Multiple sequence alignment - TraesCS7D01G311000

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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 TraesCS7D01G311000 chr7D 100.000 2477 0 0 1 2477 394370003 394367527 0.000000e+00 4575
1 TraesCS7D01G311000 chr1A 98.842 1209 14 0 1269 2477 143270483 143269275 0.000000e+00 2156
2 TraesCS7D01G311000 chr1A 98.693 612 6 1 629 1238 143271095 143270484 0.000000e+00 1085
3 TraesCS7D01G311000 chr1A 96.615 325 2 3 302 622 143271909 143271590 4.690000e-147 531
4 TraesCS7D01G311000 chr6D 99.669 302 0 1 1 301 214550712 214550411 3.600000e-153 551
5 TraesCS7D01G311000 chr6D 99.003 301 2 1 1 301 338805857 338806156 2.800000e-149 538
6 TraesCS7D01G311000 chr6D 98.671 301 3 1 1 301 4301027 4300728 1.300000e-147 532
7 TraesCS7D01G311000 chr5D 99.668 301 1 0 1 301 185206966 185206666 3.600000e-153 551
8 TraesCS7D01G311000 chr5D 98.675 302 3 1 1 301 334927132 334926831 3.630000e-148 534
9 TraesCS7D01G311000 chr2D 99.336 301 1 1 1 301 377144165 377143866 6.020000e-151 544
10 TraesCS7D01G311000 chr2D 98.689 305 2 2 1 304 286986795 286987098 7.790000e-150 540
11 TraesCS7D01G311000 chr2D 99.003 301 2 1 1 301 218029601 218029302 2.800000e-149 538
12 TraesCS7D01G311000 chr2D 98.361 305 3 2 1 304 377138927 377138624 3.630000e-148 534


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 TraesCS7D01G311000 chr7D 394367527 394370003 2476 True 4575.000000 4575 100.00 1 2477 1 chr7D.!!$R1 2476
1 TraesCS7D01G311000 chr1A 143269275 143271909 2634 True 1257.333333 2156 98.05 302 2477 3 chr1A.!!$R1 2175

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
66 67 0.035176 ACACAAATGCCATGCCAACC 59.965 50.0 0.0 0.0 0.00 3.77 F
236 237 0.185901 AACTGCCACAAGGACCATGT 59.814 50.0 0.0 0.0 36.89 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 1934 0.614812 TGCCATAAGCTGAGAGCACA 59.385 50.0 0.0 0.0 45.56 4.57 R
1726 2221 2.853235 AACAGCCCACCTACACTAAC 57.147 50.0 0.0 0.0 0.00 2.34 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
21 22 3.099905 TGGATGACACTAGGAGAGTTGG 58.900 50.000 0.00 0.00 35.64 3.77
22 23 2.432510 GGATGACACTAGGAGAGTTGGG 59.567 54.545 0.00 0.00 35.64 4.12
23 24 2.992847 TGACACTAGGAGAGTTGGGA 57.007 50.000 0.00 0.00 35.64 4.37
24 25 2.526432 TGACACTAGGAGAGTTGGGAC 58.474 52.381 0.00 0.00 35.64 4.46
25 26 2.158370 TGACACTAGGAGAGTTGGGACA 60.158 50.000 0.00 0.00 35.64 4.02
41 42 5.793030 TGGGACAATTTTCGTTGGTTTAT 57.207 34.783 0.00 0.00 31.92 1.40
42 43 6.163135 TGGGACAATTTTCGTTGGTTTATT 57.837 33.333 0.00 0.00 31.92 1.40
43 44 6.583562 TGGGACAATTTTCGTTGGTTTATTT 58.416 32.000 0.00 0.00 31.92 1.40
44 45 6.702282 TGGGACAATTTTCGTTGGTTTATTTC 59.298 34.615 0.00 0.00 31.92 2.17
45 46 6.926826 GGGACAATTTTCGTTGGTTTATTTCT 59.073 34.615 0.00 0.00 33.40 2.52
46 47 7.115805 GGGACAATTTTCGTTGGTTTATTTCTC 59.884 37.037 0.00 0.00 33.40 2.87
47 48 7.650104 GGACAATTTTCGTTGGTTTATTTCTCA 59.350 33.333 0.00 0.00 33.40 3.27
48 49 8.347729 ACAATTTTCGTTGGTTTATTTCTCAC 57.652 30.769 0.00 0.00 33.40 3.51
49 50 7.976734 ACAATTTTCGTTGGTTTATTTCTCACA 59.023 29.630 0.00 0.00 33.40 3.58
50 51 7.924103 ATTTTCGTTGGTTTATTTCTCACAC 57.076 32.000 0.00 0.00 0.00 3.82
51 52 6.438259 TTTCGTTGGTTTATTTCTCACACA 57.562 33.333 0.00 0.00 0.00 3.72
52 53 6.438259 TTCGTTGGTTTATTTCTCACACAA 57.562 33.333 0.00 0.00 0.00 3.33
53 54 6.438259 TCGTTGGTTTATTTCTCACACAAA 57.562 33.333 0.00 0.00 0.00 2.83
54 55 7.033530 TCGTTGGTTTATTTCTCACACAAAT 57.966 32.000 0.00 0.00 0.00 2.32
55 56 6.915300 TCGTTGGTTTATTTCTCACACAAATG 59.085 34.615 0.00 0.00 0.00 2.32
56 57 6.345723 CGTTGGTTTATTTCTCACACAAATGC 60.346 38.462 0.00 0.00 0.00 3.56
57 58 5.537188 TGGTTTATTTCTCACACAAATGCC 58.463 37.500 0.00 0.00 0.00 4.40
58 59 5.069648 TGGTTTATTTCTCACACAAATGCCA 59.930 36.000 0.00 0.00 0.00 4.92
59 60 6.165577 GGTTTATTTCTCACACAAATGCCAT 58.834 36.000 0.00 0.00 0.00 4.40
60 61 6.091169 GGTTTATTTCTCACACAAATGCCATG 59.909 38.462 0.00 0.00 0.00 3.66
61 62 2.728690 TTCTCACACAAATGCCATGC 57.271 45.000 0.00 0.00 0.00 4.06
62 63 0.889994 TCTCACACAAATGCCATGCC 59.110 50.000 0.00 0.00 0.00 4.40
63 64 0.604073 CTCACACAAATGCCATGCCA 59.396 50.000 0.00 0.00 0.00 4.92
64 65 1.001068 CTCACACAAATGCCATGCCAA 59.999 47.619 0.00 0.00 0.00 4.52
65 66 1.149987 CACACAAATGCCATGCCAAC 58.850 50.000 0.00 0.00 0.00 3.77
66 67 0.035176 ACACAAATGCCATGCCAACC 59.965 50.000 0.00 0.00 0.00 3.77
67 68 0.322322 CACAAATGCCATGCCAACCT 59.678 50.000 0.00 0.00 0.00 3.50
68 69 0.322322 ACAAATGCCATGCCAACCTG 59.678 50.000 0.00 0.00 0.00 4.00
69 70 0.609151 CAAATGCCATGCCAACCTGA 59.391 50.000 0.00 0.00 0.00 3.86
70 71 0.899720 AAATGCCATGCCAACCTGAG 59.100 50.000 0.00 0.00 0.00 3.35
71 72 0.974010 AATGCCATGCCAACCTGAGG 60.974 55.000 0.00 0.00 0.00 3.86
72 73 2.757099 GCCATGCCAACCTGAGGG 60.757 66.667 2.38 0.00 38.88 4.30
73 74 2.043652 CCATGCCAACCTGAGGGG 60.044 66.667 2.38 0.00 41.89 4.79
82 83 4.851784 CCTGAGGGGTTGGGGATA 57.148 61.111 0.00 0.00 0.00 2.59
83 84 2.231642 CCTGAGGGGTTGGGGATAC 58.768 63.158 0.00 0.00 0.00 2.24
84 85 0.623324 CCTGAGGGGTTGGGGATACA 60.623 60.000 0.00 0.00 39.74 2.29
85 86 1.522900 CTGAGGGGTTGGGGATACAT 58.477 55.000 0.00 0.00 39.74 2.29
86 87 2.698967 CCTGAGGGGTTGGGGATACATA 60.699 54.545 0.00 0.00 39.74 2.29
87 88 2.372172 CTGAGGGGTTGGGGATACATAC 59.628 54.545 0.00 0.00 39.74 2.39
88 89 2.021441 TGAGGGGTTGGGGATACATACT 60.021 50.000 0.00 0.00 39.74 2.12
89 90 3.053826 GAGGGGTTGGGGATACATACTT 58.946 50.000 0.00 0.00 39.74 2.24
90 91 4.237018 GAGGGGTTGGGGATACATACTTA 58.763 47.826 0.00 0.00 39.74 2.24
91 92 4.850386 GAGGGGTTGGGGATACATACTTAT 59.150 45.833 0.00 0.00 39.74 1.73
92 93 5.997094 AGGGGTTGGGGATACATACTTATA 58.003 41.667 0.00 0.00 39.74 0.98
93 94 6.030082 AGGGGTTGGGGATACATACTTATAG 58.970 44.000 0.00 0.00 39.74 1.31
94 95 5.191124 GGGGTTGGGGATACATACTTATAGG 59.809 48.000 0.00 0.00 39.74 2.57
95 96 5.338953 GGGTTGGGGATACATACTTATAGGC 60.339 48.000 0.00 0.00 39.74 3.93
96 97 5.487845 GGTTGGGGATACATACTTATAGGCT 59.512 44.000 0.00 0.00 39.74 4.58
97 98 6.407202 GTTGGGGATACATACTTATAGGCTG 58.593 44.000 0.00 0.00 39.74 4.85
98 99 4.469945 TGGGGATACATACTTATAGGCTGC 59.530 45.833 0.00 0.00 39.74 5.25
99 100 4.717280 GGGGATACATACTTATAGGCTGCT 59.283 45.833 0.00 0.00 39.74 4.24
100 101 5.897824 GGGGATACATACTTATAGGCTGCTA 59.102 44.000 0.00 0.00 39.74 3.49
101 102 6.041069 GGGGATACATACTTATAGGCTGCTAG 59.959 46.154 0.00 0.00 39.74 3.42
102 103 6.461788 GGGATACATACTTATAGGCTGCTAGC 60.462 46.154 8.10 8.10 38.65 3.42
114 115 4.885426 GCTAGCCAGCCAAGCATA 57.115 55.556 2.29 0.00 42.37 3.14
115 116 3.336122 GCTAGCCAGCCAAGCATAT 57.664 52.632 2.29 0.00 42.37 1.78
116 117 0.879765 GCTAGCCAGCCAAGCATATG 59.120 55.000 2.29 0.00 42.37 1.78
117 118 0.879765 CTAGCCAGCCAAGCATATGC 59.120 55.000 20.36 20.36 42.49 3.14
119 120 5.990447 GCTAGCCAGCCAAGCATATGCTA 62.990 52.174 29.77 10.49 46.09 3.49
134 135 7.754069 GCATATGCTAAGATGCTAGTCTAAG 57.246 40.000 20.64 0.00 45.60 2.18
135 136 7.542890 GCATATGCTAAGATGCTAGTCTAAGA 58.457 38.462 20.64 0.00 45.60 2.10
136 137 8.196771 GCATATGCTAAGATGCTAGTCTAAGAT 58.803 37.037 20.64 0.00 45.60 2.40
137 138 9.518906 CATATGCTAAGATGCTAGTCTAAGATG 57.481 37.037 0.00 0.00 0.00 2.90
138 139 5.777802 TGCTAAGATGCTAGTCTAAGATGC 58.222 41.667 0.00 0.00 0.00 3.91
139 140 5.538053 TGCTAAGATGCTAGTCTAAGATGCT 59.462 40.000 0.00 0.00 0.00 3.79
140 141 5.863397 GCTAAGATGCTAGTCTAAGATGCTG 59.137 44.000 0.00 0.00 0.00 4.41
141 142 4.255833 AGATGCTAGTCTAAGATGCTGC 57.744 45.455 0.00 0.00 0.00 5.25
142 143 3.896888 AGATGCTAGTCTAAGATGCTGCT 59.103 43.478 0.00 0.00 0.00 4.24
143 144 5.076182 AGATGCTAGTCTAAGATGCTGCTA 58.924 41.667 0.00 0.00 0.00 3.49
144 145 5.538053 AGATGCTAGTCTAAGATGCTGCTAA 59.462 40.000 0.00 0.00 0.00 3.09
145 146 5.193663 TGCTAGTCTAAGATGCTGCTAAG 57.806 43.478 0.00 0.00 0.00 2.18
146 147 4.889995 TGCTAGTCTAAGATGCTGCTAAGA 59.110 41.667 0.00 0.00 0.00 2.10
147 148 5.538053 TGCTAGTCTAAGATGCTGCTAAGAT 59.462 40.000 0.00 0.00 0.00 2.40
148 149 5.863397 GCTAGTCTAAGATGCTGCTAAGATG 59.137 44.000 0.00 0.00 0.00 2.90
149 150 4.630111 AGTCTAAGATGCTGCTAAGATGC 58.370 43.478 0.00 0.00 0.00 3.91
150 151 3.745458 GTCTAAGATGCTGCTAAGATGCC 59.255 47.826 0.00 0.00 0.00 4.40
151 152 2.723322 AAGATGCTGCTAAGATGCCA 57.277 45.000 0.00 0.00 0.00 4.92
152 153 2.257691 AGATGCTGCTAAGATGCCAG 57.742 50.000 0.00 0.00 0.00 4.85
153 154 1.489649 AGATGCTGCTAAGATGCCAGT 59.510 47.619 0.00 0.00 0.00 4.00
154 155 1.872313 GATGCTGCTAAGATGCCAGTC 59.128 52.381 0.00 0.00 0.00 3.51
155 156 0.907486 TGCTGCTAAGATGCCAGTCT 59.093 50.000 0.00 0.00 0.00 3.24
156 157 2.110578 TGCTGCTAAGATGCCAGTCTA 58.889 47.619 0.00 0.00 0.00 2.59
157 158 2.501316 TGCTGCTAAGATGCCAGTCTAA 59.499 45.455 0.00 0.00 0.00 2.10
158 159 3.129871 GCTGCTAAGATGCCAGTCTAAG 58.870 50.000 0.00 0.00 0.00 2.18
159 160 3.181471 GCTGCTAAGATGCCAGTCTAAGA 60.181 47.826 0.00 0.00 0.00 2.10
160 161 4.502950 GCTGCTAAGATGCCAGTCTAAGAT 60.503 45.833 0.00 0.00 0.00 2.40
161 162 4.953667 TGCTAAGATGCCAGTCTAAGATG 58.046 43.478 0.00 0.00 0.00 2.90
162 163 3.745458 GCTAAGATGCCAGTCTAAGATGC 59.255 47.826 0.00 0.00 0.00 3.91
163 164 4.502950 GCTAAGATGCCAGTCTAAGATGCT 60.503 45.833 0.00 0.00 0.00 3.79
164 165 5.279206 GCTAAGATGCCAGTCTAAGATGCTA 60.279 44.000 0.00 0.00 0.00 3.49
165 166 4.870123 AGATGCCAGTCTAAGATGCTAG 57.130 45.455 0.00 0.00 0.00 3.42
166 167 4.222336 AGATGCCAGTCTAAGATGCTAGT 58.778 43.478 0.00 0.00 0.00 2.57
167 168 4.280677 AGATGCCAGTCTAAGATGCTAGTC 59.719 45.833 0.00 0.00 0.00 2.59
168 169 3.636679 TGCCAGTCTAAGATGCTAGTCT 58.363 45.455 0.00 0.00 0.00 3.24
169 170 4.793201 TGCCAGTCTAAGATGCTAGTCTA 58.207 43.478 0.00 0.00 0.00 2.59
170 171 5.201243 TGCCAGTCTAAGATGCTAGTCTAA 58.799 41.667 0.00 0.00 0.00 2.10
171 172 5.300539 TGCCAGTCTAAGATGCTAGTCTAAG 59.699 44.000 0.00 0.00 0.00 2.18
172 173 5.533154 GCCAGTCTAAGATGCTAGTCTAAGA 59.467 44.000 0.00 0.00 0.00 2.10
173 174 6.208599 GCCAGTCTAAGATGCTAGTCTAAGAT 59.791 42.308 0.00 0.00 0.00 2.40
174 175 7.592938 CCAGTCTAAGATGCTAGTCTAAGATG 58.407 42.308 0.00 0.00 0.00 2.90
175 176 7.083858 CAGTCTAAGATGCTAGTCTAAGATGC 58.916 42.308 0.00 0.00 0.00 3.91
176 177 7.004086 AGTCTAAGATGCTAGTCTAAGATGCT 58.996 38.462 0.00 0.00 0.00 3.79
177 178 8.160765 AGTCTAAGATGCTAGTCTAAGATGCTA 58.839 37.037 0.00 0.00 0.00 3.49
178 179 8.956426 GTCTAAGATGCTAGTCTAAGATGCTAT 58.044 37.037 0.00 0.00 0.00 2.97
179 180 9.173021 TCTAAGATGCTAGTCTAAGATGCTATC 57.827 37.037 0.00 0.00 0.00 2.08
180 181 6.773976 AGATGCTAGTCTAAGATGCTATCC 57.226 41.667 0.00 0.00 0.00 2.59
181 182 6.493166 AGATGCTAGTCTAAGATGCTATCCT 58.507 40.000 0.00 0.00 0.00 3.24
182 183 7.638444 AGATGCTAGTCTAAGATGCTATCCTA 58.362 38.462 0.00 0.00 0.00 2.94
183 184 8.112822 AGATGCTAGTCTAAGATGCTATCCTAA 58.887 37.037 0.00 0.00 0.00 2.69
184 185 7.455641 TGCTAGTCTAAGATGCTATCCTAAC 57.544 40.000 0.00 0.00 0.00 2.34
185 186 7.235079 TGCTAGTCTAAGATGCTATCCTAACT 58.765 38.462 0.00 0.00 0.00 2.24
186 187 7.175816 TGCTAGTCTAAGATGCTATCCTAACTG 59.824 40.741 0.00 0.00 0.00 3.16
187 188 6.339587 AGTCTAAGATGCTATCCTAACTGC 57.660 41.667 0.00 0.00 0.00 4.40
188 189 5.245075 AGTCTAAGATGCTATCCTAACTGCC 59.755 44.000 0.00 0.00 0.00 4.85
189 190 5.011125 GTCTAAGATGCTATCCTAACTGCCA 59.989 44.000 0.00 0.00 0.00 4.92
190 191 4.348863 AAGATGCTATCCTAACTGCCAG 57.651 45.455 0.00 0.00 0.00 4.85
191 192 3.312890 AGATGCTATCCTAACTGCCAGT 58.687 45.455 0.00 0.00 0.00 4.00
192 193 3.323403 AGATGCTATCCTAACTGCCAGTC 59.677 47.826 0.00 0.00 0.00 3.51
193 194 1.762957 TGCTATCCTAACTGCCAGTCC 59.237 52.381 0.00 0.00 0.00 3.85
194 195 2.043227 GCTATCCTAACTGCCAGTCCT 58.957 52.381 0.00 0.00 0.00 3.85
195 196 2.436173 GCTATCCTAACTGCCAGTCCTT 59.564 50.000 0.00 0.00 0.00 3.36
196 197 3.742640 GCTATCCTAACTGCCAGTCCTTG 60.743 52.174 0.00 0.00 0.00 3.61
197 198 2.024176 TCCTAACTGCCAGTCCTTGA 57.976 50.000 0.00 0.00 0.00 3.02
198 199 2.551270 TCCTAACTGCCAGTCCTTGAT 58.449 47.619 0.00 0.00 0.00 2.57
199 200 2.237143 TCCTAACTGCCAGTCCTTGATG 59.763 50.000 0.00 0.00 0.00 3.07
200 201 2.636830 CTAACTGCCAGTCCTTGATGG 58.363 52.381 0.00 0.00 39.73 3.51
201 202 0.773644 AACTGCCAGTCCTTGATGGT 59.226 50.000 0.00 0.00 38.91 3.55
202 203 0.326264 ACTGCCAGTCCTTGATGGTC 59.674 55.000 0.00 0.00 38.91 4.02
203 204 0.325933 CTGCCAGTCCTTGATGGTCA 59.674 55.000 0.00 0.00 38.91 4.02
204 205 0.325933 TGCCAGTCCTTGATGGTCAG 59.674 55.000 0.00 0.00 38.91 3.51
205 206 0.393537 GCCAGTCCTTGATGGTCAGG 60.394 60.000 0.00 0.00 38.91 3.86
206 207 0.254178 CCAGTCCTTGATGGTCAGGG 59.746 60.000 1.98 1.98 44.20 4.45
211 212 2.850833 TCCTTGATGGTCAGGGATTCT 58.149 47.619 6.70 0.00 46.11 2.40
212 213 4.007581 TCCTTGATGGTCAGGGATTCTA 57.992 45.455 6.70 0.00 46.11 2.10
213 214 4.570926 TCCTTGATGGTCAGGGATTCTAT 58.429 43.478 6.70 0.00 46.11 1.98
214 215 4.594920 TCCTTGATGGTCAGGGATTCTATC 59.405 45.833 6.70 0.00 46.11 2.08
215 216 4.263243 CCTTGATGGTCAGGGATTCTATCC 60.263 50.000 2.20 0.00 45.53 2.59
216 217 6.466180 CCTTGATGGTCAGGGATTCTATCCT 61.466 48.000 2.20 0.00 45.53 3.24
217 218 7.209528 CCTTGATGGTCAGGGATTCTATCCTA 61.210 46.154 2.20 0.00 45.53 2.94
218 219 8.628659 CCTTGATGGTCAGGGATTCTATCCTAA 61.629 44.444 2.20 0.00 45.53 2.69
226 227 4.689612 GGATTCTATCCTAACTGCCACA 57.310 45.455 0.00 0.00 46.19 4.17
227 228 5.036117 GGATTCTATCCTAACTGCCACAA 57.964 43.478 0.00 0.00 46.19 3.33
228 229 5.059833 GGATTCTATCCTAACTGCCACAAG 58.940 45.833 0.00 0.00 46.19 3.16
229 230 4.487714 TTCTATCCTAACTGCCACAAGG 57.512 45.455 0.00 0.00 38.23 3.61
230 231 3.719871 TCTATCCTAACTGCCACAAGGA 58.280 45.455 0.00 0.00 42.17 3.36
231 232 2.789409 ATCCTAACTGCCACAAGGAC 57.211 50.000 0.00 0.00 40.83 3.85
232 233 0.690762 TCCTAACTGCCACAAGGACC 59.309 55.000 0.00 0.00 36.89 4.46
233 234 0.400213 CCTAACTGCCACAAGGACCA 59.600 55.000 0.00 0.00 36.89 4.02
234 235 1.004745 CCTAACTGCCACAAGGACCAT 59.995 52.381 0.00 0.00 36.89 3.55
235 236 2.086869 CTAACTGCCACAAGGACCATG 58.913 52.381 0.00 0.00 36.89 3.66
236 237 0.185901 AACTGCCACAAGGACCATGT 59.814 50.000 0.00 0.00 36.89 3.21
237 238 0.538057 ACTGCCACAAGGACCATGTG 60.538 55.000 20.60 20.60 46.05 3.21
238 239 1.870055 CTGCCACAAGGACCATGTGC 61.870 60.000 21.84 17.31 45.32 4.57
239 240 1.604593 GCCACAAGGACCATGTGCT 60.605 57.895 21.84 0.00 45.32 4.40
240 241 1.870055 GCCACAAGGACCATGTGCTG 61.870 60.000 21.84 11.91 45.32 4.41
241 242 1.582968 CACAAGGACCATGTGCTGC 59.417 57.895 16.36 0.00 41.42 5.25
242 243 1.151221 ACAAGGACCATGTGCTGCA 59.849 52.632 0.52 0.00 33.74 4.41
243 244 0.892358 ACAAGGACCATGTGCTGCAG 60.892 55.000 10.11 10.11 33.74 4.41
244 245 1.975407 AAGGACCATGTGCTGCAGC 60.975 57.895 31.89 31.89 33.74 5.25
245 246 3.446570 GGACCATGTGCTGCAGCC 61.447 66.667 34.64 25.13 41.18 4.85
246 247 2.674033 GACCATGTGCTGCAGCCA 60.674 61.111 34.64 29.46 41.18 4.75
247 248 2.203523 ACCATGTGCTGCAGCCAA 60.204 55.556 34.64 23.22 41.18 4.52
248 249 1.808531 GACCATGTGCTGCAGCCAAA 61.809 55.000 34.64 20.62 41.18 3.28
249 250 1.080093 CCATGTGCTGCAGCCAAAG 60.080 57.895 34.64 24.24 41.18 2.77
250 251 1.080093 CATGTGCTGCAGCCAAAGG 60.080 57.895 34.64 18.17 41.18 3.11
251 252 1.228644 ATGTGCTGCAGCCAAAGGA 60.229 52.632 34.64 13.43 41.18 3.36
252 253 1.530013 ATGTGCTGCAGCCAAAGGAC 61.530 55.000 34.64 24.37 41.18 3.85
253 254 2.598394 TGCTGCAGCCAAAGGACC 60.598 61.111 34.64 5.72 41.18 4.46
254 255 2.598394 GCTGCAGCCAAAGGACCA 60.598 61.111 28.76 0.00 34.31 4.02
255 256 1.980772 GCTGCAGCCAAAGGACCAT 60.981 57.895 28.76 0.00 34.31 3.55
256 257 1.888018 CTGCAGCCAAAGGACCATG 59.112 57.895 0.00 0.00 0.00 3.66
257 258 0.896940 CTGCAGCCAAAGGACCATGT 60.897 55.000 0.00 0.00 0.00 3.21
258 259 1.180456 TGCAGCCAAAGGACCATGTG 61.180 55.000 0.00 0.00 0.00 3.21
259 260 1.588082 CAGCCAAAGGACCATGTGC 59.412 57.895 0.00 0.00 0.00 4.57
260 261 0.896940 CAGCCAAAGGACCATGTGCT 60.897 55.000 0.00 1.32 35.27 4.40
261 262 0.896940 AGCCAAAGGACCATGTGCTG 60.897 55.000 10.41 0.00 33.74 4.41
262 263 1.588082 CCAAAGGACCATGTGCTGC 59.412 57.895 0.00 0.00 33.74 5.25
263 264 1.180456 CCAAAGGACCATGTGCTGCA 61.180 55.000 0.00 0.00 33.74 4.41
264 265 0.242825 CAAAGGACCATGTGCTGCAG 59.757 55.000 10.11 10.11 33.74 4.41
265 266 1.530013 AAAGGACCATGTGCTGCAGC 61.530 55.000 31.89 31.89 33.74 5.25
266 267 3.446570 GGACCATGTGCTGCAGCC 61.447 66.667 34.64 25.13 41.18 4.85
267 268 3.446570 GACCATGTGCTGCAGCCC 61.447 66.667 34.64 25.41 41.18 5.19
270 271 3.755628 CATGTGCTGCAGCCCCAC 61.756 66.667 34.64 25.80 41.18 4.61
271 272 4.289101 ATGTGCTGCAGCCCCACA 62.289 61.111 34.64 30.21 42.87 4.17
272 273 3.813606 ATGTGCTGCAGCCCCACAA 62.814 57.895 34.64 13.43 42.10 3.33
273 274 3.225798 GTGCTGCAGCCCCACAAA 61.226 61.111 34.64 12.62 41.18 2.83
274 275 2.913578 TGCTGCAGCCCCACAAAG 60.914 61.111 34.64 0.00 41.18 2.77
275 276 2.598394 GCTGCAGCCCCACAAAGA 60.598 61.111 28.76 0.00 34.31 2.52
276 277 2.924105 GCTGCAGCCCCACAAAGAC 61.924 63.158 28.76 0.00 34.31 3.01
277 278 2.203480 TGCAGCCCCACAAAGACC 60.203 61.111 0.00 0.00 0.00 3.85
278 279 2.116125 GCAGCCCCACAAAGACCT 59.884 61.111 0.00 0.00 0.00 3.85
279 280 1.531602 GCAGCCCCACAAAGACCTT 60.532 57.895 0.00 0.00 0.00 3.50
280 281 0.251165 GCAGCCCCACAAAGACCTTA 60.251 55.000 0.00 0.00 0.00 2.69
281 282 1.826385 CAGCCCCACAAAGACCTTAG 58.174 55.000 0.00 0.00 0.00 2.18
282 283 1.073923 CAGCCCCACAAAGACCTTAGT 59.926 52.381 0.00 0.00 0.00 2.24
283 284 2.304761 CAGCCCCACAAAGACCTTAGTA 59.695 50.000 0.00 0.00 0.00 1.82
284 285 2.305052 AGCCCCACAAAGACCTTAGTAC 59.695 50.000 0.00 0.00 0.00 2.73
285 286 2.039348 GCCCCACAAAGACCTTAGTACA 59.961 50.000 0.00 0.00 0.00 2.90
286 287 3.308188 GCCCCACAAAGACCTTAGTACAT 60.308 47.826 0.00 0.00 0.00 2.29
287 288 4.080751 GCCCCACAAAGACCTTAGTACATA 60.081 45.833 0.00 0.00 0.00 2.29
288 289 5.671493 CCCCACAAAGACCTTAGTACATAG 58.329 45.833 0.00 0.00 0.00 2.23
289 290 5.424252 CCCCACAAAGACCTTAGTACATAGA 59.576 44.000 0.00 0.00 0.00 1.98
290 291 6.338937 CCCACAAAGACCTTAGTACATAGAC 58.661 44.000 0.00 0.00 0.00 2.59
291 292 6.154706 CCCACAAAGACCTTAGTACATAGACT 59.845 42.308 0.00 0.00 0.00 3.24
292 293 7.310485 CCCACAAAGACCTTAGTACATAGACTT 60.310 40.741 0.00 0.00 0.00 3.01
293 294 8.746530 CCACAAAGACCTTAGTACATAGACTTA 58.253 37.037 0.00 0.00 0.00 2.24
296 297 9.968870 CAAAGACCTTAGTACATAGACTTATCC 57.031 37.037 0.00 0.00 0.00 2.59
297 298 9.710818 AAAGACCTTAGTACATAGACTTATCCA 57.289 33.333 0.00 0.00 0.00 3.41
298 299 9.884814 AAGACCTTAGTACATAGACTTATCCAT 57.115 33.333 0.00 0.00 0.00 3.41
299 300 9.523168 AGACCTTAGTACATAGACTTATCCATC 57.477 37.037 0.00 0.00 0.00 3.51
300 301 9.298250 GACCTTAGTACATAGACTTATCCATCA 57.702 37.037 0.00 0.00 0.00 3.07
507 508 2.010145 TAGCCTTCATGCAAGTCGTC 57.990 50.000 0.00 0.00 0.00 4.20
508 509 0.322975 AGCCTTCATGCAAGTCGTCT 59.677 50.000 0.00 0.00 0.00 4.18
509 510 1.160137 GCCTTCATGCAAGTCGTCTT 58.840 50.000 0.00 0.00 0.00 3.01
510 511 1.537202 GCCTTCATGCAAGTCGTCTTT 59.463 47.619 0.00 0.00 0.00 2.52
511 512 2.666619 GCCTTCATGCAAGTCGTCTTTG 60.667 50.000 0.00 0.00 0.00 2.77
1082 1577 1.601914 GCCGGCCTTGTTTTACTTGTG 60.602 52.381 18.11 0.00 0.00 3.33
1101 1596 1.153061 TGAGGTGACTGAGGACGGT 59.847 57.895 0.00 0.00 44.43 4.83
1238 1733 2.241160 TGCTGTGCAGGTCATCAATTT 58.759 42.857 1.11 0.00 33.32 1.82
1239 1734 2.629137 TGCTGTGCAGGTCATCAATTTT 59.371 40.909 1.11 0.00 33.32 1.82
1240 1735 3.069872 TGCTGTGCAGGTCATCAATTTTT 59.930 39.130 1.11 0.00 33.32 1.94
1259 1754 5.461032 TTTTTGCAACGAATCTATGGGTT 57.539 34.783 0.00 0.00 0.00 4.11
1260 1755 4.695217 TTTGCAACGAATCTATGGGTTC 57.305 40.909 0.00 0.00 0.00 3.62
1266 1761 3.925688 CGAATCTATGGGTTCGTTGTG 57.074 47.619 15.62 0.00 41.52 3.33
1267 1762 2.030457 CGAATCTATGGGTTCGTTGTGC 59.970 50.000 15.62 0.00 41.52 4.57
1336 1831 0.461870 TGCTGTTCTTGTCGCTGTGT 60.462 50.000 0.00 0.00 0.00 3.72
1439 1934 6.038936 CGGGGAACGTTAGATTGGAATTTATT 59.961 38.462 0.00 0.00 37.93 1.40
1480 1975 5.615544 GCATCCATGCGTAATGTGTAGATTC 60.616 44.000 0.00 0.00 44.67 2.52
1726 2221 1.767759 CCAGGATTTTAGGTGGGCTG 58.232 55.000 0.00 0.00 0.00 4.85
1820 2315 7.308589 GCTCTTGCTATCTCAACCTTGTTTTTA 60.309 37.037 0.00 0.00 36.03 1.52
1998 2493 0.813821 GCATTTCCAGTGCCCTCTTC 59.186 55.000 0.00 0.00 36.61 2.87
2154 2649 6.017275 GGCATGTCCATCTTTAGATTTCTCTG 60.017 42.308 0.00 0.00 31.21 3.35
2337 2832 2.851798 GCTCTTGTGCCTCTTCCTG 58.148 57.895 0.00 0.00 0.00 3.86
2441 2936 1.720694 CTCTTCCTCGTCCCTCTCGC 61.721 65.000 0.00 0.00 0.00 5.03
2459 2954 4.974275 TCTCGCCGTAAAAATCTTATCTCG 59.026 41.667 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.099905 CCAACTCTCCTAGTGTCATCCA 58.900 50.000 0.00 0.00 38.88 3.41
1 2 2.432510 CCCAACTCTCCTAGTGTCATCC 59.567 54.545 0.00 0.00 38.88 3.51
2 3 3.131400 GTCCCAACTCTCCTAGTGTCATC 59.869 52.174 0.00 0.00 38.88 2.92
3 4 3.100671 GTCCCAACTCTCCTAGTGTCAT 58.899 50.000 0.00 0.00 38.88 3.06
4 5 2.158370 TGTCCCAACTCTCCTAGTGTCA 60.158 50.000 0.00 0.00 38.88 3.58
5 6 2.526432 TGTCCCAACTCTCCTAGTGTC 58.474 52.381 0.00 0.00 38.88 3.67
6 7 2.696526 TGTCCCAACTCTCCTAGTGT 57.303 50.000 0.00 0.00 38.88 3.55
7 8 4.559862 AATTGTCCCAACTCTCCTAGTG 57.440 45.455 0.00 0.00 38.88 2.74
8 9 5.561679 GAAAATTGTCCCAACTCTCCTAGT 58.438 41.667 0.00 0.00 41.49 2.57
9 10 4.631813 CGAAAATTGTCCCAACTCTCCTAG 59.368 45.833 0.00 0.00 0.00 3.02
10 11 4.041198 ACGAAAATTGTCCCAACTCTCCTA 59.959 41.667 0.00 0.00 0.00 2.94
11 12 3.181443 ACGAAAATTGTCCCAACTCTCCT 60.181 43.478 0.00 0.00 0.00 3.69
12 13 3.146847 ACGAAAATTGTCCCAACTCTCC 58.853 45.455 0.00 0.00 0.00 3.71
13 14 4.537015 CAACGAAAATTGTCCCAACTCTC 58.463 43.478 0.00 0.00 0.00 3.20
14 15 3.317993 CCAACGAAAATTGTCCCAACTCT 59.682 43.478 0.00 0.00 0.00 3.24
15 16 3.067601 ACCAACGAAAATTGTCCCAACTC 59.932 43.478 0.00 0.00 0.00 3.01
16 17 3.028130 ACCAACGAAAATTGTCCCAACT 58.972 40.909 0.00 0.00 0.00 3.16
17 18 3.446310 ACCAACGAAAATTGTCCCAAC 57.554 42.857 0.00 0.00 0.00 3.77
18 19 4.473477 AAACCAACGAAAATTGTCCCAA 57.527 36.364 0.00 0.00 0.00 4.12
19 20 5.793030 ATAAACCAACGAAAATTGTCCCA 57.207 34.783 0.00 0.00 0.00 4.37
20 21 6.926826 AGAAATAAACCAACGAAAATTGTCCC 59.073 34.615 0.00 0.00 0.00 4.46
21 22 7.650104 TGAGAAATAAACCAACGAAAATTGTCC 59.350 33.333 0.00 0.00 0.00 4.02
22 23 8.476925 GTGAGAAATAAACCAACGAAAATTGTC 58.523 33.333 0.00 0.00 0.00 3.18
23 24 7.976734 TGTGAGAAATAAACCAACGAAAATTGT 59.023 29.630 0.00 0.00 0.00 2.71
24 25 8.265998 GTGTGAGAAATAAACCAACGAAAATTG 58.734 33.333 0.00 0.00 0.00 2.32
25 26 7.976734 TGTGTGAGAAATAAACCAACGAAAATT 59.023 29.630 0.00 0.00 0.00 1.82
26 27 7.484975 TGTGTGAGAAATAAACCAACGAAAAT 58.515 30.769 0.00 0.00 0.00 1.82
27 28 6.853720 TGTGTGAGAAATAAACCAACGAAAA 58.146 32.000 0.00 0.00 0.00 2.29
28 29 6.438259 TGTGTGAGAAATAAACCAACGAAA 57.562 33.333 0.00 0.00 0.00 3.46
29 30 6.438259 TTGTGTGAGAAATAAACCAACGAA 57.562 33.333 0.00 0.00 0.00 3.85
30 31 6.438259 TTTGTGTGAGAAATAAACCAACGA 57.562 33.333 0.00 0.00 0.00 3.85
31 32 6.345723 GCATTTGTGTGAGAAATAAACCAACG 60.346 38.462 0.00 0.00 0.00 4.10
32 33 6.073819 GGCATTTGTGTGAGAAATAAACCAAC 60.074 38.462 0.00 0.00 0.00 3.77
33 34 5.988561 GGCATTTGTGTGAGAAATAAACCAA 59.011 36.000 0.00 0.00 0.00 3.67
34 35 5.069648 TGGCATTTGTGTGAGAAATAAACCA 59.930 36.000 0.00 0.00 0.00 3.67
35 36 5.537188 TGGCATTTGTGTGAGAAATAAACC 58.463 37.500 0.00 0.00 0.00 3.27
36 37 6.401367 GCATGGCATTTGTGTGAGAAATAAAC 60.401 38.462 0.00 0.00 0.00 2.01
37 38 5.638657 GCATGGCATTTGTGTGAGAAATAAA 59.361 36.000 0.00 0.00 0.00 1.40
38 39 5.170021 GCATGGCATTTGTGTGAGAAATAA 58.830 37.500 0.00 0.00 0.00 1.40
39 40 4.381825 GGCATGGCATTTGTGTGAGAAATA 60.382 41.667 15.47 0.00 0.00 1.40
40 41 3.592059 GCATGGCATTTGTGTGAGAAAT 58.408 40.909 0.00 0.00 0.00 2.17
41 42 2.288948 GGCATGGCATTTGTGTGAGAAA 60.289 45.455 15.47 0.00 0.00 2.52
42 43 1.273048 GGCATGGCATTTGTGTGAGAA 59.727 47.619 15.47 0.00 0.00 2.87
43 44 0.889994 GGCATGGCATTTGTGTGAGA 59.110 50.000 15.47 0.00 0.00 3.27
44 45 0.604073 TGGCATGGCATTTGTGTGAG 59.396 50.000 19.43 0.00 0.00 3.51
45 46 1.046204 TTGGCATGGCATTTGTGTGA 58.954 45.000 23.96 1.89 0.00 3.58
46 47 1.149987 GTTGGCATGGCATTTGTGTG 58.850 50.000 23.96 0.00 0.00 3.82
47 48 0.035176 GGTTGGCATGGCATTTGTGT 59.965 50.000 23.96 0.00 0.00 3.72
48 49 0.322322 AGGTTGGCATGGCATTTGTG 59.678 50.000 23.96 0.00 0.00 3.33
49 50 0.322322 CAGGTTGGCATGGCATTTGT 59.678 50.000 23.96 5.46 0.00 2.83
50 51 0.609151 TCAGGTTGGCATGGCATTTG 59.391 50.000 23.96 19.63 0.00 2.32
51 52 0.899720 CTCAGGTTGGCATGGCATTT 59.100 50.000 23.96 8.75 0.00 2.32
52 53 0.974010 CCTCAGGTTGGCATGGCATT 60.974 55.000 23.96 9.13 0.00 3.56
53 54 1.380785 CCTCAGGTTGGCATGGCAT 60.381 57.895 23.96 5.26 0.00 4.40
54 55 2.036098 CCTCAGGTTGGCATGGCA 59.964 61.111 19.43 19.43 0.00 4.92
55 56 2.757099 CCCTCAGGTTGGCATGGC 60.757 66.667 13.29 13.29 0.00 4.40
56 57 2.043652 CCCCTCAGGTTGGCATGG 60.044 66.667 0.00 0.00 0.00 3.66
65 66 0.623324 TGTATCCCCAACCCCTCAGG 60.623 60.000 0.00 0.00 43.78 3.86
66 67 1.522900 ATGTATCCCCAACCCCTCAG 58.477 55.000 0.00 0.00 0.00 3.35
67 68 2.021441 AGTATGTATCCCCAACCCCTCA 60.021 50.000 0.00 0.00 0.00 3.86
68 69 2.702748 AGTATGTATCCCCAACCCCTC 58.297 52.381 0.00 0.00 0.00 4.30
69 70 2.910360 AGTATGTATCCCCAACCCCT 57.090 50.000 0.00 0.00 0.00 4.79
70 71 5.191124 CCTATAAGTATGTATCCCCAACCCC 59.809 48.000 0.00 0.00 0.00 4.95
71 72 5.338953 GCCTATAAGTATGTATCCCCAACCC 60.339 48.000 0.00 0.00 0.00 4.11
72 73 5.487845 AGCCTATAAGTATGTATCCCCAACC 59.512 44.000 0.00 0.00 0.00 3.77
73 74 6.407202 CAGCCTATAAGTATGTATCCCCAAC 58.593 44.000 0.00 0.00 0.00 3.77
74 75 5.045869 GCAGCCTATAAGTATGTATCCCCAA 60.046 44.000 0.00 0.00 0.00 4.12
75 76 4.469945 GCAGCCTATAAGTATGTATCCCCA 59.530 45.833 0.00 0.00 0.00 4.96
76 77 4.717280 AGCAGCCTATAAGTATGTATCCCC 59.283 45.833 0.00 0.00 0.00 4.81
77 78 5.941555 AGCAGCCTATAAGTATGTATCCC 57.058 43.478 0.00 0.00 0.00 3.85
78 79 6.508777 GCTAGCAGCCTATAAGTATGTATCC 58.491 44.000 10.63 0.00 34.48 2.59
97 98 3.079237 GCATATGCTTGGCTGGCTAGC 62.079 57.143 25.85 25.85 42.80 3.42
98 99 0.879765 GCATATGCTTGGCTGGCTAG 59.120 55.000 20.64 8.24 38.21 3.42
99 100 3.025924 GCATATGCTTGGCTGGCTA 57.974 52.632 20.64 0.00 38.21 3.93
100 101 3.851955 GCATATGCTTGGCTGGCT 58.148 55.556 20.64 0.00 38.21 4.75
111 112 9.518906 CATCTTAGACTAGCATCTTAGCATATG 57.481 37.037 0.00 0.00 36.85 1.78
112 113 8.196771 GCATCTTAGACTAGCATCTTAGCATAT 58.803 37.037 0.00 0.00 36.85 1.78
113 114 7.395772 AGCATCTTAGACTAGCATCTTAGCATA 59.604 37.037 6.06 0.00 36.85 3.14
114 115 6.211184 AGCATCTTAGACTAGCATCTTAGCAT 59.789 38.462 6.06 0.00 36.85 3.79
115 116 5.538053 AGCATCTTAGACTAGCATCTTAGCA 59.462 40.000 6.06 0.00 36.85 3.49
116 117 5.863397 CAGCATCTTAGACTAGCATCTTAGC 59.137 44.000 6.06 0.00 0.00 3.09
117 118 5.863397 GCAGCATCTTAGACTAGCATCTTAG 59.137 44.000 6.06 0.00 0.00 2.18
118 119 5.538053 AGCAGCATCTTAGACTAGCATCTTA 59.462 40.000 0.00 0.00 0.00 2.10
119 120 4.344679 AGCAGCATCTTAGACTAGCATCTT 59.655 41.667 0.00 0.00 0.00 2.40
120 121 3.896888 AGCAGCATCTTAGACTAGCATCT 59.103 43.478 0.00 0.00 0.00 2.90
121 122 4.255833 AGCAGCATCTTAGACTAGCATC 57.744 45.455 0.00 0.00 0.00 3.91
122 123 5.538053 TCTTAGCAGCATCTTAGACTAGCAT 59.462 40.000 0.00 0.00 0.00 3.79
123 124 4.889995 TCTTAGCAGCATCTTAGACTAGCA 59.110 41.667 0.00 0.00 0.00 3.49
124 125 5.446143 TCTTAGCAGCATCTTAGACTAGC 57.554 43.478 0.00 0.00 0.00 3.42
125 126 5.863397 GCATCTTAGCAGCATCTTAGACTAG 59.137 44.000 0.00 0.00 0.00 2.57
126 127 5.279206 GGCATCTTAGCAGCATCTTAGACTA 60.279 44.000 0.00 0.00 35.83 2.59
127 128 4.502950 GGCATCTTAGCAGCATCTTAGACT 60.503 45.833 0.00 0.00 35.83 3.24
128 129 3.745458 GGCATCTTAGCAGCATCTTAGAC 59.255 47.826 0.00 0.00 35.83 2.59
129 130 3.389002 TGGCATCTTAGCAGCATCTTAGA 59.611 43.478 0.00 0.00 35.83 2.10
130 131 3.736720 TGGCATCTTAGCAGCATCTTAG 58.263 45.455 0.00 0.00 35.83 2.18
131 132 3.135348 ACTGGCATCTTAGCAGCATCTTA 59.865 43.478 0.00 0.00 35.83 2.10
132 133 2.092538 ACTGGCATCTTAGCAGCATCTT 60.093 45.455 0.00 0.00 35.83 2.40
133 134 1.489649 ACTGGCATCTTAGCAGCATCT 59.510 47.619 0.00 0.00 35.83 2.90
134 135 1.872313 GACTGGCATCTTAGCAGCATC 59.128 52.381 0.00 0.00 35.83 3.91
135 136 1.489649 AGACTGGCATCTTAGCAGCAT 59.510 47.619 0.00 0.00 35.83 3.79
136 137 0.907486 AGACTGGCATCTTAGCAGCA 59.093 50.000 0.00 0.00 35.83 4.41
137 138 2.898729 TAGACTGGCATCTTAGCAGC 57.101 50.000 5.07 0.00 35.83 5.25
138 139 4.662468 TCTTAGACTGGCATCTTAGCAG 57.338 45.455 5.07 0.00 35.83 4.24
139 140 4.741837 GCATCTTAGACTGGCATCTTAGCA 60.742 45.833 5.07 0.00 35.83 3.49
140 141 3.745458 GCATCTTAGACTGGCATCTTAGC 59.255 47.826 5.07 0.00 0.00 3.09
141 142 5.212532 AGCATCTTAGACTGGCATCTTAG 57.787 43.478 5.07 5.92 0.00 2.18
142 143 5.835819 ACTAGCATCTTAGACTGGCATCTTA 59.164 40.000 5.07 0.00 0.00 2.10
143 144 4.653341 ACTAGCATCTTAGACTGGCATCTT 59.347 41.667 5.07 0.00 0.00 2.40
144 145 4.222336 ACTAGCATCTTAGACTGGCATCT 58.778 43.478 5.42 0.00 0.00 2.90
145 146 4.280677 AGACTAGCATCTTAGACTGGCATC 59.719 45.833 5.42 0.00 0.00 3.91
146 147 4.222336 AGACTAGCATCTTAGACTGGCAT 58.778 43.478 5.42 0.00 0.00 4.40
147 148 3.636679 AGACTAGCATCTTAGACTGGCA 58.363 45.455 5.42 0.00 0.00 4.92
148 149 5.533154 TCTTAGACTAGCATCTTAGACTGGC 59.467 44.000 0.00 0.00 31.19 4.85
149 150 7.592938 CATCTTAGACTAGCATCTTAGACTGG 58.407 42.308 2.27 0.00 37.24 4.00
150 151 7.040478 AGCATCTTAGACTAGCATCTTAGACTG 60.040 40.741 2.27 4.18 37.24 3.51
151 152 7.004086 AGCATCTTAGACTAGCATCTTAGACT 58.996 38.462 2.27 0.00 37.24 3.24
152 153 7.214467 AGCATCTTAGACTAGCATCTTAGAC 57.786 40.000 2.27 0.00 37.24 2.59
153 154 9.173021 GATAGCATCTTAGACTAGCATCTTAGA 57.827 37.037 2.62 2.62 38.40 2.10
154 155 8.405531 GGATAGCATCTTAGACTAGCATCTTAG 58.594 40.741 6.06 0.00 0.00 2.18
155 156 8.112822 AGGATAGCATCTTAGACTAGCATCTTA 58.887 37.037 6.06 0.00 0.00 2.10
156 157 6.953520 AGGATAGCATCTTAGACTAGCATCTT 59.046 38.462 6.06 2.25 0.00 2.40
157 158 6.493166 AGGATAGCATCTTAGACTAGCATCT 58.507 40.000 6.06 0.00 0.00 2.90
158 159 6.773976 AGGATAGCATCTTAGACTAGCATC 57.226 41.667 6.06 6.52 0.00 3.91
159 160 7.893302 AGTTAGGATAGCATCTTAGACTAGCAT 59.107 37.037 6.06 0.00 0.00 3.79
160 161 7.175816 CAGTTAGGATAGCATCTTAGACTAGCA 59.824 40.741 6.06 0.00 0.00 3.49
161 162 7.535139 CAGTTAGGATAGCATCTTAGACTAGC 58.465 42.308 0.00 0.00 0.00 3.42
162 163 7.362574 GGCAGTTAGGATAGCATCTTAGACTAG 60.363 44.444 0.00 0.00 0.00 2.57
163 164 6.434652 GGCAGTTAGGATAGCATCTTAGACTA 59.565 42.308 0.00 0.00 0.00 2.59
164 165 5.245075 GGCAGTTAGGATAGCATCTTAGACT 59.755 44.000 0.00 0.00 0.00 3.24
165 166 5.011125 TGGCAGTTAGGATAGCATCTTAGAC 59.989 44.000 0.00 0.00 0.00 2.59
166 167 5.147767 TGGCAGTTAGGATAGCATCTTAGA 58.852 41.667 0.00 0.00 0.00 2.10
167 168 5.011533 ACTGGCAGTTAGGATAGCATCTTAG 59.988 44.000 15.88 0.00 0.00 2.18
168 169 4.901849 ACTGGCAGTTAGGATAGCATCTTA 59.098 41.667 15.88 0.00 0.00 2.10
169 170 3.713764 ACTGGCAGTTAGGATAGCATCTT 59.286 43.478 15.88 0.00 0.00 2.40
170 171 3.312890 ACTGGCAGTTAGGATAGCATCT 58.687 45.455 15.88 0.00 0.00 2.90
171 172 3.556004 GGACTGGCAGTTAGGATAGCATC 60.556 52.174 22.98 3.76 0.00 3.91
172 173 2.370189 GGACTGGCAGTTAGGATAGCAT 59.630 50.000 22.98 0.00 0.00 3.79
173 174 1.762957 GGACTGGCAGTTAGGATAGCA 59.237 52.381 22.98 0.00 0.00 3.49
174 175 2.043227 AGGACTGGCAGTTAGGATAGC 58.957 52.381 22.98 5.86 0.00 2.97
175 176 3.706594 TCAAGGACTGGCAGTTAGGATAG 59.293 47.826 22.98 8.57 0.00 2.08
176 177 3.719871 TCAAGGACTGGCAGTTAGGATA 58.280 45.455 22.98 3.57 0.00 2.59
177 178 2.551270 TCAAGGACTGGCAGTTAGGAT 58.449 47.619 22.98 4.13 0.00 3.24
178 179 2.024176 TCAAGGACTGGCAGTTAGGA 57.976 50.000 22.98 13.97 0.00 2.94
179 180 2.636830 CATCAAGGACTGGCAGTTAGG 58.363 52.381 22.98 11.87 0.00 2.69
180 181 2.026822 ACCATCAAGGACTGGCAGTTAG 60.027 50.000 22.98 11.85 41.22 2.34
181 182 1.985159 ACCATCAAGGACTGGCAGTTA 59.015 47.619 22.98 5.86 41.22 2.24
182 183 0.773644 ACCATCAAGGACTGGCAGTT 59.226 50.000 22.98 3.34 41.22 3.16
183 184 0.326264 GACCATCAAGGACTGGCAGT 59.674 55.000 22.26 22.26 41.22 4.40
184 185 0.325933 TGACCATCAAGGACTGGCAG 59.674 55.000 14.16 14.16 41.22 4.85
185 186 0.325933 CTGACCATCAAGGACTGGCA 59.674 55.000 0.00 0.00 41.22 4.92
186 187 0.393537 CCTGACCATCAAGGACTGGC 60.394 60.000 0.00 0.00 42.22 4.85
187 188 0.254178 CCCTGACCATCAAGGACTGG 59.746 60.000 0.00 0.00 45.91 4.00
188 189 1.279496 TCCCTGACCATCAAGGACTG 58.721 55.000 0.00 0.00 41.22 3.51
189 190 2.277008 ATCCCTGACCATCAAGGACT 57.723 50.000 0.00 0.00 39.61 3.85
190 191 2.507471 AGAATCCCTGACCATCAAGGAC 59.493 50.000 0.00 0.00 39.61 3.85
191 192 2.850833 AGAATCCCTGACCATCAAGGA 58.149 47.619 0.00 0.00 40.93 3.36
192 193 4.263243 GGATAGAATCCCTGACCATCAAGG 60.263 50.000 0.00 0.00 43.88 3.61
193 194 4.904241 GGATAGAATCCCTGACCATCAAG 58.096 47.826 0.00 0.00 43.88 3.02
194 195 4.982241 GGATAGAATCCCTGACCATCAA 57.018 45.455 0.00 0.00 43.88 2.57
206 207 5.059833 CCTTGTGGCAGTTAGGATAGAATC 58.940 45.833 3.95 0.00 0.00 2.52
207 208 4.721776 TCCTTGTGGCAGTTAGGATAGAAT 59.278 41.667 7.81 0.00 32.00 2.40
208 209 4.081087 GTCCTTGTGGCAGTTAGGATAGAA 60.081 45.833 13.40 0.00 38.92 2.10
209 210 3.451178 GTCCTTGTGGCAGTTAGGATAGA 59.549 47.826 13.40 0.00 38.92 1.98
210 211 3.432326 GGTCCTTGTGGCAGTTAGGATAG 60.432 52.174 13.40 0.00 38.92 2.08
211 212 2.504175 GGTCCTTGTGGCAGTTAGGATA 59.496 50.000 13.40 0.00 38.92 2.59
212 213 1.282157 GGTCCTTGTGGCAGTTAGGAT 59.718 52.381 13.40 0.00 38.92 3.24
213 214 0.690762 GGTCCTTGTGGCAGTTAGGA 59.309 55.000 7.81 7.81 34.50 2.94
214 215 0.400213 TGGTCCTTGTGGCAGTTAGG 59.600 55.000 0.00 0.00 0.00 2.69
215 216 2.086869 CATGGTCCTTGTGGCAGTTAG 58.913 52.381 0.00 0.00 0.00 2.34
216 217 1.423541 ACATGGTCCTTGTGGCAGTTA 59.576 47.619 9.54 0.00 0.00 2.24
217 218 0.185901 ACATGGTCCTTGTGGCAGTT 59.814 50.000 9.54 0.00 0.00 3.16
218 219 0.538057 CACATGGTCCTTGTGGCAGT 60.538 55.000 24.03 0.00 40.60 4.40
219 220 1.870055 GCACATGGTCCTTGTGGCAG 61.870 60.000 29.47 12.39 43.69 4.85
220 221 1.902918 GCACATGGTCCTTGTGGCA 60.903 57.895 29.47 0.00 43.69 4.92
221 222 1.604593 AGCACATGGTCCTTGTGGC 60.605 57.895 29.47 22.98 43.69 5.01
222 223 1.870055 GCAGCACATGGTCCTTGTGG 61.870 60.000 29.47 19.17 43.69 4.17
223 224 1.174078 TGCAGCACATGGTCCTTGTG 61.174 55.000 26.31 26.31 45.74 3.33
224 225 0.892358 CTGCAGCACATGGTCCTTGT 60.892 55.000 0.00 4.56 0.00 3.16
225 226 1.880894 CTGCAGCACATGGTCCTTG 59.119 57.895 0.00 3.21 0.00 3.61
226 227 1.975407 GCTGCAGCACATGGTCCTT 60.975 57.895 33.36 0.00 41.59 3.36
227 228 2.360852 GCTGCAGCACATGGTCCT 60.361 61.111 33.36 0.00 41.59 3.85
228 229 3.446570 GGCTGCAGCACATGGTCC 61.447 66.667 37.63 15.84 44.36 4.46
229 230 1.808531 TTTGGCTGCAGCACATGGTC 61.809 55.000 37.63 20.06 44.36 4.02
230 231 1.812686 CTTTGGCTGCAGCACATGGT 61.813 55.000 37.63 0.00 44.36 3.55
231 232 1.080093 CTTTGGCTGCAGCACATGG 60.080 57.895 37.63 22.16 44.36 3.66
232 233 1.080093 CCTTTGGCTGCAGCACATG 60.080 57.895 37.63 23.70 44.36 3.21
233 234 1.228644 TCCTTTGGCTGCAGCACAT 60.229 52.632 37.63 0.00 44.36 3.21
234 235 2.195411 TCCTTTGGCTGCAGCACA 59.805 55.556 37.63 28.84 44.36 4.57
235 236 2.647297 GTCCTTTGGCTGCAGCAC 59.353 61.111 37.63 26.73 44.36 4.40
236 237 2.598394 GGTCCTTTGGCTGCAGCA 60.598 61.111 37.63 22.06 44.36 4.41
237 238 1.980772 ATGGTCCTTTGGCTGCAGC 60.981 57.895 30.88 30.88 41.14 5.25
238 239 0.896940 ACATGGTCCTTTGGCTGCAG 60.897 55.000 10.11 10.11 0.00 4.41
239 240 1.153524 ACATGGTCCTTTGGCTGCA 59.846 52.632 0.50 0.00 0.00 4.41
240 241 1.588082 CACATGGTCCTTTGGCTGC 59.412 57.895 0.00 0.00 0.00 5.25
241 242 0.896940 AGCACATGGTCCTTTGGCTG 60.897 55.000 0.00 0.00 0.00 4.85
242 243 0.896940 CAGCACATGGTCCTTTGGCT 60.897 55.000 0.00 0.00 0.00 4.75
243 244 1.588082 CAGCACATGGTCCTTTGGC 59.412 57.895 0.00 0.00 0.00 4.52
244 245 1.180456 TGCAGCACATGGTCCTTTGG 61.180 55.000 0.00 0.00 0.00 3.28
245 246 0.242825 CTGCAGCACATGGTCCTTTG 59.757 55.000 0.00 0.00 0.00 2.77
246 247 1.530013 GCTGCAGCACATGGTCCTTT 61.530 55.000 33.36 0.00 41.59 3.11
247 248 1.975407 GCTGCAGCACATGGTCCTT 60.975 57.895 33.36 0.00 41.59 3.36
248 249 2.360852 GCTGCAGCACATGGTCCT 60.361 61.111 33.36 0.00 41.59 3.85
249 250 3.446570 GGCTGCAGCACATGGTCC 61.447 66.667 37.63 15.84 44.36 4.46
250 251 3.446570 GGGCTGCAGCACATGGTC 61.447 66.667 37.63 19.48 45.57 4.02
256 257 3.216944 CTTTGTGGGGCTGCAGCAC 62.217 63.158 37.63 35.59 45.53 4.40
257 258 2.913578 CTTTGTGGGGCTGCAGCA 60.914 61.111 37.63 17.28 44.36 4.41
258 259 2.598394 TCTTTGTGGGGCTGCAGC 60.598 61.111 30.88 30.88 41.14 5.25
259 260 2.270986 GGTCTTTGTGGGGCTGCAG 61.271 63.158 10.11 10.11 0.00 4.41
260 261 2.203480 GGTCTTTGTGGGGCTGCA 60.203 61.111 0.50 0.00 0.00 4.41
261 262 0.251165 TAAGGTCTTTGTGGGGCTGC 60.251 55.000 0.00 0.00 0.00 5.25
262 263 1.073923 ACTAAGGTCTTTGTGGGGCTG 59.926 52.381 0.00 0.00 0.00 4.85
263 264 1.446016 ACTAAGGTCTTTGTGGGGCT 58.554 50.000 0.00 0.00 0.00 5.19
264 265 2.039348 TGTACTAAGGTCTTTGTGGGGC 59.961 50.000 7.79 0.00 31.51 5.80
265 266 4.569719 ATGTACTAAGGTCTTTGTGGGG 57.430 45.455 7.79 0.00 31.51 4.96
266 267 6.154706 AGTCTATGTACTAAGGTCTTTGTGGG 59.845 42.308 7.79 0.00 31.51 4.61
267 268 7.171630 AGTCTATGTACTAAGGTCTTTGTGG 57.828 40.000 7.79 0.00 31.51 4.17
270 271 9.968870 GGATAAGTCTATGTACTAAGGTCTTTG 57.031 37.037 0.00 0.00 0.00 2.77
271 272 9.710818 TGGATAAGTCTATGTACTAAGGTCTTT 57.289 33.333 0.00 0.00 0.00 2.52
272 273 9.884814 ATGGATAAGTCTATGTACTAAGGTCTT 57.115 33.333 0.00 3.82 0.00 3.01
273 274 9.523168 GATGGATAAGTCTATGTACTAAGGTCT 57.477 37.037 0.00 0.00 0.00 3.85
274 275 9.298250 TGATGGATAAGTCTATGTACTAAGGTC 57.702 37.037 0.00 0.00 0.00 3.85
275 276 9.080097 GTGATGGATAAGTCTATGTACTAAGGT 57.920 37.037 0.00 0.00 0.00 3.50
276 277 8.524487 GGTGATGGATAAGTCTATGTACTAAGG 58.476 40.741 0.00 0.00 0.00 2.69
277 278 9.303116 AGGTGATGGATAAGTCTATGTACTAAG 57.697 37.037 0.00 0.00 0.00 2.18
278 279 9.656323 AAGGTGATGGATAAGTCTATGTACTAA 57.344 33.333 0.00 0.00 0.00 2.24
279 280 9.298250 GAAGGTGATGGATAAGTCTATGTACTA 57.702 37.037 0.00 0.00 0.00 1.82
280 281 8.007742 AGAAGGTGATGGATAAGTCTATGTACT 58.992 37.037 0.00 0.00 0.00 2.73
281 282 8.184304 AGAAGGTGATGGATAAGTCTATGTAC 57.816 38.462 0.00 0.00 0.00 2.90
282 283 8.783660 AAGAAGGTGATGGATAAGTCTATGTA 57.216 34.615 0.00 0.00 0.00 2.29
283 284 7.202047 GGAAGAAGGTGATGGATAAGTCTATGT 60.202 40.741 0.00 0.00 0.00 2.29
284 285 7.158021 GGAAGAAGGTGATGGATAAGTCTATG 58.842 42.308 0.00 0.00 0.00 2.23
285 286 6.015010 CGGAAGAAGGTGATGGATAAGTCTAT 60.015 42.308 0.00 0.00 0.00 1.98
286 287 5.302059 CGGAAGAAGGTGATGGATAAGTCTA 59.698 44.000 0.00 0.00 0.00 2.59
287 288 4.100189 CGGAAGAAGGTGATGGATAAGTCT 59.900 45.833 0.00 0.00 0.00 3.24
288 289 4.372656 CGGAAGAAGGTGATGGATAAGTC 58.627 47.826 0.00 0.00 0.00 3.01
289 290 3.432326 GCGGAAGAAGGTGATGGATAAGT 60.432 47.826 0.00 0.00 0.00 2.24
290 291 3.134458 GCGGAAGAAGGTGATGGATAAG 58.866 50.000 0.00 0.00 0.00 1.73
291 292 2.158813 GGCGGAAGAAGGTGATGGATAA 60.159 50.000 0.00 0.00 0.00 1.75
292 293 1.416401 GGCGGAAGAAGGTGATGGATA 59.584 52.381 0.00 0.00 0.00 2.59
293 294 0.181350 GGCGGAAGAAGGTGATGGAT 59.819 55.000 0.00 0.00 0.00 3.41
294 295 1.602237 GGCGGAAGAAGGTGATGGA 59.398 57.895 0.00 0.00 0.00 3.41
295 296 1.815421 CGGCGGAAGAAGGTGATGG 60.815 63.158 0.00 0.00 0.00 3.51
296 297 0.673644 AACGGCGGAAGAAGGTGATG 60.674 55.000 13.24 0.00 0.00 3.07
297 298 0.391263 GAACGGCGGAAGAAGGTGAT 60.391 55.000 13.24 0.00 0.00 3.06
298 299 1.005394 GAACGGCGGAAGAAGGTGA 60.005 57.895 13.24 0.00 0.00 4.02
299 300 0.673644 ATGAACGGCGGAAGAAGGTG 60.674 55.000 13.24 0.00 0.00 4.00
300 301 0.391263 GATGAACGGCGGAAGAAGGT 60.391 55.000 13.24 0.00 0.00 3.50
477 478 7.977853 ACTTGCATGAAGGCTAATATTTTTCTG 59.022 33.333 6.60 0.00 35.78 3.02
625 630 9.793245 CAAACTAATACAGAAAGTAAGAACGTG 57.207 33.333 0.00 0.00 36.05 4.49
626 631 9.538508 ACAAACTAATACAGAAAGTAAGAACGT 57.461 29.630 0.00 0.00 36.05 3.99
647 1140 6.327279 ACCCATAAAGCAGTAGAAACAAAC 57.673 37.500 0.00 0.00 0.00 2.93
707 1200 5.703592 AGGTAAACGTCATACAAAATCTGCA 59.296 36.000 12.01 0.00 0.00 4.41
914 1407 4.035017 CGCAGGAACAAAACAAGTGTAAG 58.965 43.478 0.00 0.00 0.00 2.34
1082 1577 1.179814 ACCGTCCTCAGTCACCTCAC 61.180 60.000 0.00 0.00 0.00 3.51
1101 1596 1.777878 TCTACCCCAGCCAAAACAGAA 59.222 47.619 0.00 0.00 0.00 3.02
1238 1733 4.378978 CGAACCCATAGATTCGTTGCAAAA 60.379 41.667 0.00 0.00 42.11 2.44
1239 1734 3.126171 CGAACCCATAGATTCGTTGCAAA 59.874 43.478 0.00 0.00 42.11 3.68
1240 1735 2.675844 CGAACCCATAGATTCGTTGCAA 59.324 45.455 0.00 0.00 42.11 4.08
1241 1736 2.276201 CGAACCCATAGATTCGTTGCA 58.724 47.619 0.00 0.00 42.11 4.08
1247 1742 3.675467 GCACAACGAACCCATAGATTC 57.325 47.619 0.00 0.00 0.00 2.52
1262 1757 4.776795 TCATAGTTGTAGTCTCGCACAA 57.223 40.909 0.00 0.00 32.40 3.33
1263 1758 4.776795 TTCATAGTTGTAGTCTCGCACA 57.223 40.909 0.00 0.00 0.00 4.57
1264 1759 4.026475 GCATTCATAGTTGTAGTCTCGCAC 60.026 45.833 0.00 0.00 0.00 5.34
1265 1760 4.112634 GCATTCATAGTTGTAGTCTCGCA 58.887 43.478 0.00 0.00 0.00 5.10
1266 1761 4.112634 TGCATTCATAGTTGTAGTCTCGC 58.887 43.478 0.00 0.00 0.00 5.03
1267 1762 5.979517 TCATGCATTCATAGTTGTAGTCTCG 59.020 40.000 0.00 0.00 0.00 4.04
1439 1934 0.614812 TGCCATAAGCTGAGAGCACA 59.385 50.000 0.00 0.00 45.56 4.57
1508 2003 3.760580 AGCTCTCAAACAGTAAGCAGT 57.239 42.857 0.00 0.00 35.42 4.40
1726 2221 2.853235 AACAGCCCACCTACACTAAC 57.147 50.000 0.00 0.00 0.00 2.34
2026 2521 9.952188 AGTAAGAAACAAATCTAAAAGAACAGC 57.048 29.630 0.00 0.00 0.00 4.40
2154 2649 2.935849 CAAGAAAGCACCCAAACAAACC 59.064 45.455 0.00 0.00 0.00 3.27
2337 2832 0.524862 TTCTTACGACGAGAGGCACC 59.475 55.000 0.00 0.00 41.50 5.01
2441 2936 4.085210 GCCGACGAGATAAGATTTTTACGG 60.085 45.833 0.00 0.00 38.72 4.02


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

AutoCloner maintained by Alex Coulton.