Multiple sequence alignment - TraesCS7D01G074800

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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 TraesCS7D01G074800 chr7D 100.000 5185 0 0 1 5185 44304800 44299616 0.000000e+00 9575.0
1 TraesCS7D01G074800 chr7A 89.466 3389 225 72 994 4331 46726570 46723263 0.000000e+00 4159.0
2 TraesCS7D01G074800 chr7A 92.548 832 44 9 1 831 46765958 46765144 0.000000e+00 1177.0
3 TraesCS7D01G074800 chr7A 86.325 702 47 27 4506 5173 46722723 46722037 0.000000e+00 719.0
4 TraesCS7D01G074800 chr7A 95.359 237 9 2 4239 4475 46723254 46723020 4.900000e-100 375.0
5 TraesCS7D01G074800 chr4A 95.455 2354 84 12 988 3340 655264208 655261877 0.000000e+00 3733.0
6 TraesCS7D01G074800 chr4A 89.827 1386 78 28 3844 5185 655261336 655259970 0.000000e+00 1720.0
7 TraesCS7D01G074800 chr4A 94.177 498 15 8 3330 3816 655261824 655261330 0.000000e+00 747.0
8 TraesCS7D01G074800 chr4A 88.462 78 8 1 568 645 655397658 655397582 5.530000e-15 93.5
9 TraesCS7D01G074800 chr3B 79.221 231 31 14 568 794 377861779 377861996 1.500000e-30 145.0
10 TraesCS7D01G074800 chr5B 87.395 119 13 2 4471 4588 640805271 640805154 9.060000e-28 135.0
11 TraesCS7D01G074800 chr4D 93.478 46 3 0 514 559 509132326 509132281 9.320000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G074800 chr7D 44299616 44304800 5184 True 9575.000000 9575 100.000000 1 5185 1 chr7D.!!$R1 5184
1 TraesCS7D01G074800 chr7A 46722037 46726570 4533 True 1751.000000 4159 90.383333 994 5173 3 chr7A.!!$R2 4179
2 TraesCS7D01G074800 chr7A 46765144 46765958 814 True 1177.000000 1177 92.548000 1 831 1 chr7A.!!$R1 830
3 TraesCS7D01G074800 chr4A 655259970 655264208 4238 True 2066.666667 3733 93.153000 988 5185 3 chr4A.!!$R2 4197

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
914 916 0.031010 GACAGATAGGACCCACCCCT 60.031 60.000 0.0 0.0 40.05 4.79 F
981 983 0.106868 GGTAAATCGGGGTTCAGGGG 60.107 60.000 0.0 0.0 0.00 4.79 F
982 984 0.622136 GTAAATCGGGGTTCAGGGGT 59.378 55.000 0.0 0.0 0.00 4.95 F
983 985 0.913924 TAAATCGGGGTTCAGGGGTC 59.086 55.000 0.0 0.0 0.00 4.46 F
991 993 1.079057 GTTCAGGGGTCGCTCCTTC 60.079 63.158 0.0 0.0 36.25 3.46 F
2508 2510 1.272480 GCCCTTCTTGGTGGGTGTAAT 60.272 52.381 0.0 0.0 45.06 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2529 2531 1.702182 TTCTTGCTGCCAAATCACCA 58.298 45.000 0.0 0.0 0.0 4.17 R
2902 2904 2.519013 ACAAAATGCTTCCCTCTGACC 58.481 47.619 0.0 0.0 0.0 4.02 R
2981 2983 1.755380 GGTACTCACGGGCTCATAGTT 59.245 52.381 0.0 0.0 0.0 2.24 R
2983 2985 1.693627 AGGTACTCACGGGCTCATAG 58.306 55.000 0.0 0.0 0.0 2.23 R
2984 2986 3.918134 AGGTACTCACGGGCTCATA 57.082 52.632 0.0 0.0 0.0 2.15 R
4293 4495 0.178992 CCTGTTGGTGGGCTTCAAGA 60.179 55.000 0.0 0.0 0.0 3.02 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
37 38 1.080638 TGGGTCTTAATGCAAGGGGT 58.919 50.000 0.00 0.00 34.76 4.95
53 54 6.272324 TGCAAGGGGTAACATTATAGATAGCT 59.728 38.462 0.00 0.00 39.74 3.32
159 160 9.579932 AAGAAACTTCTCATGTTTTAGAGGAAT 57.420 29.630 0.00 0.00 37.70 3.01
218 219 4.876107 ACCAAACATCGTCTTACATCATCC 59.124 41.667 0.00 0.00 0.00 3.51
239 240 4.343526 TCCAGTTTGCATACAACAACCAAT 59.656 37.500 10.02 0.00 34.87 3.16
258 259 5.163513 CCAATGTGCTACCTCAAATTTGAC 58.836 41.667 16.91 7.68 32.90 3.18
285 286 7.573710 ACATAGGTTGCAGTGGATTAGATAAA 58.426 34.615 0.00 0.00 0.00 1.40
286 287 8.052748 ACATAGGTTGCAGTGGATTAGATAAAA 58.947 33.333 0.00 0.00 0.00 1.52
287 288 8.902806 CATAGGTTGCAGTGGATTAGATAAAAA 58.097 33.333 0.00 0.00 0.00 1.94
322 324 9.931210 AATCAACTTTGTCTACTTTAAGAAACG 57.069 29.630 0.00 0.00 0.00 3.60
327 329 9.369904 ACTTTGTCTACTTTAAGAAACGTGTAA 57.630 29.630 0.00 0.00 0.00 2.41
450 452 9.853555 TGATTAATAATACAACAAACTGCTTGG 57.146 29.630 0.00 0.00 39.56 3.61
479 481 5.847111 TTACTAGTTGATACACCGCTGAT 57.153 39.130 0.00 0.00 0.00 2.90
511 513 2.290367 GCAATTCTTTTGGCGGCTTTTT 59.710 40.909 11.43 0.00 0.00 1.94
538 540 3.939592 GCTGGGTAGGTGACAGTTTATTC 59.060 47.826 0.00 0.00 34.79 1.75
539 541 4.514401 CTGGGTAGGTGACAGTTTATTCC 58.486 47.826 0.00 0.00 0.00 3.01
571 573 2.979678 AGAAGCCAGAACTGACCCTTAA 59.020 45.455 3.19 0.00 0.00 1.85
575 577 3.200165 AGCCAGAACTGACCCTTAATACC 59.800 47.826 3.19 0.00 0.00 2.73
576 578 3.054655 GCCAGAACTGACCCTTAATACCA 60.055 47.826 3.19 0.00 0.00 3.25
583 585 8.925338 AGAACTGACCCTTAATACCATTACTAG 58.075 37.037 0.00 0.00 0.00 2.57
590 592 6.485648 CCCTTAATACCATTACTAGTTGGCAC 59.514 42.308 12.69 0.00 36.41 5.01
611 613 9.149225 TGGCACAAATTTAATAGTTGCTAAATG 57.851 29.630 0.00 0.00 35.28 2.32
612 614 9.364989 GGCACAAATTTAATAGTTGCTAAATGA 57.635 29.630 0.00 0.00 35.28 2.57
634 636 5.920840 TGATGTTTACTATCGATGCTAGCAC 59.079 40.000 22.07 13.05 0.00 4.40
698 700 4.536090 ACATCCTACTCCTCCAATCAAACA 59.464 41.667 0.00 0.00 0.00 2.83
701 703 4.782691 TCCTACTCCTCCAATCAAACATCA 59.217 41.667 0.00 0.00 0.00 3.07
705 707 5.006386 ACTCCTCCAATCAAACATCAAGAC 58.994 41.667 0.00 0.00 0.00 3.01
720 722 2.017049 CAAGACGGGACCATTCCATTC 58.983 52.381 0.00 0.00 44.98 2.67
728 730 2.158264 GGACCATTCCATTCCATCCCAT 60.158 50.000 0.00 0.00 42.30 4.00
737 739 3.558746 CCATTCCATCCCATGAGCTCTAC 60.559 52.174 16.19 0.00 0.00 2.59
754 756 6.963796 AGCTCTACAAAACAAGAACATGAAG 58.036 36.000 0.00 0.00 0.00 3.02
768 770 3.950397 ACATGAAGCCATTCCGTTCTAA 58.050 40.909 0.00 0.00 34.28 2.10
776 778 5.192927 AGCCATTCCGTTCTAATGAAATGA 58.807 37.500 0.00 0.00 36.61 2.57
826 828 3.195825 CCACAAACCAAACACACCCTAAA 59.804 43.478 0.00 0.00 0.00 1.85
828 830 3.449377 ACAAACCAAACACACCCTAAAGG 59.551 43.478 0.00 0.00 43.78 3.11
830 832 0.966179 CCAAACACACCCTAAAGGCC 59.034 55.000 0.00 0.00 40.58 5.19
831 833 1.480498 CCAAACACACCCTAAAGGCCT 60.480 52.381 0.00 0.00 40.58 5.19
832 834 2.224917 CCAAACACACCCTAAAGGCCTA 60.225 50.000 5.16 0.00 40.58 3.93
833 835 3.492337 CAAACACACCCTAAAGGCCTAA 58.508 45.455 5.16 0.00 40.58 2.69
834 836 3.887916 AACACACCCTAAAGGCCTAAA 57.112 42.857 5.16 0.00 40.58 1.85
835 837 3.150458 ACACACCCTAAAGGCCTAAAC 57.850 47.619 5.16 0.00 40.58 2.01
836 838 2.444010 ACACACCCTAAAGGCCTAAACA 59.556 45.455 5.16 0.00 40.58 2.83
837 839 3.075432 ACACACCCTAAAGGCCTAAACAT 59.925 43.478 5.16 0.00 40.58 2.71
838 840 4.290196 ACACACCCTAAAGGCCTAAACATA 59.710 41.667 5.16 0.00 40.58 2.29
839 841 4.881850 CACACCCTAAAGGCCTAAACATAG 59.118 45.833 5.16 4.12 40.58 2.23
840 842 4.786454 ACACCCTAAAGGCCTAAACATAGA 59.214 41.667 5.16 0.00 40.58 1.98
841 843 5.123936 CACCCTAAAGGCCTAAACATAGAC 58.876 45.833 5.16 0.00 40.58 2.59
842 844 4.165565 ACCCTAAAGGCCTAAACATAGACC 59.834 45.833 5.16 0.00 40.58 3.85
843 845 4.165372 CCCTAAAGGCCTAAACATAGACCA 59.835 45.833 5.16 0.00 0.00 4.02
844 846 5.163088 CCCTAAAGGCCTAAACATAGACCAT 60.163 44.000 5.16 0.00 0.00 3.55
845 847 6.365520 CCTAAAGGCCTAAACATAGACCATT 58.634 40.000 5.16 0.00 0.00 3.16
846 848 6.486993 CCTAAAGGCCTAAACATAGACCATTC 59.513 42.308 5.16 0.00 0.00 2.67
847 849 4.439253 AGGCCTAAACATAGACCATTCC 57.561 45.455 1.29 0.00 0.00 3.01
848 850 3.785887 AGGCCTAAACATAGACCATTCCA 59.214 43.478 1.29 0.00 0.00 3.53
849 851 4.416848 AGGCCTAAACATAGACCATTCCAT 59.583 41.667 1.29 0.00 0.00 3.41
850 852 5.103515 AGGCCTAAACATAGACCATTCCATT 60.104 40.000 1.29 0.00 0.00 3.16
851 853 5.241728 GGCCTAAACATAGACCATTCCATTC 59.758 44.000 0.00 0.00 0.00 2.67
852 854 5.827797 GCCTAAACATAGACCATTCCATTCA 59.172 40.000 0.00 0.00 0.00 2.57
853 855 6.238759 GCCTAAACATAGACCATTCCATTCAC 60.239 42.308 0.00 0.00 0.00 3.18
854 856 6.828273 CCTAAACATAGACCATTCCATTCACA 59.172 38.462 0.00 0.00 0.00 3.58
855 857 6.764308 AAACATAGACCATTCCATTCACAG 57.236 37.500 0.00 0.00 0.00 3.66
856 858 5.698741 ACATAGACCATTCCATTCACAGA 57.301 39.130 0.00 0.00 0.00 3.41
857 859 5.431765 ACATAGACCATTCCATTCACAGAC 58.568 41.667 0.00 0.00 0.00 3.51
858 860 5.190528 ACATAGACCATTCCATTCACAGACT 59.809 40.000 0.00 0.00 0.00 3.24
859 861 4.213564 AGACCATTCCATTCACAGACTC 57.786 45.455 0.00 0.00 0.00 3.36
860 862 3.843027 AGACCATTCCATTCACAGACTCT 59.157 43.478 0.00 0.00 0.00 3.24
861 863 3.937706 GACCATTCCATTCACAGACTCTG 59.062 47.826 4.36 4.36 37.52 3.35
862 864 3.276857 CCATTCCATTCACAGACTCTGG 58.723 50.000 10.86 0.24 35.51 3.86
863 865 3.054875 CCATTCCATTCACAGACTCTGGA 60.055 47.826 10.86 2.56 35.51 3.86
864 866 4.384978 CCATTCCATTCACAGACTCTGGAT 60.385 45.833 10.86 0.00 35.99 3.41
865 867 4.916041 TTCCATTCACAGACTCTGGATT 57.084 40.909 10.86 0.00 35.99 3.01
866 868 4.916041 TCCATTCACAGACTCTGGATTT 57.084 40.909 10.86 0.00 35.51 2.17
867 869 4.836825 TCCATTCACAGACTCTGGATTTC 58.163 43.478 10.86 0.00 35.51 2.17
868 870 3.944015 CCATTCACAGACTCTGGATTTCC 59.056 47.826 10.86 0.00 35.51 3.13
869 871 4.566278 CCATTCACAGACTCTGGATTTCCA 60.566 45.833 10.86 0.00 45.30 3.53
882 884 5.441718 TGGATTTCCAGATTAGACTTGCT 57.558 39.130 0.00 0.00 42.01 3.91
883 885 5.819991 TGGATTTCCAGATTAGACTTGCTT 58.180 37.500 0.00 0.00 42.01 3.91
884 886 5.649395 TGGATTTCCAGATTAGACTTGCTTG 59.351 40.000 0.00 0.00 42.01 4.01
885 887 5.882557 GGATTTCCAGATTAGACTTGCTTGA 59.117 40.000 0.00 0.00 35.64 3.02
886 888 6.545298 GGATTTCCAGATTAGACTTGCTTGAT 59.455 38.462 0.00 0.00 35.64 2.57
887 889 7.716998 GGATTTCCAGATTAGACTTGCTTGATA 59.283 37.037 0.00 0.00 35.64 2.15
888 890 8.674263 ATTTCCAGATTAGACTTGCTTGATAG 57.326 34.615 0.00 0.00 0.00 2.08
900 902 3.516981 GCTTGATAGCAGACTGACAGA 57.483 47.619 10.08 0.00 46.95 3.41
901 903 4.057406 GCTTGATAGCAGACTGACAGAT 57.943 45.455 10.08 0.00 46.95 2.90
902 904 5.193663 GCTTGATAGCAGACTGACAGATA 57.806 43.478 10.08 0.00 46.95 1.98
903 905 5.221880 GCTTGATAGCAGACTGACAGATAG 58.778 45.833 10.08 0.00 46.95 2.08
904 906 5.771469 CTTGATAGCAGACTGACAGATAGG 58.229 45.833 10.08 0.00 0.00 2.57
905 907 5.053978 TGATAGCAGACTGACAGATAGGA 57.946 43.478 10.08 0.00 0.00 2.94
906 908 4.824537 TGATAGCAGACTGACAGATAGGAC 59.175 45.833 10.08 0.00 0.00 3.85
907 909 2.383855 AGCAGACTGACAGATAGGACC 58.616 52.381 10.08 0.00 0.00 4.46
908 910 1.410882 GCAGACTGACAGATAGGACCC 59.589 57.143 10.08 0.00 0.00 4.46
909 911 2.739943 CAGACTGACAGATAGGACCCA 58.260 52.381 10.08 0.00 0.00 4.51
910 912 2.428890 CAGACTGACAGATAGGACCCAC 59.571 54.545 10.08 0.00 0.00 4.61
911 913 1.757699 GACTGACAGATAGGACCCACC 59.242 57.143 10.08 0.00 39.35 4.61
912 914 1.123928 CTGACAGATAGGACCCACCC 58.876 60.000 0.00 0.00 40.05 4.61
913 915 0.326238 TGACAGATAGGACCCACCCC 60.326 60.000 0.00 0.00 40.05 4.95
914 916 0.031010 GACAGATAGGACCCACCCCT 60.031 60.000 0.00 0.00 40.05 4.79
915 917 0.031010 ACAGATAGGACCCACCCCTC 60.031 60.000 0.00 0.00 40.05 4.30
916 918 1.115930 CAGATAGGACCCACCCCTCG 61.116 65.000 0.00 0.00 40.05 4.63
917 919 1.837499 GATAGGACCCACCCCTCGG 60.837 68.421 0.00 0.00 40.05 4.63
918 920 4.791069 TAGGACCCACCCCTCGGC 62.791 72.222 0.00 0.00 40.05 5.54
924 926 4.394712 CCACCCCTCGGCTCACAC 62.395 72.222 0.00 0.00 0.00 3.82
925 927 4.742201 CACCCCTCGGCTCACACG 62.742 72.222 0.00 0.00 0.00 4.49
927 929 4.742201 CCCCTCGGCTCACACGTG 62.742 72.222 15.48 15.48 0.00 4.49
928 930 4.742201 CCCTCGGCTCACACGTGG 62.742 72.222 21.57 9.11 42.72 4.94
929 931 4.742201 CCTCGGCTCACACGTGGG 62.742 72.222 21.57 17.59 40.27 4.61
936 938 1.513158 CTCACACGTGGGCTAGAGG 59.487 63.158 21.57 0.00 0.00 3.69
937 939 1.228769 TCACACGTGGGCTAGAGGT 60.229 57.895 21.57 0.00 0.00 3.85
938 940 0.830444 TCACACGTGGGCTAGAGGTT 60.830 55.000 21.57 0.00 0.00 3.50
939 941 0.389948 CACACGTGGGCTAGAGGTTC 60.390 60.000 21.57 0.00 0.00 3.62
940 942 1.218316 CACGTGGGCTAGAGGTTCC 59.782 63.158 7.95 0.00 0.00 3.62
941 943 1.229082 ACGTGGGCTAGAGGTTCCA 60.229 57.895 0.00 0.00 0.00 3.53
942 944 1.218316 CGTGGGCTAGAGGTTCCAC 59.782 63.158 0.00 0.00 44.39 4.02
943 945 1.218316 GTGGGCTAGAGGTTCCACG 59.782 63.158 0.00 0.00 39.97 4.94
944 946 2.187163 GGGCTAGAGGTTCCACGC 59.813 66.667 0.00 0.00 0.00 5.34
945 947 2.359967 GGGCTAGAGGTTCCACGCT 61.360 63.158 0.00 0.00 0.00 5.07
946 948 1.153549 GGCTAGAGGTTCCACGCTG 60.154 63.158 0.00 0.00 0.00 5.18
947 949 1.153549 GCTAGAGGTTCCACGCTGG 60.154 63.158 0.00 0.00 39.43 4.85
948 950 1.889530 GCTAGAGGTTCCACGCTGGT 61.890 60.000 0.00 0.00 39.03 4.00
949 951 0.608640 CTAGAGGTTCCACGCTGGTT 59.391 55.000 4.33 0.00 39.03 3.67
950 952 0.320374 TAGAGGTTCCACGCTGGTTG 59.680 55.000 4.33 0.00 39.03 3.77
951 953 1.070786 GAGGTTCCACGCTGGTTGA 59.929 57.895 4.33 0.00 39.03 3.18
952 954 1.227853 AGGTTCCACGCTGGTTGAC 60.228 57.895 4.33 3.10 39.03 3.18
953 955 2.258726 GGTTCCACGCTGGTTGACC 61.259 63.158 4.33 0.00 39.03 4.02
954 956 2.280524 TTCCACGCTGGTTGACCG 60.281 61.111 4.33 0.00 39.03 4.79
955 957 2.798364 TTCCACGCTGGTTGACCGA 61.798 57.895 4.33 0.00 39.03 4.69
956 958 2.981977 TTCCACGCTGGTTGACCGAC 62.982 60.000 4.33 0.00 39.03 4.79
957 959 3.403057 CACGCTGGTTGACCGACG 61.403 66.667 11.59 11.59 41.08 5.12
958 960 3.908081 ACGCTGGTTGACCGACGT 61.908 61.111 12.67 12.67 42.70 4.34
959 961 3.403057 CGCTGGTTGACCGACGTG 61.403 66.667 0.00 0.00 39.43 4.49
960 962 3.041940 GCTGGTTGACCGACGTGG 61.042 66.667 0.00 0.00 46.41 4.94
961 963 3.041940 CTGGTTGACCGACGTGGC 61.042 66.667 0.00 0.00 43.94 5.01
962 964 4.953868 TGGTTGACCGACGTGGCG 62.954 66.667 0.00 0.00 43.94 5.69
969 971 3.391355 CCGACGTGGCGGTAAATC 58.609 61.111 5.84 0.00 46.07 2.17
970 972 2.510594 CCGACGTGGCGGTAAATCG 61.511 63.158 5.84 0.00 46.07 3.34
971 973 2.510594 CGACGTGGCGGTAAATCGG 61.511 63.158 0.00 0.00 0.00 4.18
972 974 2.125431 ACGTGGCGGTAAATCGGG 60.125 61.111 0.00 0.00 0.00 5.14
973 975 2.893404 CGTGGCGGTAAATCGGGG 60.893 66.667 0.00 0.00 0.00 5.73
974 976 2.269883 GTGGCGGTAAATCGGGGT 59.730 61.111 0.00 0.00 0.00 4.95
975 977 1.377594 GTGGCGGTAAATCGGGGTT 60.378 57.895 0.00 0.00 0.00 4.11
976 978 1.078285 TGGCGGTAAATCGGGGTTC 60.078 57.895 0.00 0.00 0.00 3.62
977 979 1.078285 GGCGGTAAATCGGGGTTCA 60.078 57.895 0.00 0.00 0.00 3.18
978 980 1.093496 GGCGGTAAATCGGGGTTCAG 61.093 60.000 0.00 0.00 0.00 3.02
979 981 1.093496 GCGGTAAATCGGGGTTCAGG 61.093 60.000 0.00 0.00 0.00 3.86
980 982 0.463116 CGGTAAATCGGGGTTCAGGG 60.463 60.000 0.00 0.00 0.00 4.45
981 983 0.106868 GGTAAATCGGGGTTCAGGGG 60.107 60.000 0.00 0.00 0.00 4.79
982 984 0.622136 GTAAATCGGGGTTCAGGGGT 59.378 55.000 0.00 0.00 0.00 4.95
983 985 0.913924 TAAATCGGGGTTCAGGGGTC 59.086 55.000 0.00 0.00 0.00 4.46
984 986 2.193087 AAATCGGGGTTCAGGGGTCG 62.193 60.000 0.00 0.00 0.00 4.79
987 989 4.097361 GGGGTTCAGGGGTCGCTC 62.097 72.222 0.00 0.00 0.00 5.03
988 990 4.097361 GGGTTCAGGGGTCGCTCC 62.097 72.222 0.00 0.00 0.00 4.70
989 991 3.003763 GGTTCAGGGGTCGCTCCT 61.004 66.667 0.00 0.00 36.25 3.69
990 992 2.593956 GGTTCAGGGGTCGCTCCTT 61.594 63.158 0.00 0.00 36.25 3.36
991 993 1.079057 GTTCAGGGGTCGCTCCTTC 60.079 63.158 0.00 0.00 36.25 3.46
992 994 1.535444 TTCAGGGGTCGCTCCTTCA 60.535 57.895 0.00 0.00 36.25 3.02
1067 1069 1.954362 CTCGCCTCCACCTTCTCCTG 61.954 65.000 0.00 0.00 0.00 3.86
1971 1973 3.307691 GGATCAGACCAAATCAGGTGACA 60.308 47.826 0.00 0.00 43.38 3.58
1983 1985 1.411977 CAGGTGACATTTTTGGGTGCA 59.588 47.619 0.00 0.00 0.00 4.57
2109 2111 6.142798 CACTCATGAATTTATACGCCAAATGC 59.857 38.462 0.00 0.00 0.00 3.56
2356 2358 8.031277 GGATATTTGAATACATGGCAAAGGATC 58.969 37.037 0.00 8.86 35.29 3.36
2455 2457 5.572896 GCCAAAAGATTAATCAACGGTCTTG 59.427 40.000 17.56 8.89 0.00 3.02
2496 2498 2.269940 ACTGTATGGAGTGCCCTTCTT 58.730 47.619 0.00 0.00 35.38 2.52
2508 2510 1.272480 GCCCTTCTTGGTGGGTGTAAT 60.272 52.381 0.00 0.00 45.06 1.89
2529 2531 4.274602 TGCACATGGAAATGAAAGCATT 57.725 36.364 0.00 0.00 46.35 3.56
2650 2652 1.446907 AGCAGCAAAGATTCGGTCTG 58.553 50.000 0.00 0.00 37.23 3.51
2870 2872 8.770438 GATCTGGTGGATCTTCAAGTATAATC 57.230 38.462 0.00 0.00 45.38 1.75
2902 2904 6.313744 ACGAAAGTAAAGTTCCAGGATTTG 57.686 37.500 0.00 0.00 46.88 2.32
2922 2924 2.158475 TGGTCAGAGGGAAGCATTTTGT 60.158 45.455 0.00 0.00 0.00 2.83
2924 2926 3.691609 GGTCAGAGGGAAGCATTTTGTAG 59.308 47.826 0.00 0.00 0.00 2.74
2929 2931 3.084786 AGGGAAGCATTTTGTAGCACTC 58.915 45.455 0.00 0.00 0.00 3.51
2949 2951 4.101741 ACTCTATCTGACAATTGGCCTACC 59.898 45.833 9.30 0.00 0.00 3.18
2950 2952 2.736670 ATCTGACAATTGGCCTACCC 57.263 50.000 9.30 0.00 33.59 3.69
2970 2972 6.088541 ACCCTGTAGAGTTTAGACCTATGA 57.911 41.667 0.00 0.00 0.00 2.15
2980 2982 9.036980 AGAGTTTAGACCTATGATGTTAGTGTT 57.963 33.333 0.00 0.00 0.00 3.32
2990 2992 9.197694 CCTATGATGTTAGTGTTAACTATGAGC 57.802 37.037 7.22 0.00 38.69 4.26
2991 2993 9.197694 CTATGATGTTAGTGTTAACTATGAGCC 57.802 37.037 7.22 0.00 38.69 4.70
2992 2994 6.346096 TGATGTTAGTGTTAACTATGAGCCC 58.654 40.000 7.22 0.00 38.69 5.19
2993 2995 4.751060 TGTTAGTGTTAACTATGAGCCCG 58.249 43.478 7.22 0.00 38.69 6.13
3002 3004 1.063867 ACTATGAGCCCGTGAGTACCT 60.064 52.381 0.00 0.00 0.00 3.08
3025 3028 2.019984 GGCTAAGTTGCCCTCATCTTG 58.980 52.381 5.33 0.00 46.82 3.02
3064 3067 1.673665 CACCTGGGCTCTTGTCTGC 60.674 63.158 0.00 0.00 0.00 4.26
3139 3143 2.810852 CCTTGCAGAAGTCTTGACCTTC 59.189 50.000 0.00 0.00 38.87 3.46
3179 3183 4.287067 TCTTATTTCTCTGGTTCACTGGCT 59.713 41.667 0.00 0.00 0.00 4.75
3189 3193 3.289834 CACTGGCTGCGGCTTTGT 61.290 61.111 18.85 10.87 38.73 2.83
3206 3210 3.788227 TTGTCATGTTAGAGGGTGCTT 57.212 42.857 0.00 0.00 0.00 3.91
3207 3211 3.057969 TGTCATGTTAGAGGGTGCTTG 57.942 47.619 0.00 0.00 0.00 4.01
3208 3212 1.740025 GTCATGTTAGAGGGTGCTTGC 59.260 52.381 0.00 0.00 0.00 4.01
3209 3213 1.630369 TCATGTTAGAGGGTGCTTGCT 59.370 47.619 0.00 0.00 0.00 3.91
3214 3218 2.866762 GTTAGAGGGTGCTTGCTATTCG 59.133 50.000 0.00 0.00 0.00 3.34
3565 3643 2.476854 GCTGAACCATCATTTGAGCGAC 60.477 50.000 0.00 0.00 34.37 5.19
3718 3812 4.309933 TCATGTGTGACTCAACTTGCTAG 58.690 43.478 0.00 0.00 0.00 3.42
3744 3838 2.618241 TGTTACAGTTGCAGGCAAGAAG 59.382 45.455 6.99 3.12 36.52 2.85
3797 3896 4.758688 TGTGAACTCTGCCATGTATGTAG 58.241 43.478 0.00 0.00 0.00 2.74
3840 3943 1.072159 GCAGTGGCTCAGAAGGTGT 59.928 57.895 0.00 0.00 36.96 4.16
3842 3945 0.683973 CAGTGGCTCAGAAGGTGTCT 59.316 55.000 0.00 0.00 36.88 3.41
3907 4010 2.360165 ACTGTTTAGAACACTCGGACGT 59.640 45.455 0.00 0.00 36.25 4.34
3926 4029 3.175152 CGTTGCTGCAAAACTGTTTGTA 58.825 40.909 17.80 0.72 45.06 2.41
3969 4072 6.628856 GCATCGTGCATTGTAAACTGTAATAG 59.371 38.462 0.00 0.00 44.26 1.73
3974 4078 7.312899 GTGCATTGTAAACTGTAATAGCCTTT 58.687 34.615 0.00 0.00 0.00 3.11
4001 4107 5.586243 TGAGAAGCAAGTCCATTGTAATAGC 59.414 40.000 0.00 0.00 41.29 2.97
4008 4114 5.847111 AGTCCATTGTAATAGCTGTCGTA 57.153 39.130 0.00 0.00 0.00 3.43
4101 4207 3.620966 GCCTGAGATTCTTGGCACTTACT 60.621 47.826 20.02 0.00 44.34 2.24
4132 4238 1.173913 CTGTCGGGATGGGGTTTTTC 58.826 55.000 0.00 0.00 0.00 2.29
4133 4239 0.774908 TGTCGGGATGGGGTTTTTCT 59.225 50.000 0.00 0.00 0.00 2.52
4136 4242 2.230508 GTCGGGATGGGGTTTTTCTTTC 59.769 50.000 0.00 0.00 0.00 2.62
4137 4243 1.201414 CGGGATGGGGTTTTTCTTTCG 59.799 52.381 0.00 0.00 0.00 3.46
4138 4244 2.521126 GGGATGGGGTTTTTCTTTCGA 58.479 47.619 0.00 0.00 0.00 3.71
4140 4246 3.418047 GGATGGGGTTTTTCTTTCGAGA 58.582 45.455 0.00 0.00 0.00 4.04
4190 4296 6.555463 AGCATCTTCAATGGGAAATCAATT 57.445 33.333 0.00 0.00 34.44 2.32
4195 4301 9.309516 CATCTTCAATGGGAAATCAATTAGTTG 57.690 33.333 0.00 0.00 34.44 3.16
4203 4316 5.639082 GGGAAATCAATTAGTTGTTGCCAAG 59.361 40.000 6.88 0.00 34.22 3.61
4288 4490 1.828979 TACATTCCGAGGCCCAAAAC 58.171 50.000 0.00 0.00 0.00 2.43
4293 4495 2.115266 CGAGGCCCAAAACCAGGT 59.885 61.111 0.00 0.00 0.00 4.00
4308 4510 0.178992 CAGGTCTTGAAGCCCACCAA 60.179 55.000 0.00 0.00 0.00 3.67
4319 4521 2.198426 CCACCAACAGGCCCACTT 59.802 61.111 0.00 0.00 0.00 3.16
4320 4522 1.458486 CCACCAACAGGCCCACTTA 59.542 57.895 0.00 0.00 0.00 2.24
4809 5304 1.001181 TGCGTCAAGGTAGTACCAACC 59.999 52.381 21.49 6.86 41.95 3.77
4816 5311 0.459078 GGTAGTACCAACCGAGCTCC 59.541 60.000 14.82 0.00 38.42 4.70
4817 5312 1.472188 GTAGTACCAACCGAGCTCCT 58.528 55.000 8.47 0.00 0.00 3.69
4819 5314 0.971447 AGTACCAACCGAGCTCCTCC 60.971 60.000 8.47 0.00 0.00 4.30
4821 5316 2.164332 TACCAACCGAGCTCCTCCCT 62.164 60.000 8.47 0.00 0.00 4.20
4822 5317 2.294078 CCAACCGAGCTCCTCCCTT 61.294 63.158 8.47 0.00 0.00 3.95
4823 5318 1.219393 CAACCGAGCTCCTCCCTTC 59.781 63.158 8.47 0.00 0.00 3.46
4824 5319 1.079438 AACCGAGCTCCTCCCTTCT 59.921 57.895 8.47 0.00 0.00 2.85
4825 5320 1.261238 AACCGAGCTCCTCCCTTCTG 61.261 60.000 8.47 0.00 0.00 3.02
4827 5322 2.057408 CGAGCTCCTCCCTTCTGCT 61.057 63.158 8.47 0.00 36.63 4.24
4828 5323 0.753479 CGAGCTCCTCCCTTCTGCTA 60.753 60.000 8.47 0.00 33.83 3.49
4829 5324 1.039856 GAGCTCCTCCCTTCTGCTAG 58.960 60.000 0.87 0.00 33.83 3.42
4848 5355 7.290014 TCTGCTAGTCCCTTGATAATGTTCATA 59.710 37.037 0.00 0.00 0.00 2.15
4920 5432 9.856488 TTATTAAACTAAACCATTTTATGCGCA 57.144 25.926 14.96 14.96 0.00 6.09
4962 5474 8.586273 GTGATTGAATGAACGAATGTTTTATGG 58.414 33.333 0.00 0.00 38.78 2.74
4965 5477 5.047731 TGAATGAACGAATGTTTTATGGCCA 60.048 36.000 8.56 8.56 38.78 5.36
4966 5478 4.855715 TGAACGAATGTTTTATGGCCAA 57.144 36.364 10.96 0.00 38.78 4.52
4974 5486 5.697082 ATGTTTTATGGCCAACATGGATT 57.303 34.783 17.98 0.00 41.18 3.01
4986 5498 4.563993 CCAACATGGATTGAATGCTTTGGT 60.564 41.667 13.24 2.40 40.96 3.67
4988 5500 3.119388 ACATGGATTGAATGCTTTGGTCG 60.119 43.478 0.00 0.00 0.00 4.79
4990 5502 3.680490 TGGATTGAATGCTTTGGTCGTA 58.320 40.909 0.00 0.00 0.00 3.43
4996 5508 6.811253 TTGAATGCTTTGGTCGTACTTAAT 57.189 33.333 0.00 0.00 0.00 1.40
5033 5545 3.648982 TGGCGTGTGCTTGAAGCG 61.649 61.111 13.05 0.00 46.26 4.68
5100 5612 4.374702 GCGTGGTCTTGCTGCGTG 62.375 66.667 0.00 0.00 0.00 5.34
5113 5625 1.382522 CTGCGTGTCTGCCCATTATT 58.617 50.000 0.00 0.00 0.00 1.40
5115 5627 3.141398 CTGCGTGTCTGCCCATTATTAT 58.859 45.455 0.00 0.00 0.00 1.28
5116 5628 3.550820 TGCGTGTCTGCCCATTATTATT 58.449 40.909 0.00 0.00 0.00 1.40
5175 5687 5.675538 AGTAATTTCTGAGCTACCATGACC 58.324 41.667 0.00 0.00 0.00 4.02
5176 5688 2.672961 TTTCTGAGCTACCATGACCG 57.327 50.000 0.00 0.00 0.00 4.79
5179 5691 1.680522 CTGAGCTACCATGACCGGCT 61.681 60.000 0.00 0.00 35.86 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.897969 GGAATCCTCGGGCTAGTCATTA 59.102 50.000 0.00 0.00 0.00 1.90
159 160 1.768870 GAGCTAGGGTTGGAGCCATTA 59.231 52.381 0.00 0.00 39.65 1.90
218 219 5.049167 ACATTGGTTGTTGTATGCAAACTG 58.951 37.500 0.00 0.00 33.74 3.16
239 240 5.616270 TGTAGTCAAATTTGAGGTAGCACA 58.384 37.500 21.05 14.33 37.98 4.57
258 259 6.161855 TCTAATCCACTGCAACCTATGTAG 57.838 41.667 0.00 0.00 46.19 2.74
399 401 6.014647 TGCTCTAAGAGTTAAGGTAGACCAA 58.985 40.000 0.66 0.00 33.20 3.67
450 452 6.141369 GCGGTGTATCAACTAGTAATTCGTAC 59.859 42.308 0.00 0.00 0.00 3.67
511 513 2.976882 ACTGTCACCTACCCAGCTTAAA 59.023 45.455 0.00 0.00 0.00 1.52
525 527 9.774742 CTAAAATAAGCTGGAATAAACTGTCAC 57.225 33.333 0.00 0.00 0.00 3.67
526 528 9.733556 TCTAAAATAAGCTGGAATAAACTGTCA 57.266 29.630 0.00 0.00 0.00 3.58
538 540 5.649831 AGTTCTGGCTTCTAAAATAAGCTGG 59.350 40.000 7.65 2.17 46.81 4.85
539 541 6.372659 TCAGTTCTGGCTTCTAAAATAAGCTG 59.627 38.462 7.65 2.46 46.81 4.24
555 557 4.837093 TGGTATTAAGGGTCAGTTCTGG 57.163 45.455 0.00 0.00 0.00 3.86
571 573 7.954666 AATTTGTGCCAACTAGTAATGGTAT 57.045 32.000 13.87 0.00 39.00 2.73
583 585 8.527567 TTAGCAACTATTAAATTTGTGCCAAC 57.472 30.769 0.00 0.00 0.00 3.77
611 613 6.153067 AGTGCTAGCATCGATAGTAAACATC 58.847 40.000 22.51 1.48 37.40 3.06
612 614 6.090483 AGTGCTAGCATCGATAGTAAACAT 57.910 37.500 22.51 0.00 37.40 2.71
613 615 5.515797 AGTGCTAGCATCGATAGTAAACA 57.484 39.130 22.51 0.00 37.40 2.83
614 616 5.977725 TCAAGTGCTAGCATCGATAGTAAAC 59.022 40.000 22.51 2.89 37.40 2.01
615 617 6.144078 TCAAGTGCTAGCATCGATAGTAAA 57.856 37.500 22.51 0.00 37.40 2.01
616 618 5.767816 TCAAGTGCTAGCATCGATAGTAA 57.232 39.130 22.51 0.00 37.40 2.24
617 619 5.767816 TTCAAGTGCTAGCATCGATAGTA 57.232 39.130 22.51 0.21 37.40 1.82
618 620 4.655762 TTCAAGTGCTAGCATCGATAGT 57.344 40.909 22.51 0.00 37.40 2.12
619 621 5.973651 TTTTCAAGTGCTAGCATCGATAG 57.026 39.130 22.51 8.31 0.00 2.08
658 660 5.670485 AGGATGTAATACGCATCACTCAAA 58.330 37.500 7.46 0.00 43.17 2.69
698 700 1.285280 TGGAATGGTCCCGTCTTGAT 58.715 50.000 0.00 0.00 44.23 2.57
701 703 1.064685 GGAATGGAATGGTCCCGTCTT 60.065 52.381 0.00 0.00 44.23 3.01
705 707 1.609208 GATGGAATGGAATGGTCCCG 58.391 55.000 0.00 0.00 44.23 5.14
720 722 3.565764 TTTGTAGAGCTCATGGGATGG 57.434 47.619 17.77 0.00 0.00 3.51
728 730 6.054941 TCATGTTCTTGTTTTGTAGAGCTCA 58.945 36.000 17.77 0.00 0.00 4.26
737 739 5.178067 GGAATGGCTTCATGTTCTTGTTTTG 59.822 40.000 0.00 0.00 32.70 2.44
754 756 5.499139 TCATTTCATTAGAACGGAATGGC 57.501 39.130 0.00 0.00 35.42 4.40
791 793 8.428063 TGTTTGGTTTGTGGAATCAAATAGAAT 58.572 29.630 1.12 0.00 46.76 2.40
797 799 4.932200 GTGTGTTTGGTTTGTGGAATCAAA 59.068 37.500 0.00 0.00 44.06 2.69
828 830 5.827797 TGAATGGAATGGTCTATGTTTAGGC 59.172 40.000 0.00 0.00 0.00 3.93
830 832 7.770433 TCTGTGAATGGAATGGTCTATGTTTAG 59.230 37.037 0.00 0.00 0.00 1.85
831 833 7.552687 GTCTGTGAATGGAATGGTCTATGTTTA 59.447 37.037 0.00 0.00 0.00 2.01
832 834 6.375455 GTCTGTGAATGGAATGGTCTATGTTT 59.625 38.462 0.00 0.00 0.00 2.83
833 835 5.882557 GTCTGTGAATGGAATGGTCTATGTT 59.117 40.000 0.00 0.00 0.00 2.71
834 836 5.190528 AGTCTGTGAATGGAATGGTCTATGT 59.809 40.000 0.00 0.00 0.00 2.29
835 837 5.678583 AGTCTGTGAATGGAATGGTCTATG 58.321 41.667 0.00 0.00 0.00 2.23
836 838 5.664908 AGAGTCTGTGAATGGAATGGTCTAT 59.335 40.000 0.00 0.00 0.00 1.98
837 839 5.026121 AGAGTCTGTGAATGGAATGGTCTA 58.974 41.667 0.00 0.00 0.00 2.59
838 840 3.843027 AGAGTCTGTGAATGGAATGGTCT 59.157 43.478 0.00 0.00 0.00 3.85
839 841 3.937706 CAGAGTCTGTGAATGGAATGGTC 59.062 47.826 12.28 0.00 0.00 4.02
840 842 3.307975 CCAGAGTCTGTGAATGGAATGGT 60.308 47.826 18.74 0.00 32.55 3.55
841 843 3.054875 TCCAGAGTCTGTGAATGGAATGG 60.055 47.826 18.74 0.00 37.12 3.16
842 844 4.212143 TCCAGAGTCTGTGAATGGAATG 57.788 45.455 18.74 0.00 37.12 2.67
843 845 5.447778 AATCCAGAGTCTGTGAATGGAAT 57.552 39.130 18.74 0.00 42.98 3.01
844 846 4.916041 AATCCAGAGTCTGTGAATGGAA 57.084 40.909 18.74 0.00 42.98 3.53
845 847 4.323792 GGAAATCCAGAGTCTGTGAATGGA 60.324 45.833 18.74 9.05 43.82 3.41
846 848 3.944015 GGAAATCCAGAGTCTGTGAATGG 59.056 47.826 18.74 3.47 35.64 3.16
847 849 4.582869 TGGAAATCCAGAGTCTGTGAATG 58.417 43.478 18.74 3.33 42.01 2.67
848 850 4.916041 TGGAAATCCAGAGTCTGTGAAT 57.084 40.909 18.74 6.41 42.01 2.57
860 862 5.441718 AGCAAGTCTAATCTGGAAATCCA 57.558 39.130 1.53 1.53 45.30 3.41
861 863 5.882557 TCAAGCAAGTCTAATCTGGAAATCC 59.117 40.000 0.00 0.00 0.00 3.01
862 864 6.992063 TCAAGCAAGTCTAATCTGGAAATC 57.008 37.500 0.00 0.00 0.00 2.17
863 865 8.674263 CTATCAAGCAAGTCTAATCTGGAAAT 57.326 34.615 0.00 0.00 0.00 2.17
881 883 5.534278 TCCTATCTGTCAGTCTGCTATCAAG 59.466 44.000 0.00 0.00 0.00 3.02
882 884 5.300539 GTCCTATCTGTCAGTCTGCTATCAA 59.699 44.000 0.00 0.00 0.00 2.57
883 885 4.824537 GTCCTATCTGTCAGTCTGCTATCA 59.175 45.833 0.00 0.00 0.00 2.15
884 886 4.217550 GGTCCTATCTGTCAGTCTGCTATC 59.782 50.000 0.00 0.00 0.00 2.08
885 887 4.148838 GGTCCTATCTGTCAGTCTGCTAT 58.851 47.826 0.00 0.00 0.00 2.97
886 888 3.556999 GGTCCTATCTGTCAGTCTGCTA 58.443 50.000 0.00 0.00 0.00 3.49
887 889 2.383855 GGTCCTATCTGTCAGTCTGCT 58.616 52.381 0.00 0.00 0.00 4.24
888 890 1.410882 GGGTCCTATCTGTCAGTCTGC 59.589 57.143 0.00 0.00 0.00 4.26
889 891 2.428890 GTGGGTCCTATCTGTCAGTCTG 59.571 54.545 0.00 0.00 0.00 3.51
890 892 2.624557 GGTGGGTCCTATCTGTCAGTCT 60.625 54.545 0.00 0.00 0.00 3.24
891 893 1.757699 GGTGGGTCCTATCTGTCAGTC 59.242 57.143 0.00 0.00 0.00 3.51
892 894 1.622725 GGGTGGGTCCTATCTGTCAGT 60.623 57.143 0.00 0.00 36.25 3.41
893 895 1.123928 GGGTGGGTCCTATCTGTCAG 58.876 60.000 0.00 0.00 36.25 3.51
894 896 0.326238 GGGGTGGGTCCTATCTGTCA 60.326 60.000 0.00 0.00 36.25 3.58
895 897 0.031010 AGGGGTGGGTCCTATCTGTC 60.031 60.000 0.00 0.00 36.25 3.51
896 898 0.031010 GAGGGGTGGGTCCTATCTGT 60.031 60.000 0.00 0.00 34.21 3.41
897 899 1.115930 CGAGGGGTGGGTCCTATCTG 61.116 65.000 0.00 0.00 34.21 2.90
898 900 1.233369 CGAGGGGTGGGTCCTATCT 59.767 63.158 0.00 0.00 34.21 1.98
899 901 1.837499 CCGAGGGGTGGGTCCTATC 60.837 68.421 0.00 0.00 34.21 2.08
900 902 2.285868 CCGAGGGGTGGGTCCTAT 59.714 66.667 0.00 0.00 34.21 2.57
901 903 4.791069 GCCGAGGGGTGGGTCCTA 62.791 72.222 0.00 0.00 34.21 2.94
907 909 4.394712 GTGTGAGCCGAGGGGTGG 62.395 72.222 0.00 0.00 31.55 4.61
908 910 4.742201 CGTGTGAGCCGAGGGGTG 62.742 72.222 0.00 0.00 31.55 4.61
910 912 4.742201 CACGTGTGAGCCGAGGGG 62.742 72.222 7.58 0.00 0.00 4.79
911 913 4.742201 CCACGTGTGAGCCGAGGG 62.742 72.222 15.65 0.00 33.22 4.30
912 914 4.742201 CCCACGTGTGAGCCGAGG 62.742 72.222 15.65 1.51 36.07 4.63
915 917 3.989698 CTAGCCCACGTGTGAGCCG 62.990 68.421 15.65 5.10 34.65 5.52
916 918 2.125512 CTAGCCCACGTGTGAGCC 60.126 66.667 15.65 0.00 34.65 4.70
917 919 1.153745 CTCTAGCCCACGTGTGAGC 60.154 63.158 15.65 14.09 34.28 4.26
918 920 1.251527 ACCTCTAGCCCACGTGTGAG 61.252 60.000 15.65 12.48 0.00 3.51
919 921 0.830444 AACCTCTAGCCCACGTGTGA 60.830 55.000 15.65 3.83 0.00 3.58
920 922 0.389948 GAACCTCTAGCCCACGTGTG 60.390 60.000 15.65 3.72 0.00 3.82
921 923 1.542187 GGAACCTCTAGCCCACGTGT 61.542 60.000 15.65 0.00 0.00 4.49
922 924 1.218316 GGAACCTCTAGCCCACGTG 59.782 63.158 9.08 9.08 0.00 4.49
923 925 1.229082 TGGAACCTCTAGCCCACGT 60.229 57.895 0.00 0.00 0.00 4.49
924 926 1.218316 GTGGAACCTCTAGCCCACG 59.782 63.158 0.00 0.00 39.52 4.94
925 927 1.218316 CGTGGAACCTCTAGCCCAC 59.782 63.158 0.00 0.00 44.08 4.61
926 928 2.656069 GCGTGGAACCTCTAGCCCA 61.656 63.158 0.00 0.00 0.00 5.36
927 929 2.187163 GCGTGGAACCTCTAGCCC 59.813 66.667 0.00 0.00 0.00 5.19
928 930 1.153549 CAGCGTGGAACCTCTAGCC 60.154 63.158 0.00 0.00 0.00 3.93
929 931 1.153549 CCAGCGTGGAACCTCTAGC 60.154 63.158 0.00 0.00 40.96 3.42
930 932 0.608640 AACCAGCGTGGAACCTCTAG 59.391 55.000 10.46 0.00 40.96 2.43
931 933 0.320374 CAACCAGCGTGGAACCTCTA 59.680 55.000 10.46 0.00 40.96 2.43
932 934 1.071471 CAACCAGCGTGGAACCTCT 59.929 57.895 10.46 0.00 40.96 3.69
933 935 1.070786 TCAACCAGCGTGGAACCTC 59.929 57.895 10.46 0.00 40.96 3.85
934 936 1.227853 GTCAACCAGCGTGGAACCT 60.228 57.895 10.46 0.00 40.96 3.50
935 937 2.258726 GGTCAACCAGCGTGGAACC 61.259 63.158 10.46 10.13 40.96 3.62
936 938 2.604174 CGGTCAACCAGCGTGGAAC 61.604 63.158 10.46 5.98 40.96 3.62
937 939 2.280524 CGGTCAACCAGCGTGGAA 60.281 61.111 10.46 0.00 40.96 3.53
938 940 3.228017 TCGGTCAACCAGCGTGGA 61.228 61.111 10.46 0.00 46.50 4.02
939 941 3.041940 GTCGGTCAACCAGCGTGG 61.042 66.667 0.00 2.92 46.50 4.94
940 942 3.403057 CGTCGGTCAACCAGCGTG 61.403 66.667 0.00 0.00 46.50 5.34
941 943 3.908081 ACGTCGGTCAACCAGCGT 61.908 61.111 10.84 10.84 46.50 5.07
943 945 3.041940 CCACGTCGGTCAACCAGC 61.042 66.667 0.00 0.00 35.14 4.85
944 946 3.041940 GCCACGTCGGTCAACCAG 61.042 66.667 0.00 0.00 36.97 4.00
945 947 4.953868 CGCCACGTCGGTCAACCA 62.954 66.667 0.00 0.00 36.97 3.67
953 955 2.510594 CCGATTTACCGCCACGTCG 61.511 63.158 0.00 0.00 0.00 5.12
954 956 2.169146 CCCGATTTACCGCCACGTC 61.169 63.158 0.00 0.00 0.00 4.34
955 957 2.125431 CCCGATTTACCGCCACGT 60.125 61.111 0.00 0.00 0.00 4.49
956 958 2.893404 CCCCGATTTACCGCCACG 60.893 66.667 0.00 0.00 0.00 4.94
957 959 1.371337 GAACCCCGATTTACCGCCAC 61.371 60.000 0.00 0.00 0.00 5.01
958 960 1.078285 GAACCCCGATTTACCGCCA 60.078 57.895 0.00 0.00 0.00 5.69
959 961 1.078285 TGAACCCCGATTTACCGCC 60.078 57.895 0.00 0.00 0.00 6.13
960 962 1.093496 CCTGAACCCCGATTTACCGC 61.093 60.000 0.00 0.00 0.00 5.68
961 963 0.463116 CCCTGAACCCCGATTTACCG 60.463 60.000 0.00 0.00 0.00 4.02
962 964 0.106868 CCCCTGAACCCCGATTTACC 60.107 60.000 0.00 0.00 0.00 2.85
963 965 0.622136 ACCCCTGAACCCCGATTTAC 59.378 55.000 0.00 0.00 0.00 2.01
964 966 0.913924 GACCCCTGAACCCCGATTTA 59.086 55.000 0.00 0.00 0.00 1.40
965 967 1.689412 GACCCCTGAACCCCGATTT 59.311 57.895 0.00 0.00 0.00 2.17
966 968 2.666098 CGACCCCTGAACCCCGATT 61.666 63.158 0.00 0.00 0.00 3.34
967 969 3.081409 CGACCCCTGAACCCCGAT 61.081 66.667 0.00 0.00 0.00 4.18
970 972 4.097361 GAGCGACCCCTGAACCCC 62.097 72.222 0.00 0.00 0.00 4.95
971 973 4.097361 GGAGCGACCCCTGAACCC 62.097 72.222 0.00 0.00 0.00 4.11
972 974 2.523453 GAAGGAGCGACCCCTGAACC 62.523 65.000 0.00 0.00 40.05 3.62
973 975 1.079057 GAAGGAGCGACCCCTGAAC 60.079 63.158 0.00 0.00 40.05 3.18
974 976 0.909610 ATGAAGGAGCGACCCCTGAA 60.910 55.000 0.00 0.00 40.05 3.02
975 977 1.306141 ATGAAGGAGCGACCCCTGA 60.306 57.895 0.00 0.00 40.05 3.86
976 978 1.144936 GATGAAGGAGCGACCCCTG 59.855 63.158 0.00 0.00 40.05 4.45
977 979 0.261991 TAGATGAAGGAGCGACCCCT 59.738 55.000 0.00 0.00 40.05 4.79
978 980 1.069358 CTTAGATGAAGGAGCGACCCC 59.931 57.143 0.00 0.00 40.05 4.95
979 981 1.539280 GCTTAGATGAAGGAGCGACCC 60.539 57.143 0.00 0.00 40.05 4.46
980 982 1.137086 TGCTTAGATGAAGGAGCGACC 59.863 52.381 0.00 0.00 37.94 4.79
981 983 2.586258 TGCTTAGATGAAGGAGCGAC 57.414 50.000 0.00 0.00 37.94 5.19
982 984 2.224137 CCATGCTTAGATGAAGGAGCGA 60.224 50.000 0.00 0.00 39.10 4.93
983 985 2.141517 CCATGCTTAGATGAAGGAGCG 58.858 52.381 0.00 0.00 39.10 5.03
984 986 1.878734 GCCATGCTTAGATGAAGGAGC 59.121 52.381 0.00 0.00 39.10 4.70
985 987 3.139850 CTGCCATGCTTAGATGAAGGAG 58.860 50.000 0.00 0.00 39.10 3.69
986 988 2.747467 GCTGCCATGCTTAGATGAAGGA 60.747 50.000 0.00 0.00 40.16 3.36
987 989 1.607628 GCTGCCATGCTTAGATGAAGG 59.392 52.381 0.00 0.00 35.49 3.46
988 990 2.573369 AGCTGCCATGCTTAGATGAAG 58.427 47.619 0.00 0.00 40.93 3.02
989 991 2.723322 AGCTGCCATGCTTAGATGAA 57.277 45.000 0.00 0.00 40.93 2.57
1106 1108 1.537889 TTCGGGTCCTGGACATGGT 60.538 57.895 26.94 0.00 33.68 3.55
1410 1412 2.590007 GCGTAGGCCTCCAGCATG 60.590 66.667 9.68 0.00 46.50 4.06
1641 1643 1.517694 CATGCCATCAAACAGCGCC 60.518 57.895 2.29 0.00 0.00 6.53
1920 1922 4.142093 ACGAGCATACCGTTAAATACCTGT 60.142 41.667 0.00 0.00 36.83 4.00
2109 2111 2.541588 CCTTGCCAATCTAATTTCGCCG 60.542 50.000 0.00 0.00 0.00 6.46
2356 2358 2.693762 CCCGCACTGCAATGGACTG 61.694 63.158 0.00 0.00 0.00 3.51
2455 2457 7.097834 ACAGTACTTGATGTAGGCTTAAGTTC 58.902 38.462 4.02 0.00 33.93 3.01
2508 2510 3.965379 ATGCTTTCATTTCCATGTGCA 57.035 38.095 0.00 0.00 36.98 4.57
2529 2531 1.702182 TTCTTGCTGCCAAATCACCA 58.298 45.000 0.00 0.00 0.00 4.17
2902 2904 2.519013 ACAAAATGCTTCCCTCTGACC 58.481 47.619 0.00 0.00 0.00 4.02
2922 2924 4.443457 GGCCAATTGTCAGATAGAGTGCTA 60.443 45.833 4.43 0.00 0.00 3.49
2924 2926 2.615912 GGCCAATTGTCAGATAGAGTGC 59.384 50.000 4.43 0.00 0.00 4.40
2929 2931 3.392616 AGGGTAGGCCAATTGTCAGATAG 59.607 47.826 5.01 0.00 36.17 2.08
2949 2951 7.589958 ACATCATAGGTCTAAACTCTACAGG 57.410 40.000 0.00 0.00 0.00 4.00
2970 2972 5.105064 ACGGGCTCATAGTTAACACTAACAT 60.105 40.000 8.61 0.00 39.05 2.71
2980 2982 2.954318 GGTACTCACGGGCTCATAGTTA 59.046 50.000 0.00 0.00 0.00 2.24
2981 2983 1.755380 GGTACTCACGGGCTCATAGTT 59.245 52.381 0.00 0.00 0.00 2.24
2983 2985 1.693627 AGGTACTCACGGGCTCATAG 58.306 55.000 0.00 0.00 0.00 2.23
2984 2986 3.918134 AGGTACTCACGGGCTCATA 57.082 52.632 0.00 0.00 0.00 2.15
2985 2987 4.787735 AGGTACTCACGGGCTCAT 57.212 55.556 0.00 0.00 0.00 2.90
3018 3021 6.043127 TGCTAGTTATAATGCTCCCAAGATGA 59.957 38.462 8.70 0.00 0.00 2.92
3025 3028 5.008712 GGTGTTTGCTAGTTATAATGCTCCC 59.991 44.000 8.70 0.00 0.00 4.30
3139 3143 6.939132 AATAAGATTCAAGCACCAGAGATG 57.061 37.500 0.00 0.00 0.00 2.90
3179 3183 2.076100 CTCTAACATGACAAAGCCGCA 58.924 47.619 0.00 0.00 0.00 5.69
3189 3193 1.630369 AGCAAGCACCCTCTAACATGA 59.370 47.619 0.00 0.00 0.00 3.07
3206 3210 5.353394 AAAGAACATACCCTCGAATAGCA 57.647 39.130 0.00 0.00 0.00 3.49
3207 3211 7.152645 TGATAAAGAACATACCCTCGAATAGC 58.847 38.462 0.00 0.00 0.00 2.97
3208 3212 8.361139 ACTGATAAAGAACATACCCTCGAATAG 58.639 37.037 0.00 0.00 0.00 1.73
3209 3213 8.246430 ACTGATAAAGAACATACCCTCGAATA 57.754 34.615 0.00 0.00 0.00 1.75
3214 3218 8.561738 TTCAAACTGATAAAGAACATACCCTC 57.438 34.615 0.00 0.00 0.00 4.30
3310 3322 9.616156 TCAAGTTACATAACTGAAAAGGTACAA 57.384 29.630 5.08 0.00 45.17 2.41
3565 3643 2.594303 TGAAGCAGGGCAACACGG 60.594 61.111 0.00 0.00 39.74 4.94
3673 3767 4.342092 ACCTTCCACAATCCAAGACAAAAG 59.658 41.667 0.00 0.00 0.00 2.27
3718 3812 4.497473 TGCCTGCAACTGTAACAAATAC 57.503 40.909 0.00 0.00 34.92 1.89
3840 3943 3.117322 TCCCATTCCAACACCAAAAGAGA 60.117 43.478 0.00 0.00 0.00 3.10
3842 3945 3.230134 CTCCCATTCCAACACCAAAAGA 58.770 45.455 0.00 0.00 0.00 2.52
3907 4010 3.923461 GTGTACAAACAGTTTTGCAGCAA 59.077 39.130 2.83 2.83 45.32 3.91
3926 4029 1.230635 GCATCGGCTCAACTGTGTGT 61.231 55.000 0.00 0.00 36.96 3.72
3974 4078 6.707440 TTACAATGGACTTGCTTCTCAAAA 57.293 33.333 0.00 0.00 38.50 2.44
4001 4107 6.412362 CAGATTCTTTCATACGAGTACGACAG 59.588 42.308 0.00 0.00 42.66 3.51
4008 4114 4.398358 TCGTCCAGATTCTTTCATACGAGT 59.602 41.667 0.00 0.00 33.15 4.18
4101 4207 1.621317 TCCCGACAGTTTGCATCTACA 59.379 47.619 0.00 0.00 0.00 2.74
4150 4256 5.625150 AGATGCTTATAACTCATCCCAACC 58.375 41.667 14.65 0.00 37.82 3.77
4195 4301 5.444663 AAAGAGAGTTCATTCTTGGCAAC 57.555 39.130 0.00 0.00 34.09 4.17
4225 4338 7.309621 CCCAACAATCAGAGTTCATTCTCAAAT 60.310 37.037 0.00 0.00 36.97 2.32
4269 4471 1.614850 GGTTTTGGGCCTCGGAATGTA 60.615 52.381 4.53 0.00 0.00 2.29
4288 4490 1.303643 GGTGGGCTTCAAGACCTGG 60.304 63.158 11.75 0.00 46.32 4.45
4293 4495 0.178992 CCTGTTGGTGGGCTTCAAGA 60.179 55.000 0.00 0.00 0.00 3.02
4308 4510 1.072505 CCGTGTTAAGTGGGCCTGT 59.927 57.895 4.53 0.00 0.00 4.00
4319 4521 4.382320 GCTGTCCGGCCCGTGTTA 62.382 66.667 0.85 0.00 0.00 2.41
4501 4703 2.692741 GAGGGGAGGGAAGGTGGG 60.693 72.222 0.00 0.00 0.00 4.61
4504 4706 2.125225 GTGGAGGGGAGGGAAGGT 59.875 66.667 0.00 0.00 0.00 3.50
4506 4708 3.787001 GCGTGGAGGGGAGGGAAG 61.787 72.222 0.00 0.00 0.00 3.46
4668 5163 3.655810 CTCGGAGCGCCAGAAGCTT 62.656 63.158 7.44 0.00 46.13 3.74
4691 5186 3.691342 CGTGGAGGCACCCGAAGA 61.691 66.667 0.00 0.00 38.00 2.87
4809 5304 0.753479 TAGCAGAAGGGAGGAGCTCG 60.753 60.000 7.83 0.00 36.80 5.03
4816 5311 1.484240 CAAGGGACTAGCAGAAGGGAG 59.516 57.143 0.00 0.00 38.49 4.30
4817 5312 1.078823 TCAAGGGACTAGCAGAAGGGA 59.921 52.381 0.00 0.00 38.49 4.20
4819 5314 5.163258 ACATTATCAAGGGACTAGCAGAAGG 60.163 44.000 0.00 0.00 38.49 3.46
4821 5316 5.957771 ACATTATCAAGGGACTAGCAGAA 57.042 39.130 0.00 0.00 38.49 3.02
4822 5317 5.425217 TGAACATTATCAAGGGACTAGCAGA 59.575 40.000 0.00 0.00 38.49 4.26
4823 5318 5.674525 TGAACATTATCAAGGGACTAGCAG 58.325 41.667 0.00 0.00 38.49 4.24
4824 5319 5.692115 TGAACATTATCAAGGGACTAGCA 57.308 39.130 0.00 0.00 38.49 3.49
4825 5320 8.725148 CAATATGAACATTATCAAGGGACTAGC 58.275 37.037 0.00 0.00 38.49 3.42
4827 5322 9.778741 GACAATATGAACATTATCAAGGGACTA 57.221 33.333 0.00 0.00 38.49 2.59
4829 5324 7.576236 CGACAATATGAACATTATCAAGGGAC 58.424 38.462 0.00 0.00 32.06 4.46
4870 5378 3.834489 AGCACAGAGAACAGGATATGG 57.166 47.619 0.00 0.00 0.00 2.74
4871 5379 3.875727 CCAAGCACAGAGAACAGGATATG 59.124 47.826 0.00 0.00 0.00 1.78
4875 5383 1.131638 ACCAAGCACAGAGAACAGGA 58.868 50.000 0.00 0.00 0.00 3.86
4920 5432 8.509690 CATTCAATCACTGATAGTTTCACTTGT 58.490 33.333 0.00 0.00 32.78 3.16
4933 5445 6.558771 AACATTCGTTCATTCAATCACTGA 57.441 33.333 0.00 0.00 0.00 3.41
4962 5474 2.973694 AGCATTCAATCCATGTTGGC 57.026 45.000 0.00 0.00 37.47 4.52
4965 5477 4.618927 CGACCAAAGCATTCAATCCATGTT 60.619 41.667 0.00 0.00 0.00 2.71
4966 5478 3.119388 CGACCAAAGCATTCAATCCATGT 60.119 43.478 0.00 0.00 0.00 3.21
4974 5486 7.466725 GCATATTAAGTACGACCAAAGCATTCA 60.467 37.037 0.00 0.00 0.00 2.57
4986 5498 6.288294 AGCAAATCAGGCATATTAAGTACGA 58.712 36.000 0.00 0.00 0.00 3.43
4988 5500 6.638468 GCAAGCAAATCAGGCATATTAAGTAC 59.362 38.462 0.00 0.00 0.00 2.73
4990 5502 5.361857 AGCAAGCAAATCAGGCATATTAAGT 59.638 36.000 0.00 0.00 0.00 2.24
4996 5508 2.164827 CACAGCAAGCAAATCAGGCATA 59.835 45.455 0.00 0.00 0.00 3.14
5033 5545 3.907894 TCTAAACAAACACGCCCAATC 57.092 42.857 0.00 0.00 0.00 2.67
5074 5586 4.988598 AGACCACGCGCACCAAGG 62.989 66.667 5.73 3.42 0.00 3.61
5088 5600 2.553268 GCAGACACGCAGCAAGAC 59.447 61.111 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.