Multiple sequence alignment - TraesCS7A01G299800

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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 TraesCS7A01G299800 chr7A 100.000 2936 0 0 1 2936 412892948 412895883 0.000000e+00 5422
1 TraesCS7A01G299800 chr7A 85.526 304 20 13 578 858 289141598 289141900 2.210000e-76 296
2 TraesCS7A01G299800 chr7A 86.643 277 13 6 576 830 435351120 435351394 4.790000e-73 285
3 TraesCS7A01G299800 chr7A 84.588 279 36 6 581 855 29544790 29545065 1.340000e-68 270
4 TraesCS7A01G299800 chr7D 95.554 2047 59 9 895 2936 369283717 369281698 0.000000e+00 3247
5 TraesCS7A01G299800 chr7B 94.734 2089 77 10 856 2936 314930736 314928673 0.000000e+00 3217
6 TraesCS7A01G299800 chr7B 76.944 373 54 20 112 459 740524327 740523962 1.800000e-42 183
7 TraesCS7A01G299800 chr6B 86.486 518 48 8 3 499 124993418 124992902 1.540000e-152 549
8 TraesCS7A01G299800 chr4B 86.550 513 47 7 9 499 416117954 416118466 1.990000e-151 545
9 TraesCS7A01G299800 chr1B 80.989 526 68 18 3 499 629809056 629809578 3.550000e-104 388
10 TraesCS7A01G299800 chr5A 87.107 318 15 4 576 868 94080518 94080834 1.300000e-88 337
11 TraesCS7A01G299800 chr5A 86.486 296 17 8 582 855 553144370 553144076 1.320000e-78 303
12 TraesCS7A01G299800 chr5A 85.714 301 20 8 583 861 604748505 604748206 2.210000e-76 296
13 TraesCS7A01G299800 chr5A 81.908 304 20 6 579 848 488311168 488311470 1.060000e-54 224
14 TraesCS7A01G299800 chr5A 93.069 101 7 0 578 678 582978448 582978548 6.560000e-32 148
15 TraesCS7A01G299800 chr1A 87.171 304 17 6 576 857 28615957 28616260 2.820000e-85 326
16 TraesCS7A01G299800 chr1A 84.965 286 37 5 581 861 309084529 309084813 4.790000e-73 285
17 TraesCS7A01G299800 chr3A 86.435 317 18 9 568 862 57085377 57085064 1.010000e-84 324
18 TraesCS7A01G299800 chr6A 86.824 296 17 2 582 855 602490120 602489825 7.900000e-81 311
19 TraesCS7A01G299800 chrUn 85.902 305 21 5 575 857 32095228 32095532 3.680000e-79 305
20 TraesCS7A01G299800 chr5B 83.188 345 44 7 1 342 272165311 272165644 1.320000e-78 303
21 TraesCS7A01G299800 chr2A 86.093 302 19 3 579 858 146749627 146749327 1.320000e-78 303
22 TraesCS7A01G299800 chr1D 89.815 216 18 3 3 214 246672509 246672294 1.040000e-69 274


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 TraesCS7A01G299800 chr7A 412892948 412895883 2935 False 5422 5422 100.000 1 2936 1 chr7A.!!$F3 2935
1 TraesCS7A01G299800 chr7D 369281698 369283717 2019 True 3247 3247 95.554 895 2936 1 chr7D.!!$R1 2041
2 TraesCS7A01G299800 chr7B 314928673 314930736 2063 True 3217 3217 94.734 856 2936 1 chr7B.!!$R1 2080
3 TraesCS7A01G299800 chr6B 124992902 124993418 516 True 549 549 86.486 3 499 1 chr6B.!!$R1 496
4 TraesCS7A01G299800 chr4B 416117954 416118466 512 False 545 545 86.550 9 499 1 chr4B.!!$F1 490
5 TraesCS7A01G299800 chr1B 629809056 629809578 522 False 388 388 80.989 3 499 1 chr1B.!!$F1 496

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
667 697 0.031616 TTTGAGCCCCTTTGGTTGGT 60.032 50.000 0.00 0.0 36.04 3.67 F
672 702 0.113580 GCCCCTTTGGTTGGTAGGAA 59.886 55.000 0.00 0.0 36.04 3.36 F
673 703 1.273041 GCCCCTTTGGTTGGTAGGAAT 60.273 52.381 0.00 0.0 36.04 3.01 F
867 897 2.041755 AGGAGGCCTAAGTTTCCTTTGG 59.958 50.000 4.42 0.0 43.80 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 1769 0.892358 CAGCATTGCCACCTGTGTCT 60.892 55.000 4.70 0.00 0.00 3.41 R
1875 1916 1.133181 TGACCCTCTTCATGCACCCA 61.133 55.000 0.00 0.00 0.00 4.51 R
1896 1937 1.502231 GAAAGTCACGCTTGAGCTCA 58.498 50.000 13.74 13.74 37.52 4.26 R
2106 2147 2.025155 TGCCGTTTAGCTTCACCAAAA 58.975 42.857 0.00 0.00 0.00 2.44 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
91 96 5.976458 TCAACCAACATGAGAAAAAGCTTT 58.024 33.333 5.69 5.69 0.00 3.51
94 99 8.203485 TCAACCAACATGAGAAAAAGCTTTAAT 58.797 29.630 13.10 4.50 0.00 1.40
101 107 6.478512 TGAGAAAAAGCTTTAATTGGGTGT 57.521 33.333 13.10 0.00 0.00 4.16
123 129 3.503363 GGCGGCACTGAGTGATGC 61.503 66.667 18.18 17.83 41.29 3.91
198 205 0.317854 CTGCAACGACAGAGACGTCA 60.318 55.000 19.50 0.00 43.16 4.35
270 296 1.666553 GCGTGATGTCGACCACCAA 60.667 57.895 14.12 0.00 0.00 3.67
401 427 1.153289 GACTGCTCCGGATGCACAT 60.153 57.895 20.28 13.43 36.37 3.21
423 452 6.831769 CATGCGTCATGTTTCTTTTACTAGT 58.168 36.000 0.00 0.00 37.12 2.57
434 463 9.386010 TGTTTCTTTTACTAGTGAAGCAGTTTA 57.614 29.630 5.39 0.00 0.00 2.01
459 489 1.221840 GAAGGAATCCTGCGGCTGA 59.778 57.895 0.90 1.77 32.13 4.26
493 523 2.680693 TACGTGCGCTGTTTGACCGA 62.681 55.000 9.73 0.00 0.00 4.69
503 533 2.395651 TTTGACCGACCAAACACCG 58.604 52.632 0.00 0.00 31.73 4.94
505 535 3.351416 GACCGACCAAACACCGGC 61.351 66.667 0.00 0.00 46.54 6.13
509 539 4.025401 GACCAAACACCGGCGCAG 62.025 66.667 10.83 4.65 0.00 5.18
510 540 4.555709 ACCAAACACCGGCGCAGA 62.556 61.111 10.83 0.00 0.00 4.26
511 541 3.726517 CCAAACACCGGCGCAGAG 61.727 66.667 10.83 3.85 0.00 3.35
512 542 2.972505 CAAACACCGGCGCAGAGT 60.973 61.111 10.83 4.58 0.00 3.24
513 543 1.666553 CAAACACCGGCGCAGAGTA 60.667 57.895 10.83 0.00 0.00 2.59
514 544 1.374252 AAACACCGGCGCAGAGTAG 60.374 57.895 10.83 0.00 0.00 2.57
515 545 3.934391 AACACCGGCGCAGAGTAGC 62.934 63.158 10.83 0.00 0.00 3.58
521 551 3.787001 GCGCAGAGTAGCCCCCTT 61.787 66.667 0.30 0.00 0.00 3.95
522 552 2.990479 CGCAGAGTAGCCCCCTTT 59.010 61.111 0.00 0.00 0.00 3.11
523 553 1.153349 CGCAGAGTAGCCCCCTTTC 60.153 63.158 0.00 0.00 0.00 2.62
524 554 1.899437 CGCAGAGTAGCCCCCTTTCA 61.899 60.000 0.00 0.00 0.00 2.69
525 555 0.548510 GCAGAGTAGCCCCCTTTCAT 59.451 55.000 0.00 0.00 0.00 2.57
526 556 1.768870 GCAGAGTAGCCCCCTTTCATA 59.231 52.381 0.00 0.00 0.00 2.15
527 557 2.373502 GCAGAGTAGCCCCCTTTCATAT 59.626 50.000 0.00 0.00 0.00 1.78
528 558 3.181439 GCAGAGTAGCCCCCTTTCATATT 60.181 47.826 0.00 0.00 0.00 1.28
529 559 4.646572 CAGAGTAGCCCCCTTTCATATTC 58.353 47.826 0.00 0.00 0.00 1.75
530 560 3.653352 AGAGTAGCCCCCTTTCATATTCC 59.347 47.826 0.00 0.00 0.00 3.01
531 561 2.716969 AGTAGCCCCCTTTCATATTCCC 59.283 50.000 0.00 0.00 0.00 3.97
532 562 0.478507 AGCCCCCTTTCATATTCCCG 59.521 55.000 0.00 0.00 0.00 5.14
533 563 0.185175 GCCCCCTTTCATATTCCCGT 59.815 55.000 0.00 0.00 0.00 5.28
534 564 1.981256 CCCCCTTTCATATTCCCGTG 58.019 55.000 0.00 0.00 0.00 4.94
535 565 1.478654 CCCCCTTTCATATTCCCGTGG 60.479 57.143 0.00 0.00 0.00 4.94
536 566 1.214424 CCCCTTTCATATTCCCGTGGT 59.786 52.381 0.00 0.00 0.00 4.16
537 567 2.440253 CCCCTTTCATATTCCCGTGGTA 59.560 50.000 0.00 0.00 0.00 3.25
538 568 3.117813 CCCCTTTCATATTCCCGTGGTAA 60.118 47.826 0.00 0.00 0.00 2.85
539 569 3.881089 CCCTTTCATATTCCCGTGGTAAC 59.119 47.826 0.00 0.00 0.00 2.50
550 580 4.753542 TGGTAACGCATGGGCATT 57.246 50.000 10.10 0.09 41.24 3.56
551 581 2.487918 TGGTAACGCATGGGCATTC 58.512 52.632 10.10 0.00 41.24 2.67
552 582 0.322906 TGGTAACGCATGGGCATTCA 60.323 50.000 10.10 1.25 41.24 2.57
553 583 0.814457 GGTAACGCATGGGCATTCAA 59.186 50.000 10.10 0.00 41.24 2.69
554 584 1.469079 GGTAACGCATGGGCATTCAAC 60.469 52.381 10.10 0.00 41.24 3.18
555 585 1.472480 GTAACGCATGGGCATTCAACT 59.528 47.619 10.10 0.00 41.24 3.16
556 586 1.832883 AACGCATGGGCATTCAACTA 58.167 45.000 10.10 0.00 41.24 2.24
557 587 1.382522 ACGCATGGGCATTCAACTAG 58.617 50.000 10.10 0.00 41.24 2.57
558 588 1.340017 ACGCATGGGCATTCAACTAGT 60.340 47.619 10.10 0.00 41.24 2.57
559 589 1.064505 CGCATGGGCATTCAACTAGTG 59.935 52.381 0.00 0.00 41.24 2.74
560 590 2.368439 GCATGGGCATTCAACTAGTGA 58.632 47.619 0.00 0.00 40.72 3.41
561 591 2.357009 GCATGGGCATTCAACTAGTGAG 59.643 50.000 0.00 0.00 37.51 3.51
562 592 3.614092 CATGGGCATTCAACTAGTGAGT 58.386 45.455 0.00 0.00 37.61 3.41
563 593 3.334583 TGGGCATTCAACTAGTGAGTC 57.665 47.619 0.00 0.00 37.61 3.36
564 594 2.906389 TGGGCATTCAACTAGTGAGTCT 59.094 45.455 0.00 0.00 37.61 3.24
565 595 3.265791 GGGCATTCAACTAGTGAGTCTG 58.734 50.000 0.00 0.00 37.61 3.51
566 596 3.265791 GGCATTCAACTAGTGAGTCTGG 58.734 50.000 0.00 0.00 37.61 3.86
567 597 3.307059 GGCATTCAACTAGTGAGTCTGGT 60.307 47.826 0.00 0.00 39.55 4.00
568 598 3.681897 GCATTCAACTAGTGAGTCTGGTG 59.318 47.826 0.00 0.00 37.90 4.17
569 599 4.800914 GCATTCAACTAGTGAGTCTGGTGT 60.801 45.833 0.00 0.00 37.90 4.16
570 600 5.566826 GCATTCAACTAGTGAGTCTGGTGTA 60.567 44.000 0.00 0.00 37.90 2.90
571 601 5.707242 TTCAACTAGTGAGTCTGGTGTAG 57.293 43.478 0.00 0.00 37.90 2.74
572 602 4.981812 TCAACTAGTGAGTCTGGTGTAGA 58.018 43.478 0.00 0.00 37.90 2.59
573 603 5.571285 TCAACTAGTGAGTCTGGTGTAGAT 58.429 41.667 0.00 0.00 37.90 1.98
574 604 6.718294 TCAACTAGTGAGTCTGGTGTAGATA 58.282 40.000 0.00 0.00 37.90 1.98
575 605 6.598457 TCAACTAGTGAGTCTGGTGTAGATAC 59.402 42.308 0.00 0.00 37.90 2.24
576 606 6.316280 ACTAGTGAGTCTGGTGTAGATACT 57.684 41.667 0.00 0.00 36.52 2.12
577 607 6.350906 ACTAGTGAGTCTGGTGTAGATACTC 58.649 44.000 0.00 0.00 36.52 2.59
578 608 5.444744 AGTGAGTCTGGTGTAGATACTCT 57.555 43.478 0.00 0.00 37.83 3.24
579 609 6.563037 AGTGAGTCTGGTGTAGATACTCTA 57.437 41.667 0.00 0.00 37.83 2.43
580 610 6.959904 AGTGAGTCTGGTGTAGATACTCTAA 58.040 40.000 0.00 0.00 37.83 2.10
581 611 7.051623 AGTGAGTCTGGTGTAGATACTCTAAG 58.948 42.308 0.00 0.00 37.83 2.18
582 612 6.261381 GTGAGTCTGGTGTAGATACTCTAAGG 59.739 46.154 0.00 0.00 37.83 2.69
583 613 5.134661 AGTCTGGTGTAGATACTCTAAGGC 58.865 45.833 0.00 0.00 37.83 4.35
584 614 4.278919 GTCTGGTGTAGATACTCTAAGGCC 59.721 50.000 0.00 0.00 37.83 5.19
585 615 4.168283 TCTGGTGTAGATACTCTAAGGCCT 59.832 45.833 0.00 0.00 29.58 5.19
586 616 4.471548 TGGTGTAGATACTCTAAGGCCTC 58.528 47.826 5.23 0.00 29.58 4.70
587 617 3.827876 GGTGTAGATACTCTAAGGCCTCC 59.172 52.174 5.23 0.00 29.58 4.30
588 618 4.448054 GGTGTAGATACTCTAAGGCCTCCT 60.448 50.000 5.23 0.00 29.58 3.69
589 619 5.141910 GTGTAGATACTCTAAGGCCTCCTT 58.858 45.833 5.23 3.40 46.63 3.36
590 620 5.599242 GTGTAGATACTCTAAGGCCTCCTTT 59.401 44.000 5.23 0.00 41.69 3.11
591 621 5.598830 TGTAGATACTCTAAGGCCTCCTTTG 59.401 44.000 5.23 2.24 41.69 2.77
592 622 3.970640 AGATACTCTAAGGCCTCCTTTGG 59.029 47.826 5.23 0.00 41.69 3.28
593 623 2.046280 ACTCTAAGGCCTCCTTTGGT 57.954 50.000 5.23 0.00 41.69 3.67
594 624 2.349445 ACTCTAAGGCCTCCTTTGGTT 58.651 47.619 5.23 0.00 41.69 3.67
595 625 2.716969 ACTCTAAGGCCTCCTTTGGTTT 59.283 45.455 5.23 0.00 41.69 3.27
596 626 3.084786 CTCTAAGGCCTCCTTTGGTTTG 58.915 50.000 5.23 0.00 41.69 2.93
597 627 2.445525 TCTAAGGCCTCCTTTGGTTTGT 59.554 45.455 5.23 0.00 41.69 2.83
598 628 3.653836 TCTAAGGCCTCCTTTGGTTTGTA 59.346 43.478 5.23 0.00 41.69 2.41
599 629 2.586648 AGGCCTCCTTTGGTTTGTAG 57.413 50.000 0.00 0.00 0.00 2.74
600 630 1.075536 AGGCCTCCTTTGGTTTGTAGG 59.924 52.381 0.00 0.00 0.00 3.18
601 631 1.074889 GGCCTCCTTTGGTTTGTAGGA 59.925 52.381 0.00 0.00 36.65 2.94
602 632 2.490168 GGCCTCCTTTGGTTTGTAGGAA 60.490 50.000 0.00 0.00 37.61 3.36
603 633 3.431415 GCCTCCTTTGGTTTGTAGGAAT 58.569 45.455 0.00 0.00 37.61 3.01
604 634 3.193479 GCCTCCTTTGGTTTGTAGGAATG 59.807 47.826 0.00 0.00 37.61 2.67
605 635 4.407365 CCTCCTTTGGTTTGTAGGAATGT 58.593 43.478 0.00 0.00 37.61 2.71
606 636 4.459337 CCTCCTTTGGTTTGTAGGAATGTC 59.541 45.833 0.00 0.00 37.61 3.06
607 637 5.055265 TCCTTTGGTTTGTAGGAATGTCA 57.945 39.130 0.00 0.00 35.20 3.58
608 638 5.640147 TCCTTTGGTTTGTAGGAATGTCAT 58.360 37.500 0.00 0.00 35.20 3.06
609 639 6.785076 TCCTTTGGTTTGTAGGAATGTCATA 58.215 36.000 0.00 0.00 35.20 2.15
610 640 6.884295 TCCTTTGGTTTGTAGGAATGTCATAG 59.116 38.462 0.00 0.00 35.20 2.23
611 641 6.095440 CCTTTGGTTTGTAGGAATGTCATAGG 59.905 42.308 0.00 0.00 0.00 2.57
612 642 6.381498 TTGGTTTGTAGGAATGTCATAGGA 57.619 37.500 0.00 0.00 0.00 2.94
613 643 6.575244 TGGTTTGTAGGAATGTCATAGGAT 57.425 37.500 0.00 0.00 0.00 3.24
614 644 6.969043 TGGTTTGTAGGAATGTCATAGGATT 58.031 36.000 0.00 0.00 0.00 3.01
615 645 7.410174 TGGTTTGTAGGAATGTCATAGGATTT 58.590 34.615 0.00 0.00 0.00 2.17
616 646 7.556275 TGGTTTGTAGGAATGTCATAGGATTTC 59.444 37.037 0.00 0.00 0.00 2.17
617 647 7.775561 GGTTTGTAGGAATGTCATAGGATTTCT 59.224 37.037 3.93 0.00 0.00 2.52
618 648 9.832445 GTTTGTAGGAATGTCATAGGATTTCTA 57.168 33.333 3.93 0.00 0.00 2.10
619 649 9.832445 TTTGTAGGAATGTCATAGGATTTCTAC 57.168 33.333 0.00 0.00 0.00 2.59
620 650 8.547481 TGTAGGAATGTCATAGGATTTCTACA 57.453 34.615 7.49 7.49 0.00 2.74
621 651 9.159254 TGTAGGAATGTCATAGGATTTCTACAT 57.841 33.333 7.49 0.00 0.00 2.29
622 652 9.429359 GTAGGAATGTCATAGGATTTCTACATG 57.571 37.037 0.00 0.00 0.00 3.21
623 653 8.267620 AGGAATGTCATAGGATTTCTACATGA 57.732 34.615 0.00 0.00 0.00 3.07
624 654 8.888419 AGGAATGTCATAGGATTTCTACATGAT 58.112 33.333 0.00 0.00 0.00 2.45
655 685 9.705290 TTTGTATAGAAAAATTTCCTTTGAGCC 57.295 29.630 2.37 0.00 37.92 4.70
656 686 7.836842 TGTATAGAAAAATTTCCTTTGAGCCC 58.163 34.615 2.37 0.00 37.92 5.19
657 687 4.623932 AGAAAAATTTCCTTTGAGCCCC 57.376 40.909 2.37 0.00 37.92 5.80
658 688 4.234550 AGAAAAATTTCCTTTGAGCCCCT 58.765 39.130 2.37 0.00 37.92 4.79
659 689 4.660303 AGAAAAATTTCCTTTGAGCCCCTT 59.340 37.500 2.37 0.00 37.92 3.95
660 690 5.132648 AGAAAAATTTCCTTTGAGCCCCTTT 59.867 36.000 2.37 0.00 37.92 3.11
661 691 4.356405 AAATTTCCTTTGAGCCCCTTTG 57.644 40.909 0.00 0.00 0.00 2.77
662 692 1.715785 TTTCCTTTGAGCCCCTTTGG 58.284 50.000 0.00 0.00 37.09 3.28
663 693 0.560688 TTCCTTTGAGCCCCTTTGGT 59.439 50.000 0.00 0.00 36.04 3.67
664 694 0.560688 TCCTTTGAGCCCCTTTGGTT 59.439 50.000 0.00 0.00 36.04 3.67
665 695 0.681175 CCTTTGAGCCCCTTTGGTTG 59.319 55.000 0.00 0.00 36.04 3.77
666 696 0.681175 CTTTGAGCCCCTTTGGTTGG 59.319 55.000 0.00 0.00 36.04 3.77
667 697 0.031616 TTTGAGCCCCTTTGGTTGGT 60.032 50.000 0.00 0.00 36.04 3.67
668 698 0.854218 TTGAGCCCCTTTGGTTGGTA 59.146 50.000 0.00 0.00 36.04 3.25
669 699 0.404040 TGAGCCCCTTTGGTTGGTAG 59.596 55.000 0.00 0.00 36.04 3.18
670 700 0.323451 GAGCCCCTTTGGTTGGTAGG 60.323 60.000 0.00 0.00 36.04 3.18
671 701 0.774491 AGCCCCTTTGGTTGGTAGGA 60.774 55.000 0.00 0.00 36.04 2.94
672 702 0.113580 GCCCCTTTGGTTGGTAGGAA 59.886 55.000 0.00 0.00 36.04 3.36
673 703 1.273041 GCCCCTTTGGTTGGTAGGAAT 60.273 52.381 0.00 0.00 36.04 3.01
674 704 2.456577 CCCCTTTGGTTGGTAGGAATG 58.543 52.381 0.00 0.00 0.00 2.67
675 705 2.456577 CCCTTTGGTTGGTAGGAATGG 58.543 52.381 0.00 0.00 0.00 3.16
676 706 2.042433 CCCTTTGGTTGGTAGGAATGGA 59.958 50.000 0.00 0.00 0.00 3.41
677 707 3.309848 CCCTTTGGTTGGTAGGAATGGAT 60.310 47.826 0.00 0.00 0.00 3.41
678 708 4.079443 CCCTTTGGTTGGTAGGAATGGATA 60.079 45.833 0.00 0.00 0.00 2.59
679 709 5.133221 CCTTTGGTTGGTAGGAATGGATAG 58.867 45.833 0.00 0.00 0.00 2.08
680 710 4.788925 TTGGTTGGTAGGAATGGATAGG 57.211 45.455 0.00 0.00 0.00 2.57
681 711 4.015617 TGGTTGGTAGGAATGGATAGGA 57.984 45.455 0.00 0.00 0.00 2.94
682 712 4.376223 TGGTTGGTAGGAATGGATAGGAA 58.624 43.478 0.00 0.00 0.00 3.36
683 713 4.981647 TGGTTGGTAGGAATGGATAGGAAT 59.018 41.667 0.00 0.00 0.00 3.01
684 714 5.073144 TGGTTGGTAGGAATGGATAGGAATC 59.927 44.000 0.00 0.00 0.00 2.52
685 715 5.073144 GGTTGGTAGGAATGGATAGGAATCA 59.927 44.000 0.00 0.00 33.41 2.57
686 716 6.410388 GGTTGGTAGGAATGGATAGGAATCAA 60.410 42.308 0.00 0.00 33.41 2.57
687 717 7.234355 GTTGGTAGGAATGGATAGGAATCAAT 58.766 38.462 0.00 0.00 33.41 2.57
688 718 7.406620 TGGTAGGAATGGATAGGAATCAATT 57.593 36.000 0.00 0.00 38.29 2.32
689 719 7.461749 TGGTAGGAATGGATAGGAATCAATTC 58.538 38.462 6.86 6.86 46.00 2.17
690 720 7.295672 TGGTAGGAATGGATAGGAATCAATTCT 59.704 37.037 12.83 4.92 45.98 2.40
691 721 8.166726 GGTAGGAATGGATAGGAATCAATTCTT 58.833 37.037 12.83 9.32 45.98 2.52
692 722 9.225436 GTAGGAATGGATAGGAATCAATTCTTC 57.775 37.037 12.83 1.54 45.98 2.87
693 723 7.819500 AGGAATGGATAGGAATCAATTCTTCA 58.180 34.615 12.83 0.00 45.98 3.02
694 724 7.723172 AGGAATGGATAGGAATCAATTCTTCAC 59.277 37.037 12.83 0.74 45.98 3.18
695 725 7.503566 GGAATGGATAGGAATCAATTCTTCACA 59.496 37.037 12.83 0.00 45.98 3.58
696 726 9.075678 GAATGGATAGGAATCAATTCTTCACAT 57.924 33.333 7.83 0.00 44.40 3.21
697 727 9.430399 AATGGATAGGAATCAATTCTTCACATT 57.570 29.630 2.96 4.89 31.11 2.71
698 728 8.827832 TGGATAGGAATCAATTCTTCACATTT 57.172 30.769 2.96 0.00 37.00 2.32
699 729 9.258629 TGGATAGGAATCAATTCTTCACATTTT 57.741 29.630 2.96 0.00 37.00 1.82
704 734 8.964772 AGGAATCAATTCTTCACATTTTAGAGG 58.035 33.333 2.96 0.00 37.00 3.69
705 735 8.960591 GGAATCAATTCTTCACATTTTAGAGGA 58.039 33.333 2.96 0.00 37.00 3.71
759 789 8.929260 ATTTCTATCCTATGCATCAAATGACA 57.071 30.769 0.19 0.00 0.00 3.58
760 790 8.929260 TTTCTATCCTATGCATCAAATGACAT 57.071 30.769 0.19 0.00 33.67 3.06
761 791 8.557592 TTCTATCCTATGCATCAAATGACATC 57.442 34.615 0.19 0.00 32.25 3.06
762 792 7.914859 TCTATCCTATGCATCAAATGACATCT 58.085 34.615 0.19 0.00 32.25 2.90
763 793 8.039538 TCTATCCTATGCATCAAATGACATCTC 58.960 37.037 0.19 0.00 32.25 2.75
764 794 6.183810 TCCTATGCATCAAATGACATCTCT 57.816 37.500 0.19 0.00 32.25 3.10
765 795 6.598503 TCCTATGCATCAAATGACATCTCTT 58.401 36.000 0.19 0.00 32.25 2.85
766 796 7.058525 TCCTATGCATCAAATGACATCTCTTT 58.941 34.615 0.19 0.00 32.25 2.52
767 797 7.228108 TCCTATGCATCAAATGACATCTCTTTC 59.772 37.037 0.19 0.00 32.25 2.62
768 798 7.228906 CCTATGCATCAAATGACATCTCTTTCT 59.771 37.037 0.19 0.00 32.25 2.52
769 799 6.432607 TGCATCAAATGACATCTCTTTCTC 57.567 37.500 0.00 0.00 0.00 2.87
770 800 6.178324 TGCATCAAATGACATCTCTTTCTCT 58.822 36.000 0.00 0.00 0.00 3.10
771 801 7.333323 TGCATCAAATGACATCTCTTTCTCTA 58.667 34.615 0.00 0.00 0.00 2.43
772 802 7.991460 TGCATCAAATGACATCTCTTTCTCTAT 59.009 33.333 0.00 0.00 0.00 1.98
773 803 9.486497 GCATCAAATGACATCTCTTTCTCTATA 57.514 33.333 0.00 0.00 0.00 1.31
790 820 9.842775 TTTCTCTATAGAAATTGAGATGCATGT 57.157 29.630 2.46 0.00 44.85 3.21
791 821 9.486497 TTCTCTATAGAAATTGAGATGCATGTC 57.514 33.333 16.63 16.63 41.55 3.06
792 822 8.645110 TCTCTATAGAAATTGAGATGCATGTCA 58.355 33.333 21.70 21.70 38.53 3.58
793 823 9.438228 CTCTATAGAAATTGAGATGCATGTCAT 57.562 33.333 25.41 12.35 37.20 3.06
803 833 3.806380 GATGCATGTCATCTCACTTCCT 58.194 45.455 2.46 0.00 46.29 3.36
804 834 4.953667 GATGCATGTCATCTCACTTCCTA 58.046 43.478 2.46 0.00 46.29 2.94
805 835 5.549347 GATGCATGTCATCTCACTTCCTAT 58.451 41.667 2.46 0.00 46.29 2.57
806 836 4.700700 TGCATGTCATCTCACTTCCTATG 58.299 43.478 0.00 0.00 0.00 2.23
807 837 4.406649 TGCATGTCATCTCACTTCCTATGA 59.593 41.667 0.00 0.00 0.00 2.15
808 838 5.071384 TGCATGTCATCTCACTTCCTATGAT 59.929 40.000 0.00 0.00 31.49 2.45
809 839 5.996513 GCATGTCATCTCACTTCCTATGATT 59.003 40.000 0.00 0.00 31.49 2.57
810 840 6.485984 GCATGTCATCTCACTTCCTATGATTT 59.514 38.462 0.00 0.00 31.49 2.17
811 841 7.013083 GCATGTCATCTCACTTCCTATGATTTT 59.987 37.037 0.00 0.00 31.49 1.82
812 842 8.900781 CATGTCATCTCACTTCCTATGATTTTT 58.099 33.333 0.00 0.00 31.49 1.94
813 843 8.498054 TGTCATCTCACTTCCTATGATTTTTC 57.502 34.615 0.00 0.00 31.49 2.29
814 844 8.324306 TGTCATCTCACTTCCTATGATTTTTCT 58.676 33.333 0.00 0.00 31.49 2.52
815 845 9.823647 GTCATCTCACTTCCTATGATTTTTCTA 57.176 33.333 0.00 0.00 31.49 2.10
819 849 9.838339 TCTCACTTCCTATGATTTTTCTATTCC 57.162 33.333 0.00 0.00 0.00 3.01
820 850 9.844257 CTCACTTCCTATGATTTTTCTATTCCT 57.156 33.333 0.00 0.00 0.00 3.36
851 881 9.807649 CATTTTTATTCTATGAACCAAAGGAGG 57.192 33.333 0.00 0.00 0.00 4.30
852 882 7.404671 TTTTATTCTATGAACCAAAGGAGGC 57.595 36.000 0.00 0.00 0.00 4.70
853 883 3.366052 TTCTATGAACCAAAGGAGGCC 57.634 47.619 0.00 0.00 0.00 5.19
854 884 2.562296 TCTATGAACCAAAGGAGGCCT 58.438 47.619 3.86 3.86 33.87 5.19
867 897 2.041755 AGGAGGCCTAAGTTTCCTTTGG 59.958 50.000 4.42 0.00 43.80 3.28
904 945 3.399330 GTGAACCGAGTGAGGAAATTGA 58.601 45.455 0.00 0.00 34.73 2.57
911 952 3.557054 CGAGTGAGGAAATTGAGGGTTCA 60.557 47.826 0.00 0.00 0.00 3.18
918 959 5.070685 AGGAAATTGAGGGTTCAGTTGTAC 58.929 41.667 0.00 0.00 34.01 2.90
1079 1120 4.191950 CGATGCCGCCGCCAATTT 62.192 61.111 0.00 0.00 0.00 1.82
1185 1226 2.513204 TACTCCCTCGACTCGGCG 60.513 66.667 0.00 0.00 0.00 6.46
1266 1307 3.402681 CCATCCTCCGCCACTGGT 61.403 66.667 0.00 0.00 0.00 4.00
1587 1628 2.811101 CGCTGGGAGAAGATCGCT 59.189 61.111 0.00 0.00 41.37 4.93
1896 1937 0.326264 GGTGCATGAAGAGGGTCACT 59.674 55.000 0.00 0.00 0.00 3.41
1978 2019 2.808933 CGTTGTCTTCCTTGCCTGGTAA 60.809 50.000 0.00 0.00 0.00 2.85
2007 2048 2.979813 GCTTGTCATTTTAACGGCAGTG 59.020 45.455 0.00 0.00 0.00 3.66
2241 2282 6.506500 AATTTGAGTGAAGCCTAGATGTTG 57.493 37.500 0.00 0.00 0.00 3.33
2261 2302 5.617528 TTGCCCAAGAATGCAATGATATT 57.382 34.783 0.00 0.00 42.19 1.28
2262 2303 4.951254 TGCCCAAGAATGCAATGATATTG 58.049 39.130 0.00 0.00 33.87 1.90
2263 2304 4.202274 TGCCCAAGAATGCAATGATATTGG 60.202 41.667 10.05 10.05 36.35 3.16
2264 2305 4.202284 GCCCAAGAATGCAATGATATTGGT 60.202 41.667 13.81 0.00 35.11 3.67
2265 2306 5.294356 CCCAAGAATGCAATGATATTGGTG 58.706 41.667 13.81 5.74 35.11 4.17
2266 2307 5.163385 CCCAAGAATGCAATGATATTGGTGT 60.163 40.000 13.81 0.00 35.11 4.16
2267 2308 5.751509 CCAAGAATGCAATGATATTGGTGTG 59.248 40.000 0.00 0.00 32.82 3.82
2268 2309 6.406065 CCAAGAATGCAATGATATTGGTGTGA 60.406 38.462 0.00 0.00 32.82 3.58
2269 2310 6.971726 AGAATGCAATGATATTGGTGTGAT 57.028 33.333 0.00 0.00 0.00 3.06
2270 2311 7.356089 AGAATGCAATGATATTGGTGTGATT 57.644 32.000 0.00 0.00 0.00 2.57
2271 2312 7.788026 AGAATGCAATGATATTGGTGTGATTT 58.212 30.769 0.00 0.00 0.00 2.17
2272 2313 8.262227 AGAATGCAATGATATTGGTGTGATTTT 58.738 29.630 0.00 0.00 0.00 1.82
2273 2314 8.428186 AATGCAATGATATTGGTGTGATTTTC 57.572 30.769 0.00 0.00 0.00 2.29
2274 2315 7.172868 TGCAATGATATTGGTGTGATTTTCT 57.827 32.000 3.97 0.00 0.00 2.52
2275 2316 7.036829 TGCAATGATATTGGTGTGATTTTCTG 58.963 34.615 3.97 0.00 0.00 3.02
2276 2317 7.093858 TGCAATGATATTGGTGTGATTTTCTGA 60.094 33.333 3.97 0.00 0.00 3.27
2277 2318 7.434307 GCAATGATATTGGTGTGATTTTCTGAG 59.566 37.037 3.97 0.00 0.00 3.35
2278 2319 8.680001 CAATGATATTGGTGTGATTTTCTGAGA 58.320 33.333 0.00 0.00 0.00 3.27
2363 2405 6.850752 TGAAACTAGACACCTCATGATACA 57.149 37.500 0.00 0.00 0.00 2.29
2383 2425 8.519526 TGATACACTTCCAATTTGGTTTATGTC 58.480 33.333 14.98 7.58 39.03 3.06
2388 2430 3.829601 TCCAATTTGGTTTATGTCGCCTT 59.170 39.130 14.98 0.00 39.03 4.35
2390 2432 3.757745 ATTTGGTTTATGTCGCCTTCG 57.242 42.857 0.00 0.00 0.00 3.79
2417 2459 9.371136 TCATAAAGATGACATGTTACTTGTCTC 57.629 33.333 24.76 19.76 43.12 3.36
2554 2596 2.158885 GCGAGAAGCCTAGATTTTCCCT 60.159 50.000 0.00 0.00 40.81 4.20
2566 2608 8.406297 GCCTAGATTTTCCCTAACTAAACAATG 58.594 37.037 0.00 0.00 0.00 2.82
2610 2652 2.025155 AGTTGATCCTAGCGATGACGT 58.975 47.619 0.00 0.00 41.98 4.34
2668 2710 4.072839 TCACTTGTCTCACTAGATGACGT 58.927 43.478 0.00 0.00 33.30 4.34
2675 2717 3.685272 TCTCACTAGATGACGTGACAGTC 59.315 47.826 0.00 0.00 41.30 3.51
2744 2786 3.642848 TGCATTTTCTTCTTCTTTGCCCT 59.357 39.130 0.00 0.00 0.00 5.19
2771 2813 1.967066 ACCAGGATTATGCTCGAGGAG 59.033 52.381 15.58 0.00 0.00 3.69
2780 2822 1.221840 GCTCGAGGAGGAAATGCCA 59.778 57.895 15.58 0.00 40.02 4.92
2858 2904 7.308589 GCCGAAATACCTCATAATTTATGTGCT 60.309 37.037 14.48 4.49 37.45 4.40
2876 2922 9.612066 TTATGTGCTGACAAAATAGATGATGTA 57.388 29.630 0.00 0.00 35.11 2.29
2884 2930 8.902806 TGACAAAATAGATGATGTATGTTTCCC 58.097 33.333 0.00 0.00 0.00 3.97
2904 2950 3.751698 CCCTTTTCTTAACCCGTCTTCTG 59.248 47.826 0.00 0.00 0.00 3.02
2912 2958 5.244402 TCTTAACCCGTCTTCTGAACACATA 59.756 40.000 0.00 0.00 0.00 2.29
2916 2962 5.844004 ACCCGTCTTCTGAACACATATATC 58.156 41.667 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.796312 CACGGGGTTGAAGAACGATG 59.204 55.000 0.00 0.00 32.28 3.84
1 2 0.953960 GCACGGGGTTGAAGAACGAT 60.954 55.000 0.00 0.00 32.28 3.73
2 3 1.595929 GCACGGGGTTGAAGAACGA 60.596 57.895 0.00 0.00 32.28 3.85
3 4 2.943653 GCACGGGGTTGAAGAACG 59.056 61.111 0.00 0.00 32.28 3.95
4 5 1.566018 CTCGCACGGGGTTGAAGAAC 61.566 60.000 0.00 0.00 0.00 3.01
5 6 1.301401 CTCGCACGGGGTTGAAGAA 60.301 57.895 0.00 0.00 0.00 2.52
7 8 3.423154 GCTCGCACGGGGTTGAAG 61.423 66.667 0.00 0.00 0.00 3.02
55 60 4.997565 TGTTGGTTGAAGCTTTTTCTCAG 58.002 39.130 0.00 0.00 0.00 3.35
91 96 1.743623 CGCCGCTCACACCCAATTA 60.744 57.895 0.00 0.00 0.00 1.40
198 205 0.949105 CCACTCGTAGCAAAACGCCT 60.949 55.000 1.84 0.00 44.04 5.52
246 272 2.100631 GTCGACATCACGCCCTTGG 61.101 63.158 11.55 0.00 0.00 3.61
249 275 2.994995 TGGTCGACATCACGCCCT 60.995 61.111 18.91 0.00 32.35 5.19
252 278 1.666553 TTGGTGGTCGACATCACGC 60.667 57.895 18.91 11.11 40.67 5.34
253 279 1.614227 CGTTGGTGGTCGACATCACG 61.614 60.000 18.91 13.32 40.67 4.35
255 281 2.042800 TCGTTGGTGGTCGACATCA 58.957 52.632 18.91 9.16 38.77 3.07
260 286 2.640989 CTCGTCGTTGGTGGTCGA 59.359 61.111 0.00 0.00 0.00 4.20
288 314 0.526211 TGACTCCTGTCGATTCCACG 59.474 55.000 0.00 0.00 45.70 4.94
295 321 2.033602 TCGGCTGACTCCTGTCGA 59.966 61.111 0.00 0.00 45.70 4.20
353 379 0.458543 CAATACGTCAGCCTGCTCGT 60.459 55.000 16.02 16.02 39.74 4.18
359 385 0.759346 GATCCCCAATACGTCAGCCT 59.241 55.000 0.00 0.00 0.00 4.58
401 427 5.986741 TCACTAGTAAAAGAAACATGACGCA 59.013 36.000 0.00 0.00 0.00 5.24
413 439 6.371825 CCCCTAAACTGCTTCACTAGTAAAAG 59.628 42.308 11.19 11.19 0.00 2.27
423 452 3.244911 CCTTCTTCCCCTAAACTGCTTCA 60.245 47.826 0.00 0.00 0.00 3.02
434 463 0.922626 GCAGGATTCCTTCTTCCCCT 59.077 55.000 1.28 0.00 32.05 4.79
493 523 4.555709 TCTGCGCCGGTGTTTGGT 62.556 61.111 17.91 0.00 0.00 3.67
504 534 3.330992 AAAGGGGGCTACTCTGCGC 62.331 63.158 0.00 0.00 43.82 6.09
505 535 1.153349 GAAAGGGGGCTACTCTGCG 60.153 63.158 0.00 0.00 0.00 5.18
506 536 0.548510 ATGAAAGGGGGCTACTCTGC 59.451 55.000 0.00 0.00 0.00 4.26
507 537 4.505742 GGAATATGAAAGGGGGCTACTCTG 60.506 50.000 0.00 0.00 0.00 3.35
508 538 3.653352 GGAATATGAAAGGGGGCTACTCT 59.347 47.826 0.00 0.00 0.00 3.24
509 539 3.244946 GGGAATATGAAAGGGGGCTACTC 60.245 52.174 0.00 0.00 0.00 2.59
510 540 2.716969 GGGAATATGAAAGGGGGCTACT 59.283 50.000 0.00 0.00 0.00 2.57
511 541 2.552373 CGGGAATATGAAAGGGGGCTAC 60.552 54.545 0.00 0.00 0.00 3.58
512 542 1.702957 CGGGAATATGAAAGGGGGCTA 59.297 52.381 0.00 0.00 0.00 3.93
513 543 0.478507 CGGGAATATGAAAGGGGGCT 59.521 55.000 0.00 0.00 0.00 5.19
514 544 0.185175 ACGGGAATATGAAAGGGGGC 59.815 55.000 0.00 0.00 0.00 5.80
515 545 1.478654 CCACGGGAATATGAAAGGGGG 60.479 57.143 0.00 0.00 0.00 5.40
516 546 1.214424 ACCACGGGAATATGAAAGGGG 59.786 52.381 0.00 0.00 0.00 4.79
517 547 2.729028 ACCACGGGAATATGAAAGGG 57.271 50.000 0.00 0.00 0.00 3.95
518 548 3.558418 CGTTACCACGGGAATATGAAAGG 59.442 47.826 0.00 0.00 43.16 3.11
519 549 4.789095 CGTTACCACGGGAATATGAAAG 57.211 45.455 0.00 0.00 43.16 2.62
531 561 3.513784 GAATGCCCATGCGTTACCACG 62.514 57.143 0.00 0.00 46.55 4.94
532 562 0.100503 GAATGCCCATGCGTTACCAC 59.899 55.000 0.00 0.00 46.55 4.16
533 563 0.322906 TGAATGCCCATGCGTTACCA 60.323 50.000 0.00 0.00 46.55 3.25
534 564 0.814457 TTGAATGCCCATGCGTTACC 59.186 50.000 0.00 0.00 46.55 2.85
535 565 1.472480 AGTTGAATGCCCATGCGTTAC 59.528 47.619 0.00 0.00 46.55 2.50
536 566 1.832883 AGTTGAATGCCCATGCGTTA 58.167 45.000 0.00 0.00 46.55 3.18
538 568 1.340017 ACTAGTTGAATGCCCATGCGT 60.340 47.619 0.00 0.00 41.78 5.24
539 569 1.064505 CACTAGTTGAATGCCCATGCG 59.935 52.381 0.00 0.00 41.78 4.73
540 570 2.357009 CTCACTAGTTGAATGCCCATGC 59.643 50.000 0.00 0.00 32.21 4.06
541 571 3.614092 ACTCACTAGTTGAATGCCCATG 58.386 45.455 0.00 0.00 32.21 3.66
542 572 3.521126 AGACTCACTAGTTGAATGCCCAT 59.479 43.478 0.00 0.00 35.56 4.00
543 573 2.906389 AGACTCACTAGTTGAATGCCCA 59.094 45.455 0.00 0.00 35.56 5.36
544 574 3.265791 CAGACTCACTAGTTGAATGCCC 58.734 50.000 0.00 0.00 35.56 5.36
545 575 3.265791 CCAGACTCACTAGTTGAATGCC 58.734 50.000 0.00 0.00 35.56 4.40
546 576 3.681897 CACCAGACTCACTAGTTGAATGC 59.318 47.826 0.00 0.00 35.56 3.56
547 577 4.887748 ACACCAGACTCACTAGTTGAATG 58.112 43.478 0.00 0.00 35.56 2.67
548 578 6.010850 TCTACACCAGACTCACTAGTTGAAT 58.989 40.000 0.00 0.00 35.56 2.57
549 579 5.382616 TCTACACCAGACTCACTAGTTGAA 58.617 41.667 0.00 0.00 35.56 2.69
550 580 4.981812 TCTACACCAGACTCACTAGTTGA 58.018 43.478 0.00 0.00 35.56 3.18
551 581 5.906113 ATCTACACCAGACTCACTAGTTG 57.094 43.478 0.00 0.00 35.56 3.16
552 582 6.723339 AGTATCTACACCAGACTCACTAGTT 58.277 40.000 0.00 0.00 35.56 2.24
553 583 6.316280 AGTATCTACACCAGACTCACTAGT 57.684 41.667 0.00 0.00 39.21 2.57
554 584 6.854496 GAGTATCTACACCAGACTCACTAG 57.146 45.833 0.00 0.00 35.62 2.57
569 599 5.148502 CCAAAGGAGGCCTTAGAGTATCTA 58.851 45.833 6.77 0.00 44.06 1.98
570 600 3.970640 CCAAAGGAGGCCTTAGAGTATCT 59.029 47.826 6.77 0.00 43.92 1.98
571 601 3.712218 ACCAAAGGAGGCCTTAGAGTATC 59.288 47.826 6.77 0.00 43.92 2.24
572 602 3.737263 ACCAAAGGAGGCCTTAGAGTAT 58.263 45.455 6.77 0.00 43.92 2.12
573 603 3.200958 ACCAAAGGAGGCCTTAGAGTA 57.799 47.619 6.77 0.00 43.92 2.59
574 604 2.046280 ACCAAAGGAGGCCTTAGAGT 57.954 50.000 6.77 0.00 43.92 3.24
575 605 3.084786 CAAACCAAAGGAGGCCTTAGAG 58.915 50.000 6.77 0.00 43.92 2.43
576 606 2.445525 ACAAACCAAAGGAGGCCTTAGA 59.554 45.455 6.77 0.00 43.92 2.10
577 607 2.876581 ACAAACCAAAGGAGGCCTTAG 58.123 47.619 6.77 0.00 43.92 2.18
578 608 3.245122 CCTACAAACCAAAGGAGGCCTTA 60.245 47.826 6.77 0.00 43.92 2.69
580 610 1.075536 CCTACAAACCAAAGGAGGCCT 59.924 52.381 3.86 3.86 33.87 5.19
581 611 1.074889 TCCTACAAACCAAAGGAGGCC 59.925 52.381 0.00 0.00 34.46 5.19
582 612 2.579410 TCCTACAAACCAAAGGAGGC 57.421 50.000 0.00 0.00 34.46 4.70
583 613 4.407365 ACATTCCTACAAACCAAAGGAGG 58.593 43.478 0.00 0.00 40.43 4.30
584 614 5.070001 TGACATTCCTACAAACCAAAGGAG 58.930 41.667 0.00 0.00 40.43 3.69
585 615 5.055265 TGACATTCCTACAAACCAAAGGA 57.945 39.130 0.00 0.00 37.64 3.36
586 616 5.982890 ATGACATTCCTACAAACCAAAGG 57.017 39.130 0.00 0.00 0.00 3.11
587 617 6.884295 TCCTATGACATTCCTACAAACCAAAG 59.116 38.462 0.00 0.00 0.00 2.77
588 618 6.785076 TCCTATGACATTCCTACAAACCAAA 58.215 36.000 0.00 0.00 0.00 3.28
589 619 6.381498 TCCTATGACATTCCTACAAACCAA 57.619 37.500 0.00 0.00 0.00 3.67
590 620 6.575244 ATCCTATGACATTCCTACAAACCA 57.425 37.500 0.00 0.00 0.00 3.67
591 621 7.775561 AGAAATCCTATGACATTCCTACAAACC 59.224 37.037 0.00 0.00 0.00 3.27
592 622 8.738645 AGAAATCCTATGACATTCCTACAAAC 57.261 34.615 0.00 0.00 0.00 2.93
593 623 9.832445 GTAGAAATCCTATGACATTCCTACAAA 57.168 33.333 0.00 0.00 0.00 2.83
594 624 8.988060 TGTAGAAATCCTATGACATTCCTACAA 58.012 33.333 0.00 0.00 0.00 2.41
595 625 8.547481 TGTAGAAATCCTATGACATTCCTACA 57.453 34.615 0.00 0.00 0.00 2.74
596 626 9.429359 CATGTAGAAATCCTATGACATTCCTAC 57.571 37.037 0.00 0.00 0.00 3.18
597 627 9.379770 TCATGTAGAAATCCTATGACATTCCTA 57.620 33.333 0.00 0.00 0.00 2.94
598 628 8.267620 TCATGTAGAAATCCTATGACATTCCT 57.732 34.615 0.00 0.00 0.00 3.36
629 659 9.705290 GGCTCAAAGGAAATTTTTCTATACAAA 57.295 29.630 3.28 0.00 37.35 2.83
630 660 8.311109 GGGCTCAAAGGAAATTTTTCTATACAA 58.689 33.333 3.28 0.00 37.35 2.41
631 661 7.093509 GGGGCTCAAAGGAAATTTTTCTATACA 60.094 37.037 3.28 0.00 37.35 2.29
632 662 7.124298 AGGGGCTCAAAGGAAATTTTTCTATAC 59.876 37.037 3.28 0.00 37.35 1.47
633 663 7.189087 AGGGGCTCAAAGGAAATTTTTCTATA 58.811 34.615 3.28 0.00 37.35 1.31
634 664 6.025539 AGGGGCTCAAAGGAAATTTTTCTAT 58.974 36.000 3.28 0.00 37.35 1.98
635 665 5.402630 AGGGGCTCAAAGGAAATTTTTCTA 58.597 37.500 3.28 0.00 37.35 2.10
636 666 4.234550 AGGGGCTCAAAGGAAATTTTTCT 58.765 39.130 3.28 0.00 37.35 2.52
637 667 4.623932 AGGGGCTCAAAGGAAATTTTTC 57.376 40.909 0.00 0.00 36.46 2.29
638 668 5.132502 CAAAGGGGCTCAAAGGAAATTTTT 58.867 37.500 0.00 0.00 0.00 1.94
639 669 4.446167 CCAAAGGGGCTCAAAGGAAATTTT 60.446 41.667 0.00 0.00 0.00 1.82
640 670 3.072915 CCAAAGGGGCTCAAAGGAAATTT 59.927 43.478 0.00 0.00 0.00 1.82
641 671 2.639347 CCAAAGGGGCTCAAAGGAAATT 59.361 45.455 0.00 0.00 0.00 1.82
642 672 2.259917 CCAAAGGGGCTCAAAGGAAAT 58.740 47.619 0.00 0.00 0.00 2.17
643 673 1.062505 ACCAAAGGGGCTCAAAGGAAA 60.063 47.619 0.00 0.00 42.05 3.13
644 674 0.560688 ACCAAAGGGGCTCAAAGGAA 59.439 50.000 0.00 0.00 42.05 3.36
645 675 0.560688 AACCAAAGGGGCTCAAAGGA 59.439 50.000 0.00 0.00 42.05 3.36
646 676 0.681175 CAACCAAAGGGGCTCAAAGG 59.319 55.000 0.00 0.00 42.05 3.11
647 677 0.681175 CCAACCAAAGGGGCTCAAAG 59.319 55.000 0.00 0.00 42.05 2.77
648 678 0.031616 ACCAACCAAAGGGGCTCAAA 60.032 50.000 0.00 0.00 42.05 2.69
649 679 0.854218 TACCAACCAAAGGGGCTCAA 59.146 50.000 0.00 0.00 42.05 3.02
650 680 0.404040 CTACCAACCAAAGGGGCTCA 59.596 55.000 0.00 0.00 42.05 4.26
651 681 0.323451 CCTACCAACCAAAGGGGCTC 60.323 60.000 0.00 0.00 42.05 4.70
652 682 0.774491 TCCTACCAACCAAAGGGGCT 60.774 55.000 0.00 0.00 42.05 5.19
653 683 0.113580 TTCCTACCAACCAAAGGGGC 59.886 55.000 0.00 0.00 42.05 5.80
654 684 2.456577 CATTCCTACCAACCAAAGGGG 58.543 52.381 0.00 0.00 44.81 4.79
655 685 2.042433 TCCATTCCTACCAACCAAAGGG 59.958 50.000 0.00 0.00 41.29 3.95
656 686 3.449746 TCCATTCCTACCAACCAAAGG 57.550 47.619 0.00 0.00 0.00 3.11
657 687 5.104109 TCCTATCCATTCCTACCAACCAAAG 60.104 44.000 0.00 0.00 0.00 2.77
658 688 4.791334 TCCTATCCATTCCTACCAACCAAA 59.209 41.667 0.00 0.00 0.00 3.28
659 689 4.376223 TCCTATCCATTCCTACCAACCAA 58.624 43.478 0.00 0.00 0.00 3.67
660 690 4.015617 TCCTATCCATTCCTACCAACCA 57.984 45.455 0.00 0.00 0.00 3.67
661 691 5.073144 TGATTCCTATCCATTCCTACCAACC 59.927 44.000 0.00 0.00 0.00 3.77
662 692 6.187727 TGATTCCTATCCATTCCTACCAAC 57.812 41.667 0.00 0.00 0.00 3.77
663 693 6.840090 TTGATTCCTATCCATTCCTACCAA 57.160 37.500 0.00 0.00 0.00 3.67
664 694 7.295672 AGAATTGATTCCTATCCATTCCTACCA 59.704 37.037 7.80 0.00 40.91 3.25
665 695 7.694093 AGAATTGATTCCTATCCATTCCTACC 58.306 38.462 7.80 0.00 40.91 3.18
666 696 9.225436 GAAGAATTGATTCCTATCCATTCCTAC 57.775 37.037 7.80 0.17 40.91 3.18
667 697 8.948362 TGAAGAATTGATTCCTATCCATTCCTA 58.052 33.333 7.80 0.00 40.91 2.94
668 698 7.723172 GTGAAGAATTGATTCCTATCCATTCCT 59.277 37.037 7.80 0.00 40.91 3.36
669 699 7.503566 TGTGAAGAATTGATTCCTATCCATTCC 59.496 37.037 7.80 0.00 40.91 3.01
670 700 8.455903 TGTGAAGAATTGATTCCTATCCATTC 57.544 34.615 0.27 0.00 40.58 2.67
671 701 9.430399 AATGTGAAGAATTGATTCCTATCCATT 57.570 29.630 0.27 6.46 37.51 3.16
672 702 9.430399 AAATGTGAAGAATTGATTCCTATCCAT 57.570 29.630 0.27 2.12 37.51 3.41
673 703 8.827832 AAATGTGAAGAATTGATTCCTATCCA 57.172 30.769 0.27 0.33 37.51 3.41
678 708 8.964772 CCTCTAAAATGTGAAGAATTGATTCCT 58.035 33.333 0.27 0.00 37.51 3.36
679 709 8.960591 TCCTCTAAAATGTGAAGAATTGATTCC 58.039 33.333 0.27 0.00 37.51 3.01
733 763 9.358406 TGTCATTTGATGCATAGGATAGAAATT 57.642 29.630 0.00 0.00 0.00 1.82
734 764 8.929260 TGTCATTTGATGCATAGGATAGAAAT 57.071 30.769 0.00 0.00 0.00 2.17
735 765 8.929260 ATGTCATTTGATGCATAGGATAGAAA 57.071 30.769 0.00 0.00 0.00 2.52
736 766 8.380867 AGATGTCATTTGATGCATAGGATAGAA 58.619 33.333 0.00 0.00 30.80 2.10
737 767 7.914859 AGATGTCATTTGATGCATAGGATAGA 58.085 34.615 0.00 0.00 30.80 1.98
738 768 8.041919 AGAGATGTCATTTGATGCATAGGATAG 58.958 37.037 0.00 0.00 30.80 2.08
739 769 7.914859 AGAGATGTCATTTGATGCATAGGATA 58.085 34.615 0.00 0.00 30.80 2.59
740 770 6.780901 AGAGATGTCATTTGATGCATAGGAT 58.219 36.000 0.00 0.00 30.80 3.24
741 771 6.183810 AGAGATGTCATTTGATGCATAGGA 57.816 37.500 0.00 0.00 30.80 2.94
742 772 6.879276 AAGAGATGTCATTTGATGCATAGG 57.121 37.500 0.00 0.00 30.80 2.57
743 773 8.155821 AGAAAGAGATGTCATTTGATGCATAG 57.844 34.615 0.00 0.00 30.80 2.23
744 774 7.991460 AGAGAAAGAGATGTCATTTGATGCATA 59.009 33.333 0.00 0.00 30.80 3.14
745 775 6.829298 AGAGAAAGAGATGTCATTTGATGCAT 59.171 34.615 0.00 0.00 32.43 3.96
746 776 6.178324 AGAGAAAGAGATGTCATTTGATGCA 58.822 36.000 0.00 0.00 0.00 3.96
747 777 6.680874 AGAGAAAGAGATGTCATTTGATGC 57.319 37.500 0.00 0.00 0.00 3.91
765 795 9.486497 GACATGCATCTCAATTTCTATAGAGAA 57.514 33.333 0.00 0.00 40.19 2.87
766 796 8.645110 TGACATGCATCTCAATTTCTATAGAGA 58.355 33.333 1.73 0.00 40.96 3.10
767 797 8.828688 TGACATGCATCTCAATTTCTATAGAG 57.171 34.615 1.73 0.00 0.00 2.43
783 813 3.928005 AGGAAGTGAGATGACATGCAT 57.072 42.857 0.00 0.00 40.77 3.96
784 814 4.406649 TCATAGGAAGTGAGATGACATGCA 59.593 41.667 0.00 0.00 0.00 3.96
785 815 4.953667 TCATAGGAAGTGAGATGACATGC 58.046 43.478 0.00 0.00 0.00 4.06
786 816 8.447924 AAAATCATAGGAAGTGAGATGACATG 57.552 34.615 0.00 0.00 31.41 3.21
787 817 9.118300 GAAAAATCATAGGAAGTGAGATGACAT 57.882 33.333 0.00 0.00 31.41 3.06
788 818 8.324306 AGAAAAATCATAGGAAGTGAGATGACA 58.676 33.333 0.00 0.00 31.41 3.58
789 819 8.729805 AGAAAAATCATAGGAAGTGAGATGAC 57.270 34.615 0.00 0.00 31.41 3.06
793 823 9.838339 GGAATAGAAAAATCATAGGAAGTGAGA 57.162 33.333 0.00 0.00 0.00 3.27
794 824 9.844257 AGGAATAGAAAAATCATAGGAAGTGAG 57.156 33.333 0.00 0.00 0.00 3.51
825 855 9.807649 CCTCCTTTGGTTCATAGAATAAAAATG 57.192 33.333 0.00 0.00 0.00 2.32
826 856 8.478066 GCCTCCTTTGGTTCATAGAATAAAAAT 58.522 33.333 0.00 0.00 0.00 1.82
827 857 7.093509 GGCCTCCTTTGGTTCATAGAATAAAAA 60.094 37.037 0.00 0.00 0.00 1.94
828 858 6.379988 GGCCTCCTTTGGTTCATAGAATAAAA 59.620 38.462 0.00 0.00 0.00 1.52
829 859 5.891551 GGCCTCCTTTGGTTCATAGAATAAA 59.108 40.000 0.00 0.00 0.00 1.40
830 860 5.193728 AGGCCTCCTTTGGTTCATAGAATAA 59.806 40.000 0.00 0.00 0.00 1.40
831 861 4.726825 AGGCCTCCTTTGGTTCATAGAATA 59.273 41.667 0.00 0.00 0.00 1.75
832 862 3.529319 AGGCCTCCTTTGGTTCATAGAAT 59.471 43.478 0.00 0.00 0.00 2.40
833 863 2.919602 AGGCCTCCTTTGGTTCATAGAA 59.080 45.455 0.00 0.00 0.00 2.10
834 864 2.562296 AGGCCTCCTTTGGTTCATAGA 58.438 47.619 0.00 0.00 0.00 1.98
835 865 4.080299 ACTTAGGCCTCCTTTGGTTCATAG 60.080 45.833 9.68 0.00 34.61 2.23
836 866 3.850173 ACTTAGGCCTCCTTTGGTTCATA 59.150 43.478 9.68 0.00 34.61 2.15
837 867 2.649816 ACTTAGGCCTCCTTTGGTTCAT 59.350 45.455 9.68 0.00 34.61 2.57
838 868 2.062636 ACTTAGGCCTCCTTTGGTTCA 58.937 47.619 9.68 0.00 34.61 3.18
839 869 2.881111 ACTTAGGCCTCCTTTGGTTC 57.119 50.000 9.68 0.00 34.61 3.62
840 870 3.497332 GAAACTTAGGCCTCCTTTGGTT 58.503 45.455 9.68 0.21 34.61 3.67
841 871 2.225041 GGAAACTTAGGCCTCCTTTGGT 60.225 50.000 9.68 0.00 34.61 3.67
842 872 2.041755 AGGAAACTTAGGCCTCCTTTGG 59.958 50.000 9.68 0.00 37.44 3.28
843 873 3.441500 AGGAAACTTAGGCCTCCTTTG 57.558 47.619 9.68 0.00 37.44 2.77
867 897 0.810648 TCACGGGATTTGCTGCAATC 59.189 50.000 16.77 14.48 0.00 2.67
904 945 2.639839 AGAGCATGTACAACTGAACCCT 59.360 45.455 0.00 0.00 0.00 4.34
911 952 3.499918 GCAGTTTCAGAGCATGTACAACT 59.500 43.478 0.00 0.00 0.00 3.16
918 959 2.935201 GGAGTAGCAGTTTCAGAGCATG 59.065 50.000 0.00 0.00 0.00 4.06
1079 1120 0.982852 ATTCGCAGTGGGGGATGAGA 60.983 55.000 7.42 0.00 38.38 3.27
1185 1226 1.255667 TGGAGGCGAAGACCTGGTAC 61.256 60.000 0.00 0.00 41.32 3.34
1263 1304 2.994995 ACGGAGATGTCGCCACCA 60.995 61.111 3.72 0.00 35.39 4.17
1478 1519 1.892441 AACCTCCTCCTCCCTCTCCC 61.892 65.000 0.00 0.00 0.00 4.30
1728 1769 0.892358 CAGCATTGCCACCTGTGTCT 60.892 55.000 4.70 0.00 0.00 3.41
1875 1916 1.133181 TGACCCTCTTCATGCACCCA 61.133 55.000 0.00 0.00 0.00 4.51
1896 1937 1.502231 GAAAGTCACGCTTGAGCTCA 58.498 50.000 13.74 13.74 37.52 4.26
1978 2019 5.049405 CCGTTAAAATGACAAGCAGAGACTT 60.049 40.000 0.00 0.00 0.00 3.01
2106 2147 2.025155 TGCCGTTTAGCTTCACCAAAA 58.975 42.857 0.00 0.00 0.00 2.44
2157 2198 6.494893 TGACAGCCAACACATTATAGTTTC 57.505 37.500 0.00 0.00 0.00 2.78
2241 2282 4.202284 ACCAATATCATTGCATTCTTGGGC 60.202 41.667 12.59 0.00 36.76 5.36
2255 2296 7.884877 AGTTCTCAGAAAATCACACCAATATCA 59.115 33.333 0.00 0.00 0.00 2.15
2256 2297 8.180267 CAGTTCTCAGAAAATCACACCAATATC 58.820 37.037 0.00 0.00 0.00 1.63
2257 2298 7.884877 TCAGTTCTCAGAAAATCACACCAATAT 59.115 33.333 0.00 0.00 0.00 1.28
2258 2299 7.223584 TCAGTTCTCAGAAAATCACACCAATA 58.776 34.615 0.00 0.00 0.00 1.90
2259 2300 6.064060 TCAGTTCTCAGAAAATCACACCAAT 58.936 36.000 0.00 0.00 0.00 3.16
2260 2301 5.436175 TCAGTTCTCAGAAAATCACACCAA 58.564 37.500 0.00 0.00 0.00 3.67
2261 2302 5.034852 TCAGTTCTCAGAAAATCACACCA 57.965 39.130 0.00 0.00 0.00 4.17
2262 2303 6.566197 AATCAGTTCTCAGAAAATCACACC 57.434 37.500 0.00 0.00 0.00 4.16
2363 2405 4.321675 GGCGACATAAACCAAATTGGAAGT 60.322 41.667 20.25 8.89 40.96 3.01
2744 2786 4.346709 TCGAGCATAATCCTGGTAAATCCA 59.653 41.667 0.00 0.00 45.01 3.41
2771 2813 4.699257 CAGGCTATCTCTTATGGCATTTCC 59.301 45.833 4.78 0.00 0.00 3.13
2780 2822 9.717942 CAGCTAATTTAACAGGCTATCTCTTAT 57.282 33.333 0.00 0.00 0.00 1.73
2835 2881 9.884465 GTCAGCACATAAATTATGAGGTATTTC 57.116 33.333 18.78 5.35 39.45 2.17
2858 2904 8.902806 GGGAAACATACATCATCTATTTTGTCA 58.097 33.333 0.00 0.00 0.00 3.58
2876 2922 4.476297 ACGGGTTAAGAAAAGGGAAACAT 58.524 39.130 0.00 0.00 0.00 2.71
2884 2930 5.526111 TGTTCAGAAGACGGGTTAAGAAAAG 59.474 40.000 0.00 0.00 0.00 2.27
2904 2950 9.935241 ATATGGACAAGTCTGATATATGTGTTC 57.065 33.333 0.00 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.