Multiple sequence alignment - TraesCS6D01G091200

Loading Multiple Alignment...

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 TraesCS6D01G091200 chr6D 100.000 5179 0 0 1 5179 56920744 56915566 0.000000e+00 9564
1 TraesCS6D01G091200 chr6D 82.124 744 102 14 2 743 104144934 104144220 4.430000e-170 608
2 TraesCS6D01G091200 chr6D 82.845 682 102 11 7 679 382795118 382794443 9.600000e-167 597
3 TraesCS6D01G091200 chr6B 95.224 3497 138 14 969 4439 127615016 127611523 0.000000e+00 5505
4 TraesCS6D01G091200 chr6B 87.829 608 44 10 4580 5179 127610773 127610188 0.000000e+00 686
5 TraesCS6D01G091200 chr6A 93.544 2339 93 19 2420 4717 71545832 71543511 0.000000e+00 3430
6 TraesCS6D01G091200 chr6A 93.692 1300 66 10 981 2274 71548500 71547211 0.000000e+00 1932
7 TraesCS6D01G091200 chr6A 86.571 417 28 5 4768 5179 71543511 71543118 7.960000e-118 435
8 TraesCS6D01G091200 chr6A 76.500 600 98 24 177 760 298446866 298446294 2.360000e-73 287
9 TraesCS6D01G091200 chr6A 95.902 122 5 0 2308 2429 71547212 71547091 1.140000e-46 198
10 TraesCS6D01G091200 chr2B 83.528 771 109 13 2 758 107568053 107567287 0.000000e+00 704
11 TraesCS6D01G091200 chr2B 82.105 760 117 13 13 758 206761967 206761213 2.630000e-177 632
12 TraesCS6D01G091200 chr2B 81.507 146 23 4 610 754 782544823 782544681 3.280000e-22 117
13 TraesCS6D01G091200 chr4B 83.966 711 91 13 7 710 535300403 535301097 0.000000e+00 660
14 TraesCS6D01G091200 chr5D 83.590 713 101 8 2 707 414239156 414239859 0.000000e+00 654
15 TraesCS6D01G091200 chr2D 82.500 680 107 9 2 678 304267681 304268351 2.080000e-163 586
16 TraesCS6D01G091200 chr2D 81.752 685 115 7 2 678 88403889 88404571 9.740000e-157 564
17 TraesCS6D01G091200 chr4D 82.206 680 116 5 2 678 195014027 195014704 9.670000e-162 580
18 TraesCS6D01G091200 chr3B 78.921 797 136 21 2 772 12591613 12590823 3.580000e-141 512
19 TraesCS6D01G091200 chr3B 81.333 150 24 4 610 758 155627269 155627415 9.110000e-23 119
20 TraesCS6D01G091200 chr7D 89.024 164 16 2 771 933 506659989 506659827 8.790000e-48 202
21 TraesCS6D01G091200 chr7D 89.091 165 15 3 771 933 506668253 506668090 8.790000e-48 202
22 TraesCS6D01G091200 chr7D 81.333 150 18 9 610 754 209623756 209623612 4.240000e-21 113
23 TraesCS6D01G091200 chr7B 86.014 143 16 4 611 752 594329677 594329816 3.230000e-32 150


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 TraesCS6D01G091200 chr6D 56915566 56920744 5178 True 9564.00 9564 100.00000 1 5179 1 chr6D.!!$R1 5178
1 TraesCS6D01G091200 chr6D 104144220 104144934 714 True 608.00 608 82.12400 2 743 1 chr6D.!!$R2 741
2 TraesCS6D01G091200 chr6D 382794443 382795118 675 True 597.00 597 82.84500 7 679 1 chr6D.!!$R3 672
3 TraesCS6D01G091200 chr6B 127610188 127615016 4828 True 3095.50 5505 91.52650 969 5179 2 chr6B.!!$R1 4210
4 TraesCS6D01G091200 chr6A 71543118 71548500 5382 True 1498.75 3430 92.42725 981 5179 4 chr6A.!!$R2 4198
5 TraesCS6D01G091200 chr6A 298446294 298446866 572 True 287.00 287 76.50000 177 760 1 chr6A.!!$R1 583
6 TraesCS6D01G091200 chr2B 107567287 107568053 766 True 704.00 704 83.52800 2 758 1 chr2B.!!$R1 756
7 TraesCS6D01G091200 chr2B 206761213 206761967 754 True 632.00 632 82.10500 13 758 1 chr2B.!!$R2 745
8 TraesCS6D01G091200 chr4B 535300403 535301097 694 False 660.00 660 83.96600 7 710 1 chr4B.!!$F1 703
9 TraesCS6D01G091200 chr5D 414239156 414239859 703 False 654.00 654 83.59000 2 707 1 chr5D.!!$F1 705
10 TraesCS6D01G091200 chr2D 304267681 304268351 670 False 586.00 586 82.50000 2 678 1 chr2D.!!$F2 676
11 TraesCS6D01G091200 chr2D 88403889 88404571 682 False 564.00 564 81.75200 2 678 1 chr2D.!!$F1 676
12 TraesCS6D01G091200 chr4D 195014027 195014704 677 False 580.00 580 82.20600 2 678 1 chr4D.!!$F1 676
13 TraesCS6D01G091200 chr3B 12590823 12591613 790 True 512.00 512 78.92100 2 772 1 chr3B.!!$R1 770

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
835 907 0.687920 TCCAACGATAGCCCAACACA 59.312 50.000 0.00 0.00 42.67 3.72 F
1403 1475 0.174845 AATAGCGCGTCCTAGCACAA 59.825 50.000 8.43 0.00 36.85 3.33 F
2512 3859 1.680249 GGACCTTCATGAACAGGCTCC 60.680 57.143 12.58 13.59 32.79 4.70 F
3440 4799 2.495669 TGTTCAGTGTGGCGATGATAGA 59.504 45.455 0.00 0.00 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 3859 1.394917 CAGGGAAAACGCATTCGAGAG 59.605 52.381 0.00 0.0 39.41 3.20 R
2807 4164 2.226437 GTCATTGACAACCGAACATGCT 59.774 45.455 11.93 0.0 32.09 3.79 R
3682 5076 2.037641 CACATGTGAGAGAGGACAACCA 59.962 50.000 21.64 0.0 38.94 3.67 R
5137 7207 0.179029 ACTGAAAGGGTGGGTGAACG 60.179 55.000 0.00 0.0 39.30 3.95 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
108 109 2.184322 CTCCCATGACCGGTGTCG 59.816 66.667 14.63 0.00 44.86 4.35
172 181 1.604147 ATGGTGTGTCCGATGCTCGA 61.604 55.000 7.07 0.00 43.74 4.04
271 280 2.203070 CTAGCCCAGCGCCGAATT 60.203 61.111 2.29 0.00 38.78 2.17
287 296 2.795681 CGAATTCATGCGTCATTTGGGG 60.796 50.000 6.22 0.00 0.00 4.96
435 448 1.343478 ACGGATCTGGAGGTGAAGGAT 60.343 52.381 6.47 0.00 0.00 3.24
520 554 1.128188 GGGGAGTGGAGTGAAGTGGT 61.128 60.000 0.00 0.00 0.00 4.16
551 585 3.311110 GGCGAGCGGATGGGGATA 61.311 66.667 0.00 0.00 0.00 2.59
766 838 1.405526 GGTTTGAGGCGCTGTAGATGA 60.406 52.381 7.64 0.00 0.00 2.92
772 844 3.004839 TGAGGCGCTGTAGATGATCTAAC 59.995 47.826 7.64 0.03 29.58 2.34
773 845 2.297597 AGGCGCTGTAGATGATCTAACC 59.702 50.000 7.64 1.84 29.58 2.85
774 846 2.035961 GGCGCTGTAGATGATCTAACCA 59.964 50.000 7.64 0.00 29.58 3.67
775 847 3.053455 GCGCTGTAGATGATCTAACCAC 58.947 50.000 3.31 0.00 29.58 4.16
776 848 3.300857 CGCTGTAGATGATCTAACCACG 58.699 50.000 3.31 2.84 29.58 4.94
777 849 3.053455 GCTGTAGATGATCTAACCACGC 58.947 50.000 3.31 2.31 29.58 5.34
778 850 3.243569 GCTGTAGATGATCTAACCACGCT 60.244 47.826 3.31 0.00 29.58 5.07
779 851 4.023107 GCTGTAGATGATCTAACCACGCTA 60.023 45.833 3.31 0.00 29.58 4.26
780 852 5.690997 TGTAGATGATCTAACCACGCTAG 57.309 43.478 3.31 0.00 29.58 3.42
781 853 5.131067 TGTAGATGATCTAACCACGCTAGT 58.869 41.667 3.31 0.00 29.58 2.57
782 854 6.293698 TGTAGATGATCTAACCACGCTAGTA 58.706 40.000 3.31 0.00 29.58 1.82
783 855 5.692613 AGATGATCTAACCACGCTAGTAC 57.307 43.478 0.00 0.00 0.00 2.73
784 856 5.131067 AGATGATCTAACCACGCTAGTACA 58.869 41.667 0.00 0.00 0.00 2.90
785 857 5.593095 AGATGATCTAACCACGCTAGTACAA 59.407 40.000 0.00 0.00 0.00 2.41
786 858 5.244785 TGATCTAACCACGCTAGTACAAG 57.755 43.478 0.00 0.00 0.00 3.16
787 859 4.703575 TGATCTAACCACGCTAGTACAAGT 59.296 41.667 0.00 0.00 0.00 3.16
788 860 5.184479 TGATCTAACCACGCTAGTACAAGTT 59.816 40.000 0.00 0.00 0.00 2.66
789 861 5.051891 TCTAACCACGCTAGTACAAGTTC 57.948 43.478 0.00 0.00 0.00 3.01
790 862 3.738830 AACCACGCTAGTACAAGTTCA 57.261 42.857 0.00 0.00 0.00 3.18
791 863 3.022607 ACCACGCTAGTACAAGTTCAC 57.977 47.619 0.00 0.00 0.00 3.18
792 864 2.626743 ACCACGCTAGTACAAGTTCACT 59.373 45.455 0.00 0.00 0.00 3.41
793 865 3.243336 CCACGCTAGTACAAGTTCACTC 58.757 50.000 0.00 0.00 0.00 3.51
794 866 3.057456 CCACGCTAGTACAAGTTCACTCT 60.057 47.826 0.00 0.00 0.00 3.24
795 867 4.547532 CACGCTAGTACAAGTTCACTCTT 58.452 43.478 0.00 0.00 0.00 2.85
796 868 4.617645 CACGCTAGTACAAGTTCACTCTTC 59.382 45.833 0.00 0.00 0.00 2.87
797 869 4.519730 ACGCTAGTACAAGTTCACTCTTCT 59.480 41.667 0.00 0.00 0.00 2.85
798 870 5.009811 ACGCTAGTACAAGTTCACTCTTCTT 59.990 40.000 0.00 0.00 0.00 2.52
799 871 5.569823 CGCTAGTACAAGTTCACTCTTCTTC 59.430 44.000 0.00 0.00 0.00 2.87
800 872 5.865013 GCTAGTACAAGTTCACTCTTCTTCC 59.135 44.000 0.00 0.00 0.00 3.46
801 873 5.871396 AGTACAAGTTCACTCTTCTTCCA 57.129 39.130 0.00 0.00 0.00 3.53
802 874 6.235231 AGTACAAGTTCACTCTTCTTCCAA 57.765 37.500 0.00 0.00 0.00 3.53
803 875 6.650120 AGTACAAGTTCACTCTTCTTCCAAA 58.350 36.000 0.00 0.00 0.00 3.28
804 876 7.110155 AGTACAAGTTCACTCTTCTTCCAAAA 58.890 34.615 0.00 0.00 0.00 2.44
805 877 6.196079 ACAAGTTCACTCTTCTTCCAAAAC 57.804 37.500 0.00 0.00 0.00 2.43
806 878 5.710099 ACAAGTTCACTCTTCTTCCAAAACA 59.290 36.000 0.00 0.00 0.00 2.83
807 879 6.208599 ACAAGTTCACTCTTCTTCCAAAACAA 59.791 34.615 0.00 0.00 0.00 2.83
808 880 6.834168 AGTTCACTCTTCTTCCAAAACAAA 57.166 33.333 0.00 0.00 0.00 2.83
809 881 7.410120 AGTTCACTCTTCTTCCAAAACAAAT 57.590 32.000 0.00 0.00 0.00 2.32
810 882 8.519799 AGTTCACTCTTCTTCCAAAACAAATA 57.480 30.769 0.00 0.00 0.00 1.40
811 883 8.406297 AGTTCACTCTTCTTCCAAAACAAATAC 58.594 33.333 0.00 0.00 0.00 1.89
812 884 7.272037 TCACTCTTCTTCCAAAACAAATACC 57.728 36.000 0.00 0.00 0.00 2.73
813 885 6.017440 TCACTCTTCTTCCAAAACAAATACCG 60.017 38.462 0.00 0.00 0.00 4.02
814 886 5.826208 ACTCTTCTTCCAAAACAAATACCGT 59.174 36.000 0.00 0.00 0.00 4.83
815 887 6.017357 ACTCTTCTTCCAAAACAAATACCGTC 60.017 38.462 0.00 0.00 0.00 4.79
816 888 6.059484 TCTTCTTCCAAAACAAATACCGTCT 58.941 36.000 0.00 0.00 0.00 4.18
817 889 5.934935 TCTTCCAAAACAAATACCGTCTC 57.065 39.130 0.00 0.00 0.00 3.36
818 890 4.758165 TCTTCCAAAACAAATACCGTCTCC 59.242 41.667 0.00 0.00 0.00 3.71
819 891 4.088056 TCCAAAACAAATACCGTCTCCA 57.912 40.909 0.00 0.00 0.00 3.86
820 892 4.462133 TCCAAAACAAATACCGTCTCCAA 58.538 39.130 0.00 0.00 0.00 3.53
821 893 4.276431 TCCAAAACAAATACCGTCTCCAAC 59.724 41.667 0.00 0.00 0.00 3.77
832 904 1.653151 GTCTCCAACGATAGCCCAAC 58.347 55.000 0.00 0.00 42.67 3.77
833 905 1.066430 GTCTCCAACGATAGCCCAACA 60.066 52.381 0.00 0.00 42.67 3.33
834 906 1.066430 TCTCCAACGATAGCCCAACAC 60.066 52.381 0.00 0.00 42.67 3.32
835 907 0.687920 TCCAACGATAGCCCAACACA 59.312 50.000 0.00 0.00 42.67 3.72
836 908 1.072489 TCCAACGATAGCCCAACACAA 59.928 47.619 0.00 0.00 42.67 3.33
837 909 1.883275 CCAACGATAGCCCAACACAAA 59.117 47.619 0.00 0.00 42.67 2.83
838 910 2.294791 CCAACGATAGCCCAACACAAAA 59.705 45.455 0.00 0.00 42.67 2.44
839 911 3.056891 CCAACGATAGCCCAACACAAAAT 60.057 43.478 0.00 0.00 42.67 1.82
840 912 4.156922 CCAACGATAGCCCAACACAAAATA 59.843 41.667 0.00 0.00 42.67 1.40
841 913 4.957759 ACGATAGCCCAACACAAAATAC 57.042 40.909 0.00 0.00 42.67 1.89
842 914 3.372822 ACGATAGCCCAACACAAAATACG 59.627 43.478 0.00 0.00 42.67 3.06
843 915 3.619483 CGATAGCCCAACACAAAATACGA 59.381 43.478 0.00 0.00 0.00 3.43
844 916 4.093703 CGATAGCCCAACACAAAATACGAA 59.906 41.667 0.00 0.00 0.00 3.85
845 917 5.220777 CGATAGCCCAACACAAAATACGAAT 60.221 40.000 0.00 0.00 0.00 3.34
846 918 4.173036 AGCCCAACACAAAATACGAATG 57.827 40.909 0.00 0.00 0.00 2.67
847 919 3.823873 AGCCCAACACAAAATACGAATGA 59.176 39.130 0.00 0.00 0.00 2.57
848 920 4.279671 AGCCCAACACAAAATACGAATGAA 59.720 37.500 0.00 0.00 0.00 2.57
849 921 4.985409 GCCCAACACAAAATACGAATGAAA 59.015 37.500 0.00 0.00 0.00 2.69
850 922 5.463724 GCCCAACACAAAATACGAATGAAAA 59.536 36.000 0.00 0.00 0.00 2.29
851 923 6.018669 GCCCAACACAAAATACGAATGAAAAA 60.019 34.615 0.00 0.00 0.00 1.94
880 952 8.565416 ACCACTAAAAATAGTTAACACTCAAGC 58.435 33.333 8.61 0.00 34.06 4.01
881 953 8.021396 CCACTAAAAATAGTTAACACTCAAGCC 58.979 37.037 8.61 0.00 34.06 4.35
882 954 8.564574 CACTAAAAATAGTTAACACTCAAGCCA 58.435 33.333 8.61 0.00 34.06 4.75
883 955 9.127277 ACTAAAAATAGTTAACACTCAAGCCAA 57.873 29.630 8.61 0.00 34.06 4.52
884 956 9.394477 CTAAAAATAGTTAACACTCAAGCCAAC 57.606 33.333 8.61 0.00 34.06 3.77
885 957 5.959618 AATAGTTAACACTCAAGCCAACC 57.040 39.130 8.61 0.00 34.06 3.77
886 958 2.583143 AGTTAACACTCAAGCCAACCC 58.417 47.619 8.61 0.00 0.00 4.11
887 959 2.092103 AGTTAACACTCAAGCCAACCCA 60.092 45.455 8.61 0.00 0.00 4.51
888 960 2.691011 GTTAACACTCAAGCCAACCCAA 59.309 45.455 0.00 0.00 0.00 4.12
889 961 1.859302 AACACTCAAGCCAACCCAAA 58.141 45.000 0.00 0.00 0.00 3.28
890 962 2.086610 ACACTCAAGCCAACCCAAAT 57.913 45.000 0.00 0.00 0.00 2.32
891 963 3.237268 ACACTCAAGCCAACCCAAATA 57.763 42.857 0.00 0.00 0.00 1.40
892 964 3.571590 ACACTCAAGCCAACCCAAATAA 58.428 40.909 0.00 0.00 0.00 1.40
893 965 3.964031 ACACTCAAGCCAACCCAAATAAA 59.036 39.130 0.00 0.00 0.00 1.40
894 966 4.039124 ACACTCAAGCCAACCCAAATAAAG 59.961 41.667 0.00 0.00 0.00 1.85
895 967 4.039124 CACTCAAGCCAACCCAAATAAAGT 59.961 41.667 0.00 0.00 0.00 2.66
896 968 4.280929 ACTCAAGCCAACCCAAATAAAGTC 59.719 41.667 0.00 0.00 0.00 3.01
897 969 4.219115 TCAAGCCAACCCAAATAAAGTCA 58.781 39.130 0.00 0.00 0.00 3.41
898 970 4.651503 TCAAGCCAACCCAAATAAAGTCAA 59.348 37.500 0.00 0.00 0.00 3.18
899 971 5.129485 TCAAGCCAACCCAAATAAAGTCAAA 59.871 36.000 0.00 0.00 0.00 2.69
900 972 5.622346 AGCCAACCCAAATAAAGTCAAAA 57.378 34.783 0.00 0.00 0.00 2.44
901 973 6.186420 AGCCAACCCAAATAAAGTCAAAAT 57.814 33.333 0.00 0.00 0.00 1.82
902 974 5.997129 AGCCAACCCAAATAAAGTCAAAATG 59.003 36.000 0.00 0.00 0.00 2.32
903 975 5.994668 GCCAACCCAAATAAAGTCAAAATGA 59.005 36.000 0.00 0.00 0.00 2.57
904 976 6.484977 GCCAACCCAAATAAAGTCAAAATGAA 59.515 34.615 0.00 0.00 0.00 2.57
905 977 7.012799 GCCAACCCAAATAAAGTCAAAATGAAA 59.987 33.333 0.00 0.00 0.00 2.69
906 978 8.341903 CCAACCCAAATAAAGTCAAAATGAAAC 58.658 33.333 0.00 0.00 0.00 2.78
907 979 8.887717 CAACCCAAATAAAGTCAAAATGAAACA 58.112 29.630 0.00 0.00 0.00 2.83
908 980 9.454859 AACCCAAATAAAGTCAAAATGAAACAA 57.545 25.926 0.00 0.00 0.00 2.83
909 981 9.625747 ACCCAAATAAAGTCAAAATGAAACAAT 57.374 25.926 0.00 0.00 0.00 2.71
917 989 8.560576 AAGTCAAAATGAAACAATCAACTACG 57.439 30.769 0.00 0.00 42.54 3.51
918 990 7.925993 AGTCAAAATGAAACAATCAACTACGA 58.074 30.769 0.00 0.00 42.54 3.43
919 991 8.567948 AGTCAAAATGAAACAATCAACTACGAT 58.432 29.630 0.00 0.00 42.54 3.73
920 992 9.820229 GTCAAAATGAAACAATCAACTACGATA 57.180 29.630 0.00 0.00 42.54 2.92
923 995 9.620660 AAAATGAAACAATCAACTACGATAACC 57.379 29.630 0.00 0.00 42.54 2.85
924 996 8.561738 AATGAAACAATCAACTACGATAACCT 57.438 30.769 0.00 0.00 42.54 3.50
925 997 7.359262 TGAAACAATCAACTACGATAACCTG 57.641 36.000 0.00 0.00 34.30 4.00
926 998 5.796350 AACAATCAACTACGATAACCTGC 57.204 39.130 0.00 0.00 0.00 4.85
927 999 4.827692 ACAATCAACTACGATAACCTGCA 58.172 39.130 0.00 0.00 0.00 4.41
928 1000 5.242434 ACAATCAACTACGATAACCTGCAA 58.758 37.500 0.00 0.00 0.00 4.08
929 1001 5.351465 ACAATCAACTACGATAACCTGCAAG 59.649 40.000 0.00 0.00 0.00 4.01
930 1002 4.794278 TCAACTACGATAACCTGCAAGA 57.206 40.909 0.00 0.00 34.07 3.02
931 1003 4.744570 TCAACTACGATAACCTGCAAGAG 58.255 43.478 0.00 0.00 34.07 2.85
932 1004 4.461431 TCAACTACGATAACCTGCAAGAGA 59.539 41.667 0.00 0.00 34.07 3.10
933 1005 5.047590 TCAACTACGATAACCTGCAAGAGAA 60.048 40.000 0.00 0.00 34.07 2.87
934 1006 5.401531 ACTACGATAACCTGCAAGAGAAA 57.598 39.130 0.00 0.00 34.07 2.52
935 1007 5.790593 ACTACGATAACCTGCAAGAGAAAA 58.209 37.500 0.00 0.00 34.07 2.29
936 1008 6.228258 ACTACGATAACCTGCAAGAGAAAAA 58.772 36.000 0.00 0.00 34.07 1.94
955 1027 5.763876 AAAAACAGTAGCCTCTAGTCCAT 57.236 39.130 0.00 0.00 0.00 3.41
956 1028 5.346181 AAAACAGTAGCCTCTAGTCCATC 57.654 43.478 0.00 0.00 0.00 3.51
957 1029 2.952116 ACAGTAGCCTCTAGTCCATCC 58.048 52.381 0.00 0.00 0.00 3.51
958 1030 1.883275 CAGTAGCCTCTAGTCCATCCG 59.117 57.143 0.00 0.00 0.00 4.18
959 1031 1.775459 AGTAGCCTCTAGTCCATCCGA 59.225 52.381 0.00 0.00 0.00 4.55
960 1032 2.377193 AGTAGCCTCTAGTCCATCCGAT 59.623 50.000 0.00 0.00 0.00 4.18
961 1033 2.390225 AGCCTCTAGTCCATCCGATT 57.610 50.000 0.00 0.00 0.00 3.34
962 1034 2.683768 AGCCTCTAGTCCATCCGATTT 58.316 47.619 0.00 0.00 0.00 2.17
963 1035 2.630580 AGCCTCTAGTCCATCCGATTTC 59.369 50.000 0.00 0.00 0.00 2.17
964 1036 2.608261 GCCTCTAGTCCATCCGATTTCG 60.608 54.545 0.00 0.00 39.44 3.46
965 1037 2.608261 CCTCTAGTCCATCCGATTTCGC 60.608 54.545 0.00 0.00 38.18 4.70
966 1038 1.001706 TCTAGTCCATCCGATTTCGCG 60.002 52.381 0.00 0.00 38.18 5.87
967 1039 0.742505 TAGTCCATCCGATTTCGCGT 59.257 50.000 5.77 0.00 38.18 6.01
973 1045 2.365095 ATCCGATTTCGCGTCCCCTC 62.365 60.000 5.77 0.00 38.18 4.30
1378 1450 6.134061 GGATTTTATGCGAATAACCTTCGAC 58.866 40.000 11.20 3.81 43.97 4.20
1392 1464 0.248498 TTCGACTGGAGAATAGCGCG 60.248 55.000 0.00 0.00 0.00 6.86
1403 1475 0.174845 AATAGCGCGTCCTAGCACAA 59.825 50.000 8.43 0.00 36.85 3.33
1471 1543 9.632638 ACATCTGTAGCTGTTAATTCCATTATT 57.367 29.630 0.00 0.00 0.00 1.40
1496 1568 5.748402 TGAATCTGATTGAGCCATACTTGT 58.252 37.500 7.78 0.00 0.00 3.16
1498 1570 7.337938 TGAATCTGATTGAGCCATACTTGTTA 58.662 34.615 7.78 0.00 0.00 2.41
1537 1610 8.383175 TCTCACTTTCTATTTCATAGTTTGGGT 58.617 33.333 0.00 0.00 34.47 4.51
1538 1611 8.561738 TCACTTTCTATTTCATAGTTTGGGTC 57.438 34.615 0.00 0.00 34.47 4.46
1544 1620 4.365514 TTTCATAGTTTGGGTCTGCTGA 57.634 40.909 0.00 0.00 0.00 4.26
1546 1622 5.692115 TTCATAGTTTGGGTCTGCTGATA 57.308 39.130 0.00 0.00 0.00 2.15
1584 1662 8.585471 ATGTGATGATCATTTCTTTAACCTGT 57.415 30.769 10.14 0.00 0.00 4.00
1600 1678 8.934023 TTTAACCTGTTCTTATCACTTTGGAT 57.066 30.769 0.00 0.00 0.00 3.41
1617 1695 7.227512 CACTTTGGATATCTATGGTCAAGGTTC 59.772 40.741 2.05 0.00 0.00 3.62
1667 1745 4.380678 GGTTTTGTAAATTTCGCGTTCCTC 59.619 41.667 5.77 0.00 0.00 3.71
1909 1988 2.293399 CTGTTTTTCTTGTCCCTTCCGG 59.707 50.000 0.00 0.00 0.00 5.14
2077 2156 5.221303 CCAACATGTGGTTCAAATCAAGAGT 60.221 40.000 0.00 0.00 43.20 3.24
2087 2166 5.011090 TCAAATCAAGAGTCGTCCTATGG 57.989 43.478 0.00 0.00 0.00 2.74
2171 2250 3.519510 ACCTTGCCTCTCTAGTGCAATTA 59.480 43.478 0.00 0.00 43.38 1.40
2192 2271 9.282569 CAATTATTCTCCCTCTCTAATTCTTGG 57.717 37.037 0.00 0.00 0.00 3.61
2426 2505 4.836825 TCCAAGTCTTGAGCTTTATCCTG 58.163 43.478 14.42 0.00 0.00 3.86
2512 3859 1.680249 GGACCTTCATGAACAGGCTCC 60.680 57.143 12.58 13.59 32.79 4.70
2620 3974 6.165577 GGAAATTGCAGAGCTGGATTTAAAA 58.834 36.000 0.00 0.00 0.00 1.52
2934 4292 7.235079 TGAAAAATCCAAGTCCTGGTACATTA 58.765 34.615 0.00 0.00 46.51 1.90
2950 4308 7.425577 GGTACATTACCCGTGAATATTAACC 57.574 40.000 0.00 0.00 43.18 2.85
3294 4652 5.279657 GGTTCCAAATTTCTTTCTGCTGGAT 60.280 40.000 0.00 0.00 0.00 3.41
3376 4734 3.434739 GCAAGGTCCATGGATCTGAATCT 60.435 47.826 28.40 9.42 35.49 2.40
3411 4769 3.496160 GGATGGTGGTACTTGTCAGTGTT 60.496 47.826 0.00 0.00 34.06 3.32
3440 4799 2.495669 TGTTCAGTGTGGCGATGATAGA 59.504 45.455 0.00 0.00 0.00 1.98
3531 4914 8.149973 ACACCGTTATTTAATGTAGCCATAAG 57.850 34.615 0.00 0.00 0.00 1.73
3543 4926 5.674525 TGTAGCCATAAGAATCTGAACAGG 58.325 41.667 1.93 0.00 0.00 4.00
3638 5032 8.034313 TCTTAAGAAGTGATGCCCAGTTATAT 57.966 34.615 1.68 0.00 38.48 0.86
3682 5076 6.203915 TGCTGTTACATCGTCTTGTACAAATT 59.796 34.615 10.03 0.00 31.98 1.82
4180 5576 9.751542 CATAAAGATATCAGTTTCGAACTAGGT 57.248 33.333 5.32 0.00 40.46 3.08
4183 5579 6.972722 AGATATCAGTTTCGAACTAGGTAGC 58.027 40.000 5.32 0.00 40.46 3.58
4184 5580 6.546403 AGATATCAGTTTCGAACTAGGTAGCA 59.454 38.462 5.32 0.00 40.46 3.49
4241 5637 3.618150 GCACATGTAAAATTGATGGTGGC 59.382 43.478 0.00 0.00 0.00 5.01
4337 5733 2.012673 GATGTGATCCCTGTTGCTGAC 58.987 52.381 0.00 0.00 0.00 3.51
4345 5741 3.686016 TCCCTGTTGCTGACTATTTTCC 58.314 45.455 0.00 0.00 0.00 3.13
4387 5785 0.609957 TTGCCCATCAGAAGGTGCAG 60.610 55.000 7.59 0.00 35.04 4.41
4436 5834 6.694411 GCTGTAAGATTTTGATAGGCAATGTG 59.306 38.462 0.00 0.00 33.42 3.21
4498 6558 0.986019 ACCAACCACCTCACTCACCA 60.986 55.000 0.00 0.00 0.00 4.17
4535 6595 8.798975 ATATCTCCTTGTGGTCTAGGAATTAA 57.201 34.615 0.00 0.00 42.89 1.40
4559 6621 2.371841 TCCTATCAACCACTGCTTGTGT 59.628 45.455 9.00 0.00 44.81 3.72
4574 6636 4.223700 TGCTTGTGTCTCCATCTTGACTAT 59.776 41.667 0.00 0.00 34.57 2.12
4582 6644 4.892345 TCTCCATCTTGACTATCCTGTCAG 59.108 45.833 0.00 0.00 46.02 3.51
4640 6703 3.125520 CCTCTAGAGGGAGGTGAGC 57.874 63.158 28.68 0.00 45.65 4.26
4641 6704 0.821711 CCTCTAGAGGGAGGTGAGCG 60.822 65.000 28.68 1.06 45.65 5.03
4642 6705 0.106918 CTCTAGAGGGAGGTGAGCGT 60.107 60.000 12.27 0.00 0.00 5.07
4643 6706 0.394488 TCTAGAGGGAGGTGAGCGTG 60.394 60.000 0.00 0.00 0.00 5.34
4644 6707 0.681564 CTAGAGGGAGGTGAGCGTGT 60.682 60.000 0.00 0.00 0.00 4.49
4645 6708 0.622136 TAGAGGGAGGTGAGCGTGTA 59.378 55.000 0.00 0.00 0.00 2.90
4647 6710 1.668101 GAGGGAGGTGAGCGTGTAGG 61.668 65.000 0.00 0.00 0.00 3.18
4648 6711 2.184579 GGAGGTGAGCGTGTAGGC 59.815 66.667 0.00 0.00 0.00 3.93
4660 6723 2.899976 CGTGTAGGCCACAACATATGA 58.100 47.619 10.38 0.00 44.78 2.15
4717 6780 2.733956 TGGGTGTAATTGGCATCCTTC 58.266 47.619 13.14 0.00 37.96 3.46
4718 6781 2.042297 TGGGTGTAATTGGCATCCTTCA 59.958 45.455 13.14 0.00 37.96 3.02
4721 6785 2.689983 GTGTAATTGGCATCCTTCAGGG 59.310 50.000 0.00 0.00 35.41 4.45
4734 6798 1.471684 CTTCAGGGAGAAGCAATGTGC 59.528 52.381 0.00 0.00 46.54 4.57
4751 6815 4.019792 TGTGCAAGATATGTTCCACACT 57.980 40.909 5.29 0.00 28.52 3.55
4868 6933 6.611381 TGCTTTTGTCAGCATAGTATTTCAC 58.389 36.000 0.00 0.00 45.14 3.18
4878 6943 4.101741 GCATAGTATTTCACCCTCTCCTGT 59.898 45.833 0.00 0.00 0.00 4.00
4879 6944 5.740513 GCATAGTATTTCACCCTCTCCTGTC 60.741 48.000 0.00 0.00 0.00 3.51
4880 6945 3.791320 AGTATTTCACCCTCTCCTGTCA 58.209 45.455 0.00 0.00 0.00 3.58
4881 6946 4.168101 AGTATTTCACCCTCTCCTGTCAA 58.832 43.478 0.00 0.00 0.00 3.18
4916 6986 2.770164 AGTTTTGAGATGCTAGGCGT 57.230 45.000 0.00 0.00 0.00 5.68
4924 6994 3.871006 TGAGATGCTAGGCGTATGTTTTG 59.129 43.478 0.00 0.00 0.00 2.44
4925 6995 3.871594 GAGATGCTAGGCGTATGTTTTGT 59.128 43.478 0.00 0.00 0.00 2.83
4926 6996 5.018539 AGATGCTAGGCGTATGTTTTGTA 57.981 39.130 0.00 0.00 0.00 2.41
4938 7008 7.063780 GGCGTATGTTTTGTAGTAGTAATGTGT 59.936 37.037 0.00 0.00 0.00 3.72
4946 7016 7.721409 TTGTAGTAGTAATGTGTGGGTATCA 57.279 36.000 0.00 0.00 0.00 2.15
4961 7031 7.063898 GTGTGGGTATCATCATTGATAGAATCG 59.936 40.741 0.00 0.00 43.74 3.34
5029 7099 6.899393 TGCTTAGAAAGGTGTCATTTTCAT 57.101 33.333 12.53 4.20 36.11 2.57
5036 7106 8.103948 AGAAAGGTGTCATTTTCATAGAAGTG 57.896 34.615 12.53 0.00 36.11 3.16
5046 7116 8.134895 TCATTTTCATAGAAGTGCGAAAACTTT 58.865 29.630 0.00 0.00 40.48 2.66
5056 7126 3.675698 GTGCGAAAACTTTTGTTGTTCCA 59.324 39.130 0.00 0.00 42.67 3.53
5057 7127 4.328712 GTGCGAAAACTTTTGTTGTTCCAT 59.671 37.500 0.00 0.00 42.67 3.41
5058 7128 4.564769 TGCGAAAACTTTTGTTGTTCCATC 59.435 37.500 0.00 0.00 42.67 3.51
5059 7129 4.026062 GCGAAAACTTTTGTTGTTCCATCC 60.026 41.667 0.00 0.00 42.67 3.51
5060 7130 4.506288 CGAAAACTTTTGTTGTTCCATCCC 59.494 41.667 0.00 0.00 42.67 3.85
5061 7131 5.670485 GAAAACTTTTGTTGTTCCATCCCT 58.330 37.500 0.00 0.00 42.67 4.20
5062 7132 4.937201 AACTTTTGTTGTTCCATCCCTC 57.063 40.909 0.00 0.00 41.77 4.30
5063 7133 3.909732 ACTTTTGTTGTTCCATCCCTCA 58.090 40.909 0.00 0.00 0.00 3.86
5064 7134 4.285863 ACTTTTGTTGTTCCATCCCTCAA 58.714 39.130 0.00 0.00 0.00 3.02
5065 7135 4.099419 ACTTTTGTTGTTCCATCCCTCAAC 59.901 41.667 0.00 0.00 40.03 3.18
5066 7136 3.593442 TTGTTGTTCCATCCCTCAACT 57.407 42.857 0.00 0.00 40.20 3.16
5067 7137 4.715534 TTGTTGTTCCATCCCTCAACTA 57.284 40.909 0.00 0.00 40.20 2.24
5137 7207 4.864704 TCAAGTAATTTTCCAAGCACCC 57.135 40.909 0.00 0.00 0.00 4.61
5141 7211 2.812358 AATTTTCCAAGCACCCGTTC 57.188 45.000 0.00 0.00 0.00 3.95
5142 7212 1.698506 ATTTTCCAAGCACCCGTTCA 58.301 45.000 0.00 0.00 0.00 3.18
5143 7213 0.741915 TTTTCCAAGCACCCGTTCAC 59.258 50.000 0.00 0.00 0.00 3.18
5144 7214 1.104577 TTTCCAAGCACCCGTTCACC 61.105 55.000 0.00 0.00 0.00 4.02
5171 7241 5.284079 CCTTTCAGTTTGTCCATCTGTTTG 58.716 41.667 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 2.660552 CTCGCGGTGGTGAACGTT 60.661 61.111 6.13 0.00 31.08 3.99
256 265 3.704231 ATGAATTCGGCGCTGGGCT 62.704 57.895 17.88 0.00 42.94 5.19
271 280 4.335214 CCCCCAAATGACGCATGA 57.665 55.556 0.00 0.00 0.00 3.07
287 296 0.754472 TCGGGAATCCATTACGTCCC 59.246 55.000 0.09 0.00 45.50 4.46
435 448 2.812499 GCAGGTAGCGGATCCGAA 59.188 61.111 37.64 21.32 42.83 4.30
520 554 2.175035 CTCGCCGGACCAAACCCTAA 62.175 60.000 5.05 0.00 0.00 2.69
550 584 4.519213 CCACCCGACCTCACATAAATTTA 58.481 43.478 0.00 0.00 0.00 1.40
551 585 3.352648 CCACCCGACCTCACATAAATTT 58.647 45.455 0.00 0.00 0.00 1.82
729 796 1.771565 ACCCGTCTCATATGTCCGAA 58.228 50.000 1.90 0.00 0.00 4.30
730 797 1.771565 AACCCGTCTCATATGTCCGA 58.228 50.000 1.90 0.00 0.00 4.55
736 803 1.202533 CGCCTCAAACCCGTCTCATAT 60.203 52.381 0.00 0.00 0.00 1.78
766 838 5.184479 TGAACTTGTACTAGCGTGGTTAGAT 59.816 40.000 4.10 0.00 0.00 1.98
772 844 3.057456 AGAGTGAACTTGTACTAGCGTGG 60.057 47.826 4.10 0.00 0.00 4.94
773 845 4.162096 AGAGTGAACTTGTACTAGCGTG 57.838 45.455 4.10 0.00 0.00 5.34
774 846 4.519730 AGAAGAGTGAACTTGTACTAGCGT 59.480 41.667 4.10 0.00 0.00 5.07
775 847 5.049398 AGAAGAGTGAACTTGTACTAGCG 57.951 43.478 4.10 0.00 0.00 4.26
776 848 5.865013 GGAAGAAGAGTGAACTTGTACTAGC 59.135 44.000 4.10 0.00 0.00 3.42
777 849 6.982852 TGGAAGAAGAGTGAACTTGTACTAG 58.017 40.000 2.56 2.56 0.00 2.57
778 850 6.971726 TGGAAGAAGAGTGAACTTGTACTA 57.028 37.500 0.00 0.00 0.00 1.82
779 851 5.871396 TGGAAGAAGAGTGAACTTGTACT 57.129 39.130 0.00 0.00 0.00 2.73
780 852 6.920569 TTTGGAAGAAGAGTGAACTTGTAC 57.079 37.500 0.00 0.00 0.00 2.90
781 853 6.882140 TGTTTTGGAAGAAGAGTGAACTTGTA 59.118 34.615 0.00 0.00 0.00 2.41
782 854 5.710099 TGTTTTGGAAGAAGAGTGAACTTGT 59.290 36.000 0.00 0.00 0.00 3.16
783 855 6.194796 TGTTTTGGAAGAAGAGTGAACTTG 57.805 37.500 0.00 0.00 0.00 3.16
784 856 6.834168 TTGTTTTGGAAGAAGAGTGAACTT 57.166 33.333 0.00 0.00 0.00 2.66
785 857 6.834168 TTTGTTTTGGAAGAAGAGTGAACT 57.166 33.333 0.00 0.00 0.00 3.01
786 858 7.648112 GGTATTTGTTTTGGAAGAAGAGTGAAC 59.352 37.037 0.00 0.00 0.00 3.18
787 859 7.468084 CGGTATTTGTTTTGGAAGAAGAGTGAA 60.468 37.037 0.00 0.00 0.00 3.18
788 860 6.017440 CGGTATTTGTTTTGGAAGAAGAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
789 861 6.142817 CGGTATTTGTTTTGGAAGAAGAGTG 58.857 40.000 0.00 0.00 0.00 3.51
790 862 5.826208 ACGGTATTTGTTTTGGAAGAAGAGT 59.174 36.000 0.00 0.00 0.00 3.24
791 863 6.204882 AGACGGTATTTGTTTTGGAAGAAGAG 59.795 38.462 0.00 0.00 0.00 2.85
792 864 6.059484 AGACGGTATTTGTTTTGGAAGAAGA 58.941 36.000 0.00 0.00 0.00 2.87
793 865 6.313744 AGACGGTATTTGTTTTGGAAGAAG 57.686 37.500 0.00 0.00 0.00 2.85
794 866 5.239963 GGAGACGGTATTTGTTTTGGAAGAA 59.760 40.000 0.00 0.00 0.00 2.52
795 867 4.758165 GGAGACGGTATTTGTTTTGGAAGA 59.242 41.667 0.00 0.00 0.00 2.87
796 868 4.517453 TGGAGACGGTATTTGTTTTGGAAG 59.483 41.667 0.00 0.00 0.00 3.46
797 869 4.462133 TGGAGACGGTATTTGTTTTGGAA 58.538 39.130 0.00 0.00 0.00 3.53
798 870 4.088056 TGGAGACGGTATTTGTTTTGGA 57.912 40.909 0.00 0.00 0.00 3.53
799 871 4.542735 GTTGGAGACGGTATTTGTTTTGG 58.457 43.478 0.00 0.00 0.00 3.28
813 885 1.066430 TGTTGGGCTATCGTTGGAGAC 60.066 52.381 0.00 0.00 0.00 3.36
814 886 1.066430 GTGTTGGGCTATCGTTGGAGA 60.066 52.381 0.00 0.00 0.00 3.71
815 887 1.338674 TGTGTTGGGCTATCGTTGGAG 60.339 52.381 0.00 0.00 0.00 3.86
816 888 0.687920 TGTGTTGGGCTATCGTTGGA 59.312 50.000 0.00 0.00 0.00 3.53
817 889 1.529226 TTGTGTTGGGCTATCGTTGG 58.471 50.000 0.00 0.00 0.00 3.77
818 890 3.634568 TTTTGTGTTGGGCTATCGTTG 57.365 42.857 0.00 0.00 0.00 4.10
819 891 4.142773 CGTATTTTGTGTTGGGCTATCGTT 60.143 41.667 0.00 0.00 0.00 3.85
820 892 3.372822 CGTATTTTGTGTTGGGCTATCGT 59.627 43.478 0.00 0.00 0.00 3.73
821 893 3.619483 TCGTATTTTGTGTTGGGCTATCG 59.381 43.478 0.00 0.00 0.00 2.92
822 894 5.554822 TTCGTATTTTGTGTTGGGCTATC 57.445 39.130 0.00 0.00 0.00 2.08
823 895 5.650266 TCATTCGTATTTTGTGTTGGGCTAT 59.350 36.000 0.00 0.00 0.00 2.97
824 896 5.004448 TCATTCGTATTTTGTGTTGGGCTA 58.996 37.500 0.00 0.00 0.00 3.93
825 897 3.823873 TCATTCGTATTTTGTGTTGGGCT 59.176 39.130 0.00 0.00 0.00 5.19
826 898 4.167554 TCATTCGTATTTTGTGTTGGGC 57.832 40.909 0.00 0.00 0.00 5.36
827 899 7.470289 TTTTTCATTCGTATTTTGTGTTGGG 57.530 32.000 0.00 0.00 0.00 4.12
854 926 8.565416 GCTTGAGTGTTAACTATTTTTAGTGGT 58.435 33.333 7.22 0.00 36.52 4.16
855 927 8.021396 GGCTTGAGTGTTAACTATTTTTAGTGG 58.979 37.037 7.22 0.00 36.52 4.00
856 928 8.564574 TGGCTTGAGTGTTAACTATTTTTAGTG 58.435 33.333 7.22 0.00 36.52 2.74
857 929 8.685838 TGGCTTGAGTGTTAACTATTTTTAGT 57.314 30.769 7.22 0.00 36.52 2.24
858 930 9.394477 GTTGGCTTGAGTGTTAACTATTTTTAG 57.606 33.333 7.22 0.00 36.52 1.85
859 931 8.354426 GGTTGGCTTGAGTGTTAACTATTTTTA 58.646 33.333 7.22 0.00 36.52 1.52
860 932 7.207383 GGTTGGCTTGAGTGTTAACTATTTTT 58.793 34.615 7.22 0.00 36.52 1.94
861 933 6.239204 GGGTTGGCTTGAGTGTTAACTATTTT 60.239 38.462 7.22 0.00 36.52 1.82
862 934 5.243060 GGGTTGGCTTGAGTGTTAACTATTT 59.757 40.000 7.22 0.00 36.52 1.40
863 935 4.765339 GGGTTGGCTTGAGTGTTAACTATT 59.235 41.667 7.22 0.00 36.52 1.73
864 936 4.202524 TGGGTTGGCTTGAGTGTTAACTAT 60.203 41.667 7.22 0.00 36.52 2.12
865 937 3.136809 TGGGTTGGCTTGAGTGTTAACTA 59.863 43.478 7.22 0.00 36.52 2.24
866 938 2.092103 TGGGTTGGCTTGAGTGTTAACT 60.092 45.455 7.22 0.00 40.21 2.24
867 939 2.303175 TGGGTTGGCTTGAGTGTTAAC 58.697 47.619 0.00 0.00 0.00 2.01
868 940 2.738587 TGGGTTGGCTTGAGTGTTAA 57.261 45.000 0.00 0.00 0.00 2.01
869 941 2.738587 TTGGGTTGGCTTGAGTGTTA 57.261 45.000 0.00 0.00 0.00 2.41
870 942 1.859302 TTTGGGTTGGCTTGAGTGTT 58.141 45.000 0.00 0.00 0.00 3.32
871 943 2.086610 ATTTGGGTTGGCTTGAGTGT 57.913 45.000 0.00 0.00 0.00 3.55
872 944 4.039124 ACTTTATTTGGGTTGGCTTGAGTG 59.961 41.667 0.00 0.00 0.00 3.51
873 945 4.223144 ACTTTATTTGGGTTGGCTTGAGT 58.777 39.130 0.00 0.00 0.00 3.41
874 946 4.280677 TGACTTTATTTGGGTTGGCTTGAG 59.719 41.667 0.00 0.00 0.00 3.02
875 947 4.219115 TGACTTTATTTGGGTTGGCTTGA 58.781 39.130 0.00 0.00 0.00 3.02
876 948 4.599047 TGACTTTATTTGGGTTGGCTTG 57.401 40.909 0.00 0.00 0.00 4.01
877 949 5.622346 TTTGACTTTATTTGGGTTGGCTT 57.378 34.783 0.00 0.00 0.00 4.35
878 950 5.622346 TTTTGACTTTATTTGGGTTGGCT 57.378 34.783 0.00 0.00 0.00 4.75
879 951 5.994668 TCATTTTGACTTTATTTGGGTTGGC 59.005 36.000 0.00 0.00 0.00 4.52
880 952 8.341903 GTTTCATTTTGACTTTATTTGGGTTGG 58.658 33.333 0.00 0.00 0.00 3.77
881 953 8.887717 TGTTTCATTTTGACTTTATTTGGGTTG 58.112 29.630 0.00 0.00 0.00 3.77
882 954 9.454859 TTGTTTCATTTTGACTTTATTTGGGTT 57.545 25.926 0.00 0.00 0.00 4.11
883 955 9.625747 ATTGTTTCATTTTGACTTTATTTGGGT 57.374 25.926 0.00 0.00 0.00 4.51
891 963 9.019764 CGTAGTTGATTGTTTCATTTTGACTTT 57.980 29.630 0.00 0.00 33.34 2.66
892 964 8.402472 TCGTAGTTGATTGTTTCATTTTGACTT 58.598 29.630 0.00 0.00 33.34 3.01
893 965 7.925993 TCGTAGTTGATTGTTTCATTTTGACT 58.074 30.769 0.00 0.00 33.34 3.41
894 966 8.728088 ATCGTAGTTGATTGTTTCATTTTGAC 57.272 30.769 0.00 0.00 33.34 3.18
897 969 9.620660 GGTTATCGTAGTTGATTGTTTCATTTT 57.379 29.630 0.00 0.00 33.34 1.82
898 970 9.010029 AGGTTATCGTAGTTGATTGTTTCATTT 57.990 29.630 0.00 0.00 33.34 2.32
899 971 8.450964 CAGGTTATCGTAGTTGATTGTTTCATT 58.549 33.333 0.00 0.00 33.34 2.57
900 972 7.414098 GCAGGTTATCGTAGTTGATTGTTTCAT 60.414 37.037 0.00 0.00 33.34 2.57
901 973 6.128391 GCAGGTTATCGTAGTTGATTGTTTCA 60.128 38.462 0.00 0.00 0.00 2.69
902 974 6.128391 TGCAGGTTATCGTAGTTGATTGTTTC 60.128 38.462 0.00 0.00 0.00 2.78
903 975 5.703592 TGCAGGTTATCGTAGTTGATTGTTT 59.296 36.000 0.00 0.00 0.00 2.83
904 976 5.242434 TGCAGGTTATCGTAGTTGATTGTT 58.758 37.500 0.00 0.00 0.00 2.83
905 977 4.827692 TGCAGGTTATCGTAGTTGATTGT 58.172 39.130 0.00 0.00 0.00 2.71
906 978 5.580691 TCTTGCAGGTTATCGTAGTTGATTG 59.419 40.000 0.00 0.00 0.00 2.67
907 979 5.730550 TCTTGCAGGTTATCGTAGTTGATT 58.269 37.500 0.00 0.00 0.00 2.57
908 980 5.127194 TCTCTTGCAGGTTATCGTAGTTGAT 59.873 40.000 0.00 0.00 0.00 2.57
909 981 4.461431 TCTCTTGCAGGTTATCGTAGTTGA 59.539 41.667 0.00 0.00 0.00 3.18
910 982 4.744570 TCTCTTGCAGGTTATCGTAGTTG 58.255 43.478 0.00 0.00 0.00 3.16
911 983 5.401531 TTCTCTTGCAGGTTATCGTAGTT 57.598 39.130 0.00 0.00 0.00 2.24
912 984 5.401531 TTTCTCTTGCAGGTTATCGTAGT 57.598 39.130 0.00 0.00 0.00 2.73
913 985 6.721571 TTTTTCTCTTGCAGGTTATCGTAG 57.278 37.500 0.00 0.00 0.00 3.51
933 1005 5.338463 GGATGGACTAGAGGCTACTGTTTTT 60.338 44.000 0.00 0.00 0.00 1.94
934 1006 4.162509 GGATGGACTAGAGGCTACTGTTTT 59.837 45.833 0.00 0.00 0.00 2.43
935 1007 3.707102 GGATGGACTAGAGGCTACTGTTT 59.293 47.826 0.00 0.00 0.00 2.83
936 1008 3.301274 GGATGGACTAGAGGCTACTGTT 58.699 50.000 0.00 0.00 0.00 3.16
937 1009 2.750135 CGGATGGACTAGAGGCTACTGT 60.750 54.545 0.00 0.00 0.00 3.55
938 1010 1.883275 CGGATGGACTAGAGGCTACTG 59.117 57.143 0.00 0.00 0.00 2.74
939 1011 1.775459 TCGGATGGACTAGAGGCTACT 59.225 52.381 0.00 0.00 0.00 2.57
940 1012 2.273538 TCGGATGGACTAGAGGCTAC 57.726 55.000 0.00 0.00 0.00 3.58
941 1013 3.527507 AATCGGATGGACTAGAGGCTA 57.472 47.619 0.00 0.00 0.00 3.93
942 1014 2.390225 AATCGGATGGACTAGAGGCT 57.610 50.000 0.00 0.00 0.00 4.58
943 1015 2.608261 CGAAATCGGATGGACTAGAGGC 60.608 54.545 0.00 0.00 35.37 4.70
944 1016 2.608261 GCGAAATCGGATGGACTAGAGG 60.608 54.545 4.84 0.00 40.23 3.69
945 1017 2.667137 GCGAAATCGGATGGACTAGAG 58.333 52.381 4.84 0.00 40.23 2.43
946 1018 1.001706 CGCGAAATCGGATGGACTAGA 60.002 52.381 0.00 0.00 40.23 2.43
947 1019 1.269102 ACGCGAAATCGGATGGACTAG 60.269 52.381 15.93 0.00 40.23 2.57
948 1020 0.742505 ACGCGAAATCGGATGGACTA 59.257 50.000 15.93 0.00 40.23 2.59
949 1021 0.527817 GACGCGAAATCGGATGGACT 60.528 55.000 15.93 0.00 40.23 3.85
950 1022 1.488261 GGACGCGAAATCGGATGGAC 61.488 60.000 15.93 0.00 40.23 4.02
951 1023 1.227147 GGACGCGAAATCGGATGGA 60.227 57.895 15.93 0.00 40.23 3.41
952 1024 2.244651 GGGACGCGAAATCGGATGG 61.245 63.158 15.93 0.00 40.23 3.51
953 1025 2.244651 GGGGACGCGAAATCGGATG 61.245 63.158 15.93 0.00 40.23 3.51
954 1026 2.108362 GGGGACGCGAAATCGGAT 59.892 61.111 15.93 0.00 40.23 4.18
955 1027 3.072468 AGGGGACGCGAAATCGGA 61.072 61.111 15.93 0.00 40.23 4.55
956 1028 2.585247 GAGGGGACGCGAAATCGG 60.585 66.667 15.93 0.00 40.23 4.18
964 1036 1.737008 GTTCTGTTCGAGGGGACGC 60.737 63.158 0.00 0.00 0.00 5.19
965 1037 0.388649 CTGTTCTGTTCGAGGGGACG 60.389 60.000 0.00 0.00 0.00 4.79
966 1038 0.966920 TCTGTTCTGTTCGAGGGGAC 59.033 55.000 0.00 0.00 0.00 4.46
967 1039 1.257743 CTCTGTTCTGTTCGAGGGGA 58.742 55.000 0.00 0.00 0.00 4.81
973 1045 1.403514 GCTCCTCCTCTGTTCTGTTCG 60.404 57.143 0.00 0.00 0.00 3.95
1370 1442 1.405821 CGCTATTCTCCAGTCGAAGGT 59.594 52.381 5.19 0.00 0.00 3.50
1378 1450 0.952280 TAGGACGCGCTATTCTCCAG 59.048 55.000 5.73 0.00 0.00 3.86
1392 1464 2.749621 CTCAAATGGGTTGTGCTAGGAC 59.250 50.000 7.56 7.56 38.47 3.85
1403 1475 5.553123 TGTTAATCACGTACTCAAATGGGT 58.447 37.500 0.00 0.00 0.00 4.51
1471 1543 7.512130 ACAAGTATGGCTCAATCAGATTCATA 58.488 34.615 0.00 0.00 0.00 2.15
1472 1544 6.363065 ACAAGTATGGCTCAATCAGATTCAT 58.637 36.000 0.00 0.00 0.00 2.57
1473 1545 5.748402 ACAAGTATGGCTCAATCAGATTCA 58.252 37.500 0.00 0.00 0.00 2.57
1534 1607 5.023533 TCACTGTTATTATCAGCAGACCC 57.976 43.478 0.00 0.00 36.50 4.46
1537 1610 9.264719 CACATTATCACTGTTATTATCAGCAGA 57.735 33.333 0.00 2.18 36.50 4.26
1538 1611 9.264719 TCACATTATCACTGTTATTATCAGCAG 57.735 33.333 2.33 0.00 36.50 4.24
1578 1656 8.552296 AGATATCCAAAGTGATAAGAACAGGTT 58.448 33.333 0.00 0.00 31.34 3.50
1960 2039 1.566211 TAAGAGAGAGCTGCTGCCTT 58.434 50.000 7.01 10.14 40.80 4.35
2077 2156 6.776116 ACACTAGTCATTTATCCATAGGACGA 59.224 38.462 0.00 0.00 32.98 4.20
2171 2250 4.723789 TGCCAAGAATTAGAGAGGGAGAAT 59.276 41.667 0.00 0.00 0.00 2.40
2512 3859 1.394917 CAGGGAAAACGCATTCGAGAG 59.605 52.381 0.00 0.00 39.41 3.20
2620 3974 4.081406 TGATAGCATTGTCAACCTTTGCT 58.919 39.130 14.18 14.18 45.10 3.91
2806 4163 3.435327 GTCATTGACAACCGAACATGCTA 59.565 43.478 11.93 0.00 32.09 3.49
2807 4164 2.226437 GTCATTGACAACCGAACATGCT 59.774 45.455 11.93 0.00 32.09 3.79
2934 4292 3.454812 AGAGCTGGTTAATATTCACGGGT 59.545 43.478 0.00 0.00 0.00 5.28
3164 4522 3.777106 TGGTGCTTCTCATCTCAGTTT 57.223 42.857 0.00 0.00 0.00 2.66
3239 4597 6.370433 TCAAAATTGAACACTTCGATCACA 57.630 33.333 0.00 0.00 32.58 3.58
3376 4734 5.387113 ACCACCATCCTTTAAGCATCATA 57.613 39.130 0.00 0.00 0.00 2.15
3411 4769 2.494059 GCCACACTGAACAAAGCTCTA 58.506 47.619 0.00 0.00 0.00 2.43
3531 4914 9.952188 GGTTATAATTAAAGCCTGTTCAGATTC 57.048 33.333 1.00 0.00 0.00 2.52
3583 4974 7.933215 AAACCACTTAACTAGTTGTCTTTGT 57.067 32.000 18.56 5.66 31.93 2.83
3638 5032 4.157656 CAGCAGGAATAATTTTTCGGTGGA 59.842 41.667 3.04 0.00 0.00 4.02
3682 5076 2.037641 CACATGTGAGAGAGGACAACCA 59.962 50.000 21.64 0.00 38.94 3.67
4180 5576 9.590451 GGTATAGTACTTGTGTTTTGTATGCTA 57.410 33.333 0.00 0.00 0.00 3.49
4183 5579 9.444600 AAGGGTATAGTACTTGTGTTTTGTATG 57.555 33.333 0.00 0.00 0.00 2.39
4184 5580 9.444600 CAAGGGTATAGTACTTGTGTTTTGTAT 57.555 33.333 0.00 0.00 37.43 2.29
4241 5637 6.145535 GCAAGTTCAACTCCAAGAAATACAG 58.854 40.000 0.00 0.00 0.00 2.74
4337 5733 9.277783 ACATGAAATCTTATCCTCGGAAAATAG 57.722 33.333 0.00 0.00 0.00 1.73
4345 5741 7.852945 GCAAGTAAACATGAAATCTTATCCTCG 59.147 37.037 0.00 0.00 0.00 4.63
4387 5785 3.129813 TCAAGTGCATGCCAGATGAAATC 59.870 43.478 16.68 0.00 46.04 2.17
4436 5834 6.519761 CAGTAGAACATACAAAACATTCGCAC 59.480 38.462 0.00 0.00 0.00 5.34
4439 5837 8.873830 AGATCAGTAGAACATACAAAACATTCG 58.126 33.333 0.00 0.00 0.00 3.34
4445 5843 9.856488 GTCAGTAGATCAGTAGAACATACAAAA 57.144 33.333 0.00 0.00 0.00 2.44
4498 6558 6.239543 CCACAAGGAGATATAAGCATCTCTGT 60.240 42.308 11.69 7.37 46.81 3.41
4535 6595 4.460382 CACAAGCAGTGGTTGATAGGAAAT 59.540 41.667 35.01 12.47 44.69 2.17
4559 6621 4.871822 TGACAGGATAGTCAAGATGGAGA 58.128 43.478 0.00 0.00 44.92 3.71
4591 6653 2.092429 GGGTAATCAAGATGGAGCCACA 60.092 50.000 0.00 0.00 0.00 4.17
4592 6654 2.576615 GGGTAATCAAGATGGAGCCAC 58.423 52.381 0.00 0.00 0.00 5.01
4595 6657 3.117888 TCAAGGGGTAATCAAGATGGAGC 60.118 47.826 0.00 0.00 0.00 4.70
4642 6705 3.457749 TGGATCATATGTTGTGGCCTACA 59.542 43.478 3.32 6.33 37.56 2.74
4643 6706 4.085357 TGGATCATATGTTGTGGCCTAC 57.915 45.455 3.32 0.69 0.00 3.18
4644 6707 4.787135 TTGGATCATATGTTGTGGCCTA 57.213 40.909 3.32 0.00 0.00 3.93
4645 6708 3.668141 TTGGATCATATGTTGTGGCCT 57.332 42.857 3.32 0.00 0.00 5.19
4647 6710 6.579666 ACATATTGGATCATATGTTGTGGC 57.420 37.500 11.19 0.00 40.03 5.01
4648 6711 8.853126 AGAAACATATTGGATCATATGTTGTGG 58.147 33.333 22.52 0.67 46.94 4.17
4660 6723 7.884877 TCAGTCAACTCAAGAAACATATTGGAT 59.115 33.333 0.00 0.00 0.00 3.41
4717 6780 1.201647 CTTGCACATTGCTTCTCCCTG 59.798 52.381 0.00 0.00 45.31 4.45
4718 6781 1.074405 TCTTGCACATTGCTTCTCCCT 59.926 47.619 0.00 0.00 45.31 4.20
4721 6785 5.496133 ACATATCTTGCACATTGCTTCTC 57.504 39.130 0.00 0.00 45.31 2.87
4725 6789 4.018490 TGGAACATATCTTGCACATTGCT 58.982 39.130 0.00 0.00 45.31 3.91
4758 6822 1.618343 GCCCATTCGGAATATTTGGGG 59.382 52.381 22.41 18.96 45.93 4.96
4770 6835 2.757868 TCAAGGTTTTATGGCCCATTCG 59.242 45.455 0.00 0.00 0.00 3.34
4868 6933 2.900546 ACAACTAGTTGACAGGAGAGGG 59.099 50.000 36.14 10.57 42.93 4.30
4878 6943 8.208224 TCAAAACTATCAAGGACAACTAGTTGA 58.792 33.333 36.14 17.51 42.93 3.18
4879 6944 8.378172 TCAAAACTATCAAGGACAACTAGTTG 57.622 34.615 29.76 29.76 45.58 3.16
4880 6945 8.429641 TCTCAAAACTATCAAGGACAACTAGTT 58.570 33.333 1.12 1.12 34.89 2.24
4881 6946 7.963532 TCTCAAAACTATCAAGGACAACTAGT 58.036 34.615 0.00 0.00 0.00 2.57
4916 6986 8.377034 ACCCACACATTACTACTACAAAACATA 58.623 33.333 0.00 0.00 0.00 2.29
4924 6994 7.948357 TGATGATACCCACACATTACTACTAC 58.052 38.462 0.00 0.00 0.00 2.73
4925 6995 8.721133 ATGATGATACCCACACATTACTACTA 57.279 34.615 0.00 0.00 0.00 1.82
4926 6996 7.618019 ATGATGATACCCACACATTACTACT 57.382 36.000 0.00 0.00 0.00 2.57
4938 7008 6.352137 CCCGATTCTATCAATGATGATACCCA 60.352 42.308 5.91 0.00 44.50 4.51
4946 7016 6.688073 AACCTACCCGATTCTATCAATGAT 57.312 37.500 0.00 0.00 0.00 2.45
4961 7031 2.298446 GGTAGCCGAATCTAACCTACCC 59.702 54.545 0.00 0.00 41.24 3.69
5002 7072 4.708726 ATGACACCTTTCTAAGCATTGC 57.291 40.909 0.00 0.00 0.00 3.56
5011 7081 7.308830 GCACTTCTATGAAAATGACACCTTTCT 60.309 37.037 11.28 3.10 33.55 2.52
5029 7099 5.945155 ACAACAAAAGTTTTCGCACTTCTA 58.055 33.333 0.00 0.00 35.87 2.10
5056 7126 2.311542 TGGTTGGCATTAGTTGAGGGAT 59.688 45.455 0.00 0.00 0.00 3.85
5057 7127 1.707989 TGGTTGGCATTAGTTGAGGGA 59.292 47.619 0.00 0.00 0.00 4.20
5058 7128 2.214376 TGGTTGGCATTAGTTGAGGG 57.786 50.000 0.00 0.00 0.00 4.30
5059 7129 3.355378 TCATGGTTGGCATTAGTTGAGG 58.645 45.455 0.00 0.00 0.00 3.86
5060 7130 5.345702 CATTCATGGTTGGCATTAGTTGAG 58.654 41.667 0.00 0.00 0.00 3.02
5061 7131 4.381825 GCATTCATGGTTGGCATTAGTTGA 60.382 41.667 0.00 0.00 0.00 3.18
5062 7132 3.866910 GCATTCATGGTTGGCATTAGTTG 59.133 43.478 0.00 0.00 0.00 3.16
5063 7133 3.118665 GGCATTCATGGTTGGCATTAGTT 60.119 43.478 14.55 0.00 38.23 2.24
5064 7134 2.431782 GGCATTCATGGTTGGCATTAGT 59.568 45.455 14.55 0.00 38.23 2.24
5065 7135 2.431419 TGGCATTCATGGTTGGCATTAG 59.569 45.455 17.09 0.00 42.67 1.73
5066 7136 2.464782 TGGCATTCATGGTTGGCATTA 58.535 42.857 17.09 0.59 42.67 1.90
5067 7137 1.277579 TGGCATTCATGGTTGGCATT 58.722 45.000 17.09 0.00 42.67 3.56
5137 7207 0.179029 ACTGAAAGGGTGGGTGAACG 60.179 55.000 0.00 0.00 39.30 3.95
5141 7211 1.681264 GACAAACTGAAAGGGTGGGTG 59.319 52.381 0.00 0.00 39.30 4.61
5142 7212 1.411074 GGACAAACTGAAAGGGTGGGT 60.411 52.381 0.00 0.00 39.30 4.51
5143 7213 1.328279 GGACAAACTGAAAGGGTGGG 58.672 55.000 0.00 0.00 39.30 4.61
5144 7214 2.065899 TGGACAAACTGAAAGGGTGG 57.934 50.000 0.00 0.00 39.30 4.61


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

AutoCloner maintained by Alex Coulton.