Multiple sequence alignment - TraesCS4B01G254800

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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 TraesCS4B01G254800 chr4B 100.000 6442 0 0 1 6442 520208568 520215009 0.000000e+00 11897.0
1 TraesCS4B01G254800 chr4B 89.873 553 45 6 1 544 112133144 112132594 0.000000e+00 701.0
2 TraesCS4B01G254800 chr4B 89.350 554 45 10 1 544 109832449 109831900 0.000000e+00 684.0
3 TraesCS4B01G254800 chr4B 100.000 357 0 0 6779 7135 520215346 520215702 0.000000e+00 660.0
4 TraesCS4B01G254800 chr4B 90.909 66 6 0 1797 1862 149736857 149736922 9.860000e-14 89.8
5 TraesCS4B01G254800 chr4D 93.706 5720 218 63 794 6442 423588870 423594518 0.000000e+00 8438.0
6 TraesCS4B01G254800 chr4D 89.068 558 49 8 1 548 418271620 418271065 0.000000e+00 682.0
7 TraesCS4B01G254800 chr4D 90.000 360 26 7 6779 7132 423594554 423594909 2.350000e-124 457.0
8 TraesCS4B01G254800 chr4D 89.655 261 20 4 545 798 133735948 133736208 6.900000e-85 326.0
9 TraesCS4B01G254800 chr4D 100.000 28 0 0 7058 7085 108220976 108221003 1.300000e-02 52.8
10 TraesCS4B01G254800 chr4A 91.200 2875 154 36 3623 6442 40541093 40538263 0.000000e+00 3816.0
11 TraesCS4B01G254800 chr4A 90.310 1868 112 37 1797 3641 40543266 40541445 0.000000e+00 2383.0
12 TraesCS4B01G254800 chr4A 92.058 894 39 10 896 1787 40544225 40543362 0.000000e+00 1229.0
13 TraesCS4B01G254800 chr4A 88.981 363 28 9 6779 7135 40538240 40537884 8.500000e-119 438.0
14 TraesCS4B01G254800 chr3D 90.958 553 40 6 1 544 583840558 583840007 0.000000e+00 736.0
15 TraesCS4B01G254800 chr3D 87.356 261 29 3 545 801 380530058 380529798 5.410000e-76 296.0
16 TraesCS4B01G254800 chr3D 80.645 124 13 7 6885 7004 497709172 497709056 1.280000e-12 86.1
17 TraesCS4B01G254800 chr6B 90.235 553 43 6 1 544 448202240 448201690 0.000000e+00 712.0
18 TraesCS4B01G254800 chr6B 89.730 555 42 9 1 544 325200628 325201178 0.000000e+00 695.0
19 TraesCS4B01G254800 chr6B 85.475 179 24 1 5191 5367 633849743 633849565 1.220000e-42 185.0
20 TraesCS4B01G254800 chr6B 96.875 32 1 0 6860 6891 617343667 617343698 4.000000e-03 54.7
21 TraesCS4B01G254800 chr2B 90.054 553 45 5 1 544 168115851 168116402 0.000000e+00 708.0
22 TraesCS4B01G254800 chr3B 89.493 552 48 6 2 544 360185588 360186138 0.000000e+00 689.0
23 TraesCS4B01G254800 chr3B 87.143 70 3 3 6885 6953 657771485 657771421 2.760000e-09 75.0
24 TraesCS4B01G254800 chr7B 89.189 555 48 7 1 544 203733222 203733775 0.000000e+00 682.0
25 TraesCS4B01G254800 chr7B 77.996 559 80 18 1797 2336 683246741 683247275 1.930000e-80 311.0
26 TraesCS4B01G254800 chr2D 89.494 257 22 4 545 796 30431119 30431375 3.210000e-83 320.0
27 TraesCS4B01G254800 chr2D 89.272 261 21 4 545 798 629603841 629604101 3.210000e-83 320.0
28 TraesCS4B01G254800 chr2D 100.000 29 0 0 7059 7087 49619797 49619769 4.000000e-03 54.7
29 TraesCS4B01G254800 chr5B 89.231 260 20 5 545 796 419498647 419498388 1.160000e-82 318.0
30 TraesCS4B01G254800 chr5D 89.105 257 23 4 545 796 445868169 445868425 1.490000e-81 315.0
31 TraesCS4B01G254800 chr7D 88.417 259 24 3 545 798 83751861 83752118 2.500000e-79 307.0
32 TraesCS4B01G254800 chr7D 88.327 257 25 5 545 796 36452955 36453211 3.230000e-78 303.0
33 TraesCS4B01G254800 chr6D 88.235 255 27 2 545 796 437961197 437960943 1.160000e-77 302.0
34 TraesCS4B01G254800 chr6D 85.057 87 10 3 6816 6902 2835917 2836000 1.280000e-12 86.1
35 TraesCS4B01G254800 chr3A 77.652 528 71 24 1797 2300 697485202 697484698 1.960000e-70 278.0
36 TraesCS4B01G254800 chr6A 78.371 356 45 19 5006 5360 203600919 203601243 1.210000e-47 202.0
37 TraesCS4B01G254800 chr6A 78.852 331 44 12 1797 2104 103974480 103974153 4.370000e-47 200.0
38 TraesCS4B01G254800 chr1A 83.704 135 17 5 6827 6960 546036087 546036217 9.720000e-24 122.0
39 TraesCS4B01G254800 chr5A 96.875 32 1 0 7059 7090 516670096 516670127 4.000000e-03 54.7
40 TraesCS4B01G254800 chr2A 96.875 32 0 1 7055 7085 749628835 749628866 1.300000e-02 52.8
41 TraesCS4B01G254800 chr1D 80.556 72 10 3 7058 7125 396331607 396331536 1.300000e-02 52.8
42 TraesCS4B01G254800 chr1B 100.000 28 0 0 7058 7085 7122726 7122753 1.300000e-02 52.8
43 TraesCS4B01G254800 chr1B 100.000 28 0 0 7058 7085 523216293 523216320 1.300000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G254800 chr4B 520208568 520215702 7134 False 6278.5 11897 100.00000 1 7135 2 chr4B.!!$F2 7134
1 TraesCS4B01G254800 chr4B 112132594 112133144 550 True 701.0 701 89.87300 1 544 1 chr4B.!!$R2 543
2 TraesCS4B01G254800 chr4B 109831900 109832449 549 True 684.0 684 89.35000 1 544 1 chr4B.!!$R1 543
3 TraesCS4B01G254800 chr4D 423588870 423594909 6039 False 4447.5 8438 91.85300 794 7132 2 chr4D.!!$F3 6338
4 TraesCS4B01G254800 chr4D 418271065 418271620 555 True 682.0 682 89.06800 1 548 1 chr4D.!!$R1 547
5 TraesCS4B01G254800 chr4A 40537884 40544225 6341 True 1966.5 3816 90.63725 896 7135 4 chr4A.!!$R1 6239
6 TraesCS4B01G254800 chr3D 583840007 583840558 551 True 736.0 736 90.95800 1 544 1 chr3D.!!$R3 543
7 TraesCS4B01G254800 chr6B 448201690 448202240 550 True 712.0 712 90.23500 1 544 1 chr6B.!!$R1 543
8 TraesCS4B01G254800 chr6B 325200628 325201178 550 False 695.0 695 89.73000 1 544 1 chr6B.!!$F1 543
9 TraesCS4B01G254800 chr2B 168115851 168116402 551 False 708.0 708 90.05400 1 544 1 chr2B.!!$F1 543
10 TraesCS4B01G254800 chr3B 360185588 360186138 550 False 689.0 689 89.49300 2 544 1 chr3B.!!$F1 542
11 TraesCS4B01G254800 chr7B 203733222 203733775 553 False 682.0 682 89.18900 1 544 1 chr7B.!!$F1 543
12 TraesCS4B01G254800 chr7B 683246741 683247275 534 False 311.0 311 77.99600 1797 2336 1 chr7B.!!$F2 539
13 TraesCS4B01G254800 chr3A 697484698 697485202 504 True 278.0 278 77.65200 1797 2300 1 chr3A.!!$R1 503

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
795 809 0.035630 GTGGCTGTTGGAGATGCTCT 60.036 55.000 0.00 0.00 0.00 4.09 F
803 817 0.738975 TGGAGATGCTCTAACGGACG 59.261 55.000 0.00 0.00 0.00 4.79 F
804 818 1.022735 GGAGATGCTCTAACGGACGA 58.977 55.000 0.00 0.00 0.00 4.20 F
1730 1764 1.029681 AAACCTTTGTTCGTCAGGCC 58.970 50.000 0.00 0.00 32.15 5.19 F
3478 3668 1.275002 ACATGGAGGATAGGGTTGGGT 60.275 52.381 0.00 0.00 0.00 4.51 F
3697 4260 0.036952 ATGACGAGCCAGGTGTCTTG 60.037 55.000 9.24 0.00 33.81 3.02 F
4095 4661 0.698818 ATGTTCTGGACTTGTCCCCC 59.301 55.000 16.23 3.45 0.00 5.40 F
5836 6462 0.392729 CAAGAGCCCAAGAGAGCCAG 60.393 60.000 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1754 0.249120 AATGATCACGGCCTGACGAA 59.751 50.000 0.00 0.00 37.61 3.85 R
1789 1838 2.543848 GCAAAACACTCGTCACTCATCA 59.456 45.455 0.00 0.00 0.00 3.07 R
2225 2390 2.553028 GCTCACTGAATGGGGAAGAACA 60.553 50.000 0.00 0.00 0.00 3.18 R
3640 4202 1.202879 AGGCGATCAACAACTTGGGAA 60.203 47.619 0.00 0.00 0.00 3.97 R
5034 5643 1.577328 GCTGGTCATGGTTGTCGTGG 61.577 60.000 0.00 0.00 33.31 4.94 R
5681 6307 0.940126 CACCATCGCATAAGCTGACC 59.060 55.000 0.00 0.00 39.10 4.02 R
5841 6467 1.795768 AGCAGATTTCGCGTCTCAAA 58.204 45.000 5.77 0.00 0.00 2.69 R
6893 7544 8.816144 GTTTGAAGAAATTCTTGCAAACATGTA 58.184 29.630 30.89 14.52 43.69 2.29 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
94 96 4.278419 GGATAGTCTTTGCCACACAGTTTT 59.722 41.667 0.00 0.00 0.00 2.43
168 170 1.795768 ATTGTGTGCGATGAGAACGT 58.204 45.000 0.00 0.00 0.00 3.99
185 187 6.128929 TGAGAACGTCATCACAAACGATTTAG 60.129 38.462 1.52 0.00 41.29 1.85
239 242 2.061028 GAAATGTTTTCCTTGCAGCGG 58.939 47.619 0.00 0.00 0.00 5.52
290 294 0.389817 TTCGCGGAGATTGACTGTGG 60.390 55.000 6.13 0.00 0.00 4.17
307 311 4.538490 ACTGTGGGGGATGTACTTATGAAA 59.462 41.667 0.00 0.00 0.00 2.69
434 447 0.942252 GCATATCCCCGACGTTTTCC 59.058 55.000 0.00 0.00 0.00 3.13
472 486 0.469917 CCCTAATCGCCCACACTCAT 59.530 55.000 0.00 0.00 0.00 2.90
544 558 2.869646 CACCGACGCGTACCAGTA 59.130 61.111 13.97 0.00 0.00 2.74
546 560 0.179156 CACCGACGCGTACCAGTAAT 60.179 55.000 13.97 0.00 0.00 1.89
548 562 1.194495 CCGACGCGTACCAGTAATTC 58.806 55.000 13.97 0.00 0.00 2.17
549 563 0.835740 CGACGCGTACCAGTAATTCG 59.164 55.000 13.97 2.98 0.00 3.34
550 564 0.569349 GACGCGTACCAGTAATTCGC 59.431 55.000 13.97 0.00 42.78 4.70
551 565 0.803380 ACGCGTACCAGTAATTCGCC 60.803 55.000 11.67 0.00 43.18 5.54
552 566 1.804273 CGCGTACCAGTAATTCGCCG 61.804 60.000 0.00 0.00 43.18 6.46
553 567 1.485032 GCGTACCAGTAATTCGCCGG 61.485 60.000 0.00 0.00 40.83 6.13
554 568 1.485032 CGTACCAGTAATTCGCCGGC 61.485 60.000 19.07 19.07 0.00 6.13
555 569 1.227031 TACCAGTAATTCGCCGGCG 60.227 57.895 42.13 42.13 41.35 6.46
556 570 2.632136 TACCAGTAATTCGCCGGCGG 62.632 60.000 44.95 29.28 40.25 6.13
557 571 3.937062 CAGTAATTCGCCGGCGGC 61.937 66.667 44.95 39.60 46.75 6.53
602 616 3.749064 GGAGAGAGTGCGGCGTGA 61.749 66.667 9.37 0.00 0.00 4.35
603 617 2.202544 GAGAGAGTGCGGCGTGAG 60.203 66.667 9.37 0.00 0.00 3.51
615 629 3.168604 CGTGAGCGCTCGAGTGTG 61.169 66.667 30.75 13.43 33.14 3.82
616 630 3.474034 GTGAGCGCTCGAGTGTGC 61.474 66.667 30.75 20.26 43.09 4.57
617 631 4.724602 TGAGCGCTCGAGTGTGCC 62.725 66.667 30.75 15.49 43.73 5.01
640 654 3.350612 CGAAAGCGGGCGAACCAA 61.351 61.111 0.00 0.00 40.22 3.67
641 655 2.899044 CGAAAGCGGGCGAACCAAA 61.899 57.895 0.00 0.00 40.22 3.28
642 656 1.081442 GAAAGCGGGCGAACCAAAG 60.081 57.895 0.00 0.00 40.22 2.77
643 657 1.512156 GAAAGCGGGCGAACCAAAGA 61.512 55.000 0.00 0.00 40.22 2.52
644 658 1.792118 AAAGCGGGCGAACCAAAGAC 61.792 55.000 0.00 0.00 40.22 3.01
645 659 2.951475 AAGCGGGCGAACCAAAGACA 62.951 55.000 0.00 0.00 40.22 3.41
646 660 2.943653 CGGGCGAACCAAAGACAC 59.056 61.111 0.00 0.00 40.22 3.67
647 661 1.890041 CGGGCGAACCAAAGACACA 60.890 57.895 0.00 0.00 40.22 3.72
648 662 1.841663 CGGGCGAACCAAAGACACAG 61.842 60.000 0.00 0.00 40.22 3.66
649 663 1.515521 GGGCGAACCAAAGACACAGG 61.516 60.000 0.00 0.00 39.85 4.00
650 664 0.534203 GGCGAACCAAAGACACAGGA 60.534 55.000 0.00 0.00 35.26 3.86
651 665 0.586802 GCGAACCAAAGACACAGGAC 59.413 55.000 0.00 0.00 0.00 3.85
652 666 0.859232 CGAACCAAAGACACAGGACG 59.141 55.000 0.00 0.00 0.00 4.79
653 667 0.586802 GAACCAAAGACACAGGACGC 59.413 55.000 0.00 0.00 0.00 5.19
654 668 1.157870 AACCAAAGACACAGGACGCG 61.158 55.000 3.53 3.53 0.00 6.01
655 669 1.300620 CCAAAGACACAGGACGCGA 60.301 57.895 15.93 0.00 0.00 5.87
656 670 0.670546 CCAAAGACACAGGACGCGAT 60.671 55.000 15.93 0.00 0.00 4.58
657 671 0.439985 CAAAGACACAGGACGCGATG 59.560 55.000 15.93 11.34 0.00 3.84
658 672 0.317160 AAAGACACAGGACGCGATGA 59.683 50.000 15.93 0.00 0.00 2.92
659 673 0.388649 AAGACACAGGACGCGATGAC 60.389 55.000 15.93 3.36 0.00 3.06
660 674 1.080772 GACACAGGACGCGATGACA 60.081 57.895 15.93 0.00 0.00 3.58
661 675 0.666274 GACACAGGACGCGATGACAA 60.666 55.000 15.93 0.00 0.00 3.18
662 676 0.037326 ACACAGGACGCGATGACAAT 60.037 50.000 15.93 0.00 0.00 2.71
663 677 1.078709 CACAGGACGCGATGACAATT 58.921 50.000 15.93 0.00 0.00 2.32
664 678 1.061131 CACAGGACGCGATGACAATTC 59.939 52.381 15.93 0.00 0.00 2.17
665 679 0.298707 CAGGACGCGATGACAATTCG 59.701 55.000 15.93 0.00 39.55 3.34
666 680 0.172578 AGGACGCGATGACAATTCGA 59.827 50.000 15.93 0.00 38.88 3.71
667 681 0.996462 GGACGCGATGACAATTCGAA 59.004 50.000 15.93 0.00 38.88 3.71
668 682 1.266891 GGACGCGATGACAATTCGAAC 60.267 52.381 15.93 0.00 38.88 3.95
669 683 0.719465 ACGCGATGACAATTCGAACC 59.281 50.000 15.93 0.00 38.88 3.62
670 684 0.314259 CGCGATGACAATTCGAACCG 60.314 55.000 0.00 0.00 38.88 4.44
671 685 0.586502 GCGATGACAATTCGAACCGC 60.587 55.000 0.00 3.83 38.88 5.68
672 686 0.314259 CGATGACAATTCGAACCGCG 60.314 55.000 0.00 0.00 38.88 6.46
673 687 0.586502 GATGACAATTCGAACCGCGC 60.587 55.000 0.00 0.00 40.61 6.86
674 688 2.275812 GACAATTCGAACCGCGCG 60.276 61.111 25.67 25.67 40.61 6.86
675 689 4.439472 ACAATTCGAACCGCGCGC 62.439 61.111 27.36 23.91 40.61 6.86
685 699 4.891727 CCGCGCGCCCAACTCTAT 62.892 66.667 27.36 0.00 0.00 1.98
686 700 2.027024 CGCGCGCCCAACTCTATA 59.973 61.111 27.72 0.00 0.00 1.31
687 701 1.372997 CGCGCGCCCAACTCTATAT 60.373 57.895 27.72 0.00 0.00 0.86
688 702 1.617755 CGCGCGCCCAACTCTATATG 61.618 60.000 27.72 1.87 0.00 1.78
689 703 1.901650 GCGCGCCCAACTCTATATGC 61.902 60.000 23.24 0.00 0.00 3.14
690 704 1.291877 CGCGCCCAACTCTATATGCC 61.292 60.000 0.00 0.00 0.00 4.40
691 705 1.291877 GCGCCCAACTCTATATGCCG 61.292 60.000 0.00 0.00 0.00 5.69
692 706 1.291877 CGCCCAACTCTATATGCCGC 61.292 60.000 0.00 0.00 0.00 6.53
693 707 1.291877 GCCCAACTCTATATGCCGCG 61.292 60.000 0.00 0.00 0.00 6.46
694 708 1.291877 CCCAACTCTATATGCCGCGC 61.292 60.000 0.00 0.00 0.00 6.86
695 709 1.617755 CCAACTCTATATGCCGCGCG 61.618 60.000 25.67 25.67 0.00 6.86
696 710 2.022129 AACTCTATATGCCGCGCGC 61.022 57.895 27.36 23.91 38.31 6.86
697 711 2.126307 CTCTATATGCCGCGCGCT 60.126 61.111 30.48 13.20 38.78 5.92
698 712 1.734477 CTCTATATGCCGCGCGCTT 60.734 57.895 30.48 19.41 38.78 4.68
699 713 0.456142 CTCTATATGCCGCGCGCTTA 60.456 55.000 30.48 20.86 38.78 3.09
700 714 0.172578 TCTATATGCCGCGCGCTTAT 59.827 50.000 30.48 25.26 40.12 1.73
701 715 0.999406 CTATATGCCGCGCGCTTATT 59.001 50.000 30.48 13.81 38.44 1.40
702 716 0.718904 TATATGCCGCGCGCTTATTG 59.281 50.000 30.48 13.08 38.44 1.90
703 717 2.513065 ATATGCCGCGCGCTTATTGC 62.513 55.000 30.48 21.70 34.94 3.56
724 738 3.751018 TCCGCTGGAGCCCCTCTA 61.751 66.667 0.00 0.00 37.91 2.43
725 739 3.541713 CCGCTGGAGCCCCTCTAC 61.542 72.222 0.00 0.00 37.91 2.59
726 740 3.541713 CGCTGGAGCCCCTCTACC 61.542 72.222 0.00 0.00 37.91 3.18
727 741 3.541713 GCTGGAGCCCCTCTACCG 61.542 72.222 0.00 0.00 34.31 4.02
728 742 2.279073 CTGGAGCCCCTCTACCGA 59.721 66.667 0.00 0.00 0.00 4.69
729 743 1.152440 CTGGAGCCCCTCTACCGAT 60.152 63.158 0.00 0.00 0.00 4.18
730 744 0.760945 CTGGAGCCCCTCTACCGATT 60.761 60.000 0.00 0.00 0.00 3.34
731 745 1.048724 TGGAGCCCCTCTACCGATTG 61.049 60.000 0.00 0.00 0.00 2.67
732 746 1.069935 GAGCCCCTCTACCGATTGC 59.930 63.158 0.00 0.00 0.00 3.56
733 747 2.280186 GCCCCTCTACCGATTGCG 60.280 66.667 0.00 0.00 37.24 4.85
734 748 2.280186 CCCCTCTACCGATTGCGC 60.280 66.667 0.00 0.00 35.83 6.09
735 749 2.658593 CCCTCTACCGATTGCGCG 60.659 66.667 0.00 0.00 35.83 6.86
736 750 3.330853 CCTCTACCGATTGCGCGC 61.331 66.667 27.26 27.26 35.83 6.86
737 751 3.682315 CTCTACCGATTGCGCGCG 61.682 66.667 28.44 28.44 35.83 6.86
742 756 3.855589 CCGATTGCGCGCGGTAAA 61.856 61.111 33.06 15.77 42.49 2.01
743 757 2.096782 CGATTGCGCGCGGTAAAA 59.903 55.556 33.06 15.34 0.00 1.52
744 758 1.510204 CGATTGCGCGCGGTAAAAA 60.510 52.632 33.06 14.53 0.00 1.94
745 759 1.452837 CGATTGCGCGCGGTAAAAAG 61.453 55.000 33.06 9.32 0.00 2.27
746 760 1.131618 GATTGCGCGCGGTAAAAAGG 61.132 55.000 33.06 0.00 0.00 3.11
747 761 2.536323 ATTGCGCGCGGTAAAAAGGG 62.536 55.000 33.06 0.00 0.00 3.95
749 763 3.728636 CGCGCGGTAAAAAGGGCA 61.729 61.111 24.84 0.00 45.01 5.36
750 764 2.646143 GCGCGGTAAAAAGGGCAA 59.354 55.556 8.83 0.00 44.31 4.52
751 765 1.007154 GCGCGGTAAAAAGGGCAAA 60.007 52.632 8.83 0.00 44.31 3.68
752 766 0.389296 GCGCGGTAAAAAGGGCAAAT 60.389 50.000 8.83 0.00 44.31 2.32
753 767 1.937562 GCGCGGTAAAAAGGGCAAATT 60.938 47.619 8.83 0.00 44.31 1.82
754 768 2.409012 CGCGGTAAAAAGGGCAAATTT 58.591 42.857 0.00 0.00 0.00 1.82
755 769 2.156697 CGCGGTAAAAAGGGCAAATTTG 59.843 45.455 14.03 14.03 0.00 2.32
764 778 3.102668 GCAAATTTGCGGCGCGAA 61.103 55.556 33.95 33.95 45.11 4.70
765 779 3.058281 GCAAATTTGCGGCGCGAAG 62.058 57.895 34.49 23.83 45.11 3.79
783 797 2.471255 GCTCATTTAGCGTGGCTGT 58.529 52.632 0.00 0.00 42.53 4.40
784 798 0.804989 GCTCATTTAGCGTGGCTGTT 59.195 50.000 0.00 0.00 42.53 3.16
785 799 1.466360 GCTCATTTAGCGTGGCTGTTG 60.466 52.381 0.00 0.00 42.53 3.33
786 800 1.131126 CTCATTTAGCGTGGCTGTTGG 59.869 52.381 0.00 0.00 40.10 3.77
787 801 1.164411 CATTTAGCGTGGCTGTTGGA 58.836 50.000 0.00 0.00 40.10 3.53
788 802 1.131126 CATTTAGCGTGGCTGTTGGAG 59.869 52.381 0.00 0.00 40.10 3.86
789 803 0.394938 TTTAGCGTGGCTGTTGGAGA 59.605 50.000 0.00 0.00 40.10 3.71
790 804 0.613260 TTAGCGTGGCTGTTGGAGAT 59.387 50.000 0.00 0.00 40.10 2.75
791 805 0.108186 TAGCGTGGCTGTTGGAGATG 60.108 55.000 0.00 0.00 40.10 2.90
792 806 3.044059 GCGTGGCTGTTGGAGATGC 62.044 63.158 0.00 0.00 0.00 3.91
793 807 1.376424 CGTGGCTGTTGGAGATGCT 60.376 57.895 0.00 0.00 0.00 3.79
794 808 1.364626 CGTGGCTGTTGGAGATGCTC 61.365 60.000 0.00 0.00 0.00 4.26
795 809 0.035630 GTGGCTGTTGGAGATGCTCT 60.036 55.000 0.00 0.00 0.00 4.09
796 810 1.208052 GTGGCTGTTGGAGATGCTCTA 59.792 52.381 0.00 0.00 0.00 2.43
797 811 1.908619 TGGCTGTTGGAGATGCTCTAA 59.091 47.619 0.00 0.00 0.00 2.10
801 815 2.961526 GTTGGAGATGCTCTAACGGA 57.038 50.000 7.71 0.00 40.83 4.69
802 816 2.541556 GTTGGAGATGCTCTAACGGAC 58.458 52.381 7.71 0.00 40.83 4.79
803 817 0.738975 TGGAGATGCTCTAACGGACG 59.261 55.000 0.00 0.00 0.00 4.79
804 818 1.022735 GGAGATGCTCTAACGGACGA 58.977 55.000 0.00 0.00 0.00 4.20
805 819 1.404391 GGAGATGCTCTAACGGACGAA 59.596 52.381 0.00 0.00 0.00 3.85
806 820 2.541999 GGAGATGCTCTAACGGACGAAG 60.542 54.545 0.00 0.00 0.00 3.79
813 827 3.306434 GCTCTAACGGACGAAGATTTTCC 59.694 47.826 0.00 0.00 0.00 3.13
818 832 3.064931 ACGGACGAAGATTTTCCAAGTC 58.935 45.455 0.00 0.00 0.00 3.01
820 834 3.368236 CGGACGAAGATTTTCCAAGTCTC 59.632 47.826 0.00 0.00 0.00 3.36
823 837 5.238650 GGACGAAGATTTTCCAAGTCTCAAA 59.761 40.000 0.00 0.00 0.00 2.69
824 838 6.305693 ACGAAGATTTTCCAAGTCTCAAAG 57.694 37.500 0.00 0.00 0.00 2.77
825 839 5.823045 ACGAAGATTTTCCAAGTCTCAAAGT 59.177 36.000 0.00 0.00 0.00 2.66
827 841 6.396829 AAGATTTTCCAAGTCTCAAAGTGG 57.603 37.500 0.00 0.00 0.00 4.00
833 847 2.498167 CAAGTCTCAAAGTGGTCCCTG 58.502 52.381 0.00 0.00 0.00 4.45
834 848 1.059913 AGTCTCAAAGTGGTCCCTGG 58.940 55.000 0.00 0.00 0.00 4.45
867 881 5.825593 AAAAAGAGTAGATCCCTGACACA 57.174 39.130 0.00 0.00 0.00 3.72
868 882 6.380079 AAAAAGAGTAGATCCCTGACACAT 57.620 37.500 0.00 0.00 0.00 3.21
869 883 7.496346 AAAAAGAGTAGATCCCTGACACATA 57.504 36.000 0.00 0.00 0.00 2.29
871 885 7.496346 AAAGAGTAGATCCCTGACACATAAA 57.504 36.000 0.00 0.00 0.00 1.40
872 886 7.496346 AAGAGTAGATCCCTGACACATAAAA 57.504 36.000 0.00 0.00 0.00 1.52
873 887 7.118496 AGAGTAGATCCCTGACACATAAAAG 57.882 40.000 0.00 0.00 0.00 2.27
874 888 6.098982 AGAGTAGATCCCTGACACATAAAAGG 59.901 42.308 0.00 0.00 0.00 3.11
945 959 4.010349 CCTATTTTTGCTCCGGTTTCTCT 58.990 43.478 0.00 0.00 0.00 3.10
979 993 7.764141 TTTTTCTGATCCAGATTCAACATCA 57.236 32.000 0.00 0.00 40.39 3.07
1095 1121 1.608627 GATATAGGCCCGTCCCCGT 60.609 63.158 0.00 0.00 34.51 5.28
1096 1122 1.602327 GATATAGGCCCGTCCCCGTC 61.602 65.000 0.00 0.00 34.51 4.79
1097 1123 3.815407 TATAGGCCCGTCCCCGTCC 62.815 68.421 0.00 0.00 34.51 4.79
1584 1612 6.971527 ATATCGGTACATTTGTGTTCGAAA 57.028 33.333 0.00 0.00 32.44 3.46
1630 1660 1.550524 CAGAGATTGGAACGGACTGGA 59.449 52.381 0.00 0.00 0.00 3.86
1666 1700 5.984233 TGCTTGATTGATCGGTGTATTAC 57.016 39.130 0.00 0.00 0.00 1.89
1707 1741 5.153950 AGTGAACTCTGGTTTGTAGGATC 57.846 43.478 0.00 0.00 35.58 3.36
1720 1754 6.040504 GGTTTGTAGGATCTGAAAACCTTTGT 59.959 38.462 17.85 0.00 44.10 2.83
1723 1757 5.468746 TGTAGGATCTGAAAACCTTTGTTCG 59.531 40.000 6.71 0.00 35.52 3.95
1730 1764 1.029681 AAACCTTTGTTCGTCAGGCC 58.970 50.000 0.00 0.00 32.15 5.19
1770 1819 4.859798 GTGTCTGTCTAAGGTTCGATTGAG 59.140 45.833 0.00 0.00 0.00 3.02
1787 1836 7.722363 TCGATTGAGGCTGTTATTGAATACTA 58.278 34.615 0.00 0.00 0.00 1.82
1789 1838 7.653713 CGATTGAGGCTGTTATTGAATACTACT 59.346 37.037 0.00 0.00 0.00 2.57
1790 1839 8.668510 ATTGAGGCTGTTATTGAATACTACTG 57.331 34.615 0.00 0.00 0.00 2.74
1791 1840 7.418337 TGAGGCTGTTATTGAATACTACTGA 57.582 36.000 0.00 0.00 0.00 3.41
1794 1843 8.023021 AGGCTGTTATTGAATACTACTGATGA 57.977 34.615 0.00 0.00 0.00 2.92
1795 1844 8.147058 AGGCTGTTATTGAATACTACTGATGAG 58.853 37.037 0.00 0.00 0.00 2.90
1872 2025 5.818136 TGTGCTTGTTAGAATTATGCCTC 57.182 39.130 0.00 0.00 0.00 4.70
1891 2044 3.711059 GAGTGGGGCTGCATCCAGG 62.711 68.421 9.17 0.00 39.54 4.45
1934 2087 7.216494 ACTAAAACACCTGCAAAATAGCATTT 58.784 30.769 0.00 0.00 44.68 2.32
1950 2103 7.854166 ATAGCATTTATGGAGGCCATTTAAA 57.146 32.000 5.01 4.09 42.23 1.52
1958 2118 3.701040 TGGAGGCCATTTAAAATCTCTGC 59.299 43.478 5.01 0.00 0.00 4.26
1960 2120 4.440663 GGAGGCCATTTAAAATCTCTGCAC 60.441 45.833 5.01 0.00 0.00 4.57
1961 2121 4.088634 AGGCCATTTAAAATCTCTGCACA 58.911 39.130 5.01 0.00 0.00 4.57
2007 2167 2.503356 TGGAGTTGCACCAACCAAAATT 59.497 40.909 4.60 0.00 44.49 1.82
2314 2479 6.486993 ACAGTGAAGTCTTTGAAGGGATTAAC 59.513 38.462 0.00 0.00 0.00 2.01
2650 2824 7.657354 TCTTCATCCATTTACATCCATAACTCG 59.343 37.037 0.00 0.00 0.00 4.18
2697 2871 5.951747 ACCATATGATGCAACTAACCAGTTT 59.048 36.000 3.65 0.00 42.51 2.66
2742 2916 5.959618 AGGACCGAAACCTTCTAATTTTG 57.040 39.130 0.00 0.00 33.55 2.44
2808 2983 1.774110 TGCCCTTTTCAGCTGACAAA 58.226 45.000 18.03 17.62 0.00 2.83
2815 2990 1.896220 TTCAGCTGACAAATTCCGCT 58.104 45.000 18.03 0.00 45.05 5.52
2923 3104 7.936496 TCTTTGTGCTATCCAAATATGTGAA 57.064 32.000 0.00 0.00 31.85 3.18
3395 3585 6.482308 GGGTAGTGCTTATCGATTGTTACATT 59.518 38.462 1.71 0.00 0.00 2.71
3438 3628 3.370527 CGGTGAATTATCTGGGTTGGTCT 60.371 47.826 0.00 0.00 0.00 3.85
3476 3666 3.053693 TGAAACATGGAGGATAGGGTTGG 60.054 47.826 0.00 0.00 0.00 3.77
3478 3668 1.275002 ACATGGAGGATAGGGTTGGGT 60.275 52.381 0.00 0.00 0.00 4.51
3610 3802 6.500041 TGAGCGCAACAGTAAAACTTATTTT 58.500 32.000 11.47 0.00 41.07 1.82
3640 4202 5.780282 TGGCTAGTCTGGCATGTATATACTT 59.220 40.000 13.89 5.00 37.59 2.24
3697 4260 0.036952 ATGACGAGCCAGGTGTCTTG 60.037 55.000 9.24 0.00 33.81 3.02
3817 4380 3.360867 TCCTTGGCAAAAAGACTTGTCA 58.639 40.909 0.00 0.00 39.09 3.58
3856 4419 4.202111 GCCAAACCAGTGAATTGTGTTAGT 60.202 41.667 0.00 0.00 0.00 2.24
3891 4457 6.396829 AACTTTCTTCCATATGCTTATGCC 57.603 37.500 12.92 0.00 38.71 4.40
4091 4657 5.700832 TCACATTACATGTTCTGGACTTGTC 59.299 40.000 10.57 0.00 43.31 3.18
4093 4659 2.568623 ACATGTTCTGGACTTGTCCC 57.431 50.000 16.23 2.61 41.31 4.46
4094 4660 1.073923 ACATGTTCTGGACTTGTCCCC 59.926 52.381 16.23 3.76 41.31 4.81
4095 4661 0.698818 ATGTTCTGGACTTGTCCCCC 59.301 55.000 16.23 3.45 0.00 5.40
4595 5202 5.534654 TGTGCTACTTAATTTGGCAGAGTTT 59.465 36.000 0.00 0.00 33.47 2.66
4774 5381 4.517285 TGTGGATATTTTGACTGGAGCTC 58.483 43.478 4.71 4.71 0.00 4.09
4951 5560 1.261619 GACCTTGCTTCTGTGAACACG 59.738 52.381 0.57 0.00 0.00 4.49
4954 5563 2.354510 CCTTGCTTCTGTGAACACGAAA 59.645 45.455 0.00 3.89 0.00 3.46
4959 5568 3.309954 GCTTCTGTGAACACGAAAGACTT 59.690 43.478 17.17 0.00 31.23 3.01
5102 5711 7.652909 CCATTGTCACAATTGTCTTGTATTTGT 59.347 33.333 8.48 0.00 0.00 2.83
5184 5793 6.548251 TCTTTCCTTTTTCGGTTGAAGGTATT 59.452 34.615 0.00 0.00 40.60 1.89
5373 5983 4.634349 CACATTTTGCATCAGAAAACGG 57.366 40.909 0.00 0.00 0.00 4.44
5466 6092 1.808945 TCTCGTGTCCGAAGAGGTTAC 59.191 52.381 0.00 0.00 43.69 2.50
5485 6111 5.955959 GGTTACATATTTCCCCTGTTTTCCT 59.044 40.000 0.00 0.00 0.00 3.36
5681 6307 3.254903 GCTAACCAACTTGTTAACCTGGG 59.745 47.826 2.48 0.60 30.74 4.45
5836 6462 0.392729 CAAGAGCCCAAGAGAGCCAG 60.393 60.000 0.00 0.00 0.00 4.85
5841 6467 1.344191 GCCCAAGAGAGCCAGGAGAT 61.344 60.000 0.00 0.00 0.00 2.75
5855 6481 2.932614 CAGGAGATTTGAGACGCGAAAT 59.067 45.455 15.93 8.36 0.00 2.17
5947 6573 2.047274 ATGGTTGGGACGCTGTCG 60.047 61.111 3.27 0.00 42.43 4.35
5970 6596 3.134262 TGAATCTCTGATTGGCTCCTGAG 59.866 47.826 0.00 0.00 0.00 3.35
6036 6663 1.225855 CAAAACAGACAGGCTACGCA 58.774 50.000 0.00 0.00 0.00 5.24
6062 6689 9.850628 ATTGTCATGACTTGATGATTAGTTTTG 57.149 29.630 25.55 0.00 36.54 2.44
6071 6700 8.362639 ACTTGATGATTAGTTTTGATGCAACTT 58.637 29.630 0.00 0.00 35.95 2.66
6186 6834 9.662545 AAAAATATTTCTGCCGTTTCAAAAATG 57.337 25.926 0.10 0.00 0.00 2.32
6187 6835 7.961325 AATATTTCTGCCGTTTCAAAAATGT 57.039 28.000 0.00 0.00 0.00 2.71
6188 6836 7.961325 ATATTTCTGCCGTTTCAAAAATGTT 57.039 28.000 0.00 0.00 0.00 2.71
6189 6837 6.676237 ATTTCTGCCGTTTCAAAAATGTTT 57.324 29.167 0.00 0.00 0.00 2.83
6190 6838 5.462034 TTCTGCCGTTTCAAAAATGTTTG 57.538 34.783 1.55 1.55 44.71 2.93
6191 6839 3.308323 TCTGCCGTTTCAAAAATGTTTGC 59.692 39.130 3.24 0.00 43.30 3.68
6192 6840 3.002791 TGCCGTTTCAAAAATGTTTGCA 58.997 36.364 3.24 0.00 43.30 4.08
6193 6841 3.181516 TGCCGTTTCAAAAATGTTTGCAC 60.182 39.130 3.24 2.51 43.30 4.57
6194 6842 3.181516 GCCGTTTCAAAAATGTTTGCACA 60.182 39.130 3.24 0.00 43.30 4.57
6195 6843 4.670221 GCCGTTTCAAAAATGTTTGCACAA 60.670 37.500 3.24 0.00 43.30 3.33
6196 6844 4.785561 CCGTTTCAAAAATGTTTGCACAAC 59.214 37.500 3.24 5.84 43.30 3.32
6199 6847 7.230222 CGTTTCAAAAATGTTTGCACAACTTA 58.770 30.769 3.24 0.00 43.30 2.24
6202 6850 9.950680 TTTCAAAAATGTTTGCACAACTTAAAA 57.049 22.222 3.24 0.00 43.30 1.52
6371 7020 6.984474 TGTTGTGGTTTTTGTTTTTCTGTGTA 59.016 30.769 0.00 0.00 0.00 2.90
6835 7486 9.923786 TGTTGTATATTTTTCATATACACGTGC 57.076 29.630 17.22 0.00 43.27 5.34
6858 7509 9.357652 GTGCAACATTCTTTTATACACATTGAT 57.642 29.630 0.00 0.00 36.32 2.57
6915 7566 9.801714 CAAATACATGTTTGCAAGAATTTCTTC 57.198 29.630 2.30 5.43 30.09 2.87
6916 7567 9.545105 AAATACATGTTTGCAAGAATTTCTTCA 57.455 25.926 2.30 7.68 33.78 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 147 5.106442 ACGTTCTCATCGCACACAATATTA 58.894 37.500 0.00 0.00 0.00 0.98
162 164 5.389516 GCTAAATCGTTTGTGATGACGTTCT 60.390 40.000 0.00 0.00 40.03 3.01
168 170 3.616821 CCTCGCTAAATCGTTTGTGATGA 59.383 43.478 0.00 0.00 30.40 2.92
185 187 3.236816 CATCACACACAATTTTCCTCGC 58.763 45.455 0.00 0.00 0.00 5.03
239 242 4.514781 TCGTATATACATCCCACACAGC 57.485 45.455 13.22 0.00 0.00 4.40
270 273 0.716108 CACAGTCAATCTCCGCGAAC 59.284 55.000 8.23 0.00 0.00 3.95
278 281 1.673767 ACATCCCCCACAGTCAATCT 58.326 50.000 0.00 0.00 0.00 2.40
290 294 6.206498 GCGAAATTTTCATAAGTACATCCCC 58.794 40.000 9.66 0.00 0.00 4.81
342 354 5.842327 GCGCCAAATACGTTTATATGTACAC 59.158 40.000 0.00 0.00 0.00 2.90
348 360 3.120786 GCGAGCGCCAAATACGTTTATAT 60.121 43.478 2.29 0.00 34.56 0.86
429 442 2.281208 CCCACGCGACCTGGAAAA 60.281 61.111 15.93 0.00 0.00 2.29
434 447 3.691342 TCCTTCCCACGCGACCTG 61.691 66.667 15.93 0.00 0.00 4.00
472 486 1.444836 CATTTGGAACCGTCGCCTAA 58.555 50.000 0.00 0.00 0.00 2.69
504 518 7.255695 GGTGCTATACAAACAGTTTAAAACCCT 60.256 37.037 0.00 0.00 0.00 4.34
585 599 3.691744 CTCACGCCGCACTCTCTCC 62.692 68.421 0.00 0.00 0.00 3.71
586 600 2.202544 CTCACGCCGCACTCTCTC 60.203 66.667 0.00 0.00 0.00 3.20
587 601 4.427661 GCTCACGCCGCACTCTCT 62.428 66.667 0.00 0.00 0.00 3.10
598 612 3.168604 CACACTCGAGCGCTCACG 61.169 66.667 34.69 25.95 44.07 4.35
599 613 3.474034 GCACACTCGAGCGCTCAC 61.474 66.667 34.69 12.29 0.00 3.51
600 614 4.724602 GGCACACTCGAGCGCTCA 62.725 66.667 34.69 21.12 0.00 4.26
623 637 2.780149 CTTTGGTTCGCCCGCTTTCG 62.780 60.000 0.00 0.00 36.08 3.46
624 638 1.081442 CTTTGGTTCGCCCGCTTTC 60.081 57.895 0.00 0.00 36.08 2.62
625 639 1.527380 TCTTTGGTTCGCCCGCTTT 60.527 52.632 0.00 0.00 36.08 3.51
626 640 2.112297 TCTTTGGTTCGCCCGCTT 59.888 55.556 0.00 0.00 36.08 4.68
627 641 2.668550 GTCTTTGGTTCGCCCGCT 60.669 61.111 0.00 0.00 36.08 5.52
628 642 2.975799 TGTCTTTGGTTCGCCCGC 60.976 61.111 0.00 0.00 36.08 6.13
629 643 1.841663 CTGTGTCTTTGGTTCGCCCG 61.842 60.000 0.00 0.00 36.08 6.13
630 644 1.515521 CCTGTGTCTTTGGTTCGCCC 61.516 60.000 0.00 0.00 36.08 6.13
631 645 0.534203 TCCTGTGTCTTTGGTTCGCC 60.534 55.000 0.00 0.00 37.92 5.54
632 646 0.586802 GTCCTGTGTCTTTGGTTCGC 59.413 55.000 0.00 0.00 0.00 4.70
633 647 0.859232 CGTCCTGTGTCTTTGGTTCG 59.141 55.000 0.00 0.00 0.00 3.95
634 648 0.586802 GCGTCCTGTGTCTTTGGTTC 59.413 55.000 0.00 0.00 0.00 3.62
635 649 1.157870 CGCGTCCTGTGTCTTTGGTT 61.158 55.000 0.00 0.00 0.00 3.67
636 650 1.594293 CGCGTCCTGTGTCTTTGGT 60.594 57.895 0.00 0.00 0.00 3.67
637 651 0.670546 ATCGCGTCCTGTGTCTTTGG 60.671 55.000 5.77 0.00 0.00 3.28
638 652 0.439985 CATCGCGTCCTGTGTCTTTG 59.560 55.000 5.77 0.00 0.00 2.77
639 653 0.317160 TCATCGCGTCCTGTGTCTTT 59.683 50.000 5.77 0.00 0.00 2.52
640 654 0.388649 GTCATCGCGTCCTGTGTCTT 60.389 55.000 5.77 0.00 0.00 3.01
641 655 1.213013 GTCATCGCGTCCTGTGTCT 59.787 57.895 5.77 0.00 0.00 3.41
642 656 0.666274 TTGTCATCGCGTCCTGTGTC 60.666 55.000 5.77 0.00 0.00 3.67
643 657 0.037326 ATTGTCATCGCGTCCTGTGT 60.037 50.000 5.77 0.00 0.00 3.72
644 658 1.061131 GAATTGTCATCGCGTCCTGTG 59.939 52.381 5.77 0.00 0.00 3.66
645 659 1.359848 GAATTGTCATCGCGTCCTGT 58.640 50.000 5.77 0.00 0.00 4.00
646 660 0.298707 CGAATTGTCATCGCGTCCTG 59.701 55.000 5.77 2.65 33.07 3.86
647 661 0.172578 TCGAATTGTCATCGCGTCCT 59.827 50.000 5.77 0.00 40.04 3.85
648 662 0.996462 TTCGAATTGTCATCGCGTCC 59.004 50.000 5.77 0.00 40.04 4.79
649 663 1.266891 GGTTCGAATTGTCATCGCGTC 60.267 52.381 5.77 0.00 40.04 5.19
650 664 0.719465 GGTTCGAATTGTCATCGCGT 59.281 50.000 5.77 0.00 40.04 6.01
651 665 0.314259 CGGTTCGAATTGTCATCGCG 60.314 55.000 0.00 0.00 40.04 5.87
652 666 0.586502 GCGGTTCGAATTGTCATCGC 60.587 55.000 0.00 0.00 40.04 4.58
653 667 0.314259 CGCGGTTCGAATTGTCATCG 60.314 55.000 0.00 0.00 41.67 3.84
654 668 0.586502 GCGCGGTTCGAATTGTCATC 60.587 55.000 8.83 0.00 41.67 2.92
655 669 1.423845 GCGCGGTTCGAATTGTCAT 59.576 52.632 8.83 0.00 41.67 3.06
656 670 2.857448 GCGCGGTTCGAATTGTCA 59.143 55.556 8.83 0.00 41.67 3.58
657 671 2.275812 CGCGCGGTTCGAATTGTC 60.276 61.111 24.84 0.00 41.67 3.18
658 672 4.439472 GCGCGCGGTTCGAATTGT 62.439 61.111 33.06 0.00 41.67 2.71
668 682 2.765250 ATATAGAGTTGGGCGCGCGG 62.765 60.000 33.06 13.66 0.00 6.46
669 683 1.372997 ATATAGAGTTGGGCGCGCG 60.373 57.895 28.44 28.44 0.00 6.86
670 684 1.901650 GCATATAGAGTTGGGCGCGC 61.902 60.000 25.94 25.94 0.00 6.86
671 685 1.291877 GGCATATAGAGTTGGGCGCG 61.292 60.000 0.00 0.00 0.00 6.86
672 686 1.291877 CGGCATATAGAGTTGGGCGC 61.292 60.000 0.00 0.00 40.52 6.53
673 687 2.827604 CGGCATATAGAGTTGGGCG 58.172 57.895 0.00 0.00 41.00 6.13
674 688 1.291877 CGCGGCATATAGAGTTGGGC 61.292 60.000 0.00 0.00 0.00 5.36
675 689 1.291877 GCGCGGCATATAGAGTTGGG 61.292 60.000 8.83 0.00 0.00 4.12
676 690 1.617755 CGCGCGGCATATAGAGTTGG 61.618 60.000 24.84 0.00 0.00 3.77
677 691 1.775344 CGCGCGGCATATAGAGTTG 59.225 57.895 24.84 0.00 0.00 3.16
678 692 2.022129 GCGCGCGGCATATAGAGTT 61.022 57.895 33.06 0.00 42.87 3.01
679 693 2.430921 GCGCGCGGCATATAGAGT 60.431 61.111 33.06 0.00 42.87 3.24
707 721 3.751018 TAGAGGGGCTCCAGCGGA 61.751 66.667 4.79 0.00 43.26 5.54
708 722 3.541713 GTAGAGGGGCTCCAGCGG 61.542 72.222 4.79 0.00 43.26 5.52
709 723 3.541713 GGTAGAGGGGCTCCAGCG 61.542 72.222 4.79 0.00 43.26 5.18
710 724 3.541713 CGGTAGAGGGGCTCCAGC 61.542 72.222 4.79 0.00 41.14 4.85
711 725 0.760945 AATCGGTAGAGGGGCTCCAG 60.761 60.000 4.79 0.00 34.83 3.86
712 726 1.048724 CAATCGGTAGAGGGGCTCCA 61.049 60.000 4.79 0.00 34.83 3.86
713 727 1.749033 CAATCGGTAGAGGGGCTCC 59.251 63.158 0.00 0.00 0.00 4.70
714 728 1.069935 GCAATCGGTAGAGGGGCTC 59.930 63.158 0.00 0.00 0.00 4.70
715 729 2.797278 CGCAATCGGTAGAGGGGCT 61.797 63.158 0.00 0.00 0.00 5.19
716 730 2.280186 CGCAATCGGTAGAGGGGC 60.280 66.667 0.00 0.00 0.00 5.80
717 731 2.280186 GCGCAATCGGTAGAGGGG 60.280 66.667 0.30 0.00 35.95 4.79
718 732 2.658593 CGCGCAATCGGTAGAGGG 60.659 66.667 8.75 0.00 35.95 4.30
719 733 3.330853 GCGCGCAATCGGTAGAGG 61.331 66.667 29.10 0.00 35.95 3.69
720 734 3.682315 CGCGCGCAATCGGTAGAG 61.682 66.667 32.61 6.38 35.95 2.43
726 740 1.452837 CTTTTTACCGCGCGCAATCG 61.453 55.000 32.61 16.98 39.07 3.34
727 741 1.131618 CCTTTTTACCGCGCGCAATC 61.132 55.000 32.61 0.72 0.00 2.67
728 742 1.154112 CCTTTTTACCGCGCGCAAT 60.154 52.632 32.61 20.60 0.00 3.56
729 743 2.252855 CCTTTTTACCGCGCGCAA 59.747 55.556 32.61 17.78 0.00 4.85
730 744 3.728636 CCCTTTTTACCGCGCGCA 61.729 61.111 32.61 11.84 0.00 6.09
732 746 2.734756 TTTGCCCTTTTTACCGCGCG 62.735 55.000 25.67 25.67 0.00 6.86
733 747 0.389296 ATTTGCCCTTTTTACCGCGC 60.389 50.000 0.00 0.00 0.00 6.86
734 748 2.073117 AATTTGCCCTTTTTACCGCG 57.927 45.000 0.00 0.00 0.00 6.46
735 749 3.804518 CAAATTTGCCCTTTTTACCGC 57.195 42.857 5.01 0.00 0.00 5.68
748 762 3.058281 GCTTCGCGCCGCAAATTTG 62.058 57.895 14.03 14.03 0.00 2.32
749 763 2.804931 GCTTCGCGCCGCAAATTT 60.805 55.556 10.75 0.00 0.00 1.82
750 764 3.667429 GAGCTTCGCGCCGCAAATT 62.667 57.895 10.75 1.22 40.39 1.82
751 765 4.166011 GAGCTTCGCGCCGCAAAT 62.166 61.111 10.75 1.55 40.39 2.32
755 769 2.686518 CTAAATGAGCTTCGCGCCGC 62.687 60.000 0.00 6.25 40.39 6.53
756 770 1.273887 CTAAATGAGCTTCGCGCCG 59.726 57.895 0.00 0.00 40.39 6.46
766 780 1.131126 CCAACAGCCACGCTAAATGAG 59.869 52.381 0.00 0.00 36.40 2.90
767 781 1.164411 CCAACAGCCACGCTAAATGA 58.836 50.000 0.00 0.00 36.40 2.57
768 782 1.131126 CTCCAACAGCCACGCTAAATG 59.869 52.381 0.00 0.00 36.40 2.32
769 783 1.003118 TCTCCAACAGCCACGCTAAAT 59.997 47.619 0.00 0.00 36.40 1.40
770 784 0.394938 TCTCCAACAGCCACGCTAAA 59.605 50.000 0.00 0.00 36.40 1.85
771 785 0.613260 ATCTCCAACAGCCACGCTAA 59.387 50.000 0.00 0.00 36.40 3.09
772 786 0.108186 CATCTCCAACAGCCACGCTA 60.108 55.000 0.00 0.00 36.40 4.26
773 787 1.376424 CATCTCCAACAGCCACGCT 60.376 57.895 0.00 0.00 40.77 5.07
774 788 3.044059 GCATCTCCAACAGCCACGC 62.044 63.158 0.00 0.00 0.00 5.34
775 789 1.364626 GAGCATCTCCAACAGCCACG 61.365 60.000 0.00 0.00 0.00 4.94
776 790 2.475666 GAGCATCTCCAACAGCCAC 58.524 57.895 0.00 0.00 0.00 5.01
788 802 2.846039 TCTTCGTCCGTTAGAGCATC 57.154 50.000 0.00 0.00 0.00 3.91
789 803 3.802948 AATCTTCGTCCGTTAGAGCAT 57.197 42.857 0.00 0.00 0.00 3.79
790 804 3.587797 AAATCTTCGTCCGTTAGAGCA 57.412 42.857 0.00 0.00 0.00 4.26
791 805 3.306434 GGAAAATCTTCGTCCGTTAGAGC 59.694 47.826 0.00 0.00 31.77 4.09
792 806 4.491676 TGGAAAATCTTCGTCCGTTAGAG 58.508 43.478 0.00 0.00 33.87 2.43
793 807 4.524316 TGGAAAATCTTCGTCCGTTAGA 57.476 40.909 0.00 0.00 33.87 2.10
794 808 4.689345 ACTTGGAAAATCTTCGTCCGTTAG 59.311 41.667 0.00 0.00 33.87 2.34
795 809 4.634199 ACTTGGAAAATCTTCGTCCGTTA 58.366 39.130 0.00 0.00 33.87 3.18
796 810 3.473625 ACTTGGAAAATCTTCGTCCGTT 58.526 40.909 0.00 0.00 33.87 4.44
797 811 3.064931 GACTTGGAAAATCTTCGTCCGT 58.935 45.455 0.00 0.00 33.87 4.69
798 812 3.326747 AGACTTGGAAAATCTTCGTCCG 58.673 45.455 0.00 0.00 33.87 4.79
799 813 4.315803 TGAGACTTGGAAAATCTTCGTCC 58.684 43.478 0.00 0.00 31.77 4.79
800 814 5.924475 TTGAGACTTGGAAAATCTTCGTC 57.076 39.130 0.00 0.00 31.77 4.20
801 815 5.823045 ACTTTGAGACTTGGAAAATCTTCGT 59.177 36.000 0.00 0.00 31.77 3.85
802 816 6.138761 CACTTTGAGACTTGGAAAATCTTCG 58.861 40.000 0.00 0.00 31.77 3.79
803 817 6.039829 ACCACTTTGAGACTTGGAAAATCTTC 59.960 38.462 0.00 0.00 33.02 2.87
804 818 5.893824 ACCACTTTGAGACTTGGAAAATCTT 59.106 36.000 0.00 0.00 33.02 2.40
805 819 5.449553 ACCACTTTGAGACTTGGAAAATCT 58.550 37.500 0.00 0.00 33.02 2.40
806 820 5.278512 GGACCACTTTGAGACTTGGAAAATC 60.279 44.000 0.00 0.00 33.02 2.17
813 827 2.498167 CAGGGACCACTTTGAGACTTG 58.502 52.381 0.00 0.00 0.00 3.16
818 832 1.303643 GGCCAGGGACCACTTTGAG 60.304 63.158 0.00 0.00 0.00 3.02
820 834 1.153756 AAGGCCAGGGACCACTTTG 59.846 57.895 5.01 0.00 0.00 2.77
823 837 2.450502 ACAAGGCCAGGGACCACT 60.451 61.111 5.01 0.00 0.00 4.00
824 838 1.198759 TAGACAAGGCCAGGGACCAC 61.199 60.000 5.01 0.00 0.00 4.16
825 839 0.474854 TTAGACAAGGCCAGGGACCA 60.475 55.000 5.01 0.00 0.00 4.02
827 841 2.579410 TTTTAGACAAGGCCAGGGAC 57.421 50.000 5.01 0.00 0.00 4.46
850 864 6.284459 CCTTTTATGTGTCAGGGATCTACTC 58.716 44.000 0.00 0.00 0.00 2.59
851 865 6.240549 CCTTTTATGTGTCAGGGATCTACT 57.759 41.667 0.00 0.00 0.00 2.57
858 872 5.799827 TTTTTCCCTTTTATGTGTCAGGG 57.200 39.130 0.00 0.00 46.85 4.45
918 932 0.740737 CGGAGCAAAAATAGGCTGGG 59.259 55.000 0.00 0.00 41.22 4.45
922 936 2.492088 AGAAACCGGAGCAAAAATAGGC 59.508 45.455 9.46 0.00 0.00 3.93
945 959 3.013921 GGATCAGAAAAATACGGCCACA 58.986 45.455 2.24 0.00 0.00 4.17
979 993 3.006859 TGTTTGATCGGTGACTGTGAGAT 59.993 43.478 0.00 0.00 0.00 2.75
1106 1132 0.179205 CTAGGTCGTGTCGTTCGGAC 60.179 60.000 0.00 0.00 46.27 4.79
1426 1453 3.689649 CAGAGTTAGGCGCTGGTTTTATT 59.310 43.478 7.64 0.00 40.64 1.40
1427 1454 3.270877 CAGAGTTAGGCGCTGGTTTTAT 58.729 45.455 7.64 0.00 40.64 1.40
1491 1518 7.526192 CGATCCTCCCACATAATCAGTTAATCT 60.526 40.741 0.00 0.00 0.00 2.40
1505 1532 1.788229 TTAGATGCGATCCTCCCACA 58.212 50.000 0.00 0.00 0.00 4.17
1507 1534 4.141505 TGAATTTTAGATGCGATCCTCCCA 60.142 41.667 0.00 0.00 0.00 4.37
1630 1660 5.716228 TCAATCAAGCAATAGAACAACCCAT 59.284 36.000 0.00 0.00 0.00 4.00
1666 1700 4.403752 TCACTCCTATGACTCCTCATTGTG 59.596 45.833 0.00 0.00 38.21 3.33
1707 1741 3.792124 GCCTGACGAACAAAGGTTTTCAG 60.792 47.826 10.71 10.71 41.99 3.02
1720 1754 0.249120 AATGATCACGGCCTGACGAA 59.751 50.000 0.00 0.00 37.61 3.85
1757 1806 2.568623 AACAGCCTCAATCGAACCTT 57.431 45.000 0.00 0.00 0.00 3.50
1770 1819 7.928706 ACTCATCAGTAGTATTCAATAACAGCC 59.071 37.037 0.00 0.00 0.00 4.85
1787 1836 3.735237 AAACACTCGTCACTCATCAGT 57.265 42.857 0.00 0.00 0.00 3.41
1789 1838 2.543848 GCAAAACACTCGTCACTCATCA 59.456 45.455 0.00 0.00 0.00 3.07
1790 1839 2.802816 AGCAAAACACTCGTCACTCATC 59.197 45.455 0.00 0.00 0.00 2.92
1791 1840 2.838736 AGCAAAACACTCGTCACTCAT 58.161 42.857 0.00 0.00 0.00 2.90
1794 1843 4.814234 TGAAATAGCAAAACACTCGTCACT 59.186 37.500 0.00 0.00 0.00 3.41
1795 1844 5.050363 TCTGAAATAGCAAAACACTCGTCAC 60.050 40.000 0.00 0.00 0.00 3.67
1872 2025 4.100084 TGGATGCAGCCCCACTCG 62.100 66.667 20.33 0.00 0.00 4.18
1901 2054 2.814336 GCAGGTGTTTTAGTCTTCTGGG 59.186 50.000 0.00 0.00 0.00 4.45
1934 2087 5.536161 GCAGAGATTTTAAATGGCCTCCATA 59.464 40.000 3.32 0.00 44.40 2.74
1958 2118 2.724977 TGCTAAGAACGACCTCTGTG 57.275 50.000 0.00 0.00 0.00 3.66
1960 2120 3.807622 TGTTTTGCTAAGAACGACCTCTG 59.192 43.478 0.00 0.00 0.00 3.35
1961 2121 4.058817 CTGTTTTGCTAAGAACGACCTCT 58.941 43.478 0.00 0.00 0.00 3.69
2185 2350 9.991906 ACTAAGTACATAGCTACAAGAAACAAA 57.008 29.630 5.06 0.00 0.00 2.83
2225 2390 2.553028 GCTCACTGAATGGGGAAGAACA 60.553 50.000 0.00 0.00 0.00 3.18
2594 2768 2.858745 TCCCTTGACCAGCTTGTTAAC 58.141 47.619 0.00 0.00 0.00 2.01
2650 2824 3.365364 GCAAGTGGTTAGTCACAAGATGC 60.365 47.826 0.00 0.00 39.93 3.91
2742 2916 4.799428 GCTAAACTGATCTCTAACGGTGAC 59.201 45.833 0.00 0.00 0.00 3.67
2808 2983 1.612950 TCATGCACAAACAAGCGGAAT 59.387 42.857 0.00 0.00 0.00 3.01
2815 2990 3.884693 AGAGTGACATCATGCACAAACAA 59.115 39.130 12.77 0.00 37.48 2.83
2931 3115 9.652114 AATCTTTATTTCCCTCTTTATCTGCAT 57.348 29.630 0.00 0.00 0.00 3.96
3155 3345 3.480470 ACAGGTTCAACACTTCATCCAG 58.520 45.455 0.00 0.00 0.00 3.86
3292 3482 5.689383 AAAATCACAAGACGTGCAACTAT 57.311 34.783 0.00 0.00 45.92 2.12
3374 3564 6.374333 ACCAAATGTAACAATCGATAAGCACT 59.626 34.615 0.00 0.00 0.00 4.40
3476 3666 6.854381 GCACGTATTTATTGTAGCCAAATACC 59.146 38.462 9.60 0.00 39.97 2.73
3478 3668 7.496263 TCTGCACGTATTTATTGTAGCCAAATA 59.504 33.333 0.00 0.00 33.44 1.40
3610 3802 1.266867 TGCCAGACTAGCCATGCAGA 61.267 55.000 0.00 0.00 0.00 4.26
3640 4202 1.202879 AGGCGATCAACAACTTGGGAA 60.203 47.619 0.00 0.00 0.00 3.97
3817 4380 4.161754 GGTTTGGCTATCTACTACCACTGT 59.838 45.833 0.00 0.00 0.00 3.55
3957 4523 5.869579 AGAGACTAAGTGAAAATGAGCCAA 58.130 37.500 0.00 0.00 0.00 4.52
4196 4762 1.612462 CCTGAAATGTGAGCAGGCTGA 60.612 52.381 20.86 0.00 42.30 4.26
4595 5202 6.699642 GGATTCAAAATTCGGAAACAAACAGA 59.300 34.615 0.00 0.00 0.00 3.41
5034 5643 1.577328 GCTGGTCATGGTTGTCGTGG 61.577 60.000 0.00 0.00 33.31 4.94
5319 5928 6.049149 ACACCATACGAATAAGATGTTCAGG 58.951 40.000 0.00 0.00 0.00 3.86
5372 5982 2.785713 TAAGCAACAAGAAAACGGCC 57.214 45.000 0.00 0.00 0.00 6.13
5373 5983 3.242016 GTGTTAAGCAACAAGAAAACGGC 59.758 43.478 0.00 0.00 45.99 5.68
5466 6092 4.270008 ACGAGGAAAACAGGGGAAATATG 58.730 43.478 0.00 0.00 0.00 1.78
5485 6111 4.535526 TTGAGAAATGACAGATGGACGA 57.464 40.909 0.00 0.00 0.00 4.20
5681 6307 0.940126 CACCATCGCATAAGCTGACC 59.060 55.000 0.00 0.00 39.10 4.02
5766 6392 2.420687 GCCCTCACCTGATGAAAGTAGG 60.421 54.545 0.00 0.00 36.69 3.18
5767 6393 2.237143 TGCCCTCACCTGATGAAAGTAG 59.763 50.000 0.00 0.00 36.69 2.57
5836 6462 3.000724 CAGATTTCGCGTCTCAAATCTCC 59.999 47.826 23.11 5.63 44.16 3.71
5841 6467 1.795768 AGCAGATTTCGCGTCTCAAA 58.204 45.000 5.77 0.00 0.00 2.69
5947 6573 3.118482 TCAGGAGCCAATCAGAGATTCAC 60.118 47.826 0.00 0.00 0.00 3.18
6007 6634 3.381045 CTGTCTGTTTTGTAGACTCGCA 58.619 45.455 0.00 0.00 43.79 5.10
6036 6663 9.850628 CAAAACTAATCATCAAGTCATGACAAT 57.149 29.630 27.02 14.35 41.93 2.71
6125 6754 4.280819 CCTCAAATTAAGCCCAGAATCCA 58.719 43.478 0.00 0.00 0.00 3.41
6166 6814 6.485393 CAAACATTTTTGAAACGGCAGAAAT 58.515 32.000 0.00 0.00 44.38 2.17
6169 6817 3.308323 GCAAACATTTTTGAAACGGCAGA 59.692 39.130 8.51 0.00 44.38 4.26
6170 6818 3.063180 TGCAAACATTTTTGAAACGGCAG 59.937 39.130 8.51 0.00 44.38 4.85
6171 6819 3.002791 TGCAAACATTTTTGAAACGGCA 58.997 36.364 8.51 0.00 44.38 5.69
6172 6820 3.181516 TGTGCAAACATTTTTGAAACGGC 60.182 39.130 8.51 0.00 44.38 5.68
6174 6822 5.616658 AGTTGTGCAAACATTTTTGAAACG 58.383 33.333 8.51 0.00 44.38 3.60
6175 6823 8.941127 TTAAGTTGTGCAAACATTTTTGAAAC 57.059 26.923 8.51 8.61 44.38 2.78
6176 6824 9.950680 TTTTAAGTTGTGCAAACATTTTTGAAA 57.049 22.222 8.51 0.00 44.38 2.69
6893 7544 8.816144 GTTTGAAGAAATTCTTGCAAACATGTA 58.184 29.630 30.89 14.52 43.69 2.29


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

AutoCloner maintained by Alex Coulton.