Multiple sequence alignment - TraesCS2A01G105000

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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 TraesCS2A01G105000 chr2A 100.000 3517 0 0 1 3517 57916859 57913343 0.000000e+00 6495.0
1 TraesCS2A01G105000 chr2A 98.741 3177 39 1 342 3517 678124286 678121110 0.000000e+00 5644.0
2 TraesCS2A01G105000 chr2A 96.128 3177 100 11 341 3517 672845010 672848163 0.000000e+00 5164.0
3 TraesCS2A01G105000 chr2A 86.111 72 9 1 174 244 612399966 612400037 3.760000e-10 76.8
4 TraesCS2A01G105000 chr7A 98.993 3177 31 1 342 3517 299568844 299572020 0.000000e+00 5688.0
5 TraesCS2A01G105000 chr1D 98.048 3177 59 3 342 3517 283557064 283560238 0.000000e+00 5520.0
6 TraesCS2A01G105000 chr3B 97.867 3188 61 5 332 3517 245008821 245012003 0.000000e+00 5504.0
7 TraesCS2A01G105000 chr3B 96.403 3169 78 19 351 3517 259400045 259396911 0.000000e+00 5188.0
8 TraesCS2A01G105000 chr4D 97.199 3177 67 4 342 3517 281202809 281199654 0.000000e+00 5354.0
9 TraesCS2A01G105000 chr1B 96.570 3178 77 13 341 3517 682092122 682088976 0.000000e+00 5236.0
10 TraesCS2A01G105000 chr1B 98.529 2788 41 0 339 3126 611146106 611148893 0.000000e+00 4922.0
11 TraesCS2A01G105000 chr4B 95.355 3186 130 11 332 3517 637596047 637599214 0.000000e+00 5048.0
12 TraesCS2A01G105000 chr5A 90.385 104 10 0 176 279 234437513 234437410 1.700000e-28 137.0
13 TraesCS2A01G105000 chr3A 88.462 104 12 0 176 279 608104438 608104335 3.690000e-25 126.0


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 TraesCS2A01G105000 chr2A 57913343 57916859 3516 True 6495 6495 100.000 1 3517 1 chr2A.!!$R1 3516
1 TraesCS2A01G105000 chr2A 678121110 678124286 3176 True 5644 5644 98.741 342 3517 1 chr2A.!!$R2 3175
2 TraesCS2A01G105000 chr2A 672845010 672848163 3153 False 5164 5164 96.128 341 3517 1 chr2A.!!$F2 3176
3 TraesCS2A01G105000 chr7A 299568844 299572020 3176 False 5688 5688 98.993 342 3517 1 chr7A.!!$F1 3175
4 TraesCS2A01G105000 chr1D 283557064 283560238 3174 False 5520 5520 98.048 342 3517 1 chr1D.!!$F1 3175
5 TraesCS2A01G105000 chr3B 245008821 245012003 3182 False 5504 5504 97.867 332 3517 1 chr3B.!!$F1 3185
6 TraesCS2A01G105000 chr3B 259396911 259400045 3134 True 5188 5188 96.403 351 3517 1 chr3B.!!$R1 3166
7 TraesCS2A01G105000 chr4D 281199654 281202809 3155 True 5354 5354 97.199 342 3517 1 chr4D.!!$R1 3175
8 TraesCS2A01G105000 chr1B 682088976 682092122 3146 True 5236 5236 96.570 341 3517 1 chr1B.!!$R1 3176
9 TraesCS2A01G105000 chr1B 611146106 611148893 2787 False 4922 4922 98.529 339 3126 1 chr1B.!!$F1 2787
10 TraesCS2A01G105000 chr4B 637596047 637599214 3167 False 5048 5048 95.355 332 3517 1 chr4B.!!$F1 3185

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
290 291 0.108756 AGCGAGCTACGAAAAGGGAC 60.109 55.000 9.32 0.0 45.77 4.46 F
291 292 0.389426 GCGAGCTACGAAAAGGGACA 60.389 55.000 9.32 0.0 45.77 4.02 F
1899 1908 1.077993 AGAGGAGGTTACAGAGGCAGT 59.922 52.381 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 1867 2.102420 TGCCTTTGTTGTCTCTCTTCGA 59.898 45.455 0.0 0.0 0.00 3.71 R
2103 2112 2.622064 AGTCACCAAACACTGTCTCC 57.378 50.000 0.0 0.0 0.00 3.71 R
2739 2750 2.975489 CCTGAGCCCCTTACTCACATAT 59.025 50.000 0.0 0.0 39.21 1.78 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
21 22 4.756084 CCAACAATGTCCTCTCTTTGAC 57.244 45.455 0.00 0.00 0.00 3.18
22 23 4.136796 CCAACAATGTCCTCTCTTTGACA 58.863 43.478 0.00 0.00 44.86 3.58
27 28 3.685139 TGTCCTCTCTTTGACATCCAC 57.315 47.619 0.00 0.00 36.62 4.02
28 29 2.972021 TGTCCTCTCTTTGACATCCACA 59.028 45.455 0.00 0.00 36.62 4.17
29 30 3.390967 TGTCCTCTCTTTGACATCCACAA 59.609 43.478 0.00 0.00 36.62 3.33
30 31 3.748568 GTCCTCTCTTTGACATCCACAAC 59.251 47.826 0.00 0.00 0.00 3.32
31 32 3.390967 TCCTCTCTTTGACATCCACAACA 59.609 43.478 0.00 0.00 0.00 3.33
32 33 4.042062 TCCTCTCTTTGACATCCACAACAT 59.958 41.667 0.00 0.00 0.00 2.71
33 34 5.248248 TCCTCTCTTTGACATCCACAACATA 59.752 40.000 0.00 0.00 0.00 2.29
34 35 6.070021 TCCTCTCTTTGACATCCACAACATAT 60.070 38.462 0.00 0.00 0.00 1.78
35 36 7.125659 TCCTCTCTTTGACATCCACAACATATA 59.874 37.037 0.00 0.00 0.00 0.86
36 37 7.440556 CCTCTCTTTGACATCCACAACATATAG 59.559 40.741 0.00 0.00 0.00 1.31
37 38 6.763135 TCTCTTTGACATCCACAACATATAGC 59.237 38.462 0.00 0.00 0.00 2.97
38 39 5.523552 TCTTTGACATCCACAACATATAGCG 59.476 40.000 0.00 0.00 0.00 4.26
39 40 4.664150 TGACATCCACAACATATAGCGA 57.336 40.909 0.00 0.00 0.00 4.93
40 41 4.368315 TGACATCCACAACATATAGCGAC 58.632 43.478 0.00 0.00 0.00 5.19
41 42 3.728845 ACATCCACAACATATAGCGACC 58.271 45.455 0.00 0.00 0.00 4.79
42 43 3.133901 ACATCCACAACATATAGCGACCA 59.866 43.478 0.00 0.00 0.00 4.02
43 44 3.897141 TCCACAACATATAGCGACCAA 57.103 42.857 0.00 0.00 0.00 3.67
44 45 3.527533 TCCACAACATATAGCGACCAAC 58.472 45.455 0.00 0.00 0.00 3.77
45 46 3.196901 TCCACAACATATAGCGACCAACT 59.803 43.478 0.00 0.00 0.00 3.16
46 47 3.938963 CCACAACATATAGCGACCAACTT 59.061 43.478 0.00 0.00 0.00 2.66
47 48 4.394920 CCACAACATATAGCGACCAACTTT 59.605 41.667 0.00 0.00 0.00 2.66
48 49 5.447279 CCACAACATATAGCGACCAACTTTC 60.447 44.000 0.00 0.00 0.00 2.62
49 50 4.634443 ACAACATATAGCGACCAACTTTCC 59.366 41.667 0.00 0.00 0.00 3.13
50 51 4.481368 ACATATAGCGACCAACTTTCCA 57.519 40.909 0.00 0.00 0.00 3.53
51 52 5.036117 ACATATAGCGACCAACTTTCCAT 57.964 39.130 0.00 0.00 0.00 3.41
52 53 5.057149 ACATATAGCGACCAACTTTCCATC 58.943 41.667 0.00 0.00 0.00 3.51
53 54 3.627395 ATAGCGACCAACTTTCCATCA 57.373 42.857 0.00 0.00 0.00 3.07
54 55 2.496899 AGCGACCAACTTTCCATCAT 57.503 45.000 0.00 0.00 0.00 2.45
55 56 2.795329 AGCGACCAACTTTCCATCATT 58.205 42.857 0.00 0.00 0.00 2.57
56 57 2.489329 AGCGACCAACTTTCCATCATTG 59.511 45.455 0.00 0.00 0.00 2.82
57 58 2.415893 GCGACCAACTTTCCATCATTGG 60.416 50.000 0.33 0.33 45.91 3.16
58 59 2.164219 CGACCAACTTTCCATCATTGGG 59.836 50.000 6.79 0.00 44.94 4.12
59 60 3.430453 GACCAACTTTCCATCATTGGGA 58.570 45.455 6.79 0.00 44.94 4.37
60 61 3.165071 ACCAACTTTCCATCATTGGGAC 58.835 45.455 6.79 0.00 44.94 4.46
61 62 3.181418 ACCAACTTTCCATCATTGGGACT 60.181 43.478 6.79 0.00 44.94 3.85
62 63 3.194116 CCAACTTTCCATCATTGGGACTG 59.806 47.826 0.00 0.00 43.81 3.51
63 64 3.091633 ACTTTCCATCATTGGGACTGG 57.908 47.619 0.00 0.00 43.81 4.00
64 65 2.291800 ACTTTCCATCATTGGGACTGGG 60.292 50.000 0.00 0.00 43.81 4.45
65 66 1.679981 TTCCATCATTGGGACTGGGA 58.320 50.000 0.00 0.00 43.81 4.37
66 67 1.216064 TCCATCATTGGGACTGGGAG 58.784 55.000 0.00 0.00 43.81 4.30
67 68 0.466922 CCATCATTGGGACTGGGAGC 60.467 60.000 0.00 0.00 39.56 4.70
68 69 0.256752 CATCATTGGGACTGGGAGCA 59.743 55.000 0.00 0.00 0.00 4.26
69 70 1.133575 CATCATTGGGACTGGGAGCAT 60.134 52.381 0.00 0.00 0.00 3.79
70 71 0.256752 TCATTGGGACTGGGAGCATG 59.743 55.000 0.00 0.00 0.00 4.06
71 72 0.256752 CATTGGGACTGGGAGCATGA 59.743 55.000 0.00 0.00 0.00 3.07
72 73 0.549950 ATTGGGACTGGGAGCATGAG 59.450 55.000 0.00 0.00 0.00 2.90
73 74 2.191641 GGGACTGGGAGCATGAGC 59.808 66.667 0.00 0.00 42.56 4.26
118 119 9.671279 ACATATATTCTTGTTCAATCTGTCACA 57.329 29.630 0.00 0.00 0.00 3.58
122 123 9.850628 ATATTCTTGTTCAATCTGTCACATTTG 57.149 29.630 0.00 0.00 0.00 2.32
123 124 6.940831 TCTTGTTCAATCTGTCACATTTGA 57.059 33.333 0.30 0.30 0.00 2.69
124 125 7.514784 TCTTGTTCAATCTGTCACATTTGAT 57.485 32.000 4.60 0.00 33.11 2.57
125 126 8.620116 TCTTGTTCAATCTGTCACATTTGATA 57.380 30.769 4.60 0.00 33.11 2.15
126 127 9.065798 TCTTGTTCAATCTGTCACATTTGATAA 57.934 29.630 4.60 3.75 33.11 1.75
127 128 9.850628 CTTGTTCAATCTGTCACATTTGATAAT 57.149 29.630 4.60 0.00 33.11 1.28
133 134 9.608617 CAATCTGTCACATTTGATAATATCAGC 57.391 33.333 2.98 0.00 40.94 4.26
134 135 8.913487 ATCTGTCACATTTGATAATATCAGCA 57.087 30.769 2.98 0.00 40.94 4.41
135 136 8.735692 TCTGTCACATTTGATAATATCAGCAA 57.264 30.769 2.98 0.00 40.94 3.91
136 137 9.346005 TCTGTCACATTTGATAATATCAGCAAT 57.654 29.630 2.98 0.00 40.94 3.56
137 138 9.394477 CTGTCACATTTGATAATATCAGCAATG 57.606 33.333 18.76 18.76 40.64 2.82
138 139 8.905850 TGTCACATTTGATAATATCAGCAATGT 58.094 29.630 19.68 19.68 44.94 2.71
139 140 9.740239 GTCACATTTGATAATATCAGCAATGTT 57.260 29.630 21.52 10.92 43.13 2.71
140 141 9.955208 TCACATTTGATAATATCAGCAATGTTC 57.045 29.630 21.52 0.00 43.13 3.18
141 142 9.738832 CACATTTGATAATATCAGCAATGTTCA 57.261 29.630 21.52 0.00 43.13 3.18
151 152 9.511272 AATATCAGCAATGTTCATATAAGCTCA 57.489 29.630 0.00 0.00 0.00 4.26
152 153 7.997773 ATCAGCAATGTTCATATAAGCTCAT 57.002 32.000 0.00 0.00 0.00 2.90
153 154 7.198306 TCAGCAATGTTCATATAAGCTCATG 57.802 36.000 0.00 0.00 0.00 3.07
154 155 5.856986 CAGCAATGTTCATATAAGCTCATGC 59.143 40.000 0.00 0.00 40.05 4.06
171 172 6.584954 GCTCATGCTAGTATATTTGTTGACG 58.415 40.000 0.00 0.00 36.03 4.35
172 173 6.346919 GCTCATGCTAGTATATTTGTTGACGG 60.347 42.308 0.00 0.00 36.03 4.79
173 174 5.989168 TCATGCTAGTATATTTGTTGACGGG 59.011 40.000 0.00 0.00 0.00 5.28
174 175 4.124238 TGCTAGTATATTTGTTGACGGGC 58.876 43.478 0.00 0.00 0.00 6.13
175 176 4.141801 TGCTAGTATATTTGTTGACGGGCT 60.142 41.667 0.00 0.00 0.00 5.19
176 177 5.069383 TGCTAGTATATTTGTTGACGGGCTA 59.931 40.000 0.00 0.00 0.00 3.93
177 178 5.404667 GCTAGTATATTTGTTGACGGGCTAC 59.595 44.000 0.00 0.00 0.00 3.58
178 179 4.700700 AGTATATTTGTTGACGGGCTACC 58.299 43.478 0.00 0.00 0.00 3.18
179 180 3.926058 ATATTTGTTGACGGGCTACCT 57.074 42.857 0.00 0.00 33.28 3.08
180 181 2.579410 ATTTGTTGACGGGCTACCTT 57.421 45.000 0.00 0.00 33.28 3.50
181 182 1.886886 TTTGTTGACGGGCTACCTTC 58.113 50.000 0.00 0.00 35.67 3.46
182 183 1.053424 TTGTTGACGGGCTACCTTCT 58.947 50.000 0.00 0.00 36.08 2.85
183 184 1.053424 TGTTGACGGGCTACCTTCTT 58.947 50.000 0.00 0.00 36.08 2.52
184 185 1.418637 TGTTGACGGGCTACCTTCTTT 59.581 47.619 0.00 0.00 36.08 2.52
185 186 1.804748 GTTGACGGGCTACCTTCTTTG 59.195 52.381 0.00 0.00 36.08 2.77
186 187 1.053424 TGACGGGCTACCTTCTTTGT 58.947 50.000 0.00 0.00 36.08 2.83
187 188 1.001633 TGACGGGCTACCTTCTTTGTC 59.998 52.381 0.00 0.00 36.08 3.18
188 189 0.323957 ACGGGCTACCTTCTTTGTCC 59.676 55.000 0.00 0.00 33.28 4.02
189 190 0.323629 CGGGCTACCTTCTTTGTCCA 59.676 55.000 0.00 0.00 33.28 4.02
190 191 1.065418 CGGGCTACCTTCTTTGTCCAT 60.065 52.381 0.00 0.00 33.28 3.41
191 192 2.618045 CGGGCTACCTTCTTTGTCCATT 60.618 50.000 0.00 0.00 33.28 3.16
192 193 2.755103 GGGCTACCTTCTTTGTCCATTG 59.245 50.000 0.00 0.00 0.00 2.82
193 194 2.164422 GGCTACCTTCTTTGTCCATTGC 59.836 50.000 0.00 0.00 0.00 3.56
194 195 2.819608 GCTACCTTCTTTGTCCATTGCA 59.180 45.455 0.00 0.00 0.00 4.08
195 196 3.119708 GCTACCTTCTTTGTCCATTGCAG 60.120 47.826 0.00 0.00 0.00 4.41
196 197 2.949447 ACCTTCTTTGTCCATTGCAGT 58.051 42.857 0.00 0.00 0.00 4.40
197 198 2.887152 ACCTTCTTTGTCCATTGCAGTC 59.113 45.455 0.00 0.00 0.00 3.51
198 199 2.095567 CCTTCTTTGTCCATTGCAGTCG 60.096 50.000 0.00 0.00 0.00 4.18
199 200 2.542020 TCTTTGTCCATTGCAGTCGA 57.458 45.000 0.00 0.00 0.00 4.20
200 201 3.057969 TCTTTGTCCATTGCAGTCGAT 57.942 42.857 0.00 0.00 0.00 3.59
201 202 2.743664 TCTTTGTCCATTGCAGTCGATG 59.256 45.455 0.00 0.00 34.51 3.84
215 216 4.615815 GATGCCCGAGCGCCTCAT 62.616 66.667 2.29 0.00 44.31 2.90
216 217 3.226429 GATGCCCGAGCGCCTCATA 62.226 63.158 2.29 0.00 44.31 2.15
217 218 3.231889 ATGCCCGAGCGCCTCATAG 62.232 63.158 2.29 0.00 44.31 2.23
224 225 2.434317 AGCGCCTCATAGCTCATCA 58.566 52.632 2.29 0.00 39.98 3.07
225 226 0.975135 AGCGCCTCATAGCTCATCAT 59.025 50.000 2.29 0.00 39.98 2.45
226 227 1.347050 AGCGCCTCATAGCTCATCATT 59.653 47.619 2.29 0.00 39.98 2.57
227 228 1.463831 GCGCCTCATAGCTCATCATTG 59.536 52.381 0.00 0.00 0.00 2.82
228 229 2.763933 CGCCTCATAGCTCATCATTGT 58.236 47.619 0.00 0.00 0.00 2.71
229 230 3.862264 GCGCCTCATAGCTCATCATTGTA 60.862 47.826 0.00 0.00 0.00 2.41
230 231 4.502016 CGCCTCATAGCTCATCATTGTAT 58.498 43.478 0.00 0.00 0.00 2.29
231 232 4.934001 CGCCTCATAGCTCATCATTGTATT 59.066 41.667 0.00 0.00 0.00 1.89
232 233 5.063186 CGCCTCATAGCTCATCATTGTATTC 59.937 44.000 0.00 0.00 0.00 1.75
233 234 5.936372 GCCTCATAGCTCATCATTGTATTCA 59.064 40.000 0.00 0.00 0.00 2.57
234 235 6.598457 GCCTCATAGCTCATCATTGTATTCAT 59.402 38.462 0.00 0.00 0.00 2.57
235 236 7.414208 GCCTCATAGCTCATCATTGTATTCATG 60.414 40.741 0.00 0.00 0.00 3.07
236 237 7.822822 CCTCATAGCTCATCATTGTATTCATGA 59.177 37.037 0.00 0.00 0.00 3.07
237 238 9.216117 CTCATAGCTCATCATTGTATTCATGAA 57.784 33.333 11.26 11.26 0.00 2.57
238 239 9.734984 TCATAGCTCATCATTGTATTCATGAAT 57.265 29.630 23.75 23.75 34.93 2.57
241 242 7.582352 AGCTCATCATTGTATTCATGAATTCG 58.418 34.615 25.26 8.79 32.50 3.34
242 243 7.443272 AGCTCATCATTGTATTCATGAATTCGA 59.557 33.333 25.26 19.70 32.50 3.71
243 244 8.071967 GCTCATCATTGTATTCATGAATTCGAA 58.928 33.333 25.26 15.37 32.50 3.71
244 245 9.595357 CTCATCATTGTATTCATGAATTCGAAG 57.405 33.333 25.26 16.53 32.50 3.79
245 246 9.112725 TCATCATTGTATTCATGAATTCGAAGT 57.887 29.630 25.26 0.00 32.50 3.01
246 247 9.378597 CATCATTGTATTCATGAATTCGAAGTC 57.621 33.333 25.26 18.22 32.50 3.01
247 248 7.919690 TCATTGTATTCATGAATTCGAAGTCC 58.080 34.615 25.26 6.05 32.50 3.85
248 249 7.552330 TCATTGTATTCATGAATTCGAAGTCCA 59.448 33.333 25.26 10.95 32.50 4.02
249 250 7.680442 TTGTATTCATGAATTCGAAGTCCAA 57.320 32.000 25.26 13.53 32.50 3.53
250 251 7.680442 TGTATTCATGAATTCGAAGTCCAAA 57.320 32.000 25.26 13.40 32.50 3.28
251 252 8.279970 TGTATTCATGAATTCGAAGTCCAAAT 57.720 30.769 25.26 18.36 32.50 2.32
252 253 8.397906 TGTATTCATGAATTCGAAGTCCAAATC 58.602 33.333 25.26 12.20 32.50 2.17
253 254 6.816134 TTCATGAATTCGAAGTCCAAATCA 57.184 33.333 21.63 4.11 0.00 2.57
254 255 7.395190 TTCATGAATTCGAAGTCCAAATCAT 57.605 32.000 21.63 6.30 0.00 2.45
255 256 8.504812 TTCATGAATTCGAAGTCCAAATCATA 57.495 30.769 21.63 1.99 0.00 2.15
256 257 8.504812 TCATGAATTCGAAGTCCAAATCATAA 57.495 30.769 21.63 1.28 0.00 1.90
257 258 8.615211 TCATGAATTCGAAGTCCAAATCATAAG 58.385 33.333 21.63 0.00 0.00 1.73
258 259 8.615211 CATGAATTCGAAGTCCAAATCATAAGA 58.385 33.333 21.63 0.05 0.00 2.10
259 260 7.974675 TGAATTCGAAGTCCAAATCATAAGAC 58.025 34.615 21.63 0.00 0.00 3.01
260 261 6.927294 ATTCGAAGTCCAAATCATAAGACC 57.073 37.500 3.35 0.00 0.00 3.85
261 262 5.677319 TCGAAGTCCAAATCATAAGACCT 57.323 39.130 0.00 0.00 0.00 3.85
262 263 5.419542 TCGAAGTCCAAATCATAAGACCTG 58.580 41.667 0.00 0.00 0.00 4.00
263 264 5.046591 TCGAAGTCCAAATCATAAGACCTGT 60.047 40.000 0.00 0.00 0.00 4.00
264 265 6.153851 TCGAAGTCCAAATCATAAGACCTGTA 59.846 38.462 0.00 0.00 0.00 2.74
265 266 6.255887 CGAAGTCCAAATCATAAGACCTGTAC 59.744 42.308 0.00 0.00 0.00 2.90
266 267 6.620877 AGTCCAAATCATAAGACCTGTACA 57.379 37.500 0.00 0.00 0.00 2.90
267 268 7.200434 AGTCCAAATCATAAGACCTGTACAT 57.800 36.000 0.00 0.00 0.00 2.29
268 269 8.319057 AGTCCAAATCATAAGACCTGTACATA 57.681 34.615 0.00 0.00 0.00 2.29
269 270 8.768397 AGTCCAAATCATAAGACCTGTACATAA 58.232 33.333 0.00 0.00 0.00 1.90
270 271 9.046296 GTCCAAATCATAAGACCTGTACATAAG 57.954 37.037 0.00 0.00 0.00 1.73
271 272 8.988060 TCCAAATCATAAGACCTGTACATAAGA 58.012 33.333 0.00 0.00 0.00 2.10
272 273 9.265901 CCAAATCATAAGACCTGTACATAAGAG 57.734 37.037 0.00 0.00 0.00 2.85
273 274 8.768955 CAAATCATAAGACCTGTACATAAGAGC 58.231 37.037 0.00 0.00 0.00 4.09
274 275 6.073327 TCATAAGACCTGTACATAAGAGCG 57.927 41.667 0.00 0.00 0.00 5.03
275 276 5.826208 TCATAAGACCTGTACATAAGAGCGA 59.174 40.000 0.00 0.00 0.00 4.93
276 277 4.640789 AAGACCTGTACATAAGAGCGAG 57.359 45.455 0.00 0.00 0.00 5.03
277 278 2.359531 AGACCTGTACATAAGAGCGAGC 59.640 50.000 0.00 0.00 0.00 5.03
278 279 2.359531 GACCTGTACATAAGAGCGAGCT 59.640 50.000 0.00 0.00 0.00 4.09
279 280 3.552875 ACCTGTACATAAGAGCGAGCTA 58.447 45.455 0.00 0.00 0.00 3.32
280 281 3.315749 ACCTGTACATAAGAGCGAGCTAC 59.684 47.826 0.00 0.00 0.00 3.58
281 282 3.546617 CTGTACATAAGAGCGAGCTACG 58.453 50.000 0.00 0.00 45.66 3.51
282 283 3.200483 TGTACATAAGAGCGAGCTACGA 58.800 45.455 9.32 0.00 45.77 3.43
283 284 3.624410 TGTACATAAGAGCGAGCTACGAA 59.376 43.478 9.32 0.00 45.77 3.85
284 285 3.777465 ACATAAGAGCGAGCTACGAAA 57.223 42.857 9.32 0.00 45.77 3.46
285 286 4.106029 ACATAAGAGCGAGCTACGAAAA 57.894 40.909 9.32 0.00 45.77 2.29
286 287 4.106197 ACATAAGAGCGAGCTACGAAAAG 58.894 43.478 9.32 0.00 45.77 2.27
287 288 1.997669 AAGAGCGAGCTACGAAAAGG 58.002 50.000 9.32 0.00 45.77 3.11
288 289 0.173708 AGAGCGAGCTACGAAAAGGG 59.826 55.000 9.32 0.00 45.77 3.95
289 290 0.172803 GAGCGAGCTACGAAAAGGGA 59.827 55.000 9.32 0.00 45.77 4.20
290 291 0.108756 AGCGAGCTACGAAAAGGGAC 60.109 55.000 9.32 0.00 45.77 4.46
291 292 0.389426 GCGAGCTACGAAAAGGGACA 60.389 55.000 9.32 0.00 45.77 4.02
292 293 1.938016 GCGAGCTACGAAAAGGGACAA 60.938 52.381 9.32 0.00 45.77 3.18
293 294 1.725164 CGAGCTACGAAAAGGGACAAC 59.275 52.381 0.00 0.00 45.77 3.32
294 295 2.762745 GAGCTACGAAAAGGGACAACA 58.237 47.619 0.00 0.00 0.00 3.33
295 296 3.135994 GAGCTACGAAAAGGGACAACAA 58.864 45.455 0.00 0.00 0.00 2.83
296 297 3.139077 AGCTACGAAAAGGGACAACAAG 58.861 45.455 0.00 0.00 0.00 3.16
297 298 2.876550 GCTACGAAAAGGGACAACAAGT 59.123 45.455 0.00 0.00 0.00 3.16
298 299 4.060205 GCTACGAAAAGGGACAACAAGTA 58.940 43.478 0.00 0.00 0.00 2.24
299 300 4.512571 GCTACGAAAAGGGACAACAAGTAA 59.487 41.667 0.00 0.00 0.00 2.24
300 301 5.333875 GCTACGAAAAGGGACAACAAGTAAG 60.334 44.000 0.00 0.00 0.00 2.34
301 302 4.520179 ACGAAAAGGGACAACAAGTAAGT 58.480 39.130 0.00 0.00 0.00 2.24
302 303 5.673514 ACGAAAAGGGACAACAAGTAAGTA 58.326 37.500 0.00 0.00 0.00 2.24
303 304 6.293698 ACGAAAAGGGACAACAAGTAAGTAT 58.706 36.000 0.00 0.00 0.00 2.12
304 305 6.426025 ACGAAAAGGGACAACAAGTAAGTATC 59.574 38.462 0.00 0.00 0.00 2.24
305 306 6.128363 CGAAAAGGGACAACAAGTAAGTATCC 60.128 42.308 0.00 0.00 0.00 2.59
306 307 5.836024 AAGGGACAACAAGTAAGTATCCA 57.164 39.130 0.00 0.00 0.00 3.41
307 308 6.388619 AAGGGACAACAAGTAAGTATCCAT 57.611 37.500 0.00 0.00 0.00 3.41
308 309 5.745227 AGGGACAACAAGTAAGTATCCATG 58.255 41.667 0.00 0.00 0.00 3.66
309 310 5.250774 AGGGACAACAAGTAAGTATCCATGT 59.749 40.000 0.00 0.00 0.00 3.21
310 311 5.354234 GGGACAACAAGTAAGTATCCATGTG 59.646 44.000 0.00 0.00 0.00 3.21
311 312 5.938125 GGACAACAAGTAAGTATCCATGTGT 59.062 40.000 0.00 0.00 0.00 3.72
312 313 6.430000 GGACAACAAGTAAGTATCCATGTGTT 59.570 38.462 0.00 0.00 0.00 3.32
313 314 7.040686 GGACAACAAGTAAGTATCCATGTGTTT 60.041 37.037 0.00 0.00 0.00 2.83
314 315 7.871853 ACAACAAGTAAGTATCCATGTGTTTC 58.128 34.615 0.00 0.00 0.00 2.78
315 316 7.500892 ACAACAAGTAAGTATCCATGTGTTTCA 59.499 33.333 0.00 0.00 0.00 2.69
316 317 8.349245 CAACAAGTAAGTATCCATGTGTTTCAA 58.651 33.333 0.00 0.00 0.00 2.69
317 318 8.458573 ACAAGTAAGTATCCATGTGTTTCAAA 57.541 30.769 0.00 0.00 0.00 2.69
318 319 9.077885 ACAAGTAAGTATCCATGTGTTTCAAAT 57.922 29.630 0.00 0.00 0.00 2.32
319 320 9.912634 CAAGTAAGTATCCATGTGTTTCAAATT 57.087 29.630 0.00 0.00 0.00 1.82
321 322 9.295825 AGTAAGTATCCATGTGTTTCAAATTCA 57.704 29.630 0.00 0.00 0.00 2.57
322 323 9.559958 GTAAGTATCCATGTGTTTCAAATTCAG 57.440 33.333 0.00 0.00 0.00 3.02
323 324 7.161773 AGTATCCATGTGTTTCAAATTCAGG 57.838 36.000 0.00 0.00 0.00 3.86
324 325 4.255833 TCCATGTGTTTCAAATTCAGGC 57.744 40.909 0.00 0.00 0.00 4.85
325 326 3.006752 TCCATGTGTTTCAAATTCAGGCC 59.993 43.478 0.00 0.00 0.00 5.19
326 327 3.244146 CCATGTGTTTCAAATTCAGGCCA 60.244 43.478 5.01 0.00 0.00 5.36
327 328 4.563993 CCATGTGTTTCAAATTCAGGCCAT 60.564 41.667 5.01 0.00 0.00 4.40
328 329 3.992643 TGTGTTTCAAATTCAGGCCATG 58.007 40.909 5.01 0.00 0.00 3.66
329 330 3.244146 TGTGTTTCAAATTCAGGCCATGG 60.244 43.478 7.63 7.63 0.00 3.66
330 331 2.971330 TGTTTCAAATTCAGGCCATGGT 59.029 40.909 14.67 0.00 0.00 3.55
331 332 3.390639 TGTTTCAAATTCAGGCCATGGTT 59.609 39.130 14.67 0.00 0.00 3.67
332 333 4.141528 TGTTTCAAATTCAGGCCATGGTTT 60.142 37.500 14.67 1.46 0.00 3.27
333 334 5.070981 TGTTTCAAATTCAGGCCATGGTTTA 59.929 36.000 14.67 0.00 0.00 2.01
334 335 6.172630 GTTTCAAATTCAGGCCATGGTTTAT 58.827 36.000 14.67 0.00 0.00 1.40
335 336 5.341872 TCAAATTCAGGCCATGGTTTATG 57.658 39.130 14.67 7.40 36.50 1.90
336 337 5.022122 TCAAATTCAGGCCATGGTTTATGA 58.978 37.500 14.67 9.66 39.21 2.15
337 338 5.105392 TCAAATTCAGGCCATGGTTTATGAC 60.105 40.000 14.67 0.00 39.21 3.06
338 339 3.448093 TTCAGGCCATGGTTTATGACA 57.552 42.857 14.67 2.08 39.21 3.58
339 340 3.668141 TCAGGCCATGGTTTATGACAT 57.332 42.857 14.67 0.00 39.21 3.06
466 467 2.010582 GCCGCCACACACCAAGAAAA 62.011 55.000 0.00 0.00 0.00 2.29
805 806 2.736995 GACACGGCAGCAACGCTA 60.737 61.111 0.00 0.00 36.40 4.26
845 846 2.564771 CTGCAGTTTGTCTCCAAGTCA 58.435 47.619 5.25 0.00 0.00 3.41
859 860 1.270826 CAAGTCACCTTCTGCTCTCGA 59.729 52.381 0.00 0.00 0.00 4.04
899 900 3.803340 TGGTAAAGGAAGGAGAGGTGAT 58.197 45.455 0.00 0.00 0.00 3.06
1858 1867 1.788518 TTACCAGTGCACAGCCCCAT 61.789 55.000 21.04 0.00 0.00 4.00
1899 1908 1.077993 AGAGGAGGTTACAGAGGCAGT 59.922 52.381 0.00 0.00 0.00 4.40
2103 2112 0.946221 AGAGGAACGAACAGCAAGCG 60.946 55.000 0.00 0.00 0.00 4.68
2294 2305 8.405531 CCAATCGTACAATGGAACTATTCAAAT 58.594 33.333 3.11 0.00 36.27 2.32
2739 2750 4.729227 TGCTAAACACACTCGGATATCA 57.271 40.909 4.83 0.00 0.00 2.15
3201 3215 3.018598 ACCTATCTGATCAATCGCACG 57.981 47.619 0.00 0.00 0.00 5.34
3302 3317 6.809196 GTGTTTGGATGTACTTGTTTTGTCAA 59.191 34.615 0.00 0.00 0.00 3.18
3426 3441 0.246635 ATAGGCGCACTTTCGTGAGT 59.753 50.000 10.83 0.00 43.97 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.136796 TGTCAAAGAGAGGACATTGTTGG 58.863 43.478 0.00 0.00 39.00 3.77
8 9 3.685139 TGTGGATGTCAAAGAGAGGAC 57.315 47.619 0.00 0.00 34.63 3.85
9 10 3.390967 TGTTGTGGATGTCAAAGAGAGGA 59.609 43.478 0.00 0.00 0.00 3.71
10 11 3.743521 TGTTGTGGATGTCAAAGAGAGG 58.256 45.455 0.00 0.00 0.00 3.69
11 12 7.042187 GCTATATGTTGTGGATGTCAAAGAGAG 60.042 40.741 0.00 0.00 0.00 3.20
12 13 6.763135 GCTATATGTTGTGGATGTCAAAGAGA 59.237 38.462 0.00 0.00 0.00 3.10
13 14 6.292542 CGCTATATGTTGTGGATGTCAAAGAG 60.293 42.308 0.00 0.00 0.00 2.85
14 15 5.523552 CGCTATATGTTGTGGATGTCAAAGA 59.476 40.000 0.00 0.00 0.00 2.52
15 16 5.523552 TCGCTATATGTTGTGGATGTCAAAG 59.476 40.000 0.00 0.00 0.00 2.77
16 17 5.293324 GTCGCTATATGTTGTGGATGTCAAA 59.707 40.000 0.00 0.00 0.00 2.69
17 18 4.808895 GTCGCTATATGTTGTGGATGTCAA 59.191 41.667 0.00 0.00 0.00 3.18
18 19 4.368315 GTCGCTATATGTTGTGGATGTCA 58.632 43.478 0.00 0.00 0.00 3.58
19 20 3.741344 GGTCGCTATATGTTGTGGATGTC 59.259 47.826 0.00 0.00 0.00 3.06
20 21 3.133901 TGGTCGCTATATGTTGTGGATGT 59.866 43.478 0.00 0.00 0.00 3.06
21 22 3.727726 TGGTCGCTATATGTTGTGGATG 58.272 45.455 0.00 0.00 0.00 3.51
22 23 4.127171 GTTGGTCGCTATATGTTGTGGAT 58.873 43.478 0.00 0.00 0.00 3.41
23 24 3.196901 AGTTGGTCGCTATATGTTGTGGA 59.803 43.478 0.00 0.00 0.00 4.02
24 25 3.531538 AGTTGGTCGCTATATGTTGTGG 58.468 45.455 0.00 0.00 0.00 4.17
25 26 5.447279 GGAAAGTTGGTCGCTATATGTTGTG 60.447 44.000 0.00 0.00 0.00 3.33
26 27 4.634443 GGAAAGTTGGTCGCTATATGTTGT 59.366 41.667 0.00 0.00 0.00 3.32
27 28 4.634004 TGGAAAGTTGGTCGCTATATGTTG 59.366 41.667 0.00 0.00 0.00 3.33
28 29 4.839121 TGGAAAGTTGGTCGCTATATGTT 58.161 39.130 0.00 0.00 0.00 2.71
29 30 4.481368 TGGAAAGTTGGTCGCTATATGT 57.519 40.909 0.00 0.00 0.00 2.29
30 31 5.056480 TGATGGAAAGTTGGTCGCTATATG 58.944 41.667 0.00 0.00 0.00 1.78
31 32 5.290493 TGATGGAAAGTTGGTCGCTATAT 57.710 39.130 0.00 0.00 0.00 0.86
32 33 4.746535 TGATGGAAAGTTGGTCGCTATA 57.253 40.909 0.00 0.00 0.00 1.31
33 34 3.627395 TGATGGAAAGTTGGTCGCTAT 57.373 42.857 0.00 0.00 0.00 2.97
34 35 3.627395 ATGATGGAAAGTTGGTCGCTA 57.373 42.857 0.00 0.00 0.00 4.26
35 36 2.489329 CAATGATGGAAAGTTGGTCGCT 59.511 45.455 0.00 0.00 0.00 4.93
36 37 2.867429 CAATGATGGAAAGTTGGTCGC 58.133 47.619 0.00 0.00 0.00 5.19
49 50 0.256752 TGCTCCCAGTCCCAATGATG 59.743 55.000 0.00 0.00 0.00 3.07
50 51 1.133575 CATGCTCCCAGTCCCAATGAT 60.134 52.381 0.00 0.00 0.00 2.45
51 52 0.256752 CATGCTCCCAGTCCCAATGA 59.743 55.000 0.00 0.00 0.00 2.57
52 53 0.256752 TCATGCTCCCAGTCCCAATG 59.743 55.000 0.00 0.00 0.00 2.82
53 54 0.549950 CTCATGCTCCCAGTCCCAAT 59.450 55.000 0.00 0.00 0.00 3.16
54 55 1.993653 CTCATGCTCCCAGTCCCAA 59.006 57.895 0.00 0.00 0.00 4.12
55 56 2.673200 GCTCATGCTCCCAGTCCCA 61.673 63.158 0.00 0.00 36.03 4.37
56 57 2.191641 GCTCATGCTCCCAGTCCC 59.808 66.667 0.00 0.00 36.03 4.46
92 93 9.671279 TGTGACAGATTGAACAAGAATATATGT 57.329 29.630 0.00 0.00 0.00 2.29
96 97 9.850628 CAAATGTGACAGATTGAACAAGAATAT 57.149 29.630 7.83 0.00 0.00 1.28
97 98 9.065798 TCAAATGTGACAGATTGAACAAGAATA 57.934 29.630 12.41 0.00 0.00 1.75
98 99 7.944061 TCAAATGTGACAGATTGAACAAGAAT 58.056 30.769 12.41 0.00 0.00 2.40
99 100 7.332213 TCAAATGTGACAGATTGAACAAGAA 57.668 32.000 12.41 0.00 0.00 2.52
100 101 6.940831 TCAAATGTGACAGATTGAACAAGA 57.059 33.333 12.41 0.00 0.00 3.02
101 102 9.850628 ATTATCAAATGTGACAGATTGAACAAG 57.149 29.630 16.95 0.00 36.31 3.16
107 108 9.608617 GCTGATATTATCAAATGTGACAGATTG 57.391 33.333 7.73 7.37 39.11 2.67
108 109 9.346005 TGCTGATATTATCAAATGTGACAGATT 57.654 29.630 7.73 0.00 39.11 2.40
109 110 8.913487 TGCTGATATTATCAAATGTGACAGAT 57.087 30.769 7.73 0.00 39.11 2.90
110 111 8.735692 TTGCTGATATTATCAAATGTGACAGA 57.264 30.769 7.73 0.00 39.11 3.41
111 112 9.394477 CATTGCTGATATTATCAAATGTGACAG 57.606 33.333 16.33 0.00 39.11 3.51
112 113 8.905850 ACATTGCTGATATTATCAAATGTGACA 58.094 29.630 23.52 0.00 43.60 3.58
113 114 9.740239 AACATTGCTGATATTATCAAATGTGAC 57.260 29.630 24.23 7.11 44.06 3.67
114 115 9.955208 GAACATTGCTGATATTATCAAATGTGA 57.045 29.630 24.23 0.00 44.06 3.58
115 116 9.738832 TGAACATTGCTGATATTATCAAATGTG 57.261 29.630 24.23 15.95 44.06 3.21
125 126 9.511272 TGAGCTTATATGAACATTGCTGATATT 57.489 29.630 0.00 0.00 0.00 1.28
126 127 9.682465 ATGAGCTTATATGAACATTGCTGATAT 57.318 29.630 0.00 0.00 0.00 1.63
127 128 8.943002 CATGAGCTTATATGAACATTGCTGATA 58.057 33.333 0.00 0.00 0.00 2.15
128 129 7.575155 GCATGAGCTTATATGAACATTGCTGAT 60.575 37.037 0.00 0.00 37.91 2.90
129 130 6.293790 GCATGAGCTTATATGAACATTGCTGA 60.294 38.462 0.00 0.00 37.91 4.26
130 131 5.856986 GCATGAGCTTATATGAACATTGCTG 59.143 40.000 0.00 0.00 37.91 4.41
131 132 6.010294 GCATGAGCTTATATGAACATTGCT 57.990 37.500 0.00 0.00 37.91 3.91
147 148 6.346919 CCGTCAACAAATATACTAGCATGAGC 60.347 42.308 0.00 0.00 42.56 4.26
148 149 6.146184 CCCGTCAACAAATATACTAGCATGAG 59.854 42.308 0.00 0.00 0.00 2.90
149 150 5.989168 CCCGTCAACAAATATACTAGCATGA 59.011 40.000 0.00 0.00 0.00 3.07
150 151 5.334105 GCCCGTCAACAAATATACTAGCATG 60.334 44.000 0.00 0.00 0.00 4.06
151 152 4.755123 GCCCGTCAACAAATATACTAGCAT 59.245 41.667 0.00 0.00 0.00 3.79
152 153 4.124238 GCCCGTCAACAAATATACTAGCA 58.876 43.478 0.00 0.00 0.00 3.49
153 154 4.377897 AGCCCGTCAACAAATATACTAGC 58.622 43.478 0.00 0.00 0.00 3.42
154 155 5.924825 GGTAGCCCGTCAACAAATATACTAG 59.075 44.000 0.00 0.00 0.00 2.57
155 156 5.599656 AGGTAGCCCGTCAACAAATATACTA 59.400 40.000 0.00 0.00 35.12 1.82
156 157 4.407945 AGGTAGCCCGTCAACAAATATACT 59.592 41.667 0.00 0.00 35.12 2.12
157 158 4.700700 AGGTAGCCCGTCAACAAATATAC 58.299 43.478 0.00 0.00 35.12 1.47
158 159 5.129815 AGAAGGTAGCCCGTCAACAAATATA 59.870 40.000 0.00 0.00 41.25 0.86
159 160 3.926058 AGGTAGCCCGTCAACAAATAT 57.074 42.857 0.00 0.00 35.12 1.28
160 161 3.262405 AGAAGGTAGCCCGTCAACAAATA 59.738 43.478 0.00 0.00 41.25 1.40
161 162 2.039879 AGAAGGTAGCCCGTCAACAAAT 59.960 45.455 0.00 0.00 41.25 2.32
162 163 1.418637 AGAAGGTAGCCCGTCAACAAA 59.581 47.619 0.00 0.00 41.25 2.83
163 164 1.053424 AGAAGGTAGCCCGTCAACAA 58.947 50.000 0.00 0.00 41.25 2.83
164 165 1.053424 AAGAAGGTAGCCCGTCAACA 58.947 50.000 0.00 0.00 41.25 3.33
165 166 1.804748 CAAAGAAGGTAGCCCGTCAAC 59.195 52.381 0.00 0.00 41.25 3.18
166 167 1.418637 ACAAAGAAGGTAGCCCGTCAA 59.581 47.619 0.00 0.00 41.25 3.18
167 168 1.001633 GACAAAGAAGGTAGCCCGTCA 59.998 52.381 0.00 0.00 41.25 4.35
168 169 1.675116 GGACAAAGAAGGTAGCCCGTC 60.675 57.143 0.00 0.00 39.31 4.79
169 170 0.323957 GGACAAAGAAGGTAGCCCGT 59.676 55.000 0.00 0.00 35.12 5.28
170 171 0.323629 TGGACAAAGAAGGTAGCCCG 59.676 55.000 0.00 0.00 35.12 6.13
171 172 2.755103 CAATGGACAAAGAAGGTAGCCC 59.245 50.000 0.00 0.00 0.00 5.19
172 173 2.164422 GCAATGGACAAAGAAGGTAGCC 59.836 50.000 0.00 0.00 0.00 3.93
173 174 2.819608 TGCAATGGACAAAGAAGGTAGC 59.180 45.455 0.00 0.00 0.00 3.58
174 175 4.074970 ACTGCAATGGACAAAGAAGGTAG 58.925 43.478 0.00 0.00 0.00 3.18
175 176 4.072131 GACTGCAATGGACAAAGAAGGTA 58.928 43.478 0.00 0.00 0.00 3.08
176 177 2.887152 GACTGCAATGGACAAAGAAGGT 59.113 45.455 0.00 0.00 0.00 3.50
177 178 2.095567 CGACTGCAATGGACAAAGAAGG 60.096 50.000 0.00 0.00 0.00 3.46
178 179 2.807967 TCGACTGCAATGGACAAAGAAG 59.192 45.455 0.00 0.00 0.00 2.85
179 180 2.844946 TCGACTGCAATGGACAAAGAA 58.155 42.857 0.00 0.00 0.00 2.52
180 181 2.542020 TCGACTGCAATGGACAAAGA 57.458 45.000 0.00 0.00 0.00 2.52
181 182 3.127081 CATCGACTGCAATGGACAAAG 57.873 47.619 0.00 0.00 0.00 2.77
198 199 3.226429 TATGAGGCGCTCGGGCATC 62.226 63.158 8.62 12.72 45.36 3.91
199 200 3.231889 CTATGAGGCGCTCGGGCAT 62.232 63.158 8.62 6.78 45.36 4.40
200 201 3.916544 CTATGAGGCGCTCGGGCA 61.917 66.667 8.62 0.00 45.36 5.36
202 203 3.565910 GAGCTATGAGGCGCTCGGG 62.566 68.421 7.64 0.00 42.62 5.14
203 204 2.049618 GAGCTATGAGGCGCTCGG 60.050 66.667 7.64 0.00 42.62 4.63
206 207 0.975135 ATGATGAGCTATGAGGCGCT 59.025 50.000 7.64 0.00 39.61 5.92
207 208 1.463831 CAATGATGAGCTATGAGGCGC 59.536 52.381 0.00 0.00 37.29 6.53
208 209 2.763933 ACAATGATGAGCTATGAGGCG 58.236 47.619 0.00 0.00 37.29 5.52
209 210 5.936372 TGAATACAATGATGAGCTATGAGGC 59.064 40.000 0.00 0.00 0.00 4.70
210 211 7.822822 TCATGAATACAATGATGAGCTATGAGG 59.177 37.037 0.00 0.00 0.00 3.86
211 212 8.773404 TCATGAATACAATGATGAGCTATGAG 57.227 34.615 0.00 0.00 0.00 2.90
212 213 9.734984 ATTCATGAATACAATGATGAGCTATGA 57.265 29.630 19.42 0.00 0.00 2.15
215 216 8.715088 CGAATTCATGAATACAATGATGAGCTA 58.285 33.333 21.00 0.00 0.00 3.32
216 217 7.443272 TCGAATTCATGAATACAATGATGAGCT 59.557 33.333 21.00 0.81 0.00 4.09
217 218 7.578852 TCGAATTCATGAATACAATGATGAGC 58.421 34.615 21.00 0.05 0.00 4.26
218 219 9.595357 CTTCGAATTCATGAATACAATGATGAG 57.405 33.333 21.00 6.89 0.00 2.90
219 220 9.112725 ACTTCGAATTCATGAATACAATGATGA 57.887 29.630 21.00 7.76 0.00 2.92
220 221 9.378597 GACTTCGAATTCATGAATACAATGATG 57.621 33.333 21.00 16.16 0.00 3.07
221 222 8.562892 GGACTTCGAATTCATGAATACAATGAT 58.437 33.333 21.00 3.81 0.00 2.45
222 223 7.552330 TGGACTTCGAATTCATGAATACAATGA 59.448 33.333 21.00 11.47 0.00 2.57
223 224 7.696755 TGGACTTCGAATTCATGAATACAATG 58.303 34.615 21.00 13.41 0.00 2.82
224 225 7.864108 TGGACTTCGAATTCATGAATACAAT 57.136 32.000 21.00 5.71 0.00 2.71
225 226 7.680442 TTGGACTTCGAATTCATGAATACAA 57.320 32.000 21.00 8.75 0.00 2.41
226 227 7.680442 TTTGGACTTCGAATTCATGAATACA 57.320 32.000 21.00 2.53 0.00 2.29
227 228 8.397906 TGATTTGGACTTCGAATTCATGAATAC 58.602 33.333 21.00 0.00 29.85 1.89
228 229 8.504812 TGATTTGGACTTCGAATTCATGAATA 57.495 30.769 21.00 3.28 29.85 1.75
229 230 7.395190 TGATTTGGACTTCGAATTCATGAAT 57.605 32.000 15.36 15.36 29.85 2.57
230 231 6.816134 TGATTTGGACTTCGAATTCATGAA 57.184 33.333 11.26 11.26 29.85 2.57
231 232 8.504812 TTATGATTTGGACTTCGAATTCATGA 57.495 30.769 16.25 0.00 36.27 3.07
232 233 8.615211 TCTTATGATTTGGACTTCGAATTCATG 58.385 33.333 16.25 0.00 36.27 3.07
233 234 8.616076 GTCTTATGATTTGGACTTCGAATTCAT 58.384 33.333 16.25 12.83 37.89 2.57
234 235 7.065803 GGTCTTATGATTTGGACTTCGAATTCA 59.934 37.037 16.25 4.76 31.86 2.57
235 236 7.281100 AGGTCTTATGATTTGGACTTCGAATTC 59.719 37.037 6.95 6.95 29.85 2.17
236 237 7.066284 CAGGTCTTATGATTTGGACTTCGAATT 59.934 37.037 0.00 0.00 29.85 2.17
237 238 6.540189 CAGGTCTTATGATTTGGACTTCGAAT 59.460 38.462 0.00 0.00 32.31 3.34
238 239 5.874810 CAGGTCTTATGATTTGGACTTCGAA 59.125 40.000 0.00 0.00 0.00 3.71
239 240 5.046591 ACAGGTCTTATGATTTGGACTTCGA 60.047 40.000 0.00 0.00 0.00 3.71
240 241 5.178797 ACAGGTCTTATGATTTGGACTTCG 58.821 41.667 0.00 0.00 0.00 3.79
241 242 7.103641 TGTACAGGTCTTATGATTTGGACTTC 58.896 38.462 0.00 0.00 0.00 3.01
242 243 7.016153 TGTACAGGTCTTATGATTTGGACTT 57.984 36.000 0.00 0.00 0.00 3.01
243 244 6.620877 TGTACAGGTCTTATGATTTGGACT 57.379 37.500 0.00 0.00 0.00 3.85
244 245 8.958119 TTATGTACAGGTCTTATGATTTGGAC 57.042 34.615 0.33 0.00 0.00 4.02
245 246 8.988060 TCTTATGTACAGGTCTTATGATTTGGA 58.012 33.333 0.33 0.00 0.00 3.53
246 247 9.265901 CTCTTATGTACAGGTCTTATGATTTGG 57.734 37.037 0.33 0.00 0.00 3.28
247 248 8.768955 GCTCTTATGTACAGGTCTTATGATTTG 58.231 37.037 0.33 0.00 0.00 2.32
248 249 7.653713 CGCTCTTATGTACAGGTCTTATGATTT 59.346 37.037 0.33 0.00 0.00 2.17
249 250 7.014326 TCGCTCTTATGTACAGGTCTTATGATT 59.986 37.037 0.33 0.00 0.00 2.57
250 251 6.490381 TCGCTCTTATGTACAGGTCTTATGAT 59.510 38.462 0.33 0.00 0.00 2.45
251 252 5.826208 TCGCTCTTATGTACAGGTCTTATGA 59.174 40.000 0.33 0.00 0.00 2.15
252 253 6.073327 TCGCTCTTATGTACAGGTCTTATG 57.927 41.667 0.33 0.00 0.00 1.90
253 254 5.278561 GCTCGCTCTTATGTACAGGTCTTAT 60.279 44.000 0.33 0.00 0.00 1.73
254 255 4.036498 GCTCGCTCTTATGTACAGGTCTTA 59.964 45.833 0.33 0.00 0.00 2.10
255 256 3.181485 GCTCGCTCTTATGTACAGGTCTT 60.181 47.826 0.33 0.00 0.00 3.01
256 257 2.359531 GCTCGCTCTTATGTACAGGTCT 59.640 50.000 0.33 0.00 0.00 3.85
257 258 2.359531 AGCTCGCTCTTATGTACAGGTC 59.640 50.000 0.33 0.00 0.00 3.85
258 259 2.379972 AGCTCGCTCTTATGTACAGGT 58.620 47.619 0.33 0.00 0.00 4.00
259 260 3.607310 CGTAGCTCGCTCTTATGTACAGG 60.607 52.174 0.33 0.00 0.00 4.00
260 261 3.247886 TCGTAGCTCGCTCTTATGTACAG 59.752 47.826 0.33 0.00 39.67 2.74
261 262 3.200483 TCGTAGCTCGCTCTTATGTACA 58.800 45.455 0.00 0.00 39.67 2.90
262 263 3.874400 TCGTAGCTCGCTCTTATGTAC 57.126 47.619 0.00 0.00 39.67 2.90
263 264 4.888038 TTTCGTAGCTCGCTCTTATGTA 57.112 40.909 0.00 0.00 39.67 2.29
264 265 3.777465 TTTCGTAGCTCGCTCTTATGT 57.223 42.857 0.00 0.00 39.67 2.29
265 266 3.487574 CCTTTTCGTAGCTCGCTCTTATG 59.512 47.826 0.00 0.00 39.67 1.90
266 267 3.491104 CCCTTTTCGTAGCTCGCTCTTAT 60.491 47.826 0.00 0.00 39.67 1.73
267 268 2.159282 CCCTTTTCGTAGCTCGCTCTTA 60.159 50.000 0.00 0.00 39.67 2.10
268 269 1.404315 CCCTTTTCGTAGCTCGCTCTT 60.404 52.381 0.00 0.00 39.67 2.85
269 270 0.173708 CCCTTTTCGTAGCTCGCTCT 59.826 55.000 0.00 0.00 39.67 4.09
270 271 0.172803 TCCCTTTTCGTAGCTCGCTC 59.827 55.000 0.00 0.00 39.67 5.03
271 272 0.108756 GTCCCTTTTCGTAGCTCGCT 60.109 55.000 0.00 0.00 39.67 4.93
272 273 0.389426 TGTCCCTTTTCGTAGCTCGC 60.389 55.000 0.00 0.00 39.67 5.03
273 274 1.725164 GTTGTCCCTTTTCGTAGCTCG 59.275 52.381 0.00 0.00 41.41 5.03
274 275 2.762745 TGTTGTCCCTTTTCGTAGCTC 58.237 47.619 0.00 0.00 0.00 4.09
275 276 2.922740 TGTTGTCCCTTTTCGTAGCT 57.077 45.000 0.00 0.00 0.00 3.32
276 277 2.876550 ACTTGTTGTCCCTTTTCGTAGC 59.123 45.455 0.00 0.00 0.00 3.58
277 278 5.756833 ACTTACTTGTTGTCCCTTTTCGTAG 59.243 40.000 0.00 0.00 0.00 3.51
278 279 5.673514 ACTTACTTGTTGTCCCTTTTCGTA 58.326 37.500 0.00 0.00 0.00 3.43
279 280 4.520179 ACTTACTTGTTGTCCCTTTTCGT 58.480 39.130 0.00 0.00 0.00 3.85
280 281 6.128363 GGATACTTACTTGTTGTCCCTTTTCG 60.128 42.308 0.00 0.00 0.00 3.46
281 282 6.713450 TGGATACTTACTTGTTGTCCCTTTTC 59.287 38.462 0.00 0.00 37.61 2.29
282 283 6.607019 TGGATACTTACTTGTTGTCCCTTTT 58.393 36.000 0.00 0.00 37.61 2.27
283 284 6.195600 TGGATACTTACTTGTTGTCCCTTT 57.804 37.500 0.00 0.00 37.61 3.11
284 285 5.836024 TGGATACTTACTTGTTGTCCCTT 57.164 39.130 0.00 0.00 37.61 3.95
285 286 5.250774 ACATGGATACTTACTTGTTGTCCCT 59.749 40.000 0.00 0.00 37.61 4.20
286 287 5.354234 CACATGGATACTTACTTGTTGTCCC 59.646 44.000 0.00 0.00 37.61 4.46
287 288 5.938125 ACACATGGATACTTACTTGTTGTCC 59.062 40.000 0.00 0.00 37.61 4.02
288 289 7.435068 AACACATGGATACTTACTTGTTGTC 57.565 36.000 0.00 0.00 37.61 3.18
289 290 7.500892 TGAAACACATGGATACTTACTTGTTGT 59.499 33.333 0.00 0.00 37.61 3.32
290 291 7.870826 TGAAACACATGGATACTTACTTGTTG 58.129 34.615 0.00 0.00 37.61 3.33
291 292 8.458573 TTGAAACACATGGATACTTACTTGTT 57.541 30.769 0.00 0.00 37.61 2.83
292 293 8.458573 TTTGAAACACATGGATACTTACTTGT 57.541 30.769 0.00 0.00 37.61 3.16
293 294 9.912634 AATTTGAAACACATGGATACTTACTTG 57.087 29.630 0.00 0.00 37.61 3.16
295 296 9.295825 TGAATTTGAAACACATGGATACTTACT 57.704 29.630 0.00 0.00 37.61 2.24
296 297 9.559958 CTGAATTTGAAACACATGGATACTTAC 57.440 33.333 0.00 0.00 37.61 2.34
297 298 8.739039 CCTGAATTTGAAACACATGGATACTTA 58.261 33.333 0.00 0.00 37.61 2.24
298 299 7.605449 CCTGAATTTGAAACACATGGATACTT 58.395 34.615 0.00 0.00 37.61 2.24
299 300 6.350445 GCCTGAATTTGAAACACATGGATACT 60.350 38.462 0.00 0.00 37.61 2.12
300 301 5.807011 GCCTGAATTTGAAACACATGGATAC 59.193 40.000 0.00 0.00 0.00 2.24
301 302 5.105392 GGCCTGAATTTGAAACACATGGATA 60.105 40.000 0.00 0.00 0.00 2.59
302 303 4.322953 GGCCTGAATTTGAAACACATGGAT 60.323 41.667 0.00 0.00 0.00 3.41
303 304 3.006752 GGCCTGAATTTGAAACACATGGA 59.993 43.478 0.00 0.00 0.00 3.41
304 305 3.244146 TGGCCTGAATTTGAAACACATGG 60.244 43.478 3.32 0.00 0.00 3.66
305 306 3.992643 TGGCCTGAATTTGAAACACATG 58.007 40.909 3.32 0.00 0.00 3.21
306 307 4.563993 CCATGGCCTGAATTTGAAACACAT 60.564 41.667 3.32 0.00 0.00 3.21
307 308 3.244146 CCATGGCCTGAATTTGAAACACA 60.244 43.478 3.32 0.00 0.00 3.72
308 309 3.244181 ACCATGGCCTGAATTTGAAACAC 60.244 43.478 13.04 0.00 0.00 3.32
309 310 2.971330 ACCATGGCCTGAATTTGAAACA 59.029 40.909 13.04 0.00 0.00 2.83
310 311 3.683365 ACCATGGCCTGAATTTGAAAC 57.317 42.857 13.04 0.00 0.00 2.78
311 312 4.703379 AAACCATGGCCTGAATTTGAAA 57.297 36.364 13.04 0.00 0.00 2.69
312 313 5.483231 TCATAAACCATGGCCTGAATTTGAA 59.517 36.000 13.04 0.00 35.16 2.69
313 314 5.022122 TCATAAACCATGGCCTGAATTTGA 58.978 37.500 13.04 1.81 35.16 2.69
314 315 5.111293 GTCATAAACCATGGCCTGAATTTG 58.889 41.667 13.04 0.00 32.76 2.32
315 316 4.776837 TGTCATAAACCATGGCCTGAATTT 59.223 37.500 13.04 6.32 38.58 1.82
316 317 4.352009 TGTCATAAACCATGGCCTGAATT 58.648 39.130 13.04 0.00 38.58 2.17
317 318 3.979911 TGTCATAAACCATGGCCTGAAT 58.020 40.909 13.04 0.00 38.58 2.57
318 319 3.448093 TGTCATAAACCATGGCCTGAA 57.552 42.857 13.04 0.00 38.58 3.02
319 320 3.289836 CATGTCATAAACCATGGCCTGA 58.710 45.455 13.04 6.85 37.12 3.86
320 321 3.025978 ACATGTCATAAACCATGGCCTG 58.974 45.455 13.04 4.35 42.15 4.85
321 322 3.025978 CACATGTCATAAACCATGGCCT 58.974 45.455 13.04 0.75 42.15 5.19
322 323 2.760092 ACACATGTCATAAACCATGGCC 59.240 45.455 13.04 0.00 42.15 5.36
323 324 4.082300 TCAACACATGTCATAAACCATGGC 60.082 41.667 13.04 0.00 42.15 4.40
324 325 5.641783 TCAACACATGTCATAAACCATGG 57.358 39.130 11.19 11.19 42.15 3.66
325 326 5.863397 GGTTCAACACATGTCATAAACCATG 59.137 40.000 18.23 0.00 43.21 3.66
326 327 5.335583 CGGTTCAACACATGTCATAAACCAT 60.336 40.000 20.93 0.00 0.00 3.55
327 328 4.023622 CGGTTCAACACATGTCATAAACCA 60.024 41.667 20.93 0.00 0.00 3.67
328 329 4.472286 CGGTTCAACACATGTCATAAACC 58.528 43.478 15.13 15.13 0.00 3.27
329 330 4.023536 ACCGGTTCAACACATGTCATAAAC 60.024 41.667 0.00 0.00 0.00 2.01
330 331 4.138290 ACCGGTTCAACACATGTCATAAA 58.862 39.130 0.00 0.00 0.00 1.40
331 332 3.745799 ACCGGTTCAACACATGTCATAA 58.254 40.909 0.00 0.00 0.00 1.90
332 333 3.410631 ACCGGTTCAACACATGTCATA 57.589 42.857 0.00 0.00 0.00 2.15
333 334 2.270352 ACCGGTTCAACACATGTCAT 57.730 45.000 0.00 0.00 0.00 3.06
334 335 2.912690 TACCGGTTCAACACATGTCA 57.087 45.000 15.04 0.00 0.00 3.58
335 336 2.418628 CCATACCGGTTCAACACATGTC 59.581 50.000 15.04 0.00 0.00 3.06
336 337 2.432444 CCATACCGGTTCAACACATGT 58.568 47.619 15.04 0.00 0.00 3.21
337 338 1.742831 CCCATACCGGTTCAACACATG 59.257 52.381 15.04 8.51 0.00 3.21
338 339 1.953311 GCCCATACCGGTTCAACACAT 60.953 52.381 15.04 0.00 0.00 3.21
339 340 0.606944 GCCCATACCGGTTCAACACA 60.607 55.000 15.04 0.00 0.00 3.72
466 467 0.740737 GGAGCAGCTGTTGTTGTGTT 59.259 50.000 16.64 0.00 0.00 3.32
805 806 0.534412 CTTCTCGCAGTGGACCTGAT 59.466 55.000 0.00 0.00 44.49 2.90
845 846 1.000283 CAACAGTCGAGAGCAGAAGGT 60.000 52.381 0.00 0.00 0.00 3.50
859 860 0.823356 AACCCGCAGCAATCAACAGT 60.823 50.000 0.00 0.00 0.00 3.55
899 900 0.469494 TCTCAACCAGCAGCAGTTCA 59.531 50.000 0.00 0.00 0.00 3.18
1720 1729 4.021544 CACAGCTTTCAGTCTAGTCTCCTT 60.022 45.833 0.00 0.00 0.00 3.36
1858 1867 2.102420 TGCCTTTGTTGTCTCTCTTCGA 59.898 45.455 0.00 0.00 0.00 3.71
1899 1908 2.863238 TCCCCTACCATCTCCTCTGTAA 59.137 50.000 0.00 0.00 0.00 2.41
2103 2112 2.622064 AGTCACCAAACACTGTCTCC 57.378 50.000 0.00 0.00 0.00 3.71
2739 2750 2.975489 CCTGAGCCCCTTACTCACATAT 59.025 50.000 0.00 0.00 39.21 1.78
3201 3215 3.264193 TCATACCCAGTATCATGGATGGC 59.736 47.826 0.00 0.00 43.57 4.40
3302 3317 3.037851 TCACAGCAGGTCTATGATCCT 57.962 47.619 0.00 0.00 33.96 3.24
3426 3441 5.370584 AGATTCCCAGAATGTCACATCCATA 59.629 40.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.