Multiple sequence alignment - TraesCS2D01G562600

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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 TraesCS2D01G562600 chr2D 100.000 3089 0 0 1 3089 634294863 634297951 0.000000e+00 5705.0
1 TraesCS2D01G562600 chr2D 80.695 259 41 7 66 317 640825065 640825321 3.140000e-45 193.0
2 TraesCS2D01G562600 chr2D 97.727 44 1 0 2649 2692 634284276 634284319 3.300000e-10 76.8
3 TraesCS2D01G562600 chr2B 92.201 2731 134 31 401 3089 777329294 777331987 0.000000e+00 3790.0
4 TraesCS2D01G562600 chr2B 95.918 49 1 1 2649 2696 777305586 777305634 9.180000e-11 78.7
5 TraesCS2D01G562600 chr2A 92.675 2034 103 16 537 2553 779217757 779215753 0.000000e+00 2889.0
6 TraesCS2D01G562600 chr2A 92.027 439 18 8 2636 3057 779215752 779215314 4.410000e-168 601.0
7 TraesCS2D01G562600 chr2A 88.148 135 4 7 421 545 779217934 779217802 1.920000e-32 150.0
8 TraesCS2D01G562600 chr2A 97.727 44 1 0 2649 2692 779269755 779269712 3.300000e-10 76.8
9 TraesCS2D01G562600 chr6A 86.810 326 43 0 1154 1479 302779985 302780310 6.300000e-97 364.0
10 TraesCS2D01G562600 chr6D 90.206 194 19 0 1896 2089 220935752 220935559 1.420000e-63 254.0
11 TraesCS2D01G562600 chr6D 84.541 207 23 8 66 266 321949784 321949987 2.430000e-46 196.0
12 TraesCS2D01G562600 chr5A 82.331 266 33 11 66 321 28657475 28657736 5.190000e-53 219.0
13 TraesCS2D01G562600 chr5A 90.667 75 6 1 2977 3051 174263849 174263922 7.050000e-17 99.0
14 TraesCS2D01G562600 chr1A 82.308 260 34 8 67 317 34979981 34979725 6.710000e-52 215.0
15 TraesCS2D01G562600 chr1A 95.833 48 2 0 2952 2999 5661803 5661850 9.180000e-11 78.7
16 TraesCS2D01G562600 chr4D 82.061 262 32 10 66 317 501151190 501150934 3.120000e-50 209.0
17 TraesCS2D01G562600 chr1B 79.934 304 46 11 26 317 559124943 559125243 3.120000e-50 209.0
18 TraesCS2D01G562600 chr1B 81.298 262 36 7 66 317 503813722 503813464 1.880000e-47 200.0
19 TraesCS2D01G562600 chr5D 81.746 252 33 10 75 317 410443008 410442761 6.760000e-47 198.0
20 TraesCS2D01G562600 chr5B 79.377 257 43 9 66 317 454693382 454693633 4.100000e-39 172.0
21 TraesCS2D01G562600 chr5B 92.857 70 4 1 2952 3020 704167898 704167829 1.960000e-17 100.0
22 TraesCS2D01G562600 chr1D 88.785 107 6 6 2952 3056 42026213 42026315 3.230000e-25 126.0
23 TraesCS2D01G562600 chr7A 96.491 57 2 0 2952 3008 3840436 3840380 9.120000e-16 95.3
24 TraesCS2D01G562600 chr7D 94.231 52 3 0 2957 3008 4006869 4006818 2.550000e-11 80.5
25 TraesCS2D01G562600 chr7D 92.453 53 4 0 2956 3008 638657265 638657213 3.300000e-10 76.8


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 TraesCS2D01G562600 chr2D 634294863 634297951 3088 False 5705.000000 5705 100.000 1 3089 1 chr2D.!!$F2 3088
1 TraesCS2D01G562600 chr2B 777329294 777331987 2693 False 3790.000000 3790 92.201 401 3089 1 chr2B.!!$F2 2688
2 TraesCS2D01G562600 chr2A 779215314 779217934 2620 True 1213.333333 2889 90.950 421 3057 3 chr2A.!!$R2 2636

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
274 275 0.034896 ACTTGTCGCAACCTAGTGGG 59.965 55.0 0.0 0.0 41.89 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2177 0.038744 AAGGGGTGGTGCTCAATCAG 59.961 55.0 0.0 0.0 0.0 2.9 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
19 20 0.886563 AGGCACAGATTTGCTTCTGC 59.113 50.000 10.53 0.00 45.75 4.26
20 21 0.599558 GGCACAGATTTGCTTCTGCA 59.400 50.000 10.53 0.00 45.75 4.41
35 36 3.749064 GCAGTCGTGCCTCTCGGA 61.749 66.667 0.00 0.00 44.72 4.55
36 37 2.962569 CAGTCGTGCCTCTCGGAA 59.037 61.111 0.00 0.00 0.00 4.30
37 38 1.289066 CAGTCGTGCCTCTCGGAAA 59.711 57.895 0.00 0.00 0.00 3.13
38 39 0.734253 CAGTCGTGCCTCTCGGAAAG 60.734 60.000 0.00 0.00 0.00 2.62
39 40 1.446272 GTCGTGCCTCTCGGAAAGG 60.446 63.158 0.00 0.00 36.95 3.11
40 41 2.125512 CGTGCCTCTCGGAAAGGG 60.126 66.667 0.00 0.00 34.26 3.95
41 42 2.646175 CGTGCCTCTCGGAAAGGGA 61.646 63.158 0.00 0.00 34.26 4.20
42 43 1.677552 GTGCCTCTCGGAAAGGGAA 59.322 57.895 0.00 0.00 35.86 3.97
43 44 0.036306 GTGCCTCTCGGAAAGGGAAA 59.964 55.000 0.00 0.00 35.86 3.13
44 45 0.768622 TGCCTCTCGGAAAGGGAAAA 59.231 50.000 0.00 0.00 34.26 2.29
45 46 1.144093 TGCCTCTCGGAAAGGGAAAAA 59.856 47.619 0.00 0.00 34.26 1.94
64 65 4.718940 AAAAATATGCTTCCAGTTCGGG 57.281 40.909 0.00 0.00 34.36 5.14
65 66 3.366052 AAATATGCTTCCAGTTCGGGT 57.634 42.857 0.00 0.00 34.36 5.28
66 67 3.366052 AATATGCTTCCAGTTCGGGTT 57.634 42.857 0.00 0.00 34.36 4.11
67 68 2.871096 TATGCTTCCAGTTCGGGTTT 57.129 45.000 0.00 0.00 34.36 3.27
68 69 1.995376 ATGCTTCCAGTTCGGGTTTT 58.005 45.000 0.00 0.00 34.36 2.43
69 70 1.314730 TGCTTCCAGTTCGGGTTTTC 58.685 50.000 0.00 0.00 34.36 2.29
70 71 0.237498 GCTTCCAGTTCGGGTTTTCG 59.763 55.000 0.00 0.00 34.36 3.46
71 72 1.589803 CTTCCAGTTCGGGTTTTCGT 58.410 50.000 0.00 0.00 34.36 3.85
72 73 2.758009 CTTCCAGTTCGGGTTTTCGTA 58.242 47.619 0.00 0.00 34.36 3.43
73 74 2.443887 TCCAGTTCGGGTTTTCGTAG 57.556 50.000 0.00 0.00 34.36 3.51
74 75 1.962807 TCCAGTTCGGGTTTTCGTAGA 59.037 47.619 0.00 0.00 34.36 2.59
75 76 2.364970 TCCAGTTCGGGTTTTCGTAGAA 59.635 45.455 0.00 0.00 37.18 2.10
76 77 3.132925 CCAGTTCGGGTTTTCGTAGAAA 58.867 45.455 0.00 0.00 45.90 2.52
77 78 3.560896 CCAGTTCGGGTTTTCGTAGAAAA 59.439 43.478 4.07 4.07 45.90 2.29
78 79 4.035441 CCAGTTCGGGTTTTCGTAGAAAAA 59.965 41.667 9.19 0.00 45.90 1.94
103 104 9.755064 AAAAGTTCGTCGAAATCTATTAACATG 57.245 29.630 9.70 0.00 0.00 3.21
104 105 8.697846 AAGTTCGTCGAAATCTATTAACATGA 57.302 30.769 9.70 0.00 0.00 3.07
105 106 8.697846 AGTTCGTCGAAATCTATTAACATGAA 57.302 30.769 9.70 0.00 0.00 2.57
106 107 9.314321 AGTTCGTCGAAATCTATTAACATGAAT 57.686 29.630 9.70 0.00 0.00 2.57
107 108 9.569212 GTTCGTCGAAATCTATTAACATGAATC 57.431 33.333 9.70 0.00 0.00 2.52
108 109 9.529325 TTCGTCGAAATCTATTAACATGAATCT 57.471 29.630 4.91 0.00 0.00 2.40
124 125 9.956640 AACATGAATCTAGTTTTGAAGATCTCT 57.043 29.630 0.00 0.00 0.00 3.10
127 128 9.743057 ATGAATCTAGTTTTGAAGATCTCTACG 57.257 33.333 0.00 0.00 0.00 3.51
128 129 7.702772 TGAATCTAGTTTTGAAGATCTCTACGC 59.297 37.037 0.00 0.00 0.00 4.42
129 130 5.570344 TCTAGTTTTGAAGATCTCTACGCG 58.430 41.667 3.53 3.53 0.00 6.01
130 131 4.436242 AGTTTTGAAGATCTCTACGCGA 57.564 40.909 15.93 0.00 0.00 5.87
131 132 4.416620 AGTTTTGAAGATCTCTACGCGAG 58.583 43.478 15.93 6.12 41.30 5.03
132 133 3.422417 TTTGAAGATCTCTACGCGAGG 57.578 47.619 15.93 4.70 40.30 4.63
133 134 2.327200 TGAAGATCTCTACGCGAGGA 57.673 50.000 15.93 9.48 40.30 3.71
134 135 2.640184 TGAAGATCTCTACGCGAGGAA 58.360 47.619 15.93 2.15 40.30 3.36
135 136 3.215151 TGAAGATCTCTACGCGAGGAAT 58.785 45.455 15.93 6.76 40.30 3.01
136 137 3.251245 TGAAGATCTCTACGCGAGGAATC 59.749 47.826 15.93 14.25 40.30 2.52
137 138 2.156098 AGATCTCTACGCGAGGAATCC 58.844 52.381 15.93 0.00 40.30 3.01
138 139 1.880675 GATCTCTACGCGAGGAATCCA 59.119 52.381 15.93 0.00 40.30 3.41
139 140 1.758936 TCTCTACGCGAGGAATCCAA 58.241 50.000 15.93 0.00 40.30 3.53
140 141 2.307768 TCTCTACGCGAGGAATCCAAT 58.692 47.619 15.93 0.00 40.30 3.16
141 142 3.483421 TCTCTACGCGAGGAATCCAATA 58.517 45.455 15.93 0.00 40.30 1.90
142 143 3.502595 TCTCTACGCGAGGAATCCAATAG 59.497 47.826 15.93 0.00 40.30 1.73
143 144 3.220110 TCTACGCGAGGAATCCAATAGT 58.780 45.455 15.93 0.00 0.00 2.12
144 145 2.225068 ACGCGAGGAATCCAATAGTG 57.775 50.000 15.93 0.00 0.00 2.74
145 146 1.754803 ACGCGAGGAATCCAATAGTGA 59.245 47.619 15.93 0.00 0.00 3.41
146 147 2.167693 ACGCGAGGAATCCAATAGTGAA 59.832 45.455 15.93 0.00 0.00 3.18
147 148 3.194861 CGCGAGGAATCCAATAGTGAAA 58.805 45.455 0.00 0.00 0.00 2.69
148 149 3.621268 CGCGAGGAATCCAATAGTGAAAA 59.379 43.478 0.00 0.00 0.00 2.29
149 150 4.494199 CGCGAGGAATCCAATAGTGAAAAC 60.494 45.833 0.00 0.00 0.00 2.43
150 151 4.494199 GCGAGGAATCCAATAGTGAAAACG 60.494 45.833 0.61 0.00 0.00 3.60
151 152 4.868171 CGAGGAATCCAATAGTGAAAACGA 59.132 41.667 0.61 0.00 0.00 3.85
152 153 5.523916 CGAGGAATCCAATAGTGAAAACGAT 59.476 40.000 0.61 0.00 0.00 3.73
153 154 6.037172 CGAGGAATCCAATAGTGAAAACGATT 59.963 38.462 0.61 0.00 0.00 3.34
154 155 7.321745 AGGAATCCAATAGTGAAAACGATTC 57.678 36.000 0.61 9.31 35.50 2.52
155 156 6.037172 AGGAATCCAATAGTGAAAACGATTCG 59.963 38.462 0.61 4.14 36.55 3.34
156 157 6.036735 GGAATCCAATAGTGAAAACGATTCGA 59.963 38.462 13.95 0.00 36.55 3.71
157 158 5.773239 TCCAATAGTGAAAACGATTCGAC 57.227 39.130 13.95 0.00 0.00 4.20
158 159 5.231702 TCCAATAGTGAAAACGATTCGACA 58.768 37.500 13.95 4.72 0.00 4.35
159 160 5.872617 TCCAATAGTGAAAACGATTCGACAT 59.127 36.000 13.95 0.00 0.00 3.06
160 161 6.370442 TCCAATAGTGAAAACGATTCGACATT 59.630 34.615 13.95 4.38 0.00 2.71
161 162 7.021196 CCAATAGTGAAAACGATTCGACATTT 58.979 34.615 13.95 10.44 0.00 2.32
162 163 7.007367 CCAATAGTGAAAACGATTCGACATTTG 59.993 37.037 13.95 7.64 0.00 2.32
163 164 5.666969 AGTGAAAACGATTCGACATTTGA 57.333 34.783 13.95 2.87 0.00 2.69
164 165 6.055231 AGTGAAAACGATTCGACATTTGAA 57.945 33.333 13.95 0.30 0.00 2.69
165 166 6.668323 AGTGAAAACGATTCGACATTTGAAT 58.332 32.000 13.95 2.30 38.71 2.57
166 167 6.578545 AGTGAAAACGATTCGACATTTGAATG 59.421 34.615 13.95 2.29 42.10 2.67
167 168 5.341993 TGAAAACGATTCGACATTTGAATGC 59.658 36.000 13.95 0.72 40.04 3.56
168 169 4.418013 AACGATTCGACATTTGAATGCA 57.582 36.364 13.95 0.00 40.04 3.96
169 170 3.747193 ACGATTCGACATTTGAATGCAC 58.253 40.909 13.95 0.00 40.04 4.57
170 171 2.772467 CGATTCGACATTTGAATGCACG 59.228 45.455 0.00 13.62 40.04 5.34
171 172 2.610219 TTCGACATTTGAATGCACGG 57.390 45.000 17.14 2.63 40.04 4.94
172 173 1.518325 TCGACATTTGAATGCACGGT 58.482 45.000 17.14 0.00 40.04 4.83
173 174 1.876799 TCGACATTTGAATGCACGGTT 59.123 42.857 17.14 0.00 40.04 4.44
174 175 2.292016 TCGACATTTGAATGCACGGTTT 59.708 40.909 17.14 0.00 40.04 3.27
175 176 2.404693 CGACATTTGAATGCACGGTTTG 59.595 45.455 3.71 0.00 40.04 2.93
176 177 3.637432 GACATTTGAATGCACGGTTTGA 58.363 40.909 3.71 0.00 40.04 2.69
177 178 3.641648 ACATTTGAATGCACGGTTTGAG 58.358 40.909 3.71 0.00 40.04 3.02
178 179 3.317711 ACATTTGAATGCACGGTTTGAGA 59.682 39.130 3.71 0.00 40.04 3.27
179 180 3.624326 TTTGAATGCACGGTTTGAGAG 57.376 42.857 0.00 0.00 0.00 3.20
180 181 2.542020 TGAATGCACGGTTTGAGAGA 57.458 45.000 0.00 0.00 0.00 3.10
181 182 3.057969 TGAATGCACGGTTTGAGAGAT 57.942 42.857 0.00 0.00 0.00 2.75
182 183 4.200838 TGAATGCACGGTTTGAGAGATA 57.799 40.909 0.00 0.00 0.00 1.98
183 184 4.574892 TGAATGCACGGTTTGAGAGATAA 58.425 39.130 0.00 0.00 0.00 1.75
184 185 5.000591 TGAATGCACGGTTTGAGAGATAAA 58.999 37.500 0.00 0.00 0.00 1.40
185 186 5.471797 TGAATGCACGGTTTGAGAGATAAAA 59.528 36.000 0.00 0.00 0.00 1.52
186 187 4.742438 TGCACGGTTTGAGAGATAAAAC 57.258 40.909 0.00 0.00 0.00 2.43
192 193 5.981174 CGGTTTGAGAGATAAAACGTTTGA 58.019 37.500 15.46 7.57 41.77 2.69
193 194 6.423862 CGGTTTGAGAGATAAAACGTTTGAA 58.576 36.000 15.46 6.55 41.77 2.69
194 195 6.908284 CGGTTTGAGAGATAAAACGTTTGAAA 59.092 34.615 15.46 3.84 41.77 2.69
195 196 7.589954 CGGTTTGAGAGATAAAACGTTTGAAAT 59.410 33.333 15.46 8.78 41.77 2.17
196 197 9.887406 GGTTTGAGAGATAAAACGTTTGAAATA 57.113 29.630 15.46 3.32 0.00 1.40
230 231 5.514274 AAAAAGAAACTTTCAGGATGCGA 57.486 34.783 4.34 0.00 34.76 5.10
231 232 4.489679 AAAGAAACTTTCAGGATGCGAC 57.510 40.909 4.34 0.00 34.76 5.19
232 233 3.126001 AGAAACTTTCAGGATGCGACA 57.874 42.857 4.34 0.00 34.76 4.35
233 234 3.476552 AGAAACTTTCAGGATGCGACAA 58.523 40.909 4.34 0.00 34.76 3.18
234 235 3.499918 AGAAACTTTCAGGATGCGACAAG 59.500 43.478 4.34 0.00 34.76 3.16
235 236 2.550830 ACTTTCAGGATGCGACAAGT 57.449 45.000 0.00 0.00 34.76 3.16
236 237 3.678056 ACTTTCAGGATGCGACAAGTA 57.322 42.857 0.00 0.00 34.76 2.24
237 238 3.589988 ACTTTCAGGATGCGACAAGTAG 58.410 45.455 0.00 0.00 34.76 2.57
238 239 2.010145 TTCAGGATGCGACAAGTAGC 57.990 50.000 0.00 0.00 34.76 3.58
239 240 0.179137 TCAGGATGCGACAAGTAGCG 60.179 55.000 1.07 0.00 34.76 4.26
246 247 1.059369 CGACAAGTAGCGCACATGC 59.941 57.895 11.47 5.15 37.78 4.06
247 248 1.625759 CGACAAGTAGCGCACATGCA 61.626 55.000 11.47 0.00 42.21 3.96
248 249 0.095935 GACAAGTAGCGCACATGCAG 59.904 55.000 11.47 0.00 42.21 4.41
249 250 0.603707 ACAAGTAGCGCACATGCAGT 60.604 50.000 11.47 0.00 42.21 4.40
260 261 2.042686 ACATGCAGTGTGACACTTGT 57.957 45.000 16.79 15.16 42.59 3.16
261 262 1.942657 ACATGCAGTGTGACACTTGTC 59.057 47.619 16.79 8.80 42.59 3.18
262 263 1.070376 CATGCAGTGTGACACTTGTCG 60.070 52.381 16.79 5.95 42.59 4.35
271 272 2.150397 GACACTTGTCGCAACCTAGT 57.850 50.000 0.00 0.00 35.12 2.57
272 273 1.792949 GACACTTGTCGCAACCTAGTG 59.207 52.381 5.81 5.81 40.32 2.74
273 274 1.148310 CACTTGTCGCAACCTAGTGG 58.852 55.000 0.00 0.00 35.24 4.00
274 275 0.034896 ACTTGTCGCAACCTAGTGGG 59.965 55.000 0.00 0.00 41.89 4.61
275 276 0.320374 CTTGTCGCAACCTAGTGGGA 59.680 55.000 0.00 0.00 38.06 4.37
276 277 0.759959 TTGTCGCAACCTAGTGGGAA 59.240 50.000 0.00 0.00 41.55 3.97
277 278 0.759959 TGTCGCAACCTAGTGGGAAA 59.240 50.000 0.00 0.00 41.55 3.13
278 279 1.270625 TGTCGCAACCTAGTGGGAAAG 60.271 52.381 0.00 0.00 41.55 2.62
279 280 1.001633 GTCGCAACCTAGTGGGAAAGA 59.998 52.381 0.00 0.00 41.55 2.52
280 281 1.275291 TCGCAACCTAGTGGGAAAGAG 59.725 52.381 0.00 0.00 37.51 2.85
281 282 1.002087 CGCAACCTAGTGGGAAAGAGT 59.998 52.381 0.00 0.00 38.76 3.24
282 283 2.427506 GCAACCTAGTGGGAAAGAGTG 58.572 52.381 0.00 0.00 38.76 3.51
283 284 2.038557 GCAACCTAGTGGGAAAGAGTGA 59.961 50.000 0.00 0.00 38.76 3.41
284 285 3.307762 GCAACCTAGTGGGAAAGAGTGAT 60.308 47.826 0.00 0.00 38.76 3.06
285 286 4.508662 CAACCTAGTGGGAAAGAGTGATC 58.491 47.826 0.00 0.00 38.76 2.92
286 287 4.067944 ACCTAGTGGGAAAGAGTGATCT 57.932 45.455 0.00 0.00 38.76 2.75
287 288 4.430441 ACCTAGTGGGAAAGAGTGATCTT 58.570 43.478 0.00 0.00 38.76 2.40
288 289 4.846940 ACCTAGTGGGAAAGAGTGATCTTT 59.153 41.667 0.00 3.00 38.45 2.52
289 290 5.181748 CCTAGTGGGAAAGAGTGATCTTTG 58.818 45.833 7.91 0.00 39.74 2.77
290 291 3.416156 AGTGGGAAAGAGTGATCTTTGC 58.584 45.455 12.22 12.22 44.04 3.68
291 292 3.149196 GTGGGAAAGAGTGATCTTTGCA 58.851 45.455 19.43 7.19 45.73 4.08
292 293 3.569701 GTGGGAAAGAGTGATCTTTGCAA 59.430 43.478 19.43 9.27 45.73 4.08
293 294 4.037923 GTGGGAAAGAGTGATCTTTGCAAA 59.962 41.667 19.43 12.14 45.73 3.68
294 295 4.648762 TGGGAAAGAGTGATCTTTGCAAAA 59.351 37.500 19.43 5.01 45.73 2.44
295 296 5.305128 TGGGAAAGAGTGATCTTTGCAAAAT 59.695 36.000 19.43 9.59 45.73 1.82
296 297 5.636543 GGGAAAGAGTGATCTTTGCAAAATG 59.363 40.000 19.43 2.54 45.73 2.32
297 298 6.218746 GGAAAGAGTGATCTTTGCAAAATGT 58.781 36.000 13.84 1.81 44.14 2.71
298 299 7.370383 GGAAAGAGTGATCTTTGCAAAATGTA 58.630 34.615 13.84 0.00 44.14 2.29
299 300 8.031277 GGAAAGAGTGATCTTTGCAAAATGTAT 58.969 33.333 13.84 4.67 44.14 2.29
301 302 9.846248 AAAGAGTGATCTTTGCAAAATGTATAC 57.154 29.630 13.84 7.86 38.39 1.47
302 303 7.989826 AGAGTGATCTTTGCAAAATGTATACC 58.010 34.615 13.84 0.07 0.00 2.73
303 304 7.831193 AGAGTGATCTTTGCAAAATGTATACCT 59.169 33.333 13.84 2.11 0.00 3.08
304 305 8.353423 AGTGATCTTTGCAAAATGTATACCTT 57.647 30.769 13.84 0.00 0.00 3.50
305 306 9.461312 AGTGATCTTTGCAAAATGTATACCTTA 57.539 29.630 13.84 0.00 0.00 2.69
312 313 9.509855 TTTGCAAAATGTATACCTTAATTAGCG 57.490 29.630 10.02 0.00 0.00 4.26
313 314 8.439993 TGCAAAATGTATACCTTAATTAGCGA 57.560 30.769 0.00 0.00 0.00 4.93
314 315 9.062524 TGCAAAATGTATACCTTAATTAGCGAT 57.937 29.630 0.00 0.00 0.00 4.58
315 316 9.893305 GCAAAATGTATACCTTAATTAGCGATT 57.107 29.630 0.00 0.00 0.00 3.34
354 355 6.945938 TTTTTAGTGATTTTCCCGTTCTCA 57.054 33.333 0.00 0.00 0.00 3.27
355 356 6.945938 TTTTAGTGATTTTCCCGTTCTCAA 57.054 33.333 0.00 0.00 0.00 3.02
356 357 7.519032 TTTTAGTGATTTTCCCGTTCTCAAT 57.481 32.000 0.00 0.00 0.00 2.57
357 358 7.519032 TTTAGTGATTTTCCCGTTCTCAATT 57.481 32.000 0.00 0.00 0.00 2.32
358 359 7.519032 TTAGTGATTTTCCCGTTCTCAATTT 57.481 32.000 0.00 0.00 0.00 1.82
359 360 6.405278 AGTGATTTTCCCGTTCTCAATTTT 57.595 33.333 0.00 0.00 0.00 1.82
360 361 6.816136 AGTGATTTTCCCGTTCTCAATTTTT 58.184 32.000 0.00 0.00 0.00 1.94
409 410 9.936759 TTTTTAGGCAATTTCCCTTAATTAGTG 57.063 29.630 0.01 0.00 33.88 2.74
414 415 9.487442 AGGCAATTTCCCTTAATTAGTGATTTA 57.513 29.630 0.00 0.00 0.00 1.40
435 436 1.621317 CCTAATTTGTTTGGGGCCGTT 59.379 47.619 0.00 0.00 32.44 4.44
504 515 4.794655 GCTTTCACGTTGGATTGCCTAAAA 60.795 41.667 0.00 0.00 34.31 1.52
564 628 5.982516 ACATGAGTCGAGAAGATTTATCTGC 59.017 40.000 0.00 0.00 37.19 4.26
568 632 5.347342 AGTCGAGAAGATTTATCTGCTGTG 58.653 41.667 4.93 0.00 42.93 3.66
580 644 1.134007 TCTGCTGTGGCCATCCATAAG 60.134 52.381 9.72 3.95 45.62 1.73
723 791 1.878522 CCGTCGCTTTCCCTCGATG 60.879 63.158 0.00 0.00 40.33 3.84
746 814 1.474143 GCCTCCCTCCTCTCAATTTCG 60.474 57.143 0.00 0.00 0.00 3.46
747 815 1.834263 CCTCCCTCCTCTCAATTTCGT 59.166 52.381 0.00 0.00 0.00 3.85
905 986 4.042398 CGATCGAGTATGTGGAAATTCGT 58.958 43.478 10.26 0.00 0.00 3.85
907 988 4.713824 TCGAGTATGTGGAAATTCGTCT 57.286 40.909 0.00 0.00 0.00 4.18
931 1012 2.744494 GCCTGCCTAGAAATCTGGAGTG 60.744 54.545 0.00 0.00 0.00 3.51
961 1045 4.341935 GTTTGATTGTTGTTTTTGCCTGC 58.658 39.130 0.00 0.00 0.00 4.85
977 1061 0.385223 CTGCGTGCTTGTTTCAGAGC 60.385 55.000 0.00 0.00 39.33 4.09
1185 1269 3.414272 GCAGGCGTGCCAATAGAG 58.586 61.111 20.50 0.00 44.72 2.43
1203 1287 2.166664 AGAGTGGGAAGAGCATTACGTC 59.833 50.000 0.00 0.00 0.00 4.34
1224 1308 1.221840 CACGGAGGTTGATCCCAGG 59.778 63.158 0.00 0.00 35.82 4.45
1437 1521 0.605319 TGAACCTGGTGACAATCCGC 60.605 55.000 0.00 0.00 42.06 5.54
1569 1653 1.378514 CCACTACGCCAAGGCCAAT 60.379 57.895 5.01 0.00 37.98 3.16
1587 1671 3.151022 GGCAGGGAGAGGGTCTCG 61.151 72.222 0.00 0.00 44.28 4.04
1593 1677 1.228184 GGAGAGGGTCTCGGCGATA 60.228 63.158 11.27 0.00 44.28 2.92
1635 1719 1.640917 AGACAGACGGGCTTTTCCTA 58.359 50.000 0.00 0.00 34.39 2.94
1800 1884 2.359900 GATCTGTCCGCTGGTTTGATT 58.640 47.619 0.00 0.00 0.00 2.57
1807 1891 0.962356 CGCTGGTTTGATTGGAGGCT 60.962 55.000 0.00 0.00 0.00 4.58
1854 1938 0.169009 GTGAAGGCGGCATTTGTCTC 59.831 55.000 13.08 0.00 0.00 3.36
1911 1995 0.597377 GCAAGAACCTTGCAAACCCG 60.597 55.000 22.33 0.00 44.34 5.28
1942 2026 1.002773 TGCTGAGTGCTGTCATGATGT 59.997 47.619 0.00 0.00 43.37 3.06
1953 2037 1.026182 TCATGATGTTGCGCCACCTC 61.026 55.000 9.38 9.46 0.00 3.85
2046 2130 1.883638 GCTGATCTTGGTGGCAAGTCA 60.884 52.381 0.00 0.00 34.07 3.41
2052 2136 0.948623 TTGGTGGCAAGTCATCGACG 60.949 55.000 0.00 0.00 37.67 5.12
2064 2148 2.159037 GTCATCGACGTCAGACTACACA 59.841 50.000 17.16 0.00 0.00 3.72
2089 2173 2.677836 GCAGTTTGCGGTCATATCTGAA 59.322 45.455 0.00 0.00 31.71 3.02
2090 2174 3.313526 GCAGTTTGCGGTCATATCTGAAT 59.686 43.478 0.00 0.00 31.71 2.57
2091 2175 4.511454 GCAGTTTGCGGTCATATCTGAATA 59.489 41.667 0.00 0.00 31.71 1.75
2092 2176 5.180117 GCAGTTTGCGGTCATATCTGAATAT 59.820 40.000 0.00 0.00 31.71 1.28
2093 2177 6.619446 GCAGTTTGCGGTCATATCTGAATATC 60.619 42.308 0.00 0.00 31.71 1.63
2094 2178 6.648310 CAGTTTGCGGTCATATCTGAATATCT 59.352 38.462 0.00 0.00 31.85 1.98
2095 2179 6.648310 AGTTTGCGGTCATATCTGAATATCTG 59.352 38.462 0.00 0.00 31.85 2.90
2096 2180 5.982890 TGCGGTCATATCTGAATATCTGA 57.017 39.130 0.00 0.00 31.85 3.27
2109 2197 3.498774 ATATCTGATTGAGCACCACCC 57.501 47.619 0.00 0.00 0.00 4.61
2122 2210 0.853530 ACCACCCCTTGCTCTTTCTT 59.146 50.000 0.00 0.00 0.00 2.52
2156 2244 9.579932 TTTATTCCCCAAATTTTGTTTGCTATT 57.420 25.926 8.26 0.00 0.00 1.73
2205 2294 5.331607 CCGTCGAAGAATAATCGTCACATTC 60.332 44.000 0.00 0.00 39.69 2.67
2294 2383 2.863740 TCAGCGCATATAGTTTGTTCGG 59.136 45.455 11.47 0.00 0.00 4.30
2321 2410 4.275936 AGTTGTTGAAGAACTGGATTTCGG 59.724 41.667 6.94 0.00 32.30 4.30
2323 2412 3.813166 TGTTGAAGAACTGGATTTCGGTC 59.187 43.478 0.00 0.00 32.92 4.79
2343 2432 6.815142 TCGGTCTGTAAAAATAAACCTAGCTC 59.185 38.462 0.00 0.00 0.00 4.09
2371 2460 4.130118 CTCTGTTACCTCTGTTGCTGTTT 58.870 43.478 0.00 0.00 0.00 2.83
2372 2461 4.523083 TCTGTTACCTCTGTTGCTGTTTT 58.477 39.130 0.00 0.00 0.00 2.43
2373 2462 4.335315 TCTGTTACCTCTGTTGCTGTTTTG 59.665 41.667 0.00 0.00 0.00 2.44
2374 2463 3.380004 TGTTACCTCTGTTGCTGTTTTGG 59.620 43.478 0.00 0.00 0.00 3.28
2376 2465 1.750778 ACCTCTGTTGCTGTTTTGGTG 59.249 47.619 0.00 0.00 0.00 4.17
2377 2466 1.536709 CCTCTGTTGCTGTTTTGGTGC 60.537 52.381 0.00 0.00 0.00 5.01
2379 2468 0.175302 CTGTTGCTGTTTTGGTGCCA 59.825 50.000 0.00 0.00 0.00 4.92
2382 2471 0.829333 TTGCTGTTTTGGTGCCATGT 59.171 45.000 0.00 0.00 0.00 3.21
2384 2473 0.388659 GCTGTTTTGGTGCCATGTGA 59.611 50.000 0.00 0.00 0.00 3.58
2395 2504 2.482336 GTGCCATGTGATTGTTGTCGTA 59.518 45.455 0.00 0.00 0.00 3.43
2399 2508 4.260375 GCCATGTGATTGTTGTCGTATCTC 60.260 45.833 0.00 0.00 0.00 2.75
2473 2584 2.482721 CCAGTGAATCACCAAACCGTAC 59.517 50.000 10.12 0.00 34.49 3.67
2475 2586 2.105134 AGTGAATCACCAAACCGTACCA 59.895 45.455 10.12 0.00 34.49 3.25
2550 2661 2.235016 CGTTAGCCGGGCGTATGTG 61.235 63.158 14.39 0.00 0.00 3.21
2552 2663 1.142314 TTAGCCGGGCGTATGTGTC 59.858 57.895 14.39 0.00 0.00 3.67
2556 2667 2.488355 CGGGCGTATGTGTCGAGT 59.512 61.111 0.00 0.00 0.00 4.18
2563 2674 3.488721 GGCGTATGTGTCGAGTACTGAAT 60.489 47.826 0.00 0.00 0.00 2.57
2646 2758 3.788434 AAATTCGTTCTGTGCTACACG 57.212 42.857 0.00 0.00 37.14 4.49
2664 2776 2.823829 GACGCCCATCATCAACGGC 61.824 63.158 0.00 0.00 38.07 5.68
2693 2805 1.156645 GGCATGACTCGCATCTGACC 61.157 60.000 0.00 0.00 34.15 4.02
2695 2807 0.179127 CATGACTCGCATCTGACCGT 60.179 55.000 0.00 0.00 34.15 4.83
2767 2887 3.092301 TCCGTCTGTGATTCTGTGAGAT 58.908 45.455 0.00 0.00 0.00 2.75
2786 2906 6.813649 GTGAGATCATTGTTAGTGAACAGCTA 59.186 38.462 0.00 0.00 46.11 3.32
2915 3035 5.603170 ATTTATTGCTCCAGTTTGGGATG 57.397 39.130 0.00 0.00 38.32 3.51
3064 3196 3.376234 ACTGAATTTCATGGATGAGTGCG 59.624 43.478 0.00 0.00 38.19 5.34
3075 3207 1.062587 GATGAGTGCGGTGGAAAATCG 59.937 52.381 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.886563 GCAGAAGCAAATCTGTGCCT 59.113 50.000 13.52 0.00 46.85 4.75
1 2 3.413522 GCAGAAGCAAATCTGTGCC 57.586 52.632 13.52 0.00 46.85 5.01
12 13 2.358003 AGGCACGACTGCAGAAGC 60.358 61.111 23.35 17.07 46.28 3.86
13 14 0.735632 GAGAGGCACGACTGCAGAAG 60.736 60.000 23.35 15.82 46.28 2.85
14 15 1.290324 GAGAGGCACGACTGCAGAA 59.710 57.895 23.35 0.00 46.28 3.02
15 16 2.965783 GAGAGGCACGACTGCAGA 59.034 61.111 23.35 0.00 46.28 4.26
16 17 2.505777 CGAGAGGCACGACTGCAG 60.506 66.667 13.48 13.48 46.28 4.41
43 44 4.086457 ACCCGAACTGGAAGCATATTTTT 58.914 39.130 0.00 0.00 42.00 1.94
44 45 3.697166 ACCCGAACTGGAAGCATATTTT 58.303 40.909 0.00 0.00 42.00 1.82
45 46 3.366052 ACCCGAACTGGAAGCATATTT 57.634 42.857 0.00 0.00 42.00 1.40
46 47 3.366052 AACCCGAACTGGAAGCATATT 57.634 42.857 0.00 0.00 42.00 1.28
47 48 3.366052 AAACCCGAACTGGAAGCATAT 57.634 42.857 0.00 0.00 42.00 1.78
48 49 2.871096 AAACCCGAACTGGAAGCATA 57.129 45.000 0.00 0.00 42.00 3.14
49 50 1.886542 GAAAACCCGAACTGGAAGCAT 59.113 47.619 0.00 0.00 42.00 3.79
50 51 1.314730 GAAAACCCGAACTGGAAGCA 58.685 50.000 0.00 0.00 42.00 3.91
51 52 0.237498 CGAAAACCCGAACTGGAAGC 59.763 55.000 0.00 0.00 42.00 3.86
52 53 1.589803 ACGAAAACCCGAACTGGAAG 58.410 50.000 0.00 0.00 42.00 3.46
53 54 2.364970 TCTACGAAAACCCGAACTGGAA 59.635 45.455 0.00 0.00 42.00 3.53
54 55 1.962807 TCTACGAAAACCCGAACTGGA 59.037 47.619 0.00 0.00 42.00 3.86
55 56 2.443887 TCTACGAAAACCCGAACTGG 57.556 50.000 0.00 0.00 37.55 4.00
56 57 4.799419 TTTTCTACGAAAACCCGAACTG 57.201 40.909 0.00 0.00 0.00 3.16
77 78 9.755064 CATGTTAATAGATTTCGACGAACTTTT 57.245 29.630 10.38 9.03 0.00 2.27
78 79 9.146984 TCATGTTAATAGATTTCGACGAACTTT 57.853 29.630 10.38 2.89 0.00 2.66
79 80 8.697846 TCATGTTAATAGATTTCGACGAACTT 57.302 30.769 10.38 0.41 0.00 2.66
80 81 8.697846 TTCATGTTAATAGATTTCGACGAACT 57.302 30.769 10.38 4.73 0.00 3.01
81 82 9.569212 GATTCATGTTAATAGATTTCGACGAAC 57.431 33.333 10.38 0.00 0.00 3.95
82 83 9.529325 AGATTCATGTTAATAGATTTCGACGAA 57.471 29.630 6.10 6.10 0.00 3.85
98 99 9.956640 AGAGATCTTCAAAACTAGATTCATGTT 57.043 29.630 0.00 0.00 0.00 2.71
101 102 9.743057 CGTAGAGATCTTCAAAACTAGATTCAT 57.257 33.333 0.00 0.00 0.00 2.57
102 103 7.702772 GCGTAGAGATCTTCAAAACTAGATTCA 59.297 37.037 0.00 0.00 0.00 2.57
103 104 7.096803 CGCGTAGAGATCTTCAAAACTAGATTC 60.097 40.741 0.00 0.00 0.00 2.52
104 105 6.693545 CGCGTAGAGATCTTCAAAACTAGATT 59.306 38.462 0.00 0.00 0.00 2.40
105 106 6.038382 TCGCGTAGAGATCTTCAAAACTAGAT 59.962 38.462 5.77 0.00 0.00 1.98
106 107 5.353400 TCGCGTAGAGATCTTCAAAACTAGA 59.647 40.000 5.77 0.00 0.00 2.43
107 108 5.570344 TCGCGTAGAGATCTTCAAAACTAG 58.430 41.667 5.77 0.00 0.00 2.57
108 109 5.556355 TCGCGTAGAGATCTTCAAAACTA 57.444 39.130 5.77 0.00 0.00 2.24
109 110 4.436242 TCGCGTAGAGATCTTCAAAACT 57.564 40.909 5.77 0.00 0.00 2.66
121 122 2.802787 ATTGGATTCCTCGCGTAGAG 57.197 50.000 5.77 0.00 46.44 2.43
122 123 3.004419 CACTATTGGATTCCTCGCGTAGA 59.996 47.826 5.77 0.49 0.00 2.59
123 124 3.004419 TCACTATTGGATTCCTCGCGTAG 59.996 47.826 5.77 1.91 0.00 3.51
124 125 2.953648 TCACTATTGGATTCCTCGCGTA 59.046 45.455 5.77 0.00 0.00 4.42
125 126 1.754803 TCACTATTGGATTCCTCGCGT 59.245 47.619 5.77 0.00 0.00 6.01
126 127 2.509052 TCACTATTGGATTCCTCGCG 57.491 50.000 0.00 0.00 0.00 5.87
127 128 4.494199 CGTTTTCACTATTGGATTCCTCGC 60.494 45.833 3.95 0.00 0.00 5.03
128 129 4.868171 TCGTTTTCACTATTGGATTCCTCG 59.132 41.667 3.95 0.00 0.00 4.63
129 130 6.927294 ATCGTTTTCACTATTGGATTCCTC 57.073 37.500 3.95 0.00 0.00 3.71
130 131 6.037172 CGAATCGTTTTCACTATTGGATTCCT 59.963 38.462 3.95 0.00 36.55 3.36
131 132 6.036735 TCGAATCGTTTTCACTATTGGATTCC 59.963 38.462 1.52 0.00 36.55 3.01
132 133 6.900299 GTCGAATCGTTTTCACTATTGGATTC 59.100 38.462 1.52 0.00 36.55 2.52
133 134 6.370442 TGTCGAATCGTTTTCACTATTGGATT 59.630 34.615 1.52 0.00 29.43 3.01
134 135 5.872617 TGTCGAATCGTTTTCACTATTGGAT 59.127 36.000 1.52 0.00 29.43 3.41
135 136 5.231702 TGTCGAATCGTTTTCACTATTGGA 58.768 37.500 1.52 0.00 0.00 3.53
136 137 5.524511 TGTCGAATCGTTTTCACTATTGG 57.475 39.130 1.52 0.00 0.00 3.16
137 138 7.744276 TCAAATGTCGAATCGTTTTCACTATTG 59.256 33.333 1.52 3.62 0.00 1.90
138 139 7.802738 TCAAATGTCGAATCGTTTTCACTATT 58.197 30.769 1.52 0.00 0.00 1.73
139 140 7.359262 TCAAATGTCGAATCGTTTTCACTAT 57.641 32.000 1.52 0.00 0.00 2.12
140 141 6.772770 TCAAATGTCGAATCGTTTTCACTA 57.227 33.333 1.52 0.00 0.00 2.74
141 142 5.666969 TCAAATGTCGAATCGTTTTCACT 57.333 34.783 1.52 0.00 0.00 3.41
142 143 6.665055 GCATTCAAATGTCGAATCGTTTTCAC 60.665 38.462 1.52 0.00 38.65 3.18
143 144 5.341993 GCATTCAAATGTCGAATCGTTTTCA 59.658 36.000 1.52 0.00 38.65 2.69
144 145 5.341993 TGCATTCAAATGTCGAATCGTTTTC 59.658 36.000 1.52 0.00 38.65 2.29
145 146 5.116983 GTGCATTCAAATGTCGAATCGTTTT 59.883 36.000 1.52 0.00 38.65 2.43
146 147 4.616802 GTGCATTCAAATGTCGAATCGTTT 59.383 37.500 1.52 0.00 38.65 3.60
147 148 4.158384 GTGCATTCAAATGTCGAATCGTT 58.842 39.130 1.52 0.00 38.65 3.85
148 149 3.724716 CGTGCATTCAAATGTCGAATCGT 60.725 43.478 1.52 0.00 38.65 3.73
149 150 2.772467 CGTGCATTCAAATGTCGAATCG 59.228 45.455 0.00 0.00 38.65 3.34
150 151 3.100817 CCGTGCATTCAAATGTCGAATC 58.899 45.455 17.15 0.00 38.65 2.52
151 152 2.487762 ACCGTGCATTCAAATGTCGAAT 59.512 40.909 17.15 0.00 38.65 3.34
152 153 1.876799 ACCGTGCATTCAAATGTCGAA 59.123 42.857 17.15 0.00 38.65 3.71
153 154 1.518325 ACCGTGCATTCAAATGTCGA 58.482 45.000 17.15 0.00 38.65 4.20
154 155 2.330231 AACCGTGCATTCAAATGTCG 57.670 45.000 4.76 9.14 38.65 4.35
155 156 3.637432 TCAAACCGTGCATTCAAATGTC 58.363 40.909 4.76 0.00 38.65 3.06
156 157 3.317711 TCTCAAACCGTGCATTCAAATGT 59.682 39.130 4.76 0.00 38.65 2.71
157 158 3.899734 TCTCAAACCGTGCATTCAAATG 58.100 40.909 0.00 0.00 39.40 2.32
158 159 3.820467 TCTCTCAAACCGTGCATTCAAAT 59.180 39.130 0.00 0.00 0.00 2.32
159 160 3.210227 TCTCTCAAACCGTGCATTCAAA 58.790 40.909 0.00 0.00 0.00 2.69
160 161 2.844946 TCTCTCAAACCGTGCATTCAA 58.155 42.857 0.00 0.00 0.00 2.69
161 162 2.542020 TCTCTCAAACCGTGCATTCA 57.458 45.000 0.00 0.00 0.00 2.57
162 163 5.545658 TTTATCTCTCAAACCGTGCATTC 57.454 39.130 0.00 0.00 0.00 2.67
163 164 5.616866 CGTTTTATCTCTCAAACCGTGCATT 60.617 40.000 0.00 0.00 30.37 3.56
164 165 4.142902 CGTTTTATCTCTCAAACCGTGCAT 60.143 41.667 0.00 0.00 30.37 3.96
165 166 3.185594 CGTTTTATCTCTCAAACCGTGCA 59.814 43.478 0.00 0.00 30.37 4.57
166 167 3.185797 ACGTTTTATCTCTCAAACCGTGC 59.814 43.478 0.00 0.00 30.37 5.34
167 168 4.985044 ACGTTTTATCTCTCAAACCGTG 57.015 40.909 0.00 0.00 30.37 4.94
168 169 5.524646 TCAAACGTTTTATCTCTCAAACCGT 59.475 36.000 11.66 0.00 30.37 4.83
169 170 5.981174 TCAAACGTTTTATCTCTCAAACCG 58.019 37.500 11.66 0.00 30.37 4.44
170 171 8.797266 ATTTCAAACGTTTTATCTCTCAAACC 57.203 30.769 11.66 0.00 30.37 3.27
174 175 9.588774 CGTTTATTTCAAACGTTTTATCTCTCA 57.411 29.630 11.66 0.00 45.45 3.27
208 209 5.163561 TGTCGCATCCTGAAAGTTTCTTTTT 60.164 36.000 16.33 0.00 0.00 1.94
209 210 4.338118 TGTCGCATCCTGAAAGTTTCTTTT 59.662 37.500 16.33 0.00 0.00 2.27
210 211 3.882888 TGTCGCATCCTGAAAGTTTCTTT 59.117 39.130 16.33 0.00 0.00 2.52
211 212 3.476552 TGTCGCATCCTGAAAGTTTCTT 58.523 40.909 16.33 0.00 0.00 2.52
212 213 3.126001 TGTCGCATCCTGAAAGTTTCT 57.874 42.857 16.33 0.00 0.00 2.52
213 214 3.251004 ACTTGTCGCATCCTGAAAGTTTC 59.749 43.478 8.75 8.75 0.00 2.78
214 215 3.214328 ACTTGTCGCATCCTGAAAGTTT 58.786 40.909 0.00 0.00 0.00 2.66
215 216 2.851195 ACTTGTCGCATCCTGAAAGTT 58.149 42.857 0.00 0.00 0.00 2.66
216 217 2.550830 ACTTGTCGCATCCTGAAAGT 57.449 45.000 0.00 0.00 0.00 2.66
217 218 2.349886 GCTACTTGTCGCATCCTGAAAG 59.650 50.000 0.00 0.00 0.00 2.62
218 219 2.346803 GCTACTTGTCGCATCCTGAAA 58.653 47.619 0.00 0.00 0.00 2.69
219 220 1.735700 CGCTACTTGTCGCATCCTGAA 60.736 52.381 0.00 0.00 0.00 3.02
220 221 0.179137 CGCTACTTGTCGCATCCTGA 60.179 55.000 0.00 0.00 0.00 3.86
221 222 2.291843 CGCTACTTGTCGCATCCTG 58.708 57.895 0.00 0.00 0.00 3.86
222 223 4.814900 CGCTACTTGTCGCATCCT 57.185 55.556 0.00 0.00 0.00 3.24
228 229 1.059369 GCATGTGCGCTACTTGTCG 59.941 57.895 9.73 0.00 36.94 4.35
229 230 0.095935 CTGCATGTGCGCTACTTGTC 59.904 55.000 9.73 10.06 45.83 3.18
230 231 0.603707 ACTGCATGTGCGCTACTTGT 60.604 50.000 9.73 0.00 45.83 3.16
231 232 0.179207 CACTGCATGTGCGCTACTTG 60.179 55.000 9.73 14.07 45.83 3.16
232 233 2.165380 CACTGCATGTGCGCTACTT 58.835 52.632 9.73 0.56 45.83 2.24
233 234 3.880591 CACTGCATGTGCGCTACT 58.119 55.556 9.73 0.00 45.83 2.57
241 242 1.942657 GACAAGTGTCACACTGCATGT 59.057 47.619 12.33 12.51 44.62 3.21
242 243 1.070376 CGACAAGTGTCACACTGCATG 60.070 52.381 12.33 8.97 44.62 4.06
243 244 1.220529 CGACAAGTGTCACACTGCAT 58.779 50.000 12.33 0.00 44.62 3.96
244 245 1.428370 GCGACAAGTGTCACACTGCA 61.428 55.000 12.33 0.00 44.62 4.41
245 246 1.276844 GCGACAAGTGTCACACTGC 59.723 57.895 12.33 6.73 44.62 4.40
246 247 1.006086 TTGCGACAAGTGTCACACTG 58.994 50.000 12.33 8.46 44.62 3.66
248 249 0.027586 GGTTGCGACAAGTGTCACAC 59.972 55.000 11.77 0.00 44.99 3.82
249 250 0.107897 AGGTTGCGACAAGTGTCACA 60.108 50.000 11.77 5.22 44.99 3.58
250 251 1.792949 CTAGGTTGCGACAAGTGTCAC 59.207 52.381 11.77 2.53 44.99 3.67
251 252 1.411246 ACTAGGTTGCGACAAGTGTCA 59.589 47.619 11.77 0.00 44.99 3.58
252 253 1.792949 CACTAGGTTGCGACAAGTGTC 59.207 52.381 22.10 1.12 41.47 3.67
253 254 1.540363 CCACTAGGTTGCGACAAGTGT 60.540 52.381 25.57 10.30 38.58 3.55
254 255 1.148310 CCACTAGGTTGCGACAAGTG 58.852 55.000 22.91 22.91 39.31 3.16
255 256 0.034896 CCCACTAGGTTGCGACAAGT 59.965 55.000 6.39 5.98 0.00 3.16
256 257 0.320374 TCCCACTAGGTTGCGACAAG 59.680 55.000 6.39 5.32 36.75 3.16
257 258 0.759959 TTCCCACTAGGTTGCGACAA 59.240 50.000 6.39 0.00 36.75 3.18
258 259 0.759959 TTTCCCACTAGGTTGCGACA 59.240 50.000 6.39 0.00 36.75 4.35
259 260 1.001633 TCTTTCCCACTAGGTTGCGAC 59.998 52.381 0.00 0.00 36.75 5.19
260 261 1.275291 CTCTTTCCCACTAGGTTGCGA 59.725 52.381 0.00 0.00 36.75 5.10
261 262 1.002087 ACTCTTTCCCACTAGGTTGCG 59.998 52.381 0.00 0.00 36.75 4.85
262 263 2.038557 TCACTCTTTCCCACTAGGTTGC 59.961 50.000 0.00 0.00 36.75 4.17
263 264 4.223923 AGATCACTCTTTCCCACTAGGTTG 59.776 45.833 0.00 0.00 36.75 3.77
264 265 4.430441 AGATCACTCTTTCCCACTAGGTT 58.570 43.478 0.00 0.00 36.75 3.50
265 266 4.067944 AGATCACTCTTTCCCACTAGGT 57.932 45.455 0.00 0.00 36.75 3.08
266 267 5.181748 CAAAGATCACTCTTTCCCACTAGG 58.818 45.833 0.00 0.00 46.46 3.02
267 268 4.633565 GCAAAGATCACTCTTTCCCACTAG 59.366 45.833 0.00 0.00 46.46 2.57
268 269 4.041567 TGCAAAGATCACTCTTTCCCACTA 59.958 41.667 0.00 0.00 46.46 2.74
269 270 3.181440 TGCAAAGATCACTCTTTCCCACT 60.181 43.478 0.00 0.00 46.46 4.00
270 271 3.149196 TGCAAAGATCACTCTTTCCCAC 58.851 45.455 0.00 0.00 46.46 4.61
271 272 3.507162 TGCAAAGATCACTCTTTCCCA 57.493 42.857 0.00 0.00 46.46 4.37
272 273 4.853924 TTTGCAAAGATCACTCTTTCCC 57.146 40.909 8.05 0.00 46.46 3.97
273 274 6.218746 ACATTTTGCAAAGATCACTCTTTCC 58.781 36.000 12.41 0.00 46.46 3.13
274 275 8.976986 ATACATTTTGCAAAGATCACTCTTTC 57.023 30.769 12.41 0.00 46.46 2.62
276 277 8.462016 GGTATACATTTTGCAAAGATCACTCTT 58.538 33.333 12.41 0.00 43.71 2.85
277 278 7.831193 AGGTATACATTTTGCAAAGATCACTCT 59.169 33.333 12.41 3.31 0.00 3.24
278 279 7.989826 AGGTATACATTTTGCAAAGATCACTC 58.010 34.615 12.41 3.17 0.00 3.51
279 280 7.944729 AGGTATACATTTTGCAAAGATCACT 57.055 32.000 12.41 2.46 0.00 3.41
286 287 9.509855 CGCTAATTAAGGTATACATTTTGCAAA 57.490 29.630 8.05 8.05 0.00 3.68
287 288 8.894731 TCGCTAATTAAGGTATACATTTTGCAA 58.105 29.630 8.23 0.00 0.00 4.08
288 289 8.439993 TCGCTAATTAAGGTATACATTTTGCA 57.560 30.769 8.23 0.00 0.00 4.08
289 290 9.893305 AATCGCTAATTAAGGTATACATTTTGC 57.107 29.630 8.23 2.88 0.00 3.68
331 332 6.945938 TGAGAACGGGAAAATCACTAAAAA 57.054 33.333 0.00 0.00 0.00 1.94
332 333 6.945938 TTGAGAACGGGAAAATCACTAAAA 57.054 33.333 0.00 0.00 0.00 1.52
333 334 7.519032 AATTGAGAACGGGAAAATCACTAAA 57.481 32.000 0.00 0.00 0.00 1.85
334 335 7.519032 AAATTGAGAACGGGAAAATCACTAA 57.481 32.000 0.00 0.00 0.00 2.24
335 336 7.519032 AAAATTGAGAACGGGAAAATCACTA 57.481 32.000 0.00 0.00 0.00 2.74
336 337 6.405278 AAAATTGAGAACGGGAAAATCACT 57.595 33.333 0.00 0.00 0.00 3.41
383 384 9.936759 CACTAATTAAGGGAAATTGCCTAAAAA 57.063 29.630 6.44 2.56 37.13 1.94
384 385 9.315363 TCACTAATTAAGGGAAATTGCCTAAAA 57.685 29.630 6.44 5.13 37.13 1.52
385 386 8.887264 TCACTAATTAAGGGAAATTGCCTAAA 57.113 30.769 6.44 0.00 37.13 1.85
386 387 9.487442 AATCACTAATTAAGGGAAATTGCCTAA 57.513 29.630 6.44 2.48 42.28 2.69
387 388 9.487442 AAATCACTAATTAAGGGAAATTGCCTA 57.513 29.630 6.44 0.00 42.28 3.93
388 389 7.978099 AATCACTAATTAAGGGAAATTGCCT 57.022 32.000 0.00 0.00 42.28 4.75
389 390 9.529325 GTAAATCACTAATTAAGGGAAATTGCC 57.471 33.333 0.00 0.00 42.28 4.52
390 391 9.529325 GGTAAATCACTAATTAAGGGAAATTGC 57.471 33.333 0.00 0.00 42.28 3.56
409 410 5.424757 GGCCCCAAACAAATTAGGTAAATC 58.575 41.667 0.00 0.00 0.00 2.17
414 415 1.262417 CGGCCCCAAACAAATTAGGT 58.738 50.000 0.00 0.00 0.00 3.08
441 446 3.450904 AGGTCTAAGACATACAGCCCAA 58.549 45.455 0.00 0.00 33.68 4.12
452 457 4.554960 ACTGGGCTTTTAGGTCTAAGAC 57.445 45.455 0.00 0.00 0.00 3.01
457 462 3.876309 TCAAACTGGGCTTTTAGGTCT 57.124 42.857 0.00 0.00 0.00 3.85
504 515 4.616802 GCGTTTCATCGTGATCATGTTTTT 59.383 37.500 14.52 0.00 0.00 1.94
568 632 3.559384 GCTAGGGTTACTTATGGATGGCC 60.559 52.174 0.00 0.00 0.00 5.36
580 644 1.948834 GAGAGAGACGGCTAGGGTTAC 59.051 57.143 0.00 0.00 0.00 2.50
777 845 1.881252 CCGATCGGAACCGCGAATT 60.881 57.895 30.62 0.11 39.59 2.17
905 986 2.093288 CAGATTTCTAGGCAGGCACAGA 60.093 50.000 0.00 0.00 0.00 3.41
907 988 1.065199 CCAGATTTCTAGGCAGGCACA 60.065 52.381 0.00 0.00 0.00 4.57
931 1012 7.306574 GCAAAAACAACAATCAAACCTAGCTAC 60.307 37.037 0.00 0.00 0.00 3.58
961 1045 1.205064 CGGCTCTGAAACAAGCACG 59.795 57.895 0.00 0.00 40.36 5.34
1182 1266 2.166664 GACGTAATGCTCTTCCCACTCT 59.833 50.000 0.00 0.00 0.00 3.24
1185 1269 1.278238 CGACGTAATGCTCTTCCCAC 58.722 55.000 0.00 0.00 0.00 4.61
1203 1287 2.511600 GGATCAACCTCCGTGCCG 60.512 66.667 0.00 0.00 35.41 5.69
1224 1308 2.740981 CCATGTCAAGAAGCTCTGTGTC 59.259 50.000 0.00 0.00 0.00 3.67
1266 1350 4.363138 CTTTCAAGCCAACTTTGTTCCTC 58.637 43.478 0.00 0.00 32.29 3.71
1437 1521 2.256117 ACTCCCCTTCAGTGTTTTCG 57.744 50.000 0.00 0.00 0.00 3.46
1569 1653 2.039624 GAGACCCTCTCCCTGCCA 59.960 66.667 0.00 0.00 37.55 4.92
1587 1671 0.958382 TGTTGGCCTTGTGTATCGCC 60.958 55.000 3.32 0.00 41.99 5.54
1593 1677 2.165167 CTCATGATGTTGGCCTTGTGT 58.835 47.619 3.32 0.00 0.00 3.72
1653 1737 3.682292 CTCAGGGTACTTGGCGGCC 62.682 68.421 13.32 13.32 0.00 6.13
1749 1833 3.794270 CCGTACAGGTTCGGCATG 58.206 61.111 4.57 0.00 40.28 4.06
1800 1884 2.129555 GAGTCAAGCCCAAGCCTCCA 62.130 60.000 0.00 0.00 41.25 3.86
1911 1995 1.932511 GCACTCAGCATAAGAGCAGTC 59.067 52.381 0.00 0.00 44.79 3.51
1942 2026 2.975799 GAAACGGAGGTGGCGCAA 60.976 61.111 10.83 0.00 0.00 4.85
2022 2106 1.675641 GCCACCAAGATCAGCGGTT 60.676 57.895 0.00 0.00 0.00 4.44
2046 2130 3.909776 TTTGTGTAGTCTGACGTCGAT 57.090 42.857 11.62 0.00 0.00 3.59
2052 2136 5.266242 CAAACTGCTTTTGTGTAGTCTGAC 58.734 41.667 0.00 0.00 39.96 3.51
2064 2148 3.758554 AGATATGACCGCAAACTGCTTTT 59.241 39.130 0.00 0.00 42.25 2.27
2089 2173 2.107204 GGGGTGGTGCTCAATCAGATAT 59.893 50.000 0.00 0.00 0.00 1.63
2090 2174 1.490490 GGGGTGGTGCTCAATCAGATA 59.510 52.381 0.00 0.00 0.00 1.98
2091 2175 0.257039 GGGGTGGTGCTCAATCAGAT 59.743 55.000 0.00 0.00 0.00 2.90
2092 2176 0.842030 AGGGGTGGTGCTCAATCAGA 60.842 55.000 0.00 0.00 0.00 3.27
2093 2177 0.038744 AAGGGGTGGTGCTCAATCAG 59.961 55.000 0.00 0.00 0.00 2.90
2094 2178 0.251297 CAAGGGGTGGTGCTCAATCA 60.251 55.000 0.00 0.00 0.00 2.57
2095 2179 1.598701 GCAAGGGGTGGTGCTCAATC 61.599 60.000 0.00 0.00 0.00 2.67
2096 2180 1.607467 GCAAGGGGTGGTGCTCAAT 60.607 57.895 0.00 0.00 0.00 2.57
2156 2244 7.280652 GGTCTTAACTAAACCGTGCCAAATATA 59.719 37.037 0.00 0.00 0.00 0.86
2205 2294 7.817478 AGTTGGTAAAACTTTTCCAAGAACAAG 59.183 33.333 12.07 0.00 44.63 3.16
2294 2383 5.757850 ATCCAGTTCTTCAACAACTTGAC 57.242 39.130 0.00 0.00 36.06 3.18
2321 2410 6.456584 GGCGAGCTAGGTTTATTTTTACAGAC 60.457 42.308 0.00 0.00 0.00 3.51
2323 2412 5.501897 CGGCGAGCTAGGTTTATTTTTACAG 60.502 44.000 0.00 0.00 0.00 2.74
2343 2432 0.179161 CAGAGGTAACAGAGACGGCG 60.179 60.000 4.80 4.80 41.41 6.46
2371 2460 2.035704 GACAACAATCACATGGCACCAA 59.964 45.455 0.00 0.00 0.00 3.67
2372 2461 1.612950 GACAACAATCACATGGCACCA 59.387 47.619 0.00 0.00 0.00 4.17
2373 2462 1.401409 CGACAACAATCACATGGCACC 60.401 52.381 0.00 0.00 0.00 5.01
2374 2463 1.266718 ACGACAACAATCACATGGCAC 59.733 47.619 0.00 0.00 0.00 5.01
2376 2465 3.623060 AGATACGACAACAATCACATGGC 59.377 43.478 0.00 0.00 0.00 4.40
2377 2466 4.026558 CGAGATACGACAACAATCACATGG 60.027 45.833 0.00 0.00 45.77 3.66
2379 2468 3.551890 GCGAGATACGACAACAATCACAT 59.448 43.478 0.00 0.00 45.77 3.21
2382 2471 3.119637 TCTGCGAGATACGACAACAATCA 60.120 43.478 0.00 0.00 45.77 2.57
2384 2473 3.179830 GTCTGCGAGATACGACAACAAT 58.820 45.455 0.00 0.00 45.77 2.71
2473 2584 3.633235 CAAGACGAGACGAAGGATATGG 58.367 50.000 0.00 0.00 0.00 2.74
2475 2586 2.688446 TGCAAGACGAGACGAAGGATAT 59.312 45.455 0.00 0.00 0.00 1.63
2552 2663 9.878599 ACAATTAACTTCAAAATTCAGTACTCG 57.121 29.630 0.00 0.00 0.00 4.18
2634 2746 2.257371 GGCGTCGTGTAGCACAGA 59.743 61.111 0.00 0.00 33.40 3.41
2646 2758 2.823829 GCCGTTGATGATGGGCGTC 61.824 63.158 0.00 0.00 35.59 5.19
2693 2805 3.108881 CAGAGGTGTTGTCGATGATACG 58.891 50.000 0.00 0.00 0.00 3.06
2695 2807 6.709018 TTATCAGAGGTGTTGTCGATGATA 57.291 37.500 0.00 0.00 0.00 2.15
2731 2846 2.860293 GGAATCCACACACACGCG 59.140 61.111 3.53 3.53 0.00 6.01
2767 2887 6.241207 GCTTTAGCTGTTCACTAACAATGA 57.759 37.500 0.00 0.00 44.79 2.57
2786 2906 5.163216 CCTTCCTGAATCCTGATCTAGCTTT 60.163 44.000 0.00 0.00 0.00 3.51
2915 3035 0.961019 TGATGGCCAACAAGCTTCAC 59.039 50.000 14.14 0.00 0.00 3.18
2984 3106 6.152831 CCCTAATAGCATATTTTAAGGGCCAC 59.847 42.308 6.18 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.