Multiple sequence alignment - TraesCS4A01G330500

Loading Multiple Alignment...

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 TraesCS4A01G330500 chr4A 100.000 5539 0 0 1 5539 615223583 615218045 0.000000e+00 10229.0
1 TraesCS4A01G330500 chr2A 98.106 4488 61 12 705 5181 604627725 604623251 0.000000e+00 7795.0
2 TraesCS4A01G330500 chr5B 97.748 4485 72 12 704 5180 24174850 24179313 0.000000e+00 7696.0
3 TraesCS4A01G330500 chr5A 98.217 4375 60 7 706 5067 482741851 482737482 0.000000e+00 7631.0
4 TraesCS4A01G330500 chr3A 97.419 4494 80 18 706 5180 322330587 322326111 0.000000e+00 7624.0
5 TraesCS4A01G330500 chr3A 96.431 2606 85 4 1693 4297 238190195 238187597 0.000000e+00 4290.0
6 TraesCS4A01G330500 chr3A 96.637 1338 31 5 706 2035 180128422 180127091 0.000000e+00 2209.0
7 TraesCS4A01G330500 chr3A 99.519 1040 5 0 4141 5180 180127093 180126054 0.000000e+00 1893.0
8 TraesCS4A01G330500 chr3A 94.248 452 20 2 704 1149 238190645 238190194 0.000000e+00 686.0
9 TraesCS4A01G330500 chr3A 93.557 357 21 1 4598 4954 238187591 238187237 1.060000e-146 531.0
10 TraesCS4A01G330500 chr3A 95.968 248 9 1 4934 5181 238186914 238186668 8.640000e-108 401.0
11 TraesCS4A01G330500 chr7A 96.490 1339 33 5 705 2035 577148761 577147429 0.000000e+00 2200.0
12 TraesCS4A01G330500 chr7A 99.519 1040 5 0 4141 5180 577147431 577146392 0.000000e+00 1893.0
13 TraesCS4A01G330500 chr4B 90.479 1586 94 20 934 2464 332574026 332575609 0.000000e+00 2039.0
14 TraesCS4A01G330500 chr4B 95.374 454 18 3 4410 4861 332575613 332576065 0.000000e+00 719.0
15 TraesCS4A01G330500 chr4B 96.939 294 6 1 4888 5181 332576060 332576350 1.790000e-134 490.0
16 TraesCS4A01G330500 chr4B 95.217 230 11 0 702 931 332573473 332573702 1.130000e-96 364.0
17 TraesCS4A01G330500 chr4D 93.652 1276 46 8 1223 2464 118551853 118550579 0.000000e+00 1875.0
18 TraesCS4A01G330500 chr4D 96.044 455 14 4 4410 4861 118550575 118550122 0.000000e+00 737.0
19 TraesCS4A01G330500 chr4D 96.949 295 7 1 4888 5180 118550127 118549833 1.390000e-135 494.0
20 TraesCS4A01G330500 chr4D 91.080 213 19 0 4970 5182 398889799 398890011 7.020000e-74 289.0
21 TraesCS4A01G330500 chr4D 91.304 69 6 0 1344 1412 391733460 391733528 1.640000e-15 95.3
22 TraesCS4A01G330500 chr5D 96.176 706 21 6 1 705 552777657 552778357 0.000000e+00 1149.0
23 TraesCS4A01G330500 chr5D 93.733 367 16 4 5179 5539 552778348 552778713 1.360000e-150 544.0
24 TraesCS4A01G330500 chrUn 98.966 387 3 1 4135 4521 480550969 480551354 0.000000e+00 691.0
25 TraesCS4A01G330500 chr3D 84.064 502 52 8 706 1185 215763422 215763917 5.060000e-125 459.0


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 TraesCS4A01G330500 chr4A 615218045 615223583 5538 True 10229.000000 10229 100.000000 1 5539 1 chr4A.!!$R1 5538
1 TraesCS4A01G330500 chr2A 604623251 604627725 4474 True 7795.000000 7795 98.106000 705 5181 1 chr2A.!!$R1 4476
2 TraesCS4A01G330500 chr5B 24174850 24179313 4463 False 7696.000000 7696 97.748000 704 5180 1 chr5B.!!$F1 4476
3 TraesCS4A01G330500 chr5A 482737482 482741851 4369 True 7631.000000 7631 98.217000 706 5067 1 chr5A.!!$R1 4361
4 TraesCS4A01G330500 chr3A 322326111 322330587 4476 True 7624.000000 7624 97.419000 706 5180 1 chr3A.!!$R1 4474
5 TraesCS4A01G330500 chr3A 180126054 180128422 2368 True 2051.000000 2209 98.078000 706 5180 2 chr3A.!!$R2 4474
6 TraesCS4A01G330500 chr3A 238186668 238190645 3977 True 1477.000000 4290 95.051000 704 5181 4 chr3A.!!$R3 4477
7 TraesCS4A01G330500 chr7A 577146392 577148761 2369 True 2046.500000 2200 98.004500 705 5180 2 chr7A.!!$R1 4475
8 TraesCS4A01G330500 chr4B 332573473 332576350 2877 False 903.000000 2039 94.502250 702 5181 4 chr4B.!!$F1 4479
9 TraesCS4A01G330500 chr4D 118549833 118551853 2020 True 1035.333333 1875 95.548333 1223 5180 3 chr4D.!!$R1 3957
10 TraesCS4A01G330500 chr5D 552777657 552778713 1056 False 846.500000 1149 94.954500 1 5539 2 chr5D.!!$F1 5538

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
624 625 0.167908 CACTCGCTAATTGCCGCAAA 59.832 50.000 10.42 0.00 38.78 3.68 F
673 674 0.179163 GCGGCAAATAAGAGGTGCAC 60.179 55.000 8.80 8.80 40.12 4.57 F
675 676 1.135689 CGGCAAATAAGAGGTGCACAC 60.136 52.381 20.43 12.05 40.12 3.82 F
1143 1473 1.379443 ACGGCCATCACCTCGTCTA 60.379 57.895 2.24 0.00 0.00 2.59 F
1186 1542 1.831106 TGCTCTCTCTCTCTCTCTCGT 59.169 52.381 0.00 0.00 0.00 4.18 F
1330 1739 1.908793 CCCCGCCATAGAGTCCGAT 60.909 63.158 0.00 0.00 0.00 4.18 F
2948 3399 4.185394 CTGCACCACCGTTGTATAACATA 58.815 43.478 3.13 0.00 36.58 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 2122 8.756486 ATTAGTGGATGATGATTGATGAACAA 57.244 30.769 0.00 0.0 42.95 2.83 R
2948 3399 7.693969 ATGCAAAAGCTTGTTATTAGAGACT 57.306 32.000 0.00 0.0 34.79 3.24 R
3126 3578 7.979786 ACTTGGACCTATCAGATTCTCTAAA 57.020 36.000 0.00 0.0 0.00 1.85 R
3488 3941 7.331026 CCTATCACAGACTTCTCCACAAAATA 58.669 38.462 0.00 0.0 0.00 1.40 R
3615 4068 0.391597 TCCCACACTTCGACCACTTC 59.608 55.000 0.00 0.0 0.00 3.01 R
3649 4106 4.586001 TGCACTCATAGCATCTGACATAGA 59.414 41.667 0.00 0.0 40.37 1.98 R
5184 6218 0.896019 TTGCCGGGTTTATGTGGTGG 60.896 55.000 2.18 0.0 0.00 4.61 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
133 134 2.160721 AGACATGGGTCCAGTACGAT 57.839 50.000 0.00 0.00 45.48 3.73
134 135 2.032620 AGACATGGGTCCAGTACGATC 58.967 52.381 0.00 0.00 45.48 3.69
135 136 1.754803 GACATGGGTCCAGTACGATCA 59.245 52.381 0.00 0.00 38.12 2.92
136 137 2.167693 GACATGGGTCCAGTACGATCAA 59.832 50.000 0.00 0.00 38.12 2.57
137 138 2.569853 ACATGGGTCCAGTACGATCAAA 59.430 45.455 0.00 0.00 0.00 2.69
138 139 3.198068 CATGGGTCCAGTACGATCAAAG 58.802 50.000 0.00 0.00 0.00 2.77
139 140 2.253610 TGGGTCCAGTACGATCAAAGT 58.746 47.619 0.00 0.00 0.00 2.66
140 141 2.028476 TGGGTCCAGTACGATCAAAGTG 60.028 50.000 0.00 0.00 0.00 3.16
141 142 2.618053 GGTCCAGTACGATCAAAGTGG 58.382 52.381 10.62 10.62 37.52 4.00
142 143 2.618053 GTCCAGTACGATCAAAGTGGG 58.382 52.381 15.01 0.40 36.91 4.61
143 144 1.066430 TCCAGTACGATCAAAGTGGGC 60.066 52.381 15.01 0.00 36.91 5.36
144 145 1.066143 CCAGTACGATCAAAGTGGGCT 60.066 52.381 9.42 0.00 33.30 5.19
145 146 2.615493 CCAGTACGATCAAAGTGGGCTT 60.615 50.000 9.42 0.00 33.30 4.35
146 147 2.416547 CAGTACGATCAAAGTGGGCTTG 59.583 50.000 0.00 0.00 34.71 4.01
147 148 2.038557 AGTACGATCAAAGTGGGCTTGT 59.961 45.455 0.00 0.00 34.71 3.16
148 149 1.523758 ACGATCAAAGTGGGCTTGTC 58.476 50.000 0.00 0.00 34.71 3.18
149 150 1.072331 ACGATCAAAGTGGGCTTGTCT 59.928 47.619 0.00 0.00 34.71 3.41
150 151 1.734465 CGATCAAAGTGGGCTTGTCTC 59.266 52.381 0.00 0.00 34.71 3.36
151 152 1.734465 GATCAAAGTGGGCTTGTCTCG 59.266 52.381 0.00 0.00 34.71 4.04
152 153 0.884704 TCAAAGTGGGCTTGTCTCGC 60.885 55.000 0.00 0.00 34.71 5.03
153 154 0.886490 CAAAGTGGGCTTGTCTCGCT 60.886 55.000 0.00 0.00 34.71 4.93
154 155 0.179018 AAAGTGGGCTTGTCTCGCTT 60.179 50.000 0.00 0.00 34.71 4.68
155 156 0.886490 AAGTGGGCTTGTCTCGCTTG 60.886 55.000 0.00 0.00 32.92 4.01
156 157 2.032528 TGGGCTTGTCTCGCTTGG 59.967 61.111 0.00 0.00 0.00 3.61
157 158 3.435186 GGGCTTGTCTCGCTTGGC 61.435 66.667 0.00 0.00 0.00 4.52
158 159 2.669569 GGCTTGTCTCGCTTGGCA 60.670 61.111 0.00 0.00 0.00 4.92
159 160 2.042831 GGCTTGTCTCGCTTGGCAT 61.043 57.895 0.00 0.00 0.00 4.40
160 161 1.136147 GCTTGTCTCGCTTGGCATG 59.864 57.895 0.00 0.00 0.00 4.06
161 162 1.136147 CTTGTCTCGCTTGGCATGC 59.864 57.895 9.90 9.90 0.00 4.06
167 168 2.484662 CGCTTGGCATGCGCTTAA 59.515 55.556 30.28 3.51 46.72 1.85
168 169 1.154054 CGCTTGGCATGCGCTTAAA 60.154 52.632 30.28 0.13 46.72 1.52
169 170 0.732196 CGCTTGGCATGCGCTTAAAA 60.732 50.000 30.28 0.00 46.72 1.52
170 171 1.427435 GCTTGGCATGCGCTTAAAAA 58.573 45.000 12.44 0.00 38.60 1.94
171 172 2.001872 GCTTGGCATGCGCTTAAAAAT 58.998 42.857 12.44 0.00 38.60 1.82
172 173 2.416202 GCTTGGCATGCGCTTAAAAATT 59.584 40.909 12.44 0.00 38.60 1.82
173 174 3.484065 GCTTGGCATGCGCTTAAAAATTC 60.484 43.478 12.44 0.00 38.60 2.17
174 175 3.591196 TGGCATGCGCTTAAAAATTCT 57.409 38.095 12.44 0.00 38.60 2.40
175 176 3.510719 TGGCATGCGCTTAAAAATTCTC 58.489 40.909 12.44 0.00 38.60 2.87
176 177 3.193267 TGGCATGCGCTTAAAAATTCTCT 59.807 39.130 12.44 0.00 38.60 3.10
177 178 4.176271 GGCATGCGCTTAAAAATTCTCTT 58.824 39.130 12.44 0.00 38.60 2.85
178 179 4.032104 GGCATGCGCTTAAAAATTCTCTTG 59.968 41.667 12.44 0.00 38.60 3.02
179 180 4.622740 GCATGCGCTTAAAAATTCTCTTGT 59.377 37.500 9.73 0.00 34.30 3.16
180 181 5.220098 GCATGCGCTTAAAAATTCTCTTGTC 60.220 40.000 9.73 0.00 34.30 3.18
181 182 5.689383 TGCGCTTAAAAATTCTCTTGTCT 57.311 34.783 9.73 0.00 0.00 3.41
182 183 6.072112 TGCGCTTAAAAATTCTCTTGTCTT 57.928 33.333 9.73 0.00 0.00 3.01
183 184 6.503524 TGCGCTTAAAAATTCTCTTGTCTTT 58.496 32.000 9.73 0.00 0.00 2.52
184 185 6.417635 TGCGCTTAAAAATTCTCTTGTCTTTG 59.582 34.615 9.73 0.00 0.00 2.77
185 186 6.417930 GCGCTTAAAAATTCTCTTGTCTTTGT 59.582 34.615 0.00 0.00 0.00 2.83
186 187 7.357613 GCGCTTAAAAATTCTCTTGTCTTTGTC 60.358 37.037 0.00 0.00 0.00 3.18
187 188 7.149288 CGCTTAAAAATTCTCTTGTCTTTGTCG 60.149 37.037 0.00 0.00 0.00 4.35
188 189 7.855904 GCTTAAAAATTCTCTTGTCTTTGTCGA 59.144 33.333 0.00 0.00 0.00 4.20
189 190 9.716507 CTTAAAAATTCTCTTGTCTTTGTCGAA 57.283 29.630 0.00 0.00 0.00 3.71
190 191 9.716507 TTAAAAATTCTCTTGTCTTTGTCGAAG 57.283 29.630 0.00 0.00 36.67 3.79
191 192 4.999751 ATTCTCTTGTCTTTGTCGAAGC 57.000 40.909 0.00 0.00 35.24 3.86
192 193 3.735237 TCTCTTGTCTTTGTCGAAGCT 57.265 42.857 0.00 0.00 35.24 3.74
193 194 4.848562 TCTCTTGTCTTTGTCGAAGCTA 57.151 40.909 0.00 0.00 35.24 3.32
194 195 4.547532 TCTCTTGTCTTTGTCGAAGCTAC 58.452 43.478 0.00 0.00 35.24 3.58
195 196 4.278669 TCTCTTGTCTTTGTCGAAGCTACT 59.721 41.667 0.00 0.00 35.24 2.57
196 197 4.547532 TCTTGTCTTTGTCGAAGCTACTC 58.452 43.478 0.00 0.00 35.24 2.59
197 198 4.037565 TCTTGTCTTTGTCGAAGCTACTCA 59.962 41.667 0.00 0.00 35.24 3.41
198 199 3.902150 TGTCTTTGTCGAAGCTACTCAG 58.098 45.455 0.00 0.00 35.24 3.35
199 200 3.568430 TGTCTTTGTCGAAGCTACTCAGA 59.432 43.478 0.00 0.00 35.24 3.27
200 201 4.218635 TGTCTTTGTCGAAGCTACTCAGAT 59.781 41.667 0.00 0.00 35.24 2.90
201 202 4.796312 GTCTTTGTCGAAGCTACTCAGATC 59.204 45.833 0.00 0.00 35.24 2.75
202 203 4.459337 TCTTTGTCGAAGCTACTCAGATCA 59.541 41.667 0.00 0.00 35.24 2.92
203 204 4.783764 TTGTCGAAGCTACTCAGATCAA 57.216 40.909 0.00 0.00 0.00 2.57
204 205 4.362932 TGTCGAAGCTACTCAGATCAAG 57.637 45.455 0.00 0.00 0.00 3.02
205 206 3.759086 TGTCGAAGCTACTCAGATCAAGT 59.241 43.478 6.11 6.11 0.00 3.16
206 207 4.941873 TGTCGAAGCTACTCAGATCAAGTA 59.058 41.667 0.00 1.68 0.00 2.24
207 208 5.590663 TGTCGAAGCTACTCAGATCAAGTAT 59.409 40.000 8.05 0.00 0.00 2.12
208 209 6.766467 TGTCGAAGCTACTCAGATCAAGTATA 59.234 38.462 8.05 0.00 0.00 1.47
209 210 7.282450 TGTCGAAGCTACTCAGATCAAGTATAA 59.718 37.037 8.05 0.00 0.00 0.98
210 211 8.293867 GTCGAAGCTACTCAGATCAAGTATAAT 58.706 37.037 8.05 0.00 0.00 1.28
211 212 8.851145 TCGAAGCTACTCAGATCAAGTATAATT 58.149 33.333 8.05 4.80 0.00 1.40
212 213 9.469807 CGAAGCTACTCAGATCAAGTATAATTT 57.530 33.333 8.05 2.78 0.00 1.82
245 246 9.869757 ACTTTCTAAAACTAACAAAAGTTGCAT 57.130 25.926 0.00 0.00 39.62 3.96
252 253 9.606631 AAAACTAACAAAAGTTGCATTAATGGA 57.393 25.926 17.02 11.71 39.62 3.41
253 254 9.777297 AAACTAACAAAAGTTGCATTAATGGAT 57.223 25.926 17.02 0.00 39.62 3.41
291 292 8.863872 TTTTCTGGTTTTTGGAAAAATAACCA 57.136 26.923 11.10 11.10 39.75 3.67
292 293 8.863872 TTTCTGGTTTTTGGAAAAATAACCAA 57.136 26.923 12.22 0.00 43.22 3.67
293 294 7.851387 TCTGGTTTTTGGAAAAATAACCAAC 57.149 32.000 12.22 0.00 44.34 3.77
294 295 7.625469 TCTGGTTTTTGGAAAAATAACCAACT 58.375 30.769 12.22 0.00 44.34 3.16
295 296 8.103935 TCTGGTTTTTGGAAAAATAACCAACTT 58.896 29.630 12.22 0.00 44.34 2.66
296 297 8.637196 TGGTTTTTGGAAAAATAACCAACTTT 57.363 26.923 9.70 0.00 44.34 2.66
297 298 9.078990 TGGTTTTTGGAAAAATAACCAACTTTT 57.921 25.926 9.70 0.00 44.34 2.27
298 299 9.915629 GGTTTTTGGAAAAATAACCAACTTTTT 57.084 25.926 0.00 0.00 44.34 1.94
323 324 8.642908 TTGGAAGTATTATGTCACAGTTATCG 57.357 34.615 0.00 0.00 0.00 2.92
324 325 8.002984 TGGAAGTATTATGTCACAGTTATCGA 57.997 34.615 0.00 0.00 0.00 3.59
325 326 8.638873 TGGAAGTATTATGTCACAGTTATCGAT 58.361 33.333 2.16 2.16 0.00 3.59
326 327 8.916654 GGAAGTATTATGTCACAGTTATCGATG 58.083 37.037 8.54 0.00 0.00 3.84
327 328 9.464714 GAAGTATTATGTCACAGTTATCGATGT 57.535 33.333 8.54 0.00 0.00 3.06
328 329 9.817809 AAGTATTATGTCACAGTTATCGATGTT 57.182 29.630 8.54 0.00 0.00 2.71
329 330 9.817809 AGTATTATGTCACAGTTATCGATGTTT 57.182 29.630 8.54 0.00 0.00 2.83
356 357 9.658475 TTTTAAGTGTGAACATTTTCTATGACG 57.342 29.630 0.00 0.00 32.36 4.35
357 358 8.596271 TTAAGTGTGAACATTTTCTATGACGA 57.404 30.769 0.00 0.00 32.36 4.20
358 359 7.672983 AAGTGTGAACATTTTCTATGACGAT 57.327 32.000 0.00 0.00 32.36 3.73
359 360 7.295952 AGTGTGAACATTTTCTATGACGATC 57.704 36.000 0.00 0.00 32.36 3.69
360 361 6.313905 AGTGTGAACATTTTCTATGACGATCC 59.686 38.462 0.00 0.00 32.36 3.36
361 362 6.313905 GTGTGAACATTTTCTATGACGATCCT 59.686 38.462 0.00 0.00 32.36 3.24
362 363 6.313658 TGTGAACATTTTCTATGACGATCCTG 59.686 38.462 0.00 0.00 32.36 3.86
363 364 6.313905 GTGAACATTTTCTATGACGATCCTGT 59.686 38.462 0.00 0.00 32.36 4.00
364 365 7.491372 GTGAACATTTTCTATGACGATCCTGTA 59.509 37.037 0.00 0.00 32.36 2.74
365 366 7.491372 TGAACATTTTCTATGACGATCCTGTAC 59.509 37.037 0.00 0.00 32.36 2.90
366 367 6.873997 ACATTTTCTATGACGATCCTGTACA 58.126 36.000 0.00 0.00 0.00 2.90
367 368 7.500992 ACATTTTCTATGACGATCCTGTACAT 58.499 34.615 0.00 0.00 0.00 2.29
368 369 7.987458 ACATTTTCTATGACGATCCTGTACATT 59.013 33.333 0.00 0.00 0.00 2.71
369 370 8.830580 CATTTTCTATGACGATCCTGTACATTT 58.169 33.333 0.00 0.00 0.00 2.32
370 371 8.786826 TTTTCTATGACGATCCTGTACATTTT 57.213 30.769 0.00 0.00 0.00 1.82
371 372 9.878667 TTTTCTATGACGATCCTGTACATTTTA 57.121 29.630 0.00 0.00 0.00 1.52
437 438 7.754069 TGAACATTTCTTGAAACATGTGAAC 57.246 32.000 0.00 0.00 30.15 3.18
438 439 7.318893 TGAACATTTCTTGAAACATGTGAACA 58.681 30.769 0.00 0.00 30.15 3.18
439 440 7.980662 TGAACATTTCTTGAAACATGTGAACAT 59.019 29.630 0.00 0.00 36.96 2.71
440 441 8.721019 AACATTTCTTGAAACATGTGAACATT 57.279 26.923 0.00 0.00 33.61 2.71
441 442 8.721019 ACATTTCTTGAAACATGTGAACATTT 57.279 26.923 0.00 0.00 33.61 2.32
442 443 9.165035 ACATTTCTTGAAACATGTGAACATTTT 57.835 25.926 0.00 0.00 33.61 1.82
443 444 9.991388 CATTTCTTGAAACATGTGAACATTTTT 57.009 25.926 0.00 7.16 38.50 1.94
465 466 8.783833 TTTTTGAAAACATGTCATTTTCCTGA 57.216 26.923 15.52 3.43 42.77 3.86
466 467 8.783833 TTTTGAAAACATGTCATTTTCCTGAA 57.216 26.923 15.52 7.86 42.77 3.02
467 468 8.961294 TTTGAAAACATGTCATTTTCCTGAAT 57.039 26.923 15.52 0.00 42.77 2.57
468 469 8.961294 TTGAAAACATGTCATTTTCCTGAATT 57.039 26.923 15.52 0.00 42.77 2.17
469 470 8.961294 TGAAAACATGTCATTTTCCTGAATTT 57.039 26.923 15.52 1.97 42.77 1.82
470 471 9.044150 TGAAAACATGTCATTTTCCTGAATTTC 57.956 29.630 15.52 10.11 42.77 2.17
471 472 8.961294 AAAACATGTCATTTTCCTGAATTTCA 57.039 26.923 0.00 0.00 0.00 2.69
472 473 9.563748 AAAACATGTCATTTTCCTGAATTTCAT 57.436 25.926 0.00 0.00 0.00 2.57
473 474 8.542497 AACATGTCATTTTCCTGAATTTCATG 57.458 30.769 0.00 0.00 35.71 3.07
474 475 7.898918 ACATGTCATTTTCCTGAATTTCATGA 58.101 30.769 0.00 0.00 34.81 3.07
475 476 8.369424 ACATGTCATTTTCCTGAATTTCATGAA 58.631 29.630 3.38 3.38 34.81 2.57
476 477 9.378551 CATGTCATTTTCCTGAATTTCATGAAT 57.621 29.630 9.40 0.00 32.51 2.57
506 507 6.800072 TTTAACAGTTCCCAAGAAAATGGT 57.200 33.333 0.00 0.00 38.91 3.55
507 508 4.937201 AACAGTTCCCAAGAAAATGGTC 57.063 40.909 0.00 0.00 38.91 4.02
508 509 4.184649 ACAGTTCCCAAGAAAATGGTCT 57.815 40.909 0.00 0.00 38.91 3.85
509 510 5.319043 ACAGTTCCCAAGAAAATGGTCTA 57.681 39.130 0.00 0.00 38.91 2.59
510 511 5.892348 ACAGTTCCCAAGAAAATGGTCTAT 58.108 37.500 0.00 0.00 38.91 1.98
511 512 7.027874 ACAGTTCCCAAGAAAATGGTCTATA 57.972 36.000 0.00 0.00 38.91 1.31
512 513 7.466804 ACAGTTCCCAAGAAAATGGTCTATAA 58.533 34.615 0.00 0.00 38.91 0.98
513 514 7.947890 ACAGTTCCCAAGAAAATGGTCTATAAA 59.052 33.333 0.00 0.00 38.91 1.40
514 515 8.802267 CAGTTCCCAAGAAAATGGTCTATAAAA 58.198 33.333 0.00 0.00 38.91 1.52
515 516 8.803235 AGTTCCCAAGAAAATGGTCTATAAAAC 58.197 33.333 0.00 0.00 38.91 2.43
516 517 7.385778 TCCCAAGAAAATGGTCTATAAAACG 57.614 36.000 0.00 0.00 38.91 3.60
517 518 6.033966 CCCAAGAAAATGGTCTATAAAACGC 58.966 40.000 0.00 0.00 38.91 4.84
518 519 6.349777 CCCAAGAAAATGGTCTATAAAACGCA 60.350 38.462 0.00 0.00 38.91 5.24
519 520 7.087639 CCAAGAAAATGGTCTATAAAACGCAA 58.912 34.615 0.00 0.00 35.65 4.85
520 521 7.596995 CCAAGAAAATGGTCTATAAAACGCAAA 59.403 33.333 0.00 0.00 35.65 3.68
521 522 8.973378 CAAGAAAATGGTCTATAAAACGCAAAA 58.027 29.630 0.00 0.00 0.00 2.44
522 523 9.535878 AAGAAAATGGTCTATAAAACGCAAAAA 57.464 25.926 0.00 0.00 0.00 1.94
561 562 9.871175 AAAAAGGGTTATAGAACACTCCTAAAA 57.129 29.630 5.28 0.00 46.95 1.52
562 563 8.859236 AAAGGGTTATAGAACACTCCTAAAAC 57.141 34.615 5.28 0.00 46.95 2.43
563 564 6.955364 AGGGTTATAGAACACTCCTAAAACC 58.045 40.000 0.00 0.00 46.95 3.27
564 565 5.814188 GGGTTATAGAACACTCCTAAAACCG 59.186 44.000 2.17 0.00 35.94 4.44
565 566 6.351286 GGGTTATAGAACACTCCTAAAACCGA 60.351 42.308 2.17 0.00 35.94 4.69
566 567 7.099120 GGTTATAGAACACTCCTAAAACCGAA 58.901 38.462 2.17 0.00 37.29 4.30
567 568 7.063898 GGTTATAGAACACTCCTAAAACCGAAC 59.936 40.741 2.17 0.00 37.29 3.95
568 569 3.736720 AGAACACTCCTAAAACCGAACC 58.263 45.455 0.00 0.00 0.00 3.62
569 570 2.159327 ACACTCCTAAAACCGAACCG 57.841 50.000 0.00 0.00 0.00 4.44
581 582 3.025866 CGAACCGGAACCGAACTAG 57.974 57.895 9.46 0.00 42.83 2.57
582 583 1.074872 CGAACCGGAACCGAACTAGC 61.075 60.000 9.46 0.00 42.83 3.42
583 584 1.074872 GAACCGGAACCGAACTAGCG 61.075 60.000 9.46 0.00 42.83 4.26
592 593 1.578583 CCGAACTAGCGGTAATTGGG 58.421 55.000 2.55 2.55 46.07 4.12
593 594 0.935196 CGAACTAGCGGTAATTGGGC 59.065 55.000 0.00 0.00 0.00 5.36
594 595 1.306148 GAACTAGCGGTAATTGGGCC 58.694 55.000 0.00 0.00 0.00 5.80
605 606 5.539582 GGTAATTGGGCCGAAAAATTTTC 57.460 39.130 3.59 8.32 0.00 2.29
606 607 4.998033 GGTAATTGGGCCGAAAAATTTTCA 59.002 37.500 17.33 0.00 0.00 2.69
607 608 5.106869 GGTAATTGGGCCGAAAAATTTTCAC 60.107 40.000 17.33 9.08 0.00 3.18
608 609 3.828875 TTGGGCCGAAAAATTTTCACT 57.171 38.095 17.33 0.00 0.00 3.41
609 610 3.378911 TGGGCCGAAAAATTTTCACTC 57.621 42.857 17.33 9.67 0.00 3.51
610 611 2.287909 TGGGCCGAAAAATTTTCACTCG 60.288 45.455 17.33 13.91 0.00 4.18
611 612 1.719246 GGCCGAAAAATTTTCACTCGC 59.281 47.619 17.33 11.99 0.00 5.03
612 613 2.607038 GGCCGAAAAATTTTCACTCGCT 60.607 45.455 17.33 0.00 0.00 4.93
613 614 3.365565 GGCCGAAAAATTTTCACTCGCTA 60.366 43.478 17.33 0.00 0.00 4.26
614 615 4.223659 GCCGAAAAATTTTCACTCGCTAA 58.776 39.130 17.33 0.00 0.00 3.09
615 616 4.857037 GCCGAAAAATTTTCACTCGCTAAT 59.143 37.500 17.33 0.00 0.00 1.73
616 617 5.344933 GCCGAAAAATTTTCACTCGCTAATT 59.655 36.000 17.33 0.00 0.00 1.40
617 618 6.667386 GCCGAAAAATTTTCACTCGCTAATTG 60.667 38.462 17.33 5.04 0.00 2.32
618 619 6.226407 CGAAAAATTTTCACTCGCTAATTGC 58.774 36.000 17.33 0.00 38.57 3.56
619 620 6.466308 AAAAATTTTCACTCGCTAATTGCC 57.534 33.333 3.41 0.00 38.78 4.52
620 621 2.892373 TTTTCACTCGCTAATTGCCG 57.108 45.000 0.00 0.00 38.78 5.69
621 622 0.446222 TTTCACTCGCTAATTGCCGC 59.554 50.000 0.00 0.00 38.78 6.53
622 623 0.672091 TTCACTCGCTAATTGCCGCA 60.672 50.000 0.00 0.00 38.78 5.69
623 624 0.672091 TCACTCGCTAATTGCCGCAA 60.672 50.000 8.55 8.55 38.78 4.85
624 625 0.167908 CACTCGCTAATTGCCGCAAA 59.832 50.000 10.42 0.00 38.78 3.68
625 626 0.447801 ACTCGCTAATTGCCGCAAAG 59.552 50.000 10.42 5.15 38.78 2.77
626 627 0.863119 CTCGCTAATTGCCGCAAAGC 60.863 55.000 16.62 16.62 38.78 3.51
627 628 1.873572 CGCTAATTGCCGCAAAGCC 60.874 57.895 19.43 6.66 38.78 4.35
628 629 1.873572 GCTAATTGCCGCAAAGCCG 60.874 57.895 15.98 5.03 35.15 5.52
629 630 1.873572 CTAATTGCCGCAAAGCCGC 60.874 57.895 10.42 0.00 33.73 6.53
630 631 2.270297 CTAATTGCCGCAAAGCCGCT 62.270 55.000 10.42 0.00 34.21 5.52
631 632 1.027255 TAATTGCCGCAAAGCCGCTA 61.027 50.000 10.42 0.00 34.21 4.26
632 633 1.872197 AATTGCCGCAAAGCCGCTAA 61.872 50.000 10.42 0.00 34.21 3.09
633 634 1.872197 ATTGCCGCAAAGCCGCTAAA 61.872 50.000 10.42 0.00 34.21 1.85
634 635 2.076622 TTGCCGCAAAGCCGCTAAAA 62.077 50.000 2.50 0.00 34.21 1.52
635 636 1.372375 GCCGCAAAGCCGCTAAAAA 60.372 52.632 0.00 0.00 30.75 1.94
668 669 3.632189 GCAATAAGCGGCAAATAAGAGG 58.368 45.455 1.45 0.00 0.00 3.69
669 670 3.066760 GCAATAAGCGGCAAATAAGAGGT 59.933 43.478 1.45 0.00 0.00 3.85
670 671 4.601019 CAATAAGCGGCAAATAAGAGGTG 58.399 43.478 1.45 0.00 0.00 4.00
671 672 0.811281 AAGCGGCAAATAAGAGGTGC 59.189 50.000 1.45 0.00 37.55 5.01
672 673 0.322456 AGCGGCAAATAAGAGGTGCA 60.322 50.000 1.45 0.00 40.12 4.57
673 674 0.179163 GCGGCAAATAAGAGGTGCAC 60.179 55.000 8.80 8.80 40.12 4.57
674 675 1.164411 CGGCAAATAAGAGGTGCACA 58.836 50.000 20.43 0.00 40.12 4.57
675 676 1.135689 CGGCAAATAAGAGGTGCACAC 60.136 52.381 20.43 12.05 40.12 3.82
676 677 1.885887 GGCAAATAAGAGGTGCACACA 59.114 47.619 20.43 0.00 40.12 3.72
677 678 2.295909 GGCAAATAAGAGGTGCACACAA 59.704 45.455 20.43 5.14 40.12 3.33
678 679 3.056607 GGCAAATAAGAGGTGCACACAAT 60.057 43.478 20.43 4.41 40.12 2.71
679 680 3.922240 GCAAATAAGAGGTGCACACAATG 59.078 43.478 20.43 7.19 38.19 2.82
680 681 4.559300 GCAAATAAGAGGTGCACACAATGT 60.559 41.667 20.43 0.62 38.19 2.71
694 695 3.820467 ACACAATGTGAACAGGTATGTGG 59.180 43.478 21.34 0.00 40.60 4.17
695 696 3.820467 CACAATGTGAACAGGTATGTGGT 59.180 43.478 7.78 0.00 40.39 4.16
696 697 5.000591 CACAATGTGAACAGGTATGTGGTA 58.999 41.667 7.78 0.00 40.39 3.25
697 698 5.122239 CACAATGTGAACAGGTATGTGGTAG 59.878 44.000 7.78 0.00 40.39 3.18
698 699 3.973206 TGTGAACAGGTATGTGGTAGG 57.027 47.619 0.00 0.00 40.39 3.18
699 700 2.027561 TGTGAACAGGTATGTGGTAGGC 60.028 50.000 0.00 0.00 40.39 3.93
700 701 1.557832 TGAACAGGTATGTGGTAGGCC 59.442 52.381 0.00 0.00 40.39 5.19
898 899 2.556622 GGGACCCGCATTTTACATATGG 59.443 50.000 7.80 0.00 0.00 2.74
1143 1473 1.379443 ACGGCCATCACCTCGTCTA 60.379 57.895 2.24 0.00 0.00 2.59
1185 1541 2.159043 AGTGCTCTCTCTCTCTCTCTCG 60.159 54.545 0.00 0.00 0.00 4.04
1186 1542 1.831106 TGCTCTCTCTCTCTCTCTCGT 59.169 52.381 0.00 0.00 0.00 4.18
1187 1543 2.205074 GCTCTCTCTCTCTCTCTCGTG 58.795 57.143 0.00 0.00 0.00 4.35
1188 1544 2.418746 GCTCTCTCTCTCTCTCTCGTGT 60.419 54.545 0.00 0.00 0.00 4.49
1189 1545 3.181479 GCTCTCTCTCTCTCTCTCGTGTA 60.181 52.174 0.00 0.00 0.00 2.90
1190 1546 4.679639 GCTCTCTCTCTCTCTCTCGTGTAA 60.680 50.000 0.00 0.00 0.00 2.41
1210 1572 6.696148 GTGTAATCGTGTTTATCCTCTTCGAT 59.304 38.462 0.00 0.00 38.00 3.59
1330 1739 1.908793 CCCCGCCATAGAGTCCGAT 60.909 63.158 0.00 0.00 0.00 4.18
2291 2741 5.240403 ACAAGAGGAAGAAAATGAAGCAGAC 59.760 40.000 0.00 0.00 0.00 3.51
2948 3399 4.185394 CTGCACCACCGTTGTATAACATA 58.815 43.478 3.13 0.00 36.58 2.29
3126 3578 4.196193 CAAATGATGCTTGCATTCCCATT 58.804 39.130 9.59 11.23 35.06 3.16
3488 3941 4.596212 TGCTCCTAGTGATGATGATTGGAT 59.404 41.667 0.00 0.00 0.00 3.41
3649 4106 8.840321 CGAAGTGTGGGAATGAAATTATAGAAT 58.160 33.333 0.00 0.00 36.07 2.40
3846 4303 3.054875 TCCGTGAGTTAGTGTCTAGCCTA 60.055 47.826 0.00 0.00 0.00 3.93
3927 4384 3.052455 TCTGCAATGGAAGCTAACGAA 57.948 42.857 0.00 0.00 0.00 3.85
4681 5140 9.169592 TCATGTTTACCTTAAGTTAGTTATGGC 57.830 33.333 10.52 0.00 38.84 4.40
4895 5356 6.267817 CCATTATGGCTTGTTATGTGTTCAG 58.732 40.000 0.00 0.00 0.00 3.02
5181 6215 1.067762 TCCCCATTGCCATCCCTAGG 61.068 60.000 0.06 0.06 0.00 3.02
5265 6299 3.103742 GCTATTGGGAGGAGATAGAGGG 58.896 54.545 0.00 0.00 0.00 4.30
5326 6360 1.521681 GCCCGAAAGAGGACGATGG 60.522 63.158 0.00 0.00 0.00 3.51
5484 6525 0.108138 GTAGTGGTAGCTGCCCTGTG 60.108 60.000 19.07 0.00 0.00 3.66
5486 6527 1.376037 GTGGTAGCTGCCCTGTGTC 60.376 63.158 19.07 0.00 0.00 3.67
5488 6529 0.252057 TGGTAGCTGCCCTGTGTCTA 60.252 55.000 19.07 0.00 0.00 2.59
5491 6532 1.135333 GTAGCTGCCCTGTGTCTAGTC 59.865 57.143 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 0.884704 GCGAGACAAGCCCACTTTGA 60.885 55.000 0.00 0.00 32.29 2.69
134 135 0.886490 AGCGAGACAAGCCCACTTTG 60.886 55.000 0.00 0.00 32.29 2.77
135 136 0.179018 AAGCGAGACAAGCCCACTTT 60.179 50.000 0.00 0.00 32.29 2.66
136 137 0.886490 CAAGCGAGACAAGCCCACTT 60.886 55.000 0.00 0.00 36.19 3.16
137 138 1.302033 CAAGCGAGACAAGCCCACT 60.302 57.895 0.00 0.00 34.64 4.00
138 139 2.328099 CCAAGCGAGACAAGCCCAC 61.328 63.158 0.00 0.00 34.64 4.61
139 140 2.032528 CCAAGCGAGACAAGCCCA 59.967 61.111 0.00 0.00 34.64 5.36
140 141 3.435186 GCCAAGCGAGACAAGCCC 61.435 66.667 0.00 0.00 34.64 5.19
141 142 2.042831 ATGCCAAGCGAGACAAGCC 61.043 57.895 0.00 0.00 34.64 4.35
142 143 1.136147 CATGCCAAGCGAGACAAGC 59.864 57.895 0.00 0.00 0.00 4.01
143 144 1.136147 GCATGCCAAGCGAGACAAG 59.864 57.895 6.36 0.00 0.00 3.16
144 145 3.266964 GCATGCCAAGCGAGACAA 58.733 55.556 6.36 0.00 0.00 3.18
151 152 1.427435 TTTTTAAGCGCATGCCAAGC 58.573 45.000 13.15 10.20 44.31 4.01
152 153 3.928375 AGAATTTTTAAGCGCATGCCAAG 59.072 39.130 13.15 0.00 44.31 3.61
153 154 3.924144 AGAATTTTTAAGCGCATGCCAA 58.076 36.364 13.15 0.00 44.31 4.52
154 155 3.193267 AGAGAATTTTTAAGCGCATGCCA 59.807 39.130 13.15 0.00 44.31 4.92
155 156 3.774066 AGAGAATTTTTAAGCGCATGCC 58.226 40.909 13.15 4.99 44.31 4.40
156 157 4.622740 ACAAGAGAATTTTTAAGCGCATGC 59.377 37.500 11.47 7.91 43.24 4.06
157 158 6.088824 AGACAAGAGAATTTTTAAGCGCATG 58.911 36.000 11.47 0.00 0.00 4.06
158 159 6.259550 AGACAAGAGAATTTTTAAGCGCAT 57.740 33.333 11.47 0.00 0.00 4.73
159 160 5.689383 AGACAAGAGAATTTTTAAGCGCA 57.311 34.783 11.47 0.00 0.00 6.09
160 161 6.417930 ACAAAGACAAGAGAATTTTTAAGCGC 59.582 34.615 0.00 0.00 0.00 5.92
161 162 7.149288 CGACAAAGACAAGAGAATTTTTAAGCG 60.149 37.037 0.00 0.00 0.00 4.68
162 163 7.855904 TCGACAAAGACAAGAGAATTTTTAAGC 59.144 33.333 0.00 0.00 0.00 3.09
163 164 9.716507 TTCGACAAAGACAAGAGAATTTTTAAG 57.283 29.630 0.00 0.00 0.00 1.85
164 165 9.716507 CTTCGACAAAGACAAGAGAATTTTTAA 57.283 29.630 0.00 0.00 37.12 1.52
165 166 7.855904 GCTTCGACAAAGACAAGAGAATTTTTA 59.144 33.333 0.00 0.00 37.12 1.52
166 167 6.693113 GCTTCGACAAAGACAAGAGAATTTTT 59.307 34.615 0.00 0.00 37.12 1.94
167 168 6.038714 AGCTTCGACAAAGACAAGAGAATTTT 59.961 34.615 0.00 0.00 37.12 1.82
168 169 5.529060 AGCTTCGACAAAGACAAGAGAATTT 59.471 36.000 0.00 0.00 37.12 1.82
169 170 5.059833 AGCTTCGACAAAGACAAGAGAATT 58.940 37.500 0.00 0.00 37.12 2.17
170 171 4.636249 AGCTTCGACAAAGACAAGAGAAT 58.364 39.130 0.00 0.00 37.12 2.40
171 172 4.060038 AGCTTCGACAAAGACAAGAGAA 57.940 40.909 0.00 0.00 37.12 2.87
172 173 3.735237 AGCTTCGACAAAGACAAGAGA 57.265 42.857 0.00 0.00 37.12 3.10
173 174 4.551388 AGTAGCTTCGACAAAGACAAGAG 58.449 43.478 0.00 0.00 37.12 2.85
174 175 4.037565 TGAGTAGCTTCGACAAAGACAAGA 59.962 41.667 0.00 0.00 37.12 3.02
175 176 4.299155 TGAGTAGCTTCGACAAAGACAAG 58.701 43.478 0.00 0.00 37.12 3.16
176 177 4.037565 TCTGAGTAGCTTCGACAAAGACAA 59.962 41.667 0.00 0.00 37.12 3.18
177 178 3.568430 TCTGAGTAGCTTCGACAAAGACA 59.432 43.478 0.00 0.00 37.12 3.41
178 179 4.162096 TCTGAGTAGCTTCGACAAAGAC 57.838 45.455 0.00 0.00 37.12 3.01
179 180 4.459337 TGATCTGAGTAGCTTCGACAAAGA 59.541 41.667 0.00 0.00 37.12 2.52
180 181 4.738124 TGATCTGAGTAGCTTCGACAAAG 58.262 43.478 0.00 0.00 38.08 2.77
181 182 4.783764 TGATCTGAGTAGCTTCGACAAA 57.216 40.909 0.00 0.00 0.00 2.83
182 183 4.218635 ACTTGATCTGAGTAGCTTCGACAA 59.781 41.667 0.00 0.00 0.00 3.18
183 184 3.759086 ACTTGATCTGAGTAGCTTCGACA 59.241 43.478 0.00 0.00 0.00 4.35
184 185 4.364415 ACTTGATCTGAGTAGCTTCGAC 57.636 45.455 0.00 0.00 0.00 4.20
185 186 7.803279 TTATACTTGATCTGAGTAGCTTCGA 57.197 36.000 12.78 0.00 33.46 3.71
186 187 9.469807 AAATTATACTTGATCTGAGTAGCTTCG 57.530 33.333 12.78 0.00 33.46 3.79
219 220 9.869757 ATGCAACTTTTGTTAGTTTTAGAAAGT 57.130 25.926 0.00 0.00 41.35 2.66
226 227 9.606631 TCCATTAATGCAACTTTTGTTAGTTTT 57.393 25.926 10.11 0.00 41.35 2.43
227 228 9.777297 ATCCATTAATGCAACTTTTGTTAGTTT 57.223 25.926 10.11 0.00 41.35 2.66
266 267 8.863872 TGGTTATTTTTCCAAAAACCAGAAAA 57.136 26.923 1.24 0.00 40.33 2.29
267 268 8.731605 GTTGGTTATTTTTCCAAAAACCAGAAA 58.268 29.630 5.49 0.00 43.89 2.52
268 269 8.103935 AGTTGGTTATTTTTCCAAAAACCAGAA 58.896 29.630 5.49 0.00 43.89 3.02
269 270 7.625469 AGTTGGTTATTTTTCCAAAAACCAGA 58.375 30.769 5.49 0.00 43.89 3.86
270 271 7.857734 AGTTGGTTATTTTTCCAAAAACCAG 57.142 32.000 5.49 0.00 43.89 4.00
271 272 8.637196 AAAGTTGGTTATTTTTCCAAAAACCA 57.363 26.923 1.24 1.24 43.89 3.67
272 273 9.915629 AAAAAGTTGGTTATTTTTCCAAAAACC 57.084 25.926 0.00 0.00 43.89 3.27
297 298 9.093970 CGATAACTGTGACATAATACTTCCAAA 57.906 33.333 0.00 0.00 0.00 3.28
298 299 8.471609 TCGATAACTGTGACATAATACTTCCAA 58.528 33.333 0.00 0.00 0.00 3.53
299 300 8.002984 TCGATAACTGTGACATAATACTTCCA 57.997 34.615 0.00 0.00 0.00 3.53
300 301 8.916654 CATCGATAACTGTGACATAATACTTCC 58.083 37.037 0.00 0.00 0.00 3.46
301 302 9.464714 ACATCGATAACTGTGACATAATACTTC 57.535 33.333 0.00 0.00 0.00 3.01
302 303 9.817809 AACATCGATAACTGTGACATAATACTT 57.182 29.630 0.00 0.00 0.00 2.24
303 304 9.817809 AAACATCGATAACTGTGACATAATACT 57.182 29.630 0.00 0.00 0.00 2.12
330 331 9.658475 CGTCATAGAAAATGTTCACACTTAAAA 57.342 29.630 0.00 0.00 36.09 1.52
331 332 9.047371 TCGTCATAGAAAATGTTCACACTTAAA 57.953 29.630 0.00 0.00 36.09 1.52
332 333 8.596271 TCGTCATAGAAAATGTTCACACTTAA 57.404 30.769 0.00 0.00 36.09 1.85
333 334 8.771920 ATCGTCATAGAAAATGTTCACACTTA 57.228 30.769 0.00 0.00 36.09 2.24
334 335 7.148407 GGATCGTCATAGAAAATGTTCACACTT 60.148 37.037 0.00 0.00 36.09 3.16
335 336 6.313905 GGATCGTCATAGAAAATGTTCACACT 59.686 38.462 0.00 0.00 36.09 3.55
336 337 6.313905 AGGATCGTCATAGAAAATGTTCACAC 59.686 38.462 0.00 0.00 36.09 3.82
337 338 6.313658 CAGGATCGTCATAGAAAATGTTCACA 59.686 38.462 0.00 0.00 36.09 3.58
338 339 6.313905 ACAGGATCGTCATAGAAAATGTTCAC 59.686 38.462 0.00 0.00 36.09 3.18
339 340 6.406370 ACAGGATCGTCATAGAAAATGTTCA 58.594 36.000 0.00 0.00 36.09 3.18
340 341 6.910536 ACAGGATCGTCATAGAAAATGTTC 57.089 37.500 0.00 0.00 0.00 3.18
341 342 7.327975 TGTACAGGATCGTCATAGAAAATGTT 58.672 34.615 0.00 0.00 0.00 2.71
342 343 6.873997 TGTACAGGATCGTCATAGAAAATGT 58.126 36.000 0.00 0.00 0.00 2.71
343 344 7.953158 ATGTACAGGATCGTCATAGAAAATG 57.047 36.000 0.33 0.00 0.00 2.32
344 345 8.964476 AAATGTACAGGATCGTCATAGAAAAT 57.036 30.769 0.33 0.00 0.00 1.82
345 346 8.786826 AAAATGTACAGGATCGTCATAGAAAA 57.213 30.769 0.33 0.00 0.00 2.29
411 412 9.462174 GTTCACATGTTTCAAGAAATGTTCATA 57.538 29.630 0.00 0.00 32.36 2.15
412 413 7.980662 TGTTCACATGTTTCAAGAAATGTTCAT 59.019 29.630 0.00 0.00 32.36 2.57
413 414 7.318893 TGTTCACATGTTTCAAGAAATGTTCA 58.681 30.769 0.00 0.00 32.36 3.18
414 415 7.754069 TGTTCACATGTTTCAAGAAATGTTC 57.246 32.000 0.00 0.00 32.36 3.18
415 416 8.721019 AATGTTCACATGTTTCAAGAAATGTT 57.279 26.923 0.00 0.00 36.56 2.71
416 417 8.721019 AAATGTTCACATGTTTCAAGAAATGT 57.279 26.923 0.00 0.00 36.56 2.71
417 418 9.991388 AAAAATGTTCACATGTTTCAAGAAATG 57.009 25.926 0.00 0.00 38.98 2.32
440 441 8.783833 TCAGGAAAATGACATGTTTTCAAAAA 57.216 26.923 18.51 3.70 43.78 1.94
441 442 8.783833 TTCAGGAAAATGACATGTTTTCAAAA 57.216 26.923 18.51 9.53 43.78 2.44
442 443 8.961294 ATTCAGGAAAATGACATGTTTTCAAA 57.039 26.923 18.51 11.82 43.78 2.69
443 444 8.961294 AATTCAGGAAAATGACATGTTTTCAA 57.039 26.923 18.51 8.62 43.78 2.69
444 445 8.961294 AAATTCAGGAAAATGACATGTTTTCA 57.039 26.923 18.51 6.09 43.78 2.69
445 446 9.044150 TGAAATTCAGGAAAATGACATGTTTTC 57.956 29.630 11.46 11.46 42.17 2.29
446 447 8.961294 TGAAATTCAGGAAAATGACATGTTTT 57.039 26.923 0.00 0.00 0.00 2.43
447 448 8.995220 CATGAAATTCAGGAAAATGACATGTTT 58.005 29.630 0.80 0.00 33.41 2.83
448 449 8.369424 TCATGAAATTCAGGAAAATGACATGTT 58.631 29.630 7.95 0.00 33.94 2.71
449 450 7.898918 TCATGAAATTCAGGAAAATGACATGT 58.101 30.769 7.95 0.00 33.94 3.21
450 451 8.766000 TTCATGAAATTCAGGAAAATGACATG 57.234 30.769 18.95 0.00 43.11 3.21
481 482 7.625469 ACCATTTTCTTGGGAACTGTTAAAAA 58.375 30.769 0.00 0.00 41.35 1.94
482 483 7.125053 AGACCATTTTCTTGGGAACTGTTAAAA 59.875 33.333 0.00 0.00 41.35 1.52
483 484 6.609616 AGACCATTTTCTTGGGAACTGTTAAA 59.390 34.615 0.00 0.00 41.35 1.52
484 485 6.133356 AGACCATTTTCTTGGGAACTGTTAA 58.867 36.000 0.00 0.00 41.35 2.01
485 486 5.701224 AGACCATTTTCTTGGGAACTGTTA 58.299 37.500 0.00 0.00 41.35 2.41
486 487 4.546674 AGACCATTTTCTTGGGAACTGTT 58.453 39.130 0.00 0.00 41.35 3.16
487 488 4.184649 AGACCATTTTCTTGGGAACTGT 57.815 40.909 0.00 0.00 41.35 3.55
488 489 7.938140 TTATAGACCATTTTCTTGGGAACTG 57.062 36.000 0.00 0.00 41.35 3.16
489 490 8.803235 GTTTTATAGACCATTTTCTTGGGAACT 58.197 33.333 0.00 0.00 41.35 3.01
490 491 7.753580 CGTTTTATAGACCATTTTCTTGGGAAC 59.246 37.037 0.00 0.00 41.35 3.62
491 492 7.576098 GCGTTTTATAGACCATTTTCTTGGGAA 60.576 37.037 0.00 0.00 41.35 3.97
492 493 6.127842 GCGTTTTATAGACCATTTTCTTGGGA 60.128 38.462 0.00 0.00 41.35 4.37
493 494 6.033966 GCGTTTTATAGACCATTTTCTTGGG 58.966 40.000 0.00 0.00 41.35 4.12
494 495 6.616947 TGCGTTTTATAGACCATTTTCTTGG 58.383 36.000 0.00 0.00 42.82 3.61
495 496 8.514136 TTTGCGTTTTATAGACCATTTTCTTG 57.486 30.769 0.00 0.00 0.00 3.02
496 497 9.535878 TTTTTGCGTTTTATAGACCATTTTCTT 57.464 25.926 0.00 0.00 0.00 2.52
535 536 9.871175 TTTTAGGAGTGTTCTATAACCCTTTTT 57.129 29.630 0.00 0.00 34.49 1.94
536 537 9.293404 GTTTTAGGAGTGTTCTATAACCCTTTT 57.707 33.333 0.00 0.00 34.49 2.27
537 538 7.886970 GGTTTTAGGAGTGTTCTATAACCCTTT 59.113 37.037 10.36 0.00 40.10 3.11
538 539 7.400439 GGTTTTAGGAGTGTTCTATAACCCTT 58.600 38.462 10.36 0.00 40.10 3.95
539 540 6.351626 CGGTTTTAGGAGTGTTCTATAACCCT 60.352 42.308 13.68 0.00 41.50 4.34
540 541 5.814188 CGGTTTTAGGAGTGTTCTATAACCC 59.186 44.000 13.68 0.00 41.50 4.11
541 542 6.633856 TCGGTTTTAGGAGTGTTCTATAACC 58.366 40.000 11.04 11.04 41.32 2.85
542 543 7.063898 GGTTCGGTTTTAGGAGTGTTCTATAAC 59.936 40.741 0.00 0.00 36.07 1.89
543 544 7.099120 GGTTCGGTTTTAGGAGTGTTCTATAA 58.901 38.462 0.00 0.00 0.00 0.98
544 545 6.625740 CGGTTCGGTTTTAGGAGTGTTCTATA 60.626 42.308 0.00 0.00 0.00 1.31
545 546 5.485620 GGTTCGGTTTTAGGAGTGTTCTAT 58.514 41.667 0.00 0.00 0.00 1.98
546 547 4.559300 CGGTTCGGTTTTAGGAGTGTTCTA 60.559 45.833 0.00 0.00 0.00 2.10
547 548 3.736720 GGTTCGGTTTTAGGAGTGTTCT 58.263 45.455 0.00 0.00 0.00 3.01
548 549 2.477754 CGGTTCGGTTTTAGGAGTGTTC 59.522 50.000 0.00 0.00 0.00 3.18
549 550 2.486918 CGGTTCGGTTTTAGGAGTGTT 58.513 47.619 0.00 0.00 0.00 3.32
550 551 1.270465 CCGGTTCGGTTTTAGGAGTGT 60.270 52.381 0.00 0.00 42.73 3.55
551 552 1.435577 CCGGTTCGGTTTTAGGAGTG 58.564 55.000 0.00 0.00 42.73 3.51
552 553 3.921257 CCGGTTCGGTTTTAGGAGT 57.079 52.632 0.00 0.00 42.73 3.85
563 564 1.074872 GCTAGTTCGGTTCCGGTTCG 61.075 60.000 11.37 4.32 0.00 3.95
564 565 1.074872 CGCTAGTTCGGTTCCGGTTC 61.075 60.000 11.37 0.00 0.00 3.62
565 566 1.080298 CGCTAGTTCGGTTCCGGTT 60.080 57.895 11.37 0.65 0.00 4.44
566 567 2.570181 CGCTAGTTCGGTTCCGGT 59.430 61.111 11.37 0.00 0.00 5.28
567 568 2.202703 CCGCTAGTTCGGTTCCGG 60.203 66.667 11.37 0.00 44.18 5.14
574 575 0.935196 GCCCAATTACCGCTAGTTCG 59.065 55.000 0.00 0.00 0.00 3.95
575 576 1.306148 GGCCCAATTACCGCTAGTTC 58.694 55.000 0.00 0.00 0.00 3.01
576 577 0.463116 CGGCCCAATTACCGCTAGTT 60.463 55.000 0.00 0.00 43.44 2.24
577 578 1.145377 CGGCCCAATTACCGCTAGT 59.855 57.895 0.00 0.00 43.44 2.57
578 579 4.043168 CGGCCCAATTACCGCTAG 57.957 61.111 0.00 0.00 43.44 3.42
583 584 4.998033 TGAAAATTTTTCGGCCCAATTACC 59.002 37.500 15.22 0.00 0.00 2.85
584 585 5.699001 AGTGAAAATTTTTCGGCCCAATTAC 59.301 36.000 15.22 6.33 0.00 1.89
585 586 5.859495 AGTGAAAATTTTTCGGCCCAATTA 58.141 33.333 15.22 0.00 0.00 1.40
586 587 4.713553 AGTGAAAATTTTTCGGCCCAATT 58.286 34.783 15.22 0.00 0.00 2.32
587 588 4.314961 GAGTGAAAATTTTTCGGCCCAAT 58.685 39.130 15.22 0.00 0.00 3.16
588 589 3.723260 GAGTGAAAATTTTTCGGCCCAA 58.277 40.909 15.22 0.00 0.00 4.12
589 590 2.287909 CGAGTGAAAATTTTTCGGCCCA 60.288 45.455 15.22 0.72 0.00 5.36
590 591 2.324860 CGAGTGAAAATTTTTCGGCCC 58.675 47.619 15.22 5.38 0.00 5.80
591 592 1.719246 GCGAGTGAAAATTTTTCGGCC 59.281 47.619 19.59 0.00 0.00 6.13
592 593 2.661594 AGCGAGTGAAAATTTTTCGGC 58.338 42.857 19.59 14.59 0.00 5.54
593 594 6.667386 GCAATTAGCGAGTGAAAATTTTTCGG 60.667 38.462 19.59 7.71 0.00 4.30
594 595 6.226407 GCAATTAGCGAGTGAAAATTTTTCG 58.774 36.000 15.75 15.75 0.00 3.46
610 611 1.873572 CGGCTTTGCGGCAATTAGC 60.874 57.895 24.30 24.30 44.65 3.09
611 612 4.382728 CGGCTTTGCGGCAATTAG 57.617 55.556 17.19 12.85 38.27 1.73
618 619 4.955089 TTTTTAGCGGCTTTGCGG 57.045 50.000 8.26 0.00 40.67 5.69
633 634 5.442402 CGCTTATTGCAGCAAATTGTTTTT 58.558 33.333 12.97 0.00 43.06 1.94
634 635 4.083908 CCGCTTATTGCAGCAAATTGTTTT 60.084 37.500 12.97 0.00 43.06 2.43
635 636 3.432933 CCGCTTATTGCAGCAAATTGTTT 59.567 39.130 12.97 0.00 43.06 2.83
636 637 2.995258 CCGCTTATTGCAGCAAATTGTT 59.005 40.909 12.97 0.00 43.06 2.83
637 638 2.609350 CCGCTTATTGCAGCAAATTGT 58.391 42.857 12.97 0.00 43.06 2.71
638 639 1.325338 GCCGCTTATTGCAGCAAATTG 59.675 47.619 12.97 6.12 44.06 2.32
639 640 1.643880 GCCGCTTATTGCAGCAAATT 58.356 45.000 12.97 0.00 44.06 1.82
640 641 3.350766 GCCGCTTATTGCAGCAAAT 57.649 47.368 12.97 3.69 44.06 2.32
641 642 4.887290 GCCGCTTATTGCAGCAAA 57.113 50.000 12.97 0.00 44.06 3.68
644 645 2.490328 TATTTGCCGCTTATTGCAGC 57.510 45.000 0.00 0.00 44.83 5.25
645 646 4.285292 CTCTTATTTGCCGCTTATTGCAG 58.715 43.478 0.00 0.00 43.06 4.41
646 647 3.066621 CCTCTTATTTGCCGCTTATTGCA 59.933 43.478 0.00 0.00 43.06 4.08
647 648 3.066760 ACCTCTTATTTGCCGCTTATTGC 59.933 43.478 0.00 0.00 38.57 3.56
648 649 4.601019 CACCTCTTATTTGCCGCTTATTG 58.399 43.478 0.00 0.00 0.00 1.90
649 650 3.066760 GCACCTCTTATTTGCCGCTTATT 59.933 43.478 0.00 0.00 0.00 1.40
650 651 2.618709 GCACCTCTTATTTGCCGCTTAT 59.381 45.455 0.00 0.00 0.00 1.73
651 652 2.014128 GCACCTCTTATTTGCCGCTTA 58.986 47.619 0.00 0.00 0.00 3.09
652 653 0.811281 GCACCTCTTATTTGCCGCTT 59.189 50.000 0.00 0.00 0.00 4.68
653 654 0.322456 TGCACCTCTTATTTGCCGCT 60.322 50.000 0.00 0.00 35.26 5.52
654 655 0.179163 GTGCACCTCTTATTTGCCGC 60.179 55.000 5.22 0.00 35.26 6.53
655 656 1.135689 GTGTGCACCTCTTATTTGCCG 60.136 52.381 15.69 0.00 35.26 5.69
656 657 1.885887 TGTGTGCACCTCTTATTTGCC 59.114 47.619 15.69 0.00 35.26 4.52
657 658 3.641437 TTGTGTGCACCTCTTATTTGC 57.359 42.857 15.69 0.00 36.76 3.68
658 659 4.919168 CACATTGTGTGCACCTCTTATTTG 59.081 41.667 15.69 4.01 41.89 2.32
659 660 5.125100 CACATTGTGTGCACCTCTTATTT 57.875 39.130 15.69 0.00 41.89 1.40
660 661 4.771590 CACATTGTGTGCACCTCTTATT 57.228 40.909 15.69 0.00 41.89 1.40
669 670 7.220178 CACATACCTGTTCACATTGTGTGCA 62.220 44.000 16.06 14.05 39.89 4.57
670 671 4.848370 CACATACCTGTTCACATTGTGTGC 60.848 45.833 16.06 10.61 39.89 4.57
671 672 4.320421 CCACATACCTGTTCACATTGTGTG 60.320 45.833 16.06 6.41 40.77 3.82
672 673 3.820467 CCACATACCTGTTCACATTGTGT 59.180 43.478 16.06 0.00 31.97 3.72
673 674 3.820467 ACCACATACCTGTTCACATTGTG 59.180 43.478 10.64 10.64 31.62 3.33
674 675 4.098914 ACCACATACCTGTTCACATTGT 57.901 40.909 0.00 0.00 31.62 2.71
675 676 4.635765 CCTACCACATACCTGTTCACATTG 59.364 45.833 0.00 0.00 31.62 2.82
676 677 4.843728 CCTACCACATACCTGTTCACATT 58.156 43.478 0.00 0.00 31.62 2.71
677 678 3.370527 GCCTACCACATACCTGTTCACAT 60.371 47.826 0.00 0.00 31.62 3.21
678 679 2.027561 GCCTACCACATACCTGTTCACA 60.028 50.000 0.00 0.00 31.62 3.58
679 680 2.629051 GCCTACCACATACCTGTTCAC 58.371 52.381 0.00 0.00 31.62 3.18
680 681 1.557832 GGCCTACCACATACCTGTTCA 59.442 52.381 0.00 0.00 31.62 3.18
681 682 1.134189 GGGCCTACCACATACCTGTTC 60.134 57.143 0.84 0.00 39.85 3.18
682 683 0.916809 GGGCCTACCACATACCTGTT 59.083 55.000 0.84 0.00 39.85 3.16
683 684 0.986550 GGGGCCTACCACATACCTGT 60.987 60.000 0.84 0.00 40.19 4.00
684 685 1.837090 GGGGCCTACCACATACCTG 59.163 63.158 0.84 0.00 40.19 4.00
685 686 4.413074 GGGGCCTACCACATACCT 57.587 61.111 0.84 0.00 40.19 3.08
761 762 1.442886 TTTTCACCCATCCCCTGCCT 61.443 55.000 0.00 0.00 0.00 4.75
1143 1473 1.765314 GTGGAGATGGATGGCTGTAGT 59.235 52.381 0.00 0.00 0.00 2.73
1185 1541 6.032094 TCGAAGAGGATAAACACGATTACAC 58.968 40.000 0.00 0.00 0.00 2.90
1186 1542 6.198650 TCGAAGAGGATAAACACGATTACA 57.801 37.500 0.00 0.00 0.00 2.41
1187 1543 6.086502 CGATCGAAGAGGATAAACACGATTAC 59.913 42.308 10.26 0.00 43.63 1.89
1188 1544 6.017687 TCGATCGAAGAGGATAAACACGATTA 60.018 38.462 16.99 0.00 43.63 1.75
1189 1545 4.976731 CGATCGAAGAGGATAAACACGATT 59.023 41.667 10.26 0.00 43.63 3.34
1190 1546 4.275196 TCGATCGAAGAGGATAAACACGAT 59.725 41.667 16.99 0.00 43.63 3.73
1405 1818 2.354805 GCCAATCAACTAGAAGGACGGT 60.355 50.000 0.00 0.00 0.00 4.83
1684 2122 8.756486 ATTAGTGGATGATGATTGATGAACAA 57.244 30.769 0.00 0.00 42.95 2.83
2948 3399 7.693969 ATGCAAAAGCTTGTTATTAGAGACT 57.306 32.000 0.00 0.00 34.79 3.24
3126 3578 7.979786 ACTTGGACCTATCAGATTCTCTAAA 57.020 36.000 0.00 0.00 0.00 1.85
3488 3941 7.331026 CCTATCACAGACTTCTCCACAAAATA 58.669 38.462 0.00 0.00 0.00 1.40
3612 4065 1.202651 CCACACTTCGACCACTTCCTT 60.203 52.381 0.00 0.00 0.00 3.36
3613 4066 0.393077 CCACACTTCGACCACTTCCT 59.607 55.000 0.00 0.00 0.00 3.36
3614 4067 0.602905 CCCACACTTCGACCACTTCC 60.603 60.000 0.00 0.00 0.00 3.46
3615 4068 0.391597 TCCCACACTTCGACCACTTC 59.608 55.000 0.00 0.00 0.00 3.01
3649 4106 4.586001 TGCACTCATAGCATCTGACATAGA 59.414 41.667 0.00 0.00 40.37 1.98
3846 4303 7.558807 TCACTCTCCATTTGATATTCAAGCATT 59.441 33.333 0.00 0.00 37.70 3.56
3927 4384 2.303890 TGCACTGAAGATGGACATCACT 59.696 45.455 14.16 1.37 40.22 3.41
4681 5140 3.696045 TCCAACATAAGGTTCCATGTGG 58.304 45.455 0.00 0.00 37.72 4.17
4895 5356 2.026641 AGATGTTGTATGCACCATGGC 58.973 47.619 13.04 0.00 27.46 4.40
5181 6215 2.049767 CGGGTTTATGTGGTGGGGC 61.050 63.158 0.00 0.00 0.00 5.80
5182 6216 1.379309 CCGGGTTTATGTGGTGGGG 60.379 63.158 0.00 0.00 0.00 4.96
5183 6217 2.049767 GCCGGGTTTATGTGGTGGG 61.050 63.158 2.18 0.00 0.00 4.61
5184 6218 0.896019 TTGCCGGGTTTATGTGGTGG 60.896 55.000 2.18 0.00 0.00 4.61
5310 6344 1.144057 CCCCATCGTCCTCTTTCGG 59.856 63.158 0.00 0.00 0.00 4.30
5326 6360 6.796705 AAAAATACCGTCATATCGATTCCC 57.203 37.500 1.71 0.00 0.00 3.97
5375 6409 7.581213 ATTGTGAAAACCAGTTCAGTAATGA 57.419 32.000 0.00 0.00 38.17 2.57
5486 6527 1.085091 AGCCACTACGTGTCGACTAG 58.915 55.000 17.92 12.48 0.00 2.57
5488 6529 1.170919 ACAGCCACTACGTGTCGACT 61.171 55.000 17.92 0.00 0.00 4.18
5491 6532 0.318360 TTCACAGCCACTACGTGTCG 60.318 55.000 0.00 0.00 32.42 4.35
5519 6560 0.765510 AGAGAGGGAAAGTTGCGGTT 59.234 50.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.