Multiple sequence alignment - TraesCS1A01G160000

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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 TraesCS1A01G160000 chr1A 100.000 2563 0 0 1682 4244 287315226 287312664 0.000000e+00 4734
1 TraesCS1A01G160000 chr1A 100.000 1166 0 0 1 1166 287316907 287315742 0.000000e+00 2154
2 TraesCS1A01G160000 chr1A 92.439 410 23 3 1 402 287542373 287541964 2.840000e-161 579
3 TraesCS1A01G160000 chr1B 95.257 2572 107 8 1682 4244 317846534 317849099 0.000000e+00 4060
4 TraesCS1A01G160000 chr1B 90.144 416 20 7 1 398 317845725 317846137 4.860000e-144 521
5 TraesCS1A01G160000 chr1B 95.114 307 14 1 860 1166 317846232 317846537 2.290000e-132 483
6 TraesCS1A01G160000 chr1D 95.518 1919 71 7 1682 3588 221886185 221884270 0.000000e+00 3053
7 TraesCS1A01G160000 chr1D 89.737 419 26 6 1 402 221887004 221886586 1.750000e-143 520
8 TraesCS1A01G160000 chr1D 87.309 457 37 5 3590 4046 221883625 221883190 1.760000e-138 503
9 TraesCS1A01G160000 chr1D 94.620 316 12 5 855 1166 221886496 221886182 6.380000e-133 484
10 TraesCS1A01G160000 chr1D 85.417 288 30 9 3968 4244 221883186 221882900 5.370000e-74 289


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 TraesCS1A01G160000 chr1A 287312664 287316907 4243 True 3444.0 4734 100.0000 1 4244 2 chr1A.!!$R2 4243
1 TraesCS1A01G160000 chr1B 317845725 317849099 3374 False 1688.0 4060 93.5050 1 4244 3 chr1B.!!$F1 4243
2 TraesCS1A01G160000 chr1D 221882900 221887004 4104 True 969.8 3053 90.5202 1 4244 5 chr1D.!!$R1 4243

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
639 660 0.034756 TGGTTGTGTGTGGATCCGAG 59.965 55.0 7.39 0.0 0.0 4.63 F
994 1025 0.039180 CCCTCCCCTAACAAACACCC 59.961 60.0 0.00 0.0 0.0 4.61 F
996 1027 0.039180 CTCCCCTAACAAACACCCCC 59.961 60.0 0.00 0.0 0.0 5.40 F
2091 2122 0.178973 CCCCGGACCTTTTGACCTTT 60.179 55.0 0.73 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2122 0.387929 GCCCGGAGATGACGATGTTA 59.612 55.000 0.73 0.0 0.0 2.41 R
2915 2946 0.036010 CCGATGCTCTGGTTCCAAGT 60.036 55.000 0.00 0.0 0.0 3.16 R
3155 3186 3.912528 CTCCATCATCCCCTCCTTGATTA 59.087 47.826 0.00 0.0 0.0 1.75 R
3744 4431 2.162681 GTTGCACAGGTATTTGCCTCT 58.837 47.619 0.00 0.0 38.0 3.69 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
37 38 6.533730 AGACAAACCATGAGATGTAGAACAA 58.466 36.000 0.00 0.00 0.00 2.83
176 186 0.815095 CTGCTTCATGGCATCAGCAA 59.185 50.000 24.13 12.95 41.65 3.91
196 206 4.487948 CAACATTCGAAATTGGAGTGCAT 58.512 39.130 14.65 0.00 0.00 3.96
205 215 5.007921 CGAAATTGGAGTGCATATGACATGA 59.992 40.000 6.97 0.00 0.00 3.07
207 217 3.910568 TGGAGTGCATATGACATGACA 57.089 42.857 6.97 0.00 0.00 3.58
232 248 2.265182 GGCCTGCGCTTTGTGGTAA 61.265 57.895 9.73 0.00 34.44 2.85
289 306 5.412594 TCTTTTTACATTCTCGCTTGCTCAT 59.587 36.000 0.00 0.00 0.00 2.90
304 321 5.296283 GCTTGCTCATGTTCAGAGATGTAAT 59.704 40.000 0.00 0.00 35.09 1.89
312 329 8.702819 TCATGTTCAGAGATGTAATTGAGATCT 58.297 33.333 0.00 0.00 40.82 2.75
313 330 9.327628 CATGTTCAGAGATGTAATTGAGATCTT 57.672 33.333 0.00 0.00 38.28 2.40
333 350 5.003804 TCTTGGCCTGTATCTGACTTTTTC 58.996 41.667 3.32 0.00 0.00 2.29
336 353 3.942115 GGCCTGTATCTGACTTTTTCCTC 59.058 47.826 0.00 0.00 0.00 3.71
372 390 0.541764 TCCATTTGCACCAAGTCCCC 60.542 55.000 0.00 0.00 0.00 4.81
471 492 8.648557 AAAAAGAACAAGCAGATTTCTAAACC 57.351 30.769 0.00 0.00 0.00 3.27
472 493 7.588497 AAAGAACAAGCAGATTTCTAAACCT 57.412 32.000 0.00 0.00 0.00 3.50
473 494 7.588497 AAGAACAAGCAGATTTCTAAACCTT 57.412 32.000 0.00 0.00 0.00 3.50
474 495 7.588497 AGAACAAGCAGATTTCTAAACCTTT 57.412 32.000 0.00 0.00 0.00 3.11
475 496 8.691661 AGAACAAGCAGATTTCTAAACCTTTA 57.308 30.769 0.00 0.00 0.00 1.85
476 497 9.301897 AGAACAAGCAGATTTCTAAACCTTTAT 57.698 29.630 0.00 0.00 0.00 1.40
533 554 7.888424 TGAATTTCTTCATTTGCATCAAGAGA 58.112 30.769 0.00 0.00 36.46 3.10
534 555 8.027189 TGAATTTCTTCATTTGCATCAAGAGAG 58.973 33.333 0.00 0.00 36.46 3.20
535 556 7.698506 ATTTCTTCATTTGCATCAAGAGAGA 57.301 32.000 0.00 0.00 0.00 3.10
536 557 7.514784 TTTCTTCATTTGCATCAAGAGAGAA 57.485 32.000 0.00 0.00 0.00 2.87
537 558 7.514784 TTCTTCATTTGCATCAAGAGAGAAA 57.485 32.000 0.00 0.00 0.00 2.52
538 559 7.142306 TCTTCATTTGCATCAAGAGAGAAAG 57.858 36.000 0.00 0.00 0.00 2.62
539 560 6.938596 TCTTCATTTGCATCAAGAGAGAAAGA 59.061 34.615 0.00 0.00 0.00 2.52
540 561 7.446319 TCTTCATTTGCATCAAGAGAGAAAGAA 59.554 33.333 0.00 0.00 0.00 2.52
541 562 6.906659 TCATTTGCATCAAGAGAGAAAGAAC 58.093 36.000 0.00 0.00 0.00 3.01
542 563 6.487668 TCATTTGCATCAAGAGAGAAAGAACA 59.512 34.615 0.00 0.00 0.00 3.18
543 564 6.889301 TTTGCATCAAGAGAGAAAGAACAT 57.111 33.333 0.00 0.00 0.00 2.71
544 565 5.874895 TGCATCAAGAGAGAAAGAACATG 57.125 39.130 0.00 0.00 0.00 3.21
545 566 5.311265 TGCATCAAGAGAGAAAGAACATGT 58.689 37.500 0.00 0.00 0.00 3.21
546 567 6.466812 TGCATCAAGAGAGAAAGAACATGTA 58.533 36.000 0.00 0.00 0.00 2.29
547 568 6.936335 TGCATCAAGAGAGAAAGAACATGTAA 59.064 34.615 0.00 0.00 0.00 2.41
548 569 7.445096 TGCATCAAGAGAGAAAGAACATGTAAA 59.555 33.333 0.00 0.00 0.00 2.01
549 570 8.292448 GCATCAAGAGAGAAAGAACATGTAAAA 58.708 33.333 0.00 0.00 0.00 1.52
584 605 9.705290 ACTTTCTTCTCTCTTAGAATGAACTTC 57.295 33.333 0.00 0.00 43.32 3.01
585 606 9.927668 CTTTCTTCTCTCTTAGAATGAACTTCT 57.072 33.333 0.00 0.00 43.32 2.85
586 607 9.921637 TTTCTTCTCTCTTAGAATGAACTTCTC 57.078 33.333 0.00 0.00 43.32 2.87
587 608 8.062065 TCTTCTCTCTTAGAATGAACTTCTCC 57.938 38.462 0.00 0.00 43.32 3.71
588 609 7.671819 TCTTCTCTCTTAGAATGAACTTCTCCA 59.328 37.037 0.00 0.00 43.32 3.86
589 610 7.969690 TCTCTCTTAGAATGAACTTCTCCAT 57.030 36.000 0.00 0.00 43.32 3.41
590 611 8.372877 TCTCTCTTAGAATGAACTTCTCCATT 57.627 34.615 0.00 0.00 43.32 3.16
591 612 8.820831 TCTCTCTTAGAATGAACTTCTCCATTT 58.179 33.333 0.00 0.00 43.32 2.32
592 613 8.783833 TCTCTTAGAATGAACTTCTCCATTTG 57.216 34.615 0.00 0.00 43.32 2.32
593 614 7.826252 TCTCTTAGAATGAACTTCTCCATTTGG 59.174 37.037 0.00 0.00 43.32 3.28
594 615 6.886459 TCTTAGAATGAACTTCTCCATTTGGG 59.114 38.462 0.00 0.00 43.32 4.12
595 616 5.261040 AGAATGAACTTCTCCATTTGGGA 57.739 39.130 0.00 0.00 40.26 4.37
609 630 7.610580 TCCATTTGGGATAATTATTCAACCC 57.389 36.000 11.44 11.44 42.15 4.11
610 631 6.556874 TCCATTTGGGATAATTATTCAACCCC 59.443 38.462 14.45 12.68 42.15 4.95
611 632 6.454795 CATTTGGGATAATTATTCAACCCCG 58.545 40.000 14.45 0.00 36.82 5.73
612 633 4.107127 TGGGATAATTATTCAACCCCGG 57.893 45.455 14.45 0.00 36.82 5.73
613 634 2.823747 GGGATAATTATTCAACCCCGGC 59.176 50.000 6.09 0.00 0.00 6.13
614 635 2.823747 GGATAATTATTCAACCCCGGCC 59.176 50.000 0.00 0.00 0.00 6.13
615 636 3.499745 GGATAATTATTCAACCCCGGCCT 60.500 47.826 0.00 0.00 0.00 5.19
616 637 2.543037 AATTATTCAACCCCGGCCTT 57.457 45.000 0.00 0.00 0.00 4.35
617 638 1.775385 ATTATTCAACCCCGGCCTTG 58.225 50.000 0.00 0.00 0.00 3.61
618 639 0.406361 TTATTCAACCCCGGCCTTGT 59.594 50.000 0.00 0.00 0.00 3.16
619 640 0.406361 TATTCAACCCCGGCCTTGTT 59.594 50.000 0.00 0.00 0.00 2.83
620 641 0.471022 ATTCAACCCCGGCCTTGTTT 60.471 50.000 0.00 0.00 0.00 2.83
621 642 1.395826 TTCAACCCCGGCCTTGTTTG 61.396 55.000 0.00 0.00 0.00 2.93
622 643 2.523168 AACCCCGGCCTTGTTTGG 60.523 61.111 0.00 0.00 0.00 3.28
623 644 3.383031 AACCCCGGCCTTGTTTGGT 62.383 57.895 0.00 0.00 0.00 3.67
624 645 2.523168 CCCCGGCCTTGTTTGGTT 60.523 61.111 0.00 0.00 0.00 3.67
625 646 2.733945 CCCGGCCTTGTTTGGTTG 59.266 61.111 0.00 0.00 0.00 3.77
626 647 2.131067 CCCGGCCTTGTTTGGTTGT 61.131 57.895 0.00 0.00 0.00 3.32
627 648 1.067250 CCGGCCTTGTTTGGTTGTG 59.933 57.895 0.00 0.00 0.00 3.33
628 649 1.671901 CCGGCCTTGTTTGGTTGTGT 61.672 55.000 0.00 0.00 0.00 3.72
629 650 0.527385 CGGCCTTGTTTGGTTGTGTG 60.527 55.000 0.00 0.00 0.00 3.82
630 651 0.534873 GGCCTTGTTTGGTTGTGTGT 59.465 50.000 0.00 0.00 0.00 3.72
631 652 1.639280 GCCTTGTTTGGTTGTGTGTG 58.361 50.000 0.00 0.00 0.00 3.82
632 653 1.738700 GCCTTGTTTGGTTGTGTGTGG 60.739 52.381 0.00 0.00 0.00 4.17
633 654 1.821753 CCTTGTTTGGTTGTGTGTGGA 59.178 47.619 0.00 0.00 0.00 4.02
634 655 2.430332 CCTTGTTTGGTTGTGTGTGGAT 59.570 45.455 0.00 0.00 0.00 3.41
635 656 3.490761 CCTTGTTTGGTTGTGTGTGGATC 60.491 47.826 0.00 0.00 0.00 3.36
636 657 2.028130 TGTTTGGTTGTGTGTGGATCC 58.972 47.619 4.20 4.20 0.00 3.36
637 658 1.001815 GTTTGGTTGTGTGTGGATCCG 60.002 52.381 7.39 0.00 0.00 4.18
638 659 0.470341 TTGGTTGTGTGTGGATCCGA 59.530 50.000 7.39 0.00 0.00 4.55
639 660 0.034756 TGGTTGTGTGTGGATCCGAG 59.965 55.000 7.39 0.00 0.00 4.63
640 661 0.673644 GGTTGTGTGTGGATCCGAGG 60.674 60.000 7.39 0.00 0.00 4.63
641 662 0.673644 GTTGTGTGTGGATCCGAGGG 60.674 60.000 7.39 0.00 0.00 4.30
642 663 1.836999 TTGTGTGTGGATCCGAGGGG 61.837 60.000 7.39 0.00 0.00 4.79
643 664 2.121832 TGTGTGGATCCGAGGGGT 59.878 61.111 7.39 0.00 33.83 4.95
644 665 1.987855 TGTGTGGATCCGAGGGGTC 60.988 63.158 7.39 0.00 33.83 4.46
645 666 1.686110 GTGTGGATCCGAGGGGTCT 60.686 63.158 7.39 0.00 33.83 3.85
646 667 1.685765 TGTGGATCCGAGGGGTCTG 60.686 63.158 7.39 0.00 33.83 3.51
647 668 1.686110 GTGGATCCGAGGGGTCTGT 60.686 63.158 7.39 0.00 33.83 3.41
648 669 1.685765 TGGATCCGAGGGGTCTGTG 60.686 63.158 7.39 0.00 33.83 3.66
649 670 2.435693 GGATCCGAGGGGTCTGTGG 61.436 68.421 0.00 0.00 33.83 4.17
650 671 2.365635 ATCCGAGGGGTCTGTGGG 60.366 66.667 0.00 0.00 33.83 4.61
651 672 4.715130 TCCGAGGGGTCTGTGGGG 62.715 72.222 0.00 0.00 33.83 4.96
653 674 4.715130 CGAGGGGTCTGTGGGGGA 62.715 72.222 0.00 0.00 0.00 4.81
654 675 2.042930 GAGGGGTCTGTGGGGGAT 59.957 66.667 0.00 0.00 0.00 3.85
655 676 1.619669 GAGGGGTCTGTGGGGGATT 60.620 63.158 0.00 0.00 0.00 3.01
656 677 1.151361 AGGGGTCTGTGGGGGATTT 60.151 57.895 0.00 0.00 0.00 2.17
657 678 0.122435 AGGGGTCTGTGGGGGATTTA 59.878 55.000 0.00 0.00 0.00 1.40
658 679 1.004436 GGGGTCTGTGGGGGATTTAA 58.996 55.000 0.00 0.00 0.00 1.52
659 680 1.359818 GGGGTCTGTGGGGGATTTAAA 59.640 52.381 0.00 0.00 0.00 1.52
660 681 2.453521 GGGTCTGTGGGGGATTTAAAC 58.546 52.381 0.00 0.00 0.00 2.01
661 682 2.042569 GGGTCTGTGGGGGATTTAAACT 59.957 50.000 0.00 0.00 0.00 2.66
662 683 3.353557 GGTCTGTGGGGGATTTAAACTC 58.646 50.000 0.00 0.00 0.00 3.01
663 684 3.010250 GGTCTGTGGGGGATTTAAACTCT 59.990 47.826 0.00 0.00 0.00 3.24
664 685 4.508584 GGTCTGTGGGGGATTTAAACTCTT 60.509 45.833 0.00 0.00 0.00 2.85
665 686 5.280830 GGTCTGTGGGGGATTTAAACTCTTA 60.281 44.000 0.00 0.00 0.00 2.10
666 687 6.424032 GTCTGTGGGGGATTTAAACTCTTAT 58.576 40.000 0.00 0.00 0.00 1.73
667 688 7.366191 GGTCTGTGGGGGATTTAAACTCTTATA 60.366 40.741 0.00 0.00 0.00 0.98
668 689 8.050930 GTCTGTGGGGGATTTAAACTCTTATAA 58.949 37.037 0.00 0.00 0.00 0.98
669 690 8.272173 TCTGTGGGGGATTTAAACTCTTATAAG 58.728 37.037 6.11 6.11 0.00 1.73
670 691 7.935405 TGTGGGGGATTTAAACTCTTATAAGT 58.065 34.615 12.19 0.00 0.00 2.24
671 692 8.050930 TGTGGGGGATTTAAACTCTTATAAGTC 58.949 37.037 12.19 0.29 0.00 3.01
672 693 8.050930 GTGGGGGATTTAAACTCTTATAAGTCA 58.949 37.037 12.19 0.00 0.00 3.41
673 694 8.616598 TGGGGGATTTAAACTCTTATAAGTCAA 58.383 33.333 12.19 0.00 0.00 3.18
674 695 9.470399 GGGGGATTTAAACTCTTATAAGTCAAA 57.530 33.333 12.19 7.11 0.00 2.69
683 704 8.754230 AACTCTTATAAGTCAAACTACGTTCC 57.246 34.615 12.19 0.00 0.00 3.62
684 705 7.889469 ACTCTTATAAGTCAAACTACGTTCCA 58.111 34.615 12.19 0.00 0.00 3.53
685 706 8.362639 ACTCTTATAAGTCAAACTACGTTCCAA 58.637 33.333 12.19 0.00 0.00 3.53
686 707 9.367444 CTCTTATAAGTCAAACTACGTTCCAAT 57.633 33.333 12.19 0.00 0.00 3.16
687 708 9.362539 TCTTATAAGTCAAACTACGTTCCAATC 57.637 33.333 12.19 0.00 0.00 2.67
688 709 6.980051 ATAAGTCAAACTACGTTCCAATCC 57.020 37.500 0.00 0.00 0.00 3.01
689 710 4.618920 AGTCAAACTACGTTCCAATCCT 57.381 40.909 0.00 0.00 0.00 3.24
690 711 4.566987 AGTCAAACTACGTTCCAATCCTC 58.433 43.478 0.00 0.00 0.00 3.71
691 712 4.283722 AGTCAAACTACGTTCCAATCCTCT 59.716 41.667 0.00 0.00 0.00 3.69
692 713 4.995487 GTCAAACTACGTTCCAATCCTCTT 59.005 41.667 0.00 0.00 0.00 2.85
693 714 4.994852 TCAAACTACGTTCCAATCCTCTTG 59.005 41.667 0.00 0.00 0.00 3.02
694 715 4.884668 AACTACGTTCCAATCCTCTTGA 57.115 40.909 0.00 0.00 0.00 3.02
695 716 4.884668 ACTACGTTCCAATCCTCTTGAA 57.115 40.909 0.00 0.00 0.00 2.69
696 717 5.223449 ACTACGTTCCAATCCTCTTGAAA 57.777 39.130 0.00 0.00 0.00 2.69
697 718 5.238583 ACTACGTTCCAATCCTCTTGAAAG 58.761 41.667 0.00 0.00 0.00 2.62
698 719 3.412386 ACGTTCCAATCCTCTTGAAAGG 58.588 45.455 0.00 0.00 37.81 3.11
712 733 7.240414 CTCTTGAAAGGAGGATTAATCGAAC 57.760 40.000 9.32 2.12 0.00 3.95
713 734 6.707290 TCTTGAAAGGAGGATTAATCGAACA 58.293 36.000 9.32 0.93 0.00 3.18
714 735 7.165485 TCTTGAAAGGAGGATTAATCGAACAA 58.835 34.615 9.32 7.64 0.00 2.83
715 736 6.985188 TGAAAGGAGGATTAATCGAACAAG 57.015 37.500 9.32 0.00 0.00 3.16
716 737 5.354234 TGAAAGGAGGATTAATCGAACAAGC 59.646 40.000 9.32 0.00 0.00 4.01
717 738 4.487714 AGGAGGATTAATCGAACAAGCA 57.512 40.909 9.32 0.00 0.00 3.91
718 739 4.843728 AGGAGGATTAATCGAACAAGCAA 58.156 39.130 9.32 0.00 0.00 3.91
719 740 5.440610 AGGAGGATTAATCGAACAAGCAAT 58.559 37.500 9.32 0.00 0.00 3.56
720 741 6.591935 AGGAGGATTAATCGAACAAGCAATA 58.408 36.000 9.32 0.00 0.00 1.90
721 742 7.054124 AGGAGGATTAATCGAACAAGCAATAA 58.946 34.615 9.32 0.00 0.00 1.40
722 743 7.556275 AGGAGGATTAATCGAACAAGCAATAAA 59.444 33.333 9.32 0.00 0.00 1.40
723 744 8.188139 GGAGGATTAATCGAACAAGCAATAAAA 58.812 33.333 9.32 0.00 0.00 1.52
724 745 9.226345 GAGGATTAATCGAACAAGCAATAAAAG 57.774 33.333 9.32 0.00 0.00 2.27
725 746 8.956426 AGGATTAATCGAACAAGCAATAAAAGA 58.044 29.630 9.32 0.00 0.00 2.52
726 747 9.736023 GGATTAATCGAACAAGCAATAAAAGAT 57.264 29.630 9.32 0.00 0.00 2.40
829 856 7.521509 ACTCTCCGTTTCAAATTACTTATCG 57.478 36.000 0.00 0.00 0.00 2.92
830 857 7.095270 ACTCTCCGTTTCAAATTACTTATCGT 58.905 34.615 0.00 0.00 0.00 3.73
831 858 7.063074 ACTCTCCGTTTCAAATTACTTATCGTG 59.937 37.037 0.00 0.00 0.00 4.35
832 859 6.311935 TCTCCGTTTCAAATTACTTATCGTGG 59.688 38.462 0.00 0.00 0.00 4.94
833 860 6.164876 TCCGTTTCAAATTACTTATCGTGGA 58.835 36.000 0.00 0.00 0.00 4.02
834 861 6.311935 TCCGTTTCAAATTACTTATCGTGGAG 59.688 38.462 0.00 0.00 0.00 3.86
835 862 6.091713 CCGTTTCAAATTACTTATCGTGGAGT 59.908 38.462 0.00 0.00 0.00 3.85
836 863 7.276218 CCGTTTCAAATTACTTATCGTGGAGTA 59.724 37.037 0.00 0.00 0.00 2.59
837 864 8.649841 CGTTTCAAATTACTTATCGTGGAGTAA 58.350 33.333 8.77 8.77 41.18 2.24
845 872 9.847224 ATTACTTATCGTGGAGTAATTTGGAAT 57.153 29.630 11.50 0.00 43.12 3.01
846 873 7.553881 ACTTATCGTGGAGTAATTTGGAATG 57.446 36.000 0.00 0.00 0.00 2.67
847 874 6.542370 ACTTATCGTGGAGTAATTTGGAATGG 59.458 38.462 0.00 0.00 0.00 3.16
848 875 4.561500 TCGTGGAGTAATTTGGAATGGA 57.438 40.909 0.00 0.00 0.00 3.41
849 876 4.513442 TCGTGGAGTAATTTGGAATGGAG 58.487 43.478 0.00 0.00 0.00 3.86
850 877 4.224147 TCGTGGAGTAATTTGGAATGGAGA 59.776 41.667 0.00 0.00 0.00 3.71
851 878 4.572389 CGTGGAGTAATTTGGAATGGAGAG 59.428 45.833 0.00 0.00 0.00 3.20
852 879 5.626809 CGTGGAGTAATTTGGAATGGAGAGA 60.627 44.000 0.00 0.00 0.00 3.10
853 880 5.819901 GTGGAGTAATTTGGAATGGAGAGAG 59.180 44.000 0.00 0.00 0.00 3.20
860 887 4.884668 TTGGAATGGAGAGAGTACGTTT 57.115 40.909 0.00 0.00 0.00 3.60
866 893 1.467713 GGAGAGAGTACGTTTCTGCCG 60.468 57.143 6.96 0.00 0.00 5.69
883 910 1.593196 CCGTGCTTCTGGTTCTGAAA 58.407 50.000 0.00 0.00 0.00 2.69
908 935 0.468226 TGTTTGTGCCGAACTCCTCT 59.532 50.000 6.80 0.00 0.00 3.69
911 938 0.756294 TTGTGCCGAACTCCTCTTGA 59.244 50.000 0.00 0.00 0.00 3.02
994 1025 0.039180 CCCTCCCCTAACAAACACCC 59.961 60.000 0.00 0.00 0.00 4.61
996 1027 0.039180 CTCCCCTAACAAACACCCCC 59.961 60.000 0.00 0.00 0.00 5.40
997 1028 0.701659 TCCCCTAACAAACACCCCCA 60.702 55.000 0.00 0.00 0.00 4.96
1937 1968 3.766691 GGCGTACGAGGCCTTCCA 61.767 66.667 21.65 0.00 45.16 3.53
1948 1979 3.003173 CCTTCCACCTCCTCGGCA 61.003 66.667 0.00 0.00 35.61 5.69
2085 2116 1.964373 CGTGTCCCCGGACCTTTTG 60.964 63.158 0.73 0.00 43.97 2.44
2091 2122 0.178973 CCCCGGACCTTTTGACCTTT 60.179 55.000 0.73 0.00 0.00 3.11
2127 2158 2.282674 CTCTGCAAGGCTGGGCAA 60.283 61.111 14.07 6.04 39.93 4.52
2195 2226 3.260100 CCCCTCTGTGGCCACCTT 61.260 66.667 32.62 0.00 0.00 3.50
2331 2362 2.747446 CAATGTGCTGGTTACTGGGTAC 59.253 50.000 0.00 0.00 0.00 3.34
2448 2479 2.267324 GGTCTCTGCAGTGAGGGC 59.733 66.667 18.38 7.44 34.98 5.19
2513 2544 4.857251 GCTGGCGCCTAATGTAGT 57.143 55.556 29.70 0.00 0.00 2.73
2613 2644 5.297029 GGCACAGAGGAATATTGAACCTAAC 59.703 44.000 0.00 0.00 33.89 2.34
2879 2910 2.618053 CTGCAAAGGGGAAGTACGTAG 58.382 52.381 0.00 0.00 0.00 3.51
2915 2946 5.774184 TCTTGGATGAAATGTTGATGGTTGA 59.226 36.000 0.00 0.00 0.00 3.18
3155 3186 8.899771 CGTTCCAAATAAGGTTACCTATGAAAT 58.100 33.333 3.55 0.00 31.13 2.17
3205 3236 5.163437 GGTTACGTTCCTGATGTAAGAGGAT 60.163 44.000 0.00 0.00 39.70 3.24
3260 3291 2.159707 CCTGAAACGCTTGGTATGTTCG 60.160 50.000 0.00 0.00 0.00 3.95
3286 3317 6.818644 AGTAATGTACCAACATAGCTTGTCTG 59.181 38.462 0.00 0.00 45.79 3.51
3357 3388 5.668471 TGTTGTTGAAATGAGAAATTGGCA 58.332 33.333 0.00 0.00 0.00 4.92
3388 3427 5.609533 TTCTGCTAGGTCATAGTTTACCC 57.390 43.478 0.00 0.00 36.34 3.69
3389 3428 4.616553 TCTGCTAGGTCATAGTTTACCCA 58.383 43.478 0.00 0.00 36.34 4.51
3398 3437 5.941647 GGTCATAGTTTACCCACTGCTTTTA 59.058 40.000 0.00 0.00 0.00 1.52
3410 3449 4.039124 CCACTGCTTTTAGGTTTGGATGTT 59.961 41.667 0.00 0.00 0.00 2.71
3487 3526 4.200838 TCAGCCATTAACATCGTTCTCA 57.799 40.909 0.00 0.00 0.00 3.27
3527 3570 8.055986 GCAGTTCACAGTTTTAAGTTTTAATGC 58.944 33.333 0.00 0.00 0.00 3.56
3533 3576 9.522804 CACAGTTTTAAGTTTTAATGCTTGGTA 57.477 29.630 3.23 0.00 0.00 3.25
3567 3610 3.430651 CCAGTCTTTTTGGTGTGCACAAT 60.431 43.478 23.59 0.00 0.00 2.71
3636 4323 4.214980 GCATCTGTTTATGCGTGCTTAT 57.785 40.909 0.00 0.00 42.57 1.73
3753 4440 3.416156 GAAGTGAAGACCAGAGGCAAAT 58.584 45.455 0.00 0.00 0.00 2.32
3805 4492 4.284490 TGAATCTGAAAGTGCTCACCTAGT 59.716 41.667 0.00 0.00 33.76 2.57
3835 4522 3.357203 TCCTGGACACTACACTGATCTC 58.643 50.000 0.00 0.00 0.00 2.75
3930 4617 5.105877 GGTTAGGAGCCACTTTATTTGGTTC 60.106 44.000 0.00 0.00 42.17 3.62
3931 4618 4.112634 AGGAGCCACTTTATTTGGTTCA 57.887 40.909 7.42 0.00 44.10 3.18
3932 4619 4.082125 AGGAGCCACTTTATTTGGTTCAG 58.918 43.478 7.42 0.00 44.10 3.02
4067 4836 4.240096 CAAATGAAATGCAACCAGGAGTC 58.760 43.478 0.00 0.00 0.00 3.36
4160 4938 9.651913 AAAATGTTTATCACCCACATAATGAAC 57.348 29.630 0.00 0.00 30.74 3.18
4161 4939 8.593945 AATGTTTATCACCCACATAATGAACT 57.406 30.769 0.00 0.00 30.74 3.01
4162 4940 7.624360 TGTTTATCACCCACATAATGAACTC 57.376 36.000 0.00 0.00 0.00 3.01
4163 4941 7.171653 TGTTTATCACCCACATAATGAACTCA 58.828 34.615 0.00 0.00 0.00 3.41
4164 4942 7.667635 TGTTTATCACCCACATAATGAACTCAA 59.332 33.333 0.00 0.00 0.00 3.02
4199 4977 3.657634 CATATCGAGGCTTATGCACACT 58.342 45.455 2.72 0.00 41.91 3.55
4209 4987 4.082026 GGCTTATGCACACTTTTTCTCCAT 60.082 41.667 2.72 0.00 41.91 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.886523 CTCATGGTTTGTCTTCCAAGCA 59.113 45.455 0.00 0.00 36.10 3.91
6 7 3.149196 TCTCATGGTTTGTCTTCCAAGC 58.851 45.455 0.00 0.00 37.27 4.01
37 38 6.674419 AGATCTGAAACAGGATACCCTTTAGT 59.326 38.462 0.00 0.00 42.02 2.24
176 186 5.589855 TCATATGCACTCCAATTTCGAATGT 59.410 36.000 0.00 0.00 0.00 2.71
196 206 3.081061 GGCCAAACTGTGTCATGTCATA 58.919 45.455 0.00 0.00 0.00 2.15
207 217 2.127232 AAAGCGCAGGCCAAACTGT 61.127 52.632 11.47 0.00 40.59 3.55
232 248 1.653151 GCGAAAAGCCGGTAGAATCT 58.347 50.000 1.90 0.00 40.81 2.40
289 306 7.767659 CCAAGATCTCAATTACATCTCTGAACA 59.232 37.037 0.00 0.00 0.00 3.18
304 321 4.033009 TCAGATACAGGCCAAGATCTCAA 58.967 43.478 5.01 0.00 0.00 3.02
312 329 4.079253 GGAAAAAGTCAGATACAGGCCAA 58.921 43.478 5.01 0.00 0.00 4.52
313 330 3.330701 AGGAAAAAGTCAGATACAGGCCA 59.669 43.478 5.01 0.00 0.00 5.36
333 350 4.019860 TGGAGAAGTTCATTCCAAGAGAGG 60.020 45.833 10.62 0.00 38.03 3.69
336 353 6.618811 CAAATGGAGAAGTTCATTCCAAGAG 58.381 40.000 15.63 6.76 43.69 2.85
445 466 9.744468 GGTTTAGAAATCTGCTTGTTCTTTTTA 57.256 29.630 0.00 0.00 33.70 1.52
446 467 8.478066 AGGTTTAGAAATCTGCTTGTTCTTTTT 58.522 29.630 0.00 0.00 33.70 1.94
447 468 8.011844 AGGTTTAGAAATCTGCTTGTTCTTTT 57.988 30.769 0.00 0.00 33.70 2.27
448 469 7.588497 AGGTTTAGAAATCTGCTTGTTCTTT 57.412 32.000 0.00 0.00 33.70 2.52
449 470 7.588497 AAGGTTTAGAAATCTGCTTGTTCTT 57.412 32.000 0.00 0.00 33.70 2.52
450 471 7.588497 AAAGGTTTAGAAATCTGCTTGTTCT 57.412 32.000 0.00 0.00 35.77 3.01
507 528 8.528643 TCTCTTGATGCAAATGAAGAAATTCAT 58.471 29.630 0.00 0.00 43.00 2.57
508 529 7.888424 TCTCTTGATGCAAATGAAGAAATTCA 58.112 30.769 0.00 0.00 35.15 2.57
509 530 8.242053 TCTCTCTTGATGCAAATGAAGAAATTC 58.758 33.333 0.00 0.00 0.00 2.17
510 531 8.118976 TCTCTCTTGATGCAAATGAAGAAATT 57.881 30.769 0.00 0.00 0.00 1.82
511 532 7.698506 TCTCTCTTGATGCAAATGAAGAAAT 57.301 32.000 0.00 0.00 0.00 2.17
512 533 7.514784 TTCTCTCTTGATGCAAATGAAGAAA 57.485 32.000 0.00 0.00 0.00 2.52
513 534 7.446319 TCTTTCTCTCTTGATGCAAATGAAGAA 59.554 33.333 0.00 1.05 0.00 2.52
514 535 6.938596 TCTTTCTCTCTTGATGCAAATGAAGA 59.061 34.615 0.00 0.00 0.00 2.87
515 536 7.142306 TCTTTCTCTCTTGATGCAAATGAAG 57.858 36.000 0.00 0.00 0.00 3.02
516 537 7.013559 TGTTCTTTCTCTCTTGATGCAAATGAA 59.986 33.333 0.00 0.00 0.00 2.57
517 538 6.487668 TGTTCTTTCTCTCTTGATGCAAATGA 59.512 34.615 0.00 0.00 0.00 2.57
518 539 6.675026 TGTTCTTTCTCTCTTGATGCAAATG 58.325 36.000 0.00 0.00 0.00 2.32
519 540 6.889301 TGTTCTTTCTCTCTTGATGCAAAT 57.111 33.333 0.00 0.00 0.00 2.32
520 541 6.263842 ACATGTTCTTTCTCTCTTGATGCAAA 59.736 34.615 0.00 0.00 0.00 3.68
521 542 5.766670 ACATGTTCTTTCTCTCTTGATGCAA 59.233 36.000 0.00 0.00 0.00 4.08
522 543 5.311265 ACATGTTCTTTCTCTCTTGATGCA 58.689 37.500 0.00 0.00 0.00 3.96
523 544 5.876612 ACATGTTCTTTCTCTCTTGATGC 57.123 39.130 0.00 0.00 0.00 3.91
586 607 6.518200 CGGGGTTGAATAATTATCCCAAATGG 60.518 42.308 17.49 0.00 36.90 3.16
587 608 6.454795 CGGGGTTGAATAATTATCCCAAATG 58.545 40.000 17.49 5.05 36.90 2.32
588 609 5.542251 CCGGGGTTGAATAATTATCCCAAAT 59.458 40.000 17.49 0.00 36.90 2.32
589 610 4.896482 CCGGGGTTGAATAATTATCCCAAA 59.104 41.667 17.49 1.72 36.90 3.28
590 611 4.475345 CCGGGGTTGAATAATTATCCCAA 58.525 43.478 17.49 12.94 36.90 4.12
591 612 3.752542 GCCGGGGTTGAATAATTATCCCA 60.753 47.826 17.49 8.65 36.90 4.37
592 613 2.823747 GCCGGGGTTGAATAATTATCCC 59.176 50.000 2.18 10.30 34.68 3.85
593 614 2.823747 GGCCGGGGTTGAATAATTATCC 59.176 50.000 2.18 0.00 0.00 2.59
594 615 3.763057 AGGCCGGGGTTGAATAATTATC 58.237 45.455 2.18 0.00 0.00 1.75
595 616 3.895041 CAAGGCCGGGGTTGAATAATTAT 59.105 43.478 2.18 0.00 0.00 1.28
596 617 3.292460 CAAGGCCGGGGTTGAATAATTA 58.708 45.455 2.18 0.00 0.00 1.40
597 618 2.107366 CAAGGCCGGGGTTGAATAATT 58.893 47.619 2.18 0.00 0.00 1.40
598 619 1.006639 ACAAGGCCGGGGTTGAATAAT 59.993 47.619 2.18 0.00 0.00 1.28
599 620 0.406361 ACAAGGCCGGGGTTGAATAA 59.594 50.000 2.18 0.00 0.00 1.40
600 621 0.406361 AACAAGGCCGGGGTTGAATA 59.594 50.000 2.18 0.00 0.00 1.75
601 622 0.471022 AAACAAGGCCGGGGTTGAAT 60.471 50.000 2.18 0.00 0.00 2.57
602 623 1.075896 AAACAAGGCCGGGGTTGAA 60.076 52.632 2.18 0.00 0.00 2.69
603 624 1.830408 CAAACAAGGCCGGGGTTGA 60.830 57.895 19.15 0.00 0.00 3.18
604 625 2.733945 CAAACAAGGCCGGGGTTG 59.266 61.111 12.16 12.16 0.00 3.77
605 626 2.523168 CCAAACAAGGCCGGGGTT 60.523 61.111 2.18 0.00 0.00 4.11
606 627 3.383031 AACCAAACAAGGCCGGGGT 62.383 57.895 2.18 0.00 0.00 4.95
607 628 2.523168 AACCAAACAAGGCCGGGG 60.523 61.111 2.18 0.00 0.00 5.73
608 629 2.131067 ACAACCAAACAAGGCCGGG 61.131 57.895 2.18 0.00 0.00 5.73
609 630 1.067250 CACAACCAAACAAGGCCGG 59.933 57.895 0.00 0.00 0.00 6.13
610 631 0.527385 CACACAACCAAACAAGGCCG 60.527 55.000 0.00 0.00 0.00 6.13
611 632 0.534873 ACACACAACCAAACAAGGCC 59.465 50.000 0.00 0.00 0.00 5.19
612 633 1.639280 CACACACAACCAAACAAGGC 58.361 50.000 0.00 0.00 0.00 4.35
613 634 1.821753 TCCACACACAACCAAACAAGG 59.178 47.619 0.00 0.00 0.00 3.61
614 635 3.490761 GGATCCACACACAACCAAACAAG 60.491 47.826 6.95 0.00 0.00 3.16
615 636 2.428890 GGATCCACACACAACCAAACAA 59.571 45.455 6.95 0.00 0.00 2.83
616 637 2.028130 GGATCCACACACAACCAAACA 58.972 47.619 6.95 0.00 0.00 2.83
617 638 1.001815 CGGATCCACACACAACCAAAC 60.002 52.381 13.41 0.00 0.00 2.93
618 639 1.134068 TCGGATCCACACACAACCAAA 60.134 47.619 13.41 0.00 0.00 3.28
619 640 0.470341 TCGGATCCACACACAACCAA 59.530 50.000 13.41 0.00 0.00 3.67
620 641 0.034756 CTCGGATCCACACACAACCA 59.965 55.000 13.41 0.00 0.00 3.67
621 642 0.673644 CCTCGGATCCACACACAACC 60.674 60.000 13.41 0.00 0.00 3.77
622 643 0.673644 CCCTCGGATCCACACACAAC 60.674 60.000 13.41 0.00 0.00 3.32
623 644 1.676968 CCCTCGGATCCACACACAA 59.323 57.895 13.41 0.00 0.00 3.33
624 645 2.290287 CCCCTCGGATCCACACACA 61.290 63.158 13.41 0.00 0.00 3.72
625 646 2.240162 GACCCCTCGGATCCACACAC 62.240 65.000 13.41 0.00 0.00 3.82
626 647 1.987855 GACCCCTCGGATCCACACA 60.988 63.158 13.41 0.00 0.00 3.72
627 648 1.686110 AGACCCCTCGGATCCACAC 60.686 63.158 13.41 0.00 0.00 3.82
628 649 1.685765 CAGACCCCTCGGATCCACA 60.686 63.158 13.41 0.00 0.00 4.17
629 650 1.686110 ACAGACCCCTCGGATCCAC 60.686 63.158 13.41 0.00 0.00 4.02
630 651 1.685765 CACAGACCCCTCGGATCCA 60.686 63.158 13.41 0.00 0.00 3.41
631 652 2.435693 CCACAGACCCCTCGGATCC 61.436 68.421 0.00 0.00 0.00 3.36
632 653 2.435693 CCCACAGACCCCTCGGATC 61.436 68.421 0.00 0.00 0.00 3.36
633 654 2.365635 CCCACAGACCCCTCGGAT 60.366 66.667 0.00 0.00 0.00 4.18
634 655 4.715130 CCCCACAGACCCCTCGGA 62.715 72.222 0.00 0.00 0.00 4.55
636 657 4.715130 TCCCCCACAGACCCCTCG 62.715 72.222 0.00 0.00 0.00 4.63
637 658 1.214992 AAATCCCCCACAGACCCCTC 61.215 60.000 0.00 0.00 0.00 4.30
638 659 0.122435 TAAATCCCCCACAGACCCCT 59.878 55.000 0.00 0.00 0.00 4.79
639 660 1.004436 TTAAATCCCCCACAGACCCC 58.996 55.000 0.00 0.00 0.00 4.95
640 661 2.042569 AGTTTAAATCCCCCACAGACCC 59.957 50.000 0.00 0.00 0.00 4.46
641 662 3.010250 AGAGTTTAAATCCCCCACAGACC 59.990 47.826 0.00 0.00 0.00 3.85
642 663 4.302559 AGAGTTTAAATCCCCCACAGAC 57.697 45.455 0.00 0.00 0.00 3.51
643 664 6.652205 ATAAGAGTTTAAATCCCCCACAGA 57.348 37.500 0.00 0.00 0.00 3.41
644 665 8.053355 ACTTATAAGAGTTTAAATCCCCCACAG 58.947 37.037 19.38 0.00 0.00 3.66
645 666 7.935405 ACTTATAAGAGTTTAAATCCCCCACA 58.065 34.615 19.38 0.00 0.00 4.17
646 667 8.050930 TGACTTATAAGAGTTTAAATCCCCCAC 58.949 37.037 19.38 0.00 0.00 4.61
647 668 8.165267 TGACTTATAAGAGTTTAAATCCCCCA 57.835 34.615 19.38 0.00 0.00 4.96
648 669 9.470399 TTTGACTTATAAGAGTTTAAATCCCCC 57.530 33.333 19.38 0.00 0.00 5.40
672 693 8.649733 CCTTTCAAGAGGATTGGAACGTAGTTT 61.650 40.741 0.00 0.00 45.64 2.66
674 695 5.800239 CCTTTCAAGAGGATTGGAACGTAGT 60.800 44.000 0.00 0.00 40.79 2.73
675 696 4.631813 CCTTTCAAGAGGATTGGAACGTAG 59.368 45.833 0.00 0.00 39.25 3.51
676 697 4.285003 TCCTTTCAAGAGGATTGGAACGTA 59.715 41.667 0.00 0.00 40.87 3.57
677 698 3.072476 TCCTTTCAAGAGGATTGGAACGT 59.928 43.478 0.00 0.00 40.87 3.99
678 699 3.674997 TCCTTTCAAGAGGATTGGAACG 58.325 45.455 0.00 0.00 40.87 3.95
688 709 6.818644 TGTTCGATTAATCCTCCTTTCAAGAG 59.181 38.462 9.87 0.00 0.00 2.85
689 710 6.707290 TGTTCGATTAATCCTCCTTTCAAGA 58.293 36.000 9.87 0.00 0.00 3.02
690 711 6.985188 TGTTCGATTAATCCTCCTTTCAAG 57.015 37.500 9.87 0.00 0.00 3.02
691 712 6.128007 GCTTGTTCGATTAATCCTCCTTTCAA 60.128 38.462 9.87 5.62 0.00 2.69
692 713 5.354234 GCTTGTTCGATTAATCCTCCTTTCA 59.646 40.000 9.87 0.00 0.00 2.69
693 714 5.354234 TGCTTGTTCGATTAATCCTCCTTTC 59.646 40.000 9.87 0.00 0.00 2.62
694 715 5.253330 TGCTTGTTCGATTAATCCTCCTTT 58.747 37.500 9.87 0.00 0.00 3.11
695 716 4.843728 TGCTTGTTCGATTAATCCTCCTT 58.156 39.130 9.87 0.00 0.00 3.36
696 717 4.487714 TGCTTGTTCGATTAATCCTCCT 57.512 40.909 9.87 0.00 0.00 3.69
697 718 5.757850 ATTGCTTGTTCGATTAATCCTCC 57.242 39.130 9.87 0.00 0.00 4.30
698 719 9.226345 CTTTTATTGCTTGTTCGATTAATCCTC 57.774 33.333 9.87 1.78 0.00 3.71
699 720 8.956426 TCTTTTATTGCTTGTTCGATTAATCCT 58.044 29.630 9.87 0.00 0.00 3.24
700 721 9.736023 ATCTTTTATTGCTTGTTCGATTAATCC 57.264 29.630 9.87 0.00 0.00 3.01
809 836 6.164876 TCCACGATAAGTAATTTGAAACGGA 58.835 36.000 0.00 0.00 0.00 4.69
810 837 6.091713 ACTCCACGATAAGTAATTTGAAACGG 59.908 38.462 0.00 0.00 0.00 4.44
811 838 7.057149 ACTCCACGATAAGTAATTTGAAACG 57.943 36.000 0.00 0.00 0.00 3.60
819 846 9.847224 ATTCCAAATTACTCCACGATAAGTAAT 57.153 29.630 12.19 12.19 45.87 1.89
820 847 9.104965 CATTCCAAATTACTCCACGATAAGTAA 57.895 33.333 9.49 9.49 41.00 2.24
821 848 7.713507 CCATTCCAAATTACTCCACGATAAGTA 59.286 37.037 0.00 0.00 0.00 2.24
822 849 6.542370 CCATTCCAAATTACTCCACGATAAGT 59.458 38.462 0.00 0.00 0.00 2.24
823 850 6.765989 TCCATTCCAAATTACTCCACGATAAG 59.234 38.462 0.00 0.00 0.00 1.73
824 851 6.654959 TCCATTCCAAATTACTCCACGATAA 58.345 36.000 0.00 0.00 0.00 1.75
825 852 6.099125 TCTCCATTCCAAATTACTCCACGATA 59.901 38.462 0.00 0.00 0.00 2.92
826 853 5.104527 TCTCCATTCCAAATTACTCCACGAT 60.105 40.000 0.00 0.00 0.00 3.73
827 854 4.224147 TCTCCATTCCAAATTACTCCACGA 59.776 41.667 0.00 0.00 0.00 4.35
828 855 4.513442 TCTCCATTCCAAATTACTCCACG 58.487 43.478 0.00 0.00 0.00 4.94
829 856 5.745227 TCTCTCCATTCCAAATTACTCCAC 58.255 41.667 0.00 0.00 0.00 4.02
830 857 5.488919 ACTCTCTCCATTCCAAATTACTCCA 59.511 40.000 0.00 0.00 0.00 3.86
831 858 5.995446 ACTCTCTCCATTCCAAATTACTCC 58.005 41.667 0.00 0.00 0.00 3.85
832 859 6.697892 CGTACTCTCTCCATTCCAAATTACTC 59.302 42.308 0.00 0.00 0.00 2.59
833 860 6.154706 ACGTACTCTCTCCATTCCAAATTACT 59.845 38.462 0.00 0.00 0.00 2.24
834 861 6.338937 ACGTACTCTCTCCATTCCAAATTAC 58.661 40.000 0.00 0.00 0.00 1.89
835 862 6.540438 ACGTACTCTCTCCATTCCAAATTA 57.460 37.500 0.00 0.00 0.00 1.40
836 863 5.422214 ACGTACTCTCTCCATTCCAAATT 57.578 39.130 0.00 0.00 0.00 1.82
837 864 5.422214 AACGTACTCTCTCCATTCCAAAT 57.578 39.130 0.00 0.00 0.00 2.32
838 865 4.884668 AACGTACTCTCTCCATTCCAAA 57.115 40.909 0.00 0.00 0.00 3.28
839 866 4.527038 AGAAACGTACTCTCTCCATTCCAA 59.473 41.667 0.00 0.00 0.00 3.53
840 867 4.082190 CAGAAACGTACTCTCTCCATTCCA 60.082 45.833 0.00 0.00 0.00 3.53
841 868 4.425520 CAGAAACGTACTCTCTCCATTCC 58.574 47.826 0.00 0.00 0.00 3.01
842 869 3.860536 GCAGAAACGTACTCTCTCCATTC 59.139 47.826 0.00 0.00 0.00 2.67
843 870 3.368531 GGCAGAAACGTACTCTCTCCATT 60.369 47.826 0.00 0.00 0.00 3.16
844 871 2.166664 GGCAGAAACGTACTCTCTCCAT 59.833 50.000 0.00 0.00 0.00 3.41
845 872 1.544691 GGCAGAAACGTACTCTCTCCA 59.455 52.381 0.00 0.00 0.00 3.86
846 873 1.467713 CGGCAGAAACGTACTCTCTCC 60.468 57.143 0.00 0.00 0.00 3.71
847 874 1.199558 ACGGCAGAAACGTACTCTCTC 59.800 52.381 0.00 0.00 43.60 3.20
848 875 1.068472 CACGGCAGAAACGTACTCTCT 60.068 52.381 0.00 0.00 43.58 3.10
849 876 1.337821 CACGGCAGAAACGTACTCTC 58.662 55.000 0.00 0.00 43.58 3.20
850 877 0.666577 GCACGGCAGAAACGTACTCT 60.667 55.000 0.00 0.00 43.58 3.24
851 878 0.666577 AGCACGGCAGAAACGTACTC 60.667 55.000 0.00 0.00 43.58 2.59
852 879 0.249741 AAGCACGGCAGAAACGTACT 60.250 50.000 0.00 0.00 43.58 2.73
853 880 0.163146 GAAGCACGGCAGAAACGTAC 59.837 55.000 0.00 0.00 43.58 3.67
860 887 1.301716 GAACCAGAAGCACGGCAGA 60.302 57.895 0.00 0.00 0.00 4.26
866 893 2.210116 TCGTTTCAGAACCAGAAGCAC 58.790 47.619 0.00 0.00 31.93 4.40
883 910 1.673920 AGTTCGGCACAAACATTTCGT 59.326 42.857 0.00 0.00 0.00 3.85
908 935 5.924356 TGACTGACTGGAAAATACACTCAA 58.076 37.500 0.00 0.00 0.00 3.02
911 938 6.114187 TGATGACTGACTGGAAAATACACT 57.886 37.500 0.00 0.00 0.00 3.55
1937 1968 2.430367 GGTTGTTGCCGAGGAGGT 59.570 61.111 0.00 0.00 43.70 3.85
1977 2008 0.884704 GCAGGCTGTTCACCGAGAAA 60.885 55.000 17.16 0.00 38.13 2.52
2073 2104 2.555325 GTTAAAGGTCAAAAGGTCCGGG 59.445 50.000 0.00 0.00 0.00 5.73
2085 2116 3.797256 CGGAGATGACGATGTTAAAGGTC 59.203 47.826 0.00 0.00 0.00 3.85
2091 2122 0.387929 GCCCGGAGATGACGATGTTA 59.612 55.000 0.73 0.00 0.00 2.41
2195 2226 0.528466 GCCGTCGATGAGAGCATTGA 60.528 55.000 6.11 0.00 41.55 2.57
2331 2362 0.668706 CAGTGTTCGAGTCCTGGCAG 60.669 60.000 7.75 7.75 0.00 4.85
2448 2479 1.952621 TCACCCCTTCCTCTACCTTG 58.047 55.000 0.00 0.00 0.00 3.61
2613 2644 7.332430 TCAATCAAGGTATTGTAAGTAACCACG 59.668 37.037 0.00 0.00 37.94 4.94
2691 2722 1.074566 CTAATCCCCTTCCCTGCCATC 59.925 57.143 0.00 0.00 0.00 3.51
2915 2946 0.036010 CCGATGCTCTGGTTCCAAGT 60.036 55.000 0.00 0.00 0.00 3.16
3155 3186 3.912528 CTCCATCATCCCCTCCTTGATTA 59.087 47.826 0.00 0.00 0.00 1.75
3260 3291 7.010552 CAGACAAGCTATGTTGGTACATTACTC 59.989 40.741 0.00 0.00 42.29 2.59
3286 3317 9.310716 CTTTGTTTGCTAGGTATAAGTAGGTAC 57.689 37.037 0.00 0.00 0.00 3.34
3357 3388 6.789959 ACTATGACCTAGCAGAATTAGGGATT 59.210 38.462 3.60 0.00 41.66 3.01
3388 3427 4.853924 ACATCCAAACCTAAAAGCAGTG 57.146 40.909 0.00 0.00 0.00 3.66
3389 3428 6.719370 TGATAACATCCAAACCTAAAAGCAGT 59.281 34.615 0.00 0.00 0.00 4.40
3398 3437 5.422012 GGACCAAATGATAACATCCAAACCT 59.578 40.000 0.00 0.00 35.50 3.50
3410 3449 9.787435 GTTATACCACATAAGGACCAAATGATA 57.213 33.333 11.83 3.72 0.00 2.15
3487 3526 3.821033 GTGAACTGCAAGGTAGTTGGATT 59.179 43.478 4.45 0.00 38.42 3.01
3527 3570 4.407365 ACTGGGTCCAAGAAAATACCAAG 58.593 43.478 0.00 0.00 38.76 3.61
3533 3576 5.163311 CCAAAAAGACTGGGTCCAAGAAAAT 60.163 40.000 0.00 0.00 32.18 1.82
3567 3610 6.601613 AGTTTACTTCCTTCAATGTGAACACA 59.398 34.615 10.04 10.04 46.44 3.72
3629 4316 8.888579 AGTATGACATTACCACTAATAAGCAC 57.111 34.615 0.00 0.00 0.00 4.40
3636 4323 8.700973 TGAATGCTAGTATGACATTACCACTAA 58.299 33.333 0.00 0.00 34.28 2.24
3667 4354 3.506455 TCGTGCTAAGTACTCTGAAAGCT 59.494 43.478 0.00 0.00 0.00 3.74
3744 4431 2.162681 GTTGCACAGGTATTTGCCTCT 58.837 47.619 0.00 0.00 38.00 3.69
3753 4440 4.086457 TGTCAGATAGAGTTGCACAGGTA 58.914 43.478 0.00 0.00 0.00 3.08
3805 4492 2.283604 TGTCCAGGAGGCGCAGTA 60.284 61.111 10.83 0.00 33.74 2.74
3835 4522 6.696148 CCTTCAAACGTAGGCTATACAGTAAG 59.304 42.308 0.00 0.00 0.00 2.34
3930 4617 5.940192 TTTTGTCGCCCTTATATATGCTG 57.060 39.130 0.00 0.00 0.00 4.41
4164 4942 5.734220 GCCTCGATATGCACATGATGTTTTT 60.734 40.000 0.00 0.00 0.00 1.94
4171 4949 2.916702 AAGCCTCGATATGCACATGA 57.083 45.000 0.00 0.00 0.00 3.07
4209 4987 8.121305 ACCATCAGCAAGACAAACAATATTAA 57.879 30.769 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.