Multiple sequence alignment - TraesCS5D01G049700

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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 TraesCS5D01G049700 chr5D 100.000 3954 0 0 1 3954 47279641 47283594 0.000000e+00 7302.0
1 TraesCS5D01G049700 chr5D 84.019 1264 150 25 996 2222 46732787 46731539 0.000000e+00 1168.0
2 TraesCS5D01G049700 chr5D 82.401 1233 175 26 1035 2232 48315034 48313809 0.000000e+00 1037.0
3 TraesCS5D01G049700 chr5D 82.022 1207 145 39 1049 2222 46606159 46607326 0.000000e+00 961.0
4 TraesCS5D01G049700 chr5D 81.255 1179 161 31 1070 2211 46847562 46846407 0.000000e+00 898.0
5 TraesCS5D01G049700 chr5D 87.848 683 67 7 1 678 498652557 498651886 0.000000e+00 787.0
6 TraesCS5D01G049700 chr5D 74.729 1199 249 35 1053 2224 48656837 48658008 1.650000e-133 486.0
7 TraesCS5D01G049700 chr5D 85.023 434 59 2 1792 2222 47916470 47916900 1.690000e-118 436.0
8 TraesCS5D01G049700 chr5D 84.463 354 49 6 1443 1792 48032280 48032631 1.050000e-90 344.0
9 TraesCS5D01G049700 chr5D 88.387 155 18 0 1277 1431 47092673 47092519 1.880000e-43 187.0
10 TraesCS5D01G049700 chr5D 83.951 162 26 0 1240 1401 47915786 47915947 5.290000e-34 156.0
11 TraesCS5D01G049700 chr5D 89.130 92 9 1 1356 1447 48021825 48021915 3.230000e-21 113.0
12 TraesCS5D01G049700 chr5D 86.047 86 12 0 3869 3954 443636500 443636585 4.210000e-15 93.5
13 TraesCS5D01G049700 chr5B 90.627 1931 115 34 871 2749 50226503 50228419 0.000000e+00 2503.0
14 TraesCS5D01G049700 chr5B 84.711 1210 146 17 1049 2222 48931295 48930089 0.000000e+00 1173.0
15 TraesCS5D01G049700 chr5B 83.347 1225 150 25 1035 2219 51062268 51061058 0.000000e+00 1083.0
16 TraesCS5D01G049700 chr5B 83.089 1230 160 27 1029 2219 50530119 50531339 0.000000e+00 1075.0
17 TraesCS5D01G049700 chr5B 88.299 735 76 4 1401 2129 50003376 50004106 0.000000e+00 872.0
18 TraesCS5D01G049700 chr5B 93.957 513 18 5 3408 3913 50229119 50229625 0.000000e+00 763.0
19 TraesCS5D01G049700 chr5B 84.430 623 57 16 2751 3361 50228526 50229120 9.530000e-161 577.0
20 TraesCS5D01G049700 chr5B 81.569 255 29 10 3442 3686 684016198 684016444 1.120000e-45 195.0
21 TraesCS5D01G049700 chr5B 84.921 126 14 3 3722 3846 50853829 50853950 5.370000e-24 122.0
22 TraesCS5D01G049700 chr5A 81.667 1140 175 22 1120 2232 38055683 38054551 0.000000e+00 917.0
23 TraesCS5D01G049700 chr5A 85.031 815 99 14 1 800 419677401 419678207 0.000000e+00 808.0
24 TraesCS5D01G049700 chr5A 82.835 903 126 14 1316 2211 37780630 37779750 0.000000e+00 782.0
25 TraesCS5D01G049700 chr5A 78.740 127 18 5 3722 3847 37997394 37997512 4.240000e-10 76.8
26 TraesCS5D01G049700 chr5A 100.000 29 0 0 3153 3181 38054036 38054008 2.000000e-03 54.7
27 TraesCS5D01G049700 chr7B 88.205 780 71 14 6 779 19278026 19277262 0.000000e+00 911.0
28 TraesCS5D01G049700 chr2A 86.625 800 99 7 8 800 486491824 486492622 0.000000e+00 878.0
29 TraesCS5D01G049700 chr7D 87.775 728 71 10 11 730 171318624 171319341 0.000000e+00 835.0
30 TraesCS5D01G049700 chr2D 85.432 810 98 7 11 800 394533974 394534783 0.000000e+00 824.0
31 TraesCS5D01G049700 chr2D 87.169 717 62 17 11 716 45674738 45675435 0.000000e+00 787.0
32 TraesCS5D01G049700 chr2D 84.810 79 10 2 3864 3941 351973350 351973427 1.180000e-10 78.7
33 TraesCS5D01G049700 chr4A 83.892 776 110 10 11 773 184954162 184953389 0.000000e+00 726.0
34 TraesCS5D01G049700 chr4A 89.286 56 2 4 3368 3419 478341362 478341307 2.550000e-07 67.6
35 TraesCS5D01G049700 chr4D 85.408 699 95 6 4 699 141809198 141808504 0.000000e+00 719.0
36 TraesCS5D01G049700 chr4D 84.615 91 14 0 3864 3954 494829596 494829686 1.510000e-14 91.6
37 TraesCS5D01G049700 chr4D 81.915 94 15 2 3861 3953 259497368 259497276 1.180000e-10 78.7
38 TraesCS5D01G049700 chr3A 79.045 649 81 21 182 800 434768907 434768284 1.030000e-105 394.0
39 TraesCS5D01G049700 chr6A 82.297 209 19 7 3492 3686 41082564 41082360 8.790000e-37 165.0
40 TraesCS5D01G049700 chr6A 79.126 206 31 4 2684 2877 97751108 97750903 8.920000e-27 132.0
41 TraesCS5D01G049700 chr3B 86.897 145 16 1 3492 3636 45153896 45153755 4.090000e-35 159.0
42 TraesCS5D01G049700 chr4B 85.714 91 13 0 3864 3954 634340422 634340512 3.250000e-16 97.1
43 TraesCS5D01G049700 chr7A 88.462 78 9 0 3864 3941 257125984 257126061 1.170000e-15 95.3
44 TraesCS5D01G049700 chr6B 86.420 81 11 0 3864 3944 14779573 14779493 5.440000e-14 89.8
45 TraesCS5D01G049700 chr1A 81.915 94 15 2 3861 3953 11576220 11576128 1.180000e-10 78.7


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 TraesCS5D01G049700 chr5D 47279641 47283594 3953 False 7302.00 7302 100.000000 1 3954 1 chr5D.!!$F2 3953
1 TraesCS5D01G049700 chr5D 46731539 46732787 1248 True 1168.00 1168 84.019000 996 2222 1 chr5D.!!$R1 1226
2 TraesCS5D01G049700 chr5D 48313809 48315034 1225 True 1037.00 1037 82.401000 1035 2232 1 chr5D.!!$R4 1197
3 TraesCS5D01G049700 chr5D 46606159 46607326 1167 False 961.00 961 82.022000 1049 2222 1 chr5D.!!$F1 1173
4 TraesCS5D01G049700 chr5D 46846407 46847562 1155 True 898.00 898 81.255000 1070 2211 1 chr5D.!!$R2 1141
5 TraesCS5D01G049700 chr5D 498651886 498652557 671 True 787.00 787 87.848000 1 678 1 chr5D.!!$R5 677
6 TraesCS5D01G049700 chr5D 48656837 48658008 1171 False 486.00 486 74.729000 1053 2224 1 chr5D.!!$F5 1171
7 TraesCS5D01G049700 chr5D 47915786 47916900 1114 False 296.00 436 84.487000 1240 2222 2 chr5D.!!$F7 982
8 TraesCS5D01G049700 chr5B 50226503 50229625 3122 False 1281.00 2503 89.671333 871 3913 3 chr5B.!!$F5 3042
9 TraesCS5D01G049700 chr5B 48930089 48931295 1206 True 1173.00 1173 84.711000 1049 2222 1 chr5B.!!$R1 1173
10 TraesCS5D01G049700 chr5B 51061058 51062268 1210 True 1083.00 1083 83.347000 1035 2219 1 chr5B.!!$R2 1184
11 TraesCS5D01G049700 chr5B 50530119 50531339 1220 False 1075.00 1075 83.089000 1029 2219 1 chr5B.!!$F2 1190
12 TraesCS5D01G049700 chr5B 50003376 50004106 730 False 872.00 872 88.299000 1401 2129 1 chr5B.!!$F1 728
13 TraesCS5D01G049700 chr5A 419677401 419678207 806 False 808.00 808 85.031000 1 800 1 chr5A.!!$F2 799
14 TraesCS5D01G049700 chr5A 37779750 37780630 880 True 782.00 782 82.835000 1316 2211 1 chr5A.!!$R1 895
15 TraesCS5D01G049700 chr5A 38054008 38055683 1675 True 485.85 917 90.833500 1120 3181 2 chr5A.!!$R2 2061
16 TraesCS5D01G049700 chr7B 19277262 19278026 764 True 911.00 911 88.205000 6 779 1 chr7B.!!$R1 773
17 TraesCS5D01G049700 chr2A 486491824 486492622 798 False 878.00 878 86.625000 8 800 1 chr2A.!!$F1 792
18 TraesCS5D01G049700 chr7D 171318624 171319341 717 False 835.00 835 87.775000 11 730 1 chr7D.!!$F1 719
19 TraesCS5D01G049700 chr2D 394533974 394534783 809 False 824.00 824 85.432000 11 800 1 chr2D.!!$F3 789
20 TraesCS5D01G049700 chr2D 45674738 45675435 697 False 787.00 787 87.169000 11 716 1 chr2D.!!$F1 705
21 TraesCS5D01G049700 chr4A 184953389 184954162 773 True 726.00 726 83.892000 11 773 1 chr4A.!!$R1 762
22 TraesCS5D01G049700 chr4D 141808504 141809198 694 True 719.00 719 85.408000 4 699 1 chr4D.!!$R1 695
23 TraesCS5D01G049700 chr3A 434768284 434768907 623 True 394.00 394 79.045000 182 800 1 chr3A.!!$R1 618

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
830 874 0.104855 TCATCGCAGGTGTATGCTCC 59.895 55.0 0.0 0.0 44.24 4.70 F
2433 2884 0.250684 ACATGGTGGTGACGCATTGA 60.251 50.0 0.0 0.0 44.70 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 3045 0.107456 CAGCAAGGTGGTCTGAGTGT 59.893 55.0 0.0 0.0 0.0 3.55 R
3293 3920 0.392998 GTCATGAGCCCCGACAATGT 60.393 55.0 0.0 0.0 0.0 2.71 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
97 101 3.185365 CGCAGCGCCAACATCGTA 61.185 61.111 2.29 0.00 0.00 3.43
213 217 1.221840 GGCTCGCCTCCATGAAGAA 59.778 57.895 0.00 0.00 0.00 2.52
223 227 0.750911 CCATGAAGAAGGAGGCAGGC 60.751 60.000 0.00 0.00 0.00 4.85
312 316 3.518998 GCGGACGGAGCTAGAGCA 61.519 66.667 4.01 0.00 45.16 4.26
625 656 7.209471 TGTTATGTTCACCGAATTTTAGCTT 57.791 32.000 0.00 0.00 0.00 3.74
635 666 8.573035 TCACCGAATTTTAGCTTAATCTTTGTT 58.427 29.630 0.00 0.00 0.00 2.83
658 689 4.216687 TCCGTTTGTCAAATTTTAGCCGAT 59.783 37.500 0.40 0.00 0.00 4.18
716 757 4.796495 GAGCCGGCGGTTGGGAAT 62.796 66.667 28.82 0.00 0.00 3.01
781 822 2.104331 CGATCTTACGCGCCCTGT 59.896 61.111 5.73 0.00 0.00 4.00
787 831 4.627801 TACGCGCCCTGTGCCAAA 62.628 61.111 5.73 0.00 35.42 3.28
802 846 3.564262 CAAAGGCTGGAGATGCAGA 57.436 52.632 5.44 0.00 0.00 4.26
803 847 2.054232 CAAAGGCTGGAGATGCAGAT 57.946 50.000 5.44 0.00 0.00 2.90
804 848 1.948145 CAAAGGCTGGAGATGCAGATC 59.052 52.381 5.44 0.00 0.00 2.75
805 849 0.473326 AAGGCTGGAGATGCAGATCC 59.527 55.000 12.10 12.10 36.05 3.36
806 850 0.693430 AGGCTGGAGATGCAGATCCA 60.693 55.000 18.80 18.80 43.34 3.41
807 851 0.182061 GGCTGGAGATGCAGATCCAA 59.818 55.000 19.96 7.66 44.82 3.53
808 852 1.307097 GCTGGAGATGCAGATCCAAC 58.693 55.000 19.96 13.84 44.82 3.77
809 853 1.579698 CTGGAGATGCAGATCCAACG 58.420 55.000 19.96 8.83 44.82 4.10
810 854 0.178767 TGGAGATGCAGATCCAACGG 59.821 55.000 17.92 0.00 42.61 4.44
811 855 0.179000 GGAGATGCAGATCCAACGGT 59.821 55.000 13.73 0.00 35.54 4.83
812 856 1.576356 GAGATGCAGATCCAACGGTC 58.424 55.000 0.00 0.00 0.00 4.79
813 857 0.904649 AGATGCAGATCCAACGGTCA 59.095 50.000 0.00 0.00 0.00 4.02
814 858 1.487976 AGATGCAGATCCAACGGTCAT 59.512 47.619 0.00 0.00 0.00 3.06
815 859 1.869767 GATGCAGATCCAACGGTCATC 59.130 52.381 0.00 0.00 0.00 2.92
816 860 0.460109 TGCAGATCCAACGGTCATCG 60.460 55.000 0.00 0.00 45.88 3.84
817 861 1.766143 GCAGATCCAACGGTCATCGC 61.766 60.000 0.00 0.00 43.89 4.58
818 862 0.460109 CAGATCCAACGGTCATCGCA 60.460 55.000 0.00 0.00 43.89 5.10
819 863 0.179100 AGATCCAACGGTCATCGCAG 60.179 55.000 0.00 0.00 43.89 5.18
820 864 1.153369 ATCCAACGGTCATCGCAGG 60.153 57.895 0.00 0.00 43.89 4.85
821 865 1.899437 ATCCAACGGTCATCGCAGGT 61.899 55.000 0.00 0.00 43.89 4.00
822 866 2.390599 CCAACGGTCATCGCAGGTG 61.391 63.158 0.00 0.00 43.89 4.00
823 867 1.667830 CAACGGTCATCGCAGGTGT 60.668 57.895 0.00 0.00 43.89 4.16
824 868 0.389296 CAACGGTCATCGCAGGTGTA 60.389 55.000 0.00 0.00 43.89 2.90
825 869 0.535335 AACGGTCATCGCAGGTGTAT 59.465 50.000 0.00 0.00 43.89 2.29
826 870 0.179111 ACGGTCATCGCAGGTGTATG 60.179 55.000 0.00 0.00 43.89 2.39
827 871 1.490693 CGGTCATCGCAGGTGTATGC 61.491 60.000 0.00 0.00 42.95 3.14
828 872 0.179073 GGTCATCGCAGGTGTATGCT 60.179 55.000 0.00 0.00 44.24 3.79
829 873 1.212616 GTCATCGCAGGTGTATGCTC 58.787 55.000 0.00 0.00 44.24 4.26
830 874 0.104855 TCATCGCAGGTGTATGCTCC 59.895 55.000 0.00 0.00 44.24 4.70
831 875 1.068083 ATCGCAGGTGTATGCTCCG 59.932 57.895 0.00 0.00 44.24 4.63
832 876 2.369257 ATCGCAGGTGTATGCTCCGG 62.369 60.000 0.00 0.00 44.24 5.14
833 877 2.900273 GCAGGTGTATGCTCCGGA 59.100 61.111 2.93 2.93 43.07 5.14
834 878 1.447643 GCAGGTGTATGCTCCGGAT 59.552 57.895 3.57 0.00 43.07 4.18
835 879 0.882042 GCAGGTGTATGCTCCGGATG 60.882 60.000 3.57 0.00 43.07 3.51
836 880 0.465705 CAGGTGTATGCTCCGGATGT 59.534 55.000 3.57 0.00 33.72 3.06
837 881 0.753262 AGGTGTATGCTCCGGATGTC 59.247 55.000 3.57 0.00 33.72 3.06
838 882 0.753262 GGTGTATGCTCCGGATGTCT 59.247 55.000 3.57 0.00 0.00 3.41
839 883 1.961394 GGTGTATGCTCCGGATGTCTA 59.039 52.381 3.57 0.00 0.00 2.59
840 884 2.364324 GGTGTATGCTCCGGATGTCTAA 59.636 50.000 3.57 0.00 0.00 2.10
841 885 3.181469 GGTGTATGCTCCGGATGTCTAAA 60.181 47.826 3.57 0.00 0.00 1.85
842 886 4.439057 GTGTATGCTCCGGATGTCTAAAA 58.561 43.478 3.57 0.00 0.00 1.52
843 887 4.873827 GTGTATGCTCCGGATGTCTAAAAA 59.126 41.667 3.57 0.00 0.00 1.94
868 912 9.546428 AAAAGTTCAGCTGCACTTTTTATAATT 57.454 25.926 36.06 21.57 44.72 1.40
869 913 9.546428 AAAGTTCAGCTGCACTTTTTATAATTT 57.454 25.926 30.76 12.26 38.07 1.82
872 916 9.076596 GTTCAGCTGCACTTTTTATAATTTAGG 57.923 33.333 9.47 0.00 0.00 2.69
904 948 3.772060 CCTTTATTTGTCAGGCAGAGC 57.228 47.619 0.00 0.00 0.00 4.09
905 949 3.350833 CCTTTATTTGTCAGGCAGAGCT 58.649 45.455 0.00 0.00 0.00 4.09
906 950 3.128242 CCTTTATTTGTCAGGCAGAGCTG 59.872 47.826 0.00 0.00 0.00 4.24
949 1003 2.753043 GCCCATGTGCCAGGACAG 60.753 66.667 0.00 0.00 0.00 3.51
998 1060 4.175337 CATCCATCCACCGGCCGT 62.175 66.667 26.12 9.63 0.00 5.68
1122 1193 0.524414 TCGACTACACGTCCATGGTG 59.476 55.000 12.58 8.43 39.56 4.17
2061 2473 2.432628 GTCGTCCTTGACCCGCTG 60.433 66.667 0.00 0.00 32.61 5.18
2276 2715 9.561270 GTTCTAATTAACTGCCAGAAATTCTTC 57.439 33.333 0.00 0.00 0.00 2.87
2304 2743 7.823745 AAGAGCTCTTTAAGATTGGAAACAA 57.176 32.000 23.49 0.00 44.02 2.83
2305 2744 8.237811 AAGAGCTCTTTAAGATTGGAAACAAA 57.762 30.769 23.49 0.00 43.43 2.83
2306 2745 8.138074 AAGAGCTCTTTAAGATTGGAAACAAAC 58.862 33.333 23.49 0.00 43.43 2.93
2393 2844 7.442062 GGATGAATTTTGTGACTGGAAACAATT 59.558 33.333 0.00 0.00 42.06 2.32
2397 2848 5.793026 TTTGTGACTGGAAACAATTTTGC 57.207 34.783 0.00 0.00 42.06 3.68
2405 2856 0.317938 AAACAATTTTGCGGCGCGTA 60.318 45.000 28.09 15.23 0.00 4.42
2428 2879 4.816392 TCATATATACATGGTGGTGACGC 58.184 43.478 0.00 0.00 41.20 5.19
2432 2883 1.447945 TACATGGTGGTGACGCATTG 58.552 50.000 0.00 0.00 44.70 2.82
2433 2884 0.250684 ACATGGTGGTGACGCATTGA 60.251 50.000 0.00 0.00 44.70 2.57
2434 2885 1.097232 CATGGTGGTGACGCATTGAT 58.903 50.000 0.00 0.00 44.70 2.57
2435 2886 1.473677 CATGGTGGTGACGCATTGATT 59.526 47.619 0.00 0.00 44.70 2.57
2436 2887 0.880441 TGGTGGTGACGCATTGATTG 59.120 50.000 0.00 0.00 44.70 2.67
2437 2888 0.881118 GGTGGTGACGCATTGATTGT 59.119 50.000 0.00 0.00 44.70 2.71
2438 2889 1.269448 GGTGGTGACGCATTGATTGTT 59.731 47.619 0.00 0.00 44.70 2.83
2439 2890 2.318578 GTGGTGACGCATTGATTGTTG 58.681 47.619 0.00 0.00 41.67 3.33
2440 2891 1.335780 TGGTGACGCATTGATTGTTGC 60.336 47.619 0.00 0.00 35.50 4.17
2441 2892 1.068333 GGTGACGCATTGATTGTTGCT 60.068 47.619 0.00 0.00 36.71 3.91
2442 2893 2.161410 GGTGACGCATTGATTGTTGCTA 59.839 45.455 0.00 0.00 36.71 3.49
2443 2894 3.419915 GTGACGCATTGATTGTTGCTAG 58.580 45.455 0.00 0.00 36.71 3.42
2444 2895 3.125146 GTGACGCATTGATTGTTGCTAGA 59.875 43.478 0.00 0.00 36.71 2.43
2445 2896 3.750652 TGACGCATTGATTGTTGCTAGAA 59.249 39.130 0.00 0.00 36.71 2.10
2446 2897 4.083581 ACGCATTGATTGTTGCTAGAAC 57.916 40.909 0.00 0.00 36.71 3.01
2447 2898 3.753272 ACGCATTGATTGTTGCTAGAACT 59.247 39.130 0.00 0.00 36.71 3.01
2448 2899 4.093514 CGCATTGATTGTTGCTAGAACTG 58.906 43.478 0.00 0.00 36.71 3.16
2449 2900 4.142838 CGCATTGATTGTTGCTAGAACTGA 60.143 41.667 0.00 0.00 36.71 3.41
2450 2901 5.448225 CGCATTGATTGTTGCTAGAACTGAT 60.448 40.000 0.00 0.00 36.71 2.90
2451 2902 5.970023 GCATTGATTGTTGCTAGAACTGATC 59.030 40.000 0.00 4.96 35.95 2.92
2452 2903 6.403964 GCATTGATTGTTGCTAGAACTGATCA 60.404 38.462 0.00 0.00 35.95 2.92
2453 2904 7.681304 GCATTGATTGTTGCTAGAACTGATCAT 60.681 37.037 0.00 0.00 35.95 2.45
2454 2905 7.692460 TTGATTGTTGCTAGAACTGATCATT 57.308 32.000 0.00 0.00 0.00 2.57
2455 2906 7.080353 TGATTGTTGCTAGAACTGATCATTG 57.920 36.000 0.00 0.00 0.00 2.82
2456 2907 4.952262 TGTTGCTAGAACTGATCATTGC 57.048 40.909 0.00 0.00 0.00 3.56
2457 2908 3.691118 TGTTGCTAGAACTGATCATTGCC 59.309 43.478 0.00 0.00 0.00 4.52
2458 2909 2.554142 TGCTAGAACTGATCATTGCCG 58.446 47.619 0.00 0.00 0.00 5.69
2459 2910 2.093500 TGCTAGAACTGATCATTGCCGT 60.093 45.455 0.00 0.00 0.00 5.68
2460 2911 2.286294 GCTAGAACTGATCATTGCCGTG 59.714 50.000 0.00 0.00 0.00 4.94
2461 2912 2.768253 AGAACTGATCATTGCCGTGA 57.232 45.000 0.00 0.00 0.00 4.35
2462 2913 3.057969 AGAACTGATCATTGCCGTGAA 57.942 42.857 0.00 0.00 0.00 3.18
2463 2914 3.411446 AGAACTGATCATTGCCGTGAAA 58.589 40.909 0.00 0.00 0.00 2.69
2464 2915 3.820467 AGAACTGATCATTGCCGTGAAAA 59.180 39.130 0.00 0.00 0.00 2.29
2465 2916 4.278170 AGAACTGATCATTGCCGTGAAAAA 59.722 37.500 0.00 0.00 0.00 1.94
2499 2950 7.048629 TGGATCTCTGCTACTAAGATTTCAG 57.951 40.000 0.00 0.00 30.04 3.02
2541 3039 3.834489 AGGACTGGTGCTATTGATCTG 57.166 47.619 0.00 0.00 0.00 2.90
2547 3045 3.106827 TGGTGCTATTGATCTGGTCAGA 58.893 45.455 2.93 2.93 42.37 3.27
2569 3067 1.620819 ACTCAGACCACCTTGCTGTAG 59.379 52.381 0.00 0.00 0.00 2.74
2602 3109 4.269123 CAGTTTGTTAGTGTACAAGCGTGA 59.731 41.667 6.65 0.00 42.06 4.35
2603 3110 5.050363 CAGTTTGTTAGTGTACAAGCGTGAT 60.050 40.000 6.65 0.00 42.06 3.06
2620 3127 4.259970 GCGTGATGTATGTTTGCTAGTCAG 60.260 45.833 0.00 0.00 0.00 3.51
2625 3132 5.468540 TGTATGTTTGCTAGTCAGACACT 57.531 39.130 2.66 5.81 41.75 3.55
2626 3133 5.470368 TGTATGTTTGCTAGTCAGACACTC 58.530 41.667 2.66 8.65 41.75 3.51
2627 3134 3.013276 TGTTTGCTAGTCAGACACTCG 57.987 47.619 2.66 0.00 35.20 4.18
2648 3157 1.072331 GACCACCTTGCTGGAAGAAGA 59.928 52.381 10.73 0.00 39.71 2.87
2650 3159 2.089980 CCACCTTGCTGGAAGAAGATG 58.910 52.381 10.73 3.49 39.71 2.90
2652 3161 3.307691 CCACCTTGCTGGAAGAAGATGTA 60.308 47.826 10.73 0.00 39.71 2.29
2653 3162 3.937706 CACCTTGCTGGAAGAAGATGTAG 59.062 47.826 10.73 0.00 39.71 2.74
2655 3164 3.603532 CTTGCTGGAAGAAGATGTAGCA 58.396 45.455 2.37 0.00 39.17 3.49
2658 3167 4.194640 TGCTGGAAGAAGATGTAGCATTC 58.805 43.478 0.00 0.00 36.37 2.67
2659 3168 4.194640 GCTGGAAGAAGATGTAGCATTCA 58.805 43.478 0.00 0.00 34.07 2.57
2661 3170 5.277876 GCTGGAAGAAGATGTAGCATTCATG 60.278 44.000 0.00 0.00 34.07 3.07
2675 3184 4.895224 CATTCATGCAAGCTCTGTATGT 57.105 40.909 18.72 5.94 45.52 2.29
2676 3185 5.244785 CATTCATGCAAGCTCTGTATGTT 57.755 39.130 18.72 10.41 45.52 2.71
2677 3186 5.647589 CATTCATGCAAGCTCTGTATGTTT 58.352 37.500 18.72 10.19 45.52 2.83
2678 3187 4.690184 TCATGCAAGCTCTGTATGTTTG 57.310 40.909 18.72 0.72 45.52 2.93
2679 3188 4.074259 TCATGCAAGCTCTGTATGTTTGT 58.926 39.130 18.72 0.00 45.52 2.83
2680 3189 4.520111 TCATGCAAGCTCTGTATGTTTGTT 59.480 37.500 18.72 0.00 45.52 2.83
2682 3191 5.611796 TGCAAGCTCTGTATGTTTGTTAG 57.388 39.130 0.00 0.00 0.00 2.34
2683 3192 5.063204 TGCAAGCTCTGTATGTTTGTTAGT 58.937 37.500 0.00 0.00 0.00 2.24
2684 3193 5.049474 TGCAAGCTCTGTATGTTTGTTAGTG 60.049 40.000 0.00 0.00 0.00 2.74
2685 3194 5.049405 GCAAGCTCTGTATGTTTGTTAGTGT 60.049 40.000 0.00 0.00 0.00 3.55
2686 3195 6.147164 GCAAGCTCTGTATGTTTGTTAGTGTA 59.853 38.462 0.00 0.00 0.00 2.90
2688 3197 9.366216 CAAGCTCTGTATGTTTGTTAGTGTATA 57.634 33.333 0.00 0.00 0.00 1.47
2689 3198 9.938280 AAGCTCTGTATGTTTGTTAGTGTATAA 57.062 29.630 0.00 0.00 0.00 0.98
2701 3210 7.940178 TGTTAGTGTATAAGTGTGTTCTGTG 57.060 36.000 0.00 0.00 0.00 3.66
2704 3213 9.467258 GTTAGTGTATAAGTGTGTTCTGTGTTA 57.533 33.333 0.00 0.00 0.00 2.41
2719 3228 4.005650 CTGTGTTAGACAGTGGCATTCAT 58.994 43.478 0.00 0.00 46.30 2.57
2733 3242 0.454957 ATTCATGCAAGCGCGTTCAC 60.455 50.000 8.43 0.00 42.97 3.18
2743 3252 1.886861 GCGCGTTCACGTCATGTTCT 61.887 55.000 8.43 0.00 42.22 3.01
2749 3258 3.362014 CGTTCACGTCATGTTCTGTTCTG 60.362 47.826 0.00 0.00 34.11 3.02
2773 3387 6.823678 CAATGCATGCTCTTTTATTTCTCC 57.176 37.500 20.33 0.00 0.00 3.71
2778 3392 5.684626 GCATGCTCTTTTATTTCTCCAATCG 59.315 40.000 11.37 0.00 0.00 3.34
2796 3410 3.835378 TCGTGTCTATTCGCACAAGTA 57.165 42.857 0.00 0.00 35.51 2.24
2799 3413 3.918591 CGTGTCTATTCGCACAAGTACTT 59.081 43.478 1.12 1.12 35.51 2.24
2800 3414 4.384846 CGTGTCTATTCGCACAAGTACTTT 59.615 41.667 5.07 0.00 35.51 2.66
2801 3415 5.609088 GTGTCTATTCGCACAAGTACTTTG 58.391 41.667 5.07 9.09 42.68 2.77
2815 3429 4.006989 AGTACTTTGTTCACAGCAACACA 58.993 39.130 0.00 0.00 35.97 3.72
2818 3432 5.772825 ACTTTGTTCACAGCAACACATAT 57.227 34.783 0.00 0.00 35.97 1.78
2826 3440 8.240682 TGTTCACAGCAACACATATTTTATACC 58.759 33.333 0.00 0.00 31.08 2.73
2827 3441 7.010697 TCACAGCAACACATATTTTATACCG 57.989 36.000 0.00 0.00 0.00 4.02
2850 3464 2.871453 ACAAATTGTTCCGGGTTAGCT 58.129 42.857 0.00 0.00 0.00 3.32
2860 3474 1.270625 CCGGGTTAGCTTTGTGTCTGA 60.271 52.381 0.00 0.00 0.00 3.27
2865 3479 5.006746 CGGGTTAGCTTTGTGTCTGATATTC 59.993 44.000 0.00 0.00 0.00 1.75
2872 3486 8.034058 AGCTTTGTGTCTGATATTCAAGTTAC 57.966 34.615 0.00 0.00 0.00 2.50
2877 3491 9.990360 TTGTGTCTGATATTCAAGTTACTGTAA 57.010 29.630 0.00 0.00 0.00 2.41
2879 3493 8.870879 GTGTCTGATATTCAAGTTACTGTAACC 58.129 37.037 23.22 9.06 39.47 2.85
2897 3513 2.779506 ACCTGACCGAGGAAACAATTC 58.220 47.619 0.00 0.00 46.33 2.17
2924 3540 1.135721 GCAAGAAGGATGGCATGGAAC 59.864 52.381 3.81 0.00 0.00 3.62
2946 3562 4.127171 CCGACAGATGATCCGGTTAATTT 58.873 43.478 0.00 0.00 37.40 1.82
2949 3565 5.276868 CGACAGATGATCCGGTTAATTTGTC 60.277 44.000 17.96 17.96 0.00 3.18
2959 3579 9.706691 GATCCGGTTAATTTGTCTTAGATATGA 57.293 33.333 0.00 0.00 0.00 2.15
2961 3581 9.706691 TCCGGTTAATTTGTCTTAGATATGATC 57.293 33.333 0.00 0.00 0.00 2.92
2972 3592 8.043113 TGTCTTAGATATGATCAATGGGTATGC 58.957 37.037 0.00 0.00 0.00 3.14
2973 3593 8.043113 GTCTTAGATATGATCAATGGGTATGCA 58.957 37.037 0.00 0.00 0.00 3.96
2985 3605 6.942005 TCAATGGGTATGCATTAATCTACCAG 59.058 38.462 14.46 3.57 36.21 4.00
3000 3620 4.483950 TCTACCAGCCAGCTTATGTATCT 58.516 43.478 0.00 0.00 0.00 1.98
3004 3624 3.556633 CCAGCCAGCTTATGTATCTCTGG 60.557 52.174 2.43 2.43 45.26 3.86
3010 3630 5.305644 CCAGCTTATGTATCTCTGGGTACTT 59.694 44.000 0.00 0.00 40.34 2.24
3011 3631 6.451393 CAGCTTATGTATCTCTGGGTACTTC 58.549 44.000 0.00 0.00 0.00 3.01
3015 3635 7.014808 GCTTATGTATCTCTGGGTACTTCTCTT 59.985 40.741 0.00 0.00 0.00 2.85
3016 3636 9.575868 CTTATGTATCTCTGGGTACTTCTCTTA 57.424 37.037 0.00 0.00 0.00 2.10
3019 3639 5.799827 ATCTCTGGGTACTTCTCTTATGC 57.200 43.478 0.00 0.00 0.00 3.14
3020 3640 4.610333 TCTCTGGGTACTTCTCTTATGCA 58.390 43.478 0.00 0.00 0.00 3.96
3021 3641 5.023452 TCTCTGGGTACTTCTCTTATGCAA 58.977 41.667 0.00 0.00 0.00 4.08
3022 3642 5.663106 TCTCTGGGTACTTCTCTTATGCAAT 59.337 40.000 0.00 0.00 0.00 3.56
3023 3643 5.674525 TCTGGGTACTTCTCTTATGCAATG 58.325 41.667 0.00 0.00 0.00 2.82
3029 3649 6.986817 GGTACTTCTCTTATGCAATGCTTCTA 59.013 38.462 6.82 0.00 0.00 2.10
3068 3688 6.762702 ATTAGTCATTCATGTGCATTGTCA 57.237 33.333 0.00 0.00 0.00 3.58
3072 3692 3.441222 TCATTCATGTGCATTGTCAGGAC 59.559 43.478 0.00 0.00 0.00 3.85
3137 3757 9.874205 TCACTCTTGTTCTTTTTCATGAAATTT 57.126 25.926 21.10 0.00 0.00 1.82
3219 3846 9.853555 TGTTAATGATGTAATTTGGTGCTAAAG 57.146 29.630 0.00 0.00 0.00 1.85
3234 3861 5.627780 GGTGCTAAAGTAAACATTTTGTCCG 59.372 40.000 0.00 0.00 0.00 4.79
3242 3869 7.931578 AGTAAACATTTTGTCCGGATGATAA 57.068 32.000 7.81 0.06 0.00 1.75
3243 3870 7.985476 AGTAAACATTTTGTCCGGATGATAAG 58.015 34.615 7.81 0.00 0.00 1.73
3244 3871 6.834168 AAACATTTTGTCCGGATGATAAGT 57.166 33.333 7.81 0.00 0.00 2.24
3245 3872 6.834168 AACATTTTGTCCGGATGATAAGTT 57.166 33.333 7.81 6.93 0.00 2.66
3274 3901 9.520515 TTTCCTTTTAGCTTTTGTAGATCATCT 57.479 29.630 0.00 0.00 0.00 2.90
3284 3911 8.983724 GCTTTTGTAGATCATCTAGTATTGGTC 58.016 37.037 0.00 0.00 28.01 4.02
3293 3920 7.616528 TCATCTAGTATTGGTCATCCATTCA 57.383 36.000 0.00 0.00 43.91 2.57
3301 3928 3.009026 TGGTCATCCATTCACATTGTCG 58.991 45.455 0.00 0.00 39.03 4.35
3320 3947 1.680338 GGGGCTCATGACGCTTTATT 58.320 50.000 14.20 0.00 0.00 1.40
3361 3988 3.334691 TGACCGCTCTTTCCATACTTTG 58.665 45.455 0.00 0.00 0.00 2.77
3362 3989 3.244422 TGACCGCTCTTTCCATACTTTGT 60.244 43.478 0.00 0.00 0.00 2.83
3363 3990 4.020928 TGACCGCTCTTTCCATACTTTGTA 60.021 41.667 0.00 0.00 0.00 2.41
3364 3991 4.251268 ACCGCTCTTTCCATACTTTGTAC 58.749 43.478 0.00 0.00 0.00 2.90
3365 3992 4.020485 ACCGCTCTTTCCATACTTTGTACT 60.020 41.667 0.00 0.00 0.00 2.73
3366 3993 4.935808 CCGCTCTTTCCATACTTTGTACTT 59.064 41.667 0.00 0.00 0.00 2.24
3367 3994 5.163854 CCGCTCTTTCCATACTTTGTACTTG 60.164 44.000 0.00 0.00 0.00 3.16
3368 3995 5.408604 CGCTCTTTCCATACTTTGTACTTGT 59.591 40.000 0.00 0.00 0.00 3.16
3369 3996 6.588756 CGCTCTTTCCATACTTTGTACTTGTA 59.411 38.462 0.00 0.00 0.00 2.41
3370 3997 7.117236 CGCTCTTTCCATACTTTGTACTTGTAA 59.883 37.037 0.00 0.00 0.00 2.41
3371 3998 8.780249 GCTCTTTCCATACTTTGTACTTGTAAA 58.220 33.333 0.00 0.00 0.00 2.01
3407 4034 9.661563 TTATGAAGATTACCGTAGAACAATTGT 57.338 29.630 4.92 4.92 0.00 2.71
3408 4035 7.972832 TGAAGATTACCGTAGAACAATTGTT 57.027 32.000 23.49 23.49 41.64 2.83
3421 4048 4.223320 ACAATTGTTCTACAGTTTGCGG 57.777 40.909 4.92 0.00 30.77 5.69
3424 4051 4.911514 ATTGTTCTACAGTTTGCGGTTT 57.088 36.364 0.00 0.00 0.00 3.27
3429 4056 6.618811 TGTTCTACAGTTTGCGGTTTAAAAA 58.381 32.000 0.00 0.00 0.00 1.94
3460 4087 5.334569 CCGCTCTTTCCTTTTTCGTGAAATA 60.335 40.000 0.00 0.00 0.00 1.40
3587 4219 7.315890 ACTCACTTTCTTTTTCACTTTTGGAG 58.684 34.615 0.00 0.00 0.00 3.86
3602 4234 5.669447 ACTTTTGGAGGTGAGATAGATGGAT 59.331 40.000 0.00 0.00 0.00 3.41
3791 4424 1.612442 TAGGAAGGAAGCTGGCGGT 60.612 57.895 0.00 0.00 0.00 5.68
3818 4451 3.636300 TGTCAAACTCTCATTTTGGTGGG 59.364 43.478 0.00 0.00 35.12 4.61
3820 4453 4.340950 GTCAAACTCTCATTTTGGTGGGAA 59.659 41.667 0.00 0.00 35.12 3.97
3850 4483 7.902920 AGAAGTATGGGTTTATCGTAGGTTA 57.097 36.000 0.00 0.00 0.00 2.85
3890 4523 4.412199 TCCTCCATCCGGAATTAGTTGATT 59.588 41.667 9.01 0.00 42.21 2.57
3901 4534 5.414765 GGAATTAGTTGATTCTCAAACGGGT 59.585 40.000 0.00 0.00 38.22 5.28
3913 4546 4.161565 TCTCAAACGGGTGTATCTAGCATT 59.838 41.667 0.00 0.00 0.00 3.56
3914 4547 5.361571 TCTCAAACGGGTGTATCTAGCATTA 59.638 40.000 0.00 0.00 0.00 1.90
3915 4548 5.979993 TCAAACGGGTGTATCTAGCATTAA 58.020 37.500 0.00 0.00 0.00 1.40
3916 4549 6.408035 TCAAACGGGTGTATCTAGCATTAAA 58.592 36.000 0.00 0.00 0.00 1.52
3917 4550 6.879993 TCAAACGGGTGTATCTAGCATTAAAA 59.120 34.615 0.00 0.00 0.00 1.52
3918 4551 7.554835 TCAAACGGGTGTATCTAGCATTAAAAT 59.445 33.333 0.00 0.00 0.00 1.82
3919 4552 8.832521 CAAACGGGTGTATCTAGCATTAAAATA 58.167 33.333 0.00 0.00 0.00 1.40
3920 4553 7.958053 ACGGGTGTATCTAGCATTAAAATAC 57.042 36.000 0.00 0.00 0.00 1.89
3921 4554 6.643770 ACGGGTGTATCTAGCATTAAAATACG 59.356 38.462 0.00 0.00 0.00 3.06
3922 4555 6.643770 CGGGTGTATCTAGCATTAAAATACGT 59.356 38.462 0.00 0.00 0.00 3.57
3923 4556 7.148853 CGGGTGTATCTAGCATTAAAATACGTC 60.149 40.741 0.00 0.00 0.00 4.34
3924 4557 7.871463 GGGTGTATCTAGCATTAAAATACGTCT 59.129 37.037 0.00 0.00 0.00 4.18
3925 4558 9.903682 GGTGTATCTAGCATTAAAATACGTCTA 57.096 33.333 0.00 0.00 0.00 2.59
3934 4567 9.640963 AGCATTAAAATACGTCTAGATACATCC 57.359 33.333 0.00 0.00 0.00 3.51
3935 4568 8.584600 GCATTAAAATACGTCTAGATACATCCG 58.415 37.037 0.00 0.00 0.00 4.18
3936 4569 9.622004 CATTAAAATACGTCTAGATACATCCGT 57.378 33.333 8.59 8.59 0.00 4.69
3939 4572 7.925703 AAATACGTCTAGATACATCCGTTTG 57.074 36.000 8.82 0.00 0.00 2.93
3940 4573 6.872628 ATACGTCTAGATACATCCGTTTGA 57.127 37.500 8.82 0.00 0.00 2.69
3941 4574 5.571784 ACGTCTAGATACATCCGTTTGAA 57.428 39.130 0.00 0.00 0.00 2.69
3942 4575 5.338365 ACGTCTAGATACATCCGTTTGAAC 58.662 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 101 2.125673 CGTCCGCCCTCGTTGATT 60.126 61.111 0.00 0.00 0.00 2.57
121 125 2.348888 GCGGGGAGGAGTCGAAGAA 61.349 63.158 0.00 0.00 39.69 2.52
124 128 2.283676 AAGCGGGGAGGAGTCGAA 60.284 61.111 0.00 0.00 0.00 3.71
206 210 0.918310 AGGCCTGCCTCCTTCTTCAT 60.918 55.000 3.11 0.00 44.43 2.57
283 287 4.373116 GTCCGCGCCCAGTCTTCA 62.373 66.667 0.00 0.00 0.00 3.02
312 316 3.760035 CTAGGGCGCGACACTGGT 61.760 66.667 17.00 0.00 0.00 4.00
385 389 3.340253 TCGTCGTCGCTGTCGTCA 61.340 61.111 0.00 0.00 36.96 4.35
520 540 0.963962 AACTACAGGCCGAAGAACGA 59.036 50.000 8.77 0.00 45.77 3.85
590 621 5.815740 CGGTGAACATAACATTACTTAGGCT 59.184 40.000 0.00 0.00 0.00 4.58
604 635 9.391006 AGATTAAGCTAAAATTCGGTGAACATA 57.609 29.630 0.00 0.00 0.00 2.29
625 656 8.934507 AAATTTGACAAACGGAACAAAGATTA 57.065 26.923 1.94 0.00 36.07 1.75
635 666 3.564644 TCGGCTAAAATTTGACAAACGGA 59.435 39.130 1.94 0.00 0.00 4.69
700 741 4.796495 GATTCCCAACCGCCGGCT 62.796 66.667 26.68 2.78 0.00 5.52
709 750 0.251877 GGGGGTTTTCGGATTCCCAA 60.252 55.000 12.42 0.00 41.51 4.12
716 757 1.138568 TTAGTGTGGGGGTTTTCGGA 58.861 50.000 0.00 0.00 0.00 4.55
787 831 0.693430 TGGATCTGCATCTCCAGCCT 60.693 55.000 12.18 0.00 36.63 4.58
790 834 1.579698 CGTTGGATCTGCATCTCCAG 58.420 55.000 14.88 4.23 42.32 3.86
800 844 0.179100 CTGCGATGACCGTTGGATCT 60.179 55.000 0.00 0.00 41.15 2.75
801 845 1.154205 CCTGCGATGACCGTTGGATC 61.154 60.000 0.00 0.00 41.15 3.36
802 846 1.153369 CCTGCGATGACCGTTGGAT 60.153 57.895 0.00 0.00 41.15 3.41
803 847 2.264480 CCTGCGATGACCGTTGGA 59.736 61.111 0.00 0.00 41.15 3.53
804 848 2.047274 ACCTGCGATGACCGTTGG 60.047 61.111 0.00 0.00 41.15 3.77
805 849 0.389296 TACACCTGCGATGACCGTTG 60.389 55.000 0.00 0.00 41.15 4.10
806 850 0.535335 ATACACCTGCGATGACCGTT 59.465 50.000 0.00 0.00 41.15 4.44
807 851 0.179111 CATACACCTGCGATGACCGT 60.179 55.000 0.00 0.00 41.15 4.83
808 852 1.490693 GCATACACCTGCGATGACCG 61.491 60.000 0.00 0.00 42.21 4.79
809 853 0.179073 AGCATACACCTGCGATGACC 60.179 55.000 0.00 0.00 46.86 4.02
810 854 1.212616 GAGCATACACCTGCGATGAC 58.787 55.000 0.00 0.00 46.86 3.06
811 855 0.104855 GGAGCATACACCTGCGATGA 59.895 55.000 0.00 0.00 46.86 2.92
812 856 1.217585 CGGAGCATACACCTGCGATG 61.218 60.000 0.00 0.00 45.30 3.84
813 857 1.068083 CGGAGCATACACCTGCGAT 59.932 57.895 0.00 0.00 45.30 4.58
814 858 2.494445 CGGAGCATACACCTGCGA 59.506 61.111 0.00 0.00 45.30 5.10
815 859 2.369257 ATCCGGAGCATACACCTGCG 62.369 60.000 11.34 0.00 46.86 5.18
816 860 0.882042 CATCCGGAGCATACACCTGC 60.882 60.000 11.34 0.00 42.62 4.85
817 861 0.465705 ACATCCGGAGCATACACCTG 59.534 55.000 11.34 1.82 0.00 4.00
818 862 0.753262 GACATCCGGAGCATACACCT 59.247 55.000 11.34 0.00 0.00 4.00
819 863 0.753262 AGACATCCGGAGCATACACC 59.247 55.000 11.34 0.00 0.00 4.16
820 864 3.728076 TTAGACATCCGGAGCATACAC 57.272 47.619 11.34 0.00 0.00 2.90
821 865 4.746535 TTTTAGACATCCGGAGCATACA 57.253 40.909 11.34 0.00 0.00 2.29
845 889 9.846248 CTAAATTATAAAAAGTGCAGCTGAACT 57.154 29.630 22.53 22.53 34.75 3.01
846 890 9.076596 CCTAAATTATAAAAAGTGCAGCTGAAC 57.923 33.333 20.43 19.10 0.00 3.18
847 891 8.802267 ACCTAAATTATAAAAAGTGCAGCTGAA 58.198 29.630 20.43 2.96 0.00 3.02
848 892 8.348285 ACCTAAATTATAAAAAGTGCAGCTGA 57.652 30.769 20.43 0.00 0.00 4.26
849 893 8.986477 AACCTAAATTATAAAAAGTGCAGCTG 57.014 30.769 10.11 10.11 0.00 4.24
850 894 9.996554 AAAACCTAAATTATAAAAAGTGCAGCT 57.003 25.926 0.00 0.00 0.00 4.24
868 912 9.674068 ACAAATAAAGGCAAAAGAAAAACCTAA 57.326 25.926 0.00 0.00 0.00 2.69
869 913 9.320352 GACAAATAAAGGCAAAAGAAAAACCTA 57.680 29.630 0.00 0.00 0.00 3.08
872 916 8.122330 CCTGACAAATAAAGGCAAAAGAAAAAC 58.878 33.333 0.00 0.00 0.00 2.43
906 950 0.318441 TACTGTGGACTGCAGTCTGC 59.682 55.000 38.17 30.47 44.96 4.26
907 951 1.337260 GGTACTGTGGACTGCAGTCTG 60.337 57.143 38.17 27.80 44.96 3.51
908 952 0.969894 GGTACTGTGGACTGCAGTCT 59.030 55.000 38.17 24.53 44.96 3.24
949 1003 3.254892 GCTGTTGGCTACTGTAGACTTC 58.745 50.000 20.68 13.65 38.06 3.01
1362 1466 0.741221 AGACGAAGCGCTGGATTTCC 60.741 55.000 12.58 0.00 0.00 3.13
1504 1617 3.554692 GGCGACGGCGAATCTGTG 61.555 66.667 18.90 0.00 41.24 3.66
2061 2473 1.702491 GGTAGATGGCGTTGGCGTTC 61.702 60.000 0.00 0.00 41.24 3.95
2276 2715 8.972349 GTTTCCAATCTTAAAGAGCTCTTTTTG 58.028 33.333 38.82 33.01 43.07 2.44
2304 2743 5.122082 CCAGCAAGTGATTTGTTTGTTTGTT 59.878 36.000 0.00 0.00 39.08 2.83
2305 2744 4.630940 CCAGCAAGTGATTTGTTTGTTTGT 59.369 37.500 0.00 0.00 39.08 2.83
2306 2745 4.630940 ACCAGCAAGTGATTTGTTTGTTTG 59.369 37.500 0.00 0.00 39.08 2.93
2307 2746 4.630940 CACCAGCAAGTGATTTGTTTGTTT 59.369 37.500 0.00 0.00 40.34 2.83
2393 2844 2.067414 TATATGATACGCGCCGCAAA 57.933 45.000 10.75 0.00 0.00 3.68
2397 2848 3.668656 CCATGTATATATGATACGCGCCG 59.331 47.826 5.73 0.00 0.00 6.46
2405 2856 5.046663 TGCGTCACCACCATGTATATATGAT 60.047 40.000 10.79 0.00 0.00 2.45
2428 2879 7.080353 TGATCAGTTCTAGCAACAATCAATG 57.920 36.000 0.00 0.00 0.00 2.82
2432 2883 5.970023 GCAATGATCAGTTCTAGCAACAATC 59.030 40.000 0.09 9.10 0.00 2.67
2433 2884 5.163581 GGCAATGATCAGTTCTAGCAACAAT 60.164 40.000 0.09 2.23 0.00 2.71
2434 2885 4.156556 GGCAATGATCAGTTCTAGCAACAA 59.843 41.667 0.09 0.00 0.00 2.83
2435 2886 3.691118 GGCAATGATCAGTTCTAGCAACA 59.309 43.478 0.09 0.00 0.00 3.33
2436 2887 3.242543 CGGCAATGATCAGTTCTAGCAAC 60.243 47.826 0.09 0.00 0.00 4.17
2437 2888 2.938451 CGGCAATGATCAGTTCTAGCAA 59.062 45.455 0.09 0.00 0.00 3.91
2438 2889 2.093500 ACGGCAATGATCAGTTCTAGCA 60.093 45.455 0.09 0.00 0.00 3.49
2439 2890 2.286294 CACGGCAATGATCAGTTCTAGC 59.714 50.000 0.09 0.00 0.00 3.42
2440 2891 3.785486 TCACGGCAATGATCAGTTCTAG 58.215 45.455 0.09 0.00 0.00 2.43
2441 2892 3.885724 TCACGGCAATGATCAGTTCTA 57.114 42.857 0.09 0.00 0.00 2.10
2442 2893 2.768253 TCACGGCAATGATCAGTTCT 57.232 45.000 0.09 0.00 0.00 3.01
2443 2894 3.829886 TTTCACGGCAATGATCAGTTC 57.170 42.857 0.09 0.00 0.00 3.01
2444 2895 4.582701 TTTTTCACGGCAATGATCAGTT 57.417 36.364 0.09 0.00 0.00 3.16
2469 2920 7.283625 TCTTAGTAGCAGAGATCCAATTCTC 57.716 40.000 0.00 0.00 42.08 2.87
2470 2921 7.854166 ATCTTAGTAGCAGAGATCCAATTCT 57.146 36.000 0.00 0.00 0.00 2.40
2471 2922 8.900983 AAATCTTAGTAGCAGAGATCCAATTC 57.099 34.615 0.00 0.00 30.19 2.17
2472 2923 8.489489 TGAAATCTTAGTAGCAGAGATCCAATT 58.511 33.333 0.00 0.00 30.19 2.32
2473 2924 8.027524 TGAAATCTTAGTAGCAGAGATCCAAT 57.972 34.615 0.00 0.00 30.19 3.16
2474 2925 7.343057 TCTGAAATCTTAGTAGCAGAGATCCAA 59.657 37.037 0.00 0.00 30.19 3.53
2475 2926 6.836007 TCTGAAATCTTAGTAGCAGAGATCCA 59.164 38.462 0.00 0.00 30.19 3.41
2476 2927 7.145323 GTCTGAAATCTTAGTAGCAGAGATCC 58.855 42.308 0.00 0.00 33.55 3.36
2517 2971 4.586841 AGATCAATAGCACCAGTCCTAGTC 59.413 45.833 0.00 0.00 0.00 2.59
2527 2981 3.118629 TGTCTGACCAGATCAATAGCACC 60.119 47.826 5.17 0.00 39.97 5.01
2547 3045 0.107456 CAGCAAGGTGGTCTGAGTGT 59.893 55.000 0.00 0.00 0.00 3.55
2569 3067 4.269363 ACACTAACAAACTGCGAAGTACAC 59.731 41.667 0.00 0.00 0.00 2.90
2602 3109 6.042638 AGTGTCTGACTAGCAAACATACAT 57.957 37.500 9.51 0.00 30.86 2.29
2603 3110 5.468540 AGTGTCTGACTAGCAAACATACA 57.531 39.130 9.51 0.00 30.86 2.29
2620 3127 1.668151 GCAAGGTGGTCCGAGTGTC 60.668 63.158 0.00 0.00 39.05 3.67
2625 3132 2.111999 CTTCCAGCAAGGTGGTCCGA 62.112 60.000 16.99 0.00 38.88 4.55
2626 3133 1.672356 CTTCCAGCAAGGTGGTCCG 60.672 63.158 16.99 4.47 38.88 4.79
2627 3134 0.110486 TTCTTCCAGCAAGGTGGTCC 59.890 55.000 16.99 0.00 38.88 4.46
2655 3164 5.184479 ACAAACATACAGAGCTTGCATGAAT 59.816 36.000 12.97 0.00 34.69 2.57
2658 3167 4.430137 ACAAACATACAGAGCTTGCATG 57.570 40.909 0.00 0.00 36.74 4.06
2659 3168 5.707298 ACTAACAAACATACAGAGCTTGCAT 59.293 36.000 0.00 0.00 0.00 3.96
2661 3170 5.049405 ACACTAACAAACATACAGAGCTTGC 60.049 40.000 0.00 0.00 0.00 4.01
2663 3172 9.938280 TTATACACTAACAAACATACAGAGCTT 57.062 29.630 0.00 0.00 0.00 3.74
2664 3173 9.587772 CTTATACACTAACAAACATACAGAGCT 57.412 33.333 0.00 0.00 0.00 4.09
2665 3174 9.367444 ACTTATACACTAACAAACATACAGAGC 57.633 33.333 0.00 0.00 0.00 4.09
2672 3181 9.555727 AGAACACACTTATACACTAACAAACAT 57.444 29.630 0.00 0.00 0.00 2.71
2673 3182 8.822855 CAGAACACACTTATACACTAACAAACA 58.177 33.333 0.00 0.00 0.00 2.83
2675 3184 8.822855 CACAGAACACACTTATACACTAACAAA 58.177 33.333 0.00 0.00 0.00 2.83
2676 3185 7.982919 ACACAGAACACACTTATACACTAACAA 59.017 33.333 0.00 0.00 0.00 2.83
2677 3186 7.494211 ACACAGAACACACTTATACACTAACA 58.506 34.615 0.00 0.00 0.00 2.41
2678 3187 7.941795 ACACAGAACACACTTATACACTAAC 57.058 36.000 0.00 0.00 0.00 2.34
2679 3188 9.687210 CTAACACAGAACACACTTATACACTAA 57.313 33.333 0.00 0.00 0.00 2.24
2680 3189 9.070179 TCTAACACAGAACACACTTATACACTA 57.930 33.333 0.00 0.00 0.00 2.74
2682 3191 7.650504 TGTCTAACACAGAACACACTTATACAC 59.349 37.037 0.00 0.00 34.17 2.90
2683 3192 7.718525 TGTCTAACACAGAACACACTTATACA 58.281 34.615 0.00 0.00 34.17 2.29
2714 3223 0.454957 GTGAACGCGCTTGCATGAAT 60.455 50.000 5.73 0.00 39.07 2.57
2717 3226 2.866510 CGTGAACGCGCTTGCATG 60.867 61.111 5.73 1.87 39.07 4.06
2719 3228 3.995669 GACGTGAACGCGCTTGCA 61.996 61.111 5.73 0.00 44.43 4.08
2725 3234 0.179275 CAGAACATGACGTGAACGCG 60.179 55.000 3.53 3.53 44.43 6.01
2727 3236 2.794910 AGAACAGAACATGACGTGAACG 59.205 45.455 0.00 0.40 46.33 3.95
2733 3242 3.485633 CATTGCAGAACAGAACATGACG 58.514 45.455 0.00 0.00 0.00 4.35
2773 3387 3.367932 ACTTGTGCGAATAGACACGATTG 59.632 43.478 0.00 0.00 39.71 2.67
2778 3392 5.176958 ACAAAGTACTTGTGCGAATAGACAC 59.823 40.000 9.34 0.00 46.80 3.67
2796 3410 5.772825 ATATGTGTTGCTGTGAACAAAGT 57.227 34.783 0.00 0.00 37.58 2.66
2799 3413 9.619316 GTATAAAATATGTGTTGCTGTGAACAA 57.381 29.630 0.00 0.00 37.58 2.83
2800 3414 8.240682 GGTATAAAATATGTGTTGCTGTGAACA 58.759 33.333 0.00 0.00 33.36 3.18
2801 3415 7.428183 CGGTATAAAATATGTGTTGCTGTGAAC 59.572 37.037 0.00 0.00 0.00 3.18
2818 3432 6.403418 CCGGAACAATTTGTAGCGGTATAAAA 60.403 38.462 18.36 12.70 0.00 1.52
2826 3440 1.161843 ACCCGGAACAATTTGTAGCG 58.838 50.000 0.73 0.00 0.00 4.26
2827 3441 3.427098 GCTAACCCGGAACAATTTGTAGC 60.427 47.826 0.73 1.93 0.00 3.58
2850 3464 8.902540 ACAGTAACTTGAATATCAGACACAAA 57.097 30.769 0.00 0.00 0.00 2.83
2865 3479 4.235360 CTCGGTCAGGTTACAGTAACTTG 58.765 47.826 23.46 23.46 44.32 3.16
2872 3486 2.036733 TGTTTCCTCGGTCAGGTTACAG 59.963 50.000 0.00 0.00 43.95 2.74
2877 3491 2.372172 AGAATTGTTTCCTCGGTCAGGT 59.628 45.455 0.00 0.00 43.95 4.00
2879 3493 4.515191 TGAAAGAATTGTTTCCTCGGTCAG 59.485 41.667 21.49 0.00 35.85 3.51
2897 3513 1.475682 GCCATCCTTCTTGCCTGAAAG 59.524 52.381 0.00 0.00 0.00 2.62
2924 3540 2.882927 TTAACCGGATCATCTGTCGG 57.117 50.000 9.46 4.53 46.95 4.79
2946 3562 8.043113 GCATACCCATTGATCATATCTAAGACA 58.957 37.037 0.00 0.00 0.00 3.41
2949 3565 8.975663 ATGCATACCCATTGATCATATCTAAG 57.024 34.615 0.00 0.00 0.00 2.18
2959 3579 7.469343 TGGTAGATTAATGCATACCCATTGAT 58.531 34.615 10.80 0.00 37.47 2.57
2961 3581 6.349611 GCTGGTAGATTAATGCATACCCATTG 60.350 42.308 10.80 1.94 37.47 2.82
2972 3592 6.000219 ACATAAGCTGGCTGGTAGATTAATG 59.000 40.000 0.00 0.00 30.82 1.90
2973 3593 6.192970 ACATAAGCTGGCTGGTAGATTAAT 57.807 37.500 0.00 0.00 30.82 1.40
2976 3596 5.545723 AGATACATAAGCTGGCTGGTAGATT 59.454 40.000 0.00 0.00 0.00 2.40
2985 3605 2.370189 ACCCAGAGATACATAAGCTGGC 59.630 50.000 0.00 0.00 43.65 4.85
3000 3620 5.674525 CATTGCATAAGAGAAGTACCCAGA 58.325 41.667 0.00 0.00 0.00 3.86
3004 3624 5.819901 AGAAGCATTGCATAAGAGAAGTACC 59.180 40.000 11.91 0.00 0.00 3.34
3010 3630 7.955918 TCTACATAGAAGCATTGCATAAGAGA 58.044 34.615 11.91 0.55 0.00 3.10
3011 3631 8.774890 ATCTACATAGAAGCATTGCATAAGAG 57.225 34.615 11.91 0.00 35.69 2.85
3015 3635 7.767659 GGATGATCTACATAGAAGCATTGCATA 59.232 37.037 11.91 1.17 39.56 3.14
3016 3636 6.598457 GGATGATCTACATAGAAGCATTGCAT 59.402 38.462 11.91 0.00 39.56 3.96
3019 3639 7.160049 AGTGGATGATCTACATAGAAGCATTG 58.840 38.462 11.56 0.00 39.56 2.82
3020 3640 7.313740 AGTGGATGATCTACATAGAAGCATT 57.686 36.000 11.56 0.00 39.56 3.56
3021 3641 6.931790 AGTGGATGATCTACATAGAAGCAT 57.068 37.500 11.56 7.13 39.56 3.79
3022 3642 8.427902 AATAGTGGATGATCTACATAGAAGCA 57.572 34.615 11.56 0.00 39.56 3.91
3058 3678 2.703416 TCATGAGTCCTGACAATGCAC 58.297 47.619 0.00 0.00 31.63 4.57
3111 3731 9.874205 AAATTTCATGAAAAAGAACAAGAGTGA 57.126 25.926 23.91 0.00 33.56 3.41
3143 3763 8.854117 AGCTTCAGTTTTAGACTTCATCAAAAT 58.146 29.630 0.00 0.00 36.10 1.82
3146 3766 7.283127 ACAAGCTTCAGTTTTAGACTTCATCAA 59.717 33.333 0.00 0.00 36.10 2.57
3147 3767 6.767902 ACAAGCTTCAGTTTTAGACTTCATCA 59.232 34.615 0.00 0.00 36.10 3.07
3148 3768 7.195839 ACAAGCTTCAGTTTTAGACTTCATC 57.804 36.000 0.00 0.00 36.10 2.92
3151 3771 9.952188 AAATAACAAGCTTCAGTTTTAGACTTC 57.048 29.630 7.41 0.00 36.10 3.01
3219 3846 7.758495 ACTTATCATCCGGACAAAATGTTTAC 58.242 34.615 6.12 0.00 0.00 2.01
3227 3854 6.596497 GGAAAGTAACTTATCATCCGGACAAA 59.404 38.462 6.12 0.00 0.00 2.83
3234 3861 9.397280 AGCTAAAAGGAAAGTAACTTATCATCC 57.603 33.333 0.00 0.00 0.00 3.51
3242 3869 9.623000 TCTACAAAAGCTAAAAGGAAAGTAACT 57.377 29.630 0.00 0.00 0.00 2.24
3245 3872 9.787435 TGATCTACAAAAGCTAAAAGGAAAGTA 57.213 29.630 0.00 0.00 0.00 2.24
3284 3911 1.677576 CCCCGACAATGTGAATGGATG 59.322 52.381 0.00 0.00 0.00 3.51
3293 3920 0.392998 GTCATGAGCCCCGACAATGT 60.393 55.000 0.00 0.00 0.00 2.71
3301 3928 1.680338 AATAAAGCGTCATGAGCCCC 58.320 50.000 11.89 0.00 34.64 5.80
3332 3959 2.096496 GGAAAGAGCGGTCATCATTGTG 59.904 50.000 18.15 0.00 0.00 3.33
3381 4008 9.661563 ACAATTGTTCTACGGTAATCTTCATAA 57.338 29.630 4.92 0.00 0.00 1.90
3382 4009 9.661563 AACAATTGTTCTACGGTAATCTTCATA 57.338 29.630 18.13 0.00 31.64 2.15
3383 4010 8.561738 AACAATTGTTCTACGGTAATCTTCAT 57.438 30.769 18.13 0.00 31.64 2.57
3384 4011 7.972832 AACAATTGTTCTACGGTAATCTTCA 57.027 32.000 18.13 0.00 31.64 3.02
3399 4026 4.097286 ACCGCAAACTGTAGAACAATTGTT 59.903 37.500 23.49 23.49 41.64 2.83
3400 4027 3.630312 ACCGCAAACTGTAGAACAATTGT 59.370 39.130 4.92 4.92 31.48 2.71
3401 4028 4.223320 ACCGCAAACTGTAGAACAATTG 57.777 40.909 3.24 3.24 31.80 2.32
3402 4029 4.911514 AACCGCAAACTGTAGAACAATT 57.088 36.364 0.00 0.00 0.00 2.32
3403 4030 4.911514 AAACCGCAAACTGTAGAACAAT 57.088 36.364 0.00 0.00 0.00 2.71
3404 4031 5.814764 TTAAACCGCAAACTGTAGAACAA 57.185 34.783 0.00 0.00 0.00 2.83
3405 4032 5.814764 TTTAAACCGCAAACTGTAGAACA 57.185 34.783 0.00 0.00 0.00 3.18
3429 4056 1.704641 AAGGAAAGAGCGGCCTTTTT 58.295 45.000 14.67 5.95 38.85 1.94
3435 4062 0.591659 ACGAAAAAGGAAAGAGCGGC 59.408 50.000 0.00 0.00 0.00 6.53
3471 4098 9.939802 AGAAATAACGAACTTCAGTATTAGGTT 57.060 29.630 0.00 0.00 0.00 3.50
3488 4120 9.801873 ATCATTTGTTGGGAAATAGAAATAACG 57.198 29.630 0.00 0.00 0.00 3.18
3818 4451 7.711339 ACGATAAACCCATACTTCTTCAGATTC 59.289 37.037 0.00 0.00 0.00 2.52
3820 4453 7.125792 ACGATAAACCCATACTTCTTCAGAT 57.874 36.000 0.00 0.00 0.00 2.90
3850 4483 8.652290 GGATGGAGGAAGTAGTAATTAATCAGT 58.348 37.037 0.00 0.00 0.00 3.41
3868 4501 7.238037 GAGAATCAACTAATTCCGGATGGAGG 61.238 46.154 4.15 0.00 39.80 4.30
3869 4502 5.698545 GAGAATCAACTAATTCCGGATGGAG 59.301 44.000 4.15 5.13 39.80 3.86
3870 4503 5.130311 TGAGAATCAACTAATTCCGGATGGA 59.870 40.000 4.15 0.00 45.97 3.41
3871 4504 5.368145 TGAGAATCAACTAATTCCGGATGG 58.632 41.667 4.15 0.00 45.97 3.51
3890 4523 3.093814 TGCTAGATACACCCGTTTGAGA 58.906 45.455 0.00 0.00 0.00 3.27
3913 4546 9.454585 CAAACGGATGTATCTAGACGTATTTTA 57.545 33.333 0.00 0.00 33.85 1.52
3914 4547 8.192774 TCAAACGGATGTATCTAGACGTATTTT 58.807 33.333 0.00 0.00 33.85 1.82
3915 4548 7.709947 TCAAACGGATGTATCTAGACGTATTT 58.290 34.615 0.00 0.00 33.85 1.40
3916 4549 7.268199 TCAAACGGATGTATCTAGACGTATT 57.732 36.000 0.00 0.00 33.85 1.89
3917 4550 6.872628 TCAAACGGATGTATCTAGACGTAT 57.127 37.500 0.00 0.00 33.85 3.06
3918 4551 6.489675 GTTCAAACGGATGTATCTAGACGTA 58.510 40.000 0.00 0.00 33.85 3.57
3919 4552 5.338365 GTTCAAACGGATGTATCTAGACGT 58.662 41.667 0.00 0.00 35.95 4.34
3920 4553 5.868177 GTTCAAACGGATGTATCTAGACG 57.132 43.478 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.