Multiple sequence alignment - TraesCS7D01G413400

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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 TraesCS7D01G413400 chr7D 100.000 2315 0 0 1 2315 531597950 531600264 0.000000e+00 4276
1 TraesCS7D01G413400 chr7D 91.379 174 14 1 469 642 348321493 348321665 1.070000e-58 237
2 TraesCS7D01G413400 chr7A 93.241 1376 74 10 940 2313 611858387 611859745 0.000000e+00 2008
3 TraesCS7D01G413400 chr7A 91.111 315 15 7 640 942 611848911 611849224 4.600000e-112 414
4 TraesCS7D01G413400 chr7A 94.048 168 8 2 476 642 247210645 247210479 1.060000e-63 254
5 TraesCS7D01G413400 chr7A 91.667 84 7 0 376 459 611847941 611848024 1.450000e-22 117
6 TraesCS7D01G413400 chr6A 94.545 165 6 3 479 642 483259681 483259519 3.820000e-63 252
7 TraesCS7D01G413400 chr3A 95.541 157 5 2 486 642 497183165 497183319 1.370000e-62 250
8 TraesCS7D01G413400 chr2B 91.061 179 15 1 469 647 168863670 168863493 8.270000e-60 241
9 TraesCS7D01G413400 chr1A 92.353 170 11 2 479 648 564779426 564779593 8.270000e-60 241
10 TraesCS7D01G413400 chr5D 91.379 174 14 1 469 642 560778754 560778582 1.070000e-58 237
11 TraesCS7D01G413400 chr4D 91.379 174 14 1 469 642 94312404 94312232 1.070000e-58 237
12 TraesCS7D01G413400 chr1B 90.503 179 15 2 469 647 224183506 224183682 3.850000e-58 235


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 TraesCS7D01G413400 chr7D 531597950 531600264 2314 False 4276.0 4276 100.000 1 2315 1 chr7D.!!$F2 2314
1 TraesCS7D01G413400 chr7A 611858387 611859745 1358 False 2008.0 2008 93.241 940 2313 1 chr7A.!!$F1 1373
2 TraesCS7D01G413400 chr7A 611847941 611849224 1283 False 265.5 414 91.389 376 942 2 chr7A.!!$F2 566

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
422 423 0.320247 AAGGAGAGCAGCTCACGTTG 60.32 55.0 24.64 0.0 45.81 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 2465 0.107508 ACCAGAATCACCGCATGGAG 60.108 55.0 0.0 0.0 39.21 3.86 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
37 38 8.682710 ACAGTCAAATGTTTATGTTAACACTGT 58.317 29.630 11.22 11.66 40.53 3.55
38 39 9.169468 CAGTCAAATGTTTATGTTAACACTGTC 57.831 33.333 11.22 3.34 40.53 3.51
39 40 9.120538 AGTCAAATGTTTATGTTAACACTGTCT 57.879 29.630 11.22 0.00 40.53 3.41
40 41 9.730420 GTCAAATGTTTATGTTAACACTGTCTT 57.270 29.630 11.22 0.00 40.53 3.01
41 42 9.944663 TCAAATGTTTATGTTAACACTGTCTTC 57.055 29.630 11.22 0.00 40.53 2.87
42 43 9.950680 CAAATGTTTATGTTAACACTGTCTTCT 57.049 29.630 11.22 0.00 40.53 2.85
45 46 9.998106 ATGTTTATGTTAACACTGTCTTCTAGT 57.002 29.630 11.22 0.00 40.53 2.57
49 50 9.524496 TTATGTTAACACTGTCTTCTAGTAGGA 57.476 33.333 11.22 0.00 0.00 2.94
50 51 7.828508 TGTTAACACTGTCTTCTAGTAGGAA 57.171 36.000 3.59 0.00 0.00 3.36
51 52 7.883217 TGTTAACACTGTCTTCTAGTAGGAAG 58.117 38.462 3.59 0.81 42.72 3.46
52 53 7.504911 TGTTAACACTGTCTTCTAGTAGGAAGT 59.495 37.037 3.59 0.00 42.19 3.01
53 54 9.007901 GTTAACACTGTCTTCTAGTAGGAAGTA 57.992 37.037 0.00 0.00 42.19 2.24
54 55 9.578576 TTAACACTGTCTTCTAGTAGGAAGTAA 57.421 33.333 0.00 0.00 42.19 2.24
55 56 7.690952 ACACTGTCTTCTAGTAGGAAGTAAG 57.309 40.000 0.00 5.40 42.19 2.34
56 57 7.460071 ACACTGTCTTCTAGTAGGAAGTAAGA 58.540 38.462 0.00 0.00 42.19 2.10
57 58 7.608761 ACACTGTCTTCTAGTAGGAAGTAAGAG 59.391 40.741 0.00 4.57 42.19 2.85
58 59 7.608761 CACTGTCTTCTAGTAGGAAGTAAGAGT 59.391 40.741 0.00 0.00 42.19 3.24
59 60 8.165397 ACTGTCTTCTAGTAGGAAGTAAGAGTT 58.835 37.037 0.00 0.00 42.19 3.01
60 61 9.669887 CTGTCTTCTAGTAGGAAGTAAGAGTTA 57.330 37.037 0.00 0.00 42.19 2.24
65 66 8.152309 TCTAGTAGGAAGTAAGAGTTATTCGC 57.848 38.462 0.00 0.00 0.00 4.70
66 67 6.770746 AGTAGGAAGTAAGAGTTATTCGCA 57.229 37.500 0.00 0.00 0.00 5.10
67 68 7.166691 AGTAGGAAGTAAGAGTTATTCGCAA 57.833 36.000 0.00 0.00 0.00 4.85
68 69 7.609056 AGTAGGAAGTAAGAGTTATTCGCAAA 58.391 34.615 0.00 0.00 0.00 3.68
69 70 8.092687 AGTAGGAAGTAAGAGTTATTCGCAAAA 58.907 33.333 0.00 0.00 0.00 2.44
70 71 7.739498 AGGAAGTAAGAGTTATTCGCAAAAA 57.261 32.000 0.00 0.00 0.00 1.94
103 104 8.979534 AGGAAGTAAGAGTTTAGTTAGTATGGG 58.020 37.037 0.00 0.00 33.58 4.00
104 105 8.975295 GGAAGTAAGAGTTTAGTTAGTATGGGA 58.025 37.037 0.00 0.00 33.58 4.37
111 112 9.668497 AGAGTTTAGTTAGTATGGGATTTTCAC 57.332 33.333 0.00 0.00 0.00 3.18
112 113 9.668497 GAGTTTAGTTAGTATGGGATTTTCACT 57.332 33.333 0.00 0.00 0.00 3.41
126 127 9.938280 TGGGATTTTCACTATATAACGAATAGG 57.062 33.333 0.00 0.00 32.26 2.57
127 128 9.939802 GGGATTTTCACTATATAACGAATAGGT 57.060 33.333 0.00 0.00 32.26 3.08
140 141 6.476243 AACGAATAGGTAAACATGTGTCAC 57.524 37.500 0.00 0.00 0.00 3.67
141 142 5.543714 ACGAATAGGTAAACATGTGTCACA 58.456 37.500 8.40 8.40 0.00 3.58
142 143 5.992829 ACGAATAGGTAAACATGTGTCACAA 59.007 36.000 10.28 0.00 0.00 3.33
143 144 6.073440 ACGAATAGGTAAACATGTGTCACAAC 60.073 38.462 10.28 2.91 0.00 3.32
144 145 6.073494 CGAATAGGTAAACATGTGTCACAACA 60.073 38.462 10.28 0.00 0.00 3.33
159 160 6.993079 TGTCACAACACTAATACTCATCACT 58.007 36.000 0.00 0.00 0.00 3.41
160 161 7.441836 TGTCACAACACTAATACTCATCACTT 58.558 34.615 0.00 0.00 0.00 3.16
161 162 8.581578 TGTCACAACACTAATACTCATCACTTA 58.418 33.333 0.00 0.00 0.00 2.24
162 163 9.419297 GTCACAACACTAATACTCATCACTTAA 57.581 33.333 0.00 0.00 0.00 1.85
163 164 9.639601 TCACAACACTAATACTCATCACTTAAG 57.360 33.333 0.00 0.00 0.00 1.85
164 165 8.383619 CACAACACTAATACTCATCACTTAAGC 58.616 37.037 1.29 0.00 0.00 3.09
165 166 8.314751 ACAACACTAATACTCATCACTTAAGCT 58.685 33.333 1.29 0.00 0.00 3.74
166 167 9.803315 CAACACTAATACTCATCACTTAAGCTA 57.197 33.333 1.29 0.00 0.00 3.32
168 169 9.191479 ACACTAATACTCATCACTTAAGCTAGT 57.809 33.333 1.29 2.15 0.00 2.57
169 170 9.457110 CACTAATACTCATCACTTAAGCTAGTG 57.543 37.037 9.95 9.95 45.46 2.74
170 171 8.138712 ACTAATACTCATCACTTAAGCTAGTGC 58.861 37.037 11.18 0.00 44.10 4.40
171 172 4.808414 ACTCATCACTTAAGCTAGTGCA 57.192 40.909 11.18 2.44 44.10 4.57
172 173 4.753233 ACTCATCACTTAAGCTAGTGCAG 58.247 43.478 11.18 9.22 44.10 4.41
173 174 4.221703 ACTCATCACTTAAGCTAGTGCAGT 59.778 41.667 11.18 9.73 44.10 4.40
174 175 4.498241 TCATCACTTAAGCTAGTGCAGTG 58.502 43.478 11.18 9.78 44.10 3.66
175 176 3.319137 TCACTTAAGCTAGTGCAGTGG 57.681 47.619 11.18 1.51 44.10 4.00
176 177 2.632996 TCACTTAAGCTAGTGCAGTGGT 59.367 45.455 11.18 0.00 44.10 4.16
177 178 3.830178 TCACTTAAGCTAGTGCAGTGGTA 59.170 43.478 11.18 0.00 44.10 3.25
178 179 4.466370 TCACTTAAGCTAGTGCAGTGGTAT 59.534 41.667 11.18 0.00 44.10 2.73
179 180 5.655090 TCACTTAAGCTAGTGCAGTGGTATA 59.345 40.000 11.18 0.00 44.10 1.47
180 181 5.749109 CACTTAAGCTAGTGCAGTGGTATAC 59.251 44.000 3.69 0.00 39.12 1.47
181 182 3.438297 AAGCTAGTGCAGTGGTATACG 57.562 47.619 3.69 0.00 42.74 3.06
182 183 2.651455 AGCTAGTGCAGTGGTATACGA 58.349 47.619 3.69 0.00 42.74 3.43
183 184 2.619177 AGCTAGTGCAGTGGTATACGAG 59.381 50.000 3.69 0.00 42.74 4.18
184 185 2.287668 GCTAGTGCAGTGGTATACGAGG 60.288 54.545 3.69 0.00 39.41 4.63
185 186 2.139323 AGTGCAGTGGTATACGAGGA 57.861 50.000 0.00 0.00 0.00 3.71
186 187 2.453521 AGTGCAGTGGTATACGAGGAA 58.546 47.619 0.00 0.00 0.00 3.36
187 188 2.829720 AGTGCAGTGGTATACGAGGAAA 59.170 45.455 0.00 0.00 0.00 3.13
188 189 3.451178 AGTGCAGTGGTATACGAGGAAAT 59.549 43.478 0.00 0.00 0.00 2.17
189 190 4.647853 AGTGCAGTGGTATACGAGGAAATA 59.352 41.667 0.00 0.00 0.00 1.40
190 191 5.128171 AGTGCAGTGGTATACGAGGAAATAA 59.872 40.000 0.00 0.00 0.00 1.40
191 192 5.989777 GTGCAGTGGTATACGAGGAAATAAT 59.010 40.000 0.00 0.00 0.00 1.28
192 193 5.989168 TGCAGTGGTATACGAGGAAATAATG 59.011 40.000 0.00 0.00 0.00 1.90
193 194 5.408604 GCAGTGGTATACGAGGAAATAATGG 59.591 44.000 0.00 0.00 0.00 3.16
194 195 6.522054 CAGTGGTATACGAGGAAATAATGGT 58.478 40.000 0.00 0.00 0.00 3.55
195 196 6.645415 CAGTGGTATACGAGGAAATAATGGTC 59.355 42.308 0.00 0.00 0.00 4.02
196 197 6.325545 AGTGGTATACGAGGAAATAATGGTCA 59.674 38.462 0.00 0.00 0.00 4.02
197 198 6.987992 GTGGTATACGAGGAAATAATGGTCAA 59.012 38.462 0.00 0.00 0.00 3.18
198 199 7.170998 GTGGTATACGAGGAAATAATGGTCAAG 59.829 40.741 0.00 0.00 0.00 3.02
199 200 7.070198 TGGTATACGAGGAAATAATGGTCAAGA 59.930 37.037 0.00 0.00 0.00 3.02
200 201 7.384387 GGTATACGAGGAAATAATGGTCAAGAC 59.616 40.741 0.00 0.00 0.00 3.01
201 202 5.422214 ACGAGGAAATAATGGTCAAGACT 57.578 39.130 0.00 0.00 0.00 3.24
202 203 6.540438 ACGAGGAAATAATGGTCAAGACTA 57.460 37.500 0.00 0.00 0.00 2.59
203 204 6.942976 ACGAGGAAATAATGGTCAAGACTAA 58.057 36.000 0.00 0.00 0.00 2.24
204 205 7.565680 ACGAGGAAATAATGGTCAAGACTAAT 58.434 34.615 0.00 0.00 0.00 1.73
205 206 8.047310 ACGAGGAAATAATGGTCAAGACTAATT 58.953 33.333 0.00 4.08 0.00 1.40
206 207 9.542462 CGAGGAAATAATGGTCAAGACTAATTA 57.458 33.333 0.00 5.93 0.00 1.40
217 218 9.326413 TGGTCAAGACTAATTAATAAAGCTAGC 57.674 33.333 6.62 6.62 0.00 3.42
218 219 9.549078 GGTCAAGACTAATTAATAAAGCTAGCT 57.451 33.333 12.68 12.68 0.00 3.32
236 237 9.667107 AAGCTAGCTTAGTATTTGTTTGATACA 57.333 29.630 28.36 0.00 34.05 2.29
237 238 9.838339 AGCTAGCTTAGTATTTGTTTGATACAT 57.162 29.630 12.68 0.00 36.44 2.29
283 284 5.649782 ATTTTCACTCCAACATGTCATCC 57.350 39.130 0.00 0.00 0.00 3.51
284 285 4.371624 TTTCACTCCAACATGTCATCCT 57.628 40.909 0.00 0.00 0.00 3.24
285 286 5.497464 TTTCACTCCAACATGTCATCCTA 57.503 39.130 0.00 0.00 0.00 2.94
286 287 4.471904 TCACTCCAACATGTCATCCTAC 57.528 45.455 0.00 0.00 0.00 3.18
287 288 4.096681 TCACTCCAACATGTCATCCTACT 58.903 43.478 0.00 0.00 0.00 2.57
288 289 5.269189 TCACTCCAACATGTCATCCTACTA 58.731 41.667 0.00 0.00 0.00 1.82
289 290 5.899547 TCACTCCAACATGTCATCCTACTAT 59.100 40.000 0.00 0.00 0.00 2.12
290 291 5.987953 CACTCCAACATGTCATCCTACTATG 59.012 44.000 0.00 0.00 0.00 2.23
291 292 5.899547 ACTCCAACATGTCATCCTACTATGA 59.100 40.000 0.00 0.00 33.48 2.15
292 293 6.041409 ACTCCAACATGTCATCCTACTATGAG 59.959 42.308 0.00 0.00 36.57 2.90
293 294 5.899547 TCCAACATGTCATCCTACTATGAGT 59.100 40.000 0.00 0.00 36.57 3.41
294 295 7.066781 TCCAACATGTCATCCTACTATGAGTA 58.933 38.462 0.00 0.00 36.57 2.59
295 296 7.231519 TCCAACATGTCATCCTACTATGAGTAG 59.768 40.741 0.00 6.67 45.93 2.57
296 297 7.014711 CCAACATGTCATCCTACTATGAGTAGT 59.985 40.741 0.00 0.51 45.12 2.73
297 298 7.517614 ACATGTCATCCTACTATGAGTAGTG 57.482 40.000 11.66 5.69 45.12 2.74
298 299 7.063593 ACATGTCATCCTACTATGAGTAGTGT 58.936 38.462 11.66 5.73 45.12 3.55
299 300 6.944234 TGTCATCCTACTATGAGTAGTGTG 57.056 41.667 11.66 9.76 45.12 3.82
300 301 5.299531 TGTCATCCTACTATGAGTAGTGTGC 59.700 44.000 11.66 7.46 45.12 4.57
301 302 5.299531 GTCATCCTACTATGAGTAGTGTGCA 59.700 44.000 11.66 0.00 45.12 4.57
302 303 6.015856 GTCATCCTACTATGAGTAGTGTGCAT 60.016 42.308 11.66 0.00 45.12 3.96
303 304 5.774498 TCCTACTATGAGTAGTGTGCATG 57.226 43.478 11.66 0.00 45.12 4.06
304 305 4.038042 TCCTACTATGAGTAGTGTGCATGC 59.962 45.833 11.82 11.82 45.12 4.06
305 306 4.038522 CCTACTATGAGTAGTGTGCATGCT 59.961 45.833 20.33 0.00 45.12 3.79
306 307 4.478206 ACTATGAGTAGTGTGCATGCTT 57.522 40.909 20.33 4.60 39.66 3.91
307 308 4.836825 ACTATGAGTAGTGTGCATGCTTT 58.163 39.130 20.33 4.23 39.66 3.51
308 309 5.248640 ACTATGAGTAGTGTGCATGCTTTT 58.751 37.500 20.33 4.59 39.66 2.27
309 310 6.406370 ACTATGAGTAGTGTGCATGCTTTTA 58.594 36.000 20.33 3.59 39.66 1.52
310 311 5.551760 ATGAGTAGTGTGCATGCTTTTAC 57.448 39.130 20.33 14.93 0.00 2.01
311 312 4.641396 TGAGTAGTGTGCATGCTTTTACT 58.359 39.130 20.33 18.92 0.00 2.24
312 313 5.063204 TGAGTAGTGTGCATGCTTTTACTT 58.937 37.500 20.33 4.03 0.00 2.24
313 314 5.049474 TGAGTAGTGTGCATGCTTTTACTTG 60.049 40.000 20.33 0.00 0.00 3.16
314 315 5.063204 AGTAGTGTGCATGCTTTTACTTGA 58.937 37.500 20.33 1.57 0.00 3.02
315 316 4.228912 AGTGTGCATGCTTTTACTTGAC 57.771 40.909 20.33 5.64 0.00 3.18
316 317 3.631686 AGTGTGCATGCTTTTACTTGACA 59.368 39.130 20.33 8.44 0.00 3.58
317 318 4.097741 AGTGTGCATGCTTTTACTTGACAA 59.902 37.500 20.33 0.00 0.00 3.18
318 319 4.207019 GTGTGCATGCTTTTACTTGACAAC 59.793 41.667 20.33 4.10 0.00 3.32
319 320 4.097741 TGTGCATGCTTTTACTTGACAACT 59.902 37.500 20.33 0.00 0.00 3.16
320 321 4.442073 GTGCATGCTTTTACTTGACAACTG 59.558 41.667 20.33 0.00 0.00 3.16
321 322 4.097741 TGCATGCTTTTACTTGACAACTGT 59.902 37.500 20.33 0.00 0.00 3.55
322 323 5.043248 GCATGCTTTTACTTGACAACTGTT 58.957 37.500 11.37 0.00 0.00 3.16
323 324 5.519927 GCATGCTTTTACTTGACAACTGTTT 59.480 36.000 11.37 0.00 0.00 2.83
324 325 6.035975 GCATGCTTTTACTTGACAACTGTTTT 59.964 34.615 11.37 0.00 0.00 2.43
325 326 7.412891 GCATGCTTTTACTTGACAACTGTTTTT 60.413 33.333 11.37 0.00 0.00 1.94
404 405 4.450082 TCTAGAGTTGCGCATACTGAAA 57.550 40.909 23.61 11.53 0.00 2.69
415 416 2.419851 GCATACTGAAAGGAGAGCAGCT 60.420 50.000 0.00 0.00 39.30 4.24
422 423 0.320247 AAGGAGAGCAGCTCACGTTG 60.320 55.000 24.64 0.00 45.81 4.10
424 425 0.601311 GGAGAGCAGCTCACGTTGTT 60.601 55.000 24.64 1.03 45.81 2.83
434 435 3.003689 AGCTCACGTTGTTTTTCATCAGG 59.996 43.478 0.00 0.00 0.00 3.86
438 439 4.882427 TCACGTTGTTTTTCATCAGGGTAA 59.118 37.500 0.00 0.00 0.00 2.85
466 467 7.336396 AGTATGTCACTATTGTTCCTAAACCC 58.664 38.462 0.00 0.00 34.98 4.11
469 529 7.319052 TGTCACTATTGTTCCTAAACCCTAA 57.681 36.000 0.00 0.00 34.28 2.69
471 531 7.016858 TGTCACTATTGTTCCTAAACCCTAACT 59.983 37.037 0.00 0.00 34.28 2.24
472 532 7.548427 GTCACTATTGTTCCTAAACCCTAACTC 59.452 40.741 0.00 0.00 34.28 3.01
474 534 5.853572 ATTGTTCCTAAACCCTAACTCCA 57.146 39.130 0.00 0.00 34.28 3.86
476 536 5.649970 TGTTCCTAAACCCTAACTCCAAA 57.350 39.130 0.00 0.00 34.28 3.28
478 538 6.616577 TGTTCCTAAACCCTAACTCCAAATT 58.383 36.000 0.00 0.00 34.28 1.82
480 540 7.565768 TGTTCCTAAACCCTAACTCCAAATTTT 59.434 33.333 0.00 0.00 34.28 1.82
584 1025 7.861176 TCCAAACGTAATTTGTTTATGAAGC 57.139 32.000 7.83 0.00 45.45 3.86
587 1028 7.272515 CCAAACGTAATTTGTTTATGAAGCGAT 59.727 33.333 7.83 0.00 45.45 4.58
588 1029 8.635124 CAAACGTAATTTGTTTATGAAGCGATT 58.365 29.630 7.83 0.00 42.46 3.34
589 1030 8.736751 AACGTAATTTGTTTATGAAGCGATTT 57.263 26.923 0.00 0.00 32.17 2.17
590 1031 8.736751 ACGTAATTTGTTTATGAAGCGATTTT 57.263 26.923 0.00 0.00 32.17 1.82
591 1032 9.828852 ACGTAATTTGTTTATGAAGCGATTTTA 57.171 25.926 0.00 0.00 32.17 1.52
599 1040 9.997482 TGTTTATGAAGCGATTTTAAGATTACC 57.003 29.630 0.00 0.00 0.00 2.85
602 1043 6.583912 TGAAGCGATTTTAAGATTACCTCG 57.416 37.500 0.00 0.00 0.00 4.63
603 1044 5.522460 TGAAGCGATTTTAAGATTACCTCGG 59.478 40.000 0.00 0.00 0.00 4.63
605 1046 4.124970 GCGATTTTAAGATTACCTCGGGT 58.875 43.478 1.14 1.14 40.16 5.28
606 1047 4.025145 GCGATTTTAAGATTACCTCGGGTG 60.025 45.833 5.90 0.00 36.19 4.61
607 1048 4.025145 CGATTTTAAGATTACCTCGGGTGC 60.025 45.833 5.90 0.00 36.19 5.01
609 1050 3.536956 TTAAGATTACCTCGGGTGCAG 57.463 47.619 5.90 0.00 36.19 4.41
610 1051 1.568504 AAGATTACCTCGGGTGCAGA 58.431 50.000 5.90 0.00 36.19 4.26
611 1052 1.568504 AGATTACCTCGGGTGCAGAA 58.431 50.000 5.90 0.00 36.19 3.02
614 1055 3.709653 AGATTACCTCGGGTGCAGAATAA 59.290 43.478 5.90 0.00 36.19 1.40
615 1056 2.973694 TACCTCGGGTGCAGAATAAC 57.026 50.000 5.90 0.00 36.19 1.89
617 1058 1.628846 ACCTCGGGTGCAGAATAACTT 59.371 47.619 0.00 0.00 32.98 2.66
618 1059 2.835764 ACCTCGGGTGCAGAATAACTTA 59.164 45.455 0.00 0.00 32.98 2.24
620 1061 4.080526 ACCTCGGGTGCAGAATAACTTATT 60.081 41.667 0.00 0.00 32.98 1.40
621 1062 4.511826 CCTCGGGTGCAGAATAACTTATTC 59.488 45.833 12.07 12.07 43.77 1.75
622 1063 8.043668 ACCTCGGGTGCAGAATAACTTATTCT 62.044 42.308 15.62 15.62 44.21 2.40
631 1072 5.757850 GAATAACTTATTCTGCACCCTGG 57.242 43.478 12.55 0.00 41.00 4.45
632 1073 2.514458 AACTTATTCTGCACCCTGGG 57.486 50.000 12.28 12.28 0.00 4.45
635 1076 9.907723 GAATAACTTATTCTGCACCCTGGGTGA 62.908 44.444 42.58 27.49 46.15 4.02
655 1362 5.461078 GGTGATGAATAATCATTTGCTGCAC 59.539 40.000 0.00 0.00 46.90 4.57
662 1369 0.451383 TCATTTGCTGCACGTATGGC 59.549 50.000 0.00 0.00 0.00 4.40
703 1410 5.705441 GGAACTTGGAATTGTATCACACTCA 59.295 40.000 0.00 0.00 0.00 3.41
728 1435 1.764723 TCATCAGGCTATCACTGGGTG 59.235 52.381 0.00 0.00 36.62 4.61
748 1455 0.942410 TTTCGCAGAGCACGTGTACC 60.942 55.000 18.38 6.64 38.43 3.34
756 1463 1.014044 AGCACGTGTACCATCAAGCG 61.014 55.000 18.38 0.00 0.00 4.68
772 1479 2.281761 CGTCTGGTTGCTGCCCTT 60.282 61.111 0.00 0.00 0.00 3.95
793 1506 3.551846 TCACCAGTTCTTTGAGGGTTTC 58.448 45.455 0.00 0.00 0.00 2.78
801 1514 0.821711 TTTGAGGGTTTCGCACTGGG 60.822 55.000 0.00 0.00 0.00 4.45
844 1557 9.416284 GGTTAATTAACTATCTCCATTTTCCCA 57.584 33.333 23.89 0.00 36.47 4.37
852 1566 7.128077 ACTATCTCCATTTTCCCAAATCATGT 58.872 34.615 0.00 0.00 29.41 3.21
942 1661 5.357257 ACCTGCTCAACCAATAATAGTACG 58.643 41.667 0.00 0.00 0.00 3.67
954 1673 9.252962 ACCAATAATAGTACGTATGTGCTAAAC 57.747 33.333 15.63 0.00 44.77 2.01
1001 1720 8.408601 GCAAGGTATGTCATGAAACAAATCTAT 58.591 33.333 0.00 0.00 31.81 1.98
1041 1760 4.492494 TCTCTCTATGCTTTTGATGGCA 57.508 40.909 0.00 0.00 42.80 4.92
1053 1772 4.877378 TTTGATGGCATTCTTCTTTGCT 57.123 36.364 0.00 0.00 38.88 3.91
1105 1824 0.514255 CGCCATGGCATCATTCTACG 59.486 55.000 34.93 11.86 42.06 3.51
1154 1873 3.883489 GTGGAGGGTATTCTTAATGCCAC 59.117 47.826 8.69 0.00 44.50 5.01
1215 1934 1.514873 CGCGGCTGATTTTCTTGGC 60.515 57.895 0.00 0.00 0.00 4.52
1254 1973 2.354902 AACCATCTTGCAGGTTGGC 58.645 52.632 22.20 0.00 45.91 4.52
1282 2001 2.283894 CCCTGTTTCTTGGGGCCC 60.284 66.667 18.17 18.17 39.76 5.80
1287 2006 1.140134 TGTTTCTTGGGGCCCTAGCT 61.140 55.000 26.87 0.00 39.73 3.32
1316 2035 3.330701 TCCCTTGCAATCTGGACTTAGTT 59.669 43.478 0.00 0.00 0.00 2.24
1317 2036 4.534500 TCCCTTGCAATCTGGACTTAGTTA 59.466 41.667 0.00 0.00 0.00 2.24
1318 2037 4.878397 CCCTTGCAATCTGGACTTAGTTAG 59.122 45.833 0.00 0.00 0.00 2.34
1319 2038 5.491982 CCTTGCAATCTGGACTTAGTTAGT 58.508 41.667 0.00 0.00 40.71 2.24
1327 2046 4.897076 TCTGGACTTAGTTAGTGTTGGTGA 59.103 41.667 0.00 0.00 37.17 4.02
1405 2125 4.384647 GGATTGGAGTTGTAGAAGCTGGAT 60.385 45.833 0.00 0.00 0.00 3.41
1417 2137 0.620030 AGCTGGATGTACACATGGCA 59.380 50.000 0.00 0.00 36.57 4.92
1505 2225 7.509797 GTTGGTTCTTTTGTTTCTTGTTCTTG 58.490 34.615 0.00 0.00 0.00 3.02
1519 2239 4.431416 TGTTCTTGACATGGTAGTGGTT 57.569 40.909 0.00 0.00 32.00 3.67
1523 2243 3.587061 TCTTGACATGGTAGTGGTTGGAT 59.413 43.478 0.00 0.00 0.00 3.41
1525 2245 2.642311 TGACATGGTAGTGGTTGGATGT 59.358 45.455 0.00 0.00 0.00 3.06
1599 2319 4.218200 TGTGAATTTGTGATGGATGGTGAC 59.782 41.667 0.00 0.00 0.00 3.67
1617 2337 5.719563 TGGTGACACAGGAGATGAATTAGTA 59.280 40.000 8.08 0.00 33.40 1.82
1618 2338 6.043411 GGTGACACAGGAGATGAATTAGTAC 58.957 44.000 8.08 0.00 0.00 2.73
1619 2339 6.043411 GTGACACAGGAGATGAATTAGTACC 58.957 44.000 0.00 0.00 0.00 3.34
1626 2346 4.322801 GGAGATGAATTAGTACCGGGGATG 60.323 50.000 6.32 0.00 0.00 3.51
1672 2392 5.237127 TGTTCAAGTCACTAGCTCACATTTG 59.763 40.000 0.00 0.00 0.00 2.32
1679 2399 5.120830 GTCACTAGCTCACATTTGAAATCGT 59.879 40.000 0.00 0.00 0.00 3.73
1716 2437 0.108585 ACTGCACGGATCCAAAGTGT 59.891 50.000 13.41 1.66 38.10 3.55
1720 2441 0.790207 CACGGATCCAAAGTGTGACG 59.210 55.000 13.41 0.00 32.39 4.35
1735 2456 1.204941 GTGACGCAACCTACTCCATCT 59.795 52.381 0.00 0.00 0.00 2.90
1744 2465 2.171448 ACCTACTCCATCTGATTGCACC 59.829 50.000 0.00 0.00 0.00 5.01
1774 2495 3.944015 GGTGATTCTGGTTTCATCTCCTG 59.056 47.826 0.00 0.00 30.86 3.86
1782 2503 0.036388 TTTCATCTCCTGCCGTCACC 60.036 55.000 0.00 0.00 0.00 4.02
1828 2549 4.394610 AGTGCATTGGTTTTTGGTTTGAAC 59.605 37.500 0.00 0.00 0.00 3.18
1882 2603 6.150140 GCAGTTCAATTGTTCCTCTTGTATCT 59.850 38.462 5.13 0.00 0.00 1.98
2079 2800 2.560841 CCAAGAAGAAGAGAGGGGGAGA 60.561 54.545 0.00 0.00 0.00 3.71
2089 2810 0.637743 GAGGGGGAGAGGACCTTACT 59.362 60.000 0.00 0.00 34.02 2.24
2152 2873 3.983044 ACACTTCACCTAATCACCTCC 57.017 47.619 0.00 0.00 0.00 4.30
2171 2892 5.104900 ACCTCCTATCCTTGTTGTCATACAC 60.105 44.000 0.00 0.00 0.00 2.90
2180 2901 5.241506 CCTTGTTGTCATACACCATCTTGTT 59.758 40.000 0.00 0.00 0.00 2.83
2181 2902 5.940192 TGTTGTCATACACCATCTTGTTC 57.060 39.130 0.00 0.00 0.00 3.18
2193 2914 3.681897 CCATCTTGTTCAAAGTCTCCTCG 59.318 47.826 0.00 0.00 0.00 4.63
2204 2925 2.530701 AGTCTCCTCGAAGAACCATGT 58.469 47.619 0.00 0.00 34.09 3.21
2212 2933 4.564821 CCTCGAAGAACCATGTAGGGAAAA 60.565 45.833 0.00 0.00 43.89 2.29
2213 2934 5.174037 TCGAAGAACCATGTAGGGAAAAT 57.826 39.130 0.00 0.00 43.89 1.82
2214 2935 6.302535 TCGAAGAACCATGTAGGGAAAATA 57.697 37.500 0.00 0.00 43.89 1.40
2215 2936 6.895782 TCGAAGAACCATGTAGGGAAAATAT 58.104 36.000 0.00 0.00 43.89 1.28
2251 2972 8.995027 AGATATACATAACTGGCCATGAAAAA 57.005 30.769 5.51 0.00 0.00 1.94
2272 2993 3.976015 ACTCCTTCCAAAAACCAAGTGA 58.024 40.909 0.00 0.00 0.00 3.41
2289 3010 9.981460 AACCAAGTGAGAATATAAGGAGAAAAT 57.019 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.682710 ACAGTGTTAACATAAACATTTGACTGT 58.317 29.630 12.26 12.04 41.18 3.55
12 13 9.169468 GACAGTGTTAACATAAACATTTGACTG 57.831 33.333 12.26 11.43 41.18 3.51
13 14 9.120538 AGACAGTGTTAACATAAACATTTGACT 57.879 29.630 12.26 0.00 41.18 3.41
14 15 9.730420 AAGACAGTGTTAACATAAACATTTGAC 57.270 29.630 12.26 0.00 41.18 3.18
15 16 9.944663 GAAGACAGTGTTAACATAAACATTTGA 57.055 29.630 12.26 0.00 41.18 2.69
16 17 9.950680 AGAAGACAGTGTTAACATAAACATTTG 57.049 29.630 12.26 3.78 41.18 2.32
19 20 9.998106 ACTAGAAGACAGTGTTAACATAAACAT 57.002 29.630 12.26 0.00 41.18 2.71
23 24 9.524496 TCCTACTAGAAGACAGTGTTAACATAA 57.476 33.333 12.26 0.00 0.00 1.90
24 25 9.524496 TTCCTACTAGAAGACAGTGTTAACATA 57.476 33.333 12.26 0.00 0.00 2.29
25 26 8.418597 TTCCTACTAGAAGACAGTGTTAACAT 57.581 34.615 12.26 0.00 0.00 2.71
26 27 7.504911 ACTTCCTACTAGAAGACAGTGTTAACA 59.495 37.037 3.59 3.59 45.08 2.41
27 28 7.884257 ACTTCCTACTAGAAGACAGTGTTAAC 58.116 38.462 8.21 0.00 45.08 2.01
28 29 9.578576 TTACTTCCTACTAGAAGACAGTGTTAA 57.421 33.333 8.21 0.00 45.08 2.01
29 30 9.228949 CTTACTTCCTACTAGAAGACAGTGTTA 57.771 37.037 8.21 0.00 45.08 2.41
30 31 7.943447 TCTTACTTCCTACTAGAAGACAGTGTT 59.057 37.037 8.21 0.00 45.08 3.32
31 32 7.460071 TCTTACTTCCTACTAGAAGACAGTGT 58.540 38.462 8.21 0.00 45.08 3.55
32 33 7.608761 ACTCTTACTTCCTACTAGAAGACAGTG 59.391 40.741 8.21 6.64 45.08 3.66
33 34 7.692172 ACTCTTACTTCCTACTAGAAGACAGT 58.308 38.462 8.21 0.00 45.08 3.55
34 35 8.570068 AACTCTTACTTCCTACTAGAAGACAG 57.430 38.462 8.21 3.90 45.08 3.51
39 40 8.619546 GCGAATAACTCTTACTTCCTACTAGAA 58.380 37.037 0.00 0.00 0.00 2.10
40 41 7.772292 TGCGAATAACTCTTACTTCCTACTAGA 59.228 37.037 0.00 0.00 0.00 2.43
41 42 7.928103 TGCGAATAACTCTTACTTCCTACTAG 58.072 38.462 0.00 0.00 0.00 2.57
42 43 7.870509 TGCGAATAACTCTTACTTCCTACTA 57.129 36.000 0.00 0.00 0.00 1.82
43 44 6.770746 TGCGAATAACTCTTACTTCCTACT 57.229 37.500 0.00 0.00 0.00 2.57
44 45 7.823149 TTTGCGAATAACTCTTACTTCCTAC 57.177 36.000 0.00 0.00 0.00 3.18
45 46 8.836268 TTTTTGCGAATAACTCTTACTTCCTA 57.164 30.769 0.00 0.00 0.00 2.94
46 47 7.739498 TTTTTGCGAATAACTCTTACTTCCT 57.261 32.000 0.00 0.00 0.00 3.36
77 78 8.979534 CCCATACTAACTAAACTCTTACTTCCT 58.020 37.037 0.00 0.00 0.00 3.36
78 79 8.975295 TCCCATACTAACTAAACTCTTACTTCC 58.025 37.037 0.00 0.00 0.00 3.46
85 86 9.668497 GTGAAAATCCCATACTAACTAAACTCT 57.332 33.333 0.00 0.00 0.00 3.24
86 87 9.668497 AGTGAAAATCCCATACTAACTAAACTC 57.332 33.333 0.00 0.00 0.00 3.01
100 101 9.938280 CCTATTCGTTATATAGTGAAAATCCCA 57.062 33.333 3.68 0.00 0.00 4.37
101 102 9.939802 ACCTATTCGTTATATAGTGAAAATCCC 57.060 33.333 3.68 0.00 0.00 3.85
114 115 9.304731 GTGACACATGTTTACCTATTCGTTATA 57.695 33.333 0.00 0.00 0.00 0.98
115 116 7.820386 TGTGACACATGTTTACCTATTCGTTAT 59.180 33.333 3.56 0.00 0.00 1.89
116 117 7.153315 TGTGACACATGTTTACCTATTCGTTA 58.847 34.615 3.56 0.00 0.00 3.18
117 118 5.992829 TGTGACACATGTTTACCTATTCGTT 59.007 36.000 3.56 0.00 0.00 3.85
118 119 5.543714 TGTGACACATGTTTACCTATTCGT 58.456 37.500 3.56 0.00 0.00 3.85
119 120 6.073494 TGTTGTGACACATGTTTACCTATTCG 60.073 38.462 9.55 0.00 0.00 3.34
120 121 7.197071 TGTTGTGACACATGTTTACCTATTC 57.803 36.000 9.55 0.00 0.00 1.75
135 136 6.993079 AGTGATGAGTATTAGTGTTGTGACA 58.007 36.000 0.00 0.00 0.00 3.58
136 137 7.891183 AAGTGATGAGTATTAGTGTTGTGAC 57.109 36.000 0.00 0.00 0.00 3.67
137 138 9.639601 CTTAAGTGATGAGTATTAGTGTTGTGA 57.360 33.333 0.00 0.00 0.00 3.58
138 139 8.383619 GCTTAAGTGATGAGTATTAGTGTTGTG 58.616 37.037 4.02 0.00 0.00 3.33
139 140 8.314751 AGCTTAAGTGATGAGTATTAGTGTTGT 58.685 33.333 4.02 0.00 0.00 3.32
140 141 8.709386 AGCTTAAGTGATGAGTATTAGTGTTG 57.291 34.615 4.02 0.00 0.00 3.33
142 143 9.191479 ACTAGCTTAAGTGATGAGTATTAGTGT 57.809 33.333 4.02 0.00 0.00 3.55
157 158 5.450137 CGTATACCACTGCACTAGCTTAAGT 60.450 44.000 4.02 0.00 42.74 2.24
158 159 4.976731 CGTATACCACTGCACTAGCTTAAG 59.023 45.833 0.00 0.00 42.74 1.85
159 160 4.641541 TCGTATACCACTGCACTAGCTTAA 59.358 41.667 0.00 0.00 42.74 1.85
160 161 4.201657 TCGTATACCACTGCACTAGCTTA 58.798 43.478 0.00 0.00 42.74 3.09
161 162 3.021695 TCGTATACCACTGCACTAGCTT 58.978 45.455 0.00 0.00 42.74 3.74
162 163 2.619177 CTCGTATACCACTGCACTAGCT 59.381 50.000 0.00 0.00 42.74 3.32
163 164 2.287668 CCTCGTATACCACTGCACTAGC 60.288 54.545 0.00 0.00 42.57 3.42
164 165 3.211865 TCCTCGTATACCACTGCACTAG 58.788 50.000 0.00 0.00 0.00 2.57
165 166 3.286329 TCCTCGTATACCACTGCACTA 57.714 47.619 0.00 0.00 0.00 2.74
166 167 2.139323 TCCTCGTATACCACTGCACT 57.861 50.000 0.00 0.00 0.00 4.40
167 168 2.953466 TTCCTCGTATACCACTGCAC 57.047 50.000 0.00 0.00 0.00 4.57
168 169 5.601583 TTATTTCCTCGTATACCACTGCA 57.398 39.130 0.00 0.00 0.00 4.41
169 170 5.408604 CCATTATTTCCTCGTATACCACTGC 59.591 44.000 0.00 0.00 0.00 4.40
170 171 6.522054 ACCATTATTTCCTCGTATACCACTG 58.478 40.000 0.00 0.00 0.00 3.66
171 172 6.325545 TGACCATTATTTCCTCGTATACCACT 59.674 38.462 0.00 0.00 0.00 4.00
172 173 6.518493 TGACCATTATTTCCTCGTATACCAC 58.482 40.000 0.00 0.00 0.00 4.16
173 174 6.734502 TGACCATTATTTCCTCGTATACCA 57.265 37.500 0.00 0.00 0.00 3.25
174 175 7.384387 GTCTTGACCATTATTTCCTCGTATACC 59.616 40.741 0.00 0.00 0.00 2.73
175 176 8.142551 AGTCTTGACCATTATTTCCTCGTATAC 58.857 37.037 0.00 0.00 0.00 1.47
176 177 8.246430 AGTCTTGACCATTATTTCCTCGTATA 57.754 34.615 0.00 0.00 0.00 1.47
177 178 7.125792 AGTCTTGACCATTATTTCCTCGTAT 57.874 36.000 0.00 0.00 0.00 3.06
178 179 6.540438 AGTCTTGACCATTATTTCCTCGTA 57.460 37.500 0.00 0.00 0.00 3.43
179 180 5.422214 AGTCTTGACCATTATTTCCTCGT 57.578 39.130 0.00 0.00 0.00 4.18
180 181 8.438676 AATTAGTCTTGACCATTATTTCCTCG 57.561 34.615 0.00 0.00 0.00 4.63
191 192 9.326413 GCTAGCTTTATTAATTAGTCTTGACCA 57.674 33.333 7.70 0.00 0.00 4.02
192 193 9.549078 AGCTAGCTTTATTAATTAGTCTTGACC 57.451 33.333 12.68 0.00 0.00 4.02
210 211 9.667107 TGTATCAAACAAATACTAAGCTAGCTT 57.333 29.630 31.38 31.38 36.21 3.74
211 212 9.838339 ATGTATCAAACAAATACTAAGCTAGCT 57.162 29.630 12.68 12.68 42.70 3.32
257 258 8.902806 GGATGACATGTTGGAGTGAAAATAATA 58.097 33.333 0.00 0.00 0.00 0.98
258 259 7.616935 AGGATGACATGTTGGAGTGAAAATAAT 59.383 33.333 0.00 0.00 0.00 1.28
259 260 6.947733 AGGATGACATGTTGGAGTGAAAATAA 59.052 34.615 0.00 0.00 0.00 1.40
260 261 6.484288 AGGATGACATGTTGGAGTGAAAATA 58.516 36.000 0.00 0.00 0.00 1.40
261 262 5.327732 AGGATGACATGTTGGAGTGAAAAT 58.672 37.500 0.00 0.00 0.00 1.82
262 263 4.728772 AGGATGACATGTTGGAGTGAAAA 58.271 39.130 0.00 0.00 0.00 2.29
263 264 4.371624 AGGATGACATGTTGGAGTGAAA 57.628 40.909 0.00 0.00 0.00 2.69
264 265 4.532126 AGTAGGATGACATGTTGGAGTGAA 59.468 41.667 0.00 0.00 0.00 3.18
265 266 4.096681 AGTAGGATGACATGTTGGAGTGA 58.903 43.478 0.00 0.00 0.00 3.41
266 267 4.478206 AGTAGGATGACATGTTGGAGTG 57.522 45.455 0.00 0.00 0.00 3.51
267 268 5.899547 TCATAGTAGGATGACATGTTGGAGT 59.100 40.000 0.00 0.00 30.75 3.85
268 269 6.041409 ACTCATAGTAGGATGACATGTTGGAG 59.959 42.308 0.00 0.00 32.39 3.86
269 270 5.899547 ACTCATAGTAGGATGACATGTTGGA 59.100 40.000 0.00 0.00 32.39 3.53
270 271 6.166984 ACTCATAGTAGGATGACATGTTGG 57.833 41.667 0.00 0.00 32.39 3.77
284 285 5.598416 AAGCATGCACACTACTCATAGTA 57.402 39.130 21.98 0.00 39.80 1.82
285 286 4.478206 AAGCATGCACACTACTCATAGT 57.522 40.909 21.98 0.00 42.74 2.12
286 287 5.808042 AAAAGCATGCACACTACTCATAG 57.192 39.130 21.98 0.00 34.25 2.23
287 288 6.406370 AGTAAAAGCATGCACACTACTCATA 58.594 36.000 21.98 0.00 0.00 2.15
288 289 5.248640 AGTAAAAGCATGCACACTACTCAT 58.751 37.500 21.98 0.00 0.00 2.90
289 290 4.641396 AGTAAAAGCATGCACACTACTCA 58.359 39.130 21.98 0.00 0.00 3.41
290 291 5.179368 TCAAGTAAAAGCATGCACACTACTC 59.821 40.000 21.98 2.45 0.00 2.59
291 292 5.049405 GTCAAGTAAAAGCATGCACACTACT 60.049 40.000 21.98 16.48 0.00 2.57
292 293 5.147162 GTCAAGTAAAAGCATGCACACTAC 58.853 41.667 21.98 14.57 0.00 2.73
293 294 4.819088 TGTCAAGTAAAAGCATGCACACTA 59.181 37.500 21.98 2.53 0.00 2.74
294 295 3.631686 TGTCAAGTAAAAGCATGCACACT 59.368 39.130 21.98 13.45 0.00 3.55
295 296 3.963665 TGTCAAGTAAAAGCATGCACAC 58.036 40.909 21.98 11.34 0.00 3.82
296 297 4.097741 AGTTGTCAAGTAAAAGCATGCACA 59.902 37.500 21.98 9.07 0.00 4.57
297 298 4.442073 CAGTTGTCAAGTAAAAGCATGCAC 59.558 41.667 21.98 9.26 0.00 4.57
298 299 4.097741 ACAGTTGTCAAGTAAAAGCATGCA 59.902 37.500 21.98 0.00 0.00 3.96
299 300 4.610945 ACAGTTGTCAAGTAAAAGCATGC 58.389 39.130 10.51 10.51 0.00 4.06
300 301 7.524294 AAAACAGTTGTCAAGTAAAAGCATG 57.476 32.000 0.00 0.00 0.00 4.06
351 352 8.303876 GGTATGACATGTTGGTGATTAAAACTT 58.696 33.333 0.00 0.00 0.00 2.66
352 353 7.450014 TGGTATGACATGTTGGTGATTAAAACT 59.550 33.333 0.00 0.00 0.00 2.66
353 354 7.598278 TGGTATGACATGTTGGTGATTAAAAC 58.402 34.615 0.00 0.00 0.00 2.43
354 355 7.767250 TGGTATGACATGTTGGTGATTAAAA 57.233 32.000 0.00 0.00 0.00 1.52
355 356 7.147932 CCATGGTATGACATGTTGGTGATTAAA 60.148 37.037 2.57 0.00 45.21 1.52
356 357 6.320926 CCATGGTATGACATGTTGGTGATTAA 59.679 38.462 2.57 0.00 45.21 1.40
357 358 5.827267 CCATGGTATGACATGTTGGTGATTA 59.173 40.000 2.57 0.00 45.21 1.75
358 359 4.646040 CCATGGTATGACATGTTGGTGATT 59.354 41.667 2.57 0.00 45.21 2.57
359 360 4.079844 TCCATGGTATGACATGTTGGTGAT 60.080 41.667 12.58 0.00 45.21 3.06
360 361 3.265479 TCCATGGTATGACATGTTGGTGA 59.735 43.478 12.58 0.00 45.21 4.02
361 362 3.619419 TCCATGGTATGACATGTTGGTG 58.381 45.455 12.58 0.00 45.21 4.17
362 363 4.166725 AGATCCATGGTATGACATGTTGGT 59.833 41.667 12.58 0.00 45.21 3.67
363 364 4.722220 AGATCCATGGTATGACATGTTGG 58.278 43.478 12.58 1.45 45.21 3.77
364 365 6.762333 TCTAGATCCATGGTATGACATGTTG 58.238 40.000 12.58 0.00 45.21 3.33
365 366 6.556495 ACTCTAGATCCATGGTATGACATGTT 59.444 38.462 12.58 0.00 45.21 2.71
366 367 6.080682 ACTCTAGATCCATGGTATGACATGT 58.919 40.000 12.58 0.00 45.21 3.21
367 368 6.602410 ACTCTAGATCCATGGTATGACATG 57.398 41.667 12.58 0.00 46.02 3.21
368 369 6.519721 GCAACTCTAGATCCATGGTATGACAT 60.520 42.308 12.58 0.00 0.00 3.06
369 370 5.221521 GCAACTCTAGATCCATGGTATGACA 60.222 44.000 12.58 0.00 0.00 3.58
370 371 5.233988 GCAACTCTAGATCCATGGTATGAC 58.766 45.833 12.58 0.25 0.00 3.06
371 372 4.021981 CGCAACTCTAGATCCATGGTATGA 60.022 45.833 12.58 3.85 0.00 2.15
372 373 4.240888 CGCAACTCTAGATCCATGGTATG 58.759 47.826 12.58 0.00 0.00 2.39
373 374 3.306364 GCGCAACTCTAGATCCATGGTAT 60.306 47.826 12.58 3.90 0.00 2.73
374 375 2.035961 GCGCAACTCTAGATCCATGGTA 59.964 50.000 12.58 0.00 0.00 3.25
404 405 1.291588 CAACGTGAGCTGCTCTCCT 59.708 57.895 28.04 13.28 41.18 3.69
415 416 3.283751 ACCCTGATGAAAAACAACGTGA 58.716 40.909 0.00 0.00 0.00 4.35
424 425 9.391006 GTGACATACTATTTACCCTGATGAAAA 57.609 33.333 0.00 0.00 0.00 2.29
455 456 7.534723 AAATTTGGAGTTAGGGTTTAGGAAC 57.465 36.000 0.00 0.00 34.96 3.62
462 463 9.601810 AAGATAAGAAAATTTGGAGTTAGGGTT 57.398 29.630 0.00 0.00 0.00 4.11
576 1017 8.761497 CGAGGTAATCTTAAAATCGCTTCATAA 58.239 33.333 0.00 0.00 0.00 1.90
578 1019 6.202954 CCGAGGTAATCTTAAAATCGCTTCAT 59.797 38.462 0.00 0.00 0.00 2.57
580 1021 5.050295 CCCGAGGTAATCTTAAAATCGCTTC 60.050 44.000 0.00 0.00 0.00 3.86
581 1022 4.814771 CCCGAGGTAATCTTAAAATCGCTT 59.185 41.667 0.00 0.00 0.00 4.68
584 1025 4.025145 GCACCCGAGGTAATCTTAAAATCG 60.025 45.833 0.00 0.00 32.11 3.34
587 1028 4.020039 TCTGCACCCGAGGTAATCTTAAAA 60.020 41.667 0.00 0.00 32.11 1.52
588 1029 3.516300 TCTGCACCCGAGGTAATCTTAAA 59.484 43.478 0.00 0.00 32.11 1.52
589 1030 3.101437 TCTGCACCCGAGGTAATCTTAA 58.899 45.455 0.00 0.00 32.11 1.85
590 1031 2.742348 TCTGCACCCGAGGTAATCTTA 58.258 47.619 0.00 0.00 32.11 2.10
591 1032 1.568504 TCTGCACCCGAGGTAATCTT 58.431 50.000 0.00 0.00 32.11 2.40
592 1033 1.568504 TTCTGCACCCGAGGTAATCT 58.431 50.000 0.00 0.00 32.11 2.40
593 1034 2.622064 ATTCTGCACCCGAGGTAATC 57.378 50.000 0.00 0.00 32.11 1.75
594 1035 3.454812 AGTTATTCTGCACCCGAGGTAAT 59.545 43.478 0.00 0.00 32.11 1.89
596 1037 2.463752 AGTTATTCTGCACCCGAGGTA 58.536 47.619 0.00 0.00 32.11 3.08
597 1038 1.276622 AGTTATTCTGCACCCGAGGT 58.723 50.000 0.00 0.00 35.62 3.85
598 1039 2.403252 AAGTTATTCTGCACCCGAGG 57.597 50.000 0.00 0.00 0.00 4.63
599 1040 5.659048 GAATAAGTTATTCTGCACCCGAG 57.341 43.478 22.93 0.00 41.00 4.63
609 1050 4.580580 CCCAGGGTGCAGAATAAGTTATTC 59.419 45.833 22.80 22.80 43.77 1.75
610 1051 4.017499 ACCCAGGGTGCAGAATAAGTTATT 60.017 41.667 11.70 7.87 32.98 1.40
611 1052 3.527665 ACCCAGGGTGCAGAATAAGTTAT 59.472 43.478 11.70 0.00 32.98 1.89
614 1055 1.372501 ACCCAGGGTGCAGAATAAGT 58.627 50.000 11.70 0.00 32.98 2.24
622 1063 7.409582 ATGATTATTCATCACCCAGGGTGCA 62.410 44.000 31.92 20.55 45.12 4.57
623 1064 4.994099 ATGATTATTCATCACCCAGGGTGC 60.994 45.833 31.92 15.74 45.12 5.01
624 1065 4.733165 ATGATTATTCATCACCCAGGGTG 58.267 43.478 31.06 31.06 45.12 4.61
625 1066 5.408079 AATGATTATTCATCACCCAGGGT 57.592 39.130 4.76 4.76 45.12 4.34
627 1068 5.303589 AGCAAATGATTATTCATCACCCAGG 59.696 40.000 0.75 0.00 45.12 4.45
628 1069 6.213677 CAGCAAATGATTATTCATCACCCAG 58.786 40.000 0.75 0.00 45.12 4.45
630 1071 4.986659 GCAGCAAATGATTATTCATCACCC 59.013 41.667 0.75 0.00 45.12 4.61
631 1072 5.461078 GTGCAGCAAATGATTATTCATCACC 59.539 40.000 0.00 0.00 45.12 4.02
632 1073 5.172591 CGTGCAGCAAATGATTATTCATCAC 59.827 40.000 0.00 3.59 45.12 3.06
635 1076 5.252969 ACGTGCAGCAAATGATTATTCAT 57.747 34.783 0.00 0.00 44.62 2.57
636 1077 4.700268 ACGTGCAGCAAATGATTATTCA 57.300 36.364 0.00 0.00 36.00 2.57
638 1079 5.522456 CCATACGTGCAGCAAATGATTATT 58.478 37.500 12.96 0.00 0.00 1.40
639 1080 4.557296 GCCATACGTGCAGCAAATGATTAT 60.557 41.667 12.96 0.00 0.00 1.28
640 1081 3.243035 GCCATACGTGCAGCAAATGATTA 60.243 43.478 12.96 0.00 0.00 1.75
641 1082 2.480073 GCCATACGTGCAGCAAATGATT 60.480 45.455 12.96 0.00 0.00 2.57
655 1362 2.107950 TCTTGAAGGTTGGCCATACG 57.892 50.000 6.09 0.00 37.19 3.06
662 1369 5.535753 AGTTCCAAAATCTTGAAGGTTGG 57.464 39.130 13.56 13.56 40.12 3.77
713 1420 1.066143 CGAAACACCCAGTGATAGCCT 60.066 52.381 0.96 0.00 36.96 4.58
724 1431 2.946762 GTGCTCTGCGAAACACCC 59.053 61.111 0.00 0.00 0.00 4.61
728 1435 0.161024 GTACACGTGCTCTGCGAAAC 59.839 55.000 17.22 0.00 0.00 2.78
748 1455 0.167470 CAGCAACCAGACGCTTGATG 59.833 55.000 0.00 0.00 35.96 3.07
756 1463 1.228245 TGAAGGGCAGCAACCAGAC 60.228 57.895 0.00 0.00 0.00 3.51
772 1479 3.551846 GAAACCCTCAAAGAACTGGTGA 58.448 45.455 0.00 0.00 0.00 4.02
793 1506 3.907260 ATGCAGTCACCCCAGTGCG 62.907 63.158 0.00 0.00 44.53 5.34
801 1514 2.191128 ACCTGAGAAATGCAGTCACC 57.809 50.000 0.00 0.00 0.00 4.02
842 1555 6.331369 AGACCACACTTAAACATGATTTGG 57.669 37.500 0.00 0.37 0.00 3.28
844 1557 8.006298 TGAAAGACCACACTTAAACATGATTT 57.994 30.769 0.00 0.00 0.00 2.17
883 1597 9.823647 TTACAATACAAAGGCTTTGAAAAATCA 57.176 25.926 38.62 18.64 43.26 2.57
888 1607 9.474920 CTCAATTACAATACAAAGGCTTTGAAA 57.525 29.630 38.62 27.39 43.26 2.69
895 1614 8.129211 GGTACATCTCAATTACAATACAAAGGC 58.871 37.037 0.00 0.00 0.00 4.35
900 1619 7.564793 AGCAGGTACATCTCAATTACAATACA 58.435 34.615 0.00 0.00 0.00 2.29
942 1661 7.333423 TGAGGAACTGTTATGTTTAGCACATAC 59.667 37.037 0.00 0.00 43.53 2.39
954 1673 6.801539 TGCTTAAAGTGAGGAACTGTTATG 57.198 37.500 0.00 0.00 41.55 1.90
959 1678 4.137543 ACCTTGCTTAAAGTGAGGAACTG 58.862 43.478 6.24 0.00 39.81 3.16
1001 1720 1.559965 ATCCTTCAGCTGAGCCTGCA 61.560 55.000 17.43 0.00 32.87 4.41
1041 1760 5.183904 GGGTGTTGTGATAGCAAAGAAGAAT 59.816 40.000 0.00 0.00 0.00 2.40
1053 1772 2.266372 CCGGCGGGTGTTGTGATA 59.734 61.111 20.56 0.00 0.00 2.15
1083 1802 0.106569 AGAATGATGCCATGGCGGAA 60.107 50.000 30.87 18.86 45.51 4.30
1125 1844 1.633945 AGAATACCCTCCACCACCAAC 59.366 52.381 0.00 0.00 0.00 3.77
1154 1873 1.880675 AGATCAGTATACCAGCCGACG 59.119 52.381 0.00 0.00 0.00 5.12
1165 1884 5.188555 CCACCAGTGCCATATAGATCAGTAT 59.811 44.000 0.00 0.00 0.00 2.12
1215 1934 1.817099 GCTGTTGCTCATCCTCCGG 60.817 63.158 0.00 0.00 36.03 5.14
1232 1951 1.187567 AACCTGCAAGATGGTTGGGC 61.188 55.000 7.26 0.00 39.23 5.36
1236 1955 1.526575 CGCCAACCTGCAAGATGGTT 61.527 55.000 12.69 7.79 41.18 3.67
1254 1973 3.185246 AGAAACAGGGAGACATATGCG 57.815 47.619 1.58 0.00 0.00 4.73
1302 2021 6.042781 TCACCAACACTAACTAAGTCCAGATT 59.957 38.462 0.00 0.00 35.76 2.40
1316 2035 3.135712 ACTCACACCAATCACCAACACTA 59.864 43.478 0.00 0.00 0.00 2.74
1317 2036 2.092429 ACTCACACCAATCACCAACACT 60.092 45.455 0.00 0.00 0.00 3.55
1318 2037 2.297701 ACTCACACCAATCACCAACAC 58.702 47.619 0.00 0.00 0.00 3.32
1319 2038 2.727123 ACTCACACCAATCACCAACA 57.273 45.000 0.00 0.00 0.00 3.33
1368 2088 9.093458 ACAACTCCAATCCTTCATCTTATTTTT 57.907 29.630 0.00 0.00 0.00 1.94
1417 2137 3.944015 GAGCAACTCCTAGTGCATTGAAT 59.056 43.478 5.91 0.00 0.00 2.57
1505 2225 3.350219 ACATCCAACCACTACCATGTC 57.650 47.619 0.00 0.00 0.00 3.06
1519 2239 3.237268 ACAAAGGCACCTTTACATCCA 57.763 42.857 14.15 0.00 43.56 3.41
1523 2243 2.741145 ACCAACAAAGGCACCTTTACA 58.259 42.857 14.15 0.00 43.56 2.41
1525 2245 7.069578 TGTTTATTACCAACAAAGGCACCTTTA 59.930 33.333 14.15 0.00 43.56 1.85
1569 2289 5.412640 TCCATCACAAATTCACAATGCATC 58.587 37.500 0.00 0.00 0.00 3.91
1599 2319 4.501571 CCCGGTACTAATTCATCTCCTGTG 60.502 50.000 0.00 0.00 0.00 3.66
1617 2337 2.444895 GAGCTCCTCATCCCCGGT 60.445 66.667 0.87 0.00 0.00 5.28
1618 2338 3.237741 GGAGCTCCTCATCCCCGG 61.238 72.222 26.25 0.00 31.08 5.73
1619 2339 2.444706 TGGAGCTCCTCATCCCCG 60.445 66.667 32.28 0.00 34.47 5.73
1626 2346 0.534873 GTCAGTTCCTGGAGCTCCTC 59.465 60.000 32.28 16.87 36.82 3.71
1653 2373 6.128445 CGATTTCAAATGTGAGCTAGTGACTT 60.128 38.462 0.00 0.00 34.49 3.01
1654 2374 5.349817 CGATTTCAAATGTGAGCTAGTGACT 59.650 40.000 0.00 0.00 34.49 3.41
1672 2392 7.218204 GTGAACTTGTGGCATAATTACGATTTC 59.782 37.037 0.00 0.00 0.00 2.17
1679 2399 4.764308 TGCAGTGAACTTGTGGCATAATTA 59.236 37.500 0.00 0.00 0.00 1.40
1716 2437 1.204704 CAGATGGAGTAGGTTGCGTCA 59.795 52.381 0.00 0.00 0.00 4.35
1720 2441 2.615912 GCAATCAGATGGAGTAGGTTGC 59.384 50.000 0.00 0.00 34.71 4.17
1735 2456 1.750018 CCGCATGGAGGTGCAATCA 60.750 57.895 0.00 0.00 45.30 2.57
1744 2465 0.107508 ACCAGAATCACCGCATGGAG 60.108 55.000 0.00 0.00 39.21 3.86
1752 2473 3.944015 CAGGAGATGAAACCAGAATCACC 59.056 47.826 0.00 0.00 32.92 4.02
1782 2503 3.492102 ATCACGATGAGTTTATGGGGG 57.508 47.619 0.00 0.00 0.00 5.40
1786 2507 7.873739 TGCACTATATCACGATGAGTTTATG 57.126 36.000 0.00 0.00 0.00 1.90
1795 2516 6.942532 AAAACCAATGCACTATATCACGAT 57.057 33.333 0.00 0.00 0.00 3.73
1799 2520 6.849085 ACCAAAAACCAATGCACTATATCA 57.151 33.333 0.00 0.00 0.00 2.15
1800 2521 7.816995 TCAAACCAAAAACCAATGCACTATATC 59.183 33.333 0.00 0.00 0.00 1.63
1828 2549 3.678072 TCCAAACGAAGTCGAAATAGCAG 59.322 43.478 7.87 0.00 45.00 4.24
1998 2719 7.991460 ACATCATGAATGAGAATGACACATAGT 59.009 33.333 0.00 0.00 40.64 2.12
2079 2800 6.178324 GGTTTACTTATTGCAGTAAGGTCCT 58.822 40.000 26.80 12.65 39.79 3.85
2089 2810 6.016108 GTGGTTAGTTGGGTTTACTTATTGCA 60.016 38.462 0.00 0.00 0.00 4.08
2130 2851 5.091552 AGGAGGTGATTAGGTGAAGTGTTA 58.908 41.667 0.00 0.00 0.00 2.41
2138 2859 4.656112 ACAAGGATAGGAGGTGATTAGGTG 59.344 45.833 0.00 0.00 0.00 4.00
2139 2860 4.897051 ACAAGGATAGGAGGTGATTAGGT 58.103 43.478 0.00 0.00 0.00 3.08
2171 2892 3.681897 CGAGGAGACTTTGAACAAGATGG 59.318 47.826 0.00 0.00 44.43 3.51
2180 2901 2.963101 TGGTTCTTCGAGGAGACTTTGA 59.037 45.455 0.00 0.00 44.43 2.69
2181 2902 3.386768 TGGTTCTTCGAGGAGACTTTG 57.613 47.619 0.00 0.00 44.43 2.77
2251 2972 3.954258 CTCACTTGGTTTTTGGAAGGAGT 59.046 43.478 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.