Multiple sequence alignment - TraesCS7D01G379100

Loading Multiple Alignment...

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 TraesCS7D01G379100 chr7D 100.000 2664 0 0 1 2664 490882784 490880121 0.000000e+00 4920.0
1 TraesCS7D01G379100 chr7D 100.000 337 0 0 2899 3235 490879886 490879550 9.860000e-175 623.0
2 TraesCS7D01G379100 chr7D 89.916 238 22 2 48 283 409485761 409485998 4.050000e-79 305.0
3 TraesCS7D01G379100 chr7A 93.176 2286 72 23 419 2664 556921981 556919740 0.000000e+00 3280.0
4 TraesCS7D01G379100 chr7A 92.395 263 15 2 2946 3203 556919436 556919174 1.420000e-98 370.0
5 TraesCS7D01G379100 chr7A 91.983 237 16 3 50 283 159552168 159552404 2.410000e-86 329.0
6 TraesCS7D01G379100 chr7A 89.362 235 23 2 51 283 468939461 468939227 8.780000e-76 294.0
7 TraesCS7D01G379100 chr7A 90.323 93 5 3 278 366 556922227 556922135 5.670000e-23 119.0
8 TraesCS7D01G379100 chr7B 90.925 2270 78 36 381 2578 519525169 519522956 0.000000e+00 2933.0
9 TraesCS7D01G379100 chr7B 89.300 243 19 5 43 283 245662979 245662742 6.790000e-77 298.0
10 TraesCS7D01G379100 chr6B 79.472 492 85 14 1097 1583 38971330 38971810 5.170000e-88 335.0
11 TraesCS7D01G379100 chr6B 89.916 238 22 2 48 283 694442571 694442334 4.050000e-79 305.0
12 TraesCS7D01G379100 chr4D 86.032 315 32 7 2900 3203 361977741 361977428 8.650000e-86 327.0
13 TraesCS7D01G379100 chr6D 78.990 495 89 13 1097 1587 24029268 24029751 1.120000e-84 324.0
14 TraesCS7D01G379100 chr6D 89.873 237 21 3 49 283 371534941 371535176 5.250000e-78 302.0
15 TraesCS7D01G379100 chr5A 85.714 315 31 6 2901 3203 312866551 312866239 1.450000e-83 320.0
16 TraesCS7D01G379100 chr5D 90.795 239 19 3 48 283 398907420 398907182 1.870000e-82 316.0
17 TraesCS7D01G379100 chr5D 85.531 311 31 6 2902 3200 241027509 241027817 2.420000e-81 313.0
18 TraesCS7D01G379100 chr5D 85.065 308 30 7 2907 3200 164696795 164697100 1.890000e-77 300.0
19 TraesCS7D01G379100 chr6A 89.583 240 20 5 48 283 176986815 176987053 1.890000e-77 300.0
20 TraesCS7D01G379100 chr2B 84.713 314 31 11 2903 3203 263808550 263808241 6.790000e-77 298.0
21 TraesCS7D01G379100 chr1A 88.750 240 23 4 48 283 576232415 576232176 1.140000e-74 291.0
22 TraesCS7D01G379100 chr3D 87.607 234 22 5 2973 3200 124656346 124656578 6.880000e-67 265.0
23 TraesCS7D01G379100 chr3D 86.580 231 20 6 2975 3200 367379026 367379250 8.970000e-61 244.0
24 TraesCS7D01G379100 chr3B 84.083 289 28 10 2928 3200 178611323 178611609 2.480000e-66 263.0
25 TraesCS7D01G379100 chr2D 96.000 50 2 0 1186 1235 27062588 27062637 7.440000e-12 82.4


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 TraesCS7D01G379100 chr7D 490879550 490882784 3234 True 2771.500000 4920 100.000000 1 3235 2 chr7D.!!$R1 3234
1 TraesCS7D01G379100 chr7A 556919174 556922227 3053 True 1256.333333 3280 91.964667 278 3203 3 chr7A.!!$R2 2925
2 TraesCS7D01G379100 chr7B 519522956 519525169 2213 True 2933.000000 2933 90.925000 381 2578 1 chr7B.!!$R2 2197

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
243 244 0.106419 GGGAACAACAGGACACCCAA 60.106 55.000 0.00 0.0 37.5 4.12 F
269 270 0.466555 CGGGACCTAGCTAGCAGACT 60.467 60.000 18.83 0.0 0.0 3.24 F
1963 2108 1.077787 ATTGCGCCGGGAAAGATCA 60.078 52.632 4.18 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2108 0.746923 TCACCAGGACGTCGATCGAT 60.747 55.000 22.5 5.91 42.86 3.59 R
2111 2265 3.425659 GGGCAAGATCAGTTCTCCTTTT 58.574 45.455 0.0 0.00 31.78 2.27 R
3120 3366 0.042131 ACGAAGATGTACCTCCCCCA 59.958 55.000 0.0 0.00 0.00 4.96 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
20 21 2.937519 TGTAAGGCATTTGTCCACACA 58.062 42.857 0.00 0.00 0.00 3.72
21 22 3.495331 TGTAAGGCATTTGTCCACACAT 58.505 40.909 0.00 0.00 30.55 3.21
22 23 3.894427 TGTAAGGCATTTGTCCACACATT 59.106 39.130 0.00 0.00 30.55 2.71
23 24 3.665745 AAGGCATTTGTCCACACATTC 57.334 42.857 0.00 0.00 30.55 2.67
24 25 1.541147 AGGCATTTGTCCACACATTCG 59.459 47.619 0.00 0.00 30.55 3.34
25 26 1.539388 GGCATTTGTCCACACATTCGA 59.461 47.619 0.00 0.00 30.55 3.71
26 27 2.414559 GGCATTTGTCCACACATTCGAG 60.415 50.000 0.00 0.00 30.55 4.04
27 28 2.226437 GCATTTGTCCACACATTCGAGT 59.774 45.455 0.00 0.00 30.55 4.18
28 29 3.813800 CATTTGTCCACACATTCGAGTG 58.186 45.455 6.35 6.35 44.93 3.51
40 41 6.421377 CACATTCGAGTGTAATGAATTGGA 57.579 37.500 13.65 0.00 37.68 3.53
41 42 7.019774 CACATTCGAGTGTAATGAATTGGAT 57.980 36.000 13.65 0.00 37.68 3.41
42 43 7.475015 CACATTCGAGTGTAATGAATTGGATT 58.525 34.615 13.65 0.00 37.68 3.01
43 44 7.641411 CACATTCGAGTGTAATGAATTGGATTC 59.359 37.037 13.65 0.00 37.68 2.52
44 45 7.554118 ACATTCGAGTGTAATGAATTGGATTCT 59.446 33.333 12.36 0.00 39.96 2.40
45 46 7.921786 TTCGAGTGTAATGAATTGGATTCTT 57.078 32.000 2.74 0.00 39.96 2.52
46 47 9.613428 ATTCGAGTGTAATGAATTGGATTCTTA 57.387 29.630 2.74 0.00 39.96 2.10
47 48 9.613428 TTCGAGTGTAATGAATTGGATTCTTAT 57.387 29.630 2.74 0.00 39.96 1.73
48 49 9.613428 TCGAGTGTAATGAATTGGATTCTTATT 57.387 29.630 2.74 0.00 39.96 1.40
71 72 2.961531 TTTTTCAGAATCACCGGGGA 57.038 45.000 9.99 9.99 0.00 4.81
72 73 2.489938 TTTTCAGAATCACCGGGGAG 57.510 50.000 14.24 0.00 0.00 4.30
74 75 0.252513 TTCAGAATCACCGGGGAGGA 60.253 55.000 14.24 4.11 45.00 3.71
75 76 0.687757 TCAGAATCACCGGGGAGGAG 60.688 60.000 14.24 1.76 45.00 3.69
76 77 0.978146 CAGAATCACCGGGGAGGAGT 60.978 60.000 14.24 0.00 45.00 3.85
77 78 0.688087 AGAATCACCGGGGAGGAGTC 60.688 60.000 14.24 9.66 45.00 3.36
78 79 1.687297 GAATCACCGGGGAGGAGTCC 61.687 65.000 14.24 0.00 45.00 3.85
79 80 2.182858 AATCACCGGGGAGGAGTCCT 62.183 60.000 14.24 12.85 45.00 3.85
80 81 2.182858 ATCACCGGGGAGGAGTCCTT 62.183 60.000 14.24 0.00 45.00 3.36
81 82 2.039137 ACCGGGGAGGAGTCCTTC 59.961 66.667 14.41 11.80 45.00 3.46
119 120 6.949352 ATTCAAAGTGGCTATTATGTCAGG 57.051 37.500 0.00 0.00 0.00 3.86
120 121 5.692115 TCAAAGTGGCTATTATGTCAGGA 57.308 39.130 0.00 0.00 0.00 3.86
121 122 5.674525 TCAAAGTGGCTATTATGTCAGGAG 58.325 41.667 0.00 0.00 0.00 3.69
122 123 5.425217 TCAAAGTGGCTATTATGTCAGGAGA 59.575 40.000 0.00 0.00 0.00 3.71
123 124 5.543507 AAGTGGCTATTATGTCAGGAGAG 57.456 43.478 0.00 0.00 0.00 3.20
124 125 4.551671 AGTGGCTATTATGTCAGGAGAGT 58.448 43.478 0.00 0.00 0.00 3.24
125 126 4.343526 AGTGGCTATTATGTCAGGAGAGTG 59.656 45.833 0.00 0.00 0.00 3.51
126 127 4.342378 GTGGCTATTATGTCAGGAGAGTGA 59.658 45.833 0.00 0.00 0.00 3.41
127 128 5.011533 GTGGCTATTATGTCAGGAGAGTGAT 59.988 44.000 0.00 0.00 0.00 3.06
128 129 5.244851 TGGCTATTATGTCAGGAGAGTGATC 59.755 44.000 0.00 0.00 0.00 2.92
129 130 5.337169 GGCTATTATGTCAGGAGAGTGATCC 60.337 48.000 0.00 0.00 39.89 3.36
130 131 5.244851 GCTATTATGTCAGGAGAGTGATCCA 59.755 44.000 0.00 0.00 42.26 3.41
131 132 5.804944 ATTATGTCAGGAGAGTGATCCAG 57.195 43.478 0.00 0.00 42.26 3.86
132 133 2.612285 TGTCAGGAGAGTGATCCAGT 57.388 50.000 0.00 0.00 42.26 4.00
133 134 2.894731 TGTCAGGAGAGTGATCCAGTT 58.105 47.619 0.00 0.00 42.26 3.16
134 135 3.242867 TGTCAGGAGAGTGATCCAGTTT 58.757 45.455 0.00 0.00 42.26 2.66
135 136 4.416516 TGTCAGGAGAGTGATCCAGTTTA 58.583 43.478 0.00 0.00 42.26 2.01
136 137 5.026121 TGTCAGGAGAGTGATCCAGTTTAT 58.974 41.667 0.00 0.00 42.26 1.40
137 138 6.194967 TGTCAGGAGAGTGATCCAGTTTATA 58.805 40.000 0.00 0.00 42.26 0.98
138 139 6.667848 TGTCAGGAGAGTGATCCAGTTTATAA 59.332 38.462 0.00 0.00 42.26 0.98
139 140 7.147828 TGTCAGGAGAGTGATCCAGTTTATAAG 60.148 40.741 0.00 0.00 42.26 1.73
140 141 6.325028 TCAGGAGAGTGATCCAGTTTATAAGG 59.675 42.308 0.00 0.00 42.26 2.69
141 142 6.325028 CAGGAGAGTGATCCAGTTTATAAGGA 59.675 42.308 0.00 0.00 42.26 3.36
142 143 6.903534 AGGAGAGTGATCCAGTTTATAAGGAA 59.096 38.462 0.00 0.00 42.26 3.36
143 144 7.403231 AGGAGAGTGATCCAGTTTATAAGGAAA 59.597 37.037 0.00 0.00 42.26 3.13
144 145 7.496263 GGAGAGTGATCCAGTTTATAAGGAAAC 59.504 40.741 0.00 0.00 39.34 2.78
145 146 7.339482 AGAGTGATCCAGTTTATAAGGAAACC 58.661 38.462 0.00 0.00 39.66 3.27
146 147 6.113411 AGTGATCCAGTTTATAAGGAAACCG 58.887 40.000 0.00 0.00 39.66 4.44
147 148 5.296035 GTGATCCAGTTTATAAGGAAACCGG 59.704 44.000 0.00 0.00 39.66 5.28
148 149 5.190132 TGATCCAGTTTATAAGGAAACCGGA 59.810 40.000 9.46 6.47 45.49 5.14
149 150 5.703730 TCCAGTTTATAAGGAAACCGGAT 57.296 39.130 9.46 0.00 39.75 4.18
150 151 5.677567 TCCAGTTTATAAGGAAACCGGATC 58.322 41.667 9.46 5.87 39.75 3.36
151 152 4.510340 CCAGTTTATAAGGAAACCGGATCG 59.490 45.833 9.46 0.00 38.61 3.69
152 153 5.353938 CAGTTTATAAGGAAACCGGATCGA 58.646 41.667 9.46 0.00 39.66 3.59
153 154 5.813672 CAGTTTATAAGGAAACCGGATCGAA 59.186 40.000 9.46 0.00 39.66 3.71
154 155 6.314400 CAGTTTATAAGGAAACCGGATCGAAA 59.686 38.462 9.46 0.38 39.66 3.46
155 156 6.880529 AGTTTATAAGGAAACCGGATCGAAAA 59.119 34.615 9.46 0.93 39.66 2.29
156 157 7.555195 AGTTTATAAGGAAACCGGATCGAAAAT 59.445 33.333 9.46 0.00 39.66 1.82
157 158 7.486802 TTATAAGGAAACCGGATCGAAAATC 57.513 36.000 9.46 0.00 0.00 2.17
158 159 3.629142 AGGAAACCGGATCGAAAATCT 57.371 42.857 9.46 0.00 0.00 2.40
159 160 4.748277 AGGAAACCGGATCGAAAATCTA 57.252 40.909 9.46 0.00 0.00 1.98
160 161 5.093849 AGGAAACCGGATCGAAAATCTAA 57.906 39.130 9.46 0.00 0.00 2.10
161 162 5.493809 AGGAAACCGGATCGAAAATCTAAA 58.506 37.500 9.46 0.00 0.00 1.85
162 163 5.353400 AGGAAACCGGATCGAAAATCTAAAC 59.647 40.000 9.46 0.00 0.00 2.01
163 164 5.122711 GGAAACCGGATCGAAAATCTAAACA 59.877 40.000 9.46 0.00 0.00 2.83
164 165 6.348704 GGAAACCGGATCGAAAATCTAAACAA 60.349 38.462 9.46 0.00 0.00 2.83
165 166 5.796350 ACCGGATCGAAAATCTAAACAAG 57.204 39.130 9.46 0.00 0.00 3.16
166 167 5.243207 ACCGGATCGAAAATCTAAACAAGT 58.757 37.500 9.46 0.00 0.00 3.16
167 168 5.704053 ACCGGATCGAAAATCTAAACAAGTT 59.296 36.000 9.46 0.00 0.00 2.66
168 169 6.021596 CCGGATCGAAAATCTAAACAAGTTG 58.978 40.000 0.00 0.00 0.00 3.16
169 170 6.128391 CCGGATCGAAAATCTAAACAAGTTGA 60.128 38.462 10.54 0.00 0.00 3.18
170 171 6.736853 CGGATCGAAAATCTAAACAAGTTGAC 59.263 38.462 10.54 0.00 0.00 3.18
171 172 7.021790 GGATCGAAAATCTAAACAAGTTGACC 58.978 38.462 10.54 0.00 0.00 4.02
172 173 6.308371 TCGAAAATCTAAACAAGTTGACCC 57.692 37.500 10.54 0.00 0.00 4.46
173 174 5.049954 TCGAAAATCTAAACAAGTTGACCCG 60.050 40.000 10.54 0.00 0.00 5.28
174 175 5.277634 CGAAAATCTAAACAAGTTGACCCGT 60.278 40.000 10.54 0.00 0.00 5.28
175 176 6.459670 AAAATCTAAACAAGTTGACCCGTT 57.540 33.333 10.54 0.00 0.00 4.44
176 177 6.459670 AAATCTAAACAAGTTGACCCGTTT 57.540 33.333 10.54 1.80 35.79 3.60
177 178 7.571080 AAATCTAAACAAGTTGACCCGTTTA 57.429 32.000 10.54 2.92 33.79 2.01
178 179 7.754851 AATCTAAACAAGTTGACCCGTTTAT 57.245 32.000 10.54 0.00 34.35 1.40
179 180 8.851541 AATCTAAACAAGTTGACCCGTTTATA 57.148 30.769 10.54 0.00 34.35 0.98
180 181 8.851541 ATCTAAACAAGTTGACCCGTTTATAA 57.148 30.769 10.54 0.00 34.35 0.98
181 182 8.314143 TCTAAACAAGTTGACCCGTTTATAAG 57.686 34.615 10.54 0.00 34.35 1.73
182 183 5.952526 AACAAGTTGACCCGTTTATAAGG 57.047 39.130 10.54 0.00 0.00 2.69
192 193 3.812262 CCGTTTATAAGGGAAATCGGGT 58.188 45.455 0.00 0.00 38.71 5.28
193 194 4.201657 CCGTTTATAAGGGAAATCGGGTT 58.798 43.478 0.00 0.00 38.71 4.11
194 195 4.035909 CCGTTTATAAGGGAAATCGGGTTG 59.964 45.833 0.00 0.00 38.71 3.77
195 196 4.877251 CGTTTATAAGGGAAATCGGGTTGA 59.123 41.667 0.00 0.00 0.00 3.18
196 197 5.354792 CGTTTATAAGGGAAATCGGGTTGAA 59.645 40.000 0.00 0.00 0.00 2.69
197 198 6.127952 CGTTTATAAGGGAAATCGGGTTGAAA 60.128 38.462 0.00 0.00 0.00 2.69
198 199 7.575343 CGTTTATAAGGGAAATCGGGTTGAAAA 60.575 37.037 0.00 0.00 0.00 2.29
212 213 4.359971 GTTGAAAACCGTACAACAAGGT 57.640 40.909 0.00 0.00 42.21 3.50
214 215 5.878133 GTTGAAAACCGTACAACAAGGTTA 58.122 37.500 0.00 0.00 46.84 2.85
215 216 6.497437 GTTGAAAACCGTACAACAAGGTTAT 58.503 36.000 0.00 0.00 46.84 1.89
216 217 7.638134 GTTGAAAACCGTACAACAAGGTTATA 58.362 34.615 0.00 0.00 46.84 0.98
217 218 7.798596 TGAAAACCGTACAACAAGGTTATAA 57.201 32.000 2.98 0.00 46.84 0.98
218 219 7.863666 TGAAAACCGTACAACAAGGTTATAAG 58.136 34.615 2.98 0.00 46.84 1.73
219 220 6.806388 AAACCGTACAACAAGGTTATAAGG 57.194 37.500 2.98 0.00 46.84 2.69
220 221 5.743636 ACCGTACAACAAGGTTATAAGGA 57.256 39.130 6.42 0.00 35.13 3.36
221 222 5.727434 ACCGTACAACAAGGTTATAAGGAG 58.273 41.667 6.42 0.00 35.13 3.69
222 223 5.481473 ACCGTACAACAAGGTTATAAGGAGA 59.519 40.000 6.42 0.00 35.13 3.71
223 224 6.014327 ACCGTACAACAAGGTTATAAGGAGAA 60.014 38.462 6.42 0.00 35.13 2.87
224 225 6.534079 CCGTACAACAAGGTTATAAGGAGAAG 59.466 42.308 0.00 0.00 0.00 2.85
225 226 6.534079 CGTACAACAAGGTTATAAGGAGAAGG 59.466 42.308 0.00 0.00 0.00 3.46
226 227 5.816682 ACAACAAGGTTATAAGGAGAAGGG 58.183 41.667 0.00 0.00 0.00 3.95
227 228 5.550403 ACAACAAGGTTATAAGGAGAAGGGA 59.450 40.000 0.00 0.00 0.00 4.20
228 229 6.045106 ACAACAAGGTTATAAGGAGAAGGGAA 59.955 38.462 0.00 0.00 0.00 3.97
229 230 6.063496 ACAAGGTTATAAGGAGAAGGGAAC 57.937 41.667 0.00 0.00 0.00 3.62
230 231 5.550403 ACAAGGTTATAAGGAGAAGGGAACA 59.450 40.000 0.00 0.00 0.00 3.18
231 232 6.045106 ACAAGGTTATAAGGAGAAGGGAACAA 59.955 38.462 0.00 0.00 0.00 2.83
232 233 6.063496 AGGTTATAAGGAGAAGGGAACAAC 57.937 41.667 0.00 0.00 0.00 3.32
233 234 5.550403 AGGTTATAAGGAGAAGGGAACAACA 59.450 40.000 0.00 0.00 0.00 3.33
234 235 5.880887 GGTTATAAGGAGAAGGGAACAACAG 59.119 44.000 0.00 0.00 0.00 3.16
235 236 2.959465 AAGGAGAAGGGAACAACAGG 57.041 50.000 0.00 0.00 0.00 4.00
236 237 2.118403 AGGAGAAGGGAACAACAGGA 57.882 50.000 0.00 0.00 0.00 3.86
237 238 1.700186 AGGAGAAGGGAACAACAGGAC 59.300 52.381 0.00 0.00 0.00 3.85
238 239 1.420138 GGAGAAGGGAACAACAGGACA 59.580 52.381 0.00 0.00 0.00 4.02
239 240 2.495084 GAGAAGGGAACAACAGGACAC 58.505 52.381 0.00 0.00 0.00 3.67
240 241 1.143073 AGAAGGGAACAACAGGACACC 59.857 52.381 0.00 0.00 0.00 4.16
241 242 0.185175 AAGGGAACAACAGGACACCC 59.815 55.000 0.00 0.00 37.79 4.61
242 243 0.991355 AGGGAACAACAGGACACCCA 60.991 55.000 0.00 0.00 39.73 4.51
243 244 0.106419 GGGAACAACAGGACACCCAA 60.106 55.000 0.00 0.00 37.50 4.12
244 245 1.029681 GGAACAACAGGACACCCAAC 58.970 55.000 0.00 0.00 33.88 3.77
245 246 1.683629 GGAACAACAGGACACCCAACA 60.684 52.381 0.00 0.00 33.88 3.33
246 247 2.096248 GAACAACAGGACACCCAACAA 58.904 47.619 0.00 0.00 33.88 2.83
247 248 2.223803 ACAACAGGACACCCAACAAA 57.776 45.000 0.00 0.00 33.88 2.83
248 249 2.099405 ACAACAGGACACCCAACAAAG 58.901 47.619 0.00 0.00 33.88 2.77
249 250 1.408702 CAACAGGACACCCAACAAAGG 59.591 52.381 0.00 0.00 33.88 3.11
250 251 0.755327 ACAGGACACCCAACAAAGGC 60.755 55.000 0.00 0.00 33.88 4.35
251 252 1.528309 AGGACACCCAACAAAGGCG 60.528 57.895 0.00 0.00 33.88 5.52
252 253 2.561037 GGACACCCAACAAAGGCGG 61.561 63.158 0.00 0.00 0.00 6.13
253 254 2.520741 ACACCCAACAAAGGCGGG 60.521 61.111 0.00 0.00 46.22 6.13
254 255 2.203422 CACCCAACAAAGGCGGGA 60.203 61.111 0.00 0.00 43.21 5.14
255 256 2.203437 ACCCAACAAAGGCGGGAC 60.203 61.111 0.00 0.00 43.21 4.46
256 257 2.989253 CCCAACAAAGGCGGGACC 60.989 66.667 0.00 0.00 43.21 4.46
265 266 2.838225 GGCGGGACCTAGCTAGCA 60.838 66.667 18.83 1.89 34.51 3.49
266 267 2.731374 GCGGGACCTAGCTAGCAG 59.269 66.667 18.83 11.93 0.00 4.24
267 268 1.828660 GCGGGACCTAGCTAGCAGA 60.829 63.158 18.83 3.05 0.00 4.26
268 269 2.034607 CGGGACCTAGCTAGCAGAC 58.965 63.158 18.83 5.47 0.00 3.51
269 270 0.466555 CGGGACCTAGCTAGCAGACT 60.467 60.000 18.83 0.00 0.00 3.24
270 271 1.202782 CGGGACCTAGCTAGCAGACTA 60.203 57.143 18.83 0.00 0.00 2.59
271 272 2.748798 CGGGACCTAGCTAGCAGACTAA 60.749 54.545 18.83 0.00 0.00 2.24
272 273 3.297736 GGGACCTAGCTAGCAGACTAAA 58.702 50.000 18.83 0.00 0.00 1.85
273 274 3.705072 GGGACCTAGCTAGCAGACTAAAA 59.295 47.826 18.83 0.00 0.00 1.52
274 275 4.202172 GGGACCTAGCTAGCAGACTAAAAG 60.202 50.000 18.83 0.16 0.00 2.27
275 276 4.645588 GGACCTAGCTAGCAGACTAAAAGA 59.354 45.833 18.83 0.00 0.00 2.52
276 277 5.127356 GGACCTAGCTAGCAGACTAAAAGAA 59.873 44.000 18.83 0.00 0.00 2.52
302 303 9.657419 ACCATCAATTTGTAGATTGGAAAAATC 57.343 29.630 0.00 0.00 37.56 2.17
303 304 9.656040 CCATCAATTTGTAGATTGGAAAAATCA 57.344 29.630 0.00 0.00 37.56 2.57
338 343 6.779049 TGCCAAAGCATCCTCTTTATTCATAT 59.221 34.615 0.00 0.00 46.52 1.78
339 344 7.288389 TGCCAAAGCATCCTCTTTATTCATATT 59.712 33.333 0.00 0.00 46.52 1.28
378 410 3.981375 AGGTAGACTTCCCTCAAAAAGGT 59.019 43.478 0.00 0.00 44.56 3.50
389 421 7.483580 TCCCTCAAAAAGGTAAAAAGAACAA 57.516 32.000 0.00 0.00 44.56 2.83
408 440 7.078228 AGAACAATGCACTTTTCTAAATCGAC 58.922 34.615 0.00 0.00 0.00 4.20
413 445 4.000988 GCACTTTTCTAAATCGACTGGGA 58.999 43.478 0.00 0.00 0.00 4.37
434 541 9.277783 CTGGGACTTAAGAAATCTTATATGTGG 57.722 37.037 10.09 0.00 38.16 4.17
435 542 7.719633 TGGGACTTAAGAAATCTTATATGTGGC 59.280 37.037 10.09 0.00 38.16 5.01
449 556 3.895232 ATGTGGCACGACTAAAGAGAT 57.105 42.857 13.77 0.00 0.00 2.75
472 580 2.604046 ATGTACCGTCTCTCCATTGC 57.396 50.000 0.00 0.00 0.00 3.56
643 752 2.280592 GCCGACGTGTGGTCCTTT 60.281 61.111 0.00 0.00 42.99 3.11
644 753 1.890510 GCCGACGTGTGGTCCTTTT 60.891 57.895 0.00 0.00 42.99 2.27
645 754 1.441732 GCCGACGTGTGGTCCTTTTT 61.442 55.000 0.00 0.00 42.99 1.94
665 774 2.721425 TTTTGAAACGGAGTGGTCCT 57.279 45.000 0.00 0.00 45.00 3.85
666 775 2.721425 TTTGAAACGGAGTGGTCCTT 57.279 45.000 0.00 0.00 45.00 3.36
960 1071 3.834799 ATCCGGTCTTCGTCGCCC 61.835 66.667 0.00 0.00 37.11 6.13
1038 1154 2.422127 ACAACACTGTACAGTTTGCCAC 59.578 45.455 30.09 0.00 40.20 5.01
1043 1159 1.532868 CTGTACAGTTTGCCACAGCTC 59.467 52.381 15.06 0.00 40.80 4.09
1282 1410 4.988486 GTCACCGGCGTCGACGTT 62.988 66.667 35.48 17.16 42.22 3.99
1540 1668 1.380920 GACTAGGTACACCGGGGCT 60.381 63.158 1.73 0.00 42.08 5.19
1586 1714 1.658409 TGCGCGATCATGTAGCTCG 60.658 57.895 12.10 0.00 38.81 5.03
1731 1859 4.025401 GGTTGGTTCACGCGGCAG 62.025 66.667 12.47 0.00 0.00 4.85
1732 1860 4.025401 GTTGGTTCACGCGGCAGG 62.025 66.667 12.47 0.00 0.00 4.85
1883 2012 2.005370 TCTAGGTCTGGTCGTTGGTT 57.995 50.000 0.00 0.00 0.00 3.67
1914 2043 1.863662 CTGCTCTGCTGCAAGGTTGG 61.864 60.000 3.02 0.00 42.83 3.77
1948 2077 1.250328 TCTTGTGCTTCTGGGCATTG 58.750 50.000 0.00 0.00 44.34 2.82
1963 2108 1.077787 ATTGCGCCGGGAAAGATCA 60.078 52.632 4.18 0.00 0.00 2.92
1971 2116 1.269723 CCGGGAAAGATCATCGATCGA 59.730 52.381 21.86 21.86 43.17 3.59
2091 2245 1.415659 CTGGAGGCCACCTAAGATCAG 59.584 57.143 20.77 3.40 31.76 2.90
2111 2265 3.682885 CGTTGCCCAATGCCAGCA 61.683 61.111 0.00 0.00 40.16 4.41
2507 2697 6.016108 CCAAAACCTTAACCGAATTTGGTAGA 60.016 38.462 18.09 6.55 42.89 2.59
2596 2805 6.590234 TTCTTGTTAGCAGTGTCTATCTGA 57.410 37.500 0.00 0.00 35.20 3.27
2601 2810 9.371136 CTTGTTAGCAGTGTCTATCTGATTTAA 57.629 33.333 0.00 0.00 35.20 1.52
2602 2811 8.932945 TGTTAGCAGTGTCTATCTGATTTAAG 57.067 34.615 0.00 0.00 35.20 1.85
2603 2812 8.749354 TGTTAGCAGTGTCTATCTGATTTAAGA 58.251 33.333 0.00 0.00 35.20 2.10
2932 3175 2.169978 AGGCGACTAACCATCCTTAACC 59.830 50.000 0.00 0.00 40.61 2.85
2939 3182 6.755607 CGACTAACCATCCTTAACCTCTTTAC 59.244 42.308 0.00 0.00 0.00 2.01
2940 3183 6.955364 ACTAACCATCCTTAACCTCTTTACC 58.045 40.000 0.00 0.00 0.00 2.85
2941 3184 5.853572 AACCATCCTTAACCTCTTTACCA 57.146 39.130 0.00 0.00 0.00 3.25
2942 3185 5.853572 ACCATCCTTAACCTCTTTACCAA 57.146 39.130 0.00 0.00 0.00 3.67
2943 3186 6.208840 ACCATCCTTAACCTCTTTACCAAA 57.791 37.500 0.00 0.00 0.00 3.28
2944 3187 6.800890 ACCATCCTTAACCTCTTTACCAAAT 58.199 36.000 0.00 0.00 0.00 2.32
2945 3188 7.246027 ACCATCCTTAACCTCTTTACCAAATT 58.754 34.615 0.00 0.00 0.00 1.82
2946 3189 7.733047 ACCATCCTTAACCTCTTTACCAAATTT 59.267 33.333 0.00 0.00 0.00 1.82
2947 3190 8.593679 CCATCCTTAACCTCTTTACCAAATTTT 58.406 33.333 0.00 0.00 0.00 1.82
3046 3289 9.191995 AGCACAAAGTAAACATACAATAAAAGC 57.808 29.630 0.00 0.00 0.00 3.51
3075 3318 2.680577 AGTAAAGGCACGAAGTAACCG 58.319 47.619 0.00 0.00 41.61 4.44
3085 3331 2.030451 ACGAAGTAACCGAAGTGGAGTC 60.030 50.000 0.00 0.00 41.94 3.36
3094 3340 1.202200 CGAAGTGGAGTCGATGGAGAC 60.202 57.143 0.00 0.00 41.02 3.36
3119 3365 0.106918 TGTGTTGCCGAAGTTCCCTT 60.107 50.000 0.00 0.00 0.00 3.95
3120 3366 1.029681 GTGTTGCCGAAGTTCCCTTT 58.970 50.000 0.00 0.00 0.00 3.11
3121 3367 1.028905 TGTTGCCGAAGTTCCCTTTG 58.971 50.000 0.00 0.00 32.61 2.77
3137 3385 2.092375 CCTTTGGGGGAGGTACATCTTC 60.092 54.545 7.56 0.53 0.00 2.87
3156 3404 0.951040 CGTTGGAGAGGTGTGGAAGC 60.951 60.000 0.00 0.00 0.00 3.86
3161 3409 1.271597 GGAGAGGTGTGGAAGCACAAT 60.272 52.381 0.00 0.00 40.89 2.71
3168 3416 1.004277 TGTGGAAGCACAATACTCCCC 59.996 52.381 0.00 0.00 31.35 4.81
3181 3429 1.596496 ACTCCCCAAATGTCCCTAGG 58.404 55.000 0.06 0.06 0.00 3.02
3200 3448 4.014273 AGGACCACCTTATTCTCCTCAT 57.986 45.455 0.00 0.00 45.36 2.90
3203 3451 3.118531 ACCACCTTATTCTCCTCATGCT 58.881 45.455 0.00 0.00 0.00 3.79
3204 3452 3.118112 ACCACCTTATTCTCCTCATGCTG 60.118 47.826 0.00 0.00 0.00 4.41
3205 3453 3.474600 CACCTTATTCTCCTCATGCTGG 58.525 50.000 0.00 0.00 0.00 4.85
3206 3454 3.135348 CACCTTATTCTCCTCATGCTGGA 59.865 47.826 7.01 7.01 0.00 3.86
3207 3455 3.782523 ACCTTATTCTCCTCATGCTGGAA 59.217 43.478 8.30 1.93 32.61 3.53
3208 3456 4.141528 ACCTTATTCTCCTCATGCTGGAAG 60.142 45.833 8.30 3.57 32.61 3.46
3226 3474 3.446507 GCACAATGCTCCCCAAATG 57.553 52.632 0.00 0.00 40.96 2.32
3227 3475 0.609662 GCACAATGCTCCCCAAATGT 59.390 50.000 0.00 0.00 40.96 2.71
3228 3476 1.404583 GCACAATGCTCCCCAAATGTC 60.405 52.381 0.00 0.00 40.96 3.06
3229 3477 1.205417 CACAATGCTCCCCAAATGTCC 59.795 52.381 0.00 0.00 0.00 4.02
3230 3478 0.826062 CAATGCTCCCCAAATGTCCC 59.174 55.000 0.00 0.00 0.00 4.46
3231 3479 0.712380 AATGCTCCCCAAATGTCCCT 59.288 50.000 0.00 0.00 0.00 4.20
3232 3480 1.607225 ATGCTCCCCAAATGTCCCTA 58.393 50.000 0.00 0.00 0.00 3.53
3233 3481 0.918983 TGCTCCCCAAATGTCCCTAG 59.081 55.000 0.00 0.00 0.00 3.02
3234 3482 0.183731 GCTCCCCAAATGTCCCTAGG 59.816 60.000 0.06 0.06 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.937519 TGTGTGGACAAATGCCTTACA 58.062 42.857 0.00 0.00 0.00 2.41
1 2 4.485163 GAATGTGTGGACAAATGCCTTAC 58.515 43.478 0.00 0.00 35.11 2.34
2 3 3.190327 CGAATGTGTGGACAAATGCCTTA 59.810 43.478 0.00 0.00 35.11 2.69
3 4 2.030007 CGAATGTGTGGACAAATGCCTT 60.030 45.455 0.00 0.00 35.11 4.35
4 5 1.541147 CGAATGTGTGGACAAATGCCT 59.459 47.619 0.00 0.00 35.11 4.75
5 6 1.539388 TCGAATGTGTGGACAAATGCC 59.461 47.619 0.00 0.00 35.11 4.40
6 7 2.226437 ACTCGAATGTGTGGACAAATGC 59.774 45.455 0.00 0.00 35.11 3.56
7 8 3.813800 CACTCGAATGTGTGGACAAATG 58.186 45.455 0.00 0.00 36.26 2.32
17 18 6.421377 TCCAATTCATTACACTCGAATGTG 57.579 37.500 10.26 6.51 43.07 3.21
18 19 7.554118 AGAATCCAATTCATTACACTCGAATGT 59.446 33.333 4.38 4.38 41.71 2.71
19 20 7.923888 AGAATCCAATTCATTACACTCGAATG 58.076 34.615 0.00 0.00 41.71 2.67
20 21 8.511604 AAGAATCCAATTCATTACACTCGAAT 57.488 30.769 2.79 0.00 41.71 3.34
21 22 7.921786 AAGAATCCAATTCATTACACTCGAA 57.078 32.000 2.79 0.00 41.71 3.71
22 23 9.613428 AATAAGAATCCAATTCATTACACTCGA 57.387 29.630 2.79 0.00 41.71 4.04
52 53 2.554344 CCTCCCCGGTGATTCTGAAAAA 60.554 50.000 0.00 0.00 0.00 1.94
53 54 1.004277 CCTCCCCGGTGATTCTGAAAA 59.996 52.381 0.00 0.00 0.00 2.29
54 55 0.618458 CCTCCCCGGTGATTCTGAAA 59.382 55.000 0.00 0.00 0.00 2.69
55 56 0.252513 TCCTCCCCGGTGATTCTGAA 60.253 55.000 0.00 0.00 0.00 3.02
56 57 0.687757 CTCCTCCCCGGTGATTCTGA 60.688 60.000 0.00 0.00 0.00 3.27
57 58 0.978146 ACTCCTCCCCGGTGATTCTG 60.978 60.000 0.00 0.00 0.00 3.02
58 59 0.688087 GACTCCTCCCCGGTGATTCT 60.688 60.000 0.00 0.00 0.00 2.40
59 60 1.687297 GGACTCCTCCCCGGTGATTC 61.687 65.000 0.00 0.00 0.00 2.52
60 61 1.689582 GGACTCCTCCCCGGTGATT 60.690 63.158 0.00 0.00 0.00 2.57
61 62 2.041819 GGACTCCTCCCCGGTGAT 60.042 66.667 0.00 0.00 0.00 3.06
62 63 2.800159 GAAGGACTCCTCCCCGGTGA 62.800 65.000 0.00 0.00 37.25 4.02
63 64 2.284699 AAGGACTCCTCCCCGGTG 60.285 66.667 0.00 0.00 37.25 4.94
64 65 2.039137 GAAGGACTCCTCCCCGGT 59.961 66.667 0.00 0.00 37.25 5.28
65 66 2.764547 GGAAGGACTCCTCCCCGG 60.765 72.222 0.00 0.00 41.61 5.73
66 67 1.383248 ATGGAAGGACTCCTCCCCG 60.383 63.158 0.00 0.00 45.64 5.73
67 68 0.030603 AGATGGAAGGACTCCTCCCC 60.031 60.000 0.00 3.95 45.64 4.81
68 69 1.127343 CAGATGGAAGGACTCCTCCC 58.873 60.000 0.00 0.00 45.64 4.30
69 70 2.166907 TCAGATGGAAGGACTCCTCC 57.833 55.000 0.00 2.61 45.64 4.30
70 71 7.732222 ATATATTCAGATGGAAGGACTCCTC 57.268 40.000 0.00 0.00 45.64 3.71
71 72 9.796242 ATAATATATTCAGATGGAAGGACTCCT 57.204 33.333 0.00 0.00 45.64 3.69
93 94 9.071276 CCTGACATAATAGCCACTTTGAATAAT 57.929 33.333 0.00 0.00 0.00 1.28
94 95 8.271458 TCCTGACATAATAGCCACTTTGAATAA 58.729 33.333 0.00 0.00 0.00 1.40
95 96 7.801104 TCCTGACATAATAGCCACTTTGAATA 58.199 34.615 0.00 0.00 0.00 1.75
96 97 6.662755 TCCTGACATAATAGCCACTTTGAAT 58.337 36.000 0.00 0.00 0.00 2.57
97 98 6.061022 TCCTGACATAATAGCCACTTTGAA 57.939 37.500 0.00 0.00 0.00 2.69
98 99 5.425217 TCTCCTGACATAATAGCCACTTTGA 59.575 40.000 0.00 0.00 0.00 2.69
99 100 5.674525 TCTCCTGACATAATAGCCACTTTG 58.325 41.667 0.00 0.00 0.00 2.77
100 101 5.426833 ACTCTCCTGACATAATAGCCACTTT 59.573 40.000 0.00 0.00 0.00 2.66
101 102 4.965532 ACTCTCCTGACATAATAGCCACTT 59.034 41.667 0.00 0.00 0.00 3.16
102 103 4.343526 CACTCTCCTGACATAATAGCCACT 59.656 45.833 0.00 0.00 0.00 4.00
103 104 4.342378 TCACTCTCCTGACATAATAGCCAC 59.658 45.833 0.00 0.00 0.00 5.01
104 105 4.546674 TCACTCTCCTGACATAATAGCCA 58.453 43.478 0.00 0.00 0.00 4.75
105 106 5.337169 GGATCACTCTCCTGACATAATAGCC 60.337 48.000 0.00 0.00 32.18 3.93
106 107 5.244851 TGGATCACTCTCCTGACATAATAGC 59.755 44.000 0.00 0.00 36.20 2.97
107 108 6.493115 ACTGGATCACTCTCCTGACATAATAG 59.507 42.308 0.00 0.00 37.60 1.73
108 109 6.377080 ACTGGATCACTCTCCTGACATAATA 58.623 40.000 0.00 0.00 37.60 0.98
109 110 5.215069 ACTGGATCACTCTCCTGACATAAT 58.785 41.667 0.00 0.00 37.60 1.28
110 111 4.614475 ACTGGATCACTCTCCTGACATAA 58.386 43.478 0.00 0.00 37.60 1.90
111 112 4.256983 ACTGGATCACTCTCCTGACATA 57.743 45.455 0.00 0.00 37.60 2.29
112 113 3.113191 ACTGGATCACTCTCCTGACAT 57.887 47.619 0.00 0.00 37.60 3.06
113 114 2.612285 ACTGGATCACTCTCCTGACA 57.388 50.000 0.00 0.00 37.60 3.58
114 115 3.971245 AAACTGGATCACTCTCCTGAC 57.029 47.619 0.00 0.00 37.60 3.51
115 116 6.325028 CCTTATAAACTGGATCACTCTCCTGA 59.675 42.308 0.00 0.00 37.60 3.86
116 117 6.325028 TCCTTATAAACTGGATCACTCTCCTG 59.675 42.308 0.00 0.00 39.46 3.86
117 118 6.444704 TCCTTATAAACTGGATCACTCTCCT 58.555 40.000 0.00 0.00 36.20 3.69
118 119 6.732896 TCCTTATAAACTGGATCACTCTCC 57.267 41.667 0.00 0.00 35.74 3.71
119 120 7.496263 GGTTTCCTTATAAACTGGATCACTCTC 59.504 40.741 0.00 0.00 38.98 3.20
120 121 7.339482 GGTTTCCTTATAAACTGGATCACTCT 58.661 38.462 0.00 0.00 38.98 3.24
121 122 6.258068 CGGTTTCCTTATAAACTGGATCACTC 59.742 42.308 0.00 0.00 40.52 3.51
122 123 6.113411 CGGTTTCCTTATAAACTGGATCACT 58.887 40.000 0.00 0.00 40.52 3.41
123 124 6.359480 CGGTTTCCTTATAAACTGGATCAC 57.641 41.667 0.00 0.00 40.52 3.06
129 130 5.353938 TCGATCCGGTTTCCTTATAAACTG 58.646 41.667 0.00 0.00 42.76 3.16
130 131 5.603170 TCGATCCGGTTTCCTTATAAACT 57.397 39.130 0.00 0.00 38.98 2.66
131 132 6.667007 TTTCGATCCGGTTTCCTTATAAAC 57.333 37.500 0.00 0.00 38.39 2.01
132 133 7.771826 AGATTTTCGATCCGGTTTCCTTATAAA 59.228 33.333 0.00 0.00 0.00 1.40
133 134 7.277396 AGATTTTCGATCCGGTTTCCTTATAA 58.723 34.615 0.00 0.00 0.00 0.98
134 135 6.823497 AGATTTTCGATCCGGTTTCCTTATA 58.177 36.000 0.00 0.00 0.00 0.98
135 136 5.681639 AGATTTTCGATCCGGTTTCCTTAT 58.318 37.500 0.00 0.00 0.00 1.73
136 137 5.093849 AGATTTTCGATCCGGTTTCCTTA 57.906 39.130 0.00 0.00 0.00 2.69
137 138 3.951663 AGATTTTCGATCCGGTTTCCTT 58.048 40.909 0.00 0.00 0.00 3.36
138 139 3.629142 AGATTTTCGATCCGGTTTCCT 57.371 42.857 0.00 0.00 0.00 3.36
139 140 5.122711 TGTTTAGATTTTCGATCCGGTTTCC 59.877 40.000 0.00 0.00 0.00 3.13
140 141 6.173191 TGTTTAGATTTTCGATCCGGTTTC 57.827 37.500 0.00 0.00 0.00 2.78
141 142 6.206048 ACTTGTTTAGATTTTCGATCCGGTTT 59.794 34.615 0.00 0.00 0.00 3.27
142 143 5.704053 ACTTGTTTAGATTTTCGATCCGGTT 59.296 36.000 0.00 0.00 0.00 4.44
143 144 5.243207 ACTTGTTTAGATTTTCGATCCGGT 58.757 37.500 0.00 0.00 0.00 5.28
144 145 5.796350 ACTTGTTTAGATTTTCGATCCGG 57.204 39.130 0.00 0.00 0.00 5.14
145 146 6.736853 GTCAACTTGTTTAGATTTTCGATCCG 59.263 38.462 0.00 0.00 0.00 4.18
146 147 7.021790 GGTCAACTTGTTTAGATTTTCGATCC 58.978 38.462 0.00 0.00 0.00 3.36
147 148 7.021790 GGGTCAACTTGTTTAGATTTTCGATC 58.978 38.462 0.00 0.00 0.00 3.69
148 149 6.348213 CGGGTCAACTTGTTTAGATTTTCGAT 60.348 38.462 0.00 0.00 0.00 3.59
149 150 5.049954 CGGGTCAACTTGTTTAGATTTTCGA 60.050 40.000 0.00 0.00 0.00 3.71
150 151 5.144359 CGGGTCAACTTGTTTAGATTTTCG 58.856 41.667 0.00 0.00 0.00 3.46
151 152 6.068473 ACGGGTCAACTTGTTTAGATTTTC 57.932 37.500 0.00 0.00 0.00 2.29
152 153 6.459670 AACGGGTCAACTTGTTTAGATTTT 57.540 33.333 0.00 0.00 0.00 1.82
153 154 6.459670 AAACGGGTCAACTTGTTTAGATTT 57.540 33.333 0.00 0.00 33.11 2.17
154 155 7.754851 ATAAACGGGTCAACTTGTTTAGATT 57.245 32.000 12.48 0.00 39.37 2.40
155 156 8.851541 TTATAAACGGGTCAACTTGTTTAGAT 57.148 30.769 12.48 5.04 39.37 1.98
156 157 7.388500 CCTTATAAACGGGTCAACTTGTTTAGA 59.612 37.037 12.48 7.98 39.37 2.10
157 158 7.361457 CCCTTATAAACGGGTCAACTTGTTTAG 60.361 40.741 2.21 5.27 39.37 1.85
158 159 6.430616 CCCTTATAAACGGGTCAACTTGTTTA 59.569 38.462 2.21 10.58 40.04 2.01
159 160 5.242171 CCCTTATAAACGGGTCAACTTGTTT 59.758 40.000 2.21 7.87 38.10 2.83
160 161 4.763279 CCCTTATAAACGGGTCAACTTGTT 59.237 41.667 2.21 0.00 35.65 2.83
161 162 4.041938 TCCCTTATAAACGGGTCAACTTGT 59.958 41.667 9.12 0.00 41.40 3.16
162 163 4.581868 TCCCTTATAAACGGGTCAACTTG 58.418 43.478 9.12 0.00 41.40 3.16
163 164 4.914177 TCCCTTATAAACGGGTCAACTT 57.086 40.909 9.12 0.00 41.40 2.66
164 165 4.914177 TTCCCTTATAAACGGGTCAACT 57.086 40.909 9.12 0.00 41.40 3.16
165 166 5.220719 CGATTTCCCTTATAAACGGGTCAAC 60.221 44.000 9.12 1.77 41.40 3.18
166 167 4.877251 CGATTTCCCTTATAAACGGGTCAA 59.123 41.667 9.12 5.18 41.40 3.18
167 168 4.444536 CGATTTCCCTTATAAACGGGTCA 58.555 43.478 9.12 0.00 41.40 4.02
168 169 3.811497 CCGATTTCCCTTATAAACGGGTC 59.189 47.826 9.12 0.89 41.40 4.46
169 170 3.812262 CCGATTTCCCTTATAAACGGGT 58.188 45.455 9.12 0.00 41.40 5.28
171 172 3.812262 ACCCGATTTCCCTTATAAACGG 58.188 45.455 0.00 0.00 39.02 4.44
172 173 4.877251 TCAACCCGATTTCCCTTATAAACG 59.123 41.667 0.00 0.00 0.00 3.60
173 174 6.762702 TTCAACCCGATTTCCCTTATAAAC 57.237 37.500 0.00 0.00 0.00 2.01
174 175 7.309928 GGTTTTCAACCCGATTTCCCTTATAAA 60.310 37.037 0.00 0.00 46.12 1.40
175 176 6.153170 GGTTTTCAACCCGATTTCCCTTATAA 59.847 38.462 0.00 0.00 46.12 0.98
176 177 5.653330 GGTTTTCAACCCGATTTCCCTTATA 59.347 40.000 0.00 0.00 46.12 0.98
177 178 4.464951 GGTTTTCAACCCGATTTCCCTTAT 59.535 41.667 0.00 0.00 46.12 1.73
178 179 3.827876 GGTTTTCAACCCGATTTCCCTTA 59.172 43.478 0.00 0.00 46.12 2.69
179 180 2.631062 GGTTTTCAACCCGATTTCCCTT 59.369 45.455 0.00 0.00 46.12 3.95
180 181 2.244695 GGTTTTCAACCCGATTTCCCT 58.755 47.619 0.00 0.00 46.12 4.20
181 182 2.736144 GGTTTTCAACCCGATTTCCC 57.264 50.000 0.00 0.00 46.12 3.97
191 192 4.359971 ACCTTGTTGTACGGTTTTCAAC 57.640 40.909 12.91 12.91 40.91 3.18
192 193 6.696441 ATAACCTTGTTGTACGGTTTTCAA 57.304 33.333 7.33 0.00 41.09 2.69
193 194 7.041235 CCTTATAACCTTGTTGTACGGTTTTCA 60.041 37.037 7.33 0.00 41.09 2.69
194 195 7.173047 TCCTTATAACCTTGTTGTACGGTTTTC 59.827 37.037 7.33 0.00 41.09 2.29
195 196 6.997476 TCCTTATAACCTTGTTGTACGGTTTT 59.003 34.615 7.33 3.41 41.09 2.43
196 197 6.532826 TCCTTATAACCTTGTTGTACGGTTT 58.467 36.000 7.33 0.56 41.09 3.27
197 198 6.014327 TCTCCTTATAACCTTGTTGTACGGTT 60.014 38.462 7.21 7.21 43.10 4.44
198 199 5.481473 TCTCCTTATAACCTTGTTGTACGGT 59.519 40.000 6.29 0.00 0.00 4.83
199 200 5.969423 TCTCCTTATAACCTTGTTGTACGG 58.031 41.667 0.00 1.45 0.00 4.02
200 201 6.534079 CCTTCTCCTTATAACCTTGTTGTACG 59.466 42.308 0.00 0.00 0.00 3.67
201 202 6.822170 CCCTTCTCCTTATAACCTTGTTGTAC 59.178 42.308 0.00 0.00 0.00 2.90
202 203 6.731919 TCCCTTCTCCTTATAACCTTGTTGTA 59.268 38.462 0.00 0.00 0.00 2.41
203 204 5.550403 TCCCTTCTCCTTATAACCTTGTTGT 59.450 40.000 0.00 0.00 0.00 3.32
204 205 6.062258 TCCCTTCTCCTTATAACCTTGTTG 57.938 41.667 0.00 0.00 0.00 3.33
205 206 6.045106 TGTTCCCTTCTCCTTATAACCTTGTT 59.955 38.462 0.00 0.00 0.00 2.83
206 207 5.550403 TGTTCCCTTCTCCTTATAACCTTGT 59.450 40.000 0.00 0.00 0.00 3.16
207 208 6.062258 TGTTCCCTTCTCCTTATAACCTTG 57.938 41.667 0.00 0.00 0.00 3.61
208 209 6.045106 TGTTGTTCCCTTCTCCTTATAACCTT 59.955 38.462 0.00 0.00 0.00 3.50
209 210 5.550403 TGTTGTTCCCTTCTCCTTATAACCT 59.450 40.000 0.00 0.00 0.00 3.50
210 211 5.812286 TGTTGTTCCCTTCTCCTTATAACC 58.188 41.667 0.00 0.00 0.00 2.85
211 212 5.880887 CCTGTTGTTCCCTTCTCCTTATAAC 59.119 44.000 0.00 0.00 0.00 1.89
212 213 5.788533 TCCTGTTGTTCCCTTCTCCTTATAA 59.211 40.000 0.00 0.00 0.00 0.98
213 214 5.189145 GTCCTGTTGTTCCCTTCTCCTTATA 59.811 44.000 0.00 0.00 0.00 0.98
214 215 4.019231 GTCCTGTTGTTCCCTTCTCCTTAT 60.019 45.833 0.00 0.00 0.00 1.73
215 216 3.326880 GTCCTGTTGTTCCCTTCTCCTTA 59.673 47.826 0.00 0.00 0.00 2.69
216 217 2.106684 GTCCTGTTGTTCCCTTCTCCTT 59.893 50.000 0.00 0.00 0.00 3.36
217 218 1.700186 GTCCTGTTGTTCCCTTCTCCT 59.300 52.381 0.00 0.00 0.00 3.69
218 219 1.420138 TGTCCTGTTGTTCCCTTCTCC 59.580 52.381 0.00 0.00 0.00 3.71
219 220 2.495084 GTGTCCTGTTGTTCCCTTCTC 58.505 52.381 0.00 0.00 0.00 2.87
220 221 1.143073 GGTGTCCTGTTGTTCCCTTCT 59.857 52.381 0.00 0.00 0.00 2.85
221 222 1.605753 GGTGTCCTGTTGTTCCCTTC 58.394 55.000 0.00 0.00 0.00 3.46
222 223 0.185175 GGGTGTCCTGTTGTTCCCTT 59.815 55.000 0.00 0.00 32.89 3.95
223 224 0.991355 TGGGTGTCCTGTTGTTCCCT 60.991 55.000 0.00 0.00 36.23 4.20
224 225 0.106419 TTGGGTGTCCTGTTGTTCCC 60.106 55.000 0.00 0.00 35.85 3.97
225 226 1.029681 GTTGGGTGTCCTGTTGTTCC 58.970 55.000 0.00 0.00 0.00 3.62
226 227 1.757682 TGTTGGGTGTCCTGTTGTTC 58.242 50.000 0.00 0.00 0.00 3.18
227 228 2.223803 TTGTTGGGTGTCCTGTTGTT 57.776 45.000 0.00 0.00 0.00 2.83
228 229 2.099405 CTTTGTTGGGTGTCCTGTTGT 58.901 47.619 0.00 0.00 0.00 3.32
229 230 1.408702 CCTTTGTTGGGTGTCCTGTTG 59.591 52.381 0.00 0.00 0.00 3.33
230 231 1.775385 CCTTTGTTGGGTGTCCTGTT 58.225 50.000 0.00 0.00 0.00 3.16
231 232 0.755327 GCCTTTGTTGGGTGTCCTGT 60.755 55.000 0.00 0.00 0.00 4.00
232 233 1.795170 CGCCTTTGTTGGGTGTCCTG 61.795 60.000 0.00 0.00 0.00 3.86
233 234 1.528309 CGCCTTTGTTGGGTGTCCT 60.528 57.895 0.00 0.00 0.00 3.85
234 235 2.561037 CCGCCTTTGTTGGGTGTCC 61.561 63.158 0.00 0.00 32.93 4.02
235 236 2.561037 CCCGCCTTTGTTGGGTGTC 61.561 63.158 0.00 0.00 38.18 3.67
236 237 2.520741 CCCGCCTTTGTTGGGTGT 60.521 61.111 0.00 0.00 38.18 4.16
237 238 2.203422 TCCCGCCTTTGTTGGGTG 60.203 61.111 0.00 0.00 43.75 4.61
238 239 2.203437 GTCCCGCCTTTGTTGGGT 60.203 61.111 0.00 0.00 43.75 4.51
239 240 2.989253 GGTCCCGCCTTTGTTGGG 60.989 66.667 0.00 0.00 44.75 4.12
248 249 2.838225 TGCTAGCTAGGTCCCGCC 60.838 66.667 22.10 4.24 37.58 6.13
249 250 1.828660 TCTGCTAGCTAGGTCCCGC 60.829 63.158 22.10 8.11 0.00 6.13
250 251 0.466555 AGTCTGCTAGCTAGGTCCCG 60.467 60.000 22.10 2.73 0.00 5.14
251 252 2.660670 TAGTCTGCTAGCTAGGTCCC 57.339 55.000 22.10 6.04 0.00 4.46
252 253 4.645588 TCTTTTAGTCTGCTAGCTAGGTCC 59.354 45.833 22.10 6.41 0.00 4.46
253 254 5.838531 TCTTTTAGTCTGCTAGCTAGGTC 57.161 43.478 22.10 7.13 0.00 3.85
254 255 5.105269 GGTTCTTTTAGTCTGCTAGCTAGGT 60.105 44.000 22.10 0.00 0.00 3.08
255 256 5.105310 TGGTTCTTTTAGTCTGCTAGCTAGG 60.105 44.000 22.10 6.77 0.00 3.02
256 257 5.967088 TGGTTCTTTTAGTCTGCTAGCTAG 58.033 41.667 16.84 16.84 0.00 3.42
257 258 5.995565 TGGTTCTTTTAGTCTGCTAGCTA 57.004 39.130 17.23 0.72 0.00 3.32
258 259 4.891992 TGGTTCTTTTAGTCTGCTAGCT 57.108 40.909 17.23 0.00 0.00 3.32
259 260 5.178797 TGATGGTTCTTTTAGTCTGCTAGC 58.821 41.667 8.10 8.10 0.00 3.42
260 261 7.856145 ATTGATGGTTCTTTTAGTCTGCTAG 57.144 36.000 0.00 0.00 0.00 3.42
261 262 8.514594 CAAATTGATGGTTCTTTTAGTCTGCTA 58.485 33.333 0.00 0.00 0.00 3.49
262 263 7.014615 ACAAATTGATGGTTCTTTTAGTCTGCT 59.985 33.333 0.00 0.00 0.00 4.24
263 264 7.147976 ACAAATTGATGGTTCTTTTAGTCTGC 58.852 34.615 0.00 0.00 0.00 4.26
264 265 9.831737 CTACAAATTGATGGTTCTTTTAGTCTG 57.168 33.333 0.00 0.00 0.00 3.51
265 266 9.793259 TCTACAAATTGATGGTTCTTTTAGTCT 57.207 29.630 0.00 0.00 0.00 3.24
270 271 8.869109 TCCAATCTACAAATTGATGGTTCTTTT 58.131 29.630 0.00 0.00 38.64 2.27
271 272 8.421249 TCCAATCTACAAATTGATGGTTCTTT 57.579 30.769 0.00 0.00 38.64 2.52
272 273 8.421249 TTCCAATCTACAAATTGATGGTTCTT 57.579 30.769 0.00 0.00 38.64 2.52
273 274 8.421249 TTTCCAATCTACAAATTGATGGTTCT 57.579 30.769 0.00 0.00 38.64 3.01
274 275 9.487790 TTTTTCCAATCTACAAATTGATGGTTC 57.512 29.630 0.00 0.00 38.64 3.62
276 277 9.657419 GATTTTTCCAATCTACAAATTGATGGT 57.343 29.630 0.00 0.00 38.64 3.55
294 295 8.825667 TTTGGCATACTAAAACTGATTTTTCC 57.174 30.769 0.00 0.00 38.91 3.13
338 343 9.328845 AGTCTACCTCAAATAACAAAACGTAAA 57.671 29.630 0.00 0.00 0.00 2.01
339 344 8.891671 AGTCTACCTCAAATAACAAAACGTAA 57.108 30.769 0.00 0.00 0.00 3.18
373 405 8.560355 AAAAGTGCATTGTTCTTTTTACCTTT 57.440 26.923 6.25 0.00 37.90 3.11
389 421 4.396166 CCCAGTCGATTTAGAAAAGTGCAT 59.604 41.667 0.00 0.00 0.00 3.96
408 440 9.277783 CCACATATAAGATTTCTTAAGTCCCAG 57.722 37.037 1.63 0.00 41.27 4.45
413 445 7.985184 TCGTGCCACATATAAGATTTCTTAAGT 59.015 33.333 1.63 2.04 41.27 2.24
434 541 7.514747 CGGTACATTTTATCTCTTTAGTCGTGC 60.515 40.741 0.00 0.00 0.00 5.34
435 542 7.487189 ACGGTACATTTTATCTCTTTAGTCGTG 59.513 37.037 0.00 0.00 0.00 4.35
449 556 4.873827 GCAATGGAGAGACGGTACATTTTA 59.126 41.667 0.00 0.00 0.00 1.52
645 754 3.007473 AGGACCACTCCGTTTCAAAAA 57.993 42.857 0.00 0.00 42.22 1.94
646 755 2.721425 AGGACCACTCCGTTTCAAAA 57.279 45.000 0.00 0.00 42.22 2.44
647 756 2.171870 AGAAGGACCACTCCGTTTCAAA 59.828 45.455 0.00 0.00 42.22 2.69
648 757 1.766496 AGAAGGACCACTCCGTTTCAA 59.234 47.619 0.00 0.00 42.22 2.69
649 758 1.420430 AGAAGGACCACTCCGTTTCA 58.580 50.000 0.00 0.00 42.22 2.69
650 759 2.561858 AGTAGAAGGACCACTCCGTTTC 59.438 50.000 0.00 0.00 42.22 2.78
651 760 2.561858 GAGTAGAAGGACCACTCCGTTT 59.438 50.000 0.00 0.00 42.22 3.60
652 761 2.169330 GAGTAGAAGGACCACTCCGTT 58.831 52.381 0.00 0.00 42.22 4.44
653 762 1.836802 GAGTAGAAGGACCACTCCGT 58.163 55.000 0.00 0.00 42.22 4.69
654 763 0.733729 CGAGTAGAAGGACCACTCCG 59.266 60.000 4.55 0.98 42.22 4.63
655 764 1.473278 CACGAGTAGAAGGACCACTCC 59.527 57.143 4.55 0.00 36.20 3.85
656 765 1.473278 CCACGAGTAGAAGGACCACTC 59.527 57.143 0.00 0.00 36.23 3.51
657 766 1.075050 TCCACGAGTAGAAGGACCACT 59.925 52.381 0.00 0.00 0.00 4.00
658 767 1.201880 GTCCACGAGTAGAAGGACCAC 59.798 57.143 0.00 0.00 40.25 4.16
659 768 1.075050 AGTCCACGAGTAGAAGGACCA 59.925 52.381 13.03 0.00 44.00 4.02
660 769 1.744522 GAGTCCACGAGTAGAAGGACC 59.255 57.143 13.03 0.00 44.00 4.46
661 770 1.397692 CGAGTCCACGAGTAGAAGGAC 59.602 57.143 0.00 0.00 43.61 3.85
662 771 1.735386 CGAGTCCACGAGTAGAAGGA 58.265 55.000 0.00 0.00 35.09 3.36
663 772 0.099082 GCGAGTCCACGAGTAGAAGG 59.901 60.000 0.00 0.00 35.09 3.46
664 773 0.247735 CGCGAGTCCACGAGTAGAAG 60.248 60.000 0.00 0.00 35.09 2.85
665 774 0.671472 TCGCGAGTCCACGAGTAGAA 60.671 55.000 3.71 0.00 34.94 2.10
666 775 1.079612 TCGCGAGTCCACGAGTAGA 60.080 57.895 3.71 0.00 34.94 2.59
740 851 1.153588 GGCTCAGAGACTGCTGCTC 60.154 63.158 0.00 6.85 35.86 4.26
1282 1410 1.538876 CCTGTTCTCCCTGGGGACA 60.539 63.158 14.00 14.02 39.76 4.02
1519 1647 0.754587 CCCCGGTGTACCTAGTCTCC 60.755 65.000 0.00 0.00 0.00 3.71
1586 1714 3.395639 AGAGATCGATCGACCTAGTGAC 58.604 50.000 22.06 3.18 0.00 3.67
1948 2077 2.598632 CGATGATCTTTCCCGGCGC 61.599 63.158 0.00 0.00 0.00 6.53
1958 2103 1.533299 CAGGACGTCGATCGATGATCT 59.467 52.381 36.95 28.43 42.86 2.75
1963 2108 0.746923 TCACCAGGACGTCGATCGAT 60.747 55.000 22.50 5.91 42.86 3.59
2111 2265 3.425659 GGGCAAGATCAGTTCTCCTTTT 58.574 45.455 0.00 0.00 31.78 2.27
2140 2294 5.637006 TTTATTCAATCACAAAGACCCGG 57.363 39.130 0.00 0.00 0.00 5.73
2179 2333 4.759183 ACTGAAGCTGAAAGATGGAAGAAC 59.241 41.667 0.00 0.00 34.07 3.01
2507 2697 2.429927 GTTTGAGCCCAAGCCAACT 58.570 52.632 0.00 0.00 41.25 3.16
2601 2810 9.533831 AAACATCTACTTCCCACAATAAAATCT 57.466 29.630 0.00 0.00 0.00 2.40
2902 3145 2.093341 TGGTTAGTCGCCTATTCAACCC 60.093 50.000 0.00 0.00 0.00 4.11
2905 3148 3.709653 AGGATGGTTAGTCGCCTATTCAA 59.290 43.478 0.00 0.00 0.00 2.69
2944 3187 9.796120 CAACCTACTTTCTTGTTGAACATAAAA 57.204 29.630 0.00 2.42 40.30 1.52
2945 3188 7.918562 GCAACCTACTTTCTTGTTGAACATAAA 59.081 33.333 0.00 2.74 40.30 1.40
2946 3189 7.422399 GCAACCTACTTTCTTGTTGAACATAA 58.578 34.615 0.00 0.00 40.30 1.90
2947 3190 6.293190 CGCAACCTACTTTCTTGTTGAACATA 60.293 38.462 0.00 0.00 40.30 2.29
2948 3191 5.505654 CGCAACCTACTTTCTTGTTGAACAT 60.506 40.000 0.00 0.00 40.30 2.71
2949 3192 4.201871 CGCAACCTACTTTCTTGTTGAACA 60.202 41.667 0.00 0.00 40.30 3.18
2950 3193 4.279659 CGCAACCTACTTTCTTGTTGAAC 58.720 43.478 5.49 0.00 40.30 3.18
2951 3194 3.242936 GCGCAACCTACTTTCTTGTTGAA 60.243 43.478 0.30 0.00 40.30 2.69
2952 3195 2.289547 GCGCAACCTACTTTCTTGTTGA 59.710 45.455 0.30 0.00 40.30 3.18
2953 3196 2.032799 TGCGCAACCTACTTTCTTGTTG 59.967 45.455 8.16 0.00 40.71 3.33
2954 3197 2.294074 TGCGCAACCTACTTTCTTGTT 58.706 42.857 8.16 0.00 0.00 2.83
2969 3212 0.882927 GTTGTCCACCTAGTTGCGCA 60.883 55.000 5.66 5.66 0.00 6.09
2994 3237 3.443329 ACATGTTCTTGTGTTGCTTGTCA 59.557 39.130 0.00 0.00 0.00 3.58
3046 3289 5.007332 ACTTCGTGCCTTTACTTTGTACAAG 59.993 40.000 8.56 6.02 0.00 3.16
3075 3318 1.202200 CGTCTCCATCGACTCCACTTC 60.202 57.143 0.00 0.00 0.00 3.01
3085 3331 0.741326 ACACATCCTCGTCTCCATCG 59.259 55.000 0.00 0.00 0.00 3.84
3094 3340 0.670546 ACTTCGGCAACACATCCTCG 60.671 55.000 0.00 0.00 0.00 4.63
3119 3365 1.200519 CGAAGATGTACCTCCCCCAA 58.799 55.000 0.00 0.00 0.00 4.12
3120 3366 0.042131 ACGAAGATGTACCTCCCCCA 59.958 55.000 0.00 0.00 0.00 4.96
3121 3367 1.134491 CAACGAAGATGTACCTCCCCC 60.134 57.143 0.00 0.00 0.00 5.40
3137 3385 0.951040 GCTTCCACACCTCTCCAACG 60.951 60.000 0.00 0.00 0.00 4.10
3156 3404 3.023832 GGGACATTTGGGGAGTATTGTG 58.976 50.000 0.00 0.00 0.00 3.33
3161 3409 2.319747 TCCTAGGGACATTTGGGGAGTA 59.680 50.000 9.46 0.00 0.00 2.59
3181 3429 3.135530 AGCATGAGGAGAATAAGGTGGTC 59.864 47.826 0.00 0.00 0.00 4.02
3208 3456 0.609662 ACATTTGGGGAGCATTGTGC 59.390 50.000 0.00 0.00 45.46 4.57
3209 3457 1.205417 GGACATTTGGGGAGCATTGTG 59.795 52.381 0.00 0.00 0.00 3.33
3210 3458 1.560505 GGACATTTGGGGAGCATTGT 58.439 50.000 0.00 0.00 0.00 2.71
3211 3459 0.826062 GGGACATTTGGGGAGCATTG 59.174 55.000 0.00 0.00 0.00 2.82
3212 3460 0.712380 AGGGACATTTGGGGAGCATT 59.288 50.000 0.00 0.00 0.00 3.56
3213 3461 1.496429 CTAGGGACATTTGGGGAGCAT 59.504 52.381 0.00 0.00 0.00 3.79
3214 3462 0.918983 CTAGGGACATTTGGGGAGCA 59.081 55.000 0.00 0.00 0.00 4.26
3215 3463 0.183731 CCTAGGGACATTTGGGGAGC 59.816 60.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.