Multiple sequence alignment - TraesCS1B01G417700

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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 TraesCS1B01G417700 chr1B 100.000 1972 0 0 685 2656 642049502 642047531 0.000000e+00 3642.0
1 TraesCS1B01G417700 chr1B 85.852 933 97 24 896 1801 264357070 264356146 0.000000e+00 959.0
2 TraesCS1B01G417700 chr1B 100.000 278 0 0 1 278 642050186 642049909 5.070000e-142 514.0
3 TraesCS1B01G417700 chr1B 89.655 174 16 2 2483 2654 264353865 264353692 1.240000e-53 220.0
4 TraesCS1B01G417700 chr1B 89.231 65 2 1 1800 1859 264355269 264355205 2.840000e-10 76.8
5 TraesCS1B01G417700 chr1D 89.874 1827 98 35 899 2656 465085341 465083533 0.000000e+00 2268.0
6 TraesCS1B01G417700 chr1D 86.069 926 95 21 896 1801 190778316 190777405 0.000000e+00 965.0
7 TraesCS1B01G417700 chr1A 85.637 926 98 19 896 1801 168579935 168579025 0.000000e+00 941.0
8 TraesCS1B01G417700 chr1A 88.571 70 2 2 1800 1864 168578333 168578265 2.190000e-11 80.5


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 TraesCS1B01G417700 chr1B 642047531 642050186 2655 True 2078.00 3642 100.000 1 2656 2 chr1B.!!$R2 2655
1 TraesCS1B01G417700 chr1B 264353692 264357070 3378 True 418.60 959 88.246 896 2654 3 chr1B.!!$R1 1758
2 TraesCS1B01G417700 chr1D 465083533 465085341 1808 True 2268.00 2268 89.874 899 2656 1 chr1D.!!$R2 1757
3 TraesCS1B01G417700 chr1D 190777405 190778316 911 True 965.00 965 86.069 896 1801 1 chr1D.!!$R1 905
4 TraesCS1B01G417700 chr1A 168578265 168579935 1670 True 510.75 941 87.104 896 1864 2 chr1A.!!$R1 968

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
743 744 0.038343 TGTAGGTTTACGGTGGCGAC 60.038 55.0 0.0 0.0 32.21 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 3647 0.603569 AGCACCACAGTAAGAGTCCG 59.396 55.0 0.0 0.0 0.0 4.79 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
19 20 2.279935 TTCCCTTGCTCCGCTAAAAA 57.720 45.000 0.00 0.00 0.00 1.94
45 46 5.975693 AAAGATTTATTTCTTGGTGCGGA 57.024 34.783 0.00 0.00 36.12 5.54
46 47 4.965119 AGATTTATTTCTTGGTGCGGAC 57.035 40.909 0.00 0.00 0.00 4.79
47 48 4.589908 AGATTTATTTCTTGGTGCGGACT 58.410 39.130 7.11 0.00 0.00 3.85
48 49 4.396166 AGATTTATTTCTTGGTGCGGACTG 59.604 41.667 7.11 0.00 0.00 3.51
49 50 1.448985 TATTTCTTGGTGCGGACTGC 58.551 50.000 7.11 0.00 46.70 4.40
61 62 4.500116 GACTGCGAGGCCCGTCTC 62.500 72.222 13.97 0.00 41.15 3.36
85 86 3.056458 CCGCAGGCCCGATGTATA 58.944 61.111 0.00 0.00 46.14 1.47
86 87 1.079819 CCGCAGGCCCGATGTATAG 60.080 63.158 0.00 0.00 46.14 1.31
87 88 1.738099 CGCAGGCCCGATGTATAGC 60.738 63.158 0.00 0.00 0.00 2.97
88 89 1.738099 GCAGGCCCGATGTATAGCG 60.738 63.158 0.00 0.00 35.03 4.26
94 95 4.148230 CGATGTATAGCGGGCGTC 57.852 61.111 0.00 0.00 30.81 5.19
95 96 1.796355 CGATGTATAGCGGGCGTCG 60.796 63.158 0.00 0.00 42.76 5.12
105 106 4.821589 GGGCGTCGCTGGAAGAGG 62.822 72.222 18.11 0.00 34.07 3.69
112 113 4.443266 GCTGGAAGAGGCGCTCGT 62.443 66.667 7.64 0.62 35.36 4.18
113 114 2.262915 CTGGAAGAGGCGCTCGTT 59.737 61.111 7.64 0.00 35.36 3.85
114 115 1.807573 CTGGAAGAGGCGCTCGTTC 60.808 63.158 7.64 7.48 35.36 3.95
115 116 2.881352 GGAAGAGGCGCTCGTTCG 60.881 66.667 7.64 0.00 35.36 3.95
116 117 2.881352 GAAGAGGCGCTCGTTCGG 60.881 66.667 7.64 0.00 35.36 4.30
125 126 4.137872 CTCGTTCGGCGCCCCTAA 62.138 66.667 23.46 10.37 41.07 2.69
126 127 3.652539 CTCGTTCGGCGCCCCTAAA 62.653 63.158 23.46 7.53 41.07 1.85
127 128 2.743149 CGTTCGGCGCCCCTAAAA 60.743 61.111 23.46 4.74 0.00 1.52
128 129 2.326589 CGTTCGGCGCCCCTAAAAA 61.327 57.895 23.46 2.77 0.00 1.94
146 147 4.494515 AAAAACACTCCTCCGGGC 57.505 55.556 0.00 0.00 0.00 6.13
147 148 1.844130 AAAAACACTCCTCCGGGCT 59.156 52.632 0.00 0.00 0.00 5.19
148 149 0.250770 AAAAACACTCCTCCGGGCTC 60.251 55.000 0.00 0.00 0.00 4.70
149 150 2.125766 AAAACACTCCTCCGGGCTCC 62.126 60.000 0.00 0.00 0.00 4.70
168 169 3.025619 GCAATTGCCTCCGATCGG 58.974 61.111 28.62 28.62 34.31 4.18
169 170 2.546494 GCAATTGCCTCCGATCGGG 61.546 63.158 32.79 22.45 33.38 5.14
170 171 1.893808 CAATTGCCTCCGATCGGGG 60.894 63.158 32.79 30.43 36.01 5.73
180 181 4.996434 GATCGGGGGCGGATGCTG 62.996 72.222 0.00 0.00 42.25 4.41
215 216 1.811679 GCAGTAGCTTGAGGCGACC 60.812 63.158 0.00 0.00 45.57 4.79
216 217 1.517257 CAGTAGCTTGAGGCGACCG 60.517 63.158 0.00 0.00 45.57 4.79
217 218 3.358076 AGTAGCTTGAGGCGACCGC 62.358 63.158 5.75 5.75 45.57 5.68
220 221 3.127533 GCTTGAGGCGACCGCATT 61.128 61.111 16.47 3.59 44.11 3.56
221 222 2.787249 CTTGAGGCGACCGCATTG 59.213 61.111 16.47 0.63 44.11 2.82
222 223 2.745884 TTGAGGCGACCGCATTGG 60.746 61.111 16.47 0.00 44.11 3.16
223 224 4.776322 TGAGGCGACCGCATTGGG 62.776 66.667 16.47 0.00 44.64 4.12
256 257 4.101448 CGGGGCTTGTGGGAGGAG 62.101 72.222 0.00 0.00 0.00 3.69
257 258 3.732849 GGGGCTTGTGGGAGGAGG 61.733 72.222 0.00 0.00 0.00 4.30
258 259 3.732849 GGGCTTGTGGGAGGAGGG 61.733 72.222 0.00 0.00 0.00 4.30
259 260 3.732849 GGCTTGTGGGAGGAGGGG 61.733 72.222 0.00 0.00 0.00 4.79
260 261 4.432741 GCTTGTGGGAGGAGGGGC 62.433 72.222 0.00 0.00 0.00 5.80
261 262 4.101448 CTTGTGGGAGGAGGGGCG 62.101 72.222 0.00 0.00 0.00 6.13
262 263 4.649705 TTGTGGGAGGAGGGGCGA 62.650 66.667 0.00 0.00 0.00 5.54
266 267 4.565850 GGGAGGAGGGGCGAGGAT 62.566 72.222 0.00 0.00 0.00 3.24
267 268 3.237741 GGAGGAGGGGCGAGGATG 61.238 72.222 0.00 0.00 0.00 3.51
268 269 2.123251 GAGGAGGGGCGAGGATGA 60.123 66.667 0.00 0.00 0.00 2.92
269 270 2.123077 AGGAGGGGCGAGGATGAG 60.123 66.667 0.00 0.00 0.00 2.90
270 271 3.237741 GGAGGGGCGAGGATGAGG 61.238 72.222 0.00 0.00 0.00 3.86
271 272 2.444895 GAGGGGCGAGGATGAGGT 60.445 66.667 0.00 0.00 0.00 3.85
272 273 2.765807 AGGGGCGAGGATGAGGTG 60.766 66.667 0.00 0.00 0.00 4.00
273 274 2.764128 GGGGCGAGGATGAGGTGA 60.764 66.667 0.00 0.00 0.00 4.02
274 275 2.801631 GGGGCGAGGATGAGGTGAG 61.802 68.421 0.00 0.00 0.00 3.51
275 276 2.801631 GGGCGAGGATGAGGTGAGG 61.802 68.421 0.00 0.00 0.00 3.86
276 277 2.801631 GGCGAGGATGAGGTGAGGG 61.802 68.421 0.00 0.00 0.00 4.30
277 278 2.801631 GCGAGGATGAGGTGAGGGG 61.802 68.421 0.00 0.00 0.00 4.79
701 702 4.278956 GTGAGGTGCCCGTTACAG 57.721 61.111 0.00 0.00 0.00 2.74
702 703 1.375523 GTGAGGTGCCCGTTACAGG 60.376 63.158 0.00 0.00 0.00 4.00
709 710 2.125269 CCCGTTACAGGGGAAGCG 60.125 66.667 4.71 0.00 46.04 4.68
710 711 2.125269 CCGTTACAGGGGAAGCGG 60.125 66.667 0.00 0.00 0.00 5.52
711 712 2.818274 CGTTACAGGGGAAGCGGC 60.818 66.667 0.00 0.00 0.00 6.53
712 713 2.818274 GTTACAGGGGAAGCGGCG 60.818 66.667 0.51 0.51 0.00 6.46
713 714 4.090588 TTACAGGGGAAGCGGCGG 62.091 66.667 9.78 0.00 0.00 6.13
733 734 2.125431 GCGCGGGCTGTAGGTTTA 60.125 61.111 18.33 0.00 35.83 2.01
734 735 2.458610 GCGCGGGCTGTAGGTTTAC 61.459 63.158 18.33 0.00 35.83 2.01
735 736 2.162754 CGCGGGCTGTAGGTTTACG 61.163 63.158 0.00 0.00 32.21 3.18
736 737 1.812507 GCGGGCTGTAGGTTTACGG 60.813 63.158 0.00 0.00 38.87 4.02
737 738 1.593265 CGGGCTGTAGGTTTACGGT 59.407 57.895 0.00 0.00 38.25 4.83
738 739 0.738412 CGGGCTGTAGGTTTACGGTG 60.738 60.000 0.00 0.00 38.25 4.94
739 740 0.392060 GGGCTGTAGGTTTACGGTGG 60.392 60.000 0.00 0.00 38.25 4.61
740 741 1.022982 GGCTGTAGGTTTACGGTGGC 61.023 60.000 0.00 0.00 38.25 5.01
741 742 1.356527 GCTGTAGGTTTACGGTGGCG 61.357 60.000 0.00 0.00 38.25 5.69
742 743 0.244450 CTGTAGGTTTACGGTGGCGA 59.756 55.000 0.00 0.00 32.51 5.54
743 744 0.038343 TGTAGGTTTACGGTGGCGAC 60.038 55.000 0.00 0.00 32.21 5.19
744 745 0.737367 GTAGGTTTACGGTGGCGACC 60.737 60.000 8.02 8.02 39.14 4.79
780 781 4.227134 CGCAGCGCTGGTAGGGAT 62.227 66.667 36.47 0.00 0.00 3.85
781 782 2.190578 GCAGCGCTGGTAGGGATT 59.809 61.111 36.47 0.00 0.00 3.01
782 783 1.452108 GCAGCGCTGGTAGGGATTT 60.452 57.895 36.47 0.00 0.00 2.17
783 784 1.032114 GCAGCGCTGGTAGGGATTTT 61.032 55.000 36.47 0.00 0.00 1.82
784 785 0.734889 CAGCGCTGGTAGGGATTTTG 59.265 55.000 29.88 0.00 0.00 2.44
785 786 0.394352 AGCGCTGGTAGGGATTTTGG 60.394 55.000 10.39 0.00 0.00 3.28
786 787 1.384222 GCGCTGGTAGGGATTTTGGG 61.384 60.000 0.00 0.00 0.00 4.12
787 788 0.254747 CGCTGGTAGGGATTTTGGGA 59.745 55.000 0.00 0.00 0.00 4.37
788 789 1.747206 CGCTGGTAGGGATTTTGGGAG 60.747 57.143 0.00 0.00 0.00 4.30
789 790 1.410224 GCTGGTAGGGATTTTGGGAGG 60.410 57.143 0.00 0.00 0.00 4.30
790 791 2.205342 CTGGTAGGGATTTTGGGAGGA 58.795 52.381 0.00 0.00 0.00 3.71
791 792 2.173569 CTGGTAGGGATTTTGGGAGGAG 59.826 54.545 0.00 0.00 0.00 3.69
792 793 1.495148 GGTAGGGATTTTGGGAGGAGG 59.505 57.143 0.00 0.00 0.00 4.30
793 794 1.495148 GTAGGGATTTTGGGAGGAGGG 59.505 57.143 0.00 0.00 0.00 4.30
794 795 0.926220 AGGGATTTTGGGAGGAGGGG 60.926 60.000 0.00 0.00 0.00 4.79
795 796 1.075970 GGATTTTGGGAGGAGGGGC 60.076 63.158 0.00 0.00 0.00 5.80
796 797 1.453928 GATTTTGGGAGGAGGGGCG 60.454 63.158 0.00 0.00 0.00 6.13
797 798 2.211468 GATTTTGGGAGGAGGGGCGT 62.211 60.000 0.00 0.00 0.00 5.68
798 799 2.499303 ATTTTGGGAGGAGGGGCGTG 62.499 60.000 0.00 0.00 0.00 5.34
836 837 3.610669 CGAGGAGCGGGATGGGAG 61.611 72.222 0.00 0.00 36.03 4.30
837 838 3.237741 GAGGAGCGGGATGGGAGG 61.238 72.222 0.00 0.00 0.00 4.30
838 839 4.888325 AGGAGCGGGATGGGAGGG 62.888 72.222 0.00 0.00 0.00 4.30
839 840 4.880426 GGAGCGGGATGGGAGGGA 62.880 72.222 0.00 0.00 0.00 4.20
840 841 3.237741 GAGCGGGATGGGAGGGAG 61.238 72.222 0.00 0.00 0.00 4.30
841 842 4.888325 AGCGGGATGGGAGGGAGG 62.888 72.222 0.00 0.00 0.00 4.30
846 847 4.880426 GATGGGAGGGAGGCGGGA 62.880 72.222 0.00 0.00 0.00 5.14
847 848 4.888325 ATGGGAGGGAGGCGGGAG 62.888 72.222 0.00 0.00 0.00 4.30
855 856 4.144727 GAGGCGGGAGAGGGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
856 857 4.150454 AGGCGGGAGAGGGGAGAG 62.150 72.222 0.00 0.00 0.00 3.20
859 860 3.430497 CGGGAGAGGGGAGAGGGA 61.430 72.222 0.00 0.00 0.00 4.20
860 861 2.612251 GGGAGAGGGGAGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
861 862 2.329399 GGGAGAGGGGAGAGGGAGT 61.329 68.421 0.00 0.00 0.00 3.85
862 863 1.075600 GGAGAGGGGAGAGGGAGTG 60.076 68.421 0.00 0.00 0.00 3.51
863 864 1.700985 GAGAGGGGAGAGGGAGTGT 59.299 63.158 0.00 0.00 0.00 3.55
864 865 0.686112 GAGAGGGGAGAGGGAGTGTG 60.686 65.000 0.00 0.00 0.00 3.82
865 866 1.079438 GAGGGGAGAGGGAGTGTGT 59.921 63.158 0.00 0.00 0.00 3.72
866 867 0.973496 GAGGGGAGAGGGAGTGTGTC 60.973 65.000 0.00 0.00 0.00 3.67
867 868 1.229209 GGGGAGAGGGAGTGTGTCA 60.229 63.158 0.00 0.00 0.00 3.58
868 869 1.261238 GGGGAGAGGGAGTGTGTCAG 61.261 65.000 0.00 0.00 0.00 3.51
869 870 0.251832 GGGAGAGGGAGTGTGTCAGA 60.252 60.000 0.00 0.00 0.00 3.27
870 871 1.633774 GGAGAGGGAGTGTGTCAGAA 58.366 55.000 0.00 0.00 0.00 3.02
871 872 1.971357 GGAGAGGGAGTGTGTCAGAAA 59.029 52.381 0.00 0.00 0.00 2.52
872 873 2.569404 GGAGAGGGAGTGTGTCAGAAAT 59.431 50.000 0.00 0.00 0.00 2.17
873 874 3.594134 GAGAGGGAGTGTGTCAGAAATG 58.406 50.000 0.00 0.00 0.00 2.32
874 875 2.304180 AGAGGGAGTGTGTCAGAAATGG 59.696 50.000 0.00 0.00 0.00 3.16
875 876 1.168714 GGGAGTGTGTCAGAAATGGC 58.831 55.000 0.00 0.00 0.00 4.40
876 877 1.271597 GGGAGTGTGTCAGAAATGGCT 60.272 52.381 0.00 0.00 0.00 4.75
877 878 2.079925 GGAGTGTGTCAGAAATGGCTC 58.920 52.381 0.00 0.00 0.00 4.70
878 879 2.079925 GAGTGTGTCAGAAATGGCTCC 58.920 52.381 0.00 0.00 0.00 4.70
879 880 1.421268 AGTGTGTCAGAAATGGCTCCA 59.579 47.619 0.00 0.00 0.00 3.86
880 881 1.537202 GTGTGTCAGAAATGGCTCCAC 59.463 52.381 0.00 0.00 0.00 4.02
881 882 1.421268 TGTGTCAGAAATGGCTCCACT 59.579 47.619 0.00 0.00 0.00 4.00
882 883 2.158623 TGTGTCAGAAATGGCTCCACTT 60.159 45.455 0.00 0.00 0.00 3.16
883 884 2.887152 GTGTCAGAAATGGCTCCACTTT 59.113 45.455 0.00 0.00 0.00 2.66
884 885 4.072131 GTGTCAGAAATGGCTCCACTTTA 58.928 43.478 0.00 0.00 0.00 1.85
885 886 4.154918 GTGTCAGAAATGGCTCCACTTTAG 59.845 45.833 0.00 0.00 0.00 1.85
886 887 4.041567 TGTCAGAAATGGCTCCACTTTAGA 59.958 41.667 0.00 0.00 0.00 2.10
887 888 4.633565 GTCAGAAATGGCTCCACTTTAGAG 59.366 45.833 0.00 0.00 0.00 2.43
888 889 3.944015 CAGAAATGGCTCCACTTTAGAGG 59.056 47.826 0.00 0.00 0.00 3.69
889 890 3.846588 AGAAATGGCTCCACTTTAGAGGA 59.153 43.478 0.00 0.00 33.74 3.71
890 891 4.289672 AGAAATGGCTCCACTTTAGAGGAA 59.710 41.667 0.00 0.00 34.44 3.36
891 892 4.870021 AATGGCTCCACTTTAGAGGAAT 57.130 40.909 0.00 0.00 34.44 3.01
892 893 3.634397 TGGCTCCACTTTAGAGGAATG 57.366 47.619 0.00 0.00 34.44 2.67
893 894 2.293170 GGCTCCACTTTAGAGGAATGC 58.707 52.381 0.00 0.00 34.44 3.56
894 895 2.293170 GCTCCACTTTAGAGGAATGCC 58.707 52.381 0.00 0.00 34.44 4.40
910 911 1.376037 GCCGCCTCTGTTGCTAACT 60.376 57.895 0.00 0.00 0.00 2.24
912 913 0.320771 CCGCCTCTGTTGCTAACTGT 60.321 55.000 0.00 0.00 0.00 3.55
918 919 3.632145 CCTCTGTTGCTAACTGTTGGTTT 59.368 43.478 2.69 0.00 39.17 3.27
923 924 2.303175 TGCTAACTGTTGGTTTGACCC 58.697 47.619 2.69 0.00 37.50 4.46
928 929 1.005450 ACTGTTGGTTTGACCCACTGT 59.995 47.619 7.68 7.68 39.89 3.55
929 930 2.099405 CTGTTGGTTTGACCCACTGTT 58.901 47.619 3.43 0.00 37.50 3.16
930 931 2.495669 CTGTTGGTTTGACCCACTGTTT 59.504 45.455 3.43 0.00 37.50 2.83
932 933 0.820871 TGGTTTGACCCACTGTTTGC 59.179 50.000 0.00 0.00 37.50 3.68
943 944 2.094286 CCACTGTTTGCAAGTGGTTTGA 60.094 45.455 22.77 0.00 45.74 2.69
949 950 6.128309 ACTGTTTGCAAGTGGTTTGAAAAATC 60.128 34.615 0.00 0.00 44.12 2.17
966 967 4.685169 AAATCCACAGTCGTATGCTTTG 57.315 40.909 0.00 0.00 0.00 2.77
997 999 9.248291 CTAACAAACTCACTTGCATTGTTAAAT 57.752 29.630 16.21 0.00 42.52 1.40
1005 1007 5.583061 CACTTGCATTGTTAAATCCATGCAT 59.417 36.000 6.51 0.00 43.32 3.96
1009 1011 9.478768 CTTGCATTGTTAAATCCATGCATTATA 57.521 29.630 6.51 0.00 43.32 0.98
1078 1082 3.561143 ACAGTGTTGCTTGGGTTCATAA 58.439 40.909 0.00 0.00 0.00 1.90
1081 1085 1.892474 TGTTGCTTGGGTTCATAAGGC 59.108 47.619 0.00 0.00 0.00 4.35
1089 1093 2.375174 TGGGTTCATAAGGCAGTCAAGT 59.625 45.455 0.00 0.00 0.00 3.16
1111 1115 9.099454 CAAGTACAATGAGTAAATCCCTAGTTC 57.901 37.037 0.00 0.00 33.72 3.01
1125 1129 5.338632 TCCCTAGTTCACTATGGAGAACAA 58.661 41.667 18.70 0.17 42.62 2.83
1161 1171 1.792949 ACTACAGCGAAAAGACTTGCG 59.207 47.619 6.41 6.41 36.58 4.85
1179 1189 1.950216 GCGGAATTCCTTGGAGATTCC 59.050 52.381 22.05 20.90 37.88 3.01
1223 1233 3.758554 CACTGCCAATATATAGTTGCCCC 59.241 47.826 4.07 0.00 0.00 5.80
1231 1241 6.169094 CAATATATAGTTGCCCCAGAGTCAG 58.831 44.000 0.00 0.00 0.00 3.51
1237 1247 1.561643 TGCCCCAGAGTCAGAAGTAG 58.438 55.000 0.00 0.00 0.00 2.57
1321 1339 3.650281 TTCAGCATCTGGGCAAAGATA 57.350 42.857 2.04 0.00 35.09 1.98
1340 1358 6.699242 AGATACCCTCATTCATGTGATGAT 57.301 37.500 12.62 4.32 39.39 2.45
1471 1500 4.072131 GGTGGCTGTTTTTGAGACAGATA 58.928 43.478 8.33 0.00 45.72 1.98
1498 1528 5.522460 GGTACTACTTTCATGCAAATCGCTA 59.478 40.000 0.00 0.00 43.06 4.26
1509 1539 4.257731 TGCAAATCGCTACTTTGGTATCA 58.742 39.130 0.00 0.00 43.06 2.15
1519 1549 2.890945 ACTTTGGTATCACCCAAACTGC 59.109 45.455 1.38 0.00 46.80 4.40
1534 1564 5.298276 CCCAAACTGCTCAACTTACTTACAA 59.702 40.000 0.00 0.00 0.00 2.41
1536 1566 6.857964 CCAAACTGCTCAACTTACTTACAATG 59.142 38.462 0.00 0.00 0.00 2.82
1540 1570 6.647067 ACTGCTCAACTTACTTACAATGTCTC 59.353 38.462 0.00 0.00 0.00 3.36
1541 1571 6.759272 TGCTCAACTTACTTACAATGTCTCT 58.241 36.000 0.00 0.00 0.00 3.10
1612 1643 2.554032 CAAAGTCTCCACGGAAGCAAAT 59.446 45.455 0.00 0.00 0.00 2.32
1669 1700 2.618709 GCGCCTAAGCTTGGTTATTCAT 59.381 45.455 9.86 0.00 36.60 2.57
1940 3556 1.062488 AGAGTGTGTTTCCCTGGCCT 61.062 55.000 3.32 0.00 0.00 5.19
1971 3587 2.802816 GCTTGTAAGTCCATATGCCGAG 59.197 50.000 0.00 0.00 0.00 4.63
2031 3647 2.332063 TGTTAGCTATTGCCTGCCTC 57.668 50.000 0.00 0.00 40.80 4.70
2054 3698 3.430929 GGACTCTTACTGTGGTGCTATGG 60.431 52.174 0.00 0.00 0.00 2.74
2278 3922 3.008157 TGGCCAATCAATGCTCATGTTTT 59.992 39.130 0.61 0.00 0.00 2.43
2351 4041 3.949113 GTGGGAATCGGCCTACATTTTTA 59.051 43.478 0.00 0.00 39.06 1.52
2433 4192 3.441496 TTTTCTTGCTTGCTCCAAGTG 57.559 42.857 6.80 0.00 42.77 3.16
2472 4231 1.317431 TGCATGGGCTGTTGCTGATC 61.317 55.000 0.00 0.00 41.91 2.92
2473 4232 1.317431 GCATGGGCTGTTGCTGATCA 61.317 55.000 0.00 0.00 39.59 2.92
2475 4234 1.067060 CATGGGCTGTTGCTGATCATG 59.933 52.381 0.00 0.00 39.59 3.07
2477 4236 1.180029 GGGCTGTTGCTGATCATGTT 58.820 50.000 0.00 0.00 39.59 2.71
2478 4237 1.133790 GGGCTGTTGCTGATCATGTTC 59.866 52.381 0.00 0.00 39.59 3.18
2479 4238 1.814394 GGCTGTTGCTGATCATGTTCA 59.186 47.619 6.32 6.32 39.59 3.18
2480 4239 2.229543 GGCTGTTGCTGATCATGTTCAA 59.770 45.455 7.82 0.00 39.59 2.69
2481 4240 3.240069 GCTGTTGCTGATCATGTTCAAC 58.760 45.455 16.62 16.62 37.94 3.18
2637 4418 6.920569 AACTAACTAGGGATGCAATTTACG 57.079 37.500 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.645003 GTCCGCACCAAGAAATAAATCTTTTT 59.355 34.615 0.00 0.00 37.56 1.94
22 23 6.015434 AGTCCGCACCAAGAAATAAATCTTTT 60.015 34.615 0.00 0.00 37.56 2.27
23 24 5.476945 AGTCCGCACCAAGAAATAAATCTTT 59.523 36.000 0.00 0.00 37.56 2.52
24 25 5.010282 AGTCCGCACCAAGAAATAAATCTT 58.990 37.500 0.00 0.00 40.23 2.40
25 26 4.396166 CAGTCCGCACCAAGAAATAAATCT 59.604 41.667 0.00 0.00 0.00 2.40
26 27 4.662145 CAGTCCGCACCAAGAAATAAATC 58.338 43.478 0.00 0.00 0.00 2.17
27 28 3.119495 GCAGTCCGCACCAAGAAATAAAT 60.119 43.478 0.00 0.00 41.79 1.40
28 29 2.227865 GCAGTCCGCACCAAGAAATAAA 59.772 45.455 0.00 0.00 41.79 1.40
29 30 1.810151 GCAGTCCGCACCAAGAAATAA 59.190 47.619 0.00 0.00 41.79 1.40
30 31 1.448985 GCAGTCCGCACCAAGAAATA 58.551 50.000 0.00 0.00 41.79 1.40
31 32 1.577328 CGCAGTCCGCACCAAGAAAT 61.577 55.000 0.00 0.00 42.60 2.17
32 33 2.250939 CGCAGTCCGCACCAAGAAA 61.251 57.895 0.00 0.00 42.60 2.52
33 34 2.664851 CGCAGTCCGCACCAAGAA 60.665 61.111 0.00 0.00 42.60 2.52
34 35 3.573772 CTCGCAGTCCGCACCAAGA 62.574 63.158 0.00 0.00 42.60 3.02
35 36 3.114616 CTCGCAGTCCGCACCAAG 61.115 66.667 0.00 0.00 42.60 3.61
36 37 4.680237 CCTCGCAGTCCGCACCAA 62.680 66.667 0.00 0.00 42.60 3.67
44 45 4.500116 GAGACGGGCCTCGCAGTC 62.500 72.222 12.78 9.83 43.89 3.51
67 68 2.507110 CTATACATCGGGCCTGCGGG 62.507 65.000 7.41 7.41 0.00 6.13
68 69 1.079819 CTATACATCGGGCCTGCGG 60.080 63.158 6.73 3.44 0.00 5.69
69 70 1.738099 GCTATACATCGGGCCTGCG 60.738 63.158 6.73 0.00 0.00 5.18
70 71 1.738099 CGCTATACATCGGGCCTGC 60.738 63.158 6.73 0.00 0.00 4.85
71 72 1.079819 CCGCTATACATCGGGCCTG 60.080 63.158 4.71 4.71 41.82 4.85
72 73 3.377656 CCGCTATACATCGGGCCT 58.622 61.111 0.84 0.00 41.82 5.19
76 77 1.443872 GACGCCCGCTATACATCGG 60.444 63.158 0.00 0.00 44.89 4.18
77 78 1.796355 CGACGCCCGCTATACATCG 60.796 63.158 0.00 0.00 0.00 3.84
78 79 4.148230 CGACGCCCGCTATACATC 57.852 61.111 0.00 0.00 0.00 3.06
88 89 4.821589 CCTCTTCCAGCGACGCCC 62.822 72.222 17.79 0.00 0.00 6.13
95 96 3.941657 AACGAGCGCCTCTTCCAGC 62.942 63.158 2.29 0.00 0.00 4.85
96 97 1.807573 GAACGAGCGCCTCTTCCAG 60.808 63.158 2.29 0.00 0.00 3.86
97 98 2.261671 GAACGAGCGCCTCTTCCA 59.738 61.111 2.29 0.00 0.00 3.53
98 99 2.881352 CGAACGAGCGCCTCTTCC 60.881 66.667 2.29 0.00 0.00 3.46
99 100 2.881352 CCGAACGAGCGCCTCTTC 60.881 66.667 2.29 0.62 0.00 2.87
111 112 3.670989 TTTTTAGGGGCGCCGAAC 58.329 55.556 22.54 13.58 0.00 3.95
151 152 2.546494 CCCGATCGGAGGCAATTGC 61.546 63.158 35.42 22.47 37.50 3.56
152 153 1.893808 CCCCGATCGGAGGCAATTG 60.894 63.158 35.42 15.32 37.50 2.32
153 154 2.510906 CCCCGATCGGAGGCAATT 59.489 61.111 35.42 0.00 37.50 2.32
154 155 3.560251 CCCCCGATCGGAGGCAAT 61.560 66.667 35.42 0.00 37.50 3.56
163 164 4.996434 CAGCATCCGCCCCCGATC 62.996 72.222 0.00 0.00 39.83 3.69
191 192 0.392193 CCTCAAGCTACTGCCTGTGG 60.392 60.000 0.00 0.00 37.75 4.17
192 193 1.023513 GCCTCAAGCTACTGCCTGTG 61.024 60.000 0.00 0.00 40.80 3.66
193 194 1.298014 GCCTCAAGCTACTGCCTGT 59.702 57.895 0.00 0.00 40.80 4.00
194 195 1.812922 CGCCTCAAGCTACTGCCTG 60.813 63.158 0.00 0.00 40.39 4.85
195 196 1.984570 TCGCCTCAAGCTACTGCCT 60.985 57.895 0.00 0.00 40.39 4.75
196 197 1.811679 GTCGCCTCAAGCTACTGCC 60.812 63.158 0.00 0.00 40.39 4.85
197 198 1.811679 GGTCGCCTCAAGCTACTGC 60.812 63.158 0.00 0.00 40.39 4.40
198 199 1.517257 CGGTCGCCTCAAGCTACTG 60.517 63.158 0.00 0.00 40.39 2.74
199 200 2.885861 CGGTCGCCTCAAGCTACT 59.114 61.111 0.00 0.00 40.39 2.57
200 201 2.886124 GCGGTCGCCTCAAGCTAC 60.886 66.667 3.73 0.00 40.39 3.58
201 202 2.238847 AATGCGGTCGCCTCAAGCTA 62.239 55.000 12.94 0.00 40.39 3.32
202 203 3.612247 AATGCGGTCGCCTCAAGCT 62.612 57.895 12.94 0.00 40.39 3.74
203 204 3.127533 AATGCGGTCGCCTCAAGC 61.128 61.111 12.94 0.00 41.09 4.01
204 205 2.753966 CCAATGCGGTCGCCTCAAG 61.754 63.158 12.94 0.00 41.09 3.02
205 206 2.745884 CCAATGCGGTCGCCTCAA 60.746 61.111 12.94 0.00 41.09 3.02
206 207 4.776322 CCCAATGCGGTCGCCTCA 62.776 66.667 12.94 0.00 41.09 3.86
239 240 4.101448 CTCCTCCCACAAGCCCCG 62.101 72.222 0.00 0.00 0.00 5.73
240 241 3.732849 CCTCCTCCCACAAGCCCC 61.733 72.222 0.00 0.00 0.00 5.80
241 242 3.732849 CCCTCCTCCCACAAGCCC 61.733 72.222 0.00 0.00 0.00 5.19
242 243 3.732849 CCCCTCCTCCCACAAGCC 61.733 72.222 0.00 0.00 0.00 4.35
243 244 4.432741 GCCCCTCCTCCCACAAGC 62.433 72.222 0.00 0.00 0.00 4.01
244 245 4.101448 CGCCCCTCCTCCCACAAG 62.101 72.222 0.00 0.00 0.00 3.16
245 246 4.649705 TCGCCCCTCCTCCCACAA 62.650 66.667 0.00 0.00 0.00 3.33
249 250 4.565850 ATCCTCGCCCCTCCTCCC 62.566 72.222 0.00 0.00 0.00 4.30
250 251 3.237741 CATCCTCGCCCCTCCTCC 61.238 72.222 0.00 0.00 0.00 4.30
251 252 2.123251 TCATCCTCGCCCCTCCTC 60.123 66.667 0.00 0.00 0.00 3.71
252 253 2.123077 CTCATCCTCGCCCCTCCT 60.123 66.667 0.00 0.00 0.00 3.69
253 254 3.237741 CCTCATCCTCGCCCCTCC 61.238 72.222 0.00 0.00 0.00 4.30
254 255 2.444895 ACCTCATCCTCGCCCCTC 60.445 66.667 0.00 0.00 0.00 4.30
255 256 2.765807 CACCTCATCCTCGCCCCT 60.766 66.667 0.00 0.00 0.00 4.79
256 257 2.764128 TCACCTCATCCTCGCCCC 60.764 66.667 0.00 0.00 0.00 5.80
257 258 2.801631 CCTCACCTCATCCTCGCCC 61.802 68.421 0.00 0.00 0.00 6.13
258 259 2.801631 CCCTCACCTCATCCTCGCC 61.802 68.421 0.00 0.00 0.00 5.54
259 260 2.801631 CCCCTCACCTCATCCTCGC 61.802 68.421 0.00 0.00 0.00 5.03
260 261 3.543537 CCCCTCACCTCATCCTCG 58.456 66.667 0.00 0.00 0.00 4.63
689 690 1.376812 CTTCCCCTGTAACGGGCAC 60.377 63.158 0.00 0.00 43.25 5.01
690 691 3.074281 CTTCCCCTGTAACGGGCA 58.926 61.111 0.00 0.00 43.25 5.36
691 692 2.437895 GCTTCCCCTGTAACGGGC 60.438 66.667 0.00 0.00 43.25 6.13
692 693 2.125269 CGCTTCCCCTGTAACGGG 60.125 66.667 0.00 0.00 44.27 5.28
693 694 2.125269 CCGCTTCCCCTGTAACGG 60.125 66.667 0.00 0.00 0.00 4.44
694 695 2.818274 GCCGCTTCCCCTGTAACG 60.818 66.667 0.00 0.00 0.00 3.18
695 696 2.818274 CGCCGCTTCCCCTGTAAC 60.818 66.667 0.00 0.00 0.00 2.50
696 697 4.090588 CCGCCGCTTCCCCTGTAA 62.091 66.667 0.00 0.00 0.00 2.41
716 717 2.125431 TAAACCTACAGCCCGCGC 60.125 61.111 0.00 0.00 0.00 6.86
717 718 2.162754 CGTAAACCTACAGCCCGCG 61.163 63.158 0.00 0.00 0.00 6.46
718 719 1.812507 CCGTAAACCTACAGCCCGC 60.813 63.158 0.00 0.00 0.00 6.13
719 720 0.738412 CACCGTAAACCTACAGCCCG 60.738 60.000 0.00 0.00 0.00 6.13
720 721 0.392060 CCACCGTAAACCTACAGCCC 60.392 60.000 0.00 0.00 0.00 5.19
721 722 1.022982 GCCACCGTAAACCTACAGCC 61.023 60.000 0.00 0.00 0.00 4.85
722 723 1.356527 CGCCACCGTAAACCTACAGC 61.357 60.000 0.00 0.00 0.00 4.40
723 724 0.244450 TCGCCACCGTAAACCTACAG 59.756 55.000 0.00 0.00 35.54 2.74
724 725 0.038343 GTCGCCACCGTAAACCTACA 60.038 55.000 0.00 0.00 35.54 2.74
725 726 0.737367 GGTCGCCACCGTAAACCTAC 60.737 60.000 0.00 0.00 35.54 3.18
726 727 1.591183 GGTCGCCACCGTAAACCTA 59.409 57.895 0.00 0.00 35.54 3.08
727 728 2.344872 GGTCGCCACCGTAAACCT 59.655 61.111 0.00 0.00 35.54 3.50
763 764 3.740128 AATCCCTACCAGCGCTGCG 62.740 63.158 31.96 25.19 0.00 5.18
764 765 1.032114 AAAATCCCTACCAGCGCTGC 61.032 55.000 31.96 0.00 0.00 5.25
765 766 0.734889 CAAAATCCCTACCAGCGCTG 59.265 55.000 30.52 30.52 0.00 5.18
766 767 0.394352 CCAAAATCCCTACCAGCGCT 60.394 55.000 2.64 2.64 0.00 5.92
767 768 1.384222 CCCAAAATCCCTACCAGCGC 61.384 60.000 0.00 0.00 0.00 5.92
768 769 0.254747 TCCCAAAATCCCTACCAGCG 59.745 55.000 0.00 0.00 0.00 5.18
769 770 1.410224 CCTCCCAAAATCCCTACCAGC 60.410 57.143 0.00 0.00 0.00 4.85
770 771 2.173569 CTCCTCCCAAAATCCCTACCAG 59.826 54.545 0.00 0.00 0.00 4.00
771 772 2.205342 CTCCTCCCAAAATCCCTACCA 58.795 52.381 0.00 0.00 0.00 3.25
772 773 1.495148 CCTCCTCCCAAAATCCCTACC 59.505 57.143 0.00 0.00 0.00 3.18
773 774 1.495148 CCCTCCTCCCAAAATCCCTAC 59.505 57.143 0.00 0.00 0.00 3.18
774 775 1.630894 CCCCTCCTCCCAAAATCCCTA 60.631 57.143 0.00 0.00 0.00 3.53
775 776 0.926220 CCCCTCCTCCCAAAATCCCT 60.926 60.000 0.00 0.00 0.00 4.20
776 777 1.620818 CCCCTCCTCCCAAAATCCC 59.379 63.158 0.00 0.00 0.00 3.85
777 778 1.075970 GCCCCTCCTCCCAAAATCC 60.076 63.158 0.00 0.00 0.00 3.01
778 779 1.453928 CGCCCCTCCTCCCAAAATC 60.454 63.158 0.00 0.00 0.00 2.17
779 780 2.238701 ACGCCCCTCCTCCCAAAAT 61.239 57.895 0.00 0.00 0.00 1.82
780 781 2.856988 ACGCCCCTCCTCCCAAAA 60.857 61.111 0.00 0.00 0.00 2.44
781 782 3.646715 CACGCCCCTCCTCCCAAA 61.647 66.667 0.00 0.00 0.00 3.28
819 820 3.610669 CTCCCATCCCGCTCCTCG 61.611 72.222 0.00 0.00 38.08 4.63
820 821 3.237741 CCTCCCATCCCGCTCCTC 61.238 72.222 0.00 0.00 0.00 3.71
821 822 4.888325 CCCTCCCATCCCGCTCCT 62.888 72.222 0.00 0.00 0.00 3.69
822 823 4.880426 TCCCTCCCATCCCGCTCC 62.880 72.222 0.00 0.00 0.00 4.70
823 824 3.237741 CTCCCTCCCATCCCGCTC 61.238 72.222 0.00 0.00 0.00 5.03
824 825 4.888325 CCTCCCTCCCATCCCGCT 62.888 72.222 0.00 0.00 0.00 5.52
829 830 4.880426 TCCCGCCTCCCTCCCATC 62.880 72.222 0.00 0.00 0.00 3.51
830 831 4.888325 CTCCCGCCTCCCTCCCAT 62.888 72.222 0.00 0.00 0.00 4.00
838 839 4.144727 TCTCCCCTCTCCCGCCTC 62.145 72.222 0.00 0.00 0.00 4.70
839 840 4.150454 CTCTCCCCTCTCCCGCCT 62.150 72.222 0.00 0.00 0.00 5.52
842 843 3.430497 TCCCTCTCCCCTCTCCCG 61.430 72.222 0.00 0.00 0.00 5.14
843 844 2.329399 ACTCCCTCTCCCCTCTCCC 61.329 68.421 0.00 0.00 0.00 4.30
844 845 1.075600 CACTCCCTCTCCCCTCTCC 60.076 68.421 0.00 0.00 0.00 3.71
845 846 0.686112 CACACTCCCTCTCCCCTCTC 60.686 65.000 0.00 0.00 0.00 3.20
846 847 1.390125 CACACTCCCTCTCCCCTCT 59.610 63.158 0.00 0.00 0.00 3.69
847 848 0.973496 GACACACTCCCTCTCCCCTC 60.973 65.000 0.00 0.00 0.00 4.30
848 849 1.079438 GACACACTCCCTCTCCCCT 59.921 63.158 0.00 0.00 0.00 4.79
849 850 1.229209 TGACACACTCCCTCTCCCC 60.229 63.158 0.00 0.00 0.00 4.81
850 851 0.251832 TCTGACACACTCCCTCTCCC 60.252 60.000 0.00 0.00 0.00 4.30
851 852 1.633774 TTCTGACACACTCCCTCTCC 58.366 55.000 0.00 0.00 0.00 3.71
852 853 3.594134 CATTTCTGACACACTCCCTCTC 58.406 50.000 0.00 0.00 0.00 3.20
853 854 2.304180 CCATTTCTGACACACTCCCTCT 59.696 50.000 0.00 0.00 0.00 3.69
854 855 2.704572 CCATTTCTGACACACTCCCTC 58.295 52.381 0.00 0.00 0.00 4.30
855 856 1.271597 GCCATTTCTGACACACTCCCT 60.272 52.381 0.00 0.00 0.00 4.20
856 857 1.168714 GCCATTTCTGACACACTCCC 58.831 55.000 0.00 0.00 0.00 4.30
857 858 2.079925 GAGCCATTTCTGACACACTCC 58.920 52.381 0.00 0.00 0.00 3.85
858 859 2.079925 GGAGCCATTTCTGACACACTC 58.920 52.381 0.00 0.00 0.00 3.51
859 860 1.421268 TGGAGCCATTTCTGACACACT 59.579 47.619 0.00 0.00 0.00 3.55
860 861 1.537202 GTGGAGCCATTTCTGACACAC 59.463 52.381 0.00 0.00 0.00 3.82
861 862 1.421268 AGTGGAGCCATTTCTGACACA 59.579 47.619 0.00 0.00 0.00 3.72
862 863 2.191128 AGTGGAGCCATTTCTGACAC 57.809 50.000 0.00 0.00 0.00 3.67
863 864 2.957402 AAGTGGAGCCATTTCTGACA 57.043 45.000 0.00 0.00 0.00 3.58
864 865 4.579869 TCTAAAGTGGAGCCATTTCTGAC 58.420 43.478 0.00 0.00 0.00 3.51
865 866 4.323792 CCTCTAAAGTGGAGCCATTTCTGA 60.324 45.833 0.00 0.12 0.00 3.27
866 867 3.944015 CCTCTAAAGTGGAGCCATTTCTG 59.056 47.826 0.00 0.00 0.00 3.02
867 868 3.846588 TCCTCTAAAGTGGAGCCATTTCT 59.153 43.478 0.00 0.00 33.24 2.52
868 869 4.222124 TCCTCTAAAGTGGAGCCATTTC 57.778 45.455 0.00 0.00 33.24 2.17
869 870 4.657814 TTCCTCTAAAGTGGAGCCATTT 57.342 40.909 1.41 0.00 38.72 2.32
870 871 4.530875 CATTCCTCTAAAGTGGAGCCATT 58.469 43.478 1.41 0.00 38.72 3.16
871 872 3.686691 GCATTCCTCTAAAGTGGAGCCAT 60.687 47.826 1.41 0.00 38.72 4.40
872 873 2.356125 GCATTCCTCTAAAGTGGAGCCA 60.356 50.000 1.41 0.00 38.72 4.75
873 874 2.293170 GCATTCCTCTAAAGTGGAGCC 58.707 52.381 1.41 0.00 38.72 4.70
874 875 2.293170 GGCATTCCTCTAAAGTGGAGC 58.707 52.381 1.41 3.15 38.72 4.70
875 876 2.555199 CGGCATTCCTCTAAAGTGGAG 58.445 52.381 1.41 0.00 38.72 3.86
876 877 1.406887 GCGGCATTCCTCTAAAGTGGA 60.407 52.381 0.00 0.00 36.07 4.02
877 878 1.017387 GCGGCATTCCTCTAAAGTGG 58.983 55.000 0.00 0.00 0.00 4.00
878 879 1.017387 GGCGGCATTCCTCTAAAGTG 58.983 55.000 3.07 0.00 0.00 3.16
879 880 0.912486 AGGCGGCATTCCTCTAAAGT 59.088 50.000 13.08 0.00 0.00 2.66
880 881 1.587547 GAGGCGGCATTCCTCTAAAG 58.412 55.000 13.08 0.00 45.13 1.85
881 882 3.780624 GAGGCGGCATTCCTCTAAA 57.219 52.632 13.08 0.00 45.13 1.85
886 887 1.377725 CAACAGAGGCGGCATTCCT 60.378 57.895 13.08 0.00 36.46 3.36
887 888 3.056313 GCAACAGAGGCGGCATTCC 62.056 63.158 13.08 0.00 0.00 3.01
888 889 0.744414 TAGCAACAGAGGCGGCATTC 60.744 55.000 13.08 0.00 36.08 2.67
889 890 0.322456 TTAGCAACAGAGGCGGCATT 60.322 50.000 13.08 0.00 36.08 3.56
890 891 1.026718 GTTAGCAACAGAGGCGGCAT 61.027 55.000 13.08 0.00 36.08 4.40
891 892 1.671054 GTTAGCAACAGAGGCGGCA 60.671 57.895 13.08 0.00 36.08 5.69
892 893 1.376037 AGTTAGCAACAGAGGCGGC 60.376 57.895 0.00 0.00 36.08 6.53
893 894 0.320771 ACAGTTAGCAACAGAGGCGG 60.321 55.000 0.00 0.00 36.08 6.13
894 895 1.195448 CAACAGTTAGCAACAGAGGCG 59.805 52.381 0.00 0.00 36.08 5.52
910 911 2.223803 AACAGTGGGTCAAACCAACA 57.776 45.000 6.43 0.00 44.92 3.33
912 913 1.205893 GCAAACAGTGGGTCAAACCAA 59.794 47.619 0.00 0.00 43.34 3.67
918 919 1.102154 CACTTGCAAACAGTGGGTCA 58.898 50.000 8.84 0.00 0.00 4.02
923 924 3.229276 TCAAACCACTTGCAAACAGTG 57.771 42.857 9.63 9.63 34.76 3.66
928 929 5.248640 TGGATTTTTCAAACCACTTGCAAA 58.751 33.333 0.00 0.00 34.76 3.68
929 930 4.836825 TGGATTTTTCAAACCACTTGCAA 58.163 34.783 0.00 0.00 34.76 4.08
930 931 4.478206 TGGATTTTTCAAACCACTTGCA 57.522 36.364 0.00 0.00 34.76 4.08
943 944 5.240623 TCAAAGCATACGACTGTGGATTTTT 59.759 36.000 0.00 0.00 0.00 1.94
949 950 3.067106 ACTTCAAAGCATACGACTGTGG 58.933 45.455 0.00 0.00 0.00 4.17
954 955 6.462073 TTGTTAGACTTCAAAGCATACGAC 57.538 37.500 0.00 0.00 0.00 4.34
966 967 5.734855 TGCAAGTGAGTTTGTTAGACTTC 57.265 39.130 0.00 0.00 0.00 3.01
1009 1011 8.246180 CCTGCAACAGACAAATATTGTTAGATT 58.754 33.333 0.00 0.00 45.52 2.40
1078 1082 5.483685 TTACTCATTGTACTTGACTGCCT 57.516 39.130 0.00 0.00 0.00 4.75
1081 1085 7.106239 AGGGATTTACTCATTGTACTTGACTG 58.894 38.462 0.00 0.00 0.00 3.51
1089 1093 8.375493 AGTGAACTAGGGATTTACTCATTGTA 57.625 34.615 0.00 0.00 0.00 2.41
1111 1115 6.605849 CACATGACTTTTGTTCTCCATAGTG 58.394 40.000 0.00 0.00 0.00 2.74
1149 1159 4.229876 CAAGGAATTCCGCAAGTCTTTTC 58.770 43.478 18.82 0.00 42.08 2.29
1179 1189 4.278170 TGCAGTCCTTTGTCTTTAACCATG 59.722 41.667 0.00 0.00 0.00 3.66
1223 1233 5.941058 TCTTCAGTACCTACTTCTGACTCTG 59.059 44.000 0.00 0.00 37.84 3.35
1254 1270 9.467796 AATATAAGAATTTATAAGCTCTGGGGC 57.532 33.333 0.00 0.00 35.84 5.80
1287 1303 4.718276 AGATGCTGAAAGGGCCATAATTTT 59.282 37.500 6.18 0.00 0.00 1.82
1296 1312 3.930504 CCCAGATGCTGAAAGGGC 58.069 61.111 0.00 0.00 32.44 5.19
1321 1339 7.982252 ACTATTATCATCACATGAATGAGGGT 58.018 34.615 16.64 5.60 43.50 4.34
1350 1368 9.750125 GATTCAAATGGGTCAAAATTATAGGAC 57.250 33.333 0.00 0.00 0.00 3.85
1363 1386 9.019764 CATTAAATACAACGATTCAAATGGGTC 57.980 33.333 0.00 0.00 0.00 4.46
1365 1388 8.806634 CACATTAAATACAACGATTCAAATGGG 58.193 33.333 0.00 0.00 32.06 4.00
1406 1429 4.218312 GGCCTACATGATTTGGGAAAGAT 58.782 43.478 0.00 0.00 0.00 2.40
1471 1500 5.351465 CGATTTGCATGAAAGTAGTACCAGT 59.649 40.000 0.00 0.00 0.00 4.00
1509 1539 3.577805 AGTAAGTTGAGCAGTTTGGGT 57.422 42.857 0.00 0.00 0.00 4.51
1534 1564 8.311395 TGTCAAATACAAGGATAGAGAGACAT 57.689 34.615 0.00 0.00 34.29 3.06
1536 1566 8.001881 TCTGTCAAATACAAGGATAGAGAGAC 57.998 38.462 0.00 0.00 37.74 3.36
1541 1571 8.677300 GCAATTTCTGTCAAATACAAGGATAGA 58.323 33.333 0.00 0.00 37.74 1.98
1580 1611 1.269448 GGAGACTTTGCGCCATTTTCA 59.731 47.619 4.18 0.00 0.00 2.69
1669 1700 5.369404 TGCTCCAGGAATGGTTATGATCTTA 59.631 40.000 0.00 0.00 0.00 2.10
1781 1813 1.003696 GGAAGAACTCAGGGAACAGGG 59.996 57.143 0.00 0.00 0.00 4.45
1837 2760 0.990374 AGCCAGGAAAGTCTCTGCAT 59.010 50.000 0.00 0.00 0.00 3.96
1930 3546 1.004745 CTGAAGCTAAAGGCCAGGGAA 59.995 52.381 5.01 0.00 43.05 3.97
2031 3647 0.603569 AGCACCACAGTAAGAGTCCG 59.396 55.000 0.00 0.00 0.00 4.79
2054 3698 1.160137 CTGAAACCTGGTGCAGCTAC 58.840 55.000 18.08 3.01 0.00 3.58
2201 3845 7.286546 AGTCTCAATTGCATTAGTAGCTCTAGA 59.713 37.037 0.00 0.00 0.00 2.43
2278 3922 4.287067 AGCCAACCTGATAGAAACAGAAGA 59.713 41.667 0.00 0.00 37.54 2.87
2351 4041 8.655935 ATCTAAAGAGGGACAATTGTTTGAAT 57.344 30.769 13.36 0.00 36.64 2.57
2472 4231 6.371825 GGTAGAAAACTCTAGGGTTGAACATG 59.628 42.308 9.23 0.00 0.00 3.21
2473 4232 6.272558 AGGTAGAAAACTCTAGGGTTGAACAT 59.727 38.462 9.23 0.17 0.00 2.71
2475 4234 6.111669 AGGTAGAAAACTCTAGGGTTGAAC 57.888 41.667 9.23 5.13 0.00 3.18
2477 4236 7.511714 AGTTTAGGTAGAAAACTCTAGGGTTGA 59.488 37.037 9.23 0.00 42.09 3.18
2478 4237 7.677892 AGTTTAGGTAGAAAACTCTAGGGTTG 58.322 38.462 9.23 0.00 42.09 3.77
2479 4238 7.868792 AGTTTAGGTAGAAAACTCTAGGGTT 57.131 36.000 0.85 0.85 42.09 4.11


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

AutoCloner maintained by Alex Coulton.