Multiple sequence alignment - TraesCS5B01G212600

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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 TraesCS5B01G212600 chr5B 100.000 2671 0 0 1 2671 383210266 383207596 0.000000e+00 4933.0
1 TraesCS5B01G212600 chr5B 91.057 123 11 0 297 419 594746990 594747112 1.640000e-37 167.0
2 TraesCS5B01G212600 chr5A 89.766 1710 82 44 413 2048 426708580 426710270 0.000000e+00 2102.0
3 TraesCS5B01G212600 chr5A 86.644 584 37 21 2108 2671 426710295 426710857 2.270000e-170 608.0
4 TraesCS5B01G212600 chr5D 90.171 1465 75 40 830 2248 330121397 330119956 0.000000e+00 1844.0
5 TraesCS5B01G212600 chr5D 90.758 422 18 8 2259 2671 330119861 330119452 6.500000e-151 544.0
6 TraesCS5B01G212600 chr5D 86.026 458 29 6 415 838 330122939 330122483 2.420000e-125 459.0
7 TraesCS5B01G212600 chr5D 91.736 121 10 0 302 422 47538620 47538500 4.570000e-38 169.0
8 TraesCS5B01G212600 chr1B 91.803 122 10 0 302 423 573577806 573577685 1.270000e-38 171.0
9 TraesCS5B01G212600 chr1B 91.453 117 10 0 302 418 641942049 641941933 7.650000e-36 161.0
10 TraesCS5B01G212600 chr1B 86.806 144 14 5 298 437 545428538 545428396 3.560000e-34 156.0
11 TraesCS5B01G212600 chr3B 91.736 121 10 0 299 419 712995671 712995791 4.570000e-38 169.0
12 TraesCS5B01G212600 chr3B 79.006 181 31 5 77 250 41661862 41662042 1.680000e-22 117.0
13 TraesCS5B01G212600 chr2B 90.909 121 10 1 300 419 413865149 413865029 7.650000e-36 161.0
14 TraesCS5B01G212600 chr2B 89.683 126 13 0 293 418 709798637 709798762 7.650000e-36 161.0
15 TraesCS5B01G212600 chr2B 84.000 125 16 4 417 539 237044784 237044906 1.680000e-22 117.0
16 TraesCS5B01G212600 chr3A 82.065 184 30 3 70 250 568448880 568448697 1.280000e-33 154.0
17 TraesCS5B01G212600 chr1D 83.041 171 24 5 299 467 453059914 453060081 1.660000e-32 150.0
18 TraesCS5B01G212600 chr6B 79.348 184 33 5 72 250 624880876 624881059 1.000000e-24 124.0
19 TraesCS5B01G212600 chr7B 79.070 172 31 5 83 250 568392078 568391908 2.170000e-21 113.0
20 TraesCS5B01G212600 chr1A 77.957 186 34 6 70 250 124347110 124346927 2.810000e-20 110.0
21 TraesCS5B01G212600 chr1A 77.193 171 33 6 83 250 586084431 586084264 7.870000e-16 95.3
22 TraesCS5B01G212600 chr2D 80.882 136 20 5 119 250 420735657 420735524 4.700000e-18 102.0
23 TraesCS5B01G212600 chr2D 77.778 117 18 5 139 250 612733002 612732889 6.170000e-07 65.8
24 TraesCS5B01G212600 chr2A 76.543 162 32 5 94 250 592467034 592466874 1.700000e-12 84.2


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 TraesCS5B01G212600 chr5B 383207596 383210266 2670 True 4933 4933 100.000 1 2671 1 chr5B.!!$R1 2670
1 TraesCS5B01G212600 chr5A 426708580 426710857 2277 False 1355 2102 88.205 413 2671 2 chr5A.!!$F1 2258
2 TraesCS5B01G212600 chr5D 330119452 330122939 3487 True 949 1844 88.985 415 2671 3 chr5D.!!$R2 2256

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
219 220 0.026674 GTCGTTATTTAACCGGCCGC 59.973 55.0 22.85 0.75 32.69 6.53 F
220 221 0.108233 TCGTTATTTAACCGGCCGCT 60.108 50.0 22.85 11.86 32.69 5.52 F
1042 2191 0.038744 CCAGCTGAACCCAAGACCAT 59.961 55.0 17.39 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1026 2175 0.038166 TGGATGGTCTTGGGTTCAGC 59.962 55.000 0.0 0.0 0.0 4.26 R
1045 2194 1.006281 TGGCCATTGAAAGCAGAGGAT 59.994 47.619 0.0 0.0 0.0 3.24 R
2495 3820 0.321919 GAAGCACCATGACAGCCAGA 60.322 55.000 0.0 0.0 0.0 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.925700 CATTTAAGGAACAAATTTAGGACAAGC 58.074 33.333 0.00 0.00 0.00 4.01
32 33 7.833285 TTAAGGAACAAATTTAGGACAAGCT 57.167 32.000 0.00 0.00 0.00 3.74
33 34 6.731292 AAGGAACAAATTTAGGACAAGCTT 57.269 33.333 0.00 0.00 0.00 3.74
34 35 6.731292 AGGAACAAATTTAGGACAAGCTTT 57.269 33.333 0.00 0.00 0.00 3.51
35 36 7.124573 AGGAACAAATTTAGGACAAGCTTTT 57.875 32.000 0.00 0.00 0.00 2.27
36 37 7.564793 AGGAACAAATTTAGGACAAGCTTTTT 58.435 30.769 0.00 0.00 0.00 1.94
54 55 4.470334 TTTTTAATACGCGGGAGTACCT 57.530 40.909 12.47 0.00 36.97 3.08
55 56 3.441496 TTTAATACGCGGGAGTACCTG 57.559 47.619 12.47 0.00 44.87 4.00
61 62 4.857251 CGGGAGTACCTGCCAATC 57.143 61.111 2.65 0.00 42.30 2.67
62 63 1.904771 CGGGAGTACCTGCCAATCA 59.095 57.895 2.65 0.00 42.30 2.57
63 64 0.462047 CGGGAGTACCTGCCAATCAC 60.462 60.000 2.65 0.00 42.30 3.06
64 65 0.107165 GGGAGTACCTGCCAATCACC 60.107 60.000 0.00 0.00 41.77 4.02
65 66 0.107165 GGAGTACCTGCCAATCACCC 60.107 60.000 0.00 0.00 0.00 4.61
66 67 0.912486 GAGTACCTGCCAATCACCCT 59.088 55.000 0.00 0.00 0.00 4.34
67 68 2.116238 GAGTACCTGCCAATCACCCTA 58.884 52.381 0.00 0.00 0.00 3.53
68 69 2.103263 GAGTACCTGCCAATCACCCTAG 59.897 54.545 0.00 0.00 0.00 3.02
69 70 1.141053 GTACCTGCCAATCACCCTAGG 59.859 57.143 0.06 0.06 0.00 3.02
70 71 1.281925 ACCTGCCAATCACCCTAGGG 61.282 60.000 27.36 27.36 42.03 3.53
84 85 4.790718 CCCTAGGGGCATAGTAAACTTT 57.209 45.455 21.44 0.00 35.35 2.66
85 86 5.899631 CCCTAGGGGCATAGTAAACTTTA 57.100 43.478 21.44 0.00 35.35 1.85
86 87 6.256643 CCCTAGGGGCATAGTAAACTTTAA 57.743 41.667 21.44 0.00 35.35 1.52
87 88 6.296803 CCCTAGGGGCATAGTAAACTTTAAG 58.703 44.000 21.44 0.00 35.35 1.85
88 89 6.126565 CCCTAGGGGCATAGTAAACTTTAAGT 60.127 42.308 21.44 0.00 35.35 2.24
89 90 7.344134 CCTAGGGGCATAGTAAACTTTAAGTT 58.656 38.462 4.30 4.30 40.80 2.66
91 92 7.698506 AGGGGCATAGTAAACTTTAAGTTTC 57.301 36.000 23.96 15.96 44.47 2.78
92 93 7.235804 AGGGGCATAGTAAACTTTAAGTTTCA 58.764 34.615 23.96 12.58 44.47 2.69
93 94 7.393515 AGGGGCATAGTAAACTTTAAGTTTCAG 59.606 37.037 23.96 12.67 44.47 3.02
94 95 7.176165 GGGGCATAGTAAACTTTAAGTTTCAGT 59.824 37.037 23.96 15.60 44.47 3.41
95 96 8.573885 GGGCATAGTAAACTTTAAGTTTCAGTT 58.426 33.333 23.96 12.01 44.47 3.16
96 97 9.394477 GGCATAGTAAACTTTAAGTTTCAGTTG 57.606 33.333 23.96 17.92 44.47 3.16
97 98 9.946165 GCATAGTAAACTTTAAGTTTCAGTTGT 57.054 29.630 23.96 4.02 44.47 3.32
128 129 9.846248 ACTTATGATATTTCAACTGAAACTTGC 57.154 29.630 7.02 0.00 45.55 4.01
129 130 9.844790 CTTATGATATTTCAACTGAAACTTGCA 57.155 29.630 7.02 4.68 45.55 4.08
132 133 9.715121 ATGATATTTCAACTGAAACTTGCAATT 57.285 25.926 7.02 0.00 45.55 2.32
133 134 9.195411 TGATATTTCAACTGAAACTTGCAATTC 57.805 29.630 7.02 2.33 45.55 2.17
134 135 9.415544 GATATTTCAACTGAAACTTGCAATTCT 57.584 29.630 12.67 0.00 45.55 2.40
135 136 9.768662 ATATTTCAACTGAAACTTGCAATTCTT 57.231 25.926 12.67 1.69 45.55 2.52
136 137 6.890663 TTCAACTGAAACTTGCAATTCTTG 57.109 33.333 12.67 10.00 0.00 3.02
137 138 6.183360 TTTCAACTGAAACTTGCAATTCTTGC 60.183 34.615 12.67 4.93 46.03 4.01
138 139 8.271535 TTTCAACTGAAACTTGCAATTCTTGCT 61.272 33.333 12.67 0.00 46.02 3.91
150 151 5.475273 CAATTCTTGCTCGCTCTTATCAA 57.525 39.130 0.00 0.00 0.00 2.57
151 152 5.499935 CAATTCTTGCTCGCTCTTATCAAG 58.500 41.667 0.00 0.00 36.42 3.02
152 153 3.876274 TCTTGCTCGCTCTTATCAAGT 57.124 42.857 0.00 0.00 36.47 3.16
153 154 4.193826 TCTTGCTCGCTCTTATCAAGTT 57.806 40.909 0.00 0.00 36.47 2.66
154 155 4.569943 TCTTGCTCGCTCTTATCAAGTTT 58.430 39.130 0.00 0.00 36.47 2.66
155 156 4.627467 TCTTGCTCGCTCTTATCAAGTTTC 59.373 41.667 0.00 0.00 36.47 2.78
156 157 3.925379 TGCTCGCTCTTATCAAGTTTCA 58.075 40.909 0.00 0.00 0.00 2.69
157 158 3.679980 TGCTCGCTCTTATCAAGTTTCAC 59.320 43.478 0.00 0.00 0.00 3.18
158 159 3.241804 GCTCGCTCTTATCAAGTTTCACG 60.242 47.826 0.00 0.00 0.00 4.35
159 160 3.250744 TCGCTCTTATCAAGTTTCACGG 58.749 45.455 0.00 0.00 0.00 4.94
160 161 3.057104 TCGCTCTTATCAAGTTTCACGGA 60.057 43.478 0.00 0.00 0.00 4.69
161 162 3.865745 CGCTCTTATCAAGTTTCACGGAT 59.134 43.478 0.00 0.00 0.00 4.18
162 163 5.041287 CGCTCTTATCAAGTTTCACGGATA 58.959 41.667 0.00 0.00 0.00 2.59
163 164 5.518847 CGCTCTTATCAAGTTTCACGGATAA 59.481 40.000 0.00 0.00 32.49 1.75
164 165 6.035650 CGCTCTTATCAAGTTTCACGGATAAA 59.964 38.462 0.00 0.00 32.80 1.40
165 166 7.254455 CGCTCTTATCAAGTTTCACGGATAAAT 60.254 37.037 0.00 0.00 32.80 1.40
166 167 8.398665 GCTCTTATCAAGTTTCACGGATAAATT 58.601 33.333 0.00 0.00 32.80 1.82
203 204 7.534085 TTATTAGTCACAGGCATAAAAGTCG 57.466 36.000 0.00 0.00 0.00 4.18
204 205 3.402628 AGTCACAGGCATAAAAGTCGT 57.597 42.857 0.00 0.00 0.00 4.34
205 206 3.740115 AGTCACAGGCATAAAAGTCGTT 58.260 40.909 0.00 0.00 0.00 3.85
206 207 4.890088 AGTCACAGGCATAAAAGTCGTTA 58.110 39.130 0.00 0.00 0.00 3.18
207 208 5.488341 AGTCACAGGCATAAAAGTCGTTAT 58.512 37.500 0.00 0.00 0.00 1.89
208 209 5.938125 AGTCACAGGCATAAAAGTCGTTATT 59.062 36.000 0.00 0.00 0.00 1.40
209 210 6.430000 AGTCACAGGCATAAAAGTCGTTATTT 59.570 34.615 0.00 0.00 0.00 1.40
210 211 7.604927 AGTCACAGGCATAAAAGTCGTTATTTA 59.395 33.333 0.00 0.00 0.00 1.40
211 212 8.231837 GTCACAGGCATAAAAGTCGTTATTTAA 58.768 33.333 0.00 0.00 0.00 1.52
212 213 8.231837 TCACAGGCATAAAAGTCGTTATTTAAC 58.768 33.333 0.00 0.00 0.00 2.01
213 214 7.483691 CACAGGCATAAAAGTCGTTATTTAACC 59.516 37.037 0.00 0.00 32.69 2.85
214 215 6.685403 CAGGCATAAAAGTCGTTATTTAACCG 59.315 38.462 0.00 0.00 31.58 4.44
215 216 5.967088 GGCATAAAAGTCGTTATTTAACCGG 59.033 40.000 0.00 0.00 32.69 5.28
216 217 5.453266 GCATAAAAGTCGTTATTTAACCGGC 59.547 40.000 0.00 0.00 32.69 6.13
217 218 4.424061 AAAAGTCGTTATTTAACCGGCC 57.576 40.909 0.00 0.00 32.69 6.13
218 219 1.643880 AGTCGTTATTTAACCGGCCG 58.356 50.000 21.04 21.04 32.69 6.13
219 220 0.026674 GTCGTTATTTAACCGGCCGC 59.973 55.000 22.85 0.75 32.69 6.53
220 221 0.108233 TCGTTATTTAACCGGCCGCT 60.108 50.000 22.85 11.86 32.69 5.52
221 222 0.302589 CGTTATTTAACCGGCCGCTC 59.697 55.000 22.85 0.34 32.69 5.03
222 223 0.302589 GTTATTTAACCGGCCGCTCG 59.697 55.000 22.85 9.35 0.00 5.03
223 224 0.108233 TTATTTAACCGGCCGCTCGT 60.108 50.000 22.85 10.16 0.00 4.18
224 225 0.743688 TATTTAACCGGCCGCTCGTA 59.256 50.000 22.85 5.35 0.00 3.43
225 226 0.807275 ATTTAACCGGCCGCTCGTAC 60.807 55.000 22.85 0.00 0.00 3.67
226 227 1.876497 TTTAACCGGCCGCTCGTACT 61.876 55.000 22.85 0.62 0.00 2.73
227 228 1.029408 TTAACCGGCCGCTCGTACTA 61.029 55.000 22.85 0.00 0.00 1.82
228 229 1.029408 TAACCGGCCGCTCGTACTAA 61.029 55.000 22.85 0.00 0.00 2.24
229 230 2.025727 CCGGCCGCTCGTACTAAG 59.974 66.667 22.85 0.00 0.00 2.18
230 231 2.768492 CCGGCCGCTCGTACTAAGT 61.768 63.158 22.85 0.00 0.00 2.24
231 232 1.138247 CGGCCGCTCGTACTAAGTT 59.862 57.895 14.67 0.00 0.00 2.66
232 233 0.457337 CGGCCGCTCGTACTAAGTTT 60.457 55.000 14.67 0.00 0.00 2.66
233 234 1.275505 GGCCGCTCGTACTAAGTTTC 58.724 55.000 0.00 0.00 0.00 2.78
234 235 1.403249 GGCCGCTCGTACTAAGTTTCA 60.403 52.381 0.00 0.00 0.00 2.69
235 236 2.331194 GCCGCTCGTACTAAGTTTCAA 58.669 47.619 0.00 0.00 0.00 2.69
236 237 2.344741 GCCGCTCGTACTAAGTTTCAAG 59.655 50.000 0.00 0.00 0.00 3.02
237 238 3.829948 CCGCTCGTACTAAGTTTCAAGA 58.170 45.455 0.00 0.00 0.00 3.02
238 239 3.852536 CCGCTCGTACTAAGTTTCAAGAG 59.147 47.826 0.00 0.00 0.00 2.85
239 240 4.474113 CGCTCGTACTAAGTTTCAAGAGT 58.526 43.478 0.00 0.00 0.00 3.24
240 241 4.916249 CGCTCGTACTAAGTTTCAAGAGTT 59.084 41.667 0.00 0.00 0.00 3.01
241 242 5.164177 CGCTCGTACTAAGTTTCAAGAGTTG 60.164 44.000 0.00 0.00 0.00 3.16
242 243 5.919141 GCTCGTACTAAGTTTCAAGAGTTGA 59.081 40.000 0.00 0.00 38.04 3.18
284 285 8.924511 AAACAGATCTTATTTGAAAGGTCTCA 57.075 30.769 0.00 0.00 42.08 3.27
285 286 9.525826 AAACAGATCTTATTTGAAAGGTCTCAT 57.474 29.630 0.00 0.00 42.08 2.90
286 287 8.729805 ACAGATCTTATTTGAAAGGTCTCATC 57.270 34.615 0.00 0.00 42.08 2.92
287 288 8.324306 ACAGATCTTATTTGAAAGGTCTCATCA 58.676 33.333 0.00 0.00 42.08 3.07
288 289 9.339850 CAGATCTTATTTGAAAGGTCTCATCAT 57.660 33.333 0.00 0.00 42.08 2.45
289 290 9.917887 AGATCTTATTTGAAAGGTCTCATCATT 57.082 29.630 0.00 0.00 42.08 2.57
297 298 9.528018 TTTGAAAGGTCTCATCATTAAAAACAC 57.472 29.630 0.00 0.00 0.00 3.32
298 299 8.231692 TGAAAGGTCTCATCATTAAAAACACA 57.768 30.769 0.00 0.00 0.00 3.72
299 300 8.690884 TGAAAGGTCTCATCATTAAAAACACAA 58.309 29.630 0.00 0.00 0.00 3.33
300 301 9.528018 GAAAGGTCTCATCATTAAAAACACAAA 57.472 29.630 0.00 0.00 0.00 2.83
307 308 9.573133 CTCATCATTAAAAACACAAATACTCCC 57.427 33.333 0.00 0.00 0.00 4.30
308 309 9.308000 TCATCATTAAAAACACAAATACTCCCT 57.692 29.630 0.00 0.00 0.00 4.20
311 312 8.723311 TCATTAAAAACACAAATACTCCCTACG 58.277 33.333 0.00 0.00 0.00 3.51
312 313 8.508875 CATTAAAAACACAAATACTCCCTACGT 58.491 33.333 0.00 0.00 0.00 3.57
313 314 6.549912 AAAAACACAAATACTCCCTACGTC 57.450 37.500 0.00 0.00 0.00 4.34
314 315 3.881937 ACACAAATACTCCCTACGTCC 57.118 47.619 0.00 0.00 0.00 4.79
315 316 2.165030 ACACAAATACTCCCTACGTCCG 59.835 50.000 0.00 0.00 0.00 4.79
316 317 2.424601 CACAAATACTCCCTACGTCCGA 59.575 50.000 0.00 0.00 0.00 4.55
317 318 3.091545 ACAAATACTCCCTACGTCCGAA 58.908 45.455 0.00 0.00 0.00 4.30
318 319 3.511146 ACAAATACTCCCTACGTCCGAAA 59.489 43.478 0.00 0.00 0.00 3.46
319 320 4.021192 ACAAATACTCCCTACGTCCGAAAA 60.021 41.667 0.00 0.00 0.00 2.29
320 321 5.114081 CAAATACTCCCTACGTCCGAAAAT 58.886 41.667 0.00 0.00 0.00 1.82
321 322 6.127366 ACAAATACTCCCTACGTCCGAAAATA 60.127 38.462 0.00 0.00 0.00 1.40
322 323 3.790152 ACTCCCTACGTCCGAAAATAC 57.210 47.619 0.00 0.00 0.00 1.89
323 324 3.359950 ACTCCCTACGTCCGAAAATACT 58.640 45.455 0.00 0.00 0.00 2.12
324 325 3.766051 ACTCCCTACGTCCGAAAATACTT 59.234 43.478 0.00 0.00 0.00 2.24
325 326 4.110482 CTCCCTACGTCCGAAAATACTTG 58.890 47.826 0.00 0.00 0.00 3.16
326 327 3.511146 TCCCTACGTCCGAAAATACTTGT 59.489 43.478 0.00 0.00 0.00 3.16
327 328 3.861689 CCCTACGTCCGAAAATACTTGTC 59.138 47.826 0.00 0.00 0.00 3.18
328 329 3.545078 CCTACGTCCGAAAATACTTGTCG 59.455 47.826 0.00 0.00 34.58 4.35
329 330 1.723003 ACGTCCGAAAATACTTGTCGC 59.277 47.619 0.00 0.00 33.46 5.19
330 331 1.722464 CGTCCGAAAATACTTGTCGCA 59.278 47.619 0.00 0.00 33.46 5.10
331 332 2.347452 CGTCCGAAAATACTTGTCGCAT 59.653 45.455 0.00 0.00 33.46 4.73
332 333 3.548668 CGTCCGAAAATACTTGTCGCATA 59.451 43.478 0.00 0.00 33.46 3.14
333 334 4.031991 CGTCCGAAAATACTTGTCGCATAA 59.968 41.667 0.00 0.00 33.46 1.90
334 335 5.444877 CGTCCGAAAATACTTGTCGCATAAA 60.445 40.000 0.00 0.00 33.46 1.40
335 336 6.483687 GTCCGAAAATACTTGTCGCATAAAT 58.516 36.000 0.00 0.00 33.46 1.40
336 337 6.410914 GTCCGAAAATACTTGTCGCATAAATG 59.589 38.462 0.00 0.00 33.46 2.32
337 338 5.681105 CCGAAAATACTTGTCGCATAAATGG 59.319 40.000 0.00 0.00 33.46 3.16
338 339 6.457663 CCGAAAATACTTGTCGCATAAATGGA 60.458 38.462 0.00 0.00 33.46 3.41
339 340 7.132213 CGAAAATACTTGTCGCATAAATGGAT 58.868 34.615 0.00 0.00 0.00 3.41
340 341 7.112009 CGAAAATACTTGTCGCATAAATGGATG 59.888 37.037 0.00 0.00 0.00 3.51
341 342 7.566760 AAATACTTGTCGCATAAATGGATGA 57.433 32.000 0.00 0.00 0.00 2.92
342 343 7.566760 AATACTTGTCGCATAAATGGATGAA 57.433 32.000 0.00 0.00 0.00 2.57
343 344 5.895636 ACTTGTCGCATAAATGGATGAAA 57.104 34.783 0.00 0.00 0.00 2.69
344 345 6.266168 ACTTGTCGCATAAATGGATGAAAA 57.734 33.333 0.00 0.00 0.00 2.29
345 346 6.866480 ACTTGTCGCATAAATGGATGAAAAT 58.134 32.000 0.00 0.00 0.00 1.82
346 347 6.753279 ACTTGTCGCATAAATGGATGAAAATG 59.247 34.615 0.00 0.00 0.00 2.32
347 348 6.448207 TGTCGCATAAATGGATGAAAATGA 57.552 33.333 0.00 0.00 0.00 2.57
348 349 6.861144 TGTCGCATAAATGGATGAAAATGAA 58.139 32.000 0.00 0.00 0.00 2.57
349 350 7.490840 TGTCGCATAAATGGATGAAAATGAAT 58.509 30.769 0.00 0.00 0.00 2.57
350 351 7.435784 TGTCGCATAAATGGATGAAAATGAATG 59.564 33.333 0.00 0.00 0.00 2.67
351 352 7.436080 GTCGCATAAATGGATGAAAATGAATGT 59.564 33.333 0.00 0.00 0.00 2.71
352 353 8.628280 TCGCATAAATGGATGAAAATGAATGTA 58.372 29.630 0.00 0.00 0.00 2.29
353 354 9.414295 CGCATAAATGGATGAAAATGAATGTAT 57.586 29.630 0.00 0.00 0.00 2.29
412 413 9.996554 TTAATGACAAGTATTTTCAGACAGAGA 57.003 29.630 0.00 0.00 0.00 3.10
413 414 8.908786 AATGACAAGTATTTTCAGACAGAGAA 57.091 30.769 0.00 0.00 0.00 2.87
414 415 8.908786 ATGACAAGTATTTTCAGACAGAGAAA 57.091 30.769 0.00 0.00 33.48 2.52
415 416 8.370493 TGACAAGTATTTTCAGACAGAGAAAG 57.630 34.615 0.00 0.00 36.45 2.62
416 417 7.987458 TGACAAGTATTTTCAGACAGAGAAAGT 59.013 33.333 0.00 0.00 36.45 2.66
417 418 9.477484 GACAAGTATTTTCAGACAGAGAAAGTA 57.523 33.333 0.00 0.00 36.45 2.24
427 428 8.731275 TCAGACAGAGAAAGTATGAAAAACAA 57.269 30.769 0.00 0.00 34.62 2.83
491 492 7.683746 TGAAAATCAAAAGCCGAAAGAAAAAG 58.316 30.769 0.00 0.00 0.00 2.27
601 632 4.988598 CTCGTGCAAGTGGCCGGT 62.989 66.667 1.90 0.00 43.89 5.28
604 635 3.660111 GTGCAAGTGGCCGGTGAC 61.660 66.667 1.90 0.00 43.89 3.67
650 693 0.679505 TGACATATACCAGCTCGGCC 59.320 55.000 0.00 0.00 39.03 6.13
664 707 0.745845 TCGGCCTACTACCTGACGAC 60.746 60.000 0.00 0.00 0.00 4.34
665 708 1.722636 CGGCCTACTACCTGACGACC 61.723 65.000 0.00 0.00 0.00 4.79
667 710 1.722636 GCCTACTACCTGACGACCGG 61.723 65.000 0.00 0.00 0.00 5.28
700 743 0.313672 TTGCAAATTCACAGTCGGGC 59.686 50.000 0.00 0.00 0.00 6.13
793 840 1.811266 CGGAGCATCACCACTTCCG 60.811 63.158 0.00 0.00 36.25 4.30
828 1969 1.062488 AGTTGCCTCCCCACTGTTCT 61.062 55.000 0.00 0.00 0.00 3.01
842 1983 2.291540 ACTGTTCTCCTCTCCTCTCCTG 60.292 54.545 0.00 0.00 0.00 3.86
863 2004 2.554893 GCAGGTTCGGTTTTACCATCAA 59.445 45.455 0.00 0.00 38.47 2.57
864 2005 3.192633 GCAGGTTCGGTTTTACCATCAAT 59.807 43.478 0.00 0.00 38.47 2.57
865 2006 4.674362 GCAGGTTCGGTTTTACCATCAATC 60.674 45.833 0.00 0.00 38.47 2.67
866 2007 4.457603 CAGGTTCGGTTTTACCATCAATCA 59.542 41.667 0.00 0.00 38.47 2.57
867 2008 4.457949 AGGTTCGGTTTTACCATCAATCAC 59.542 41.667 0.00 0.00 38.47 3.06
868 2009 4.380128 GGTTCGGTTTTACCATCAATCACC 60.380 45.833 0.00 0.00 38.47 4.02
869 2010 4.022413 TCGGTTTTACCATCAATCACCA 57.978 40.909 0.00 0.00 38.47 4.17
870 2011 4.594970 TCGGTTTTACCATCAATCACCAT 58.405 39.130 0.00 0.00 38.47 3.55
871 2012 4.397730 TCGGTTTTACCATCAATCACCATG 59.602 41.667 0.00 0.00 38.47 3.66
872 2013 4.439974 CGGTTTTACCATCAATCACCATGG 60.440 45.833 11.19 11.19 44.68 3.66
1025 2174 0.251832 ACGCCTCCTCTCTCTTTCCA 60.252 55.000 0.00 0.00 0.00 3.53
1026 2175 0.459489 CGCCTCCTCTCTCTTTCCAG 59.541 60.000 0.00 0.00 0.00 3.86
1035 2184 1.349026 CTCTCTTTCCAGCTGAACCCA 59.651 52.381 17.39 0.00 31.05 4.51
1037 2186 2.157738 CTCTTTCCAGCTGAACCCAAG 58.842 52.381 17.39 9.33 31.05 3.61
1038 2187 1.774254 TCTTTCCAGCTGAACCCAAGA 59.226 47.619 17.39 11.46 31.05 3.02
1039 2188 1.882623 CTTTCCAGCTGAACCCAAGAC 59.117 52.381 17.39 0.00 31.05 3.01
1040 2189 0.110486 TTCCAGCTGAACCCAAGACC 59.890 55.000 17.39 0.00 0.00 3.85
1041 2190 1.059584 TCCAGCTGAACCCAAGACCA 61.060 55.000 17.39 0.00 0.00 4.02
1042 2191 0.038744 CCAGCTGAACCCAAGACCAT 59.961 55.000 17.39 0.00 0.00 3.55
1043 2192 1.457346 CAGCTGAACCCAAGACCATC 58.543 55.000 8.42 0.00 0.00 3.51
1045 2194 0.038166 GCTGAACCCAAGACCATCCA 59.962 55.000 0.00 0.00 0.00 3.41
1056 2214 2.203584 AGACCATCCATCCTCTGCTTT 58.796 47.619 0.00 0.00 0.00 3.51
1064 2222 1.407979 CATCCTCTGCTTTCAATGGCC 59.592 52.381 0.00 0.00 0.00 5.36
1066 2224 0.815734 CCTCTGCTTTCAATGGCCAG 59.184 55.000 13.05 0.00 0.00 4.85
1115 2273 3.315142 GATCAGGCGGTGGCACTCA 62.315 63.158 18.45 0.00 42.47 3.41
1493 2669 0.242017 AGTACTACGCGTGTTGACCC 59.758 55.000 24.59 2.94 0.00 4.46
1536 2715 2.515290 CATCATCCGCAGCTGGCA 60.515 61.111 17.12 0.00 45.17 4.92
1565 2747 2.856000 AGAGTTGGTGGCCTGGCT 60.856 61.111 19.68 0.00 0.00 4.75
1568 2750 2.991540 GTTGGTGGCCTGGCTTCC 60.992 66.667 19.68 19.84 0.00 3.46
1599 2781 6.316140 GGGGCAATTTGGTAATCATTTCTTTC 59.684 38.462 0.00 0.00 0.00 2.62
1716 2912 1.648504 GTTCGTGGTAATTCGGGGAG 58.351 55.000 0.00 0.00 0.00 4.30
1769 2965 4.159506 TGATGCTGTTTTGGGGCTATTAAC 59.840 41.667 0.00 0.00 0.00 2.01
1900 3096 3.002656 GCATCCACGTACATTTCCATCTG 59.997 47.826 0.00 0.00 0.00 2.90
1901 3097 3.973206 TCCACGTACATTTCCATCTGT 57.027 42.857 0.00 0.00 0.00 3.41
1902 3098 3.595173 TCCACGTACATTTCCATCTGTG 58.405 45.455 0.00 0.00 0.00 3.66
1903 3099 3.007506 TCCACGTACATTTCCATCTGTGT 59.992 43.478 0.00 0.00 0.00 3.72
1904 3100 4.221041 TCCACGTACATTTCCATCTGTGTA 59.779 41.667 0.00 0.00 0.00 2.90
1905 3101 5.105106 TCCACGTACATTTCCATCTGTGTAT 60.105 40.000 0.00 0.00 30.65 2.29
1906 3102 6.097129 TCCACGTACATTTCCATCTGTGTATA 59.903 38.462 0.00 0.00 30.65 1.47
1907 3103 6.759356 CCACGTACATTTCCATCTGTGTATAA 59.241 38.462 0.00 0.00 30.65 0.98
1908 3104 7.279090 CCACGTACATTTCCATCTGTGTATAAA 59.721 37.037 0.00 0.00 30.65 1.40
1912 3108 7.088589 ACATTTCCATCTGTGTATAAAGTGC 57.911 36.000 0.00 0.00 0.00 4.40
1929 3138 0.533491 TGCATGCAAGCTCATTTCCC 59.467 50.000 20.30 0.00 34.99 3.97
2018 3248 1.702182 TGAAGGCATTTTCACCAGCA 58.298 45.000 0.00 0.00 32.39 4.41
2103 3334 5.546621 TCTTTCACAAAGTAGCTGGTAGT 57.453 39.130 0.00 0.00 39.52 2.73
2104 3335 6.659745 TCTTTCACAAAGTAGCTGGTAGTA 57.340 37.500 0.00 0.00 39.52 1.82
2109 3340 7.241042 TCACAAAGTAGCTGGTAGTAGAATT 57.759 36.000 0.00 0.00 0.00 2.17
2115 3346 6.879400 AGTAGCTGGTAGTAGAATTTCAAGG 58.121 40.000 0.00 0.00 0.00 3.61
2168 3401 3.133183 TCCTGGGCCAAAAGTAACAAAAC 59.867 43.478 8.04 0.00 0.00 2.43
2181 3414 6.800072 AGTAACAAAACCCCAATCAAGAAA 57.200 33.333 0.00 0.00 0.00 2.52
2188 3421 6.686484 AAACCCCAATCAAGAAAGCTTAAT 57.314 33.333 0.00 0.00 31.81 1.40
2242 3475 4.496840 GGTTTACAAAGTCCCACAAAGACG 60.497 45.833 0.00 0.00 39.31 4.18
2250 3483 0.034059 CCCACAAAGACGAGACAGCT 59.966 55.000 0.00 0.00 0.00 4.24
2251 3484 1.272490 CCCACAAAGACGAGACAGCTA 59.728 52.381 0.00 0.00 0.00 3.32
2252 3485 2.093973 CCCACAAAGACGAGACAGCTAT 60.094 50.000 0.00 0.00 0.00 2.97
2253 3486 2.926200 CCACAAAGACGAGACAGCTATG 59.074 50.000 0.00 0.00 0.00 2.23
2254 3487 2.926200 CACAAAGACGAGACAGCTATGG 59.074 50.000 0.00 0.00 0.00 2.74
2256 3489 1.853963 AAGACGAGACAGCTATGGGT 58.146 50.000 0.00 0.00 0.00 4.51
2407 3727 0.955428 TCAAAGACTGGTCGCCATGC 60.955 55.000 0.00 0.00 30.82 4.06
2448 3769 5.959618 ATCACAGGGTTTTAAGTAAGTGC 57.040 39.130 0.00 0.00 0.00 4.40
2454 3775 6.153851 ACAGGGTTTTAAGTAAGTGCAAGTTT 59.846 34.615 0.00 0.00 0.00 2.66
2495 3820 0.732196 TACGTACGCGCGTCCAATTT 60.732 50.000 41.35 20.27 44.55 1.82
2527 3854 4.170468 TGGTGCTTCTTTTTCTCTTCCT 57.830 40.909 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.925700 GCTTGTCCTAAATTTGTTCCTTAAATG 58.074 33.333 0.00 0.00 0.00 2.32
6 7 8.870116 AGCTTGTCCTAAATTTGTTCCTTAAAT 58.130 29.630 0.00 0.00 0.00 1.40
7 8 8.245195 AGCTTGTCCTAAATTTGTTCCTTAAA 57.755 30.769 0.00 0.00 0.00 1.52
8 9 7.833285 AGCTTGTCCTAAATTTGTTCCTTAA 57.167 32.000 0.00 0.00 0.00 1.85
9 10 7.833285 AAGCTTGTCCTAAATTTGTTCCTTA 57.167 32.000 0.00 0.00 0.00 2.69
10 11 6.731292 AAGCTTGTCCTAAATTTGTTCCTT 57.269 33.333 0.00 0.00 0.00 3.36
11 12 6.731292 AAAGCTTGTCCTAAATTTGTTCCT 57.269 33.333 0.00 0.00 0.00 3.36
12 13 7.786178 AAAAAGCTTGTCCTAAATTTGTTCC 57.214 32.000 0.00 0.00 0.00 3.62
33 34 4.183101 CAGGTACTCCCGCGTATTAAAAA 58.817 43.478 4.92 0.00 34.60 1.94
34 35 3.784338 CAGGTACTCCCGCGTATTAAAA 58.216 45.455 4.92 0.00 34.60 1.52
35 36 2.481795 GCAGGTACTCCCGCGTATTAAA 60.482 50.000 4.92 0.00 34.60 1.52
36 37 1.067516 GCAGGTACTCCCGCGTATTAA 59.932 52.381 4.92 0.00 34.60 1.40
37 38 0.670162 GCAGGTACTCCCGCGTATTA 59.330 55.000 4.92 0.00 34.60 0.98
38 39 1.440476 GCAGGTACTCCCGCGTATT 59.560 57.895 4.92 0.00 34.60 1.89
39 40 2.496291 GGCAGGTACTCCCGCGTAT 61.496 63.158 4.92 0.00 34.60 3.06
40 41 3.142838 GGCAGGTACTCCCGCGTA 61.143 66.667 4.92 0.00 34.60 4.42
42 43 3.385749 ATTGGCAGGTACTCCCGCG 62.386 63.158 0.00 0.00 34.60 6.46
43 44 1.523938 GATTGGCAGGTACTCCCGC 60.524 63.158 0.00 0.00 34.60 6.13
44 45 0.462047 GTGATTGGCAGGTACTCCCG 60.462 60.000 0.00 0.00 34.60 5.14
45 46 0.107165 GGTGATTGGCAGGTACTCCC 60.107 60.000 0.00 0.00 34.60 4.30
46 47 0.107165 GGGTGATTGGCAGGTACTCC 60.107 60.000 0.00 0.00 34.60 3.85
47 48 0.912486 AGGGTGATTGGCAGGTACTC 59.088 55.000 0.00 0.00 34.60 2.59
48 49 2.119495 CTAGGGTGATTGGCAGGTACT 58.881 52.381 0.00 0.00 43.88 2.73
49 50 1.141053 CCTAGGGTGATTGGCAGGTAC 59.859 57.143 0.00 0.00 0.00 3.34
50 51 1.507140 CCTAGGGTGATTGGCAGGTA 58.493 55.000 0.00 0.00 0.00 3.08
51 52 1.281925 CCCTAGGGTGATTGGCAGGT 61.282 60.000 20.88 0.00 0.00 4.00
52 53 1.533711 CCCTAGGGTGATTGGCAGG 59.466 63.158 20.88 0.00 0.00 4.85
53 54 1.533711 CCCCTAGGGTGATTGGCAG 59.466 63.158 26.66 3.71 38.25 4.85
54 55 2.689691 GCCCCTAGGGTGATTGGCA 61.690 63.158 26.66 0.00 46.51 4.92
55 56 2.011617 ATGCCCCTAGGGTGATTGGC 62.012 60.000 26.66 20.53 46.51 4.52
56 57 1.352352 CTATGCCCCTAGGGTGATTGG 59.648 57.143 26.66 11.00 46.51 3.16
57 58 2.057922 ACTATGCCCCTAGGGTGATTG 58.942 52.381 26.66 18.67 46.51 2.67
58 59 2.514726 ACTATGCCCCTAGGGTGATT 57.485 50.000 26.66 10.65 46.51 2.57
59 60 3.648683 TTACTATGCCCCTAGGGTGAT 57.351 47.619 26.66 18.70 46.51 3.06
60 61 3.043418 GTTTACTATGCCCCTAGGGTGA 58.957 50.000 26.66 12.70 46.51 4.02
61 62 3.046374 AGTTTACTATGCCCCTAGGGTG 58.954 50.000 26.66 18.19 46.51 4.61
62 63 3.433088 AGTTTACTATGCCCCTAGGGT 57.567 47.619 26.66 10.93 46.51 4.34
63 64 7.584794 AACTTAAAGTTTACTATGCCCCTAGGG 60.585 40.741 22.25 22.25 39.84 3.53
64 65 6.896883 ACTTAAAGTTTACTATGCCCCTAGG 58.103 40.000 0.06 0.06 0.00 3.02
65 66 8.803397 AAACTTAAAGTTTACTATGCCCCTAG 57.197 34.615 0.00 0.00 45.75 3.02
102 103 9.846248 GCAAGTTTCAGTTGAAATATCATAAGT 57.154 29.630 10.20 0.00 44.69 2.24
103 104 9.844790 TGCAAGTTTCAGTTGAAATATCATAAG 57.155 29.630 10.20 0.00 44.69 1.73
106 107 9.715121 AATTGCAAGTTTCAGTTGAAATATCAT 57.285 25.926 4.94 0.00 44.69 2.45
107 108 9.195411 GAATTGCAAGTTTCAGTTGAAATATCA 57.805 29.630 4.94 4.75 44.69 2.15
108 109 9.415544 AGAATTGCAAGTTTCAGTTGAAATATC 57.584 29.630 13.74 0.00 44.69 1.63
109 110 9.768662 AAGAATTGCAAGTTTCAGTTGAAATAT 57.231 25.926 13.74 1.02 44.69 1.28
110 111 9.033481 CAAGAATTGCAAGTTTCAGTTGAAATA 57.967 29.630 13.74 0.00 41.82 1.40
111 112 7.912383 CAAGAATTGCAAGTTTCAGTTGAAAT 58.088 30.769 13.74 0.00 41.82 2.17
112 113 7.293402 CAAGAATTGCAAGTTTCAGTTGAAA 57.707 32.000 13.74 3.28 40.39 2.69
113 114 6.890663 CAAGAATTGCAAGTTTCAGTTGAA 57.109 33.333 13.74 0.00 40.39 2.69
129 130 5.181748 ACTTGATAAGAGCGAGCAAGAATT 58.818 37.500 13.38 0.00 41.73 2.17
130 131 4.764172 ACTTGATAAGAGCGAGCAAGAAT 58.236 39.130 13.38 0.00 41.73 2.40
131 132 4.193826 ACTTGATAAGAGCGAGCAAGAA 57.806 40.909 13.38 0.00 41.73 2.52
132 133 3.876274 ACTTGATAAGAGCGAGCAAGA 57.124 42.857 13.38 0.00 41.73 3.02
133 134 4.389992 TGAAACTTGATAAGAGCGAGCAAG 59.610 41.667 0.00 0.00 44.11 4.01
134 135 4.152402 GTGAAACTTGATAAGAGCGAGCAA 59.848 41.667 0.00 0.00 0.00 3.91
135 136 3.679980 GTGAAACTTGATAAGAGCGAGCA 59.320 43.478 0.00 0.00 0.00 4.26
136 137 3.241804 CGTGAAACTTGATAAGAGCGAGC 60.242 47.826 0.00 0.00 31.75 5.03
137 138 3.304559 CCGTGAAACTTGATAAGAGCGAG 59.695 47.826 0.00 0.00 31.75 5.03
138 139 3.057104 TCCGTGAAACTTGATAAGAGCGA 60.057 43.478 0.00 0.00 31.75 4.93
139 140 3.250744 TCCGTGAAACTTGATAAGAGCG 58.749 45.455 0.00 0.00 31.75 5.03
140 141 6.903883 TTATCCGTGAAACTTGATAAGAGC 57.096 37.500 0.00 0.00 35.03 4.09
177 178 8.447833 CGACTTTTATGCCTGTGACTAATAAAA 58.552 33.333 0.00 0.00 33.76 1.52
178 179 7.604927 ACGACTTTTATGCCTGTGACTAATAAA 59.395 33.333 0.00 0.00 0.00 1.40
179 180 7.101054 ACGACTTTTATGCCTGTGACTAATAA 58.899 34.615 0.00 0.00 0.00 1.40
180 181 6.636705 ACGACTTTTATGCCTGTGACTAATA 58.363 36.000 0.00 0.00 0.00 0.98
181 182 5.488341 ACGACTTTTATGCCTGTGACTAAT 58.512 37.500 0.00 0.00 0.00 1.73
182 183 4.890088 ACGACTTTTATGCCTGTGACTAA 58.110 39.130 0.00 0.00 0.00 2.24
183 184 4.530710 ACGACTTTTATGCCTGTGACTA 57.469 40.909 0.00 0.00 0.00 2.59
184 185 3.402628 ACGACTTTTATGCCTGTGACT 57.597 42.857 0.00 0.00 0.00 3.41
185 186 5.796350 ATAACGACTTTTATGCCTGTGAC 57.204 39.130 0.00 0.00 0.00 3.67
186 187 6.811253 AAATAACGACTTTTATGCCTGTGA 57.189 33.333 0.00 0.00 0.00 3.58
187 188 7.483691 GGTTAAATAACGACTTTTATGCCTGTG 59.516 37.037 0.00 0.00 37.07 3.66
188 189 7.532571 GGTTAAATAACGACTTTTATGCCTGT 58.467 34.615 0.00 0.00 37.07 4.00
189 190 6.685403 CGGTTAAATAACGACTTTTATGCCTG 59.315 38.462 0.00 0.00 37.07 4.85
190 191 6.183360 CCGGTTAAATAACGACTTTTATGCCT 60.183 38.462 0.00 0.00 37.07 4.75
191 192 5.967088 CCGGTTAAATAACGACTTTTATGCC 59.033 40.000 0.00 0.00 37.07 4.40
192 193 5.453266 GCCGGTTAAATAACGACTTTTATGC 59.547 40.000 1.90 0.00 37.07 3.14
193 194 5.967088 GGCCGGTTAAATAACGACTTTTATG 59.033 40.000 1.90 0.00 37.07 1.90
194 195 5.220643 CGGCCGGTTAAATAACGACTTTTAT 60.221 40.000 20.10 0.00 37.07 1.40
195 196 4.092675 CGGCCGGTTAAATAACGACTTTTA 59.907 41.667 20.10 0.00 37.07 1.52
196 197 3.120234 CGGCCGGTTAAATAACGACTTTT 60.120 43.478 20.10 0.00 37.07 2.27
197 198 2.416202 CGGCCGGTTAAATAACGACTTT 59.584 45.455 20.10 0.00 37.07 2.66
198 199 2.001872 CGGCCGGTTAAATAACGACTT 58.998 47.619 20.10 0.00 37.07 3.01
199 200 1.643880 CGGCCGGTTAAATAACGACT 58.356 50.000 20.10 0.00 37.07 4.18
200 201 0.026674 GCGGCCGGTTAAATAACGAC 59.973 55.000 29.38 0.17 37.07 4.34
201 202 0.108233 AGCGGCCGGTTAAATAACGA 60.108 50.000 26.97 0.00 37.07 3.85
202 203 0.302589 GAGCGGCCGGTTAAATAACG 59.697 55.000 32.91 0.00 37.07 3.18
203 204 0.302589 CGAGCGGCCGGTTAAATAAC 59.697 55.000 32.91 15.58 35.50 1.89
204 205 0.108233 ACGAGCGGCCGGTTAAATAA 60.108 50.000 32.91 0.00 0.00 1.40
205 206 0.743688 TACGAGCGGCCGGTTAAATA 59.256 50.000 32.91 17.68 0.00 1.40
206 207 0.807275 GTACGAGCGGCCGGTTAAAT 60.807 55.000 32.91 18.72 0.00 1.40
207 208 1.445926 GTACGAGCGGCCGGTTAAA 60.446 57.895 32.91 16.55 0.00 1.52
208 209 1.029408 TAGTACGAGCGGCCGGTTAA 61.029 55.000 32.91 16.93 0.00 2.01
209 210 1.029408 TTAGTACGAGCGGCCGGTTA 61.029 55.000 32.91 18.28 0.00 2.85
210 211 2.275547 CTTAGTACGAGCGGCCGGTT 62.276 60.000 32.91 19.47 0.00 4.44
211 212 2.751436 TTAGTACGAGCGGCCGGT 60.751 61.111 33.01 33.01 0.00 5.28
212 213 2.025727 CTTAGTACGAGCGGCCGG 59.974 66.667 29.38 13.36 0.00 6.13
213 214 0.457337 AAACTTAGTACGAGCGGCCG 60.457 55.000 24.05 24.05 0.00 6.13
214 215 1.275505 GAAACTTAGTACGAGCGGCC 58.724 55.000 0.00 0.00 0.00 6.13
215 216 1.986698 TGAAACTTAGTACGAGCGGC 58.013 50.000 0.00 0.00 0.00 6.53
216 217 3.829948 TCTTGAAACTTAGTACGAGCGG 58.170 45.455 0.00 0.00 0.00 5.52
217 218 4.474113 ACTCTTGAAACTTAGTACGAGCG 58.526 43.478 0.00 0.00 0.00 5.03
218 219 5.919141 TCAACTCTTGAAACTTAGTACGAGC 59.081 40.000 0.00 0.00 36.59 5.03
219 220 7.925703 TTCAACTCTTGAAACTTAGTACGAG 57.074 36.000 0.00 0.00 45.94 4.18
258 259 9.354673 TGAGACCTTTCAAATAAGATCTGTTTT 57.645 29.630 0.00 0.00 27.81 2.43
259 260 8.924511 TGAGACCTTTCAAATAAGATCTGTTT 57.075 30.769 0.00 0.00 27.81 2.83
260 261 9.171877 GATGAGACCTTTCAAATAAGATCTGTT 57.828 33.333 0.00 0.00 27.81 3.16
261 262 8.324306 TGATGAGACCTTTCAAATAAGATCTGT 58.676 33.333 0.00 0.00 27.81 3.41
262 263 8.728337 TGATGAGACCTTTCAAATAAGATCTG 57.272 34.615 0.00 0.00 27.81 2.90
263 264 9.917887 AATGATGAGACCTTTCAAATAAGATCT 57.082 29.630 0.00 0.00 30.42 2.75
271 272 9.528018 GTGTTTTTAATGATGAGACCTTTCAAA 57.472 29.630 0.00 0.00 0.00 2.69
272 273 8.690884 TGTGTTTTTAATGATGAGACCTTTCAA 58.309 29.630 0.00 0.00 0.00 2.69
273 274 8.231692 TGTGTTTTTAATGATGAGACCTTTCA 57.768 30.769 0.00 0.00 0.00 2.69
274 275 9.528018 TTTGTGTTTTTAATGATGAGACCTTTC 57.472 29.630 0.00 0.00 0.00 2.62
281 282 9.573133 GGGAGTATTTGTGTTTTTAATGATGAG 57.427 33.333 0.00 0.00 0.00 2.90
282 283 9.308000 AGGGAGTATTTGTGTTTTTAATGATGA 57.692 29.630 0.00 0.00 0.00 2.92
285 286 8.723311 CGTAGGGAGTATTTGTGTTTTTAATGA 58.277 33.333 0.00 0.00 0.00 2.57
286 287 8.508875 ACGTAGGGAGTATTTGTGTTTTTAATG 58.491 33.333 0.00 0.00 0.00 1.90
287 288 8.625786 ACGTAGGGAGTATTTGTGTTTTTAAT 57.374 30.769 0.00 0.00 0.00 1.40
288 289 7.173047 GGACGTAGGGAGTATTTGTGTTTTTAA 59.827 37.037 0.00 0.00 0.00 1.52
289 290 6.650390 GGACGTAGGGAGTATTTGTGTTTTTA 59.350 38.462 0.00 0.00 0.00 1.52
290 291 5.471116 GGACGTAGGGAGTATTTGTGTTTTT 59.529 40.000 0.00 0.00 0.00 1.94
291 292 4.999311 GGACGTAGGGAGTATTTGTGTTTT 59.001 41.667 0.00 0.00 0.00 2.43
292 293 4.572909 GGACGTAGGGAGTATTTGTGTTT 58.427 43.478 0.00 0.00 0.00 2.83
293 294 3.367703 CGGACGTAGGGAGTATTTGTGTT 60.368 47.826 0.00 0.00 0.00 3.32
294 295 2.165030 CGGACGTAGGGAGTATTTGTGT 59.835 50.000 0.00 0.00 0.00 3.72
295 296 2.424601 TCGGACGTAGGGAGTATTTGTG 59.575 50.000 0.00 0.00 0.00 3.33
296 297 2.726821 TCGGACGTAGGGAGTATTTGT 58.273 47.619 0.00 0.00 0.00 2.83
297 298 3.788333 TTCGGACGTAGGGAGTATTTG 57.212 47.619 0.00 0.00 0.00 2.32
298 299 4.806640 TTTTCGGACGTAGGGAGTATTT 57.193 40.909 0.00 0.00 0.00 1.40
299 300 5.595952 AGTATTTTCGGACGTAGGGAGTATT 59.404 40.000 0.00 0.00 0.00 1.89
300 301 5.136105 AGTATTTTCGGACGTAGGGAGTAT 58.864 41.667 0.00 0.00 0.00 2.12
301 302 4.526970 AGTATTTTCGGACGTAGGGAGTA 58.473 43.478 0.00 0.00 0.00 2.59
302 303 3.359950 AGTATTTTCGGACGTAGGGAGT 58.640 45.455 0.00 0.00 0.00 3.85
303 304 4.110482 CAAGTATTTTCGGACGTAGGGAG 58.890 47.826 0.00 0.00 0.00 4.30
304 305 3.511146 ACAAGTATTTTCGGACGTAGGGA 59.489 43.478 0.00 0.00 0.00 4.20
305 306 3.853475 ACAAGTATTTTCGGACGTAGGG 58.147 45.455 0.00 0.00 0.00 3.53
306 307 3.545078 CGACAAGTATTTTCGGACGTAGG 59.455 47.826 0.00 0.00 0.00 3.18
307 308 3.001365 GCGACAAGTATTTTCGGACGTAG 60.001 47.826 0.00 0.00 33.28 3.51
308 309 2.916716 GCGACAAGTATTTTCGGACGTA 59.083 45.455 0.00 0.00 33.28 3.57
309 310 1.723003 GCGACAAGTATTTTCGGACGT 59.277 47.619 0.00 0.00 33.28 4.34
310 311 1.722464 TGCGACAAGTATTTTCGGACG 59.278 47.619 0.00 0.00 33.28 4.79
311 312 5.459110 TTATGCGACAAGTATTTTCGGAC 57.541 39.130 0.00 0.00 35.86 4.79
312 313 6.457663 CCATTTATGCGACAAGTATTTTCGGA 60.458 38.462 0.00 0.00 37.51 4.55
313 314 5.681105 CCATTTATGCGACAAGTATTTTCGG 59.319 40.000 0.00 0.00 33.28 4.30
314 315 6.482835 TCCATTTATGCGACAAGTATTTTCG 58.517 36.000 0.00 0.00 35.82 3.46
315 316 8.128582 TCATCCATTTATGCGACAAGTATTTTC 58.871 33.333 0.00 0.00 0.00 2.29
316 317 7.995289 TCATCCATTTATGCGACAAGTATTTT 58.005 30.769 0.00 0.00 0.00 1.82
317 318 7.566760 TCATCCATTTATGCGACAAGTATTT 57.433 32.000 0.00 0.00 0.00 1.40
318 319 7.566760 TTCATCCATTTATGCGACAAGTATT 57.433 32.000 0.00 0.00 0.00 1.89
319 320 7.566760 TTTCATCCATTTATGCGACAAGTAT 57.433 32.000 0.00 0.00 0.00 2.12
320 321 6.993786 TTTCATCCATTTATGCGACAAGTA 57.006 33.333 0.00 0.00 0.00 2.24
321 322 5.895636 TTTCATCCATTTATGCGACAAGT 57.104 34.783 0.00 0.00 0.00 3.16
322 323 6.974048 TCATTTTCATCCATTTATGCGACAAG 59.026 34.615 0.00 0.00 0.00 3.16
323 324 6.861144 TCATTTTCATCCATTTATGCGACAA 58.139 32.000 0.00 0.00 0.00 3.18
324 325 6.448207 TCATTTTCATCCATTTATGCGACA 57.552 33.333 0.00 0.00 0.00 4.35
325 326 7.436080 ACATTCATTTTCATCCATTTATGCGAC 59.564 33.333 0.00 0.00 0.00 5.19
326 327 7.490840 ACATTCATTTTCATCCATTTATGCGA 58.509 30.769 0.00 0.00 0.00 5.10
327 328 7.703298 ACATTCATTTTCATCCATTTATGCG 57.297 32.000 0.00 0.00 0.00 4.73
386 387 9.996554 TCTCTGTCTGAAAATACTTGTCATTAA 57.003 29.630 0.00 0.00 0.00 1.40
387 388 9.996554 TTCTCTGTCTGAAAATACTTGTCATTA 57.003 29.630 0.00 0.00 0.00 1.90
388 389 8.908786 TTCTCTGTCTGAAAATACTTGTCATT 57.091 30.769 0.00 0.00 0.00 2.57
389 390 8.908786 TTTCTCTGTCTGAAAATACTTGTCAT 57.091 30.769 0.00 0.00 31.45 3.06
390 391 7.987458 ACTTTCTCTGTCTGAAAATACTTGTCA 59.013 33.333 0.00 0.00 33.70 3.58
391 392 8.371770 ACTTTCTCTGTCTGAAAATACTTGTC 57.628 34.615 0.00 0.00 33.70 3.18
400 401 9.173021 TGTTTTTCATACTTTCTCTGTCTGAAA 57.827 29.630 0.00 0.00 38.12 2.69
401 402 8.731275 TGTTTTTCATACTTTCTCTGTCTGAA 57.269 30.769 0.00 0.00 31.69 3.02
402 403 8.731275 TTGTTTTTCATACTTTCTCTGTCTGA 57.269 30.769 0.00 0.00 0.00 3.27
403 404 9.787532 TTTTGTTTTTCATACTTTCTCTGTCTG 57.212 29.630 0.00 0.00 0.00 3.51
459 460 7.784633 TTCGGCTTTTGATTTTCAATCTTTT 57.215 28.000 0.00 0.00 36.11 2.27
464 465 7.784633 TTTCTTTCGGCTTTTGATTTTCAAT 57.215 28.000 0.00 0.00 36.11 2.57
601 632 6.701340 AGATTTAAGCCATATATGCTCGTCA 58.299 36.000 7.24 0.00 38.34 4.35
604 635 9.926751 CATTTAGATTTAAGCCATATATGCTCG 57.073 33.333 7.24 0.00 38.34 5.03
631 670 0.679505 GGCCGAGCTGGTATATGTCA 59.320 55.000 0.00 0.00 41.21 3.58
635 678 2.606751 AGTAGGCCGAGCTGGTATAT 57.393 50.000 0.00 0.00 41.21 0.86
636 679 2.553904 GGTAGTAGGCCGAGCTGGTATA 60.554 54.545 0.00 0.00 41.21 1.47
640 683 1.455959 AGGTAGTAGGCCGAGCTGG 60.456 63.158 0.00 0.00 42.50 4.85
650 693 1.028330 TGCCGGTCGTCAGGTAGTAG 61.028 60.000 1.90 0.00 0.00 2.57
665 708 2.047274 AAGGACCGTGACATGCCG 60.047 61.111 0.00 0.00 0.00 5.69
667 710 1.514678 TTGCAAGGACCGTGACATGC 61.515 55.000 12.01 5.22 0.00 4.06
780 827 1.447838 CCGTCCGGAAGTGGTGATG 60.448 63.158 16.46 0.00 37.50 3.07
828 1969 1.309347 CCTGCAGGAGAGGAGAGGA 59.691 63.158 29.88 0.00 37.39 3.71
842 1983 2.156098 TGATGGTAAAACCGAACCTGC 58.844 47.619 0.00 0.00 42.58 4.85
872 2013 4.197498 GACGGTGCATGGCATGGC 62.197 66.667 27.48 19.51 41.91 4.40
951 2098 3.601537 GAGGTTATATAGGGGGAGGAGGA 59.398 52.174 0.00 0.00 0.00 3.71
957 2104 2.292061 GGCGAGAGGTTATATAGGGGGA 60.292 54.545 0.00 0.00 0.00 4.81
1025 2174 0.329596 GGATGGTCTTGGGTTCAGCT 59.670 55.000 0.00 0.00 0.00 4.24
1026 2175 0.038166 TGGATGGTCTTGGGTTCAGC 59.962 55.000 0.00 0.00 0.00 4.26
1035 2184 1.890552 AGCAGAGGATGGATGGTCTT 58.109 50.000 0.00 0.00 0.00 3.01
1037 2186 2.092753 TGAAAGCAGAGGATGGATGGTC 60.093 50.000 0.00 0.00 0.00 4.02
1038 2187 1.918262 TGAAAGCAGAGGATGGATGGT 59.082 47.619 0.00 0.00 0.00 3.55
1039 2188 2.723322 TGAAAGCAGAGGATGGATGG 57.277 50.000 0.00 0.00 0.00 3.51
1040 2189 3.318275 CCATTGAAAGCAGAGGATGGATG 59.682 47.826 3.20 0.00 36.92 3.51
1041 2190 3.563223 CCATTGAAAGCAGAGGATGGAT 58.437 45.455 3.20 0.00 36.92 3.41
1042 2191 2.947243 GCCATTGAAAGCAGAGGATGGA 60.947 50.000 11.23 0.00 36.92 3.41
1043 2192 1.407979 GCCATTGAAAGCAGAGGATGG 59.592 52.381 0.00 0.00 37.64 3.51
1045 2194 1.006281 TGGCCATTGAAAGCAGAGGAT 59.994 47.619 0.00 0.00 0.00 3.24
1536 2715 1.302033 CAACTCTGGCGAGCTTGGT 60.302 57.895 2.37 0.00 41.09 3.67
1577 2759 7.332678 AGCTGAAAGAAATGATTACCAAATTGC 59.667 33.333 0.00 0.00 34.07 3.56
1590 2772 5.104735 ACTCTACCCCTAGCTGAAAGAAATG 60.105 44.000 0.00 0.00 34.07 2.32
1591 2773 5.033522 ACTCTACCCCTAGCTGAAAGAAAT 58.966 41.667 0.00 0.00 34.07 2.17
1599 2781 6.919775 ATATTACAACTCTACCCCTAGCTG 57.080 41.667 0.00 0.00 0.00 4.24
1716 2912 1.810197 CGCGGTAATTGCAAAGCTAC 58.190 50.000 1.71 5.72 0.00 3.58
1789 2985 6.969828 AGAAGAATAAAAGAAGCTACCACG 57.030 37.500 0.00 0.00 0.00 4.94
1856 3052 7.559335 TGCATTGATCCCTACATCTTATAGT 57.441 36.000 0.00 0.00 0.00 2.12
1857 3053 7.714377 GGATGCATTGATCCCTACATCTTATAG 59.286 40.741 0.00 0.00 36.61 1.31
1900 3096 4.142622 TGAGCTTGCATGCACTTTATACAC 60.143 41.667 22.58 5.89 34.99 2.90
1901 3097 4.009002 TGAGCTTGCATGCACTTTATACA 58.991 39.130 22.58 11.40 34.99 2.29
1902 3098 4.621068 TGAGCTTGCATGCACTTTATAC 57.379 40.909 22.58 8.93 34.99 1.47
1903 3099 5.840243 AATGAGCTTGCATGCACTTTATA 57.160 34.783 22.58 3.16 34.99 0.98
1904 3100 4.730949 AATGAGCTTGCATGCACTTTAT 57.269 36.364 22.58 10.87 34.99 1.40
1905 3101 4.487948 GAAATGAGCTTGCATGCACTTTA 58.512 39.130 22.58 4.47 34.99 1.85
1906 3102 3.323243 GAAATGAGCTTGCATGCACTTT 58.677 40.909 22.58 18.87 34.99 2.66
1907 3103 2.353406 GGAAATGAGCTTGCATGCACTT 60.353 45.455 22.58 14.50 34.99 3.16
1908 3104 1.203994 GGAAATGAGCTTGCATGCACT 59.796 47.619 22.58 15.80 34.99 4.40
1912 3108 2.099263 CAGAGGGAAATGAGCTTGCATG 59.901 50.000 0.00 0.00 0.00 4.06
2018 3248 7.390027 ACATCTTATCTGTAGCAGTTTTGTCT 58.610 34.615 0.00 0.00 32.61 3.41
2115 3346 2.287373 GCTATGCTCACATCAAGTCTGC 59.713 50.000 0.00 0.00 37.74 4.26
2168 3401 4.436332 GCATTAAGCTTTCTTGATTGGGG 58.564 43.478 3.20 0.00 41.15 4.96
2188 3421 4.947147 GTCCCACCAACGCCAGCA 62.947 66.667 0.00 0.00 0.00 4.41
2242 3475 0.386113 GACCGACCCATAGCTGTCTC 59.614 60.000 0.00 0.00 0.00 3.36
2250 3483 2.807392 GTTTTTGAACGACCGACCCATA 59.193 45.455 0.00 0.00 0.00 2.74
2251 3484 1.605232 GTTTTTGAACGACCGACCCAT 59.395 47.619 0.00 0.00 0.00 4.00
2252 3485 1.015868 GTTTTTGAACGACCGACCCA 58.984 50.000 0.00 0.00 0.00 4.51
2253 3486 1.015868 TGTTTTTGAACGACCGACCC 58.984 50.000 0.00 0.00 0.00 4.46
2254 3487 2.711885 CTTGTTTTTGAACGACCGACC 58.288 47.619 0.00 0.00 0.00 4.79
2256 3489 1.064357 GGCTTGTTTTTGAACGACCGA 59.936 47.619 0.00 0.00 0.00 4.69
2324 3642 3.906879 TGCATGCGCATGATGGCC 61.907 61.111 45.47 30.07 45.36 5.36
2342 3660 2.536761 AGGCTGTACGTGTTGCTTTA 57.463 45.000 0.00 0.00 0.00 1.85
2407 3727 7.362660 CCTGTGATTGGATTAGAATATGCATGG 60.363 40.741 10.16 0.00 0.00 3.66
2448 3769 2.016318 TCTGACTGTGCACCAAACTTG 58.984 47.619 15.69 0.00 0.00 3.16
2454 3775 1.339342 CCATCATCTGACTGTGCACCA 60.339 52.381 15.69 4.09 0.00 4.17
2461 3782 3.548214 CGTACGTACCCATCATCTGACTG 60.548 52.174 19.67 0.00 0.00 3.51
2495 3820 0.321919 GAAGCACCATGACAGCCAGA 60.322 55.000 0.00 0.00 0.00 3.86
2527 3854 3.982475 TGCAAATACGAACCATGCAAAA 58.018 36.364 0.00 0.00 43.39 2.44
2563 3890 1.060553 CGTTACCAGTAAGCATGCGTG 59.939 52.381 16.84 10.47 0.00 5.34
2577 3904 3.668980 TAAGCGCAGGCCCGTTACC 62.669 63.158 11.47 0.00 41.24 2.85


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

AutoCloner maintained by Alex Coulton.