Multiple sequence alignment - TraesCS5A01G123300

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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 TraesCS5A01G123300 chr5A 100.000 3227 0 0 1 3227 269321806 269318580 0.000000e+00 5960
1 TraesCS5A01G123300 chr5A 97.837 601 11 2 2628 3227 382789789 382789190 0.000000e+00 1037
2 TraesCS5A01G123300 chr5D 95.023 2170 57 19 492 2621 208537660 208535502 0.000000e+00 3362
3 TraesCS5A01G123300 chr5B 94.137 2166 80 19 489 2623 222128234 222126085 0.000000e+00 3253
4 TraesCS5A01G123300 chr3A 98.336 601 9 1 2628 3227 395744541 395745141 0.000000e+00 1053
5 TraesCS5A01G123300 chr3A 94.521 292 8 1 1 284 452940471 452940762 8.220000e-121 444
6 TraesCS5A01G123300 chr2D 95.710 606 24 2 2623 3227 447158706 447158102 0.000000e+00 974
7 TraesCS5A01G123300 chr2D 83.251 406 55 7 1 397 90314039 90313638 8.510000e-96 361
8 TraesCS5A01G123300 chr4A 81.871 1037 169 12 1195 2220 501976228 501975200 0.000000e+00 856
9 TraesCS5A01G123300 chr4A 94.949 396 10 2 1 387 97379316 97378922 2.130000e-171 612
10 TraesCS5A01G123300 chr4D 81.660 1036 173 10 1195 2220 89435846 89434818 0.000000e+00 845
11 TraesCS5A01G123300 chr4B 81.232 1039 172 14 1195 2220 126508469 126507441 0.000000e+00 817
12 TraesCS5A01G123300 chr4B 76.658 407 69 20 1 394 630132746 630132353 5.460000e-48 202
13 TraesCS5A01G123300 chr1A 94.304 316 9 1 3 309 361191912 361191597 2.910000e-130 475
14 TraesCS5A01G123300 chr6D 94.656 262 11 3 2624 2883 306062290 306062030 1.390000e-108 403
15 TraesCS5A01G123300 chr7A 84.949 392 44 11 1 383 291525845 291526230 1.820000e-102 383
16 TraesCS5A01G123300 chrUn 81.193 218 25 11 182 394 360427606 360427400 9.260000e-36 161


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 TraesCS5A01G123300 chr5A 269318580 269321806 3226 True 5960 5960 100.000 1 3227 1 chr5A.!!$R1 3226
1 TraesCS5A01G123300 chr5A 382789190 382789789 599 True 1037 1037 97.837 2628 3227 1 chr5A.!!$R2 599
2 TraesCS5A01G123300 chr5D 208535502 208537660 2158 True 3362 3362 95.023 492 2621 1 chr5D.!!$R1 2129
3 TraesCS5A01G123300 chr5B 222126085 222128234 2149 True 3253 3253 94.137 489 2623 1 chr5B.!!$R1 2134
4 TraesCS5A01G123300 chr3A 395744541 395745141 600 False 1053 1053 98.336 2628 3227 1 chr3A.!!$F1 599
5 TraesCS5A01G123300 chr2D 447158102 447158706 604 True 974 974 95.710 2623 3227 1 chr2D.!!$R2 604
6 TraesCS5A01G123300 chr4A 501975200 501976228 1028 True 856 856 81.871 1195 2220 1 chr4A.!!$R2 1025
7 TraesCS5A01G123300 chr4D 89434818 89435846 1028 True 845 845 81.660 1195 2220 1 chr4D.!!$R1 1025
8 TraesCS5A01G123300 chr4B 126507441 126508469 1028 True 817 817 81.232 1195 2220 1 chr4B.!!$R1 1025

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
303 304 0.03831 GGAGAACAAAGGGGGAGGTG 59.962 60.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2232 2294 0.03392 CCGATCAATGGCGAGATGGA 59.966 55.0 0.0 0.0 0.0 3.41 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
27 28 4.559063 CCCCAGCTGGCAGATCCG 62.559 72.222 28.39 11.59 37.80 4.18
29 30 4.478371 CCAGCTGGCAGATCCGCA 62.478 66.667 22.33 0.00 37.01 5.69
30 31 3.200593 CAGCTGGCAGATCCGCAC 61.201 66.667 20.86 0.00 37.01 5.34
31 32 4.479993 AGCTGGCAGATCCGCACC 62.480 66.667 20.86 0.00 37.01 5.01
33 34 4.100084 CTGGCAGATCCGCACCCA 62.100 66.667 9.42 0.00 37.80 4.51
34 35 3.410628 TGGCAGATCCGCACCCAT 61.411 61.111 2.82 0.00 37.80 4.00
35 36 2.592861 GGCAGATCCGCACCCATC 60.593 66.667 2.82 0.00 0.00 3.51
36 37 2.592861 GCAGATCCGCACCCATCC 60.593 66.667 0.00 0.00 0.00 3.51
37 38 3.112205 GCAGATCCGCACCCATCCT 62.112 63.158 0.00 0.00 0.00 3.24
38 39 1.070445 CAGATCCGCACCCATCCTC 59.930 63.158 0.00 0.00 0.00 3.71
39 40 2.143419 AGATCCGCACCCATCCTCC 61.143 63.158 0.00 0.00 0.00 4.30
40 41 2.040464 ATCCGCACCCATCCTCCT 60.040 61.111 0.00 0.00 0.00 3.69
41 42 2.105806 GATCCGCACCCATCCTCCTC 62.106 65.000 0.00 0.00 0.00 3.71
42 43 2.611964 ATCCGCACCCATCCTCCTCT 62.612 60.000 0.00 0.00 0.00 3.69
43 44 2.370445 CCGCACCCATCCTCCTCTT 61.370 63.158 0.00 0.00 0.00 2.85
44 45 1.144936 CGCACCCATCCTCCTCTTC 59.855 63.158 0.00 0.00 0.00 2.87
45 46 1.529309 GCACCCATCCTCCTCTTCC 59.471 63.158 0.00 0.00 0.00 3.46
46 47 1.274703 GCACCCATCCTCCTCTTCCA 61.275 60.000 0.00 0.00 0.00 3.53
47 48 1.516110 CACCCATCCTCCTCTTCCAT 58.484 55.000 0.00 0.00 0.00 3.41
48 49 2.694397 CACCCATCCTCCTCTTCCATA 58.306 52.381 0.00 0.00 0.00 2.74
49 50 2.636893 CACCCATCCTCCTCTTCCATAG 59.363 54.545 0.00 0.00 0.00 2.23
50 51 2.264455 CCCATCCTCCTCTTCCATAGG 58.736 57.143 0.00 0.00 35.26 2.57
51 52 2.264455 CCATCCTCCTCTTCCATAGGG 58.736 57.143 0.00 0.00 34.66 3.53
52 53 2.428484 CCATCCTCCTCTTCCATAGGGT 60.428 54.545 0.00 0.00 34.66 4.34
53 54 2.777459 TCCTCCTCTTCCATAGGGTC 57.223 55.000 0.00 0.00 34.66 4.46
54 55 2.227703 TCCTCCTCTTCCATAGGGTCT 58.772 52.381 0.00 0.00 34.66 3.85
55 56 2.592512 TCCTCCTCTTCCATAGGGTCTT 59.407 50.000 0.00 0.00 34.66 3.01
56 57 2.969262 CCTCCTCTTCCATAGGGTCTTC 59.031 54.545 0.00 0.00 34.66 2.87
57 58 3.374762 CCTCCTCTTCCATAGGGTCTTCT 60.375 52.174 0.00 0.00 34.66 2.85
58 59 4.294347 CTCCTCTTCCATAGGGTCTTCTT 58.706 47.826 0.00 0.00 34.66 2.52
59 60 4.290942 TCCTCTTCCATAGGGTCTTCTTC 58.709 47.826 0.00 0.00 34.66 2.87
60 61 3.068873 CCTCTTCCATAGGGTCTTCTTCG 59.931 52.174 0.00 0.00 34.93 3.79
61 62 3.954904 CTCTTCCATAGGGTCTTCTTCGA 59.045 47.826 0.00 0.00 34.93 3.71
62 63 4.350245 TCTTCCATAGGGTCTTCTTCGAA 58.650 43.478 0.00 0.00 34.93 3.71
63 64 4.402793 TCTTCCATAGGGTCTTCTTCGAAG 59.597 45.833 19.35 19.35 34.93 3.79
64 65 2.431057 TCCATAGGGTCTTCTTCGAAGC 59.569 50.000 20.56 6.14 34.93 3.86
65 66 2.168521 CCATAGGGTCTTCTTCGAAGCA 59.831 50.000 20.56 8.99 0.00 3.91
66 67 3.452474 CATAGGGTCTTCTTCGAAGCAG 58.548 50.000 20.56 18.91 0.00 4.24
67 68 0.610687 AGGGTCTTCTTCGAAGCAGG 59.389 55.000 22.03 13.40 0.00 4.85
68 69 0.391793 GGGTCTTCTTCGAAGCAGGG 60.392 60.000 22.03 11.26 0.00 4.45
69 70 0.391793 GGTCTTCTTCGAAGCAGGGG 60.392 60.000 22.03 9.75 0.00 4.79
70 71 1.021920 GTCTTCTTCGAAGCAGGGGC 61.022 60.000 22.03 10.85 41.61 5.80
71 72 1.746991 CTTCTTCGAAGCAGGGGCC 60.747 63.158 20.56 0.00 42.56 5.80
72 73 3.605749 TTCTTCGAAGCAGGGGCCG 62.606 63.158 20.56 0.00 42.56 6.13
126 127 4.463879 CGGCACCCTCCAGCAGAG 62.464 72.222 0.00 0.00 42.83 3.35
171 172 4.570663 CCACGTCCTCGGCGGATC 62.571 72.222 7.21 0.00 45.44 3.36
172 173 3.518998 CACGTCCTCGGCGGATCT 61.519 66.667 7.21 0.00 45.44 2.75
173 174 3.210528 ACGTCCTCGGCGGATCTC 61.211 66.667 7.21 0.00 45.44 2.75
174 175 2.902846 CGTCCTCGGCGGATCTCT 60.903 66.667 7.21 0.00 45.44 3.10
175 176 2.899044 CGTCCTCGGCGGATCTCTC 61.899 68.421 7.21 0.00 45.44 3.20
176 177 2.592001 TCCTCGGCGGATCTCTCG 60.592 66.667 7.21 0.00 36.69 4.04
177 178 2.592001 CCTCGGCGGATCTCTCGA 60.592 66.667 7.21 0.00 33.16 4.04
178 179 2.187493 CCTCGGCGGATCTCTCGAA 61.187 63.158 7.21 0.00 33.16 3.71
179 180 1.725557 CCTCGGCGGATCTCTCGAAA 61.726 60.000 7.21 0.00 33.16 3.46
180 181 0.317436 CTCGGCGGATCTCTCGAAAG 60.317 60.000 7.21 0.00 0.00 2.62
181 182 1.946650 CGGCGGATCTCTCGAAAGC 60.947 63.158 0.00 0.00 0.00 3.51
182 183 1.592939 GGCGGATCTCTCGAAAGCC 60.593 63.158 0.00 0.00 36.08 4.35
183 184 1.946650 GCGGATCTCTCGAAAGCCG 60.947 63.158 12.80 12.80 41.51 5.52
184 185 1.728069 CGGATCTCTCGAAAGCCGA 59.272 57.895 12.00 0.00 46.35 5.54
192 193 2.116383 TCGAAAGCCGAGGAGATCC 58.884 57.895 0.00 0.00 43.23 3.36
193 194 1.068250 CGAAAGCCGAGGAGATCCC 59.932 63.158 0.00 0.00 41.76 3.85
194 195 1.448069 GAAAGCCGAGGAGATCCCC 59.552 63.158 0.00 0.00 36.42 4.81
195 196 1.306997 AAAGCCGAGGAGATCCCCA 60.307 57.895 0.00 0.00 36.42 4.96
196 197 1.341156 AAAGCCGAGGAGATCCCCAG 61.341 60.000 0.00 0.00 36.42 4.45
197 198 2.123251 GCCGAGGAGATCCCCAGA 60.123 66.667 0.00 0.00 36.42 3.86
198 199 2.503382 GCCGAGGAGATCCCCAGAC 61.503 68.421 0.00 0.00 36.42 3.51
199 200 1.834822 CCGAGGAGATCCCCAGACC 60.835 68.421 0.00 0.00 36.42 3.85
200 201 1.075970 CGAGGAGATCCCCAGACCA 60.076 63.158 0.00 0.00 36.42 4.02
201 202 1.112315 CGAGGAGATCCCCAGACCAG 61.112 65.000 0.00 0.00 36.42 4.00
202 203 0.263172 GAGGAGATCCCCAGACCAGA 59.737 60.000 0.00 0.00 36.42 3.86
203 204 0.264359 AGGAGATCCCCAGACCAGAG 59.736 60.000 0.00 0.00 36.42 3.35
204 205 0.263172 GGAGATCCCCAGACCAGAGA 59.737 60.000 0.00 0.00 0.00 3.10
205 206 1.408969 GAGATCCCCAGACCAGAGAC 58.591 60.000 0.00 0.00 0.00 3.36
206 207 0.396417 AGATCCCCAGACCAGAGACG 60.396 60.000 0.00 0.00 0.00 4.18
207 208 0.395862 GATCCCCAGACCAGAGACGA 60.396 60.000 0.00 0.00 0.00 4.20
208 209 0.684805 ATCCCCAGACCAGAGACGAC 60.685 60.000 0.00 0.00 0.00 4.34
209 210 2.701780 CCCCAGACCAGAGACGACG 61.702 68.421 0.00 0.00 0.00 5.12
210 211 2.701780 CCCAGACCAGAGACGACGG 61.702 68.421 0.00 0.00 0.00 4.79
211 212 2.701780 CCAGACCAGAGACGACGGG 61.702 68.421 0.00 0.00 0.00 5.28
212 213 3.063084 AGACCAGAGACGACGGGC 61.063 66.667 0.00 0.00 0.00 6.13
213 214 4.131088 GACCAGAGACGACGGGCC 62.131 72.222 0.00 0.00 0.00 5.80
214 215 4.680537 ACCAGAGACGACGGGCCT 62.681 66.667 0.84 0.00 0.00 5.19
215 216 3.827898 CCAGAGACGACGGGCCTC 61.828 72.222 0.84 3.00 0.00 4.70
216 217 2.752238 CAGAGACGACGGGCCTCT 60.752 66.667 0.84 5.38 37.74 3.69
217 218 2.438795 AGAGACGACGGGCCTCTC 60.439 66.667 11.53 11.53 32.23 3.20
218 219 3.519930 GAGACGACGGGCCTCTCC 61.520 72.222 0.84 0.00 0.00 3.71
230 231 2.885861 CTCTCCCGAGGGAACACG 59.114 66.667 12.54 0.55 44.66 4.49
236 237 4.261888 CGAGGGAACACGGAGTTG 57.738 61.111 0.00 0.00 41.61 3.16
237 238 1.663739 CGAGGGAACACGGAGTTGA 59.336 57.895 0.00 0.00 41.61 3.18
238 239 0.666577 CGAGGGAACACGGAGTTGAC 60.667 60.000 0.00 0.00 41.61 3.18
239 240 0.666577 GAGGGAACACGGAGTTGACG 60.667 60.000 0.00 0.00 41.61 4.35
240 241 1.666872 GGGAACACGGAGTTGACGG 60.667 63.158 0.00 0.00 41.61 4.79
241 242 1.364901 GGAACACGGAGTTGACGGA 59.635 57.895 0.00 0.00 41.61 4.69
242 243 0.666577 GGAACACGGAGTTGACGGAG 60.667 60.000 0.00 0.00 41.61 4.63
243 244 1.282930 GAACACGGAGTTGACGGAGC 61.283 60.000 0.00 0.00 41.61 4.70
244 245 2.805353 CACGGAGTTGACGGAGCG 60.805 66.667 0.00 0.00 41.61 5.03
245 246 4.052229 ACGGAGTTGACGGAGCGG 62.052 66.667 0.00 0.00 37.78 5.52
246 247 4.796231 CGGAGTTGACGGAGCGGG 62.796 72.222 0.00 0.00 0.00 6.13
247 248 4.452733 GGAGTTGACGGAGCGGGG 62.453 72.222 0.00 0.00 0.00 5.73
248 249 4.452733 GAGTTGACGGAGCGGGGG 62.453 72.222 0.00 0.00 0.00 5.40
266 267 4.559063 CTCTCCGCCATGGCCAGG 62.559 72.222 30.79 25.66 37.80 4.45
268 269 4.113815 CTCCGCCATGGCCAGGAA 62.114 66.667 30.79 14.90 37.80 3.36
269 270 4.113815 TCCGCCATGGCCAGGAAG 62.114 66.667 30.79 15.29 37.80 3.46
272 273 3.145551 GCCATGGCCAGGAAGCAG 61.146 66.667 27.24 2.04 34.56 4.24
273 274 2.679092 CCATGGCCAGGAAGCAGA 59.321 61.111 21.32 0.00 0.00 4.26
274 275 1.453379 CCATGGCCAGGAAGCAGAG 60.453 63.158 21.32 0.00 0.00 3.35
275 276 1.605992 CATGGCCAGGAAGCAGAGA 59.394 57.895 13.35 0.00 0.00 3.10
276 277 0.464013 CATGGCCAGGAAGCAGAGAG 60.464 60.000 13.35 0.00 0.00 3.20
277 278 2.124778 GGCCAGGAAGCAGAGAGC 60.125 66.667 0.00 0.00 46.19 4.09
294 295 2.746277 CGGGGGCGGAGAACAAAG 60.746 66.667 0.00 0.00 0.00 2.77
295 296 2.361230 GGGGGCGGAGAACAAAGG 60.361 66.667 0.00 0.00 0.00 3.11
296 297 2.361230 GGGGCGGAGAACAAAGGG 60.361 66.667 0.00 0.00 0.00 3.95
297 298 2.361230 GGGCGGAGAACAAAGGGG 60.361 66.667 0.00 0.00 0.00 4.79
298 299 2.361230 GGCGGAGAACAAAGGGGG 60.361 66.667 0.00 0.00 0.00 5.40
299 300 2.754375 GCGGAGAACAAAGGGGGA 59.246 61.111 0.00 0.00 0.00 4.81
300 301 1.377333 GCGGAGAACAAAGGGGGAG 60.377 63.158 0.00 0.00 0.00 4.30
301 302 1.299976 CGGAGAACAAAGGGGGAGG 59.700 63.158 0.00 0.00 0.00 4.30
302 303 1.489560 CGGAGAACAAAGGGGGAGGT 61.490 60.000 0.00 0.00 0.00 3.85
303 304 0.038310 GGAGAACAAAGGGGGAGGTG 59.962 60.000 0.00 0.00 0.00 4.00
304 305 0.038310 GAGAACAAAGGGGGAGGTGG 59.962 60.000 0.00 0.00 0.00 4.61
305 306 1.606601 GAACAAAGGGGGAGGTGGC 60.607 63.158 0.00 0.00 0.00 5.01
306 307 3.160478 AACAAAGGGGGAGGTGGCC 62.160 63.158 0.00 0.00 0.00 5.36
307 308 4.740822 CAAAGGGGGAGGTGGCCG 62.741 72.222 0.00 0.00 0.00 6.13
337 338 3.186047 CGGCAAGCGACGGGTTAG 61.186 66.667 0.00 0.00 41.23 2.34
338 339 2.818274 GGCAAGCGACGGGTTAGG 60.818 66.667 0.00 0.00 31.46 2.69
339 340 2.047560 GCAAGCGACGGGTTAGGT 60.048 61.111 0.00 0.00 31.46 3.08
340 341 2.388232 GCAAGCGACGGGTTAGGTG 61.388 63.158 0.00 0.00 31.46 4.00
341 342 1.740296 CAAGCGACGGGTTAGGTGG 60.740 63.158 0.00 0.00 31.46 4.61
342 343 1.909781 AAGCGACGGGTTAGGTGGA 60.910 57.895 0.00 0.00 30.73 4.02
343 344 2.125793 GCGACGGGTTAGGTGGAC 60.126 66.667 0.00 0.00 0.00 4.02
344 345 2.180017 CGACGGGTTAGGTGGACG 59.820 66.667 0.00 0.00 0.00 4.79
345 346 2.125793 GACGGGTTAGGTGGACGC 60.126 66.667 0.00 0.00 0.00 5.19
346 347 3.654173 GACGGGTTAGGTGGACGCC 62.654 68.421 0.00 0.00 0.00 5.68
347 348 4.807039 CGGGTTAGGTGGACGCCG 62.807 72.222 0.00 0.00 0.00 6.46
348 349 4.462280 GGGTTAGGTGGACGCCGG 62.462 72.222 0.00 0.00 0.00 6.13
366 367 2.880879 CGTCGGAGTGATGCACGG 60.881 66.667 0.00 0.00 39.64 4.94
367 368 3.188786 GTCGGAGTGATGCACGGC 61.189 66.667 0.00 0.00 39.64 5.68
368 369 4.794439 TCGGAGTGATGCACGGCG 62.794 66.667 4.80 4.80 39.64 6.46
369 370 4.794439 CGGAGTGATGCACGGCGA 62.794 66.667 16.62 0.00 39.64 5.54
370 371 2.434185 GGAGTGATGCACGGCGAA 60.434 61.111 16.62 0.00 39.64 4.70
371 372 2.456119 GGAGTGATGCACGGCGAAG 61.456 63.158 16.62 6.85 39.64 3.79
372 373 2.434884 AGTGATGCACGGCGAAGG 60.435 61.111 16.62 3.42 39.64 3.46
373 374 3.499737 GTGATGCACGGCGAAGGG 61.500 66.667 16.62 0.49 0.00 3.95
374 375 3.700970 TGATGCACGGCGAAGGGA 61.701 61.111 16.62 3.99 0.00 4.20
375 376 2.892425 GATGCACGGCGAAGGGAG 60.892 66.667 16.62 0.00 0.00 4.30
376 377 4.473520 ATGCACGGCGAAGGGAGG 62.474 66.667 16.62 0.00 0.00 4.30
382 383 3.855853 GGCGAAGGGAGGGCTCTC 61.856 72.222 4.50 4.50 39.25 3.20
383 384 3.077556 GCGAAGGGAGGGCTCTCA 61.078 66.667 17.22 0.00 41.69 3.27
384 385 2.896443 CGAAGGGAGGGCTCTCAC 59.104 66.667 17.22 13.11 43.64 3.51
388 389 4.459089 GGGAGGGCTCTCACGCAC 62.459 72.222 17.22 0.00 41.69 5.34
391 392 2.283532 AGGGCTCTCACGCACTCT 60.284 61.111 0.00 0.00 40.21 3.24
392 393 2.183046 GGGCTCTCACGCACTCTC 59.817 66.667 0.00 0.00 0.00 3.20
393 394 2.202544 GGCTCTCACGCACTCTCG 60.203 66.667 0.00 0.00 0.00 4.04
394 395 2.878520 GCTCTCACGCACTCTCGC 60.879 66.667 0.00 0.00 0.00 5.03
395 396 2.874019 CTCTCACGCACTCTCGCT 59.126 61.111 0.00 0.00 0.00 4.93
396 397 1.226267 CTCTCACGCACTCTCGCTC 60.226 63.158 0.00 0.00 0.00 5.03
397 398 1.643868 CTCTCACGCACTCTCGCTCT 61.644 60.000 0.00 0.00 0.00 4.09
398 399 1.226267 CTCACGCACTCTCGCTCTC 60.226 63.158 0.00 0.00 0.00 3.20
399 400 2.575525 CACGCACTCTCGCTCTCG 60.576 66.667 0.00 0.00 0.00 4.04
400 401 4.468615 ACGCACTCTCGCTCTCGC 62.469 66.667 0.00 0.00 35.26 5.03
401 402 4.172772 CGCACTCTCGCTCTCGCT 62.173 66.667 0.00 0.00 35.26 4.93
402 403 2.277884 GCACTCTCGCTCTCGCTC 60.278 66.667 0.00 0.00 35.26 5.03
403 404 2.760159 GCACTCTCGCTCTCGCTCT 61.760 63.158 0.00 0.00 35.26 4.09
404 405 1.351707 CACTCTCGCTCTCGCTCTC 59.648 63.158 0.00 0.00 35.26 3.20
405 406 1.089481 CACTCTCGCTCTCGCTCTCT 61.089 60.000 0.00 0.00 35.26 3.10
406 407 0.810031 ACTCTCGCTCTCGCTCTCTC 60.810 60.000 0.00 0.00 35.26 3.20
407 408 1.498865 CTCTCGCTCTCGCTCTCTCC 61.499 65.000 0.00 0.00 35.26 3.71
408 409 2.515057 TCGCTCTCGCTCTCTCCC 60.515 66.667 0.00 0.00 35.26 4.30
409 410 2.515991 CGCTCTCGCTCTCTCCCT 60.516 66.667 0.00 0.00 0.00 4.20
410 411 2.118404 CGCTCTCGCTCTCTCCCTT 61.118 63.158 0.00 0.00 0.00 3.95
411 412 1.733526 GCTCTCGCTCTCTCCCTTC 59.266 63.158 0.00 0.00 0.00 3.46
412 413 0.751643 GCTCTCGCTCTCTCCCTTCT 60.752 60.000 0.00 0.00 0.00 2.85
413 414 1.308998 CTCTCGCTCTCTCCCTTCTC 58.691 60.000 0.00 0.00 0.00 2.87
414 415 0.916086 TCTCGCTCTCTCCCTTCTCT 59.084 55.000 0.00 0.00 0.00 3.10
415 416 2.104111 CTCTCGCTCTCTCCCTTCTCTA 59.896 54.545 0.00 0.00 0.00 2.43
416 417 2.104111 TCTCGCTCTCTCCCTTCTCTAG 59.896 54.545 0.00 0.00 0.00 2.43
417 418 1.841277 TCGCTCTCTCCCTTCTCTAGT 59.159 52.381 0.00 0.00 0.00 2.57
418 419 3.039743 TCGCTCTCTCCCTTCTCTAGTA 58.960 50.000 0.00 0.00 0.00 1.82
419 420 3.455177 TCGCTCTCTCCCTTCTCTAGTAA 59.545 47.826 0.00 0.00 0.00 2.24
420 421 3.562557 CGCTCTCTCCCTTCTCTAGTAAC 59.437 52.174 0.00 0.00 0.00 2.50
421 422 4.685030 CGCTCTCTCCCTTCTCTAGTAACT 60.685 50.000 0.00 0.00 0.00 2.24
422 423 4.820173 GCTCTCTCCCTTCTCTAGTAACTC 59.180 50.000 0.00 0.00 0.00 3.01
423 424 5.630539 GCTCTCTCCCTTCTCTAGTAACTCA 60.631 48.000 0.00 0.00 0.00 3.41
424 425 6.390048 TCTCTCCCTTCTCTAGTAACTCAA 57.610 41.667 0.00 0.00 0.00 3.02
425 426 6.419791 TCTCTCCCTTCTCTAGTAACTCAAG 58.580 44.000 0.00 0.00 0.00 3.02
426 427 4.951094 TCTCCCTTCTCTAGTAACTCAAGC 59.049 45.833 0.00 0.00 0.00 4.01
427 428 4.673968 TCCCTTCTCTAGTAACTCAAGCA 58.326 43.478 0.00 0.00 0.00 3.91
428 429 4.463186 TCCCTTCTCTAGTAACTCAAGCAC 59.537 45.833 0.00 0.00 0.00 4.40
429 430 4.220821 CCCTTCTCTAGTAACTCAAGCACA 59.779 45.833 0.00 0.00 0.00 4.57
430 431 5.105146 CCCTTCTCTAGTAACTCAAGCACAT 60.105 44.000 0.00 0.00 0.00 3.21
431 432 6.096987 CCCTTCTCTAGTAACTCAAGCACATA 59.903 42.308 0.00 0.00 0.00 2.29
432 433 6.975772 CCTTCTCTAGTAACTCAAGCACATAC 59.024 42.308 0.00 0.00 0.00 2.39
433 434 6.120378 TCTCTAGTAACTCAAGCACATACG 57.880 41.667 0.00 0.00 0.00 3.06
434 435 5.066117 TCTCTAGTAACTCAAGCACATACGG 59.934 44.000 0.00 0.00 0.00 4.02
435 436 4.945543 TCTAGTAACTCAAGCACATACGGA 59.054 41.667 0.00 0.00 0.00 4.69
436 437 4.530710 AGTAACTCAAGCACATACGGAA 57.469 40.909 0.00 0.00 0.00 4.30
437 438 4.890088 AGTAACTCAAGCACATACGGAAA 58.110 39.130 0.00 0.00 0.00 3.13
438 439 4.929808 AGTAACTCAAGCACATACGGAAAG 59.070 41.667 0.00 0.00 0.00 2.62
439 440 3.678056 ACTCAAGCACATACGGAAAGA 57.322 42.857 0.00 0.00 0.00 2.52
440 441 4.207891 ACTCAAGCACATACGGAAAGAT 57.792 40.909 0.00 0.00 0.00 2.40
441 442 4.579869 ACTCAAGCACATACGGAAAGATT 58.420 39.130 0.00 0.00 0.00 2.40
442 443 5.003804 ACTCAAGCACATACGGAAAGATTT 58.996 37.500 0.00 0.00 0.00 2.17
443 444 5.473504 ACTCAAGCACATACGGAAAGATTTT 59.526 36.000 0.00 0.00 0.00 1.82
444 445 5.698832 TCAAGCACATACGGAAAGATTTTG 58.301 37.500 0.00 0.00 0.00 2.44
445 446 4.096732 AGCACATACGGAAAGATTTTGC 57.903 40.909 0.00 0.00 0.00 3.68
446 447 3.758554 AGCACATACGGAAAGATTTTGCT 59.241 39.130 0.00 0.00 33.02 3.91
447 448 4.098416 GCACATACGGAAAGATTTTGCTC 58.902 43.478 0.00 0.00 0.00 4.26
448 449 4.142600 GCACATACGGAAAGATTTTGCTCT 60.143 41.667 0.00 0.00 0.00 4.09
449 450 5.064707 GCACATACGGAAAGATTTTGCTCTA 59.935 40.000 0.00 0.00 0.00 2.43
450 451 6.478588 CACATACGGAAAGATTTTGCTCTAC 58.521 40.000 0.00 0.00 0.00 2.59
451 452 6.313905 CACATACGGAAAGATTTTGCTCTACT 59.686 38.462 0.00 0.00 0.00 2.57
452 453 7.491372 CACATACGGAAAGATTTTGCTCTACTA 59.509 37.037 0.00 0.00 0.00 1.82
453 454 7.491696 ACATACGGAAAGATTTTGCTCTACTAC 59.508 37.037 0.00 0.00 0.00 2.73
454 455 5.790593 ACGGAAAGATTTTGCTCTACTACA 58.209 37.500 0.00 0.00 0.00 2.74
455 456 6.407202 ACGGAAAGATTTTGCTCTACTACAT 58.593 36.000 0.00 0.00 0.00 2.29
456 457 6.879458 ACGGAAAGATTTTGCTCTACTACATT 59.121 34.615 0.00 0.00 0.00 2.71
457 458 7.064728 ACGGAAAGATTTTGCTCTACTACATTC 59.935 37.037 0.00 0.00 0.00 2.67
458 459 7.064609 CGGAAAGATTTTGCTCTACTACATTCA 59.935 37.037 0.00 0.00 0.00 2.57
459 460 8.897752 GGAAAGATTTTGCTCTACTACATTCAT 58.102 33.333 0.00 0.00 0.00 2.57
463 464 9.979578 AGATTTTGCTCTACTACATTCATAGAG 57.020 33.333 3.62 3.62 43.22 2.43
468 469 6.176975 CTCTACTACATTCATAGAGCTCCG 57.823 45.833 10.93 0.00 36.53 4.63
469 470 3.651803 ACTACATTCATAGAGCTCCGC 57.348 47.619 10.93 0.00 0.00 5.54
470 471 3.226777 ACTACATTCATAGAGCTCCGCT 58.773 45.455 10.93 0.00 43.88 5.52
471 472 2.522836 ACATTCATAGAGCTCCGCTG 57.477 50.000 10.93 5.77 39.88 5.18
472 473 1.069823 ACATTCATAGAGCTCCGCTGG 59.930 52.381 10.93 0.00 39.88 4.85
473 474 1.069823 CATTCATAGAGCTCCGCTGGT 59.930 52.381 10.93 0.00 39.88 4.00
474 475 0.461548 TTCATAGAGCTCCGCTGGTG 59.538 55.000 10.93 0.86 39.88 4.17
475 476 0.684479 TCATAGAGCTCCGCTGGTGT 60.684 55.000 10.93 0.00 39.88 4.16
476 477 0.249238 CATAGAGCTCCGCTGGTGTC 60.249 60.000 10.93 0.00 39.88 3.67
477 478 1.395826 ATAGAGCTCCGCTGGTGTCC 61.396 60.000 10.93 0.00 39.88 4.02
478 479 2.781431 TAGAGCTCCGCTGGTGTCCA 62.781 60.000 10.93 0.00 39.88 4.02
479 480 3.941657 GAGCTCCGCTGGTGTCCAC 62.942 68.421 0.87 0.00 39.88 4.02
497 498 1.726791 CACCACGCATGAGTTGAGTAC 59.273 52.381 7.67 0.00 36.07 2.73
506 507 4.611943 CATGAGTTGAGTACGGTATGGAG 58.388 47.826 0.00 0.00 0.00 3.86
544 546 5.239744 TCATCCGTTGCTTAACTGCTTTTTA 59.760 36.000 0.00 0.00 0.00 1.52
563 567 6.478512 TTTTACAAAGCAAGGAAGTCCAAT 57.521 33.333 0.00 0.00 38.89 3.16
592 596 7.114811 CCATGCTAAAAACATGCGATTATTACC 59.885 37.037 0.00 0.00 42.89 2.85
595 599 8.841300 TGCTAAAAACATGCGATTATTACCATA 58.159 29.630 0.00 0.00 0.00 2.74
637 648 5.001874 GGTAAGGACTTTCTGGTGGTAAAG 58.998 45.833 0.00 0.00 38.41 1.85
687 709 1.067635 CAGGCACAAAAGAATTCCCCG 60.068 52.381 0.65 0.00 0.00 5.73
767 789 9.657419 CTCCCAAAAACAAGCTCATTATTAAAT 57.343 29.630 0.00 0.00 0.00 1.40
860 909 2.495866 GCATTGCCACATTCCCCG 59.504 61.111 0.00 0.00 0.00 5.73
866 915 2.437716 CCACATTCCCCGTTCCCG 60.438 66.667 0.00 0.00 0.00 5.14
882 931 0.755327 CCCGTTCCCATTCCATTCCC 60.755 60.000 0.00 0.00 0.00 3.97
884 933 1.680338 CGTTCCCATTCCATTCCCTC 58.320 55.000 0.00 0.00 0.00 4.30
888 937 1.151450 CCATTCCATTCCCTCCCCG 59.849 63.158 0.00 0.00 0.00 5.73
1776 1838 3.900892 CTCGTGGCGCCGGTCTAT 61.901 66.667 23.90 0.00 0.00 1.98
2001 2063 2.154462 CTCAAGGAAATCCACGTGCTT 58.846 47.619 10.91 3.90 38.89 3.91
2004 2066 2.489329 CAAGGAAATCCACGTGCTTGAT 59.511 45.455 20.12 11.52 43.59 2.57
2025 2087 2.358003 GCCACACAGAAGCTCGCT 60.358 61.111 0.00 0.00 0.00 4.93
2232 2294 5.079689 TGCACAATGCTGATTGATTCATT 57.920 34.783 3.92 0.00 45.31 2.57
2265 2327 0.970427 GATCGGGCAATTTGGTGGGT 60.970 55.000 0.00 0.00 0.00 4.51
2356 2424 1.918609 GTACGTGCCTTCGTCTTCATC 59.081 52.381 0.00 0.00 43.12 2.92
2358 2426 1.000955 ACGTGCCTTCGTCTTCATCTT 59.999 47.619 0.00 0.00 40.04 2.40
2359 2427 1.656095 CGTGCCTTCGTCTTCATCTTC 59.344 52.381 0.00 0.00 0.00 2.87
2361 2429 3.265791 GTGCCTTCGTCTTCATCTTCAT 58.734 45.455 0.00 0.00 0.00 2.57
2363 2431 3.265791 GCCTTCGTCTTCATCTTCATGT 58.734 45.455 0.00 0.00 0.00 3.21
2364 2432 4.081697 TGCCTTCGTCTTCATCTTCATGTA 60.082 41.667 0.00 0.00 0.00 2.29
2440 2508 8.898761 GGTTCTCCCATGTTAATTTTTGTTTTT 58.101 29.630 0.00 0.00 0.00 1.94
2510 2578 1.785518 CGTCAACGGCTAATTTGTCGC 60.786 52.381 13.69 0.00 38.79 5.19
2536 2604 6.155221 TGAGTTTATGTTCCAGAGCTCACTAT 59.845 38.462 17.77 4.05 0.00 2.12
2564 2632 6.211384 TCACTTTGATCTCTCTCATGGTTACA 59.789 38.462 0.00 0.00 0.00 2.41
2598 2666 5.996219 TGTTCTGTAATTACACATGCACAC 58.004 37.500 14.35 0.60 31.93 3.82
2600 2668 6.073276 TGTTCTGTAATTACACATGCACACTC 60.073 38.462 14.35 0.00 31.93 3.51
2623 2691 2.039084 GGGGTGTGAGATTGTCTGTCTT 59.961 50.000 0.00 0.00 0.00 3.01
2624 2692 3.496870 GGGGTGTGAGATTGTCTGTCTTT 60.497 47.826 0.00 0.00 0.00 2.52
2625 2693 4.137543 GGGTGTGAGATTGTCTGTCTTTT 58.862 43.478 0.00 0.00 0.00 2.27
2626 2694 4.214332 GGGTGTGAGATTGTCTGTCTTTTC 59.786 45.833 0.00 0.00 0.00 2.29
2912 2981 0.456142 CGCCGTCAGATGAACGAGAA 60.456 55.000 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.559063 CGGATCTGCCAGCTGGGG 62.559 72.222 33.46 10.63 37.04 4.96
12 13 4.478371 TGCGGATCTGCCAGCTGG 62.478 66.667 29.34 29.34 37.18 4.85
13 14 3.200593 GTGCGGATCTGCCAGCTG 61.201 66.667 23.64 6.78 37.18 4.24
14 15 4.479993 GGTGCGGATCTGCCAGCT 62.480 66.667 23.64 0.00 37.18 4.24
16 17 3.411114 ATGGGTGCGGATCTGCCAG 62.411 63.158 23.64 0.00 35.94 4.85
17 18 3.405093 GATGGGTGCGGATCTGCCA 62.405 63.158 23.64 14.59 35.94 4.92
18 19 2.592861 GATGGGTGCGGATCTGCC 60.593 66.667 23.64 14.31 0.00 4.85
19 20 2.592861 GGATGGGTGCGGATCTGC 60.593 66.667 20.08 20.08 0.00 4.26
20 21 1.070445 GAGGATGGGTGCGGATCTG 59.930 63.158 0.00 0.00 0.00 2.90
21 22 2.143419 GGAGGATGGGTGCGGATCT 61.143 63.158 0.00 0.00 0.00 2.75
22 23 2.105806 GAGGAGGATGGGTGCGGATC 62.106 65.000 0.00 0.00 0.00 3.36
23 24 2.040464 AGGAGGATGGGTGCGGAT 60.040 61.111 0.00 0.00 0.00 4.18
24 25 2.764128 GAGGAGGATGGGTGCGGA 60.764 66.667 0.00 0.00 0.00 5.54
25 26 2.317149 GAAGAGGAGGATGGGTGCGG 62.317 65.000 0.00 0.00 0.00 5.69
26 27 1.144936 GAAGAGGAGGATGGGTGCG 59.855 63.158 0.00 0.00 0.00 5.34
27 28 1.274703 TGGAAGAGGAGGATGGGTGC 61.275 60.000 0.00 0.00 0.00 5.01
28 29 1.516110 ATGGAAGAGGAGGATGGGTG 58.484 55.000 0.00 0.00 0.00 4.61
29 30 2.428484 CCTATGGAAGAGGAGGATGGGT 60.428 54.545 0.00 0.00 35.99 4.51
30 31 2.264455 CCTATGGAAGAGGAGGATGGG 58.736 57.143 0.00 0.00 35.99 4.00
31 32 2.264455 CCCTATGGAAGAGGAGGATGG 58.736 57.143 0.00 0.00 35.99 3.51
32 33 2.903135 GACCCTATGGAAGAGGAGGATG 59.097 54.545 0.00 0.00 35.99 3.51
33 34 2.800788 AGACCCTATGGAAGAGGAGGAT 59.199 50.000 0.00 0.00 35.99 3.24
34 35 2.227703 AGACCCTATGGAAGAGGAGGA 58.772 52.381 0.00 0.00 35.99 3.71
35 36 2.785357 AGACCCTATGGAAGAGGAGG 57.215 55.000 0.00 0.00 35.99 4.30
36 37 3.922375 AGAAGACCCTATGGAAGAGGAG 58.078 50.000 0.00 0.00 35.99 3.69
37 38 4.290942 GAAGAAGACCCTATGGAAGAGGA 58.709 47.826 0.00 0.00 35.99 3.71
38 39 3.068873 CGAAGAAGACCCTATGGAAGAGG 59.931 52.174 0.00 0.00 34.81 3.69
39 40 3.954904 TCGAAGAAGACCCTATGGAAGAG 59.045 47.826 0.00 0.00 34.81 2.85
40 41 3.977312 TCGAAGAAGACCCTATGGAAGA 58.023 45.455 0.00 0.00 34.81 2.87
41 42 4.688021 CTTCGAAGAAGACCCTATGGAAG 58.312 47.826 20.74 0.00 45.90 3.46
42 43 3.118738 GCTTCGAAGAAGACCCTATGGAA 60.119 47.826 28.95 0.00 45.90 3.53
43 44 2.431057 GCTTCGAAGAAGACCCTATGGA 59.569 50.000 28.95 0.00 45.90 3.41
44 45 2.168521 TGCTTCGAAGAAGACCCTATGG 59.831 50.000 28.95 0.00 45.90 2.74
45 46 3.452474 CTGCTTCGAAGAAGACCCTATG 58.548 50.000 26.62 0.00 45.90 2.23
46 47 2.432510 CCTGCTTCGAAGAAGACCCTAT 59.567 50.000 31.25 0.00 45.90 2.57
47 48 1.825474 CCTGCTTCGAAGAAGACCCTA 59.175 52.381 31.25 5.44 45.90 3.53
48 49 0.610687 CCTGCTTCGAAGAAGACCCT 59.389 55.000 31.25 0.00 45.90 4.34
49 50 0.391793 CCCTGCTTCGAAGAAGACCC 60.392 60.000 31.25 12.35 45.90 4.46
50 51 0.391793 CCCCTGCTTCGAAGAAGACC 60.392 60.000 31.25 13.05 45.90 3.85
51 52 1.021920 GCCCCTGCTTCGAAGAAGAC 61.022 60.000 31.25 17.49 45.90 3.01
52 53 1.296715 GCCCCTGCTTCGAAGAAGA 59.703 57.895 31.25 12.40 45.90 2.87
53 54 1.746991 GGCCCCTGCTTCGAAGAAG 60.747 63.158 28.95 26.51 45.90 2.85
54 55 2.351276 GGCCCCTGCTTCGAAGAA 59.649 61.111 28.95 18.16 45.90 2.52
55 56 4.082523 CGGCCCCTGCTTCGAAGA 62.083 66.667 28.95 12.53 37.74 2.87
109 110 4.463879 CTCTGCTGGAGGGTGCCG 62.464 72.222 0.00 0.00 38.35 5.69
160 161 1.725557 TTTCGAGAGATCCGCCGAGG 61.726 60.000 0.00 0.00 41.60 4.63
161 162 0.317436 CTTTCGAGAGATCCGCCGAG 60.317 60.000 0.00 0.00 41.60 4.63
162 163 1.728069 CTTTCGAGAGATCCGCCGA 59.272 57.895 0.00 0.00 41.60 5.54
163 164 1.946650 GCTTTCGAGAGATCCGCCG 60.947 63.158 7.23 0.00 41.60 6.46
164 165 1.592939 GGCTTTCGAGAGATCCGCC 60.593 63.158 7.23 0.00 41.60 6.13
165 166 1.946650 CGGCTTTCGAGAGATCCGC 60.947 63.158 7.23 0.00 42.43 5.54
166 167 1.728069 TCGGCTTTCGAGAGATCCG 59.272 57.895 13.57 13.57 43.74 4.18
174 175 1.392710 GGGATCTCCTCGGCTTTCGA 61.393 60.000 0.00 0.00 46.77 3.71
175 176 1.068250 GGGATCTCCTCGGCTTTCG 59.932 63.158 0.00 0.00 40.90 3.46
176 177 1.338136 TGGGGATCTCCTCGGCTTTC 61.338 60.000 14.22 0.00 40.19 2.62
177 178 1.306997 TGGGGATCTCCTCGGCTTT 60.307 57.895 14.22 0.00 40.19 3.51
178 179 1.764054 CTGGGGATCTCCTCGGCTT 60.764 63.158 14.22 0.00 40.19 4.35
179 180 2.123077 CTGGGGATCTCCTCGGCT 60.123 66.667 14.22 0.00 40.19 5.52
180 181 2.123251 TCTGGGGATCTCCTCGGC 60.123 66.667 14.22 0.00 42.80 5.54
181 182 1.834822 GGTCTGGGGATCTCCTCGG 60.835 68.421 14.22 3.33 44.51 4.63
182 183 1.075970 TGGTCTGGGGATCTCCTCG 60.076 63.158 14.22 4.06 40.19 4.63
183 184 0.263172 TCTGGTCTGGGGATCTCCTC 59.737 60.000 14.22 3.37 36.90 3.71
184 185 0.264359 CTCTGGTCTGGGGATCTCCT 59.736 60.000 14.22 0.00 35.95 3.69
185 186 0.263172 TCTCTGGTCTGGGGATCTCC 59.737 60.000 3.99 3.99 0.00 3.71
186 187 1.408969 GTCTCTGGTCTGGGGATCTC 58.591 60.000 0.00 0.00 0.00 2.75
187 188 0.396417 CGTCTCTGGTCTGGGGATCT 60.396 60.000 0.00 0.00 0.00 2.75
188 189 0.395862 TCGTCTCTGGTCTGGGGATC 60.396 60.000 0.00 0.00 0.00 3.36
189 190 0.684805 GTCGTCTCTGGTCTGGGGAT 60.685 60.000 0.00 0.00 0.00 3.85
190 191 1.304217 GTCGTCTCTGGTCTGGGGA 60.304 63.158 0.00 0.00 0.00 4.81
191 192 2.701780 CGTCGTCTCTGGTCTGGGG 61.702 68.421 0.00 0.00 0.00 4.96
192 193 2.701780 CCGTCGTCTCTGGTCTGGG 61.702 68.421 0.00 0.00 0.00 4.45
193 194 2.701780 CCCGTCGTCTCTGGTCTGG 61.702 68.421 0.00 0.00 0.00 3.86
194 195 2.878429 CCCGTCGTCTCTGGTCTG 59.122 66.667 0.00 0.00 0.00 3.51
195 196 3.063084 GCCCGTCGTCTCTGGTCT 61.063 66.667 0.00 0.00 0.00 3.85
196 197 4.131088 GGCCCGTCGTCTCTGGTC 62.131 72.222 0.00 0.00 0.00 4.02
197 198 4.680537 AGGCCCGTCGTCTCTGGT 62.681 66.667 0.00 0.00 0.00 4.00
198 199 3.827898 GAGGCCCGTCGTCTCTGG 61.828 72.222 0.00 0.00 0.00 3.86
199 200 2.752238 AGAGGCCCGTCGTCTCTG 60.752 66.667 0.00 0.00 35.13 3.35
214 215 2.678934 CCGTGTTCCCTCGGGAGA 60.679 66.667 4.63 0.00 46.06 3.71
215 216 2.678934 TCCGTGTTCCCTCGGGAG 60.679 66.667 4.63 0.00 46.06 4.30
216 217 2.678934 CTCCGTGTTCCCTCGGGA 60.679 66.667 0.00 0.00 45.48 5.14
217 218 2.580601 AACTCCGTGTTCCCTCGGG 61.581 63.158 0.00 0.00 45.48 5.14
218 219 1.374252 CAACTCCGTGTTCCCTCGG 60.374 63.158 0.00 0.00 46.50 4.63
219 220 0.666577 GTCAACTCCGTGTTCCCTCG 60.667 60.000 0.00 0.00 36.63 4.63
220 221 0.666577 CGTCAACTCCGTGTTCCCTC 60.667 60.000 0.00 0.00 36.63 4.30
221 222 1.366366 CGTCAACTCCGTGTTCCCT 59.634 57.895 0.00 0.00 36.63 4.20
222 223 1.666872 CCGTCAACTCCGTGTTCCC 60.667 63.158 0.00 0.00 36.63 3.97
223 224 0.666577 CTCCGTCAACTCCGTGTTCC 60.667 60.000 0.00 0.00 36.63 3.62
224 225 1.282930 GCTCCGTCAACTCCGTGTTC 61.283 60.000 0.00 0.00 36.63 3.18
225 226 1.300697 GCTCCGTCAACTCCGTGTT 60.301 57.895 0.00 0.00 39.92 3.32
226 227 2.338984 GCTCCGTCAACTCCGTGT 59.661 61.111 0.00 0.00 0.00 4.49
227 228 2.805353 CGCTCCGTCAACTCCGTG 60.805 66.667 0.00 0.00 0.00 4.94
228 229 4.052229 CCGCTCCGTCAACTCCGT 62.052 66.667 0.00 0.00 0.00 4.69
229 230 4.796231 CCCGCTCCGTCAACTCCG 62.796 72.222 0.00 0.00 0.00 4.63
230 231 4.452733 CCCCGCTCCGTCAACTCC 62.453 72.222 0.00 0.00 0.00 3.85
231 232 4.452733 CCCCCGCTCCGTCAACTC 62.453 72.222 0.00 0.00 0.00 3.01
249 250 4.559063 CCTGGCCATGGCGGAGAG 62.559 72.222 29.90 20.74 43.06 3.20
251 252 4.113815 TTCCTGGCCATGGCGGAG 62.114 66.667 29.90 25.46 43.06 4.63
252 253 4.113815 CTTCCTGGCCATGGCGGA 62.114 66.667 29.90 27.11 43.06 5.54
255 256 3.145551 CTGCTTCCTGGCCATGGC 61.146 66.667 29.47 29.47 41.06 4.40
256 257 1.453379 CTCTGCTTCCTGGCCATGG 60.453 63.158 5.51 7.63 0.00 3.66
257 258 0.464013 CTCTCTGCTTCCTGGCCATG 60.464 60.000 5.51 2.84 0.00 3.66
258 259 1.913722 CTCTCTGCTTCCTGGCCAT 59.086 57.895 5.51 0.00 0.00 4.40
259 260 2.964310 GCTCTCTGCTTCCTGGCCA 61.964 63.158 4.71 4.71 38.95 5.36
260 261 2.124778 GCTCTCTGCTTCCTGGCC 60.125 66.667 0.00 0.00 38.95 5.36
261 262 2.511145 CGCTCTCTGCTTCCTGGC 60.511 66.667 0.00 0.00 40.11 4.85
262 263 2.186384 CCGCTCTCTGCTTCCTGG 59.814 66.667 0.00 0.00 40.11 4.45
263 264 2.186384 CCCGCTCTCTGCTTCCTG 59.814 66.667 0.00 0.00 40.11 3.86
264 265 3.080121 CCCCGCTCTCTGCTTCCT 61.080 66.667 0.00 0.00 40.11 3.36
265 266 4.168291 CCCCCGCTCTCTGCTTCC 62.168 72.222 0.00 0.00 40.11 3.46
266 267 4.847444 GCCCCCGCTCTCTGCTTC 62.847 72.222 0.00 0.00 40.11 3.86
277 278 2.746277 CTTTGTTCTCCGCCCCCG 60.746 66.667 0.00 0.00 0.00 5.73
278 279 2.361230 CCTTTGTTCTCCGCCCCC 60.361 66.667 0.00 0.00 0.00 5.40
279 280 2.361230 CCCTTTGTTCTCCGCCCC 60.361 66.667 0.00 0.00 0.00 5.80
280 281 2.361230 CCCCTTTGTTCTCCGCCC 60.361 66.667 0.00 0.00 0.00 6.13
281 282 2.361230 CCCCCTTTGTTCTCCGCC 60.361 66.667 0.00 0.00 0.00 6.13
282 283 1.377333 CTCCCCCTTTGTTCTCCGC 60.377 63.158 0.00 0.00 0.00 5.54
283 284 1.299976 CCTCCCCCTTTGTTCTCCG 59.700 63.158 0.00 0.00 0.00 4.63
284 285 0.038310 CACCTCCCCCTTTGTTCTCC 59.962 60.000 0.00 0.00 0.00 3.71
285 286 0.038310 CCACCTCCCCCTTTGTTCTC 59.962 60.000 0.00 0.00 0.00 2.87
286 287 2.081585 GCCACCTCCCCCTTTGTTCT 62.082 60.000 0.00 0.00 0.00 3.01
287 288 1.606601 GCCACCTCCCCCTTTGTTC 60.607 63.158 0.00 0.00 0.00 3.18
288 289 2.526110 GCCACCTCCCCCTTTGTT 59.474 61.111 0.00 0.00 0.00 2.83
289 290 3.590574 GGCCACCTCCCCCTTTGT 61.591 66.667 0.00 0.00 0.00 2.83
290 291 4.740822 CGGCCACCTCCCCCTTTG 62.741 72.222 2.24 0.00 0.00 2.77
320 321 3.186047 CTAACCCGTCGCTTGCCG 61.186 66.667 0.00 0.00 38.61 5.69
321 322 2.818274 CCTAACCCGTCGCTTGCC 60.818 66.667 0.00 0.00 0.00 4.52
322 323 2.047560 ACCTAACCCGTCGCTTGC 60.048 61.111 0.00 0.00 0.00 4.01
323 324 1.740296 CCACCTAACCCGTCGCTTG 60.740 63.158 0.00 0.00 0.00 4.01
324 325 1.909781 TCCACCTAACCCGTCGCTT 60.910 57.895 0.00 0.00 0.00 4.68
325 326 2.283388 TCCACCTAACCCGTCGCT 60.283 61.111 0.00 0.00 0.00 4.93
326 327 2.125793 GTCCACCTAACCCGTCGC 60.126 66.667 0.00 0.00 0.00 5.19
327 328 2.180017 CGTCCACCTAACCCGTCG 59.820 66.667 0.00 0.00 0.00 5.12
328 329 2.125793 GCGTCCACCTAACCCGTC 60.126 66.667 0.00 0.00 0.00 4.79
329 330 3.698820 GGCGTCCACCTAACCCGT 61.699 66.667 0.00 0.00 0.00 5.28
330 331 4.807039 CGGCGTCCACCTAACCCG 62.807 72.222 0.00 0.00 0.00 5.28
331 332 4.462280 CCGGCGTCCACCTAACCC 62.462 72.222 6.01 0.00 0.00 4.11
346 347 4.794439 TGCATCACTCCGACGCCG 62.794 66.667 0.00 0.00 0.00 6.46
347 348 3.188786 GTGCATCACTCCGACGCC 61.189 66.667 0.00 0.00 0.00 5.68
348 349 3.545481 CGTGCATCACTCCGACGC 61.545 66.667 0.00 0.00 31.34 5.19
349 350 2.880879 CCGTGCATCACTCCGACG 60.881 66.667 0.00 0.00 31.34 5.12
350 351 3.188786 GCCGTGCATCACTCCGAC 61.189 66.667 0.00 0.00 31.34 4.79
351 352 4.794439 CGCCGTGCATCACTCCGA 62.794 66.667 0.00 0.00 31.06 4.55
352 353 4.794439 TCGCCGTGCATCACTCCG 62.794 66.667 0.00 0.00 31.34 4.63
353 354 2.434185 TTCGCCGTGCATCACTCC 60.434 61.111 0.00 0.00 31.34 3.85
354 355 2.456119 CCTTCGCCGTGCATCACTC 61.456 63.158 0.00 0.00 31.34 3.51
355 356 2.434884 CCTTCGCCGTGCATCACT 60.435 61.111 0.00 0.00 31.34 3.41
356 357 3.499737 CCCTTCGCCGTGCATCAC 61.500 66.667 0.00 0.00 0.00 3.06
357 358 3.664025 CTCCCTTCGCCGTGCATCA 62.664 63.158 0.00 0.00 0.00 3.07
358 359 2.892425 CTCCCTTCGCCGTGCATC 60.892 66.667 0.00 0.00 0.00 3.91
359 360 4.473520 CCTCCCTTCGCCGTGCAT 62.474 66.667 0.00 0.00 0.00 3.96
365 366 3.855853 GAGAGCCCTCCCTTCGCC 61.856 72.222 0.00 0.00 33.30 5.54
366 367 3.077556 TGAGAGCCCTCCCTTCGC 61.078 66.667 0.00 0.00 38.66 4.70
367 368 2.896443 GTGAGAGCCCTCCCTTCG 59.104 66.667 0.00 0.00 38.66 3.79
368 369 2.896443 CGTGAGAGCCCTCCCTTC 59.104 66.667 0.00 0.00 38.66 3.46
369 370 3.394836 GCGTGAGAGCCCTCCCTT 61.395 66.667 0.00 0.00 38.66 3.95
370 371 4.704103 TGCGTGAGAGCCCTCCCT 62.704 66.667 0.00 0.00 38.66 4.20
371 372 4.459089 GTGCGTGAGAGCCCTCCC 62.459 72.222 0.00 0.00 38.66 4.30
372 373 3.363844 GAGTGCGTGAGAGCCCTCC 62.364 68.421 0.00 0.00 35.96 4.30
373 374 2.183046 GAGTGCGTGAGAGCCCTC 59.817 66.667 0.00 0.00 39.86 4.30
374 375 2.283532 AGAGTGCGTGAGAGCCCT 60.284 61.111 0.00 0.00 36.02 5.19
375 376 2.183046 GAGAGTGCGTGAGAGCCC 59.817 66.667 0.00 0.00 36.02 5.19
376 377 2.202544 CGAGAGTGCGTGAGAGCC 60.203 66.667 0.00 0.00 36.02 4.70
377 378 2.878520 GCGAGAGTGCGTGAGAGC 60.879 66.667 0.00 0.00 37.71 4.09
378 379 1.226267 GAGCGAGAGTGCGTGAGAG 60.226 63.158 0.00 0.00 40.67 3.20
379 380 1.640210 GAGAGCGAGAGTGCGTGAGA 61.640 60.000 0.00 0.00 40.67 3.27
380 381 1.226267 GAGAGCGAGAGTGCGTGAG 60.226 63.158 0.00 0.00 40.67 3.51
381 382 2.871099 GAGAGCGAGAGTGCGTGA 59.129 61.111 0.00 0.00 40.67 4.35
382 383 2.575525 CGAGAGCGAGAGTGCGTG 60.576 66.667 0.00 0.00 40.82 5.34
394 395 1.134098 AGAGAAGGGAGAGAGCGAGAG 60.134 57.143 0.00 0.00 0.00 3.20
395 396 0.916086 AGAGAAGGGAGAGAGCGAGA 59.084 55.000 0.00 0.00 0.00 4.04
396 397 2.158813 ACTAGAGAAGGGAGAGAGCGAG 60.159 54.545 0.00 0.00 0.00 5.03
397 398 1.841277 ACTAGAGAAGGGAGAGAGCGA 59.159 52.381 0.00 0.00 0.00 4.93
398 399 2.341846 ACTAGAGAAGGGAGAGAGCG 57.658 55.000 0.00 0.00 0.00 5.03
399 400 4.788679 AGTTACTAGAGAAGGGAGAGAGC 58.211 47.826 0.00 0.00 0.00 4.09
400 401 5.996644 TGAGTTACTAGAGAAGGGAGAGAG 58.003 45.833 0.00 0.00 0.00 3.20
401 402 6.390048 TTGAGTTACTAGAGAAGGGAGAGA 57.610 41.667 0.00 0.00 0.00 3.10
402 403 5.067283 GCTTGAGTTACTAGAGAAGGGAGAG 59.933 48.000 0.00 0.00 0.00 3.20
403 404 4.951094 GCTTGAGTTACTAGAGAAGGGAGA 59.049 45.833 0.00 0.00 0.00 3.71
404 405 4.707448 TGCTTGAGTTACTAGAGAAGGGAG 59.293 45.833 0.00 0.00 0.00 4.30
405 406 4.463186 GTGCTTGAGTTACTAGAGAAGGGA 59.537 45.833 0.00 0.00 0.00 4.20
406 407 4.220821 TGTGCTTGAGTTACTAGAGAAGGG 59.779 45.833 0.00 0.00 0.00 3.95
407 408 5.392767 TGTGCTTGAGTTACTAGAGAAGG 57.607 43.478 0.00 0.00 0.00 3.46
408 409 6.689241 CGTATGTGCTTGAGTTACTAGAGAAG 59.311 42.308 0.00 0.00 0.00 2.85
409 410 6.404403 CCGTATGTGCTTGAGTTACTAGAGAA 60.404 42.308 0.00 0.00 0.00 2.87
410 411 5.066117 CCGTATGTGCTTGAGTTACTAGAGA 59.934 44.000 0.00 0.00 0.00 3.10
411 412 5.066117 TCCGTATGTGCTTGAGTTACTAGAG 59.934 44.000 0.00 0.00 0.00 2.43
412 413 4.945543 TCCGTATGTGCTTGAGTTACTAGA 59.054 41.667 0.00 0.00 0.00 2.43
413 414 5.244785 TCCGTATGTGCTTGAGTTACTAG 57.755 43.478 0.00 0.00 0.00 2.57
414 415 5.648178 TTCCGTATGTGCTTGAGTTACTA 57.352 39.130 0.00 0.00 0.00 1.82
415 416 4.530710 TTCCGTATGTGCTTGAGTTACT 57.469 40.909 0.00 0.00 0.00 2.24
416 417 4.927425 TCTTTCCGTATGTGCTTGAGTTAC 59.073 41.667 0.00 0.00 0.00 2.50
417 418 5.142061 TCTTTCCGTATGTGCTTGAGTTA 57.858 39.130 0.00 0.00 0.00 2.24
418 419 4.002906 TCTTTCCGTATGTGCTTGAGTT 57.997 40.909 0.00 0.00 0.00 3.01
419 420 3.678056 TCTTTCCGTATGTGCTTGAGT 57.322 42.857 0.00 0.00 0.00 3.41
420 421 5.551760 AAATCTTTCCGTATGTGCTTGAG 57.448 39.130 0.00 0.00 0.00 3.02
421 422 5.698832 CAAAATCTTTCCGTATGTGCTTGA 58.301 37.500 0.00 0.00 0.00 3.02
422 423 4.324402 GCAAAATCTTTCCGTATGTGCTTG 59.676 41.667 0.00 0.00 0.00 4.01
423 424 4.218417 AGCAAAATCTTTCCGTATGTGCTT 59.782 37.500 0.00 0.00 36.45 3.91
424 425 3.758554 AGCAAAATCTTTCCGTATGTGCT 59.241 39.130 0.00 0.00 35.09 4.40
425 426 4.096732 AGCAAAATCTTTCCGTATGTGC 57.903 40.909 0.00 0.00 0.00 4.57
426 427 5.551760 AGAGCAAAATCTTTCCGTATGTG 57.448 39.130 0.00 0.00 0.00 3.21
427 428 6.407202 AGTAGAGCAAAATCTTTCCGTATGT 58.593 36.000 0.00 0.00 0.00 2.29
428 429 6.910536 AGTAGAGCAAAATCTTTCCGTATG 57.089 37.500 0.00 0.00 0.00 2.39
429 430 7.553334 TGTAGTAGAGCAAAATCTTTCCGTAT 58.447 34.615 0.00 0.00 0.00 3.06
430 431 6.927416 TGTAGTAGAGCAAAATCTTTCCGTA 58.073 36.000 0.00 0.00 0.00 4.02
431 432 5.790593 TGTAGTAGAGCAAAATCTTTCCGT 58.209 37.500 0.00 0.00 0.00 4.69
432 433 6.910536 ATGTAGTAGAGCAAAATCTTTCCG 57.089 37.500 0.00 0.00 0.00 4.30
433 434 8.268850 TGAATGTAGTAGAGCAAAATCTTTCC 57.731 34.615 0.00 0.00 0.00 3.13
437 438 9.979578 CTCTATGAATGTAGTAGAGCAAAATCT 57.020 33.333 0.00 0.00 36.22 2.40
445 446 6.176975 CGGAGCTCTATGAATGTAGTAGAG 57.823 45.833 14.64 4.67 42.65 2.43
472 473 0.884704 AACTCATGCGTGGTGGACAC 60.885 55.000 5.98 0.00 46.78 3.67
473 474 0.884259 CAACTCATGCGTGGTGGACA 60.884 55.000 5.98 0.00 0.00 4.02
474 475 0.602638 TCAACTCATGCGTGGTGGAC 60.603 55.000 5.98 0.00 0.00 4.02
475 476 0.320683 CTCAACTCATGCGTGGTGGA 60.321 55.000 5.98 5.38 0.00 4.02
476 477 0.603707 ACTCAACTCATGCGTGGTGG 60.604 55.000 5.98 0.93 0.00 4.61
477 478 1.726791 GTACTCAACTCATGCGTGGTG 59.273 52.381 5.98 2.62 0.00 4.17
478 479 1.668919 CGTACTCAACTCATGCGTGGT 60.669 52.381 5.98 0.00 0.00 4.16
479 480 0.992072 CGTACTCAACTCATGCGTGG 59.008 55.000 5.98 0.00 0.00 4.94
480 481 0.992072 CCGTACTCAACTCATGCGTG 59.008 55.000 0.00 0.00 0.00 5.34
481 482 0.601558 ACCGTACTCAACTCATGCGT 59.398 50.000 0.00 0.00 0.00 5.24
482 483 2.554806 TACCGTACTCAACTCATGCG 57.445 50.000 0.00 0.00 0.00 4.73
483 484 3.123804 CCATACCGTACTCAACTCATGC 58.876 50.000 0.00 0.00 0.00 4.06
484 485 4.338400 TCTCCATACCGTACTCAACTCATG 59.662 45.833 0.00 0.00 0.00 3.07
485 486 4.533815 TCTCCATACCGTACTCAACTCAT 58.466 43.478 0.00 0.00 0.00 2.90
486 487 3.945921 CTCTCCATACCGTACTCAACTCA 59.054 47.826 0.00 0.00 0.00 3.41
487 488 3.243134 GCTCTCCATACCGTACTCAACTC 60.243 52.174 0.00 0.00 0.00 3.01
497 498 3.674528 ATCTCATTGCTCTCCATACCG 57.325 47.619 0.00 0.00 0.00 4.02
506 507 3.201290 ACGGATGACAATCTCATTGCTC 58.799 45.455 0.00 0.00 43.98 4.26
544 546 3.507622 GCTATTGGACTTCCTTGCTTTGT 59.492 43.478 0.00 0.00 36.82 2.83
557 561 5.323371 TGTTTTTAGCATGGCTATTGGAC 57.677 39.130 0.00 0.00 41.01 4.02
563 567 3.013219 TCGCATGTTTTTAGCATGGCTA 58.987 40.909 7.29 0.00 42.72 3.93
592 596 6.329496 ACCGGTGTTGATATTGCTTTTTATG 58.671 36.000 6.12 0.00 0.00 1.90
595 599 4.864704 ACCGGTGTTGATATTGCTTTTT 57.135 36.364 6.12 0.00 0.00 1.94
637 648 0.891904 TACGCCTCCTTTTGGGTTGC 60.892 55.000 0.00 0.00 40.87 4.17
687 709 6.901081 AATGCTTCCACTTATTTATAGGCC 57.099 37.500 0.00 0.00 0.00 5.19
803 828 5.492895 TGGAGTTTTATATGAAGGCGTTCA 58.507 37.500 22.83 22.83 46.81 3.18
860 909 1.749063 GAATGGAATGGGAACGGGAAC 59.251 52.381 0.00 0.00 0.00 3.62
866 915 1.411644 GGGAGGGAATGGAATGGGAAC 60.412 57.143 0.00 0.00 0.00 3.62
1500 1556 3.404141 GACGAGCAGGACGGAGAGC 62.404 68.421 0.00 0.00 34.93 4.09
2001 2063 3.338249 GAGCTTCTGTGTGGCTTTATCA 58.662 45.455 0.00 0.00 36.37 2.15
2004 2066 1.795768 CGAGCTTCTGTGTGGCTTTA 58.204 50.000 0.00 0.00 36.37 1.85
2232 2294 0.033920 CCGATCAATGGCGAGATGGA 59.966 55.000 0.00 0.00 0.00 3.41
2265 2327 5.307196 ACCAAGAAGAAGAAAGCTACCTACA 59.693 40.000 0.00 0.00 0.00 2.74
2356 2424 6.900194 TCTAATCCCCTTCCTTTACATGAAG 58.100 40.000 0.00 0.00 38.14 3.02
2358 2426 6.901615 TTCTAATCCCCTTCCTTTACATGA 57.098 37.500 0.00 0.00 0.00 3.07
2359 2427 6.547510 CCTTTCTAATCCCCTTCCTTTACATG 59.452 42.308 0.00 0.00 0.00 3.21
2361 2429 5.044402 CCCTTTCTAATCCCCTTCCTTTACA 60.044 44.000 0.00 0.00 0.00 2.41
2363 2431 4.480908 CCCCTTTCTAATCCCCTTCCTTTA 59.519 45.833 0.00 0.00 0.00 1.85
2364 2432 3.272285 CCCCTTTCTAATCCCCTTCCTTT 59.728 47.826 0.00 0.00 0.00 3.11
2480 2548 1.011242 CCGTTGACGCACACAACTG 60.011 57.895 13.09 5.73 43.40 3.16
2510 2578 4.629200 GTGAGCTCTGGAACATAAACTCAG 59.371 45.833 16.19 0.00 38.20 3.35
2536 2604 4.081254 CCATGAGAGAGATCAAAGTGACCA 60.081 45.833 0.00 0.00 31.76 4.02
2598 2666 0.108138 GACAATCTCACACCCCCGAG 60.108 60.000 0.00 0.00 0.00 4.63
2600 2668 0.391661 CAGACAATCTCACACCCCCG 60.392 60.000 0.00 0.00 0.00 5.73
2912 2981 3.604582 CGAGAAGAAAGGGCTTGATCTT 58.395 45.455 0.00 0.00 34.96 2.40
2959 3028 2.087646 GCCTTCAAGGACTGGATGTTC 58.912 52.381 7.98 0.00 37.67 3.18


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

AutoCloner maintained by Alex Coulton.