Multiple sequence alignment - TraesCS7A01G208400

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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 TraesCS7A01G208400 chr7A 100.000 2957 0 0 1 2957 171275484 171272528 0.000000e+00 5461
1 TraesCS7A01G208400 chr7A 81.519 395 57 15 2520 2905 83699615 83700002 7.960000e-81 311
2 TraesCS7A01G208400 chr6A 98.126 1014 19 0 1 1014 85765095 85766108 0.000000e+00 1768
3 TraesCS7A01G208400 chr6A 78.590 383 58 21 2564 2930 604200507 604200881 6.370000e-57 231
4 TraesCS7A01G208400 chr4B 95.964 991 39 1 1 990 629782375 629783365 0.000000e+00 1607
5 TraesCS7A01G208400 chr7D 89.526 1117 69 19 1876 2954 168811103 168809997 0.000000e+00 1371
6 TraesCS7A01G208400 chr7D 91.074 661 44 9 1359 2014 168811856 168811206 0.000000e+00 880
7 TraesCS7A01G208400 chr7D 81.361 338 47 15 2585 2911 25486123 25486455 8.130000e-66 261
8 TraesCS7A01G208400 chr7B 90.090 999 79 11 1026 2014 134304726 134303738 0.000000e+00 1279
9 TraesCS7A01G208400 chr7B 88.230 1113 69 28 1876 2954 134303638 134302554 0.000000e+00 1273
10 TraesCS7A01G208400 chr7B 80.627 351 55 11 2573 2915 588283748 588283403 2.920000e-65 259
11 TraesCS7A01G208400 chr7B 80.994 342 43 18 2589 2915 588258845 588258511 4.890000e-63 252
12 TraesCS7A01G208400 chr1B 74.502 1004 177 39 1027 1995 517507788 517506829 2.170000e-96 363
13 TraesCS7A01G208400 chr1B 90.090 111 9 2 1853 1962 402041870 402041761 3.070000e-30 143
14 TraesCS7A01G208400 chr2B 81.233 373 58 10 2548 2911 782575522 782575891 1.040000e-74 291
15 TraesCS7A01G208400 chr3D 77.753 445 70 21 2494 2915 94737926 94738364 2.280000e-61 246
16 TraesCS7A01G208400 chr1D 83.846 260 32 7 1739 1995 385052082 385051830 3.810000e-59 239
17 TraesCS7A01G208400 chr1D 85.398 226 29 4 1739 1962 298605932 298605709 6.370000e-57 231
18 TraesCS7A01G208400 chr2A 76.667 210 45 4 1441 1648 47767485 47767692 2.410000e-21 113


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 TraesCS7A01G208400 chr7A 171272528 171275484 2956 True 5461.0 5461 100.000 1 2957 1 chr7A.!!$R1 2956
1 TraesCS7A01G208400 chr6A 85765095 85766108 1013 False 1768.0 1768 98.126 1 1014 1 chr6A.!!$F1 1013
2 TraesCS7A01G208400 chr4B 629782375 629783365 990 False 1607.0 1607 95.964 1 990 1 chr4B.!!$F1 989
3 TraesCS7A01G208400 chr7D 168809997 168811856 1859 True 1125.5 1371 90.300 1359 2954 2 chr7D.!!$R1 1595
4 TraesCS7A01G208400 chr7B 134302554 134304726 2172 True 1276.0 1279 89.160 1026 2954 2 chr7B.!!$R3 1928
5 TraesCS7A01G208400 chr1B 517506829 517507788 959 True 363.0 363 74.502 1027 1995 1 chr1B.!!$R2 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
711 713 0.036875 CCTCCTTGAAAGCTTCCGGT 59.963 55.0 0.00 0.0 0.00 5.28 F
1009 1011 0.107508 CCAGCTCGTGATGTGGGATT 60.108 55.0 1.77 0.0 0.00 3.01 F
1722 1773 0.250295 TTTGCCTTGTGGAGACGGAG 60.250 55.0 0.00 0.0 34.57 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1773 0.250338 AGCCGTCAAACTCCAGTTCC 60.250 55.0 0.00 0.0 37.25 3.62 R
1886 2202 0.393820 CAACCAAGCCAAACAGCCAT 59.606 50.0 0.00 0.0 0.00 4.40 R
2867 3237 5.777732 ACCTTTTTCTAATACATGGCCAACA 59.222 36.0 10.96 0.0 0.00 3.33 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
29 30 3.190849 CTGATGTGGGTGCGCGAG 61.191 66.667 12.10 0.00 0.00 5.03
487 489 2.159393 GCGATTTGAATGCTTGTAGCCA 60.159 45.455 0.00 0.00 41.51 4.75
584 586 1.678123 GCAAGATCTGAAGAGCAGGCA 60.678 52.381 0.00 0.00 44.98 4.75
688 690 2.031919 CCACCAGCGGCAGTAACA 59.968 61.111 1.45 0.00 0.00 2.41
689 691 2.325082 CCACCAGCGGCAGTAACAC 61.325 63.158 1.45 0.00 0.00 3.32
690 692 2.357034 ACCAGCGGCAGTAACACG 60.357 61.111 1.45 0.00 0.00 4.49
695 697 2.813908 CGGCAGTAACACGCCCTC 60.814 66.667 0.00 0.00 46.04 4.30
696 698 2.436115 GGCAGTAACACGCCCTCC 60.436 66.667 0.00 0.00 42.82 4.30
697 699 2.663196 GCAGTAACACGCCCTCCT 59.337 61.111 0.00 0.00 0.00 3.69
698 700 1.003718 GCAGTAACACGCCCTCCTT 60.004 57.895 0.00 0.00 0.00 3.36
699 701 1.298859 GCAGTAACACGCCCTCCTTG 61.299 60.000 0.00 0.00 0.00 3.61
700 702 0.320374 CAGTAACACGCCCTCCTTGA 59.680 55.000 0.00 0.00 0.00 3.02
701 703 1.053424 AGTAACACGCCCTCCTTGAA 58.947 50.000 0.00 0.00 0.00 2.69
702 704 1.418637 AGTAACACGCCCTCCTTGAAA 59.581 47.619 0.00 0.00 0.00 2.69
703 705 1.804748 GTAACACGCCCTCCTTGAAAG 59.195 52.381 0.00 0.00 0.00 2.62
704 706 1.172812 AACACGCCCTCCTTGAAAGC 61.173 55.000 0.00 0.00 0.00 3.51
705 707 1.302832 CACGCCCTCCTTGAAAGCT 60.303 57.895 0.00 0.00 0.00 3.74
706 708 0.890996 CACGCCCTCCTTGAAAGCTT 60.891 55.000 0.00 0.00 0.00 3.74
707 709 0.606673 ACGCCCTCCTTGAAAGCTTC 60.607 55.000 0.00 0.00 0.00 3.86
708 710 1.308783 CGCCCTCCTTGAAAGCTTCC 61.309 60.000 0.00 0.00 0.00 3.46
709 711 1.308783 GCCCTCCTTGAAAGCTTCCG 61.309 60.000 0.00 0.00 0.00 4.30
710 712 0.678048 CCCTCCTTGAAAGCTTCCGG 60.678 60.000 0.00 0.00 0.00 5.14
711 713 0.036875 CCTCCTTGAAAGCTTCCGGT 59.963 55.000 0.00 0.00 0.00 5.28
712 714 1.160137 CTCCTTGAAAGCTTCCGGTG 58.840 55.000 0.00 0.00 0.00 4.94
713 715 0.762418 TCCTTGAAAGCTTCCGGTGA 59.238 50.000 0.00 0.00 0.00 4.02
714 716 1.160137 CCTTGAAAGCTTCCGGTGAG 58.840 55.000 0.00 1.83 0.00 3.51
715 717 1.270839 CCTTGAAAGCTTCCGGTGAGA 60.271 52.381 0.00 0.00 0.00 3.27
716 718 2.072298 CTTGAAAGCTTCCGGTGAGAG 58.928 52.381 0.00 0.00 0.00 3.20
717 719 0.320771 TGAAAGCTTCCGGTGAGAGC 60.321 55.000 0.00 7.55 36.68 4.09
719 721 3.798758 AGCTTCCGGTGAGAGCTT 58.201 55.556 15.20 4.32 43.84 3.74
720 722 1.294780 AGCTTCCGGTGAGAGCTTG 59.705 57.895 15.20 0.00 43.84 4.01
721 723 1.188219 AGCTTCCGGTGAGAGCTTGA 61.188 55.000 15.20 0.00 43.84 3.02
722 724 1.016653 GCTTCCGGTGAGAGCTTGAC 61.017 60.000 0.00 0.00 33.72 3.18
723 725 0.605589 CTTCCGGTGAGAGCTTGACT 59.394 55.000 0.00 0.00 0.00 3.41
724 726 1.001406 CTTCCGGTGAGAGCTTGACTT 59.999 52.381 0.00 0.00 0.00 3.01
725 727 0.318441 TCCGGTGAGAGCTTGACTTG 59.682 55.000 0.00 0.00 0.00 3.16
726 728 0.318441 CCGGTGAGAGCTTGACTTGA 59.682 55.000 0.00 0.00 0.00 3.02
727 729 1.671261 CCGGTGAGAGCTTGACTTGAG 60.671 57.143 0.00 0.00 0.00 3.02
728 730 1.437625 GGTGAGAGCTTGACTTGAGC 58.562 55.000 0.00 0.00 40.43 4.26
733 735 2.866028 GCTTGACTTGAGCTGGCG 59.134 61.111 0.00 0.00 37.18 5.69
734 736 1.963338 GCTTGACTTGAGCTGGCGT 60.963 57.895 0.00 0.00 37.18 5.68
735 737 1.510480 GCTTGACTTGAGCTGGCGTT 61.510 55.000 0.00 0.00 37.18 4.84
736 738 0.236711 CTTGACTTGAGCTGGCGTTG 59.763 55.000 0.00 0.00 0.00 4.10
737 739 1.165907 TTGACTTGAGCTGGCGTTGG 61.166 55.000 0.00 0.00 0.00 3.77
738 740 2.970974 GACTTGAGCTGGCGTTGGC 61.971 63.158 0.00 0.00 38.90 4.52
739 741 2.670934 CTTGAGCTGGCGTTGGCT 60.671 61.111 0.00 0.00 41.88 4.75
740 742 2.203337 TTGAGCTGGCGTTGGCTT 60.203 55.556 0.00 0.00 39.05 4.35
741 743 2.467946 CTTGAGCTGGCGTTGGCTTG 62.468 60.000 0.00 0.00 39.05 4.01
742 744 3.741476 GAGCTGGCGTTGGCTTGG 61.741 66.667 0.00 0.00 39.05 3.61
743 745 4.269523 AGCTGGCGTTGGCTTGGA 62.270 61.111 0.00 0.00 39.81 3.53
744 746 3.741476 GCTGGCGTTGGCTTGGAG 61.741 66.667 0.00 0.00 39.81 3.86
745 747 3.741476 CTGGCGTTGGCTTGGAGC 61.741 66.667 0.00 0.00 41.46 4.70
749 751 3.121030 CGTTGGCTTGGAGCGGAG 61.121 66.667 0.00 0.00 43.62 4.63
750 752 2.032681 GTTGGCTTGGAGCGGAGT 59.967 61.111 0.00 0.00 43.62 3.85
751 753 1.600916 GTTGGCTTGGAGCGGAGTT 60.601 57.895 0.00 0.00 43.62 3.01
752 754 1.150536 TTGGCTTGGAGCGGAGTTT 59.849 52.632 0.00 0.00 43.62 2.66
753 755 0.467290 TTGGCTTGGAGCGGAGTTTT 60.467 50.000 0.00 0.00 43.62 2.43
754 756 0.889186 TGGCTTGGAGCGGAGTTTTC 60.889 55.000 0.00 0.00 43.62 2.29
755 757 1.497722 GCTTGGAGCGGAGTTTTCG 59.502 57.895 0.00 0.00 0.00 3.46
756 758 1.912371 GCTTGGAGCGGAGTTTTCGG 61.912 60.000 0.00 0.00 0.00 4.30
757 759 1.298859 CTTGGAGCGGAGTTTTCGGG 61.299 60.000 0.00 0.00 0.00 5.14
758 760 2.436115 GGAGCGGAGTTTTCGGGG 60.436 66.667 0.00 0.00 0.00 5.73
759 761 3.125573 GAGCGGAGTTTTCGGGGC 61.126 66.667 0.00 0.00 0.00 5.80
760 762 3.894547 GAGCGGAGTTTTCGGGGCA 62.895 63.158 0.00 0.00 0.00 5.36
761 763 2.981350 GCGGAGTTTTCGGGGCAA 60.981 61.111 0.00 0.00 0.00 4.52
762 764 2.557372 GCGGAGTTTTCGGGGCAAA 61.557 57.895 0.00 0.00 0.00 3.68
763 765 1.579429 CGGAGTTTTCGGGGCAAAG 59.421 57.895 0.00 0.00 0.00 2.77
764 766 1.862602 CGGAGTTTTCGGGGCAAAGG 61.863 60.000 0.00 0.00 0.00 3.11
765 767 0.538746 GGAGTTTTCGGGGCAAAGGA 60.539 55.000 0.00 0.00 0.00 3.36
766 768 0.596577 GAGTTTTCGGGGCAAAGGAC 59.403 55.000 0.00 0.00 0.00 3.85
767 769 1.170290 AGTTTTCGGGGCAAAGGACG 61.170 55.000 0.00 0.00 0.00 4.79
768 770 1.148723 TTTTCGGGGCAAAGGACGA 59.851 52.632 0.00 0.00 0.00 4.20
769 771 0.465824 TTTTCGGGGCAAAGGACGAA 60.466 50.000 0.00 0.00 42.71 3.85
770 772 1.167781 TTTCGGGGCAAAGGACGAAC 61.168 55.000 0.00 0.00 43.88 3.95
771 773 3.053896 CGGGGCAAAGGACGAACC 61.054 66.667 0.00 0.00 39.35 3.62
780 782 4.353437 GGACGAACCTGACGGCGT 62.353 66.667 14.65 14.65 39.91 5.68
781 783 2.804090 GACGAACCTGACGGCGTC 60.804 66.667 31.68 31.68 44.83 5.19
782 784 4.695231 ACGAACCTGACGGCGTCG 62.695 66.667 31.90 25.24 43.26 5.12
808 810 4.851179 GCGTTGGGGGACGGGATC 62.851 72.222 0.00 0.00 42.98 3.36
809 811 3.081409 CGTTGGGGGACGGGATCT 61.081 66.667 0.00 0.00 39.27 2.75
810 812 2.590092 GTTGGGGGACGGGATCTG 59.410 66.667 0.00 0.00 0.00 2.90
811 813 2.690881 TTGGGGGACGGGATCTGG 60.691 66.667 0.00 0.00 0.00 3.86
812 814 3.261315 TTGGGGGACGGGATCTGGA 62.261 63.158 0.00 0.00 0.00 3.86
813 815 2.122369 GGGGGACGGGATCTGGAT 60.122 66.667 0.00 0.00 0.00 3.41
814 816 2.217745 GGGGGACGGGATCTGGATC 61.218 68.421 2.24 2.24 37.11 3.36
830 832 3.151710 TCCGGTAGGATGGTGGCG 61.152 66.667 0.00 0.00 42.75 5.69
831 833 4.235762 CCGGTAGGATGGTGGCGG 62.236 72.222 0.00 0.00 41.02 6.13
832 834 3.467226 CGGTAGGATGGTGGCGGT 61.467 66.667 0.00 0.00 0.00 5.68
833 835 2.189521 GGTAGGATGGTGGCGGTG 59.810 66.667 0.00 0.00 0.00 4.94
834 836 2.189521 GTAGGATGGTGGCGGTGG 59.810 66.667 0.00 0.00 0.00 4.61
835 837 3.087253 TAGGATGGTGGCGGTGGG 61.087 66.667 0.00 0.00 0.00 4.61
838 840 3.404438 GATGGTGGCGGTGGGGTA 61.404 66.667 0.00 0.00 0.00 3.69
839 841 3.400599 GATGGTGGCGGTGGGGTAG 62.401 68.421 0.00 0.00 0.00 3.18
843 845 4.660611 TGGCGGTGGGGTAGGGAA 62.661 66.667 0.00 0.00 0.00 3.97
844 846 3.793888 GGCGGTGGGGTAGGGAAG 61.794 72.222 0.00 0.00 0.00 3.46
845 847 4.484872 GCGGTGGGGTAGGGAAGC 62.485 72.222 0.00 0.00 0.00 3.86
846 848 3.793888 CGGTGGGGTAGGGAAGCC 61.794 72.222 0.00 0.00 45.69 4.35
851 853 3.097162 GGGTAGGGAAGCCAGGGG 61.097 72.222 0.00 0.00 45.71 4.79
852 854 3.097162 GGTAGGGAAGCCAGGGGG 61.097 72.222 0.00 0.00 37.18 5.40
853 855 2.286197 GTAGGGAAGCCAGGGGGT 60.286 66.667 0.00 0.00 36.17 4.95
854 856 1.929088 GTAGGGAAGCCAGGGGGTT 60.929 63.158 0.00 0.00 46.75 4.11
855 857 1.151452 TAGGGAAGCCAGGGGGTTT 60.151 57.895 0.77 0.00 43.92 3.27
856 858 1.506028 TAGGGAAGCCAGGGGGTTTG 61.506 60.000 0.77 0.00 43.92 2.93
857 859 2.283894 GGAAGCCAGGGGGTTTGG 60.284 66.667 0.77 0.00 43.92 3.28
858 860 2.851045 GAAGCCAGGGGGTTTGGA 59.149 61.111 0.77 0.00 43.92 3.53
859 861 1.606601 GAAGCCAGGGGGTTTGGAC 60.607 63.158 0.77 0.00 43.92 4.02
860 862 3.507377 AAGCCAGGGGGTTTGGACG 62.507 63.158 0.00 0.00 40.84 4.79
861 863 3.961414 GCCAGGGGGTTTGGACGA 61.961 66.667 0.00 0.00 37.96 4.20
862 864 2.351276 CCAGGGGGTTTGGACGAG 59.649 66.667 0.00 0.00 37.96 4.18
863 865 2.351276 CAGGGGGTTTGGACGAGG 59.649 66.667 0.00 0.00 0.00 4.63
864 866 2.122099 AGGGGGTTTGGACGAGGT 60.122 61.111 0.00 0.00 0.00 3.85
865 867 2.033602 GGGGGTTTGGACGAGGTG 59.966 66.667 0.00 0.00 0.00 4.00
866 868 2.033602 GGGGTTTGGACGAGGTGG 59.966 66.667 0.00 0.00 0.00 4.61
867 869 2.671963 GGGTTTGGACGAGGTGGC 60.672 66.667 0.00 0.00 0.00 5.01
868 870 2.671963 GGTTTGGACGAGGTGGCC 60.672 66.667 0.00 0.00 0.00 5.36
869 871 3.047877 GTTTGGACGAGGTGGCCG 61.048 66.667 0.00 0.00 0.00 6.13
870 872 3.552384 TTTGGACGAGGTGGCCGT 61.552 61.111 0.00 0.00 43.56 5.68
871 873 3.109592 TTTGGACGAGGTGGCCGTT 62.110 57.895 0.00 0.00 40.67 4.44
872 874 3.818121 TTGGACGAGGTGGCCGTTG 62.818 63.158 0.00 0.00 40.67 4.10
874 876 4.681978 GACGAGGTGGCCGTTGCT 62.682 66.667 0.00 0.00 40.67 3.91
875 877 4.988598 ACGAGGTGGCCGTTGCTG 62.989 66.667 0.00 0.00 36.83 4.41
876 878 4.988598 CGAGGTGGCCGTTGCTGT 62.989 66.667 0.00 0.00 37.74 4.40
877 879 3.357079 GAGGTGGCCGTTGCTGTG 61.357 66.667 0.00 0.00 37.74 3.66
878 880 4.954970 AGGTGGCCGTTGCTGTGG 62.955 66.667 0.00 0.00 37.74 4.17
879 881 4.947147 GGTGGCCGTTGCTGTGGA 62.947 66.667 0.00 0.00 37.74 4.02
880 882 2.904866 GTGGCCGTTGCTGTGGAA 60.905 61.111 0.00 0.00 37.74 3.53
881 883 2.594303 TGGCCGTTGCTGTGGAAG 60.594 61.111 0.00 0.00 37.74 3.46
890 892 4.730487 CTGTGGAAGCAGGGGAAG 57.270 61.111 0.00 0.00 33.11 3.46
891 893 1.676967 CTGTGGAAGCAGGGGAAGC 60.677 63.158 0.00 0.00 33.11 3.86
892 894 2.416107 CTGTGGAAGCAGGGGAAGCA 62.416 60.000 0.00 0.00 33.11 3.91
893 895 1.676967 GTGGAAGCAGGGGAAGCAG 60.677 63.158 0.00 0.00 0.00 4.24
894 896 2.044551 GGAAGCAGGGGAAGCAGG 60.045 66.667 0.00 0.00 0.00 4.85
895 897 2.044551 GAAGCAGGGGAAGCAGGG 60.045 66.667 0.00 0.00 0.00 4.45
896 898 3.651980 GAAGCAGGGGAAGCAGGGG 62.652 68.421 0.00 0.00 0.00 4.79
897 899 4.682714 AGCAGGGGAAGCAGGGGA 62.683 66.667 0.00 0.00 0.00 4.81
898 900 3.424105 GCAGGGGAAGCAGGGGAT 61.424 66.667 0.00 0.00 0.00 3.85
899 901 2.599597 CAGGGGAAGCAGGGGATG 59.400 66.667 0.00 0.00 0.00 3.51
919 921 3.214123 CGGGATGCTGGCACCATG 61.214 66.667 0.00 0.00 0.00 3.66
920 922 2.836360 GGGATGCTGGCACCATGG 60.836 66.667 11.19 11.19 0.00 3.66
921 923 3.534056 GGATGCTGGCACCATGGC 61.534 66.667 13.04 0.00 44.03 4.40
922 924 2.441532 GATGCTGGCACCATGGCT 60.442 61.111 13.04 0.00 44.10 4.75
923 925 2.038329 ATGCTGGCACCATGGCTT 59.962 55.556 13.04 0.00 44.10 4.35
924 926 2.292794 GATGCTGGCACCATGGCTTG 62.293 60.000 13.04 4.59 44.10 4.01
925 927 2.993264 GCTGGCACCATGGCTTGT 60.993 61.111 13.04 0.00 44.10 3.16
926 928 2.967397 CTGGCACCATGGCTTGTG 59.033 61.111 13.04 3.31 44.10 3.33
927 929 2.601067 TGGCACCATGGCTTGTGG 60.601 61.111 13.04 1.46 44.10 4.17
929 931 2.993264 GCACCATGGCTTGTGGCT 60.993 61.111 13.04 0.00 40.49 4.75
930 932 2.967397 CACCATGGCTTGTGGCTG 59.033 61.111 13.04 0.00 40.49 4.85
931 933 2.993264 ACCATGGCTTGTGGCTGC 60.993 61.111 13.04 0.00 40.49 5.25
932 934 4.124351 CCATGGCTTGTGGCTGCG 62.124 66.667 0.00 0.00 41.46 5.18
933 935 4.124351 CATGGCTTGTGGCTGCGG 62.124 66.667 0.00 0.00 41.46 5.69
995 997 4.148825 CTTAGCCGTCGCCCAGCT 62.149 66.667 0.00 0.00 40.66 4.24
996 998 4.143333 TTAGCCGTCGCCCAGCTC 62.143 66.667 0.00 0.00 38.06 4.09
1001 1003 4.498520 CGTCGCCCAGCTCGTGAT 62.499 66.667 0.00 0.00 0.00 3.06
1002 1004 2.887568 GTCGCCCAGCTCGTGATG 60.888 66.667 0.00 0.00 0.00 3.07
1003 1005 3.381983 TCGCCCAGCTCGTGATGT 61.382 61.111 1.77 0.00 0.00 3.06
1004 1006 3.190849 CGCCCAGCTCGTGATGTG 61.191 66.667 1.77 0.00 0.00 3.21
1005 1007 2.821366 GCCCAGCTCGTGATGTGG 60.821 66.667 1.77 4.25 0.00 4.17
1006 1008 2.124983 CCCAGCTCGTGATGTGGG 60.125 66.667 1.77 4.09 43.83 4.61
1007 1009 2.981302 CCAGCTCGTGATGTGGGA 59.019 61.111 1.77 0.00 0.00 4.37
1008 1010 1.524002 CCAGCTCGTGATGTGGGAT 59.476 57.895 1.77 0.00 0.00 3.85
1009 1011 0.107508 CCAGCTCGTGATGTGGGATT 60.108 55.000 1.77 0.00 0.00 3.01
1010 1012 1.679944 CCAGCTCGTGATGTGGGATTT 60.680 52.381 1.77 0.00 0.00 2.17
1011 1013 1.667724 CAGCTCGTGATGTGGGATTTC 59.332 52.381 0.00 0.00 0.00 2.17
1012 1014 1.278985 AGCTCGTGATGTGGGATTTCA 59.721 47.619 0.00 0.00 0.00 2.69
1013 1015 1.398390 GCTCGTGATGTGGGATTTCAC 59.602 52.381 0.00 0.00 37.10 3.18
1014 1016 2.009774 CTCGTGATGTGGGATTTCACC 58.990 52.381 0.00 0.00 37.13 4.02
1015 1017 0.726827 CGTGATGTGGGATTTCACCG 59.273 55.000 0.00 0.00 37.13 4.94
1016 1018 0.451783 GTGATGTGGGATTTCACCGC 59.548 55.000 0.00 0.00 36.87 5.68
1017 1019 0.327924 TGATGTGGGATTTCACCGCT 59.672 50.000 0.00 0.00 39.24 5.52
1018 1020 1.271871 TGATGTGGGATTTCACCGCTT 60.272 47.619 0.00 0.00 39.24 4.68
1019 1021 1.818674 GATGTGGGATTTCACCGCTTT 59.181 47.619 0.00 0.00 39.24 3.51
1020 1022 1.243902 TGTGGGATTTCACCGCTTTC 58.756 50.000 0.00 0.00 39.24 2.62
1021 1023 1.243902 GTGGGATTTCACCGCTTTCA 58.756 50.000 0.00 0.00 35.64 2.69
1022 1024 1.611491 GTGGGATTTCACCGCTTTCAA 59.389 47.619 0.00 0.00 35.64 2.69
1023 1025 1.611491 TGGGATTTCACCGCTTTCAAC 59.389 47.619 0.00 0.00 0.00 3.18
1024 1026 1.886542 GGGATTTCACCGCTTTCAACT 59.113 47.619 0.00 0.00 0.00 3.16
1044 1046 4.070009 ACTTTTATCCCGTGAACTTCACC 58.930 43.478 14.98 0.03 44.20 4.02
1047 1049 1.827399 ATCCCGTGAACTTCACCGCT 61.827 55.000 14.98 0.00 44.20 5.52
1355 1357 1.109323 CCGCCATTCCCCAAGGATTC 61.109 60.000 0.00 0.00 43.54 2.52
1357 1359 0.760567 GCCATTCCCCAAGGATTCCC 60.761 60.000 0.00 0.00 43.54 3.97
1421 1423 1.388547 GTGTCTTGTGGAAGCAACCA 58.611 50.000 0.00 0.00 37.63 3.67
1434 1436 1.719117 CAACCACGACACACACCAC 59.281 57.895 0.00 0.00 0.00 4.16
1435 1437 1.450669 AACCACGACACACACCACC 60.451 57.895 0.00 0.00 0.00 4.61
1436 1438 2.186602 AACCACGACACACACCACCA 62.187 55.000 0.00 0.00 0.00 4.17
1722 1773 0.250295 TTTGCCTTGTGGAGACGGAG 60.250 55.000 0.00 0.00 34.57 4.63
1737 1788 1.070289 ACGGAGGAACTGGAGTTTGAC 59.930 52.381 0.00 0.00 41.55 3.18
1804 1881 2.743928 GAGAGCTGCAACCCACCG 60.744 66.667 1.02 0.00 0.00 4.94
1831 1908 1.135689 GCACCACCAAATCATGTCGAC 60.136 52.381 9.11 9.11 0.00 4.20
1834 1911 1.131126 CCACCAAATCATGTCGACTGC 59.869 52.381 17.92 0.00 0.00 4.40
1835 1912 1.805943 CACCAAATCATGTCGACTGCA 59.194 47.619 17.92 0.00 0.00 4.41
1886 2202 3.687698 GCGTTCTGGTTATAGCTTGGAAA 59.312 43.478 0.00 0.00 0.00 3.13
2015 2332 9.943163 GGAACCTACTAAGTTATCTTTACTACG 57.057 37.037 0.00 0.00 35.36 3.51
2111 2429 3.491405 AACCCCACCCGTCGGTTT 61.491 61.111 11.06 0.00 42.04 3.27
2112 2430 3.778097 AACCCCACCCGTCGGTTTG 62.778 63.158 11.06 6.83 42.04 2.93
2113 2431 4.259131 CCCCACCCGTCGGTTTGT 62.259 66.667 11.06 0.00 42.04 2.83
2115 2433 1.071128 CCCACCCGTCGGTTTGTAA 59.929 57.895 11.06 0.00 42.04 2.41
2116 2434 1.229975 CCCACCCGTCGGTTTGTAAC 61.230 60.000 11.06 0.00 42.04 2.50
2157 2485 1.873591 TGCTCGCTTCTTTCTTGTTCC 59.126 47.619 0.00 0.00 0.00 3.62
2158 2486 1.197949 GCTCGCTTCTTTCTTGTTCCC 59.802 52.381 0.00 0.00 0.00 3.97
2159 2487 2.772287 CTCGCTTCTTTCTTGTTCCCT 58.228 47.619 0.00 0.00 0.00 4.20
2160 2488 2.739379 CTCGCTTCTTTCTTGTTCCCTC 59.261 50.000 0.00 0.00 0.00 4.30
2161 2489 1.807142 CGCTTCTTTCTTGTTCCCTCC 59.193 52.381 0.00 0.00 0.00 4.30
2162 2490 2.163509 GCTTCTTTCTTGTTCCCTCCC 58.836 52.381 0.00 0.00 0.00 4.30
2163 2491 2.796557 CTTCTTTCTTGTTCCCTCCCC 58.203 52.381 0.00 0.00 0.00 4.81
2164 2492 1.827792 TCTTTCTTGTTCCCTCCCCA 58.172 50.000 0.00 0.00 0.00 4.96
2165 2493 2.358258 TCTTTCTTGTTCCCTCCCCAT 58.642 47.619 0.00 0.00 0.00 4.00
2166 2494 2.308866 TCTTTCTTGTTCCCTCCCCATC 59.691 50.000 0.00 0.00 0.00 3.51
2185 2513 1.689243 CCCGCCTGATGTCTCCATGA 61.689 60.000 0.00 0.00 0.00 3.07
2231 2559 2.418060 GGCAAGGTCTCTCTAGCACTTC 60.418 54.545 0.00 0.00 0.00 3.01
2232 2560 2.495669 GCAAGGTCTCTCTAGCACTTCT 59.504 50.000 0.00 0.00 0.00 2.85
2233 2561 3.428862 GCAAGGTCTCTCTAGCACTTCTC 60.429 52.174 0.00 0.00 0.00 2.87
2234 2562 3.012934 AGGTCTCTCTAGCACTTCTCC 57.987 52.381 0.00 0.00 0.00 3.71
2242 2572 4.464597 TCTCTAGCACTTCTCCTTTCCTTC 59.535 45.833 0.00 0.00 0.00 3.46
2277 2607 6.409704 AGCATCTCTAGCACATCTTGTAAAA 58.590 36.000 0.00 0.00 0.00 1.52
2291 2621 5.250200 TCTTGTAAAAGTCCATACCGCAAT 58.750 37.500 0.00 0.00 0.00 3.56
2324 2679 6.164176 CGATATACCCTAAAACATGGGAGAC 58.836 44.000 4.93 0.00 46.15 3.36
2419 2775 5.631512 TGTTTGTTCGACCTTTTGTTTTCTG 59.368 36.000 0.00 0.00 0.00 3.02
2889 3259 8.776376 AAATGTTGGCCATGTATTAGAAAAAG 57.224 30.769 6.09 0.00 32.82 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.019278 ACATCGCCAACGTCATCCAC 61.019 55.000 0.00 0.00 41.18 4.02
194 195 1.451028 GTCTGAGACAGCCATGCCC 60.451 63.158 7.90 0.00 32.09 5.36
457 459 2.159393 GCATTCAAATCGCAGCTACCAA 60.159 45.455 0.00 0.00 0.00 3.67
680 682 1.003718 AAGGAGGGCGTGTTACTGC 60.004 57.895 0.00 0.00 0.00 4.40
681 683 0.320374 TCAAGGAGGGCGTGTTACTG 59.680 55.000 0.00 0.00 0.00 2.74
682 684 1.053424 TTCAAGGAGGGCGTGTTACT 58.947 50.000 0.00 0.00 0.00 2.24
683 685 1.804748 CTTTCAAGGAGGGCGTGTTAC 59.195 52.381 0.00 0.00 0.00 2.50
684 686 1.880646 GCTTTCAAGGAGGGCGTGTTA 60.881 52.381 0.00 0.00 0.00 2.41
685 687 1.172812 GCTTTCAAGGAGGGCGTGTT 61.173 55.000 0.00 0.00 0.00 3.32
686 688 1.600916 GCTTTCAAGGAGGGCGTGT 60.601 57.895 0.00 0.00 0.00 4.49
687 689 0.890996 AAGCTTTCAAGGAGGGCGTG 60.891 55.000 0.00 0.00 0.00 5.34
688 690 0.606673 GAAGCTTTCAAGGAGGGCGT 60.607 55.000 0.00 0.00 0.00 5.68
689 691 1.308783 GGAAGCTTTCAAGGAGGGCG 61.309 60.000 0.00 0.00 0.00 6.13
690 692 1.308783 CGGAAGCTTTCAAGGAGGGC 61.309 60.000 5.39 0.00 0.00 5.19
691 693 0.678048 CCGGAAGCTTTCAAGGAGGG 60.678 60.000 5.39 0.00 32.80 4.30
692 694 0.036875 ACCGGAAGCTTTCAAGGAGG 59.963 55.000 9.46 0.00 34.45 4.30
693 695 1.160137 CACCGGAAGCTTTCAAGGAG 58.840 55.000 9.46 0.11 34.45 3.69
694 696 0.762418 TCACCGGAAGCTTTCAAGGA 59.238 50.000 9.46 0.00 34.45 3.36
695 697 1.160137 CTCACCGGAAGCTTTCAAGG 58.840 55.000 9.46 7.17 35.82 3.61
696 698 2.072298 CTCTCACCGGAAGCTTTCAAG 58.928 52.381 9.46 0.00 0.00 3.02
697 699 1.878102 GCTCTCACCGGAAGCTTTCAA 60.878 52.381 9.46 0.00 0.00 2.69
698 700 0.320771 GCTCTCACCGGAAGCTTTCA 60.321 55.000 9.46 0.00 0.00 2.69
699 701 0.036858 AGCTCTCACCGGAAGCTTTC 60.037 55.000 9.46 0.00 31.02 2.62
700 702 0.398318 AAGCTCTCACCGGAAGCTTT 59.602 50.000 22.95 13.02 42.31 3.51
701 703 0.321122 CAAGCTCTCACCGGAAGCTT 60.321 55.000 22.95 22.95 45.31 3.74
702 704 1.188219 TCAAGCTCTCACCGGAAGCT 61.188 55.000 9.46 13.92 37.45 3.74
703 705 1.016653 GTCAAGCTCTCACCGGAAGC 61.017 60.000 9.46 11.65 0.00 3.86
704 706 0.605589 AGTCAAGCTCTCACCGGAAG 59.394 55.000 9.46 5.18 0.00 3.46
705 707 1.048601 AAGTCAAGCTCTCACCGGAA 58.951 50.000 9.46 0.00 0.00 4.30
706 708 0.318441 CAAGTCAAGCTCTCACCGGA 59.682 55.000 9.46 0.00 0.00 5.14
707 709 0.318441 TCAAGTCAAGCTCTCACCGG 59.682 55.000 0.00 0.00 0.00 5.28
708 710 1.707632 CTCAAGTCAAGCTCTCACCG 58.292 55.000 0.00 0.00 0.00 4.94
709 711 1.437625 GCTCAAGTCAAGCTCTCACC 58.562 55.000 0.00 0.00 36.80 4.02
716 718 1.510480 AACGCCAGCTCAAGTCAAGC 61.510 55.000 0.00 0.00 40.14 4.01
717 719 0.236711 CAACGCCAGCTCAAGTCAAG 59.763 55.000 0.00 0.00 0.00 3.02
718 720 1.165907 CCAACGCCAGCTCAAGTCAA 61.166 55.000 0.00 0.00 0.00 3.18
719 721 1.597854 CCAACGCCAGCTCAAGTCA 60.598 57.895 0.00 0.00 0.00 3.41
720 722 2.970974 GCCAACGCCAGCTCAAGTC 61.971 63.158 0.00 0.00 0.00 3.01
721 723 2.965716 AAGCCAACGCCAGCTCAAGT 62.966 55.000 0.00 0.00 38.74 3.16
722 724 2.263741 AAGCCAACGCCAGCTCAAG 61.264 57.895 0.00 0.00 38.74 3.02
723 725 2.203337 AAGCCAACGCCAGCTCAA 60.203 55.556 0.00 0.00 38.74 3.02
724 726 2.979676 CAAGCCAACGCCAGCTCA 60.980 61.111 0.00 0.00 38.74 4.26
725 727 3.741476 CCAAGCCAACGCCAGCTC 61.741 66.667 0.00 0.00 38.74 4.09
726 728 4.269523 TCCAAGCCAACGCCAGCT 62.270 61.111 0.00 0.00 42.40 4.24
727 729 3.741476 CTCCAAGCCAACGCCAGC 61.741 66.667 0.00 0.00 34.57 4.85
728 730 3.741476 GCTCCAAGCCAACGCCAG 61.741 66.667 0.00 0.00 34.48 4.85
732 734 3.121030 CTCCGCTCCAAGCCAACG 61.121 66.667 0.00 0.00 38.18 4.10
733 735 1.172812 AAACTCCGCTCCAAGCCAAC 61.173 55.000 0.00 0.00 38.18 3.77
734 736 0.467290 AAAACTCCGCTCCAAGCCAA 60.467 50.000 0.00 0.00 38.18 4.52
735 737 0.889186 GAAAACTCCGCTCCAAGCCA 60.889 55.000 0.00 0.00 38.18 4.75
736 738 1.876664 GAAAACTCCGCTCCAAGCC 59.123 57.895 0.00 0.00 38.18 4.35
737 739 1.497722 CGAAAACTCCGCTCCAAGC 59.502 57.895 0.00 0.00 38.02 4.01
738 740 1.298859 CCCGAAAACTCCGCTCCAAG 61.299 60.000 0.00 0.00 0.00 3.61
739 741 1.302192 CCCGAAAACTCCGCTCCAA 60.302 57.895 0.00 0.00 0.00 3.53
740 742 2.345991 CCCGAAAACTCCGCTCCA 59.654 61.111 0.00 0.00 0.00 3.86
741 743 2.436115 CCCCGAAAACTCCGCTCC 60.436 66.667 0.00 0.00 0.00 4.70
742 744 3.125573 GCCCCGAAAACTCCGCTC 61.126 66.667 0.00 0.00 0.00 5.03
743 745 2.969300 TTTGCCCCGAAAACTCCGCT 62.969 55.000 0.00 0.00 0.00 5.52
744 746 2.472232 CTTTGCCCCGAAAACTCCGC 62.472 60.000 0.00 0.00 0.00 5.54
745 747 1.579429 CTTTGCCCCGAAAACTCCG 59.421 57.895 0.00 0.00 0.00 4.63
746 748 0.538746 TCCTTTGCCCCGAAAACTCC 60.539 55.000 0.00 0.00 0.00 3.85
747 749 0.596577 GTCCTTTGCCCCGAAAACTC 59.403 55.000 0.00 0.00 0.00 3.01
748 750 1.170290 CGTCCTTTGCCCCGAAAACT 61.170 55.000 0.00 0.00 0.00 2.66
749 751 1.167781 TCGTCCTTTGCCCCGAAAAC 61.168 55.000 0.00 0.00 0.00 2.43
750 752 0.465824 TTCGTCCTTTGCCCCGAAAA 60.466 50.000 0.00 0.00 36.49 2.29
751 753 1.148723 TTCGTCCTTTGCCCCGAAA 59.851 52.632 0.00 0.00 36.49 3.46
752 754 1.598685 GTTCGTCCTTTGCCCCGAA 60.599 57.895 0.00 0.00 37.02 4.30
753 755 2.031465 GTTCGTCCTTTGCCCCGA 59.969 61.111 0.00 0.00 0.00 5.14
754 756 3.053896 GGTTCGTCCTTTGCCCCG 61.054 66.667 0.00 0.00 0.00 5.73
755 757 1.971695 CAGGTTCGTCCTTTGCCCC 60.972 63.158 0.00 0.00 45.67 5.80
756 758 1.072505 TCAGGTTCGTCCTTTGCCC 59.927 57.895 0.00 0.00 45.67 5.36
757 759 1.566018 CGTCAGGTTCGTCCTTTGCC 61.566 60.000 0.00 0.00 45.67 4.52
758 760 1.566018 CCGTCAGGTTCGTCCTTTGC 61.566 60.000 0.00 0.00 45.67 3.68
759 761 1.566018 GCCGTCAGGTTCGTCCTTTG 61.566 60.000 0.00 0.00 45.67 2.77
760 762 1.301479 GCCGTCAGGTTCGTCCTTT 60.301 57.895 0.00 0.00 45.67 3.11
761 763 2.342648 GCCGTCAGGTTCGTCCTT 59.657 61.111 0.00 0.00 45.67 3.36
763 765 4.353437 ACGCCGTCAGGTTCGTCC 62.353 66.667 0.00 0.00 40.50 4.79
764 766 2.804090 GACGCCGTCAGGTTCGTC 60.804 66.667 13.23 0.00 42.58 4.20
765 767 4.695231 CGACGCCGTCAGGTTCGT 62.695 66.667 18.40 0.00 39.08 3.85
791 793 4.851179 GATCCCGTCCCCCAACGC 62.851 72.222 0.00 0.00 41.26 4.84
792 794 3.081409 AGATCCCGTCCCCCAACG 61.081 66.667 0.00 0.00 42.24 4.10
793 795 2.590092 CAGATCCCGTCCCCCAAC 59.410 66.667 0.00 0.00 0.00 3.77
794 796 2.561378 ATCCAGATCCCGTCCCCCAA 62.561 60.000 0.00 0.00 0.00 4.12
795 797 2.965226 GATCCAGATCCCGTCCCCCA 62.965 65.000 0.00 0.00 31.76 4.96
796 798 2.122369 ATCCAGATCCCGTCCCCC 60.122 66.667 0.00 0.00 0.00 5.40
797 799 3.472809 GATCCAGATCCCGTCCCC 58.527 66.667 0.00 0.00 31.76 4.81
813 815 3.151710 CGCCACCATCCTACCGGA 61.152 66.667 9.46 0.00 45.16 5.14
814 816 4.235762 CCGCCACCATCCTACCGG 62.236 72.222 0.00 0.00 0.00 5.28
815 817 3.467226 ACCGCCACCATCCTACCG 61.467 66.667 0.00 0.00 0.00 4.02
816 818 2.189521 CACCGCCACCATCCTACC 59.810 66.667 0.00 0.00 0.00 3.18
817 819 2.189521 CCACCGCCACCATCCTAC 59.810 66.667 0.00 0.00 0.00 3.18
818 820 3.087253 CCCACCGCCACCATCCTA 61.087 66.667 0.00 0.00 0.00 2.94
821 823 3.400599 CTACCCCACCGCCACCATC 62.401 68.421 0.00 0.00 0.00 3.51
822 824 3.407967 CTACCCCACCGCCACCAT 61.408 66.667 0.00 0.00 0.00 3.55
826 828 4.660611 TTCCCTACCCCACCGCCA 62.661 66.667 0.00 0.00 0.00 5.69
827 829 3.793888 CTTCCCTACCCCACCGCC 61.794 72.222 0.00 0.00 0.00 6.13
828 830 4.484872 GCTTCCCTACCCCACCGC 62.485 72.222 0.00 0.00 0.00 5.68
829 831 3.793888 GGCTTCCCTACCCCACCG 61.794 72.222 0.00 0.00 0.00 4.94
830 832 2.612746 TGGCTTCCCTACCCCACC 60.613 66.667 0.00 0.00 0.00 4.61
831 833 2.680370 CCTGGCTTCCCTACCCCAC 61.680 68.421 0.00 0.00 0.00 4.61
832 834 2.286121 CCTGGCTTCCCTACCCCA 60.286 66.667 0.00 0.00 0.00 4.96
833 835 3.097162 CCCTGGCTTCCCTACCCC 61.097 72.222 0.00 0.00 0.00 4.95
834 836 3.097162 CCCCTGGCTTCCCTACCC 61.097 72.222 0.00 0.00 0.00 3.69
835 837 3.097162 CCCCCTGGCTTCCCTACC 61.097 72.222 0.00 0.00 0.00 3.18
836 838 1.506907 AAACCCCCTGGCTTCCCTAC 61.507 60.000 0.00 0.00 33.59 3.18
837 839 1.151452 AAACCCCCTGGCTTCCCTA 60.151 57.895 0.00 0.00 33.59 3.53
838 840 2.454511 AAACCCCCTGGCTTCCCT 60.455 61.111 0.00 0.00 33.59 4.20
839 841 2.283894 CAAACCCCCTGGCTTCCC 60.284 66.667 0.00 0.00 33.59 3.97
840 842 2.283894 CCAAACCCCCTGGCTTCC 60.284 66.667 0.00 0.00 33.59 3.46
841 843 1.606601 GTCCAAACCCCCTGGCTTC 60.607 63.158 0.00 0.00 33.63 3.86
842 844 2.526110 GTCCAAACCCCCTGGCTT 59.474 61.111 0.00 0.00 33.63 4.35
843 845 3.966543 CGTCCAAACCCCCTGGCT 61.967 66.667 0.00 0.00 33.63 4.75
844 846 3.920093 CTCGTCCAAACCCCCTGGC 62.920 68.421 0.00 0.00 33.63 4.85
845 847 2.351276 CTCGTCCAAACCCCCTGG 59.649 66.667 0.00 0.00 35.05 4.45
846 848 2.351276 CCTCGTCCAAACCCCCTG 59.649 66.667 0.00 0.00 0.00 4.45
847 849 2.122099 ACCTCGTCCAAACCCCCT 60.122 61.111 0.00 0.00 0.00 4.79
848 850 2.033602 CACCTCGTCCAAACCCCC 59.966 66.667 0.00 0.00 0.00 5.40
849 851 2.033602 CCACCTCGTCCAAACCCC 59.966 66.667 0.00 0.00 0.00 4.95
850 852 2.671963 GCCACCTCGTCCAAACCC 60.672 66.667 0.00 0.00 0.00 4.11
851 853 2.671963 GGCCACCTCGTCCAAACC 60.672 66.667 0.00 0.00 0.00 3.27
852 854 3.047877 CGGCCACCTCGTCCAAAC 61.048 66.667 2.24 0.00 0.00 2.93
853 855 3.109592 AACGGCCACCTCGTCCAAA 62.110 57.895 2.24 0.00 40.18 3.28
854 856 3.552384 AACGGCCACCTCGTCCAA 61.552 61.111 2.24 0.00 40.18 3.53
855 857 4.308458 CAACGGCCACCTCGTCCA 62.308 66.667 2.24 0.00 40.18 4.02
857 859 4.681978 AGCAACGGCCACCTCGTC 62.682 66.667 2.24 0.00 42.56 4.20
858 860 4.988598 CAGCAACGGCCACCTCGT 62.989 66.667 2.24 0.00 42.56 4.18
859 861 4.988598 ACAGCAACGGCCACCTCG 62.989 66.667 2.24 0.00 42.56 4.63
860 862 3.357079 CACAGCAACGGCCACCTC 61.357 66.667 2.24 0.00 42.56 3.85
861 863 4.954970 CCACAGCAACGGCCACCT 62.955 66.667 2.24 0.00 42.56 4.00
862 864 4.947147 TCCACAGCAACGGCCACC 62.947 66.667 2.24 0.00 42.56 4.61
863 865 2.904866 TTCCACAGCAACGGCCAC 60.905 61.111 2.24 0.00 42.56 5.01
864 866 2.594303 CTTCCACAGCAACGGCCA 60.594 61.111 2.24 0.00 42.56 5.36
873 875 1.676967 GCTTCCCCTGCTTCCACAG 60.677 63.158 0.00 0.00 37.42 3.66
874 876 2.416107 CTGCTTCCCCTGCTTCCACA 62.416 60.000 0.00 0.00 0.00 4.17
875 877 1.676967 CTGCTTCCCCTGCTTCCAC 60.677 63.158 0.00 0.00 0.00 4.02
876 878 2.759114 CTGCTTCCCCTGCTTCCA 59.241 61.111 0.00 0.00 0.00 3.53
877 879 2.044551 CCTGCTTCCCCTGCTTCC 60.045 66.667 0.00 0.00 0.00 3.46
878 880 2.044551 CCCTGCTTCCCCTGCTTC 60.045 66.667 0.00 0.00 0.00 3.86
879 881 3.665971 CCCCTGCTTCCCCTGCTT 61.666 66.667 0.00 0.00 0.00 3.91
880 882 3.978241 ATCCCCTGCTTCCCCTGCT 62.978 63.158 0.00 0.00 0.00 4.24
881 883 3.424105 ATCCCCTGCTTCCCCTGC 61.424 66.667 0.00 0.00 0.00 4.85
882 884 2.599597 CATCCCCTGCTTCCCCTG 59.400 66.667 0.00 0.00 0.00 4.45
902 904 3.214123 CATGGTGCCAGCATCCCG 61.214 66.667 6.38 0.00 33.46 5.14
903 905 2.836360 CCATGGTGCCAGCATCCC 60.836 66.667 6.38 0.00 33.46 3.85
904 906 3.534056 GCCATGGTGCCAGCATCC 61.534 66.667 14.67 2.65 33.46 3.51
905 907 2.056223 AAGCCATGGTGCCAGCATC 61.056 57.895 14.67 0.00 33.46 3.91
906 908 2.038329 AAGCCATGGTGCCAGCAT 59.962 55.556 14.67 2.99 36.65 3.79
907 909 2.992689 CAAGCCATGGTGCCAGCA 60.993 61.111 14.67 0.00 0.00 4.41
908 910 2.993264 ACAAGCCATGGTGCCAGC 60.993 61.111 14.67 0.00 0.00 4.85
909 911 2.642254 CCACAAGCCATGGTGCCAG 61.642 63.158 14.67 2.01 33.72 4.85
910 912 2.601067 CCACAAGCCATGGTGCCA 60.601 61.111 14.67 0.00 33.72 4.92
911 913 4.073200 GCCACAAGCCATGGTGCC 62.073 66.667 14.67 0.00 39.63 5.01
912 914 2.993264 AGCCACAAGCCATGGTGC 60.993 61.111 14.67 6.97 45.47 5.01
913 915 2.967397 CAGCCACAAGCCATGGTG 59.033 61.111 14.67 7.25 45.47 4.17
914 916 2.993264 GCAGCCACAAGCCATGGT 60.993 61.111 14.67 0.00 45.47 3.55
915 917 4.124351 CGCAGCCACAAGCCATGG 62.124 66.667 7.63 7.63 45.47 3.66
916 918 4.124351 CCGCAGCCACAAGCCATG 62.124 66.667 0.00 0.00 45.47 3.66
984 986 4.498520 ATCACGAGCTGGGCGACG 62.499 66.667 0.00 0.00 38.52 5.12
985 987 2.887568 CATCACGAGCTGGGCGAC 60.888 66.667 0.00 0.00 0.00 5.19
986 988 3.381983 ACATCACGAGCTGGGCGA 61.382 61.111 0.00 0.00 0.00 5.54
987 989 3.190849 CACATCACGAGCTGGGCG 61.191 66.667 0.00 0.00 0.00 6.13
988 990 2.821366 CCACATCACGAGCTGGGC 60.821 66.667 0.00 0.00 0.00 5.36
989 991 1.976132 ATCCCACATCACGAGCTGGG 61.976 60.000 0.00 0.00 44.41 4.45
990 992 0.107508 AATCCCACATCACGAGCTGG 60.108 55.000 0.00 0.00 0.00 4.85
991 993 1.667724 GAAATCCCACATCACGAGCTG 59.332 52.381 0.00 0.00 0.00 4.24
992 994 1.278985 TGAAATCCCACATCACGAGCT 59.721 47.619 0.00 0.00 0.00 4.09
993 995 1.398390 GTGAAATCCCACATCACGAGC 59.602 52.381 0.00 0.00 37.04 5.03
994 996 2.009774 GGTGAAATCCCACATCACGAG 58.990 52.381 0.00 0.00 43.38 4.18
995 997 1.674519 CGGTGAAATCCCACATCACGA 60.675 52.381 0.00 0.00 43.38 4.35
996 998 0.726827 CGGTGAAATCCCACATCACG 59.273 55.000 0.00 0.00 43.38 4.35
997 999 0.451783 GCGGTGAAATCCCACATCAC 59.548 55.000 0.00 0.00 42.08 3.06
998 1000 0.327924 AGCGGTGAAATCCCACATCA 59.672 50.000 0.00 0.00 38.74 3.07
999 1001 1.463674 AAGCGGTGAAATCCCACATC 58.536 50.000 0.00 0.00 38.74 3.06
1000 1002 1.818674 GAAAGCGGTGAAATCCCACAT 59.181 47.619 0.00 0.00 38.74 3.21
1001 1003 1.243902 GAAAGCGGTGAAATCCCACA 58.756 50.000 0.00 0.00 38.74 4.17
1002 1004 1.243902 TGAAAGCGGTGAAATCCCAC 58.756 50.000 0.00 0.00 36.37 4.61
1003 1005 1.611491 GTTGAAAGCGGTGAAATCCCA 59.389 47.619 0.00 0.00 0.00 4.37
1004 1006 1.886542 AGTTGAAAGCGGTGAAATCCC 59.113 47.619 0.00 0.00 0.00 3.85
1005 1007 3.643159 AAGTTGAAAGCGGTGAAATCC 57.357 42.857 0.00 0.00 0.00 3.01
1006 1008 6.308041 GGATAAAAGTTGAAAGCGGTGAAATC 59.692 38.462 0.00 0.00 0.00 2.17
1007 1009 6.156519 GGATAAAAGTTGAAAGCGGTGAAAT 58.843 36.000 0.00 0.00 0.00 2.17
1008 1010 5.508320 GGGATAAAAGTTGAAAGCGGTGAAA 60.508 40.000 0.00 0.00 0.00 2.69
1009 1011 4.022676 GGGATAAAAGTTGAAAGCGGTGAA 60.023 41.667 0.00 0.00 0.00 3.18
1010 1012 3.504520 GGGATAAAAGTTGAAAGCGGTGA 59.495 43.478 0.00 0.00 0.00 4.02
1011 1013 3.669557 CGGGATAAAAGTTGAAAGCGGTG 60.670 47.826 0.00 0.00 0.00 4.94
1012 1014 2.486592 CGGGATAAAAGTTGAAAGCGGT 59.513 45.455 0.00 0.00 0.00 5.68
1013 1015 2.486592 ACGGGATAAAAGTTGAAAGCGG 59.513 45.455 0.00 0.00 0.00 5.52
1014 1016 3.187637 TCACGGGATAAAAGTTGAAAGCG 59.812 43.478 0.00 0.00 0.00 4.68
1015 1017 4.759516 TCACGGGATAAAAGTTGAAAGC 57.240 40.909 0.00 0.00 0.00 3.51
1016 1018 6.313744 AGTTCACGGGATAAAAGTTGAAAG 57.686 37.500 0.00 0.00 0.00 2.62
1017 1019 6.319152 TGAAGTTCACGGGATAAAAGTTGAAA 59.681 34.615 0.08 0.00 0.00 2.69
1018 1020 5.823570 TGAAGTTCACGGGATAAAAGTTGAA 59.176 36.000 0.08 0.00 0.00 2.69
1019 1021 5.237779 GTGAAGTTCACGGGATAAAAGTTGA 59.762 40.000 19.71 0.00 37.67 3.18
1020 1022 5.449304 GTGAAGTTCACGGGATAAAAGTTG 58.551 41.667 19.71 0.00 37.67 3.16
1021 1023 5.684550 GTGAAGTTCACGGGATAAAAGTT 57.315 39.130 19.71 0.00 37.67 2.66
1047 1049 0.401356 TGAAGATGTTGCTGCCCAGA 59.599 50.000 0.00 0.00 0.00 3.86
1218 1220 1.460504 CCTGCTGCATGTCACAGATT 58.539 50.000 1.31 0.00 37.32 2.40
1283 1285 0.969149 GCTTGGGTTTGGGAAAGAGG 59.031 55.000 0.00 0.00 0.00 3.69
1355 1357 2.417516 CGTAGGCGGTGATCAGGG 59.582 66.667 0.00 0.00 0.00 4.45
1421 1423 2.188469 GGTGGTGGTGTGTGTCGT 59.812 61.111 0.00 0.00 0.00 4.34
1434 1436 0.246635 CGAAGGAGTAGGTGTGGTGG 59.753 60.000 0.00 0.00 0.00 4.61
1435 1437 1.067776 GTCGAAGGAGTAGGTGTGGTG 60.068 57.143 0.00 0.00 0.00 4.17
1436 1438 1.254954 GTCGAAGGAGTAGGTGTGGT 58.745 55.000 0.00 0.00 0.00 4.16
1684 1726 2.751436 CCTGGCGTTCCCCATGTG 60.751 66.667 0.00 0.00 33.64 3.21
1722 1773 0.250338 AGCCGTCAAACTCCAGTTCC 60.250 55.000 0.00 0.00 37.25 3.62
1857 1934 0.676782 ATAACCAGAACGCCACAGGC 60.677 55.000 0.00 0.00 46.75 4.85
1886 2202 0.393820 CAACCAAGCCAAACAGCCAT 59.606 50.000 0.00 0.00 0.00 4.40
1962 2278 7.227314 ACAAAAATGGGCAAGAGAAGAATTTTC 59.773 33.333 0.00 0.00 0.00 2.29
2006 2323 3.306166 CGGGCATTCAGTTCGTAGTAAAG 59.694 47.826 0.00 0.00 0.00 1.85
2015 2332 1.210155 GCACACGGGCATTCAGTTC 59.790 57.895 0.00 0.00 0.00 3.01
2020 2337 4.120331 GGCAGCACACGGGCATTC 62.120 66.667 0.00 0.00 36.53 2.67
2077 2394 7.446319 GGGTGGGGTTGTAATACATAACTTATC 59.554 40.741 0.00 0.00 0.00 1.75
2158 2486 2.851102 ATCAGGCGGGATGGGGAG 60.851 66.667 0.00 0.00 0.00 4.30
2159 2487 3.170672 CATCAGGCGGGATGGGGA 61.171 66.667 12.56 0.00 40.75 4.81
2164 2492 1.383109 TGGAGACATCAGGCGGGAT 60.383 57.895 0.00 0.00 33.40 3.85
2165 2493 2.038813 TGGAGACATCAGGCGGGA 59.961 61.111 0.00 0.00 33.40 5.14
2185 2513 2.905736 AGGCCCAATAGCACATGTTTTT 59.094 40.909 0.00 0.00 0.00 1.94
2213 2541 3.011257 AGGAGAAGTGCTAGAGAGACCTT 59.989 47.826 0.00 0.00 0.00 3.50
2242 2572 3.243501 GCTAGAGATGCTCTCAGTCCAAG 60.244 52.174 13.42 0.00 45.73 3.61
2266 2596 4.634004 TGCGGTATGGACTTTTACAAGATG 59.366 41.667 0.00 0.00 33.72 2.90
2270 2600 6.408035 TCTATTGCGGTATGGACTTTTACAA 58.592 36.000 0.00 0.00 0.00 2.41
2277 2607 4.443034 GGAAACTCTATTGCGGTATGGACT 60.443 45.833 0.00 0.00 0.00 3.85
2291 2621 8.537728 TGTTTTAGGGTATATCGGAAACTCTA 57.462 34.615 8.18 0.00 0.00 2.43
2352 2707 2.856628 CGAGCTGTGCCGGCCTATA 61.857 63.158 26.77 0.59 36.20 1.31
2483 2849 8.770438 ACACATTTAACATTTCAAAACACTGT 57.230 26.923 0.00 0.00 0.00 3.55
2606 2974 9.488124 CACATTTAACATTTTTCAAACACTTGG 57.512 29.630 0.00 0.00 33.01 3.61
2790 3158 9.828039 TGCAATATTACATTTTTAATGCATGGA 57.172 25.926 0.00 0.00 0.00 3.41
2867 3237 5.777732 ACCTTTTTCTAATACATGGCCAACA 59.222 36.000 10.96 0.00 0.00 3.33
2872 3242 8.000780 AGATTGACCTTTTTCTAATACATGGC 57.999 34.615 0.00 0.00 0.00 4.40
2889 3259 6.106003 ACTTTTTCCAAACACAAGATTGACC 58.894 36.000 0.00 0.00 29.78 4.02


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

AutoCloner maintained by Alex Coulton.