Multiple sequence alignment - TraesCS2B01G195600

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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 TraesCS2B01G195600 chr2B 100.000 3618 0 0 1 3618 173206940 173203323 0.000000e+00 6682
1 TraesCS2B01G195600 chr2D 89.437 1723 94 32 274 1942 120257155 120255467 0.000000e+00 2093
2 TraesCS2B01G195600 chr2D 95.257 738 33 1 1941 2676 120255435 120254698 0.000000e+00 1168
3 TraesCS2B01G195600 chr2D 94.394 660 18 7 2671 3319 120254660 120254009 0.000000e+00 996
4 TraesCS2B01G195600 chr2D 93.277 357 13 3 3263 3618 120254013 120253667 1.930000e-142 516
5 TraesCS2B01G195600 chr2A 89.177 1737 105 37 243 1939 124214305 124212612 0.000000e+00 2089
6 TraesCS2B01G195600 chr2A 93.828 956 44 9 2671 3618 124211793 124210845 0.000000e+00 1424
7 TraesCS2B01G195600 chr2A 95.168 745 27 6 1941 2676 124212577 124211833 0.000000e+00 1168
8 TraesCS2B01G195600 chr3D 92.373 236 17 1 8 242 568056533 568056298 5.790000e-88 335
9 TraesCS2B01G195600 chr1B 91.358 243 19 2 5 246 642155025 642155266 7.490000e-87 331
10 TraesCS2B01G195600 chrUn 91.739 230 18 1 8 236 164079 163850 5.830000e-83 318
11 TraesCS2B01G195600 chr1D 91.739 230 18 1 8 236 18763813 18763584 5.830000e-83 318
12 TraesCS2B01G195600 chr1D 91.304 230 19 1 8 236 362518779 362518550 2.710000e-81 313
13 TraesCS2B01G195600 chr7B 90.948 232 18 3 8 236 550029556 550029325 3.510000e-80 309
14 TraesCS2B01G195600 chr1A 90.476 231 19 3 8 236 509706137 509706366 5.870000e-78 302
15 TraesCS2B01G195600 chr1A 90.043 231 20 3 8 236 509779402 509779631 2.730000e-76 296
16 TraesCS2B01G195600 chr7D 90.086 232 20 3 8 236 503935609 503935378 7.590000e-77 298


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 TraesCS2B01G195600 chr2B 173203323 173206940 3617 True 6682.000000 6682 100.000000 1 3618 1 chr2B.!!$R1 3617
1 TraesCS2B01G195600 chr2D 120253667 120257155 3488 True 1193.250000 2093 93.091250 274 3618 4 chr2D.!!$R1 3344
2 TraesCS2B01G195600 chr2A 124210845 124214305 3460 True 1560.333333 2089 92.724333 243 3618 3 chr2A.!!$R1 3375

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
97 98 0.034756 GTGTGGTTGCAATTTCCCCC 59.965 55.0 0.59 0.0 0.00 5.40 F
244 245 0.175760 GCCAGAGATGCACCTACGAA 59.824 55.0 0.00 0.0 0.00 3.85 F
337 343 0.182299 GGGAGAGCAAGATTGGGAGG 59.818 60.0 0.00 0.0 0.00 4.30 F
439 460 0.603707 CTGCACCACAGTACCACAGG 60.604 60.0 0.00 0.0 41.86 4.00 F
1556 1628 0.106419 TTGGACCACACCACTTTCCC 60.106 55.0 0.00 0.0 39.85 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1133 1198 0.100503 CGCCCAAATCCCGAAACATC 59.899 55.000 0.0 0.0 0.00 3.06 R
1278 1348 0.892358 GACCTTCGTCCCCCAAAACC 60.892 60.000 0.0 0.0 32.40 3.27 R
1312 1384 1.077663 AGCCACCAAATTCCAGACCAT 59.922 47.619 0.0 0.0 0.00 3.55 R
2213 2335 1.202582 GACGAGCAGACTTAGGAGCAA 59.797 52.381 0.0 0.0 0.00 3.91 R
3227 3416 1.690633 GGGATCTGCCTGACCCTCA 60.691 63.158 0.0 0.0 39.28 3.86 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
60 61 8.999431 TGTGATGATGAACTATGAATGATCATG 58.001 33.333 9.46 0.00 45.82 3.07
61 62 9.000486 GTGATGATGAACTATGAATGATCATGT 58.000 33.333 9.46 0.00 45.82 3.21
75 76 9.264719 TGAATGATCATGTAGTATGTGATGAAC 57.735 33.333 9.46 0.00 33.03 3.18
76 77 9.486497 GAATGATCATGTAGTATGTGATGAACT 57.514 33.333 9.46 0.00 33.03 3.01
79 80 9.136323 TGATCATGTAGTATGTGATGAACTAGT 57.864 33.333 0.00 0.00 33.03 2.57
80 81 9.404348 GATCATGTAGTATGTGATGAACTAGTG 57.596 37.037 0.00 0.00 33.03 2.74
81 82 8.293699 TCATGTAGTATGTGATGAACTAGTGT 57.706 34.615 0.00 0.00 0.00 3.55
82 83 8.190784 TCATGTAGTATGTGATGAACTAGTGTG 58.809 37.037 0.00 0.00 0.00 3.82
83 84 6.863275 TGTAGTATGTGATGAACTAGTGTGG 58.137 40.000 0.00 0.00 0.00 4.17
84 85 6.436218 TGTAGTATGTGATGAACTAGTGTGGT 59.564 38.462 0.00 0.00 0.00 4.16
85 86 6.360370 AGTATGTGATGAACTAGTGTGGTT 57.640 37.500 0.00 0.00 0.00 3.67
86 87 6.166279 AGTATGTGATGAACTAGTGTGGTTG 58.834 40.000 0.00 0.00 0.00 3.77
87 88 3.138304 TGTGATGAACTAGTGTGGTTGC 58.862 45.455 0.00 0.00 0.00 4.17
88 89 3.138304 GTGATGAACTAGTGTGGTTGCA 58.862 45.455 0.00 0.00 0.00 4.08
89 90 3.563808 GTGATGAACTAGTGTGGTTGCAA 59.436 43.478 0.00 0.00 0.00 4.08
90 91 4.216257 GTGATGAACTAGTGTGGTTGCAAT 59.784 41.667 0.59 0.00 0.00 3.56
91 92 4.826733 TGATGAACTAGTGTGGTTGCAATT 59.173 37.500 0.59 0.00 0.00 2.32
92 93 5.301551 TGATGAACTAGTGTGGTTGCAATTT 59.698 36.000 0.59 0.00 0.00 1.82
93 94 5.181690 TGAACTAGTGTGGTTGCAATTTC 57.818 39.130 0.59 0.00 0.00 2.17
94 95 4.037446 TGAACTAGTGTGGTTGCAATTTCC 59.963 41.667 0.59 0.00 0.00 3.13
95 96 2.890945 ACTAGTGTGGTTGCAATTTCCC 59.109 45.455 0.59 0.00 0.00 3.97
96 97 1.047801 AGTGTGGTTGCAATTTCCCC 58.952 50.000 0.59 0.00 0.00 4.81
97 98 0.034756 GTGTGGTTGCAATTTCCCCC 59.965 55.000 0.59 0.00 0.00 5.40
98 99 1.291906 GTGGTTGCAATTTCCCCCG 59.708 57.895 0.59 0.00 0.00 5.73
99 100 2.264480 GGTTGCAATTTCCCCCGC 59.736 61.111 0.59 0.00 0.00 6.13
100 101 2.126110 GTTGCAATTTCCCCCGCG 60.126 61.111 0.59 0.00 0.00 6.46
101 102 2.282532 TTGCAATTTCCCCCGCGA 60.283 55.556 8.23 0.00 0.00 5.87
102 103 1.903890 TTGCAATTTCCCCCGCGAA 60.904 52.632 8.23 0.00 0.00 4.70
103 104 1.872197 TTGCAATTTCCCCCGCGAAG 61.872 55.000 8.23 0.00 0.00 3.79
122 123 6.450845 CGAAGCACTTTTTCAAATTATGCA 57.549 33.333 0.00 0.00 34.03 3.96
123 124 6.519315 CGAAGCACTTTTTCAAATTATGCAG 58.481 36.000 0.00 0.00 34.03 4.41
124 125 6.144402 CGAAGCACTTTTTCAAATTATGCAGT 59.856 34.615 0.00 0.00 34.03 4.40
125 126 7.306749 CGAAGCACTTTTTCAAATTATGCAGTT 60.307 33.333 0.00 0.00 34.03 3.16
126 127 7.790823 AGCACTTTTTCAAATTATGCAGTTT 57.209 28.000 0.00 0.00 34.03 2.66
127 128 7.854534 AGCACTTTTTCAAATTATGCAGTTTC 58.145 30.769 0.00 0.00 34.03 2.78
128 129 7.495279 AGCACTTTTTCAAATTATGCAGTTTCA 59.505 29.630 0.00 0.00 34.03 2.69
129 130 8.284693 GCACTTTTTCAAATTATGCAGTTTCAT 58.715 29.630 0.00 0.00 0.00 2.57
135 136 9.729023 TTTCAAATTATGCAGTTTCATATACGG 57.271 29.630 0.00 0.00 0.00 4.02
136 137 7.870826 TCAAATTATGCAGTTTCATATACGGG 58.129 34.615 0.00 0.00 0.00 5.28
137 138 7.500892 TCAAATTATGCAGTTTCATATACGGGT 59.499 33.333 0.00 0.00 0.00 5.28
138 139 7.817418 AATTATGCAGTTTCATATACGGGTT 57.183 32.000 0.00 0.00 0.00 4.11
139 140 6.854496 TTATGCAGTTTCATATACGGGTTC 57.146 37.500 0.00 0.00 0.00 3.62
140 141 4.481368 TGCAGTTTCATATACGGGTTCT 57.519 40.909 0.00 0.00 0.00 3.01
141 142 5.601583 TGCAGTTTCATATACGGGTTCTA 57.398 39.130 0.00 0.00 0.00 2.10
142 143 5.353938 TGCAGTTTCATATACGGGTTCTAC 58.646 41.667 0.00 0.00 0.00 2.59
143 144 5.128171 TGCAGTTTCATATACGGGTTCTACT 59.872 40.000 0.00 0.00 0.00 2.57
144 145 5.690857 GCAGTTTCATATACGGGTTCTACTC 59.309 44.000 0.00 0.00 0.00 2.59
145 146 6.461231 GCAGTTTCATATACGGGTTCTACTCT 60.461 42.308 0.00 0.00 0.00 3.24
146 147 6.918569 CAGTTTCATATACGGGTTCTACTCTG 59.081 42.308 0.00 0.00 0.00 3.35
147 148 5.449107 TTCATATACGGGTTCTACTCTGC 57.551 43.478 0.00 0.00 0.00 4.26
148 149 3.825014 TCATATACGGGTTCTACTCTGCC 59.175 47.826 0.00 0.00 0.00 4.85
149 150 2.456073 ATACGGGTTCTACTCTGCCT 57.544 50.000 0.00 0.00 0.00 4.75
150 151 2.226962 TACGGGTTCTACTCTGCCTT 57.773 50.000 0.00 0.00 0.00 4.35
151 152 0.608640 ACGGGTTCTACTCTGCCTTG 59.391 55.000 0.00 0.00 0.00 3.61
152 153 0.741221 CGGGTTCTACTCTGCCTTGC 60.741 60.000 0.00 0.00 0.00 4.01
153 154 0.324943 GGGTTCTACTCTGCCTTGCA 59.675 55.000 0.00 0.00 36.92 4.08
154 155 1.443802 GGTTCTACTCTGCCTTGCAC 58.556 55.000 0.00 0.00 33.79 4.57
155 156 1.071605 GTTCTACTCTGCCTTGCACG 58.928 55.000 0.00 0.00 33.79 5.34
156 157 0.966179 TTCTACTCTGCCTTGCACGA 59.034 50.000 0.00 0.00 33.79 4.35
157 158 1.186200 TCTACTCTGCCTTGCACGAT 58.814 50.000 0.00 0.00 33.79 3.73
158 159 1.550524 TCTACTCTGCCTTGCACGATT 59.449 47.619 0.00 0.00 33.79 3.34
159 160 2.028112 TCTACTCTGCCTTGCACGATTT 60.028 45.455 0.00 0.00 33.79 2.17
160 161 1.609208 ACTCTGCCTTGCACGATTTT 58.391 45.000 0.00 0.00 33.79 1.82
161 162 1.267806 ACTCTGCCTTGCACGATTTTG 59.732 47.619 0.00 0.00 33.79 2.44
162 163 1.536766 CTCTGCCTTGCACGATTTTGA 59.463 47.619 0.00 0.00 33.79 2.69
163 164 1.266718 TCTGCCTTGCACGATTTTGAC 59.733 47.619 0.00 0.00 33.79 3.18
164 165 0.313672 TGCCTTGCACGATTTTGACC 59.686 50.000 0.00 0.00 31.71 4.02
165 166 0.598065 GCCTTGCACGATTTTGACCT 59.402 50.000 0.00 0.00 0.00 3.85
166 167 1.666888 GCCTTGCACGATTTTGACCTG 60.667 52.381 0.00 0.00 0.00 4.00
167 168 1.666888 CCTTGCACGATTTTGACCTGC 60.667 52.381 0.00 0.00 0.00 4.85
168 169 1.001487 CTTGCACGATTTTGACCTGCA 60.001 47.619 0.00 0.00 36.08 4.41
169 170 1.028130 TGCACGATTTTGACCTGCAA 58.972 45.000 0.00 0.00 34.97 4.08
170 171 1.406898 TGCACGATTTTGACCTGCAAA 59.593 42.857 0.00 0.00 44.38 3.68
181 182 6.820470 TTTGACCTGCAAAATAGTTTTTCG 57.180 33.333 0.00 0.00 43.18 3.46
182 183 5.508200 TGACCTGCAAAATAGTTTTTCGT 57.492 34.783 0.00 0.00 32.72 3.85
183 184 5.516090 TGACCTGCAAAATAGTTTTTCGTC 58.484 37.500 0.00 0.00 32.72 4.20
184 185 4.533222 ACCTGCAAAATAGTTTTTCGTCG 58.467 39.130 0.00 0.00 32.72 5.12
185 186 4.273969 ACCTGCAAAATAGTTTTTCGTCGA 59.726 37.500 0.00 0.00 32.72 4.20
186 187 5.209240 CCTGCAAAATAGTTTTTCGTCGAA 58.791 37.500 2.90 2.90 32.72 3.71
187 188 5.115021 CCTGCAAAATAGTTTTTCGTCGAAC 59.885 40.000 7.29 0.00 32.72 3.95
188 189 5.812652 TGCAAAATAGTTTTTCGTCGAACT 58.187 33.333 7.29 5.22 39.32 3.01
189 190 5.679355 TGCAAAATAGTTTTTCGTCGAACTG 59.321 36.000 7.29 0.00 36.79 3.16
190 191 5.679792 GCAAAATAGTTTTTCGTCGAACTGT 59.320 36.000 7.29 0.00 36.79 3.55
191 192 6.847289 GCAAAATAGTTTTTCGTCGAACTGTA 59.153 34.615 7.29 0.00 36.79 2.74
192 193 7.373966 GCAAAATAGTTTTTCGTCGAACTGTAA 59.626 33.333 7.29 0.00 36.79 2.41
193 194 9.212687 CAAAATAGTTTTTCGTCGAACTGTAAA 57.787 29.630 7.29 2.84 36.79 2.01
194 195 8.757817 AAATAGTTTTTCGTCGAACTGTAAAC 57.242 30.769 18.65 18.65 36.79 2.01
195 196 4.814465 AGTTTTTCGTCGAACTGTAAACG 58.186 39.130 19.52 3.92 34.96 3.60
196 197 2.909076 TTTCGTCGAACTGTAAACGC 57.091 45.000 7.29 0.00 35.22 4.84
197 198 1.130955 TTCGTCGAACTGTAAACGCC 58.869 50.000 2.90 0.00 35.22 5.68
198 199 0.311790 TCGTCGAACTGTAAACGCCT 59.688 50.000 0.00 0.00 35.22 5.52
199 200 1.134226 CGTCGAACTGTAAACGCCTT 58.866 50.000 0.00 0.00 0.00 4.35
200 201 2.031245 TCGTCGAACTGTAAACGCCTTA 60.031 45.455 0.00 0.00 35.22 2.69
201 202 2.919229 CGTCGAACTGTAAACGCCTTAT 59.081 45.455 0.00 0.00 0.00 1.73
202 203 3.241552 CGTCGAACTGTAAACGCCTTATG 60.242 47.826 0.00 0.00 0.00 1.90
203 204 2.669434 TCGAACTGTAAACGCCTTATGC 59.331 45.455 0.00 0.00 0.00 3.14
219 220 4.138109 GCGGGTCGCGGTTTTACG 62.138 66.667 6.13 4.20 44.55 3.18
220 221 3.481024 CGGGTCGCGGTTTTACGG 61.481 66.667 6.13 0.00 0.00 4.02
221 222 2.048316 GGGTCGCGGTTTTACGGA 60.048 61.111 6.13 0.00 0.00 4.69
222 223 1.448365 GGGTCGCGGTTTTACGGAT 60.448 57.895 6.13 0.00 0.00 4.18
223 224 1.423721 GGGTCGCGGTTTTACGGATC 61.424 60.000 6.13 0.00 0.00 3.36
224 225 0.459063 GGTCGCGGTTTTACGGATCT 60.459 55.000 6.13 0.00 0.00 2.75
225 226 0.643820 GTCGCGGTTTTACGGATCTG 59.356 55.000 6.13 0.00 0.00 2.90
226 227 1.079875 TCGCGGTTTTACGGATCTGC 61.080 55.000 6.13 0.00 0.00 4.26
227 228 1.719709 GCGGTTTTACGGATCTGCC 59.280 57.895 0.00 0.00 0.00 4.85
228 229 1.022451 GCGGTTTTACGGATCTGCCA 61.022 55.000 0.00 0.00 35.94 4.92
229 230 1.006832 CGGTTTTACGGATCTGCCAG 58.993 55.000 0.00 0.00 35.94 4.85
230 231 1.404986 CGGTTTTACGGATCTGCCAGA 60.405 52.381 0.00 0.00 35.94 3.86
231 232 2.280628 GGTTTTACGGATCTGCCAGAG 58.719 52.381 0.00 0.00 35.94 3.35
232 233 2.093658 GGTTTTACGGATCTGCCAGAGA 60.094 50.000 0.00 0.00 35.94 3.10
233 234 3.432326 GGTTTTACGGATCTGCCAGAGAT 60.432 47.826 0.00 0.00 44.78 2.75
234 235 3.459232 TTTACGGATCTGCCAGAGATG 57.541 47.619 0.00 0.00 41.91 2.90
235 236 0.676184 TACGGATCTGCCAGAGATGC 59.324 55.000 0.00 0.00 41.91 3.91
237 238 3.003740 GGATCTGCCAGAGATGCAC 57.996 57.895 0.00 0.00 46.33 4.57
238 239 0.534652 GGATCTGCCAGAGATGCACC 60.535 60.000 0.00 0.00 46.33 5.01
239 240 0.469070 GATCTGCCAGAGATGCACCT 59.531 55.000 0.00 0.00 41.91 4.00
240 241 1.690893 GATCTGCCAGAGATGCACCTA 59.309 52.381 0.00 0.00 41.91 3.08
241 242 0.826715 TCTGCCAGAGATGCACCTAC 59.173 55.000 0.00 0.00 34.46 3.18
242 243 0.529337 CTGCCAGAGATGCACCTACG 60.529 60.000 0.00 0.00 34.46 3.51
243 244 0.970427 TGCCAGAGATGCACCTACGA 60.970 55.000 0.00 0.00 32.85 3.43
244 245 0.175760 GCCAGAGATGCACCTACGAA 59.824 55.000 0.00 0.00 0.00 3.85
245 246 1.804372 GCCAGAGATGCACCTACGAAG 60.804 57.143 0.00 0.00 0.00 3.79
264 265 5.163893 ACGAAGTTTACGAAGTTATGCATGG 60.164 40.000 10.16 0.00 31.82 3.66
265 266 5.163893 CGAAGTTTACGAAGTTATGCATGGT 60.164 40.000 10.16 0.36 37.78 3.55
266 267 6.035220 CGAAGTTTACGAAGTTATGCATGGTA 59.965 38.462 10.16 0.00 37.78 3.25
267 268 6.903883 AGTTTACGAAGTTATGCATGGTAG 57.096 37.500 10.16 0.00 37.78 3.18
268 269 6.403878 AGTTTACGAAGTTATGCATGGTAGT 58.596 36.000 10.16 4.66 37.78 2.73
269 270 6.534079 AGTTTACGAAGTTATGCATGGTAGTC 59.466 38.462 10.16 0.00 37.78 2.59
270 271 3.444916 ACGAAGTTATGCATGGTAGTCG 58.555 45.455 10.16 13.67 37.78 4.18
271 272 3.119245 ACGAAGTTATGCATGGTAGTCGT 60.119 43.478 10.16 14.29 37.78 4.34
272 273 4.096833 ACGAAGTTATGCATGGTAGTCGTA 59.903 41.667 19.12 0.00 37.78 3.43
282 283 4.260948 GCATGGTAGTCGTAGTACAGTACC 60.261 50.000 19.58 19.58 0.00 3.34
288 289 5.667539 AGTCGTAGTACAGTACCAGTCTA 57.332 43.478 7.13 0.00 0.00 2.59
290 291 5.872070 AGTCGTAGTACAGTACCAGTCTAAC 59.128 44.000 7.13 0.00 0.00 2.34
291 292 5.064071 GTCGTAGTACAGTACCAGTCTAACC 59.936 48.000 7.13 0.00 0.00 2.85
292 293 5.046304 TCGTAGTACAGTACCAGTCTAACCT 60.046 44.000 7.13 0.00 0.00 3.50
293 294 6.154534 TCGTAGTACAGTACCAGTCTAACCTA 59.845 42.308 7.13 0.00 0.00 3.08
315 321 4.864916 TTTCACAGCGCAAGAGATATTC 57.135 40.909 11.47 0.00 43.02 1.75
337 343 0.182299 GGGAGAGCAAGATTGGGAGG 59.818 60.000 0.00 0.00 0.00 4.30
438 459 2.918571 CTGCACCACAGTACCACAG 58.081 57.895 0.00 0.00 41.86 3.66
439 460 0.603707 CTGCACCACAGTACCACAGG 60.604 60.000 0.00 0.00 41.86 4.00
440 461 1.302511 GCACCACAGTACCACAGGG 60.303 63.158 0.00 0.00 41.29 4.45
441 462 1.302511 CACCACAGTACCACAGGGC 60.303 63.158 0.00 0.00 37.90 5.19
442 463 2.351276 CCACAGTACCACAGGGCC 59.649 66.667 0.00 0.00 37.90 5.80
570 602 5.707764 AGAAGGAAAGAGAATTTCGAAAGGG 59.292 40.000 16.80 0.00 0.00 3.95
604 645 3.700350 CCACCTCCCCCTCCTCCT 61.700 72.222 0.00 0.00 0.00 3.69
605 646 2.041405 CACCTCCCCCTCCTCCTC 60.041 72.222 0.00 0.00 0.00 3.71
606 647 3.369388 ACCTCCCCCTCCTCCTCC 61.369 72.222 0.00 0.00 0.00 4.30
607 648 3.039526 CCTCCCCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
608 649 2.612251 CTCCCCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
609 650 3.036959 TCCCCCTCCTCCTCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
633 674 1.070175 CGAACCACGTGCGAAATTTCT 60.070 47.619 10.91 0.00 36.57 2.52
654 695 1.595382 CAATCATCGCGGTCCCTCC 60.595 63.158 6.13 0.00 0.00 4.30
765 806 2.897350 GCGGGGGCGAGATTTCAG 60.897 66.667 0.00 0.00 0.00 3.02
830 872 2.660552 GTACGCACACGGCACACT 60.661 61.111 0.00 0.00 46.04 3.55
1133 1198 2.484287 ATCAACAAGGGTGAGCGGGG 62.484 60.000 0.00 0.00 0.00 5.73
1134 1199 2.852075 AACAAGGGTGAGCGGGGA 60.852 61.111 0.00 0.00 0.00 4.81
1222 1291 3.641986 TTGCGTTCCGGTTCGTGC 61.642 61.111 18.26 10.31 0.00 5.34
1236 1306 2.730183 TCGTGCGAACAAAGTTCTTG 57.270 45.000 8.11 0.00 0.00 3.02
1237 1307 1.112459 CGTGCGAACAAAGTTCTTGC 58.888 50.000 8.11 5.77 0.00 4.01
1278 1348 3.423645 GCGAGATCTGAGTTTGTTTTCCG 60.424 47.826 0.00 0.00 0.00 4.30
1284 1356 4.739195 TCTGAGTTTGTTTTCCGGTTTTG 58.261 39.130 0.00 0.00 0.00 2.44
1312 1384 2.528743 GGTCCTCGTCGCGTCGATA 61.529 63.158 27.02 16.24 38.42 2.92
1336 1408 0.890683 CTGGAATTTGGTGGCTGGTC 59.109 55.000 0.00 0.00 0.00 4.02
1352 1424 3.498397 GCTGGTCGAGTGAATTGAGAAAA 59.502 43.478 0.00 0.00 0.00 2.29
1409 1481 4.704103 AGGCCGAGGCTCACAGGA 62.704 66.667 15.95 0.00 41.60 3.86
1435 1507 1.228675 CACCAAGAGCCCTTTGCCT 60.229 57.895 0.00 0.00 42.71 4.75
1556 1628 0.106419 TTGGACCACACCACTTTCCC 60.106 55.000 0.00 0.00 39.85 3.97
1620 1702 9.553064 GAATCCATACAGATAAAAGTCAGATGT 57.447 33.333 0.00 0.00 0.00 3.06
1696 1785 3.439857 TTGCAAGGCCTGAAATCTAGT 57.560 42.857 5.69 0.00 0.00 2.57
1709 1798 6.036953 CCTGAAATCTAGTTGAGAGTGATTGC 59.963 42.308 0.00 0.00 37.70 3.56
1823 1912 9.636789 TGAGTGATAATAGTACTAGGTTTGCTA 57.363 33.333 8.85 0.00 0.00 3.49
1866 1955 5.248870 TCGACCTTAAACCGTATCCTTAC 57.751 43.478 0.00 0.00 0.00 2.34
1878 1967 5.419788 ACCGTATCCTTACTGATACAACACA 59.580 40.000 10.71 0.00 44.77 3.72
1973 2095 5.511363 AGAGTAGTCTGCAGGTGTACTTAT 58.489 41.667 15.13 8.41 0.00 1.73
2213 2335 0.981183 TTGCCTAGTGATCCGGTTGT 59.019 50.000 0.00 0.00 0.00 3.32
2252 2374 3.242413 CGTCCGAATGCTTCTGGTAATTG 60.242 47.826 0.00 0.00 0.00 2.32
2256 2378 1.392589 ATGCTTCTGGTAATTGCCCG 58.607 50.000 10.34 3.72 0.00 6.13
2281 2403 7.415095 CGGTGATTTGTTGTACATATCCATTGT 60.415 37.037 0.00 0.00 36.25 2.71
2455 2586 9.118300 GAACTCATGATCATCTTTTCTTACCAT 57.882 33.333 4.86 0.00 0.00 3.55
2480 2611 8.234136 TCGAAGTATATGGATCTAACTTGTGT 57.766 34.615 0.00 0.00 30.83 3.72
2494 2625 8.658171 TCTAACTTGTGTTTTTGTTTTCGTAC 57.342 30.769 0.00 0.00 37.59 3.67
2654 2785 2.688446 GCCTTATGCCCTTACCAGAAAC 59.312 50.000 0.00 0.00 0.00 2.78
2701 2880 5.627780 GCGTTTTGTTTAGGTTATGGTTCTG 59.372 40.000 0.00 0.00 0.00 3.02
2964 3143 9.995594 ATATTATGTTTGTATTCCCATATGGCT 57.004 29.630 16.97 5.64 0.00 4.75
2965 3144 7.759489 TTATGTTTGTATTCCCATATGGCTC 57.241 36.000 16.97 4.83 0.00 4.70
2966 3145 5.387113 TGTTTGTATTCCCATATGGCTCT 57.613 39.130 16.97 4.93 0.00 4.09
3002 3181 5.400066 TTCGGTTGTCAGATCTGTATGAA 57.600 39.130 21.92 14.53 0.00 2.57
3012 3191 7.550551 TGTCAGATCTGTATGAATTCTTGTTCC 59.449 37.037 21.92 0.00 0.00 3.62
3068 3253 5.668135 TGGATAATGATTTCCCATGGACT 57.332 39.130 15.22 0.00 0.00 3.85
3069 3254 6.778542 TGGATAATGATTTCCCATGGACTA 57.221 37.500 15.22 0.00 0.00 2.59
3071 3256 7.768643 TGGATAATGATTTCCCATGGACTAAT 58.231 34.615 15.22 9.40 0.00 1.73
3072 3257 8.899765 TGGATAATGATTTCCCATGGACTAATA 58.100 33.333 15.22 0.00 0.00 0.98
3073 3258 9.927081 GGATAATGATTTCCCATGGACTAATAT 57.073 33.333 15.22 1.37 0.00 1.28
3103 3292 4.223659 ACGGAAACAAATTTCGCATGTAC 58.776 39.130 0.00 0.00 44.53 2.90
3117 3306 3.120889 CGCATGTACTCAACAAGTGACAG 60.121 47.826 0.00 0.00 42.70 3.51
3192 3381 9.132521 GTAAAGTTGCTTTCGTCTATAGTTGTA 57.867 33.333 0.00 0.00 35.21 2.41
3295 3537 3.208692 AGGATAGGGTGTGAGAGGAAGAT 59.791 47.826 0.00 0.00 0.00 2.40
3463 3706 1.134551 TGTTTGGAAGTTGCAAAGGGC 60.135 47.619 21.21 11.42 38.34 5.19
3499 3743 0.600057 CAACTTGCTGCCTTTCTCCC 59.400 55.000 0.00 0.00 0.00 4.30
3509 3753 2.091885 TGCCTTTCTCCCTCAACTTGTT 60.092 45.455 0.00 0.00 0.00 2.83
3512 3756 3.243535 CCTTTCTCCCTCAACTTGTTTGC 60.244 47.826 0.00 0.00 34.88 3.68
3548 3792 3.807622 GTGCTTGCTAATATAAGACCGCA 59.192 43.478 0.00 0.00 0.00 5.69
3581 3828 4.093472 TGATGGTGATGATGATGATGCA 57.907 40.909 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.740710 ATGATCATTCATAGTTCATCATCACAT 57.259 29.630 1.18 0.00 40.87 3.21
34 35 8.999431 CATGATCATTCATAGTTCATCATCACA 58.001 33.333 5.16 0.00 40.70 3.58
35 36 9.000486 ACATGATCATTCATAGTTCATCATCAC 58.000 33.333 5.16 0.00 40.70 3.06
49 50 9.264719 GTTCATCACATACTACATGATCATTCA 57.735 33.333 5.16 0.00 36.00 2.57
50 51 9.486497 AGTTCATCACATACTACATGATCATTC 57.514 33.333 5.16 0.00 30.58 2.67
53 54 9.136323 ACTAGTTCATCACATACTACATGATCA 57.864 33.333 0.00 0.00 30.58 2.92
54 55 9.404348 CACTAGTTCATCACATACTACATGATC 57.596 37.037 0.00 0.00 30.58 2.92
55 56 8.918116 ACACTAGTTCATCACATACTACATGAT 58.082 33.333 0.00 0.00 33.28 2.45
56 57 8.190784 CACACTAGTTCATCACATACTACATGA 58.809 37.037 0.00 0.00 0.00 3.07
57 58 7.436376 CCACACTAGTTCATCACATACTACATG 59.564 40.741 0.00 0.00 0.00 3.21
58 59 7.124298 ACCACACTAGTTCATCACATACTACAT 59.876 37.037 0.00 0.00 0.00 2.29
59 60 6.436218 ACCACACTAGTTCATCACATACTACA 59.564 38.462 0.00 0.00 0.00 2.74
60 61 6.864342 ACCACACTAGTTCATCACATACTAC 58.136 40.000 0.00 0.00 0.00 2.73
61 62 7.320399 CAACCACACTAGTTCATCACATACTA 58.680 38.462 0.00 0.00 0.00 1.82
62 63 6.166279 CAACCACACTAGTTCATCACATACT 58.834 40.000 0.00 0.00 0.00 2.12
63 64 5.163854 GCAACCACACTAGTTCATCACATAC 60.164 44.000 0.00 0.00 0.00 2.39
64 65 4.935205 GCAACCACACTAGTTCATCACATA 59.065 41.667 0.00 0.00 0.00 2.29
65 66 3.753272 GCAACCACACTAGTTCATCACAT 59.247 43.478 0.00 0.00 0.00 3.21
66 67 3.138304 GCAACCACACTAGTTCATCACA 58.862 45.455 0.00 0.00 0.00 3.58
67 68 3.138304 TGCAACCACACTAGTTCATCAC 58.862 45.455 0.00 0.00 0.00 3.06
68 69 3.483808 TGCAACCACACTAGTTCATCA 57.516 42.857 0.00 0.00 0.00 3.07
69 70 5.376854 AATTGCAACCACACTAGTTCATC 57.623 39.130 0.00 0.00 0.00 2.92
70 71 5.278957 GGAAATTGCAACCACACTAGTTCAT 60.279 40.000 0.00 0.00 0.00 2.57
71 72 4.037446 GGAAATTGCAACCACACTAGTTCA 59.963 41.667 0.00 0.00 0.00 3.18
72 73 4.546570 GGAAATTGCAACCACACTAGTTC 58.453 43.478 0.00 0.00 0.00 3.01
73 74 3.320826 GGGAAATTGCAACCACACTAGTT 59.679 43.478 0.00 0.00 0.00 2.24
74 75 2.890945 GGGAAATTGCAACCACACTAGT 59.109 45.455 0.00 0.00 0.00 2.57
75 76 2.231235 GGGGAAATTGCAACCACACTAG 59.769 50.000 0.00 0.00 0.00 2.57
76 77 2.243810 GGGGAAATTGCAACCACACTA 58.756 47.619 0.00 0.00 0.00 2.74
77 78 1.047801 GGGGAAATTGCAACCACACT 58.952 50.000 0.00 0.00 0.00 3.55
78 79 0.034756 GGGGGAAATTGCAACCACAC 59.965 55.000 0.00 0.00 0.00 3.82
79 80 1.467678 CGGGGGAAATTGCAACCACA 61.468 55.000 0.00 0.00 0.00 4.17
80 81 1.291906 CGGGGGAAATTGCAACCAC 59.708 57.895 0.00 0.00 0.00 4.16
81 82 2.578714 GCGGGGGAAATTGCAACCA 61.579 57.895 0.00 0.00 0.00 3.67
82 83 2.264480 GCGGGGGAAATTGCAACC 59.736 61.111 0.00 0.00 0.00 3.77
83 84 2.126110 CGCGGGGGAAATTGCAAC 60.126 61.111 0.00 0.00 0.00 4.17
84 85 1.872197 CTTCGCGGGGGAAATTGCAA 61.872 55.000 6.13 0.00 0.00 4.08
85 86 2.282532 TTCGCGGGGGAAATTGCA 60.283 55.556 6.13 0.00 0.00 4.08
86 87 2.489751 CTTCGCGGGGGAAATTGC 59.510 61.111 6.13 0.00 0.00 3.56
87 88 2.339556 TGCTTCGCGGGGGAAATTG 61.340 57.895 6.13 0.00 0.00 2.32
88 89 2.034999 TGCTTCGCGGGGGAAATT 59.965 55.556 6.13 0.00 0.00 1.82
89 90 2.750237 GTGCTTCGCGGGGGAAAT 60.750 61.111 6.13 0.00 0.00 2.17
90 91 2.969300 AAAGTGCTTCGCGGGGGAAA 62.969 55.000 6.13 0.00 0.00 3.13
91 92 2.969300 AAAAGTGCTTCGCGGGGGAA 62.969 55.000 6.13 0.00 0.00 3.97
92 93 2.969300 AAAAAGTGCTTCGCGGGGGA 62.969 55.000 6.13 0.00 0.00 4.81
93 94 2.472232 GAAAAAGTGCTTCGCGGGGG 62.472 60.000 6.13 0.00 0.00 5.40
94 95 1.081442 GAAAAAGTGCTTCGCGGGG 60.081 57.895 6.13 0.00 0.00 5.73
95 96 0.030101 TTGAAAAAGTGCTTCGCGGG 59.970 50.000 6.13 0.11 0.00 6.13
96 97 1.833860 TTTGAAAAAGTGCTTCGCGG 58.166 45.000 6.13 0.00 0.00 6.46
97 98 5.532041 CATAATTTGAAAAAGTGCTTCGCG 58.468 37.500 0.00 0.00 0.00 5.87
98 99 5.107530 TGCATAATTTGAAAAAGTGCTTCGC 60.108 36.000 11.20 0.00 32.67 4.70
99 100 6.144402 ACTGCATAATTTGAAAAAGTGCTTCG 59.856 34.615 11.20 4.99 32.67 3.79
100 101 7.412137 ACTGCATAATTTGAAAAAGTGCTTC 57.588 32.000 11.20 0.00 32.67 3.86
101 102 7.790823 AACTGCATAATTTGAAAAAGTGCTT 57.209 28.000 11.20 0.00 32.67 3.91
102 103 7.495279 TGAAACTGCATAATTTGAAAAAGTGCT 59.505 29.630 11.20 0.00 32.67 4.40
103 104 7.629130 TGAAACTGCATAATTTGAAAAAGTGC 58.371 30.769 0.00 5.28 0.00 4.40
109 110 9.729023 CCGTATATGAAACTGCATAATTTGAAA 57.271 29.630 0.00 0.00 34.67 2.69
110 111 8.349245 CCCGTATATGAAACTGCATAATTTGAA 58.651 33.333 0.00 0.00 34.67 2.69
111 112 7.500892 ACCCGTATATGAAACTGCATAATTTGA 59.499 33.333 0.00 0.00 34.67 2.69
112 113 7.648142 ACCCGTATATGAAACTGCATAATTTG 58.352 34.615 0.00 0.00 34.67 2.32
113 114 7.817418 ACCCGTATATGAAACTGCATAATTT 57.183 32.000 0.00 0.00 34.67 1.82
114 115 7.719633 AGAACCCGTATATGAAACTGCATAATT 59.280 33.333 0.00 0.00 34.67 1.40
115 116 7.224297 AGAACCCGTATATGAAACTGCATAAT 58.776 34.615 0.00 0.00 34.67 1.28
116 117 6.588204 AGAACCCGTATATGAAACTGCATAA 58.412 36.000 0.00 0.00 34.67 1.90
117 118 6.169557 AGAACCCGTATATGAAACTGCATA 57.830 37.500 0.00 0.00 35.41 3.14
118 119 5.036117 AGAACCCGTATATGAAACTGCAT 57.964 39.130 0.00 0.00 0.00 3.96
119 120 4.481368 AGAACCCGTATATGAAACTGCA 57.519 40.909 0.00 0.00 0.00 4.41
120 121 5.598769 AGTAGAACCCGTATATGAAACTGC 58.401 41.667 0.00 0.00 0.00 4.40
121 122 6.918569 CAGAGTAGAACCCGTATATGAAACTG 59.081 42.308 0.00 0.00 0.00 3.16
122 123 6.461231 GCAGAGTAGAACCCGTATATGAAACT 60.461 42.308 0.00 0.00 0.00 2.66
123 124 5.690857 GCAGAGTAGAACCCGTATATGAAAC 59.309 44.000 0.00 0.00 0.00 2.78
124 125 5.221382 GGCAGAGTAGAACCCGTATATGAAA 60.221 44.000 0.00 0.00 0.00 2.69
125 126 4.280174 GGCAGAGTAGAACCCGTATATGAA 59.720 45.833 0.00 0.00 0.00 2.57
126 127 3.825014 GGCAGAGTAGAACCCGTATATGA 59.175 47.826 0.00 0.00 0.00 2.15
127 128 3.827302 AGGCAGAGTAGAACCCGTATATG 59.173 47.826 0.00 0.00 0.00 1.78
128 129 4.115398 AGGCAGAGTAGAACCCGTATAT 57.885 45.455 0.00 0.00 0.00 0.86
129 130 3.589951 AGGCAGAGTAGAACCCGTATA 57.410 47.619 0.00 0.00 0.00 1.47
130 131 2.431057 CAAGGCAGAGTAGAACCCGTAT 59.569 50.000 0.00 0.00 0.00 3.06
131 132 1.822990 CAAGGCAGAGTAGAACCCGTA 59.177 52.381 0.00 0.00 0.00 4.02
132 133 0.608640 CAAGGCAGAGTAGAACCCGT 59.391 55.000 0.00 0.00 0.00 5.28
133 134 0.741221 GCAAGGCAGAGTAGAACCCG 60.741 60.000 0.00 0.00 0.00 5.28
134 135 0.324943 TGCAAGGCAGAGTAGAACCC 59.675 55.000 0.00 0.00 33.32 4.11
135 136 1.443802 GTGCAAGGCAGAGTAGAACC 58.556 55.000 0.00 0.00 40.08 3.62
136 137 1.071605 CGTGCAAGGCAGAGTAGAAC 58.928 55.000 0.00 0.00 40.08 3.01
137 138 0.966179 TCGTGCAAGGCAGAGTAGAA 59.034 50.000 0.00 0.00 40.08 2.10
138 139 1.186200 ATCGTGCAAGGCAGAGTAGA 58.814 50.000 0.00 0.00 40.08 2.59
139 140 2.015736 AATCGTGCAAGGCAGAGTAG 57.984 50.000 0.00 0.00 40.08 2.57
140 141 2.472695 AAATCGTGCAAGGCAGAGTA 57.527 45.000 0.00 0.00 40.08 2.59
141 142 1.267806 CAAAATCGTGCAAGGCAGAGT 59.732 47.619 0.00 0.00 40.08 3.24
142 143 1.536766 TCAAAATCGTGCAAGGCAGAG 59.463 47.619 0.00 0.00 40.08 3.35
143 144 1.266718 GTCAAAATCGTGCAAGGCAGA 59.733 47.619 0.00 0.00 40.08 4.26
144 145 1.666888 GGTCAAAATCGTGCAAGGCAG 60.667 52.381 0.00 0.00 40.08 4.85
145 146 0.313672 GGTCAAAATCGTGCAAGGCA 59.686 50.000 0.00 0.00 35.60 4.75
146 147 0.598065 AGGTCAAAATCGTGCAAGGC 59.402 50.000 0.00 0.00 0.00 4.35
147 148 1.666888 GCAGGTCAAAATCGTGCAAGG 60.667 52.381 0.00 0.00 43.30 3.61
148 149 1.689959 GCAGGTCAAAATCGTGCAAG 58.310 50.000 0.00 0.00 43.30 4.01
149 150 3.863681 GCAGGTCAAAATCGTGCAA 57.136 47.368 0.00 0.00 43.30 4.08
150 151 2.159184 TTTTGCAGGTCAAAATCGTGCA 60.159 40.909 8.77 8.77 46.44 4.57
151 152 2.132740 TTTGCAGGTCAAAATCGTGC 57.867 45.000 0.00 0.00 41.36 5.34
158 159 6.334202 ACGAAAAACTATTTTGCAGGTCAAA 58.666 32.000 0.00 0.00 42.50 2.69
159 160 5.897050 ACGAAAAACTATTTTGCAGGTCAA 58.103 33.333 0.00 0.00 38.83 3.18
160 161 5.508200 ACGAAAAACTATTTTGCAGGTCA 57.492 34.783 0.00 0.00 38.83 4.02
161 162 4.611366 CGACGAAAAACTATTTTGCAGGTC 59.389 41.667 0.00 0.00 38.83 3.85
162 163 4.273969 TCGACGAAAAACTATTTTGCAGGT 59.726 37.500 0.00 0.00 38.83 4.00
163 164 4.778904 TCGACGAAAAACTATTTTGCAGG 58.221 39.130 0.00 0.00 38.83 4.85
164 165 5.907391 AGTTCGACGAAAAACTATTTTGCAG 59.093 36.000 12.67 0.00 38.83 4.41
165 166 5.679355 CAGTTCGACGAAAAACTATTTTGCA 59.321 36.000 12.67 0.00 38.83 4.08
166 167 5.679792 ACAGTTCGACGAAAAACTATTTTGC 59.320 36.000 12.67 0.00 38.83 3.68
167 168 8.756376 TTACAGTTCGACGAAAAACTATTTTG 57.244 30.769 12.67 0.00 38.83 2.44
168 169 9.213819 GTTTACAGTTCGACGAAAAACTATTTT 57.786 29.630 20.44 3.59 41.37 1.82
169 170 7.580165 CGTTTACAGTTCGACGAAAAACTATTT 59.420 33.333 23.00 7.33 37.69 1.40
170 171 7.059212 CGTTTACAGTTCGACGAAAAACTATT 58.941 34.615 23.00 9.12 37.69 1.73
171 172 6.575132 CGTTTACAGTTCGACGAAAAACTAT 58.425 36.000 23.00 8.51 37.69 2.12
172 173 5.554324 GCGTTTACAGTTCGACGAAAAACTA 60.554 40.000 23.00 7.40 37.69 2.24
173 174 4.780013 GCGTTTACAGTTCGACGAAAAACT 60.780 41.667 23.00 12.50 37.69 2.66
174 175 3.412186 GCGTTTACAGTTCGACGAAAAAC 59.588 43.478 12.67 16.63 37.69 2.43
175 176 3.543852 GGCGTTTACAGTTCGACGAAAAA 60.544 43.478 12.67 6.47 37.69 1.94
176 177 2.033832 GGCGTTTACAGTTCGACGAAAA 60.034 45.455 12.67 0.00 37.69 2.29
177 178 1.522258 GGCGTTTACAGTTCGACGAAA 59.478 47.619 12.67 0.00 37.69 3.46
178 179 1.130955 GGCGTTTACAGTTCGACGAA 58.869 50.000 6.10 6.10 37.69 3.85
179 180 0.311790 AGGCGTTTACAGTTCGACGA 59.688 50.000 0.00 0.00 37.69 4.20
180 181 1.134226 AAGGCGTTTACAGTTCGACG 58.866 50.000 0.00 0.00 37.69 5.12
181 182 3.483085 GCATAAGGCGTTTACAGTTCGAC 60.483 47.826 0.00 0.00 0.00 4.20
182 183 2.669434 GCATAAGGCGTTTACAGTTCGA 59.331 45.455 0.00 0.00 0.00 3.71
183 184 3.034406 GCATAAGGCGTTTACAGTTCG 57.966 47.619 0.00 0.00 0.00 3.95
203 204 3.481024 CCGTAAAACCGCGACCCG 61.481 66.667 8.23 0.22 0.00 5.28
204 205 1.423721 GATCCGTAAAACCGCGACCC 61.424 60.000 8.23 0.00 0.00 4.46
205 206 0.459063 AGATCCGTAAAACCGCGACC 60.459 55.000 8.23 0.00 0.00 4.79
206 207 0.643820 CAGATCCGTAAAACCGCGAC 59.356 55.000 8.23 0.00 0.00 5.19
207 208 1.079875 GCAGATCCGTAAAACCGCGA 61.080 55.000 8.23 0.00 0.00 5.87
208 209 1.347221 GCAGATCCGTAAAACCGCG 59.653 57.895 0.00 0.00 0.00 6.46
209 210 1.022451 TGGCAGATCCGTAAAACCGC 61.022 55.000 0.00 0.00 37.80 5.68
210 211 1.006832 CTGGCAGATCCGTAAAACCG 58.993 55.000 9.42 0.00 37.80 4.44
211 212 2.093658 TCTCTGGCAGATCCGTAAAACC 60.094 50.000 19.11 0.00 37.80 3.27
212 213 3.247006 TCTCTGGCAGATCCGTAAAAC 57.753 47.619 19.11 0.00 37.80 2.43
213 214 3.797039 CATCTCTGGCAGATCCGTAAAA 58.203 45.455 19.11 0.00 40.20 1.52
214 215 2.483714 GCATCTCTGGCAGATCCGTAAA 60.484 50.000 19.11 0.00 40.20 2.01
215 216 1.069204 GCATCTCTGGCAGATCCGTAA 59.931 52.381 19.11 0.19 40.20 3.18
216 217 0.676184 GCATCTCTGGCAGATCCGTA 59.324 55.000 19.11 1.98 40.20 4.02
217 218 1.332889 TGCATCTCTGGCAGATCCGT 61.333 55.000 19.11 1.43 40.20 4.69
218 219 0.879400 GTGCATCTCTGGCAGATCCG 60.879 60.000 19.11 10.03 40.20 4.18
219 220 0.534652 GGTGCATCTCTGGCAGATCC 60.535 60.000 19.11 9.87 40.20 3.36
220 221 0.469070 AGGTGCATCTCTGGCAGATC 59.531 55.000 19.11 8.29 40.20 2.75
221 222 1.415659 GTAGGTGCATCTCTGGCAGAT 59.584 52.381 19.11 0.21 43.33 2.90
222 223 0.826715 GTAGGTGCATCTCTGGCAGA 59.173 55.000 17.68 17.68 42.85 4.26
223 224 0.529337 CGTAGGTGCATCTCTGGCAG 60.529 60.000 0.56 8.58 42.85 4.85
224 225 0.970427 TCGTAGGTGCATCTCTGGCA 60.970 55.000 0.56 0.00 39.32 4.92
225 226 0.175760 TTCGTAGGTGCATCTCTGGC 59.824 55.000 0.56 0.00 0.00 4.85
226 227 1.478510 ACTTCGTAGGTGCATCTCTGG 59.521 52.381 0.56 0.00 0.00 3.86
227 228 2.949451 ACTTCGTAGGTGCATCTCTG 57.051 50.000 0.56 0.00 0.00 3.35
228 229 3.963428 AAACTTCGTAGGTGCATCTCT 57.037 42.857 0.56 0.00 0.00 3.10
229 230 3.546670 CGTAAACTTCGTAGGTGCATCTC 59.453 47.826 0.56 0.00 0.00 2.75
230 231 3.192001 TCGTAAACTTCGTAGGTGCATCT 59.808 43.478 4.13 4.13 0.00 2.90
231 232 3.504863 TCGTAAACTTCGTAGGTGCATC 58.495 45.455 0.00 0.00 0.00 3.91
232 233 3.581024 TCGTAAACTTCGTAGGTGCAT 57.419 42.857 0.00 0.00 0.00 3.96
233 234 3.243501 ACTTCGTAAACTTCGTAGGTGCA 60.244 43.478 0.00 0.00 31.83 4.57
234 235 3.311966 ACTTCGTAAACTTCGTAGGTGC 58.688 45.455 0.00 0.00 31.83 5.01
235 236 6.453396 GCATAACTTCGTAAACTTCGTAGGTG 60.453 42.308 0.00 0.00 31.83 4.00
236 237 5.574443 GCATAACTTCGTAAACTTCGTAGGT 59.426 40.000 0.00 0.00 31.83 3.08
237 238 5.574055 TGCATAACTTCGTAAACTTCGTAGG 59.426 40.000 0.00 0.00 31.83 3.18
238 239 6.621737 TGCATAACTTCGTAAACTTCGTAG 57.378 37.500 0.00 0.00 33.31 3.51
239 240 6.035220 CCATGCATAACTTCGTAAACTTCGTA 59.965 38.462 0.00 0.00 0.00 3.43
240 241 5.163893 CCATGCATAACTTCGTAAACTTCGT 60.164 40.000 0.00 0.00 0.00 3.85
241 242 5.163893 ACCATGCATAACTTCGTAAACTTCG 60.164 40.000 0.00 0.00 0.00 3.79
242 243 6.178239 ACCATGCATAACTTCGTAAACTTC 57.822 37.500 0.00 0.00 0.00 3.01
243 244 6.877322 ACTACCATGCATAACTTCGTAAACTT 59.123 34.615 0.00 0.00 0.00 2.66
244 245 6.403878 ACTACCATGCATAACTTCGTAAACT 58.596 36.000 0.00 0.00 0.00 2.66
245 246 6.507456 CGACTACCATGCATAACTTCGTAAAC 60.507 42.308 0.00 0.00 0.00 2.01
246 247 5.517411 CGACTACCATGCATAACTTCGTAAA 59.483 40.000 0.00 0.00 0.00 2.01
264 265 5.415221 AGACTGGTACTGTACTACGACTAC 58.585 45.833 16.79 0.00 41.64 2.73
265 266 5.667539 AGACTGGTACTGTACTACGACTA 57.332 43.478 16.79 0.00 41.64 2.59
266 267 4.550076 AGACTGGTACTGTACTACGACT 57.450 45.455 16.79 8.34 41.64 4.18
267 268 5.064071 GGTTAGACTGGTACTGTACTACGAC 59.936 48.000 16.79 6.55 41.64 4.34
268 269 5.046304 AGGTTAGACTGGTACTGTACTACGA 60.046 44.000 16.79 0.00 41.64 3.43
269 270 5.181748 AGGTTAGACTGGTACTGTACTACG 58.818 45.833 16.79 8.16 41.64 3.51
270 271 8.744568 AATAGGTTAGACTGGTACTGTACTAC 57.255 38.462 16.79 2.96 41.64 2.73
271 272 9.401058 GAAATAGGTTAGACTGGTACTGTACTA 57.599 37.037 16.79 10.60 41.64 1.82
272 273 7.892241 TGAAATAGGTTAGACTGGTACTGTACT 59.108 37.037 16.79 0.00 41.64 2.73
282 283 3.307242 GCGCTGTGAAATAGGTTAGACTG 59.693 47.826 0.00 0.00 0.00 3.51
288 289 2.744202 CTCTTGCGCTGTGAAATAGGTT 59.256 45.455 9.73 0.00 0.00 3.50
290 291 2.621338 TCTCTTGCGCTGTGAAATAGG 58.379 47.619 9.73 0.00 0.00 2.57
291 292 6.536731 AATATCTCTTGCGCTGTGAAATAG 57.463 37.500 9.73 0.00 0.00 1.73
292 293 5.175673 CGAATATCTCTTGCGCTGTGAAATA 59.824 40.000 9.73 1.23 0.00 1.40
293 294 4.025396 CGAATATCTCTTGCGCTGTGAAAT 60.025 41.667 9.73 0.00 0.00 2.17
315 321 0.179062 CCCAATCTTGCTCTCCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
337 343 3.315749 CCTCGTGACTCCTACTACCATTC 59.684 52.174 0.00 0.00 0.00 2.67
424 445 2.526046 GGCCCTGTGGTACTGTGGT 61.526 63.158 0.00 0.00 0.00 4.16
441 462 2.040213 GAATGCGATCGTGGCTGTGG 62.040 60.000 17.81 0.00 0.00 4.17
442 463 1.349627 GAATGCGATCGTGGCTGTG 59.650 57.895 17.81 0.00 0.00 3.66
463 485 4.439472 CGCGTGCTTAACCACCGC 62.439 66.667 0.00 0.00 34.38 5.68
604 645 2.732016 CGTGGTTCGTGTGGAGGA 59.268 61.111 0.00 0.00 34.52 3.71
665 706 0.948678 GCATTTATTAAGCGGGGCGA 59.051 50.000 0.00 0.00 0.00 5.54
756 797 2.297033 TGGCTTGGCAAACTGAAATCTC 59.703 45.455 0.00 0.00 0.00 2.75
757 798 2.298163 CTGGCTTGGCAAACTGAAATCT 59.702 45.455 0.00 0.00 0.00 2.40
765 806 0.597377 CGGTTTCTGGCTTGGCAAAC 60.597 55.000 0.00 0.00 0.00 2.93
830 872 4.460683 GTGCGGTGCGGGATGGTA 62.461 66.667 0.00 0.00 0.00 3.25
1133 1198 0.100503 CGCCCAAATCCCGAAACATC 59.899 55.000 0.00 0.00 0.00 3.06
1134 1199 1.944234 GCGCCCAAATCCCGAAACAT 61.944 55.000 0.00 0.00 0.00 2.71
1222 1291 2.031682 CAGAGGGCAAGAACTTTGTTCG 60.032 50.000 5.02 0.00 0.00 3.95
1226 1295 1.251251 CCCAGAGGGCAAGAACTTTG 58.749 55.000 0.00 0.00 35.35 2.77
1278 1348 0.892358 GACCTTCGTCCCCCAAAACC 60.892 60.000 0.00 0.00 32.40 3.27
1312 1384 1.077663 AGCCACCAAATTCCAGACCAT 59.922 47.619 0.00 0.00 0.00 3.55
1336 1408 3.499918 AGCTGGTTTTCTCAATTCACTCG 59.500 43.478 0.00 0.00 0.00 4.18
1352 1424 1.779221 CCTCAGATCAGAGAGCTGGT 58.221 55.000 16.18 0.00 44.89 4.00
1409 1481 4.681978 GCTCTTGGTGTCCGCCGT 62.682 66.667 0.00 0.00 0.00 5.68
1546 1618 2.361085 ATGGAGTAGGGGAAAGTGGT 57.639 50.000 0.00 0.00 0.00 4.16
1556 1628 4.142381 GCACAAGGCTAAAAATGGAGTAGG 60.142 45.833 0.00 0.00 40.25 3.18
1696 1785 5.000591 TCGGTTAATTGCAATCACTCTCAA 58.999 37.500 13.38 0.00 0.00 3.02
1797 1886 8.534954 AGCAAACCTAGTACTATTATCACTCA 57.465 34.615 2.33 0.00 0.00 3.41
1802 1891 9.930693 AGCATTAGCAAACCTAGTACTATTATC 57.069 33.333 2.33 0.00 45.49 1.75
1866 1955 4.032217 GCTCGATCAGTTGTGTTGTATCAG 59.968 45.833 0.00 0.00 0.00 2.90
1878 1967 3.393089 ACAAACTCAGCTCGATCAGTT 57.607 42.857 0.00 0.00 0.00 3.16
1929 2018 5.060506 TCTTCAGTTTTGCCAAACGATCTA 58.939 37.500 7.67 0.00 46.14 1.98
1933 2022 3.013921 ACTCTTCAGTTTTGCCAAACGA 58.986 40.909 7.67 5.95 46.14 3.85
1939 2028 3.187432 GCAGACTACTCTTCAGTTTTGCC 59.813 47.826 0.00 0.00 33.94 4.52
1963 2085 5.176407 TGCACACAACAAATAAGTACACC 57.824 39.130 0.00 0.00 0.00 4.16
1973 2095 7.201679 CCCTGAAATTTATTTGCACACAACAAA 60.202 33.333 0.00 0.00 40.98 2.83
2076 2198 1.601419 CCAACTGCATCAGGCCCTTG 61.601 60.000 0.00 0.00 43.89 3.61
2112 2234 3.896317 AGAGACGTTCTGAGCAACC 57.104 52.632 0.00 0.00 33.93 3.77
2213 2335 1.202582 GACGAGCAGACTTAGGAGCAA 59.797 52.381 0.00 0.00 0.00 3.91
2252 2374 1.240256 TGTACAACAAATCACCGGGC 58.760 50.000 6.32 0.00 0.00 6.13
2256 2378 7.701924 CACAATGGATATGTACAACAAATCACC 59.298 37.037 0.00 0.00 0.00 4.02
2281 2403 2.033577 GCGACGTACATGTCAAACAACA 60.034 45.455 0.00 0.00 38.84 3.33
2455 2586 8.234136 ACACAAGTTAGATCCATATACTTCGA 57.766 34.615 0.00 0.00 0.00 3.71
2480 2611 5.298197 TGCAGACTGTACGAAAACAAAAA 57.702 34.783 3.99 0.00 0.00 1.94
2494 2625 1.961378 TGCCTTTGCATGCAGACTG 59.039 52.632 21.50 11.81 44.23 3.51
2654 2785 4.778534 AGGACAAAGCACATTTCAGATG 57.221 40.909 0.00 0.00 0.00 2.90
2701 2880 3.808174 GGAACTATGGAGGCGAATAACAC 59.192 47.826 0.00 0.00 0.00 3.32
2959 3138 6.205464 CCGAATCATGTAAACATAAGAGCCAT 59.795 38.462 0.00 0.00 34.26 4.40
2960 3139 5.527214 CCGAATCATGTAAACATAAGAGCCA 59.473 40.000 0.00 0.00 34.26 4.75
2961 3140 5.527582 ACCGAATCATGTAAACATAAGAGCC 59.472 40.000 0.00 0.00 34.26 4.70
2962 3141 6.604735 ACCGAATCATGTAAACATAAGAGC 57.395 37.500 0.00 0.00 34.26 4.09
2964 3143 7.604545 TGACAACCGAATCATGTAAACATAAGA 59.395 33.333 0.00 0.00 34.26 2.10
2965 3144 7.747888 TGACAACCGAATCATGTAAACATAAG 58.252 34.615 0.00 0.00 34.26 1.73
2966 3145 7.604545 TCTGACAACCGAATCATGTAAACATAA 59.395 33.333 0.00 0.00 34.26 1.90
3002 3181 3.242936 CCACGAACAAACGGAACAAGAAT 60.243 43.478 0.00 0.00 37.61 2.40
3012 3191 1.841663 CTCCCTGCCACGAACAAACG 61.842 60.000 0.00 0.00 39.31 3.60
3071 3256 9.919348 GCGAAATTTGTTTCCGTAGTTATAATA 57.081 29.630 0.00 0.00 0.00 0.98
3072 3257 8.452534 TGCGAAATTTGTTTCCGTAGTTATAAT 58.547 29.630 0.00 0.00 0.00 1.28
3073 3258 7.804712 TGCGAAATTTGTTTCCGTAGTTATAA 58.195 30.769 0.00 0.00 0.00 0.98
3103 3292 4.543590 AGATACCCTGTCACTTGTTGAG 57.456 45.455 0.00 0.00 33.71 3.02
3117 3306 9.099454 CTTGTGTTTGTAGAGAATTAGATACCC 57.901 37.037 0.00 0.00 0.00 3.69
3192 3381 6.321945 TGCTCTGTATTTGCATGATTGGTTAT 59.678 34.615 0.00 0.00 0.00 1.89
3227 3416 1.690633 GGGATCTGCCTGACCCTCA 60.691 63.158 0.00 0.00 39.28 3.86
3228 3417 2.801631 CGGGATCTGCCTGACCCTC 61.802 68.421 0.00 0.00 46.81 4.30
3229 3418 2.765807 CGGGATCTGCCTGACCCT 60.766 66.667 0.00 0.00 46.81 4.34
3230 3419 3.866582 CCGGGATCTGCCTGACCC 61.867 72.222 0.00 0.00 46.81 4.46
3364 3606 2.037772 CCCTATCACCTCCCAATTCTCG 59.962 54.545 0.00 0.00 0.00 4.04
3499 3743 8.389603 ACAAACATAAAATGCAAACAAGTTGAG 58.610 29.630 10.54 0.13 39.87 3.02
3509 3753 5.503683 GCAAGCACACAAACATAAAATGCAA 60.504 36.000 0.00 0.00 34.03 4.08
3512 3756 5.910637 AGCAAGCACACAAACATAAAATG 57.089 34.783 0.00 0.00 0.00 2.32
3548 3792 2.068821 ACCATCATCCCTCTGCGCT 61.069 57.895 9.73 0.00 0.00 5.92
3581 3828 2.435586 GCTGCGAGGATGTGCACT 60.436 61.111 19.41 3.19 35.90 4.40


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

AutoCloner maintained by Alex Coulton.