Multiple sequence alignment - TraesCS5D01G338600

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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 TraesCS5D01G338600 chr5D 100.000 2112 0 0 1 2112 428037007 428039118 0.000000e+00 3901
1 TraesCS5D01G338600 chr5D 100.000 530 0 0 2342 2871 428039348 428039877 0.000000e+00 979
2 TraesCS5D01G338600 chr5D 78.491 530 82 17 1225 1740 428307471 428307982 4.620000e-83 318
3 TraesCS5D01G338600 chr5D 94.444 90 2 3 1 88 30982561 30982473 4.990000e-28 135
4 TraesCS5D01G338600 chr5D 94.253 87 3 2 1 85 220901967 220901881 6.450000e-27 132
5 TraesCS5D01G338600 chr5A 89.405 1529 130 9 246 1744 542526193 542527719 0.000000e+00 1897
6 TraesCS5D01G338600 chr5A 91.509 530 39 5 2342 2871 542528180 542528703 0.000000e+00 725
7 TraesCS5D01G338600 chr5A 91.644 371 27 1 1742 2108 542527750 542528120 7.100000e-141 510
8 TraesCS5D01G338600 chr5A 86.335 161 22 0 71 231 200975380 200975220 2.940000e-40 176
9 TraesCS5D01G338600 chr5A 84.472 161 25 0 71 231 200874451 200874291 2.960000e-35 159
10 TraesCS5D01G338600 chr5B 83.959 1066 120 21 703 1743 517246539 517247578 0.000000e+00 974
11 TraesCS5D01G338600 chr5B 90.029 341 31 3 253 592 517245744 517246082 3.400000e-119 438
12 TraesCS5D01G338600 chr7D 88.344 163 16 2 71 231 297153857 297154018 2.920000e-45 193
13 TraesCS5D01G338600 chr7D 85.714 161 22 1 71 231 325316353 325316512 4.920000e-38 169
14 TraesCS5D01G338600 chr7D 85.714 161 22 1 71 231 325323589 325323748 4.920000e-38 169
15 TraesCS5D01G338600 chr7D 100.000 74 0 0 1 74 262558626 262558699 1.390000e-28 137
16 TraesCS5D01G338600 chr3A 88.199 161 17 2 71 231 330447098 330447256 1.050000e-44 191
17 TraesCS5D01G338600 chr6D 86.250 160 21 1 72 231 254641794 254641952 3.800000e-39 172
18 TraesCS5D01G338600 chr3D 85.890 163 20 3 71 231 316299672 316299511 1.370000e-38 171
19 TraesCS5D01G338600 chr3D 93.182 88 4 2 4 90 307616223 307616137 8.350000e-26 128
20 TraesCS5D01G338600 chr4A 85.185 162 23 1 71 231 319537136 319536975 6.360000e-37 165
21 TraesCS5D01G338600 chr4A 91.579 95 4 2 1 94 75726811 75726720 8.350000e-26 128
22 TraesCS5D01G338600 chr3B 98.734 79 0 1 1 78 709536571 709536493 3.860000e-29 139
23 TraesCS5D01G338600 chr1D 95.455 88 2 2 1 87 406194164 406194078 3.860000e-29 139
24 TraesCS5D01G338600 chr2D 93.333 90 4 2 1 88 162748552 162748463 6.450000e-27 132
25 TraesCS5D01G338600 chr2B 93.407 91 3 3 1 88 563949078 563948988 6.450000e-27 132


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 TraesCS5D01G338600 chr5D 428037007 428039877 2870 False 2440 3901 100.000000 1 2871 2 chr5D.!!$F2 2870
1 TraesCS5D01G338600 chr5D 428307471 428307982 511 False 318 318 78.491000 1225 1740 1 chr5D.!!$F1 515
2 TraesCS5D01G338600 chr5A 542526193 542528703 2510 False 1044 1897 90.852667 246 2871 3 chr5A.!!$F1 2625
3 TraesCS5D01G338600 chr5B 517245744 517247578 1834 False 706 974 86.994000 253 1743 2 chr5B.!!$F1 1490

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
113 114 0.107654 CCCGAGCCTGGGTAAAAGAG 60.108 60.0 0.0 0.0 44.76 2.85 F
878 1230 0.251519 AAAAGCCAAGCCCCTCTCTG 60.252 55.0 0.0 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1890 0.042431 AGACTCTGCCTCCTGGTGAT 59.958 55.0 0.0 0.0 35.27 3.06 R
1989 2419 0.537188 TTGGATGAAGAGACTCGGCC 59.463 55.0 0.0 0.0 0.00 6.13 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
46 47 2.892784 AAAAATTCGTTCGGCCCAAA 57.107 40.000 0.00 0.00 0.00 3.28
47 48 2.892784 AAAATTCGTTCGGCCCAAAA 57.107 40.000 0.00 0.00 0.00 2.44
48 49 3.394674 AAAATTCGTTCGGCCCAAAAT 57.605 38.095 0.00 0.00 0.00 1.82
49 50 2.362169 AATTCGTTCGGCCCAAAATG 57.638 45.000 0.00 0.00 0.00 2.32
50 51 1.253100 ATTCGTTCGGCCCAAAATGT 58.747 45.000 0.00 0.00 0.00 2.71
51 52 0.594110 TTCGTTCGGCCCAAAATGTC 59.406 50.000 0.00 0.00 0.00 3.06
52 53 0.535328 TCGTTCGGCCCAAAATGTCA 60.535 50.000 0.00 0.00 0.00 3.58
53 54 0.386731 CGTTCGGCCCAAAATGTCAC 60.387 55.000 0.00 0.00 0.00 3.67
54 55 0.386731 GTTCGGCCCAAAATGTCACG 60.387 55.000 0.00 0.00 0.00 4.35
55 56 1.519751 TTCGGCCCAAAATGTCACGG 61.520 55.000 0.00 0.00 0.00 4.94
56 57 1.969064 CGGCCCAAAATGTCACGGA 60.969 57.895 0.00 0.00 0.00 4.69
57 58 1.312371 CGGCCCAAAATGTCACGGAT 61.312 55.000 0.00 0.00 0.00 4.18
58 59 0.173255 GGCCCAAAATGTCACGGATG 59.827 55.000 0.00 0.00 0.00 3.51
59 60 0.887933 GCCCAAAATGTCACGGATGT 59.112 50.000 0.00 0.00 0.00 3.06
61 62 1.885887 CCCAAAATGTCACGGATGTGT 59.114 47.619 0.00 0.00 46.49 3.72
62 63 2.095263 CCCAAAATGTCACGGATGTGTC 60.095 50.000 0.00 0.00 46.49 3.67
63 64 2.813754 CCAAAATGTCACGGATGTGTCT 59.186 45.455 0.00 0.00 46.49 3.41
64 65 3.253188 CCAAAATGTCACGGATGTGTCTT 59.747 43.478 0.00 0.00 46.49 3.01
65 66 4.261572 CCAAAATGTCACGGATGTGTCTTT 60.262 41.667 0.00 0.00 46.49 2.52
66 67 5.280945 CAAAATGTCACGGATGTGTCTTTT 58.719 37.500 0.00 0.00 46.49 2.27
67 68 5.514274 AAATGTCACGGATGTGTCTTTTT 57.486 34.783 0.00 0.00 46.49 1.94
90 91 8.568732 TTTTTGTAGGATTTTACGCTTCAAAG 57.431 30.769 0.00 0.00 0.00 2.77
101 102 1.581447 CTTCAAAGCAACCCGAGCC 59.419 57.895 0.00 0.00 0.00 4.70
102 103 0.890996 CTTCAAAGCAACCCGAGCCT 60.891 55.000 0.00 0.00 0.00 4.58
103 104 1.172180 TTCAAAGCAACCCGAGCCTG 61.172 55.000 0.00 0.00 0.00 4.85
104 105 2.282462 AAAGCAACCCGAGCCTGG 60.282 61.111 0.00 0.00 0.00 4.45
111 112 4.637771 CCCGAGCCTGGGTAAAAG 57.362 61.111 0.00 0.00 44.76 2.27
112 113 1.988015 CCCGAGCCTGGGTAAAAGA 59.012 57.895 0.00 0.00 44.76 2.52
113 114 0.107654 CCCGAGCCTGGGTAAAAGAG 60.108 60.000 0.00 0.00 44.76 2.85
114 115 0.902531 CCGAGCCTGGGTAAAAGAGA 59.097 55.000 0.00 0.00 0.00 3.10
115 116 1.278127 CCGAGCCTGGGTAAAAGAGAA 59.722 52.381 0.00 0.00 0.00 2.87
116 117 2.347731 CGAGCCTGGGTAAAAGAGAAC 58.652 52.381 0.00 0.00 0.00 3.01
117 118 2.028020 CGAGCCTGGGTAAAAGAGAACT 60.028 50.000 0.00 0.00 0.00 3.01
118 119 3.339141 GAGCCTGGGTAAAAGAGAACTG 58.661 50.000 0.00 0.00 0.00 3.16
119 120 2.711547 AGCCTGGGTAAAAGAGAACTGT 59.288 45.455 0.00 0.00 0.00 3.55
120 121 3.075148 GCCTGGGTAAAAGAGAACTGTC 58.925 50.000 0.00 0.00 0.00 3.51
121 122 3.676093 CCTGGGTAAAAGAGAACTGTCC 58.324 50.000 0.00 0.00 0.00 4.02
122 123 3.072476 CCTGGGTAAAAGAGAACTGTCCA 59.928 47.826 0.00 0.00 0.00 4.02
123 124 4.263506 CCTGGGTAAAAGAGAACTGTCCAT 60.264 45.833 0.00 0.00 0.00 3.41
124 125 4.906618 TGGGTAAAAGAGAACTGTCCATC 58.093 43.478 0.00 0.00 0.00 3.51
125 126 4.349636 TGGGTAAAAGAGAACTGTCCATCA 59.650 41.667 0.00 0.00 0.00 3.07
126 127 4.695928 GGGTAAAAGAGAACTGTCCATCAC 59.304 45.833 0.00 0.00 0.00 3.06
127 128 4.695928 GGTAAAAGAGAACTGTCCATCACC 59.304 45.833 0.00 0.00 0.00 4.02
128 129 2.751166 AAGAGAACTGTCCATCACCG 57.249 50.000 0.00 0.00 0.00 4.94
129 130 1.633774 AGAGAACTGTCCATCACCGT 58.366 50.000 0.00 0.00 0.00 4.83
130 131 1.273606 AGAGAACTGTCCATCACCGTG 59.726 52.381 0.00 0.00 0.00 4.94
131 132 0.320771 AGAACTGTCCATCACCGTGC 60.321 55.000 0.00 0.00 0.00 5.34
132 133 0.320771 GAACTGTCCATCACCGTGCT 60.321 55.000 0.00 0.00 0.00 4.40
133 134 0.603707 AACTGTCCATCACCGTGCTG 60.604 55.000 0.00 0.00 0.00 4.41
134 135 2.358615 TGTCCATCACCGTGCTGC 60.359 61.111 0.00 0.00 0.00 5.25
135 136 3.127533 GTCCATCACCGTGCTGCC 61.128 66.667 0.00 0.00 0.00 4.85
136 137 3.321648 TCCATCACCGTGCTGCCT 61.322 61.111 0.00 0.00 0.00 4.75
137 138 2.360350 CCATCACCGTGCTGCCTT 60.360 61.111 0.00 0.00 0.00 4.35
138 139 2.693762 CCATCACCGTGCTGCCTTG 61.694 63.158 0.00 0.00 0.00 3.61
139 140 3.058160 ATCACCGTGCTGCCTTGC 61.058 61.111 0.00 0.00 0.00 4.01
140 141 3.557903 ATCACCGTGCTGCCTTGCT 62.558 57.895 0.00 0.00 0.00 3.91
141 142 2.184020 ATCACCGTGCTGCCTTGCTA 62.184 55.000 0.00 0.00 0.00 3.49
142 143 2.358737 ACCGTGCTGCCTTGCTAC 60.359 61.111 0.00 0.00 0.00 3.58
143 144 2.046892 CCGTGCTGCCTTGCTACT 60.047 61.111 0.00 0.00 0.00 2.57
144 145 1.672356 CCGTGCTGCCTTGCTACTT 60.672 57.895 0.00 0.00 0.00 2.24
145 146 1.639298 CCGTGCTGCCTTGCTACTTC 61.639 60.000 0.00 0.00 0.00 3.01
146 147 0.671781 CGTGCTGCCTTGCTACTTCT 60.672 55.000 0.00 0.00 0.00 2.85
147 148 0.801251 GTGCTGCCTTGCTACTTCTG 59.199 55.000 0.00 0.00 0.00 3.02
148 149 0.957395 TGCTGCCTTGCTACTTCTGC 60.957 55.000 0.00 0.00 0.00 4.26
149 150 0.676151 GCTGCCTTGCTACTTCTGCT 60.676 55.000 0.00 0.00 0.00 4.24
150 151 1.367659 CTGCCTTGCTACTTCTGCTC 58.632 55.000 0.00 0.00 0.00 4.26
151 152 0.979665 TGCCTTGCTACTTCTGCTCT 59.020 50.000 0.00 0.00 0.00 4.09
152 153 1.349026 TGCCTTGCTACTTCTGCTCTT 59.651 47.619 0.00 0.00 0.00 2.85
153 154 2.224621 TGCCTTGCTACTTCTGCTCTTT 60.225 45.455 0.00 0.00 0.00 2.52
154 155 2.161211 GCCTTGCTACTTCTGCTCTTTG 59.839 50.000 0.00 0.00 0.00 2.77
155 156 2.746362 CCTTGCTACTTCTGCTCTTTGG 59.254 50.000 0.00 0.00 0.00 3.28
156 157 2.479566 TGCTACTTCTGCTCTTTGGG 57.520 50.000 0.00 0.00 0.00 4.12
157 158 1.090728 GCTACTTCTGCTCTTTGGGC 58.909 55.000 0.00 0.00 0.00 5.36
158 159 1.611673 GCTACTTCTGCTCTTTGGGCA 60.612 52.381 0.00 0.00 38.10 5.36
159 160 2.783135 CTACTTCTGCTCTTTGGGCAA 58.217 47.619 0.00 0.00 39.30 4.52
160 161 2.299326 ACTTCTGCTCTTTGGGCAAT 57.701 45.000 0.00 0.00 39.30 3.56
161 162 1.891150 ACTTCTGCTCTTTGGGCAATG 59.109 47.619 0.00 0.00 39.30 2.82
162 163 1.891150 CTTCTGCTCTTTGGGCAATGT 59.109 47.619 0.00 0.00 39.30 2.71
163 164 1.250328 TCTGCTCTTTGGGCAATGTG 58.750 50.000 0.00 0.00 39.30 3.21
164 165 1.202915 TCTGCTCTTTGGGCAATGTGA 60.203 47.619 0.00 0.00 39.30 3.58
165 166 0.961019 TGCTCTTTGGGCAATGTGAC 59.039 50.000 0.00 0.00 36.71 3.67
172 173 3.939564 GGCAATGTGACCATCCCC 58.060 61.111 0.00 0.00 0.00 4.81
173 174 1.307647 GGCAATGTGACCATCCCCT 59.692 57.895 0.00 0.00 0.00 4.79
174 175 0.324645 GGCAATGTGACCATCCCCTT 60.325 55.000 0.00 0.00 0.00 3.95
175 176 0.819582 GCAATGTGACCATCCCCTTG 59.180 55.000 0.00 0.00 0.00 3.61
176 177 0.819582 CAATGTGACCATCCCCTTGC 59.180 55.000 0.00 0.00 0.00 4.01
177 178 0.324645 AATGTGACCATCCCCTTGCC 60.325 55.000 0.00 0.00 0.00 4.52
178 179 2.438434 GTGACCATCCCCTTGCCG 60.438 66.667 0.00 0.00 0.00 5.69
179 180 2.609299 TGACCATCCCCTTGCCGA 60.609 61.111 0.00 0.00 0.00 5.54
180 181 2.227757 TGACCATCCCCTTGCCGAA 61.228 57.895 0.00 0.00 0.00 4.30
181 182 1.749258 GACCATCCCCTTGCCGAAC 60.749 63.158 0.00 0.00 0.00 3.95
182 183 2.440247 CCATCCCCTTGCCGAACC 60.440 66.667 0.00 0.00 0.00 3.62
183 184 2.354729 CATCCCCTTGCCGAACCA 59.645 61.111 0.00 0.00 0.00 3.67
184 185 2.046285 CATCCCCTTGCCGAACCAC 61.046 63.158 0.00 0.00 0.00 4.16
185 186 2.534396 ATCCCCTTGCCGAACCACA 61.534 57.895 0.00 0.00 0.00 4.17
186 187 2.075355 ATCCCCTTGCCGAACCACAA 62.075 55.000 0.00 0.00 0.00 3.33
187 188 1.830408 CCCCTTGCCGAACCACAAA 60.830 57.895 0.00 0.00 0.00 2.83
188 189 1.659794 CCCTTGCCGAACCACAAAG 59.340 57.895 0.00 0.00 0.00 2.77
189 190 1.659794 CCTTGCCGAACCACAAAGG 59.340 57.895 0.00 0.00 45.67 3.11
190 191 1.659794 CTTGCCGAACCACAAAGGG 59.340 57.895 0.00 0.00 43.89 3.95
191 192 1.805428 CTTGCCGAACCACAAAGGGG 61.805 60.000 0.00 0.00 43.89 4.79
192 193 2.203437 GCCGAACCACAAAGGGGT 60.203 61.111 0.00 0.00 43.89 4.95
193 194 1.073548 GCCGAACCACAAAGGGGTA 59.926 57.895 0.00 0.00 43.89 3.69
194 195 0.958876 GCCGAACCACAAAGGGGTAG 60.959 60.000 0.00 0.00 43.89 3.18
195 196 0.958876 CCGAACCACAAAGGGGTAGC 60.959 60.000 0.00 0.00 43.89 3.58
196 197 0.958876 CGAACCACAAAGGGGTAGCC 60.959 60.000 1.07 1.07 43.89 3.93
197 198 0.611062 GAACCACAAAGGGGTAGCCC 60.611 60.000 23.15 23.15 44.51 5.19
198 199 1.071909 AACCACAAAGGGGTAGCCCT 61.072 55.000 27.44 27.44 44.66 5.19
199 200 1.000896 CCACAAAGGGGTAGCCCTG 60.001 63.158 32.93 23.61 44.66 4.45
200 201 1.678970 CACAAAGGGGTAGCCCTGC 60.679 63.158 32.93 5.34 44.66 4.85
201 202 2.043953 CAAAGGGGTAGCCCTGCC 60.044 66.667 32.93 4.94 44.66 4.85
207 208 4.209866 GGTAGCCCTGCCCCATGG 62.210 72.222 4.14 4.14 0.00 3.66
209 210 4.777546 TAGCCCTGCCCCATGGGT 62.778 66.667 29.33 11.53 46.51 4.51
212 213 3.432335 CCCTGCCCCATGGGTGAT 61.432 66.667 29.33 0.00 46.51 3.06
213 214 2.196776 CCTGCCCCATGGGTGATC 59.803 66.667 29.33 15.13 46.51 2.92
214 215 2.203252 CTGCCCCATGGGTGATCG 60.203 66.667 29.33 14.59 46.51 3.69
215 216 3.014538 TGCCCCATGGGTGATCGT 61.015 61.111 29.33 0.00 46.51 3.73
216 217 2.516930 GCCCCATGGGTGATCGTG 60.517 66.667 29.33 13.08 46.51 4.35
217 218 2.516930 CCCCATGGGTGATCGTGC 60.517 66.667 29.33 0.00 38.25 5.34
218 219 2.591753 CCCATGGGTGATCGTGCT 59.408 61.111 23.93 0.00 0.00 4.40
219 220 1.077501 CCCATGGGTGATCGTGCTT 60.078 57.895 23.93 0.00 0.00 3.91
220 221 1.097547 CCCATGGGTGATCGTGCTTC 61.098 60.000 23.93 0.00 0.00 3.86
221 222 1.097547 CCATGGGTGATCGTGCTTCC 61.098 60.000 2.85 0.00 0.00 3.46
222 223 0.392863 CATGGGTGATCGTGCTTCCA 60.393 55.000 0.00 0.00 0.00 3.53
223 224 0.392998 ATGGGTGATCGTGCTTCCAC 60.393 55.000 0.00 0.00 38.62 4.02
231 232 3.414700 GTGCTTCCACGCCGACAG 61.415 66.667 0.00 0.00 31.34 3.51
234 235 4.680237 CTTCCACGCCGACAGCCA 62.680 66.667 0.00 0.00 38.78 4.75
235 236 4.980805 TTCCACGCCGACAGCCAC 62.981 66.667 0.00 0.00 38.78 5.01
238 239 4.662961 CACGCCGACAGCCACAGA 62.663 66.667 0.00 0.00 38.78 3.41
239 240 4.664677 ACGCCGACAGCCACAGAC 62.665 66.667 0.00 0.00 38.78 3.51
240 241 4.662961 CGCCGACAGCCACAGACA 62.663 66.667 0.00 0.00 38.78 3.41
241 242 2.046892 GCCGACAGCCACAGACAT 60.047 61.111 0.00 0.00 34.35 3.06
242 243 2.393768 GCCGACAGCCACAGACATG 61.394 63.158 0.00 0.00 34.35 3.21
243 244 2.393768 CCGACAGCCACAGACATGC 61.394 63.158 0.00 0.00 0.00 4.06
244 245 2.733671 CGACAGCCACAGACATGCG 61.734 63.158 0.00 0.00 0.00 4.73
251 252 0.992072 CCACAGACATGCGTTCTACG 59.008 55.000 0.00 0.00 45.88 3.51
259 260 0.320421 ATGCGTTCTACGTGGCAACT 60.320 50.000 0.00 0.00 44.73 3.16
279 280 3.243975 ACTCGTTCGTGTTGGATTAAGGT 60.244 43.478 0.00 0.00 0.00 3.50
294 295 9.535170 TTGGATTAAGGTTCAATGGTAATACAA 57.465 29.630 0.00 0.00 34.24 2.41
329 330 5.575157 TGGTCAGGCCAAATCTATTTAACA 58.425 37.500 5.01 0.00 45.94 2.41
479 480 1.674441 CCTAGCCATGTGAATGTGCAG 59.326 52.381 0.00 0.00 0.00 4.41
480 481 2.362736 CTAGCCATGTGAATGTGCAGT 58.637 47.619 0.00 0.00 0.00 4.40
592 593 4.365514 AACATACAACATGTGAGGACCA 57.634 40.909 0.00 0.00 31.80 4.02
593 594 4.574674 ACATACAACATGTGAGGACCAT 57.425 40.909 0.00 0.00 0.00 3.55
598 599 3.244875 ACAACATGTGAGGACCATTAGCA 60.245 43.478 0.00 0.00 0.00 3.49
632 633 2.698274 GGTTGTCCTGACCCAACAATTT 59.302 45.455 0.00 0.00 42.09 1.82
659 660 4.973663 GGACAAAACCAATTAGACGTGTTG 59.026 41.667 0.00 0.00 32.11 3.33
695 696 3.002656 CCAGACAACTCACAATGTGACAC 59.997 47.826 12.63 0.00 37.67 3.67
730 1077 2.254918 TGCGTATTTGCGTTGGATTG 57.745 45.000 0.00 0.00 37.81 2.67
758 1105 6.535865 AGATAATGGTAATTACGCGTGAAACA 59.464 34.615 24.59 9.21 30.66 2.83
878 1230 0.251519 AAAAGCCAAGCCCCTCTCTG 60.252 55.000 0.00 0.00 0.00 3.35
890 1242 3.812167 GCCCCTCTCTGTCAGAAAACAAT 60.812 47.826 3.67 0.00 0.00 2.71
930 1296 3.850173 AGACTAGAAGAGAGAGTGGAGGT 59.150 47.826 0.00 0.00 0.00 3.85
942 1308 3.054802 AGAGTGGAGGTGAAATTAGCCAG 60.055 47.826 0.00 0.00 0.00 4.85
944 1310 1.354031 TGGAGGTGAAATTAGCCAGCA 59.646 47.619 0.00 0.00 33.61 4.41
948 1314 0.521291 GTGAAATTAGCCAGCACGCA 59.479 50.000 0.00 0.00 0.00 5.24
969 1336 1.532794 TCCATGCAACCAACCCACC 60.533 57.895 0.00 0.00 0.00 4.61
971 1338 2.203773 ATGCAACCAACCCACCCC 60.204 61.111 0.00 0.00 0.00 4.95
994 1361 5.480073 CCAATCTCCCATGAAAAACCTACAA 59.520 40.000 0.00 0.00 0.00 2.41
1007 1374 3.412237 ACCTACAACGCAAGGTACAAT 57.588 42.857 0.00 0.00 44.40 2.71
1009 1376 2.347452 CCTACAACGCAAGGTACAATCG 59.653 50.000 0.00 0.00 46.39 3.34
1087 1454 1.185618 CGGAGGTGGAGGACTTCACA 61.186 60.000 12.51 0.00 35.74 3.58
1123 1490 4.521062 GCCGAGCAGCTCATCCGT 62.521 66.667 22.49 0.00 0.00 4.69
1150 1517 1.891150 GAGAGTAACGTGTCCTTGGGA 59.109 52.381 0.00 0.00 0.00 4.37
1177 1547 4.716977 GTCCCCGTCTCCCCCTGT 62.717 72.222 0.00 0.00 0.00 4.00
1182 1552 2.603473 CGTCTCCCCCTGTGTGGA 60.603 66.667 0.00 0.00 38.35 4.02
1190 1560 1.483595 CCCCTGTGTGGAGCTCTCAA 61.484 60.000 14.64 0.00 38.35 3.02
1292 1662 1.773653 AGGATTGGGAGGAAGATGAGC 59.226 52.381 0.00 0.00 0.00 4.26
1362 1732 2.556792 CGAGATCTACGCCGCGAT 59.443 61.111 21.79 1.80 0.00 4.58
1409 1782 4.227864 AGCAACCATAAGAAGAAGAGGG 57.772 45.455 0.00 0.00 0.00 4.30
1474 1851 4.402155 TGTAATTCATGTGATTTCCAGGGC 59.598 41.667 0.00 0.00 0.00 5.19
1512 1890 3.269906 AGCTTGTAGTCCTCTCCTTCCTA 59.730 47.826 0.00 0.00 0.00 2.94
1525 1903 1.500474 CTTCCTATCACCAGGAGGCA 58.500 55.000 0.00 0.00 45.45 4.75
1531 1909 0.042431 ATCACCAGGAGGCAGAGTCT 59.958 55.000 0.00 0.00 39.06 3.24
1537 1915 1.879380 CAGGAGGCAGAGTCTCTATCG 59.121 57.143 0.94 0.00 34.33 2.92
1571 1950 7.280876 TCTCGCTGTTAAATCTTATCTTTGCAT 59.719 33.333 0.00 0.00 0.00 3.96
1596 1985 3.393278 AGAGTTACTTGTTGGTTGGGCTA 59.607 43.478 0.00 0.00 0.00 3.93
1602 1991 0.251916 TGTTGGTTGGGCTAGATCCG 59.748 55.000 0.00 0.00 0.00 4.18
1623 2012 1.133513 TCCATGGTGGCTTGTGAACTT 60.134 47.619 12.58 0.00 37.47 2.66
1655 2044 9.883142 TGAATTGGTTTTGTTTTTCTCATACTT 57.117 25.926 0.00 0.00 0.00 2.24
1763 2193 2.046988 CCACCGCTGCATGACTGA 60.047 61.111 0.00 0.00 0.00 3.41
1777 2207 3.375782 TGACTGATCGATGCCTATGTG 57.624 47.619 0.54 0.00 0.00 3.21
1778 2208 2.064762 GACTGATCGATGCCTATGTGC 58.935 52.381 0.54 0.00 0.00 4.57
1845 2275 8.030692 TCTGATTCGCAAAAATCTTGATTGAAT 58.969 29.630 0.00 2.06 36.73 2.57
1853 2283 8.932791 GCAAAAATCTTGATTGAATGATTCAGT 58.067 29.630 8.01 5.37 41.38 3.41
1863 2293 9.642327 TGATTGAATGATTCAGTAAATTTGGTG 57.358 29.630 8.01 0.00 41.38 4.17
1899 2329 1.070134 TCTGGTAACACTGAGGTGCAC 59.930 52.381 8.80 8.80 46.57 4.57
1919 2349 2.779506 CCTCACTGGTTTGGGAGTTAC 58.220 52.381 0.00 0.00 0.00 2.50
1929 2359 2.507407 TGGGAGTTACATTTCCTGCC 57.493 50.000 0.00 0.00 37.24 4.85
1930 2360 1.339631 TGGGAGTTACATTTCCTGCCG 60.340 52.381 0.00 0.00 39.36 5.69
1984 2414 2.180086 TCAGTAGATATGGTGGAGGGCT 59.820 50.000 0.00 0.00 0.00 5.19
1989 2419 0.769776 ATATGGTGGAGGGCTGGAGG 60.770 60.000 0.00 0.00 0.00 4.30
2006 2436 1.045911 AGGGCCGAGTCTCTTCATCC 61.046 60.000 0.00 0.00 0.00 3.51
2011 2441 2.831333 CCGAGTCTCTTCATCCAATGG 58.169 52.381 0.00 0.00 0.00 3.16
2013 2443 2.208431 GAGTCTCTTCATCCAATGGCG 58.792 52.381 0.00 0.00 0.00 5.69
2017 2447 0.252761 TCTTCATCCAATGGCGAGCA 59.747 50.000 0.00 0.00 0.00 4.26
2053 2483 1.009829 CCTTGCCTCGTCACATTAGC 58.990 55.000 0.00 0.00 0.00 3.09
2054 2484 1.406069 CCTTGCCTCGTCACATTAGCT 60.406 52.381 0.00 0.00 0.00 3.32
2095 2529 2.313717 CTTGCACGCGACATGATGGG 62.314 60.000 15.93 1.83 0.00 4.00
2108 2542 3.203710 ACATGATGGGATGTGGTCAATCT 59.796 43.478 0.00 0.00 35.17 2.40
2109 2543 3.286329 TGATGGGATGTGGTCAATCTG 57.714 47.619 0.00 0.00 0.00 2.90
2110 2544 2.092267 TGATGGGATGTGGTCAATCTGG 60.092 50.000 0.00 0.00 0.00 3.86
2378 2812 2.359900 GGTGGGAGACAATGCAAGTAG 58.640 52.381 0.00 0.00 0.00 2.57
2397 2831 2.500229 AGCTAGCCACGAGAGAGATAC 58.500 52.381 12.13 0.00 0.00 2.24
2414 2848 3.954904 AGATACACATCTTGCCTCTACGT 59.045 43.478 0.00 0.00 38.41 3.57
2424 2858 1.278238 GCCTCTACGTGGTTCATTCG 58.722 55.000 0.00 0.00 0.00 3.34
2438 2872 3.529634 TCATTCGTTTTACACCAAGCG 57.470 42.857 0.00 0.00 0.00 4.68
2439 2873 1.976045 CATTCGTTTTACACCAAGCGC 59.024 47.619 0.00 0.00 0.00 5.92
2441 2875 0.863144 TCGTTTTACACCAAGCGCTC 59.137 50.000 12.06 0.00 0.00 5.03
2459 2893 4.468643 CGCTCGAGGTTATAATCTGAGAC 58.531 47.826 20.37 13.79 0.00 3.36
2462 2896 5.688176 GCTCGAGGTTATAATCTGAGACAAC 59.312 44.000 20.37 6.90 0.00 3.32
2537 2971 8.307483 AGGTGATCCTACAAATATGATAGTTCG 58.693 37.037 0.00 0.00 43.12 3.95
2538 2972 8.304596 GGTGATCCTACAAATATGATAGTTCGA 58.695 37.037 0.00 0.00 0.00 3.71
2541 2975 9.562583 GATCCTACAAATATGATAGTTCGAGTC 57.437 37.037 0.00 0.00 0.00 3.36
2544 2978 5.529791 ACAAATATGATAGTTCGAGTCCGG 58.470 41.667 0.00 0.00 36.24 5.14
2554 2988 3.064931 GTTCGAGTCCGGAATGAGTTTT 58.935 45.455 10.26 0.00 36.24 2.43
2558 2992 2.924290 GAGTCCGGAATGAGTTTTCGAG 59.076 50.000 10.26 0.00 0.00 4.04
2559 2993 2.299297 AGTCCGGAATGAGTTTTCGAGT 59.701 45.455 5.23 0.00 0.00 4.18
2577 3011 2.618241 GAGTGTTGGTGCAAGATGACAA 59.382 45.455 0.00 0.00 0.00 3.18
2590 3024 6.751425 TGCAAGATGACAACTTTTGTTTGTAG 59.249 34.615 0.00 0.00 45.52 2.74
2622 3056 3.319137 AACTTCAGATTGAGCGCACTA 57.681 42.857 11.47 0.00 0.00 2.74
2627 3061 2.736721 TCAGATTGAGCGCACTAACAAC 59.263 45.455 11.47 3.65 0.00 3.32
2628 3062 1.726791 AGATTGAGCGCACTAACAACG 59.273 47.619 11.47 0.00 0.00 4.10
2664 3098 2.285083 TCAGTTCCACCACAAAGTTCG 58.715 47.619 0.00 0.00 0.00 3.95
2665 3099 2.093394 TCAGTTCCACCACAAAGTTCGA 60.093 45.455 0.00 0.00 0.00 3.71
2681 3115 2.456119 CGATCGGCTGGTGTGAAGC 61.456 63.158 7.38 0.00 40.06 3.86
2719 3153 3.339141 CTTGGAAGGTTGGTTCTAGCTC 58.661 50.000 0.00 0.00 0.00 4.09
2741 3175 9.871238 AGCTCGTAGAAGAAAATAAAGATACAA 57.129 29.630 0.00 0.00 34.09 2.41
2837 3271 5.604565 ACTGTGATGATGAGCATTTCGATA 58.395 37.500 0.00 0.00 37.34 2.92
2847 3281 8.506437 TGATGAGCATTTCGATAATTCCATAAC 58.494 33.333 0.00 0.00 0.00 1.89
2854 3288 9.273016 CATTTCGATAATTCCATAACTGGTACT 57.727 33.333 0.00 0.00 43.61 2.73
2857 3291 7.600065 TCGATAATTCCATAACTGGTACTAGC 58.400 38.462 6.09 0.00 43.61 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.892784 TTTGGGCCGAACGAATTTTT 57.107 40.000 0.79 0.00 0.00 1.94
28 29 2.892784 TTTTGGGCCGAACGAATTTT 57.107 40.000 5.46 0.00 0.00 1.82
29 30 2.036604 ACATTTTGGGCCGAACGAATTT 59.963 40.909 5.46 0.00 0.00 1.82
30 31 1.616374 ACATTTTGGGCCGAACGAATT 59.384 42.857 5.46 0.00 0.00 2.17
31 32 1.201414 GACATTTTGGGCCGAACGAAT 59.799 47.619 5.46 0.00 0.00 3.34
32 33 0.594110 GACATTTTGGGCCGAACGAA 59.406 50.000 5.46 0.00 0.00 3.85
33 34 0.535328 TGACATTTTGGGCCGAACGA 60.535 50.000 5.46 0.00 0.00 3.85
34 35 0.386731 GTGACATTTTGGGCCGAACG 60.387 55.000 5.46 3.01 0.00 3.95
35 36 0.386731 CGTGACATTTTGGGCCGAAC 60.387 55.000 5.46 0.00 0.00 3.95
36 37 1.519751 CCGTGACATTTTGGGCCGAA 61.520 55.000 0.79 0.79 0.00 4.30
37 38 1.969064 CCGTGACATTTTGGGCCGA 60.969 57.895 0.00 0.00 0.00 5.54
38 39 1.312371 ATCCGTGACATTTTGGGCCG 61.312 55.000 0.00 0.00 0.00 6.13
39 40 0.173255 CATCCGTGACATTTTGGGCC 59.827 55.000 0.00 0.00 0.00 5.80
40 41 0.887933 ACATCCGTGACATTTTGGGC 59.112 50.000 0.00 0.00 0.00 5.36
41 42 1.885887 ACACATCCGTGACATTTTGGG 59.114 47.619 0.00 0.00 46.80 4.12
42 43 2.813754 AGACACATCCGTGACATTTTGG 59.186 45.455 0.00 0.00 46.80 3.28
43 44 4.488126 AAGACACATCCGTGACATTTTG 57.512 40.909 0.00 0.00 46.80 2.44
44 45 5.514274 AAAAGACACATCCGTGACATTTT 57.486 34.783 0.00 1.58 46.80 1.82
45 46 5.514274 AAAAAGACACATCCGTGACATTT 57.486 34.783 0.00 0.00 46.80 2.32
65 66 7.168469 GCTTTGAAGCGTAAAATCCTACAAAAA 59.832 33.333 0.00 0.00 42.88 1.94
66 67 6.639279 GCTTTGAAGCGTAAAATCCTACAAAA 59.361 34.615 0.00 0.00 42.88 2.44
67 68 6.146898 GCTTTGAAGCGTAAAATCCTACAAA 58.853 36.000 0.00 0.00 42.88 2.83
68 69 5.695818 GCTTTGAAGCGTAAAATCCTACAA 58.304 37.500 0.00 0.00 42.88 2.41
69 70 5.291293 GCTTTGAAGCGTAAAATCCTACA 57.709 39.130 0.00 0.00 42.88 2.74
83 84 0.890996 AGGCTCGGGTTGCTTTGAAG 60.891 55.000 0.00 0.00 0.00 3.02
84 85 1.150536 AGGCTCGGGTTGCTTTGAA 59.849 52.632 0.00 0.00 0.00 2.69
85 86 1.600636 CAGGCTCGGGTTGCTTTGA 60.601 57.895 0.00 0.00 0.00 2.69
86 87 2.629656 CCAGGCTCGGGTTGCTTTG 61.630 63.158 0.00 0.00 0.00 2.77
87 88 2.282462 CCAGGCTCGGGTTGCTTT 60.282 61.111 0.00 0.00 0.00 3.51
88 89 4.351054 CCCAGGCTCGGGTTGCTT 62.351 66.667 12.34 0.00 41.83 3.91
95 96 0.902531 TCTCTTTTACCCAGGCTCGG 59.097 55.000 0.00 0.00 0.00 4.63
96 97 2.028020 AGTTCTCTTTTACCCAGGCTCG 60.028 50.000 0.00 0.00 0.00 5.03
97 98 3.244596 ACAGTTCTCTTTTACCCAGGCTC 60.245 47.826 0.00 0.00 0.00 4.70
98 99 2.711547 ACAGTTCTCTTTTACCCAGGCT 59.288 45.455 0.00 0.00 0.00 4.58
99 100 3.075148 GACAGTTCTCTTTTACCCAGGC 58.925 50.000 0.00 0.00 0.00 4.85
100 101 3.072476 TGGACAGTTCTCTTTTACCCAGG 59.928 47.826 0.00 0.00 0.00 4.45
101 102 4.351874 TGGACAGTTCTCTTTTACCCAG 57.648 45.455 0.00 0.00 0.00 4.45
102 103 4.349636 TGATGGACAGTTCTCTTTTACCCA 59.650 41.667 0.00 0.00 0.00 4.51
103 104 4.695928 GTGATGGACAGTTCTCTTTTACCC 59.304 45.833 0.00 0.00 0.00 3.69
104 105 4.695928 GGTGATGGACAGTTCTCTTTTACC 59.304 45.833 0.00 0.00 0.00 2.85
105 106 4.389077 CGGTGATGGACAGTTCTCTTTTAC 59.611 45.833 0.00 0.00 0.00 2.01
106 107 4.039973 ACGGTGATGGACAGTTCTCTTTTA 59.960 41.667 0.00 0.00 26.83 1.52
107 108 3.181454 ACGGTGATGGACAGTTCTCTTTT 60.181 43.478 0.00 0.00 26.83 2.27
108 109 2.368875 ACGGTGATGGACAGTTCTCTTT 59.631 45.455 0.00 0.00 26.83 2.52
109 110 1.971357 ACGGTGATGGACAGTTCTCTT 59.029 47.619 0.00 0.00 26.83 2.85
110 111 1.273606 CACGGTGATGGACAGTTCTCT 59.726 52.381 0.74 0.00 29.43 3.10
111 112 1.714794 CACGGTGATGGACAGTTCTC 58.285 55.000 0.74 0.00 29.43 2.87
112 113 0.320771 GCACGGTGATGGACAGTTCT 60.321 55.000 13.29 0.00 29.43 3.01
113 114 0.320771 AGCACGGTGATGGACAGTTC 60.321 55.000 13.29 0.00 29.43 3.01
114 115 0.603707 CAGCACGGTGATGGACAGTT 60.604 55.000 18.14 0.00 29.43 3.16
115 116 1.004560 CAGCACGGTGATGGACAGT 60.005 57.895 18.14 0.00 32.54 3.55
116 117 2.393768 GCAGCACGGTGATGGACAG 61.394 63.158 25.68 2.49 33.75 3.51
117 118 2.358615 GCAGCACGGTGATGGACA 60.359 61.111 25.68 0.00 33.75 4.02
118 119 3.127533 GGCAGCACGGTGATGGAC 61.128 66.667 25.68 11.37 33.75 4.02
119 120 2.894257 AAGGCAGCACGGTGATGGA 61.894 57.895 25.68 0.00 33.75 3.41
120 121 2.360350 AAGGCAGCACGGTGATGG 60.360 61.111 25.68 9.53 33.75 3.51
121 122 2.872557 CAAGGCAGCACGGTGATG 59.127 61.111 21.24 21.24 36.74 3.07
122 123 2.184020 TAGCAAGGCAGCACGGTGAT 62.184 55.000 13.29 1.50 36.85 3.06
123 124 2.878089 TAGCAAGGCAGCACGGTGA 61.878 57.895 13.29 0.00 36.85 4.02
124 125 2.358615 TAGCAAGGCAGCACGGTG 60.359 61.111 3.15 3.15 36.85 4.94
125 126 2.358737 GTAGCAAGGCAGCACGGT 60.359 61.111 4.78 0.00 36.85 4.83
126 127 1.639298 GAAGTAGCAAGGCAGCACGG 61.639 60.000 4.78 0.00 36.85 4.94
127 128 0.671781 AGAAGTAGCAAGGCAGCACG 60.672 55.000 4.78 0.00 36.85 5.34
128 129 0.801251 CAGAAGTAGCAAGGCAGCAC 59.199 55.000 4.78 1.64 36.85 4.40
129 130 0.957395 GCAGAAGTAGCAAGGCAGCA 60.957 55.000 4.78 0.00 36.85 4.41
130 131 0.676151 AGCAGAAGTAGCAAGGCAGC 60.676 55.000 0.00 0.00 0.00 5.25
131 132 1.066286 AGAGCAGAAGTAGCAAGGCAG 60.066 52.381 0.00 0.00 0.00 4.85
132 133 0.979665 AGAGCAGAAGTAGCAAGGCA 59.020 50.000 0.00 0.00 0.00 4.75
133 134 2.106477 AAGAGCAGAAGTAGCAAGGC 57.894 50.000 0.00 0.00 0.00 4.35
134 135 2.746362 CCAAAGAGCAGAAGTAGCAAGG 59.254 50.000 0.00 0.00 0.00 3.61
135 136 2.746362 CCCAAAGAGCAGAAGTAGCAAG 59.254 50.000 0.00 0.00 0.00 4.01
136 137 2.783135 CCCAAAGAGCAGAAGTAGCAA 58.217 47.619 0.00 0.00 0.00 3.91
137 138 1.611673 GCCCAAAGAGCAGAAGTAGCA 60.612 52.381 0.00 0.00 0.00 3.49
138 139 1.090728 GCCCAAAGAGCAGAAGTAGC 58.909 55.000 0.00 0.00 0.00 3.58
139 140 2.479566 TGCCCAAAGAGCAGAAGTAG 57.520 50.000 0.00 0.00 34.69 2.57
140 141 2.949177 TTGCCCAAAGAGCAGAAGTA 57.051 45.000 0.00 0.00 42.17 2.24
141 142 1.891150 CATTGCCCAAAGAGCAGAAGT 59.109 47.619 0.00 0.00 42.17 3.01
142 143 1.891150 ACATTGCCCAAAGAGCAGAAG 59.109 47.619 0.00 0.00 42.17 2.85
143 144 1.614903 CACATTGCCCAAAGAGCAGAA 59.385 47.619 0.00 0.00 42.17 3.02
144 145 1.202915 TCACATTGCCCAAAGAGCAGA 60.203 47.619 0.00 0.00 42.17 4.26
145 146 1.068055 GTCACATTGCCCAAAGAGCAG 60.068 52.381 0.00 0.00 42.17 4.24
146 147 0.961019 GTCACATTGCCCAAAGAGCA 59.039 50.000 0.00 0.00 38.81 4.26
147 148 0.244721 GGTCACATTGCCCAAAGAGC 59.755 55.000 0.00 0.00 0.00 4.09
148 149 1.619654 TGGTCACATTGCCCAAAGAG 58.380 50.000 0.00 0.00 0.00 2.85
149 150 2.170166 GATGGTCACATTGCCCAAAGA 58.830 47.619 0.00 0.00 37.47 2.52
150 151 1.205417 GGATGGTCACATTGCCCAAAG 59.795 52.381 0.00 0.00 37.47 2.77
151 152 1.265236 GGATGGTCACATTGCCCAAA 58.735 50.000 0.00 0.00 37.47 3.28
152 153 0.614415 GGGATGGTCACATTGCCCAA 60.614 55.000 0.00 0.00 39.70 4.12
153 154 1.000233 GGGATGGTCACATTGCCCA 60.000 57.895 0.00 0.00 39.70 5.36
154 155 1.758122 GGGGATGGTCACATTGCCC 60.758 63.158 0.00 0.00 39.37 5.36
155 156 0.324645 AAGGGGATGGTCACATTGCC 60.325 55.000 0.00 0.00 37.47 4.52
156 157 0.819582 CAAGGGGATGGTCACATTGC 59.180 55.000 0.00 0.00 34.71 3.56
157 158 0.819582 GCAAGGGGATGGTCACATTG 59.180 55.000 2.50 2.50 43.70 2.82
158 159 0.324645 GGCAAGGGGATGGTCACATT 60.325 55.000 0.00 0.00 37.47 2.71
159 160 1.307647 GGCAAGGGGATGGTCACAT 59.692 57.895 0.00 0.00 40.85 3.21
160 161 2.763215 GGCAAGGGGATGGTCACA 59.237 61.111 0.00 0.00 0.00 3.58
161 162 2.438434 CGGCAAGGGGATGGTCAC 60.438 66.667 0.00 0.00 0.00 3.67
162 163 2.227757 TTCGGCAAGGGGATGGTCA 61.228 57.895 0.00 0.00 0.00 4.02
163 164 1.749258 GTTCGGCAAGGGGATGGTC 60.749 63.158 0.00 0.00 0.00 4.02
164 165 2.355115 GTTCGGCAAGGGGATGGT 59.645 61.111 0.00 0.00 0.00 3.55
165 166 2.440247 GGTTCGGCAAGGGGATGG 60.440 66.667 0.00 0.00 0.00 3.51
166 167 2.046285 GTGGTTCGGCAAGGGGATG 61.046 63.158 0.00 0.00 0.00 3.51
167 168 2.075355 TTGTGGTTCGGCAAGGGGAT 62.075 55.000 0.00 0.00 0.00 3.85
168 169 2.285889 TTTGTGGTTCGGCAAGGGGA 62.286 55.000 0.00 0.00 0.00 4.81
169 170 1.805428 CTTTGTGGTTCGGCAAGGGG 61.805 60.000 0.00 0.00 0.00 4.79
170 171 1.659794 CTTTGTGGTTCGGCAAGGG 59.340 57.895 0.00 0.00 0.00 3.95
171 172 1.659794 CCTTTGTGGTTCGGCAAGG 59.340 57.895 0.00 0.00 0.00 3.61
172 173 1.659794 CCCTTTGTGGTTCGGCAAG 59.340 57.895 0.00 0.00 0.00 4.01
173 174 1.830408 CCCCTTTGTGGTTCGGCAA 60.830 57.895 0.00 0.00 0.00 4.52
174 175 1.706995 TACCCCTTTGTGGTTCGGCA 61.707 55.000 0.00 0.00 37.31 5.69
175 176 0.958876 CTACCCCTTTGTGGTTCGGC 60.959 60.000 0.00 0.00 37.31 5.54
176 177 0.958876 GCTACCCCTTTGTGGTTCGG 60.959 60.000 0.00 0.00 37.31 4.30
177 178 0.958876 GGCTACCCCTTTGTGGTTCG 60.959 60.000 0.00 0.00 37.31 3.95
178 179 2.957060 GGCTACCCCTTTGTGGTTC 58.043 57.895 0.00 0.00 37.31 3.62
189 190 4.209866 CATGGGGCAGGGCTACCC 62.210 72.222 0.00 0.00 45.90 3.69
190 191 4.209866 CCATGGGGCAGGGCTACC 62.210 72.222 2.85 0.00 0.00 3.18
191 192 4.209866 CCCATGGGGCAGGGCTAC 62.210 72.222 24.53 0.00 38.44 3.58
201 202 1.077501 AAGCACGATCACCCATGGG 60.078 57.895 30.23 30.23 42.03 4.00
202 203 1.097547 GGAAGCACGATCACCCATGG 61.098 60.000 4.14 4.14 0.00 3.66
203 204 0.392863 TGGAAGCACGATCACCCATG 60.393 55.000 0.00 0.00 0.00 3.66
204 205 0.392998 GTGGAAGCACGATCACCCAT 60.393 55.000 0.00 0.00 0.00 4.00
205 206 1.003839 GTGGAAGCACGATCACCCA 60.004 57.895 0.00 0.00 0.00 4.51
206 207 3.890674 GTGGAAGCACGATCACCC 58.109 61.111 0.00 0.00 0.00 4.61
214 215 3.414700 CTGTCGGCGTGGAAGCAC 61.415 66.667 6.85 0.00 39.27 4.40
217 218 4.680237 TGGCTGTCGGCGTGGAAG 62.680 66.667 6.85 1.60 42.94 3.46
218 219 4.980805 GTGGCTGTCGGCGTGGAA 62.981 66.667 6.85 0.00 42.94 3.53
221 222 4.662961 TCTGTGGCTGTCGGCGTG 62.663 66.667 6.85 0.00 42.94 5.34
222 223 4.664677 GTCTGTGGCTGTCGGCGT 62.665 66.667 6.85 0.00 42.94 5.68
223 224 3.939837 ATGTCTGTGGCTGTCGGCG 62.940 63.158 0.00 0.00 42.94 6.46
224 225 2.046892 ATGTCTGTGGCTGTCGGC 60.047 61.111 0.00 0.00 40.90 5.54
225 226 2.393768 GCATGTCTGTGGCTGTCGG 61.394 63.158 0.00 0.00 0.00 4.79
226 227 2.733671 CGCATGTCTGTGGCTGTCG 61.734 63.158 0.00 0.00 0.00 4.35
227 228 1.230635 AACGCATGTCTGTGGCTGTC 61.231 55.000 0.00 0.00 37.19 3.51
228 229 1.227943 AACGCATGTCTGTGGCTGT 60.228 52.632 0.00 0.00 37.19 4.40
229 230 0.952497 AGAACGCATGTCTGTGGCTG 60.952 55.000 0.00 0.00 37.19 4.85
230 231 0.608130 TAGAACGCATGTCTGTGGCT 59.392 50.000 0.00 0.00 37.19 4.75
231 232 0.721718 GTAGAACGCATGTCTGTGGC 59.278 55.000 0.00 0.00 37.19 5.01
232 233 0.992072 CGTAGAACGCATGTCTGTGG 59.008 55.000 0.00 0.00 37.19 4.17
244 245 1.454653 GAACGAGTTGCCACGTAGAAC 59.545 52.381 0.00 0.00 41.87 3.01
251 252 0.315869 CAACACGAACGAGTTGCCAC 60.316 55.000 19.74 0.00 39.12 5.01
259 260 3.389925 ACCTTAATCCAACACGAACGA 57.610 42.857 0.14 0.00 0.00 3.85
279 280 9.357161 AGGTTTTACACTTGTATTACCATTGAA 57.643 29.630 16.66 0.00 37.07 2.69
326 327 6.493115 TCTTTTGGACACATCAATATGGTGTT 59.507 34.615 0.00 0.00 38.88 3.32
327 328 6.009589 TCTTTTGGACACATCAATATGGTGT 58.990 36.000 0.00 0.00 43.61 4.16
328 329 6.513806 TCTTTTGGACACATCAATATGGTG 57.486 37.500 0.00 0.00 37.43 4.17
329 330 5.126061 GCTCTTTTGGACACATCAATATGGT 59.874 40.000 0.00 0.00 37.43 3.55
479 480 3.242511 GGTTTCACACTCGTTGTAACCAC 60.243 47.826 14.54 2.99 42.83 4.16
480 481 2.937799 GGTTTCACACTCGTTGTAACCA 59.062 45.455 14.54 0.00 42.83 3.67
566 567 6.597672 GGTCCTCACATGTTGTATGTTTATGA 59.402 38.462 0.00 0.00 0.00 2.15
570 571 4.724399 TGGTCCTCACATGTTGTATGTTT 58.276 39.130 0.00 0.00 0.00 2.83
598 599 3.916580 GGACAACCATCGACGTGTCGT 62.917 57.143 20.44 4.93 43.55 4.34
610 611 0.626382 TTGTTGGGTCAGGACAACCA 59.374 50.000 1.41 0.00 44.72 3.67
659 660 3.889196 TGTCTGGTTAATCAAACGTGC 57.111 42.857 0.00 0.00 39.13 5.34
695 696 3.478394 CATCACCGTGTGGACGCG 61.478 66.667 3.53 3.53 44.68 6.01
730 1077 5.050634 TCACGCGTAATTACCATTATCTTGC 60.051 40.000 13.44 3.57 0.00 4.01
758 1105 3.129287 GGAATCGATTTGGCATGACAACT 59.871 43.478 15.21 9.10 0.00 3.16
821 1173 7.578203 TCCCCTTGTATTTTTGGAAATGTTTT 58.422 30.769 0.00 0.00 36.22 2.43
878 1230 6.385649 TGGTTGTTCCTATTGTTTTCTGAC 57.614 37.500 0.00 0.00 37.07 3.51
890 1242 7.798071 TCTAGTCTTTTCTTTGGTTGTTCCTA 58.202 34.615 0.00 0.00 37.07 2.94
930 1296 1.132834 CATGCGTGCTGGCTAATTTCA 59.867 47.619 0.00 0.00 0.00 2.69
948 1314 0.178938 TGGGTTGGTTGCATGGACAT 60.179 50.000 0.00 0.00 0.00 3.06
962 1329 0.855400 ATGGGAGATTGGGGTGGGTT 60.855 55.000 0.00 0.00 0.00 4.11
969 1336 3.444029 AGGTTTTTCATGGGAGATTGGG 58.556 45.455 0.00 0.00 0.00 4.12
971 1338 6.389906 GTTGTAGGTTTTTCATGGGAGATTG 58.610 40.000 0.00 0.00 0.00 2.67
994 1361 0.319083 TCACCGATTGTACCTTGCGT 59.681 50.000 0.00 0.00 0.00 5.24
1007 1374 0.252513 TCCATCTTCCCCTTCACCGA 60.253 55.000 0.00 0.00 0.00 4.69
1009 1376 0.106967 GCTCCATCTTCCCCTTCACC 60.107 60.000 0.00 0.00 0.00 4.02
1063 1430 3.992641 TCCTCCACCTCCGCTGGA 61.993 66.667 0.00 0.00 36.34 3.86
1069 1436 0.610687 CTGTGAAGTCCTCCACCTCC 59.389 60.000 0.00 0.00 32.61 4.30
1123 1490 2.417933 GGACACGTTACTCTCGCTAAGA 59.582 50.000 0.00 0.00 0.00 2.10
1177 1547 1.615883 GACTGACTTGAGAGCTCCACA 59.384 52.381 10.93 8.66 0.00 4.17
1182 1552 1.077005 AGGAGGACTGACTTGAGAGCT 59.923 52.381 0.00 0.00 0.00 4.09
1190 1560 0.629058 GGAGGAGAGGAGGACTGACT 59.371 60.000 0.00 0.00 0.00 3.41
1249 1619 2.481276 GGAACCGCCAAGAATTATTGCC 60.481 50.000 7.31 0.00 36.34 4.52
1409 1782 3.075283 TCATCTCTCCTCATCTACTCCCC 59.925 52.174 0.00 0.00 0.00 4.81
1474 1851 2.656560 AGCTCAACCTACAAGCTACG 57.343 50.000 0.00 0.00 44.28 3.51
1512 1890 0.042431 AGACTCTGCCTCCTGGTGAT 59.958 55.000 0.00 0.00 35.27 3.06
1525 1903 6.073440 GCGAGAAAGATAACGATAGAGACTCT 60.073 42.308 10.47 10.47 41.38 3.24
1531 1909 5.752892 ACAGCGAGAAAGATAACGATAGA 57.247 39.130 0.00 0.00 41.38 1.98
1571 1950 4.581409 GCCCAACCAACAAGTAACTCTTAA 59.419 41.667 0.00 0.00 34.66 1.85
1577 1956 3.746940 TCTAGCCCAACCAACAAGTAAC 58.253 45.455 0.00 0.00 0.00 2.50
1596 1985 1.274703 AAGCCACCATGGACGGATCT 61.275 55.000 21.47 8.81 40.96 2.75
1602 1991 0.598065 GTTCACAAGCCACCATGGAC 59.402 55.000 21.47 7.45 40.96 4.02
1623 2012 9.097257 GAGAAAAACAAAACCAATTCATCTCAA 57.903 29.630 0.00 0.00 0.00 3.02
1655 2044 0.392998 GCCTAGCCAGCTAGCAACAA 60.393 55.000 18.83 0.00 43.35 2.83
1748 2178 1.520120 CGATCAGTCATGCAGCGGT 60.520 57.895 0.00 0.00 0.00 5.68
1777 2207 8.255394 AGTAATTAATTGCCAAAGTTGAATGC 57.745 30.769 11.05 0.00 0.00 3.56
1778 2208 8.872845 GGAGTAATTAATTGCCAAAGTTGAATG 58.127 33.333 11.05 0.00 0.00 2.67
1899 2329 2.105821 TGTAACTCCCAAACCAGTGAGG 59.894 50.000 0.00 0.00 45.67 3.86
1909 2339 2.802719 GGCAGGAAATGTAACTCCCAA 58.197 47.619 0.00 0.00 31.50 4.12
1929 2359 2.640684 GCACACGGCAATCATTTCG 58.359 52.632 0.00 0.00 43.97 3.46
1984 2414 1.682684 GAAGAGACTCGGCCCTCCA 60.683 63.158 0.00 0.00 0.00 3.86
1989 2419 0.537188 TTGGATGAAGAGACTCGGCC 59.463 55.000 0.00 0.00 0.00 6.13
2006 2436 1.530441 CGAAGAACATGCTCGCCATTG 60.530 52.381 0.00 0.00 29.71 2.82
2011 2441 2.603110 TGTATTCGAAGAACATGCTCGC 59.397 45.455 11.04 0.00 45.90 5.03
2013 2443 4.631813 AGGTTGTATTCGAAGAACATGCTC 59.368 41.667 14.71 0.00 45.90 4.26
2017 2447 4.156008 GGCAAGGTTGTATTCGAAGAACAT 59.844 41.667 14.71 7.62 45.90 2.71
2053 2483 1.734465 GACTTGCCTGAATCGACCAAG 59.266 52.381 0.00 0.00 38.95 3.61
2054 2484 1.610624 GGACTTGCCTGAATCGACCAA 60.611 52.381 0.00 0.00 0.00 3.67
2355 2789 2.438434 GCATTGTCTCCCACCCCG 60.438 66.667 0.00 0.00 0.00 5.73
2378 2812 2.031508 GTGTATCTCTCTCGTGGCTAGC 60.032 54.545 6.04 6.04 0.00 3.42
2397 2831 1.066858 ACCACGTAGAGGCAAGATGTG 60.067 52.381 0.00 0.00 43.95 3.21
2414 2848 4.498345 GCTTGGTGTAAAACGAATGAACCA 60.498 41.667 0.00 0.00 34.52 3.67
2424 2858 0.863144 TCGAGCGCTTGGTGTAAAAC 59.137 50.000 24.31 0.00 0.00 2.43
2438 2872 5.440234 TGTCTCAGATTATAACCTCGAGC 57.560 43.478 6.99 0.00 0.00 5.03
2439 2873 7.033530 AGTTGTCTCAGATTATAACCTCGAG 57.966 40.000 5.13 5.13 0.00 4.04
2441 2875 6.858993 GCTAGTTGTCTCAGATTATAACCTCG 59.141 42.308 0.00 0.00 0.00 4.63
2507 2941 9.442047 CTATCATATTTGTAGGATCACCTTTCC 57.558 37.037 0.00 0.00 45.36 3.13
2512 2946 8.304596 TCGAACTATCATATTTGTAGGATCACC 58.695 37.037 0.00 0.00 0.00 4.02
2537 2971 2.924290 CTCGAAAACTCATTCCGGACTC 59.076 50.000 1.83 0.00 0.00 3.36
2538 2972 2.299297 ACTCGAAAACTCATTCCGGACT 59.701 45.455 1.83 0.00 0.00 3.85
2541 2975 2.413837 ACACTCGAAAACTCATTCCGG 58.586 47.619 0.00 0.00 0.00 5.14
2544 2978 4.527564 CACCAACACTCGAAAACTCATTC 58.472 43.478 0.00 0.00 0.00 2.67
2554 2988 1.069978 TCATCTTGCACCAACACTCGA 59.930 47.619 0.00 0.00 0.00 4.04
2558 2992 2.358898 AGTTGTCATCTTGCACCAACAC 59.641 45.455 0.00 0.00 38.24 3.32
2559 2993 2.653726 AGTTGTCATCTTGCACCAACA 58.346 42.857 0.00 0.00 38.24 3.33
2590 3024 8.599774 GCTCAATCTGAAGTTATGAACTAGAAC 58.400 37.037 0.00 0.00 41.91 3.01
2601 3035 3.319137 AGTGCGCTCAATCTGAAGTTA 57.681 42.857 9.73 0.00 0.00 2.24
2629 3063 2.054687 ACTGAAAACATGCATGCGTG 57.945 45.000 33.18 33.18 38.78 5.34
2630 3064 2.607771 GGAACTGAAAACATGCATGCGT 60.608 45.455 26.53 10.53 0.00 5.24
2631 3065 1.987770 GGAACTGAAAACATGCATGCG 59.012 47.619 26.53 4.36 0.00 4.73
2664 3098 1.364626 CTGCTTCACACCAGCCGATC 61.365 60.000 0.00 0.00 36.33 3.69
2665 3099 1.376424 CTGCTTCACACCAGCCGAT 60.376 57.895 0.00 0.00 36.33 4.18
2681 3115 8.409358 CCTTCCAAGGGAAAATATATAACCTG 57.591 38.462 0.00 0.00 41.54 4.00
2847 3281 3.081804 CCTTTGGTTTGGCTAGTACCAG 58.918 50.000 6.31 0.00 42.48 4.00


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

AutoCloner maintained by Alex Coulton.