Multiple sequence alignment - TraesCS2D01G333900

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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 TraesCS2D01G333900 chr2D 100.000 2960 0 0 1 2960 427570025 427572984 0.000000e+00 5467.0
1 TraesCS2D01G333900 chr2B 93.012 2075 71 21 316 2323 504468020 504470087 0.000000e+00 2961.0
2 TraesCS2D01G333900 chr2B 91.872 406 26 4 2544 2942 504470621 504471026 7.160000e-156 560.0
3 TraesCS2D01G333900 chr2B 94.141 256 13 1 316 569 504444374 504444629 3.580000e-104 388.0
4 TraesCS2D01G333900 chr2B 91.000 200 14 3 2316 2515 504470241 504470436 1.750000e-67 267.0
5 TraesCS2D01G333900 chr2A 91.266 1809 59 30 318 2076 560784498 560782739 0.000000e+00 2374.0
6 TraesCS2D01G333900 chr2A 84.363 518 29 25 2133 2630 560782743 560782258 7.480000e-126 460.0
7 TraesCS2D01G333900 chr2A 90.295 237 16 5 2633 2863 560782171 560781936 1.330000e-78 303.0
8 TraesCS2D01G333900 chr2A 94.118 102 6 0 2859 2960 560776492 560776391 3.950000e-34 156.0
9 TraesCS2D01G333900 chr7A 85.632 174 25 0 4 177 528304112 528303939 1.810000e-42 183.0
10 TraesCS2D01G333900 chr7A 96.774 31 1 0 223 253 700813208 700813238 5.000000e-03 52.8
11 TraesCS2D01G333900 chrUn 100.000 29 0 0 1788 1816 356020608 356020636 1.000000e-03 54.7
12 TraesCS2D01G333900 chr4D 96.774 31 1 0 222 252 503141342 503141372 5.000000e-03 52.8


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 TraesCS2D01G333900 chr2D 427570025 427572984 2959 False 5467.000000 5467 100.000000 1 2960 1 chr2D.!!$F1 2959
1 TraesCS2D01G333900 chr2B 504468020 504471026 3006 False 1262.666667 2961 91.961333 316 2942 3 chr2B.!!$F2 2626
2 TraesCS2D01G333900 chr2A 560781936 560784498 2562 True 1045.666667 2374 88.641333 318 2863 3 chr2A.!!$R2 2545

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
274 275 0.038251 AGCAACAACATCGAGCGAGA 60.038 50.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2255 0.112995 TCTGTGGAAAATGCCTGGCT 59.887 50.0 21.03 0.0 0.0 4.75 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
26 27 9.575783 TTGACGCTTAAATCAAAAGTTAAAGTT 57.424 25.926 0.00 0.00 31.95 2.66
27 28 9.575783 TGACGCTTAAATCAAAAGTTAAAGTTT 57.424 25.926 0.00 0.00 0.00 2.66
57 58 8.601845 AACTTTTTGAACCACCTAATAAATGC 57.398 30.769 0.00 0.00 0.00 3.56
58 59 7.731054 ACTTTTTGAACCACCTAATAAATGCA 58.269 30.769 0.00 0.00 0.00 3.96
59 60 7.655732 ACTTTTTGAACCACCTAATAAATGCAC 59.344 33.333 0.00 0.00 0.00 4.57
60 61 4.955925 TGAACCACCTAATAAATGCACG 57.044 40.909 0.00 0.00 0.00 5.34
61 62 4.328536 TGAACCACCTAATAAATGCACGT 58.671 39.130 0.00 0.00 0.00 4.49
62 63 4.155099 TGAACCACCTAATAAATGCACGTG 59.845 41.667 12.28 12.28 0.00 4.49
63 64 3.681593 ACCACCTAATAAATGCACGTGT 58.318 40.909 18.38 0.00 0.00 4.49
64 65 3.438781 ACCACCTAATAAATGCACGTGTG 59.561 43.478 18.38 2.37 0.00 3.82
65 66 3.181501 CCACCTAATAAATGCACGTGTGG 60.182 47.826 18.38 8.18 35.30 4.17
66 67 3.687212 CACCTAATAAATGCACGTGTGGA 59.313 43.478 18.38 1.70 34.81 4.02
67 68 3.687698 ACCTAATAAATGCACGTGTGGAC 59.312 43.478 18.38 0.09 32.58 4.02
68 69 3.687212 CCTAATAAATGCACGTGTGGACA 59.313 43.478 18.38 6.74 32.58 4.02
69 70 4.155099 CCTAATAAATGCACGTGTGGACAA 59.845 41.667 18.38 0.00 32.58 3.18
70 71 3.829886 ATAAATGCACGTGTGGACAAG 57.170 42.857 18.38 0.00 32.58 3.16
71 72 1.674359 AAATGCACGTGTGGACAAGA 58.326 45.000 18.38 0.00 32.58 3.02
72 73 1.896220 AATGCACGTGTGGACAAGAT 58.104 45.000 18.38 0.00 32.58 2.40
73 74 1.896220 ATGCACGTGTGGACAAGATT 58.104 45.000 18.38 0.00 32.58 2.40
74 75 2.535012 TGCACGTGTGGACAAGATTA 57.465 45.000 18.38 0.00 0.00 1.75
75 76 2.139917 TGCACGTGTGGACAAGATTAC 58.860 47.619 18.38 0.00 0.00 1.89
76 77 2.224185 TGCACGTGTGGACAAGATTACT 60.224 45.455 18.38 0.00 0.00 2.24
77 78 2.806244 GCACGTGTGGACAAGATTACTT 59.194 45.455 18.38 0.00 36.73 2.24
78 79 3.250040 GCACGTGTGGACAAGATTACTTT 59.750 43.478 18.38 0.00 33.70 2.66
79 80 4.261031 GCACGTGTGGACAAGATTACTTTT 60.261 41.667 18.38 0.00 33.70 2.27
80 81 5.732247 GCACGTGTGGACAAGATTACTTTTT 60.732 40.000 18.38 0.00 33.70 1.94
99 100 3.804786 TTTGACGGACTGTGTAGAACA 57.195 42.857 0.00 0.00 37.22 3.18
100 101 4.330944 TTTGACGGACTGTGTAGAACAT 57.669 40.909 0.00 0.00 38.39 2.71
101 102 3.297830 TGACGGACTGTGTAGAACATG 57.702 47.619 0.00 0.00 38.39 3.21
102 103 2.626266 TGACGGACTGTGTAGAACATGT 59.374 45.455 0.00 0.00 38.39 3.21
103 104 2.987149 GACGGACTGTGTAGAACATGTG 59.013 50.000 0.00 0.00 38.39 3.21
104 105 2.288825 ACGGACTGTGTAGAACATGTGG 60.289 50.000 0.00 0.00 38.39 4.17
105 106 2.699954 GGACTGTGTAGAACATGTGGG 58.300 52.381 0.00 0.00 38.39 4.61
106 107 2.076863 GACTGTGTAGAACATGTGGGC 58.923 52.381 0.00 0.00 38.39 5.36
107 108 1.699634 ACTGTGTAGAACATGTGGGCT 59.300 47.619 0.00 0.00 38.39 5.19
108 109 2.903784 ACTGTGTAGAACATGTGGGCTA 59.096 45.455 0.00 0.00 38.39 3.93
109 110 3.262420 CTGTGTAGAACATGTGGGCTAC 58.738 50.000 19.21 19.21 38.39 3.58
110 111 2.903784 TGTGTAGAACATGTGGGCTACT 59.096 45.455 23.19 10.90 35.45 2.57
111 112 3.056107 TGTGTAGAACATGTGGGCTACTC 60.056 47.826 23.19 20.99 35.45 2.59
112 113 2.500098 TGTAGAACATGTGGGCTACTCC 59.500 50.000 23.19 8.16 35.45 3.85
113 114 1.958288 AGAACATGTGGGCTACTCCT 58.042 50.000 0.00 0.00 34.39 3.69
114 115 2.269940 AGAACATGTGGGCTACTCCTT 58.730 47.619 0.00 0.00 34.39 3.36
115 116 2.237392 AGAACATGTGGGCTACTCCTTC 59.763 50.000 0.00 0.35 34.39 3.46
116 117 0.912486 ACATGTGGGCTACTCCTTCC 59.088 55.000 0.00 0.00 34.39 3.46
117 118 0.911769 CATGTGGGCTACTCCTTCCA 59.088 55.000 1.79 0.00 34.39 3.53
118 119 1.492176 CATGTGGGCTACTCCTTCCAT 59.508 52.381 1.79 0.00 34.39 3.41
119 120 2.561209 TGTGGGCTACTCCTTCCATA 57.439 50.000 1.79 0.00 34.39 2.74
120 121 3.060479 TGTGGGCTACTCCTTCCATAT 57.940 47.619 1.79 0.00 34.39 1.78
121 122 3.393687 TGTGGGCTACTCCTTCCATATT 58.606 45.455 1.79 0.00 34.39 1.28
122 123 3.785887 TGTGGGCTACTCCTTCCATATTT 59.214 43.478 1.79 0.00 34.39 1.40
123 124 4.137543 GTGGGCTACTCCTTCCATATTTG 58.862 47.826 0.00 0.00 34.39 2.32
124 125 3.138283 TGGGCTACTCCTTCCATATTTGG 59.862 47.826 0.00 0.00 38.58 3.28
135 136 3.344904 CCATATTTGGAAGAGCGCTTG 57.655 47.619 13.26 0.54 46.92 4.01
136 137 2.945008 CCATATTTGGAAGAGCGCTTGA 59.055 45.455 13.26 0.00 46.92 3.02
137 138 3.567164 CCATATTTGGAAGAGCGCTTGAT 59.433 43.478 13.26 0.00 46.92 2.57
138 139 4.320057 CCATATTTGGAAGAGCGCTTGATC 60.320 45.833 13.26 10.50 46.92 2.92
139 140 1.453155 TTTGGAAGAGCGCTTGATCC 58.547 50.000 22.84 22.84 33.61 3.36
140 141 0.392998 TTGGAAGAGCGCTTGATCCC 60.393 55.000 25.14 17.05 33.61 3.85
141 142 1.267574 TGGAAGAGCGCTTGATCCCT 61.268 55.000 25.14 10.67 33.61 4.20
142 143 0.107459 GGAAGAGCGCTTGATCCCTT 60.107 55.000 13.26 9.21 33.61 3.95
143 144 1.294857 GAAGAGCGCTTGATCCCTTC 58.705 55.000 13.26 14.86 33.61 3.46
144 145 0.615331 AAGAGCGCTTGATCCCTTCA 59.385 50.000 13.26 0.00 31.83 3.02
145 146 0.615331 AGAGCGCTTGATCCCTTCAA 59.385 50.000 13.26 0.00 42.09 2.69
146 147 0.729690 GAGCGCTTGATCCCTTCAAC 59.270 55.000 13.26 0.00 39.44 3.18
147 148 1.021390 AGCGCTTGATCCCTTCAACG 61.021 55.000 2.64 0.00 39.44 4.10
148 149 1.982073 GCGCTTGATCCCTTCAACGG 61.982 60.000 0.00 0.00 39.44 4.44
149 150 1.369091 CGCTTGATCCCTTCAACGGG 61.369 60.000 0.00 0.00 46.13 5.28
150 151 1.657751 GCTTGATCCCTTCAACGGGC 61.658 60.000 0.00 0.00 44.30 6.13
151 152 1.369091 CTTGATCCCTTCAACGGGCG 61.369 60.000 0.00 0.00 44.30 6.13
152 153 3.202706 GATCCCTTCAACGGGCGC 61.203 66.667 0.00 0.00 44.30 6.53
153 154 3.682292 GATCCCTTCAACGGGCGCT 62.682 63.158 7.64 0.00 44.30 5.92
154 155 3.682292 ATCCCTTCAACGGGCGCTC 62.682 63.158 7.64 0.06 44.30 5.03
165 166 4.148825 GGCGCTCGGGTGTCATCT 62.149 66.667 7.64 0.00 0.00 2.90
166 167 2.782222 GGCGCTCGGGTGTCATCTA 61.782 63.158 7.64 0.00 0.00 1.98
167 168 1.299468 GCGCTCGGGTGTCATCTAG 60.299 63.158 0.00 0.00 0.00 2.43
168 169 1.299468 CGCTCGGGTGTCATCTAGC 60.299 63.158 0.00 2.04 0.00 3.42
169 170 1.068250 GCTCGGGTGTCATCTAGCC 59.932 63.158 0.91 0.00 0.00 3.93
172 173 4.835927 GGGTGTCATCTAGCCGTG 57.164 61.111 0.00 0.00 0.00 4.94
173 174 1.898154 GGGTGTCATCTAGCCGTGT 59.102 57.895 0.00 0.00 0.00 4.49
174 175 0.179108 GGGTGTCATCTAGCCGTGTC 60.179 60.000 0.00 0.00 0.00 3.67
175 176 0.179108 GGTGTCATCTAGCCGTGTCC 60.179 60.000 0.00 0.00 0.00 4.02
176 177 0.530744 GTGTCATCTAGCCGTGTCCA 59.469 55.000 0.00 0.00 0.00 4.02
177 178 1.137086 GTGTCATCTAGCCGTGTCCAT 59.863 52.381 0.00 0.00 0.00 3.41
178 179 2.361119 GTGTCATCTAGCCGTGTCCATA 59.639 50.000 0.00 0.00 0.00 2.74
179 180 3.005897 GTGTCATCTAGCCGTGTCCATAT 59.994 47.826 0.00 0.00 0.00 1.78
180 181 3.641436 TGTCATCTAGCCGTGTCCATATT 59.359 43.478 0.00 0.00 0.00 1.28
181 182 4.100963 TGTCATCTAGCCGTGTCCATATTT 59.899 41.667 0.00 0.00 0.00 1.40
182 183 5.057149 GTCATCTAGCCGTGTCCATATTTT 58.943 41.667 0.00 0.00 0.00 1.82
183 184 5.527582 GTCATCTAGCCGTGTCCATATTTTT 59.472 40.000 0.00 0.00 0.00 1.94
210 211 9.563748 TTGCTAATATACCCAACAATTACTACC 57.436 33.333 0.00 0.00 0.00 3.18
211 212 8.158789 TGCTAATATACCCAACAATTACTACCC 58.841 37.037 0.00 0.00 0.00 3.69
212 213 7.332678 GCTAATATACCCAACAATTACTACCCG 59.667 40.741 0.00 0.00 0.00 5.28
213 214 2.793288 ACCCAACAATTACTACCCGG 57.207 50.000 0.00 0.00 0.00 5.73
214 215 1.987368 ACCCAACAATTACTACCCGGT 59.013 47.619 0.00 0.00 0.00 5.28
215 216 2.376181 ACCCAACAATTACTACCCGGTT 59.624 45.455 0.00 0.00 0.00 4.44
216 217 3.586618 ACCCAACAATTACTACCCGGTTA 59.413 43.478 0.00 0.00 0.00 2.85
217 218 3.940852 CCCAACAATTACTACCCGGTTAC 59.059 47.826 0.00 0.00 0.00 2.50
218 219 4.323715 CCCAACAATTACTACCCGGTTACT 60.324 45.833 0.00 0.00 0.00 2.24
219 220 5.104982 CCCAACAATTACTACCCGGTTACTA 60.105 44.000 0.00 0.00 0.00 1.82
220 221 6.408434 CCCAACAATTACTACCCGGTTACTAT 60.408 42.308 0.00 0.00 0.00 2.12
221 222 7.049754 CCAACAATTACTACCCGGTTACTATT 58.950 38.462 0.00 0.00 0.00 1.73
222 223 7.553760 CCAACAATTACTACCCGGTTACTATTT 59.446 37.037 0.00 0.00 0.00 1.40
223 224 8.949177 CAACAATTACTACCCGGTTACTATTTT 58.051 33.333 0.00 0.00 0.00 1.82
224 225 9.519191 AACAATTACTACCCGGTTACTATTTTT 57.481 29.630 0.00 0.00 0.00 1.94
225 226 8.949177 ACAATTACTACCCGGTTACTATTTTTG 58.051 33.333 0.00 0.00 0.00 2.44
226 227 8.400186 CAATTACTACCCGGTTACTATTTTTGG 58.600 37.037 0.00 0.00 0.00 3.28
227 228 4.847198 ACTACCCGGTTACTATTTTTGGG 58.153 43.478 0.00 0.00 41.06 4.12
228 229 3.090210 ACCCGGTTACTATTTTTGGGG 57.910 47.619 0.00 0.00 39.54 4.96
229 230 2.291735 ACCCGGTTACTATTTTTGGGGG 60.292 50.000 0.00 0.00 39.54 5.40
230 231 2.291735 CCCGGTTACTATTTTTGGGGGT 60.292 50.000 0.00 0.00 0.00 4.95
231 232 2.756207 CCGGTTACTATTTTTGGGGGTG 59.244 50.000 0.00 0.00 0.00 4.61
232 233 3.423749 CGGTTACTATTTTTGGGGGTGT 58.576 45.455 0.00 0.00 0.00 4.16
233 234 3.827876 CGGTTACTATTTTTGGGGGTGTT 59.172 43.478 0.00 0.00 0.00 3.32
234 235 4.281435 CGGTTACTATTTTTGGGGGTGTTT 59.719 41.667 0.00 0.00 0.00 2.83
235 236 5.543714 GGTTACTATTTTTGGGGGTGTTTG 58.456 41.667 0.00 0.00 0.00 2.93
236 237 5.511716 GGTTACTATTTTTGGGGGTGTTTGG 60.512 44.000 0.00 0.00 0.00 3.28
237 238 3.659841 ACTATTTTTGGGGGTGTTTGGT 58.340 40.909 0.00 0.00 0.00 3.67
238 239 4.041464 ACTATTTTTGGGGGTGTTTGGTT 58.959 39.130 0.00 0.00 0.00 3.67
239 240 3.569194 ATTTTTGGGGGTGTTTGGTTC 57.431 42.857 0.00 0.00 0.00 3.62
240 241 1.205055 TTTTGGGGGTGTTTGGTTCC 58.795 50.000 0.00 0.00 0.00 3.62
241 242 0.042731 TTTGGGGGTGTTTGGTTCCA 59.957 50.000 0.00 0.00 0.00 3.53
242 243 0.397816 TTGGGGGTGTTTGGTTCCAG 60.398 55.000 0.00 0.00 0.00 3.86
243 244 1.289982 TGGGGGTGTTTGGTTCCAGA 61.290 55.000 0.00 0.00 0.00 3.86
244 245 0.539669 GGGGGTGTTTGGTTCCAGAG 60.540 60.000 0.00 0.00 0.00 3.35
245 246 0.476771 GGGGTGTTTGGTTCCAGAGA 59.523 55.000 0.00 0.00 0.00 3.10
246 247 1.605753 GGGTGTTTGGTTCCAGAGAC 58.394 55.000 1.90 1.90 0.00 3.36
247 248 1.143073 GGGTGTTTGGTTCCAGAGACT 59.857 52.381 8.93 0.00 0.00 3.24
248 249 2.422945 GGGTGTTTGGTTCCAGAGACTT 60.423 50.000 8.93 0.00 0.00 3.01
249 250 3.288092 GGTGTTTGGTTCCAGAGACTTT 58.712 45.455 8.93 0.00 0.00 2.66
250 251 3.699538 GGTGTTTGGTTCCAGAGACTTTT 59.300 43.478 8.93 0.00 0.00 2.27
251 252 4.159693 GGTGTTTGGTTCCAGAGACTTTTT 59.840 41.667 8.93 0.00 0.00 1.94
252 253 5.102313 GTGTTTGGTTCCAGAGACTTTTTG 58.898 41.667 3.12 0.00 0.00 2.44
253 254 4.159506 TGTTTGGTTCCAGAGACTTTTTGG 59.840 41.667 0.00 0.00 0.00 3.28
254 255 3.662759 TGGTTCCAGAGACTTTTTGGT 57.337 42.857 2.67 0.00 33.65 3.67
255 256 4.781775 TGGTTCCAGAGACTTTTTGGTA 57.218 40.909 2.67 0.00 33.65 3.25
256 257 4.714632 TGGTTCCAGAGACTTTTTGGTAG 58.285 43.478 2.67 0.00 33.65 3.18
257 258 3.502595 GGTTCCAGAGACTTTTTGGTAGC 59.497 47.826 2.67 0.00 33.65 3.58
258 259 4.134563 GTTCCAGAGACTTTTTGGTAGCA 58.865 43.478 0.00 0.00 33.65 3.49
259 260 4.431416 TCCAGAGACTTTTTGGTAGCAA 57.569 40.909 2.54 2.54 33.65 3.91
260 261 4.134563 TCCAGAGACTTTTTGGTAGCAAC 58.865 43.478 6.90 0.00 33.65 4.17
261 262 3.882888 CCAGAGACTTTTTGGTAGCAACA 59.117 43.478 6.90 0.00 0.00 3.33
262 263 4.338118 CCAGAGACTTTTTGGTAGCAACAA 59.662 41.667 6.90 6.46 0.00 2.83
263 264 5.273944 CAGAGACTTTTTGGTAGCAACAAC 58.726 41.667 6.90 0.00 0.00 3.32
264 265 4.947388 AGAGACTTTTTGGTAGCAACAACA 59.053 37.500 6.90 0.00 0.00 3.33
265 266 5.594317 AGAGACTTTTTGGTAGCAACAACAT 59.406 36.000 6.90 0.00 0.00 2.71
266 267 5.831997 AGACTTTTTGGTAGCAACAACATC 58.168 37.500 6.90 6.00 0.00 3.06
267 268 4.606961 ACTTTTTGGTAGCAACAACATCG 58.393 39.130 6.90 0.00 0.00 3.84
268 269 4.336993 ACTTTTTGGTAGCAACAACATCGA 59.663 37.500 6.90 0.00 0.00 3.59
269 270 4.481930 TTTTGGTAGCAACAACATCGAG 57.518 40.909 6.90 0.00 0.00 4.04
270 271 1.438651 TGGTAGCAACAACATCGAGC 58.561 50.000 0.00 0.00 0.00 5.03
271 272 0.370273 GGTAGCAACAACATCGAGCG 59.630 55.000 0.00 0.00 0.00 5.03
272 273 1.346365 GTAGCAACAACATCGAGCGA 58.654 50.000 0.00 0.00 0.00 4.93
273 274 1.321743 GTAGCAACAACATCGAGCGAG 59.678 52.381 0.00 0.00 0.00 5.03
274 275 0.038251 AGCAACAACATCGAGCGAGA 60.038 50.000 0.00 0.00 0.00 4.04
275 276 0.790207 GCAACAACATCGAGCGAGAA 59.210 50.000 0.00 0.00 0.00 2.87
276 277 1.194547 GCAACAACATCGAGCGAGAAA 59.805 47.619 0.00 0.00 0.00 2.52
277 278 2.723010 GCAACAACATCGAGCGAGAAAG 60.723 50.000 0.00 0.00 0.00 2.62
278 279 2.440539 ACAACATCGAGCGAGAAAGT 57.559 45.000 0.00 0.00 0.00 2.66
279 280 3.570926 ACAACATCGAGCGAGAAAGTA 57.429 42.857 0.00 0.00 0.00 2.24
280 281 3.502920 ACAACATCGAGCGAGAAAGTAG 58.497 45.455 0.00 0.00 0.00 2.57
281 282 2.196295 ACATCGAGCGAGAAAGTAGC 57.804 50.000 0.00 0.00 0.00 3.58
282 283 1.472878 ACATCGAGCGAGAAAGTAGCA 59.527 47.619 0.00 0.00 0.00 3.49
283 284 2.094700 ACATCGAGCGAGAAAGTAGCAA 60.095 45.455 0.00 0.00 0.00 3.91
284 285 1.978542 TCGAGCGAGAAAGTAGCAAC 58.021 50.000 0.00 0.00 0.00 4.17
285 286 1.268625 TCGAGCGAGAAAGTAGCAACA 59.731 47.619 0.00 0.00 0.00 3.33
286 287 2.058798 CGAGCGAGAAAGTAGCAACAA 58.941 47.619 0.00 0.00 0.00 2.83
287 288 2.159960 CGAGCGAGAAAGTAGCAACAAC 60.160 50.000 0.00 0.00 0.00 3.32
288 289 3.060602 GAGCGAGAAAGTAGCAACAACT 58.939 45.455 0.00 0.00 0.00 3.16
289 290 4.235360 GAGCGAGAAAGTAGCAACAACTA 58.765 43.478 0.00 0.00 0.00 2.24
290 291 4.628074 AGCGAGAAAGTAGCAACAACTAA 58.372 39.130 0.00 0.00 0.00 2.24
291 292 5.054477 AGCGAGAAAGTAGCAACAACTAAA 58.946 37.500 0.00 0.00 0.00 1.85
292 293 5.701290 AGCGAGAAAGTAGCAACAACTAAAT 59.299 36.000 0.00 0.00 0.00 1.40
293 294 6.204882 AGCGAGAAAGTAGCAACAACTAAATT 59.795 34.615 0.00 0.00 0.00 1.82
294 295 6.856426 GCGAGAAAGTAGCAACAACTAAATTT 59.144 34.615 0.00 0.00 0.00 1.82
295 296 7.378728 GCGAGAAAGTAGCAACAACTAAATTTT 59.621 33.333 0.00 0.00 0.00 1.82
296 297 8.892905 CGAGAAAGTAGCAACAACTAAATTTTC 58.107 33.333 0.00 0.00 0.00 2.29
297 298 9.952188 GAGAAAGTAGCAACAACTAAATTTTCT 57.048 29.630 0.00 0.00 35.04 2.52
302 303 9.961265 AGTAGCAACAACTAAATTTTCTTAACC 57.039 29.630 0.00 0.00 0.00 2.85
303 304 9.738832 GTAGCAACAACTAAATTTTCTTAACCA 57.261 29.630 0.00 0.00 0.00 3.67
305 306 9.660180 AGCAACAACTAAATTTTCTTAACCAAA 57.340 25.926 0.00 0.00 0.00 3.28
351 352 8.055279 TGATTGAGAATAAAGTCAACCCAATC 57.945 34.615 0.00 0.00 0.00 2.67
384 386 1.496934 CCATTTTGGTTTCGGTGCAC 58.503 50.000 8.80 8.80 31.35 4.57
642 648 5.403166 CGATAATTCAAAATCCGCCGTACTA 59.597 40.000 0.00 0.00 0.00 1.82
885 910 0.396811 ACCAACACCTCCTTCCTTCG 59.603 55.000 0.00 0.00 0.00 3.79
979 1006 0.254638 TCTAGGAGGAGGGAGGGGAA 60.255 60.000 0.00 0.00 0.00 3.97
1159 1224 2.223947 TGCATCTAACGTGTCTGTGTGT 60.224 45.455 0.00 0.00 0.00 3.72
1167 1232 1.438651 GTGTCTGTGTGTGTGTGTGT 58.561 50.000 0.00 0.00 0.00 3.72
1168 1233 1.128507 GTGTCTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1169 1234 1.270571 TGTCTGTGTGTGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
1170 1235 1.128507 GTCTGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1296 1361 2.425592 CAGGACAAGGACGTGGCA 59.574 61.111 0.00 0.00 0.00 4.92
1503 1574 2.103042 GCTGATGACGCTGGTGTCC 61.103 63.158 11.09 0.00 38.11 4.02
1773 1844 2.501610 GACTCGGCCTCCACATCC 59.498 66.667 0.00 0.00 0.00 3.51
1885 1956 1.274167 CCACGCCTCCTAACAACAGTA 59.726 52.381 0.00 0.00 0.00 2.74
1972 2043 9.791820 TGCACATAAATTAGACAGAAATGATTG 57.208 29.630 0.00 0.00 0.00 2.67
2011 2082 1.522668 CAGTCTTTCGTGCCCATCAA 58.477 50.000 0.00 0.00 0.00 2.57
2015 2086 2.352960 GTCTTTCGTGCCCATCAATCTC 59.647 50.000 0.00 0.00 0.00 2.75
2027 2098 3.607741 CATCAATCTCACAGAAGCAGGT 58.392 45.455 0.00 0.00 0.00 4.00
2112 2183 1.672356 ATGTCGTCCTGCTTGTGCC 60.672 57.895 0.00 0.00 38.71 5.01
2134 2215 0.036388 TGCCCCTGAAGACGTCATTC 60.036 55.000 19.50 17.45 35.07 2.67
2138 2219 2.028112 CCCCTGAAGACGTCATTCTCAA 60.028 50.000 19.50 2.88 35.07 3.02
2145 2226 7.254252 CCTGAAGACGTCATTCTCAATTGTATC 60.254 40.741 19.50 0.00 35.07 2.24
2146 2227 6.253512 TGAAGACGTCATTCTCAATTGTATCG 59.746 38.462 19.50 5.17 0.00 2.92
2147 2228 5.891451 AGACGTCATTCTCAATTGTATCGA 58.109 37.500 19.50 0.00 0.00 3.59
2148 2229 6.507900 AGACGTCATTCTCAATTGTATCGAT 58.492 36.000 19.50 2.16 0.00 3.59
2149 2230 6.419116 AGACGTCATTCTCAATTGTATCGATG 59.581 38.462 19.50 5.54 0.00 3.84
2150 2231 5.050769 ACGTCATTCTCAATTGTATCGATGC 60.051 40.000 8.54 7.48 0.00 3.91
2172 2255 2.649190 TCTGCAAGGCTGTAAACAACA 58.351 42.857 0.00 0.00 36.42 3.33
2187 2270 0.680618 CAACAGCCAGGCATTTTCCA 59.319 50.000 15.80 0.00 0.00 3.53
2188 2271 0.681175 AACAGCCAGGCATTTTCCAC 59.319 50.000 15.80 0.00 0.00 4.02
2189 2272 0.469705 ACAGCCAGGCATTTTCCACA 60.470 50.000 15.80 0.00 0.00 4.17
2190 2273 0.245539 CAGCCAGGCATTTTCCACAG 59.754 55.000 15.80 0.00 0.00 3.66
2191 2274 0.112995 AGCCAGGCATTTTCCACAGA 59.887 50.000 15.80 0.00 0.00 3.41
2192 2275 0.529378 GCCAGGCATTTTCCACAGAG 59.471 55.000 6.55 0.00 0.00 3.35
2220 2303 0.825010 CTTGGGCAGTTGGAGCAGTT 60.825 55.000 0.00 0.00 0.00 3.16
2233 2316 3.005897 TGGAGCAGTTAAGATCGGCTATC 59.994 47.826 0.00 0.00 36.59 2.08
2244 2334 2.438868 TCGGCTATCGATGGAACATG 57.561 50.000 13.60 0.00 43.74 3.21
2245 2335 1.960689 TCGGCTATCGATGGAACATGA 59.039 47.619 13.60 0.00 43.74 3.07
2323 2417 2.432510 GCTACACAGTTCTGGGAGCTAT 59.567 50.000 9.16 0.00 0.00 2.97
2324 2418 3.637229 GCTACACAGTTCTGGGAGCTATA 59.363 47.826 9.16 0.00 0.00 1.31
2325 2419 4.282195 GCTACACAGTTCTGGGAGCTATAT 59.718 45.833 9.16 0.00 0.00 0.86
2326 2420 5.477291 GCTACACAGTTCTGGGAGCTATATA 59.523 44.000 9.16 0.00 0.00 0.86
2368 2620 2.582636 AGAATTACTCCATTGCCCAGGT 59.417 45.455 0.00 0.00 0.00 4.00
2372 2624 1.136329 ACTCCATTGCCCAGGTCTGT 61.136 55.000 0.00 0.00 0.00 3.41
2436 2688 1.311859 TCGCCTCATGGATCAATTGC 58.688 50.000 0.00 0.00 34.57 3.56
2460 2712 2.096069 CACCTTTGTGAGATTGCTCGTG 60.096 50.000 0.00 0.00 45.76 4.35
2508 2760 6.999871 AGAATGTTATGCATGGATGTATGACA 59.000 34.615 10.16 14.60 46.89 3.58
2535 2950 6.110707 TCTAGTTTGTATTCGGTGAAATCCC 58.889 40.000 0.00 0.00 0.00 3.85
2536 2951 4.918588 AGTTTGTATTCGGTGAAATCCCT 58.081 39.130 0.00 0.00 0.00 4.20
2537 2952 5.321927 AGTTTGTATTCGGTGAAATCCCTT 58.678 37.500 0.00 0.00 0.00 3.95
2538 2953 5.773176 AGTTTGTATTCGGTGAAATCCCTTT 59.227 36.000 0.00 0.00 0.00 3.11
2539 2954 6.943718 AGTTTGTATTCGGTGAAATCCCTTTA 59.056 34.615 0.00 0.00 0.00 1.85
2540 2955 7.614192 AGTTTGTATTCGGTGAAATCCCTTTAT 59.386 33.333 0.00 0.00 0.00 1.40
2541 2956 6.935741 TGTATTCGGTGAAATCCCTTTATG 57.064 37.500 0.00 0.00 0.00 1.90
2542 2957 5.825679 TGTATTCGGTGAAATCCCTTTATGG 59.174 40.000 0.00 0.00 0.00 2.74
2564 2979 5.359576 TGGTTTATGCCATTGTGAGTAATCC 59.640 40.000 0.00 0.00 32.81 3.01
2608 3026 6.998673 ACCCATTCTGCTTGGAATATTACTAC 59.001 38.462 0.00 0.00 36.26 2.73
2611 3029 8.153550 CCATTCTGCTTGGAATATTACTACTCT 58.846 37.037 0.00 0.00 36.26 3.24
2683 3187 6.376299 TGACTAGAGATAACCTTGCTAAACGA 59.624 38.462 0.00 0.00 0.00 3.85
2685 3189 4.756502 AGAGATAACCTTGCTAAACGACC 58.243 43.478 0.00 0.00 0.00 4.79
2742 3247 5.467902 TTTTGTGCTGAAAATGAAAGTGC 57.532 34.783 0.00 0.00 0.00 4.40
2820 3328 1.737793 GTACTTTCGCTTGACATGGGG 59.262 52.381 0.00 0.00 0.00 4.96
2821 3329 0.110486 ACTTTCGCTTGACATGGGGT 59.890 50.000 0.00 0.00 0.00 4.95
2822 3330 1.247567 CTTTCGCTTGACATGGGGTT 58.752 50.000 0.00 0.00 0.00 4.11
2873 3382 4.391155 ACAAAATGCCTGCAATGTTGATT 58.609 34.783 15.38 0.00 0.00 2.57
2883 3392 2.666508 GCAATGTTGATTTCTGCTGCTG 59.333 45.455 0.00 0.00 0.00 4.41
2900 3409 3.785486 TGCTGTATCATGGACTCTTTCG 58.215 45.455 0.00 0.00 0.00 3.46
2902 3411 4.047822 GCTGTATCATGGACTCTTTCGAG 58.952 47.826 0.00 0.00 43.10 4.04
2919 3428 1.198867 CGAGCTATCGCAGTGCTATCT 59.801 52.381 14.33 1.96 42.97 1.98
2942 3451 5.083122 TGTTTCCAGGGCAATAGATGAAAA 58.917 37.500 0.00 0.00 0.00 2.29
2943 3452 5.185635 TGTTTCCAGGGCAATAGATGAAAAG 59.814 40.000 0.00 0.00 0.00 2.27
2944 3453 3.902218 TCCAGGGCAATAGATGAAAAGG 58.098 45.455 0.00 0.00 0.00 3.11
2945 3454 2.363359 CCAGGGCAATAGATGAAAAGGC 59.637 50.000 0.00 0.00 0.00 4.35
2946 3455 3.294214 CAGGGCAATAGATGAAAAGGCT 58.706 45.455 0.00 0.00 0.00 4.58
2947 3456 3.703052 CAGGGCAATAGATGAAAAGGCTT 59.297 43.478 0.00 0.00 0.00 4.35
2948 3457 3.703052 AGGGCAATAGATGAAAAGGCTTG 59.297 43.478 0.00 0.00 0.00 4.01
2949 3458 3.451526 GGCAATAGATGAAAAGGCTTGC 58.548 45.455 0.00 0.00 37.40 4.01
2950 3459 3.131755 GGCAATAGATGAAAAGGCTTGCT 59.868 43.478 0.00 0.00 38.03 3.91
2951 3460 4.110482 GCAATAGATGAAAAGGCTTGCTG 58.890 43.478 0.00 0.00 35.75 4.41
2952 3461 4.679662 CAATAGATGAAAAGGCTTGCTGG 58.320 43.478 0.00 0.00 0.00 4.85
2953 3462 2.592102 AGATGAAAAGGCTTGCTGGA 57.408 45.000 0.00 0.00 0.00 3.86
2954 3463 3.097342 AGATGAAAAGGCTTGCTGGAT 57.903 42.857 0.00 0.00 0.00 3.41
2955 3464 2.758979 AGATGAAAAGGCTTGCTGGATG 59.241 45.455 0.00 0.00 0.00 3.51
2956 3465 1.999648 TGAAAAGGCTTGCTGGATGT 58.000 45.000 0.00 0.00 0.00 3.06
2957 3466 3.153369 TGAAAAGGCTTGCTGGATGTA 57.847 42.857 0.00 0.00 0.00 2.29
2958 3467 3.700538 TGAAAAGGCTTGCTGGATGTAT 58.299 40.909 0.00 0.00 0.00 2.29
2959 3468 3.444742 TGAAAAGGCTTGCTGGATGTATG 59.555 43.478 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.575783 AACTTTAACTTTTGATTTAAGCGTCAA 57.424 25.926 0.00 0.00 32.86 3.18
1 2 9.575783 AAACTTTAACTTTTGATTTAAGCGTCA 57.424 25.926 0.00 0.00 0.00 4.35
31 32 9.051679 GCATTTATTAGGTGGTTCAAAAAGTTT 57.948 29.630 0.00 0.00 0.00 2.66
32 33 8.207545 TGCATTTATTAGGTGGTTCAAAAAGTT 58.792 29.630 0.00 0.00 0.00 2.66
33 34 7.655732 GTGCATTTATTAGGTGGTTCAAAAAGT 59.344 33.333 0.00 0.00 0.00 2.66
34 35 7.148820 CGTGCATTTATTAGGTGGTTCAAAAAG 60.149 37.037 0.00 0.00 0.00 2.27
35 36 6.642950 CGTGCATTTATTAGGTGGTTCAAAAA 59.357 34.615 0.00 0.00 0.00 1.94
36 37 6.153067 CGTGCATTTATTAGGTGGTTCAAAA 58.847 36.000 0.00 0.00 0.00 2.44
37 38 5.241949 ACGTGCATTTATTAGGTGGTTCAAA 59.758 36.000 0.00 0.00 0.00 2.69
38 39 4.762765 ACGTGCATTTATTAGGTGGTTCAA 59.237 37.500 0.00 0.00 0.00 2.69
39 40 4.155099 CACGTGCATTTATTAGGTGGTTCA 59.845 41.667 0.82 0.00 0.00 3.18
40 41 4.155280 ACACGTGCATTTATTAGGTGGTTC 59.845 41.667 17.22 0.00 35.26 3.62
41 42 4.076394 ACACGTGCATTTATTAGGTGGTT 58.924 39.130 17.22 0.00 35.26 3.67
42 43 3.438781 CACACGTGCATTTATTAGGTGGT 59.561 43.478 17.22 0.00 35.26 4.16
43 44 3.181501 CCACACGTGCATTTATTAGGTGG 60.182 47.826 17.22 7.26 37.53 4.61
44 45 3.687212 TCCACACGTGCATTTATTAGGTG 59.313 43.478 17.22 1.15 36.56 4.00
45 46 3.687698 GTCCACACGTGCATTTATTAGGT 59.312 43.478 17.22 0.00 0.00 3.08
46 47 3.687212 TGTCCACACGTGCATTTATTAGG 59.313 43.478 17.22 4.05 0.00 2.69
47 48 4.937696 TGTCCACACGTGCATTTATTAG 57.062 40.909 17.22 0.00 0.00 1.73
48 49 4.998033 TCTTGTCCACACGTGCATTTATTA 59.002 37.500 17.22 0.00 0.00 0.98
49 50 3.818210 TCTTGTCCACACGTGCATTTATT 59.182 39.130 17.22 0.00 0.00 1.40
50 51 3.407698 TCTTGTCCACACGTGCATTTAT 58.592 40.909 17.22 0.00 0.00 1.40
51 52 2.839975 TCTTGTCCACACGTGCATTTA 58.160 42.857 17.22 0.00 0.00 1.40
52 53 1.674359 TCTTGTCCACACGTGCATTT 58.326 45.000 17.22 0.00 0.00 2.32
53 54 1.896220 ATCTTGTCCACACGTGCATT 58.104 45.000 17.22 0.00 0.00 3.56
54 55 1.896220 AATCTTGTCCACACGTGCAT 58.104 45.000 17.22 0.00 0.00 3.96
55 56 2.139917 GTAATCTTGTCCACACGTGCA 58.860 47.619 17.22 1.90 0.00 4.57
56 57 2.413837 AGTAATCTTGTCCACACGTGC 58.586 47.619 17.22 0.00 0.00 5.34
57 58 5.418310 AAAAGTAATCTTGTCCACACGTG 57.582 39.130 15.48 15.48 33.79 4.49
77 78 4.505808 TGTTCTACACAGTCCGTCAAAAA 58.494 39.130 0.00 0.00 0.00 1.94
78 79 4.126208 TGTTCTACACAGTCCGTCAAAA 57.874 40.909 0.00 0.00 0.00 2.44
79 80 3.804786 TGTTCTACACAGTCCGTCAAA 57.195 42.857 0.00 0.00 0.00 2.69
80 81 3.069016 ACATGTTCTACACAGTCCGTCAA 59.931 43.478 0.00 0.00 39.40 3.18
81 82 2.626266 ACATGTTCTACACAGTCCGTCA 59.374 45.455 0.00 0.00 39.40 4.35
82 83 2.987149 CACATGTTCTACACAGTCCGTC 59.013 50.000 0.00 0.00 39.40 4.79
83 84 2.288825 CCACATGTTCTACACAGTCCGT 60.289 50.000 0.00 0.00 39.40 4.69
84 85 2.337583 CCACATGTTCTACACAGTCCG 58.662 52.381 0.00 0.00 39.40 4.79
85 86 2.699954 CCCACATGTTCTACACAGTCC 58.300 52.381 0.00 0.00 39.40 3.85
86 87 2.076863 GCCCACATGTTCTACACAGTC 58.923 52.381 0.00 0.00 39.40 3.51
87 88 1.699634 AGCCCACATGTTCTACACAGT 59.300 47.619 0.00 0.00 39.40 3.55
88 89 2.479566 AGCCCACATGTTCTACACAG 57.520 50.000 0.00 0.00 39.40 3.66
89 90 2.903784 AGTAGCCCACATGTTCTACACA 59.096 45.455 21.86 0.00 40.71 3.72
90 91 3.522553 GAGTAGCCCACATGTTCTACAC 58.477 50.000 21.86 15.91 35.19 2.90
91 92 2.500098 GGAGTAGCCCACATGTTCTACA 59.500 50.000 21.86 0.00 35.19 2.74
92 93 2.766828 AGGAGTAGCCCACATGTTCTAC 59.233 50.000 16.24 16.24 37.37 2.59
93 94 3.116096 AGGAGTAGCCCACATGTTCTA 57.884 47.619 0.00 0.00 37.37 2.10
94 95 1.958288 AGGAGTAGCCCACATGTTCT 58.042 50.000 0.00 0.00 37.37 3.01
95 96 2.633488 GAAGGAGTAGCCCACATGTTC 58.367 52.381 0.00 0.00 37.37 3.18
96 97 1.282157 GGAAGGAGTAGCCCACATGTT 59.718 52.381 0.00 0.00 37.37 2.71
97 98 0.912486 GGAAGGAGTAGCCCACATGT 59.088 55.000 0.00 0.00 37.37 3.21
98 99 0.911769 TGGAAGGAGTAGCCCACATG 59.088 55.000 0.00 0.00 37.37 3.21
99 100 1.898863 ATGGAAGGAGTAGCCCACAT 58.101 50.000 0.00 0.00 37.37 3.21
100 101 2.561209 TATGGAAGGAGTAGCCCACA 57.439 50.000 0.00 0.00 37.37 4.17
101 102 4.137543 CAAATATGGAAGGAGTAGCCCAC 58.862 47.826 0.00 0.00 37.37 4.61
102 103 4.437682 CAAATATGGAAGGAGTAGCCCA 57.562 45.455 0.00 0.00 37.37 5.36
116 117 4.320057 GGATCAAGCGCTCTTCCAAATATG 60.320 45.833 21.75 9.58 0.00 1.78
117 118 3.817647 GGATCAAGCGCTCTTCCAAATAT 59.182 43.478 21.75 0.00 0.00 1.28
118 119 3.206150 GGATCAAGCGCTCTTCCAAATA 58.794 45.455 21.75 0.00 0.00 1.40
119 120 2.019984 GGATCAAGCGCTCTTCCAAAT 58.980 47.619 21.75 5.80 0.00 2.32
120 121 1.453155 GGATCAAGCGCTCTTCCAAA 58.547 50.000 21.75 1.63 0.00 3.28
121 122 0.392998 GGGATCAAGCGCTCTTCCAA 60.393 55.000 25.55 5.87 0.00 3.53
122 123 1.221840 GGGATCAAGCGCTCTTCCA 59.778 57.895 25.55 6.01 0.00 3.53
123 124 0.107459 AAGGGATCAAGCGCTCTTCC 60.107 55.000 12.06 17.11 0.00 3.46
124 125 1.294857 GAAGGGATCAAGCGCTCTTC 58.705 55.000 12.06 14.46 0.00 2.87
125 126 0.615331 TGAAGGGATCAAGCGCTCTT 59.385 50.000 12.06 8.69 34.30 2.85
126 127 0.615331 TTGAAGGGATCAAGCGCTCT 59.385 50.000 12.06 0.00 43.08 4.09
127 128 3.159298 TTGAAGGGATCAAGCGCTC 57.841 52.632 12.06 0.00 43.08 5.03
148 149 2.685387 CTAGATGACACCCGAGCGCC 62.685 65.000 2.29 0.00 0.00 6.53
149 150 1.299468 CTAGATGACACCCGAGCGC 60.299 63.158 0.00 0.00 0.00 5.92
150 151 1.299468 GCTAGATGACACCCGAGCG 60.299 63.158 0.00 0.00 0.00 5.03
151 152 1.068250 GGCTAGATGACACCCGAGC 59.932 63.158 0.00 4.04 0.00 5.03
152 153 1.360551 CGGCTAGATGACACCCGAG 59.639 63.158 0.00 0.00 41.34 4.63
153 154 1.379443 ACGGCTAGATGACACCCGA 60.379 57.895 9.31 0.00 41.34 5.14
154 155 1.226974 CACGGCTAGATGACACCCG 60.227 63.158 0.00 0.00 44.19 5.28
155 156 0.179108 GACACGGCTAGATGACACCC 60.179 60.000 0.00 0.00 0.00 4.61
156 157 0.179108 GGACACGGCTAGATGACACC 60.179 60.000 0.00 0.00 0.00 4.16
157 158 0.530744 TGGACACGGCTAGATGACAC 59.469 55.000 0.00 0.00 0.00 3.67
158 159 1.485124 ATGGACACGGCTAGATGACA 58.515 50.000 0.00 0.00 0.00 3.58
159 160 3.944055 ATATGGACACGGCTAGATGAC 57.056 47.619 0.00 0.00 0.00 3.06
160 161 4.955811 AAATATGGACACGGCTAGATGA 57.044 40.909 0.00 0.00 0.00 2.92
184 185 9.563748 GGTAGTAATTGTTGGGTATATTAGCAA 57.436 33.333 0.00 0.00 0.00 3.91
185 186 8.158789 GGGTAGTAATTGTTGGGTATATTAGCA 58.841 37.037 0.00 0.00 0.00 3.49
186 187 7.332678 CGGGTAGTAATTGTTGGGTATATTAGC 59.667 40.741 0.00 0.00 0.00 3.09
187 188 7.820872 CCGGGTAGTAATTGTTGGGTATATTAG 59.179 40.741 0.00 0.00 0.00 1.73
188 189 7.292120 ACCGGGTAGTAATTGTTGGGTATATTA 59.708 37.037 6.32 0.00 0.00 0.98
189 190 6.101588 ACCGGGTAGTAATTGTTGGGTATATT 59.898 38.462 6.32 0.00 0.00 1.28
190 191 5.608015 ACCGGGTAGTAATTGTTGGGTATAT 59.392 40.000 6.32 0.00 0.00 0.86
191 192 4.968080 ACCGGGTAGTAATTGTTGGGTATA 59.032 41.667 6.32 0.00 0.00 1.47
192 193 3.781965 ACCGGGTAGTAATTGTTGGGTAT 59.218 43.478 6.32 0.00 0.00 2.73
193 194 3.180507 ACCGGGTAGTAATTGTTGGGTA 58.819 45.455 6.32 0.00 0.00 3.69
194 195 1.987368 ACCGGGTAGTAATTGTTGGGT 59.013 47.619 6.32 0.00 0.00 4.51
195 196 2.793288 ACCGGGTAGTAATTGTTGGG 57.207 50.000 6.32 0.00 0.00 4.12
196 197 4.835678 AGTAACCGGGTAGTAATTGTTGG 58.164 43.478 4.61 0.00 0.00 3.77
197 198 8.496707 AAATAGTAACCGGGTAGTAATTGTTG 57.503 34.615 17.91 0.00 0.00 3.33
198 199 9.519191 AAAAATAGTAACCGGGTAGTAATTGTT 57.481 29.630 17.91 10.86 0.00 2.83
199 200 8.949177 CAAAAATAGTAACCGGGTAGTAATTGT 58.051 33.333 17.91 8.50 0.00 2.71
200 201 8.400186 CCAAAAATAGTAACCGGGTAGTAATTG 58.600 37.037 17.91 19.52 0.00 2.32
201 202 7.557358 CCCAAAAATAGTAACCGGGTAGTAATT 59.443 37.037 17.91 13.06 0.00 1.40
202 203 7.056006 CCCAAAAATAGTAACCGGGTAGTAAT 58.944 38.462 17.91 7.15 0.00 1.89
203 204 6.413892 CCCAAAAATAGTAACCGGGTAGTAA 58.586 40.000 17.91 2.37 0.00 2.24
204 205 5.104569 CCCCAAAAATAGTAACCGGGTAGTA 60.105 44.000 16.41 16.41 0.00 1.82
205 206 4.324486 CCCCAAAAATAGTAACCGGGTAGT 60.324 45.833 12.50 12.50 0.00 2.73
206 207 4.201657 CCCCAAAAATAGTAACCGGGTAG 58.798 47.826 6.32 0.00 0.00 3.18
207 208 3.053768 CCCCCAAAAATAGTAACCGGGTA 60.054 47.826 6.32 0.00 0.00 3.69
208 209 2.291735 CCCCCAAAAATAGTAACCGGGT 60.292 50.000 6.32 0.00 0.00 5.28
209 210 2.291735 ACCCCCAAAAATAGTAACCGGG 60.292 50.000 6.32 0.00 0.00 5.73
210 211 2.756207 CACCCCCAAAAATAGTAACCGG 59.244 50.000 0.00 0.00 0.00 5.28
211 212 3.423749 ACACCCCCAAAAATAGTAACCG 58.576 45.455 0.00 0.00 0.00 4.44
212 213 5.511716 CCAAACACCCCCAAAAATAGTAACC 60.512 44.000 0.00 0.00 0.00 2.85
213 214 5.070714 ACCAAACACCCCCAAAAATAGTAAC 59.929 40.000 0.00 0.00 0.00 2.50
214 215 5.217400 ACCAAACACCCCCAAAAATAGTAA 58.783 37.500 0.00 0.00 0.00 2.24
215 216 4.817286 ACCAAACACCCCCAAAAATAGTA 58.183 39.130 0.00 0.00 0.00 1.82
216 217 3.659841 ACCAAACACCCCCAAAAATAGT 58.340 40.909 0.00 0.00 0.00 2.12
217 218 4.504165 GGAACCAAACACCCCCAAAAATAG 60.504 45.833 0.00 0.00 0.00 1.73
218 219 3.391626 GGAACCAAACACCCCCAAAAATA 59.608 43.478 0.00 0.00 0.00 1.40
219 220 2.173782 GGAACCAAACACCCCCAAAAAT 59.826 45.455 0.00 0.00 0.00 1.82
220 221 1.560146 GGAACCAAACACCCCCAAAAA 59.440 47.619 0.00 0.00 0.00 1.94
221 222 1.205055 GGAACCAAACACCCCCAAAA 58.795 50.000 0.00 0.00 0.00 2.44
222 223 0.042731 TGGAACCAAACACCCCCAAA 59.957 50.000 0.00 0.00 0.00 3.28
223 224 0.397816 CTGGAACCAAACACCCCCAA 60.398 55.000 0.00 0.00 0.00 4.12
224 225 1.231641 CTGGAACCAAACACCCCCA 59.768 57.895 0.00 0.00 0.00 4.96
225 226 0.539669 CTCTGGAACCAAACACCCCC 60.540 60.000 0.00 0.00 0.00 5.40
226 227 0.476771 TCTCTGGAACCAAACACCCC 59.523 55.000 0.00 0.00 0.00 4.95
227 228 1.143073 AGTCTCTGGAACCAAACACCC 59.857 52.381 0.00 0.00 0.00 4.61
228 229 2.640316 AGTCTCTGGAACCAAACACC 57.360 50.000 0.00 0.00 0.00 4.16
229 230 4.983671 AAAAGTCTCTGGAACCAAACAC 57.016 40.909 0.00 0.00 0.00 3.32
230 231 4.159506 CCAAAAAGTCTCTGGAACCAAACA 59.840 41.667 0.00 0.00 31.38 2.83
231 232 4.159693 ACCAAAAAGTCTCTGGAACCAAAC 59.840 41.667 3.25 0.00 34.16 2.93
232 233 4.349365 ACCAAAAAGTCTCTGGAACCAAA 58.651 39.130 3.25 0.00 34.16 3.28
233 234 3.976015 ACCAAAAAGTCTCTGGAACCAA 58.024 40.909 3.25 0.00 34.16 3.67
234 235 3.662759 ACCAAAAAGTCTCTGGAACCA 57.337 42.857 3.25 0.00 34.16 3.67
235 236 3.502595 GCTACCAAAAAGTCTCTGGAACC 59.497 47.826 3.25 0.00 34.16 3.62
236 237 4.134563 TGCTACCAAAAAGTCTCTGGAAC 58.865 43.478 3.25 0.00 34.16 3.62
237 238 4.431416 TGCTACCAAAAAGTCTCTGGAA 57.569 40.909 3.25 0.00 34.16 3.53
238 239 4.134563 GTTGCTACCAAAAAGTCTCTGGA 58.865 43.478 3.25 0.00 34.16 3.86
239 240 3.882888 TGTTGCTACCAAAAAGTCTCTGG 59.117 43.478 0.00 0.00 36.24 3.86
240 241 5.163663 TGTTGTTGCTACCAAAAAGTCTCTG 60.164 40.000 0.00 0.00 29.02 3.35
241 242 4.947388 TGTTGTTGCTACCAAAAAGTCTCT 59.053 37.500 0.00 0.00 29.02 3.10
242 243 5.243426 TGTTGTTGCTACCAAAAAGTCTC 57.757 39.130 0.00 0.00 29.02 3.36
243 244 5.505654 CGATGTTGTTGCTACCAAAAAGTCT 60.506 40.000 0.00 0.00 29.02 3.24
244 245 4.675114 CGATGTTGTTGCTACCAAAAAGTC 59.325 41.667 0.00 0.00 29.02 3.01
245 246 4.336993 TCGATGTTGTTGCTACCAAAAAGT 59.663 37.500 0.00 0.00 29.02 2.66
246 247 4.854399 TCGATGTTGTTGCTACCAAAAAG 58.146 39.130 0.00 0.00 29.02 2.27
247 248 4.791411 GCTCGATGTTGTTGCTACCAAAAA 60.791 41.667 0.00 0.00 31.68 1.94
248 249 3.304391 GCTCGATGTTGTTGCTACCAAAA 60.304 43.478 0.00 0.00 31.68 2.44
249 250 2.225491 GCTCGATGTTGTTGCTACCAAA 59.775 45.455 0.00 0.00 31.68 3.28
250 251 1.804151 GCTCGATGTTGTTGCTACCAA 59.196 47.619 0.00 0.00 0.00 3.67
251 252 1.438651 GCTCGATGTTGTTGCTACCA 58.561 50.000 0.00 0.00 0.00 3.25
252 253 0.370273 CGCTCGATGTTGTTGCTACC 59.630 55.000 0.00 0.00 0.00 3.18
253 254 1.321743 CTCGCTCGATGTTGTTGCTAC 59.678 52.381 0.00 0.00 0.00 3.58
254 255 1.201414 TCTCGCTCGATGTTGTTGCTA 59.799 47.619 0.00 0.00 0.00 3.49
255 256 0.038251 TCTCGCTCGATGTTGTTGCT 60.038 50.000 0.00 0.00 0.00 3.91
256 257 0.790207 TTCTCGCTCGATGTTGTTGC 59.210 50.000 0.00 0.00 0.00 4.17
257 258 2.476619 ACTTTCTCGCTCGATGTTGTTG 59.523 45.455 0.00 0.00 0.00 3.33
258 259 2.755650 ACTTTCTCGCTCGATGTTGTT 58.244 42.857 0.00 0.00 0.00 2.83
259 260 2.440539 ACTTTCTCGCTCGATGTTGT 57.559 45.000 0.00 0.00 0.00 3.32
260 261 2.280183 GCTACTTTCTCGCTCGATGTTG 59.720 50.000 0.00 0.00 0.00 3.33
261 262 2.094700 TGCTACTTTCTCGCTCGATGTT 60.095 45.455 0.00 0.00 0.00 2.71
262 263 1.472878 TGCTACTTTCTCGCTCGATGT 59.527 47.619 0.00 0.00 0.00 3.06
263 264 2.194800 TGCTACTTTCTCGCTCGATG 57.805 50.000 0.00 0.00 0.00 3.84
264 265 2.094700 TGTTGCTACTTTCTCGCTCGAT 60.095 45.455 0.00 0.00 0.00 3.59
265 266 1.268625 TGTTGCTACTTTCTCGCTCGA 59.731 47.619 0.00 0.00 0.00 4.04
266 267 1.698165 TGTTGCTACTTTCTCGCTCG 58.302 50.000 0.00 0.00 0.00 5.03
267 268 3.060602 AGTTGTTGCTACTTTCTCGCTC 58.939 45.455 0.00 0.00 0.00 5.03
268 269 3.113260 AGTTGTTGCTACTTTCTCGCT 57.887 42.857 0.00 0.00 0.00 4.93
269 270 4.985044 TTAGTTGTTGCTACTTTCTCGC 57.015 40.909 0.00 0.00 0.00 5.03
270 271 8.782533 AAAATTTAGTTGTTGCTACTTTCTCG 57.217 30.769 0.00 0.00 0.00 4.04
271 272 9.952188 AGAAAATTTAGTTGTTGCTACTTTCTC 57.048 29.630 0.00 0.00 28.74 2.87
276 277 9.961265 GGTTAAGAAAATTTAGTTGTTGCTACT 57.039 29.630 0.00 0.00 0.00 2.57
277 278 9.738832 TGGTTAAGAAAATTTAGTTGTTGCTAC 57.261 29.630 0.00 0.00 0.00 3.58
279 280 9.660180 TTTGGTTAAGAAAATTTAGTTGTTGCT 57.340 25.926 0.00 0.00 0.00 3.91
384 386 3.848019 CCATCTTCGCGTTTGAATTGAAG 59.152 43.478 5.77 0.00 37.87 3.02
771 780 2.203181 GATCTGGGGCAGCAGAGC 60.203 66.667 0.00 0.00 0.00 4.09
784 800 1.227089 GCGCGTGTCCATCTGATCT 60.227 57.895 8.43 0.00 0.00 2.75
885 910 1.301677 CTGCTCCGAAAACTCTGGCC 61.302 60.000 0.00 0.00 0.00 5.36
1159 1224 1.941975 CTTCATCTGCACACACACACA 59.058 47.619 0.00 0.00 0.00 3.72
1167 1232 2.703416 GACATGGACTTCATCTGCACA 58.297 47.619 0.00 0.00 32.92 4.57
1168 1233 1.662629 CGACATGGACTTCATCTGCAC 59.337 52.381 0.00 0.00 32.92 4.57
1169 1234 2.008543 GCGACATGGACTTCATCTGCA 61.009 52.381 0.00 0.00 32.92 4.41
1170 1235 0.654683 GCGACATGGACTTCATCTGC 59.345 55.000 0.00 0.00 32.92 4.26
1845 1916 1.359475 GACGACGAGGCCCAGTATC 59.641 63.158 0.00 0.00 0.00 2.24
1885 1956 3.790416 TTTTGTCGCCCCTGCTGCT 62.790 57.895 0.00 0.00 34.43 4.24
1899 1970 2.344872 GCTTGGCCTGGGCTTTTG 59.655 61.111 21.72 9.46 41.60 2.44
1901 1972 2.919328 GTGCTTGGCCTGGGCTTT 60.919 61.111 21.72 0.00 41.60 3.51
1984 2055 2.616842 GGCACGAAAGACTGGAGAAAAA 59.383 45.455 0.00 0.00 0.00 1.94
2011 2082 1.554160 CCAGACCTGCTTCTGTGAGAT 59.446 52.381 8.97 0.00 41.40 2.75
2015 2086 0.394192 TGACCAGACCTGCTTCTGTG 59.606 55.000 8.97 4.58 41.40 3.66
2027 2098 1.541670 GCTGTAAAACCCGTGACCAGA 60.542 52.381 0.00 0.00 0.00 3.86
2032 2103 3.018149 ACAAAAGCTGTAAAACCCGTGA 58.982 40.909 0.00 0.00 36.10 4.35
2112 2183 1.374758 GACGTCTTCAGGGGCACAG 60.375 63.158 8.70 0.00 0.00 3.66
2134 2215 4.770287 GCAGAAGCATCGATACAATTGAG 58.230 43.478 13.59 0.69 41.58 3.02
2149 2230 1.608590 TGTTTACAGCCTTGCAGAAGC 59.391 47.619 0.00 0.00 42.57 3.86
2150 2231 3.066621 TGTTGTTTACAGCCTTGCAGAAG 59.933 43.478 0.00 0.00 31.68 2.85
2172 2255 0.112995 TCTGTGGAAAATGCCTGGCT 59.887 50.000 21.03 0.00 0.00 4.75
2187 2270 2.227036 CCAAGCCACCCCTCTCTGT 61.227 63.158 0.00 0.00 0.00 3.41
2188 2271 2.673523 CCAAGCCACCCCTCTCTG 59.326 66.667 0.00 0.00 0.00 3.35
2189 2272 2.612115 CCCAAGCCACCCCTCTCT 60.612 66.667 0.00 0.00 0.00 3.10
2190 2273 4.432741 GCCCAAGCCACCCCTCTC 62.433 72.222 0.00 0.00 0.00 3.20
2192 2275 4.748144 CTGCCCAAGCCACCCCTC 62.748 72.222 0.00 0.00 38.69 4.30
2233 2316 5.812127 TCTTGTCATTACTCATGTTCCATCG 59.188 40.000 0.00 0.00 34.06 3.84
2256 2350 6.830838 AGACATCCTCCCAGAATTAAACATTC 59.169 38.462 0.00 0.00 0.00 2.67
2353 2605 1.136329 ACAGACCTGGGCAATGGAGT 61.136 55.000 0.47 0.00 34.19 3.85
2368 2620 2.565046 TGAATGCACACCATCACAGA 57.435 45.000 0.00 0.00 31.43 3.41
2372 2624 2.241160 AGCTTTGAATGCACACCATCA 58.759 42.857 5.84 0.00 31.43 3.07
2460 2712 1.466950 CTCGTCAGACAGAGAGACACC 59.533 57.143 13.93 0.00 36.65 4.16
2508 2760 7.280205 GGATTTCACCGAATACAAACTAGATGT 59.720 37.037 0.00 3.89 34.81 3.06
2522 2937 4.310022 ACCATAAAGGGATTTCACCGAA 57.690 40.909 0.00 0.00 43.89 4.30
2540 2955 5.359576 GGATTACTCACAATGGCATAAACCA 59.640 40.000 0.00 0.00 45.82 3.67
2541 2956 5.359576 TGGATTACTCACAATGGCATAAACC 59.640 40.000 0.00 0.00 0.00 3.27
2542 2957 6.449635 TGGATTACTCACAATGGCATAAAC 57.550 37.500 0.00 0.00 0.00 2.01
2608 3026 3.944422 AACACGTGCACACTTTAAGAG 57.056 42.857 17.22 0.00 0.00 2.85
2611 3029 4.688511 AAGAAACACGTGCACACTTTAA 57.311 36.364 17.22 0.00 0.00 1.52
2620 3038 6.260377 ACTTAAAAACCTAAGAAACACGTGC 58.740 36.000 17.22 0.00 33.78 5.34
2623 3041 9.771915 TTGTTACTTAAAAACCTAAGAAACACG 57.228 29.630 0.00 0.00 33.78 4.49
2683 3187 1.768684 ATGAGCCGTCCACAGTTGGT 61.769 55.000 0.00 0.00 44.35 3.67
2685 3189 0.320683 TGATGAGCCGTCCACAGTTG 60.321 55.000 0.00 0.00 0.00 3.16
2742 3247 3.441572 CCCAAGCAAAGACTAAGTGATGG 59.558 47.826 0.00 0.00 0.00 3.51
2752 3257 1.136891 AGCAAACACCCAAGCAAAGAC 59.863 47.619 0.00 0.00 0.00 3.01
2826 3334 1.065401 CAGCGAGCAACAGGTTGAAAA 59.935 47.619 15.88 0.00 42.93 2.29
2830 3339 1.165907 TTCCAGCGAGCAACAGGTTG 61.166 55.000 7.77 7.77 43.14 3.77
2873 3382 2.502947 AGTCCATGATACAGCAGCAGAA 59.497 45.455 0.00 0.00 0.00 3.02
2919 3428 4.314522 TTCATCTATTGCCCTGGAAACA 57.685 40.909 0.00 0.00 39.59 2.83


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

AutoCloner maintained by Alex Coulton.