Multiple sequence alignment - TraesCS5D01G016200

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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 TraesCS5D01G016200 chr5D 100.000 2669 0 0 1 2669 9289817 9292485 0.000000e+00 4929
1 TraesCS5D01G016200 chr5A 89.602 2385 139 53 352 2669 7486476 7488818 0.000000e+00 2929
2 TraesCS5D01G016200 chr5B 88.261 1610 98 43 1135 2667 9298809 9300404 0.000000e+00 1842
3 TraesCS5D01G016200 chr5B 85.172 580 40 20 674 1222 9298407 9298971 1.080000e-153 553
4 TraesCS5D01G016200 chr5B 89.493 276 16 5 410 673 9297808 9298082 1.180000e-88 337
5 TraesCS5D01G016200 chr5B 86.755 302 38 2 1 301 489275971 489276271 4.260000e-88 335
6 TraesCS5D01G016200 chr2D 88.742 302 33 1 1 302 372702884 372702584 4.200000e-98 368
7 TraesCS5D01G016200 chr2D 88.079 302 34 2 1 302 190599950 190600249 9.090000e-95 357
8 TraesCS5D01G016200 chr2D 87.417 302 31 5 1 300 78708546 78708842 9.150000e-90 340
9 TraesCS5D01G016200 chr1D 87.748 302 36 1 1 302 337998963 337998663 4.230000e-93 351
10 TraesCS5D01G016200 chr6B 88.014 292 34 1 1 292 590915018 590914728 7.070000e-91 344
11 TraesCS5D01G016200 chr6D 86.842 304 35 5 1 302 287031599 287031299 4.260000e-88 335
12 TraesCS5D01G016200 chr7D 86.755 302 36 2 1 302 511648133 511648430 1.530000e-87 333
13 TraesCS5D01G016200 chr1B 86.755 302 37 3 1 301 119293945 119294244 1.530000e-87 333


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 TraesCS5D01G016200 chr5D 9289817 9292485 2668 False 4929.000000 4929 100.000 1 2669 1 chr5D.!!$F1 2668
1 TraesCS5D01G016200 chr5A 7486476 7488818 2342 False 2929.000000 2929 89.602 352 2669 1 chr5A.!!$F1 2317
2 TraesCS5D01G016200 chr5B 9297808 9300404 2596 False 910.666667 1842 87.642 410 2667 3 chr5B.!!$F2 2257

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
238 239 0.039074 GATGGAGTAGCCGGACGATG 60.039 60.0 5.05 0.0 40.66 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 2313 0.027716 GATGTTCGAGCAGCAGCATG 59.972 55.0 12.87 0.0 45.49 4.06 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
33 34 3.598273 CGAAGGAGGAGAAGGAGGA 57.402 57.895 0.00 0.00 0.00 3.71
34 35 1.107945 CGAAGGAGGAGAAGGAGGAC 58.892 60.000 0.00 0.00 0.00 3.85
35 36 1.107945 GAAGGAGGAGAAGGAGGACG 58.892 60.000 0.00 0.00 0.00 4.79
36 37 0.324830 AAGGAGGAGAAGGAGGACGG 60.325 60.000 0.00 0.00 0.00 4.79
37 38 2.428085 GGAGGAGAAGGAGGACGGC 61.428 68.421 0.00 0.00 0.00 5.68
38 39 2.756283 AGGAGAAGGAGGACGGCG 60.756 66.667 4.80 4.80 0.00 6.46
39 40 2.754658 GGAGAAGGAGGACGGCGA 60.755 66.667 16.62 0.00 0.00 5.54
40 41 2.490685 GAGAAGGAGGACGGCGAC 59.509 66.667 16.62 7.58 0.00 5.19
41 42 2.282958 AGAAGGAGGACGGCGACA 60.283 61.111 16.62 0.00 0.00 4.35
42 43 2.182030 GAAGGAGGACGGCGACAG 59.818 66.667 16.62 0.00 0.00 3.51
43 44 3.991536 GAAGGAGGACGGCGACAGC 62.992 68.421 16.62 2.68 44.18 4.40
46 47 4.838486 GAGGACGGCGACAGCGAG 62.838 72.222 16.62 0.00 46.35 5.03
54 55 2.259818 CGACAGCGAGGACAGCTT 59.740 61.111 0.00 0.00 44.06 3.74
55 56 1.803519 CGACAGCGAGGACAGCTTC 60.804 63.158 0.00 0.00 44.06 3.86
56 57 1.290324 GACAGCGAGGACAGCTTCA 59.710 57.895 0.00 0.00 44.06 3.02
57 58 0.735632 GACAGCGAGGACAGCTTCAG 60.736 60.000 0.00 0.00 44.06 3.02
58 59 2.099431 CAGCGAGGACAGCTTCAGC 61.099 63.158 0.00 0.00 44.06 4.26
75 76 3.102985 CGACGAGCAGATCCGACT 58.897 61.111 0.00 0.00 0.00 4.18
76 77 1.010574 CGACGAGCAGATCCGACTC 60.011 63.158 0.00 0.00 0.00 3.36
80 81 3.765349 GAGCAGATCCGACTCGATC 57.235 57.895 0.00 1.85 39.21 3.69
81 82 0.239879 GAGCAGATCCGACTCGATCC 59.760 60.000 0.00 0.00 39.67 3.36
82 83 1.081774 GCAGATCCGACTCGATCCG 60.082 63.158 0.00 0.00 39.67 4.18
83 84 1.787057 GCAGATCCGACTCGATCCGT 61.787 60.000 0.00 0.00 39.67 4.69
84 85 1.509703 CAGATCCGACTCGATCCGTA 58.490 55.000 0.00 0.00 39.67 4.02
85 86 1.194997 CAGATCCGACTCGATCCGTAC 59.805 57.143 0.00 0.00 39.67 3.67
86 87 1.070445 AGATCCGACTCGATCCGTACT 59.930 52.381 0.00 0.81 39.67 2.73
87 88 1.194997 GATCCGACTCGATCCGTACTG 59.805 57.143 0.00 0.00 33.83 2.74
88 89 1.009900 CCGACTCGATCCGTACTGC 60.010 63.158 0.00 0.00 0.00 4.40
89 90 1.367782 CGACTCGATCCGTACTGCG 60.368 63.158 0.00 0.00 40.95 5.18
90 91 1.759293 CGACTCGATCCGTACTGCGA 61.759 60.000 0.00 0.00 44.77 5.10
91 92 0.587285 GACTCGATCCGTACTGCGAT 59.413 55.000 0.00 0.00 44.77 4.58
92 93 1.002684 GACTCGATCCGTACTGCGATT 60.003 52.381 0.00 0.00 44.77 3.34
93 94 1.404391 ACTCGATCCGTACTGCGATTT 59.596 47.619 0.00 0.00 44.77 2.17
94 95 2.044860 CTCGATCCGTACTGCGATTTC 58.955 52.381 0.00 0.00 44.77 2.17
95 96 0.770590 CGATCCGTACTGCGATTTCG 59.229 55.000 0.00 0.00 44.77 3.46
96 97 1.596220 CGATCCGTACTGCGATTTCGA 60.596 52.381 3.77 0.00 44.77 3.71
97 98 1.779724 GATCCGTACTGCGATTTCGAC 59.220 52.381 3.77 0.00 44.77 4.20
98 99 0.806868 TCCGTACTGCGATTTCGACT 59.193 50.000 3.77 0.00 44.77 4.18
99 100 0.914551 CCGTACTGCGATTTCGACTG 59.085 55.000 3.77 2.59 44.77 3.51
100 101 0.914551 CGTACTGCGATTTCGACTGG 59.085 55.000 3.77 0.00 44.77 4.00
101 102 1.731424 CGTACTGCGATTTCGACTGGT 60.731 52.381 3.77 0.00 44.77 4.00
102 103 2.476686 CGTACTGCGATTTCGACTGGTA 60.477 50.000 3.77 0.00 44.77 3.25
103 104 1.992170 ACTGCGATTTCGACTGGTAC 58.008 50.000 3.77 0.00 43.02 3.34
104 105 1.544691 ACTGCGATTTCGACTGGTACT 59.455 47.619 3.77 0.00 43.02 2.73
105 106 2.029290 ACTGCGATTTCGACTGGTACTT 60.029 45.455 3.77 0.00 43.02 2.24
106 107 2.599082 CTGCGATTTCGACTGGTACTTC 59.401 50.000 3.77 0.00 43.02 3.01
107 108 1.925185 GCGATTTCGACTGGTACTTCC 59.075 52.381 3.77 0.00 43.02 3.46
108 109 2.182825 CGATTTCGACTGGTACTTCCG 58.817 52.381 0.00 0.00 43.02 4.30
109 110 1.925185 GATTTCGACTGGTACTTCCGC 59.075 52.381 0.00 0.00 39.52 5.54
110 111 0.387622 TTTCGACTGGTACTTCCGCG 60.388 55.000 0.00 0.00 39.52 6.46
111 112 1.236616 TTCGACTGGTACTTCCGCGA 61.237 55.000 8.23 0.00 39.52 5.87
112 113 1.226323 CGACTGGTACTTCCGCGAG 60.226 63.158 8.23 0.00 39.52 5.03
113 114 1.642037 CGACTGGTACTTCCGCGAGA 61.642 60.000 8.23 0.00 39.52 4.04
114 115 0.524862 GACTGGTACTTCCGCGAGAA 59.475 55.000 8.23 8.88 39.52 2.87
121 122 4.430765 TTCCGCGAGAAGGACGGC 62.431 66.667 8.23 0.00 46.49 5.68
123 124 4.735132 CCGCGAGAAGGACGGCAA 62.735 66.667 8.23 0.00 40.55 4.52
124 125 3.181967 CGCGAGAAGGACGGCAAG 61.182 66.667 0.00 0.00 0.00 4.01
125 126 2.815647 GCGAGAAGGACGGCAAGG 60.816 66.667 0.00 0.00 0.00 3.61
126 127 2.125512 CGAGAAGGACGGCAAGGG 60.126 66.667 0.00 0.00 0.00 3.95
127 128 2.436824 GAGAAGGACGGCAAGGGC 60.437 66.667 0.00 0.00 40.13 5.19
146 147 4.426313 CCGGGGAAGGGCAAGGAC 62.426 72.222 0.00 0.00 0.00 3.85
147 148 3.646715 CGGGGAAGGGCAAGGACA 61.647 66.667 0.00 0.00 0.00 4.02
148 149 2.356667 GGGGAAGGGCAAGGACAG 59.643 66.667 0.00 0.00 0.00 3.51
149 150 2.361737 GGGAAGGGCAAGGACAGC 60.362 66.667 0.00 0.00 0.00 4.40
155 156 4.329545 GGCAAGGACAGCCGTGGA 62.330 66.667 0.00 0.00 42.99 4.02
156 157 2.045926 GCAAGGACAGCCGTGGAT 60.046 61.111 0.00 0.00 42.99 3.41
157 158 2.401766 GCAAGGACAGCCGTGGATG 61.402 63.158 1.93 1.93 42.99 3.51
158 159 1.296392 CAAGGACAGCCGTGGATGA 59.704 57.895 11.72 0.00 39.63 2.92
159 160 0.321564 CAAGGACAGCCGTGGATGAA 60.322 55.000 11.72 0.00 39.63 2.57
160 161 0.321653 AAGGACAGCCGTGGATGAAC 60.322 55.000 11.72 3.08 39.96 3.18
161 162 1.194781 AGGACAGCCGTGGATGAACT 61.195 55.000 11.72 5.41 39.96 3.01
162 163 0.741221 GGACAGCCGTGGATGAACTC 60.741 60.000 11.72 0.00 35.26 3.01
163 164 0.741221 GACAGCCGTGGATGAACTCC 60.741 60.000 11.72 0.00 45.19 3.85
172 173 2.640316 GGATGAACTCCACCATACCC 57.360 55.000 0.00 0.00 44.26 3.69
173 174 1.843851 GGATGAACTCCACCATACCCA 59.156 52.381 0.00 0.00 44.26 4.51
174 175 2.241176 GGATGAACTCCACCATACCCAA 59.759 50.000 0.00 0.00 44.26 4.12
175 176 3.308832 GGATGAACTCCACCATACCCAAA 60.309 47.826 0.00 0.00 44.26 3.28
176 177 4.536765 GATGAACTCCACCATACCCAAAT 58.463 43.478 0.00 0.00 0.00 2.32
177 178 5.398581 GGATGAACTCCACCATACCCAAATA 60.399 44.000 0.00 0.00 44.26 1.40
178 179 5.725551 TGAACTCCACCATACCCAAATAT 57.274 39.130 0.00 0.00 0.00 1.28
179 180 5.445069 TGAACTCCACCATACCCAAATATG 58.555 41.667 0.00 0.00 33.10 1.78
180 181 3.832527 ACTCCACCATACCCAAATATGC 58.167 45.455 0.00 0.00 32.12 3.14
181 182 3.157087 CTCCACCATACCCAAATATGCC 58.843 50.000 0.00 0.00 32.12 4.40
182 183 2.515853 TCCACCATACCCAAATATGCCA 59.484 45.455 0.00 0.00 32.12 4.92
183 184 3.052566 TCCACCATACCCAAATATGCCAA 60.053 43.478 0.00 0.00 32.12 4.52
184 185 3.708631 CCACCATACCCAAATATGCCAAA 59.291 43.478 0.00 0.00 32.12 3.28
185 186 4.347583 CCACCATACCCAAATATGCCAAAT 59.652 41.667 0.00 0.00 32.12 2.32
186 187 5.163216 CCACCATACCCAAATATGCCAAATT 60.163 40.000 0.00 0.00 32.12 1.82
187 188 6.355747 CACCATACCCAAATATGCCAAATTT 58.644 36.000 0.00 0.00 32.12 1.82
188 189 6.827762 CACCATACCCAAATATGCCAAATTTT 59.172 34.615 0.00 0.00 32.12 1.82
189 190 6.827762 ACCATACCCAAATATGCCAAATTTTG 59.172 34.615 1.99 1.99 32.12 2.44
202 203 5.835113 CCAAATTTTGGTAGTCCGATGAT 57.165 39.130 18.34 0.00 45.93 2.45
203 204 6.935741 CCAAATTTTGGTAGTCCGATGATA 57.064 37.500 18.34 0.00 45.93 2.15
204 205 7.510549 CCAAATTTTGGTAGTCCGATGATAT 57.489 36.000 18.34 0.00 45.93 1.63
205 206 7.362662 CCAAATTTTGGTAGTCCGATGATATG 58.637 38.462 18.34 0.00 45.93 1.78
206 207 6.560253 AATTTTGGTAGTCCGATGATATGC 57.440 37.500 0.00 0.00 36.30 3.14
207 208 4.955811 TTTGGTAGTCCGATGATATGCT 57.044 40.909 0.00 0.00 36.30 3.79
208 209 6.413783 TTTTGGTAGTCCGATGATATGCTA 57.586 37.500 0.00 0.00 36.30 3.49
209 210 6.413783 TTTGGTAGTCCGATGATATGCTAA 57.586 37.500 0.00 0.00 36.30 3.09
210 211 5.644977 TGGTAGTCCGATGATATGCTAAG 57.355 43.478 0.00 0.00 36.30 2.18
211 212 5.077564 TGGTAGTCCGATGATATGCTAAGT 58.922 41.667 0.00 0.00 36.30 2.24
212 213 6.243148 TGGTAGTCCGATGATATGCTAAGTA 58.757 40.000 0.00 0.00 36.30 2.24
213 214 6.890268 TGGTAGTCCGATGATATGCTAAGTAT 59.110 38.462 0.00 0.00 36.30 2.12
214 215 8.050930 TGGTAGTCCGATGATATGCTAAGTATA 58.949 37.037 0.00 0.00 36.30 1.47
215 216 8.561212 GGTAGTCCGATGATATGCTAAGTATAG 58.439 40.741 0.00 0.00 0.00 1.31
216 217 9.111613 GTAGTCCGATGATATGCTAAGTATAGT 57.888 37.037 0.00 0.00 0.00 2.12
217 218 7.990917 AGTCCGATGATATGCTAAGTATAGTG 58.009 38.462 0.00 0.00 0.00 2.74
218 219 7.612244 AGTCCGATGATATGCTAAGTATAGTGT 59.388 37.037 0.00 0.00 0.00 3.55
219 220 7.698550 GTCCGATGATATGCTAAGTATAGTGTG 59.301 40.741 0.00 0.00 0.00 3.82
220 221 7.610305 TCCGATGATATGCTAAGTATAGTGTGA 59.390 37.037 0.00 0.00 0.00 3.58
221 222 8.409371 CCGATGATATGCTAAGTATAGTGTGAT 58.591 37.037 0.00 0.00 0.00 3.06
222 223 9.230932 CGATGATATGCTAAGTATAGTGTGATG 57.769 37.037 0.00 0.00 0.00 3.07
223 224 9.526713 GATGATATGCTAAGTATAGTGTGATGG 57.473 37.037 0.00 0.00 0.00 3.51
224 225 8.650143 TGATATGCTAAGTATAGTGTGATGGA 57.350 34.615 0.00 0.00 0.00 3.41
225 226 8.743714 TGATATGCTAAGTATAGTGTGATGGAG 58.256 37.037 0.00 0.00 0.00 3.86
226 227 6.985653 ATGCTAAGTATAGTGTGATGGAGT 57.014 37.500 0.00 0.00 0.00 3.85
227 228 9.755122 ATATGCTAAGTATAGTGTGATGGAGTA 57.245 33.333 0.00 0.00 0.00 2.59
228 229 7.511959 TGCTAAGTATAGTGTGATGGAGTAG 57.488 40.000 0.00 0.00 0.00 2.57
229 230 6.016192 TGCTAAGTATAGTGTGATGGAGTAGC 60.016 42.308 0.00 0.00 0.00 3.58
230 231 5.793030 AAGTATAGTGTGATGGAGTAGCC 57.207 43.478 0.00 0.00 37.10 3.93
231 232 3.821600 AGTATAGTGTGATGGAGTAGCCG 59.178 47.826 0.00 0.00 40.66 5.52
232 233 1.399714 TAGTGTGATGGAGTAGCCGG 58.600 55.000 0.00 0.00 40.66 6.13
233 234 0.324368 AGTGTGATGGAGTAGCCGGA 60.324 55.000 5.05 0.00 40.66 5.14
234 235 0.179108 GTGTGATGGAGTAGCCGGAC 60.179 60.000 5.05 0.00 40.66 4.79
235 236 1.065928 GTGATGGAGTAGCCGGACG 59.934 63.158 5.05 0.00 40.66 4.79
236 237 1.077285 TGATGGAGTAGCCGGACGA 60.077 57.895 5.05 0.00 40.66 4.20
237 238 0.467474 TGATGGAGTAGCCGGACGAT 60.467 55.000 5.05 0.00 40.66 3.73
238 239 0.039074 GATGGAGTAGCCGGACGATG 60.039 60.000 5.05 0.00 40.66 3.84
239 240 2.027751 GGAGTAGCCGGACGATGC 59.972 66.667 5.05 0.00 0.00 3.91
240 241 2.782222 GGAGTAGCCGGACGATGCA 61.782 63.158 5.05 0.00 0.00 3.96
241 242 1.364171 GAGTAGCCGGACGATGCAT 59.636 57.895 5.05 0.00 0.00 3.96
242 243 0.596577 GAGTAGCCGGACGATGCATA 59.403 55.000 5.05 0.00 0.00 3.14
243 244 1.202582 GAGTAGCCGGACGATGCATAT 59.797 52.381 5.05 0.00 0.00 1.78
244 245 1.067565 AGTAGCCGGACGATGCATATG 60.068 52.381 5.05 0.00 0.00 1.78
245 246 0.389817 TAGCCGGACGATGCATATGC 60.390 55.000 21.09 21.09 42.50 3.14
246 247 3.015293 GCCGGACGATGCATATGCG 62.015 63.158 22.21 14.98 45.83 4.73
247 248 1.664649 CCGGACGATGCATATGCGT 60.665 57.895 22.29 22.29 45.83 5.24
253 254 2.506544 GATGCATATGCGTCGACGT 58.493 52.632 35.48 21.51 45.68 4.34
254 255 1.681825 GATGCATATGCGTCGACGTA 58.318 50.000 35.48 32.87 45.68 3.57
255 256 1.644295 GATGCATATGCGTCGACGTAG 59.356 52.381 35.48 21.96 45.68 3.51
256 257 0.379316 TGCATATGCGTCGACGTAGT 59.621 50.000 35.48 22.45 46.22 2.73
257 258 1.202211 TGCATATGCGTCGACGTAGTT 60.202 47.619 35.48 21.56 43.89 2.24
258 259 3.353423 TGCATATGCGTCGACGTAGTTG 61.353 50.000 35.48 29.85 43.89 3.16
302 303 9.616156 TTAAAATATGCTAATTTAGGTGTCCGA 57.384 29.630 5.61 0.00 0.00 4.55
303 304 8.514330 AAAATATGCTAATTTAGGTGTCCGAA 57.486 30.769 5.61 0.00 0.00 4.30
304 305 7.730364 AATATGCTAATTTAGGTGTCCGAAG 57.270 36.000 5.61 0.00 0.00 3.79
305 306 4.546829 TGCTAATTTAGGTGTCCGAAGT 57.453 40.909 5.61 0.00 0.00 3.01
306 307 4.501071 TGCTAATTTAGGTGTCCGAAGTC 58.499 43.478 5.61 0.00 0.00 3.01
307 308 3.869832 GCTAATTTAGGTGTCCGAAGTCC 59.130 47.826 5.61 0.00 0.00 3.85
308 309 2.667473 ATTTAGGTGTCCGAAGTCCG 57.333 50.000 0.00 0.00 38.18 4.79
317 318 4.787999 CGAAGTCCGGCTGTAGAC 57.212 61.111 0.00 0.00 33.91 2.59
324 325 2.566529 CGGCTGTAGACGCTCACA 59.433 61.111 0.00 0.00 40.91 3.58
325 326 1.139734 CGGCTGTAGACGCTCACAT 59.860 57.895 0.00 0.00 40.91 3.21
326 327 0.458543 CGGCTGTAGACGCTCACATT 60.459 55.000 0.00 0.00 40.91 2.71
327 328 1.002366 GGCTGTAGACGCTCACATTG 58.998 55.000 0.00 0.00 0.00 2.82
328 329 1.404181 GGCTGTAGACGCTCACATTGA 60.404 52.381 0.00 0.00 0.00 2.57
329 330 1.923204 GCTGTAGACGCTCACATTGAG 59.077 52.381 0.00 0.00 46.90 3.02
337 338 4.284123 TCACATTGAGAGGTGCGC 57.716 55.556 0.00 0.00 37.48 6.09
338 339 1.375908 TCACATTGAGAGGTGCGCC 60.376 57.895 8.71 8.71 37.48 6.53
339 340 2.434884 ACATTGAGAGGTGCGCCG 60.435 61.111 11.42 0.00 40.50 6.46
340 341 3.197790 CATTGAGAGGTGCGCCGG 61.198 66.667 11.42 0.00 40.50 6.13
341 342 3.390521 ATTGAGAGGTGCGCCGGA 61.391 61.111 11.42 0.00 40.50 5.14
342 343 3.665675 ATTGAGAGGTGCGCCGGAC 62.666 63.158 11.42 0.00 40.50 4.79
344 345 4.500116 GAGAGGTGCGCCGGACTC 62.500 72.222 19.28 19.28 40.50 3.36
352 353 2.813474 CGCCGGACTCGCAATCAA 60.813 61.111 5.05 0.00 34.56 2.57
353 354 2.387445 CGCCGGACTCGCAATCAAA 61.387 57.895 5.05 0.00 34.56 2.69
354 355 1.425428 GCCGGACTCGCAATCAAAG 59.575 57.895 5.05 0.00 34.56 2.77
355 356 1.019278 GCCGGACTCGCAATCAAAGA 61.019 55.000 5.05 0.00 34.56 2.52
356 357 1.002366 CCGGACTCGCAATCAAAGAG 58.998 55.000 0.00 0.00 37.96 2.85
361 362 3.000724 GGACTCGCAATCAAAGAGAATCG 59.999 47.826 0.00 0.00 42.67 3.34
362 363 3.589988 ACTCGCAATCAAAGAGAATCGT 58.410 40.909 0.00 0.00 42.67 3.73
380 381 5.927954 ATCGTTCGGTAGTTTAGCAAAAA 57.072 34.783 0.00 0.00 0.00 1.94
381 382 5.081888 TCGTTCGGTAGTTTAGCAAAAAC 57.918 39.130 6.59 6.59 0.00 2.43
383 384 4.317980 CGTTCGGTAGTTTAGCAAAAACGA 60.318 41.667 8.51 2.21 37.90 3.85
384 385 5.613142 CGTTCGGTAGTTTAGCAAAAACGAT 60.613 40.000 8.51 0.00 37.90 3.73
385 386 5.927954 TCGGTAGTTTAGCAAAAACGATT 57.072 34.783 8.51 0.00 35.42 3.34
393 394 3.518634 AGCAAAAACGATTTGGTGTGT 57.481 38.095 17.61 0.00 38.51 3.72
398 399 4.712122 AAAACGATTTGGTGTGTCAGTT 57.288 36.364 0.00 0.00 0.00 3.16
399 400 3.691049 AACGATTTGGTGTGTCAGTTG 57.309 42.857 0.00 0.00 0.00 3.16
403 404 3.568538 GATTTGGTGTGTCAGTTGCATC 58.431 45.455 0.00 0.00 0.00 3.91
406 407 2.653726 TGGTGTGTCAGTTGCATCTTT 58.346 42.857 0.00 0.00 0.00 2.52
412 413 4.572795 TGTGTCAGTTGCATCTTTCGTTAA 59.427 37.500 0.00 0.00 0.00 2.01
421 422 8.230486 AGTTGCATCTTTCGTTAACTAATTGAG 58.770 33.333 3.71 0.00 0.00 3.02
427 428 6.876789 TCTTTCGTTAACTAATTGAGCCATGA 59.123 34.615 3.71 0.00 0.00 3.07
436 437 5.663106 ACTAATTGAGCCATGAGGACTTCTA 59.337 40.000 0.00 0.00 36.89 2.10
439 440 2.497675 TGAGCCATGAGGACTTCTACAC 59.502 50.000 0.00 0.00 36.89 2.90
468 469 5.818136 AACCCATGAAATTACATGTCTCG 57.182 39.130 0.00 0.00 44.00 4.04
488 491 5.243954 TCTCGATATATCCTGGTTGACCAAG 59.756 44.000 7.15 0.00 46.97 3.61
574 590 7.278629 CGTGAGGTAATTAATTAACGAATCGG 58.721 38.462 18.71 6.18 35.17 4.18
652 675 4.345859 TTTAACCTTGTGACCATCGAGT 57.654 40.909 0.00 0.00 0.00 4.18
653 676 2.169832 AACCTTGTGACCATCGAGTG 57.830 50.000 0.00 0.00 0.00 3.51
667 691 5.835257 CCATCGAGTGGCAATCAATAAATT 58.165 37.500 15.84 0.00 42.12 1.82
674 698 8.905702 CGAGTGGCAATCAATAAATTAATTAGC 58.094 33.333 15.84 0.00 0.00 3.09
675 699 9.748708 GAGTGGCAATCAATAAATTAATTAGCA 57.251 29.630 10.50 0.00 0.00 3.49
676 700 9.754382 AGTGGCAATCAATAAATTAATTAGCAG 57.246 29.630 0.01 0.00 0.00 4.24
678 702 8.202811 TGGCAATCAATAAATTAATTAGCAGCA 58.797 29.630 0.01 0.00 0.00 4.41
851 1209 3.070576 GAGGTGGGCCCAATGTGC 61.071 66.667 30.64 14.31 34.66 4.57
981 1349 3.741830 GACGCTTCTGCCCCTAGCC 62.742 68.421 0.00 0.00 42.71 3.93
1199 1609 1.622607 CCGCTGGAAGTACCCATGGA 61.623 60.000 15.22 0.00 35.03 3.41
1209 1619 1.925415 TACCCATGGACACGTCGTCG 61.925 60.000 15.22 0.00 46.42 5.12
1745 2164 0.287143 GATCGAACGAACGAACGACG 59.713 55.000 16.99 14.49 45.16 5.12
1746 2165 0.110688 ATCGAACGAACGAACGACGA 60.111 50.000 21.55 21.55 45.16 4.20
1768 2198 1.983605 CGTACGGGCTGCTATTAATCG 59.016 52.381 7.57 0.00 0.00 3.34
1769 2199 2.351060 CGTACGGGCTGCTATTAATCGA 60.351 50.000 7.57 0.00 0.00 3.59
1845 2285 2.990066 ACGGAAAATGGCACCAAAAA 57.010 40.000 0.00 0.00 0.00 1.94
1865 2313 1.726853 ACGTACTTGCTGCTTGATCC 58.273 50.000 0.00 0.00 0.00 3.36
1904 2355 1.450312 CCGATTTCTGCGCTCCCTT 60.450 57.895 9.73 0.00 0.00 3.95
1915 2366 0.727398 CGCTCCCTTTGATCGGAAAC 59.273 55.000 0.00 0.00 0.00 2.78
1959 2412 3.682766 CATGAGATGCTCTTCCGCT 57.317 52.632 0.00 0.00 0.00 5.52
1961 2414 0.031857 ATGAGATGCTCTTCCGCTCG 59.968 55.000 0.00 0.00 0.00 5.03
2116 2569 1.681666 CACCTGTCACCCTCATGCT 59.318 57.895 0.00 0.00 0.00 3.79
2164 2620 2.613506 CGGCCGAAAGTTGGTGGAC 61.614 63.158 24.07 0.00 0.00 4.02
2223 2679 1.162951 TCTCTCCCCTCCCTCCCTTT 61.163 60.000 0.00 0.00 0.00 3.11
2224 2680 0.985490 CTCTCCCCTCCCTCCCTTTG 60.985 65.000 0.00 0.00 0.00 2.77
2226 2682 1.541368 TCCCCTCCCTCCCTTTGTG 60.541 63.158 0.00 0.00 0.00 3.33
2228 2684 0.549169 CCCCTCCCTCCCTTTGTGTA 60.549 60.000 0.00 0.00 0.00 2.90
2245 2711 3.254060 GTGTATGTGTGTGCGAGAGAAT 58.746 45.455 0.00 0.00 0.00 2.40
2256 2726 4.082463 TGTGCGAGAGAATGTGTGTGTATA 60.082 41.667 0.00 0.00 0.00 1.47
2261 2731 6.863645 GCGAGAGAATGTGTGTGTATATATGT 59.136 38.462 0.00 0.00 0.00 2.29
2270 2740 8.293114 TGTGTGTGTATATATGTATGAAAGCG 57.707 34.615 0.00 0.00 0.00 4.68
2271 2741 8.138712 TGTGTGTGTATATATGTATGAAAGCGA 58.861 33.333 0.00 0.00 0.00 4.93
2374 2854 5.665916 TGCTCATCTATGTCTGTTTCTGA 57.334 39.130 0.00 0.00 0.00 3.27
2406 2886 1.136984 GAGTCGTCGTCGGAAGCAT 59.863 57.895 1.55 0.00 37.69 3.79
2433 2913 2.159627 GCGAGGTAGTCATTGTGGTTTG 59.840 50.000 0.00 0.00 0.00 2.93
2515 2998 3.163630 TGTGTTGCTTTTTCCAAGCTC 57.836 42.857 8.00 2.70 43.38 4.09
2522 3008 2.989166 GCTTTTTCCAAGCTCATTTCGG 59.011 45.455 0.00 0.00 40.01 4.30
2536 3022 0.886938 TTTCGGTGATGGCGCTTTCA 60.887 50.000 7.64 8.13 0.00 2.69
2615 3105 4.990426 CACCAGCCATAAGAAAAACCTTTG 59.010 41.667 0.00 0.00 0.00 2.77
2616 3106 4.040339 ACCAGCCATAAGAAAAACCTTTGG 59.960 41.667 0.00 0.00 32.50 3.28
2622 3112 2.882927 AGAAAAACCTTTGGGAACGC 57.117 45.000 0.00 0.00 36.25 4.84
2626 3116 1.037493 AAACCTTTGGGAACGCCTTC 58.963 50.000 0.00 0.00 36.25 3.46
2634 3124 2.661718 TGGGAACGCCTTCTTCTTTTT 58.338 42.857 0.00 0.00 0.00 1.94
2641 3131 4.921547 ACGCCTTCTTCTTTTTGAGAAAC 58.078 39.130 0.00 0.00 43.56 2.78
2650 3142 6.374894 TCTTCTTTTTGAGAAACCGGTTTACA 59.625 34.615 31.70 27.98 43.56 2.41
2653 3145 7.641760 TCTTTTTGAGAAACCGGTTTACATAC 58.358 34.615 31.70 18.80 32.11 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.232298 CTCCTCCTTCGGTGGCACTC 62.232 65.000 18.45 6.81 36.40 3.51
7 8 2.203788 TCCTCCTTCGGTGGCACT 60.204 61.111 18.45 0.00 36.40 4.40
8 9 1.827399 TTCTCCTCCTTCGGTGGCAC 61.827 60.000 9.70 9.70 36.40 5.01
9 10 1.535444 TTCTCCTCCTTCGGTGGCA 60.535 57.895 0.00 0.00 36.40 4.92
10 11 1.219393 CTTCTCCTCCTTCGGTGGC 59.781 63.158 0.00 0.00 36.40 5.01
11 12 0.614979 TCCTTCTCCTCCTTCGGTGG 60.615 60.000 0.00 0.00 37.67 4.61
12 13 0.820871 CTCCTTCTCCTCCTTCGGTG 59.179 60.000 0.00 0.00 0.00 4.94
13 14 0.324830 CCTCCTTCTCCTCCTTCGGT 60.325 60.000 0.00 0.00 0.00 4.69
14 15 0.033011 TCCTCCTTCTCCTCCTTCGG 60.033 60.000 0.00 0.00 0.00 4.30
15 16 1.107945 GTCCTCCTTCTCCTCCTTCG 58.892 60.000 0.00 0.00 0.00 3.79
16 17 1.107945 CGTCCTCCTTCTCCTCCTTC 58.892 60.000 0.00 0.00 0.00 3.46
17 18 0.324830 CCGTCCTCCTTCTCCTCCTT 60.325 60.000 0.00 0.00 0.00 3.36
18 19 1.308326 CCGTCCTCCTTCTCCTCCT 59.692 63.158 0.00 0.00 0.00 3.69
19 20 2.428085 GCCGTCCTCCTTCTCCTCC 61.428 68.421 0.00 0.00 0.00 4.30
20 21 2.776913 CGCCGTCCTCCTTCTCCTC 61.777 68.421 0.00 0.00 0.00 3.71
21 22 2.756283 CGCCGTCCTCCTTCTCCT 60.756 66.667 0.00 0.00 0.00 3.69
22 23 2.754658 TCGCCGTCCTCCTTCTCC 60.755 66.667 0.00 0.00 0.00 3.71
23 24 2.272918 CTGTCGCCGTCCTCCTTCTC 62.273 65.000 0.00 0.00 0.00 2.87
24 25 2.282958 TGTCGCCGTCCTCCTTCT 60.283 61.111 0.00 0.00 0.00 2.85
25 26 2.182030 CTGTCGCCGTCCTCCTTC 59.818 66.667 0.00 0.00 0.00 3.46
26 27 4.070552 GCTGTCGCCGTCCTCCTT 62.071 66.667 0.00 0.00 0.00 3.36
29 30 4.838486 CTCGCTGTCGCCGTCCTC 62.838 72.222 0.00 0.00 35.26 3.71
36 37 3.923563 AAGCTGTCCTCGCTGTCGC 62.924 63.158 0.00 0.00 37.87 5.19
37 38 1.803519 GAAGCTGTCCTCGCTGTCG 60.804 63.158 0.00 0.00 37.87 4.35
38 39 0.735632 CTGAAGCTGTCCTCGCTGTC 60.736 60.000 0.00 0.00 37.87 3.51
39 40 1.291588 CTGAAGCTGTCCTCGCTGT 59.708 57.895 0.00 0.00 37.87 4.40
40 41 2.099431 GCTGAAGCTGTCCTCGCTG 61.099 63.158 0.00 0.00 37.87 5.18
41 42 2.264166 GCTGAAGCTGTCCTCGCT 59.736 61.111 0.00 0.00 39.94 4.93
42 43 3.184683 CGCTGAAGCTGTCCTCGC 61.185 66.667 0.10 0.00 39.32 5.03
43 44 1.803519 GTCGCTGAAGCTGTCCTCG 60.804 63.158 0.10 0.00 39.32 4.63
44 45 1.803519 CGTCGCTGAAGCTGTCCTC 60.804 63.158 0.10 0.00 39.32 3.71
45 46 2.206515 CTCGTCGCTGAAGCTGTCCT 62.207 60.000 0.10 0.00 39.32 3.85
46 47 1.803519 CTCGTCGCTGAAGCTGTCC 60.804 63.158 0.10 0.00 39.32 4.02
47 48 2.440569 GCTCGTCGCTGAAGCTGTC 61.441 63.158 0.10 0.00 39.32 3.51
48 49 2.431601 GCTCGTCGCTGAAGCTGT 60.432 61.111 0.10 0.00 39.32 4.40
49 50 2.431430 TGCTCGTCGCTGAAGCTG 60.431 61.111 5.40 0.00 40.11 4.24
50 51 2.126149 CTGCTCGTCGCTGAAGCT 60.126 61.111 5.40 0.00 39.69 3.74
51 52 2.126307 TCTGCTCGTCGCTGAAGC 60.126 61.111 6.58 0.00 42.63 3.86
55 56 2.653448 CGGATCTGCTCGTCGCTG 60.653 66.667 0.00 1.45 40.11 5.18
56 57 2.824489 TCGGATCTGCTCGTCGCT 60.824 61.111 0.00 0.00 40.11 4.93
57 58 2.652496 GTCGGATCTGCTCGTCGC 60.652 66.667 0.00 0.00 39.77 5.19
58 59 1.010574 GAGTCGGATCTGCTCGTCG 60.011 63.158 9.32 0.00 0.00 5.12
59 60 1.010574 CGAGTCGGATCTGCTCGTC 60.011 63.158 26.63 8.55 44.69 4.20
60 61 3.102985 CGAGTCGGATCTGCTCGT 58.897 61.111 26.63 3.25 44.69 4.18
62 63 0.239879 GGATCGAGTCGGATCTGCTC 59.760 60.000 13.54 13.10 41.99 4.26
63 64 1.511318 CGGATCGAGTCGGATCTGCT 61.511 60.000 13.54 0.00 41.48 4.24
64 65 1.081774 CGGATCGAGTCGGATCTGC 60.082 63.158 13.54 0.07 41.48 4.26
66 67 1.070445 AGTACGGATCGAGTCGGATCT 59.930 52.381 13.54 3.01 41.99 2.75
67 68 1.194997 CAGTACGGATCGAGTCGGATC 59.805 57.143 13.54 13.42 41.67 3.36
68 69 1.227639 CAGTACGGATCGAGTCGGAT 58.772 55.000 13.54 4.94 0.00 4.18
69 70 1.434622 GCAGTACGGATCGAGTCGGA 61.435 60.000 13.54 3.37 0.00 4.55
70 71 1.009900 GCAGTACGGATCGAGTCGG 60.010 63.158 13.54 0.00 0.00 4.79
71 72 1.367782 CGCAGTACGGATCGAGTCG 60.368 63.158 6.09 6.09 38.44 4.18
72 73 0.587285 ATCGCAGTACGGATCGAGTC 59.413 55.000 0.00 0.00 43.89 3.36
73 74 1.022735 AATCGCAGTACGGATCGAGT 58.977 50.000 0.00 0.00 43.89 4.18
74 75 2.044860 GAAATCGCAGTACGGATCGAG 58.955 52.381 0.00 0.00 43.89 4.04
75 76 1.596220 CGAAATCGCAGTACGGATCGA 60.596 52.381 0.00 0.00 43.89 3.59
76 77 0.770590 CGAAATCGCAGTACGGATCG 59.229 55.000 0.00 0.00 43.89 3.69
77 78 1.779724 GTCGAAATCGCAGTACGGATC 59.220 52.381 0.00 0.00 43.89 3.36
78 79 1.404391 AGTCGAAATCGCAGTACGGAT 59.596 47.619 0.00 0.00 43.89 4.18
79 80 0.806868 AGTCGAAATCGCAGTACGGA 59.193 50.000 0.00 0.00 43.89 4.69
80 81 0.914551 CAGTCGAAATCGCAGTACGG 59.085 55.000 0.00 0.00 43.89 4.02
81 82 0.914551 CCAGTCGAAATCGCAGTACG 59.085 55.000 0.00 0.00 45.62 3.67
82 83 1.992170 ACCAGTCGAAATCGCAGTAC 58.008 50.000 0.00 0.00 39.60 2.73
83 84 2.751259 AGTACCAGTCGAAATCGCAGTA 59.249 45.455 0.00 0.00 39.60 2.74
84 85 1.544691 AGTACCAGTCGAAATCGCAGT 59.455 47.619 0.00 0.00 39.60 4.40
85 86 2.279582 AGTACCAGTCGAAATCGCAG 57.720 50.000 0.00 0.00 39.60 5.18
86 87 2.602878 GAAGTACCAGTCGAAATCGCA 58.397 47.619 0.00 0.00 39.60 5.10
87 88 1.925185 GGAAGTACCAGTCGAAATCGC 59.075 52.381 0.00 0.00 37.70 4.58
88 89 2.182825 CGGAAGTACCAGTCGAAATCG 58.817 52.381 0.00 0.00 38.90 3.34
89 90 1.925185 GCGGAAGTACCAGTCGAAATC 59.075 52.381 0.00 0.00 38.90 2.17
90 91 1.734707 CGCGGAAGTACCAGTCGAAAT 60.735 52.381 0.00 0.00 38.90 2.17
91 92 0.387622 CGCGGAAGTACCAGTCGAAA 60.388 55.000 0.00 0.00 38.90 3.46
92 93 1.210931 CGCGGAAGTACCAGTCGAA 59.789 57.895 0.00 0.00 38.90 3.71
93 94 1.642037 CTCGCGGAAGTACCAGTCGA 61.642 60.000 6.13 0.00 38.90 4.20
94 95 1.226323 CTCGCGGAAGTACCAGTCG 60.226 63.158 6.13 0.00 38.90 4.18
95 96 0.524862 TTCTCGCGGAAGTACCAGTC 59.475 55.000 6.13 0.00 38.90 3.51
96 97 0.526662 CTTCTCGCGGAAGTACCAGT 59.473 55.000 21.80 0.00 44.59 4.00
97 98 3.330766 CTTCTCGCGGAAGTACCAG 57.669 57.895 21.80 5.24 44.59 4.00
107 108 3.181967 CTTGCCGTCCTTCTCGCG 61.182 66.667 0.00 0.00 0.00 5.87
108 109 2.815647 CCTTGCCGTCCTTCTCGC 60.816 66.667 0.00 0.00 0.00 5.03
109 110 2.125512 CCCTTGCCGTCCTTCTCG 60.126 66.667 0.00 0.00 0.00 4.04
110 111 2.436824 GCCCTTGCCGTCCTTCTC 60.437 66.667 0.00 0.00 0.00 2.87
111 112 4.394712 CGCCCTTGCCGTCCTTCT 62.395 66.667 0.00 0.00 0.00 2.85
129 130 4.426313 GTCCTTGCCCTTCCCCGG 62.426 72.222 0.00 0.00 0.00 5.73
130 131 3.628646 CTGTCCTTGCCCTTCCCCG 62.629 68.421 0.00 0.00 0.00 5.73
131 132 2.356667 CTGTCCTTGCCCTTCCCC 59.643 66.667 0.00 0.00 0.00 4.81
132 133 2.361737 GCTGTCCTTGCCCTTCCC 60.362 66.667 0.00 0.00 0.00 3.97
133 134 2.361737 GGCTGTCCTTGCCCTTCC 60.362 66.667 0.00 0.00 44.32 3.46
138 139 3.628646 ATCCACGGCTGTCCTTGCC 62.629 63.158 0.00 0.00 46.42 4.52
139 140 2.045926 ATCCACGGCTGTCCTTGC 60.046 61.111 0.00 0.00 30.77 4.01
140 141 0.321564 TTCATCCACGGCTGTCCTTG 60.322 55.000 0.00 0.00 0.00 3.61
141 142 0.321653 GTTCATCCACGGCTGTCCTT 60.322 55.000 0.00 0.00 0.00 3.36
142 143 1.194781 AGTTCATCCACGGCTGTCCT 61.195 55.000 0.00 0.00 0.00 3.85
143 144 0.741221 GAGTTCATCCACGGCTGTCC 60.741 60.000 0.00 0.00 0.00 4.02
144 145 2.755929 GAGTTCATCCACGGCTGTC 58.244 57.895 0.00 0.00 0.00 3.51
154 155 3.644966 TTGGGTATGGTGGAGTTCATC 57.355 47.619 0.00 0.00 0.00 2.92
155 156 4.608170 ATTTGGGTATGGTGGAGTTCAT 57.392 40.909 0.00 0.00 0.00 2.57
156 157 5.445069 CATATTTGGGTATGGTGGAGTTCA 58.555 41.667 0.00 0.00 0.00 3.18
157 158 4.278419 GCATATTTGGGTATGGTGGAGTTC 59.722 45.833 0.00 0.00 33.61 3.01
158 159 4.215109 GCATATTTGGGTATGGTGGAGTT 58.785 43.478 0.00 0.00 33.61 3.01
159 160 3.436470 GGCATATTTGGGTATGGTGGAGT 60.436 47.826 0.00 0.00 33.61 3.85
160 161 3.157087 GGCATATTTGGGTATGGTGGAG 58.843 50.000 0.00 0.00 33.61 3.86
161 162 2.515853 TGGCATATTTGGGTATGGTGGA 59.484 45.455 0.00 0.00 33.61 4.02
162 163 2.956132 TGGCATATTTGGGTATGGTGG 58.044 47.619 0.00 0.00 33.61 4.61
163 164 5.549742 ATTTGGCATATTTGGGTATGGTG 57.450 39.130 0.00 0.00 33.61 4.17
164 165 6.573712 AAATTTGGCATATTTGGGTATGGT 57.426 33.333 13.94 0.00 33.61 3.55
165 166 6.262720 CCAAAATTTGGCATATTTGGGTATGG 59.737 38.462 21.97 17.40 45.09 2.74
166 167 7.261829 CCAAAATTTGGCATATTTGGGTATG 57.738 36.000 21.97 13.66 45.09 2.39
181 182 6.857964 GCATATCATCGGACTACCAAAATTTG 59.142 38.462 0.00 0.00 35.59 2.32
182 183 6.772716 AGCATATCATCGGACTACCAAAATTT 59.227 34.615 0.00 0.00 35.59 1.82
183 184 6.299141 AGCATATCATCGGACTACCAAAATT 58.701 36.000 0.00 0.00 35.59 1.82
184 185 5.869579 AGCATATCATCGGACTACCAAAAT 58.130 37.500 0.00 0.00 35.59 1.82
185 186 5.290493 AGCATATCATCGGACTACCAAAA 57.710 39.130 0.00 0.00 35.59 2.44
186 187 4.955811 AGCATATCATCGGACTACCAAA 57.044 40.909 0.00 0.00 35.59 3.28
187 188 5.538813 ACTTAGCATATCATCGGACTACCAA 59.461 40.000 0.00 0.00 35.59 3.67
188 189 5.077564 ACTTAGCATATCATCGGACTACCA 58.922 41.667 0.00 0.00 35.59 3.25
189 190 5.646577 ACTTAGCATATCATCGGACTACC 57.353 43.478 0.00 0.00 0.00 3.18
190 191 9.111613 ACTATACTTAGCATATCATCGGACTAC 57.888 37.037 0.00 0.00 0.00 2.73
191 192 9.110502 CACTATACTTAGCATATCATCGGACTA 57.889 37.037 0.00 0.00 0.00 2.59
192 193 7.612244 ACACTATACTTAGCATATCATCGGACT 59.388 37.037 0.00 0.00 0.00 3.85
193 194 7.698550 CACACTATACTTAGCATATCATCGGAC 59.301 40.741 0.00 0.00 0.00 4.79
194 195 7.610305 TCACACTATACTTAGCATATCATCGGA 59.390 37.037 0.00 0.00 0.00 4.55
195 196 7.762382 TCACACTATACTTAGCATATCATCGG 58.238 38.462 0.00 0.00 0.00 4.18
196 197 9.230932 CATCACACTATACTTAGCATATCATCG 57.769 37.037 0.00 0.00 0.00 3.84
197 198 9.526713 CCATCACACTATACTTAGCATATCATC 57.473 37.037 0.00 0.00 0.00 2.92
198 199 9.259832 TCCATCACACTATACTTAGCATATCAT 57.740 33.333 0.00 0.00 0.00 2.45
199 200 8.650143 TCCATCACACTATACTTAGCATATCA 57.350 34.615 0.00 0.00 0.00 2.15
200 201 8.744652 ACTCCATCACACTATACTTAGCATATC 58.255 37.037 0.00 0.00 0.00 1.63
201 202 8.657387 ACTCCATCACACTATACTTAGCATAT 57.343 34.615 0.00 0.00 0.00 1.78
202 203 9.232473 CTACTCCATCACACTATACTTAGCATA 57.768 37.037 0.00 0.00 0.00 3.14
203 204 6.985653 ACTCCATCACACTATACTTAGCAT 57.014 37.500 0.00 0.00 0.00 3.79
204 205 6.016192 GCTACTCCATCACACTATACTTAGCA 60.016 42.308 0.00 0.00 0.00 3.49
205 206 6.383415 GCTACTCCATCACACTATACTTAGC 58.617 44.000 0.00 0.00 0.00 3.09
206 207 6.348622 CGGCTACTCCATCACACTATACTTAG 60.349 46.154 0.00 0.00 34.01 2.18
207 208 5.472478 CGGCTACTCCATCACACTATACTTA 59.528 44.000 0.00 0.00 34.01 2.24
208 209 4.278669 CGGCTACTCCATCACACTATACTT 59.721 45.833 0.00 0.00 34.01 2.24
209 210 3.821600 CGGCTACTCCATCACACTATACT 59.178 47.826 0.00 0.00 34.01 2.12
210 211 3.057456 CCGGCTACTCCATCACACTATAC 60.057 52.174 0.00 0.00 34.01 1.47
211 212 3.154710 CCGGCTACTCCATCACACTATA 58.845 50.000 0.00 0.00 34.01 1.31
212 213 1.964223 CCGGCTACTCCATCACACTAT 59.036 52.381 0.00 0.00 34.01 2.12
213 214 1.064240 TCCGGCTACTCCATCACACTA 60.064 52.381 0.00 0.00 34.01 2.74
214 215 0.324368 TCCGGCTACTCCATCACACT 60.324 55.000 0.00 0.00 34.01 3.55
215 216 0.179108 GTCCGGCTACTCCATCACAC 60.179 60.000 0.00 0.00 34.01 3.82
216 217 1.663379 CGTCCGGCTACTCCATCACA 61.663 60.000 0.00 0.00 34.01 3.58
217 218 1.065928 CGTCCGGCTACTCCATCAC 59.934 63.158 0.00 0.00 34.01 3.06
218 219 0.467474 ATCGTCCGGCTACTCCATCA 60.467 55.000 0.00 0.00 34.01 3.07
219 220 0.039074 CATCGTCCGGCTACTCCATC 60.039 60.000 0.00 0.00 34.01 3.51
220 221 2.041976 CATCGTCCGGCTACTCCAT 58.958 57.895 0.00 0.00 34.01 3.41
221 222 2.782222 GCATCGTCCGGCTACTCCA 61.782 63.158 0.00 0.00 34.01 3.86
222 223 2.027751 GCATCGTCCGGCTACTCC 59.972 66.667 0.00 0.00 0.00 3.85
223 224 0.596577 TATGCATCGTCCGGCTACTC 59.403 55.000 0.19 0.00 0.00 2.59
224 225 1.067565 CATATGCATCGTCCGGCTACT 60.068 52.381 0.19 0.00 0.00 2.57
225 226 1.350193 CATATGCATCGTCCGGCTAC 58.650 55.000 0.19 0.00 0.00 3.58
226 227 0.389817 GCATATGCATCGTCCGGCTA 60.390 55.000 22.84 0.00 41.59 3.93
227 228 1.669115 GCATATGCATCGTCCGGCT 60.669 57.895 22.84 0.00 41.59 5.52
228 229 2.863153 GCATATGCATCGTCCGGC 59.137 61.111 22.84 0.00 41.59 6.13
229 230 1.617755 GACGCATATGCATCGTCCGG 61.618 60.000 26.52 10.54 44.62 5.14
230 231 1.775344 GACGCATATGCATCGTCCG 59.225 57.895 26.52 14.87 44.62 4.79
235 236 1.644295 CTACGTCGACGCATATGCATC 59.356 52.381 35.92 20.38 44.43 3.91
236 237 1.001706 ACTACGTCGACGCATATGCAT 60.002 47.619 35.92 17.45 44.43 3.96
237 238 0.379316 ACTACGTCGACGCATATGCA 59.621 50.000 35.92 12.45 44.43 3.96
238 239 1.187271 CAACTACGTCGACGCATATGC 59.813 52.381 35.92 18.08 44.43 3.14
239 240 1.187271 GCAACTACGTCGACGCATATG 59.813 52.381 35.92 27.92 44.43 1.78
240 241 1.202211 TGCAACTACGTCGACGCATAT 60.202 47.619 35.92 20.06 44.43 1.78
241 242 0.168568 TGCAACTACGTCGACGCATA 59.831 50.000 35.92 21.16 44.43 3.14
242 243 0.457853 ATGCAACTACGTCGACGCAT 60.458 50.000 35.92 25.57 44.43 4.73
243 244 0.168568 TATGCAACTACGTCGACGCA 59.831 50.000 35.92 24.21 44.43 5.24
244 245 1.252015 CTTATGCAACTACGTCGACGC 59.748 52.381 35.92 19.70 44.43 5.19
245 246 2.512885 ACTTATGCAACTACGTCGACG 58.487 47.619 34.58 34.58 46.33 5.12
246 247 5.032863 ACATACTTATGCAACTACGTCGAC 58.967 41.667 5.18 5.18 37.19 4.20
247 248 5.239359 ACATACTTATGCAACTACGTCGA 57.761 39.130 0.00 0.00 37.19 4.20
248 249 8.225777 TCTATACATACTTATGCAACTACGTCG 58.774 37.037 0.00 0.00 37.19 5.12
276 277 9.616156 TCGGACACCTAAATTAGCATATTTTAA 57.384 29.630 0.00 0.00 29.30 1.52
277 278 9.616156 TTCGGACACCTAAATTAGCATATTTTA 57.384 29.630 0.00 0.00 0.00 1.52
278 279 8.514330 TTCGGACACCTAAATTAGCATATTTT 57.486 30.769 0.00 0.00 0.00 1.82
279 280 7.773690 ACTTCGGACACCTAAATTAGCATATTT 59.226 33.333 0.00 0.00 0.00 1.40
280 281 7.280356 ACTTCGGACACCTAAATTAGCATATT 58.720 34.615 0.00 0.00 0.00 1.28
281 282 6.827727 ACTTCGGACACCTAAATTAGCATAT 58.172 36.000 0.00 0.00 0.00 1.78
282 283 6.229936 ACTTCGGACACCTAAATTAGCATA 57.770 37.500 0.00 0.00 0.00 3.14
283 284 5.099042 ACTTCGGACACCTAAATTAGCAT 57.901 39.130 0.00 0.00 0.00 3.79
284 285 4.501071 GACTTCGGACACCTAAATTAGCA 58.499 43.478 0.00 0.00 0.00 3.49
285 286 3.869832 GGACTTCGGACACCTAAATTAGC 59.130 47.826 0.00 0.00 0.00 3.09
286 287 4.110482 CGGACTTCGGACACCTAAATTAG 58.890 47.826 0.00 0.00 34.75 1.73
287 288 4.114058 CGGACTTCGGACACCTAAATTA 57.886 45.455 0.00 0.00 34.75 1.40
288 289 2.968675 CGGACTTCGGACACCTAAATT 58.031 47.619 0.00 0.00 34.75 1.82
289 290 2.667473 CGGACTTCGGACACCTAAAT 57.333 50.000 0.00 0.00 34.75 1.40
300 301 1.226323 CGTCTACAGCCGGACTTCG 60.226 63.158 5.05 0.00 38.88 3.79
301 302 1.516603 GCGTCTACAGCCGGACTTC 60.517 63.158 5.05 0.00 0.00 3.01
302 303 1.935327 GAGCGTCTACAGCCGGACTT 61.935 60.000 5.05 0.00 34.64 3.01
303 304 2.361357 AGCGTCTACAGCCGGACT 60.361 61.111 5.05 0.00 34.64 3.85
304 305 2.102553 GAGCGTCTACAGCCGGAC 59.897 66.667 5.05 0.00 34.64 4.79
305 306 2.360726 TGAGCGTCTACAGCCGGA 60.361 61.111 5.05 0.00 34.64 5.14
306 307 2.202623 GTGAGCGTCTACAGCCGG 60.203 66.667 0.00 0.00 34.64 6.13
307 308 0.458543 AATGTGAGCGTCTACAGCCG 60.459 55.000 0.00 0.00 34.64 5.52
308 309 1.002366 CAATGTGAGCGTCTACAGCC 58.998 55.000 0.00 0.00 34.64 4.85
309 310 1.923204 CTCAATGTGAGCGTCTACAGC 59.077 52.381 0.00 0.00 37.72 4.40
310 311 3.433709 CTCTCAATGTGAGCGTCTACAG 58.566 50.000 0.00 0.00 43.95 2.74
311 312 2.164422 CCTCTCAATGTGAGCGTCTACA 59.836 50.000 6.79 0.00 43.95 2.74
312 313 2.164624 ACCTCTCAATGTGAGCGTCTAC 59.835 50.000 6.79 0.00 43.95 2.59
313 314 2.164422 CACCTCTCAATGTGAGCGTCTA 59.836 50.000 6.79 0.00 43.95 2.59
314 315 1.067283 CACCTCTCAATGTGAGCGTCT 60.067 52.381 6.79 0.00 43.95 4.18
315 316 1.354040 CACCTCTCAATGTGAGCGTC 58.646 55.000 6.79 0.00 43.95 5.19
316 317 0.671781 GCACCTCTCAATGTGAGCGT 60.672 55.000 6.79 4.23 43.95 5.07
317 318 1.690283 CGCACCTCTCAATGTGAGCG 61.690 60.000 6.79 5.14 43.95 5.03
318 319 2.084844 CGCACCTCTCAATGTGAGC 58.915 57.895 6.79 0.00 43.95 4.26
319 320 1.364626 GGCGCACCTCTCAATGTGAG 61.365 60.000 10.83 5.41 45.59 3.51
320 321 1.375908 GGCGCACCTCTCAATGTGA 60.376 57.895 10.83 0.00 34.37 3.58
321 322 2.743752 CGGCGCACCTCTCAATGTG 61.744 63.158 10.83 0.00 35.58 3.21
322 323 2.434884 CGGCGCACCTCTCAATGT 60.435 61.111 10.83 0.00 0.00 2.71
323 324 3.197790 CCGGCGCACCTCTCAATG 61.198 66.667 10.83 0.00 0.00 2.82
324 325 3.390521 TCCGGCGCACCTCTCAAT 61.391 61.111 10.83 0.00 0.00 2.57
325 326 4.373116 GTCCGGCGCACCTCTCAA 62.373 66.667 10.83 0.00 0.00 3.02
327 328 4.500116 GAGTCCGGCGCACCTCTC 62.500 72.222 10.83 7.93 0.00 3.20
335 336 2.296692 CTTTGATTGCGAGTCCGGCG 62.297 60.000 0.00 0.00 36.06 6.46
336 337 1.019278 TCTTTGATTGCGAGTCCGGC 61.019 55.000 0.00 0.00 36.06 6.13
337 338 1.002366 CTCTTTGATTGCGAGTCCGG 58.998 55.000 0.00 0.00 36.06 5.14
338 339 1.996292 TCTCTTTGATTGCGAGTCCG 58.004 50.000 0.00 0.00 39.16 4.79
339 340 3.000724 CGATTCTCTTTGATTGCGAGTCC 59.999 47.826 0.00 0.00 0.00 3.85
340 341 3.614616 ACGATTCTCTTTGATTGCGAGTC 59.385 43.478 0.00 0.00 0.00 3.36
341 342 3.589988 ACGATTCTCTTTGATTGCGAGT 58.410 40.909 0.00 0.00 0.00 4.18
342 343 4.572845 GAACGATTCTCTTTGATTGCGAG 58.427 43.478 0.00 0.00 0.00 5.03
343 344 3.060761 CGAACGATTCTCTTTGATTGCGA 59.939 43.478 0.00 0.00 0.00 5.10
344 345 3.337130 CGAACGATTCTCTTTGATTGCG 58.663 45.455 0.00 0.00 0.00 4.85
345 346 3.125316 ACCGAACGATTCTCTTTGATTGC 59.875 43.478 0.00 0.00 0.00 3.56
346 347 4.928661 ACCGAACGATTCTCTTTGATTG 57.071 40.909 0.00 0.00 0.00 2.67
347 348 5.721232 ACTACCGAACGATTCTCTTTGATT 58.279 37.500 0.00 0.00 0.00 2.57
348 349 5.326200 ACTACCGAACGATTCTCTTTGAT 57.674 39.130 0.00 0.00 0.00 2.57
349 350 4.778534 ACTACCGAACGATTCTCTTTGA 57.221 40.909 0.00 0.00 0.00 2.69
350 351 5.840940 AAACTACCGAACGATTCTCTTTG 57.159 39.130 0.00 0.00 0.00 2.77
351 352 5.575995 GCTAAACTACCGAACGATTCTCTTT 59.424 40.000 0.00 0.00 0.00 2.52
352 353 5.100943 GCTAAACTACCGAACGATTCTCTT 58.899 41.667 0.00 0.00 0.00 2.85
353 354 4.157289 TGCTAAACTACCGAACGATTCTCT 59.843 41.667 0.00 0.00 0.00 3.10
354 355 4.418392 TGCTAAACTACCGAACGATTCTC 58.582 43.478 0.00 0.00 0.00 2.87
355 356 4.445452 TGCTAAACTACCGAACGATTCT 57.555 40.909 0.00 0.00 0.00 2.40
356 357 5.520022 TTTGCTAAACTACCGAACGATTC 57.480 39.130 0.00 0.00 0.00 2.52
361 362 5.081888 TCGTTTTTGCTAAACTACCGAAC 57.918 39.130 11.45 0.00 0.00 3.95
362 363 5.927954 ATCGTTTTTGCTAAACTACCGAA 57.072 34.783 11.45 0.00 0.00 4.30
380 381 1.333619 GCAACTGACACACCAAATCGT 59.666 47.619 0.00 0.00 0.00 3.73
381 382 1.333308 TGCAACTGACACACCAAATCG 59.667 47.619 0.00 0.00 0.00 3.34
383 384 3.225104 AGATGCAACTGACACACCAAAT 58.775 40.909 0.00 0.00 0.00 2.32
384 385 2.653726 AGATGCAACTGACACACCAAA 58.346 42.857 0.00 0.00 0.00 3.28
385 386 2.346766 AGATGCAACTGACACACCAA 57.653 45.000 0.00 0.00 0.00 3.67
393 394 7.667043 ATTAGTTAACGAAAGATGCAACTGA 57.333 32.000 5.21 0.00 0.00 3.41
398 399 6.403200 GGCTCAATTAGTTAACGAAAGATGCA 60.403 38.462 5.21 0.00 0.00 3.96
399 400 5.965918 GGCTCAATTAGTTAACGAAAGATGC 59.034 40.000 5.21 10.68 0.00 3.91
403 404 7.072177 TCATGGCTCAATTAGTTAACGAAAG 57.928 36.000 5.21 0.44 0.00 2.62
406 407 5.105106 TCCTCATGGCTCAATTAGTTAACGA 60.105 40.000 0.00 0.00 0.00 3.85
412 413 4.472833 AGAAGTCCTCATGGCTCAATTAGT 59.527 41.667 0.00 0.00 0.00 2.24
421 422 2.497675 TCTGTGTAGAAGTCCTCATGGC 59.502 50.000 0.00 0.00 0.00 4.40
427 428 5.546499 TGGGTTAATTCTGTGTAGAAGTCCT 59.454 40.000 0.00 0.00 45.53 3.85
436 437 8.415950 TGTAATTTCATGGGTTAATTCTGTGT 57.584 30.769 0.00 0.00 0.00 3.72
439 440 9.520204 GACATGTAATTTCATGGGTTAATTCTG 57.480 33.333 23.76 2.20 46.39 3.02
488 491 2.543777 TTAGCCGGTGATATCCAAGC 57.456 50.000 1.90 0.00 0.00 4.01
568 584 2.793237 GCTCGACTGAGACTTCCGATTC 60.793 54.545 0.00 0.00 45.57 2.52
573 589 1.064952 GCTAGCTCGACTGAGACTTCC 59.935 57.143 7.70 0.00 45.57 3.46
574 590 2.014128 AGCTAGCTCGACTGAGACTTC 58.986 52.381 12.68 0.00 45.57 3.01
652 675 8.202811 TGCTGCTAATTAATTTATTGATTGCCA 58.797 29.630 5.91 1.00 30.12 4.92
653 676 8.592105 TGCTGCTAATTAATTTATTGATTGCC 57.408 30.769 5.91 0.00 30.12 4.52
678 702 4.062991 ACGTCGAGGTAGCAAATCTTTTT 58.937 39.130 9.40 0.00 0.00 1.94
683 1030 1.189403 CGACGTCGAGGTAGCAAATC 58.811 55.000 33.35 0.00 43.02 2.17
832 1190 2.535317 ACATTGGGCCCACCTCCT 60.535 61.111 28.70 3.76 41.11 3.69
1716 2135 0.989164 TCGTTCGATCGATGTTGCAC 59.011 50.000 20.18 11.82 34.85 4.57
1717 2136 1.388768 GTTCGTTCGATCGATGTTGCA 59.611 47.619 20.18 0.00 39.57 4.08
1718 2137 1.586679 CGTTCGTTCGATCGATGTTGC 60.587 52.381 20.18 8.81 39.57 4.17
1744 2163 0.526954 AATAGCAGCCCGTACGTTCG 60.527 55.000 15.21 7.68 0.00 3.95
1745 2164 2.497107 TAATAGCAGCCCGTACGTTC 57.503 50.000 15.21 5.20 0.00 3.95
1746 2165 2.965572 TTAATAGCAGCCCGTACGTT 57.034 45.000 15.21 1.57 0.00 3.99
1750 2180 4.053295 GTTTCGATTAATAGCAGCCCGTA 58.947 43.478 0.00 0.00 0.00 4.02
1768 2198 7.510549 TGCATAATAGCTTCTTATGGGTTTC 57.489 36.000 21.15 10.80 37.16 2.78
1769 2199 7.725397 TCATGCATAATAGCTTCTTATGGGTTT 59.275 33.333 21.15 0.00 37.16 3.27
1845 2285 2.076863 GGATCAAGCAGCAAGTACGTT 58.923 47.619 0.00 0.00 0.00 3.99
1865 2313 0.027716 GATGTTCGAGCAGCAGCATG 59.972 55.000 12.87 0.00 45.49 4.06
1904 2355 1.738830 GCCGTCCGTTTCCGATCAA 60.739 57.895 0.00 0.00 35.63 2.57
1915 2366 3.559657 GATCGATCCTGGCCGTCCG 62.560 68.421 14.76 0.00 34.14 4.79
1959 2412 0.750249 TAATTGAGATCCAGCGGCGA 59.250 50.000 12.98 0.00 0.00 5.54
1961 2414 2.880890 ACAATAATTGAGATCCAGCGGC 59.119 45.455 0.00 0.00 0.00 6.53
2066 2519 5.420421 TGAGGAATAAGAAGGACACAGAGAG 59.580 44.000 0.00 0.00 0.00 3.20
2067 2520 5.333581 TGAGGAATAAGAAGGACACAGAGA 58.666 41.667 0.00 0.00 0.00 3.10
2136 2589 4.697756 TTCGGCCGGTGAGCAAGG 62.698 66.667 27.83 0.00 0.00 3.61
2223 2679 1.611491 TCTCTCGCACACACATACACA 59.389 47.619 0.00 0.00 0.00 3.72
2224 2680 2.347697 TCTCTCGCACACACATACAC 57.652 50.000 0.00 0.00 0.00 2.90
2226 2682 3.061295 CACATTCTCTCGCACACACATAC 59.939 47.826 0.00 0.00 0.00 2.39
2228 2684 2.071540 CACATTCTCTCGCACACACAT 58.928 47.619 0.00 0.00 0.00 3.21
2245 2711 8.138712 TCGCTTTCATACATATATACACACACA 58.861 33.333 0.00 0.00 0.00 3.72
2256 2726 5.460571 CGCATCATCGCTTTCATACATAT 57.539 39.130 0.00 0.00 0.00 1.78
2269 2739 7.697710 ACAAAATTAATATATGGCGCATCATCG 59.302 33.333 10.83 0.00 0.00 3.84
2270 2740 8.915871 ACAAAATTAATATATGGCGCATCATC 57.084 30.769 10.83 0.00 0.00 2.92
2271 2741 9.142515 CAACAAAATTAATATATGGCGCATCAT 57.857 29.630 10.83 7.10 0.00 2.45
2312 2782 3.514309 GGCGTATGTACCCATAGGAGAAT 59.486 47.826 6.60 0.00 40.32 2.40
2374 2854 3.249189 ACTCGCCACCACCACCAT 61.249 61.111 0.00 0.00 0.00 3.55
2400 2880 0.666913 TACCTCGCGGTCTATGCTTC 59.333 55.000 6.13 0.00 44.21 3.86
2406 2886 1.674441 CAATGACTACCTCGCGGTCTA 59.326 52.381 6.13 0.00 44.21 2.59
2448 2928 6.708285 ACACTAGGGACGTAAATTGATTTCT 58.292 36.000 0.00 0.00 0.00 2.52
2456 2938 5.415701 TCGTAAAGACACTAGGGACGTAAAT 59.584 40.000 0.00 0.00 0.00 1.40
2465 2947 4.235360 CAGTGGTTCGTAAAGACACTAGG 58.765 47.826 0.00 0.00 40.14 3.02
2515 2998 0.171007 AAAGCGCCATCACCGAAATG 59.829 50.000 2.29 0.00 0.00 2.32
2536 3022 3.412386 CGTTCTTCCCAGAAAGAATGGT 58.588 45.455 9.65 0.00 44.64 3.55
2540 3026 3.625764 CACAACGTTCTTCCCAGAAAGAA 59.374 43.478 0.00 0.00 40.90 2.52
2615 3105 2.621526 TCAAAAAGAAGAAGGCGTTCCC 59.378 45.455 15.23 8.08 32.48 3.97
2616 3106 3.564225 TCTCAAAAAGAAGAAGGCGTTCC 59.436 43.478 15.23 1.64 32.48 3.62
2622 3112 4.338400 ACCGGTTTCTCAAAAAGAAGAAGG 59.662 41.667 0.00 0.00 44.69 3.46
2626 3116 6.557110 TGTAAACCGGTTTCTCAAAAAGAAG 58.443 36.000 34.79 0.00 44.69 2.85
2634 3124 4.529377 AGAGGTATGTAAACCGGTTTCTCA 59.471 41.667 34.79 30.56 44.77 3.27
2641 3131 3.492137 GGCACTAGAGGTATGTAAACCGG 60.492 52.174 0.00 0.00 44.77 5.28


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

AutoCloner maintained by Alex Coulton.