Multiple sequence alignment - TraesCS6A01G229100

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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 TraesCS6A01G229100 chr6A 100.000 2543 0 0 1 2543 431923880 431921338 0 4697
1 TraesCS6A01G229100 chr6D 94.823 2260 80 16 307 2543 291489881 291492126 0 3491
2 TraesCS6A01G229100 chr6B 93.934 2110 99 14 451 2543 452616338 452618435 0 3160


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 TraesCS6A01G229100 chr6A 431921338 431923880 2542 True 4697 4697 100.000 1 2543 1 chr6A.!!$R1 2542
1 TraesCS6A01G229100 chr6D 291489881 291492126 2245 False 3491 3491 94.823 307 2543 1 chr6D.!!$F1 2236
2 TraesCS6A01G229100 chr6B 452616338 452618435 2097 False 3160 3160 93.934 451 2543 1 chr6B.!!$F1 2092

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
141 142 0.033228 CTATGAGGCGGGCTCTCAAG 59.967 60.0 28.62 19.31 43.43 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1846 0.247736 ACGACCAGGATCTGACAAGC 59.752 55.0 0.0 0.0 32.44 4.01 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 3.233355 CGGCTTATCACCATAGGGC 57.767 57.895 0.00 0.00 37.90 5.19
19 20 0.396435 CGGCTTATCACCATAGGGCA 59.604 55.000 0.00 0.00 37.06 5.36
20 21 1.609061 CGGCTTATCACCATAGGGCAG 60.609 57.143 0.00 0.00 37.06 4.85
21 22 1.271597 GGCTTATCACCATAGGGCAGG 60.272 57.143 0.00 0.00 37.17 4.85
22 23 1.699634 GCTTATCACCATAGGGCAGGA 59.300 52.381 0.00 0.00 37.90 3.86
23 24 2.289945 GCTTATCACCATAGGGCAGGAG 60.290 54.545 0.00 0.00 37.90 3.69
24 25 1.352083 TATCACCATAGGGCAGGAGC 58.648 55.000 0.00 0.00 37.90 4.70
25 26 0.695462 ATCACCATAGGGCAGGAGCA 60.695 55.000 0.00 0.00 44.61 4.26
26 27 1.147824 CACCATAGGGCAGGAGCAG 59.852 63.158 0.00 0.00 44.61 4.24
27 28 2.074948 ACCATAGGGCAGGAGCAGG 61.075 63.158 0.00 0.00 44.61 4.85
28 29 2.112718 CATAGGGCAGGAGCAGGC 59.887 66.667 0.00 0.00 44.61 4.85
41 42 2.825836 CAGGCCGGCCTCATGTTC 60.826 66.667 45.31 16.63 46.28 3.18
42 43 3.329889 AGGCCGGCCTCATGTTCA 61.330 61.111 42.84 0.00 44.43 3.18
43 44 2.825836 GGCCGGCCTCATGTTCAG 60.826 66.667 38.76 0.00 0.00 3.02
44 45 2.825836 GCCGGCCTCATGTTCAGG 60.826 66.667 18.11 0.00 0.00 3.86
45 46 2.124570 CCGGCCTCATGTTCAGGG 60.125 66.667 0.00 0.00 0.00 4.45
47 48 2.825836 GGCCTCATGTTCAGGGCG 60.826 66.667 9.38 0.00 45.87 6.13
48 49 2.825836 GCCTCATGTTCAGGGCGG 60.826 66.667 1.42 0.00 35.08 6.13
49 50 2.124570 CCTCATGTTCAGGGCGGG 60.125 66.667 0.00 0.00 0.00 6.13
50 51 2.124570 CTCATGTTCAGGGCGGGG 60.125 66.667 0.00 0.00 0.00 5.73
51 52 2.609299 TCATGTTCAGGGCGGGGA 60.609 61.111 0.00 0.00 0.00 4.81
52 53 2.196997 CTCATGTTCAGGGCGGGGAA 62.197 60.000 0.00 0.00 0.00 3.97
53 54 1.750399 CATGTTCAGGGCGGGGAAG 60.750 63.158 0.00 0.00 0.00 3.46
54 55 1.923395 ATGTTCAGGGCGGGGAAGA 60.923 57.895 0.00 0.00 0.00 2.87
55 56 1.281925 ATGTTCAGGGCGGGGAAGAT 61.282 55.000 0.00 0.00 0.00 2.40
56 57 1.153147 GTTCAGGGCGGGGAAGATC 60.153 63.158 0.00 0.00 0.00 2.75
57 58 2.375345 TTCAGGGCGGGGAAGATCC 61.375 63.158 0.00 0.00 35.23 3.36
64 65 4.587189 GGGGAAGATCCGCGTCCG 62.587 72.222 4.92 0.00 45.00 4.79
81 82 3.562635 GGCTTGGAGTCCGAAACG 58.437 61.111 4.30 0.00 0.00 3.60
82 83 1.301479 GGCTTGGAGTCCGAAACGT 60.301 57.895 4.30 0.00 0.00 3.99
83 84 1.566018 GGCTTGGAGTCCGAAACGTG 61.566 60.000 4.30 0.00 0.00 4.49
84 85 1.566018 GCTTGGAGTCCGAAACGTGG 61.566 60.000 4.30 0.00 0.00 4.94
85 86 0.949105 CTTGGAGTCCGAAACGTGGG 60.949 60.000 4.30 0.00 0.00 4.61
86 87 1.401318 TTGGAGTCCGAAACGTGGGA 61.401 55.000 4.30 0.00 0.00 4.37
87 88 1.189524 TGGAGTCCGAAACGTGGGAT 61.190 55.000 4.30 0.00 33.70 3.85
88 89 0.036671 GGAGTCCGAAACGTGGGATT 60.037 55.000 6.54 2.89 33.70 3.01
89 90 1.356938 GAGTCCGAAACGTGGGATTC 58.643 55.000 6.54 8.06 33.70 2.52
90 91 0.389426 AGTCCGAAACGTGGGATTCG 60.389 55.000 12.05 12.05 44.90 3.34
92 93 2.782615 CGAAACGTGGGATTCGGC 59.217 61.111 11.33 0.00 42.57 5.54
93 94 2.746803 CGAAACGTGGGATTCGGCC 61.747 63.158 11.33 0.00 42.57 6.13
94 95 2.744709 AAACGTGGGATTCGGCCG 60.745 61.111 22.12 22.12 0.00 6.13
95 96 3.540367 AAACGTGGGATTCGGCCGT 62.540 57.895 27.15 6.47 0.00 5.68
96 97 4.752879 ACGTGGGATTCGGCCGTG 62.753 66.667 27.15 8.29 0.00 4.94
107 108 3.053291 GGCCGTGGCGAATTGTCA 61.053 61.111 4.53 0.00 43.06 3.58
108 109 2.480555 GCCGTGGCGAATTGTCAG 59.519 61.111 0.00 0.00 28.53 3.51
109 110 3.039202 GCCGTGGCGAATTGTCAGG 62.039 63.158 0.00 0.00 37.80 3.86
110 111 2.480555 CGTGGCGAATTGTCAGGC 59.519 61.111 0.00 0.00 30.49 4.85
111 112 2.324330 CGTGGCGAATTGTCAGGCA 61.324 57.895 0.00 0.00 38.13 4.75
112 113 1.503542 GTGGCGAATTGTCAGGCAG 59.496 57.895 0.00 0.00 41.08 4.85
113 114 1.073025 TGGCGAATTGTCAGGCAGT 59.927 52.632 0.00 0.00 35.49 4.40
114 115 1.236616 TGGCGAATTGTCAGGCAGTG 61.237 55.000 0.00 0.00 35.49 3.66
115 116 0.955428 GGCGAATTGTCAGGCAGTGA 60.955 55.000 0.00 0.00 0.00 3.41
116 117 0.874390 GCGAATTGTCAGGCAGTGAA 59.126 50.000 0.00 0.00 36.74 3.18
117 118 1.135859 GCGAATTGTCAGGCAGTGAAG 60.136 52.381 0.00 0.00 36.74 3.02
118 119 2.416747 CGAATTGTCAGGCAGTGAAGA 58.583 47.619 0.00 0.00 36.74 2.87
119 120 3.005554 CGAATTGTCAGGCAGTGAAGAT 58.994 45.455 0.00 0.00 36.74 2.40
120 121 3.181513 CGAATTGTCAGGCAGTGAAGATG 60.182 47.826 0.00 0.00 36.74 2.90
121 122 2.936919 TTGTCAGGCAGTGAAGATGT 57.063 45.000 0.00 0.00 36.74 3.06
122 123 2.462456 TGTCAGGCAGTGAAGATGTC 57.538 50.000 0.00 0.00 36.74 3.06
123 124 1.973515 TGTCAGGCAGTGAAGATGTCT 59.026 47.619 0.00 0.00 36.74 3.41
124 125 3.165071 TGTCAGGCAGTGAAGATGTCTA 58.835 45.455 0.00 0.00 36.74 2.59
125 126 3.771479 TGTCAGGCAGTGAAGATGTCTAT 59.229 43.478 0.00 0.00 36.74 1.98
126 127 4.118410 GTCAGGCAGTGAAGATGTCTATG 58.882 47.826 0.00 0.00 36.74 2.23
127 128 4.026052 TCAGGCAGTGAAGATGTCTATGA 58.974 43.478 0.00 0.00 29.71 2.15
128 129 4.099113 TCAGGCAGTGAAGATGTCTATGAG 59.901 45.833 0.00 0.00 29.71 2.90
129 130 3.387374 AGGCAGTGAAGATGTCTATGAGG 59.613 47.826 0.00 0.00 28.80 3.86
130 131 3.129871 GCAGTGAAGATGTCTATGAGGC 58.870 50.000 0.00 0.00 0.00 4.70
131 132 3.379240 CAGTGAAGATGTCTATGAGGCG 58.621 50.000 0.00 0.00 0.00 5.52
132 133 2.363680 AGTGAAGATGTCTATGAGGCGG 59.636 50.000 0.00 0.00 0.00 6.13
133 134 1.688735 TGAAGATGTCTATGAGGCGGG 59.311 52.381 0.00 0.00 0.00 6.13
134 135 0.394565 AAGATGTCTATGAGGCGGGC 59.605 55.000 0.00 0.00 0.00 6.13
135 136 0.470833 AGATGTCTATGAGGCGGGCT 60.471 55.000 2.69 2.69 0.00 5.19
136 137 0.037790 GATGTCTATGAGGCGGGCTC 60.038 60.000 23.32 23.32 0.00 4.70
137 138 0.470833 ATGTCTATGAGGCGGGCTCT 60.471 55.000 28.62 17.77 0.00 4.09
138 139 1.109920 TGTCTATGAGGCGGGCTCTC 61.110 60.000 28.62 15.38 0.00 3.20
139 140 1.109920 GTCTATGAGGCGGGCTCTCA 61.110 60.000 28.62 16.72 44.19 3.27
140 141 0.397114 TCTATGAGGCGGGCTCTCAA 60.397 55.000 28.62 12.26 43.43 3.02
141 142 0.033228 CTATGAGGCGGGCTCTCAAG 59.967 60.000 28.62 19.31 43.43 3.02
142 143 1.402896 TATGAGGCGGGCTCTCAAGG 61.403 60.000 28.62 0.00 43.43 3.61
149 150 4.021925 GGCTCTCAAGGCGTGGGT 62.022 66.667 0.00 0.00 38.44 4.51
150 151 2.656069 GGCTCTCAAGGCGTGGGTA 61.656 63.158 0.00 0.00 38.44 3.69
151 152 1.522569 GCTCTCAAGGCGTGGGTAT 59.477 57.895 0.00 0.00 0.00 2.73
152 153 0.530870 GCTCTCAAGGCGTGGGTATC 60.531 60.000 0.00 0.00 0.00 2.24
153 154 0.824109 CTCTCAAGGCGTGGGTATCA 59.176 55.000 0.00 0.00 0.00 2.15
154 155 1.207089 CTCTCAAGGCGTGGGTATCAA 59.793 52.381 0.00 0.00 0.00 2.57
155 156 1.626321 TCTCAAGGCGTGGGTATCAAA 59.374 47.619 0.00 0.00 0.00 2.69
156 157 2.009774 CTCAAGGCGTGGGTATCAAAG 58.990 52.381 0.00 0.00 0.00 2.77
157 158 1.094785 CAAGGCGTGGGTATCAAAGG 58.905 55.000 0.00 0.00 0.00 3.11
158 159 0.034477 AAGGCGTGGGTATCAAAGGG 60.034 55.000 0.00 0.00 0.00 3.95
159 160 0.912487 AGGCGTGGGTATCAAAGGGA 60.912 55.000 0.00 0.00 0.00 4.20
160 161 0.463833 GGCGTGGGTATCAAAGGGAG 60.464 60.000 0.00 0.00 0.00 4.30
161 162 0.252197 GCGTGGGTATCAAAGGGAGT 59.748 55.000 0.00 0.00 0.00 3.85
162 163 2.012051 GCGTGGGTATCAAAGGGAGTG 61.012 57.143 0.00 0.00 0.00 3.51
163 164 1.406887 CGTGGGTATCAAAGGGAGTGG 60.407 57.143 0.00 0.00 0.00 4.00
164 165 1.913419 GTGGGTATCAAAGGGAGTGGA 59.087 52.381 0.00 0.00 0.00 4.02
165 166 2.092914 GTGGGTATCAAAGGGAGTGGAG 60.093 54.545 0.00 0.00 0.00 3.86
166 167 1.490910 GGGTATCAAAGGGAGTGGAGG 59.509 57.143 0.00 0.00 0.00 4.30
167 168 2.197465 GGTATCAAAGGGAGTGGAGGT 58.803 52.381 0.00 0.00 0.00 3.85
168 169 2.092914 GGTATCAAAGGGAGTGGAGGTG 60.093 54.545 0.00 0.00 0.00 4.00
169 170 1.747444 ATCAAAGGGAGTGGAGGTGT 58.253 50.000 0.00 0.00 0.00 4.16
170 171 1.518367 TCAAAGGGAGTGGAGGTGTT 58.482 50.000 0.00 0.00 0.00 3.32
171 172 1.142870 TCAAAGGGAGTGGAGGTGTTG 59.857 52.381 0.00 0.00 0.00 3.33
172 173 1.133792 CAAAGGGAGTGGAGGTGTTGT 60.134 52.381 0.00 0.00 0.00 3.32
173 174 1.222567 AAGGGAGTGGAGGTGTTGTT 58.777 50.000 0.00 0.00 0.00 2.83
174 175 0.474184 AGGGAGTGGAGGTGTTGTTG 59.526 55.000 0.00 0.00 0.00 3.33
175 176 0.472471 GGGAGTGGAGGTGTTGTTGA 59.528 55.000 0.00 0.00 0.00 3.18
176 177 1.543429 GGGAGTGGAGGTGTTGTTGAG 60.543 57.143 0.00 0.00 0.00 3.02
177 178 1.543429 GGAGTGGAGGTGTTGTTGAGG 60.543 57.143 0.00 0.00 0.00 3.86
178 179 1.141053 GAGTGGAGGTGTTGTTGAGGT 59.859 52.381 0.00 0.00 0.00 3.85
179 180 1.134098 AGTGGAGGTGTTGTTGAGGTG 60.134 52.381 0.00 0.00 0.00 4.00
180 181 0.182537 TGGAGGTGTTGTTGAGGTGG 59.817 55.000 0.00 0.00 0.00 4.61
181 182 0.182775 GGAGGTGTTGTTGAGGTGGT 59.817 55.000 0.00 0.00 0.00 4.16
182 183 1.308998 GAGGTGTTGTTGAGGTGGTG 58.691 55.000 0.00 0.00 0.00 4.17
183 184 0.106719 AGGTGTTGTTGAGGTGGTGG 60.107 55.000 0.00 0.00 0.00 4.61
184 185 0.395173 GGTGTTGTTGAGGTGGTGGT 60.395 55.000 0.00 0.00 0.00 4.16
185 186 0.738389 GTGTTGTTGAGGTGGTGGTG 59.262 55.000 0.00 0.00 0.00 4.17
186 187 1.034838 TGTTGTTGAGGTGGTGGTGC 61.035 55.000 0.00 0.00 0.00 5.01
187 188 1.821759 TTGTTGAGGTGGTGGTGCG 60.822 57.895 0.00 0.00 0.00 5.34
188 189 2.978010 GTTGAGGTGGTGGTGCGG 60.978 66.667 0.00 0.00 0.00 5.69
189 190 4.263572 TTGAGGTGGTGGTGCGGG 62.264 66.667 0.00 0.00 0.00 6.13
205 206 3.909651 GGCTGGTGGGGGTTGGAA 61.910 66.667 0.00 0.00 0.00 3.53
206 207 2.283173 GCTGGTGGGGGTTGGAAG 60.283 66.667 0.00 0.00 0.00 3.46
207 208 2.840753 GCTGGTGGGGGTTGGAAGA 61.841 63.158 0.00 0.00 0.00 2.87
208 209 1.850549 CTGGTGGGGGTTGGAAGAA 59.149 57.895 0.00 0.00 0.00 2.52
209 210 0.409484 CTGGTGGGGGTTGGAAGAAT 59.591 55.000 0.00 0.00 0.00 2.40
210 211 0.407918 TGGTGGGGGTTGGAAGAATC 59.592 55.000 0.00 0.00 0.00 2.52
211 212 0.324368 GGTGGGGGTTGGAAGAATCC 60.324 60.000 0.00 0.00 46.76 3.01
212 213 0.324368 GTGGGGGTTGGAAGAATCCC 60.324 60.000 0.00 0.00 45.95 3.85
213 214 1.076995 GGGGGTTGGAAGAATCCCG 60.077 63.158 0.00 0.00 45.95 5.14
214 215 1.076995 GGGGTTGGAAGAATCCCGG 60.077 63.158 0.00 0.00 45.95 5.73
215 216 1.076995 GGGTTGGAAGAATCCCGGG 60.077 63.158 16.85 16.85 45.95 5.73
216 217 1.753078 GGTTGGAAGAATCCCGGGC 60.753 63.158 18.49 0.83 45.95 6.13
217 218 1.303282 GTTGGAAGAATCCCGGGCT 59.697 57.895 18.49 1.75 45.95 5.19
218 219 0.323451 GTTGGAAGAATCCCGGGCTT 60.323 55.000 18.49 14.08 45.95 4.35
219 220 0.407918 TTGGAAGAATCCCGGGCTTT 59.592 50.000 18.49 12.43 45.95 3.51
220 221 0.323360 TGGAAGAATCCCGGGCTTTG 60.323 55.000 18.49 0.00 45.95 2.77
221 222 0.323451 GGAAGAATCCCGGGCTTTGT 60.323 55.000 18.49 7.80 40.10 2.83
222 223 1.095600 GAAGAATCCCGGGCTTTGTC 58.904 55.000 18.49 10.35 0.00 3.18
223 224 0.698818 AAGAATCCCGGGCTTTGTCT 59.301 50.000 18.49 10.45 0.00 3.41
224 225 1.580059 AGAATCCCGGGCTTTGTCTA 58.420 50.000 18.49 0.00 0.00 2.59
225 226 1.913419 AGAATCCCGGGCTTTGTCTAA 59.087 47.619 18.49 0.00 0.00 2.10
226 227 2.014857 GAATCCCGGGCTTTGTCTAAC 58.985 52.381 18.49 0.00 0.00 2.34
227 228 1.286248 ATCCCGGGCTTTGTCTAACT 58.714 50.000 18.49 0.00 0.00 2.24
228 229 0.323629 TCCCGGGCTTTGTCTAACTG 59.676 55.000 18.49 0.00 0.00 3.16
229 230 1.305930 CCCGGGCTTTGTCTAACTGC 61.306 60.000 8.08 0.00 0.00 4.40
230 231 0.605319 CCGGGCTTTGTCTAACTGCA 60.605 55.000 0.00 0.00 0.00 4.41
231 232 0.798776 CGGGCTTTGTCTAACTGCAG 59.201 55.000 13.48 13.48 0.00 4.41
232 233 1.608025 CGGGCTTTGTCTAACTGCAGA 60.608 52.381 23.35 0.00 0.00 4.26
233 234 2.504367 GGGCTTTGTCTAACTGCAGAA 58.496 47.619 23.35 7.06 0.00 3.02
234 235 3.084786 GGGCTTTGTCTAACTGCAGAAT 58.915 45.455 23.35 11.42 0.00 2.40
235 236 3.127721 GGGCTTTGTCTAACTGCAGAATC 59.872 47.826 23.35 6.47 0.00 2.52
236 237 3.753272 GGCTTTGTCTAACTGCAGAATCA 59.247 43.478 23.35 9.02 0.00 2.57
237 238 4.378874 GGCTTTGTCTAACTGCAGAATCAC 60.379 45.833 23.35 11.79 0.00 3.06
238 239 4.378874 GCTTTGTCTAACTGCAGAATCACC 60.379 45.833 23.35 3.95 0.00 4.02
239 240 3.334583 TGTCTAACTGCAGAATCACCC 57.665 47.619 23.35 2.27 0.00 4.61
240 241 2.637382 TGTCTAACTGCAGAATCACCCA 59.363 45.455 23.35 5.00 0.00 4.51
241 242 3.072330 TGTCTAACTGCAGAATCACCCAA 59.928 43.478 23.35 0.00 0.00 4.12
242 243 4.263462 TGTCTAACTGCAGAATCACCCAAT 60.263 41.667 23.35 0.00 0.00 3.16
243 244 4.702131 GTCTAACTGCAGAATCACCCAATT 59.298 41.667 23.35 2.14 0.00 2.32
244 245 4.943705 TCTAACTGCAGAATCACCCAATTC 59.056 41.667 23.35 0.00 36.16 2.17
245 246 3.159213 ACTGCAGAATCACCCAATTCA 57.841 42.857 23.35 0.00 37.98 2.57
246 247 2.821969 ACTGCAGAATCACCCAATTCAC 59.178 45.455 23.35 0.00 37.98 3.18
247 248 2.821378 CTGCAGAATCACCCAATTCACA 59.179 45.455 8.42 0.00 37.98 3.58
248 249 3.229293 TGCAGAATCACCCAATTCACAA 58.771 40.909 0.00 0.00 37.98 3.33
249 250 3.833650 TGCAGAATCACCCAATTCACAAT 59.166 39.130 0.00 0.00 37.98 2.71
250 251 4.082081 TGCAGAATCACCCAATTCACAATC 60.082 41.667 0.00 0.00 37.98 2.67
251 252 4.082081 GCAGAATCACCCAATTCACAATCA 60.082 41.667 0.00 0.00 37.98 2.57
252 253 5.404946 CAGAATCACCCAATTCACAATCAC 58.595 41.667 0.00 0.00 37.98 3.06
253 254 5.047872 CAGAATCACCCAATTCACAATCACA 60.048 40.000 0.00 0.00 37.98 3.58
254 255 5.539574 AGAATCACCCAATTCACAATCACAA 59.460 36.000 0.00 0.00 37.98 3.33
255 256 6.211986 AGAATCACCCAATTCACAATCACAAT 59.788 34.615 0.00 0.00 37.98 2.71
256 257 5.804944 TCACCCAATTCACAATCACAATT 57.195 34.783 0.00 0.00 0.00 2.32
257 258 6.172136 TCACCCAATTCACAATCACAATTT 57.828 33.333 0.00 0.00 0.00 1.82
258 259 5.990386 TCACCCAATTCACAATCACAATTTG 59.010 36.000 0.00 0.00 0.00 2.32
259 260 5.759273 CACCCAATTCACAATCACAATTTGT 59.241 36.000 0.00 0.00 37.79 2.83
260 261 5.990996 ACCCAATTCACAATCACAATTTGTC 59.009 36.000 0.00 0.00 35.18 3.18
261 262 5.118971 CCCAATTCACAATCACAATTTGTCG 59.881 40.000 0.00 0.00 35.18 4.35
262 263 5.691305 CCAATTCACAATCACAATTTGTCGT 59.309 36.000 0.00 0.00 35.18 4.34
263 264 6.200665 CCAATTCACAATCACAATTTGTCGTT 59.799 34.615 0.00 0.00 35.18 3.85
264 265 7.254387 CCAATTCACAATCACAATTTGTCGTTT 60.254 33.333 0.00 0.00 35.18 3.60
265 266 6.566310 TTCACAATCACAATTTGTCGTTTG 57.434 33.333 0.00 9.25 35.18 2.93
266 267 5.884771 TCACAATCACAATTTGTCGTTTGA 58.115 33.333 18.78 8.50 35.18 2.69
267 268 5.741510 TCACAATCACAATTTGTCGTTTGAC 59.258 36.000 18.78 0.00 45.71 3.18
276 277 3.472263 GTCGTTTGACATTGCCCAC 57.528 52.632 0.00 0.00 44.82 4.61
277 278 0.951558 GTCGTTTGACATTGCCCACT 59.048 50.000 0.00 0.00 44.82 4.00
278 279 1.336755 GTCGTTTGACATTGCCCACTT 59.663 47.619 0.00 0.00 44.82 3.16
279 280 2.028130 TCGTTTGACATTGCCCACTTT 58.972 42.857 0.00 0.00 0.00 2.66
280 281 2.428890 TCGTTTGACATTGCCCACTTTT 59.571 40.909 0.00 0.00 0.00 2.27
281 282 2.794350 CGTTTGACATTGCCCACTTTTC 59.206 45.455 0.00 0.00 0.00 2.29
282 283 3.490761 CGTTTGACATTGCCCACTTTTCT 60.491 43.478 0.00 0.00 0.00 2.52
283 284 4.051237 GTTTGACATTGCCCACTTTTCTC 58.949 43.478 0.00 0.00 0.00 2.87
284 285 3.228188 TGACATTGCCCACTTTTCTCT 57.772 42.857 0.00 0.00 0.00 3.10
285 286 4.365514 TGACATTGCCCACTTTTCTCTA 57.634 40.909 0.00 0.00 0.00 2.43
286 287 4.724399 TGACATTGCCCACTTTTCTCTAA 58.276 39.130 0.00 0.00 0.00 2.10
287 288 4.518970 TGACATTGCCCACTTTTCTCTAAC 59.481 41.667 0.00 0.00 0.00 2.34
288 289 3.826729 ACATTGCCCACTTTTCTCTAACC 59.173 43.478 0.00 0.00 0.00 2.85
289 290 2.579410 TGCCCACTTTTCTCTAACCC 57.421 50.000 0.00 0.00 0.00 4.11
290 291 1.777878 TGCCCACTTTTCTCTAACCCA 59.222 47.619 0.00 0.00 0.00 4.51
291 292 2.175931 TGCCCACTTTTCTCTAACCCAA 59.824 45.455 0.00 0.00 0.00 4.12
292 293 3.227614 GCCCACTTTTCTCTAACCCAAA 58.772 45.455 0.00 0.00 0.00 3.28
293 294 3.639561 GCCCACTTTTCTCTAACCCAAAA 59.360 43.478 0.00 0.00 0.00 2.44
294 295 4.283467 GCCCACTTTTCTCTAACCCAAAAT 59.717 41.667 0.00 0.00 0.00 1.82
295 296 5.783111 CCCACTTTTCTCTAACCCAAAATG 58.217 41.667 0.00 0.00 0.00 2.32
296 297 5.304357 CCCACTTTTCTCTAACCCAAAATGT 59.696 40.000 0.00 0.00 0.00 2.71
297 298 6.183360 CCCACTTTTCTCTAACCCAAAATGTT 60.183 38.462 0.00 0.00 0.00 2.71
298 299 7.014808 CCCACTTTTCTCTAACCCAAAATGTTA 59.985 37.037 0.00 0.00 0.00 2.41
299 300 7.865889 CCACTTTTCTCTAACCCAAAATGTTAC 59.134 37.037 0.00 0.00 0.00 2.50
300 301 8.630037 CACTTTTCTCTAACCCAAAATGTTACT 58.370 33.333 0.00 0.00 0.00 2.24
301 302 8.630037 ACTTTTCTCTAACCCAAAATGTTACTG 58.370 33.333 0.00 0.00 0.00 2.74
302 303 8.754991 TTTTCTCTAACCCAAAATGTTACTGA 57.245 30.769 0.00 0.00 0.00 3.41
303 304 8.934023 TTTCTCTAACCCAAAATGTTACTGAT 57.066 30.769 0.00 0.00 0.00 2.90
305 306 9.444600 TTCTCTAACCCAAAATGTTACTGATAC 57.555 33.333 0.00 0.00 0.00 2.24
316 317 5.677319 TGTTACTGATACTTAGCAGGCTT 57.323 39.130 6.48 0.00 43.58 4.35
414 415 6.322712 TGAATATATTTGAAAGTTTCCCCCGG 59.677 38.462 13.01 0.00 0.00 5.73
465 466 9.315363 GAAGGGATTCACTATAGAATTCTCCTA 57.685 37.037 12.24 4.48 38.30 2.94
477 478 3.498774 ATTCTCCTATGTGGTCATGCC 57.501 47.619 0.00 0.00 35.70 4.40
484 485 3.381272 CCTATGTGGTCATGCCGAATTTT 59.619 43.478 0.00 0.00 41.21 1.82
497 498 3.826466 CCGAATTTTCTCTCTGGTTTGC 58.174 45.455 0.00 0.00 0.00 3.68
504 505 1.134220 TCTCTCTGGTTTGCCAAACGT 60.134 47.619 13.75 0.00 45.51 3.99
511 512 1.202475 GGTTTGCCAAACGTGAACCAT 60.202 47.619 13.75 0.00 42.29 3.55
549 553 7.214467 TCTCTTATTTGATGAAAGGCGTTTT 57.786 32.000 5.76 0.00 0.00 2.43
564 568 1.066587 TTTTGCCGCACCTTTTCCG 59.933 52.632 0.00 0.00 0.00 4.30
566 570 4.572571 TGCCGCACCTTTTCCGGT 62.573 61.111 0.00 0.00 43.70 5.28
708 713 5.699458 TCTTTCGAATCTACCAACTTTCCAC 59.301 40.000 0.00 0.00 0.00 4.02
728 733 2.968574 ACTTCCACGGCATCTAGATCAT 59.031 45.455 1.03 0.00 0.00 2.45
756 761 0.736325 AGAAGATTCAACGACGGCCG 60.736 55.000 26.86 26.86 45.44 6.13
822 827 0.739813 GTCAGTATCGGCACCACCAC 60.740 60.000 0.00 0.00 39.03 4.16
823 828 1.449601 CAGTATCGGCACCACCACC 60.450 63.158 0.00 0.00 39.03 4.61
824 829 1.612442 AGTATCGGCACCACCACCT 60.612 57.895 0.00 0.00 39.03 4.00
857 862 1.318158 CCTGCTTGACCAATGAGCCC 61.318 60.000 0.00 0.00 35.59 5.19
1044 1058 1.144936 GAAGTCGAGCCCCATGGAG 59.855 63.158 15.22 0.00 0.00 3.86
1352 1366 2.593468 TACGCCAGCTTCATCCCTGC 62.593 60.000 0.00 0.00 0.00 4.85
1424 1438 1.052287 GCAACGCAAAGAATTCCGTG 58.948 50.000 8.00 5.16 36.36 4.94
1582 1608 1.815421 CCTGGTCATCTTTCGCGGG 60.815 63.158 6.13 0.00 0.00 6.13
1612 1638 2.660802 GATCGGGTCGGTGGTGTT 59.339 61.111 0.00 0.00 0.00 3.32
1820 1846 1.003262 CGATGCAAAGCCCGTTGTTG 61.003 55.000 0.00 0.00 0.00 3.33
1841 1867 2.611518 CTTGTCAGATCCTGGTCGTTC 58.388 52.381 0.00 0.00 31.51 3.95
1847 1873 2.630592 GATCCTGGTCGTTCCGGAGC 62.631 65.000 8.48 8.48 45.09 4.70
2054 2080 2.892425 GATGCCGACCTCGCCTTG 60.892 66.667 0.00 0.00 38.18 3.61
2114 2140 4.899239 GCCGCCTCGATCACCAGG 62.899 72.222 0.00 0.00 0.00 4.45
2357 2383 4.514569 GCGTTACGCGGCATGTGG 62.515 66.667 15.43 0.00 44.55 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.396435 TGCCCTATGGTGATAAGCCG 59.604 55.000 0.00 0.00 0.00 5.52
1 2 1.271597 CCTGCCCTATGGTGATAAGCC 60.272 57.143 0.00 0.00 0.00 4.35
2 3 1.699634 TCCTGCCCTATGGTGATAAGC 59.300 52.381 0.00 0.00 0.00 3.09
3 4 2.289945 GCTCCTGCCCTATGGTGATAAG 60.290 54.545 0.00 0.00 0.00 1.73
4 5 1.699634 GCTCCTGCCCTATGGTGATAA 59.300 52.381 0.00 0.00 0.00 1.75
5 6 1.352083 GCTCCTGCCCTATGGTGATA 58.648 55.000 0.00 0.00 0.00 2.15
6 7 0.695462 TGCTCCTGCCCTATGGTGAT 60.695 55.000 0.00 0.00 38.71 3.06
7 8 1.306911 TGCTCCTGCCCTATGGTGA 60.307 57.895 0.00 0.00 38.71 4.02
8 9 1.147824 CTGCTCCTGCCCTATGGTG 59.852 63.158 0.00 0.00 38.71 4.17
9 10 2.074948 CCTGCTCCTGCCCTATGGT 61.075 63.158 0.00 0.00 38.71 3.55
10 11 2.834688 CCTGCTCCTGCCCTATGG 59.165 66.667 0.00 0.00 38.71 2.74
11 12 2.112718 GCCTGCTCCTGCCCTATG 59.887 66.667 0.00 0.00 38.71 2.23
12 13 3.174265 GGCCTGCTCCTGCCCTAT 61.174 66.667 0.00 0.00 41.97 2.57
26 27 2.825836 CTGAACATGAGGCCGGCC 60.826 66.667 39.29 39.29 0.00 6.13
27 28 2.825836 CCTGAACATGAGGCCGGC 60.826 66.667 21.18 21.18 0.00 6.13
28 29 2.124570 CCCTGAACATGAGGCCGG 60.125 66.667 0.00 0.00 0.00 6.13
29 30 2.825836 GCCCTGAACATGAGGCCG 60.826 66.667 0.00 0.00 39.60 6.13
30 31 2.825836 CGCCCTGAACATGAGGCC 60.826 66.667 0.00 0.00 42.66 5.19
31 32 2.825836 CCGCCCTGAACATGAGGC 60.826 66.667 0.00 2.54 42.18 4.70
32 33 2.124570 CCCGCCCTGAACATGAGG 60.125 66.667 0.00 0.00 0.00 3.86
33 34 2.124570 CCCCGCCCTGAACATGAG 60.125 66.667 0.00 0.00 0.00 2.90
34 35 2.196997 CTTCCCCGCCCTGAACATGA 62.197 60.000 0.00 0.00 0.00 3.07
35 36 1.750399 CTTCCCCGCCCTGAACATG 60.750 63.158 0.00 0.00 0.00 3.21
36 37 1.281925 ATCTTCCCCGCCCTGAACAT 61.282 55.000 0.00 0.00 0.00 2.71
37 38 1.910580 GATCTTCCCCGCCCTGAACA 61.911 60.000 0.00 0.00 0.00 3.18
38 39 1.153147 GATCTTCCCCGCCCTGAAC 60.153 63.158 0.00 0.00 0.00 3.18
39 40 2.375345 GGATCTTCCCCGCCCTGAA 61.375 63.158 0.00 0.00 0.00 3.02
40 41 2.768344 GGATCTTCCCCGCCCTGA 60.768 66.667 0.00 0.00 0.00 3.86
41 42 4.241555 CGGATCTTCCCCGCCCTG 62.242 72.222 0.00 0.00 40.54 4.45
47 48 4.587189 CGGACGCGGATCTTCCCC 62.587 72.222 12.47 0.00 31.13 4.81
48 49 4.587189 CCGGACGCGGATCTTCCC 62.587 72.222 12.47 0.00 31.13 3.97
50 51 3.718210 AAGCCGGACGCGGATCTTC 62.718 63.158 12.47 0.00 44.76 2.87
51 52 3.771160 AAGCCGGACGCGGATCTT 61.771 61.111 12.47 3.24 44.76 2.40
52 53 4.514577 CAAGCCGGACGCGGATCT 62.515 66.667 12.47 0.00 44.76 2.75
59 60 4.796231 CGGACTCCAAGCCGGACG 62.796 72.222 5.05 0.00 43.67 4.79
64 65 1.301479 ACGTTTCGGACTCCAAGCC 60.301 57.895 0.00 0.00 0.00 4.35
65 66 1.566018 CCACGTTTCGGACTCCAAGC 61.566 60.000 0.00 0.00 0.00 4.01
66 67 0.949105 CCCACGTTTCGGACTCCAAG 60.949 60.000 0.00 0.00 0.00 3.61
67 68 1.070105 CCCACGTTTCGGACTCCAA 59.930 57.895 0.00 0.00 0.00 3.53
68 69 1.189524 ATCCCACGTTTCGGACTCCA 61.190 55.000 0.00 0.00 0.00 3.86
69 70 0.036671 AATCCCACGTTTCGGACTCC 60.037 55.000 0.00 0.00 0.00 3.85
70 71 1.356938 GAATCCCACGTTTCGGACTC 58.643 55.000 0.00 0.00 0.00 3.36
71 72 0.389426 CGAATCCCACGTTTCGGACT 60.389 55.000 11.33 0.00 40.67 3.85
72 73 2.075761 CGAATCCCACGTTTCGGAC 58.924 57.895 11.33 0.00 40.67 4.79
73 74 4.582760 CGAATCCCACGTTTCGGA 57.417 55.556 11.33 5.37 40.67 4.55
75 76 2.746803 GGCCGAATCCCACGTTTCG 61.747 63.158 12.05 12.05 43.21 3.46
76 77 2.746803 CGGCCGAATCCCACGTTTC 61.747 63.158 24.07 0.00 0.00 2.78
77 78 2.744709 CGGCCGAATCCCACGTTT 60.745 61.111 24.07 0.00 0.00 3.60
78 79 4.011517 ACGGCCGAATCCCACGTT 62.012 61.111 35.90 0.68 33.54 3.99
79 80 4.752879 CACGGCCGAATCCCACGT 62.753 66.667 35.90 1.64 38.43 4.49
85 86 2.469516 AATTCGCCACGGCCGAATC 61.470 57.895 35.90 18.12 40.49 2.52
86 87 2.437716 AATTCGCCACGGCCGAAT 60.438 55.556 35.90 18.15 41.85 3.34
87 88 3.427425 CAATTCGCCACGGCCGAA 61.427 61.111 35.90 16.38 37.75 4.30
88 89 4.690719 ACAATTCGCCACGGCCGA 62.691 61.111 35.90 8.69 37.98 5.54
89 90 4.160635 GACAATTCGCCACGGCCG 62.161 66.667 26.86 26.86 37.98 6.13
90 91 3.039202 CTGACAATTCGCCACGGCC 62.039 63.158 1.63 0.00 37.98 6.13
91 92 2.480555 CTGACAATTCGCCACGGC 59.519 61.111 0.00 0.00 37.85 5.68
92 93 3.039202 GCCTGACAATTCGCCACGG 62.039 63.158 0.00 0.00 0.00 4.94
93 94 2.244436 CTGCCTGACAATTCGCCACG 62.244 60.000 0.00 0.00 0.00 4.94
94 95 1.237285 ACTGCCTGACAATTCGCCAC 61.237 55.000 0.00 0.00 0.00 5.01
95 96 1.073025 ACTGCCTGACAATTCGCCA 59.927 52.632 0.00 0.00 0.00 5.69
96 97 0.955428 TCACTGCCTGACAATTCGCC 60.955 55.000 0.00 0.00 0.00 5.54
97 98 0.874390 TTCACTGCCTGACAATTCGC 59.126 50.000 0.00 0.00 0.00 4.70
98 99 2.416747 TCTTCACTGCCTGACAATTCG 58.583 47.619 0.00 0.00 0.00 3.34
99 100 3.755378 ACATCTTCACTGCCTGACAATTC 59.245 43.478 0.00 0.00 0.00 2.17
100 101 3.755378 GACATCTTCACTGCCTGACAATT 59.245 43.478 0.00 0.00 0.00 2.32
101 102 3.008813 AGACATCTTCACTGCCTGACAAT 59.991 43.478 0.00 0.00 0.00 2.71
102 103 2.369860 AGACATCTTCACTGCCTGACAA 59.630 45.455 0.00 0.00 0.00 3.18
103 104 1.973515 AGACATCTTCACTGCCTGACA 59.026 47.619 0.00 0.00 0.00 3.58
104 105 2.758736 AGACATCTTCACTGCCTGAC 57.241 50.000 0.00 0.00 0.00 3.51
105 106 4.026052 TCATAGACATCTTCACTGCCTGA 58.974 43.478 0.00 0.00 0.00 3.86
106 107 4.370049 CTCATAGACATCTTCACTGCCTG 58.630 47.826 0.00 0.00 0.00 4.85
107 108 3.387374 CCTCATAGACATCTTCACTGCCT 59.613 47.826 0.00 0.00 0.00 4.75
108 109 3.726607 CCTCATAGACATCTTCACTGCC 58.273 50.000 0.00 0.00 0.00 4.85
109 110 3.129871 GCCTCATAGACATCTTCACTGC 58.870 50.000 0.00 0.00 0.00 4.40
110 111 3.379240 CGCCTCATAGACATCTTCACTG 58.621 50.000 0.00 0.00 0.00 3.66
111 112 2.363680 CCGCCTCATAGACATCTTCACT 59.636 50.000 0.00 0.00 0.00 3.41
112 113 2.546795 CCCGCCTCATAGACATCTTCAC 60.547 54.545 0.00 0.00 0.00 3.18
113 114 1.688735 CCCGCCTCATAGACATCTTCA 59.311 52.381 0.00 0.00 0.00 3.02
114 115 1.606737 GCCCGCCTCATAGACATCTTC 60.607 57.143 0.00 0.00 0.00 2.87
115 116 0.394565 GCCCGCCTCATAGACATCTT 59.605 55.000 0.00 0.00 0.00 2.40
116 117 0.470833 AGCCCGCCTCATAGACATCT 60.471 55.000 0.00 0.00 0.00 2.90
117 118 0.037790 GAGCCCGCCTCATAGACATC 60.038 60.000 0.00 0.00 40.45 3.06
118 119 0.470833 AGAGCCCGCCTCATAGACAT 60.471 55.000 4.47 0.00 43.31 3.06
119 120 1.075970 AGAGCCCGCCTCATAGACA 60.076 57.895 4.47 0.00 43.31 3.41
120 121 1.109920 TGAGAGCCCGCCTCATAGAC 61.110 60.000 4.47 0.00 43.31 2.59
121 122 0.397114 TTGAGAGCCCGCCTCATAGA 60.397 55.000 8.17 0.00 43.31 1.98
122 123 0.033228 CTTGAGAGCCCGCCTCATAG 59.967 60.000 8.17 6.12 43.31 2.23
123 124 1.402896 CCTTGAGAGCCCGCCTCATA 61.403 60.000 8.17 1.79 43.31 2.15
124 125 2.739996 CCTTGAGAGCCCGCCTCAT 61.740 63.158 8.17 0.00 43.31 2.90
125 126 3.393970 CCTTGAGAGCCCGCCTCA 61.394 66.667 4.47 4.40 43.31 3.86
126 127 4.847444 GCCTTGAGAGCCCGCCTC 62.847 72.222 0.00 0.00 41.07 4.70
131 132 4.785453 CCCACGCCTTGAGAGCCC 62.785 72.222 0.00 0.00 0.00 5.19
132 133 1.972660 ATACCCACGCCTTGAGAGCC 61.973 60.000 0.00 0.00 0.00 4.70
133 134 0.530870 GATACCCACGCCTTGAGAGC 60.531 60.000 0.00 0.00 0.00 4.09
134 135 0.824109 TGATACCCACGCCTTGAGAG 59.176 55.000 0.00 0.00 0.00 3.20
135 136 1.271856 TTGATACCCACGCCTTGAGA 58.728 50.000 0.00 0.00 0.00 3.27
136 137 2.009774 CTTTGATACCCACGCCTTGAG 58.990 52.381 0.00 0.00 0.00 3.02
137 138 1.339631 CCTTTGATACCCACGCCTTGA 60.340 52.381 0.00 0.00 0.00 3.02
138 139 1.094785 CCTTTGATACCCACGCCTTG 58.905 55.000 0.00 0.00 0.00 3.61
139 140 0.034477 CCCTTTGATACCCACGCCTT 60.034 55.000 0.00 0.00 0.00 4.35
140 141 0.912487 TCCCTTTGATACCCACGCCT 60.912 55.000 0.00 0.00 0.00 5.52
141 142 0.463833 CTCCCTTTGATACCCACGCC 60.464 60.000 0.00 0.00 0.00 5.68
142 143 0.252197 ACTCCCTTTGATACCCACGC 59.748 55.000 0.00 0.00 0.00 5.34
143 144 1.406887 CCACTCCCTTTGATACCCACG 60.407 57.143 0.00 0.00 0.00 4.94
144 145 1.913419 TCCACTCCCTTTGATACCCAC 59.087 52.381 0.00 0.00 0.00 4.61
145 146 2.196595 CTCCACTCCCTTTGATACCCA 58.803 52.381 0.00 0.00 0.00 4.51
146 147 1.490910 CCTCCACTCCCTTTGATACCC 59.509 57.143 0.00 0.00 0.00 3.69
147 148 2.092914 CACCTCCACTCCCTTTGATACC 60.093 54.545 0.00 0.00 0.00 2.73
148 149 2.572104 ACACCTCCACTCCCTTTGATAC 59.428 50.000 0.00 0.00 0.00 2.24
149 150 2.915869 ACACCTCCACTCCCTTTGATA 58.084 47.619 0.00 0.00 0.00 2.15
150 151 1.747444 ACACCTCCACTCCCTTTGAT 58.253 50.000 0.00 0.00 0.00 2.57
151 152 1.142870 CAACACCTCCACTCCCTTTGA 59.857 52.381 0.00 0.00 0.00 2.69
152 153 1.133792 ACAACACCTCCACTCCCTTTG 60.134 52.381 0.00 0.00 0.00 2.77
153 154 1.222567 ACAACACCTCCACTCCCTTT 58.777 50.000 0.00 0.00 0.00 3.11
154 155 1.133792 CAACAACACCTCCACTCCCTT 60.134 52.381 0.00 0.00 0.00 3.95
155 156 0.474184 CAACAACACCTCCACTCCCT 59.526 55.000 0.00 0.00 0.00 4.20
156 157 0.472471 TCAACAACACCTCCACTCCC 59.528 55.000 0.00 0.00 0.00 4.30
157 158 1.543429 CCTCAACAACACCTCCACTCC 60.543 57.143 0.00 0.00 0.00 3.85
158 159 1.141053 ACCTCAACAACACCTCCACTC 59.859 52.381 0.00 0.00 0.00 3.51
159 160 1.134098 CACCTCAACAACACCTCCACT 60.134 52.381 0.00 0.00 0.00 4.00
160 161 1.308998 CACCTCAACAACACCTCCAC 58.691 55.000 0.00 0.00 0.00 4.02
161 162 0.182537 CCACCTCAACAACACCTCCA 59.817 55.000 0.00 0.00 0.00 3.86
162 163 0.182775 ACCACCTCAACAACACCTCC 59.817 55.000 0.00 0.00 0.00 4.30
163 164 1.308998 CACCACCTCAACAACACCTC 58.691 55.000 0.00 0.00 0.00 3.85
164 165 0.106719 CCACCACCTCAACAACACCT 60.107 55.000 0.00 0.00 0.00 4.00
165 166 0.395173 ACCACCACCTCAACAACACC 60.395 55.000 0.00 0.00 0.00 4.16
166 167 0.738389 CACCACCACCTCAACAACAC 59.262 55.000 0.00 0.00 0.00 3.32
167 168 1.034838 GCACCACCACCTCAACAACA 61.035 55.000 0.00 0.00 0.00 3.33
168 169 1.733526 GCACCACCACCTCAACAAC 59.266 57.895 0.00 0.00 0.00 3.32
169 170 1.821759 CGCACCACCACCTCAACAA 60.822 57.895 0.00 0.00 0.00 2.83
170 171 2.203139 CGCACCACCACCTCAACA 60.203 61.111 0.00 0.00 0.00 3.33
171 172 2.978010 CCGCACCACCACCTCAAC 60.978 66.667 0.00 0.00 0.00 3.18
172 173 4.263572 CCCGCACCACCACCTCAA 62.264 66.667 0.00 0.00 0.00 3.02
188 189 3.886550 CTTCCAACCCCCACCAGCC 62.887 68.421 0.00 0.00 0.00 4.85
189 190 2.283173 CTTCCAACCCCCACCAGC 60.283 66.667 0.00 0.00 0.00 4.85
190 191 0.409484 ATTCTTCCAACCCCCACCAG 59.591 55.000 0.00 0.00 0.00 4.00
191 192 0.407918 GATTCTTCCAACCCCCACCA 59.592 55.000 0.00 0.00 0.00 4.17
192 193 0.324368 GGATTCTTCCAACCCCCACC 60.324 60.000 0.00 0.00 42.12 4.61
193 194 0.324368 GGGATTCTTCCAACCCCCAC 60.324 60.000 0.00 0.00 44.60 4.61
194 195 1.858739 CGGGATTCTTCCAACCCCCA 61.859 60.000 0.00 0.00 44.60 4.96
195 196 1.076995 CGGGATTCTTCCAACCCCC 60.077 63.158 0.00 0.00 44.60 5.40
196 197 1.076995 CCGGGATTCTTCCAACCCC 60.077 63.158 0.00 0.00 44.60 4.95
197 198 1.076995 CCCGGGATTCTTCCAACCC 60.077 63.158 18.48 0.00 44.60 4.11
198 199 1.753078 GCCCGGGATTCTTCCAACC 60.753 63.158 29.31 0.00 44.60 3.77
199 200 0.323451 AAGCCCGGGATTCTTCCAAC 60.323 55.000 29.31 1.00 44.60 3.77
200 201 0.407918 AAAGCCCGGGATTCTTCCAA 59.592 50.000 27.06 0.00 44.60 3.53
201 202 0.323360 CAAAGCCCGGGATTCTTCCA 60.323 55.000 27.06 0.00 44.60 3.53
202 203 0.323451 ACAAAGCCCGGGATTCTTCC 60.323 55.000 27.06 3.76 41.77 3.46
203 204 1.095600 GACAAAGCCCGGGATTCTTC 58.904 55.000 27.06 19.74 0.00 2.87
204 205 0.698818 AGACAAAGCCCGGGATTCTT 59.301 50.000 27.06 15.57 0.00 2.52
205 206 1.580059 TAGACAAAGCCCGGGATTCT 58.420 50.000 27.06 20.48 0.00 2.40
206 207 2.014857 GTTAGACAAAGCCCGGGATTC 58.985 52.381 27.06 13.29 0.00 2.52
207 208 1.633945 AGTTAGACAAAGCCCGGGATT 59.366 47.619 29.31 25.02 0.00 3.01
208 209 1.065418 CAGTTAGACAAAGCCCGGGAT 60.065 52.381 29.31 18.54 0.00 3.85
209 210 0.323629 CAGTTAGACAAAGCCCGGGA 59.676 55.000 29.31 0.00 0.00 5.14
210 211 1.305930 GCAGTTAGACAAAGCCCGGG 61.306 60.000 19.09 19.09 0.00 5.73
211 212 0.605319 TGCAGTTAGACAAAGCCCGG 60.605 55.000 0.00 0.00 0.00 5.73
212 213 0.798776 CTGCAGTTAGACAAAGCCCG 59.201 55.000 5.25 0.00 0.00 6.13
213 214 2.185004 TCTGCAGTTAGACAAAGCCC 57.815 50.000 14.67 0.00 0.00 5.19
214 215 3.753272 TGATTCTGCAGTTAGACAAAGCC 59.247 43.478 14.67 0.00 0.00 4.35
215 216 4.378874 GGTGATTCTGCAGTTAGACAAAGC 60.379 45.833 14.67 1.81 0.00 3.51
216 217 4.154918 GGGTGATTCTGCAGTTAGACAAAG 59.845 45.833 14.67 0.00 0.00 2.77
217 218 4.072131 GGGTGATTCTGCAGTTAGACAAA 58.928 43.478 14.67 0.00 0.00 2.83
218 219 3.072330 TGGGTGATTCTGCAGTTAGACAA 59.928 43.478 14.67 0.00 0.00 3.18
219 220 2.637382 TGGGTGATTCTGCAGTTAGACA 59.363 45.455 14.67 5.76 0.00 3.41
220 221 3.334583 TGGGTGATTCTGCAGTTAGAC 57.665 47.619 14.67 6.86 0.00 2.59
221 222 4.574674 ATTGGGTGATTCTGCAGTTAGA 57.425 40.909 14.67 0.00 0.00 2.10
222 223 4.701651 TGAATTGGGTGATTCTGCAGTTAG 59.298 41.667 14.67 0.00 37.04 2.34
223 224 4.458989 GTGAATTGGGTGATTCTGCAGTTA 59.541 41.667 14.67 3.52 37.04 2.24
224 225 3.256631 GTGAATTGGGTGATTCTGCAGTT 59.743 43.478 14.67 2.24 37.04 3.16
225 226 2.821969 GTGAATTGGGTGATTCTGCAGT 59.178 45.455 14.67 0.00 37.04 4.40
226 227 2.821378 TGTGAATTGGGTGATTCTGCAG 59.179 45.455 7.63 7.63 37.04 4.41
227 228 2.874014 TGTGAATTGGGTGATTCTGCA 58.126 42.857 0.00 0.00 37.04 4.41
228 229 3.940209 TTGTGAATTGGGTGATTCTGC 57.060 42.857 0.00 0.00 37.04 4.26
229 230 5.047872 TGTGATTGTGAATTGGGTGATTCTG 60.048 40.000 0.00 0.00 37.04 3.02
230 231 5.078949 TGTGATTGTGAATTGGGTGATTCT 58.921 37.500 0.00 0.00 37.04 2.40
231 232 5.389859 TGTGATTGTGAATTGGGTGATTC 57.610 39.130 0.00 0.00 36.73 2.52
232 233 5.804944 TTGTGATTGTGAATTGGGTGATT 57.195 34.783 0.00 0.00 0.00 2.57
233 234 6.363167 AATTGTGATTGTGAATTGGGTGAT 57.637 33.333 0.00 0.00 0.00 3.06
234 235 5.804944 AATTGTGATTGTGAATTGGGTGA 57.195 34.783 0.00 0.00 0.00 4.02
235 236 5.759273 ACAAATTGTGATTGTGAATTGGGTG 59.241 36.000 0.00 0.00 39.43 4.61
236 237 5.927819 ACAAATTGTGATTGTGAATTGGGT 58.072 33.333 0.00 0.00 39.43 4.51
237 238 5.118971 CGACAAATTGTGATTGTGAATTGGG 59.881 40.000 2.20 0.00 40.90 4.12
238 239 5.691305 ACGACAAATTGTGATTGTGAATTGG 59.309 36.000 2.20 0.00 40.90 3.16
239 240 6.752335 ACGACAAATTGTGATTGTGAATTG 57.248 33.333 2.20 0.00 40.90 2.32
240 241 7.490725 TCAAACGACAAATTGTGATTGTGAATT 59.509 29.630 2.20 0.00 40.90 2.17
241 242 6.977502 TCAAACGACAAATTGTGATTGTGAAT 59.022 30.769 2.20 0.00 40.90 2.57
242 243 6.252441 GTCAAACGACAAATTGTGATTGTGAA 59.748 34.615 2.20 0.00 40.90 3.18
243 244 5.741510 GTCAAACGACAAATTGTGATTGTGA 59.258 36.000 2.20 0.00 40.90 3.58
244 245 5.514559 TGTCAAACGACAAATTGTGATTGTG 59.485 36.000 2.20 0.00 40.90 3.33
245 246 5.645624 TGTCAAACGACAAATTGTGATTGT 58.354 33.333 2.20 0.00 43.37 2.71
246 247 6.752335 ATGTCAAACGACAAATTGTGATTG 57.248 33.333 2.20 7.61 46.16 2.67
247 248 6.292274 GCAATGTCAAACGACAAATTGTGATT 60.292 34.615 2.20 0.00 46.16 2.57
248 249 5.175491 GCAATGTCAAACGACAAATTGTGAT 59.825 36.000 2.20 0.00 46.16 3.06
249 250 4.502282 GCAATGTCAAACGACAAATTGTGA 59.498 37.500 2.20 0.00 46.16 3.58
250 251 4.317980 GGCAATGTCAAACGACAAATTGTG 60.318 41.667 2.20 0.00 46.16 3.33
251 252 3.801594 GGCAATGTCAAACGACAAATTGT 59.198 39.130 0.00 0.00 46.16 2.71
252 253 3.184178 GGGCAATGTCAAACGACAAATTG 59.816 43.478 0.00 2.50 46.16 2.32
253 254 3.181471 TGGGCAATGTCAAACGACAAATT 60.181 39.130 0.00 0.00 46.16 1.82
254 255 2.363680 TGGGCAATGTCAAACGACAAAT 59.636 40.909 0.00 0.00 46.16 2.32
255 256 1.751351 TGGGCAATGTCAAACGACAAA 59.249 42.857 0.00 0.00 46.16 2.83
256 257 1.066303 GTGGGCAATGTCAAACGACAA 59.934 47.619 0.00 0.00 46.16 3.18
258 259 0.951558 AGTGGGCAATGTCAAACGAC 59.048 50.000 0.00 0.00 0.00 4.34
259 260 1.686355 AAGTGGGCAATGTCAAACGA 58.314 45.000 0.00 0.00 0.00 3.85
260 261 2.507339 AAAGTGGGCAATGTCAAACG 57.493 45.000 0.00 0.00 0.00 3.60
261 262 4.051237 GAGAAAAGTGGGCAATGTCAAAC 58.949 43.478 0.00 0.00 0.00 2.93
262 263 3.960102 AGAGAAAAGTGGGCAATGTCAAA 59.040 39.130 0.00 0.00 0.00 2.69
263 264 3.565307 AGAGAAAAGTGGGCAATGTCAA 58.435 40.909 0.00 0.00 0.00 3.18
264 265 3.228188 AGAGAAAAGTGGGCAATGTCA 57.772 42.857 0.00 0.00 0.00 3.58
265 266 4.082733 GGTTAGAGAAAAGTGGGCAATGTC 60.083 45.833 0.00 0.00 0.00 3.06
266 267 3.826729 GGTTAGAGAAAAGTGGGCAATGT 59.173 43.478 0.00 0.00 0.00 2.71
267 268 3.193479 GGGTTAGAGAAAAGTGGGCAATG 59.807 47.826 0.00 0.00 0.00 2.82
268 269 3.181423 TGGGTTAGAGAAAAGTGGGCAAT 60.181 43.478 0.00 0.00 0.00 3.56
269 270 2.175931 TGGGTTAGAGAAAAGTGGGCAA 59.824 45.455 0.00 0.00 0.00 4.52
270 271 1.777878 TGGGTTAGAGAAAAGTGGGCA 59.222 47.619 0.00 0.00 0.00 5.36
271 272 2.579410 TGGGTTAGAGAAAAGTGGGC 57.421 50.000 0.00 0.00 0.00 5.36
272 273 5.304357 ACATTTTGGGTTAGAGAAAAGTGGG 59.696 40.000 0.00 0.00 0.00 4.61
273 274 6.405278 ACATTTTGGGTTAGAGAAAAGTGG 57.595 37.500 0.00 0.00 0.00 4.00
274 275 8.630037 AGTAACATTTTGGGTTAGAGAAAAGTG 58.370 33.333 0.00 0.00 31.82 3.16
275 276 8.630037 CAGTAACATTTTGGGTTAGAGAAAAGT 58.370 33.333 0.00 0.00 31.82 2.66
276 277 8.846211 TCAGTAACATTTTGGGTTAGAGAAAAG 58.154 33.333 0.00 0.00 31.82 2.27
277 278 8.754991 TCAGTAACATTTTGGGTTAGAGAAAA 57.245 30.769 0.00 0.00 31.82 2.29
278 279 8.934023 ATCAGTAACATTTTGGGTTAGAGAAA 57.066 30.769 0.00 0.00 31.82 2.52
279 280 9.444600 GTATCAGTAACATTTTGGGTTAGAGAA 57.555 33.333 0.00 0.00 31.82 2.87
280 281 8.822805 AGTATCAGTAACATTTTGGGTTAGAGA 58.177 33.333 0.00 0.00 31.82 3.10
281 282 9.449719 AAGTATCAGTAACATTTTGGGTTAGAG 57.550 33.333 0.00 0.00 31.82 2.43
284 285 9.169592 GCTAAGTATCAGTAACATTTTGGGTTA 57.830 33.333 0.00 0.00 0.00 2.85
285 286 7.668052 TGCTAAGTATCAGTAACATTTTGGGTT 59.332 33.333 0.00 0.00 0.00 4.11
286 287 7.172342 TGCTAAGTATCAGTAACATTTTGGGT 58.828 34.615 0.00 0.00 0.00 4.51
287 288 7.201732 CCTGCTAAGTATCAGTAACATTTTGGG 60.202 40.741 0.00 0.00 0.00 4.12
288 289 7.679638 GCCTGCTAAGTATCAGTAACATTTTGG 60.680 40.741 0.00 0.00 0.00 3.28
289 290 7.066284 AGCCTGCTAAGTATCAGTAACATTTTG 59.934 37.037 0.00 0.00 0.00 2.44
290 291 7.112779 AGCCTGCTAAGTATCAGTAACATTTT 58.887 34.615 0.00 0.00 0.00 1.82
291 292 6.653989 AGCCTGCTAAGTATCAGTAACATTT 58.346 36.000 0.00 0.00 0.00 2.32
292 293 6.240549 AGCCTGCTAAGTATCAGTAACATT 57.759 37.500 0.00 0.00 0.00 2.71
293 294 5.878406 AGCCTGCTAAGTATCAGTAACAT 57.122 39.130 0.00 0.00 0.00 2.71
294 295 5.186992 TCAAGCCTGCTAAGTATCAGTAACA 59.813 40.000 0.00 0.00 0.00 2.41
295 296 5.661458 TCAAGCCTGCTAAGTATCAGTAAC 58.339 41.667 0.00 0.00 0.00 2.50
296 297 5.932619 TCAAGCCTGCTAAGTATCAGTAA 57.067 39.130 0.00 0.00 0.00 2.24
297 298 5.163405 CCTTCAAGCCTGCTAAGTATCAGTA 60.163 44.000 0.00 0.00 0.00 2.74
298 299 4.383552 CCTTCAAGCCTGCTAAGTATCAGT 60.384 45.833 0.00 0.00 0.00 3.41
299 300 4.125703 CCTTCAAGCCTGCTAAGTATCAG 58.874 47.826 0.00 0.00 0.00 2.90
300 301 3.118261 CCCTTCAAGCCTGCTAAGTATCA 60.118 47.826 0.00 0.00 0.00 2.15
301 302 3.134804 TCCCTTCAAGCCTGCTAAGTATC 59.865 47.826 0.00 0.00 0.00 2.24
302 303 3.115390 TCCCTTCAAGCCTGCTAAGTAT 58.885 45.455 0.00 0.00 0.00 2.12
303 304 2.546899 TCCCTTCAAGCCTGCTAAGTA 58.453 47.619 0.00 0.00 0.00 2.24
304 305 1.362224 TCCCTTCAAGCCTGCTAAGT 58.638 50.000 0.00 0.00 0.00 2.24
305 306 2.092753 TGATCCCTTCAAGCCTGCTAAG 60.093 50.000 0.00 0.00 0.00 2.18
316 317 2.182827 CTGAGGTGACTGATCCCTTCA 58.817 52.381 0.00 0.00 44.43 3.02
355 356 1.896660 GAACAGAAGGCGGCCACAA 60.897 57.895 23.09 0.00 0.00 3.33
356 357 2.281484 GAACAGAAGGCGGCCACA 60.281 61.111 23.09 0.00 0.00 4.17
360 361 0.674895 ATGACAGAACAGAAGGCGGC 60.675 55.000 0.00 0.00 0.00 6.53
361 362 1.081892 CATGACAGAACAGAAGGCGG 58.918 55.000 0.00 0.00 0.00 6.13
394 395 4.325084 TCCGGGGGAAACTTTCAAATAT 57.675 40.909 0.00 0.00 0.00 1.28
419 420 2.490115 TCGTTTTCTTGGTGTGTGCTTT 59.510 40.909 0.00 0.00 0.00 3.51
430 431 6.743575 ATAGTGAATCCCTTCGTTTTCTTG 57.256 37.500 0.00 0.00 33.86 3.02
465 466 3.091545 AGAAAATTCGGCATGACCACAT 58.908 40.909 0.00 0.00 39.03 3.21
477 478 3.253188 TGGCAAACCAGAGAGAAAATTCG 59.747 43.478 0.00 0.00 42.67 3.34
497 498 0.110238 CGAGCATGGTTCACGTTTGG 60.110 55.000 0.00 0.00 0.00 3.28
504 505 2.198827 ATTTCCACGAGCATGGTTCA 57.801 45.000 0.00 0.00 40.95 3.18
511 512 6.429692 TCAAATAAGAGAAATTTCCACGAGCA 59.570 34.615 14.61 0.00 0.00 4.26
638 643 0.793250 GCTCACCTTCGTTCTTCTGC 59.207 55.000 0.00 0.00 0.00 4.26
686 691 5.617252 AGTGGAAAGTTGGTAGATTCGAAA 58.383 37.500 0.00 0.00 0.00 3.46
708 713 3.674528 ATGATCTAGATGCCGTGGAAG 57.325 47.619 10.74 0.00 0.00 3.46
728 733 4.798907 GTCGTTGAATCTTCTCGCTGATAA 59.201 41.667 0.00 0.00 0.00 1.75
756 761 1.662044 CAGCTGCAGGTTTTCCCAC 59.338 57.895 17.45 0.00 41.86 4.61
781 786 3.019564 GCGTGGGTTAGGACTTACTAGA 58.980 50.000 0.00 0.00 0.00 2.43
783 788 1.745087 CGCGTGGGTTAGGACTTACTA 59.255 52.381 0.00 0.00 0.00 1.82
784 789 0.529378 CGCGTGGGTTAGGACTTACT 59.471 55.000 0.00 0.00 0.00 2.24
785 790 0.244721 ACGCGTGGGTTAGGACTTAC 59.755 55.000 12.93 0.00 0.00 2.34
822 827 1.401905 GCAGGAGTTAATGGCGAAAGG 59.598 52.381 0.00 0.00 0.00 3.11
823 828 2.359900 AGCAGGAGTTAATGGCGAAAG 58.640 47.619 0.00 0.00 0.00 2.62
824 829 2.487762 CAAGCAGGAGTTAATGGCGAAA 59.512 45.455 0.00 0.00 0.00 3.46
857 862 1.745653 TGTGAGAGATAGCGACAGGTG 59.254 52.381 0.00 0.00 0.00 4.00
1352 1366 3.849645 GCTGAACAGGTTCGTTGATTGTG 60.850 47.826 7.58 0.00 42.28 3.33
1582 1608 1.452108 CCGATCCAGGAAACCAGGC 60.452 63.158 0.00 0.00 0.00 4.85
1612 1638 0.874390 GCTCATCAACTTTGCACCGA 59.126 50.000 0.00 0.00 0.00 4.69
1781 1807 4.575973 AGGATGGGCATGCCGCTC 62.576 66.667 29.90 25.74 43.80 5.03
1820 1846 0.247736 ACGACCAGGATCTGACAAGC 59.752 55.000 0.00 0.00 32.44 4.01
1847 1873 4.214327 GGAAGCCTCTCGAGCCCG 62.214 72.222 7.81 0.00 37.07 6.13
1865 1891 1.073722 CAGCAAGAAGTGGCTCCCA 59.926 57.895 0.00 0.00 38.56 4.37
2304 2330 2.338984 GGGTGCTCGTGAAGTCGT 59.661 61.111 0.00 0.00 0.00 4.34
2428 2454 2.130395 CATATATGGCGCTATGGCTCG 58.870 52.381 17.43 0.00 45.14 5.03
2479 2505 3.770040 CCATGTCCACCTCGCCGA 61.770 66.667 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.