Multiple sequence alignment - TraesCS5A01G052000

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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 TraesCS5A01G052000 chr5A 100.000 3083 0 0 1 3083 47445033 47441951 0.000000e+00 5694
1 TraesCS5A01G052000 chr5A 97.368 988 22 4 1 984 73032573 73033560 0.000000e+00 1677
2 TraesCS5A01G052000 chr7B 93.739 1773 75 11 1073 2844 698143816 698145553 0.000000e+00 2627
3 TraesCS5A01G052000 chr1B 93.739 1773 75 11 1073 2844 683730487 683728750 0.000000e+00 2627
4 TraesCS5A01G052000 chr1B 93.627 1773 76 13 1073 2844 49802073 49803809 0.000000e+00 2614
5 TraesCS5A01G052000 chr1B 93.175 1773 85 9 1073 2844 583533115 583531378 0.000000e+00 2571
6 TraesCS5A01G052000 chr1B 97.467 987 22 3 1 984 638749028 638748042 0.000000e+00 1681
7 TraesCS5A01G052000 chrUn 93.457 1773 79 12 1073 2844 40089516 40091252 0.000000e+00 2597
8 TraesCS5A01G052000 chrUn 93.678 174 4 2 918 1085 233525248 233525076 1.420000e-63 254
9 TraesCS5A01G052000 chrUn 94.152 171 3 2 918 1082 257944132 257944301 1.420000e-63 254
10 TraesCS5A01G052000 chr4D 92.946 1772 116 7 1073 2844 241100096 241098334 0.000000e+00 2571
11 TraesCS5A01G052000 chr4D 92.841 1774 120 4 1073 2844 241188039 241186271 0.000000e+00 2566
12 TraesCS5A01G052000 chr4D 94.152 171 3 2 918 1082 123688981 123689150 1.420000e-63 254
13 TraesCS5A01G052000 chr3A 92.837 1773 118 6 1073 2844 401673525 401671761 0.000000e+00 2562
14 TraesCS5A01G052000 chr3A 97.507 1083 24 3 1 1082 151100392 151101472 0.000000e+00 1847
15 TraesCS5A01G052000 chr4A 92.381 1772 128 5 1073 2844 295226822 295228586 0.000000e+00 2518
16 TraesCS5A01G052000 chr4A 96.317 1086 36 4 1 1085 350272468 350271386 0.000000e+00 1781
17 TraesCS5A01G052000 chr6D 94.572 1529 82 1 1316 2844 108473792 108472265 0.000000e+00 2362
18 TraesCS5A01G052000 chr6B 93.338 1516 68 10 1330 2844 388302590 388304073 0.000000e+00 2209
19 TraesCS5A01G052000 chr6B 93.605 172 6 2 918 1085 236482390 236482560 5.100000e-63 252
20 TraesCS5A01G052000 chr1A 97.957 1077 20 2 1 1076 94749508 94748433 0.000000e+00 1866
21 TraesCS5A01G052000 chr2D 96.802 1063 29 3 1 1061 189855946 189857005 0.000000e+00 1770
22 TraesCS5A01G052000 chr3D 93.071 1169 80 1 1071 2239 478073551 478074718 0.000000e+00 1709
23 TraesCS5A01G052000 chr2B 97.940 971 19 1 2 971 500715101 500716071 0.000000e+00 1681
24 TraesCS5A01G052000 chr2B 97.062 987 25 4 1 984 357760544 357759559 0.000000e+00 1659
25 TraesCS5A01G052000 chr3B 97.366 987 23 3 1 984 575753742 575752756 0.000000e+00 1676
26 TraesCS5A01G052000 chr3B 92.301 1169 88 2 1071 2239 39820935 39819769 0.000000e+00 1659
27 TraesCS5A01G052000 chr1D 94.152 171 3 2 918 1082 212428888 212429057 1.420000e-63 254
28 TraesCS5A01G052000 chr1D 92.632 95 6 1 2089 2183 362741533 362741440 5.360000e-28 135
29 TraesCS5A01G052000 chr5B 91.034 145 11 2 2939 3083 72115745 72115887 8.720000e-46 195
30 TraesCS5A01G052000 chr5B 89.773 88 7 2 2858 2945 72112000 72112085 9.040000e-21 111


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 TraesCS5A01G052000 chr5A 47441951 47445033 3082 True 5694 5694 100.000 1 3083 1 chr5A.!!$R1 3082
1 TraesCS5A01G052000 chr5A 73032573 73033560 987 False 1677 1677 97.368 1 984 1 chr5A.!!$F1 983
2 TraesCS5A01G052000 chr7B 698143816 698145553 1737 False 2627 2627 93.739 1073 2844 1 chr7B.!!$F1 1771
3 TraesCS5A01G052000 chr1B 683728750 683730487 1737 True 2627 2627 93.739 1073 2844 1 chr1B.!!$R3 1771
4 TraesCS5A01G052000 chr1B 49802073 49803809 1736 False 2614 2614 93.627 1073 2844 1 chr1B.!!$F1 1771
5 TraesCS5A01G052000 chr1B 583531378 583533115 1737 True 2571 2571 93.175 1073 2844 1 chr1B.!!$R1 1771
6 TraesCS5A01G052000 chr1B 638748042 638749028 986 True 1681 1681 97.467 1 984 1 chr1B.!!$R2 983
7 TraesCS5A01G052000 chrUn 40089516 40091252 1736 False 2597 2597 93.457 1073 2844 1 chrUn.!!$F1 1771
8 TraesCS5A01G052000 chr4D 241098334 241100096 1762 True 2571 2571 92.946 1073 2844 1 chr4D.!!$R1 1771
9 TraesCS5A01G052000 chr4D 241186271 241188039 1768 True 2566 2566 92.841 1073 2844 1 chr4D.!!$R2 1771
10 TraesCS5A01G052000 chr3A 401671761 401673525 1764 True 2562 2562 92.837 1073 2844 1 chr3A.!!$R1 1771
11 TraesCS5A01G052000 chr3A 151100392 151101472 1080 False 1847 1847 97.507 1 1082 1 chr3A.!!$F1 1081
12 TraesCS5A01G052000 chr4A 295226822 295228586 1764 False 2518 2518 92.381 1073 2844 1 chr4A.!!$F1 1771
13 TraesCS5A01G052000 chr4A 350271386 350272468 1082 True 1781 1781 96.317 1 1085 1 chr4A.!!$R1 1084
14 TraesCS5A01G052000 chr6D 108472265 108473792 1527 True 2362 2362 94.572 1316 2844 1 chr6D.!!$R1 1528
15 TraesCS5A01G052000 chr6B 388302590 388304073 1483 False 2209 2209 93.338 1330 2844 1 chr6B.!!$F2 1514
16 TraesCS5A01G052000 chr1A 94748433 94749508 1075 True 1866 1866 97.957 1 1076 1 chr1A.!!$R1 1075
17 TraesCS5A01G052000 chr2D 189855946 189857005 1059 False 1770 1770 96.802 1 1061 1 chr2D.!!$F1 1060
18 TraesCS5A01G052000 chr3D 478073551 478074718 1167 False 1709 1709 93.071 1071 2239 1 chr3D.!!$F1 1168
19 TraesCS5A01G052000 chr2B 500715101 500716071 970 False 1681 1681 97.940 2 971 1 chr2B.!!$F1 969
20 TraesCS5A01G052000 chr2B 357759559 357760544 985 True 1659 1659 97.062 1 984 1 chr2B.!!$R1 983
21 TraesCS5A01G052000 chr3B 575752756 575753742 986 True 1676 1676 97.366 1 984 1 chr3B.!!$R2 983
22 TraesCS5A01G052000 chr3B 39819769 39820935 1166 True 1659 1659 92.301 1071 2239 1 chr3B.!!$R1 1168

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
498 502 1.306141 TCCCTTCATCCGGAGCTGT 60.306 57.895 11.34 0.0 0.00 4.40 F
971 975 1.693627 AGATTGTAGATCCGAGCCGT 58.306 50.000 0.00 0.0 0.00 5.68 F
1091 1095 4.412199 TGGAATTGGATCCGGAAGTAATCT 59.588 41.667 9.01 0.0 42.76 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1409 1414 0.106318 ATCTGCTGAAAGGGATGGGC 60.106 55.0 0.0 0.0 0.00 5.36 R
1819 1829 0.108329 AGAACACCTTCATACCGGCG 60.108 55.0 0.0 0.0 0.00 6.46 R
2475 2485 0.249398 GGCAGGTAGACCGAACACAT 59.751 55.0 0.0 0.0 42.08 3.21 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
356 358 5.482878 AGTCTCGGAGGTTATGTTCCTTTTA 59.517 40.000 4.96 0.00 35.20 1.52
498 502 1.306141 TCCCTTCATCCGGAGCTGT 60.306 57.895 11.34 0.00 0.00 4.40
817 821 3.003897 GGCATTTTGTAGACGTGGTTCAA 59.996 43.478 0.00 0.00 0.00 2.69
963 967 6.716934 TTGGAGAGGTGTAGATTGTAGATC 57.283 41.667 0.00 0.00 0.00 2.75
965 969 4.216687 GGAGAGGTGTAGATTGTAGATCCG 59.783 50.000 0.00 0.00 0.00 4.18
971 975 1.693627 AGATTGTAGATCCGAGCCGT 58.306 50.000 0.00 0.00 0.00 5.68
1080 1084 5.993055 ACAAAAATGGATGGAATTGGATCC 58.007 37.500 4.20 4.20 38.98 3.36
1081 1085 4.942761 AAAATGGATGGAATTGGATCCG 57.057 40.909 7.39 0.00 42.76 4.18
1091 1095 4.412199 TGGAATTGGATCCGGAAGTAATCT 59.588 41.667 9.01 0.00 42.76 2.40
1092 1096 5.104109 TGGAATTGGATCCGGAAGTAATCTT 60.104 40.000 9.01 0.00 42.76 2.40
1578 1587 9.227777 GGTCAAAGTGGTGTAGATAAAATAGTT 57.772 33.333 0.00 0.00 0.00 2.24
1598 1607 4.704540 AGTTTGTGTGGATTTGAGTCACAA 59.295 37.500 0.00 0.00 43.84 3.33
1646 1655 7.709613 ACGTCTATGGAATACATTAAAGTGTCC 59.290 37.037 7.92 7.92 41.03 4.02
1737 1747 6.183347 CACTAACCTCCAAATTCCTCATTCT 58.817 40.000 0.00 0.00 0.00 2.40
1738 1748 6.660949 CACTAACCTCCAAATTCCTCATTCTT 59.339 38.462 0.00 0.00 0.00 2.52
1881 1891 2.288825 TGTCCTTCTAGCTTCAACACGG 60.289 50.000 0.00 0.00 0.00 4.94
1887 1897 1.394917 CTAGCTTCAACACGGCATGAC 59.605 52.381 0.00 0.00 0.00 3.06
2004 2014 2.622436 CTCGTGAACCCTGAGAAATCC 58.378 52.381 0.00 0.00 31.31 3.01
2083 2093 7.860373 GTGAGACTGACTATGATAGTGAATGAC 59.140 40.741 10.29 0.00 39.59 3.06
2094 2104 5.600898 TGATAGTGAATGACTCCGGGAATTA 59.399 40.000 0.00 0.00 35.96 1.40
2176 2186 3.190535 GGAAACACGCATGTCCTATTTGT 59.809 43.478 0.00 0.00 38.45 2.83
2444 2454 2.378547 AGGAAGGAACCAATAAGCCACA 59.621 45.455 0.00 0.00 0.00 4.17
2835 2845 4.724293 CCTTTTCCTAAGGAGGGAGAGAAT 59.276 45.833 0.00 0.00 43.94 2.40
2844 2854 3.032459 GGAGGGAGAGAATACGGTTCTT 58.968 50.000 6.76 0.00 0.00 2.52
2845 2855 3.068448 GGAGGGAGAGAATACGGTTCTTC 59.932 52.174 6.76 6.62 0.00 2.87
2846 2856 3.700038 GAGGGAGAGAATACGGTTCTTCA 59.300 47.826 6.76 0.00 0.00 3.02
2847 2857 4.290942 AGGGAGAGAATACGGTTCTTCAT 58.709 43.478 6.76 0.00 0.00 2.57
2848 2858 5.455872 AGGGAGAGAATACGGTTCTTCATA 58.544 41.667 6.76 0.00 0.00 2.15
2849 2859 6.078664 AGGGAGAGAATACGGTTCTTCATAT 58.921 40.000 6.76 0.00 0.00 1.78
2850 2860 6.015010 AGGGAGAGAATACGGTTCTTCATATG 60.015 42.308 6.76 0.00 0.00 1.78
2851 2861 6.239345 GGGAGAGAATACGGTTCTTCATATGT 60.239 42.308 1.90 0.00 0.00 2.29
2852 2862 7.210873 GGAGAGAATACGGTTCTTCATATGTT 58.789 38.462 1.90 0.00 0.00 2.71
2853 2863 7.382759 GGAGAGAATACGGTTCTTCATATGTTC 59.617 40.741 1.90 0.00 0.00 3.18
2854 2864 8.012957 AGAGAATACGGTTCTTCATATGTTCT 57.987 34.615 1.90 0.37 0.00 3.01
2855 2865 8.138712 AGAGAATACGGTTCTTCATATGTTCTC 58.861 37.037 13.44 13.44 38.56 2.87
2856 2866 8.012957 AGAATACGGTTCTTCATATGTTCTCT 57.987 34.615 1.90 0.00 0.00 3.10
2857 2867 8.478877 AGAATACGGTTCTTCATATGTTCTCTT 58.521 33.333 1.90 0.00 0.00 2.85
2858 2868 8.425577 AATACGGTTCTTCATATGTTCTCTTG 57.574 34.615 1.90 0.00 0.00 3.02
2859 2869 6.037786 ACGGTTCTTCATATGTTCTCTTGA 57.962 37.500 1.90 0.00 0.00 3.02
2860 2870 6.644347 ACGGTTCTTCATATGTTCTCTTGAT 58.356 36.000 1.90 0.00 0.00 2.57
2861 2871 7.106239 ACGGTTCTTCATATGTTCTCTTGATT 58.894 34.615 1.90 0.00 0.00 2.57
2862 2872 7.607991 ACGGTTCTTCATATGTTCTCTTGATTT 59.392 33.333 1.90 0.00 0.00 2.17
2863 2873 7.907045 CGGTTCTTCATATGTTCTCTTGATTTG 59.093 37.037 1.90 0.00 0.00 2.32
2864 2874 7.699812 GGTTCTTCATATGTTCTCTTGATTTGC 59.300 37.037 1.90 0.00 0.00 3.68
2865 2875 7.926674 TCTTCATATGTTCTCTTGATTTGCA 57.073 32.000 1.90 0.00 0.00 4.08
2866 2876 8.515695 TCTTCATATGTTCTCTTGATTTGCAT 57.484 30.769 1.90 0.00 0.00 3.96
2867 2877 8.403236 TCTTCATATGTTCTCTTGATTTGCATG 58.597 33.333 1.90 0.00 0.00 4.06
2868 2878 7.634671 TCATATGTTCTCTTGATTTGCATGT 57.365 32.000 1.90 0.00 0.00 3.21
2869 2879 8.735692 TCATATGTTCTCTTGATTTGCATGTA 57.264 30.769 1.90 0.00 0.00 2.29
2870 2880 9.176460 TCATATGTTCTCTTGATTTGCATGTAA 57.824 29.630 1.90 0.00 0.00 2.41
2871 2881 9.229784 CATATGTTCTCTTGATTTGCATGTAAC 57.770 33.333 0.00 0.00 0.00 2.50
2872 2882 6.012658 TGTTCTCTTGATTTGCATGTAACC 57.987 37.500 0.00 0.00 0.00 2.85
2873 2883 5.534278 TGTTCTCTTGATTTGCATGTAACCA 59.466 36.000 0.00 0.00 0.00 3.67
2874 2884 6.040278 TGTTCTCTTGATTTGCATGTAACCAA 59.960 34.615 0.00 3.37 0.00 3.67
2875 2885 6.012658 TCTCTTGATTTGCATGTAACCAAC 57.987 37.500 0.00 0.00 0.00 3.77
2876 2886 4.793071 TCTTGATTTGCATGTAACCAACG 58.207 39.130 0.00 0.08 0.00 4.10
2877 2887 2.940147 TGATTTGCATGTAACCAACGC 58.060 42.857 0.00 0.00 0.00 4.84
2878 2888 2.294512 TGATTTGCATGTAACCAACGCA 59.705 40.909 0.00 0.00 32.91 5.24
2879 2889 3.056962 TGATTTGCATGTAACCAACGCAT 60.057 39.130 0.00 0.00 34.29 4.73
2880 2890 2.344504 TTGCATGTAACCAACGCATG 57.655 45.000 0.00 0.00 41.89 4.06
2881 2891 1.242989 TGCATGTAACCAACGCATGT 58.757 45.000 0.00 0.00 41.27 3.21
2882 2892 2.427506 TGCATGTAACCAACGCATGTA 58.572 42.857 0.00 0.00 41.27 2.29
2883 2893 2.814336 TGCATGTAACCAACGCATGTAA 59.186 40.909 0.00 0.00 41.27 2.41
2884 2894 3.441922 TGCATGTAACCAACGCATGTAAT 59.558 39.130 0.00 0.00 41.27 1.89
2885 2895 4.082517 TGCATGTAACCAACGCATGTAATT 60.083 37.500 0.00 0.00 41.27 1.40
2886 2896 4.265085 GCATGTAACCAACGCATGTAATTG 59.735 41.667 0.00 0.00 41.27 2.32
2887 2897 5.398169 CATGTAACCAACGCATGTAATTGT 58.602 37.500 0.00 0.00 36.28 2.71
2888 2898 5.440234 TGTAACCAACGCATGTAATTGTT 57.560 34.783 0.00 0.00 0.00 2.83
2889 2899 5.215903 TGTAACCAACGCATGTAATTGTTG 58.784 37.500 0.00 2.69 38.91 3.33
2890 2900 4.314740 AACCAACGCATGTAATTGTTGT 57.685 36.364 0.00 0.00 38.03 3.32
2891 2901 4.314740 ACCAACGCATGTAATTGTTGTT 57.685 36.364 0.00 0.00 38.03 2.83
2892 2902 4.688021 ACCAACGCATGTAATTGTTGTTT 58.312 34.783 0.00 0.00 38.03 2.83
2893 2903 4.742659 ACCAACGCATGTAATTGTTGTTTC 59.257 37.500 0.00 0.00 38.03 2.78
2894 2904 4.981674 CCAACGCATGTAATTGTTGTTTCT 59.018 37.500 0.00 0.00 38.03 2.52
2895 2905 5.461737 CCAACGCATGTAATTGTTGTTTCTT 59.538 36.000 0.00 0.00 38.03 2.52
2896 2906 6.345723 CCAACGCATGTAATTGTTGTTTCTTC 60.346 38.462 0.00 0.00 38.03 2.87
2897 2907 5.219633 ACGCATGTAATTGTTGTTTCTTCC 58.780 37.500 0.00 0.00 0.00 3.46
2898 2908 5.009610 ACGCATGTAATTGTTGTTTCTTCCT 59.990 36.000 0.00 0.00 0.00 3.36
2899 2909 5.569059 CGCATGTAATTGTTGTTTCTTCCTC 59.431 40.000 0.00 0.00 0.00 3.71
2900 2910 5.569059 GCATGTAATTGTTGTTTCTTCCTCG 59.431 40.000 0.00 0.00 0.00 4.63
2901 2911 6.567701 GCATGTAATTGTTGTTTCTTCCTCGA 60.568 38.462 0.00 0.00 0.00 4.04
2902 2912 6.295039 TGTAATTGTTGTTTCTTCCTCGAC 57.705 37.500 0.00 0.00 0.00 4.20
2903 2913 5.818336 TGTAATTGTTGTTTCTTCCTCGACA 59.182 36.000 0.00 0.00 0.00 4.35
2904 2914 4.813296 ATTGTTGTTTCTTCCTCGACAC 57.187 40.909 0.00 0.00 0.00 3.67
2905 2915 2.557317 TGTTGTTTCTTCCTCGACACC 58.443 47.619 0.00 0.00 0.00 4.16
2906 2916 2.093394 TGTTGTTTCTTCCTCGACACCA 60.093 45.455 0.00 0.00 0.00 4.17
2907 2917 2.234300 TGTTTCTTCCTCGACACCAC 57.766 50.000 0.00 0.00 0.00 4.16
2908 2918 1.483004 TGTTTCTTCCTCGACACCACA 59.517 47.619 0.00 0.00 0.00 4.17
2909 2919 1.865340 GTTTCTTCCTCGACACCACAC 59.135 52.381 0.00 0.00 0.00 3.82
2910 2920 1.116308 TTCTTCCTCGACACCACACA 58.884 50.000 0.00 0.00 0.00 3.72
2911 2921 1.116308 TCTTCCTCGACACCACACAA 58.884 50.000 0.00 0.00 0.00 3.33
2912 2922 1.068588 TCTTCCTCGACACCACACAAG 59.931 52.381 0.00 0.00 0.00 3.16
2913 2923 1.068588 CTTCCTCGACACCACACAAGA 59.931 52.381 0.00 0.00 0.00 3.02
2914 2924 1.116308 TCCTCGACACCACACAAGAA 58.884 50.000 0.00 0.00 0.00 2.52
2915 2925 1.483004 TCCTCGACACCACACAAGAAA 59.517 47.619 0.00 0.00 0.00 2.52
2916 2926 1.597663 CCTCGACACCACACAAGAAAC 59.402 52.381 0.00 0.00 0.00 2.78
2917 2927 2.276201 CTCGACACCACACAAGAAACA 58.724 47.619 0.00 0.00 0.00 2.83
2918 2928 2.276201 TCGACACCACACAAGAAACAG 58.724 47.619 0.00 0.00 0.00 3.16
2919 2929 1.268032 CGACACCACACAAGAAACAGC 60.268 52.381 0.00 0.00 0.00 4.40
2920 2930 2.017049 GACACCACACAAGAAACAGCT 58.983 47.619 0.00 0.00 0.00 4.24
2921 2931 3.202906 GACACCACACAAGAAACAGCTA 58.797 45.455 0.00 0.00 0.00 3.32
2922 2932 3.206150 ACACCACACAAGAAACAGCTAG 58.794 45.455 0.00 0.00 0.00 3.42
2923 2933 2.031682 CACCACACAAGAAACAGCTAGC 60.032 50.000 6.62 6.62 0.00 3.42
2924 2934 2.221169 CCACACAAGAAACAGCTAGCA 58.779 47.619 18.83 0.00 0.00 3.49
2925 2935 2.225019 CCACACAAGAAACAGCTAGCAG 59.775 50.000 18.83 12.15 0.00 4.24
2926 2936 2.874701 CACACAAGAAACAGCTAGCAGT 59.125 45.455 18.83 12.94 0.00 4.40
2927 2937 4.058124 CACACAAGAAACAGCTAGCAGTA 58.942 43.478 18.83 0.00 0.00 2.74
2928 2938 4.151335 CACACAAGAAACAGCTAGCAGTAG 59.849 45.833 18.83 6.22 0.00 2.57
2929 2939 4.202264 ACACAAGAAACAGCTAGCAGTAGT 60.202 41.667 18.83 6.79 0.00 2.73
2930 2940 4.387256 CACAAGAAACAGCTAGCAGTAGTC 59.613 45.833 18.83 15.32 0.00 2.59
2931 2941 4.282195 ACAAGAAACAGCTAGCAGTAGTCT 59.718 41.667 18.83 17.22 0.00 3.24
2932 2942 5.477291 ACAAGAAACAGCTAGCAGTAGTCTA 59.523 40.000 18.83 0.00 0.00 2.59
2933 2943 6.153680 ACAAGAAACAGCTAGCAGTAGTCTAT 59.846 38.462 18.83 10.18 0.00 1.98
2934 2944 7.339721 ACAAGAAACAGCTAGCAGTAGTCTATA 59.660 37.037 18.83 0.00 0.00 1.31
2935 2945 7.504924 AGAAACAGCTAGCAGTAGTCTATAG 57.495 40.000 18.83 0.00 0.00 1.31
2936 2946 6.488683 AGAAACAGCTAGCAGTAGTCTATAGG 59.511 42.308 18.83 0.00 0.00 2.57
2937 2947 4.076394 ACAGCTAGCAGTAGTCTATAGGC 58.924 47.826 18.83 0.00 0.00 3.93
2938 2948 3.126171 CAGCTAGCAGTAGTCTATAGGCG 59.874 52.174 18.83 0.00 0.00 5.52
2939 2949 3.008157 AGCTAGCAGTAGTCTATAGGCGA 59.992 47.826 18.83 0.00 0.00 5.54
2940 2950 3.125658 GCTAGCAGTAGTCTATAGGCGAC 59.874 52.174 10.63 9.35 0.00 5.19
2941 2951 2.144730 AGCAGTAGTCTATAGGCGACG 58.855 52.381 11.30 8.09 36.53 5.12
2942 2952 2.141517 GCAGTAGTCTATAGGCGACGA 58.858 52.381 11.30 0.00 36.53 4.20
2943 2953 2.158058 GCAGTAGTCTATAGGCGACGAG 59.842 54.545 11.30 9.54 36.53 4.18
2944 2954 3.391965 CAGTAGTCTATAGGCGACGAGT 58.608 50.000 11.30 0.00 36.53 4.18
2945 2955 3.808726 CAGTAGTCTATAGGCGACGAGTT 59.191 47.826 11.30 0.00 36.53 3.01
2946 2956 4.272991 CAGTAGTCTATAGGCGACGAGTTT 59.727 45.833 11.30 0.00 36.53 2.66
2947 2957 3.694535 AGTCTATAGGCGACGAGTTTG 57.305 47.619 0.00 0.00 36.53 2.93
2948 2958 3.015327 AGTCTATAGGCGACGAGTTTGT 58.985 45.455 0.00 0.00 36.53 2.83
2949 2959 3.442977 AGTCTATAGGCGACGAGTTTGTT 59.557 43.478 0.00 0.00 36.53 2.83
2950 2960 4.082354 AGTCTATAGGCGACGAGTTTGTTT 60.082 41.667 0.00 0.00 36.53 2.83
2951 2961 5.124457 AGTCTATAGGCGACGAGTTTGTTTA 59.876 40.000 0.00 0.00 36.53 2.01
2952 2962 5.228843 GTCTATAGGCGACGAGTTTGTTTAC 59.771 44.000 0.00 0.00 0.00 2.01
2953 2963 1.505425 AGGCGACGAGTTTGTTTACC 58.495 50.000 0.00 0.00 0.00 2.85
2954 2964 0.514255 GGCGACGAGTTTGTTTACCC 59.486 55.000 0.00 0.00 0.00 3.69
2955 2965 1.505425 GCGACGAGTTTGTTTACCCT 58.495 50.000 0.00 0.00 0.00 4.34
2956 2966 1.869132 GCGACGAGTTTGTTTACCCTT 59.131 47.619 0.00 0.00 0.00 3.95
2957 2967 2.288729 GCGACGAGTTTGTTTACCCTTT 59.711 45.455 0.00 0.00 0.00 3.11
2958 2968 3.847105 GCGACGAGTTTGTTTACCCTTTG 60.847 47.826 0.00 0.00 0.00 2.77
2959 2969 3.556775 CGACGAGTTTGTTTACCCTTTGA 59.443 43.478 0.00 0.00 0.00 2.69
2960 2970 4.034279 CGACGAGTTTGTTTACCCTTTGAA 59.966 41.667 0.00 0.00 0.00 2.69
2961 2971 5.494632 ACGAGTTTGTTTACCCTTTGAAG 57.505 39.130 0.00 0.00 0.00 3.02
2962 2972 4.945543 ACGAGTTTGTTTACCCTTTGAAGT 59.054 37.500 0.00 0.00 0.00 3.01
2963 2973 5.416639 ACGAGTTTGTTTACCCTTTGAAGTT 59.583 36.000 0.00 0.00 0.00 2.66
2964 2974 5.741982 CGAGTTTGTTTACCCTTTGAAGTTG 59.258 40.000 0.00 0.00 0.00 3.16
2965 2975 5.416083 AGTTTGTTTACCCTTTGAAGTTGC 58.584 37.500 0.00 0.00 0.00 4.17
2966 2976 4.394439 TTGTTTACCCTTTGAAGTTGCC 57.606 40.909 0.00 0.00 0.00 4.52
2967 2977 3.366396 TGTTTACCCTTTGAAGTTGCCA 58.634 40.909 0.00 0.00 0.00 4.92
2968 2978 3.769844 TGTTTACCCTTTGAAGTTGCCAA 59.230 39.130 0.00 0.00 0.00 4.52
2969 2979 4.116961 GTTTACCCTTTGAAGTTGCCAAC 58.883 43.478 0.00 0.00 0.00 3.77
2970 2980 0.744281 ACCCTTTGAAGTTGCCAACG 59.256 50.000 1.20 0.00 36.23 4.10
2971 2981 0.597377 CCCTTTGAAGTTGCCAACGC 60.597 55.000 1.20 0.00 36.23 4.84
2972 2982 0.597377 CCTTTGAAGTTGCCAACGCC 60.597 55.000 1.20 0.00 36.23 5.68
2973 2983 0.597377 CTTTGAAGTTGCCAACGCCC 60.597 55.000 1.20 0.00 36.23 6.13
2974 2984 2.022240 TTTGAAGTTGCCAACGCCCC 62.022 55.000 1.20 0.00 36.23 5.80
2975 2985 2.909965 GAAGTTGCCAACGCCCCA 60.910 61.111 1.20 0.00 36.23 4.96
2976 2986 2.912025 AAGTTGCCAACGCCCCAG 60.912 61.111 1.20 0.00 36.23 4.45
2977 2987 3.731766 AAGTTGCCAACGCCCCAGT 62.732 57.895 1.20 0.00 36.23 4.00
2978 2988 2.281900 GTTGCCAACGCCCCAGTA 60.282 61.111 0.00 0.00 0.00 2.74
2979 2989 2.281900 TTGCCAACGCCCCAGTAC 60.282 61.111 0.00 0.00 0.00 2.73
2980 2990 3.121406 TTGCCAACGCCCCAGTACA 62.121 57.895 0.00 0.00 0.00 2.90
2981 2991 2.045340 GCCAACGCCCCAGTACAT 60.045 61.111 0.00 0.00 0.00 2.29
2982 2992 2.406616 GCCAACGCCCCAGTACATG 61.407 63.158 0.00 0.00 0.00 3.21
2983 2993 2.406616 CCAACGCCCCAGTACATGC 61.407 63.158 0.00 0.00 0.00 4.06
2984 2994 1.377202 CAACGCCCCAGTACATGCT 60.377 57.895 0.00 0.00 0.00 3.79
2985 2995 0.960364 CAACGCCCCAGTACATGCTT 60.960 55.000 0.00 0.00 0.00 3.91
2986 2996 0.251165 AACGCCCCAGTACATGCTTT 60.251 50.000 0.00 0.00 0.00 3.51
2987 2997 0.251165 ACGCCCCAGTACATGCTTTT 60.251 50.000 0.00 0.00 0.00 2.27
2988 2998 0.451783 CGCCCCAGTACATGCTTTTC 59.548 55.000 0.00 0.00 0.00 2.29
2989 2999 0.817654 GCCCCAGTACATGCTTTTCC 59.182 55.000 0.00 0.00 0.00 3.13
2990 3000 1.890573 GCCCCAGTACATGCTTTTCCA 60.891 52.381 0.00 0.00 0.00 3.53
2991 3001 2.738743 CCCCAGTACATGCTTTTCCAT 58.261 47.619 0.00 0.00 0.00 3.41
2992 3002 2.428171 CCCCAGTACATGCTTTTCCATG 59.572 50.000 0.00 0.94 46.19 3.66
2993 3003 2.159198 CCCAGTACATGCTTTTCCATGC 60.159 50.000 0.00 0.00 44.98 4.06
2994 3004 2.159198 CCAGTACATGCTTTTCCATGCC 60.159 50.000 0.00 0.00 44.98 4.40
2995 3005 2.492881 CAGTACATGCTTTTCCATGCCA 59.507 45.455 0.00 0.00 44.98 4.92
2996 3006 3.131577 CAGTACATGCTTTTCCATGCCAT 59.868 43.478 0.00 0.00 44.98 4.40
2997 3007 4.338964 CAGTACATGCTTTTCCATGCCATA 59.661 41.667 0.00 0.00 44.98 2.74
2998 3008 4.955450 AGTACATGCTTTTCCATGCCATAA 59.045 37.500 0.00 0.00 44.98 1.90
2999 3009 5.599656 AGTACATGCTTTTCCATGCCATAAT 59.400 36.000 0.00 0.00 44.98 1.28
3000 3010 5.362105 ACATGCTTTTCCATGCCATAATT 57.638 34.783 0.00 0.00 44.98 1.40
3001 3011 5.747342 ACATGCTTTTCCATGCCATAATTT 58.253 33.333 0.00 0.00 44.98 1.82
3002 3012 6.181908 ACATGCTTTTCCATGCCATAATTTT 58.818 32.000 0.00 0.00 44.98 1.82
3003 3013 6.316890 ACATGCTTTTCCATGCCATAATTTTC 59.683 34.615 0.00 0.00 44.98 2.29
3004 3014 5.802465 TGCTTTTCCATGCCATAATTTTCA 58.198 33.333 0.00 0.00 0.00 2.69
3005 3015 6.416415 TGCTTTTCCATGCCATAATTTTCAT 58.584 32.000 0.00 0.00 0.00 2.57
3006 3016 6.539464 TGCTTTTCCATGCCATAATTTTCATC 59.461 34.615 0.00 0.00 0.00 2.92
3007 3017 6.764560 GCTTTTCCATGCCATAATTTTCATCT 59.235 34.615 0.00 0.00 0.00 2.90
3008 3018 7.281549 GCTTTTCCATGCCATAATTTTCATCTT 59.718 33.333 0.00 0.00 0.00 2.40
3009 3019 9.820725 CTTTTCCATGCCATAATTTTCATCTTA 57.179 29.630 0.00 0.00 0.00 2.10
3013 3023 8.729756 TCCATGCCATAATTTTCATCTTATACG 58.270 33.333 0.00 0.00 0.00 3.06
3014 3024 8.729756 CCATGCCATAATTTTCATCTTATACGA 58.270 33.333 0.00 0.00 0.00 3.43
3017 3027 9.944663 TGCCATAATTTTCATCTTATACGAAAC 57.055 29.630 0.00 0.00 0.00 2.78
3018 3028 9.394477 GCCATAATTTTCATCTTATACGAAACC 57.606 33.333 0.00 0.00 0.00 3.27
3023 3033 9.620660 AATTTTCATCTTATACGAAACCACAAC 57.379 29.630 0.00 0.00 0.00 3.32
3024 3034 7.972832 TTTCATCTTATACGAAACCACAACT 57.027 32.000 0.00 0.00 0.00 3.16
3025 3035 7.591006 TTCATCTTATACGAAACCACAACTC 57.409 36.000 0.00 0.00 0.00 3.01
3026 3036 6.693466 TCATCTTATACGAAACCACAACTCA 58.307 36.000 0.00 0.00 0.00 3.41
3027 3037 6.588756 TCATCTTATACGAAACCACAACTCAC 59.411 38.462 0.00 0.00 0.00 3.51
3028 3038 5.232463 TCTTATACGAAACCACAACTCACC 58.768 41.667 0.00 0.00 0.00 4.02
3029 3039 2.983907 TACGAAACCACAACTCACCA 57.016 45.000 0.00 0.00 0.00 4.17
3030 3040 2.341846 ACGAAACCACAACTCACCAT 57.658 45.000 0.00 0.00 0.00 3.55
3031 3041 3.478857 ACGAAACCACAACTCACCATA 57.521 42.857 0.00 0.00 0.00 2.74
3032 3042 4.015872 ACGAAACCACAACTCACCATAT 57.984 40.909 0.00 0.00 0.00 1.78
3033 3043 4.000988 ACGAAACCACAACTCACCATATC 58.999 43.478 0.00 0.00 0.00 1.63
3034 3044 4.000325 CGAAACCACAACTCACCATATCA 59.000 43.478 0.00 0.00 0.00 2.15
3035 3045 4.454161 CGAAACCACAACTCACCATATCAA 59.546 41.667 0.00 0.00 0.00 2.57
3036 3046 5.390885 CGAAACCACAACTCACCATATCAAG 60.391 44.000 0.00 0.00 0.00 3.02
3037 3047 3.347216 ACCACAACTCACCATATCAAGC 58.653 45.455 0.00 0.00 0.00 4.01
3038 3048 3.009473 ACCACAACTCACCATATCAAGCT 59.991 43.478 0.00 0.00 0.00 3.74
3039 3049 3.624861 CCACAACTCACCATATCAAGCTC 59.375 47.826 0.00 0.00 0.00 4.09
3040 3050 3.624861 CACAACTCACCATATCAAGCTCC 59.375 47.826 0.00 0.00 0.00 4.70
3041 3051 3.264193 ACAACTCACCATATCAAGCTCCA 59.736 43.478 0.00 0.00 0.00 3.86
3042 3052 4.080129 ACAACTCACCATATCAAGCTCCAT 60.080 41.667 0.00 0.00 0.00 3.41
3043 3053 5.130975 ACAACTCACCATATCAAGCTCCATA 59.869 40.000 0.00 0.00 0.00 2.74
3044 3054 5.480642 ACTCACCATATCAAGCTCCATAG 57.519 43.478 0.00 0.00 0.00 2.23
3069 3079 5.611796 TTTTTGTCACCATCGAGATGAAG 57.388 39.130 14.12 6.54 41.20 3.02
3070 3080 4.535526 TTTGTCACCATCGAGATGAAGA 57.464 40.909 14.12 8.56 41.20 2.87
3071 3081 3.510388 TGTCACCATCGAGATGAAGAC 57.490 47.619 20.51 20.51 41.20 3.01
3072 3082 2.166459 TGTCACCATCGAGATGAAGACC 59.834 50.000 22.51 12.76 41.20 3.85
3073 3083 1.757118 TCACCATCGAGATGAAGACCC 59.243 52.381 14.12 0.00 41.20 4.46
3074 3084 0.747255 ACCATCGAGATGAAGACCCG 59.253 55.000 14.12 0.00 41.20 5.28
3075 3085 1.032794 CCATCGAGATGAAGACCCGA 58.967 55.000 14.12 0.00 41.20 5.14
3076 3086 1.269309 CCATCGAGATGAAGACCCGAC 60.269 57.143 14.12 0.00 41.20 4.79
3077 3087 1.405463 CATCGAGATGAAGACCCGACA 59.595 52.381 7.26 0.00 41.20 4.35
3078 3088 0.809385 TCGAGATGAAGACCCGACAC 59.191 55.000 0.00 0.00 0.00 3.67
3079 3089 0.526211 CGAGATGAAGACCCGACACA 59.474 55.000 0.00 0.00 0.00 3.72
3080 3090 1.732732 CGAGATGAAGACCCGACACAC 60.733 57.143 0.00 0.00 0.00 3.82
3081 3091 0.608640 AGATGAAGACCCGACACACC 59.391 55.000 0.00 0.00 0.00 4.16
3082 3092 0.608640 GATGAAGACCCGACACACCT 59.391 55.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
369 373 5.184671 GGTGCCAAAGAAGAATGAGAAGAAT 59.815 40.000 0.00 0.00 0.00 2.40
498 502 2.905075 CATGATGAGCCCAAGTTACGA 58.095 47.619 0.00 0.00 0.00 3.43
722 726 3.186409 CCAAGATATTGGCGAATACCACG 59.814 47.826 6.10 0.00 40.19 4.94
785 789 5.583061 CGTCTACAAAATGCCAGTACCATAA 59.417 40.000 0.00 0.00 0.00 1.90
786 790 5.113383 CGTCTACAAAATGCCAGTACCATA 58.887 41.667 0.00 0.00 0.00 2.74
963 967 2.125912 CTGGTCTTCACGGCTCGG 60.126 66.667 0.00 0.00 0.00 4.63
965 969 0.034896 TTTCCTGGTCTTCACGGCTC 59.965 55.000 0.00 0.00 0.00 4.70
971 975 6.642733 ATCCTTATCTTTTCCTGGTCTTCA 57.357 37.500 0.00 0.00 0.00 3.02
1080 1084 6.701432 AAAGTGACGTTAAGATTACTTCCG 57.299 37.500 0.00 0.00 37.53 4.30
1081 1085 8.307921 AGAAAAGTGACGTTAAGATTACTTCC 57.692 34.615 0.00 0.00 37.53 3.46
1092 1096 9.483916 TGAAATCTCATAAGAAAAGTGACGTTA 57.516 29.630 0.00 0.00 34.49 3.18
1109 1113 8.112822 TCCTAAAACCACCATTATGAAATCTCA 58.887 33.333 0.00 0.00 35.56 3.27
1409 1414 0.106318 ATCTGCTGAAAGGGATGGGC 60.106 55.000 0.00 0.00 0.00 5.36
1453 1458 7.116948 CACTAGAAACTCCCGCATTAAGATATG 59.883 40.741 0.00 0.00 0.00 1.78
1598 1607 5.563475 CGTTCCGTAGAAACATACCGGATAT 60.563 44.000 9.46 0.00 32.58 1.63
1646 1655 3.441572 GGAAATCACTCCCAGATTGTGTG 59.558 47.826 0.00 0.00 35.96 3.82
1659 1668 6.139679 TCCTTTAAGATGTGGGAAATCACT 57.860 37.500 0.00 0.00 38.40 3.41
1818 1828 0.390735 GAACACCTTCATACCGGCGT 60.391 55.000 6.01 0.00 0.00 5.68
1819 1829 0.108329 AGAACACCTTCATACCGGCG 60.108 55.000 0.00 0.00 0.00 6.46
1881 1891 3.755378 GGTCAAGATGATATGGGTCATGC 59.245 47.826 0.00 0.00 38.88 4.06
1887 1897 2.368548 TGGACGGTCAAGATGATATGGG 59.631 50.000 10.76 0.00 0.00 4.00
2004 2014 5.568423 GCCATCTACACTGAGGAATATCTGG 60.568 48.000 0.00 0.00 0.00 3.86
2083 2093 8.345565 CAAAAACATTCTATCTAATTCCCGGAG 58.654 37.037 0.73 0.00 0.00 4.63
2161 2171 3.270027 TCCTTCACAAATAGGACATGCG 58.730 45.455 0.00 0.00 35.66 4.73
2176 2186 7.889873 TCTTTGAACCTTTGTTATTCCTTCA 57.110 32.000 0.00 0.00 33.97 3.02
2444 2454 2.303022 CCCAATGACTGGTACACTGACT 59.697 50.000 0.00 0.00 44.76 3.41
2475 2485 0.249398 GGCAGGTAGACCGAACACAT 59.751 55.000 0.00 0.00 42.08 3.21
2835 2845 7.165460 TCAAGAGAACATATGAAGAACCGTA 57.835 36.000 10.38 0.00 0.00 4.02
2844 2854 7.634671 ACATGCAAATCAAGAGAACATATGA 57.365 32.000 10.38 0.00 0.00 2.15
2845 2855 9.229784 GTTACATGCAAATCAAGAGAACATATG 57.770 33.333 0.00 0.00 0.00 1.78
2846 2856 8.408601 GGTTACATGCAAATCAAGAGAACATAT 58.591 33.333 0.00 0.00 0.00 1.78
2847 2857 7.392953 TGGTTACATGCAAATCAAGAGAACATA 59.607 33.333 0.00 0.00 0.00 2.29
2848 2858 6.209192 TGGTTACATGCAAATCAAGAGAACAT 59.791 34.615 0.00 0.00 0.00 2.71
2849 2859 5.534278 TGGTTACATGCAAATCAAGAGAACA 59.466 36.000 0.00 0.00 0.00 3.18
2850 2860 6.012658 TGGTTACATGCAAATCAAGAGAAC 57.987 37.500 0.00 0.00 0.00 3.01
2851 2861 6.446318 GTTGGTTACATGCAAATCAAGAGAA 58.554 36.000 7.20 0.00 0.00 2.87
2852 2862 5.334802 CGTTGGTTACATGCAAATCAAGAGA 60.335 40.000 7.20 0.00 0.00 3.10
2853 2863 4.853196 CGTTGGTTACATGCAAATCAAGAG 59.147 41.667 7.20 2.74 0.00 2.85
2854 2864 4.793071 CGTTGGTTACATGCAAATCAAGA 58.207 39.130 7.20 0.00 0.00 3.02
2855 2865 3.364621 GCGTTGGTTACATGCAAATCAAG 59.635 43.478 7.20 4.38 0.00 3.02
2856 2866 3.243535 TGCGTTGGTTACATGCAAATCAA 60.244 39.130 3.57 3.57 36.01 2.57
2857 2867 2.294512 TGCGTTGGTTACATGCAAATCA 59.705 40.909 0.00 0.00 36.01 2.57
2858 2868 2.940147 TGCGTTGGTTACATGCAAATC 58.060 42.857 0.00 0.00 36.01 2.17
2859 2869 3.252400 CATGCGTTGGTTACATGCAAAT 58.748 40.909 0.00 0.00 40.32 2.32
2860 2870 2.035193 ACATGCGTTGGTTACATGCAAA 59.965 40.909 0.00 0.00 43.96 3.68
2861 2871 1.611006 ACATGCGTTGGTTACATGCAA 59.389 42.857 0.00 0.00 43.96 4.08
2862 2872 1.242989 ACATGCGTTGGTTACATGCA 58.757 45.000 0.00 0.00 43.96 3.96
2863 2873 3.479505 TTACATGCGTTGGTTACATGC 57.520 42.857 0.00 0.00 43.96 4.06
2864 2874 5.398169 ACAATTACATGCGTTGGTTACATG 58.602 37.500 9.30 0.00 45.28 3.21
2865 2875 5.637006 ACAATTACATGCGTTGGTTACAT 57.363 34.783 9.30 0.00 0.00 2.29
2866 2876 5.215903 CAACAATTACATGCGTTGGTTACA 58.784 37.500 9.30 0.00 36.06 2.41
2867 2877 5.216648 ACAACAATTACATGCGTTGGTTAC 58.783 37.500 13.59 0.00 42.35 2.50
2868 2878 5.440234 ACAACAATTACATGCGTTGGTTA 57.560 34.783 13.59 0.00 42.35 2.85
2869 2879 4.314740 ACAACAATTACATGCGTTGGTT 57.685 36.364 13.59 3.24 42.35 3.67
2870 2880 4.314740 AACAACAATTACATGCGTTGGT 57.685 36.364 13.59 7.16 42.35 3.67
2871 2881 4.981674 AGAAACAACAATTACATGCGTTGG 59.018 37.500 13.59 0.00 42.35 3.77
2872 2882 6.345723 GGAAGAAACAACAATTACATGCGTTG 60.346 38.462 0.00 1.98 43.40 4.10
2873 2883 5.689961 GGAAGAAACAACAATTACATGCGTT 59.310 36.000 0.00 0.00 0.00 4.84
2874 2884 5.009610 AGGAAGAAACAACAATTACATGCGT 59.990 36.000 0.00 0.00 0.00 5.24
2875 2885 5.460646 AGGAAGAAACAACAATTACATGCG 58.539 37.500 0.00 0.00 0.00 4.73
2876 2886 5.569059 CGAGGAAGAAACAACAATTACATGC 59.431 40.000 0.00 0.00 0.00 4.06
2877 2887 6.797033 GTCGAGGAAGAAACAACAATTACATG 59.203 38.462 0.00 0.00 0.00 3.21
2878 2888 6.485313 TGTCGAGGAAGAAACAACAATTACAT 59.515 34.615 0.00 0.00 0.00 2.29
2879 2889 5.818336 TGTCGAGGAAGAAACAACAATTACA 59.182 36.000 0.00 0.00 0.00 2.41
2880 2890 6.134061 GTGTCGAGGAAGAAACAACAATTAC 58.866 40.000 0.00 0.00 0.00 1.89
2881 2891 5.237779 GGTGTCGAGGAAGAAACAACAATTA 59.762 40.000 0.00 0.00 30.04 1.40
2882 2892 4.036380 GGTGTCGAGGAAGAAACAACAATT 59.964 41.667 0.00 0.00 30.04 2.32
2883 2893 3.564225 GGTGTCGAGGAAGAAACAACAAT 59.436 43.478 0.00 0.00 30.04 2.71
2884 2894 2.940410 GGTGTCGAGGAAGAAACAACAA 59.060 45.455 0.00 0.00 30.04 2.83
2885 2895 2.093394 TGGTGTCGAGGAAGAAACAACA 60.093 45.455 0.00 0.00 37.01 3.33
2886 2896 2.287103 GTGGTGTCGAGGAAGAAACAAC 59.713 50.000 0.00 0.00 30.04 3.32
2887 2897 2.093394 TGTGGTGTCGAGGAAGAAACAA 60.093 45.455 0.00 0.00 30.04 2.83
2888 2898 1.483004 TGTGGTGTCGAGGAAGAAACA 59.517 47.619 0.00 0.00 30.04 2.83
2889 2899 1.865340 GTGTGGTGTCGAGGAAGAAAC 59.135 52.381 0.00 0.00 0.00 2.78
2890 2900 1.483004 TGTGTGGTGTCGAGGAAGAAA 59.517 47.619 0.00 0.00 0.00 2.52
2891 2901 1.116308 TGTGTGGTGTCGAGGAAGAA 58.884 50.000 0.00 0.00 0.00 2.52
2892 2902 1.068588 CTTGTGTGGTGTCGAGGAAGA 59.931 52.381 0.00 0.00 0.00 2.87
2893 2903 1.068588 TCTTGTGTGGTGTCGAGGAAG 59.931 52.381 0.00 0.00 0.00 3.46
2894 2904 1.116308 TCTTGTGTGGTGTCGAGGAA 58.884 50.000 0.00 0.00 0.00 3.36
2895 2905 1.116308 TTCTTGTGTGGTGTCGAGGA 58.884 50.000 0.00 0.00 0.00 3.71
2896 2906 1.597663 GTTTCTTGTGTGGTGTCGAGG 59.402 52.381 0.00 0.00 0.00 4.63
2897 2907 2.276201 TGTTTCTTGTGTGGTGTCGAG 58.724 47.619 0.00 0.00 0.00 4.04
2898 2908 2.276201 CTGTTTCTTGTGTGGTGTCGA 58.724 47.619 0.00 0.00 0.00 4.20
2899 2909 1.268032 GCTGTTTCTTGTGTGGTGTCG 60.268 52.381 0.00 0.00 0.00 4.35
2900 2910 2.017049 AGCTGTTTCTTGTGTGGTGTC 58.983 47.619 0.00 0.00 0.00 3.67
2901 2911 2.128771 AGCTGTTTCTTGTGTGGTGT 57.871 45.000 0.00 0.00 0.00 4.16
2902 2912 2.031682 GCTAGCTGTTTCTTGTGTGGTG 60.032 50.000 7.70 0.00 0.00 4.17
2903 2913 2.222027 GCTAGCTGTTTCTTGTGTGGT 58.778 47.619 7.70 0.00 0.00 4.16
2904 2914 2.221169 TGCTAGCTGTTTCTTGTGTGG 58.779 47.619 17.23 0.00 0.00 4.17
2905 2915 2.874701 ACTGCTAGCTGTTTCTTGTGTG 59.125 45.455 20.37 0.00 0.00 3.82
2906 2916 3.199880 ACTGCTAGCTGTTTCTTGTGT 57.800 42.857 20.37 0.00 0.00 3.72
2907 2917 4.310769 ACTACTGCTAGCTGTTTCTTGTG 58.689 43.478 29.02 14.19 0.00 3.33
2908 2918 4.282195 AGACTACTGCTAGCTGTTTCTTGT 59.718 41.667 29.02 19.40 0.00 3.16
2909 2919 4.815269 AGACTACTGCTAGCTGTTTCTTG 58.185 43.478 29.02 16.98 0.00 3.02
2910 2920 6.783708 ATAGACTACTGCTAGCTGTTTCTT 57.216 37.500 29.02 17.64 0.00 2.52
2911 2921 6.488683 CCTATAGACTACTGCTAGCTGTTTCT 59.511 42.308 29.02 27.85 0.00 2.52
2912 2922 6.674066 CCTATAGACTACTGCTAGCTGTTTC 58.326 44.000 29.02 23.73 0.00 2.78
2913 2923 5.010213 GCCTATAGACTACTGCTAGCTGTTT 59.990 44.000 29.02 17.93 0.00 2.83
2914 2924 4.521256 GCCTATAGACTACTGCTAGCTGTT 59.479 45.833 29.02 14.73 0.00 3.16
2915 2925 4.076394 GCCTATAGACTACTGCTAGCTGT 58.924 47.826 27.37 27.37 0.00 4.40
2916 2926 3.126171 CGCCTATAGACTACTGCTAGCTG 59.874 52.174 19.01 19.01 0.00 4.24
2917 2927 3.008157 TCGCCTATAGACTACTGCTAGCT 59.992 47.826 17.23 0.00 0.00 3.32
2918 2928 3.125658 GTCGCCTATAGACTACTGCTAGC 59.874 52.174 8.10 8.10 35.84 3.42
2919 2929 3.368539 CGTCGCCTATAGACTACTGCTAG 59.631 52.174 0.00 0.00 36.53 3.42
2920 2930 3.006217 TCGTCGCCTATAGACTACTGCTA 59.994 47.826 0.00 0.00 36.53 3.49
2921 2931 2.144730 CGTCGCCTATAGACTACTGCT 58.855 52.381 0.00 0.00 36.53 4.24
2922 2932 2.141517 TCGTCGCCTATAGACTACTGC 58.858 52.381 0.00 0.00 36.53 4.40
2923 2933 3.391965 ACTCGTCGCCTATAGACTACTG 58.608 50.000 0.00 0.00 36.53 2.74
2924 2934 3.749665 ACTCGTCGCCTATAGACTACT 57.250 47.619 0.00 0.00 36.53 2.57
2925 2935 4.034975 ACAAACTCGTCGCCTATAGACTAC 59.965 45.833 0.00 0.00 36.53 2.73
2926 2936 4.194640 ACAAACTCGTCGCCTATAGACTA 58.805 43.478 0.00 0.00 36.53 2.59
2927 2937 3.015327 ACAAACTCGTCGCCTATAGACT 58.985 45.455 0.00 0.00 36.53 3.24
2928 2938 3.417690 ACAAACTCGTCGCCTATAGAC 57.582 47.619 0.00 0.00 35.41 2.59
2929 2939 4.445452 AAACAAACTCGTCGCCTATAGA 57.555 40.909 0.00 0.00 0.00 1.98
2930 2940 4.501921 GGTAAACAAACTCGTCGCCTATAG 59.498 45.833 0.00 0.00 0.00 1.31
2931 2941 4.423732 GGTAAACAAACTCGTCGCCTATA 58.576 43.478 0.00 0.00 0.00 1.31
2932 2942 3.256558 GGTAAACAAACTCGTCGCCTAT 58.743 45.455 0.00 0.00 0.00 2.57
2933 2943 2.610232 GGGTAAACAAACTCGTCGCCTA 60.610 50.000 0.00 0.00 0.00 3.93
2934 2944 1.505425 GGTAAACAAACTCGTCGCCT 58.495 50.000 0.00 0.00 0.00 5.52
2935 2945 0.514255 GGGTAAACAAACTCGTCGCC 59.486 55.000 0.00 0.00 0.00 5.54
2936 2946 1.505425 AGGGTAAACAAACTCGTCGC 58.495 50.000 0.00 0.00 0.00 5.19
2937 2947 3.556775 TCAAAGGGTAAACAAACTCGTCG 59.443 43.478 0.00 0.00 0.00 5.12
2938 2948 5.065602 ACTTCAAAGGGTAAACAAACTCGTC 59.934 40.000 0.00 0.00 0.00 4.20
2939 2949 4.945543 ACTTCAAAGGGTAAACAAACTCGT 59.054 37.500 0.00 0.00 0.00 4.18
2940 2950 5.494632 ACTTCAAAGGGTAAACAAACTCG 57.505 39.130 0.00 0.00 0.00 4.18
2941 2951 5.518847 GCAACTTCAAAGGGTAAACAAACTC 59.481 40.000 0.00 0.00 0.00 3.01
2942 2952 5.416083 GCAACTTCAAAGGGTAAACAAACT 58.584 37.500 0.00 0.00 0.00 2.66
2943 2953 4.569162 GGCAACTTCAAAGGGTAAACAAAC 59.431 41.667 0.00 0.00 0.00 2.93
2944 2954 4.223032 TGGCAACTTCAAAGGGTAAACAAA 59.777 37.500 0.00 0.00 37.61 2.83
2945 2955 3.769844 TGGCAACTTCAAAGGGTAAACAA 59.230 39.130 0.00 0.00 37.61 2.83
2946 2956 3.366396 TGGCAACTTCAAAGGGTAAACA 58.634 40.909 0.00 0.00 37.61 2.83
2947 2957 4.116961 GTTGGCAACTTCAAAGGGTAAAC 58.883 43.478 22.66 0.00 37.61 2.01
2948 2958 3.181485 CGTTGGCAACTTCAAAGGGTAAA 60.181 43.478 26.26 0.00 37.61 2.01
2949 2959 2.359531 CGTTGGCAACTTCAAAGGGTAA 59.640 45.455 26.26 0.00 37.61 2.85
2950 2960 1.950909 CGTTGGCAACTTCAAAGGGTA 59.049 47.619 26.26 0.00 37.61 3.69
2951 2961 0.744281 CGTTGGCAACTTCAAAGGGT 59.256 50.000 26.26 0.00 37.61 4.34
2952 2962 0.597377 GCGTTGGCAACTTCAAAGGG 60.597 55.000 26.26 10.52 39.62 3.95
2953 2963 0.597377 GGCGTTGGCAACTTCAAAGG 60.597 55.000 26.26 11.21 42.47 3.11
2954 2964 0.597377 GGGCGTTGGCAACTTCAAAG 60.597 55.000 26.26 11.90 42.47 2.77
2955 2965 1.439644 GGGCGTTGGCAACTTCAAA 59.560 52.632 26.26 0.00 42.47 2.69
2956 2966 2.494530 GGGGCGTTGGCAACTTCAA 61.495 57.895 26.26 0.00 42.47 2.69
2957 2967 2.909965 GGGGCGTTGGCAACTTCA 60.910 61.111 26.26 0.00 42.47 3.02
2958 2968 2.909965 TGGGGCGTTGGCAACTTC 60.910 61.111 26.26 17.53 42.47 3.01
2959 2969 2.346284 TACTGGGGCGTTGGCAACTT 62.346 55.000 26.26 5.98 42.47 2.66
2960 2970 2.824880 TACTGGGGCGTTGGCAACT 61.825 57.895 26.26 9.74 42.47 3.16
2961 2971 2.281900 TACTGGGGCGTTGGCAAC 60.282 61.111 20.27 20.27 42.47 4.17
2962 2972 2.281900 GTACTGGGGCGTTGGCAA 60.282 61.111 0.00 0.00 42.47 4.52
2963 2973 2.901281 ATGTACTGGGGCGTTGGCA 61.901 57.895 0.00 0.00 42.47 4.92
2964 2974 2.045340 ATGTACTGGGGCGTTGGC 60.045 61.111 0.00 0.00 38.90 4.52
2965 2975 2.406616 GCATGTACTGGGGCGTTGG 61.407 63.158 0.00 0.00 0.00 3.77
2966 2976 0.960364 AAGCATGTACTGGGGCGTTG 60.960 55.000 0.00 0.00 0.00 4.10
2967 2977 0.251165 AAAGCATGTACTGGGGCGTT 60.251 50.000 0.00 0.00 0.00 4.84
2968 2978 0.251165 AAAAGCATGTACTGGGGCGT 60.251 50.000 0.00 0.00 0.00 5.68
2969 2979 0.451783 GAAAAGCATGTACTGGGGCG 59.548 55.000 0.00 0.00 0.00 6.13
2970 2980 0.817654 GGAAAAGCATGTACTGGGGC 59.182 55.000 0.00 0.00 0.00 5.80
2971 2981 2.214376 TGGAAAAGCATGTACTGGGG 57.786 50.000 0.00 0.00 0.00 4.96
2972 2982 2.159198 GCATGGAAAAGCATGTACTGGG 60.159 50.000 0.00 0.00 0.00 4.45
2973 2983 2.159198 GGCATGGAAAAGCATGTACTGG 60.159 50.000 0.00 0.00 0.00 4.00
2974 2984 2.492881 TGGCATGGAAAAGCATGTACTG 59.507 45.455 0.00 0.00 0.00 2.74
2975 2985 2.806434 TGGCATGGAAAAGCATGTACT 58.194 42.857 0.00 0.00 0.00 2.73
2976 2986 3.806625 ATGGCATGGAAAAGCATGTAC 57.193 42.857 0.00 0.00 0.00 2.90
2977 2987 6.482898 AATTATGGCATGGAAAAGCATGTA 57.517 33.333 10.98 0.00 0.00 2.29
2978 2988 5.362105 AATTATGGCATGGAAAAGCATGT 57.638 34.783 10.98 0.00 0.00 3.21
2979 2989 6.316640 TGAAAATTATGGCATGGAAAAGCATG 59.683 34.615 10.98 0.00 0.00 4.06
2980 2990 6.416415 TGAAAATTATGGCATGGAAAAGCAT 58.584 32.000 10.98 0.00 0.00 3.79
2981 2991 5.802465 TGAAAATTATGGCATGGAAAAGCA 58.198 33.333 10.98 0.00 0.00 3.91
2982 2992 6.764560 AGATGAAAATTATGGCATGGAAAAGC 59.235 34.615 10.98 0.00 0.00 3.51
2983 2993 8.726870 AAGATGAAAATTATGGCATGGAAAAG 57.273 30.769 10.98 0.00 0.00 2.27
2987 2997 8.729756 CGTATAAGATGAAAATTATGGCATGGA 58.270 33.333 10.98 0.00 0.00 3.41
2988 2998 8.729756 TCGTATAAGATGAAAATTATGGCATGG 58.270 33.333 10.98 0.00 0.00 3.66
2991 3001 9.944663 GTTTCGTATAAGATGAAAATTATGGCA 57.055 29.630 0.00 0.00 43.20 4.92
2992 3002 9.394477 GGTTTCGTATAAGATGAAAATTATGGC 57.606 33.333 0.00 0.00 43.20 4.40
2997 3007 9.620660 GTTGTGGTTTCGTATAAGATGAAAATT 57.379 29.630 0.00 0.00 43.20 1.82
2998 3008 9.010029 AGTTGTGGTTTCGTATAAGATGAAAAT 57.990 29.630 0.00 0.00 43.20 1.82
2999 3009 8.385898 AGTTGTGGTTTCGTATAAGATGAAAA 57.614 30.769 0.00 0.00 43.20 2.29
3000 3010 7.658167 TGAGTTGTGGTTTCGTATAAGATGAAA 59.342 33.333 0.00 0.00 40.13 2.69
3001 3011 7.117236 GTGAGTTGTGGTTTCGTATAAGATGAA 59.883 37.037 0.00 0.00 0.00 2.57
3002 3012 6.588756 GTGAGTTGTGGTTTCGTATAAGATGA 59.411 38.462 0.00 0.00 0.00 2.92
3003 3013 6.183360 GGTGAGTTGTGGTTTCGTATAAGATG 60.183 42.308 0.00 0.00 0.00 2.90
3004 3014 5.873164 GGTGAGTTGTGGTTTCGTATAAGAT 59.127 40.000 0.00 0.00 0.00 2.40
3005 3015 5.221481 TGGTGAGTTGTGGTTTCGTATAAGA 60.221 40.000 0.00 0.00 0.00 2.10
3006 3016 4.992319 TGGTGAGTTGTGGTTTCGTATAAG 59.008 41.667 0.00 0.00 0.00 1.73
3007 3017 4.958509 TGGTGAGTTGTGGTTTCGTATAA 58.041 39.130 0.00 0.00 0.00 0.98
3008 3018 4.603989 TGGTGAGTTGTGGTTTCGTATA 57.396 40.909 0.00 0.00 0.00 1.47
3009 3019 3.478857 TGGTGAGTTGTGGTTTCGTAT 57.521 42.857 0.00 0.00 0.00 3.06
3010 3020 2.983907 TGGTGAGTTGTGGTTTCGTA 57.016 45.000 0.00 0.00 0.00 3.43
3011 3021 2.341846 ATGGTGAGTTGTGGTTTCGT 57.658 45.000 0.00 0.00 0.00 3.85
3012 3022 4.000325 TGATATGGTGAGTTGTGGTTTCG 59.000 43.478 0.00 0.00 0.00 3.46
3013 3023 5.619981 GCTTGATATGGTGAGTTGTGGTTTC 60.620 44.000 0.00 0.00 0.00 2.78
3014 3024 4.218417 GCTTGATATGGTGAGTTGTGGTTT 59.782 41.667 0.00 0.00 0.00 3.27
3015 3025 3.758554 GCTTGATATGGTGAGTTGTGGTT 59.241 43.478 0.00 0.00 0.00 3.67
3016 3026 3.009473 AGCTTGATATGGTGAGTTGTGGT 59.991 43.478 0.00 0.00 0.00 4.16
3017 3027 3.614092 AGCTTGATATGGTGAGTTGTGG 58.386 45.455 0.00 0.00 0.00 4.17
3018 3028 3.624861 GGAGCTTGATATGGTGAGTTGTG 59.375 47.826 0.00 0.00 0.00 3.33
3019 3029 3.264193 TGGAGCTTGATATGGTGAGTTGT 59.736 43.478 0.00 0.00 0.00 3.32
3020 3030 3.877559 TGGAGCTTGATATGGTGAGTTG 58.122 45.455 0.00 0.00 0.00 3.16
3021 3031 4.785346 ATGGAGCTTGATATGGTGAGTT 57.215 40.909 0.00 0.00 0.00 3.01
3022 3032 4.262808 GCTATGGAGCTTGATATGGTGAGT 60.263 45.833 0.00 0.00 45.98 3.41
3023 3033 4.252073 GCTATGGAGCTTGATATGGTGAG 58.748 47.826 0.00 0.00 45.98 3.51
3024 3034 4.277515 GCTATGGAGCTTGATATGGTGA 57.722 45.455 0.00 0.00 45.98 4.02
3052 3062 2.482142 GGGTCTTCATCTCGATGGTGAC 60.482 54.545 16.90 16.90 39.24 3.67
3053 3063 1.757118 GGGTCTTCATCTCGATGGTGA 59.243 52.381 7.03 3.59 39.24 4.02
3054 3064 1.536922 CGGGTCTTCATCTCGATGGTG 60.537 57.143 7.03 1.51 39.24 4.17
3055 3065 0.747255 CGGGTCTTCATCTCGATGGT 59.253 55.000 7.03 0.00 39.24 3.55
3056 3066 1.032794 TCGGGTCTTCATCTCGATGG 58.967 55.000 7.03 0.00 39.24 3.51
3057 3067 1.405463 TGTCGGGTCTTCATCTCGATG 59.595 52.381 0.45 0.45 40.09 3.84
3058 3068 1.405821 GTGTCGGGTCTTCATCTCGAT 59.594 52.381 0.00 0.00 32.46 3.59
3059 3069 0.809385 GTGTCGGGTCTTCATCTCGA 59.191 55.000 0.00 0.00 0.00 4.04
3060 3070 0.526211 TGTGTCGGGTCTTCATCTCG 59.474 55.000 0.00 0.00 0.00 4.04
3061 3071 1.404315 GGTGTGTCGGGTCTTCATCTC 60.404 57.143 0.00 0.00 0.00 2.75
3062 3072 0.608640 GGTGTGTCGGGTCTTCATCT 59.391 55.000 0.00 0.00 0.00 2.90
3063 3073 0.608640 AGGTGTGTCGGGTCTTCATC 59.391 55.000 0.00 0.00 0.00 2.92
3064 3074 2.759985 AGGTGTGTCGGGTCTTCAT 58.240 52.632 0.00 0.00 0.00 2.57
3065 3075 4.288234 AGGTGTGTCGGGTCTTCA 57.712 55.556 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.