Multiple sequence alignment - TraesCS5A01G325900

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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 TraesCS5A01G325900 chr5A 100.000 4091 0 0 1 4091 536351303 536355393 0.000000e+00 7555.0
1 TraesCS5A01G325900 chr5A 85.714 483 50 8 3335 3798 536293214 536292732 3.670000e-135 492.0
2 TraesCS5A01G325900 chr5B 93.165 3058 178 16 862 3917 510509242 510512270 0.000000e+00 4460.0
3 TraesCS5A01G325900 chr5B 88.272 2234 211 24 1003 3211 510561528 510559321 0.000000e+00 2627.0
4 TraesCS5A01G325900 chr5B 91.195 477 41 1 3615 4091 510516753 510517228 0.000000e+00 647.0
5 TraesCS5A01G325900 chr5B 85.921 483 49 8 3335 3798 510401725 510401243 7.900000e-137 497.0
6 TraesCS5A01G325900 chr5B 84.536 485 52 12 3335 3798 510703784 510704266 3.730000e-125 459.0
7 TraesCS5A01G325900 chr5B 93.000 300 18 3 564 861 510563683 510563385 6.280000e-118 435.0
8 TraesCS5A01G325900 chr5B 96.667 240 8 0 620 859 510508672 510508911 2.290000e-107 399.0
9 TraesCS5A01G325900 chr5B 93.725 255 15 1 3338 3591 510516051 510516305 8.300000e-102 381.0
10 TraesCS5A01G325900 chr5B 95.489 133 5 1 392 523 510505760 510505892 1.150000e-50 211.0
11 TraesCS5A01G325900 chr5B 88.889 72 6 2 71 140 510505526 510505597 2.030000e-13 87.9
12 TraesCS5A01G325900 chr5D 88.770 2431 224 20 862 3265 422948477 422946069 0.000000e+00 2931.0
13 TraesCS5A01G325900 chr5D 84.536 485 52 13 3335 3798 423069602 423070084 3.730000e-125 459.0
14 TraesCS5A01G325900 chr5D 92.642 299 13 3 564 861 422949096 422948806 4.890000e-114 422.0
15 TraesCS5A01G325900 chr5D 96.903 226 7 0 3630 3855 422942282 422942057 2.980000e-101 379.0
16 TraesCS5A01G325900 chr5D 81.679 262 32 10 3846 4091 423071496 423071757 1.930000e-48 204.0
17 TraesCS5A01G325900 chr5D 92.188 128 9 1 3964 4091 422942278 422942404 3.250000e-41 180.0
18 TraesCS5A01G325900 chr5D 100.000 29 0 0 3791 3819 422942021 422941993 2.000000e-03 54.7
19 TraesCS5A01G325900 chr2D 72.427 1273 248 52 1274 2463 603209418 603210670 1.100000e-80 311.0
20 TraesCS5A01G325900 chr4A 72.793 1110 217 49 1275 2319 731408160 731409249 8.600000e-77 298.0
21 TraesCS5A01G325900 chr4A 83.761 117 8 2 165 270 310741279 310741163 2.600000e-17 100.0
22 TraesCS5A01G325900 chr7A 71.787 1276 257 52 1275 2467 9009389 9010644 2.420000e-67 267.0
23 TraesCS5A01G325900 chr7A 72.256 811 165 33 1770 2538 2828902 2829694 3.230000e-46 196.0
24 TraesCS5A01G325900 chr7A 71.921 755 154 31 1825 2538 2095006 2095743 2.530000e-37 167.0
25 TraesCS5A01G325900 chr7A 70.099 1311 288 67 1308 2539 3780717 3782002 1.970000e-33 154.0
26 TraesCS5A01G325900 chr7A 91.837 49 3 1 3800 3847 8787547 8787595 2.640000e-07 67.6
27 TraesCS5A01G325900 chr7A 92.857 42 2 1 3807 3847 2812378 2812419 4.420000e-05 60.2
28 TraesCS5A01G325900 chr7A 87.755 49 5 1 3800 3847 2079915 2079963 5.710000e-04 56.5
29 TraesCS5A01G325900 chr7D 71.376 814 166 44 1773 2539 2409915 2410708 2.550000e-32 150.0
30 TraesCS5A01G325900 chr7D 71.467 750 156 37 1830 2538 3857116 3856384 3.300000e-31 147.0
31 TraesCS5A01G325900 chr7D 73.318 431 83 19 2059 2463 3689283 3689707 3.320000e-26 130.0
32 TraesCS5A01G325900 chr7D 87.755 49 5 1 3800 3847 3824298 3824346 5.710000e-04 56.5
33 TraesCS5A01G325900 chr4D 85.345 116 6 4 165 269 19931255 19931140 4.320000e-20 110.0
34 TraesCS5A01G325900 chr4D 83.838 99 5 2 182 269 348380905 348381003 2.620000e-12 84.2
35 TraesCS5A01G325900 chrUn 84.483 116 7 2 165 269 421834939 421834824 2.010000e-18 104.0
36 TraesCS5A01G325900 chrUn 82.759 116 9 2 165 269 216515921 216516036 4.350000e-15 93.5
37 TraesCS5A01G325900 chrUn 82.759 116 9 2 165 269 286267462 286267347 4.350000e-15 93.5
38 TraesCS5A01G325900 chrUn 82.418 91 5 2 190 269 389361792 389361702 7.340000e-08 69.4
39 TraesCS5A01G325900 chr6B 91.667 72 6 0 166 237 261644157 261644228 2.600000e-17 100.0
40 TraesCS5A01G325900 chr6B 92.857 42 2 1 3807 3847 77782625 77782666 4.420000e-05 60.2
41 TraesCS5A01G325900 chr6D 82.759 116 9 2 165 269 135461763 135461878 4.350000e-15 93.5
42 TraesCS5A01G325900 chr6D 82.759 116 9 2 165 269 168257608 168257493 4.350000e-15 93.5
43 TraesCS5A01G325900 chr6A 92.857 42 2 1 3807 3847 45333594 45333635 4.420000e-05 60.2


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 TraesCS5A01G325900 chr5A 536351303 536355393 4090 False 7555.000000 7555 100.000000 1 4091 1 chr5A.!!$F1 4090
1 TraesCS5A01G325900 chr5B 510559321 510563683 4362 True 1531.000000 2627 90.636000 564 3211 2 chr5B.!!$R2 2647
2 TraesCS5A01G325900 chr5B 510505526 510517228 11702 False 1030.983333 4460 93.188333 71 4091 6 chr5B.!!$F2 4020
3 TraesCS5A01G325900 chr5D 422941993 422949096 7103 True 946.675000 2931 94.578750 564 3855 4 chr5D.!!$R1 3291
4 TraesCS5A01G325900 chr5D 423069602 423071757 2155 False 331.500000 459 83.107500 3335 4091 2 chr5D.!!$F2 756
5 TraesCS5A01G325900 chr2D 603209418 603210670 1252 False 311.000000 311 72.427000 1274 2463 1 chr2D.!!$F1 1189
6 TraesCS5A01G325900 chr4A 731408160 731409249 1089 False 298.000000 298 72.793000 1275 2319 1 chr4A.!!$F1 1044
7 TraesCS5A01G325900 chr7A 9009389 9010644 1255 False 267.000000 267 71.787000 1275 2467 1 chr7A.!!$F7 1192

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
269 271 0.250513 GGGCGCCATATTCTAGGAGG 59.749 60.0 30.85 0.0 0.00 4.30 F
271 273 0.250513 GCGCCATATTCTAGGAGGGG 59.749 60.0 0.00 0.0 35.61 4.79 F
336 338 0.320771 CTTGACACCTCTTGACCGGG 60.321 60.0 6.32 0.0 0.00 5.73 F
342 344 0.763223 ACCTCTTGACCGGGTGAACT 60.763 55.0 3.30 0.0 31.48 3.01 F
1063 5464 0.890683 AAAATGCCTCGAGCCAAAGG 59.109 50.0 6.99 0.0 42.71 3.11 F
2289 6764 0.394488 AAGTCATCGAGCTCCCGAGA 60.394 55.0 8.47 0.0 42.21 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 5717 0.321210 TGTACTGAATGGGCGTGGTG 60.321 55.000 0.00 0.0 0.00 4.17 R
1977 6443 0.392336 CTGGACTCATCCTAGCCTGC 59.608 60.000 0.00 0.0 46.43 4.85 R
1979 6445 1.133199 CCTCTGGACTCATCCTAGCCT 60.133 57.143 0.00 0.0 46.43 4.58 R
2013 6479 2.029290 GCCAAAGACTGTTAGAGACCGA 60.029 50.000 0.00 0.0 0.00 4.69 R
2748 7241 0.824109 AGGAGCGCACTATGCTTACA 59.176 50.000 11.47 0.0 44.18 2.41 R
3858 9747 0.253044 AACACTAGTGCCATGCGGAT 59.747 50.000 22.90 0.0 0.00 4.18 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
20 21 3.668596 GGTCAATCCGTAACCGATTTG 57.331 47.619 0.00 0.00 35.63 2.32
21 22 3.004862 GGTCAATCCGTAACCGATTTGT 58.995 45.455 0.00 0.00 35.63 2.83
22 23 4.183101 GGTCAATCCGTAACCGATTTGTA 58.817 43.478 0.00 0.00 35.63 2.41
23 24 4.812626 GGTCAATCCGTAACCGATTTGTAT 59.187 41.667 0.00 0.00 35.63 2.29
24 25 5.295045 GGTCAATCCGTAACCGATTTGTATT 59.705 40.000 0.00 0.00 35.63 1.89
25 26 6.479660 GGTCAATCCGTAACCGATTTGTATTA 59.520 38.462 0.00 0.00 35.63 0.98
26 27 7.172019 GGTCAATCCGTAACCGATTTGTATTAT 59.828 37.037 0.00 0.00 35.63 1.28
27 28 8.007716 GTCAATCCGTAACCGATTTGTATTATG 58.992 37.037 0.00 0.00 35.63 1.90
28 29 7.927092 TCAATCCGTAACCGATTTGTATTATGA 59.073 33.333 0.00 0.00 35.63 2.15
29 30 8.717821 CAATCCGTAACCGATTTGTATTATGAT 58.282 33.333 0.00 0.00 35.63 2.45
30 31 8.842358 ATCCGTAACCGATTTGTATTATGATT 57.158 30.769 0.00 0.00 35.63 2.57
31 32 8.665643 TCCGTAACCGATTTGTATTATGATTT 57.334 30.769 0.00 0.00 35.63 2.17
32 33 9.111613 TCCGTAACCGATTTGTATTATGATTTT 57.888 29.630 0.00 0.00 35.63 1.82
96 97 1.445582 GTCGTTAGGGTGCTGACGG 60.446 63.158 0.00 0.00 37.03 4.79
154 156 9.482627 AAAGTGACATTTACTTTGTTTTGACAA 57.517 25.926 0.00 0.00 44.29 3.18
165 167 8.141835 ACTTTGTTTTGACAATTTATCAAGCC 57.858 30.769 2.91 0.18 37.38 4.35
169 171 8.729805 TGTTTTGACAATTTATCAAGCCTTTT 57.270 26.923 2.91 0.00 37.38 2.27
170 172 8.610896 TGTTTTGACAATTTATCAAGCCTTTTG 58.389 29.630 2.91 0.00 37.38 2.44
171 173 7.727331 TTTGACAATTTATCAAGCCTTTTGG 57.273 32.000 2.91 0.00 37.38 3.28
172 174 6.418057 TGACAATTTATCAAGCCTTTTGGT 57.582 33.333 0.00 0.00 42.99 3.67
173 175 6.454795 TGACAATTTATCAAGCCTTTTGGTC 58.545 36.000 0.00 0.00 42.99 4.02
174 176 6.267471 TGACAATTTATCAAGCCTTTTGGTCT 59.733 34.615 0.00 0.00 42.99 3.85
175 177 7.066307 ACAATTTATCAAGCCTTTTGGTCTT 57.934 32.000 0.00 0.00 42.99 3.01
176 178 6.930722 ACAATTTATCAAGCCTTTTGGTCTTG 59.069 34.615 10.67 10.67 45.96 3.02
184 186 6.327934 CAAGCCTTTTGGTCTTGAATATCAG 58.672 40.000 11.16 0.00 46.73 2.90
185 187 5.819991 AGCCTTTTGGTCTTGAATATCAGA 58.180 37.500 0.00 0.00 42.99 3.27
186 188 6.248433 AGCCTTTTGGTCTTGAATATCAGAA 58.752 36.000 0.00 0.00 42.99 3.02
187 189 6.894103 AGCCTTTTGGTCTTGAATATCAGAAT 59.106 34.615 0.00 0.00 42.99 2.40
188 190 8.055181 AGCCTTTTGGTCTTGAATATCAGAATA 58.945 33.333 0.00 0.00 42.99 1.75
189 191 8.348507 GCCTTTTGGTCTTGAATATCAGAATAG 58.651 37.037 0.00 0.00 42.99 1.73
190 192 8.844244 CCTTTTGGTCTTGAATATCAGAATAGG 58.156 37.037 0.00 0.00 34.07 2.57
192 194 8.964476 TTTGGTCTTGAATATCAGAATAGGAC 57.036 34.615 0.00 0.00 0.00 3.85
194 196 8.089625 TGGTCTTGAATATCAGAATAGGACAA 57.910 34.615 0.00 0.00 0.00 3.18
195 197 8.548025 TGGTCTTGAATATCAGAATAGGACAAA 58.452 33.333 0.00 0.00 0.00 2.83
196 198 9.566432 GGTCTTGAATATCAGAATAGGACAAAT 57.434 33.333 0.00 0.00 0.00 2.32
201 203 9.342308 TGAATATCAGAATAGGACAAATGAACC 57.658 33.333 0.00 0.00 0.00 3.62
202 204 9.342308 GAATATCAGAATAGGACAAATGAACCA 57.658 33.333 0.00 0.00 0.00 3.67
203 205 8.915057 ATATCAGAATAGGACAAATGAACCAG 57.085 34.615 0.00 0.00 0.00 4.00
204 206 4.943705 TCAGAATAGGACAAATGAACCAGC 59.056 41.667 0.00 0.00 0.00 4.85
205 207 4.096984 CAGAATAGGACAAATGAACCAGCC 59.903 45.833 0.00 0.00 0.00 4.85
206 208 4.018050 AGAATAGGACAAATGAACCAGCCT 60.018 41.667 0.00 0.00 0.00 4.58
207 209 2.206576 AGGACAAATGAACCAGCCTC 57.793 50.000 0.00 0.00 0.00 4.70
209 211 0.804989 GACAAATGAACCAGCCTCCG 59.195 55.000 0.00 0.00 0.00 4.63
210 212 1.244019 ACAAATGAACCAGCCTCCGC 61.244 55.000 0.00 0.00 0.00 5.54
211 213 2.040544 AAATGAACCAGCCTCCGCG 61.041 57.895 0.00 0.00 41.18 6.46
212 214 2.748058 AAATGAACCAGCCTCCGCGT 62.748 55.000 4.92 0.00 41.18 6.01
213 215 1.895020 AATGAACCAGCCTCCGCGTA 61.895 55.000 4.92 0.00 41.18 4.42
215 217 1.038681 TGAACCAGCCTCCGCGTATA 61.039 55.000 4.92 0.00 41.18 1.47
216 218 0.317479 GAACCAGCCTCCGCGTATAT 59.683 55.000 4.92 0.00 41.18 0.86
217 219 0.317479 AACCAGCCTCCGCGTATATC 59.683 55.000 4.92 0.00 41.18 1.63
219 221 0.603569 CCAGCCTCCGCGTATATCTT 59.396 55.000 4.92 0.00 41.18 2.40
220 222 1.000955 CCAGCCTCCGCGTATATCTTT 59.999 52.381 4.92 0.00 41.18 2.52
221 223 2.230508 CCAGCCTCCGCGTATATCTTTA 59.769 50.000 4.92 0.00 41.18 1.85
222 224 3.243336 CAGCCTCCGCGTATATCTTTAC 58.757 50.000 4.92 0.00 41.18 2.01
224 226 3.573110 AGCCTCCGCGTATATCTTTACTT 59.427 43.478 4.92 0.00 41.18 2.24
225 227 3.919197 GCCTCCGCGTATATCTTTACTTC 59.081 47.826 4.92 0.00 0.00 3.01
226 228 4.156915 CCTCCGCGTATATCTTTACTTCG 58.843 47.826 4.92 0.00 0.00 3.79
227 229 4.151258 TCCGCGTATATCTTTACTTCGG 57.849 45.455 4.92 0.00 37.29 4.30
228 230 3.814842 TCCGCGTATATCTTTACTTCGGA 59.185 43.478 4.92 0.00 39.89 4.55
229 231 4.275689 TCCGCGTATATCTTTACTTCGGAA 59.724 41.667 4.92 0.00 39.57 4.30
235 237 7.633664 GCGTATATCTTTACTTCGGAACAAAAC 59.366 37.037 0.00 0.00 0.00 2.43
236 238 8.112449 CGTATATCTTTACTTCGGAACAAAACC 58.888 37.037 0.00 0.00 0.00 3.27
238 240 6.894339 ATCTTTACTTCGGAACAAAACCAT 57.106 33.333 0.00 0.00 0.00 3.55
239 241 6.067263 TCTTTACTTCGGAACAAAACCATG 57.933 37.500 0.00 0.00 0.00 3.66
240 242 5.823570 TCTTTACTTCGGAACAAAACCATGA 59.176 36.000 0.00 0.00 0.00 3.07
241 243 6.488683 TCTTTACTTCGGAACAAAACCATGAT 59.511 34.615 0.00 0.00 0.00 2.45
243 245 4.870363 ACTTCGGAACAAAACCATGATTG 58.130 39.130 0.00 0.00 0.00 2.67
244 246 4.340950 ACTTCGGAACAAAACCATGATTGT 59.659 37.500 0.00 0.00 41.31 2.71
245 247 4.497473 TCGGAACAAAACCATGATTGTC 57.503 40.909 10.55 6.17 38.75 3.18
246 248 3.254657 TCGGAACAAAACCATGATTGTCC 59.745 43.478 10.55 11.52 38.75 4.02
247 249 3.613910 CGGAACAAAACCATGATTGTCCC 60.614 47.826 10.55 7.69 38.75 4.46
248 250 3.323403 GGAACAAAACCATGATTGTCCCA 59.677 43.478 8.61 0.00 38.75 4.37
250 252 4.605640 ACAAAACCATGATTGTCCCAAG 57.394 40.909 0.00 0.00 34.84 3.61
252 254 2.236489 AACCATGATTGTCCCAAGGG 57.764 50.000 0.00 0.00 0.00 3.95
253 255 0.324645 ACCATGATTGTCCCAAGGGC 60.325 55.000 0.00 0.00 34.68 5.19
254 256 1.386525 CCATGATTGTCCCAAGGGCG 61.387 60.000 0.00 0.00 34.68 6.13
255 257 1.754234 ATGATTGTCCCAAGGGCGC 60.754 57.895 0.00 0.00 34.68 6.53
256 258 3.140814 GATTGTCCCAAGGGCGCC 61.141 66.667 21.18 21.18 34.68 6.53
258 260 3.301222 ATTGTCCCAAGGGCGCCAT 62.301 57.895 30.85 21.35 34.68 4.40
260 262 1.932156 TTGTCCCAAGGGCGCCATAT 61.932 55.000 30.85 10.95 34.68 1.78
261 263 1.152756 GTCCCAAGGGCGCCATATT 60.153 57.895 30.85 16.95 34.68 1.28
262 264 1.150536 TCCCAAGGGCGCCATATTC 59.849 57.895 30.85 10.59 34.68 1.75
263 265 1.151450 CCCAAGGGCGCCATATTCT 59.849 57.895 30.85 13.15 0.00 2.40
264 266 0.400213 CCCAAGGGCGCCATATTCTA 59.600 55.000 30.85 0.00 0.00 2.10
265 267 1.611673 CCCAAGGGCGCCATATTCTAG 60.612 57.143 30.85 10.35 0.00 2.43
266 268 1.611673 CCAAGGGCGCCATATTCTAGG 60.612 57.143 30.85 13.07 0.00 3.02
267 269 1.347707 CAAGGGCGCCATATTCTAGGA 59.652 52.381 30.85 0.00 0.00 2.94
268 270 1.270907 AGGGCGCCATATTCTAGGAG 58.729 55.000 30.85 0.00 0.00 3.69
269 271 0.250513 GGGCGCCATATTCTAGGAGG 59.749 60.000 30.85 0.00 0.00 4.30
270 272 0.250513 GGCGCCATATTCTAGGAGGG 59.749 60.000 24.80 0.00 0.00 4.30
271 273 0.250513 GCGCCATATTCTAGGAGGGG 59.749 60.000 0.00 0.00 35.61 4.79
272 274 1.938585 CGCCATATTCTAGGAGGGGA 58.061 55.000 0.00 0.00 34.56 4.81
273 275 1.827969 CGCCATATTCTAGGAGGGGAG 59.172 57.143 0.00 0.00 34.56 4.30
274 276 2.823535 CGCCATATTCTAGGAGGGGAGT 60.824 54.545 0.00 0.00 34.56 3.85
294 296 6.923508 GGGAGTTTTAGTCAATTGGAAAACAG 59.076 38.462 27.29 0.00 41.88 3.16
302 304 5.004922 TCAATTGGAAAACAGTTGACACC 57.995 39.130 5.42 0.00 46.73 4.16
303 305 4.464244 TCAATTGGAAAACAGTTGACACCA 59.536 37.500 5.42 0.00 46.73 4.17
304 306 3.859411 TTGGAAAACAGTTGACACCAC 57.141 42.857 0.00 0.00 0.00 4.16
305 307 2.796557 TGGAAAACAGTTGACACCACA 58.203 42.857 0.00 0.00 0.00 4.17
306 308 3.157881 TGGAAAACAGTTGACACCACAA 58.842 40.909 0.00 0.00 0.00 3.33
307 309 3.574396 TGGAAAACAGTTGACACCACAAA 59.426 39.130 0.00 0.00 0.00 2.83
308 310 4.039245 TGGAAAACAGTTGACACCACAAAA 59.961 37.500 0.00 0.00 0.00 2.44
309 311 4.991687 GGAAAACAGTTGACACCACAAAAA 59.008 37.500 0.00 0.00 0.00 1.94
332 334 4.965119 AAAACACTTGACACCTCTTGAC 57.035 40.909 0.00 0.00 0.00 3.18
333 335 2.622064 ACACTTGACACCTCTTGACC 57.378 50.000 0.00 0.00 0.00 4.02
334 336 1.202533 ACACTTGACACCTCTTGACCG 60.203 52.381 0.00 0.00 0.00 4.79
335 337 0.393077 ACTTGACACCTCTTGACCGG 59.607 55.000 0.00 0.00 0.00 5.28
336 338 0.320771 CTTGACACCTCTTGACCGGG 60.321 60.000 6.32 0.00 0.00 5.73
337 339 1.052124 TTGACACCTCTTGACCGGGT 61.052 55.000 6.32 0.00 0.00 5.28
340 342 4.306245 ACCTCTTGACCGGGTGAA 57.694 55.556 3.30 0.15 31.48 3.18
341 343 1.752833 ACCTCTTGACCGGGTGAAC 59.247 57.895 3.30 0.00 31.48 3.18
342 344 0.763223 ACCTCTTGACCGGGTGAACT 60.763 55.000 3.30 0.00 31.48 3.01
343 345 1.263356 CCTCTTGACCGGGTGAACTA 58.737 55.000 3.30 0.00 0.00 2.24
344 346 1.831736 CCTCTTGACCGGGTGAACTAT 59.168 52.381 3.30 0.00 0.00 2.12
345 347 2.418746 CCTCTTGACCGGGTGAACTATG 60.419 54.545 3.30 0.00 0.00 2.23
346 348 2.233922 CTCTTGACCGGGTGAACTATGT 59.766 50.000 3.30 0.00 0.00 2.29
347 349 3.433343 TCTTGACCGGGTGAACTATGTA 58.567 45.455 3.30 0.00 0.00 2.29
348 350 3.833650 TCTTGACCGGGTGAACTATGTAA 59.166 43.478 3.30 0.00 0.00 2.41
349 351 3.880047 TGACCGGGTGAACTATGTAAG 57.120 47.619 3.30 0.00 0.00 2.34
350 352 3.433343 TGACCGGGTGAACTATGTAAGA 58.567 45.455 3.30 0.00 0.00 2.10
351 353 3.833650 TGACCGGGTGAACTATGTAAGAA 59.166 43.478 3.30 0.00 0.00 2.52
352 354 4.468510 TGACCGGGTGAACTATGTAAGAAT 59.531 41.667 3.30 0.00 0.00 2.40
353 355 5.046159 TGACCGGGTGAACTATGTAAGAATT 60.046 40.000 3.30 0.00 0.00 2.17
354 356 5.812286 ACCGGGTGAACTATGTAAGAATTT 58.188 37.500 6.32 0.00 0.00 1.82
355 357 6.243148 ACCGGGTGAACTATGTAAGAATTTT 58.757 36.000 6.32 0.00 0.00 1.82
356 358 6.717997 ACCGGGTGAACTATGTAAGAATTTTT 59.282 34.615 6.32 0.00 0.00 1.94
386 388 4.740902 ACTTTTATTCCAAAGTCCTGCCT 58.259 39.130 0.00 0.00 42.25 4.75
387 389 5.147767 ACTTTTATTCCAAAGTCCTGCCTT 58.852 37.500 0.00 0.00 42.25 4.35
388 390 5.011023 ACTTTTATTCCAAAGTCCTGCCTTG 59.989 40.000 0.00 0.00 42.25 3.61
389 391 2.978156 ATTCCAAAGTCCTGCCTTGA 57.022 45.000 0.00 0.00 0.00 3.02
390 392 2.978156 TTCCAAAGTCCTGCCTTGAT 57.022 45.000 0.00 0.00 0.00 2.57
395 397 4.534500 TCCAAAGTCCTGCCTTGATAACTA 59.466 41.667 0.00 0.00 0.00 2.24
455 458 3.933048 CTGTCAGCAAGCCCCTGGG 62.933 68.421 5.50 5.50 38.57 4.45
538 564 5.012328 AGTACATACACCAGAGCTTAAGC 57.988 43.478 20.09 20.09 42.49 3.09
539 565 3.981071 ACATACACCAGAGCTTAAGCA 57.019 42.857 28.39 6.27 45.16 3.91
541 567 2.762535 TACACCAGAGCTTAAGCACC 57.237 50.000 28.39 18.92 45.16 5.01
545 3011 1.639298 CCAGAGCTTAAGCACCGCAC 61.639 60.000 28.39 12.12 45.16 5.34
640 3326 1.178276 TTGTGGCCACGACTTTTGTT 58.822 45.000 30.07 0.00 0.00 2.83
661 3347 1.139734 TCGGATCGCACTGAAGCTC 59.860 57.895 0.00 0.00 0.00 4.09
786 3472 4.753877 CGACCGTCGCTCGAGCAA 62.754 66.667 34.69 17.41 42.86 3.91
968 3982 4.025401 GGACAAAGGCGCGGTGTG 62.025 66.667 8.83 5.57 0.00 3.82
976 3990 3.712881 GCGCGGTGTGTGTTCTCC 61.713 66.667 8.83 0.00 0.00 3.71
1031 5432 1.452833 GGGATGCCAGGAAGCTCAC 60.453 63.158 0.00 0.00 0.00 3.51
1057 5458 2.015736 TCTCAGAAAATGCCTCGAGC 57.984 50.000 6.99 3.23 44.14 5.03
1063 5464 0.890683 AAAATGCCTCGAGCCAAAGG 59.109 50.000 6.99 0.00 42.71 3.11
1076 5477 1.580059 CCAAAGGGGTGAGCCTACTA 58.420 55.000 0.00 0.00 34.45 1.82
1086 5487 3.322541 GGTGAGCCTACTAGAGAAATCCC 59.677 52.174 0.00 0.00 0.00 3.85
1088 5489 4.651962 GTGAGCCTACTAGAGAAATCCCTT 59.348 45.833 0.00 0.00 0.00 3.95
1089 5490 5.129650 GTGAGCCTACTAGAGAAATCCCTTT 59.870 44.000 0.00 0.00 0.00 3.11
1090 5491 5.726793 TGAGCCTACTAGAGAAATCCCTTTT 59.273 40.000 0.00 0.00 0.00 2.27
1091 5492 6.127026 TGAGCCTACTAGAGAAATCCCTTTTC 60.127 42.308 0.00 0.00 43.45 2.29
1165 5583 4.563580 GGATGTCCTCTGCTGACTTGTTAA 60.564 45.833 0.00 0.00 33.83 2.01
1168 5586 4.756642 TGTCCTCTGCTGACTTGTTAATTG 59.243 41.667 0.00 0.00 33.83 2.32
1169 5587 4.757149 GTCCTCTGCTGACTTGTTAATTGT 59.243 41.667 0.00 0.00 0.00 2.71
1170 5588 5.239525 GTCCTCTGCTGACTTGTTAATTGTT 59.760 40.000 0.00 0.00 0.00 2.83
1171 5589 6.426937 GTCCTCTGCTGACTTGTTAATTGTTA 59.573 38.462 0.00 0.00 0.00 2.41
1172 5590 7.119846 GTCCTCTGCTGACTTGTTAATTGTTAT 59.880 37.037 0.00 0.00 0.00 1.89
1176 5594 8.296713 TCTGCTGACTTGTTAATTGTTATTTCC 58.703 33.333 0.00 0.00 0.00 3.13
1177 5595 7.081349 TGCTGACTTGTTAATTGTTATTTCCG 58.919 34.615 0.00 0.00 0.00 4.30
1179 5597 7.593644 GCTGACTTGTTAATTGTTATTTCCGTT 59.406 33.333 0.00 0.00 0.00 4.44
1180 5598 9.113876 CTGACTTGTTAATTGTTATTTCCGTTC 57.886 33.333 0.00 0.00 0.00 3.95
1195 5613 1.669795 CCGTTCTTTGATTTGCCCTGC 60.670 52.381 0.00 0.00 0.00 4.85
1556 5989 3.677648 GTGGGCAAGGCTGTGCAG 61.678 66.667 18.66 0.00 46.81 4.41
1630 6063 2.511373 TTCGCCACAGCTATGCCG 60.511 61.111 0.00 0.00 36.60 5.69
1674 6107 6.528321 CAAGACATTCTTGCTATATCTGGGA 58.472 40.000 3.07 0.00 46.03 4.37
1701 6134 2.885113 CGTGATCGCCCAGTGAGA 59.115 61.111 0.00 0.00 0.00 3.27
1786 6234 3.664107 ACGTGCTATTTCAAGAAGCTGA 58.336 40.909 0.00 0.00 37.16 4.26
1816 6264 5.702670 CACAGTATCATTCGGCCTATTGATT 59.297 40.000 16.96 1.45 31.59 2.57
1817 6265 5.702670 ACAGTATCATTCGGCCTATTGATTG 59.297 40.000 16.96 13.24 31.59 2.67
1878 6335 3.553715 GCATGATGCTCGAGTTCATCCTA 60.554 47.826 22.35 10.94 40.96 2.94
1971 6437 3.693085 GGCTTTCTCTGCATCATGAAAGA 59.307 43.478 22.99 2.72 44.58 2.52
1974 6440 3.908643 TCTCTGCATCATGAAAGAGCT 57.091 42.857 20.60 0.00 36.84 4.09
1977 6443 1.676529 CTGCATCATGAAAGAGCTGGG 59.323 52.381 0.00 0.00 0.00 4.45
1979 6445 1.758936 CATCATGAAAGAGCTGGGCA 58.241 50.000 0.00 0.00 0.00 5.36
1994 6460 1.751563 GGCAGGCTAGGATGAGTCC 59.248 63.158 0.00 0.00 45.45 3.85
2013 6479 4.354087 AGTCCAGAGGATTTACCCTTTGTT 59.646 41.667 0.00 0.00 36.88 2.83
2148 6617 6.587206 CATCTCAGAGAGATATGCAACCTA 57.413 41.667 6.24 0.00 46.25 3.08
2283 6758 3.004839 TGCCTATACAAGTCATCGAGCTC 59.995 47.826 2.73 2.73 0.00 4.09
2287 6762 0.965866 ACAAGTCATCGAGCTCCCGA 60.966 55.000 8.47 3.70 43.16 5.14
2289 6764 0.394488 AAGTCATCGAGCTCCCGAGA 60.394 55.000 8.47 0.00 42.21 4.04
2705 7198 1.214062 CTGGTCTCACCGAGCTGTC 59.786 63.158 0.00 0.00 42.58 3.51
2706 7199 1.228583 TGGTCTCACCGAGCTGTCT 60.229 57.895 0.00 0.00 42.58 3.41
2721 7214 0.537188 TGTCTCTTTCATCCCTCGGC 59.463 55.000 0.00 0.00 0.00 5.54
2748 7241 2.105477 CACTGGGGATATACTTGCTGCT 59.895 50.000 0.00 0.00 0.00 4.24
2749 7242 2.105477 ACTGGGGATATACTTGCTGCTG 59.895 50.000 0.00 0.00 0.00 4.41
2838 7331 4.907875 AGAAAGGGGCAGCTCAATATACTA 59.092 41.667 0.00 0.00 0.00 1.82
2892 7385 5.303333 GGAAGACCTAGAAATCGAAGAGGAT 59.697 44.000 8.03 0.00 43.63 3.24
2907 7400 1.154225 GGATGCGCTTCCGTGTTTG 60.154 57.895 24.65 0.00 36.67 2.93
2927 7420 1.675720 GAGTCCCTCCAGCTGCTCTC 61.676 65.000 8.66 5.39 0.00 3.20
2964 7457 4.020662 GGTTTTGGTGGCATAAGAATGGAA 60.021 41.667 0.00 0.00 33.38 3.53
3048 7541 2.362077 GTGGGAAGAAGCAGCAAAGAAA 59.638 45.455 0.00 0.00 0.00 2.52
3161 7664 1.078143 CCTGCAACACTAGCTCCCC 60.078 63.158 0.00 0.00 0.00 4.81
3213 7716 1.741032 GAGCTGAGCAGACTGTGGC 60.741 63.158 7.39 3.98 0.00 5.01
3214 7717 2.031616 GCTGAGCAGACTGTGGCA 59.968 61.111 0.00 0.00 0.00 4.92
3342 7845 2.494059 GCCTTCTATTTCGGCAGCATA 58.506 47.619 0.00 0.00 43.25 3.14
3452 7955 2.172505 CTCTGGGCTCTCTACTCTCAGA 59.827 54.545 0.00 0.00 0.00 3.27
3524 8027 0.592247 GTTGTGGTTCGCAGTGCTTG 60.592 55.000 14.33 0.00 0.00 4.01
3531 8035 0.662619 TTCGCAGTGCTTGAAAGTGG 59.337 50.000 14.33 0.00 0.00 4.00
3533 8037 1.789078 CGCAGTGCTTGAAAGTGGCT 61.789 55.000 14.33 0.00 0.00 4.75
3570 8074 0.790993 AGTACCTCCCCCACTTCTCA 59.209 55.000 0.00 0.00 0.00 3.27
3581 8085 3.490348 CCCACTTCTCAAGGTGTTTGAT 58.510 45.455 0.00 0.00 44.48 2.57
3729 8251 4.409718 TCCTTGTATTTGCATACGGCTA 57.590 40.909 0.00 0.00 45.15 3.93
3780 8302 4.937620 TGGGATTCTGAATTCTCAACTTCG 59.062 41.667 8.51 0.00 0.00 3.79
3785 8307 6.530913 TTCTGAATTCTCAACTTCGTGAAG 57.469 37.500 7.05 8.04 43.79 3.02
3834 8375 2.416680 AATCTCTGGAAGCTCAAGCC 57.583 50.000 0.00 0.00 43.38 4.35
3858 9747 0.187117 TCAATGCCCTGGTGGTTTCA 59.813 50.000 0.00 0.00 36.04 2.69
3959 16125 9.214957 TGTTTTGACTATGTATTGTCTGTAAGG 57.785 33.333 7.70 0.00 34.39 2.69
3980 16146 2.925563 GCCTGTTTTGCAATATGTGAGC 59.074 45.455 0.00 0.00 0.00 4.26
4030 16197 8.631480 GGACTGTTCCTTTTAATCCTTTTCTA 57.369 34.615 0.00 0.00 39.13 2.10
4080 16250 9.524106 AAAGAGTAAAGAAAATTGGTTTAACCG 57.476 29.630 9.77 0.00 42.58 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.004862 ACAAATCGGTTACGGATTGACC 58.995 45.455 16.78 0.00 41.39 4.02
1 2 5.978934 ATACAAATCGGTTACGGATTGAC 57.021 39.130 16.78 0.00 41.39 3.18
2 3 7.927092 TCATAATACAAATCGGTTACGGATTGA 59.073 33.333 16.78 7.10 41.39 2.57
3 4 8.078959 TCATAATACAAATCGGTTACGGATTG 57.921 34.615 16.78 13.29 41.39 2.67
6 7 8.665643 AAATCATAATACAAATCGGTTACGGA 57.334 30.769 0.00 0.00 41.39 4.69
72 73 2.158726 TCAGCACCCTAACGACCTTTTT 60.159 45.455 0.00 0.00 0.00 1.94
73 74 1.418637 TCAGCACCCTAACGACCTTTT 59.581 47.619 0.00 0.00 0.00 2.27
74 75 1.053424 TCAGCACCCTAACGACCTTT 58.947 50.000 0.00 0.00 0.00 3.11
75 76 0.320697 GTCAGCACCCTAACGACCTT 59.679 55.000 0.00 0.00 0.00 3.50
76 77 1.874345 CGTCAGCACCCTAACGACCT 61.874 60.000 0.00 0.00 37.31 3.85
79 80 2.967397 CCGTCAGCACCCTAACGA 59.033 61.111 0.00 0.00 37.31 3.85
96 97 2.057137 TGGACCCAAATATCTGCTGC 57.943 50.000 0.00 0.00 0.00 5.25
105 107 7.552050 TTGATAGAATTGTTTGGACCCAAAT 57.448 32.000 16.27 1.68 45.90 2.32
144 146 8.610896 CAAAAGGCTTGATAAATTGTCAAAACA 58.389 29.630 0.00 0.00 35.36 2.83
145 147 8.069574 CCAAAAGGCTTGATAAATTGTCAAAAC 58.930 33.333 0.00 3.08 35.36 2.43
146 148 7.772757 ACCAAAAGGCTTGATAAATTGTCAAAA 59.227 29.630 0.00 0.00 35.36 2.44
147 149 7.278875 ACCAAAAGGCTTGATAAATTGTCAAA 58.721 30.769 0.00 0.00 35.36 2.69
150 152 6.691508 AGACCAAAAGGCTTGATAAATTGTC 58.308 36.000 0.00 1.83 0.00 3.18
151 153 6.670695 AGACCAAAAGGCTTGATAAATTGT 57.329 33.333 0.00 0.00 0.00 2.71
152 154 7.153985 TCAAGACCAAAAGGCTTGATAAATTG 58.846 34.615 6.88 0.00 42.03 2.32
153 155 7.301868 TCAAGACCAAAAGGCTTGATAAATT 57.698 32.000 6.88 0.00 42.03 1.82
154 156 6.916360 TCAAGACCAAAAGGCTTGATAAAT 57.084 33.333 6.88 0.00 42.03 1.40
157 159 7.833682 TGATATTCAAGACCAAAAGGCTTGATA 59.166 33.333 11.56 7.18 45.06 2.15
158 160 6.664816 TGATATTCAAGACCAAAAGGCTTGAT 59.335 34.615 11.56 5.43 45.06 2.57
160 162 6.151648 TCTGATATTCAAGACCAAAAGGCTTG 59.848 38.462 0.00 1.71 40.16 4.01
161 163 6.248433 TCTGATATTCAAGACCAAAAGGCTT 58.752 36.000 0.00 0.00 0.00 4.35
162 164 5.819991 TCTGATATTCAAGACCAAAAGGCT 58.180 37.500 0.00 0.00 0.00 4.58
163 165 6.515272 TTCTGATATTCAAGACCAAAAGGC 57.485 37.500 0.00 0.00 0.00 4.35
164 166 8.844244 CCTATTCTGATATTCAAGACCAAAAGG 58.156 37.037 0.00 0.00 0.00 3.11
165 167 9.618890 TCCTATTCTGATATTCAAGACCAAAAG 57.381 33.333 0.00 0.00 0.00 2.27
169 171 7.675161 TGTCCTATTCTGATATTCAAGACCA 57.325 36.000 0.00 0.00 0.00 4.02
170 172 8.964476 TTTGTCCTATTCTGATATTCAAGACC 57.036 34.615 0.00 0.00 0.00 3.85
175 177 9.342308 GGTTCATTTGTCCTATTCTGATATTCA 57.658 33.333 0.00 0.00 0.00 2.57
176 178 9.342308 TGGTTCATTTGTCCTATTCTGATATTC 57.658 33.333 0.00 0.00 0.00 1.75
178 180 7.446625 GCTGGTTCATTTGTCCTATTCTGATAT 59.553 37.037 0.00 0.00 0.00 1.63
179 181 6.767902 GCTGGTTCATTTGTCCTATTCTGATA 59.232 38.462 0.00 0.00 0.00 2.15
180 182 5.591877 GCTGGTTCATTTGTCCTATTCTGAT 59.408 40.000 0.00 0.00 0.00 2.90
181 183 4.943705 GCTGGTTCATTTGTCCTATTCTGA 59.056 41.667 0.00 0.00 0.00 3.27
184 186 4.273318 AGGCTGGTTCATTTGTCCTATTC 58.727 43.478 0.00 0.00 0.00 1.75
185 187 4.273318 GAGGCTGGTTCATTTGTCCTATT 58.727 43.478 0.00 0.00 0.00 1.73
186 188 3.372025 GGAGGCTGGTTCATTTGTCCTAT 60.372 47.826 0.00 0.00 0.00 2.57
187 189 2.026262 GGAGGCTGGTTCATTTGTCCTA 60.026 50.000 0.00 0.00 0.00 2.94
188 190 1.272147 GGAGGCTGGTTCATTTGTCCT 60.272 52.381 0.00 0.00 0.00 3.85
189 191 1.177401 GGAGGCTGGTTCATTTGTCC 58.823 55.000 0.00 0.00 0.00 4.02
190 192 0.804989 CGGAGGCTGGTTCATTTGTC 59.195 55.000 0.00 0.00 0.00 3.18
192 194 1.508088 GCGGAGGCTGGTTCATTTG 59.492 57.895 0.00 0.00 35.83 2.32
194 196 1.895020 TACGCGGAGGCTGGTTCATT 61.895 55.000 12.47 0.00 36.88 2.57
195 197 1.686325 ATACGCGGAGGCTGGTTCAT 61.686 55.000 12.47 0.00 36.88 2.57
196 198 1.038681 TATACGCGGAGGCTGGTTCA 61.039 55.000 12.47 0.00 36.88 3.18
197 199 0.317479 ATATACGCGGAGGCTGGTTC 59.683 55.000 12.47 0.00 36.88 3.62
198 200 0.317479 GATATACGCGGAGGCTGGTT 59.683 55.000 12.47 0.00 36.88 3.67
199 201 0.539901 AGATATACGCGGAGGCTGGT 60.540 55.000 12.47 0.00 36.88 4.00
200 202 0.603569 AAGATATACGCGGAGGCTGG 59.396 55.000 12.47 0.00 36.88 4.85
201 203 2.440539 AAAGATATACGCGGAGGCTG 57.559 50.000 12.47 0.00 36.88 4.85
202 204 3.155501 AGTAAAGATATACGCGGAGGCT 58.844 45.455 12.47 0.00 36.88 4.58
203 205 3.572604 AGTAAAGATATACGCGGAGGC 57.427 47.619 12.47 0.00 0.00 4.70
204 206 4.156915 CGAAGTAAAGATATACGCGGAGG 58.843 47.826 12.47 0.00 0.00 4.30
205 207 4.083643 TCCGAAGTAAAGATATACGCGGAG 60.084 45.833 12.47 0.00 44.65 4.63
206 208 3.814842 TCCGAAGTAAAGATATACGCGGA 59.185 43.478 12.47 0.00 45.91 5.54
207 209 4.151258 TCCGAAGTAAAGATATACGCGG 57.849 45.455 12.47 12.41 43.55 6.46
209 211 6.817270 TTGTTCCGAAGTAAAGATATACGC 57.183 37.500 0.00 0.00 0.00 4.42
210 212 8.112449 GGTTTTGTTCCGAAGTAAAGATATACG 58.888 37.037 0.00 0.00 0.00 3.06
211 213 8.938906 TGGTTTTGTTCCGAAGTAAAGATATAC 58.061 33.333 0.00 0.00 0.00 1.47
212 214 9.675464 ATGGTTTTGTTCCGAAGTAAAGATATA 57.325 29.630 0.00 0.00 0.00 0.86
213 215 7.989416 TGGTTTTGTTCCGAAGTAAAGATAT 57.011 32.000 0.00 0.00 0.00 1.63
215 217 6.488683 TCATGGTTTTGTTCCGAAGTAAAGAT 59.511 34.615 0.00 0.00 0.00 2.40
216 218 5.823570 TCATGGTTTTGTTCCGAAGTAAAGA 59.176 36.000 0.00 0.00 0.00 2.52
217 219 6.067263 TCATGGTTTTGTTCCGAAGTAAAG 57.933 37.500 0.00 0.00 0.00 1.85
219 221 6.039941 ACAATCATGGTTTTGTTCCGAAGTAA 59.960 34.615 0.00 0.00 32.28 2.24
220 222 5.533154 ACAATCATGGTTTTGTTCCGAAGTA 59.467 36.000 0.00 0.00 32.28 2.24
221 223 4.340950 ACAATCATGGTTTTGTTCCGAAGT 59.659 37.500 0.00 0.00 32.28 3.01
222 224 4.870363 ACAATCATGGTTTTGTTCCGAAG 58.130 39.130 0.00 0.00 32.28 3.79
224 226 3.254657 GGACAATCATGGTTTTGTTCCGA 59.745 43.478 9.81 0.00 36.25 4.55
225 227 3.574614 GGACAATCATGGTTTTGTTCCG 58.425 45.455 9.81 0.00 36.25 4.30
226 228 3.925379 GGGACAATCATGGTTTTGTTCC 58.075 45.455 14.65 14.65 42.67 3.62
227 229 4.599047 TGGGACAATCATGGTTTTGTTC 57.401 40.909 9.81 8.27 36.25 3.18
239 241 3.808692 TATGGCGCCCTTGGGACAATC 62.809 57.143 26.77 0.00 46.73 2.67
240 242 1.932156 TATGGCGCCCTTGGGACAAT 61.932 55.000 26.77 9.84 46.73 2.71
241 243 1.932156 ATATGGCGCCCTTGGGACAA 61.932 55.000 26.77 0.73 46.73 3.18
243 245 1.152756 AATATGGCGCCCTTGGGAC 60.153 57.895 26.77 0.00 0.00 4.46
244 246 1.150536 GAATATGGCGCCCTTGGGA 59.849 57.895 26.77 3.54 0.00 4.37
245 247 0.400213 TAGAATATGGCGCCCTTGGG 59.600 55.000 26.77 0.32 0.00 4.12
246 248 1.611673 CCTAGAATATGGCGCCCTTGG 60.612 57.143 26.77 18.94 0.00 3.61
247 249 1.347707 TCCTAGAATATGGCGCCCTTG 59.652 52.381 26.77 13.75 0.00 3.61
248 250 1.625818 CTCCTAGAATATGGCGCCCTT 59.374 52.381 26.77 15.12 0.00 3.95
250 252 0.250513 CCTCCTAGAATATGGCGCCC 59.749 60.000 26.77 7.94 0.00 6.13
252 254 0.250513 CCCCTCCTAGAATATGGCGC 59.749 60.000 0.00 0.00 0.00 6.53
253 255 1.827969 CTCCCCTCCTAGAATATGGCG 59.172 57.143 0.00 0.00 0.00 5.69
254 256 2.909217 ACTCCCCTCCTAGAATATGGC 58.091 52.381 0.00 0.00 0.00 4.40
255 257 5.913946 AAAACTCCCCTCCTAGAATATGG 57.086 43.478 0.00 0.00 0.00 2.74
256 258 7.290248 TGACTAAAACTCCCCTCCTAGAATATG 59.710 40.741 0.00 0.00 0.00 1.78
258 260 6.748969 TGACTAAAACTCCCCTCCTAGAATA 58.251 40.000 0.00 0.00 0.00 1.75
260 262 5.019657 TGACTAAAACTCCCCTCCTAGAA 57.980 43.478 0.00 0.00 0.00 2.10
261 263 4.687262 TGACTAAAACTCCCCTCCTAGA 57.313 45.455 0.00 0.00 0.00 2.43
262 264 5.959583 ATTGACTAAAACTCCCCTCCTAG 57.040 43.478 0.00 0.00 0.00 3.02
263 265 5.045140 CCAATTGACTAAAACTCCCCTCCTA 60.045 44.000 7.12 0.00 0.00 2.94
264 266 4.263949 CCAATTGACTAAAACTCCCCTCCT 60.264 45.833 7.12 0.00 0.00 3.69
265 267 4.017126 CCAATTGACTAAAACTCCCCTCC 58.983 47.826 7.12 0.00 0.00 4.30
266 268 4.918588 TCCAATTGACTAAAACTCCCCTC 58.081 43.478 7.12 0.00 0.00 4.30
267 269 5.333566 TTCCAATTGACTAAAACTCCCCT 57.666 39.130 7.12 0.00 0.00 4.79
268 270 6.183360 TGTTTTCCAATTGACTAAAACTCCCC 60.183 38.462 26.26 12.99 40.67 4.81
269 271 6.811954 TGTTTTCCAATTGACTAAAACTCCC 58.188 36.000 26.26 13.21 40.67 4.30
270 272 7.489160 ACTGTTTTCCAATTGACTAAAACTCC 58.511 34.615 26.26 13.42 40.67 3.85
271 273 8.807581 CAACTGTTTTCCAATTGACTAAAACTC 58.192 33.333 26.26 13.85 40.67 3.01
272 274 8.527810 TCAACTGTTTTCCAATTGACTAAAACT 58.472 29.630 26.26 15.29 40.67 2.66
273 275 8.592155 GTCAACTGTTTTCCAATTGACTAAAAC 58.408 33.333 23.00 23.00 43.68 2.43
274 276 8.307483 TGTCAACTGTTTTCCAATTGACTAAAA 58.693 29.630 15.02 7.94 46.00 1.52
310 312 4.157840 GGTCAAGAGGTGTCAAGTGTTTTT 59.842 41.667 0.00 0.00 0.00 1.94
311 313 3.694566 GGTCAAGAGGTGTCAAGTGTTTT 59.305 43.478 0.00 0.00 0.00 2.43
312 314 3.279434 GGTCAAGAGGTGTCAAGTGTTT 58.721 45.455 0.00 0.00 0.00 2.83
313 315 2.741878 CGGTCAAGAGGTGTCAAGTGTT 60.742 50.000 0.00 0.00 0.00 3.32
314 316 1.202533 CGGTCAAGAGGTGTCAAGTGT 60.203 52.381 0.00 0.00 0.00 3.55
315 317 1.502231 CGGTCAAGAGGTGTCAAGTG 58.498 55.000 0.00 0.00 0.00 3.16
316 318 0.393077 CCGGTCAAGAGGTGTCAAGT 59.607 55.000 0.00 0.00 0.00 3.16
317 319 0.320771 CCCGGTCAAGAGGTGTCAAG 60.321 60.000 0.00 0.00 0.00 3.02
318 320 1.052124 ACCCGGTCAAGAGGTGTCAA 61.052 55.000 0.00 0.00 30.97 3.18
319 321 1.458777 ACCCGGTCAAGAGGTGTCA 60.459 57.895 0.00 0.00 30.97 3.58
320 322 1.004918 CACCCGGTCAAGAGGTGTC 60.005 63.158 0.00 0.00 44.95 3.67
321 323 3.148084 CACCCGGTCAAGAGGTGT 58.852 61.111 0.00 0.00 44.95 4.16
323 325 0.763223 AGTTCACCCGGTCAAGAGGT 60.763 55.000 0.00 0.00 0.00 3.85
324 326 1.263356 TAGTTCACCCGGTCAAGAGG 58.737 55.000 0.00 0.00 0.00 3.69
325 327 2.233922 ACATAGTTCACCCGGTCAAGAG 59.766 50.000 0.00 0.00 0.00 2.85
326 328 2.253610 ACATAGTTCACCCGGTCAAGA 58.746 47.619 0.00 0.00 0.00 3.02
327 329 2.762535 ACATAGTTCACCCGGTCAAG 57.237 50.000 0.00 0.00 0.00 3.02
328 330 3.833650 TCTTACATAGTTCACCCGGTCAA 59.166 43.478 0.00 0.00 0.00 3.18
329 331 3.433343 TCTTACATAGTTCACCCGGTCA 58.567 45.455 0.00 0.00 0.00 4.02
330 332 4.460948 TTCTTACATAGTTCACCCGGTC 57.539 45.455 0.00 0.00 0.00 4.79
331 333 5.431179 AATTCTTACATAGTTCACCCGGT 57.569 39.130 0.00 0.00 0.00 5.28
332 334 6.753107 AAAATTCTTACATAGTTCACCCGG 57.247 37.500 0.00 0.00 0.00 5.73
365 367 5.243730 TCAAGGCAGGACTTTGGAATAAAAG 59.756 40.000 0.00 0.00 41.91 2.27
366 368 5.144100 TCAAGGCAGGACTTTGGAATAAAA 58.856 37.500 0.00 0.00 0.00 1.52
367 369 4.735369 TCAAGGCAGGACTTTGGAATAAA 58.265 39.130 0.00 0.00 0.00 1.40
368 370 4.380843 TCAAGGCAGGACTTTGGAATAA 57.619 40.909 0.00 0.00 0.00 1.40
369 371 4.591321 ATCAAGGCAGGACTTTGGAATA 57.409 40.909 0.00 0.00 0.00 1.75
370 372 2.978156 TCAAGGCAGGACTTTGGAAT 57.022 45.000 0.00 0.00 0.00 3.01
371 373 2.978156 ATCAAGGCAGGACTTTGGAA 57.022 45.000 0.00 0.00 0.00 3.53
372 374 3.330701 AGTTATCAAGGCAGGACTTTGGA 59.669 43.478 0.00 0.00 0.00 3.53
373 375 3.690460 AGTTATCAAGGCAGGACTTTGG 58.310 45.455 0.00 0.00 0.00 3.28
374 376 5.220931 GCATAGTTATCAAGGCAGGACTTTG 60.221 44.000 0.00 0.00 0.00 2.77
375 377 4.884164 GCATAGTTATCAAGGCAGGACTTT 59.116 41.667 0.00 0.00 0.00 2.66
376 378 4.080356 TGCATAGTTATCAAGGCAGGACTT 60.080 41.667 0.00 0.00 0.00 3.01
377 379 3.455910 TGCATAGTTATCAAGGCAGGACT 59.544 43.478 0.00 0.00 0.00 3.85
378 380 3.808728 TGCATAGTTATCAAGGCAGGAC 58.191 45.455 0.00 0.00 0.00 3.85
379 381 4.164030 TCTTGCATAGTTATCAAGGCAGGA 59.836 41.667 0.00 0.00 38.13 3.86
380 382 4.454678 TCTTGCATAGTTATCAAGGCAGG 58.545 43.478 0.00 0.00 38.13 4.85
381 383 6.630444 ATTCTTGCATAGTTATCAAGGCAG 57.370 37.500 0.00 0.00 38.13 4.85
382 384 8.405531 GTTAATTCTTGCATAGTTATCAAGGCA 58.594 33.333 0.00 0.00 38.13 4.75
383 385 7.862873 GGTTAATTCTTGCATAGTTATCAAGGC 59.137 37.037 0.00 0.00 38.13 4.35
384 386 8.070171 CGGTTAATTCTTGCATAGTTATCAAGG 58.930 37.037 0.00 0.00 38.13 3.61
385 387 8.070171 CCGGTTAATTCTTGCATAGTTATCAAG 58.930 37.037 0.00 0.00 38.73 3.02
386 388 7.771361 TCCGGTTAATTCTTGCATAGTTATCAA 59.229 33.333 0.00 0.00 0.00 2.57
387 389 7.276658 TCCGGTTAATTCTTGCATAGTTATCA 58.723 34.615 0.00 0.00 0.00 2.15
388 390 7.724305 TCCGGTTAATTCTTGCATAGTTATC 57.276 36.000 0.00 0.00 0.00 1.75
389 391 8.691661 AATCCGGTTAATTCTTGCATAGTTAT 57.308 30.769 0.00 0.00 0.00 1.89
390 392 9.048446 GTAATCCGGTTAATTCTTGCATAGTTA 57.952 33.333 0.00 0.00 0.00 2.24
395 397 5.120399 TCGTAATCCGGTTAATTCTTGCAT 58.880 37.500 0.00 0.00 37.11 3.96
455 458 1.294659 CTGCTTCTGGAGTTGACCGC 61.295 60.000 0.00 0.00 0.00 5.68
480 483 3.080121 CCCTTGCGGCTCCTCTCT 61.080 66.667 0.00 0.00 0.00 3.10
515 518 5.044558 GCTTAAGCTCTGGTGTATGTACTC 58.955 45.833 20.38 0.00 38.21 2.59
539 565 3.941188 CACTCACCCCTGTGCGGT 61.941 66.667 0.00 0.00 42.46 5.68
541 567 4.704833 CCCACTCACCCCTGTGCG 62.705 72.222 0.00 0.00 42.46 5.34
598 3072 1.127343 CCATCTTCTCCACTCCCCTC 58.873 60.000 0.00 0.00 0.00 4.30
599 3073 0.719015 TCCATCTTCTCCACTCCCCT 59.281 55.000 0.00 0.00 0.00 4.79
600 3074 1.127343 CTCCATCTTCTCCACTCCCC 58.873 60.000 0.00 0.00 0.00 4.81
601 3075 2.166907 TCTCCATCTTCTCCACTCCC 57.833 55.000 0.00 0.00 0.00 4.30
602 3076 3.454082 ACAATCTCCATCTTCTCCACTCC 59.546 47.826 0.00 0.00 0.00 3.85
603 3077 4.440880 CACAATCTCCATCTTCTCCACTC 58.559 47.826 0.00 0.00 0.00 3.51
604 3078 3.199508 CCACAATCTCCATCTTCTCCACT 59.800 47.826 0.00 0.00 0.00 4.00
605 3079 3.539604 CCACAATCTCCATCTTCTCCAC 58.460 50.000 0.00 0.00 0.00 4.02
606 3080 2.092753 GCCACAATCTCCATCTTCTCCA 60.093 50.000 0.00 0.00 0.00 3.86
640 3326 1.215382 CTTCAGTGCGATCCGACCA 59.785 57.895 0.00 0.00 0.00 4.02
661 3347 7.453034 TGTAATTTTCATCTAGAAACGCGAAG 58.547 34.615 15.93 1.72 45.48 3.79
885 3899 2.674357 GTCACTCTCGTACACCTCTCTC 59.326 54.545 0.00 0.00 0.00 3.20
888 3902 2.152830 GTGTCACTCTCGTACACCTCT 58.847 52.381 0.00 0.00 38.02 3.69
903 3917 3.157949 TGGCAGACCACGGTGTCA 61.158 61.111 7.45 0.00 42.67 3.58
967 3981 2.630889 AGGATCTCCTGGAGAACACA 57.369 50.000 28.84 7.51 46.55 3.72
1031 5432 3.087031 AGGCATTTTCTGAGATGTGTGG 58.913 45.455 0.00 0.00 0.00 4.17
1057 5458 1.486726 CTAGTAGGCTCACCCCTTTGG 59.513 57.143 0.00 0.00 36.41 3.28
1063 5464 3.322541 GGATTTCTCTAGTAGGCTCACCC 59.677 52.174 0.00 0.00 36.11 4.61
1105 5520 9.013490 CAGAAACAAAAACAATCAGTGAAGTAG 57.987 33.333 0.00 0.00 0.00 2.57
1106 5521 8.519526 ACAGAAACAAAAACAATCAGTGAAGTA 58.480 29.630 0.00 0.00 0.00 2.24
1117 5532 8.877779 CCATTGTTCATACAGAAACAAAAACAA 58.122 29.630 4.94 0.00 38.13 2.83
1119 5534 8.641499 TCCATTGTTCATACAGAAACAAAAAC 57.359 30.769 4.94 0.00 38.13 2.43
1120 5535 9.258826 CATCCATTGTTCATACAGAAACAAAAA 57.741 29.630 4.94 0.00 38.13 1.94
1165 5583 7.117667 GGCAAATCAAAGAACGGAAATAACAAT 59.882 33.333 0.00 0.00 0.00 2.71
1168 5586 5.347635 GGGCAAATCAAAGAACGGAAATAAC 59.652 40.000 0.00 0.00 0.00 1.89
1169 5587 5.245075 AGGGCAAATCAAAGAACGGAAATAA 59.755 36.000 0.00 0.00 0.00 1.40
1170 5588 4.770010 AGGGCAAATCAAAGAACGGAAATA 59.230 37.500 0.00 0.00 0.00 1.40
1171 5589 3.578282 AGGGCAAATCAAAGAACGGAAAT 59.422 39.130 0.00 0.00 0.00 2.17
1172 5590 2.962421 AGGGCAAATCAAAGAACGGAAA 59.038 40.909 0.00 0.00 0.00 3.13
1176 5594 1.270550 AGCAGGGCAAATCAAAGAACG 59.729 47.619 0.00 0.00 0.00 3.95
1177 5595 2.297033 TCAGCAGGGCAAATCAAAGAAC 59.703 45.455 0.00 0.00 0.00 3.01
1179 5597 1.888512 GTCAGCAGGGCAAATCAAAGA 59.111 47.619 0.00 0.00 0.00 2.52
1180 5598 1.067354 GGTCAGCAGGGCAAATCAAAG 60.067 52.381 0.00 0.00 0.00 2.77
1187 5605 2.697147 GAACCTGGTCAGCAGGGCAA 62.697 60.000 26.71 0.00 43.89 4.52
1195 5613 6.430925 TCAATAACAATGAAGAACCTGGTCAG 59.569 38.462 0.00 0.00 0.00 3.51
1299 5717 0.321210 TGTACTGAATGGGCGTGGTG 60.321 55.000 0.00 0.00 0.00 4.17
1556 5989 1.270550 CCAGATGTTCACCCAAGTTGC 59.729 52.381 0.00 0.00 0.00 4.17
1561 5994 2.226330 CGTTTCCAGATGTTCACCCAA 58.774 47.619 0.00 0.00 0.00 4.12
1701 6134 4.755266 TCGCCTTATTAGCCTTTCTCTT 57.245 40.909 0.00 0.00 0.00 2.85
1786 6234 2.545952 GCCGAATGATACTGTGGTCGAT 60.546 50.000 0.00 0.00 0.00 3.59
1816 6264 2.357881 CTCTGCGTTGCTGCTCCA 60.358 61.111 0.00 0.00 35.36 3.86
1817 6265 3.123620 CCTCTGCGTTGCTGCTCC 61.124 66.667 0.00 0.00 35.36 4.70
1878 6335 3.389329 AGTTCTCACATCTGGACTTGTGT 59.611 43.478 3.30 0.00 42.95 3.72
1971 6437 2.040043 ATCCTAGCCTGCCCAGCT 60.040 61.111 0.00 0.00 44.49 4.24
1974 6440 1.003442 ACTCATCCTAGCCTGCCCA 59.997 57.895 0.00 0.00 0.00 5.36
1977 6443 0.392336 CTGGACTCATCCTAGCCTGC 59.608 60.000 0.00 0.00 46.43 4.85
1979 6445 1.133199 CCTCTGGACTCATCCTAGCCT 60.133 57.143 0.00 0.00 46.43 4.58
1994 6460 3.689649 CCGAACAAAGGGTAAATCCTCTG 59.310 47.826 0.00 0.00 35.80 3.35
2013 6479 2.029290 GCCAAAGACTGTTAGAGACCGA 60.029 50.000 0.00 0.00 0.00 4.69
2283 6758 4.036027 CCAAACAGATGAATCAATCTCGGG 59.964 45.833 0.00 0.00 34.60 5.14
2287 6762 6.251471 ACCTTCCAAACAGATGAATCAATCT 58.749 36.000 0.00 0.00 37.39 2.40
2289 6764 6.494491 TGAACCTTCCAAACAGATGAATCAAT 59.506 34.615 0.00 0.00 0.00 2.57
2517 7010 1.144936 GCCTCTCTGGATGAACCCG 59.855 63.158 0.00 0.00 38.35 5.28
2553 7046 5.991328 TGAAATTCAGTGAGAGTGAACAC 57.009 39.130 0.00 0.00 40.03 3.32
2554 7047 5.879777 TGTTGAAATTCAGTGAGAGTGAACA 59.120 36.000 0.00 0.00 40.03 3.18
2644 7137 5.140454 AGGTAAACTCAAGATGTTGCCTTT 58.860 37.500 0.00 0.89 33.19 3.11
2705 7198 1.065854 ACTTGCCGAGGGATGAAAGAG 60.066 52.381 3.69 0.00 0.00 2.85
2706 7199 0.984230 ACTTGCCGAGGGATGAAAGA 59.016 50.000 3.69 0.00 0.00 2.52
2721 7214 4.576463 GCAAGTATATCCCCAGTGAACTTG 59.424 45.833 7.71 7.71 43.14 3.16
2748 7241 0.824109 AGGAGCGCACTATGCTTACA 59.176 50.000 11.47 0.00 44.18 2.41
2749 7242 1.594862 CAAGGAGCGCACTATGCTTAC 59.405 52.381 11.47 0.00 44.18 2.34
2838 7331 1.446099 CACGATGCACAGGCGTAGT 60.446 57.895 5.60 0.00 44.32 2.73
2892 7385 2.203084 TCCAAACACGGAAGCGCA 60.203 55.556 11.47 0.00 29.93 6.09
2927 7420 6.405842 GCCACCAAAACCATCTAAATCCTTAG 60.406 42.308 0.00 0.00 36.59 2.18
3048 7541 2.095978 CTTTGGGTCGTCTCGGGTGT 62.096 60.000 0.00 0.00 0.00 4.16
3161 7664 2.815211 CACCTGGGCGTCATGTCG 60.815 66.667 8.03 8.03 0.00 4.35
3213 7716 2.263741 GGAGTTGGCTGCACCTGTG 61.264 63.158 0.50 0.00 40.22 3.66
3214 7717 2.113986 GGAGTTGGCTGCACCTGT 59.886 61.111 0.50 0.00 40.22 4.00
3302 7805 6.656632 AGGCATACTCTCGATTCTCAAATA 57.343 37.500 0.00 0.00 0.00 1.40
3313 7816 4.230657 CCGAAATAGAAGGCATACTCTCG 58.769 47.826 0.00 0.00 0.00 4.04
3342 7845 1.975660 TTAGCTTGCCAACGAACCTT 58.024 45.000 0.00 0.00 0.00 3.50
3452 7955 5.048013 GCTAGAGTTTTTAGGTTGCCATGTT 60.048 40.000 0.00 0.00 0.00 2.71
3524 8027 0.322008 CCCAGGAGACAGCCACTTTC 60.322 60.000 0.00 0.00 0.00 2.62
3531 8035 1.919600 AAGCCATCCCAGGAGACAGC 61.920 60.000 0.00 0.00 0.00 4.40
3533 8037 1.273838 ACTAAGCCATCCCAGGAGACA 60.274 52.381 0.00 0.00 0.00 3.41
3570 8074 1.981256 AGCGACCAATCAAACACCTT 58.019 45.000 0.00 0.00 0.00 3.50
3597 8101 7.707035 CCACTTCAGAATACAAGACAGTATACC 59.293 40.741 0.00 0.00 33.73 2.73
3729 8251 5.652014 TGTCAAAGACAATCCTTTCAACAGT 59.348 36.000 0.00 0.00 39.78 3.55
3780 8302 2.358003 ACTGCGCCTGAGCTTCAC 60.358 61.111 4.18 0.00 38.13 3.18
3858 9747 0.253044 AACACTAGTGCCATGCGGAT 59.747 50.000 22.90 0.00 0.00 4.18
3959 16125 2.925563 GCTCACATATTGCAAAACAGGC 59.074 45.455 1.71 0.00 0.00 4.85
3980 16146 9.722056 CCTTCCATATCACGAAGAAATTTAAAG 57.278 33.333 0.00 0.00 38.18 1.85
4055 16222 7.650504 GCGGTTAAACCAATTTTCTTTACTCTT 59.349 33.333 0.00 0.00 38.47 2.85
4070 16237 2.430546 CAATGCTTGCGGTTAAACCA 57.569 45.000 0.00 0.00 38.47 3.67


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

AutoCloner maintained by Alex Coulton.