Multiple sequence alignment - TraesCS2B01G016400

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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 TraesCS2B01G016400 chr2B 100.000 2441 0 0 1 2441 7688244 7690684 0.000000e+00 4508.0
1 TraesCS2B01G016400 chr2B 74.721 269 53 13 2017 2275 767669336 767669073 3.320000e-19 106.0
2 TraesCS2B01G016400 chr2A 90.941 2285 164 21 175 2441 2712990 2715249 0.000000e+00 3033.0
3 TraesCS2B01G016400 chr2A 87.925 265 32 0 2011 2275 499490718 499490982 1.820000e-81 313.0
4 TraesCS2B01G016400 chr2D 90.680 1749 144 8 278 2018 2961656 2959919 0.000000e+00 2309.0
5 TraesCS2B01G016400 chr2D 92.982 171 5 1 2278 2441 2959930 2959760 2.420000e-60 243.0
6 TraesCS2B01G016400 chr2D 92.523 107 8 0 178 284 2998788 2998682 1.170000e-33 154.0
7 TraesCS2B01G016400 chr1D 83.650 263 35 6 2017 2279 484472712 484472458 8.720000e-60 241.0
8 TraesCS2B01G016400 chr1D 75.094 265 49 13 2017 2274 133989728 133989474 9.230000e-20 108.0
9 TraesCS2B01G016400 chr6B 75.758 264 54 9 2017 2274 459272268 459272009 9.160000e-25 124.0
10 TraesCS2B01G016400 chr5D 75.285 263 52 8 2017 2272 41838422 41838166 1.980000e-21 113.0
11 TraesCS2B01G016400 chr7B 75.090 277 45 18 2011 2277 720493101 720493363 9.230000e-20 108.0
12 TraesCS2B01G016400 chr3B 82.524 103 13 4 2177 2276 817346101 817346201 4.320000e-13 86.1


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 TraesCS2B01G016400 chr2B 7688244 7690684 2440 False 4508 4508 100.000 1 2441 1 chr2B.!!$F1 2440
1 TraesCS2B01G016400 chr2A 2712990 2715249 2259 False 3033 3033 90.941 175 2441 1 chr2A.!!$F1 2266
2 TraesCS2B01G016400 chr2D 2959760 2961656 1896 True 1276 2309 91.831 278 2441 2 chr2D.!!$R2 2163

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
130 131 0.033504 GGTCTCTTGTGGCTTCGACA 59.966 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2059 0.251608 AAACCACGCCCTAAGCCATT 60.252 50.0 0.0 0.0 38.78 3.16 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
25 26 2.587753 ACAGTGTGTGTTCGCCGG 60.588 61.111 0.00 0.00 34.94 6.13
26 27 2.279851 CAGTGTGTGTTCGCCGGA 60.280 61.111 5.05 0.00 0.00 5.14
27 28 2.279918 AGTGTGTGTTCGCCGGAC 60.280 61.111 5.05 0.00 0.00 4.79
28 29 2.586635 GTGTGTGTTCGCCGGACA 60.587 61.111 5.05 0.00 0.00 4.02
29 30 1.959226 GTGTGTGTTCGCCGGACAT 60.959 57.895 5.05 0.00 0.00 3.06
30 31 1.666553 TGTGTGTTCGCCGGACATC 60.667 57.895 5.05 0.00 0.00 3.06
31 32 2.431771 TGTGTTCGCCGGACATCG 60.432 61.111 5.05 0.00 38.88 3.84
40 41 3.617824 CGGACATCGGCGAGATTG 58.382 61.111 17.22 11.79 37.52 2.67
41 42 1.951130 CGGACATCGGCGAGATTGG 60.951 63.158 17.22 4.78 37.52 3.16
42 43 1.144057 GGACATCGGCGAGATTGGT 59.856 57.895 17.22 8.16 37.52 3.67
43 44 0.462047 GGACATCGGCGAGATTGGTT 60.462 55.000 17.22 0.00 37.52 3.67
44 45 0.652592 GACATCGGCGAGATTGGTTG 59.347 55.000 17.22 9.39 37.52 3.77
45 46 0.744414 ACATCGGCGAGATTGGTTGG 60.744 55.000 17.22 0.00 37.52 3.77
46 47 0.461870 CATCGGCGAGATTGGTTGGA 60.462 55.000 17.22 0.00 37.52 3.53
47 48 0.462047 ATCGGCGAGATTGGTTGGAC 60.462 55.000 17.22 0.00 35.73 4.02
48 49 1.375396 CGGCGAGATTGGTTGGACA 60.375 57.895 0.00 0.00 0.00 4.02
49 50 0.744414 CGGCGAGATTGGTTGGACAT 60.744 55.000 0.00 0.00 0.00 3.06
50 51 1.017387 GGCGAGATTGGTTGGACATC 58.983 55.000 0.00 0.00 0.00 3.06
51 52 1.407437 GGCGAGATTGGTTGGACATCT 60.407 52.381 0.00 0.00 0.00 2.90
52 53 2.158957 GGCGAGATTGGTTGGACATCTA 60.159 50.000 0.00 0.00 0.00 1.98
53 54 3.126831 GCGAGATTGGTTGGACATCTAG 58.873 50.000 0.00 0.00 0.00 2.43
54 55 3.181475 GCGAGATTGGTTGGACATCTAGA 60.181 47.826 0.00 0.00 0.00 2.43
55 56 4.502259 GCGAGATTGGTTGGACATCTAGAT 60.502 45.833 0.00 0.00 0.00 1.98
56 57 5.226396 CGAGATTGGTTGGACATCTAGATC 58.774 45.833 1.03 0.00 0.00 2.75
57 58 5.010516 CGAGATTGGTTGGACATCTAGATCT 59.989 44.000 1.03 0.00 0.00 2.75
58 59 6.462207 CGAGATTGGTTGGACATCTAGATCTT 60.462 42.308 1.03 0.00 0.00 2.40
59 60 6.825610 AGATTGGTTGGACATCTAGATCTTC 58.174 40.000 1.03 2.33 0.00 2.87
60 61 6.385176 AGATTGGTTGGACATCTAGATCTTCA 59.615 38.462 1.03 0.00 0.00 3.02
61 62 6.373005 TTGGTTGGACATCTAGATCTTCAA 57.627 37.500 1.03 0.00 0.00 2.69
62 63 6.566079 TGGTTGGACATCTAGATCTTCAAT 57.434 37.500 1.03 0.00 0.00 2.57
63 64 7.675161 TGGTTGGACATCTAGATCTTCAATA 57.325 36.000 1.03 0.00 0.00 1.90
64 65 8.267620 TGGTTGGACATCTAGATCTTCAATAT 57.732 34.615 1.03 0.00 0.00 1.28
65 66 8.717717 TGGTTGGACATCTAGATCTTCAATATT 58.282 33.333 1.03 0.00 0.00 1.28
66 67 9.213799 GGTTGGACATCTAGATCTTCAATATTC 57.786 37.037 1.03 0.00 0.00 1.75
67 68 9.770097 GTTGGACATCTAGATCTTCAATATTCA 57.230 33.333 1.03 0.00 0.00 2.57
75 76 9.481340 TCTAGATCTTCAATATTCATTGGTTCG 57.519 33.333 0.00 0.00 41.66 3.95
76 77 7.502120 AGATCTTCAATATTCATTGGTTCGG 57.498 36.000 0.00 0.00 41.66 4.30
77 78 5.499139 TCTTCAATATTCATTGGTTCGGC 57.501 39.130 0.00 0.00 41.66 5.54
78 79 4.338118 TCTTCAATATTCATTGGTTCGGCC 59.662 41.667 0.00 0.00 41.66 6.13
79 80 2.955660 TCAATATTCATTGGTTCGGCCC 59.044 45.455 0.00 0.00 41.66 5.80
80 81 2.958355 CAATATTCATTGGTTCGGCCCT 59.042 45.455 0.00 0.00 38.31 5.19
81 82 2.818751 TATTCATTGGTTCGGCCCTT 57.181 45.000 0.00 0.00 36.04 3.95
82 83 1.937191 ATTCATTGGTTCGGCCCTTT 58.063 45.000 0.00 0.00 36.04 3.11
83 84 1.253100 TTCATTGGTTCGGCCCTTTC 58.747 50.000 0.00 0.00 36.04 2.62
84 85 0.958382 TCATTGGTTCGGCCCTTTCG 60.958 55.000 0.00 0.00 36.04 3.46
85 86 1.677633 ATTGGTTCGGCCCTTTCGG 60.678 57.895 0.00 0.00 36.04 4.30
86 87 2.420466 ATTGGTTCGGCCCTTTCGGT 62.420 55.000 0.00 0.00 36.04 4.69
87 88 1.766625 TTGGTTCGGCCCTTTCGGTA 61.767 55.000 0.00 0.00 36.04 4.02
88 89 1.449070 GGTTCGGCCCTTTCGGTAG 60.449 63.158 0.00 0.00 0.00 3.18
89 90 1.294459 GTTCGGCCCTTTCGGTAGT 59.706 57.895 0.00 0.00 0.00 2.73
90 91 1.017701 GTTCGGCCCTTTCGGTAGTG 61.018 60.000 0.00 0.00 0.00 2.74
91 92 2.125269 CGGCCCTTTCGGTAGTGG 60.125 66.667 0.00 0.00 0.00 4.00
92 93 2.652095 CGGCCCTTTCGGTAGTGGA 61.652 63.158 0.00 0.00 0.00 4.02
93 94 1.681076 GGCCCTTTCGGTAGTGGAA 59.319 57.895 0.00 0.00 0.00 3.53
94 95 0.037160 GGCCCTTTCGGTAGTGGAAA 59.963 55.000 0.00 0.00 32.81 3.13
95 96 1.162698 GCCCTTTCGGTAGTGGAAAC 58.837 55.000 0.00 0.00 30.73 2.78
96 97 1.435577 CCCTTTCGGTAGTGGAAACG 58.564 55.000 0.00 0.00 30.73 3.60
97 98 1.435577 CCTTTCGGTAGTGGAAACGG 58.564 55.000 0.00 0.00 30.73 4.44
98 99 1.270465 CCTTTCGGTAGTGGAAACGGT 60.270 52.381 0.00 0.00 30.73 4.83
99 100 1.796459 CTTTCGGTAGTGGAAACGGTG 59.204 52.381 0.00 0.00 30.73 4.94
100 101 0.033781 TTCGGTAGTGGAAACGGTGG 59.966 55.000 0.00 0.00 0.00 4.61
101 102 1.114722 TCGGTAGTGGAAACGGTGGT 61.115 55.000 0.00 0.00 0.00 4.16
102 103 0.947180 CGGTAGTGGAAACGGTGGTG 60.947 60.000 0.00 0.00 0.00 4.17
103 104 1.232621 GGTAGTGGAAACGGTGGTGC 61.233 60.000 0.00 0.00 0.00 5.01
104 105 0.250166 GTAGTGGAAACGGTGGTGCT 60.250 55.000 0.00 0.00 0.00 4.40
105 106 0.034337 TAGTGGAAACGGTGGTGCTC 59.966 55.000 0.00 0.00 0.00 4.26
106 107 1.525077 GTGGAAACGGTGGTGCTCA 60.525 57.895 0.00 0.00 0.00 4.26
107 108 1.098712 GTGGAAACGGTGGTGCTCAA 61.099 55.000 0.00 0.00 0.00 3.02
108 109 0.179004 TGGAAACGGTGGTGCTCAAT 60.179 50.000 0.00 0.00 0.00 2.57
109 110 1.072489 TGGAAACGGTGGTGCTCAATA 59.928 47.619 0.00 0.00 0.00 1.90
110 111 2.156098 GGAAACGGTGGTGCTCAATAA 58.844 47.619 0.00 0.00 0.00 1.40
111 112 2.161609 GGAAACGGTGGTGCTCAATAAG 59.838 50.000 0.00 0.00 0.00 1.73
112 113 1.821216 AACGGTGGTGCTCAATAAGG 58.179 50.000 0.00 0.00 0.00 2.69
113 114 0.690762 ACGGTGGTGCTCAATAAGGT 59.309 50.000 0.00 0.00 0.00 3.50
114 115 1.338769 ACGGTGGTGCTCAATAAGGTC 60.339 52.381 0.00 0.00 0.00 3.85
115 116 1.066143 CGGTGGTGCTCAATAAGGTCT 60.066 52.381 0.00 0.00 0.00 3.85
116 117 2.633488 GGTGGTGCTCAATAAGGTCTC 58.367 52.381 0.00 0.00 0.00 3.36
117 118 2.237392 GGTGGTGCTCAATAAGGTCTCT 59.763 50.000 0.00 0.00 0.00 3.10
118 119 3.307762 GGTGGTGCTCAATAAGGTCTCTT 60.308 47.826 0.00 0.00 37.03 2.85
119 120 3.686726 GTGGTGCTCAATAAGGTCTCTTG 59.313 47.826 0.00 0.00 34.59 3.02
120 121 3.327757 TGGTGCTCAATAAGGTCTCTTGT 59.672 43.478 0.00 0.00 34.59 3.16
121 122 3.686726 GGTGCTCAATAAGGTCTCTTGTG 59.313 47.826 0.00 0.00 34.59 3.33
122 123 3.686726 GTGCTCAATAAGGTCTCTTGTGG 59.313 47.826 0.00 0.00 34.59 4.17
123 124 2.680339 GCTCAATAAGGTCTCTTGTGGC 59.320 50.000 0.00 0.00 34.59 5.01
124 125 3.620966 GCTCAATAAGGTCTCTTGTGGCT 60.621 47.826 0.00 0.00 34.59 4.75
125 126 4.583871 CTCAATAAGGTCTCTTGTGGCTT 58.416 43.478 0.00 0.00 34.59 4.35
126 127 4.579869 TCAATAAGGTCTCTTGTGGCTTC 58.420 43.478 0.00 0.00 34.59 3.86
127 128 2.743636 TAAGGTCTCTTGTGGCTTCG 57.256 50.000 0.00 0.00 34.59 3.79
128 129 1.048601 AAGGTCTCTTGTGGCTTCGA 58.951 50.000 0.00 0.00 0.00 3.71
129 130 0.318762 AGGTCTCTTGTGGCTTCGAC 59.681 55.000 0.00 0.00 0.00 4.20
130 131 0.033504 GGTCTCTTGTGGCTTCGACA 59.966 55.000 0.00 0.00 0.00 4.35
131 132 1.423395 GTCTCTTGTGGCTTCGACAG 58.577 55.000 0.00 0.00 0.00 3.51
132 133 1.040646 TCTCTTGTGGCTTCGACAGT 58.959 50.000 0.00 0.00 0.00 3.55
133 134 1.143305 CTCTTGTGGCTTCGACAGTG 58.857 55.000 0.00 0.00 0.00 3.66
134 135 0.750249 TCTTGTGGCTTCGACAGTGA 59.250 50.000 0.00 0.00 0.00 3.41
135 136 1.143305 CTTGTGGCTTCGACAGTGAG 58.857 55.000 0.00 0.00 0.00 3.51
136 137 0.464036 TTGTGGCTTCGACAGTGAGT 59.536 50.000 0.00 0.00 0.00 3.41
137 138 0.249447 TGTGGCTTCGACAGTGAGTG 60.249 55.000 0.00 0.00 0.00 3.51
138 139 0.249489 GTGGCTTCGACAGTGAGTGT 60.249 55.000 0.00 0.00 44.49 3.55
139 140 0.249447 TGGCTTCGACAGTGAGTGTG 60.249 55.000 0.00 0.00 40.56 3.82
140 141 0.249489 GGCTTCGACAGTGAGTGTGT 60.249 55.000 0.00 0.00 40.56 3.72
141 142 1.132588 GCTTCGACAGTGAGTGTGTC 58.867 55.000 0.00 0.00 40.56 3.67
142 143 1.536072 GCTTCGACAGTGAGTGTGTCA 60.536 52.381 0.00 0.00 43.90 3.58
143 144 2.864097 GCTTCGACAGTGAGTGTGTCAT 60.864 50.000 0.00 0.00 43.90 3.06
144 145 3.384668 CTTCGACAGTGAGTGTGTCATT 58.615 45.455 0.00 0.00 43.90 2.57
145 146 2.742774 TCGACAGTGAGTGTGTCATTG 58.257 47.619 0.00 0.00 46.03 2.82
146 147 1.794701 CGACAGTGAGTGTGTCATTGG 59.205 52.381 0.00 0.00 45.11 3.16
147 148 2.545742 CGACAGTGAGTGTGTCATTGGA 60.546 50.000 0.00 0.00 45.11 3.53
148 149 3.668447 GACAGTGAGTGTGTCATTGGAT 58.332 45.455 0.00 0.00 45.11 3.41
149 150 3.668447 ACAGTGAGTGTGTCATTGGATC 58.332 45.455 0.00 0.00 45.11 3.36
150 151 3.326006 ACAGTGAGTGTGTCATTGGATCT 59.674 43.478 0.00 0.00 45.11 2.75
151 152 4.528206 ACAGTGAGTGTGTCATTGGATCTA 59.472 41.667 0.00 0.00 45.11 1.98
152 153 5.107824 CAGTGAGTGTGTCATTGGATCTAG 58.892 45.833 0.00 0.00 38.85 2.43
153 154 3.868077 GTGAGTGTGTCATTGGATCTAGC 59.132 47.826 0.00 0.00 37.56 3.42
154 155 3.119291 GAGTGTGTCATTGGATCTAGCG 58.881 50.000 0.00 0.00 0.00 4.26
155 156 2.760650 AGTGTGTCATTGGATCTAGCGA 59.239 45.455 0.00 0.00 0.00 4.93
156 157 3.386078 AGTGTGTCATTGGATCTAGCGAT 59.614 43.478 0.00 0.00 0.00 4.58
157 158 3.492383 GTGTGTCATTGGATCTAGCGATG 59.508 47.826 0.00 0.00 0.00 3.84
158 159 3.384467 TGTGTCATTGGATCTAGCGATGA 59.616 43.478 0.00 0.00 0.00 2.92
159 160 3.986572 GTGTCATTGGATCTAGCGATGAG 59.013 47.826 0.00 0.00 0.00 2.90
160 161 3.891366 TGTCATTGGATCTAGCGATGAGA 59.109 43.478 0.00 0.00 0.00 3.27
161 162 4.233789 GTCATTGGATCTAGCGATGAGAC 58.766 47.826 0.00 0.00 0.00 3.36
162 163 4.022416 GTCATTGGATCTAGCGATGAGACT 60.022 45.833 0.00 0.00 0.00 3.24
163 164 3.998099 TTGGATCTAGCGATGAGACTG 57.002 47.619 0.00 0.00 0.00 3.51
164 165 2.234143 TGGATCTAGCGATGAGACTGG 58.766 52.381 0.00 0.00 0.00 4.00
165 166 2.235016 GGATCTAGCGATGAGACTGGT 58.765 52.381 0.00 0.00 0.00 4.00
166 167 2.030363 GGATCTAGCGATGAGACTGGTG 60.030 54.545 0.00 0.00 0.00 4.17
167 168 1.393603 TCTAGCGATGAGACTGGTGG 58.606 55.000 0.00 0.00 0.00 4.61
168 169 1.064685 TCTAGCGATGAGACTGGTGGA 60.065 52.381 0.00 0.00 0.00 4.02
169 170 1.066303 CTAGCGATGAGACTGGTGGAC 59.934 57.143 0.00 0.00 0.00 4.02
170 171 1.517257 GCGATGAGACTGGTGGACG 60.517 63.158 0.00 0.00 0.00 4.79
171 172 1.139734 CGATGAGACTGGTGGACGG 59.860 63.158 0.00 0.00 0.00 4.79
172 173 1.595993 CGATGAGACTGGTGGACGGT 61.596 60.000 0.00 0.00 42.79 4.83
173 174 0.608640 GATGAGACTGGTGGACGGTT 59.391 55.000 0.00 0.00 39.29 4.44
174 175 1.002087 GATGAGACTGGTGGACGGTTT 59.998 52.381 0.00 0.00 39.29 3.27
175 176 0.105964 TGAGACTGGTGGACGGTTTG 59.894 55.000 0.00 0.00 39.29 2.93
176 177 1.227853 AGACTGGTGGACGGTTTGC 60.228 57.895 0.00 0.00 39.29 3.68
177 178 2.203294 ACTGGTGGACGGTTTGCC 60.203 61.111 0.00 0.00 34.09 4.52
178 179 2.113139 CTGGTGGACGGTTTGCCT 59.887 61.111 0.00 0.00 0.00 4.75
179 180 1.528309 CTGGTGGACGGTTTGCCTT 60.528 57.895 0.00 0.00 0.00 4.35
180 181 1.515521 CTGGTGGACGGTTTGCCTTC 61.516 60.000 0.00 0.00 32.75 3.46
181 182 2.613506 GGTGGACGGTTTGCCTTCG 61.614 63.158 0.00 0.00 34.18 3.79
191 192 3.818121 TTGCCTTCGACGGTGGGTG 62.818 63.158 9.98 0.00 0.00 4.61
192 193 4.309950 GCCTTCGACGGTGGGTGT 62.310 66.667 9.98 0.00 0.00 4.16
196 197 2.358193 CTTCGACGGTGGGTGTGTCA 62.358 60.000 0.00 0.00 32.91 3.58
199 200 1.565156 CGACGGTGGGTGTGTCATTG 61.565 60.000 0.00 0.00 32.91 2.82
225 226 2.494918 GATGAGACCGGGTGGACG 59.505 66.667 3.30 0.00 39.21 4.79
243 247 1.133915 ACGGTTTGCCTTTTCCTCTGA 60.134 47.619 0.00 0.00 0.00 3.27
246 250 2.959030 GGTTTGCCTTTTCCTCTGAAGT 59.041 45.455 0.00 0.00 0.00 3.01
250 254 2.003301 GCCTTTTCCTCTGAAGTAGCG 58.997 52.381 0.00 0.00 0.00 4.26
258 262 0.331954 TCTGAAGTAGCGAGGGGAGT 59.668 55.000 0.00 0.00 0.00 3.85
273 277 2.027469 GGGGAGTTGGTTATGTCTTCGT 60.027 50.000 0.00 0.00 0.00 3.85
280 284 1.066430 GGTTATGTCTTCGTGAGGCCA 60.066 52.381 5.01 0.00 0.00 5.36
311 315 4.156922 TCCAACAATAATGTCGCCGATTTT 59.843 37.500 0.00 0.00 39.40 1.82
329 333 4.735662 TTTTGTTATTCCGTCGACTTGG 57.264 40.909 14.70 8.62 0.00 3.61
338 342 0.387622 CGTCGACTTGGGCGAAAGTA 60.388 55.000 14.70 0.00 40.48 2.24
356 360 3.223435 AGTATAGGTGTGATCGACCCAG 58.777 50.000 9.58 0.00 33.51 4.45
373 377 2.568956 CCCAGTGTCATCTTCTTCTCCA 59.431 50.000 0.00 0.00 0.00 3.86
376 380 3.513119 CAGTGTCATCTTCTTCTCCAGGA 59.487 47.826 0.00 0.00 0.00 3.86
396 400 3.434739 GGACATGGATCCTTCAAGCTCAT 60.435 47.826 14.23 0.00 35.68 2.90
398 402 2.609427 TGGATCCTTCAAGCTCATCG 57.391 50.000 14.23 0.00 0.00 3.84
400 404 2.237143 TGGATCCTTCAAGCTCATCGTT 59.763 45.455 14.23 0.00 0.00 3.85
416 420 2.646930 TCGTTGCCGATACTTCTAGGA 58.353 47.619 0.00 0.00 38.40 2.94
418 422 3.444742 TCGTTGCCGATACTTCTAGGAAA 59.555 43.478 0.00 0.00 38.40 3.13
461 465 5.130311 TGCCTATGTGGATGCTACTTTCTTA 59.870 40.000 0.00 0.00 38.35 2.10
465 469 6.851222 ATGTGGATGCTACTTTCTTATTCG 57.149 37.500 0.00 0.00 0.00 3.34
469 473 2.914059 TGCTACTTTCTTATTCGGGCC 58.086 47.619 0.00 0.00 0.00 5.80
478 482 1.944024 CTTATTCGGGCCATTACGCAA 59.056 47.619 4.39 0.00 0.00 4.85
505 509 0.615331 AATATCGGCTGGCCATCGAT 59.385 50.000 32.29 32.29 44.39 3.59
508 512 1.485124 ATCGGCTGGCCATCGATATA 58.515 50.000 30.40 13.71 41.12 0.86
553 557 1.134818 TGACTTCCCGATGAATGGACG 60.135 52.381 0.00 0.00 31.06 4.79
714 723 8.760103 TCCAATCATATGTTGTCACAATTTTG 57.240 30.769 1.90 0.00 36.16 2.44
744 753 6.945218 AGCCAAGATAATAACCAAAATTGCA 58.055 32.000 0.00 0.00 0.00 4.08
899 909 5.867716 GTGTATATATAAACACCAGCCCTCG 59.132 44.000 8.02 0.00 40.07 4.63
923 933 5.283247 GTCTAAACGTACATTCAGTGAGACG 59.717 44.000 13.90 13.90 42.36 4.18
1053 1067 2.345244 CTCAGGGCGAACACTGCT 59.655 61.111 0.00 0.00 34.76 4.24
1150 1167 3.636313 TCCGTGATGGAACGCGTCC 62.636 63.158 14.44 16.38 46.38 4.79
1477 1497 2.012673 GTGCCACTAGCTGGAATCTTG 58.987 52.381 3.17 0.00 43.95 3.02
1524 1544 3.057596 AGTTGGTGTGTGTTTGACTGTTG 60.058 43.478 0.00 0.00 0.00 3.33
1539 1559 3.674997 ACTGTTGGTACATGTGGATGTC 58.325 45.455 9.11 0.00 42.14 3.06
1551 1571 1.349688 GTGGATGTCTGTTGGGTGGTA 59.650 52.381 0.00 0.00 0.00 3.25
1558 1578 0.951558 CTGTTGGGTGGTAGTTGCAC 59.048 55.000 0.00 0.00 0.00 4.57
1578 1598 2.259618 CGCATGTGTAGTGTGGTAGAC 58.740 52.381 0.00 0.00 0.00 2.59
1606 1626 5.344128 GGCGTACGTGTTGGATGTATATAAG 59.656 44.000 17.90 0.00 0.00 1.73
1609 1629 6.087687 CGTACGTGTTGGATGTATATAAGCAG 59.912 42.308 7.22 0.00 0.00 4.24
1628 1648 5.343249 AGCAGAGTTTTGTGCAAGTTTAAG 58.657 37.500 0.00 0.00 45.49 1.85
1653 1673 2.358898 CCCAACTTGTCAAGTGGAGTTG 59.641 50.000 24.35 16.75 45.21 3.16
1871 1891 4.526970 ACCACAAGATGTGTCTTCAAGTT 58.473 39.130 9.42 0.00 46.45 2.66
1927 1947 0.394352 GGCGAGATCCATGGTGGTTT 60.394 55.000 12.58 0.00 39.03 3.27
1947 1967 1.603739 GGTCAGGGTTCACAAGGCC 60.604 63.158 0.00 0.00 0.00 5.19
2039 2059 3.138798 GCTAGGGAGCCGACGACA 61.139 66.667 0.00 0.00 43.49 4.35
2041 2061 2.017559 GCTAGGGAGCCGACGACAAT 62.018 60.000 0.00 0.00 43.49 2.71
2082 2102 3.698765 TCTCATGGCGAGACTGCA 58.301 55.556 0.00 0.00 46.18 4.41
2100 2120 0.741221 CACGCTCTGTAGGGGCTTTC 60.741 60.000 0.00 0.00 39.91 2.62
2125 2145 3.064987 TAAGACTGCTCGCGGCCTC 62.065 63.158 6.13 6.29 40.92 4.70
2161 2181 5.260027 ACTTACGACGTTTTCATGCTTAC 57.740 39.130 5.50 0.00 0.00 2.34
2185 2205 1.976474 TCGGGATGGCTTTTGGTGC 60.976 57.895 0.00 0.00 0.00 5.01
2211 2231 9.577110 CTGTAATCTAACTTATGTTTCGGTACA 57.423 33.333 0.00 4.26 37.59 2.90
2216 2236 3.332034 ACTTATGTTTCGGTACACTGCC 58.668 45.455 0.00 0.00 0.00 4.85
2241 2261 8.311109 CCTGTTGTGGGCTTTATTAAGTTAAAT 58.689 33.333 0.00 0.00 33.74 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.668419 GAACACACACTGTTGAGGCT 58.332 50.000 0.00 0.00 43.60 4.58
4 5 0.304705 GGCGAACACACACTGTTGAG 59.695 55.000 0.00 0.00 43.60 3.02
8 9 2.587753 CCGGCGAACACACACTGT 60.588 61.111 9.30 0.00 32.89 3.55
9 10 2.279851 TCCGGCGAACACACACTG 60.280 61.111 9.30 0.00 0.00 3.66
10 11 2.279918 GTCCGGCGAACACACACT 60.280 61.111 9.30 0.00 0.00 3.55
11 12 1.897398 GATGTCCGGCGAACACACAC 61.897 60.000 9.30 3.03 0.00 3.82
12 13 1.666553 GATGTCCGGCGAACACACA 60.667 57.895 9.30 3.13 0.00 3.72
13 14 2.726691 CGATGTCCGGCGAACACAC 61.727 63.158 9.30 1.23 33.91 3.82
14 15 2.431771 CGATGTCCGGCGAACACA 60.432 61.111 9.30 8.73 33.91 3.72
23 24 1.951130 CCAATCTCGCCGATGTCCG 60.951 63.158 0.00 0.00 38.18 4.79
24 25 0.462047 AACCAATCTCGCCGATGTCC 60.462 55.000 0.00 0.00 31.20 4.02
25 26 0.652592 CAACCAATCTCGCCGATGTC 59.347 55.000 0.00 0.00 31.20 3.06
26 27 0.744414 CCAACCAATCTCGCCGATGT 60.744 55.000 0.00 0.00 31.20 3.06
27 28 0.461870 TCCAACCAATCTCGCCGATG 60.462 55.000 0.00 0.00 31.20 3.84
28 29 0.462047 GTCCAACCAATCTCGCCGAT 60.462 55.000 0.00 0.00 0.00 4.18
29 30 1.079405 GTCCAACCAATCTCGCCGA 60.079 57.895 0.00 0.00 0.00 5.54
30 31 0.744414 ATGTCCAACCAATCTCGCCG 60.744 55.000 0.00 0.00 0.00 6.46
31 32 1.017387 GATGTCCAACCAATCTCGCC 58.983 55.000 0.00 0.00 0.00 5.54
32 33 2.029838 AGATGTCCAACCAATCTCGC 57.970 50.000 0.00 0.00 0.00 5.03
33 34 4.655762 TCTAGATGTCCAACCAATCTCG 57.344 45.455 0.00 0.00 0.00 4.04
34 35 6.418057 AGATCTAGATGTCCAACCAATCTC 57.582 41.667 10.74 0.00 0.00 2.75
35 36 6.385176 TGAAGATCTAGATGTCCAACCAATCT 59.615 38.462 10.74 0.00 0.00 2.40
36 37 6.586344 TGAAGATCTAGATGTCCAACCAATC 58.414 40.000 10.74 0.00 0.00 2.67
37 38 6.566079 TGAAGATCTAGATGTCCAACCAAT 57.434 37.500 10.74 0.00 0.00 3.16
38 39 6.373005 TTGAAGATCTAGATGTCCAACCAA 57.627 37.500 10.74 4.18 0.00 3.67
39 40 6.566079 ATTGAAGATCTAGATGTCCAACCA 57.434 37.500 10.74 0.00 0.00 3.67
40 41 9.213799 GAATATTGAAGATCTAGATGTCCAACC 57.786 37.037 10.74 0.00 0.00 3.77
41 42 9.770097 TGAATATTGAAGATCTAGATGTCCAAC 57.230 33.333 10.74 0.00 0.00 3.77
49 50 9.481340 CGAACCAATGAATATTGAAGATCTAGA 57.519 33.333 0.00 0.00 45.21 2.43
50 51 8.715998 CCGAACCAATGAATATTGAAGATCTAG 58.284 37.037 0.00 0.00 45.21 2.43
51 52 7.173218 GCCGAACCAATGAATATTGAAGATCTA 59.827 37.037 0.00 0.00 45.21 1.98
52 53 6.016777 GCCGAACCAATGAATATTGAAGATCT 60.017 38.462 0.00 0.00 45.21 2.75
53 54 6.145535 GCCGAACCAATGAATATTGAAGATC 58.854 40.000 0.00 0.00 45.21 2.75
54 55 5.010012 GGCCGAACCAATGAATATTGAAGAT 59.990 40.000 0.00 0.00 45.21 2.40
55 56 4.338118 GGCCGAACCAATGAATATTGAAGA 59.662 41.667 0.00 0.00 45.21 2.87
56 57 4.499696 GGGCCGAACCAATGAATATTGAAG 60.500 45.833 0.00 0.00 45.21 3.02
57 58 3.383185 GGGCCGAACCAATGAATATTGAA 59.617 43.478 0.00 0.00 45.21 2.69
58 59 2.955660 GGGCCGAACCAATGAATATTGA 59.044 45.455 0.00 0.00 45.21 2.57
59 60 2.958355 AGGGCCGAACCAATGAATATTG 59.042 45.455 0.00 0.00 42.66 1.90
60 61 3.312736 AGGGCCGAACCAATGAATATT 57.687 42.857 0.00 0.00 42.05 1.28
61 62 3.312736 AAGGGCCGAACCAATGAATAT 57.687 42.857 0.00 0.00 42.05 1.28
62 63 2.818751 AAGGGCCGAACCAATGAATA 57.181 45.000 0.00 0.00 42.05 1.75
63 64 1.824852 GAAAGGGCCGAACCAATGAAT 59.175 47.619 0.00 0.00 42.05 2.57
64 65 1.253100 GAAAGGGCCGAACCAATGAA 58.747 50.000 0.00 0.00 42.05 2.57
65 66 0.958382 CGAAAGGGCCGAACCAATGA 60.958 55.000 0.00 0.00 42.05 2.57
66 67 1.506262 CGAAAGGGCCGAACCAATG 59.494 57.895 0.00 0.00 42.05 2.82
67 68 3.996614 CGAAAGGGCCGAACCAAT 58.003 55.556 0.00 0.00 42.05 3.16
79 80 1.796459 CACCGTTTCCACTACCGAAAG 59.204 52.381 0.00 0.00 30.11 2.62
80 81 1.540797 CCACCGTTTCCACTACCGAAA 60.541 52.381 0.00 0.00 0.00 3.46
81 82 0.033781 CCACCGTTTCCACTACCGAA 59.966 55.000 0.00 0.00 0.00 4.30
82 83 1.114722 ACCACCGTTTCCACTACCGA 61.115 55.000 0.00 0.00 0.00 4.69
83 84 0.947180 CACCACCGTTTCCACTACCG 60.947 60.000 0.00 0.00 0.00 4.02
84 85 1.232621 GCACCACCGTTTCCACTACC 61.233 60.000 0.00 0.00 0.00 3.18
85 86 0.250166 AGCACCACCGTTTCCACTAC 60.250 55.000 0.00 0.00 0.00 2.73
86 87 0.034337 GAGCACCACCGTTTCCACTA 59.966 55.000 0.00 0.00 0.00 2.74
87 88 1.227853 GAGCACCACCGTTTCCACT 60.228 57.895 0.00 0.00 0.00 4.00
88 89 1.098712 TTGAGCACCACCGTTTCCAC 61.099 55.000 0.00 0.00 0.00 4.02
89 90 0.179004 ATTGAGCACCACCGTTTCCA 60.179 50.000 0.00 0.00 0.00 3.53
90 91 1.816074 TATTGAGCACCACCGTTTCC 58.184 50.000 0.00 0.00 0.00 3.13
91 92 2.161609 CCTTATTGAGCACCACCGTTTC 59.838 50.000 0.00 0.00 0.00 2.78
92 93 2.159382 CCTTATTGAGCACCACCGTTT 58.841 47.619 0.00 0.00 0.00 3.60
93 94 1.073284 ACCTTATTGAGCACCACCGTT 59.927 47.619 0.00 0.00 0.00 4.44
94 95 0.690762 ACCTTATTGAGCACCACCGT 59.309 50.000 0.00 0.00 0.00 4.83
95 96 1.066143 AGACCTTATTGAGCACCACCG 60.066 52.381 0.00 0.00 0.00 4.94
96 97 2.237392 AGAGACCTTATTGAGCACCACC 59.763 50.000 0.00 0.00 0.00 4.61
97 98 3.618690 AGAGACCTTATTGAGCACCAC 57.381 47.619 0.00 0.00 0.00 4.16
98 99 3.327757 ACAAGAGACCTTATTGAGCACCA 59.672 43.478 0.00 0.00 0.00 4.17
99 100 3.686726 CACAAGAGACCTTATTGAGCACC 59.313 47.826 0.00 0.00 0.00 5.01
100 101 3.686726 CCACAAGAGACCTTATTGAGCAC 59.313 47.826 0.00 0.00 0.00 4.40
101 102 3.869912 GCCACAAGAGACCTTATTGAGCA 60.870 47.826 0.00 0.00 0.00 4.26
102 103 2.680339 GCCACAAGAGACCTTATTGAGC 59.320 50.000 0.00 0.00 0.00 4.26
103 104 4.213564 AGCCACAAGAGACCTTATTGAG 57.786 45.455 0.00 0.00 0.00 3.02
104 105 4.579869 GAAGCCACAAGAGACCTTATTGA 58.420 43.478 0.00 0.00 0.00 2.57
105 106 3.372206 CGAAGCCACAAGAGACCTTATTG 59.628 47.826 0.00 0.00 0.00 1.90
106 107 3.260884 TCGAAGCCACAAGAGACCTTATT 59.739 43.478 0.00 0.00 0.00 1.40
107 108 2.832129 TCGAAGCCACAAGAGACCTTAT 59.168 45.455 0.00 0.00 0.00 1.73
108 109 2.029290 GTCGAAGCCACAAGAGACCTTA 60.029 50.000 0.00 0.00 0.00 2.69
109 110 1.048601 TCGAAGCCACAAGAGACCTT 58.951 50.000 0.00 0.00 0.00 3.50
110 111 0.318762 GTCGAAGCCACAAGAGACCT 59.681 55.000 0.00 0.00 0.00 3.85
111 112 0.033504 TGTCGAAGCCACAAGAGACC 59.966 55.000 0.00 0.00 0.00 3.85
112 113 1.269831 ACTGTCGAAGCCACAAGAGAC 60.270 52.381 0.00 0.00 0.00 3.36
113 114 1.040646 ACTGTCGAAGCCACAAGAGA 58.959 50.000 0.00 0.00 0.00 3.10
114 115 1.143305 CACTGTCGAAGCCACAAGAG 58.857 55.000 0.00 0.00 0.00 2.85
115 116 0.750249 TCACTGTCGAAGCCACAAGA 59.250 50.000 0.00 0.00 0.00 3.02
116 117 1.143305 CTCACTGTCGAAGCCACAAG 58.857 55.000 0.00 0.00 0.00 3.16
117 118 0.464036 ACTCACTGTCGAAGCCACAA 59.536 50.000 0.00 0.00 0.00 3.33
118 119 0.249447 CACTCACTGTCGAAGCCACA 60.249 55.000 0.00 0.00 0.00 4.17
119 120 0.249489 ACACTCACTGTCGAAGCCAC 60.249 55.000 0.00 0.00 0.00 5.01
120 121 0.249447 CACACTCACTGTCGAAGCCA 60.249 55.000 0.00 0.00 0.00 4.75
121 122 0.249489 ACACACTCACTGTCGAAGCC 60.249 55.000 0.00 0.00 0.00 4.35
122 123 1.132588 GACACACTCACTGTCGAAGC 58.867 55.000 0.00 0.00 0.00 3.86
123 124 2.492019 TGACACACTCACTGTCGAAG 57.508 50.000 0.00 0.00 40.92 3.79
124 125 3.123050 CAATGACACACTCACTGTCGAA 58.877 45.455 0.00 0.00 40.92 3.71
125 126 2.545742 CCAATGACACACTCACTGTCGA 60.546 50.000 0.00 0.00 40.92 4.20
126 127 1.794701 CCAATGACACACTCACTGTCG 59.205 52.381 0.00 0.00 40.92 4.35
127 128 3.111853 TCCAATGACACACTCACTGTC 57.888 47.619 0.00 0.00 38.86 3.51
128 129 3.326006 AGATCCAATGACACACTCACTGT 59.674 43.478 0.00 0.00 0.00 3.55
129 130 3.935315 AGATCCAATGACACACTCACTG 58.065 45.455 0.00 0.00 0.00 3.66
130 131 4.382470 GCTAGATCCAATGACACACTCACT 60.382 45.833 0.00 0.00 0.00 3.41
131 132 3.868077 GCTAGATCCAATGACACACTCAC 59.132 47.826 0.00 0.00 0.00 3.51
132 133 3.429410 CGCTAGATCCAATGACACACTCA 60.429 47.826 0.00 0.00 0.00 3.41
133 134 3.119291 CGCTAGATCCAATGACACACTC 58.881 50.000 0.00 0.00 0.00 3.51
134 135 2.760650 TCGCTAGATCCAATGACACACT 59.239 45.455 0.00 0.00 0.00 3.55
135 136 3.165058 TCGCTAGATCCAATGACACAC 57.835 47.619 0.00 0.00 0.00 3.82
136 137 3.384467 TCATCGCTAGATCCAATGACACA 59.616 43.478 0.00 0.00 34.23 3.72
137 138 3.982475 TCATCGCTAGATCCAATGACAC 58.018 45.455 0.00 0.00 34.23 3.67
138 139 3.891366 TCTCATCGCTAGATCCAATGACA 59.109 43.478 0.00 0.00 34.23 3.58
139 140 4.022416 AGTCTCATCGCTAGATCCAATGAC 60.022 45.833 0.00 0.00 34.23 3.06
140 141 4.022503 CAGTCTCATCGCTAGATCCAATGA 60.023 45.833 0.00 0.00 34.23 2.57
141 142 4.236147 CAGTCTCATCGCTAGATCCAATG 58.764 47.826 0.00 0.00 34.23 2.82
142 143 3.257873 CCAGTCTCATCGCTAGATCCAAT 59.742 47.826 0.00 0.00 34.23 3.16
143 144 2.625314 CCAGTCTCATCGCTAGATCCAA 59.375 50.000 0.00 0.00 34.23 3.53
144 145 2.234143 CCAGTCTCATCGCTAGATCCA 58.766 52.381 0.00 0.00 34.23 3.41
145 146 2.030363 CACCAGTCTCATCGCTAGATCC 60.030 54.545 0.00 0.00 34.23 3.36
146 147 2.030363 CCACCAGTCTCATCGCTAGATC 60.030 54.545 0.00 0.00 34.23 2.75
147 148 1.959985 CCACCAGTCTCATCGCTAGAT 59.040 52.381 0.00 0.00 37.65 1.98
148 149 1.064685 TCCACCAGTCTCATCGCTAGA 60.065 52.381 0.00 0.00 0.00 2.43
149 150 1.066303 GTCCACCAGTCTCATCGCTAG 59.934 57.143 0.00 0.00 0.00 3.42
150 151 1.103803 GTCCACCAGTCTCATCGCTA 58.896 55.000 0.00 0.00 0.00 4.26
151 152 1.893786 GTCCACCAGTCTCATCGCT 59.106 57.895 0.00 0.00 0.00 4.93
152 153 1.517257 CGTCCACCAGTCTCATCGC 60.517 63.158 0.00 0.00 0.00 4.58
153 154 1.139734 CCGTCCACCAGTCTCATCG 59.860 63.158 0.00 0.00 0.00 3.84
154 155 0.608640 AACCGTCCACCAGTCTCATC 59.391 55.000 0.00 0.00 0.00 2.92
155 156 1.056660 AAACCGTCCACCAGTCTCAT 58.943 50.000 0.00 0.00 0.00 2.90
156 157 0.105964 CAAACCGTCCACCAGTCTCA 59.894 55.000 0.00 0.00 0.00 3.27
157 158 1.228657 GCAAACCGTCCACCAGTCTC 61.229 60.000 0.00 0.00 0.00 3.36
158 159 1.227853 GCAAACCGTCCACCAGTCT 60.228 57.895 0.00 0.00 0.00 3.24
159 160 2.258726 GGCAAACCGTCCACCAGTC 61.259 63.158 0.00 0.00 0.00 3.51
160 161 2.203294 GGCAAACCGTCCACCAGT 60.203 61.111 0.00 0.00 0.00 4.00
161 162 1.515521 GAAGGCAAACCGTCCACCAG 61.516 60.000 0.00 0.00 42.76 4.00
162 163 1.527380 GAAGGCAAACCGTCCACCA 60.527 57.895 0.00 0.00 42.76 4.17
163 164 2.613506 CGAAGGCAAACCGTCCACC 61.614 63.158 0.00 0.00 41.02 4.61
164 165 1.595929 TCGAAGGCAAACCGTCCAC 60.596 57.895 0.00 0.00 41.02 4.02
165 166 1.595929 GTCGAAGGCAAACCGTCCA 60.596 57.895 0.00 0.00 41.02 4.02
166 167 2.664436 CGTCGAAGGCAAACCGTCC 61.664 63.158 0.00 0.00 41.02 4.79
167 168 2.664436 CCGTCGAAGGCAAACCGTC 61.664 63.158 3.92 0.00 42.76 4.79
168 169 2.663852 CCGTCGAAGGCAAACCGT 60.664 61.111 3.92 0.00 42.76 4.83
169 170 2.663852 ACCGTCGAAGGCAAACCG 60.664 61.111 17.91 0.00 42.76 4.44
170 171 2.613506 CCACCGTCGAAGGCAAACC 61.614 63.158 17.91 0.00 33.69 3.27
171 172 2.613506 CCCACCGTCGAAGGCAAAC 61.614 63.158 17.91 0.00 33.69 2.93
172 173 2.281208 CCCACCGTCGAAGGCAAA 60.281 61.111 17.91 0.00 33.69 3.68
173 174 3.552384 ACCCACCGTCGAAGGCAA 61.552 61.111 17.91 0.00 33.69 4.52
174 175 4.308458 CACCCACCGTCGAAGGCA 62.308 66.667 17.91 0.00 33.69 4.75
175 176 4.309950 ACACCCACCGTCGAAGGC 62.310 66.667 17.91 0.00 33.69 4.35
176 177 2.357034 CACACCCACCGTCGAAGG 60.357 66.667 16.38 16.38 37.30 3.46
177 178 1.663702 GACACACCCACCGTCGAAG 60.664 63.158 0.00 0.00 0.00 3.79
178 179 1.750341 ATGACACACCCACCGTCGAA 61.750 55.000 0.00 0.00 32.17 3.71
179 180 1.750341 AATGACACACCCACCGTCGA 61.750 55.000 0.00 0.00 32.17 4.20
180 181 1.301401 AATGACACACCCACCGTCG 60.301 57.895 0.00 0.00 32.17 5.12
181 182 1.234615 CCAATGACACACCCACCGTC 61.235 60.000 0.00 0.00 0.00 4.79
191 192 3.982475 TCATCGCTAGATCCAATGACAC 58.018 45.455 0.00 0.00 34.23 3.67
192 193 3.891366 TCTCATCGCTAGATCCAATGACA 59.109 43.478 0.00 0.00 34.23 3.58
196 197 2.230025 CGGTCTCATCGCTAGATCCAAT 59.770 50.000 0.00 0.00 34.23 3.16
199 200 0.523966 CCGGTCTCATCGCTAGATCC 59.476 60.000 0.00 0.00 34.23 3.36
225 226 2.959030 ACTTCAGAGGAAAAGGCAAACC 59.041 45.455 0.00 0.00 31.35 3.27
243 247 0.544595 ACCAACTCCCCTCGCTACTT 60.545 55.000 0.00 0.00 0.00 2.24
246 250 1.760613 CATAACCAACTCCCCTCGCTA 59.239 52.381 0.00 0.00 0.00 4.26
250 254 3.679083 CGAAGACATAACCAACTCCCCTC 60.679 52.174 0.00 0.00 0.00 4.30
258 262 2.614481 GGCCTCACGAAGACATAACCAA 60.614 50.000 0.00 0.00 0.00 3.67
273 277 3.640407 GGAGCACCACTGGCCTCA 61.640 66.667 3.32 0.00 35.97 3.86
280 284 3.758554 GACATTATTGTTGGAGCACCACT 59.241 43.478 0.85 0.00 46.80 4.00
311 315 1.673626 GCCCAAGTCGACGGAATAACA 60.674 52.381 10.46 0.00 0.00 2.41
329 333 3.050619 CGATCACACCTATACTTTCGCC 58.949 50.000 0.00 0.00 0.00 5.54
338 342 1.757118 CACTGGGTCGATCACACCTAT 59.243 52.381 10.06 0.00 33.96 2.57
356 360 3.259374 TGTCCTGGAGAAGAAGATGACAC 59.741 47.826 0.00 0.00 0.00 3.67
376 380 3.743584 CGATGAGCTTGAAGGATCCATGT 60.744 47.826 15.82 0.00 0.00 3.21
398 402 5.416947 TCTTTTCCTAGAAGTATCGGCAAC 58.583 41.667 0.00 0.00 0.00 4.17
400 404 5.507482 CGATCTTTTCCTAGAAGTATCGGCA 60.507 44.000 0.00 0.00 34.42 5.69
412 416 5.221461 GCTAGGATTCACCGATCTTTTCCTA 60.221 44.000 0.00 0.00 44.74 2.94
416 420 4.446371 CAGCTAGGATTCACCGATCTTTT 58.554 43.478 0.00 0.00 44.74 2.27
418 422 2.224161 GCAGCTAGGATTCACCGATCTT 60.224 50.000 0.00 0.00 44.74 2.40
461 465 1.711060 CGTTGCGTAATGGCCCGAAT 61.711 55.000 0.00 0.00 0.00 3.34
465 469 1.433837 CTACCGTTGCGTAATGGCCC 61.434 60.000 22.66 0.00 45.21 5.80
469 473 4.663140 CGATATTGCTACCGTTGCGTAATG 60.663 45.833 0.00 0.00 0.00 1.90
478 482 0.033504 CCAGCCGATATTGCTACCGT 59.966 55.000 0.88 0.00 36.81 4.83
505 509 4.035814 CCTCCCTCTCCATCATGCATATA 58.964 47.826 0.00 0.00 0.00 0.86
508 512 1.065647 CCTCCCTCTCCATCATGCAT 58.934 55.000 0.00 0.00 0.00 3.96
626 635 7.489113 GGTCAAAGCAACTGAACATTATATTGG 59.511 37.037 0.09 0.00 30.46 3.16
644 653 6.450545 AGAATTAAAGAAAGCTGGTCAAAGC 58.549 36.000 0.00 0.00 43.88 3.51
685 694 9.631257 AATTGTGACAACATATGATTGGATCTA 57.369 29.630 10.38 3.57 35.83 1.98
714 723 5.036117 TGGTTATTATCTTGGCTCTCCAC 57.964 43.478 0.00 0.00 43.33 4.02
717 726 7.436376 GCAATTTTGGTTATTATCTTGGCTCTC 59.564 37.037 0.00 0.00 0.00 3.20
720 729 6.945218 TGCAATTTTGGTTATTATCTTGGCT 58.055 32.000 0.00 0.00 0.00 4.75
734 743 3.181493 CGGGAGAGAGAATGCAATTTTGG 60.181 47.826 0.00 0.00 36.07 3.28
781 790 4.221041 TGTTGATCCACATGTTGCATGAAT 59.779 37.500 15.03 6.22 0.00 2.57
782 791 3.573110 TGTTGATCCACATGTTGCATGAA 59.427 39.130 15.03 0.00 0.00 2.57
783 792 3.155501 TGTTGATCCACATGTTGCATGA 58.844 40.909 15.03 0.00 0.00 3.07
784 793 3.579335 TGTTGATCCACATGTTGCATG 57.421 42.857 0.00 7.48 0.00 4.06
899 909 5.283247 CGTCTCACTGAATGTACGTTTAGAC 59.717 44.000 22.47 16.90 35.46 2.59
923 933 0.029834 CAACTGGTGTGTGCTTGCTC 59.970 55.000 0.00 0.00 0.00 4.26
964 978 3.100862 CTTGCTTAGCCGCTTCGCC 62.101 63.158 0.29 0.00 0.00 5.54
1053 1067 2.758327 AGCCTCGGGATGCACGTA 60.758 61.111 0.00 0.00 0.00 3.57
1477 1497 3.561310 TGCGTGGATCTTGCAGAATAATC 59.439 43.478 3.49 0.00 34.03 1.75
1524 1544 3.009723 CCAACAGACATCCACATGTACC 58.990 50.000 0.00 0.00 43.79 3.34
1539 1559 0.951558 GTGCAACTACCACCCAACAG 59.048 55.000 0.00 0.00 0.00 3.16
1558 1578 2.259618 GTCTACCACACTACACATGCG 58.740 52.381 0.00 0.00 0.00 4.73
1606 1626 5.102313 ACTTAAACTTGCACAAAACTCTGC 58.898 37.500 0.00 0.00 0.00 4.26
1609 1629 5.975344 GGGTACTTAAACTTGCACAAAACTC 59.025 40.000 0.00 0.00 0.00 3.01
1628 1648 2.158726 TCCACTTGACAAGTTGGGGTAC 60.159 50.000 24.44 0.00 40.46 3.34
1717 1737 1.400142 CCAGCGGATAAAACGAATGCA 59.600 47.619 0.00 0.00 0.00 3.96
1871 1891 4.578928 CCATCATCATCTGATCAAGCACAA 59.421 41.667 0.00 0.00 42.91 3.33
1916 1936 0.968405 CCTGACCAAAACCACCATGG 59.032 55.000 11.19 11.19 45.02 3.66
1927 1947 0.467290 GCCTTGTGAACCCTGACCAA 60.467 55.000 0.00 0.00 0.00 3.67
2039 2059 0.251608 AAACCACGCCCTAAGCCATT 60.252 50.000 0.00 0.00 38.78 3.16
2041 2061 1.302993 GAAACCACGCCCTAAGCCA 60.303 57.895 0.00 0.00 38.78 4.75
2082 2102 1.597461 GAAAGCCCCTACAGAGCGT 59.403 57.895 0.00 0.00 0.00 5.07
2100 2120 1.687494 GCGAGCAGTCTTACAAGGCG 61.687 60.000 0.00 0.00 35.32 5.52
2125 2145 2.100252 TCGTAAGTTATGGAGGCCGAAG 59.900 50.000 0.00 0.00 39.48 3.79
2130 2150 2.573941 ACGTCGTAAGTTATGGAGGC 57.426 50.000 0.00 0.00 39.48 4.70
2136 2156 6.476243 AAGCATGAAAACGTCGTAAGTTAT 57.524 33.333 0.00 0.00 39.48 1.89
2161 2181 0.748005 AAAAGCCATCCCGACCATCG 60.748 55.000 0.00 0.00 40.07 3.84
2185 2205 9.577110 TGTACCGAAACATAAGTTAGATTACAG 57.423 33.333 0.00 0.00 36.84 2.74
2216 2236 9.353999 GATTTAACTTAATAAAGCCCACAACAG 57.646 33.333 0.00 0.00 36.05 3.16
2276 2296 2.009774 CATTGCTGACCGAAACCCTAG 58.990 52.381 0.00 0.00 0.00 3.02
2279 2299 0.958822 AACATTGCTGACCGAAACCC 59.041 50.000 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.