Multiple sequence alignment - TraesCS6A01G421000

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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 TraesCS6A01G421000 chr6A 100.000 3819 0 0 1 3819 617655899 617659717 0.000000e+00 7053.0
1 TraesCS6A01G421000 chr6A 81.713 432 73 6 1189 1617 484608438 484608866 4.690000e-94 355.0
2 TraesCS6A01G421000 chr6D 93.488 1766 68 20 2067 3813 472357824 472356087 0.000000e+00 2580.0
3 TraesCS6A01G421000 chr6D 98.225 1465 24 1 585 2049 472359529 472358067 0.000000e+00 2560.0
4 TraesCS6A01G421000 chr6D 92.466 438 17 6 1 438 472359952 472359531 2.520000e-171 612.0
5 TraesCS6A01G421000 chr6D 81.481 432 74 6 1189 1617 344207866 344208294 2.180000e-92 350.0
6 TraesCS6A01G421000 chr6B 92.993 1313 40 28 777 2049 717077279 717075979 0.000000e+00 1868.0
7 TraesCS6A01G421000 chr6B 90.430 1233 69 19 2067 3286 717075716 717074520 0.000000e+00 1578.0
8 TraesCS6A01G421000 chr6B 90.745 443 29 6 3 438 717077865 717077428 7.110000e-162 580.0
9 TraesCS6A01G421000 chr6B 88.139 489 42 8 3335 3819 717060256 717059780 5.540000e-158 568.0
10 TraesCS6A01G421000 chr6B 87.959 490 42 8 3335 3819 717074505 717074028 2.580000e-156 562.0
11 TraesCS6A01G421000 chr6B 81.019 432 76 6 1189 1617 519720394 519720822 4.730000e-89 339.0
12 TraesCS6A01G421000 chr6B 91.852 135 7 1 585 715 717077419 717077285 6.510000e-43 185.0
13 TraesCS6A01G421000 chr6B 91.667 96 8 0 3724 3819 717026757 717026662 2.390000e-27 134.0
14 TraesCS6A01G421000 chr6B 91.667 96 8 0 3724 3819 717043395 717043300 2.390000e-27 134.0
15 TraesCS6A01G421000 chr6B 84.783 92 7 5 2974 3064 717060186 717060101 6.800000e-13 86.1
16 TraesCS6A01G421000 chr6B 84.783 92 7 5 2974 3064 717074434 717074349 6.800000e-13 86.1
17 TraesCS6A01G421000 chr2D 84.813 428 61 4 1213 1638 564095486 564095061 9.800000e-116 427.0
18 TraesCS6A01G421000 chr2A 84.813 428 61 4 1213 1638 704776741 704776316 9.800000e-116 427.0
19 TraesCS6A01G421000 chr2B 84.579 428 62 4 1213 1638 675356172 675355747 4.560000e-114 422.0
20 TraesCS6A01G421000 chr5A 82.469 405 62 8 1220 1620 611652918 611652519 2.820000e-91 346.0
21 TraesCS6A01G421000 chr5A 78.333 300 57 6 1704 1999 310874436 310874141 1.810000e-43 187.0
22 TraesCS6A01G421000 chr5A 82.703 185 30 2 1703 1886 505612649 505612466 3.050000e-36 163.0
23 TraesCS6A01G421000 chr1A 80.795 302 50 6 1703 2000 500342868 500342571 2.970000e-56 230.0
24 TraesCS6A01G421000 chr4A 79.139 302 57 6 1703 2001 466926509 466926807 1.800000e-48 204.0
25 TraesCS6A01G421000 chr4D 78.477 302 59 6 1703 2001 109911468 109911170 3.890000e-45 193.0
26 TraesCS6A01G421000 chr5B 78.261 299 59 5 1704 1999 259538749 259539044 1.810000e-43 187.0
27 TraesCS6A01G421000 chr5D 82.162 185 31 2 1703 1886 400280928 400280745 1.420000e-34 158.0
28 TraesCS6A01G421000 chr1D 97.674 86 2 0 443 528 416093197 416093282 8.550000e-32 148.0
29 TraesCS6A01G421000 chr7D 96.512 86 3 0 443 528 565622203 565622288 3.980000e-30 143.0
30 TraesCS6A01G421000 chr7D 96.512 86 3 0 443 528 565624000 565624085 3.980000e-30 143.0
31 TraesCS6A01G421000 chr7D 96.512 86 3 0 443 528 565638072 565638157 3.980000e-30 143.0
32 TraesCS6A01G421000 chr7D 96.512 86 2 1 443 528 565636747 565636831 1.430000e-29 141.0
33 TraesCS6A01G421000 chr7D 96.386 83 2 1 443 525 565637887 565637968 6.650000e-28 135.0
34 TraesCS6A01G421000 chr7D 95.181 83 4 0 446 528 565639319 565639401 8.610000e-27 132.0
35 TraesCS6A01G421000 chr7D 94.186 86 4 1 443 528 565639501 565639585 3.100000e-26 130.0
36 TraesCS6A01G421000 chr7D 93.182 88 4 1 443 528 565624187 565624274 1.110000e-25 128.0
37 TraesCS6A01G421000 chr7D 93.443 61 3 1 523 583 565623917 565623976 5.250000e-14 89.8
38 TraesCS6A01G421000 chr7D 90.625 64 4 1 534 595 565636859 565636922 2.440000e-12 84.2
39 TraesCS6A01G421000 chr7D 96.000 50 2 0 534 583 565622316 565622365 8.790000e-12 82.4
40 TraesCS6A01G421000 chr7D 92.857 56 4 0 528 583 565624108 565624163 8.790000e-12 82.4
41 TraesCS6A01G421000 chr7D 95.455 44 2 0 540 583 54923438 54923395 1.900000e-08 71.3
42 TraesCS6A01G421000 chr7A 93.976 83 5 0 446 528 256015841 256015759 4.010000e-25 126.0
43 TraesCS6A01G421000 chr3D 83.898 118 15 3 161 277 548494951 548494837 4.030000e-20 110.0
44 TraesCS6A01G421000 chr3D 92.857 56 4 0 528 583 427818713 427818658 8.790000e-12 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G421000 chr6A 617655899 617659717 3818 False 7053.000000 7053 100.000000 1 3819 1 chr6A.!!$F2 3818
1 TraesCS6A01G421000 chr6D 472356087 472359952 3865 True 1917.333333 2580 94.726333 1 3813 3 chr6D.!!$R1 3812
2 TraesCS6A01G421000 chr6B 717074028 717077865 3837 True 809.850000 1868 89.793667 3 3819 6 chr6B.!!$R4 3816

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
451 459 0.161024 GCGACGTGCAGTGAAGTTAC 59.839 55.000 0.00 0.00 45.45 2.50 F
576 584 0.169672 GCTCGTTCGTAGGTGTAGCA 59.830 55.000 0.00 0.00 0.00 3.49 F
786 798 1.154016 ACGACGAAGCTCGACATGG 60.154 57.895 0.00 0.00 43.74 3.66 F
1299 1333 1.874019 CGAGATCTCAACCGGCGTG 60.874 63.158 22.31 0.00 0.00 5.34 F
1301 1335 1.945354 GAGATCTCAACCGGCGTGGA 61.945 60.000 18.11 0.26 42.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2398 0.323633 TGATCCATGGGTGGCACAAG 60.324 55.000 20.82 5.46 45.63 3.16 R
2350 2650 1.077068 CTCCGAGTCCCTGAGCTCT 60.077 63.158 16.19 0.00 0.00 4.09 R
2389 2689 1.595382 GCTGTTGTCCACGTCAGCT 60.595 57.895 15.22 0.00 46.35 4.24 R
2667 2979 2.494471 TCCTGCATTTGAGCCATTCAAG 59.506 45.455 0.00 0.00 46.01 3.02 R
2989 3305 5.182380 GGTCTTCAAATCCACGGTAAATGAA 59.818 40.000 0.00 0.00 0.00 2.57 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
85 86 3.325425 TGTGAACCGACCCTTTCTATTCA 59.675 43.478 0.00 0.00 0.00 2.57
138 139 6.060028 ACGAGTACTACTACTACTCTCTCG 57.940 45.833 0.00 0.00 44.67 4.04
376 381 9.936759 TTTAAGGTTTGACTTGAGACAAATTTT 57.063 25.926 10.77 10.44 40.50 1.82
447 455 3.767230 CCGCGACGTGCAGTGAAG 61.767 66.667 8.23 0.00 46.97 3.02
448 456 3.030308 CGCGACGTGCAGTGAAGT 61.030 61.111 0.00 0.00 46.97 3.01
449 457 2.585869 CGCGACGTGCAGTGAAGTT 61.586 57.895 0.00 0.00 46.97 2.66
450 458 1.272784 CGCGACGTGCAGTGAAGTTA 61.273 55.000 0.00 0.00 46.97 2.24
451 459 0.161024 GCGACGTGCAGTGAAGTTAC 59.839 55.000 0.00 0.00 45.45 2.50
452 460 0.429736 CGACGTGCAGTGAAGTTACG 59.570 55.000 0.00 0.00 40.30 3.18
453 461 3.654178 ACGTGCAGTGAAGTTACGT 57.346 47.368 0.00 0.00 42.40 3.57
454 462 1.189446 GACGTGCAGTGAAGTTACGTG 59.811 52.381 5.41 0.00 46.47 4.49
455 463 1.202325 ACGTGCAGTGAAGTTACGTGA 60.202 47.619 0.00 0.00 45.03 4.35
456 464 1.452025 CGTGCAGTGAAGTTACGTGAG 59.548 52.381 0.00 0.00 0.00 3.51
457 465 2.739292 GTGCAGTGAAGTTACGTGAGA 58.261 47.619 0.00 0.00 0.00 3.27
458 466 3.318017 GTGCAGTGAAGTTACGTGAGAT 58.682 45.455 0.00 0.00 0.00 2.75
459 467 3.741344 GTGCAGTGAAGTTACGTGAGATT 59.259 43.478 0.00 0.00 0.00 2.40
460 468 4.211374 GTGCAGTGAAGTTACGTGAGATTT 59.789 41.667 0.00 0.00 0.00 2.17
461 469 4.814234 TGCAGTGAAGTTACGTGAGATTTT 59.186 37.500 0.00 0.00 0.00 1.82
462 470 5.295787 TGCAGTGAAGTTACGTGAGATTTTT 59.704 36.000 0.00 0.00 0.00 1.94
463 471 6.480651 TGCAGTGAAGTTACGTGAGATTTTTA 59.519 34.615 0.00 0.00 0.00 1.52
464 472 6.790825 GCAGTGAAGTTACGTGAGATTTTTAC 59.209 38.462 0.00 0.00 0.00 2.01
465 473 7.001922 CAGTGAAGTTACGTGAGATTTTTACG 58.998 38.462 0.00 0.00 42.98 3.18
473 481 5.526010 CGTGAGATTTTTACGTAAAGGCT 57.474 39.130 19.31 16.83 33.48 4.58
474 482 5.313623 CGTGAGATTTTTACGTAAAGGCTG 58.686 41.667 19.31 5.10 33.48 4.85
475 483 5.119588 CGTGAGATTTTTACGTAAAGGCTGA 59.880 40.000 19.31 10.37 33.48 4.26
476 484 6.304882 GTGAGATTTTTACGTAAAGGCTGAC 58.695 40.000 19.31 16.74 0.00 3.51
477 485 6.147328 GTGAGATTTTTACGTAAAGGCTGACT 59.853 38.462 19.31 13.73 0.00 3.41
478 486 6.708949 TGAGATTTTTACGTAAAGGCTGACTT 59.291 34.615 19.31 0.00 42.52 3.01
479 487 6.899114 AGATTTTTACGTAAAGGCTGACTTG 58.101 36.000 19.31 0.00 39.96 3.16
480 488 5.427036 TTTTTACGTAAAGGCTGACTTGG 57.573 39.130 19.31 0.00 39.96 3.61
481 489 3.756933 TTACGTAAAGGCTGACTTGGT 57.243 42.857 5.31 0.00 39.96 3.67
482 490 1.878953 ACGTAAAGGCTGACTTGGTG 58.121 50.000 0.00 0.00 39.96 4.17
483 491 1.156736 CGTAAAGGCTGACTTGGTGG 58.843 55.000 0.00 0.00 39.96 4.61
484 492 0.881796 GTAAAGGCTGACTTGGTGGC 59.118 55.000 0.00 0.00 39.96 5.01
485 493 0.476338 TAAAGGCTGACTTGGTGGCA 59.524 50.000 0.00 0.00 39.96 4.92
493 501 4.164822 CTGACTTGGTGGCAGTTAATTG 57.835 45.455 0.00 0.00 46.57 2.32
494 502 2.890311 TGACTTGGTGGCAGTTAATTGG 59.110 45.455 0.00 0.00 0.00 3.16
495 503 3.153919 GACTTGGTGGCAGTTAATTGGA 58.846 45.455 0.00 0.00 0.00 3.53
496 504 3.763897 GACTTGGTGGCAGTTAATTGGAT 59.236 43.478 0.00 0.00 0.00 3.41
497 505 4.159557 ACTTGGTGGCAGTTAATTGGATT 58.840 39.130 0.00 0.00 0.00 3.01
498 506 5.329399 ACTTGGTGGCAGTTAATTGGATTA 58.671 37.500 0.00 0.00 0.00 1.75
499 507 5.418840 ACTTGGTGGCAGTTAATTGGATTAG 59.581 40.000 0.00 0.00 0.00 1.73
500 508 4.277476 TGGTGGCAGTTAATTGGATTAGG 58.723 43.478 0.00 0.00 0.00 2.69
501 509 4.017958 TGGTGGCAGTTAATTGGATTAGGA 60.018 41.667 0.00 0.00 0.00 2.94
502 510 5.140454 GGTGGCAGTTAATTGGATTAGGAT 58.860 41.667 0.00 0.00 0.00 3.24
503 511 5.598417 GGTGGCAGTTAATTGGATTAGGATT 59.402 40.000 0.00 0.00 0.00 3.01
504 512 6.775629 GGTGGCAGTTAATTGGATTAGGATTA 59.224 38.462 0.00 0.00 0.00 1.75
505 513 7.040409 GGTGGCAGTTAATTGGATTAGGATTAG 60.040 40.741 0.00 0.00 0.00 1.73
506 514 7.502561 GTGGCAGTTAATTGGATTAGGATTAGT 59.497 37.037 0.00 0.00 0.00 2.24
507 515 7.502226 TGGCAGTTAATTGGATTAGGATTAGTG 59.498 37.037 0.00 0.00 0.00 2.74
508 516 7.040409 GGCAGTTAATTGGATTAGGATTAGTGG 60.040 40.741 0.00 0.00 0.00 4.00
509 517 7.522236 GCAGTTAATTGGATTAGGATTAGTGGC 60.522 40.741 0.00 0.00 0.00 5.01
510 518 7.721399 CAGTTAATTGGATTAGGATTAGTGGCT 59.279 37.037 0.00 0.00 0.00 4.75
511 519 7.721399 AGTTAATTGGATTAGGATTAGTGGCTG 59.279 37.037 0.00 0.00 0.00 4.85
512 520 4.437682 TTGGATTAGGATTAGTGGCTGG 57.562 45.455 0.00 0.00 0.00 4.85
513 521 2.711009 TGGATTAGGATTAGTGGCTGGG 59.289 50.000 0.00 0.00 0.00 4.45
514 522 2.040412 GGATTAGGATTAGTGGCTGGGG 59.960 54.545 0.00 0.00 0.00 4.96
515 523 0.843984 TTAGGATTAGTGGCTGGGGC 59.156 55.000 0.00 0.00 37.82 5.80
531 539 3.681909 GGCCCACCCAGTTAATTGA 57.318 52.632 0.00 0.00 0.00 2.57
532 540 1.931635 GGCCCACCCAGTTAATTGAA 58.068 50.000 0.00 0.00 0.00 2.69
533 541 1.824852 GGCCCACCCAGTTAATTGAAG 59.175 52.381 0.00 0.00 0.00 3.02
534 542 1.824852 GCCCACCCAGTTAATTGAAGG 59.175 52.381 0.00 0.00 0.00 3.46
535 543 2.556559 GCCCACCCAGTTAATTGAAGGA 60.557 50.000 0.00 0.00 0.00 3.36
536 544 3.773560 CCCACCCAGTTAATTGAAGGAA 58.226 45.455 0.00 0.00 0.00 3.36
537 545 4.156477 CCCACCCAGTTAATTGAAGGAAA 58.844 43.478 0.00 0.00 0.00 3.13
538 546 4.220602 CCCACCCAGTTAATTGAAGGAAAG 59.779 45.833 0.00 0.00 0.00 2.62
539 547 4.832823 CCACCCAGTTAATTGAAGGAAAGT 59.167 41.667 0.00 0.00 0.00 2.66
540 548 5.304357 CCACCCAGTTAATTGAAGGAAAGTT 59.696 40.000 0.00 0.00 0.00 2.66
541 549 6.492087 CCACCCAGTTAATTGAAGGAAAGTTA 59.508 38.462 0.00 0.00 0.00 2.24
542 550 7.309194 CCACCCAGTTAATTGAAGGAAAGTTAG 60.309 40.741 0.00 0.00 0.00 2.34
543 551 6.719829 ACCCAGTTAATTGAAGGAAAGTTAGG 59.280 38.462 0.00 0.00 0.00 2.69
544 552 6.719829 CCCAGTTAATTGAAGGAAAGTTAGGT 59.280 38.462 0.00 0.00 0.00 3.08
545 553 7.886446 CCCAGTTAATTGAAGGAAAGTTAGGTA 59.114 37.037 0.00 0.00 0.00 3.08
546 554 9.292195 CCAGTTAATTGAAGGAAAGTTAGGTAA 57.708 33.333 0.00 0.00 0.00 2.85
552 560 8.622948 ATTGAAGGAAAGTTAGGTAAGTCTTG 57.377 34.615 0.00 0.00 0.00 3.02
553 561 6.531021 TGAAGGAAAGTTAGGTAAGTCTTGG 58.469 40.000 0.00 0.00 0.00 3.61
554 562 6.100714 TGAAGGAAAGTTAGGTAAGTCTTGGT 59.899 38.462 0.00 0.00 0.00 3.67
555 563 7.290714 TGAAGGAAAGTTAGGTAAGTCTTGGTA 59.709 37.037 0.00 0.00 0.00 3.25
556 564 7.622502 AGGAAAGTTAGGTAAGTCTTGGTAA 57.377 36.000 0.00 0.00 0.00 2.85
557 565 7.677892 AGGAAAGTTAGGTAAGTCTTGGTAAG 58.322 38.462 0.00 0.00 0.00 2.34
558 566 6.370994 GGAAAGTTAGGTAAGTCTTGGTAAGC 59.629 42.308 0.00 0.00 0.00 3.09
559 567 6.683312 AAGTTAGGTAAGTCTTGGTAAGCT 57.317 37.500 0.00 0.00 0.00 3.74
560 568 6.283544 AGTTAGGTAAGTCTTGGTAAGCTC 57.716 41.667 0.00 0.00 0.00 4.09
561 569 3.870633 AGGTAAGTCTTGGTAAGCTCG 57.129 47.619 0.00 0.00 0.00 5.03
562 570 3.163467 AGGTAAGTCTTGGTAAGCTCGT 58.837 45.455 0.00 0.00 0.00 4.18
563 571 3.577415 AGGTAAGTCTTGGTAAGCTCGTT 59.423 43.478 0.00 0.00 0.00 3.85
564 572 3.925299 GGTAAGTCTTGGTAAGCTCGTTC 59.075 47.826 0.00 0.00 0.00 3.95
565 573 2.349297 AGTCTTGGTAAGCTCGTTCG 57.651 50.000 0.00 0.00 0.00 3.95
566 574 1.612463 AGTCTTGGTAAGCTCGTTCGT 59.388 47.619 0.00 0.00 0.00 3.85
567 575 2.816087 AGTCTTGGTAAGCTCGTTCGTA 59.184 45.455 0.00 0.00 0.00 3.43
568 576 3.119919 AGTCTTGGTAAGCTCGTTCGTAG 60.120 47.826 0.00 0.00 0.00 3.51
569 577 2.163010 TCTTGGTAAGCTCGTTCGTAGG 59.837 50.000 0.00 0.00 0.00 3.18
570 578 1.538047 TGGTAAGCTCGTTCGTAGGT 58.462 50.000 0.00 0.00 0.00 3.08
571 579 1.200716 TGGTAAGCTCGTTCGTAGGTG 59.799 52.381 0.00 0.00 0.00 4.00
572 580 1.200948 GGTAAGCTCGTTCGTAGGTGT 59.799 52.381 0.00 0.00 0.00 4.16
573 581 2.420022 GGTAAGCTCGTTCGTAGGTGTA 59.580 50.000 0.00 0.00 0.00 2.90
574 582 2.915738 AAGCTCGTTCGTAGGTGTAG 57.084 50.000 0.00 0.00 0.00 2.74
575 583 0.450983 AGCTCGTTCGTAGGTGTAGC 59.549 55.000 0.00 0.00 0.00 3.58
576 584 0.169672 GCTCGTTCGTAGGTGTAGCA 59.830 55.000 0.00 0.00 0.00 3.49
577 585 1.202268 GCTCGTTCGTAGGTGTAGCAT 60.202 52.381 0.00 0.00 0.00 3.79
578 586 2.734492 GCTCGTTCGTAGGTGTAGCATT 60.734 50.000 0.00 0.00 0.00 3.56
579 587 3.488047 GCTCGTTCGTAGGTGTAGCATTA 60.488 47.826 0.00 0.00 0.00 1.90
580 588 4.792057 GCTCGTTCGTAGGTGTAGCATTAT 60.792 45.833 0.00 0.00 0.00 1.28
581 589 5.252969 TCGTTCGTAGGTGTAGCATTATT 57.747 39.130 0.00 0.00 0.00 1.40
582 590 5.038683 TCGTTCGTAGGTGTAGCATTATTG 58.961 41.667 0.00 0.00 0.00 1.90
583 591 5.038683 CGTTCGTAGGTGTAGCATTATTGA 58.961 41.667 0.00 0.00 0.00 2.57
664 676 1.160329 GCCGCACCTACTAATGCCAG 61.160 60.000 0.00 0.00 38.69 4.85
786 798 1.154016 ACGACGAAGCTCGACATGG 60.154 57.895 0.00 0.00 43.74 3.66
832 844 4.467769 CTCAAATTAGGAGGGACATGCAT 58.532 43.478 0.00 0.00 0.00 3.96
833 845 4.209538 TCAAATTAGGAGGGACATGCATG 58.790 43.478 25.09 25.09 0.00 4.06
1111 1145 4.444081 ACTCCTCCTCCCCCGTCG 62.444 72.222 0.00 0.00 0.00 5.12
1228 1262 2.360726 TCCTGCGCGACCTCTACA 60.361 61.111 12.10 0.00 0.00 2.74
1299 1333 1.874019 CGAGATCTCAACCGGCGTG 60.874 63.158 22.31 0.00 0.00 5.34
1301 1335 1.945354 GAGATCTCAACCGGCGTGGA 61.945 60.000 18.11 0.26 42.00 4.02
1965 2020 2.819595 CCGTGGCCCAACATCTCG 60.820 66.667 0.00 0.00 0.00 4.04
2042 2097 2.746277 GGCGCACCAGGTAACCAG 60.746 66.667 10.83 0.00 35.26 4.00
2049 2104 2.237392 GCACCAGGTAACCAGAGATTCT 59.763 50.000 0.00 0.00 37.17 2.40
2050 2105 3.307762 GCACCAGGTAACCAGAGATTCTT 60.308 47.826 0.00 0.00 37.17 2.52
2051 2106 4.256920 CACCAGGTAACCAGAGATTCTTG 58.743 47.826 0.00 0.00 37.17 3.02
2053 2108 4.256920 CCAGGTAACCAGAGATTCTTGTG 58.743 47.826 0.00 0.00 37.17 3.33
2054 2109 4.020218 CCAGGTAACCAGAGATTCTTGTGA 60.020 45.833 0.00 0.00 37.17 3.58
2055 2110 5.513094 CCAGGTAACCAGAGATTCTTGTGAA 60.513 44.000 0.00 0.00 34.72 3.18
2057 2112 6.486657 CAGGTAACCAGAGATTCTTGTGAAAA 59.513 38.462 0.00 0.00 34.08 2.29
2058 2113 6.712547 AGGTAACCAGAGATTCTTGTGAAAAG 59.287 38.462 0.00 0.00 34.08 2.27
2059 2114 6.486993 GGTAACCAGAGATTCTTGTGAAAAGT 59.513 38.462 0.00 0.00 35.63 2.66
2060 2115 7.013369 GGTAACCAGAGATTCTTGTGAAAAGTT 59.987 37.037 0.00 0.00 35.63 2.66
2062 2117 7.410120 ACCAGAGATTCTTGTGAAAAGTTTT 57.590 32.000 0.00 0.00 35.63 2.43
2063 2118 7.260603 ACCAGAGATTCTTGTGAAAAGTTTTG 58.739 34.615 5.36 0.00 35.63 2.44
2064 2119 7.093771 ACCAGAGATTCTTGTGAAAAGTTTTGT 60.094 33.333 5.36 0.00 35.63 2.83
2065 2120 7.221452 CCAGAGATTCTTGTGAAAAGTTTTGTG 59.779 37.037 5.36 0.00 35.63 3.33
2079 2379 6.779115 AAGTTTTGTGTGAAACCAAAAGTC 57.221 33.333 5.86 0.00 43.39 3.01
2084 2384 8.878769 GTTTTGTGTGAAACCAAAAGTCATAAT 58.121 29.630 0.00 0.00 42.93 1.28
2085 2385 9.442047 TTTTGTGTGAAACCAAAAGTCATAATT 57.558 25.926 0.00 0.00 39.94 1.40
2098 2398 7.631717 AAAGTCATAATTAAAGGAGCAGGTC 57.368 36.000 0.00 0.00 0.00 3.85
2287 2587 3.072915 AGATGTTCAAGACCATGGACACA 59.927 43.478 21.47 12.96 41.49 3.72
2509 2809 3.119424 CCTTCTCCTACTTCGACAAGGAC 60.119 52.174 5.65 0.00 34.46 3.85
2847 3159 3.866582 GCATAGCTCCACCGGCCT 61.867 66.667 0.00 0.00 0.00 5.19
2898 3214 8.200792 TGCCAATTACATTGTACTTGAAGTTTT 58.799 29.630 21.80 0.00 38.59 2.43
2939 3255 6.522625 AGAAGAGAACGATGATGAAGAAGA 57.477 37.500 0.00 0.00 0.00 2.87
2940 3256 6.929625 AGAAGAGAACGATGATGAAGAAGAA 58.070 36.000 0.00 0.00 0.00 2.52
2941 3257 7.382110 AGAAGAGAACGATGATGAAGAAGAAA 58.618 34.615 0.00 0.00 0.00 2.52
2942 3258 7.545265 AGAAGAGAACGATGATGAAGAAGAAAG 59.455 37.037 0.00 0.00 0.00 2.62
3078 3394 2.541466 ACTTAACTAGCAGAGTGGCCT 58.459 47.619 3.32 0.00 38.87 5.19
3525 3849 8.387813 TGGGAGAAAGTAATTAAATGTACCTGT 58.612 33.333 0.00 0.00 0.00 4.00
3575 3899 1.621107 GCTCGTTCAAACATGCATGG 58.379 50.000 29.41 12.93 0.00 3.66
3583 3907 5.050227 CGTTCAAACATGCATGGTTTTCATT 60.050 36.000 27.21 8.89 35.04 2.57
3596 3920 8.682710 GCATGGTTTTCATTAAGTCTATTACCA 58.317 33.333 0.00 0.00 36.49 3.25
3644 3970 5.633182 CCAAATTCTCCCATTGTTAAACACG 59.367 40.000 0.00 0.00 0.00 4.49
3645 3971 3.907894 TTCTCCCATTGTTAAACACGC 57.092 42.857 0.00 0.00 0.00 5.34
3646 3972 2.156098 TCTCCCATTGTTAAACACGCC 58.844 47.619 0.00 0.00 0.00 5.68
3647 3973 1.201414 CTCCCATTGTTAAACACGCCC 59.799 52.381 0.00 0.00 0.00 6.13
3648 3974 0.962489 CCCATTGTTAAACACGCCCA 59.038 50.000 0.00 0.00 0.00 5.36
3649 3975 1.548269 CCCATTGTTAAACACGCCCAT 59.452 47.619 0.00 0.00 0.00 4.00
3650 3976 2.605030 CCATTGTTAAACACGCCCATG 58.395 47.619 0.00 0.00 0.00 3.66
3651 3977 2.605030 CATTGTTAAACACGCCCATGG 58.395 47.619 4.14 4.14 0.00 3.66
3652 3978 0.315568 TTGTTAAACACGCCCATGGC 59.684 50.000 6.09 0.58 46.75 4.40
3680 4006 2.817396 GAGCGCACTGAGAAGCCC 60.817 66.667 11.47 0.00 0.00 5.19
3681 4007 3.308014 GAGCGCACTGAGAAGCCCT 62.308 63.158 11.47 0.00 0.00 5.19
3686 4012 2.359900 CGCACTGAGAAGCCCTTAATT 58.640 47.619 0.00 0.00 0.00 1.40
3799 4126 4.200851 CGCTGTCTGCATCGCGTG 62.201 66.667 5.77 5.06 43.06 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.525100 AGGTAACAAGAGAGAACTGACTCC 59.475 45.833 0.00 0.00 36.94 3.85
9 10 7.598759 AACTAAGGTAACAAGAGAGAACTGA 57.401 36.000 0.00 0.00 41.41 3.41
12 13 8.658499 TCAAAACTAAGGTAACAAGAGAGAAC 57.342 34.615 0.00 0.00 41.41 3.01
85 86 1.188863 GACTTTTGGGCATGGCATCT 58.811 50.000 22.06 0.00 0.00 2.90
173 176 7.277760 GGCAACACTTTACAAAGTTTGATTTCT 59.722 33.333 22.23 1.80 46.52 2.52
290 293 9.031360 ACATTCATAACACGTGATCAGTATTAC 57.969 33.333 25.01 0.00 0.00 1.89
434 442 1.189446 CACGTAACTTCACTGCACGTC 59.811 52.381 0.00 0.00 43.37 4.34
438 446 3.660501 ATCTCACGTAACTTCACTGCA 57.339 42.857 0.00 0.00 0.00 4.41
439 447 4.992381 AAATCTCACGTAACTTCACTGC 57.008 40.909 0.00 0.00 0.00 4.40
440 448 7.001922 CGTAAAAATCTCACGTAACTTCACTG 58.998 38.462 0.00 0.00 0.00 3.66
441 449 6.698766 ACGTAAAAATCTCACGTAACTTCACT 59.301 34.615 0.00 0.00 46.23 3.41
442 450 6.870517 ACGTAAAAATCTCACGTAACTTCAC 58.129 36.000 0.00 0.00 46.23 3.18
449 457 6.089820 CAGCCTTTACGTAAAAATCTCACGTA 59.910 38.462 20.47 2.38 46.23 3.57
451 459 5.119588 TCAGCCTTTACGTAAAAATCTCACG 59.880 40.000 20.47 7.32 41.32 4.35
452 460 6.147328 AGTCAGCCTTTACGTAAAAATCTCAC 59.853 38.462 20.47 13.68 0.00 3.51
453 461 6.228258 AGTCAGCCTTTACGTAAAAATCTCA 58.772 36.000 20.47 3.30 0.00 3.27
454 462 6.723131 AGTCAGCCTTTACGTAAAAATCTC 57.277 37.500 20.47 10.28 0.00 2.75
455 463 6.072673 CCAAGTCAGCCTTTACGTAAAAATCT 60.073 38.462 20.47 14.16 0.00 2.40
456 464 6.084277 CCAAGTCAGCCTTTACGTAAAAATC 58.916 40.000 20.47 12.40 0.00 2.17
457 465 5.533528 ACCAAGTCAGCCTTTACGTAAAAAT 59.466 36.000 20.47 7.67 0.00 1.82
458 466 4.883006 ACCAAGTCAGCCTTTACGTAAAAA 59.117 37.500 20.47 2.81 0.00 1.94
459 467 4.273969 CACCAAGTCAGCCTTTACGTAAAA 59.726 41.667 20.47 3.89 0.00 1.52
460 468 3.810941 CACCAAGTCAGCCTTTACGTAAA 59.189 43.478 19.12 19.12 0.00 2.01
461 469 3.395639 CACCAAGTCAGCCTTTACGTAA 58.604 45.455 3.29 3.29 0.00 3.18
462 470 2.289195 CCACCAAGTCAGCCTTTACGTA 60.289 50.000 0.00 0.00 0.00 3.57
463 471 1.542547 CCACCAAGTCAGCCTTTACGT 60.543 52.381 0.00 0.00 0.00 3.57
464 472 1.156736 CCACCAAGTCAGCCTTTACG 58.843 55.000 0.00 0.00 0.00 3.18
465 473 0.881796 GCCACCAAGTCAGCCTTTAC 59.118 55.000 0.00 0.00 0.00 2.01
466 474 0.476338 TGCCACCAAGTCAGCCTTTA 59.524 50.000 0.00 0.00 0.00 1.85
467 475 0.825010 CTGCCACCAAGTCAGCCTTT 60.825 55.000 0.00 0.00 0.00 3.11
468 476 1.228367 CTGCCACCAAGTCAGCCTT 60.228 57.895 0.00 0.00 0.00 4.35
469 477 1.999634 AACTGCCACCAAGTCAGCCT 62.000 55.000 0.00 0.00 0.00 4.58
470 478 0.250727 TAACTGCCACCAAGTCAGCC 60.251 55.000 0.00 0.00 0.00 4.85
471 479 1.604604 TTAACTGCCACCAAGTCAGC 58.395 50.000 0.00 0.00 0.00 4.26
472 480 3.057315 CCAATTAACTGCCACCAAGTCAG 60.057 47.826 0.00 0.00 0.00 3.51
473 481 2.890311 CCAATTAACTGCCACCAAGTCA 59.110 45.455 0.00 0.00 0.00 3.41
474 482 3.153919 TCCAATTAACTGCCACCAAGTC 58.846 45.455 0.00 0.00 0.00 3.01
475 483 3.237268 TCCAATTAACTGCCACCAAGT 57.763 42.857 0.00 0.00 0.00 3.16
476 484 4.806640 AATCCAATTAACTGCCACCAAG 57.193 40.909 0.00 0.00 0.00 3.61
477 485 4.709397 CCTAATCCAATTAACTGCCACCAA 59.291 41.667 0.00 0.00 0.00 3.67
478 486 4.017958 TCCTAATCCAATTAACTGCCACCA 60.018 41.667 0.00 0.00 0.00 4.17
479 487 4.532834 TCCTAATCCAATTAACTGCCACC 58.467 43.478 0.00 0.00 0.00 4.61
480 488 6.715347 AATCCTAATCCAATTAACTGCCAC 57.285 37.500 0.00 0.00 0.00 5.01
481 489 7.502226 CACTAATCCTAATCCAATTAACTGCCA 59.498 37.037 0.00 0.00 0.00 4.92
482 490 7.040409 CCACTAATCCTAATCCAATTAACTGCC 60.040 40.741 0.00 0.00 0.00 4.85
483 491 7.522236 GCCACTAATCCTAATCCAATTAACTGC 60.522 40.741 0.00 0.00 0.00 4.40
484 492 7.721399 AGCCACTAATCCTAATCCAATTAACTG 59.279 37.037 0.00 0.00 0.00 3.16
485 493 7.721399 CAGCCACTAATCCTAATCCAATTAACT 59.279 37.037 0.00 0.00 0.00 2.24
486 494 7.040409 CCAGCCACTAATCCTAATCCAATTAAC 60.040 40.741 0.00 0.00 0.00 2.01
487 495 7.004086 CCAGCCACTAATCCTAATCCAATTAA 58.996 38.462 0.00 0.00 0.00 1.40
488 496 6.467194 CCCAGCCACTAATCCTAATCCAATTA 60.467 42.308 0.00 0.00 0.00 1.40
489 497 5.388654 CCAGCCACTAATCCTAATCCAATT 58.611 41.667 0.00 0.00 0.00 2.32
490 498 4.202609 CCCAGCCACTAATCCTAATCCAAT 60.203 45.833 0.00 0.00 0.00 3.16
491 499 3.138283 CCCAGCCACTAATCCTAATCCAA 59.862 47.826 0.00 0.00 0.00 3.53
492 500 2.711009 CCCAGCCACTAATCCTAATCCA 59.289 50.000 0.00 0.00 0.00 3.41
493 501 2.040412 CCCCAGCCACTAATCCTAATCC 59.960 54.545 0.00 0.00 0.00 3.01
494 502 2.553247 GCCCCAGCCACTAATCCTAATC 60.553 54.545 0.00 0.00 0.00 1.75
495 503 1.425448 GCCCCAGCCACTAATCCTAAT 59.575 52.381 0.00 0.00 0.00 1.73
496 504 0.843984 GCCCCAGCCACTAATCCTAA 59.156 55.000 0.00 0.00 0.00 2.69
497 505 2.539983 GCCCCAGCCACTAATCCTA 58.460 57.895 0.00 0.00 0.00 2.94
498 506 3.335711 GCCCCAGCCACTAATCCT 58.664 61.111 0.00 0.00 0.00 3.24
513 521 1.824852 CTTCAATTAACTGGGTGGGCC 59.175 52.381 0.00 0.00 0.00 5.80
514 522 1.824852 CCTTCAATTAACTGGGTGGGC 59.175 52.381 0.00 0.00 0.00 5.36
515 523 3.449746 TCCTTCAATTAACTGGGTGGG 57.550 47.619 0.00 0.00 0.00 4.61
516 524 4.832823 ACTTTCCTTCAATTAACTGGGTGG 59.167 41.667 0.00 0.00 0.00 4.61
517 525 6.405278 AACTTTCCTTCAATTAACTGGGTG 57.595 37.500 0.00 0.00 0.00 4.61
518 526 6.719829 CCTAACTTTCCTTCAATTAACTGGGT 59.280 38.462 0.00 0.00 0.00 4.51
519 527 6.719829 ACCTAACTTTCCTTCAATTAACTGGG 59.280 38.462 0.00 0.00 0.00 4.45
520 528 7.761038 ACCTAACTTTCCTTCAATTAACTGG 57.239 36.000 0.00 0.00 0.00 4.00
526 534 9.067986 CAAGACTTACCTAACTTTCCTTCAATT 57.932 33.333 0.00 0.00 0.00 2.32
527 535 7.665974 CCAAGACTTACCTAACTTTCCTTCAAT 59.334 37.037 0.00 0.00 0.00 2.57
528 536 6.996282 CCAAGACTTACCTAACTTTCCTTCAA 59.004 38.462 0.00 0.00 0.00 2.69
529 537 6.100714 ACCAAGACTTACCTAACTTTCCTTCA 59.899 38.462 0.00 0.00 0.00 3.02
530 538 6.531923 ACCAAGACTTACCTAACTTTCCTTC 58.468 40.000 0.00 0.00 0.00 3.46
531 539 6.511017 ACCAAGACTTACCTAACTTTCCTT 57.489 37.500 0.00 0.00 0.00 3.36
532 540 7.622502 TTACCAAGACTTACCTAACTTTCCT 57.377 36.000 0.00 0.00 0.00 3.36
533 541 6.370994 GCTTACCAAGACTTACCTAACTTTCC 59.629 42.308 0.00 0.00 0.00 3.13
534 542 7.160049 AGCTTACCAAGACTTACCTAACTTTC 58.840 38.462 0.00 0.00 0.00 2.62
535 543 7.075851 AGCTTACCAAGACTTACCTAACTTT 57.924 36.000 0.00 0.00 0.00 2.66
536 544 6.571925 CGAGCTTACCAAGACTTACCTAACTT 60.572 42.308 0.00 0.00 0.00 2.66
537 545 5.105837 CGAGCTTACCAAGACTTACCTAACT 60.106 44.000 0.00 0.00 0.00 2.24
538 546 5.100943 CGAGCTTACCAAGACTTACCTAAC 58.899 45.833 0.00 0.00 0.00 2.34
539 547 4.768968 ACGAGCTTACCAAGACTTACCTAA 59.231 41.667 0.00 0.00 0.00 2.69
540 548 4.338879 ACGAGCTTACCAAGACTTACCTA 58.661 43.478 0.00 0.00 0.00 3.08
541 549 3.163467 ACGAGCTTACCAAGACTTACCT 58.837 45.455 0.00 0.00 0.00 3.08
542 550 3.589495 ACGAGCTTACCAAGACTTACC 57.411 47.619 0.00 0.00 0.00 2.85
543 551 3.607209 CGAACGAGCTTACCAAGACTTAC 59.393 47.826 0.00 0.00 0.00 2.34
544 552 3.254166 ACGAACGAGCTTACCAAGACTTA 59.746 43.478 0.14 0.00 0.00 2.24
545 553 2.035576 ACGAACGAGCTTACCAAGACTT 59.964 45.455 0.14 0.00 0.00 3.01
546 554 1.612463 ACGAACGAGCTTACCAAGACT 59.388 47.619 0.14 0.00 0.00 3.24
547 555 2.061740 ACGAACGAGCTTACCAAGAC 57.938 50.000 0.14 0.00 0.00 3.01
548 556 2.163010 CCTACGAACGAGCTTACCAAGA 59.837 50.000 0.14 0.00 0.00 3.02
549 557 2.094854 ACCTACGAACGAGCTTACCAAG 60.095 50.000 0.14 0.00 0.00 3.61
550 558 1.888512 ACCTACGAACGAGCTTACCAA 59.111 47.619 0.14 0.00 0.00 3.67
551 559 1.200716 CACCTACGAACGAGCTTACCA 59.799 52.381 0.14 0.00 0.00 3.25
552 560 1.200948 ACACCTACGAACGAGCTTACC 59.799 52.381 0.14 0.00 0.00 2.85
553 561 2.626088 ACACCTACGAACGAGCTTAC 57.374 50.000 0.14 0.00 0.00 2.34
554 562 2.096496 GCTACACCTACGAACGAGCTTA 59.904 50.000 0.14 0.00 0.00 3.09
555 563 1.135460 GCTACACCTACGAACGAGCTT 60.135 52.381 0.14 0.00 0.00 3.74
556 564 0.450983 GCTACACCTACGAACGAGCT 59.549 55.000 0.14 0.00 0.00 4.09
557 565 0.169672 TGCTACACCTACGAACGAGC 59.830 55.000 0.14 0.00 0.00 5.03
558 566 2.846039 ATGCTACACCTACGAACGAG 57.154 50.000 0.14 0.00 0.00 4.18
559 567 4.906065 ATAATGCTACACCTACGAACGA 57.094 40.909 0.14 0.00 0.00 3.85
560 568 5.038683 TCAATAATGCTACACCTACGAACG 58.961 41.667 0.00 0.00 0.00 3.95
561 569 5.462398 CCTCAATAATGCTACACCTACGAAC 59.538 44.000 0.00 0.00 0.00 3.95
562 570 5.452776 CCCTCAATAATGCTACACCTACGAA 60.453 44.000 0.00 0.00 0.00 3.85
563 571 4.038763 CCCTCAATAATGCTACACCTACGA 59.961 45.833 0.00 0.00 0.00 3.43
564 572 4.038763 TCCCTCAATAATGCTACACCTACG 59.961 45.833 0.00 0.00 0.00 3.51
565 573 5.511545 CCTCCCTCAATAATGCTACACCTAC 60.512 48.000 0.00 0.00 0.00 3.18
566 574 4.593206 CCTCCCTCAATAATGCTACACCTA 59.407 45.833 0.00 0.00 0.00 3.08
567 575 3.392616 CCTCCCTCAATAATGCTACACCT 59.607 47.826 0.00 0.00 0.00 4.00
568 576 3.496870 CCCTCCCTCAATAATGCTACACC 60.497 52.174 0.00 0.00 0.00 4.16
569 577 3.391296 TCCCTCCCTCAATAATGCTACAC 59.609 47.826 0.00 0.00 0.00 2.90
570 578 3.664320 TCCCTCCCTCAATAATGCTACA 58.336 45.455 0.00 0.00 0.00 2.74
571 579 4.583871 CATCCCTCCCTCAATAATGCTAC 58.416 47.826 0.00 0.00 0.00 3.58
572 580 3.009473 GCATCCCTCCCTCAATAATGCTA 59.991 47.826 0.00 0.00 36.12 3.49
573 581 2.224967 GCATCCCTCCCTCAATAATGCT 60.225 50.000 0.00 0.00 36.12 3.79
574 582 2.165998 GCATCCCTCCCTCAATAATGC 58.834 52.381 0.00 0.00 0.00 3.56
575 583 3.152341 GTGCATCCCTCCCTCAATAATG 58.848 50.000 0.00 0.00 0.00 1.90
576 584 2.224621 CGTGCATCCCTCCCTCAATAAT 60.225 50.000 0.00 0.00 0.00 1.28
577 585 1.140852 CGTGCATCCCTCCCTCAATAA 59.859 52.381 0.00 0.00 0.00 1.40
578 586 0.758734 CGTGCATCCCTCCCTCAATA 59.241 55.000 0.00 0.00 0.00 1.90
579 587 0.982852 TCGTGCATCCCTCCCTCAAT 60.983 55.000 0.00 0.00 0.00 2.57
580 588 1.612146 TCGTGCATCCCTCCCTCAA 60.612 57.895 0.00 0.00 0.00 3.02
581 589 2.038813 TCGTGCATCCCTCCCTCA 59.961 61.111 0.00 0.00 0.00 3.86
582 590 2.501610 GTCGTGCATCCCTCCCTC 59.498 66.667 0.00 0.00 0.00 4.30
583 591 3.461773 CGTCGTGCATCCCTCCCT 61.462 66.667 0.00 0.00 0.00 4.20
664 676 3.564027 GACTACGTGCATGCCGCC 61.564 66.667 22.90 8.42 41.33 6.13
832 844 0.893270 CTCCATTGTTTCGGGGTGCA 60.893 55.000 0.00 0.00 0.00 4.57
833 845 0.608035 TCTCCATTGTTTCGGGGTGC 60.608 55.000 0.00 0.00 0.00 5.01
963 997 2.432146 TCAACGATGGATCCTCCTCAAG 59.568 50.000 14.23 0.18 37.46 3.02
1299 1333 3.567473 GACTTGCAGGCGAAGTCC 58.433 61.111 17.89 7.32 42.36 3.85
1301 1335 0.674895 GATGGACTTGCAGGCGAAGT 60.675 55.000 0.00 8.23 36.33 3.01
1341 1375 4.753662 TCCTCCACGTCCTCCGGG 62.754 72.222 0.00 0.00 42.24 5.73
2042 2097 7.754924 TCACACAAAACTTTTCACAAGAATCTC 59.245 33.333 0.00 0.00 32.89 2.75
2049 2104 6.049149 TGGTTTCACACAAAACTTTTCACAA 58.951 32.000 0.00 0.00 38.81 3.33
2050 2105 5.601662 TGGTTTCACACAAAACTTTTCACA 58.398 33.333 0.00 0.00 38.81 3.58
2051 2106 6.532365 TTGGTTTCACACAAAACTTTTCAC 57.468 33.333 0.00 0.00 38.81 3.18
2053 2108 7.635423 ACTTTTGGTTTCACACAAAACTTTTC 58.365 30.769 0.00 0.00 40.48 2.29
2054 2109 7.281100 TGACTTTTGGTTTCACACAAAACTTTT 59.719 29.630 0.00 0.00 40.48 2.27
2055 2110 6.763610 TGACTTTTGGTTTCACACAAAACTTT 59.236 30.769 0.00 0.00 40.48 2.66
2057 2112 5.848406 TGACTTTTGGTTTCACACAAAACT 58.152 33.333 0.00 0.00 40.48 2.66
2058 2113 6.720012 ATGACTTTTGGTTTCACACAAAAC 57.280 33.333 0.00 0.00 40.48 2.43
2059 2114 9.442047 AATTATGACTTTTGGTTTCACACAAAA 57.558 25.926 0.00 0.00 42.38 2.44
2064 2119 9.757227 CCTTTAATTATGACTTTTGGTTTCACA 57.243 29.630 0.00 0.00 0.00 3.58
2065 2120 9.974980 TCCTTTAATTATGACTTTTGGTTTCAC 57.025 29.630 0.00 0.00 0.00 3.18
2079 2379 6.678900 GCACAAGACCTGCTCCTTTAATTATG 60.679 42.308 0.00 0.00 0.00 1.90
2084 2384 2.504367 GCACAAGACCTGCTCCTTTAA 58.496 47.619 0.00 0.00 0.00 1.52
2085 2385 1.271379 GGCACAAGACCTGCTCCTTTA 60.271 52.381 0.00 0.00 34.84 1.85
2086 2386 0.538287 GGCACAAGACCTGCTCCTTT 60.538 55.000 0.00 0.00 34.84 3.11
2087 2387 1.073897 GGCACAAGACCTGCTCCTT 59.926 57.895 0.00 0.00 34.84 3.36
2088 2388 2.149383 TGGCACAAGACCTGCTCCT 61.149 57.895 0.00 0.00 34.84 3.69
2089 2389 1.968540 GTGGCACAAGACCTGCTCC 60.969 63.158 13.86 0.00 44.16 4.70
2092 2392 2.985847 GGGTGGCACAAGACCTGC 60.986 66.667 20.82 0.00 44.16 4.85
2098 2398 0.323633 TGATCCATGGGTGGCACAAG 60.324 55.000 20.82 5.46 45.63 3.16
2158 2458 1.447489 CTTGAGCCTGGAGAGCACG 60.447 63.158 0.00 0.00 0.00 5.34
2350 2650 1.077068 CTCCGAGTCCCTGAGCTCT 60.077 63.158 16.19 0.00 0.00 4.09
2389 2689 1.595382 GCTGTTGTCCACGTCAGCT 60.595 57.895 15.22 0.00 46.35 4.24
2509 2809 2.890474 GTGATGTACCCGCTGCCG 60.890 66.667 0.00 0.00 0.00 5.69
2533 2833 4.007644 CACGCCACCTCCAGCTCA 62.008 66.667 0.00 0.00 0.00 4.26
2667 2979 2.494471 TCCTGCATTTGAGCCATTCAAG 59.506 45.455 0.00 0.00 46.01 3.02
2898 3214 8.759481 TCTCTTCTTCTTGCTCATCTTCTATA 57.241 34.615 0.00 0.00 0.00 1.31
2985 3301 6.825944 TCAAATCCACGGTAAATGAAATGA 57.174 33.333 0.00 0.00 0.00 2.57
2986 3302 7.273381 GTCTTCAAATCCACGGTAAATGAAATG 59.727 37.037 0.00 0.00 0.00 2.32
2987 3303 7.312899 GTCTTCAAATCCACGGTAAATGAAAT 58.687 34.615 0.00 0.00 0.00 2.17
2988 3304 6.294286 GGTCTTCAAATCCACGGTAAATGAAA 60.294 38.462 0.00 0.00 0.00 2.69
2989 3305 5.182380 GGTCTTCAAATCCACGGTAAATGAA 59.818 40.000 0.00 0.00 0.00 2.57
3194 3511 9.189156 AGAGGCAATCTATGTTAAAGCATTTAA 57.811 29.630 0.00 0.00 41.50 1.52
3498 3822 9.408648 CAGGTACATTTAATTACTTTCTCCCAT 57.591 33.333 0.00 0.00 0.00 4.00
3525 3849 4.379813 GCCTCTGCTTGAAAATCGATTGAA 60.380 41.667 12.25 4.53 33.53 2.69
3599 3923 7.835634 TTGGACCTTCAAATTTGTGTTTAAC 57.164 32.000 17.47 5.52 0.00 2.01
3610 3934 4.750941 TGGGAGAATTTGGACCTTCAAAT 58.249 39.130 0.00 0.00 45.86 2.32
3611 3935 4.191804 TGGGAGAATTTGGACCTTCAAA 57.808 40.909 0.00 0.00 40.37 2.69
3612 3936 3.893753 TGGGAGAATTTGGACCTTCAA 57.106 42.857 0.00 0.00 0.00 2.69
3645 3971 1.468520 CTCAACACGTAAAGCCATGGG 59.531 52.381 15.13 0.00 0.00 4.00
3646 3972 1.135689 GCTCAACACGTAAAGCCATGG 60.136 52.381 7.63 7.63 0.00 3.66
3647 3973 1.464023 CGCTCAACACGTAAAGCCATG 60.464 52.381 0.00 0.00 0.00 3.66
3648 3974 0.796312 CGCTCAACACGTAAAGCCAT 59.204 50.000 0.00 0.00 0.00 4.40
3649 3975 1.837538 GCGCTCAACACGTAAAGCCA 61.838 55.000 0.00 0.00 0.00 4.75
3650 3976 1.154469 GCGCTCAACACGTAAAGCC 60.154 57.895 0.00 0.00 0.00 4.35
3651 3977 0.721483 GTGCGCTCAACACGTAAAGC 60.721 55.000 9.73 0.00 0.00 3.51
3652 3978 0.859232 AGTGCGCTCAACACGTAAAG 59.141 50.000 9.73 0.00 42.94 1.85
3653 3979 0.579630 CAGTGCGCTCAACACGTAAA 59.420 50.000 9.73 0.00 42.94 2.01
3654 3980 0.249114 TCAGTGCGCTCAACACGTAA 60.249 50.000 9.73 0.00 42.94 3.18
3655 3981 0.663269 CTCAGTGCGCTCAACACGTA 60.663 55.000 9.73 0.00 42.94 3.57
3656 3982 1.951130 CTCAGTGCGCTCAACACGT 60.951 57.895 9.73 0.00 42.94 4.49
3657 3983 1.215014 TTCTCAGTGCGCTCAACACG 61.215 55.000 9.73 0.00 42.94 4.49
3658 3984 0.510359 CTTCTCAGTGCGCTCAACAC 59.490 55.000 9.73 0.00 38.35 3.32
3706 4032 5.195185 TGGATGACGAACCAGTACATAGTA 58.805 41.667 0.00 0.00 0.00 1.82
3754 4081 2.713967 GCATGGGCGTGCAGGAAAT 61.714 57.895 11.29 0.00 44.43 2.17
3799 4126 1.228094 GCAGAAGGCTAGATGGGGC 60.228 63.158 0.00 0.00 40.25 5.80


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

AutoCloner maintained by Alex Coulton.