Multiple sequence alignment - TraesCS1B01G261100

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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 TraesCS1B01G261100 chr1B 100.000 2696 0 0 1 2696 458725597 458728292 0.000000e+00 4979.0
1 TraesCS1B01G261100 chr1B 95.413 109 4 1 148 255 458725642 458725750 3.570000e-39 172.0
2 TraesCS1B01G261100 chr1B 95.413 109 4 1 46 154 458725744 458725851 3.570000e-39 172.0
3 TraesCS1B01G261100 chr1D 90.046 1738 112 31 445 2159 342489025 342490724 0.000000e+00 2194.0
4 TraesCS1B01G261100 chr1D 93.573 529 34 0 2168 2696 342490792 342491320 0.000000e+00 789.0
5 TraesCS1B01G261100 chr1A 90.532 940 54 16 1185 2114 442155182 442156096 0.000000e+00 1210.0
6 TraesCS1B01G261100 chr1A 88.655 714 52 14 438 1139 442154405 442155101 0.000000e+00 843.0
7 TraesCS1B01G261100 chr1A 94.118 527 29 2 2168 2694 442156209 442156733 0.000000e+00 800.0
8 TraesCS1B01G261100 chr1A 99.032 310 3 0 1 310 77471674 77471983 8.430000e-155 556.0
9 TraesCS1B01G261100 chr1A 95.413 109 4 1 148 255 77471719 77471827 3.570000e-39 172.0
10 TraesCS1B01G261100 chr1A 95.413 109 4 1 46 154 77471821 77471928 3.570000e-39 172.0
11 TraesCS1B01G261100 chr1A 80.000 130 8 18 269 397 335110852 335110964 2.230000e-11 80.5
12 TraesCS1B01G261100 chr2B 99.057 318 3 0 1 318 547854891 547854574 3.010000e-159 571.0
13 TraesCS1B01G261100 chr2B 97.170 106 2 1 49 154 547854741 547854637 7.670000e-41 178.0
14 TraesCS1B01G261100 chr2B 96.226 106 3 1 151 255 547854843 547854738 3.570000e-39 172.0
15 TraesCS1B01G261100 chr2B 96.040 101 3 1 279 378 57156997 57156897 2.150000e-36 163.0
16 TraesCS1B01G261100 chr4B 97.460 315 8 0 1 315 197208761 197209075 3.050000e-149 538.0
17 TraesCS1B01G261100 chr4B 96.330 109 3 1 46 154 197208908 197209015 7.670000e-41 178.0
18 TraesCS1B01G261100 chr4B 91.743 109 8 1 148 255 197208806 197208914 1.670000e-32 150.0
19 TraesCS1B01G261100 chr4B 94.505 91 5 0 278 368 290362115 290362205 1.010000e-29 141.0
20 TraesCS1B01G261100 chr7B 90.751 173 12 2 151 319 580609219 580609047 7.510000e-56 228.0
21 TraesCS1B01G261100 chr7B 93.548 155 5 4 4 154 580609264 580609111 2.700000e-55 226.0
22 TraesCS1B01G261100 chr7B 85.345 116 6 11 282 397 535631261 535631157 2.840000e-20 110.0
23 TraesCS1B01G261100 chr4A 92.903 155 6 4 4 154 695236602 695236755 1.260000e-53 220.0
24 TraesCS1B01G261100 chr6D 95.699 93 4 0 277 369 19201402 19201494 1.670000e-32 150.0
25 TraesCS1B01G261100 chr6D 80.672 119 9 14 282 397 291698965 291699072 2.230000e-11 80.5
26 TraesCS1B01G261100 chr2A 86.000 100 9 5 273 372 443988708 443988614 4.750000e-18 102.0
27 TraesCS1B01G261100 chr6B 83.471 121 4 16 278 397 250780592 250780487 6.140000e-17 99.0
28 TraesCS1B01G261100 chr3A 82.759 116 6 14 282 397 747669397 747669498 1.030000e-14 91.6
29 TraesCS1B01G261100 chr3B 100.000 37 0 0 748 784 396348482 396348518 4.820000e-08 69.4


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 TraesCS1B01G261100 chr1B 458725597 458728292 2695 False 1774.333333 4979 96.942000 1 2696 3 chr1B.!!$F1 2695
1 TraesCS1B01G261100 chr1D 342489025 342491320 2295 False 1491.500000 2194 91.809500 445 2696 2 chr1D.!!$F1 2251
2 TraesCS1B01G261100 chr1A 442154405 442156733 2328 False 951.000000 1210 91.101667 438 2694 3 chr1A.!!$F3 2256

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
269 270 0.107017 GGTAGCCTCATGGTGCATGT 60.107 55.0 9.54 0.0 41.98 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2142 0.531753 TGTTCAGTTACGCAGCTGCA 60.532 50.0 36.03 17.26 42.21 4.41 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
75 76 5.526479 GGTTGCTACCTTGGTTATTACTAGC 59.474 44.000 10.33 0.00 41.53 3.42
76 77 5.286267 TGCTACCTTGGTTATTACTAGCC 57.714 43.478 0.00 0.00 0.00 3.93
77 78 4.102054 TGCTACCTTGGTTATTACTAGCCC 59.898 45.833 0.00 0.00 0.00 5.19
78 79 4.347292 GCTACCTTGGTTATTACTAGCCCT 59.653 45.833 0.00 0.00 0.00 5.19
79 80 5.541484 GCTACCTTGGTTATTACTAGCCCTA 59.459 44.000 0.00 0.00 0.00 3.53
80 81 6.042437 GCTACCTTGGTTATTACTAGCCCTAA 59.958 42.308 0.00 0.00 0.00 2.69
81 82 7.256583 GCTACCTTGGTTATTACTAGCCCTAAT 60.257 40.741 0.00 0.00 0.00 1.73
82 83 7.461633 ACCTTGGTTATTACTAGCCCTAATT 57.538 36.000 0.00 0.00 0.00 1.40
83 84 8.571460 ACCTTGGTTATTACTAGCCCTAATTA 57.429 34.615 0.00 0.00 0.00 1.40
84 85 9.006405 ACCTTGGTTATTACTAGCCCTAATTAA 57.994 33.333 0.00 0.00 0.00 1.40
94 95 7.932683 ACTAGCCCTAATTAATTACTCCACT 57.067 36.000 3.71 1.53 0.00 4.00
95 96 8.333226 ACTAGCCCTAATTAATTACTCCACTT 57.667 34.615 3.71 0.00 0.00 3.16
96 97 8.211629 ACTAGCCCTAATTAATTACTCCACTTG 58.788 37.037 3.71 2.69 0.00 3.16
97 98 6.970191 AGCCCTAATTAATTACTCCACTTGT 58.030 36.000 3.71 0.00 0.00 3.16
98 99 7.054751 AGCCCTAATTAATTACTCCACTTGTC 58.945 38.462 3.71 0.00 0.00 3.18
99 100 6.826741 GCCCTAATTAATTACTCCACTTGTCA 59.173 38.462 3.71 0.00 0.00 3.58
100 101 7.502561 GCCCTAATTAATTACTCCACTTGTCAT 59.497 37.037 3.71 0.00 0.00 3.06
133 134 6.947258 AGAAATTTTTGCAAACTACACATGC 58.053 32.000 12.39 0.00 40.45 4.06
134 135 5.671742 AATTTTTGCAAACTACACATGCC 57.328 34.783 12.39 0.00 39.31 4.40
135 136 4.399004 TTTTTGCAAACTACACATGCCT 57.601 36.364 12.39 0.00 39.31 4.75
136 137 3.367992 TTTGCAAACTACACATGCCTG 57.632 42.857 8.05 0.00 39.31 4.85
137 138 0.597568 TGCAAACTACACATGCCTGC 59.402 50.000 0.00 0.00 39.31 4.85
138 139 0.597568 GCAAACTACACATGCCTGCA 59.402 50.000 0.00 0.00 34.03 4.41
139 140 1.000385 GCAAACTACACATGCCTGCAA 60.000 47.619 0.00 0.00 34.03 4.08
140 141 2.353011 GCAAACTACACATGCCTGCAAT 60.353 45.455 0.00 0.00 34.03 3.56
141 142 3.119531 GCAAACTACACATGCCTGCAATA 60.120 43.478 0.00 0.00 34.03 1.90
142 143 4.617995 GCAAACTACACATGCCTGCAATAA 60.618 41.667 0.00 0.00 34.03 1.40
143 144 4.970662 AACTACACATGCCTGCAATAAG 57.029 40.909 0.00 0.00 0.00 1.73
144 145 4.220693 ACTACACATGCCTGCAATAAGA 57.779 40.909 0.00 0.00 0.00 2.10
145 146 4.194640 ACTACACATGCCTGCAATAAGAG 58.805 43.478 0.00 0.00 0.00 2.85
146 147 3.354948 ACACATGCCTGCAATAAGAGA 57.645 42.857 0.00 0.00 0.00 3.10
147 148 3.276857 ACACATGCCTGCAATAAGAGAG 58.723 45.455 0.00 0.00 0.00 3.20
148 149 2.033049 CACATGCCTGCAATAAGAGAGC 59.967 50.000 0.00 0.00 0.00 4.09
149 150 1.263484 CATGCCTGCAATAAGAGAGCG 59.737 52.381 0.00 0.00 0.00 5.03
150 151 0.462581 TGCCTGCAATAAGAGAGCGG 60.463 55.000 0.00 0.00 0.00 5.52
151 152 0.462759 GCCTGCAATAAGAGAGCGGT 60.463 55.000 0.00 0.00 32.85 5.68
152 153 1.202533 GCCTGCAATAAGAGAGCGGTA 60.203 52.381 0.00 0.00 32.85 4.02
153 154 2.748605 CCTGCAATAAGAGAGCGGTAG 58.251 52.381 0.00 0.00 32.85 3.18
154 155 2.101582 CCTGCAATAAGAGAGCGGTAGT 59.898 50.000 0.00 0.00 32.85 2.73
155 156 3.430929 CCTGCAATAAGAGAGCGGTAGTT 60.431 47.826 0.00 0.00 32.85 2.24
156 157 3.521560 TGCAATAAGAGAGCGGTAGTTG 58.478 45.455 0.00 0.00 0.00 3.16
157 158 2.285488 GCAATAAGAGAGCGGTAGTTGC 59.715 50.000 0.00 0.00 34.71 4.17
159 160 4.736759 GCAATAAGAGAGCGGTAGTTGCTA 60.737 45.833 0.00 0.00 44.18 3.49
160 161 2.943449 AAGAGAGCGGTAGTTGCTAC 57.057 50.000 0.00 0.00 44.18 3.58
175 176 8.868635 GTAGTTGCTACCTTGGTTATTACTAG 57.131 38.462 0.00 0.00 31.38 2.57
176 177 6.346896 AGTTGCTACCTTGGTTATTACTAGC 58.653 40.000 0.00 0.00 0.00 3.42
177 178 5.286267 TGCTACCTTGGTTATTACTAGCC 57.714 43.478 0.00 0.00 0.00 3.93
178 179 4.102054 TGCTACCTTGGTTATTACTAGCCC 59.898 45.833 0.00 0.00 0.00 5.19
179 180 4.347292 GCTACCTTGGTTATTACTAGCCCT 59.653 45.833 0.00 0.00 0.00 5.19
180 181 5.541484 GCTACCTTGGTTATTACTAGCCCTA 59.459 44.000 0.00 0.00 0.00 3.53
181 182 6.042437 GCTACCTTGGTTATTACTAGCCCTAA 59.958 42.308 0.00 0.00 0.00 2.69
182 183 7.256583 GCTACCTTGGTTATTACTAGCCCTAAT 60.257 40.741 0.00 0.00 0.00 1.73
183 184 7.461633 ACCTTGGTTATTACTAGCCCTAATT 57.538 36.000 0.00 0.00 0.00 1.40
184 185 8.571460 ACCTTGGTTATTACTAGCCCTAATTA 57.429 34.615 0.00 0.00 0.00 1.40
185 186 9.006405 ACCTTGGTTATTACTAGCCCTAATTAA 57.994 33.333 0.00 0.00 0.00 1.40
194 195 9.631056 ATTACTAGCCCTAATTAATTACTCCCT 57.369 33.333 3.71 2.14 0.00 4.20
195 196 7.949468 ACTAGCCCTAATTAATTACTCCCTT 57.051 36.000 3.71 0.00 0.00 3.95
196 197 8.346247 ACTAGCCCTAATTAATTACTCCCTTT 57.654 34.615 3.71 0.00 0.00 3.11
197 198 8.218488 ACTAGCCCTAATTAATTACTCCCTTTG 58.782 37.037 3.71 0.00 0.00 2.77
198 199 6.981737 AGCCCTAATTAATTACTCCCTTTGT 58.018 36.000 3.71 0.00 0.00 2.83
199 200 7.061054 AGCCCTAATTAATTACTCCCTTTGTC 58.939 38.462 3.71 0.00 0.00 3.18
200 201 6.831868 GCCCTAATTAATTACTCCCTTTGTCA 59.168 38.462 3.71 0.00 0.00 3.58
201 202 7.505923 GCCCTAATTAATTACTCCCTTTGTCAT 59.494 37.037 3.71 0.00 0.00 3.06
231 232 9.973450 TTATAAGAAATTTTTGCAAGCTACACA 57.027 25.926 0.00 0.00 0.00 3.72
233 234 6.774354 AGAAATTTTTGCAAGCTACACATG 57.226 33.333 0.00 0.00 0.00 3.21
234 235 4.996062 AATTTTTGCAAGCTACACATGC 57.004 36.364 0.00 0.21 40.45 4.06
235 236 2.437200 TTTTGCAAGCTACACATGCC 57.563 45.000 0.00 0.00 39.31 4.40
236 237 1.619654 TTTGCAAGCTACACATGCCT 58.380 45.000 0.00 0.00 39.31 4.75
237 238 0.883153 TTGCAAGCTACACATGCCTG 59.117 50.000 4.93 0.00 39.31 4.85
238 239 1.138247 GCAAGCTACACATGCCTGC 59.862 57.895 0.00 0.00 40.05 4.85
239 240 1.588824 GCAAGCTACACATGCCTGCA 61.589 55.000 4.69 0.00 44.52 4.41
240 241 0.883153 CAAGCTACACATGCCTGCAA 59.117 50.000 0.00 0.00 0.00 4.08
241 242 1.475280 CAAGCTACACATGCCTGCAAT 59.525 47.619 0.00 0.00 0.00 3.56
242 243 2.684374 CAAGCTACACATGCCTGCAATA 59.316 45.455 0.00 0.00 0.00 1.90
243 244 3.003394 AGCTACACATGCCTGCAATAA 57.997 42.857 0.00 0.00 0.00 1.40
244 245 2.947652 AGCTACACATGCCTGCAATAAG 59.052 45.455 0.00 0.00 0.00 1.73
245 246 2.945008 GCTACACATGCCTGCAATAAGA 59.055 45.455 0.00 0.00 0.00 2.10
246 247 3.003068 GCTACACATGCCTGCAATAAGAG 59.997 47.826 0.00 0.00 0.00 2.85
247 248 3.354948 ACACATGCCTGCAATAAGAGA 57.645 42.857 0.00 0.00 0.00 3.10
248 249 3.276857 ACACATGCCTGCAATAAGAGAG 58.723 45.455 0.00 0.00 0.00 3.20
249 250 2.033049 CACATGCCTGCAATAAGAGAGC 59.967 50.000 0.00 0.00 0.00 4.09
250 251 1.263484 CATGCCTGCAATAAGAGAGCG 59.737 52.381 0.00 0.00 0.00 5.03
251 252 0.462581 TGCCTGCAATAAGAGAGCGG 60.463 55.000 0.00 0.00 0.00 5.52
252 253 0.462759 GCCTGCAATAAGAGAGCGGT 60.463 55.000 0.00 0.00 32.85 5.68
253 254 1.202533 GCCTGCAATAAGAGAGCGGTA 60.203 52.381 0.00 0.00 32.85 4.02
254 255 2.748605 CCTGCAATAAGAGAGCGGTAG 58.251 52.381 0.00 0.00 32.85 3.18
255 256 2.131183 CTGCAATAAGAGAGCGGTAGC 58.869 52.381 0.00 0.00 45.58 3.58
256 257 1.202533 TGCAATAAGAGAGCGGTAGCC 60.203 52.381 0.00 0.00 46.67 3.93
257 258 1.069358 GCAATAAGAGAGCGGTAGCCT 59.931 52.381 0.00 0.00 46.67 4.58
258 259 2.864489 GCAATAAGAGAGCGGTAGCCTC 60.864 54.545 0.00 0.00 46.67 4.70
259 260 2.362397 CAATAAGAGAGCGGTAGCCTCA 59.638 50.000 11.39 0.00 46.67 3.86
260 261 2.366640 TAAGAGAGCGGTAGCCTCAT 57.633 50.000 11.39 0.00 46.67 2.90
261 262 0.749649 AAGAGAGCGGTAGCCTCATG 59.250 55.000 11.39 0.00 46.67 3.07
262 263 1.112315 AGAGAGCGGTAGCCTCATGG 61.112 60.000 11.39 0.00 46.67 3.66
263 264 1.381872 AGAGCGGTAGCCTCATGGT 60.382 57.895 11.39 0.00 46.67 3.55
264 265 1.227380 GAGCGGTAGCCTCATGGTG 60.227 63.158 0.00 0.00 46.67 4.17
265 266 2.897350 GCGGTAGCCTCATGGTGC 60.897 66.667 0.00 0.00 37.42 5.01
266 267 2.584064 CGGTAGCCTCATGGTGCA 59.416 61.111 9.54 0.00 35.27 4.57
267 268 1.146930 CGGTAGCCTCATGGTGCAT 59.853 57.895 9.54 0.00 35.27 3.96
268 269 1.162181 CGGTAGCCTCATGGTGCATG 61.162 60.000 9.54 0.00 42.60 4.06
269 270 0.107017 GGTAGCCTCATGGTGCATGT 60.107 55.000 9.54 0.00 41.98 3.21
270 271 1.140852 GGTAGCCTCATGGTGCATGTA 59.859 52.381 9.54 0.00 41.98 2.29
271 272 2.421388 GGTAGCCTCATGGTGCATGTAA 60.421 50.000 9.54 0.00 41.98 2.41
272 273 2.512692 AGCCTCATGGTGCATGTAAA 57.487 45.000 9.54 0.00 41.98 2.01
273 274 2.806434 AGCCTCATGGTGCATGTAAAA 58.194 42.857 9.54 0.00 41.98 1.52
274 275 2.756760 AGCCTCATGGTGCATGTAAAAG 59.243 45.455 9.54 0.00 41.98 2.27
275 276 2.493278 GCCTCATGGTGCATGTAAAAGT 59.507 45.455 0.00 0.00 41.98 2.66
276 277 3.674138 GCCTCATGGTGCATGTAAAAGTG 60.674 47.826 0.00 0.00 41.98 3.16
277 278 3.507233 CCTCATGGTGCATGTAAAAGTGT 59.493 43.478 0.00 0.00 41.98 3.55
278 279 4.022068 CCTCATGGTGCATGTAAAAGTGTT 60.022 41.667 0.00 0.00 41.98 3.32
279 280 5.509501 CCTCATGGTGCATGTAAAAGTGTTT 60.510 40.000 0.00 0.00 41.98 2.83
280 281 5.288015 TCATGGTGCATGTAAAAGTGTTTG 58.712 37.500 0.00 0.00 41.98 2.93
281 282 4.727507 TGGTGCATGTAAAAGTGTTTGT 57.272 36.364 0.00 0.00 0.00 2.83
282 283 5.078411 TGGTGCATGTAAAAGTGTTTGTT 57.922 34.783 0.00 0.00 0.00 2.83
283 284 5.482908 TGGTGCATGTAAAAGTGTTTGTTT 58.517 33.333 0.00 0.00 0.00 2.83
284 285 5.578727 TGGTGCATGTAAAAGTGTTTGTTTC 59.421 36.000 0.00 0.00 0.00 2.78
285 286 5.810074 GGTGCATGTAAAAGTGTTTGTTTCT 59.190 36.000 0.00 0.00 0.00 2.52
286 287 6.019881 GGTGCATGTAAAAGTGTTTGTTTCTC 60.020 38.462 0.00 0.00 0.00 2.87
287 288 6.019881 GTGCATGTAAAAGTGTTTGTTTCTCC 60.020 38.462 0.00 0.00 0.00 3.71
288 289 5.462068 GCATGTAAAAGTGTTTGTTTCTCCC 59.538 40.000 0.00 0.00 0.00 4.30
289 290 5.238006 TGTAAAAGTGTTTGTTTCTCCCG 57.762 39.130 0.00 0.00 0.00 5.14
290 291 4.701171 TGTAAAAGTGTTTGTTTCTCCCGT 59.299 37.500 0.00 0.00 0.00 5.28
291 292 4.794278 AAAAGTGTTTGTTTCTCCCGTT 57.206 36.364 0.00 0.00 0.00 4.44
292 293 3.775661 AAGTGTTTGTTTCTCCCGTTG 57.224 42.857 0.00 0.00 0.00 4.10
293 294 1.404035 AGTGTTTGTTTCTCCCGTTGC 59.596 47.619 0.00 0.00 0.00 4.17
294 295 1.133407 GTGTTTGTTTCTCCCGTTGCA 59.867 47.619 0.00 0.00 0.00 4.08
295 296 1.819288 TGTTTGTTTCTCCCGTTGCAA 59.181 42.857 0.00 0.00 0.00 4.08
296 297 2.190161 GTTTGTTTCTCCCGTTGCAAC 58.810 47.619 19.89 19.89 0.00 4.17
306 307 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
307 308 2.669910 TTGCAACGCACGGGCATA 60.670 55.556 11.77 0.00 38.71 3.14
308 309 2.043405 TTGCAACGCACGGGCATAT 61.043 52.632 11.77 0.00 38.71 1.78
309 310 1.590610 TTGCAACGCACGGGCATATT 61.591 50.000 11.77 0.00 38.71 1.28
310 311 1.298339 GCAACGCACGGGCATATTC 60.298 57.895 11.77 0.00 41.24 1.75
311 312 1.355210 CAACGCACGGGCATATTCC 59.645 57.895 11.77 0.00 41.24 3.01
312 313 1.822186 AACGCACGGGCATATTCCC 60.822 57.895 11.77 0.00 43.02 3.97
313 314 2.111043 CGCACGGGCATATTCCCT 59.889 61.111 11.77 0.00 44.30 4.20
314 315 1.369692 CGCACGGGCATATTCCCTA 59.630 57.895 11.77 0.00 44.30 3.53
315 316 0.250124 CGCACGGGCATATTCCCTAA 60.250 55.000 11.77 0.00 44.30 2.69
316 317 1.610624 CGCACGGGCATATTCCCTAAT 60.611 52.381 11.77 0.00 44.30 1.73
317 318 2.354303 CGCACGGGCATATTCCCTAATA 60.354 50.000 11.77 0.00 44.30 0.98
318 319 3.681594 CGCACGGGCATATTCCCTAATAT 60.682 47.826 11.77 0.00 44.30 1.28
319 320 4.442332 CGCACGGGCATATTCCCTAATATA 60.442 45.833 11.77 0.00 44.30 0.86
320 321 5.621193 GCACGGGCATATTCCCTAATATAT 58.379 41.667 3.77 0.00 44.30 0.86
321 322 6.517697 CGCACGGGCATATTCCCTAATATATA 60.518 42.308 11.77 0.00 44.30 0.86
322 323 7.394816 GCACGGGCATATTCCCTAATATATAT 58.605 38.462 3.77 0.00 44.30 0.86
323 324 8.537016 GCACGGGCATATTCCCTAATATATATA 58.463 37.037 3.77 0.00 44.30 0.86
422 423 3.535280 AGGAGAAATCCTCTTTCGCTC 57.465 47.619 0.00 0.00 41.66 5.03
423 424 2.834549 AGGAGAAATCCTCTTTCGCTCA 59.165 45.455 0.00 0.00 41.66 4.26
424 425 3.261897 AGGAGAAATCCTCTTTCGCTCAA 59.738 43.478 0.00 0.00 41.66 3.02
425 426 4.003648 GGAGAAATCCTCTTTCGCTCAAA 58.996 43.478 0.00 0.00 41.66 2.69
426 427 4.455877 GGAGAAATCCTCTTTCGCTCAAAA 59.544 41.667 0.00 0.00 41.66 2.44
427 428 5.048713 GGAGAAATCCTCTTTCGCTCAAAAA 60.049 40.000 0.00 0.00 41.66 1.94
459 460 8.918961 TTTGTTTTGTGTTAAAGTGTCCATAG 57.081 30.769 0.00 0.00 0.00 2.23
462 463 8.908903 TGTTTTGTGTTAAAGTGTCCATAGAAT 58.091 29.630 0.00 0.00 0.00 2.40
463 464 9.180678 GTTTTGTGTTAAAGTGTCCATAGAATG 57.819 33.333 0.00 0.00 0.00 2.67
464 465 8.458573 TTTGTGTTAAAGTGTCCATAGAATGT 57.541 30.769 0.00 0.00 0.00 2.71
497 498 4.642437 TGTGGTCAATTGCTAAGTTGTCAA 59.358 37.500 0.00 0.00 0.00 3.18
500 501 6.198966 GTGGTCAATTGCTAAGTTGTCAAAAG 59.801 38.462 0.00 0.00 0.00 2.27
501 502 5.691754 GGTCAATTGCTAAGTTGTCAAAAGG 59.308 40.000 0.00 0.00 0.00 3.11
502 503 6.273071 GTCAATTGCTAAGTTGTCAAAAGGT 58.727 36.000 0.00 0.00 0.00 3.50
504 505 6.756074 TCAATTGCTAAGTTGTCAAAAGGTTG 59.244 34.615 0.00 0.00 35.95 3.77
507 508 5.406649 TGCTAAGTTGTCAAAAGGTTGTTG 58.593 37.500 0.00 0.00 36.07 3.33
508 509 5.047660 TGCTAAGTTGTCAAAAGGTTGTTGT 60.048 36.000 0.00 0.00 36.07 3.32
511 512 6.538189 AAGTTGTCAAAAGGTTGTTGTTTG 57.462 33.333 0.00 0.00 36.07 2.93
512 513 5.848406 AGTTGTCAAAAGGTTGTTGTTTGA 58.152 33.333 0.00 0.00 38.57 2.69
513 514 6.463360 AGTTGTCAAAAGGTTGTTGTTTGAT 58.537 32.000 1.80 0.00 41.77 2.57
514 515 7.607250 AGTTGTCAAAAGGTTGTTGTTTGATA 58.393 30.769 1.80 0.00 41.77 2.15
523 528 6.790319 AGGTTGTTGTTTGATACTAATCCCT 58.210 36.000 0.00 0.00 0.00 4.20
525 530 8.387813 AGGTTGTTGTTTGATACTAATCCCTTA 58.612 33.333 0.00 0.00 0.00 2.69
602 613 1.308783 GCCGAGCAAGAGGGAAAAGG 61.309 60.000 0.00 0.00 0.00 3.11
683 694 2.813754 TCACCTGCCGAAGAAAAGAATG 59.186 45.455 0.00 0.00 0.00 2.67
689 700 2.162681 CCGAAGAAAAGAATGCCTGGT 58.837 47.619 0.00 0.00 0.00 4.00
703 714 2.525629 TGGTCCCGTGCAAGGAGA 60.526 61.111 21.23 12.57 32.84 3.71
704 715 2.266055 GGTCCCGTGCAAGGAGAG 59.734 66.667 21.23 3.52 32.84 3.20
705 716 2.266055 GTCCCGTGCAAGGAGAGG 59.734 66.667 21.23 3.13 32.84 3.69
706 717 2.119611 TCCCGTGCAAGGAGAGGA 59.880 61.111 21.23 5.73 0.00 3.71
707 718 1.984570 TCCCGTGCAAGGAGAGGAG 60.985 63.158 21.23 1.94 0.00 3.69
796 815 4.458989 TGCAAAGAAACGGCAGAATATCTT 59.541 37.500 0.00 0.00 32.95 2.40
813 832 0.662619 CTTTGGCTTCTTCGTGTGCA 59.337 50.000 0.00 0.00 0.00 4.57
826 845 1.012841 GTGTGCATCTCTTAGCTGCC 58.987 55.000 0.00 0.00 36.59 4.85
827 846 0.907486 TGTGCATCTCTTAGCTGCCT 59.093 50.000 0.00 0.00 36.59 4.75
828 847 1.134580 TGTGCATCTCTTAGCTGCCTC 60.135 52.381 0.00 0.00 36.59 4.70
838 857 1.198759 TAGCTGCCTCCCGACCTTTT 61.199 55.000 0.00 0.00 0.00 2.27
857 876 6.622833 CTTTTCACCAAAGGAATGCATTTT 57.377 33.333 14.33 1.55 38.67 1.82
866 885 0.109319 GAATGCATTTTCCGTGGCGT 60.109 50.000 14.33 0.00 0.00 5.68
875 894 5.793457 GCATTTTCCGTGGCGTTTATATATC 59.207 40.000 0.00 0.00 0.00 1.63
896 915 1.301716 GCCGATCACCACGCCATAT 60.302 57.895 0.00 0.00 0.00 1.78
910 929 1.811558 GCCATATCAGCACACCACGAT 60.812 52.381 0.00 0.00 0.00 3.73
916 935 2.509336 GCACACCACGATCGGAGG 60.509 66.667 20.98 21.86 0.00 4.30
917 936 3.001902 GCACACCACGATCGGAGGA 62.002 63.158 28.49 0.00 0.00 3.71
949 968 2.734723 GCGAGCTGAGCACACGAA 60.735 61.111 18.80 0.00 34.19 3.85
979 998 2.796383 GCGCATCTATCTCGTGTTCAGT 60.796 50.000 0.30 0.00 0.00 3.41
984 1003 5.734786 GCATCTATCTCGTGTTCAGTAGCTT 60.735 44.000 0.00 0.00 0.00 3.74
1203 1258 3.057596 ACGGTATGTTTGATTTGCTGTGG 60.058 43.478 0.00 0.00 0.00 4.17
1339 1394 1.893062 CATCTCCACCTCGCTCACA 59.107 57.895 0.00 0.00 0.00 3.58
1440 1495 4.181010 CCTCGCCATGGGACTGGG 62.181 72.222 15.13 3.51 36.75 4.45
1493 1548 1.593006 CGAGCCTGGTAATTAAGCACG 59.407 52.381 0.00 0.00 0.00 5.34
1519 1574 5.808042 AAATCAATGGAGAATCTGTCGTG 57.192 39.130 0.00 0.00 33.73 4.35
1534 1589 1.272490 GTCGTGTCCATCTCTTGTCCA 59.728 52.381 0.00 0.00 0.00 4.02
1559 1614 2.353607 CCTAGCTAACGCGGCTCG 60.354 66.667 12.47 5.69 42.32 5.03
1678 1735 0.174845 CGTTCAGACGCCTATGGGAA 59.825 55.000 0.00 0.00 43.03 3.97
1707 1767 2.648102 GTCTGATCGGTCGACGCG 60.648 66.667 17.01 17.01 43.86 6.01
1778 1847 4.075682 TGACAAGGATTATTGGTTTGCGA 58.924 39.130 0.00 0.00 34.36 5.10
1779 1848 4.155826 TGACAAGGATTATTGGTTTGCGAG 59.844 41.667 0.00 0.00 34.36 5.03
1780 1849 4.079253 ACAAGGATTATTGGTTTGCGAGT 58.921 39.130 0.00 0.00 34.36 4.18
1781 1850 4.082787 ACAAGGATTATTGGTTTGCGAGTG 60.083 41.667 0.00 0.00 34.36 3.51
1782 1851 2.423538 AGGATTATTGGTTTGCGAGTGC 59.576 45.455 0.00 0.00 43.20 4.40
1793 1862 3.756677 CGAGTGCGTGCGTGAGTG 61.757 66.667 0.00 0.00 0.00 3.51
1794 1863 4.064491 GAGTGCGTGCGTGAGTGC 62.064 66.667 0.00 0.00 0.00 4.40
1818 1887 4.328712 GTGTGTGCGTGTGATGTGAATATA 59.671 41.667 0.00 0.00 0.00 0.86
1819 1888 5.006649 GTGTGTGCGTGTGATGTGAATATAT 59.993 40.000 0.00 0.00 0.00 0.86
1838 1907 9.698309 GAATATATGCGGATTATATGTGCTACT 57.302 33.333 0.00 0.00 0.00 2.57
1840 1909 3.325870 TGCGGATTATATGTGCTACTGC 58.674 45.455 0.00 0.00 40.20 4.40
1850 1919 2.813908 GCTACTGCGTCGGGGTTG 60.814 66.667 0.00 0.00 0.00 3.77
1858 1927 2.833957 GTCGGGGTTGTCAGGGTT 59.166 61.111 0.00 0.00 0.00 4.11
1878 1947 2.977456 TGTGCGCTTGCGGTGAAT 60.977 55.556 16.79 0.00 43.34 2.57
1906 1976 1.964373 GCCGGTGGTTGTGACGATT 60.964 57.895 1.90 0.00 0.00 3.34
1913 1983 4.201647 CGGTGGTTGTGACGATTACATAAC 60.202 45.833 0.00 0.00 38.17 1.89
1960 2034 1.832608 TGGGACTGTCGCACTCTGT 60.833 57.895 21.76 0.00 34.23 3.41
1988 2062 8.967218 CAAAATCTGGCAAATATATAACGTTGG 58.033 33.333 11.99 0.00 0.00 3.77
2085 2160 0.798776 ATGCAGCTGCGTAACTGAAC 59.201 50.000 31.61 2.47 45.83 3.18
2094 2169 2.288213 TGCGTAACTGAACAGAGACAGG 60.288 50.000 8.87 0.00 38.30 4.00
2119 2238 4.924305 AGCAGAGCTTTCACAAATTCAA 57.076 36.364 0.00 0.00 33.89 2.69
2122 2241 6.108015 AGCAGAGCTTTCACAAATTCAAAAA 58.892 32.000 0.00 0.00 33.89 1.94
2159 2280 1.788258 TGAGACAAAGAAGCAGCTCG 58.212 50.000 0.00 0.00 0.00 5.03
2160 2281 1.069204 TGAGACAAAGAAGCAGCTCGT 59.931 47.619 0.00 0.00 0.00 4.18
2161 2282 2.296190 TGAGACAAAGAAGCAGCTCGTA 59.704 45.455 0.00 0.00 0.00 3.43
2162 2283 2.664085 GAGACAAAGAAGCAGCTCGTAC 59.336 50.000 0.00 0.00 0.00 3.67
2163 2284 1.387084 GACAAAGAAGCAGCTCGTACG 59.613 52.381 9.53 9.53 0.00 3.67
2165 2286 2.030540 ACAAAGAAGCAGCTCGTACGTA 60.031 45.455 16.05 0.00 0.00 3.57
2166 2287 2.259505 AAGAAGCAGCTCGTACGTAC 57.740 50.000 15.90 15.90 0.00 3.67
2174 2354 0.643820 GCTCGTACGTACAATGTGGC 59.356 55.000 24.50 14.03 0.00 5.01
2196 2377 2.359975 CCAGTCGGAGGCCCAAAC 60.360 66.667 0.00 0.00 0.00 2.93
2407 2588 1.520564 CGCGCCACACAGCCTATTA 60.521 57.895 0.00 0.00 0.00 0.98
2408 2589 1.762222 CGCGCCACACAGCCTATTAC 61.762 60.000 0.00 0.00 0.00 1.89
2425 2606 9.640963 AGCCTATTACTATCAAAGTTATAAGCG 57.359 33.333 0.00 0.00 40.04 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.091537 TAGCAACCTACGGCAATTGC 58.908 50.000 22.47 22.47 46.21 3.56
40 41 1.400494 GGTAGCAACCTACGGCAATTG 59.600 52.381 0.00 0.00 43.95 2.32
41 42 1.746470 GGTAGCAACCTACGGCAATT 58.254 50.000 0.00 0.00 43.95 2.32
42 43 3.471354 GGTAGCAACCTACGGCAAT 57.529 52.632 0.00 0.00 43.95 3.56
52 53 5.526479 GGCTAGTAATAACCAAGGTAGCAAC 59.474 44.000 9.39 0.12 0.00 4.17
53 54 5.397109 GGGCTAGTAATAACCAAGGTAGCAA 60.397 44.000 9.39 0.00 0.00 3.91
54 55 4.102054 GGGCTAGTAATAACCAAGGTAGCA 59.898 45.833 9.39 0.00 0.00 3.49
55 56 4.347292 AGGGCTAGTAATAACCAAGGTAGC 59.653 45.833 0.00 0.00 0.00 3.58
56 57 7.607615 TTAGGGCTAGTAATAACCAAGGTAG 57.392 40.000 0.00 0.00 0.00 3.18
57 58 8.571460 AATTAGGGCTAGTAATAACCAAGGTA 57.429 34.615 0.00 0.00 0.00 3.08
58 59 7.461633 AATTAGGGCTAGTAATAACCAAGGT 57.538 36.000 0.00 0.00 0.00 3.50
68 69 9.443365 AGTGGAGTAATTAATTAGGGCTAGTAA 57.557 33.333 8.18 0.00 0.00 2.24
69 70 9.443365 AAGTGGAGTAATTAATTAGGGCTAGTA 57.557 33.333 8.18 0.00 0.00 1.82
70 71 7.932683 AGTGGAGTAATTAATTAGGGCTAGT 57.067 36.000 8.18 0.33 0.00 2.57
71 72 8.211629 ACAAGTGGAGTAATTAATTAGGGCTAG 58.788 37.037 8.18 0.00 0.00 3.42
72 73 8.097791 ACAAGTGGAGTAATTAATTAGGGCTA 57.902 34.615 8.18 0.00 0.00 3.93
73 74 6.970191 ACAAGTGGAGTAATTAATTAGGGCT 58.030 36.000 8.18 2.69 0.00 5.19
74 75 6.826741 TGACAAGTGGAGTAATTAATTAGGGC 59.173 38.462 8.18 1.58 0.00 5.19
75 76 8.980481 ATGACAAGTGGAGTAATTAATTAGGG 57.020 34.615 8.18 0.00 0.00 3.53
107 108 8.547069 GCATGTGTAGTTTGCAAAAATTTCTTA 58.453 29.630 14.67 0.00 36.40 2.10
108 109 7.408910 GCATGTGTAGTTTGCAAAAATTTCTT 58.591 30.769 14.67 1.15 36.40 2.52
109 110 6.018016 GGCATGTGTAGTTTGCAAAAATTTCT 60.018 34.615 14.67 8.91 38.12 2.52
110 111 6.018016 AGGCATGTGTAGTTTGCAAAAATTTC 60.018 34.615 14.67 0.55 38.12 2.17
111 112 5.821995 AGGCATGTGTAGTTTGCAAAAATTT 59.178 32.000 14.67 2.86 38.12 1.82
112 113 5.236911 CAGGCATGTGTAGTTTGCAAAAATT 59.763 36.000 14.67 5.43 38.12 1.82
113 114 4.751098 CAGGCATGTGTAGTTTGCAAAAAT 59.249 37.500 14.67 8.40 38.12 1.82
114 115 4.118410 CAGGCATGTGTAGTTTGCAAAAA 58.882 39.130 14.67 2.08 38.12 1.94
115 116 3.715495 CAGGCATGTGTAGTTTGCAAAA 58.285 40.909 14.67 0.00 38.12 2.44
116 117 2.545532 GCAGGCATGTGTAGTTTGCAAA 60.546 45.455 8.05 8.05 38.12 3.68
117 118 1.000385 GCAGGCATGTGTAGTTTGCAA 60.000 47.619 0.00 0.00 38.12 4.08
118 119 0.597568 GCAGGCATGTGTAGTTTGCA 59.402 50.000 0.00 0.00 38.12 4.08
119 120 0.597568 TGCAGGCATGTGTAGTTTGC 59.402 50.000 0.00 0.00 35.64 3.68
120 121 3.581024 ATTGCAGGCATGTGTAGTTTG 57.419 42.857 0.00 0.00 0.00 2.93
121 122 5.009631 TCTTATTGCAGGCATGTGTAGTTT 58.990 37.500 0.00 0.00 0.00 2.66
122 123 4.588899 TCTTATTGCAGGCATGTGTAGTT 58.411 39.130 0.00 0.00 0.00 2.24
123 124 4.080919 TCTCTTATTGCAGGCATGTGTAGT 60.081 41.667 0.00 0.00 0.00 2.73
124 125 4.445453 TCTCTTATTGCAGGCATGTGTAG 58.555 43.478 0.00 0.00 0.00 2.74
125 126 4.445453 CTCTCTTATTGCAGGCATGTGTA 58.555 43.478 0.00 0.00 0.00 2.90
126 127 3.276857 CTCTCTTATTGCAGGCATGTGT 58.723 45.455 0.00 0.00 0.00 3.72
127 128 2.033049 GCTCTCTTATTGCAGGCATGTG 59.967 50.000 0.00 0.00 0.00 3.21
128 129 2.295885 GCTCTCTTATTGCAGGCATGT 58.704 47.619 0.00 0.00 0.00 3.21
129 130 1.263484 CGCTCTCTTATTGCAGGCATG 59.737 52.381 0.00 0.00 0.00 4.06
130 131 1.590932 CGCTCTCTTATTGCAGGCAT 58.409 50.000 0.00 0.00 0.00 4.40
131 132 0.462581 CCGCTCTCTTATTGCAGGCA 60.463 55.000 0.00 0.00 0.00 4.75
132 133 0.462759 ACCGCTCTCTTATTGCAGGC 60.463 55.000 0.00 0.00 0.00 4.85
133 134 2.101582 ACTACCGCTCTCTTATTGCAGG 59.898 50.000 0.00 0.00 0.00 4.85
134 135 3.444703 ACTACCGCTCTCTTATTGCAG 57.555 47.619 0.00 0.00 0.00 4.41
135 136 3.521560 CAACTACCGCTCTCTTATTGCA 58.478 45.455 0.00 0.00 0.00 4.08
136 137 2.285488 GCAACTACCGCTCTCTTATTGC 59.715 50.000 0.00 0.00 34.98 3.56
137 138 3.786635 AGCAACTACCGCTCTCTTATTG 58.213 45.455 0.00 0.00 33.35 1.90
138 139 4.202131 GGTAGCAACTACCGCTCTCTTATT 60.202 45.833 7.99 0.00 45.49 1.40
139 140 3.318557 GGTAGCAACTACCGCTCTCTTAT 59.681 47.826 7.99 0.00 45.49 1.73
140 141 2.686915 GGTAGCAACTACCGCTCTCTTA 59.313 50.000 7.99 0.00 45.49 2.10
141 142 1.477295 GGTAGCAACTACCGCTCTCTT 59.523 52.381 7.99 0.00 45.49 2.85
142 143 1.104630 GGTAGCAACTACCGCTCTCT 58.895 55.000 7.99 0.00 45.49 3.10
143 144 3.644774 GGTAGCAACTACCGCTCTC 57.355 57.895 7.99 0.00 45.49 3.20
150 151 7.437565 GCTAGTAATAACCAAGGTAGCAACTAC 59.562 40.741 0.00 0.00 36.33 2.73
151 152 7.418254 GGCTAGTAATAACCAAGGTAGCAACTA 60.418 40.741 9.39 7.07 0.00 2.24
152 153 6.346896 GCTAGTAATAACCAAGGTAGCAACT 58.653 40.000 0.00 0.00 0.00 3.16
153 154 5.526479 GGCTAGTAATAACCAAGGTAGCAAC 59.474 44.000 9.39 0.12 0.00 4.17
154 155 5.397109 GGGCTAGTAATAACCAAGGTAGCAA 60.397 44.000 9.39 0.00 0.00 3.91
155 156 4.102054 GGGCTAGTAATAACCAAGGTAGCA 59.898 45.833 9.39 0.00 0.00 3.49
156 157 4.347292 AGGGCTAGTAATAACCAAGGTAGC 59.653 45.833 0.00 0.00 0.00 3.58
157 158 7.607615 TTAGGGCTAGTAATAACCAAGGTAG 57.392 40.000 0.00 0.00 0.00 3.18
158 159 8.571460 AATTAGGGCTAGTAATAACCAAGGTA 57.429 34.615 0.00 0.00 0.00 3.08
159 160 7.461633 AATTAGGGCTAGTAATAACCAAGGT 57.538 36.000 0.00 0.00 0.00 3.50
168 169 9.631056 AGGGAGTAATTAATTAGGGCTAGTAAT 57.369 33.333 8.18 0.00 0.00 1.89
169 170 9.456459 AAGGGAGTAATTAATTAGGGCTAGTAA 57.544 33.333 8.18 0.00 0.00 2.24
170 171 9.456459 AAAGGGAGTAATTAATTAGGGCTAGTA 57.544 33.333 8.18 0.00 0.00 1.82
171 172 7.949468 AAGGGAGTAATTAATTAGGGCTAGT 57.051 36.000 8.18 0.00 0.00 2.57
172 173 8.218488 ACAAAGGGAGTAATTAATTAGGGCTAG 58.782 37.037 8.18 0.00 0.00 3.42
173 174 8.109560 ACAAAGGGAGTAATTAATTAGGGCTA 57.890 34.615 8.18 0.00 0.00 3.93
174 175 6.981737 ACAAAGGGAGTAATTAATTAGGGCT 58.018 36.000 8.18 2.69 0.00 5.19
175 176 6.831868 TGACAAAGGGAGTAATTAATTAGGGC 59.168 38.462 8.18 1.58 0.00 5.19
176 177 8.996651 ATGACAAAGGGAGTAATTAATTAGGG 57.003 34.615 8.18 0.00 0.00 3.53
205 206 9.973450 TGTGTAGCTTGCAAAAATTTCTTATAA 57.027 25.926 0.00 0.00 0.00 0.98
207 208 8.928733 CATGTGTAGCTTGCAAAAATTTCTTAT 58.071 29.630 0.00 0.00 0.00 1.73
208 209 7.095691 GCATGTGTAGCTTGCAAAAATTTCTTA 60.096 33.333 0.00 0.00 44.67 2.10
209 210 6.293027 GCATGTGTAGCTTGCAAAAATTTCTT 60.293 34.615 0.00 0.00 44.67 2.52
210 211 5.178067 GCATGTGTAGCTTGCAAAAATTTCT 59.822 36.000 0.00 0.00 44.67 2.52
211 212 5.376537 GCATGTGTAGCTTGCAAAAATTTC 58.623 37.500 0.00 0.00 44.67 2.17
212 213 4.213906 GGCATGTGTAGCTTGCAAAAATTT 59.786 37.500 9.41 0.00 46.39 1.82
213 214 3.747529 GGCATGTGTAGCTTGCAAAAATT 59.252 39.130 9.41 0.00 46.39 1.82
214 215 3.007182 AGGCATGTGTAGCTTGCAAAAAT 59.993 39.130 9.41 0.00 46.39 1.82
215 216 2.364970 AGGCATGTGTAGCTTGCAAAAA 59.635 40.909 9.41 0.00 46.39 1.94
216 217 1.962807 AGGCATGTGTAGCTTGCAAAA 59.037 42.857 9.41 0.00 46.39 2.44
217 218 1.270274 CAGGCATGTGTAGCTTGCAAA 59.730 47.619 9.41 0.00 46.39 3.68
218 219 0.883153 CAGGCATGTGTAGCTTGCAA 59.117 50.000 9.41 0.00 46.39 4.08
219 220 2.558617 CAGGCATGTGTAGCTTGCA 58.441 52.632 9.41 0.00 46.39 4.08
221 222 0.883153 TTGCAGGCATGTGTAGCTTG 59.117 50.000 0.00 0.00 41.45 4.01
222 223 1.843368 ATTGCAGGCATGTGTAGCTT 58.157 45.000 0.00 0.00 0.00 3.74
223 224 2.715749 TATTGCAGGCATGTGTAGCT 57.284 45.000 0.00 0.00 0.00 3.32
224 225 2.945008 TCTTATTGCAGGCATGTGTAGC 59.055 45.455 0.00 0.00 0.00 3.58
225 226 4.445453 TCTCTTATTGCAGGCATGTGTAG 58.555 43.478 0.00 0.00 0.00 2.74
226 227 4.445453 CTCTCTTATTGCAGGCATGTGTA 58.555 43.478 0.00 0.00 0.00 2.90
227 228 3.276857 CTCTCTTATTGCAGGCATGTGT 58.723 45.455 0.00 0.00 0.00 3.72
228 229 2.033049 GCTCTCTTATTGCAGGCATGTG 59.967 50.000 0.00 0.00 0.00 3.21
229 230 2.295885 GCTCTCTTATTGCAGGCATGT 58.704 47.619 0.00 0.00 0.00 3.21
230 231 1.263484 CGCTCTCTTATTGCAGGCATG 59.737 52.381 0.00 0.00 0.00 4.06
231 232 1.590932 CGCTCTCTTATTGCAGGCAT 58.409 50.000 0.00 0.00 0.00 4.40
232 233 0.462581 CCGCTCTCTTATTGCAGGCA 60.463 55.000 0.00 0.00 0.00 4.75
233 234 0.462759 ACCGCTCTCTTATTGCAGGC 60.463 55.000 0.00 0.00 0.00 4.85
234 235 2.748605 CTACCGCTCTCTTATTGCAGG 58.251 52.381 0.00 0.00 0.00 4.85
235 236 2.131183 GCTACCGCTCTCTTATTGCAG 58.869 52.381 0.00 0.00 0.00 4.41
236 237 1.202533 GGCTACCGCTCTCTTATTGCA 60.203 52.381 0.00 0.00 36.09 4.08
237 238 1.069358 AGGCTACCGCTCTCTTATTGC 59.931 52.381 0.00 0.00 36.09 3.56
238 239 2.362397 TGAGGCTACCGCTCTCTTATTG 59.638 50.000 0.00 0.00 35.66 1.90
239 240 2.667470 TGAGGCTACCGCTCTCTTATT 58.333 47.619 0.00 0.00 35.66 1.40
240 241 2.366640 TGAGGCTACCGCTCTCTTAT 57.633 50.000 0.00 0.00 35.66 1.73
241 242 1.957177 CATGAGGCTACCGCTCTCTTA 59.043 52.381 0.00 0.00 35.66 2.10
242 243 0.749649 CATGAGGCTACCGCTCTCTT 59.250 55.000 0.00 0.00 35.66 2.85
243 244 1.112315 CCATGAGGCTACCGCTCTCT 61.112 60.000 0.00 0.00 35.66 3.10
244 245 1.365633 CCATGAGGCTACCGCTCTC 59.634 63.158 0.00 0.00 35.40 3.20
245 246 1.381872 ACCATGAGGCTACCGCTCT 60.382 57.895 0.00 0.00 39.06 4.09
246 247 1.227380 CACCATGAGGCTACCGCTC 60.227 63.158 0.00 0.00 39.06 5.03
247 248 2.903357 CACCATGAGGCTACCGCT 59.097 61.111 0.00 0.00 39.06 5.52
248 249 2.897350 GCACCATGAGGCTACCGC 60.897 66.667 0.00 0.00 39.06 5.68
249 250 1.146930 ATGCACCATGAGGCTACCG 59.853 57.895 9.48 0.00 39.06 4.02
250 251 0.107017 ACATGCACCATGAGGCTACC 60.107 55.000 11.78 0.00 43.81 3.18
251 252 2.620251 TACATGCACCATGAGGCTAC 57.380 50.000 11.78 0.00 43.81 3.58
252 253 3.643199 TTTACATGCACCATGAGGCTA 57.357 42.857 11.78 0.00 43.81 3.93
253 254 2.512692 TTTACATGCACCATGAGGCT 57.487 45.000 11.78 0.00 43.81 4.58
254 255 2.493278 ACTTTTACATGCACCATGAGGC 59.507 45.455 11.78 0.00 43.81 4.70
255 256 3.507233 ACACTTTTACATGCACCATGAGG 59.493 43.478 11.78 0.00 43.81 3.86
256 257 4.771590 ACACTTTTACATGCACCATGAG 57.228 40.909 11.78 1.96 43.81 2.90
257 258 5.163468 ACAAACACTTTTACATGCACCATGA 60.163 36.000 11.78 0.00 43.81 3.07
258 259 5.049167 ACAAACACTTTTACATGCACCATG 58.951 37.500 3.80 3.80 46.18 3.66
259 260 5.275067 ACAAACACTTTTACATGCACCAT 57.725 34.783 0.00 0.00 0.00 3.55
260 261 4.727507 ACAAACACTTTTACATGCACCA 57.272 36.364 0.00 0.00 0.00 4.17
261 262 5.810074 AGAAACAAACACTTTTACATGCACC 59.190 36.000 0.00 0.00 0.00 5.01
262 263 6.019881 GGAGAAACAAACACTTTTACATGCAC 60.020 38.462 0.00 0.00 0.00 4.57
263 264 6.039616 GGAGAAACAAACACTTTTACATGCA 58.960 36.000 0.00 0.00 0.00 3.96
264 265 5.462068 GGGAGAAACAAACACTTTTACATGC 59.538 40.000 0.00 0.00 0.00 4.06
265 266 5.685511 CGGGAGAAACAAACACTTTTACATG 59.314 40.000 0.00 0.00 0.00 3.21
266 267 5.358725 ACGGGAGAAACAAACACTTTTACAT 59.641 36.000 0.00 0.00 0.00 2.29
267 268 4.701171 ACGGGAGAAACAAACACTTTTACA 59.299 37.500 0.00 0.00 0.00 2.41
268 269 5.239359 ACGGGAGAAACAAACACTTTTAC 57.761 39.130 0.00 0.00 0.00 2.01
269 270 5.642686 CAACGGGAGAAACAAACACTTTTA 58.357 37.500 0.00 0.00 0.00 1.52
270 271 4.490743 CAACGGGAGAAACAAACACTTTT 58.509 39.130 0.00 0.00 0.00 2.27
271 272 3.674955 GCAACGGGAGAAACAAACACTTT 60.675 43.478 0.00 0.00 0.00 2.66
272 273 2.159296 GCAACGGGAGAAACAAACACTT 60.159 45.455 0.00 0.00 0.00 3.16
273 274 1.404035 GCAACGGGAGAAACAAACACT 59.596 47.619 0.00 0.00 0.00 3.55
274 275 1.133407 TGCAACGGGAGAAACAAACAC 59.867 47.619 0.00 0.00 0.00 3.32
275 276 1.464734 TGCAACGGGAGAAACAAACA 58.535 45.000 0.00 0.00 0.00 2.83
276 277 2.190161 GTTGCAACGGGAGAAACAAAC 58.810 47.619 14.90 0.00 0.00 2.93
277 278 2.570442 GTTGCAACGGGAGAAACAAA 57.430 45.000 14.90 0.00 0.00 2.83
289 290 2.265073 ATATGCCCGTGCGTTGCAAC 62.265 55.000 19.89 19.89 41.47 4.17
290 291 1.590610 AATATGCCCGTGCGTTGCAA 61.591 50.000 0.00 0.00 41.47 4.08
291 292 1.987704 GAATATGCCCGTGCGTTGCA 61.988 55.000 8.11 8.11 41.78 4.08
292 293 1.298339 GAATATGCCCGTGCGTTGC 60.298 57.895 0.00 0.00 41.78 4.17
293 294 1.355210 GGAATATGCCCGTGCGTTG 59.645 57.895 0.00 0.00 41.78 4.10
294 295 1.822186 GGGAATATGCCCGTGCGTT 60.822 57.895 1.81 0.00 41.78 4.84
295 296 2.203153 GGGAATATGCCCGTGCGT 60.203 61.111 1.81 0.00 41.78 5.24
403 404 3.252974 TGAGCGAAAGAGGATTTCTCC 57.747 47.619 0.00 0.00 43.44 3.71
404 405 5.613358 TTTTGAGCGAAAGAGGATTTCTC 57.387 39.130 0.00 0.00 42.75 2.87
433 434 9.528018 CTATGGACACTTTAACACAAAACAAAT 57.472 29.630 0.00 0.00 0.00 2.32
434 435 8.740906 TCTATGGACACTTTAACACAAAACAAA 58.259 29.630 0.00 0.00 0.00 2.83
435 436 8.282455 TCTATGGACACTTTAACACAAAACAA 57.718 30.769 0.00 0.00 0.00 2.83
436 437 7.867305 TCTATGGACACTTTAACACAAAACA 57.133 32.000 0.00 0.00 0.00 2.83
497 498 7.728532 AGGGATTAGTATCAAACAACAACCTTT 59.271 33.333 0.00 0.00 32.09 3.11
500 501 7.462571 AAGGGATTAGTATCAAACAACAACC 57.537 36.000 0.00 0.00 32.09 3.77
689 700 1.984570 CTCCTCTCCTTGCACGGGA 60.985 63.158 9.71 8.34 0.00 5.14
703 714 0.771127 CGGATCTCCTCTCCTCTCCT 59.229 60.000 0.00 0.00 0.00 3.69
704 715 0.476771 ACGGATCTCCTCTCCTCTCC 59.523 60.000 0.00 0.00 0.00 3.71
705 716 1.544759 GGACGGATCTCCTCTCCTCTC 60.545 61.905 0.00 0.00 31.29 3.20
706 717 0.476771 GGACGGATCTCCTCTCCTCT 59.523 60.000 0.00 0.00 31.29 3.69
707 718 0.538746 GGGACGGATCTCCTCTCCTC 60.539 65.000 1.35 0.00 33.34 3.71
765 784 2.307049 CCGTTTCTTTGCAAGTAAGCG 58.693 47.619 18.58 18.58 37.31 4.68
773 792 4.009675 AGATATTCTGCCGTTTCTTTGCA 58.990 39.130 0.00 0.00 0.00 4.08
796 815 0.874390 GATGCACACGAAGAAGCCAA 59.126 50.000 0.00 0.00 0.00 4.52
813 832 0.105964 TCGGGAGGCAGCTAAGAGAT 60.106 55.000 0.00 0.00 0.00 2.75
826 845 1.880027 CTTTGGTGAAAAGGTCGGGAG 59.120 52.381 0.00 0.00 41.46 4.30
827 846 1.975660 CTTTGGTGAAAAGGTCGGGA 58.024 50.000 0.00 0.00 41.46 5.14
838 857 3.305950 CGGAAAATGCATTCCTTTGGTGA 60.306 43.478 13.38 0.00 45.54 4.02
857 876 2.094597 CGGGATATATAAACGCCACGGA 60.095 50.000 0.00 0.00 0.00 4.69
866 885 3.770388 TGGTGATCGGCGGGATATATAAA 59.230 43.478 7.21 0.00 34.82 1.40
893 912 1.269778 CCGATCGTGGTGTGCTGATAT 60.270 52.381 15.09 0.00 0.00 1.63
896 915 2.212900 CTCCGATCGTGGTGTGCTGA 62.213 60.000 15.09 0.00 0.00 4.26
910 929 0.465705 CCTTTGCTATGCTCCTCCGA 59.534 55.000 0.00 0.00 0.00 4.55
916 935 0.179073 TCGCTCCCTTTGCTATGCTC 60.179 55.000 0.00 0.00 0.00 4.26
917 936 0.179062 CTCGCTCCCTTTGCTATGCT 60.179 55.000 0.00 0.00 0.00 3.79
965 984 3.192633 TGCAAGCTACTGAACACGAGATA 59.807 43.478 0.00 0.00 0.00 1.98
1015 1035 4.409342 CGAGGCCATCGTCTTGAG 57.591 61.111 5.01 0.00 46.62 3.02
1183 1203 3.253230 GCCACAGCAAATCAAACATACC 58.747 45.455 0.00 0.00 39.53 2.73
1203 1258 2.401766 CCCCTCACTGCATCAACGC 61.402 63.158 0.00 0.00 0.00 4.84
1440 1495 1.307097 GATGCTGATCTCCTTGCACC 58.693 55.000 0.00 0.00 38.29 5.01
1493 1548 6.758886 ACGACAGATTCTCCATTGATTTACTC 59.241 38.462 0.00 0.00 0.00 2.59
1519 1574 3.340814 ACACATGGACAAGAGATGGAC 57.659 47.619 0.00 0.00 0.00 4.02
1534 1589 2.480759 CCGCGTTAGCTAGGTTACACAT 60.481 50.000 4.92 0.00 42.32 3.21
1559 1614 4.360027 CGCGCTGCACACACAGAC 62.360 66.667 5.56 0.00 40.25 3.51
1662 1719 1.688735 CTGATTCCCATAGGCGTCTGA 59.311 52.381 0.00 0.00 0.00 3.27
1671 1728 2.439507 GACCCTTGCTCTGATTCCCATA 59.560 50.000 0.00 0.00 0.00 2.74
1711 1771 2.680352 ACACTCCATCGACGGCCT 60.680 61.111 0.00 0.00 0.00 5.19
1782 1851 4.339809 CACACGCACTCACGCACG 62.340 66.667 0.00 0.00 36.19 5.34
1783 1852 3.261951 ACACACGCACTCACGCAC 61.262 61.111 0.00 0.00 36.19 5.34
1784 1853 3.261216 CACACACGCACTCACGCA 61.261 61.111 0.00 0.00 36.19 5.24
1785 1854 4.649954 GCACACACGCACTCACGC 62.650 66.667 0.00 0.00 36.19 5.34
1786 1855 4.339809 CGCACACACGCACTCACG 62.340 66.667 0.00 0.00 39.50 4.35
1787 1856 3.261951 ACGCACACACGCACTCAC 61.262 61.111 0.00 0.00 36.19 3.51
1788 1857 3.261216 CACGCACACACGCACTCA 61.261 61.111 0.00 0.00 36.19 3.41
1789 1858 3.261951 ACACGCACACACGCACTC 61.262 61.111 0.00 0.00 36.19 3.51
1790 1859 3.563088 CACACGCACACACGCACT 61.563 61.111 0.00 0.00 36.19 4.40
1791 1860 2.881266 ATCACACGCACACACGCAC 61.881 57.895 0.00 0.00 36.19 5.34
1792 1861 2.587473 ATCACACGCACACACGCA 60.587 55.556 0.00 0.00 36.19 5.24
1793 1862 2.127646 CATCACACGCACACACGC 60.128 61.111 0.00 0.00 36.19 5.34
1794 1863 1.083465 CACATCACACGCACACACG 60.083 57.895 0.00 0.00 39.50 4.49
1798 1867 4.024977 GCATATATTCACATCACACGCACA 60.025 41.667 0.00 0.00 0.00 4.57
1818 1887 3.935203 GCAGTAGCACATATAATCCGCAT 59.065 43.478 0.00 0.00 41.58 4.73
1819 1888 3.325870 GCAGTAGCACATATAATCCGCA 58.674 45.455 0.00 0.00 41.58 5.69
1838 1907 4.308458 CCTGACAACCCCGACGCA 62.308 66.667 0.00 0.00 0.00 5.24
1840 1909 2.669777 AAACCCTGACAACCCCGACG 62.670 60.000 0.00 0.00 0.00 5.12
1850 1919 1.724582 AAGCGCACACAAACCCTGAC 61.725 55.000 11.47 0.00 0.00 3.51
1858 1927 4.249020 CACCGCAAGCGCACACAA 62.249 61.111 11.47 0.00 38.40 3.33
1896 1966 6.094061 TCGACATGTTATGTAATCGTCACAA 58.906 36.000 0.00 0.00 45.03 3.33
1897 1967 5.642686 TCGACATGTTATGTAATCGTCACA 58.357 37.500 0.00 0.00 45.03 3.58
1988 2062 6.913873 AATATTTGCCAGATTTTGCATGAC 57.086 33.333 0.00 0.00 37.33 3.06
2053 2127 0.655733 GCTGCATGCGTACCGTTTAT 59.344 50.000 14.09 0.00 0.00 1.40
2064 2139 1.226211 CAGTTACGCAGCTGCATGC 60.226 57.895 36.03 22.29 42.21 4.06
2065 2140 0.798159 TTCAGTTACGCAGCTGCATG 59.202 50.000 36.03 23.84 42.21 4.06
2066 2141 0.798776 GTTCAGTTACGCAGCTGCAT 59.201 50.000 36.03 26.43 42.21 3.96
2067 2142 0.531753 TGTTCAGTTACGCAGCTGCA 60.532 50.000 36.03 17.26 42.21 4.41
2078 2153 3.742640 GCTTCACCTGTCTCTGTTCAGTT 60.743 47.826 0.00 0.00 0.00 3.16
2085 2160 1.672441 GCTCTGCTTCACCTGTCTCTG 60.672 57.143 0.00 0.00 0.00 3.35
2145 2266 1.419374 ACGTACGAGCTGCTTCTTTG 58.581 50.000 24.41 0.00 0.00 2.77
2147 2268 1.538512 TGTACGTACGAGCTGCTTCTT 59.461 47.619 24.41 0.00 0.00 2.52
2149 2270 1.973138 TTGTACGTACGAGCTGCTTC 58.027 50.000 24.41 0.00 0.00 3.86
2159 2280 2.925563 GGTGTAGCCACATTGTACGTAC 59.074 50.000 18.90 18.90 43.71 3.67
2160 2281 2.561858 TGGTGTAGCCACATTGTACGTA 59.438 45.455 0.00 0.00 43.61 3.57
2161 2282 1.345089 TGGTGTAGCCACATTGTACGT 59.655 47.619 0.00 0.00 43.61 3.57
2162 2283 1.999735 CTGGTGTAGCCACATTGTACG 59.000 52.381 0.00 0.00 43.61 3.67
2163 2284 3.000727 GACTGGTGTAGCCACATTGTAC 58.999 50.000 0.00 0.00 43.61 2.90
2165 2286 1.608025 CGACTGGTGTAGCCACATTGT 60.608 52.381 0.00 0.00 43.61 2.71
2166 2287 1.078709 CGACTGGTGTAGCCACATTG 58.921 55.000 0.00 0.00 43.61 2.82
2174 2354 2.722201 GGGCCTCCGACTGGTGTAG 61.722 68.421 0.84 0.00 36.30 2.74
2196 2377 2.052590 CGTCACGTTTGTTGGCGG 60.053 61.111 0.00 0.00 0.00 6.13
2404 2585 6.128634 GCGGCGCTTATAACTTTGATAGTAAT 60.129 38.462 26.86 0.00 35.54 1.89
2407 2588 3.493503 GCGGCGCTTATAACTTTGATAGT 59.506 43.478 26.86 0.00 39.32 2.12
2408 2589 3.120649 GGCGGCGCTTATAACTTTGATAG 60.121 47.826 32.30 0.00 0.00 2.08
2497 2678 0.824182 CCGCCTACCTCGAGATCCTT 60.824 60.000 15.71 0.00 0.00 3.36
2677 2858 2.193532 CTTGCCGAGCTACCTGAGA 58.806 57.895 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.