Multiple sequence alignment - TraesCS3A01G330700

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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 TraesCS3A01G330700 chr3A 100.000 4262 0 0 1 4262 575412390 575408129 0.000000e+00 7871.0
1 TraesCS3A01G330700 chr3B 93.695 3394 148 26 894 4262 572670764 572667412 0.000000e+00 5022.0
2 TraesCS3A01G330700 chr3D 91.156 1583 79 32 297 1869 437359259 437357728 0.000000e+00 2091.0
3 TraesCS3A01G330700 chr3D 93.045 1294 71 9 2983 4262 437356391 437355103 0.000000e+00 1873.0
4 TraesCS3A01G330700 chr3D 83.915 1032 118 31 1859 2871 437357642 437356640 0.000000e+00 942.0
5 TraesCS3A01G330700 chr3D 90.268 298 19 7 14 307 437394666 437394375 8.650000e-102 381.0
6 TraesCS3A01G330700 chr5A 88.945 199 17 5 2317 2512 34717294 34717490 1.530000e-59 241.0
7 TraesCS3A01G330700 chr5A 97.619 42 1 0 2469 2510 34717558 34717599 5.910000e-09 73.1


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 TraesCS3A01G330700 chr3A 575408129 575412390 4261 True 7871.000000 7871 100.000 1 4262 1 chr3A.!!$R1 4261
1 TraesCS3A01G330700 chr3B 572667412 572670764 3352 True 5022.000000 5022 93.695 894 4262 1 chr3B.!!$R1 3368
2 TraesCS3A01G330700 chr3D 437355103 437359259 4156 True 1635.333333 2091 89.372 297 4262 3 chr3D.!!$R2 3965

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
625 628 0.029035 CGGTTGTACTCTCCGATCGG 59.971 60.0 28.62 28.62 46.05 4.18 F
626 629 0.248949 GGTTGTACTCTCCGATCGGC 60.249 60.0 29.62 14.47 34.68 5.54 F
1335 1347 0.316689 CGTGGGACAAGCGTTTTCAC 60.317 55.0 0.00 0.00 44.16 3.18 F
3069 3338 0.250467 AGTGCCACAAGTACAGCAGG 60.250 55.0 0.00 0.00 35.56 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 2469 0.582005 GCAAACAGTGACTCCGTGTC 59.418 55.000 0.00 0.00 45.54 3.67 R
2570 2698 3.127791 ACAGGACCTCATCAGGATCTT 57.872 47.619 0.00 0.00 43.65 2.40 R
3207 3476 0.404426 TCGGAGTCTCCCTCTTCACA 59.596 55.000 13.54 0.00 40.30 3.58 R
3895 4177 0.654683 CTGCCTCGTTCTAAGCATGC 59.345 55.000 10.51 10.51 34.16 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
24 25 7.769272 CCGTGAATGTGCCAAAAATATTAAT 57.231 32.000 0.00 0.00 0.00 1.40
25 26 8.195617 CCGTGAATGTGCCAAAAATATTAATT 57.804 30.769 0.00 0.00 0.00 1.40
26 27 8.663911 CCGTGAATGTGCCAAAAATATTAATTT 58.336 29.630 0.00 0.00 36.87 1.82
97 98 8.838452 TTTCAAATGAAAAATGCATTGTTCAC 57.162 26.923 36.11 17.70 44.30 3.18
98 99 7.549615 TCAAATGAAAAATGCATTGTTCACA 57.450 28.000 36.11 21.96 44.30 3.58
99 100 8.155821 TCAAATGAAAAATGCATTGTTCACAT 57.844 26.923 36.11 27.38 44.30 3.21
100 101 8.070769 TCAAATGAAAAATGCATTGTTCACATG 58.929 29.630 36.11 33.16 44.30 3.21
101 102 7.499321 AATGAAAAATGCATTGTTCACATGT 57.501 28.000 36.11 23.06 44.30 3.21
102 103 6.922247 TGAAAAATGCATTGTTCACATGTT 57.078 29.167 32.17 10.51 38.67 2.71
103 104 7.317842 TGAAAAATGCATTGTTCACATGTTT 57.682 28.000 32.17 17.39 38.67 2.83
104 105 7.759465 TGAAAAATGCATTGTTCACATGTTTT 58.241 26.923 32.17 16.76 38.67 2.43
105 106 8.242053 TGAAAAATGCATTGTTCACATGTTTTT 58.758 25.926 32.17 16.90 38.67 1.94
106 107 7.972623 AAAATGCATTGTTCACATGTTTTTG 57.027 28.000 13.82 0.00 0.00 2.44
107 108 5.676532 ATGCATTGTTCACATGTTTTTGG 57.323 34.783 0.00 0.00 0.00 3.28
108 109 3.311871 TGCATTGTTCACATGTTTTTGGC 59.688 39.130 0.00 0.00 0.00 4.52
109 110 3.604314 GCATTGTTCACATGTTTTTGGCG 60.604 43.478 0.00 0.00 0.00 5.69
110 111 2.215907 TGTTCACATGTTTTTGGCGG 57.784 45.000 0.00 0.00 0.00 6.13
111 112 1.751351 TGTTCACATGTTTTTGGCGGA 59.249 42.857 0.00 0.00 0.00 5.54
112 113 2.124122 GTTCACATGTTTTTGGCGGAC 58.876 47.619 0.00 0.00 0.00 4.79
113 114 1.686355 TCACATGTTTTTGGCGGACT 58.314 45.000 0.00 0.00 0.00 3.85
114 115 1.606668 TCACATGTTTTTGGCGGACTC 59.393 47.619 0.00 0.00 0.00 3.36
115 116 0.591170 ACATGTTTTTGGCGGACTCG 59.409 50.000 0.00 0.00 39.81 4.18
116 117 0.109781 CATGTTTTTGGCGGACTCGG 60.110 55.000 0.00 0.00 36.79 4.63
117 118 1.241315 ATGTTTTTGGCGGACTCGGG 61.241 55.000 0.00 0.00 36.79 5.14
118 119 2.981350 TTTTTGGCGGACTCGGGC 60.981 61.111 3.43 3.43 36.79 6.13
119 120 3.485346 TTTTTGGCGGACTCGGGCT 62.485 57.895 10.89 0.00 36.79 5.19
120 121 2.969300 TTTTTGGCGGACTCGGGCTT 62.969 55.000 10.89 0.00 36.79 4.35
121 122 4.697756 TTGGCGGACTCGGGCTTG 62.698 66.667 10.89 0.00 36.79 4.01
123 124 4.821589 GGCGGACTCGGGCTTGAG 62.822 72.222 3.17 5.88 41.86 3.02
124 125 3.760035 GCGGACTCGGGCTTGAGA 61.760 66.667 12.99 0.00 39.35 3.27
125 126 3.082579 GCGGACTCGGGCTTGAGAT 62.083 63.158 12.99 0.00 39.35 2.75
126 127 1.517832 CGGACTCGGGCTTGAGATT 59.482 57.895 12.99 0.00 39.35 2.40
127 128 0.108138 CGGACTCGGGCTTGAGATTT 60.108 55.000 12.99 0.00 39.35 2.17
128 129 1.676014 CGGACTCGGGCTTGAGATTTT 60.676 52.381 12.99 0.00 39.35 1.82
129 130 2.010497 GGACTCGGGCTTGAGATTTTC 58.990 52.381 12.99 1.97 39.35 2.29
130 131 2.615493 GGACTCGGGCTTGAGATTTTCA 60.615 50.000 12.99 0.00 39.35 2.69
131 132 2.416893 GACTCGGGCTTGAGATTTTCAC 59.583 50.000 12.99 0.00 39.35 3.18
132 133 1.740025 CTCGGGCTTGAGATTTTCACC 59.260 52.381 1.75 0.00 38.28 4.02
133 134 1.351017 TCGGGCTTGAGATTTTCACCT 59.649 47.619 0.00 0.00 34.94 4.00
134 135 1.470098 CGGGCTTGAGATTTTCACCTG 59.530 52.381 0.00 0.00 34.94 4.00
135 136 1.821136 GGGCTTGAGATTTTCACCTGG 59.179 52.381 0.00 0.00 34.94 4.45
136 137 1.821136 GGCTTGAGATTTTCACCTGGG 59.179 52.381 0.00 0.00 34.94 4.45
137 138 2.519013 GCTTGAGATTTTCACCTGGGT 58.481 47.619 0.00 0.00 34.94 4.51
138 139 2.893489 GCTTGAGATTTTCACCTGGGTT 59.107 45.455 0.00 0.00 34.94 4.11
139 140 3.057245 GCTTGAGATTTTCACCTGGGTTC 60.057 47.826 0.00 0.00 34.94 3.62
140 141 4.401925 CTTGAGATTTTCACCTGGGTTCT 58.598 43.478 0.00 0.00 34.94 3.01
141 142 3.754965 TGAGATTTTCACCTGGGTTCTG 58.245 45.455 0.00 0.00 0.00 3.02
142 143 3.138283 TGAGATTTTCACCTGGGTTCTGT 59.862 43.478 0.00 0.00 0.00 3.41
143 144 3.753797 GAGATTTTCACCTGGGTTCTGTC 59.246 47.826 0.00 0.00 0.00 3.51
144 145 3.138283 AGATTTTCACCTGGGTTCTGTCA 59.862 43.478 0.00 0.00 0.00 3.58
145 146 3.374042 TTTTCACCTGGGTTCTGTCAA 57.626 42.857 0.00 0.00 0.00 3.18
146 147 2.638480 TTCACCTGGGTTCTGTCAAG 57.362 50.000 0.00 0.00 0.00 3.02
147 148 0.108585 TCACCTGGGTTCTGTCAAGC 59.891 55.000 0.00 0.00 0.00 4.01
148 149 0.890996 CACCTGGGTTCTGTCAAGCC 60.891 60.000 0.00 0.00 38.25 4.35
149 150 1.303643 CCTGGGTTCTGTCAAGCCC 60.304 63.158 0.28 0.00 41.42 5.19
150 151 1.672356 CTGGGTTCTGTCAAGCCCG 60.672 63.158 0.28 0.00 43.89 6.13
151 152 2.111999 CTGGGTTCTGTCAAGCCCGA 62.112 60.000 0.28 0.00 43.89 5.14
152 153 1.671379 GGGTTCTGTCAAGCCCGAC 60.671 63.158 0.00 0.00 36.40 4.79
153 154 2.027625 GGTTCTGTCAAGCCCGACG 61.028 63.158 0.00 0.00 38.84 5.12
154 155 1.006571 GTTCTGTCAAGCCCGACGA 60.007 57.895 0.00 0.00 38.84 4.20
155 156 1.009389 GTTCTGTCAAGCCCGACGAG 61.009 60.000 0.00 0.00 38.84 4.18
156 157 1.176619 TTCTGTCAAGCCCGACGAGA 61.177 55.000 0.00 1.42 38.84 4.04
157 158 1.176619 TCTGTCAAGCCCGACGAGAA 61.177 55.000 0.00 0.00 38.84 2.87
158 159 0.319555 CTGTCAAGCCCGACGAGAAA 60.320 55.000 0.00 0.00 38.84 2.52
159 160 0.599204 TGTCAAGCCCGACGAGAAAC 60.599 55.000 0.00 0.00 38.84 2.78
160 161 1.005394 TCAAGCCCGACGAGAAACC 60.005 57.895 0.00 0.00 0.00 3.27
161 162 1.004918 CAAGCCCGACGAGAAACCT 60.005 57.895 0.00 0.00 0.00 3.50
162 163 0.245539 CAAGCCCGACGAGAAACCTA 59.754 55.000 0.00 0.00 0.00 3.08
163 164 0.531200 AAGCCCGACGAGAAACCTAG 59.469 55.000 0.00 0.00 0.00 3.02
164 165 1.518792 GCCCGACGAGAAACCTAGC 60.519 63.158 0.00 0.00 0.00 3.42
165 166 1.946475 GCCCGACGAGAAACCTAGCT 61.946 60.000 0.00 0.00 0.00 3.32
166 167 0.100861 CCCGACGAGAAACCTAGCTC 59.899 60.000 0.00 0.00 0.00 4.09
170 171 4.838046 GAGAAACCTAGCTCGGCC 57.162 61.111 3.73 0.00 0.00 6.13
171 172 1.144276 GAGAAACCTAGCTCGGCCC 59.856 63.158 3.73 0.00 0.00 5.80
172 173 2.202892 GAAACCTAGCTCGGCCCG 60.203 66.667 3.73 0.00 0.00 6.13
173 174 2.682494 AAACCTAGCTCGGCCCGA 60.682 61.111 5.37 5.37 0.00 5.14
174 175 2.902759 GAAACCTAGCTCGGCCCGAC 62.903 65.000 0.00 0.00 0.00 4.79
175 176 3.959329 AACCTAGCTCGGCCCGACT 62.959 63.158 0.00 7.63 0.00 4.18
176 177 2.203308 CCTAGCTCGGCCCGACTA 60.203 66.667 0.00 8.43 0.00 2.59
177 178 2.262303 CCTAGCTCGGCCCGACTAG 61.262 68.421 24.04 24.04 37.36 2.57
178 179 2.203308 TAGCTCGGCCCGACTAGG 60.203 66.667 0.00 0.00 40.63 3.02
179 180 2.962142 CTAGCTCGGCCCGACTAGGT 62.962 65.000 23.62 14.83 35.80 3.08
180 181 1.699054 TAGCTCGGCCCGACTAGGTA 61.699 60.000 0.00 0.00 38.74 3.08
181 182 1.902432 GCTCGGCCCGACTAGGTAT 60.902 63.158 0.00 0.00 38.74 2.73
182 183 1.957562 CTCGGCCCGACTAGGTATG 59.042 63.158 0.00 0.00 38.74 2.39
183 184 0.536687 CTCGGCCCGACTAGGTATGA 60.537 60.000 0.00 0.00 38.74 2.15
184 185 0.111832 TCGGCCCGACTAGGTATGAT 59.888 55.000 0.00 0.00 38.74 2.45
185 186 0.526662 CGGCCCGACTAGGTATGATC 59.473 60.000 0.00 0.00 38.74 2.92
186 187 1.629043 GGCCCGACTAGGTATGATCA 58.371 55.000 0.00 0.00 38.74 2.92
187 188 1.546476 GGCCCGACTAGGTATGATCAG 59.454 57.143 0.09 0.00 38.74 2.90
188 189 1.546476 GCCCGACTAGGTATGATCAGG 59.454 57.143 0.09 0.00 38.74 3.86
189 190 2.877866 CCCGACTAGGTATGATCAGGT 58.122 52.381 0.09 0.00 38.74 4.00
190 191 3.231818 CCCGACTAGGTATGATCAGGTT 58.768 50.000 0.09 0.00 38.74 3.50
191 192 3.641906 CCCGACTAGGTATGATCAGGTTT 59.358 47.826 0.09 0.00 38.74 3.27
192 193 4.831155 CCCGACTAGGTATGATCAGGTTTA 59.169 45.833 0.09 0.00 38.74 2.01
193 194 5.480772 CCCGACTAGGTATGATCAGGTTTAT 59.519 44.000 0.09 0.00 38.74 1.40
194 195 6.390721 CCGACTAGGTATGATCAGGTTTATG 58.609 44.000 0.09 0.00 34.51 1.90
195 196 5.864474 CGACTAGGTATGATCAGGTTTATGC 59.136 44.000 0.09 0.00 0.00 3.14
196 197 6.294787 CGACTAGGTATGATCAGGTTTATGCT 60.295 42.308 0.09 0.00 0.00 3.79
197 198 6.763355 ACTAGGTATGATCAGGTTTATGCTG 58.237 40.000 0.09 0.00 0.00 4.41
198 199 4.978099 AGGTATGATCAGGTTTATGCTGG 58.022 43.478 0.09 0.00 0.00 4.85
199 200 4.660303 AGGTATGATCAGGTTTATGCTGGA 59.340 41.667 0.09 0.00 0.00 3.86
200 201 4.999950 GGTATGATCAGGTTTATGCTGGAG 59.000 45.833 0.09 0.00 0.00 3.86
201 202 2.923121 TGATCAGGTTTATGCTGGAGC 58.077 47.619 0.00 0.00 42.50 4.70
232 233 5.853572 TTTTTGACCTAACCCCTCATACT 57.146 39.130 0.00 0.00 0.00 2.12
233 234 6.956102 TTTTTGACCTAACCCCTCATACTA 57.044 37.500 0.00 0.00 0.00 1.82
234 235 6.956102 TTTTGACCTAACCCCTCATACTAA 57.044 37.500 0.00 0.00 0.00 2.24
235 236 6.555463 TTTGACCTAACCCCTCATACTAAG 57.445 41.667 0.00 0.00 0.00 2.18
236 237 5.476950 TGACCTAACCCCTCATACTAAGA 57.523 43.478 0.00 0.00 0.00 2.10
237 238 5.845734 TGACCTAACCCCTCATACTAAGAA 58.154 41.667 0.00 0.00 0.00 2.52
238 239 6.449956 TGACCTAACCCCTCATACTAAGAAT 58.550 40.000 0.00 0.00 0.00 2.40
239 240 6.326583 TGACCTAACCCCTCATACTAAGAATG 59.673 42.308 0.00 0.00 0.00 2.67
240 241 6.210522 ACCTAACCCCTCATACTAAGAATGT 58.789 40.000 0.00 0.00 0.00 2.71
241 242 6.677076 ACCTAACCCCTCATACTAAGAATGTT 59.323 38.462 0.00 0.00 0.00 2.71
242 243 7.184022 ACCTAACCCCTCATACTAAGAATGTTT 59.816 37.037 0.00 0.00 0.00 2.83
243 244 8.053355 CCTAACCCCTCATACTAAGAATGTTTT 58.947 37.037 0.00 0.00 0.00 2.43
244 245 9.462606 CTAACCCCTCATACTAAGAATGTTTTT 57.537 33.333 0.00 0.00 0.00 1.94
245 246 7.703058 ACCCCTCATACTAAGAATGTTTTTG 57.297 36.000 0.00 0.00 0.00 2.44
246 247 7.466804 ACCCCTCATACTAAGAATGTTTTTGA 58.533 34.615 0.00 0.00 0.00 2.69
247 248 7.947890 ACCCCTCATACTAAGAATGTTTTTGAA 59.052 33.333 0.00 0.00 0.00 2.69
248 249 8.802267 CCCCTCATACTAAGAATGTTTTTGAAA 58.198 33.333 0.00 0.00 0.00 2.69
281 282 7.621428 TCTTTTGAAGATGATCTAAAGCCAG 57.379 36.000 10.06 0.00 40.01 4.85
282 283 5.824904 TTTGAAGATGATCTAAAGCCAGC 57.175 39.130 0.00 0.00 0.00 4.85
283 284 4.767578 TGAAGATGATCTAAAGCCAGCT 57.232 40.909 0.00 0.00 0.00 4.24
284 285 5.876651 TGAAGATGATCTAAAGCCAGCTA 57.123 39.130 0.00 0.00 0.00 3.32
285 286 6.239217 TGAAGATGATCTAAAGCCAGCTAA 57.761 37.500 0.00 0.00 0.00 3.09
286 287 6.835174 TGAAGATGATCTAAAGCCAGCTAAT 58.165 36.000 0.00 0.00 0.00 1.73
287 288 6.709397 TGAAGATGATCTAAAGCCAGCTAATG 59.291 38.462 0.00 0.00 0.00 1.90
288 289 5.002516 AGATGATCTAAAGCCAGCTAATGC 58.997 41.667 0.00 0.00 40.05 3.56
289 290 3.133691 TGATCTAAAGCCAGCTAATGCG 58.866 45.455 0.00 0.00 45.42 4.73
290 291 2.979814 TCTAAAGCCAGCTAATGCGA 57.020 45.000 0.00 0.00 45.42 5.10
291 292 3.260475 TCTAAAGCCAGCTAATGCGAA 57.740 42.857 0.00 0.00 45.42 4.70
292 293 2.936498 TCTAAAGCCAGCTAATGCGAAC 59.064 45.455 0.00 0.00 45.42 3.95
293 294 0.811281 AAAGCCAGCTAATGCGAACC 59.189 50.000 0.00 0.00 45.42 3.62
294 295 0.322456 AAGCCAGCTAATGCGAACCA 60.322 50.000 0.00 0.00 45.42 3.67
295 296 0.322456 AGCCAGCTAATGCGAACCAA 60.322 50.000 0.00 0.00 45.42 3.67
309 310 4.023878 TGCGAACCAAACCATTAGTTGTAC 60.024 41.667 0.00 0.00 39.19 2.90
312 313 5.182380 CGAACCAAACCATTAGTTGTACCAT 59.818 40.000 0.00 0.00 39.19 3.55
319 320 3.857093 CCATTAGTTGTACCATTTTGCGC 59.143 43.478 0.00 0.00 0.00 6.09
350 351 1.729586 AGAGTTCCCACTTAGCACCA 58.270 50.000 0.00 0.00 31.22 4.17
367 368 2.753452 CACCAGATCTACCACTACACGT 59.247 50.000 0.00 0.00 0.00 4.49
400 401 6.237901 TGTGAGAAAACACATATACAAGGCT 58.762 36.000 0.00 0.00 44.29 4.58
430 431 8.517062 AGGATCTAAATATAAGATGCATTGCC 57.483 34.615 16.74 7.29 42.44 4.52
431 432 8.334734 AGGATCTAAATATAAGATGCATTGCCT 58.665 33.333 16.74 0.00 42.44 4.75
436 437 2.804986 TAAGATGCATTGCCTGGACA 57.195 45.000 6.12 0.00 0.00 4.02
456 457 1.072505 TTCCTTGCCCCGTTCTCAC 59.927 57.895 0.00 0.00 0.00 3.51
488 489 2.782222 GGGCGGCGACTGATCTACA 61.782 63.158 14.66 0.00 0.00 2.74
529 530 0.694783 CCTTCTACCCTCCCCCTTCC 60.695 65.000 0.00 0.00 0.00 3.46
538 539 1.497161 CTCCCCCTTCCGTCTATTGT 58.503 55.000 0.00 0.00 0.00 2.71
559 560 1.108776 CCCACGATAAGAAGGGACGA 58.891 55.000 0.00 0.00 39.80 4.20
574 575 2.062519 GGACGAAGACTTCAAGTGCTC 58.937 52.381 15.36 0.00 0.00 4.26
591 593 1.202428 GCTCCGGCTAGTGAAGTTAGG 60.202 57.143 0.00 0.00 35.22 2.69
620 623 5.233689 GGATAAATTTCGGTTGTACTCTCCG 59.766 44.000 14.39 14.39 44.76 4.63
625 628 0.029035 CGGTTGTACTCTCCGATCGG 59.971 60.000 28.62 28.62 46.05 4.18
626 629 0.248949 GGTTGTACTCTCCGATCGGC 60.249 60.000 29.62 14.47 34.68 5.54
627 630 0.454600 GTTGTACTCTCCGATCGGCA 59.545 55.000 29.62 17.03 34.68 5.69
628 631 1.135199 GTTGTACTCTCCGATCGGCAA 60.135 52.381 29.62 21.71 34.68 4.52
629 632 1.399714 TGTACTCTCCGATCGGCAAT 58.600 50.000 29.62 16.07 34.68 3.56
630 633 1.067060 TGTACTCTCCGATCGGCAATG 59.933 52.381 29.62 19.45 34.68 2.82
631 634 0.673985 TACTCTCCGATCGGCAATGG 59.326 55.000 29.62 17.71 34.68 3.16
632 635 1.330655 ACTCTCCGATCGGCAATGGT 61.331 55.000 29.62 18.31 34.68 3.55
633 636 0.598680 CTCTCCGATCGGCAATGGTC 60.599 60.000 29.62 0.00 34.68 4.02
634 637 1.143838 CTCCGATCGGCAATGGTCA 59.856 57.895 29.62 8.54 34.68 4.02
635 638 0.877649 CTCCGATCGGCAATGGTCAG 60.878 60.000 29.62 14.68 34.68 3.51
636 639 1.143838 CCGATCGGCAATGGTCAGA 59.856 57.895 23.37 0.00 0.00 3.27
637 640 1.154205 CCGATCGGCAATGGTCAGAC 61.154 60.000 23.37 0.00 0.00 3.51
638 641 1.482621 CGATCGGCAATGGTCAGACG 61.483 60.000 7.38 0.00 0.00 4.18
643 646 1.080093 GCAATGGTCAGACGACGGA 60.080 57.895 0.00 0.00 43.61 4.69
669 672 3.431856 TCGTCGATGTGAAATAAGGTCG 58.568 45.455 4.21 0.00 0.00 4.79
672 675 3.000322 GTCGATGTGAAATAAGGTCGCTG 60.000 47.826 0.00 0.00 0.00 5.18
673 676 2.285834 CGATGTGAAATAAGGTCGCTGC 60.286 50.000 0.00 0.00 0.00 5.25
682 685 4.408821 GGTCGCTGCACCCCATCA 62.409 66.667 0.00 0.00 0.00 3.07
687 690 0.464373 CGCTGCACCCCATCATAGTT 60.464 55.000 0.00 0.00 0.00 2.24
708 711 1.277842 TGGTGGTGCATCTTCGTATGT 59.722 47.619 0.00 0.00 0.00 2.29
754 757 2.297937 GGATCTGGTTCTCCGGGTT 58.702 57.895 0.00 0.00 40.36 4.11
763 766 1.497309 TTCTCCGGGTTTGGCTCCAT 61.497 55.000 0.00 0.00 0.00 3.41
772 775 1.305219 TTTGGCTCCATTTCCTCGCG 61.305 55.000 0.00 0.00 0.00 5.87
782 785 3.550030 CCATTTCCTCGCGTTTTGACTTT 60.550 43.478 5.77 0.00 0.00 2.66
793 796 5.510323 CGCGTTTTGACTTTTCACTAAGTTT 59.490 36.000 0.00 0.00 38.43 2.66
794 797 6.504180 CGCGTTTTGACTTTTCACTAAGTTTG 60.504 38.462 0.00 0.00 38.43 2.93
795 798 6.307077 GCGTTTTGACTTTTCACTAAGTTTGT 59.693 34.615 0.00 0.00 38.43 2.83
796 799 7.148869 GCGTTTTGACTTTTCACTAAGTTTGTT 60.149 33.333 0.00 0.00 38.43 2.83
797 800 9.332301 CGTTTTGACTTTTCACTAAGTTTGTTA 57.668 29.630 0.00 0.00 38.43 2.41
863 866 5.613358 AGCAAAAGTCTTTTCAGGATACG 57.387 39.130 7.62 0.00 46.39 3.06
864 867 5.305585 AGCAAAAGTCTTTTCAGGATACGA 58.694 37.500 7.62 0.00 46.39 3.43
910 913 3.527253 TCAGATTAGATGGGCCTGGAAAA 59.473 43.478 4.53 0.00 0.00 2.29
919 922 1.793414 GGCCTGGAAAATTAGCCCAT 58.207 50.000 0.00 0.00 37.66 4.00
921 924 2.110578 GCCTGGAAAATTAGCCCATGT 58.889 47.619 0.00 0.00 0.00 3.21
930 934 1.635817 TTAGCCCATGTCTGCCCCTC 61.636 60.000 0.00 0.00 0.00 4.30
932 936 3.813724 CCCATGTCTGCCCCTCCC 61.814 72.222 0.00 0.00 0.00 4.30
933 937 3.016971 CCATGTCTGCCCCTCCCA 61.017 66.667 0.00 0.00 0.00 4.37
985 997 2.713967 GCGGCAGCCCAATCACAAT 61.714 57.895 5.63 0.00 37.42 2.71
1098 1110 2.363018 CTCCGCTCCCTCTCCACA 60.363 66.667 0.00 0.00 0.00 4.17
1335 1347 0.316689 CGTGGGACAAGCGTTTTCAC 60.317 55.000 0.00 0.00 44.16 3.18
1482 1494 3.423154 GCCAAGGACTTCCGCGTG 61.423 66.667 4.92 0.00 42.08 5.34
1618 1630 5.336849 CCAGAGTACGTGAAGAGATCCTTTT 60.337 44.000 0.00 0.00 34.68 2.27
1620 1632 6.090088 CAGAGTACGTGAAGAGATCCTTTTTG 59.910 42.308 0.00 0.00 34.68 2.44
1621 1633 4.691216 AGTACGTGAAGAGATCCTTTTTGC 59.309 41.667 0.00 0.00 34.68 3.68
1629 1641 4.006319 AGAGATCCTTTTTGCTTCCTTCG 58.994 43.478 0.00 0.00 0.00 3.79
1640 1652 3.280295 TGCTTCCTTCGGTTTTGTGTTA 58.720 40.909 0.00 0.00 0.00 2.41
1697 1714 4.780275 AGGGTTCTAGTTCGTAAGTCAC 57.220 45.455 0.00 0.00 39.48 3.67
1699 1716 8.316956 CTAGGGTTCTAGTTCGTAAGTCACGG 62.317 50.000 0.00 0.00 42.76 4.94
1870 1887 3.937778 TCCAATGCTCTGGATCATGAA 57.062 42.857 0.00 0.00 40.71 2.57
1877 1894 3.131577 TGCTCTGGATCATGAAAATTGGC 59.868 43.478 0.00 1.87 0.00 4.52
2004 2121 9.223099 TGTGACTATATATGCTTGATGAAATGG 57.777 33.333 0.00 0.00 0.00 3.16
2025 2142 4.469945 TGGTATGGAGTCGAGGAATTCTTT 59.530 41.667 5.23 0.00 0.00 2.52
2027 2144 5.524281 GGTATGGAGTCGAGGAATTCTTTTC 59.476 44.000 5.23 0.76 0.00 2.29
2062 2179 2.409975 GCGTTGAGCTAGGTGTTTGTA 58.590 47.619 0.00 0.00 44.04 2.41
2093 2210 9.847224 AAATGTACTAATATAGTTGTTCCAGGG 57.153 33.333 0.00 0.00 40.14 4.45
2138 2256 2.468777 GCAAGCAAAACAGTCATTGACG 59.531 45.455 11.01 8.72 37.67 4.35
2142 2260 3.002656 AGCAAAACAGTCATTGACGTCAG 59.997 43.478 19.11 8.46 37.67 3.51
2215 2339 8.936864 AGTTTGTATTACTGATTAGCTCAACAC 58.063 33.333 0.00 0.00 32.14 3.32
2219 2343 7.913821 TGTATTACTGATTAGCTCAACACTACG 59.086 37.037 0.00 0.00 32.14 3.51
2250 2374 6.096673 AGTCAATGGTGGAAATTGGTAAAC 57.903 37.500 0.00 0.00 36.01 2.01
2312 2436 7.039784 ACCATTTCAGTTTGCATGTTATGTACT 60.040 33.333 0.00 0.00 0.00 2.73
2313 2437 8.458052 CCATTTCAGTTTGCATGTTATGTACTA 58.542 33.333 0.00 0.00 0.00 1.82
2314 2438 9.277565 CATTTCAGTTTGCATGTTATGTACTAC 57.722 33.333 0.00 0.00 0.00 2.73
2383 2509 6.817641 TGTTTGCAAATTGATGTGTTTCTCTT 59.182 30.769 16.21 0.00 0.00 2.85
2570 2698 1.971167 GCTGGGATGGCACGACAAA 60.971 57.895 0.00 0.00 0.00 2.83
2707 2837 6.639632 TGCTCCCTTTTATGATATTTGCTC 57.360 37.500 0.00 0.00 0.00 4.26
2783 2913 7.941790 TCCTGCAGCAGACCTATATATAGATAG 59.058 40.741 24.90 7.32 32.44 2.08
2810 2940 4.357918 AAGAGTATGGTTGTGCTGTTCT 57.642 40.909 0.00 0.00 0.00 3.01
2811 2941 3.668447 AGAGTATGGTTGTGCTGTTCTG 58.332 45.455 0.00 0.00 0.00 3.02
2815 2945 4.997395 AGTATGGTTGTGCTGTTCTGTTAG 59.003 41.667 0.00 0.00 0.00 2.34
2828 2958 6.203723 GCTGTTCTGTTAGTTCTTCTGTGATT 59.796 38.462 0.00 0.00 0.00 2.57
2851 2981 4.357918 AGTACAAATTCCTGCAGTCTGT 57.642 40.909 13.81 10.24 0.00 3.41
2855 2985 3.054878 CAAATTCCTGCAGTCTGTTTGC 58.945 45.455 13.81 0.00 41.86 3.68
2856 2986 2.283145 ATTCCTGCAGTCTGTTTGCT 57.717 45.000 13.81 0.00 42.02 3.91
3016 3285 0.392193 CCACTGGTCATCTGCCTCAC 60.392 60.000 0.00 0.00 0.00 3.51
3069 3338 0.250467 AGTGCCACAAGTACAGCAGG 60.250 55.000 0.00 0.00 35.56 4.85
3174 3443 0.321564 TCAGTTTGCCTGATGGGTCG 60.322 55.000 0.00 0.00 45.34 4.79
3207 3476 5.360999 TCTGAATGACACGGAGAAGATGTAT 59.639 40.000 0.00 0.00 0.00 2.29
3290 3560 2.224548 GGCCCCTCTGCTCGTTATAATT 60.225 50.000 0.00 0.00 0.00 1.40
3311 3581 2.034939 TGCAGGAGTTCTACGAACGAAA 59.965 45.455 0.14 0.00 0.00 3.46
3422 3697 0.936297 CTTGTTTTGCTGCAGCGGAC 60.936 55.000 32.11 27.34 45.83 4.79
3491 3766 8.725148 CCACTTTAGGCAGATGAATAATATGTC 58.275 37.037 0.00 0.00 32.03 3.06
3538 3813 0.038343 CCACAACATTTCCGGGCAAG 60.038 55.000 0.00 0.00 0.00 4.01
3539 3814 0.673437 CACAACATTTCCGGGCAAGT 59.327 50.000 0.00 0.00 0.00 3.16
3540 3815 1.068434 CACAACATTTCCGGGCAAGTT 59.932 47.619 0.00 0.00 0.00 2.66
3547 3822 0.534203 TTCCGGGCAAGTTGTCACTC 60.534 55.000 10.13 0.00 30.45 3.51
3571 3846 1.574428 GCAGTACCAGGCAAACACG 59.426 57.895 0.00 0.00 0.00 4.49
3599 3874 7.087409 TGCAGTCAACATTTCATATAACCTG 57.913 36.000 0.00 0.00 0.00 4.00
3604 3879 9.407380 AGTCAACATTTCATATAACCTGCAATA 57.593 29.630 0.00 0.00 0.00 1.90
3618 3894 9.717942 ATAACCTGCAATATTTTTGCTTACAAA 57.282 25.926 12.12 0.00 45.13 2.83
3619 3895 7.420184 ACCTGCAATATTTTTGCTTACAAAC 57.580 32.000 12.12 0.00 45.29 2.93
3716 3998 4.072131 TGATTTCCTTTCCTGCTGTACAC 58.928 43.478 0.00 0.00 0.00 2.90
3748 4030 1.085501 GCCCAATCATTTGCTTGCCG 61.086 55.000 0.00 0.00 0.00 5.69
3798 4080 4.100529 GGATTGCGACAAATGTGATTCAG 58.899 43.478 0.00 0.00 0.00 3.02
3869 4151 7.571026 CGAAAGAGTAGGATTTTATGCATCTG 58.429 38.462 0.19 0.00 0.00 2.90
3895 4177 2.002586 CTCACCTGTCCGCATGTTAAG 58.997 52.381 0.00 0.00 0.00 1.85
3956 4238 6.262944 ACTGACTTGCTTGATGATGTTGTAAA 59.737 34.615 0.00 0.00 0.00 2.01
3976 4258 1.062587 AGCGCTTTAATGTGCATCGTC 59.937 47.619 23.80 0.00 44.96 4.20
4002 4284 2.894602 GTCGAAAATTCTTTGCGTCGAC 59.105 45.455 5.18 5.18 41.03 4.20
4037 4319 0.959553 TAGATCGGCCGATGTCCTTC 59.040 55.000 43.46 28.51 34.60 3.46
4078 4365 4.274950 CACCAACCACCTACTACAACAAAG 59.725 45.833 0.00 0.00 0.00 2.77
4084 4371 5.071384 ACCACCTACTACAACAAAGCTAACT 59.929 40.000 0.00 0.00 0.00 2.24
4243 4531 8.169268 GTCTTCTATCAGTTGGTTACGAATTTG 58.831 37.037 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.769272 ATTAATATTTTTGGCACATTCACGG 57.231 32.000 0.00 0.00 39.30 4.94
71 72 9.453325 GTGAACAATGCATTTTTCATTTGAAAT 57.547 25.926 32.44 2.15 42.83 2.17
72 73 8.456471 TGTGAACAATGCATTTTTCATTTGAAA 58.544 25.926 32.44 17.36 41.77 2.69
73 74 7.982224 TGTGAACAATGCATTTTTCATTTGAA 58.018 26.923 32.44 18.64 32.30 2.69
74 75 7.549615 TGTGAACAATGCATTTTTCATTTGA 57.450 28.000 32.44 19.36 32.30 2.69
75 76 7.858382 ACATGTGAACAATGCATTTTTCATTTG 59.142 29.630 32.44 30.47 32.30 2.32
76 77 7.932335 ACATGTGAACAATGCATTTTTCATTT 58.068 26.923 32.44 23.26 32.30 2.32
77 78 7.499321 ACATGTGAACAATGCATTTTTCATT 57.501 28.000 32.44 23.52 34.74 2.57
78 79 7.499321 AACATGTGAACAATGCATTTTTCAT 57.501 28.000 32.44 20.75 30.96 2.57
79 80 6.922247 AACATGTGAACAATGCATTTTTCA 57.078 29.167 28.59 28.59 0.00 2.69
80 81 8.525071 CAAAAACATGTGAACAATGCATTTTTC 58.475 29.630 24.87 24.87 0.00 2.29
81 82 7.488471 CCAAAAACATGTGAACAATGCATTTTT 59.512 29.630 9.83 10.21 0.00 1.94
82 83 6.973474 CCAAAAACATGTGAACAATGCATTTT 59.027 30.769 9.83 7.81 0.00 1.82
83 84 6.496571 CCAAAAACATGTGAACAATGCATTT 58.503 32.000 9.83 0.00 0.00 2.32
84 85 5.505985 GCCAAAAACATGTGAACAATGCATT 60.506 36.000 5.99 5.99 0.00 3.56
85 86 4.023878 GCCAAAAACATGTGAACAATGCAT 60.024 37.500 0.00 0.00 0.00 3.96
86 87 3.311871 GCCAAAAACATGTGAACAATGCA 59.688 39.130 0.00 0.00 0.00 3.96
87 88 3.604314 CGCCAAAAACATGTGAACAATGC 60.604 43.478 0.00 0.00 0.00 3.56
88 89 3.059733 CCGCCAAAAACATGTGAACAATG 60.060 43.478 0.00 0.00 0.00 2.82
89 90 3.129871 CCGCCAAAAACATGTGAACAAT 58.870 40.909 0.00 0.00 0.00 2.71
90 91 2.166459 TCCGCCAAAAACATGTGAACAA 59.834 40.909 0.00 0.00 0.00 2.83
91 92 1.751351 TCCGCCAAAAACATGTGAACA 59.249 42.857 0.00 0.00 0.00 3.18
92 93 2.124122 GTCCGCCAAAAACATGTGAAC 58.876 47.619 0.00 0.00 0.00 3.18
93 94 2.028130 AGTCCGCCAAAAACATGTGAA 58.972 42.857 0.00 0.00 0.00 3.18
94 95 1.606668 GAGTCCGCCAAAAACATGTGA 59.393 47.619 0.00 0.00 0.00 3.58
95 96 1.662876 CGAGTCCGCCAAAAACATGTG 60.663 52.381 0.00 0.00 0.00 3.21
96 97 0.591170 CGAGTCCGCCAAAAACATGT 59.409 50.000 0.00 0.00 0.00 3.21
97 98 0.109781 CCGAGTCCGCCAAAAACATG 60.110 55.000 0.00 0.00 0.00 3.21
98 99 1.241315 CCCGAGTCCGCCAAAAACAT 61.241 55.000 0.00 0.00 0.00 2.71
99 100 1.894756 CCCGAGTCCGCCAAAAACA 60.895 57.895 0.00 0.00 0.00 2.83
100 101 2.951458 CCCGAGTCCGCCAAAAAC 59.049 61.111 0.00 0.00 0.00 2.43
101 102 2.969300 AAGCCCGAGTCCGCCAAAAA 62.969 55.000 0.00 0.00 0.00 1.94
102 103 3.485346 AAGCCCGAGTCCGCCAAAA 62.485 57.895 0.00 0.00 0.00 2.44
103 104 3.948719 AAGCCCGAGTCCGCCAAA 61.949 61.111 0.00 0.00 0.00 3.28
104 105 4.697756 CAAGCCCGAGTCCGCCAA 62.698 66.667 0.00 0.00 0.00 4.52
106 107 4.821589 CTCAAGCCCGAGTCCGCC 62.822 72.222 0.00 0.00 0.00 6.13
107 108 2.579684 AATCTCAAGCCCGAGTCCGC 62.580 60.000 0.31 0.00 34.46 5.54
108 109 0.108138 AAATCTCAAGCCCGAGTCCG 60.108 55.000 0.31 0.00 34.46 4.79
109 110 2.010497 GAAAATCTCAAGCCCGAGTCC 58.990 52.381 0.31 0.00 34.46 3.85
110 111 2.416893 GTGAAAATCTCAAGCCCGAGTC 59.583 50.000 0.31 0.00 35.22 3.36
111 112 2.427506 GTGAAAATCTCAAGCCCGAGT 58.572 47.619 0.31 0.00 35.22 4.18
112 113 1.740025 GGTGAAAATCTCAAGCCCGAG 59.260 52.381 0.00 0.00 35.22 4.63
113 114 1.351017 AGGTGAAAATCTCAAGCCCGA 59.649 47.619 0.00 0.00 35.22 5.14
114 115 1.470098 CAGGTGAAAATCTCAAGCCCG 59.530 52.381 0.00 0.00 35.22 6.13
115 116 1.821136 CCAGGTGAAAATCTCAAGCCC 59.179 52.381 0.00 0.00 35.22 5.19
116 117 1.821136 CCCAGGTGAAAATCTCAAGCC 59.179 52.381 0.00 0.00 35.22 4.35
117 118 2.519013 ACCCAGGTGAAAATCTCAAGC 58.481 47.619 0.00 0.00 35.22 4.01
118 119 4.217118 CAGAACCCAGGTGAAAATCTCAAG 59.783 45.833 0.00 0.00 35.22 3.02
119 120 4.144297 CAGAACCCAGGTGAAAATCTCAA 58.856 43.478 0.00 0.00 35.22 3.02
120 121 3.138283 ACAGAACCCAGGTGAAAATCTCA 59.862 43.478 0.00 0.00 0.00 3.27
121 122 3.753797 GACAGAACCCAGGTGAAAATCTC 59.246 47.826 0.00 0.00 0.00 2.75
122 123 3.138283 TGACAGAACCCAGGTGAAAATCT 59.862 43.478 0.00 0.00 0.00 2.40
123 124 3.486383 TGACAGAACCCAGGTGAAAATC 58.514 45.455 0.00 0.00 0.00 2.17
124 125 3.593442 TGACAGAACCCAGGTGAAAAT 57.407 42.857 0.00 0.00 0.00 1.82
125 126 3.287222 CTTGACAGAACCCAGGTGAAAA 58.713 45.455 0.00 0.00 0.00 2.29
126 127 2.930950 CTTGACAGAACCCAGGTGAAA 58.069 47.619 0.00 0.00 0.00 2.69
127 128 1.476833 GCTTGACAGAACCCAGGTGAA 60.477 52.381 0.00 0.00 0.00 3.18
128 129 0.108585 GCTTGACAGAACCCAGGTGA 59.891 55.000 0.00 0.00 0.00 4.02
129 130 0.890996 GGCTTGACAGAACCCAGGTG 60.891 60.000 0.00 0.00 0.00 4.00
130 131 1.456287 GGCTTGACAGAACCCAGGT 59.544 57.895 0.00 0.00 0.00 4.00
131 132 1.303643 GGGCTTGACAGAACCCAGG 60.304 63.158 4.97 0.00 42.33 4.45
132 133 1.672356 CGGGCTTGACAGAACCCAG 60.672 63.158 9.45 0.75 42.97 4.45
133 134 2.144078 TCGGGCTTGACAGAACCCA 61.144 57.895 9.45 0.00 42.97 4.51
134 135 1.671379 GTCGGGCTTGACAGAACCC 60.671 63.158 5.71 0.00 38.75 4.11
135 136 2.027625 CGTCGGGCTTGACAGAACC 61.028 63.158 10.22 0.00 38.84 3.62
136 137 1.006571 TCGTCGGGCTTGACAGAAC 60.007 57.895 10.22 0.00 38.84 3.01
137 138 1.176619 TCTCGTCGGGCTTGACAGAA 61.177 55.000 10.22 0.00 38.84 3.02
138 139 1.176619 TTCTCGTCGGGCTTGACAGA 61.177 55.000 10.22 8.81 38.84 3.41
139 140 0.319555 TTTCTCGTCGGGCTTGACAG 60.320 55.000 10.22 7.14 38.84 3.51
140 141 0.599204 GTTTCTCGTCGGGCTTGACA 60.599 55.000 10.22 0.00 38.84 3.58
141 142 1.289800 GGTTTCTCGTCGGGCTTGAC 61.290 60.000 0.00 1.12 35.49 3.18
142 143 1.005394 GGTTTCTCGTCGGGCTTGA 60.005 57.895 0.00 0.00 0.00 3.02
143 144 0.245539 TAGGTTTCTCGTCGGGCTTG 59.754 55.000 0.00 0.00 0.00 4.01
144 145 0.531200 CTAGGTTTCTCGTCGGGCTT 59.469 55.000 0.00 0.00 0.00 4.35
145 146 1.946475 GCTAGGTTTCTCGTCGGGCT 61.946 60.000 0.00 0.00 0.00 5.19
146 147 1.518792 GCTAGGTTTCTCGTCGGGC 60.519 63.158 0.00 0.00 0.00 6.13
147 148 0.100861 GAGCTAGGTTTCTCGTCGGG 59.899 60.000 0.00 0.00 0.00 5.14
148 149 0.248134 CGAGCTAGGTTTCTCGTCGG 60.248 60.000 8.75 0.00 44.95 4.79
149 150 3.221834 CGAGCTAGGTTTCTCGTCG 57.778 57.895 8.75 0.00 44.95 5.12
153 154 1.144276 GGGCCGAGCTAGGTTTCTC 59.856 63.158 14.88 0.00 0.00 2.87
154 155 2.722201 CGGGCCGAGCTAGGTTTCT 61.722 63.158 24.41 0.00 0.00 2.52
155 156 2.202892 CGGGCCGAGCTAGGTTTC 60.203 66.667 24.41 4.80 0.00 2.78
156 157 2.682494 TCGGGCCGAGCTAGGTTT 60.682 61.111 27.46 0.00 0.00 3.27
157 158 2.563013 TAGTCGGGCCGAGCTAGGTT 62.563 60.000 31.98 11.22 36.23 3.50
158 159 2.962142 CTAGTCGGGCCGAGCTAGGT 62.962 65.000 33.90 19.65 36.23 3.08
159 160 2.203308 TAGTCGGGCCGAGCTAGG 60.203 66.667 31.98 8.78 36.23 3.02
160 161 2.262303 CCTAGTCGGGCCGAGCTAG 61.262 68.421 34.21 34.21 36.23 3.42
161 162 1.699054 TACCTAGTCGGGCCGAGCTA 61.699 60.000 31.98 27.92 36.23 3.32
162 163 2.354755 ATACCTAGTCGGGCCGAGCT 62.355 60.000 31.98 28.29 36.23 4.09
163 164 1.902432 ATACCTAGTCGGGCCGAGC 60.902 63.158 31.98 23.11 36.23 5.03
164 165 0.536687 TCATACCTAGTCGGGCCGAG 60.537 60.000 31.98 20.29 36.23 4.63
165 166 0.111832 ATCATACCTAGTCGGGCCGA 59.888 55.000 27.46 27.46 36.97 5.54
166 167 0.526662 GATCATACCTAGTCGGGCCG 59.473 60.000 22.51 22.51 36.97 6.13
167 168 1.546476 CTGATCATACCTAGTCGGGCC 59.454 57.143 0.00 0.00 36.97 5.80
168 169 1.546476 CCTGATCATACCTAGTCGGGC 59.454 57.143 0.00 0.00 36.97 6.13
169 170 2.877866 ACCTGATCATACCTAGTCGGG 58.122 52.381 0.00 2.79 41.80 5.14
170 171 4.939052 AAACCTGATCATACCTAGTCGG 57.061 45.455 0.00 0.00 39.35 4.79
171 172 5.864474 GCATAAACCTGATCATACCTAGTCG 59.136 44.000 0.00 0.00 0.00 4.18
172 173 6.870965 CAGCATAAACCTGATCATACCTAGTC 59.129 42.308 0.00 0.00 32.03 2.59
173 174 6.239714 CCAGCATAAACCTGATCATACCTAGT 60.240 42.308 0.00 0.00 32.03 2.57
174 175 6.014242 TCCAGCATAAACCTGATCATACCTAG 60.014 42.308 0.00 0.00 32.03 3.02
175 176 5.843969 TCCAGCATAAACCTGATCATACCTA 59.156 40.000 0.00 0.00 32.03 3.08
176 177 4.660303 TCCAGCATAAACCTGATCATACCT 59.340 41.667 0.00 0.00 32.03 3.08
177 178 4.973168 TCCAGCATAAACCTGATCATACC 58.027 43.478 0.00 0.00 32.03 2.73
178 179 4.453819 GCTCCAGCATAAACCTGATCATAC 59.546 45.833 0.00 0.00 41.59 2.39
179 180 4.645535 GCTCCAGCATAAACCTGATCATA 58.354 43.478 0.00 0.00 41.59 2.15
180 181 3.484407 GCTCCAGCATAAACCTGATCAT 58.516 45.455 0.00 0.00 41.59 2.45
181 182 2.923121 GCTCCAGCATAAACCTGATCA 58.077 47.619 0.00 0.00 41.59 2.92
210 211 5.853572 AGTATGAGGGGTTAGGTCAAAAA 57.146 39.130 0.00 0.00 0.00 1.94
211 212 6.731919 TCTTAGTATGAGGGGTTAGGTCAAAA 59.268 38.462 0.00 0.00 0.00 2.44
212 213 6.266080 TCTTAGTATGAGGGGTTAGGTCAAA 58.734 40.000 0.00 0.00 0.00 2.69
213 214 5.845734 TCTTAGTATGAGGGGTTAGGTCAA 58.154 41.667 0.00 0.00 0.00 3.18
214 215 5.476950 TCTTAGTATGAGGGGTTAGGTCA 57.523 43.478 0.00 0.00 0.00 4.02
215 216 6.326843 ACATTCTTAGTATGAGGGGTTAGGTC 59.673 42.308 5.86 0.00 0.00 3.85
216 217 6.210522 ACATTCTTAGTATGAGGGGTTAGGT 58.789 40.000 5.86 0.00 0.00 3.08
217 218 6.749036 ACATTCTTAGTATGAGGGGTTAGG 57.251 41.667 5.86 0.00 0.00 2.69
218 219 9.462606 AAAAACATTCTTAGTATGAGGGGTTAG 57.537 33.333 5.86 0.00 0.00 2.34
219 220 9.238368 CAAAAACATTCTTAGTATGAGGGGTTA 57.762 33.333 5.86 0.00 0.00 2.85
220 221 7.947890 TCAAAAACATTCTTAGTATGAGGGGTT 59.052 33.333 5.86 0.00 0.00 4.11
221 222 7.466804 TCAAAAACATTCTTAGTATGAGGGGT 58.533 34.615 5.86 0.00 0.00 4.95
222 223 7.938140 TCAAAAACATTCTTAGTATGAGGGG 57.062 36.000 5.86 0.00 0.00 4.79
252 253 9.328845 GCTTTAGATCATCTTCAAAAGATCTCT 57.671 33.333 11.23 12.44 46.20 3.10
253 254 8.558700 GGCTTTAGATCATCTTCAAAAGATCTC 58.441 37.037 11.23 1.27 46.20 2.75
254 255 8.051535 TGGCTTTAGATCATCTTCAAAAGATCT 58.948 33.333 11.23 8.60 46.20 2.75
255 256 8.218338 TGGCTTTAGATCATCTTCAAAAGATC 57.782 34.615 11.23 4.73 46.20 2.75
257 258 6.094603 GCTGGCTTTAGATCATCTTCAAAAGA 59.905 38.462 11.23 0.00 42.69 2.52
258 259 6.095160 AGCTGGCTTTAGATCATCTTCAAAAG 59.905 38.462 0.00 0.00 0.00 2.27
259 260 5.948162 AGCTGGCTTTAGATCATCTTCAAAA 59.052 36.000 0.00 0.00 0.00 2.44
260 261 5.503927 AGCTGGCTTTAGATCATCTTCAAA 58.496 37.500 0.00 0.00 0.00 2.69
261 262 5.108187 AGCTGGCTTTAGATCATCTTCAA 57.892 39.130 0.00 0.00 0.00 2.69
262 263 4.767578 AGCTGGCTTTAGATCATCTTCA 57.232 40.909 0.00 0.00 0.00 3.02
263 264 6.348376 GCATTAGCTGGCTTTAGATCATCTTC 60.348 42.308 0.00 0.00 37.91 2.87
264 265 5.472820 GCATTAGCTGGCTTTAGATCATCTT 59.527 40.000 0.00 0.00 37.91 2.40
265 266 5.002516 GCATTAGCTGGCTTTAGATCATCT 58.997 41.667 0.00 0.00 37.91 2.90
266 267 4.142945 CGCATTAGCTGGCTTTAGATCATC 60.143 45.833 0.00 0.00 39.10 2.92
267 268 3.750130 CGCATTAGCTGGCTTTAGATCAT 59.250 43.478 0.00 0.00 39.10 2.45
268 269 3.133691 CGCATTAGCTGGCTTTAGATCA 58.866 45.455 0.00 0.00 39.10 2.92
269 270 3.393800 TCGCATTAGCTGGCTTTAGATC 58.606 45.455 0.00 0.00 39.10 2.75
270 271 3.475566 TCGCATTAGCTGGCTTTAGAT 57.524 42.857 0.00 0.00 39.10 1.98
271 272 2.936498 GTTCGCATTAGCTGGCTTTAGA 59.064 45.455 0.00 0.00 39.10 2.10
272 273 2.032178 GGTTCGCATTAGCTGGCTTTAG 59.968 50.000 0.00 0.00 39.10 1.85
273 274 2.014128 GGTTCGCATTAGCTGGCTTTA 58.986 47.619 0.00 0.00 39.10 1.85
274 275 0.811281 GGTTCGCATTAGCTGGCTTT 59.189 50.000 0.00 0.00 39.10 3.51
275 276 0.322456 TGGTTCGCATTAGCTGGCTT 60.322 50.000 0.00 0.00 39.10 4.35
276 277 0.322456 TTGGTTCGCATTAGCTGGCT 60.322 50.000 0.00 0.00 39.10 4.75
277 278 0.525761 TTTGGTTCGCATTAGCTGGC 59.474 50.000 0.00 0.00 39.10 4.85
278 279 1.135402 GGTTTGGTTCGCATTAGCTGG 60.135 52.381 0.00 0.00 39.10 4.85
279 280 1.539388 TGGTTTGGTTCGCATTAGCTG 59.461 47.619 0.00 0.00 39.10 4.24
280 281 1.904287 TGGTTTGGTTCGCATTAGCT 58.096 45.000 0.00 0.00 39.10 3.32
281 282 2.939460 ATGGTTTGGTTCGCATTAGC 57.061 45.000 0.00 0.00 37.42 3.09
282 283 5.560966 ACTAATGGTTTGGTTCGCATTAG 57.439 39.130 2.11 2.11 38.12 1.73
283 284 5.241949 ACAACTAATGGTTTGGTTCGCATTA 59.758 36.000 0.00 0.00 34.66 1.90
284 285 4.038642 ACAACTAATGGTTTGGTTCGCATT 59.961 37.500 0.00 0.00 34.66 3.56
285 286 3.572255 ACAACTAATGGTTTGGTTCGCAT 59.428 39.130 0.00 0.00 34.66 4.73
286 287 2.952978 ACAACTAATGGTTTGGTTCGCA 59.047 40.909 0.00 0.00 34.66 5.10
287 288 3.636282 ACAACTAATGGTTTGGTTCGC 57.364 42.857 0.00 0.00 34.66 4.70
288 289 4.515944 TGGTACAACTAATGGTTTGGTTCG 59.484 41.667 0.00 0.00 34.66 3.95
309 310 1.726248 GCAAAACCTAGCGCAAAATGG 59.274 47.619 11.47 6.39 0.00 3.16
312 313 2.099921 TCTTGCAAAACCTAGCGCAAAA 59.900 40.909 11.47 0.00 43.25 2.44
319 320 3.253432 GTGGGAACTCTTGCAAAACCTAG 59.747 47.826 0.00 0.00 0.00 3.02
350 351 5.095145 TCAGTACGTGTAGTGGTAGATCT 57.905 43.478 13.39 0.00 37.17 2.75
421 422 1.180029 GAACTGTCCAGGCAATGCAT 58.820 50.000 7.79 0.00 0.00 3.96
456 457 4.426313 GCCCCTTCCCTTGGGTCG 62.426 72.222 5.51 0.00 44.20 4.79
488 489 2.494677 CGGTCTCGTCAGGGAAGAT 58.505 57.895 0.00 0.00 0.00 2.40
529 530 2.502213 TATCGTGGGCACAATAGACG 57.498 50.000 0.00 0.00 0.00 4.18
538 539 0.539986 GTCCCTTCTTATCGTGGGCA 59.460 55.000 0.00 0.00 39.49 5.36
559 560 0.603975 GCCGGAGCACTTGAAGTCTT 60.604 55.000 5.05 0.00 39.53 3.01
574 575 3.821421 AATCCTAACTTCACTAGCCGG 57.179 47.619 0.00 0.00 0.00 6.13
591 593 9.543783 AGAGTACAACCGAAATTTATCCTAATC 57.456 33.333 0.00 0.00 0.00 1.75
606 609 0.029035 CCGATCGGAGAGTACAACCG 59.971 60.000 30.62 15.68 43.63 4.44
620 623 0.179111 TCGTCTGACCATTGCCGATC 60.179 55.000 1.55 0.00 0.00 3.69
621 624 0.460284 GTCGTCTGACCATTGCCGAT 60.460 55.000 1.55 0.00 39.30 4.18
622 625 1.080093 GTCGTCTGACCATTGCCGA 60.080 57.895 1.55 0.00 39.30 5.54
623 626 2.444624 CGTCGTCTGACCATTGCCG 61.445 63.158 1.55 0.00 42.37 5.69
625 628 1.078759 CTCCGTCGTCTGACCATTGC 61.079 60.000 1.55 0.00 42.37 3.56
626 629 0.243907 ACTCCGTCGTCTGACCATTG 59.756 55.000 1.55 0.00 42.37 2.82
627 630 0.526662 GACTCCGTCGTCTGACCATT 59.473 55.000 1.55 0.00 42.37 3.16
628 631 0.608308 TGACTCCGTCGTCTGACCAT 60.608 55.000 1.55 0.00 42.37 3.55
629 632 0.608308 ATGACTCCGTCGTCTGACCA 60.608 55.000 1.55 0.00 42.37 4.02
630 633 0.099082 GATGACTCCGTCGTCTGACC 59.901 60.000 1.55 0.00 43.07 4.02
631 634 0.247735 CGATGACTCCGTCGTCTGAC 60.248 60.000 12.72 0.00 43.89 3.51
632 635 2.087344 CGATGACTCCGTCGTCTGA 58.913 57.895 12.72 0.00 43.89 3.27
633 636 4.672550 CGATGACTCCGTCGTCTG 57.327 61.111 12.72 4.83 43.89 3.51
643 646 5.043903 CCTTATTTCACATCGACGATGACT 58.956 41.667 37.26 18.32 42.09 3.41
669 672 1.406539 CAAACTATGATGGGGTGCAGC 59.593 52.381 7.55 7.55 0.00 5.25
672 675 1.750778 CACCAAACTATGATGGGGTGC 59.249 52.381 0.00 0.00 41.17 5.01
673 676 2.291540 ACCACCAAACTATGATGGGGTG 60.292 50.000 0.00 0.00 44.09 4.61
682 685 3.009723 CGAAGATGCACCACCAAACTAT 58.990 45.455 0.00 0.00 0.00 2.12
687 690 2.290008 ACATACGAAGATGCACCACCAA 60.290 45.455 0.00 0.00 0.00 3.67
708 711 0.396435 ACATTCTTCACACGCCTCCA 59.604 50.000 0.00 0.00 0.00 3.86
754 757 1.745115 CGCGAGGAAATGGAGCCAA 60.745 57.895 0.00 0.00 0.00 4.52
763 766 3.127203 TGAAAAGTCAAAACGCGAGGAAA 59.873 39.130 15.93 0.00 0.00 3.13
839 842 7.103641 TCGTATCCTGAAAAGACTTTTGCTAT 58.896 34.615 17.76 8.30 31.94 2.97
851 854 6.567701 GCAAAGAACACATCGTATCCTGAAAA 60.568 38.462 0.00 0.00 0.00 2.29
852 855 5.106712 GCAAAGAACACATCGTATCCTGAAA 60.107 40.000 0.00 0.00 0.00 2.69
853 856 4.391830 GCAAAGAACACATCGTATCCTGAA 59.608 41.667 0.00 0.00 0.00 3.02
854 857 3.932710 GCAAAGAACACATCGTATCCTGA 59.067 43.478 0.00 0.00 0.00 3.86
855 858 3.063997 GGCAAAGAACACATCGTATCCTG 59.936 47.826 0.00 0.00 0.00 3.86
856 859 3.055094 AGGCAAAGAACACATCGTATCCT 60.055 43.478 0.00 0.00 0.00 3.24
857 860 3.270877 AGGCAAAGAACACATCGTATCC 58.729 45.455 0.00 0.00 0.00 2.59
858 861 4.946784 AAGGCAAAGAACACATCGTATC 57.053 40.909 0.00 0.00 0.00 2.24
859 862 5.003804 AGAAAGGCAAAGAACACATCGTAT 58.996 37.500 0.00 0.00 0.00 3.06
860 863 4.213270 CAGAAAGGCAAAGAACACATCGTA 59.787 41.667 0.00 0.00 0.00 3.43
861 864 3.003689 CAGAAAGGCAAAGAACACATCGT 59.996 43.478 0.00 0.00 0.00 3.73
862 865 3.558505 CAGAAAGGCAAAGAACACATCG 58.441 45.455 0.00 0.00 0.00 3.84
863 866 3.243501 TGCAGAAAGGCAAAGAACACATC 60.244 43.478 0.00 0.00 41.65 3.06
864 867 2.694628 TGCAGAAAGGCAAAGAACACAT 59.305 40.909 0.00 0.00 41.65 3.21
910 913 0.995675 AGGGGCAGACATGGGCTAAT 60.996 55.000 0.00 0.00 0.00 1.73
930 934 0.816825 CAATGGAGGAGATGCGTGGG 60.817 60.000 0.00 0.00 0.00 4.61
932 936 2.028420 TTCAATGGAGGAGATGCGTG 57.972 50.000 0.00 0.00 0.00 5.34
933 937 2.359900 GTTTCAATGGAGGAGATGCGT 58.640 47.619 0.00 0.00 0.00 5.24
985 997 0.878416 AACATTTTTCGGCTGCGCTA 59.122 45.000 9.73 0.00 0.00 4.26
1335 1347 4.767841 AGCAGCTCGCACGTCTCG 62.768 66.667 10.16 0.67 46.13 4.04
1661 1673 8.896722 ACTAGAACCCTAGATCTTTTTACTCA 57.103 34.615 0.00 0.00 44.00 3.41
1697 1714 4.266714 TCTCTTAAATAAAACAGGGGCCG 58.733 43.478 0.00 0.00 0.00 6.13
1699 1716 6.584185 TGTTCTCTTAAATAAAACAGGGGC 57.416 37.500 0.00 0.00 0.00 5.80
1833 1850 7.779073 AGCATTGGAAATTTCTATTCAGGAAG 58.221 34.615 17.42 0.00 0.00 3.46
1870 1887 1.559368 TGCCATGCTACTGCCAATTT 58.441 45.000 0.00 0.00 38.71 1.82
1877 1894 2.105477 ACCTAGGATTGCCATGCTACTG 59.895 50.000 17.98 0.00 36.29 2.74
1920 2036 8.024145 TCATTTAAAAACCATACACCCAGTTT 57.976 30.769 0.00 0.00 34.02 2.66
2004 2121 5.232414 CGAAAAGAATTCCTCGACTCCATAC 59.768 44.000 13.98 0.00 35.95 2.39
2009 2126 3.860536 CCTCGAAAAGAATTCCTCGACTC 59.139 47.826 16.57 0.92 37.41 3.36
2025 2142 1.829222 ACGCTTTCTTATCCCCTCGAA 59.171 47.619 0.00 0.00 0.00 3.71
2027 2144 1.933853 CAACGCTTTCTTATCCCCTCG 59.066 52.381 0.00 0.00 0.00 4.63
2080 2197 3.434453 CCAACTTCACCCTGGAACAACTA 60.434 47.826 0.00 0.00 38.70 2.24
2093 2210 7.170658 TGCAAAATAACATTAAGCCAACTTCAC 59.829 33.333 0.00 0.00 37.33 3.18
2138 2256 5.540911 GAGATGAATCTCCAAGGATCTGAC 58.459 45.833 8.84 0.00 45.88 3.51
2189 2313 8.936864 GTGTTGAGCTAATCAGTAATACAAACT 58.063 33.333 0.00 0.00 39.68 2.66
2215 2339 2.607635 ACCATTGACTTTATGCGCGTAG 59.392 45.455 8.43 3.49 0.00 3.51
2219 2343 1.742831 TCCACCATTGACTTTATGCGC 59.257 47.619 0.00 0.00 0.00 6.09
2250 2374 6.816136 AGAAGTTAAAACCAAATTCCCACTG 58.184 36.000 0.00 0.00 33.99 3.66
2345 2469 0.582005 GCAAACAGTGACTCCGTGTC 59.418 55.000 0.00 0.00 45.54 3.67
2570 2698 3.127791 ACAGGACCTCATCAGGATCTT 57.872 47.619 0.00 0.00 43.65 2.40
2707 2837 3.755378 AGCAGTAACAGCCATTCTCTTTG 59.245 43.478 0.00 0.00 0.00 2.77
2747 2877 1.802960 CTGCTGCAGGAGTTTGTACTG 59.197 52.381 25.76 0.00 33.84 2.74
2783 2913 3.503748 AGCACAACCATACTCTTTTCTGC 59.496 43.478 0.00 0.00 0.00 4.26
2791 2921 3.403038 ACAGAACAGCACAACCATACTC 58.597 45.455 0.00 0.00 0.00 2.59
2815 2945 9.827411 GGAATTTGTACTAAATCACAGAAGAAC 57.173 33.333 7.30 0.00 0.00 3.01
2828 2958 5.865085 ACAGACTGCAGGAATTTGTACTAA 58.135 37.500 19.93 0.00 0.00 2.24
2851 2981 3.211045 GGGTCTTACAAGTCACAGCAAA 58.789 45.455 0.00 0.00 0.00 3.68
2855 2985 3.007940 TCATGGGGTCTTACAAGTCACAG 59.992 47.826 0.00 0.00 0.00 3.66
2856 2986 2.976185 TCATGGGGTCTTACAAGTCACA 59.024 45.455 0.00 0.00 0.00 3.58
2992 3261 2.042162 AGGCAGATGACCAGTGGAAAAT 59.958 45.455 18.40 5.91 0.00 1.82
3016 3285 1.788308 CACCTGCAAAACAATGAAGCG 59.212 47.619 0.00 0.00 0.00 4.68
3069 3338 2.337749 ATCCATCGTCTGGTCGTCGC 62.338 60.000 6.66 0.00 46.08 5.19
3171 3440 0.526524 CATTCAGAGGACGGCTCGAC 60.527 60.000 1.50 0.00 0.00 4.20
3174 3443 0.532573 TGTCATTCAGAGGACGGCTC 59.467 55.000 0.00 0.00 39.36 4.70
3207 3476 0.404426 TCGGAGTCTCCCTCTTCACA 59.596 55.000 13.54 0.00 40.30 3.58
3252 3521 3.308904 GGGGCCTTTCCTGTTACTTGTAT 60.309 47.826 0.84 0.00 34.39 2.29
3290 3560 1.241165 TCGTTCGTAGAACTCCTGCA 58.759 50.000 10.62 0.00 45.90 4.41
3294 3564 4.882508 GAACTTTCGTTCGTAGAACTCC 57.117 45.455 10.62 0.00 45.90 3.85
3311 3581 3.467803 CCTGGAGAACGACAAAAGAACT 58.532 45.455 0.00 0.00 0.00 3.01
3422 3697 5.303747 TGCCAAGAATACATTAAACCACG 57.696 39.130 0.00 0.00 0.00 4.94
3491 3766 1.008995 CACGCCAACGGTTCAAAGG 60.009 57.895 0.00 0.00 46.04 3.11
3538 3813 0.317479 ACTGCCTACCGAGTGACAAC 59.683 55.000 0.00 0.00 0.00 3.32
3539 3814 1.542915 GTACTGCCTACCGAGTGACAA 59.457 52.381 0.00 0.00 0.00 3.18
3540 3815 1.171308 GTACTGCCTACCGAGTGACA 58.829 55.000 0.00 0.00 0.00 3.58
3571 3846 7.009540 GGTTATATGAAATGTTGACTGCAAAGC 59.990 37.037 0.00 0.00 35.42 3.51
3599 3874 9.191995 AGTACTGTTTGTAAGCAAAAATATTGC 57.808 29.630 5.06 5.06 45.01 3.56
3604 3879 7.704899 GTCCAAGTACTGTTTGTAAGCAAAAAT 59.295 33.333 0.00 0.00 45.01 1.82
3618 3894 9.227777 GTAGGAAATTTTATGTCCAAGTACTGT 57.772 33.333 0.00 0.00 33.57 3.55
3619 3895 9.449719 AGTAGGAAATTTTATGTCCAAGTACTG 57.550 33.333 0.00 0.00 33.57 2.74
3716 3998 1.747355 GATTGGGCACAACAGGAGATG 59.253 52.381 1.86 0.00 39.87 2.90
3748 4030 0.944386 TTGAAAGTCGAAGCACCAGC 59.056 50.000 0.00 0.00 42.56 4.85
3780 4062 4.378356 GCTTACTGAATCACATTTGTCGCA 60.378 41.667 0.00 0.00 0.00 5.10
3869 4151 2.029844 GCGGACAGGTGAGCAGTTC 61.030 63.158 0.00 0.00 0.00 3.01
3895 4177 0.654683 CTGCCTCGTTCTAAGCATGC 59.345 55.000 10.51 10.51 34.16 4.06
3956 4238 1.062587 GACGATGCACATTAAAGCGCT 59.937 47.619 2.64 2.64 0.00 5.92
4002 4284 3.642778 CTACAGTCCGCACGGTGGG 62.643 68.421 17.36 17.36 32.61 4.61
4084 4371 7.094848 TGTCGTTTCATGATTATTTTCTGCTGA 60.095 33.333 0.00 0.00 0.00 4.26
4120 4408 2.670905 TGGCGTGTCATGATTAAGTTCG 59.329 45.455 0.00 0.00 0.00 3.95
4243 4531 1.062525 GCCGTTTCACCATCATCGC 59.937 57.895 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.