Multiple sequence alignment - TraesCS5A01G230100

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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 TraesCS5A01G230100 chr5A 100.000 3050 0 0 1 3050 445241076 445244125 0.000000 5633.0
1 TraesCS5A01G230100 chr5D 93.766 2791 105 29 268 3048 345961403 345958672 0.000000 4126.0
2 TraesCS5A01G230100 chr5B 93.669 2780 113 22 287 3039 405592467 405595210 0.000000 4100.0
3 TraesCS5A01G230100 chr5B 97.143 35 1 0 265 299 405592414 405592448 0.000033 60.2


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 TraesCS5A01G230100 chr5A 445241076 445244125 3049 False 5633.0 5633 100.000 1 3050 1 chr5A.!!$F1 3049
1 TraesCS5A01G230100 chr5D 345958672 345961403 2731 True 4126.0 4126 93.766 268 3048 1 chr5D.!!$R1 2780
2 TraesCS5A01G230100 chr5B 405592414 405595210 2796 False 2080.1 4100 95.406 265 3039 2 chr5B.!!$F1 2774

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
96 97 0.097499 CTCGTCGCCATGTACACGTA 59.903 55.0 0.0 0.0 33.89 3.57 F
98 99 0.097499 CGTCGCCATGTACACGTAGA 59.903 55.0 0.0 0.0 0.00 2.59 F
366 398 0.301687 CATCGGAAGCAAATCGACGG 59.698 55.0 0.0 0.0 35.70 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1835 0.462047 CCCACACGGCCTCATTAGAC 60.462 60.000 0.00 0.00 0.00 2.59 R
1908 1961 2.352651 CGCATACATGTTTGACAGGAGG 59.647 50.000 18.99 0.00 33.56 4.30 R
2159 2212 1.081242 CACCTGATGGTTGCAACGC 60.081 57.895 22.67 15.82 46.05 4.84 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
35 36 8.816640 ATGAAATTAACACCAATGACAAAGTC 57.183 30.769 0.00 0.00 0.00 3.01
36 37 8.006298 TGAAATTAACACCAATGACAAAGTCT 57.994 30.769 0.00 0.00 33.15 3.24
37 38 9.126151 TGAAATTAACACCAATGACAAAGTCTA 57.874 29.630 0.00 0.00 33.15 2.59
38 39 9.394477 GAAATTAACACCAATGACAAAGTCTAC 57.606 33.333 0.00 0.00 33.15 2.59
39 40 8.691661 AATTAACACCAATGACAAAGTCTACT 57.308 30.769 0.00 0.00 33.15 2.57
40 41 8.691661 ATTAACACCAATGACAAAGTCTACTT 57.308 30.769 0.00 0.00 37.91 2.24
41 42 6.619801 AACACCAATGACAAAGTCTACTTC 57.380 37.500 0.00 0.00 34.61 3.01
42 43 5.930135 ACACCAATGACAAAGTCTACTTCT 58.070 37.500 0.00 0.00 34.61 2.85
43 44 6.357367 ACACCAATGACAAAGTCTACTTCTT 58.643 36.000 0.00 0.00 34.61 2.52
44 45 6.828785 ACACCAATGACAAAGTCTACTTCTTT 59.171 34.615 0.00 0.00 34.61 2.52
45 46 7.012421 ACACCAATGACAAAGTCTACTTCTTTC 59.988 37.037 0.00 0.00 34.61 2.62
46 47 6.202954 ACCAATGACAAAGTCTACTTCTTTCG 59.797 38.462 0.00 0.00 34.61 3.46
47 48 6.202954 CCAATGACAAAGTCTACTTCTTTCGT 59.797 38.462 0.00 0.00 34.61 3.85
48 49 7.384115 CCAATGACAAAGTCTACTTCTTTCGTA 59.616 37.037 0.00 0.00 34.61 3.43
49 50 8.761497 CAATGACAAAGTCTACTTCTTTCGTAA 58.239 33.333 0.00 0.00 34.61 3.18
50 51 7.689953 TGACAAAGTCTACTTCTTTCGTAAC 57.310 36.000 0.00 0.00 34.61 2.50
51 52 6.415867 TGACAAAGTCTACTTCTTTCGTAACG 59.584 38.462 0.00 0.00 34.61 3.18
52 53 5.174579 ACAAAGTCTACTTCTTTCGTAACGC 59.825 40.000 0.00 0.00 34.61 4.84
53 54 3.831112 AGTCTACTTCTTTCGTAACGCC 58.169 45.455 0.00 0.00 0.00 5.68
54 55 3.505293 AGTCTACTTCTTTCGTAACGCCT 59.495 43.478 0.00 0.00 0.00 5.52
55 56 3.850837 GTCTACTTCTTTCGTAACGCCTC 59.149 47.826 0.00 0.00 0.00 4.70
56 57 2.806608 ACTTCTTTCGTAACGCCTCA 57.193 45.000 0.00 0.00 0.00 3.86
57 58 3.102052 ACTTCTTTCGTAACGCCTCAA 57.898 42.857 0.00 0.00 0.00 3.02
58 59 3.460103 ACTTCTTTCGTAACGCCTCAAA 58.540 40.909 0.00 0.00 0.00 2.69
59 60 3.493503 ACTTCTTTCGTAACGCCTCAAAG 59.506 43.478 0.00 0.00 0.00 2.77
60 61 3.374220 TCTTTCGTAACGCCTCAAAGA 57.626 42.857 0.00 0.00 32.03 2.52
61 62 3.314553 TCTTTCGTAACGCCTCAAAGAG 58.685 45.455 0.00 0.00 31.13 2.85
62 63 3.005050 TCTTTCGTAACGCCTCAAAGAGA 59.995 43.478 0.00 0.00 31.13 3.10
63 64 2.631418 TCGTAACGCCTCAAAGAGAG 57.369 50.000 0.00 0.00 44.31 3.20
76 77 4.495422 TCAAAGAGAGAGAAATACACGCC 58.505 43.478 0.00 0.00 0.00 5.68
77 78 3.528597 AAGAGAGAGAAATACACGCCC 57.471 47.619 0.00 0.00 0.00 6.13
78 79 2.741145 AGAGAGAGAAATACACGCCCT 58.259 47.619 0.00 0.00 0.00 5.19
79 80 2.691011 AGAGAGAGAAATACACGCCCTC 59.309 50.000 0.00 0.00 0.00 4.30
80 81 1.405821 AGAGAGAAATACACGCCCTCG 59.594 52.381 0.00 0.00 42.43 4.63
90 91 4.201679 CGCCCTCGTCGCCATGTA 62.202 66.667 0.00 0.00 0.00 2.29
91 92 2.585247 GCCCTCGTCGCCATGTAC 60.585 66.667 0.00 0.00 0.00 2.90
92 93 2.889617 CCCTCGTCGCCATGTACA 59.110 61.111 0.00 0.00 0.00 2.90
93 94 1.518572 CCCTCGTCGCCATGTACAC 60.519 63.158 0.00 0.00 0.00 2.90
94 95 1.872234 CCTCGTCGCCATGTACACG 60.872 63.158 0.00 0.00 0.00 4.49
95 96 1.154093 CTCGTCGCCATGTACACGT 60.154 57.895 0.00 0.00 33.89 4.49
96 97 0.097499 CTCGTCGCCATGTACACGTA 59.903 55.000 0.00 0.00 33.89 3.57
97 98 0.097499 TCGTCGCCATGTACACGTAG 59.903 55.000 0.00 0.00 33.89 3.51
98 99 0.097499 CGTCGCCATGTACACGTAGA 59.903 55.000 0.00 0.00 0.00 2.59
99 100 1.823828 GTCGCCATGTACACGTAGAG 58.176 55.000 0.00 0.00 0.00 2.43
100 101 1.399440 GTCGCCATGTACACGTAGAGA 59.601 52.381 0.00 0.00 0.00 3.10
101 102 2.033049 GTCGCCATGTACACGTAGAGAT 59.967 50.000 0.00 0.00 0.00 2.75
102 103 2.032924 TCGCCATGTACACGTAGAGATG 59.967 50.000 0.00 0.00 0.00 2.90
103 104 2.032924 CGCCATGTACACGTAGAGATGA 59.967 50.000 0.00 0.00 0.00 2.92
104 105 3.372954 GCCATGTACACGTAGAGATGAC 58.627 50.000 0.00 0.00 0.00 3.06
105 106 3.181490 GCCATGTACACGTAGAGATGACA 60.181 47.826 0.00 0.00 0.00 3.58
106 107 4.676986 GCCATGTACACGTAGAGATGACAA 60.677 45.833 0.00 0.00 0.00 3.18
107 108 5.037385 CCATGTACACGTAGAGATGACAAG 58.963 45.833 0.00 0.00 0.00 3.16
108 109 4.696899 TGTACACGTAGAGATGACAAGG 57.303 45.455 0.00 0.00 0.00 3.61
109 110 4.329392 TGTACACGTAGAGATGACAAGGA 58.671 43.478 0.00 0.00 0.00 3.36
110 111 3.851976 ACACGTAGAGATGACAAGGAC 57.148 47.619 0.00 0.00 0.00 3.85
111 112 3.154710 ACACGTAGAGATGACAAGGACA 58.845 45.455 0.00 0.00 0.00 4.02
112 113 3.572682 ACACGTAGAGATGACAAGGACAA 59.427 43.478 0.00 0.00 0.00 3.18
113 114 4.169508 CACGTAGAGATGACAAGGACAAG 58.830 47.826 0.00 0.00 0.00 3.16
114 115 3.193691 ACGTAGAGATGACAAGGACAAGG 59.806 47.826 0.00 0.00 0.00 3.61
115 116 3.444034 CGTAGAGATGACAAGGACAAGGA 59.556 47.826 0.00 0.00 0.00 3.36
116 117 4.098654 CGTAGAGATGACAAGGACAAGGAT 59.901 45.833 0.00 0.00 0.00 3.24
117 118 4.751767 AGAGATGACAAGGACAAGGATC 57.248 45.455 0.00 0.00 0.00 3.36
118 119 4.360889 AGAGATGACAAGGACAAGGATCT 58.639 43.478 0.00 0.00 0.00 2.75
119 120 4.782156 AGAGATGACAAGGACAAGGATCTT 59.218 41.667 0.00 0.00 0.00 2.40
120 121 5.096443 AGATGACAAGGACAAGGATCTTC 57.904 43.478 0.00 0.00 0.00 2.87
121 122 4.533707 AGATGACAAGGACAAGGATCTTCA 59.466 41.667 0.00 0.00 0.00 3.02
122 123 4.008074 TGACAAGGACAAGGATCTTCAC 57.992 45.455 0.00 0.00 0.00 3.18
123 124 3.244561 TGACAAGGACAAGGATCTTCACC 60.245 47.826 0.00 0.00 0.00 4.02
124 125 2.040412 ACAAGGACAAGGATCTTCACCC 59.960 50.000 0.00 0.00 0.00 4.61
125 126 0.905357 AGGACAAGGATCTTCACCCG 59.095 55.000 0.00 0.00 0.00 5.28
126 127 0.902531 GGACAAGGATCTTCACCCGA 59.097 55.000 0.00 0.00 0.00 5.14
127 128 1.278127 GGACAAGGATCTTCACCCGAA 59.722 52.381 0.00 0.00 0.00 4.30
128 129 2.290071 GGACAAGGATCTTCACCCGAAA 60.290 50.000 0.00 0.00 0.00 3.46
129 130 3.610911 GACAAGGATCTTCACCCGAAAT 58.389 45.455 0.00 0.00 0.00 2.17
130 131 4.010349 GACAAGGATCTTCACCCGAAATT 58.990 43.478 0.00 0.00 0.00 1.82
131 132 4.010349 ACAAGGATCTTCACCCGAAATTC 58.990 43.478 0.00 0.00 0.00 2.17
132 133 4.009675 CAAGGATCTTCACCCGAAATTCA 58.990 43.478 0.00 0.00 0.00 2.57
133 134 4.301072 AGGATCTTCACCCGAAATTCAA 57.699 40.909 0.00 0.00 0.00 2.69
134 135 4.010349 AGGATCTTCACCCGAAATTCAAC 58.990 43.478 0.00 0.00 0.00 3.18
135 136 3.128764 GGATCTTCACCCGAAATTCAACC 59.871 47.826 0.00 0.00 0.00 3.77
136 137 3.216187 TCTTCACCCGAAATTCAACCA 57.784 42.857 0.00 0.00 0.00 3.67
137 138 3.556999 TCTTCACCCGAAATTCAACCAA 58.443 40.909 0.00 0.00 0.00 3.67
138 139 4.148838 TCTTCACCCGAAATTCAACCAAT 58.851 39.130 0.00 0.00 0.00 3.16
139 140 5.317808 TCTTCACCCGAAATTCAACCAATA 58.682 37.500 0.00 0.00 0.00 1.90
140 141 5.770663 TCTTCACCCGAAATTCAACCAATAA 59.229 36.000 0.00 0.00 0.00 1.40
141 142 6.265649 TCTTCACCCGAAATTCAACCAATAAA 59.734 34.615 0.00 0.00 0.00 1.40
142 143 6.406692 TCACCCGAAATTCAACCAATAAAA 57.593 33.333 0.00 0.00 0.00 1.52
143 144 6.451393 TCACCCGAAATTCAACCAATAAAAG 58.549 36.000 0.00 0.00 0.00 2.27
144 145 6.041069 TCACCCGAAATTCAACCAATAAAAGT 59.959 34.615 0.00 0.00 0.00 2.66
145 146 6.704050 CACCCGAAATTCAACCAATAAAAGTT 59.296 34.615 0.00 0.00 0.00 2.66
146 147 7.868415 CACCCGAAATTCAACCAATAAAAGTTA 59.132 33.333 0.00 0.00 0.00 2.24
147 148 8.085909 ACCCGAAATTCAACCAATAAAAGTTAG 58.914 33.333 0.00 0.00 0.00 2.34
148 149 7.062956 CCCGAAATTCAACCAATAAAAGTTAGC 59.937 37.037 0.00 0.00 0.00 3.09
149 150 7.596995 CCGAAATTCAACCAATAAAAGTTAGCA 59.403 33.333 0.00 0.00 0.00 3.49
150 151 8.424731 CGAAATTCAACCAATAAAAGTTAGCAC 58.575 33.333 0.00 0.00 0.00 4.40
151 152 9.255304 GAAATTCAACCAATAAAAGTTAGCACA 57.745 29.630 0.00 0.00 0.00 4.57
152 153 9.606631 AAATTCAACCAATAAAAGTTAGCACAA 57.393 25.926 0.00 0.00 0.00 3.33
153 154 7.995463 TTCAACCAATAAAAGTTAGCACAAC 57.005 32.000 0.00 0.00 0.00 3.32
154 155 7.101652 TCAACCAATAAAAGTTAGCACAACA 57.898 32.000 4.30 0.00 0.00 3.33
155 156 7.548097 TCAACCAATAAAAGTTAGCACAACAA 58.452 30.769 4.30 0.00 0.00 2.83
156 157 7.489757 TCAACCAATAAAAGTTAGCACAACAAC 59.510 33.333 4.30 0.00 0.00 3.32
157 158 6.868622 ACCAATAAAAGTTAGCACAACAACA 58.131 32.000 4.30 0.00 0.00 3.33
158 159 7.324178 ACCAATAAAAGTTAGCACAACAACAA 58.676 30.769 4.30 0.00 0.00 2.83
159 160 7.984617 ACCAATAAAAGTTAGCACAACAACAAT 59.015 29.630 4.30 0.00 0.00 2.71
160 161 9.469807 CCAATAAAAGTTAGCACAACAACAATA 57.530 29.630 4.30 0.00 0.00 1.90
164 165 7.444558 AAAGTTAGCACAACAACAATAAACG 57.555 32.000 4.30 0.00 0.00 3.60
165 166 6.366315 AGTTAGCACAACAACAATAAACGA 57.634 33.333 0.00 0.00 0.00 3.85
166 167 6.966021 AGTTAGCACAACAACAATAAACGAT 58.034 32.000 0.00 0.00 0.00 3.73
167 168 6.855914 AGTTAGCACAACAACAATAAACGATG 59.144 34.615 0.00 0.00 0.00 3.84
168 169 5.181690 AGCACAACAACAATAAACGATGT 57.818 34.783 0.00 0.00 0.00 3.06
169 170 5.587289 AGCACAACAACAATAAACGATGTT 58.413 33.333 0.00 0.00 40.24 2.71
170 171 6.039616 AGCACAACAACAATAAACGATGTTT 58.960 32.000 0.00 0.22 37.66 2.83
171 172 6.533367 AGCACAACAACAATAAACGATGTTTT 59.467 30.769 0.00 0.00 37.66 2.43
172 173 6.838806 GCACAACAACAATAAACGATGTTTTC 59.161 34.615 0.00 0.00 37.66 2.29
173 174 7.463383 GCACAACAACAATAAACGATGTTTTCA 60.463 33.333 0.00 0.00 37.66 2.69
174 175 8.376203 CACAACAACAATAAACGATGTTTTCAA 58.624 29.630 0.00 0.00 37.66 2.69
175 176 8.376942 ACAACAACAATAAACGATGTTTTCAAC 58.623 29.630 0.00 0.00 37.66 3.18
176 177 8.376203 CAACAACAATAAACGATGTTTTCAACA 58.624 29.630 0.00 0.00 46.94 3.33
177 178 8.467402 ACAACAATAAACGATGTTTTCAACAA 57.533 26.923 0.00 0.00 45.86 2.83
178 179 8.591312 ACAACAATAAACGATGTTTTCAACAAG 58.409 29.630 0.00 0.00 45.86 3.16
179 180 8.802856 CAACAATAAACGATGTTTTCAACAAGA 58.197 29.630 0.00 0.00 45.86 3.02
180 181 9.528018 AACAATAAACGATGTTTTCAACAAGAT 57.472 25.926 0.00 0.00 45.86 2.40
185 186 8.782533 AAACGATGTTTTCAACAAGATAAGAC 57.217 30.769 0.00 0.00 45.86 3.01
186 187 6.590357 ACGATGTTTTCAACAAGATAAGACG 58.410 36.000 0.00 0.00 45.86 4.18
187 188 6.422701 ACGATGTTTTCAACAAGATAAGACGA 59.577 34.615 0.00 0.00 45.86 4.20
188 189 7.042321 ACGATGTTTTCAACAAGATAAGACGAA 60.042 33.333 0.00 0.00 45.86 3.85
189 190 7.796660 CGATGTTTTCAACAAGATAAGACGAAA 59.203 33.333 0.00 0.00 45.86 3.46
190 191 9.107367 GATGTTTTCAACAAGATAAGACGAAAG 57.893 33.333 0.00 0.00 45.86 2.62
191 192 7.981142 TGTTTTCAACAAGATAAGACGAAAGT 58.019 30.769 0.00 0.00 43.36 2.66
192 193 8.455682 TGTTTTCAACAAGATAAGACGAAAGTT 58.544 29.630 0.00 0.00 41.45 2.66
201 202 3.233331 ACGAAAGTTGGTCCCCGT 58.767 55.556 0.00 0.00 46.40 5.28
202 203 1.528339 ACGAAAGTTGGTCCCCGTT 59.472 52.632 0.00 0.00 46.40 4.44
203 204 0.816421 ACGAAAGTTGGTCCCCGTTG 60.816 55.000 0.00 0.00 46.40 4.10
204 205 0.533308 CGAAAGTTGGTCCCCGTTGA 60.533 55.000 0.00 0.00 0.00 3.18
205 206 1.235724 GAAAGTTGGTCCCCGTTGAG 58.764 55.000 0.00 0.00 0.00 3.02
206 207 0.822121 AAAGTTGGTCCCCGTTGAGC 60.822 55.000 0.00 0.00 0.00 4.26
207 208 2.671963 GTTGGTCCCCGTTGAGCC 60.672 66.667 0.00 0.00 31.79 4.70
208 209 3.961414 TTGGTCCCCGTTGAGCCC 61.961 66.667 0.00 0.00 31.79 5.19
211 212 4.754667 GTCCCCGTTGAGCCCGAC 62.755 72.222 0.00 0.00 0.00 4.79
213 214 3.072468 CCCCGTTGAGCCCGACTA 61.072 66.667 0.00 0.00 0.00 2.59
214 215 2.652095 CCCCGTTGAGCCCGACTAA 61.652 63.158 0.00 0.00 0.00 2.24
215 216 1.520666 CCCGTTGAGCCCGACTAAT 59.479 57.895 0.00 0.00 0.00 1.73
216 217 0.748450 CCCGTTGAGCCCGACTAATA 59.252 55.000 0.00 0.00 0.00 0.98
217 218 1.137479 CCCGTTGAGCCCGACTAATAA 59.863 52.381 0.00 0.00 0.00 1.40
218 219 2.419021 CCCGTTGAGCCCGACTAATAAA 60.419 50.000 0.00 0.00 0.00 1.40
219 220 3.264104 CCGTTGAGCCCGACTAATAAAA 58.736 45.455 0.00 0.00 0.00 1.52
220 221 3.685756 CCGTTGAGCCCGACTAATAAAAA 59.314 43.478 0.00 0.00 0.00 1.94
221 222 4.436451 CCGTTGAGCCCGACTAATAAAAAC 60.436 45.833 0.00 0.00 0.00 2.43
222 223 4.436451 CGTTGAGCCCGACTAATAAAAACC 60.436 45.833 0.00 0.00 0.00 3.27
223 224 4.289238 TGAGCCCGACTAATAAAAACCA 57.711 40.909 0.00 0.00 0.00 3.67
224 225 4.850680 TGAGCCCGACTAATAAAAACCAT 58.149 39.130 0.00 0.00 0.00 3.55
225 226 5.258051 TGAGCCCGACTAATAAAAACCATT 58.742 37.500 0.00 0.00 0.00 3.16
226 227 5.124776 TGAGCCCGACTAATAAAAACCATTG 59.875 40.000 0.00 0.00 0.00 2.82
227 228 4.109766 GCCCGACTAATAAAAACCATTGC 58.890 43.478 0.00 0.00 0.00 3.56
228 229 4.381079 GCCCGACTAATAAAAACCATTGCA 60.381 41.667 0.00 0.00 0.00 4.08
229 230 5.715070 CCCGACTAATAAAAACCATTGCAA 58.285 37.500 0.00 0.00 0.00 4.08
230 231 6.159988 CCCGACTAATAAAAACCATTGCAAA 58.840 36.000 1.71 0.00 0.00 3.68
231 232 6.310224 CCCGACTAATAAAAACCATTGCAAAG 59.690 38.462 1.71 0.00 0.00 2.77
232 233 6.310224 CCGACTAATAAAAACCATTGCAAAGG 59.690 38.462 18.90 18.90 0.00 3.11
233 234 6.866248 CGACTAATAAAAACCATTGCAAAGGT 59.134 34.615 20.35 20.35 40.61 3.50
240 241 3.733443 ACCATTGCAAAGGTTTCTCAC 57.267 42.857 20.35 0.00 33.39 3.51
241 242 3.181466 AACCATTGCAAAGGTTTCTCACC 60.181 43.478 28.69 0.00 45.46 4.02
248 249 3.153825 GGTTTCTCACCCCGGACA 58.846 61.111 0.73 0.00 40.19 4.02
249 250 1.302271 GGTTTCTCACCCCGGACAC 60.302 63.158 0.73 0.00 40.19 3.67
250 251 1.666872 GTTTCTCACCCCGGACACG 60.667 63.158 0.73 0.00 40.55 4.49
251 252 1.833492 TTTCTCACCCCGGACACGA 60.833 57.895 0.73 0.00 44.60 4.35
252 253 1.401318 TTTCTCACCCCGGACACGAA 61.401 55.000 0.73 0.00 44.60 3.85
253 254 1.812686 TTCTCACCCCGGACACGAAG 61.813 60.000 0.73 0.00 44.60 3.79
254 255 3.934391 CTCACCCCGGACACGAAGC 62.934 68.421 0.73 0.00 44.60 3.86
255 256 4.308458 CACCCCGGACACGAAGCA 62.308 66.667 0.73 0.00 44.60 3.91
256 257 3.552384 ACCCCGGACACGAAGCAA 61.552 61.111 0.73 0.00 44.60 3.91
257 258 2.046314 CCCCGGACACGAAGCAAT 60.046 61.111 0.73 0.00 44.60 3.56
258 259 2.398554 CCCCGGACACGAAGCAATG 61.399 63.158 0.73 0.00 44.60 2.82
259 260 1.671054 CCCGGACACGAAGCAATGT 60.671 57.895 0.73 0.00 44.60 2.71
260 261 1.497278 CCGGACACGAAGCAATGTG 59.503 57.895 0.00 1.29 44.60 3.21
261 262 1.154413 CGGACACGAAGCAATGTGC 60.154 57.895 0.00 0.00 43.25 4.57
326 358 3.487202 GATCTGCAAACCGCGCGA 61.487 61.111 34.63 9.08 46.97 5.87
327 359 3.425938 GATCTGCAAACCGCGCGAG 62.426 63.158 34.63 23.58 46.97 5.03
364 396 0.657840 CCCATCGGAAGCAAATCGAC 59.342 55.000 0.00 0.00 35.70 4.20
366 398 0.301687 CATCGGAAGCAAATCGACGG 59.698 55.000 0.00 0.00 35.70 4.79
395 427 1.175983 AAACCATTCCCGCGCAGAAA 61.176 50.000 8.75 0.00 0.00 2.52
396 428 1.175983 AACCATTCCCGCGCAGAAAA 61.176 50.000 8.75 0.00 0.00 2.29
397 429 1.154035 CCATTCCCGCGCAGAAAAC 60.154 57.895 8.75 0.00 0.00 2.43
398 430 1.578926 CATTCCCGCGCAGAAAACA 59.421 52.632 8.75 0.00 0.00 2.83
399 431 0.729140 CATTCCCGCGCAGAAAACAC 60.729 55.000 8.75 0.00 0.00 3.32
401 433 2.051345 CCCGCGCAGAAAACACAC 60.051 61.111 8.75 0.00 0.00 3.82
402 434 2.051345 CCGCGCAGAAAACACACC 60.051 61.111 8.75 0.00 0.00 4.16
406 438 1.999071 GCGCAGAAAACACACCACCA 61.999 55.000 0.30 0.00 0.00 4.17
408 440 1.533756 CGCAGAAAACACACCACCAAG 60.534 52.381 0.00 0.00 0.00 3.61
414 446 0.324275 AACACACCACCAAGCCAAGT 60.324 50.000 0.00 0.00 0.00 3.16
473 505 4.796231 CCAAGCCCCTCGTCGTCG 62.796 72.222 0.00 0.00 38.55 5.12
489 521 2.272797 CGTCGTCCTCCTCCTCCT 59.727 66.667 0.00 0.00 0.00 3.69
490 522 1.820481 CGTCGTCCTCCTCCTCCTC 60.820 68.421 0.00 0.00 0.00 3.71
491 523 1.454295 GTCGTCCTCCTCCTCCTCC 60.454 68.421 0.00 0.00 0.00 4.30
492 524 1.619975 TCGTCCTCCTCCTCCTCCT 60.620 63.158 0.00 0.00 0.00 3.69
1076 1129 2.030401 TGTTCGACGAAATGCCCGG 61.030 57.895 12.67 0.00 0.00 5.73
1083 1136 3.508840 GAAATGCCCGGCAGGACG 61.509 66.667 18.96 0.00 43.65 4.79
1113 1166 2.482374 GCGTGGAACTGCATGCTC 59.518 61.111 20.33 8.13 36.60 4.26
1284 1337 0.609406 GGAAGGCAAGGGTCAAGGAC 60.609 60.000 0.00 0.00 0.00 3.85
1309 1362 1.374252 GTGACGATGGTCGCCTTGT 60.374 57.895 10.04 0.00 45.75 3.16
1320 1373 4.683334 GCCTTGTTGACGGCGTGC 62.683 66.667 21.19 9.23 36.45 5.34
1521 1574 3.279434 GACTACAATGATTTCCGGGCTT 58.721 45.455 0.00 0.00 0.00 4.35
1564 1617 5.746284 AGGAGGCTCTAGAATTGTTTAACC 58.254 41.667 15.23 0.00 0.00 2.85
1764 1817 2.023771 CGAAGCACTTGAGCTCGCA 61.024 57.895 9.64 0.00 45.89 5.10
1940 1993 0.742990 ATGTATGCGGGTGTTGGTCG 60.743 55.000 0.00 0.00 0.00 4.79
2041 2094 2.254546 AAACGAGACCAGCATGTTGA 57.745 45.000 11.60 0.00 0.00 3.18
2050 2103 3.819337 GACCAGCATGTTGATAGCATGAT 59.181 43.478 11.60 0.00 44.60 2.45
2064 2117 7.700505 TGATAGCATGATCTCAACAAATTGTC 58.299 34.615 0.00 0.00 37.11 3.18
2066 2119 8.969260 ATAGCATGATCTCAACAAATTGTCTA 57.031 30.769 0.00 0.00 37.11 2.59
2153 2206 0.539669 TCAGAACTCGAGGGAGCACA 60.540 55.000 18.41 0.00 44.48 4.57
2154 2207 0.534412 CAGAACTCGAGGGAGCACAT 59.466 55.000 18.41 0.00 44.48 3.21
2155 2208 1.066573 CAGAACTCGAGGGAGCACATT 60.067 52.381 18.41 0.00 44.48 2.71
2156 2209 1.066573 AGAACTCGAGGGAGCACATTG 60.067 52.381 18.41 0.00 44.48 2.82
2157 2210 0.036010 AACTCGAGGGAGCACATTGG 60.036 55.000 18.41 0.00 44.48 3.16
2158 2211 1.153289 CTCGAGGGAGCACATTGGG 60.153 63.158 3.91 0.00 32.61 4.12
2159 2212 2.124570 CGAGGGAGCACATTGGGG 60.125 66.667 0.00 0.00 0.00 4.96
2272 2325 4.021544 TGCCACACACTTTCTTTTGACTTT 60.022 37.500 0.00 0.00 0.00 2.66
2315 2368 1.072331 ACCAGTTTCCATCTTCGCTGT 59.928 47.619 0.00 0.00 0.00 4.40
2316 2369 2.154462 CCAGTTTCCATCTTCGCTGTT 58.846 47.619 0.00 0.00 0.00 3.16
2482 2535 3.027974 AGCGTAAACTTCTCTGTCCAC 57.972 47.619 0.00 0.00 0.00 4.02
2505 2558 9.423061 CCACCTTAATTCATTTTTGTAGGAAAG 57.577 33.333 0.00 0.00 0.00 2.62
2523 2576 0.322975 AGAGTGTCATGACAGCCCAC 59.677 55.000 28.54 16.16 42.74 4.61
2526 2579 2.044946 GTCATGACAGCCCACCCC 60.045 66.667 21.07 0.00 0.00 4.95
2555 2608 8.394877 TCTCGCAGTAATAATTAAACACCAATG 58.605 33.333 0.00 0.00 0.00 2.82
2556 2609 6.970043 TCGCAGTAATAATTAAACACCAATGC 59.030 34.615 0.00 0.00 0.00 3.56
2587 2641 2.413765 GCAGAACTACATGCACAAGCTG 60.414 50.000 0.00 0.00 42.11 4.24
2640 2694 6.214191 TCTTTCTGAGAGATACGAAAGCAT 57.786 37.500 0.00 0.00 41.11 3.79
2648 2702 5.355596 AGAGATACGAAAGCATTCTTCTGG 58.644 41.667 0.00 0.00 33.17 3.86
2650 2704 6.096987 AGAGATACGAAAGCATTCTTCTGGTA 59.903 38.462 0.00 0.00 33.17 3.25
2670 2724 5.716228 TGGTATCAATTTGAACAATGCTCCT 59.284 36.000 2.68 0.00 0.00 3.69
2671 2725 6.038356 GGTATCAATTTGAACAATGCTCCTG 58.962 40.000 2.68 0.00 0.00 3.86
2672 2726 5.733620 ATCAATTTGAACAATGCTCCTGT 57.266 34.783 2.68 0.00 0.00 4.00
2673 2727 5.534207 TCAATTTGAACAATGCTCCTGTT 57.466 34.783 0.00 0.00 39.69 3.16
2679 2733 3.936564 GAACAATGCTCCTGTTCTCTCT 58.063 45.455 14.84 0.00 46.01 3.10
2703 2757 8.910944 TCTTCTATGTAACCTATTCTGTACACC 58.089 37.037 0.00 0.00 0.00 4.16
2757 2812 7.936301 GCTGAATCTAACTCCTTCTGGATAAAT 59.064 37.037 0.00 0.00 42.29 1.40
2766 2821 8.517062 ACTCCTTCTGGATAAATTGAAATCAG 57.483 34.615 0.00 0.00 42.29 2.90
2948 3003 3.932710 ACATCTTGTGCAGGTTATGTACG 59.067 43.478 0.00 0.00 46.57 3.67
3000 3060 0.539438 TGCGAAGGAAACCTGCCATT 60.539 50.000 0.00 0.00 32.13 3.16
3021 3081 9.213799 GCCATTTAAACAGTTTGATTTATCCAA 57.786 29.630 8.93 0.00 0.00 3.53
3048 3108 6.808704 AGTTTTCTTTCAACAAAGACTTGCTC 59.191 34.615 0.00 0.00 46.38 4.26
3049 3109 5.895636 TTCTTTCAACAAAGACTTGCTCA 57.104 34.783 0.00 0.00 46.38 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.906660 GACTTTGTCATTGGTGTTAATTTCATA 57.093 29.630 0.00 0.00 32.09 2.15
10 11 8.641541 AGACTTTGTCATTGGTGTTAATTTCAT 58.358 29.630 0.46 0.00 34.60 2.57
11 12 8.006298 AGACTTTGTCATTGGTGTTAATTTCA 57.994 30.769 0.46 0.00 34.60 2.69
12 13 9.394477 GTAGACTTTGTCATTGGTGTTAATTTC 57.606 33.333 0.46 0.00 34.60 2.17
13 14 9.131791 AGTAGACTTTGTCATTGGTGTTAATTT 57.868 29.630 0.46 0.00 34.60 1.82
14 15 8.691661 AGTAGACTTTGTCATTGGTGTTAATT 57.308 30.769 0.46 0.00 34.60 1.40
15 16 8.691661 AAGTAGACTTTGTCATTGGTGTTAAT 57.308 30.769 0.46 0.00 34.60 1.40
16 17 7.990886 AGAAGTAGACTTTGTCATTGGTGTTAA 59.009 33.333 0.00 0.00 36.11 2.01
17 18 7.506114 AGAAGTAGACTTTGTCATTGGTGTTA 58.494 34.615 0.00 0.00 36.11 2.41
18 19 6.357367 AGAAGTAGACTTTGTCATTGGTGTT 58.643 36.000 0.00 0.00 36.11 3.32
19 20 5.930135 AGAAGTAGACTTTGTCATTGGTGT 58.070 37.500 0.00 0.00 36.11 4.16
20 21 6.867662 AAGAAGTAGACTTTGTCATTGGTG 57.132 37.500 0.00 0.00 36.11 4.17
21 22 6.202954 CGAAAGAAGTAGACTTTGTCATTGGT 59.797 38.462 0.00 0.00 37.64 3.67
22 23 6.202954 ACGAAAGAAGTAGACTTTGTCATTGG 59.797 38.462 0.00 0.00 37.64 3.16
23 24 7.178712 ACGAAAGAAGTAGACTTTGTCATTG 57.821 36.000 0.00 0.00 37.64 2.82
24 25 8.762426 GTTACGAAAGAAGTAGACTTTGTCATT 58.238 33.333 0.00 0.00 37.64 2.57
25 26 7.114529 CGTTACGAAAGAAGTAGACTTTGTCAT 59.885 37.037 0.00 0.00 37.64 3.06
26 27 6.415867 CGTTACGAAAGAAGTAGACTTTGTCA 59.584 38.462 0.00 0.00 37.64 3.58
27 28 6.613120 GCGTTACGAAAGAAGTAGACTTTGTC 60.613 42.308 9.62 0.00 37.64 3.18
28 29 5.174579 GCGTTACGAAAGAAGTAGACTTTGT 59.825 40.000 9.62 0.00 37.64 2.83
29 30 5.388164 GGCGTTACGAAAGAAGTAGACTTTG 60.388 44.000 9.62 0.00 37.64 2.77
30 31 4.683320 GGCGTTACGAAAGAAGTAGACTTT 59.317 41.667 9.62 0.00 39.76 2.66
31 32 4.022503 AGGCGTTACGAAAGAAGTAGACTT 60.023 41.667 9.62 0.00 39.23 3.01
32 33 3.505293 AGGCGTTACGAAAGAAGTAGACT 59.495 43.478 9.62 0.00 0.00 3.24
33 34 3.831112 AGGCGTTACGAAAGAAGTAGAC 58.169 45.455 9.62 0.00 0.00 2.59
34 35 3.503363 TGAGGCGTTACGAAAGAAGTAGA 59.497 43.478 9.62 0.00 0.00 2.59
35 36 3.829948 TGAGGCGTTACGAAAGAAGTAG 58.170 45.455 9.62 0.00 0.00 2.57
36 37 3.921119 TGAGGCGTTACGAAAGAAGTA 57.079 42.857 9.62 0.00 0.00 2.24
37 38 2.806608 TGAGGCGTTACGAAAGAAGT 57.193 45.000 9.62 0.00 0.00 3.01
38 39 3.739300 TCTTTGAGGCGTTACGAAAGAAG 59.261 43.478 9.62 5.57 31.38 2.85
39 40 3.719924 TCTTTGAGGCGTTACGAAAGAA 58.280 40.909 9.62 0.00 31.38 2.52
40 41 3.005050 TCTCTTTGAGGCGTTACGAAAGA 59.995 43.478 9.62 13.23 32.95 2.52
41 42 3.314553 TCTCTTTGAGGCGTTACGAAAG 58.685 45.455 9.62 9.49 0.00 2.62
42 43 3.005050 TCTCTCTTTGAGGCGTTACGAAA 59.995 43.478 9.62 0.00 42.86 3.46
43 44 2.555325 TCTCTCTTTGAGGCGTTACGAA 59.445 45.455 9.62 0.00 42.86 3.85
44 45 2.156917 TCTCTCTTTGAGGCGTTACGA 58.843 47.619 9.62 0.00 42.86 3.43
45 46 2.161808 TCTCTCTCTTTGAGGCGTTACG 59.838 50.000 0.00 0.00 42.86 3.18
46 47 3.851976 TCTCTCTCTTTGAGGCGTTAC 57.148 47.619 0.00 0.00 42.86 2.50
47 48 4.866508 TTTCTCTCTCTTTGAGGCGTTA 57.133 40.909 0.00 0.00 42.86 3.18
48 49 3.753294 TTTCTCTCTCTTTGAGGCGTT 57.247 42.857 0.00 0.00 42.86 4.84
49 50 3.971245 ATTTCTCTCTCTTTGAGGCGT 57.029 42.857 0.00 0.00 42.86 5.68
50 51 4.564769 GTGTATTTCTCTCTCTTTGAGGCG 59.435 45.833 0.00 0.00 42.86 5.52
51 52 4.564769 CGTGTATTTCTCTCTCTTTGAGGC 59.435 45.833 0.00 0.00 42.86 4.70
52 53 4.564769 GCGTGTATTTCTCTCTCTTTGAGG 59.435 45.833 0.00 0.00 42.86 3.86
53 54 4.564769 GGCGTGTATTTCTCTCTCTTTGAG 59.435 45.833 0.00 0.00 43.96 3.02
54 55 4.495422 GGCGTGTATTTCTCTCTCTTTGA 58.505 43.478 0.00 0.00 0.00 2.69
55 56 3.619038 GGGCGTGTATTTCTCTCTCTTTG 59.381 47.826 0.00 0.00 0.00 2.77
56 57 3.515901 AGGGCGTGTATTTCTCTCTCTTT 59.484 43.478 0.00 0.00 0.00 2.52
57 58 3.100671 AGGGCGTGTATTTCTCTCTCTT 58.899 45.455 0.00 0.00 0.00 2.85
58 59 2.691011 GAGGGCGTGTATTTCTCTCTCT 59.309 50.000 0.00 0.00 0.00 3.10
59 60 2.541999 CGAGGGCGTGTATTTCTCTCTC 60.542 54.545 0.00 0.00 0.00 3.20
60 61 1.405821 CGAGGGCGTGTATTTCTCTCT 59.594 52.381 0.00 0.00 0.00 3.10
61 62 1.841450 CGAGGGCGTGTATTTCTCTC 58.159 55.000 0.00 0.00 0.00 3.20
73 74 4.201679 TACATGGCGACGAGGGCG 62.202 66.667 0.00 0.00 44.79 6.13
74 75 2.585247 GTACATGGCGACGAGGGC 60.585 66.667 0.00 0.00 0.00 5.19
75 76 1.518572 GTGTACATGGCGACGAGGG 60.519 63.158 0.00 0.00 0.00 4.30
76 77 1.872234 CGTGTACATGGCGACGAGG 60.872 63.158 7.22 0.00 33.64 4.63
77 78 0.097499 TACGTGTACATGGCGACGAG 59.903 55.000 19.05 4.41 35.77 4.18
78 79 0.097499 CTACGTGTACATGGCGACGA 59.903 55.000 19.05 0.40 35.77 4.20
79 80 0.097499 TCTACGTGTACATGGCGACG 59.903 55.000 19.05 9.64 37.82 5.12
80 81 1.399440 TCTCTACGTGTACATGGCGAC 59.601 52.381 19.05 0.00 0.00 5.19
81 82 1.741528 TCTCTACGTGTACATGGCGA 58.258 50.000 19.05 12.81 0.00 5.54
82 83 2.032924 TCATCTCTACGTGTACATGGCG 59.967 50.000 19.05 11.07 0.00 5.69
83 84 3.181490 TGTCATCTCTACGTGTACATGGC 60.181 47.826 19.05 3.38 0.00 4.40
84 85 4.632538 TGTCATCTCTACGTGTACATGG 57.367 45.455 19.05 7.61 0.00 3.66
85 86 5.037385 CCTTGTCATCTCTACGTGTACATG 58.963 45.833 13.64 13.64 0.00 3.21
86 87 4.948004 TCCTTGTCATCTCTACGTGTACAT 59.052 41.667 0.00 0.00 0.00 2.29
87 88 4.155462 GTCCTTGTCATCTCTACGTGTACA 59.845 45.833 0.00 0.00 0.00 2.90
88 89 4.155462 TGTCCTTGTCATCTCTACGTGTAC 59.845 45.833 0.00 0.00 0.00 2.90
89 90 4.329392 TGTCCTTGTCATCTCTACGTGTA 58.671 43.478 0.00 0.00 0.00 2.90
90 91 3.154710 TGTCCTTGTCATCTCTACGTGT 58.845 45.455 0.00 0.00 0.00 4.49
91 92 3.850122 TGTCCTTGTCATCTCTACGTG 57.150 47.619 0.00 0.00 0.00 4.49
92 93 3.193691 CCTTGTCCTTGTCATCTCTACGT 59.806 47.826 0.00 0.00 0.00 3.57
93 94 3.444034 TCCTTGTCCTTGTCATCTCTACG 59.556 47.826 0.00 0.00 0.00 3.51
94 95 5.362430 AGATCCTTGTCCTTGTCATCTCTAC 59.638 44.000 0.00 0.00 0.00 2.59
95 96 5.523588 AGATCCTTGTCCTTGTCATCTCTA 58.476 41.667 0.00 0.00 0.00 2.43
96 97 4.360889 AGATCCTTGTCCTTGTCATCTCT 58.639 43.478 0.00 0.00 0.00 3.10
97 98 4.751767 AGATCCTTGTCCTTGTCATCTC 57.248 45.455 0.00 0.00 0.00 2.75
98 99 4.533707 TGAAGATCCTTGTCCTTGTCATCT 59.466 41.667 0.00 0.00 0.00 2.90
99 100 4.633565 GTGAAGATCCTTGTCCTTGTCATC 59.366 45.833 0.00 0.00 0.00 2.92
100 101 4.566488 GGTGAAGATCCTTGTCCTTGTCAT 60.566 45.833 0.00 0.00 0.00 3.06
101 102 3.244561 GGTGAAGATCCTTGTCCTTGTCA 60.245 47.826 0.00 0.00 0.00 3.58
102 103 3.339141 GGTGAAGATCCTTGTCCTTGTC 58.661 50.000 0.00 0.00 0.00 3.18
103 104 2.040412 GGGTGAAGATCCTTGTCCTTGT 59.960 50.000 0.00 0.00 0.00 3.16
104 105 2.716217 GGGTGAAGATCCTTGTCCTTG 58.284 52.381 0.00 0.00 0.00 3.61
105 106 1.279271 CGGGTGAAGATCCTTGTCCTT 59.721 52.381 0.00 0.00 0.00 3.36
106 107 0.905357 CGGGTGAAGATCCTTGTCCT 59.095 55.000 0.00 0.00 0.00 3.85
107 108 0.902531 TCGGGTGAAGATCCTTGTCC 59.097 55.000 0.00 0.00 0.00 4.02
108 109 2.762535 TTCGGGTGAAGATCCTTGTC 57.237 50.000 0.00 0.00 0.00 3.18
109 110 3.721087 ATTTCGGGTGAAGATCCTTGT 57.279 42.857 0.00 0.00 35.06 3.16
110 111 4.009675 TGAATTTCGGGTGAAGATCCTTG 58.990 43.478 0.00 0.00 35.06 3.61
111 112 4.301072 TGAATTTCGGGTGAAGATCCTT 57.699 40.909 0.00 0.00 35.06 3.36
112 113 4.010349 GTTGAATTTCGGGTGAAGATCCT 58.990 43.478 0.00 0.00 35.06 3.24
113 114 3.128764 GGTTGAATTTCGGGTGAAGATCC 59.871 47.826 0.00 0.00 35.06 3.36
114 115 3.756434 TGGTTGAATTTCGGGTGAAGATC 59.244 43.478 0.00 0.00 35.06 2.75
115 116 3.761897 TGGTTGAATTTCGGGTGAAGAT 58.238 40.909 0.00 0.00 35.06 2.40
116 117 3.216187 TGGTTGAATTTCGGGTGAAGA 57.784 42.857 0.00 0.00 35.06 2.87
117 118 4.519540 ATTGGTTGAATTTCGGGTGAAG 57.480 40.909 0.00 0.00 35.06 3.02
118 119 6.406692 TTTATTGGTTGAATTTCGGGTGAA 57.593 33.333 0.00 0.00 0.00 3.18
119 120 6.041069 ACTTTTATTGGTTGAATTTCGGGTGA 59.959 34.615 0.00 0.00 0.00 4.02
120 121 6.220201 ACTTTTATTGGTTGAATTTCGGGTG 58.780 36.000 0.00 0.00 0.00 4.61
121 122 6.413783 ACTTTTATTGGTTGAATTTCGGGT 57.586 33.333 0.00 0.00 0.00 5.28
122 123 7.062956 GCTAACTTTTATTGGTTGAATTTCGGG 59.937 37.037 0.00 0.00 0.00 5.14
123 124 7.596995 TGCTAACTTTTATTGGTTGAATTTCGG 59.403 33.333 0.00 0.00 0.00 4.30
124 125 8.424731 GTGCTAACTTTTATTGGTTGAATTTCG 58.575 33.333 0.00 0.00 0.00 3.46
125 126 9.255304 TGTGCTAACTTTTATTGGTTGAATTTC 57.745 29.630 0.00 0.00 0.00 2.17
126 127 9.606631 TTGTGCTAACTTTTATTGGTTGAATTT 57.393 25.926 0.00 0.00 0.00 1.82
127 128 9.040939 GTTGTGCTAACTTTTATTGGTTGAATT 57.959 29.630 0.00 0.00 0.00 2.17
128 129 8.200792 TGTTGTGCTAACTTTTATTGGTTGAAT 58.799 29.630 6.10 0.00 0.00 2.57
129 130 7.548097 TGTTGTGCTAACTTTTATTGGTTGAA 58.452 30.769 6.10 0.00 0.00 2.69
130 131 7.101652 TGTTGTGCTAACTTTTATTGGTTGA 57.898 32.000 6.10 0.00 0.00 3.18
131 132 7.276658 TGTTGTTGTGCTAACTTTTATTGGTTG 59.723 33.333 6.10 0.00 0.00 3.77
132 133 7.324178 TGTTGTTGTGCTAACTTTTATTGGTT 58.676 30.769 6.10 0.00 0.00 3.67
133 134 6.868622 TGTTGTTGTGCTAACTTTTATTGGT 58.131 32.000 6.10 0.00 0.00 3.67
134 135 7.763172 TTGTTGTTGTGCTAACTTTTATTGG 57.237 32.000 6.10 0.00 0.00 3.16
138 139 9.011407 CGTTTATTGTTGTTGTGCTAACTTTTA 57.989 29.630 6.10 0.00 0.00 1.52
139 140 7.755822 TCGTTTATTGTTGTTGTGCTAACTTTT 59.244 29.630 6.10 0.00 0.00 2.27
140 141 7.251994 TCGTTTATTGTTGTTGTGCTAACTTT 58.748 30.769 6.10 0.00 0.00 2.66
141 142 6.787225 TCGTTTATTGTTGTTGTGCTAACTT 58.213 32.000 6.10 0.00 0.00 2.66
142 143 6.366315 TCGTTTATTGTTGTTGTGCTAACT 57.634 33.333 6.10 0.00 0.00 2.24
143 144 6.635239 ACATCGTTTATTGTTGTTGTGCTAAC 59.365 34.615 0.00 0.00 0.00 2.34
144 145 6.730175 ACATCGTTTATTGTTGTTGTGCTAA 58.270 32.000 0.00 0.00 0.00 3.09
145 146 6.307031 ACATCGTTTATTGTTGTTGTGCTA 57.693 33.333 0.00 0.00 0.00 3.49
146 147 5.181690 ACATCGTTTATTGTTGTTGTGCT 57.818 34.783 0.00 0.00 0.00 4.40
147 148 5.881637 AACATCGTTTATTGTTGTTGTGC 57.118 34.783 0.00 0.00 34.87 4.57
148 149 7.889745 TGAAAACATCGTTTATTGTTGTTGTG 58.110 30.769 0.00 0.00 36.26 3.33
149 150 8.467402 TTGAAAACATCGTTTATTGTTGTTGT 57.533 26.923 0.00 0.00 36.26 3.32
168 169 7.913297 CCAACTTTCGTCTTATCTTGTTGAAAA 59.087 33.333 0.00 0.00 36.60 2.29
169 170 7.066525 ACCAACTTTCGTCTTATCTTGTTGAAA 59.933 33.333 0.00 0.00 36.60 2.69
170 171 6.540914 ACCAACTTTCGTCTTATCTTGTTGAA 59.459 34.615 0.00 0.00 36.60 2.69
171 172 6.053005 ACCAACTTTCGTCTTATCTTGTTGA 58.947 36.000 0.00 0.00 36.60 3.18
172 173 6.300354 ACCAACTTTCGTCTTATCTTGTTG 57.700 37.500 0.00 0.00 34.96 3.33
173 174 5.469084 GGACCAACTTTCGTCTTATCTTGTT 59.531 40.000 0.00 0.00 0.00 2.83
174 175 4.995487 GGACCAACTTTCGTCTTATCTTGT 59.005 41.667 0.00 0.00 0.00 3.16
175 176 4.392138 GGGACCAACTTTCGTCTTATCTTG 59.608 45.833 0.00 0.00 0.00 3.02
176 177 4.576879 GGGACCAACTTTCGTCTTATCTT 58.423 43.478 0.00 0.00 0.00 2.40
177 178 4.203654 GGGACCAACTTTCGTCTTATCT 57.796 45.455 0.00 0.00 0.00 1.98
194 195 4.754667 GTCGGGCTCAACGGGGAC 62.755 72.222 0.00 0.00 0.00 4.46
195 196 3.588817 TAGTCGGGCTCAACGGGGA 62.589 63.158 0.00 0.00 0.00 4.81
196 197 1.968050 ATTAGTCGGGCTCAACGGGG 61.968 60.000 0.00 0.00 0.00 5.73
197 198 0.748450 TATTAGTCGGGCTCAACGGG 59.252 55.000 0.00 0.00 0.00 5.28
198 199 2.589798 TTATTAGTCGGGCTCAACGG 57.410 50.000 0.00 0.00 0.00 4.44
199 200 4.436451 GGTTTTTATTAGTCGGGCTCAACG 60.436 45.833 0.00 0.00 0.00 4.10
200 201 4.456566 TGGTTTTTATTAGTCGGGCTCAAC 59.543 41.667 0.00 0.00 0.00 3.18
201 202 4.653868 TGGTTTTTATTAGTCGGGCTCAA 58.346 39.130 0.00 0.00 0.00 3.02
202 203 4.289238 TGGTTTTTATTAGTCGGGCTCA 57.711 40.909 0.00 0.00 0.00 4.26
203 204 5.578776 CAATGGTTTTTATTAGTCGGGCTC 58.421 41.667 0.00 0.00 0.00 4.70
204 205 4.142249 GCAATGGTTTTTATTAGTCGGGCT 60.142 41.667 0.00 0.00 0.00 5.19
205 206 4.109766 GCAATGGTTTTTATTAGTCGGGC 58.890 43.478 0.00 0.00 0.00 6.13
206 207 5.317733 TGCAATGGTTTTTATTAGTCGGG 57.682 39.130 0.00 0.00 0.00 5.14
207 208 6.310224 CCTTTGCAATGGTTTTTATTAGTCGG 59.690 38.462 20.54 0.00 0.00 4.79
208 209 6.866248 ACCTTTGCAATGGTTTTTATTAGTCG 59.134 34.615 26.80 3.23 33.06 4.18
209 210 8.601845 AACCTTTGCAATGGTTTTTATTAGTC 57.398 30.769 33.05 0.00 41.93 2.59
219 220 3.181466 GGTGAGAAACCTTTGCAATGGTT 60.181 43.478 33.05 33.05 46.55 3.67
220 221 2.365293 GGTGAGAAACCTTTGCAATGGT 59.635 45.455 26.80 26.80 46.55 3.55
221 222 3.030668 GGTGAGAAACCTTTGCAATGG 57.969 47.619 25.55 25.55 46.55 3.16
232 233 1.666872 CGTGTCCGGGGTGAGAAAC 60.667 63.158 0.00 0.00 0.00 2.78
233 234 1.401318 TTCGTGTCCGGGGTGAGAAA 61.401 55.000 0.00 0.00 33.95 2.52
234 235 1.812686 CTTCGTGTCCGGGGTGAGAA 61.813 60.000 0.00 0.81 33.95 2.87
235 236 2.203523 TTCGTGTCCGGGGTGAGA 60.204 61.111 0.00 0.00 33.95 3.27
236 237 2.261671 CTTCGTGTCCGGGGTGAG 59.738 66.667 0.00 0.00 33.95 3.51
237 238 3.998672 GCTTCGTGTCCGGGGTGA 61.999 66.667 0.00 0.00 33.95 4.02
238 239 3.818121 TTGCTTCGTGTCCGGGGTG 62.818 63.158 0.00 0.00 33.95 4.61
239 240 2.890766 ATTGCTTCGTGTCCGGGGT 61.891 57.895 0.00 0.00 33.95 4.95
240 241 2.046314 ATTGCTTCGTGTCCGGGG 60.046 61.111 0.00 0.00 33.95 5.73
241 242 1.671054 ACATTGCTTCGTGTCCGGG 60.671 57.895 0.00 0.00 33.95 5.73
242 243 1.497278 CACATTGCTTCGTGTCCGG 59.503 57.895 0.00 0.00 33.95 5.14
243 244 1.154413 GCACATTGCTTCGTGTCCG 60.154 57.895 0.00 0.00 40.96 4.79
244 245 4.847255 GCACATTGCTTCGTGTCC 57.153 55.556 0.00 0.00 40.96 4.02
253 254 0.038892 CTGGTGTTGGAGCACATTGC 60.039 55.000 0.00 0.00 45.46 3.56
254 255 1.538512 CTCTGGTGTTGGAGCACATTG 59.461 52.381 0.00 0.00 40.89 2.82
255 256 1.901591 CTCTGGTGTTGGAGCACATT 58.098 50.000 0.00 0.00 40.89 2.71
256 257 3.639099 CTCTGGTGTTGGAGCACAT 57.361 52.632 0.00 0.00 40.89 3.21
261 262 1.079543 CCTCGCTCTGGTGTTGGAG 60.080 63.158 0.00 0.00 0.00 3.86
262 263 2.583441 CCCTCGCTCTGGTGTTGGA 61.583 63.158 0.00 0.00 0.00 3.53
263 264 2.046892 CCCTCGCTCTGGTGTTGG 60.047 66.667 0.00 0.00 0.00 3.77
326 358 3.124921 CGAAAATGGGTCGCGCCT 61.125 61.111 17.07 0.00 37.43 5.52
364 396 2.141122 AATGGTTTTCTGCCGCACCG 62.141 55.000 0.00 0.00 31.24 4.94
366 398 0.388520 GGAATGGTTTTCTGCCGCAC 60.389 55.000 0.00 0.00 0.00 5.34
395 427 0.324275 ACTTGGCTTGGTGGTGTGTT 60.324 50.000 0.00 0.00 0.00 3.32
396 428 0.751643 GACTTGGCTTGGTGGTGTGT 60.752 55.000 0.00 0.00 0.00 3.72
397 429 0.751277 TGACTTGGCTTGGTGGTGTG 60.751 55.000 0.00 0.00 0.00 3.82
398 430 0.466189 CTGACTTGGCTTGGTGGTGT 60.466 55.000 0.00 0.00 0.00 4.16
399 431 0.179020 TCTGACTTGGCTTGGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
401 433 1.230635 CGTCTGACTTGGCTTGGTGG 61.231 60.000 6.21 0.00 0.00 4.61
402 434 1.845809 GCGTCTGACTTGGCTTGGTG 61.846 60.000 6.21 0.00 0.00 4.17
406 438 0.320247 CTCTGCGTCTGACTTGGCTT 60.320 55.000 6.21 0.00 0.00 4.35
408 440 1.739562 CCTCTGCGTCTGACTTGGC 60.740 63.158 6.21 2.83 0.00 4.52
441 473 0.811616 CTTGGCTAGACATGGTCGGC 60.812 60.000 0.00 8.19 37.67 5.54
442 474 0.811616 GCTTGGCTAGACATGGTCGG 60.812 60.000 13.06 0.00 37.67 4.79
443 475 0.811616 GGCTTGGCTAGACATGGTCG 60.812 60.000 13.06 0.00 37.67 4.79
444 476 0.464554 GGGCTTGGCTAGACATGGTC 60.465 60.000 13.06 4.52 31.29 4.02
473 505 1.454295 GGAGGAGGAGGAGGACGAC 60.454 68.421 0.00 0.00 0.00 4.34
489 521 1.538876 CAGGTTGGGTGGGAGAGGA 60.539 63.158 0.00 0.00 0.00 3.71
490 522 3.081554 CAGGTTGGGTGGGAGAGG 58.918 66.667 0.00 0.00 0.00 3.69
491 523 2.352805 GCAGGTTGGGTGGGAGAG 59.647 66.667 0.00 0.00 0.00 3.20
492 524 3.256960 GGCAGGTTGGGTGGGAGA 61.257 66.667 0.00 0.00 0.00 3.71
821 874 1.002792 AAGAGGGAGAGGAGCTGGG 59.997 63.158 0.00 0.00 0.00 4.45
981 1034 3.268965 GACGTGCGAGCTGGACAGA 62.269 63.158 0.00 0.00 39.19 3.41
1113 1166 2.730672 GCACCGCACGTAAGCAGAG 61.731 63.158 0.00 0.00 45.62 3.35
1362 1415 2.266055 CCTTCCTGGTCCACTCGC 59.734 66.667 0.00 0.00 0.00 5.03
1365 1418 1.142688 AATGGCCTTCCTGGTCCACT 61.143 55.000 3.32 0.00 42.08 4.00
1564 1617 1.141881 CAGGACGTTCCTCCATCCG 59.858 63.158 3.87 0.00 45.66 4.18
1627 1680 4.351938 TCCGTCGTCAACCTGCCG 62.352 66.667 0.00 0.00 0.00 5.69
1630 1683 2.430244 CCGTCCGTCGTCAACCTG 60.430 66.667 0.00 0.00 37.94 4.00
1695 1748 1.244816 CCATGCATCCATAGTGCTGG 58.755 55.000 0.00 0.00 42.92 4.85
1755 1808 0.738762 GCATTGTCTCTGCGAGCTCA 60.739 55.000 15.40 0.00 0.00 4.26
1776 1829 1.009829 CGGCCTCATTAGACTGCAAC 58.990 55.000 0.00 0.00 0.00 4.17
1782 1835 0.462047 CCCACACGGCCTCATTAGAC 60.462 60.000 0.00 0.00 0.00 2.59
1908 1961 2.352651 CGCATACATGTTTGACAGGAGG 59.647 50.000 18.99 0.00 33.56 4.30
2041 2094 7.876936 AGACAATTTGTTGAGATCATGCTAT 57.123 32.000 3.08 0.00 0.00 2.97
2153 2206 1.887344 GATGGTTGCAACGCCCCAAT 61.887 55.000 22.67 9.36 33.50 3.16
2154 2207 2.522923 ATGGTTGCAACGCCCCAA 60.523 55.556 22.67 5.01 33.50 4.12
2155 2208 2.988684 GATGGTTGCAACGCCCCA 60.989 61.111 22.67 15.61 34.10 4.96
2156 2209 2.988684 TGATGGTTGCAACGCCCC 60.989 61.111 22.67 10.09 0.00 5.80
2157 2210 2.568090 CTGATGGTTGCAACGCCC 59.432 61.111 22.67 10.46 0.00 6.13
2158 2211 2.268076 ACCTGATGGTTGCAACGCC 61.268 57.895 22.67 11.22 46.05 5.68
2159 2212 1.081242 CACCTGATGGTTGCAACGC 60.081 57.895 22.67 15.82 46.05 4.84
2236 2289 3.076621 TGTGTGGCAGACTGATCATTTC 58.923 45.455 16.26 0.00 0.00 2.17
2272 2325 3.305950 GCATAATTCCACAGTTGCACCAA 60.306 43.478 0.00 0.00 0.00 3.67
2316 2369 9.513906 TCAAATGTATCATGTTCTAACCTTGAA 57.486 29.630 0.00 0.00 0.00 2.69
2437 2490 9.388506 CTTCAAAGACCTCATCATTACAACTAT 57.611 33.333 0.00 0.00 0.00 2.12
2438 2491 7.334421 GCTTCAAAGACCTCATCATTACAACTA 59.666 37.037 0.00 0.00 0.00 2.24
2505 2558 0.674895 GGTGGGCTGTCATGACACTC 60.675 60.000 24.56 19.90 36.21 3.51
2530 2583 7.165812 GCATTGGTGTTTAATTATTACTGCGAG 59.834 37.037 0.00 0.00 0.00 5.03
2533 2586 8.472683 TTGCATTGGTGTTTAATTATTACTGC 57.527 30.769 0.00 0.00 0.00 4.40
2555 2608 5.684626 GCATGTAGTTCTGCTATGATTTTGC 59.315 40.000 0.00 0.00 35.49 3.68
2556 2609 6.690098 GTGCATGTAGTTCTGCTATGATTTTG 59.310 38.462 0.00 0.00 39.16 2.44
2587 2641 5.074584 AGGAAAATGAGACGAACTAGGTC 57.925 43.478 0.00 0.00 34.62 3.85
2640 2694 7.814107 GCATTGTTCAAATTGATACCAGAAGAA 59.186 33.333 0.00 0.00 0.00 2.52
2648 2702 6.624423 ACAGGAGCATTGTTCAAATTGATAC 58.376 36.000 0.00 0.00 0.00 2.24
2650 2704 5.733620 ACAGGAGCATTGTTCAAATTGAT 57.266 34.783 0.00 0.00 0.00 2.57
2670 2724 9.702253 AGAATAGGTTACATAGAAGAGAGAACA 57.298 33.333 0.00 0.00 0.00 3.18
2671 2725 9.959749 CAGAATAGGTTACATAGAAGAGAGAAC 57.040 37.037 0.00 0.00 0.00 3.01
2672 2726 9.702253 ACAGAATAGGTTACATAGAAGAGAGAA 57.298 33.333 0.00 0.00 0.00 2.87
2675 2729 9.916360 TGTACAGAATAGGTTACATAGAAGAGA 57.084 33.333 0.00 0.00 0.00 3.10
2676 2730 9.953697 GTGTACAGAATAGGTTACATAGAAGAG 57.046 37.037 0.00 0.00 0.00 2.85
2677 2731 8.910944 GGTGTACAGAATAGGTTACATAGAAGA 58.089 37.037 0.00 0.00 0.00 2.87
2678 2732 7.861372 CGGTGTACAGAATAGGTTACATAGAAG 59.139 40.741 0.00 0.00 0.00 2.85
2679 2733 7.340232 ACGGTGTACAGAATAGGTTACATAGAA 59.660 37.037 0.00 0.00 0.00 2.10
2757 2812 6.948353 GCTATCAACGAATAGCTGATTTCAA 58.052 36.000 16.50 0.00 46.94 2.69
2873 2928 2.223525 CGACGATTACTTCCCAGAGACC 60.224 54.545 0.00 0.00 0.00 3.85
2948 3003 2.147150 GTTGAACCAGAGCTCAGAACC 58.853 52.381 17.77 2.51 0.00 3.62


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

AutoCloner maintained by Alex Coulton.