Multiple sequence alignment - TraesCS7A01G393500

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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 TraesCS7A01G393500 chr7A 100.000 2378 0 0 1 2378 571647837 571650214 0.000000e+00 4392
1 TraesCS7A01G393500 chr4D 95.887 2188 82 4 193 2378 483696953 483699134 0.000000e+00 3535
2 TraesCS7A01G393500 chr4D 95.107 2187 101 5 193 2378 135005627 135003446 0.000000e+00 3441
3 TraesCS7A01G393500 chr4D 94.648 2186 112 4 194 2378 241142650 241140469 0.000000e+00 3384
4 TraesCS7A01G393500 chr5D 94.239 2187 121 4 193 2378 79865849 79868031 0.000000e+00 3336
5 TraesCS7A01G393500 chr5D 93.004 2187 142 9 193 2378 197839304 197837128 0.000000e+00 3181
6 TraesCS7A01G393500 chr5D 96.954 197 5 1 1 196 88953255 88953059 1.760000e-86 329
7 TraesCS7A01G393500 chr5D 96.447 197 6 1 1 196 436527390 436527586 8.200000e-85 324
8 TraesCS7A01G393500 chr1B 93.827 2187 119 6 193 2378 286167194 286169365 0.000000e+00 3277
9 TraesCS7A01G393500 chr1B 94.013 2021 118 3 359 2378 286025634 286023616 0.000000e+00 3059
10 TraesCS7A01G393500 chr6B 94.774 1435 67 3 193 1627 53079609 53081035 0.000000e+00 2228
11 TraesCS7A01G393500 chr3A 96.092 1305 51 0 193 1497 191856143 191857447 0.000000e+00 2128
12 TraesCS7A01G393500 chr1D 96.458 1214 41 2 1165 2378 185763599 185764810 0.000000e+00 2002
13 TraesCS7A01G393500 chr2A 96.851 921 25 2 1460 2378 735187105 735188023 0.000000e+00 1537
14 TraesCS7A01G393500 chr3D 96.954 197 4 2 1 195 312667192 312667388 1.760000e-86 329
15 TraesCS7A01G393500 chr3D 96.482 199 6 1 1 198 325752728 325752530 6.340000e-86 327
16 TraesCS7A01G393500 chr2D 96.954 197 5 1 1 196 75072656 75072460 1.760000e-86 329
17 TraesCS7A01G393500 chr2D 95.146 206 9 1 1 205 396569350 396569555 8.200000e-85 324
18 TraesCS7A01G393500 chr2D 94.686 207 10 1 1 206 112801752 112801958 1.060000e-83 320
19 TraesCS7A01G393500 chr6D 96.020 201 5 3 1 198 218295428 218295628 8.200000e-85 324
20 TraesCS7A01G393500 chr6D 95.960 198 7 1 1 197 293479891 293480088 1.060000e-83 320


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 TraesCS7A01G393500 chr7A 571647837 571650214 2377 False 4392 4392 100.000 1 2378 1 chr7A.!!$F1 2377
1 TraesCS7A01G393500 chr4D 483696953 483699134 2181 False 3535 3535 95.887 193 2378 1 chr4D.!!$F1 2185
2 TraesCS7A01G393500 chr4D 135003446 135005627 2181 True 3441 3441 95.107 193 2378 1 chr4D.!!$R1 2185
3 TraesCS7A01G393500 chr4D 241140469 241142650 2181 True 3384 3384 94.648 194 2378 1 chr4D.!!$R2 2184
4 TraesCS7A01G393500 chr5D 79865849 79868031 2182 False 3336 3336 94.239 193 2378 1 chr5D.!!$F1 2185
5 TraesCS7A01G393500 chr5D 197837128 197839304 2176 True 3181 3181 93.004 193 2378 1 chr5D.!!$R2 2185
6 TraesCS7A01G393500 chr1B 286167194 286169365 2171 False 3277 3277 93.827 193 2378 1 chr1B.!!$F1 2185
7 TraesCS7A01G393500 chr1B 286023616 286025634 2018 True 3059 3059 94.013 359 2378 1 chr1B.!!$R1 2019
8 TraesCS7A01G393500 chr6B 53079609 53081035 1426 False 2228 2228 94.774 193 1627 1 chr6B.!!$F1 1434
9 TraesCS7A01G393500 chr3A 191856143 191857447 1304 False 2128 2128 96.092 193 1497 1 chr3A.!!$F1 1304
10 TraesCS7A01G393500 chr1D 185763599 185764810 1211 False 2002 2002 96.458 1165 2378 1 chr1D.!!$F1 1213
11 TraesCS7A01G393500 chr2A 735187105 735188023 918 False 1537 1537 96.851 1460 2378 1 chr2A.!!$F1 918

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
137 138 0.036294 GCCTCCTATTACCATCCGCC 60.036 60.0 0.0 0.0 0.0 6.13 F
145 146 0.103572 TTACCATCCGCCTTAGACGC 59.896 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1064 1070 1.408822 GGGGACATTGATCCGAAGCTT 60.409 52.381 0.0 0.0 39.97 3.74 R
1663 1670 2.224523 CGGCAAGGGAAATATCTGGCTA 60.225 50.000 0.0 0.0 0.00 3.93 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
27 28 4.703645 TCTCGTGGTAGATCAACTCTTG 57.296 45.455 0.00 0.00 35.28 3.02
28 29 4.079970 TCTCGTGGTAGATCAACTCTTGT 58.920 43.478 0.00 0.00 35.28 3.16
29 30 5.250982 TCTCGTGGTAGATCAACTCTTGTA 58.749 41.667 0.00 0.00 35.28 2.41
30 31 5.708697 TCTCGTGGTAGATCAACTCTTGTAA 59.291 40.000 0.00 0.00 35.28 2.41
31 32 6.377429 TCTCGTGGTAGATCAACTCTTGTAAT 59.623 38.462 0.00 0.00 35.28 1.89
32 33 7.555195 TCTCGTGGTAGATCAACTCTTGTAATA 59.445 37.037 0.00 0.00 35.28 0.98
33 34 7.478322 TCGTGGTAGATCAACTCTTGTAATAC 58.522 38.462 0.00 0.00 35.28 1.89
34 35 7.338703 TCGTGGTAGATCAACTCTTGTAATACT 59.661 37.037 0.00 0.00 35.28 2.12
35 36 7.644551 CGTGGTAGATCAACTCTTGTAATACTC 59.355 40.741 0.00 0.00 35.28 2.59
36 37 8.467598 GTGGTAGATCAACTCTTGTAATACTCA 58.532 37.037 0.00 0.00 35.28 3.41
37 38 9.201989 TGGTAGATCAACTCTTGTAATACTCAT 57.798 33.333 0.00 0.00 35.28 2.90
58 59 9.676861 ACTCATATCATCAAGTTCAATCAAGAA 57.323 29.630 0.00 0.00 0.00 2.52
60 61 9.117183 TCATATCATCAAGTTCAATCAAGAAGG 57.883 33.333 0.00 0.00 0.00 3.46
61 62 9.117183 CATATCATCAAGTTCAATCAAGAAGGA 57.883 33.333 0.00 0.00 0.00 3.36
62 63 9.690913 ATATCATCAAGTTCAATCAAGAAGGAA 57.309 29.630 0.00 0.00 0.00 3.36
63 64 7.444629 TCATCAAGTTCAATCAAGAAGGAAG 57.555 36.000 0.00 0.00 0.00 3.46
64 65 7.000472 TCATCAAGTTCAATCAAGAAGGAAGT 59.000 34.615 0.00 0.00 0.00 3.01
65 66 8.156820 TCATCAAGTTCAATCAAGAAGGAAGTA 58.843 33.333 0.00 0.00 0.00 2.24
66 67 7.969536 TCAAGTTCAATCAAGAAGGAAGTAG 57.030 36.000 0.00 0.00 0.00 2.57
67 68 7.735917 TCAAGTTCAATCAAGAAGGAAGTAGA 58.264 34.615 0.00 0.00 0.00 2.59
68 69 7.875041 TCAAGTTCAATCAAGAAGGAAGTAGAG 59.125 37.037 0.00 0.00 0.00 2.43
69 70 7.309770 AGTTCAATCAAGAAGGAAGTAGAGT 57.690 36.000 0.00 0.00 0.00 3.24
70 71 8.423906 AGTTCAATCAAGAAGGAAGTAGAGTA 57.576 34.615 0.00 0.00 0.00 2.59
71 72 9.041354 AGTTCAATCAAGAAGGAAGTAGAGTAT 57.959 33.333 0.00 0.00 0.00 2.12
72 73 9.660180 GTTCAATCAAGAAGGAAGTAGAGTATT 57.340 33.333 0.00 0.00 0.00 1.89
75 76 9.535878 CAATCAAGAAGGAAGTAGAGTATTACC 57.464 37.037 0.00 0.00 0.00 2.85
76 77 9.495382 AATCAAGAAGGAAGTAGAGTATTACCT 57.505 33.333 0.00 0.00 0.00 3.08
77 78 8.522542 TCAAGAAGGAAGTAGAGTATTACCTC 57.477 38.462 0.00 0.00 0.00 3.85
78 79 7.560626 TCAAGAAGGAAGTAGAGTATTACCTCC 59.439 40.741 0.00 0.00 35.33 4.30
79 80 6.982899 AGAAGGAAGTAGAGTATTACCTCCA 58.017 40.000 4.23 0.00 36.85 3.86
80 81 7.597327 AGAAGGAAGTAGAGTATTACCTCCAT 58.403 38.462 4.23 0.00 36.85 3.41
81 82 7.726738 AGAAGGAAGTAGAGTATTACCTCCATC 59.273 40.741 4.23 2.15 36.85 3.51
82 83 6.005198 AGGAAGTAGAGTATTACCTCCATCG 58.995 44.000 4.23 0.00 36.85 3.84
83 84 6.002704 GGAAGTAGAGTATTACCTCCATCGA 58.997 44.000 0.00 0.00 35.25 3.59
84 85 6.149807 GGAAGTAGAGTATTACCTCCATCGAG 59.850 46.154 0.00 0.00 35.25 4.04
85 86 6.436738 AGTAGAGTATTACCTCCATCGAGA 57.563 41.667 0.00 0.00 38.52 4.04
86 87 6.469410 AGTAGAGTATTACCTCCATCGAGAG 58.531 44.000 0.00 0.00 38.52 3.20
92 93 3.610669 CTCCATCGAGAGGGCCCG 61.611 72.222 18.44 4.06 38.52 6.13
93 94 4.137615 TCCATCGAGAGGGCCCGA 62.138 66.667 18.44 10.63 39.25 5.14
94 95 3.154473 CCATCGAGAGGGCCCGAA 61.154 66.667 18.44 1.01 38.36 4.30
95 96 2.107141 CATCGAGAGGGCCCGAAC 59.893 66.667 18.44 12.45 38.36 3.95
96 97 3.155167 ATCGAGAGGGCCCGAACC 61.155 66.667 18.44 7.31 38.36 3.62
97 98 3.680920 ATCGAGAGGGCCCGAACCT 62.681 63.158 18.44 12.55 42.18 3.50
98 99 4.148825 CGAGAGGGCCCGAACCTG 62.149 72.222 18.44 1.23 38.79 4.00
99 100 3.787001 GAGAGGGCCCGAACCTGG 61.787 72.222 18.44 0.00 38.79 4.45
107 108 3.970205 CCCGAACCTGGGTAAACAT 57.030 52.632 0.00 0.00 44.76 2.71
108 109 2.209690 CCCGAACCTGGGTAAACATT 57.790 50.000 0.00 0.00 44.76 2.71
109 110 1.816224 CCCGAACCTGGGTAAACATTG 59.184 52.381 0.00 0.00 44.76 2.82
110 111 2.510613 CCGAACCTGGGTAAACATTGT 58.489 47.619 0.00 0.00 0.00 2.71
111 112 2.227865 CCGAACCTGGGTAAACATTGTG 59.772 50.000 0.00 0.00 0.00 3.33
112 113 2.882137 CGAACCTGGGTAAACATTGTGT 59.118 45.455 0.00 0.00 0.00 3.72
113 114 3.058501 CGAACCTGGGTAAACATTGTGTC 60.059 47.826 0.00 0.00 0.00 3.67
114 115 2.871453 ACCTGGGTAAACATTGTGTCC 58.129 47.619 0.00 0.00 0.00 4.02
115 116 2.167662 CCTGGGTAAACATTGTGTCCC 58.832 52.381 13.79 13.79 35.85 4.46
116 117 2.167662 CTGGGTAAACATTGTGTCCCC 58.832 52.381 16.40 10.25 34.88 4.81
117 118 1.203075 TGGGTAAACATTGTGTCCCCC 60.203 52.381 5.22 6.45 33.96 5.40
118 119 1.170442 GGTAAACATTGTGTCCCCCG 58.830 55.000 0.00 0.00 0.00 5.73
119 120 0.524414 GTAAACATTGTGTCCCCCGC 59.476 55.000 0.00 0.00 0.00 6.13
120 121 0.609681 TAAACATTGTGTCCCCCGCC 60.610 55.000 0.00 0.00 0.00 6.13
121 122 2.366153 AAACATTGTGTCCCCCGCCT 62.366 55.000 0.00 0.00 0.00 5.52
122 123 2.438434 CATTGTGTCCCCCGCCTC 60.438 66.667 0.00 0.00 0.00 4.70
123 124 3.728373 ATTGTGTCCCCCGCCTCC 61.728 66.667 0.00 0.00 0.00 4.30
124 125 4.974438 TTGTGTCCCCCGCCTCCT 62.974 66.667 0.00 0.00 0.00 3.69
125 126 2.833151 ATTGTGTCCCCCGCCTCCTA 62.833 60.000 0.00 0.00 0.00 2.94
126 127 2.446036 GTGTCCCCCGCCTCCTAT 60.446 66.667 0.00 0.00 0.00 2.57
127 128 2.070650 GTGTCCCCCGCCTCCTATT 61.071 63.158 0.00 0.00 0.00 1.73
128 129 0.761702 GTGTCCCCCGCCTCCTATTA 60.762 60.000 0.00 0.00 0.00 0.98
129 130 0.761702 TGTCCCCCGCCTCCTATTAC 60.762 60.000 0.00 0.00 0.00 1.89
130 131 1.152183 TCCCCCGCCTCCTATTACC 60.152 63.158 0.00 0.00 0.00 2.85
131 132 1.460689 CCCCCGCCTCCTATTACCA 60.461 63.158 0.00 0.00 0.00 3.25
132 133 0.840722 CCCCCGCCTCCTATTACCAT 60.841 60.000 0.00 0.00 0.00 3.55
133 134 0.613777 CCCCGCCTCCTATTACCATC 59.386 60.000 0.00 0.00 0.00 3.51
134 135 0.613777 CCCGCCTCCTATTACCATCC 59.386 60.000 0.00 0.00 0.00 3.51
135 136 0.246635 CCGCCTCCTATTACCATCCG 59.753 60.000 0.00 0.00 0.00 4.18
136 137 0.389948 CGCCTCCTATTACCATCCGC 60.390 60.000 0.00 0.00 0.00 5.54
137 138 0.036294 GCCTCCTATTACCATCCGCC 60.036 60.000 0.00 0.00 0.00 6.13
138 139 1.645710 CCTCCTATTACCATCCGCCT 58.354 55.000 0.00 0.00 0.00 5.52
139 140 1.978580 CCTCCTATTACCATCCGCCTT 59.021 52.381 0.00 0.00 0.00 4.35
140 141 3.170717 CCTCCTATTACCATCCGCCTTA 58.829 50.000 0.00 0.00 0.00 2.69
141 142 3.195825 CCTCCTATTACCATCCGCCTTAG 59.804 52.174 0.00 0.00 0.00 2.18
142 143 4.087182 CTCCTATTACCATCCGCCTTAGA 58.913 47.826 0.00 0.00 0.00 2.10
143 144 3.830755 TCCTATTACCATCCGCCTTAGAC 59.169 47.826 0.00 0.00 0.00 2.59
144 145 2.814280 ATTACCATCCGCCTTAGACG 57.186 50.000 0.00 0.00 0.00 4.18
145 146 0.103572 TTACCATCCGCCTTAGACGC 59.896 55.000 0.00 0.00 0.00 5.19
146 147 1.038681 TACCATCCGCCTTAGACGCA 61.039 55.000 0.00 0.00 0.00 5.24
147 148 1.883084 CCATCCGCCTTAGACGCAC 60.883 63.158 0.00 0.00 0.00 5.34
148 149 1.153647 CATCCGCCTTAGACGCACA 60.154 57.895 0.00 0.00 0.00 4.57
149 150 1.141881 ATCCGCCTTAGACGCACAG 59.858 57.895 0.00 0.00 0.00 3.66
150 151 1.605058 ATCCGCCTTAGACGCACAGT 61.605 55.000 0.00 0.00 0.00 3.55
151 152 0.961857 TCCGCCTTAGACGCACAGTA 60.962 55.000 0.00 0.00 0.00 2.74
152 153 0.801067 CCGCCTTAGACGCACAGTAC 60.801 60.000 0.00 0.00 0.00 2.73
153 154 1.132199 CGCCTTAGACGCACAGTACG 61.132 60.000 0.00 0.00 0.00 3.67
154 155 0.801067 GCCTTAGACGCACAGTACGG 60.801 60.000 0.00 0.00 34.00 4.02
155 156 0.179145 CCTTAGACGCACAGTACGGG 60.179 60.000 0.00 0.00 34.00 5.28
156 157 0.806868 CTTAGACGCACAGTACGGGA 59.193 55.000 0.00 0.00 34.00 5.14
157 158 0.523072 TTAGACGCACAGTACGGGAC 59.477 55.000 0.00 0.00 34.00 4.46
158 159 1.308069 TAGACGCACAGTACGGGACC 61.308 60.000 0.00 0.00 34.00 4.46
159 160 3.637926 GACGCACAGTACGGGACCC 62.638 68.421 0.00 0.00 34.00 4.46
160 161 4.446413 CGCACAGTACGGGACCCC 62.446 72.222 4.46 0.00 0.00 4.95
161 162 4.091939 GCACAGTACGGGACCCCC 62.092 72.222 4.46 0.00 41.09 5.40
162 163 2.284405 CACAGTACGGGACCCCCT 60.284 66.667 4.46 0.00 42.67 4.79
163 164 1.000739 CACAGTACGGGACCCCCTA 59.999 63.158 4.46 0.00 42.67 3.53
164 165 1.000866 ACAGTACGGGACCCCCTAC 59.999 63.158 4.46 4.93 42.67 3.18
165 166 1.759692 CAGTACGGGACCCCCTACC 60.760 68.421 4.46 0.00 42.67 3.18
170 171 2.613421 GGGACCCCCTACCGAGAT 59.387 66.667 0.00 0.00 41.34 2.75
171 172 1.533513 GGGACCCCCTACCGAGATC 60.534 68.421 0.00 0.00 41.34 2.75
172 173 1.533513 GGACCCCCTACCGAGATCC 60.534 68.421 0.00 0.00 0.00 3.36
173 174 1.902432 GACCCCCTACCGAGATCCG 60.902 68.421 0.00 0.00 38.18 4.18
174 175 3.303928 CCCCCTACCGAGATCCGC 61.304 72.222 0.00 0.00 36.84 5.54
175 176 3.303928 CCCCTACCGAGATCCGCC 61.304 72.222 0.00 0.00 36.84 6.13
176 177 3.671411 CCCTACCGAGATCCGCCG 61.671 72.222 0.00 0.00 36.84 6.46
181 182 2.125269 CCGAGATCCGCCGGTTTT 60.125 61.111 1.63 0.00 40.78 2.43
182 183 2.461110 CCGAGATCCGCCGGTTTTG 61.461 63.158 1.63 0.00 40.78 2.44
183 184 1.447140 CGAGATCCGCCGGTTTTGA 60.447 57.895 1.63 0.00 0.00 2.69
184 185 1.693083 CGAGATCCGCCGGTTTTGAC 61.693 60.000 1.63 0.00 0.00 3.18
185 186 0.672401 GAGATCCGCCGGTTTTGACA 60.672 55.000 1.63 0.00 0.00 3.58
186 187 0.953960 AGATCCGCCGGTTTTGACAC 60.954 55.000 1.63 0.00 0.00 3.67
187 188 1.918868 GATCCGCCGGTTTTGACACC 61.919 60.000 1.63 0.00 0.00 4.16
219 220 2.069273 CTTGTTCTTGGTGGCGTCTAG 58.931 52.381 0.00 0.00 0.00 2.43
296 297 1.123861 TGAGCAAGCTCCTCCACTGT 61.124 55.000 18.54 0.00 42.09 3.55
314 315 4.830046 CACTGTAGGTAGGATGCTCATAGT 59.170 45.833 0.00 0.00 0.00 2.12
344 345 4.439253 AGAGACTTTAGGCAAGTGGTTT 57.561 40.909 0.00 0.00 46.53 3.27
394 395 4.013267 AGCAACAGATTGAGCAACTAGT 57.987 40.909 0.00 0.00 38.15 2.57
396 397 3.499918 GCAACAGATTGAGCAACTAGTGT 59.500 43.478 0.00 0.00 38.15 3.55
451 452 2.036217 TGCTGGACTGCAAATCCTTTTG 59.964 45.455 15.82 6.68 44.18 2.44
501 502 3.306919 GCATTGCCCTTGAAATCCTTCAA 60.307 43.478 0.00 0.77 46.88 2.69
591 594 1.179814 AGCGAGAGAACGAAGTGGGT 61.180 55.000 0.00 0.00 45.00 4.51
671 675 4.610605 TCTTTGATTCCACTCGGTGTTA 57.389 40.909 3.82 0.00 0.00 2.41
693 697 8.592809 TGTTACTTTTCCATTTGCTTCCAATAT 58.407 29.630 0.00 0.00 0.00 1.28
772 776 3.857052 TGCCAGAAGTCGTTTCGATATT 58.143 40.909 0.00 0.00 40.86 1.28
818 822 9.476928 TTTTATTTGTTATCCCTAATCCGGAAA 57.523 29.630 9.01 0.00 31.75 3.13
852 856 1.123928 CCTTGGGCAGTACCTCCTAG 58.876 60.000 0.00 0.00 39.10 3.02
856 860 1.132500 GGGCAGTACCTCCTAGCAAT 58.868 55.000 0.00 0.00 39.10 3.56
863 867 6.234177 GCAGTACCTCCTAGCAATATTGATT 58.766 40.000 19.73 8.66 0.00 2.57
999 1004 3.116174 GGGAAGGACATAGGAAAGAGGT 58.884 50.000 0.00 0.00 0.00 3.85
1064 1070 1.138883 GACGCACGGAGCATACTCA 59.861 57.895 3.06 0.00 45.42 3.41
1115 1121 1.006832 GTATGCCTGCGTGTTTCGAT 58.993 50.000 0.00 0.00 42.86 3.59
1121 1127 1.798223 CCTGCGTGTTTCGATGAGAAA 59.202 47.619 0.00 0.00 45.76 2.52
1327 1333 2.230130 TTTGCTGGGAATTCCGGATT 57.770 45.000 18.30 0.00 44.90 3.01
1481 1487 4.162320 ACCATTTCTCTCCGCTATTCTTCA 59.838 41.667 0.00 0.00 0.00 3.02
1507 1513 4.907809 AGAAGGGCTTGACTTACTTAACC 58.092 43.478 0.00 0.00 0.00 2.85
1608 1614 1.676006 CTGTCGGTATGGGCAATTTCC 59.324 52.381 0.00 0.00 0.00 3.13
1660 1667 5.940470 AGTGCTACCAAAGTTCCTCTAATTG 59.060 40.000 0.00 0.00 0.00 2.32
1663 1670 5.416013 GCTACCAAAGTTCCTCTAATTGCTT 59.584 40.000 0.00 0.00 0.00 3.91
1684 1691 0.954452 GCCAGATATTTCCCTTGCCG 59.046 55.000 0.00 0.00 0.00 5.69
1726 1733 2.034179 CGATAGATGTTACCACGGAGCA 59.966 50.000 0.00 0.00 39.76 4.26
1775 1782 2.300723 TCCGTCTTGCCTTTGCTACTTA 59.699 45.455 0.00 0.00 38.71 2.24
1796 1803 1.902508 AGAGAATGCCTTTGACCGAGA 59.097 47.619 0.00 0.00 0.00 4.04
1926 1933 1.136891 TCCGCTATGACATGACCAGTG 59.863 52.381 0.00 0.08 0.00 3.66
1949 1956 7.999545 AGTGCACTAATAAGTCAGGTATCTCTA 59.000 37.037 20.16 0.00 31.97 2.43
2220 2231 4.112634 CTGCGAGGTTCTTTGATCGAATA 58.887 43.478 0.00 0.00 37.35 1.75
2230 2241 7.361286 GGTTCTTTGATCGAATAAGCTCTTTGT 60.361 37.037 13.16 0.00 0.00 2.83
2276 2287 8.818057 CACTCTCTTTCTTCTTTCGTTTTAAGA 58.182 33.333 0.00 0.00 0.00 2.10
2277 2288 9.379791 ACTCTCTTTCTTCTTTCGTTTTAAGAA 57.620 29.630 0.00 0.00 38.82 2.52
2339 2352 8.650490 TCTATACAATCCAATCATGCAGTCTAA 58.350 33.333 0.00 0.00 0.00 2.10
2370 2383 8.540492 ACTTTACAACGATATATCTCGCTTTTG 58.460 33.333 10.14 9.71 42.35 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.707448 ACAAGAGTTGATCTACCACGAGAT 59.293 41.667 3.54 0.00 37.23 2.75
6 7 4.079970 ACAAGAGTTGATCTACCACGAGA 58.920 43.478 3.54 0.00 37.23 4.04
7 8 4.442375 ACAAGAGTTGATCTACCACGAG 57.558 45.455 3.54 1.07 37.23 4.18
8 9 5.970317 TTACAAGAGTTGATCTACCACGA 57.030 39.130 3.54 0.00 37.23 4.35
9 10 7.481642 AGTATTACAAGAGTTGATCTACCACG 58.518 38.462 3.54 0.00 37.23 4.94
10 11 8.467598 TGAGTATTACAAGAGTTGATCTACCAC 58.532 37.037 3.54 0.00 37.23 4.16
11 12 8.589701 TGAGTATTACAAGAGTTGATCTACCA 57.410 34.615 3.54 0.00 37.23 3.25
32 33 9.676861 TTCTTGATTGAACTTGATGATATGAGT 57.323 29.630 0.00 0.00 0.00 3.41
34 35 9.117183 CCTTCTTGATTGAACTTGATGATATGA 57.883 33.333 0.00 0.00 0.00 2.15
35 36 9.117183 TCCTTCTTGATTGAACTTGATGATATG 57.883 33.333 0.00 0.00 0.00 1.78
36 37 9.690913 TTCCTTCTTGATTGAACTTGATGATAT 57.309 29.630 0.00 0.00 0.00 1.63
37 38 9.170734 CTTCCTTCTTGATTGAACTTGATGATA 57.829 33.333 0.00 0.00 0.00 2.15
38 39 7.668886 ACTTCCTTCTTGATTGAACTTGATGAT 59.331 33.333 0.00 0.00 0.00 2.45
39 40 7.000472 ACTTCCTTCTTGATTGAACTTGATGA 59.000 34.615 0.00 0.00 0.00 2.92
40 41 7.211966 ACTTCCTTCTTGATTGAACTTGATG 57.788 36.000 0.00 0.00 0.00 3.07
41 42 8.378565 TCTACTTCCTTCTTGATTGAACTTGAT 58.621 33.333 0.00 0.00 0.00 2.57
42 43 7.735917 TCTACTTCCTTCTTGATTGAACTTGA 58.264 34.615 0.00 0.00 0.00 3.02
43 44 7.659390 ACTCTACTTCCTTCTTGATTGAACTTG 59.341 37.037 0.00 0.00 0.00 3.16
44 45 7.740805 ACTCTACTTCCTTCTTGATTGAACTT 58.259 34.615 0.00 0.00 0.00 2.66
45 46 7.309770 ACTCTACTTCCTTCTTGATTGAACT 57.690 36.000 0.00 0.00 0.00 3.01
46 47 9.660180 AATACTCTACTTCCTTCTTGATTGAAC 57.340 33.333 0.00 0.00 0.00 3.18
49 50 9.535878 GGTAATACTCTACTTCCTTCTTGATTG 57.464 37.037 0.00 0.00 0.00 2.67
50 51 9.495382 AGGTAATACTCTACTTCCTTCTTGATT 57.505 33.333 0.00 0.00 0.00 2.57
51 52 9.138596 GAGGTAATACTCTACTTCCTTCTTGAT 57.861 37.037 0.00 0.00 34.65 2.57
52 53 7.560626 GGAGGTAATACTCTACTTCCTTCTTGA 59.439 40.741 5.03 0.00 42.18 3.02
53 54 7.342284 TGGAGGTAATACTCTACTTCCTTCTTG 59.658 40.741 11.71 0.00 44.50 3.02
54 55 7.420029 TGGAGGTAATACTCTACTTCCTTCTT 58.580 38.462 11.71 0.00 44.50 2.52
55 56 6.982899 TGGAGGTAATACTCTACTTCCTTCT 58.017 40.000 11.71 0.00 44.50 2.85
56 57 7.308710 CGATGGAGGTAATACTCTACTTCCTTC 60.309 44.444 11.71 12.67 44.50 3.46
57 58 6.490721 CGATGGAGGTAATACTCTACTTCCTT 59.509 42.308 11.71 6.71 44.50 3.36
58 59 6.005198 CGATGGAGGTAATACTCTACTTCCT 58.995 44.000 11.71 0.00 44.50 3.36
59 60 6.002704 TCGATGGAGGTAATACTCTACTTCC 58.997 44.000 5.26 5.26 44.47 3.46
60 61 6.935771 TCTCGATGGAGGTAATACTCTACTTC 59.064 42.308 4.78 0.00 40.85 3.01
61 62 6.839454 TCTCGATGGAGGTAATACTCTACTT 58.161 40.000 4.78 0.00 40.85 2.24
62 63 6.436738 TCTCGATGGAGGTAATACTCTACT 57.563 41.667 4.78 0.00 40.85 2.57
63 64 5.644636 CCTCTCGATGGAGGTAATACTCTAC 59.355 48.000 11.66 0.00 45.65 2.59
64 65 5.806818 CCTCTCGATGGAGGTAATACTCTA 58.193 45.833 11.66 0.00 45.65 2.43
65 66 4.658063 CCTCTCGATGGAGGTAATACTCT 58.342 47.826 11.66 0.00 45.65 3.24
75 76 3.610669 CGGGCCCTCTCGATGGAG 61.611 72.222 22.43 0.00 41.89 3.86
76 77 3.672338 TTCGGGCCCTCTCGATGGA 62.672 63.158 22.43 3.53 35.25 3.41
77 78 3.154473 TTCGGGCCCTCTCGATGG 61.154 66.667 22.43 0.54 35.25 3.51
78 79 2.107141 GTTCGGGCCCTCTCGATG 59.893 66.667 22.43 1.43 35.25 3.84
79 80 3.155167 GGTTCGGGCCCTCTCGAT 61.155 66.667 22.43 0.00 35.25 3.59
80 81 4.377760 AGGTTCGGGCCCTCTCGA 62.378 66.667 22.43 9.26 0.00 4.04
81 82 4.148825 CAGGTTCGGGCCCTCTCG 62.149 72.222 22.43 6.49 0.00 4.04
82 83 3.787001 CCAGGTTCGGGCCCTCTC 61.787 72.222 22.43 9.34 0.00 3.20
90 91 2.227865 CACAATGTTTACCCAGGTTCGG 59.772 50.000 0.00 0.00 0.00 4.30
91 92 2.882137 ACACAATGTTTACCCAGGTTCG 59.118 45.455 0.00 0.00 0.00 3.95
92 93 3.254903 GGACACAATGTTTACCCAGGTTC 59.745 47.826 0.00 0.00 0.00 3.62
93 94 3.227614 GGACACAATGTTTACCCAGGTT 58.772 45.455 0.00 0.00 0.00 3.50
94 95 2.490168 GGGACACAATGTTTACCCAGGT 60.490 50.000 12.30 0.00 37.50 4.00
95 96 2.167662 GGGACACAATGTTTACCCAGG 58.832 52.381 12.30 0.00 37.50 4.45
96 97 2.167662 GGGGACACAATGTTTACCCAG 58.832 52.381 14.80 0.00 38.30 4.45
97 98 1.203075 GGGGGACACAATGTTTACCCA 60.203 52.381 20.61 0.00 39.39 4.51
98 99 1.552578 GGGGGACACAATGTTTACCC 58.447 55.000 11.42 11.42 37.95 3.69
99 100 1.170442 CGGGGGACACAATGTTTACC 58.830 55.000 0.00 0.00 0.00 2.85
100 101 0.524414 GCGGGGGACACAATGTTTAC 59.476 55.000 0.00 0.00 0.00 2.01
101 102 0.609681 GGCGGGGGACACAATGTTTA 60.610 55.000 0.00 0.00 0.00 2.01
102 103 1.906333 GGCGGGGGACACAATGTTT 60.906 57.895 0.00 0.00 0.00 2.83
103 104 2.282887 GGCGGGGGACACAATGTT 60.283 61.111 0.00 0.00 0.00 2.71
104 105 3.256960 AGGCGGGGGACACAATGT 61.257 61.111 0.00 0.00 0.00 2.71
105 106 2.438434 GAGGCGGGGGACACAATG 60.438 66.667 0.00 0.00 0.00 2.82
106 107 2.833151 TAGGAGGCGGGGGACACAAT 62.833 60.000 0.00 0.00 0.00 2.71
107 108 2.833151 ATAGGAGGCGGGGGACACAA 62.833 60.000 0.00 0.00 0.00 3.33
108 109 2.833151 AATAGGAGGCGGGGGACACA 62.833 60.000 0.00 0.00 0.00 3.72
109 110 0.761702 TAATAGGAGGCGGGGGACAC 60.762 60.000 0.00 0.00 0.00 3.67
110 111 0.761702 GTAATAGGAGGCGGGGGACA 60.762 60.000 0.00 0.00 0.00 4.02
111 112 1.478526 GGTAATAGGAGGCGGGGGAC 61.479 65.000 0.00 0.00 0.00 4.46
112 113 1.152183 GGTAATAGGAGGCGGGGGA 60.152 63.158 0.00 0.00 0.00 4.81
113 114 0.840722 ATGGTAATAGGAGGCGGGGG 60.841 60.000 0.00 0.00 0.00 5.40
114 115 0.613777 GATGGTAATAGGAGGCGGGG 59.386 60.000 0.00 0.00 0.00 5.73
115 116 0.613777 GGATGGTAATAGGAGGCGGG 59.386 60.000 0.00 0.00 0.00 6.13
116 117 0.246635 CGGATGGTAATAGGAGGCGG 59.753 60.000 0.00 0.00 0.00 6.13
117 118 0.389948 GCGGATGGTAATAGGAGGCG 60.390 60.000 0.00 0.00 0.00 5.52
118 119 0.036294 GGCGGATGGTAATAGGAGGC 60.036 60.000 0.00 0.00 0.00 4.70
119 120 1.645710 AGGCGGATGGTAATAGGAGG 58.354 55.000 0.00 0.00 0.00 4.30
120 121 4.082136 GTCTAAGGCGGATGGTAATAGGAG 60.082 50.000 0.00 0.00 0.00 3.69
121 122 3.830755 GTCTAAGGCGGATGGTAATAGGA 59.169 47.826 0.00 0.00 0.00 2.94
122 123 3.367087 CGTCTAAGGCGGATGGTAATAGG 60.367 52.174 0.00 0.00 0.00 2.57
123 124 3.834610 CGTCTAAGGCGGATGGTAATAG 58.165 50.000 0.00 0.00 0.00 1.73
124 125 2.029649 GCGTCTAAGGCGGATGGTAATA 60.030 50.000 0.00 0.00 0.00 0.98
125 126 1.270147 GCGTCTAAGGCGGATGGTAAT 60.270 52.381 0.00 0.00 0.00 1.89
126 127 0.103572 GCGTCTAAGGCGGATGGTAA 59.896 55.000 0.00 0.00 0.00 2.85
127 128 1.038681 TGCGTCTAAGGCGGATGGTA 61.039 55.000 0.00 0.00 0.00 3.25
128 129 2.355986 TGCGTCTAAGGCGGATGGT 61.356 57.895 0.00 0.00 0.00 3.55
129 130 1.883084 GTGCGTCTAAGGCGGATGG 60.883 63.158 0.00 0.00 31.50 3.51
130 131 1.148157 CTGTGCGTCTAAGGCGGATG 61.148 60.000 0.00 0.00 31.50 3.51
131 132 1.141881 CTGTGCGTCTAAGGCGGAT 59.858 57.895 0.00 0.00 31.50 4.18
132 133 0.961857 TACTGTGCGTCTAAGGCGGA 60.962 55.000 0.00 0.00 0.00 5.54
133 134 0.801067 GTACTGTGCGTCTAAGGCGG 60.801 60.000 0.00 0.00 0.00 6.13
134 135 1.132199 CGTACTGTGCGTCTAAGGCG 61.132 60.000 10.19 0.00 0.00 5.52
135 136 0.801067 CCGTACTGTGCGTCTAAGGC 60.801 60.000 16.66 0.00 0.00 4.35
136 137 0.179145 CCCGTACTGTGCGTCTAAGG 60.179 60.000 16.66 6.81 0.00 2.69
137 138 0.806868 TCCCGTACTGTGCGTCTAAG 59.193 55.000 16.66 1.44 0.00 2.18
138 139 0.523072 GTCCCGTACTGTGCGTCTAA 59.477 55.000 16.66 0.00 0.00 2.10
139 140 1.308069 GGTCCCGTACTGTGCGTCTA 61.308 60.000 16.66 0.00 0.00 2.59
140 141 2.633509 GGTCCCGTACTGTGCGTCT 61.634 63.158 16.66 0.00 0.00 4.18
141 142 2.126189 GGTCCCGTACTGTGCGTC 60.126 66.667 16.66 7.08 0.00 5.19
142 143 3.688159 GGGTCCCGTACTGTGCGT 61.688 66.667 16.66 0.00 0.00 5.24
143 144 4.446413 GGGGTCCCGTACTGTGCG 62.446 72.222 11.42 11.42 0.00 5.34
144 145 4.091939 GGGGGTCCCGTACTGTGC 62.092 72.222 0.48 0.00 36.85 4.57
153 154 1.533513 GATCTCGGTAGGGGGTCCC 60.534 68.421 0.00 0.00 45.90 4.46
154 155 1.533513 GGATCTCGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
155 156 1.902432 CGGATCTCGGTAGGGGGTC 60.902 68.421 0.00 0.00 34.75 4.46
156 157 2.197875 CGGATCTCGGTAGGGGGT 59.802 66.667 0.00 0.00 34.75 4.95
157 158 3.303928 GCGGATCTCGGTAGGGGG 61.304 72.222 5.87 0.00 39.69 5.40
158 159 3.303928 GGCGGATCTCGGTAGGGG 61.304 72.222 5.87 0.00 39.69 4.79
159 160 3.671411 CGGCGGATCTCGGTAGGG 61.671 72.222 0.00 0.00 39.69 3.53
160 161 3.671411 CCGGCGGATCTCGGTAGG 61.671 72.222 24.41 0.00 41.23 3.18
165 166 1.447140 TCAAAACCGGCGGATCTCG 60.447 57.895 35.78 16.34 42.76 4.04
166 167 0.672401 TGTCAAAACCGGCGGATCTC 60.672 55.000 35.78 16.90 0.00 2.75
167 168 0.953960 GTGTCAAAACCGGCGGATCT 60.954 55.000 35.78 13.84 0.00 2.75
168 169 1.500396 GTGTCAAAACCGGCGGATC 59.500 57.895 35.78 9.52 0.00 3.36
169 170 1.969589 GGTGTCAAAACCGGCGGAT 60.970 57.895 35.78 20.37 0.00 4.18
170 171 2.592287 GGTGTCAAAACCGGCGGA 60.592 61.111 35.78 6.54 0.00 5.54
176 177 1.449726 GGGGTGTCGGTGTCAAAACC 61.450 60.000 0.00 0.00 36.82 3.27
177 178 0.464916 AGGGGTGTCGGTGTCAAAAC 60.465 55.000 0.00 0.00 0.00 2.43
178 179 0.256464 AAGGGGTGTCGGTGTCAAAA 59.744 50.000 0.00 0.00 0.00 2.44
179 180 0.256464 AAAGGGGTGTCGGTGTCAAA 59.744 50.000 0.00 0.00 0.00 2.69
180 181 0.179040 GAAAGGGGTGTCGGTGTCAA 60.179 55.000 0.00 0.00 0.00 3.18
181 182 1.052124 AGAAAGGGGTGTCGGTGTCA 61.052 55.000 0.00 0.00 0.00 3.58
182 183 0.108019 AAGAAAGGGGTGTCGGTGTC 59.892 55.000 0.00 0.00 0.00 3.67
183 184 0.179029 CAAGAAAGGGGTGTCGGTGT 60.179 55.000 0.00 0.00 0.00 4.16
184 185 0.179029 ACAAGAAAGGGGTGTCGGTG 60.179 55.000 0.00 0.00 0.00 4.94
185 186 0.549469 AACAAGAAAGGGGTGTCGGT 59.451 50.000 0.00 0.00 0.00 4.69
186 187 1.202770 AGAACAAGAAAGGGGTGTCGG 60.203 52.381 0.00 0.00 0.00 4.79
187 188 2.256117 AGAACAAGAAAGGGGTGTCG 57.744 50.000 0.00 0.00 0.00 4.35
188 189 2.623416 CCAAGAACAAGAAAGGGGTGTC 59.377 50.000 0.00 0.00 0.00 3.67
189 190 2.024369 ACCAAGAACAAGAAAGGGGTGT 60.024 45.455 0.00 0.00 0.00 4.16
190 191 2.362077 CACCAAGAACAAGAAAGGGGTG 59.638 50.000 0.00 0.00 38.64 4.61
191 192 2.666317 CACCAAGAACAAGAAAGGGGT 58.334 47.619 0.00 0.00 0.00 4.95
219 220 1.002087 TCGGGAAGGTCTTCTTTGCTC 59.998 52.381 10.13 0.00 39.45 4.26
296 297 6.373759 TCTTCAACTATGAGCATCCTACCTA 58.626 40.000 0.00 0.00 36.78 3.08
314 315 6.828785 ACTTGCCTAAAGTCTCTTTTCTTCAA 59.171 34.615 0.15 1.41 46.60 2.69
344 345 2.497675 CTCTAACCAGCTGAGCTACCAA 59.502 50.000 17.39 0.00 36.40 3.67
451 452 4.578928 TGCTCTTCCCACTAAAACAAGAAC 59.421 41.667 0.00 0.00 0.00 3.01
501 502 4.067896 GCTCATATGTGGATTCGAACCAT 58.932 43.478 18.29 12.42 39.69 3.55
591 594 5.049167 GTGCAAATTCTGACATCACCAAAA 58.951 37.500 0.00 0.00 0.00 2.44
671 675 9.657419 CTAAATATTGGAAGCAAATGGAAAAGT 57.343 29.630 0.00 0.00 0.00 2.66
693 697 9.158233 CCGACAATTTTTCTGTATAGGTCTAAA 57.842 33.333 0.00 0.00 0.00 1.85
696 700 5.585047 GCCGACAATTTTTCTGTATAGGTCT 59.415 40.000 0.00 0.00 0.00 3.85
704 708 2.482721 CGTAGGCCGACAATTTTTCTGT 59.517 45.455 16.75 0.00 39.56 3.41
727 731 1.065854 CCAGAGGGATCAGAACCACAC 60.066 57.143 0.00 0.00 35.59 3.82
800 804 5.001874 GGTGATTTCCGGATTAGGGATAAC 58.998 45.833 4.15 0.00 32.58 1.89
809 813 6.419484 AAAAGAAAAGGTGATTTCCGGATT 57.581 33.333 4.15 0.00 39.59 3.01
818 822 3.324846 GCCCAAGGAAAAGAAAAGGTGAT 59.675 43.478 0.00 0.00 0.00 3.06
852 856 7.550196 ACCAAGATCCAAACAAATCAATATTGC 59.450 33.333 10.76 0.00 0.00 3.56
856 860 6.723515 TGGACCAAGATCCAAACAAATCAATA 59.276 34.615 0.00 0.00 46.08 1.90
1056 1062 2.826428 TGATCCGAAGCTTGAGTATGC 58.174 47.619 2.10 0.00 0.00 3.14
1064 1070 1.408822 GGGGACATTGATCCGAAGCTT 60.409 52.381 0.00 0.00 39.97 3.74
1327 1333 9.225682 ACCATATTTAGATCTTCCCTTTCTACA 57.774 33.333 0.00 0.00 0.00 2.74
1481 1487 5.827326 AAGTAAGTCAAGCCCTTCTAAGT 57.173 39.130 0.00 0.00 0.00 2.24
1507 1513 2.537401 CTAGTTTCGGGAAAGCGGTAG 58.463 52.381 0.00 0.00 0.00 3.18
1608 1614 7.244192 GGGACGAAATCAATCAAAGAACTTAG 58.756 38.462 0.00 0.00 0.00 2.18
1660 1667 3.254411 GCAAGGGAAATATCTGGCTAAGC 59.746 47.826 0.00 0.00 0.00 3.09
1663 1670 2.224523 CGGCAAGGGAAATATCTGGCTA 60.225 50.000 0.00 0.00 0.00 3.93
1726 1733 4.080863 CAGGAATGAAGGTTGCTAGGTACT 60.081 45.833 0.00 0.00 46.37 2.73
1775 1782 2.303022 TCTCGGTCAAAGGCATTCTCTT 59.697 45.455 0.00 0.00 0.00 2.85
1796 1803 6.886459 TGCTAATAAAATGAGTGGAAGAGCTT 59.114 34.615 0.00 0.00 0.00 3.74
1949 1956 4.504514 GGGAAGAGGACGGTCTTACTTTTT 60.505 45.833 8.23 0.00 37.52 1.94
2155 2166 5.037385 TCGAAAGCACTCATCTTTATCGAG 58.963 41.667 0.00 0.00 34.24 4.04
2220 2231 6.239036 GGGATGAAAGTAAACACAAAGAGCTT 60.239 38.462 0.00 0.00 0.00 3.74
2230 2241 4.044065 AGTGGGATGGGATGAAAGTAAACA 59.956 41.667 0.00 0.00 0.00 2.83
2299 2312 8.816894 TGGATTGTATAGAAGGATAAGATGGAC 58.183 37.037 0.00 0.00 0.00 4.02
2339 2352 8.229137 GCGAGATATATCGTTGTAAAGTAGAGT 58.771 37.037 19.91 0.00 44.53 3.24


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

AutoCloner maintained by Alex Coulton.