Multiple sequence alignment - TraesCS1A01G302900

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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 TraesCS1A01G302900 chr1A 100.000 2290 0 0 1 2290 496475849 496478138 0.000000e+00 4229
1 TraesCS1A01G302900 chr1D 89.128 2134 136 43 218 2290 400060316 400062414 0.000000e+00 2567
2 TraesCS1A01G302900 chr1B 87.593 669 36 14 773 1412 536770443 536771093 0.000000e+00 732
3 TraesCS1A01G302900 chr1B 82.990 776 92 30 1458 2210 536771310 536772068 0.000000e+00 665
4 TraesCS1A01G302900 chr1B 92.342 444 18 9 219 655 536769782 536770216 3.230000e-173 617


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 TraesCS1A01G302900 chr1A 496475849 496478138 2289 False 4229.000000 4229 100.000000 1 2290 1 chr1A.!!$F1 2289
1 TraesCS1A01G302900 chr1D 400060316 400062414 2098 False 2567.000000 2567 89.128000 218 2290 1 chr1D.!!$F1 2072
2 TraesCS1A01G302900 chr1B 536769782 536772068 2286 False 671.333333 732 87.641667 219 2210 3 chr1B.!!$F1 1991

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
114 115 0.03309 GGGTTTACCGGATCCGCTAG 59.967 60.0 29.12 17.53 38.24 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1309 1487 0.179062 CCGGCAGGAGATTCAGAAGG 60.179 60.0 0.0 0.0 41.02 3.46 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
26 27 2.939022 GCGTTTGCGAGCTCTGTT 59.061 55.556 12.85 0.00 41.33 3.16
27 28 1.279840 GCGTTTGCGAGCTCTGTTT 59.720 52.632 12.85 0.00 41.33 2.83
28 29 0.993746 GCGTTTGCGAGCTCTGTTTG 60.994 55.000 12.85 0.00 41.33 2.93
29 30 0.384725 CGTTTGCGAGCTCTGTTTGG 60.385 55.000 12.85 0.00 41.33 3.28
30 31 0.661483 GTTTGCGAGCTCTGTTTGGC 60.661 55.000 12.85 7.12 0.00 4.52
31 32 1.795170 TTTGCGAGCTCTGTTTGGCC 61.795 55.000 12.85 0.00 0.00 5.36
32 33 3.793144 GCGAGCTCTGTTTGGCCG 61.793 66.667 12.85 0.00 0.00 6.13
33 34 3.121030 CGAGCTCTGTTTGGCCGG 61.121 66.667 12.85 0.00 0.00 6.13
34 35 2.347490 GAGCTCTGTTTGGCCGGA 59.653 61.111 5.05 0.00 0.00 5.14
35 36 1.743252 GAGCTCTGTTTGGCCGGAG 60.743 63.158 5.05 1.72 40.23 4.63
37 38 3.121030 CTCTGTTTGGCCGGAGCG 61.121 66.667 5.05 0.00 41.24 5.03
40 41 3.950794 CTGTTTGGCCGGAGCGCTA 62.951 63.158 11.50 0.00 41.24 4.26
41 42 3.195698 GTTTGGCCGGAGCGCTAG 61.196 66.667 11.50 7.80 41.24 3.42
52 53 2.956964 GCGCTAGCTGCACCGTAG 60.957 66.667 21.32 2.00 43.06 3.51
53 54 2.798689 CGCTAGCTGCACCGTAGA 59.201 61.111 13.93 0.00 43.06 2.59
54 55 1.138883 CGCTAGCTGCACCGTAGAA 59.861 57.895 13.93 0.00 43.06 2.10
55 56 0.457853 CGCTAGCTGCACCGTAGAAA 60.458 55.000 13.93 0.00 43.06 2.52
56 57 1.000145 GCTAGCTGCACCGTAGAAAC 59.000 55.000 7.70 0.00 42.31 2.78
57 58 1.671850 GCTAGCTGCACCGTAGAAACA 60.672 52.381 7.70 0.00 42.31 2.83
58 59 2.683968 CTAGCTGCACCGTAGAAACAA 58.316 47.619 1.02 0.00 0.00 2.83
59 60 2.185004 AGCTGCACCGTAGAAACAAT 57.815 45.000 1.02 0.00 0.00 2.71
60 61 2.504367 AGCTGCACCGTAGAAACAATT 58.496 42.857 1.02 0.00 0.00 2.32
61 62 2.484264 AGCTGCACCGTAGAAACAATTC 59.516 45.455 1.02 0.00 35.70 2.17
62 63 2.724839 GCTGCACCGTAGAAACAATTCG 60.725 50.000 0.00 0.00 40.63 3.34
63 64 2.478894 CTGCACCGTAGAAACAATTCGT 59.521 45.455 0.00 0.00 40.63 3.85
64 65 3.651206 TGCACCGTAGAAACAATTCGTA 58.349 40.909 0.00 0.00 40.63 3.43
65 66 3.676172 TGCACCGTAGAAACAATTCGTAG 59.324 43.478 0.00 0.00 40.63 3.51
66 67 3.061697 GCACCGTAGAAACAATTCGTAGG 59.938 47.826 0.00 0.00 40.63 3.18
67 68 4.487948 CACCGTAGAAACAATTCGTAGGA 58.512 43.478 0.00 0.00 40.63 2.94
68 69 4.561606 CACCGTAGAAACAATTCGTAGGAG 59.438 45.833 0.00 0.00 40.63 3.69
69 70 4.219288 ACCGTAGAAACAATTCGTAGGAGT 59.781 41.667 0.00 0.00 40.63 3.85
70 71 4.797349 CCGTAGAAACAATTCGTAGGAGTC 59.203 45.833 0.00 0.00 40.63 3.36
71 72 4.797349 CGTAGAAACAATTCGTAGGAGTCC 59.203 45.833 0.00 0.00 40.63 3.85
72 73 5.392811 CGTAGAAACAATTCGTAGGAGTCCT 60.393 44.000 17.78 17.78 40.63 3.85
73 74 5.074584 AGAAACAATTCGTAGGAGTCCTC 57.925 43.478 17.09 6.76 40.63 3.71
74 75 4.527038 AGAAACAATTCGTAGGAGTCCTCA 59.473 41.667 17.09 0.00 40.63 3.86
75 76 5.187967 AGAAACAATTCGTAGGAGTCCTCAT 59.812 40.000 17.09 0.92 40.63 2.90
76 77 6.380274 AGAAACAATTCGTAGGAGTCCTCATA 59.620 38.462 17.09 0.00 40.63 2.15
77 78 5.517322 ACAATTCGTAGGAGTCCTCATAC 57.483 43.478 17.09 7.81 41.76 2.39
78 79 5.202004 ACAATTCGTAGGAGTCCTCATACT 58.798 41.667 17.09 0.00 42.66 2.12
79 80 5.657302 ACAATTCGTAGGAGTCCTCATACTT 59.343 40.000 17.09 2.66 42.66 2.24
80 81 5.776173 ATTCGTAGGAGTCCTCATACTTG 57.224 43.478 17.09 0.00 42.66 3.16
81 82 4.232188 TCGTAGGAGTCCTCATACTTGT 57.768 45.455 17.09 0.00 42.66 3.16
82 83 4.597004 TCGTAGGAGTCCTCATACTTGTT 58.403 43.478 17.09 0.00 42.66 2.83
83 84 5.014858 TCGTAGGAGTCCTCATACTTGTTT 58.985 41.667 17.09 0.00 42.66 2.83
84 85 5.479375 TCGTAGGAGTCCTCATACTTGTTTT 59.521 40.000 17.09 0.00 42.66 2.43
85 86 5.577164 CGTAGGAGTCCTCATACTTGTTTTG 59.423 44.000 17.09 0.00 42.66 2.44
86 87 5.568620 AGGAGTCCTCATACTTGTTTTGT 57.431 39.130 5.62 0.00 0.00 2.83
87 88 5.308825 AGGAGTCCTCATACTTGTTTTGTG 58.691 41.667 5.62 0.00 0.00 3.33
88 89 4.455877 GGAGTCCTCATACTTGTTTTGTGG 59.544 45.833 0.41 0.00 0.00 4.17
89 90 4.398319 AGTCCTCATACTTGTTTTGTGGG 58.602 43.478 0.00 0.00 0.00 4.61
90 91 4.104102 AGTCCTCATACTTGTTTTGTGGGA 59.896 41.667 0.00 0.00 0.00 4.37
91 92 4.215613 GTCCTCATACTTGTTTTGTGGGAC 59.784 45.833 0.00 0.00 33.90 4.46
92 93 3.188460 CCTCATACTTGTTTTGTGGGACG 59.812 47.826 0.00 0.00 0.00 4.79
93 94 2.550606 TCATACTTGTTTTGTGGGACGC 59.449 45.455 0.00 0.00 40.62 5.19
94 95 0.938713 TACTTGTTTTGTGGGACGCG 59.061 50.000 3.53 3.53 45.01 6.01
95 96 1.008995 CTTGTTTTGTGGGACGCGG 60.009 57.895 12.47 0.00 45.01 6.46
96 97 2.400896 CTTGTTTTGTGGGACGCGGG 62.401 60.000 12.47 0.00 45.01 6.13
97 98 3.666253 GTTTTGTGGGACGCGGGG 61.666 66.667 12.47 0.00 45.01 5.73
98 99 4.192453 TTTTGTGGGACGCGGGGT 62.192 61.111 12.47 0.00 45.01 4.95
99 100 3.717924 TTTTGTGGGACGCGGGGTT 62.718 57.895 12.47 0.00 45.01 4.11
100 101 3.717924 TTTGTGGGACGCGGGGTTT 62.718 57.895 12.47 0.00 45.01 3.27
101 102 2.335092 TTTGTGGGACGCGGGGTTTA 62.335 55.000 12.47 0.00 45.01 2.01
102 103 2.743538 GTGGGACGCGGGGTTTAC 60.744 66.667 12.47 0.00 0.00 2.01
103 104 4.019312 TGGGACGCGGGGTTTACC 62.019 66.667 12.47 0.00 39.11 2.85
111 112 2.203112 GGGGTTTACCGGATCCGC 60.203 66.667 29.12 14.25 41.60 5.54
112 113 2.738938 GGGGTTTACCGGATCCGCT 61.739 63.158 29.12 18.34 41.60 5.52
113 114 1.402107 GGGGTTTACCGGATCCGCTA 61.402 60.000 29.12 17.15 41.60 4.26
114 115 0.033090 GGGTTTACCGGATCCGCTAG 59.967 60.000 29.12 17.53 38.24 3.42
115 116 1.035139 GGTTTACCGGATCCGCTAGA 58.965 55.000 29.12 12.16 38.24 2.43
116 117 1.000496 GGTTTACCGGATCCGCTAGAG 60.000 57.143 29.12 16.76 38.24 2.43
117 118 1.952296 GTTTACCGGATCCGCTAGAGA 59.048 52.381 29.12 8.72 38.24 3.10
118 119 2.557490 GTTTACCGGATCCGCTAGAGAT 59.443 50.000 29.12 9.30 38.24 2.75
119 120 1.822506 TACCGGATCCGCTAGAGATG 58.177 55.000 29.12 14.51 38.24 2.90
120 121 1.214062 CCGGATCCGCTAGAGATGC 59.786 63.158 29.12 0.00 38.24 3.91
121 122 1.247419 CCGGATCCGCTAGAGATGCT 61.247 60.000 29.12 0.00 38.24 3.79
122 123 0.170116 CGGATCCGCTAGAGATGCTC 59.830 60.000 23.37 0.00 30.52 4.26
123 124 1.544724 GGATCCGCTAGAGATGCTCT 58.455 55.000 0.00 2.22 43.83 4.09
124 125 1.472480 GGATCCGCTAGAGATGCTCTC 59.528 57.143 0.00 5.36 43.70 3.20
125 126 2.158559 GATCCGCTAGAGATGCTCTCA 58.841 52.381 13.42 2.40 45.73 3.27
126 127 2.058593 TCCGCTAGAGATGCTCTCAA 57.941 50.000 13.42 0.00 45.73 3.02
127 128 2.591923 TCCGCTAGAGATGCTCTCAAT 58.408 47.619 13.42 0.17 45.73 2.57
128 129 2.295629 TCCGCTAGAGATGCTCTCAATG 59.704 50.000 13.42 6.09 45.73 2.82
129 130 2.609984 CCGCTAGAGATGCTCTCAATGG 60.610 54.545 13.42 7.31 45.73 3.16
130 131 2.035704 CGCTAGAGATGCTCTCAATGGT 59.964 50.000 13.42 0.00 45.73 3.55
131 132 3.492309 CGCTAGAGATGCTCTCAATGGTT 60.492 47.826 13.42 0.00 45.73 3.67
132 133 4.450053 GCTAGAGATGCTCTCAATGGTTT 58.550 43.478 13.42 0.00 45.73 3.27
133 134 4.880696 GCTAGAGATGCTCTCAATGGTTTT 59.119 41.667 13.42 0.00 45.73 2.43
134 135 5.356470 GCTAGAGATGCTCTCAATGGTTTTT 59.644 40.000 13.42 0.00 45.73 1.94
135 136 5.893897 AGAGATGCTCTCAATGGTTTTTC 57.106 39.130 13.42 0.00 45.73 2.29
136 137 4.394300 AGAGATGCTCTCAATGGTTTTTCG 59.606 41.667 13.42 0.00 45.73 3.46
137 138 3.441572 AGATGCTCTCAATGGTTTTTCGG 59.558 43.478 0.00 0.00 0.00 4.30
138 139 2.582052 TGCTCTCAATGGTTTTTCGGT 58.418 42.857 0.00 0.00 0.00 4.69
139 140 2.955660 TGCTCTCAATGGTTTTTCGGTT 59.044 40.909 0.00 0.00 0.00 4.44
140 141 3.383185 TGCTCTCAATGGTTTTTCGGTTT 59.617 39.130 0.00 0.00 0.00 3.27
141 142 4.142049 TGCTCTCAATGGTTTTTCGGTTTT 60.142 37.500 0.00 0.00 0.00 2.43
142 143 4.808895 GCTCTCAATGGTTTTTCGGTTTTT 59.191 37.500 0.00 0.00 0.00 1.94
143 144 5.051039 GCTCTCAATGGTTTTTCGGTTTTTC 60.051 40.000 0.00 0.00 0.00 2.29
144 145 6.215495 TCTCAATGGTTTTTCGGTTTTTCT 57.785 33.333 0.00 0.00 0.00 2.52
145 146 6.635755 TCTCAATGGTTTTTCGGTTTTTCTT 58.364 32.000 0.00 0.00 0.00 2.52
146 147 7.100409 TCTCAATGGTTTTTCGGTTTTTCTTT 58.900 30.769 0.00 0.00 0.00 2.52
147 148 8.251721 TCTCAATGGTTTTTCGGTTTTTCTTTA 58.748 29.630 0.00 0.00 0.00 1.85
148 149 8.413899 TCAATGGTTTTTCGGTTTTTCTTTAG 57.586 30.769 0.00 0.00 0.00 1.85
149 150 7.492994 TCAATGGTTTTTCGGTTTTTCTTTAGG 59.507 33.333 0.00 0.00 0.00 2.69
150 151 5.662456 TGGTTTTTCGGTTTTTCTTTAGGG 58.338 37.500 0.00 0.00 0.00 3.53
151 152 5.051816 GGTTTTTCGGTTTTTCTTTAGGGG 58.948 41.667 0.00 0.00 0.00 4.79
152 153 5.163426 GGTTTTTCGGTTTTTCTTTAGGGGA 60.163 40.000 0.00 0.00 0.00 4.81
153 154 6.339730 GTTTTTCGGTTTTTCTTTAGGGGAA 58.660 36.000 0.00 0.00 0.00 3.97
154 155 5.777850 TTTCGGTTTTTCTTTAGGGGAAG 57.222 39.130 0.00 0.00 0.00 3.46
155 156 4.710313 TCGGTTTTTCTTTAGGGGAAGA 57.290 40.909 0.00 0.00 34.00 2.87
156 157 5.051409 TCGGTTTTTCTTTAGGGGAAGAA 57.949 39.130 0.00 0.00 42.28 2.52
161 162 4.463050 TTTCTTTAGGGGAAGAAAGCCA 57.537 40.909 8.30 0.00 45.66 4.75
162 163 3.434940 TCTTTAGGGGAAGAAAGCCAC 57.565 47.619 0.00 0.00 32.95 5.01
163 164 2.986728 TCTTTAGGGGAAGAAAGCCACT 59.013 45.455 0.00 0.00 43.02 4.00
164 165 3.009143 TCTTTAGGGGAAGAAAGCCACTC 59.991 47.826 0.00 0.00 38.80 3.51
165 166 2.038863 TAGGGGAAGAAAGCCACTCA 57.961 50.000 0.00 0.00 38.80 3.41
166 167 1.149101 AGGGGAAGAAAGCCACTCAA 58.851 50.000 0.00 0.00 32.40 3.02
167 168 1.202940 AGGGGAAGAAAGCCACTCAAC 60.203 52.381 0.00 0.00 32.40 3.18
168 169 0.875059 GGGAAGAAAGCCACTCAACG 59.125 55.000 0.00 0.00 0.00 4.10
169 170 0.875059 GGAAGAAAGCCACTCAACGG 59.125 55.000 0.00 0.00 0.00 4.44
170 171 1.594331 GAAGAAAGCCACTCAACGGT 58.406 50.000 0.00 0.00 0.00 4.83
171 172 1.264288 GAAGAAAGCCACTCAACGGTG 59.736 52.381 0.00 0.00 37.00 4.94
172 173 0.468226 AGAAAGCCACTCAACGGTGA 59.532 50.000 1.69 1.69 39.34 4.02
173 174 1.072331 AGAAAGCCACTCAACGGTGAT 59.928 47.619 2.20 0.00 39.34 3.06
174 175 1.197721 GAAAGCCACTCAACGGTGATG 59.802 52.381 2.20 4.72 39.34 3.07
175 176 0.108585 AAGCCACTCAACGGTGATGT 59.891 50.000 2.20 1.11 39.34 3.06
176 177 0.973632 AGCCACTCAACGGTGATGTA 59.026 50.000 2.20 0.00 39.34 2.29
177 178 1.555075 AGCCACTCAACGGTGATGTAT 59.445 47.619 2.20 0.00 39.34 2.29
178 179 2.764010 AGCCACTCAACGGTGATGTATA 59.236 45.455 2.20 0.00 39.34 1.47
179 180 3.196901 AGCCACTCAACGGTGATGTATAA 59.803 43.478 2.20 0.00 39.34 0.98
180 181 3.308866 GCCACTCAACGGTGATGTATAAC 59.691 47.826 2.20 0.00 39.34 1.89
181 182 4.755411 CCACTCAACGGTGATGTATAACT 58.245 43.478 2.20 0.00 39.34 2.24
182 183 5.175859 CCACTCAACGGTGATGTATAACTT 58.824 41.667 2.20 0.00 39.34 2.66
183 184 5.063438 CCACTCAACGGTGATGTATAACTTG 59.937 44.000 2.20 0.00 39.34 3.16
184 185 5.637810 CACTCAACGGTGATGTATAACTTGT 59.362 40.000 2.20 0.00 39.34 3.16
185 186 5.637810 ACTCAACGGTGATGTATAACTTGTG 59.362 40.000 2.20 0.00 31.85 3.33
186 187 4.932799 TCAACGGTGATGTATAACTTGTGG 59.067 41.667 0.00 0.00 0.00 4.17
187 188 3.869065 ACGGTGATGTATAACTTGTGGG 58.131 45.455 0.00 0.00 0.00 4.61
188 189 2.612212 CGGTGATGTATAACTTGTGGGC 59.388 50.000 0.00 0.00 0.00 5.36
189 190 3.616219 GGTGATGTATAACTTGTGGGCA 58.384 45.455 0.00 0.00 0.00 5.36
190 191 3.627577 GGTGATGTATAACTTGTGGGCAG 59.372 47.826 0.00 0.00 0.00 4.85
191 192 4.261801 GTGATGTATAACTTGTGGGCAGT 58.738 43.478 0.00 0.00 0.00 4.40
192 193 4.094887 GTGATGTATAACTTGTGGGCAGTG 59.905 45.833 0.00 0.00 0.00 3.66
193 194 4.019771 TGATGTATAACTTGTGGGCAGTGA 60.020 41.667 0.00 0.00 0.00 3.41
194 195 3.670625 TGTATAACTTGTGGGCAGTGAC 58.329 45.455 0.00 0.00 0.00 3.67
195 196 1.808411 ATAACTTGTGGGCAGTGACG 58.192 50.000 0.00 0.00 0.00 4.35
196 197 0.466543 TAACTTGTGGGCAGTGACGT 59.533 50.000 0.00 0.00 0.00 4.34
197 198 1.095228 AACTTGTGGGCAGTGACGTG 61.095 55.000 0.00 0.00 0.00 4.49
198 199 1.227527 CTTGTGGGCAGTGACGTGA 60.228 57.895 0.00 0.00 0.00 4.35
199 200 0.813610 CTTGTGGGCAGTGACGTGAA 60.814 55.000 0.00 0.00 0.00 3.18
200 201 0.813610 TTGTGGGCAGTGACGTGAAG 60.814 55.000 0.00 0.00 0.00 3.02
201 202 1.961277 GTGGGCAGTGACGTGAAGG 60.961 63.158 0.00 0.00 0.00 3.46
202 203 2.426023 GGGCAGTGACGTGAAGGT 59.574 61.111 0.00 0.00 0.00 3.50
203 204 1.668151 GGGCAGTGACGTGAAGGTC 60.668 63.158 0.00 0.00 37.45 3.85
204 205 1.069090 GGCAGTGACGTGAAGGTCA 59.931 57.895 0.00 1.85 44.25 4.02
205 206 0.946221 GGCAGTGACGTGAAGGTCAG 60.946 60.000 6.11 0.00 46.81 3.51
206 207 1.560860 GCAGTGACGTGAAGGTCAGC 61.561 60.000 6.11 4.27 46.81 4.26
207 208 0.946221 CAGTGACGTGAAGGTCAGCC 60.946 60.000 6.11 0.00 46.81 4.85
208 209 1.115930 AGTGACGTGAAGGTCAGCCT 61.116 55.000 6.11 0.00 46.81 4.58
209 210 0.667792 GTGACGTGAAGGTCAGCCTC 60.668 60.000 6.11 0.00 46.81 4.70
210 211 1.444553 GACGTGAAGGTCAGCCTCG 60.445 63.158 0.00 0.00 46.33 4.63
211 212 2.143594 GACGTGAAGGTCAGCCTCGT 62.144 60.000 0.00 0.00 46.33 4.18
212 213 0.892358 ACGTGAAGGTCAGCCTCGTA 60.892 55.000 0.00 0.00 46.33 3.43
213 214 0.456312 CGTGAAGGTCAGCCTCGTAC 60.456 60.000 0.00 0.00 46.33 3.67
214 215 0.889306 GTGAAGGTCAGCCTCGTACT 59.111 55.000 0.00 0.00 46.33 2.73
215 216 2.089980 GTGAAGGTCAGCCTCGTACTA 58.910 52.381 0.00 0.00 46.33 1.82
216 217 2.089980 TGAAGGTCAGCCTCGTACTAC 58.910 52.381 0.00 0.00 46.33 2.73
272 278 1.401148 CGAGGGCATACGGAAGATACG 60.401 57.143 0.00 0.00 37.36 3.06
273 279 0.317479 AGGGCATACGGAAGATACGC 59.683 55.000 0.00 0.00 34.00 4.42
274 280 0.317479 GGGCATACGGAAGATACGCT 59.683 55.000 0.00 0.00 34.00 5.07
275 281 1.270147 GGGCATACGGAAGATACGCTT 60.270 52.381 0.00 0.00 40.25 4.68
470 476 1.065418 CCCTTGTCACCCACAGTATCC 60.065 57.143 0.00 0.00 35.97 2.59
472 478 1.909302 CTTGTCACCCACAGTATCCCT 59.091 52.381 0.00 0.00 35.97 4.20
474 480 1.078823 TGTCACCCACAGTATCCCTCT 59.921 52.381 0.00 0.00 0.00 3.69
495 501 3.669939 TCCTCCTTTTTCCATGATCCC 57.330 47.619 0.00 0.00 0.00 3.85
508 514 5.806818 TCCATGATCCCGTTTAGTGTAAAA 58.193 37.500 0.00 0.00 0.00 1.52
509 515 6.239396 TCCATGATCCCGTTTAGTGTAAAAA 58.761 36.000 0.00 0.00 0.00 1.94
589 595 4.284123 GCTGATGAGCACGACCAA 57.716 55.556 0.00 0.00 45.46 3.67
594 600 2.227968 GATGAGCACGACCAACGCAC 62.228 60.000 0.00 0.00 46.94 5.34
597 603 3.712881 GCACGACCAACGCACCTC 61.713 66.667 0.00 0.00 46.94 3.85
600 606 4.308458 CGACCAACGCACCTCCCA 62.308 66.667 0.00 0.00 34.51 4.37
611 617 1.073284 GCACCTCCCAAACTCCAGTTA 59.927 52.381 0.00 0.00 37.25 2.24
612 618 2.876079 GCACCTCCCAAACTCCAGTTAG 60.876 54.545 0.00 0.00 37.25 2.34
617 623 4.082125 CTCCCAAACTCCAGTTAGCATTT 58.918 43.478 0.00 0.00 37.25 2.32
650 656 8.227119 GTGGCCAACAACATTTTATACAAATTC 58.773 33.333 7.24 0.00 0.00 2.17
746 821 1.419381 TCTATGACGCCATTAGCCCA 58.581 50.000 0.00 0.00 38.78 5.36
756 831 2.026356 GCCATTAGCCCAAACCCATTTT 60.026 45.455 0.00 0.00 34.35 1.82
760 835 5.499313 CATTAGCCCAAACCCATTTTCAAT 58.501 37.500 0.00 0.00 0.00 2.57
763 838 2.819019 GCCCAAACCCATTTTCAATTGG 59.181 45.455 5.42 0.00 37.61 3.16
765 840 4.810376 GCCCAAACCCATTTTCAATTGGAT 60.810 41.667 5.42 0.00 39.69 3.41
766 841 5.572475 GCCCAAACCCATTTTCAATTGGATA 60.572 40.000 5.42 0.00 39.69 2.59
768 843 6.598850 CCCAAACCCATTTTCAATTGGATAAG 59.401 38.462 5.42 0.00 39.69 1.73
775 912 4.683766 TTTCAATTGGATAAGACCCCCA 57.316 40.909 5.42 0.00 0.00 4.96
812 949 2.770164 AAACTCGGTCAAGGATCCAG 57.230 50.000 15.82 6.17 0.00 3.86
891 1028 0.683973 CACAGACCAAGTCCAGAGCT 59.316 55.000 0.00 0.00 32.18 4.09
896 1033 2.752358 CAAGTCCAGAGCTGCCCA 59.248 61.111 0.00 0.00 0.00 5.36
1182 1360 0.395586 ATCTCTCTCGTGCTGAGGCT 60.396 55.000 6.69 0.00 45.32 4.58
1183 1361 0.610509 TCTCTCTCGTGCTGAGGCTT 60.611 55.000 6.69 0.00 45.32 4.35
1311 1489 3.555967 GGATCTGATCCCACGCCT 58.444 61.111 23.45 0.00 43.88 5.52
1312 1490 1.832912 GGATCTGATCCCACGCCTT 59.167 57.895 23.45 0.00 43.88 4.35
1313 1491 0.250081 GGATCTGATCCCACGCCTTC 60.250 60.000 23.45 0.00 43.88 3.46
1314 1492 0.755686 GATCTGATCCCACGCCTTCT 59.244 55.000 6.37 0.00 0.00 2.85
1315 1493 0.467384 ATCTGATCCCACGCCTTCTG 59.533 55.000 0.00 0.00 0.00 3.02
1316 1494 0.614697 TCTGATCCCACGCCTTCTGA 60.615 55.000 0.00 0.00 0.00 3.27
1317 1495 0.250234 CTGATCCCACGCCTTCTGAA 59.750 55.000 0.00 0.00 0.00 3.02
1318 1496 0.911769 TGATCCCACGCCTTCTGAAT 59.088 50.000 0.00 0.00 0.00 2.57
1319 1497 1.134401 TGATCCCACGCCTTCTGAATC 60.134 52.381 0.00 0.00 0.00 2.52
1320 1498 1.139853 GATCCCACGCCTTCTGAATCT 59.860 52.381 0.00 0.00 0.00 2.40
1321 1499 0.537188 TCCCACGCCTTCTGAATCTC 59.463 55.000 0.00 0.00 0.00 2.75
1322 1500 0.462759 CCCACGCCTTCTGAATCTCC 60.463 60.000 0.00 0.00 0.00 3.71
1328 1506 0.179062 CCTTCTGAATCTCCTGCCGG 60.179 60.000 0.00 0.00 0.00 6.13
1329 1507 0.539051 CTTCTGAATCTCCTGCCGGT 59.461 55.000 1.90 0.00 0.00 5.28
1354 1548 0.183731 CTATCAGGTTTCTGGGGGCC 59.816 60.000 0.00 0.00 41.23 5.80
1384 1578 3.418047 ACGTGAAATTCTAGGGTTTGGG 58.582 45.455 0.00 0.00 0.00 4.12
1401 1595 3.695830 TGGGCTGGTGTTAAGTTAGAG 57.304 47.619 0.00 0.00 0.00 2.43
1412 1606 7.095910 GGTGTTAAGTTAGAGTAGTTCCCTTC 58.904 42.308 0.00 0.00 0.00 3.46
1422 1617 3.714798 AGTAGTTCCCTTCTGTTGTTGGA 59.285 43.478 0.00 0.00 0.00 3.53
1435 1630 4.958509 TGTTGTTGGATACGAGGTGTTTA 58.041 39.130 0.00 0.00 42.51 2.01
1461 1826 1.548719 GGGGTTACAAATTGGGAGTGC 59.451 52.381 0.00 0.00 0.00 4.40
1495 1860 1.154205 CGCATTTCTCCGTAGCTGGG 61.154 60.000 0.00 0.00 0.00 4.45
1501 1866 3.682292 CTCCGTAGCTGGGTTGCCC 62.682 68.421 0.00 0.00 45.71 5.36
1542 1907 1.203523 GCAGATCACTGGAGACTTCGT 59.796 52.381 0.00 0.00 43.62 3.85
1659 2036 2.689983 AGCCCCATTTTCGCTATCAAAG 59.310 45.455 0.00 0.00 0.00 2.77
1667 2044 4.944962 TTTCGCTATCAAAGTGATGGTG 57.055 40.909 8.39 8.39 44.10 4.17
1677 2054 2.036098 TGATGGTGCAGCTTGGGG 59.964 61.111 18.08 0.00 0.00 4.96
1683 2060 1.529244 GTGCAGCTTGGGGTCTTGT 60.529 57.895 0.00 0.00 0.00 3.16
1716 2093 8.758829 TGAATGTAAGGCTAGTTTAGAAGATGA 58.241 33.333 0.00 0.00 0.00 2.92
1743 2133 2.094803 CACGCAATGAGGTAAATGCCAA 60.095 45.455 0.00 0.00 35.41 4.52
1773 2164 2.104963 GTCTTTGAGGTGGGAGAAGTGT 59.895 50.000 0.00 0.00 0.00 3.55
1807 2198 2.507324 GCGCTTCCTCTGGTCGTC 60.507 66.667 0.00 0.00 0.00 4.20
1813 2204 2.163509 CTTCCTCTGGTCGTCTTCTCA 58.836 52.381 0.00 0.00 0.00 3.27
1887 2278 5.964958 TTGCCTAGTCTTTTGAAGAATGG 57.035 39.130 1.32 0.00 39.67 3.16
1942 2335 4.019858 CTCTCCAGTCTCCTGTGAATACA 58.980 47.826 0.00 0.00 36.95 2.29
2082 2476 5.012893 GGTCCATTCTTGTCTTCCTCAATT 58.987 41.667 0.00 0.00 0.00 2.32
2103 2497 4.431416 TGTATTATCCTTCCCGTGCATT 57.569 40.909 0.00 0.00 0.00 3.56
2171 2565 8.524487 TGTTTTAACTGTTTACCACTTCACATT 58.476 29.630 0.00 0.00 0.00 2.71
2190 2584 4.931002 ACATTGGCATTGTTTGAGCAATAC 59.069 37.500 9.11 0.00 37.00 1.89
2250 2644 1.874872 CTTCGTTTTCCCGTTGCCTTA 59.125 47.619 0.00 0.00 0.00 2.69
2255 2649 2.477845 TTTCCCGTTGCCTTACTACC 57.522 50.000 0.00 0.00 0.00 3.18
2262 2656 2.224784 CGTTGCCTTACTACCAACAACC 59.775 50.000 0.00 0.00 38.92 3.77
2271 2665 4.216411 ACTACCAACAACCGCTATTGAT 57.784 40.909 4.02 0.00 33.57 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.520846 GCTCGCAAACGCATCCCG 62.521 66.667 0.00 0.00 44.21 5.14
4 5 3.100862 GAGCTCGCAAACGCATCCC 62.101 63.158 0.00 0.00 39.84 3.85
5 6 2.103042 AGAGCTCGCAAACGCATCC 61.103 57.895 8.37 0.00 39.84 3.51
6 7 1.059994 CAGAGCTCGCAAACGCATC 59.940 57.895 8.37 0.00 39.84 3.91
7 8 1.230635 AACAGAGCTCGCAAACGCAT 61.231 50.000 8.37 0.00 39.84 4.73
8 9 1.436195 AAACAGAGCTCGCAAACGCA 61.436 50.000 8.37 0.00 39.84 5.24
9 10 0.993746 CAAACAGAGCTCGCAAACGC 60.994 55.000 8.37 0.00 39.84 4.84
10 11 0.384725 CCAAACAGAGCTCGCAAACG 60.385 55.000 8.37 0.00 42.01 3.60
11 12 0.661483 GCCAAACAGAGCTCGCAAAC 60.661 55.000 8.37 0.00 0.00 2.93
12 13 1.654220 GCCAAACAGAGCTCGCAAA 59.346 52.632 8.37 0.00 0.00 3.68
13 14 2.260869 GGCCAAACAGAGCTCGCAA 61.261 57.895 8.37 0.00 0.00 4.85
14 15 2.669569 GGCCAAACAGAGCTCGCA 60.670 61.111 8.37 0.00 0.00 5.10
15 16 3.793144 CGGCCAAACAGAGCTCGC 61.793 66.667 8.37 4.16 0.00 5.03
16 17 3.121030 CCGGCCAAACAGAGCTCG 61.121 66.667 8.37 6.04 0.00 5.03
17 18 1.743252 CTCCGGCCAAACAGAGCTC 60.743 63.158 5.27 5.27 0.00 4.09
18 19 2.348998 CTCCGGCCAAACAGAGCT 59.651 61.111 2.24 0.00 0.00 4.09
19 20 3.435186 GCTCCGGCCAAACAGAGC 61.435 66.667 2.24 8.25 44.36 4.09
20 21 3.121030 CGCTCCGGCCAAACAGAG 61.121 66.667 2.24 1.22 34.44 3.35
22 23 3.950794 TAGCGCTCCGGCCAAACAG 62.951 63.158 16.34 0.00 34.44 3.16
23 24 3.950794 CTAGCGCTCCGGCCAAACA 62.951 63.158 16.34 0.00 34.44 2.83
24 25 3.195698 CTAGCGCTCCGGCCAAAC 61.196 66.667 16.34 0.00 34.44 2.93
37 38 1.000145 GTTTCTACGGTGCAGCTAGC 59.000 55.000 14.92 6.62 45.96 3.42
38 39 2.363788 TGTTTCTACGGTGCAGCTAG 57.636 50.000 14.92 13.80 0.00 3.42
39 40 2.823924 TTGTTTCTACGGTGCAGCTA 57.176 45.000 14.92 4.77 0.00 3.32
40 41 2.185004 ATTGTTTCTACGGTGCAGCT 57.815 45.000 14.92 3.76 0.00 4.24
41 42 2.724839 CGAATTGTTTCTACGGTGCAGC 60.725 50.000 5.64 5.64 0.00 5.25
42 43 2.478894 ACGAATTGTTTCTACGGTGCAG 59.521 45.455 0.00 0.00 0.00 4.41
43 44 2.485903 ACGAATTGTTTCTACGGTGCA 58.514 42.857 0.00 0.00 0.00 4.57
44 45 3.061697 CCTACGAATTGTTTCTACGGTGC 59.938 47.826 0.00 0.00 0.00 5.01
45 46 4.487948 TCCTACGAATTGTTTCTACGGTG 58.512 43.478 0.00 0.00 0.00 4.94
46 47 4.219288 ACTCCTACGAATTGTTTCTACGGT 59.781 41.667 0.00 0.00 0.00 4.83
47 48 4.741342 ACTCCTACGAATTGTTTCTACGG 58.259 43.478 0.00 0.00 0.00 4.02
48 49 4.797349 GGACTCCTACGAATTGTTTCTACG 59.203 45.833 0.00 0.00 0.00 3.51
49 50 5.963594 AGGACTCCTACGAATTGTTTCTAC 58.036 41.667 0.00 0.00 28.47 2.59
50 51 5.713389 TGAGGACTCCTACGAATTGTTTCTA 59.287 40.000 0.00 0.00 31.76 2.10
51 52 4.527038 TGAGGACTCCTACGAATTGTTTCT 59.473 41.667 0.00 0.00 31.76 2.52
52 53 4.817517 TGAGGACTCCTACGAATTGTTTC 58.182 43.478 0.00 0.00 31.76 2.78
53 54 4.884668 TGAGGACTCCTACGAATTGTTT 57.115 40.909 0.00 0.00 31.76 2.83
54 55 5.657302 AGTATGAGGACTCCTACGAATTGTT 59.343 40.000 0.00 0.00 36.32 2.83
55 56 5.202004 AGTATGAGGACTCCTACGAATTGT 58.798 41.667 0.00 0.00 36.32 2.71
56 57 5.776173 AGTATGAGGACTCCTACGAATTG 57.224 43.478 0.00 0.00 36.32 2.32
57 58 5.657302 ACAAGTATGAGGACTCCTACGAATT 59.343 40.000 0.00 0.00 36.32 2.17
58 59 5.202004 ACAAGTATGAGGACTCCTACGAAT 58.798 41.667 0.00 0.00 36.32 3.34
59 60 4.597004 ACAAGTATGAGGACTCCTACGAA 58.403 43.478 0.00 0.00 36.32 3.85
60 61 4.232188 ACAAGTATGAGGACTCCTACGA 57.768 45.455 0.00 0.00 36.32 3.43
61 62 4.985538 AACAAGTATGAGGACTCCTACG 57.014 45.455 0.00 0.00 36.32 3.51
62 63 6.369065 CACAAAACAAGTATGAGGACTCCTAC 59.631 42.308 0.00 6.65 31.76 3.18
63 64 6.464222 CACAAAACAAGTATGAGGACTCCTA 58.536 40.000 0.00 0.00 31.76 2.94
64 65 5.308825 CACAAAACAAGTATGAGGACTCCT 58.691 41.667 0.00 0.00 36.03 3.69
65 66 4.455877 CCACAAAACAAGTATGAGGACTCC 59.544 45.833 0.00 0.00 0.00 3.85
66 67 4.455877 CCCACAAAACAAGTATGAGGACTC 59.544 45.833 4.68 0.00 0.00 3.36
67 68 4.104102 TCCCACAAAACAAGTATGAGGACT 59.896 41.667 4.68 0.00 0.00 3.85
68 69 4.215613 GTCCCACAAAACAAGTATGAGGAC 59.784 45.833 12.33 12.33 35.52 3.85
69 70 4.394729 GTCCCACAAAACAAGTATGAGGA 58.605 43.478 4.68 0.00 0.00 3.71
70 71 3.188460 CGTCCCACAAAACAAGTATGAGG 59.812 47.826 0.00 0.00 0.00 3.86
71 72 3.364964 GCGTCCCACAAAACAAGTATGAG 60.365 47.826 0.00 0.00 0.00 2.90
72 73 2.550606 GCGTCCCACAAAACAAGTATGA 59.449 45.455 0.00 0.00 0.00 2.15
73 74 2.664424 CGCGTCCCACAAAACAAGTATG 60.664 50.000 0.00 0.00 0.00 2.39
74 75 1.533731 CGCGTCCCACAAAACAAGTAT 59.466 47.619 0.00 0.00 0.00 2.12
75 76 0.938713 CGCGTCCCACAAAACAAGTA 59.061 50.000 0.00 0.00 0.00 2.24
76 77 1.720694 CCGCGTCCCACAAAACAAGT 61.721 55.000 4.92 0.00 0.00 3.16
77 78 1.008995 CCGCGTCCCACAAAACAAG 60.009 57.895 4.92 0.00 0.00 3.16
78 79 2.482333 CCCGCGTCCCACAAAACAA 61.482 57.895 4.92 0.00 0.00 2.83
79 80 2.902846 CCCGCGTCCCACAAAACA 60.903 61.111 4.92 0.00 0.00 2.83
80 81 3.666253 CCCCGCGTCCCACAAAAC 61.666 66.667 4.92 0.00 0.00 2.43
81 82 3.717924 AACCCCGCGTCCCACAAAA 62.718 57.895 4.92 0.00 0.00 2.44
82 83 2.335092 TAAACCCCGCGTCCCACAAA 62.335 55.000 4.92 0.00 0.00 2.83
83 84 2.815945 TAAACCCCGCGTCCCACAA 61.816 57.895 4.92 0.00 0.00 3.33
84 85 3.240011 TAAACCCCGCGTCCCACA 61.240 61.111 4.92 0.00 0.00 4.17
85 86 2.743538 GTAAACCCCGCGTCCCAC 60.744 66.667 4.92 0.00 0.00 4.61
86 87 4.019312 GGTAAACCCCGCGTCCCA 62.019 66.667 4.92 0.00 0.00 4.37
89 90 3.375472 ATCCGGTAAACCCCGCGTC 62.375 63.158 4.92 0.00 46.71 5.19
90 91 3.375472 GATCCGGTAAACCCCGCGT 62.375 63.158 4.92 0.00 46.71 6.01
91 92 2.586914 GATCCGGTAAACCCCGCG 60.587 66.667 0.00 0.00 46.71 6.46
92 93 2.203112 GGATCCGGTAAACCCCGC 60.203 66.667 0.00 0.00 46.71 6.13
94 95 2.203112 GCGGATCCGGTAAACCCC 60.203 66.667 33.98 12.15 40.19 4.95
102 103 1.214062 GCATCTCTAGCGGATCCGG 59.786 63.158 33.98 18.59 40.19 5.14
103 104 0.170116 GAGCATCTCTAGCGGATCCG 59.830 60.000 30.03 30.03 43.09 4.18
116 117 3.191371 ACCGAAAAACCATTGAGAGCATC 59.809 43.478 0.00 0.00 0.00 3.91
117 118 3.157087 ACCGAAAAACCATTGAGAGCAT 58.843 40.909 0.00 0.00 0.00 3.79
118 119 2.582052 ACCGAAAAACCATTGAGAGCA 58.418 42.857 0.00 0.00 0.00 4.26
119 120 3.643159 AACCGAAAAACCATTGAGAGC 57.357 42.857 0.00 0.00 0.00 4.09
120 121 6.273071 AGAAAAACCGAAAAACCATTGAGAG 58.727 36.000 0.00 0.00 0.00 3.20
121 122 6.215495 AGAAAAACCGAAAAACCATTGAGA 57.785 33.333 0.00 0.00 0.00 3.27
122 123 6.902224 AAGAAAAACCGAAAAACCATTGAG 57.098 33.333 0.00 0.00 0.00 3.02
123 124 7.492994 CCTAAAGAAAAACCGAAAAACCATTGA 59.507 33.333 0.00 0.00 0.00 2.57
124 125 7.254624 CCCTAAAGAAAAACCGAAAAACCATTG 60.255 37.037 0.00 0.00 0.00 2.82
125 126 6.764085 CCCTAAAGAAAAACCGAAAAACCATT 59.236 34.615 0.00 0.00 0.00 3.16
126 127 6.285224 CCCTAAAGAAAAACCGAAAAACCAT 58.715 36.000 0.00 0.00 0.00 3.55
127 128 5.395435 CCCCTAAAGAAAAACCGAAAAACCA 60.395 40.000 0.00 0.00 0.00 3.67
128 129 5.051816 CCCCTAAAGAAAAACCGAAAAACC 58.948 41.667 0.00 0.00 0.00 3.27
129 130 5.904941 TCCCCTAAAGAAAAACCGAAAAAC 58.095 37.500 0.00 0.00 0.00 2.43
130 131 6.380560 TCTTCCCCTAAAGAAAAACCGAAAAA 59.619 34.615 0.00 0.00 32.42 1.94
131 132 5.892686 TCTTCCCCTAAAGAAAAACCGAAAA 59.107 36.000 0.00 0.00 32.42 2.29
132 133 5.447757 TCTTCCCCTAAAGAAAAACCGAAA 58.552 37.500 0.00 0.00 32.42 3.46
133 134 5.051409 TCTTCCCCTAAAGAAAAACCGAA 57.949 39.130 0.00 0.00 32.42 4.30
134 135 4.710313 TCTTCCCCTAAAGAAAAACCGA 57.290 40.909 0.00 0.00 32.42 4.69
135 136 5.777850 TTTCTTCCCCTAAAGAAAAACCG 57.222 39.130 8.85 0.00 46.77 4.44
141 142 3.397955 AGTGGCTTTCTTCCCCTAAAGAA 59.602 43.478 0.00 0.00 42.12 2.52
142 143 2.986728 AGTGGCTTTCTTCCCCTAAAGA 59.013 45.455 0.00 0.00 35.19 2.52
143 144 3.244911 TGAGTGGCTTTCTTCCCCTAAAG 60.245 47.826 0.00 0.00 36.09 1.85
144 145 2.714250 TGAGTGGCTTTCTTCCCCTAAA 59.286 45.455 0.00 0.00 0.00 1.85
145 146 2.344592 TGAGTGGCTTTCTTCCCCTAA 58.655 47.619 0.00 0.00 0.00 2.69
146 147 2.038863 TGAGTGGCTTTCTTCCCCTA 57.961 50.000 0.00 0.00 0.00 3.53
147 148 1.149101 TTGAGTGGCTTTCTTCCCCT 58.851 50.000 0.00 0.00 0.00 4.79
148 149 1.248486 GTTGAGTGGCTTTCTTCCCC 58.752 55.000 0.00 0.00 0.00 4.81
149 150 0.875059 CGTTGAGTGGCTTTCTTCCC 59.125 55.000 0.00 0.00 0.00 3.97
150 151 0.875059 CCGTTGAGTGGCTTTCTTCC 59.125 55.000 0.00 0.00 0.00 3.46
151 152 1.264288 CACCGTTGAGTGGCTTTCTTC 59.736 52.381 0.00 0.00 33.95 2.87
152 153 1.134220 TCACCGTTGAGTGGCTTTCTT 60.134 47.619 0.00 0.00 38.34 2.52
153 154 0.468226 TCACCGTTGAGTGGCTTTCT 59.532 50.000 0.00 0.00 38.34 2.52
154 155 1.197721 CATCACCGTTGAGTGGCTTTC 59.802 52.381 0.00 0.00 38.34 2.62
155 156 1.238439 CATCACCGTTGAGTGGCTTT 58.762 50.000 0.00 0.00 38.34 3.51
156 157 0.108585 ACATCACCGTTGAGTGGCTT 59.891 50.000 0.00 0.00 38.34 4.35
157 158 0.973632 TACATCACCGTTGAGTGGCT 59.026 50.000 0.00 0.00 38.34 4.75
158 159 2.024176 ATACATCACCGTTGAGTGGC 57.976 50.000 0.00 0.00 38.34 5.01
159 160 4.755411 AGTTATACATCACCGTTGAGTGG 58.245 43.478 0.00 0.00 38.34 4.00
160 161 5.637810 ACAAGTTATACATCACCGTTGAGTG 59.362 40.000 0.00 0.00 39.20 3.51
161 162 5.637810 CACAAGTTATACATCACCGTTGAGT 59.362 40.000 0.00 0.00 34.35 3.41
162 163 5.063438 CCACAAGTTATACATCACCGTTGAG 59.937 44.000 0.00 0.00 34.35 3.02
163 164 4.932799 CCACAAGTTATACATCACCGTTGA 59.067 41.667 0.00 0.00 35.73 3.18
164 165 4.094294 CCCACAAGTTATACATCACCGTTG 59.906 45.833 0.00 0.00 0.00 4.10
165 166 4.258543 CCCACAAGTTATACATCACCGTT 58.741 43.478 0.00 0.00 0.00 4.44
166 167 3.869065 CCCACAAGTTATACATCACCGT 58.131 45.455 0.00 0.00 0.00 4.83
167 168 2.612212 GCCCACAAGTTATACATCACCG 59.388 50.000 0.00 0.00 0.00 4.94
168 169 3.616219 TGCCCACAAGTTATACATCACC 58.384 45.455 0.00 0.00 0.00 4.02
169 170 4.094887 CACTGCCCACAAGTTATACATCAC 59.905 45.833 0.00 0.00 0.00 3.06
170 171 4.019771 TCACTGCCCACAAGTTATACATCA 60.020 41.667 0.00 0.00 0.00 3.07
171 172 4.332819 GTCACTGCCCACAAGTTATACATC 59.667 45.833 0.00 0.00 0.00 3.06
172 173 4.261801 GTCACTGCCCACAAGTTATACAT 58.738 43.478 0.00 0.00 0.00 2.29
173 174 3.670625 GTCACTGCCCACAAGTTATACA 58.329 45.455 0.00 0.00 0.00 2.29
174 175 2.671396 CGTCACTGCCCACAAGTTATAC 59.329 50.000 0.00 0.00 0.00 1.47
175 176 2.300723 ACGTCACTGCCCACAAGTTATA 59.699 45.455 0.00 0.00 0.00 0.98
176 177 1.071699 ACGTCACTGCCCACAAGTTAT 59.928 47.619 0.00 0.00 0.00 1.89
177 178 0.466543 ACGTCACTGCCCACAAGTTA 59.533 50.000 0.00 0.00 0.00 2.24
178 179 1.095228 CACGTCACTGCCCACAAGTT 61.095 55.000 0.00 0.00 0.00 2.66
179 180 1.523711 CACGTCACTGCCCACAAGT 60.524 57.895 0.00 0.00 0.00 3.16
180 181 0.813610 TTCACGTCACTGCCCACAAG 60.814 55.000 0.00 0.00 0.00 3.16
181 182 0.813610 CTTCACGTCACTGCCCACAA 60.814 55.000 0.00 0.00 0.00 3.33
182 183 1.227527 CTTCACGTCACTGCCCACA 60.228 57.895 0.00 0.00 0.00 4.17
183 184 1.961277 CCTTCACGTCACTGCCCAC 60.961 63.158 0.00 0.00 0.00 4.61
184 185 2.377628 GACCTTCACGTCACTGCCCA 62.378 60.000 0.00 0.00 32.74 5.36
185 186 1.668151 GACCTTCACGTCACTGCCC 60.668 63.158 0.00 0.00 32.74 5.36
186 187 0.946221 CTGACCTTCACGTCACTGCC 60.946 60.000 0.00 0.00 37.85 4.85
187 188 1.560860 GCTGACCTTCACGTCACTGC 61.561 60.000 0.00 0.00 37.85 4.40
188 189 0.946221 GGCTGACCTTCACGTCACTG 60.946 60.000 0.00 0.00 37.85 3.66
189 190 1.367840 GGCTGACCTTCACGTCACT 59.632 57.895 0.00 0.00 37.85 3.41
190 191 3.952811 GGCTGACCTTCACGTCAC 58.047 61.111 0.00 0.00 37.85 3.67
200 201 4.708726 TTTTAGTAGTACGAGGCTGACC 57.291 45.455 0.00 0.00 0.00 4.02
201 202 5.888105 TCATTTTAGTAGTACGAGGCTGAC 58.112 41.667 0.00 0.00 0.00 3.51
202 203 5.450137 GCTCATTTTAGTAGTACGAGGCTGA 60.450 44.000 0.00 0.00 0.00 4.26
203 204 4.740695 GCTCATTTTAGTAGTACGAGGCTG 59.259 45.833 0.00 0.00 0.00 4.85
204 205 4.401519 TGCTCATTTTAGTAGTACGAGGCT 59.598 41.667 0.00 0.00 0.00 4.58
205 206 4.679662 TGCTCATTTTAGTAGTACGAGGC 58.320 43.478 0.00 0.00 0.00 4.70
206 207 6.132791 TCTGCTCATTTTAGTAGTACGAGG 57.867 41.667 0.00 0.00 31.77 4.63
207 208 8.462143 TTTTCTGCTCATTTTAGTAGTACGAG 57.538 34.615 0.00 0.00 31.77 4.18
208 209 8.821147 TTTTTCTGCTCATTTTAGTAGTACGA 57.179 30.769 0.00 0.00 31.77 3.43
376 382 0.179062 AGCGAGCATGGAAAGCTAGG 60.179 55.000 0.00 0.00 43.58 3.02
470 476 4.307032 TCATGGAAAAAGGAGGAAGAGG 57.693 45.455 0.00 0.00 0.00 3.69
472 478 4.325344 GGGATCATGGAAAAAGGAGGAAGA 60.325 45.833 0.00 0.00 0.00 2.87
474 480 3.624707 CGGGATCATGGAAAAAGGAGGAA 60.625 47.826 0.00 0.00 0.00 3.36
589 595 2.397413 CTGGAGTTTGGGAGGTGCGT 62.397 60.000 0.00 0.00 0.00 5.24
594 600 1.351017 TGCTAACTGGAGTTTGGGAGG 59.649 52.381 0.00 0.00 39.31 4.30
597 603 4.871933 AAAATGCTAACTGGAGTTTGGG 57.128 40.909 0.00 0.00 39.31 4.12
620 626 1.786937 AAATGTTGTTGGCCACTCCA 58.213 45.000 3.88 0.00 44.85 3.86
692 747 3.879427 TGTGTTTTCCGCTACGAAAATG 58.121 40.909 0.00 0.00 42.16 2.32
698 753 3.740044 ATGAATGTGTTTTCCGCTACG 57.260 42.857 0.00 0.00 0.00 3.51
699 754 7.472543 AGAAATATGAATGTGTTTTCCGCTAC 58.527 34.615 0.00 0.00 0.00 3.58
746 821 7.394016 GGTCTTATCCAATTGAAAATGGGTTT 58.606 34.615 7.12 0.00 37.31 3.27
756 831 4.898014 AATGGGGGTCTTATCCAATTGA 57.102 40.909 7.12 0.00 33.90 2.57
760 835 3.010808 ACGAAAATGGGGGTCTTATCCAA 59.989 43.478 0.00 0.00 33.90 3.53
763 838 6.117488 TCTTTACGAAAATGGGGGTCTTATC 58.883 40.000 0.00 0.00 0.00 1.75
765 840 5.502089 TCTTTACGAAAATGGGGGTCTTA 57.498 39.130 0.00 0.00 0.00 2.10
766 841 4.376225 TCTTTACGAAAATGGGGGTCTT 57.624 40.909 0.00 0.00 0.00 3.01
768 843 5.456548 TTTTCTTTACGAAAATGGGGGTC 57.543 39.130 0.00 0.00 44.42 4.46
812 949 2.677979 GCTTCGGCGGTCCAGAAAC 61.678 63.158 7.21 0.00 0.00 2.78
896 1033 4.733542 CGGTTGCGGGTGGGGAAT 62.734 66.667 0.00 0.00 0.00 3.01
1006 1171 3.353836 CCAGTGCAACCGGAACCG 61.354 66.667 9.46 6.25 37.80 4.44
1129 1298 1.152139 GGGGAGAGAGAGATGGGGG 60.152 68.421 0.00 0.00 0.00 5.40
1182 1360 1.729470 ATCCAACAAACCACGCGCAA 61.729 50.000 5.73 0.00 0.00 4.85
1183 1361 2.190170 ATCCAACAAACCACGCGCA 61.190 52.632 5.73 0.00 0.00 6.09
1187 1365 0.664166 GCTGCATCCAACAAACCACG 60.664 55.000 0.00 0.00 0.00 4.94
1307 1485 0.813210 GGCAGGAGATTCAGAAGGCG 60.813 60.000 0.00 0.00 0.00 5.52
1308 1486 0.813210 CGGCAGGAGATTCAGAAGGC 60.813 60.000 0.00 0.00 0.00 4.35
1309 1487 0.179062 CCGGCAGGAGATTCAGAAGG 60.179 60.000 0.00 0.00 41.02 3.46
1310 1488 0.539051 ACCGGCAGGAGATTCAGAAG 59.461 55.000 10.86 0.00 41.02 2.85
1311 1489 0.250234 CACCGGCAGGAGATTCAGAA 59.750 55.000 10.86 0.00 41.02 3.02
1312 1490 1.617018 CCACCGGCAGGAGATTCAGA 61.617 60.000 10.86 0.00 41.02 3.27
1313 1491 1.153289 CCACCGGCAGGAGATTCAG 60.153 63.158 10.86 0.00 41.02 3.02
1314 1492 2.989639 CCACCGGCAGGAGATTCA 59.010 61.111 10.86 0.00 41.02 2.57
1328 1506 0.919710 AGAAACCTGATAGGGGCCAC 59.080 55.000 4.39 0.00 40.58 5.01
1329 1507 0.918983 CAGAAACCTGATAGGGGCCA 59.081 55.000 4.39 0.00 40.58 5.36
1337 1531 1.544917 AGGCCCCCAGAAACCTGAT 60.545 57.895 0.00 0.00 33.56 2.90
1339 1533 2.036256 CAGGCCCCCAGAAACCTG 59.964 66.667 0.00 0.00 43.45 4.00
1340 1534 3.268032 CCAGGCCCCCAGAAACCT 61.268 66.667 0.00 0.00 0.00 3.50
1354 1548 2.693069 AGAATTTCACGTCAGAGCCAG 58.307 47.619 0.00 0.00 0.00 4.85
1364 1558 2.163613 GCCCAAACCCTAGAATTTCACG 59.836 50.000 0.00 0.00 0.00 4.35
1365 1559 3.193479 CAGCCCAAACCCTAGAATTTCAC 59.807 47.826 0.00 0.00 0.00 3.18
1384 1578 5.868258 GGAACTACTCTAACTTAACACCAGC 59.132 44.000 0.00 0.00 0.00 4.85
1401 1595 4.081322 TCCAACAACAGAAGGGAACTAC 57.919 45.455 0.00 0.00 42.68 2.73
1412 1606 3.040147 ACACCTCGTATCCAACAACAG 57.960 47.619 0.00 0.00 0.00 3.16
1422 1617 2.171870 CCCCCACATAAACACCTCGTAT 59.828 50.000 0.00 0.00 0.00 3.06
1449 1644 0.542702 CCACCAGGCACTCCCAATTT 60.543 55.000 0.00 0.00 34.60 1.82
1461 1826 1.606885 ATGCGCAAATTCCCACCAGG 61.607 55.000 17.11 0.00 0.00 4.45
1495 1860 2.890945 ACTACCAATCAAACAGGGCAAC 59.109 45.455 0.00 0.00 0.00 4.17
1501 1866 3.554524 CAACGCACTACCAATCAAACAG 58.445 45.455 0.00 0.00 0.00 3.16
1542 1907 5.711506 AGCCAAACATGACAATCAAGTATCA 59.288 36.000 0.00 0.00 27.21 2.15
1625 1998 1.636148 TGGGGCTACGAGTAACAACT 58.364 50.000 0.00 0.00 0.00 3.16
1659 2036 2.345760 CCCCAAGCTGCACCATCAC 61.346 63.158 1.02 0.00 0.00 3.06
1667 2044 2.270986 CCACAAGACCCCAAGCTGC 61.271 63.158 0.00 0.00 0.00 5.25
1677 2054 6.151144 AGCCTTACATTCAAATACCACAAGAC 59.849 38.462 0.00 0.00 0.00 3.01
1683 2060 9.391006 CTAAACTAGCCTTACATTCAAATACCA 57.609 33.333 0.00 0.00 0.00 3.25
1712 2089 2.735663 CCTCATTGCGTGCTCTATCATC 59.264 50.000 0.00 0.00 0.00 2.92
1716 2093 3.819564 TTACCTCATTGCGTGCTCTAT 57.180 42.857 0.00 0.00 0.00 1.98
1743 2133 1.133792 CACCTCAAAGACCCAACCAGT 60.134 52.381 0.00 0.00 0.00 4.00
1773 2164 1.302993 GCTGCCAACCCCGAAGTAA 60.303 57.895 0.00 0.00 0.00 2.24
1783 2174 2.359230 AGAGGAAGCGCTGCCAAC 60.359 61.111 35.98 27.04 0.00 3.77
1807 2198 1.998315 CCACTGCGATGACTTGAGAAG 59.002 52.381 0.00 0.00 0.00 2.85
1813 2204 5.957842 TTTATTTTCCACTGCGATGACTT 57.042 34.783 0.00 0.00 0.00 3.01
1942 2335 0.995675 ATTCTGGGGCCAGCCTACAT 60.996 55.000 4.39 0.00 43.31 2.29
2082 2476 4.385825 GAATGCACGGGAAGGATAATACA 58.614 43.478 0.00 0.00 0.00 2.29
2103 2497 7.710475 TGCTAATGTTATTCATGAAGTGATCGA 59.290 33.333 14.54 0.00 36.54 3.59
2171 2565 4.081406 AGAGTATTGCTCAAACAATGCCA 58.919 39.130 4.53 0.00 46.47 4.92
2220 2614 5.179703 CGGGAAAACGAAGGCAAAATTGC 62.180 47.826 9.61 9.61 44.33 3.56
2234 2628 2.485426 GGTAGTAAGGCAACGGGAAAAC 59.515 50.000 0.00 0.00 46.39 2.43
2250 2644 3.688694 TCAATAGCGGTTGTTGGTAGT 57.311 42.857 11.03 0.00 0.00 2.73
2255 2649 5.294306 AGTGTGATATCAATAGCGGTTGTTG 59.706 40.000 7.07 0.00 0.00 3.33
2262 2656 4.149571 GTGAGCAGTGTGATATCAATAGCG 59.850 45.833 7.07 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.