Multiple sequence alignment - TraesCS5B01G186100

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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 TraesCS5B01G186100 chr5B 100.000 4497 0 0 1 4497 337907633 337903137 0.000000e+00 8305.0
1 TraesCS5B01G186100 chr5B 91.860 86 5 2 3883 3967 629934766 629934850 7.900000e-23 119.0
2 TraesCS5B01G186100 chr5D 95.465 3903 132 20 1 3884 297581030 297577154 0.000000e+00 6185.0
3 TraesCS5B01G186100 chr5D 81.292 449 31 14 3965 4390 297577156 297576738 9.390000e-82 315.0
4 TraesCS5B01G186100 chr5D 91.111 90 6 2 3876 3964 370946050 370945962 2.200000e-23 121.0
5 TraesCS5B01G186100 chr5A 95.624 2765 85 13 1 2759 401438330 401441064 0.000000e+00 4403.0
6 TraesCS5B01G186100 chr5A 95.296 1148 40 4 2744 3883 401441077 401442218 0.000000e+00 1808.0
7 TraesCS5B01G186100 chr5A 84.043 470 33 8 3965 4402 401442217 401442676 9.000000e-112 414.0
8 TraesCS5B01G186100 chr4D 84.239 920 121 17 1535 2452 416763170 416762273 0.000000e+00 874.0
9 TraesCS5B01G186100 chr4D 90.503 358 34 0 994 1351 416763700 416763343 1.460000e-129 473.0
10 TraesCS5B01G186100 chr4D 89.062 256 28 0 3243 3498 416760680 416760425 7.260000e-83 318.0
11 TraesCS5B01G186100 chr4D 87.417 151 18 1 2511 2660 416762165 416762015 5.980000e-39 172.0
12 TraesCS5B01G186100 chr4B 84.256 921 111 19 1535 2452 513726133 513725244 0.000000e+00 867.0
13 TraesCS5B01G186100 chr4B 86.682 428 49 5 954 1379 513726816 513726395 6.810000e-128 468.0
14 TraesCS5B01G186100 chr4B 87.891 256 31 0 3243 3498 513724202 513723947 7.310000e-78 302.0
15 TraesCS5B01G186100 chr4B 87.500 144 18 0 2517 2660 513725129 513724986 2.780000e-37 167.0
16 TraesCS5B01G186100 chr4B 91.209 91 4 4 3883 3971 4556841 4556753 2.200000e-23 121.0
17 TraesCS5B01G186100 chr4B 85.577 104 10 5 3868 3968 653519334 653519435 2.210000e-18 104.0
18 TraesCS5B01G186100 chr4A 84.108 925 107 25 1535 2452 47390232 47391123 0.000000e+00 857.0
19 TraesCS5B01G186100 chr4A 88.689 389 40 4 966 1351 47389670 47390057 5.270000e-129 472.0
20 TraesCS5B01G186100 chr4A 88.168 262 30 1 3237 3498 47392143 47392403 1.210000e-80 311.0
21 TraesCS5B01G186100 chr4A 87.500 144 18 0 2517 2660 47391230 47391373 2.780000e-37 167.0
22 TraesCS5B01G186100 chr4A 90.805 87 7 1 3883 3969 159510148 159510063 1.020000e-21 115.0
23 TraesCS5B01G186100 chr2A 90.857 175 13 2 126 300 775658234 775658405 9.730000e-57 231.0
24 TraesCS5B01G186100 chr2A 100.000 30 0 0 642 671 775658405 775658434 6.280000e-04 56.5
25 TraesCS5B01G186100 chr7D 93.103 87 4 2 3883 3968 633878851 633878766 4.720000e-25 126.0
26 TraesCS5B01G186100 chr7D 90.426 94 7 2 3883 3975 261817972 261817880 6.110000e-24 122.0
27 TraesCS5B01G186100 chr1B 91.111 90 5 2 3883 3970 681691006 681691094 7.900000e-23 119.0
28 TraesCS5B01G186100 chr7B 90.805 87 5 3 3882 3967 43549670 43549586 3.680000e-21 113.0


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 TraesCS5B01G186100 chr5B 337903137 337907633 4496 True 8305.000000 8305 100.000000 1 4497 1 chr5B.!!$R1 4496
1 TraesCS5B01G186100 chr5D 297576738 297581030 4292 True 3250.000000 6185 88.378500 1 4390 2 chr5D.!!$R2 4389
2 TraesCS5B01G186100 chr5A 401438330 401442676 4346 False 2208.333333 4403 91.654333 1 4402 3 chr5A.!!$F1 4401
3 TraesCS5B01G186100 chr4D 416760425 416763700 3275 True 459.250000 874 87.805250 994 3498 4 chr4D.!!$R1 2504
4 TraesCS5B01G186100 chr4B 513723947 513726816 2869 True 451.000000 867 86.582250 954 3498 4 chr4B.!!$R2 2544
5 TraesCS5B01G186100 chr4A 47389670 47392403 2733 False 451.750000 857 87.116250 966 3498 4 chr4A.!!$F1 2532

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
469 474 0.393537 CTGTGCTTGATCCCAGGGTC 60.394 60.0 5.01 3.16 0.00 4.46 F
886 893 1.271856 TCGCAACCATGACTTAGGGA 58.728 50.0 0.00 0.00 33.45 4.20 F
2644 2842 0.099968 CATCAGCCAAGGATGTTGCG 59.900 55.0 4.07 0.00 37.85 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 2009 0.327924 TGTTGATGGTGGTAGGGCTG 59.672 55.0 0.0 0.0 0.00 4.85 R
2765 2993 0.034337 TACCCCACGTGAAAGCAGTC 59.966 55.0 19.3 0.0 0.00 3.51 R
4471 5727 0.106894 GGACGAGCCTAATTGAGGGG 59.893 60.0 0.0 0.0 46.81 4.79 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
18 19 2.600731 CTCTCTCTCCTCGCCCCT 59.399 66.667 0.00 0.00 0.00 4.79
171 173 4.735358 GGTCCGTCCTTTGCCCCC 62.735 72.222 0.00 0.00 0.00 5.40
177 179 1.753078 GTCCTTTGCCCCCGATTCC 60.753 63.158 0.00 0.00 0.00 3.01
270 272 1.062365 CGCCTTGTGTGTGTGTGTG 59.938 57.895 0.00 0.00 0.00 3.82
275 277 1.060553 CTTGTGTGTGTGTGTGTCGAC 59.939 52.381 9.11 9.11 0.00 4.20
310 315 1.693083 CGGCTGGTTTACGTGCTAGC 61.693 60.000 8.10 8.10 38.29 3.42
427 432 0.890996 GGCGGATGGGAATGATGTCC 60.891 60.000 0.00 0.00 36.90 4.02
469 474 0.393537 CTGTGCTTGATCCCAGGGTC 60.394 60.000 5.01 3.16 0.00 4.46
502 508 6.005823 TCCTATTCTGGTGCATTTGATATGG 58.994 40.000 0.00 0.00 0.00 2.74
503 509 4.595762 ATTCTGGTGCATTTGATATGGC 57.404 40.909 0.00 0.00 0.00 4.40
550 556 5.803020 ATCTGGTCGCTTAGTTTTGAATC 57.197 39.130 0.00 0.00 0.00 2.52
606 612 7.041098 GCTGATGGACCCAATTAATGTTACTAG 60.041 40.741 0.00 0.00 0.00 2.57
630 637 6.431234 AGAAAATTGTCTGAGCGGTCTAATTT 59.569 34.615 16.64 17.42 0.00 1.82
713 720 9.923143 AGGCATTAATAAAAGTACAAGTTTTCC 57.077 29.630 0.00 0.00 33.25 3.13
714 721 8.856247 GGCATTAATAAAAGTACAAGTTTTCCG 58.144 33.333 0.00 0.00 33.25 4.30
783 790 1.467713 GCAGCTGAGCAAGAAATCTGC 60.468 52.381 20.43 0.58 39.78 4.26
800 807 8.306761 AGAAATCTGCGGTTTTCATTTTATTCT 58.693 29.630 24.26 4.35 35.04 2.40
834 841 7.521099 GCTTGTCAATATCTGGGTATGTTCATG 60.521 40.741 0.00 0.00 0.00 3.07
886 893 1.271856 TCGCAACCATGACTTAGGGA 58.728 50.000 0.00 0.00 33.45 4.20
894 901 4.389374 ACCATGACTTAGGGAATAATGCG 58.611 43.478 0.00 0.00 33.45 4.73
1473 1589 5.346822 GTGCAGTGAATGACCAATGAAAATC 59.653 40.000 0.00 0.00 34.40 2.17
1557 1680 2.158623 ACTCAGGAATGGTGCACAGAAA 60.159 45.455 20.43 0.80 0.00 2.52
1886 2009 7.014038 AGTGAGAATATCATTTGGAAGGCATTC 59.986 37.037 1.60 1.60 40.92 2.67
2084 2207 2.038387 TCTATTTCCAAGGCTTCCGC 57.962 50.000 0.00 0.00 0.00 5.54
2159 2282 5.123979 CCCAATTAAGCTGTTCTACACTTCC 59.876 44.000 0.00 0.00 0.00 3.46
2189 2312 0.694771 TCATTCTGCACTCTGCCCTT 59.305 50.000 0.00 0.00 44.23 3.95
2241 2378 1.474143 GGGCTGCAGTTCCAGATCTAC 60.474 57.143 16.64 0.00 34.77 2.59
2243 2380 2.548875 GCTGCAGTTCCAGATCTACAG 58.451 52.381 16.64 2.74 34.77 2.74
2245 2382 3.618507 GCTGCAGTTCCAGATCTACAGTT 60.619 47.826 16.64 0.00 34.77 3.16
2246 2383 4.180057 CTGCAGTTCCAGATCTACAGTTC 58.820 47.826 5.25 0.00 34.77 3.01
2248 2385 3.055819 GCAGTTCCAGATCTACAGTTCCA 60.056 47.826 0.00 0.00 0.00 3.53
2249 2386 4.753233 CAGTTCCAGATCTACAGTTCCAG 58.247 47.826 0.00 0.00 0.00 3.86
2250 2387 4.464244 CAGTTCCAGATCTACAGTTCCAGA 59.536 45.833 0.00 0.00 0.00 3.86
2251 2388 5.128499 CAGTTCCAGATCTACAGTTCCAGAT 59.872 44.000 0.00 0.00 34.19 2.90
2252 2389 5.362430 AGTTCCAGATCTACAGTTCCAGATC 59.638 44.000 0.00 4.23 44.99 2.75
2262 2399 9.989296 ATCTACAGTTCCAGATCTATAATAGCT 57.011 33.333 0.00 0.00 0.00 3.32
2468 2617 8.273780 AGGTGAATATTGATTTCTTGTCACTC 57.726 34.615 0.00 0.00 0.00 3.51
2514 2665 8.331931 TCAGTATACTTACCCTTTGATGGAAT 57.668 34.615 1.56 0.00 0.00 3.01
2644 2842 0.099968 CATCAGCCAAGGATGTTGCG 59.900 55.000 4.07 0.00 37.85 4.85
2706 2904 4.991687 GTCCTGTCTGGTTACTCTTTCTTG 59.008 45.833 0.00 0.00 37.07 3.02
2728 2926 7.922811 TCTTGTTACATATAGCATGTCTCACAG 59.077 37.037 0.00 0.00 33.76 3.66
2861 3089 4.736759 GCCATGCAATTTCATCTCTTCCAG 60.737 45.833 0.00 0.00 0.00 3.86
2862 3090 4.401519 CCATGCAATTTCATCTCTTCCAGT 59.598 41.667 0.00 0.00 0.00 4.00
2938 3498 7.327975 TGTTTCTAGAACTTGTTTGTCTCTCA 58.672 34.615 4.18 0.00 0.00 3.27
2989 3549 1.073897 GGCACCAGCAGTCCTTCTT 59.926 57.895 0.00 0.00 44.61 2.52
3006 3687 6.879458 GTCCTTCTTATGTGTAATGTGGAAGT 59.121 38.462 0.00 0.00 0.00 3.01
3026 3707 6.183360 GGAAGTGTTTAACTAGGATGACATGC 60.183 42.308 0.00 0.00 38.56 4.06
3093 3933 3.586470 TTGTAGGGTTCTTGGAAAGCA 57.414 42.857 0.00 0.00 45.70 3.91
3180 4388 5.279456 GGGGTGATTCATTAGCTGTTTTTGT 60.279 40.000 0.00 0.00 0.00 2.83
3373 4584 1.014044 TCGGCGCATTGACTGTTCTC 61.014 55.000 10.83 0.00 0.00 2.87
3566 4777 2.638556 TCTTTCTAGACAGTCGCAGC 57.361 50.000 5.82 0.00 0.00 5.25
3825 5036 4.142491 TGGTATATGTTTTTCTTGCCTGCG 60.142 41.667 0.00 0.00 0.00 5.18
3832 5043 1.172180 TTTCTTGCCTGCGACCCTTG 61.172 55.000 0.00 0.00 0.00 3.61
3843 5054 2.093658 TGCGACCCTTGTTAATCTCTCC 60.094 50.000 0.00 0.00 0.00 3.71
3872 5083 5.728351 TTCAACTGTCGAGTAGGTTTTTG 57.272 39.130 0.00 0.00 0.00 2.44
3883 5094 6.370994 TCGAGTAGGTTTTTGTGTGTTTTGTA 59.629 34.615 0.00 0.00 0.00 2.41
3884 5095 7.066043 TCGAGTAGGTTTTTGTGTGTTTTGTAT 59.934 33.333 0.00 0.00 0.00 2.29
3885 5096 7.698970 CGAGTAGGTTTTTGTGTGTTTTGTATT 59.301 33.333 0.00 0.00 0.00 1.89
3887 5098 9.791820 AGTAGGTTTTTGTGTGTTTTGTATTAC 57.208 29.630 0.00 0.00 0.00 1.89
3888 5099 9.022915 GTAGGTTTTTGTGTGTTTTGTATTACC 57.977 33.333 0.00 0.00 0.00 2.85
3889 5100 7.842982 AGGTTTTTGTGTGTTTTGTATTACCT 58.157 30.769 0.00 0.00 0.00 3.08
3890 5101 8.968969 AGGTTTTTGTGTGTTTTGTATTACCTA 58.031 29.630 0.00 0.00 0.00 3.08
3891 5102 9.752961 GGTTTTTGTGTGTTTTGTATTACCTAT 57.247 29.630 0.00 0.00 0.00 2.57
3895 5106 9.953697 TTTGTGTGTTTTGTATTACCTATGTTC 57.046 29.630 0.00 0.00 0.00 3.18
3896 5107 8.101654 TGTGTGTTTTGTATTACCTATGTTCC 57.898 34.615 0.00 0.00 0.00 3.62
3897 5108 7.940137 TGTGTGTTTTGTATTACCTATGTTCCT 59.060 33.333 0.00 0.00 0.00 3.36
3898 5109 8.234546 GTGTGTTTTGTATTACCTATGTTCCTG 58.765 37.037 0.00 0.00 0.00 3.86
3899 5110 8.158132 TGTGTTTTGTATTACCTATGTTCCTGA 58.842 33.333 0.00 0.00 0.00 3.86
3900 5111 9.005777 GTGTTTTGTATTACCTATGTTCCTGAA 57.994 33.333 0.00 0.00 0.00 3.02
3901 5112 9.747898 TGTTTTGTATTACCTATGTTCCTGAAT 57.252 29.630 0.00 0.00 0.00 2.57
3910 5121 7.598759 ACCTATGTTCCTGAATATAAGTCGT 57.401 36.000 0.00 0.00 0.00 4.34
3911 5122 8.019656 ACCTATGTTCCTGAATATAAGTCGTT 57.980 34.615 0.00 0.00 0.00 3.85
3912 5123 7.926555 ACCTATGTTCCTGAATATAAGTCGTTG 59.073 37.037 0.00 0.00 0.00 4.10
3913 5124 7.385205 CCTATGTTCCTGAATATAAGTCGTTGG 59.615 40.741 0.00 0.00 0.00 3.77
3914 5125 5.424757 TGTTCCTGAATATAAGTCGTTGGG 58.575 41.667 0.00 0.00 0.00 4.12
3915 5126 4.682778 TCCTGAATATAAGTCGTTGGGG 57.317 45.455 0.00 0.00 0.00 4.96
3916 5127 3.389983 TCCTGAATATAAGTCGTTGGGGG 59.610 47.826 0.00 0.00 0.00 5.40
3917 5128 3.389983 CCTGAATATAAGTCGTTGGGGGA 59.610 47.826 0.00 0.00 0.00 4.81
3918 5129 4.503296 CCTGAATATAAGTCGTTGGGGGAG 60.503 50.000 0.00 0.00 0.00 4.30
3919 5130 4.035112 TGAATATAAGTCGTTGGGGGAGT 58.965 43.478 0.00 0.00 0.00 3.85
3920 5131 4.472108 TGAATATAAGTCGTTGGGGGAGTT 59.528 41.667 0.00 0.00 0.00 3.01
3921 5132 4.684484 ATATAAGTCGTTGGGGGAGTTC 57.316 45.455 0.00 0.00 0.00 3.01
3922 5133 1.719529 TAAGTCGTTGGGGGAGTTCA 58.280 50.000 0.00 0.00 0.00 3.18
3923 5134 0.396811 AAGTCGTTGGGGGAGTTCAG 59.603 55.000 0.00 0.00 0.00 3.02
3924 5135 0.763223 AGTCGTTGGGGGAGTTCAGT 60.763 55.000 0.00 0.00 0.00 3.41
3925 5136 0.108019 GTCGTTGGGGGAGTTCAGTT 59.892 55.000 0.00 0.00 0.00 3.16
3926 5137 0.841289 TCGTTGGGGGAGTTCAGTTT 59.159 50.000 0.00 0.00 0.00 2.66
3927 5138 1.213430 TCGTTGGGGGAGTTCAGTTTT 59.787 47.619 0.00 0.00 0.00 2.43
3928 5139 2.438763 TCGTTGGGGGAGTTCAGTTTTA 59.561 45.455 0.00 0.00 0.00 1.52
3929 5140 2.551032 CGTTGGGGGAGTTCAGTTTTAC 59.449 50.000 0.00 0.00 0.00 2.01
3930 5141 3.558033 GTTGGGGGAGTTCAGTTTTACA 58.442 45.455 0.00 0.00 0.00 2.41
3931 5142 3.217681 TGGGGGAGTTCAGTTTTACAC 57.782 47.619 0.00 0.00 0.00 2.90
3932 5143 2.781174 TGGGGGAGTTCAGTTTTACACT 59.219 45.455 0.00 0.00 35.35 3.55
3933 5144 3.181448 TGGGGGAGTTCAGTTTTACACTC 60.181 47.826 0.00 0.00 35.82 3.51
3936 5147 3.409570 GGAGTTCAGTTTTACACTCCCC 58.590 50.000 5.99 0.00 46.76 4.81
3937 5148 3.181448 GGAGTTCAGTTTTACACTCCCCA 60.181 47.826 5.99 0.00 46.76 4.96
3938 5149 4.457466 GAGTTCAGTTTTACACTCCCCAA 58.543 43.478 0.00 0.00 30.92 4.12
3939 5150 4.204799 AGTTCAGTTTTACACTCCCCAAC 58.795 43.478 0.00 0.00 30.92 3.77
3940 5151 2.841215 TCAGTTTTACACTCCCCAACG 58.159 47.619 0.00 0.00 30.92 4.10
3941 5152 2.435069 TCAGTTTTACACTCCCCAACGA 59.565 45.455 0.00 0.00 30.92 3.85
3942 5153 2.546789 CAGTTTTACACTCCCCAACGAC 59.453 50.000 0.00 0.00 30.92 4.34
3943 5154 2.436911 AGTTTTACACTCCCCAACGACT 59.563 45.455 0.00 0.00 0.00 4.18
3944 5155 3.118149 AGTTTTACACTCCCCAACGACTT 60.118 43.478 0.00 0.00 0.00 3.01
3945 5156 4.101430 AGTTTTACACTCCCCAACGACTTA 59.899 41.667 0.00 0.00 0.00 2.24
3946 5157 4.895668 TTTACACTCCCCAACGACTTAT 57.104 40.909 0.00 0.00 0.00 1.73
3947 5158 5.999205 TTTACACTCCCCAACGACTTATA 57.001 39.130 0.00 0.00 0.00 0.98
3948 5159 6.549433 TTTACACTCCCCAACGACTTATAT 57.451 37.500 0.00 0.00 0.00 0.86
3949 5160 6.549433 TTACACTCCCCAACGACTTATATT 57.451 37.500 0.00 0.00 0.00 1.28
3950 5161 5.431179 ACACTCCCCAACGACTTATATTT 57.569 39.130 0.00 0.00 0.00 1.40
3951 5162 6.549433 ACACTCCCCAACGACTTATATTTA 57.451 37.500 0.00 0.00 0.00 1.40
3952 5163 6.579865 ACACTCCCCAACGACTTATATTTAG 58.420 40.000 0.00 0.00 0.00 1.85
3953 5164 5.989777 CACTCCCCAACGACTTATATTTAGG 59.010 44.000 0.00 0.00 0.00 2.69
3954 5165 5.901276 ACTCCCCAACGACTTATATTTAGGA 59.099 40.000 0.00 0.00 0.00 2.94
3955 5166 6.384886 ACTCCCCAACGACTTATATTTAGGAA 59.615 38.462 0.00 0.00 0.00 3.36
3956 5167 6.585416 TCCCCAACGACTTATATTTAGGAAC 58.415 40.000 0.00 0.00 0.00 3.62
3957 5168 5.464389 CCCCAACGACTTATATTTAGGAACG 59.536 44.000 0.00 0.00 0.00 3.95
3958 5169 5.464389 CCCAACGACTTATATTTAGGAACGG 59.536 44.000 0.00 0.00 0.00 4.44
3959 5170 6.275335 CCAACGACTTATATTTAGGAACGGA 58.725 40.000 0.00 0.00 0.00 4.69
3960 5171 6.420008 CCAACGACTTATATTTAGGAACGGAG 59.580 42.308 0.00 0.00 0.00 4.63
3961 5172 6.081872 ACGACTTATATTTAGGAACGGAGG 57.918 41.667 0.00 0.00 0.00 4.30
3962 5173 5.010415 ACGACTTATATTTAGGAACGGAGGG 59.990 44.000 0.00 0.00 0.00 4.30
3963 5174 5.242393 CGACTTATATTTAGGAACGGAGGGA 59.758 44.000 0.00 0.00 0.00 4.20
3964 5175 6.569994 CGACTTATATTTAGGAACGGAGGGAG 60.570 46.154 0.00 0.00 0.00 4.30
3965 5176 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
3999 5213 3.904717 CCTGACCCAGTCTCATAGTACT 58.095 50.000 0.00 0.00 33.15 2.73
4004 5218 2.292016 CCCAGTCTCATAGTACTCTGCG 59.708 54.545 0.00 0.00 0.00 5.18
4071 5287 1.347707 TGAGGTGAACGAATTCTGGCT 59.652 47.619 3.52 0.00 35.69 4.75
4112 5362 5.528870 GTGTGGACGGAAGAAATGAAAAAT 58.471 37.500 0.00 0.00 0.00 1.82
4123 5373 8.576442 GGAAGAAATGAAAAATCCTTGTGTAGA 58.424 33.333 0.00 0.00 0.00 2.59
4175 5427 8.959734 AACAGACTAAATACATTTAAAACGCC 57.040 30.769 0.00 0.00 32.39 5.68
4182 5434 1.067915 ACATTTAAAACGCCGCTGCAT 60.068 42.857 0.00 0.00 37.32 3.96
4229 5485 2.131183 GATCGAGCAAAGGAAGATCGG 58.869 52.381 0.00 0.00 44.24 4.18
4260 5516 7.395206 TGATGCCATCCTATTTTATTCCATCTG 59.605 37.037 1.49 0.00 0.00 2.90
4293 5549 7.889589 AAAAGCTATAACTTTTGAACCATGC 57.110 32.000 12.04 0.00 45.68 4.06
4294 5550 6.588719 AAGCTATAACTTTTGAACCATGCA 57.411 33.333 0.00 0.00 0.00 3.96
4295 5551 6.780457 AGCTATAACTTTTGAACCATGCAT 57.220 33.333 0.00 0.00 0.00 3.96
4296 5552 7.880160 AGCTATAACTTTTGAACCATGCATA 57.120 32.000 0.00 0.00 0.00 3.14
4306 5562 3.010027 TGAACCATGCATAGTCCCTTTGA 59.990 43.478 0.00 0.00 0.00 2.69
4308 5564 3.825328 ACCATGCATAGTCCCTTTGATC 58.175 45.455 0.00 0.00 0.00 2.92
4309 5565 3.202818 ACCATGCATAGTCCCTTTGATCA 59.797 43.478 0.00 0.00 0.00 2.92
4362 5618 8.982685 CAACTATGGAGTATATGTTGTGATGAC 58.017 37.037 0.00 0.00 33.58 3.06
4402 5658 0.246635 ATGCCTTCTTGCGTCGTACT 59.753 50.000 0.00 0.00 0.00 2.73
4403 5659 0.032952 TGCCTTCTTGCGTCGTACTT 59.967 50.000 0.00 0.00 0.00 2.24
4404 5660 0.438830 GCCTTCTTGCGTCGTACTTG 59.561 55.000 0.00 0.00 0.00 3.16
4405 5661 1.779569 CCTTCTTGCGTCGTACTTGT 58.220 50.000 0.00 0.00 0.00 3.16
4406 5662 1.455786 CCTTCTTGCGTCGTACTTGTG 59.544 52.381 0.00 0.00 0.00 3.33
4407 5663 1.455786 CTTCTTGCGTCGTACTTGTGG 59.544 52.381 0.00 0.00 0.00 4.17
4408 5664 0.319211 TCTTGCGTCGTACTTGTGGG 60.319 55.000 0.00 0.00 0.00 4.61
4409 5665 1.289109 CTTGCGTCGTACTTGTGGGG 61.289 60.000 0.00 0.00 0.00 4.96
4410 5666 2.433664 GCGTCGTACTTGTGGGGG 60.434 66.667 0.00 0.00 0.00 5.40
4411 5667 2.934570 GCGTCGTACTTGTGGGGGA 61.935 63.158 0.00 0.00 0.00 4.81
4412 5668 1.895238 CGTCGTACTTGTGGGGGAT 59.105 57.895 0.00 0.00 0.00 3.85
4413 5669 0.459585 CGTCGTACTTGTGGGGGATG 60.460 60.000 0.00 0.00 0.00 3.51
4414 5670 0.899720 GTCGTACTTGTGGGGGATGA 59.100 55.000 0.00 0.00 0.00 2.92
4415 5671 0.899720 TCGTACTTGTGGGGGATGAC 59.100 55.000 0.00 0.00 0.00 3.06
4416 5672 0.107848 CGTACTTGTGGGGGATGACC 60.108 60.000 0.00 0.00 39.11 4.02
4417 5673 0.988832 GTACTTGTGGGGGATGACCA 59.011 55.000 0.00 0.00 42.91 4.02
4429 5685 4.277009 TGACCACCGGGCATGCAA 62.277 61.111 21.36 0.00 34.69 4.08
4430 5686 2.988684 GACCACCGGGCATGCAAA 60.989 61.111 21.36 0.00 37.90 3.68
4431 5687 2.990967 ACCACCGGGCATGCAAAG 60.991 61.111 21.36 9.29 37.90 2.77
4432 5688 3.762247 CCACCGGGCATGCAAAGG 61.762 66.667 21.36 20.26 0.00 3.11
4433 5689 2.676121 CACCGGGCATGCAAAGGA 60.676 61.111 25.45 0.00 0.00 3.36
4434 5690 2.117206 ACCGGGCATGCAAAGGAA 59.883 55.556 25.45 0.00 0.00 3.36
4435 5691 2.275380 ACCGGGCATGCAAAGGAAC 61.275 57.895 25.45 5.90 0.00 3.62
4436 5692 2.573340 CGGGCATGCAAAGGAACC 59.427 61.111 21.36 8.45 0.00 3.62
4437 5693 2.981302 GGGCATGCAAAGGAACCC 59.019 61.111 21.36 4.69 0.00 4.11
4438 5694 2.573340 GGCATGCAAAGGAACCCG 59.427 61.111 21.36 0.00 0.00 5.28
4439 5695 2.573340 GCATGCAAAGGAACCCGG 59.427 61.111 14.21 0.00 0.00 5.73
4440 5696 1.976474 GCATGCAAAGGAACCCGGA 60.976 57.895 14.21 0.00 0.00 5.14
4441 5697 1.322538 GCATGCAAAGGAACCCGGAT 61.323 55.000 14.21 0.00 0.00 4.18
4442 5698 0.740737 CATGCAAAGGAACCCGGATC 59.259 55.000 0.73 0.00 0.00 3.36
4443 5699 0.395724 ATGCAAAGGAACCCGGATCC 60.396 55.000 16.17 16.17 37.22 3.36
4444 5700 1.001393 GCAAAGGAACCCGGATCCA 60.001 57.895 23.26 0.00 39.55 3.41
4445 5701 0.395724 GCAAAGGAACCCGGATCCAT 60.396 55.000 23.26 12.34 39.55 3.41
4446 5702 1.959989 GCAAAGGAACCCGGATCCATT 60.960 52.381 23.26 16.76 39.55 3.16
4447 5703 2.456577 CAAAGGAACCCGGATCCATTT 58.543 47.619 23.26 17.50 39.55 2.32
4448 5704 2.427095 CAAAGGAACCCGGATCCATTTC 59.573 50.000 23.26 10.18 39.55 2.17
4449 5705 1.295020 AGGAACCCGGATCCATTTCA 58.705 50.000 23.26 0.00 39.55 2.69
4450 5706 1.638589 AGGAACCCGGATCCATTTCAA 59.361 47.619 23.26 0.00 39.55 2.69
4451 5707 2.042433 AGGAACCCGGATCCATTTCAAA 59.958 45.455 23.26 0.00 39.55 2.69
4452 5708 2.829120 GGAACCCGGATCCATTTCAAAA 59.171 45.455 18.31 0.00 36.92 2.44
4453 5709 3.259625 GGAACCCGGATCCATTTCAAAAA 59.740 43.478 18.31 0.00 36.92 1.94
4454 5710 4.081142 GGAACCCGGATCCATTTCAAAAAT 60.081 41.667 18.31 0.00 36.92 1.82
4455 5711 5.128008 GGAACCCGGATCCATTTCAAAAATA 59.872 40.000 18.31 0.00 36.92 1.40
4456 5712 6.183360 GGAACCCGGATCCATTTCAAAAATAT 60.183 38.462 18.31 0.00 36.92 1.28
4457 5713 6.806668 ACCCGGATCCATTTCAAAAATATT 57.193 33.333 13.41 0.00 0.00 1.28
4458 5714 6.581712 ACCCGGATCCATTTCAAAAATATTG 58.418 36.000 13.41 0.00 0.00 1.90
4459 5715 5.990996 CCCGGATCCATTTCAAAAATATTGG 59.009 40.000 13.41 0.00 0.00 3.16
4460 5716 5.990996 CCGGATCCATTTCAAAAATATTGGG 59.009 40.000 13.41 0.00 0.00 4.12
4461 5717 6.183360 CCGGATCCATTTCAAAAATATTGGGA 60.183 38.462 13.41 0.00 0.00 4.37
4462 5718 6.701400 CGGATCCATTTCAAAAATATTGGGAC 59.299 38.462 13.41 0.00 0.00 4.46
4463 5719 6.992123 GGATCCATTTCAAAAATATTGGGACC 59.008 38.462 6.95 0.00 0.00 4.46
4464 5720 5.971763 TCCATTTCAAAAATATTGGGACCG 58.028 37.500 0.00 0.00 0.00 4.79
4465 5721 5.105146 TCCATTTCAAAAATATTGGGACCGG 60.105 40.000 0.00 0.00 0.00 5.28
4466 5722 3.878160 TTCAAAAATATTGGGACCGGC 57.122 42.857 0.00 0.00 0.00 6.13
4467 5723 1.746220 TCAAAAATATTGGGACCGGCG 59.254 47.619 0.00 0.00 0.00 6.46
4468 5724 1.474879 CAAAAATATTGGGACCGGCGT 59.525 47.619 6.01 0.00 0.00 5.68
4469 5725 1.385528 AAAATATTGGGACCGGCGTC 58.614 50.000 6.01 3.39 38.38 5.19
4470 5726 0.812412 AAATATTGGGACCGGCGTCG 60.812 55.000 0.29 0.29 40.17 5.12
4481 5737 2.188469 GGCGTCGCCCCTCAATTA 59.812 61.111 26.23 0.00 44.06 1.40
4482 5738 1.887707 GGCGTCGCCCCTCAATTAG 60.888 63.158 26.23 0.00 44.06 1.73
4483 5739 1.887707 GCGTCGCCCCTCAATTAGG 60.888 63.158 5.75 0.00 46.09 2.69
4484 5740 1.887707 CGTCGCCCCTCAATTAGGC 60.888 63.158 0.00 0.00 45.03 3.93
4485 5741 1.527370 GTCGCCCCTCAATTAGGCT 59.473 57.895 0.00 0.00 45.03 4.58
4486 5742 0.533085 GTCGCCCCTCAATTAGGCTC 60.533 60.000 0.00 0.00 45.03 4.70
4487 5743 1.595382 CGCCCCTCAATTAGGCTCG 60.595 63.158 0.00 0.00 45.03 5.03
4488 5744 1.527370 GCCCCTCAATTAGGCTCGT 59.473 57.895 0.00 0.00 45.03 4.18
4489 5745 0.533085 GCCCCTCAATTAGGCTCGTC 60.533 60.000 0.00 0.00 45.03 4.20
4490 5746 0.106894 CCCCTCAATTAGGCTCGTCC 59.893 60.000 0.00 0.00 45.03 4.79
4492 5748 1.486726 CCCTCAATTAGGCTCGTCCTT 59.513 52.381 0.00 0.00 44.75 3.36
4493 5749 2.555199 CCTCAATTAGGCTCGTCCTTG 58.445 52.381 0.00 0.00 44.75 3.61
4494 5750 2.555199 CTCAATTAGGCTCGTCCTTGG 58.445 52.381 0.00 0.00 44.75 3.61
4495 5751 1.017387 CAATTAGGCTCGTCCTTGGC 58.983 55.000 0.00 0.00 44.75 4.52
4496 5752 0.107165 AATTAGGCTCGTCCTTGGCC 60.107 55.000 0.00 0.00 44.75 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.308481 TAGGAGGGGAGGACGGAGA 60.308 63.158 0.00 0.00 0.00 3.71
96 97 4.929707 GCGGGATTACCTGGCCGG 62.930 72.222 3.88 3.88 42.48 6.13
131 132 2.983930 GATCGCCTCGAGATCCGGG 61.984 68.421 15.71 5.54 39.91 5.73
256 258 1.072391 GTCGACACACACACACACAA 58.928 50.000 11.55 0.00 0.00 3.33
270 272 2.659291 GCATGAACAAACACGAGTCGAC 60.659 50.000 21.50 7.70 0.00 4.20
275 277 0.725784 GCCGCATGAACAAACACGAG 60.726 55.000 0.00 0.00 0.00 4.18
310 315 0.395311 TGGACGCCTCACCTACCTAG 60.395 60.000 0.00 0.00 0.00 3.02
411 416 1.820877 GCCAGGACATCATTCCCATCC 60.821 57.143 0.00 0.00 36.12 3.51
469 474 2.416547 CACCAGAATAGGAAACTGTGCG 59.583 50.000 0.00 0.00 43.88 5.34
511 517 1.211457 AGATAGCTGCCCCAACTCTTG 59.789 52.381 0.00 0.00 0.00 3.02
515 521 0.916358 ACCAGATAGCTGCCCCAACT 60.916 55.000 1.39 0.00 40.91 3.16
550 556 1.523095 GGAGCAATTTAGCTAGCGTCG 59.477 52.381 9.55 0.00 46.75 5.12
606 612 5.803020 ATTAGACCGCTCAGACAATTTTC 57.197 39.130 0.00 0.00 0.00 2.29
630 637 2.169769 CGGCCTATCCAGAAAGTAACCA 59.830 50.000 0.00 0.00 34.01 3.67
667 674 4.318332 CCTGACAGCTACAATTCTGTTCA 58.682 43.478 0.00 0.26 42.97 3.18
712 719 6.736807 CACATATGCATCACAATTAAACGG 57.263 37.500 0.19 0.00 0.00 4.44
783 790 8.003784 GCAGACAAAAGAATAAAATGAAAACCG 58.996 33.333 0.00 0.00 0.00 4.44
800 807 5.183713 CCCAGATATTGACAAGCAGACAAAA 59.816 40.000 0.00 0.00 35.63 2.44
834 841 3.733443 ACCAATTTGGCTGAAACAGAC 57.267 42.857 15.49 0.00 42.67 3.51
886 893 4.050553 CAATTCCCATTTCGCGCATTATT 58.949 39.130 8.75 0.00 0.00 1.40
894 901 1.202114 TCACAGCAATTCCCATTTCGC 59.798 47.619 0.00 0.00 0.00 4.70
1473 1589 7.910162 ACAACATATGAATAAGCAAGCTTTACG 59.090 33.333 13.06 0.00 37.47 3.18
1557 1680 2.590821 GCAATCAGGATACCCAGCAAT 58.409 47.619 0.00 0.00 33.88 3.56
1886 2009 0.327924 TGTTGATGGTGGTAGGGCTG 59.672 55.000 0.00 0.00 0.00 4.85
2084 2207 0.532862 ACCTCACTGGAAGCACAACG 60.533 55.000 0.00 0.00 37.60 4.10
2159 2282 1.478916 TGCAGAATGATGGGCATGTTG 59.521 47.619 0.00 0.00 39.69 3.33
2189 2312 8.950480 TGGGATATGAAATACAGGTTGGTAATA 58.050 33.333 0.00 0.00 0.00 0.98
2226 2363 3.055819 TGGAACTGTAGATCTGGAACTGC 60.056 47.826 5.18 0.00 0.00 4.40
2243 2380 9.649316 ACCCTATAGCTATTATAGATCTGGAAC 57.351 37.037 12.39 0.00 42.58 3.62
2245 2382 9.015146 TCACCCTATAGCTATTATAGATCTGGA 57.985 37.037 12.39 0.00 42.58 3.86
2246 2383 9.295825 CTCACCCTATAGCTATTATAGATCTGG 57.704 40.741 12.39 2.97 42.58 3.86
2248 2385 8.506921 TGCTCACCCTATAGCTATTATAGATCT 58.493 37.037 12.39 0.00 42.58 2.75
2249 2386 8.698973 TGCTCACCCTATAGCTATTATAGATC 57.301 38.462 12.39 1.49 42.58 2.75
2250 2387 9.667607 AATGCTCACCCTATAGCTATTATAGAT 57.332 33.333 12.39 0.00 42.58 1.98
2251 2388 9.494055 AAATGCTCACCCTATAGCTATTATAGA 57.506 33.333 12.39 3.82 42.58 1.98
2252 2389 9.539825 CAAATGCTCACCCTATAGCTATTATAG 57.460 37.037 12.39 3.20 40.58 1.31
2253 2390 7.987458 GCAAATGCTCACCCTATAGCTATTATA 59.013 37.037 12.39 0.00 39.53 0.98
2254 2391 6.825721 GCAAATGCTCACCCTATAGCTATTAT 59.174 38.462 12.39 0.00 39.53 1.28
2255 2392 6.173339 GCAAATGCTCACCCTATAGCTATTA 58.827 40.000 12.39 0.00 39.53 0.98
2256 2393 5.006386 GCAAATGCTCACCCTATAGCTATT 58.994 41.667 12.39 0.00 39.53 1.73
2257 2394 4.042062 TGCAAATGCTCACCCTATAGCTAT 59.958 41.667 11.77 11.77 42.66 2.97
2258 2395 3.390967 TGCAAATGCTCACCCTATAGCTA 59.609 43.478 6.97 0.00 42.66 3.32
2259 2396 2.173356 TGCAAATGCTCACCCTATAGCT 59.827 45.455 6.97 0.00 42.66 3.32
2260 2397 2.575532 TGCAAATGCTCACCCTATAGC 58.424 47.619 6.97 0.00 42.66 2.97
2261 2398 3.057736 GCATGCAAATGCTCACCCTATAG 60.058 47.826 14.21 0.00 43.79 1.31
2262 2399 2.886523 GCATGCAAATGCTCACCCTATA 59.113 45.455 14.21 0.00 43.79 1.31
2263 2400 1.684983 GCATGCAAATGCTCACCCTAT 59.315 47.619 14.21 0.00 43.79 2.57
2468 2617 8.608844 ACTGAACAGTATTTTCTTGACTAAGG 57.391 34.615 5.62 0.00 40.43 2.69
2514 2665 4.262765 CCAGAATATCAGCCATACTGCAGA 60.263 45.833 23.35 4.31 46.76 4.26
2644 2842 2.096218 CGTTTGTACCTTCAGCTGCTTC 60.096 50.000 9.47 0.00 0.00 3.86
2686 2884 6.984474 TGTAACAAGAAAGAGTAACCAGACAG 59.016 38.462 0.00 0.00 0.00 3.51
2706 2904 6.219473 AGCTGTGAGACATGCTATATGTAAC 58.781 40.000 0.00 0.00 33.20 2.50
2728 2926 8.445493 CAAATCAATATTTTCCACAAAAGGAGC 58.555 33.333 0.00 0.00 39.25 4.70
2759 2957 3.002791 CCACGTGAAAGCAGTCACATAT 58.997 45.455 19.30 2.65 46.90 1.78
2765 2993 0.034337 TACCCCACGTGAAAGCAGTC 59.966 55.000 19.30 0.00 0.00 3.51
2766 2994 0.250166 GTACCCCACGTGAAAGCAGT 60.250 55.000 19.30 7.18 0.00 4.40
2770 2998 1.519408 CTTGGTACCCCACGTGAAAG 58.481 55.000 19.30 7.53 41.67 2.62
2780 3008 2.092323 GAATTGGACAGCTTGGTACCC 58.908 52.381 10.07 0.00 0.00 3.69
2814 3042 6.212955 CCGTTTGTACAAATCTTTGGTGATT 58.787 36.000 23.11 0.00 42.34 2.57
2862 3090 9.238368 CCTATACCAAAACAATTGAGGTTTAGA 57.762 33.333 24.29 11.39 37.47 2.10
2938 3498 9.866655 TCAGGCTGGATTTTATAAACATCTTAT 57.133 29.630 15.73 0.00 0.00 1.73
2941 3501 7.781693 ACATCAGGCTGGATTTTATAAACATCT 59.218 33.333 15.73 0.00 0.00 2.90
2987 3547 9.607285 GTTAAACACTTCCACATTACACATAAG 57.393 33.333 0.00 0.00 0.00 1.73
2989 3549 8.911918 AGTTAAACACTTCCACATTACACATA 57.088 30.769 0.00 0.00 27.32 2.29
3026 3707 8.890718 ACAGATAATGATGATGTTTTCTGACAG 58.109 33.333 10.88 0.00 37.08 3.51
3180 4388 7.027161 GTCTTTGCAAGTTGAAACTAAGTCAA 58.973 34.615 7.16 0.00 38.57 3.18
3565 4776 4.052229 CAGCCAGCCAAGCAGTGC 62.052 66.667 7.13 7.13 0.00 4.40
3566 4777 3.371063 CCAGCCAGCCAAGCAGTG 61.371 66.667 0.00 0.00 0.00 3.66
3825 5036 4.674281 ATCGGAGAGATTAACAAGGGTC 57.326 45.455 0.00 0.00 43.63 4.46
3832 5043 7.760340 ACAGTTGAAAGTATCGGAGAGATTAAC 59.240 37.037 0.00 0.00 43.63 2.01
3843 5054 5.029014 CCTACTCGACAGTTGAAAGTATCG 58.971 45.833 0.00 0.00 33.62 2.92
3872 5083 8.234546 CAGGAACATAGGTAATACAAAACACAC 58.765 37.037 0.00 0.00 0.00 3.82
3884 5095 9.139734 ACGACTTATATTCAGGAACATAGGTAA 57.860 33.333 0.00 0.00 0.00 2.85
3885 5096 8.701908 ACGACTTATATTCAGGAACATAGGTA 57.298 34.615 0.00 0.00 0.00 3.08
3886 5097 7.598759 ACGACTTATATTCAGGAACATAGGT 57.401 36.000 0.00 0.00 0.00 3.08
3887 5098 7.385205 CCAACGACTTATATTCAGGAACATAGG 59.615 40.741 0.00 0.00 0.00 2.57
3888 5099 7.385205 CCCAACGACTTATATTCAGGAACATAG 59.615 40.741 0.00 0.00 0.00 2.23
3889 5100 7.214381 CCCAACGACTTATATTCAGGAACATA 58.786 38.462 0.00 0.00 0.00 2.29
3890 5101 6.055588 CCCAACGACTTATATTCAGGAACAT 58.944 40.000 0.00 0.00 0.00 2.71
3891 5102 5.424757 CCCAACGACTTATATTCAGGAACA 58.575 41.667 0.00 0.00 0.00 3.18
3892 5103 4.814771 CCCCAACGACTTATATTCAGGAAC 59.185 45.833 0.00 0.00 0.00 3.62
3893 5104 4.141574 CCCCCAACGACTTATATTCAGGAA 60.142 45.833 0.00 0.00 0.00 3.36
3894 5105 3.389983 CCCCCAACGACTTATATTCAGGA 59.610 47.826 0.00 0.00 0.00 3.86
3895 5106 3.389983 TCCCCCAACGACTTATATTCAGG 59.610 47.826 0.00 0.00 0.00 3.86
3896 5107 4.101119 ACTCCCCCAACGACTTATATTCAG 59.899 45.833 0.00 0.00 0.00 3.02
3897 5108 4.035112 ACTCCCCCAACGACTTATATTCA 58.965 43.478 0.00 0.00 0.00 2.57
3898 5109 4.684484 ACTCCCCCAACGACTTATATTC 57.316 45.455 0.00 0.00 0.00 1.75
3899 5110 4.472108 TGAACTCCCCCAACGACTTATATT 59.528 41.667 0.00 0.00 0.00 1.28
3900 5111 4.035112 TGAACTCCCCCAACGACTTATAT 58.965 43.478 0.00 0.00 0.00 0.86
3901 5112 3.443052 TGAACTCCCCCAACGACTTATA 58.557 45.455 0.00 0.00 0.00 0.98
3902 5113 2.236395 CTGAACTCCCCCAACGACTTAT 59.764 50.000 0.00 0.00 0.00 1.73
3903 5114 1.621814 CTGAACTCCCCCAACGACTTA 59.378 52.381 0.00 0.00 0.00 2.24
3904 5115 0.396811 CTGAACTCCCCCAACGACTT 59.603 55.000 0.00 0.00 0.00 3.01
3905 5116 0.763223 ACTGAACTCCCCCAACGACT 60.763 55.000 0.00 0.00 0.00 4.18
3906 5117 0.108019 AACTGAACTCCCCCAACGAC 59.892 55.000 0.00 0.00 0.00 4.34
3907 5118 0.841289 AAACTGAACTCCCCCAACGA 59.159 50.000 0.00 0.00 0.00 3.85
3908 5119 1.687563 AAAACTGAACTCCCCCAACG 58.312 50.000 0.00 0.00 0.00 4.10
3909 5120 3.317149 GTGTAAAACTGAACTCCCCCAAC 59.683 47.826 0.00 0.00 0.00 3.77
3910 5121 3.203487 AGTGTAAAACTGAACTCCCCCAA 59.797 43.478 0.00 0.00 37.88 4.12
3911 5122 2.781174 AGTGTAAAACTGAACTCCCCCA 59.219 45.455 0.00 0.00 37.88 4.96
3912 5123 3.409570 GAGTGTAAAACTGAACTCCCCC 58.590 50.000 0.00 0.00 40.07 5.40
3916 5127 4.081322 TGGGGAGTGTAAAACTGAACTC 57.919 45.455 0.00 0.00 40.07 3.01
3917 5128 4.204799 GTTGGGGAGTGTAAAACTGAACT 58.795 43.478 0.00 0.00 40.07 3.01
3918 5129 3.002965 CGTTGGGGAGTGTAAAACTGAAC 59.997 47.826 0.00 0.00 40.07 3.18
3919 5130 3.118334 TCGTTGGGGAGTGTAAAACTGAA 60.118 43.478 0.00 0.00 40.07 3.02
3920 5131 2.435069 TCGTTGGGGAGTGTAAAACTGA 59.565 45.455 0.00 0.00 40.07 3.41
3921 5132 2.546789 GTCGTTGGGGAGTGTAAAACTG 59.453 50.000 0.00 0.00 40.07 3.16
3922 5133 2.436911 AGTCGTTGGGGAGTGTAAAACT 59.563 45.455 0.00 0.00 43.85 2.66
3923 5134 2.842457 AGTCGTTGGGGAGTGTAAAAC 58.158 47.619 0.00 0.00 0.00 2.43
3924 5135 3.564053 AAGTCGTTGGGGAGTGTAAAA 57.436 42.857 0.00 0.00 0.00 1.52
3925 5136 4.895668 ATAAGTCGTTGGGGAGTGTAAA 57.104 40.909 0.00 0.00 0.00 2.01
3926 5137 6.549433 AATATAAGTCGTTGGGGAGTGTAA 57.451 37.500 0.00 0.00 0.00 2.41
3927 5138 6.549433 AAATATAAGTCGTTGGGGAGTGTA 57.451 37.500 0.00 0.00 0.00 2.90
3928 5139 5.431179 AAATATAAGTCGTTGGGGAGTGT 57.569 39.130 0.00 0.00 0.00 3.55
3929 5140 5.989777 CCTAAATATAAGTCGTTGGGGAGTG 59.010 44.000 0.00 0.00 0.00 3.51
3930 5141 5.901276 TCCTAAATATAAGTCGTTGGGGAGT 59.099 40.000 0.00 0.00 0.00 3.85
3931 5142 6.415206 TCCTAAATATAAGTCGTTGGGGAG 57.585 41.667 0.00 0.00 0.00 4.30
3932 5143 6.585416 GTTCCTAAATATAAGTCGTTGGGGA 58.415 40.000 0.00 0.00 0.00 4.81
3933 5144 5.464389 CGTTCCTAAATATAAGTCGTTGGGG 59.536 44.000 0.00 0.00 0.00 4.96
3934 5145 5.464389 CCGTTCCTAAATATAAGTCGTTGGG 59.536 44.000 0.00 0.00 0.00 4.12
3935 5146 6.275335 TCCGTTCCTAAATATAAGTCGTTGG 58.725 40.000 0.00 0.00 0.00 3.77
3936 5147 6.420008 CCTCCGTTCCTAAATATAAGTCGTTG 59.580 42.308 0.00 0.00 0.00 4.10
3937 5148 6.462067 CCCTCCGTTCCTAAATATAAGTCGTT 60.462 42.308 0.00 0.00 0.00 3.85
3938 5149 5.010415 CCCTCCGTTCCTAAATATAAGTCGT 59.990 44.000 0.00 0.00 0.00 4.34
3939 5150 5.242393 TCCCTCCGTTCCTAAATATAAGTCG 59.758 44.000 0.00 0.00 0.00 4.18
3940 5151 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3941 5152 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3942 5153 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3943 5154 7.529555 TCTACTCCCTCCGTTCCTAAATATAA 58.470 38.462 0.00 0.00 0.00 0.98
3944 5155 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
3945 5156 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
3946 5157 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
3947 5158 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
3948 5159 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
3949 5160 3.245371 TGTTCTACTCCCTCCGTTCCTAA 60.245 47.826 0.00 0.00 0.00 2.69
3950 5161 2.309755 TGTTCTACTCCCTCCGTTCCTA 59.690 50.000 0.00 0.00 0.00 2.94
3951 5162 1.076677 TGTTCTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 0.00 3.36
3952 5163 1.553706 TGTTCTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
3953 5164 3.672767 TTTGTTCTACTCCCTCCGTTC 57.327 47.619 0.00 0.00 0.00 3.95
3954 5165 4.426736 TTTTTGTTCTACTCCCTCCGTT 57.573 40.909 0.00 0.00 0.00 4.44
3955 5166 4.324267 CATTTTTGTTCTACTCCCTCCGT 58.676 43.478 0.00 0.00 0.00 4.69
3956 5167 3.127030 GCATTTTTGTTCTACTCCCTCCG 59.873 47.826 0.00 0.00 0.00 4.63
3957 5168 3.444034 GGCATTTTTGTTCTACTCCCTCC 59.556 47.826 0.00 0.00 0.00 4.30
3958 5169 4.156739 CAGGCATTTTTGTTCTACTCCCTC 59.843 45.833 0.00 0.00 0.00 4.30
3959 5170 4.082125 CAGGCATTTTTGTTCTACTCCCT 58.918 43.478 0.00 0.00 0.00 4.20
3960 5171 4.079253 TCAGGCATTTTTGTTCTACTCCC 58.921 43.478 0.00 0.00 0.00 4.30
3961 5172 4.082733 GGTCAGGCATTTTTGTTCTACTCC 60.083 45.833 0.00 0.00 0.00 3.85
3962 5173 4.082733 GGGTCAGGCATTTTTGTTCTACTC 60.083 45.833 0.00 0.00 0.00 2.59
3963 5174 3.826729 GGGTCAGGCATTTTTGTTCTACT 59.173 43.478 0.00 0.00 0.00 2.57
3964 5175 3.572255 TGGGTCAGGCATTTTTGTTCTAC 59.428 43.478 0.00 0.00 0.00 2.59
3965 5176 3.826157 CTGGGTCAGGCATTTTTGTTCTA 59.174 43.478 0.00 0.00 0.00 2.10
4004 5218 3.182972 GCAAACTCATTCAACATGCACAC 59.817 43.478 0.00 0.00 32.80 3.82
4060 5276 0.443869 CGAACACCAGCCAGAATTCG 59.556 55.000 0.00 0.00 33.79 3.34
4071 5287 1.595328 CACGTCATCAAACGAACACCA 59.405 47.619 3.16 0.00 45.37 4.17
4152 5402 6.193959 GCGGCGTTTTAAATGTATTTAGTCTG 59.806 38.462 9.37 0.00 34.13 3.51
4175 5427 5.393124 TCACTTCTTTCAAATAATGCAGCG 58.607 37.500 0.00 0.00 0.00 5.18
4182 5434 4.274705 TGTGCGCTCACTTCTTTCAAATAA 59.725 37.500 9.73 0.00 43.49 1.40
4290 5546 9.986157 ATAATATTGATCAAAGGGACTATGCAT 57.014 29.630 13.09 3.79 38.49 3.96
4291 5547 9.812347 AATAATATTGATCAAAGGGACTATGCA 57.188 29.630 13.09 0.00 38.49 3.96
4295 5551 9.077885 GGCAAATAATATTGATCAAAGGGACTA 57.922 33.333 13.09 0.00 32.15 2.59
4296 5552 7.255590 CGGCAAATAATATTGATCAAAGGGACT 60.256 37.037 13.09 0.00 33.51 3.85
4362 5618 6.906678 GGCATCAAAGTTGCTTTTAAAACAAG 59.093 34.615 12.97 0.05 40.03 3.16
4408 5664 3.809013 ATGCCCGGTGGTCATCCC 61.809 66.667 0.00 0.00 0.00 3.85
4409 5665 2.516930 CATGCCCGGTGGTCATCC 60.517 66.667 0.00 0.00 0.00 3.51
4410 5666 3.211963 GCATGCCCGGTGGTCATC 61.212 66.667 6.36 0.00 0.00 2.92
4411 5667 3.582242 TTGCATGCCCGGTGGTCAT 62.582 57.895 16.68 0.00 0.00 3.06
4412 5668 3.799286 TTTGCATGCCCGGTGGTCA 62.799 57.895 16.68 0.00 0.00 4.02
4413 5669 2.988684 TTTGCATGCCCGGTGGTC 60.989 61.111 16.68 0.00 0.00 4.02
4414 5670 2.990967 CTTTGCATGCCCGGTGGT 60.991 61.111 16.68 0.00 0.00 4.16
4415 5671 3.762247 CCTTTGCATGCCCGGTGG 61.762 66.667 16.68 6.57 0.00 4.61
4416 5672 2.274645 TTCCTTTGCATGCCCGGTG 61.275 57.895 16.68 0.00 0.00 4.94
4417 5673 2.117206 TTCCTTTGCATGCCCGGT 59.883 55.556 16.68 0.00 0.00 5.28
4418 5674 2.573340 GTTCCTTTGCATGCCCGG 59.427 61.111 16.68 12.71 0.00 5.73
4419 5675 2.573340 GGTTCCTTTGCATGCCCG 59.427 61.111 16.68 2.97 0.00 6.13
4420 5676 2.981302 GGGTTCCTTTGCATGCCC 59.019 61.111 16.68 6.80 0.00 5.36
4421 5677 2.573340 CGGGTTCCTTTGCATGCC 59.427 61.111 16.68 0.00 0.00 4.40
4422 5678 1.322538 ATCCGGGTTCCTTTGCATGC 61.323 55.000 11.82 11.82 0.00 4.06
4423 5679 0.740737 GATCCGGGTTCCTTTGCATG 59.259 55.000 0.00 0.00 0.00 4.06
4424 5680 0.395724 GGATCCGGGTTCCTTTGCAT 60.396 55.000 15.57 0.00 0.00 3.96
4425 5681 1.001393 GGATCCGGGTTCCTTTGCA 60.001 57.895 15.57 0.00 0.00 4.08
4426 5682 0.395724 ATGGATCCGGGTTCCTTTGC 60.396 55.000 21.70 0.00 34.17 3.68
4427 5683 2.143876 AATGGATCCGGGTTCCTTTG 57.856 50.000 21.70 0.00 34.17 2.77
4428 5684 2.042433 TGAAATGGATCCGGGTTCCTTT 59.958 45.455 21.70 18.65 33.39 3.11
4429 5685 1.638589 TGAAATGGATCCGGGTTCCTT 59.361 47.619 21.70 14.42 34.17 3.36
4430 5686 1.295020 TGAAATGGATCCGGGTTCCT 58.705 50.000 21.70 5.10 34.17 3.36
4431 5687 2.137810 TTGAAATGGATCCGGGTTCC 57.862 50.000 15.91 15.91 0.00 3.62
4432 5688 4.529109 TTTTTGAAATGGATCCGGGTTC 57.471 40.909 7.39 10.66 0.00 3.62
4433 5689 6.806668 ATATTTTTGAAATGGATCCGGGTT 57.193 33.333 7.39 0.22 0.00 4.11
4434 5690 6.407979 CCAATATTTTTGAAATGGATCCGGGT 60.408 38.462 7.39 0.00 0.00 5.28
4435 5691 5.990996 CCAATATTTTTGAAATGGATCCGGG 59.009 40.000 7.39 0.00 0.00 5.73
4436 5692 5.990996 CCCAATATTTTTGAAATGGATCCGG 59.009 40.000 7.39 0.00 0.00 5.14
4437 5693 6.701400 GTCCCAATATTTTTGAAATGGATCCG 59.299 38.462 7.39 0.00 0.00 4.18
4438 5694 6.992123 GGTCCCAATATTTTTGAAATGGATCC 59.008 38.462 4.20 4.20 0.00 3.36
4439 5695 6.701400 CGGTCCCAATATTTTTGAAATGGATC 59.299 38.462 0.00 0.00 0.00 3.36
4440 5696 6.407979 CCGGTCCCAATATTTTTGAAATGGAT 60.408 38.462 0.00 0.00 0.00 3.41
4441 5697 5.105146 CCGGTCCCAATATTTTTGAAATGGA 60.105 40.000 0.00 0.00 0.00 3.41
4442 5698 5.115480 CCGGTCCCAATATTTTTGAAATGG 58.885 41.667 0.00 0.00 0.00 3.16
4443 5699 4.570369 GCCGGTCCCAATATTTTTGAAATG 59.430 41.667 1.90 0.00 0.00 2.32
4444 5700 4.679372 CGCCGGTCCCAATATTTTTGAAAT 60.679 41.667 1.90 0.00 0.00 2.17
4445 5701 3.367498 CGCCGGTCCCAATATTTTTGAAA 60.367 43.478 1.90 0.00 0.00 2.69
4446 5702 2.164624 CGCCGGTCCCAATATTTTTGAA 59.835 45.455 1.90 0.00 0.00 2.69
4447 5703 1.746220 CGCCGGTCCCAATATTTTTGA 59.254 47.619 1.90 0.00 0.00 2.69
4448 5704 1.474879 ACGCCGGTCCCAATATTTTTG 59.525 47.619 1.90 0.00 0.00 2.44
4449 5705 1.746787 GACGCCGGTCCCAATATTTTT 59.253 47.619 1.90 0.00 37.19 1.94
4450 5706 1.385528 GACGCCGGTCCCAATATTTT 58.614 50.000 1.90 0.00 37.19 1.82
4451 5707 0.812412 CGACGCCGGTCCCAATATTT 60.812 55.000 1.90 0.00 40.17 1.40
4452 5708 1.227438 CGACGCCGGTCCCAATATT 60.227 57.895 1.90 0.00 40.17 1.28
4453 5709 2.420043 CGACGCCGGTCCCAATAT 59.580 61.111 1.90 0.00 40.17 1.28
4454 5710 4.517815 GCGACGCCGGTCCCAATA 62.518 66.667 9.14 0.00 40.17 1.90
4465 5721 1.887707 CCTAATTGAGGGGCGACGC 60.888 63.158 12.43 12.43 42.39 5.19
4466 5722 1.887707 GCCTAATTGAGGGGCGACG 60.888 63.158 0.00 0.00 46.81 5.12
4467 5723 4.142780 GCCTAATTGAGGGGCGAC 57.857 61.111 0.00 0.00 46.81 5.19
4470 5726 0.533085 GACGAGCCTAATTGAGGGGC 60.533 60.000 0.00 0.00 46.81 5.80
4471 5727 0.106894 GGACGAGCCTAATTGAGGGG 59.893 60.000 0.00 0.00 46.81 4.79
4472 5728 3.688553 GGACGAGCCTAATTGAGGG 57.311 57.895 0.00 0.00 46.81 4.30


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

AutoCloner maintained by Alex Coulton.