Multiple sequence alignment - TraesCS7B01G390100

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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 TraesCS7B01G390100 chr7B 100.000 5194 0 0 1 5194 656515384 656520577 0.000000e+00 9592
1 TraesCS7B01G390100 chr7B 96.461 876 27 3 4 878 99919111 99918239 0.000000e+00 1443
2 TraesCS7B01G390100 chr7A 93.823 1797 86 15 2850 4628 677700613 677702402 0.000000e+00 2680
3 TraesCS7B01G390100 chr7A 93.821 1489 71 7 1246 2727 677699141 677700615 0.000000e+00 2220
4 TraesCS7B01G390100 chr7A 88.915 424 29 10 4613 5034 677702605 677703012 1.670000e-139 507
5 TraesCS7B01G390100 chr7A 88.037 326 24 8 904 1219 677698824 677699144 6.350000e-99 372
6 TraesCS7B01G390100 chr7A 94.737 171 7 2 5024 5194 677703031 677703199 1.110000e-66 265
7 TraesCS7B01G390100 chr7A 95.714 140 4 2 2721 2859 597530151 597530289 1.880000e-54 224
8 TraesCS7B01G390100 chr7D 91.703 1856 98 23 903 2727 586489497 586491327 0.000000e+00 2523
9 TraesCS7B01G390100 chr7D 92.489 1398 65 17 2850 4212 586491325 586492717 0.000000e+00 1964
10 TraesCS7B01G390100 chr7D 92.841 908 57 6 4293 5194 586492745 586493650 0.000000e+00 1310
11 TraesCS7B01G390100 chr6B 98.516 876 10 3 1 875 644464169 644463296 0.000000e+00 1543
12 TraesCS7B01G390100 chr3B 91.393 883 62 9 1 877 685819880 685819006 0.000000e+00 1197
13 TraesCS7B01G390100 chr3B 87.964 889 88 15 1 877 572847157 572848038 0.000000e+00 1031
14 TraesCS7B01G390100 chr4A 88.552 891 82 17 1 882 725322759 725323638 0.000000e+00 1062
15 TraesCS7B01G390100 chr5A 88.536 881 85 15 3 878 659423722 659424591 0.000000e+00 1053
16 TraesCS7B01G390100 chr1A 86.922 887 98 14 1 880 517637470 517638345 0.000000e+00 979
17 TraesCS7B01G390100 chr6A 86.486 888 103 14 1 880 520926989 520926111 0.000000e+00 959
18 TraesCS7B01G390100 chr4D 85.959 876 106 13 13 880 358101344 358100478 0.000000e+00 920
19 TraesCS7B01G390100 chr2B 86.567 335 34 6 879 1205 606487212 606486881 4.950000e-95 359
20 TraesCS7B01G390100 chr2B 95.070 142 5 2 2712 2852 518742247 518742387 6.770000e-54 222
21 TraesCS7B01G390100 chr2B 92.958 142 9 1 2720 2860 138812223 138812082 6.820000e-49 206
22 TraesCS7B01G390100 chr2A 97.059 136 3 1 2721 2856 202049212 202049346 1.460000e-55 228
23 TraesCS7B01G390100 chr5B 97.037 135 3 1 2722 2855 254980438 254980572 5.230000e-55 226
24 TraesCS7B01G390100 chr5B 95.070 142 5 2 2725 2864 710617935 710618076 6.770000e-54 222
25 TraesCS7B01G390100 chr5B 91.139 158 9 5 2703 2856 560436719 560436875 5.270000e-50 209
26 TraesCS7B01G390100 chr3D 96.350 137 4 1 2720 2855 283321119 283321255 1.880000e-54 224
27 TraesCS7B01G390100 chr2D 96.324 136 5 0 2721 2856 536091022 536091157 1.880000e-54 224


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 TraesCS7B01G390100 chr7B 656515384 656520577 5193 False 9592.000000 9592 100.000000 1 5194 1 chr7B.!!$F1 5193
1 TraesCS7B01G390100 chr7B 99918239 99919111 872 True 1443.000000 1443 96.461000 4 878 1 chr7B.!!$R1 874
2 TraesCS7B01G390100 chr7A 677698824 677703199 4375 False 1208.800000 2680 91.866600 904 5194 5 chr7A.!!$F2 4290
3 TraesCS7B01G390100 chr7D 586489497 586493650 4153 False 1932.333333 2523 92.344333 903 5194 3 chr7D.!!$F1 4291
4 TraesCS7B01G390100 chr6B 644463296 644464169 873 True 1543.000000 1543 98.516000 1 875 1 chr6B.!!$R1 874
5 TraesCS7B01G390100 chr3B 685819006 685819880 874 True 1197.000000 1197 91.393000 1 877 1 chr3B.!!$R1 876
6 TraesCS7B01G390100 chr3B 572847157 572848038 881 False 1031.000000 1031 87.964000 1 877 1 chr3B.!!$F1 876
7 TraesCS7B01G390100 chr4A 725322759 725323638 879 False 1062.000000 1062 88.552000 1 882 1 chr4A.!!$F1 881
8 TraesCS7B01G390100 chr5A 659423722 659424591 869 False 1053.000000 1053 88.536000 3 878 1 chr5A.!!$F1 875
9 TraesCS7B01G390100 chr1A 517637470 517638345 875 False 979.000000 979 86.922000 1 880 1 chr1A.!!$F1 879
10 TraesCS7B01G390100 chr6A 520926111 520926989 878 True 959.000000 959 86.486000 1 880 1 chr6A.!!$R1 879
11 TraesCS7B01G390100 chr4D 358100478 358101344 866 True 920.000000 920 85.959000 13 880 1 chr4D.!!$R1 867

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
989 1016 0.540597 AGCCCAAAGCCCAGAGAAAC 60.541 55.0 0.0 0.0 45.47 2.78 F
1565 1617 0.030101 GAGCTCGAACTCGGATCAGG 59.970 60.0 0.0 0.0 40.29 3.86 F
2741 2828 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.0 0.0 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2834 2921 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.0 0.0 0.0 0.0 3.28 R
2835 2922 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.0 0.0 0.0 0.0 4.12 R
4673 5023 0.671251 CTGCTGGTATCTCGTCTCCC 59.329 60.0 0.0 0.0 0.0 4.30 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
157 158 3.940221 AGTCATAGTCGTCTGGTGTAGTC 59.060 47.826 0.00 0.00 0.00 2.59
197 198 0.890683 CATGCCAGTTCCCAAGTTCC 59.109 55.000 0.00 0.00 0.00 3.62
345 362 4.057432 CTCCGCAACCAACAATTCAAAAT 58.943 39.130 0.00 0.00 0.00 1.82
884 911 7.801716 ATTTTGGACTTTTTCCTTTTTAGGC 57.198 32.000 0.00 0.00 46.10 3.93
885 912 5.941555 TTGGACTTTTTCCTTTTTAGGCA 57.058 34.783 0.00 0.00 46.10 4.75
886 913 5.941555 TGGACTTTTTCCTTTTTAGGCAA 57.058 34.783 0.00 0.00 46.10 4.52
887 914 6.301169 TGGACTTTTTCCTTTTTAGGCAAA 57.699 33.333 0.00 0.00 46.10 3.68
888 915 6.894682 TGGACTTTTTCCTTTTTAGGCAAAT 58.105 32.000 0.00 0.00 46.10 2.32
889 916 6.989759 TGGACTTTTTCCTTTTTAGGCAAATC 59.010 34.615 0.00 0.00 46.10 2.17
890 917 6.989759 GGACTTTTTCCTTTTTAGGCAAATCA 59.010 34.615 0.00 0.00 41.95 2.57
891 918 7.497579 GGACTTTTTCCTTTTTAGGCAAATCAA 59.502 33.333 0.00 0.00 41.95 2.57
892 919 8.437360 ACTTTTTCCTTTTTAGGCAAATCAAG 57.563 30.769 0.00 0.00 0.00 3.02
893 920 7.498900 ACTTTTTCCTTTTTAGGCAAATCAAGG 59.501 33.333 0.00 0.00 34.75 3.61
894 921 6.739331 TTTCCTTTTTAGGCAAATCAAGGA 57.261 33.333 9.54 9.54 38.23 3.36
895 922 5.982890 TCCTTTTTAGGCAAATCAAGGAG 57.017 39.130 9.54 0.00 36.43 3.69
896 923 4.772100 TCCTTTTTAGGCAAATCAAGGAGG 59.228 41.667 9.54 0.00 36.43 4.30
897 924 4.772100 CCTTTTTAGGCAAATCAAGGAGGA 59.228 41.667 0.00 0.00 35.15 3.71
898 925 5.245977 CCTTTTTAGGCAAATCAAGGAGGAA 59.754 40.000 0.00 0.00 35.15 3.36
899 926 6.070596 CCTTTTTAGGCAAATCAAGGAGGAAT 60.071 38.462 0.00 0.00 35.15 3.01
900 927 6.933514 TTTTAGGCAAATCAAGGAGGAATT 57.066 33.333 0.00 0.00 0.00 2.17
901 928 5.920193 TTAGGCAAATCAAGGAGGAATTG 57.080 39.130 0.00 0.00 32.17 2.32
902 929 3.782992 AGGCAAATCAAGGAGGAATTGT 58.217 40.909 0.00 0.00 31.75 2.71
919 946 8.218423 AGGAATTGTTTTTAGGGGAAATCAAT 57.782 30.769 0.00 0.00 39.10 2.57
983 1010 1.106285 GTTATCAGCCCAAAGCCCAG 58.894 55.000 0.00 0.00 45.47 4.45
985 1012 0.548031 TATCAGCCCAAAGCCCAGAG 59.452 55.000 0.00 0.00 45.47 3.35
989 1016 0.540597 AGCCCAAAGCCCAGAGAAAC 60.541 55.000 0.00 0.00 45.47 2.78
990 1017 0.827507 GCCCAAAGCCCAGAGAAACA 60.828 55.000 0.00 0.00 34.35 2.83
993 1020 2.036346 CCCAAAGCCCAGAGAAACAAAG 59.964 50.000 0.00 0.00 0.00 2.77
994 1021 2.958355 CCAAAGCCCAGAGAAACAAAGA 59.042 45.455 0.00 0.00 0.00 2.52
995 1022 3.243535 CCAAAGCCCAGAGAAACAAAGAC 60.244 47.826 0.00 0.00 0.00 3.01
997 1024 2.856222 AGCCCAGAGAAACAAAGACAG 58.144 47.619 0.00 0.00 0.00 3.51
999 1026 2.550180 GCCCAGAGAAACAAAGACAGAC 59.450 50.000 0.00 0.00 0.00 3.51
1014 1050 4.985538 AGACAGACAAAGAGAGAGAGAGT 58.014 43.478 0.00 0.00 0.00 3.24
1092 1128 1.557443 CCGCCGTGACAAGTGAGAAC 61.557 60.000 0.00 0.00 0.00 3.01
1158 1194 1.147153 GCCCTAATCGGAAGCTGCT 59.853 57.895 0.00 0.00 33.16 4.24
1160 1196 0.465705 CCCTAATCGGAAGCTGCTGA 59.534 55.000 5.44 5.44 33.16 4.26
1224 1261 0.882042 CGATTCCTCAATCCCCAGCG 60.882 60.000 0.00 0.00 35.81 5.18
1232 1269 1.173043 CAATCCCCAGCGCTTGTTAA 58.827 50.000 7.50 0.00 0.00 2.01
1233 1270 1.543802 CAATCCCCAGCGCTTGTTAAA 59.456 47.619 7.50 0.00 0.00 1.52
1246 1283 2.012937 TGTTAAACGAATCGCCCGAT 57.987 45.000 1.15 0.00 36.23 4.18
1250 1287 0.810031 AAACGAATCGCCCGATCCAG 60.810 55.000 1.15 1.80 33.08 3.86
1269 1306 4.766891 TCCAGCTTGAAATTCCTAGGTTTG 59.233 41.667 9.08 0.00 0.00 2.93
1332 1369 3.581101 CCAGAAGGGTGATGGATAGAGA 58.419 50.000 0.00 0.00 36.09 3.10
1339 1376 4.109435 AGGGTGATGGATAGAGAAGGAGAT 59.891 45.833 0.00 0.00 0.00 2.75
1415 1467 6.875726 CCAATCTATCGATTCCATGAGCTTTA 59.124 38.462 1.71 0.00 37.77 1.85
1545 1597 1.723220 GAGTGGTCTTTACCTTCGGC 58.277 55.000 0.00 0.00 46.91 5.54
1565 1617 0.030101 GAGCTCGAACTCGGATCAGG 59.970 60.000 0.00 0.00 40.29 3.86
1577 1629 1.348008 GGATCAGGGTGATGCCAGGA 61.348 60.000 0.00 0.00 39.00 3.86
1667 1719 1.074775 GTGGTGGTTCTGGATGCCA 59.925 57.895 0.00 0.00 0.00 4.92
1702 1754 2.796383 CGTCCATGAGGAGTTCGATGTC 60.796 54.545 0.00 0.00 46.92 3.06
1820 1872 8.564574 GTTTGGAACAGTGAAAATATAGACACA 58.435 33.333 0.00 0.00 42.39 3.72
1858 1924 5.584649 TGGTAGACACTTTGTTCTTCAGTTG 59.415 40.000 0.00 0.00 0.00 3.16
1859 1925 5.007724 GGTAGACACTTTGTTCTTCAGTTGG 59.992 44.000 0.00 0.00 0.00 3.77
1860 1926 4.843728 AGACACTTTGTTCTTCAGTTGGA 58.156 39.130 0.00 0.00 0.00 3.53
1861 1927 4.636206 AGACACTTTGTTCTTCAGTTGGAC 59.364 41.667 0.00 0.00 0.00 4.02
1862 1928 3.694566 ACACTTTGTTCTTCAGTTGGACC 59.305 43.478 0.00 0.00 0.00 4.46
1863 1929 3.947834 CACTTTGTTCTTCAGTTGGACCT 59.052 43.478 0.00 0.00 0.00 3.85
1864 1930 4.035675 CACTTTGTTCTTCAGTTGGACCTC 59.964 45.833 0.00 0.00 0.00 3.85
1865 1931 4.080299 ACTTTGTTCTTCAGTTGGACCTCT 60.080 41.667 0.00 0.00 0.00 3.69
1866 1932 5.130477 ACTTTGTTCTTCAGTTGGACCTCTA 59.870 40.000 0.00 0.00 0.00 2.43
1867 1933 4.602340 TGTTCTTCAGTTGGACCTCTAC 57.398 45.455 0.00 0.00 0.00 2.59
1868 1934 3.964688 TGTTCTTCAGTTGGACCTCTACA 59.035 43.478 0.00 0.00 0.00 2.74
1869 1935 4.039245 TGTTCTTCAGTTGGACCTCTACAG 59.961 45.833 0.00 0.00 0.00 2.74
1870 1936 3.845860 TCTTCAGTTGGACCTCTACAGT 58.154 45.455 0.00 0.00 0.00 3.55
1871 1937 4.223953 TCTTCAGTTGGACCTCTACAGTT 58.776 43.478 0.00 0.00 0.00 3.16
1886 1952 7.502561 ACCTCTACAGTTTAATTTGCTTTGACT 59.497 33.333 0.00 0.00 0.00 3.41
1947 2014 7.602644 TGTATCACTGAACAATCTTGTCTTACC 59.397 37.037 0.00 0.00 41.31 2.85
2006 2074 3.825328 AGTCTCAAAGGTGCAAATCAGT 58.175 40.909 0.00 0.00 0.00 3.41
2019 2092 6.703165 GGTGCAAATCAGTCTGAAAAAGATTT 59.297 34.615 6.64 0.00 38.91 2.17
2101 2174 4.756642 CAGAAGTGAGTCTTGTATTGCCAA 59.243 41.667 0.00 0.00 36.40 4.52
2118 2191 4.558538 GCCAAGGCAATGTCTAGTTATG 57.441 45.455 6.14 0.00 41.49 1.90
2148 2221 5.011125 ACATAGGAGAGGTAATCGTGATTGG 59.989 44.000 5.37 0.00 32.50 3.16
2336 2418 5.297029 GGTAGAATTATCCTTTGTGGTGCTC 59.703 44.000 0.00 0.00 37.07 4.26
2587 2673 0.108377 TATCTCATGGCGTTGCGTGT 60.108 50.000 0.00 0.00 0.00 4.49
2724 2811 9.862371 ACAGTAGTAGTCTTCTAATTCAACATG 57.138 33.333 0.00 0.00 0.00 3.21
2725 2812 9.862371 CAGTAGTAGTCTTCTAATTCAACATGT 57.138 33.333 0.00 0.00 0.00 3.21
2730 2817 9.303537 GTAGTCTTCTAATTCAACATGTACTCC 57.696 37.037 0.00 0.00 0.00 3.85
2731 2818 7.331791 AGTCTTCTAATTCAACATGTACTCCC 58.668 38.462 0.00 0.00 0.00 4.30
2732 2819 7.181125 AGTCTTCTAATTCAACATGTACTCCCT 59.819 37.037 0.00 0.00 0.00 4.20
2733 2820 7.492994 GTCTTCTAATTCAACATGTACTCCCTC 59.507 40.741 0.00 0.00 0.00 4.30
2734 2821 6.235231 TCTAATTCAACATGTACTCCCTCC 57.765 41.667 0.00 0.00 0.00 4.30
2735 2822 3.543680 ATTCAACATGTACTCCCTCCG 57.456 47.619 0.00 0.00 0.00 4.63
2736 2823 1.933021 TCAACATGTACTCCCTCCGT 58.067 50.000 0.00 0.00 0.00 4.69
2737 2824 1.822990 TCAACATGTACTCCCTCCGTC 59.177 52.381 0.00 0.00 0.00 4.79
2738 2825 1.134788 CAACATGTACTCCCTCCGTCC 60.135 57.143 0.00 0.00 0.00 4.79
2739 2826 0.686769 ACATGTACTCCCTCCGTCCC 60.687 60.000 0.00 0.00 0.00 4.46
2740 2827 0.686441 CATGTACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
2741 2828 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2742 2829 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2743 2830 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2744 2831 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2745 2832 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2746 2833 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2747 2834 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2748 2835 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2749 2836 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2750 2837 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2751 2838 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2752 2839 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2753 2840 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2754 2841 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2755 2842 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2756 2843 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2757 2844 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2758 2845 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2759 2846 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2760 2847 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2761 2848 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2762 2849 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2763 2850 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2822 2909 6.859112 ATACATCCGTATCTAGGCAAATCT 57.141 37.500 0.00 0.00 32.66 2.40
2823 2910 7.956328 ATACATCCGTATCTAGGCAAATCTA 57.044 36.000 0.00 0.00 32.66 1.98
2824 2911 6.665992 ACATCCGTATCTAGGCAAATCTAA 57.334 37.500 0.00 0.00 0.00 2.10
2825 2912 6.692486 ACATCCGTATCTAGGCAAATCTAAG 58.308 40.000 0.00 0.00 0.00 2.18
2826 2913 6.493802 ACATCCGTATCTAGGCAAATCTAAGA 59.506 38.462 0.00 0.00 0.00 2.10
2827 2914 6.328641 TCCGTATCTAGGCAAATCTAAGAC 57.671 41.667 0.00 0.00 0.00 3.01
2828 2915 5.831525 TCCGTATCTAGGCAAATCTAAGACA 59.168 40.000 0.00 0.00 0.00 3.41
2829 2916 6.322969 TCCGTATCTAGGCAAATCTAAGACAA 59.677 38.462 0.00 0.00 0.00 3.18
2830 2917 6.642950 CCGTATCTAGGCAAATCTAAGACAAG 59.357 42.308 0.00 0.00 0.00 3.16
2831 2918 7.426410 CGTATCTAGGCAAATCTAAGACAAGA 58.574 38.462 0.00 0.00 0.00 3.02
2832 2919 7.921214 CGTATCTAGGCAAATCTAAGACAAGAA 59.079 37.037 0.00 0.00 0.00 2.52
2833 2920 9.771534 GTATCTAGGCAAATCTAAGACAAGAAT 57.228 33.333 0.00 0.00 0.00 2.40
2835 2922 9.692325 ATCTAGGCAAATCTAAGACAAGAATTT 57.308 29.630 0.00 0.00 0.00 1.82
2836 2923 9.520515 TCTAGGCAAATCTAAGACAAGAATTTT 57.479 29.630 0.00 0.00 0.00 1.82
2837 2924 9.565213 CTAGGCAAATCTAAGACAAGAATTTTG 57.435 33.333 0.00 0.00 32.40 2.44
2838 2925 7.381323 AGGCAAATCTAAGACAAGAATTTTGG 58.619 34.615 0.00 0.00 30.97 3.28
2839 2926 6.591448 GGCAAATCTAAGACAAGAATTTTGGG 59.409 38.462 0.00 0.00 30.97 4.12
2840 2927 7.378181 GCAAATCTAAGACAAGAATTTTGGGA 58.622 34.615 0.00 0.00 30.97 4.37
2841 2928 7.329471 GCAAATCTAAGACAAGAATTTTGGGAC 59.671 37.037 0.00 0.00 30.97 4.46
2842 2929 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2843 2930 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2844 2931 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2845 2932 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2846 2933 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2847 2934 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2848 2935 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2987 3076 4.923871 AGTCACACTTATGCACTCTTTACG 59.076 41.667 0.00 0.00 0.00 3.18
3002 3091 7.743400 GCACTCTTTACGGTTTTCAAGTAATAC 59.257 37.037 0.00 0.00 31.47 1.89
3029 3129 5.642063 GCAAGTTTGGCAGTAGTAGAATACA 59.358 40.000 0.00 0.00 46.26 2.29
3042 3142 5.171476 AGTAGAATACACTGCACATGTGAC 58.829 41.667 29.80 19.67 46.26 3.67
3416 3532 4.585955 TGTAGCGTCTTGAGTTCTTCTT 57.414 40.909 0.00 0.00 0.00 2.52
3510 3626 9.782193 TGGTCTTGACCAATCTGAAGTCAGAAG 62.782 44.444 18.98 10.30 44.29 2.85
3568 3684 6.092670 AATGTATTTCATTGACTGGACAGTCG 59.907 38.462 23.02 12.13 46.57 4.18
3597 3713 0.627451 TGGGGAGCGGTAAGAGACTA 59.373 55.000 0.00 0.00 0.00 2.59
3601 3717 4.087907 GGGGAGCGGTAAGAGACTATATT 58.912 47.826 0.00 0.00 0.00 1.28
3602 3718 5.222192 TGGGGAGCGGTAAGAGACTATATTA 60.222 44.000 0.00 0.00 0.00 0.98
3607 3725 5.180868 AGCGGTAAGAGACTATATTACACCG 59.819 44.000 5.03 5.03 37.33 4.94
3608 3726 5.618640 GCGGTAAGAGACTATATTACACCGG 60.619 48.000 0.00 0.00 37.33 5.28
3615 3733 9.543783 AAGAGACTATATTACACCGGAAATTTC 57.456 33.333 9.46 9.83 0.00 2.17
3628 3746 8.567948 ACACCGGAAATTTCTATTATATTGCTG 58.432 33.333 17.42 0.00 0.00 4.41
3655 3773 3.884693 TGTAACGGGGTTTCCTTTCTTTC 59.115 43.478 0.00 0.00 0.00 2.62
3719 3841 2.162681 ACAACTTGTCCTAGGCAATGC 58.837 47.619 15.95 0.00 0.00 3.56
3726 3848 1.599542 GTCCTAGGCAATGCGTTCATC 59.400 52.381 5.55 0.00 31.27 2.92
3738 3860 1.955208 GCGTTCATCCCCTGGTTCATT 60.955 52.381 0.00 0.00 0.00 2.57
4070 4192 0.036732 AGAAACTGGCGAGGCATTGA 59.963 50.000 0.00 0.00 0.00 2.57
4253 4379 3.350833 CAAGAAGAATCAAGGACCTGGG 58.649 50.000 0.00 0.00 0.00 4.45
4261 4387 5.672194 AGAATCAAGGACCTGGGTATACATT 59.328 40.000 5.01 0.00 0.00 2.71
4359 4487 6.212955 TCTTGCAGTAAAATAAAGCCACAAC 58.787 36.000 0.00 0.00 0.00 3.32
4360 4488 5.521906 TGCAGTAAAATAAAGCCACAACA 57.478 34.783 0.00 0.00 0.00 3.33
4361 4489 6.095432 TGCAGTAAAATAAAGCCACAACAT 57.905 33.333 0.00 0.00 0.00 2.71
4416 4544 8.731605 AGCATATCTTCTGCATTTAATCTGATG 58.268 33.333 0.00 0.00 42.15 3.07
4459 4588 7.379529 GCATTTTCCCAATTATCAACGTATCTG 59.620 37.037 0.00 0.00 0.00 2.90
4479 4608 6.030548 TCTGTCTCTGATTTACACTTCAGG 57.969 41.667 0.00 0.00 39.84 3.86
4488 4617 4.911514 TTTACACTTCAGGAAAAGCACC 57.088 40.909 0.00 0.00 0.00 5.01
4495 4624 3.255969 TCAGGAAAAGCACCGGTATAC 57.744 47.619 6.87 0.00 0.00 1.47
4496 4625 2.568062 TCAGGAAAAGCACCGGTATACA 59.432 45.455 6.87 0.00 0.00 2.29
4512 4644 8.266473 ACCGGTATACATTCCAGTACAATAAAA 58.734 33.333 4.49 0.00 0.00 1.52
4548 4680 4.035675 GGCATTGTACTGCTGTAAATCTCC 59.964 45.833 4.88 7.47 41.95 3.71
4662 5012 2.415090 GCTCTTTAATGCACACTGCCTG 60.415 50.000 0.00 0.00 44.23 4.85
4673 5023 3.181497 GCACACTGCCTGTATAAACATGG 60.181 47.826 0.00 0.00 37.42 3.66
4735 5085 4.932200 ACTTCTGCTTAATTTCCAGAGACG 59.068 41.667 0.00 0.00 36.99 4.18
4738 5088 6.222038 TCTGCTTAATTTCCAGAGACGTAT 57.778 37.500 0.00 0.00 32.30 3.06
4749 5099 3.487042 CCAGAGACGTATGTAGACAACGG 60.487 52.174 16.21 1.00 40.81 4.44
4795 5145 4.828939 TCTGTCATTTGCAAGATCCTTGTT 59.171 37.500 0.00 0.00 0.00 2.83
4804 5154 6.381481 TGCAAGATCCTTGTTATTGCTATG 57.619 37.500 12.90 0.00 44.99 2.23
4837 5187 4.712476 CCCTCCTTTTCTCATCAGGTATG 58.288 47.826 0.00 0.00 36.88 2.39
4838 5188 4.445448 CCCTCCTTTTCTCATCAGGTATGG 60.445 50.000 0.00 0.00 36.15 2.74
4844 5194 5.378230 TTTCTCATCAGGTATGGATGCTT 57.622 39.130 0.00 0.00 41.46 3.91
4845 5195 4.613925 TCTCATCAGGTATGGATGCTTC 57.386 45.455 0.00 0.00 41.46 3.86
4846 5196 4.229639 TCTCATCAGGTATGGATGCTTCT 58.770 43.478 0.00 0.00 41.46 2.85
4849 5201 5.397360 TCATCAGGTATGGATGCTTCTCTA 58.603 41.667 0.00 0.00 41.46 2.43
4872 5224 4.021719 ACTCCATCCAAATCTGCTTTTGTG 60.022 41.667 6.60 1.26 35.30 3.33
4895 5247 8.579006 TGTGAATCTAAGATCAGCACAATTTTT 58.421 29.630 0.00 0.00 32.54 1.94
4913 5265 8.784043 ACAATTTTTCATCTGTACAACCTCTAC 58.216 33.333 0.00 0.00 0.00 2.59
4923 5275 8.880991 TCTGTACAACCTCTACTCTTAAATCT 57.119 34.615 0.00 0.00 0.00 2.40
4926 5278 9.524496 TGTACAACCTCTACTCTTAAATCTGTA 57.476 33.333 0.00 0.00 0.00 2.74
4957 5309 5.673818 GCTGTAACTGGTTAAATGCACTAGC 60.674 44.000 0.00 0.00 42.57 3.42
4971 5323 2.740256 GCACTAGCCCTCAGAAGTTAGC 60.740 54.545 0.00 0.00 33.58 3.09
4999 5351 6.596888 CACTTCTCATCCAAATACACACATCT 59.403 38.462 0.00 0.00 0.00 2.90
5091 5470 1.133199 AGGGTTTTGGATGCAGGAACA 60.133 47.619 14.36 0.00 0.00 3.18
5145 5524 1.466856 TACCCGACTGCGACAACTAT 58.533 50.000 0.00 0.00 40.82 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 158 1.324736 GTTGACCTGATTTCGCTAGCG 59.675 52.381 30.91 30.91 41.35 4.26
249 262 7.935338 ACGAGACGTAAAAATTCTTTCTGTA 57.065 32.000 0.00 0.00 38.73 2.74
882 909 4.541973 AACAATTCCTCCTTGATTTGCC 57.458 40.909 0.00 0.00 31.83 4.52
883 910 6.866010 AAAAACAATTCCTCCTTGATTTGC 57.134 33.333 0.00 0.00 31.53 3.68
884 911 7.603784 CCCTAAAAACAATTCCTCCTTGATTTG 59.396 37.037 0.00 0.00 31.53 2.32
885 912 7.256655 CCCCTAAAAACAATTCCTCCTTGATTT 60.257 37.037 0.00 0.00 32.17 2.17
886 913 6.213397 CCCCTAAAAACAATTCCTCCTTGATT 59.787 38.462 0.00 0.00 0.00 2.57
887 914 5.721480 CCCCTAAAAACAATTCCTCCTTGAT 59.279 40.000 0.00 0.00 0.00 2.57
888 915 5.083821 CCCCTAAAAACAATTCCTCCTTGA 58.916 41.667 0.00 0.00 0.00 3.02
889 916 5.083821 TCCCCTAAAAACAATTCCTCCTTG 58.916 41.667 0.00 0.00 0.00 3.61
890 917 5.348259 TCCCCTAAAAACAATTCCTCCTT 57.652 39.130 0.00 0.00 0.00 3.36
891 918 5.348259 TTCCCCTAAAAACAATTCCTCCT 57.652 39.130 0.00 0.00 0.00 3.69
892 919 6.212589 TGATTTCCCCTAAAAACAATTCCTCC 59.787 38.462 0.00 0.00 0.00 4.30
893 920 7.239763 TGATTTCCCCTAAAAACAATTCCTC 57.760 36.000 0.00 0.00 0.00 3.71
894 921 7.625498 TTGATTTCCCCTAAAAACAATTCCT 57.375 32.000 0.00 0.00 0.00 3.36
895 922 8.100164 TCATTGATTTCCCCTAAAAACAATTCC 58.900 33.333 3.14 0.00 36.71 3.01
896 923 9.154847 CTCATTGATTTCCCCTAAAAACAATTC 57.845 33.333 3.14 0.00 36.71 2.17
897 924 8.102676 CCTCATTGATTTCCCCTAAAAACAATT 58.897 33.333 3.14 0.00 36.71 2.32
898 925 7.457535 TCCTCATTGATTTCCCCTAAAAACAAT 59.542 33.333 0.00 0.00 37.98 2.71
899 926 6.784969 TCCTCATTGATTTCCCCTAAAAACAA 59.215 34.615 0.00 0.00 34.43 2.83
900 927 6.318913 TCCTCATTGATTTCCCCTAAAAACA 58.681 36.000 0.00 0.00 0.00 2.83
901 928 6.850752 TCCTCATTGATTTCCCCTAAAAAC 57.149 37.500 0.00 0.00 0.00 2.43
902 929 7.524698 CGTTTCCTCATTGATTTCCCCTAAAAA 60.525 37.037 0.00 0.00 0.00 1.94
919 946 2.940410 GGTGTTCACTTTCGTTTCCTCA 59.060 45.455 2.98 0.00 0.00 3.86
983 1010 6.758886 TCTCTCTTTGTCTGTCTTTGTTTCTC 59.241 38.462 0.00 0.00 0.00 2.87
985 1012 6.758886 TCTCTCTCTTTGTCTGTCTTTGTTTC 59.241 38.462 0.00 0.00 0.00 2.78
989 1016 6.083098 TCTCTCTCTCTTTGTCTGTCTTTG 57.917 41.667 0.00 0.00 0.00 2.77
990 1017 5.833131 ACTCTCTCTCTCTTTGTCTGTCTTT 59.167 40.000 0.00 0.00 0.00 2.52
993 1020 4.759693 TCACTCTCTCTCTCTTTGTCTGTC 59.240 45.833 0.00 0.00 0.00 3.51
994 1021 4.724399 TCACTCTCTCTCTCTTTGTCTGT 58.276 43.478 0.00 0.00 0.00 3.41
995 1022 4.761739 ACTCACTCTCTCTCTCTTTGTCTG 59.238 45.833 0.00 0.00 0.00 3.51
997 1024 4.142902 CGACTCACTCTCTCTCTCTTTGTC 60.143 50.000 0.00 0.00 0.00 3.18
999 1026 3.751175 ACGACTCACTCTCTCTCTCTTTG 59.249 47.826 0.00 0.00 0.00 2.77
1014 1050 2.649034 GAACAGGCCGACGACTCA 59.351 61.111 0.00 0.00 0.00 3.41
1133 1169 3.570212 CCGATTAGGGCCAGGGGG 61.570 72.222 6.18 0.00 35.97 5.40
1141 1177 0.465705 TCAGCAGCTTCCGATTAGGG 59.534 55.000 0.00 0.00 41.52 3.53
1224 1261 1.789054 CGGGCGATTCGTTTAACAAGC 60.789 52.381 8.03 0.00 0.00 4.01
1232 1269 1.227263 CTGGATCGGGCGATTCGTT 60.227 57.895 8.03 0.00 32.88 3.85
1233 1270 2.417516 CTGGATCGGGCGATTCGT 59.582 61.111 8.03 0.00 32.88 3.85
1246 1283 4.657814 AACCTAGGAATTTCAAGCTGGA 57.342 40.909 17.98 0.00 0.00 3.86
1250 1287 4.519540 TGCAAACCTAGGAATTTCAAGC 57.480 40.909 17.98 9.90 0.00 4.01
1332 1369 2.048601 CCAGATCAGAGCCATCTCCTT 58.951 52.381 0.00 0.00 40.22 3.36
1415 1467 3.007940 TCAACCGGAGATGAACTGAATGT 59.992 43.478 9.46 0.00 0.00 2.71
1561 1613 2.673200 GCTCCTGGCATCACCCTGA 61.673 63.158 0.00 0.00 41.35 3.86
1577 1629 4.040952 CCCACCTATATACTTCAGCTTGCT 59.959 45.833 0.00 0.00 0.00 3.91
1702 1754 3.499737 GGCACTTGCATCCGGACG 61.500 66.667 6.12 0.00 44.36 4.79
1833 1885 5.116882 ACTGAAGAACAAAGTGTCTACCAC 58.883 41.667 0.00 0.00 44.89 4.16
1858 1924 6.819397 AAGCAAATTAAACTGTAGAGGTCC 57.181 37.500 0.00 0.00 0.00 4.46
1859 1925 7.803659 GTCAAAGCAAATTAAACTGTAGAGGTC 59.196 37.037 0.00 0.00 0.00 3.85
1860 1926 7.502561 AGTCAAAGCAAATTAAACTGTAGAGGT 59.497 33.333 0.00 0.00 0.00 3.85
1861 1927 7.805071 CAGTCAAAGCAAATTAAACTGTAGAGG 59.195 37.037 0.00 0.00 32.66 3.69
1862 1928 8.345565 ACAGTCAAAGCAAATTAAACTGTAGAG 58.654 33.333 3.60 0.00 41.45 2.43
1863 1929 8.220755 ACAGTCAAAGCAAATTAAACTGTAGA 57.779 30.769 3.60 0.00 41.45 2.59
1864 1930 9.944663 TTACAGTCAAAGCAAATTAAACTGTAG 57.055 29.630 11.04 0.00 43.14 2.74
1865 1931 9.944663 CTTACAGTCAAAGCAAATTAAACTGTA 57.055 29.630 8.04 8.04 41.45 2.74
1866 1932 8.466798 ACTTACAGTCAAAGCAAATTAAACTGT 58.533 29.630 9.81 9.81 43.64 3.55
1867 1933 8.856490 ACTTACAGTCAAAGCAAATTAAACTG 57.144 30.769 0.00 0.00 38.55 3.16
1947 2014 4.836125 AAACTTTGTACCACTGATGCAG 57.164 40.909 0.00 0.00 37.52 4.41
1977 2044 2.927014 GCACCTTTGAGACTACTGTCCG 60.927 54.545 0.00 0.00 43.91 4.79
2019 2092 6.218019 AGCACGTAACAAATAACACTGAGTA 58.782 36.000 0.00 0.00 0.00 2.59
2101 2174 8.023021 TGTTCTATCATAACTAGACATTGCCT 57.977 34.615 0.00 0.00 0.00 4.75
2118 2191 7.390996 TCACGATTACCTCTCCTATGTTCTATC 59.609 40.741 0.00 0.00 0.00 2.08
2148 2221 2.602257 ACCAAACAAGGAAGCAAAGC 57.398 45.000 0.00 0.00 0.00 3.51
2205 2287 8.693542 TCTTACATATGATACATGCAGATTCG 57.306 34.615 10.38 0.00 0.00 3.34
2336 2418 7.277981 ACCAAATCTAAGATTAGTACAGTTGCG 59.722 37.037 0.00 0.00 32.61 4.85
2522 2604 5.712917 ACCCTATTTGCCAAAGAATCGTTAA 59.287 36.000 0.00 0.00 0.00 2.01
2587 2673 3.153919 GGCACACCAACAGGAAATAAGA 58.846 45.455 0.00 0.00 35.26 2.10
2724 2811 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
2725 2812 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2726 2813 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2727 2814 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2728 2815 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2729 2816 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2730 2817 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2731 2818 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2732 2819 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2733 2820 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2734 2821 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2735 2822 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2736 2823 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2737 2824 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2799 2886 6.859112 AGATTTGCCTAGATACGGATGTAT 57.141 37.500 0.00 0.00 43.97 2.29
2800 2887 7.668469 TCTTAGATTTGCCTAGATACGGATGTA 59.332 37.037 0.00 0.00 34.45 2.29
2801 2888 6.493802 TCTTAGATTTGCCTAGATACGGATGT 59.506 38.462 0.00 0.00 0.00 3.06
2802 2889 6.809196 GTCTTAGATTTGCCTAGATACGGATG 59.191 42.308 0.00 0.00 0.00 3.51
2803 2890 6.493802 TGTCTTAGATTTGCCTAGATACGGAT 59.506 38.462 0.00 0.00 0.00 4.18
2804 2891 5.831525 TGTCTTAGATTTGCCTAGATACGGA 59.168 40.000 0.00 0.00 0.00 4.69
2805 2892 6.085555 TGTCTTAGATTTGCCTAGATACGG 57.914 41.667 0.00 0.00 0.00 4.02
2806 2893 7.426410 TCTTGTCTTAGATTTGCCTAGATACG 58.574 38.462 0.00 0.00 0.00 3.06
2807 2894 9.771534 ATTCTTGTCTTAGATTTGCCTAGATAC 57.228 33.333 0.00 0.00 0.00 2.24
2809 2896 9.692325 AAATTCTTGTCTTAGATTTGCCTAGAT 57.308 29.630 0.00 0.00 0.00 1.98
2810 2897 9.520515 AAAATTCTTGTCTTAGATTTGCCTAGA 57.479 29.630 0.00 0.00 0.00 2.43
2811 2898 9.565213 CAAAATTCTTGTCTTAGATTTGCCTAG 57.435 33.333 0.00 0.00 0.00 3.02
2812 2899 8.522830 CCAAAATTCTTGTCTTAGATTTGCCTA 58.477 33.333 0.00 0.00 29.17 3.93
2813 2900 7.381323 CCAAAATTCTTGTCTTAGATTTGCCT 58.619 34.615 0.00 0.00 29.17 4.75
2814 2901 6.591448 CCCAAAATTCTTGTCTTAGATTTGCC 59.409 38.462 0.00 0.00 29.17 4.52
2815 2902 7.329471 GTCCCAAAATTCTTGTCTTAGATTTGC 59.671 37.037 0.00 0.00 29.17 3.68
2816 2903 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2817 2904 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2818 2905 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2819 2906 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2820 2907 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2821 2908 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2822 2909 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2823 2910 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2824 2911 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2825 2912 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2826 2913 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2827 2914 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2828 2915 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2829 2916 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2830 2917 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2831 2918 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2832 2919 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
2833 2920 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
2834 2921 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2835 2922 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
2836 2923 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2837 2924 2.237643 GATTACTACTCCCTCCGTCCC 58.762 57.143 0.00 0.00 0.00 4.46
2838 2925 2.941480 TGATTACTACTCCCTCCGTCC 58.059 52.381 0.00 0.00 0.00 4.79
2839 2926 4.400120 AGATGATTACTACTCCCTCCGTC 58.600 47.826 0.00 0.00 0.00 4.79
2840 2927 4.456662 AGATGATTACTACTCCCTCCGT 57.543 45.455 0.00 0.00 0.00 4.69
2841 2928 5.536916 AGAAAGATGATTACTACTCCCTCCG 59.463 44.000 0.00 0.00 0.00 4.63
2842 2929 6.987403 AGAAAGATGATTACTACTCCCTCC 57.013 41.667 0.00 0.00 0.00 4.30
2843 2930 7.225734 GCAAAGAAAGATGATTACTACTCCCTC 59.774 40.741 0.00 0.00 0.00 4.30
2844 2931 7.051000 GCAAAGAAAGATGATTACTACTCCCT 58.949 38.462 0.00 0.00 0.00 4.20
2845 2932 6.261158 GGCAAAGAAAGATGATTACTACTCCC 59.739 42.308 0.00 0.00 0.00 4.30
2846 2933 6.823689 TGGCAAAGAAAGATGATTACTACTCC 59.176 38.462 0.00 0.00 0.00 3.85
2847 2934 7.550906 ACTGGCAAAGAAAGATGATTACTACTC 59.449 37.037 0.00 0.00 0.00 2.59
2848 2935 7.335422 CACTGGCAAAGAAAGATGATTACTACT 59.665 37.037 0.00 0.00 0.00 2.57
2987 3076 9.394477 CAAACTTGCTAGTATTACTTGAAAACC 57.606 33.333 0.00 0.00 33.17 3.27
3002 3091 5.073311 TCTACTACTGCCAAACTTGCTAG 57.927 43.478 0.00 0.00 0.00 3.42
3029 3129 3.423539 ACCTAATGTCACATGTGCAGT 57.576 42.857 21.38 21.06 0.00 4.40
3109 3209 7.304497 ACACAGAAATCACCTTAGTCTTACT 57.696 36.000 0.00 0.00 0.00 2.24
3151 3257 2.378547 AGGGCTTCAGGGATTACAAACA 59.621 45.455 0.00 0.00 0.00 2.83
3215 3321 1.205179 TGCAGCTTGCCACAAATATGG 59.795 47.619 5.82 0.00 44.23 2.74
3283 3390 5.407407 TGCTAAACCAAAACCTGTTGAAA 57.593 34.783 0.00 0.00 0.00 2.69
3288 3395 3.957497 TGACATGCTAAACCAAAACCTGT 59.043 39.130 0.00 0.00 0.00 4.00
3400 3507 3.717707 TGTGGAAGAAGAACTCAAGACG 58.282 45.455 0.00 0.00 0.00 4.18
3405 3521 4.487714 ACAACTGTGGAAGAAGAACTCA 57.512 40.909 0.00 0.00 0.00 3.41
3416 3532 5.367352 TCTTCCCTAAAAGTACAACTGTGGA 59.633 40.000 0.00 0.00 0.00 4.02
3523 3639 3.011566 TCCTTGTTGCAGTTTCCTTCA 57.988 42.857 0.00 0.00 0.00 3.02
3524 3640 4.202151 ACATTCCTTGTTGCAGTTTCCTTC 60.202 41.667 0.00 0.00 33.74 3.46
3538 3654 7.094248 TGTCCAGTCAATGAAATACATTCCTTG 60.094 37.037 0.00 0.00 46.01 3.61
3568 3684 2.943978 CGCTCCCCATATCGTCCCC 61.944 68.421 0.00 0.00 0.00 4.81
3576 3692 1.217183 AGTCTCTTACCGCTCCCCATA 59.783 52.381 0.00 0.00 0.00 2.74
3601 3717 9.787435 AGCAATATAATAGAAATTTCCGGTGTA 57.213 29.630 14.61 0.77 0.00 2.90
3602 3718 8.567948 CAGCAATATAATAGAAATTTCCGGTGT 58.432 33.333 14.61 0.00 0.00 4.16
3615 3733 8.443160 CCCGTTACATGTTCAGCAATATAATAG 58.557 37.037 2.30 0.00 0.00 1.73
3628 3746 2.786777 AGGAAACCCCGTTACATGTTC 58.213 47.619 2.30 0.00 40.87 3.18
3632 3750 3.801307 AGAAAGGAAACCCCGTTACAT 57.199 42.857 0.00 0.00 36.74 2.29
3719 3841 1.745087 CAATGAACCAGGGGATGAACG 59.255 52.381 0.00 0.00 0.00 3.95
3726 3848 1.380380 GGCCTCAATGAACCAGGGG 60.380 63.158 0.00 0.00 0.00 4.79
3738 3860 3.378512 ACTGAGATGTAGATTGGCCTCA 58.621 45.455 3.32 0.00 0.00 3.86
4070 4192 2.736670 ACAGAGGTTGCTTGAGGTTT 57.263 45.000 0.00 0.00 0.00 3.27
4216 4342 3.950087 TCTTGCTAATTGCTATGTGCG 57.050 42.857 0.00 0.00 46.63 5.34
4345 4473 6.403866 TGTCTTCATGTTGTGGCTTTATTT 57.596 33.333 0.00 0.00 0.00 1.40
4361 4489 9.665719 TGATATTAAAGCAGTACAATGTCTTCA 57.334 29.630 0.00 0.00 0.00 3.02
4434 4563 8.405531 ACAGATACGTTGATAATTGGGAAAATG 58.594 33.333 0.00 0.00 0.00 2.32
4459 4588 7.572168 GCTTTTCCTGAAGTGTAAATCAGAGAC 60.572 40.741 4.43 0.00 44.64 3.36
4479 4608 3.942748 TGGAATGTATACCGGTGCTTTTC 59.057 43.478 19.93 13.16 0.00 2.29
4488 4617 8.553696 GGTTTTATTGTACTGGAATGTATACCG 58.446 37.037 0.00 0.00 0.00 4.02
4495 4624 7.922278 CCATCATGGTTTTATTGTACTGGAATG 59.078 37.037 0.00 0.00 31.35 2.67
4496 4625 7.069826 CCCATCATGGTTTTATTGTACTGGAAT 59.930 37.037 2.07 0.00 35.17 3.01
4512 4644 1.007479 ACAATGCCTTCCCATCATGGT 59.993 47.619 2.07 0.00 35.17 3.55
4548 4680 6.291067 TCAGATTAAATGCAAGATACGCTG 57.709 37.500 0.00 0.00 0.00 5.18
4623 4757 7.707624 AAAGAGCATAAGATTTGGTCAATCA 57.292 32.000 5.77 0.00 43.63 2.57
4627 4761 7.122501 TGCATTAAAGAGCATAAGATTTGGTCA 59.877 33.333 5.77 0.00 42.58 4.02
4628 4762 7.433425 GTGCATTAAAGAGCATAAGATTTGGTC 59.567 37.037 0.00 0.00 43.44 4.02
4629 4763 7.093814 TGTGCATTAAAGAGCATAAGATTTGGT 60.094 33.333 0.00 0.00 43.44 3.67
4631 4765 7.972277 AGTGTGCATTAAAGAGCATAAGATTTG 59.028 33.333 0.00 0.00 43.44 2.32
4632 4766 7.972277 CAGTGTGCATTAAAGAGCATAAGATTT 59.028 33.333 0.00 0.00 43.44 2.17
4662 5012 4.931661 TCTCGTCTCCCCATGTTTATAC 57.068 45.455 0.00 0.00 0.00 1.47
4673 5023 0.671251 CTGCTGGTATCTCGTCTCCC 59.329 60.000 0.00 0.00 0.00 4.30
4735 5085 4.360563 CCATCTCACCGTTGTCTACATAC 58.639 47.826 0.00 0.00 0.00 2.39
4738 5088 1.067142 GCCATCTCACCGTTGTCTACA 60.067 52.381 0.00 0.00 0.00 2.74
4749 5099 2.294233 TGAAAAGTTGCAGCCATCTCAC 59.706 45.455 0.00 0.00 0.00 3.51
4795 5145 2.426738 GGCAGCACAAACCATAGCAATA 59.573 45.455 0.00 0.00 0.00 1.90
4804 5154 1.115326 AAAGGAGGGCAGCACAAACC 61.115 55.000 0.00 0.00 0.00 3.27
4837 5187 2.968574 TGGATGGAGTAGAGAAGCATCC 59.031 50.000 0.00 0.00 38.01 3.51
4838 5188 4.679373 TTGGATGGAGTAGAGAAGCATC 57.321 45.455 0.00 0.00 0.00 3.91
4844 5194 4.293494 AGCAGATTTGGATGGAGTAGAGA 58.707 43.478 0.00 0.00 0.00 3.10
4845 5195 4.686191 AGCAGATTTGGATGGAGTAGAG 57.314 45.455 0.00 0.00 0.00 2.43
4846 5196 5.441718 AAAGCAGATTTGGATGGAGTAGA 57.558 39.130 0.00 0.00 0.00 2.59
4849 5201 4.021719 CACAAAAGCAGATTTGGATGGAGT 60.022 41.667 12.37 0.00 43.10 3.85
4872 5224 9.798994 ATGAAAAATTGTGCTGATCTTAGATTC 57.201 29.630 0.00 0.00 0.00 2.52
4895 5247 8.645814 TTTAAGAGTAGAGGTTGTACAGATGA 57.354 34.615 0.00 0.00 0.00 2.92
4913 5265 9.856488 TTACAGCTTACACTACAGATTTAAGAG 57.144 33.333 0.00 0.00 0.00 2.85
4923 5275 5.540400 AACCAGTTACAGCTTACACTACA 57.460 39.130 0.00 0.00 0.00 2.74
4926 5278 6.072673 GCATTTAACCAGTTACAGCTTACACT 60.073 38.462 0.00 0.00 0.00 3.55
4957 5309 1.277557 AGTGCTGCTAACTTCTGAGGG 59.722 52.381 0.00 0.00 0.00 4.30
4971 5323 4.696877 TGTGTATTTGGATGAGAAGTGCTG 59.303 41.667 0.00 0.00 0.00 4.41
4999 5351 7.757941 TGAATGATGTTTTATCAGGTCACAA 57.242 32.000 0.00 0.00 0.00 3.33
5016 5368 9.911788 AAAGTAACAAGATATGTCCTGAATGAT 57.088 29.630 0.00 0.00 42.99 2.45
5091 5470 1.371337 CCATGCACATGTACTGCGCT 61.371 55.000 9.73 0.00 37.46 5.92
5145 5524 0.468226 ACACTCCCTTCGTCTTGCAA 59.532 50.000 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.