Multiple sequence alignment - TraesCS1B01G014600

Loading Multiple Alignment...

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 TraesCS1B01G014600 chr1B 100.000 3280 0 0 1 3280 7131118 7127839 0.000000e+00 6058
1 TraesCS1B01G014600 chr1B 96.888 2731 67 9 266 2981 7929018 7926291 0.000000e+00 4556
2 TraesCS1B01G014600 chr1B 96.592 2670 73 10 321 2981 6325796 6328456 0.000000e+00 4410
3 TraesCS1B01G014600 chr1B 82.762 1137 166 19 905 2026 6340600 6341721 0.000000e+00 987
4 TraesCS1B01G014600 chr1B 82.616 1139 166 22 905 2026 6693306 6692183 0.000000e+00 977
5 TraesCS1B01G014600 chr1B 82.296 1141 165 26 905 2026 629702644 629703766 0.000000e+00 953
6 TraesCS1B01G014600 chr1B 98.315 178 3 0 2987 3164 7925800 7925623 2.460000e-81 313
7 TraesCS1B01G014600 chr1B 96.133 181 7 0 2984 3164 6328944 6329124 2.470000e-76 296
8 TraesCS1B01G014600 chr1B 90.860 186 17 0 81 266 3163650 3163465 1.950000e-62 250
9 TraesCS1B01G014600 chr1B 90.374 187 18 0 81 267 63917061 63916875 2.530000e-61 246
10 TraesCS1B01G014600 chr1B 97.581 124 1 2 3157 3280 69721292 69721413 9.220000e-51 211
11 TraesCS1B01G014600 chr1B 92.623 122 9 0 3043 3164 17146292 17146413 3.360000e-40 176
12 TraesCS1B01G014600 chr1B 90.217 92 9 0 3074 3165 7294761 7294852 1.600000e-23 121
13 TraesCS1B01G014600 chr1D 86.555 2261 231 32 765 2981 3122848 3125079 0.000000e+00 2423
14 TraesCS1B01G014600 chr1D 91.085 1447 92 21 266 1685 3613848 3615284 0.000000e+00 1923
15 TraesCS1B01G014600 chr1D 79.757 2554 367 87 481 2972 3227500 3229965 0.000000e+00 1714
16 TraesCS1B01G014600 chr1D 87.904 835 79 6 1730 2542 3615294 3616128 0.000000e+00 963
17 TraesCS1B01G014600 chr1D 92.409 303 18 4 436 737 3122551 3122849 8.410000e-116 427
18 TraesCS1B01G014600 chr1D 94.375 160 8 1 3010 3169 4232866 4232708 9.090000e-61 244
19 TraesCS1B01G014600 chr1D 84.937 239 30 6 2534 2769 3616158 3616393 1.520000e-58 237
20 TraesCS1B01G014600 chrUn 91.723 1027 73 6 436 1455 9821106 9820085 0.000000e+00 1415
21 TraesCS1B01G014600 chrUn 91.351 659 49 5 1744 2395 9819760 9819103 0.000000e+00 894
22 TraesCS1B01G014600 chrUn 90.881 318 25 2 1396 1709 9820074 9819757 1.090000e-114 424
23 TraesCS1B01G014600 chr1A 84.986 1392 174 19 1118 2487 6499036 6497658 0.000000e+00 1380
24 TraesCS1B01G014600 chr1A 81.988 644 81 22 905 1542 6439195 6438581 6.280000e-142 514
25 TraesCS1B01G014600 chr1A 88.088 319 30 6 789 1099 6500315 6499997 4.000000e-99 372
26 TraesCS1B01G014600 chr1A 91.444 187 16 0 81 267 577580064 577579878 1.170000e-64 257
27 TraesCS1B01G014600 chr1A 97.436 117 3 0 3164 3280 3694142 3694026 2.000000e-47 200
28 TraesCS1B01G014600 chr1A 92.727 110 7 1 3056 3164 6052891 6052782 1.220000e-34 158
29 TraesCS1B01G014600 chr1A 88.542 96 4 5 663 758 6440317 6440229 3.460000e-20 110
30 TraesCS1B01G014600 chr7B 90.875 263 24 0 4 266 684288566 684288828 1.450000e-93 353
31 TraesCS1B01G014600 chr5D 88.755 249 20 5 18 266 37696924 37697164 6.880000e-77 298
32 TraesCS1B01G014600 chr3A 91.038 212 19 0 58 269 163806891 163806680 1.490000e-73 287
33 TraesCS1B01G014600 chr3A 98.276 116 2 0 3165 3280 695225996 695226111 1.540000e-48 204
34 TraesCS1B01G014600 chr3A 98.276 116 2 0 3165 3280 735872304 735872419 1.540000e-48 204
35 TraesCS1B01G014600 chr6B 90.909 187 17 0 81 267 579030577 579030391 5.430000e-63 252
36 TraesCS1B01G014600 chr3B 90.000 190 19 0 81 270 16112051 16111862 2.530000e-61 246
37 TraesCS1B01G014600 chr3B 88.038 209 21 2 58 266 814365647 814365851 9.090000e-61 244
38 TraesCS1B01G014600 chr4A 98.333 120 1 1 3162 3280 632660623 632660742 3.320000e-50 209
39 TraesCS1B01G014600 chr4B 97.436 117 3 0 3164 3280 71707766 71707882 2.000000e-47 200
40 TraesCS1B01G014600 chr5B 94.531 128 5 2 3155 3280 517566731 517566604 2.580000e-46 196
41 TraesCS1B01G014600 chr2B 94.488 127 5 2 3156 3280 56426564 56426438 9.290000e-46 195
42 TraesCS1B01G014600 chr2B 94.488 127 4 2 3156 3280 56328276 56328151 3.340000e-45 193


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 TraesCS1B01G014600 chr1B 7127839 7131118 3279 True 6058.0 6058 100.000000 1 3280 1 chr1B.!!$R3 3279
1 TraesCS1B01G014600 chr1B 7925623 7929018 3395 True 2434.5 4556 97.601500 266 3164 2 chr1B.!!$R5 2898
2 TraesCS1B01G014600 chr1B 6325796 6329124 3328 False 2353.0 4410 96.362500 321 3164 2 chr1B.!!$F6 2843
3 TraesCS1B01G014600 chr1B 6340600 6341721 1121 False 987.0 987 82.762000 905 2026 1 chr1B.!!$F1 1121
4 TraesCS1B01G014600 chr1B 6692183 6693306 1123 True 977.0 977 82.616000 905 2026 1 chr1B.!!$R2 1121
5 TraesCS1B01G014600 chr1B 629702644 629703766 1122 False 953.0 953 82.296000 905 2026 1 chr1B.!!$F5 1121
6 TraesCS1B01G014600 chr1D 3227500 3229965 2465 False 1714.0 1714 79.757000 481 2972 1 chr1D.!!$F1 2491
7 TraesCS1B01G014600 chr1D 3122551 3125079 2528 False 1425.0 2423 89.482000 436 2981 2 chr1D.!!$F2 2545
8 TraesCS1B01G014600 chr1D 3613848 3616393 2545 False 1041.0 1923 87.975333 266 2769 3 chr1D.!!$F3 2503
9 TraesCS1B01G014600 chrUn 9819103 9821106 2003 True 911.0 1415 91.318333 436 2395 3 chrUn.!!$R1 1959
10 TraesCS1B01G014600 chr1A 6497658 6500315 2657 True 876.0 1380 86.537000 789 2487 2 chr1A.!!$R5 1698
11 TraesCS1B01G014600 chr1A 6438581 6440317 1736 True 312.0 514 85.265000 663 1542 2 chr1A.!!$R4 879

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
108 109 0.030908 GGCTGTATCTTCGGTCCGAG 59.969 60.0 14.79 9.05 37.14 4.63 F
201 202 0.181824 TTATTAAGCGGGCCAGGACC 59.818 55.0 0.00 0.00 0.00 4.46 F
1915 3930 0.600057 GCCAGAAGAAAACTGCTGGG 59.400 55.0 21.36 7.54 46.20 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 4136 0.471780 TCTCTCCTCCAACTGCACCA 60.472 55.000 0.00 0.00 0.00 4.17 R
2193 4242 4.772100 CCCAATGTTGTTACCTTCTGGAAT 59.228 41.667 0.00 0.00 37.04 3.01 R
3201 5810 0.810031 CAAAGGACCTATGCCGACGG 60.810 60.000 10.29 10.29 0.00 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 4.101790 CCAACGGCCATCGCACAC 62.102 66.667 2.24 0.00 43.89 3.82
19 20 4.444024 CAACGGCCATCGCACACG 62.444 66.667 2.24 0.00 43.89 4.49
20 21 4.980805 AACGGCCATCGCACACGT 62.981 61.111 2.24 0.00 43.89 4.49
24 25 2.819595 GCCATCGCACACGTGGAT 60.820 61.111 21.57 10.20 40.62 3.41
25 26 2.813179 GCCATCGCACACGTGGATC 61.813 63.158 21.57 7.18 40.62 3.36
26 27 2.516589 CCATCGCACACGTGGATCG 61.517 63.158 21.57 18.59 40.62 3.69
27 28 2.202743 ATCGCACACGTGGATCGG 60.203 61.111 21.57 4.85 44.69 4.18
28 29 2.706834 ATCGCACACGTGGATCGGA 61.707 57.895 21.57 9.77 44.69 4.55
29 30 2.613739 ATCGCACACGTGGATCGGAG 62.614 60.000 21.57 5.74 44.69 4.63
30 31 2.509336 GCACACGTGGATCGGAGG 60.509 66.667 21.57 0.00 44.69 4.30
31 32 3.001902 GCACACGTGGATCGGAGGA 62.002 63.158 21.57 0.00 44.69 3.71
32 33 1.139734 CACACGTGGATCGGAGGAG 59.860 63.158 21.57 0.00 44.69 3.69
33 34 2.052690 ACACGTGGATCGGAGGAGG 61.053 63.158 21.57 0.00 44.69 4.30
34 35 1.753078 CACGTGGATCGGAGGAGGA 60.753 63.158 7.95 0.00 44.69 3.71
35 36 1.454111 ACGTGGATCGGAGGAGGAG 60.454 63.158 0.00 0.00 44.69 3.69
36 37 2.196925 CGTGGATCGGAGGAGGAGG 61.197 68.421 0.00 0.00 35.71 4.30
37 38 1.230497 GTGGATCGGAGGAGGAGGA 59.770 63.158 0.00 0.00 0.00 3.71
38 39 0.178947 GTGGATCGGAGGAGGAGGAT 60.179 60.000 0.00 0.00 0.00 3.24
39 40 0.178950 TGGATCGGAGGAGGAGGATG 60.179 60.000 0.00 0.00 0.00 3.51
40 41 0.113385 GGATCGGAGGAGGAGGATGA 59.887 60.000 0.00 0.00 0.00 2.92
41 42 1.253100 GATCGGAGGAGGAGGATGAC 58.747 60.000 0.00 0.00 0.00 3.06
42 43 0.856982 ATCGGAGGAGGAGGATGACT 59.143 55.000 0.00 0.00 0.00 3.41
43 44 0.106469 TCGGAGGAGGAGGATGACTG 60.106 60.000 0.00 0.00 0.00 3.51
44 45 1.743321 CGGAGGAGGAGGATGACTGC 61.743 65.000 0.00 0.00 37.90 4.40
45 46 0.689080 GGAGGAGGAGGATGACTGCA 60.689 60.000 0.00 0.00 40.51 4.41
46 47 1.422531 GAGGAGGAGGATGACTGCAT 58.577 55.000 0.00 0.00 40.51 3.96
47 48 1.070445 GAGGAGGAGGATGACTGCATG 59.930 57.143 0.00 0.00 40.51 4.06
48 49 1.126488 GGAGGAGGATGACTGCATGA 58.874 55.000 0.00 0.00 40.51 3.07
49 50 1.070445 GGAGGAGGATGACTGCATGAG 59.930 57.143 0.00 0.00 40.51 2.90
50 51 0.469070 AGGAGGATGACTGCATGAGC 59.531 55.000 0.00 0.00 40.51 4.26
75 76 3.190849 CACGATCTGCGGGTGCTG 61.191 66.667 0.00 0.00 46.49 4.41
78 79 4.479993 GATCTGCGGGTGCTGCCT 62.480 66.667 0.00 0.00 43.34 4.75
79 80 4.479993 ATCTGCGGGTGCTGCCTC 62.480 66.667 0.00 0.00 43.34 4.70
81 82 4.790962 CTGCGGGTGCTGCCTCAT 62.791 66.667 0.00 0.00 43.34 2.90
82 83 4.783621 TGCGGGTGCTGCCTCATC 62.784 66.667 0.00 0.00 43.34 2.92
83 84 4.479993 GCGGGTGCTGCCTCATCT 62.480 66.667 0.00 0.00 38.39 2.90
84 85 2.513204 CGGGTGCTGCCTCATCTG 60.513 66.667 0.00 0.00 37.43 2.90
85 86 2.827642 GGGTGCTGCCTCATCTGC 60.828 66.667 0.00 0.00 37.43 4.26
86 87 2.827642 GGTGCTGCCTCATCTGCC 60.828 66.667 0.00 0.00 0.00 4.85
87 88 2.271497 GTGCTGCCTCATCTGCCT 59.729 61.111 0.00 0.00 0.00 4.75
88 89 2.113433 GTGCTGCCTCATCTGCCTG 61.113 63.158 0.00 0.00 0.00 4.85
89 90 2.516460 GCTGCCTCATCTGCCTGG 60.516 66.667 0.00 0.00 0.00 4.45
90 91 2.192443 CTGCCTCATCTGCCTGGG 59.808 66.667 0.00 0.00 0.00 4.45
91 92 4.119363 TGCCTCATCTGCCTGGGC 62.119 66.667 4.43 4.43 42.73 5.36
92 93 3.806667 GCCTCATCTGCCTGGGCT 61.807 66.667 13.05 0.00 42.51 5.19
93 94 2.192443 CCTCATCTGCCTGGGCTG 59.808 66.667 13.05 12.22 42.51 4.85
94 95 2.677289 CCTCATCTGCCTGGGCTGT 61.677 63.158 13.05 1.30 42.51 4.40
95 96 1.340399 CCTCATCTGCCTGGGCTGTA 61.340 60.000 13.05 3.68 42.51 2.74
96 97 0.763652 CTCATCTGCCTGGGCTGTAT 59.236 55.000 13.05 5.63 42.51 2.29
97 98 0.761187 TCATCTGCCTGGGCTGTATC 59.239 55.000 13.05 0.00 42.51 2.24
98 99 0.763652 CATCTGCCTGGGCTGTATCT 59.236 55.000 13.05 0.00 42.51 1.98
99 100 1.142465 CATCTGCCTGGGCTGTATCTT 59.858 52.381 13.05 0.00 42.51 2.40
100 101 0.833287 TCTGCCTGGGCTGTATCTTC 59.167 55.000 13.05 0.00 42.51 2.87
101 102 0.531532 CTGCCTGGGCTGTATCTTCG 60.532 60.000 13.05 0.00 42.51 3.79
102 103 1.227674 GCCTGGGCTGTATCTTCGG 60.228 63.158 4.12 0.00 38.26 4.30
103 104 1.972660 GCCTGGGCTGTATCTTCGGT 61.973 60.000 4.12 0.00 38.26 4.69
104 105 0.105039 CCTGGGCTGTATCTTCGGTC 59.895 60.000 0.00 0.00 0.00 4.79
105 106 0.105039 CTGGGCTGTATCTTCGGTCC 59.895 60.000 0.00 0.00 38.79 4.46
106 107 1.067582 GGGCTGTATCTTCGGTCCG 59.932 63.158 4.39 4.39 0.00 4.79
107 108 1.389609 GGGCTGTATCTTCGGTCCGA 61.390 60.000 10.71 10.71 0.00 4.55
108 109 0.030908 GGCTGTATCTTCGGTCCGAG 59.969 60.000 14.79 9.05 37.14 4.63
109 110 0.595310 GCTGTATCTTCGGTCCGAGC 60.595 60.000 14.79 8.84 37.14 5.03
110 111 0.317103 CTGTATCTTCGGTCCGAGCG 60.317 60.000 14.79 13.77 40.97 5.03
117 118 4.838486 CGGTCCGAGCGAGCAGAC 62.838 72.222 14.76 1.41 42.41 3.51
118 119 4.500116 GGTCCGAGCGAGCAGACC 62.500 72.222 13.47 13.47 41.87 3.85
119 120 4.838486 GTCCGAGCGAGCAGACCG 62.838 72.222 0.00 0.00 0.00 4.79
126 127 2.577059 CGAGCAGACCGGGCTTTA 59.423 61.111 7.41 0.00 42.78 1.85
127 128 1.079405 CGAGCAGACCGGGCTTTAA 60.079 57.895 7.41 0.00 42.78 1.52
128 129 1.359459 CGAGCAGACCGGGCTTTAAC 61.359 60.000 7.41 0.00 42.78 2.01
129 130 1.002502 AGCAGACCGGGCTTTAACC 60.003 57.895 7.41 0.00 38.81 2.85
136 137 4.313819 GGGCTTTAACCGGACTGG 57.686 61.111 9.46 0.00 46.41 4.00
137 138 1.681076 GGGCTTTAACCGGACTGGA 59.319 57.895 9.46 0.00 42.00 3.86
138 139 0.675837 GGGCTTTAACCGGACTGGAC 60.676 60.000 9.46 0.00 42.00 4.02
139 140 0.675837 GGCTTTAACCGGACTGGACC 60.676 60.000 9.46 0.00 42.00 4.46
151 152 2.415512 GGACTGGACCGAAGAATTTTCG 59.584 50.000 12.76 12.76 41.21 3.46
163 164 6.781138 CGAAGAATTTTCGGTCCATATTTCA 58.219 36.000 12.18 0.00 38.19 2.69
164 165 6.687105 CGAAGAATTTTCGGTCCATATTTCAC 59.313 38.462 12.18 0.00 38.19 3.18
165 166 7.461182 AAGAATTTTCGGTCCATATTTCACA 57.539 32.000 0.00 0.00 0.00 3.58
166 167 7.088589 AGAATTTTCGGTCCATATTTCACAG 57.911 36.000 0.00 0.00 0.00 3.66
167 168 6.884295 AGAATTTTCGGTCCATATTTCACAGA 59.116 34.615 0.00 0.00 0.00 3.41
168 169 5.873179 TTTTCGGTCCATATTTCACAGAC 57.127 39.130 0.00 0.00 0.00 3.51
169 170 3.536956 TCGGTCCATATTTCACAGACC 57.463 47.619 0.00 0.00 42.94 3.85
171 172 2.561569 GGTCCATATTTCACAGACCGG 58.438 52.381 0.00 0.00 37.83 5.28
172 173 2.169769 GGTCCATATTTCACAGACCGGA 59.830 50.000 9.46 0.00 37.83 5.14
173 174 3.195661 GTCCATATTTCACAGACCGGAC 58.804 50.000 9.46 0.10 35.34 4.79
174 175 2.169769 TCCATATTTCACAGACCGGACC 59.830 50.000 9.46 0.00 0.00 4.46
175 176 2.201732 CATATTTCACAGACCGGACCG 58.798 52.381 9.46 6.99 0.00 4.79
185 186 4.571243 CCGGACCGGCCATTTTAT 57.429 55.556 22.37 0.00 41.17 1.40
186 187 2.801859 CCGGACCGGCCATTTTATT 58.198 52.632 22.37 0.00 41.17 1.40
187 188 1.970092 CCGGACCGGCCATTTTATTA 58.030 50.000 22.37 0.00 41.17 0.98
188 189 2.299521 CCGGACCGGCCATTTTATTAA 58.700 47.619 22.37 0.00 41.17 1.40
189 190 2.292292 CCGGACCGGCCATTTTATTAAG 59.708 50.000 22.37 0.00 41.17 1.85
190 191 2.287368 CGGACCGGCCATTTTATTAAGC 60.287 50.000 5.81 0.00 35.94 3.09
191 192 2.287368 GGACCGGCCATTTTATTAAGCG 60.287 50.000 0.00 0.00 36.34 4.68
192 193 1.679153 ACCGGCCATTTTATTAAGCGG 59.321 47.619 0.00 0.00 0.00 5.52
193 194 1.000717 CCGGCCATTTTATTAAGCGGG 60.001 52.381 2.24 0.00 37.55 6.13
194 195 1.601914 CGGCCATTTTATTAAGCGGGC 60.602 52.381 2.24 0.00 39.18 6.13
195 196 2.148916 GCCATTTTATTAAGCGGGCC 57.851 50.000 0.00 0.00 33.93 5.80
196 197 1.410882 GCCATTTTATTAAGCGGGCCA 59.589 47.619 4.39 0.00 33.93 5.36
197 198 2.545742 GCCATTTTATTAAGCGGGCCAG 60.546 50.000 4.39 0.00 33.93 4.85
198 199 2.035832 CCATTTTATTAAGCGGGCCAGG 59.964 50.000 4.39 0.00 0.00 4.45
199 200 2.810870 TTTTATTAAGCGGGCCAGGA 57.189 45.000 4.39 0.00 0.00 3.86
200 201 2.047002 TTTATTAAGCGGGCCAGGAC 57.953 50.000 4.39 0.00 0.00 3.85
201 202 0.181824 TTATTAAGCGGGCCAGGACC 59.818 55.000 0.00 0.00 0.00 4.46
230 231 4.436998 GACCGAGTGGGCCACGAG 62.437 72.222 29.76 25.39 37.27 4.18
234 235 4.767255 GAGTGGGCCACGAGCAGG 62.767 72.222 29.76 0.00 46.50 4.85
240 241 3.294493 GCCACGAGCAGGCCAAAA 61.294 61.111 5.01 0.00 46.50 2.44
241 242 2.855514 GCCACGAGCAGGCCAAAAA 61.856 57.895 5.01 0.00 46.50 1.94
242 243 1.286880 CCACGAGCAGGCCAAAAAG 59.713 57.895 5.01 0.00 0.00 2.27
243 244 1.372128 CACGAGCAGGCCAAAAAGC 60.372 57.895 5.01 0.05 0.00 3.51
251 252 3.670377 GCCAAAAAGCCCGCTCGT 61.670 61.111 0.00 0.00 0.00 4.18
252 253 2.255252 CCAAAAAGCCCGCTCGTG 59.745 61.111 0.00 0.00 0.00 4.35
253 254 2.551912 CCAAAAAGCCCGCTCGTGT 61.552 57.895 0.00 0.00 0.00 4.49
254 255 1.082104 CAAAAAGCCCGCTCGTGTC 60.082 57.895 0.00 0.00 0.00 3.67
255 256 2.604174 AAAAAGCCCGCTCGTGTCG 61.604 57.895 0.00 0.00 0.00 4.35
256 257 3.802418 AAAAGCCCGCTCGTGTCGT 62.802 57.895 0.00 0.00 0.00 4.34
257 258 4.719369 AAGCCCGCTCGTGTCGTC 62.719 66.667 0.00 0.00 0.00 4.20
263 264 3.681835 GCTCGTGTCGTCCACCCT 61.682 66.667 3.10 0.00 41.26 4.34
264 265 2.258591 CTCGTGTCGTCCACCCTG 59.741 66.667 3.10 0.00 41.26 4.45
421 435 7.502561 AGTTGTAACTAGCTTGAAATGTCCTTT 59.497 33.333 1.04 0.00 37.52 3.11
422 436 7.817418 TGTAACTAGCTTGAAATGTCCTTTT 57.183 32.000 1.04 0.00 0.00 2.27
657 685 2.100087 TGCATGCATGTTAAGCCATGAG 59.900 45.455 26.79 0.00 43.99 2.90
680 713 7.720074 TGAGAAATCGACGCCCTAGATATATAT 59.280 37.037 0.00 0.00 0.00 0.86
681 714 9.217278 GAGAAATCGACGCCCTAGATATATATA 57.783 37.037 0.00 0.00 0.00 0.86
768 802 6.215495 TGGACCAAAAGGACAAAGTTTAAG 57.785 37.500 0.00 0.00 0.00 1.85
780 814 7.170489 AGGACAAAGTTTAAGTAAAGCTCGTAC 59.830 37.037 0.00 0.00 0.00 3.67
867 948 9.388506 AGAACATATTTTAACTGGATCTGACTG 57.611 33.333 0.00 0.00 0.00 3.51
886 973 2.216148 AGCATCTAGTGGCTCACCC 58.784 57.895 5.29 0.00 34.76 4.61
903 1868 2.345991 CGACACACGGAACCCCAT 59.654 61.111 0.00 0.00 38.46 4.00
1558 3556 2.635915 CCAAACTGTACCACCTACTCCA 59.364 50.000 0.00 0.00 0.00 3.86
1757 3772 3.717507 TCACCTATACCCAGATCCCAA 57.282 47.619 0.00 0.00 0.00 4.12
1915 3930 0.600057 GCCAGAAGAAAACTGCTGGG 59.400 55.000 21.36 7.54 46.20 4.45
2087 4136 9.569122 TTTATAAAGCAAGTTCTTGGAACTACT 57.431 29.630 12.43 10.44 0.00 2.57
2193 4242 1.206371 GTACCCCTTTTAGCAGCGAGA 59.794 52.381 0.00 0.00 0.00 4.04
2201 4250 3.610040 TTTAGCAGCGAGATTCCAGAA 57.390 42.857 0.00 0.00 0.00 3.02
2237 4286 1.656652 GATTCTATGCACGTGCTGGT 58.343 50.000 37.59 25.71 42.66 4.00
2424 4494 3.413327 TCCTTTTTATTGTGCGTGCCTA 58.587 40.909 0.00 0.00 0.00 3.93
2554 4671 6.162777 ACTTCTCTCTCTTATTTGTGTGCTC 58.837 40.000 0.00 0.00 0.00 4.26
2803 4926 5.046878 CGGGATATGTAGGTATTAGTGGCAA 60.047 44.000 0.00 0.00 0.00 4.52
2906 5030 6.931838 TGTCAACTTGTTATTCTAGATCCGT 58.068 36.000 0.00 0.00 0.00 4.69
2985 5594 9.620660 GAACAAACATAACAACCTAGGTAAATG 57.379 33.333 16.67 17.30 0.00 2.32
3171 5780 8.671921 TCTCAAGTATTTAGTTACTCACTACCG 58.328 37.037 0.00 0.00 37.74 4.02
3172 5781 7.765307 TCAAGTATTTAGTTACTCACTACCGG 58.235 38.462 0.00 0.00 37.74 5.28
3173 5782 7.611467 TCAAGTATTTAGTTACTCACTACCGGA 59.389 37.037 9.46 0.00 37.74 5.14
3174 5783 7.326968 AGTATTTAGTTACTCACTACCGGAC 57.673 40.000 9.46 0.00 37.74 4.79
3175 5784 7.115414 AGTATTTAGTTACTCACTACCGGACT 58.885 38.462 9.46 0.00 37.74 3.85
3176 5785 5.886960 TTTAGTTACTCACTACCGGACTC 57.113 43.478 9.46 0.00 37.74 3.36
3177 5786 2.354259 AGTTACTCACTACCGGACTCG 58.646 52.381 9.46 0.00 31.97 4.18
3178 5787 1.089920 TTACTCACTACCGGACTCGC 58.910 55.000 9.46 0.00 34.56 5.03
3179 5788 1.086067 TACTCACTACCGGACTCGCG 61.086 60.000 9.46 0.00 34.56 5.87
3180 5789 3.109612 CTCACTACCGGACTCGCGG 62.110 68.421 9.46 0.00 34.56 6.46
3181 5790 4.189188 CACTACCGGACTCGCGGG 62.189 72.222 9.46 3.27 42.39 6.13
3184 5793 4.488136 TACCGGACTCGCGGGCTA 62.488 66.667 9.46 0.00 40.47 3.93
3185 5794 3.779850 TACCGGACTCGCGGGCTAT 62.780 63.158 9.46 0.00 40.47 2.97
3186 5795 4.647615 CCGGACTCGCGGGCTATG 62.648 72.222 5.51 0.00 34.56 2.23
3218 5827 3.217231 CCGTCGGCATAGGTCCTT 58.783 61.111 0.00 0.00 0.00 3.36
3219 5828 1.520666 CCGTCGGCATAGGTCCTTT 59.479 57.895 0.00 0.00 0.00 3.11
3220 5829 0.810031 CCGTCGGCATAGGTCCTTTG 60.810 60.000 0.00 0.00 0.00 2.77
3221 5830 1.429148 CGTCGGCATAGGTCCTTTGC 61.429 60.000 22.29 22.29 37.63 3.68
3223 5832 3.827634 GGCATAGGTCCTTTGCCG 58.172 61.111 30.38 3.46 45.36 5.69
3224 5833 1.077716 GGCATAGGTCCTTTGCCGT 60.078 57.895 30.38 0.00 45.36 5.68
3225 5834 1.095807 GGCATAGGTCCTTTGCCGTC 61.096 60.000 30.38 13.61 45.36 4.79
3226 5835 1.429148 GCATAGGTCCTTTGCCGTCG 61.429 60.000 20.40 0.00 33.51 5.12
3227 5836 0.810031 CATAGGTCCTTTGCCGTCGG 60.810 60.000 6.99 6.99 0.00 4.79
3279 5888 3.214123 CCCCGTCGGCGTAGATCA 61.214 66.667 9.28 0.00 36.15 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.101790 GTGTGCGATGGCCGTTGG 62.102 66.667 14.36 3.48 41.15 3.77
3 4 4.980805 ACGTGTGCGATGGCCGTT 62.981 61.111 0.00 0.00 42.00 4.44
7 8 2.813179 GATCCACGTGTGCGATGGC 61.813 63.158 15.65 0.00 42.00 4.40
8 9 2.516589 CGATCCACGTGTGCGATGG 61.517 63.158 15.65 7.76 42.00 3.51
9 10 2.516589 CCGATCCACGTGTGCGATG 61.517 63.158 15.65 0.00 42.00 3.84
10 11 2.202743 CCGATCCACGTGTGCGAT 60.203 61.111 15.65 10.13 42.00 4.58
11 12 3.336715 CTCCGATCCACGTGTGCGA 62.337 63.158 15.65 5.04 42.00 5.10
12 13 2.880879 CTCCGATCCACGTGTGCG 60.881 66.667 15.65 14.06 44.93 5.34
13 14 2.509336 CCTCCGATCCACGTGTGC 60.509 66.667 15.65 2.09 40.78 4.57
14 15 1.139734 CTCCTCCGATCCACGTGTG 59.860 63.158 15.65 6.24 40.78 3.82
15 16 2.052690 CCTCCTCCGATCCACGTGT 61.053 63.158 15.65 0.00 40.78 4.49
16 17 1.729470 CTCCTCCTCCGATCCACGTG 61.729 65.000 9.08 9.08 40.78 4.49
17 18 1.454111 CTCCTCCTCCGATCCACGT 60.454 63.158 0.00 0.00 40.78 4.49
18 19 2.196925 CCTCCTCCTCCGATCCACG 61.197 68.421 0.00 0.00 42.18 4.94
19 20 0.178947 ATCCTCCTCCTCCGATCCAC 60.179 60.000 0.00 0.00 0.00 4.02
20 21 0.178950 CATCCTCCTCCTCCGATCCA 60.179 60.000 0.00 0.00 0.00 3.41
21 22 0.113385 TCATCCTCCTCCTCCGATCC 59.887 60.000 0.00 0.00 0.00 3.36
22 23 1.203001 AGTCATCCTCCTCCTCCGATC 60.203 57.143 0.00 0.00 0.00 3.69
23 24 0.856982 AGTCATCCTCCTCCTCCGAT 59.143 55.000 0.00 0.00 0.00 4.18
24 25 0.106469 CAGTCATCCTCCTCCTCCGA 60.106 60.000 0.00 0.00 0.00 4.55
25 26 1.743321 GCAGTCATCCTCCTCCTCCG 61.743 65.000 0.00 0.00 0.00 4.63
26 27 0.689080 TGCAGTCATCCTCCTCCTCC 60.689 60.000 0.00 0.00 0.00 4.30
27 28 1.070445 CATGCAGTCATCCTCCTCCTC 59.930 57.143 0.00 0.00 0.00 3.71
28 29 1.129917 CATGCAGTCATCCTCCTCCT 58.870 55.000 0.00 0.00 0.00 3.69
29 30 1.070445 CTCATGCAGTCATCCTCCTCC 59.930 57.143 0.00 0.00 0.00 4.30
30 31 1.540797 GCTCATGCAGTCATCCTCCTC 60.541 57.143 0.00 0.00 39.41 3.71
31 32 0.469070 GCTCATGCAGTCATCCTCCT 59.531 55.000 0.00 0.00 39.41 3.69
32 33 0.179702 TGCTCATGCAGTCATCCTCC 59.820 55.000 0.00 0.00 45.31 4.30
33 34 3.774616 TGCTCATGCAGTCATCCTC 57.225 52.632 0.00 0.00 45.31 3.71
58 59 3.190849 CAGCACCCGCAGATCGTG 61.191 66.667 0.00 0.00 42.27 4.35
61 62 4.479993 AGGCAGCACCCGCAGATC 62.480 66.667 0.00 0.00 42.27 2.75
62 63 4.479993 GAGGCAGCACCCGCAGAT 62.480 66.667 0.00 0.00 42.27 2.90
64 65 4.790962 ATGAGGCAGCACCCGCAG 62.791 66.667 0.00 0.00 42.27 5.18
65 66 4.783621 GATGAGGCAGCACCCGCA 62.784 66.667 0.00 1.89 42.27 5.69
66 67 4.479993 AGATGAGGCAGCACCCGC 62.480 66.667 0.00 0.00 40.58 6.13
67 68 2.513204 CAGATGAGGCAGCACCCG 60.513 66.667 0.00 0.00 40.58 5.28
68 69 2.827642 GCAGATGAGGCAGCACCC 60.828 66.667 0.00 0.00 40.58 4.61
69 70 2.827642 GGCAGATGAGGCAGCACC 60.828 66.667 0.00 0.00 39.61 5.01
70 71 2.113433 CAGGCAGATGAGGCAGCAC 61.113 63.158 0.00 0.00 36.37 4.40
71 72 2.271173 CAGGCAGATGAGGCAGCA 59.729 61.111 0.00 0.00 36.37 4.41
72 73 2.516460 CCAGGCAGATGAGGCAGC 60.516 66.667 0.00 0.00 36.37 5.25
73 74 2.192443 CCCAGGCAGATGAGGCAG 59.808 66.667 0.00 0.00 36.37 4.85
74 75 4.119363 GCCCAGGCAGATGAGGCA 62.119 66.667 3.12 0.00 43.32 4.75
75 76 3.806667 AGCCCAGGCAGATGAGGC 61.807 66.667 12.03 0.00 44.88 4.70
76 77 1.340399 TACAGCCCAGGCAGATGAGG 61.340 60.000 12.03 0.00 44.88 3.86
77 78 0.763652 ATACAGCCCAGGCAGATGAG 59.236 55.000 12.03 0.00 44.88 2.90
78 79 0.761187 GATACAGCCCAGGCAGATGA 59.239 55.000 12.03 0.00 44.88 2.92
79 80 0.763652 AGATACAGCCCAGGCAGATG 59.236 55.000 12.03 3.03 44.88 2.90
80 81 1.419387 GAAGATACAGCCCAGGCAGAT 59.581 52.381 12.03 0.39 44.88 2.90
81 82 0.833287 GAAGATACAGCCCAGGCAGA 59.167 55.000 12.03 0.00 44.88 4.26
82 83 0.531532 CGAAGATACAGCCCAGGCAG 60.532 60.000 12.03 5.35 44.88 4.85
83 84 1.522092 CGAAGATACAGCCCAGGCA 59.478 57.895 12.03 0.00 44.88 4.75
84 85 1.227674 CCGAAGATACAGCCCAGGC 60.228 63.158 0.00 0.00 42.33 4.85
85 86 0.105039 GACCGAAGATACAGCCCAGG 59.895 60.000 0.00 0.00 0.00 4.45
86 87 0.105039 GGACCGAAGATACAGCCCAG 59.895 60.000 0.00 0.00 0.00 4.45
87 88 1.672854 CGGACCGAAGATACAGCCCA 61.673 60.000 8.64 0.00 0.00 5.36
88 89 1.067582 CGGACCGAAGATACAGCCC 59.932 63.158 8.64 0.00 0.00 5.19
89 90 0.030908 CTCGGACCGAAGATACAGCC 59.969 60.000 18.93 0.00 34.74 4.85
90 91 0.595310 GCTCGGACCGAAGATACAGC 60.595 60.000 18.93 12.01 34.74 4.40
91 92 0.317103 CGCTCGGACCGAAGATACAG 60.317 60.000 18.93 5.34 34.74 2.74
92 93 0.745486 TCGCTCGGACCGAAGATACA 60.745 55.000 18.93 0.00 34.74 2.29
93 94 0.041135 CTCGCTCGGACCGAAGATAC 60.041 60.000 18.93 4.41 34.74 2.24
94 95 1.783031 GCTCGCTCGGACCGAAGATA 61.783 60.000 18.93 3.01 34.74 1.98
95 96 3.111939 CTCGCTCGGACCGAAGAT 58.888 61.111 18.93 0.00 34.74 2.40
96 97 3.812019 GCTCGCTCGGACCGAAGA 61.812 66.667 18.93 18.04 34.74 2.87
97 98 4.116328 TGCTCGCTCGGACCGAAG 62.116 66.667 18.93 13.62 34.74 3.79
98 99 4.116328 CTGCTCGCTCGGACCGAA 62.116 66.667 18.93 1.89 34.74 4.30
100 101 4.838486 GTCTGCTCGCTCGGACCG 62.838 72.222 7.84 7.84 36.58 4.79
102 103 4.838486 CGGTCTGCTCGCTCGGAC 62.838 72.222 7.04 7.04 40.68 4.79
108 109 3.659089 TAAAGCCCGGTCTGCTCGC 62.659 63.158 4.05 0.00 38.34 5.03
109 110 1.079405 TTAAAGCCCGGTCTGCTCG 60.079 57.895 4.05 0.00 38.34 5.03
110 111 1.025113 GGTTAAAGCCCGGTCTGCTC 61.025 60.000 4.05 0.00 38.34 4.26
111 112 1.002502 GGTTAAAGCCCGGTCTGCT 60.003 57.895 0.00 0.00 41.89 4.24
112 113 2.396157 CGGTTAAAGCCCGGTCTGC 61.396 63.158 0.00 0.00 41.78 4.26
113 114 3.884900 CGGTTAAAGCCCGGTCTG 58.115 61.111 0.00 0.00 41.78 3.51
118 119 1.743995 CCAGTCCGGTTAAAGCCCG 60.744 63.158 0.00 0.00 45.07 6.13
119 120 0.675837 GTCCAGTCCGGTTAAAGCCC 60.676 60.000 0.00 0.00 35.57 5.19
120 121 0.675837 GGTCCAGTCCGGTTAAAGCC 60.676 60.000 0.00 0.00 35.57 4.35
121 122 1.017701 CGGTCCAGTCCGGTTAAAGC 61.018 60.000 0.00 0.00 45.88 3.51
122 123 3.132863 CGGTCCAGTCCGGTTAAAG 57.867 57.895 0.00 0.00 45.88 1.85
130 131 2.415512 CGAAAATTCTTCGGTCCAGTCC 59.584 50.000 12.18 0.00 38.19 3.85
131 132 3.724295 CGAAAATTCTTCGGTCCAGTC 57.276 47.619 12.18 0.00 38.19 3.51
139 140 6.687105 GTGAAATATGGACCGAAAATTCTTCG 59.313 38.462 12.76 12.76 41.21 3.79
140 141 7.535139 TGTGAAATATGGACCGAAAATTCTTC 58.465 34.615 0.00 0.00 0.00 2.87
141 142 7.393234 TCTGTGAAATATGGACCGAAAATTCTT 59.607 33.333 0.00 0.00 0.00 2.52
142 143 6.884295 TCTGTGAAATATGGACCGAAAATTCT 59.116 34.615 0.00 0.00 0.00 2.40
143 144 6.967199 GTCTGTGAAATATGGACCGAAAATTC 59.033 38.462 0.00 0.00 0.00 2.17
144 145 6.127730 GGTCTGTGAAATATGGACCGAAAATT 60.128 38.462 0.00 0.00 37.34 1.82
145 146 5.357032 GGTCTGTGAAATATGGACCGAAAAT 59.643 40.000 0.00 0.00 37.34 1.82
146 147 4.698304 GGTCTGTGAAATATGGACCGAAAA 59.302 41.667 0.00 0.00 37.34 2.29
147 148 4.258543 GGTCTGTGAAATATGGACCGAAA 58.741 43.478 0.00 0.00 37.34 3.46
148 149 3.869065 GGTCTGTGAAATATGGACCGAA 58.131 45.455 0.00 0.00 37.34 4.30
149 150 3.536956 GGTCTGTGAAATATGGACCGA 57.463 47.619 0.00 0.00 37.34 4.69
151 152 2.169769 TCCGGTCTGTGAAATATGGACC 59.830 50.000 0.00 0.00 41.92 4.46
152 153 3.195661 GTCCGGTCTGTGAAATATGGAC 58.804 50.000 0.00 0.00 38.01 4.02
153 154 2.169769 GGTCCGGTCTGTGAAATATGGA 59.830 50.000 0.00 0.00 0.00 3.41
154 155 2.561569 GGTCCGGTCTGTGAAATATGG 58.438 52.381 0.00 0.00 0.00 2.74
155 156 2.201732 CGGTCCGGTCTGTGAAATATG 58.798 52.381 2.34 0.00 0.00 1.78
156 157 1.138266 CCGGTCCGGTCTGTGAAATAT 59.862 52.381 23.02 0.00 42.73 1.28
157 158 0.533491 CCGGTCCGGTCTGTGAAATA 59.467 55.000 23.02 0.00 42.73 1.40
158 159 1.295423 CCGGTCCGGTCTGTGAAAT 59.705 57.895 23.02 0.00 42.73 2.17
159 160 2.738480 CCGGTCCGGTCTGTGAAA 59.262 61.111 23.02 0.00 42.73 2.69
169 170 2.287368 GCTTAATAAAATGGCCGGTCCG 60.287 50.000 2.12 3.60 37.80 4.79
170 171 2.287368 CGCTTAATAAAATGGCCGGTCC 60.287 50.000 2.12 5.67 0.00 4.46
171 172 2.287368 CCGCTTAATAAAATGGCCGGTC 60.287 50.000 0.00 0.00 0.00 4.79
172 173 1.679153 CCGCTTAATAAAATGGCCGGT 59.321 47.619 1.90 0.00 0.00 5.28
173 174 1.000717 CCCGCTTAATAAAATGGCCGG 60.001 52.381 0.00 0.00 0.00 6.13
174 175 1.601914 GCCCGCTTAATAAAATGGCCG 60.602 52.381 0.00 0.00 0.00 6.13
175 176 2.148916 GCCCGCTTAATAAAATGGCC 57.851 50.000 0.00 0.00 0.00 5.36
176 177 1.410882 TGGCCCGCTTAATAAAATGGC 59.589 47.619 0.00 0.00 36.68 4.40
177 178 2.035832 CCTGGCCCGCTTAATAAAATGG 59.964 50.000 0.00 0.00 0.00 3.16
178 179 2.955660 TCCTGGCCCGCTTAATAAAATG 59.044 45.455 0.00 0.00 0.00 2.32
179 180 2.956333 GTCCTGGCCCGCTTAATAAAAT 59.044 45.455 0.00 0.00 0.00 1.82
180 181 2.371306 GTCCTGGCCCGCTTAATAAAA 58.629 47.619 0.00 0.00 0.00 1.52
181 182 1.409101 GGTCCTGGCCCGCTTAATAAA 60.409 52.381 0.00 0.00 0.00 1.40
182 183 0.181824 GGTCCTGGCCCGCTTAATAA 59.818 55.000 0.00 0.00 0.00 1.40
183 184 1.834301 GGTCCTGGCCCGCTTAATA 59.166 57.895 0.00 0.00 0.00 0.98
184 185 2.595655 GGTCCTGGCCCGCTTAAT 59.404 61.111 0.00 0.00 0.00 1.40
185 186 4.090588 CGGTCCTGGCCCGCTTAA 62.091 66.667 2.08 0.00 38.85 1.85
213 214 4.436998 CTCGTGGCCCACTCGGTC 62.437 72.222 12.94 0.00 36.76 4.79
217 218 4.767255 CCTGCTCGTGGCCCACTC 62.767 72.222 12.94 1.54 40.92 3.51
224 225 1.286880 CTTTTTGGCCTGCTCGTGG 59.713 57.895 3.32 0.00 0.00 4.94
225 226 1.372128 GCTTTTTGGCCTGCTCGTG 60.372 57.895 3.32 0.00 0.00 4.35
226 227 3.042560 GCTTTTTGGCCTGCTCGT 58.957 55.556 3.32 0.00 0.00 4.18
234 235 3.670377 ACGAGCGGGCTTTTTGGC 61.670 61.111 0.00 0.00 40.96 4.52
235 236 2.255252 CACGAGCGGGCTTTTTGG 59.745 61.111 0.00 0.00 0.00 3.28
236 237 1.082104 GACACGAGCGGGCTTTTTG 60.082 57.895 0.00 0.00 0.00 2.44
237 238 2.604174 CGACACGAGCGGGCTTTTT 61.604 57.895 0.00 0.00 0.00 1.94
238 239 3.041940 CGACACGAGCGGGCTTTT 61.042 61.111 0.00 0.00 0.00 2.27
239 240 4.295119 ACGACACGAGCGGGCTTT 62.295 61.111 0.00 0.00 0.00 3.51
240 241 4.719369 GACGACACGAGCGGGCTT 62.719 66.667 0.00 0.00 0.00 4.35
251 252 3.311110 GGCTCAGGGTGGACGACA 61.311 66.667 0.00 0.00 0.00 4.35
252 253 2.997897 AGGCTCAGGGTGGACGAC 60.998 66.667 0.00 0.00 0.00 4.34
253 254 2.997315 CAGGCTCAGGGTGGACGA 60.997 66.667 0.00 0.00 0.00 4.20
254 255 3.314331 ACAGGCTCAGGGTGGACG 61.314 66.667 0.00 0.00 0.00 4.79
255 256 2.348998 CACAGGCTCAGGGTGGAC 59.651 66.667 0.00 0.00 0.00 4.02
256 257 3.640407 GCACAGGCTCAGGGTGGA 61.640 66.667 5.05 0.00 36.96 4.02
424 438 1.610624 CCTCTAAGCTGACCCGCAAAA 60.611 52.381 0.00 0.00 0.00 2.44
425 439 0.036388 CCTCTAAGCTGACCCGCAAA 60.036 55.000 0.00 0.00 0.00 3.68
426 440 1.596934 CCTCTAAGCTGACCCGCAA 59.403 57.895 0.00 0.00 0.00 4.85
428 442 2.202946 GCCTCTAAGCTGACCCGC 60.203 66.667 0.00 0.00 0.00 6.13
429 443 0.179097 GAAGCCTCTAAGCTGACCCG 60.179 60.000 0.00 0.00 44.11 5.28
430 444 0.905357 TGAAGCCTCTAAGCTGACCC 59.095 55.000 0.00 0.00 44.11 4.46
431 445 2.626840 CTTGAAGCCTCTAAGCTGACC 58.373 52.381 0.00 0.00 44.11 4.02
433 447 1.404717 CGCTTGAAGCCTCTAAGCTGA 60.405 52.381 12.13 0.00 44.11 4.26
434 448 1.005340 CGCTTGAAGCCTCTAAGCTG 58.995 55.000 12.13 0.00 44.11 4.24
439 460 2.076863 GCTTTTCGCTTGAAGCCTCTA 58.923 47.619 12.13 0.00 41.78 2.43
768 802 4.111198 GGAGCTTAAGGTACGAGCTTTAC 58.889 47.826 7.26 0.00 46.08 2.01
780 814 7.503566 TGAAGATAAATTCATGGGAGCTTAAGG 59.496 37.037 4.29 0.00 34.31 2.69
886 973 1.740296 GATGGGGTTCCGTGTGTCG 60.740 63.158 0.00 0.00 39.52 4.35
903 1868 6.042777 CAGAGTGAAGGTCGCAATTTATAGA 58.957 40.000 0.00 0.00 0.00 1.98
1558 3556 1.900545 GAAGCTCCCAAGTACGCCCT 61.901 60.000 0.00 0.00 0.00 5.19
1673 3679 5.692115 TCCAAGTAATTAGGTGAGATGCA 57.308 39.130 0.00 0.00 0.00 3.96
1757 3772 2.291800 CCCAAGGTCCCATCTTTGTCAT 60.292 50.000 0.00 0.00 0.00 3.06
2087 4136 0.471780 TCTCTCCTCCAACTGCACCA 60.472 55.000 0.00 0.00 0.00 4.17
2193 4242 4.772100 CCCAATGTTGTTACCTTCTGGAAT 59.228 41.667 0.00 0.00 37.04 3.01
2201 4250 3.336694 AGAATCCCCCAATGTTGTTACCT 59.663 43.478 0.00 0.00 0.00 3.08
2237 4286 1.608055 CAAGTGCATTGACAGACCCA 58.392 50.000 0.00 0.00 41.83 4.51
2297 4352 3.256631 GGGCAAGAAGATTCTGAAGCAAA 59.743 43.478 8.50 0.00 37.65 3.68
2424 4494 5.812642 GCAAGTACATGTAGACAGTAGCAAT 59.187 40.000 5.62 0.00 0.00 3.56
2554 4671 8.682936 ATTATTTAGCCTTGTCATGTAGGAAG 57.317 34.615 13.17 3.22 33.13 3.46
2906 5030 4.151121 TCTCCATGAACCATTTGCTTTCA 58.849 39.130 0.00 0.00 33.89 2.69
2950 5074 8.567948 AGGTTGTTATGTTTGTTCTTATGACTG 58.432 33.333 0.00 0.00 0.00 3.51
2981 5105 6.099557 AGCTTTGATCTAGCCTCTCTACATTT 59.900 38.462 14.29 0.00 39.47 2.32
2985 5594 5.768164 ACTAGCTTTGATCTAGCCTCTCTAC 59.232 44.000 14.29 0.00 39.47 2.59
3164 5773 4.189188 CCCGCGAGTCCGGTAGTG 62.189 72.222 8.23 0.00 46.71 2.74
3167 5776 3.779850 ATAGCCCGCGAGTCCGGTA 62.780 63.158 8.23 0.00 46.71 4.02
3171 5780 4.971125 GGCATAGCCCGCGAGTCC 62.971 72.222 8.23 0.00 44.06 3.85
3201 5810 0.810031 CAAAGGACCTATGCCGACGG 60.810 60.000 10.29 10.29 0.00 4.79
3202 5811 1.429148 GCAAAGGACCTATGCCGACG 61.429 60.000 0.00 0.00 34.03 5.12
3203 5812 2.394604 GCAAAGGACCTATGCCGAC 58.605 57.895 0.00 0.00 34.03 4.79
3204 5813 4.954933 GCAAAGGACCTATGCCGA 57.045 55.556 0.00 0.00 34.03 5.54
3207 5816 1.429148 CGACGGCAAAGGACCTATGC 61.429 60.000 0.00 0.00 39.33 3.14
3208 5817 0.810031 CCGACGGCAAAGGACCTATG 60.810 60.000 0.00 0.00 0.00 2.23
3209 5818 1.520666 CCGACGGCAAAGGACCTAT 59.479 57.895 0.00 0.00 0.00 2.57
3210 5819 2.975536 CCGACGGCAAAGGACCTA 59.024 61.111 0.00 0.00 0.00 3.08
3262 5871 3.214123 TGATCTACGCCGACGGGG 61.214 66.667 27.56 27.56 46.04 5.73


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

AutoCloner maintained by Alex Coulton.