Multiple sequence alignment - TraesCS6B01G354400

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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 TraesCS6B01G354400 chr6B 100.000 2839 0 0 1 2839 620266871 620264033 0.000000e+00 5243.0
1 TraesCS6B01G354400 chr6D 90.921 2346 163 31 513 2839 412002455 412000141 0.000000e+00 3107.0
2 TraesCS6B01G354400 chr6A 90.131 993 48 21 516 1481 557095481 557094512 0.000000e+00 1245.0
3 TraesCS6B01G354400 chr6A 91.181 669 53 6 2172 2839 557093861 557093198 0.000000e+00 904.0
4 TraesCS6B01G354400 chr6A 90.705 624 52 6 1484 2104 557094481 557093861 0.000000e+00 826.0
5 TraesCS6B01G354400 chr6A 90.335 269 20 3 257 519 557095787 557095519 5.820000e-92 348.0
6 TraesCS6B01G354400 chr2A 97.358 265 5 2 2 266 36021793 36021531 1.550000e-122 449.0
7 TraesCS6B01G354400 chr1A 97.683 259 6 0 3 261 387338390 387338648 2.010000e-121 446.0
8 TraesCS6B01G354400 chr1A 80.723 83 15 1 320 401 511109447 511109529 2.360000e-06 63.9
9 TraesCS6B01G354400 chr5A 96.552 261 8 1 3 262 663324667 663324407 5.620000e-117 431.0
10 TraesCS6B01G354400 chrUn 95.802 262 10 1 2 262 35797602 35797341 3.380000e-114 422.0
11 TraesCS6B01G354400 chr3A 95.489 266 9 2 2 264 8568512 8568247 3.380000e-114 422.0
12 TraesCS6B01G354400 chr4A 95.420 262 11 1 2 262 701953133 701952872 1.570000e-112 416.0
13 TraesCS6B01G354400 chr4A 94.757 267 9 1 2 263 731081659 731081925 7.320000e-111 411.0
14 TraesCS6B01G354400 chr3B 94.231 260 14 1 2 261 112836701 112836443 2.050000e-106 396.0
15 TraesCS6B01G354400 chr3B 93.680 269 10 3 2 263 576048424 576048156 2.050000e-106 396.0
16 TraesCS6B01G354400 chr1B 86.702 188 23 2 1235 1421 641602374 641602560 1.030000e-49 207.0
17 TraesCS6B01G354400 chr4B 85.638 188 25 2 1235 1421 28267988 28268174 2.230000e-46 196.0


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 TraesCS6B01G354400 chr6B 620264033 620266871 2838 True 5243.00 5243 100.000 1 2839 1 chr6B.!!$R1 2838
1 TraesCS6B01G354400 chr6D 412000141 412002455 2314 True 3107.00 3107 90.921 513 2839 1 chr6D.!!$R1 2326
2 TraesCS6B01G354400 chr6A 557093198 557095787 2589 True 830.75 1245 90.588 257 2839 4 chr6A.!!$R1 2582

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
202 203 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.0 4.96 0.0 31.08 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2046 0.820226 GCCAGGAAATCCAAAGAGGC 59.18 55.0 1.67 3.6 38.89 4.7 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
19 20 2.024176 CGGTTGAGATGGTTAGGTGG 57.976 55.000 0.00 0.00 0.00 4.61
20 21 1.553248 CGGTTGAGATGGTTAGGTGGA 59.447 52.381 0.00 0.00 0.00 4.02
21 22 2.170607 CGGTTGAGATGGTTAGGTGGAT 59.829 50.000 0.00 0.00 0.00 3.41
22 23 3.386726 CGGTTGAGATGGTTAGGTGGATA 59.613 47.826 0.00 0.00 0.00 2.59
23 24 4.501571 CGGTTGAGATGGTTAGGTGGATAG 60.502 50.000 0.00 0.00 0.00 2.08
24 25 4.409247 GGTTGAGATGGTTAGGTGGATAGT 59.591 45.833 0.00 0.00 0.00 2.12
25 26 5.360591 GTTGAGATGGTTAGGTGGATAGTG 58.639 45.833 0.00 0.00 0.00 2.74
26 27 3.967326 TGAGATGGTTAGGTGGATAGTGG 59.033 47.826 0.00 0.00 0.00 4.00
27 28 3.967987 GAGATGGTTAGGTGGATAGTGGT 59.032 47.826 0.00 0.00 0.00 4.16
28 29 5.145564 GAGATGGTTAGGTGGATAGTGGTA 58.854 45.833 0.00 0.00 0.00 3.25
29 30 5.727630 AGATGGTTAGGTGGATAGTGGTAT 58.272 41.667 0.00 0.00 0.00 2.73
30 31 5.780793 AGATGGTTAGGTGGATAGTGGTATC 59.219 44.000 0.00 0.00 35.19 2.24
41 42 3.844063 TGGTATCCCCAACCCACC 58.156 61.111 0.00 0.00 41.50 4.61
42 43 1.151565 TGGTATCCCCAACCCACCA 60.152 57.895 0.00 0.00 41.50 4.17
43 44 1.211567 TGGTATCCCCAACCCACCAG 61.212 60.000 0.00 0.00 41.50 4.00
44 45 1.613061 GTATCCCCAACCCACCAGG 59.387 63.158 0.00 0.00 43.78 4.45
60 61 3.363787 AGGGTTCAAATCCTGGTGC 57.636 52.632 0.00 0.00 38.36 5.01
61 62 0.779997 AGGGTTCAAATCCTGGTGCT 59.220 50.000 0.00 0.00 38.36 4.40
62 63 1.177401 GGGTTCAAATCCTGGTGCTC 58.823 55.000 0.00 0.00 0.00 4.26
63 64 0.804989 GGTTCAAATCCTGGTGCTCG 59.195 55.000 0.00 0.00 0.00 5.03
64 65 0.169009 GTTCAAATCCTGGTGCTCGC 59.831 55.000 0.00 0.00 0.00 5.03
65 66 0.250684 TTCAAATCCTGGTGCTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
66 67 0.035152 TCAAATCCTGGTGCTCGCAT 60.035 50.000 0.00 0.00 0.00 4.73
67 68 0.813184 CAAATCCTGGTGCTCGCATT 59.187 50.000 0.00 0.00 0.00 3.56
68 69 2.016318 CAAATCCTGGTGCTCGCATTA 58.984 47.619 0.00 0.00 0.00 1.90
69 70 2.620115 CAAATCCTGGTGCTCGCATTAT 59.380 45.455 0.00 0.00 0.00 1.28
70 71 2.645838 ATCCTGGTGCTCGCATTATT 57.354 45.000 0.00 0.00 0.00 1.40
71 72 1.953559 TCCTGGTGCTCGCATTATTC 58.046 50.000 0.00 0.00 0.00 1.75
72 73 0.947244 CCTGGTGCTCGCATTATTCC 59.053 55.000 0.00 0.00 0.00 3.01
73 74 1.475751 CCTGGTGCTCGCATTATTCCT 60.476 52.381 0.00 0.00 0.00 3.36
74 75 1.600957 CTGGTGCTCGCATTATTCCTG 59.399 52.381 0.00 0.00 0.00 3.86
75 76 0.947244 GGTGCTCGCATTATTCCTGG 59.053 55.000 0.00 0.00 0.00 4.45
76 77 1.475034 GGTGCTCGCATTATTCCTGGA 60.475 52.381 0.00 0.00 0.00 3.86
77 78 2.498167 GTGCTCGCATTATTCCTGGAT 58.502 47.619 0.00 0.00 0.00 3.41
78 79 2.880890 GTGCTCGCATTATTCCTGGATT 59.119 45.455 0.00 0.00 0.00 3.01
79 80 3.316308 GTGCTCGCATTATTCCTGGATTT 59.684 43.478 0.00 0.00 0.00 2.17
80 81 4.515191 GTGCTCGCATTATTCCTGGATTTA 59.485 41.667 0.00 0.00 0.00 1.40
81 82 5.182001 GTGCTCGCATTATTCCTGGATTTAT 59.818 40.000 0.00 0.00 0.00 1.40
82 83 5.769662 TGCTCGCATTATTCCTGGATTTATT 59.230 36.000 0.00 0.00 0.00 1.40
83 84 6.265196 TGCTCGCATTATTCCTGGATTTATTT 59.735 34.615 0.00 0.00 0.00 1.40
84 85 6.803807 GCTCGCATTATTCCTGGATTTATTTC 59.196 38.462 0.00 0.00 0.00 2.17
85 86 7.522073 GCTCGCATTATTCCTGGATTTATTTCA 60.522 37.037 0.00 0.00 0.00 2.69
86 87 7.874940 TCGCATTATTCCTGGATTTATTTCAG 58.125 34.615 0.00 0.00 0.00 3.02
87 88 7.040478 TCGCATTATTCCTGGATTTATTTCAGG 60.040 37.037 0.00 0.00 46.91 3.86
95 96 6.076981 CTGGATTTATTTCAGGATTTCCGG 57.923 41.667 0.00 0.00 42.08 5.14
96 97 4.340950 TGGATTTATTTCAGGATTTCCGGC 59.659 41.667 0.00 0.00 42.08 6.13
97 98 4.537015 GATTTATTTCAGGATTTCCGGCG 58.463 43.478 0.00 0.00 42.08 6.46
98 99 2.992124 TATTTCAGGATTTCCGGCGA 57.008 45.000 9.30 0.00 42.08 5.54
99 100 2.348411 ATTTCAGGATTTCCGGCGAT 57.652 45.000 9.30 0.00 42.08 4.58
100 101 1.378531 TTTCAGGATTTCCGGCGATG 58.621 50.000 9.30 0.00 42.08 3.84
101 102 1.095228 TTCAGGATTTCCGGCGATGC 61.095 55.000 9.30 0.00 42.08 3.91
102 103 2.588877 AGGATTTCCGGCGATGCG 60.589 61.111 9.30 0.00 42.08 4.73
113 114 2.787249 CGATGCGCTTTCAGTGGG 59.213 61.111 9.73 0.00 0.00 4.61
114 115 1.741401 CGATGCGCTTTCAGTGGGA 60.741 57.895 9.73 0.00 0.00 4.37
115 116 1.699656 CGATGCGCTTTCAGTGGGAG 61.700 60.000 9.73 0.00 0.00 4.30
116 117 1.372087 GATGCGCTTTCAGTGGGAGG 61.372 60.000 9.73 0.00 0.00 4.30
117 118 1.841302 ATGCGCTTTCAGTGGGAGGA 61.841 55.000 9.73 0.00 0.00 3.71
118 119 1.743252 GCGCTTTCAGTGGGAGGAG 60.743 63.158 0.00 0.00 0.00 3.69
119 120 1.975327 CGCTTTCAGTGGGAGGAGA 59.025 57.895 0.00 0.00 0.00 3.71
120 121 0.390472 CGCTTTCAGTGGGAGGAGAC 60.390 60.000 0.00 0.00 0.00 3.36
121 122 0.390472 GCTTTCAGTGGGAGGAGACG 60.390 60.000 0.00 0.00 0.00 4.18
122 123 0.969894 CTTTCAGTGGGAGGAGACGT 59.030 55.000 0.00 0.00 0.00 4.34
123 124 1.344763 CTTTCAGTGGGAGGAGACGTT 59.655 52.381 0.00 0.00 0.00 3.99
124 125 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
147 148 4.883300 GACGACGAGGCGCCTACG 62.883 72.222 32.91 32.91 44.07 3.51
150 151 4.849329 GACGAGGCGCCTACGGTG 62.849 72.222 34.97 23.88 40.57 4.94
152 153 4.849329 CGAGGCGCCTACGGTGAC 62.849 72.222 32.97 14.51 42.50 3.67
155 156 2.508663 GGCGCCTACGGTGACTTC 60.509 66.667 22.15 0.00 38.38 3.01
156 157 2.879462 GCGCCTACGGTGACTTCG 60.879 66.667 0.00 0.00 40.57 3.79
157 158 2.564975 CGCCTACGGTGACTTCGT 59.435 61.111 0.00 0.00 43.64 3.85
158 159 1.796151 CGCCTACGGTGACTTCGTA 59.204 57.895 0.00 0.00 41.38 3.43
159 160 0.168788 CGCCTACGGTGACTTCGTAA 59.831 55.000 0.00 0.00 41.62 3.18
160 161 1.622232 GCCTACGGTGACTTCGTAAC 58.378 55.000 0.00 0.00 41.62 2.50
161 162 1.200948 GCCTACGGTGACTTCGTAACT 59.799 52.381 0.00 0.00 41.62 2.24
162 163 2.730402 GCCTACGGTGACTTCGTAACTC 60.730 54.545 0.00 0.00 41.62 3.01
163 164 2.746362 CCTACGGTGACTTCGTAACTCT 59.254 50.000 0.00 0.00 41.62 3.24
164 165 2.985406 ACGGTGACTTCGTAACTCTC 57.015 50.000 0.00 0.00 39.22 3.20
165 166 2.224606 ACGGTGACTTCGTAACTCTCA 58.775 47.619 0.00 0.00 39.22 3.27
166 167 2.620115 ACGGTGACTTCGTAACTCTCAA 59.380 45.455 0.00 0.00 39.22 3.02
167 168 3.235195 CGGTGACTTCGTAACTCTCAAG 58.765 50.000 0.00 0.00 0.00 3.02
168 169 3.058432 CGGTGACTTCGTAACTCTCAAGA 60.058 47.826 0.00 0.00 0.00 3.02
169 170 4.379603 CGGTGACTTCGTAACTCTCAAGAT 60.380 45.833 0.00 0.00 0.00 2.40
170 171 4.859798 GGTGACTTCGTAACTCTCAAGATG 59.140 45.833 0.00 0.00 0.00 2.90
171 172 5.335740 GGTGACTTCGTAACTCTCAAGATGA 60.336 44.000 0.00 0.00 0.00 2.92
172 173 6.326375 GTGACTTCGTAACTCTCAAGATGAT 58.674 40.000 0.00 0.00 0.00 2.45
173 174 7.415318 GGTGACTTCGTAACTCTCAAGATGATA 60.415 40.741 0.00 0.00 0.00 2.15
174 175 8.132362 GTGACTTCGTAACTCTCAAGATGATAT 58.868 37.037 0.00 0.00 0.00 1.63
175 176 8.131731 TGACTTCGTAACTCTCAAGATGATATG 58.868 37.037 0.00 0.00 0.00 1.78
176 177 6.920758 ACTTCGTAACTCTCAAGATGATATGC 59.079 38.462 0.00 0.00 0.00 3.14
177 178 5.773575 TCGTAACTCTCAAGATGATATGCC 58.226 41.667 0.00 0.00 0.00 4.40
178 179 4.618912 CGTAACTCTCAAGATGATATGCCG 59.381 45.833 0.00 0.00 0.00 5.69
179 180 3.674528 ACTCTCAAGATGATATGCCGG 57.325 47.619 0.00 0.00 0.00 6.13
180 181 2.289320 ACTCTCAAGATGATATGCCGGC 60.289 50.000 22.73 22.73 0.00 6.13
181 182 1.973515 TCTCAAGATGATATGCCGGCT 59.026 47.619 29.70 15.76 0.00 5.52
182 183 2.028658 TCTCAAGATGATATGCCGGCTC 60.029 50.000 29.70 17.89 0.00 4.70
183 184 1.693606 TCAAGATGATATGCCGGCTCA 59.306 47.619 29.70 23.34 0.00 4.26
184 185 2.074576 CAAGATGATATGCCGGCTCAG 58.925 52.381 29.70 7.35 0.00 3.35
185 186 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
186 187 1.274728 AGATGATATGCCGGCTCAGTC 59.725 52.381 29.70 19.55 0.00 3.51
187 188 1.274728 GATGATATGCCGGCTCAGTCT 59.725 52.381 29.70 8.26 0.00 3.24
188 189 0.676184 TGATATGCCGGCTCAGTCTC 59.324 55.000 29.70 15.31 0.00 3.36
189 190 0.965439 GATATGCCGGCTCAGTCTCT 59.035 55.000 29.70 3.16 0.00 3.10
190 191 0.965439 ATATGCCGGCTCAGTCTCTC 59.035 55.000 29.70 0.00 0.00 3.20
191 192 1.448119 TATGCCGGCTCAGTCTCTCG 61.448 60.000 29.70 0.00 0.00 4.04
192 193 4.200283 GCCGGCTCAGTCTCTCGG 62.200 72.222 22.15 0.00 43.13 4.63
193 194 2.438614 CCGGCTCAGTCTCTCGGA 60.439 66.667 0.00 0.00 42.94 4.55
194 195 2.477176 CCGGCTCAGTCTCTCGGAG 61.477 68.421 0.00 0.00 42.94 4.63
195 196 2.477176 CGGCTCAGTCTCTCGGAGG 61.477 68.421 4.96 0.00 38.48 4.30
196 197 1.379309 GGCTCAGTCTCTCGGAGGT 60.379 63.158 4.96 0.00 38.48 3.85
197 198 1.662438 GGCTCAGTCTCTCGGAGGTG 61.662 65.000 4.96 0.00 38.48 4.00
198 199 1.806568 CTCAGTCTCTCGGAGGTGC 59.193 63.158 4.96 0.00 35.32 5.01
199 200 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
200 201 0.678366 TCAGTCTCTCGGAGGTGCTC 60.678 60.000 4.96 0.00 0.00 4.26
201 202 0.962855 CAGTCTCTCGGAGGTGCTCA 60.963 60.000 4.96 0.00 31.08 4.26
202 203 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
203 204 1.213182 AGTCTCTCGGAGGTGCTCATA 59.787 52.381 4.96 0.00 31.08 2.15
204 205 1.606668 GTCTCTCGGAGGTGCTCATAG 59.393 57.143 4.96 0.00 31.08 2.23
205 206 0.958091 CTCTCGGAGGTGCTCATAGG 59.042 60.000 4.96 0.00 31.08 2.57
206 207 0.468214 TCTCGGAGGTGCTCATAGGG 60.468 60.000 4.96 0.00 31.08 3.53
207 208 1.457643 TCGGAGGTGCTCATAGGGG 60.458 63.158 0.00 0.00 31.08 4.79
208 209 1.762460 CGGAGGTGCTCATAGGGGT 60.762 63.158 0.00 0.00 31.08 4.95
209 210 1.832912 GGAGGTGCTCATAGGGGTG 59.167 63.158 0.00 0.00 31.08 4.61
210 211 0.691078 GGAGGTGCTCATAGGGGTGA 60.691 60.000 0.00 0.00 31.08 4.02
211 212 0.755686 GAGGTGCTCATAGGGGTGAG 59.244 60.000 0.00 0.00 46.59 3.51
212 213 0.043334 AGGTGCTCATAGGGGTGAGT 59.957 55.000 5.87 0.00 45.80 3.41
213 214 0.179000 GGTGCTCATAGGGGTGAGTG 59.821 60.000 5.87 0.00 45.80 3.51
214 215 0.905357 GTGCTCATAGGGGTGAGTGT 59.095 55.000 5.87 0.00 45.80 3.55
215 216 2.108168 GTGCTCATAGGGGTGAGTGTA 58.892 52.381 5.87 0.00 45.80 2.90
216 217 2.700897 GTGCTCATAGGGGTGAGTGTAT 59.299 50.000 5.87 0.00 45.80 2.29
217 218 2.700371 TGCTCATAGGGGTGAGTGTATG 59.300 50.000 5.87 0.00 45.80 2.39
218 219 2.548920 GCTCATAGGGGTGAGTGTATGC 60.549 54.545 5.87 0.00 45.80 3.14
219 220 1.686587 TCATAGGGGTGAGTGTATGCG 59.313 52.381 0.00 0.00 0.00 4.73
220 221 0.393077 ATAGGGGTGAGTGTATGCGC 59.607 55.000 0.00 0.00 0.00 6.09
221 222 2.011741 TAGGGGTGAGTGTATGCGCG 62.012 60.000 0.00 0.00 0.00 6.86
222 223 2.125673 GGGTGAGTGTATGCGCGT 60.126 61.111 8.43 7.55 0.00 6.01
223 224 2.452813 GGGTGAGTGTATGCGCGTG 61.453 63.158 13.61 0.00 0.00 5.34
224 225 1.736645 GGTGAGTGTATGCGCGTGT 60.737 57.895 13.61 0.00 0.00 4.49
225 226 0.457166 GGTGAGTGTATGCGCGTGTA 60.457 55.000 13.61 0.00 0.00 2.90
226 227 1.556564 GTGAGTGTATGCGCGTGTAT 58.443 50.000 13.61 4.63 0.00 2.29
227 228 2.542205 GGTGAGTGTATGCGCGTGTATA 60.542 50.000 13.61 2.40 0.00 1.47
228 229 3.305964 GTGAGTGTATGCGCGTGTATAT 58.694 45.455 13.61 0.00 0.00 0.86
229 230 3.119628 GTGAGTGTATGCGCGTGTATATG 59.880 47.826 13.61 0.00 0.00 1.78
230 231 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
231 232 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
232 233 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
235 236 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
236 237 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
237 238 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
238 239 1.209128 GCGTGTATATGAGCGCTTGT 58.791 50.000 13.26 5.98 45.48 3.16
239 240 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
240 241 2.193447 CGTGTATATGAGCGCTTGTGT 58.807 47.619 13.26 4.27 0.00 3.72
241 242 2.216488 CGTGTATATGAGCGCTTGTGTC 59.784 50.000 13.26 0.00 0.00 3.67
242 243 3.448686 GTGTATATGAGCGCTTGTGTCT 58.551 45.455 13.26 0.00 0.00 3.41
243 244 3.243877 GTGTATATGAGCGCTTGTGTCTG 59.756 47.826 13.26 0.00 0.00 3.51
244 245 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
245 246 3.801114 ATATGAGCGCTTGTGTCTGTA 57.199 42.857 13.26 0.00 0.00 2.74
246 247 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
247 248 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
248 249 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
249 250 0.673985 AGCGCTTGTGTCTGTACTGA 59.326 50.000 2.64 0.00 0.00 3.41
250 251 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
251 252 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
252 253 1.391485 CGCTTGTGTCTGTACTGATGC 59.609 52.381 5.69 3.20 0.00 3.91
253 254 2.693069 GCTTGTGTCTGTACTGATGCT 58.307 47.619 5.69 0.00 0.00 3.79
254 255 3.673323 CGCTTGTGTCTGTACTGATGCTA 60.673 47.826 5.69 0.00 0.00 3.49
255 256 4.245660 GCTTGTGTCTGTACTGATGCTAA 58.754 43.478 5.69 0.07 0.00 3.09
318 319 6.012745 AGATGGGTAAATTAATGGCAGGATC 58.987 40.000 0.00 0.00 0.00 3.36
373 374 7.745620 ATATGGAAAGATTAATCACGGGAAC 57.254 36.000 17.56 2.19 0.00 3.62
375 376 5.505780 TGGAAAGATTAATCACGGGAACAT 58.494 37.500 17.56 0.00 0.00 2.71
376 377 6.654959 TGGAAAGATTAATCACGGGAACATA 58.345 36.000 17.56 0.00 0.00 2.29
377 378 6.765989 TGGAAAGATTAATCACGGGAACATAG 59.234 38.462 17.56 0.00 0.00 2.23
415 422 2.255430 TGCATCGCATGTGCAGAAA 58.745 47.368 5.43 0.00 46.76 2.52
416 423 0.597072 TGCATCGCATGTGCAGAAAA 59.403 45.000 5.43 0.00 46.76 2.29
423 430 4.864633 TCGCATGTGCAGAAAATAACAAA 58.135 34.783 0.00 0.00 42.21 2.83
425 432 5.174761 TCGCATGTGCAGAAAATAACAAAAC 59.825 36.000 0.00 0.00 42.21 2.43
430 437 7.066374 TGTGCAGAAAATAACAAAACCAAAC 57.934 32.000 0.00 0.00 0.00 2.93
435 442 7.480229 GCAGAAAATAACAAAACCAAACAACAC 59.520 33.333 0.00 0.00 0.00 3.32
439 446 6.820470 ATAACAAAACCAAACAACACGATG 57.180 33.333 0.00 0.00 0.00 3.84
441 448 3.186119 CAAAACCAAACAACACGATGCT 58.814 40.909 0.00 0.00 0.00 3.79
504 511 1.496934 CAAACCACGCCACCAAAATC 58.503 50.000 0.00 0.00 0.00 2.17
509 516 0.958091 CACGCCACCAAAATCTCCAA 59.042 50.000 0.00 0.00 0.00 3.53
541 589 3.381949 CCACATTTAAAACGGCCGAAAA 58.618 40.909 35.90 24.16 0.00 2.29
691 744 1.383799 CCATCTGGCAAGGACCCAA 59.616 57.895 0.00 0.00 30.66 4.12
693 746 0.251297 CATCTGGCAAGGACCCAACA 60.251 55.000 0.00 0.00 30.66 3.33
697 750 3.365265 GCAAGGACCCAACAGCCG 61.365 66.667 0.00 0.00 0.00 5.52
700 753 2.448582 AAGGACCCAACAGCCGTGA 61.449 57.895 0.00 0.00 0.00 4.35
701 754 2.358737 GGACCCAACAGCCGTGAG 60.359 66.667 0.00 0.00 0.00 3.51
702 755 2.741092 GACCCAACAGCCGTGAGA 59.259 61.111 0.00 0.00 0.00 3.27
760 813 0.335019 AGGAATAAAGCCACCACCCC 59.665 55.000 0.00 0.00 0.00 4.95
761 814 1.035385 GGAATAAAGCCACCACCCCG 61.035 60.000 0.00 0.00 0.00 5.73
829 884 0.302890 GCAACTTCGCGATCATCAGG 59.697 55.000 10.88 0.00 0.00 3.86
846 901 2.307392 TCAGGGGCTATTTTGCTGTACA 59.693 45.455 0.00 0.00 0.00 2.90
878 933 3.340034 CAACCACCTTAAATACCGCTGA 58.660 45.455 0.00 0.00 0.00 4.26
911 969 5.717119 ATCCTTAACCCAGAAATAGCACT 57.283 39.130 0.00 0.00 0.00 4.40
912 970 4.843728 TCCTTAACCCAGAAATAGCACTG 58.156 43.478 0.00 0.00 0.00 3.66
913 971 3.378427 CCTTAACCCAGAAATAGCACTGC 59.622 47.826 0.00 0.00 33.40 4.40
914 972 2.887151 AACCCAGAAATAGCACTGCT 57.113 45.000 8.95 8.95 43.41 4.24
929 987 1.881973 ACTGCTGCACATTGGTTAGTG 59.118 47.619 0.00 0.00 38.74 2.74
996 1066 0.671796 TTCGTCCAGAAACTCTCGCA 59.328 50.000 0.00 0.00 35.61 5.10
1186 1256 1.065358 CACCGGTTCACGTATGTGTC 58.935 55.000 2.97 9.17 46.49 3.67
1187 1257 0.037975 ACCGGTTCACGTATGTGTCC 60.038 55.000 14.63 15.68 46.49 4.02
1188 1258 0.038067 CCGGTTCACGTATGTGTCCA 60.038 55.000 21.93 6.58 46.49 4.02
1189 1259 1.346365 CGGTTCACGTATGTGTCCAG 58.654 55.000 21.93 14.86 46.49 3.86
1190 1260 1.068125 CGGTTCACGTATGTGTCCAGA 60.068 52.381 21.93 2.25 46.49 3.86
1194 1264 1.816835 TCACGTATGTGTCCAGACTCC 59.183 52.381 14.63 0.00 46.49 3.85
1226 1301 2.698274 TCCTCTGTTCTGTTGTGTAGCA 59.302 45.455 0.00 0.00 0.00 3.49
1252 1327 4.806330 TCGACTCTTTTCTGTTTCGCTAT 58.194 39.130 0.00 0.00 0.00 2.97
1290 1365 3.054276 TCGTTTGTGTTTTTACCTGCG 57.946 42.857 0.00 0.00 0.00 5.18
1418 1493 3.654273 AGTCCAAGCAGGTAATAGCCTA 58.346 45.455 0.00 0.00 37.04 3.93
1510 1623 5.465051 TGTGCTGCTAATTAGAGATCGATC 58.535 41.667 17.91 17.91 0.00 3.69
1693 1806 8.427276 TGTCGAGTAAACTATGAGGATCTAGTA 58.573 37.037 0.00 0.00 31.78 1.82
1694 1807 9.270640 GTCGAGTAAACTATGAGGATCTAGTAA 57.729 37.037 0.00 0.00 31.78 2.24
1867 1980 2.158696 ACTTCTGGAATGATGGGCTAGC 60.159 50.000 6.04 6.04 0.00 3.42
1892 2005 0.107643 TGTTCATTGGTCCGTCAGCA 59.892 50.000 0.00 0.00 0.00 4.41
1936 2050 9.732130 ATTTAAGAGGATAGTGATATTTGCCTC 57.268 33.333 0.00 0.00 40.48 4.70
1940 2054 7.222872 AGAGGATAGTGATATTTGCCTCTTTG 58.777 38.462 0.00 0.00 46.23 2.77
1942 2056 6.101734 AGGATAGTGATATTTGCCTCTTTGGA 59.898 38.462 0.00 0.00 38.35 3.53
1943 2057 6.944862 GGATAGTGATATTTGCCTCTTTGGAT 59.055 38.462 0.00 0.00 38.35 3.41
1949 2063 4.813750 ATTTGCCTCTTTGGATTTCCTG 57.186 40.909 0.00 0.00 38.35 3.86
1983 2097 5.070770 AGTGCAAATTCAGTGTGTTTTCA 57.929 34.783 0.00 0.00 0.00 2.69
2066 2180 3.838244 TGCCTACAGACTTGTTCAGTT 57.162 42.857 0.00 0.00 38.76 3.16
2069 2183 3.877508 GCCTACAGACTTGTTCAGTTGTT 59.122 43.478 0.00 0.00 38.76 2.83
2070 2184 4.335594 GCCTACAGACTTGTTCAGTTGTTT 59.664 41.667 0.00 0.00 38.76 2.83
2103 2217 0.913934 TGAATGACTAGGCAGGCCCA 60.914 55.000 3.72 0.00 36.58 5.36
2105 2219 1.926426 AATGACTAGGCAGGCCCACC 61.926 60.000 3.72 0.00 36.58 4.61
2106 2220 3.009115 GACTAGGCAGGCCCACCA 61.009 66.667 13.90 0.00 39.06 4.17
2116 2230 1.001181 CAGGCCCACCAAAGTTGAATG 59.999 52.381 0.00 0.00 39.06 2.67
2203 2318 1.888512 GCTTCTCAATGAAACCCAGCA 59.111 47.619 0.00 0.00 33.79 4.41
2239 2355 6.037172 CCTGTTAGTTGGCAGTTGATGTATAC 59.963 42.308 0.00 0.00 0.00 1.47
2264 2380 2.225019 CAGAATGATCGGGCATAAGCAC 59.775 50.000 0.00 0.00 40.48 4.40
2283 2399 3.100671 CACCTACTGCTAGGAAGGTCTT 58.899 50.000 4.72 0.00 42.34 3.01
2310 2426 6.916909 TGGAATATCCAGGCCTGTATTTTTA 58.083 36.000 30.63 14.92 42.67 1.52
2313 2430 9.700831 GGAATATCCAGGCCTGTATTTTTATAT 57.299 33.333 30.63 16.70 36.28 0.86
2395 2514 7.524294 ACAAATAGCTAAATTTCAAATGGCG 57.476 32.000 0.00 0.00 0.00 5.69
2444 2563 4.640201 TCAACATTTTACTCCATGCTAGCC 59.360 41.667 13.29 0.00 0.00 3.93
2514 2633 4.952335 AGATGGAATGACATTTCTGGAACC 59.048 41.667 7.96 1.03 0.00 3.62
2516 2635 3.075882 TGGAATGACATTTCTGGAACCCT 59.924 43.478 7.96 0.00 0.00 4.34
2544 2663 3.795688 AATGGAAGCAGTTTCTGGAGA 57.204 42.857 0.00 0.00 36.03 3.71
2816 2935 9.896645 AGCAAGATAGATGTTAAATCTCTTCAA 57.103 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.553248 TCCACCTAACCATCTCAACCG 59.447 52.381 0.00 0.00 0.00 4.44
1 2 3.933861 ATCCACCTAACCATCTCAACC 57.066 47.619 0.00 0.00 0.00 3.77
2 3 5.360591 CACTATCCACCTAACCATCTCAAC 58.639 45.833 0.00 0.00 0.00 3.18
3 4 4.408921 CCACTATCCACCTAACCATCTCAA 59.591 45.833 0.00 0.00 0.00 3.02
4 5 3.967326 CCACTATCCACCTAACCATCTCA 59.033 47.826 0.00 0.00 0.00 3.27
5 6 3.967987 ACCACTATCCACCTAACCATCTC 59.032 47.826 0.00 0.00 0.00 2.75
6 7 4.008916 ACCACTATCCACCTAACCATCT 57.991 45.455 0.00 0.00 0.00 2.90
7 8 5.046520 GGATACCACTATCCACCTAACCATC 60.047 48.000 2.40 0.00 45.82 3.51
8 9 4.844655 GGATACCACTATCCACCTAACCAT 59.155 45.833 2.40 0.00 45.82 3.55
9 10 4.228824 GGATACCACTATCCACCTAACCA 58.771 47.826 2.40 0.00 45.82 3.67
10 11 4.886496 GGATACCACTATCCACCTAACC 57.114 50.000 2.40 0.00 45.82 2.85
26 27 1.613061 CCTGGTGGGTTGGGGATAC 59.387 63.158 0.00 0.00 0.00 2.24
27 28 4.179896 CCTGGTGGGTTGGGGATA 57.820 61.111 0.00 0.00 0.00 2.59
37 38 1.549203 CAGGATTTGAACCCTGGTGG 58.451 55.000 0.00 0.00 44.68 4.61
42 43 0.779997 AGCACCAGGATTTGAACCCT 59.220 50.000 0.00 0.00 0.00 4.34
43 44 1.177401 GAGCACCAGGATTTGAACCC 58.823 55.000 0.00 0.00 0.00 4.11
44 45 0.804989 CGAGCACCAGGATTTGAACC 59.195 55.000 0.00 0.00 0.00 3.62
45 46 0.169009 GCGAGCACCAGGATTTGAAC 59.831 55.000 0.00 0.00 0.00 3.18
46 47 0.250684 TGCGAGCACCAGGATTTGAA 60.251 50.000 0.00 0.00 0.00 2.69
47 48 0.035152 ATGCGAGCACCAGGATTTGA 60.035 50.000 0.00 0.00 0.00 2.69
48 49 0.813184 AATGCGAGCACCAGGATTTG 59.187 50.000 0.00 0.00 0.00 2.32
49 50 2.418368 TAATGCGAGCACCAGGATTT 57.582 45.000 0.00 0.00 31.11 2.17
50 51 2.645838 ATAATGCGAGCACCAGGATT 57.354 45.000 0.00 0.00 33.17 3.01
51 52 2.498167 GAATAATGCGAGCACCAGGAT 58.502 47.619 0.00 0.00 0.00 3.24
52 53 1.475034 GGAATAATGCGAGCACCAGGA 60.475 52.381 0.00 0.00 0.00 3.86
53 54 0.947244 GGAATAATGCGAGCACCAGG 59.053 55.000 0.00 0.00 0.00 4.45
54 55 1.600957 CAGGAATAATGCGAGCACCAG 59.399 52.381 0.00 0.00 0.00 4.00
55 56 1.667236 CAGGAATAATGCGAGCACCA 58.333 50.000 0.00 0.00 0.00 4.17
56 57 0.947244 CCAGGAATAATGCGAGCACC 59.053 55.000 0.00 0.00 0.00 5.01
57 58 1.953559 TCCAGGAATAATGCGAGCAC 58.046 50.000 0.00 0.00 0.00 4.40
58 59 2.936919 ATCCAGGAATAATGCGAGCA 57.063 45.000 0.00 0.00 0.00 4.26
59 60 5.886960 ATAAATCCAGGAATAATGCGAGC 57.113 39.130 0.00 0.00 0.00 5.03
60 61 7.874940 TGAAATAAATCCAGGAATAATGCGAG 58.125 34.615 0.00 0.00 0.00 5.03
61 62 7.815840 TGAAATAAATCCAGGAATAATGCGA 57.184 32.000 0.00 0.00 0.00 5.10
71 72 5.010012 CCGGAAATCCTGAAATAAATCCAGG 59.990 44.000 0.00 0.00 46.64 4.45
72 73 5.507985 GCCGGAAATCCTGAAATAAATCCAG 60.508 44.000 5.05 0.00 0.00 3.86
73 74 4.340950 GCCGGAAATCCTGAAATAAATCCA 59.659 41.667 5.05 0.00 0.00 3.41
74 75 4.556699 CGCCGGAAATCCTGAAATAAATCC 60.557 45.833 5.05 0.00 0.00 3.01
75 76 4.274950 TCGCCGGAAATCCTGAAATAAATC 59.725 41.667 5.05 0.00 0.00 2.17
76 77 4.204012 TCGCCGGAAATCCTGAAATAAAT 58.796 39.130 5.05 0.00 0.00 1.40
77 78 3.611970 TCGCCGGAAATCCTGAAATAAA 58.388 40.909 5.05 0.00 0.00 1.40
78 79 3.269538 TCGCCGGAAATCCTGAAATAA 57.730 42.857 5.05 0.00 0.00 1.40
79 80 2.992124 TCGCCGGAAATCCTGAAATA 57.008 45.000 5.05 0.00 0.00 1.40
80 81 1.949525 CATCGCCGGAAATCCTGAAAT 59.050 47.619 5.05 0.00 0.00 2.17
81 82 1.378531 CATCGCCGGAAATCCTGAAA 58.621 50.000 5.05 0.00 0.00 2.69
82 83 1.095228 GCATCGCCGGAAATCCTGAA 61.095 55.000 5.05 0.00 0.00 3.02
83 84 1.523711 GCATCGCCGGAAATCCTGA 60.524 57.895 5.05 0.00 0.00 3.86
84 85 2.885676 CGCATCGCCGGAAATCCTG 61.886 63.158 5.05 0.00 0.00 3.86
85 86 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
96 97 1.699656 CTCCCACTGAAAGCGCATCG 61.700 60.000 11.47 6.82 37.60 3.84
97 98 1.372087 CCTCCCACTGAAAGCGCATC 61.372 60.000 11.47 8.39 37.60 3.91
98 99 1.377725 CCTCCCACTGAAAGCGCAT 60.378 57.895 11.47 0.00 37.60 4.73
99 100 2.032528 CCTCCCACTGAAAGCGCA 59.967 61.111 11.47 0.00 37.60 6.09
100 101 1.743252 CTCCTCCCACTGAAAGCGC 60.743 63.158 0.00 0.00 37.60 5.92
101 102 0.390472 GTCTCCTCCCACTGAAAGCG 60.390 60.000 0.00 0.00 37.60 4.68
102 103 0.390472 CGTCTCCTCCCACTGAAAGC 60.390 60.000 0.00 0.00 37.60 3.51
103 104 0.969894 ACGTCTCCTCCCACTGAAAG 59.030 55.000 0.00 0.00 42.29 2.62
104 105 1.343465 GAACGTCTCCTCCCACTGAAA 59.657 52.381 0.00 0.00 0.00 2.69
105 106 0.966920 GAACGTCTCCTCCCACTGAA 59.033 55.000 0.00 0.00 0.00 3.02
106 107 0.898789 GGAACGTCTCCTCCCACTGA 60.899 60.000 8.87 0.00 41.61 3.41
107 108 1.592223 GGAACGTCTCCTCCCACTG 59.408 63.158 8.87 0.00 41.61 3.66
108 109 4.115270 GGAACGTCTCCTCCCACT 57.885 61.111 8.87 0.00 41.61 4.00
129 130 4.883300 GTAGGCGCCTCGTCGTCG 62.883 72.222 36.73 0.00 39.34 5.12
130 131 4.883300 CGTAGGCGCCTCGTCGTC 62.883 72.222 36.73 15.88 36.23 4.20
143 144 3.434641 TGAGAGTTACGAAGTCACCGTAG 59.565 47.826 0.00 0.00 43.93 3.51
144 145 3.402110 TGAGAGTTACGAAGTCACCGTA 58.598 45.455 0.00 0.00 43.93 4.02
145 146 2.224606 TGAGAGTTACGAAGTCACCGT 58.775 47.619 0.00 0.00 43.93 4.83
146 147 2.983402 TGAGAGTTACGAAGTCACCG 57.017 50.000 0.00 0.00 43.93 4.94
147 148 4.500603 TCTTGAGAGTTACGAAGTCACC 57.499 45.455 0.00 0.00 43.93 4.02
148 149 5.700846 TCATCTTGAGAGTTACGAAGTCAC 58.299 41.667 0.00 0.00 43.93 3.67
149 150 5.959618 TCATCTTGAGAGTTACGAAGTCA 57.040 39.130 0.00 0.00 43.93 3.41
150 151 7.114247 GCATATCATCTTGAGAGTTACGAAGTC 59.886 40.741 0.00 0.00 43.93 3.01
152 153 6.364706 GGCATATCATCTTGAGAGTTACGAAG 59.635 42.308 0.00 0.00 0.00 3.79
153 154 6.216569 GGCATATCATCTTGAGAGTTACGAA 58.783 40.000 0.00 0.00 0.00 3.85
154 155 5.562890 CGGCATATCATCTTGAGAGTTACGA 60.563 44.000 0.00 0.00 0.00 3.43
155 156 4.618912 CGGCATATCATCTTGAGAGTTACG 59.381 45.833 0.00 0.00 0.00 3.18
156 157 4.926238 CCGGCATATCATCTTGAGAGTTAC 59.074 45.833 0.00 0.00 0.00 2.50
157 158 4.561530 GCCGGCATATCATCTTGAGAGTTA 60.562 45.833 24.80 0.00 0.00 2.24
158 159 3.805108 GCCGGCATATCATCTTGAGAGTT 60.805 47.826 24.80 0.00 0.00 3.01
159 160 2.289320 GCCGGCATATCATCTTGAGAGT 60.289 50.000 24.80 0.00 0.00 3.24
160 161 2.028294 AGCCGGCATATCATCTTGAGAG 60.028 50.000 31.54 0.00 0.00 3.20
161 162 1.973515 AGCCGGCATATCATCTTGAGA 59.026 47.619 31.54 0.00 0.00 3.27
162 163 2.289257 TGAGCCGGCATATCATCTTGAG 60.289 50.000 31.54 0.00 0.00 3.02
163 164 1.693606 TGAGCCGGCATATCATCTTGA 59.306 47.619 31.54 0.00 0.00 3.02
164 165 2.074576 CTGAGCCGGCATATCATCTTG 58.925 52.381 31.54 7.95 0.00 3.02
165 166 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
166 167 1.274728 GACTGAGCCGGCATATCATCT 59.725 52.381 31.54 11.40 0.00 2.90
167 168 1.274728 AGACTGAGCCGGCATATCATC 59.725 52.381 31.54 19.98 0.00 2.92
168 169 1.274728 GAGACTGAGCCGGCATATCAT 59.725 52.381 31.54 13.17 0.00 2.45
169 170 0.676184 GAGACTGAGCCGGCATATCA 59.324 55.000 31.54 22.44 0.00 2.15
170 171 0.965439 AGAGACTGAGCCGGCATATC 59.035 55.000 31.54 18.63 0.00 1.63
171 172 0.965439 GAGAGACTGAGCCGGCATAT 59.035 55.000 31.54 8.11 0.00 1.78
172 173 1.448119 CGAGAGACTGAGCCGGCATA 61.448 60.000 31.54 16.21 0.00 3.14
173 174 2.780094 CGAGAGACTGAGCCGGCAT 61.780 63.158 31.54 14.28 0.00 4.40
174 175 3.443925 CGAGAGACTGAGCCGGCA 61.444 66.667 31.54 7.98 0.00 5.69
175 176 4.200283 CCGAGAGACTGAGCCGGC 62.200 72.222 21.89 21.89 33.47 6.13
176 177 2.438614 TCCGAGAGACTGAGCCGG 60.439 66.667 0.00 0.00 41.36 6.13
177 178 2.477176 CCTCCGAGAGACTGAGCCG 61.477 68.421 0.00 0.00 0.00 5.52
178 179 1.379309 ACCTCCGAGAGACTGAGCC 60.379 63.158 0.00 0.00 0.00 4.70
179 180 1.806568 CACCTCCGAGAGACTGAGC 59.193 63.158 0.00 0.00 0.00 4.26
180 181 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
181 182 0.678366 GAGCACCTCCGAGAGACTGA 60.678 60.000 0.00 0.00 0.00 3.41
182 183 0.962855 TGAGCACCTCCGAGAGACTG 60.963 60.000 0.00 0.22 0.00 3.51
183 184 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.000 0.00 0.00 0.00 3.24
184 185 1.606668 CTATGAGCACCTCCGAGAGAC 59.393 57.143 0.00 0.00 0.00 3.36
185 186 1.477740 CCTATGAGCACCTCCGAGAGA 60.478 57.143 0.00 0.00 0.00 3.10
186 187 0.958091 CCTATGAGCACCTCCGAGAG 59.042 60.000 0.00 0.00 0.00 3.20
187 188 0.468214 CCCTATGAGCACCTCCGAGA 60.468 60.000 0.00 0.00 0.00 4.04
188 189 1.467678 CCCCTATGAGCACCTCCGAG 61.468 65.000 0.00 0.00 0.00 4.63
189 190 1.457643 CCCCTATGAGCACCTCCGA 60.458 63.158 0.00 0.00 0.00 4.55
190 191 1.762460 ACCCCTATGAGCACCTCCG 60.762 63.158 0.00 0.00 0.00 4.63
191 192 0.691078 TCACCCCTATGAGCACCTCC 60.691 60.000 0.00 0.00 0.00 4.30
192 193 0.755686 CTCACCCCTATGAGCACCTC 59.244 60.000 0.00 0.00 39.77 3.85
193 194 2.922162 CTCACCCCTATGAGCACCT 58.078 57.895 0.00 0.00 39.77 4.00
199 200 1.686587 CGCATACACTCACCCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
200 201 1.873903 GCGCATACACTCACCCCTATG 60.874 57.143 0.30 0.00 0.00 2.23
201 202 0.393077 GCGCATACACTCACCCCTAT 59.607 55.000 0.30 0.00 0.00 2.57
202 203 1.820581 GCGCATACACTCACCCCTA 59.179 57.895 0.30 0.00 0.00 3.53
203 204 2.584608 GCGCATACACTCACCCCT 59.415 61.111 0.30 0.00 0.00 4.79
204 205 2.890474 CGCGCATACACTCACCCC 60.890 66.667 8.75 0.00 0.00 4.95
205 206 2.125673 ACGCGCATACACTCACCC 60.126 61.111 5.73 0.00 0.00 4.61
206 207 0.457166 TACACGCGCATACACTCACC 60.457 55.000 5.73 0.00 0.00 4.02
207 208 1.556564 ATACACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
208 209 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
209 210 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
210 211 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
211 212 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
212 213 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
213 214 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
214 215 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
215 216 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
216 217 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
220 221 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
221 222 3.243877 CAGACACAAGCGCTCATATACAC 59.756 47.826 12.06 0.00 0.00 2.90
222 223 3.119137 ACAGACACAAGCGCTCATATACA 60.119 43.478 12.06 0.00 0.00 2.29
223 224 3.448686 ACAGACACAAGCGCTCATATAC 58.551 45.455 12.06 1.00 0.00 1.47
224 225 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
225 226 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
226 227 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
227 228 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
228 229 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
229 230 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
230 231 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
231 232 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
232 233 1.391485 GCATCAGTACAGACACAAGCG 59.609 52.381 0.00 0.00 0.00 4.68
233 234 2.693069 AGCATCAGTACAGACACAAGC 58.307 47.619 0.00 0.00 0.00 4.01
234 235 6.785488 TTTTAGCATCAGTACAGACACAAG 57.215 37.500 0.00 0.00 0.00 3.16
412 419 7.730778 TCGTGTTGTTTGGTTTTGTTATTTTC 58.269 30.769 0.00 0.00 0.00 2.29
413 420 7.653767 TCGTGTTGTTTGGTTTTGTTATTTT 57.346 28.000 0.00 0.00 0.00 1.82
415 422 6.237969 GCATCGTGTTGTTTGGTTTTGTTATT 60.238 34.615 0.00 0.00 0.00 1.40
416 423 5.233263 GCATCGTGTTGTTTGGTTTTGTTAT 59.767 36.000 0.00 0.00 0.00 1.89
423 430 1.336755 GGAGCATCGTGTTGTTTGGTT 59.663 47.619 0.00 0.00 34.37 3.67
425 432 0.110238 CGGAGCATCGTGTTGTTTGG 60.110 55.000 0.00 0.00 34.37 3.28
453 460 1.304254 CTTTTTGCAAAAACCGGGGG 58.696 50.000 28.85 16.61 34.46 5.40
504 511 1.270625 TGTGGCGTAGAGGTTTTGGAG 60.271 52.381 0.00 0.00 0.00 3.86
509 516 5.561339 CGTTTTAAATGTGGCGTAGAGGTTT 60.561 40.000 0.00 0.00 0.00 3.27
562 613 2.158726 AGTAAAACTCCGGCTGGAAACA 60.159 45.455 16.91 0.00 45.87 2.83
691 744 2.341846 TTCCTTTTTCTCACGGCTGT 57.658 45.000 0.00 0.00 0.00 4.40
693 746 3.208747 TCTTTCCTTTTTCTCACGGCT 57.791 42.857 0.00 0.00 0.00 5.52
697 750 7.175641 TCTGATGGATTCTTTCCTTTTTCTCAC 59.824 37.037 0.00 0.00 45.68 3.51
700 753 6.152492 GCTCTGATGGATTCTTTCCTTTTTCT 59.848 38.462 0.00 0.00 45.68 2.52
701 754 6.071728 TGCTCTGATGGATTCTTTCCTTTTTC 60.072 38.462 0.00 0.00 45.68 2.29
702 755 5.776716 TGCTCTGATGGATTCTTTCCTTTTT 59.223 36.000 0.00 0.00 45.68 1.94
774 828 5.906838 GCTTTTGGTTTTATTCGCCTTTTTG 59.093 36.000 0.00 0.00 0.00 2.44
829 884 2.442413 TGGTGTACAGCAAAATAGCCC 58.558 47.619 24.69 5.12 35.69 5.19
846 901 1.084018 AGGTGGTTGGATTGGATGGT 58.916 50.000 0.00 0.00 0.00 3.55
878 933 2.466846 GGTTAAGGATTGTGCCCCAAT 58.533 47.619 0.00 0.00 46.51 3.16
929 987 1.904990 GAGGTGTTGGGAGAGGAGGC 61.905 65.000 0.00 0.00 0.00 4.70
1104 1174 1.690893 AGGACGTGGATGAGGATGATG 59.309 52.381 0.00 0.00 0.00 3.07
1155 1225 1.831652 AACCGGTGCTCTTCCAGAGG 61.832 60.000 8.52 0.00 42.54 3.69
1186 1256 2.093764 GGATTCAGTGTCTGGAGTCTGG 60.094 54.545 0.00 0.00 31.51 3.86
1187 1257 2.830923 AGGATTCAGTGTCTGGAGTCTG 59.169 50.000 0.00 0.00 31.51 3.51
1188 1258 3.096092 GAGGATTCAGTGTCTGGAGTCT 58.904 50.000 0.00 0.00 31.51 3.24
1189 1259 3.096092 AGAGGATTCAGTGTCTGGAGTC 58.904 50.000 0.00 0.00 31.51 3.36
1190 1260 2.830923 CAGAGGATTCAGTGTCTGGAGT 59.169 50.000 0.77 0.00 34.06 3.85
1194 1264 4.244066 CAGAACAGAGGATTCAGTGTCTG 58.756 47.826 6.23 6.23 41.88 3.51
1226 1301 3.797256 CGAAACAGAAAAGAGTCGAGTGT 59.203 43.478 0.00 0.00 0.00 3.55
1232 1307 6.654793 ATCATAGCGAAACAGAAAAGAGTC 57.345 37.500 0.00 0.00 0.00 3.36
1252 1327 1.805943 CGATGGTGTCAGTTGCAATCA 59.194 47.619 0.59 0.00 0.00 2.57
1279 1354 2.806244 GAGCTTCAGTCGCAGGTAAAAA 59.194 45.455 0.00 0.00 0.00 1.94
1290 1365 2.101249 CAGAGGGATCAGAGCTTCAGTC 59.899 54.545 0.00 0.00 0.00 3.51
1359 1434 1.194781 TCTCCAGCACCTCCTTGTCC 61.195 60.000 0.00 0.00 0.00 4.02
1418 1493 7.394016 TGTATGGACAATTCAGTAGTTGATGT 58.606 34.615 0.00 0.00 32.95 3.06
1510 1623 1.272648 ACCTGATCCAACCAACATGGG 60.273 52.381 0.00 0.00 43.37 4.00
1693 1806 7.951347 ATGAGAAAACTCTGATTAGCCATTT 57.049 32.000 0.00 0.00 0.00 2.32
1694 1807 9.638176 AATATGAGAAAACTCTGATTAGCCATT 57.362 29.630 0.00 0.00 0.00 3.16
1814 1927 1.133025 GCAAGTGATCCATTTGGTCCG 59.867 52.381 0.00 0.00 32.85 4.79
1918 2031 6.299141 TCCAAAGAGGCAAATATCACTATCC 58.701 40.000 0.00 0.00 37.29 2.59
1932 2046 0.820226 GCCAGGAAATCCAAAGAGGC 59.180 55.000 1.67 3.60 38.89 4.70
1933 2047 2.521547 AGCCAGGAAATCCAAAGAGG 57.478 50.000 1.67 0.00 38.89 3.69
1935 2049 3.788142 AGGATAGCCAGGAAATCCAAAGA 59.212 43.478 18.41 0.00 41.44 2.52
1936 2050 4.176120 AGGATAGCCAGGAAATCCAAAG 57.824 45.455 18.41 0.00 41.44 2.77
1940 2054 3.584733 ACAAGGATAGCCAGGAAATCC 57.415 47.619 11.15 11.15 39.64 3.01
1942 2056 4.687219 GCACTACAAGGATAGCCAGGAAAT 60.687 45.833 0.00 0.00 36.29 2.17
1943 2057 3.370527 GCACTACAAGGATAGCCAGGAAA 60.371 47.826 0.00 0.00 36.29 3.13
1949 2063 4.640201 TGAATTTGCACTACAAGGATAGCC 59.360 41.667 0.00 0.00 40.06 3.93
2070 2184 8.609176 GCCTAGTCATTCACATAAACGAAAATA 58.391 33.333 0.00 0.00 0.00 1.40
2086 2200 1.609783 GTGGGCCTGCCTAGTCATT 59.390 57.895 4.53 0.00 36.10 2.57
2105 2219 8.190784 AGAAACTTGAGTAACCATTCAACTTTG 58.809 33.333 0.00 0.00 30.66 2.77
2106 2220 8.190784 CAGAAACTTGAGTAACCATTCAACTTT 58.809 33.333 0.00 0.00 30.66 2.66
2116 2230 5.057149 TGCTCTTCAGAAACTTGAGTAACC 58.943 41.667 0.00 0.00 0.00 2.85
2124 2238 7.716998 TCACTTTTAGATGCTCTTCAGAAACTT 59.283 33.333 0.00 0.00 0.00 2.66
2164 2279 6.981722 AGAAGCAACCGAAAGAATTTTGTAT 58.018 32.000 0.00 0.00 39.27 2.29
2165 2280 6.038825 TGAGAAGCAACCGAAAGAATTTTGTA 59.961 34.615 0.00 0.00 39.27 2.41
2168 2283 5.514274 TGAGAAGCAACCGAAAGAATTTT 57.486 34.783 0.00 0.00 39.27 1.82
2178 2293 2.351738 GGGTTTCATTGAGAAGCAACCG 60.352 50.000 9.86 0.00 39.78 4.44
2203 2318 2.031495 ACTAACAGGTCCCAGCTTCT 57.969 50.000 0.00 0.00 0.00 2.85
2217 2332 5.878116 TGGTATACATCAACTGCCAACTAAC 59.122 40.000 5.01 0.00 0.00 2.34
2239 2355 2.195741 ATGCCCGATCATTCTGATGG 57.804 50.000 0.00 0.00 37.20 3.51
2251 2367 0.464036 CAGTAGGTGCTTATGCCCGA 59.536 55.000 0.00 0.00 38.71 5.14
2252 2368 2.992089 CAGTAGGTGCTTATGCCCG 58.008 57.895 0.00 0.00 38.71 6.13
2264 2380 4.027437 AGAAAGACCTTCCTAGCAGTAGG 58.973 47.826 0.00 0.00 46.85 3.18
2274 2390 5.373812 TGGATATTCCAGAAAGACCTTCC 57.626 43.478 0.00 0.00 42.67 3.46
2374 2492 6.463995 TCCGCCATTTGAAATTTAGCTATT 57.536 33.333 0.00 0.00 0.00 1.73
2381 2499 4.392754 GCATCTTTCCGCCATTTGAAATTT 59.607 37.500 0.00 0.00 30.67 1.82
2382 2500 3.934579 GCATCTTTCCGCCATTTGAAATT 59.065 39.130 0.00 0.00 30.67 1.82
2429 2548 1.776662 AGACGGCTAGCATGGAGTAA 58.223 50.000 18.24 0.00 0.00 2.24
2431 2550 2.002505 ATAGACGGCTAGCATGGAGT 57.997 50.000 18.24 7.84 0.00 3.85
2495 2614 3.701664 AGGGTTCCAGAAATGTCATTCC 58.298 45.455 0.00 0.00 0.00 3.01
2514 2633 4.170468 ACTGCTTCCATTATGGGTTAGG 57.830 45.455 11.76 2.64 38.32 2.69
2516 2635 5.652014 CAGAAACTGCTTCCATTATGGGTTA 59.348 40.000 11.76 0.00 38.32 2.85
2544 2663 9.334947 CACTGGTAAGATGTTCTGATTGATATT 57.665 33.333 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.