Multiple sequence alignment - TraesCS3A01G508900

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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 TraesCS3A01G508900 chr3A 100.000 2582 0 0 1 2582 729877063 729879644 0.000000e+00 4769
1 TraesCS3A01G508900 chr3A 97.479 714 14 2 1869 2582 729885861 729886570 0.000000e+00 1216
2 TraesCS3A01G508900 chr3A 96.919 714 22 0 1869 2582 79529983 79529270 0.000000e+00 1197
3 TraesCS3A01G508900 chr3A 96.503 715 24 1 1869 2582 530461313 530462027 0.000000e+00 1181
4 TraesCS3A01G508900 chr3A 90.256 195 12 3 173 366 466062744 466062932 5.520000e-62 248
5 TraesCS3A01G508900 chr4D 95.613 1459 61 3 409 1867 119369760 119368305 0.000000e+00 2337
6 TraesCS3A01G508900 chrUn 95.423 1464 63 3 410 1872 105335964 105334504 0.000000e+00 2329
7 TraesCS3A01G508900 chr6D 95.280 1462 64 3 407 1867 347439908 347438451 0.000000e+00 2313
8 TraesCS3A01G508900 chr6D 88.947 190 13 5 175 363 399222108 399222290 7.190000e-56 228
9 TraesCS3A01G508900 chr7D 95.274 1460 61 3 410 1869 126988444 126989895 0.000000e+00 2307
10 TraesCS3A01G508900 chr7D 95.082 1464 63 7 409 1869 85019321 85020778 0.000000e+00 2296
11 TraesCS3A01G508900 chr7D 89.418 189 14 4 175 363 605142730 605142912 1.540000e-57 233
12 TraesCS3A01G508900 chr1D 95.150 1464 64 5 411 1869 303344960 303346421 0.000000e+00 2303
13 TraesCS3A01G508900 chr5D 94.959 1468 72 2 400 1867 426404714 426403249 0.000000e+00 2300
14 TraesCS3A01G508900 chr2D 95.017 1465 70 3 406 1869 603142393 603143855 0.000000e+00 2298
15 TraesCS3A01G508900 chr2D 89.583 192 14 2 172 363 12588329 12588514 3.320000e-59 239
16 TraesCS3A01G508900 chr2D 88.557 201 16 6 164 363 142440891 142441085 1.190000e-58 237
17 TraesCS3A01G508900 chr7B 94.809 1464 70 4 410 1869 442357638 442359099 0.000000e+00 2278
18 TraesCS3A01G508900 chr6A 97.759 714 15 1 1869 2582 536417106 536417818 0.000000e+00 1229
19 TraesCS3A01G508900 chr6A 97.479 714 15 2 1869 2582 536423994 536424704 0.000000e+00 1216
20 TraesCS3A01G508900 chr6A 97.343 715 18 1 1869 2582 536428130 536428844 0.000000e+00 1214
21 TraesCS3A01G508900 chr5A 97.059 714 21 0 1869 2582 493635444 493636157 0.000000e+00 1203
22 TraesCS3A01G508900 chr5A 88.889 198 15 6 172 368 515773708 515773899 1.190000e-58 237
23 TraesCS3A01G508900 chr7A 96.783 715 21 2 1869 2582 19878213 19878926 0.000000e+00 1192
24 TraesCS3A01G508900 chr7A 89.418 189 13 3 175 363 595642483 595642664 5.560000e-57 231
25 TraesCS3A01G508900 chr1A 96.499 714 25 0 1869 2582 506509631 506508918 0.000000e+00 1181
26 TraesCS3A01G508900 chr3D 93.605 172 5 6 1 169 600126970 600127138 4.270000e-63 252
27 TraesCS3A01G508900 chr3D 88.889 198 11 7 175 370 308822429 308822241 1.540000e-57 233
28 TraesCS3A01G508900 chr1B 86.473 207 16 10 173 376 364224708 364224511 1.560000e-52 217
29 TraesCS3A01G508900 chr3B 83.230 161 6 9 1 155 807289564 807289709 7.500000e-26 128


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 TraesCS3A01G508900 chr3A 729877063 729879644 2581 False 4769 4769 100.000 1 2582 1 chr3A.!!$F3 2581
1 TraesCS3A01G508900 chr3A 729885861 729886570 709 False 1216 1216 97.479 1869 2582 1 chr3A.!!$F4 713
2 TraesCS3A01G508900 chr3A 79529270 79529983 713 True 1197 1197 96.919 1869 2582 1 chr3A.!!$R1 713
3 TraesCS3A01G508900 chr3A 530461313 530462027 714 False 1181 1181 96.503 1869 2582 1 chr3A.!!$F2 713
4 TraesCS3A01G508900 chr4D 119368305 119369760 1455 True 2337 2337 95.613 409 1867 1 chr4D.!!$R1 1458
5 TraesCS3A01G508900 chrUn 105334504 105335964 1460 True 2329 2329 95.423 410 1872 1 chrUn.!!$R1 1462
6 TraesCS3A01G508900 chr6D 347438451 347439908 1457 True 2313 2313 95.280 407 1867 1 chr6D.!!$R1 1460
7 TraesCS3A01G508900 chr7D 126988444 126989895 1451 False 2307 2307 95.274 410 1869 1 chr7D.!!$F2 1459
8 TraesCS3A01G508900 chr7D 85019321 85020778 1457 False 2296 2296 95.082 409 1869 1 chr7D.!!$F1 1460
9 TraesCS3A01G508900 chr1D 303344960 303346421 1461 False 2303 2303 95.150 411 1869 1 chr1D.!!$F1 1458
10 TraesCS3A01G508900 chr5D 426403249 426404714 1465 True 2300 2300 94.959 400 1867 1 chr5D.!!$R1 1467
11 TraesCS3A01G508900 chr2D 603142393 603143855 1462 False 2298 2298 95.017 406 1869 1 chr2D.!!$F3 1463
12 TraesCS3A01G508900 chr7B 442357638 442359099 1461 False 2278 2278 94.809 410 1869 1 chr7B.!!$F1 1459
13 TraesCS3A01G508900 chr6A 536417106 536417818 712 False 1229 1229 97.759 1869 2582 1 chr6A.!!$F1 713
14 TraesCS3A01G508900 chr6A 536423994 536428844 4850 False 1215 1216 97.411 1869 2582 2 chr6A.!!$F2 713
15 TraesCS3A01G508900 chr5A 493635444 493636157 713 False 1203 1203 97.059 1869 2582 1 chr5A.!!$F1 713
16 TraesCS3A01G508900 chr7A 19878213 19878926 713 False 1192 1192 96.783 1869 2582 1 chr7A.!!$F1 713
17 TraesCS3A01G508900 chr1A 506508918 506509631 713 True 1181 1181 96.499 1869 2582 1 chr1A.!!$R1 713

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
19 20 0.028770 ATGTCGTGTGTTGGCGTTTG 59.971 50.0 0.0 0.0 0.0 2.93 F
180 181 0.034059 CGTGCTTCTTCTGAGGTGGT 59.966 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1135 1148 0.417437 TGGATCCTCTCCTGTTCCCA 59.583 55.0 14.23 0.00 45.21 4.37 R
1792 1805 0.830648 TTGATCCCATCAGGTCGACC 59.169 55.0 27.67 27.67 40.94 4.79 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
17 18 4.134623 ATGTCGTGTGTTGGCGTT 57.865 50.000 0.00 0.00 0.00 4.84
18 19 2.399856 ATGTCGTGTGTTGGCGTTT 58.600 47.368 0.00 0.00 0.00 3.60
19 20 0.028770 ATGTCGTGTGTTGGCGTTTG 59.971 50.000 0.00 0.00 0.00 2.93
20 21 1.937362 GTCGTGTGTTGGCGTTTGC 60.937 57.895 0.00 0.00 41.71 3.68
21 22 2.109739 TCGTGTGTTGGCGTTTGCT 61.110 52.632 0.00 0.00 42.25 3.91
22 23 1.654137 CGTGTGTTGGCGTTTGCTC 60.654 57.895 0.00 0.00 42.25 4.26
23 24 1.299089 GTGTGTTGGCGTTTGCTCC 60.299 57.895 0.00 0.00 42.25 4.70
24 25 1.453015 TGTGTTGGCGTTTGCTCCT 60.453 52.632 0.00 0.00 42.25 3.69
25 26 1.282875 GTGTTGGCGTTTGCTCCTC 59.717 57.895 0.00 0.00 42.25 3.71
26 27 1.896660 TGTTGGCGTTTGCTCCTCC 60.897 57.895 0.00 0.00 42.25 4.30
27 28 2.668212 TTGGCGTTTGCTCCTCCG 60.668 61.111 0.00 0.00 42.25 4.63
28 29 4.697756 TGGCGTTTGCTCCTCCGG 62.698 66.667 0.00 0.00 42.25 5.14
29 30 4.699522 GGCGTTTGCTCCTCCGGT 62.700 66.667 0.00 0.00 42.25 5.28
30 31 2.668550 GCGTTTGCTCCTCCGGTT 60.669 61.111 0.00 0.00 38.39 4.44
31 32 2.677979 GCGTTTGCTCCTCCGGTTC 61.678 63.158 0.00 0.00 38.39 3.62
32 33 2.380410 CGTTTGCTCCTCCGGTTCG 61.380 63.158 0.00 0.00 0.00 3.95
51 52 4.657824 CGGTTGGTCGCGTGGACT 62.658 66.667 5.77 0.00 45.35 3.85
52 53 3.041940 GGTTGGTCGCGTGGACTG 61.042 66.667 5.77 0.00 45.35 3.51
53 54 3.712881 GTTGGTCGCGTGGACTGC 61.713 66.667 5.77 0.00 45.35 4.40
54 55 3.923864 TTGGTCGCGTGGACTGCT 61.924 61.111 5.77 0.00 45.35 4.24
55 56 4.662961 TGGTCGCGTGGACTGCTG 62.663 66.667 5.77 0.00 45.35 4.41
82 83 4.947147 CGGGTGTGGTGGGTGGTG 62.947 72.222 0.00 0.00 0.00 4.17
131 132 4.143333 CCGTAGGCCTGGTCCACG 62.143 72.222 17.99 17.08 46.14 4.94
132 133 4.143333 CGTAGGCCTGGTCCACGG 62.143 72.222 17.99 0.00 31.65 4.94
133 134 2.682494 GTAGGCCTGGTCCACGGA 60.682 66.667 17.99 0.00 0.00 4.69
134 135 2.363795 TAGGCCTGGTCCACGGAG 60.364 66.667 17.99 0.00 0.00 4.63
135 136 2.926326 TAGGCCTGGTCCACGGAGA 61.926 63.158 17.99 0.00 0.00 3.71
136 137 2.449967 TAGGCCTGGTCCACGGAGAA 62.450 60.000 17.99 0.00 0.00 2.87
137 138 2.047179 GCCTGGTCCACGGAGAAC 60.047 66.667 10.58 0.00 0.00 3.01
138 139 2.663196 CCTGGTCCACGGAGAACC 59.337 66.667 2.08 0.00 0.00 3.62
139 140 2.214216 CCTGGTCCACGGAGAACCA 61.214 63.158 2.08 0.00 40.70 3.67
140 141 1.752198 CTGGTCCACGGAGAACCAA 59.248 57.895 0.00 0.00 42.28 3.67
141 142 0.602905 CTGGTCCACGGAGAACCAAC 60.603 60.000 0.00 0.00 42.28 3.77
142 143 1.666872 GGTCCACGGAGAACCAACG 60.667 63.158 0.00 0.00 35.59 4.10
143 144 1.666872 GTCCACGGAGAACCAACGG 60.667 63.158 0.00 0.00 35.59 4.44
144 145 3.047877 CCACGGAGAACCAACGGC 61.048 66.667 0.00 0.00 35.59 5.68
145 146 2.030562 CACGGAGAACCAACGGCT 59.969 61.111 0.00 0.00 35.59 5.52
146 147 2.030562 ACGGAGAACCAACGGCTG 59.969 61.111 0.00 0.00 35.59 4.85
147 148 3.423154 CGGAGAACCAACGGCTGC 61.423 66.667 0.00 0.00 35.59 5.25
148 149 3.423154 GGAGAACCAACGGCTGCG 61.423 66.667 0.00 0.00 35.97 5.18
149 150 2.665185 GAGAACCAACGGCTGCGT 60.665 61.111 0.00 0.00 0.00 5.24
150 151 1.373748 GAGAACCAACGGCTGCGTA 60.374 57.895 0.00 0.00 0.00 4.42
151 152 1.352156 GAGAACCAACGGCTGCGTAG 61.352 60.000 0.00 0.00 0.00 3.51
152 153 1.373748 GAACCAACGGCTGCGTAGA 60.374 57.895 4.08 0.00 0.00 2.59
153 154 1.623973 GAACCAACGGCTGCGTAGAC 61.624 60.000 4.08 0.00 0.00 2.59
154 155 2.095978 AACCAACGGCTGCGTAGACT 62.096 55.000 4.08 0.00 0.00 3.24
155 156 1.805945 CCAACGGCTGCGTAGACTC 60.806 63.158 4.08 0.00 0.00 3.36
156 157 2.152699 CAACGGCTGCGTAGACTCG 61.153 63.158 4.08 7.22 0.00 4.18
164 165 4.189188 CGTAGACTCGCCCCCGTG 62.189 72.222 0.00 0.00 35.54 4.94
165 166 4.509737 GTAGACTCGCCCCCGTGC 62.510 72.222 0.00 0.00 35.54 5.34
166 167 4.753662 TAGACTCGCCCCCGTGCT 62.754 66.667 0.00 0.00 35.54 4.40
170 171 4.394712 CTCGCCCCCGTGCTTCTT 62.395 66.667 0.00 0.00 35.54 2.52
171 172 4.388499 TCGCCCCCGTGCTTCTTC 62.388 66.667 0.00 0.00 35.54 2.87
172 173 4.394712 CGCCCCCGTGCTTCTTCT 62.395 66.667 0.00 0.00 0.00 2.85
173 174 2.747855 GCCCCCGTGCTTCTTCTG 60.748 66.667 0.00 0.00 0.00 3.02
174 175 3.068881 CCCCCGTGCTTCTTCTGA 58.931 61.111 0.00 0.00 0.00 3.27
175 176 1.078848 CCCCCGTGCTTCTTCTGAG 60.079 63.158 0.00 0.00 0.00 3.35
176 177 1.078848 CCCCGTGCTTCTTCTGAGG 60.079 63.158 0.00 0.00 0.00 3.86
177 178 1.674057 CCCGTGCTTCTTCTGAGGT 59.326 57.895 0.00 0.00 0.00 3.85
178 179 0.671781 CCCGTGCTTCTTCTGAGGTG 60.672 60.000 0.00 0.00 0.00 4.00
179 180 0.671781 CCGTGCTTCTTCTGAGGTGG 60.672 60.000 0.00 0.00 0.00 4.61
180 181 0.034059 CGTGCTTCTTCTGAGGTGGT 59.966 55.000 0.00 0.00 0.00 4.16
181 182 1.517242 GTGCTTCTTCTGAGGTGGTG 58.483 55.000 0.00 0.00 0.00 4.17
182 183 1.131638 TGCTTCTTCTGAGGTGGTGT 58.868 50.000 0.00 0.00 0.00 4.16
183 184 1.490490 TGCTTCTTCTGAGGTGGTGTT 59.510 47.619 0.00 0.00 0.00 3.32
184 185 2.092429 TGCTTCTTCTGAGGTGGTGTTT 60.092 45.455 0.00 0.00 0.00 2.83
185 186 2.291741 GCTTCTTCTGAGGTGGTGTTTG 59.708 50.000 0.00 0.00 0.00 2.93
186 187 2.638480 TCTTCTGAGGTGGTGTTTGG 57.362 50.000 0.00 0.00 0.00 3.28
187 188 1.843851 TCTTCTGAGGTGGTGTTTGGT 59.156 47.619 0.00 0.00 0.00 3.67
188 189 2.241176 TCTTCTGAGGTGGTGTTTGGTT 59.759 45.455 0.00 0.00 0.00 3.67
189 190 2.341846 TCTGAGGTGGTGTTTGGTTC 57.658 50.000 0.00 0.00 0.00 3.62
190 191 1.843851 TCTGAGGTGGTGTTTGGTTCT 59.156 47.619 0.00 0.00 0.00 3.01
191 192 2.158813 TCTGAGGTGGTGTTTGGTTCTC 60.159 50.000 0.00 0.00 0.00 2.87
192 193 1.843851 TGAGGTGGTGTTTGGTTCTCT 59.156 47.619 0.00 0.00 0.00 3.10
193 194 3.042682 TGAGGTGGTGTTTGGTTCTCTA 58.957 45.455 0.00 0.00 0.00 2.43
194 195 3.071023 TGAGGTGGTGTTTGGTTCTCTAG 59.929 47.826 0.00 0.00 0.00 2.43
195 196 3.046374 AGGTGGTGTTTGGTTCTCTAGT 58.954 45.455 0.00 0.00 0.00 2.57
196 197 4.228824 AGGTGGTGTTTGGTTCTCTAGTA 58.771 43.478 0.00 0.00 0.00 1.82
197 198 4.040095 AGGTGGTGTTTGGTTCTCTAGTAC 59.960 45.833 0.00 0.00 0.00 2.73
198 199 4.040095 GGTGGTGTTTGGTTCTCTAGTACT 59.960 45.833 0.00 0.00 0.00 2.73
199 200 5.244626 GGTGGTGTTTGGTTCTCTAGTACTA 59.755 44.000 1.89 1.89 0.00 1.82
200 201 6.388278 GTGGTGTTTGGTTCTCTAGTACTAG 58.612 44.000 21.87 21.87 34.56 2.57
201 202 6.015603 GTGGTGTTTGGTTCTCTAGTACTAGT 60.016 42.308 25.58 0.00 34.84 2.57
202 203 7.175641 GTGGTGTTTGGTTCTCTAGTACTAGTA 59.824 40.741 25.58 14.64 34.84 1.82
203 204 7.175641 TGGTGTTTGGTTCTCTAGTACTAGTAC 59.824 40.741 25.58 23.03 34.84 2.73
205 206 9.442047 GTGTTTGGTTCTCTAGTACTAGTACTA 57.558 37.037 31.39 31.39 43.98 1.82
239 240 9.689501 TTCTAGTCCCTAGAACTTTTTGAAAAA 57.310 29.630 9.14 2.83 44.85 1.94
240 241 9.338622 TCTAGTCCCTAGAACTTTTTGAAAAAG 57.661 33.333 24.36 24.36 39.74 2.27
241 242 9.338622 CTAGTCCCTAGAACTTTTTGAAAAAGA 57.661 33.333 30.55 12.07 36.26 2.52
242 243 7.997482 AGTCCCTAGAACTTTTTGAAAAAGAC 58.003 34.615 30.55 22.96 0.00 3.01
243 244 7.834681 AGTCCCTAGAACTTTTTGAAAAAGACT 59.165 33.333 30.55 26.88 0.00 3.24
244 245 8.467598 GTCCCTAGAACTTTTTGAAAAAGACTT 58.532 33.333 30.55 18.34 0.00 3.01
245 246 9.031537 TCCCTAGAACTTTTTGAAAAAGACTTT 57.968 29.630 30.55 17.73 0.00 2.66
246 247 9.302345 CCCTAGAACTTTTTGAAAAAGACTTTC 57.698 33.333 30.55 23.28 0.00 2.62
247 248 9.855021 CCTAGAACTTTTTGAAAAAGACTTTCA 57.145 29.630 30.55 15.56 36.71 2.69
256 257 5.650543 TGAAAAAGACTTTCAAAGAGGTGC 58.349 37.500 3.49 0.00 35.69 5.01
257 258 5.418840 TGAAAAAGACTTTCAAAGAGGTGCT 59.581 36.000 3.49 0.00 35.69 4.40
258 259 5.921962 AAAAGACTTTCAAAGAGGTGCTT 57.078 34.783 3.49 0.00 38.88 3.91
259 260 5.506686 AAAGACTTTCAAAGAGGTGCTTC 57.493 39.130 3.49 0.00 35.24 3.86
260 261 4.429854 AGACTTTCAAAGAGGTGCTTCT 57.570 40.909 3.49 0.00 35.24 2.85
261 262 5.552870 AGACTTTCAAAGAGGTGCTTCTA 57.447 39.130 3.49 0.00 35.24 2.10
262 263 5.930135 AGACTTTCAAAGAGGTGCTTCTAA 58.070 37.500 3.49 0.00 35.24 2.10
263 264 5.994668 AGACTTTCAAAGAGGTGCTTCTAAG 59.005 40.000 3.49 0.00 35.24 2.18
264 265 5.066593 ACTTTCAAAGAGGTGCTTCTAAGG 58.933 41.667 3.49 0.00 35.24 2.69
265 266 4.974645 TTCAAAGAGGTGCTTCTAAGGA 57.025 40.909 0.00 0.00 35.24 3.36
266 267 5.505181 TTCAAAGAGGTGCTTCTAAGGAT 57.495 39.130 0.00 0.00 35.24 3.24
267 268 5.505181 TCAAAGAGGTGCTTCTAAGGATT 57.495 39.130 0.00 0.00 35.24 3.01
268 269 5.880901 TCAAAGAGGTGCTTCTAAGGATTT 58.119 37.500 0.00 0.00 35.24 2.17
269 270 6.306987 TCAAAGAGGTGCTTCTAAGGATTTT 58.693 36.000 0.00 0.00 35.24 1.82
270 271 6.777580 TCAAAGAGGTGCTTCTAAGGATTTTT 59.222 34.615 0.00 0.00 35.24 1.94
271 272 7.942341 TCAAAGAGGTGCTTCTAAGGATTTTTA 59.058 33.333 0.00 0.00 35.24 1.52
272 273 7.929941 AAGAGGTGCTTCTAAGGATTTTTAG 57.070 36.000 0.00 0.00 28.17 1.85
273 274 5.883115 AGAGGTGCTTCTAAGGATTTTTAGC 59.117 40.000 0.00 0.00 32.01 3.09
274 275 5.570320 AGGTGCTTCTAAGGATTTTTAGCA 58.430 37.500 0.00 0.00 35.05 3.49
275 276 6.010219 AGGTGCTTCTAAGGATTTTTAGCAA 58.990 36.000 0.00 0.00 38.69 3.91
276 277 6.493458 AGGTGCTTCTAAGGATTTTTAGCAAA 59.507 34.615 0.00 0.00 38.69 3.68
277 278 7.015195 AGGTGCTTCTAAGGATTTTTAGCAAAA 59.985 33.333 0.00 0.00 38.69 2.44
278 279 7.655732 GGTGCTTCTAAGGATTTTTAGCAAAAA 59.344 33.333 0.00 8.54 43.76 1.94
279 280 8.703336 GTGCTTCTAAGGATTTTTAGCAAAAAG 58.297 33.333 0.00 0.00 42.97 2.27
280 281 8.421002 TGCTTCTAAGGATTTTTAGCAAAAAGT 58.579 29.630 10.88 0.00 42.97 2.66
281 282 9.261180 GCTTCTAAGGATTTTTAGCAAAAAGTT 57.739 29.630 10.88 7.83 42.97 2.66
308 309 6.544928 AAAAAGTCTCACCCTGTTTGATTT 57.455 33.333 0.00 0.00 0.00 2.17
309 310 5.520376 AAAGTCTCACCCTGTTTGATTTG 57.480 39.130 0.00 0.00 0.00 2.32
310 311 2.887152 AGTCTCACCCTGTTTGATTTGC 59.113 45.455 0.00 0.00 0.00 3.68
311 312 2.887152 GTCTCACCCTGTTTGATTTGCT 59.113 45.455 0.00 0.00 0.00 3.91
312 313 4.072131 GTCTCACCCTGTTTGATTTGCTA 58.928 43.478 0.00 0.00 0.00 3.49
313 314 4.154918 GTCTCACCCTGTTTGATTTGCTAG 59.845 45.833 0.00 0.00 0.00 3.42
314 315 3.420893 TCACCCTGTTTGATTTGCTAGG 58.579 45.455 0.00 0.00 0.00 3.02
316 317 2.378547 ACCCTGTTTGATTTGCTAGGGA 59.621 45.455 13.68 0.00 46.19 4.20
317 318 2.755103 CCCTGTTTGATTTGCTAGGGAC 59.245 50.000 0.00 0.00 46.19 4.46
318 319 3.562176 CCCTGTTTGATTTGCTAGGGACT 60.562 47.826 0.00 0.00 46.19 3.85
319 320 4.082125 CCTGTTTGATTTGCTAGGGACTT 58.918 43.478 0.00 0.00 41.75 3.01
320 321 4.524328 CCTGTTTGATTTGCTAGGGACTTT 59.476 41.667 0.00 0.00 41.75 2.66
321 322 5.011023 CCTGTTTGATTTGCTAGGGACTTTT 59.989 40.000 0.00 0.00 41.75 2.27
322 323 6.462909 CCTGTTTGATTTGCTAGGGACTTTTT 60.463 38.462 0.00 0.00 41.75 1.94
323 324 6.512297 TGTTTGATTTGCTAGGGACTTTTTC 58.488 36.000 0.00 0.00 41.75 2.29
324 325 6.323739 TGTTTGATTTGCTAGGGACTTTTTCT 59.676 34.615 0.00 0.00 41.75 2.52
325 326 7.504238 TGTTTGATTTGCTAGGGACTTTTTCTA 59.496 33.333 0.00 0.00 41.75 2.10
326 327 7.687941 TTGATTTGCTAGGGACTTTTTCTAG 57.312 36.000 0.00 0.00 41.75 2.43
327 328 6.779860 TGATTTGCTAGGGACTTTTTCTAGT 58.220 36.000 0.00 0.00 41.75 2.57
328 329 6.879458 TGATTTGCTAGGGACTTTTTCTAGTC 59.121 38.462 0.00 0.00 43.05 2.59
359 360 4.465632 AAAAGTCCCTGAAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
360 361 2.067365 AGTCCCTGAAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
361 362 1.037493 GTCCCTGAAACCAAACACCC 58.963 55.000 0.00 0.00 0.00 4.61
362 363 0.105913 TCCCTGAAACCAAACACCCC 60.106 55.000 0.00 0.00 0.00 4.95
363 364 0.105709 CCCTGAAACCAAACACCCCT 60.106 55.000 0.00 0.00 0.00 4.79
364 365 1.039856 CCTGAAACCAAACACCCCTG 58.960 55.000 0.00 0.00 0.00 4.45
365 366 1.410932 CCTGAAACCAAACACCCCTGA 60.411 52.381 0.00 0.00 0.00 3.86
366 367 1.956477 CTGAAACCAAACACCCCTGAG 59.044 52.381 0.00 0.00 0.00 3.35
367 368 1.286553 TGAAACCAAACACCCCTGAGT 59.713 47.619 0.00 0.00 0.00 3.41
368 369 2.291930 TGAAACCAAACACCCCTGAGTT 60.292 45.455 0.00 0.00 0.00 3.01
369 370 2.543037 AACCAAACACCCCTGAGTTT 57.457 45.000 0.00 0.00 38.40 2.66
370 371 2.067365 ACCAAACACCCCTGAGTTTC 57.933 50.000 0.00 0.00 35.90 2.78
371 372 1.569072 ACCAAACACCCCTGAGTTTCT 59.431 47.619 0.00 0.00 35.90 2.52
372 373 2.781174 ACCAAACACCCCTGAGTTTCTA 59.219 45.455 0.00 0.00 35.90 2.10
373 374 3.203487 ACCAAACACCCCTGAGTTTCTAA 59.797 43.478 0.00 0.00 35.90 2.10
374 375 3.568430 CCAAACACCCCTGAGTTTCTAAC 59.432 47.826 0.00 0.00 35.90 2.34
375 376 4.204012 CAAACACCCCTGAGTTTCTAACA 58.796 43.478 0.00 0.00 35.90 2.41
376 377 4.513406 AACACCCCTGAGTTTCTAACAA 57.487 40.909 0.00 0.00 0.00 2.83
377 378 4.724279 ACACCCCTGAGTTTCTAACAAT 57.276 40.909 0.00 0.00 0.00 2.71
378 379 4.652822 ACACCCCTGAGTTTCTAACAATC 58.347 43.478 0.00 0.00 0.00 2.67
379 380 3.684788 CACCCCTGAGTTTCTAACAATCG 59.315 47.826 0.00 0.00 0.00 3.34
380 381 3.326880 ACCCCTGAGTTTCTAACAATCGT 59.673 43.478 0.00 0.00 0.00 3.73
381 382 3.684788 CCCCTGAGTTTCTAACAATCGTG 59.315 47.826 0.00 0.00 0.00 4.35
382 383 3.125316 CCCTGAGTTTCTAACAATCGTGC 59.875 47.826 0.00 0.00 0.00 5.34
383 384 3.181530 CCTGAGTTTCTAACAATCGTGCG 60.182 47.826 0.00 0.00 0.00 5.34
384 385 3.386486 TGAGTTTCTAACAATCGTGCGT 58.614 40.909 0.00 0.00 0.00 5.24
385 386 3.183574 TGAGTTTCTAACAATCGTGCGTG 59.816 43.478 0.00 0.00 0.00 5.34
386 387 2.096417 AGTTTCTAACAATCGTGCGTGC 60.096 45.455 0.00 0.00 0.00 5.34
387 388 0.436913 TTCTAACAATCGTGCGTGCG 59.563 50.000 0.00 0.00 0.00 5.34
388 389 1.058748 CTAACAATCGTGCGTGCGG 59.941 57.895 1.42 0.00 0.00 5.69
389 390 1.348538 CTAACAATCGTGCGTGCGGA 61.349 55.000 1.42 0.00 0.00 5.54
390 391 0.738063 TAACAATCGTGCGTGCGGAT 60.738 50.000 1.42 0.00 0.00 4.18
391 392 1.573829 AACAATCGTGCGTGCGGATT 61.574 50.000 5.45 5.45 0.00 3.01
392 393 1.134487 CAATCGTGCGTGCGGATTT 59.866 52.632 7.85 0.00 0.00 2.17
393 394 1.127571 CAATCGTGCGTGCGGATTTG 61.128 55.000 7.85 0.01 0.00 2.32
394 395 1.573829 AATCGTGCGTGCGGATTTGT 61.574 50.000 5.45 0.00 0.00 2.83
395 396 2.239341 ATCGTGCGTGCGGATTTGTG 62.239 55.000 1.42 0.00 0.00 3.33
396 397 2.637025 GTGCGTGCGGATTTGTGT 59.363 55.556 0.00 0.00 0.00 3.72
397 398 1.008995 GTGCGTGCGGATTTGTGTT 60.009 52.632 0.00 0.00 0.00 3.32
398 399 0.996727 GTGCGTGCGGATTTGTGTTC 60.997 55.000 0.00 0.00 0.00 3.18
399 400 1.163420 TGCGTGCGGATTTGTGTTCT 61.163 50.000 0.00 0.00 0.00 3.01
400 401 0.725784 GCGTGCGGATTTGTGTTCTG 60.726 55.000 0.00 0.00 0.00 3.02
401 402 0.865111 CGTGCGGATTTGTGTTCTGA 59.135 50.000 0.00 0.00 0.00 3.27
402 403 1.464608 CGTGCGGATTTGTGTTCTGAT 59.535 47.619 0.00 0.00 0.00 2.90
403 404 2.474526 CGTGCGGATTTGTGTTCTGATC 60.475 50.000 0.00 0.00 0.00 2.92
404 405 2.083774 TGCGGATTTGTGTTCTGATCC 58.916 47.619 0.00 0.00 35.73 3.36
405 406 2.290260 TGCGGATTTGTGTTCTGATCCT 60.290 45.455 0.00 0.00 36.70 3.24
406 407 2.352960 GCGGATTTGTGTTCTGATCCTC 59.647 50.000 0.00 0.00 36.70 3.71
407 408 3.599343 CGGATTTGTGTTCTGATCCTCA 58.401 45.455 0.00 0.00 36.70 3.86
466 467 4.722535 TGCGGGAAGGGAGAGGCT 62.723 66.667 0.00 0.00 0.00 4.58
554 555 1.602237 GCTGGAAACCCTCGGATCA 59.398 57.895 0.00 0.00 0.00 2.92
555 556 0.181350 GCTGGAAACCCTCGGATCAT 59.819 55.000 0.00 0.00 0.00 2.45
573 574 0.037326 ATCAGTTTCTCGCGAGCCAA 60.037 50.000 30.97 21.81 0.00 4.52
648 649 1.728490 GGCGGGACATGGAAATCTGC 61.728 60.000 0.00 0.00 0.00 4.26
651 652 0.394352 GGGACATGGAAATCTGCCGT 60.394 55.000 0.00 0.00 0.00 5.68
837 847 2.284112 CCCCTTGCTGTTGGCCAT 60.284 61.111 6.09 0.00 40.92 4.40
898 908 2.892425 CCTTGTCTCCGATGCCGC 60.892 66.667 0.00 0.00 0.00 6.53
971 984 3.318313 AGGTGTAGGATCGATTTCCCAT 58.682 45.455 0.00 0.00 36.35 4.00
1009 1022 2.034305 GTCGACTAGGTTATGGACGCAT 59.966 50.000 8.70 0.00 0.00 4.73
1135 1148 2.683742 CGCTATGGTCCATTGTTTCCCT 60.684 50.000 10.33 0.00 0.00 4.20
1195 1208 0.179137 CTGCAATGACGTCGAGGCTA 60.179 55.000 20.71 10.18 0.00 3.93
1257 1270 1.153667 CGAGACCTTCAGGAGCAGC 60.154 63.158 0.00 0.00 38.94 5.25
1369 1382 2.971660 TCACAACACGTTCAGGAGAA 57.028 45.000 0.00 0.00 0.00 2.87
1553 1566 8.462589 TTTTCATGGCTTGATATGCTTGTATA 57.537 30.769 3.72 0.00 33.34 1.47
1575 1588 3.555956 AGTTCAAGTTCAGCACTAACACG 59.444 43.478 0.00 0.00 32.94 4.49
1615 1628 1.006998 AGGACTGCATTGGGGCAATAA 59.993 47.619 0.00 0.00 44.40 1.40
1742 1755 4.005650 CTCAAGTTCACATATGTGCTGGT 58.994 43.478 27.71 12.33 45.25 4.00
1792 1805 2.708051 ACATTCTCACTGACAGCATGG 58.292 47.619 1.25 0.00 43.62 3.66
1834 1847 1.590147 CCCGACGGCAAGTTCTACT 59.410 57.895 8.86 0.00 0.00 2.57
1861 1874 1.524621 GCTGGCTATGCATGTCGGT 60.525 57.895 10.16 0.00 0.00 4.69
1941 1954 7.365497 TCAATCTATGGAGTCATCTAGCAAA 57.635 36.000 0.00 0.00 34.96 3.68
2439 6590 0.546122 TTATCTCTTGGCGCATGGGT 59.454 50.000 10.83 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.028770 CAAACGCCAACACACGACAT 59.971 50.000 0.00 0.00 0.00 3.06
1 2 1.425825 CAAACGCCAACACACGACA 59.574 52.632 0.00 0.00 0.00 4.35
2 3 1.937362 GCAAACGCCAACACACGAC 60.937 57.895 0.00 0.00 0.00 4.34
5 6 1.299089 GGAGCAAACGCCAACACAC 60.299 57.895 0.00 0.00 35.48 3.82
7 8 1.282875 GAGGAGCAAACGCCAACAC 59.717 57.895 0.00 0.00 38.42 3.32
9 10 2.954611 GGAGGAGCAAACGCCAAC 59.045 61.111 0.00 0.00 38.42 3.77
10 11 2.668212 CGGAGGAGCAAACGCCAA 60.668 61.111 0.00 0.00 38.42 4.52
34 35 4.657824 AGTCCACGCGACCAACCG 62.658 66.667 15.93 0.00 43.08 4.44
35 36 3.041940 CAGTCCACGCGACCAACC 61.042 66.667 15.93 0.00 43.08 3.77
36 37 3.712881 GCAGTCCACGCGACCAAC 61.713 66.667 15.93 5.27 43.08 3.77
37 38 3.923864 AGCAGTCCACGCGACCAA 61.924 61.111 15.93 0.00 43.08 3.67
38 39 4.662961 CAGCAGTCCACGCGACCA 62.663 66.667 15.93 0.00 43.08 4.02
65 66 4.947147 CACCACCCACCACACCCG 62.947 72.222 0.00 0.00 0.00 5.28
107 108 3.834799 CAGGCCTACGGTCCGGAC 61.835 72.222 27.04 27.04 0.00 4.79
110 111 3.834799 GACCAGGCCTACGGTCCG 61.835 72.222 25.46 10.48 45.03 4.79
113 114 3.001406 GTGGACCAGGCCTACGGT 61.001 66.667 14.53 14.53 38.56 4.83
114 115 4.143333 CGTGGACCAGGCCTACGG 62.143 72.222 15.77 11.99 32.57 4.02
115 116 4.143333 CCGTGGACCAGGCCTACG 62.143 72.222 16.47 16.47 34.48 3.51
116 117 2.682494 TCCGTGGACCAGGCCTAC 60.682 66.667 3.98 0.00 0.00 3.18
117 118 2.363795 CTCCGTGGACCAGGCCTA 60.364 66.667 3.98 0.00 0.00 3.93
118 119 3.846405 TTCTCCGTGGACCAGGCCT 62.846 63.158 0.00 0.00 0.00 5.19
119 120 3.319198 TTCTCCGTGGACCAGGCC 61.319 66.667 8.75 0.00 0.00 5.19
120 121 2.047179 GTTCTCCGTGGACCAGGC 60.047 66.667 8.75 0.00 0.00 4.85
121 122 1.764571 TTGGTTCTCCGTGGACCAGG 61.765 60.000 7.23 7.23 36.30 4.45
122 123 0.602905 GTTGGTTCTCCGTGGACCAG 60.603 60.000 0.00 0.00 36.30 4.00
123 124 1.448497 GTTGGTTCTCCGTGGACCA 59.552 57.895 2.07 2.07 36.30 4.02
124 125 1.666872 CGTTGGTTCTCCGTGGACC 60.667 63.158 0.00 0.00 36.30 4.46
125 126 1.666872 CCGTTGGTTCTCCGTGGAC 60.667 63.158 0.00 0.00 36.30 4.02
126 127 2.738480 CCGTTGGTTCTCCGTGGA 59.262 61.111 0.00 0.00 36.30 4.02
127 128 3.047877 GCCGTTGGTTCTCCGTGG 61.048 66.667 0.00 0.00 36.30 4.94
128 129 2.030562 AGCCGTTGGTTCTCCGTG 59.969 61.111 0.00 0.00 36.30 4.94
129 130 2.030562 CAGCCGTTGGTTCTCCGT 59.969 61.111 0.00 0.00 36.30 4.69
130 131 3.423154 GCAGCCGTTGGTTCTCCG 61.423 66.667 0.00 0.00 36.30 4.63
131 132 3.423154 CGCAGCCGTTGGTTCTCC 61.423 66.667 0.00 0.00 0.00 3.71
147 148 4.189188 CACGGGGGCGAGTCTACG 62.189 72.222 0.00 0.00 0.00 3.51
148 149 4.509737 GCACGGGGGCGAGTCTAC 62.510 72.222 0.00 0.00 0.00 2.59
149 150 4.753662 AGCACGGGGGCGAGTCTA 62.754 66.667 0.00 0.00 39.27 2.59
153 154 4.394712 AAGAAGCACGGGGGCGAG 62.395 66.667 0.00 0.00 39.27 5.03
154 155 4.388499 GAAGAAGCACGGGGGCGA 62.388 66.667 0.00 0.00 39.27 5.54
155 156 4.394712 AGAAGAAGCACGGGGGCG 62.395 66.667 0.00 0.00 39.27 6.13
156 157 2.747855 CAGAAGAAGCACGGGGGC 60.748 66.667 0.00 0.00 0.00 5.80
157 158 1.078848 CTCAGAAGAAGCACGGGGG 60.079 63.158 0.00 0.00 0.00 5.40
158 159 1.078848 CCTCAGAAGAAGCACGGGG 60.079 63.158 0.00 0.00 0.00 5.73
159 160 0.671781 CACCTCAGAAGAAGCACGGG 60.672 60.000 0.00 0.00 0.00 5.28
160 161 0.671781 CCACCTCAGAAGAAGCACGG 60.672 60.000 0.00 0.00 0.00 4.94
161 162 0.034059 ACCACCTCAGAAGAAGCACG 59.966 55.000 0.00 0.00 0.00 5.34
162 163 1.202698 ACACCACCTCAGAAGAAGCAC 60.203 52.381 0.00 0.00 0.00 4.40
163 164 1.131638 ACACCACCTCAGAAGAAGCA 58.868 50.000 0.00 0.00 0.00 3.91
164 165 2.262423 AACACCACCTCAGAAGAAGC 57.738 50.000 0.00 0.00 0.00 3.86
165 166 2.880890 CCAAACACCACCTCAGAAGAAG 59.119 50.000 0.00 0.00 0.00 2.85
166 167 2.241176 ACCAAACACCACCTCAGAAGAA 59.759 45.455 0.00 0.00 0.00 2.52
167 168 1.843851 ACCAAACACCACCTCAGAAGA 59.156 47.619 0.00 0.00 0.00 2.87
168 169 2.348411 ACCAAACACCACCTCAGAAG 57.652 50.000 0.00 0.00 0.00 2.85
169 170 2.241176 AGAACCAAACACCACCTCAGAA 59.759 45.455 0.00 0.00 0.00 3.02
170 171 1.843851 AGAACCAAACACCACCTCAGA 59.156 47.619 0.00 0.00 0.00 3.27
171 172 2.158755 AGAGAACCAAACACCACCTCAG 60.159 50.000 0.00 0.00 0.00 3.35
172 173 1.843851 AGAGAACCAAACACCACCTCA 59.156 47.619 0.00 0.00 0.00 3.86
173 174 2.640316 AGAGAACCAAACACCACCTC 57.360 50.000 0.00 0.00 0.00 3.85
174 175 3.046374 ACTAGAGAACCAAACACCACCT 58.954 45.455 0.00 0.00 0.00 4.00
175 176 3.487120 ACTAGAGAACCAAACACCACC 57.513 47.619 0.00 0.00 0.00 4.61
176 177 5.211174 AGTACTAGAGAACCAAACACCAC 57.789 43.478 0.00 0.00 0.00 4.16
177 178 6.073314 ACTAGTACTAGAGAACCAAACACCA 58.927 40.000 31.93 0.00 36.97 4.17
178 179 6.587206 ACTAGTACTAGAGAACCAAACACC 57.413 41.667 31.93 0.00 36.97 4.16
179 180 8.334263 AGTACTAGTACTAGAGAACCAAACAC 57.666 38.462 31.93 14.24 43.98 3.32
216 217 9.117183 GTCTTTTTCAAAAAGTTCTAGGGACTA 57.883 33.333 19.82 0.00 41.75 2.59
217 218 7.834681 AGTCTTTTTCAAAAAGTTCTAGGGACT 59.165 33.333 19.82 11.77 46.37 3.85
218 219 7.997482 AGTCTTTTTCAAAAAGTTCTAGGGAC 58.003 34.615 19.82 9.96 0.00 4.46
219 220 8.589701 AAGTCTTTTTCAAAAAGTTCTAGGGA 57.410 30.769 19.82 0.00 0.00 4.20
220 221 9.302345 GAAAGTCTTTTTCAAAAAGTTCTAGGG 57.698 33.333 19.82 0.00 0.00 3.53
221 222 9.855021 TGAAAGTCTTTTTCAAAAAGTTCTAGG 57.145 29.630 19.82 0.00 35.69 3.02
232 233 6.071391 AGCACCTCTTTGAAAGTCTTTTTCAA 60.071 34.615 10.14 10.14 43.99 2.69
233 234 5.418840 AGCACCTCTTTGAAAGTCTTTTTCA 59.581 36.000 4.68 0.00 36.71 2.69
234 235 5.895928 AGCACCTCTTTGAAAGTCTTTTTC 58.104 37.500 4.68 0.00 0.00 2.29
235 236 5.921962 AGCACCTCTTTGAAAGTCTTTTT 57.078 34.783 4.68 0.00 0.00 1.94
236 237 5.654209 AGAAGCACCTCTTTGAAAGTCTTTT 59.346 36.000 4.68 0.00 34.56 2.27
237 238 5.196695 AGAAGCACCTCTTTGAAAGTCTTT 58.803 37.500 4.68 0.00 34.56 2.52
238 239 4.786425 AGAAGCACCTCTTTGAAAGTCTT 58.214 39.130 4.68 2.68 34.56 3.01
239 240 4.429854 AGAAGCACCTCTTTGAAAGTCT 57.570 40.909 4.68 0.00 34.56 3.24
240 241 5.180304 CCTTAGAAGCACCTCTTTGAAAGTC 59.820 44.000 4.68 0.00 34.56 3.01
241 242 5.066593 CCTTAGAAGCACCTCTTTGAAAGT 58.933 41.667 4.68 0.00 34.56 2.66
242 243 5.308825 TCCTTAGAAGCACCTCTTTGAAAG 58.691 41.667 0.00 0.00 34.56 2.62
243 244 5.304686 TCCTTAGAAGCACCTCTTTGAAA 57.695 39.130 0.00 0.00 34.56 2.69
244 245 4.974645 TCCTTAGAAGCACCTCTTTGAA 57.025 40.909 0.00 0.00 34.56 2.69
245 246 5.505181 AATCCTTAGAAGCACCTCTTTGA 57.495 39.130 0.00 0.00 34.56 2.69
246 247 6.581171 AAAATCCTTAGAAGCACCTCTTTG 57.419 37.500 0.00 0.00 34.56 2.77
247 248 7.094162 GCTAAAAATCCTTAGAAGCACCTCTTT 60.094 37.037 0.00 0.00 34.56 2.52
248 249 6.375736 GCTAAAAATCCTTAGAAGCACCTCTT 59.624 38.462 0.00 0.00 37.83 2.85
249 250 5.883115 GCTAAAAATCCTTAGAAGCACCTCT 59.117 40.000 0.00 0.00 31.59 3.69
250 251 5.648092 TGCTAAAAATCCTTAGAAGCACCTC 59.352 40.000 0.00 0.00 33.84 3.85
251 252 5.570320 TGCTAAAAATCCTTAGAAGCACCT 58.430 37.500 0.00 0.00 33.84 4.00
252 253 5.897377 TGCTAAAAATCCTTAGAAGCACC 57.103 39.130 0.00 0.00 33.84 5.01
253 254 8.587952 TTTTTGCTAAAAATCCTTAGAAGCAC 57.412 30.769 3.49 0.00 38.15 4.40
254 255 8.421002 ACTTTTTGCTAAAAATCCTTAGAAGCA 58.579 29.630 7.45 0.00 39.43 3.91
255 256 8.818141 ACTTTTTGCTAAAAATCCTTAGAAGC 57.182 30.769 7.45 0.00 39.43 3.86
285 286 6.340522 CAAATCAAACAGGGTGAGACTTTTT 58.659 36.000 0.00 0.00 0.00 1.94
286 287 5.682212 GCAAATCAAACAGGGTGAGACTTTT 60.682 40.000 0.00 0.00 0.00 2.27
287 288 4.202151 GCAAATCAAACAGGGTGAGACTTT 60.202 41.667 0.00 0.00 0.00 2.66
288 289 3.319122 GCAAATCAAACAGGGTGAGACTT 59.681 43.478 0.00 0.00 0.00 3.01
289 290 2.887152 GCAAATCAAACAGGGTGAGACT 59.113 45.455 0.00 0.00 0.00 3.24
290 291 2.887152 AGCAAATCAAACAGGGTGAGAC 59.113 45.455 0.00 0.00 0.00 3.36
291 292 3.228188 AGCAAATCAAACAGGGTGAGA 57.772 42.857 0.00 0.00 0.00 3.27
292 293 3.441572 CCTAGCAAATCAAACAGGGTGAG 59.558 47.826 0.00 0.00 0.00 3.51
293 294 3.420893 CCTAGCAAATCAAACAGGGTGA 58.579 45.455 0.00 0.00 0.00 4.02
294 295 2.493278 CCCTAGCAAATCAAACAGGGTG 59.507 50.000 0.00 0.00 38.34 4.61
295 296 2.378547 TCCCTAGCAAATCAAACAGGGT 59.621 45.455 4.47 0.00 42.84 4.34
296 297 2.755103 GTCCCTAGCAAATCAAACAGGG 59.245 50.000 0.00 0.00 43.52 4.45
297 298 3.690460 AGTCCCTAGCAAATCAAACAGG 58.310 45.455 0.00 0.00 0.00 4.00
298 299 5.712152 AAAGTCCCTAGCAAATCAAACAG 57.288 39.130 0.00 0.00 0.00 3.16
299 300 6.323739 AGAAAAAGTCCCTAGCAAATCAAACA 59.676 34.615 0.00 0.00 0.00 2.83
300 301 6.749139 AGAAAAAGTCCCTAGCAAATCAAAC 58.251 36.000 0.00 0.00 0.00 2.93
301 302 6.976934 AGAAAAAGTCCCTAGCAAATCAAA 57.023 33.333 0.00 0.00 0.00 2.69
302 303 7.231467 ACTAGAAAAAGTCCCTAGCAAATCAA 58.769 34.615 0.00 0.00 34.70 2.57
303 304 6.779860 ACTAGAAAAAGTCCCTAGCAAATCA 58.220 36.000 0.00 0.00 34.70 2.57
304 305 7.310072 GACTAGAAAAAGTCCCTAGCAAATC 57.690 40.000 0.00 0.00 40.06 2.17
337 338 4.323180 GGTGTTTGGTTTCAGGGACTTTTT 60.323 41.667 0.00 0.00 34.60 1.94
338 339 3.196901 GGTGTTTGGTTTCAGGGACTTTT 59.803 43.478 0.00 0.00 34.60 2.27
339 340 2.764010 GGTGTTTGGTTTCAGGGACTTT 59.236 45.455 0.00 0.00 34.60 2.66
340 341 2.384828 GGTGTTTGGTTTCAGGGACTT 58.615 47.619 0.00 0.00 34.60 3.01
341 342 1.411074 GGGTGTTTGGTTTCAGGGACT 60.411 52.381 0.00 0.00 43.88 3.85
342 343 1.037493 GGGTGTTTGGTTTCAGGGAC 58.963 55.000 0.00 0.00 0.00 4.46
343 344 0.105913 GGGGTGTTTGGTTTCAGGGA 60.106 55.000 0.00 0.00 0.00 4.20
344 345 0.105709 AGGGGTGTTTGGTTTCAGGG 60.106 55.000 0.00 0.00 0.00 4.45
345 346 1.039856 CAGGGGTGTTTGGTTTCAGG 58.960 55.000 0.00 0.00 0.00 3.86
346 347 1.956477 CTCAGGGGTGTTTGGTTTCAG 59.044 52.381 0.00 0.00 0.00 3.02
347 348 1.286553 ACTCAGGGGTGTTTGGTTTCA 59.713 47.619 0.00 0.00 0.00 2.69
348 349 2.067365 ACTCAGGGGTGTTTGGTTTC 57.933 50.000 0.00 0.00 0.00 2.78
349 350 2.543037 AACTCAGGGGTGTTTGGTTT 57.457 45.000 0.00 0.00 0.00 3.27
350 351 2.024369 AGAAACTCAGGGGTGTTTGGTT 60.024 45.455 0.00 0.00 39.91 3.67
351 352 1.569072 AGAAACTCAGGGGTGTTTGGT 59.431 47.619 0.00 0.00 39.91 3.67
352 353 2.364972 AGAAACTCAGGGGTGTTTGG 57.635 50.000 0.00 0.00 39.91 3.28
353 354 4.204012 TGTTAGAAACTCAGGGGTGTTTG 58.796 43.478 0.00 0.00 39.91 2.93
354 355 4.513406 TGTTAGAAACTCAGGGGTGTTT 57.487 40.909 0.00 0.00 41.83 2.83
355 356 4.513406 TTGTTAGAAACTCAGGGGTGTT 57.487 40.909 0.00 0.00 32.43 3.32
356 357 4.652822 GATTGTTAGAAACTCAGGGGTGT 58.347 43.478 0.00 0.00 0.00 4.16
357 358 3.684788 CGATTGTTAGAAACTCAGGGGTG 59.315 47.826 0.00 0.00 0.00 4.61
358 359 3.326880 ACGATTGTTAGAAACTCAGGGGT 59.673 43.478 0.00 0.00 0.00 4.95
359 360 3.684788 CACGATTGTTAGAAACTCAGGGG 59.315 47.826 0.00 0.00 0.00 4.79
360 361 3.125316 GCACGATTGTTAGAAACTCAGGG 59.875 47.826 0.00 0.00 0.00 4.45
361 362 3.181530 CGCACGATTGTTAGAAACTCAGG 60.182 47.826 0.00 0.00 0.00 3.86
362 363 3.428870 ACGCACGATTGTTAGAAACTCAG 59.571 43.478 0.00 0.00 0.00 3.35
363 364 3.183574 CACGCACGATTGTTAGAAACTCA 59.816 43.478 0.00 0.00 0.00 3.41
364 365 3.722123 CACGCACGATTGTTAGAAACTC 58.278 45.455 0.00 0.00 0.00 3.01
365 366 2.096417 GCACGCACGATTGTTAGAAACT 60.096 45.455 0.00 0.00 0.00 2.66
366 367 2.230864 GCACGCACGATTGTTAGAAAC 58.769 47.619 0.00 0.00 0.00 2.78
367 368 1.136474 CGCACGCACGATTGTTAGAAA 60.136 47.619 0.00 0.00 34.06 2.52
368 369 0.436913 CGCACGCACGATTGTTAGAA 59.563 50.000 0.00 0.00 34.06 2.10
369 370 1.348538 CCGCACGCACGATTGTTAGA 61.349 55.000 0.00 0.00 34.06 2.10
370 371 1.058748 CCGCACGCACGATTGTTAG 59.941 57.895 0.00 0.00 34.06 2.34
371 372 0.738063 ATCCGCACGCACGATTGTTA 60.738 50.000 0.00 0.00 34.06 2.41
372 373 1.573829 AATCCGCACGCACGATTGTT 61.574 50.000 0.00 0.00 34.06 2.83
373 374 1.573829 AAATCCGCACGCACGATTGT 61.574 50.000 0.00 0.00 34.06 2.71
374 375 1.127571 CAAATCCGCACGCACGATTG 61.128 55.000 0.00 0.00 34.06 2.67
375 376 1.134487 CAAATCCGCACGCACGATT 59.866 52.632 0.00 0.00 34.06 3.34
376 377 2.032634 ACAAATCCGCACGCACGAT 61.033 52.632 0.00 0.00 34.06 3.73
377 378 2.663520 ACAAATCCGCACGCACGA 60.664 55.556 0.00 0.00 34.06 4.35
378 379 2.499520 CACAAATCCGCACGCACG 60.500 61.111 0.00 0.00 0.00 5.34
379 380 0.996727 GAACACAAATCCGCACGCAC 60.997 55.000 0.00 0.00 0.00 5.34
380 381 1.163420 AGAACACAAATCCGCACGCA 61.163 50.000 0.00 0.00 0.00 5.24
381 382 0.725784 CAGAACACAAATCCGCACGC 60.726 55.000 0.00 0.00 0.00 5.34
382 383 0.865111 TCAGAACACAAATCCGCACG 59.135 50.000 0.00 0.00 0.00 5.34
383 384 2.159517 GGATCAGAACACAAATCCGCAC 60.160 50.000 0.00 0.00 0.00 5.34
384 385 2.083774 GGATCAGAACACAAATCCGCA 58.916 47.619 0.00 0.00 0.00 5.69
385 386 2.352960 GAGGATCAGAACACAAATCCGC 59.647 50.000 0.00 0.00 42.09 5.54
386 387 3.599343 TGAGGATCAGAACACAAATCCG 58.401 45.455 0.00 0.00 42.56 4.18
400 401 0.804989 CAAACACGCCCTTGAGGATC 59.195 55.000 0.00 0.00 38.24 3.36
401 402 0.609131 CCAAACACGCCCTTGAGGAT 60.609 55.000 0.00 0.00 38.24 3.24
402 403 1.228124 CCAAACACGCCCTTGAGGA 60.228 57.895 0.00 0.00 38.24 3.71
403 404 1.106944 AACCAAACACGCCCTTGAGG 61.107 55.000 0.00 0.00 39.47 3.86
404 405 0.030638 CAACCAAACACGCCCTTGAG 59.969 55.000 0.00 0.00 0.00 3.02
405 406 2.010582 GCAACCAAACACGCCCTTGA 62.011 55.000 0.00 0.00 0.00 3.02
406 407 1.591327 GCAACCAAACACGCCCTTG 60.591 57.895 0.00 0.00 0.00 3.61
407 408 2.791868 GGCAACCAAACACGCCCTT 61.792 57.895 0.00 0.00 38.67 3.95
449 450 4.722535 AGCCTCTCCCTTCCCGCA 62.723 66.667 0.00 0.00 0.00 5.69
466 467 3.835395 AGGAAAACCAGACAACCAAACAA 59.165 39.130 0.00 0.00 0.00 2.83
554 555 0.037326 TTGGCTCGCGAGAAACTGAT 60.037 50.000 38.74 0.00 41.32 2.90
555 556 0.667487 CTTGGCTCGCGAGAAACTGA 60.667 55.000 38.74 17.79 41.32 3.41
636 637 1.434696 GGCACGGCAGATTTCCATG 59.565 57.895 0.00 0.00 0.00 3.66
688 689 2.280457 GGCTATGGGTGAGCGAGC 60.280 66.667 0.00 0.00 41.06 5.03
898 908 2.592308 GGAGGGGGTGCTGCTTAG 59.408 66.667 0.00 0.00 0.00 2.18
971 984 1.411394 GACATCGACGGTTCGTTCAA 58.589 50.000 0.00 0.00 46.01 2.69
1009 1022 2.641321 CCTGGATTATCAGCCTCATCCA 59.359 50.000 0.00 0.00 42.44 3.41
1135 1148 0.417437 TGGATCCTCTCCTGTTCCCA 59.583 55.000 14.23 0.00 45.21 4.37
1157 1170 5.470368 TGCAGTTGTAGATGTAGTTCAGAC 58.530 41.667 0.00 0.00 0.00 3.51
1195 1208 6.238320 GCTCTTTTCATTCTAAGCATCGACAT 60.238 38.462 0.00 0.00 0.00 3.06
1257 1270 2.309528 TGCTATCTTGTAACAGGCCG 57.690 50.000 0.00 0.00 0.00 6.13
1553 1566 3.555956 CGTGTTAGTGCTGAACTTGAACT 59.444 43.478 0.00 0.00 40.56 3.01
1615 1628 2.305635 TGGCAGTGACATGAGTACCATT 59.694 45.455 0.00 0.00 31.94 3.16
1742 1755 2.935481 CTGACCCCTCCCAGCCAA 60.935 66.667 0.00 0.00 0.00 4.52
1761 1774 4.157105 TCAGTGAGAATGTTTGCATCATGG 59.843 41.667 5.81 0.00 33.50 3.66
1792 1805 0.830648 TTGATCCCATCAGGTCGACC 59.169 55.000 27.67 27.67 40.94 4.79
1834 1847 1.064537 TGCATAGCCAGCATCTCCAAA 60.065 47.619 0.00 0.00 37.02 3.28
1861 1874 1.193462 ACGTTCCCCAACATACCCGA 61.193 55.000 0.00 0.00 32.14 5.14
1941 1954 2.218673 TGTAGATCCACTCCTCCCTCT 58.781 52.381 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.