Multiple sequence alignment - TraesCS1B01G314000

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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 TraesCS1B01G314000 chr1B 100.000 2627 0 0 1 2627 538166317 538163691 0.000000e+00 4852.0
1 TraesCS1B01G314000 chr1D 92.780 1759 64 30 569 2274 400956974 400955226 0.000000e+00 2486.0
2 TraesCS1B01G314000 chr1D 91.209 273 19 5 2313 2584 400955125 400954857 1.490000e-97 366.0
3 TraesCS1B01G314000 chr1D 79.027 329 30 19 292 584 400957314 400956989 3.450000e-44 189.0
4 TraesCS1B01G314000 chr1A 91.433 1856 75 30 439 2272 497193315 497191522 0.000000e+00 2470.0
5 TraesCS1B01G314000 chr1A 89.328 253 21 6 2341 2590 497191261 497191012 1.960000e-81 313.0
6 TraesCS1B01G314000 chr4D 76.410 195 26 13 1082 1260 102534312 102534122 1.300000e-13 87.9
7 TraesCS1B01G314000 chr4B 82.759 87 15 0 1082 1168 147066773 147066687 7.800000e-11 78.7
8 TraesCS1B01G314000 chr4B 100.000 30 0 0 2598 2627 619602715 619602744 3.650000e-04 56.5
9 TraesCS1B01G314000 chr6A 97.368 38 1 0 2590 2627 57688773 57688810 6.070000e-07 65.8
10 TraesCS1B01G314000 chr3B 94.737 38 2 0 2590 2627 24006950 24006913 2.820000e-05 60.2
11 TraesCS1B01G314000 chr6B 100.000 30 0 0 2598 2627 449774358 449774329 3.650000e-04 56.5
12 TraesCS1B01G314000 chr6B 100.000 30 0 0 2598 2627 693800755 693800726 3.650000e-04 56.5
13 TraesCS1B01G314000 chr6B 85.185 54 7 1 2365 2417 546528507 546528454 1.000000e-03 54.7
14 TraesCS1B01G314000 chr7A 94.444 36 1 1 2365 2399 410601806 410601841 1.000000e-03 54.7


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 TraesCS1B01G314000 chr1B 538163691 538166317 2626 True 4852.000000 4852 100.0000 1 2627 1 chr1B.!!$R1 2626
1 TraesCS1B01G314000 chr1D 400954857 400957314 2457 True 1013.666667 2486 87.6720 292 2584 3 chr1D.!!$R1 2292
2 TraesCS1B01G314000 chr1A 497191012 497193315 2303 True 1391.500000 2470 90.3805 439 2590 2 chr1A.!!$R1 2151

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
247 248 0.038166 TCACCCTCCTCATTGGTTGC 59.962 55.0 0.0 0.0 37.07 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2194 0.108567 GAGGAAGTCCGGTTCTGCTC 60.109 60.0 0.0 3.21 42.08 4.26 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
28 29 2.646121 CCAGTCCTTGGTCCAAAGC 58.354 57.895 5.64 0.00 42.41 3.51
29 30 0.178992 CCAGTCCTTGGTCCAAAGCA 60.179 55.000 5.64 0.00 42.41 3.91
30 31 1.691196 CAGTCCTTGGTCCAAAGCAA 58.309 50.000 5.64 0.00 40.44 3.91
37 38 3.297134 TTGGTCCAAAGCAAGAGTTCT 57.703 42.857 0.40 0.00 37.94 3.01
38 39 2.575532 TGGTCCAAAGCAAGAGTTCTG 58.424 47.619 0.00 0.00 0.00 3.02
39 40 2.092429 TGGTCCAAAGCAAGAGTTCTGT 60.092 45.455 0.00 0.00 0.00 3.41
40 41 2.952310 GGTCCAAAGCAAGAGTTCTGTT 59.048 45.455 0.00 0.00 0.00 3.16
41 42 3.243201 GGTCCAAAGCAAGAGTTCTGTTG 60.243 47.826 5.51 5.51 0.00 3.33
47 48 3.978718 GCAAGAGTTCTGTTGCTTTCT 57.021 42.857 21.70 0.00 44.68 2.52
48 49 4.298744 GCAAGAGTTCTGTTGCTTTCTT 57.701 40.909 21.70 0.00 44.68 2.52
49 50 4.676546 GCAAGAGTTCTGTTGCTTTCTTT 58.323 39.130 21.70 0.00 44.68 2.52
50 51 5.105063 GCAAGAGTTCTGTTGCTTTCTTTT 58.895 37.500 21.70 0.00 44.68 2.27
51 52 6.265577 GCAAGAGTTCTGTTGCTTTCTTTTA 58.734 36.000 21.70 0.00 44.68 1.52
52 53 6.416161 GCAAGAGTTCTGTTGCTTTCTTTTAG 59.584 38.462 21.70 0.00 44.68 1.85
53 54 7.679638 GCAAGAGTTCTGTTGCTTTCTTTTAGA 60.680 37.037 21.70 0.00 44.68 2.10
54 55 7.865706 AGAGTTCTGTTGCTTTCTTTTAGAA 57.134 32.000 0.00 0.00 31.28 2.10
55 56 8.281212 AGAGTTCTGTTGCTTTCTTTTAGAAA 57.719 30.769 2.27 2.27 41.51 2.52
56 57 8.184848 AGAGTTCTGTTGCTTTCTTTTAGAAAC 58.815 33.333 0.00 0.00 39.13 2.78
57 58 7.826690 AGTTCTGTTGCTTTCTTTTAGAAACA 58.173 30.769 0.00 0.00 39.13 2.83
58 59 7.755373 AGTTCTGTTGCTTTCTTTTAGAAACAC 59.245 33.333 0.00 0.00 39.13 3.32
59 60 6.560711 TCTGTTGCTTTCTTTTAGAAACACC 58.439 36.000 0.00 0.00 39.13 4.16
60 61 5.336744 TGTTGCTTTCTTTTAGAAACACCG 58.663 37.500 0.00 0.00 39.13 4.94
61 62 5.106078 TGTTGCTTTCTTTTAGAAACACCGT 60.106 36.000 0.00 0.00 39.13 4.83
62 63 6.093771 TGTTGCTTTCTTTTAGAAACACCGTA 59.906 34.615 0.00 0.00 39.13 4.02
63 64 6.870971 TGCTTTCTTTTAGAAACACCGTAT 57.129 33.333 0.00 0.00 39.13 3.06
64 65 6.664515 TGCTTTCTTTTAGAAACACCGTATG 58.335 36.000 0.00 0.00 39.13 2.39
65 66 6.483974 TGCTTTCTTTTAGAAACACCGTATGA 59.516 34.615 0.00 0.00 39.13 2.15
66 67 7.174253 TGCTTTCTTTTAGAAACACCGTATGAT 59.826 33.333 0.00 0.00 39.13 2.45
67 68 8.662141 GCTTTCTTTTAGAAACACCGTATGATA 58.338 33.333 0.00 0.00 39.13 2.15
100 101 3.284793 TCCGAAAAGGAGGTTGAAACA 57.715 42.857 0.00 0.00 45.98 2.83
101 102 2.946990 TCCGAAAAGGAGGTTGAAACAC 59.053 45.455 0.00 0.00 45.98 3.32
102 103 2.685897 CCGAAAAGGAGGTTGAAACACA 59.314 45.455 0.00 0.00 45.00 3.72
103 104 3.243068 CCGAAAAGGAGGTTGAAACACAG 60.243 47.826 0.00 0.00 45.00 3.66
104 105 3.377172 CGAAAAGGAGGTTGAAACACAGT 59.623 43.478 0.00 0.00 0.00 3.55
105 106 4.573201 CGAAAAGGAGGTTGAAACACAGTA 59.427 41.667 0.00 0.00 0.00 2.74
106 107 5.503520 CGAAAAGGAGGTTGAAACACAGTAC 60.504 44.000 0.00 0.00 0.00 2.73
107 108 4.497291 AAGGAGGTTGAAACACAGTACA 57.503 40.909 0.00 0.00 0.00 2.90
108 109 4.497291 AGGAGGTTGAAACACAGTACAA 57.503 40.909 0.00 0.00 0.00 2.41
109 110 4.451900 AGGAGGTTGAAACACAGTACAAG 58.548 43.478 0.00 0.00 0.00 3.16
110 111 4.163458 AGGAGGTTGAAACACAGTACAAGA 59.837 41.667 0.00 0.00 0.00 3.02
111 112 5.063880 GGAGGTTGAAACACAGTACAAGAT 58.936 41.667 0.00 0.00 0.00 2.40
112 113 5.531287 GGAGGTTGAAACACAGTACAAGATT 59.469 40.000 0.00 0.00 0.00 2.40
113 114 6.039382 GGAGGTTGAAACACAGTACAAGATTT 59.961 38.462 0.00 0.00 0.00 2.17
114 115 6.795399 AGGTTGAAACACAGTACAAGATTTG 58.205 36.000 0.00 0.00 0.00 2.32
116 117 7.033185 GGTTGAAACACAGTACAAGATTTGTT 58.967 34.615 0.00 0.00 42.22 2.83
117 118 7.009174 GGTTGAAACACAGTACAAGATTTGTTG 59.991 37.037 0.00 0.00 42.22 3.33
118 119 6.033341 TGAAACACAGTACAAGATTTGTTGC 58.967 36.000 0.00 0.00 42.22 4.17
119 120 5.574891 AACACAGTACAAGATTTGTTGCA 57.425 34.783 0.00 0.00 42.22 4.08
120 121 5.772825 ACACAGTACAAGATTTGTTGCAT 57.227 34.783 0.00 0.00 42.22 3.96
121 122 6.147864 ACACAGTACAAGATTTGTTGCATT 57.852 33.333 0.00 0.00 42.22 3.56
122 123 6.208644 ACACAGTACAAGATTTGTTGCATTC 58.791 36.000 0.00 0.00 42.22 2.67
123 124 5.630680 CACAGTACAAGATTTGTTGCATTCC 59.369 40.000 0.00 0.00 42.22 3.01
124 125 5.301551 ACAGTACAAGATTTGTTGCATTCCA 59.698 36.000 0.00 0.00 42.22 3.53
125 126 6.015180 ACAGTACAAGATTTGTTGCATTCCAT 60.015 34.615 0.00 0.00 42.22 3.41
126 127 6.869913 CAGTACAAGATTTGTTGCATTCCATT 59.130 34.615 0.00 0.00 42.22 3.16
127 128 7.062605 CAGTACAAGATTTGTTGCATTCCATTC 59.937 37.037 0.00 0.00 42.22 2.67
128 129 5.856156 ACAAGATTTGTTGCATTCCATTCA 58.144 33.333 0.00 0.00 42.22 2.57
129 130 5.697633 ACAAGATTTGTTGCATTCCATTCAC 59.302 36.000 0.00 0.00 42.22 3.18
130 131 5.471556 AGATTTGTTGCATTCCATTCACA 57.528 34.783 0.00 0.00 0.00 3.58
131 132 6.045072 AGATTTGTTGCATTCCATTCACAT 57.955 33.333 0.00 0.00 0.00 3.21
132 133 5.872617 AGATTTGTTGCATTCCATTCACATG 59.127 36.000 0.00 0.00 0.00 3.21
143 144 4.587211 CCATTCACATGGCAAATTTTCG 57.413 40.909 0.00 0.00 43.95 3.46
144 145 3.995705 CCATTCACATGGCAAATTTTCGT 59.004 39.130 0.00 0.00 43.95 3.85
145 146 4.451774 CCATTCACATGGCAAATTTTCGTT 59.548 37.500 0.00 0.00 43.95 3.85
146 147 5.049543 CCATTCACATGGCAAATTTTCGTTT 60.050 36.000 0.00 0.00 43.95 3.60
147 148 5.649602 TTCACATGGCAAATTTTCGTTTC 57.350 34.783 0.00 0.00 0.00 2.78
148 149 4.942852 TCACATGGCAAATTTTCGTTTCT 58.057 34.783 0.00 0.00 0.00 2.52
149 150 4.981674 TCACATGGCAAATTTTCGTTTCTC 59.018 37.500 0.00 0.00 0.00 2.87
150 151 3.980775 ACATGGCAAATTTTCGTTTCTCG 59.019 39.130 0.00 0.00 41.41 4.04
151 152 2.389998 TGGCAAATTTTCGTTTCTCGC 58.610 42.857 0.00 0.00 39.67 5.03
152 153 2.223595 TGGCAAATTTTCGTTTCTCGCA 60.224 40.909 0.00 0.00 39.67 5.10
153 154 2.792116 GGCAAATTTTCGTTTCTCGCAA 59.208 40.909 0.00 0.00 39.67 4.85
154 155 3.244111 GGCAAATTTTCGTTTCTCGCAAA 59.756 39.130 0.00 0.00 38.73 3.68
155 156 4.193380 GCAAATTTTCGTTTCTCGCAAAC 58.807 39.130 0.00 0.91 37.47 2.93
159 160 3.796709 CGTTTCTCGCAAACGTGC 58.203 55.556 18.62 0.00 45.45 5.34
173 174 5.124847 CAAACGTGCTAAAAAGTGTTTGG 57.875 39.130 7.54 0.00 41.29 3.28
174 175 4.443913 AACGTGCTAAAAAGTGTTTGGT 57.556 36.364 0.00 0.00 0.00 3.67
175 176 3.765026 ACGTGCTAAAAAGTGTTTGGTG 58.235 40.909 0.00 0.00 0.00 4.17
176 177 3.112580 CGTGCTAAAAAGTGTTTGGTGG 58.887 45.455 0.00 0.00 0.00 4.61
177 178 3.181495 CGTGCTAAAAAGTGTTTGGTGGA 60.181 43.478 0.00 0.00 0.00 4.02
178 179 4.499019 CGTGCTAAAAAGTGTTTGGTGGAT 60.499 41.667 0.00 0.00 0.00 3.41
179 180 5.356426 GTGCTAAAAAGTGTTTGGTGGATT 58.644 37.500 0.00 0.00 0.00 3.01
180 181 5.234116 GTGCTAAAAAGTGTTTGGTGGATTG 59.766 40.000 0.00 0.00 0.00 2.67
181 182 5.127845 TGCTAAAAAGTGTTTGGTGGATTGA 59.872 36.000 0.00 0.00 0.00 2.57
182 183 6.045955 GCTAAAAAGTGTTTGGTGGATTGAA 58.954 36.000 0.00 0.00 0.00 2.69
183 184 6.200854 GCTAAAAAGTGTTTGGTGGATTGAAG 59.799 38.462 0.00 0.00 0.00 3.02
184 185 4.670896 AAAGTGTTTGGTGGATTGAAGG 57.329 40.909 0.00 0.00 0.00 3.46
185 186 1.963515 AGTGTTTGGTGGATTGAAGGC 59.036 47.619 0.00 0.00 0.00 4.35
186 187 1.686052 GTGTTTGGTGGATTGAAGGCA 59.314 47.619 0.00 0.00 0.00 4.75
187 188 2.299867 GTGTTTGGTGGATTGAAGGCAT 59.700 45.455 0.00 0.00 0.00 4.40
188 189 2.299582 TGTTTGGTGGATTGAAGGCATG 59.700 45.455 0.00 0.00 0.00 4.06
189 190 2.562298 GTTTGGTGGATTGAAGGCATGA 59.438 45.455 0.00 0.00 0.00 3.07
190 191 1.838112 TGGTGGATTGAAGGCATGAC 58.162 50.000 0.00 0.00 0.00 3.06
191 192 1.106285 GGTGGATTGAAGGCATGACC 58.894 55.000 0.00 0.00 39.61 4.02
192 193 1.616725 GGTGGATTGAAGGCATGACCA 60.617 52.381 0.00 0.00 43.14 4.02
193 194 2.381911 GTGGATTGAAGGCATGACCAT 58.618 47.619 0.00 0.00 43.14 3.55
194 195 2.762327 GTGGATTGAAGGCATGACCATT 59.238 45.455 0.00 0.00 43.14 3.16
195 196 3.025978 TGGATTGAAGGCATGACCATTC 58.974 45.455 0.00 0.00 43.14 2.67
196 197 2.033801 GGATTGAAGGCATGACCATTCG 59.966 50.000 0.00 0.00 43.14 3.34
197 198 1.462616 TTGAAGGCATGACCATTCGG 58.537 50.000 0.00 0.00 43.14 4.30
198 199 0.394216 TGAAGGCATGACCATTCGGG 60.394 55.000 0.00 0.00 43.14 5.14
199 200 1.728490 GAAGGCATGACCATTCGGGC 61.728 60.000 0.00 0.00 43.14 6.13
200 201 2.124151 GGCATGACCATTCGGGCT 60.124 61.111 0.00 0.00 43.17 5.19
201 202 1.148273 GGCATGACCATTCGGGCTA 59.852 57.895 0.00 0.00 43.17 3.93
202 203 0.250901 GGCATGACCATTCGGGCTAT 60.251 55.000 0.00 0.00 43.17 2.97
203 204 1.003118 GGCATGACCATTCGGGCTATA 59.997 52.381 0.00 0.00 43.17 1.31
204 205 2.350522 GCATGACCATTCGGGCTATAG 58.649 52.381 0.00 0.00 43.17 1.31
205 206 2.350522 CATGACCATTCGGGCTATAGC 58.649 52.381 16.78 16.78 43.17 2.97
217 218 2.859165 GCTATAGCCCTATGGTGCAA 57.141 50.000 14.13 0.00 34.31 4.08
218 219 2.427506 GCTATAGCCCTATGGTGCAAC 58.572 52.381 14.13 0.00 34.31 4.17
219 220 2.224523 GCTATAGCCCTATGGTGCAACA 60.225 50.000 7.04 7.04 34.36 3.33
220 221 2.348411 ATAGCCCTATGGTGCAACAC 57.652 50.000 6.58 0.00 39.98 3.32
229 230 4.703703 GTGCAACACCTCCTCCTC 57.296 61.111 0.00 0.00 36.32 3.71
230 231 1.754745 GTGCAACACCTCCTCCTCA 59.245 57.895 0.00 0.00 36.32 3.86
231 232 0.603975 GTGCAACACCTCCTCCTCAC 60.604 60.000 0.00 0.00 36.32 3.51
232 233 1.003233 GCAACACCTCCTCCTCACC 60.003 63.158 0.00 0.00 0.00 4.02
233 234 1.679898 CAACACCTCCTCCTCACCC 59.320 63.158 0.00 0.00 0.00 4.61
234 235 0.838122 CAACACCTCCTCCTCACCCT 60.838 60.000 0.00 0.00 0.00 4.34
235 236 0.545548 AACACCTCCTCCTCACCCTC 60.546 60.000 0.00 0.00 0.00 4.30
236 237 1.687493 CACCTCCTCCTCACCCTCC 60.687 68.421 0.00 0.00 0.00 4.30
237 238 1.864559 ACCTCCTCCTCACCCTCCT 60.865 63.158 0.00 0.00 0.00 3.69
238 239 1.075600 CCTCCTCCTCACCCTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
239 240 1.700368 CTCCTCCTCACCCTCCTCA 59.300 63.158 0.00 0.00 0.00 3.86
240 241 0.264359 CTCCTCCTCACCCTCCTCAT 59.736 60.000 0.00 0.00 0.00 2.90
241 242 0.719015 TCCTCCTCACCCTCCTCATT 59.281 55.000 0.00 0.00 0.00 2.57
242 243 0.835941 CCTCCTCACCCTCCTCATTG 59.164 60.000 0.00 0.00 0.00 2.82
243 244 0.835941 CTCCTCACCCTCCTCATTGG 59.164 60.000 0.00 0.00 37.10 3.16
244 245 0.119155 TCCTCACCCTCCTCATTGGT 59.881 55.000 0.00 0.00 37.07 3.67
245 246 0.995024 CCTCACCCTCCTCATTGGTT 59.005 55.000 0.00 0.00 37.07 3.67
246 247 1.340405 CCTCACCCTCCTCATTGGTTG 60.340 57.143 0.00 0.00 37.07 3.77
247 248 0.038166 TCACCCTCCTCATTGGTTGC 59.962 55.000 0.00 0.00 37.07 4.17
248 249 0.251297 CACCCTCCTCATTGGTTGCA 60.251 55.000 0.00 0.00 37.07 4.08
249 250 0.706433 ACCCTCCTCATTGGTTGCAT 59.294 50.000 0.00 0.00 37.07 3.96
250 251 1.077663 ACCCTCCTCATTGGTTGCATT 59.922 47.619 0.00 0.00 37.07 3.56
251 252 2.181975 CCCTCCTCATTGGTTGCATTT 58.818 47.619 0.00 0.00 37.07 2.32
252 253 3.245586 ACCCTCCTCATTGGTTGCATTTA 60.246 43.478 0.00 0.00 37.07 1.40
253 254 3.962718 CCCTCCTCATTGGTTGCATTTAT 59.037 43.478 0.00 0.00 37.07 1.40
254 255 4.202182 CCCTCCTCATTGGTTGCATTTATG 60.202 45.833 0.00 0.00 37.07 1.90
255 256 4.403432 CCTCCTCATTGGTTGCATTTATGT 59.597 41.667 0.00 0.00 37.07 2.29
256 257 5.450965 CCTCCTCATTGGTTGCATTTATGTC 60.451 44.000 0.00 0.00 37.07 3.06
257 258 5.263599 TCCTCATTGGTTGCATTTATGTCT 58.736 37.500 0.00 0.00 37.07 3.41
258 259 5.716228 TCCTCATTGGTTGCATTTATGTCTT 59.284 36.000 0.00 0.00 37.07 3.01
259 260 6.038356 CCTCATTGGTTGCATTTATGTCTTC 58.962 40.000 0.00 0.00 0.00 2.87
260 261 6.127535 CCTCATTGGTTGCATTTATGTCTTCT 60.128 38.462 0.00 0.00 0.00 2.85
261 262 6.855836 TCATTGGTTGCATTTATGTCTTCTC 58.144 36.000 0.00 0.00 0.00 2.87
262 263 6.433716 TCATTGGTTGCATTTATGTCTTCTCA 59.566 34.615 0.00 0.00 0.00 3.27
263 264 5.627499 TGGTTGCATTTATGTCTTCTCAC 57.373 39.130 0.00 0.00 0.00 3.51
264 265 5.069318 TGGTTGCATTTATGTCTTCTCACA 58.931 37.500 0.00 0.00 0.00 3.58
265 266 5.534278 TGGTTGCATTTATGTCTTCTCACAA 59.466 36.000 0.00 0.00 0.00 3.33
266 267 6.209192 TGGTTGCATTTATGTCTTCTCACAAT 59.791 34.615 0.00 0.00 0.00 2.71
267 268 6.749118 GGTTGCATTTATGTCTTCTCACAATC 59.251 38.462 0.00 0.00 0.00 2.67
268 269 7.362401 GGTTGCATTTATGTCTTCTCACAATCT 60.362 37.037 0.00 0.00 0.00 2.40
269 270 7.312657 TGCATTTATGTCTTCTCACAATCTC 57.687 36.000 0.00 0.00 0.00 2.75
270 271 6.317140 TGCATTTATGTCTTCTCACAATCTCC 59.683 38.462 0.00 0.00 0.00 3.71
271 272 6.317140 GCATTTATGTCTTCTCACAATCTCCA 59.683 38.462 0.00 0.00 0.00 3.86
272 273 7.678218 GCATTTATGTCTTCTCACAATCTCCAC 60.678 40.741 0.00 0.00 0.00 4.02
273 274 3.685139 TGTCTTCTCACAATCTCCACC 57.315 47.619 0.00 0.00 0.00 4.61
274 275 2.303022 TGTCTTCTCACAATCTCCACCC 59.697 50.000 0.00 0.00 0.00 4.61
275 276 1.909302 TCTTCTCACAATCTCCACCCC 59.091 52.381 0.00 0.00 0.00 4.95
276 277 1.912043 CTTCTCACAATCTCCACCCCT 59.088 52.381 0.00 0.00 0.00 4.79
277 278 1.279496 TCTCACAATCTCCACCCCTG 58.721 55.000 0.00 0.00 0.00 4.45
278 279 0.987294 CTCACAATCTCCACCCCTGT 59.013 55.000 0.00 0.00 0.00 4.00
279 280 1.352352 CTCACAATCTCCACCCCTGTT 59.648 52.381 0.00 0.00 0.00 3.16
280 281 1.780309 TCACAATCTCCACCCCTGTTT 59.220 47.619 0.00 0.00 0.00 2.83
281 282 1.888512 CACAATCTCCACCCCTGTTTG 59.111 52.381 0.00 0.00 0.00 2.93
282 283 1.499007 ACAATCTCCACCCCTGTTTGT 59.501 47.619 0.00 0.00 0.00 2.83
283 284 2.162681 CAATCTCCACCCCTGTTTGTC 58.837 52.381 0.00 0.00 0.00 3.18
284 285 1.747444 ATCTCCACCCCTGTTTGTCT 58.253 50.000 0.00 0.00 0.00 3.41
285 286 2.409064 TCTCCACCCCTGTTTGTCTA 57.591 50.000 0.00 0.00 0.00 2.59
286 287 2.696775 TCTCCACCCCTGTTTGTCTAA 58.303 47.619 0.00 0.00 0.00 2.10
287 288 3.256704 TCTCCACCCCTGTTTGTCTAAT 58.743 45.455 0.00 0.00 0.00 1.73
288 289 4.431378 TCTCCACCCCTGTTTGTCTAATA 58.569 43.478 0.00 0.00 0.00 0.98
289 290 4.847512 TCTCCACCCCTGTTTGTCTAATAA 59.152 41.667 0.00 0.00 0.00 1.40
290 291 5.311121 TCTCCACCCCTGTTTGTCTAATAAA 59.689 40.000 0.00 0.00 0.00 1.40
325 326 3.458163 CCGGCACCGCTCCTCTAA 61.458 66.667 2.83 0.00 38.24 2.10
326 327 2.202756 CGGCACCGCTCCTCTAAC 60.203 66.667 0.00 0.00 0.00 2.34
331 332 0.173708 CACCGCTCCTCTAACTGTCC 59.826 60.000 0.00 0.00 0.00 4.02
334 335 0.970937 CGCTCCTCTAACTGTCCCCA 60.971 60.000 0.00 0.00 0.00 4.96
376 383 7.492344 CACTTCCTTTAACTTTCTTGCAACAAT 59.508 33.333 0.00 0.00 0.00 2.71
379 386 8.195617 TCCTTTAACTTTCTTGCAACAATTTG 57.804 30.769 0.00 0.00 35.62 2.32
411 418 9.494271 AATTAGCACACACTACCTATAATGATG 57.506 33.333 0.00 0.00 0.00 3.07
417 425 8.612619 CACACACTACCTATAATGATGGAAAAC 58.387 37.037 0.00 0.00 0.00 2.43
418 426 7.773690 ACACACTACCTATAATGATGGAAAACC 59.226 37.037 0.00 0.00 0.00 3.27
419 427 7.993183 CACACTACCTATAATGATGGAAAACCT 59.007 37.037 0.00 0.00 0.00 3.50
420 428 7.993183 ACACTACCTATAATGATGGAAAACCTG 59.007 37.037 0.00 0.00 0.00 4.00
429 437 5.549742 TGATGGAAAACCTGCAAGAAAAT 57.450 34.783 0.00 0.00 34.07 1.82
436 444 7.772757 TGGAAAACCTGCAAGAAAATAAACATT 59.227 29.630 0.00 0.00 34.07 2.71
459 495 3.766151 TGCGACCATTCTAAGTCTAACG 58.234 45.455 0.00 0.00 0.00 3.18
567 610 4.881850 CCACTAATCTCACCCCACATTAAC 59.118 45.833 0.00 0.00 0.00 2.01
755 829 1.610967 TGCCCCCATACACGTGAGA 60.611 57.895 25.01 10.16 0.00 3.27
771 845 0.879400 GAGAGCCATGAGCCACATCG 60.879 60.000 0.00 0.00 45.47 3.84
822 896 1.465188 ATTCCTGTCCACCACCCCA 60.465 57.895 0.00 0.00 0.00 4.96
890 964 5.925397 CCATTGATCTATTCTTCGTCTCCAG 59.075 44.000 0.00 0.00 0.00 3.86
897 971 0.679960 TCTTCGTCTCCAGCGATCCA 60.680 55.000 0.00 0.00 38.21 3.41
907 982 2.026729 TCCAGCGATCCATTGGTAAACA 60.027 45.455 1.86 0.00 33.65 2.83
940 1020 0.624254 TCTTCGCTCACCTCTCCCTA 59.376 55.000 0.00 0.00 0.00 3.53
989 1074 2.054232 TGATCCACCGGTCTAGTCTC 57.946 55.000 2.59 0.00 0.00 3.36
990 1075 1.283905 TGATCCACCGGTCTAGTCTCA 59.716 52.381 2.59 0.00 0.00 3.27
1046 1131 3.083997 GCCGTCTCTGGGGATGGT 61.084 66.667 10.08 0.00 42.63 3.55
1425 1513 1.000107 GTACGAGGTGGAGGGGTCT 60.000 63.158 0.00 0.00 0.00 3.85
1590 1678 3.200593 GCGCTGGACCAGATGCTG 61.201 66.667 26.25 9.39 33.66 4.41
1668 1756 1.628340 TCCTTCGATTTGCCTCCTTCA 59.372 47.619 0.00 0.00 0.00 3.02
1675 1771 3.193267 CGATTTGCCTCCTTCAATTTCCA 59.807 43.478 0.00 0.00 0.00 3.53
1719 1815 4.990910 AGCTCCTGTGTGCCCCCT 62.991 66.667 0.00 0.00 0.00 4.79
1799 1898 4.996788 ATGTGCATGGAAATCCTTCTTC 57.003 40.909 0.44 0.00 36.82 2.87
1801 1900 4.151121 TGTGCATGGAAATCCTTCTTCAA 58.849 39.130 0.44 0.00 36.82 2.69
1886 2003 5.964477 AGGAGGGATGAAAGTGTATTACTCA 59.036 40.000 0.00 0.00 39.18 3.41
1933 2050 3.788227 AGGCCAATTTCACTGTCTACA 57.212 42.857 5.01 0.00 0.00 2.74
1948 2065 6.367422 CACTGTCTACATTCTCTCCAACTTTC 59.633 42.308 0.00 0.00 0.00 2.62
1968 2088 1.667722 CAGCACCAAAGGCCTTTCC 59.332 57.895 28.16 15.66 0.00 3.13
1971 2091 1.820010 GCACCAAAGGCCTTTCCCAG 61.820 60.000 28.16 18.10 34.51 4.45
1977 2097 2.700371 CAAAGGCCTTTCCCAGAAGTTT 59.300 45.455 28.16 0.00 34.51 2.66
1988 2108 3.573967 TCCCAGAAGTTTGCTGAAATTCC 59.426 43.478 9.03 0.00 41.90 3.01
2001 2121 4.580580 GCTGAAATTCCCCGATGTAGAATT 59.419 41.667 0.00 0.00 40.92 2.17
2007 2127 5.890424 TTCCCCGATGTAGAATTTGAAAC 57.110 39.130 0.00 0.00 0.00 2.78
2027 2148 1.336440 CCTGAACCAATTGCGTGTCAA 59.664 47.619 0.00 0.00 39.32 3.18
2028 2149 2.223688 CCTGAACCAATTGCGTGTCAAA 60.224 45.455 0.00 0.00 38.34 2.69
2029 2150 3.552684 CCTGAACCAATTGCGTGTCAAAT 60.553 43.478 0.00 0.00 38.34 2.32
2030 2151 4.050553 CTGAACCAATTGCGTGTCAAATT 58.949 39.130 0.00 0.00 38.34 1.82
2066 2187 1.868498 CGTTCCTTTCCACGTAGCAAA 59.132 47.619 0.00 0.00 0.00 3.68
2073 2194 0.666274 TCCACGTAGCAAAGCAGTCG 60.666 55.000 0.00 0.00 0.00 4.18
2093 2214 0.832135 AGCAGAACCGGACTTCCTCA 60.832 55.000 9.46 0.00 0.00 3.86
2129 2251 2.031930 GCTCACTCCAGCTAGTACGTAC 59.968 54.545 18.10 18.10 36.38 3.67
2165 2290 1.264288 GATCCGCGTTGAATTCCCATC 59.736 52.381 4.92 0.00 0.00 3.51
2291 2444 9.807921 AAAATATTTCCTGTCCAGAGAAAACTA 57.192 29.630 0.10 5.34 34.09 2.24
2325 2517 3.507622 GCCATGGCCATCCTAAATTCTAC 59.492 47.826 27.24 0.00 34.56 2.59
2334 2526 7.285401 GGCCATCCTAAATTCTACAATGAAGAA 59.715 37.037 0.00 0.00 37.38 2.52
2401 2725 1.474855 GCAAGGCAACAACCCACAATT 60.475 47.619 0.00 0.00 41.41 2.32
2457 2782 2.073816 CGTCATACACAAACAGGGGAC 58.926 52.381 0.00 0.00 0.00 4.46
2458 2783 2.289444 CGTCATACACAAACAGGGGACT 60.289 50.000 0.00 0.00 46.44 3.85
2466 2794 6.894339 ACACAAACAGGGGACTAAAAATAG 57.106 37.500 0.00 0.00 40.21 1.73
2469 2797 6.940298 CACAAACAGGGGACTAAAAATAGAGA 59.060 38.462 0.00 0.00 40.21 3.10
2470 2798 7.447238 CACAAACAGGGGACTAAAAATAGAGAA 59.553 37.037 0.00 0.00 40.21 2.87
2471 2799 8.002459 ACAAACAGGGGACTAAAAATAGAGAAA 58.998 33.333 0.00 0.00 40.21 2.52
2475 2803 8.225416 ACAGGGGACTAAAAATAGAGAAAAAGT 58.775 33.333 0.00 0.00 40.21 2.66
2496 2824 9.990868 AAAAGTGGAAGAAAACCTATATACCAT 57.009 29.630 0.00 0.00 0.00 3.55
2506 2834 8.577164 AAAACCTATATACCATGGAACCTACT 57.423 34.615 21.47 0.00 0.00 2.57
2584 2912 8.948631 TTCTATGGTAAAACAGAGTCATCATC 57.051 34.615 0.00 0.00 31.85 2.92
2585 2913 8.311395 TCTATGGTAAAACAGAGTCATCATCT 57.689 34.615 0.00 0.00 31.85 2.90
2590 2918 6.989169 GGTAAAACAGAGTCATCATCTATGCT 59.011 38.462 0.00 0.00 35.38 3.79
2591 2919 8.144478 GGTAAAACAGAGTCATCATCTATGCTA 58.856 37.037 0.00 0.00 35.38 3.49
2592 2920 9.703892 GTAAAACAGAGTCATCATCTATGCTAT 57.296 33.333 0.00 0.00 35.38 2.97
2593 2921 8.604640 AAAACAGAGTCATCATCTATGCTATG 57.395 34.615 0.00 0.00 37.17 2.23
2594 2922 6.914654 ACAGAGTCATCATCTATGCTATGT 57.085 37.500 0.00 0.00 38.34 2.29
2595 2923 8.414629 AACAGAGTCATCATCTATGCTATGTA 57.585 34.615 8.82 0.00 40.27 2.29
2596 2924 8.054152 ACAGAGTCATCATCTATGCTATGTAG 57.946 38.462 0.00 0.00 39.83 2.74
2617 2945 2.334307 CCGATACGGTGATACGGGT 58.666 57.895 0.00 0.00 42.73 5.28
2618 2946 1.522668 CCGATACGGTGATACGGGTA 58.477 55.000 0.00 0.00 42.73 3.69
2619 2947 1.197721 CCGATACGGTGATACGGGTAC 59.802 57.143 0.00 0.00 42.73 3.34
2620 2948 4.306489 CCGATACGGTGATACGGGTACG 62.306 59.091 0.00 0.00 42.73 3.67
2621 2949 1.197721 GATACGGTGATACGGGTACGG 59.802 57.143 0.00 0.00 46.48 4.02
2622 2950 1.444119 TACGGTGATACGGGTACGGC 61.444 60.000 0.00 0.00 46.48 5.68
2623 2951 2.026590 GGTGATACGGGTACGGCG 59.973 66.667 4.80 4.80 46.48 6.46
2624 2952 2.480610 GGTGATACGGGTACGGCGA 61.481 63.158 16.62 0.00 46.48 5.54
2625 2953 1.656441 GTGATACGGGTACGGCGAT 59.344 57.895 16.62 0.00 46.48 4.58
2626 2954 0.874390 GTGATACGGGTACGGCGATA 59.126 55.000 16.62 0.00 46.48 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.610522 CTTGCTTTGGACCAAGGACTG 59.389 52.381 19.90 4.79 35.86 3.51
12 13 1.494721 TCTTGCTTTGGACCAAGGACT 59.505 47.619 19.90 0.00 39.07 3.85
13 14 1.882623 CTCTTGCTTTGGACCAAGGAC 59.117 52.381 19.90 11.28 39.07 3.85
14 15 1.494721 ACTCTTGCTTTGGACCAAGGA 59.505 47.619 19.90 7.10 39.07 3.36
15 16 1.986882 ACTCTTGCTTTGGACCAAGG 58.013 50.000 11.90 11.90 39.07 3.61
16 17 3.004106 CAGAACTCTTGCTTTGGACCAAG 59.996 47.826 7.07 3.37 39.74 3.61
17 18 2.951642 CAGAACTCTTGCTTTGGACCAA 59.048 45.455 1.69 1.69 0.00 3.67
18 19 2.092429 ACAGAACTCTTGCTTTGGACCA 60.092 45.455 0.00 0.00 0.00 4.02
19 20 2.576615 ACAGAACTCTTGCTTTGGACC 58.423 47.619 0.00 0.00 0.00 4.46
20 21 3.793465 GCAACAGAACTCTTGCTTTGGAC 60.793 47.826 7.37 0.00 39.79 4.02
21 22 2.358898 GCAACAGAACTCTTGCTTTGGA 59.641 45.455 7.37 0.00 39.79 3.53
22 23 2.735823 GCAACAGAACTCTTGCTTTGG 58.264 47.619 7.37 0.00 39.79 3.28
27 28 3.978718 AGAAAGCAACAGAACTCTTGC 57.021 42.857 6.68 6.68 42.67 4.01
28 29 7.697691 TCTAAAAGAAAGCAACAGAACTCTTG 58.302 34.615 0.00 0.00 0.00 3.02
29 30 7.865706 TCTAAAAGAAAGCAACAGAACTCTT 57.134 32.000 0.00 0.00 0.00 2.85
30 31 7.865706 TTCTAAAAGAAAGCAACAGAACTCT 57.134 32.000 0.00 0.00 29.99 3.24
31 32 7.968405 TGTTTCTAAAAGAAAGCAACAGAACTC 59.032 33.333 2.42 0.00 44.07 3.01
32 33 7.755373 GTGTTTCTAAAAGAAAGCAACAGAACT 59.245 33.333 2.42 0.00 44.07 3.01
33 34 7.009265 GGTGTTTCTAAAAGAAAGCAACAGAAC 59.991 37.037 2.42 0.00 44.07 3.01
34 35 7.033185 GGTGTTTCTAAAAGAAAGCAACAGAA 58.967 34.615 2.42 0.00 44.07 3.02
35 36 6.560711 GGTGTTTCTAAAAGAAAGCAACAGA 58.439 36.000 2.42 0.00 44.07 3.41
36 37 5.455525 CGGTGTTTCTAAAAGAAAGCAACAG 59.544 40.000 2.42 0.71 44.07 3.16
37 38 5.106078 ACGGTGTTTCTAAAAGAAAGCAACA 60.106 36.000 2.42 0.00 44.07 3.33
38 39 5.337554 ACGGTGTTTCTAAAAGAAAGCAAC 58.662 37.500 2.42 6.26 44.07 4.17
39 40 5.570234 ACGGTGTTTCTAAAAGAAAGCAA 57.430 34.783 2.42 0.00 44.07 3.91
40 41 6.483974 TCATACGGTGTTTCTAAAAGAAAGCA 59.516 34.615 2.42 2.52 44.07 3.91
41 42 6.894828 TCATACGGTGTTTCTAAAAGAAAGC 58.105 36.000 2.42 0.20 44.07 3.51
77 78 3.849563 TTCAACCTCCTTTTCGGAAGA 57.150 42.857 1.68 0.00 42.53 2.87
78 79 3.630312 TGTTTCAACCTCCTTTTCGGAAG 59.370 43.478 0.00 0.00 42.53 3.46
79 80 3.379057 GTGTTTCAACCTCCTTTTCGGAA 59.621 43.478 0.00 0.00 42.53 4.30
80 81 2.946990 GTGTTTCAACCTCCTTTTCGGA 59.053 45.455 0.00 0.00 40.30 4.55
81 82 2.685897 TGTGTTTCAACCTCCTTTTCGG 59.314 45.455 0.00 0.00 0.00 4.30
82 83 3.377172 ACTGTGTTTCAACCTCCTTTTCG 59.623 43.478 0.00 0.00 0.00 3.46
83 84 4.983671 ACTGTGTTTCAACCTCCTTTTC 57.016 40.909 0.00 0.00 0.00 2.29
84 85 5.258051 TGTACTGTGTTTCAACCTCCTTTT 58.742 37.500 0.00 0.00 0.00 2.27
85 86 4.850680 TGTACTGTGTTTCAACCTCCTTT 58.149 39.130 0.00 0.00 0.00 3.11
86 87 4.497291 TGTACTGTGTTTCAACCTCCTT 57.503 40.909 0.00 0.00 0.00 3.36
87 88 4.163458 TCTTGTACTGTGTTTCAACCTCCT 59.837 41.667 0.00 0.00 0.00 3.69
88 89 4.448210 TCTTGTACTGTGTTTCAACCTCC 58.552 43.478 0.00 0.00 0.00 4.30
89 90 6.619801 AATCTTGTACTGTGTTTCAACCTC 57.380 37.500 0.00 0.00 0.00 3.85
90 91 6.377146 ACAAATCTTGTACTGTGTTTCAACCT 59.623 34.615 0.00 0.00 43.27 3.50
91 92 6.560711 ACAAATCTTGTACTGTGTTTCAACC 58.439 36.000 0.00 0.00 43.27 3.77
92 93 7.462724 GCAACAAATCTTGTACTGTGTTTCAAC 60.463 37.037 0.00 0.00 44.59 3.18
93 94 6.529829 GCAACAAATCTTGTACTGTGTTTCAA 59.470 34.615 0.00 0.00 44.59 2.69
94 95 6.033341 GCAACAAATCTTGTACTGTGTTTCA 58.967 36.000 0.00 0.00 44.59 2.69
95 96 6.033341 TGCAACAAATCTTGTACTGTGTTTC 58.967 36.000 0.00 0.00 44.59 2.78
96 97 5.960113 TGCAACAAATCTTGTACTGTGTTT 58.040 33.333 0.00 0.00 44.59 2.83
97 98 5.574891 TGCAACAAATCTTGTACTGTGTT 57.425 34.783 0.00 0.00 44.59 3.32
98 99 5.772825 ATGCAACAAATCTTGTACTGTGT 57.227 34.783 0.00 0.00 44.59 3.72
99 100 5.630680 GGAATGCAACAAATCTTGTACTGTG 59.369 40.000 0.00 0.00 44.59 3.66
100 101 5.301551 TGGAATGCAACAAATCTTGTACTGT 59.698 36.000 0.00 0.00 44.59 3.55
101 102 5.771469 TGGAATGCAACAAATCTTGTACTG 58.229 37.500 0.00 0.00 44.59 2.74
102 103 6.594788 ATGGAATGCAACAAATCTTGTACT 57.405 33.333 0.00 0.00 44.59 2.73
103 104 6.867816 TGAATGGAATGCAACAAATCTTGTAC 59.132 34.615 0.00 0.00 44.59 2.90
104 105 6.867816 GTGAATGGAATGCAACAAATCTTGTA 59.132 34.615 0.00 0.00 44.59 2.41
106 107 5.697178 TGTGAATGGAATGCAACAAATCTTG 59.303 36.000 0.00 0.00 29.98 3.02
107 108 5.856156 TGTGAATGGAATGCAACAAATCTT 58.144 33.333 0.00 0.00 29.98 2.40
108 109 5.471556 TGTGAATGGAATGCAACAAATCT 57.528 34.783 0.00 0.00 29.98 2.40
109 110 5.064198 CCATGTGAATGGAATGCAACAAATC 59.936 40.000 0.00 0.00 44.39 2.17
110 111 4.938832 CCATGTGAATGGAATGCAACAAAT 59.061 37.500 0.00 0.00 44.39 2.32
111 112 4.316645 CCATGTGAATGGAATGCAACAAA 58.683 39.130 0.00 0.00 44.39 2.83
112 113 3.865302 GCCATGTGAATGGAATGCAACAA 60.865 43.478 8.93 0.00 44.39 2.83
113 114 2.353903 GCCATGTGAATGGAATGCAACA 60.354 45.455 8.93 0.00 44.39 3.33
114 115 2.273557 GCCATGTGAATGGAATGCAAC 58.726 47.619 8.93 0.00 44.39 4.17
115 116 1.900486 TGCCATGTGAATGGAATGCAA 59.100 42.857 8.93 0.00 44.39 4.08
116 117 1.558233 TGCCATGTGAATGGAATGCA 58.442 45.000 8.93 0.00 44.39 3.96
117 118 2.676632 TTGCCATGTGAATGGAATGC 57.323 45.000 8.93 0.00 44.39 3.56
118 119 6.503589 AAAATTTGCCATGTGAATGGAATG 57.496 33.333 8.93 0.00 44.39 2.67
119 120 5.352016 CGAAAATTTGCCATGTGAATGGAAT 59.648 36.000 8.93 0.00 44.39 3.01
120 121 4.689812 CGAAAATTTGCCATGTGAATGGAA 59.310 37.500 8.93 0.00 44.39 3.53
121 122 4.244066 CGAAAATTTGCCATGTGAATGGA 58.756 39.130 8.93 0.00 44.39 3.41
122 123 3.995705 ACGAAAATTTGCCATGTGAATGG 59.004 39.130 0.15 0.15 44.44 3.16
123 124 5.594724 AACGAAAATTTGCCATGTGAATG 57.405 34.783 0.00 0.00 0.00 2.67
124 125 5.990996 AGAAACGAAAATTTGCCATGTGAAT 59.009 32.000 0.00 0.00 0.00 2.57
125 126 5.355596 AGAAACGAAAATTTGCCATGTGAA 58.644 33.333 0.00 0.00 0.00 3.18
126 127 4.942852 AGAAACGAAAATTTGCCATGTGA 58.057 34.783 0.00 0.00 0.00 3.58
127 128 4.143556 CGAGAAACGAAAATTTGCCATGTG 60.144 41.667 0.00 0.00 45.77 3.21
128 129 3.980775 CGAGAAACGAAAATTTGCCATGT 59.019 39.130 0.00 0.00 45.77 3.21
129 130 3.181541 GCGAGAAACGAAAATTTGCCATG 60.182 43.478 0.00 0.00 45.77 3.66
130 131 2.986479 GCGAGAAACGAAAATTTGCCAT 59.014 40.909 0.00 0.00 45.77 4.40
131 132 2.223595 TGCGAGAAACGAAAATTTGCCA 60.224 40.909 0.00 0.00 45.77 4.92
132 133 2.389998 TGCGAGAAACGAAAATTTGCC 58.610 42.857 0.00 0.00 45.77 4.52
133 134 4.430407 TTTGCGAGAAACGAAAATTTGC 57.570 36.364 0.00 0.00 43.53 3.68
151 152 4.623595 ACCAAACACTTTTTAGCACGTTTG 59.376 37.500 0.00 0.00 41.64 2.93
152 153 4.623595 CACCAAACACTTTTTAGCACGTTT 59.376 37.500 0.00 0.00 0.00 3.60
153 154 4.170256 CACCAAACACTTTTTAGCACGTT 58.830 39.130 0.00 0.00 0.00 3.99
154 155 3.428316 CCACCAAACACTTTTTAGCACGT 60.428 43.478 0.00 0.00 0.00 4.49
155 156 3.112580 CCACCAAACACTTTTTAGCACG 58.887 45.455 0.00 0.00 0.00 5.34
156 157 4.379339 TCCACCAAACACTTTTTAGCAC 57.621 40.909 0.00 0.00 0.00 4.40
157 158 5.127845 TCAATCCACCAAACACTTTTTAGCA 59.872 36.000 0.00 0.00 0.00 3.49
158 159 5.596845 TCAATCCACCAAACACTTTTTAGC 58.403 37.500 0.00 0.00 0.00 3.09
159 160 6.701400 CCTTCAATCCACCAAACACTTTTTAG 59.299 38.462 0.00 0.00 0.00 1.85
160 161 6.578023 CCTTCAATCCACCAAACACTTTTTA 58.422 36.000 0.00 0.00 0.00 1.52
161 162 5.427378 CCTTCAATCCACCAAACACTTTTT 58.573 37.500 0.00 0.00 0.00 1.94
162 163 4.683129 GCCTTCAATCCACCAAACACTTTT 60.683 41.667 0.00 0.00 0.00 2.27
163 164 3.181466 GCCTTCAATCCACCAAACACTTT 60.181 43.478 0.00 0.00 0.00 2.66
164 165 2.365293 GCCTTCAATCCACCAAACACTT 59.635 45.455 0.00 0.00 0.00 3.16
165 166 1.963515 GCCTTCAATCCACCAAACACT 59.036 47.619 0.00 0.00 0.00 3.55
166 167 1.686052 TGCCTTCAATCCACCAAACAC 59.314 47.619 0.00 0.00 0.00 3.32
167 168 2.079170 TGCCTTCAATCCACCAAACA 57.921 45.000 0.00 0.00 0.00 2.83
168 169 2.562298 TCATGCCTTCAATCCACCAAAC 59.438 45.455 0.00 0.00 0.00 2.93
169 170 2.562298 GTCATGCCTTCAATCCACCAAA 59.438 45.455 0.00 0.00 0.00 3.28
170 171 2.170166 GTCATGCCTTCAATCCACCAA 58.830 47.619 0.00 0.00 0.00 3.67
171 172 1.616725 GGTCATGCCTTCAATCCACCA 60.617 52.381 0.00 0.00 0.00 4.17
172 173 1.106285 GGTCATGCCTTCAATCCACC 58.894 55.000 0.00 0.00 0.00 4.61
173 174 1.838112 TGGTCATGCCTTCAATCCAC 58.162 50.000 7.54 0.00 38.35 4.02
174 175 2.832643 ATGGTCATGCCTTCAATCCA 57.167 45.000 7.54 0.00 38.35 3.41
175 176 2.033801 CGAATGGTCATGCCTTCAATCC 59.966 50.000 7.54 0.00 38.35 3.01
176 177 2.033801 CCGAATGGTCATGCCTTCAATC 59.966 50.000 7.54 0.00 38.35 2.67
177 178 2.026641 CCGAATGGTCATGCCTTCAAT 58.973 47.619 7.54 0.00 38.35 2.57
178 179 1.462616 CCGAATGGTCATGCCTTCAA 58.537 50.000 7.54 0.00 38.35 2.69
179 180 0.394216 CCCGAATGGTCATGCCTTCA 60.394 55.000 7.54 0.00 38.35 3.02
180 181 1.728490 GCCCGAATGGTCATGCCTTC 61.728 60.000 7.54 7.56 38.35 3.46
181 182 1.754234 GCCCGAATGGTCATGCCTT 60.754 57.895 7.54 0.00 38.35 4.35
182 183 1.344953 TAGCCCGAATGGTCATGCCT 61.345 55.000 7.54 0.00 38.35 4.75
183 184 0.250901 ATAGCCCGAATGGTCATGCC 60.251 55.000 0.00 0.00 36.04 4.40
184 185 2.350522 CTATAGCCCGAATGGTCATGC 58.649 52.381 0.00 0.00 36.04 4.06
185 186 2.350522 GCTATAGCCCGAATGGTCATG 58.649 52.381 14.13 0.00 36.04 3.07
186 187 2.770164 GCTATAGCCCGAATGGTCAT 57.230 50.000 14.13 0.00 36.04 3.06
198 199 2.224523 TGTTGCACCATAGGGCTATAGC 60.225 50.000 16.78 16.78 37.90 2.97
199 200 3.403038 GTGTTGCACCATAGGGCTATAG 58.597 50.000 0.00 0.00 37.90 1.31
200 201 3.485463 GTGTTGCACCATAGGGCTATA 57.515 47.619 0.00 0.00 37.90 1.31
201 202 2.348411 GTGTTGCACCATAGGGCTAT 57.652 50.000 0.00 0.00 37.90 2.97
202 203 3.873781 GTGTTGCACCATAGGGCTA 57.126 52.632 0.00 0.00 37.90 3.93
203 204 4.743018 GTGTTGCACCATAGGGCT 57.257 55.556 0.00 0.00 37.90 5.19
212 213 0.603975 GTGAGGAGGAGGTGTTGCAC 60.604 60.000 0.00 0.00 0.00 4.57
213 214 1.754745 GTGAGGAGGAGGTGTTGCA 59.245 57.895 0.00 0.00 0.00 4.08
214 215 1.003233 GGTGAGGAGGAGGTGTTGC 60.003 63.158 0.00 0.00 0.00 4.17
215 216 0.838122 AGGGTGAGGAGGAGGTGTTG 60.838 60.000 0.00 0.00 0.00 3.33
216 217 0.545548 GAGGGTGAGGAGGAGGTGTT 60.546 60.000 0.00 0.00 0.00 3.32
217 218 1.079438 GAGGGTGAGGAGGAGGTGT 59.921 63.158 0.00 0.00 0.00 4.16
218 219 1.687493 GGAGGGTGAGGAGGAGGTG 60.687 68.421 0.00 0.00 0.00 4.00
219 220 1.864559 AGGAGGGTGAGGAGGAGGT 60.865 63.158 0.00 0.00 0.00 3.85
220 221 1.075600 GAGGAGGGTGAGGAGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
221 222 0.264359 ATGAGGAGGGTGAGGAGGAG 59.736 60.000 0.00 0.00 0.00 3.69
222 223 0.719015 AATGAGGAGGGTGAGGAGGA 59.281 55.000 0.00 0.00 0.00 3.71
223 224 0.835941 CAATGAGGAGGGTGAGGAGG 59.164 60.000 0.00 0.00 0.00 4.30
224 225 0.835941 CCAATGAGGAGGGTGAGGAG 59.164 60.000 0.00 0.00 41.22 3.69
225 226 0.119155 ACCAATGAGGAGGGTGAGGA 59.881 55.000 0.00 0.00 41.22 3.71
226 227 0.995024 AACCAATGAGGAGGGTGAGG 59.005 55.000 0.00 0.00 41.22 3.86
227 228 1.952367 GCAACCAATGAGGAGGGTGAG 60.952 57.143 0.00 0.00 45.60 3.51
228 229 0.038166 GCAACCAATGAGGAGGGTGA 59.962 55.000 0.00 0.00 45.60 4.02
229 230 0.251297 TGCAACCAATGAGGAGGGTG 60.251 55.000 0.00 0.00 45.51 4.61
230 231 0.706433 ATGCAACCAATGAGGAGGGT 59.294 50.000 0.00 0.00 41.22 4.34
231 232 1.856629 AATGCAACCAATGAGGAGGG 58.143 50.000 0.00 0.00 41.22 4.30
232 233 4.403432 ACATAAATGCAACCAATGAGGAGG 59.597 41.667 0.00 0.00 41.22 4.30
233 234 5.359009 AGACATAAATGCAACCAATGAGGAG 59.641 40.000 0.00 0.00 41.22 3.69
234 235 5.263599 AGACATAAATGCAACCAATGAGGA 58.736 37.500 0.00 0.00 41.22 3.71
235 236 5.587388 AGACATAAATGCAACCAATGAGG 57.413 39.130 0.00 0.00 45.67 3.86
236 237 6.860080 AGAAGACATAAATGCAACCAATGAG 58.140 36.000 0.00 0.00 0.00 2.90
237 238 6.433716 TGAGAAGACATAAATGCAACCAATGA 59.566 34.615 0.00 0.00 0.00 2.57
238 239 6.529125 GTGAGAAGACATAAATGCAACCAATG 59.471 38.462 0.00 0.00 0.00 2.82
239 240 6.209192 TGTGAGAAGACATAAATGCAACCAAT 59.791 34.615 0.00 0.00 0.00 3.16
240 241 5.534278 TGTGAGAAGACATAAATGCAACCAA 59.466 36.000 0.00 0.00 0.00 3.67
241 242 5.069318 TGTGAGAAGACATAAATGCAACCA 58.931 37.500 0.00 0.00 0.00 3.67
242 243 5.627499 TGTGAGAAGACATAAATGCAACC 57.373 39.130 0.00 0.00 0.00 3.77
243 244 7.533426 AGATTGTGAGAAGACATAAATGCAAC 58.467 34.615 0.00 0.00 0.00 4.17
244 245 7.148188 GGAGATTGTGAGAAGACATAAATGCAA 60.148 37.037 0.00 0.00 0.00 4.08
245 246 6.317140 GGAGATTGTGAGAAGACATAAATGCA 59.683 38.462 0.00 0.00 0.00 3.96
246 247 6.317140 TGGAGATTGTGAGAAGACATAAATGC 59.683 38.462 0.00 0.00 0.00 3.56
247 248 7.201679 GGTGGAGATTGTGAGAAGACATAAATG 60.202 40.741 0.00 0.00 0.00 2.32
248 249 6.825721 GGTGGAGATTGTGAGAAGACATAAAT 59.174 38.462 0.00 0.00 0.00 1.40
249 250 6.173339 GGTGGAGATTGTGAGAAGACATAAA 58.827 40.000 0.00 0.00 0.00 1.40
250 251 5.338381 GGGTGGAGATTGTGAGAAGACATAA 60.338 44.000 0.00 0.00 0.00 1.90
251 252 4.162320 GGGTGGAGATTGTGAGAAGACATA 59.838 45.833 0.00 0.00 0.00 2.29
252 253 3.054802 GGGTGGAGATTGTGAGAAGACAT 60.055 47.826 0.00 0.00 0.00 3.06
253 254 2.303022 GGGTGGAGATTGTGAGAAGACA 59.697 50.000 0.00 0.00 0.00 3.41
254 255 2.355209 GGGGTGGAGATTGTGAGAAGAC 60.355 54.545 0.00 0.00 0.00 3.01
255 256 1.909302 GGGGTGGAGATTGTGAGAAGA 59.091 52.381 0.00 0.00 0.00 2.87
256 257 1.912043 AGGGGTGGAGATTGTGAGAAG 59.088 52.381 0.00 0.00 0.00 2.85
257 258 1.630369 CAGGGGTGGAGATTGTGAGAA 59.370 52.381 0.00 0.00 0.00 2.87
258 259 1.279496 CAGGGGTGGAGATTGTGAGA 58.721 55.000 0.00 0.00 0.00 3.27
259 260 0.987294 ACAGGGGTGGAGATTGTGAG 59.013 55.000 0.00 0.00 0.00 3.51
260 261 1.444933 AACAGGGGTGGAGATTGTGA 58.555 50.000 0.00 0.00 0.00 3.58
261 262 1.888512 CAAACAGGGGTGGAGATTGTG 59.111 52.381 0.00 0.00 0.00 3.33
262 263 1.499007 ACAAACAGGGGTGGAGATTGT 59.501 47.619 0.00 0.00 0.00 2.71
263 264 2.162681 GACAAACAGGGGTGGAGATTG 58.837 52.381 0.00 0.00 0.00 2.67
264 265 2.065799 AGACAAACAGGGGTGGAGATT 58.934 47.619 0.00 0.00 0.00 2.40
265 266 1.747444 AGACAAACAGGGGTGGAGAT 58.253 50.000 0.00 0.00 0.00 2.75
266 267 2.409064 TAGACAAACAGGGGTGGAGA 57.591 50.000 0.00 0.00 0.00 3.71
267 268 3.721087 ATTAGACAAACAGGGGTGGAG 57.279 47.619 0.00 0.00 0.00 3.86
268 269 5.586155 TTTATTAGACAAACAGGGGTGGA 57.414 39.130 0.00 0.00 0.00 4.02
269 270 6.658188 TTTTTATTAGACAAACAGGGGTGG 57.342 37.500 0.00 0.00 0.00 4.61
270 271 8.122472 AGATTTTTATTAGACAAACAGGGGTG 57.878 34.615 0.00 0.00 0.00 4.61
271 272 7.396339 GGAGATTTTTATTAGACAAACAGGGGT 59.604 37.037 0.00 0.00 0.00 4.95
272 273 7.396055 TGGAGATTTTTATTAGACAAACAGGGG 59.604 37.037 0.00 0.00 0.00 4.79
273 274 8.244113 GTGGAGATTTTTATTAGACAAACAGGG 58.756 37.037 0.00 0.00 0.00 4.45
274 275 8.244113 GGTGGAGATTTTTATTAGACAAACAGG 58.756 37.037 0.00 0.00 0.00 4.00
275 276 8.244113 GGGTGGAGATTTTTATTAGACAAACAG 58.756 37.037 0.00 0.00 0.00 3.16
276 277 7.177744 GGGGTGGAGATTTTTATTAGACAAACA 59.822 37.037 0.00 0.00 0.00 2.83
277 278 7.363530 GGGGGTGGAGATTTTTATTAGACAAAC 60.364 40.741 0.00 0.00 0.00 2.93
278 279 6.666113 GGGGGTGGAGATTTTTATTAGACAAA 59.334 38.462 0.00 0.00 0.00 2.83
279 280 6.192044 GGGGGTGGAGATTTTTATTAGACAA 58.808 40.000 0.00 0.00 0.00 3.18
280 281 5.762279 GGGGGTGGAGATTTTTATTAGACA 58.238 41.667 0.00 0.00 0.00 3.41
316 317 2.992476 TGGGGACAGTTAGAGGAGC 58.008 57.895 0.00 0.00 35.01 4.70
331 332 0.883814 GGCAGAGAAGCGATGATGGG 60.884 60.000 0.00 0.00 34.64 4.00
334 335 0.829333 AGTGGCAGAGAAGCGATGAT 59.171 50.000 0.00 0.00 34.64 2.45
376 383 5.590530 AGTGTGTGCTAATTTCCAACAAA 57.409 34.783 0.00 0.00 0.00 2.83
379 386 4.760204 AGGTAGTGTGTGCTAATTTCCAAC 59.240 41.667 0.00 0.00 0.00 3.77
383 390 9.542462 TCATTATAGGTAGTGTGTGCTAATTTC 57.458 33.333 0.00 0.00 0.00 2.17
389 396 5.602561 TCCATCATTATAGGTAGTGTGTGCT 59.397 40.000 0.00 0.00 0.00 4.40
410 417 6.644347 TGTTTATTTTCTTGCAGGTTTTCCA 58.356 32.000 0.00 0.00 43.73 3.53
411 418 7.728847 ATGTTTATTTTCTTGCAGGTTTTCC 57.271 32.000 0.00 0.00 41.05 3.13
417 425 6.751425 TCGCATAATGTTTATTTTCTTGCAGG 59.249 34.615 0.00 0.00 0.00 4.85
418 426 7.253750 GGTCGCATAATGTTTATTTTCTTGCAG 60.254 37.037 0.00 0.00 0.00 4.41
419 427 6.529829 GGTCGCATAATGTTTATTTTCTTGCA 59.470 34.615 0.00 0.00 0.00 4.08
420 428 6.529829 TGGTCGCATAATGTTTATTTTCTTGC 59.470 34.615 0.00 0.00 0.00 4.01
429 437 7.985184 AGACTTAGAATGGTCGCATAATGTTTA 59.015 33.333 0.00 0.00 37.52 2.01
436 444 5.516996 CGTTAGACTTAGAATGGTCGCATA 58.483 41.667 0.00 0.00 37.52 3.14
567 610 2.291741 GTGACTTTTCTGCAGACCCAAG 59.708 50.000 18.03 19.70 0.00 3.61
822 896 7.774157 CACGGTGGTATCAGGAGTATATATACT 59.226 40.741 22.67 22.67 45.73 2.12
890 964 3.380004 TGGATTGTTTACCAATGGATCGC 59.620 43.478 6.16 0.00 43.87 4.58
897 971 3.164268 TGCTGCTGGATTGTTTACCAAT 58.836 40.909 0.00 0.00 46.51 3.16
925 1000 1.104577 GGAGTAGGGAGAGGTGAGCG 61.105 65.000 0.00 0.00 0.00 5.03
940 1020 6.901300 ACCTAGAGATAGATAGATCGAGGAGT 59.099 42.308 7.13 0.00 33.10 3.85
989 1074 2.203972 CTTCGCCATGGCCACACTTG 62.204 60.000 30.79 14.90 37.98 3.16
990 1075 1.973281 CTTCGCCATGGCCACACTT 60.973 57.895 30.79 0.00 37.98 3.16
1261 1349 4.641645 CAGCCACTGGTCGCCCAA 62.642 66.667 0.00 0.00 41.27 4.12
1675 1771 2.242043 CTCTCAGGCCCAAACAATGTT 58.758 47.619 0.00 0.00 0.00 2.71
1801 1900 9.528018 CAGTAAAAATGAACAAAACCATACACT 57.472 29.630 0.00 0.00 0.00 3.55
1863 1962 6.235231 TGAGTAATACACTTTCATCCCTCC 57.765 41.667 0.00 0.00 37.72 4.30
1933 2050 2.079925 GCTGCGAAAGTTGGAGAGAAT 58.920 47.619 0.00 0.00 0.00 2.40
1948 2065 2.753931 GAAAGGCCTTTGGTGCTGCG 62.754 60.000 35.05 0.00 32.11 5.18
1968 2088 3.306294 GGGGAATTTCAGCAAACTTCTGG 60.306 47.826 0.00 0.00 32.63 3.86
1971 2091 2.556622 TCGGGGAATTTCAGCAAACTTC 59.443 45.455 0.00 0.00 0.00 3.01
1977 2097 2.503765 TCTACATCGGGGAATTTCAGCA 59.496 45.455 0.00 0.00 0.00 4.41
1988 2108 4.941263 TCAGGTTTCAAATTCTACATCGGG 59.059 41.667 0.00 0.00 0.00 5.14
2001 2121 2.428890 ACGCAATTGGTTCAGGTTTCAA 59.571 40.909 7.72 0.00 0.00 2.69
2007 2127 0.950836 TGACACGCAATTGGTTCAGG 59.049 50.000 7.72 0.00 0.00 3.86
2066 2187 2.259818 CGGTTCTGCTCGACTGCT 59.740 61.111 0.00 0.00 0.00 4.24
2073 2194 0.108567 GAGGAAGTCCGGTTCTGCTC 60.109 60.000 0.00 3.21 42.08 4.26
2129 2251 3.832237 ATCATTGGCCGGCGCTAGG 62.832 63.158 22.54 16.25 34.44 3.02
2291 2444 1.003464 GGCCATGGCTGGTTTCAAATT 59.997 47.619 34.70 0.00 45.10 1.82
2440 2765 6.642707 TTTTTAGTCCCCTGTTTGTGTATG 57.357 37.500 0.00 0.00 0.00 2.39
2443 2768 6.607019 TCTATTTTTAGTCCCCTGTTTGTGT 58.393 36.000 0.00 0.00 0.00 3.72
2444 2769 6.940298 TCTCTATTTTTAGTCCCCTGTTTGTG 59.060 38.462 0.00 0.00 0.00 3.33
2452 2777 7.668469 TCCACTTTTTCTCTATTTTTAGTCCCC 59.332 37.037 0.00 0.00 0.00 4.81
2469 2797 9.816787 TGGTATATAGGTTTTCTTCCACTTTTT 57.183 29.630 0.00 0.00 0.00 1.94
2470 2798 9.990868 ATGGTATATAGGTTTTCTTCCACTTTT 57.009 29.630 0.00 0.00 0.00 2.27
2471 2799 9.408648 CATGGTATATAGGTTTTCTTCCACTTT 57.591 33.333 0.00 0.00 0.00 2.66
2475 2803 7.699709 TCCATGGTATATAGGTTTTCTTCCA 57.300 36.000 12.58 0.00 0.00 3.53
2490 2818 3.073062 GCCATCAGTAGGTTCCATGGTAT 59.927 47.826 12.58 0.00 37.02 2.73
2496 2824 1.281867 CCTTGCCATCAGTAGGTTCCA 59.718 52.381 0.00 0.00 0.00 3.53
2506 2834 3.454719 TGGATTTCTTCCTTGCCATCA 57.545 42.857 0.00 0.00 45.68 3.07
2600 2928 1.136252 CGTACCCGTATCACCGTATCG 60.136 57.143 0.00 0.00 0.00 2.92
2601 2929 1.197721 CCGTACCCGTATCACCGTATC 59.802 57.143 0.00 0.00 0.00 2.24
2602 2930 1.238439 CCGTACCCGTATCACCGTAT 58.762 55.000 0.00 0.00 0.00 3.06
2603 2931 1.444119 GCCGTACCCGTATCACCGTA 61.444 60.000 0.00 0.00 0.00 4.02
2604 2932 2.774799 GCCGTACCCGTATCACCGT 61.775 63.158 0.00 0.00 0.00 4.83
2605 2933 2.026590 GCCGTACCCGTATCACCG 59.973 66.667 0.00 0.00 0.00 4.94
2606 2934 1.799258 ATCGCCGTACCCGTATCACC 61.799 60.000 1.22 0.00 0.00 4.02
2607 2935 0.874390 TATCGCCGTACCCGTATCAC 59.126 55.000 1.22 0.00 0.00 3.06
2608 2936 3.320823 TATCGCCGTACCCGTATCA 57.679 52.632 1.22 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.