Multiple sequence alignment - TraesCS7D01G535300

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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 TraesCS7D01G535300 chr7D 100.000 2897 0 0 1 2897 627316639 627313743 0.000000e+00 5350.0
1 TraesCS7D01G535300 chr7B 86.699 2293 164 73 308 2505 728698950 728701196 0.000000e+00 2414.0
2 TraesCS7D01G535300 chr7B 88.584 1165 71 25 865 1979 728288882 728287730 0.000000e+00 1358.0
3 TraesCS7D01G535300 chr7A 89.687 1406 74 28 873 2241 723256389 723255018 0.000000e+00 1727.0
4 TraesCS7D01G535300 chr7A 91.573 356 27 2 2544 2897 723251828 723251474 3.360000e-134 488.0
5 TraesCS7D01G535300 chr7A 93.069 303 20 1 2241 2542 723254972 723254670 2.650000e-120 442.0
6 TraesCS7D01G535300 chr7A 86.400 125 10 4 19 139 723256821 723256700 2.340000e-26 130.0
7 TraesCS7D01G535300 chr7A 91.209 91 3 4 134 221 162920412 162920324 5.070000e-23 119.0
8 TraesCS7D01G535300 chr4B 85.766 274 33 5 1284 1557 619774540 619774273 4.720000e-73 285.0
9 TraesCS7D01G535300 chr4B 84.532 278 37 5 1284 1558 619589592 619589318 1.320000e-68 270.0
10 TraesCS7D01G535300 chr4B 83.942 274 38 5 1284 1557 619787578 619787311 1.030000e-64 257.0
11 TraesCS7D01G535300 chr4B 83.273 275 40 6 1284 1558 619659118 619658850 6.200000e-62 248.0
12 TraesCS7D01G535300 chr4B 86.207 58 8 0 1036 1093 619774866 619774809 2.410000e-06 63.9
13 TraesCS7D01G535300 chr4D 84.727 275 36 6 1284 1558 485683327 485683059 1.320000e-68 270.0
14 TraesCS7D01G535300 chr4D 89.888 89 7 2 138 226 397690494 397690580 2.360000e-21 113.0
15 TraesCS7D01G535300 chr4D 87.931 58 7 0 1036 1093 485683639 485683582 5.180000e-08 69.4
16 TraesCS7D01G535300 chr4D 86.207 58 8 0 1036 1093 485764466 485764409 2.410000e-06 63.9
17 TraesCS7D01G535300 chr5A 84.000 275 38 6 1284 1558 666525224 666524956 2.860000e-65 259.0
18 TraesCS7D01G535300 chr5A 97.403 77 1 1 138 213 4610133 4610209 2.340000e-26 130.0
19 TraesCS7D01G535300 chr5A 87.931 58 7 0 1036 1093 666525529 666525472 5.180000e-08 69.4
20 TraesCS7D01G535300 chr2A 94.048 84 3 2 132 215 48870640 48870559 3.030000e-25 126.0
21 TraesCS7D01G535300 chr5D 93.103 87 3 2 134 217 480427662 480427576 1.090000e-24 124.0
22 TraesCS7D01G535300 chr1D 96.104 77 2 1 137 213 433912678 433912603 1.090000e-24 124.0
23 TraesCS7D01G535300 chr1D 90.000 90 7 2 133 222 433912598 433912685 6.560000e-22 115.0
24 TraesCS7D01G535300 chr2D 89.583 96 6 4 136 229 407254410 407254503 5.070000e-23 119.0
25 TraesCS7D01G535300 chr1B 88.000 100 6 2 129 228 332084455 332084548 2.360000e-21 113.0
26 TraesCS7D01G535300 chr3D 84.000 75 12 0 1064 1138 30409201 30409275 4.000000e-09 73.1
27 TraesCS7D01G535300 chr3D 100.000 28 0 0 1610 1637 172359644 172359671 5.000000e-03 52.8
28 TraesCS7D01G535300 chr3A 84.000 75 12 0 1064 1138 42364680 42364754 4.000000e-09 73.1


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 TraesCS7D01G535300 chr7D 627313743 627316639 2896 True 5350.00 5350 100.00000 1 2897 1 chr7D.!!$R1 2896
1 TraesCS7D01G535300 chr7B 728698950 728701196 2246 False 2414.00 2414 86.69900 308 2505 1 chr7B.!!$F1 2197
2 TraesCS7D01G535300 chr7B 728287730 728288882 1152 True 1358.00 1358 88.58400 865 1979 1 chr7B.!!$R1 1114
3 TraesCS7D01G535300 chr7A 723251474 723256821 5347 True 696.75 1727 90.18225 19 2897 4 chr7A.!!$R2 2878

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
150 155 0.175989 CTTTGCTACTCCCTCCGTCC 59.824 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2112 0.098376 AGATTCGACGACCGCTACAC 59.902 55.0 0.0 0.0 38.37 2.9 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
32 33 7.398332 ACAAATTGAGCCCATTCTTTAGATCTT 59.602 33.333 0.00 0.00 0.00 2.40
34 35 9.479549 AAATTGAGCCCATTCTTTAGATCTTTA 57.520 29.630 0.00 0.00 0.00 1.85
36 37 9.652114 ATTGAGCCCATTCTTTAGATCTTTATT 57.348 29.630 0.00 0.00 0.00 1.40
139 144 3.696051 TCATTGAGCCCAATCTTTGCTAC 59.304 43.478 0.00 0.00 40.81 3.58
140 145 3.439857 TTGAGCCCAATCTTTGCTACT 57.560 42.857 0.00 0.00 34.99 2.57
141 146 2.991250 TGAGCCCAATCTTTGCTACTC 58.009 47.619 0.00 0.00 34.99 2.59
142 147 2.293170 GAGCCCAATCTTTGCTACTCC 58.707 52.381 0.00 0.00 34.99 3.85
143 148 1.064389 AGCCCAATCTTTGCTACTCCC 60.064 52.381 0.00 0.00 32.56 4.30
144 149 1.064389 GCCCAATCTTTGCTACTCCCT 60.064 52.381 0.00 0.00 0.00 4.20
145 150 2.924421 CCCAATCTTTGCTACTCCCTC 58.076 52.381 0.00 0.00 0.00 4.30
146 151 2.422093 CCCAATCTTTGCTACTCCCTCC 60.422 54.545 0.00 0.00 0.00 4.30
147 152 2.555199 CAATCTTTGCTACTCCCTCCG 58.445 52.381 0.00 0.00 0.00 4.63
148 153 1.867363 ATCTTTGCTACTCCCTCCGT 58.133 50.000 0.00 0.00 0.00 4.69
149 154 1.183549 TCTTTGCTACTCCCTCCGTC 58.816 55.000 0.00 0.00 0.00 4.79
150 155 0.175989 CTTTGCTACTCCCTCCGTCC 59.824 60.000 0.00 0.00 0.00 4.79
151 156 1.262640 TTTGCTACTCCCTCCGTCCC 61.263 60.000 0.00 0.00 0.00 4.46
152 157 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
153 158 1.457831 GCTACTCCCTCCGTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
154 159 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.00 0.00 2.74
155 160 1.756690 GCTACTCCCTCCGTCCCATAA 60.757 57.143 0.00 0.00 0.00 1.90
156 161 2.890814 CTACTCCCTCCGTCCCATAAT 58.109 52.381 0.00 0.00 0.00 1.28
157 162 3.816842 GCTACTCCCTCCGTCCCATAATA 60.817 52.174 0.00 0.00 0.00 0.98
158 163 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
159 164 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
160 165 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
161 166 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
162 167 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
163 168 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
164 169 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
165 170 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
166 171 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
167 172 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
168 173 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
169 174 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
170 175 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
171 176 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
172 177 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
173 178 8.784043 GTCCCATAATATAAGAGCGTTTTTGAT 58.216 33.333 0.00 0.00 0.00 2.57
174 179 8.783093 TCCCATAATATAAGAGCGTTTTTGATG 58.217 33.333 0.00 0.00 0.00 3.07
175 180 8.567948 CCCATAATATAAGAGCGTTTTTGATGT 58.432 33.333 0.00 0.00 0.00 3.06
176 181 9.385902 CCATAATATAAGAGCGTTTTTGATGTG 57.614 33.333 0.00 0.00 0.00 3.21
177 182 8.895845 CATAATATAAGAGCGTTTTTGATGTGC 58.104 33.333 0.00 0.00 0.00 4.57
178 183 2.422276 AAGAGCGTTTTTGATGTGCC 57.578 45.000 0.00 0.00 0.00 5.01
179 184 1.317613 AGAGCGTTTTTGATGTGCCA 58.682 45.000 0.00 0.00 0.00 4.92
180 185 1.680735 AGAGCGTTTTTGATGTGCCAA 59.319 42.857 0.00 0.00 0.00 4.52
181 186 2.100584 AGAGCGTTTTTGATGTGCCAAA 59.899 40.909 0.00 0.00 34.56 3.28
182 187 2.863137 GAGCGTTTTTGATGTGCCAAAA 59.137 40.909 0.00 0.00 42.30 2.44
186 191 3.665173 TTTTTGATGTGCCAAAAACGC 57.335 38.095 9.60 0.00 45.53 4.84
187 192 2.593346 TTTGATGTGCCAAAAACGCT 57.407 40.000 0.00 0.00 33.56 5.07
188 193 2.132740 TTGATGTGCCAAAAACGCTC 57.867 45.000 0.00 0.00 0.00 5.03
189 194 1.317613 TGATGTGCCAAAAACGCTCT 58.682 45.000 0.00 0.00 0.00 4.09
190 195 1.680735 TGATGTGCCAAAAACGCTCTT 59.319 42.857 0.00 0.00 0.00 2.85
191 196 2.881513 TGATGTGCCAAAAACGCTCTTA 59.118 40.909 0.00 0.00 0.00 2.10
192 197 3.505680 TGATGTGCCAAAAACGCTCTTAT 59.494 39.130 0.00 0.00 0.00 1.73
193 198 4.697828 TGATGTGCCAAAAACGCTCTTATA 59.302 37.500 0.00 0.00 0.00 0.98
194 199 5.356751 TGATGTGCCAAAAACGCTCTTATAT 59.643 36.000 0.00 0.00 0.00 0.86
195 200 5.637006 TGTGCCAAAAACGCTCTTATATT 57.363 34.783 0.00 0.00 0.00 1.28
196 201 6.745159 TGTGCCAAAAACGCTCTTATATTA 57.255 33.333 0.00 0.00 0.00 0.98
197 202 7.328277 TGTGCCAAAAACGCTCTTATATTAT 57.672 32.000 0.00 0.00 0.00 1.28
198 203 7.192913 TGTGCCAAAAACGCTCTTATATTATG 58.807 34.615 0.00 0.00 0.00 1.90
199 204 6.636850 GTGCCAAAAACGCTCTTATATTATGG 59.363 38.462 0.00 0.00 0.00 2.74
200 205 6.149633 GCCAAAAACGCTCTTATATTATGGG 58.850 40.000 0.00 0.00 0.00 4.00
201 206 6.016610 GCCAAAAACGCTCTTATATTATGGGA 60.017 38.462 0.00 0.00 0.00 4.37
202 207 7.360361 CCAAAAACGCTCTTATATTATGGGAC 58.640 38.462 0.00 0.00 0.00 4.46
203 208 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
204 209 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
205 210 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
206 211 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
207 212 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
208 213 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
209 214 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
210 215 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
211 216 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
212 217 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
213 218 3.562108 ATTATGGGACGGAGGGAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
214 219 2.304221 TATGGGACGGAGGGAGTATG 57.696 55.000 0.00 0.00 0.00 2.39
234 239 5.633830 ATGTTTCTATGACAACTTGCCAG 57.366 39.130 0.00 0.00 0.00 4.85
235 240 3.253188 TGTTTCTATGACAACTTGCCAGC 59.747 43.478 0.00 0.00 0.00 4.85
237 242 1.630369 TCTATGACAACTTGCCAGCCT 59.370 47.619 0.00 0.00 0.00 4.58
238 243 1.741706 CTATGACAACTTGCCAGCCTG 59.258 52.381 0.00 0.00 0.00 4.85
239 244 1.530013 ATGACAACTTGCCAGCCTGC 61.530 55.000 0.00 0.00 0.00 4.85
240 245 2.914097 ACAACTTGCCAGCCTGCC 60.914 61.111 0.00 0.00 0.00 4.85
241 246 2.599578 CAACTTGCCAGCCTGCCT 60.600 61.111 0.00 0.00 0.00 4.75
242 247 2.199535 AACTTGCCAGCCTGCCTT 59.800 55.556 0.00 0.00 0.00 4.35
243 248 1.458209 AACTTGCCAGCCTGCCTTT 60.458 52.632 0.00 0.00 0.00 3.11
245 250 1.005394 CTTGCCAGCCTGCCTTTTG 60.005 57.895 0.00 0.00 0.00 2.44
246 251 2.444700 CTTGCCAGCCTGCCTTTTGG 62.445 60.000 0.00 0.00 44.18 3.28
247 252 3.698820 GCCAGCCTGCCTTTTGGG 61.699 66.667 0.00 0.00 40.82 4.12
256 261 4.041617 CCTTTTGGGCGGTTTTGC 57.958 55.556 0.00 0.00 35.46 3.68
258 263 0.879839 CCTTTTGGGCGGTTTTGCTG 60.880 55.000 0.00 0.00 35.46 4.41
265 270 2.670251 CGGTTTTGCTGCGGGGTA 60.670 61.111 0.00 0.00 0.00 3.69
266 271 2.262303 CGGTTTTGCTGCGGGGTAA 61.262 57.895 0.00 0.00 0.00 2.85
267 272 1.287815 GGTTTTGCTGCGGGGTAAC 59.712 57.895 0.00 0.00 0.00 2.50
428 434 4.801521 TGACCAATCATGATTCTCCCAT 57.198 40.909 18.16 0.68 0.00 4.00
438 444 6.122277 TCATGATTCTCCCATTAACTTGGAC 58.878 40.000 0.00 0.00 39.25 4.02
442 448 6.443849 TGATTCTCCCATTAACTTGGACTAGT 59.556 38.462 0.00 0.00 39.25 2.57
443 449 5.677319 TCTCCCATTAACTTGGACTAGTG 57.323 43.478 0.00 0.00 39.25 2.74
471 480 6.868339 GGGGAAACTTCATCATGTAAAACTTG 59.132 38.462 0.00 0.00 0.00 3.16
519 530 5.763204 ACACACAAACATAACTTCCTACCAG 59.237 40.000 0.00 0.00 0.00 4.00
540 551 8.950007 ACCAGTTTCCTTTCTTAATTAATCCA 57.050 30.769 0.00 0.00 0.00 3.41
583 595 6.104665 TCATCAACTTGAGATGAGATCACAC 58.895 40.000 0.00 0.00 44.98 3.82
584 596 5.473066 TCAACTTGAGATGAGATCACACA 57.527 39.130 0.00 0.00 29.59 3.72
585 597 5.476614 TCAACTTGAGATGAGATCACACAG 58.523 41.667 0.00 0.00 29.59 3.66
586 598 4.468765 ACTTGAGATGAGATCACACAGG 57.531 45.455 0.00 0.00 29.59 4.00
588 600 4.529769 ACTTGAGATGAGATCACACAGGAA 59.470 41.667 0.00 0.00 29.59 3.36
630 645 4.256110 CAACAGTAGATGCAGACCATTGA 58.744 43.478 0.00 0.00 33.29 2.57
637 652 4.970711 AGATGCAGACCATTGATTCCTAG 58.029 43.478 0.00 0.00 33.29 3.02
638 653 3.565764 TGCAGACCATTGATTCCTAGG 57.434 47.619 0.82 0.82 0.00 3.02
639 654 2.846206 TGCAGACCATTGATTCCTAGGT 59.154 45.455 9.08 0.00 34.76 3.08
640 655 3.266772 TGCAGACCATTGATTCCTAGGTT 59.733 43.478 9.08 0.00 31.57 3.50
641 656 4.473196 TGCAGACCATTGATTCCTAGGTTA 59.527 41.667 9.08 0.00 31.57 2.85
642 657 4.816925 GCAGACCATTGATTCCTAGGTTAC 59.183 45.833 9.08 1.95 31.57 2.50
669 686 5.105513 CCACTAAACAAATCACCATTACCCC 60.106 44.000 0.00 0.00 0.00 4.95
672 689 5.482163 AAACAAATCACCATTACCCCAAG 57.518 39.130 0.00 0.00 0.00 3.61
683 700 3.818295 TTACCCCAAGTTGGCAGTTAT 57.182 42.857 17.07 0.23 35.79 1.89
684 701 2.694616 ACCCCAAGTTGGCAGTTATT 57.305 45.000 17.07 0.00 35.79 1.40
695 712 9.289303 CAAGTTGGCAGTTATTTAATCACATAC 57.711 33.333 0.00 0.00 0.00 2.39
697 714 9.019656 AGTTGGCAGTTATTTAATCACATACAA 57.980 29.630 0.00 0.00 0.00 2.41
699 716 9.632807 TTGGCAGTTATTTAATCACATACAAAC 57.367 29.630 0.00 0.00 0.00 2.93
718 743 1.202651 ACCACACTCACACCTTGTAGC 60.203 52.381 0.00 0.00 0.00 3.58
721 746 3.055819 CCACACTCACACCTTGTAGCTAT 60.056 47.826 0.00 0.00 0.00 2.97
723 748 3.195825 ACACTCACACCTTGTAGCTATCC 59.804 47.826 0.00 0.00 0.00 2.59
725 750 3.838317 ACTCACACCTTGTAGCTATCCAA 59.162 43.478 0.00 0.00 0.00 3.53
726 751 4.081420 ACTCACACCTTGTAGCTATCCAAG 60.081 45.833 14.33 14.33 38.21 3.61
727 752 4.093743 TCACACCTTGTAGCTATCCAAGA 58.906 43.478 20.27 3.32 40.36 3.02
750 779 3.459710 AACCCCCGGTCAATTAATCAA 57.540 42.857 0.00 0.00 33.12 2.57
763 792 8.921670 GGTCAATTAATCAACACAAATTACCAC 58.078 33.333 0.00 0.00 0.00 4.16
779 809 9.203421 CAAATTACCACTTAAAATTCCAAGTCC 57.797 33.333 2.48 0.00 32.72 3.85
806 836 2.360483 CACTCACACTCACTCACTGTCT 59.640 50.000 0.00 0.00 0.00 3.41
828 858 2.604614 GCAGTTTGGCCAGTAAAAGTCG 60.605 50.000 5.11 0.00 0.00 4.18
832 862 0.887387 TGGCCAGTAAAAGTCGTGCC 60.887 55.000 0.00 0.00 37.90 5.01
833 863 0.887387 GGCCAGTAAAAGTCGTGCCA 60.887 55.000 0.00 0.00 37.36 4.92
854 884 5.772825 CAAGACTTGGAATTTGGACAGAA 57.227 39.130 7.35 0.00 0.00 3.02
855 885 6.147864 CAAGACTTGGAATTTGGACAGAAA 57.852 37.500 7.35 0.00 0.00 2.52
857 887 4.279420 AGACTTGGAATTTGGACAGAAAGC 59.721 41.667 0.00 0.00 0.00 3.51
906 936 2.710377 CCGGCCTATATATGCTGCAAA 58.290 47.619 6.36 0.00 32.40 3.68
908 938 2.420022 CGGCCTATATATGCTGCAAACC 59.580 50.000 6.36 0.00 0.00 3.27
938 968 4.338879 CTCTTTCCCAACACATTCATCCT 58.661 43.478 0.00 0.00 0.00 3.24
939 969 4.335416 TCTTTCCCAACACATTCATCCTC 58.665 43.478 0.00 0.00 0.00 3.71
940 970 4.043310 TCTTTCCCAACACATTCATCCTCT 59.957 41.667 0.00 0.00 0.00 3.69
941 971 3.354948 TCCCAACACATTCATCCTCTG 57.645 47.619 0.00 0.00 0.00 3.35
942 972 1.747355 CCCAACACATTCATCCTCTGC 59.253 52.381 0.00 0.00 0.00 4.26
943 973 2.619849 CCCAACACATTCATCCTCTGCT 60.620 50.000 0.00 0.00 0.00 4.24
944 974 3.370846 CCCAACACATTCATCCTCTGCTA 60.371 47.826 0.00 0.00 0.00 3.49
945 975 3.875727 CCAACACATTCATCCTCTGCTAG 59.124 47.826 0.00 0.00 0.00 3.42
946 976 3.191078 ACACATTCATCCTCTGCTAGC 57.809 47.619 8.10 8.10 0.00 3.42
947 977 2.770802 ACACATTCATCCTCTGCTAGCT 59.229 45.455 17.23 0.00 0.00 3.32
948 978 3.199508 ACACATTCATCCTCTGCTAGCTT 59.800 43.478 17.23 0.00 0.00 3.74
953 992 2.158986 TCATCCTCTGCTAGCTTTGCTC 60.159 50.000 17.23 0.00 40.44 4.26
968 1007 1.059098 TGCTCACCACACTGGAATCT 58.941 50.000 0.00 0.00 40.96 2.40
999 1038 1.067635 GCTAGCTAGCTGATCTGAGCC 60.068 57.143 33.71 7.85 45.62 4.70
1101 1142 2.237392 GGAGTTCTACCTCAAGCACCAT 59.763 50.000 0.00 0.00 32.91 3.55
1133 1183 0.752743 AACAAGCAGCAGCACCTCAA 60.753 50.000 3.17 0.00 45.49 3.02
1628 1681 2.122729 CTCCCACTCCCACTCCCA 59.877 66.667 0.00 0.00 0.00 4.37
1644 1697 4.694233 CACTCCCACTGCAGCGCT 62.694 66.667 15.27 2.64 0.00 5.92
1790 1874 4.388499 GGAGACCGCGAAGGCCAA 62.388 66.667 8.23 0.00 46.52 4.52
1898 1991 1.067565 CAGCGTCCTCAACTTCTAGCA 60.068 52.381 0.00 0.00 0.00 3.49
1949 2074 2.553904 CCAGTAATCCATGGAGCCATCC 60.554 54.545 21.33 4.69 46.87 3.51
1984 2109 3.370840 AAAATACATCAGCCAGCAGGA 57.629 42.857 0.00 0.00 36.89 3.86
1987 2112 0.538584 TACATCAGCCAGCAGGAGTG 59.461 55.000 0.00 0.00 36.89 3.51
2024 2149 3.741476 GGCAACAGGCGCTCTTGG 61.741 66.667 7.64 0.00 46.16 3.61
2043 2168 3.248024 TGGAATGGAGTCTACTGGTTGT 58.752 45.455 0.00 0.00 0.00 3.32
2046 2177 4.262894 GGAATGGAGTCTACTGGTTGTCAA 60.263 45.833 0.00 0.00 0.00 3.18
2051 2182 5.013079 TGGAGTCTACTGGTTGTCAAATGAT 59.987 40.000 0.00 0.00 0.00 2.45
2061 2199 8.896744 ACTGGTTGTCAAATGATACTCAATATG 58.103 33.333 0.00 0.00 0.00 1.78
2075 2214 9.457110 GATACTCAATATGTGACACAACTAGAG 57.543 37.037 13.23 18.06 31.13 2.43
2080 2219 9.554395 TCAATATGTGACACAACTAGAGAAAAA 57.446 29.630 13.23 0.00 0.00 1.94
2134 2273 5.884792 AGATAGAGGAGCCAAATTTTCACTG 59.115 40.000 0.00 0.00 0.00 3.66
2182 2328 8.286191 GGAGTTTGTCCAGAATTCATAGATTT 57.714 34.615 8.44 0.00 46.10 2.17
2193 2339 8.523658 CAGAATTCATAGATTTGATGGATGCAT 58.476 33.333 8.44 0.00 0.00 3.96
2276 2473 3.524541 GGCATTCACACCAAATTCCATC 58.475 45.455 0.00 0.00 0.00 3.51
2280 2477 3.524095 TCACACCAAATTCCATCACCT 57.476 42.857 0.00 0.00 0.00 4.00
2350 2561 1.257743 TGTGAGTCGGAGAAAGAGGG 58.742 55.000 0.00 0.00 39.69 4.30
2361 2572 3.882288 GGAGAAAGAGGGAATTGATGAGC 59.118 47.826 0.00 0.00 0.00 4.26
2378 2589 8.662781 TTGATGAGCTAGAAATACATGTAACC 57.337 34.615 10.14 2.24 0.00 2.85
2528 2742 0.981183 TACAACGAGGGATGGCTGTT 59.019 50.000 0.00 0.00 0.00 3.16
2534 2748 1.808133 CGAGGGATGGCTGTTTCTAGC 60.808 57.143 0.00 0.00 42.94 3.42
2542 2756 2.239654 TGGCTGTTTCTAGCTGCCTAAT 59.760 45.455 14.68 0.00 46.69 1.73
2568 5622 5.856126 TTGGCTTGAACTTATACTTGTCG 57.144 39.130 0.00 0.00 0.00 4.35
2637 5691 9.730705 AATGTTACTAAAACTAGGGGTTAAGAC 57.269 33.333 0.00 0.00 37.12 3.01
2640 5694 8.588472 GTTACTAAAACTAGGGGTTAAGACTCA 58.412 37.037 0.00 0.00 37.12 3.41
2646 5700 4.593634 ACTAGGGGTTAAGACTCATATGCC 59.406 45.833 0.00 0.00 0.00 4.40
2651 5705 5.456763 GGGGTTAAGACTCATATGCCTGATT 60.457 44.000 0.00 0.00 0.00 2.57
2671 5725 1.003464 TGGGCTAAAGTTTACGGGGAC 59.997 52.381 0.00 0.00 0.00 4.46
2676 5730 3.126343 GCTAAAGTTTACGGGGACACATG 59.874 47.826 0.00 0.00 0.00 3.21
2691 5745 1.149101 ACATGGTCCCTCAACCTGTT 58.851 50.000 0.00 0.00 40.20 3.16
2709 5763 5.654650 ACCTGTTGATTTACCACACAAAAGA 59.345 36.000 0.00 0.00 31.55 2.52
2736 5790 5.324784 TCTCACTTACTGCGATGTACAAT 57.675 39.130 0.00 0.00 0.00 2.71
2745 5799 2.028567 TGCGATGTACAATGAGTGACCA 60.029 45.455 0.00 0.00 0.00 4.02
2747 5801 2.930040 CGATGTACAATGAGTGACCACC 59.070 50.000 0.00 0.00 0.00 4.61
2750 5804 1.628846 GTACAATGAGTGACCACCCCT 59.371 52.381 0.00 0.00 0.00 4.79
2753 5807 0.401738 AATGAGTGACCACCCCTGTG 59.598 55.000 0.00 0.00 42.39 3.66
2853 5909 9.114952 TCTTGTTTTGTTTTCAGTTTTCCTTTT 57.885 25.926 0.00 0.00 0.00 2.27
2866 5922 8.151596 TCAGTTTTCCTTTTTGTGTTTTTACCT 58.848 29.630 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.922931 AAAGAATGGGCTCAATTTGTATTTTT 57.077 26.923 0.00 0.00 0.00 1.94
1 2 9.657419 CTAAAGAATGGGCTCAATTTGTATTTT 57.343 29.630 0.00 0.00 0.00 1.82
2 3 9.034800 TCTAAAGAATGGGCTCAATTTGTATTT 57.965 29.630 0.00 0.00 0.00 1.40
3 4 8.593945 TCTAAAGAATGGGCTCAATTTGTATT 57.406 30.769 0.00 0.00 0.00 1.89
4 5 8.773033 ATCTAAAGAATGGGCTCAATTTGTAT 57.227 30.769 0.00 0.00 0.00 2.29
5 6 8.055181 AGATCTAAAGAATGGGCTCAATTTGTA 58.945 33.333 0.00 0.00 0.00 2.41
6 7 6.894103 AGATCTAAAGAATGGGCTCAATTTGT 59.106 34.615 0.00 0.00 0.00 2.83
7 8 7.344095 AGATCTAAAGAATGGGCTCAATTTG 57.656 36.000 0.00 0.00 0.00 2.32
8 9 7.968014 AAGATCTAAAGAATGGGCTCAATTT 57.032 32.000 0.00 0.00 0.00 1.82
9 10 7.968014 AAAGATCTAAAGAATGGGCTCAATT 57.032 32.000 0.00 0.00 0.00 2.32
10 11 9.652114 AATAAAGATCTAAAGAATGGGCTCAAT 57.348 29.630 0.00 0.00 0.00 2.57
34 35 9.646522 ACAAATCAAACAAGGCCTATAGATAAT 57.353 29.630 5.16 0.00 0.00 1.28
36 37 9.778741 CTACAAATCAAACAAGGCCTATAGATA 57.221 33.333 5.16 0.00 0.00 1.98
37 38 7.721399 CCTACAAATCAAACAAGGCCTATAGAT 59.279 37.037 5.16 2.77 0.00 1.98
38 39 7.054124 CCTACAAATCAAACAAGGCCTATAGA 58.946 38.462 5.16 0.00 0.00 1.98
39 40 7.054124 TCCTACAAATCAAACAAGGCCTATAG 58.946 38.462 5.16 1.10 0.00 1.31
40 41 6.964464 TCCTACAAATCAAACAAGGCCTATA 58.036 36.000 5.16 0.00 0.00 1.31
45 47 8.825667 TTTTTATCCTACAAATCAAACAAGGC 57.174 30.769 0.00 0.00 0.00 4.35
80 85 8.000709 TCCATGCAAAGTAGATCATAGGAAAAT 58.999 33.333 0.00 0.00 0.00 1.82
81 86 7.345691 TCCATGCAAAGTAGATCATAGGAAAA 58.654 34.615 0.00 0.00 0.00 2.29
82 87 6.899089 TCCATGCAAAGTAGATCATAGGAAA 58.101 36.000 0.00 0.00 0.00 3.13
116 121 2.758979 AGCAAAGATTGGGCTCAATGAG 59.241 45.455 18.65 5.78 43.08 2.90
117 122 2.811410 AGCAAAGATTGGGCTCAATGA 58.189 42.857 18.65 0.00 43.08 2.57
139 144 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
140 145 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
141 146 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
142 147 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
143 148 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
144 149 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
145 150 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
146 151 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
147 152 8.149973 TCAAAAACGCTCTTATATTATGGGAC 57.850 34.615 0.00 0.00 0.00 4.46
148 153 8.783093 CATCAAAAACGCTCTTATATTATGGGA 58.217 33.333 0.00 0.00 0.00 4.37
149 154 8.567948 ACATCAAAAACGCTCTTATATTATGGG 58.432 33.333 0.00 0.00 0.00 4.00
150 155 9.385902 CACATCAAAAACGCTCTTATATTATGG 57.614 33.333 0.00 0.00 0.00 2.74
151 156 8.895845 GCACATCAAAAACGCTCTTATATTATG 58.104 33.333 0.00 0.00 0.00 1.90
152 157 8.076178 GGCACATCAAAAACGCTCTTATATTAT 58.924 33.333 0.00 0.00 0.00 1.28
153 158 7.066404 TGGCACATCAAAAACGCTCTTATATTA 59.934 33.333 0.00 0.00 0.00 0.98
154 159 6.127758 TGGCACATCAAAAACGCTCTTATATT 60.128 34.615 0.00 0.00 0.00 1.28
155 160 5.356751 TGGCACATCAAAAACGCTCTTATAT 59.643 36.000 0.00 0.00 0.00 0.86
156 161 4.697828 TGGCACATCAAAAACGCTCTTATA 59.302 37.500 0.00 0.00 0.00 0.98
157 162 3.505680 TGGCACATCAAAAACGCTCTTAT 59.494 39.130 0.00 0.00 0.00 1.73
158 163 2.881513 TGGCACATCAAAAACGCTCTTA 59.118 40.909 0.00 0.00 0.00 2.10
159 164 1.680735 TGGCACATCAAAAACGCTCTT 59.319 42.857 0.00 0.00 0.00 2.85
160 165 1.317613 TGGCACATCAAAAACGCTCT 58.682 45.000 0.00 0.00 0.00 4.09
161 166 2.132740 TTGGCACATCAAAAACGCTC 57.867 45.000 0.00 0.00 39.30 5.03
162 167 2.593346 TTTGGCACATCAAAAACGCT 57.407 40.000 0.00 0.00 39.30 5.07
163 168 3.665173 TTTTTGGCACATCAAAAACGC 57.335 38.095 10.29 0.00 45.75 4.84
167 172 2.863137 GAGCGTTTTTGGCACATCAAAA 59.137 40.909 0.00 0.00 42.63 2.44
168 173 2.100584 AGAGCGTTTTTGGCACATCAAA 59.899 40.909 0.00 0.00 39.30 2.69
169 174 1.680735 AGAGCGTTTTTGGCACATCAA 59.319 42.857 0.00 0.00 39.30 2.57
170 175 1.317613 AGAGCGTTTTTGGCACATCA 58.682 45.000 0.00 0.00 39.30 3.07
171 176 2.422276 AAGAGCGTTTTTGGCACATC 57.578 45.000 0.00 0.00 39.30 3.06
172 177 5.835113 ATATAAGAGCGTTTTTGGCACAT 57.165 34.783 0.00 0.00 39.30 3.21
173 178 5.637006 AATATAAGAGCGTTTTTGGCACA 57.363 34.783 0.00 0.00 0.00 4.57
174 179 6.636850 CCATAATATAAGAGCGTTTTTGGCAC 59.363 38.462 0.00 0.00 0.00 5.01
175 180 6.238897 CCCATAATATAAGAGCGTTTTTGGCA 60.239 38.462 0.00 0.00 0.00 4.92
176 181 6.016610 TCCCATAATATAAGAGCGTTTTTGGC 60.017 38.462 0.00 0.00 0.00 4.52
177 182 7.360361 GTCCCATAATATAAGAGCGTTTTTGG 58.640 38.462 0.00 0.00 0.00 3.28
178 183 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
179 184 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
180 185 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
181 186 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
182 187 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
183 188 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
184 189 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
185 190 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
186 191 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
187 192 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
188 193 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
189 194 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
190 195 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
191 196 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
192 197 4.202749 ACATACTCCCTCCGTCCCATAATA 60.203 45.833 0.00 0.00 0.00 0.98
193 198 3.173965 CATACTCCCTCCGTCCCATAAT 58.826 50.000 0.00 0.00 0.00 1.28
194 199 2.090943 ACATACTCCCTCCGTCCCATAA 60.091 50.000 0.00 0.00 0.00 1.90
195 200 1.502039 ACATACTCCCTCCGTCCCATA 59.498 52.381 0.00 0.00 0.00 2.74
196 201 0.264955 ACATACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
197 202 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
198 203 1.138464 GAAACATACTCCCTCCGTCCC 59.862 57.143 0.00 0.00 0.00 4.46
199 204 2.108970 AGAAACATACTCCCTCCGTCC 58.891 52.381 0.00 0.00 0.00 4.79
200 205 4.583489 TCATAGAAACATACTCCCTCCGTC 59.417 45.833 0.00 0.00 0.00 4.79
201 206 4.341520 GTCATAGAAACATACTCCCTCCGT 59.658 45.833 0.00 0.00 0.00 4.69
202 207 4.341235 TGTCATAGAAACATACTCCCTCCG 59.659 45.833 0.00 0.00 0.00 4.63
203 208 5.871396 TGTCATAGAAACATACTCCCTCC 57.129 43.478 0.00 0.00 0.00 4.30
204 209 6.879400 AGTTGTCATAGAAACATACTCCCTC 58.121 40.000 0.00 0.00 0.00 4.30
205 210 6.875972 AGTTGTCATAGAAACATACTCCCT 57.124 37.500 0.00 0.00 0.00 4.20
206 211 6.183360 GCAAGTTGTCATAGAAACATACTCCC 60.183 42.308 4.48 0.00 0.00 4.30
207 212 6.183360 GGCAAGTTGTCATAGAAACATACTCC 60.183 42.308 1.68 0.00 0.00 3.85
208 213 6.371548 TGGCAAGTTGTCATAGAAACATACTC 59.628 38.462 5.94 0.00 0.00 2.59
209 214 6.237901 TGGCAAGTTGTCATAGAAACATACT 58.762 36.000 5.94 0.00 0.00 2.12
210 215 6.494893 TGGCAAGTTGTCATAGAAACATAC 57.505 37.500 5.94 0.00 0.00 2.39
211 216 5.123820 GCTGGCAAGTTGTCATAGAAACATA 59.876 40.000 11.23 0.00 28.30 2.29
212 217 4.082571 GCTGGCAAGTTGTCATAGAAACAT 60.083 41.667 11.23 0.00 28.30 2.71
213 218 3.253188 GCTGGCAAGTTGTCATAGAAACA 59.747 43.478 11.23 0.00 28.30 2.83
214 219 3.366374 GGCTGGCAAGTTGTCATAGAAAC 60.366 47.826 11.23 0.00 28.30 2.78
239 244 0.879839 CAGCAAAACCGCCCAAAAGG 60.880 55.000 0.00 0.00 39.47 3.11
240 245 1.498043 GCAGCAAAACCGCCCAAAAG 61.498 55.000 0.00 0.00 0.00 2.27
241 246 1.522580 GCAGCAAAACCGCCCAAAA 60.523 52.632 0.00 0.00 0.00 2.44
242 247 2.107953 GCAGCAAAACCGCCCAAA 59.892 55.556 0.00 0.00 0.00 3.28
243 248 4.277593 CGCAGCAAAACCGCCCAA 62.278 61.111 0.00 0.00 0.00 4.12
248 253 2.262303 TTACCCCGCAGCAAAACCG 61.262 57.895 0.00 0.00 0.00 4.44
250 255 1.287815 GGTTACCCCGCAGCAAAAC 59.712 57.895 0.00 0.00 0.00 2.43
251 256 0.755698 TTGGTTACCCCGCAGCAAAA 60.756 50.000 0.00 0.00 35.15 2.44
252 257 1.152735 TTGGTTACCCCGCAGCAAA 60.153 52.632 0.00 0.00 35.15 3.68
254 259 2.281900 GTTGGTTACCCCGCAGCA 60.282 61.111 0.00 0.00 35.15 4.41
255 260 1.583495 GAAGTTGGTTACCCCGCAGC 61.583 60.000 0.00 0.00 35.15 5.25
256 261 0.036306 AGAAGTTGGTTACCCCGCAG 59.964 55.000 0.00 0.00 35.15 5.18
258 263 2.704464 ATAGAAGTTGGTTACCCCGC 57.296 50.000 0.00 0.00 35.15 6.13
259 264 5.088680 TGTAATAGAAGTTGGTTACCCCG 57.911 43.478 0.00 0.00 35.15 5.73
260 265 9.281371 GAATATGTAATAGAAGTTGGTTACCCC 57.719 37.037 0.00 0.00 28.50 4.95
297 302 9.515226 ACATTTTAGCTTCATAACTTTACCTGA 57.485 29.630 0.00 0.00 0.00 3.86
428 434 4.495565 TCCCCTTCACTAGTCCAAGTTAA 58.504 43.478 0.00 0.00 0.00 2.01
443 449 6.834168 TTTACATGATGAAGTTTCCCCTTC 57.166 37.500 0.00 0.00 41.01 3.46
471 480 7.612633 TGTAGTGGTTCCTTATTAAAATCCACC 59.387 37.037 0.00 0.00 43.20 4.61
483 492 5.100344 TGTTTGTGTGTAGTGGTTCCTTA 57.900 39.130 0.00 0.00 0.00 2.69
485 494 3.637911 TGTTTGTGTGTAGTGGTTCCT 57.362 42.857 0.00 0.00 0.00 3.36
555 566 4.449131 TCTCATCTCAAGTTGATGATGGC 58.551 43.478 27.10 0.00 46.01 4.40
556 567 6.203145 GTGATCTCATCTCAAGTTGATGATGG 59.797 42.308 27.10 21.60 46.01 3.51
586 598 6.770746 TGTGGATGTACCTTCTAGTACTTC 57.229 41.667 0.00 8.45 42.58 3.01
588 600 6.014647 TGTTGTGGATGTACCTTCTAGTACT 58.985 40.000 0.00 0.00 42.58 2.73
638 653 5.299782 TGGTGATTTGTTTAGTGGTGGTAAC 59.700 40.000 0.00 0.00 0.00 2.50
639 654 5.446860 TGGTGATTTGTTTAGTGGTGGTAA 58.553 37.500 0.00 0.00 0.00 2.85
640 655 5.050126 TGGTGATTTGTTTAGTGGTGGTA 57.950 39.130 0.00 0.00 0.00 3.25
641 656 3.904717 TGGTGATTTGTTTAGTGGTGGT 58.095 40.909 0.00 0.00 0.00 4.16
642 657 5.467035 AATGGTGATTTGTTTAGTGGTGG 57.533 39.130 0.00 0.00 0.00 4.61
657 674 1.549037 GCCAACTTGGGGTAATGGTGA 60.549 52.381 9.95 0.00 38.19 4.02
669 686 9.289303 GTATGTGATTAAATAACTGCCAACTTG 57.711 33.333 0.00 0.00 0.00 3.16
672 689 9.632807 TTTGTATGTGATTAAATAACTGCCAAC 57.367 29.630 0.00 0.00 0.00 3.77
683 700 7.283354 TGTGAGTGTGGTTTGTATGTGATTAAA 59.717 33.333 0.00 0.00 0.00 1.52
684 701 6.768381 TGTGAGTGTGGTTTGTATGTGATTAA 59.232 34.615 0.00 0.00 0.00 1.40
695 712 2.091541 ACAAGGTGTGAGTGTGGTTTG 58.908 47.619 0.00 0.00 0.00 2.93
697 714 2.745152 GCTACAAGGTGTGAGTGTGGTT 60.745 50.000 0.00 0.00 0.00 3.67
699 716 1.070758 AGCTACAAGGTGTGAGTGTGG 59.929 52.381 0.00 0.00 0.00 4.17
718 743 2.709397 ACCGGGGGTTAATCTTGGATAG 59.291 50.000 6.32 0.00 27.29 2.08
721 746 0.913924 GACCGGGGGTTAATCTTGGA 59.086 55.000 6.32 0.00 35.25 3.53
723 748 2.500392 TTGACCGGGGGTTAATCTTG 57.500 50.000 6.32 0.00 35.25 3.02
725 750 4.866327 TTAATTGACCGGGGGTTAATCT 57.134 40.909 6.32 0.71 40.29 2.40
726 751 5.134661 TGATTAATTGACCGGGGGTTAATC 58.865 41.667 23.02 23.02 40.29 1.75
727 752 5.132043 TGATTAATTGACCGGGGGTTAAT 57.868 39.130 6.32 10.82 42.45 1.40
750 779 9.541143 CTTGGAATTTTAAGTGGTAATTTGTGT 57.459 29.630 0.00 0.00 0.00 3.72
763 792 5.977129 GTGTGTGTGGACTTGGAATTTTAAG 59.023 40.000 2.22 2.22 0.00 1.85
779 809 2.196749 GAGTGAGTGTGAGTGTGTGTG 58.803 52.381 0.00 0.00 0.00 3.82
806 836 2.360801 GACTTTTACTGGCCAAACTGCA 59.639 45.455 7.01 0.00 0.00 4.41
832 862 5.772825 TTCTGTCCAAATTCCAAGTCTTG 57.227 39.130 5.53 5.53 0.00 3.02
833 863 5.221322 GCTTTCTGTCCAAATTCCAAGTCTT 60.221 40.000 0.00 0.00 0.00 3.01
851 881 0.323451 GGGAAATGGGGTCGCTTTCT 60.323 55.000 0.00 0.00 0.00 2.52
854 884 1.208165 AGAGGGAAATGGGGTCGCTT 61.208 55.000 0.00 0.00 38.31 4.68
855 885 1.208165 AAGAGGGAAATGGGGTCGCT 61.208 55.000 0.00 0.00 40.66 4.93
857 887 0.618458 TCAAGAGGGAAATGGGGTCG 59.382 55.000 0.00 0.00 0.00 4.79
906 936 0.178891 TGGGAAAGAGCAGAGGAGGT 60.179 55.000 0.00 0.00 0.00 3.85
908 938 1.349026 TGTTGGGAAAGAGCAGAGGAG 59.651 52.381 0.00 0.00 0.00 3.69
938 968 0.686789 TGGTGAGCAAAGCTAGCAGA 59.313 50.000 18.83 0.00 39.88 4.26
939 969 0.801251 GTGGTGAGCAAAGCTAGCAG 59.199 55.000 18.83 7.50 39.88 4.24
940 970 0.108396 TGTGGTGAGCAAAGCTAGCA 59.892 50.000 18.83 0.00 39.88 3.49
941 971 0.519077 GTGTGGTGAGCAAAGCTAGC 59.481 55.000 6.62 6.62 39.88 3.42
942 972 1.802960 CAGTGTGGTGAGCAAAGCTAG 59.197 52.381 0.00 0.00 39.88 3.42
943 973 1.543208 CCAGTGTGGTGAGCAAAGCTA 60.543 52.381 0.00 0.00 33.50 3.32
944 974 0.820891 CCAGTGTGGTGAGCAAAGCT 60.821 55.000 0.00 0.00 35.29 3.74
945 975 0.819259 TCCAGTGTGGTGAGCAAAGC 60.819 55.000 0.00 0.00 39.03 3.51
946 976 1.679139 TTCCAGTGTGGTGAGCAAAG 58.321 50.000 0.00 0.00 39.03 2.77
947 977 2.158623 AGATTCCAGTGTGGTGAGCAAA 60.159 45.455 0.00 0.00 39.03 3.68
948 978 1.421268 AGATTCCAGTGTGGTGAGCAA 59.579 47.619 0.00 0.00 39.03 3.91
953 992 5.360999 TGAGTAGATAGATTCCAGTGTGGTG 59.639 44.000 0.00 0.00 39.03 4.17
999 1038 4.598894 CCTCCTCGCCGCTCCATG 62.599 72.222 0.00 0.00 0.00 3.66
1101 1142 0.736053 GCTTGTTGTTTCGGGTGACA 59.264 50.000 0.00 0.00 0.00 3.58
1383 1436 3.022981 GACGAGCGTCTTCTTGAGG 57.977 57.895 15.13 0.00 41.57 3.86
1437 1490 0.608640 ACTCGTTCATGACCCAGTCC 59.391 55.000 0.00 0.00 0.00 3.85
1608 1661 3.403558 GAGTGGGAGTGGGAGGCC 61.404 72.222 0.00 0.00 0.00 5.19
1609 1662 3.403558 GGAGTGGGAGTGGGAGGC 61.404 72.222 0.00 0.00 0.00 4.70
1611 1664 2.122729 TGGGAGTGGGAGTGGGAG 59.877 66.667 0.00 0.00 0.00 4.30
1612 1665 2.203938 GTGGGAGTGGGAGTGGGA 60.204 66.667 0.00 0.00 0.00 4.37
1614 1667 2.294078 GGAGTGGGAGTGGGAGTGG 61.294 68.421 0.00 0.00 0.00 4.00
1615 1668 2.294078 GGGAGTGGGAGTGGGAGTG 61.294 68.421 0.00 0.00 0.00 3.51
1616 1669 2.122954 GGGAGTGGGAGTGGGAGT 59.877 66.667 0.00 0.00 0.00 3.85
1620 1673 3.072476 CAGTGGGAGTGGGAGTGG 58.928 66.667 0.00 0.00 0.00 4.00
1622 1675 2.122413 TGCAGTGGGAGTGGGAGT 60.122 61.111 0.00 0.00 0.00 3.85
1628 1681 4.694233 CAGCGCTGCAGTGGGAGT 62.694 66.667 26.68 0.00 34.49 3.85
1693 1759 1.375908 CGTGGTGGACATGGTGGAG 60.376 63.158 0.00 0.00 32.27 3.86
1842 1932 2.459086 GCAGAGGCCCTCCATCCAT 61.459 63.158 7.26 0.00 33.74 3.41
1931 2035 1.425066 TGGGATGGCTCCATGGATTAC 59.575 52.381 16.63 9.15 44.08 1.89
1984 2109 1.509644 TTCGACGACCGCTACACACT 61.510 55.000 0.00 0.00 38.37 3.55
1987 2112 0.098376 AGATTCGACGACCGCTACAC 59.902 55.000 0.00 0.00 38.37 2.90
2015 2140 0.107945 AGACTCCATTCCAAGAGCGC 60.108 55.000 0.00 0.00 33.18 5.92
2024 2149 4.537135 TGACAACCAGTAGACTCCATTC 57.463 45.455 0.00 0.00 0.00 2.67
2051 2182 8.575649 TCTCTAGTTGTGTCACATATTGAGTA 57.424 34.615 19.31 8.29 33.71 2.59
2061 2199 7.012421 ACCATTCTTTTTCTCTAGTTGTGTCAC 59.988 37.037 0.00 0.00 0.00 3.67
2101 2240 8.958060 ATTTGGCTCCTCTATCTGTACTATAA 57.042 34.615 0.00 0.00 0.00 0.98
2182 2328 1.886886 CACCGATCATGCATCCATCA 58.113 50.000 13.31 0.00 0.00 3.07
2193 2339 0.179032 AACACACCTTGCACCGATCA 60.179 50.000 0.00 0.00 0.00 2.92
2244 2395 5.704354 TGGTGTGAATGCCCAATCTATTAT 58.296 37.500 0.00 0.00 0.00 1.28
2305 2503 0.957395 AGTGAGTTTCATGCGCCCAG 60.957 55.000 4.18 0.00 0.00 4.45
2378 2589 7.061326 CGACCCTTTGTATTCAAAATTAAACGG 59.939 37.037 0.00 0.00 42.02 4.44
2476 2690 5.045012 AGGCAGCTCAAGATCATCATTTA 57.955 39.130 0.00 0.00 0.00 1.40
2542 2756 8.447833 CGACAAGTATAAGTTCAAGCCAATTAA 58.552 33.333 0.00 0.00 0.00 1.40
2566 5620 2.884980 TTGCCAATCGTGACCCCGA 61.885 57.895 0.00 0.00 41.73 5.14
2568 5622 1.175983 TTGTTGCCAATCGTGACCCC 61.176 55.000 0.00 0.00 0.00 4.95
2614 5668 8.588472 TGAGTCTTAACCCCTAGTTTTAGTAAC 58.412 37.037 0.00 0.00 40.05 2.50
2623 5677 4.593634 GGCATATGAGTCTTAACCCCTAGT 59.406 45.833 6.97 0.00 0.00 2.57
2646 5700 3.377172 CCCGTAAACTTTAGCCCAATCAG 59.623 47.826 0.00 0.00 0.00 2.90
2651 5705 1.003464 GTCCCCGTAAACTTTAGCCCA 59.997 52.381 0.00 0.00 0.00 5.36
2671 5725 0.401738 ACAGGTTGAGGGACCATGTG 59.598 55.000 0.00 0.00 42.35 3.21
2698 5752 9.823647 AGTAAGTGAGATATATCTTTTGTGTGG 57.176 33.333 16.37 0.00 37.25 4.17
2703 5757 8.803201 TCGCAGTAAGTGAGATATATCTTTTG 57.197 34.615 16.37 5.18 37.25 2.44
2709 5763 8.336801 TGTACATCGCAGTAAGTGAGATATAT 57.663 34.615 0.00 0.00 43.25 0.86
2736 5790 3.562250 CACAGGGGTGGTCACTCA 58.438 61.111 3.23 0.00 41.45 3.41


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

AutoCloner maintained by Alex Coulton.