Multiple sequence alignment - TraesCS3B01G334900

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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 TraesCS3B01G334900 chr3B 100.000 4099 0 0 521 4619 540762164 540758066 0.000000e+00 7570.0
1 TraesCS3B01G334900 chr3B 100.000 247 0 0 1 247 540762684 540762438 1.510000e-124 457.0
2 TraesCS3B01G334900 chr3B 92.391 92 7 0 154 245 540762162 540762071 1.040000e-26 132.0
3 TraesCS3B01G334900 chr3B 92.391 92 7 0 523 614 540762531 540762440 1.040000e-26 132.0
4 TraesCS3B01G334900 chr3A 95.499 2844 100 18 1796 4619 535217605 535220440 0.000000e+00 4518.0
5 TraesCS3B01G334900 chr3A 88.106 866 62 23 523 1356 535216035 535216891 0.000000e+00 990.0
6 TraesCS3B01G334900 chr3A 90.893 560 30 8 1384 1942 535216892 535217431 0.000000e+00 732.0
7 TraesCS3B01G334900 chr3A 94.558 147 8 0 1796 1942 535217445 535217591 1.290000e-55 228.0
8 TraesCS3B01G334900 chr3D 96.814 2417 54 14 1796 4203 414914839 414912437 0.000000e+00 4015.0
9 TraesCS3B01G334900 chr3D 91.748 1442 67 19 522 1942 414916263 414914853 0.000000e+00 1956.0
10 TraesCS3B01G334900 chr3D 90.610 426 22 7 4202 4619 414912281 414911866 2.430000e-152 549.0
11 TraesCS3B01G334900 chr7A 87.013 77 7 3 4545 4619 94913417 94913342 2.960000e-12 84.2


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 TraesCS3B01G334900 chr3B 540758066 540762684 4618 True 2072.750000 7570 96.195500 1 4619 4 chr3B.!!$R1 4618
1 TraesCS3B01G334900 chr3A 535216035 535220440 4405 False 1617.000000 4518 92.264000 523 4619 4 chr3A.!!$F1 4096
2 TraesCS3B01G334900 chr3D 414911866 414916263 4397 True 2173.333333 4015 93.057333 522 4619 3 chr3D.!!$R1 4097

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
49 50 0.037139 TATTGACGACCAACCCCACG 60.037 55.000 0.00 0.00 37.63 4.94 F
172 173 0.103937 CACCTCGCTTTGGCCAAAAA 59.896 50.000 29.93 17.63 34.44 1.94 F
546 547 0.103937 CGCCTTGGCCAAAAACTTGA 59.896 50.000 20.91 0.00 0.00 3.02 F
724 743 0.109086 CACAGCACCTCACCTCTACG 60.109 60.000 0.00 0.00 0.00 3.51 F
725 744 1.251527 ACAGCACCTCACCTCTACGG 61.252 60.000 0.00 0.00 39.35 4.02 F
753 777 1.343465 GGGACGACCACTTCAAAGAGA 59.657 52.381 6.20 0.00 39.85 3.10 F
2888 3244 1.159713 CCAGTGCTCTTTGCGACACA 61.160 55.000 0.00 0.00 46.63 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1283 0.106217 AAATCACCGGCCCCCAATAG 60.106 55.000 0.00 0.0 0.00 1.73 R
1381 1416 1.274167 ACCGAAGCAACGATGGACTTA 59.726 47.619 4.23 0.0 35.09 2.24 R
1836 2174 3.066064 TGCACATACGTTTGCAGAAAGTT 59.934 39.130 13.38 0.0 43.79 2.66 R
2343 2686 4.290722 AGATCTTCTGGAAAGAATGGGTGT 59.709 41.667 0.00 0.0 0.00 4.16 R
2557 2912 8.786826 ATGCTAGTTGCTAACAAGTAACAATA 57.213 30.769 8.67 0.0 39.80 1.90 R
2907 3263 7.342026 TCAAAGACCAGCAGTATTGATCTAGTA 59.658 37.037 0.00 0.0 32.36 1.82 R
4577 5101 0.741221 GCTCGACGGGCTTCTTCATT 60.741 55.000 13.71 0.0 0.00 2.57 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
18 19 3.935371 TGGAACCTTTTTCCTGCCA 57.065 47.368 4.73 0.00 39.31 4.92
19 20 1.408969 TGGAACCTTTTTCCTGCCAC 58.591 50.000 4.73 0.00 39.31 5.01
20 21 0.313987 GGAACCTTTTTCCTGCCACG 59.686 55.000 0.00 0.00 35.73 4.94
21 22 1.029681 GAACCTTTTTCCTGCCACGT 58.970 50.000 0.00 0.00 0.00 4.49
22 23 2.223745 GAACCTTTTTCCTGCCACGTA 58.776 47.619 0.00 0.00 0.00 3.57
23 24 2.579410 ACCTTTTTCCTGCCACGTAT 57.421 45.000 0.00 0.00 0.00 3.06
24 25 3.706600 ACCTTTTTCCTGCCACGTATA 57.293 42.857 0.00 0.00 0.00 1.47
25 26 4.023726 ACCTTTTTCCTGCCACGTATAA 57.976 40.909 0.00 0.00 0.00 0.98
26 27 4.595986 ACCTTTTTCCTGCCACGTATAAT 58.404 39.130 0.00 0.00 0.00 1.28
27 28 4.398044 ACCTTTTTCCTGCCACGTATAATG 59.602 41.667 0.00 0.00 0.00 1.90
28 29 4.398044 CCTTTTTCCTGCCACGTATAATGT 59.602 41.667 0.00 0.00 0.00 2.71
29 30 5.105917 CCTTTTTCCTGCCACGTATAATGTT 60.106 40.000 0.00 0.00 0.00 2.71
30 31 5.968528 TTTTCCTGCCACGTATAATGTTT 57.031 34.783 0.00 0.00 0.00 2.83
31 32 7.362229 CCTTTTTCCTGCCACGTATAATGTTTA 60.362 37.037 0.00 0.00 0.00 2.01
32 33 7.633193 TTTTCCTGCCACGTATAATGTTTAT 57.367 32.000 0.00 0.00 0.00 1.40
33 34 7.633193 TTTCCTGCCACGTATAATGTTTATT 57.367 32.000 0.00 0.00 0.00 1.40
34 35 6.612247 TCCTGCCACGTATAATGTTTATTG 57.388 37.500 0.00 0.00 0.00 1.90
35 36 6.350103 TCCTGCCACGTATAATGTTTATTGA 58.650 36.000 0.00 0.00 0.00 2.57
36 37 6.259167 TCCTGCCACGTATAATGTTTATTGAC 59.741 38.462 0.00 0.00 0.00 3.18
37 38 6.038601 TGCCACGTATAATGTTTATTGACG 57.961 37.500 0.00 0.00 40.17 4.35
38 39 5.811100 TGCCACGTATAATGTTTATTGACGA 59.189 36.000 12.87 0.00 38.32 4.20
39 40 6.124759 GCCACGTATAATGTTTATTGACGAC 58.875 40.000 12.87 0.00 38.32 4.34
40 41 6.642917 CCACGTATAATGTTTATTGACGACC 58.357 40.000 12.87 0.00 38.32 4.79
41 42 6.256104 CCACGTATAATGTTTATTGACGACCA 59.744 38.462 12.87 0.00 38.32 4.02
42 43 7.201539 CCACGTATAATGTTTATTGACGACCAA 60.202 37.037 12.87 0.00 38.32 3.67
43 44 7.633281 CACGTATAATGTTTATTGACGACCAAC 59.367 37.037 12.87 0.00 38.32 3.77
44 45 7.121272 CGTATAATGTTTATTGACGACCAACC 58.879 38.462 0.00 0.00 38.32 3.77
45 46 4.776795 AATGTTTATTGACGACCAACCC 57.223 40.909 0.00 0.00 37.63 4.11
46 47 2.506444 TGTTTATTGACGACCAACCCC 58.494 47.619 0.00 0.00 37.63 4.95
47 48 2.158652 TGTTTATTGACGACCAACCCCA 60.159 45.455 0.00 0.00 37.63 4.96
48 49 2.188062 TTATTGACGACCAACCCCAC 57.812 50.000 0.00 0.00 37.63 4.61
49 50 0.037139 TATTGACGACCAACCCCACG 60.037 55.000 0.00 0.00 37.63 4.94
50 51 3.964641 TATTGACGACCAACCCCACGC 62.965 57.143 0.00 0.00 37.63 5.34
57 58 4.263572 CAACCCCACGCCACCTCA 62.264 66.667 0.00 0.00 0.00 3.86
58 59 4.265056 AACCCCACGCCACCTCAC 62.265 66.667 0.00 0.00 0.00 3.51
61 62 4.394712 CCCACGCCACCTCACCTC 62.395 72.222 0.00 0.00 0.00 3.85
62 63 4.742201 CCACGCCACCTCACCTCG 62.742 72.222 0.00 0.00 0.00 4.63
63 64 4.742201 CACGCCACCTCACCTCGG 62.742 72.222 0.00 0.00 0.00 4.63
67 68 3.636231 CCACCTCACCTCGGCCAA 61.636 66.667 2.24 0.00 0.00 4.52
68 69 2.429930 CACCTCACCTCGGCCAAA 59.570 61.111 2.24 0.00 0.00 3.28
69 70 1.228124 CACCTCACCTCGGCCAAAA 60.228 57.895 2.24 0.00 0.00 2.44
70 71 1.073199 ACCTCACCTCGGCCAAAAG 59.927 57.895 2.24 0.00 0.00 2.27
71 72 1.073199 CCTCACCTCGGCCAAAAGT 59.927 57.895 2.24 0.00 0.00 2.66
72 73 0.537371 CCTCACCTCGGCCAAAAGTT 60.537 55.000 2.24 0.00 0.00 2.66
73 74 1.318576 CTCACCTCGGCCAAAAGTTT 58.681 50.000 2.24 0.00 0.00 2.66
74 75 1.001378 CTCACCTCGGCCAAAAGTTTG 60.001 52.381 2.24 0.00 37.90 2.93
101 102 9.470399 GGACTACCCCTTCTCAATAAAAATAAA 57.530 33.333 0.00 0.00 0.00 1.40
117 118 9.869757 ATAAAAATAAAATCTTTTCCTCACCGG 57.130 29.630 0.00 0.00 0.00 5.28
118 119 7.533289 AAAATAAAATCTTTTCCTCACCGGA 57.467 32.000 9.46 0.00 41.06 5.14
119 120 6.510879 AATAAAATCTTTTCCTCACCGGAC 57.489 37.500 9.46 0.00 42.97 4.79
120 121 3.502123 AAATCTTTTCCTCACCGGACA 57.498 42.857 9.46 0.00 42.97 4.02
121 122 3.721087 AATCTTTTCCTCACCGGACAT 57.279 42.857 9.46 0.00 42.97 3.06
122 123 2.472695 TCTTTTCCTCACCGGACATG 57.527 50.000 9.46 0.00 42.97 3.21
123 124 1.697432 TCTTTTCCTCACCGGACATGT 59.303 47.619 9.46 0.00 42.97 3.21
124 125 2.901192 TCTTTTCCTCACCGGACATGTA 59.099 45.455 9.46 0.00 42.97 2.29
125 126 2.754946 TTTCCTCACCGGACATGTAC 57.245 50.000 9.46 0.00 42.97 2.90
126 127 1.634960 TTCCTCACCGGACATGTACA 58.365 50.000 9.46 0.00 42.97 2.90
127 128 1.634960 TCCTCACCGGACATGTACAA 58.365 50.000 9.46 0.00 36.69 2.41
128 129 2.184533 TCCTCACCGGACATGTACAAT 58.815 47.619 9.46 0.00 36.69 2.71
129 130 2.093711 TCCTCACCGGACATGTACAATG 60.094 50.000 9.46 5.54 36.69 2.82
130 131 1.665679 CTCACCGGACATGTACAATGC 59.334 52.381 9.46 0.00 0.00 3.56
131 132 1.277842 TCACCGGACATGTACAATGCT 59.722 47.619 9.46 0.00 0.00 3.79
132 133 2.083774 CACCGGACATGTACAATGCTT 58.916 47.619 9.46 0.00 0.00 3.91
133 134 3.055747 TCACCGGACATGTACAATGCTTA 60.056 43.478 9.46 0.00 0.00 3.09
134 135 3.876914 CACCGGACATGTACAATGCTTAT 59.123 43.478 9.46 0.00 0.00 1.73
135 136 4.335315 CACCGGACATGTACAATGCTTATT 59.665 41.667 9.46 0.00 0.00 1.40
136 137 4.335315 ACCGGACATGTACAATGCTTATTG 59.665 41.667 9.46 0.00 37.54 1.90
137 138 4.261155 CCGGACATGTACAATGCTTATTGG 60.261 45.833 9.21 0.00 35.93 3.16
138 139 4.610945 GGACATGTACAATGCTTATTGGC 58.389 43.478 2.19 0.00 35.93 4.52
139 140 4.282068 GACATGTACAATGCTTATTGGCG 58.718 43.478 0.00 0.00 35.93 5.69
140 141 3.944650 ACATGTACAATGCTTATTGGCGA 59.055 39.130 0.00 0.00 35.93 5.54
141 142 4.201910 ACATGTACAATGCTTATTGGCGAC 60.202 41.667 0.00 0.00 35.93 5.19
142 143 2.680841 TGTACAATGCTTATTGGCGACC 59.319 45.455 0.00 0.00 35.93 4.79
143 144 1.832883 ACAATGCTTATTGGCGACCA 58.167 45.000 5.17 0.00 35.93 4.02
145 146 2.094752 ACAATGCTTATTGGCGACCAAC 60.095 45.455 12.53 2.69 46.95 3.77
146 147 1.102978 ATGCTTATTGGCGACCAACC 58.897 50.000 12.53 4.29 46.95 3.77
147 148 0.963355 TGCTTATTGGCGACCAACCC 60.963 55.000 12.53 4.01 46.95 4.11
148 149 1.663379 GCTTATTGGCGACCAACCCC 61.663 60.000 12.53 0.79 46.95 4.95
149 150 1.373590 CTTATTGGCGACCAACCCCG 61.374 60.000 12.53 0.00 46.95 5.73
150 151 3.980442 TATTGGCGACCAACCCCGC 62.980 63.158 12.53 0.00 46.95 6.13
167 168 3.423154 CGTCACCTCGCTTTGGCC 61.423 66.667 0.00 0.00 34.44 5.36
168 169 2.281484 GTCACCTCGCTTTGGCCA 60.281 61.111 0.00 0.00 34.44 5.36
169 170 1.896660 GTCACCTCGCTTTGGCCAA 60.897 57.895 16.05 16.05 34.44 4.52
170 171 1.152860 TCACCTCGCTTTGGCCAAA 60.153 52.632 28.65 28.65 34.44 3.28
171 172 0.753479 TCACCTCGCTTTGGCCAAAA 60.753 50.000 29.93 15.84 34.44 2.44
172 173 0.103937 CACCTCGCTTTGGCCAAAAA 59.896 50.000 29.93 17.63 34.44 1.94
173 174 0.104120 ACCTCGCTTTGGCCAAAAAC 59.896 50.000 29.93 22.97 34.44 2.43
174 175 0.389025 CCTCGCTTTGGCCAAAAACT 59.611 50.000 29.93 0.00 34.44 2.66
175 176 1.202521 CCTCGCTTTGGCCAAAAACTT 60.203 47.619 29.93 0.00 34.44 2.66
176 177 1.860326 CTCGCTTTGGCCAAAAACTTG 59.140 47.619 29.93 19.28 34.44 3.16
177 178 1.478510 TCGCTTTGGCCAAAAACTTGA 59.521 42.857 29.93 19.39 34.44 3.02
178 179 1.860326 CGCTTTGGCCAAAAACTTGAG 59.140 47.619 29.93 18.13 34.44 3.02
179 180 2.481104 CGCTTTGGCCAAAAACTTGAGA 60.481 45.455 29.93 6.45 34.44 3.27
180 181 2.866156 GCTTTGGCCAAAAACTTGAGAC 59.134 45.455 29.93 10.25 0.00 3.36
181 182 3.430790 GCTTTGGCCAAAAACTTGAGACT 60.431 43.478 29.93 0.00 0.00 3.24
182 183 4.202111 GCTTTGGCCAAAAACTTGAGACTA 60.202 41.667 29.93 4.94 0.00 2.59
183 184 4.911514 TTGGCCAAAAACTTGAGACTAC 57.088 40.909 17.98 0.00 0.00 2.73
184 185 3.219281 TGGCCAAAAACTTGAGACTACC 58.781 45.455 0.61 0.00 0.00 3.18
185 186 2.557056 GGCCAAAAACTTGAGACTACCC 59.443 50.000 0.00 0.00 0.00 3.69
186 187 2.557056 GCCAAAAACTTGAGACTACCCC 59.443 50.000 0.00 0.00 0.00 4.95
187 188 3.750922 GCCAAAAACTTGAGACTACCCCT 60.751 47.826 0.00 0.00 0.00 4.79
188 189 4.470602 CCAAAAACTTGAGACTACCCCTT 58.529 43.478 0.00 0.00 0.00 3.95
189 190 4.893524 CCAAAAACTTGAGACTACCCCTTT 59.106 41.667 0.00 0.00 0.00 3.11
190 191 5.362717 CCAAAAACTTGAGACTACCCCTTTT 59.637 40.000 0.00 0.00 0.00 2.27
191 192 6.461092 CCAAAAACTTGAGACTACCCCTTTTC 60.461 42.308 0.00 0.00 0.00 2.29
192 193 5.382664 AAACTTGAGACTACCCCTTTTCA 57.617 39.130 0.00 0.00 0.00 2.69
193 194 5.382664 AACTTGAGACTACCCCTTTTCAA 57.617 39.130 0.00 0.00 0.00 2.69
194 195 5.584551 ACTTGAGACTACCCCTTTTCAAT 57.415 39.130 0.00 0.00 0.00 2.57
195 196 6.697641 ACTTGAGACTACCCCTTTTCAATA 57.302 37.500 0.00 0.00 0.00 1.90
196 197 7.086685 ACTTGAGACTACCCCTTTTCAATAA 57.913 36.000 0.00 0.00 0.00 1.40
197 198 7.523415 ACTTGAGACTACCCCTTTTCAATAAA 58.477 34.615 0.00 0.00 0.00 1.40
198 199 8.002459 ACTTGAGACTACCCCTTTTCAATAAAA 58.998 33.333 0.00 0.00 33.58 1.52
199 200 8.770010 TTGAGACTACCCCTTTTCAATAAAAA 57.230 30.769 0.00 0.00 34.26 1.94
200 201 8.950007 TGAGACTACCCCTTTTCAATAAAAAT 57.050 30.769 0.00 0.00 36.30 1.82
222 223 8.786826 AAATAGAATATTTTCGTCACCAGACA 57.213 30.769 0.00 0.00 45.23 3.41
223 224 7.772332 ATAGAATATTTTCGTCACCAGACAC 57.228 36.000 0.00 0.00 45.23 3.67
224 225 4.625742 AGAATATTTTCGTCACCAGACACG 59.374 41.667 0.00 0.00 45.23 4.49
225 226 2.234300 ATTTTCGTCACCAGACACGT 57.766 45.000 0.00 0.00 45.23 4.49
226 227 2.867287 TTTTCGTCACCAGACACGTA 57.133 45.000 0.00 0.00 45.23 3.57
227 228 2.124011 TTTCGTCACCAGACACGTAC 57.876 50.000 0.00 0.00 45.23 3.67
228 229 1.023502 TTCGTCACCAGACACGTACA 58.976 50.000 0.00 0.00 45.23 2.90
229 230 1.023502 TCGTCACCAGACACGTACAA 58.976 50.000 0.00 0.00 45.23 2.41
230 231 1.610038 TCGTCACCAGACACGTACAAT 59.390 47.619 0.00 0.00 45.23 2.71
231 232 1.719246 CGTCACCAGACACGTACAATG 59.281 52.381 0.00 0.00 45.23 2.82
232 233 1.459592 GTCACCAGACACGTACAATGC 59.540 52.381 0.00 0.00 44.34 3.56
233 234 1.343142 TCACCAGACACGTACAATGCT 59.657 47.619 0.00 0.00 0.00 3.79
234 235 2.143122 CACCAGACACGTACAATGCTT 58.857 47.619 0.00 0.00 0.00 3.91
235 236 3.006003 TCACCAGACACGTACAATGCTTA 59.994 43.478 0.00 0.00 0.00 3.09
236 237 3.932710 CACCAGACACGTACAATGCTTAT 59.067 43.478 0.00 0.00 0.00 1.73
237 238 4.391830 CACCAGACACGTACAATGCTTATT 59.608 41.667 0.00 0.00 0.00 1.40
238 239 4.391830 ACCAGACACGTACAATGCTTATTG 59.608 41.667 0.00 0.00 37.54 1.90
239 240 4.201812 CCAGACACGTACAATGCTTATTGG 60.202 45.833 5.17 0.00 35.93 3.16
240 241 3.374058 AGACACGTACAATGCTTATTGGC 59.626 43.478 5.17 0.00 35.93 4.52
241 242 2.095213 ACACGTACAATGCTTATTGGCG 59.905 45.455 13.45 13.45 38.74 5.69
242 243 2.350192 CACGTACAATGCTTATTGGCGA 59.650 45.455 18.49 0.00 37.42 5.54
243 244 2.350498 ACGTACAATGCTTATTGGCGAC 59.650 45.455 18.49 0.00 37.42 5.19
244 245 2.286184 CGTACAATGCTTATTGGCGACC 60.286 50.000 11.11 0.00 36.72 4.79
245 246 1.832883 ACAATGCTTATTGGCGACCA 58.167 45.000 5.17 0.00 35.93 4.02
546 547 0.103937 CGCCTTGGCCAAAAACTTGA 59.896 50.000 20.91 0.00 0.00 3.02
553 554 4.164843 TGGCCAAAAACTTGAGACTACT 57.835 40.909 0.61 0.00 0.00 2.57
570 571 9.475620 TGAGACTACTCCTTCTCAATACAAATA 57.524 33.333 0.00 0.00 44.19 1.40
601 603 1.726791 CTCACCAGACACGTACAATGC 59.273 52.381 0.00 0.00 0.00 3.56
614 616 0.732571 ACAATGCTTATTGGCGACCG 59.267 50.000 5.17 0.00 35.93 4.79
615 617 0.592247 CAATGCTTATTGGCGACCGC 60.592 55.000 5.75 5.75 41.06 5.68
616 618 2.047151 AATGCTTATTGGCGACCGCG 62.047 55.000 8.36 0.00 43.06 6.46
641 651 2.032620 TGCCTCGGCCAAAAACTTAAA 58.967 42.857 2.24 0.00 41.09 1.52
644 654 3.738590 GCCTCGGCCAAAAACTTAAAACA 60.739 43.478 2.24 0.00 34.56 2.83
708 727 1.780107 TATTGGCGACCAACCCCACA 61.780 55.000 12.53 0.00 46.95 4.17
709 728 3.668981 TATTGGCGACCAACCCCACAG 62.669 57.143 12.53 0.00 46.95 3.66
714 733 3.103213 ACCAACCCCACAGCACCT 61.103 61.111 0.00 0.00 0.00 4.00
724 743 0.109086 CACAGCACCTCACCTCTACG 60.109 60.000 0.00 0.00 0.00 3.51
725 744 1.251527 ACAGCACCTCACCTCTACGG 61.252 60.000 0.00 0.00 39.35 4.02
753 777 1.343465 GGGACGACCACTTCAAAGAGA 59.657 52.381 6.20 0.00 39.85 3.10
1216 1251 2.634600 CGACATTGATTCCCCCGTTTA 58.365 47.619 0.00 0.00 0.00 2.01
1237 1272 7.271653 CGTTTATTTTGCTTTGCTTACGGATAA 59.728 33.333 0.00 0.00 0.00 1.75
1248 1283 4.879545 TGCTTACGGATAAGGATGTTTTCC 59.120 41.667 0.00 0.00 45.85 3.13
1344 1379 8.903820 AGTTATGAAATATTAAGTCTGGTTGCC 58.096 33.333 0.00 0.00 0.00 4.52
1362 1397 5.356426 GTTGCCCTGTTTTCAGTTACAATT 58.644 37.500 0.00 0.00 45.68 2.32
1430 1465 9.178758 GAAGTTAATGATTGAGTTATCCCAAGT 57.821 33.333 0.00 0.00 0.00 3.16
1463 1499 5.711036 AGGTACTCTAGTTTGACTCGTGATT 59.289 40.000 0.00 0.00 0.00 2.57
1537 1573 3.551846 ACCAACTTCTTGTCGGTGAAAT 58.448 40.909 0.00 0.00 0.00 2.17
1542 1578 6.238648 CCAACTTCTTGTCGGTGAAATAGTTT 60.239 38.462 0.00 0.00 0.00 2.66
1544 1580 8.504005 CAACTTCTTGTCGGTGAAATAGTTTAT 58.496 33.333 0.00 0.00 0.00 1.40
1776 1812 5.815581 TGATTAACTTTGACTAGGGCATGT 58.184 37.500 0.00 0.00 0.00 3.21
1789 1985 4.307032 AGGGCATGTCTGTAATGTCTTT 57.693 40.909 0.00 0.00 30.25 2.52
1790 1986 4.666512 AGGGCATGTCTGTAATGTCTTTT 58.333 39.130 0.00 0.00 30.25 2.27
1926 2264 8.607713 TGGATTAACCTGGTTCTGATAACTTTA 58.392 33.333 16.75 0.00 39.86 1.85
2078 2421 1.788229 TGGACAGTGTCAGAACCTCA 58.212 50.000 24.20 8.64 33.68 3.86
2343 2686 3.389329 GGAGATACAAGAGCCCAGATGAA 59.611 47.826 0.00 0.00 0.00 2.57
2557 2912 6.318648 TGAACAATACTGTGCTTCTGTTTTCT 59.681 34.615 0.00 0.00 35.37 2.52
2888 3244 1.159713 CCAGTGCTCTTTGCGACACA 61.160 55.000 0.00 0.00 46.63 3.72
2950 3306 2.010145 TGAGTCGGACAGCTAATTGC 57.990 50.000 11.27 0.00 43.29 3.56
3088 3445 1.190643 AGCTGAGGTTCACTAGAGGC 58.809 55.000 0.00 0.00 0.00 4.70
3143 3500 6.014840 ACATTTTGCTCATCTGTCTTTTCCAT 60.015 34.615 0.00 0.00 0.00 3.41
3236 3593 2.761208 AGAGTCCCCTGAAGATTACACG 59.239 50.000 0.00 0.00 0.00 4.49
3246 3603 3.871006 TGAAGATTACACGCCTGCAATAG 59.129 43.478 0.00 0.00 0.00 1.73
3257 3614 2.286872 CCTGCAATAGAAGCTCAGGTG 58.713 52.381 7.11 0.00 39.45 4.00
3327 3684 4.621034 CGCTTACATTGTTTCAAATGGACC 59.379 41.667 0.00 0.00 41.06 4.46
3328 3685 4.621034 GCTTACATTGTTTCAAATGGACCG 59.379 41.667 0.00 0.00 41.06 4.79
3329 3686 5.768317 CTTACATTGTTTCAAATGGACCGT 58.232 37.500 0.00 0.00 41.06 4.83
3330 3687 3.976169 ACATTGTTTCAAATGGACCGTG 58.024 40.909 2.34 0.00 41.06 4.94
3344 3701 1.312371 ACCGTGGCAATTTGATCCCG 61.312 55.000 0.00 0.00 0.00 5.14
3360 3717 1.036707 CCCGTTGTGGAAACAACCAT 58.963 50.000 14.30 0.00 45.07 3.55
3403 3760 1.001974 ACGGTGCTCAACTAATGCAGA 59.998 47.619 0.00 0.00 37.39 4.26
3411 3768 3.785486 TCAACTAATGCAGATCCTCACG 58.215 45.455 0.00 0.00 0.00 4.35
3620 3977 1.962402 GCTAAGGAGGCTGGACTGAGA 60.962 57.143 0.00 0.00 0.00 3.27
3625 3982 2.003658 GAGGCTGGACTGAGAGCTCG 62.004 65.000 8.37 0.00 35.42 5.03
3647 4004 0.250858 AATGTGCAGTGCAGTGCCTA 60.251 50.000 36.86 27.33 43.28 3.93
3661 4018 2.185494 GCCTACTCCGTCGTCCGAT 61.185 63.158 0.00 0.00 39.56 4.18
3728 4085 4.836825 AGGCATATTCATATTGGGACTCG 58.163 43.478 0.00 0.00 0.00 4.18
3878 4235 4.855937 GCAAAGCTTTGAATCTTAGAGCAC 59.144 41.667 37.14 14.58 40.55 4.40
4102 4459 0.883833 AAGCGAGCATGGAGGTTTTG 59.116 50.000 0.00 0.00 0.00 2.44
4528 5045 2.023741 GCAACTGCCATCATCGCG 59.976 61.111 0.00 0.00 34.31 5.87
4531 5048 1.815421 AACTGCCATCATCGCGGTC 60.815 57.895 6.13 0.00 45.06 4.79
4532 5049 3.333189 CTGCCATCATCGCGGTCG 61.333 66.667 6.13 0.00 0.00 4.79
4589 5113 0.813821 GTGAGCCAATGAAGAAGCCC 59.186 55.000 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.408969 GTGGCAGGAAAAAGGTTCCA 58.591 50.000 7.80 0.00 41.00 3.53
1 2 0.313987 CGTGGCAGGAAAAAGGTTCC 59.686 55.000 0.00 0.00 38.86 3.62
2 3 1.029681 ACGTGGCAGGAAAAAGGTTC 58.970 50.000 14.98 0.00 0.00 3.62
3 4 2.351706 TACGTGGCAGGAAAAAGGTT 57.648 45.000 14.98 0.00 0.00 3.50
4 5 2.579410 ATACGTGGCAGGAAAAAGGT 57.421 45.000 14.98 0.00 0.00 3.50
5 6 4.398044 ACATTATACGTGGCAGGAAAAAGG 59.602 41.667 14.98 8.39 0.00 3.11
6 7 5.560966 ACATTATACGTGGCAGGAAAAAG 57.439 39.130 14.98 4.74 0.00 2.27
7 8 5.968528 AACATTATACGTGGCAGGAAAAA 57.031 34.783 14.98 4.93 0.00 1.94
8 9 5.968528 AAACATTATACGTGGCAGGAAAA 57.031 34.783 14.98 5.27 0.00 2.29
9 10 7.337184 TCAATAAACATTATACGTGGCAGGAAA 59.663 33.333 14.98 5.62 0.00 3.13
10 11 6.824196 TCAATAAACATTATACGTGGCAGGAA 59.176 34.615 14.98 0.00 0.00 3.36
11 12 6.259167 GTCAATAAACATTATACGTGGCAGGA 59.741 38.462 14.98 0.00 0.00 3.86
12 13 6.427150 GTCAATAAACATTATACGTGGCAGG 58.573 40.000 5.50 5.50 0.00 4.85
13 14 6.019398 TCGTCAATAAACATTATACGTGGCAG 60.019 38.462 0.00 0.00 0.00 4.85
14 15 5.811100 TCGTCAATAAACATTATACGTGGCA 59.189 36.000 0.00 0.00 0.00 4.92
15 16 6.124759 GTCGTCAATAAACATTATACGTGGC 58.875 40.000 0.00 0.00 0.00 5.01
16 17 6.256104 TGGTCGTCAATAAACATTATACGTGG 59.744 38.462 0.00 0.00 0.00 4.94
17 18 7.224290 TGGTCGTCAATAAACATTATACGTG 57.776 36.000 0.00 0.00 0.00 4.49
18 19 7.201548 GGTTGGTCGTCAATAAACATTATACGT 60.202 37.037 0.00 0.00 37.73 3.57
19 20 7.121272 GGTTGGTCGTCAATAAACATTATACG 58.879 38.462 0.00 0.00 37.73 3.06
20 21 7.412063 GGGTTGGTCGTCAATAAACATTATAC 58.588 38.462 0.00 0.00 37.73 1.47
21 22 6.543100 GGGGTTGGTCGTCAATAAACATTATA 59.457 38.462 0.00 0.00 37.73 0.98
22 23 5.358725 GGGGTTGGTCGTCAATAAACATTAT 59.641 40.000 0.00 0.00 37.73 1.28
23 24 4.701171 GGGGTTGGTCGTCAATAAACATTA 59.299 41.667 0.00 0.00 37.73 1.90
24 25 3.508402 GGGGTTGGTCGTCAATAAACATT 59.492 43.478 0.00 0.00 37.73 2.71
25 26 3.086282 GGGGTTGGTCGTCAATAAACAT 58.914 45.455 0.00 0.00 37.73 2.71
26 27 2.158652 TGGGGTTGGTCGTCAATAAACA 60.159 45.455 0.00 0.00 37.73 2.83
27 28 2.227149 GTGGGGTTGGTCGTCAATAAAC 59.773 50.000 0.00 0.00 37.73 2.01
28 29 2.506444 GTGGGGTTGGTCGTCAATAAA 58.494 47.619 0.00 0.00 37.73 1.40
29 30 1.608542 CGTGGGGTTGGTCGTCAATAA 60.609 52.381 0.00 0.00 37.73 1.40
30 31 0.037139 CGTGGGGTTGGTCGTCAATA 60.037 55.000 0.00 0.00 37.73 1.90
31 32 1.302192 CGTGGGGTTGGTCGTCAAT 60.302 57.895 0.00 0.00 37.73 2.57
32 33 2.109387 CGTGGGGTTGGTCGTCAA 59.891 61.111 0.00 0.00 0.00 3.18
33 34 4.612412 GCGTGGGGTTGGTCGTCA 62.612 66.667 0.00 0.00 0.00 4.35
40 41 4.263572 TGAGGTGGCGTGGGGTTG 62.264 66.667 0.00 0.00 0.00 3.77
41 42 4.265056 GTGAGGTGGCGTGGGGTT 62.265 66.667 0.00 0.00 0.00 4.11
44 45 4.394712 GAGGTGAGGTGGCGTGGG 62.395 72.222 0.00 0.00 0.00 4.61
45 46 4.742201 CGAGGTGAGGTGGCGTGG 62.742 72.222 0.00 0.00 0.00 4.94
46 47 4.742201 CCGAGGTGAGGTGGCGTG 62.742 72.222 0.00 0.00 0.00 5.34
50 51 2.690653 TTTTGGCCGAGGTGAGGTGG 62.691 60.000 0.00 0.00 0.00 4.61
51 52 1.228124 TTTTGGCCGAGGTGAGGTG 60.228 57.895 0.00 0.00 0.00 4.00
52 53 1.073199 CTTTTGGCCGAGGTGAGGT 59.927 57.895 0.00 0.00 0.00 3.85
53 54 0.537371 AACTTTTGGCCGAGGTGAGG 60.537 55.000 0.00 0.00 0.00 3.86
54 55 1.001378 CAAACTTTTGGCCGAGGTGAG 60.001 52.381 0.00 0.00 34.59 3.51
55 56 1.028905 CAAACTTTTGGCCGAGGTGA 58.971 50.000 0.00 0.00 34.59 4.02
56 57 3.568093 CAAACTTTTGGCCGAGGTG 57.432 52.632 0.00 0.00 34.59 4.00
75 76 9.470399 TTTATTTTTATTGAGAAGGGGTAGTCC 57.530 33.333 0.00 0.00 0.00 3.85
91 92 9.869757 CCGGTGAGGAAAAGATTTTATTTTTAT 57.130 29.630 0.00 0.00 45.00 1.40
109 110 2.279741 CATTGTACATGTCCGGTGAGG 58.720 52.381 0.00 0.00 42.97 3.86
110 111 1.665679 GCATTGTACATGTCCGGTGAG 59.334 52.381 0.00 0.00 0.00 3.51
111 112 1.277842 AGCATTGTACATGTCCGGTGA 59.722 47.619 0.00 0.00 0.00 4.02
112 113 1.737838 AGCATTGTACATGTCCGGTG 58.262 50.000 0.00 0.00 0.00 4.94
113 114 2.489938 AAGCATTGTACATGTCCGGT 57.510 45.000 0.00 0.00 0.00 5.28
114 115 4.261155 CCAATAAGCATTGTACATGTCCGG 60.261 45.833 0.00 0.00 40.04 5.14
115 116 4.789481 GCCAATAAGCATTGTACATGTCCG 60.789 45.833 0.00 0.00 40.04 4.79
116 117 4.610945 GCCAATAAGCATTGTACATGTCC 58.389 43.478 0.00 0.00 40.04 4.02
117 118 4.035091 TCGCCAATAAGCATTGTACATGTC 59.965 41.667 0.00 0.00 40.04 3.06
118 119 3.944650 TCGCCAATAAGCATTGTACATGT 59.055 39.130 2.69 2.69 40.04 3.21
119 120 4.282068 GTCGCCAATAAGCATTGTACATG 58.718 43.478 0.00 0.00 40.04 3.21
120 121 3.315191 GGTCGCCAATAAGCATTGTACAT 59.685 43.478 0.00 0.00 40.04 2.29
121 122 2.680841 GGTCGCCAATAAGCATTGTACA 59.319 45.455 0.00 0.00 40.04 2.90
122 123 2.680841 TGGTCGCCAATAAGCATTGTAC 59.319 45.455 0.00 0.00 40.04 2.90
123 124 2.992593 TGGTCGCCAATAAGCATTGTA 58.007 42.857 0.00 0.00 40.04 2.41
124 125 1.832883 TGGTCGCCAATAAGCATTGT 58.167 45.000 0.00 0.00 40.04 2.71
125 126 2.529151 GTTGGTCGCCAATAAGCATTG 58.471 47.619 13.23 0.00 45.80 2.82
126 127 1.476488 GGTTGGTCGCCAATAAGCATT 59.524 47.619 13.23 0.00 45.80 3.56
127 128 1.102978 GGTTGGTCGCCAATAAGCAT 58.897 50.000 13.23 0.00 45.80 3.79
128 129 0.963355 GGGTTGGTCGCCAATAAGCA 60.963 55.000 13.23 0.00 45.80 3.91
129 130 1.663379 GGGGTTGGTCGCCAATAAGC 61.663 60.000 13.23 3.01 45.80 3.09
130 131 1.373590 CGGGGTTGGTCGCCAATAAG 61.374 60.000 13.23 4.17 45.80 1.73
131 132 1.377463 CGGGGTTGGTCGCCAATAA 60.377 57.895 13.23 0.00 45.80 1.40
132 133 2.269562 CGGGGTTGGTCGCCAATA 59.730 61.111 13.23 0.00 45.80 1.90
150 151 3.423154 GGCCAAAGCGAGGTGACG 61.423 66.667 0.00 0.00 41.24 4.35
151 152 1.452145 TTTGGCCAAAGCGAGGTGAC 61.452 55.000 27.13 0.00 41.24 3.67
152 153 0.753479 TTTTGGCCAAAGCGAGGTGA 60.753 50.000 28.79 10.77 41.24 4.02
153 154 0.103937 TTTTTGGCCAAAGCGAGGTG 59.896 50.000 28.79 0.00 41.24 4.00
154 155 0.104120 GTTTTTGGCCAAAGCGAGGT 59.896 50.000 28.79 0.00 41.24 3.85
155 156 0.389025 AGTTTTTGGCCAAAGCGAGG 59.611 50.000 28.79 0.00 41.24 4.63
156 157 1.860326 CAAGTTTTTGGCCAAAGCGAG 59.140 47.619 28.79 18.47 41.24 5.03
157 158 1.478510 TCAAGTTTTTGGCCAAAGCGA 59.521 42.857 28.79 18.65 41.24 4.93
158 159 1.860326 CTCAAGTTTTTGGCCAAAGCG 59.140 47.619 28.79 16.89 41.24 4.68
159 160 2.866156 GTCTCAAGTTTTTGGCCAAAGC 59.134 45.455 28.79 24.15 34.97 3.51
160 161 4.391405 AGTCTCAAGTTTTTGGCCAAAG 57.609 40.909 28.79 17.99 34.97 2.77
161 162 4.098807 GGTAGTCTCAAGTTTTTGGCCAAA 59.901 41.667 27.13 27.13 34.97 3.28
162 163 3.634910 GGTAGTCTCAAGTTTTTGGCCAA 59.365 43.478 16.05 16.05 34.97 4.52
163 164 3.219281 GGTAGTCTCAAGTTTTTGGCCA 58.781 45.455 0.00 0.00 34.97 5.36
164 165 2.557056 GGGTAGTCTCAAGTTTTTGGCC 59.443 50.000 0.00 0.00 34.97 5.36
165 166 2.557056 GGGGTAGTCTCAAGTTTTTGGC 59.443 50.000 0.00 0.00 34.97 4.52
166 167 4.100279 AGGGGTAGTCTCAAGTTTTTGG 57.900 45.455 0.00 0.00 34.97 3.28
167 168 6.096282 TGAAAAGGGGTAGTCTCAAGTTTTTG 59.904 38.462 0.00 0.00 35.57 2.44
168 169 6.192044 TGAAAAGGGGTAGTCTCAAGTTTTT 58.808 36.000 0.00 0.00 0.00 1.94
169 170 5.762279 TGAAAAGGGGTAGTCTCAAGTTTT 58.238 37.500 0.00 0.00 0.00 2.43
170 171 5.382664 TGAAAAGGGGTAGTCTCAAGTTT 57.617 39.130 0.00 0.00 0.00 2.66
171 172 5.382664 TTGAAAAGGGGTAGTCTCAAGTT 57.617 39.130 0.00 0.00 0.00 2.66
172 173 5.584551 ATTGAAAAGGGGTAGTCTCAAGT 57.415 39.130 0.00 0.00 0.00 3.16
173 174 7.996098 TTTATTGAAAAGGGGTAGTCTCAAG 57.004 36.000 0.00 0.00 0.00 3.02
174 175 8.770010 TTTTTATTGAAAAGGGGTAGTCTCAA 57.230 30.769 0.00 0.00 35.96 3.02
175 176 8.950007 ATTTTTATTGAAAAGGGGTAGTCTCA 57.050 30.769 0.00 0.00 40.35 3.27
196 197 9.226606 TGTCTGGTGACGAAAATATTCTATTTT 57.773 29.630 4.90 4.90 45.70 1.82
197 198 8.665685 GTGTCTGGTGACGAAAATATTCTATTT 58.334 33.333 0.00 0.00 45.70 1.40
198 199 7.010183 CGTGTCTGGTGACGAAAATATTCTATT 59.990 37.037 0.00 0.00 45.70 1.73
199 200 6.475727 CGTGTCTGGTGACGAAAATATTCTAT 59.524 38.462 0.00 0.00 45.70 1.98
200 201 5.803461 CGTGTCTGGTGACGAAAATATTCTA 59.197 40.000 0.00 0.00 45.70 2.10
201 202 4.625742 CGTGTCTGGTGACGAAAATATTCT 59.374 41.667 0.00 0.00 45.70 2.40
202 203 4.387862 ACGTGTCTGGTGACGAAAATATTC 59.612 41.667 0.00 0.00 45.70 1.75
203 204 4.312443 ACGTGTCTGGTGACGAAAATATT 58.688 39.130 0.00 0.00 45.70 1.28
204 205 3.921677 ACGTGTCTGGTGACGAAAATAT 58.078 40.909 0.00 0.00 45.70 1.28
205 206 3.374220 ACGTGTCTGGTGACGAAAATA 57.626 42.857 0.00 0.00 45.70 1.40
206 207 2.234300 ACGTGTCTGGTGACGAAAAT 57.766 45.000 0.00 0.00 45.70 1.82
207 208 2.159268 TGTACGTGTCTGGTGACGAAAA 60.159 45.455 0.00 0.00 45.70 2.29
208 209 1.404748 TGTACGTGTCTGGTGACGAAA 59.595 47.619 0.00 0.00 45.70 3.46
209 210 1.023502 TGTACGTGTCTGGTGACGAA 58.976 50.000 0.00 0.00 45.70 3.85
210 211 1.023502 TTGTACGTGTCTGGTGACGA 58.976 50.000 0.00 0.00 45.70 4.20
211 212 1.719246 CATTGTACGTGTCTGGTGACG 59.281 52.381 0.00 0.00 45.70 4.35
212 213 1.459592 GCATTGTACGTGTCTGGTGAC 59.540 52.381 0.00 0.00 43.20 3.67
213 214 1.343142 AGCATTGTACGTGTCTGGTGA 59.657 47.619 0.00 0.00 0.00 4.02
214 215 1.795768 AGCATTGTACGTGTCTGGTG 58.204 50.000 0.00 0.00 0.00 4.17
215 216 2.543777 AAGCATTGTACGTGTCTGGT 57.456 45.000 0.00 0.00 0.00 4.00
216 217 4.201812 CCAATAAGCATTGTACGTGTCTGG 60.202 45.833 0.00 0.00 40.04 3.86
217 218 4.727734 GCCAATAAGCATTGTACGTGTCTG 60.728 45.833 0.00 0.00 40.04 3.51
218 219 3.374058 GCCAATAAGCATTGTACGTGTCT 59.626 43.478 0.00 0.00 40.04 3.41
219 220 3.680789 GCCAATAAGCATTGTACGTGTC 58.319 45.455 0.00 0.00 40.04 3.67
220 221 2.095213 CGCCAATAAGCATTGTACGTGT 59.905 45.455 0.00 0.00 40.04 4.49
221 222 2.350192 TCGCCAATAAGCATTGTACGTG 59.650 45.455 0.00 0.00 40.04 4.49
222 223 2.350498 GTCGCCAATAAGCATTGTACGT 59.650 45.455 0.00 0.00 40.04 3.57
223 224 2.286184 GGTCGCCAATAAGCATTGTACG 60.286 50.000 0.00 0.00 40.04 3.67
224 225 2.680841 TGGTCGCCAATAAGCATTGTAC 59.319 45.455 0.00 0.00 40.04 2.90
225 226 2.992593 TGGTCGCCAATAAGCATTGTA 58.007 42.857 0.00 0.00 40.04 2.41
226 227 1.832883 TGGTCGCCAATAAGCATTGT 58.167 45.000 0.00 0.00 40.04 2.71
227 228 2.937469 TTGGTCGCCAATAAGCATTG 57.063 45.000 7.15 0.00 38.75 2.82
532 533 4.134563 GAGTAGTCTCAAGTTTTTGGCCA 58.865 43.478 0.00 0.00 40.18 5.36
546 547 9.702253 TCTATTTGTATTGAGAAGGAGTAGTCT 57.298 33.333 0.00 0.00 0.00 3.24
565 566 8.786898 TGTCTGGTGAGAAAAAGATTCTATTTG 58.213 33.333 0.00 0.00 0.00 2.32
570 571 4.752101 CGTGTCTGGTGAGAAAAAGATTCT 59.248 41.667 0.00 0.00 0.00 2.40
585 587 4.201812 CCAATAAGCATTGTACGTGTCTGG 60.202 45.833 0.00 0.00 40.04 3.86
619 621 0.755327 AAGTTTTTGGCCGAGGCAGT 60.755 50.000 16.65 0.00 44.11 4.40
620 622 1.243902 TAAGTTTTTGGCCGAGGCAG 58.756 50.000 16.65 0.00 44.11 4.85
621 623 1.693627 TTAAGTTTTTGGCCGAGGCA 58.306 45.000 16.65 0.00 44.11 4.75
672 682 9.683069 GTCGCCAATAAATATTTGATGAAGAAT 57.317 29.630 11.05 0.00 0.00 2.40
678 688 6.420604 GGTTGGTCGCCAATAAATATTTGATG 59.579 38.462 11.05 9.05 45.80 3.07
679 689 6.462347 GGGTTGGTCGCCAATAAATATTTGAT 60.462 38.462 11.05 0.00 45.80 2.57
680 690 5.163499 GGGTTGGTCGCCAATAAATATTTGA 60.163 40.000 11.05 0.00 45.80 2.69
681 691 5.047188 GGGTTGGTCGCCAATAAATATTTG 58.953 41.667 11.05 0.00 45.80 2.32
708 727 0.251653 TTCCGTAGAGGTGAGGTGCT 60.252 55.000 0.00 0.00 41.99 4.40
709 728 0.606604 TTTCCGTAGAGGTGAGGTGC 59.393 55.000 0.00 0.00 41.99 5.01
714 733 2.038033 CCCAAGTTTTCCGTAGAGGTGA 59.962 50.000 0.00 0.00 41.99 4.02
724 743 3.407443 TGGTCGTCCCAAGTTTTCC 57.593 52.632 0.00 0.00 41.50 3.13
794 818 3.695825 GGGAGGGTGAGGAGGGGA 61.696 72.222 0.00 0.00 0.00 4.81
1168 1203 0.618458 AACATGACGCCATACCTGGT 59.382 50.000 4.05 4.05 45.10 4.00
1180 1215 5.293324 TCAATGTCGGTAAGCATAACATGAC 59.707 40.000 0.00 0.00 31.29 3.06
1216 1251 5.417580 TCCTTATCCGTAAGCAAAGCAAAAT 59.582 36.000 0.00 0.00 36.74 1.82
1248 1283 0.106217 AAATCACCGGCCCCCAATAG 60.106 55.000 0.00 0.00 0.00 1.73
1370 1405 7.042925 AGCAACGATGGACTTAATATTTCGTAC 60.043 37.037 8.93 5.80 37.36 3.67
1381 1416 1.274167 ACCGAAGCAACGATGGACTTA 59.726 47.619 4.23 0.00 35.09 2.24
1438 1474 5.068636 TCACGAGTCAAACTAGAGTACCTT 58.931 41.667 0.00 0.00 0.00 3.50
1537 1573 8.817100 CACATGCTATGTTTCGAAGATAAACTA 58.183 33.333 0.00 0.00 42.70 2.24
1542 1578 5.753438 GGTCACATGCTATGTTTCGAAGATA 59.247 40.000 0.00 0.00 42.70 1.98
1544 1580 3.932710 GGTCACATGCTATGTTTCGAAGA 59.067 43.478 0.00 0.00 42.70 2.87
1836 2174 3.066064 TGCACATACGTTTGCAGAAAGTT 59.934 39.130 13.38 0.00 43.79 2.66
2078 2421 8.016301 TGATGCTGTCTTCTAGTCTAATCAAT 57.984 34.615 0.00 0.00 0.00 2.57
2126 2469 7.015226 TGTATCAGCATTGTAACAATACTGC 57.985 36.000 0.00 5.94 34.87 4.40
2343 2686 4.290722 AGATCTTCTGGAAAGAATGGGTGT 59.709 41.667 0.00 0.00 0.00 4.16
2557 2912 8.786826 ATGCTAGTTGCTAACAAGTAACAATA 57.213 30.769 8.67 0.00 39.80 1.90
2907 3263 7.342026 TCAAAGACCAGCAGTATTGATCTAGTA 59.658 37.037 0.00 0.00 32.36 1.82
2950 3306 9.853555 TTGTGGCATAGTAAAAATGATTTACAG 57.146 29.630 12.15 4.64 37.35 2.74
3088 3445 5.159209 CAAAGAAATGCTTAGTTGCAGGAG 58.841 41.667 0.00 0.00 46.71 3.69
3236 3593 1.307097 CCTGAGCTTCTATTGCAGGC 58.693 55.000 2.71 0.00 39.60 4.85
3246 3603 0.607620 AGAGCACTCACCTGAGCTTC 59.392 55.000 2.01 0.00 45.79 3.86
3257 3614 5.053145 CCCTCATTGTAACATAGAGCACTC 58.947 45.833 0.00 0.00 0.00 3.51
3327 3684 0.525761 AACGGGATCAAATTGCCACG 59.474 50.000 7.95 7.95 0.00 4.94
3328 3685 1.272212 ACAACGGGATCAAATTGCCAC 59.728 47.619 0.00 0.00 0.00 5.01
3329 3686 1.271934 CACAACGGGATCAAATTGCCA 59.728 47.619 0.00 0.00 0.00 4.92
3330 3687 1.404047 CCACAACGGGATCAAATTGCC 60.404 52.381 0.00 0.00 0.00 4.52
3360 3717 2.598985 AATGGCCGCCCGACAAAA 60.599 55.556 7.03 0.00 0.00 2.44
3387 3744 3.198417 TGAGGATCTGCATTAGTTGAGCA 59.802 43.478 0.00 0.00 34.92 4.26
3411 3768 2.021106 CGCTCGACCGTCTCGTAC 59.979 66.667 0.00 0.00 43.45 3.67
3556 3913 1.221414 GTTAGCGGCATGATCCTGTC 58.779 55.000 1.45 0.00 0.00 3.51
3661 4018 4.804608 TTCTTTGATGACGCGAGAAAAA 57.195 36.364 15.93 5.86 0.00 1.94
3728 4085 6.369065 ACGTCTCAAATATGTTCTTCCAAGTC 59.631 38.462 0.00 0.00 0.00 3.01
3878 4235 5.006386 AGGTTTTACAGAATCAGCAAGAGG 58.994 41.667 0.00 0.00 0.00 3.69
3979 4336 9.598517 AGTTTGATTTTGCTCAACTCAAAAATA 57.401 25.926 15.33 0.00 43.77 1.40
4102 4459 1.014352 ACAAGTCACAAACACTCCGC 58.986 50.000 0.00 0.00 0.00 5.54
4528 5045 4.216731 GTTTTCCTTCGAATTTGACGACC 58.783 43.478 0.00 0.00 39.46 4.79
4530 5047 3.878103 TGGTTTTCCTTCGAATTTGACGA 59.122 39.130 0.00 0.00 41.38 4.20
4531 5048 4.217754 TGGTTTTCCTTCGAATTTGACG 57.782 40.909 0.00 0.00 41.38 4.35
4532 5049 5.800438 GCTATGGTTTTCCTTCGAATTTGAC 59.200 40.000 0.00 0.00 41.38 3.18
4577 5101 0.741221 GCTCGACGGGCTTCTTCATT 60.741 55.000 13.71 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.