Multiple sequence alignment - TraesCS6D01G176100

Loading Multiple Alignment...

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 TraesCS6D01G176100 chr6D 100.000 2231 0 0 1 2231 168757564 168759794 0.000000e+00 4120
1 TraesCS6D01G176100 chr6D 98.180 2033 35 2 201 2231 124519396 124521428 0.000000e+00 3548
2 TraesCS6D01G176100 chr6D 97.640 2034 45 1 201 2231 458900056 458902089 0.000000e+00 3487
3 TraesCS6D01G176100 chr6D 98.049 205 4 0 1 205 124519988 124520192 7.580000e-95 357
4 TraesCS6D01G176100 chr6D 98.049 205 4 0 1 205 168758356 168758560 7.580000e-95 357
5 TraesCS6D01G176100 chr7D 98.523 2031 30 0 201 2231 382051953 382053983 0.000000e+00 3585
6 TraesCS6D01G176100 chr7D 98.227 2031 36 0 201 2231 381925875 381927905 0.000000e+00 3552
7 TraesCS6D01G176100 chr7D 98.085 2037 33 2 201 2231 381971896 381969860 0.000000e+00 3541
8 TraesCS6D01G176100 chr7D 97.931 2030 35 5 203 2231 203501875 203503898 0.000000e+00 3509
9 TraesCS6D01G176100 chr7D 98.049 205 4 0 1 205 203502465 203502669 7.580000e-95 357
10 TraesCS6D01G176100 chr7D 98.049 205 4 0 1 205 381926467 381926671 7.580000e-95 357
11 TraesCS6D01G176100 chr7D 98.049 205 4 0 1 205 381971299 381971095 7.580000e-95 357
12 TraesCS6D01G176100 chr7D 100.000 55 0 0 2172 2226 606916351 606916297 3.920000e-18 102
13 TraesCS6D01G176100 chr7D 96.774 62 1 1 2171 2231 626693989 626693928 3.920000e-18 102
14 TraesCS6D01G176100 chr1D 97.638 2032 46 2 201 2231 269408674 269410704 0.000000e+00 3485
15 TraesCS6D01G176100 chr1D 98.049 205 4 0 1 205 43234249 43234045 7.580000e-95 357
16 TraesCS6D01G176100 chr5A 97.988 1988 40 0 201 2188 238820934 238818947 0.000000e+00 3450
17 TraesCS6D01G176100 chr7A 97.888 1989 36 2 201 2188 60281187 60283170 0.000000e+00 3435
18 TraesCS6D01G176100 chrUn 98.049 205 4 0 1 205 186205960 186205756 7.580000e-95 357
19 TraesCS6D01G176100 chrUn 98.049 205 4 0 1 205 434806041 434806245 7.580000e-95 357
20 TraesCS6D01G176100 chr1A 98.049 205 4 0 1 205 498688766 498688562 7.580000e-95 357
21 TraesCS6D01G176100 chr3A 98.361 61 1 0 2171 2231 227648530 227648590 8.420000e-20 108
22 TraesCS6D01G176100 chr7B 96.774 62 1 1 2171 2231 247490142 247490081 3.920000e-18 102


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 TraesCS6D01G176100 chr6D 168757564 168759794 2230 False 2238.5 4120 99.0245 1 2231 2 chr6D.!!$F3 2230
1 TraesCS6D01G176100 chr6D 458900056 458902089 2033 False 3487.0 3487 97.6400 201 2231 1 chr6D.!!$F1 2030
2 TraesCS6D01G176100 chr6D 124519396 124521428 2032 False 1952.5 3548 98.1145 1 2231 2 chr6D.!!$F2 2230
3 TraesCS6D01G176100 chr7D 382051953 382053983 2030 False 3585.0 3585 98.5230 201 2231 1 chr7D.!!$F1 2030
4 TraesCS6D01G176100 chr7D 381925875 381927905 2030 False 1954.5 3552 98.1380 1 2231 2 chr7D.!!$F3 2230
5 TraesCS6D01G176100 chr7D 381969860 381971896 2036 True 1949.0 3541 98.0670 1 2231 2 chr7D.!!$R3 2230
6 TraesCS6D01G176100 chr7D 203501875 203503898 2023 False 1933.0 3509 97.9900 1 2231 2 chr7D.!!$F2 2230
7 TraesCS6D01G176100 chr1D 269408674 269410704 2030 False 3485.0 3485 97.6380 201 2231 1 chr1D.!!$F1 2030
8 TraesCS6D01G176100 chr5A 238818947 238820934 1987 True 3450.0 3450 97.9880 201 2188 1 chr5A.!!$R1 1987
9 TraesCS6D01G176100 chr7A 60281187 60283170 1983 False 3435.0 3435 97.8880 201 2188 1 chr7A.!!$F1 1987

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
22 23 0.179034 CCATCTCAGGCCAGGCTAAC 60.179 60.0 12.43 0.0 0.0 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 1953 1.195442 TTCGGTAGTGATGGGGTGCA 61.195 55.0 0.0 0.0 0.0 4.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.367377 TCCCCATCTCAGGCCAGG 60.367 66.667 5.01 0.00 0.00 4.45
18 19 4.201122 CCCCATCTCAGGCCAGGC 62.201 72.222 5.01 1.26 0.00 4.85
19 20 3.095163 CCCATCTCAGGCCAGGCT 61.095 66.667 12.43 0.00 0.00 4.58
20 21 1.767672 CCCATCTCAGGCCAGGCTA 60.768 63.158 12.43 0.00 0.00 3.93
21 22 1.348008 CCCATCTCAGGCCAGGCTAA 61.348 60.000 12.43 0.00 0.00 3.09
22 23 0.179034 CCATCTCAGGCCAGGCTAAC 60.179 60.000 12.43 0.00 0.00 2.34
23 24 0.531532 CATCTCAGGCCAGGCTAACG 60.532 60.000 12.43 0.00 0.00 3.18
24 25 1.690219 ATCTCAGGCCAGGCTAACGG 61.690 60.000 12.43 0.00 0.00 4.44
25 26 2.284331 TCAGGCCAGGCTAACGGA 60.284 61.111 12.43 0.00 0.00 4.69
26 27 2.187946 CAGGCCAGGCTAACGGAG 59.812 66.667 12.43 0.00 0.00 4.63
36 37 2.892784 GCTAACGGAGCCTGACTTAT 57.107 50.000 0.27 0.00 46.41 1.73
37 38 3.180891 GCTAACGGAGCCTGACTTATT 57.819 47.619 0.27 0.00 46.41 1.40
38 39 3.124560 GCTAACGGAGCCTGACTTATTC 58.875 50.000 0.27 0.00 46.41 1.75
39 40 3.430374 GCTAACGGAGCCTGACTTATTCA 60.430 47.826 0.27 0.00 46.41 2.57
50 51 4.338795 TGACTTATTCAGGGGAGAGAGT 57.661 45.455 0.00 0.00 0.00 3.24
51 52 4.026744 TGACTTATTCAGGGGAGAGAGTG 58.973 47.826 0.00 0.00 0.00 3.51
52 53 3.379452 ACTTATTCAGGGGAGAGAGTGG 58.621 50.000 0.00 0.00 0.00 4.00
53 54 3.012959 ACTTATTCAGGGGAGAGAGTGGA 59.987 47.826 0.00 0.00 0.00 4.02
54 55 2.173126 ATTCAGGGGAGAGAGTGGAG 57.827 55.000 0.00 0.00 0.00 3.86
55 56 0.616111 TTCAGGGGAGAGAGTGGAGC 60.616 60.000 0.00 0.00 0.00 4.70
56 57 2.063378 CAGGGGAGAGAGTGGAGCC 61.063 68.421 0.00 0.00 0.00 4.70
57 58 2.252898 AGGGGAGAGAGTGGAGCCT 61.253 63.158 0.00 0.00 0.00 4.58
58 59 0.926720 AGGGGAGAGAGTGGAGCCTA 60.927 60.000 0.00 0.00 0.00 3.93
59 60 0.189822 GGGGAGAGAGTGGAGCCTAT 59.810 60.000 0.00 0.00 0.00 2.57
60 61 1.627864 GGGAGAGAGTGGAGCCTATC 58.372 60.000 0.00 0.00 0.00 2.08
61 62 1.243902 GGAGAGAGTGGAGCCTATCG 58.756 60.000 0.00 0.00 0.00 2.92
62 63 1.202830 GGAGAGAGTGGAGCCTATCGA 60.203 57.143 0.00 0.00 0.00 3.59
63 64 2.577700 GAGAGAGTGGAGCCTATCGAA 58.422 52.381 0.00 0.00 0.00 3.71
64 65 2.552315 GAGAGAGTGGAGCCTATCGAAG 59.448 54.545 0.00 0.00 0.00 3.79
65 66 1.000717 GAGAGTGGAGCCTATCGAAGC 60.001 57.143 0.00 0.00 0.00 3.86
66 67 0.747255 GAGTGGAGCCTATCGAAGCA 59.253 55.000 8.00 0.00 0.00 3.91
67 68 0.461961 AGTGGAGCCTATCGAAGCAC 59.538 55.000 8.00 2.01 0.00 4.40
68 69 0.461961 GTGGAGCCTATCGAAGCACT 59.538 55.000 8.00 0.00 0.00 4.40
69 70 0.747255 TGGAGCCTATCGAAGCACTC 59.253 55.000 8.00 4.66 0.00 3.51
70 71 1.036707 GGAGCCTATCGAAGCACTCT 58.963 55.000 8.00 0.00 31.08 3.24
71 72 1.410882 GGAGCCTATCGAAGCACTCTT 59.589 52.381 8.00 0.00 34.68 2.85
72 73 2.468831 GAGCCTATCGAAGCACTCTTG 58.531 52.381 8.00 0.00 31.48 3.02
73 74 2.099921 GAGCCTATCGAAGCACTCTTGA 59.900 50.000 8.00 0.00 31.48 3.02
74 75 2.100584 AGCCTATCGAAGCACTCTTGAG 59.899 50.000 8.00 0.00 31.48 3.02
75 76 2.099921 GCCTATCGAAGCACTCTTGAGA 59.900 50.000 4.49 0.00 31.48 3.27
90 91 5.976458 CTCTTGAGAGTAAGATCTTTGGCT 58.024 41.667 14.36 9.68 36.21 4.75
91 92 5.971763 TCTTGAGAGTAAGATCTTTGGCTC 58.028 41.667 14.36 17.17 32.02 4.70
92 93 4.744795 TGAGAGTAAGATCTTTGGCTCC 57.255 45.455 14.36 12.30 0.00 4.70
93 94 4.357325 TGAGAGTAAGATCTTTGGCTCCT 58.643 43.478 14.36 8.91 0.00 3.69
94 95 4.404073 TGAGAGTAAGATCTTTGGCTCCTC 59.596 45.833 14.36 15.56 0.00 3.71
95 96 4.619679 AGAGTAAGATCTTTGGCTCCTCT 58.380 43.478 14.36 11.26 0.00 3.69
96 97 5.029474 AGAGTAAGATCTTTGGCTCCTCTT 58.971 41.667 14.36 1.62 0.00 2.85
97 98 5.128663 AGAGTAAGATCTTTGGCTCCTCTTC 59.871 44.000 14.36 0.00 0.00 2.87
98 99 4.780021 AGTAAGATCTTTGGCTCCTCTTCA 59.220 41.667 14.36 0.00 0.00 3.02
99 100 4.858965 AAGATCTTTGGCTCCTCTTCAT 57.141 40.909 0.88 0.00 0.00 2.57
100 101 4.858965 AGATCTTTGGCTCCTCTTCATT 57.141 40.909 0.00 0.00 0.00 2.57
101 102 4.779696 AGATCTTTGGCTCCTCTTCATTC 58.220 43.478 0.00 0.00 0.00 2.67
102 103 4.474287 AGATCTTTGGCTCCTCTTCATTCT 59.526 41.667 0.00 0.00 0.00 2.40
103 104 4.213564 TCTTTGGCTCCTCTTCATTCTC 57.786 45.455 0.00 0.00 0.00 2.87
104 105 3.843027 TCTTTGGCTCCTCTTCATTCTCT 59.157 43.478 0.00 0.00 0.00 3.10
105 106 5.026121 TCTTTGGCTCCTCTTCATTCTCTA 58.974 41.667 0.00 0.00 0.00 2.43
106 107 4.744795 TTGGCTCCTCTTCATTCTCTAC 57.255 45.455 0.00 0.00 0.00 2.59
107 108 3.713003 TGGCTCCTCTTCATTCTCTACA 58.287 45.455 0.00 0.00 0.00 2.74
108 109 3.703556 TGGCTCCTCTTCATTCTCTACAG 59.296 47.826 0.00 0.00 0.00 2.74
109 110 3.069443 GGCTCCTCTTCATTCTCTACAGG 59.931 52.174 0.00 0.00 0.00 4.00
110 111 3.069443 GCTCCTCTTCATTCTCTACAGGG 59.931 52.174 0.00 0.00 0.00 4.45
111 112 3.640967 CTCCTCTTCATTCTCTACAGGGG 59.359 52.174 0.00 0.00 0.00 4.79
112 113 3.012959 TCCTCTTCATTCTCTACAGGGGT 59.987 47.826 0.00 0.00 0.00 4.95
113 114 3.386402 CCTCTTCATTCTCTACAGGGGTC 59.614 52.174 0.00 0.00 0.00 4.46
114 115 4.285863 CTCTTCATTCTCTACAGGGGTCT 58.714 47.826 0.00 0.00 0.00 3.85
115 116 4.689062 TCTTCATTCTCTACAGGGGTCTT 58.311 43.478 0.00 0.00 0.00 3.01
116 117 5.094387 TCTTCATTCTCTACAGGGGTCTTT 58.906 41.667 0.00 0.00 0.00 2.52
117 118 4.826274 TCATTCTCTACAGGGGTCTTTG 57.174 45.455 0.00 0.00 0.00 2.77
118 119 3.055094 TCATTCTCTACAGGGGTCTTTGC 60.055 47.826 0.00 0.00 0.00 3.68
119 120 1.276622 TCTCTACAGGGGTCTTTGCC 58.723 55.000 0.00 0.00 0.00 4.52
127 128 4.841441 GGTCTTTGCCCACATGGA 57.159 55.556 0.00 0.00 37.39 3.41
128 129 3.050089 GGTCTTTGCCCACATGGAA 57.950 52.632 0.00 0.00 37.39 3.53
129 130 0.890683 GGTCTTTGCCCACATGGAAG 59.109 55.000 0.00 0.00 37.39 3.46
130 131 0.244721 GTCTTTGCCCACATGGAAGC 59.755 55.000 0.00 0.00 37.39 3.86
131 132 1.213537 CTTTGCCCACATGGAAGCG 59.786 57.895 0.00 0.00 37.39 4.68
132 133 2.216750 CTTTGCCCACATGGAAGCGG 62.217 60.000 0.00 0.00 37.39 5.52
133 134 4.738998 TGCCCACATGGAAGCGGG 62.739 66.667 0.00 0.00 42.03 6.13
136 137 4.738998 CCACATGGAAGCGGGGCA 62.739 66.667 0.00 0.00 37.39 5.36
137 138 3.136123 CACATGGAAGCGGGGCAG 61.136 66.667 0.00 0.00 0.00 4.85
138 139 3.329889 ACATGGAAGCGGGGCAGA 61.330 61.111 0.00 0.00 0.00 4.26
139 140 2.515523 CATGGAAGCGGGGCAGAG 60.516 66.667 0.00 0.00 0.00 3.35
140 141 2.688666 ATGGAAGCGGGGCAGAGA 60.689 61.111 0.00 0.00 0.00 3.10
141 142 2.074948 ATGGAAGCGGGGCAGAGAT 61.075 57.895 0.00 0.00 0.00 2.75
142 143 2.203126 GGAAGCGGGGCAGAGATG 60.203 66.667 0.00 0.00 0.00 2.90
143 144 2.203126 GAAGCGGGGCAGAGATGG 60.203 66.667 0.00 0.00 0.00 3.51
144 145 2.688666 AAGCGGGGCAGAGATGGA 60.689 61.111 0.00 0.00 0.00 3.41
145 146 2.049627 GAAGCGGGGCAGAGATGGAT 62.050 60.000 0.00 0.00 0.00 3.41
146 147 0.764369 AAGCGGGGCAGAGATGGATA 60.764 55.000 0.00 0.00 0.00 2.59
147 148 0.764369 AGCGGGGCAGAGATGGATAA 60.764 55.000 0.00 0.00 0.00 1.75
148 149 0.321122 GCGGGGCAGAGATGGATAAG 60.321 60.000 0.00 0.00 0.00 1.73
149 150 1.342074 CGGGGCAGAGATGGATAAGA 58.658 55.000 0.00 0.00 0.00 2.10
150 151 1.905215 CGGGGCAGAGATGGATAAGAT 59.095 52.381 0.00 0.00 0.00 2.40
151 152 2.093764 CGGGGCAGAGATGGATAAGATC 60.094 54.545 0.00 0.00 0.00 2.75
152 153 2.909006 GGGGCAGAGATGGATAAGATCA 59.091 50.000 0.00 0.00 0.00 2.92
153 154 3.328931 GGGGCAGAGATGGATAAGATCAA 59.671 47.826 0.00 0.00 0.00 2.57
154 155 4.202503 GGGGCAGAGATGGATAAGATCAAA 60.203 45.833 0.00 0.00 0.00 2.69
155 156 4.759183 GGGCAGAGATGGATAAGATCAAAC 59.241 45.833 0.00 0.00 0.00 2.93
156 157 5.371526 GGCAGAGATGGATAAGATCAAACA 58.628 41.667 0.00 0.00 0.00 2.83
157 158 5.238214 GGCAGAGATGGATAAGATCAAACAC 59.762 44.000 0.00 0.00 0.00 3.32
158 159 5.050499 GCAGAGATGGATAAGATCAAACACG 60.050 44.000 0.00 0.00 0.00 4.49
159 160 5.464722 CAGAGATGGATAAGATCAAACACGG 59.535 44.000 0.00 0.00 0.00 4.94
160 161 4.708177 AGATGGATAAGATCAAACACGGG 58.292 43.478 0.00 0.00 0.00 5.28
161 162 4.408921 AGATGGATAAGATCAAACACGGGA 59.591 41.667 0.00 0.00 0.00 5.14
162 163 4.561500 TGGATAAGATCAAACACGGGAA 57.438 40.909 0.00 0.00 0.00 3.97
163 164 5.110814 TGGATAAGATCAAACACGGGAAT 57.889 39.130 0.00 0.00 0.00 3.01
164 165 6.241882 TGGATAAGATCAAACACGGGAATA 57.758 37.500 0.00 0.00 0.00 1.75
165 166 6.654959 TGGATAAGATCAAACACGGGAATAA 58.345 36.000 0.00 0.00 0.00 1.40
166 167 6.765989 TGGATAAGATCAAACACGGGAATAAG 59.234 38.462 0.00 0.00 0.00 1.73
167 168 6.990349 GGATAAGATCAAACACGGGAATAAGA 59.010 38.462 0.00 0.00 0.00 2.10
168 169 7.497909 GGATAAGATCAAACACGGGAATAAGAA 59.502 37.037 0.00 0.00 0.00 2.52
169 170 6.743575 AAGATCAAACACGGGAATAAGAAG 57.256 37.500 0.00 0.00 0.00 2.85
170 171 4.636206 AGATCAAACACGGGAATAAGAAGC 59.364 41.667 0.00 0.00 0.00 3.86
171 172 3.745799 TCAAACACGGGAATAAGAAGCA 58.254 40.909 0.00 0.00 0.00 3.91
172 173 4.331968 TCAAACACGGGAATAAGAAGCAT 58.668 39.130 0.00 0.00 0.00 3.79
173 174 4.764823 TCAAACACGGGAATAAGAAGCATT 59.235 37.500 0.00 0.00 0.00 3.56
174 175 5.242838 TCAAACACGGGAATAAGAAGCATTT 59.757 36.000 0.00 0.00 0.00 2.32
175 176 4.701956 ACACGGGAATAAGAAGCATTTG 57.298 40.909 0.00 0.00 0.00 2.32
176 177 4.331968 ACACGGGAATAAGAAGCATTTGA 58.668 39.130 0.00 0.00 0.00 2.69
177 178 4.764823 ACACGGGAATAAGAAGCATTTGAA 59.235 37.500 0.00 0.00 0.00 2.69
178 179 5.242838 ACACGGGAATAAGAAGCATTTGAAA 59.757 36.000 0.00 0.00 0.00 2.69
179 180 6.071391 ACACGGGAATAAGAAGCATTTGAAAT 60.071 34.615 0.00 0.00 0.00 2.17
180 181 6.254157 CACGGGAATAAGAAGCATTTGAAATG 59.746 38.462 13.32 13.32 0.00 2.32
181 182 5.232838 CGGGAATAAGAAGCATTTGAAATGC 59.767 40.000 29.88 29.88 44.85 3.56
182 183 5.525012 GGGAATAAGAAGCATTTGAAATGCC 59.475 40.000 32.26 21.05 45.59 4.40
183 184 6.343703 GGAATAAGAAGCATTTGAAATGCCT 58.656 36.000 32.26 23.70 45.59 4.75
184 185 6.820152 GGAATAAGAAGCATTTGAAATGCCTT 59.180 34.615 32.26 28.70 45.59 4.35
185 186 7.335171 GGAATAAGAAGCATTTGAAATGCCTTT 59.665 33.333 32.26 25.38 45.59 3.11
186 187 8.625786 AATAAGAAGCATTTGAAATGCCTTTT 57.374 26.923 32.26 24.47 45.59 2.27
187 188 6.947644 AAGAAGCATTTGAAATGCCTTTTT 57.052 29.167 32.26 22.43 45.59 1.94
188 189 6.308371 AGAAGCATTTGAAATGCCTTTTTG 57.692 33.333 32.26 3.11 45.59 2.44
189 190 6.056884 AGAAGCATTTGAAATGCCTTTTTGA 58.943 32.000 32.26 0.00 45.59 2.69
190 191 6.713450 AGAAGCATTTGAAATGCCTTTTTGAT 59.287 30.769 32.26 13.81 45.59 2.57
191 192 6.490566 AGCATTTGAAATGCCTTTTTGATC 57.509 33.333 32.26 7.77 45.59 2.92
192 193 5.998981 AGCATTTGAAATGCCTTTTTGATCA 59.001 32.000 32.26 0.00 45.59 2.92
193 194 6.657541 AGCATTTGAAATGCCTTTTTGATCAT 59.342 30.769 32.26 12.04 45.59 2.45
194 195 7.175990 AGCATTTGAAATGCCTTTTTGATCATT 59.824 29.630 32.26 11.86 45.59 2.57
195 196 7.810759 GCATTTGAAATGCCTTTTTGATCATTT 59.189 29.630 27.65 0.00 40.55 2.32
196 197 9.685828 CATTTGAAATGCCTTTTTGATCATTTT 57.314 25.926 4.82 0.00 38.71 1.82
392 393 3.756963 GGGCACGGAGAAATAAAGAAGTT 59.243 43.478 0.00 0.00 0.00 2.66
423 424 0.393537 CAGCCGAGCTCATTCCCTTT 60.394 55.000 15.40 0.00 36.40 3.11
907 913 4.689062 TCTTCATTCTCTACAGGGGTCTT 58.311 43.478 0.00 0.00 0.00 3.01
1090 1100 9.403110 CGACAAAGAAAGAATCATCTTGAAAAT 57.597 29.630 2.77 0.00 45.19 1.82
1138 1148 6.459298 CGTGTATAGTAAGTGATCCGAACCTT 60.459 42.308 0.00 0.00 0.00 3.50
1159 1170 2.187163 GGAGCGAGCCCCACTTAC 59.813 66.667 0.00 0.00 0.00 2.34
1188 1199 2.271800 GAAGTTGGTGAGCCGTATGAG 58.728 52.381 0.00 0.00 37.67 2.90
1211 1222 1.405526 GCAACTATCTCCTGCGGTTCA 60.406 52.381 0.00 0.00 0.00 3.18
1384 1395 7.010339 ACTACTAGCAATGACTTCCTCTTTT 57.990 36.000 0.00 0.00 0.00 2.27
1411 1422 4.352298 ACTTCATCCTTTCCATATCCCTCC 59.648 45.833 0.00 0.00 0.00 4.30
1413 1424 3.115803 TCATCCTTTCCATATCCCTCCCT 60.116 47.826 0.00 0.00 0.00 4.20
1457 1468 3.548745 TGGCACTCAGTTCATATCTGG 57.451 47.619 0.00 0.00 34.15 3.86
1870 1883 3.198953 TTGCCGTTTCCCCATCGGT 62.199 57.895 0.00 0.00 45.11 4.69
1940 1953 6.901857 AGAACTAGGCCTACTTAGGTAAACAT 59.098 38.462 8.91 0.00 45.42 2.71
1958 1971 0.980754 ATGCACCCCATCACTACCGA 60.981 55.000 0.00 0.00 0.00 4.69
2035 2048 3.555795 GCGATTCTGAGATCCAGCCATTA 60.556 47.826 6.38 0.00 42.62 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.367377 CCTGGCCTGAGATGGGGA 60.367 66.667 11.88 0.00 0.00 4.81
1 2 4.201122 GCCTGGCCTGAGATGGGG 62.201 72.222 11.88 0.00 0.00 4.96
2 3 1.348008 TTAGCCTGGCCTGAGATGGG 61.348 60.000 16.57 0.00 0.00 4.00
3 4 0.179034 GTTAGCCTGGCCTGAGATGG 60.179 60.000 16.57 1.37 0.00 3.51
4 5 0.531532 CGTTAGCCTGGCCTGAGATG 60.532 60.000 16.57 0.00 0.00 2.90
5 6 1.690219 CCGTTAGCCTGGCCTGAGAT 61.690 60.000 16.57 2.71 0.00 2.75
6 7 2.359169 CCGTTAGCCTGGCCTGAGA 61.359 63.158 16.57 0.00 0.00 3.27
7 8 2.187946 CCGTTAGCCTGGCCTGAG 59.812 66.667 16.57 4.93 0.00 3.35
8 9 2.284331 TCCGTTAGCCTGGCCTGA 60.284 61.111 16.57 1.99 0.00 3.86
9 10 2.187946 CTCCGTTAGCCTGGCCTG 59.812 66.667 16.57 2.54 0.00 4.85
10 11 3.787001 GCTCCGTTAGCCTGGCCT 61.787 66.667 16.57 5.44 46.25 5.19
18 19 4.386867 TGAATAAGTCAGGCTCCGTTAG 57.613 45.455 0.00 0.00 0.00 2.34
29 30 4.026744 CACTCTCTCCCCTGAATAAGTCA 58.973 47.826 0.00 0.00 34.17 3.41
30 31 3.386402 CCACTCTCTCCCCTGAATAAGTC 59.614 52.174 0.00 0.00 0.00 3.01
31 32 3.012959 TCCACTCTCTCCCCTGAATAAGT 59.987 47.826 0.00 0.00 0.00 2.24
32 33 3.640967 CTCCACTCTCTCCCCTGAATAAG 59.359 52.174 0.00 0.00 0.00 1.73
33 34 3.647636 CTCCACTCTCTCCCCTGAATAA 58.352 50.000 0.00 0.00 0.00 1.40
34 35 2.691241 GCTCCACTCTCTCCCCTGAATA 60.691 54.545 0.00 0.00 0.00 1.75
35 36 1.969240 GCTCCACTCTCTCCCCTGAAT 60.969 57.143 0.00 0.00 0.00 2.57
36 37 0.616111 GCTCCACTCTCTCCCCTGAA 60.616 60.000 0.00 0.00 0.00 3.02
37 38 1.000993 GCTCCACTCTCTCCCCTGA 59.999 63.158 0.00 0.00 0.00 3.86
38 39 2.063378 GGCTCCACTCTCTCCCCTG 61.063 68.421 0.00 0.00 0.00 4.45
39 40 0.926720 TAGGCTCCACTCTCTCCCCT 60.927 60.000 0.00 0.00 0.00 4.79
40 41 0.189822 ATAGGCTCCACTCTCTCCCC 59.810 60.000 0.00 0.00 0.00 4.81
41 42 1.627864 GATAGGCTCCACTCTCTCCC 58.372 60.000 0.00 0.00 0.00 4.30
42 43 1.202830 TCGATAGGCTCCACTCTCTCC 60.203 57.143 0.00 0.00 0.00 3.71
43 44 2.264005 TCGATAGGCTCCACTCTCTC 57.736 55.000 0.00 0.00 0.00 3.20
44 45 2.582052 CTTCGATAGGCTCCACTCTCT 58.418 52.381 0.00 0.00 0.00 3.10
45 46 1.000717 GCTTCGATAGGCTCCACTCTC 60.001 57.143 0.00 0.00 0.00 3.20
46 47 1.036707 GCTTCGATAGGCTCCACTCT 58.963 55.000 0.00 0.00 0.00 3.24
47 48 0.747255 TGCTTCGATAGGCTCCACTC 59.253 55.000 0.00 0.00 0.00 3.51
48 49 0.461961 GTGCTTCGATAGGCTCCACT 59.538 55.000 0.00 0.00 0.00 4.00
49 50 0.461961 AGTGCTTCGATAGGCTCCAC 59.538 55.000 0.00 0.00 0.00 4.02
50 51 0.747255 GAGTGCTTCGATAGGCTCCA 59.253 55.000 0.00 0.00 0.00 3.86
51 52 1.036707 AGAGTGCTTCGATAGGCTCC 58.963 55.000 0.00 0.00 0.00 4.70
52 53 2.099921 TCAAGAGTGCTTCGATAGGCTC 59.900 50.000 0.00 4.01 30.14 4.70
53 54 2.100584 CTCAAGAGTGCTTCGATAGGCT 59.899 50.000 0.00 0.00 30.14 4.58
54 55 2.099921 TCTCAAGAGTGCTTCGATAGGC 59.900 50.000 0.00 0.00 30.14 3.93
55 56 3.963665 CTCTCAAGAGTGCTTCGATAGG 58.036 50.000 0.00 0.00 37.40 2.57
68 69 5.105146 GGAGCCAAAGATCTTACTCTCAAGA 60.105 44.000 22.44 0.00 38.84 3.02
69 70 5.104982 AGGAGCCAAAGATCTTACTCTCAAG 60.105 44.000 22.44 5.38 0.00 3.02
70 71 4.780021 AGGAGCCAAAGATCTTACTCTCAA 59.220 41.667 22.44 0.00 0.00 3.02
71 72 4.357325 AGGAGCCAAAGATCTTACTCTCA 58.643 43.478 22.44 0.00 0.00 3.27
72 73 4.649218 AGAGGAGCCAAAGATCTTACTCTC 59.351 45.833 22.44 19.47 0.00 3.20
73 74 4.619679 AGAGGAGCCAAAGATCTTACTCT 58.380 43.478 22.44 13.87 0.00 3.24
74 75 5.105146 TGAAGAGGAGCCAAAGATCTTACTC 60.105 44.000 8.75 14.91 30.62 2.59
75 76 4.780021 TGAAGAGGAGCCAAAGATCTTACT 59.220 41.667 8.75 6.83 30.62 2.24
76 77 5.091261 TGAAGAGGAGCCAAAGATCTTAC 57.909 43.478 8.75 1.64 30.62 2.34
77 78 5.965033 ATGAAGAGGAGCCAAAGATCTTA 57.035 39.130 8.75 0.00 30.62 2.10
78 79 4.858965 ATGAAGAGGAGCCAAAGATCTT 57.141 40.909 0.88 0.88 33.07 2.40
79 80 4.474287 AGAATGAAGAGGAGCCAAAGATCT 59.526 41.667 0.00 0.00 0.00 2.75
80 81 4.779696 AGAATGAAGAGGAGCCAAAGATC 58.220 43.478 0.00 0.00 0.00 2.75
81 82 4.474287 AGAGAATGAAGAGGAGCCAAAGAT 59.526 41.667 0.00 0.00 0.00 2.40
82 83 3.843027 AGAGAATGAAGAGGAGCCAAAGA 59.157 43.478 0.00 0.00 0.00 2.52
83 84 4.219264 AGAGAATGAAGAGGAGCCAAAG 57.781 45.455 0.00 0.00 0.00 2.77
84 85 4.532126 TGTAGAGAATGAAGAGGAGCCAAA 59.468 41.667 0.00 0.00 0.00 3.28
85 86 4.096681 TGTAGAGAATGAAGAGGAGCCAA 58.903 43.478 0.00 0.00 0.00 4.52
86 87 3.703556 CTGTAGAGAATGAAGAGGAGCCA 59.296 47.826 0.00 0.00 0.00 4.75
87 88 3.069443 CCTGTAGAGAATGAAGAGGAGCC 59.931 52.174 0.00 0.00 0.00 4.70
88 89 3.069443 CCCTGTAGAGAATGAAGAGGAGC 59.931 52.174 0.00 0.00 0.00 4.70
89 90 3.640967 CCCCTGTAGAGAATGAAGAGGAG 59.359 52.174 0.00 0.00 0.00 3.69
90 91 3.012959 ACCCCTGTAGAGAATGAAGAGGA 59.987 47.826 0.00 0.00 0.00 3.71
91 92 3.379452 ACCCCTGTAGAGAATGAAGAGG 58.621 50.000 0.00 0.00 0.00 3.69
92 93 4.285863 AGACCCCTGTAGAGAATGAAGAG 58.714 47.826 0.00 0.00 0.00 2.85
93 94 4.338795 AGACCCCTGTAGAGAATGAAGA 57.661 45.455 0.00 0.00 0.00 2.87
94 95 5.181748 CAAAGACCCCTGTAGAGAATGAAG 58.818 45.833 0.00 0.00 0.00 3.02
95 96 4.565652 GCAAAGACCCCTGTAGAGAATGAA 60.566 45.833 0.00 0.00 0.00 2.57
96 97 3.055094 GCAAAGACCCCTGTAGAGAATGA 60.055 47.826 0.00 0.00 0.00 2.57
97 98 3.274288 GCAAAGACCCCTGTAGAGAATG 58.726 50.000 0.00 0.00 0.00 2.67
98 99 2.239907 GGCAAAGACCCCTGTAGAGAAT 59.760 50.000 0.00 0.00 0.00 2.40
99 100 1.628846 GGCAAAGACCCCTGTAGAGAA 59.371 52.381 0.00 0.00 0.00 2.87
100 101 1.276622 GGCAAAGACCCCTGTAGAGA 58.723 55.000 0.00 0.00 0.00 3.10
101 102 0.253327 GGGCAAAGACCCCTGTAGAG 59.747 60.000 0.00 0.00 45.00 2.43
102 103 2.383608 GGGCAAAGACCCCTGTAGA 58.616 57.895 0.00 0.00 45.00 2.59
110 111 0.890683 CTTCCATGTGGGCAAAGACC 59.109 55.000 0.00 0.00 36.21 3.85
111 112 0.244721 GCTTCCATGTGGGCAAAGAC 59.755 55.000 0.00 0.00 36.21 3.01
112 113 1.243342 CGCTTCCATGTGGGCAAAGA 61.243 55.000 0.00 0.00 36.21 2.52
113 114 1.213537 CGCTTCCATGTGGGCAAAG 59.786 57.895 0.00 0.00 36.21 2.77
114 115 2.274645 CCGCTTCCATGTGGGCAAA 61.275 57.895 0.00 0.00 36.21 3.68
115 116 2.676121 CCGCTTCCATGTGGGCAA 60.676 61.111 0.00 0.00 36.21 4.52
119 120 4.738998 TGCCCCGCTTCCATGTGG 62.739 66.667 0.00 0.00 37.35 4.17
120 121 3.136123 CTGCCCCGCTTCCATGTG 61.136 66.667 0.00 0.00 0.00 3.21
121 122 3.329889 TCTGCCCCGCTTCCATGT 61.330 61.111 0.00 0.00 0.00 3.21
122 123 2.335092 ATCTCTGCCCCGCTTCCATG 62.335 60.000 0.00 0.00 0.00 3.66
123 124 2.074948 ATCTCTGCCCCGCTTCCAT 61.075 57.895 0.00 0.00 0.00 3.41
124 125 2.688666 ATCTCTGCCCCGCTTCCA 60.689 61.111 0.00 0.00 0.00 3.53
125 126 2.203126 CATCTCTGCCCCGCTTCC 60.203 66.667 0.00 0.00 0.00 3.46
126 127 2.049627 ATCCATCTCTGCCCCGCTTC 62.050 60.000 0.00 0.00 0.00 3.86
127 128 0.764369 TATCCATCTCTGCCCCGCTT 60.764 55.000 0.00 0.00 0.00 4.68
128 129 0.764369 TTATCCATCTCTGCCCCGCT 60.764 55.000 0.00 0.00 0.00 5.52
129 130 0.321122 CTTATCCATCTCTGCCCCGC 60.321 60.000 0.00 0.00 0.00 6.13
130 131 1.342074 TCTTATCCATCTCTGCCCCG 58.658 55.000 0.00 0.00 0.00 5.73
131 132 2.909006 TGATCTTATCCATCTCTGCCCC 59.091 50.000 0.00 0.00 0.00 5.80
132 133 4.630644 TTGATCTTATCCATCTCTGCCC 57.369 45.455 0.00 0.00 0.00 5.36
133 134 5.238214 GTGTTTGATCTTATCCATCTCTGCC 59.762 44.000 0.00 0.00 0.00 4.85
134 135 5.050499 CGTGTTTGATCTTATCCATCTCTGC 60.050 44.000 0.00 0.00 0.00 4.26
135 136 5.464722 CCGTGTTTGATCTTATCCATCTCTG 59.535 44.000 0.00 0.00 0.00 3.35
136 137 5.453903 CCCGTGTTTGATCTTATCCATCTCT 60.454 44.000 0.00 0.00 0.00 3.10
137 138 4.752101 CCCGTGTTTGATCTTATCCATCTC 59.248 45.833 0.00 0.00 0.00 2.75
138 139 4.408921 TCCCGTGTTTGATCTTATCCATCT 59.591 41.667 0.00 0.00 0.00 2.90
139 140 4.703897 TCCCGTGTTTGATCTTATCCATC 58.296 43.478 0.00 0.00 0.00 3.51
140 141 4.771114 TCCCGTGTTTGATCTTATCCAT 57.229 40.909 0.00 0.00 0.00 3.41
141 142 4.561500 TTCCCGTGTTTGATCTTATCCA 57.438 40.909 0.00 0.00 0.00 3.41
142 143 6.990349 TCTTATTCCCGTGTTTGATCTTATCC 59.010 38.462 0.00 0.00 0.00 2.59
143 144 8.433421 TTCTTATTCCCGTGTTTGATCTTATC 57.567 34.615 0.00 0.00 0.00 1.75
144 145 7.012421 GCTTCTTATTCCCGTGTTTGATCTTAT 59.988 37.037 0.00 0.00 0.00 1.73
145 146 6.315393 GCTTCTTATTCCCGTGTTTGATCTTA 59.685 38.462 0.00 0.00 0.00 2.10
146 147 5.123979 GCTTCTTATTCCCGTGTTTGATCTT 59.876 40.000 0.00 0.00 0.00 2.40
147 148 4.636206 GCTTCTTATTCCCGTGTTTGATCT 59.364 41.667 0.00 0.00 0.00 2.75
148 149 4.394920 TGCTTCTTATTCCCGTGTTTGATC 59.605 41.667 0.00 0.00 0.00 2.92
149 150 4.331968 TGCTTCTTATTCCCGTGTTTGAT 58.668 39.130 0.00 0.00 0.00 2.57
150 151 3.745799 TGCTTCTTATTCCCGTGTTTGA 58.254 40.909 0.00 0.00 0.00 2.69
151 152 4.701956 ATGCTTCTTATTCCCGTGTTTG 57.298 40.909 0.00 0.00 0.00 2.93
152 153 5.242838 TCAAATGCTTCTTATTCCCGTGTTT 59.757 36.000 0.00 0.00 0.00 2.83
153 154 4.764823 TCAAATGCTTCTTATTCCCGTGTT 59.235 37.500 0.00 0.00 0.00 3.32
154 155 4.331968 TCAAATGCTTCTTATTCCCGTGT 58.668 39.130 0.00 0.00 0.00 4.49
155 156 4.963276 TCAAATGCTTCTTATTCCCGTG 57.037 40.909 0.00 0.00 0.00 4.94
156 157 5.975693 TTTCAAATGCTTCTTATTCCCGT 57.024 34.783 0.00 0.00 0.00 5.28
157 158 5.232838 GCATTTCAAATGCTTCTTATTCCCG 59.767 40.000 25.16 0.00 41.52 5.14
158 159 5.525012 GGCATTTCAAATGCTTCTTATTCCC 59.475 40.000 29.61 9.45 44.02 3.97
159 160 6.343703 AGGCATTTCAAATGCTTCTTATTCC 58.656 36.000 29.61 13.10 44.02 3.01
160 161 7.838771 AAGGCATTTCAAATGCTTCTTATTC 57.161 32.000 29.61 13.73 44.02 1.75
161 162 8.625786 AAAAGGCATTTCAAATGCTTCTTATT 57.374 26.923 29.61 18.51 44.02 1.40
162 163 8.508875 CAAAAAGGCATTTCAAATGCTTCTTAT 58.491 29.630 29.61 16.45 44.02 1.73
163 164 7.714377 TCAAAAAGGCATTTCAAATGCTTCTTA 59.286 29.630 29.61 11.18 44.02 2.10
164 165 6.543100 TCAAAAAGGCATTTCAAATGCTTCTT 59.457 30.769 29.61 22.64 44.02 2.52
165 166 6.056884 TCAAAAAGGCATTTCAAATGCTTCT 58.943 32.000 29.61 18.74 44.02 2.85
166 167 6.303021 TCAAAAAGGCATTTCAAATGCTTC 57.697 33.333 29.61 16.96 44.02 3.86
167 168 6.487331 TGATCAAAAAGGCATTTCAAATGCTT 59.513 30.769 29.61 22.41 44.02 3.91
168 169 5.998981 TGATCAAAAAGGCATTTCAAATGCT 59.001 32.000 29.61 15.88 44.02 3.79
169 170 6.243811 TGATCAAAAAGGCATTTCAAATGC 57.756 33.333 24.58 24.58 43.85 3.56
170 171 9.685828 AAAATGATCAAAAAGGCATTTCAAATG 57.314 25.926 5.68 5.68 39.31 2.32
179 180 9.034800 ACCTCTATAAAAATGATCAAAAAGGCA 57.965 29.630 0.00 0.00 0.00 4.75
180 181 9.305925 CACCTCTATAAAAATGATCAAAAAGGC 57.694 33.333 0.00 0.00 0.00 4.35
190 191 9.847224 GGGAATTAGTCACCTCTATAAAAATGA 57.153 33.333 0.00 0.00 0.00 2.57
255 256 5.949354 ACGAAAATGGAAAGGGATGTATCAA 59.051 36.000 0.00 0.00 0.00 2.57
263 264 2.158445 TCCCAACGAAAATGGAAAGGGA 60.158 45.455 0.00 0.00 40.56 4.20
392 393 4.033776 CGGCTGCTTCTCCCCCAA 62.034 66.667 0.00 0.00 0.00 4.12
423 424 2.118076 CTTTGGGCCCAGGAAGCA 59.882 61.111 26.87 5.91 0.00 3.91
451 452 2.925966 TCCTTGATTTGGCCAGGAAT 57.074 45.000 5.11 3.41 0.00 3.01
760 766 1.550072 CGATTGAAGCCCCCAACATTT 59.450 47.619 0.00 0.00 0.00 2.32
763 769 0.608035 GACGATTGAAGCCCCCAACA 60.608 55.000 0.00 0.00 0.00 3.33
907 913 2.676121 CCGCTTCCATGTGGGCAA 60.676 61.111 0.00 0.00 36.21 4.52
1090 1100 1.481871 CTACGAAGGGGTTAGGAGCA 58.518 55.000 0.00 0.00 0.00 4.26
1154 1165 3.214328 CCAACTTCACTTGCCTGTAAGT 58.786 45.455 0.00 0.00 41.37 2.24
1159 1170 1.605710 CTCACCAACTTCACTTGCCTG 59.394 52.381 0.00 0.00 0.00 4.85
1188 1199 1.227674 CGCAGGAGATAGTTGCCCC 60.228 63.158 0.00 0.00 34.42 5.80
1211 1222 3.449746 ACTAACAGCTGAGTCCTCTCT 57.550 47.619 23.35 0.00 40.98 3.10
1384 1395 8.757307 AGGGATATGGAAAGGATGAAGTAATA 57.243 34.615 0.00 0.00 0.00 0.98
1411 1422 5.895928 TGATGAGTAAGATCGAACAAGAGG 58.104 41.667 0.00 0.00 0.00 3.69
1413 1424 7.278646 CCATTTGATGAGTAAGATCGAACAAGA 59.721 37.037 0.00 0.00 0.00 3.02
1457 1468 4.903638 TGTCAATGATCGAACGAACTTC 57.096 40.909 0.12 0.00 0.00 3.01
1870 1883 3.496331 GGGGACTTTGATCCAACTTCAA 58.504 45.455 0.00 0.00 40.96 2.69
1940 1953 1.195442 TTCGGTAGTGATGGGGTGCA 61.195 55.000 0.00 0.00 0.00 4.57
1958 1971 9.930693 CACCTAAGTTAGAGATTTCAACTACTT 57.069 33.333 11.66 0.00 32.35 2.24
2035 2048 0.032615 AGCGGGGATCTCTCAGTTCT 60.033 55.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.