Multiple sequence alignment - TraesCS2D01G225000

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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 TraesCS2D01G225000 chr2D 100.000 2609 0 0 1 2609 192735354 192737962 0.000000e+00 4819
1 TraesCS2D01G225000 chr2B 92.883 2192 63 33 222 2366 247937715 247935570 0.000000e+00 3097
2 TraesCS2D01G225000 chr2B 95.556 180 8 0 1 180 247937895 247937716 3.290000e-74 289
3 TraesCS2D01G225000 chr2B 84.926 272 16 1 2363 2609 545406466 545406195 4.310000e-63 252
4 TraesCS2D01G225000 chr2B 84.337 166 16 4 2059 2215 107965229 107965065 1.250000e-33 154
5 TraesCS2D01G225000 chr2A 94.730 1480 58 10 585 2047 205219544 205218068 0.000000e+00 2283
6 TraesCS2D01G225000 chr3A 86.617 269 11 6 2366 2609 419510630 419510362 9.200000e-70 274
7 TraesCS2D01G225000 chr4D 85.890 163 16 4 2059 2215 498687919 498687758 1.610000e-37 167
8 TraesCS2D01G225000 chr3D 84.146 164 20 3 2058 2216 137981641 137981479 1.250000e-33 154
9 TraesCS2D01G225000 chr3D 83.537 164 20 4 2059 2216 500129016 500128854 2.090000e-31 147
10 TraesCS2D01G225000 chr3D 82.081 173 21 4 2056 2219 247038638 247038809 3.500000e-29 139
11 TraesCS2D01G225000 chr4A 82.955 176 18 6 2059 2226 665175110 665174939 5.820000e-32 148
12 TraesCS2D01G225000 chr1D 83.234 167 18 4 2059 2216 466603290 466603455 7.530000e-31 145
13 TraesCS2D01G225000 chr1B 82.840 169 17 8 2055 2215 329488318 329488482 9.730000e-30 141


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 TraesCS2D01G225000 chr2D 192735354 192737962 2608 False 4819 4819 100.0000 1 2609 1 chr2D.!!$F1 2608
1 TraesCS2D01G225000 chr2B 247935570 247937895 2325 True 1693 3097 94.2195 1 2366 2 chr2B.!!$R3 2365
2 TraesCS2D01G225000 chr2A 205218068 205219544 1476 True 2283 2283 94.7300 585 2047 1 chr2A.!!$R1 1462

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
247 248 0.179081 GCCAGGTTCACGAGGATACC 60.179 60.0 0.0 0.0 37.17 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2114 1.187087 AAGAACGGAGGGAGTAGCTG 58.813 55.0 0.0 0.0 0.0 4.24 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
59 60 3.749088 CAGCGTCCAACAAACTACCATTA 59.251 43.478 0.00 0.00 0.00 1.90
71 72 3.865446 ACTACCATTAGGGCACGTAAAC 58.135 45.455 0.00 0.00 42.09 2.01
104 105 5.195940 ACTGTATATGCTTGCCTTGTCAAT 58.804 37.500 0.00 0.00 0.00 2.57
123 124 2.380084 TCACCACTCGCCAATTAGTC 57.620 50.000 0.00 0.00 0.00 2.59
141 142 2.747686 GGGACCGCTCCTTGTTGA 59.252 61.111 0.00 0.00 36.68 3.18
188 189 1.979809 TCCTTGGGAAGATAAGGGCA 58.020 50.000 0.00 0.00 42.92 5.36
189 190 1.846439 TCCTTGGGAAGATAAGGGCAG 59.154 52.381 0.00 0.00 42.92 4.85
190 191 1.685148 CTTGGGAAGATAAGGGCAGC 58.315 55.000 0.00 0.00 0.00 5.25
191 192 0.258774 TTGGGAAGATAAGGGCAGCC 59.741 55.000 1.26 1.26 0.00 4.85
192 193 0.624500 TGGGAAGATAAGGGCAGCCT 60.625 55.000 12.43 0.00 0.00 4.58
193 194 0.553333 GGGAAGATAAGGGCAGCCTT 59.447 55.000 12.43 0.00 0.00 4.35
194 195 1.685148 GGAAGATAAGGGCAGCCTTG 58.315 55.000 12.43 0.00 0.00 3.61
195 196 1.064389 GGAAGATAAGGGCAGCCTTGT 60.064 52.381 12.43 1.89 0.00 3.16
196 197 2.621668 GGAAGATAAGGGCAGCCTTGTT 60.622 50.000 12.43 5.45 0.00 2.83
197 198 2.907458 AGATAAGGGCAGCCTTGTTT 57.093 45.000 12.43 3.96 0.00 2.83
198 199 4.270008 GAAGATAAGGGCAGCCTTGTTTA 58.730 43.478 12.43 6.10 0.00 2.01
199 200 3.621558 AGATAAGGGCAGCCTTGTTTAC 58.378 45.455 12.43 0.00 0.00 2.01
200 201 1.816074 TAAGGGCAGCCTTGTTTACG 58.184 50.000 12.43 0.00 0.00 3.18
201 202 0.893727 AAGGGCAGCCTTGTTTACGG 60.894 55.000 12.43 0.00 0.00 4.02
202 203 2.340328 GGGCAGCCTTGTTTACGGG 61.340 63.158 12.43 0.00 0.00 5.28
203 204 2.566529 GCAGCCTTGTTTACGGGC 59.433 61.111 8.11 8.11 45.57 6.13
207 208 3.969995 GCCTTGTTTACGGGCAAAA 57.030 47.368 10.43 0.00 44.69 2.44
208 209 1.778334 GCCTTGTTTACGGGCAAAAG 58.222 50.000 10.43 0.00 44.69 2.27
209 210 1.778334 CCTTGTTTACGGGCAAAAGC 58.222 50.000 0.00 0.00 0.00 3.51
210 211 1.404477 CTTGTTTACGGGCAAAAGCG 58.596 50.000 0.00 0.00 0.00 4.68
211 212 1.002251 CTTGTTTACGGGCAAAAGCGA 60.002 47.619 0.00 0.00 0.00 4.93
212 213 1.022735 TGTTTACGGGCAAAAGCGAA 58.977 45.000 0.00 0.00 0.00 4.70
213 214 1.002251 TGTTTACGGGCAAAAGCGAAG 60.002 47.619 0.00 0.00 0.00 3.79
214 215 1.264826 GTTTACGGGCAAAAGCGAAGA 59.735 47.619 0.00 0.00 0.00 2.87
215 216 0.869730 TTACGGGCAAAAGCGAAGAC 59.130 50.000 0.00 0.00 0.00 3.01
216 217 1.286354 TACGGGCAAAAGCGAAGACG 61.286 55.000 0.00 0.00 42.93 4.18
217 218 2.314647 CGGGCAAAAGCGAAGACGA 61.315 57.895 0.00 0.00 42.66 4.20
218 219 1.837538 CGGGCAAAAGCGAAGACGAA 61.838 55.000 0.00 0.00 42.66 3.85
219 220 0.521735 GGGCAAAAGCGAAGACGAAT 59.478 50.000 0.00 0.00 42.66 3.34
220 221 1.068541 GGGCAAAAGCGAAGACGAATT 60.069 47.619 0.00 0.00 42.66 2.17
245 246 0.535335 GTGCCAGGTTCACGAGGATA 59.465 55.000 0.00 0.00 0.00 2.59
246 247 0.535335 TGCCAGGTTCACGAGGATAC 59.465 55.000 0.00 0.00 0.00 2.24
247 248 0.179081 GCCAGGTTCACGAGGATACC 60.179 60.000 0.00 0.00 37.17 2.73
248 249 1.486211 CCAGGTTCACGAGGATACCT 58.514 55.000 0.00 0.00 37.44 3.08
249 250 1.831736 CCAGGTTCACGAGGATACCTT 59.168 52.381 0.00 0.00 35.90 3.50
250 251 2.236395 CCAGGTTCACGAGGATACCTTT 59.764 50.000 0.00 0.00 35.90 3.11
251 252 3.522553 CAGGTTCACGAGGATACCTTTC 58.477 50.000 0.00 0.00 35.90 2.62
252 253 3.195825 CAGGTTCACGAGGATACCTTTCT 59.804 47.826 0.00 0.00 35.90 2.52
271 272 4.897509 TCTGGATATGCAATACCTGAGG 57.102 45.455 0.00 0.00 30.61 3.86
288 289 9.907229 ATACCTGAGGTATTTTCTTTAGAAAGG 57.093 33.333 18.22 3.75 45.54 3.11
350 353 5.006941 GGTTGAAGTTGTACTAAAGCAACGA 59.993 40.000 0.00 0.00 46.66 3.85
351 354 6.293244 GGTTGAAGTTGTACTAAAGCAACGAT 60.293 38.462 0.00 0.00 46.66 3.73
358 361 9.162764 AGTTGTACTAAAGCAACGATAATCAAT 57.837 29.630 0.00 0.00 46.66 2.57
365 368 9.979270 CTAAAGCAACGATAATCAATATGGATC 57.021 33.333 0.00 0.00 0.00 3.36
367 370 6.398095 AGCAACGATAATCAATATGGATCGA 58.602 36.000 8.28 0.00 41.42 3.59
379 382 2.241281 TGGATCGAAGGGAGTACCAA 57.759 50.000 0.00 0.00 43.89 3.67
396 399 3.697166 ACCAAATTACCAGTGACATCCC 58.303 45.455 0.00 0.00 0.00 3.85
413 416 6.042781 TGACATCCCCATAGACCATAGTAAAC 59.957 42.308 0.00 0.00 0.00 2.01
421 424 7.442656 CCATAGACCATAGTAAACTTAGGTGG 58.557 42.308 9.95 6.49 33.79 4.61
445 448 6.095021 GGTTTTAGCTAACGAATCCAAGGAAT 59.905 38.462 5.45 0.00 0.00 3.01
455 458 3.512978 CCAAGGAATGGTTTTGCCG 57.487 52.632 0.00 0.00 44.85 5.69
459 462 1.247567 AGGAATGGTTTTGCCGTCTG 58.752 50.000 0.00 0.00 41.21 3.51
460 463 0.958822 GGAATGGTTTTGCCGTCTGT 59.041 50.000 0.00 0.00 41.21 3.41
567 570 9.267096 GCAAAGAATTCAAGAATAAGTTAGTCG 57.733 33.333 8.44 0.00 0.00 4.18
683 686 6.369065 AGAATCATACCACGACAGAGAAAAAC 59.631 38.462 0.00 0.00 0.00 2.43
710 717 7.144661 TCCGTAAACAAACAGAAGAACGTATA 58.855 34.615 0.00 0.00 0.00 1.47
797 804 0.694771 TCTGTCAAAGCCAGCCTCAT 59.305 50.000 0.00 0.00 0.00 2.90
818 825 1.940613 GGGAATCAACATCCAGTACGC 59.059 52.381 0.00 0.00 38.80 4.42
819 826 1.940613 GGAATCAACATCCAGTACGCC 59.059 52.381 0.00 0.00 36.92 5.68
824 831 1.134401 CAACATCCAGTACGCCCATCT 60.134 52.381 0.00 0.00 0.00 2.90
1014 1046 2.591715 GCCATGCCGCGGAACTAT 60.592 61.111 33.48 14.14 0.00 2.12
1274 1306 2.650813 ATCGGCATCCACTTCGAGGC 62.651 60.000 0.00 0.00 38.81 4.70
1276 1308 2.892425 GCATCCACTTCGAGGCCG 60.892 66.667 0.00 0.00 33.52 6.13
1277 1309 2.579201 CATCCACTTCGAGGCCGT 59.421 61.111 0.00 0.00 37.05 5.68
1278 1310 1.519455 CATCCACTTCGAGGCCGTC 60.519 63.158 0.00 0.00 37.05 4.79
1279 1311 1.682684 ATCCACTTCGAGGCCGTCT 60.683 57.895 0.00 0.00 37.05 4.18
1280 1312 0.395311 ATCCACTTCGAGGCCGTCTA 60.395 55.000 0.00 0.00 37.05 2.59
1281 1313 1.139095 CCACTTCGAGGCCGTCTAC 59.861 63.158 0.00 0.00 37.05 2.59
1282 1314 1.226323 CACTTCGAGGCCGTCTACG 60.226 63.158 0.00 0.00 37.05 3.51
2071 2131 1.142097 GCAGCTACTCCCTCCGTTC 59.858 63.158 0.00 0.00 0.00 3.95
2072 2132 1.324005 GCAGCTACTCCCTCCGTTCT 61.324 60.000 0.00 0.00 0.00 3.01
2144 2210 5.109903 ACATGGTTTAGAGCGTAGATTCAC 58.890 41.667 0.00 0.00 0.00 3.18
2155 2221 4.697352 AGCGTAGATTCACTCATTTTGCTT 59.303 37.500 0.00 0.00 0.00 3.91
2156 2222 5.024555 GCGTAGATTCACTCATTTTGCTTC 58.975 41.667 0.00 0.00 0.00 3.86
2157 2223 5.251081 CGTAGATTCACTCATTTTGCTTCG 58.749 41.667 0.00 0.00 0.00 3.79
2158 2224 5.163953 CGTAGATTCACTCATTTTGCTTCGT 60.164 40.000 0.00 0.00 0.00 3.85
2159 2225 6.034577 CGTAGATTCACTCATTTTGCTTCGTA 59.965 38.462 0.00 0.00 0.00 3.43
2160 2226 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
2161 2227 9.031360 GTAGATTCACTCATTTTGCTTCGTATA 57.969 33.333 0.00 0.00 0.00 1.47
2162 2228 8.668510 AGATTCACTCATTTTGCTTCGTATAT 57.331 30.769 0.00 0.00 0.00 0.86
2163 2229 9.764363 AGATTCACTCATTTTGCTTCGTATATA 57.236 29.630 0.00 0.00 0.00 0.86
2165 2231 8.942338 TTCACTCATTTTGCTTCGTATATAGT 57.058 30.769 0.00 0.00 0.00 2.12
2166 2232 8.575565 TCACTCATTTTGCTTCGTATATAGTC 57.424 34.615 0.00 0.00 0.00 2.59
2167 2233 8.414003 TCACTCATTTTGCTTCGTATATAGTCT 58.586 33.333 0.00 0.00 0.00 3.24
2174 2240 9.731819 TTTTGCTTCGTATATAGTCTCTTACTG 57.268 33.333 0.00 0.00 39.39 2.74
2258 2325 2.047274 GGCACGCTGCTGGTTCTA 60.047 61.111 9.31 0.00 44.28 2.10
2306 2375 7.807977 ACATATATGCTTAACCTTTCACCAG 57.192 36.000 12.79 0.00 0.00 4.00
2379 2453 5.766222 GAGCATCTAAGGGCATTTACAATG 58.234 41.667 0.00 0.00 0.00 2.82
2380 2454 4.038402 AGCATCTAAGGGCATTTACAATGC 59.962 41.667 12.21 12.21 43.85 3.56
2381 2455 4.202141 GCATCTAAGGGCATTTACAATGCA 60.202 41.667 20.19 0.00 46.21 3.96
2382 2456 5.526115 CATCTAAGGGCATTTACAATGCAG 58.474 41.667 20.19 10.73 46.21 4.41
2383 2457 4.854173 TCTAAGGGCATTTACAATGCAGA 58.146 39.130 20.19 12.53 46.21 4.26
2384 2458 4.883585 TCTAAGGGCATTTACAATGCAGAG 59.116 41.667 20.19 12.03 46.21 3.35
2385 2459 1.753073 AGGGCATTTACAATGCAGAGC 59.247 47.619 20.19 5.59 46.21 4.09
2386 2460 1.534595 GGGCATTTACAATGCAGAGCG 60.535 52.381 20.19 0.00 46.21 5.03
2387 2461 1.194495 GCATTTACAATGCAGAGCGC 58.806 50.000 15.11 0.00 44.00 5.92
2388 2462 1.202222 GCATTTACAATGCAGAGCGCT 60.202 47.619 11.27 11.27 44.00 5.92
2389 2463 2.032054 GCATTTACAATGCAGAGCGCTA 59.968 45.455 11.50 0.00 44.00 4.26
2390 2464 3.487376 GCATTTACAATGCAGAGCGCTAA 60.487 43.478 11.50 0.00 44.00 3.09
2391 2465 4.277258 CATTTACAATGCAGAGCGCTAAG 58.723 43.478 11.50 7.13 43.06 2.18
2392 2466 1.939974 TACAATGCAGAGCGCTAAGG 58.060 50.000 11.50 3.57 43.06 2.69
2393 2467 1.354506 CAATGCAGAGCGCTAAGGC 59.645 57.895 11.50 15.46 43.06 4.35
2403 2477 4.971125 GCTAAGGCGGGCGCTAGG 62.971 72.222 7.64 0.00 41.60 3.02
2404 2478 4.301027 CTAAGGCGGGCGCTAGGG 62.301 72.222 7.64 1.65 41.60 3.53
2411 2485 2.844839 GGGCGCTAGGGTCAGGAT 60.845 66.667 13.90 0.00 0.00 3.24
2412 2486 2.737830 GGCGCTAGGGTCAGGATC 59.262 66.667 7.64 0.00 0.00 3.36
2413 2487 2.737830 GCGCTAGGGTCAGGATCC 59.262 66.667 2.48 2.48 0.00 3.36
2414 2488 2.873525 GCGCTAGGGTCAGGATCCC 61.874 68.421 8.55 0.00 44.90 3.85
2419 2493 3.537874 GGGTCAGGATCCCGGTCG 61.538 72.222 8.55 0.00 35.27 4.79
2420 2494 2.758737 GGTCAGGATCCCGGTCGT 60.759 66.667 8.55 0.00 0.00 4.34
2421 2495 2.356780 GGTCAGGATCCCGGTCGTT 61.357 63.158 8.55 0.00 0.00 3.85
2422 2496 1.595357 GTCAGGATCCCGGTCGTTT 59.405 57.895 8.55 0.00 0.00 3.60
2423 2497 0.036671 GTCAGGATCCCGGTCGTTTT 60.037 55.000 8.55 0.00 0.00 2.43
2424 2498 0.036765 TCAGGATCCCGGTCGTTTTG 60.037 55.000 8.55 0.00 0.00 2.44
2425 2499 1.376812 AGGATCCCGGTCGTTTTGC 60.377 57.895 8.55 0.00 0.00 3.68
2426 2500 1.376812 GGATCCCGGTCGTTTTGCT 60.377 57.895 0.00 0.00 0.00 3.91
2427 2501 0.958876 GGATCCCGGTCGTTTTGCTT 60.959 55.000 0.00 0.00 0.00 3.91
2428 2502 1.676615 GGATCCCGGTCGTTTTGCTTA 60.677 52.381 0.00 0.00 0.00 3.09
2429 2503 1.664151 GATCCCGGTCGTTTTGCTTAG 59.336 52.381 0.00 0.00 0.00 2.18
2430 2504 0.393820 TCCCGGTCGTTTTGCTTAGT 59.606 50.000 0.00 0.00 0.00 2.24
2431 2505 1.202675 TCCCGGTCGTTTTGCTTAGTT 60.203 47.619 0.00 0.00 0.00 2.24
2432 2506 1.196127 CCCGGTCGTTTTGCTTAGTTC 59.804 52.381 0.00 0.00 0.00 3.01
2433 2507 1.196127 CCGGTCGTTTTGCTTAGTTCC 59.804 52.381 0.00 0.00 0.00 3.62
2434 2508 1.196127 CGGTCGTTTTGCTTAGTTCCC 59.804 52.381 0.00 0.00 0.00 3.97
2435 2509 1.196127 GGTCGTTTTGCTTAGTTCCCG 59.804 52.381 0.00 0.00 0.00 5.14
2436 2510 1.869132 GTCGTTTTGCTTAGTTCCCGT 59.131 47.619 0.00 0.00 0.00 5.28
2437 2511 2.288729 GTCGTTTTGCTTAGTTCCCGTT 59.711 45.455 0.00 0.00 0.00 4.44
2438 2512 2.545106 TCGTTTTGCTTAGTTCCCGTTC 59.455 45.455 0.00 0.00 0.00 3.95
2439 2513 2.288458 CGTTTTGCTTAGTTCCCGTTCA 59.712 45.455 0.00 0.00 0.00 3.18
2440 2514 3.242804 CGTTTTGCTTAGTTCCCGTTCAA 60.243 43.478 0.00 0.00 0.00 2.69
2441 2515 4.674475 GTTTTGCTTAGTTCCCGTTCAAA 58.326 39.130 0.00 0.00 0.00 2.69
2442 2516 5.286438 GTTTTGCTTAGTTCCCGTTCAAAT 58.714 37.500 0.00 0.00 0.00 2.32
2443 2517 4.759516 TTGCTTAGTTCCCGTTCAAATC 57.240 40.909 0.00 0.00 0.00 2.17
2444 2518 4.015872 TGCTTAGTTCCCGTTCAAATCT 57.984 40.909 0.00 0.00 0.00 2.40
2445 2519 3.751175 TGCTTAGTTCCCGTTCAAATCTG 59.249 43.478 0.00 0.00 0.00 2.90
2446 2520 3.127030 GCTTAGTTCCCGTTCAAATCTGG 59.873 47.826 0.00 0.00 0.00 3.86
2447 2521 2.200373 AGTTCCCGTTCAAATCTGGG 57.800 50.000 0.00 0.00 43.36 4.45
2452 2526 3.782889 CCCGTTCAAATCTGGGAATTC 57.217 47.619 0.00 0.00 44.88 2.17
2453 2527 2.097466 CCCGTTCAAATCTGGGAATTCG 59.903 50.000 0.00 0.00 44.88 3.34
2454 2528 2.097466 CCGTTCAAATCTGGGAATTCGG 59.903 50.000 0.00 0.00 0.00 4.30
2455 2529 2.477863 CGTTCAAATCTGGGAATTCGGC 60.478 50.000 0.00 0.00 0.00 5.54
2456 2530 1.378531 TCAAATCTGGGAATTCGGCG 58.621 50.000 0.00 0.00 0.00 6.46
2457 2531 0.381801 CAAATCTGGGAATTCGGCGG 59.618 55.000 7.21 0.00 0.00 6.13
2458 2532 0.751643 AAATCTGGGAATTCGGCGGG 60.752 55.000 7.21 0.00 0.00 6.13
2459 2533 3.774599 ATCTGGGAATTCGGCGGGC 62.775 63.158 7.21 0.00 0.00 6.13
2463 2537 4.903010 GGAATTCGGCGGGCGCTA 62.903 66.667 19.97 9.99 41.60 4.26
2464 2538 2.893404 GAATTCGGCGGGCGCTAA 60.893 61.111 19.97 9.85 41.60 3.09
2465 2539 3.164390 GAATTCGGCGGGCGCTAAC 62.164 63.158 19.97 7.13 41.60 2.34
2474 2548 4.716003 GGCGCTAACCCTGTTTCT 57.284 55.556 7.64 0.00 0.00 2.52
2475 2549 2.467962 GGCGCTAACCCTGTTTCTC 58.532 57.895 7.64 0.00 0.00 2.87
2476 2550 1.359459 GGCGCTAACCCTGTTTCTCG 61.359 60.000 7.64 0.00 0.00 4.04
2477 2551 0.669625 GCGCTAACCCTGTTTCTCGT 60.670 55.000 0.00 0.00 0.00 4.18
2478 2552 1.792006 CGCTAACCCTGTTTCTCGTT 58.208 50.000 0.00 0.00 0.00 3.85
2479 2553 1.725164 CGCTAACCCTGTTTCTCGTTC 59.275 52.381 0.00 0.00 0.00 3.95
2480 2554 2.609737 CGCTAACCCTGTTTCTCGTTCT 60.610 50.000 0.00 0.00 0.00 3.01
2481 2555 3.366679 CGCTAACCCTGTTTCTCGTTCTA 60.367 47.826 0.00 0.00 0.00 2.10
2482 2556 4.563061 GCTAACCCTGTTTCTCGTTCTAA 58.437 43.478 0.00 0.00 0.00 2.10
2483 2557 5.176592 GCTAACCCTGTTTCTCGTTCTAAT 58.823 41.667 0.00 0.00 0.00 1.73
2484 2558 5.642491 GCTAACCCTGTTTCTCGTTCTAATT 59.358 40.000 0.00 0.00 0.00 1.40
2485 2559 6.148976 GCTAACCCTGTTTCTCGTTCTAATTT 59.851 38.462 0.00 0.00 0.00 1.82
2486 2560 6.954487 AACCCTGTTTCTCGTTCTAATTTT 57.046 33.333 0.00 0.00 0.00 1.82
2487 2561 6.555812 ACCCTGTTTCTCGTTCTAATTTTC 57.444 37.500 0.00 0.00 0.00 2.29
2488 2562 6.296803 ACCCTGTTTCTCGTTCTAATTTTCT 58.703 36.000 0.00 0.00 0.00 2.52
2489 2563 6.204882 ACCCTGTTTCTCGTTCTAATTTTCTG 59.795 38.462 0.00 0.00 0.00 3.02
2490 2564 6.426937 CCCTGTTTCTCGTTCTAATTTTCTGA 59.573 38.462 0.00 0.00 0.00 3.27
2491 2565 7.360438 CCCTGTTTCTCGTTCTAATTTTCTGAG 60.360 40.741 0.00 0.00 0.00 3.35
2492 2566 7.171678 CCTGTTTCTCGTTCTAATTTTCTGAGT 59.828 37.037 0.00 0.00 0.00 3.41
2493 2567 9.193133 CTGTTTCTCGTTCTAATTTTCTGAGTA 57.807 33.333 0.00 0.00 0.00 2.59
2494 2568 9.706691 TGTTTCTCGTTCTAATTTTCTGAGTAT 57.293 29.630 0.00 0.00 0.00 2.12
2497 2571 9.517609 TTCTCGTTCTAATTTTCTGAGTATAGC 57.482 33.333 0.00 0.00 0.00 2.97
2498 2572 7.856398 TCTCGTTCTAATTTTCTGAGTATAGCG 59.144 37.037 0.00 0.00 0.00 4.26
2499 2573 6.417044 TCGTTCTAATTTTCTGAGTATAGCGC 59.583 38.462 0.00 0.00 0.00 5.92
2500 2574 6.418226 CGTTCTAATTTTCTGAGTATAGCGCT 59.582 38.462 17.26 17.26 0.00 5.92
2501 2575 7.559845 GTTCTAATTTTCTGAGTATAGCGCTG 58.440 38.462 22.90 0.17 0.00 5.18
2502 2576 6.216569 TCTAATTTTCTGAGTATAGCGCTGG 58.783 40.000 22.90 1.31 0.00 4.85
2503 2577 3.887621 TTTTCTGAGTATAGCGCTGGT 57.112 42.857 22.90 11.51 0.00 4.00
2504 2578 4.994907 TTTTCTGAGTATAGCGCTGGTA 57.005 40.909 22.90 10.36 0.00 3.25
2505 2579 3.984508 TTCTGAGTATAGCGCTGGTAC 57.015 47.619 22.90 21.49 0.00 3.34
2506 2580 2.927028 TCTGAGTATAGCGCTGGTACA 58.073 47.619 26.36 16.93 0.00 2.90
2507 2581 2.617308 TCTGAGTATAGCGCTGGTACAC 59.383 50.000 26.36 22.36 0.00 2.90
2508 2582 2.357952 CTGAGTATAGCGCTGGTACACA 59.642 50.000 26.36 24.60 0.00 3.72
2517 2591 3.432517 CTGGTACACAGCTCTCAGC 57.567 57.895 0.00 0.00 40.97 4.26
2526 2600 2.175322 GCTCTCAGCGTTGCAAGC 59.825 61.111 0.00 6.05 0.00 4.01
2527 2601 2.610694 GCTCTCAGCGTTGCAAGCA 61.611 57.895 18.74 0.00 37.01 3.91
2528 2602 1.496393 CTCTCAGCGTTGCAAGCAG 59.504 57.895 18.74 12.92 37.01 4.24
2529 2603 0.947660 CTCTCAGCGTTGCAAGCAGA 60.948 55.000 18.74 15.63 37.01 4.26
2530 2604 0.947660 TCTCAGCGTTGCAAGCAGAG 60.948 55.000 24.18 24.18 45.66 3.35
2531 2605 1.226686 CTCAGCGTTGCAAGCAGAGT 61.227 55.000 22.95 5.39 41.41 3.24
2532 2606 1.206072 CAGCGTTGCAAGCAGAGTC 59.794 57.895 18.74 0.00 37.01 3.36
2533 2607 2.171940 GCGTTGCAAGCAGAGTCG 59.828 61.111 0.00 0.00 34.19 4.18
2534 2608 2.171940 CGTTGCAAGCAGAGTCGC 59.828 61.111 0.00 0.00 0.00 5.19
2535 2609 2.313172 CGTTGCAAGCAGAGTCGCT 61.313 57.895 0.00 4.01 46.67 4.93
2541 2615 3.700109 AGCAGAGTCGCTTAGCCA 58.300 55.556 0.00 0.00 39.99 4.75
2542 2616 1.515020 AGCAGAGTCGCTTAGCCAG 59.485 57.895 0.00 0.00 39.99 4.85
2543 2617 1.520342 GCAGAGTCGCTTAGCCAGG 60.520 63.158 0.00 0.00 0.00 4.45
2544 2618 1.520342 CAGAGTCGCTTAGCCAGGC 60.520 63.158 1.84 1.84 0.00 4.85
2555 2629 4.537433 GCCAGGCGCTAGGACCAG 62.537 72.222 20.29 0.00 0.00 4.00
2556 2630 2.759973 CCAGGCGCTAGGACCAGA 60.760 66.667 7.64 0.00 0.00 3.86
2557 2631 2.359169 CCAGGCGCTAGGACCAGAA 61.359 63.158 7.64 0.00 0.00 3.02
2558 2632 1.690219 CCAGGCGCTAGGACCAGAAT 61.690 60.000 7.64 0.00 0.00 2.40
2559 2633 1.040646 CAGGCGCTAGGACCAGAATA 58.959 55.000 7.64 0.00 0.00 1.75
2560 2634 1.412710 CAGGCGCTAGGACCAGAATAA 59.587 52.381 7.64 0.00 0.00 1.40
2561 2635 2.037772 CAGGCGCTAGGACCAGAATAAT 59.962 50.000 7.64 0.00 0.00 1.28
2562 2636 3.258372 CAGGCGCTAGGACCAGAATAATA 59.742 47.826 7.64 0.00 0.00 0.98
2563 2637 4.081420 CAGGCGCTAGGACCAGAATAATAT 60.081 45.833 7.64 0.00 0.00 1.28
2564 2638 4.532521 AGGCGCTAGGACCAGAATAATATT 59.467 41.667 7.64 0.00 0.00 1.28
2565 2639 5.013183 AGGCGCTAGGACCAGAATAATATTT 59.987 40.000 7.64 0.00 0.00 1.40
2566 2640 5.705905 GGCGCTAGGACCAGAATAATATTTT 59.294 40.000 7.64 0.00 0.00 1.82
2567 2641 6.877322 GGCGCTAGGACCAGAATAATATTTTA 59.123 38.462 7.64 0.00 0.00 1.52
2568 2642 7.553044 GGCGCTAGGACCAGAATAATATTTTAT 59.447 37.037 7.64 0.00 0.00 1.40
2569 2643 8.947115 GCGCTAGGACCAGAATAATATTTTATT 58.053 33.333 0.00 1.30 40.04 1.40
2591 2665 6.861065 TTTCTAATCAAGCGCCTAATTAGG 57.139 37.500 24.90 24.90 46.42 2.69
2600 2674 2.142220 CCTAATTAGGCGCCTCCCA 58.858 57.895 36.73 19.40 36.53 4.37
2601 2675 0.693049 CCTAATTAGGCGCCTCCCAT 59.307 55.000 36.73 20.91 36.53 4.00
2602 2676 1.073923 CCTAATTAGGCGCCTCCCATT 59.926 52.381 36.73 28.71 36.53 3.16
2603 2677 2.154462 CTAATTAGGCGCCTCCCATTG 58.846 52.381 36.73 16.24 34.51 2.82
2604 2678 0.468029 AATTAGGCGCCTCCCATTGG 60.468 55.000 36.73 0.00 34.51 3.16
2605 2679 1.352622 ATTAGGCGCCTCCCATTGGA 61.353 55.000 36.73 10.36 38.75 3.53
2606 2680 2.265467 TTAGGCGCCTCCCATTGGAC 62.265 60.000 36.73 0.00 35.03 4.02
2607 2681 4.424711 GGCGCCTCCCATTGGACA 62.425 66.667 22.15 0.00 35.03 4.02
2608 2682 2.124151 GCGCCTCCCATTGGACAT 60.124 61.111 3.62 0.00 35.03 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.700352 TGGCAATTCTTTTGAAATAGGGAAG 58.300 36.000 0.00 0.00 42.31 3.46
9 10 6.690530 TCACTGGCAATTCTTTTGAAATAGG 58.309 36.000 0.00 0.00 42.31 2.57
10 11 8.592105 TTTCACTGGCAATTCTTTTGAAATAG 57.408 30.769 0.00 0.00 42.31 1.73
59 60 1.485066 CCCTGATAGTTTACGTGCCCT 59.515 52.381 0.00 0.00 0.00 5.19
71 72 6.102663 GCAAGCATATACAGTACCCTGATAG 58.897 44.000 0.00 0.00 41.50 2.08
104 105 2.380084 GACTAATTGGCGAGTGGTGA 57.620 50.000 0.00 0.00 0.00 4.02
123 124 2.725203 TTCAACAAGGAGCGGTCCCG 62.725 60.000 29.33 22.51 45.26 5.14
183 184 1.303317 CCGTAAACAAGGCTGCCCT 60.303 57.895 16.57 0.00 45.77 5.19
184 185 2.340328 CCCGTAAACAAGGCTGCCC 61.340 63.158 16.57 0.00 0.00 5.36
185 186 2.989881 GCCCGTAAACAAGGCTGCC 61.990 63.158 11.65 11.65 43.62 4.85
186 187 2.566529 GCCCGTAAACAAGGCTGC 59.433 61.111 0.00 0.00 43.62 5.25
190 191 1.778334 GCTTTTGCCCGTAAACAAGG 58.222 50.000 0.00 0.00 40.15 3.61
191 192 1.002251 TCGCTTTTGCCCGTAAACAAG 60.002 47.619 0.00 0.00 43.93 3.16
192 193 1.022735 TCGCTTTTGCCCGTAAACAA 58.977 45.000 0.00 0.00 43.93 2.83
193 194 1.002251 CTTCGCTTTTGCCCGTAAACA 60.002 47.619 0.00 0.00 43.93 2.83
194 195 1.264826 TCTTCGCTTTTGCCCGTAAAC 59.735 47.619 0.00 0.00 43.93 2.01
195 196 1.264826 GTCTTCGCTTTTGCCCGTAAA 59.735 47.619 0.00 0.00 43.93 2.01
196 197 0.869730 GTCTTCGCTTTTGCCCGTAA 59.130 50.000 0.00 0.00 43.93 3.18
197 198 1.286354 CGTCTTCGCTTTTGCCCGTA 61.286 55.000 0.00 0.00 43.93 4.02
198 199 2.604174 CGTCTTCGCTTTTGCCCGT 61.604 57.895 0.00 0.00 43.93 5.28
199 200 1.837538 TTCGTCTTCGCTTTTGCCCG 61.838 55.000 0.00 0.00 43.93 6.13
200 201 0.521735 ATTCGTCTTCGCTTTTGCCC 59.478 50.000 0.00 0.00 43.93 5.36
201 202 2.331809 AATTCGTCTTCGCTTTTGCC 57.668 45.000 0.00 0.00 43.93 4.52
202 203 2.335610 CGAAATTCGTCTTCGCTTTTGC 59.664 45.455 7.29 0.00 39.22 3.68
215 216 1.722011 ACCTGGCACTACGAAATTCG 58.278 50.000 14.35 14.35 46.93 3.34
216 217 3.071479 TGAACCTGGCACTACGAAATTC 58.929 45.455 0.00 0.00 0.00 2.17
217 218 2.812011 GTGAACCTGGCACTACGAAATT 59.188 45.455 0.00 0.00 33.57 1.82
218 219 2.423577 GTGAACCTGGCACTACGAAAT 58.576 47.619 0.00 0.00 33.57 2.17
219 220 1.870580 CGTGAACCTGGCACTACGAAA 60.871 52.381 7.35 0.00 34.18 3.46
220 221 0.319211 CGTGAACCTGGCACTACGAA 60.319 55.000 7.35 0.00 34.18 3.85
245 246 5.132648 TCAGGTATTGCATATCCAGAAAGGT 59.867 40.000 0.00 0.00 39.02 3.50
246 247 5.624159 TCAGGTATTGCATATCCAGAAAGG 58.376 41.667 0.00 0.00 39.47 3.11
247 248 5.704515 CCTCAGGTATTGCATATCCAGAAAG 59.295 44.000 0.00 0.00 0.00 2.62
248 249 5.132648 ACCTCAGGTATTGCATATCCAGAAA 59.867 40.000 0.00 0.00 32.11 2.52
249 250 4.660303 ACCTCAGGTATTGCATATCCAGAA 59.340 41.667 0.00 0.00 32.11 3.02
250 251 4.234550 ACCTCAGGTATTGCATATCCAGA 58.765 43.478 0.00 0.00 32.11 3.86
251 252 4.630644 ACCTCAGGTATTGCATATCCAG 57.369 45.455 0.00 0.00 32.11 3.86
316 319 7.739498 AGTACAACTTCAACCATTTTCGTAT 57.261 32.000 0.00 0.00 0.00 3.06
350 353 7.502060 ACTCCCTTCGATCCATATTGATTAT 57.498 36.000 0.00 0.00 0.00 1.28
351 354 6.935240 ACTCCCTTCGATCCATATTGATTA 57.065 37.500 0.00 0.00 0.00 1.75
358 361 3.605726 TGGTACTCCCTTCGATCCATA 57.394 47.619 0.00 0.00 0.00 2.74
365 368 4.189231 CTGGTAATTTGGTACTCCCTTCG 58.811 47.826 0.00 0.00 0.00 3.79
367 370 4.600111 TCACTGGTAATTTGGTACTCCCTT 59.400 41.667 0.00 0.00 0.00 3.95
379 382 4.975147 TCTATGGGGATGTCACTGGTAATT 59.025 41.667 0.00 0.00 0.00 1.40
396 399 7.070821 ACCACCTAAGTTTACTATGGTCTATGG 59.929 40.741 4.43 0.00 33.73 2.74
413 416 6.036844 GGATTCGTTAGCTAAAACCACCTAAG 59.963 42.308 7.99 0.00 0.00 2.18
421 424 6.490566 TTCCTTGGATTCGTTAGCTAAAAC 57.509 37.500 7.99 0.00 0.00 2.43
445 448 1.077357 ACCACAGACGGCAAAACCA 60.077 52.632 0.00 0.00 39.03 3.67
449 452 1.891919 GCAGACCACAGACGGCAAA 60.892 57.895 0.00 0.00 0.00 3.68
455 458 1.198637 GAAATGCTGCAGACCACAGAC 59.801 52.381 20.43 0.00 37.32 3.51
459 462 0.610232 AGGGAAATGCTGCAGACCAC 60.610 55.000 20.43 0.00 0.00 4.16
460 463 0.112995 AAGGGAAATGCTGCAGACCA 59.887 50.000 20.43 7.27 0.00 4.02
534 537 6.906157 ATTCTTGAATTCTTTGCTTGAGGA 57.094 33.333 7.05 0.00 0.00 3.71
567 570 2.821991 ACTACATATTCTGCGGCTCC 57.178 50.000 0.00 0.00 0.00 4.70
609 612 6.875948 TCATGTACATGTTGTAAAGCAAGT 57.124 33.333 30.03 0.00 39.72 3.16
683 686 5.137403 CGTTCTTCTGTTTGTTTACGGATG 58.863 41.667 0.00 0.00 33.62 3.51
710 717 3.074412 CTGTTTAAGCGGATTGGTGAGT 58.926 45.455 0.00 0.00 0.00 3.41
750 757 1.946768 TGCTGGAAAGTGAAACCGAAG 59.053 47.619 0.00 0.00 37.80 3.79
797 804 2.679639 GCGTACTGGATGTTGATTCCCA 60.680 50.000 0.00 0.00 31.87 4.37
818 825 4.240096 GCAAAACTGTTGATGAAGATGGG 58.760 43.478 9.89 0.00 0.00 4.00
819 826 3.916172 CGCAAAACTGTTGATGAAGATGG 59.084 43.478 9.89 0.00 0.00 3.51
824 831 2.098934 AGCACGCAAAACTGTTGATGAA 59.901 40.909 9.89 0.00 0.00 2.57
1464 1508 2.029073 ACCGTGGAGTTGAGCACG 59.971 61.111 0.00 0.00 40.30 5.34
2054 2114 1.187087 AAGAACGGAGGGAGTAGCTG 58.813 55.000 0.00 0.00 0.00 4.24
2109 2175 7.265673 GCTCTAAACCATGTCTACTTACATCA 58.734 38.462 0.00 0.00 38.01 3.07
2144 2210 9.469807 AAGAGACTATATACGAAGCAAAATGAG 57.530 33.333 0.00 0.00 0.00 2.90
2222 2289 3.245586 TGCCCTTTCAGACCATGGTTAAT 60.246 43.478 20.85 5.55 0.00 1.40
2283 2350 7.807977 ACTGGTGAAAGGTTAAGCATATATG 57.192 36.000 8.45 8.45 0.00 1.78
2306 2375 2.726241 GGCTGCATGACTTTCGAAAAAC 59.274 45.455 12.41 9.20 0.00 2.43
2366 2440 1.534595 CGCTCTGCATTGTAAATGCCC 60.535 52.381 19.30 7.06 43.94 5.36
2367 2441 1.831343 CGCTCTGCATTGTAAATGCC 58.169 50.000 19.30 5.87 43.94 4.40
2368 2442 1.194495 GCGCTCTGCATTGTAAATGC 58.806 50.000 16.20 16.20 45.45 3.56
2386 2460 4.971125 CCTAGCGCCCGCCTTAGC 62.971 72.222 2.29 0.00 43.17 3.09
2387 2461 4.301027 CCCTAGCGCCCGCCTTAG 62.301 72.222 2.29 5.60 43.17 2.18
2394 2468 2.844839 ATCCTGACCCTAGCGCCC 60.845 66.667 2.29 0.00 0.00 6.13
2395 2469 2.737830 GATCCTGACCCTAGCGCC 59.262 66.667 2.29 0.00 0.00 6.53
2396 2470 2.737830 GGATCCTGACCCTAGCGC 59.262 66.667 3.84 0.00 0.00 5.92
2397 2471 2.565645 CGGGATCCTGACCCTAGCG 61.566 68.421 16.28 0.25 44.72 4.26
2398 2472 2.210711 CCGGGATCCTGACCCTAGC 61.211 68.421 23.02 0.00 44.72 3.42
2399 2473 0.828343 GACCGGGATCCTGACCCTAG 60.828 65.000 23.02 6.43 44.72 3.02
2400 2474 1.232216 GACCGGGATCCTGACCCTA 59.768 63.158 23.02 0.00 44.72 3.53
2401 2475 2.041819 GACCGGGATCCTGACCCT 60.042 66.667 23.02 0.85 44.72 4.34
2402 2476 3.537874 CGACCGGGATCCTGACCC 61.538 72.222 23.02 9.18 43.57 4.46
2403 2477 1.896122 AAACGACCGGGATCCTGACC 61.896 60.000 23.02 11.64 0.00 4.02
2404 2478 0.036671 AAAACGACCGGGATCCTGAC 60.037 55.000 23.02 13.94 0.00 3.51
2405 2479 0.036765 CAAAACGACCGGGATCCTGA 60.037 55.000 23.02 0.00 0.00 3.86
2406 2480 1.644786 GCAAAACGACCGGGATCCTG 61.645 60.000 14.26 14.26 0.00 3.86
2407 2481 1.376812 GCAAAACGACCGGGATCCT 60.377 57.895 12.58 0.00 0.00 3.24
2408 2482 0.958876 AAGCAAAACGACCGGGATCC 60.959 55.000 6.32 1.92 0.00 3.36
2409 2483 1.664151 CTAAGCAAAACGACCGGGATC 59.336 52.381 6.32 0.00 0.00 3.36
2410 2484 1.002773 ACTAAGCAAAACGACCGGGAT 59.997 47.619 6.32 0.00 0.00 3.85
2411 2485 0.393820 ACTAAGCAAAACGACCGGGA 59.606 50.000 6.32 0.00 0.00 5.14
2412 2486 1.196127 GAACTAAGCAAAACGACCGGG 59.804 52.381 6.32 0.00 0.00 5.73
2413 2487 1.196127 GGAACTAAGCAAAACGACCGG 59.804 52.381 0.00 0.00 0.00 5.28
2414 2488 1.196127 GGGAACTAAGCAAAACGACCG 59.804 52.381 0.00 0.00 0.00 4.79
2415 2489 1.196127 CGGGAACTAAGCAAAACGACC 59.804 52.381 0.00 0.00 0.00 4.79
2416 2490 1.869132 ACGGGAACTAAGCAAAACGAC 59.131 47.619 0.00 0.00 0.00 4.34
2417 2491 2.243602 ACGGGAACTAAGCAAAACGA 57.756 45.000 0.00 0.00 0.00 3.85
2418 2492 2.288458 TGAACGGGAACTAAGCAAAACG 59.712 45.455 0.00 0.00 0.00 3.60
2419 2493 3.974871 TGAACGGGAACTAAGCAAAAC 57.025 42.857 0.00 0.00 0.00 2.43
2420 2494 4.985538 TTTGAACGGGAACTAAGCAAAA 57.014 36.364 0.00 0.00 0.00 2.44
2421 2495 4.825085 AGATTTGAACGGGAACTAAGCAAA 59.175 37.500 0.00 0.00 0.00 3.68
2422 2496 4.215399 CAGATTTGAACGGGAACTAAGCAA 59.785 41.667 0.00 0.00 0.00 3.91
2423 2497 3.751175 CAGATTTGAACGGGAACTAAGCA 59.249 43.478 0.00 0.00 0.00 3.91
2424 2498 3.127030 CCAGATTTGAACGGGAACTAAGC 59.873 47.826 0.00 0.00 0.00 3.09
2425 2499 3.689649 CCCAGATTTGAACGGGAACTAAG 59.310 47.826 0.00 0.00 41.62 2.18
2426 2500 3.328343 TCCCAGATTTGAACGGGAACTAA 59.672 43.478 0.00 0.00 44.87 2.24
2427 2501 2.907696 TCCCAGATTTGAACGGGAACTA 59.092 45.455 0.00 0.00 44.87 2.24
2428 2502 1.702957 TCCCAGATTTGAACGGGAACT 59.297 47.619 0.00 0.00 44.87 3.01
2429 2503 2.194201 TCCCAGATTTGAACGGGAAC 57.806 50.000 0.00 0.00 44.87 3.62
2431 2505 3.352648 GAATTCCCAGATTTGAACGGGA 58.647 45.455 0.00 0.00 46.19 5.14
2432 2506 2.097466 CGAATTCCCAGATTTGAACGGG 59.903 50.000 0.00 0.00 40.32 5.28
2433 2507 2.097466 CCGAATTCCCAGATTTGAACGG 59.903 50.000 0.00 0.00 0.00 4.44
2434 2508 2.477863 GCCGAATTCCCAGATTTGAACG 60.478 50.000 0.00 0.00 0.00 3.95
2435 2509 2.477863 CGCCGAATTCCCAGATTTGAAC 60.478 50.000 0.00 0.00 0.00 3.18
2436 2510 1.742831 CGCCGAATTCCCAGATTTGAA 59.257 47.619 0.00 0.00 0.00 2.69
2437 2511 1.378531 CGCCGAATTCCCAGATTTGA 58.621 50.000 0.00 0.00 0.00 2.69
2438 2512 0.381801 CCGCCGAATTCCCAGATTTG 59.618 55.000 0.00 0.00 0.00 2.32
2439 2513 0.751643 CCCGCCGAATTCCCAGATTT 60.752 55.000 0.00 0.00 0.00 2.17
2440 2514 1.152963 CCCGCCGAATTCCCAGATT 60.153 57.895 0.00 0.00 0.00 2.40
2441 2515 2.510906 CCCGCCGAATTCCCAGAT 59.489 61.111 0.00 0.00 0.00 2.90
2442 2516 4.483243 GCCCGCCGAATTCCCAGA 62.483 66.667 0.00 0.00 0.00 3.86
2446 2520 4.903010 TAGCGCCCGCCGAATTCC 62.903 66.667 2.29 0.00 43.17 3.01
2447 2521 2.893404 TTAGCGCCCGCCGAATTC 60.893 61.111 2.29 0.00 43.17 2.17
2448 2522 3.199891 GTTAGCGCCCGCCGAATT 61.200 61.111 2.29 0.00 43.17 2.17
2457 2531 1.359459 CGAGAAACAGGGTTAGCGCC 61.359 60.000 2.29 0.00 0.00 6.53
2458 2532 0.669625 ACGAGAAACAGGGTTAGCGC 60.670 55.000 0.00 0.00 0.00 5.92
2459 2533 1.725164 GAACGAGAAACAGGGTTAGCG 59.275 52.381 0.00 0.00 0.00 4.26
2460 2534 3.041508 AGAACGAGAAACAGGGTTAGC 57.958 47.619 0.00 0.00 0.00 3.09
2461 2535 7.668525 AAATTAGAACGAGAAACAGGGTTAG 57.331 36.000 0.00 0.00 0.00 2.34
2462 2536 7.935210 AGAAAATTAGAACGAGAAACAGGGTTA 59.065 33.333 0.00 0.00 0.00 2.85
2463 2537 6.771267 AGAAAATTAGAACGAGAAACAGGGTT 59.229 34.615 0.00 0.00 0.00 4.11
2464 2538 6.204882 CAGAAAATTAGAACGAGAAACAGGGT 59.795 38.462 0.00 0.00 0.00 4.34
2465 2539 6.426937 TCAGAAAATTAGAACGAGAAACAGGG 59.573 38.462 0.00 0.00 0.00 4.45
2466 2540 7.171678 ACTCAGAAAATTAGAACGAGAAACAGG 59.828 37.037 0.00 0.00 0.00 4.00
2467 2541 8.077836 ACTCAGAAAATTAGAACGAGAAACAG 57.922 34.615 0.00 0.00 0.00 3.16
2468 2542 9.706691 ATACTCAGAAAATTAGAACGAGAAACA 57.293 29.630 0.00 0.00 0.00 2.83
2471 2545 9.517609 GCTATACTCAGAAAATTAGAACGAGAA 57.482 33.333 0.00 0.00 0.00 2.87
2472 2546 7.856398 CGCTATACTCAGAAAATTAGAACGAGA 59.144 37.037 0.00 0.00 0.00 4.04
2473 2547 7.357695 GCGCTATACTCAGAAAATTAGAACGAG 60.358 40.741 0.00 0.00 0.00 4.18
2474 2548 6.417044 GCGCTATACTCAGAAAATTAGAACGA 59.583 38.462 0.00 0.00 0.00 3.85
2475 2549 6.418226 AGCGCTATACTCAGAAAATTAGAACG 59.582 38.462 8.99 0.00 0.00 3.95
2476 2550 7.306866 CCAGCGCTATACTCAGAAAATTAGAAC 60.307 40.741 10.99 0.00 0.00 3.01
2477 2551 6.701841 CCAGCGCTATACTCAGAAAATTAGAA 59.298 38.462 10.99 0.00 0.00 2.10
2478 2552 6.183360 ACCAGCGCTATACTCAGAAAATTAGA 60.183 38.462 10.99 0.00 0.00 2.10
2479 2553 5.986135 ACCAGCGCTATACTCAGAAAATTAG 59.014 40.000 10.99 0.00 0.00 1.73
2480 2554 5.914033 ACCAGCGCTATACTCAGAAAATTA 58.086 37.500 10.99 0.00 0.00 1.40
2481 2555 4.770795 ACCAGCGCTATACTCAGAAAATT 58.229 39.130 10.99 0.00 0.00 1.82
2482 2556 4.408182 ACCAGCGCTATACTCAGAAAAT 57.592 40.909 10.99 0.00 0.00 1.82
2483 2557 3.887621 ACCAGCGCTATACTCAGAAAA 57.112 42.857 10.99 0.00 0.00 2.29
2484 2558 3.697542 TGTACCAGCGCTATACTCAGAAA 59.302 43.478 23.91 7.23 0.00 2.52
2485 2559 3.066342 GTGTACCAGCGCTATACTCAGAA 59.934 47.826 23.91 7.79 0.00 3.02
2486 2560 2.617308 GTGTACCAGCGCTATACTCAGA 59.383 50.000 23.91 8.08 0.00 3.27
2487 2561 2.357952 TGTGTACCAGCGCTATACTCAG 59.642 50.000 23.91 7.04 0.00 3.35
2488 2562 2.357952 CTGTGTACCAGCGCTATACTCA 59.642 50.000 23.91 23.69 33.59 3.41
2489 2563 3.001395 CTGTGTACCAGCGCTATACTC 57.999 52.381 23.91 21.35 33.59 2.59
2499 2573 0.457509 CGCTGAGAGCTGTGTACCAG 60.458 60.000 0.00 6.91 44.53 4.00
2500 2574 1.179174 ACGCTGAGAGCTGTGTACCA 61.179 55.000 0.00 0.00 39.60 3.25
2501 2575 0.038159 AACGCTGAGAGCTGTGTACC 60.038 55.000 0.00 0.00 39.60 3.34
2502 2576 1.063806 CAACGCTGAGAGCTGTGTAC 58.936 55.000 0.00 0.00 39.60 2.90
2503 2577 0.667487 GCAACGCTGAGAGCTGTGTA 60.667 55.000 0.00 0.00 39.60 2.90
2504 2578 1.958205 GCAACGCTGAGAGCTGTGT 60.958 57.895 0.00 0.00 39.60 3.72
2505 2579 1.501337 TTGCAACGCTGAGAGCTGTG 61.501 55.000 0.00 0.00 39.60 3.66
2506 2580 1.226686 CTTGCAACGCTGAGAGCTGT 61.227 55.000 0.00 0.00 39.60 4.40
2507 2581 1.496393 CTTGCAACGCTGAGAGCTG 59.504 57.895 0.00 0.00 39.60 4.24
2508 2582 2.323580 GCTTGCAACGCTGAGAGCT 61.324 57.895 11.98 0.00 39.60 4.09
2509 2583 2.175322 GCTTGCAACGCTGAGAGC 59.825 61.111 11.98 0.84 38.02 4.09
2510 2584 0.947660 TCTGCTTGCAACGCTGAGAG 60.948 55.000 19.04 10.75 32.63 3.20
2511 2585 1.069596 TCTGCTTGCAACGCTGAGA 59.930 52.632 19.04 13.02 32.63 3.27
2512 2586 1.496393 CTCTGCTTGCAACGCTGAG 59.504 57.895 26.69 26.69 43.60 3.35
2513 2587 1.224069 GACTCTGCTTGCAACGCTGA 61.224 55.000 20.55 20.55 34.76 4.26
2514 2588 1.206072 GACTCTGCTTGCAACGCTG 59.794 57.895 17.72 16.93 0.00 5.18
2515 2589 2.313172 CGACTCTGCTTGCAACGCT 61.313 57.895 17.72 2.48 0.00 5.07
2516 2590 2.171940 CGACTCTGCTTGCAACGC 59.828 61.111 12.25 12.25 0.00 4.84
2517 2591 2.171940 GCGACTCTGCTTGCAACG 59.828 61.111 0.00 0.00 0.00 4.10
2518 2592 3.647824 AGCGACTCTGCTTGCAAC 58.352 55.556 0.00 0.00 44.46 4.17
2525 2599 1.520342 CCTGGCTAAGCGACTCTGC 60.520 63.158 0.00 0.00 0.00 4.26
2526 2600 1.520342 GCCTGGCTAAGCGACTCTG 60.520 63.158 12.43 0.00 0.00 3.35
2527 2601 2.896443 GCCTGGCTAAGCGACTCT 59.104 61.111 12.43 0.00 0.00 3.24
2538 2612 4.537433 CTGGTCCTAGCGCCTGGC 62.537 72.222 9.11 9.11 44.05 4.85
2539 2613 1.690219 ATTCTGGTCCTAGCGCCTGG 61.690 60.000 2.29 6.90 0.00 4.45
2540 2614 1.040646 TATTCTGGTCCTAGCGCCTG 58.959 55.000 2.29 0.00 0.00 4.85
2541 2615 1.789523 TTATTCTGGTCCTAGCGCCT 58.210 50.000 2.29 0.00 0.00 5.52
2542 2616 2.841442 ATTATTCTGGTCCTAGCGCC 57.159 50.000 2.29 0.00 0.00 6.53
2543 2617 6.803154 AAAATATTATTCTGGTCCTAGCGC 57.197 37.500 0.00 0.00 0.00 5.92
2565 2639 8.999431 CCTAATTAGGCGCTTGATTAGAAATAA 58.001 33.333 32.27 8.80 36.53 1.40
2566 2640 8.547967 CCTAATTAGGCGCTTGATTAGAAATA 57.452 34.615 32.27 9.39 36.53 1.40
2567 2641 7.440523 CCTAATTAGGCGCTTGATTAGAAAT 57.559 36.000 32.27 9.95 36.53 2.17
2568 2642 6.861065 CCTAATTAGGCGCTTGATTAGAAA 57.139 37.500 32.27 10.30 36.53 2.52
2582 2656 0.693049 ATGGGAGGCGCCTAATTAGG 59.307 55.000 32.97 24.90 46.42 2.69
2583 2657 2.154462 CAATGGGAGGCGCCTAATTAG 58.846 52.381 32.97 18.05 36.66 1.73
2584 2658 1.202879 CCAATGGGAGGCGCCTAATTA 60.203 52.381 32.97 16.85 35.59 1.40
2585 2659 0.468029 CCAATGGGAGGCGCCTAATT 60.468 55.000 32.97 25.12 35.59 1.40
2586 2660 1.151450 CCAATGGGAGGCGCCTAAT 59.849 57.895 32.97 20.64 35.59 1.73
2587 2661 1.998438 TCCAATGGGAGGCGCCTAA 60.998 57.895 32.97 19.13 38.64 2.69
2588 2662 2.366301 TCCAATGGGAGGCGCCTA 60.366 61.111 32.97 15.82 38.64 3.93
2589 2663 4.115199 GTCCAATGGGAGGCGCCT 62.115 66.667 33.48 33.48 46.12 5.52
2590 2664 3.721370 ATGTCCAATGGGAGGCGCC 62.721 63.158 21.89 21.89 46.12 6.53
2591 2665 2.124151 ATGTCCAATGGGAGGCGC 60.124 61.111 0.00 0.00 46.12 6.53


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

AutoCloner maintained by Alex Coulton.