Multiple sequence alignment - TraesCS6D01G086100

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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 TraesCS6D01G086100 chr6D 100.000 3092 0 0 1 3092 51499189 51502280 0.000000e+00 5710
1 TraesCS6D01G086100 chr6D 98.404 2819 38 5 276 3092 472510963 472513776 0.000000e+00 4950
2 TraesCS6D01G086100 chr6D 79.791 287 43 11 1 275 43643300 43643583 8.750000e-46 195
3 TraesCS6D01G086100 chr7D 98.866 2823 31 1 271 3092 115100267 115103089 0.000000e+00 5035
4 TraesCS6D01G086100 chr7D 98.616 2818 36 3 276 3092 54583766 54580951 0.000000e+00 4985
5 TraesCS6D01G086100 chr7D 98.510 2818 41 1 276 3092 245402431 245399614 0.000000e+00 4970
6 TraesCS6D01G086100 chr7D 82.158 241 29 9 8 237 511655759 511655522 8.750000e-46 195
7 TraesCS6D01G086100 chr5D 98.722 2818 36 0 275 3092 260689963 260687146 0.000000e+00 5005
8 TraesCS6D01G086100 chr5D 98.722 2818 34 2 276 3092 565815802 565818618 0.000000e+00 5003
9 TraesCS6D01G086100 chr5D 98.687 2818 34 3 276 3092 75136832 75134017 0.000000e+00 4996
10 TraesCS6D01G086100 chr4D 98.740 2777 33 2 317 3092 417387796 417390571 0.000000e+00 4933
11 TraesCS6D01G086100 chr4D 98.156 2820 45 4 274 3092 164897178 164899991 0.000000e+00 4913
12 TraesCS6D01G086100 chr6B 89.324 281 24 4 1 275 118211684 118211404 6.350000e-92 348
13 TraesCS6D01G086100 chr6A 86.121 281 33 3 1 275 62122478 62122198 6.480000e-77 298
14 TraesCS6D01G086100 chr6A 92.195 205 10 2 1 199 62622885 62622681 5.050000e-73 285
15 TraesCS6D01G086100 chr1B 85.401 274 33 6 7 275 674664988 674664717 8.440000e-71 278
16 TraesCS6D01G086100 chr7A 82.079 279 38 6 7 275 584085747 584085471 8.630000e-56 228
17 TraesCS6D01G086100 chrUn 80.769 286 38 12 1 274 69024788 69025068 1.120000e-49 207
18 TraesCS6D01G086100 chr3B 79.021 286 47 7 1 275 59165683 59165966 1.890000e-42 183
19 TraesCS6D01G086100 chr2D 82.081 173 28 3 267 437 82834278 82834107 8.940000e-31 145


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 TraesCS6D01G086100 chr6D 51499189 51502280 3091 False 5710 5710 100.000 1 3092 1 chr6D.!!$F2 3091
1 TraesCS6D01G086100 chr6D 472510963 472513776 2813 False 4950 4950 98.404 276 3092 1 chr6D.!!$F3 2816
2 TraesCS6D01G086100 chr7D 115100267 115103089 2822 False 5035 5035 98.866 271 3092 1 chr7D.!!$F1 2821
3 TraesCS6D01G086100 chr7D 54580951 54583766 2815 True 4985 4985 98.616 276 3092 1 chr7D.!!$R1 2816
4 TraesCS6D01G086100 chr7D 245399614 245402431 2817 True 4970 4970 98.510 276 3092 1 chr7D.!!$R2 2816
5 TraesCS6D01G086100 chr5D 260687146 260689963 2817 True 5005 5005 98.722 275 3092 1 chr5D.!!$R2 2817
6 TraesCS6D01G086100 chr5D 565815802 565818618 2816 False 5003 5003 98.722 276 3092 1 chr5D.!!$F1 2816
7 TraesCS6D01G086100 chr5D 75134017 75136832 2815 True 4996 4996 98.687 276 3092 1 chr5D.!!$R1 2816
8 TraesCS6D01G086100 chr4D 417387796 417390571 2775 False 4933 4933 98.740 317 3092 1 chr4D.!!$F2 2775
9 TraesCS6D01G086100 chr4D 164897178 164899991 2813 False 4913 4913 98.156 274 3092 1 chr4D.!!$F1 2818

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
251 252 0.031994 AATTCCAACACCGCTTGCAC 59.968 50.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 2288 3.679389 AGTGGTTCAAATACAGGCAGAG 58.321 45.455 0.0 0.0 0.0 3.35 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
25 26 6.908825 TGACGAATTTCAAGAAATGGTTAGG 58.091 36.000 8.66 0.00 40.57 2.69
26 27 6.712998 TGACGAATTTCAAGAAATGGTTAGGA 59.287 34.615 8.66 0.00 40.57 2.94
27 28 6.909909 ACGAATTTCAAGAAATGGTTAGGAC 58.090 36.000 8.66 0.00 40.57 3.85
28 29 6.488683 ACGAATTTCAAGAAATGGTTAGGACA 59.511 34.615 8.66 0.00 40.57 4.02
29 30 7.176690 ACGAATTTCAAGAAATGGTTAGGACAT 59.823 33.333 8.66 0.00 40.57 3.06
30 31 8.673711 CGAATTTCAAGAAATGGTTAGGACATA 58.326 33.333 8.66 0.00 40.57 2.29
33 34 9.753674 ATTTCAAGAAATGGTTAGGACATAAGA 57.246 29.630 7.21 0.00 39.36 2.10
34 35 8.792830 TTCAAGAAATGGTTAGGACATAAGAG 57.207 34.615 0.00 0.00 0.00 2.85
35 36 8.146053 TCAAGAAATGGTTAGGACATAAGAGA 57.854 34.615 0.00 0.00 0.00 3.10
36 37 8.602424 TCAAGAAATGGTTAGGACATAAGAGAA 58.398 33.333 0.00 0.00 0.00 2.87
37 38 9.401058 CAAGAAATGGTTAGGACATAAGAGAAT 57.599 33.333 0.00 0.00 0.00 2.40
38 39 8.970859 AGAAATGGTTAGGACATAAGAGAATG 57.029 34.615 0.00 0.00 0.00 2.67
39 40 8.552296 AGAAATGGTTAGGACATAAGAGAATGT 58.448 33.333 0.00 0.00 42.75 2.71
40 41 9.178758 GAAATGGTTAGGACATAAGAGAATGTT 57.821 33.333 0.00 0.00 40.17 2.71
41 42 8.738645 AATGGTTAGGACATAAGAGAATGTTC 57.261 34.615 0.00 0.00 40.17 3.18
42 43 7.252612 TGGTTAGGACATAAGAGAATGTTCA 57.747 36.000 0.00 0.00 40.17 3.18
43 44 7.861629 TGGTTAGGACATAAGAGAATGTTCAT 58.138 34.615 0.00 0.00 40.17 2.57
44 45 7.770433 TGGTTAGGACATAAGAGAATGTTCATG 59.230 37.037 0.00 0.00 40.17 3.07
45 46 7.770897 GGTTAGGACATAAGAGAATGTTCATGT 59.229 37.037 0.00 0.00 40.17 3.21
46 47 9.167311 GTTAGGACATAAGAGAATGTTCATGTT 57.833 33.333 0.00 0.00 40.17 2.71
49 50 9.911788 AGGACATAAGAGAATGTTCATGTTAAT 57.088 29.630 0.00 0.00 40.17 1.40
96 97 9.476202 ACAAGCATTCAAATTAGGAAAAACTAC 57.524 29.630 0.00 0.00 0.00 2.73
97 98 9.474920 CAAGCATTCAAATTAGGAAAAACTACA 57.525 29.630 0.00 0.00 0.00 2.74
99 100 9.643693 AGCATTCAAATTAGGAAAAACTACATG 57.356 29.630 0.00 0.00 0.00 3.21
100 101 8.382875 GCATTCAAATTAGGAAAAACTACATGC 58.617 33.333 0.00 0.00 0.00 4.06
101 102 9.643693 CATTCAAATTAGGAAAAACTACATGCT 57.356 29.630 0.00 0.00 0.00 3.79
102 103 9.860898 ATTCAAATTAGGAAAAACTACATGCTC 57.139 29.630 0.00 0.00 0.00 4.26
103 104 8.402798 TCAAATTAGGAAAAACTACATGCTCA 57.597 30.769 0.00 0.00 0.00 4.26
104 105 8.296713 TCAAATTAGGAAAAACTACATGCTCAC 58.703 33.333 0.00 0.00 0.00 3.51
105 106 5.856126 TTAGGAAAAACTACATGCTCACG 57.144 39.130 0.00 0.00 0.00 4.35
106 107 3.074412 AGGAAAAACTACATGCTCACGG 58.926 45.455 0.00 0.00 0.00 4.94
107 108 3.071479 GGAAAAACTACATGCTCACGGA 58.929 45.455 0.00 0.00 0.00 4.69
108 109 3.689649 GGAAAAACTACATGCTCACGGAT 59.310 43.478 0.00 0.00 0.00 4.18
109 110 4.437390 GGAAAAACTACATGCTCACGGATG 60.437 45.833 0.00 0.00 43.76 3.51
110 111 1.656652 AACTACATGCTCACGGATGC 58.343 50.000 0.00 0.00 42.11 3.91
111 112 0.536724 ACTACATGCTCACGGATGCA 59.463 50.000 0.00 0.00 42.11 3.96
112 113 0.933097 CTACATGCTCACGGATGCAC 59.067 55.000 0.00 0.00 42.11 4.57
113 114 0.461870 TACATGCTCACGGATGCACC 60.462 55.000 0.00 0.00 42.11 5.01
114 115 1.450848 CATGCTCACGGATGCACCT 60.451 57.895 0.00 0.00 42.26 4.00
115 116 1.450848 ATGCTCACGGATGCACCTG 60.451 57.895 0.00 0.00 42.26 4.00
116 117 3.503363 GCTCACGGATGCACCTGC 61.503 66.667 0.00 0.00 42.50 4.85
117 118 2.267006 CTCACGGATGCACCTGCT 59.733 61.111 0.00 0.00 42.66 4.24
118 119 1.376424 CTCACGGATGCACCTGCTT 60.376 57.895 0.00 0.00 42.66 3.91
119 120 1.642037 CTCACGGATGCACCTGCTTG 61.642 60.000 0.00 0.00 42.66 4.01
120 121 2.360350 ACGGATGCACCTGCTTGG 60.360 61.111 0.00 0.00 42.66 3.61
121 122 2.046023 CGGATGCACCTGCTTGGA 60.046 61.111 0.00 0.00 42.66 3.53
122 123 2.401766 CGGATGCACCTGCTTGGAC 61.402 63.158 0.00 0.00 42.66 4.02
123 124 1.001641 GGATGCACCTGCTTGGACT 60.002 57.895 0.00 0.00 42.66 3.85
124 125 0.253044 GGATGCACCTGCTTGGACTA 59.747 55.000 0.00 0.00 42.66 2.59
125 126 1.661341 GATGCACCTGCTTGGACTAG 58.339 55.000 0.00 0.00 42.66 2.57
126 127 0.987294 ATGCACCTGCTTGGACTAGT 59.013 50.000 0.00 0.00 42.66 2.57
127 128 0.764890 TGCACCTGCTTGGACTAGTT 59.235 50.000 0.00 0.00 42.66 2.24
128 129 1.142870 TGCACCTGCTTGGACTAGTTT 59.857 47.619 0.00 0.00 42.66 2.66
129 130 2.370519 TGCACCTGCTTGGACTAGTTTA 59.629 45.455 0.00 0.00 42.66 2.01
130 131 2.742589 GCACCTGCTTGGACTAGTTTAC 59.257 50.000 0.00 0.00 39.71 2.01
131 132 3.335579 CACCTGCTTGGACTAGTTTACC 58.664 50.000 0.00 0.00 39.71 2.85
132 133 2.976882 ACCTGCTTGGACTAGTTTACCA 59.023 45.455 0.00 0.00 39.71 3.25
133 134 3.244457 ACCTGCTTGGACTAGTTTACCAC 60.244 47.826 0.00 0.00 39.71 4.16
134 135 3.244422 CCTGCTTGGACTAGTTTACCACA 60.244 47.826 0.00 0.00 38.35 4.17
135 136 3.735591 TGCTTGGACTAGTTTACCACAC 58.264 45.455 0.00 0.00 33.20 3.82
136 137 3.389983 TGCTTGGACTAGTTTACCACACT 59.610 43.478 0.00 0.00 33.20 3.55
137 138 3.995048 GCTTGGACTAGTTTACCACACTC 59.005 47.826 0.00 0.00 33.20 3.51
138 139 4.566987 CTTGGACTAGTTTACCACACTCC 58.433 47.826 0.00 0.00 33.20 3.85
139 140 3.853207 TGGACTAGTTTACCACACTCCT 58.147 45.455 0.00 0.00 0.00 3.69
140 141 3.830755 TGGACTAGTTTACCACACTCCTC 59.169 47.826 0.00 0.00 0.00 3.71
141 142 3.195182 GGACTAGTTTACCACACTCCTCC 59.805 52.174 0.00 0.00 0.00 4.30
142 143 3.171528 ACTAGTTTACCACACTCCTCCC 58.828 50.000 0.00 0.00 0.00 4.30
143 144 2.112279 AGTTTACCACACTCCTCCCA 57.888 50.000 0.00 0.00 0.00 4.37
144 145 2.414612 AGTTTACCACACTCCTCCCAA 58.585 47.619 0.00 0.00 0.00 4.12
145 146 2.105993 AGTTTACCACACTCCTCCCAAC 59.894 50.000 0.00 0.00 0.00 3.77
146 147 2.105993 GTTTACCACACTCCTCCCAACT 59.894 50.000 0.00 0.00 0.00 3.16
147 148 3.263369 TTACCACACTCCTCCCAACTA 57.737 47.619 0.00 0.00 0.00 2.24
148 149 1.645710 ACCACACTCCTCCCAACTAG 58.354 55.000 0.00 0.00 0.00 2.57
149 150 1.132817 ACCACACTCCTCCCAACTAGT 60.133 52.381 0.00 0.00 0.00 2.57
150 151 1.276421 CCACACTCCTCCCAACTAGTG 59.724 57.143 0.00 0.00 43.90 2.74
178 179 7.639113 TTTTGGACTATGGATAAATGACCAC 57.361 36.000 0.00 0.00 39.06 4.16
179 180 5.966853 TGGACTATGGATAAATGACCACA 57.033 39.130 0.00 0.00 39.06 4.17
180 181 6.514012 TGGACTATGGATAAATGACCACAT 57.486 37.500 0.00 0.00 39.06 3.21
181 182 6.533730 TGGACTATGGATAAATGACCACATC 58.466 40.000 0.00 0.00 39.06 3.06
182 183 6.329986 TGGACTATGGATAAATGACCACATCT 59.670 38.462 0.00 0.00 39.06 2.90
183 184 7.147320 TGGACTATGGATAAATGACCACATCTT 60.147 37.037 0.00 0.00 39.06 2.40
184 185 7.721399 GGACTATGGATAAATGACCACATCTTT 59.279 37.037 0.00 0.00 39.06 2.52
185 186 9.125026 GACTATGGATAAATGACCACATCTTTT 57.875 33.333 0.00 0.00 39.06 2.27
186 187 8.906867 ACTATGGATAAATGACCACATCTTTTG 58.093 33.333 0.00 0.00 39.06 2.44
187 188 5.964758 TGGATAAATGACCACATCTTTTGC 58.035 37.500 0.00 0.00 35.89 3.68
188 189 5.479724 TGGATAAATGACCACATCTTTTGCA 59.520 36.000 0.00 0.00 35.89 4.08
189 190 6.014755 TGGATAAATGACCACATCTTTTGCAA 60.015 34.615 0.00 0.00 35.89 4.08
190 191 6.532657 GGATAAATGACCACATCTTTTGCAAG 59.467 38.462 0.00 0.00 35.89 4.01
191 192 2.798976 TGACCACATCTTTTGCAAGC 57.201 45.000 0.00 0.00 0.00 4.01
192 193 2.030371 TGACCACATCTTTTGCAAGCA 58.970 42.857 0.00 0.00 0.00 3.91
193 194 2.034939 TGACCACATCTTTTGCAAGCAG 59.965 45.455 0.00 0.00 0.00 4.24
194 195 1.342174 ACCACATCTTTTGCAAGCAGG 59.658 47.619 0.00 0.00 0.00 4.85
195 196 1.342174 CCACATCTTTTGCAAGCAGGT 59.658 47.619 0.00 0.00 0.00 4.00
196 197 2.400399 CACATCTTTTGCAAGCAGGTG 58.600 47.619 15.94 15.94 0.00 4.00
197 198 1.342174 ACATCTTTTGCAAGCAGGTGG 59.658 47.619 19.75 8.40 0.00 4.61
198 199 0.971386 ATCTTTTGCAAGCAGGTGGG 59.029 50.000 0.00 0.00 0.00 4.61
199 200 1.301165 CTTTTGCAAGCAGGTGGGC 60.301 57.895 0.00 0.00 0.00 5.36
200 201 2.030490 CTTTTGCAAGCAGGTGGGCA 62.030 55.000 0.00 0.00 35.83 5.36
201 202 1.409251 TTTTGCAAGCAGGTGGGCAT 61.409 50.000 0.00 0.00 35.98 4.40
202 203 2.102109 TTTGCAAGCAGGTGGGCATG 62.102 55.000 0.00 0.00 35.98 4.06
222 223 3.946606 TGCCCATATGCATCTATGTCAG 58.053 45.455 0.19 0.00 36.04 3.51
223 224 3.276857 GCCCATATGCATCTATGTCAGG 58.723 50.000 0.19 0.76 0.00 3.86
224 225 3.307975 GCCCATATGCATCTATGTCAGGT 60.308 47.826 0.19 0.00 0.00 4.00
225 226 4.808665 GCCCATATGCATCTATGTCAGGTT 60.809 45.833 0.19 0.00 0.00 3.50
226 227 5.319453 CCCATATGCATCTATGTCAGGTTT 58.681 41.667 0.19 0.00 0.00 3.27
227 228 5.182570 CCCATATGCATCTATGTCAGGTTTG 59.817 44.000 0.19 0.00 0.00 2.93
228 229 5.999600 CCATATGCATCTATGTCAGGTTTGA 59.000 40.000 0.19 0.00 0.00 2.69
229 230 6.487668 CCATATGCATCTATGTCAGGTTTGAA 59.512 38.462 0.19 0.00 34.49 2.69
230 231 5.824904 ATGCATCTATGTCAGGTTTGAAC 57.175 39.130 0.00 0.00 34.49 3.18
231 232 3.684305 TGCATCTATGTCAGGTTTGAACG 59.316 43.478 0.00 0.00 34.49 3.95
232 233 3.932710 GCATCTATGTCAGGTTTGAACGA 59.067 43.478 0.00 0.00 34.49 3.85
233 234 4.391830 GCATCTATGTCAGGTTTGAACGAA 59.608 41.667 0.00 0.00 34.49 3.85
234 235 5.065218 GCATCTATGTCAGGTTTGAACGAAT 59.935 40.000 0.00 0.00 34.49 3.34
235 236 6.403636 GCATCTATGTCAGGTTTGAACGAATT 60.404 38.462 0.00 0.00 34.49 2.17
236 237 6.721571 TCTATGTCAGGTTTGAACGAATTC 57.278 37.500 0.00 0.00 34.49 2.17
237 238 4.766404 ATGTCAGGTTTGAACGAATTCC 57.234 40.909 0.00 0.00 34.49 3.01
238 239 3.546724 TGTCAGGTTTGAACGAATTCCA 58.453 40.909 0.00 0.00 34.49 3.53
239 240 3.948473 TGTCAGGTTTGAACGAATTCCAA 59.052 39.130 0.00 0.00 34.49 3.53
240 241 4.201970 TGTCAGGTTTGAACGAATTCCAAC 60.202 41.667 0.00 0.00 38.93 3.77
241 242 3.948473 TCAGGTTTGAACGAATTCCAACA 59.052 39.130 0.00 0.00 40.57 3.33
242 243 4.041723 CAGGTTTGAACGAATTCCAACAC 58.958 43.478 0.00 1.24 40.57 3.32
243 244 3.067601 AGGTTTGAACGAATTCCAACACC 59.932 43.478 0.00 8.76 40.57 4.16
244 245 3.040099 GTTTGAACGAATTCCAACACCG 58.960 45.455 0.00 0.00 39.28 4.94
245 246 0.589223 TGAACGAATTCCAACACCGC 59.411 50.000 0.00 0.00 33.49 5.68
246 247 0.872388 GAACGAATTCCAACACCGCT 59.128 50.000 0.00 0.00 0.00 5.52
247 248 1.265905 GAACGAATTCCAACACCGCTT 59.734 47.619 0.00 0.00 0.00 4.68
248 249 0.591170 ACGAATTCCAACACCGCTTG 59.409 50.000 0.00 0.00 0.00 4.01
249 250 0.729140 CGAATTCCAACACCGCTTGC 60.729 55.000 0.00 0.00 0.00 4.01
250 251 0.313672 GAATTCCAACACCGCTTGCA 59.686 50.000 0.00 0.00 0.00 4.08
251 252 0.031994 AATTCCAACACCGCTTGCAC 59.968 50.000 0.00 0.00 0.00 4.57
252 253 2.128853 ATTCCAACACCGCTTGCACG 62.129 55.000 0.00 0.00 0.00 5.34
253 254 3.582120 CCAACACCGCTTGCACGT 61.582 61.111 0.00 0.00 0.00 4.49
254 255 2.407210 CAACACCGCTTGCACGTT 59.593 55.556 0.00 0.00 0.00 3.99
255 256 1.938814 CAACACCGCTTGCACGTTG 60.939 57.895 0.00 0.00 0.00 4.10
256 257 3.749735 AACACCGCTTGCACGTTGC 62.750 57.895 0.00 3.44 45.29 4.17
268 269 4.059459 CGTTGCGACACGTCCTGC 62.059 66.667 4.64 0.00 35.34 4.85
269 270 3.712881 GTTGCGACACGTCCTGCC 61.713 66.667 0.00 0.00 0.00 4.85
270 271 4.228567 TTGCGACACGTCCTGCCA 62.229 61.111 0.00 0.00 0.00 4.92
271 272 3.529341 TTGCGACACGTCCTGCCAT 62.529 57.895 0.00 0.00 0.00 4.40
272 273 2.742372 GCGACACGTCCTGCCATT 60.742 61.111 0.00 0.00 0.00 3.16
423 424 5.177725 AGCGTTTTAAACCGTTTTCTGAT 57.822 34.783 7.01 0.00 0.00 2.90
563 564 2.365586 CCCCTGCCCTCACTCTCAG 61.366 68.421 0.00 0.00 0.00 3.35
745 747 0.892755 CACAAGCATGGACATGGCTT 59.107 50.000 13.63 13.15 39.16 4.35
762 764 5.685520 TGGCTTTTTGGGTAAGTTTTTCT 57.314 34.783 0.00 0.00 0.00 2.52
2286 2288 8.936864 AGTTATGAACTAAGTTGTAATGACTGC 58.063 33.333 0.00 0.00 40.69 4.40
2305 2307 2.224744 TGCTCTGCCTGTATTTGAACCA 60.225 45.455 0.00 0.00 0.00 3.67
2462 2464 1.080354 CTCCACCCACCCTCCACTA 59.920 63.158 0.00 0.00 0.00 2.74
2760 2762 1.842562 CAGGGAAGATCATCAGGTGGT 59.157 52.381 0.00 0.00 0.00 4.16
2811 2813 2.079925 CTTCTACCAGAGCAAAGTGGC 58.920 52.381 0.00 0.00 37.34 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.229707 TCCTAACCATTTCTTGAAATTCGTCAA 59.770 33.333 5.92 0.00 36.15 3.18
2 3 7.021790 GTCCTAACCATTTCTTGAAATTCGTC 58.978 38.462 5.92 0.00 0.00 4.20
3 4 6.488683 TGTCCTAACCATTTCTTGAAATTCGT 59.511 34.615 5.92 3.58 0.00 3.85
4 5 6.908825 TGTCCTAACCATTTCTTGAAATTCG 58.091 36.000 5.92 3.04 0.00 3.34
7 8 9.753674 TCTTATGTCCTAACCATTTCTTGAAAT 57.246 29.630 3.04 3.04 0.00 2.17
8 9 9.231297 CTCTTATGTCCTAACCATTTCTTGAAA 57.769 33.333 0.00 0.00 0.00 2.69
9 10 8.602424 TCTCTTATGTCCTAACCATTTCTTGAA 58.398 33.333 0.00 0.00 0.00 2.69
10 11 8.146053 TCTCTTATGTCCTAACCATTTCTTGA 57.854 34.615 0.00 0.00 0.00 3.02
11 12 8.792830 TTCTCTTATGTCCTAACCATTTCTTG 57.207 34.615 0.00 0.00 0.00 3.02
12 13 9.401058 CATTCTCTTATGTCCTAACCATTTCTT 57.599 33.333 0.00 0.00 0.00 2.52
13 14 8.552296 ACATTCTCTTATGTCCTAACCATTTCT 58.448 33.333 0.00 0.00 33.58 2.52
14 15 8.738645 ACATTCTCTTATGTCCTAACCATTTC 57.261 34.615 0.00 0.00 33.58 2.17
15 16 9.178758 GAACATTCTCTTATGTCCTAACCATTT 57.821 33.333 0.00 0.00 37.76 2.32
16 17 8.328758 TGAACATTCTCTTATGTCCTAACCATT 58.671 33.333 0.00 0.00 37.76 3.16
17 18 7.861629 TGAACATTCTCTTATGTCCTAACCAT 58.138 34.615 0.00 0.00 37.76 3.55
18 19 7.252612 TGAACATTCTCTTATGTCCTAACCA 57.747 36.000 0.00 0.00 37.76 3.67
19 20 7.770897 ACATGAACATTCTCTTATGTCCTAACC 59.229 37.037 0.00 0.00 37.76 2.85
20 21 8.723942 ACATGAACATTCTCTTATGTCCTAAC 57.276 34.615 0.00 0.00 37.76 2.34
23 24 9.911788 ATTAACATGAACATTCTCTTATGTCCT 57.088 29.630 0.00 0.00 37.76 3.85
70 71 9.476202 GTAGTTTTTCCTAATTTGAATGCTTGT 57.524 29.630 0.00 0.00 0.00 3.16
71 72 9.474920 TGTAGTTTTTCCTAATTTGAATGCTTG 57.525 29.630 0.00 0.00 0.00 4.01
73 74 9.643693 CATGTAGTTTTTCCTAATTTGAATGCT 57.356 29.630 0.00 0.00 0.00 3.79
74 75 8.382875 GCATGTAGTTTTTCCTAATTTGAATGC 58.617 33.333 0.00 0.00 0.00 3.56
75 76 9.643693 AGCATGTAGTTTTTCCTAATTTGAATG 57.356 29.630 0.00 0.00 0.00 2.67
76 77 9.860898 GAGCATGTAGTTTTTCCTAATTTGAAT 57.139 29.630 0.00 0.00 0.00 2.57
77 78 8.855110 TGAGCATGTAGTTTTTCCTAATTTGAA 58.145 29.630 0.00 0.00 0.00 2.69
78 79 8.296713 GTGAGCATGTAGTTTTTCCTAATTTGA 58.703 33.333 0.00 0.00 0.00 2.69
79 80 7.271223 CGTGAGCATGTAGTTTTTCCTAATTTG 59.729 37.037 0.00 0.00 0.00 2.32
80 81 7.305474 CGTGAGCATGTAGTTTTTCCTAATTT 58.695 34.615 0.00 0.00 0.00 1.82
81 82 6.128007 CCGTGAGCATGTAGTTTTTCCTAATT 60.128 38.462 0.00 0.00 0.00 1.40
82 83 5.354234 CCGTGAGCATGTAGTTTTTCCTAAT 59.646 40.000 0.00 0.00 0.00 1.73
83 84 4.693566 CCGTGAGCATGTAGTTTTTCCTAA 59.306 41.667 0.00 0.00 0.00 2.69
84 85 4.020928 TCCGTGAGCATGTAGTTTTTCCTA 60.021 41.667 0.00 0.00 0.00 2.94
85 86 3.074412 CCGTGAGCATGTAGTTTTTCCT 58.926 45.455 0.00 0.00 0.00 3.36
86 87 3.071479 TCCGTGAGCATGTAGTTTTTCC 58.929 45.455 0.00 0.00 0.00 3.13
87 88 4.651994 CATCCGTGAGCATGTAGTTTTTC 58.348 43.478 0.00 0.00 0.00 2.29
88 89 3.119849 GCATCCGTGAGCATGTAGTTTTT 60.120 43.478 0.00 0.00 0.00 1.94
89 90 2.420022 GCATCCGTGAGCATGTAGTTTT 59.580 45.455 0.00 0.00 0.00 2.43
90 91 2.009774 GCATCCGTGAGCATGTAGTTT 58.990 47.619 0.00 0.00 0.00 2.66
91 92 1.066215 TGCATCCGTGAGCATGTAGTT 60.066 47.619 0.00 0.00 35.51 2.24
92 93 0.536724 TGCATCCGTGAGCATGTAGT 59.463 50.000 0.00 0.00 35.51 2.73
93 94 0.933097 GTGCATCCGTGAGCATGTAG 59.067 55.000 0.00 0.00 43.44 2.74
94 95 0.461870 GGTGCATCCGTGAGCATGTA 60.462 55.000 0.00 0.00 43.44 2.29
95 96 1.746615 GGTGCATCCGTGAGCATGT 60.747 57.895 0.00 0.00 43.44 3.21
96 97 1.450848 AGGTGCATCCGTGAGCATG 60.451 57.895 0.00 0.00 43.44 4.06
97 98 1.450848 CAGGTGCATCCGTGAGCAT 60.451 57.895 0.00 0.00 43.44 3.79
98 99 2.046988 CAGGTGCATCCGTGAGCA 60.047 61.111 0.00 0.00 41.99 4.26
99 100 3.503363 GCAGGTGCATCCGTGAGC 61.503 66.667 0.00 0.00 41.99 4.26
100 101 1.376424 AAGCAGGTGCATCCGTGAG 60.376 57.895 4.48 0.00 45.16 3.51
101 102 1.672030 CAAGCAGGTGCATCCGTGA 60.672 57.895 4.48 0.00 45.16 4.35
102 103 2.693762 CCAAGCAGGTGCATCCGTG 61.694 63.158 4.48 0.00 45.16 4.94
103 104 2.360350 CCAAGCAGGTGCATCCGT 60.360 61.111 4.48 0.00 45.16 4.69
104 105 2.046023 TCCAAGCAGGTGCATCCG 60.046 61.111 4.48 0.00 45.16 4.18
105 106 0.253044 TAGTCCAAGCAGGTGCATCC 59.747 55.000 4.48 0.00 45.16 3.51
106 107 1.065854 ACTAGTCCAAGCAGGTGCATC 60.066 52.381 4.48 0.00 45.16 3.91
107 108 0.987294 ACTAGTCCAAGCAGGTGCAT 59.013 50.000 4.48 0.00 45.16 3.96
108 109 0.764890 AACTAGTCCAAGCAGGTGCA 59.235 50.000 4.48 0.00 45.16 4.57
109 110 1.897560 AAACTAGTCCAAGCAGGTGC 58.102 50.000 0.00 0.00 42.49 5.01
110 111 3.244422 TGGTAAACTAGTCCAAGCAGGTG 60.244 47.826 0.00 0.00 39.02 4.00
111 112 2.976882 TGGTAAACTAGTCCAAGCAGGT 59.023 45.455 0.00 0.00 39.02 4.00
112 113 3.244422 TGTGGTAAACTAGTCCAAGCAGG 60.244 47.826 3.46 0.00 39.47 4.85
113 114 3.746492 GTGTGGTAAACTAGTCCAAGCAG 59.254 47.826 3.46 0.00 32.82 4.24
114 115 3.389983 AGTGTGGTAAACTAGTCCAAGCA 59.610 43.478 3.46 2.22 32.82 3.91
115 116 3.995048 GAGTGTGGTAAACTAGTCCAAGC 59.005 47.826 3.46 0.00 32.82 4.01
116 117 4.283722 AGGAGTGTGGTAAACTAGTCCAAG 59.716 45.833 3.46 0.00 34.42 3.61
117 118 4.228824 AGGAGTGTGGTAAACTAGTCCAA 58.771 43.478 3.46 0.00 34.42 3.53
118 119 3.830755 GAGGAGTGTGGTAAACTAGTCCA 59.169 47.826 0.00 0.00 34.42 4.02
119 120 3.195182 GGAGGAGTGTGGTAAACTAGTCC 59.805 52.174 0.00 0.00 33.21 3.85
120 121 3.195182 GGGAGGAGTGTGGTAAACTAGTC 59.805 52.174 0.00 0.00 0.00 2.59
121 122 3.171528 GGGAGGAGTGTGGTAAACTAGT 58.828 50.000 0.00 0.00 0.00 2.57
122 123 3.170717 TGGGAGGAGTGTGGTAAACTAG 58.829 50.000 0.00 0.00 0.00 2.57
123 124 3.263369 TGGGAGGAGTGTGGTAAACTA 57.737 47.619 0.00 0.00 0.00 2.24
124 125 2.105993 GTTGGGAGGAGTGTGGTAAACT 59.894 50.000 0.00 0.00 0.00 2.66
125 126 2.105993 AGTTGGGAGGAGTGTGGTAAAC 59.894 50.000 0.00 0.00 0.00 2.01
126 127 2.414612 AGTTGGGAGGAGTGTGGTAAA 58.585 47.619 0.00 0.00 0.00 2.01
127 128 2.112279 AGTTGGGAGGAGTGTGGTAA 57.888 50.000 0.00 0.00 0.00 2.85
128 129 2.111255 ACTAGTTGGGAGGAGTGTGGTA 59.889 50.000 0.00 0.00 0.00 3.25
129 130 1.132817 ACTAGTTGGGAGGAGTGTGGT 60.133 52.381 0.00 0.00 0.00 4.16
130 131 1.276421 CACTAGTTGGGAGGAGTGTGG 59.724 57.143 0.00 0.00 35.61 4.17
131 132 1.276421 CCACTAGTTGGGAGGAGTGTG 59.724 57.143 0.00 0.00 42.54 3.82
132 133 1.645710 CCACTAGTTGGGAGGAGTGT 58.354 55.000 0.00 0.00 42.54 3.55
153 154 7.671819 TGTGGTCATTTATCCATAGTCCAAAAA 59.328 33.333 0.00 0.00 36.09 1.94
154 155 7.178573 TGTGGTCATTTATCCATAGTCCAAAA 58.821 34.615 0.00 0.00 36.09 2.44
155 156 6.726379 TGTGGTCATTTATCCATAGTCCAAA 58.274 36.000 0.00 0.00 36.09 3.28
156 157 6.320434 TGTGGTCATTTATCCATAGTCCAA 57.680 37.500 0.00 0.00 36.09 3.53
157 158 5.966853 TGTGGTCATTTATCCATAGTCCA 57.033 39.130 0.00 0.00 36.09 4.02
158 159 6.773638 AGATGTGGTCATTTATCCATAGTCC 58.226 40.000 0.00 0.00 36.09 3.85
159 160 8.682936 AAAGATGTGGTCATTTATCCATAGTC 57.317 34.615 0.00 0.00 36.09 2.59
160 161 8.906867 CAAAAGATGTGGTCATTTATCCATAGT 58.093 33.333 0.00 0.00 36.09 2.12
161 162 7.864379 GCAAAAGATGTGGTCATTTATCCATAG 59.136 37.037 0.00 0.00 36.09 2.23
162 163 7.341512 TGCAAAAGATGTGGTCATTTATCCATA 59.658 33.333 0.00 0.00 36.09 2.74
163 164 6.154877 TGCAAAAGATGTGGTCATTTATCCAT 59.845 34.615 0.00 0.00 36.09 3.41
164 165 5.479724 TGCAAAAGATGTGGTCATTTATCCA 59.520 36.000 0.00 0.00 34.06 3.41
165 166 5.964758 TGCAAAAGATGTGGTCATTTATCC 58.035 37.500 0.00 0.00 34.06 2.59
166 167 6.035327 GCTTGCAAAAGATGTGGTCATTTATC 59.965 38.462 0.00 0.00 34.06 1.75
167 168 5.870978 GCTTGCAAAAGATGTGGTCATTTAT 59.129 36.000 0.00 0.00 34.06 1.40
168 169 5.221402 TGCTTGCAAAAGATGTGGTCATTTA 60.221 36.000 0.00 0.00 34.06 1.40
169 170 4.060205 GCTTGCAAAAGATGTGGTCATTT 58.940 39.130 0.00 0.00 34.06 2.32
170 171 3.069872 TGCTTGCAAAAGATGTGGTCATT 59.930 39.130 0.00 0.00 34.06 2.57
171 172 2.629137 TGCTTGCAAAAGATGTGGTCAT 59.371 40.909 0.00 0.00 36.95 3.06
172 173 2.030371 TGCTTGCAAAAGATGTGGTCA 58.970 42.857 0.00 0.00 0.00 4.02
173 174 2.608752 CCTGCTTGCAAAAGATGTGGTC 60.609 50.000 0.00 0.00 0.00 4.02
174 175 1.342174 CCTGCTTGCAAAAGATGTGGT 59.658 47.619 0.00 0.00 0.00 4.16
175 176 1.342174 ACCTGCTTGCAAAAGATGTGG 59.658 47.619 0.00 0.00 0.00 4.17
176 177 2.400399 CACCTGCTTGCAAAAGATGTG 58.600 47.619 0.00 1.14 0.00 3.21
177 178 1.342174 CCACCTGCTTGCAAAAGATGT 59.658 47.619 0.00 0.00 0.00 3.06
178 179 1.337447 CCCACCTGCTTGCAAAAGATG 60.337 52.381 0.00 0.00 0.00 2.90
179 180 0.971386 CCCACCTGCTTGCAAAAGAT 59.029 50.000 0.00 0.00 0.00 2.40
180 181 1.747325 GCCCACCTGCTTGCAAAAGA 61.747 55.000 0.00 0.00 0.00 2.52
181 182 1.301165 GCCCACCTGCTTGCAAAAG 60.301 57.895 0.00 0.89 0.00 2.27
182 183 1.409251 ATGCCCACCTGCTTGCAAAA 61.409 50.000 0.00 0.00 37.27 2.44
183 184 1.837947 ATGCCCACCTGCTTGCAAA 60.838 52.632 0.00 0.00 37.27 3.68
184 185 2.203669 ATGCCCACCTGCTTGCAA 60.204 55.556 0.00 0.00 37.27 4.08
185 186 2.992689 CATGCCCACCTGCTTGCA 60.993 61.111 0.00 0.00 38.23 4.08
187 188 3.766691 GGCATGCCCACCTGCTTG 61.767 66.667 27.24 0.00 38.45 4.01
202 203 3.276857 CCTGACATAGATGCATATGGGC 58.723 50.000 12.87 4.39 37.45 5.36
203 204 4.564782 ACCTGACATAGATGCATATGGG 57.435 45.455 12.87 7.69 37.45 4.00
204 205 5.999600 TCAAACCTGACATAGATGCATATGG 59.000 40.000 12.87 3.44 37.45 2.74
205 206 7.358066 GTTCAAACCTGACATAGATGCATATG 58.642 38.462 3.54 5.99 38.79 1.78
206 207 6.203530 CGTTCAAACCTGACATAGATGCATAT 59.796 38.462 0.00 0.00 0.00 1.78
207 208 5.523552 CGTTCAAACCTGACATAGATGCATA 59.476 40.000 0.00 0.00 0.00 3.14
208 209 4.333649 CGTTCAAACCTGACATAGATGCAT 59.666 41.667 0.00 0.00 0.00 3.96
209 210 3.684305 CGTTCAAACCTGACATAGATGCA 59.316 43.478 0.00 0.00 0.00 3.96
210 211 3.932710 TCGTTCAAACCTGACATAGATGC 59.067 43.478 0.00 0.00 0.00 3.91
211 212 6.668541 ATTCGTTCAAACCTGACATAGATG 57.331 37.500 0.00 0.00 0.00 2.90
212 213 6.316390 GGAATTCGTTCAAACCTGACATAGAT 59.684 38.462 0.00 0.00 0.00 1.98
213 214 5.642063 GGAATTCGTTCAAACCTGACATAGA 59.358 40.000 0.00 0.00 0.00 1.98
214 215 5.411361 TGGAATTCGTTCAAACCTGACATAG 59.589 40.000 0.00 0.00 0.00 2.23
215 216 5.309638 TGGAATTCGTTCAAACCTGACATA 58.690 37.500 0.00 0.00 0.00 2.29
216 217 4.141287 TGGAATTCGTTCAAACCTGACAT 58.859 39.130 0.00 0.00 0.00 3.06
217 218 3.546724 TGGAATTCGTTCAAACCTGACA 58.453 40.909 0.00 0.00 0.00 3.58
218 219 4.201970 TGTTGGAATTCGTTCAAACCTGAC 60.202 41.667 0.00 0.00 34.69 3.51
219 220 3.948473 TGTTGGAATTCGTTCAAACCTGA 59.052 39.130 0.00 0.00 34.69 3.86
220 221 4.041723 GTGTTGGAATTCGTTCAAACCTG 58.958 43.478 0.00 0.00 34.69 4.00
221 222 3.067601 GGTGTTGGAATTCGTTCAAACCT 59.932 43.478 0.00 0.00 34.69 3.50
222 223 3.377439 GGTGTTGGAATTCGTTCAAACC 58.623 45.455 0.00 5.73 34.69 3.27
223 224 3.040099 CGGTGTTGGAATTCGTTCAAAC 58.960 45.455 0.00 2.26 35.84 2.93
224 225 2.541999 GCGGTGTTGGAATTCGTTCAAA 60.542 45.455 0.00 0.00 0.00 2.69
225 226 1.002251 GCGGTGTTGGAATTCGTTCAA 60.002 47.619 0.00 0.00 0.00 2.69
226 227 0.589223 GCGGTGTTGGAATTCGTTCA 59.411 50.000 0.00 0.00 0.00 3.18
227 228 0.872388 AGCGGTGTTGGAATTCGTTC 59.128 50.000 0.00 0.00 0.00 3.95
228 229 1.001815 CAAGCGGTGTTGGAATTCGTT 60.002 47.619 0.00 0.00 0.00 3.85
229 230 0.591170 CAAGCGGTGTTGGAATTCGT 59.409 50.000 0.00 0.00 0.00 3.85
230 231 0.729140 GCAAGCGGTGTTGGAATTCG 60.729 55.000 0.00 0.00 0.00 3.34
231 232 0.313672 TGCAAGCGGTGTTGGAATTC 59.686 50.000 0.00 0.00 0.00 2.17
232 233 0.031994 GTGCAAGCGGTGTTGGAATT 59.968 50.000 0.00 0.00 28.58 2.17
233 234 1.659794 GTGCAAGCGGTGTTGGAAT 59.340 52.632 0.00 0.00 28.58 3.01
234 235 2.829206 CGTGCAAGCGGTGTTGGAA 61.829 57.895 0.00 0.00 28.58 3.53
235 236 3.276091 CGTGCAAGCGGTGTTGGA 61.276 61.111 0.00 0.00 0.00 3.53
236 237 3.119709 AACGTGCAAGCGGTGTTGG 62.120 57.895 0.00 0.00 35.98 3.77
237 238 1.938814 CAACGTGCAAGCGGTGTTG 60.939 57.895 6.59 8.66 43.76 3.33
238 239 2.407210 CAACGTGCAAGCGGTGTT 59.593 55.556 6.59 0.00 43.76 3.32
244 245 2.722188 GTGTCGCAACGTGCAAGC 60.722 61.111 0.00 0.00 45.36 4.01
245 246 2.423517 CGTGTCGCAACGTGCAAG 60.424 61.111 0.00 0.00 45.36 4.01
252 253 3.712881 GGCAGGACGTGTCGCAAC 61.713 66.667 0.00 0.00 0.00 4.17
253 254 3.529341 ATGGCAGGACGTGTCGCAA 62.529 57.895 0.00 0.00 31.02 4.85
254 255 3.529341 AATGGCAGGACGTGTCGCA 62.529 57.895 0.00 0.00 31.02 5.10
255 256 1.017177 TAAATGGCAGGACGTGTCGC 61.017 55.000 0.00 0.00 31.02 5.19
256 257 0.999406 CTAAATGGCAGGACGTGTCG 59.001 55.000 0.00 0.00 31.02 4.35
257 258 2.271800 CTCTAAATGGCAGGACGTGTC 58.728 52.381 0.00 0.00 0.00 3.67
258 259 1.623811 ACTCTAAATGGCAGGACGTGT 59.376 47.619 0.00 0.00 0.00 4.49
259 260 2.386661 ACTCTAAATGGCAGGACGTG 57.613 50.000 0.00 0.00 0.00 4.49
260 261 4.546829 TTTACTCTAAATGGCAGGACGT 57.453 40.909 0.00 0.00 0.00 4.34
261 262 6.771188 CTATTTACTCTAAATGGCAGGACG 57.229 41.667 0.00 0.00 38.70 4.79
745 747 7.504238 TCAGCAGATAGAAAAACTTACCCAAAA 59.496 33.333 0.00 0.00 0.00 2.44
762 764 3.501349 CCTAACCCTAGCTCAGCAGATA 58.499 50.000 0.00 0.00 0.00 1.98
2286 2288 3.679389 AGTGGTTCAAATACAGGCAGAG 58.321 45.455 0.00 0.00 0.00 3.35
2305 2307 5.423610 ACTGACTCCATAACATAGCAGAAGT 59.576 40.000 0.00 0.00 0.00 3.01
2462 2464 4.593634 GGGTGGAGTAGGCTATTTATGAGT 59.406 45.833 0.00 0.00 0.00 3.41
2708 2710 2.359975 CCGCCAGGGACAAGAACC 60.360 66.667 0.00 0.00 38.47 3.62
2760 2762 2.420269 CGAGTACTGCCTGTCTCCTAGA 60.420 54.545 0.00 0.00 0.00 2.43
2811 2813 2.037873 CGTAACGATCGAAGAAACGACG 60.038 50.000 24.34 13.78 44.84 5.12


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

AutoCloner maintained by Alex Coulton.