Multiple sequence alignment - TraesCS5D01G246200

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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 TraesCS5D01G246200 chr5D 100.000 2665 0 0 1 2665 354268099 354270763 0.000000e+00 4922
1 TraesCS5D01G246200 chr5B 91.032 1405 63 26 555 1916 418549351 418550735 0.000000e+00 1838
2 TraesCS5D01G246200 chr5B 87.001 777 61 12 1918 2664 418552026 418552792 0.000000e+00 839
3 TraesCS5D01G246200 chr5B 88.055 293 28 6 283 571 418549042 418549331 9.140000e-90 340
4 TraesCS5D01G246200 chr5B 79.810 421 71 6 2201 2608 35697216 35697635 7.210000e-76 294
5 TraesCS5D01G246200 chr5A 90.169 885 48 20 815 1685 455206203 455207062 0.000000e+00 1116
6 TraesCS5D01G246200 chr5A 88.991 545 46 9 282 818 455205620 455206158 0.000000e+00 662
7 TraesCS5D01G246200 chr1B 83.373 421 64 6 2201 2617 300743691 300744109 4.160000e-103 385
8 TraesCS5D01G246200 chr2A 81.915 470 69 10 2201 2658 598965071 598965536 1.500000e-102 383
9 TraesCS5D01G246200 chr7D 81.604 424 71 5 2197 2617 213444114 213443695 7.060000e-91 344
10 TraesCS5D01G246200 chr7D 79.294 425 74 8 2197 2617 165361177 165360763 4.340000e-73 285
11 TraesCS5D01G246200 chr3B 81.106 434 66 10 2201 2619 472743248 472742816 1.530000e-87 333
12 TraesCS5D01G246200 chr4D 81.019 432 68 11 2192 2617 152830888 152831311 5.500000e-87 331
13 TraesCS5D01G246200 chr1D 84.362 243 31 6 2353 2593 443715730 443715493 5.740000e-57 231
14 TraesCS5D01G246200 chrUn 83.824 204 30 3 2416 2617 105540223 105540425 9.740000e-45 191


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 TraesCS5D01G246200 chr5D 354268099 354270763 2664 False 4922.000000 4922 100.000 1 2665 1 chr5D.!!$F1 2664
1 TraesCS5D01G246200 chr5B 418549042 418552792 3750 False 1005.666667 1838 88.696 283 2664 3 chr5B.!!$F2 2381
2 TraesCS5D01G246200 chr5A 455205620 455207062 1442 False 889.000000 1116 89.580 282 1685 2 chr5A.!!$F1 1403

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
134 135 0.035056 AGCATCGGTTCTTCCCAAGG 60.035 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 2006 0.10852 ATGCGGCTGCTCAAATTTGG 60.109 50.0 20.27 9.84 43.34 3.28 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
23 24 5.860941 TGGTTTAGCAACTCAAATTTCCA 57.139 34.783 0.00 0.00 32.90 3.53
24 25 6.227298 TGGTTTAGCAACTCAAATTTCCAA 57.773 33.333 0.00 0.00 32.90 3.53
25 26 6.045955 TGGTTTAGCAACTCAAATTTCCAAC 58.954 36.000 0.00 0.00 32.90 3.77
26 27 5.174943 GGTTTAGCAACTCAAATTTCCAACG 59.825 40.000 0.00 0.00 32.90 4.10
27 28 3.369546 AGCAACTCAAATTTCCAACGG 57.630 42.857 0.00 0.00 0.00 4.44
28 29 2.955660 AGCAACTCAAATTTCCAACGGA 59.044 40.909 0.00 0.00 0.00 4.69
29 30 3.573967 AGCAACTCAAATTTCCAACGGAT 59.426 39.130 0.00 0.00 0.00 4.18
30 31 4.764823 AGCAACTCAAATTTCCAACGGATA 59.235 37.500 0.00 0.00 0.00 2.59
31 32 5.095490 GCAACTCAAATTTCCAACGGATAG 58.905 41.667 0.00 0.00 0.00 2.08
32 33 5.335661 GCAACTCAAATTTCCAACGGATAGT 60.336 40.000 0.00 0.00 0.00 2.12
33 34 6.677913 CAACTCAAATTTCCAACGGATAGTT 58.322 36.000 0.00 0.00 45.45 2.24
66 67 8.491331 TTTTTGTTGCTAAGCTTCTTTCATTT 57.509 26.923 0.00 0.00 0.00 2.32
67 68 9.593134 TTTTTGTTGCTAAGCTTCTTTCATTTA 57.407 25.926 0.00 0.00 0.00 1.40
68 69 9.593134 TTTTGTTGCTAAGCTTCTTTCATTTAA 57.407 25.926 0.00 0.00 0.00 1.52
69 70 9.762933 TTTGTTGCTAAGCTTCTTTCATTTAAT 57.237 25.926 0.00 0.00 0.00 1.40
70 71 9.762933 TTGTTGCTAAGCTTCTTTCATTTAATT 57.237 25.926 0.00 0.00 0.00 1.40
90 91 9.768662 TTTAATTAGTTTTAGACTCAGAACGGT 57.231 29.630 0.00 0.00 39.86 4.83
91 92 7.653767 AATTAGTTTTAGACTCAGAACGGTG 57.346 36.000 0.00 0.00 39.86 4.94
92 93 4.667519 AGTTTTAGACTCAGAACGGTGT 57.332 40.909 0.00 0.00 31.20 4.16
93 94 5.019785 AGTTTTAGACTCAGAACGGTGTT 57.980 39.130 0.00 0.00 31.20 3.32
94 95 5.425630 AGTTTTAGACTCAGAACGGTGTTT 58.574 37.500 0.00 0.00 31.20 2.83
95 96 5.878669 AGTTTTAGACTCAGAACGGTGTTTT 59.121 36.000 0.00 0.00 31.20 2.43
96 97 5.978934 TTTAGACTCAGAACGGTGTTTTC 57.021 39.130 0.00 0.00 0.00 2.29
97 98 3.536956 AGACTCAGAACGGTGTTTTCA 57.463 42.857 0.00 0.00 0.00 2.69
108 109 1.873698 GTGTTTTCACCTAGGCACGA 58.126 50.000 9.30 0.00 44.31 4.35
109 110 1.798813 GTGTTTTCACCTAGGCACGAG 59.201 52.381 9.30 0.00 44.31 4.18
119 120 2.190578 GGCACGAGGGCTTAGCAT 59.809 61.111 6.53 0.00 39.42 3.79
120 121 1.889573 GGCACGAGGGCTTAGCATC 60.890 63.158 6.53 2.44 39.42 3.91
121 122 2.240500 GCACGAGGGCTTAGCATCG 61.241 63.158 23.02 23.02 42.23 3.84
122 123 1.592669 CACGAGGGCTTAGCATCGG 60.593 63.158 26.33 15.85 41.34 4.18
123 124 2.058595 ACGAGGGCTTAGCATCGGT 61.059 57.895 26.33 14.35 41.34 4.69
124 125 1.144057 CGAGGGCTTAGCATCGGTT 59.856 57.895 18.91 0.00 36.27 4.44
125 126 0.876342 CGAGGGCTTAGCATCGGTTC 60.876 60.000 18.91 2.20 36.27 3.62
126 127 0.466124 GAGGGCTTAGCATCGGTTCT 59.534 55.000 6.53 0.00 0.00 3.01
127 128 0.912486 AGGGCTTAGCATCGGTTCTT 59.088 50.000 6.53 0.00 0.00 2.52
128 129 1.134371 AGGGCTTAGCATCGGTTCTTC 60.134 52.381 6.53 0.00 0.00 2.87
129 130 1.300481 GGCTTAGCATCGGTTCTTCC 58.700 55.000 6.53 0.00 0.00 3.46
130 131 1.300481 GCTTAGCATCGGTTCTTCCC 58.700 55.000 0.00 0.00 0.00 3.97
131 132 1.406887 GCTTAGCATCGGTTCTTCCCA 60.407 52.381 0.00 0.00 0.00 4.37
132 133 2.939640 GCTTAGCATCGGTTCTTCCCAA 60.940 50.000 0.00 0.00 0.00 4.12
133 134 2.691409 TAGCATCGGTTCTTCCCAAG 57.309 50.000 0.00 0.00 0.00 3.61
134 135 0.035056 AGCATCGGTTCTTCCCAAGG 60.035 55.000 0.00 0.00 0.00 3.61
135 136 0.322546 GCATCGGTTCTTCCCAAGGT 60.323 55.000 0.00 0.00 0.00 3.50
136 137 1.739067 CATCGGTTCTTCCCAAGGTC 58.261 55.000 0.00 0.00 0.00 3.85
137 138 1.003118 CATCGGTTCTTCCCAAGGTCA 59.997 52.381 0.00 0.00 0.00 4.02
138 139 1.358152 TCGGTTCTTCCCAAGGTCAT 58.642 50.000 0.00 0.00 0.00 3.06
139 140 1.278127 TCGGTTCTTCCCAAGGTCATC 59.722 52.381 0.00 0.00 0.00 2.92
140 141 1.003118 CGGTTCTTCCCAAGGTCATCA 59.997 52.381 0.00 0.00 0.00 3.07
141 142 2.552155 CGGTTCTTCCCAAGGTCATCAA 60.552 50.000 0.00 0.00 0.00 2.57
142 143 3.496331 GGTTCTTCCCAAGGTCATCAAA 58.504 45.455 0.00 0.00 0.00 2.69
143 144 3.255888 GGTTCTTCCCAAGGTCATCAAAC 59.744 47.826 0.00 0.00 0.00 2.93
144 145 4.145052 GTTCTTCCCAAGGTCATCAAACT 58.855 43.478 0.00 0.00 0.00 2.66
145 146 5.313712 GTTCTTCCCAAGGTCATCAAACTA 58.686 41.667 0.00 0.00 0.00 2.24
146 147 4.906618 TCTTCCCAAGGTCATCAAACTAC 58.093 43.478 0.00 0.00 0.00 2.73
147 148 4.597507 TCTTCCCAAGGTCATCAAACTACT 59.402 41.667 0.00 0.00 0.00 2.57
148 149 5.783360 TCTTCCCAAGGTCATCAAACTACTA 59.217 40.000 0.00 0.00 0.00 1.82
149 150 6.443849 TCTTCCCAAGGTCATCAAACTACTAT 59.556 38.462 0.00 0.00 0.00 2.12
150 151 6.235231 TCCCAAGGTCATCAAACTACTATC 57.765 41.667 0.00 0.00 0.00 2.08
151 152 5.964477 TCCCAAGGTCATCAAACTACTATCT 59.036 40.000 0.00 0.00 0.00 1.98
152 153 6.098409 TCCCAAGGTCATCAAACTACTATCTC 59.902 42.308 0.00 0.00 0.00 2.75
153 154 6.098982 CCCAAGGTCATCAAACTACTATCTCT 59.901 42.308 0.00 0.00 0.00 3.10
154 155 7.365117 CCCAAGGTCATCAAACTACTATCTCTT 60.365 40.741 0.00 0.00 0.00 2.85
155 156 7.708752 CCAAGGTCATCAAACTACTATCTCTTC 59.291 40.741 0.00 0.00 0.00 2.87
156 157 8.474025 CAAGGTCATCAAACTACTATCTCTTCT 58.526 37.037 0.00 0.00 0.00 2.85
157 158 8.602472 AGGTCATCAAACTACTATCTCTTCTT 57.398 34.615 0.00 0.00 0.00 2.52
158 159 9.702253 AGGTCATCAAACTACTATCTCTTCTTA 57.298 33.333 0.00 0.00 0.00 2.10
170 171 8.950208 ACTATCTCTTCTTAATTTACCTGCAC 57.050 34.615 0.00 0.00 0.00 4.57
171 172 8.540388 ACTATCTCTTCTTAATTTACCTGCACA 58.460 33.333 0.00 0.00 0.00 4.57
172 173 9.553064 CTATCTCTTCTTAATTTACCTGCACAT 57.447 33.333 0.00 0.00 0.00 3.21
173 174 8.814038 ATCTCTTCTTAATTTACCTGCACATT 57.186 30.769 0.00 0.00 0.00 2.71
174 175 9.905713 ATCTCTTCTTAATTTACCTGCACATTA 57.094 29.630 0.00 0.00 0.00 1.90
175 176 9.733556 TCTCTTCTTAATTTACCTGCACATTAA 57.266 29.630 0.00 0.00 0.00 1.40
185 186 9.664332 ATTTACCTGCACATTAAATTTTATGCA 57.336 25.926 15.29 14.56 40.57 3.96
186 187 9.664332 TTTACCTGCACATTAAATTTTATGCAT 57.336 25.926 15.29 3.79 41.83 3.96
188 189 8.647143 ACCTGCACATTAAATTTTATGCATAC 57.353 30.769 15.29 5.19 41.83 2.39
189 190 8.477256 ACCTGCACATTAAATTTTATGCATACT 58.523 29.630 15.29 0.00 41.83 2.12
190 191 9.316730 CCTGCACATTAAATTTTATGCATACTT 57.683 29.630 15.29 0.75 41.83 2.24
192 193 9.096160 TGCACATTAAATTTTATGCATACTTGG 57.904 29.630 15.29 0.00 38.11 3.61
193 194 8.063630 GCACATTAAATTTTATGCATACTTGGC 58.936 33.333 15.29 5.11 33.27 4.52
194 195 8.268052 CACATTAAATTTTATGCATACTTGGCG 58.732 33.333 15.29 0.00 0.00 5.69
195 196 7.437862 ACATTAAATTTTATGCATACTTGGCGG 59.562 33.333 15.29 0.00 0.00 6.13
196 197 5.337578 AAATTTTATGCATACTTGGCGGT 57.662 34.783 5.74 0.00 0.00 5.68
197 198 4.568152 ATTTTATGCATACTTGGCGGTC 57.432 40.909 5.74 0.00 0.00 4.79
198 199 3.275617 TTTATGCATACTTGGCGGTCT 57.724 42.857 5.74 0.00 0.00 3.85
199 200 3.275617 TTATGCATACTTGGCGGTCTT 57.724 42.857 5.74 0.00 0.00 3.01
200 201 4.409718 TTATGCATACTTGGCGGTCTTA 57.590 40.909 5.74 0.00 0.00 2.10
201 202 3.492102 ATGCATACTTGGCGGTCTTAT 57.508 42.857 0.00 0.00 0.00 1.73
202 203 2.560504 TGCATACTTGGCGGTCTTATG 58.439 47.619 0.00 0.00 0.00 1.90
203 204 2.169561 TGCATACTTGGCGGTCTTATGA 59.830 45.455 0.00 0.00 0.00 2.15
204 205 2.544267 GCATACTTGGCGGTCTTATGAC 59.456 50.000 0.10 0.10 42.22 3.06
205 206 2.572191 TACTTGGCGGTCTTATGACG 57.428 50.000 2.93 0.71 43.79 4.35
206 207 0.108329 ACTTGGCGGTCTTATGACGG 60.108 55.000 10.80 10.80 43.79 4.79
207 208 0.810031 CTTGGCGGTCTTATGACGGG 60.810 60.000 15.26 6.35 43.79 5.28
208 209 1.259142 TTGGCGGTCTTATGACGGGA 61.259 55.000 15.26 0.00 43.79 5.14
209 210 1.227176 GGCGGTCTTATGACGGGAC 60.227 63.158 15.26 4.12 43.79 4.46
210 211 1.514087 GCGGTCTTATGACGGGACA 59.486 57.895 15.26 0.00 43.79 4.02
211 212 0.108520 GCGGTCTTATGACGGGACAA 60.109 55.000 15.26 0.00 43.79 3.18
212 213 1.673626 GCGGTCTTATGACGGGACAAA 60.674 52.381 15.26 0.00 43.79 2.83
213 214 2.901249 CGGTCTTATGACGGGACAAAT 58.099 47.619 8.06 0.00 43.79 2.32
214 215 3.267483 CGGTCTTATGACGGGACAAATT 58.733 45.455 8.06 0.00 43.79 1.82
215 216 3.687698 CGGTCTTATGACGGGACAAATTT 59.312 43.478 8.06 0.00 43.79 1.82
216 217 4.201783 CGGTCTTATGACGGGACAAATTTC 60.202 45.833 8.06 0.00 43.79 2.17
217 218 4.941873 GGTCTTATGACGGGACAAATTTCT 59.058 41.667 2.93 0.00 43.79 2.52
218 219 6.110707 GGTCTTATGACGGGACAAATTTCTA 58.889 40.000 2.93 0.00 43.79 2.10
219 220 6.766467 GGTCTTATGACGGGACAAATTTCTAT 59.234 38.462 2.93 0.00 43.79 1.98
220 221 7.929785 GGTCTTATGACGGGACAAATTTCTATA 59.070 37.037 2.93 0.00 43.79 1.31
221 222 9.321562 GTCTTATGACGGGACAAATTTCTATAA 57.678 33.333 0.00 0.00 33.15 0.98
222 223 9.893634 TCTTATGACGGGACAAATTTCTATAAA 57.106 29.630 0.00 0.00 0.00 1.40
223 224 9.931210 CTTATGACGGGACAAATTTCTATAAAC 57.069 33.333 0.00 0.00 0.00 2.01
224 225 7.931578 ATGACGGGACAAATTTCTATAAACA 57.068 32.000 0.00 0.00 0.00 2.83
225 226 7.747155 TGACGGGACAAATTTCTATAAACAA 57.253 32.000 0.00 0.00 0.00 2.83
226 227 8.343168 TGACGGGACAAATTTCTATAAACAAT 57.657 30.769 0.00 0.00 0.00 2.71
227 228 9.451002 TGACGGGACAAATTTCTATAAACAATA 57.549 29.630 0.00 0.00 0.00 1.90
254 255 9.771534 TTAAACTTATGGAAATTTTGACTTGGG 57.228 29.630 0.00 0.00 0.00 4.12
255 256 6.358974 ACTTATGGAAATTTTGACTTGGGG 57.641 37.500 0.00 0.00 0.00 4.96
256 257 3.701205 ATGGAAATTTTGACTTGGGGC 57.299 42.857 0.00 0.00 0.00 5.80
257 258 2.402564 TGGAAATTTTGACTTGGGGCA 58.597 42.857 0.00 0.00 0.00 5.36
258 259 2.774234 TGGAAATTTTGACTTGGGGCAA 59.226 40.909 0.00 0.00 0.00 4.52
259 260 3.393941 TGGAAATTTTGACTTGGGGCAAT 59.606 39.130 0.00 0.00 0.00 3.56
260 261 4.141298 TGGAAATTTTGACTTGGGGCAATT 60.141 37.500 0.00 0.00 0.00 2.32
261 262 4.826733 GGAAATTTTGACTTGGGGCAATTT 59.173 37.500 0.00 0.00 0.00 1.82
262 263 6.000840 GGAAATTTTGACTTGGGGCAATTTA 58.999 36.000 0.00 0.00 0.00 1.40
263 264 6.072728 GGAAATTTTGACTTGGGGCAATTTAC 60.073 38.462 0.00 0.00 0.00 2.01
264 265 5.823861 ATTTTGACTTGGGGCAATTTACT 57.176 34.783 0.00 0.00 0.00 2.24
265 266 5.622346 TTTTGACTTGGGGCAATTTACTT 57.378 34.783 0.00 0.00 0.00 2.24
266 267 5.622346 TTTGACTTGGGGCAATTTACTTT 57.378 34.783 0.00 0.00 0.00 2.66
267 268 5.622346 TTGACTTGGGGCAATTTACTTTT 57.378 34.783 0.00 0.00 0.00 2.27
268 269 5.622346 TGACTTGGGGCAATTTACTTTTT 57.378 34.783 0.00 0.00 0.00 1.94
331 332 7.112528 TGTTTAGTGCTAATTGAGTTACACG 57.887 36.000 0.00 0.00 33.44 4.49
338 339 4.142902 GCTAATTGAGTTACACGCACATGT 60.143 41.667 0.00 0.00 36.56 3.21
352 353 5.855925 CACGCACATGTACACACAATTATTT 59.144 36.000 0.00 0.00 38.42 1.40
372 373 1.686052 TCCACAATGCTGGAAAACCAC 59.314 47.619 2.80 0.00 37.39 4.16
374 375 2.472816 CACAATGCTGGAAAACCACAC 58.527 47.619 0.00 0.00 0.00 3.82
375 376 2.106566 ACAATGCTGGAAAACCACACA 58.893 42.857 0.00 0.00 0.00 3.72
394 395 6.143758 CCACACATGGTTTTATTTTCGACTTG 59.856 38.462 0.00 0.00 41.64 3.16
411 413 2.459934 CTTGGTCGCAACAAGGAAAAC 58.540 47.619 6.16 0.00 41.16 2.43
439 441 4.282195 ACGGATTTTAACTTGCCATTTCCA 59.718 37.500 0.00 0.00 0.00 3.53
443 445 7.416213 CGGATTTTAACTTGCCATTTCCATCTA 60.416 37.037 0.00 0.00 0.00 1.98
512 514 6.976349 TCTAGACGCGTGTACAATAATTTCAT 59.024 34.615 20.70 0.00 0.00 2.57
592 632 3.863424 TGTAGAAATTCGATGCGGAAGTC 59.137 43.478 0.00 0.00 0.00 3.01
740 780 1.068055 GCCACTTGGTGCAGATTCTTG 60.068 52.381 0.00 0.00 37.57 3.02
742 782 1.884579 CACTTGGTGCAGATTCTTGCT 59.115 47.619 0.00 0.00 44.38 3.91
760 800 2.888513 CTCCTTTCAACGAGCATGTG 57.111 50.000 0.00 0.00 0.00 3.21
774 819 1.610522 GCATGTGTAGATGGCCCAATC 59.389 52.381 0.00 0.00 0.00 2.67
782 827 3.173953 AGATGGCCCAATCAAAACAGA 57.826 42.857 0.00 0.00 0.00 3.41
783 828 3.094572 AGATGGCCCAATCAAAACAGAG 58.905 45.455 0.00 0.00 0.00 3.35
790 835 4.322650 GCCCAATCAAAACAGAGCCAAATA 60.323 41.667 0.00 0.00 0.00 1.40
796 843 9.027129 CAATCAAAACAGAGCCAAATATATGTG 57.973 33.333 0.00 0.00 0.00 3.21
798 845 6.152492 TCAAAACAGAGCCAAATATATGTGCA 59.848 34.615 0.00 0.00 0.00 4.57
827 921 8.809159 ACAACGAGTATCAATCAAGAGATATG 57.191 34.615 0.00 0.00 33.08 1.78
837 931 6.495181 TCAATCAAGAGATATGTAGAGTCCCC 59.505 42.308 0.00 0.00 33.08 4.81
1011 1113 1.370609 CAGCTGCACATTCAGAGAGG 58.629 55.000 0.00 0.00 36.19 3.69
1012 1114 0.392729 AGCTGCACATTCAGAGAGGC 60.393 55.000 1.02 0.00 36.19 4.70
1013 1115 1.703438 GCTGCACATTCAGAGAGGCG 61.703 60.000 0.00 0.00 36.19 5.52
1020 1122 2.103771 ACATTCAGAGAGGCGCATACAT 59.896 45.455 10.83 0.00 0.00 2.29
1021 1123 2.988010 TTCAGAGAGGCGCATACATT 57.012 45.000 10.83 0.00 0.00 2.71
1031 1133 6.230472 AGAGGCGCATACATTTTCATACATA 58.770 36.000 10.83 0.00 0.00 2.29
1045 1147 3.319972 TCATACATAGACGGCCAAGGTAC 59.680 47.826 2.24 0.00 0.00 3.34
1074 1178 4.475135 GCAAGGAGGCCGGAGACC 62.475 72.222 5.05 4.08 0.00 3.85
1383 1487 0.106335 TCGTCGCCTACTAGAGAGGG 59.894 60.000 14.70 7.29 34.35 4.30
1388 1492 1.816183 CGCCTACTAGAGAGGGGTCTG 60.816 61.905 18.25 0.00 41.08 3.51
1397 1501 1.762858 GAGGGGTCTGGCTAGGTCC 60.763 68.421 0.00 0.40 0.00 4.46
1429 1535 4.285863 AGCTAGCTCCATATCTACCCATC 58.714 47.826 12.68 0.00 0.00 3.51
1432 1538 4.085854 AGCTCCATATCTACCCATCCAT 57.914 45.455 0.00 0.00 0.00 3.41
1433 1539 3.779183 AGCTCCATATCTACCCATCCATG 59.221 47.826 0.00 0.00 0.00 3.66
1434 1540 3.683847 GCTCCATATCTACCCATCCATGC 60.684 52.174 0.00 0.00 0.00 4.06
1435 1541 3.520721 CTCCATATCTACCCATCCATGCA 59.479 47.826 0.00 0.00 0.00 3.96
1436 1542 4.113841 TCCATATCTACCCATCCATGCAT 58.886 43.478 0.00 0.00 0.00 3.96
1478 1584 1.070975 GCGCTGATCTATCGTTTGCTG 60.071 52.381 0.00 0.00 0.00 4.41
1534 1640 1.269166 CTAATCTGTGCACCGACGTC 58.731 55.000 15.69 5.18 0.00 4.34
1561 1670 5.968261 CGTCGGTGATCTATCATGATGTATC 59.032 44.000 18.72 18.53 39.30 2.24
1609 1734 3.883744 CTCGCCTTTCCTGCACGGT 62.884 63.158 2.68 0.00 0.00 4.83
1629 1754 3.797796 GGTTTGCCGTCGTTGTTAATTTT 59.202 39.130 0.00 0.00 0.00 1.82
1639 1764 4.517453 TCGTTGTTAATTTTCCCTGTCTGG 59.483 41.667 0.00 0.00 0.00 3.86
1640 1765 4.517453 CGTTGTTAATTTTCCCTGTCTGGA 59.483 41.667 0.00 0.00 38.35 3.86
1685 1810 2.215196 GATCTGGCGCCCGTTTATTTA 58.785 47.619 26.77 0.00 0.00 1.40
1693 1818 4.207635 GGCGCCCGTTTATTTATTTTTAGC 59.792 41.667 18.11 0.00 0.00 3.09
1698 1823 7.168138 GCCCGTTTATTTATTTTTAGCGTTTG 58.832 34.615 0.00 0.00 0.00 2.93
1713 1838 2.393764 CGTTTGTTCTGGTGATTTGGC 58.606 47.619 0.00 0.00 0.00 4.52
1769 1894 2.912956 TCAACCTGAGGGCAACTCTAAT 59.087 45.455 2.38 0.00 46.72 1.73
1881 2006 0.519077 CAAAAGTTGCCTCTCTCGCC 59.481 55.000 0.00 0.00 0.00 5.54
1907 2032 2.437359 AGCAGCCGCATCCACTTC 60.437 61.111 0.00 0.00 42.27 3.01
1916 2041 4.040952 AGCCGCATCCACTTCTCTAATTAT 59.959 41.667 0.00 0.00 0.00 1.28
1919 2044 6.595716 GCCGCATCCACTTCTCTAATTATAAT 59.404 38.462 0.00 0.00 0.00 1.28
1960 3374 3.578272 CGCTCCTCCTCTCCGACG 61.578 72.222 0.00 0.00 0.00 5.12
1973 3387 4.143333 CGACGCTCCCCGGTGATT 62.143 66.667 0.00 0.00 42.52 2.57
2042 3479 2.733517 GAACTCCGACGAGAATCCATC 58.266 52.381 0.00 0.00 38.52 3.51
2076 3513 0.246360 ATCACTCGTCGTTCATGCCA 59.754 50.000 0.00 0.00 0.00 4.92
2083 3520 2.189257 CGTTCATGCCATCCCCGA 59.811 61.111 0.00 0.00 0.00 5.14
2104 3541 4.722535 TGGCCTCGCTTCTCCCCT 62.723 66.667 3.32 0.00 0.00 4.79
2105 3542 3.855853 GGCCTCGCTTCTCCCCTC 61.856 72.222 0.00 0.00 0.00 4.30
2118 3555 3.738481 CCCTCCATCCCCGGCAAA 61.738 66.667 0.00 0.00 0.00 3.68
2119 3556 2.358619 CCTCCATCCCCGGCAAAA 59.641 61.111 0.00 0.00 0.00 2.44
2144 3582 1.592669 CGCTCTTACAGCCATCCCG 60.593 63.158 0.00 0.00 46.74 5.14
2149 3587 3.338275 TTACAGCCATCCCGCCCAC 62.338 63.158 0.00 0.00 0.00 4.61
2179 3617 2.018542 ACAGCAACACGTACAACACT 57.981 45.000 0.00 0.00 0.00 3.55
2197 3635 5.892160 ACACTGACACACACGTATATACT 57.108 39.130 11.05 0.00 0.00 2.12
2199 3637 6.779117 ACACTGACACACACGTATATACTAC 58.221 40.000 11.05 0.00 0.00 2.73
2216 3654 2.009774 CTACGGGCTGAAAATGGAGTG 58.990 52.381 0.00 0.00 0.00 3.51
2225 3663 6.462347 GGGCTGAAAATGGAGTGAAAAGTTTA 60.462 38.462 0.00 0.00 0.00 2.01
2240 3678 6.399639 AAAAGTTTATGCTTTTCCGGAGAA 57.600 33.333 3.34 5.58 42.90 2.87
2241 3679 6.590234 AAAGTTTATGCTTTTCCGGAGAAT 57.410 33.333 8.03 0.00 35.37 2.40
2252 3690 5.554822 TTTCCGGAGAATAAATGGAAACG 57.445 39.130 3.34 0.00 33.63 3.60
2257 3695 5.220605 CCGGAGAATAAATGGAAACGAAGAC 60.221 44.000 0.00 0.00 0.00 3.01
2335 3773 9.443283 TTTTATGCGAAATGAAAACAAAAATGG 57.557 25.926 0.00 0.00 0.00 3.16
2368 3806 4.150994 TGGAACAGGCGTGGAAAC 57.849 55.556 11.67 0.00 0.00 2.78
2377 3815 0.040692 GGCGTGGAAACGGAACTTTC 60.041 55.000 0.00 0.00 0.00 2.62
2378 3816 0.942252 GCGTGGAAACGGAACTTTCT 59.058 50.000 0.00 0.00 31.76 2.52
2464 3903 7.028962 CCACCAAACAATACACAATGACATAG 58.971 38.462 0.00 0.00 0.00 2.23
2469 3908 6.668541 ACAATACACAATGACATAGTGAGC 57.331 37.500 0.00 0.00 37.05 4.26
2476 3915 4.880120 ACAATGACATAGTGAGCAGAATGG 59.120 41.667 0.00 0.00 35.86 3.16
2487 3926 4.639310 GTGAGCAGAATGGATCATTTGAGT 59.361 41.667 0.00 0.00 35.41 3.41
2488 3927 4.880120 TGAGCAGAATGGATCATTTGAGTC 59.120 41.667 0.00 0.00 33.90 3.36
2494 3933 6.005823 AGAATGGATCATTTGAGTCACAACA 58.994 36.000 0.00 0.00 38.29 3.33
2502 3941 9.371136 GATCATTTGAGTCACAACATCTACTAA 57.629 33.333 0.00 0.00 38.29 2.24
2520 3959 7.605449 TCTACTAACACACACATACTTAACCC 58.395 38.462 0.00 0.00 0.00 4.11
2525 3964 2.027837 ACACACATACTTAACCCGACCC 60.028 50.000 0.00 0.00 0.00 4.46
2531 3970 5.302568 CACATACTTAACCCGACCCTATACA 59.697 44.000 0.00 0.00 0.00 2.29
2579 4018 7.823149 ACTTCGTTAAGTCGCTAACATAATT 57.177 32.000 0.00 0.00 42.42 1.40
2644 4088 8.157476 TCTCTATGATTCAAGGGGTTATTAAGC 58.843 37.037 0.00 0.00 0.00 3.09
2664 4108 3.047877 CGGTCAACGCCCACTTCC 61.048 66.667 0.00 0.00 34.82 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.174943 CGTTGGAAATTTGAGTTGCTAAACC 59.825 40.000 0.00 0.00 36.94 3.27
3 4 5.174943 CCGTTGGAAATTTGAGTTGCTAAAC 59.825 40.000 0.00 0.00 36.47 2.01
5 6 4.580995 TCCGTTGGAAATTTGAGTTGCTAA 59.419 37.500 0.00 0.00 0.00 3.09
6 7 4.138290 TCCGTTGGAAATTTGAGTTGCTA 58.862 39.130 0.00 0.00 0.00 3.49
7 8 2.955660 TCCGTTGGAAATTTGAGTTGCT 59.044 40.909 0.00 0.00 0.00 3.91
8 9 3.363341 TCCGTTGGAAATTTGAGTTGC 57.637 42.857 0.00 0.00 0.00 4.17
9 10 6.254281 ACTATCCGTTGGAAATTTGAGTTG 57.746 37.500 0.00 0.00 34.34 3.16
10 11 6.894339 AACTATCCGTTGGAAATTTGAGTT 57.106 33.333 0.00 0.00 34.34 3.01
41 42 8.491331 AAATGAAAGAAGCTTAGCAACAAAAA 57.509 26.923 7.07 0.00 0.00 1.94
42 43 9.593134 TTAAATGAAAGAAGCTTAGCAACAAAA 57.407 25.926 7.07 0.00 0.00 2.44
43 44 9.762933 ATTAAATGAAAGAAGCTTAGCAACAAA 57.237 25.926 7.07 0.00 0.00 2.83
44 45 9.762933 AATTAAATGAAAGAAGCTTAGCAACAA 57.237 25.926 7.07 0.00 0.00 2.83
64 65 9.768662 ACCGTTCTGAGTCTAAAACTAATTAAA 57.231 29.630 0.00 0.00 38.74 1.52
65 66 9.199982 CACCGTTCTGAGTCTAAAACTAATTAA 57.800 33.333 0.00 0.00 38.74 1.40
66 67 8.362639 ACACCGTTCTGAGTCTAAAACTAATTA 58.637 33.333 0.00 0.00 38.74 1.40
67 68 7.215085 ACACCGTTCTGAGTCTAAAACTAATT 58.785 34.615 0.00 0.00 38.74 1.40
68 69 6.756221 ACACCGTTCTGAGTCTAAAACTAAT 58.244 36.000 0.00 0.00 38.74 1.73
69 70 6.152932 ACACCGTTCTGAGTCTAAAACTAA 57.847 37.500 0.00 0.00 38.74 2.24
70 71 5.779529 ACACCGTTCTGAGTCTAAAACTA 57.220 39.130 0.00 0.00 38.74 2.24
71 72 4.667519 ACACCGTTCTGAGTCTAAAACT 57.332 40.909 0.00 0.00 42.42 2.66
72 73 5.729974 AAACACCGTTCTGAGTCTAAAAC 57.270 39.130 0.00 0.00 0.00 2.43
73 74 5.875910 TGAAAACACCGTTCTGAGTCTAAAA 59.124 36.000 0.00 0.00 0.00 1.52
74 75 5.292589 GTGAAAACACCGTTCTGAGTCTAAA 59.707 40.000 0.00 0.00 0.00 1.85
75 76 4.807304 GTGAAAACACCGTTCTGAGTCTAA 59.193 41.667 0.00 0.00 0.00 2.10
76 77 4.365723 GTGAAAACACCGTTCTGAGTCTA 58.634 43.478 0.00 0.00 0.00 2.59
77 78 3.195661 GTGAAAACACCGTTCTGAGTCT 58.804 45.455 0.00 0.00 0.00 3.24
78 79 2.287103 GGTGAAAACACCGTTCTGAGTC 59.713 50.000 3.65 0.00 35.30 3.36
79 80 2.285977 GGTGAAAACACCGTTCTGAGT 58.714 47.619 3.65 0.00 35.30 3.41
88 89 0.872388 CGTGCCTAGGTGAAAACACC 59.128 55.000 11.31 10.91 45.31 4.16
89 90 1.798813 CTCGTGCCTAGGTGAAAACAC 59.201 52.381 11.31 7.72 0.00 3.32
90 91 1.270625 CCTCGTGCCTAGGTGAAAACA 60.271 52.381 11.31 0.00 0.00 2.83
91 92 1.439679 CCTCGTGCCTAGGTGAAAAC 58.560 55.000 11.31 0.99 0.00 2.43
92 93 0.323629 CCCTCGTGCCTAGGTGAAAA 59.676 55.000 11.31 0.00 31.70 2.29
93 94 1.980052 CCCTCGTGCCTAGGTGAAA 59.020 57.895 11.31 0.00 31.70 2.69
94 95 2.656069 GCCCTCGTGCCTAGGTGAA 61.656 63.158 11.31 0.00 31.70 3.18
95 96 3.075005 GCCCTCGTGCCTAGGTGA 61.075 66.667 11.31 5.52 31.70 4.02
96 97 1.327690 TAAGCCCTCGTGCCTAGGTG 61.328 60.000 11.31 0.80 31.70 4.00
97 98 1.001248 TAAGCCCTCGTGCCTAGGT 59.999 57.895 11.31 0.00 31.70 3.08
98 99 1.742768 CTAAGCCCTCGTGCCTAGG 59.257 63.158 3.67 3.67 0.00 3.02
99 100 1.068250 GCTAAGCCCTCGTGCCTAG 59.932 63.158 0.00 0.00 0.00 3.02
100 101 1.048724 ATGCTAAGCCCTCGTGCCTA 61.049 55.000 0.00 0.00 0.00 3.93
101 102 2.317149 GATGCTAAGCCCTCGTGCCT 62.317 60.000 0.00 0.00 0.00 4.75
102 103 1.889573 GATGCTAAGCCCTCGTGCC 60.890 63.158 0.00 0.00 0.00 5.01
103 104 2.240500 CGATGCTAAGCCCTCGTGC 61.241 63.158 0.00 0.00 31.39 5.34
104 105 1.592669 CCGATGCTAAGCCCTCGTG 60.593 63.158 0.00 0.00 33.16 4.35
105 106 1.614241 AACCGATGCTAAGCCCTCGT 61.614 55.000 0.00 0.00 33.16 4.18
106 107 0.876342 GAACCGATGCTAAGCCCTCG 60.876 60.000 0.00 0.00 34.22 4.63
107 108 0.466124 AGAACCGATGCTAAGCCCTC 59.534 55.000 0.00 0.00 0.00 4.30
108 109 0.912486 AAGAACCGATGCTAAGCCCT 59.088 50.000 0.00 0.00 0.00 5.19
109 110 1.300481 GAAGAACCGATGCTAAGCCC 58.700 55.000 0.00 0.00 0.00 5.19
110 111 1.300481 GGAAGAACCGATGCTAAGCC 58.700 55.000 0.00 0.00 0.00 4.35
111 112 1.300481 GGGAAGAACCGATGCTAAGC 58.700 55.000 0.00 0.00 40.11 3.09
112 113 2.691409 TGGGAAGAACCGATGCTAAG 57.309 50.000 0.00 0.00 40.11 2.18
113 114 2.355716 CCTTGGGAAGAACCGATGCTAA 60.356 50.000 0.00 0.00 40.11 3.09
114 115 1.209504 CCTTGGGAAGAACCGATGCTA 59.790 52.381 0.00 0.00 40.11 3.49
115 116 0.035056 CCTTGGGAAGAACCGATGCT 60.035 55.000 0.00 0.00 40.11 3.79
116 117 0.322546 ACCTTGGGAAGAACCGATGC 60.323 55.000 0.00 0.00 40.11 3.91
117 118 1.003118 TGACCTTGGGAAGAACCGATG 59.997 52.381 0.00 0.00 40.11 3.84
118 119 1.358152 TGACCTTGGGAAGAACCGAT 58.642 50.000 0.00 0.00 40.11 4.18
119 120 1.278127 GATGACCTTGGGAAGAACCGA 59.722 52.381 0.00 0.00 40.11 4.69
120 121 1.003118 TGATGACCTTGGGAAGAACCG 59.997 52.381 0.00 0.00 40.11 4.44
121 122 2.879103 TGATGACCTTGGGAAGAACC 57.121 50.000 0.00 0.00 38.08 3.62
122 123 4.145052 AGTTTGATGACCTTGGGAAGAAC 58.855 43.478 0.00 0.00 0.00 3.01
123 124 4.453480 AGTTTGATGACCTTGGGAAGAA 57.547 40.909 0.00 0.00 0.00 2.52
124 125 4.597507 AGTAGTTTGATGACCTTGGGAAGA 59.402 41.667 0.00 0.00 0.00 2.87
125 126 4.911390 AGTAGTTTGATGACCTTGGGAAG 58.089 43.478 0.00 0.00 0.00 3.46
126 127 4.993705 AGTAGTTTGATGACCTTGGGAA 57.006 40.909 0.00 0.00 0.00 3.97
127 128 5.964477 AGATAGTAGTTTGATGACCTTGGGA 59.036 40.000 0.00 0.00 0.00 4.37
128 129 6.098982 AGAGATAGTAGTTTGATGACCTTGGG 59.901 42.308 0.00 0.00 0.00 4.12
129 130 7.118496 AGAGATAGTAGTTTGATGACCTTGG 57.882 40.000 0.00 0.00 0.00 3.61
130 131 8.474025 AGAAGAGATAGTAGTTTGATGACCTTG 58.526 37.037 0.00 0.00 0.00 3.61
131 132 8.602472 AGAAGAGATAGTAGTTTGATGACCTT 57.398 34.615 0.00 0.00 0.00 3.50
132 133 8.602472 AAGAAGAGATAGTAGTTTGATGACCT 57.398 34.615 0.00 0.00 0.00 3.85
145 146 8.540388 TGTGCAGGTAAATTAAGAAGAGATAGT 58.460 33.333 0.00 0.00 0.00 2.12
146 147 8.948631 TGTGCAGGTAAATTAAGAAGAGATAG 57.051 34.615 0.00 0.00 0.00 2.08
147 148 9.905713 AATGTGCAGGTAAATTAAGAAGAGATA 57.094 29.630 0.00 0.00 0.00 1.98
148 149 8.814038 AATGTGCAGGTAAATTAAGAAGAGAT 57.186 30.769 0.00 0.00 0.00 2.75
149 150 9.733556 TTAATGTGCAGGTAAATTAAGAAGAGA 57.266 29.630 0.00 0.00 0.00 3.10
159 160 9.664332 TGCATAAAATTTAATGTGCAGGTAAAT 57.336 25.926 9.45 0.00 37.63 1.40
160 161 9.664332 ATGCATAAAATTTAATGTGCAGGTAAA 57.336 25.926 16.23 0.00 44.55 2.01
162 163 9.743057 GTATGCATAAAATTTAATGTGCAGGTA 57.257 29.630 16.23 5.92 44.55 3.08
163 164 8.477256 AGTATGCATAAAATTTAATGTGCAGGT 58.523 29.630 16.23 6.67 44.55 4.00
164 165 8.876275 AGTATGCATAAAATTTAATGTGCAGG 57.124 30.769 16.23 0.00 44.55 4.85
166 167 9.096160 CCAAGTATGCATAAAATTTAATGTGCA 57.904 29.630 14.25 14.25 45.28 4.57
167 168 8.063630 GCCAAGTATGCATAAAATTTAATGTGC 58.936 33.333 8.28 5.03 0.00 4.57
168 169 8.268052 CGCCAAGTATGCATAAAATTTAATGTG 58.732 33.333 8.28 0.00 0.00 3.21
169 170 7.437862 CCGCCAAGTATGCATAAAATTTAATGT 59.562 33.333 8.28 0.00 0.00 2.71
170 171 7.437862 ACCGCCAAGTATGCATAAAATTTAATG 59.562 33.333 8.28 0.00 0.00 1.90
171 172 7.496747 ACCGCCAAGTATGCATAAAATTTAAT 58.503 30.769 8.28 0.00 0.00 1.40
172 173 6.868622 ACCGCCAAGTATGCATAAAATTTAA 58.131 32.000 8.28 0.00 0.00 1.52
173 174 6.320164 AGACCGCCAAGTATGCATAAAATTTA 59.680 34.615 8.28 0.00 0.00 1.40
174 175 5.127031 AGACCGCCAAGTATGCATAAAATTT 59.873 36.000 8.28 0.00 0.00 1.82
175 176 4.644685 AGACCGCCAAGTATGCATAAAATT 59.355 37.500 8.28 1.16 0.00 1.82
176 177 4.207165 AGACCGCCAAGTATGCATAAAAT 58.793 39.130 8.28 0.00 0.00 1.82
177 178 3.616219 AGACCGCCAAGTATGCATAAAA 58.384 40.909 8.28 0.00 0.00 1.52
178 179 3.275617 AGACCGCCAAGTATGCATAAA 57.724 42.857 8.28 0.00 0.00 1.40
179 180 3.275617 AAGACCGCCAAGTATGCATAA 57.724 42.857 8.28 0.00 0.00 1.90
180 181 4.039852 TCATAAGACCGCCAAGTATGCATA 59.960 41.667 1.16 1.16 0.00 3.14
181 182 3.141398 CATAAGACCGCCAAGTATGCAT 58.859 45.455 3.79 3.79 0.00 3.96
182 183 2.169561 TCATAAGACCGCCAAGTATGCA 59.830 45.455 0.00 0.00 0.00 3.96
183 184 2.544267 GTCATAAGACCGCCAAGTATGC 59.456 50.000 0.00 0.00 38.89 3.14
184 185 2.794910 CGTCATAAGACCGCCAAGTATG 59.205 50.000 0.00 0.00 41.87 2.39
185 186 2.223971 CCGTCATAAGACCGCCAAGTAT 60.224 50.000 0.00 0.00 41.87 2.12
186 187 1.135527 CCGTCATAAGACCGCCAAGTA 59.864 52.381 0.00 0.00 41.87 2.24
187 188 0.108329 CCGTCATAAGACCGCCAAGT 60.108 55.000 0.00 0.00 41.87 3.16
188 189 0.810031 CCCGTCATAAGACCGCCAAG 60.810 60.000 0.00 0.00 41.87 3.61
189 190 1.219664 CCCGTCATAAGACCGCCAA 59.780 57.895 0.00 0.00 41.87 4.52
190 191 1.683025 TCCCGTCATAAGACCGCCA 60.683 57.895 0.00 0.00 41.87 5.69
191 192 1.227176 GTCCCGTCATAAGACCGCC 60.227 63.158 0.00 0.00 41.87 6.13
192 193 0.108520 TTGTCCCGTCATAAGACCGC 60.109 55.000 0.00 0.00 41.87 5.68
193 194 2.373540 TTTGTCCCGTCATAAGACCG 57.626 50.000 0.00 0.00 41.87 4.79
194 195 4.941873 AGAAATTTGTCCCGTCATAAGACC 59.058 41.667 0.00 0.00 41.87 3.85
195 196 7.787725 ATAGAAATTTGTCCCGTCATAAGAC 57.212 36.000 0.00 0.00 41.46 3.01
196 197 9.893634 TTTATAGAAATTTGTCCCGTCATAAGA 57.106 29.630 0.00 0.00 0.00 2.10
197 198 9.931210 GTTTATAGAAATTTGTCCCGTCATAAG 57.069 33.333 0.00 0.00 0.00 1.73
198 199 9.451002 TGTTTATAGAAATTTGTCCCGTCATAA 57.549 29.630 0.00 0.00 0.00 1.90
199 200 9.451002 TTGTTTATAGAAATTTGTCCCGTCATA 57.549 29.630 0.00 0.00 0.00 2.15
200 201 7.931578 TGTTTATAGAAATTTGTCCCGTCAT 57.068 32.000 0.00 0.00 0.00 3.06
201 202 7.747155 TTGTTTATAGAAATTTGTCCCGTCA 57.253 32.000 0.00 0.00 0.00 4.35
228 229 9.771534 CCCAAGTCAAAATTTCCATAAGTTTAA 57.228 29.630 0.00 0.00 0.00 1.52
229 230 8.371699 CCCCAAGTCAAAATTTCCATAAGTTTA 58.628 33.333 0.00 0.00 0.00 2.01
230 231 7.223584 CCCCAAGTCAAAATTTCCATAAGTTT 58.776 34.615 0.00 0.00 0.00 2.66
231 232 6.744056 GCCCCAAGTCAAAATTTCCATAAGTT 60.744 38.462 0.00 0.00 0.00 2.66
232 233 5.279960 GCCCCAAGTCAAAATTTCCATAAGT 60.280 40.000 0.00 0.00 0.00 2.24
233 234 5.178061 GCCCCAAGTCAAAATTTCCATAAG 58.822 41.667 0.00 0.00 0.00 1.73
234 235 4.594920 TGCCCCAAGTCAAAATTTCCATAA 59.405 37.500 0.00 0.00 0.00 1.90
235 236 4.163427 TGCCCCAAGTCAAAATTTCCATA 58.837 39.130 0.00 0.00 0.00 2.74
236 237 2.978278 TGCCCCAAGTCAAAATTTCCAT 59.022 40.909 0.00 0.00 0.00 3.41
237 238 2.402564 TGCCCCAAGTCAAAATTTCCA 58.597 42.857 0.00 0.00 0.00 3.53
238 239 3.483808 TTGCCCCAAGTCAAAATTTCC 57.516 42.857 0.00 0.00 0.00 3.13
239 240 6.710295 AGTAAATTGCCCCAAGTCAAAATTTC 59.290 34.615 0.00 0.00 31.62 2.17
240 241 6.600388 AGTAAATTGCCCCAAGTCAAAATTT 58.400 32.000 0.00 0.00 33.26 1.82
241 242 6.186420 AGTAAATTGCCCCAAGTCAAAATT 57.814 33.333 0.00 0.00 0.00 1.82
242 243 5.823861 AGTAAATTGCCCCAAGTCAAAAT 57.176 34.783 0.00 0.00 0.00 1.82
243 244 5.622346 AAGTAAATTGCCCCAAGTCAAAA 57.378 34.783 0.00 0.00 0.00 2.44
244 245 5.622346 AAAGTAAATTGCCCCAAGTCAAA 57.378 34.783 0.00 0.00 0.00 2.69
245 246 5.622346 AAAAGTAAATTGCCCCAAGTCAA 57.378 34.783 0.00 0.00 0.00 3.18
246 247 5.622346 AAAAAGTAAATTGCCCCAAGTCA 57.378 34.783 0.00 0.00 0.00 3.41
272 273 9.950680 CCACACACAAAATAATATTACATCTCC 57.049 33.333 0.00 0.00 0.00 3.71
287 288 9.737427 CTAAACATTGTAATACCACACACAAAA 57.263 29.630 0.00 0.00 34.79 2.44
331 332 6.307800 GTGGAAATAATTGTGTGTACATGTGC 59.692 38.462 9.11 8.01 36.53 4.57
338 339 7.089538 CAGCATTGTGGAAATAATTGTGTGTA 58.910 34.615 0.00 0.00 0.00 2.90
352 353 2.079170 TGGTTTTCCAGCATTGTGGA 57.921 45.000 4.48 4.48 46.22 4.02
372 373 6.212955 ACCAAGTCGAAAATAAAACCATGTG 58.787 36.000 0.00 0.00 0.00 3.21
374 375 6.927933 GACCAAGTCGAAAATAAAACCATG 57.072 37.500 0.00 0.00 0.00 3.66
394 395 0.741915 TGGTTTTCCTTGTTGCGACC 59.258 50.000 0.45 0.00 41.38 4.79
411 413 3.243569 TGGCAAGTTAAAATCCGTTGTGG 60.244 43.478 0.00 0.00 40.09 4.17
439 441 5.468072 GCATCATTTTCCTCATGTCGTAGAT 59.532 40.000 0.00 0.00 40.67 1.98
443 445 3.127548 GTGCATCATTTTCCTCATGTCGT 59.872 43.478 0.00 0.00 0.00 4.34
512 514 0.249447 CAGGATGCGACGATTAGGCA 60.249 55.000 0.00 0.00 41.48 4.75
592 632 0.602905 GTGGGATTATTCGAGGGGCG 60.603 60.000 0.00 0.00 42.69 6.13
742 782 2.254546 ACACATGCTCGTTGAAAGGA 57.745 45.000 0.00 0.00 0.00 3.36
758 798 3.509575 TGTTTTGATTGGGCCATCTACAC 59.490 43.478 7.26 8.16 0.00 2.90
759 799 3.763360 CTGTTTTGATTGGGCCATCTACA 59.237 43.478 7.26 11.47 0.00 2.74
760 800 4.016444 TCTGTTTTGATTGGGCCATCTAC 58.984 43.478 7.26 7.94 0.00 2.59
774 819 6.331845 TGCACATATATTTGGCTCTGTTTTG 58.668 36.000 1.22 0.00 0.00 2.44
782 827 4.388485 TGTCGATGCACATATATTTGGCT 58.612 39.130 0.00 0.00 0.00 4.75
783 828 4.747540 TGTCGATGCACATATATTTGGC 57.252 40.909 0.00 0.00 0.00 4.52
790 835 3.165058 ACTCGTTGTCGATGCACATAT 57.835 42.857 0.00 0.00 45.21 1.78
796 843 3.796717 TGATTGATACTCGTTGTCGATGC 59.203 43.478 0.00 0.00 45.21 3.91
798 845 5.891451 TCTTGATTGATACTCGTTGTCGAT 58.109 37.500 0.00 0.00 45.21 3.59
814 861 6.385443 TGGGGACTCTACATATCTCTTGATT 58.615 40.000 0.00 0.00 34.32 2.57
819 871 6.444704 TCTTTTGGGGACTCTACATATCTCT 58.555 40.000 0.00 0.00 0.00 3.10
820 872 6.732896 TCTTTTGGGGACTCTACATATCTC 57.267 41.667 0.00 0.00 0.00 2.75
827 921 5.805728 TCTTGATTCTTTTGGGGACTCTAC 58.194 41.667 0.00 0.00 0.00 2.59
834 928 5.951747 TCCACTTATCTTGATTCTTTTGGGG 59.048 40.000 0.00 0.00 0.00 4.96
1011 1113 6.009474 CGTCTATGTATGAAAATGTATGCGC 58.991 40.000 0.00 0.00 0.00 6.09
1012 1114 6.525355 CCGTCTATGTATGAAAATGTATGCG 58.475 40.000 0.00 0.00 0.00 4.73
1013 1115 6.307155 GCCGTCTATGTATGAAAATGTATGC 58.693 40.000 0.00 0.00 0.00 3.14
1020 1122 4.196193 CCTTGGCCGTCTATGTATGAAAA 58.804 43.478 0.00 0.00 0.00 2.29
1021 1123 3.199071 ACCTTGGCCGTCTATGTATGAAA 59.801 43.478 0.00 0.00 0.00 2.69
1031 1133 0.971447 GAGAGGTACCTTGGCCGTCT 60.971 60.000 17.53 6.58 0.00 4.18
1045 1147 1.999071 CTCCTTGCTCCGACGAGAGG 61.999 65.000 13.06 5.81 38.52 3.69
1074 1178 1.934589 TCGCCATACCAAACTGATCG 58.065 50.000 0.00 0.00 0.00 3.69
1085 1189 1.202371 TCACGTTCCTGATCGCCATAC 60.202 52.381 0.00 0.00 0.00 2.39
1326 1430 1.655654 CTGCGCGTACTCGATGAGG 60.656 63.158 9.88 0.00 39.71 3.86
1383 1487 2.485657 GCTTAATGGACCTAGCCAGACC 60.486 54.545 0.00 0.00 42.15 3.85
1388 1492 2.484889 CTTCGCTTAATGGACCTAGCC 58.515 52.381 0.00 0.00 0.00 3.93
1397 1501 2.826428 TGGAGCTAGCTTCGCTTAATG 58.174 47.619 20.42 0.00 40.44 1.90
1444 1550 1.069204 TCAGCGCTTATTCTAGCAGGG 59.931 52.381 7.50 0.00 41.28 4.45
1478 1584 0.895559 AAGCAAAGGTACAGGGCAGC 60.896 55.000 0.00 0.00 0.00 5.25
1534 1640 2.030805 TCATGATAGATCACCGACGCAG 60.031 50.000 0.00 0.00 40.03 5.18
1540 1646 5.747675 GCAGATACATCATGATAGATCACCG 59.252 44.000 22.07 14.61 40.03 4.94
1541 1647 6.637657 TGCAGATACATCATGATAGATCACC 58.362 40.000 22.07 15.51 40.03 4.02
1561 1670 4.021631 CTGTGCCACACGCTGCAG 62.022 66.667 10.11 10.11 38.34 4.41
1609 1734 4.043073 GGAAAATTAACAACGACGGCAAA 58.957 39.130 0.00 0.00 0.00 3.68
1629 1754 4.722526 TTCATTTTCTTCCAGACAGGGA 57.277 40.909 0.00 0.00 38.24 4.20
1639 1764 7.044706 CGACAAGAACACACTTTCATTTTCTTC 60.045 37.037 0.00 0.00 32.32 2.87
1640 1765 6.747280 CGACAAGAACACACTTTCATTTTCTT 59.253 34.615 0.00 0.00 34.41 2.52
1646 1771 5.178252 CAGATCGACAAGAACACACTTTCAT 59.822 40.000 0.00 0.00 0.00 2.57
1685 1810 5.508200 TCACCAGAACAAACGCTAAAAAT 57.492 34.783 0.00 0.00 0.00 1.82
1693 1818 2.393764 GCCAAATCACCAGAACAAACG 58.606 47.619 0.00 0.00 0.00 3.60
1698 1823 1.620822 ACAGGCCAAATCACCAGAAC 58.379 50.000 5.01 0.00 0.00 3.01
1713 1838 1.202417 AGACCATCGACGCATTACAGG 60.202 52.381 0.00 0.00 0.00 4.00
1769 1894 9.333724 AGGAGTAAAAGACTTTTTATTGTTCGA 57.666 29.630 17.92 0.00 40.01 3.71
1800 1925 7.995488 AGTGCTTAACTGCTTAATATGGAATCT 59.005 33.333 0.00 0.00 37.88 2.40
1833 1958 2.178912 TCAACCGTTTGAGGGATCAC 57.821 50.000 0.00 0.00 36.79 3.06
1881 2006 0.108520 ATGCGGCTGCTCAAATTTGG 60.109 50.000 20.27 9.84 43.34 3.28
1919 2044 7.559170 GCGAGGTAGGAGGGATACTTATAATTA 59.441 40.741 0.00 0.00 0.00 1.40
1925 3339 2.715336 AGCGAGGTAGGAGGGATACTTA 59.285 50.000 0.00 0.00 0.00 2.24
1939 3353 2.277404 GGAGAGGAGGAGCGAGGT 59.723 66.667 0.00 0.00 0.00 3.85
1960 3374 1.227973 GGATCAATCACCGGGGAGC 60.228 63.158 14.24 0.50 0.00 4.70
1970 3384 1.224965 GCCAGAAGCTCGGATCAATC 58.775 55.000 0.00 0.00 38.99 2.67
1972 3386 1.153568 CGCCAGAAGCTCGGATCAA 60.154 57.895 0.00 0.00 40.39 2.57
1973 3387 2.496341 CGCCAGAAGCTCGGATCA 59.504 61.111 0.00 0.00 40.39 2.92
2076 3513 3.171388 GAGGCCATGGTCGGGGAT 61.171 66.667 14.67 0.00 0.00 3.85
2083 3520 2.586792 GAGAAGCGAGGCCATGGT 59.413 61.111 14.67 0.00 0.00 3.55
2104 3541 1.453015 CGATTTTGCCGGGGATGGA 60.453 57.895 2.18 0.00 0.00 3.41
2105 3542 3.119193 CGATTTTGCCGGGGATGG 58.881 61.111 2.18 0.00 0.00 3.51
2117 3554 1.421410 CTGTAAGAGCGCGGCGATTT 61.421 55.000 28.54 13.25 34.07 2.17
2118 3555 1.878522 CTGTAAGAGCGCGGCGATT 60.879 57.895 28.54 18.45 34.07 3.34
2119 3556 2.278857 CTGTAAGAGCGCGGCGAT 60.279 61.111 28.54 22.42 34.07 4.58
2144 3582 3.116531 GTTACTGCGACCGTGGGC 61.117 66.667 0.00 0.00 0.00 5.36
2149 3587 1.218875 TGTTGCTGTTACTGCGACCG 61.219 55.000 24.87 0.00 40.46 4.79
2151 3589 0.111266 CGTGTTGCTGTTACTGCGAC 60.111 55.000 22.36 22.36 41.19 5.19
2154 3592 1.862201 TGTACGTGTTGCTGTTACTGC 59.138 47.619 7.29 7.29 0.00 4.40
2157 3595 3.307782 AGTGTTGTACGTGTTGCTGTTAC 59.692 43.478 0.00 0.00 0.00 2.50
2179 3617 4.273235 CCCGTAGTATATACGTGTGTGTCA 59.727 45.833 7.23 0.00 39.09 3.58
2197 3635 1.626321 TCACTCCATTTTCAGCCCGTA 59.374 47.619 0.00 0.00 0.00 4.02
2199 3637 1.533625 TTCACTCCATTTTCAGCCCG 58.466 50.000 0.00 0.00 0.00 6.13
2203 3641 7.869429 AGCATAAACTTTTCACTCCATTTTCAG 59.131 33.333 0.00 0.00 0.00 3.02
2225 3663 5.200483 TCCATTTATTCTCCGGAAAAGCAT 58.800 37.500 5.23 0.00 34.90 3.79
2232 3670 4.475051 TCGTTTCCATTTATTCTCCGGA 57.525 40.909 2.93 2.93 0.00 5.14
2234 3672 5.350365 TGTCTTCGTTTCCATTTATTCTCCG 59.650 40.000 0.00 0.00 0.00 4.63
2235 3673 6.737254 TGTCTTCGTTTCCATTTATTCTCC 57.263 37.500 0.00 0.00 0.00 3.71
2236 3674 9.626045 ATTTTGTCTTCGTTTCCATTTATTCTC 57.374 29.630 0.00 0.00 0.00 2.87
2265 3703 6.874288 TCGCAAAATTCCATTTCCATTTTT 57.126 29.167 0.00 0.00 29.49 1.94
2271 3709 2.666022 CCGTTCGCAAAATTCCATTTCC 59.334 45.455 0.00 0.00 0.00 3.13
2272 3710 3.570559 TCCGTTCGCAAAATTCCATTTC 58.429 40.909 0.00 0.00 0.00 2.17
2281 3719 2.539346 TTTCGTTTCCGTTCGCAAAA 57.461 40.000 0.00 0.00 35.01 2.44
2287 3725 3.891056 AGTCCATTTTCGTTTCCGTTC 57.109 42.857 0.00 0.00 35.01 3.95
2335 3773 6.385033 CCTGTTCCATCTGAAAAGATTGTTC 58.615 40.000 0.00 0.00 40.29 3.18
2347 3785 0.321564 TTCCACGCCTGTTCCATCTG 60.322 55.000 0.00 0.00 0.00 2.90
2348 3786 0.400213 TTTCCACGCCTGTTCCATCT 59.600 50.000 0.00 0.00 0.00 2.90
2350 3788 1.234615 CGTTTCCACGCCTGTTCCAT 61.235 55.000 0.00 0.00 40.18 3.41
2353 3791 1.161563 TTCCGTTTCCACGCCTGTTC 61.162 55.000 0.00 0.00 45.72 3.18
2377 3815 8.840321 ACTGAAATTCCATATTCACGGAAATAG 58.160 33.333 0.00 0.00 44.25 1.73
2378 3816 8.746052 ACTGAAATTCCATATTCACGGAAATA 57.254 30.769 0.00 0.00 44.25 1.40
2464 3903 4.639310 ACTCAAATGATCCATTCTGCTCAC 59.361 41.667 0.00 0.00 32.43 3.51
2469 3908 6.072342 TGTTGTGACTCAAATGATCCATTCTG 60.072 38.462 0.00 0.00 37.81 3.02
2476 3915 7.840342 AGTAGATGTTGTGACTCAAATGATC 57.160 36.000 0.00 0.00 37.81 2.92
2487 3926 5.908341 TGTGTGTGTTAGTAGATGTTGTGA 58.092 37.500 0.00 0.00 0.00 3.58
2488 3927 6.785488 ATGTGTGTGTTAGTAGATGTTGTG 57.215 37.500 0.00 0.00 0.00 3.33
2494 3933 8.255905 GGGTTAAGTATGTGTGTGTTAGTAGAT 58.744 37.037 0.00 0.00 0.00 1.98
2502 3941 3.555586 GGTCGGGTTAAGTATGTGTGTGT 60.556 47.826 0.00 0.00 0.00 3.72
2520 3959 6.097915 ACTGGACAATTATGTATAGGGTCG 57.902 41.667 0.00 0.00 40.74 4.79
2553 3992 9.525409 AATTATGTTAGCGACTTAACGAAGTAT 57.475 29.630 0.00 0.00 46.23 2.12
2624 4068 5.445964 GGAGCTTAATAACCCCTTGAATCA 58.554 41.667 0.00 0.00 0.00 2.57
2627 4071 3.371166 CCGGAGCTTAATAACCCCTTGAA 60.371 47.826 0.00 0.00 0.00 2.69
2633 4077 2.941064 GTTGACCGGAGCTTAATAACCC 59.059 50.000 9.46 0.00 0.00 4.11
2644 4088 3.530910 AAGTGGGCGTTGACCGGAG 62.531 63.158 9.46 0.00 36.94 4.63


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

AutoCloner maintained by Alex Coulton.