Multiple sequence alignment - TraesCS3A01G349000

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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 TraesCS3A01G349000 chr3A 100.000 4365 0 0 1 4365 597848337 597852701 0.000000e+00 8061.0
1 TraesCS3A01G349000 chr3A 91.555 746 38 8 2 723 597835811 597836555 0.000000e+00 1005.0
2 TraesCS3A01G349000 chr3A 92.453 212 11 4 751 960 726233190 726233398 9.180000e-77 298.0
3 TraesCS3A01G349000 chr3A 91.905 210 15 2 751 960 712050964 712050757 4.270000e-75 292.0
4 TraesCS3A01G349000 chr3A 91.204 216 14 4 749 961 16250136 16249923 5.520000e-74 289.0
5 TraesCS3A01G349000 chr3A 91.469 211 13 3 750 957 697524364 697524572 7.140000e-73 285.0
6 TraesCS3A01G349000 chr3A 90.047 211 17 3 751 959 76343839 76343631 2.000000e-68 270.0
7 TraesCS3A01G349000 chr3A 88.800 125 8 5 3669 3791 64733805 64733925 9.780000e-32 148.0
8 TraesCS3A01G349000 chr3B 93.064 1586 75 17 961 2538 598908461 598910019 0.000000e+00 2287.0
9 TraesCS3A01G349000 chr3B 92.295 623 30 11 2577 3184 598910012 598910631 0.000000e+00 869.0
10 TraesCS3A01G349000 chr3B 89.310 580 48 8 3795 4365 598972564 598973138 0.000000e+00 715.0
11 TraesCS3A01G349000 chr3B 85.166 391 41 11 3176 3562 598913231 598913608 6.850000e-103 385.0
12 TraesCS3A01G349000 chr3B 86.769 325 36 6 3168 3488 598972301 598972622 5.370000e-94 355.0
13 TraesCS3A01G349000 chr3B 87.391 230 24 3 386 611 598906716 598906944 4.330000e-65 259.0
14 TraesCS3A01G349000 chr3B 86.792 212 26 2 2958 3168 598969934 598970144 7.300000e-58 235.0
15 TraesCS3A01G349000 chr3B 90.000 140 7 4 3669 3807 598913587 598913720 1.610000e-39 174.0
16 TraesCS3A01G349000 chr3B 89.516 124 8 4 3669 3791 83832021 83832140 7.560000e-33 152.0
17 TraesCS3A01G349000 chr3B 90.361 83 7 1 3563 3645 598972540 598972621 1.660000e-19 108.0
18 TraesCS3A01G349000 chr3D 94.033 1324 63 8 961 2273 455593965 455595283 0.000000e+00 1993.0
19 TraesCS3A01G349000 chr3D 92.280 842 32 10 2998 3807 455595960 455596800 0.000000e+00 1164.0
20 TraesCS3A01G349000 chr3D 93.210 648 33 8 2374 3013 455595302 455595946 0.000000e+00 942.0
21 TraesCS3A01G349000 chr3D 95.238 567 18 6 3804 4365 455596954 455597516 0.000000e+00 889.0
22 TraesCS3A01G349000 chr3D 90.123 648 39 8 2 625 455591481 455592127 0.000000e+00 819.0
23 TraesCS3A01G349000 chr3D 88.095 126 9 6 3669 3792 53385930 53386051 1.270000e-30 145.0
24 TraesCS3A01G349000 chr3D 92.553 94 7 0 3563 3656 455596374 455596467 7.610000e-28 135.0
25 TraesCS3A01G349000 chr1A 91.469 211 13 5 751 958 376995047 376995255 7.140000e-73 285.0
26 TraesCS3A01G349000 chr1A 90.141 213 17 4 751 961 352839718 352839928 1.550000e-69 274.0
27 TraesCS3A01G349000 chr1A 90.094 212 16 4 751 960 454420471 454420263 2.000000e-68 270.0
28 TraesCS3A01G349000 chr5A 89.671 213 18 4 748 957 27547997 27548208 7.200000e-68 268.0
29 TraesCS3A01G349000 chr2D 88.976 127 7 5 3669 3792 493001267 493001389 2.720000e-32 150.0
30 TraesCS3A01G349000 chr2D 88.189 127 8 5 3669 3792 492997624 492997746 1.270000e-30 145.0
31 TraesCS3A01G349000 chr2B 87.805 123 11 3 3669 3791 579570571 579570689 1.640000e-29 141.0
32 TraesCS3A01G349000 chr2B 85.271 129 14 4 3669 3796 579570895 579571019 1.270000e-25 128.0
33 TraesCS3A01G349000 chr6B 100.000 29 0 0 3216 3244 656486025 656485997 2.000000e-03 54.7


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 TraesCS3A01G349000 chr3A 597848337 597852701 4364 False 8061.000000 8061 100.000000 1 4365 1 chr3A.!!$F3 4364
1 TraesCS3A01G349000 chr3A 597835811 597836555 744 False 1005.000000 1005 91.555000 2 723 1 chr3A.!!$F2 721
2 TraesCS3A01G349000 chr3B 598906716 598913720 7004 False 794.800000 2287 89.583200 386 3807 5 chr3B.!!$F2 3421
3 TraesCS3A01G349000 chr3B 598969934 598973138 3204 False 353.250000 715 88.308000 2958 4365 4 chr3B.!!$F3 1407
4 TraesCS3A01G349000 chr3D 455591481 455597516 6035 False 990.333333 1993 92.906167 2 4365 6 chr3D.!!$F2 4363

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
839 3852 0.038166 TCACAAAGCATCTCCACCCC 59.962 55.0 0.0 0.0 0.00 4.95 F
842 3855 0.038744 CAAAGCATCTCCACCCCACT 59.961 55.0 0.0 0.0 0.00 4.00 F
2352 5375 0.112995 AGGCTGGACATCTTTTGCCA 59.887 50.0 0.0 0.0 42.46 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 5303 0.450583 GCCTCATGTGTGTGCAGATG 59.549 55.0 0.00 0.0 44.77 2.90 R
2641 5666 0.681564 ACCAGCTCTCCAGTACTCCG 60.682 60.0 0.00 0.0 0.00 4.63 R
4249 12290 0.952280 GGGCTATGACGACATCTCGA 59.048 55.0 3.03 0.0 43.06 4.04 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
105 106 3.047796 GAGACAACGTACGAGCTTTCAA 58.952 45.455 24.41 0.00 0.00 2.69
480 498 8.980481 TTACTCCTTTTTCTTTTGAGATGTCT 57.020 30.769 0.00 0.00 0.00 3.41
599 625 5.732331 AAAATCATGTATTCCCTCCTCCA 57.268 39.130 0.00 0.00 0.00 3.86
703 3716 7.500892 TCAAAGAAGGTAGCAGTAAATTCAACA 59.499 33.333 0.00 0.00 0.00 3.33
719 3732 0.399949 AACAGTGAGAGGGGACACCA 60.400 55.000 0.00 0.00 43.89 4.17
720 3733 1.122019 ACAGTGAGAGGGGACACCAC 61.122 60.000 0.00 0.00 43.89 4.16
721 3734 1.536662 AGTGAGAGGGGACACCACC 60.537 63.158 0.00 0.00 43.89 4.61
722 3735 1.841556 GTGAGAGGGGACACCACCA 60.842 63.158 0.00 0.00 43.89 4.17
725 3738 2.113243 GAGAGGGGACACCACCACAC 62.113 65.000 0.00 0.00 43.89 3.82
726 3739 3.175710 AGGGGACACCACCACACC 61.176 66.667 0.00 0.00 43.89 4.16
751 3764 1.010419 GCAGCAGTGGCAAAATTCGG 61.010 55.000 0.00 0.00 44.61 4.30
752 3765 0.597568 CAGCAGTGGCAAAATTCGGA 59.402 50.000 0.00 0.00 44.61 4.55
753 3766 1.000385 CAGCAGTGGCAAAATTCGGAA 60.000 47.619 0.00 0.00 44.61 4.30
754 3767 1.686052 AGCAGTGGCAAAATTCGGAAA 59.314 42.857 0.00 0.00 44.61 3.13
755 3768 2.102252 AGCAGTGGCAAAATTCGGAAAA 59.898 40.909 0.00 0.00 44.61 2.29
756 3769 2.476241 GCAGTGGCAAAATTCGGAAAAG 59.524 45.455 0.00 0.00 40.72 2.27
757 3770 3.798548 GCAGTGGCAAAATTCGGAAAAGA 60.799 43.478 0.00 0.00 40.72 2.52
758 3771 4.367450 CAGTGGCAAAATTCGGAAAAGAA 58.633 39.130 0.00 0.00 34.31 2.52
759 3772 4.990426 CAGTGGCAAAATTCGGAAAAGAAT 59.010 37.500 0.00 0.00 42.13 2.40
760 3773 7.940636 GCAGTGGCAAAATTCGGAAAAGAATT 61.941 38.462 0.00 0.00 44.42 2.17
761 3774 5.696270 AGTGGCAAAATTCGGAAAAGAATTC 59.304 36.000 0.00 0.00 46.55 2.17
762 3775 5.696270 GTGGCAAAATTCGGAAAAGAATTCT 59.304 36.000 0.88 0.88 46.55 2.40
763 3776 6.866248 GTGGCAAAATTCGGAAAAGAATTCTA 59.134 34.615 8.75 0.00 46.55 2.10
764 3777 7.545615 GTGGCAAAATTCGGAAAAGAATTCTAT 59.454 33.333 8.75 0.41 46.55 1.98
765 3778 7.545265 TGGCAAAATTCGGAAAAGAATTCTATG 59.455 33.333 8.75 6.84 46.55 2.23
766 3779 7.759433 GGCAAAATTCGGAAAAGAATTCTATGA 59.241 33.333 8.75 0.00 46.55 2.15
767 3780 8.801913 GCAAAATTCGGAAAAGAATTCTATGAG 58.198 33.333 8.75 0.26 46.55 2.90
770 3783 7.793927 ATTCGGAAAAGAATTCTATGAGACC 57.206 36.000 8.75 6.24 37.56 3.85
771 3784 6.294361 TCGGAAAAGAATTCTATGAGACCA 57.706 37.500 8.75 0.00 0.00 4.02
772 3785 6.341316 TCGGAAAAGAATTCTATGAGACCAG 58.659 40.000 8.75 4.64 0.00 4.00
773 3786 5.525378 CGGAAAAGAATTCTATGAGACCAGG 59.475 44.000 8.75 0.00 0.00 4.45
774 3787 6.418946 GGAAAAGAATTCTATGAGACCAGGT 58.581 40.000 8.75 0.00 0.00 4.00
775 3788 6.540551 GGAAAAGAATTCTATGAGACCAGGTC 59.459 42.308 12.25 12.25 0.00 3.85
776 3789 6.882768 AAAGAATTCTATGAGACCAGGTCT 57.117 37.500 23.18 23.18 46.42 3.85
798 3811 4.969484 TCACATGAGATCCATTCTGATGG 58.031 43.478 0.00 0.00 46.76 3.51
799 3812 4.411212 TCACATGAGATCCATTCTGATGGT 59.589 41.667 0.00 0.00 46.76 3.55
800 3813 5.104235 TCACATGAGATCCATTCTGATGGTT 60.104 40.000 0.00 0.00 46.76 3.67
801 3814 5.008712 CACATGAGATCCATTCTGATGGTTG 59.991 44.000 0.00 0.00 46.76 3.77
802 3815 5.104235 ACATGAGATCCATTCTGATGGTTGA 60.104 40.000 0.00 0.00 46.76 3.18
803 3816 7.134303 ACATGAGATCCATTCTGATGGTTGAC 61.134 42.308 0.00 0.00 46.76 3.18
804 3817 9.433836 ACATGAGATCCATTCTGATGGTTGACA 62.434 40.741 0.00 3.88 46.76 3.58
807 3820 2.426522 CCATTCTGATGGTTGACACGT 58.573 47.619 0.00 0.00 46.48 4.49
808 3821 2.160219 CCATTCTGATGGTTGACACGTG 59.840 50.000 15.48 15.48 46.48 4.49
809 3822 2.900716 TTCTGATGGTTGACACGTGA 57.099 45.000 25.01 0.00 0.00 4.35
810 3823 2.148916 TCTGATGGTTGACACGTGAC 57.851 50.000 25.01 17.68 0.00 3.67
811 3824 1.410882 TCTGATGGTTGACACGTGACA 59.589 47.619 25.01 20.51 0.00 3.58
812 3825 2.037121 TCTGATGGTTGACACGTGACAT 59.963 45.455 25.01 16.68 0.00 3.06
813 3826 2.807967 CTGATGGTTGACACGTGACATT 59.192 45.455 25.01 7.70 0.00 2.71
814 3827 2.805671 TGATGGTTGACACGTGACATTC 59.194 45.455 25.01 17.02 0.00 2.67
815 3828 2.317530 TGGTTGACACGTGACATTCA 57.682 45.000 25.01 18.93 0.00 2.57
816 3829 1.937223 TGGTTGACACGTGACATTCAC 59.063 47.619 25.01 16.72 43.65 3.18
828 3841 5.565723 GTGACATTCACAAATCACAAAGC 57.434 39.130 1.34 0.00 46.22 3.51
829 3842 5.042593 GTGACATTCACAAATCACAAAGCA 58.957 37.500 1.34 0.00 46.22 3.91
830 3843 5.693104 GTGACATTCACAAATCACAAAGCAT 59.307 36.000 1.34 0.00 46.22 3.79
831 3844 5.921976 TGACATTCACAAATCACAAAGCATC 59.078 36.000 0.00 0.00 0.00 3.91
832 3845 6.092955 ACATTCACAAATCACAAAGCATCT 57.907 33.333 0.00 0.00 0.00 2.90
833 3846 6.154445 ACATTCACAAATCACAAAGCATCTC 58.846 36.000 0.00 0.00 0.00 2.75
834 3847 4.771590 TCACAAATCACAAAGCATCTCC 57.228 40.909 0.00 0.00 0.00 3.71
835 3848 4.143543 TCACAAATCACAAAGCATCTCCA 58.856 39.130 0.00 0.00 0.00 3.86
836 3849 4.022935 TCACAAATCACAAAGCATCTCCAC 60.023 41.667 0.00 0.00 0.00 4.02
837 3850 3.256631 ACAAATCACAAAGCATCTCCACC 59.743 43.478 0.00 0.00 0.00 4.61
838 3851 2.134789 ATCACAAAGCATCTCCACCC 57.865 50.000 0.00 0.00 0.00 4.61
839 3852 0.038166 TCACAAAGCATCTCCACCCC 59.962 55.000 0.00 0.00 0.00 4.95
840 3853 0.251297 CACAAAGCATCTCCACCCCA 60.251 55.000 0.00 0.00 0.00 4.96
841 3854 0.251341 ACAAAGCATCTCCACCCCAC 60.251 55.000 0.00 0.00 0.00 4.61
842 3855 0.038744 CAAAGCATCTCCACCCCACT 59.961 55.000 0.00 0.00 0.00 4.00
843 3856 0.779997 AAAGCATCTCCACCCCACTT 59.220 50.000 0.00 0.00 0.00 3.16
844 3857 1.668826 AAGCATCTCCACCCCACTTA 58.331 50.000 0.00 0.00 0.00 2.24
845 3858 1.668826 AGCATCTCCACCCCACTTAA 58.331 50.000 0.00 0.00 0.00 1.85
846 3859 1.992557 AGCATCTCCACCCCACTTAAA 59.007 47.619 0.00 0.00 0.00 1.52
847 3860 2.378547 AGCATCTCCACCCCACTTAAAA 59.621 45.455 0.00 0.00 0.00 1.52
848 3861 3.011708 AGCATCTCCACCCCACTTAAAAT 59.988 43.478 0.00 0.00 0.00 1.82
849 3862 3.381590 GCATCTCCACCCCACTTAAAATC 59.618 47.826 0.00 0.00 0.00 2.17
850 3863 4.599041 CATCTCCACCCCACTTAAAATCA 58.401 43.478 0.00 0.00 0.00 2.57
851 3864 4.301072 TCTCCACCCCACTTAAAATCAG 57.699 45.455 0.00 0.00 0.00 2.90
852 3865 3.913799 TCTCCACCCCACTTAAAATCAGA 59.086 43.478 0.00 0.00 0.00 3.27
853 3866 4.019321 TCTCCACCCCACTTAAAATCAGAG 60.019 45.833 0.00 0.00 0.00 3.35
854 3867 3.010138 TCCACCCCACTTAAAATCAGAGG 59.990 47.826 0.00 0.00 0.00 3.69
855 3868 3.356290 CACCCCACTTAAAATCAGAGGG 58.644 50.000 0.00 0.00 40.86 4.30
878 3891 6.901300 GGGGGAGAGAGATTAAATACTTTGT 58.099 40.000 0.00 0.00 0.00 2.83
879 3892 6.768381 GGGGGAGAGAGATTAAATACTTTGTG 59.232 42.308 0.00 0.00 0.00 3.33
880 3893 7.365652 GGGGGAGAGAGATTAAATACTTTGTGA 60.366 40.741 0.00 0.00 0.00 3.58
881 3894 8.214364 GGGGAGAGAGATTAAATACTTTGTGAT 58.786 37.037 0.00 0.00 0.00 3.06
882 3895 9.620259 GGGAGAGAGATTAAATACTTTGTGATT 57.380 33.333 0.00 0.00 0.00 2.57
906 3919 5.165911 GTGAATGTCACATGTCATCCATC 57.834 43.478 0.00 0.00 46.22 3.51
907 3920 4.637091 GTGAATGTCACATGTCATCCATCA 59.363 41.667 0.00 0.00 46.22 3.07
908 3921 4.879545 TGAATGTCACATGTCATCCATCAG 59.120 41.667 0.00 0.00 0.00 2.90
909 3922 3.271055 TGTCACATGTCATCCATCAGG 57.729 47.619 0.00 0.00 0.00 3.86
919 3932 3.924576 TCCATCAGGACGGATCTCA 57.075 52.632 0.00 0.00 39.61 3.27
920 3933 1.403814 TCCATCAGGACGGATCTCAC 58.596 55.000 0.00 0.00 39.61 3.51
921 3934 0.390860 CCATCAGGACGGATCTCACC 59.609 60.000 0.00 0.00 36.89 4.02
922 3935 1.407936 CATCAGGACGGATCTCACCT 58.592 55.000 0.00 0.00 0.00 4.00
924 3937 1.142748 CAGGACGGATCTCACCTGC 59.857 63.158 15.37 0.00 42.30 4.85
925 3938 1.000993 AGGACGGATCTCACCTGCT 59.999 57.895 0.00 0.00 0.00 4.24
926 3939 0.259065 AGGACGGATCTCACCTGCTA 59.741 55.000 0.00 0.00 0.00 3.49
927 3940 1.112113 GGACGGATCTCACCTGCTAA 58.888 55.000 0.00 0.00 0.00 3.09
928 3941 1.689273 GGACGGATCTCACCTGCTAAT 59.311 52.381 0.00 0.00 0.00 1.73
929 3942 2.288518 GGACGGATCTCACCTGCTAATC 60.289 54.545 0.00 0.00 0.00 1.75
930 3943 2.362397 GACGGATCTCACCTGCTAATCA 59.638 50.000 0.00 0.00 0.00 2.57
931 3944 2.968574 ACGGATCTCACCTGCTAATCAT 59.031 45.455 0.00 0.00 0.00 2.45
932 3945 3.244009 ACGGATCTCACCTGCTAATCATG 60.244 47.826 0.00 0.00 0.00 3.07
933 3946 3.006217 CGGATCTCACCTGCTAATCATGA 59.994 47.826 0.00 0.00 0.00 3.07
934 3947 4.567971 GGATCTCACCTGCTAATCATGAG 58.432 47.826 0.09 0.00 38.51 2.90
936 3949 4.662468 TCTCACCTGCTAATCATGAGAC 57.338 45.455 0.09 0.00 40.59 3.36
937 3950 3.386078 TCTCACCTGCTAATCATGAGACC 59.614 47.826 0.09 0.00 40.59 3.85
938 3951 3.378512 TCACCTGCTAATCATGAGACCT 58.621 45.455 0.09 0.00 0.00 3.85
939 3952 3.133542 TCACCTGCTAATCATGAGACCTG 59.866 47.826 0.09 0.00 0.00 4.00
940 3953 2.437281 ACCTGCTAATCATGAGACCTGG 59.563 50.000 0.09 5.81 0.00 4.45
941 3954 2.437281 CCTGCTAATCATGAGACCTGGT 59.563 50.000 0.00 0.00 0.00 4.00
942 3955 3.494048 CCTGCTAATCATGAGACCTGGTC 60.494 52.174 19.20 19.20 0.00 4.02
943 3956 3.378512 TGCTAATCATGAGACCTGGTCT 58.621 45.455 28.70 28.70 46.42 3.85
944 3957 3.776969 TGCTAATCATGAGACCTGGTCTT 59.223 43.478 28.90 15.21 43.53 3.01
945 3958 4.962362 TGCTAATCATGAGACCTGGTCTTA 59.038 41.667 28.90 25.26 43.53 2.10
946 3959 5.604231 TGCTAATCATGAGACCTGGTCTTAT 59.396 40.000 28.90 26.29 43.53 1.73
947 3960 6.782494 TGCTAATCATGAGACCTGGTCTTATA 59.218 38.462 27.59 18.82 43.53 0.98
948 3961 7.455953 TGCTAATCATGAGACCTGGTCTTATAT 59.544 37.037 27.59 19.95 43.53 0.86
949 3962 8.972127 GCTAATCATGAGACCTGGTCTTATATA 58.028 37.037 27.59 20.44 43.53 0.86
1038 4051 0.966920 TTTCTTCTCCGTCGGCTTCT 59.033 50.000 6.34 0.00 0.00 2.85
1050 4063 2.815647 GCTTCTGCCGTCTTCCCG 60.816 66.667 0.00 0.00 0.00 5.14
1103 4116 2.607134 TTAAACCCTCGGCCCCGA 60.607 61.111 9.31 9.31 46.87 5.14
1283 4299 2.176273 CAGAATCCAGAAGGCGCCG 61.176 63.158 23.20 6.32 33.74 6.46
1439 4455 0.962356 CCAAGGCAAAGGCGACATCT 60.962 55.000 0.00 0.00 42.47 2.90
1495 4511 2.446802 GAGCCCGGGGAGGAAGAT 60.447 66.667 25.28 0.00 45.00 2.40
1780 4796 3.066900 CGTCCATTCCTAGTGTCTACTGG 59.933 52.174 0.00 0.00 37.78 4.00
1922 4939 5.115480 GCCTCAGAGAAATTAAGTCTCCAG 58.885 45.833 12.97 10.10 42.17 3.86
1986 5006 0.804989 CGGCTGACAATTGGAGGTTC 59.195 55.000 10.83 0.00 0.00 3.62
2019 5039 8.743636 AATTGGAGAAGGCTACTAAGGTATAT 57.256 34.615 0.00 0.00 0.00 0.86
2075 5095 7.254898 GGTGTGTGAATCATATCATGGTTACTG 60.255 40.741 0.00 0.00 32.79 2.74
2077 5097 7.828717 TGTGTGAATCATATCATGGTTACTGTT 59.171 33.333 0.00 0.00 32.79 3.16
2087 5107 6.961359 TCATGGTTACTGTTCGATTAACTG 57.039 37.500 0.00 0.00 41.45 3.16
2089 5109 6.588756 TCATGGTTACTGTTCGATTAACTGTC 59.411 38.462 2.04 0.00 44.27 3.51
2093 5115 6.588756 GGTTACTGTTCGATTAACTGTCATGA 59.411 38.462 0.00 0.00 44.27 3.07
2114 5136 8.522003 TCATGATTGCTCTGCTAATTTAACAAA 58.478 29.630 0.00 0.00 0.00 2.83
2160 5182 6.162079 TCAGACTGTGAAGATTGATCTGAAC 58.838 40.000 1.59 0.00 38.45 3.18
2196 5218 2.480759 GGCATATGCACTCCAAGCAAAG 60.481 50.000 28.07 0.00 46.27 2.77
2280 5303 8.634475 AGTCAAATTTGTCTAAGAAAAACTGC 57.366 30.769 17.47 0.00 0.00 4.40
2299 5322 0.450583 CATCTGCACACACATGAGGC 59.549 55.000 0.00 0.00 0.00 4.70
2310 5333 4.022068 ACACACATGAGGCTTATTGTTTGG 60.022 41.667 0.00 4.16 0.00 3.28
2313 5336 4.403432 CACATGAGGCTTATTGTTTGGGAT 59.597 41.667 0.00 0.00 0.00 3.85
2330 5353 4.415596 TGGGATGCTAAAGGTGACAATTT 58.584 39.130 0.00 0.00 0.00 1.82
2336 5359 4.217550 TGCTAAAGGTGACAATTTGTAGGC 59.782 41.667 1.15 0.00 0.00 3.93
2337 5360 4.459337 GCTAAAGGTGACAATTTGTAGGCT 59.541 41.667 1.15 0.00 0.00 4.58
2339 5362 2.795329 AGGTGACAATTTGTAGGCTGG 58.205 47.619 1.15 0.00 0.00 4.85
2348 5371 5.539955 ACAATTTGTAGGCTGGACATCTTTT 59.460 36.000 0.00 0.00 0.00 2.27
2349 5372 5.649782 ATTTGTAGGCTGGACATCTTTTG 57.350 39.130 0.00 0.00 0.00 2.44
2350 5373 2.436417 TGTAGGCTGGACATCTTTTGC 58.564 47.619 0.00 0.00 0.00 3.68
2351 5374 1.745653 GTAGGCTGGACATCTTTTGCC 59.254 52.381 0.00 0.00 40.54 4.52
2352 5375 0.112995 AGGCTGGACATCTTTTGCCA 59.887 50.000 0.00 0.00 42.46 4.92
2353 5376 0.529378 GGCTGGACATCTTTTGCCAG 59.471 55.000 0.00 0.00 45.16 4.85
2354 5377 1.251251 GCTGGACATCTTTTGCCAGT 58.749 50.000 0.00 0.00 44.66 4.00
2355 5378 1.615392 GCTGGACATCTTTTGCCAGTT 59.385 47.619 0.00 0.00 44.66 3.16
2356 5379 2.352127 GCTGGACATCTTTTGCCAGTTC 60.352 50.000 0.00 0.00 44.66 3.01
2357 5380 3.152341 CTGGACATCTTTTGCCAGTTCT 58.848 45.455 0.00 0.00 41.18 3.01
2358 5381 3.565307 TGGACATCTTTTGCCAGTTCTT 58.435 40.909 0.00 0.00 30.91 2.52
2359 5382 3.960102 TGGACATCTTTTGCCAGTTCTTT 59.040 39.130 0.00 0.00 30.91 2.52
2360 5383 4.037923 TGGACATCTTTTGCCAGTTCTTTC 59.962 41.667 0.00 0.00 30.91 2.62
2361 5384 4.279420 GGACATCTTTTGCCAGTTCTTTCT 59.721 41.667 0.00 0.00 0.00 2.52
2362 5385 5.221322 GGACATCTTTTGCCAGTTCTTTCTT 60.221 40.000 0.00 0.00 0.00 2.52
2363 5386 6.016276 GGACATCTTTTGCCAGTTCTTTCTTA 60.016 38.462 0.00 0.00 0.00 2.10
2364 5387 6.974965 ACATCTTTTGCCAGTTCTTTCTTAG 58.025 36.000 0.00 0.00 0.00 2.18
2365 5388 6.015940 ACATCTTTTGCCAGTTCTTTCTTAGG 60.016 38.462 0.00 0.00 0.00 2.69
2366 5389 4.827284 TCTTTTGCCAGTTCTTTCTTAGGG 59.173 41.667 0.00 0.00 0.00 3.53
2367 5390 2.879103 TGCCAGTTCTTTCTTAGGGG 57.121 50.000 0.00 0.00 0.00 4.79
2368 5391 2.062636 TGCCAGTTCTTTCTTAGGGGT 58.937 47.619 0.00 0.00 0.00 4.95
2369 5392 2.224769 TGCCAGTTCTTTCTTAGGGGTG 60.225 50.000 0.00 0.00 0.00 4.61
2370 5393 2.880167 GCCAGTTCTTTCTTAGGGGTGG 60.880 54.545 0.00 0.00 0.00 4.61
2371 5394 2.290960 CCAGTTCTTTCTTAGGGGTGGG 60.291 54.545 0.00 0.00 0.00 4.61
2372 5395 2.642807 CAGTTCTTTCTTAGGGGTGGGA 59.357 50.000 0.00 0.00 0.00 4.37
2400 5423 8.532186 ACTCACTCTGACTGTATCTGATTATT 57.468 34.615 0.00 0.00 35.00 1.40
2484 5508 7.495934 GCCTATTTCTACTACAATGCAAAGAGA 59.504 37.037 0.00 0.00 0.00 3.10
2544 5568 5.609533 TCTAAGTTCCTGGTATACAAGCC 57.390 43.478 5.01 0.00 0.00 4.35
2566 5590 3.562505 CTGAGATTGTCAGCTTTTGTGC 58.437 45.455 0.00 0.00 46.41 4.57
2596 5620 6.485830 AGCACTGATATTACCTTCTGCTAA 57.514 37.500 0.00 0.00 32.03 3.09
2600 5624 8.713271 GCACTGATATTACCTTCTGCTAATAAC 58.287 37.037 0.00 0.00 0.00 1.89
2611 5636 8.322091 ACCTTCTGCTAATAACACTTGTCTATT 58.678 33.333 0.00 0.00 0.00 1.73
2612 5637 9.817809 CCTTCTGCTAATAACACTTGTCTATTA 57.182 33.333 0.00 0.00 0.00 0.98
2641 5666 0.741915 TCGGTTTGCCTGTTGAAACC 59.258 50.000 0.00 0.00 45.23 3.27
2654 5682 2.297698 TGAAACCGGAGTACTGGAGA 57.702 50.000 9.46 0.00 44.87 3.71
2662 5690 1.205893 GGAGTACTGGAGAGCTGGTTG 59.794 57.143 0.00 0.00 0.00 3.77
2665 5693 2.300437 AGTACTGGAGAGCTGGTTGTTC 59.700 50.000 0.00 0.00 0.00 3.18
2782 5812 3.199880 ACCTGGATAAGATGCGAAAGG 57.800 47.619 0.00 0.00 0.00 3.11
3005 6046 2.093128 AGGATTTGGGGTTAGCTACGTG 60.093 50.000 0.00 0.00 0.00 4.49
3082 6152 2.855599 TGTATGGATTCCATTGGGACCA 59.144 45.455 22.87 14.95 42.23 4.02
3088 6158 3.321968 GGATTCCATTGGGACCAAATAGC 59.678 47.826 8.00 0.00 44.89 2.97
3147 6217 6.592994 TGAGTGACAGCTTCATCTTCTAAATG 59.407 38.462 2.61 0.00 36.32 2.32
3154 6226 7.012138 ACAGCTTCATCTTCTAAATGCATACAG 59.988 37.037 0.00 0.00 0.00 2.74
3262 11099 1.134401 ACATCACCTAGCCGACCATTG 60.134 52.381 0.00 0.00 0.00 2.82
3393 11234 7.667219 TCAAGCTCTTTCCTTGAATAGAACATT 59.333 33.333 1.68 0.00 43.98 2.71
3439 11280 5.489792 TTCTGGTTTGAGCAATCTAGTCT 57.510 39.130 5.09 0.00 0.00 3.24
3473 11314 8.193438 AGCAAAATTATGAGTAATTGGCTCTTC 58.807 33.333 11.44 0.00 42.22 2.87
3515 11356 7.665690 ACATTGAGCGTCTAGAGAATATGAAT 58.334 34.615 0.00 0.00 0.00 2.57
3755 11626 7.113658 TGAGCTACAGGACCTTATTTCTTAG 57.886 40.000 0.00 0.00 0.00 2.18
3758 11629 8.240267 AGCTACAGGACCTTATTTCTTAGTAG 57.760 38.462 0.00 0.00 0.00 2.57
3759 11630 7.840210 AGCTACAGGACCTTATTTCTTAGTAGT 59.160 37.037 10.07 0.00 0.00 2.73
3807 11680 5.670149 TTAAAAACGACAATTACGCTCCA 57.330 34.783 0.00 0.00 0.00 3.86
3985 12019 9.609950 AAAATATATTTTGTGCACATGCAAAAC 57.390 25.926 22.39 0.00 46.92 2.43
4100 12139 8.482943 TCACCTATACAGTGCAGTATTAACATT 58.517 33.333 4.15 0.00 36.23 2.71
4109 12148 5.283717 GTGCAGTATTAACATTGTCTTTGCG 59.716 40.000 0.00 0.00 0.00 4.85
4123 12163 4.152938 TGTCTTTGCGATCAACTCTGAATG 59.847 41.667 0.00 0.00 34.49 2.67
4136 12176 0.804989 CTGAATGGGAGACGCAAACC 59.195 55.000 0.00 0.00 0.00 3.27
4262 12303 0.456824 GCAGCTTCGAGATGTCGTCA 60.457 55.000 12.41 0.00 46.85 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.561478 AGTGGATTGTGTTTACCGCT 57.439 45.000 0.00 0.00 38.25 5.52
29 30 7.624360 TGATCATTAGTGGATTGTGTTTACC 57.376 36.000 0.00 0.00 0.00 2.85
61 62 2.890311 CAGGAGATCTCACGATAGCCTT 59.110 50.000 23.85 0.00 42.67 4.35
68 69 2.789409 TCTCACAGGAGATCTCACGA 57.211 50.000 23.85 12.50 45.12 4.35
164 165 7.448161 TGCGAATCAAATAATCACCATAGGAAT 59.552 33.333 0.00 0.00 0.00 3.01
265 266 5.163652 ACAAACAAGAAACTCTACAAGTGGC 60.164 40.000 0.00 0.00 38.58 5.01
330 332 5.844301 ACCGCATGAATTTGAATGAAAAC 57.156 34.783 0.00 0.00 0.00 2.43
331 333 6.857777 AAACCGCATGAATTTGAATGAAAA 57.142 29.167 0.00 0.00 0.00 2.29
407 424 5.840693 CCTAAGGAATTGGGGCATAAGAATT 59.159 40.000 0.00 0.00 0.00 2.17
677 3690 7.500892 TGTTGAATTTACTGCTACCTTCTTTGA 59.499 33.333 0.00 0.00 0.00 2.69
703 3716 1.536662 GGTGGTGTCCCCTCTCACT 60.537 63.158 0.00 0.00 35.26 3.41
734 3747 1.327303 TTCCGAATTTTGCCACTGCT 58.673 45.000 0.00 0.00 38.71 4.24
751 3764 7.334858 AGACCTGGTCTCATAGAATTCTTTTC 58.665 38.462 23.49 0.00 38.71 2.29
752 3765 7.264294 AGACCTGGTCTCATAGAATTCTTTT 57.736 36.000 23.49 0.00 38.71 2.27
753 3766 6.882768 AGACCTGGTCTCATAGAATTCTTT 57.117 37.500 23.49 2.41 38.71 2.52
766 3779 2.612285 TCTCATGTGAGACCTGGTCT 57.388 50.000 28.70 28.70 45.48 3.85
770 3783 8.087802 TCAGAATGGATCTCATGTGAGACCTG 62.088 46.154 14.46 13.34 45.26 4.00
771 3784 6.107325 TCAGAATGGATCTCATGTGAGACCT 61.107 44.000 14.46 0.51 45.26 3.85
772 3785 4.100653 TCAGAATGGATCTCATGTGAGACC 59.899 45.833 14.46 16.27 45.26 3.85
773 3786 5.273674 TCAGAATGGATCTCATGTGAGAC 57.726 43.478 14.46 8.87 45.26 3.36
774 3787 5.855045 CATCAGAATGGATCTCATGTGAGA 58.145 41.667 14.52 14.52 45.99 3.27
788 3801 3.066380 TCACGTGTCAACCATCAGAATG 58.934 45.455 16.51 0.00 37.54 2.67
789 3802 3.067106 GTCACGTGTCAACCATCAGAAT 58.933 45.455 16.51 0.00 0.00 2.40
790 3803 2.159028 TGTCACGTGTCAACCATCAGAA 60.159 45.455 16.51 0.00 0.00 3.02
791 3804 1.410882 TGTCACGTGTCAACCATCAGA 59.589 47.619 16.51 0.00 0.00 3.27
792 3805 1.864565 TGTCACGTGTCAACCATCAG 58.135 50.000 16.51 0.00 0.00 2.90
793 3806 2.542020 ATGTCACGTGTCAACCATCA 57.458 45.000 18.96 5.91 0.00 3.07
794 3807 2.805671 TGAATGTCACGTGTCAACCATC 59.194 45.455 18.96 14.36 0.00 3.51
795 3808 2.548057 GTGAATGTCACGTGTCAACCAT 59.452 45.455 18.96 9.84 37.67 3.55
796 3809 1.937223 GTGAATGTCACGTGTCAACCA 59.063 47.619 18.96 15.66 37.67 3.67
797 3810 2.663279 GTGAATGTCACGTGTCAACC 57.337 50.000 18.96 13.52 37.67 3.77
807 3820 5.259832 TGCTTTGTGATTTGTGAATGTCA 57.740 34.783 0.00 0.00 0.00 3.58
808 3821 6.154445 AGATGCTTTGTGATTTGTGAATGTC 58.846 36.000 0.00 0.00 0.00 3.06
809 3822 6.092955 AGATGCTTTGTGATTTGTGAATGT 57.907 33.333 0.00 0.00 0.00 2.71
810 3823 5.575606 GGAGATGCTTTGTGATTTGTGAATG 59.424 40.000 0.00 0.00 0.00 2.67
811 3824 5.244402 TGGAGATGCTTTGTGATTTGTGAAT 59.756 36.000 0.00 0.00 0.00 2.57
812 3825 4.583907 TGGAGATGCTTTGTGATTTGTGAA 59.416 37.500 0.00 0.00 0.00 3.18
813 3826 4.022935 GTGGAGATGCTTTGTGATTTGTGA 60.023 41.667 0.00 0.00 0.00 3.58
814 3827 4.232221 GTGGAGATGCTTTGTGATTTGTG 58.768 43.478 0.00 0.00 0.00 3.33
815 3828 3.256631 GGTGGAGATGCTTTGTGATTTGT 59.743 43.478 0.00 0.00 0.00 2.83
816 3829 3.367703 GGGTGGAGATGCTTTGTGATTTG 60.368 47.826 0.00 0.00 0.00 2.32
817 3830 2.827921 GGGTGGAGATGCTTTGTGATTT 59.172 45.455 0.00 0.00 0.00 2.17
818 3831 2.450476 GGGTGGAGATGCTTTGTGATT 58.550 47.619 0.00 0.00 0.00 2.57
819 3832 1.341383 GGGGTGGAGATGCTTTGTGAT 60.341 52.381 0.00 0.00 0.00 3.06
820 3833 0.038166 GGGGTGGAGATGCTTTGTGA 59.962 55.000 0.00 0.00 0.00 3.58
821 3834 0.251297 TGGGGTGGAGATGCTTTGTG 60.251 55.000 0.00 0.00 0.00 3.33
822 3835 0.251341 GTGGGGTGGAGATGCTTTGT 60.251 55.000 0.00 0.00 0.00 2.83
823 3836 0.038744 AGTGGGGTGGAGATGCTTTG 59.961 55.000 0.00 0.00 0.00 2.77
824 3837 0.779997 AAGTGGGGTGGAGATGCTTT 59.220 50.000 0.00 0.00 0.00 3.51
825 3838 1.668826 TAAGTGGGGTGGAGATGCTT 58.331 50.000 0.00 0.00 0.00 3.91
826 3839 1.668826 TTAAGTGGGGTGGAGATGCT 58.331 50.000 0.00 0.00 0.00 3.79
827 3840 2.507407 TTTAAGTGGGGTGGAGATGC 57.493 50.000 0.00 0.00 0.00 3.91
828 3841 4.599041 TGATTTTAAGTGGGGTGGAGATG 58.401 43.478 0.00 0.00 0.00 2.90
829 3842 4.540099 TCTGATTTTAAGTGGGGTGGAGAT 59.460 41.667 0.00 0.00 0.00 2.75
830 3843 3.913799 TCTGATTTTAAGTGGGGTGGAGA 59.086 43.478 0.00 0.00 0.00 3.71
831 3844 4.265073 CTCTGATTTTAAGTGGGGTGGAG 58.735 47.826 0.00 0.00 0.00 3.86
832 3845 3.010138 CCTCTGATTTTAAGTGGGGTGGA 59.990 47.826 0.00 0.00 0.00 4.02
833 3846 3.356290 CCTCTGATTTTAAGTGGGGTGG 58.644 50.000 0.00 0.00 0.00 4.61
834 3847 3.356290 CCCTCTGATTTTAAGTGGGGTG 58.644 50.000 3.16 0.00 42.41 4.61
835 3848 3.739401 CCCTCTGATTTTAAGTGGGGT 57.261 47.619 3.16 0.00 42.41 4.95
837 3850 3.018423 CCCCCTCTGATTTTAAGTGGG 57.982 52.381 3.99 3.99 44.67 4.61
854 3867 6.768381 CACAAAGTATTTAATCTCTCTCCCCC 59.232 42.308 0.00 0.00 35.03 5.40
855 3868 7.565680 TCACAAAGTATTTAATCTCTCTCCCC 58.434 38.462 0.00 0.00 35.03 4.81
856 3869 9.620259 AATCACAAAGTATTTAATCTCTCTCCC 57.380 33.333 0.00 0.00 35.03 4.30
868 3881 9.248291 GTGACATTCACAAATCACAAAGTATTT 57.752 29.630 1.34 0.00 46.22 1.40
869 3882 8.801715 GTGACATTCACAAATCACAAAGTATT 57.198 30.769 1.34 0.00 46.22 1.89
884 3897 8.111097 CCTGATGGATGACATGTGACATTCAC 62.111 46.154 1.15 2.81 38.23 3.18
885 3898 4.846040 TGATGGATGACATGTGACATTCA 58.154 39.130 1.15 7.05 40.72 2.57
886 3899 4.275196 CCTGATGGATGACATGTGACATTC 59.725 45.833 1.15 0.31 40.72 2.67
887 3900 4.080186 TCCTGATGGATGACATGTGACATT 60.080 41.667 1.15 0.00 40.72 2.71
888 3901 3.457012 TCCTGATGGATGACATGTGACAT 59.543 43.478 1.15 0.36 40.72 3.06
889 3902 2.839425 TCCTGATGGATGACATGTGACA 59.161 45.455 1.15 0.00 40.72 3.58
890 3903 3.201290 GTCCTGATGGATGACATGTGAC 58.799 50.000 1.15 0.00 45.29 3.67
891 3904 3.548745 GTCCTGATGGATGACATGTGA 57.451 47.619 1.15 0.00 45.29 3.58
902 3915 0.390860 GGTGAGATCCGTCCTGATGG 59.609 60.000 0.00 0.00 38.85 3.51
903 3916 1.407936 AGGTGAGATCCGTCCTGATG 58.592 55.000 0.00 0.00 0.00 3.07
904 3917 3.935371 AGGTGAGATCCGTCCTGAT 57.065 52.632 0.00 0.00 0.00 2.90
906 3919 1.142748 GCAGGTGAGATCCGTCCTG 59.857 63.158 17.81 17.81 46.96 3.86
907 3920 0.259065 TAGCAGGTGAGATCCGTCCT 59.741 55.000 0.00 0.00 0.00 3.85
908 3921 1.112113 TTAGCAGGTGAGATCCGTCC 58.888 55.000 0.00 0.00 0.00 4.79
909 3922 2.362397 TGATTAGCAGGTGAGATCCGTC 59.638 50.000 0.00 0.00 0.00 4.79
910 3923 2.388735 TGATTAGCAGGTGAGATCCGT 58.611 47.619 0.00 0.00 0.00 4.69
911 3924 3.006217 TCATGATTAGCAGGTGAGATCCG 59.994 47.826 0.00 0.00 0.00 4.18
912 3925 4.282957 TCTCATGATTAGCAGGTGAGATCC 59.717 45.833 0.00 0.00 37.59 3.36
913 3926 5.229423 GTCTCATGATTAGCAGGTGAGATC 58.771 45.833 6.99 0.00 41.90 2.75
914 3927 4.040217 GGTCTCATGATTAGCAGGTGAGAT 59.960 45.833 6.99 0.00 41.90 2.75
915 3928 3.386078 GGTCTCATGATTAGCAGGTGAGA 59.614 47.826 0.00 0.33 39.25 3.27
916 3929 3.387374 AGGTCTCATGATTAGCAGGTGAG 59.613 47.826 0.00 0.00 35.76 3.51
917 3930 3.133542 CAGGTCTCATGATTAGCAGGTGA 59.866 47.826 0.00 0.00 0.00 4.02
918 3931 3.464907 CAGGTCTCATGATTAGCAGGTG 58.535 50.000 0.00 0.00 0.00 4.00
919 3932 2.437281 CCAGGTCTCATGATTAGCAGGT 59.563 50.000 0.00 0.00 0.00 4.00
920 3933 2.437281 ACCAGGTCTCATGATTAGCAGG 59.563 50.000 13.81 13.81 0.00 4.85
921 3934 3.387374 AGACCAGGTCTCATGATTAGCAG 59.613 47.826 17.31 0.00 38.71 4.24
922 3935 3.378512 AGACCAGGTCTCATGATTAGCA 58.621 45.455 17.31 0.00 38.71 3.49
923 3936 4.414337 AAGACCAGGTCTCATGATTAGC 57.586 45.455 23.17 0.00 42.59 3.09
953 3966 5.777802 TGCTATCTGAATTTTGCGGAAAAA 58.222 33.333 18.91 2.36 41.88 1.94
954 3967 5.384063 TGCTATCTGAATTTTGCGGAAAA 57.616 34.783 17.38 17.38 35.52 2.29
955 3968 5.450412 GGATGCTATCTGAATTTTGCGGAAA 60.450 40.000 0.00 0.00 0.00 3.13
956 3969 4.036734 GGATGCTATCTGAATTTTGCGGAA 59.963 41.667 0.00 0.00 0.00 4.30
957 3970 3.565482 GGATGCTATCTGAATTTTGCGGA 59.435 43.478 0.00 0.00 0.00 5.54
958 3971 3.316029 TGGATGCTATCTGAATTTTGCGG 59.684 43.478 0.00 0.00 0.00 5.69
959 3972 4.285292 GTGGATGCTATCTGAATTTTGCG 58.715 43.478 0.00 0.00 0.00 4.85
960 3973 4.098349 TGGTGGATGCTATCTGAATTTTGC 59.902 41.667 0.00 0.00 0.00 3.68
961 3974 5.735354 GCTGGTGGATGCTATCTGAATTTTG 60.735 44.000 0.00 0.00 0.00 2.44
962 3975 4.340381 GCTGGTGGATGCTATCTGAATTTT 59.660 41.667 0.00 0.00 0.00 1.82
963 3976 3.887716 GCTGGTGGATGCTATCTGAATTT 59.112 43.478 0.00 0.00 0.00 1.82
964 3977 3.484407 GCTGGTGGATGCTATCTGAATT 58.516 45.455 0.00 0.00 0.00 2.17
965 3978 2.549563 CGCTGGTGGATGCTATCTGAAT 60.550 50.000 0.00 0.00 0.00 2.57
966 3979 1.202568 CGCTGGTGGATGCTATCTGAA 60.203 52.381 0.00 0.00 0.00 3.02
967 3980 0.390492 CGCTGGTGGATGCTATCTGA 59.610 55.000 0.00 0.00 0.00 3.27
968 3981 1.226686 GCGCTGGTGGATGCTATCTG 61.227 60.000 0.00 0.00 0.00 2.90
969 3982 1.070445 GCGCTGGTGGATGCTATCT 59.930 57.895 0.00 0.00 0.00 1.98
1103 4116 3.654143 GGGGTTTAGGCCGGTGGT 61.654 66.667 1.90 0.00 0.00 4.16
1258 4274 2.290021 CTTCTGGATTCTGGGGGCCC 62.290 65.000 15.76 15.76 0.00 5.80
1439 4455 1.352352 CTCCTCCTCCTTTGGCTTCAA 59.648 52.381 0.00 0.00 0.00 2.69
1495 4511 2.203788 ACCGTCTTCTGCTCCCCA 60.204 61.111 0.00 0.00 0.00 4.96
1570 4586 1.226239 GTCGAAGTACTCCGACGCC 60.226 63.158 19.03 0.00 44.23 5.68
1780 4796 4.164843 TCCCCAATGGTTTACAGCTATC 57.835 45.455 0.00 0.00 34.77 2.08
1922 4939 6.089551 CACACTACATCTGTAAACAGTGCTAC 59.910 42.308 9.81 0.00 44.12 3.58
2001 5021 6.930068 TCCCAATATACCTTAGTAGCCTTC 57.070 41.667 0.00 0.00 0.00 3.46
2019 5039 3.644966 AGCCGATCTTTTGTATCCCAA 57.355 42.857 0.00 0.00 0.00 4.12
2075 5095 6.036517 AGAGCAATCATGACAGTTAATCGAAC 59.963 38.462 0.00 0.00 38.44 3.95
2077 5097 5.521372 CAGAGCAATCATGACAGTTAATCGA 59.479 40.000 0.00 0.00 0.00 3.59
2087 5107 7.475015 TGTTAAATTAGCAGAGCAATCATGAC 58.525 34.615 0.00 0.00 0.00 3.06
2089 5109 8.692110 TTTGTTAAATTAGCAGAGCAATCATG 57.308 30.769 0.00 0.00 0.00 3.07
2093 5115 7.325694 AGCATTTGTTAAATTAGCAGAGCAAT 58.674 30.769 10.69 0.00 0.00 3.56
2127 5149 7.755373 TCAATCTTCACAGTCTGAAATACGTAG 59.245 37.037 6.91 0.00 38.47 3.51
2129 5151 6.455647 TCAATCTTCACAGTCTGAAATACGT 58.544 36.000 6.91 0.00 38.47 3.57
2130 5152 6.951256 TCAATCTTCACAGTCTGAAATACG 57.049 37.500 6.91 0.00 38.47 3.06
2160 5182 1.039068 ATGCCAGGTCTCTCTCGATG 58.961 55.000 0.00 0.00 0.00 3.84
2280 5303 0.450583 GCCTCATGTGTGTGCAGATG 59.549 55.000 0.00 0.00 44.77 2.90
2299 5322 6.152661 TCACCTTTAGCATCCCAAACAATAAG 59.847 38.462 0.00 0.00 0.00 1.73
2310 5333 5.391312 ACAAATTGTCACCTTTAGCATCC 57.609 39.130 0.00 0.00 0.00 3.51
2313 5336 4.217550 GCCTACAAATTGTCACCTTTAGCA 59.782 41.667 0.22 0.00 0.00 3.49
2330 5353 2.436417 GCAAAAGATGTCCAGCCTACA 58.564 47.619 0.00 0.00 0.00 2.74
2337 5360 3.228188 AGAACTGGCAAAAGATGTCCA 57.772 42.857 0.00 0.00 35.07 4.02
2339 5362 5.444663 AGAAAGAACTGGCAAAAGATGTC 57.555 39.130 0.00 0.00 0.00 3.06
2348 5371 2.062636 ACCCCTAAGAAAGAACTGGCA 58.937 47.619 0.00 0.00 0.00 4.92
2349 5372 2.437413 CACCCCTAAGAAAGAACTGGC 58.563 52.381 0.00 0.00 0.00 4.85
2350 5373 2.290960 CCCACCCCTAAGAAAGAACTGG 60.291 54.545 0.00 0.00 0.00 4.00
2351 5374 2.642807 TCCCACCCCTAAGAAAGAACTG 59.357 50.000 0.00 0.00 0.00 3.16
2352 5375 2.999928 TCCCACCCCTAAGAAAGAACT 58.000 47.619 0.00 0.00 0.00 3.01
2353 5376 3.801307 TTCCCACCCCTAAGAAAGAAC 57.199 47.619 0.00 0.00 0.00 3.01
2354 5377 5.105853 AGTATTCCCACCCCTAAGAAAGAA 58.894 41.667 0.00 0.00 0.00 2.52
2355 5378 4.706616 AGTATTCCCACCCCTAAGAAAGA 58.293 43.478 0.00 0.00 0.00 2.52
2356 5379 4.473559 TGAGTATTCCCACCCCTAAGAAAG 59.526 45.833 0.00 0.00 0.00 2.62
2357 5380 4.226620 GTGAGTATTCCCACCCCTAAGAAA 59.773 45.833 0.00 0.00 0.00 2.52
2358 5381 3.778629 GTGAGTATTCCCACCCCTAAGAA 59.221 47.826 0.00 0.00 0.00 2.52
2359 5382 3.013648 AGTGAGTATTCCCACCCCTAAGA 59.986 47.826 0.00 0.00 34.00 2.10
2360 5383 3.385115 AGTGAGTATTCCCACCCCTAAG 58.615 50.000 0.00 0.00 34.00 2.18
2361 5384 3.013648 AGAGTGAGTATTCCCACCCCTAA 59.986 47.826 0.00 0.00 34.00 2.69
2362 5385 2.590611 AGAGTGAGTATTCCCACCCCTA 59.409 50.000 0.00 0.00 34.00 3.53
2363 5386 1.366435 AGAGTGAGTATTCCCACCCCT 59.634 52.381 0.00 0.00 34.00 4.79
2364 5387 1.486726 CAGAGTGAGTATTCCCACCCC 59.513 57.143 0.00 0.00 34.00 4.95
2365 5388 2.168728 GTCAGAGTGAGTATTCCCACCC 59.831 54.545 0.00 0.00 34.00 4.61
2366 5389 3.100671 AGTCAGAGTGAGTATTCCCACC 58.899 50.000 0.00 0.00 34.00 4.61
2367 5390 3.511934 ACAGTCAGAGTGAGTATTCCCAC 59.488 47.826 12.54 0.00 0.00 4.61
2368 5391 3.779444 ACAGTCAGAGTGAGTATTCCCA 58.221 45.455 12.54 0.00 0.00 4.37
2369 5392 5.830991 AGATACAGTCAGAGTGAGTATTCCC 59.169 44.000 12.54 0.00 0.00 3.97
2370 5393 6.544197 TCAGATACAGTCAGAGTGAGTATTCC 59.456 42.308 12.54 0.00 0.00 3.01
2371 5394 7.561021 TCAGATACAGTCAGAGTGAGTATTC 57.439 40.000 12.54 1.86 0.00 1.75
2372 5395 8.532186 AATCAGATACAGTCAGAGTGAGTATT 57.468 34.615 12.54 0.98 0.00 1.89
2400 5423 8.078060 TCTCTGTTAATACAATCCATGAGACA 57.922 34.615 0.00 0.00 32.92 3.41
2418 5442 4.218635 TCGTCAGCTGTTCTTATCTCTGTT 59.781 41.667 14.67 0.00 0.00 3.16
2484 5508 1.559219 TCGGGATTGACACATGATGGT 59.441 47.619 0.00 0.00 0.00 3.55
2544 5568 3.611057 GCACAAAAGCTGACAATCTCAGG 60.611 47.826 0.00 0.00 46.08 3.86
2566 5590 9.416794 CAGAAGGTAATATCAGTGCTACAATAG 57.583 37.037 0.00 0.00 0.00 1.73
2611 5636 6.827586 ACAGGCAAACCGAATAAGAATTTA 57.172 33.333 0.00 0.00 42.76 1.40
2612 5637 5.722021 ACAGGCAAACCGAATAAGAATTT 57.278 34.783 0.00 0.00 42.76 1.82
2626 5651 1.028905 CTCCGGTTTCAACAGGCAAA 58.971 50.000 0.00 0.00 42.93 3.68
2641 5666 0.681564 ACCAGCTCTCCAGTACTCCG 60.682 60.000 0.00 0.00 0.00 4.63
2654 5682 2.435805 TGTCAGAGAAGAACAACCAGCT 59.564 45.455 0.00 0.00 0.00 4.24
2662 5690 6.313411 CAGAGGATCAAATGTCAGAGAAGAAC 59.687 42.308 0.00 0.00 37.82 3.01
2665 5693 5.975282 TCAGAGGATCAAATGTCAGAGAAG 58.025 41.667 0.00 0.00 37.82 2.85
2782 5812 4.520492 CACTATAGGCATCCAAAATGTCCC 59.480 45.833 4.43 0.00 0.00 4.46
2927 5960 9.168451 CTAGAACATCACTACTAGAAACTGAGA 57.832 37.037 0.00 0.00 35.69 3.27
3005 6046 6.640907 CACTAGTGGAAATTGCACCTTAAAAC 59.359 38.462 15.49 0.00 39.72 2.43
3147 6217 8.023706 TCTGTAAATGATCTCGATACTGTATGC 58.976 37.037 4.79 0.00 0.00 3.14
3184 8412 3.077359 CTGGTGACTTCTTTTAGCCAGG 58.923 50.000 0.00 0.00 38.56 4.45
3393 11234 5.994250 AGCAGAATAGGCAGACTTTATTCA 58.006 37.500 2.19 0.00 36.64 2.57
3410 11251 2.653726 TGCTCAAACCAGAAAGCAGAA 58.346 42.857 0.00 0.00 39.69 3.02
3656 11497 2.359900 GGACCAATTGCGATGACTCTT 58.640 47.619 0.00 0.00 0.00 2.85
3657 11498 1.407437 GGGACCAATTGCGATGACTCT 60.407 52.381 0.00 0.00 0.00 3.24
3694 11565 3.202818 TGGTCTGATATGCCAAAGGTCAT 59.797 43.478 0.00 0.00 0.00 3.06
3985 12019 3.634397 TCCCCTGAGCAGTTCTAAATG 57.366 47.619 0.00 0.00 0.00 2.32
4100 12139 3.385193 TCAGAGTTGATCGCAAAGACA 57.615 42.857 0.00 0.00 35.42 3.41
4109 12148 3.452474 CGTCTCCCATTCAGAGTTGATC 58.548 50.000 0.00 0.00 32.27 2.92
4123 12163 3.056328 GCCTGGTTTGCGTCTCCC 61.056 66.667 0.00 0.00 0.00 4.30
4136 12176 2.936919 TATCCTGTGCATAAGGCCTG 57.063 50.000 5.69 0.00 43.89 4.85
4249 12290 0.952280 GGGCTATGACGACATCTCGA 59.048 55.000 3.03 0.00 43.06 4.04


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

AutoCloner maintained by Alex Coulton.