Multiple sequence alignment - TraesCS4D01G045000

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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 TraesCS4D01G045000 chr4D 100.000 2882 0 0 1 2882 20508823 20511704 0.000000e+00 5323.0
1 TraesCS4D01G045000 chr4D 94.823 734 38 0 43 776 33288692 33289425 0.000000e+00 1146.0
2 TraesCS4D01G045000 chr3A 91.291 2021 162 7 863 2882 693114507 693116514 0.000000e+00 2745.0
3 TraesCS4D01G045000 chr3A 91.127 1916 157 9 968 2882 20245077 20243174 0.000000e+00 2584.0
4 TraesCS4D01G045000 chr5B 90.752 1622 137 9 1262 2882 111204447 111206056 0.000000e+00 2152.0
5 TraesCS4D01G045000 chr5B 78.987 671 140 1 2208 2877 508001400 508000730 9.410000e-125 457.0
6 TraesCS4D01G045000 chr3D 95.646 735 30 2 43 776 550246675 550245942 0.000000e+00 1179.0
7 TraesCS4D01G045000 chr3D 94.844 737 34 2 43 776 610604544 610603809 0.000000e+00 1147.0
8 TraesCS4D01G045000 chr3D 94.687 734 38 1 43 775 476513339 476514072 0.000000e+00 1138.0
9 TraesCS4D01G045000 chr2D 95.212 731 34 1 43 773 584262180 584262909 0.000000e+00 1155.0
10 TraesCS4D01G045000 chr2D 94.837 736 34 3 43 775 333507251 333507985 0.000000e+00 1146.0
11 TraesCS4D01G045000 chr6D 95.436 723 33 0 43 765 62204330 62205052 0.000000e+00 1153.0
12 TraesCS4D01G045000 chr6D 79.331 658 134 2 2226 2882 28988528 28987872 7.280000e-126 460.0
13 TraesCS4D01G045000 chr7D 94.844 737 35 2 43 776 175660166 175659430 0.000000e+00 1147.0
14 TraesCS4D01G045000 chr1D 94.694 735 37 1 43 775 421078961 421078227 0.000000e+00 1140.0
15 TraesCS4D01G045000 chr5A 94.730 721 37 1 2162 2882 42692724 42692005 0.000000e+00 1120.0
16 TraesCS4D01G045000 chr1A 79.815 649 127 4 2205 2851 497355145 497355791 1.210000e-128 470.0
17 TraesCS4D01G045000 chr3B 78.902 692 140 6 2193 2881 125933433 125934121 5.620000e-127 464.0
18 TraesCS4D01G045000 chr3B 78.466 678 139 4 2208 2881 403437854 403437180 1.230000e-118 436.0
19 TraesCS4D01G045000 chr3B 78.512 484 99 4 1108 1587 530268084 530268566 2.160000e-81 313.0
20 TraesCS4D01G045000 chr2A 78.988 514 105 3 1064 1575 555421017 555420505 5.910000e-92 348.0
21 TraesCS4D01G045000 chr6A 75.281 178 40 3 1190 1365 72977021 72977196 6.620000e-12 82.4


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 TraesCS4D01G045000 chr4D 20508823 20511704 2881 False 5323 5323 100.000 1 2882 1 chr4D.!!$F1 2881
1 TraesCS4D01G045000 chr4D 33288692 33289425 733 False 1146 1146 94.823 43 776 1 chr4D.!!$F2 733
2 TraesCS4D01G045000 chr3A 693114507 693116514 2007 False 2745 2745 91.291 863 2882 1 chr3A.!!$F1 2019
3 TraesCS4D01G045000 chr3A 20243174 20245077 1903 True 2584 2584 91.127 968 2882 1 chr3A.!!$R1 1914
4 TraesCS4D01G045000 chr5B 111204447 111206056 1609 False 2152 2152 90.752 1262 2882 1 chr5B.!!$F1 1620
5 TraesCS4D01G045000 chr5B 508000730 508001400 670 True 457 457 78.987 2208 2877 1 chr5B.!!$R1 669
6 TraesCS4D01G045000 chr3D 550245942 550246675 733 True 1179 1179 95.646 43 776 1 chr3D.!!$R1 733
7 TraesCS4D01G045000 chr3D 610603809 610604544 735 True 1147 1147 94.844 43 776 1 chr3D.!!$R2 733
8 TraesCS4D01G045000 chr3D 476513339 476514072 733 False 1138 1138 94.687 43 775 1 chr3D.!!$F1 732
9 TraesCS4D01G045000 chr2D 584262180 584262909 729 False 1155 1155 95.212 43 773 1 chr2D.!!$F2 730
10 TraesCS4D01G045000 chr2D 333507251 333507985 734 False 1146 1146 94.837 43 775 1 chr2D.!!$F1 732
11 TraesCS4D01G045000 chr6D 62204330 62205052 722 False 1153 1153 95.436 43 765 1 chr6D.!!$F1 722
12 TraesCS4D01G045000 chr6D 28987872 28988528 656 True 460 460 79.331 2226 2882 1 chr6D.!!$R1 656
13 TraesCS4D01G045000 chr7D 175659430 175660166 736 True 1147 1147 94.844 43 776 1 chr7D.!!$R1 733
14 TraesCS4D01G045000 chr1D 421078227 421078961 734 True 1140 1140 94.694 43 775 1 chr1D.!!$R1 732
15 TraesCS4D01G045000 chr5A 42692005 42692724 719 True 1120 1120 94.730 2162 2882 1 chr5A.!!$R1 720
16 TraesCS4D01G045000 chr1A 497355145 497355791 646 False 470 470 79.815 2205 2851 1 chr1A.!!$F1 646
17 TraesCS4D01G045000 chr3B 125933433 125934121 688 False 464 464 78.902 2193 2881 1 chr3B.!!$F1 688
18 TraesCS4D01G045000 chr3B 403437180 403437854 674 True 436 436 78.466 2208 2881 1 chr3B.!!$R1 673
19 TraesCS4D01G045000 chr2A 555420505 555421017 512 True 348 348 78.988 1064 1575 1 chr2A.!!$R1 511

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
341 343 0.036388 TCGGAGTTTGATGTGGGAGC 60.036 55.0 0.0 0.0 0.00 4.70 F
861 864 0.106167 TGTGTAGGGAGCCGCTATCT 60.106 55.0 0.0 0.0 31.86 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1690 0.035036 CATGCTCTCCATCTCCGCAT 59.965 55.0 0.0 0.0 41.56 4.73 R
2091 2095 0.178961 GGGGGAACTTGAGGCTGTTT 60.179 55.0 0.0 0.0 0.00 2.83 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
24 25 7.558435 GATTTCACTTTGTGCATAGACTTTG 57.442 36.000 0.00 0.00 32.98 2.77
25 26 6.449635 TTTCACTTTGTGCATAGACTTTGT 57.550 33.333 0.00 0.00 32.98 2.83
26 27 5.673337 TCACTTTGTGCATAGACTTTGTC 57.327 39.130 0.00 0.00 32.98 3.18
27 28 5.368145 TCACTTTGTGCATAGACTTTGTCT 58.632 37.500 5.53 5.53 38.76 3.41
28 29 6.521162 TCACTTTGTGCATAGACTTTGTCTA 58.479 36.000 9.47 9.47 40.01 2.59
29 30 6.646653 TCACTTTGTGCATAGACTTTGTCTAG 59.353 38.462 12.15 6.68 39.57 2.43
30 31 5.934625 ACTTTGTGCATAGACTTTGTCTAGG 59.065 40.000 13.06 13.06 46.35 3.02
31 32 4.471904 TGTGCATAGACTTTGTCTAGGG 57.528 45.455 17.26 11.15 46.35 3.53
32 33 3.198872 GTGCATAGACTTTGTCTAGGGC 58.801 50.000 17.26 18.06 46.35 5.19
33 34 3.107601 TGCATAGACTTTGTCTAGGGCT 58.892 45.455 22.51 4.97 46.35 5.19
34 35 3.133003 TGCATAGACTTTGTCTAGGGCTC 59.867 47.826 22.51 10.04 46.35 4.70
35 36 3.133003 GCATAGACTTTGTCTAGGGCTCA 59.867 47.826 17.26 0.00 46.35 4.26
36 37 4.202305 GCATAGACTTTGTCTAGGGCTCAT 60.202 45.833 17.26 0.00 46.35 2.90
37 38 3.902881 AGACTTTGTCTAGGGCTCATG 57.097 47.619 0.00 0.00 41.51 3.07
38 39 2.503356 AGACTTTGTCTAGGGCTCATGG 59.497 50.000 0.00 0.00 41.51 3.66
39 40 1.561542 ACTTTGTCTAGGGCTCATGGG 59.438 52.381 0.00 0.00 0.00 4.00
40 41 0.255890 TTTGTCTAGGGCTCATGGGC 59.744 55.000 9.80 9.80 40.05 5.36
95 96 5.163248 TGCCCTTATCATCGTTTCCTTCATA 60.163 40.000 0.00 0.00 0.00 2.15
118 119 1.661341 GCATCATCGAGGTGAAGCTT 58.339 50.000 0.00 0.00 39.15 3.74
330 332 1.160137 GCAGTGCAGATTCGGAGTTT 58.840 50.000 11.09 0.00 0.00 2.66
341 343 0.036388 TCGGAGTTTGATGTGGGAGC 60.036 55.000 0.00 0.00 0.00 4.70
370 372 2.651361 CAGGAGGACGACGCTGTT 59.349 61.111 0.00 0.00 0.00 3.16
421 423 0.464373 CCTGGCACGGTAGATGCAAT 60.464 55.000 0.00 0.00 45.27 3.56
429 431 4.499188 GCACGGTAGATGCAATAGTACAGA 60.499 45.833 0.00 0.00 42.88 3.41
632 635 3.496692 CGCCCCTTCATCAATTGGATAGA 60.497 47.826 5.42 0.00 33.95 1.98
642 645 5.791336 TCAATTGGATAGATGTAGCGACT 57.209 39.130 5.42 0.00 0.00 4.18
692 695 9.502091 AGTCTTGCTGTTGTATGACTTTATAAA 57.498 29.630 0.00 0.00 39.12 1.40
791 794 4.980339 AAAAATGGGCCTCAATTGAGTT 57.020 36.364 29.03 16.33 40.48 3.01
792 795 3.967332 AAATGGGCCTCAATTGAGTTG 57.033 42.857 29.03 18.18 40.48 3.16
793 796 2.905415 ATGGGCCTCAATTGAGTTGA 57.095 45.000 29.03 13.60 44.36 3.18
794 797 2.673775 TGGGCCTCAATTGAGTTGAA 57.326 45.000 29.03 12.87 45.74 2.69
795 798 2.517959 TGGGCCTCAATTGAGTTGAAG 58.482 47.619 29.03 16.91 45.74 3.02
796 799 2.108075 TGGGCCTCAATTGAGTTGAAGA 59.892 45.455 29.03 9.25 45.74 2.87
797 800 3.245371 TGGGCCTCAATTGAGTTGAAGAT 60.245 43.478 29.03 0.00 45.74 2.40
798 801 3.379688 GGGCCTCAATTGAGTTGAAGATC 59.620 47.826 29.03 12.09 45.74 2.75
799 802 4.012374 GGCCTCAATTGAGTTGAAGATCA 58.988 43.478 29.03 0.00 45.74 2.92
800 803 4.643784 GGCCTCAATTGAGTTGAAGATCAT 59.356 41.667 29.03 0.00 45.74 2.45
801 804 5.126707 GGCCTCAATTGAGTTGAAGATCATT 59.873 40.000 29.03 0.00 45.74 2.57
802 805 6.034591 GCCTCAATTGAGTTGAAGATCATTG 58.965 40.000 29.03 13.17 45.74 2.82
803 806 6.349944 GCCTCAATTGAGTTGAAGATCATTGT 60.350 38.462 29.03 0.00 45.74 2.71
804 807 7.027760 CCTCAATTGAGTTGAAGATCATTGTG 58.972 38.462 29.03 8.38 45.74 3.33
805 808 7.309012 CCTCAATTGAGTTGAAGATCATTGTGT 60.309 37.037 29.03 0.00 45.74 3.72
806 809 7.364970 TCAATTGAGTTGAAGATCATTGTGTG 58.635 34.615 3.38 0.00 43.64 3.82
807 810 7.229106 TCAATTGAGTTGAAGATCATTGTGTGA 59.771 33.333 3.38 0.00 43.64 3.58
808 811 5.929697 TGAGTTGAAGATCATTGTGTGAC 57.070 39.130 0.00 0.00 40.28 3.67
809 812 5.614308 TGAGTTGAAGATCATTGTGTGACT 58.386 37.500 0.00 0.00 40.28 3.41
810 813 6.057533 TGAGTTGAAGATCATTGTGTGACTT 58.942 36.000 0.00 0.00 40.28 3.01
811 814 6.017687 TGAGTTGAAGATCATTGTGTGACTTG 60.018 38.462 0.00 0.00 40.28 3.16
812 815 4.754372 TGAAGATCATTGTGTGACTTGC 57.246 40.909 0.00 0.00 40.28 4.01
813 816 3.187022 TGAAGATCATTGTGTGACTTGCG 59.813 43.478 0.00 0.00 40.28 4.85
814 817 2.771089 AGATCATTGTGTGACTTGCGT 58.229 42.857 0.00 0.00 40.28 5.24
815 818 2.481568 AGATCATTGTGTGACTTGCGTG 59.518 45.455 0.00 0.00 40.28 5.34
816 819 1.946745 TCATTGTGTGACTTGCGTGA 58.053 45.000 0.00 0.00 0.00 4.35
817 820 2.493035 TCATTGTGTGACTTGCGTGAT 58.507 42.857 0.00 0.00 0.00 3.06
818 821 3.658709 TCATTGTGTGACTTGCGTGATA 58.341 40.909 0.00 0.00 0.00 2.15
819 822 4.061596 TCATTGTGTGACTTGCGTGATAA 58.938 39.130 0.00 0.00 0.00 1.75
820 823 4.513318 TCATTGTGTGACTTGCGTGATAAA 59.487 37.500 0.00 0.00 0.00 1.40
821 824 3.870723 TGTGTGACTTGCGTGATAAAC 57.129 42.857 0.00 0.00 0.00 2.01
822 825 2.546368 TGTGTGACTTGCGTGATAAACC 59.454 45.455 0.00 0.00 0.00 3.27
823 826 2.546368 GTGTGACTTGCGTGATAAACCA 59.454 45.455 0.00 0.00 0.00 3.67
824 827 3.002862 GTGTGACTTGCGTGATAAACCAA 59.997 43.478 0.00 0.00 0.00 3.67
825 828 3.002862 TGTGACTTGCGTGATAAACCAAC 59.997 43.478 0.00 0.00 0.00 3.77
826 829 3.250040 GTGACTTGCGTGATAAACCAACT 59.750 43.478 0.00 0.00 0.00 3.16
827 830 3.249799 TGACTTGCGTGATAAACCAACTG 59.750 43.478 0.00 0.00 0.00 3.16
828 831 3.472652 ACTTGCGTGATAAACCAACTGA 58.527 40.909 0.00 0.00 0.00 3.41
829 832 3.498397 ACTTGCGTGATAAACCAACTGAG 59.502 43.478 0.00 0.00 0.00 3.35
830 833 1.804151 TGCGTGATAAACCAACTGAGC 59.196 47.619 0.00 0.00 0.00 4.26
831 834 1.130561 GCGTGATAAACCAACTGAGCC 59.869 52.381 0.00 0.00 0.00 4.70
832 835 2.422597 CGTGATAAACCAACTGAGCCA 58.577 47.619 0.00 0.00 0.00 4.75
833 836 2.811431 CGTGATAAACCAACTGAGCCAA 59.189 45.455 0.00 0.00 0.00 4.52
834 837 3.364964 CGTGATAAACCAACTGAGCCAAC 60.365 47.826 0.00 0.00 0.00 3.77
835 838 3.821033 GTGATAAACCAACTGAGCCAACT 59.179 43.478 0.00 0.00 0.00 3.16
836 839 5.001232 GTGATAAACCAACTGAGCCAACTA 58.999 41.667 0.00 0.00 0.00 2.24
837 840 5.472137 GTGATAAACCAACTGAGCCAACTAA 59.528 40.000 0.00 0.00 0.00 2.24
838 841 5.472137 TGATAAACCAACTGAGCCAACTAAC 59.528 40.000 0.00 0.00 0.00 2.34
839 842 1.878953 ACCAACTGAGCCAACTAACG 58.121 50.000 0.00 0.00 0.00 3.18
840 843 1.414919 ACCAACTGAGCCAACTAACGA 59.585 47.619 0.00 0.00 0.00 3.85
841 844 2.038557 ACCAACTGAGCCAACTAACGAT 59.961 45.455 0.00 0.00 0.00 3.73
842 845 3.074412 CCAACTGAGCCAACTAACGATT 58.926 45.455 0.00 0.00 0.00 3.34
843 846 3.120199 CCAACTGAGCCAACTAACGATTG 60.120 47.826 0.00 0.00 0.00 2.67
844 847 3.402628 ACTGAGCCAACTAACGATTGT 57.597 42.857 0.00 0.00 0.00 2.71
845 848 3.067106 ACTGAGCCAACTAACGATTGTG 58.933 45.455 0.00 0.00 0.00 3.33
846 849 3.067106 CTGAGCCAACTAACGATTGTGT 58.933 45.455 0.00 0.00 0.00 3.72
847 850 4.242475 CTGAGCCAACTAACGATTGTGTA 58.758 43.478 0.00 0.00 0.00 2.90
848 851 4.242475 TGAGCCAACTAACGATTGTGTAG 58.758 43.478 0.00 0.00 0.00 2.74
849 852 3.596214 AGCCAACTAACGATTGTGTAGG 58.404 45.455 0.00 0.00 0.00 3.18
850 853 2.676342 GCCAACTAACGATTGTGTAGGG 59.324 50.000 0.00 0.00 0.00 3.53
851 854 3.618019 GCCAACTAACGATTGTGTAGGGA 60.618 47.826 0.00 0.00 0.00 4.20
852 855 4.181578 CCAACTAACGATTGTGTAGGGAG 58.818 47.826 0.00 0.00 0.00 4.30
853 856 3.521947 ACTAACGATTGTGTAGGGAGC 57.478 47.619 0.00 0.00 0.00 4.70
854 857 2.167900 ACTAACGATTGTGTAGGGAGCC 59.832 50.000 0.00 0.00 0.00 4.70
855 858 0.108329 AACGATTGTGTAGGGAGCCG 60.108 55.000 0.00 0.00 0.00 5.52
856 859 1.883084 CGATTGTGTAGGGAGCCGC 60.883 63.158 0.00 0.00 0.00 6.53
857 860 1.522569 GATTGTGTAGGGAGCCGCT 59.477 57.895 0.00 0.00 0.00 5.52
858 861 0.750850 GATTGTGTAGGGAGCCGCTA 59.249 55.000 0.00 0.00 0.00 4.26
859 862 1.344763 GATTGTGTAGGGAGCCGCTAT 59.655 52.381 0.00 0.00 31.86 2.97
860 863 0.750850 TTGTGTAGGGAGCCGCTATC 59.249 55.000 0.00 0.00 31.86 2.08
861 864 0.106167 TGTGTAGGGAGCCGCTATCT 60.106 55.000 0.00 0.00 31.86 1.98
871 874 0.542232 GCCGCTATCTTCCCCTAGGA 60.542 60.000 11.48 0.00 41.88 2.94
880 883 2.917600 TCTTCCCCTAGGAGAAAAACCC 59.082 50.000 11.48 0.00 45.19 4.11
881 884 2.755019 TCCCCTAGGAGAAAAACCCT 57.245 50.000 11.48 0.00 37.19 4.34
902 905 0.909623 GGGTTTCCATCTCTTCCGGA 59.090 55.000 0.00 0.00 0.00 5.14
911 914 1.595466 TCTCTTCCGGAGATCTACGC 58.405 55.000 22.46 0.00 45.20 4.42
922 925 2.161030 AGATCTACGCCGGAATCTACC 58.839 52.381 5.05 0.00 0.00 3.18
927 930 1.734163 ACGCCGGAATCTACCTTTTG 58.266 50.000 5.05 0.00 0.00 2.44
966 969 2.423446 CCGGCTGCCATAGACTCC 59.577 66.667 20.29 0.00 29.52 3.85
977 980 1.448922 ATAGACTCCGCGCTGTCTCC 61.449 60.000 27.04 7.03 41.92 3.71
1037 1040 1.079405 CGCAGCGTAGGAAGGGAAA 60.079 57.895 6.65 0.00 0.00 3.13
1043 1046 3.108376 AGCGTAGGAAGGGAAAAGAGAT 58.892 45.455 0.00 0.00 0.00 2.75
1050 1053 0.543749 AGGGAAAAGAGATGGCGGAG 59.456 55.000 0.00 0.00 0.00 4.63
1053 1056 1.141858 GGAAAAGAGATGGCGGAGGAT 59.858 52.381 0.00 0.00 0.00 3.24
1056 1059 1.799933 AAGAGATGGCGGAGGATCTT 58.200 50.000 0.00 0.00 33.73 2.40
1117 1120 1.203013 TCGTCTGGGAGGAAGAGTTGA 60.203 52.381 0.00 0.00 0.00 3.18
1137 1140 1.064758 ACTGACAGTTTGGAACCTGCA 60.065 47.619 1.07 0.00 0.00 4.41
1362 1366 4.624843 GCGGTGATCATGGAGGAATATGAT 60.625 45.833 0.00 0.00 36.56 2.45
1365 1369 4.639310 GTGATCATGGAGGAATATGATGGC 59.361 45.833 0.00 0.00 34.28 4.40
1393 1397 6.702716 AAAACCCTGATTCGTTTAAACTCA 57.297 33.333 16.01 11.65 32.05 3.41
1428 1432 2.134287 GGCTCAGATCCACCGGCTA 61.134 63.158 0.00 0.00 0.00 3.93
1460 1464 4.572985 TTTTGATTGAACCAGCAGTGAG 57.427 40.909 0.00 0.00 0.00 3.51
1461 1465 2.189594 TGATTGAACCAGCAGTGAGG 57.810 50.000 0.00 0.00 0.00 3.86
1464 1468 1.059584 TTGAACCAGCAGTGAGGGGA 61.060 55.000 0.00 0.00 0.00 4.81
1485 1489 4.292178 GCCTCCAGGATCGGCGAG 62.292 72.222 17.22 0.43 37.39 5.03
1501 1505 2.067013 GCGAGGTGGAAGAAGTACAAC 58.933 52.381 0.00 0.00 0.00 3.32
1530 1534 1.614317 CCTGCAGGTTACTTTGGGGAG 60.614 57.143 25.53 0.00 0.00 4.30
1575 1579 7.445121 AGATAGATATCAACGCCAAGATCAAA 58.555 34.615 5.32 0.00 35.17 2.69
1587 1591 4.475944 CCAAGATCAAACATTTCGTCACC 58.524 43.478 0.00 0.00 0.00 4.02
1622 1626 6.179040 GGGATGAGAGGATCAAATATCAAGG 58.821 44.000 0.00 0.00 42.53 3.61
1653 1657 3.903090 AGAAGCTGCCTATCTTCTGCTAT 59.097 43.478 3.96 0.00 45.09 2.97
1686 1690 2.601240 TTGGTCATTGGCATGAGGAA 57.399 45.000 0.00 0.00 40.28 3.36
1700 1704 1.043816 GAGGAATGCGGAGATGGAGA 58.956 55.000 0.00 0.00 0.00 3.71
1766 1770 0.251341 AATGTTCGCTTCAGGCCCTT 60.251 50.000 0.00 0.00 37.74 3.95
1854 1858 4.142004 GGACGTGAACAGTATAACCCAGAT 60.142 45.833 0.00 0.00 0.00 2.90
1857 1861 4.439700 CGTGAACAGTATAACCCAGATCGT 60.440 45.833 0.00 0.00 0.00 3.73
1866 1870 2.659897 CCAGATCGTAGCTGGCGC 60.660 66.667 0.00 0.00 45.66 6.53
1893 1897 2.191128 CTCAGTAGCAGCAAAACCCT 57.809 50.000 0.00 0.00 0.00 4.34
1894 1898 3.334583 CTCAGTAGCAGCAAAACCCTA 57.665 47.619 0.00 0.00 0.00 3.53
1895 1899 3.265791 CTCAGTAGCAGCAAAACCCTAG 58.734 50.000 0.00 0.00 0.00 3.02
1896 1900 2.903784 TCAGTAGCAGCAAAACCCTAGA 59.096 45.455 0.00 0.00 0.00 2.43
1897 1901 3.326588 TCAGTAGCAGCAAAACCCTAGAA 59.673 43.478 0.00 0.00 0.00 2.10
1898 1902 4.072131 CAGTAGCAGCAAAACCCTAGAAA 58.928 43.478 0.00 0.00 0.00 2.52
1899 1903 4.154918 CAGTAGCAGCAAAACCCTAGAAAG 59.845 45.833 0.00 0.00 0.00 2.62
1900 1904 2.519013 AGCAGCAAAACCCTAGAAAGG 58.481 47.619 0.00 0.00 43.25 3.11
1936 1940 6.379703 TCAGAGAATACAGAGAAGGAGAAAGG 59.620 42.308 0.00 0.00 0.00 3.11
1937 1941 5.128663 AGAGAATACAGAGAAGGAGAAAGGC 59.871 44.000 0.00 0.00 0.00 4.35
1939 1943 1.343069 ACAGAGAAGGAGAAAGGCGT 58.657 50.000 0.00 0.00 0.00 5.68
1950 1954 0.459585 GAAAGGCGTGACTGCGGATA 60.460 55.000 0.00 0.00 35.06 2.59
1952 1956 1.605058 AAGGCGTGACTGCGGATAGT 61.605 55.000 0.00 0.00 35.06 2.12
1953 1957 0.750546 AGGCGTGACTGCGGATAGTA 60.751 55.000 0.00 0.00 35.06 1.82
1982 1986 0.687354 GGATGATGAGTACGGGGCAT 59.313 55.000 0.00 0.00 0.00 4.40
1989 1993 1.676678 GAGTACGGGGCATGAGCAGA 61.677 60.000 0.00 0.00 44.61 4.26
2011 2015 6.521133 CAGATTCAGAACTCAAATAAACGCAC 59.479 38.462 0.00 0.00 0.00 5.34
2013 2017 4.130857 TCAGAACTCAAATAAACGCACCA 58.869 39.130 0.00 0.00 0.00 4.17
2021 2025 2.489938 ATAAACGCACCACTGTGGAT 57.510 45.000 32.30 14.25 40.96 3.41
2024 2028 2.489938 AACGCACCACTGTGGATAAT 57.510 45.000 32.30 12.50 40.96 1.28
2034 2038 5.369699 ACCACTGTGGATAATATGGCTAGTT 59.630 40.000 32.30 1.63 40.96 2.24
2036 2040 5.635280 CACTGTGGATAATATGGCTAGTTCG 59.365 44.000 0.00 0.00 0.00 3.95
2041 2045 6.874134 GTGGATAATATGGCTAGTTCGTCAAT 59.126 38.462 0.00 0.00 0.00 2.57
2042 2046 8.033038 GTGGATAATATGGCTAGTTCGTCAATA 58.967 37.037 0.00 0.00 0.00 1.90
2056 2060 2.095768 CGTCAATAAGCAACAGTGTGGG 60.096 50.000 0.00 0.00 0.00 4.61
2061 2065 2.282462 GCAACAGTGTGGGAGGGG 60.282 66.667 0.00 0.00 0.00 4.79
2090 2094 2.289382 TGACACTTTAGCGCTGATTCCA 60.289 45.455 22.90 6.41 0.00 3.53
2091 2095 2.742053 GACACTTTAGCGCTGATTCCAA 59.258 45.455 22.90 1.07 0.00 3.53
2092 2096 3.146066 ACACTTTAGCGCTGATTCCAAA 58.854 40.909 22.90 10.49 0.00 3.28
2144 2148 4.927267 TTATGTGTCACCAAGGAAGGAT 57.073 40.909 0.00 0.00 0.00 3.24
2145 2149 2.859165 TGTGTCACCAAGGAAGGATC 57.141 50.000 0.00 0.00 0.00 3.36
2181 2185 2.575921 AGGGATGGATGAGTCAGGAA 57.424 50.000 0.00 0.00 0.00 3.36
2182 2186 2.850833 AGGGATGGATGAGTCAGGAAA 58.149 47.619 0.00 0.00 0.00 3.13
2199 2203 1.407656 AAAGACGGTGGAGACAGGCA 61.408 55.000 0.00 0.00 44.46 4.75
2228 2232 3.243805 CCAACACCAATGAAGCACAATCA 60.244 43.478 0.00 0.00 0.00 2.57
2422 2426 1.859080 GCTGGTTCGATCGGTTATGAC 59.141 52.381 16.41 4.91 0.00 3.06
2437 2441 4.261322 GGTTATGACAATGGCTATGCTGTG 60.261 45.833 0.00 0.00 0.00 3.66
2570 2574 2.103771 AGTGATCCATGGAGAATGACGG 59.896 50.000 21.33 0.00 38.72 4.79
2573 2577 0.541392 TCCATGGAGAATGACGGTGG 59.459 55.000 11.44 0.00 38.72 4.61
2684 2689 5.587043 TGTATAGGCGATTTTAACAAGGTGG 59.413 40.000 0.00 0.00 0.00 4.61
2688 2693 3.004944 GGCGATTTTAACAAGGTGGTTCA 59.995 43.478 0.00 0.00 32.29 3.18
2839 2844 1.125633 TGGGAGGAAGTTATACCCGC 58.874 55.000 0.00 0.00 43.04 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.318648 AGACAAAGTCTATGCACAAAGTGAAA 59.681 34.615 0.58 0.00 41.51 2.69
3 4 5.822519 AGACAAAGTCTATGCACAAAGTGAA 59.177 36.000 0.58 0.00 41.51 3.18
5 6 5.679734 AGACAAAGTCTATGCACAAAGTG 57.320 39.130 0.00 0.00 41.51 3.16
6 7 5.934625 CCTAGACAAAGTCTATGCACAAAGT 59.065 40.000 7.28 0.00 43.08 2.66
7 8 5.352569 CCCTAGACAAAGTCTATGCACAAAG 59.647 44.000 7.28 0.00 43.08 2.77
8 9 5.245531 CCCTAGACAAAGTCTATGCACAAA 58.754 41.667 7.28 0.00 43.08 2.83
9 10 4.832248 CCCTAGACAAAGTCTATGCACAA 58.168 43.478 7.28 0.00 43.08 3.33
10 11 3.369471 GCCCTAGACAAAGTCTATGCACA 60.369 47.826 17.04 0.00 43.08 4.57
12 13 3.107601 AGCCCTAGACAAAGTCTATGCA 58.892 45.455 20.90 0.00 43.08 3.96
13 14 3.133003 TGAGCCCTAGACAAAGTCTATGC 59.867 47.826 15.38 15.38 43.08 3.14
14 15 5.295950 CATGAGCCCTAGACAAAGTCTATG 58.704 45.833 7.28 5.18 43.08 2.23
16 17 3.706594 CCATGAGCCCTAGACAAAGTCTA 59.293 47.826 6.70 6.70 41.51 2.59
18 19 2.420687 CCCATGAGCCCTAGACAAAGTC 60.421 54.545 0.00 0.00 0.00 3.01
19 20 1.561542 CCCATGAGCCCTAGACAAAGT 59.438 52.381 0.00 0.00 0.00 2.66
21 22 0.255890 GCCCATGAGCCCTAGACAAA 59.744 55.000 0.00 0.00 0.00 2.83
22 23 1.915228 GCCCATGAGCCCTAGACAA 59.085 57.895 0.00 0.00 0.00 3.18
23 24 3.647367 GCCCATGAGCCCTAGACA 58.353 61.111 0.00 0.00 0.00 3.41
32 33 3.550431 ATCGACCGGGCCCATGAG 61.550 66.667 24.92 10.45 0.00 2.90
33 34 3.860605 CATCGACCGGGCCCATGA 61.861 66.667 24.92 13.75 0.00 3.07
34 35 4.935495 CCATCGACCGGGCCCATG 62.935 72.222 24.92 17.19 0.00 3.66
95 96 2.636830 CTTCACCTCGATGATGCCTTT 58.363 47.619 0.00 0.00 0.00 3.11
118 119 3.056107 CGAAGGTATTGAGTGGAGTTGGA 60.056 47.826 0.00 0.00 0.00 3.53
205 206 0.610232 GTGCACCTCCAAGAATGCCT 60.610 55.000 5.22 0.00 37.26 4.75
330 332 0.543277 GAGTCCATGCTCCCACATCA 59.457 55.000 0.00 0.00 0.00 3.07
341 343 1.153489 CCTCCTGCACGAGTCCATG 60.153 63.158 11.15 0.00 0.00 3.66
421 423 5.760743 CGAGTCCATCTTCAGATCTGTACTA 59.239 44.000 21.92 7.34 31.21 1.82
429 431 1.137872 GCCACGAGTCCATCTTCAGAT 59.862 52.381 0.00 0.00 34.56 2.90
499 501 3.702048 GCACCTACCAGTCCGGCA 61.702 66.667 0.00 0.00 39.03 5.69
632 635 2.169832 AGCAACAACAGTCGCTACAT 57.830 45.000 0.00 0.00 31.60 2.29
642 645 1.588674 CCACCGTCTAAGCAACAACA 58.411 50.000 0.00 0.00 0.00 3.33
781 784 7.229106 TCACACAATGATCTTCAACTCAATTGA 59.771 33.333 8.12 8.12 37.75 2.57
782 785 7.325338 GTCACACAATGATCTTCAACTCAATTG 59.675 37.037 0.00 0.00 40.28 2.32
783 786 7.230108 AGTCACACAATGATCTTCAACTCAATT 59.770 33.333 0.00 0.00 40.28 2.32
784 787 6.713903 AGTCACACAATGATCTTCAACTCAAT 59.286 34.615 0.00 0.00 40.28 2.57
785 788 6.057533 AGTCACACAATGATCTTCAACTCAA 58.942 36.000 0.00 0.00 40.28 3.02
786 789 5.614308 AGTCACACAATGATCTTCAACTCA 58.386 37.500 0.00 0.00 40.28 3.41
787 790 6.369005 CAAGTCACACAATGATCTTCAACTC 58.631 40.000 0.00 0.00 40.28 3.01
788 791 5.278169 GCAAGTCACACAATGATCTTCAACT 60.278 40.000 0.00 0.00 40.28 3.16
789 792 4.913924 GCAAGTCACACAATGATCTTCAAC 59.086 41.667 0.00 0.00 40.28 3.18
790 793 4.319694 CGCAAGTCACACAATGATCTTCAA 60.320 41.667 0.00 0.00 40.28 2.69
791 794 3.187022 CGCAAGTCACACAATGATCTTCA 59.813 43.478 0.00 0.00 40.28 3.02
792 795 3.740590 CGCAAGTCACACAATGATCTTC 58.259 45.455 0.00 0.00 40.28 2.87
793 796 3.818961 CGCAAGTCACACAATGATCTT 57.181 42.857 0.00 0.00 40.28 2.40
809 812 2.225491 GCTCAGTTGGTTTATCACGCAA 59.775 45.455 0.00 0.00 0.00 4.85
810 813 1.804151 GCTCAGTTGGTTTATCACGCA 59.196 47.619 0.00 0.00 0.00 5.24
811 814 1.130561 GGCTCAGTTGGTTTATCACGC 59.869 52.381 0.00 0.00 0.00 5.34
812 815 2.422597 TGGCTCAGTTGGTTTATCACG 58.577 47.619 0.00 0.00 0.00 4.35
813 816 3.821033 AGTTGGCTCAGTTGGTTTATCAC 59.179 43.478 0.00 0.00 0.00 3.06
814 817 4.098914 AGTTGGCTCAGTTGGTTTATCA 57.901 40.909 0.00 0.00 0.00 2.15
815 818 5.390567 CGTTAGTTGGCTCAGTTGGTTTATC 60.391 44.000 0.00 0.00 0.00 1.75
816 819 4.454504 CGTTAGTTGGCTCAGTTGGTTTAT 59.545 41.667 0.00 0.00 0.00 1.40
817 820 3.810941 CGTTAGTTGGCTCAGTTGGTTTA 59.189 43.478 0.00 0.00 0.00 2.01
818 821 2.616842 CGTTAGTTGGCTCAGTTGGTTT 59.383 45.455 0.00 0.00 0.00 3.27
819 822 2.158871 TCGTTAGTTGGCTCAGTTGGTT 60.159 45.455 0.00 0.00 0.00 3.67
820 823 1.414919 TCGTTAGTTGGCTCAGTTGGT 59.585 47.619 0.00 0.00 0.00 3.67
821 824 2.163818 TCGTTAGTTGGCTCAGTTGG 57.836 50.000 0.00 0.00 0.00 3.77
822 825 3.498397 ACAATCGTTAGTTGGCTCAGTTG 59.502 43.478 0.00 0.00 0.00 3.16
823 826 3.498397 CACAATCGTTAGTTGGCTCAGTT 59.502 43.478 0.00 0.00 0.00 3.16
824 827 3.067106 CACAATCGTTAGTTGGCTCAGT 58.933 45.455 0.00 0.00 0.00 3.41
825 828 3.067106 ACACAATCGTTAGTTGGCTCAG 58.933 45.455 0.00 0.00 0.00 3.35
826 829 3.120321 ACACAATCGTTAGTTGGCTCA 57.880 42.857 0.00 0.00 0.00 4.26
827 830 3.617263 CCTACACAATCGTTAGTTGGCTC 59.383 47.826 0.00 0.00 0.00 4.70
828 831 3.596214 CCTACACAATCGTTAGTTGGCT 58.404 45.455 0.00 0.00 0.00 4.75
829 832 2.676342 CCCTACACAATCGTTAGTTGGC 59.324 50.000 0.00 0.00 0.00 4.52
830 833 4.181578 CTCCCTACACAATCGTTAGTTGG 58.818 47.826 0.00 0.00 0.00 3.77
831 834 3.617263 GCTCCCTACACAATCGTTAGTTG 59.383 47.826 0.00 0.00 0.00 3.16
832 835 3.369157 GGCTCCCTACACAATCGTTAGTT 60.369 47.826 0.00 0.00 0.00 2.24
833 836 2.167900 GGCTCCCTACACAATCGTTAGT 59.832 50.000 0.00 0.00 0.00 2.24
834 837 2.798499 CGGCTCCCTACACAATCGTTAG 60.798 54.545 0.00 0.00 0.00 2.34
835 838 1.135527 CGGCTCCCTACACAATCGTTA 59.864 52.381 0.00 0.00 0.00 3.18
836 839 0.108329 CGGCTCCCTACACAATCGTT 60.108 55.000 0.00 0.00 0.00 3.85
837 840 1.515954 CGGCTCCCTACACAATCGT 59.484 57.895 0.00 0.00 0.00 3.73
838 841 1.883084 GCGGCTCCCTACACAATCG 60.883 63.158 0.00 0.00 0.00 3.34
839 842 0.750850 TAGCGGCTCCCTACACAATC 59.249 55.000 5.39 0.00 0.00 2.67
840 843 1.344763 GATAGCGGCTCCCTACACAAT 59.655 52.381 5.39 0.00 0.00 2.71
841 844 0.750850 GATAGCGGCTCCCTACACAA 59.249 55.000 5.39 0.00 0.00 3.33
842 845 0.106167 AGATAGCGGCTCCCTACACA 60.106 55.000 5.39 0.00 0.00 3.72
843 846 1.000052 GAAGATAGCGGCTCCCTACAC 60.000 57.143 5.39 0.00 0.00 2.90
844 847 1.329256 GAAGATAGCGGCTCCCTACA 58.671 55.000 5.39 0.00 0.00 2.74
845 848 0.604073 GGAAGATAGCGGCTCCCTAC 59.396 60.000 5.39 0.00 0.00 3.18
846 849 0.542232 GGGAAGATAGCGGCTCCCTA 60.542 60.000 15.06 0.00 34.71 3.53
847 850 1.839296 GGGAAGATAGCGGCTCCCT 60.839 63.158 15.06 7.47 34.71 4.20
848 851 2.744377 GGGAAGATAGCGGCTCCC 59.256 66.667 5.39 7.19 0.00 4.30
849 852 0.542232 TAGGGGAAGATAGCGGCTCC 60.542 60.000 5.39 0.30 0.00 4.70
850 853 0.892063 CTAGGGGAAGATAGCGGCTC 59.108 60.000 5.39 0.00 0.00 4.70
851 854 0.543174 CCTAGGGGAAGATAGCGGCT 60.543 60.000 7.98 7.98 33.58 5.52
852 855 0.542232 TCCTAGGGGAAGATAGCGGC 60.542 60.000 9.46 0.00 38.93 6.53
853 856 1.075698 TCTCCTAGGGGAAGATAGCGG 59.924 57.143 9.61 0.00 41.69 5.52
854 857 2.588464 TCTCCTAGGGGAAGATAGCG 57.412 55.000 9.61 0.00 41.69 4.26
855 858 5.369833 GTTTTTCTCCTAGGGGAAGATAGC 58.630 45.833 23.22 11.67 41.69 2.97
856 859 5.163184 GGGTTTTTCTCCTAGGGGAAGATAG 60.163 48.000 23.22 4.63 41.69 2.08
857 860 4.725304 GGGTTTTTCTCCTAGGGGAAGATA 59.275 45.833 23.22 7.18 41.69 1.98
858 861 3.528078 GGGTTTTTCTCCTAGGGGAAGAT 59.472 47.826 23.22 0.00 41.69 2.40
859 862 2.917600 GGGTTTTTCTCCTAGGGGAAGA 59.082 50.000 23.22 17.13 41.69 2.87
860 863 2.920271 AGGGTTTTTCTCCTAGGGGAAG 59.080 50.000 23.22 6.91 41.69 3.46
861 864 3.013984 AGGGTTTTTCTCCTAGGGGAA 57.986 47.619 20.80 20.80 41.69 3.97
880 883 2.103263 CCGGAAGAGATGGAAACCCTAG 59.897 54.545 0.00 0.00 0.00 3.02
881 884 2.116238 CCGGAAGAGATGGAAACCCTA 58.884 52.381 0.00 0.00 0.00 3.53
902 905 2.161030 GGTAGATTCCGGCGTAGATCT 58.839 52.381 17.04 17.04 0.00 2.75
911 914 1.389555 GGCCAAAAGGTAGATTCCGG 58.610 55.000 0.00 0.00 0.00 5.14
913 916 1.340697 ACGGGCCAAAAGGTAGATTCC 60.341 52.381 4.39 0.00 0.00 3.01
922 925 2.966309 GAGCACGACGGGCCAAAAG 61.966 63.158 20.44 0.00 0.00 2.27
959 962 2.113433 GGAGACAGCGCGGAGTCTA 61.113 63.158 25.53 0.00 44.61 2.59
991 994 3.209812 CTCCGTCATCCTCGGCGA 61.210 66.667 10.14 10.14 46.49 5.54
993 996 2.725008 CTCTCCGTCATCCTCGGC 59.275 66.667 0.00 0.00 46.49 5.54
1037 1040 1.691434 GAAGATCCTCCGCCATCTCTT 59.309 52.381 0.00 0.00 0.00 2.85
1043 1046 2.735772 GCCAGAAGATCCTCCGCCA 61.736 63.158 0.00 0.00 0.00 5.69
1050 1053 0.254178 TGAGCCTTGCCAGAAGATCC 59.746 55.000 0.00 0.00 0.00 3.36
1053 1056 0.767375 AAGTGAGCCTTGCCAGAAGA 59.233 50.000 0.00 0.00 30.18 2.87
1056 1059 1.174712 GCAAAGTGAGCCTTGCCAGA 61.175 55.000 0.00 0.00 32.32 3.86
1117 1120 1.064758 TGCAGGTTCCAAACTGTCAGT 60.065 47.619 0.00 0.00 37.07 3.41
1168 1171 1.365699 TTAGGGCTGAACGATTTCGC 58.634 50.000 0.00 0.00 44.43 4.70
1224 1227 2.283529 CCACACCACCGGTCTAGCT 61.284 63.158 2.59 0.00 31.02 3.32
1365 1369 9.524106 AGTTTAAACGAATCAGGGTTTTTAAAG 57.476 29.630 12.54 0.00 37.52 1.85
1393 1397 2.031674 GCCCAAACAGCCAGCTTGTT 62.032 55.000 0.00 0.00 0.00 2.83
1428 1432 5.106442 GGTTCAATCAAAAAGTTGTTCGGT 58.894 37.500 0.00 0.00 36.07 4.69
1431 1435 5.580297 TGCTGGTTCAATCAAAAAGTTGTTC 59.420 36.000 0.00 0.00 36.07 3.18
1437 1441 4.935702 TCACTGCTGGTTCAATCAAAAAG 58.064 39.130 0.00 0.00 0.00 2.27
1485 1489 5.007724 CAGTTTCAGTTGTACTTCTTCCACC 59.992 44.000 0.00 0.00 0.00 4.61
1501 1505 1.537202 GTAACCTGCAGGCAGTTTCAG 59.463 52.381 33.06 5.94 42.15 3.02
1530 1534 8.041323 TCTATCTTTATCTTCACCCTGACAAAC 58.959 37.037 0.00 0.00 0.00 2.93
1599 1603 6.777782 ACCTTGATATTTGATCCTCTCATCC 58.222 40.000 0.00 0.00 32.72 3.51
1622 1626 6.339587 AGATAGGCAGCTTCTCATACTTAC 57.660 41.667 0.00 0.00 0.00 2.34
1632 1636 2.618442 AGCAGAAGATAGGCAGCTTC 57.382 50.000 6.78 6.78 45.62 3.86
1653 1657 5.046014 CCAATGACCAAATTCCCCACAATTA 60.046 40.000 0.00 0.00 0.00 1.40
1686 1690 0.035036 CATGCTCTCCATCTCCGCAT 59.965 55.000 0.00 0.00 41.56 4.73
1700 1704 4.141981 ACTCGAAAGACATCTCATCATGCT 60.142 41.667 0.00 0.00 35.39 3.79
1878 1882 3.440522 CCTTTCTAGGGTTTTGCTGCTAC 59.559 47.826 0.00 0.00 37.94 3.58
1879 1883 3.329520 TCCTTTCTAGGGTTTTGCTGCTA 59.670 43.478 0.00 0.00 42.26 3.49
1908 1912 4.844884 TCCTTCTCTGTATTCTCTGACGA 58.155 43.478 0.00 0.00 0.00 4.20
1911 1915 6.379703 CCTTTCTCCTTCTCTGTATTCTCTGA 59.620 42.308 0.00 0.00 0.00 3.27
1919 1923 2.231478 CACGCCTTTCTCCTTCTCTGTA 59.769 50.000 0.00 0.00 0.00 2.74
1936 1940 0.928908 CGTACTATCCGCAGTCACGC 60.929 60.000 0.00 0.00 0.00 5.34
1937 1941 3.144300 CGTACTATCCGCAGTCACG 57.856 57.895 0.00 0.00 0.00 4.35
1950 1954 1.971357 CATCATCCCTTAGGGCGTACT 59.029 52.381 13.54 0.00 43.94 2.73
1952 1956 2.248248 CTCATCATCCCTTAGGGCGTA 58.752 52.381 13.54 0.00 43.94 4.42
1953 1957 1.051812 CTCATCATCCCTTAGGGCGT 58.948 55.000 13.54 0.18 43.94 5.68
1956 1960 2.563179 CCGTACTCATCATCCCTTAGGG 59.437 54.545 11.94 11.94 46.11 3.53
1959 1963 2.605257 CCCCGTACTCATCATCCCTTA 58.395 52.381 0.00 0.00 0.00 2.69
1961 1965 1.122019 GCCCCGTACTCATCATCCCT 61.122 60.000 0.00 0.00 0.00 4.20
1965 1969 1.345741 CTCATGCCCCGTACTCATCAT 59.654 52.381 0.00 0.00 0.00 2.45
1982 1986 7.360353 CGTTTATTTGAGTTCTGAATCTGCTCA 60.360 37.037 4.80 4.80 34.80 4.26
1989 1993 5.240623 TGGTGCGTTTATTTGAGTTCTGAAT 59.759 36.000 0.00 0.00 0.00 2.57
2011 2015 5.489792 ACTAGCCATATTATCCACAGTGG 57.510 43.478 14.19 14.19 39.43 4.00
2013 2017 5.304614 ACGAACTAGCCATATTATCCACAGT 59.695 40.000 0.00 0.00 0.00 3.55
2021 2025 7.438564 TGCTTATTGACGAACTAGCCATATTA 58.561 34.615 0.00 0.00 0.00 0.98
2024 2028 5.270893 TGCTTATTGACGAACTAGCCATA 57.729 39.130 0.00 0.00 0.00 2.74
2034 2038 2.805671 CCACACTGTTGCTTATTGACGA 59.194 45.455 0.00 0.00 0.00 4.20
2036 2040 3.146066 TCCCACACTGTTGCTTATTGAC 58.854 45.455 0.00 0.00 0.00 3.18
2041 2045 0.400213 CCCTCCCACACTGTTGCTTA 59.600 55.000 0.00 0.00 0.00 3.09
2042 2046 1.151450 CCCTCCCACACTGTTGCTT 59.849 57.895 0.00 0.00 0.00 3.91
2056 2060 2.692368 TGTCATCCTGGGCCCCTC 60.692 66.667 22.27 2.12 0.00 4.30
2061 2065 1.383523 GCTAAAGTGTCATCCTGGGC 58.616 55.000 0.00 0.00 0.00 5.36
2090 2094 1.704641 GGGGAACTTGAGGCTGTTTT 58.295 50.000 0.00 0.00 0.00 2.43
2091 2095 0.178961 GGGGGAACTTGAGGCTGTTT 60.179 55.000 0.00 0.00 0.00 2.83
2092 2096 1.068352 AGGGGGAACTTGAGGCTGTT 61.068 55.000 0.00 0.00 0.00 3.16
2100 2104 1.685820 GTGGGAGAGGGGGAACTTG 59.314 63.158 0.00 0.00 0.00 3.16
2144 2148 1.960689 CCTTTCTTTGGCCTTTTCCGA 59.039 47.619 3.32 0.00 0.00 4.55
2145 2149 1.000843 CCCTTTCTTTGGCCTTTTCCG 59.999 52.381 3.32 0.00 0.00 4.30
2181 2185 1.407656 TTGCCTGTCTCCACCGTCTT 61.408 55.000 0.00 0.00 0.00 3.01
2182 2186 1.407656 TTTGCCTGTCTCCACCGTCT 61.408 55.000 0.00 0.00 0.00 4.18
2199 2203 1.786937 TCATTGGTGTTGGTGGCTTT 58.213 45.000 0.00 0.00 0.00 3.51
2210 2214 2.602878 GCTGATTGTGCTTCATTGGTG 58.397 47.619 0.00 0.00 0.00 4.17
2228 2232 4.761058 TCCTCGAAGGAGCCCGCT 62.761 66.667 0.00 0.00 40.06 5.52
2261 2265 4.593206 ACAGTTCCAACTCAGGATACTCAA 59.407 41.667 0.00 0.00 41.33 3.02
2322 2326 2.727916 GCAAAATCCTTCGCGAAATCGT 60.728 45.455 23.54 5.98 42.22 3.73
2422 2426 3.801698 ACTACTCACAGCATAGCCATTG 58.198 45.455 0.00 0.00 0.00 2.82
2437 2441 4.082136 CCACCACTTCTACCTTGACTACTC 60.082 50.000 0.00 0.00 0.00 2.59
2570 2574 1.204146 TGAGCTTCCCCATAGACCAC 58.796 55.000 0.00 0.00 0.00 4.16
2573 2577 3.350219 TGTTTGAGCTTCCCCATAGAC 57.650 47.619 0.00 0.00 0.00 2.59
2688 2693 0.902531 ACCTTCATGTTCGTCCGGAT 59.097 50.000 7.81 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.