Multiple sequence alignment - TraesCS6D01G208200

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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 TraesCS6D01G208200 chr6D 100.000 3512 0 0 1 3512 293800964 293804475 0.000000e+00 6486.0
1 TraesCS6D01G208200 chr6D 84.426 244 22 11 1 232 412489601 412489840 3.530000e-55 226.0
2 TraesCS6D01G208200 chr6D 83.636 165 24 2 86 250 417885408 417885569 6.070000e-33 152.0
3 TraesCS6D01G208200 chr6D 78.543 247 27 13 3 249 443749357 443749137 4.730000e-29 139.0
4 TraesCS6D01G208200 chr6B 94.908 2553 73 24 268 2772 458485381 458487924 0.000000e+00 3941.0
5 TraesCS6D01G208200 chr6B 88.594 754 69 11 2759 3512 458494399 458495135 0.000000e+00 900.0
6 TraesCS6D01G208200 chr6A 97.473 1820 38 7 741 2556 426967748 426965933 0.000000e+00 3099.0
7 TraesCS6D01G208200 chr6A 91.584 202 9 4 2548 2746 426964063 426963867 4.470000e-69 272.0
8 TraesCS6D01G208200 chr6A 81.944 360 24 15 312 654 427052190 427051855 2.080000e-67 267.0
9 TraesCS6D01G208200 chr6A 89.231 130 5 9 3355 3478 426963863 426963737 1.690000e-33 154.0
10 TraesCS6D01G208200 chr2D 88.181 1396 158 7 1005 2398 468856181 468857571 0.000000e+00 1657.0
11 TraesCS6D01G208200 chr2D 87.195 164 19 1 86 249 538756662 538756823 5.990000e-43 185.0
12 TraesCS6D01G208200 chr2D 91.453 117 10 0 133 249 43079504 43079620 1.010000e-35 161.0
13 TraesCS6D01G208200 chr2D 84.348 115 18 0 3038 3152 599276460 599276574 2.870000e-21 113.0
14 TraesCS6D01G208200 chr2A 88.037 1396 160 7 1005 2398 608871064 608872454 0.000000e+00 1646.0
15 TraesCS6D01G208200 chr2B 87.894 1396 162 7 1005 2398 547057079 547058469 0.000000e+00 1635.0
16 TraesCS6D01G208200 chr2B 83.333 120 11 6 3033 3152 554288686 554288796 6.200000e-18 102.0
17 TraesCS6D01G208200 chr1A 83.267 251 28 6 1 247 16897863 16897623 5.900000e-53 219.0
18 TraesCS6D01G208200 chr1A 98.000 50 1 0 1 50 16484423 16484472 1.740000e-13 87.9
19 TraesCS6D01G208200 chr4A 82.609 253 36 7 1 247 636041794 636042044 2.120000e-52 217.0
20 TraesCS6D01G208200 chr5A 81.679 262 30 7 1 247 457259726 457259468 5.940000e-48 202.0
21 TraesCS6D01G208200 chr5A 90.741 108 9 1 3041 3148 19490247 19490353 3.650000e-30 143.0
22 TraesCS6D01G208200 chr5D 81.600 250 35 8 1 249 404103732 404103493 2.770000e-46 196.0
23 TraesCS6D01G208200 chr5D 81.250 192 27 7 2929 3119 243879053 243878870 2.820000e-31 147.0
24 TraesCS6D01G208200 chr5D 80.180 222 21 9 1 206 499408388 499408602 1.020000e-30 145.0
25 TraesCS6D01G208200 chr3A 81.154 260 31 10 1 247 81665303 81665049 3.580000e-45 193.0
26 TraesCS6D01G208200 chr3A 85.976 164 23 0 86 249 336872066 336871903 3.600000e-40 176.0
27 TraesCS6D01G208200 chr3D 87.037 162 21 0 86 247 424650612 424650773 2.150000e-42 183.0
28 TraesCS6D01G208200 chr7D 86.335 161 20 1 86 246 34062453 34062611 1.300000e-39 174.0
29 TraesCS6D01G208200 chr7D 82.474 97 12 5 3053 3148 146234532 146234624 2.910000e-11 80.5
30 TraesCS6D01G208200 chr1B 79.675 246 41 8 2910 3152 460580627 460580388 6.030000e-38 169.0
31 TraesCS6D01G208200 chr1D 77.308 260 43 11 2862 3113 343363774 343363523 4.730000e-29 139.0
32 TraesCS6D01G208200 chr4D 76.096 251 36 14 3 247 489629165 489628933 3.710000e-20 110.0
33 TraesCS6D01G208200 chr7A 81.818 110 20 0 3042 3151 13399400 13399291 3.730000e-15 93.5


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 TraesCS6D01G208200 chr6D 293800964 293804475 3511 False 6486 6486 100.000000 1 3512 1 chr6D.!!$F1 3511
1 TraesCS6D01G208200 chr6B 458485381 458487924 2543 False 3941 3941 94.908000 268 2772 1 chr6B.!!$F1 2504
2 TraesCS6D01G208200 chr6B 458494399 458495135 736 False 900 900 88.594000 2759 3512 1 chr6B.!!$F2 753
3 TraesCS6D01G208200 chr6A 426963737 426967748 4011 True 1175 3099 92.762667 741 3478 3 chr6A.!!$R2 2737
4 TraesCS6D01G208200 chr2D 468856181 468857571 1390 False 1657 1657 88.181000 1005 2398 1 chr2D.!!$F2 1393
5 TraesCS6D01G208200 chr2A 608871064 608872454 1390 False 1646 1646 88.037000 1005 2398 1 chr2A.!!$F1 1393
6 TraesCS6D01G208200 chr2B 547057079 547058469 1390 False 1635 1635 87.894000 1005 2398 1 chr2B.!!$F1 1393

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
186 187 0.039527 GCCGCGTTTTTCCAGACAAT 60.040 50.0 4.92 0.00 0.00 2.71 F
204 205 0.165944 ATGAACGCGCTGCAAAGTAC 59.834 50.0 5.73 0.00 0.00 2.73 F
206 207 0.234884 GAACGCGCTGCAAAGTACTT 59.765 50.0 5.73 1.12 0.00 2.24 F
756 778 0.325933 TCATCAACCACCAGGAGCAG 59.674 55.0 0.00 0.00 38.69 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1279 3.128242 CGAAGCCGAAGAGGTAGTAGAAA 59.872 47.826 0.00 0.00 43.70 2.52 R
2343 2377 4.758251 CGCGTCTGGTCCATGCCA 62.758 66.667 0.00 0.00 36.97 4.92 R
2370 2404 1.870901 GGTGTAGGCGTACGCGAAG 60.871 63.158 31.78 4.23 40.10 3.79 R
2808 4722 0.819582 GGCATCACATTGTTGAGGGG 59.180 55.000 0.00 0.00 0.00 4.79 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
72 73 8.984891 ATGCATCATTTTATCGTTTTGAGAAA 57.015 26.923 0.00 0.00 36.07 2.52
73 74 8.984891 TGCATCATTTTATCGTTTTGAGAAAT 57.015 26.923 0.00 0.00 37.61 2.17
86 87 9.123709 TCGTTTTGAGAAATATGTATTGTTTGC 57.876 29.630 0.00 0.00 0.00 3.68
87 88 8.095512 CGTTTTGAGAAATATGTATTGTTTGCG 58.904 33.333 0.00 0.00 0.00 4.85
88 89 7.504922 TTTGAGAAATATGTATTGTTTGCGC 57.495 32.000 0.00 0.00 0.00 6.09
89 90 5.262422 TGAGAAATATGTATTGTTTGCGCG 58.738 37.500 0.00 0.00 0.00 6.86
90 91 4.035017 AGAAATATGTATTGTTTGCGCGC 58.965 39.130 27.26 27.26 0.00 6.86
91 92 2.017357 ATATGTATTGTTTGCGCGCG 57.983 45.000 28.44 28.44 0.00 6.86
92 93 0.587737 TATGTATTGTTTGCGCGCGC 60.588 50.000 45.02 45.02 42.35 6.86
102 103 4.173659 GCGCGCGCTGTATTTTAG 57.826 55.556 44.38 11.16 38.26 1.85
103 104 1.998772 GCGCGCGCTGTATTTTAGC 60.999 57.895 44.38 17.67 38.26 3.09
108 109 4.589967 GCTGTATTTTAGCGCGGC 57.410 55.556 8.83 0.00 0.00 6.53
109 110 2.014594 GCTGTATTTTAGCGCGGCT 58.985 52.632 8.83 8.38 43.41 5.52
110 111 0.377203 GCTGTATTTTAGCGCGGCTT 59.623 50.000 8.83 0.00 40.44 4.35
111 112 1.594760 GCTGTATTTTAGCGCGGCTTC 60.595 52.381 8.83 0.00 40.44 3.86
112 113 1.933853 CTGTATTTTAGCGCGGCTTCT 59.066 47.619 8.83 0.00 40.44 2.85
113 114 1.663643 TGTATTTTAGCGCGGCTTCTG 59.336 47.619 8.83 0.00 40.44 3.02
114 115 1.003866 GTATTTTAGCGCGGCTTCTGG 60.004 52.381 8.83 0.00 40.44 3.86
115 116 0.392461 ATTTTAGCGCGGCTTCTGGA 60.392 50.000 8.83 0.00 40.44 3.86
116 117 1.019278 TTTTAGCGCGGCTTCTGGAG 61.019 55.000 8.83 0.00 40.44 3.86
139 140 4.255507 CGCGCGCGCTAAATTTTA 57.744 50.000 45.97 0.00 39.32 1.52
140 141 2.105045 CGCGCGCGCTAAATTTTAG 58.895 52.632 45.97 27.04 39.32 1.85
141 142 1.830981 GCGCGCGCTAAATTTTAGC 59.169 52.632 44.38 24.84 38.26 3.09
147 148 3.918102 GCTAAATTTTAGCGCGGCT 57.082 47.368 21.75 8.38 43.41 5.52
148 149 1.466855 GCTAAATTTTAGCGCGGCTG 58.533 50.000 21.75 0.00 40.10 4.85
149 150 1.466855 CTAAATTTTAGCGCGGCTGC 58.533 50.000 8.83 7.70 40.10 5.25
151 152 0.456653 AAATTTTAGCGCGGCTGCTG 60.457 50.000 22.96 10.42 46.70 4.41
152 153 1.305219 AATTTTAGCGCGGCTGCTGA 61.305 50.000 22.96 15.42 46.70 4.26
153 154 1.305219 ATTTTAGCGCGGCTGCTGAA 61.305 50.000 22.96 19.26 46.70 3.02
154 155 1.911293 TTTTAGCGCGGCTGCTGAAG 61.911 55.000 22.96 6.33 46.70 3.02
177 178 4.322385 GCTGTCCGCCGCGTTTTT 62.322 61.111 12.58 0.00 0.00 1.94
178 179 2.127383 CTGTCCGCCGCGTTTTTC 60.127 61.111 12.58 0.00 0.00 2.29
179 180 3.588891 CTGTCCGCCGCGTTTTTCC 62.589 63.158 12.58 0.00 0.00 3.13
180 181 3.652000 GTCCGCCGCGTTTTTCCA 61.652 61.111 12.58 0.00 0.00 3.53
181 182 3.350612 TCCGCCGCGTTTTTCCAG 61.351 61.111 12.58 0.00 0.00 3.86
182 183 3.350612 CCGCCGCGTTTTTCCAGA 61.351 61.111 12.58 0.00 0.00 3.86
183 184 2.127383 CGCCGCGTTTTTCCAGAC 60.127 61.111 4.92 0.00 0.00 3.51
184 185 2.887889 CGCCGCGTTTTTCCAGACA 61.888 57.895 4.92 0.00 0.00 3.41
185 186 1.357334 GCCGCGTTTTTCCAGACAA 59.643 52.632 4.92 0.00 0.00 3.18
186 187 0.039527 GCCGCGTTTTTCCAGACAAT 60.040 50.000 4.92 0.00 0.00 2.71
187 188 1.685302 CCGCGTTTTTCCAGACAATG 58.315 50.000 4.92 0.00 0.00 2.82
188 189 1.265635 CCGCGTTTTTCCAGACAATGA 59.734 47.619 4.92 0.00 0.00 2.57
189 190 2.287308 CCGCGTTTTTCCAGACAATGAA 60.287 45.455 4.92 0.00 0.00 2.57
190 191 2.719046 CGCGTTTTTCCAGACAATGAAC 59.281 45.455 0.00 0.00 0.00 3.18
191 192 2.719046 GCGTTTTTCCAGACAATGAACG 59.281 45.455 0.00 0.00 40.70 3.95
192 193 2.719046 CGTTTTTCCAGACAATGAACGC 59.281 45.455 0.00 0.00 33.25 4.84
193 194 2.679355 TTTTCCAGACAATGAACGCG 57.321 45.000 3.53 3.53 0.00 6.01
194 195 0.237235 TTTCCAGACAATGAACGCGC 59.763 50.000 5.73 0.00 0.00 6.86
195 196 0.602638 TTCCAGACAATGAACGCGCT 60.603 50.000 5.73 0.00 0.00 5.92
196 197 1.133253 CCAGACAATGAACGCGCTG 59.867 57.895 5.73 2.09 0.00 5.18
197 198 1.510623 CAGACAATGAACGCGCTGC 60.511 57.895 5.73 0.00 0.00 5.25
198 199 1.960763 AGACAATGAACGCGCTGCA 60.961 52.632 5.73 1.45 0.00 4.41
199 200 1.082169 GACAATGAACGCGCTGCAA 60.082 52.632 5.73 0.00 0.00 4.08
200 201 0.660005 GACAATGAACGCGCTGCAAA 60.660 50.000 5.73 0.00 0.00 3.68
201 202 0.661187 ACAATGAACGCGCTGCAAAG 60.661 50.000 5.73 1.65 0.00 2.77
202 203 0.661187 CAATGAACGCGCTGCAAAGT 60.661 50.000 5.73 0.00 0.00 2.66
203 204 0.871722 AATGAACGCGCTGCAAAGTA 59.128 45.000 5.73 0.00 0.00 2.24
204 205 0.165944 ATGAACGCGCTGCAAAGTAC 59.834 50.000 5.73 0.00 0.00 2.73
205 206 0.878523 TGAACGCGCTGCAAAGTACT 60.879 50.000 5.73 0.00 0.00 2.73
206 207 0.234884 GAACGCGCTGCAAAGTACTT 59.765 50.000 5.73 1.12 0.00 2.24
207 208 0.661020 AACGCGCTGCAAAGTACTTT 59.339 45.000 15.22 15.22 0.00 2.66
208 209 0.661020 ACGCGCTGCAAAGTACTTTT 59.339 45.000 18.25 1.50 0.00 2.27
209 210 1.064952 ACGCGCTGCAAAGTACTTTTT 59.935 42.857 18.25 0.00 0.00 1.94
210 211 2.288458 ACGCGCTGCAAAGTACTTTTTA 59.712 40.909 18.25 9.25 0.00 1.52
211 212 2.902484 CGCGCTGCAAAGTACTTTTTAG 59.098 45.455 18.25 18.13 0.00 1.85
212 213 2.656897 GCGCTGCAAAGTACTTTTTAGC 59.343 45.455 27.86 27.86 36.44 3.09
213 214 2.902484 CGCTGCAAAGTACTTTTTAGCG 59.098 45.455 35.98 35.98 46.13 4.26
214 215 2.656897 GCTGCAAAGTACTTTTTAGCGC 59.343 45.455 25.70 21.51 32.81 5.92
215 216 2.902484 CTGCAAAGTACTTTTTAGCGCG 59.098 45.455 18.25 0.00 0.00 6.86
216 217 1.642360 GCAAAGTACTTTTTAGCGCGC 59.358 47.619 26.66 26.66 0.00 6.86
217 218 2.239201 CAAAGTACTTTTTAGCGCGCC 58.761 47.619 30.33 10.31 0.00 6.53
218 219 0.441145 AAGTACTTTTTAGCGCGCCG 59.559 50.000 30.33 11.84 0.00 6.46
219 220 0.668401 AGTACTTTTTAGCGCGCCGT 60.668 50.000 30.33 13.66 0.00 5.68
220 221 0.517742 GTACTTTTTAGCGCGCCGTG 60.518 55.000 30.33 14.57 0.00 4.94
221 222 0.945265 TACTTTTTAGCGCGCCGTGT 60.945 50.000 30.33 19.46 0.00 4.49
222 223 1.792057 CTTTTTAGCGCGCCGTGTG 60.792 57.895 30.33 10.42 0.00 3.82
223 224 2.438385 CTTTTTAGCGCGCCGTGTGT 62.438 55.000 30.33 11.01 0.00 3.72
224 225 2.049475 TTTTTAGCGCGCCGTGTGTT 62.049 50.000 30.33 10.14 0.00 3.32
225 226 2.432841 TTTTAGCGCGCCGTGTGTTC 62.433 55.000 30.33 0.00 0.00 3.18
235 236 3.276846 GTGTGTTCGGCGGCTGTT 61.277 61.111 7.21 0.00 0.00 3.16
236 237 3.276091 TGTGTTCGGCGGCTGTTG 61.276 61.111 7.21 0.00 0.00 3.33
237 238 4.025401 GTGTTCGGCGGCTGTTGG 62.025 66.667 7.21 0.00 0.00 3.77
238 239 4.243008 TGTTCGGCGGCTGTTGGA 62.243 61.111 7.21 0.00 0.00 3.53
239 240 3.423154 GTTCGGCGGCTGTTGGAG 61.423 66.667 7.21 0.00 0.00 3.86
240 241 3.621805 TTCGGCGGCTGTTGGAGA 61.622 61.111 7.21 0.00 0.00 3.71
241 242 2.954684 TTCGGCGGCTGTTGGAGAT 61.955 57.895 7.21 0.00 0.00 2.75
242 243 3.197790 CGGCGGCTGTTGGAGATG 61.198 66.667 7.61 0.00 0.00 2.90
243 244 3.512516 GGCGGCTGTTGGAGATGC 61.513 66.667 0.00 0.00 0.00 3.91
244 245 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
245 246 2.467826 GCGGCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 0.00 4.26
246 247 1.220206 CGGCTGTTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
247 248 0.461548 CGGCTGTTGGAGATGCTCTA 59.538 55.000 0.00 0.00 0.00 2.43
248 249 1.134699 CGGCTGTTGGAGATGCTCTAA 60.135 52.381 0.00 0.00 0.00 2.10
249 250 2.484417 CGGCTGTTGGAGATGCTCTAAT 60.484 50.000 0.00 0.00 33.81 1.73
250 251 3.243873 CGGCTGTTGGAGATGCTCTAATA 60.244 47.826 0.00 0.00 33.81 0.98
251 252 4.708177 GGCTGTTGGAGATGCTCTAATAA 58.292 43.478 0.00 0.00 33.81 1.40
252 253 5.312079 GGCTGTTGGAGATGCTCTAATAAT 58.688 41.667 0.00 0.00 33.81 1.28
253 254 5.411053 GGCTGTTGGAGATGCTCTAATAATC 59.589 44.000 0.00 0.00 33.81 1.75
254 255 5.411053 GCTGTTGGAGATGCTCTAATAATCC 59.589 44.000 0.00 0.00 33.81 3.01
255 256 6.743773 GCTGTTGGAGATGCTCTAATAATCCT 60.744 42.308 0.00 0.00 33.81 3.24
256 257 7.141758 TGTTGGAGATGCTCTAATAATCCTT 57.858 36.000 0.00 0.00 33.81 3.36
257 258 8.262601 TGTTGGAGATGCTCTAATAATCCTTA 57.737 34.615 0.00 0.00 33.81 2.69
258 259 8.884323 TGTTGGAGATGCTCTAATAATCCTTAT 58.116 33.333 0.00 0.00 33.81 1.73
261 262 9.775539 TGGAGATGCTCTAATAATCCTTATACT 57.224 33.333 0.00 0.00 0.00 2.12
274 275 4.523083 TCCTTATACTCAACAACCATGGC 58.477 43.478 13.04 0.00 0.00 4.40
306 307 0.537371 TCACACGGTCTCTCAGCTGA 60.537 55.000 17.19 17.19 0.00 4.26
328 329 1.133025 CTGCTGCCTAAACAAATCGGG 59.867 52.381 0.00 0.00 0.00 5.14
382 393 2.422803 GCCTGATAATTGTGGCACCCTA 60.423 50.000 16.26 4.04 44.34 3.53
461 474 1.365368 CGTATTGACGCCCACATGCA 61.365 55.000 0.00 0.00 43.21 3.96
464 477 0.966875 ATTGACGCCCACATGCACAT 60.967 50.000 0.00 0.00 0.00 3.21
500 513 2.362503 ACGACGGCAGATCAGGGA 60.363 61.111 0.00 0.00 0.00 4.20
510 523 1.698532 CAGATCAGGGAAGATCAGGGG 59.301 57.143 6.70 0.00 45.39 4.79
556 569 2.069273 AGCACGTATCAACTGAACAGC 58.931 47.619 1.46 0.00 0.00 4.40
561 574 2.805671 CGTATCAACTGAACAGCACCAA 59.194 45.455 1.46 0.00 0.00 3.67
566 579 2.191128 ACTGAACAGCACCAAGGATC 57.809 50.000 1.46 0.00 0.00 3.36
574 587 3.201290 CAGCACCAAGGATCTGACATAC 58.799 50.000 0.00 0.00 0.00 2.39
584 597 3.932710 GGATCTGACATACAAAAGCGACA 59.067 43.478 0.00 0.00 0.00 4.35
604 617 4.210331 ACACAAAATGGAGAAGCAAGTCT 58.790 39.130 0.00 0.00 0.00 3.24
618 631 2.544685 CAAGTCTGATACAAGCTCCGG 58.455 52.381 0.00 0.00 0.00 5.14
630 643 1.256812 AGCTCCGGGTTTTCCATTTG 58.743 50.000 0.00 0.00 42.91 2.32
667 684 6.119144 ACAAACACAATTGCTATACGGATC 57.881 37.500 5.05 0.00 33.52 3.36
699 716 1.927174 CCAAATCGCTACTCAGTTCCG 59.073 52.381 0.00 0.00 0.00 4.30
715 732 7.384387 ACTCAGTTCCGTACTTTATTCAAGTTC 59.616 37.037 0.00 0.00 43.89 3.01
722 739 6.702897 CGTACTTTATTCAAGTTCGGATTCC 58.297 40.000 6.01 0.00 46.84 3.01
725 742 7.321745 ACTTTATTCAAGTTCGGATTCCATC 57.678 36.000 3.09 0.00 43.89 3.51
726 743 6.884295 ACTTTATTCAAGTTCGGATTCCATCA 59.116 34.615 3.09 0.00 43.89 3.07
727 744 7.393234 ACTTTATTCAAGTTCGGATTCCATCAA 59.607 33.333 3.09 0.00 43.89 2.57
728 745 7.880160 TTATTCAAGTTCGGATTCCATCAAT 57.120 32.000 3.09 0.00 0.00 2.57
729 746 6.780457 ATTCAAGTTCGGATTCCATCAATT 57.220 33.333 3.09 0.00 0.00 2.32
730 747 6.588719 TTCAAGTTCGGATTCCATCAATTT 57.411 33.333 3.09 0.00 0.00 1.82
731 748 6.194796 TCAAGTTCGGATTCCATCAATTTC 57.805 37.500 3.09 0.00 0.00 2.17
732 749 5.709631 TCAAGTTCGGATTCCATCAATTTCA 59.290 36.000 3.09 0.00 0.00 2.69
756 778 0.325933 TCATCAACCACCAGGAGCAG 59.674 55.000 0.00 0.00 38.69 4.24
829 861 3.780294 TGAATATTCACTGGCAGGTAGGT 59.220 43.478 20.34 3.29 31.01 3.08
836 868 4.162690 GGCAGGTAGGTCCCAGCG 62.163 72.222 0.00 0.00 38.23 5.18
889 921 1.402456 CCGTCTCGCCTATAAATCCGG 60.402 57.143 0.00 0.00 0.00 5.14
952 986 3.455469 GCACCTGCCATTGCTCCC 61.455 66.667 0.00 0.00 38.71 4.30
976 1010 4.580580 TGAGCAGCAGAGTATTCGATAAGA 59.419 41.667 0.00 0.00 0.00 2.10
1740 1774 0.675633 CCTTCTTGCTGTGGTTTGGG 59.324 55.000 0.00 0.00 0.00 4.12
1830 1864 4.143333 CAGTGGTCGGCGGTAGGG 62.143 72.222 7.21 0.00 0.00 3.53
2343 2377 3.532155 GCCGAGGACGAGATGGCT 61.532 66.667 0.00 0.00 42.44 4.75
2674 4586 9.914131 ACGTGAGTACTACTACGTGATTATATA 57.086 33.333 23.33 0.00 46.55 0.86
2749 4663 3.007516 CGCGTGTGTGGAACGAAA 58.992 55.556 0.00 0.00 43.68 3.46
2790 4704 0.872021 CGAAGCTCGATGGTAGTGGC 60.872 60.000 0.00 0.00 43.74 5.01
2800 4714 3.063997 CGATGGTAGTGGCAAATCTCAAC 59.936 47.826 0.00 0.00 0.00 3.18
2804 4718 1.238439 AGTGGCAAATCTCAACGTGG 58.762 50.000 0.00 0.00 0.00 4.94
2808 4722 2.034053 TGGCAAATCTCAACGTGGTTTC 59.966 45.455 0.00 0.00 0.00 2.78
2875 4789 4.739793 TGGAGTTCAGAAATTGTTGGGAT 58.260 39.130 0.00 0.00 0.00 3.85
2886 4800 5.524971 AATTGTTGGGATCGACTATACGA 57.475 39.130 0.00 0.00 46.04 3.43
2964 4878 1.033574 ATCGAACGGCCCAAAACAAA 58.966 45.000 0.00 0.00 0.00 2.83
2966 4880 1.001158 TCGAACGGCCCAAAACAAATC 60.001 47.619 0.00 0.00 0.00 2.17
2967 4881 1.790755 GAACGGCCCAAAACAAATCC 58.209 50.000 0.00 0.00 0.00 3.01
2970 4884 1.890489 ACGGCCCAAAACAAATCCTAC 59.110 47.619 0.00 0.00 0.00 3.18
2973 4887 2.353704 GGCCCAAAACAAATCCTACTGC 60.354 50.000 0.00 0.00 0.00 4.40
2996 4910 3.272285 TCATCTTCAACCTCCCTCCTCTA 59.728 47.826 0.00 0.00 0.00 2.43
2999 4913 4.290942 TCTTCAACCTCCCTCCTCTATTC 58.709 47.826 0.00 0.00 0.00 1.75
3003 4917 2.952116 ACCTCCCTCCTCTATTCTTCG 58.048 52.381 0.00 0.00 0.00 3.79
3006 4920 2.888414 CTCCCTCCTCTATTCTTCGTCC 59.112 54.545 0.00 0.00 0.00 4.79
3014 4928 2.306255 TATTCTTCGTCCCGCAGCCC 62.306 60.000 0.00 0.00 0.00 5.19
3086 5000 3.411418 CTATCGCGCACCACCTCGT 62.411 63.158 8.75 0.00 0.00 4.18
3109 5023 3.787001 CGCCCTCCCCTCAACCTC 61.787 72.222 0.00 0.00 0.00 3.85
3110 5024 3.412408 GCCCTCCCCTCAACCTCC 61.412 72.222 0.00 0.00 0.00 4.30
3166 5080 3.303928 CTACTCCGGCGATCCCCC 61.304 72.222 9.30 0.00 0.00 5.40
3186 5100 0.765510 GCACCCCACCCCTAAGATAG 59.234 60.000 0.00 0.00 0.00 2.08
3206 5120 1.967779 GATAGTGGGGCTCTCTTCTCC 59.032 57.143 0.00 0.00 0.00 3.71
3208 5122 1.682684 GTGGGGCTCTCTTCTCCGA 60.683 63.158 0.00 0.00 0.00 4.55
3216 5130 2.442413 CTCTCTTCTCCGACAAGGTCT 58.558 52.381 0.00 0.00 41.99 3.85
3217 5131 3.611970 CTCTCTTCTCCGACAAGGTCTA 58.388 50.000 0.00 0.00 41.99 2.59
3218 5132 4.011023 CTCTCTTCTCCGACAAGGTCTAA 58.989 47.826 0.00 0.00 41.99 2.10
3226 5140 1.455786 CGACAAGGTCTAACGTGCAAG 59.544 52.381 0.00 0.00 0.00 4.01
3227 5141 2.750948 GACAAGGTCTAACGTGCAAGA 58.249 47.619 6.65 0.00 0.00 3.02
3228 5142 3.128349 GACAAGGTCTAACGTGCAAGAA 58.872 45.455 6.65 0.00 0.00 2.52
3229 5143 3.131396 ACAAGGTCTAACGTGCAAGAAG 58.869 45.455 6.65 3.59 0.00 2.85
3230 5144 2.457366 AGGTCTAACGTGCAAGAAGG 57.543 50.000 6.65 0.00 0.00 3.46
3231 5145 1.968493 AGGTCTAACGTGCAAGAAGGA 59.032 47.619 6.65 0.00 0.00 3.36
3232 5146 2.367567 AGGTCTAACGTGCAAGAAGGAA 59.632 45.455 6.65 0.00 0.00 3.36
3233 5147 2.737252 GGTCTAACGTGCAAGAAGGAAG 59.263 50.000 6.65 0.00 0.00 3.46
3250 5164 2.290387 GGAAGGAAGGAAGAAGGTGACC 60.290 54.545 0.00 0.00 0.00 4.02
3253 5167 1.346722 GGAAGGAAGAAGGTGACCGAA 59.653 52.381 0.00 0.00 0.00 4.30
3261 5175 3.100671 AGAAGGTGACCGAAGCTAGAAT 58.899 45.455 0.00 0.00 0.00 2.40
3262 5176 3.515901 AGAAGGTGACCGAAGCTAGAATT 59.484 43.478 0.00 0.00 0.00 2.17
3263 5177 3.528597 AGGTGACCGAAGCTAGAATTC 57.471 47.619 0.00 0.00 0.00 2.17
3273 5187 5.412904 CCGAAGCTAGAATTCTTTTCAGGTT 59.587 40.000 14.36 15.67 0.00 3.50
3275 5189 7.119262 CCGAAGCTAGAATTCTTTTCAGGTTTA 59.881 37.037 14.36 0.00 0.00 2.01
3277 5191 9.995957 GAAGCTAGAATTCTTTTCAGGTTTATC 57.004 33.333 14.36 2.00 0.00 1.75
3279 5193 9.520515 AGCTAGAATTCTTTTCAGGTTTATCAA 57.479 29.630 14.36 0.00 0.00 2.57
3303 5217 9.922305 CAAAAATAGCAAAACCGAAAAATGTTA 57.078 25.926 0.00 0.00 0.00 2.41
3310 5224 6.474102 GCAAAACCGAAAAATGTTAGAGTTGA 59.526 34.615 0.00 0.00 0.00 3.18
3320 5234 8.634475 AAAATGTTAGAGTTGAAAGCTCAAAC 57.366 30.769 0.00 0.00 43.18 2.93
3323 5237 5.583061 TGTTAGAGTTGAAAGCTCAAACGAA 59.417 36.000 0.00 0.00 43.18 3.85
3328 5242 5.752712 AGTTGAAAGCTCAAACGAAGATTC 58.247 37.500 0.00 0.00 43.18 2.52
3341 5255 2.096496 CGAAGATTCTCTTTTGCCGCAT 59.904 45.455 0.00 0.00 36.73 4.73
3342 5256 3.309682 CGAAGATTCTCTTTTGCCGCATA 59.690 43.478 0.00 0.00 36.73 3.14
3349 5263 2.689983 CTCTTTTGCCGCATAAGGGAAT 59.310 45.455 16.10 0.00 41.25 3.01
3436 5355 5.431765 ACATCATCTACCTTTCTCGCAAAT 58.568 37.500 0.00 0.00 0.00 2.32
3446 5365 7.272037 ACCTTTCTCGCAAATAAAAAGAAGA 57.728 32.000 0.00 0.00 0.00 2.87
3447 5366 7.712797 ACCTTTCTCGCAAATAAAAAGAAGAA 58.287 30.769 0.00 0.00 0.00 2.52
3448 5367 7.862873 ACCTTTCTCGCAAATAAAAAGAAGAAG 59.137 33.333 0.00 0.00 0.00 2.85
3449 5368 7.862873 CCTTTCTCGCAAATAAAAAGAAGAAGT 59.137 33.333 0.00 0.00 0.00 3.01
3485 5404 2.673368 GGCACTTTACAAGAGATGTCGG 59.327 50.000 0.00 0.00 42.70 4.79
3486 5405 2.094417 GCACTTTACAAGAGATGTCGGC 59.906 50.000 0.00 0.00 42.70 5.54
3488 5407 2.230508 ACTTTACAAGAGATGTCGGCGA 59.769 45.455 4.99 4.99 42.70 5.54
3498 5417 1.609555 GATGTCGGCGACTCCTCTAAT 59.390 52.381 36.17 21.73 33.15 1.73
3503 5422 2.617308 TCGGCGACTCCTCTAATTACAG 59.383 50.000 4.99 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 8.984891 TTTCTCAAAACGATAAAATGATGCAT 57.015 26.923 0.00 0.00 0.00 3.96
48 49 8.984891 ATTTCTCAAAACGATAAAATGATGCA 57.015 26.923 0.00 0.00 0.00 3.96
60 61 9.123709 GCAAACAATACATATTTCTCAAAACGA 57.876 29.630 0.00 0.00 0.00 3.85
61 62 8.095512 CGCAAACAATACATATTTCTCAAAACG 58.904 33.333 0.00 0.00 0.00 3.60
62 63 7.892731 GCGCAAACAATACATATTTCTCAAAAC 59.107 33.333 0.30 0.00 0.00 2.43
63 64 7.201308 CGCGCAAACAATACATATTTCTCAAAA 60.201 33.333 8.75 0.00 0.00 2.44
64 65 6.250315 CGCGCAAACAATACATATTTCTCAAA 59.750 34.615 8.75 0.00 0.00 2.69
65 66 5.736824 CGCGCAAACAATACATATTTCTCAA 59.263 36.000 8.75 0.00 0.00 3.02
66 67 5.262422 CGCGCAAACAATACATATTTCTCA 58.738 37.500 8.75 0.00 0.00 3.27
67 68 4.144731 GCGCGCAAACAATACATATTTCTC 59.855 41.667 29.10 0.00 0.00 2.87
68 69 4.035017 GCGCGCAAACAATACATATTTCT 58.965 39.130 29.10 0.00 0.00 2.52
69 70 3.122157 CGCGCGCAAACAATACATATTTC 60.122 43.478 32.61 0.00 0.00 2.17
70 71 2.781101 CGCGCGCAAACAATACATATTT 59.219 40.909 32.61 0.00 0.00 1.40
71 72 2.371432 CGCGCGCAAACAATACATATT 58.629 42.857 32.61 0.00 0.00 1.28
72 73 1.919839 GCGCGCGCAAACAATACATAT 60.920 47.619 46.11 0.00 41.49 1.78
73 74 0.587737 GCGCGCGCAAACAATACATA 60.588 50.000 46.11 0.00 41.49 2.29
74 75 1.867373 GCGCGCGCAAACAATACAT 60.867 52.632 46.11 0.00 41.49 2.29
75 76 2.500795 GCGCGCGCAAACAATACA 60.501 55.556 46.11 0.00 41.49 2.29
85 86 1.998772 GCTAAAATACAGCGCGCGC 60.999 57.895 45.10 45.10 42.33 6.86
86 87 4.173659 GCTAAAATACAGCGCGCG 57.826 55.556 28.44 28.44 0.00 6.86
91 92 0.377203 AAGCCGCGCTAAAATACAGC 59.623 50.000 5.56 0.00 38.25 4.40
92 93 1.933853 AGAAGCCGCGCTAAAATACAG 59.066 47.619 5.56 0.00 38.25 2.74
93 94 1.663643 CAGAAGCCGCGCTAAAATACA 59.336 47.619 5.56 0.00 38.25 2.29
94 95 1.003866 CCAGAAGCCGCGCTAAAATAC 60.004 52.381 5.56 0.00 38.25 1.89
95 96 1.134640 TCCAGAAGCCGCGCTAAAATA 60.135 47.619 5.56 0.00 38.25 1.40
96 97 0.392461 TCCAGAAGCCGCGCTAAAAT 60.392 50.000 5.56 0.00 38.25 1.82
97 98 1.004320 TCCAGAAGCCGCGCTAAAA 60.004 52.632 5.56 0.00 38.25 1.52
98 99 1.447838 CTCCAGAAGCCGCGCTAAA 60.448 57.895 5.56 0.00 38.25 1.85
99 100 2.184322 CTCCAGAAGCCGCGCTAA 59.816 61.111 5.56 0.00 38.25 3.09
100 101 4.514577 GCTCCAGAAGCCGCGCTA 62.515 66.667 5.56 0.00 45.92 4.26
123 124 1.830981 GCTAAAATTTAGCGCGCGC 59.169 52.632 45.10 45.10 42.33 6.86
129 130 1.466855 CAGCCGCGCTAAAATTTAGC 58.533 50.000 23.64 23.64 36.40 3.09
130 131 1.064060 AGCAGCCGCGCTAAAATTTAG 59.936 47.619 5.56 8.32 45.49 1.85
131 132 1.091537 AGCAGCCGCGCTAAAATTTA 58.908 45.000 5.56 0.00 45.49 1.40
132 133 0.456653 CAGCAGCCGCGCTAAAATTT 60.457 50.000 5.56 0.00 45.49 1.82
133 134 1.137404 CAGCAGCCGCGCTAAAATT 59.863 52.632 5.56 0.00 45.49 1.82
134 135 1.305219 TTCAGCAGCCGCGCTAAAAT 61.305 50.000 5.56 0.00 45.49 1.82
135 136 1.911293 CTTCAGCAGCCGCGCTAAAA 61.911 55.000 5.56 6.68 45.49 1.52
136 137 2.358125 TTCAGCAGCCGCGCTAAA 60.358 55.556 5.56 0.00 45.49 1.85
137 138 2.815211 CTTCAGCAGCCGCGCTAA 60.815 61.111 5.56 0.00 45.49 3.09
161 162 2.127383 GAAAAACGCGGCGGACAG 60.127 61.111 27.37 0.00 0.00 3.51
162 163 3.652000 GGAAAAACGCGGCGGACA 61.652 61.111 27.37 0.00 0.00 4.02
163 164 3.588891 CTGGAAAAACGCGGCGGAC 62.589 63.158 27.37 11.89 0.00 4.79
164 165 3.350612 CTGGAAAAACGCGGCGGA 61.351 61.111 27.37 0.27 0.00 5.54
165 166 3.350612 TCTGGAAAAACGCGGCGG 61.351 61.111 27.37 8.79 0.00 6.13
166 167 2.127383 GTCTGGAAAAACGCGGCG 60.127 61.111 22.36 22.36 0.00 6.46
167 168 0.039527 ATTGTCTGGAAAAACGCGGC 60.040 50.000 12.47 0.00 0.00 6.53
168 169 1.265635 TCATTGTCTGGAAAAACGCGG 59.734 47.619 12.47 0.00 0.00 6.46
169 170 2.679355 TCATTGTCTGGAAAAACGCG 57.321 45.000 3.53 3.53 0.00 6.01
170 171 2.719046 CGTTCATTGTCTGGAAAAACGC 59.281 45.455 0.00 0.00 32.81 4.84
171 172 2.719046 GCGTTCATTGTCTGGAAAAACG 59.281 45.455 0.00 0.00 40.50 3.60
172 173 2.719046 CGCGTTCATTGTCTGGAAAAAC 59.281 45.455 0.00 0.00 0.00 2.43
173 174 2.856720 GCGCGTTCATTGTCTGGAAAAA 60.857 45.455 8.43 0.00 0.00 1.94
174 175 1.334599 GCGCGTTCATTGTCTGGAAAA 60.335 47.619 8.43 0.00 0.00 2.29
175 176 0.237235 GCGCGTTCATTGTCTGGAAA 59.763 50.000 8.43 0.00 0.00 3.13
176 177 0.602638 AGCGCGTTCATTGTCTGGAA 60.603 50.000 8.43 0.00 0.00 3.53
177 178 1.005037 AGCGCGTTCATTGTCTGGA 60.005 52.632 8.43 0.00 0.00 3.86
178 179 1.133253 CAGCGCGTTCATTGTCTGG 59.867 57.895 8.43 0.00 0.00 3.86
179 180 1.510623 GCAGCGCGTTCATTGTCTG 60.511 57.895 8.43 4.75 0.00 3.51
180 181 1.506309 TTGCAGCGCGTTCATTGTCT 61.506 50.000 8.43 0.00 0.00 3.41
181 182 0.660005 TTTGCAGCGCGTTCATTGTC 60.660 50.000 8.43 0.00 0.00 3.18
182 183 0.661187 CTTTGCAGCGCGTTCATTGT 60.661 50.000 8.43 0.00 0.00 2.71
183 184 0.661187 ACTTTGCAGCGCGTTCATTG 60.661 50.000 8.43 0.00 0.00 2.82
184 185 0.871722 TACTTTGCAGCGCGTTCATT 59.128 45.000 8.43 0.00 0.00 2.57
185 186 0.165944 GTACTTTGCAGCGCGTTCAT 59.834 50.000 8.43 0.00 0.00 2.57
186 187 0.878523 AGTACTTTGCAGCGCGTTCA 60.879 50.000 8.43 0.00 0.00 3.18
187 188 0.234884 AAGTACTTTGCAGCGCGTTC 59.765 50.000 8.43 0.00 0.00 3.95
188 189 0.661020 AAAGTACTTTGCAGCGCGTT 59.339 45.000 19.94 0.00 0.00 4.84
189 190 0.661020 AAAAGTACTTTGCAGCGCGT 59.339 45.000 21.22 0.36 32.36 6.01
190 191 1.753956 AAAAAGTACTTTGCAGCGCG 58.246 45.000 21.22 0.00 32.36 6.86
191 192 2.656897 GCTAAAAAGTACTTTGCAGCGC 59.343 45.455 26.22 18.59 33.51 5.92
192 193 2.902484 CGCTAAAAAGTACTTTGCAGCG 59.098 45.455 36.44 36.44 46.72 5.18
193 194 2.656897 GCGCTAAAAAGTACTTTGCAGC 59.343 45.455 28.35 28.35 37.09 5.25
194 195 2.902484 CGCGCTAAAAAGTACTTTGCAG 59.098 45.455 21.22 19.64 32.36 4.41
195 196 2.911120 CGCGCTAAAAAGTACTTTGCA 58.089 42.857 21.22 11.08 32.36 4.08
196 197 1.642360 GCGCGCTAAAAAGTACTTTGC 59.358 47.619 26.67 18.02 32.36 3.68
197 198 2.239201 GGCGCGCTAAAAAGTACTTTG 58.761 47.619 32.29 10.31 32.36 2.77
198 199 1.136169 CGGCGCGCTAAAAAGTACTTT 60.136 47.619 32.29 15.22 0.00 2.66
199 200 0.441145 CGGCGCGCTAAAAAGTACTT 59.559 50.000 32.29 1.12 0.00 2.24
200 201 0.668401 ACGGCGCGCTAAAAAGTACT 60.668 50.000 32.29 0.00 0.00 2.73
201 202 0.517742 CACGGCGCGCTAAAAAGTAC 60.518 55.000 32.29 9.74 0.00 2.73
202 203 0.945265 ACACGGCGCGCTAAAAAGTA 60.945 50.000 32.29 0.00 0.00 2.24
203 204 2.248835 ACACGGCGCGCTAAAAAGT 61.249 52.632 32.29 17.43 0.00 2.66
204 205 1.792057 CACACGGCGCGCTAAAAAG 60.792 57.895 32.29 16.78 0.00 2.27
205 206 2.049475 AACACACGGCGCGCTAAAAA 62.049 50.000 32.29 0.00 0.00 1.94
206 207 2.432841 GAACACACGGCGCGCTAAAA 62.433 55.000 32.29 0.00 0.00 1.52
207 208 2.945615 GAACACACGGCGCGCTAAA 61.946 57.895 32.29 0.00 0.00 1.85
208 209 3.408020 GAACACACGGCGCGCTAA 61.408 61.111 32.29 0.00 0.00 3.09
218 219 3.276846 AACAGCCGCCGAACACAC 61.277 61.111 0.00 0.00 0.00 3.82
219 220 3.276091 CAACAGCCGCCGAACACA 61.276 61.111 0.00 0.00 0.00 3.72
220 221 4.025401 CCAACAGCCGCCGAACAC 62.025 66.667 0.00 0.00 0.00 3.32
221 222 4.243008 TCCAACAGCCGCCGAACA 62.243 61.111 0.00 0.00 0.00 3.18
222 223 3.423154 CTCCAACAGCCGCCGAAC 61.423 66.667 0.00 0.00 0.00 3.95
223 224 2.954684 ATCTCCAACAGCCGCCGAA 61.955 57.895 0.00 0.00 0.00 4.30
224 225 3.390521 ATCTCCAACAGCCGCCGA 61.391 61.111 0.00 0.00 0.00 5.54
225 226 3.197790 CATCTCCAACAGCCGCCG 61.198 66.667 0.00 0.00 0.00 6.46
226 227 3.512516 GCATCTCCAACAGCCGCC 61.513 66.667 0.00 0.00 0.00 6.13
227 228 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
228 229 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
232 233 8.884323 ATAAGGATTATTAGAGCATCTCCAACA 58.116 33.333 0.00 0.00 38.91 3.33
235 236 9.775539 AGTATAAGGATTATTAGAGCATCTCCA 57.224 33.333 0.00 0.00 38.91 3.86
247 248 9.354673 CCATGGTTGTTGAGTATAAGGATTATT 57.645 33.333 2.57 0.00 38.31 1.40
248 249 7.448469 GCCATGGTTGTTGAGTATAAGGATTAT 59.552 37.037 14.67 0.00 44.82 1.28
249 250 6.770785 GCCATGGTTGTTGAGTATAAGGATTA 59.229 38.462 14.67 0.00 33.48 1.75
250 251 5.594317 GCCATGGTTGTTGAGTATAAGGATT 59.406 40.000 14.67 0.00 0.00 3.01
251 252 5.103940 AGCCATGGTTGTTGAGTATAAGGAT 60.104 40.000 14.67 0.00 0.00 3.24
252 253 4.227300 AGCCATGGTTGTTGAGTATAAGGA 59.773 41.667 14.67 0.00 0.00 3.36
253 254 4.336433 CAGCCATGGTTGTTGAGTATAAGG 59.664 45.833 19.77 0.00 0.00 2.69
254 255 4.201950 GCAGCCATGGTTGTTGAGTATAAG 60.202 45.833 27.01 0.42 0.00 1.73
255 256 3.694072 GCAGCCATGGTTGTTGAGTATAA 59.306 43.478 27.01 0.00 0.00 0.98
256 257 3.278574 GCAGCCATGGTTGTTGAGTATA 58.721 45.455 27.01 0.00 0.00 1.47
257 258 2.094675 GCAGCCATGGTTGTTGAGTAT 58.905 47.619 27.01 0.00 0.00 2.12
258 259 1.533625 GCAGCCATGGTTGTTGAGTA 58.466 50.000 27.01 0.00 0.00 2.59
259 260 1.518056 CGCAGCCATGGTTGTTGAGT 61.518 55.000 27.01 0.00 0.00 3.41
260 261 1.210931 CGCAGCCATGGTTGTTGAG 59.789 57.895 27.01 13.90 0.00 3.02
261 262 1.106351 AACGCAGCCATGGTTGTTGA 61.106 50.000 27.01 0.00 0.00 3.18
262 263 0.249405 AAACGCAGCCATGGTTGTTG 60.249 50.000 27.01 21.67 0.00 3.33
263 264 0.249405 CAAACGCAGCCATGGTTGTT 60.249 50.000 27.01 16.42 0.00 2.83
264 265 1.363443 CAAACGCAGCCATGGTTGT 59.637 52.632 27.01 11.70 0.00 3.32
265 266 2.023223 GCAAACGCAGCCATGGTTG 61.023 57.895 23.26 23.26 0.00 3.77
266 267 1.818959 ATGCAAACGCAGCCATGGTT 61.819 50.000 14.67 3.81 44.13 3.67
269 270 1.065851 TGATATGCAAACGCAGCCATG 59.934 47.619 0.00 0.00 44.13 3.66
306 307 1.470098 CGATTTGTTTAGGCAGCAGCT 59.530 47.619 0.00 0.00 41.70 4.24
328 329 2.438434 CCCCACCAGCGATCAACC 60.438 66.667 0.00 0.00 0.00 3.77
362 364 2.442236 AGGGTGCCACAATTATCAGG 57.558 50.000 0.00 0.00 0.00 3.86
382 393 5.070685 AGCTTAGAAACTTTCCGGTCAAAT 58.929 37.500 0.00 0.00 0.00 2.32
484 497 1.227089 CTTCCCTGATCTGCCGTCG 60.227 63.158 0.00 0.00 0.00 5.12
500 513 0.840722 ACCGGTGAACCCCTGATCTT 60.841 55.000 6.12 0.00 0.00 2.40
524 537 4.598062 TGATACGTGCTTATTCTCAGTCG 58.402 43.478 0.00 0.00 0.00 4.18
556 569 5.392380 GCTTTTGTATGTCAGATCCTTGGTG 60.392 44.000 0.00 0.00 0.00 4.17
561 574 4.184629 GTCGCTTTTGTATGTCAGATCCT 58.815 43.478 0.00 0.00 0.00 3.24
566 579 4.466567 TTGTGTCGCTTTTGTATGTCAG 57.533 40.909 0.00 0.00 0.00 3.51
574 587 3.963665 TCTCCATTTTGTGTCGCTTTTG 58.036 40.909 0.00 0.00 0.00 2.44
584 597 4.464008 TCAGACTTGCTTCTCCATTTTGT 58.536 39.130 0.00 0.00 0.00 2.83
604 617 2.617021 GGAAAACCCGGAGCTTGTATCA 60.617 50.000 0.73 0.00 0.00 2.15
667 684 4.621068 AGCGATTTGGTGTGTGATATTG 57.379 40.909 0.00 0.00 0.00 1.90
699 716 8.336080 GATGGAATCCGAACTTGAATAAAGTAC 58.664 37.037 0.00 0.00 42.37 2.73
715 732 6.331845 TGAAACATGAAATTGATGGAATCCG 58.668 36.000 0.00 0.00 44.73 4.18
716 733 7.982919 TGATGAAACATGAAATTGATGGAATCC 59.017 33.333 0.00 0.00 44.73 3.01
717 734 8.936070 TGATGAAACATGAAATTGATGGAATC 57.064 30.769 0.00 0.00 45.83 2.52
719 736 7.603404 GGTTGATGAAACATGAAATTGATGGAA 59.397 33.333 0.00 0.00 40.86 3.53
720 737 7.098477 GGTTGATGAAACATGAAATTGATGGA 58.902 34.615 0.00 0.00 40.86 3.41
721 738 6.874664 TGGTTGATGAAACATGAAATTGATGG 59.125 34.615 0.00 0.00 40.86 3.51
722 739 7.148540 GGTGGTTGATGAAACATGAAATTGATG 60.149 37.037 0.00 0.00 40.86 3.07
725 742 5.990386 TGGTGGTTGATGAAACATGAAATTG 59.010 36.000 0.00 0.00 40.86 2.32
726 743 6.172136 TGGTGGTTGATGAAACATGAAATT 57.828 33.333 0.00 0.00 40.86 1.82
727 744 5.279607 CCTGGTGGTTGATGAAACATGAAAT 60.280 40.000 0.00 0.00 40.86 2.17
728 745 4.039004 CCTGGTGGTTGATGAAACATGAAA 59.961 41.667 0.00 0.00 40.86 2.69
729 746 3.573538 CCTGGTGGTTGATGAAACATGAA 59.426 43.478 0.00 0.00 40.86 2.57
730 747 3.156293 CCTGGTGGTTGATGAAACATGA 58.844 45.455 0.00 0.00 40.86 3.07
731 748 3.156293 TCCTGGTGGTTGATGAAACATG 58.844 45.455 0.00 0.00 40.86 3.21
732 749 3.424703 CTCCTGGTGGTTGATGAAACAT 58.575 45.455 0.00 0.00 40.86 2.71
756 778 1.405105 TGTGGTTGCTTGTTGCTCTTC 59.595 47.619 0.00 0.00 43.37 2.87
829 861 1.218047 CGTTCAGATTCCGCTGGGA 59.782 57.895 0.00 0.00 41.83 4.37
836 868 1.814169 GCCGACCCGTTCAGATTCC 60.814 63.158 0.00 0.00 0.00 3.01
932 965 1.676635 GAGCAATGGCAGGTGCAGA 60.677 57.895 23.16 0.00 43.42 4.26
952 986 2.859526 TCGAATACTCTGCTGCTCAG 57.140 50.000 0.00 0.00 44.21 3.35
969 1003 2.939103 CCTTGCTTCCCTTGTCTTATCG 59.061 50.000 0.00 0.00 0.00 2.92
976 1010 2.282462 CCGCCTTGCTTCCCTTGT 60.282 61.111 0.00 0.00 0.00 3.16
1176 1210 4.011517 TTCTTGGCCCGGACGGAC 62.012 66.667 13.13 0.00 42.05 4.79
1245 1279 3.128242 CGAAGCCGAAGAGGTAGTAGAAA 59.872 47.826 0.00 0.00 43.70 2.52
2343 2377 4.758251 CGCGTCTGGTCCATGCCA 62.758 66.667 0.00 0.00 36.97 4.92
2370 2404 1.870901 GGTGTAGGCGTACGCGAAG 60.871 63.158 31.78 4.23 40.10 3.79
2670 4582 7.458170 ACTTCCTCCCGTGGATCTTATTTATAT 59.542 37.037 0.00 0.00 35.83 0.86
2674 4586 3.780850 ACTTCCTCCCGTGGATCTTATTT 59.219 43.478 0.00 0.00 35.83 1.40
2749 4663 4.197750 GCATGTCTCATTCTCATTGTCCT 58.802 43.478 0.00 0.00 0.00 3.85
2804 4718 3.614870 GCATCACATTGTTGAGGGGAAAC 60.615 47.826 0.00 0.00 0.00 2.78
2808 4722 0.819582 GGCATCACATTGTTGAGGGG 59.180 55.000 0.00 0.00 0.00 4.79
2848 4762 6.239402 CCCAACAATTTCTGAACTCCATTTCT 60.239 38.462 0.00 0.00 0.00 2.52
2860 4774 6.074302 CGTATAGTCGATCCCAACAATTTCTG 60.074 42.308 0.00 0.00 0.00 3.02
2875 4789 4.039609 TCAGGTACCTGATCGTATAGTCGA 59.960 45.833 35.91 13.13 46.80 4.20
2964 4878 4.036518 AGGTTGAAGATGAGCAGTAGGAT 58.963 43.478 0.00 0.00 0.00 3.24
2966 4880 3.431486 GGAGGTTGAAGATGAGCAGTAGG 60.431 52.174 0.00 0.00 0.00 3.18
2967 4881 3.431486 GGGAGGTTGAAGATGAGCAGTAG 60.431 52.174 0.00 0.00 0.00 2.57
2970 4884 1.558756 AGGGAGGTTGAAGATGAGCAG 59.441 52.381 0.00 0.00 0.00 4.24
2973 4887 2.433970 GAGGAGGGAGGTTGAAGATGAG 59.566 54.545 0.00 0.00 0.00 2.90
3143 5057 1.152525 ATCGCCGGAGTAGTGGGAT 60.153 57.895 5.05 0.00 0.00 3.85
3148 5062 2.521224 GGGGATCGCCGGAGTAGT 60.521 66.667 13.74 0.00 33.83 2.73
3166 5080 1.052124 TATCTTAGGGGTGGGGTGCG 61.052 60.000 0.00 0.00 0.00 5.34
3186 5100 1.967779 GGAGAAGAGAGCCCCACTATC 59.032 57.143 0.00 0.00 36.85 2.08
3206 5120 1.455786 CTTGCACGTTAGACCTTGTCG 59.544 52.381 0.00 0.00 37.67 4.35
3208 5122 2.902705 TCTTGCACGTTAGACCTTGT 57.097 45.000 0.00 0.00 0.00 3.16
3216 5130 3.399330 CTTCCTTCCTTCTTGCACGTTA 58.601 45.455 0.00 0.00 0.00 3.18
3217 5131 2.222027 CTTCCTTCCTTCTTGCACGTT 58.778 47.619 0.00 0.00 0.00 3.99
3218 5132 1.543429 CCTTCCTTCCTTCTTGCACGT 60.543 52.381 0.00 0.00 0.00 4.49
3226 5140 3.328050 TCACCTTCTTCCTTCCTTCCTTC 59.672 47.826 0.00 0.00 0.00 3.46
3227 5141 3.073209 GTCACCTTCTTCCTTCCTTCCTT 59.927 47.826 0.00 0.00 0.00 3.36
3228 5142 2.640332 GTCACCTTCTTCCTTCCTTCCT 59.360 50.000 0.00 0.00 0.00 3.36
3229 5143 2.290387 GGTCACCTTCTTCCTTCCTTCC 60.290 54.545 0.00 0.00 0.00 3.46
3230 5144 2.613223 CGGTCACCTTCTTCCTTCCTTC 60.613 54.545 0.00 0.00 0.00 3.46
3231 5145 1.348036 CGGTCACCTTCTTCCTTCCTT 59.652 52.381 0.00 0.00 0.00 3.36
3232 5146 0.977395 CGGTCACCTTCTTCCTTCCT 59.023 55.000 0.00 0.00 0.00 3.36
3233 5147 0.974383 TCGGTCACCTTCTTCCTTCC 59.026 55.000 0.00 0.00 0.00 3.46
3250 5164 6.487689 AACCTGAAAAGAATTCTAGCTTCG 57.512 37.500 8.75 8.41 0.00 3.79
3253 5167 9.520515 TTGATAAACCTGAAAAGAATTCTAGCT 57.479 29.630 8.75 0.00 0.00 3.32
3275 5189 8.835439 ACATTTTTCGGTTTTGCTATTTTTGAT 58.165 25.926 0.00 0.00 0.00 2.57
3277 5191 8.833976 AACATTTTTCGGTTTTGCTATTTTTG 57.166 26.923 0.00 0.00 0.00 2.44
3279 5193 9.535878 TCTAACATTTTTCGGTTTTGCTATTTT 57.464 25.926 0.00 0.00 0.00 1.82
3298 5212 5.758296 TCGTTTGAGCTTTCAACTCTAACAT 59.242 36.000 14.95 0.00 44.70 2.71
3303 5217 4.442706 TCTTCGTTTGAGCTTTCAACTCT 58.557 39.130 0.00 0.00 35.12 3.24
3328 5242 1.750193 TCCCTTATGCGGCAAAAGAG 58.250 50.000 6.82 2.60 0.00 2.85
3341 5255 3.134574 AGCAACACACGAATTCCCTTA 57.865 42.857 0.00 0.00 0.00 2.69
3342 5256 1.981256 AGCAACACACGAATTCCCTT 58.019 45.000 0.00 0.00 0.00 3.95
3384 5300 8.161699 TGTTCTTTAATCTGACAAAGTTACCC 57.838 34.615 11.29 1.69 34.17 3.69
3421 5340 8.385898 TCTTCTTTTTATTTGCGAGAAAGGTA 57.614 30.769 0.00 0.00 0.00 3.08
3436 5355 9.010029 GGTGGATGATGTAACTTCTTCTTTTTA 57.990 33.333 0.00 0.00 0.00 1.52
3446 5365 2.308570 TGCCTGGTGGATGATGTAACTT 59.691 45.455 0.00 0.00 34.57 2.66
3447 5366 1.915489 TGCCTGGTGGATGATGTAACT 59.085 47.619 0.00 0.00 34.57 2.24
3448 5367 2.017049 GTGCCTGGTGGATGATGTAAC 58.983 52.381 0.00 0.00 34.57 2.50
3449 5368 1.915489 AGTGCCTGGTGGATGATGTAA 59.085 47.619 0.00 0.00 34.57 2.41
3485 5404 4.553156 CGTCTCTGTAATTAGAGGAGTCGC 60.553 50.000 9.57 2.44 43.48 5.19
3486 5405 4.571580 ACGTCTCTGTAATTAGAGGAGTCG 59.428 45.833 9.57 14.59 43.48 4.18
3488 5407 6.197364 CAACGTCTCTGTAATTAGAGGAGT 57.803 41.667 9.57 5.54 43.48 3.85


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

AutoCloner maintained by Alex Coulton.