Multiple sequence alignment - TraesCS5A01G229700

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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 TraesCS5A01G229700 chr5A 100.000 5360 0 0 1 5360 445205029 445210388 0.000000e+00 9899.0
1 TraesCS5A01G229700 chr5A 99.445 901 4 1 4461 5360 445219266 445220166 0.000000e+00 1635.0
2 TraesCS5A01G229700 chr5A 99.445 901 4 1 4461 5360 445226185 445227085 0.000000e+00 1635.0
3 TraesCS5A01G229700 chr5A 99.334 901 5 1 4461 5360 445231654 445232554 0.000000e+00 1629.0
4 TraesCS5A01G229700 chr5A 99.223 901 6 1 4461 5360 445220716 445221616 0.000000e+00 1624.0
5 TraesCS5A01G229700 chr5A 100.000 343 0 0 4461 4803 445214957 445215299 7.570000e-178 634.0
6 TraesCS5A01G229700 chr5B 92.624 4067 203 48 831 4858 405558117 405562125 0.000000e+00 5758.0
7 TraesCS5A01G229700 chr5B 86.852 540 24 19 4854 5360 405562203 405562728 1.300000e-155 560.0
8 TraesCS5A01G229700 chr5B 90.560 339 21 4 12 339 405557464 405557802 6.370000e-119 438.0
9 TraesCS5A01G229700 chr5D 93.558 3710 175 31 831 4518 345973787 345970120 0.000000e+00 5469.0
10 TraesCS5A01G229700 chr5D 86.944 697 41 18 4552 5215 345970120 345969441 0.000000e+00 737.0
11 TraesCS5A01G229700 chr5D 88.547 358 20 7 1 339 345974455 345974100 1.070000e-111 414.0
12 TraesCS5A01G229700 chr5D 86.190 210 18 7 339 539 345974071 345973864 3.250000e-52 217.0
13 TraesCS5A01G229700 chrUn 100.000 343 0 0 4461 4803 361785549 361785207 7.570000e-178 634.0
14 TraesCS5A01G229700 chrUn 100.000 258 0 0 4461 4718 366899933 366899676 1.350000e-130 477.0
15 TraesCS5A01G229700 chrUn 89.362 47 3 2 4820 4865 36502695 36502650 2.090000e-04 58.4
16 TraesCS5A01G229700 chr3D 97.059 34 1 0 4820 4853 5071456 5071423 2.090000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G229700 chr5A 445205029 445210388 5359 False 9899.000000 9899 100.00000 1 5360 1 chr5A.!!$F1 5359
1 TraesCS5A01G229700 chr5A 445226185 445227085 900 False 1635.000000 1635 99.44500 4461 5360 1 chr5A.!!$F2 899
2 TraesCS5A01G229700 chr5A 445231654 445232554 900 False 1629.000000 1629 99.33400 4461 5360 1 chr5A.!!$F3 899
3 TraesCS5A01G229700 chr5A 445214957 445221616 6659 False 1297.666667 1635 99.55600 4461 5360 3 chr5A.!!$F4 899
4 TraesCS5A01G229700 chr5B 405557464 405562728 5264 False 2252.000000 5758 90.01200 12 5360 3 chr5B.!!$F1 5348
5 TraesCS5A01G229700 chr5D 345969441 345974455 5014 True 1709.250000 5469 88.80975 1 5215 4 chr5D.!!$R1 5214

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
677 751 0.032813 CACAAGGGCCAATCTGGGAT 60.033 55.000 6.18 0.00 38.19 3.85 F
678 752 0.032813 ACAAGGGCCAATCTGGGATG 60.033 55.000 6.18 0.00 38.19 3.51 F
735 809 0.102481 CGAGGGCAGCAACGTAGTAT 59.898 55.000 0.00 0.00 45.00 2.12 F
737 811 0.462047 AGGGCAGCAACGTAGTATGC 60.462 55.000 1.65 1.65 45.00 3.14 F
1618 1704 0.462047 GGGATATAGCGATTGGCCCG 60.462 60.000 0.00 0.00 45.17 6.13 F
1937 2027 2.151202 CAGCTGAAATACGTGTTGGGT 58.849 47.619 8.42 0.00 0.00 4.51 F
2170 2261 2.170397 TCATGCCGTGTTGATATGGAGT 59.830 45.455 0.00 0.00 0.00 3.85 F
3951 4060 0.025001 GATCGTGGAAATGTCGCGTG 59.975 55.000 5.77 0.00 38.95 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 1879 1.002033 AGTCCAACACGTCGACACTAC 60.002 52.381 17.16 3.47 0.00 2.73 R
2675 2775 2.030540 CCACACAACTGAGCCTGAATTG 60.031 50.000 0.00 0.00 0.00 2.32 R
2725 2825 4.279169 CCTGATGACCAAGTGACAACAAAT 59.721 41.667 0.00 0.00 0.00 2.32 R
3164 3265 5.446741 CGAACGTGAGAAAGAACCTGAAAAA 60.447 40.000 0.00 0.00 0.00 1.94 R
3320 3421 1.353103 GCCGATCACCGCAGAAATG 59.647 57.895 0.00 0.00 36.84 2.32 R
3848 3957 1.005097 AGAATTCTGCCATGGAGCACA 59.995 47.619 18.40 2.27 38.00 4.57 R
4169 4286 0.625316 ACATTATCAGTGGCCCAGCA 59.375 50.000 0.00 0.00 0.00 4.41 R
5275 11270 2.728690 TTGGAATGAGCATTGCACAC 57.271 45.000 15.51 0.00 46.36 3.82 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
74 82 8.454894 GGATTCAAAGAGAATAGTTGGAACTTC 58.545 37.037 0.00 0.00 46.76 3.01
105 116 7.336679 ACCAATTATTGCTTTTTGAATAAGCCC 59.663 33.333 15.85 0.00 45.73 5.19
106 117 7.336427 CCAATTATTGCTTTTTGAATAAGCCCA 59.664 33.333 15.85 5.18 45.73 5.36
189 219 8.933807 CCATTATTATCTGCTATTCACACTGAG 58.066 37.037 0.00 0.00 0.00 3.35
277 308 8.894768 AACAGATGGTTGTTCTATATAAGAGC 57.105 34.615 0.00 0.00 36.60 4.09
301 332 9.440773 AGCGAGCATCAAATATCAAATAGATTA 57.559 29.630 0.00 0.00 34.71 1.75
351 411 2.221169 TCACTGTTTTGCCTGCTAGTG 58.779 47.619 0.00 0.00 37.47 2.74
355 415 1.142870 TGTTTTGCCTGCTAGTGGTCT 59.857 47.619 5.94 0.00 0.00 3.85
369 429 1.618837 GTGGTCTGAGCTCAAGGTACA 59.381 52.381 18.85 9.70 0.00 2.90
380 440 5.564550 AGCTCAAGGTACATGTTCATCTTT 58.435 37.500 2.30 0.00 0.00 2.52
425 485 6.374333 TCTCCCAAAACGAAAATTCAGGATAG 59.626 38.462 0.00 0.00 0.00 2.08
426 486 6.007703 TCCCAAAACGAAAATTCAGGATAGT 58.992 36.000 0.00 0.00 0.00 2.12
437 497 7.496346 AAATTCAGGATAGTCTGTACTCCAA 57.504 36.000 0.00 0.00 37.15 3.53
440 500 5.519808 TCAGGATAGTCTGTACTCCAACAT 58.480 41.667 0.00 0.00 37.15 2.71
462 527 7.983307 ACATTGCTGATTCAATCTCTTTCTAC 58.017 34.615 0.00 0.00 34.68 2.59
490 559 9.887406 ACGAAAATTAGTCACGACAAAATTTAT 57.113 25.926 16.84 10.95 37.76 1.40
544 613 9.710900 AAAATTTAAGGCTCAAATTCAACCTAG 57.289 29.630 8.77 0.00 35.15 3.02
545 614 5.897377 TTAAGGCTCAAATTCAACCTAGC 57.103 39.130 0.00 0.00 0.00 3.42
546 615 3.728385 AGGCTCAAATTCAACCTAGCT 57.272 42.857 0.00 0.00 0.00 3.32
547 616 4.844349 AGGCTCAAATTCAACCTAGCTA 57.156 40.909 0.00 0.00 0.00 3.32
548 617 5.379706 AGGCTCAAATTCAACCTAGCTAT 57.620 39.130 0.00 0.00 0.00 2.97
549 618 5.128919 AGGCTCAAATTCAACCTAGCTATG 58.871 41.667 0.00 0.00 0.00 2.23
550 619 4.884164 GGCTCAAATTCAACCTAGCTATGT 59.116 41.667 0.00 0.00 0.00 2.29
551 620 5.008118 GGCTCAAATTCAACCTAGCTATGTC 59.992 44.000 1.87 0.00 0.00 3.06
552 621 5.586243 GCTCAAATTCAACCTAGCTATGTCA 59.414 40.000 1.87 0.00 0.00 3.58
553 622 6.238320 GCTCAAATTCAACCTAGCTATGTCAG 60.238 42.308 1.87 0.00 0.00 3.51
659 733 9.567776 TTATAAATATCGATGAAAAGGGAAGCA 57.432 29.630 8.54 0.00 0.00 3.91
660 734 5.757850 AATATCGATGAAAAGGGAAGCAC 57.242 39.130 8.54 0.00 0.00 4.40
661 735 2.559698 TCGATGAAAAGGGAAGCACA 57.440 45.000 0.00 0.00 0.00 4.57
663 737 2.813754 TCGATGAAAAGGGAAGCACAAG 59.186 45.455 0.00 0.00 0.00 3.16
666 740 0.318441 GAAAAGGGAAGCACAAGGGC 59.682 55.000 0.00 0.00 0.00 5.19
667 741 1.121407 AAAAGGGAAGCACAAGGGCC 61.121 55.000 0.00 0.00 0.00 5.80
668 742 2.310930 AAAGGGAAGCACAAGGGCCA 62.311 55.000 6.18 0.00 0.00 5.36
669 743 2.203625 GGGAAGCACAAGGGCCAA 60.204 61.111 6.18 0.00 0.00 4.52
670 744 1.610379 GGGAAGCACAAGGGCCAAT 60.610 57.895 6.18 0.00 0.00 3.16
671 745 1.607801 GGGAAGCACAAGGGCCAATC 61.608 60.000 6.18 0.00 0.00 2.67
672 746 0.613012 GGAAGCACAAGGGCCAATCT 60.613 55.000 6.18 0.00 0.00 2.40
673 747 0.529378 GAAGCACAAGGGCCAATCTG 59.471 55.000 6.18 0.00 0.00 2.90
674 748 0.901580 AAGCACAAGGGCCAATCTGG 60.902 55.000 6.18 0.00 41.55 3.86
675 749 2.353610 GCACAAGGGCCAATCTGGG 61.354 63.158 6.18 0.00 38.19 4.45
676 750 1.383799 CACAAGGGCCAATCTGGGA 59.616 57.895 6.18 0.00 38.19 4.37
677 751 0.032813 CACAAGGGCCAATCTGGGAT 60.033 55.000 6.18 0.00 38.19 3.85
678 752 0.032813 ACAAGGGCCAATCTGGGATG 60.033 55.000 6.18 0.00 38.19 3.51
679 753 0.259647 CAAGGGCCAATCTGGGATGA 59.740 55.000 6.18 0.00 38.19 2.92
680 754 0.554792 AAGGGCCAATCTGGGATGAG 59.445 55.000 6.18 0.00 38.19 2.90
681 755 0.327867 AGGGCCAATCTGGGATGAGA 60.328 55.000 6.18 0.00 38.19 3.27
682 756 0.552848 GGGCCAATCTGGGATGAGAA 59.447 55.000 4.39 0.00 38.19 2.87
683 757 1.146566 GGGCCAATCTGGGATGAGAAT 59.853 52.381 4.39 0.00 38.19 2.40
684 758 2.376518 GGGCCAATCTGGGATGAGAATA 59.623 50.000 4.39 0.00 38.19 1.75
685 759 3.416156 GGCCAATCTGGGATGAGAATAC 58.584 50.000 0.00 0.00 38.19 1.89
686 760 3.181440 GGCCAATCTGGGATGAGAATACA 60.181 47.826 0.00 0.00 38.19 2.29
687 761 4.508047 GGCCAATCTGGGATGAGAATACAT 60.508 45.833 0.00 0.00 38.19 2.29
688 762 5.280676 GGCCAATCTGGGATGAGAATACATA 60.281 44.000 0.00 0.00 38.19 2.29
689 763 6.240894 GCCAATCTGGGATGAGAATACATAA 58.759 40.000 0.00 0.00 38.19 1.90
690 764 6.888632 GCCAATCTGGGATGAGAATACATAAT 59.111 38.462 0.00 0.00 38.19 1.28
691 765 7.395489 GCCAATCTGGGATGAGAATACATAATT 59.605 37.037 0.00 0.00 38.19 1.40
692 766 9.964354 CCAATCTGGGATGAGAATACATAATTA 57.036 33.333 0.00 0.00 32.67 1.40
716 790 9.953565 TTAATATTGTACAACTATATGAGGGGC 57.046 33.333 11.22 0.00 29.41 5.80
717 791 4.330944 TTGTACAACTATATGAGGGGCG 57.669 45.455 3.59 0.00 0.00 6.13
718 792 3.568443 TGTACAACTATATGAGGGGCGA 58.432 45.455 0.00 0.00 0.00 5.54
719 793 3.572682 TGTACAACTATATGAGGGGCGAG 59.427 47.826 0.00 0.00 0.00 5.03
720 794 1.971357 ACAACTATATGAGGGGCGAGG 59.029 52.381 0.00 0.00 0.00 4.63
721 795 1.276421 CAACTATATGAGGGGCGAGGG 59.724 57.143 0.00 0.00 0.00 4.30
722 796 0.905337 ACTATATGAGGGGCGAGGGC 60.905 60.000 0.00 0.00 38.90 5.19
723 797 0.904865 CTATATGAGGGGCGAGGGCA 60.905 60.000 0.00 0.00 42.47 5.36
724 798 0.904865 TATATGAGGGGCGAGGGCAG 60.905 60.000 0.00 0.00 42.47 4.85
731 805 4.752879 GGCGAGGGCAGCAACGTA 62.753 66.667 0.00 0.00 42.47 3.57
732 806 3.188786 GCGAGGGCAGCAACGTAG 61.189 66.667 0.00 0.00 39.62 3.51
733 807 3.934391 GCGAGGGCAGCAACGTAGT 62.934 63.158 0.00 0.00 41.17 2.73
734 808 1.509463 CGAGGGCAGCAACGTAGTA 59.491 57.895 0.00 0.00 45.00 1.82
735 809 0.102481 CGAGGGCAGCAACGTAGTAT 59.898 55.000 0.00 0.00 45.00 2.12
736 810 1.571919 GAGGGCAGCAACGTAGTATG 58.428 55.000 0.00 0.00 45.00 2.39
737 811 0.462047 AGGGCAGCAACGTAGTATGC 60.462 55.000 1.65 1.65 45.00 3.14
739 813 2.762360 GCAGCAACGTAGTATGCCA 58.238 52.632 6.34 0.00 45.00 4.92
740 814 1.299541 GCAGCAACGTAGTATGCCAT 58.700 50.000 6.34 0.00 45.00 4.40
741 815 1.670811 GCAGCAACGTAGTATGCCATT 59.329 47.619 6.34 0.00 45.00 3.16
742 816 2.097466 GCAGCAACGTAGTATGCCATTT 59.903 45.455 6.34 0.00 45.00 2.32
743 817 3.427503 GCAGCAACGTAGTATGCCATTTT 60.428 43.478 6.34 0.00 45.00 1.82
744 818 4.732784 CAGCAACGTAGTATGCCATTTTT 58.267 39.130 6.34 0.00 45.00 1.94
745 819 5.675071 GCAGCAACGTAGTATGCCATTTTTA 60.675 40.000 6.34 0.00 45.00 1.52
746 820 6.494842 CAGCAACGTAGTATGCCATTTTTAT 58.505 36.000 6.34 0.00 45.00 1.40
747 821 6.972328 CAGCAACGTAGTATGCCATTTTTATT 59.028 34.615 6.34 0.00 45.00 1.40
748 822 7.165812 CAGCAACGTAGTATGCCATTTTTATTC 59.834 37.037 6.34 0.00 45.00 1.75
749 823 6.416750 GCAACGTAGTATGCCATTTTTATTCC 59.583 38.462 0.00 0.00 45.00 3.01
750 824 7.476667 CAACGTAGTATGCCATTTTTATTCCA 58.523 34.615 0.00 0.00 45.00 3.53
751 825 7.817418 ACGTAGTATGCCATTTTTATTCCAT 57.183 32.000 0.00 0.00 41.94 3.41
752 826 8.232913 ACGTAGTATGCCATTTTTATTCCATT 57.767 30.769 0.00 0.00 41.94 3.16
753 827 8.691797 ACGTAGTATGCCATTTTTATTCCATTT 58.308 29.630 0.00 0.00 41.94 2.32
754 828 9.528018 CGTAGTATGCCATTTTTATTCCATTTT 57.472 29.630 0.00 0.00 0.00 1.82
757 831 9.603921 AGTATGCCATTTTTATTCCATTTTCTG 57.396 29.630 0.00 0.00 0.00 3.02
759 833 6.179040 TGCCATTTTTATTCCATTTTCTGGG 58.821 36.000 0.00 0.00 45.98 4.45
760 834 6.013032 TGCCATTTTTATTCCATTTTCTGGGA 60.013 34.615 0.00 0.00 45.98 4.37
761 835 6.883756 GCCATTTTTATTCCATTTTCTGGGAA 59.116 34.615 0.00 0.00 45.98 3.97
762 836 7.148255 GCCATTTTTATTCCATTTTCTGGGAAC 60.148 37.037 0.00 0.00 45.35 3.62
763 837 7.882271 CCATTTTTATTCCATTTTCTGGGAACA 59.118 33.333 0.00 0.00 45.35 3.18
764 838 9.452287 CATTTTTATTCCATTTTCTGGGAACAT 57.548 29.630 0.00 0.00 45.35 2.71
766 840 9.859152 TTTTTATTCCATTTTCTGGGAACATTT 57.141 25.926 0.00 0.00 45.35 2.32
767 841 9.500785 TTTTATTCCATTTTCTGGGAACATTTC 57.499 29.630 0.00 0.00 45.35 2.17
768 842 6.940430 ATTCCATTTTCTGGGAACATTTCT 57.060 33.333 0.00 0.00 45.35 2.52
769 843 5.726980 TCCATTTTCTGGGAACATTTCTG 57.273 39.130 0.00 0.00 45.98 3.02
770 844 5.147032 TCCATTTTCTGGGAACATTTCTGT 58.853 37.500 0.00 0.00 45.98 3.41
771 845 5.602145 TCCATTTTCTGGGAACATTTCTGTT 59.398 36.000 0.00 0.00 45.08 3.16
772 846 6.099557 TCCATTTTCTGGGAACATTTCTGTTT 59.900 34.615 0.00 0.00 43.70 2.83
773 847 6.203338 CCATTTTCTGGGAACATTTCTGTTTG 59.797 38.462 0.00 0.00 40.94 2.93
774 848 6.537453 TTTTCTGGGAACATTTCTGTTTGA 57.463 33.333 0.00 0.00 45.57 2.69
775 849 6.729690 TTTCTGGGAACATTTCTGTTTGAT 57.270 33.333 0.00 0.00 45.57 2.57
776 850 6.729690 TTCTGGGAACATTTCTGTTTGATT 57.270 33.333 0.00 0.00 45.57 2.57
777 851 6.088016 TCTGGGAACATTTCTGTTTGATTG 57.912 37.500 0.00 0.00 45.57 2.67
778 852 5.832595 TCTGGGAACATTTCTGTTTGATTGA 59.167 36.000 0.00 0.00 45.57 2.57
779 853 5.841810 TGGGAACATTTCTGTTTGATTGAC 58.158 37.500 0.00 0.00 45.57 3.18
780 854 5.221422 TGGGAACATTTCTGTTTGATTGACC 60.221 40.000 0.00 0.00 45.57 4.02
781 855 5.221422 GGGAACATTTCTGTTTGATTGACCA 60.221 40.000 0.00 0.00 45.57 4.02
782 856 6.279882 GGAACATTTCTGTTTGATTGACCAA 58.720 36.000 0.00 0.00 45.57 3.67
783 857 6.200854 GGAACATTTCTGTTTGATTGACCAAC 59.799 38.462 0.00 0.00 45.57 3.77
784 858 6.469782 ACATTTCTGTTTGATTGACCAACT 57.530 33.333 0.00 0.00 28.70 3.16
785 859 6.877236 ACATTTCTGTTTGATTGACCAACTT 58.123 32.000 0.00 0.00 28.70 2.66
786 860 7.330262 ACATTTCTGTTTGATTGACCAACTTT 58.670 30.769 0.00 0.00 28.70 2.66
787 861 7.823799 ACATTTCTGTTTGATTGACCAACTTTT 59.176 29.630 0.00 0.00 28.70 2.27
788 862 7.593875 TTTCTGTTTGATTGACCAACTTTTG 57.406 32.000 0.00 0.00 0.00 2.44
789 863 6.279513 TCTGTTTGATTGACCAACTTTTGT 57.720 33.333 0.00 0.00 0.00 2.83
790 864 6.098679 TCTGTTTGATTGACCAACTTTTGTG 58.901 36.000 0.00 0.00 0.00 3.33
791 865 5.788450 TGTTTGATTGACCAACTTTTGTGT 58.212 33.333 0.00 0.00 0.00 3.72
792 866 5.636965 TGTTTGATTGACCAACTTTTGTGTG 59.363 36.000 0.00 0.00 0.00 3.82
793 867 5.651387 TTGATTGACCAACTTTTGTGTGA 57.349 34.783 0.00 0.00 0.00 3.58
794 868 5.850557 TGATTGACCAACTTTTGTGTGAT 57.149 34.783 0.00 0.00 0.00 3.06
795 869 6.951062 TGATTGACCAACTTTTGTGTGATA 57.049 33.333 0.00 0.00 0.00 2.15
796 870 7.523293 TGATTGACCAACTTTTGTGTGATAT 57.477 32.000 0.00 0.00 0.00 1.63
797 871 8.628630 TGATTGACCAACTTTTGTGTGATATA 57.371 30.769 0.00 0.00 0.00 0.86
798 872 8.729756 TGATTGACCAACTTTTGTGTGATATAG 58.270 33.333 0.00 0.00 0.00 1.31
799 873 6.494893 TGACCAACTTTTGTGTGATATAGC 57.505 37.500 0.00 0.00 0.00 2.97
800 874 5.121611 TGACCAACTTTTGTGTGATATAGCG 59.878 40.000 0.00 0.00 0.00 4.26
801 875 5.242434 ACCAACTTTTGTGTGATATAGCGA 58.758 37.500 0.00 0.00 0.00 4.93
802 876 5.880332 ACCAACTTTTGTGTGATATAGCGAT 59.120 36.000 0.00 0.00 0.00 4.58
803 877 6.374333 ACCAACTTTTGTGTGATATAGCGATT 59.626 34.615 0.00 0.00 0.00 3.34
804 878 6.688385 CCAACTTTTGTGTGATATAGCGATTG 59.312 38.462 0.00 0.00 0.00 2.67
805 879 5.810525 ACTTTTGTGTGATATAGCGATTGC 58.189 37.500 0.00 0.00 43.24 3.56
806 880 5.353956 ACTTTTGTGTGATATAGCGATTGCA 59.646 36.000 7.90 0.00 46.23 4.08
807 881 6.038603 ACTTTTGTGTGATATAGCGATTGCAT 59.961 34.615 7.90 1.60 46.23 3.96
808 882 5.596268 TTGTGTGATATAGCGATTGCATC 57.404 39.130 7.90 2.26 46.23 3.91
820 894 3.070429 GATTGCATCGTCCATTGTTCC 57.930 47.619 0.00 0.00 0.00 3.62
821 895 1.902938 TTGCATCGTCCATTGTTCCA 58.097 45.000 0.00 0.00 0.00 3.53
822 896 1.902938 TGCATCGTCCATTGTTCCAA 58.097 45.000 0.00 0.00 0.00 3.53
823 897 2.234143 TGCATCGTCCATTGTTCCAAA 58.766 42.857 0.00 0.00 0.00 3.28
824 898 2.228582 TGCATCGTCCATTGTTCCAAAG 59.771 45.455 0.00 0.00 0.00 2.77
825 899 2.228822 GCATCGTCCATTGTTCCAAAGT 59.771 45.455 0.00 0.00 0.00 2.66
826 900 3.438781 GCATCGTCCATTGTTCCAAAGTA 59.561 43.478 0.00 0.00 0.00 2.24
827 901 4.437390 GCATCGTCCATTGTTCCAAAGTAG 60.437 45.833 0.00 0.00 0.00 2.57
828 902 4.610605 TCGTCCATTGTTCCAAAGTAGA 57.389 40.909 0.00 0.00 0.00 2.59
829 903 4.312443 TCGTCCATTGTTCCAAAGTAGAC 58.688 43.478 0.00 0.00 0.00 2.59
835 909 2.695359 TGTTCCAAAGTAGACCATCGC 58.305 47.619 0.00 0.00 0.00 4.58
843 917 1.132643 AGTAGACCATCGCTTCGTGAC 59.867 52.381 0.00 0.00 0.00 3.67
851 925 2.334971 TCGCTTCGTGACGTCATTTA 57.665 45.000 23.12 7.45 0.00 1.40
862 936 4.035909 GTGACGTCATTTAGGTGGTGTTTT 59.964 41.667 23.12 0.00 0.00 2.43
903 981 5.762045 TGTTGGAGTACTGTAAACGTCTAC 58.238 41.667 0.00 0.00 0.00 2.59
907 985 4.460731 GGAGTACTGTAAACGTCTACCCTT 59.539 45.833 0.00 0.00 0.00 3.95
922 1000 1.153005 CCTTCATGCCCTCTCCAGC 60.153 63.158 0.00 0.00 0.00 4.85
924 1002 1.126488 CTTCATGCCCTCTCCAGCTA 58.874 55.000 0.00 0.00 0.00 3.32
925 1003 1.698532 CTTCATGCCCTCTCCAGCTAT 59.301 52.381 0.00 0.00 0.00 2.97
926 1004 1.811778 TCATGCCCTCTCCAGCTATT 58.188 50.000 0.00 0.00 0.00 1.73
927 1005 2.130193 TCATGCCCTCTCCAGCTATTT 58.870 47.619 0.00 0.00 0.00 1.40
928 1006 2.511218 TCATGCCCTCTCCAGCTATTTT 59.489 45.455 0.00 0.00 0.00 1.82
929 1007 3.053395 TCATGCCCTCTCCAGCTATTTTT 60.053 43.478 0.00 0.00 0.00 1.94
981 1059 6.884280 ACTGTTTCTCCAGGATAACAAAAG 57.116 37.500 14.91 8.68 36.75 2.27
1263 1341 2.617207 TTGGGTGGGGTAGGGATTAT 57.383 50.000 0.00 0.00 0.00 1.28
1365 1443 1.073923 ACTAGTCCACCTTGGCTTTGG 59.926 52.381 0.00 0.00 37.47 3.28
1464 1550 3.181510 CGCAGTATGGGCTTTGTAAGTTC 60.182 47.826 0.00 0.00 43.90 3.01
1496 1582 4.978099 ACTCTGTTGTGGAGATTTGATGT 58.022 39.130 0.00 0.00 35.10 3.06
1615 1701 3.265791 CTCAAGGGATATAGCGATTGGC 58.734 50.000 4.57 0.00 44.05 4.52
1618 1704 0.462047 GGGATATAGCGATTGGCCCG 60.462 60.000 0.00 0.00 45.17 6.13
1729 1815 2.563427 GCAACCTTCTTCGCTGGC 59.437 61.111 0.00 0.00 0.00 4.85
1789 1878 7.546358 TGCAAACATATACTAAAAGCTTGCAT 58.454 30.769 0.00 0.00 41.04 3.96
1790 1879 7.488792 TGCAAACATATACTAAAAGCTTGCATG 59.511 33.333 0.00 0.00 41.04 4.06
1822 1911 4.282703 ACGTGTTGGACTAAGAGTTGGTAT 59.717 41.667 0.00 0.00 0.00 2.73
1825 1914 6.869913 CGTGTTGGACTAAGAGTTGGTATTTA 59.130 38.462 0.00 0.00 0.00 1.40
1937 2027 2.151202 CAGCTGAAATACGTGTTGGGT 58.849 47.619 8.42 0.00 0.00 4.51
2013 2103 3.309296 AGATCAGTTCATCACGGGGTAT 58.691 45.455 0.00 0.00 0.00 2.73
2018 2108 4.407621 TCAGTTCATCACGGGGTATGTATT 59.592 41.667 0.00 0.00 0.00 1.89
2022 2112 4.956085 TCATCACGGGGTATGTATTTCAG 58.044 43.478 0.00 0.00 0.00 3.02
2029 2120 7.123997 TCACGGGGTATGTATTTCAGTACTTAA 59.876 37.037 0.00 0.00 0.00 1.85
2085 2176 2.964174 TGCGCTGCATTTTCTGGG 59.036 55.556 9.73 0.00 31.71 4.45
2156 2247 8.002107 CGTTATTAGTAAAAGTATGTCATGCCG 58.998 37.037 0.00 0.00 0.00 5.69
2160 2251 5.001232 AGTAAAAGTATGTCATGCCGTGTT 58.999 37.500 0.00 0.00 0.00 3.32
2169 2260 2.545526 GTCATGCCGTGTTGATATGGAG 59.454 50.000 0.00 0.00 0.00 3.86
2170 2261 2.170397 TCATGCCGTGTTGATATGGAGT 59.830 45.455 0.00 0.00 0.00 3.85
2261 2353 6.713762 TGTTATATTCATTTGGAAGCTGGG 57.286 37.500 0.00 0.00 39.30 4.45
2275 2367 2.962859 AGCTGGGAGGTGAATTTGTTT 58.037 42.857 0.00 0.00 0.00 2.83
2304 2396 2.578163 TTCTGGATCTTCCTGCGCCG 62.578 60.000 4.18 0.00 37.46 6.46
2354 2446 8.721019 ATAGTACTACTGTCTGTCTGAGTTAC 57.279 38.462 4.31 0.00 0.00 2.50
2361 2455 6.069331 ACTGTCTGTCTGAGTTACCTAAAGA 58.931 40.000 0.00 0.00 0.00 2.52
2377 2471 5.181748 CCTAAAGAACTGACAAGGAGATGG 58.818 45.833 0.00 0.00 0.00 3.51
2711 2811 3.892284 TGTGTGGACCATACACTGTTTT 58.108 40.909 19.20 0.00 46.49 2.43
2791 2891 4.842531 TCAACCCATCATCAGTACACAT 57.157 40.909 0.00 0.00 0.00 3.21
2810 2910 3.625764 ACATGATTTATTTCACCGGTCCG 59.374 43.478 2.59 3.60 0.00 4.79
2941 3041 6.148976 CAGATTTCTCATCAATCTGTGTGTGT 59.851 38.462 12.57 0.00 46.89 3.72
3320 3421 2.300152 TGCAATCCTAGGGTCGATCATC 59.700 50.000 9.46 0.00 0.00 2.92
3368 3469 5.994054 GGACTATGAAGCAGCAATTCTCATA 59.006 40.000 0.00 0.00 0.00 2.15
3470 3571 4.922206 TCTTGATTGCTGTAAGGACCAAT 58.078 39.130 0.00 0.00 29.42 3.16
3471 3572 4.701651 TCTTGATTGCTGTAAGGACCAATG 59.298 41.667 0.00 0.00 29.42 2.82
3486 3587 6.131264 AGGACCAATGCATTATCTTTGATGA 58.869 36.000 12.53 0.00 0.00 2.92
3488 3589 6.921857 GGACCAATGCATTATCTTTGATGAAG 59.078 38.462 12.53 0.00 36.67 3.02
3489 3590 6.278363 ACCAATGCATTATCTTTGATGAAGC 58.722 36.000 12.53 0.00 35.24 3.86
3491 3592 6.929049 CCAATGCATTATCTTTGATGAAGCAT 59.071 34.615 12.53 8.50 41.43 3.79
3492 3593 8.085909 CCAATGCATTATCTTTGATGAAGCATA 58.914 33.333 12.53 0.00 39.04 3.14
3532 3634 9.052759 GTCTTTTTGTGGAGACATAACTAGAAA 57.947 33.333 0.00 0.00 46.14 2.52
3893 4002 1.895798 TGGCTGACAGACGAAGAAGAT 59.104 47.619 6.65 0.00 0.00 2.40
3935 4044 6.515272 TTGCCTAAAATCAGTTCCTTGATC 57.485 37.500 0.00 0.00 36.81 2.92
3951 4060 0.025001 GATCGTGGAAATGTCGCGTG 59.975 55.000 5.77 0.00 38.95 5.34
3968 4077 7.641760 TGTCGCGTGAGTAGAATTATATGTTA 58.358 34.615 5.77 0.00 0.00 2.41
3973 4082 9.119329 GCGTGAGTAGAATTATATGTTAGTCTG 57.881 37.037 0.00 0.00 0.00 3.51
4073 4186 7.011219 CGACATCGATACAAGTGGCATACAC 62.011 48.000 0.00 0.00 45.85 2.90
4139 4252 3.523564 AGGTACACCCATTCAAGCTACAT 59.476 43.478 0.00 0.00 36.42 2.29
4141 4257 5.057149 GGTACACCCATTCAAGCTACATAG 58.943 45.833 0.00 0.00 0.00 2.23
4143 4259 5.636903 ACACCCATTCAAGCTACATAGAT 57.363 39.130 0.00 0.00 0.00 1.98
4151 4267 8.557864 CCATTCAAGCTACATAGATTTTCAGAG 58.442 37.037 0.00 0.00 27.90 3.35
4177 4294 3.893326 ATAATCTTGTTTTGCTGGGCC 57.107 42.857 0.00 0.00 0.00 5.80
4178 4295 1.422531 AATCTTGTTTTGCTGGGCCA 58.577 45.000 5.85 5.85 0.00 5.36
4194 4311 3.257873 TGGGCCACTGATAATGTTGTTTG 59.742 43.478 0.00 0.00 0.00 2.93
4195 4312 3.258123 GGGCCACTGATAATGTTGTTTGT 59.742 43.478 4.39 0.00 0.00 2.83
4196 4313 4.461081 GGGCCACTGATAATGTTGTTTGTA 59.539 41.667 4.39 0.00 0.00 2.41
4197 4314 5.127031 GGGCCACTGATAATGTTGTTTGTAT 59.873 40.000 4.39 0.00 0.00 2.29
4198 4315 6.350949 GGGCCACTGATAATGTTGTTTGTATT 60.351 38.462 4.39 0.00 0.00 1.89
4199 4316 6.531240 GGCCACTGATAATGTTGTTTGTATTG 59.469 38.462 0.00 0.00 0.00 1.90
4266 4383 5.098211 GTCATAGAAAAACTGCAAGCATCC 58.902 41.667 0.00 0.00 37.60 3.51
4368 4485 1.135083 CAGGAACCGTGAGCGAAGTAT 60.135 52.381 0.00 0.00 41.33 2.12
4388 4505 2.819984 TTCGGAGGAATGGCTGGTGC 62.820 60.000 0.00 0.00 38.76 5.01
4409 4526 1.004628 TGCCATGGTGCTAGTGTTGAT 59.995 47.619 14.67 0.00 0.00 2.57
5275 11270 5.116882 TCAGCTGATGACAAGATCAAGATG 58.883 41.667 13.74 0.00 41.93 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 82 4.996122 TCAAAAAGCAATAATTGGTGCAGG 59.004 37.500 15.16 3.08 43.42 4.85
153 164 6.058183 AGCAGATAATAATGGTGGACTGTTC 58.942 40.000 0.00 0.00 0.00 3.18
189 219 2.960819 AGGTCGACTGTATTGTTCAGC 58.039 47.619 16.46 0.00 36.50 4.26
327 358 1.267806 AGCAGGCAAAACAGTGAATCG 59.732 47.619 0.00 0.00 0.00 3.34
351 411 2.234908 ACATGTACCTTGAGCTCAGACC 59.765 50.000 17.43 5.37 0.00 3.85
355 415 4.223700 AGATGAACATGTACCTTGAGCTCA 59.776 41.667 13.74 13.74 0.00 4.26
380 440 9.400208 TGGGAGAAATATAGGTGATGGTTATTA 57.600 33.333 0.00 0.00 0.00 0.98
386 446 6.017109 CGTTTTGGGAGAAATATAGGTGATGG 60.017 42.308 0.00 0.00 0.00 3.51
425 485 3.664107 TCAGCAATGTTGGAGTACAGAC 58.336 45.455 0.00 0.00 0.00 3.51
426 486 4.558226 ATCAGCAATGTTGGAGTACAGA 57.442 40.909 0.00 0.00 0.00 3.41
437 497 7.828223 AGTAGAAAGAGATTGAATCAGCAATGT 59.172 33.333 8.03 0.00 38.53 2.71
440 500 7.489435 CGTAGTAGAAAGAGATTGAATCAGCAA 59.511 37.037 8.03 0.00 0.00 3.91
462 527 8.928844 AATTTTGTCGTGACTAATTTTCGTAG 57.071 30.769 1.23 0.00 0.00 3.51
527 596 4.884164 ACATAGCTAGGTTGAATTTGAGCC 59.116 41.667 4.95 0.00 0.00 4.70
528 597 5.586243 TGACATAGCTAGGTTGAATTTGAGC 59.414 40.000 13.02 0.00 0.00 4.26
529 598 7.244166 CTGACATAGCTAGGTTGAATTTGAG 57.756 40.000 13.02 0.00 0.00 3.02
634 708 8.999431 GTGCTTCCCTTTTCATCGATATTTATA 58.001 33.333 0.00 0.00 0.00 0.98
647 721 0.318441 GCCCTTGTGCTTCCCTTTTC 59.682 55.000 0.00 0.00 0.00 2.29
648 722 1.121407 GGCCCTTGTGCTTCCCTTTT 61.121 55.000 0.00 0.00 0.00 2.27
649 723 1.533994 GGCCCTTGTGCTTCCCTTT 60.534 57.895 0.00 0.00 0.00 3.11
650 724 2.118294 GGCCCTTGTGCTTCCCTT 59.882 61.111 0.00 0.00 0.00 3.95
651 725 2.097978 ATTGGCCCTTGTGCTTCCCT 62.098 55.000 0.00 0.00 0.00 4.20
652 726 1.607801 GATTGGCCCTTGTGCTTCCC 61.608 60.000 0.00 0.00 0.00 3.97
654 728 0.529378 CAGATTGGCCCTTGTGCTTC 59.471 55.000 0.00 0.00 0.00 3.86
655 729 0.901580 CCAGATTGGCCCTTGTGCTT 60.902 55.000 0.00 0.00 0.00 3.91
656 730 1.304713 CCAGATTGGCCCTTGTGCT 60.305 57.895 0.00 0.00 0.00 4.40
657 731 2.353610 CCCAGATTGGCCCTTGTGC 61.354 63.158 0.00 0.00 35.79 4.57
658 732 0.032813 ATCCCAGATTGGCCCTTGTG 60.033 55.000 0.00 0.00 35.79 3.33
659 733 0.032813 CATCCCAGATTGGCCCTTGT 60.033 55.000 0.00 0.00 35.79 3.16
660 734 0.259647 TCATCCCAGATTGGCCCTTG 59.740 55.000 0.00 0.00 35.79 3.61
661 735 0.554792 CTCATCCCAGATTGGCCCTT 59.445 55.000 0.00 0.00 35.79 3.95
663 737 0.552848 TTCTCATCCCAGATTGGCCC 59.447 55.000 0.00 0.00 35.79 5.80
666 740 8.874744 AATTATGTATTCTCATCCCAGATTGG 57.125 34.615 0.00 0.00 37.25 3.16
690 764 9.953565 GCCCCTCATATAGTTGTACAATATTAA 57.046 33.333 12.26 0.00 0.00 1.40
691 765 8.255206 CGCCCCTCATATAGTTGTACAATATTA 58.745 37.037 12.26 5.82 0.00 0.98
692 766 7.038587 TCGCCCCTCATATAGTTGTACAATATT 60.039 37.037 12.26 3.69 0.00 1.28
693 767 6.439375 TCGCCCCTCATATAGTTGTACAATAT 59.561 38.462 12.26 12.27 0.00 1.28
694 768 5.776208 TCGCCCCTCATATAGTTGTACAATA 59.224 40.000 12.26 5.96 0.00 1.90
695 769 4.591498 TCGCCCCTCATATAGTTGTACAAT 59.409 41.667 12.26 3.86 0.00 2.71
696 770 3.962063 TCGCCCCTCATATAGTTGTACAA 59.038 43.478 3.59 3.59 0.00 2.41
697 771 3.568443 TCGCCCCTCATATAGTTGTACA 58.432 45.455 0.00 0.00 0.00 2.90
698 772 3.056749 CCTCGCCCCTCATATAGTTGTAC 60.057 52.174 0.00 0.00 0.00 2.90
699 773 3.162666 CCTCGCCCCTCATATAGTTGTA 58.837 50.000 0.00 0.00 0.00 2.41
700 774 1.971357 CCTCGCCCCTCATATAGTTGT 59.029 52.381 0.00 0.00 0.00 3.32
701 775 1.276421 CCCTCGCCCCTCATATAGTTG 59.724 57.143 0.00 0.00 0.00 3.16
702 776 1.645710 CCCTCGCCCCTCATATAGTT 58.354 55.000 0.00 0.00 0.00 2.24
703 777 0.905337 GCCCTCGCCCCTCATATAGT 60.905 60.000 0.00 0.00 0.00 2.12
704 778 0.904865 TGCCCTCGCCCCTCATATAG 60.905 60.000 0.00 0.00 0.00 1.31
705 779 0.904865 CTGCCCTCGCCCCTCATATA 60.905 60.000 0.00 0.00 0.00 0.86
706 780 2.122413 TGCCCTCGCCCCTCATAT 60.122 61.111 0.00 0.00 0.00 1.78
707 781 2.844362 CTGCCCTCGCCCCTCATA 60.844 66.667 0.00 0.00 0.00 2.15
714 788 4.752879 TACGTTGCTGCCCTCGCC 62.753 66.667 0.00 0.00 0.00 5.54
715 789 2.552585 TACTACGTTGCTGCCCTCGC 62.553 60.000 0.00 0.00 0.00 5.03
716 790 0.102481 ATACTACGTTGCTGCCCTCG 59.898 55.000 0.00 1.89 0.00 4.63
717 791 1.571919 CATACTACGTTGCTGCCCTC 58.428 55.000 0.00 0.00 0.00 4.30
718 792 0.462047 GCATACTACGTTGCTGCCCT 60.462 55.000 12.07 0.00 35.95 5.19
719 793 1.436983 GGCATACTACGTTGCTGCCC 61.437 60.000 24.09 12.36 45.26 5.36
720 794 2.014594 GGCATACTACGTTGCTGCC 58.985 57.895 21.74 21.74 44.91 4.85
721 795 1.299541 ATGGCATACTACGTTGCTGC 58.700 50.000 13.95 13.95 38.88 5.25
722 796 4.355543 AAAATGGCATACTACGTTGCTG 57.644 40.909 9.61 3.30 38.88 4.41
723 797 6.693315 ATAAAAATGGCATACTACGTTGCT 57.307 33.333 9.61 0.00 38.88 3.91
724 798 6.416750 GGAATAAAAATGGCATACTACGTTGC 59.583 38.462 0.00 0.00 38.14 4.17
725 799 7.476667 TGGAATAAAAATGGCATACTACGTTG 58.523 34.615 0.00 0.00 0.00 4.10
726 800 7.633193 TGGAATAAAAATGGCATACTACGTT 57.367 32.000 0.00 0.00 0.00 3.99
727 801 7.817418 ATGGAATAAAAATGGCATACTACGT 57.183 32.000 0.00 0.00 0.00 3.57
728 802 9.528018 AAAATGGAATAAAAATGGCATACTACG 57.472 29.630 0.00 0.00 0.00 3.51
731 805 9.603921 CAGAAAATGGAATAAAAATGGCATACT 57.396 29.630 0.00 0.00 0.00 2.12
749 823 6.985645 TCAAACAGAAATGTTCCCAGAAAATG 59.014 34.615 0.00 0.00 0.00 2.32
750 824 7.123355 TCAAACAGAAATGTTCCCAGAAAAT 57.877 32.000 0.00 0.00 0.00 1.82
751 825 6.537453 TCAAACAGAAATGTTCCCAGAAAA 57.463 33.333 0.00 0.00 0.00 2.29
752 826 6.729690 ATCAAACAGAAATGTTCCCAGAAA 57.270 33.333 0.00 0.00 0.00 2.52
753 827 6.323482 TCAATCAAACAGAAATGTTCCCAGAA 59.677 34.615 0.00 0.00 0.00 3.02
754 828 5.832595 TCAATCAAACAGAAATGTTCCCAGA 59.167 36.000 0.00 0.00 0.00 3.86
755 829 5.922544 GTCAATCAAACAGAAATGTTCCCAG 59.077 40.000 0.00 0.00 0.00 4.45
756 830 5.221422 GGTCAATCAAACAGAAATGTTCCCA 60.221 40.000 0.00 0.00 0.00 4.37
757 831 5.221422 TGGTCAATCAAACAGAAATGTTCCC 60.221 40.000 0.00 0.00 0.00 3.97
758 832 5.841810 TGGTCAATCAAACAGAAATGTTCC 58.158 37.500 0.00 0.00 0.00 3.62
759 833 6.980397 AGTTGGTCAATCAAACAGAAATGTTC 59.020 34.615 0.00 0.00 0.00 3.18
760 834 6.877236 AGTTGGTCAATCAAACAGAAATGTT 58.123 32.000 0.00 0.00 0.00 2.71
761 835 6.469782 AGTTGGTCAATCAAACAGAAATGT 57.530 33.333 0.00 0.00 0.00 2.71
762 836 7.775397 AAAGTTGGTCAATCAAACAGAAATG 57.225 32.000 0.00 0.00 0.00 2.32
763 837 7.823799 ACAAAAGTTGGTCAATCAAACAGAAAT 59.176 29.630 0.00 0.00 34.12 2.17
764 838 7.117523 CACAAAAGTTGGTCAATCAAACAGAAA 59.882 33.333 0.00 0.00 34.12 2.52
765 839 6.589523 CACAAAAGTTGGTCAATCAAACAGAA 59.410 34.615 0.00 0.00 34.12 3.02
766 840 6.098679 CACAAAAGTTGGTCAATCAAACAGA 58.901 36.000 0.00 0.00 34.12 3.41
767 841 5.868801 ACACAAAAGTTGGTCAATCAAACAG 59.131 36.000 0.00 0.00 34.12 3.16
768 842 5.636965 CACACAAAAGTTGGTCAATCAAACA 59.363 36.000 0.00 0.00 34.12 2.83
769 843 5.866633 TCACACAAAAGTTGGTCAATCAAAC 59.133 36.000 0.00 0.00 34.12 2.93
770 844 6.030548 TCACACAAAAGTTGGTCAATCAAA 57.969 33.333 0.00 0.00 34.12 2.69
771 845 5.651387 TCACACAAAAGTTGGTCAATCAA 57.349 34.783 0.00 0.00 34.12 2.57
772 846 5.850557 ATCACACAAAAGTTGGTCAATCA 57.149 34.783 0.00 0.00 34.12 2.57
773 847 7.698130 GCTATATCACACAAAAGTTGGTCAATC 59.302 37.037 0.00 0.00 34.12 2.67
774 848 7.538575 GCTATATCACACAAAAGTTGGTCAAT 58.461 34.615 0.00 0.00 34.12 2.57
775 849 6.348132 CGCTATATCACACAAAAGTTGGTCAA 60.348 38.462 0.00 0.00 34.12 3.18
776 850 5.121611 CGCTATATCACACAAAAGTTGGTCA 59.878 40.000 0.00 0.00 34.12 4.02
777 851 5.350365 TCGCTATATCACACAAAAGTTGGTC 59.650 40.000 0.00 0.00 34.12 4.02
778 852 5.242434 TCGCTATATCACACAAAAGTTGGT 58.758 37.500 0.00 0.00 34.12 3.67
779 853 5.794687 TCGCTATATCACACAAAAGTTGG 57.205 39.130 0.00 0.00 34.12 3.77
780 854 6.195244 GCAATCGCTATATCACACAAAAGTTG 59.805 38.462 0.00 0.00 34.30 3.16
781 855 6.128035 TGCAATCGCTATATCACACAAAAGTT 60.128 34.615 0.00 0.00 39.64 2.66
782 856 5.353956 TGCAATCGCTATATCACACAAAAGT 59.646 36.000 0.00 0.00 39.64 2.66
783 857 5.809464 TGCAATCGCTATATCACACAAAAG 58.191 37.500 0.00 0.00 39.64 2.27
784 858 5.809719 TGCAATCGCTATATCACACAAAA 57.190 34.783 0.00 0.00 39.64 2.44
785 859 5.989249 GATGCAATCGCTATATCACACAAA 58.011 37.500 0.00 0.00 39.64 2.83
786 860 5.596268 GATGCAATCGCTATATCACACAA 57.404 39.130 0.00 0.00 39.64 3.33
800 874 2.423185 TGGAACAATGGACGATGCAATC 59.577 45.455 0.00 0.00 35.64 2.67
801 875 2.445427 TGGAACAATGGACGATGCAAT 58.555 42.857 0.00 0.00 31.92 3.56
802 876 1.902938 TGGAACAATGGACGATGCAA 58.097 45.000 0.00 0.00 31.92 4.08
803 877 3.641017 TGGAACAATGGACGATGCA 57.359 47.368 0.00 0.00 31.92 3.96
815 889 2.301870 AGCGATGGTCTACTTTGGAACA 59.698 45.455 0.00 0.00 34.75 3.18
816 890 2.973945 AGCGATGGTCTACTTTGGAAC 58.026 47.619 0.00 0.00 0.00 3.62
817 891 3.596214 GAAGCGATGGTCTACTTTGGAA 58.404 45.455 0.00 0.00 0.00 3.53
818 892 2.416836 CGAAGCGATGGTCTACTTTGGA 60.417 50.000 0.00 0.00 0.00 3.53
819 893 1.927174 CGAAGCGATGGTCTACTTTGG 59.073 52.381 0.00 0.00 0.00 3.28
820 894 2.345641 CACGAAGCGATGGTCTACTTTG 59.654 50.000 0.00 0.00 0.00 2.77
821 895 2.230508 TCACGAAGCGATGGTCTACTTT 59.769 45.455 0.00 0.00 0.00 2.66
822 896 1.816835 TCACGAAGCGATGGTCTACTT 59.183 47.619 0.00 0.00 0.00 2.24
823 897 1.132643 GTCACGAAGCGATGGTCTACT 59.867 52.381 0.00 0.00 0.00 2.57
824 898 1.546834 GTCACGAAGCGATGGTCTAC 58.453 55.000 0.00 0.00 0.00 2.59
825 899 0.098200 CGTCACGAAGCGATGGTCTA 59.902 55.000 0.00 0.00 0.00 2.59
826 900 1.154016 CGTCACGAAGCGATGGTCT 60.154 57.895 0.00 0.00 0.00 3.85
827 901 1.403972 GACGTCACGAAGCGATGGTC 61.404 60.000 11.55 0.00 28.45 4.02
828 902 1.443872 GACGTCACGAAGCGATGGT 60.444 57.895 11.55 0.00 28.45 3.55
829 903 0.802222 ATGACGTCACGAAGCGATGG 60.802 55.000 22.71 0.00 28.45 3.51
835 909 2.666508 CCACCTAAATGACGTCACGAAG 59.333 50.000 22.71 16.90 0.00 3.79
843 917 6.090129 CCATAAAAACACCACCTAAATGACG 58.910 40.000 0.00 0.00 0.00 4.35
851 925 8.038351 GCAAATATAACCATAAAAACACCACCT 58.962 33.333 0.00 0.00 0.00 4.00
862 936 8.976353 ACTCCAACATTGCAAATATAACCATAA 58.024 29.630 1.71 0.00 0.00 1.90
903 981 1.530771 CTGGAGAGGGCATGAAGGG 59.469 63.158 0.00 0.00 0.00 3.95
907 985 1.811778 AATAGCTGGAGAGGGCATGA 58.188 50.000 0.00 0.00 0.00 3.07
936 1014 9.498176 ACAGTTGAATTAATTTTAGTAGACGGT 57.502 29.630 1.43 0.00 0.00 4.83
981 1059 3.265791 CATCTCTGCTACTGGAACAACC 58.734 50.000 0.00 0.00 38.70 3.77
1113 1191 4.326504 AAATTCTGTGGCCAAGTTCTTG 57.673 40.909 7.24 5.66 0.00 3.02
1131 1209 9.566432 AAAGTCTCTCTCAATGTTTCTGTAAAT 57.434 29.630 0.00 0.00 0.00 1.40
1263 1341 3.807622 CGCCTTTGAACTTGTTGAGACTA 59.192 43.478 0.00 0.00 0.00 2.59
1387 1473 7.228314 TGTCCTATTAGAGTCCAATATTCGG 57.772 40.000 0.00 0.00 0.00 4.30
1388 1474 9.144747 CAATGTCCTATTAGAGTCCAATATTCG 57.855 37.037 0.00 0.00 0.00 3.34
1393 1479 5.370880 AGCCAATGTCCTATTAGAGTCCAAT 59.629 40.000 0.00 0.00 0.00 3.16
1464 1550 2.289320 CCACAACAGAGTCAAGAGGAGG 60.289 54.545 0.00 0.00 0.00 4.30
1496 1582 8.885494 ATAGCAAAACAAGCTTAAATGTTTCA 57.115 26.923 13.22 2.63 46.09 2.69
1618 1704 1.029681 AAAGAGAAACCACGGCAACC 58.970 50.000 0.00 0.00 0.00 3.77
1729 1815 2.093288 TCCTAAGGCTGCTTGAGTGATG 60.093 50.000 0.00 0.00 0.00 3.07
1789 1878 1.023502 TCCAACACGTCGACACTACA 58.976 50.000 17.16 0.00 0.00 2.74
1790 1879 1.002033 AGTCCAACACGTCGACACTAC 60.002 52.381 17.16 3.47 0.00 2.73
1793 1882 2.049228 CTTAGTCCAACACGTCGACAC 58.951 52.381 17.16 4.02 0.00 3.67
1822 1911 6.616577 AGGAACCCTAACCTGACAAAATAAA 58.383 36.000 0.00 0.00 34.99 1.40
1825 1914 4.741928 AGGAACCCTAACCTGACAAAAT 57.258 40.909 0.00 0.00 34.99 1.82
1830 1919 5.898397 ACTCTATAAGGAACCCTAACCTGAC 59.102 44.000 0.00 0.00 36.56 3.51
1937 2027 6.440436 GGTTTTCCTTGTAAAGTTTGCGATA 58.560 36.000 0.00 0.00 44.25 2.92
2047 2138 5.333875 CGCATGATGTTCTGACCAAGATATG 60.334 44.000 0.00 0.00 33.93 1.78
2131 2222 8.823818 ACGGCATGACATACTTTTACTAATAAC 58.176 33.333 0.00 0.00 0.00 1.89
2138 2229 4.939509 ACACGGCATGACATACTTTTAC 57.060 40.909 0.00 0.00 0.00 2.01
2141 2232 3.407698 TCAACACGGCATGACATACTTT 58.592 40.909 0.00 0.00 0.00 2.66
2147 2238 2.093235 TCCATATCAACACGGCATGACA 60.093 45.455 0.00 0.00 0.00 3.58
2148 2239 2.545526 CTCCATATCAACACGGCATGAC 59.454 50.000 0.00 0.00 0.00 3.06
2156 2247 8.612619 CCACATAAGTTAACTCCATATCAACAC 58.387 37.037 8.95 0.00 0.00 3.32
2160 2251 6.617784 TCCCCACATAAGTTAACTCCATATCA 59.382 38.462 8.95 0.00 0.00 2.15
2194 2286 6.439675 AAACAATTCAGCACTTGCAAAAAT 57.560 29.167 0.00 0.00 45.16 1.82
2258 2350 2.178984 AGGGAAACAAATTCACCTCCCA 59.821 45.455 14.70 0.00 42.85 4.37
2261 2353 5.791336 AAAGAGGGAAACAAATTCACCTC 57.209 39.130 13.40 13.40 45.93 3.85
2287 2379 2.587194 CGGCGCAGGAAGATCCAG 60.587 66.667 10.83 0.00 39.61 3.86
2298 2390 3.084646 TAATCCCTTCCCGGCGCA 61.085 61.111 10.83 0.00 0.00 6.09
2304 2396 2.498644 GCCTATGCTAATCCCTTCCC 57.501 55.000 0.00 0.00 33.53 3.97
2354 2446 5.181748 CCATCTCCTTGTCAGTTCTTTAGG 58.818 45.833 0.00 0.00 0.00 2.69
2361 2455 3.864789 ACAACCATCTCCTTGTCAGTT 57.135 42.857 0.00 0.00 0.00 3.16
2377 2471 3.065371 GCCAGTTCCACTGCATATACAAC 59.935 47.826 0.00 0.00 44.63 3.32
2530 2630 6.648879 TTTCTTCTTTCCCTGTGTAAATGG 57.351 37.500 0.00 0.00 0.00 3.16
2675 2775 2.030540 CCACACAACTGAGCCTGAATTG 60.031 50.000 0.00 0.00 0.00 2.32
2711 2811 7.986320 AGTGACAACAAATTTTTCATCCATGAA 59.014 29.630 0.00 0.00 44.42 2.57
2725 2825 4.279169 CCTGATGACCAAGTGACAACAAAT 59.721 41.667 0.00 0.00 0.00 2.32
2791 2891 3.337694 ACGGACCGGTGAAATAAATCA 57.662 42.857 14.63 0.00 0.00 2.57
2810 2910 5.854431 TCTTGAAACCTTTTGCAACAAAC 57.146 34.783 0.00 0.00 0.00 2.93
2882 2982 7.867403 ACATGACAGGAAAAACAAATATGTGTC 59.133 33.333 0.00 0.00 40.46 3.67
3164 3265 5.446741 CGAACGTGAGAAAGAACCTGAAAAA 60.447 40.000 0.00 0.00 0.00 1.94
3320 3421 1.353103 GCCGATCACCGCAGAAATG 59.647 57.895 0.00 0.00 36.84 2.32
3368 3469 6.098124 TGAAGTCCAATTTGTCAACTTTCCAT 59.902 34.615 9.20 0.00 30.68 3.41
3494 3595 9.513906 TCTCCACAAAAAGACATGAACATATTA 57.486 29.630 0.00 0.00 0.00 0.98
3495 3596 8.299570 GTCTCCACAAAAAGACATGAACATATT 58.700 33.333 0.00 0.00 41.26 1.28
3497 3598 6.770303 TGTCTCCACAAAAAGACATGAACATA 59.230 34.615 0.00 0.00 45.18 2.29
3498 3599 5.593909 TGTCTCCACAAAAAGACATGAACAT 59.406 36.000 0.00 0.00 45.18 2.71
3499 3600 4.946772 TGTCTCCACAAAAAGACATGAACA 59.053 37.500 0.00 0.00 45.18 3.18
3500 3601 5.499139 TGTCTCCACAAAAAGACATGAAC 57.501 39.130 0.00 0.00 45.18 3.18
3807 3916 7.828717 TGAGGCTGAAATTACTGAATTCATGTA 59.171 33.333 8.96 10.52 34.01 2.29
3848 3957 1.005097 AGAATTCTGCCATGGAGCACA 59.995 47.619 18.40 2.27 38.00 4.57
3893 4002 3.682718 GCAATCCCAGTGCTTTAGCTCTA 60.683 47.826 6.04 0.00 42.25 2.43
3935 4044 1.282248 ACTCACGCGACATTTCCACG 61.282 55.000 15.93 0.00 0.00 4.94
3999 4111 4.036027 GGACTGCATGAGTACAATGATTGG 59.964 45.833 10.27 0.00 35.25 3.16
4013 4125 1.733389 GCATTTTCACCGGACTGCATG 60.733 52.381 9.46 5.87 0.00 4.06
4064 4177 1.275010 TCTTCAAGAGCGTGTATGCCA 59.725 47.619 0.00 0.00 34.65 4.92
4073 4186 8.081633 AGATTCTTGTATAGATCTTCAAGAGCG 58.918 37.037 23.51 9.62 44.13 5.03
4151 4267 6.531594 GCCCAGCAAAACAAGATTATAGTTTC 59.468 38.462 0.00 0.00 34.64 2.78
4169 4286 0.625316 ACATTATCAGTGGCCCAGCA 59.375 50.000 0.00 0.00 0.00 4.41
4170 4287 1.406539 CAACATTATCAGTGGCCCAGC 59.593 52.381 0.00 0.00 0.00 4.85
4177 4294 9.462174 ACAACAATACAAACAACATTATCAGTG 57.538 29.630 0.00 0.00 0.00 3.66
4178 4295 9.462174 CACAACAATACAAACAACATTATCAGT 57.538 29.630 0.00 0.00 0.00 3.41
4194 4311 5.469479 AGCTGCCAAAATACACAACAATAC 58.531 37.500 0.00 0.00 0.00 1.89
4195 4312 5.242615 TGAGCTGCCAAAATACACAACAATA 59.757 36.000 0.00 0.00 0.00 1.90
4196 4313 4.039004 TGAGCTGCCAAAATACACAACAAT 59.961 37.500 0.00 0.00 0.00 2.71
4197 4314 3.382865 TGAGCTGCCAAAATACACAACAA 59.617 39.130 0.00 0.00 0.00 2.83
4198 4315 2.954989 TGAGCTGCCAAAATACACAACA 59.045 40.909 0.00 0.00 0.00 3.33
4199 4316 3.641437 TGAGCTGCCAAAATACACAAC 57.359 42.857 0.00 0.00 0.00 3.32
4206 4323 2.163010 CGACAGAATGAGCTGCCAAAAT 59.837 45.455 0.00 0.00 39.69 1.82
4368 4485 0.322456 CACCAGCCATTCCTCCGAAA 60.322 55.000 0.00 0.00 0.00 3.46
4388 4505 0.806868 CAACACTAGCACCATGGCAG 59.193 55.000 13.04 5.97 35.83 4.85
4409 4526 4.042311 TCACAGGGAGCACCAAAACTATTA 59.958 41.667 1.58 0.00 43.89 0.98
5275 11270 2.728690 TTGGAATGAGCATTGCACAC 57.271 45.000 15.51 0.00 46.36 3.82


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

AutoCloner maintained by Alex Coulton.