Multiple sequence alignment - TraesCS6D01G115800

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 TraesCS6D01G115800 chr6D 100.000 4232 0 0 1 4232 82204972 82200741 0.000000e+00 7816.0
1 TraesCS6D01G115800 chr6D 87.267 3322 386 30 868 4171 82220616 82217314 0.000000e+00 3757.0
2 TraesCS6D01G115800 chr6D 82.525 3239 509 41 982 4196 81773871 81770666 0.000000e+00 2793.0
3 TraesCS6D01G115800 chr6D 81.691 3370 550 53 895 4232 81926272 81922938 0.000000e+00 2743.0
4 TraesCS6D01G115800 chr6D 80.422 3269 591 44 895 4138 81759805 81756561 0.000000e+00 2446.0
5 TraesCS6D01G115800 chr6D 85.914 2144 294 8 857 2996 83108674 83106535 0.000000e+00 2279.0
6 TraesCS6D01G115800 chr6D 80.919 2112 324 47 914 3012 46901397 46903442 0.000000e+00 1594.0
7 TraesCS6D01G115800 chr6D 79.849 794 147 12 937 1722 82209781 82208993 6.140000e-158 568.0
8 TraesCS6D01G115800 chr6B 96.133 3388 122 5 851 4232 157109527 157106143 0.000000e+00 5522.0
9 TraesCS6D01G115800 chr6B 82.043 3269 553 29 977 4225 156550968 156547714 0.000000e+00 2754.0
10 TraesCS6D01G115800 chr6B 81.393 3402 594 33 851 4232 157489441 157486059 0.000000e+00 2739.0
11 TraesCS6D01G115800 chr6B 81.532 3368 559 49 895 4232 156654927 156651593 0.000000e+00 2715.0
12 TraesCS6D01G115800 chr6B 93.667 300 16 1 561 857 157111144 157110845 3.000000e-121 446.0
13 TraesCS6D01G115800 chr6B 93.548 186 8 1 374 559 157111906 157111725 1.500000e-69 274.0
14 TraesCS6D01G115800 chr6A 91.699 3385 270 4 858 4232 98888238 98884855 0.000000e+00 4684.0
15 TraesCS6D01G115800 chr6A 87.732 3391 385 22 851 4232 99016319 99012951 0.000000e+00 3928.0
16 TraesCS6D01G115800 chr6A 84.618 3387 487 28 858 4232 98982506 98979142 0.000000e+00 3338.0
17 TraesCS6D01G115800 chr6A 82.492 3267 528 35 977 4225 98309995 98306755 0.000000e+00 2824.0
18 TraesCS6D01G115800 chr6A 82.007 3368 543 51 895 4232 98316058 98312724 0.000000e+00 2804.0
19 TraesCS6D01G115800 chrUn 96.610 59 2 0 796 854 137731333 137731391 9.680000e-17 99.0
20 TraesCS6D01G115800 chr2D 92.188 64 3 2 795 857 342571363 342571301 5.830000e-14 89.8
21 TraesCS6D01G115800 chr2D 92.593 54 4 0 801 854 467062459 467062512 1.260000e-10 78.7
22 TraesCS6D01G115800 chr3B 94.444 54 3 0 804 857 217998252 217998305 2.710000e-12 84.2
23 TraesCS6D01G115800 chr2A 92.727 55 4 0 803 857 452797900 452797846 3.510000e-11 80.5
24 TraesCS6D01G115800 chr1B 94.231 52 3 0 803 854 1733431 1733380 3.510000e-11 80.5
25 TraesCS6D01G115800 chr7D 92.453 53 4 0 802 854 42644590 42644642 4.540000e-10 76.8
26 TraesCS6D01G115800 chr1A 89.655 58 4 2 798 854 13786635 13786691 5.870000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G115800 chr6D 82200741 82204972 4231 True 7816.000000 7816 100.000000 1 4232 1 chr6D.!!$R4 4231
1 TraesCS6D01G115800 chr6D 82217314 82220616 3302 True 3757.000000 3757 87.267000 868 4171 1 chr6D.!!$R6 3303
2 TraesCS6D01G115800 chr6D 81770666 81773871 3205 True 2793.000000 2793 82.525000 982 4196 1 chr6D.!!$R2 3214
3 TraesCS6D01G115800 chr6D 81922938 81926272 3334 True 2743.000000 2743 81.691000 895 4232 1 chr6D.!!$R3 3337
4 TraesCS6D01G115800 chr6D 81756561 81759805 3244 True 2446.000000 2446 80.422000 895 4138 1 chr6D.!!$R1 3243
5 TraesCS6D01G115800 chr6D 83106535 83108674 2139 True 2279.000000 2279 85.914000 857 2996 1 chr6D.!!$R7 2139
6 TraesCS6D01G115800 chr6D 46901397 46903442 2045 False 1594.000000 1594 80.919000 914 3012 1 chr6D.!!$F1 2098
7 TraesCS6D01G115800 chr6D 82208993 82209781 788 True 568.000000 568 79.849000 937 1722 1 chr6D.!!$R5 785
8 TraesCS6D01G115800 chr6B 156547714 156550968 3254 True 2754.000000 2754 82.043000 977 4225 1 chr6B.!!$R1 3248
9 TraesCS6D01G115800 chr6B 157486059 157489441 3382 True 2739.000000 2739 81.393000 851 4232 1 chr6B.!!$R3 3381
10 TraesCS6D01G115800 chr6B 156651593 156654927 3334 True 2715.000000 2715 81.532000 895 4232 1 chr6B.!!$R2 3337
11 TraesCS6D01G115800 chr6B 157106143 157111906 5763 True 2080.666667 5522 94.449333 374 4232 3 chr6B.!!$R4 3858
12 TraesCS6D01G115800 chr6A 98884855 98888238 3383 True 4684.000000 4684 91.699000 858 4232 1 chr6A.!!$R1 3374
13 TraesCS6D01G115800 chr6A 99012951 99016319 3368 True 3928.000000 3928 87.732000 851 4232 1 chr6A.!!$R3 3381
14 TraesCS6D01G115800 chr6A 98979142 98982506 3364 True 3338.000000 3338 84.618000 858 4232 1 chr6A.!!$R2 3374
15 TraesCS6D01G115800 chr6A 98306755 98316058 9303 True 2814.000000 2824 82.249500 895 4232 2 chr6A.!!$R4 3337

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
321 322 0.034477 CCTGGTATTTTCAGGCCCGT 60.034 55.0 0.0 0.00 44.29 5.28 F
334 335 0.035458 GGCCCGTTATGATCTGAGGG 59.965 60.0 0.0 1.27 41.65 4.30 F
411 412 0.107703 CTCGCCCAACCAAGCATCTA 60.108 55.0 0.0 0.00 0.00 1.98 F
1961 3878 0.388659 GAGCTGCCATCGAGTCTGAT 59.611 55.0 0.0 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 3596 1.338864 CCTTGAGCACTCTGAGCATGT 60.339 52.381 4.19 0.0 0.00 3.21 R
1961 3878 4.761227 TGCTTATGAGATTTGTGCAGTTGA 59.239 37.500 0.00 0.0 0.00 3.18 R
2371 10263 3.961477 TTGTCCAAATAATCCGCATCG 57.039 42.857 0.00 0.0 0.00 3.84 R
3358 11254 1.589716 GCCATCAGACAACACTGCCC 61.590 60.000 0.00 0.0 37.75 5.36 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
28 29 8.973378 ACGTGTATTTGGAAAACATTAAATGTG 58.027 29.630 0.00 0.00 44.07 3.21
29 30 8.973378 CGTGTATTTGGAAAACATTAAATGTGT 58.027 29.630 0.00 0.00 44.07 3.72
140 141 2.082140 GGAAGGTTCCCAAAACCACT 57.918 50.000 9.45 0.00 42.69 4.00
141 142 1.961394 GGAAGGTTCCCAAAACCACTC 59.039 52.381 9.45 5.41 42.69 3.51
142 143 1.961394 GAAGGTTCCCAAAACCACTCC 59.039 52.381 9.45 0.00 42.69 3.85
143 144 0.930726 AGGTTCCCAAAACCACTCCA 59.069 50.000 9.45 0.00 42.69 3.86
144 145 1.503347 AGGTTCCCAAAACCACTCCAT 59.497 47.619 9.45 0.00 42.69 3.41
145 146 1.893137 GGTTCCCAAAACCACTCCATC 59.107 52.381 2.12 0.00 40.03 3.51
146 147 2.490902 GGTTCCCAAAACCACTCCATCT 60.491 50.000 2.12 0.00 40.03 2.90
147 148 3.245122 GGTTCCCAAAACCACTCCATCTA 60.245 47.826 2.12 0.00 40.03 1.98
148 149 4.569865 GGTTCCCAAAACCACTCCATCTAT 60.570 45.833 2.12 0.00 40.03 1.98
149 150 5.339695 GGTTCCCAAAACCACTCCATCTATA 60.340 44.000 2.12 0.00 40.03 1.31
150 151 5.367945 TCCCAAAACCACTCCATCTATAC 57.632 43.478 0.00 0.00 0.00 1.47
151 152 5.036916 TCCCAAAACCACTCCATCTATACT 58.963 41.667 0.00 0.00 0.00 2.12
152 153 5.130477 TCCCAAAACCACTCCATCTATACTC 59.870 44.000 0.00 0.00 0.00 2.59
153 154 5.368989 CCAAAACCACTCCATCTATACTCC 58.631 45.833 0.00 0.00 0.00 3.85
154 155 5.368989 CAAAACCACTCCATCTATACTCCC 58.631 45.833 0.00 0.00 0.00 4.30
155 156 3.993658 ACCACTCCATCTATACTCCCA 57.006 47.619 0.00 0.00 0.00 4.37
156 157 4.280789 ACCACTCCATCTATACTCCCAA 57.719 45.455 0.00 0.00 0.00 4.12
157 158 3.967987 ACCACTCCATCTATACTCCCAAC 59.032 47.826 0.00 0.00 0.00 3.77
158 159 3.967326 CCACTCCATCTATACTCCCAACA 59.033 47.826 0.00 0.00 0.00 3.33
159 160 4.594920 CCACTCCATCTATACTCCCAACAT 59.405 45.833 0.00 0.00 0.00 2.71
160 161 5.072329 CCACTCCATCTATACTCCCAACATT 59.928 44.000 0.00 0.00 0.00 2.71
161 162 5.994054 CACTCCATCTATACTCCCAACATTG 59.006 44.000 0.00 0.00 0.00 2.82
162 163 4.973168 TCCATCTATACTCCCAACATTGC 58.027 43.478 0.00 0.00 0.00 3.56
163 164 4.074970 CCATCTATACTCCCAACATTGCC 58.925 47.826 0.00 0.00 0.00 4.52
164 165 3.857157 TCTATACTCCCAACATTGCCC 57.143 47.619 0.00 0.00 0.00 5.36
165 166 2.441750 TCTATACTCCCAACATTGCCCC 59.558 50.000 0.00 0.00 0.00 5.80
166 167 1.006813 ATACTCCCAACATTGCCCCA 58.993 50.000 0.00 0.00 0.00 4.96
167 168 0.331278 TACTCCCAACATTGCCCCAG 59.669 55.000 0.00 0.00 0.00 4.45
168 169 1.077265 CTCCCAACATTGCCCCAGT 59.923 57.895 0.00 0.00 0.00 4.00
169 170 1.228831 TCCCAACATTGCCCCAGTG 60.229 57.895 0.00 0.00 0.00 3.66
170 171 2.285024 CCCAACATTGCCCCAGTGG 61.285 63.158 0.63 0.63 37.09 4.00
171 172 1.533753 CCAACATTGCCCCAGTGGT 60.534 57.895 8.74 0.00 36.04 4.16
172 173 0.251564 CCAACATTGCCCCAGTGGTA 60.252 55.000 8.74 0.00 36.04 3.25
173 174 1.619432 CCAACATTGCCCCAGTGGTAT 60.619 52.381 8.74 0.00 36.04 2.73
174 175 2.357673 CCAACATTGCCCCAGTGGTATA 60.358 50.000 8.74 0.00 36.04 1.47
175 176 2.951642 CAACATTGCCCCAGTGGTATAG 59.048 50.000 8.74 0.00 36.04 1.31
176 177 2.205342 ACATTGCCCCAGTGGTATAGT 58.795 47.619 8.74 0.00 36.04 2.12
177 178 3.389866 ACATTGCCCCAGTGGTATAGTA 58.610 45.455 8.74 0.00 36.04 1.82
178 179 3.783642 ACATTGCCCCAGTGGTATAGTAA 59.216 43.478 8.74 0.27 36.04 2.24
179 180 3.918294 TTGCCCCAGTGGTATAGTAAC 57.082 47.619 8.74 0.00 36.04 2.50
180 181 3.124856 TGCCCCAGTGGTATAGTAACT 57.875 47.619 8.74 0.00 36.04 2.24
181 182 3.456842 TGCCCCAGTGGTATAGTAACTT 58.543 45.455 8.74 0.00 36.04 2.66
182 183 3.847780 TGCCCCAGTGGTATAGTAACTTT 59.152 43.478 8.74 0.00 36.04 2.66
183 184 4.196971 GCCCCAGTGGTATAGTAACTTTG 58.803 47.826 8.74 0.00 36.04 2.77
184 185 4.324022 GCCCCAGTGGTATAGTAACTTTGT 60.324 45.833 8.74 0.00 36.04 2.83
185 186 5.805424 GCCCCAGTGGTATAGTAACTTTGTT 60.805 44.000 8.74 0.00 36.04 2.83
186 187 6.576840 GCCCCAGTGGTATAGTAACTTTGTTA 60.577 42.308 8.74 0.00 36.04 2.41
187 188 7.396418 CCCCAGTGGTATAGTAACTTTGTTAA 58.604 38.462 8.74 0.00 0.00 2.01
188 189 8.050930 CCCCAGTGGTATAGTAACTTTGTTAAT 58.949 37.037 8.74 0.00 0.00 1.40
189 190 8.889717 CCCAGTGGTATAGTAACTTTGTTAATG 58.110 37.037 8.74 0.00 0.00 1.90
190 191 8.395633 CCAGTGGTATAGTAACTTTGTTAATGC 58.604 37.037 0.00 0.00 0.00 3.56
191 192 9.162764 CAGTGGTATAGTAACTTTGTTAATGCT 57.837 33.333 1.43 0.00 0.00 3.79
192 193 9.379791 AGTGGTATAGTAACTTTGTTAATGCTC 57.620 33.333 1.43 0.00 0.00 4.26
193 194 8.610035 GTGGTATAGTAACTTTGTTAATGCTCC 58.390 37.037 1.43 2.23 0.00 4.70
194 195 8.322828 TGGTATAGTAACTTTGTTAATGCTCCA 58.677 33.333 1.43 4.21 0.00 3.86
195 196 8.827677 GGTATAGTAACTTTGTTAATGCTCCAG 58.172 37.037 1.43 0.00 0.00 3.86
196 197 5.629079 AGTAACTTTGTTAATGCTCCAGC 57.371 39.130 0.00 0.00 42.50 4.85
197 198 3.942130 AACTTTGTTAATGCTCCAGCC 57.058 42.857 0.00 0.00 41.18 4.85
198 199 2.171003 ACTTTGTTAATGCTCCAGCCC 58.829 47.619 0.00 0.00 41.18 5.19
199 200 1.478105 CTTTGTTAATGCTCCAGCCCC 59.522 52.381 0.00 0.00 41.18 5.80
200 201 0.679640 TTGTTAATGCTCCAGCCCCG 60.680 55.000 0.00 0.00 41.18 5.73
201 202 1.823899 GTTAATGCTCCAGCCCCGG 60.824 63.158 0.00 0.00 41.18 5.73
202 203 1.998438 TTAATGCTCCAGCCCCGGA 60.998 57.895 0.73 0.00 41.18 5.14
203 204 1.352622 TTAATGCTCCAGCCCCGGAT 61.353 55.000 0.73 0.00 41.18 4.18
204 205 2.055689 TAATGCTCCAGCCCCGGATG 62.056 60.000 0.73 0.00 41.18 3.51
206 207 4.554036 GCTCCAGCCCCGGATGAC 62.554 72.222 0.73 0.00 33.56 3.06
207 208 3.866582 CTCCAGCCCCGGATGACC 61.867 72.222 0.73 0.00 33.56 4.02
219 220 1.949465 GGATGACCGTTGTGGGTATC 58.051 55.000 0.00 0.00 44.64 2.24
220 221 1.208535 GGATGACCGTTGTGGGTATCA 59.791 52.381 0.00 0.00 44.64 2.15
221 222 2.277084 GATGACCGTTGTGGGTATCAC 58.723 52.381 0.00 0.00 44.64 3.06
222 223 1.344065 TGACCGTTGTGGGTATCACT 58.656 50.000 0.00 0.00 46.20 3.41
223 224 1.274167 TGACCGTTGTGGGTATCACTC 59.726 52.381 0.00 0.00 46.20 3.51
224 225 1.274167 GACCGTTGTGGGTATCACTCA 59.726 52.381 0.00 0.00 46.20 3.41
234 235 4.188462 TGGGTATCACTCACAATAAAGCG 58.812 43.478 0.00 0.00 0.00 4.68
235 236 4.081365 TGGGTATCACTCACAATAAAGCGA 60.081 41.667 0.00 0.00 0.00 4.93
236 237 5.057149 GGGTATCACTCACAATAAAGCGAT 58.943 41.667 0.00 0.00 0.00 4.58
237 238 6.183360 TGGGTATCACTCACAATAAAGCGATA 60.183 38.462 0.00 0.00 0.00 2.92
238 239 6.145696 GGGTATCACTCACAATAAAGCGATAC 59.854 42.308 0.00 0.00 37.05 2.24
239 240 6.145696 GGTATCACTCACAATAAAGCGATACC 59.854 42.308 11.64 11.64 44.29 2.73
240 241 5.339008 TCACTCACAATAAAGCGATACCT 57.661 39.130 0.00 0.00 0.00 3.08
241 242 6.459670 TCACTCACAATAAAGCGATACCTA 57.540 37.500 0.00 0.00 0.00 3.08
242 243 6.504398 TCACTCACAATAAAGCGATACCTAG 58.496 40.000 0.00 0.00 0.00 3.02
243 244 5.175856 CACTCACAATAAAGCGATACCTAGC 59.824 44.000 0.00 0.00 0.00 3.42
244 245 5.163447 ACTCACAATAAAGCGATACCTAGCA 60.163 40.000 0.00 0.00 35.48 3.49
245 246 5.853936 TCACAATAAAGCGATACCTAGCAT 58.146 37.500 0.00 0.00 35.48 3.79
246 247 6.288294 TCACAATAAAGCGATACCTAGCATT 58.712 36.000 0.00 0.00 35.48 3.56
247 248 6.765989 TCACAATAAAGCGATACCTAGCATTT 59.234 34.615 0.00 0.00 35.48 2.32
248 249 6.852853 CACAATAAAGCGATACCTAGCATTTG 59.147 38.462 0.00 0.00 35.48 2.32
249 250 6.542370 ACAATAAAGCGATACCTAGCATTTGT 59.458 34.615 0.00 0.00 35.48 2.83
250 251 4.882671 AAAGCGATACCTAGCATTTGTG 57.117 40.909 0.00 0.00 35.48 3.33
251 252 3.819564 AGCGATACCTAGCATTTGTGA 57.180 42.857 0.00 0.00 35.48 3.58
252 253 4.137116 AGCGATACCTAGCATTTGTGAA 57.863 40.909 0.00 0.00 35.48 3.18
253 254 4.513442 AGCGATACCTAGCATTTGTGAAA 58.487 39.130 0.00 0.00 35.48 2.69
254 255 4.572389 AGCGATACCTAGCATTTGTGAAAG 59.428 41.667 0.00 0.00 35.48 2.62
255 256 4.332819 GCGATACCTAGCATTTGTGAAAGT 59.667 41.667 0.00 0.00 0.00 2.66
256 257 5.727791 GCGATACCTAGCATTTGTGAAAGTG 60.728 44.000 0.00 0.00 0.00 3.16
257 258 5.580691 CGATACCTAGCATTTGTGAAAGTGA 59.419 40.000 0.00 0.00 0.00 3.41
258 259 6.092122 CGATACCTAGCATTTGTGAAAGTGAA 59.908 38.462 0.00 0.00 0.00 3.18
259 260 7.360861 CGATACCTAGCATTTGTGAAAGTGAAA 60.361 37.037 0.00 0.00 0.00 2.69
260 261 6.076981 ACCTAGCATTTGTGAAAGTGAAAG 57.923 37.500 0.00 0.00 0.00 2.62
261 262 5.827797 ACCTAGCATTTGTGAAAGTGAAAGA 59.172 36.000 0.00 0.00 0.00 2.52
262 263 6.145535 CCTAGCATTTGTGAAAGTGAAAGAC 58.854 40.000 0.00 0.00 0.00 3.01
263 264 5.841957 AGCATTTGTGAAAGTGAAAGACT 57.158 34.783 0.00 0.00 35.94 3.24
264 265 6.942532 AGCATTTGTGAAAGTGAAAGACTA 57.057 33.333 0.00 0.00 33.09 2.59
265 266 7.516198 AGCATTTGTGAAAGTGAAAGACTAT 57.484 32.000 0.00 0.00 33.09 2.12
266 267 7.365741 AGCATTTGTGAAAGTGAAAGACTATG 58.634 34.615 0.00 0.00 33.09 2.23
267 268 6.583806 GCATTTGTGAAAGTGAAAGACTATGG 59.416 38.462 0.00 0.00 33.09 2.74
268 269 7.522073 GCATTTGTGAAAGTGAAAGACTATGGA 60.522 37.037 0.00 0.00 33.09 3.41
269 270 7.496529 TTTGTGAAAGTGAAAGACTATGGAG 57.503 36.000 0.00 0.00 33.09 3.86
270 271 6.419484 TGTGAAAGTGAAAGACTATGGAGA 57.581 37.500 0.00 0.00 33.09 3.71
271 272 6.459066 TGTGAAAGTGAAAGACTATGGAGAG 58.541 40.000 0.00 0.00 33.09 3.20
272 273 6.267699 TGTGAAAGTGAAAGACTATGGAGAGA 59.732 38.462 0.00 0.00 33.09 3.10
273 274 7.038729 TGTGAAAGTGAAAGACTATGGAGAGAT 60.039 37.037 0.00 0.00 33.09 2.75
274 275 7.821846 GTGAAAGTGAAAGACTATGGAGAGATT 59.178 37.037 0.00 0.00 33.09 2.40
275 276 8.378565 TGAAAGTGAAAGACTATGGAGAGATTT 58.621 33.333 0.00 0.00 33.09 2.17
276 277 8.785329 AAAGTGAAAGACTATGGAGAGATTTC 57.215 34.615 0.00 0.00 33.09 2.17
277 278 7.732222 AGTGAAAGACTATGGAGAGATTTCT 57.268 36.000 0.00 0.00 31.75 2.52
278 279 7.781056 AGTGAAAGACTATGGAGAGATTTCTC 58.219 38.462 4.66 4.66 40.33 2.87
279 280 7.619302 AGTGAAAGACTATGGAGAGATTTCTCT 59.381 37.037 12.62 9.82 44.14 3.10
294 295 8.546597 GAGATTTCTCTAGCTTCTGAGTTTTT 57.453 34.615 0.00 0.00 39.81 1.94
295 296 8.546597 AGATTTCTCTAGCTTCTGAGTTTTTC 57.453 34.615 0.00 0.00 0.00 2.29
296 297 7.606073 AGATTTCTCTAGCTTCTGAGTTTTTCC 59.394 37.037 0.00 0.00 0.00 3.13
297 298 6.426646 TTCTCTAGCTTCTGAGTTTTTCCT 57.573 37.500 0.00 0.00 0.00 3.36
298 299 7.540474 TTCTCTAGCTTCTGAGTTTTTCCTA 57.460 36.000 0.00 0.00 0.00 2.94
299 300 7.540474 TCTCTAGCTTCTGAGTTTTTCCTAA 57.460 36.000 0.00 0.00 0.00 2.69
300 301 7.607250 TCTCTAGCTTCTGAGTTTTTCCTAAG 58.393 38.462 0.00 0.00 0.00 2.18
301 302 7.233757 TCTCTAGCTTCTGAGTTTTTCCTAAGT 59.766 37.037 0.00 0.00 0.00 2.24
302 303 7.379750 TCTAGCTTCTGAGTTTTTCCTAAGTC 58.620 38.462 0.00 0.00 0.00 3.01
303 304 5.309638 AGCTTCTGAGTTTTTCCTAAGTCC 58.690 41.667 0.00 0.00 0.00 3.85
304 305 5.072464 AGCTTCTGAGTTTTTCCTAAGTCCT 59.928 40.000 0.00 0.00 0.00 3.85
305 306 5.180304 GCTTCTGAGTTTTTCCTAAGTCCTG 59.820 44.000 0.00 0.00 0.00 3.86
306 307 5.228945 TCTGAGTTTTTCCTAAGTCCTGG 57.771 43.478 0.00 0.00 0.00 4.45
307 308 4.658901 TCTGAGTTTTTCCTAAGTCCTGGT 59.341 41.667 0.00 0.00 0.00 4.00
308 309 5.842328 TCTGAGTTTTTCCTAAGTCCTGGTA 59.158 40.000 0.00 0.00 0.00 3.25
309 310 6.500751 TCTGAGTTTTTCCTAAGTCCTGGTAT 59.499 38.462 0.00 0.00 0.00 2.73
310 311 7.017254 TCTGAGTTTTTCCTAAGTCCTGGTATT 59.983 37.037 0.00 0.00 0.00 1.89
311 312 7.523415 TGAGTTTTTCCTAAGTCCTGGTATTT 58.477 34.615 0.00 0.00 0.00 1.40
312 313 8.002459 TGAGTTTTTCCTAAGTCCTGGTATTTT 58.998 33.333 0.00 0.00 0.00 1.82
313 314 8.405418 AGTTTTTCCTAAGTCCTGGTATTTTC 57.595 34.615 0.00 0.00 0.00 2.29
314 315 8.002459 AGTTTTTCCTAAGTCCTGGTATTTTCA 58.998 33.333 0.00 0.00 0.00 2.69
315 316 7.996098 TTTTCCTAAGTCCTGGTATTTTCAG 57.004 36.000 0.00 0.00 0.00 3.02
320 321 2.793831 CCTGGTATTTTCAGGCCCG 58.206 57.895 0.00 0.00 44.29 6.13
321 322 0.034477 CCTGGTATTTTCAGGCCCGT 60.034 55.000 0.00 0.00 44.29 5.28
322 323 1.615919 CCTGGTATTTTCAGGCCCGTT 60.616 52.381 0.00 0.00 44.29 4.44
323 324 2.356330 CCTGGTATTTTCAGGCCCGTTA 60.356 50.000 0.00 0.00 44.29 3.18
324 325 3.551846 CTGGTATTTTCAGGCCCGTTAT 58.448 45.455 0.00 0.00 0.00 1.89
325 326 3.283751 TGGTATTTTCAGGCCCGTTATG 58.716 45.455 0.00 0.00 0.00 1.90
326 327 3.054287 TGGTATTTTCAGGCCCGTTATGA 60.054 43.478 0.00 0.00 0.00 2.15
327 328 4.142038 GGTATTTTCAGGCCCGTTATGAT 58.858 43.478 0.00 0.00 0.00 2.45
328 329 4.215613 GGTATTTTCAGGCCCGTTATGATC 59.784 45.833 0.00 0.00 0.00 2.92
329 330 3.644966 TTTTCAGGCCCGTTATGATCT 57.355 42.857 0.00 0.00 0.00 2.75
330 331 2.620251 TTCAGGCCCGTTATGATCTG 57.380 50.000 0.00 0.00 0.00 2.90
331 332 1.788229 TCAGGCCCGTTATGATCTGA 58.212 50.000 0.00 0.00 0.00 3.27
332 333 1.688735 TCAGGCCCGTTATGATCTGAG 59.311 52.381 0.00 0.00 0.00 3.35
333 334 1.051812 AGGCCCGTTATGATCTGAGG 58.948 55.000 0.00 0.00 0.00 3.86
334 335 0.035458 GGCCCGTTATGATCTGAGGG 59.965 60.000 0.00 1.27 41.65 4.30
335 336 3.614399 CCCGTTATGATCTGAGGGC 57.386 57.895 0.00 0.00 31.58 5.19
336 337 0.758734 CCCGTTATGATCTGAGGGCA 59.241 55.000 0.00 0.00 31.58 5.36
337 338 1.140852 CCCGTTATGATCTGAGGGCAA 59.859 52.381 0.00 0.00 31.58 4.52
338 339 2.487934 CCGTTATGATCTGAGGGCAAG 58.512 52.381 0.00 0.00 0.00 4.01
339 340 2.158900 CCGTTATGATCTGAGGGCAAGT 60.159 50.000 0.00 0.00 0.00 3.16
340 341 2.868583 CGTTATGATCTGAGGGCAAGTG 59.131 50.000 0.00 0.00 0.00 3.16
341 342 2.615912 GTTATGATCTGAGGGCAAGTGC 59.384 50.000 0.00 0.00 41.14 4.40
353 354 2.877043 GCAAGTGCCCTGGATTAATG 57.123 50.000 0.00 0.00 34.31 1.90
354 355 2.102578 GCAAGTGCCCTGGATTAATGT 58.897 47.619 0.00 0.00 34.31 2.71
355 356 2.159198 GCAAGTGCCCTGGATTAATGTG 60.159 50.000 0.00 0.00 34.31 3.21
356 357 3.355378 CAAGTGCCCTGGATTAATGTGA 58.645 45.455 0.00 0.00 0.00 3.58
357 358 3.956199 CAAGTGCCCTGGATTAATGTGAT 59.044 43.478 0.00 0.00 0.00 3.06
358 359 4.255510 AGTGCCCTGGATTAATGTGATT 57.744 40.909 0.00 0.00 0.00 2.57
359 360 3.956199 AGTGCCCTGGATTAATGTGATTG 59.044 43.478 0.00 0.00 0.00 2.67
360 361 2.694628 TGCCCTGGATTAATGTGATTGC 59.305 45.455 0.00 0.00 0.00 3.56
361 362 2.287788 GCCCTGGATTAATGTGATTGCG 60.288 50.000 0.00 0.00 0.00 4.85
362 363 2.951642 CCCTGGATTAATGTGATTGCGT 59.048 45.455 0.00 0.00 0.00 5.24
363 364 3.381272 CCCTGGATTAATGTGATTGCGTT 59.619 43.478 0.00 0.00 0.00 4.84
364 365 4.142182 CCCTGGATTAATGTGATTGCGTTT 60.142 41.667 0.00 0.00 0.00 3.60
365 366 4.799949 CCTGGATTAATGTGATTGCGTTTG 59.200 41.667 0.00 0.00 0.00 2.93
366 367 5.384063 TGGATTAATGTGATTGCGTTTGT 57.616 34.783 0.00 0.00 0.00 2.83
367 368 5.159925 TGGATTAATGTGATTGCGTTTGTG 58.840 37.500 0.00 0.00 0.00 3.33
368 369 4.031652 GGATTAATGTGATTGCGTTTGTGC 59.968 41.667 0.00 0.00 0.00 4.57
369 370 2.798976 AATGTGATTGCGTTTGTGCT 57.201 40.000 0.00 0.00 35.36 4.40
370 371 2.336554 ATGTGATTGCGTTTGTGCTC 57.663 45.000 0.00 0.00 35.36 4.26
371 372 1.308047 TGTGATTGCGTTTGTGCTCT 58.692 45.000 0.00 0.00 35.36 4.09
372 373 1.002576 TGTGATTGCGTTTGTGCTCTG 60.003 47.619 0.00 0.00 35.36 3.35
409 410 0.749454 ATCTCGCCCAACCAAGCATC 60.749 55.000 0.00 0.00 0.00 3.91
410 411 1.377725 CTCGCCCAACCAAGCATCT 60.378 57.895 0.00 0.00 0.00 2.90
411 412 0.107703 CTCGCCCAACCAAGCATCTA 60.108 55.000 0.00 0.00 0.00 1.98
412 413 0.546122 TCGCCCAACCAAGCATCTAT 59.454 50.000 0.00 0.00 0.00 1.98
413 414 1.064758 TCGCCCAACCAAGCATCTATT 60.065 47.619 0.00 0.00 0.00 1.73
443 444 4.044426 GTGGAGCTCAACACAATGTTTTC 58.956 43.478 16.79 0.00 38.77 2.29
457 458 8.264347 ACACAATGTTTTCAGAAGGGTTTTTAT 58.736 29.630 0.00 0.00 0.00 1.40
497 498 1.669795 GCCACGCTGCTAATTTTTGCT 60.670 47.619 0.00 0.00 0.00 3.91
504 505 6.580791 CACGCTGCTAATTTTTGCTACTAAAA 59.419 34.615 0.00 0.00 0.00 1.52
505 506 7.114247 CACGCTGCTAATTTTTGCTACTAAAAA 59.886 33.333 0.00 0.00 41.94 1.94
541 542 4.702131 AGAAATGCCACTGTTCCATTAGAC 59.298 41.667 3.87 1.20 0.00 2.59
636 1216 8.742777 TCACTAAAATGTATGTACCGAGTAGTT 58.257 33.333 0.00 0.00 0.00 2.24
641 1221 8.836268 AAATGTATGTACCGAGTAGTTTTCAA 57.164 30.769 0.00 0.00 0.00 2.69
648 1228 6.814644 TGTACCGAGTAGTTTTCAATGGTATG 59.185 38.462 0.00 0.00 33.68 2.39
652 1232 6.202954 CCGAGTAGTTTTCAATGGTATGATCC 59.797 42.308 0.00 0.00 0.00 3.36
754 1334 2.380084 TATGTTCTTCAGTCCGCACC 57.620 50.000 0.00 0.00 0.00 5.01
761 1341 1.174078 TTCAGTCCGCACCGTGTCTA 61.174 55.000 0.00 0.00 0.00 2.59
775 1355 7.116376 CGCACCGTGTCTAAATATCTGATAAAT 59.884 37.037 0.81 0.00 0.00 1.40
798 1378 5.824904 AACATGCACAAATCCTCTGATAC 57.175 39.130 0.00 0.00 0.00 2.24
808 1388 5.736951 AATCCTCTGATACATGCTACTCC 57.263 43.478 0.00 0.00 0.00 3.85
854 2761 8.929827 TGTTTTGCATATTTCAATATGGACTG 57.070 30.769 17.46 0.00 45.43 3.51
856 2763 6.712179 TTGCATATTTCAATATGGACTGCA 57.288 33.333 17.46 9.97 45.43 4.41
1101 3012 2.478872 TATGCTTGGCCTCTCCTACT 57.521 50.000 3.32 0.00 35.26 2.57
1107 3018 3.637769 CTTGGCCTCTCCTACTAGTTCT 58.362 50.000 3.32 0.00 35.26 3.01
1444 3358 1.160329 AGACCTGCACAAGTTGTCGC 61.160 55.000 17.98 17.98 0.00 5.19
1679 3596 1.555075 CCCTGAACTTGGTAGCTGCTA 59.445 52.381 5.02 5.02 0.00 3.49
1961 3878 0.388659 GAGCTGCCATCGAGTCTGAT 59.611 55.000 0.00 0.00 0.00 2.90
2371 10263 5.978934 TCTTCAGGTTTTTAGTGTCGAAC 57.021 39.130 0.00 0.00 0.00 3.95
2394 10286 4.676471 CGATGCGGATTATTTGGACAAATG 59.324 41.667 17.92 4.59 40.83 2.32
2536 10428 2.227036 AACAGCCTCACAGGGGGAG 61.227 63.158 0.00 0.00 35.37 4.30
2543 10435 0.771127 CTCACAGGGGGAGTTCCAAA 59.229 55.000 0.00 0.00 37.91 3.28
2664 10556 5.941647 ACAATACCGTGTACCTATTGCTTTT 59.058 36.000 0.00 0.00 33.06 2.27
3013 10905 5.233988 GCTCTACTCTCACTCACAAATGTT 58.766 41.667 0.00 0.00 0.00 2.71
3014 10906 6.390721 GCTCTACTCTCACTCACAAATGTTA 58.609 40.000 0.00 0.00 0.00 2.41
3133 11025 0.320421 GTTGCTGGTGCGTCTCCTTA 60.320 55.000 0.00 0.00 43.34 2.69
3168 11060 4.956085 AGAAGGGTTTTATGGCAAAACAC 58.044 39.130 14.73 11.87 42.28 3.32
3186 11081 5.413309 AACACAGAAGAGGGAGTAATGAG 57.587 43.478 0.00 0.00 0.00 2.90
3358 11254 6.323996 TGTGGAGGTTATGGATTAGTCTACAG 59.676 42.308 0.00 0.00 0.00 2.74
3448 11344 2.427506 GGAGTTTAGTGCAGAGGTTGG 58.572 52.381 0.00 0.00 0.00 3.77
3487 11383 5.920273 CACAACATGAAAATCTTGTACCACC 59.080 40.000 0.00 0.00 34.23 4.61
3589 11485 6.631763 TCATAACAGGGATGATGATGCTAT 57.368 37.500 0.00 0.00 0.00 2.97
3934 11830 4.034510 GCGACCTGTTTCAATCCTATCAAG 59.965 45.833 0.00 0.00 0.00 3.02
4156 12056 0.379669 GACCCGCAGATGCAAAGATG 59.620 55.000 5.55 0.00 42.21 2.90
4197 12105 8.899427 AACCACACATGATAGATAATCTTGAG 57.101 34.615 0.00 3.38 40.53 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.535878 ACATTTAATGTTTTCCAAATACACGTT 57.464 25.926 4.56 0.00 41.63 3.99
2 3 8.973378 CACATTTAATGTTTTCCAAATACACGT 58.027 29.630 7.97 0.00 42.70 4.49
3 4 8.973378 ACACATTTAATGTTTTCCAAATACACG 58.027 29.630 7.97 0.00 42.70 4.49
126 127 2.876581 AGATGGAGTGGTTTTGGGAAC 58.123 47.619 0.00 0.00 0.00 3.62
127 128 4.946160 ATAGATGGAGTGGTTTTGGGAA 57.054 40.909 0.00 0.00 0.00 3.97
128 129 5.036916 AGTATAGATGGAGTGGTTTTGGGA 58.963 41.667 0.00 0.00 0.00 4.37
129 130 5.368989 GAGTATAGATGGAGTGGTTTTGGG 58.631 45.833 0.00 0.00 0.00 4.12
130 131 5.368989 GGAGTATAGATGGAGTGGTTTTGG 58.631 45.833 0.00 0.00 0.00 3.28
131 132 5.104527 TGGGAGTATAGATGGAGTGGTTTTG 60.105 44.000 0.00 0.00 0.00 2.44
132 133 5.036916 TGGGAGTATAGATGGAGTGGTTTT 58.963 41.667 0.00 0.00 0.00 2.43
133 134 4.631234 TGGGAGTATAGATGGAGTGGTTT 58.369 43.478 0.00 0.00 0.00 3.27
134 135 4.280789 TGGGAGTATAGATGGAGTGGTT 57.719 45.455 0.00 0.00 0.00 3.67
135 136 3.967987 GTTGGGAGTATAGATGGAGTGGT 59.032 47.826 0.00 0.00 0.00 4.16
136 137 3.967326 TGTTGGGAGTATAGATGGAGTGG 59.033 47.826 0.00 0.00 0.00 4.00
137 138 5.815233 ATGTTGGGAGTATAGATGGAGTG 57.185 43.478 0.00 0.00 0.00 3.51
138 139 5.455326 GCAATGTTGGGAGTATAGATGGAGT 60.455 44.000 0.00 0.00 0.00 3.85
139 140 4.999950 GCAATGTTGGGAGTATAGATGGAG 59.000 45.833 0.00 0.00 0.00 3.86
140 141 4.202461 GGCAATGTTGGGAGTATAGATGGA 60.202 45.833 0.00 0.00 0.00 3.41
141 142 4.074970 GGCAATGTTGGGAGTATAGATGG 58.925 47.826 0.00 0.00 0.00 3.51
142 143 4.074970 GGGCAATGTTGGGAGTATAGATG 58.925 47.826 0.00 0.00 0.00 2.90
143 144 3.074538 GGGGCAATGTTGGGAGTATAGAT 59.925 47.826 0.00 0.00 0.00 1.98
144 145 2.441750 GGGGCAATGTTGGGAGTATAGA 59.558 50.000 0.00 0.00 0.00 1.98
145 146 2.174639 TGGGGCAATGTTGGGAGTATAG 59.825 50.000 0.00 0.00 0.00 1.31
146 147 2.174639 CTGGGGCAATGTTGGGAGTATA 59.825 50.000 0.00 0.00 0.00 1.47
147 148 1.006813 TGGGGCAATGTTGGGAGTAT 58.993 50.000 0.00 0.00 0.00 2.12
148 149 0.331278 CTGGGGCAATGTTGGGAGTA 59.669 55.000 0.00 0.00 0.00 2.59
149 150 1.077265 CTGGGGCAATGTTGGGAGT 59.923 57.895 0.00 0.00 0.00 3.85
150 151 1.077265 ACTGGGGCAATGTTGGGAG 59.923 57.895 0.00 0.00 0.00 4.30
151 152 1.228831 CACTGGGGCAATGTTGGGA 60.229 57.895 0.00 0.00 0.00 4.37
152 153 2.285024 CCACTGGGGCAATGTTGGG 61.285 63.158 0.00 0.00 0.00 4.12
153 154 0.251564 TACCACTGGGGCAATGTTGG 60.252 55.000 0.00 0.00 42.05 3.77
154 155 1.851304 ATACCACTGGGGCAATGTTG 58.149 50.000 0.00 0.00 42.05 3.33
155 156 2.580783 ACTATACCACTGGGGCAATGTT 59.419 45.455 0.00 0.00 42.05 2.71
156 157 2.205342 ACTATACCACTGGGGCAATGT 58.795 47.619 0.00 0.00 42.05 2.71
157 158 4.134563 GTTACTATACCACTGGGGCAATG 58.865 47.826 0.00 0.00 42.05 2.82
158 159 4.045022 AGTTACTATACCACTGGGGCAAT 58.955 43.478 0.00 0.00 42.05 3.56
159 160 3.456842 AGTTACTATACCACTGGGGCAA 58.543 45.455 0.00 0.00 42.05 4.52
160 161 3.124856 AGTTACTATACCACTGGGGCA 57.875 47.619 0.00 0.00 42.05 5.36
161 162 4.196971 CAAAGTTACTATACCACTGGGGC 58.803 47.826 0.00 0.00 42.05 5.80
162 163 5.431179 ACAAAGTTACTATACCACTGGGG 57.569 43.478 0.00 0.00 44.81 4.96
163 164 8.889717 CATTAACAAAGTTACTATACCACTGGG 58.110 37.037 0.00 0.00 41.29 4.45
164 165 8.395633 GCATTAACAAAGTTACTATACCACTGG 58.604 37.037 0.00 0.00 0.00 4.00
165 166 9.162764 AGCATTAACAAAGTTACTATACCACTG 57.837 33.333 0.00 0.00 0.00 3.66
166 167 9.379791 GAGCATTAACAAAGTTACTATACCACT 57.620 33.333 0.00 0.00 0.00 4.00
167 168 8.610035 GGAGCATTAACAAAGTTACTATACCAC 58.390 37.037 0.00 0.00 0.00 4.16
168 169 8.322828 TGGAGCATTAACAAAGTTACTATACCA 58.677 33.333 0.00 0.00 0.00 3.25
169 170 8.726870 TGGAGCATTAACAAAGTTACTATACC 57.273 34.615 0.00 0.00 0.00 2.73
170 171 8.336080 GCTGGAGCATTAACAAAGTTACTATAC 58.664 37.037 0.00 0.00 41.59 1.47
171 172 7.497909 GGCTGGAGCATTAACAAAGTTACTATA 59.502 37.037 0.20 0.00 44.36 1.31
172 173 6.318900 GGCTGGAGCATTAACAAAGTTACTAT 59.681 38.462 0.20 0.00 44.36 2.12
173 174 5.646360 GGCTGGAGCATTAACAAAGTTACTA 59.354 40.000 0.20 0.00 44.36 1.82
174 175 4.459337 GGCTGGAGCATTAACAAAGTTACT 59.541 41.667 0.20 0.00 44.36 2.24
175 176 4.380550 GGGCTGGAGCATTAACAAAGTTAC 60.381 45.833 0.20 0.00 44.36 2.50
176 177 3.761752 GGGCTGGAGCATTAACAAAGTTA 59.238 43.478 0.20 0.00 44.36 2.24
177 178 2.562738 GGGCTGGAGCATTAACAAAGTT 59.437 45.455 0.20 0.00 44.36 2.66
178 179 2.171003 GGGCTGGAGCATTAACAAAGT 58.829 47.619 0.20 0.00 44.36 2.66
179 180 1.478105 GGGGCTGGAGCATTAACAAAG 59.522 52.381 0.20 0.00 44.36 2.77
180 181 1.555967 GGGGCTGGAGCATTAACAAA 58.444 50.000 0.20 0.00 44.36 2.83
181 182 0.679640 CGGGGCTGGAGCATTAACAA 60.680 55.000 0.20 0.00 44.36 2.83
182 183 1.077787 CGGGGCTGGAGCATTAACA 60.078 57.895 0.20 0.00 44.36 2.41
183 184 1.823899 CCGGGGCTGGAGCATTAAC 60.824 63.158 0.00 0.00 44.36 2.01
184 185 1.352622 ATCCGGGGCTGGAGCATTAA 61.353 55.000 0.00 0.00 42.45 1.40
185 186 1.770110 ATCCGGGGCTGGAGCATTA 60.770 57.895 0.00 0.00 42.45 1.90
186 187 3.099170 ATCCGGGGCTGGAGCATT 61.099 61.111 0.00 0.00 42.45 3.56
187 188 3.882326 CATCCGGGGCTGGAGCAT 61.882 66.667 0.00 0.00 42.45 3.79
189 190 4.554036 GTCATCCGGGGCTGGAGC 62.554 72.222 0.00 0.00 42.45 4.70
190 191 3.866582 GGTCATCCGGGGCTGGAG 61.867 72.222 0.00 0.00 42.45 3.86
200 201 1.208535 TGATACCCACAACGGTCATCC 59.791 52.381 0.00 0.00 37.34 3.51
201 202 2.277084 GTGATACCCACAACGGTCATC 58.723 52.381 0.00 0.00 45.03 2.92
202 203 2.396590 GTGATACCCACAACGGTCAT 57.603 50.000 0.00 0.00 45.03 3.06
203 204 3.919163 GTGATACCCACAACGGTCA 57.081 52.632 0.00 0.00 45.03 4.02
211 212 4.034048 CGCTTTATTGTGAGTGATACCCAC 59.966 45.833 0.00 0.00 46.03 4.61
212 213 4.081365 TCGCTTTATTGTGAGTGATACCCA 60.081 41.667 0.00 0.00 0.00 4.51
213 214 4.439057 TCGCTTTATTGTGAGTGATACCC 58.561 43.478 0.00 0.00 0.00 3.69
216 217 7.050970 AGGTATCGCTTTATTGTGAGTGATA 57.949 36.000 3.30 3.30 41.75 2.15
217 218 5.918608 AGGTATCGCTTTATTGTGAGTGAT 58.081 37.500 4.99 4.99 43.41 3.06
218 219 5.339008 AGGTATCGCTTTATTGTGAGTGA 57.661 39.130 0.00 0.00 36.89 3.41
219 220 5.175856 GCTAGGTATCGCTTTATTGTGAGTG 59.824 44.000 0.00 0.00 0.00 3.51
220 221 5.163447 TGCTAGGTATCGCTTTATTGTGAGT 60.163 40.000 0.00 0.00 0.00 3.41
221 222 5.289595 TGCTAGGTATCGCTTTATTGTGAG 58.710 41.667 0.00 0.00 0.00 3.51
222 223 5.270893 TGCTAGGTATCGCTTTATTGTGA 57.729 39.130 0.00 0.00 0.00 3.58
223 224 6.545504 AATGCTAGGTATCGCTTTATTGTG 57.454 37.500 0.00 0.00 0.00 3.33
224 225 6.542370 ACAAATGCTAGGTATCGCTTTATTGT 59.458 34.615 0.00 0.00 0.00 2.71
225 226 6.852853 CACAAATGCTAGGTATCGCTTTATTG 59.147 38.462 0.00 0.00 0.00 1.90
226 227 6.765989 TCACAAATGCTAGGTATCGCTTTATT 59.234 34.615 0.00 0.00 0.00 1.40
227 228 6.288294 TCACAAATGCTAGGTATCGCTTTAT 58.712 36.000 0.00 0.00 0.00 1.40
228 229 5.666462 TCACAAATGCTAGGTATCGCTTTA 58.334 37.500 0.00 0.00 0.00 1.85
229 230 4.513442 TCACAAATGCTAGGTATCGCTTT 58.487 39.130 0.00 0.00 0.00 3.51
230 231 4.137116 TCACAAATGCTAGGTATCGCTT 57.863 40.909 0.00 0.00 0.00 4.68
231 232 3.819564 TCACAAATGCTAGGTATCGCT 57.180 42.857 0.00 0.00 0.00 4.93
232 233 4.332819 ACTTTCACAAATGCTAGGTATCGC 59.667 41.667 0.00 0.00 0.00 4.58
233 234 5.580691 TCACTTTCACAAATGCTAGGTATCG 59.419 40.000 0.00 0.00 0.00 2.92
234 235 6.985188 TCACTTTCACAAATGCTAGGTATC 57.015 37.500 0.00 0.00 0.00 2.24
235 236 7.665559 TCTTTCACTTTCACAAATGCTAGGTAT 59.334 33.333 0.00 0.00 0.00 2.73
236 237 6.995686 TCTTTCACTTTCACAAATGCTAGGTA 59.004 34.615 0.00 0.00 0.00 3.08
237 238 5.827797 TCTTTCACTTTCACAAATGCTAGGT 59.172 36.000 0.00 0.00 0.00 3.08
238 239 6.016777 AGTCTTTCACTTTCACAAATGCTAGG 60.017 38.462 0.00 0.00 26.56 3.02
239 240 6.963796 AGTCTTTCACTTTCACAAATGCTAG 58.036 36.000 0.00 0.00 26.56 3.42
240 241 6.942532 AGTCTTTCACTTTCACAAATGCTA 57.057 33.333 0.00 0.00 26.56 3.49
241 242 5.841957 AGTCTTTCACTTTCACAAATGCT 57.158 34.783 0.00 0.00 26.56 3.79
242 243 6.583806 CCATAGTCTTTCACTTTCACAAATGC 59.416 38.462 0.00 0.00 36.43 3.56
243 244 7.874940 TCCATAGTCTTTCACTTTCACAAATG 58.125 34.615 0.00 0.00 36.43 2.32
244 245 7.939039 TCTCCATAGTCTTTCACTTTCACAAAT 59.061 33.333 0.00 0.00 36.43 2.32
245 246 7.279615 TCTCCATAGTCTTTCACTTTCACAAA 58.720 34.615 0.00 0.00 36.43 2.83
246 247 6.826668 TCTCCATAGTCTTTCACTTTCACAA 58.173 36.000 0.00 0.00 36.43 3.33
247 248 6.267699 TCTCTCCATAGTCTTTCACTTTCACA 59.732 38.462 0.00 0.00 36.43 3.58
248 249 6.692486 TCTCTCCATAGTCTTTCACTTTCAC 58.308 40.000 0.00 0.00 36.43 3.18
249 250 6.918067 TCTCTCCATAGTCTTTCACTTTCA 57.082 37.500 0.00 0.00 36.43 2.69
250 251 8.785329 AAATCTCTCCATAGTCTTTCACTTTC 57.215 34.615 0.00 0.00 36.43 2.62
251 252 8.601546 AGAAATCTCTCCATAGTCTTTCACTTT 58.398 33.333 0.00 0.00 36.43 2.66
252 253 8.144862 AGAAATCTCTCCATAGTCTTTCACTT 57.855 34.615 0.00 0.00 36.43 3.16
253 254 7.732222 AGAAATCTCTCCATAGTCTTTCACT 57.268 36.000 0.00 0.00 39.41 3.41
269 270 8.546597 AAAAACTCAGAAGCTAGAGAAATCTC 57.453 34.615 15.27 2.10 43.17 2.75
270 271 7.606073 GGAAAAACTCAGAAGCTAGAGAAATCT 59.394 37.037 15.27 0.00 35.83 2.40
271 272 7.606073 AGGAAAAACTCAGAAGCTAGAGAAATC 59.394 37.037 15.27 8.75 35.83 2.17
272 273 7.457561 AGGAAAAACTCAGAAGCTAGAGAAAT 58.542 34.615 15.27 1.89 35.83 2.17
273 274 6.831976 AGGAAAAACTCAGAAGCTAGAGAAA 58.168 36.000 15.27 0.00 35.83 2.52
274 275 6.426646 AGGAAAAACTCAGAAGCTAGAGAA 57.573 37.500 15.27 0.00 35.83 2.87
275 276 7.233757 ACTTAGGAAAAACTCAGAAGCTAGAGA 59.766 37.037 15.27 0.56 35.83 3.10
276 277 7.382898 ACTTAGGAAAAACTCAGAAGCTAGAG 58.617 38.462 8.68 8.68 37.87 2.43
277 278 7.304497 ACTTAGGAAAAACTCAGAAGCTAGA 57.696 36.000 0.00 0.00 0.00 2.43
278 279 6.592220 GGACTTAGGAAAAACTCAGAAGCTAG 59.408 42.308 0.00 0.00 0.00 3.42
279 280 6.270231 AGGACTTAGGAAAAACTCAGAAGCTA 59.730 38.462 0.00 0.00 0.00 3.32
280 281 5.072464 AGGACTTAGGAAAAACTCAGAAGCT 59.928 40.000 0.00 0.00 0.00 3.74
281 282 5.180304 CAGGACTTAGGAAAAACTCAGAAGC 59.820 44.000 0.00 0.00 0.00 3.86
282 283 5.703130 CCAGGACTTAGGAAAAACTCAGAAG 59.297 44.000 0.00 0.00 0.00 2.85
283 284 5.132144 ACCAGGACTTAGGAAAAACTCAGAA 59.868 40.000 0.00 0.00 0.00 3.02
284 285 4.658901 ACCAGGACTTAGGAAAAACTCAGA 59.341 41.667 0.00 0.00 0.00 3.27
285 286 4.974399 ACCAGGACTTAGGAAAAACTCAG 58.026 43.478 0.00 0.00 0.00 3.35
286 287 6.697641 ATACCAGGACTTAGGAAAAACTCA 57.302 37.500 0.00 0.00 0.00 3.41
287 288 7.997773 AAATACCAGGACTTAGGAAAAACTC 57.002 36.000 0.00 0.00 0.00 3.01
288 289 8.002459 TGAAAATACCAGGACTTAGGAAAAACT 58.998 33.333 0.00 0.00 0.00 2.66
289 290 8.173542 TGAAAATACCAGGACTTAGGAAAAAC 57.826 34.615 0.00 0.00 0.00 2.43
290 291 8.404107 CTGAAAATACCAGGACTTAGGAAAAA 57.596 34.615 0.00 0.00 0.00 1.94
291 292 7.996098 CTGAAAATACCAGGACTTAGGAAAA 57.004 36.000 0.00 0.00 0.00 2.29
303 304 1.834188 AACGGGCCTGAAAATACCAG 58.166 50.000 21.41 0.00 0.00 4.00
304 305 3.054287 TCATAACGGGCCTGAAAATACCA 60.054 43.478 21.41 0.00 0.00 3.25
305 306 3.547746 TCATAACGGGCCTGAAAATACC 58.452 45.455 21.41 0.00 0.00 2.73
306 307 5.049405 CAGATCATAACGGGCCTGAAAATAC 60.049 44.000 21.41 3.97 0.00 1.89
307 308 5.063204 CAGATCATAACGGGCCTGAAAATA 58.937 41.667 21.41 6.10 0.00 1.40
308 309 3.885297 CAGATCATAACGGGCCTGAAAAT 59.115 43.478 21.41 5.36 0.00 1.82
309 310 3.054728 TCAGATCATAACGGGCCTGAAAA 60.055 43.478 21.41 2.79 0.00 2.29
310 311 2.503765 TCAGATCATAACGGGCCTGAAA 59.496 45.455 21.41 5.74 0.00 2.69
311 312 2.103094 CTCAGATCATAACGGGCCTGAA 59.897 50.000 21.41 6.16 31.33 3.02
312 313 1.688735 CTCAGATCATAACGGGCCTGA 59.311 52.381 21.41 6.29 0.00 3.86
313 314 1.270518 CCTCAGATCATAACGGGCCTG 60.271 57.143 11.02 11.02 0.00 4.85
314 315 1.051812 CCTCAGATCATAACGGGCCT 58.948 55.000 0.84 0.00 0.00 5.19
315 316 0.035458 CCCTCAGATCATAACGGGCC 59.965 60.000 0.00 0.00 0.00 5.80
316 317 3.614399 CCCTCAGATCATAACGGGC 57.386 57.895 0.00 0.00 0.00 6.13
317 318 0.758734 TGCCCTCAGATCATAACGGG 59.241 55.000 0.00 0.00 34.79 5.28
318 319 2.158900 ACTTGCCCTCAGATCATAACGG 60.159 50.000 0.00 0.00 0.00 4.44
319 320 2.868583 CACTTGCCCTCAGATCATAACG 59.131 50.000 0.00 0.00 0.00 3.18
320 321 2.615912 GCACTTGCCCTCAGATCATAAC 59.384 50.000 0.00 0.00 34.31 1.89
321 322 2.923121 GCACTTGCCCTCAGATCATAA 58.077 47.619 0.00 0.00 34.31 1.90
322 323 2.627515 GCACTTGCCCTCAGATCATA 57.372 50.000 0.00 0.00 34.31 2.15
323 324 3.491208 GCACTTGCCCTCAGATCAT 57.509 52.632 0.00 0.00 34.31 2.45
334 335 2.102578 ACATTAATCCAGGGCACTTGC 58.897 47.619 0.00 0.00 41.14 4.01
335 336 3.355378 TCACATTAATCCAGGGCACTTG 58.645 45.455 0.00 0.00 0.00 3.16
336 337 3.737559 TCACATTAATCCAGGGCACTT 57.262 42.857 0.00 0.00 0.00 3.16
337 338 3.956199 CAATCACATTAATCCAGGGCACT 59.044 43.478 0.00 0.00 0.00 4.40
338 339 3.491447 GCAATCACATTAATCCAGGGCAC 60.491 47.826 0.00 0.00 0.00 5.01
339 340 2.694628 GCAATCACATTAATCCAGGGCA 59.305 45.455 0.00 0.00 0.00 5.36
340 341 2.287788 CGCAATCACATTAATCCAGGGC 60.288 50.000 0.00 0.00 0.00 5.19
341 342 2.951642 ACGCAATCACATTAATCCAGGG 59.048 45.455 0.00 0.00 0.00 4.45
342 343 4.637483 AACGCAATCACATTAATCCAGG 57.363 40.909 0.00 0.00 0.00 4.45
343 344 5.286797 CACAAACGCAATCACATTAATCCAG 59.713 40.000 0.00 0.00 0.00 3.86
344 345 5.159925 CACAAACGCAATCACATTAATCCA 58.840 37.500 0.00 0.00 0.00 3.41
345 346 4.031652 GCACAAACGCAATCACATTAATCC 59.968 41.667 0.00 0.00 0.00 3.01
346 347 4.858692 AGCACAAACGCAATCACATTAATC 59.141 37.500 0.00 0.00 0.00 1.75
347 348 4.808558 AGCACAAACGCAATCACATTAAT 58.191 34.783 0.00 0.00 0.00 1.40
348 349 4.023279 AGAGCACAAACGCAATCACATTAA 60.023 37.500 0.00 0.00 0.00 1.40
349 350 3.501828 AGAGCACAAACGCAATCACATTA 59.498 39.130 0.00 0.00 0.00 1.90
350 351 2.294233 AGAGCACAAACGCAATCACATT 59.706 40.909 0.00 0.00 0.00 2.71
351 352 1.881973 AGAGCACAAACGCAATCACAT 59.118 42.857 0.00 0.00 0.00 3.21
352 353 1.002576 CAGAGCACAAACGCAATCACA 60.003 47.619 0.00 0.00 0.00 3.58
353 354 1.002468 ACAGAGCACAAACGCAATCAC 60.002 47.619 0.00 0.00 0.00 3.06
354 355 1.002576 CACAGAGCACAAACGCAATCA 60.003 47.619 0.00 0.00 0.00 2.57
355 356 1.002468 ACACAGAGCACAAACGCAATC 60.002 47.619 0.00 0.00 0.00 2.67
356 357 1.024271 ACACAGAGCACAAACGCAAT 58.976 45.000 0.00 0.00 0.00 3.56
357 358 0.098552 CACACAGAGCACAAACGCAA 59.901 50.000 0.00 0.00 0.00 4.85
358 359 1.720894 CACACAGAGCACAAACGCA 59.279 52.632 0.00 0.00 0.00 5.24
359 360 1.655350 GCACACAGAGCACAAACGC 60.655 57.895 0.00 0.00 0.00 4.84
360 361 0.378257 AAGCACACAGAGCACAAACG 59.622 50.000 0.00 0.00 0.00 3.60
361 362 2.566952 AAAGCACACAGAGCACAAAC 57.433 45.000 0.00 0.00 0.00 2.93
362 363 3.278574 AGTAAAGCACACAGAGCACAAA 58.721 40.909 0.00 0.00 0.00 2.83
363 364 2.872245 GAGTAAAGCACACAGAGCACAA 59.128 45.455 0.00 0.00 0.00 3.33
364 365 2.103094 AGAGTAAAGCACACAGAGCACA 59.897 45.455 0.00 0.00 0.00 4.57
365 366 2.760374 AGAGTAAAGCACACAGAGCAC 58.240 47.619 0.00 0.00 0.00 4.40
366 367 3.475566 AAGAGTAAAGCACACAGAGCA 57.524 42.857 0.00 0.00 0.00 4.26
367 368 3.809832 TCAAAGAGTAAAGCACACAGAGC 59.190 43.478 0.00 0.00 0.00 4.09
368 369 5.991328 TTCAAAGAGTAAAGCACACAGAG 57.009 39.130 0.00 0.00 0.00 3.35
369 370 6.291377 AGATTCAAAGAGTAAAGCACACAGA 58.709 36.000 0.00 0.00 0.00 3.41
370 371 6.551385 AGATTCAAAGAGTAAAGCACACAG 57.449 37.500 0.00 0.00 0.00 3.66
371 372 5.177511 CGAGATTCAAAGAGTAAAGCACACA 59.822 40.000 0.00 0.00 0.00 3.72
372 373 5.612865 CGAGATTCAAAGAGTAAAGCACAC 58.387 41.667 0.00 0.00 0.00 3.82
409 410 5.647658 TGTTGAGCTCCACCATTGTAAATAG 59.352 40.000 14.87 0.00 0.00 1.73
410 411 5.414454 GTGTTGAGCTCCACCATTGTAAATA 59.586 40.000 14.87 0.00 0.00 1.40
411 412 4.218417 GTGTTGAGCTCCACCATTGTAAAT 59.782 41.667 14.87 0.00 0.00 1.40
412 413 3.568007 GTGTTGAGCTCCACCATTGTAAA 59.432 43.478 14.87 0.00 0.00 2.01
413 414 3.146066 GTGTTGAGCTCCACCATTGTAA 58.854 45.455 14.87 0.00 0.00 2.41
443 444 6.515832 AGCAAAAGTGATAAAAACCCTTCTG 58.484 36.000 0.00 0.00 0.00 3.02
457 458 3.813166 GGCACAACTAGTAGCAAAAGTGA 59.187 43.478 14.42 0.00 0.00 3.41
504 505 6.494835 AGTGGCATTTCTGAGTAGGAAAAATT 59.505 34.615 0.00 0.00 36.47 1.82
505 506 6.012745 AGTGGCATTTCTGAGTAGGAAAAAT 58.987 36.000 0.00 0.00 36.47 1.82
512 513 3.686726 GGAACAGTGGCATTTCTGAGTAG 59.313 47.826 10.22 0.00 35.84 2.57
656 1236 9.823647 TGCTTAAACTTTGACCAATAATTTCAA 57.176 25.926 0.00 0.00 0.00 2.69
775 1355 6.413892 TGTATCAGAGGATTTGTGCATGTTA 58.586 36.000 0.00 0.00 34.89 2.41
798 1378 3.877559 TGTGAATGAAGGGAGTAGCATG 58.122 45.455 0.00 0.00 0.00 4.06
837 1417 7.931407 TCGTAGTTGCAGTCCATATTGAAATAT 59.069 33.333 0.00 0.00 31.93 1.28
854 2761 0.108756 GTCCTGTCCCTCGTAGTTGC 60.109 60.000 0.00 0.00 0.00 4.17
856 2763 2.005370 TTGTCCTGTCCCTCGTAGTT 57.995 50.000 0.00 0.00 0.00 2.24
1140 3051 3.541713 GAGAGCCCGCCGAGGAAT 61.542 66.667 0.00 0.00 45.00 3.01
1679 3596 1.338864 CCTTGAGCACTCTGAGCATGT 60.339 52.381 4.19 0.00 0.00 3.21
1961 3878 4.761227 TGCTTATGAGATTTGTGCAGTTGA 59.239 37.500 0.00 0.00 0.00 3.18
2371 10263 3.961477 TTGTCCAAATAATCCGCATCG 57.039 42.857 0.00 0.00 0.00 3.84
2436 10328 4.024556 CCAGTGAGTTGATTGTCAGACAAC 60.025 45.833 18.49 12.40 41.40 3.32
2543 10435 3.901570 TTGGCATATCCATAAGGGCTT 57.098 42.857 0.00 0.00 46.04 4.35
2664 10556 3.132111 TGCTTAGATCCAGCACATTACGA 59.868 43.478 12.21 0.00 42.49 3.43
2707 10599 0.252513 TGACCAATCTCGAGGGGGAA 60.253 55.000 20.05 7.78 0.00 3.97
3013 10905 6.012508 GGGGATGGAGGTATTGAATCTGAATA 60.013 42.308 0.00 0.00 0.00 1.75
3014 10906 5.222213 GGGGATGGAGGTATTGAATCTGAAT 60.222 44.000 0.00 0.00 0.00 2.57
3133 11025 5.527026 AAACCCTTCTTCTGGATTGAGAT 57.473 39.130 0.00 0.00 0.00 2.75
3168 11060 4.653341 ACATCCTCATTACTCCCTCTTCTG 59.347 45.833 0.00 0.00 0.00 3.02
3248 11144 1.620822 TTTCTTCTCCCTTGCCTTGC 58.379 50.000 0.00 0.00 0.00 4.01
3358 11254 1.589716 GCCATCAGACAACACTGCCC 61.590 60.000 0.00 0.00 37.75 5.36
3448 11344 2.359230 GTGCCCTGGAGAGTGCAC 60.359 66.667 9.40 9.40 46.09 4.57
3589 11485 1.623311 TCGGCCAGTCAAGAAATGAGA 59.377 47.619 2.24 0.00 39.19 3.27
4156 12056 4.009675 TGTGGTTCATTGTATCTTGGCTC 58.990 43.478 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.