Multiple sequence alignment - TraesCS4B01G029500

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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 TraesCS4B01G029500 chr4B 100.000 2445 0 0 1 2445 21609125 21606681 0.000000e+00 4516.0
1 TraesCS4B01G029500 chr2B 97.837 2219 46 2 229 2445 777095408 777093190 0.000000e+00 3831.0
2 TraesCS4B01G029500 chr2B 97.833 2215 47 1 232 2445 160162454 160164668 0.000000e+00 3823.0
3 TraesCS4B01G029500 chr2B 97.743 2215 49 1 232 2445 412260062 412257848 0.000000e+00 3812.0
4 TraesCS4B01G029500 chr2B 97.742 2214 49 1 233 2445 786136938 786134725 0.000000e+00 3810.0
5 TraesCS4B01G029500 chr2B 93.878 49 2 1 1 48 649947976 649948024 3.370000e-09 73.1
6 TraesCS4B01G029500 chr3B 97.833 2215 47 1 232 2445 781496214 781498428 0.000000e+00 3823.0
7 TraesCS4B01G029500 chr5B 97.832 2214 46 2 233 2445 515110359 515108147 0.000000e+00 3821.0
8 TraesCS4B01G029500 chr5B 97.789 2216 47 2 231 2445 334680527 334678313 0.000000e+00 3819.0
9 TraesCS4B01G029500 chr5B 87.931 58 2 5 1 56 520553352 520553298 2.030000e-06 63.9
10 TraesCS4B01G029500 chr1B 97.743 2215 49 1 232 2445 31865928 31868142 0.000000e+00 3812.0
11 TraesCS4B01G029500 chr7B 97.743 2215 47 3 232 2445 222316414 222318626 0.000000e+00 3810.0
12 TraesCS4B01G029500 chr3A 93.878 49 1 2 1 48 726995345 726995392 3.370000e-09 73.1
13 TraesCS4B01G029500 chr6A 90.741 54 3 2 1 53 594849345 594849293 1.210000e-08 71.3
14 TraesCS4B01G029500 chr7D 90.909 55 0 5 6 56 282157759 282157812 4.360000e-08 69.4
15 TraesCS4B01G029500 chr6B 92.000 50 3 1 1 49 691786662 691786613 4.360000e-08 69.4
16 TraesCS4B01G029500 chr2A 89.091 55 4 2 2 54 657955016 657954962 1.570000e-07 67.6
17 TraesCS4B01G029500 chr1A 89.091 55 2 4 1 52 85356825 85356878 5.640000e-07 65.8
18 TraesCS4B01G029500 chr4D 87.500 56 5 2 1 56 37490635 37490582 2.030000e-06 63.9


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 TraesCS4B01G029500 chr4B 21606681 21609125 2444 True 4516 4516 100.000 1 2445 1 chr4B.!!$R1 2444
1 TraesCS4B01G029500 chr2B 777093190 777095408 2218 True 3831 3831 97.837 229 2445 1 chr2B.!!$R2 2216
2 TraesCS4B01G029500 chr2B 160162454 160164668 2214 False 3823 3823 97.833 232 2445 1 chr2B.!!$F1 2213
3 TraesCS4B01G029500 chr2B 412257848 412260062 2214 True 3812 3812 97.743 232 2445 1 chr2B.!!$R1 2213
4 TraesCS4B01G029500 chr2B 786134725 786136938 2213 True 3810 3810 97.742 233 2445 1 chr2B.!!$R3 2212
5 TraesCS4B01G029500 chr3B 781496214 781498428 2214 False 3823 3823 97.833 232 2445 1 chr3B.!!$F1 2213
6 TraesCS4B01G029500 chr5B 515108147 515110359 2212 True 3821 3821 97.832 233 2445 1 chr5B.!!$R2 2212
7 TraesCS4B01G029500 chr5B 334678313 334680527 2214 True 3819 3819 97.789 231 2445 1 chr5B.!!$R1 2214
8 TraesCS4B01G029500 chr1B 31865928 31868142 2214 False 3812 3812 97.743 232 2445 1 chr1B.!!$F1 2213
9 TraesCS4B01G029500 chr7B 222316414 222318626 2212 False 3810 3810 97.743 232 2445 1 chr7B.!!$F1 2213

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
168 169 0.03438 CGAGGTCTCTCAGGTGGGTA 60.034 60.0 0.0 0.0 39.95 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2076 0.178981 AGCAATTCCAGTGTGGTGCT 60.179 50.0 4.2 4.2 40.99 4.4 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
31 32 3.721706 CCTGCTGGTCCCCCTGTC 61.722 72.222 0.51 0.00 32.49 3.51
32 33 2.608988 CTGCTGGTCCCCCTGTCT 60.609 66.667 0.00 0.00 32.49 3.41
33 34 2.607750 TGCTGGTCCCCCTGTCTC 60.608 66.667 0.00 0.00 32.49 3.36
34 35 3.403558 GCTGGTCCCCCTGTCTCC 61.404 72.222 0.00 0.00 32.49 3.71
35 36 3.077556 CTGGTCCCCCTGTCTCCG 61.078 72.222 0.00 0.00 0.00 4.63
41 42 4.087892 CCCCTGTCTCCGCCACTG 62.088 72.222 0.00 0.00 0.00 3.66
42 43 3.314331 CCCTGTCTCCGCCACTGT 61.314 66.667 0.00 0.00 0.00 3.55
43 44 2.047844 CCTGTCTCCGCCACTGTG 60.048 66.667 0.00 0.00 0.00 3.66
44 45 2.737180 CTGTCTCCGCCACTGTGT 59.263 61.111 7.08 0.00 0.00 3.72
45 46 1.532604 CCTGTCTCCGCCACTGTGTA 61.533 60.000 7.08 0.00 0.00 2.90
46 47 0.532573 CTGTCTCCGCCACTGTGTAT 59.467 55.000 7.08 0.00 0.00 2.29
47 48 0.246360 TGTCTCCGCCACTGTGTATG 59.754 55.000 7.08 0.00 0.00 2.39
48 49 0.246635 GTCTCCGCCACTGTGTATGT 59.753 55.000 7.08 0.00 0.00 2.29
49 50 1.475280 GTCTCCGCCACTGTGTATGTA 59.525 52.381 7.08 0.00 0.00 2.29
50 51 2.100916 GTCTCCGCCACTGTGTATGTAT 59.899 50.000 7.08 0.00 0.00 2.29
51 52 2.100749 TCTCCGCCACTGTGTATGTATG 59.899 50.000 7.08 0.00 0.00 2.39
52 53 0.937304 CCGCCACTGTGTATGTATGC 59.063 55.000 7.08 0.13 0.00 3.14
53 54 1.650825 CGCCACTGTGTATGTATGCA 58.349 50.000 7.08 0.00 0.00 3.96
54 55 2.212652 CGCCACTGTGTATGTATGCAT 58.787 47.619 3.79 3.79 39.03 3.96
55 56 2.032636 CGCCACTGTGTATGTATGCATG 60.033 50.000 10.16 0.00 36.58 4.06
56 57 2.287188 GCCACTGTGTATGTATGCATGC 60.287 50.000 11.82 11.82 38.06 4.06
57 58 2.291465 CCACTGTGTATGTATGCATGCC 59.709 50.000 16.68 0.00 36.98 4.40
58 59 3.208594 CACTGTGTATGTATGCATGCCT 58.791 45.455 16.68 8.18 36.98 4.75
59 60 3.628942 CACTGTGTATGTATGCATGCCTT 59.371 43.478 16.68 5.27 36.98 4.35
60 61 3.628942 ACTGTGTATGTATGCATGCCTTG 59.371 43.478 16.68 0.86 36.98 3.61
61 62 2.950975 TGTGTATGTATGCATGCCTTGG 59.049 45.455 16.68 0.00 36.98 3.61
62 63 2.951642 GTGTATGTATGCATGCCTTGGT 59.048 45.455 16.68 1.04 36.98 3.67
63 64 3.381272 GTGTATGTATGCATGCCTTGGTT 59.619 43.478 16.68 0.00 36.98 3.67
64 65 4.022603 TGTATGTATGCATGCCTTGGTTT 58.977 39.130 16.68 0.00 36.98 3.27
65 66 4.465660 TGTATGTATGCATGCCTTGGTTTT 59.534 37.500 16.68 0.00 36.98 2.43
66 67 3.316071 TGTATGCATGCCTTGGTTTTG 57.684 42.857 16.68 0.00 0.00 2.44
67 68 2.028294 TGTATGCATGCCTTGGTTTTGG 60.028 45.455 16.68 0.00 0.00 3.28
77 78 3.917988 CCTTGGTTTTGGCAGAAGAATC 58.082 45.455 0.00 0.00 0.00 2.52
78 79 3.568538 CTTGGTTTTGGCAGAAGAATCG 58.431 45.455 0.00 0.00 0.00 3.34
79 80 1.269448 TGGTTTTGGCAGAAGAATCGC 59.731 47.619 0.00 0.00 0.00 4.58
80 81 1.606606 GTTTTGGCAGAAGAATCGCG 58.393 50.000 0.00 0.00 0.00 5.87
81 82 1.069227 GTTTTGGCAGAAGAATCGCGT 60.069 47.619 5.77 0.00 0.00 6.01
82 83 2.087501 TTTGGCAGAAGAATCGCGTA 57.912 45.000 5.77 0.00 0.00 4.42
83 84 2.309528 TTGGCAGAAGAATCGCGTAT 57.690 45.000 5.77 0.00 0.00 3.06
84 85 1.570813 TGGCAGAAGAATCGCGTATG 58.429 50.000 5.77 0.00 0.00 2.39
85 86 1.134818 TGGCAGAAGAATCGCGTATGT 60.135 47.619 5.77 0.00 0.00 2.29
86 87 2.100087 TGGCAGAAGAATCGCGTATGTA 59.900 45.455 5.77 0.00 0.00 2.29
87 88 3.243737 TGGCAGAAGAATCGCGTATGTAT 60.244 43.478 5.77 0.00 0.00 2.29
88 89 4.022676 TGGCAGAAGAATCGCGTATGTATA 60.023 41.667 5.77 0.00 0.00 1.47
89 90 4.559251 GGCAGAAGAATCGCGTATGTATAG 59.441 45.833 5.77 0.00 0.00 1.31
90 91 4.030753 GCAGAAGAATCGCGTATGTATAGC 59.969 45.833 5.77 0.00 0.00 2.97
91 92 5.394802 CAGAAGAATCGCGTATGTATAGCT 58.605 41.667 5.77 0.00 0.00 3.32
92 93 5.509972 CAGAAGAATCGCGTATGTATAGCTC 59.490 44.000 5.77 0.00 0.00 4.09
93 94 5.181433 AGAAGAATCGCGTATGTATAGCTCA 59.819 40.000 5.77 0.00 0.00 4.26
94 95 4.724303 AGAATCGCGTATGTATAGCTCAC 58.276 43.478 5.77 0.00 0.00 3.51
95 96 4.456222 AGAATCGCGTATGTATAGCTCACT 59.544 41.667 5.77 0.00 0.00 3.41
96 97 5.642491 AGAATCGCGTATGTATAGCTCACTA 59.358 40.000 5.77 0.00 0.00 2.74
97 98 4.923264 TCGCGTATGTATAGCTCACTAG 57.077 45.455 5.77 0.00 0.00 2.57
109 110 2.119801 CTCACTAGCAATGCTTGGGT 57.880 50.000 14.85 7.70 40.44 4.51
110 111 3.266510 CTCACTAGCAATGCTTGGGTA 57.733 47.619 14.85 2.09 40.44 3.69
111 112 3.609853 CTCACTAGCAATGCTTGGGTAA 58.390 45.455 14.85 0.00 40.44 2.85
112 113 4.009675 CTCACTAGCAATGCTTGGGTAAA 58.990 43.478 14.85 0.00 40.44 2.01
113 114 4.009675 TCACTAGCAATGCTTGGGTAAAG 58.990 43.478 14.85 5.12 40.44 1.85
114 115 3.758554 CACTAGCAATGCTTGGGTAAAGT 59.241 43.478 14.85 5.85 40.44 2.66
115 116 4.941263 CACTAGCAATGCTTGGGTAAAGTA 59.059 41.667 14.85 0.00 40.44 2.24
116 117 4.941873 ACTAGCAATGCTTGGGTAAAGTAC 59.058 41.667 14.85 0.00 40.44 2.73
117 118 3.761897 AGCAATGCTTGGGTAAAGTACA 58.238 40.909 0.00 0.00 33.89 2.90
118 119 3.506067 AGCAATGCTTGGGTAAAGTACAC 59.494 43.478 0.00 0.00 33.89 2.90
119 120 3.254657 GCAATGCTTGGGTAAAGTACACA 59.745 43.478 0.00 0.00 41.05 3.72
127 128 5.113446 TGGGTAAAGTACACAAAACAGGA 57.887 39.130 0.00 0.00 39.56 3.86
128 129 4.883006 TGGGTAAAGTACACAAAACAGGAC 59.117 41.667 0.00 0.00 39.56 3.85
129 130 4.276678 GGGTAAAGTACACAAAACAGGACC 59.723 45.833 0.00 0.00 30.72 4.46
130 131 4.883006 GGTAAAGTACACAAAACAGGACCA 59.117 41.667 0.00 0.00 0.00 4.02
131 132 4.976224 AAAGTACACAAAACAGGACCAC 57.024 40.909 0.00 0.00 0.00 4.16
132 133 2.927028 AGTACACAAAACAGGACCACC 58.073 47.619 0.00 0.00 0.00 4.61
134 135 2.052782 ACACAAAACAGGACCACCTC 57.947 50.000 0.00 0.00 45.94 3.85
135 136 1.283613 ACACAAAACAGGACCACCTCA 59.716 47.619 0.00 0.00 45.94 3.86
136 137 1.676006 CACAAAACAGGACCACCTCAC 59.324 52.381 0.00 0.00 45.94 3.51
137 138 1.318576 CAAAACAGGACCACCTCACC 58.681 55.000 0.00 0.00 45.94 4.02
138 139 0.179029 AAAACAGGACCACCTCACCG 60.179 55.000 0.00 0.00 45.94 4.94
139 140 1.052124 AAACAGGACCACCTCACCGA 61.052 55.000 0.00 0.00 45.94 4.69
140 141 1.052124 AACAGGACCACCTCACCGAA 61.052 55.000 0.00 0.00 45.94 4.30
141 142 1.004918 CAGGACCACCTCACCGAAC 60.005 63.158 0.00 0.00 45.94 3.95
142 143 1.458777 AGGACCACCTCACCGAACA 60.459 57.895 0.00 0.00 44.13 3.18
143 144 1.301479 GGACCACCTCACCGAACAC 60.301 63.158 0.00 0.00 0.00 3.32
144 145 1.663702 GACCACCTCACCGAACACG 60.664 63.158 0.00 0.00 0.00 4.49
145 146 3.041940 CCACCTCACCGAACACGC 61.042 66.667 0.00 0.00 0.00 5.34
146 147 2.279851 CACCTCACCGAACACGCA 60.280 61.111 0.00 0.00 0.00 5.24
147 148 2.279918 ACCTCACCGAACACGCAC 60.280 61.111 0.00 0.00 0.00 5.34
148 149 2.029073 CCTCACCGAACACGCACT 59.971 61.111 0.00 0.00 0.00 4.40
149 150 2.022129 CCTCACCGAACACGCACTC 61.022 63.158 0.00 0.00 0.00 3.51
150 151 2.354188 TCACCGAACACGCACTCG 60.354 61.111 0.00 0.00 42.43 4.18
151 152 2.354188 CACCGAACACGCACTCGA 60.354 61.111 2.54 0.00 37.23 4.04
152 153 2.050351 ACCGAACACGCACTCGAG 60.050 61.111 11.84 11.84 37.23 4.04
153 154 2.805353 CCGAACACGCACTCGAGG 60.805 66.667 18.41 6.97 37.23 4.63
154 155 2.050351 CGAACACGCACTCGAGGT 60.050 61.111 18.41 1.73 37.23 3.85
155 156 2.081212 CGAACACGCACTCGAGGTC 61.081 63.158 18.41 6.75 39.17 3.85
156 157 1.286260 GAACACGCACTCGAGGTCT 59.714 57.895 18.41 0.00 39.40 3.85
157 158 0.729816 GAACACGCACTCGAGGTCTC 60.730 60.000 18.41 1.50 39.40 3.36
158 159 1.173444 AACACGCACTCGAGGTCTCT 61.173 55.000 18.41 0.00 39.41 3.10
159 160 1.135731 CACGCACTCGAGGTCTCTC 59.864 63.158 18.41 0.00 39.41 3.20
160 161 1.302591 ACGCACTCGAGGTCTCTCA 60.303 57.895 18.41 0.00 39.95 3.27
161 162 1.302383 ACGCACTCGAGGTCTCTCAG 61.302 60.000 18.41 1.71 39.95 3.35
162 163 1.806568 GCACTCGAGGTCTCTCAGG 59.193 63.158 18.41 0.00 39.95 3.86
163 164 0.963355 GCACTCGAGGTCTCTCAGGT 60.963 60.000 18.41 0.00 39.95 4.00
164 165 0.808125 CACTCGAGGTCTCTCAGGTG 59.192 60.000 18.41 0.00 39.95 4.00
165 166 0.322997 ACTCGAGGTCTCTCAGGTGG 60.323 60.000 18.41 0.00 39.95 4.61
166 167 1.000771 TCGAGGTCTCTCAGGTGGG 60.001 63.158 0.00 0.00 39.95 4.61
167 168 1.304547 CGAGGTCTCTCAGGTGGGT 60.305 63.158 0.00 0.00 39.95 4.51
168 169 0.034380 CGAGGTCTCTCAGGTGGGTA 60.034 60.000 0.00 0.00 39.95 3.69
169 170 1.616187 CGAGGTCTCTCAGGTGGGTAA 60.616 57.143 0.00 0.00 39.95 2.85
170 171 2.104170 GAGGTCTCTCAGGTGGGTAAG 58.896 57.143 0.00 0.00 39.74 2.34
171 172 1.196012 GGTCTCTCAGGTGGGTAAGG 58.804 60.000 0.00 0.00 0.00 2.69
172 173 1.196012 GTCTCTCAGGTGGGTAAGGG 58.804 60.000 0.00 0.00 0.00 3.95
173 174 0.617820 TCTCTCAGGTGGGTAAGGGC 60.618 60.000 0.00 0.00 0.00 5.19
174 175 0.909610 CTCTCAGGTGGGTAAGGGCA 60.910 60.000 0.00 0.00 0.00 5.36
175 176 0.253160 TCTCAGGTGGGTAAGGGCAT 60.253 55.000 0.00 0.00 0.00 4.40
176 177 0.181350 CTCAGGTGGGTAAGGGCATC 59.819 60.000 0.00 0.00 0.00 3.91
177 178 0.253160 TCAGGTGGGTAAGGGCATCT 60.253 55.000 0.00 0.00 0.00 2.90
178 179 0.181350 CAGGTGGGTAAGGGCATCTC 59.819 60.000 0.00 0.00 0.00 2.75
179 180 0.988678 AGGTGGGTAAGGGCATCTCC 60.989 60.000 0.00 0.00 0.00 3.71
180 181 1.279025 GGTGGGTAAGGGCATCTCCA 61.279 60.000 0.00 0.00 36.21 3.86
181 182 0.623723 GTGGGTAAGGGCATCTCCAA 59.376 55.000 0.00 0.00 36.21 3.53
182 183 0.623723 TGGGTAAGGGCATCTCCAAC 59.376 55.000 0.00 0.00 36.21 3.77
183 184 0.623723 GGGTAAGGGCATCTCCAACA 59.376 55.000 0.00 0.00 36.21 3.33
184 185 1.682087 GGGTAAGGGCATCTCCAACAC 60.682 57.143 0.00 0.00 36.21 3.32
185 186 1.004277 GGTAAGGGCATCTCCAACACA 59.996 52.381 0.00 0.00 36.21 3.72
186 187 2.084546 GTAAGGGCATCTCCAACACAC 58.915 52.381 0.00 0.00 36.21 3.82
187 188 0.251341 AAGGGCATCTCCAACACACC 60.251 55.000 0.00 0.00 36.21 4.16
188 189 1.678970 GGGCATCTCCAACACACCC 60.679 63.158 0.00 0.00 36.21 4.61
189 190 1.380302 GGCATCTCCAACACACCCT 59.620 57.895 0.00 0.00 34.01 4.34
190 191 0.678048 GGCATCTCCAACACACCCTC 60.678 60.000 0.00 0.00 34.01 4.30
191 192 0.036732 GCATCTCCAACACACCCTCA 59.963 55.000 0.00 0.00 0.00 3.86
192 193 1.545428 GCATCTCCAACACACCCTCAA 60.545 52.381 0.00 0.00 0.00 3.02
193 194 2.862541 CATCTCCAACACACCCTCAAA 58.137 47.619 0.00 0.00 0.00 2.69
194 195 2.341846 TCTCCAACACACCCTCAAAC 57.658 50.000 0.00 0.00 0.00 2.93
195 196 1.133915 TCTCCAACACACCCTCAAACC 60.134 52.381 0.00 0.00 0.00 3.27
196 197 0.464735 TCCAACACACCCTCAAACCG 60.465 55.000 0.00 0.00 0.00 4.44
197 198 0.750182 CCAACACACCCTCAAACCGT 60.750 55.000 0.00 0.00 0.00 4.83
198 199 0.661020 CAACACACCCTCAAACCGTC 59.339 55.000 0.00 0.00 0.00 4.79
199 200 0.544697 AACACACCCTCAAACCGTCT 59.455 50.000 0.00 0.00 0.00 4.18
200 201 0.179056 ACACACCCTCAAACCGTCTG 60.179 55.000 0.00 0.00 0.00 3.51
201 202 0.884704 CACACCCTCAAACCGTCTGG 60.885 60.000 0.00 0.00 42.84 3.86
202 203 1.052124 ACACCCTCAAACCGTCTGGA 61.052 55.000 0.00 0.00 39.21 3.86
203 204 0.324943 CACCCTCAAACCGTCTGGAT 59.675 55.000 0.00 0.00 39.21 3.41
204 205 1.553248 CACCCTCAAACCGTCTGGATA 59.447 52.381 0.00 0.00 39.21 2.59
205 206 2.170607 CACCCTCAAACCGTCTGGATAT 59.829 50.000 0.00 0.00 39.21 1.63
206 207 2.170607 ACCCTCAAACCGTCTGGATATG 59.829 50.000 0.00 0.00 39.21 1.78
207 208 2.170607 CCCTCAAACCGTCTGGATATGT 59.829 50.000 0.00 0.00 39.21 2.29
208 209 3.458189 CCTCAAACCGTCTGGATATGTC 58.542 50.000 0.00 0.00 39.21 3.06
209 210 3.458189 CTCAAACCGTCTGGATATGTCC 58.542 50.000 0.60 0.60 45.31 4.02
218 219 2.121645 GGATATGTCCGGACCGTGT 58.878 57.895 31.19 18.00 34.13 4.49
219 220 0.249322 GGATATGTCCGGACCGTGTG 60.249 60.000 31.19 0.00 34.13 3.82
220 221 0.249322 GATATGTCCGGACCGTGTGG 60.249 60.000 31.19 0.00 42.84 4.17
240 241 0.035152 TCCGGACCGCTCACTAGTAA 60.035 55.000 8.86 0.00 0.00 2.24
481 482 1.067635 GGCACGAACCGGTACTAAAGA 60.068 52.381 8.00 0.00 0.00 2.52
894 896 3.161557 ACCTTGTGGTGAGCCTCC 58.838 61.111 0.00 0.00 46.51 4.30
1013 1015 8.710749 ATACATAGTGCCATGGTTTTGATATT 57.289 30.769 14.67 0.00 0.00 1.28
1333 1335 5.475273 TGCGCTTGAAGATTAGAAAGATG 57.525 39.130 9.73 0.00 0.00 2.90
1402 1404 5.417580 TGGATCAATTGTTACCTTAGTTGCC 59.582 40.000 5.13 0.00 0.00 4.52
1571 1573 1.333931 GTACGATGACCGATGCTCTCA 59.666 52.381 0.00 0.00 41.76 3.27
1572 1574 1.035923 ACGATGACCGATGCTCTCAT 58.964 50.000 0.00 0.00 41.76 2.90
1657 1659 2.512692 TATGCCTTGTCCATGTGCTT 57.487 45.000 0.00 0.00 0.00 3.91
1672 1674 3.221771 TGTGCTTGCTGTAAGAATGGTT 58.778 40.909 9.78 0.00 38.76 3.67
1699 1701 7.360946 GCAATTACTCTACGTCAAGAACCATTT 60.361 37.037 0.00 0.00 0.00 2.32
1803 1805 5.186797 AGACAATGAAGAAGAAGAGGACGAT 59.813 40.000 0.00 0.00 0.00 3.73
1816 1818 3.073209 AGAGGACGATGACAGCTATCCTA 59.927 47.826 12.01 0.00 36.70 2.94
1978 1980 1.603456 TGCCGATGCAAAGAGAAACA 58.397 45.000 0.00 0.00 46.66 2.83
2074 2076 3.807622 CGTAGGTGACAAGAAAAAGCTGA 59.192 43.478 0.00 0.00 0.00 4.26
2186 2188 2.582052 TCCAAAGGACAACGAATTGCT 58.418 42.857 0.00 0.00 39.66 3.91
2188 2190 2.293122 CCAAAGGACAACGAATTGCTCA 59.707 45.455 0.00 0.00 39.66 4.26
2196 2198 4.377021 ACAACGAATTGCTCAAGAGTACA 58.623 39.130 0.00 0.00 39.66 2.90
2298 2300 1.064505 CGCGGTGAGTACGAGGATTTA 59.935 52.381 0.00 0.00 0.00 1.40
2307 2309 4.563061 AGTACGAGGATTTAAACGCTTGT 58.437 39.130 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.246635 ACATACACAGTGGCGGAGAC 59.753 55.000 5.31 0.00 0.00 3.36
30 31 1.842052 TACATACACAGTGGCGGAGA 58.158 50.000 5.31 0.00 0.00 3.71
31 32 2.473816 CATACATACACAGTGGCGGAG 58.526 52.381 5.31 0.00 0.00 4.63
32 33 1.472552 GCATACATACACAGTGGCGGA 60.473 52.381 5.31 0.00 0.00 5.54
33 34 0.937304 GCATACATACACAGTGGCGG 59.063 55.000 5.31 0.00 0.00 6.13
34 35 1.650825 TGCATACATACACAGTGGCG 58.349 50.000 5.31 0.00 0.00 5.69
35 36 2.287188 GCATGCATACATACACAGTGGC 60.287 50.000 14.21 0.00 33.67 5.01
36 37 2.291465 GGCATGCATACATACACAGTGG 59.709 50.000 21.36 0.00 33.67 4.00
37 38 3.208594 AGGCATGCATACATACACAGTG 58.791 45.455 21.36 0.00 33.67 3.66
38 39 3.565764 AGGCATGCATACATACACAGT 57.434 42.857 21.36 0.00 33.67 3.55
39 40 3.004002 CCAAGGCATGCATACATACACAG 59.996 47.826 21.36 0.00 33.67 3.66
40 41 2.950975 CCAAGGCATGCATACATACACA 59.049 45.455 21.36 0.00 33.67 3.72
41 42 2.951642 ACCAAGGCATGCATACATACAC 59.048 45.455 21.36 0.00 33.67 2.90
42 43 3.295585 ACCAAGGCATGCATACATACA 57.704 42.857 21.36 0.00 33.67 2.29
43 44 4.654091 AAACCAAGGCATGCATACATAC 57.346 40.909 21.36 0.00 33.67 2.39
44 45 4.141981 CCAAAACCAAGGCATGCATACATA 60.142 41.667 21.36 0.00 33.67 2.29
45 46 3.369681 CCAAAACCAAGGCATGCATACAT 60.370 43.478 21.36 0.00 36.79 2.29
46 47 2.028294 CCAAAACCAAGGCATGCATACA 60.028 45.455 21.36 0.00 0.00 2.29
47 48 2.620242 CCAAAACCAAGGCATGCATAC 58.380 47.619 21.36 1.57 0.00 2.39
49 50 3.940229 CCAAAACCAAGGCATGCAT 57.060 47.368 21.36 10.32 0.00 3.96
56 57 3.612479 CGATTCTTCTGCCAAAACCAAGG 60.612 47.826 0.00 0.00 0.00 3.61
57 58 3.568538 CGATTCTTCTGCCAAAACCAAG 58.431 45.455 0.00 0.00 0.00 3.61
58 59 2.288152 GCGATTCTTCTGCCAAAACCAA 60.288 45.455 0.00 0.00 0.00 3.67
59 60 1.269448 GCGATTCTTCTGCCAAAACCA 59.731 47.619 0.00 0.00 0.00 3.67
60 61 1.729149 CGCGATTCTTCTGCCAAAACC 60.729 52.381 0.00 0.00 0.00 3.27
61 62 1.069227 ACGCGATTCTTCTGCCAAAAC 60.069 47.619 15.93 0.00 0.00 2.43
62 63 1.234821 ACGCGATTCTTCTGCCAAAA 58.765 45.000 15.93 0.00 0.00 2.44
63 64 2.087501 TACGCGATTCTTCTGCCAAA 57.912 45.000 15.93 0.00 0.00 3.28
64 65 1.933181 CATACGCGATTCTTCTGCCAA 59.067 47.619 15.93 0.00 0.00 4.52
65 66 1.134818 ACATACGCGATTCTTCTGCCA 60.135 47.619 15.93 0.00 0.00 4.92
66 67 1.571919 ACATACGCGATTCTTCTGCC 58.428 50.000 15.93 0.00 0.00 4.85
67 68 4.030753 GCTATACATACGCGATTCTTCTGC 59.969 45.833 15.93 5.02 0.00 4.26
68 69 5.394802 AGCTATACATACGCGATTCTTCTG 58.605 41.667 15.93 1.38 0.00 3.02
69 70 5.181433 TGAGCTATACATACGCGATTCTTCT 59.819 40.000 15.93 0.00 0.00 2.85
70 71 5.284188 GTGAGCTATACATACGCGATTCTTC 59.716 44.000 15.93 0.00 0.00 2.87
71 72 5.048643 AGTGAGCTATACATACGCGATTCTT 60.049 40.000 15.93 0.00 0.00 2.52
72 73 4.456222 AGTGAGCTATACATACGCGATTCT 59.544 41.667 15.93 0.00 0.00 2.40
73 74 4.724303 AGTGAGCTATACATACGCGATTC 58.276 43.478 15.93 0.00 0.00 2.52
74 75 4.768130 AGTGAGCTATACATACGCGATT 57.232 40.909 15.93 0.00 0.00 3.34
75 76 4.201832 GCTAGTGAGCTATACATACGCGAT 60.202 45.833 15.93 0.00 45.98 4.58
76 77 3.124806 GCTAGTGAGCTATACATACGCGA 59.875 47.826 15.93 0.00 45.98 5.87
77 78 3.418094 GCTAGTGAGCTATACATACGCG 58.582 50.000 3.53 3.53 45.98 6.01
99 100 6.127310 TGTTTTGTGTACTTTACCCAAGCATT 60.127 34.615 0.00 0.00 35.65 3.56
100 101 5.361285 TGTTTTGTGTACTTTACCCAAGCAT 59.639 36.000 0.00 0.00 35.65 3.79
101 102 4.705507 TGTTTTGTGTACTTTACCCAAGCA 59.294 37.500 0.00 0.00 35.65 3.91
102 103 5.251601 TGTTTTGTGTACTTTACCCAAGC 57.748 39.130 0.00 0.00 35.65 4.01
103 104 5.591067 TCCTGTTTTGTGTACTTTACCCAAG 59.409 40.000 0.00 0.00 38.64 3.61
104 105 5.357596 GTCCTGTTTTGTGTACTTTACCCAA 59.642 40.000 0.00 0.00 0.00 4.12
105 106 4.883006 GTCCTGTTTTGTGTACTTTACCCA 59.117 41.667 0.00 0.00 0.00 4.51
106 107 4.276678 GGTCCTGTTTTGTGTACTTTACCC 59.723 45.833 0.00 0.00 0.00 3.69
107 108 4.883006 TGGTCCTGTTTTGTGTACTTTACC 59.117 41.667 0.00 0.00 0.00 2.85
108 109 5.220912 GGTGGTCCTGTTTTGTGTACTTTAC 60.221 44.000 0.00 0.00 0.00 2.01
109 110 4.883006 GGTGGTCCTGTTTTGTGTACTTTA 59.117 41.667 0.00 0.00 0.00 1.85
110 111 3.697542 GGTGGTCCTGTTTTGTGTACTTT 59.302 43.478 0.00 0.00 0.00 2.66
111 112 3.053917 AGGTGGTCCTGTTTTGTGTACTT 60.054 43.478 0.00 0.00 43.33 2.24
112 113 2.508300 AGGTGGTCCTGTTTTGTGTACT 59.492 45.455 0.00 0.00 43.33 2.73
113 114 2.876550 GAGGTGGTCCTGTTTTGTGTAC 59.123 50.000 0.00 0.00 45.24 2.90
114 115 2.506231 TGAGGTGGTCCTGTTTTGTGTA 59.494 45.455 0.00 0.00 45.24 2.90
115 116 1.283613 TGAGGTGGTCCTGTTTTGTGT 59.716 47.619 0.00 0.00 45.24 3.72
116 117 1.676006 GTGAGGTGGTCCTGTTTTGTG 59.324 52.381 0.00 0.00 45.24 3.33
117 118 1.409661 GGTGAGGTGGTCCTGTTTTGT 60.410 52.381 0.00 0.00 45.24 2.83
118 119 1.318576 GGTGAGGTGGTCCTGTTTTG 58.681 55.000 0.00 0.00 45.24 2.44
119 120 0.179029 CGGTGAGGTGGTCCTGTTTT 60.179 55.000 0.00 0.00 45.24 2.43
120 121 1.052124 TCGGTGAGGTGGTCCTGTTT 61.052 55.000 0.00 0.00 45.24 2.83
121 122 1.052124 TTCGGTGAGGTGGTCCTGTT 61.052 55.000 0.00 0.00 45.24 3.16
122 123 1.458777 TTCGGTGAGGTGGTCCTGT 60.459 57.895 0.00 0.00 45.24 4.00
123 124 1.004918 GTTCGGTGAGGTGGTCCTG 60.005 63.158 0.00 0.00 45.24 3.86
125 126 1.301479 GTGTTCGGTGAGGTGGTCC 60.301 63.158 0.00 0.00 0.00 4.46
126 127 1.663702 CGTGTTCGGTGAGGTGGTC 60.664 63.158 0.00 0.00 0.00 4.02
127 128 2.420043 CGTGTTCGGTGAGGTGGT 59.580 61.111 0.00 0.00 0.00 4.16
128 129 3.041940 GCGTGTTCGGTGAGGTGG 61.042 66.667 0.00 0.00 37.56 4.61
129 130 2.279851 TGCGTGTTCGGTGAGGTG 60.280 61.111 0.00 0.00 37.56 4.00
130 131 2.279918 GTGCGTGTTCGGTGAGGT 60.280 61.111 0.00 0.00 37.56 3.85
131 132 2.022129 GAGTGCGTGTTCGGTGAGG 61.022 63.158 0.00 0.00 37.56 3.86
132 133 2.365068 CGAGTGCGTGTTCGGTGAG 61.365 63.158 0.00 0.00 37.56 3.51
133 134 2.354188 CGAGTGCGTGTTCGGTGA 60.354 61.111 0.00 0.00 37.56 4.02
134 135 2.354188 TCGAGTGCGTGTTCGGTG 60.354 61.111 5.12 0.00 37.42 4.94
135 136 2.050351 CTCGAGTGCGTGTTCGGT 60.050 61.111 3.62 0.00 37.42 4.69
136 137 2.805353 CCTCGAGTGCGTGTTCGG 60.805 66.667 12.31 0.00 37.42 4.30
137 138 2.050351 ACCTCGAGTGCGTGTTCG 60.050 61.111 12.31 0.00 38.98 3.95
138 139 0.729816 GAGACCTCGAGTGCGTGTTC 60.730 60.000 12.31 0.00 38.98 3.18
139 140 1.173444 AGAGACCTCGAGTGCGTGTT 61.173 55.000 12.31 0.00 38.98 3.32
140 141 1.579084 GAGAGACCTCGAGTGCGTGT 61.579 60.000 12.31 0.78 38.98 4.49
141 142 1.135731 GAGAGACCTCGAGTGCGTG 59.864 63.158 12.31 0.00 38.98 5.34
142 143 1.302383 CTGAGAGACCTCGAGTGCGT 61.302 60.000 12.31 1.61 42.33 5.24
143 144 1.427419 CTGAGAGACCTCGAGTGCG 59.573 63.158 12.31 0.00 42.33 5.34
144 145 0.963355 ACCTGAGAGACCTCGAGTGC 60.963 60.000 12.31 2.49 42.33 4.40
145 146 0.808125 CACCTGAGAGACCTCGAGTG 59.192 60.000 12.31 5.52 42.33 3.51
146 147 0.322997 CCACCTGAGAGACCTCGAGT 60.323 60.000 12.31 0.00 42.33 4.18
147 148 1.034838 CCCACCTGAGAGACCTCGAG 61.035 65.000 5.13 5.13 42.33 4.04
148 149 1.000771 CCCACCTGAGAGACCTCGA 60.001 63.158 0.00 0.00 42.33 4.04
149 150 0.034380 TACCCACCTGAGAGACCTCG 60.034 60.000 0.00 0.00 42.33 4.63
150 151 2.104170 CTTACCCACCTGAGAGACCTC 58.896 57.143 0.00 0.00 39.86 3.85
151 152 1.273324 CCTTACCCACCTGAGAGACCT 60.273 57.143 0.00 0.00 0.00 3.85
152 153 1.196012 CCTTACCCACCTGAGAGACC 58.804 60.000 0.00 0.00 0.00 3.85
153 154 1.196012 CCCTTACCCACCTGAGAGAC 58.804 60.000 0.00 0.00 0.00 3.36
154 155 0.617820 GCCCTTACCCACCTGAGAGA 60.618 60.000 0.00 0.00 0.00 3.10
155 156 0.909610 TGCCCTTACCCACCTGAGAG 60.910 60.000 0.00 0.00 0.00 3.20
156 157 0.253160 ATGCCCTTACCCACCTGAGA 60.253 55.000 0.00 0.00 0.00 3.27
157 158 0.181350 GATGCCCTTACCCACCTGAG 59.819 60.000 0.00 0.00 0.00 3.35
158 159 0.253160 AGATGCCCTTACCCACCTGA 60.253 55.000 0.00 0.00 0.00 3.86
159 160 0.181350 GAGATGCCCTTACCCACCTG 59.819 60.000 0.00 0.00 0.00 4.00
160 161 0.988678 GGAGATGCCCTTACCCACCT 60.989 60.000 0.00 0.00 0.00 4.00
161 162 1.279025 TGGAGATGCCCTTACCCACC 61.279 60.000 0.00 0.00 34.97 4.61
162 163 0.623723 TTGGAGATGCCCTTACCCAC 59.376 55.000 0.00 0.00 34.97 4.61
163 164 0.623723 GTTGGAGATGCCCTTACCCA 59.376 55.000 0.00 0.00 34.97 4.51
164 165 0.623723 TGTTGGAGATGCCCTTACCC 59.376 55.000 0.00 0.00 34.97 3.69
165 166 1.004277 TGTGTTGGAGATGCCCTTACC 59.996 52.381 0.00 0.00 34.97 2.85
166 167 2.084546 GTGTGTTGGAGATGCCCTTAC 58.915 52.381 0.00 0.00 34.97 2.34
167 168 1.004277 GGTGTGTTGGAGATGCCCTTA 59.996 52.381 0.00 0.00 34.97 2.69
168 169 0.251341 GGTGTGTTGGAGATGCCCTT 60.251 55.000 0.00 0.00 34.97 3.95
169 170 1.380302 GGTGTGTTGGAGATGCCCT 59.620 57.895 0.00 0.00 34.97 5.19
170 171 1.678970 GGGTGTGTTGGAGATGCCC 60.679 63.158 0.00 0.00 34.97 5.36
171 172 0.678048 GAGGGTGTGTTGGAGATGCC 60.678 60.000 0.00 0.00 37.10 4.40
172 173 0.036732 TGAGGGTGTGTTGGAGATGC 59.963 55.000 0.00 0.00 0.00 3.91
173 174 2.554032 GTTTGAGGGTGTGTTGGAGATG 59.446 50.000 0.00 0.00 0.00 2.90
174 175 2.489073 GGTTTGAGGGTGTGTTGGAGAT 60.489 50.000 0.00 0.00 0.00 2.75
175 176 1.133915 GGTTTGAGGGTGTGTTGGAGA 60.134 52.381 0.00 0.00 0.00 3.71
176 177 1.318576 GGTTTGAGGGTGTGTTGGAG 58.681 55.000 0.00 0.00 0.00 3.86
177 178 0.464735 CGGTTTGAGGGTGTGTTGGA 60.465 55.000 0.00 0.00 0.00 3.53
178 179 0.750182 ACGGTTTGAGGGTGTGTTGG 60.750 55.000 0.00 0.00 0.00 3.77
179 180 0.661020 GACGGTTTGAGGGTGTGTTG 59.339 55.000 0.00 0.00 0.00 3.33
180 181 0.544697 AGACGGTTTGAGGGTGTGTT 59.455 50.000 0.00 0.00 0.00 3.32
181 182 0.179056 CAGACGGTTTGAGGGTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
182 183 0.884704 CCAGACGGTTTGAGGGTGTG 60.885 60.000 0.00 0.00 0.00 3.82
183 184 1.052124 TCCAGACGGTTTGAGGGTGT 61.052 55.000 0.00 0.00 0.00 4.16
184 185 0.324943 ATCCAGACGGTTTGAGGGTG 59.675 55.000 0.00 0.00 0.00 4.61
185 186 1.946984 TATCCAGACGGTTTGAGGGT 58.053 50.000 0.00 0.00 0.00 4.34
186 187 2.170607 ACATATCCAGACGGTTTGAGGG 59.829 50.000 0.00 0.00 0.00 4.30
187 188 3.458189 GACATATCCAGACGGTTTGAGG 58.542 50.000 0.00 0.00 0.00 3.86
188 189 3.458189 GGACATATCCAGACGGTTTGAG 58.542 50.000 0.00 0.00 45.47 3.02
189 190 2.159156 CGGACATATCCAGACGGTTTGA 60.159 50.000 0.00 0.00 46.67 2.69
190 191 2.201732 CGGACATATCCAGACGGTTTG 58.798 52.381 0.00 0.00 46.67 2.93
191 192 1.138266 CCGGACATATCCAGACGGTTT 59.862 52.381 0.00 0.00 46.67 3.27
192 193 0.750850 CCGGACATATCCAGACGGTT 59.249 55.000 0.00 0.00 46.67 4.44
193 194 0.106369 TCCGGACATATCCAGACGGT 60.106 55.000 0.00 0.00 46.67 4.83
194 195 0.314302 GTCCGGACATATCCAGACGG 59.686 60.000 29.75 0.00 46.67 4.79
195 196 3.867723 GTCCGGACATATCCAGACG 57.132 57.895 29.75 0.00 46.67 4.18
197 198 0.106369 ACGGTCCGGACATATCCAGA 60.106 55.000 34.40 0.00 46.67 3.86
198 199 0.032130 CACGGTCCGGACATATCCAG 59.968 60.000 34.40 17.75 46.67 3.86
199 200 0.685131 ACACGGTCCGGACATATCCA 60.685 55.000 34.40 0.00 46.67 3.41
200 201 0.249322 CACACGGTCCGGACATATCC 60.249 60.000 34.40 17.10 42.28 2.59
201 202 0.249322 CCACACGGTCCGGACATATC 60.249 60.000 34.40 16.97 0.00 1.63
202 203 0.974010 ACCACACGGTCCGGACATAT 60.974 55.000 34.40 17.12 44.71 1.78
203 204 1.607178 ACCACACGGTCCGGACATA 60.607 57.895 34.40 0.00 44.71 2.29
204 205 2.920912 ACCACACGGTCCGGACAT 60.921 61.111 34.40 20.13 44.71 3.06
220 221 0.745845 TACTAGTGAGCGGTCCGGAC 60.746 60.000 27.04 27.04 0.00 4.79
221 222 0.035152 TTACTAGTGAGCGGTCCGGA 60.035 55.000 14.38 0.00 0.00 5.14
222 223 0.813184 TTTACTAGTGAGCGGTCCGG 59.187 55.000 14.38 0.00 0.00 5.14
223 224 2.642139 TTTTACTAGTGAGCGGTCCG 57.358 50.000 12.85 6.99 0.00 4.79
481 482 5.184671 GGACGAAGGGTTTATATAGGACGAT 59.815 44.000 0.00 0.00 0.00 3.73
916 918 7.712264 TCCAAATCACACAAACATCAATTTC 57.288 32.000 0.00 0.00 0.00 2.17
1333 1335 6.312426 CCTCACTATCGATGGCATATTTTCTC 59.688 42.308 8.54 0.00 0.00 2.87
1402 1404 4.201551 GCAACAACAAATGCGATCAAGATG 60.202 41.667 0.00 0.00 32.17 2.90
1571 1573 0.670546 CACGCCCTCAACGAACTGAT 60.671 55.000 0.00 0.00 0.00 2.90
1572 1574 1.300620 CACGCCCTCAACGAACTGA 60.301 57.895 0.00 0.00 0.00 3.41
1657 1659 4.870123 AATTGCAACCATTCTTACAGCA 57.130 36.364 0.00 0.00 0.00 4.41
1672 1674 4.927425 GGTTCTTGACGTAGAGTAATTGCA 59.073 41.667 0.00 0.00 0.00 4.08
1699 1701 2.424601 CGGACTCAAATAGGTGGACGTA 59.575 50.000 0.00 0.00 0.00 3.57
1978 1980 1.808945 CTTCTCCAAATCACTTGCGCT 59.191 47.619 9.73 0.00 33.27 5.92
2074 2076 0.178981 AGCAATTCCAGTGTGGTGCT 60.179 50.000 4.20 4.20 40.99 4.40
2186 2188 6.020971 TCTTTGCTTCGTATGTACTCTTGA 57.979 37.500 0.00 0.00 0.00 3.02
2188 2190 5.869888 CCTTCTTTGCTTCGTATGTACTCTT 59.130 40.000 0.00 0.00 0.00 2.85
2196 2198 4.872691 CAGACATCCTTCTTTGCTTCGTAT 59.127 41.667 0.00 0.00 0.00 3.06
2298 2300 2.151202 CCACATACTGGACAAGCGTTT 58.849 47.619 0.00 0.00 43.95 3.60
2307 2309 1.462616 GCAATGCACCACATACTGGA 58.537 50.000 0.00 0.00 43.95 3.86


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

AutoCloner maintained by Alex Coulton.