Multiple sequence alignment - TraesCS4A01G120300

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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 TraesCS4A01G120300 chr4A 100.000 3302 0 0 1 3302 148125342 148128643 0.000000e+00 6098.0
1 TraesCS4A01G120300 chr4A 79.359 1061 177 27 1265 2295 147653519 147652471 0.000000e+00 708.0
2 TraesCS4A01G120300 chr4D 96.394 1969 62 5 400 2363 323584185 323582221 0.000000e+00 3234.0
3 TraesCS4A01G120300 chr4D 93.767 722 28 8 2595 3302 323580445 323579727 0.000000e+00 1068.0
4 TraesCS4A01G120300 chr4D 79.340 1060 179 26 1265 2295 323603301 323604349 0.000000e+00 708.0
5 TraesCS4A01G120300 chr4D 90.863 197 10 4 2360 2556 323580634 323580446 1.180000e-64 257.0
6 TraesCS4A01G120300 chr4D 86.486 111 14 1 268 378 323598911 323598802 1.610000e-23 121.0
7 TraesCS4A01G120300 chr4B 79.830 1061 172 28 1265 2295 404124080 404125128 0.000000e+00 736.0
8 TraesCS4A01G120300 chr4B 73.485 396 81 20 1446 1828 666788434 666788818 9.620000e-26 128.0
9 TraesCS4A01G120300 chr7D 78.476 1050 182 32 1277 2295 560892658 560893694 0.000000e+00 647.0
10 TraesCS4A01G120300 chr7D 77.370 981 160 38 1346 2295 560982799 560983748 2.920000e-145 525.0
11 TraesCS4A01G120300 chr7A 78.314 1056 185 29 1271 2295 645038844 645039886 2.780000e-180 641.0
12 TraesCS4A01G120300 chr7B 78.586 1004 173 31 1322 2295 608876206 608875215 2.800000e-175 625.0
13 TraesCS4A01G120300 chr2D 87.622 307 29 6 81 378 373808207 373807901 6.780000e-92 348.0
14 TraesCS4A01G120300 chr2A 85.993 307 28 10 81 378 505337739 505337439 6.880000e-82 315.0
15 TraesCS4A01G120300 chr2A 84.706 85 10 3 147 229 29808164 29808081 7.590000e-12 82.4
16 TraesCS4A01G120300 chr2B 85.016 307 30 9 81 378 443281663 443281364 6.930000e-77 298.0
17 TraesCS4A01G120300 chr1D 78.230 418 47 26 1 378 365247981 365247568 9.220000e-56 228.0
18 TraesCS4A01G120300 chr3D 83.871 217 34 1 2827 3042 25966234 25966450 4.320000e-49 206.0
19 TraesCS4A01G120300 chr3B 82.949 217 36 1 2827 3042 43041741 43041957 9.350000e-46 195.0
20 TraesCS4A01G120300 chrUn 73.138 376 88 12 1446 1814 291826090 291826459 4.470000e-24 122.0
21 TraesCS4A01G120300 chr6B 83.838 99 13 3 130 226 720130180 720130083 1.260000e-14 91.6
22 TraesCS4A01G120300 chr6B 85.714 84 10 2 144 226 720042702 720042620 1.630000e-13 87.9
23 TraesCS4A01G120300 chr6B 82.653 98 16 1 130 226 720093008 720092911 5.870000e-13 86.1
24 TraesCS4A01G120300 chr1B 90.000 70 6 1 303 371 488714950 488714881 4.540000e-14 89.8
25 TraesCS4A01G120300 chr5A 94.000 50 3 0 135 184 510468463 510468512 3.530000e-10 76.8


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 TraesCS4A01G120300 chr4A 148125342 148128643 3301 False 6098.000000 6098 100.000000 1 3302 1 chr4A.!!$F1 3301
1 TraesCS4A01G120300 chr4A 147652471 147653519 1048 True 708.000000 708 79.359000 1265 2295 1 chr4A.!!$R1 1030
2 TraesCS4A01G120300 chr4D 323579727 323584185 4458 True 1519.666667 3234 93.674667 400 3302 3 chr4D.!!$R2 2902
3 TraesCS4A01G120300 chr4D 323603301 323604349 1048 False 708.000000 708 79.340000 1265 2295 1 chr4D.!!$F1 1030
4 TraesCS4A01G120300 chr4B 404124080 404125128 1048 False 736.000000 736 79.830000 1265 2295 1 chr4B.!!$F1 1030
5 TraesCS4A01G120300 chr7D 560892658 560893694 1036 False 647.000000 647 78.476000 1277 2295 1 chr7D.!!$F1 1018
6 TraesCS4A01G120300 chr7D 560982799 560983748 949 False 525.000000 525 77.370000 1346 2295 1 chr7D.!!$F2 949
7 TraesCS4A01G120300 chr7A 645038844 645039886 1042 False 641.000000 641 78.314000 1271 2295 1 chr7A.!!$F1 1024
8 TraesCS4A01G120300 chr7B 608875215 608876206 991 True 625.000000 625 78.586000 1322 2295 1 chr7B.!!$R1 973

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
983 988 0.459237 CGGACAGCTTCTGTGGCTAG 60.459 60.0 3.98 0.0 45.44 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 4032 0.03438 AATCCCTGGACTCGACTCGA 60.034 55.0 0.29 0.29 0.0 4.04 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
35 36 6.793505 TCTTGTTAGGACTAAATCTCTCCC 57.206 41.667 0.00 0.00 0.00 4.30
36 37 6.261435 TCTTGTTAGGACTAAATCTCTCCCA 58.739 40.000 0.00 0.00 0.00 4.37
37 38 6.903534 TCTTGTTAGGACTAAATCTCTCCCAT 59.096 38.462 0.00 0.00 0.00 4.00
38 39 8.065627 TCTTGTTAGGACTAAATCTCTCCCATA 58.934 37.037 0.00 0.00 0.00 2.74
39 40 8.618240 TTGTTAGGACTAAATCTCTCCCATAA 57.382 34.615 0.00 0.00 0.00 1.90
40 41 8.251383 TGTTAGGACTAAATCTCTCCCATAAG 57.749 38.462 0.00 0.00 0.00 1.73
41 42 7.844779 TGTTAGGACTAAATCTCTCCCATAAGT 59.155 37.037 0.00 0.00 0.00 2.24
42 43 6.987403 AGGACTAAATCTCTCCCATAAGTC 57.013 41.667 0.00 0.00 33.10 3.01
43 44 6.444704 AGGACTAAATCTCTCCCATAAGTCA 58.555 40.000 0.00 0.00 35.04 3.41
44 45 7.079048 AGGACTAAATCTCTCCCATAAGTCAT 58.921 38.462 0.00 0.00 35.04 3.06
45 46 7.570607 AGGACTAAATCTCTCCCATAAGTCATT 59.429 37.037 0.00 0.00 35.04 2.57
46 47 7.875554 GGACTAAATCTCTCCCATAAGTCATTC 59.124 40.741 0.00 0.00 35.04 2.67
47 48 8.560124 ACTAAATCTCTCCCATAAGTCATTCT 57.440 34.615 0.00 0.00 0.00 2.40
48 49 8.997734 ACTAAATCTCTCCCATAAGTCATTCTT 58.002 33.333 0.00 0.00 39.89 2.52
49 50 9.844257 CTAAATCTCTCCCATAAGTCATTCTTT 57.156 33.333 0.00 0.00 37.56 2.52
50 51 8.744568 AAATCTCTCCCATAAGTCATTCTTTC 57.255 34.615 0.00 0.00 37.56 2.62
51 52 7.688918 ATCTCTCCCATAAGTCATTCTTTCT 57.311 36.000 0.00 0.00 37.56 2.52
52 53 7.502060 TCTCTCCCATAAGTCATTCTTTCTT 57.498 36.000 0.00 0.00 37.56 2.52
53 54 8.609617 TCTCTCCCATAAGTCATTCTTTCTTA 57.390 34.615 0.00 0.00 37.56 2.10
54 55 8.700051 TCTCTCCCATAAGTCATTCTTTCTTAG 58.300 37.037 0.00 0.00 37.56 2.18
55 56 8.609617 TCTCCCATAAGTCATTCTTTCTTAGA 57.390 34.615 0.00 0.00 37.56 2.10
56 57 9.046846 TCTCCCATAAGTCATTCTTTCTTAGAA 57.953 33.333 0.00 0.00 46.50 2.10
57 58 9.672673 CTCCCATAAGTCATTCTTTCTTAGAAA 57.327 33.333 7.22 7.22 45.62 2.52
85 86 9.918630 AAATGTGTTCTTCCTTATCTGAATTTG 57.081 29.630 0.00 0.00 0.00 2.32
86 87 8.641498 ATGTGTTCTTCCTTATCTGAATTTGT 57.359 30.769 0.00 0.00 0.00 2.83
87 88 9.739276 ATGTGTTCTTCCTTATCTGAATTTGTA 57.261 29.630 0.00 0.00 0.00 2.41
88 89 8.999431 TGTGTTCTTCCTTATCTGAATTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
89 90 9.220767 GTGTTCTTCCTTATCTGAATTTGTACT 57.779 33.333 0.00 0.00 0.00 2.73
96 97 9.959721 TCCTTATCTGAATTTGTACTAAAAGCT 57.040 29.630 0.00 0.00 0.00 3.74
102 103 9.840427 TCTGAATTTGTACTAAAAGCTAAATGC 57.160 29.630 0.00 0.00 43.29 3.56
176 177 7.875327 TCTTCTTTTAGGTAATACCAATGGC 57.125 36.000 12.54 0.00 41.95 4.40
177 178 6.831868 TCTTCTTTTAGGTAATACCAATGGCC 59.168 38.462 12.54 0.00 41.95 5.36
178 179 6.335781 TCTTTTAGGTAATACCAATGGCCT 57.664 37.500 12.54 0.00 41.95 5.19
179 180 6.737608 TCTTTTAGGTAATACCAATGGCCTT 58.262 36.000 12.54 0.00 41.95 4.35
180 181 7.874252 TCTTTTAGGTAATACCAATGGCCTTA 58.126 34.615 12.54 0.00 41.95 2.69
181 182 8.337739 TCTTTTAGGTAATACCAATGGCCTTAA 58.662 33.333 12.54 0.00 41.95 1.85
182 183 9.143155 CTTTTAGGTAATACCAATGGCCTTAAT 57.857 33.333 12.54 0.00 41.95 1.40
183 184 9.495382 TTTTAGGTAATACCAATGGCCTTAATT 57.505 29.630 12.54 0.00 41.95 1.40
184 185 9.495382 TTTAGGTAATACCAATGGCCTTAATTT 57.505 29.630 12.54 0.00 41.95 1.82
185 186 7.360113 AGGTAATACCAATGGCCTTAATTTG 57.640 36.000 12.54 0.18 41.95 2.32
186 187 6.900743 AGGTAATACCAATGGCCTTAATTTGT 59.099 34.615 12.54 0.00 41.95 2.83
187 188 7.401782 AGGTAATACCAATGGCCTTAATTTGTT 59.598 33.333 12.54 0.00 41.95 2.83
188 189 7.709182 GGTAATACCAATGGCCTTAATTTGTTC 59.291 37.037 3.32 0.00 38.42 3.18
189 190 7.494922 AATACCAATGGCCTTAATTTGTTCT 57.505 32.000 3.32 0.00 0.00 3.01
190 191 5.823861 ACCAATGGCCTTAATTTGTTCTT 57.176 34.783 3.32 0.00 0.00 2.52
191 192 5.793817 ACCAATGGCCTTAATTTGTTCTTC 58.206 37.500 3.32 0.00 0.00 2.87
192 193 5.178061 CCAATGGCCTTAATTTGTTCTTCC 58.822 41.667 3.32 0.00 0.00 3.46
193 194 5.046376 CCAATGGCCTTAATTTGTTCTTCCT 60.046 40.000 3.32 0.00 0.00 3.36
194 195 6.466812 CAATGGCCTTAATTTGTTCTTCCTT 58.533 36.000 3.32 0.00 0.00 3.36
195 196 7.310361 CCAATGGCCTTAATTTGTTCTTCCTTA 60.310 37.037 3.32 0.00 0.00 2.69
196 197 6.834168 TGGCCTTAATTTGTTCTTCCTTAG 57.166 37.500 3.32 0.00 0.00 2.18
197 198 6.548321 TGGCCTTAATTTGTTCTTCCTTAGA 58.452 36.000 3.32 0.00 0.00 2.10
198 199 7.007723 TGGCCTTAATTTGTTCTTCCTTAGAA 58.992 34.615 3.32 0.00 40.57 2.10
199 200 7.673926 TGGCCTTAATTTGTTCTTCCTTAGAAT 59.326 33.333 3.32 0.00 44.39 2.40
200 201 9.185680 GGCCTTAATTTGTTCTTCCTTAGAATA 57.814 33.333 0.00 0.00 44.39 1.75
208 209 7.303634 TGTTCTTCCTTAGAATAAATGTCGC 57.696 36.000 0.00 0.00 44.39 5.19
209 210 7.103641 TGTTCTTCCTTAGAATAAATGTCGCT 58.896 34.615 0.00 0.00 44.39 4.93
210 211 7.606456 TGTTCTTCCTTAGAATAAATGTCGCTT 59.394 33.333 0.00 0.00 44.39 4.68
211 212 8.451748 GTTCTTCCTTAGAATAAATGTCGCTTT 58.548 33.333 0.00 0.00 44.39 3.51
212 213 9.661563 TTCTTCCTTAGAATAAATGTCGCTTTA 57.338 29.630 0.00 0.00 37.96 1.85
213 214 9.832445 TCTTCCTTAGAATAAATGTCGCTTTAT 57.168 29.630 0.00 0.00 33.72 1.40
228 229 9.862585 ATGTCGCTTTATTTTCATTTTTGTTTC 57.137 25.926 0.00 0.00 0.00 2.78
229 230 8.873830 TGTCGCTTTATTTTCATTTTTGTTTCA 58.126 25.926 0.00 0.00 0.00 2.69
230 231 9.356929 GTCGCTTTATTTTCATTTTTGTTTCAG 57.643 29.630 0.00 0.00 0.00 3.02
231 232 8.547069 TCGCTTTATTTTCATTTTTGTTTCAGG 58.453 29.630 0.00 0.00 0.00 3.86
232 233 8.334632 CGCTTTATTTTCATTTTTGTTTCAGGT 58.665 29.630 0.00 0.00 0.00 4.00
238 239 7.835634 TTTCATTTTTGTTTCAGGTAACACC 57.164 32.000 0.00 0.00 37.72 4.16
239 240 6.531503 TCATTTTTGTTTCAGGTAACACCA 57.468 33.333 0.00 0.00 41.95 4.17
240 241 6.334202 TCATTTTTGTTTCAGGTAACACCAC 58.666 36.000 0.00 0.00 41.95 4.16
241 242 5.986501 TTTTTGTTTCAGGTAACACCACT 57.013 34.783 0.00 0.00 41.95 4.00
242 243 5.986501 TTTTGTTTCAGGTAACACCACTT 57.013 34.783 0.00 0.00 41.95 3.16
243 244 7.463961 TTTTTGTTTCAGGTAACACCACTTA 57.536 32.000 0.00 0.00 41.95 2.24
244 245 6.687081 TTTGTTTCAGGTAACACCACTTAG 57.313 37.500 0.00 0.00 41.95 2.18
245 246 4.131596 TGTTTCAGGTAACACCACTTAGC 58.868 43.478 0.00 0.00 41.95 3.09
246 247 4.141574 TGTTTCAGGTAACACCACTTAGCT 60.142 41.667 0.00 0.00 41.95 3.32
247 248 4.699925 TTCAGGTAACACCACTTAGCTT 57.300 40.909 0.00 0.00 41.95 3.74
248 249 4.002906 TCAGGTAACACCACTTAGCTTG 57.997 45.455 0.00 0.00 41.95 4.01
249 250 3.644265 TCAGGTAACACCACTTAGCTTGA 59.356 43.478 0.00 0.00 41.95 3.02
250 251 3.746492 CAGGTAACACCACTTAGCTTGAC 59.254 47.826 0.00 0.00 41.95 3.18
251 252 3.646637 AGGTAACACCACTTAGCTTGACT 59.353 43.478 0.00 0.00 41.95 3.41
252 253 4.102681 AGGTAACACCACTTAGCTTGACTT 59.897 41.667 0.00 0.00 41.95 3.01
253 254 4.820173 GGTAACACCACTTAGCTTGACTTT 59.180 41.667 0.00 0.00 38.42 2.66
254 255 4.900635 AACACCACTTAGCTTGACTTTG 57.099 40.909 0.00 0.00 0.00 2.77
255 256 4.150897 ACACCACTTAGCTTGACTTTGA 57.849 40.909 0.00 0.00 0.00 2.69
256 257 4.718961 ACACCACTTAGCTTGACTTTGAT 58.281 39.130 0.00 0.00 0.00 2.57
257 258 5.865085 ACACCACTTAGCTTGACTTTGATA 58.135 37.500 0.00 0.00 0.00 2.15
258 259 6.296026 ACACCACTTAGCTTGACTTTGATAA 58.704 36.000 0.00 0.00 0.00 1.75
259 260 6.942576 ACACCACTTAGCTTGACTTTGATAAT 59.057 34.615 0.00 0.00 0.00 1.28
260 261 7.448469 ACACCACTTAGCTTGACTTTGATAATT 59.552 33.333 0.00 0.00 0.00 1.40
261 262 8.299570 CACCACTTAGCTTGACTTTGATAATTT 58.700 33.333 0.00 0.00 0.00 1.82
262 263 8.860088 ACCACTTAGCTTGACTTTGATAATTTT 58.140 29.630 0.00 0.00 0.00 1.82
263 264 9.696917 CCACTTAGCTTGACTTTGATAATTTTT 57.303 29.630 0.00 0.00 0.00 1.94
288 289 7.745620 TCTTCCTTAGAAAGAAATGTGTTCC 57.254 36.000 0.00 0.00 0.00 3.62
289 290 7.518188 TCTTCCTTAGAAAGAAATGTGTTCCT 58.482 34.615 0.00 0.00 0.00 3.36
290 291 7.661847 TCTTCCTTAGAAAGAAATGTGTTCCTC 59.338 37.037 0.00 0.00 0.00 3.71
291 292 7.079451 TCCTTAGAAAGAAATGTGTTCCTCT 57.921 36.000 0.00 0.00 0.00 3.69
292 293 7.518188 TCCTTAGAAAGAAATGTGTTCCTCTT 58.482 34.615 0.00 0.00 0.00 2.85
293 294 7.998964 TCCTTAGAAAGAAATGTGTTCCTCTTT 59.001 33.333 0.00 0.00 40.06 2.52
301 302 9.803315 AAGAAATGTGTTCCTCTTTCTTTTAAC 57.197 29.630 3.89 0.00 42.35 2.01
302 303 9.190317 AGAAATGTGTTCCTCTTTCTTTTAACT 57.810 29.630 0.00 0.00 35.06 2.24
303 304 9.803315 GAAATGTGTTCCTCTTTCTTTTAACTT 57.197 29.630 0.00 0.00 0.00 2.66
307 308 9.418045 TGTGTTCCTCTTTCTTTTAACTTTTTG 57.582 29.630 0.00 0.00 0.00 2.44
308 309 9.419297 GTGTTCCTCTTTCTTTTAACTTTTTGT 57.581 29.630 0.00 0.00 0.00 2.83
309 310 9.990360 TGTTCCTCTTTCTTTTAACTTTTTGTT 57.010 25.926 0.00 0.00 42.31 2.83
325 326 8.441312 ACTTTTTGTTATTCTTTGAGGTACGA 57.559 30.769 0.00 0.00 0.00 3.43
326 327 9.063615 ACTTTTTGTTATTCTTTGAGGTACGAT 57.936 29.630 0.00 0.00 0.00 3.73
330 331 8.657074 TTGTTATTCTTTGAGGTACGATATGG 57.343 34.615 0.00 0.00 0.00 2.74
331 332 8.014070 TGTTATTCTTTGAGGTACGATATGGA 57.986 34.615 0.00 0.00 0.00 3.41
332 333 7.924412 TGTTATTCTTTGAGGTACGATATGGAC 59.076 37.037 0.00 0.00 0.00 4.02
333 334 5.925506 TTCTTTGAGGTACGATATGGACA 57.074 39.130 0.00 0.00 0.00 4.02
334 335 6.479972 TTCTTTGAGGTACGATATGGACAT 57.520 37.500 0.00 0.00 0.00 3.06
335 336 5.842907 TCTTTGAGGTACGATATGGACATG 58.157 41.667 0.00 0.00 0.00 3.21
336 337 5.362717 TCTTTGAGGTACGATATGGACATGT 59.637 40.000 0.00 0.00 0.00 3.21
337 338 4.848562 TGAGGTACGATATGGACATGTC 57.151 45.455 17.91 17.91 0.00 3.06
338 339 4.470602 TGAGGTACGATATGGACATGTCT 58.529 43.478 24.50 9.24 0.00 3.41
339 340 4.278419 TGAGGTACGATATGGACATGTCTG 59.722 45.833 24.50 10.56 0.00 3.51
340 341 3.005897 AGGTACGATATGGACATGTCTGC 59.994 47.826 24.50 10.25 0.00 4.26
341 342 3.005897 GGTACGATATGGACATGTCTGCT 59.994 47.826 24.50 12.16 0.00 4.24
342 343 3.827008 ACGATATGGACATGTCTGCTT 57.173 42.857 24.50 10.14 0.00 3.91
343 344 3.722147 ACGATATGGACATGTCTGCTTC 58.278 45.455 24.50 15.13 0.00 3.86
344 345 3.062763 CGATATGGACATGTCTGCTTCC 58.937 50.000 24.50 8.85 0.00 3.46
345 346 2.602257 TATGGACATGTCTGCTTCCG 57.398 50.000 24.50 0.00 0.00 4.30
346 347 0.904649 ATGGACATGTCTGCTTCCGA 59.095 50.000 24.50 0.00 0.00 4.55
347 348 0.904649 TGGACATGTCTGCTTCCGAT 59.095 50.000 24.50 0.00 0.00 4.18
348 349 2.107366 TGGACATGTCTGCTTCCGATA 58.893 47.619 24.50 0.00 0.00 2.92
349 350 2.700371 TGGACATGTCTGCTTCCGATAT 59.300 45.455 24.50 0.00 0.00 1.63
350 351 3.062763 GGACATGTCTGCTTCCGATATG 58.937 50.000 24.50 0.00 36.46 1.78
351 352 3.243873 GGACATGTCTGCTTCCGATATGA 60.244 47.826 24.50 0.00 34.73 2.15
352 353 3.722147 ACATGTCTGCTTCCGATATGAC 58.278 45.455 0.00 0.00 34.73 3.06
353 354 2.890808 TGTCTGCTTCCGATATGACC 57.109 50.000 0.00 0.00 0.00 4.02
354 355 2.107366 TGTCTGCTTCCGATATGACCA 58.893 47.619 0.00 0.00 0.00 4.02
355 356 2.499693 TGTCTGCTTCCGATATGACCAA 59.500 45.455 0.00 0.00 0.00 3.67
356 357 3.055458 TGTCTGCTTCCGATATGACCAAA 60.055 43.478 0.00 0.00 0.00 3.28
357 358 3.557595 GTCTGCTTCCGATATGACCAAAG 59.442 47.826 0.00 0.00 0.00 2.77
358 359 3.450817 TCTGCTTCCGATATGACCAAAGA 59.549 43.478 0.00 0.00 0.00 2.52
359 360 3.797039 TGCTTCCGATATGACCAAAGAG 58.203 45.455 0.00 0.00 0.00 2.85
360 361 3.450817 TGCTTCCGATATGACCAAAGAGA 59.549 43.478 0.00 0.00 0.00 3.10
361 362 4.101585 TGCTTCCGATATGACCAAAGAGAT 59.898 41.667 0.00 0.00 0.00 2.75
362 363 5.059833 GCTTCCGATATGACCAAAGAGATT 58.940 41.667 0.00 0.00 0.00 2.40
363 364 6.183360 TGCTTCCGATATGACCAAAGAGATTA 60.183 38.462 0.00 0.00 0.00 1.75
364 365 6.146347 GCTTCCGATATGACCAAAGAGATTAC 59.854 42.308 0.00 0.00 0.00 1.89
365 366 6.724893 TCCGATATGACCAAAGAGATTACA 57.275 37.500 0.00 0.00 0.00 2.41
366 367 7.303182 TCCGATATGACCAAAGAGATTACAT 57.697 36.000 0.00 0.00 0.00 2.29
367 368 7.154656 TCCGATATGACCAAAGAGATTACATG 58.845 38.462 0.00 0.00 0.00 3.21
368 369 6.128445 CCGATATGACCAAAGAGATTACATGC 60.128 42.308 0.00 0.00 0.00 4.06
369 370 6.424812 CGATATGACCAAAGAGATTACATGCA 59.575 38.462 0.00 0.00 0.00 3.96
370 371 7.118825 CGATATGACCAAAGAGATTACATGCAT 59.881 37.037 0.00 0.00 0.00 3.96
371 372 9.440773 GATATGACCAAAGAGATTACATGCATA 57.559 33.333 0.00 0.00 0.00 3.14
372 373 6.925610 TGACCAAAGAGATTACATGCATAC 57.074 37.500 0.00 0.00 0.00 2.39
373 374 6.413892 TGACCAAAGAGATTACATGCATACA 58.586 36.000 0.00 0.00 0.00 2.29
374 375 7.056006 TGACCAAAGAGATTACATGCATACAT 58.944 34.615 0.00 0.00 36.79 2.29
375 376 8.210265 TGACCAAAGAGATTACATGCATACATA 58.790 33.333 0.00 0.00 33.67 2.29
376 377 9.224267 GACCAAAGAGATTACATGCATACATAT 57.776 33.333 0.00 0.00 33.67 1.78
381 382 9.881649 AAGAGATTACATGCATACATATAGGTG 57.118 33.333 0.00 0.00 33.67 4.00
382 383 7.984050 AGAGATTACATGCATACATATAGGTGC 59.016 37.037 0.00 0.00 33.67 5.01
391 392 8.916628 TGCATACATATAGGTGCATAGAAAAA 57.083 30.769 0.00 0.00 42.13 1.94
451 452 8.739972 ACATATAGGTGCTCCTTTTAGTTTTTG 58.260 33.333 13.50 3.73 42.12 2.44
453 454 5.262588 AGGTGCTCCTTTTAGTTTTTGTG 57.737 39.130 0.18 0.00 42.12 3.33
454 455 4.709886 AGGTGCTCCTTTTAGTTTTTGTGT 59.290 37.500 0.18 0.00 42.12 3.72
457 458 7.036829 GGTGCTCCTTTTAGTTTTTGTGTTTA 58.963 34.615 0.00 0.00 0.00 2.01
474 475 5.637810 TGTGTTTAGTTAGTGTAGATGCAGC 59.362 40.000 0.00 0.00 0.00 5.25
485 486 3.781770 GATGCAGCTCCGTCCTCCG 62.782 68.421 0.00 0.00 0.00 4.63
611 612 3.545078 GTCTAGTACATACGCACCGTTTG 59.455 47.826 6.65 6.65 42.57 2.93
798 800 2.388526 ATAACCTACGGTACCCCCTC 57.611 55.000 6.25 0.00 33.12 4.30
800 802 1.522018 AACCTACGGTACCCCCTCCT 61.522 60.000 6.25 0.00 33.12 3.69
801 803 1.312437 CCTACGGTACCCCCTCCTT 59.688 63.158 6.25 0.00 0.00 3.36
905 907 2.678934 CCCCTCTCCCGTTGACGA 60.679 66.667 4.91 0.00 43.02 4.20
906 908 2.572284 CCCTCTCCCGTTGACGAC 59.428 66.667 4.91 0.00 43.02 4.34
915 920 2.542896 GTTGACGACGTTCGCCAC 59.457 61.111 0.13 0.00 45.12 5.01
948 953 4.812476 TCGCCGATGGAAGGTGCG 62.812 66.667 0.00 0.00 46.09 5.34
978 983 3.114616 CGCCGGACAGCTTCTGTG 61.115 66.667 5.05 0.00 45.44 3.66
983 988 0.459237 CGGACAGCTTCTGTGGCTAG 60.459 60.000 3.98 0.00 45.44 3.42
987 992 1.080995 CAGCTTCTGTGGCTAGCGAC 61.081 60.000 21.67 21.67 39.82 5.19
1000 1005 4.502263 GCGACAGCATAGCAGTGA 57.498 55.556 0.00 0.00 44.35 3.41
1005 1010 0.812811 ACAGCATAGCAGTGATGGCG 60.813 55.000 10.64 0.00 39.69 5.69
1095 1100 3.009115 ACCACCATCCCCCTCGTG 61.009 66.667 0.00 0.00 0.00 4.35
1157 1162 1.433879 CGACCGACTCCATCCTCAC 59.566 63.158 0.00 0.00 0.00 3.51
1204 1209 0.903924 CAACCCCATCCACATTGCCA 60.904 55.000 0.00 0.00 0.00 4.92
2298 2324 2.113139 CCCACGTTCAGGGCAACT 59.887 61.111 0.00 0.00 39.96 3.16
2312 2338 2.095059 GGGCAACTTAGACGACGACTTA 60.095 50.000 4.95 0.00 0.00 2.24
2357 2383 1.068954 CGTGGCTGGCTTCTTCTTTTC 60.069 52.381 2.00 0.00 0.00 2.29
2366 3982 3.321968 GGCTTCTTCTTTTCCCATGTTGT 59.678 43.478 0.00 0.00 0.00 3.32
2418 4034 6.987992 AGAGAACTCAATAGTACTAGGACTCG 59.012 42.308 12.02 1.61 33.75 4.18
2419 4035 6.887013 AGAACTCAATAGTACTAGGACTCGA 58.113 40.000 12.02 6.27 33.75 4.04
2420 4036 6.987992 AGAACTCAATAGTACTAGGACTCGAG 59.012 42.308 12.02 17.39 33.75 4.04
2446 4062 1.995542 TCCAGGGATTTTGCCTTCTCT 59.004 47.619 0.00 0.00 35.31 3.10
2462 4078 6.706270 TGCCTTCTCTTTATCGATGATTTACC 59.294 38.462 8.54 0.00 0.00 2.85
2469 4085 6.491062 TCTTTATCGATGATTTACCCGGTCTA 59.509 38.462 8.54 0.00 0.00 2.59
2479 4095 7.491682 TGATTTACCCGGTCTACTATACAAAC 58.508 38.462 0.00 0.00 0.00 2.93
2513 4129 5.044030 TGGTAGGGCATTTCCTTTACCATAA 60.044 40.000 11.20 0.00 43.51 1.90
2515 4131 6.553476 GGTAGGGCATTTCCTTTACCATAATT 59.447 38.462 0.00 0.00 41.03 1.40
2531 4147 9.776158 TTACCATAATTTACACGTTAGCATTTG 57.224 29.630 0.00 0.00 0.00 2.32
2556 4172 4.792521 TCTCTAACAAGGCTCTCAAGTC 57.207 45.455 0.00 0.00 0.00 3.01
2557 4173 4.411927 TCTCTAACAAGGCTCTCAAGTCT 58.588 43.478 0.00 0.00 39.86 3.24
2558 4174 4.461081 TCTCTAACAAGGCTCTCAAGTCTC 59.539 45.833 0.00 0.00 36.07 3.36
2559 4175 4.152647 TCTAACAAGGCTCTCAAGTCTCA 58.847 43.478 0.00 0.00 36.07 3.27
2560 4176 3.845781 AACAAGGCTCTCAAGTCTCAA 57.154 42.857 0.00 0.00 36.07 3.02
2561 4177 3.399440 ACAAGGCTCTCAAGTCTCAAG 57.601 47.619 0.00 0.00 36.07 3.02
2562 4178 2.703007 ACAAGGCTCTCAAGTCTCAAGT 59.297 45.455 0.00 0.00 36.07 3.16
2563 4179 3.135530 ACAAGGCTCTCAAGTCTCAAGTT 59.864 43.478 0.00 0.00 36.07 2.66
2564 4180 3.676291 AGGCTCTCAAGTCTCAAGTTC 57.324 47.619 0.00 0.00 28.90 3.01
2565 4181 3.238597 AGGCTCTCAAGTCTCAAGTTCT 58.761 45.455 0.00 0.00 28.90 3.01
2566 4182 3.645687 AGGCTCTCAAGTCTCAAGTTCTT 59.354 43.478 0.00 0.00 28.90 2.52
2567 4183 4.835615 AGGCTCTCAAGTCTCAAGTTCTTA 59.164 41.667 0.00 0.00 28.90 2.10
2568 4184 5.483583 AGGCTCTCAAGTCTCAAGTTCTTAT 59.516 40.000 0.00 0.00 28.90 1.73
2569 4185 6.013812 AGGCTCTCAAGTCTCAAGTTCTTATT 60.014 38.462 0.00 0.00 28.90 1.40
2570 4186 6.652900 GGCTCTCAAGTCTCAAGTTCTTATTT 59.347 38.462 0.00 0.00 0.00 1.40
2571 4187 7.174080 GGCTCTCAAGTCTCAAGTTCTTATTTT 59.826 37.037 0.00 0.00 0.00 1.82
2572 4188 8.563732 GCTCTCAAGTCTCAAGTTCTTATTTTT 58.436 33.333 0.00 0.00 0.00 1.94
2602 4218 4.842948 TCCAATAGGATCCCATCTCTCTTG 59.157 45.833 8.55 0.00 39.61 3.02
2646 4262 5.011840 TGGTCAGGATTTCAATTTGCATCAA 59.988 36.000 0.00 0.00 0.00 2.57
2653 4269 7.278424 AGGATTTCAATTTGCATCAATAAACCG 59.722 33.333 0.00 0.00 0.00 4.44
2659 4275 2.582052 TGCATCAATAAACCGGGGATC 58.418 47.619 6.32 0.00 0.00 3.36
2660 4276 1.535462 GCATCAATAAACCGGGGATCG 59.465 52.381 6.32 0.00 38.88 3.69
2689 4305 6.980397 CAGATATAGTTTCAAAATGTTGGGCC 59.020 38.462 0.00 0.00 35.29 5.80
2727 4343 2.632512 CCAACCTGCCAACTATTTTGGT 59.367 45.455 4.99 0.00 41.53 3.67
2766 4383 2.498761 ATGCTTCTGCGACGCAAACG 62.499 55.000 24.51 9.88 40.03 3.60
2778 4395 2.002586 ACGCAAACGGAGAATCATCTG 58.997 47.619 0.00 0.00 46.04 2.90
2791 4408 0.461548 TCATCTGACGGGATGAGTGC 59.538 55.000 11.90 0.00 44.65 4.40
2792 4409 0.176449 CATCTGACGGGATGAGTGCA 59.824 55.000 8.84 0.00 44.01 4.57
2793 4410 0.904649 ATCTGACGGGATGAGTGCAA 59.095 50.000 0.00 0.00 0.00 4.08
2820 4437 3.091545 CTGCTAAAAGGGAAGAATGCCA 58.908 45.455 0.00 0.00 32.29 4.92
2821 4438 3.505386 TGCTAAAAGGGAAGAATGCCAA 58.495 40.909 0.00 0.00 32.29 4.52
2823 4440 3.368427 GCTAAAAGGGAAGAATGCCAACC 60.368 47.826 0.00 0.00 32.29 3.77
2824 4441 1.644509 AAAGGGAAGAATGCCAACCC 58.355 50.000 0.00 0.00 32.29 4.11
2873 4490 7.072202 AGTGATAGAATCTTGTCTTGGATCCAT 59.928 37.037 17.06 0.00 0.00 3.41
2915 4532 1.298157 TGGTCATTTCGCCGCTCTTG 61.298 55.000 0.00 0.00 0.00 3.02
2973 4590 1.399440 CATCATGTTTGACAGCCTCCG 59.601 52.381 0.00 0.00 33.85 4.63
3080 4699 8.753497 ACAGAGAAAAATCTTTTAAGACAGGT 57.247 30.769 0.00 0.00 37.98 4.00
3082 4701 7.592903 CAGAGAAAAATCTTTTAAGACAGGTGC 59.407 37.037 0.00 0.00 37.98 5.01
3101 4720 7.615365 ACAGGTGCTCCTTCATCATAAATAAAA 59.385 33.333 4.10 0.00 43.07 1.52
3103 4722 8.470002 AGGTGCTCCTTCATCATAAATAAAAAC 58.530 33.333 0.18 0.00 42.12 2.43
3117 4745 6.730960 AAATAAAAACGATACGCTTCCAGA 57.269 33.333 0.00 0.00 0.00 3.86
3209 4837 5.185635 TGGCCTCATAACTGAAATGGAAAAG 59.814 40.000 3.32 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.925338 GGGAGAGATTTAGTCCTAACAAGAATA 58.075 37.037 0.00 0.00 0.00 1.75
10 11 7.403231 TGGGAGAGATTTAGTCCTAACAAGAAT 59.597 37.037 0.00 0.00 0.00 2.40
11 12 6.729100 TGGGAGAGATTTAGTCCTAACAAGAA 59.271 38.462 0.00 0.00 0.00 2.52
12 13 6.261435 TGGGAGAGATTTAGTCCTAACAAGA 58.739 40.000 0.00 0.00 0.00 3.02
13 14 6.546428 TGGGAGAGATTTAGTCCTAACAAG 57.454 41.667 0.00 0.00 0.00 3.16
14 15 8.618240 TTATGGGAGAGATTTAGTCCTAACAA 57.382 34.615 0.00 0.00 0.00 2.83
15 16 7.844779 ACTTATGGGAGAGATTTAGTCCTAACA 59.155 37.037 0.00 0.00 0.00 2.41
16 17 8.252624 ACTTATGGGAGAGATTTAGTCCTAAC 57.747 38.462 0.00 0.00 0.00 2.34
17 18 8.065627 TGACTTATGGGAGAGATTTAGTCCTAA 58.934 37.037 0.00 0.00 31.99 2.69
18 19 7.592736 TGACTTATGGGAGAGATTTAGTCCTA 58.407 38.462 0.00 0.00 31.99 2.94
19 20 6.444704 TGACTTATGGGAGAGATTTAGTCCT 58.555 40.000 0.00 0.00 31.99 3.85
20 21 6.732896 TGACTTATGGGAGAGATTTAGTCC 57.267 41.667 0.00 0.00 31.99 3.85
21 22 8.646900 AGAATGACTTATGGGAGAGATTTAGTC 58.353 37.037 0.00 0.00 33.25 2.59
22 23 8.560124 AGAATGACTTATGGGAGAGATTTAGT 57.440 34.615 0.00 0.00 0.00 2.24
23 24 9.844257 AAAGAATGACTTATGGGAGAGATTTAG 57.156 33.333 0.00 0.00 37.93 1.85
24 25 9.838339 GAAAGAATGACTTATGGGAGAGATTTA 57.162 33.333 0.00 0.00 37.93 1.40
25 26 8.555729 AGAAAGAATGACTTATGGGAGAGATTT 58.444 33.333 0.00 0.00 37.93 2.17
26 27 8.100135 AGAAAGAATGACTTATGGGAGAGATT 57.900 34.615 0.00 0.00 37.93 2.40
27 28 7.688918 AGAAAGAATGACTTATGGGAGAGAT 57.311 36.000 0.00 0.00 37.93 2.75
28 29 7.502060 AAGAAAGAATGACTTATGGGAGAGA 57.498 36.000 0.00 0.00 37.93 3.10
29 30 8.700051 TCTAAGAAAGAATGACTTATGGGAGAG 58.300 37.037 0.00 0.00 37.93 3.20
30 31 8.609617 TCTAAGAAAGAATGACTTATGGGAGA 57.390 34.615 0.00 0.00 37.93 3.71
31 32 9.672673 TTTCTAAGAAAGAATGACTTATGGGAG 57.327 33.333 0.00 0.00 43.75 4.30
59 60 9.918630 CAAATTCAGATAAGGAAGAACACATTT 57.081 29.630 0.00 0.00 0.00 2.32
60 61 9.082313 ACAAATTCAGATAAGGAAGAACACATT 57.918 29.630 0.00 0.00 0.00 2.71
61 62 8.641498 ACAAATTCAGATAAGGAAGAACACAT 57.359 30.769 0.00 0.00 0.00 3.21
62 63 8.999431 GTACAAATTCAGATAAGGAAGAACACA 58.001 33.333 0.00 0.00 0.00 3.72
63 64 9.220767 AGTACAAATTCAGATAAGGAAGAACAC 57.779 33.333 0.00 0.00 0.00 3.32
70 71 9.959721 AGCTTTTAGTACAAATTCAGATAAGGA 57.040 29.630 0.00 0.00 0.00 3.36
76 77 9.840427 GCATTTAGCTTTTAGTACAAATTCAGA 57.160 29.630 0.00 0.00 41.15 3.27
150 151 8.745590 GCCATTGGTATTACCTAAAAGAAGAAA 58.254 33.333 13.90 0.00 39.58 2.52
151 152 7.340999 GGCCATTGGTATTACCTAAAAGAAGAA 59.659 37.037 13.90 0.00 39.58 2.52
152 153 6.831868 GGCCATTGGTATTACCTAAAAGAAGA 59.168 38.462 13.90 0.00 39.58 2.87
153 154 6.833933 AGGCCATTGGTATTACCTAAAAGAAG 59.166 38.462 13.90 0.00 39.58 2.85
154 155 6.737608 AGGCCATTGGTATTACCTAAAAGAA 58.262 36.000 13.90 0.00 39.58 2.52
155 156 6.335781 AGGCCATTGGTATTACCTAAAAGA 57.664 37.500 13.90 0.00 39.58 2.52
156 157 8.528044 TTAAGGCCATTGGTATTACCTAAAAG 57.472 34.615 13.90 0.00 39.58 2.27
157 158 9.495382 AATTAAGGCCATTGGTATTACCTAAAA 57.505 29.630 13.90 0.87 39.58 1.52
158 159 9.495382 AAATTAAGGCCATTGGTATTACCTAAA 57.505 29.630 13.90 1.57 39.58 1.85
159 160 8.919145 CAAATTAAGGCCATTGGTATTACCTAA 58.081 33.333 13.90 7.19 39.58 2.69
160 161 8.062536 ACAAATTAAGGCCATTGGTATTACCTA 58.937 33.333 13.90 6.93 39.58 3.08
161 162 6.900743 ACAAATTAAGGCCATTGGTATTACCT 59.099 34.615 13.90 0.00 39.58 3.08
162 163 7.119709 ACAAATTAAGGCCATTGGTATTACC 57.880 36.000 5.01 5.87 39.22 2.85
163 164 8.474831 AGAACAAATTAAGGCCATTGGTATTAC 58.525 33.333 5.01 0.00 0.00 1.89
164 165 8.602472 AGAACAAATTAAGGCCATTGGTATTA 57.398 30.769 5.01 1.44 0.00 0.98
165 166 7.494922 AGAACAAATTAAGGCCATTGGTATT 57.505 32.000 5.01 2.40 0.00 1.89
166 167 7.364673 GGAAGAACAAATTAAGGCCATTGGTAT 60.365 37.037 5.01 0.00 0.00 2.73
167 168 6.071051 GGAAGAACAAATTAAGGCCATTGGTA 60.071 38.462 5.01 0.00 0.00 3.25
168 169 5.279960 GGAAGAACAAATTAAGGCCATTGGT 60.280 40.000 5.01 0.00 0.00 3.67
169 170 5.046376 AGGAAGAACAAATTAAGGCCATTGG 60.046 40.000 5.01 0.00 0.00 3.16
170 171 6.041423 AGGAAGAACAAATTAAGGCCATTG 57.959 37.500 5.01 4.60 0.00 2.82
171 172 6.686484 AAGGAAGAACAAATTAAGGCCATT 57.314 33.333 5.01 0.00 0.00 3.16
172 173 7.182060 TCTAAGGAAGAACAAATTAAGGCCAT 58.818 34.615 5.01 0.00 0.00 4.40
173 174 6.548321 TCTAAGGAAGAACAAATTAAGGCCA 58.452 36.000 5.01 0.00 0.00 5.36
174 175 7.462571 TTCTAAGGAAGAACAAATTAAGGCC 57.537 36.000 0.00 0.00 39.36 5.19
182 183 8.234546 GCGACATTTATTCTAAGGAAGAACAAA 58.765 33.333 0.00 0.00 46.90 2.83
183 184 7.606456 AGCGACATTTATTCTAAGGAAGAACAA 59.394 33.333 0.00 0.00 46.90 2.83
184 185 7.103641 AGCGACATTTATTCTAAGGAAGAACA 58.896 34.615 0.00 0.00 46.90 3.18
185 186 7.541122 AGCGACATTTATTCTAAGGAAGAAC 57.459 36.000 0.00 0.00 46.90 3.01
187 188 9.832445 ATAAAGCGACATTTATTCTAAGGAAGA 57.168 29.630 0.00 0.00 32.66 2.87
202 203 9.862585 GAAACAAAAATGAAAATAAAGCGACAT 57.137 25.926 0.00 0.00 0.00 3.06
203 204 8.873830 TGAAACAAAAATGAAAATAAAGCGACA 58.126 25.926 0.00 0.00 0.00 4.35
204 205 9.356929 CTGAAACAAAAATGAAAATAAAGCGAC 57.643 29.630 0.00 0.00 0.00 5.19
205 206 8.547069 CCTGAAACAAAAATGAAAATAAAGCGA 58.453 29.630 0.00 0.00 0.00 4.93
206 207 8.334632 ACCTGAAACAAAAATGAAAATAAAGCG 58.665 29.630 0.00 0.00 0.00 4.68
212 213 8.888716 GGTGTTACCTGAAACAAAAATGAAAAT 58.111 29.630 0.00 0.00 40.85 1.82
213 214 7.878127 TGGTGTTACCTGAAACAAAAATGAAAA 59.122 29.630 0.00 0.00 40.85 2.29
214 215 7.332182 GTGGTGTTACCTGAAACAAAAATGAAA 59.668 33.333 0.00 0.00 40.85 2.69
215 216 6.814146 GTGGTGTTACCTGAAACAAAAATGAA 59.186 34.615 0.00 0.00 40.85 2.57
216 217 6.153680 AGTGGTGTTACCTGAAACAAAAATGA 59.846 34.615 0.00 0.00 40.85 2.57
217 218 6.337356 AGTGGTGTTACCTGAAACAAAAATG 58.663 36.000 0.00 0.00 40.85 2.32
218 219 6.538945 AGTGGTGTTACCTGAAACAAAAAT 57.461 33.333 0.00 0.00 40.85 1.82
219 220 5.986501 AGTGGTGTTACCTGAAACAAAAA 57.013 34.783 0.00 0.00 40.85 1.94
220 221 5.986501 AAGTGGTGTTACCTGAAACAAAA 57.013 34.783 0.00 0.00 40.85 2.44
221 222 5.066764 GCTAAGTGGTGTTACCTGAAACAAA 59.933 40.000 0.00 0.00 40.85 2.83
222 223 4.577283 GCTAAGTGGTGTTACCTGAAACAA 59.423 41.667 0.00 0.00 40.85 2.83
223 224 4.131596 GCTAAGTGGTGTTACCTGAAACA 58.868 43.478 0.00 0.00 39.58 2.83
224 225 4.386711 AGCTAAGTGGTGTTACCTGAAAC 58.613 43.478 0.00 0.00 39.58 2.78
225 226 4.699925 AGCTAAGTGGTGTTACCTGAAA 57.300 40.909 0.00 0.00 39.58 2.69
226 227 4.101898 TCAAGCTAAGTGGTGTTACCTGAA 59.898 41.667 0.00 0.00 39.58 3.02
227 228 3.644265 TCAAGCTAAGTGGTGTTACCTGA 59.356 43.478 0.00 0.00 39.58 3.86
228 229 3.746492 GTCAAGCTAAGTGGTGTTACCTG 59.254 47.826 0.00 0.00 39.58 4.00
229 230 3.646637 AGTCAAGCTAAGTGGTGTTACCT 59.353 43.478 0.00 0.00 39.58 3.08
230 231 4.004196 AGTCAAGCTAAGTGGTGTTACC 57.996 45.455 0.00 0.00 39.22 2.85
231 232 5.526111 TCAAAGTCAAGCTAAGTGGTGTTAC 59.474 40.000 0.00 0.00 0.00 2.50
232 233 5.676552 TCAAAGTCAAGCTAAGTGGTGTTA 58.323 37.500 0.00 0.00 0.00 2.41
233 234 4.523083 TCAAAGTCAAGCTAAGTGGTGTT 58.477 39.130 0.00 0.00 0.00 3.32
234 235 4.150897 TCAAAGTCAAGCTAAGTGGTGT 57.849 40.909 0.00 0.00 0.00 4.16
235 236 6.801539 TTATCAAAGTCAAGCTAAGTGGTG 57.198 37.500 0.00 0.00 0.00 4.17
236 237 8.409358 AAATTATCAAAGTCAAGCTAAGTGGT 57.591 30.769 0.00 0.00 0.00 4.16
237 238 9.696917 AAAAATTATCAAAGTCAAGCTAAGTGG 57.303 29.630 0.00 0.00 0.00 4.00
263 264 7.998964 AGGAACACATTTCTTTCTAAGGAAGAA 59.001 33.333 1.60 1.60 42.62 2.52
264 265 7.518188 AGGAACACATTTCTTTCTAAGGAAGA 58.482 34.615 0.00 0.00 32.61 2.87
265 266 7.663493 AGAGGAACACATTTCTTTCTAAGGAAG 59.337 37.037 0.00 0.00 32.61 3.46
266 267 7.518188 AGAGGAACACATTTCTTTCTAAGGAA 58.482 34.615 0.00 0.00 0.00 3.36
267 268 7.079451 AGAGGAACACATTTCTTTCTAAGGA 57.921 36.000 0.00 0.00 0.00 3.36
268 269 7.751768 AAGAGGAACACATTTCTTTCTAAGG 57.248 36.000 0.00 0.00 0.00 2.69
276 277 9.190317 AGTTAAAAGAAAGAGGAACACATTTCT 57.810 29.630 0.00 0.00 42.30 2.52
277 278 9.803315 AAGTTAAAAGAAAGAGGAACACATTTC 57.197 29.630 0.00 0.00 32.95 2.17
281 282 9.418045 CAAAAAGTTAAAAGAAAGAGGAACACA 57.582 29.630 0.00 0.00 0.00 3.72
282 283 9.419297 ACAAAAAGTTAAAAGAAAGAGGAACAC 57.581 29.630 0.00 0.00 0.00 3.32
283 284 9.990360 AACAAAAAGTTAAAAGAAAGAGGAACA 57.010 25.926 0.00 0.00 39.09 3.18
299 300 8.895737 TCGTACCTCAAAGAATAACAAAAAGTT 58.104 29.630 0.00 0.00 44.27 2.66
300 301 8.441312 TCGTACCTCAAAGAATAACAAAAAGT 57.559 30.769 0.00 0.00 0.00 2.66
304 305 9.104965 CCATATCGTACCTCAAAGAATAACAAA 57.895 33.333 0.00 0.00 0.00 2.83
305 306 8.479689 TCCATATCGTACCTCAAAGAATAACAA 58.520 33.333 0.00 0.00 0.00 2.83
306 307 7.924412 GTCCATATCGTACCTCAAAGAATAACA 59.076 37.037 0.00 0.00 0.00 2.41
307 308 7.924412 TGTCCATATCGTACCTCAAAGAATAAC 59.076 37.037 0.00 0.00 0.00 1.89
308 309 8.014070 TGTCCATATCGTACCTCAAAGAATAA 57.986 34.615 0.00 0.00 0.00 1.40
309 310 7.591421 TGTCCATATCGTACCTCAAAGAATA 57.409 36.000 0.00 0.00 0.00 1.75
310 311 6.479972 TGTCCATATCGTACCTCAAAGAAT 57.520 37.500 0.00 0.00 0.00 2.40
311 312 5.925506 TGTCCATATCGTACCTCAAAGAA 57.074 39.130 0.00 0.00 0.00 2.52
312 313 5.362717 ACATGTCCATATCGTACCTCAAAGA 59.637 40.000 0.00 0.00 0.00 2.52
313 314 5.601662 ACATGTCCATATCGTACCTCAAAG 58.398 41.667 0.00 0.00 0.00 2.77
314 315 5.362717 AGACATGTCCATATCGTACCTCAAA 59.637 40.000 22.21 0.00 0.00 2.69
315 316 4.893524 AGACATGTCCATATCGTACCTCAA 59.106 41.667 22.21 0.00 0.00 3.02
316 317 4.278419 CAGACATGTCCATATCGTACCTCA 59.722 45.833 22.21 0.00 0.00 3.86
317 318 4.799678 CAGACATGTCCATATCGTACCTC 58.200 47.826 22.21 0.00 0.00 3.85
318 319 3.005897 GCAGACATGTCCATATCGTACCT 59.994 47.826 22.21 0.00 0.00 3.08
319 320 3.005897 AGCAGACATGTCCATATCGTACC 59.994 47.826 22.21 0.00 0.00 3.34
320 321 4.244425 AGCAGACATGTCCATATCGTAC 57.756 45.455 22.21 0.00 0.00 3.67
321 322 4.262036 GGAAGCAGACATGTCCATATCGTA 60.262 45.833 22.21 0.00 0.00 3.43
322 323 3.493350 GGAAGCAGACATGTCCATATCGT 60.493 47.826 22.21 5.54 0.00 3.73
323 324 3.062763 GGAAGCAGACATGTCCATATCG 58.937 50.000 22.21 5.56 0.00 2.92
324 325 3.062763 CGGAAGCAGACATGTCCATATC 58.937 50.000 22.21 14.87 0.00 1.63
325 326 2.700371 TCGGAAGCAGACATGTCCATAT 59.300 45.455 22.21 6.87 0.00 1.78
326 327 2.107366 TCGGAAGCAGACATGTCCATA 58.893 47.619 22.21 0.00 0.00 2.74
327 328 0.904649 TCGGAAGCAGACATGTCCAT 59.095 50.000 22.21 5.74 0.00 3.41
328 329 0.904649 ATCGGAAGCAGACATGTCCA 59.095 50.000 22.21 0.00 0.00 4.02
329 330 2.890808 TATCGGAAGCAGACATGTCC 57.109 50.000 22.21 8.10 0.00 4.02
330 331 3.738282 GTCATATCGGAAGCAGACATGTC 59.262 47.826 18.47 18.47 0.00 3.06
331 332 3.493350 GGTCATATCGGAAGCAGACATGT 60.493 47.826 0.00 0.00 0.00 3.21
332 333 3.062763 GGTCATATCGGAAGCAGACATG 58.937 50.000 0.00 0.00 0.00 3.21
333 334 2.700371 TGGTCATATCGGAAGCAGACAT 59.300 45.455 0.00 0.00 0.00 3.06
334 335 2.107366 TGGTCATATCGGAAGCAGACA 58.893 47.619 0.00 0.00 0.00 3.41
335 336 2.890808 TGGTCATATCGGAAGCAGAC 57.109 50.000 0.00 0.00 0.00 3.51
336 337 3.450817 TCTTTGGTCATATCGGAAGCAGA 59.549 43.478 0.00 0.00 0.00 4.26
337 338 3.797039 TCTTTGGTCATATCGGAAGCAG 58.203 45.455 0.00 0.00 0.00 4.24
338 339 3.450817 TCTCTTTGGTCATATCGGAAGCA 59.549 43.478 0.00 0.00 0.00 3.91
339 340 4.060038 TCTCTTTGGTCATATCGGAAGC 57.940 45.455 0.00 0.00 0.00 3.86
340 341 7.210174 TGTAATCTCTTTGGTCATATCGGAAG 58.790 38.462 0.00 0.00 0.00 3.46
341 342 7.119709 TGTAATCTCTTTGGTCATATCGGAA 57.880 36.000 0.00 0.00 0.00 4.30
342 343 6.724893 TGTAATCTCTTTGGTCATATCGGA 57.275 37.500 0.00 0.00 0.00 4.55
343 344 6.128445 GCATGTAATCTCTTTGGTCATATCGG 60.128 42.308 0.00 0.00 0.00 4.18
344 345 6.424812 TGCATGTAATCTCTTTGGTCATATCG 59.575 38.462 0.00 0.00 0.00 2.92
345 346 7.734924 TGCATGTAATCTCTTTGGTCATATC 57.265 36.000 0.00 0.00 0.00 1.63
346 347 9.224267 GTATGCATGTAATCTCTTTGGTCATAT 57.776 33.333 10.16 0.00 0.00 1.78
347 348 8.210265 TGTATGCATGTAATCTCTTTGGTCATA 58.790 33.333 10.16 0.00 0.00 2.15
348 349 7.056006 TGTATGCATGTAATCTCTTTGGTCAT 58.944 34.615 10.16 0.00 0.00 3.06
349 350 6.413892 TGTATGCATGTAATCTCTTTGGTCA 58.586 36.000 10.16 0.00 0.00 4.02
350 351 6.925610 TGTATGCATGTAATCTCTTTGGTC 57.074 37.500 10.16 0.00 0.00 4.02
355 356 9.881649 CACCTATATGTATGCATGTAATCTCTT 57.118 33.333 10.16 0.00 36.58 2.85
356 357 7.984050 GCACCTATATGTATGCATGTAATCTCT 59.016 37.037 10.16 0.00 38.00 3.10
357 358 7.765819 TGCACCTATATGTATGCATGTAATCTC 59.234 37.037 10.16 0.00 42.92 2.75
358 359 7.623630 TGCACCTATATGTATGCATGTAATCT 58.376 34.615 10.16 0.00 42.92 2.40
359 360 7.848223 TGCACCTATATGTATGCATGTAATC 57.152 36.000 10.16 0.00 42.92 1.75
393 394 9.860898 GCCTGAATTTTATGTAATTTTCAGTCT 57.139 29.630 16.06 0.00 0.00 3.24
394 395 9.638239 TGCCTGAATTTTATGTAATTTTCAGTC 57.362 29.630 16.06 9.60 0.00 3.51
415 416 3.007723 AGCACCTATATGTCAGATGCCTG 59.992 47.826 0.00 0.00 41.74 4.85
432 433 5.006153 ACACAAAAACTAAAAGGAGCACC 57.994 39.130 0.00 0.00 0.00 5.01
451 452 5.869888 AGCTGCATCTACACTAACTAAACAC 59.130 40.000 1.02 0.00 0.00 3.32
453 454 5.520649 GGAGCTGCATCTACACTAACTAAAC 59.479 44.000 0.00 0.00 0.00 2.01
454 455 5.661458 GGAGCTGCATCTACACTAACTAAA 58.339 41.667 0.00 0.00 0.00 1.85
457 458 2.099921 CGGAGCTGCATCTACACTAACT 59.900 50.000 5.91 0.00 0.00 2.24
485 486 5.422012 ACACCATCCTTTCAAATTGTATCCC 59.578 40.000 0.00 0.00 0.00 3.85
488 489 6.493115 TGTGACACCATCCTTTCAAATTGTAT 59.507 34.615 2.45 0.00 0.00 2.29
589 590 3.411415 AACGGTGCGTATGTACTAGAC 57.589 47.619 0.00 0.00 39.99 2.59
611 612 1.139095 CGGTGCCGAAGAGGTAGAC 59.861 63.158 4.35 0.00 43.70 2.59
798 800 0.687757 TCACGATGAGGGAGGGAAGG 60.688 60.000 0.00 0.00 0.00 3.46
800 802 1.414158 GATCACGATGAGGGAGGGAA 58.586 55.000 0.00 0.00 34.57 3.97
801 803 0.470080 GGATCACGATGAGGGAGGGA 60.470 60.000 0.00 0.00 34.57 4.20
905 907 3.889227 CCATCATGTGGCGAACGT 58.111 55.556 0.00 0.00 42.12 3.99
976 981 1.218230 GCTATGCTGTCGCTAGCCAC 61.218 60.000 9.66 7.44 43.02 5.01
978 983 0.943359 CTGCTATGCTGTCGCTAGCC 60.943 60.000 9.66 0.00 43.02 3.93
983 988 0.580578 CATCACTGCTATGCTGTCGC 59.419 55.000 0.00 0.00 38.59 5.19
987 992 1.504647 CCGCCATCACTGCTATGCTG 61.505 60.000 0.00 0.00 0.00 4.41
993 998 3.677284 CTGCTCCGCCATCACTGCT 62.677 63.158 0.00 0.00 0.00 4.24
997 1002 3.503363 GTGCTGCTCCGCCATCAC 61.503 66.667 0.00 0.00 0.00 3.06
1095 1100 1.433534 CGGTGAGCAAGAGAAGGAAC 58.566 55.000 0.00 0.00 0.00 3.62
1123 1128 3.610669 CGGGCCGAGGATGAGGAG 61.611 72.222 24.41 0.00 0.00 3.69
1145 1150 1.003573 GGGAGGGTGAGGATGGAGT 59.996 63.158 0.00 0.00 0.00 3.85
1150 1155 2.367512 GCTGGGGAGGGTGAGGAT 60.368 66.667 0.00 0.00 0.00 3.24
2298 2324 1.741706 CCAGGCTAAGTCGTCGTCTAA 59.258 52.381 0.00 0.00 0.00 2.10
2312 2338 1.270907 ACAAGAGTCGATTCCAGGCT 58.729 50.000 4.05 0.00 0.00 4.58
2357 2383 4.279169 ACATCAGACTGAAAACAACATGGG 59.721 41.667 9.70 0.00 0.00 4.00
2416 4032 0.034380 AATCCCTGGACTCGACTCGA 60.034 55.000 0.29 0.29 0.00 4.04
2417 4033 0.818296 AAATCCCTGGACTCGACTCG 59.182 55.000 0.00 0.00 0.00 4.18
2418 4034 2.622436 CAAAATCCCTGGACTCGACTC 58.378 52.381 0.00 0.00 0.00 3.36
2419 4035 1.339151 GCAAAATCCCTGGACTCGACT 60.339 52.381 0.00 0.00 0.00 4.18
2420 4036 1.087501 GCAAAATCCCTGGACTCGAC 58.912 55.000 0.00 0.00 0.00 4.20
2446 4062 5.540400 AGACCGGGTAAATCATCGATAAA 57.460 39.130 6.32 0.00 0.00 1.40
2462 4078 3.703052 ACTGGGTTTGTATAGTAGACCGG 59.297 47.826 0.00 0.00 0.00 5.28
2531 4147 3.931578 TGAGAGCCTTGTTAGAGAAAGC 58.068 45.455 0.00 0.00 0.00 3.51
2569 4185 4.703093 GGGATCCTATTGGACGAACAAAAA 59.297 41.667 12.58 0.00 46.51 1.94
2570 4186 4.263550 TGGGATCCTATTGGACGAACAAAA 60.264 41.667 12.58 0.00 46.51 2.44
2571 4187 3.264706 TGGGATCCTATTGGACGAACAAA 59.735 43.478 12.58 0.00 46.51 2.83
2572 4188 2.841266 TGGGATCCTATTGGACGAACAA 59.159 45.455 12.58 0.00 46.51 2.83
2573 4189 2.473070 TGGGATCCTATTGGACGAACA 58.527 47.619 12.58 0.00 46.51 3.18
2574 4190 3.325135 AGATGGGATCCTATTGGACGAAC 59.675 47.826 12.49 0.00 46.51 3.95
2575 4191 3.578716 GAGATGGGATCCTATTGGACGAA 59.421 47.826 12.49 0.00 46.51 3.85
2576 4192 3.165875 GAGATGGGATCCTATTGGACGA 58.834 50.000 12.49 0.00 46.51 4.20
2577 4193 3.169099 AGAGATGGGATCCTATTGGACG 58.831 50.000 12.49 0.00 46.51 4.79
2578 4194 4.424842 AGAGAGATGGGATCCTATTGGAC 58.575 47.826 12.49 5.33 46.51 4.02
2580 4196 4.842948 TCAAGAGAGATGGGATCCTATTGG 59.157 45.833 12.49 0.00 33.53 3.16
2581 4197 5.566429 CGTCAAGAGAGATGGGATCCTATTG 60.566 48.000 12.49 6.31 33.76 1.90
2582 4198 4.526262 CGTCAAGAGAGATGGGATCCTATT 59.474 45.833 12.49 2.45 0.00 1.73
2583 4199 4.085733 CGTCAAGAGAGATGGGATCCTAT 58.914 47.826 10.93 10.93 0.00 2.57
2584 4200 3.491342 CGTCAAGAGAGATGGGATCCTA 58.509 50.000 12.58 5.82 0.00 2.94
2585 4201 2.315176 CGTCAAGAGAGATGGGATCCT 58.685 52.381 12.58 0.00 0.00 3.24
2586 4202 1.342819 CCGTCAAGAGAGATGGGATCC 59.657 57.143 1.92 1.92 40.34 3.36
2587 4203 1.270041 GCCGTCAAGAGAGATGGGATC 60.270 57.143 4.54 0.00 43.51 3.36
2588 4204 0.755686 GCCGTCAAGAGAGATGGGAT 59.244 55.000 4.54 0.00 43.51 3.85
2589 4205 0.614697 TGCCGTCAAGAGAGATGGGA 60.615 55.000 4.54 0.00 43.51 4.37
2590 4206 0.250234 TTGCCGTCAAGAGAGATGGG 59.750 55.000 4.54 0.00 43.51 4.00
2591 4207 1.734465 GTTTGCCGTCAAGAGAGATGG 59.266 52.381 0.00 0.00 45.59 3.51
2592 4208 2.416747 TGTTTGCCGTCAAGAGAGATG 58.583 47.619 0.00 0.00 33.12 2.90
2593 4209 2.839486 TGTTTGCCGTCAAGAGAGAT 57.161 45.000 0.00 0.00 33.12 2.75
2597 4213 0.593128 CCCTTGTTTGCCGTCAAGAG 59.407 55.000 11.58 0.00 42.22 2.85
2602 4218 0.741915 TTTGACCCTTGTTTGCCGTC 59.258 50.000 0.00 0.00 0.00 4.79
2653 4269 5.422331 TGAAACTATATCTGATCCGATCCCC 59.578 44.000 2.55 0.00 0.00 4.81
2659 4275 9.655769 CAACATTTTGAAACTATATCTGATCCG 57.344 33.333 0.00 0.00 34.24 4.18
2660 4276 9.956720 CCAACATTTTGAAACTATATCTGATCC 57.043 33.333 0.00 0.00 34.24 3.36
2661 4277 9.956720 CCCAACATTTTGAAACTATATCTGATC 57.043 33.333 0.00 0.00 34.24 2.92
2663 4279 7.147915 GGCCCAACATTTTGAAACTATATCTGA 60.148 37.037 0.00 0.00 34.24 3.27
2664 4280 6.980397 GGCCCAACATTTTGAAACTATATCTG 59.020 38.462 0.00 0.00 34.24 2.90
2665 4281 6.667414 TGGCCCAACATTTTGAAACTATATCT 59.333 34.615 0.00 0.00 34.24 1.98
2666 4282 6.756542 GTGGCCCAACATTTTGAAACTATATC 59.243 38.462 0.00 0.00 34.24 1.63
2668 4284 5.540337 TGTGGCCCAACATTTTGAAACTATA 59.460 36.000 0.00 0.00 34.24 1.31
2689 4305 2.558359 GTTGGGAGGGATTTCTTGTGTG 59.442 50.000 0.00 0.00 0.00 3.82
2727 4343 7.288810 AGCATGTTTTTGTTAGAGGAATGAA 57.711 32.000 0.00 0.00 0.00 2.57
2766 4383 2.630098 TCATCCCGTCAGATGATTCTCC 59.370 50.000 6.06 0.00 45.98 3.71
2778 4395 3.191371 AGAATTTTTGCACTCATCCCGTC 59.809 43.478 0.00 0.00 0.00 4.79
2791 4408 8.715088 CATTCTTCCCTTTTAGCAGAATTTTTG 58.285 33.333 0.00 0.00 32.91 2.44
2792 4409 7.388776 GCATTCTTCCCTTTTAGCAGAATTTTT 59.611 33.333 0.00 0.00 32.91 1.94
2793 4410 6.875726 GCATTCTTCCCTTTTAGCAGAATTTT 59.124 34.615 0.00 0.00 32.91 1.82
2832 4449 1.399714 TCACTATAGTGGGAGGTGCG 58.600 55.000 28.33 4.13 45.65 5.34
2842 4459 9.647918 TCCAAGACAAGATTCTATCACTATAGT 57.352 33.333 0.00 0.00 37.06 2.12
2861 4478 5.226194 AGCTATCTGAATGGATCCAAGAC 57.774 43.478 20.67 13.29 0.00 3.01
2873 4490 3.827008 AAGATCCGCAAGCTATCTGAA 57.173 42.857 7.31 0.00 38.21 3.02
2915 4532 4.631377 GCCAATGCCAAGTCTTATTTTTCC 59.369 41.667 0.00 0.00 0.00 3.13
2973 4590 4.096682 ACAGAGCGATTACTACAGAACTCC 59.903 45.833 0.00 0.00 0.00 3.85
3080 4699 8.275015 TCGTTTTTATTTATGATGAAGGAGCA 57.725 30.769 0.00 0.00 0.00 4.26
3101 4720 3.795826 GCATACTCTGGAAGCGTATCGTT 60.796 47.826 0.00 0.00 40.62 3.85
3103 4722 2.287608 TGCATACTCTGGAAGCGTATCG 60.288 50.000 0.00 0.00 40.62 2.92
3209 4837 1.617233 TGTACCCCTACAAGGCCCC 60.617 63.158 0.00 0.00 32.73 5.80


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

AutoCloner maintained by Alex Coulton.