Multiple sequence alignment - TraesCS5A01G386900

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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 TraesCS5A01G386900 chr5A 100.000 3311 0 0 1 3311 584457012 584453702 0.000000e+00 6115.0
1 TraesCS5A01G386900 chr5D 92.235 2743 128 38 602 3311 464073353 464070663 0.000000e+00 3807.0
2 TraesCS5A01G386900 chr5D 86.654 532 20 16 1 497 464073865 464073350 2.910000e-150 542.0
3 TraesCS5A01G386900 chr5B 92.441 2474 125 27 879 3311 570930793 570928341 0.000000e+00 3476.0
4 TraesCS5A01G386900 chr5B 85.530 387 25 15 1 376 570931273 570930907 3.120000e-100 375.0
5 TraesCS5A01G386900 chr3D 89.286 84 6 2 3030 3111 250931493 250931575 5.850000e-18 102.0
6 TraesCS5A01G386900 chr2D 88.235 85 6 1 3029 3109 425742653 425742569 7.560000e-17 99.0
7 TraesCS5A01G386900 chr6A 88.889 81 4 2 3030 3109 301951364 301951288 9.780000e-16 95.3
8 TraesCS5A01G386900 chr6D 86.207 87 8 3 3030 3116 211443945 211444027 1.270000e-14 91.6
9 TraesCS5A01G386900 chr3B 86.905 84 8 2 3030 3110 194074772 194074855 1.270000e-14 91.6
10 TraesCS5A01G386900 chr1D 87.059 85 6 4 3030 3109 279101460 279101376 1.270000e-14 91.6
11 TraesCS5A01G386900 chr1B 86.905 84 8 3 3028 3109 539869610 539869528 1.270000e-14 91.6


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 TraesCS5A01G386900 chr5A 584453702 584457012 3310 True 6115.0 6115 100.0000 1 3311 1 chr5A.!!$R1 3310
1 TraesCS5A01G386900 chr5D 464070663 464073865 3202 True 2174.5 3807 89.4445 1 3311 2 chr5D.!!$R1 3310
2 TraesCS5A01G386900 chr5B 570928341 570931273 2932 True 1925.5 3476 88.9855 1 3311 2 chr5B.!!$R1 3310

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
680 728 0.179132 GCCATGCATGACATTTGCGA 60.179 50.0 28.31 0.0 43.1 5.10 F
1829 1895 0.187851 CCCCCGGACTACTACTCCAT 59.812 60.0 0.73 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2231 0.331954 TACAGCTCCTCGAACCCTCT 59.668 55.0 0.00 0.00 0.00 3.69 R
2962 3066 0.710567 CTGCAGTCGCGTTCAAGTAG 59.289 55.0 5.77 3.56 42.97 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
110 112 4.533311 AGCCATTTGTCCCATCTGAAAATT 59.467 37.500 0.00 0.00 0.00 1.82
209 217 4.925054 TGTGTGTATTGCTCTTTACCGTAC 59.075 41.667 0.00 0.00 0.00 3.67
257 269 4.566545 TTATTGGCAAGTCAACTGTGTG 57.433 40.909 5.96 0.00 0.00 3.82
258 270 1.832883 TTGGCAAGTCAACTGTGTGT 58.167 45.000 0.00 0.00 0.00 3.72
261 273 1.202177 GGCAAGTCAACTGTGTGTGTG 60.202 52.381 0.00 0.00 0.00 3.82
265 277 2.076100 AGTCAACTGTGTGTGTGTGTG 58.924 47.619 0.00 0.00 0.00 3.82
288 300 3.767131 TGTGTGTTAGCTAGCATACCTGA 59.233 43.478 26.63 11.81 29.84 3.86
290 302 4.747108 GTGTGTTAGCTAGCATACCTGATG 59.253 45.833 21.66 0.00 38.73 3.07
294 306 1.615883 AGCTAGCATACCTGATGTCCG 59.384 52.381 18.83 0.00 37.90 4.79
360 374 6.804677 TGTGCATTGAAGTAGTTGAAAATGT 58.195 32.000 0.00 0.00 0.00 2.71
379 400 7.972832 AAATGTCATTGCTGTGATTTTGATT 57.027 28.000 0.00 0.00 0.00 2.57
380 401 7.972832 AATGTCATTGCTGTGATTTTGATTT 57.027 28.000 0.00 0.00 0.00 2.17
381 402 7.972832 ATGTCATTGCTGTGATTTTGATTTT 57.027 28.000 0.00 0.00 0.00 1.82
383 404 6.985059 TGTCATTGCTGTGATTTTGATTTTGA 59.015 30.769 0.00 0.00 0.00 2.69
384 405 7.042590 TGTCATTGCTGTGATTTTGATTTTGAC 60.043 33.333 0.00 0.00 0.00 3.18
385 406 7.170320 GTCATTGCTGTGATTTTGATTTTGACT 59.830 33.333 0.00 0.00 0.00 3.41
386 407 8.358895 TCATTGCTGTGATTTTGATTTTGACTA 58.641 29.630 0.00 0.00 0.00 2.59
387 408 8.644619 CATTGCTGTGATTTTGATTTTGACTAG 58.355 33.333 0.00 0.00 0.00 2.57
388 409 7.275888 TGCTGTGATTTTGATTTTGACTAGT 57.724 32.000 0.00 0.00 0.00 2.57
474 522 7.587037 TCACAAGAGGATTTTCAATTGAGTT 57.413 32.000 8.41 0.00 0.00 3.01
476 524 8.477256 TCACAAGAGGATTTTCAATTGAGTTTT 58.523 29.630 8.41 0.00 0.00 2.43
503 551 7.707624 TCTAGTGAACGATTAAAACTAGGGA 57.292 36.000 7.97 0.00 40.37 4.20
504 552 8.302515 TCTAGTGAACGATTAAAACTAGGGAT 57.697 34.615 7.97 0.00 40.37 3.85
505 553 8.411683 TCTAGTGAACGATTAAAACTAGGGATC 58.588 37.037 7.97 0.00 40.37 3.36
506 554 7.184067 AGTGAACGATTAAAACTAGGGATCT 57.816 36.000 0.00 0.00 0.00 2.75
507 555 7.266400 AGTGAACGATTAAAACTAGGGATCTC 58.734 38.462 0.00 0.00 0.00 2.75
508 556 6.198591 GTGAACGATTAAAACTAGGGATCTCG 59.801 42.308 0.00 0.00 0.00 4.04
509 557 6.095860 TGAACGATTAAAACTAGGGATCTCGA 59.904 38.462 9.01 0.00 0.00 4.04
510 558 6.651975 ACGATTAAAACTAGGGATCTCGAT 57.348 37.500 9.01 0.00 0.00 3.59
511 559 6.679843 ACGATTAAAACTAGGGATCTCGATC 58.320 40.000 9.01 0.00 37.11 3.69
512 560 5.795939 CGATTAAAACTAGGGATCTCGATCG 59.204 44.000 9.36 9.36 38.69 3.69
513 561 6.568081 CGATTAAAACTAGGGATCTCGATCGT 60.568 42.308 15.94 0.00 38.69 3.73
514 562 6.461110 TTAAAACTAGGGATCTCGATCGTT 57.539 37.500 15.94 1.08 38.69 3.85
515 563 5.340439 AAAACTAGGGATCTCGATCGTTT 57.660 39.130 15.94 1.07 38.69 3.60
516 564 4.571372 AACTAGGGATCTCGATCGTTTC 57.429 45.455 15.94 10.16 38.69 2.78
517 565 3.552875 ACTAGGGATCTCGATCGTTTCA 58.447 45.455 15.94 0.00 38.69 2.69
518 566 3.566322 ACTAGGGATCTCGATCGTTTCAG 59.434 47.826 15.94 5.03 38.69 3.02
519 567 1.683917 AGGGATCTCGATCGTTTCAGG 59.316 52.381 15.94 0.43 38.69 3.86
520 568 1.409427 GGGATCTCGATCGTTTCAGGT 59.591 52.381 15.94 0.24 38.69 4.00
521 569 2.159085 GGGATCTCGATCGTTTCAGGTT 60.159 50.000 15.94 0.00 38.69 3.50
522 570 3.067742 GGGATCTCGATCGTTTCAGGTTA 59.932 47.826 15.94 0.00 38.69 2.85
523 571 4.262079 GGGATCTCGATCGTTTCAGGTTAT 60.262 45.833 15.94 0.00 38.69 1.89
524 572 4.918583 GGATCTCGATCGTTTCAGGTTATC 59.081 45.833 15.94 4.43 38.69 1.75
525 573 5.278561 GGATCTCGATCGTTTCAGGTTATCT 60.279 44.000 15.94 0.00 38.69 1.98
526 574 6.072618 GGATCTCGATCGTTTCAGGTTATCTA 60.073 42.308 15.94 0.00 38.69 1.98
527 575 6.688637 TCTCGATCGTTTCAGGTTATCTAA 57.311 37.500 15.94 0.00 0.00 2.10
528 576 7.273320 TCTCGATCGTTTCAGGTTATCTAAT 57.727 36.000 15.94 0.00 0.00 1.73
529 577 7.361127 TCTCGATCGTTTCAGGTTATCTAATC 58.639 38.462 15.94 0.00 0.00 1.75
530 578 7.012989 TCTCGATCGTTTCAGGTTATCTAATCA 59.987 37.037 15.94 0.00 0.00 2.57
531 579 7.658261 TCGATCGTTTCAGGTTATCTAATCAT 58.342 34.615 15.94 0.00 0.00 2.45
532 580 7.808381 TCGATCGTTTCAGGTTATCTAATCATC 59.192 37.037 15.94 0.00 0.00 2.92
533 581 7.062371 CGATCGTTTCAGGTTATCTAATCATCC 59.938 40.741 7.03 0.00 0.00 3.51
534 582 6.213677 TCGTTTCAGGTTATCTAATCATCCG 58.786 40.000 0.00 0.00 0.00 4.18
535 583 5.983720 CGTTTCAGGTTATCTAATCATCCGT 59.016 40.000 0.00 0.00 0.00 4.69
536 584 6.074302 CGTTTCAGGTTATCTAATCATCCGTG 60.074 42.308 0.00 0.00 0.00 4.94
537 585 6.479972 TTCAGGTTATCTAATCATCCGTGT 57.520 37.500 0.00 0.00 0.00 4.49
538 586 6.479972 TCAGGTTATCTAATCATCCGTGTT 57.520 37.500 0.00 0.00 0.00 3.32
539 587 6.280643 TCAGGTTATCTAATCATCCGTGTTG 58.719 40.000 0.00 0.00 0.00 3.33
540 588 6.049149 CAGGTTATCTAATCATCCGTGTTGT 58.951 40.000 0.00 0.00 0.00 3.32
541 589 6.538742 CAGGTTATCTAATCATCCGTGTTGTT 59.461 38.462 0.00 0.00 0.00 2.83
542 590 6.538742 AGGTTATCTAATCATCCGTGTTGTTG 59.461 38.462 0.00 0.00 0.00 3.33
543 591 6.315393 GGTTATCTAATCATCCGTGTTGTTGT 59.685 38.462 0.00 0.00 0.00 3.32
544 592 7.399523 GTTATCTAATCATCCGTGTTGTTGTC 58.600 38.462 0.00 0.00 0.00 3.18
545 593 4.250464 TCTAATCATCCGTGTTGTTGTCC 58.750 43.478 0.00 0.00 0.00 4.02
546 594 2.859165 ATCATCCGTGTTGTTGTCCT 57.141 45.000 0.00 0.00 0.00 3.85
547 595 2.631160 TCATCCGTGTTGTTGTCCTT 57.369 45.000 0.00 0.00 0.00 3.36
548 596 3.755112 TCATCCGTGTTGTTGTCCTTA 57.245 42.857 0.00 0.00 0.00 2.69
549 597 4.074627 TCATCCGTGTTGTTGTCCTTAA 57.925 40.909 0.00 0.00 0.00 1.85
550 598 3.810941 TCATCCGTGTTGTTGTCCTTAAC 59.189 43.478 0.00 0.00 0.00 2.01
551 599 3.547054 TCCGTGTTGTTGTCCTTAACT 57.453 42.857 0.00 0.00 0.00 2.24
552 600 3.199677 TCCGTGTTGTTGTCCTTAACTG 58.800 45.455 0.00 0.00 0.00 3.16
553 601 2.940410 CCGTGTTGTTGTCCTTAACTGT 59.060 45.455 0.00 0.00 0.00 3.55
554 602 3.242608 CCGTGTTGTTGTCCTTAACTGTG 60.243 47.826 0.00 0.00 0.00 3.66
555 603 3.372822 CGTGTTGTTGTCCTTAACTGTGT 59.627 43.478 0.00 0.00 0.00 3.72
556 604 4.493545 CGTGTTGTTGTCCTTAACTGTGTC 60.494 45.833 0.00 0.00 0.00 3.67
557 605 4.393680 GTGTTGTTGTCCTTAACTGTGTCA 59.606 41.667 0.00 0.00 0.00 3.58
558 606 5.065988 GTGTTGTTGTCCTTAACTGTGTCAT 59.934 40.000 0.00 0.00 0.00 3.06
559 607 5.065859 TGTTGTTGTCCTTAACTGTGTCATG 59.934 40.000 0.00 0.00 0.00 3.07
560 608 5.029807 TGTTGTCCTTAACTGTGTCATGA 57.970 39.130 0.00 0.00 0.00 3.07
561 609 5.432645 TGTTGTCCTTAACTGTGTCATGAA 58.567 37.500 0.00 0.00 0.00 2.57
562 610 5.883115 TGTTGTCCTTAACTGTGTCATGAAA 59.117 36.000 0.00 0.00 0.00 2.69
563 611 6.183360 TGTTGTCCTTAACTGTGTCATGAAAC 60.183 38.462 9.25 9.25 0.00 2.78
564 612 4.509970 TGTCCTTAACTGTGTCATGAAACG 59.490 41.667 11.43 8.60 0.00 3.60
565 613 4.510340 GTCCTTAACTGTGTCATGAAACGT 59.490 41.667 11.43 9.20 0.00 3.99
566 614 4.509970 TCCTTAACTGTGTCATGAAACGTG 59.490 41.667 11.43 9.05 0.00 4.49
567 615 4.272504 CCTTAACTGTGTCATGAAACGTGT 59.727 41.667 11.43 9.65 0.00 4.49
568 616 3.673746 AACTGTGTCATGAAACGTGTG 57.326 42.857 11.43 4.44 0.00 3.82
569 617 2.899976 ACTGTGTCATGAAACGTGTGA 58.100 42.857 11.43 0.00 0.00 3.58
570 618 3.266636 ACTGTGTCATGAAACGTGTGAA 58.733 40.909 11.43 0.00 0.00 3.18
571 619 3.687212 ACTGTGTCATGAAACGTGTGAAA 59.313 39.130 11.43 0.00 0.00 2.69
572 620 4.155099 ACTGTGTCATGAAACGTGTGAAAA 59.845 37.500 11.43 0.00 0.00 2.29
573 621 5.048153 TGTGTCATGAAACGTGTGAAAAA 57.952 34.783 11.43 0.00 0.00 1.94
574 622 5.092105 TGTGTCATGAAACGTGTGAAAAAG 58.908 37.500 11.43 0.00 0.00 2.27
575 623 5.092781 GTGTCATGAAACGTGTGAAAAAGT 58.907 37.500 0.00 0.00 0.00 2.66
576 624 5.227184 GTGTCATGAAACGTGTGAAAAAGTC 59.773 40.000 0.00 0.00 0.00 3.01
577 625 4.433304 GTCATGAAACGTGTGAAAAAGTCG 59.567 41.667 0.00 0.00 0.00 4.18
578 626 3.392769 TGAAACGTGTGAAAAAGTCGG 57.607 42.857 0.00 0.00 0.00 4.79
579 627 2.106418 GAAACGTGTGAAAAAGTCGGC 58.894 47.619 0.00 0.00 0.00 5.54
580 628 1.088306 AACGTGTGAAAAAGTCGGCA 58.912 45.000 0.00 0.00 0.00 5.69
581 629 1.305201 ACGTGTGAAAAAGTCGGCAT 58.695 45.000 0.00 0.00 0.00 4.40
582 630 2.485903 ACGTGTGAAAAAGTCGGCATA 58.514 42.857 0.00 0.00 0.00 3.14
583 631 2.478894 ACGTGTGAAAAAGTCGGCATAG 59.521 45.455 0.00 0.00 0.00 2.23
584 632 2.734606 CGTGTGAAAAAGTCGGCATAGA 59.265 45.455 0.00 0.00 0.00 1.98
585 633 3.181530 CGTGTGAAAAAGTCGGCATAGAG 60.182 47.826 0.00 0.00 0.00 2.43
586 634 2.742053 TGTGAAAAAGTCGGCATAGAGC 59.258 45.455 0.00 0.00 44.65 4.09
599 647 4.480386 GCATAGAGCATTTTAGTCCAGC 57.520 45.455 0.00 0.00 44.79 4.85
632 680 5.538433 ACTTGCCTCCTGCTATTTTGTTTTA 59.462 36.000 0.00 0.00 42.00 1.52
636 684 5.360999 GCCTCCTGCTATTTTGTTTTAGGAT 59.639 40.000 0.00 0.00 36.87 3.24
638 686 6.378280 CCTCCTGCTATTTTGTTTTAGGATGT 59.622 38.462 0.00 0.00 32.87 3.06
661 709 2.317609 CCCCAGCGAACGTTCACTG 61.318 63.158 30.45 30.45 37.16 3.66
677 725 2.094442 TCACTGCCATGCATGACATTTG 60.094 45.455 28.31 20.37 38.13 2.32
678 726 1.286501 CTGCCATGCATGACATTTGC 58.713 50.000 28.31 20.36 38.13 3.68
679 727 0.458716 TGCCATGCATGACATTTGCG 60.459 50.000 28.31 9.48 43.10 4.85
680 728 0.179132 GCCATGCATGACATTTGCGA 60.179 50.000 28.31 0.00 43.10 5.10
681 729 1.736364 GCCATGCATGACATTTGCGAA 60.736 47.619 28.31 0.00 43.10 4.70
682 730 1.921887 CCATGCATGACATTTGCGAAC 59.078 47.619 28.31 0.00 43.10 3.95
683 731 2.416296 CCATGCATGACATTTGCGAACT 60.416 45.455 28.31 0.00 43.10 3.01
684 732 2.617250 TGCATGACATTTGCGAACTC 57.383 45.000 0.00 0.00 43.10 3.01
685 733 1.136000 TGCATGACATTTGCGAACTCG 60.136 47.619 0.00 0.00 43.10 4.18
686 734 1.135972 GCATGACATTTGCGAACTCGT 60.136 47.619 0.00 0.00 42.22 4.18
687 735 2.498905 CATGACATTTGCGAACTCGTG 58.501 47.619 0.51 0.00 42.22 4.35
688 736 0.865111 TGACATTTGCGAACTCGTGG 59.135 50.000 0.51 0.00 42.22 4.94
702 750 1.201414 CTCGTGGGGTGGCAATTTTAC 59.799 52.381 0.00 0.00 0.00 2.01
715 763 4.083565 GCAATTTTACTGTTAGGGGGTGA 58.916 43.478 0.00 0.00 0.00 4.02
718 766 4.792513 TTTTACTGTTAGGGGGTGACAA 57.207 40.909 0.00 0.00 0.00 3.18
725 773 4.148838 TGTTAGGGGGTGACAATTTTCAG 58.851 43.478 0.00 0.00 0.00 3.02
728 776 3.922375 AGGGGGTGACAATTTTCAGAAA 58.078 40.909 0.00 0.00 0.00 2.52
781 829 7.530010 CAATTTTCGTCAATTACTGTCATCCT 58.470 34.615 0.00 0.00 0.00 3.24
783 831 7.504924 TTTTCGTCAATTACTGTCATCCTTT 57.495 32.000 0.00 0.00 0.00 3.11
791 839 3.641434 ACTGTCATCCTTTGGATCTGG 57.359 47.619 0.00 0.00 40.98 3.86
798 846 1.134401 TCCTTTGGATCTGGATCGTGC 60.134 52.381 4.75 0.00 38.69 5.34
854 902 2.921754 GCGAACGTCAGCTAGTTAACAT 59.078 45.455 8.61 0.00 0.00 2.71
856 904 4.721226 GCGAACGTCAGCTAGTTAACATTG 60.721 45.833 8.61 0.76 0.00 2.82
867 915 7.171337 CAGCTAGTTAACATTGCCATTGTTTTT 59.829 33.333 9.94 0.89 38.26 1.94
868 916 8.364142 AGCTAGTTAACATTGCCATTGTTTTTA 58.636 29.630 9.94 1.83 38.26 1.52
869 917 9.150348 GCTAGTTAACATTGCCATTGTTTTTAT 57.850 29.630 9.94 0.00 38.26 1.40
915 963 6.604735 AACGATTCAAAATATCGAAGAGGG 57.395 37.500 11.66 0.00 45.79 4.30
1080 1137 1.703438 CGAGCTCATGGAAGCACAGC 61.703 60.000 15.40 0.98 45.00 4.40
1093 1150 0.607489 GCACAGCACCATCACCTTCT 60.607 55.000 0.00 0.00 0.00 2.85
1452 1512 1.125093 TGTCCATGGACTTCCGGTGT 61.125 55.000 37.92 1.19 44.80 4.16
1651 1717 4.111016 CGCTGGCGTCCGAGTACA 62.111 66.667 6.83 0.00 34.35 2.90
1809 1875 0.532573 TGTCCGAGTTCAGCATCCTC 59.467 55.000 0.00 0.00 0.00 3.71
1812 1878 1.144936 CGAGTTCAGCATCCTCCCC 59.855 63.158 0.00 0.00 0.00 4.81
1827 1893 4.595031 CCCCCGGACTACTACTCC 57.405 66.667 0.73 0.00 0.00 3.85
1829 1895 0.187851 CCCCCGGACTACTACTCCAT 59.812 60.000 0.73 0.00 0.00 3.41
1836 1905 2.022195 GACTACTACTCCATGCCGTCA 58.978 52.381 0.00 0.00 0.00 4.35
2027 2096 0.609957 ACCGTCATCGACAGGGTACA 60.610 55.000 8.48 0.00 39.71 2.90
2053 2122 5.976458 ACAAATGCAAAACTGAAGAAGGAA 58.024 33.333 0.00 0.00 0.00 3.36
2054 2123 6.585416 ACAAATGCAAAACTGAAGAAGGAAT 58.415 32.000 0.00 0.00 0.00 3.01
2055 2124 6.480981 ACAAATGCAAAACTGAAGAAGGAATG 59.519 34.615 0.00 0.00 0.00 2.67
2056 2125 6.409524 AATGCAAAACTGAAGAAGGAATGA 57.590 33.333 0.00 0.00 0.00 2.57
2059 2128 6.275335 TGCAAAACTGAAGAAGGAATGAAAG 58.725 36.000 0.00 0.00 0.00 2.62
2060 2129 6.096705 TGCAAAACTGAAGAAGGAATGAAAGA 59.903 34.615 0.00 0.00 0.00 2.52
2061 2130 7.150640 GCAAAACTGAAGAAGGAATGAAAGAT 58.849 34.615 0.00 0.00 0.00 2.40
2062 2131 7.328005 GCAAAACTGAAGAAGGAATGAAAGATC 59.672 37.037 0.00 0.00 0.00 2.75
2063 2132 8.355169 CAAAACTGAAGAAGGAATGAAAGATCA 58.645 33.333 0.00 0.00 40.57 2.92
2064 2133 8.469309 AAACTGAAGAAGGAATGAAAGATCAA 57.531 30.769 0.00 0.00 39.49 2.57
2065 2134 8.469309 AACTGAAGAAGGAATGAAAGATCAAA 57.531 30.769 0.00 0.00 39.49 2.69
2066 2135 8.469309 ACTGAAGAAGGAATGAAAGATCAAAA 57.531 30.769 0.00 0.00 39.49 2.44
2067 2136 8.355913 ACTGAAGAAGGAATGAAAGATCAAAAC 58.644 33.333 0.00 0.00 39.49 2.43
2068 2137 8.469309 TGAAGAAGGAATGAAAGATCAAAACT 57.531 30.769 0.00 0.00 39.49 2.66
2069 2138 8.355169 TGAAGAAGGAATGAAAGATCAAAACTG 58.645 33.333 0.00 0.00 39.49 3.16
2085 2165 9.305925 GATCAAAACTGAACTGAAAAACTGATT 57.694 29.630 0.00 0.00 0.00 2.57
2277 2359 2.903357 CCAGGAGCTACGTGGCAT 59.097 61.111 26.36 11.00 45.45 4.40
2331 2413 3.649981 AGGCATAGCTTGTCTGGATGTAT 59.350 43.478 0.00 0.00 39.37 2.29
2361 2446 8.681486 TCATTTGTAGATAATACTGCAGCAAT 57.319 30.769 15.27 4.81 34.42 3.56
2574 2677 4.242475 TGACGCTCACGATCAAAGTAAAT 58.758 39.130 0.00 0.00 43.93 1.40
2575 2678 4.091365 TGACGCTCACGATCAAAGTAAATG 59.909 41.667 0.00 0.00 43.93 2.32
2577 2680 3.370978 CGCTCACGATCAAAGTAAATGGT 59.629 43.478 0.00 0.00 43.93 3.55
2589 2693 8.983702 TCAAAGTAAATGGTTTACAGGTTACT 57.016 30.769 13.27 0.00 46.11 2.24
2607 2711 3.802948 ACTGACATCCGGAACTATGAC 57.197 47.619 9.01 2.91 0.00 3.06
2613 2717 5.596772 TGACATCCGGAACTATGACAGATTA 59.403 40.000 9.01 0.00 0.00 1.75
2619 2723 5.527214 CCGGAACTATGACAGATTATTTGCA 59.473 40.000 0.00 0.00 0.00 4.08
2622 2726 6.038603 GGAACTATGACAGATTATTTGCAGCA 59.961 38.462 0.00 0.00 0.00 4.41
2666 2770 4.957759 GCCAAGCGTTTTTATCCTTCTA 57.042 40.909 0.00 0.00 0.00 2.10
2667 2771 4.659088 GCCAAGCGTTTTTATCCTTCTAC 58.341 43.478 0.00 0.00 0.00 2.59
2681 2785 3.131396 CCTTCTACAGAACAGTTGCGTT 58.869 45.455 0.00 0.00 0.00 4.84
2799 2903 3.786368 AGAAAAGCTTCTGAGAGCCTT 57.214 42.857 0.00 0.00 43.74 4.35
2823 2927 2.189594 TGAAGAGTCCTGCATGTTGG 57.810 50.000 0.00 0.00 0.00 3.77
2825 2929 0.610232 AAGAGTCCTGCATGTTGGGC 60.610 55.000 3.07 3.07 0.00 5.36
2835 2939 1.619654 CATGTTGGGCAAAGTCTGGA 58.380 50.000 0.00 0.00 0.00 3.86
2869 2973 1.672030 CGCCTCATCAACACTGGCA 60.672 57.895 0.00 0.00 43.38 4.92
2962 3066 2.035442 GGCTGACTTCAAGGGACGC 61.035 63.158 0.00 0.00 0.00 5.19
2993 3097 1.202348 CGACTGCAGGTACATGTGAGA 59.798 52.381 19.93 0.00 0.00 3.27
3088 3197 5.215160 CACTGGCTGTCAAAAATGTCTTAC 58.785 41.667 0.00 0.00 0.00 2.34
3192 3301 6.036470 GGGTGTTTTTCTCAATAGCTTATGC 58.964 40.000 0.00 0.00 40.05 3.14
3234 3343 5.229423 GCCTTTTATGTGAAATTGCAGTGA 58.771 37.500 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.179129 CTTTGTCATTGATGGCCGGC 60.179 55.000 21.18 21.18 0.00 6.13
110 112 2.285083 GTTTGTCTATGGCATGCGGTA 58.715 47.619 12.44 6.06 0.00 4.02
209 217 6.671614 TTTTATACATGCTAGAAACCGTGG 57.328 37.500 0.00 0.00 0.00 4.94
242 254 1.468520 ACACACACACAGTTGACTTGC 59.531 47.619 0.00 0.00 0.00 4.01
257 269 2.006888 AGCTAACACACACACACACAC 58.993 47.619 0.00 0.00 0.00 3.82
258 270 2.394930 AGCTAACACACACACACACA 57.605 45.000 0.00 0.00 0.00 3.72
261 273 2.479837 TGCTAGCTAACACACACACAC 58.520 47.619 17.23 0.00 0.00 3.82
265 277 3.865745 CAGGTATGCTAGCTAACACACAC 59.134 47.826 17.23 3.11 34.67 3.82
288 300 3.006323 GCTCATGAACTAGATCCGGACAT 59.994 47.826 6.12 0.00 0.00 3.06
290 302 2.288518 GGCTCATGAACTAGATCCGGAC 60.289 54.545 6.12 0.11 0.00 4.79
294 306 9.107177 CAATATAATGGCTCATGAACTAGATCC 57.893 37.037 0.00 0.00 0.00 3.36
360 374 7.211573 AGTCAAAATCAAAATCACAGCAATGA 58.788 30.769 0.00 0.00 0.00 2.57
380 401 6.085555 ACTCGAGTTCATTTGACTAGTCAA 57.914 37.500 30.07 30.07 46.72 3.18
381 402 5.707242 ACTCGAGTTCATTTGACTAGTCA 57.293 39.130 21.74 21.74 37.91 3.41
383 404 7.603651 ACATTACTCGAGTTCATTTGACTAGT 58.396 34.615 25.44 0.00 0.00 2.57
384 405 8.467402 AACATTACTCGAGTTCATTTGACTAG 57.533 34.615 25.44 5.44 0.00 2.57
385 406 7.272731 CGAACATTACTCGAGTTCATTTGACTA 59.727 37.037 25.44 0.00 41.17 2.59
386 407 6.089551 CGAACATTACTCGAGTTCATTTGACT 59.910 38.462 25.44 7.45 41.17 3.41
387 408 6.089016 TCGAACATTACTCGAGTTCATTTGAC 59.911 38.462 25.44 8.10 40.25 3.18
388 409 6.153756 TCGAACATTACTCGAGTTCATTTGA 58.846 36.000 25.44 17.70 40.25 2.69
497 545 3.057876 CCTGAAACGATCGAGATCCCTAG 60.058 52.174 24.34 9.57 34.40 3.02
498 546 2.885266 CCTGAAACGATCGAGATCCCTA 59.115 50.000 24.34 0.68 34.40 3.53
499 547 1.683917 CCTGAAACGATCGAGATCCCT 59.316 52.381 24.34 0.00 34.40 4.20
500 548 1.409427 ACCTGAAACGATCGAGATCCC 59.591 52.381 24.34 5.06 34.40 3.85
501 549 2.873133 ACCTGAAACGATCGAGATCC 57.127 50.000 24.34 6.47 34.40 3.36
502 550 5.764131 AGATAACCTGAAACGATCGAGATC 58.236 41.667 24.34 16.12 34.56 2.75
503 551 5.776173 AGATAACCTGAAACGATCGAGAT 57.224 39.130 24.34 6.96 0.00 2.75
504 552 6.688637 TTAGATAACCTGAAACGATCGAGA 57.311 37.500 24.34 0.97 0.00 4.04
505 553 7.139392 TGATTAGATAACCTGAAACGATCGAG 58.861 38.462 24.34 8.44 0.00 4.04
506 554 7.034685 TGATTAGATAACCTGAAACGATCGA 57.965 36.000 24.34 0.00 0.00 3.59
507 555 7.062371 GGATGATTAGATAACCTGAAACGATCG 59.938 40.741 14.88 14.88 0.00 3.69
508 556 7.062371 CGGATGATTAGATAACCTGAAACGATC 59.938 40.741 0.00 0.00 0.00 3.69
509 557 6.868864 CGGATGATTAGATAACCTGAAACGAT 59.131 38.462 0.00 0.00 0.00 3.73
510 558 6.183360 ACGGATGATTAGATAACCTGAAACGA 60.183 38.462 0.00 0.00 0.00 3.85
511 559 5.983720 ACGGATGATTAGATAACCTGAAACG 59.016 40.000 0.00 0.00 0.00 3.60
512 560 6.761714 ACACGGATGATTAGATAACCTGAAAC 59.238 38.462 0.00 0.00 0.00 2.78
513 561 6.884832 ACACGGATGATTAGATAACCTGAAA 58.115 36.000 0.00 0.00 0.00 2.69
514 562 6.479972 ACACGGATGATTAGATAACCTGAA 57.520 37.500 0.00 0.00 0.00 3.02
515 563 6.127168 ACAACACGGATGATTAGATAACCTGA 60.127 38.462 0.00 0.00 0.00 3.86
516 564 6.049149 ACAACACGGATGATTAGATAACCTG 58.951 40.000 0.00 0.00 0.00 4.00
517 565 6.235231 ACAACACGGATGATTAGATAACCT 57.765 37.500 0.00 0.00 0.00 3.50
518 566 6.315393 ACAACAACACGGATGATTAGATAACC 59.685 38.462 0.00 0.00 0.00 2.85
519 567 7.303634 ACAACAACACGGATGATTAGATAAC 57.696 36.000 0.00 0.00 0.00 1.89
520 568 6.537301 GGACAACAACACGGATGATTAGATAA 59.463 38.462 0.00 0.00 0.00 1.75
521 569 6.046593 GGACAACAACACGGATGATTAGATA 58.953 40.000 0.00 0.00 0.00 1.98
522 570 4.876107 GGACAACAACACGGATGATTAGAT 59.124 41.667 0.00 0.00 0.00 1.98
523 571 4.020573 AGGACAACAACACGGATGATTAGA 60.021 41.667 0.00 0.00 0.00 2.10
524 572 4.253685 AGGACAACAACACGGATGATTAG 58.746 43.478 0.00 0.00 0.00 1.73
525 573 4.280436 AGGACAACAACACGGATGATTA 57.720 40.909 0.00 0.00 0.00 1.75
526 574 3.140325 AGGACAACAACACGGATGATT 57.860 42.857 0.00 0.00 0.00 2.57
527 575 2.859165 AGGACAACAACACGGATGAT 57.141 45.000 0.00 0.00 0.00 2.45
528 576 2.631160 AAGGACAACAACACGGATGA 57.369 45.000 0.00 0.00 0.00 2.92
529 577 3.813166 AGTTAAGGACAACAACACGGATG 59.187 43.478 0.00 0.00 0.00 3.51
530 578 3.813166 CAGTTAAGGACAACAACACGGAT 59.187 43.478 0.00 0.00 0.00 4.18
531 579 3.199677 CAGTTAAGGACAACAACACGGA 58.800 45.455 0.00 0.00 0.00 4.69
532 580 2.940410 ACAGTTAAGGACAACAACACGG 59.060 45.455 0.00 0.00 0.00 4.94
533 581 3.372822 ACACAGTTAAGGACAACAACACG 59.627 43.478 0.00 0.00 0.00 4.49
534 582 4.393680 TGACACAGTTAAGGACAACAACAC 59.606 41.667 0.00 0.00 0.00 3.32
535 583 4.580868 TGACACAGTTAAGGACAACAACA 58.419 39.130 0.00 0.00 0.00 3.33
536 584 5.295787 TCATGACACAGTTAAGGACAACAAC 59.704 40.000 0.00 0.00 0.00 3.32
537 585 5.432645 TCATGACACAGTTAAGGACAACAA 58.567 37.500 0.00 0.00 0.00 2.83
538 586 5.029807 TCATGACACAGTTAAGGACAACA 57.970 39.130 0.00 0.00 0.00 3.33
539 587 6.199393 GTTTCATGACACAGTTAAGGACAAC 58.801 40.000 7.13 0.00 0.00 3.32
540 588 5.007234 CGTTTCATGACACAGTTAAGGACAA 59.993 40.000 12.28 0.00 0.00 3.18
541 589 4.509970 CGTTTCATGACACAGTTAAGGACA 59.490 41.667 12.28 0.00 0.00 4.02
542 590 4.510340 ACGTTTCATGACACAGTTAAGGAC 59.490 41.667 12.28 0.00 0.00 3.85
543 591 4.509970 CACGTTTCATGACACAGTTAAGGA 59.490 41.667 12.28 0.00 0.00 3.36
544 592 4.272504 ACACGTTTCATGACACAGTTAAGG 59.727 41.667 12.28 3.03 0.00 2.69
545 593 5.006261 TCACACGTTTCATGACACAGTTAAG 59.994 40.000 12.28 0.00 0.00 1.85
546 594 4.870991 TCACACGTTTCATGACACAGTTAA 59.129 37.500 12.28 0.00 0.00 2.01
547 595 4.434520 TCACACGTTTCATGACACAGTTA 58.565 39.130 12.28 0.00 0.00 2.24
548 596 3.266636 TCACACGTTTCATGACACAGTT 58.733 40.909 12.28 0.00 0.00 3.16
549 597 2.899976 TCACACGTTTCATGACACAGT 58.100 42.857 12.28 6.98 0.00 3.55
550 598 3.942539 TTCACACGTTTCATGACACAG 57.057 42.857 12.28 6.39 0.00 3.66
551 599 4.686839 TTTTCACACGTTTCATGACACA 57.313 36.364 12.28 0.00 0.00 3.72
552 600 5.092781 ACTTTTTCACACGTTTCATGACAC 58.907 37.500 1.70 1.70 0.00 3.67
553 601 5.303747 ACTTTTTCACACGTTTCATGACA 57.696 34.783 0.00 0.00 0.00 3.58
554 602 4.433304 CGACTTTTTCACACGTTTCATGAC 59.567 41.667 0.00 0.00 0.00 3.06
555 603 4.495019 CCGACTTTTTCACACGTTTCATGA 60.495 41.667 0.00 0.00 0.00 3.07
556 604 3.723764 CCGACTTTTTCACACGTTTCATG 59.276 43.478 0.00 0.00 0.00 3.07
557 605 3.790789 GCCGACTTTTTCACACGTTTCAT 60.791 43.478 0.00 0.00 0.00 2.57
558 606 2.476519 GCCGACTTTTTCACACGTTTCA 60.477 45.455 0.00 0.00 0.00 2.69
559 607 2.106418 GCCGACTTTTTCACACGTTTC 58.894 47.619 0.00 0.00 0.00 2.78
560 608 1.469308 TGCCGACTTTTTCACACGTTT 59.531 42.857 0.00 0.00 0.00 3.60
561 609 1.088306 TGCCGACTTTTTCACACGTT 58.912 45.000 0.00 0.00 0.00 3.99
562 610 1.305201 ATGCCGACTTTTTCACACGT 58.695 45.000 0.00 0.00 0.00 4.49
563 611 2.734606 TCTATGCCGACTTTTTCACACG 59.265 45.455 0.00 0.00 0.00 4.49
564 612 3.424962 GCTCTATGCCGACTTTTTCACAC 60.425 47.826 0.00 0.00 35.15 3.82
565 613 2.742053 GCTCTATGCCGACTTTTTCACA 59.258 45.455 0.00 0.00 35.15 3.58
566 614 2.742053 TGCTCTATGCCGACTTTTTCAC 59.258 45.455 0.00 0.00 42.00 3.18
567 615 3.052455 TGCTCTATGCCGACTTTTTCA 57.948 42.857 0.00 0.00 42.00 2.69
568 616 4.622701 AATGCTCTATGCCGACTTTTTC 57.377 40.909 0.00 0.00 42.00 2.29
569 617 5.391312 AAAATGCTCTATGCCGACTTTTT 57.609 34.783 0.00 0.00 42.00 1.94
570 618 5.648092 ACTAAAATGCTCTATGCCGACTTTT 59.352 36.000 0.00 0.00 42.00 2.27
571 619 5.186198 ACTAAAATGCTCTATGCCGACTTT 58.814 37.500 0.00 0.00 42.00 2.66
572 620 4.770795 ACTAAAATGCTCTATGCCGACTT 58.229 39.130 0.00 0.00 42.00 3.01
573 621 4.372656 GACTAAAATGCTCTATGCCGACT 58.627 43.478 0.00 0.00 42.00 4.18
574 622 3.495001 GGACTAAAATGCTCTATGCCGAC 59.505 47.826 0.00 0.00 42.00 4.79
575 623 3.133901 TGGACTAAAATGCTCTATGCCGA 59.866 43.478 0.00 0.00 42.00 5.54
576 624 3.466836 TGGACTAAAATGCTCTATGCCG 58.533 45.455 0.00 0.00 42.00 5.69
577 625 3.251972 GCTGGACTAAAATGCTCTATGCC 59.748 47.826 0.00 0.00 42.00 4.40
578 626 3.879295 TGCTGGACTAAAATGCTCTATGC 59.121 43.478 0.00 0.00 43.25 3.14
579 627 6.441093 TTTGCTGGACTAAAATGCTCTATG 57.559 37.500 0.00 0.00 0.00 2.23
580 628 7.394359 TCTTTTTGCTGGACTAAAATGCTCTAT 59.606 33.333 0.00 0.00 33.50 1.98
581 629 6.714810 TCTTTTTGCTGGACTAAAATGCTCTA 59.285 34.615 0.00 0.00 33.50 2.43
582 630 5.536161 TCTTTTTGCTGGACTAAAATGCTCT 59.464 36.000 0.00 0.00 33.50 4.09
583 631 5.772521 TCTTTTTGCTGGACTAAAATGCTC 58.227 37.500 0.00 0.00 33.50 4.26
584 632 5.789643 TCTTTTTGCTGGACTAAAATGCT 57.210 34.783 0.00 0.00 33.50 3.79
585 633 7.315890 AGTATCTTTTTGCTGGACTAAAATGC 58.684 34.615 0.00 0.00 33.50 3.56
586 634 9.132521 CAAGTATCTTTTTGCTGGACTAAAATG 57.867 33.333 0.00 0.00 33.50 2.32
587 635 7.814587 GCAAGTATCTTTTTGCTGGACTAAAAT 59.185 33.333 2.22 0.00 44.70 1.82
588 636 7.145323 GCAAGTATCTTTTTGCTGGACTAAAA 58.855 34.615 2.22 0.00 44.70 1.52
589 637 6.294508 GGCAAGTATCTTTTTGCTGGACTAAA 60.295 38.462 8.82 0.00 46.69 1.85
590 638 5.183140 GGCAAGTATCTTTTTGCTGGACTAA 59.817 40.000 8.82 0.00 46.69 2.24
591 639 4.700213 GGCAAGTATCTTTTTGCTGGACTA 59.300 41.667 8.82 0.00 46.69 2.59
592 640 3.507622 GGCAAGTATCTTTTTGCTGGACT 59.492 43.478 8.82 0.00 46.69 3.85
593 641 3.507622 AGGCAAGTATCTTTTTGCTGGAC 59.492 43.478 8.82 0.00 46.69 4.02
594 642 3.758554 GAGGCAAGTATCTTTTTGCTGGA 59.241 43.478 8.82 0.00 46.69 3.86
595 643 3.119352 GGAGGCAAGTATCTTTTTGCTGG 60.119 47.826 8.82 0.00 46.69 4.85
596 644 3.760684 AGGAGGCAAGTATCTTTTTGCTG 59.239 43.478 8.82 0.00 46.69 4.41
597 645 3.760684 CAGGAGGCAAGTATCTTTTTGCT 59.239 43.478 8.82 0.00 46.69 3.91
598 646 3.674410 GCAGGAGGCAAGTATCTTTTTGC 60.674 47.826 0.81 0.81 46.76 3.68
599 647 4.102035 GCAGGAGGCAAGTATCTTTTTG 57.898 45.455 0.00 0.00 43.97 2.44
636 684 0.322322 ACGTTCGCTGGGGATTAACA 59.678 50.000 0.00 0.00 0.00 2.41
638 686 1.002201 TGAACGTTCGCTGGGGATTAA 59.998 47.619 22.48 0.00 0.00 1.40
661 709 0.179132 TCGCAAATGTCATGCATGGC 60.179 50.000 24.40 24.40 44.01 4.40
678 726 3.818121 TTGCCACCCCACGAGTTCG 62.818 63.158 0.00 0.00 46.33 3.95
679 727 0.893727 AATTGCCACCCCACGAGTTC 60.894 55.000 0.00 0.00 0.00 3.01
680 728 0.469144 AAATTGCCACCCCACGAGTT 60.469 50.000 0.00 0.00 0.00 3.01
681 729 0.469144 AAAATTGCCACCCCACGAGT 60.469 50.000 0.00 0.00 0.00 4.18
682 730 1.201414 GTAAAATTGCCACCCCACGAG 59.799 52.381 0.00 0.00 0.00 4.18
683 731 1.202952 AGTAAAATTGCCACCCCACGA 60.203 47.619 0.00 0.00 0.00 4.35
684 732 1.067915 CAGTAAAATTGCCACCCCACG 60.068 52.381 0.00 0.00 0.00 4.94
685 733 1.967779 ACAGTAAAATTGCCACCCCAC 59.032 47.619 0.00 0.00 0.00 4.61
686 734 2.390225 ACAGTAAAATTGCCACCCCA 57.610 45.000 0.00 0.00 0.00 4.96
687 735 3.194755 CCTAACAGTAAAATTGCCACCCC 59.805 47.826 0.00 0.00 0.00 4.95
688 736 3.194755 CCCTAACAGTAAAATTGCCACCC 59.805 47.826 0.00 0.00 0.00 4.61
702 750 4.148838 TGAAAATTGTCACCCCCTAACAG 58.851 43.478 0.00 0.00 0.00 3.16
728 776 9.830975 ATTAAAAGTAAAGAACTGCCATGTTTT 57.169 25.926 0.00 0.00 38.88 2.43
732 780 6.867816 TGCATTAAAAGTAAAGAACTGCCATG 59.132 34.615 0.00 0.00 38.88 3.66
734 782 6.398234 TGCATTAAAAGTAAAGAACTGCCA 57.602 33.333 0.00 0.00 38.88 4.92
735 783 7.889589 ATTGCATTAAAAGTAAAGAACTGCC 57.110 32.000 0.00 0.00 38.88 4.85
751 799 8.293157 TGACAGTAATTGACGAAAATTGCATTA 58.707 29.630 14.21 1.96 35.37 1.90
781 829 0.461870 CCGCACGATCCAGATCCAAA 60.462 55.000 2.11 0.00 34.40 3.28
783 831 2.814604 CCGCACGATCCAGATCCA 59.185 61.111 2.11 0.00 34.40 3.41
791 839 2.279120 CTCCAGAGCCGCACGATC 60.279 66.667 0.00 0.00 0.00 3.69
798 846 3.473647 TGGATGCCTCCAGAGCCG 61.474 66.667 6.63 0.00 46.95 5.52
831 879 2.539346 TAACTAGCTGACGTTCGCTC 57.461 50.000 14.62 0.00 37.68 5.03
898 946 3.938963 GTGTGCCCTCTTCGATATTTTGA 59.061 43.478 0.00 0.00 0.00 2.69
1058 1115 1.086634 GTGCTTCCATGAGCTCGGTC 61.087 60.000 9.64 0.74 43.11 4.79
1080 1137 2.354259 GAGCTGAAGAAGGTGATGGTG 58.646 52.381 0.00 0.00 36.52 4.17
1093 1150 1.683917 GATTAGCCTCGAGGAGCTGAA 59.316 52.381 35.69 18.96 40.28 3.02
1200 1260 2.813908 GCCAGGTACTCCGCGTTG 60.814 66.667 4.92 0.00 34.60 4.10
1644 1710 1.056464 CGTTCGTCACCGTGTACTCG 61.056 60.000 10.28 10.28 35.01 4.18
1812 1878 0.674534 GCATGGAGTAGTAGTCCGGG 59.325 60.000 17.51 13.16 40.67 5.73
1825 1891 3.860605 CGGGGATGACGGCATGGA 61.861 66.667 9.52 0.00 34.11 3.41
1827 1893 4.854924 TGCGGGGATGACGGCATG 62.855 66.667 9.52 0.00 41.00 4.06
2027 2096 5.987347 CCTTCTTCAGTTTTGCATTTGTCAT 59.013 36.000 0.00 0.00 0.00 3.06
2053 2122 9.874205 TTTTTCAGTTCAGTTTTGATCTTTCAT 57.126 25.926 0.00 0.00 32.36 2.57
2054 2123 9.139174 GTTTTTCAGTTCAGTTTTGATCTTTCA 57.861 29.630 0.00 0.00 32.36 2.69
2055 2124 9.358872 AGTTTTTCAGTTCAGTTTTGATCTTTC 57.641 29.630 0.00 0.00 32.36 2.62
2056 2125 9.143631 CAGTTTTTCAGTTCAGTTTTGATCTTT 57.856 29.630 0.00 0.00 32.36 2.52
2059 2128 8.862550 ATCAGTTTTTCAGTTCAGTTTTGATC 57.137 30.769 0.00 0.00 32.27 2.92
2149 2231 0.331954 TACAGCTCCTCGAACCCTCT 59.668 55.000 0.00 0.00 0.00 3.69
2262 2344 2.735772 CCCATGCCACGTAGCTCCT 61.736 63.158 7.64 0.00 0.00 3.69
2331 2413 9.264719 CTGCAGTATTATCTACAAATGATGTGA 57.735 33.333 5.25 0.00 43.77 3.58
2403 2493 2.170187 CTGCAAAGCCTACTGATCTCCT 59.830 50.000 0.00 0.00 0.00 3.69
2479 2569 0.469494 TCTGTTGAGCTGAAGGTGCA 59.531 50.000 0.00 0.00 0.00 4.57
2574 2677 4.561938 CGGATGTCAGTAACCTGTAAACCA 60.562 45.833 0.00 0.00 39.82 3.67
2575 2678 3.930848 CGGATGTCAGTAACCTGTAAACC 59.069 47.826 0.00 0.00 39.82 3.27
2577 2680 3.833650 TCCGGATGTCAGTAACCTGTAAA 59.166 43.478 0.00 0.00 39.82 2.01
2589 2693 3.361786 TCTGTCATAGTTCCGGATGTCA 58.638 45.455 4.15 3.61 0.00 3.58
2590 2694 4.592485 ATCTGTCATAGTTCCGGATGTC 57.408 45.455 4.15 0.00 0.00 3.06
2594 2698 5.758296 GCAAATAATCTGTCATAGTTCCGGA 59.242 40.000 0.00 0.00 0.00 5.14
2596 2700 6.603237 TGCAAATAATCTGTCATAGTTCCG 57.397 37.500 0.00 0.00 0.00 4.30
2607 2711 7.252708 TGTATCTTGTTGCTGCAAATAATCTG 58.747 34.615 17.80 4.68 0.00 2.90
2613 2717 5.199024 TGTTGTATCTTGTTGCTGCAAAT 57.801 34.783 17.80 9.47 0.00 2.32
2619 2723 5.356751 TGTTCTGTTGTTGTATCTTGTTGCT 59.643 36.000 0.00 0.00 0.00 3.91
2622 2726 5.729454 GCGTGTTCTGTTGTTGTATCTTGTT 60.729 40.000 0.00 0.00 0.00 2.83
2681 2785 8.664669 TGGTAATAATGTATATGCTGGAGAGA 57.335 34.615 0.00 0.00 0.00 3.10
2731 2835 5.539955 ACATGTTTCAATTTGTAAGGAGGCT 59.460 36.000 0.00 0.00 0.00 4.58
2799 2903 2.158769 ACATGCAGGACTCTTCAACACA 60.159 45.455 4.84 0.00 0.00 3.72
2823 2927 3.967715 GTCGGTCCAGACTTTGCC 58.032 61.111 6.61 0.00 38.09 4.52
2835 2939 4.052229 CGAGCGGTTCCAGTCGGT 62.052 66.667 0.00 0.00 39.89 4.69
2912 3016 3.311596 CGGGATAATTCTTGGGTCGTTTC 59.688 47.826 0.00 0.00 0.00 2.78
2962 3066 0.710567 CTGCAGTCGCGTTCAAGTAG 59.289 55.000 5.77 3.56 42.97 2.57
2993 3097 2.859538 CGCCGCATGCTTTAATCATTTT 59.140 40.909 17.13 0.00 38.05 1.82
3069 3173 4.483476 ACGTAAGACATTTTTGACAGCC 57.517 40.909 0.00 0.00 43.62 4.85
3070 3174 6.470877 TCAAAACGTAAGACATTTTTGACAGC 59.529 34.615 4.18 0.00 41.01 4.40
3071 3175 7.962934 TCAAAACGTAAGACATTTTTGACAG 57.037 32.000 4.18 0.00 41.01 3.51
3072 3176 9.440784 GTATCAAAACGTAAGACATTTTTGACA 57.559 29.630 9.29 0.00 45.74 3.58
3073 3177 8.615585 CGTATCAAAACGTAAGACATTTTTGAC 58.384 33.333 9.29 0.36 45.74 3.18
3075 3179 7.799447 TCCGTATCAAAACGTAAGACATTTTTG 59.201 33.333 0.00 0.00 41.27 2.44
3088 3197 2.667473 ACTCCCTCCGTATCAAAACG 57.333 50.000 0.00 0.00 42.49 3.60
3192 3301 5.997384 AGGCCCTATAGTTAATTACCGAG 57.003 43.478 0.00 0.00 0.00 4.63
3204 3313 7.147976 GCAATTTCACATAAAAGGCCCTATAG 58.852 38.462 0.00 0.00 0.00 1.31
3276 3385 9.717942 ATTAAGCTTATCCAGAGACATATCAAC 57.282 33.333 7.08 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.