643 0.607112 TTGGCGGATACAACGGTACA 59.393 50.000 0.00 0.00 30.94 2.90
2861 6701 4.083802 GGTGATGAAAGTGAGCAGTTACAC 60.084 45.833 0.00 0.00 37.30 2.90
2888 6728 4.142381 GCGCTTTCCAGAAACCTAATTCAT 60.142 41.667 0.00 0.00 0.00 2.57
2896 6736 7.470192 TCCAGAAACCTAATTCATCCTTTTCT 58.530 34.615 0.00 0.00 33.21 2.52
2898 6738 7.542025 CAGAAACCTAATTCATCCTTTTCTGG 58.458 38.462 11.58 0.00 42.17 3.86
2908 6748 2.426522 TCCTTTTCTGGTGCAAGATCG 58.573 47.619 0.00 0.00 0.00 3.69
2931 6771 2.575805 AGGCAAGAGGTTCCAAAGAG 57.424 50.000 0.00 0.00 0.00 2.85
2941 6781 2.155279 GTTCCAAAGAGTTGCTCTCCC 58.845 52.381 0.00 0.00 40.28 4.30
2969 6809 1.885388 TGGACACACCAGCGTTTCG 60.885 57.895 0.00 0.00 44.64 3.46
2974 6814 1.070786 ACACCAGCGTTTCGGATGT 59.929 52.632 0.00 0.00 0.00 3.06
2987 6827 0.464193 CGGATGTGGACATGATGGCA 60.464 55.000 0.00 0.00 36.57 4.92
2988 6828 1.766494 GGATGTGGACATGATGGCAA 58.234 50.000 0.00 0.00 36.57 4.52
3025 6865 9.353999 CTAACTTGATTTTATGTACCTTTTGGC 57.646 33.333 0.00 0.00 45.59 4.52
3027 6867 6.207810 ACTTGATTTTATGTACCTTTTGGCGA 59.792 34.615 0.00 0.00 45.59 5.54
3037 6877 2.233271 CCTTTTGGCGATGGCTGATAT 58.767 47.619 0.00 0.00 39.81 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.213402 CCGACGCCCCTCTCTCTC 61.213 72.222 0.00 0.00 0.00 3.20
18 19 4.082523 TCTTTGCCTCCCTCGCCG 62.083 66.667 0.00 0.00 0.00 6.46
19 20 2.436824 GTCTTTGCCTCCCTCGCC 60.437 66.667 0.00 0.00 0.00 5.54
20 21 1.003233 AAGTCTTTGCCTCCCTCGC 60.003 57.895 0.00 0.00 0.00 5.03
21 22 0.321671 TGAAGTCTTTGCCTCCCTCG 59.678 55.000 0.00 0.00 0.00 4.63
22 23 1.611936 GGTGAAGTCTTTGCCTCCCTC 60.612 57.143 0.00 0.00 0.00 4.30
23 24 0.402121 GGTGAAGTCTTTGCCTCCCT 59.598 55.000 0.00 0.00 0.00 4.20
24 25 0.955919 CGGTGAAGTCTTTGCCTCCC 60.956 60.000 5.28 0.00 0.00 4.30
25 26 0.034896 TCGGTGAAGTCTTTGCCTCC 59.965 55.000 5.28 0.00 0.00 4.30
26 27 1.433534 CTCGGTGAAGTCTTTGCCTC 58.566 55.000 5.28 0.00 0.00 4.70
27 28 0.035458 CCTCGGTGAAGTCTTTGCCT 59.965 55.000 5.28 0.00 0.00 4.75
28 29 2.544726 CCTCGGTGAAGTCTTTGCC 58.455 57.895 0.00 0.00 0.00 4.52
360 361 2.044946 GCCGGTCAGCCTTCCATT 60.045 61.111 1.90 0.00 0.00 3.16
361 362 4.473520 CGCCGGTCAGCCTTCCAT 62.474 66.667 1.90 0.00 0.00 3.41
369 370 4.379243 AAGACAGCCGCCGGTCAG 62.379 66.667 4.45 0.00 38.44 3.51
370 371 4.680237 CAAGACAGCCGCCGGTCA 62.680 66.667 4.45 0.00 38.44 4.02
375 376 3.064324 AATGCCAAGACAGCCGCC 61.064 61.111 0.00 0.00 0.00 6.13
376 377 1.660560 ATCAATGCCAAGACAGCCGC 61.661 55.000 0.00 0.00 0.00 6.53
377 378 0.813184 AATCAATGCCAAGACAGCCG 59.187 50.000 0.00 0.00 0.00 5.52
378 379 1.135721 GGAATCAATGCCAAGACAGCC 59.864 52.381 0.00 0.00 0.00 4.85
379 380 1.135721 GGGAATCAATGCCAAGACAGC 59.864 52.381 0.00 0.00 39.85 4.40
380 381 1.753073 GGGGAATCAATGCCAAGACAG 59.247 52.381 0.00 0.00 42.44 3.51
381 382 1.851304 GGGGAATCAATGCCAAGACA 58.149 50.000 0.00 0.00 42.44 3.41
382 383 0.740737 CGGGGAATCAATGCCAAGAC 59.259 55.000 0.00 0.00 42.44 3.01
383 384 1.037030 GCGGGGAATCAATGCCAAGA 61.037 55.000 0.00 0.00 42.44 3.02
384 385 1.438814 GCGGGGAATCAATGCCAAG 59.561 57.895 0.00 0.00 42.44 3.61
385 386 2.413963 CGCGGGGAATCAATGCCAA 61.414 57.895 0.00 0.00 42.44 4.52
386 387 2.828095 CGCGGGGAATCAATGCCA 60.828 61.111 0.00 0.00 42.44 4.92
387 388 3.595758 CCGCGGGGAATCAATGCC 61.596 66.667 20.10 0.00 39.22 4.40
410 411 4.570663 GTCATCCCCGTCGCCTCG 62.571 72.222 0.00 0.00 0.00 4.63
411 412 2.515996 TTTGTCATCCCCGTCGCCTC 62.516 60.000 0.00 0.00 0.00 4.70
412 413 1.910580 ATTTGTCATCCCCGTCGCCT 61.911 55.000 0.00 0.00 0.00 5.52
413 414 1.451387 ATTTGTCATCCCCGTCGCC 60.451 57.895 0.00 0.00 0.00 5.54
414 415 1.721487 CATTTGTCATCCCCGTCGC 59.279 57.895 0.00 0.00 0.00 5.19
415 416 1.721487 GCATTTGTCATCCCCGTCG 59.279 57.895 0.00 0.00 0.00 5.12
416 417 1.714899 CCGCATTTGTCATCCCCGTC 61.715 60.000 0.00 0.00 0.00 4.79
417 418 1.748879 CCGCATTTGTCATCCCCGT 60.749 57.895 0.00 0.00 0.00 5.28
418 419 3.110139 CCGCATTTGTCATCCCCG 58.890 61.111 0.00 0.00 0.00 5.73
419 420 2.807622 GCCGCATTTGTCATCCCC 59.192 61.111 0.00 0.00 0.00 4.81
420 421 2.408835 CGCCGCATTTGTCATCCC 59.591 61.111 0.00 0.00 0.00 3.85
421 422 2.408835 CCGCCGCATTTGTCATCC 59.591 61.111 0.00 0.00 0.00 3.51
422 423 2.322999 GACCCGCCGCATTTGTCATC 62.323 60.000 0.00 0.00 0.00 2.92
423 424 2.361104 ACCCGCCGCATTTGTCAT 60.361 55.556 0.00 0.00 0.00 3.06
424 425 3.053291 GACCCGCCGCATTTGTCA 61.053 61.111 0.00 0.00 0.00 3.58
425 426 3.810896 GGACCCGCCGCATTTGTC 61.811 66.667 0.00 0.00 0.00 3.18
426 427 4.652131 TGGACCCGCCGCATTTGT 62.652 61.111 0.00 0.00 40.66 2.83
427 428 4.114997 GTGGACCCGCCGCATTTG 62.115 66.667 0.00 0.00 46.72 2.32
435 436 4.660938 AAAGCCTGGTGGACCCGC 62.661 66.667 0.00 0.00 35.15 6.13
436 437 2.359975 GAAAGCCTGGTGGACCCG 60.360 66.667 0.00 0.00 35.15 5.28
437 438 2.359975 CGAAAGCCTGGTGGACCC 60.360 66.667 0.00 0.00 34.57 4.46
449 450 2.093783 AGAGCCGAATTTAACGCGAAAG 59.906 45.455 15.93 0.00 0.00 2.62
450 451 2.070783 AGAGCCGAATTTAACGCGAAA 58.929 42.857 15.93 3.76 0.00 3.46
451 452 1.717194 AGAGCCGAATTTAACGCGAA 58.283 45.000 15.93 0.00 0.00 4.70
452 453 2.565210 TAGAGCCGAATTTAACGCGA 57.435 45.000 15.93 0.00 0.00 5.87
453 454 3.854286 ATTAGAGCCGAATTTAACGCG 57.146 42.857 3.53 3.53 0.00 6.01
454 455 5.138095 GCTAATTAGAGCCGAATTTAACGC 58.862 41.667 16.85 0.00 36.38 4.84
455 456 6.281848 TGCTAATTAGAGCCGAATTTAACG 57.718 37.500 16.85 0.00 42.11 3.18
456 457 8.905103 TTTTGCTAATTAGAGCCGAATTTAAC 57.095 30.769 16.85 0.00 42.11 2.01
457 458 9.567848 CTTTTTGCTAATTAGAGCCGAATTTAA 57.432 29.630 16.85 0.00 42.11 1.52
458 459 8.736244 ACTTTTTGCTAATTAGAGCCGAATTTA 58.264 29.630 16.85 0.00 42.11 1.40
459 460 7.542130 CACTTTTTGCTAATTAGAGCCGAATTT 59.458 33.333 16.85 0.00 42.11 1.82
460 461 7.029563 CACTTTTTGCTAATTAGAGCCGAATT 58.970 34.615 16.85 0.00 42.11 2.17
461 462 6.404734 CCACTTTTTGCTAATTAGAGCCGAAT 60.405 38.462 16.85 0.00 42.11 3.34
462 463 5.106317 CCACTTTTTGCTAATTAGAGCCGAA 60.106 40.000 16.85 2.32 42.11 4.30
463 464 4.394920 CCACTTTTTGCTAATTAGAGCCGA 59.605 41.667 16.85 0.00 42.11 5.54
464 465 4.156008 ACCACTTTTTGCTAATTAGAGCCG 59.844 41.667 16.85 1.75 42.11 5.52
465 466 5.644977 ACCACTTTTTGCTAATTAGAGCC 57.355 39.130 16.85 0.00 42.11 4.70
466 467 7.145323 TGAAACCACTTTTTGCTAATTAGAGC 58.855 34.615 16.85 4.90 43.16 4.09
467 468 7.809806 CCTGAAACCACTTTTTGCTAATTAGAG 59.190 37.037 16.85 6.62 0.00 2.43
468 469 7.504238 TCCTGAAACCACTTTTTGCTAATTAGA 59.496 33.333 16.85 0.00 0.00 2.10
469 470 7.657336 TCCTGAAACCACTTTTTGCTAATTAG 58.343 34.615 8.20 8.20 0.00 1.73
470 471 7.255801 CCTCCTGAAACCACTTTTTGCTAATTA 60.256 37.037 0.00 0.00 0.00 1.40
471 472 6.462909 CCTCCTGAAACCACTTTTTGCTAATT 60.463 38.462 0.00 0.00 0.00 1.40
472 473 5.011023 CCTCCTGAAACCACTTTTTGCTAAT 59.989 40.000 0.00 0.00 0.00 1.73
473 474 4.340950 CCTCCTGAAACCACTTTTTGCTAA 59.659 41.667 0.00 0.00 0.00 3.09
474 475 3.888930 CCTCCTGAAACCACTTTTTGCTA 59.111 43.478 0.00 0.00 0.00 3.49
475 476 2.695147 CCTCCTGAAACCACTTTTTGCT 59.305 45.455 0.00 0.00 0.00 3.91
476 477 2.803133 GCCTCCTGAAACCACTTTTTGC 60.803 50.000 0.00 0.00 0.00 3.68
477 478 2.543653 CGCCTCCTGAAACCACTTTTTG 60.544 50.000 0.00 0.00 0.00 2.44
478 479 1.681264 CGCCTCCTGAAACCACTTTTT 59.319 47.619 0.00 0.00 0.00 1.94
479 480 1.318576 CGCCTCCTGAAACCACTTTT 58.681 50.000 0.00 0.00 0.00 2.27
480 481 1.172812 GCGCCTCCTGAAACCACTTT 61.173 55.000 0.00 0.00 0.00 2.66
481 482 1.600916 GCGCCTCCTGAAACCACTT 60.601 57.895 0.00 0.00 0.00 3.16
482 483 2.032681 GCGCCTCCTGAAACCACT 59.967 61.111 0.00 0.00 0.00 4.00
483 484 3.423154 CGCGCCTCCTGAAACCAC 61.423 66.667 0.00 0.00 0.00 4.16
484 485 3.621805 TCGCGCCTCCTGAAACCA 61.622 61.111 0.00 0.00 0.00 3.67
485 486 3.119096 GTCGCGCCTCCTGAAACC 61.119 66.667 0.00 0.00 0.00 3.27
486 487 2.048127 AGTCGCGCCTCCTGAAAC 60.048 61.111 0.00 0.00 0.00 2.78
487 488 2.048222 CAGTCGCGCCTCCTGAAA 60.048 61.111 0.00 0.00 0.00 2.69
488 489 2.989253 TCAGTCGCGCCTCCTGAA 60.989 61.111 13.90 1.40 32.55 3.02
489 490 3.443925 CTCAGTCGCGCCTCCTGA 61.444 66.667 15.04 15.04 34.28 3.86
490 491 3.691744 GACTCAGTCGCGCCTCCTG 62.692 68.421 0.00 5.48 0.00 3.86
491 492 3.444805 GACTCAGTCGCGCCTCCT 61.445 66.667 0.00 0.00 0.00 3.69
492 493 2.493907 AAAGACTCAGTCGCGCCTCC 62.494 60.000 0.00 0.00 37.67 4.30
493 494 0.667792 AAAAGACTCAGTCGCGCCTC 60.668 55.000 0.00 0.00 37.67 4.70
494 495 0.249911 AAAAAGACTCAGTCGCGCCT 60.250 50.000 0.00 0.00 37.67 5.52
495 496 2.235546 AAAAAGACTCAGTCGCGCC 58.764 52.632 0.00 0.00 37.67 6.53
536 537 2.604382 CCCAACAAGCCCCCAAGG 60.604 66.667 0.00 0.00 39.47 3.61
537 538 2.604382 CCCCAACAAGCCCCCAAG 60.604 66.667 0.00 0.00 0.00 3.61
538 539 4.247130 CCCCCAACAAGCCCCCAA 62.247 66.667 0.00 0.00 0.00 4.12
552 553 1.640917 TCCGACTTCTATATGCCCCC 58.359 55.000 0.00 0.00 0.00 5.40
553 554 2.567615 ACATCCGACTTCTATATGCCCC 59.432 50.000 0.00 0.00 0.00 5.80
554 555 3.963428 ACATCCGACTTCTATATGCCC 57.037 47.619 0.00 0.00 0.00 5.36
555 556 4.082895 ACGTACATCCGACTTCTATATGCC 60.083 45.833 0.00 0.00 0.00 4.40
556 557 5.044428 ACGTACATCCGACTTCTATATGC 57.956 43.478 0.00 0.00 0.00 3.14
571 572 6.366877 GTGGTACAGACACAATAAACGTACAT 59.633 38.462 0.00 0.00 41.80 2.29
574 575 5.010922 AGGTGGTACAGACACAATAAACGTA 59.989 40.000 0.00 0.00 41.80 3.57
576 577 4.312443 AGGTGGTACAGACACAATAAACG 58.688 43.478 0.00 0.00 41.80 3.60
578 579 7.604927 GTGAATAGGTGGTACAGACACAATAAA 59.395 37.037 0.00 0.00 41.80 1.40
588 2080 8.786826 TTAATGAAAGTGAATAGGTGGTACAG 57.213 34.615 0.00 0.00 41.80 2.74
593 2085 7.645058 ACCATTAATGAAAGTGAATAGGTGG 57.355 36.000 17.23 0.00 0.00 4.61
605 2097 9.976255 CGTTCTTCGTTATTACCATTAATGAAA 57.024 29.630 17.23 10.74 35.34 2.69
624 2116 9.518906 TTTTATTTTTGGTAAAGGACGTTCTTC 57.481 29.630 10.16 0.00 0.00 2.87
631 2123 9.005777 GGGGAATTTTTATTTTTGGTAAAGGAC 57.994 33.333 0.00 0.00 0.00 3.85
633 2125 9.226606 GAGGGGAATTTTTATTTTTGGTAAAGG 57.773 33.333 0.00 0.00 0.00 3.11
634 2126 8.931775 CGAGGGGAATTTTTATTTTTGGTAAAG 58.068 33.333 0.00 0.00 0.00 1.85
660 2152 1.130955 CAATTCACTGCGTGTTTGGC 58.869 50.000 8.22 0.00 34.79 4.52
691 2183 2.158711 TCTCTATGCCAGCTCCCATTTG 60.159 50.000 1.32 0.00 0.00 2.32
694 2186 1.629353 CATCTCTATGCCAGCTCCCAT 59.371 52.381 1.65 1.65 0.00 4.00
766 2274 0.036765 GGGCAGACGACAATACACCA 60.037 55.000 0.00 0.00 0.00 4.17
768 2276 2.953466 TAGGGCAGACGACAATACAC 57.047 50.000 0.00 0.00 0.00 2.90
769 2277 4.481368 AAATAGGGCAGACGACAATACA 57.519 40.909 0.00 0.00 0.00 2.29
770 2278 5.116882 AGAAAATAGGGCAGACGACAATAC 58.883 41.667 0.00 0.00 0.00 1.89
771 2279 5.353394 AGAAAATAGGGCAGACGACAATA 57.647 39.130 0.00 0.00 0.00 1.90
772 2280 4.222124 AGAAAATAGGGCAGACGACAAT 57.778 40.909 0.00 0.00 0.00 2.71
773 2281 3.695830 AGAAAATAGGGCAGACGACAA 57.304 42.857 0.00 0.00 0.00 3.18
840 2354 4.511454 GCAGATATAGAAACGCACATCCAA 59.489 41.667 0.00 0.00 0.00 3.53
945 2589 1.258445 ACTGTAGAAGGACGCAGGGG 61.258 60.000 0.00 0.00 33.35 4.79
964 2608 0.830444 ACTACTGCGGTGGAGTGGAA 60.830 55.000 16.89 0.00 0.00 3.53
965 2609 1.228769 ACTACTGCGGTGGAGTGGA 60.229 57.895 16.89 0.00 0.00 4.02
966 2610 1.215647 GACTACTGCGGTGGAGTGG 59.784 63.158 16.89 0.00 0.00 4.00
967 2611 0.317160 TTGACTACTGCGGTGGAGTG 59.683 55.000 16.89 0.00 0.00 3.51
968 2612 0.603569 CTTGACTACTGCGGTGGAGT 59.396 55.000 16.89 8.55 0.00 3.85
969 2613 0.603569 ACTTGACTACTGCGGTGGAG 59.396 55.000 16.89 4.86 0.00 3.86
970 2614 1.816835 CTACTTGACTACTGCGGTGGA 59.183 52.381 16.89 0.00 0.00 4.02
971 2615 1.816835 TCTACTTGACTACTGCGGTGG 59.183 52.381 8.92 8.23 0.00 4.61
973 2617 3.418995 TCTTCTACTTGACTACTGCGGT 58.581 45.455 2.42 2.42 0.00 5.68
974 2618 4.156190 TCTTCTTCTACTTGACTACTGCGG 59.844 45.833 0.00 0.00 0.00 5.69
976 2620 6.262193 ACTCTTCTTCTACTTGACTACTGC 57.738 41.667 0.00 0.00 0.00 4.40
977 2621 7.913297 GCATACTCTTCTTCTACTTGACTACTG 59.087 40.741 0.00 0.00 0.00 2.74
978 2622 7.067737 GGCATACTCTTCTTCTACTTGACTACT 59.932 40.741 0.00 0.00 0.00 2.57
980 2624 6.038382 CGGCATACTCTTCTTCTACTTGACTA 59.962 42.308 0.00 0.00 0.00 2.59
981 2625 5.163602 CGGCATACTCTTCTTCTACTTGACT 60.164 44.000 0.00 0.00 0.00 3.41
982 2626 5.038033 CGGCATACTCTTCTTCTACTTGAC 58.962 45.833 0.00 0.00 0.00 3.18
984 2628 5.038033 GTCGGCATACTCTTCTTCTACTTG 58.962 45.833 0.00 0.00 0.00 3.16
985 2629 4.098196 GGTCGGCATACTCTTCTTCTACTT 59.902 45.833 0.00 0.00 0.00 2.24
1084 2765 1.299014 GATGCTGCGACGAGGAGAG 60.299 63.158 0.00 0.00 41.23 3.20
1101 2782 2.202797 GCATGCTCTTCCTCGCGA 60.203 61.111 11.37 9.26 0.00 5.87
1716 3434 2.045242 AGCTCCTCGTACCGCAGA 60.045 61.111 0.00 0.00 0.00 4.26
1752 3470 2.680913 CGCCAGCTTTCGGACCTTG 61.681 63.158 0.00 0.00 0.00 3.61
1794 3512 4.742201 GCGTCTTCCTCCGCTGCA 62.742 66.667 0.00 0.00 46.08 4.41
1851 3569 2.206900 TCCAGGCCCTTGAGGTGA 59.793 61.111 0.00 0.00 38.26 4.02
1991 3712 2.285834 CGCATTTTGTCAGCTACGATCC 60.286 50.000 0.00 0.00 0.00 3.36
2027 3748 3.951680 ACAGGTCAAAAGTCACCGAAAAT 59.048 39.130 0.00 0.00 37.79 1.82
2048 3769 6.074142 ACGACCAGAAAAGTAATTACGTGAAC 60.074 38.462 9.91 3.13 0.00 3.18
2230 3991 6.408035 TGGTACCGTGAATGCTCTTTTTATA 58.592 36.000 7.57 0.00 0.00 0.98
2232 3993 4.643463 TGGTACCGTGAATGCTCTTTTTA 58.357 39.130 7.57 0.00 0.00 1.52
2257 6084 3.792401 TCATGACGGACACATGGTATTC 58.208 45.455 0.00 0.00 43.38 1.75
2359 6192 9.088987 ACATATTTGGTTGGTCTTAAGTCAAAT 57.911 29.630 12.87 14.53 37.23 2.32
2360 6193 8.356657 CACATATTTGGTTGGTCTTAAGTCAAA 58.643 33.333 12.87 10.31 0.00 2.69
2399 6232 7.177744 AGTTCACCAAAACTACTCTTTCCAAAA 59.822 33.333 0.00 0.00 37.71 2.44
2400 6233 6.661805 AGTTCACCAAAACTACTCTTTCCAAA 59.338 34.615 0.00 0.00 37.71 3.28
2401 6234 6.184789 AGTTCACCAAAACTACTCTTTCCAA 58.815 36.000 0.00 0.00 37.71 3.53
2485 6321 8.767085 CGGATTACGTATATGTGGTTGTAAATT 58.233 33.333 7.89 0.00 37.93 1.82
2488 6324 7.036996 TCGGATTACGTATATGTGGTTGTAA 57.963 36.000 7.89 0.00 44.69 2.41
2500 6336 6.112058 GGGTATAGAGACTCGGATTACGTAT 58.888 44.000 0.00 0.00 44.69 3.06
2509 6345 1.618487 GTGGGGGTATAGAGACTCGG 58.382 60.000 0.00 0.00 0.00 4.63
2534 6370 3.936203 GGTCAGTGTCCACGGGCA 61.936 66.667 1.10 0.00 32.78 5.36
2546 6386 0.105964 TTTGATATCCGCCCGGTCAG 59.894 55.000 6.61 0.00 36.47 3.51
2554 6394 5.004726 GCAAATGTCAAGTTTTGATATCCGC 59.995 40.000 0.00 4.68 40.08 5.54
2571 6411 2.268076 GGACCGTGGCTGCAAATGT 61.268 57.895 0.50 0.00 0.00 2.71
2577 6417 0.679960 AAAATAGGGACCGTGGCTGC 60.680 55.000 0.00 0.00 0.00 5.25
2616 6456 2.466870 TGAACAACGTGCATGTGTTC 57.533 45.000 28.56 28.56 39.24 3.18
2632 6472 8.121305 AGCTATGTATGTTTGTCCAAAATGAA 57.879 30.769 0.00 0.00 31.33 2.57
2642 6482 5.469479 GCAACCAAAGCTATGTATGTTTGT 58.531 37.500 0.00 0.00 0.00 2.83
2643 6483 4.558470 CGCAACCAAAGCTATGTATGTTTG 59.442 41.667 0.00 0.00 0.00 2.93
2644 6484 4.457603 TCGCAACCAAAGCTATGTATGTTT 59.542 37.500 0.00 0.00 0.00 2.83
2649 6489 3.435327 CACTTCGCAACCAAAGCTATGTA 59.565 43.478 0.00 0.00 0.00 2.29
2685 6525 2.033299 CGTCAATCAGGTTGTGTGCTTT 59.967 45.455 0.00 0.00 38.95 3.51
2690 6530 1.542547 GGGTCGTCAATCAGGTTGTGT 60.543 52.381 0.00 0.00 38.95 3.72
2751 6591 1.203052 CCGCTCTTTGCCACAATCATT 59.797 47.619 0.00 0.00 38.78 2.57
2758 6598 1.901650 CTTCGACCGCTCTTTGCCAC 61.902 60.000 0.00 0.00 38.78 5.01
2784 6624 0.607112 TGTACCGTTGTATCCGCCAA 59.393 50.000 0.00 0.00 0.00 4.52
2803 6643 1.003355 CCAAGTCAGGTGCCATCGT 60.003 57.895 0.00 0.00 0.00 3.73
2809 6649 1.981256 TTTCCTTCCAAGTCAGGTGC 58.019 50.000 0.00 0.00 0.00 5.01
2861 6701 0.442699 GGTTTCTGGAAAGCGCTACG 59.557 55.000 12.05 0.00 38.73 3.51
2888 6728 2.426522 CGATCTTGCACCAGAAAAGGA 58.573 47.619 0.00 0.00 0.00 3.36
2896 6736 1.865788 GCCTTTGCGATCTTGCACCA 61.866 55.000 0.00 0.00 46.25 4.17
2898 6738 0.039256 TTGCCTTTGCGATCTTGCAC 60.039 50.000 0.00 0.00 46.25 4.57
2908 6748 1.039856 TTGGAACCTCTTGCCTTTGC 58.960 50.000 0.00 0.00 38.26 3.68
2958 6798 1.671054 CCACATCCGAAACGCTGGT 60.671 57.895 0.00 0.00 0.00 4.00
2967 6807 0.179048 GCCATCATGTCCACATCCGA 60.179 55.000 0.00 0.00 33.61 4.55
2969 6809 1.406539 GTTGCCATCATGTCCACATCC 59.593 52.381 0.00 0.00 33.61 3.51
2974 6814 4.343231 AGTTTATGTTGCCATCATGTCCA 58.657 39.130 0.00 0.00 32.29 4.02
3005 6845 6.405286 CCATCGCCAAAAGGTACATAAAATCA 60.405 38.462 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.