Multiple sequence alignment - TraesCS3D01G191500

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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 TraesCS3D01G191500 chr3D 100.000 3710 0 0 1 3710 181102841 181106550 0.000000e+00 6852.0
1 TraesCS3D01G191500 chr3B 94.907 3024 133 9 213 3224 259369857 259372871 0.000000e+00 4711.0
2 TraesCS3D01G191500 chr3B 90.155 193 18 1 3519 3710 259372873 259373065 2.210000e-62 250.0
3 TraesCS3D01G191500 chr3A 97.194 2566 64 3 737 3294 227923657 227921092 0.000000e+00 4333.0
4 TraesCS3D01G191500 chr3A 96.000 450 17 1 242 690 227924100 227923651 0.000000e+00 730.0
5 TraesCS3D01G191500 chr3A 92.632 380 17 1 3331 3710 227921090 227920722 1.520000e-148 536.0
6 TraesCS3D01G191500 chr7D 90.326 2150 196 10 714 2860 576333005 576335145 0.000000e+00 2808.0
7 TraesCS3D01G191500 chr7D 86.066 122 10 7 3549 3669 576335438 576335553 1.400000e-24 124.0
8 TraesCS3D01G191500 chr7B 90.306 1991 186 4 737 2727 639083168 639085151 0.000000e+00 2601.0
9 TraesCS3D01G191500 chr7B 88.636 88 6 1 2754 2837 639085150 639085237 1.820000e-18 104.0
10 TraesCS3D01G191500 chr7B 82.692 104 6 8 3566 3669 704092969 704092878 8.540000e-12 82.4
11 TraesCS3D01G191500 chr7A 90.630 1857 167 2 1093 2945 667475057 667476910 0.000000e+00 2459.0
12 TraesCS3D01G191500 chr7A 83.200 125 12 8 3546 3669 667477143 667477259 5.070000e-19 106.0
13 TraesCS3D01G191500 chr7A 100.000 30 0 0 3640 3669 705142176 705142147 5.180000e-04 56.5


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 TraesCS3D01G191500 chr3D 181102841 181106550 3709 False 6852.000000 6852 100.000000 1 3710 1 chr3D.!!$F1 3709
1 TraesCS3D01G191500 chr3B 259369857 259373065 3208 False 2480.500000 4711 92.531000 213 3710 2 chr3B.!!$F1 3497
2 TraesCS3D01G191500 chr3A 227920722 227924100 3378 True 1866.333333 4333 95.275333 242 3710 3 chr3A.!!$R1 3468
3 TraesCS3D01G191500 chr7D 576333005 576335553 2548 False 1466.000000 2808 88.196000 714 3669 2 chr7D.!!$F1 2955
4 TraesCS3D01G191500 chr7B 639083168 639085237 2069 False 1352.500000 2601 89.471000 737 2837 2 chr7B.!!$F1 2100
5 TraesCS3D01G191500 chr7A 667475057 667477259 2202 False 1282.500000 2459 86.915000 1093 3669 2 chr7A.!!$F1 2576

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
31 32 0.176680 CACGTAGGATCCTTGCTGCT 59.823 55.000 22.03 0.0 0.00 4.24 F
86 87 0.231279 AAGTTTCGCGCTGTAACACG 59.769 50.000 18.11 0.0 30.87 4.49 F
141 142 0.248289 TAGGCTACGTGTTTCTGGGC 59.752 55.000 0.00 0.0 0.00 5.36 F
179 180 0.393808 AGTTCCATAAACCGGCGCAT 60.394 50.000 10.83 0.0 38.76 4.73 F
180 181 1.134340 AGTTCCATAAACCGGCGCATA 60.134 47.619 10.83 0.0 38.76 3.14 F
188 189 1.169577 AACCGGCGCATAAAATGTCA 58.830 45.000 10.83 0.0 0.00 3.58 F
513 515 1.174712 AGTGCCCAAGTGTGTCATGC 61.175 55.000 0.00 0.0 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1141 1150 0.666274 GCCACACACAGACGAATCGA 60.666 55.000 10.55 0.00 0.00 3.59 R
1480 1489 1.593196 TGCAACTCCACAAGTAGCAC 58.407 50.000 0.00 0.00 37.17 4.40 R
1670 1679 2.008329 GACAAGCATTCTCCAGCTGAG 58.992 52.381 17.39 10.96 41.70 3.35 R
1818 1827 4.158394 GTGGCAAATGTGATGTCATTAGGT 59.842 41.667 0.00 0.00 37.09 3.08 R
2568 2577 8.220755 TGTTTTCTGCTGTGAAAGTATAAACT 57.779 30.769 0.00 0.00 37.27 2.66 R
2601 2610 4.592778 AGGACATTGTTTATTTGGTGGCTT 59.407 37.500 0.00 0.00 0.00 4.35 R
2886 2908 3.071167 GTCAGGTGGGAAAACTCTACTGT 59.929 47.826 0.00 0.00 0.00 3.55 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 2.991434 CGAGATGGTATCCACGTAGG 57.009 55.000 0.00 0.00 35.80 3.18
28 29 3.300032 TCCACGTAGGATCCTTGCT 57.700 52.632 22.03 0.00 43.07 3.91
29 30 0.824109 TCCACGTAGGATCCTTGCTG 59.176 55.000 22.03 11.97 43.07 4.41
30 31 0.811616 CCACGTAGGATCCTTGCTGC 60.812 60.000 22.03 4.85 41.22 5.25
31 32 0.176680 CACGTAGGATCCTTGCTGCT 59.823 55.000 22.03 0.00 0.00 4.24
32 33 0.905357 ACGTAGGATCCTTGCTGCTT 59.095 50.000 22.03 0.00 0.00 3.91
33 34 1.293924 CGTAGGATCCTTGCTGCTTG 58.706 55.000 22.03 0.00 0.00 4.01
34 35 1.134699 CGTAGGATCCTTGCTGCTTGA 60.135 52.381 22.03 0.00 0.00 3.02
35 36 2.484417 CGTAGGATCCTTGCTGCTTGAT 60.484 50.000 22.03 0.00 0.00 2.57
36 37 2.054232 AGGATCCTTGCTGCTTGATG 57.946 50.000 9.02 0.00 0.00 3.07
37 38 1.030457 GGATCCTTGCTGCTTGATGG 58.970 55.000 3.84 0.00 0.00 3.51
38 39 1.409241 GGATCCTTGCTGCTTGATGGA 60.409 52.381 3.84 0.00 0.00 3.41
39 40 2.584236 GATCCTTGCTGCTTGATGGAT 58.416 47.619 0.00 3.49 37.06 3.41
40 41 1.758936 TCCTTGCTGCTTGATGGATG 58.241 50.000 0.00 0.00 0.00 3.51
41 42 0.744874 CCTTGCTGCTTGATGGATGG 59.255 55.000 0.00 0.00 0.00 3.51
42 43 1.683938 CCTTGCTGCTTGATGGATGGA 60.684 52.381 0.00 0.00 0.00 3.41
43 44 2.307768 CTTGCTGCTTGATGGATGGAT 58.692 47.619 0.00 0.00 0.00 3.41
44 45 3.483421 CTTGCTGCTTGATGGATGGATA 58.517 45.455 0.00 0.00 0.00 2.59
45 46 3.136009 TGCTGCTTGATGGATGGATAG 57.864 47.619 0.00 0.00 0.00 2.08
46 47 1.811359 GCTGCTTGATGGATGGATAGC 59.189 52.381 0.00 0.00 0.00 2.97
47 48 2.074576 CTGCTTGATGGATGGATAGCG 58.925 52.381 0.00 0.00 0.00 4.26
48 49 0.801251 GCTTGATGGATGGATAGCGC 59.199 55.000 0.00 0.00 0.00 5.92
49 50 1.073964 CTTGATGGATGGATAGCGCG 58.926 55.000 0.00 0.00 0.00 6.86
50 51 0.320683 TTGATGGATGGATAGCGCGG 60.321 55.000 8.83 0.00 0.00 6.46
51 52 1.448540 GATGGATGGATAGCGCGGG 60.449 63.158 8.83 0.00 0.00 6.13
52 53 2.172483 GATGGATGGATAGCGCGGGT 62.172 60.000 8.83 0.00 0.00 5.28
53 54 2.357517 GGATGGATAGCGCGGGTG 60.358 66.667 8.83 0.00 0.00 4.61
54 55 3.044305 GATGGATAGCGCGGGTGC 61.044 66.667 8.83 0.00 37.91 5.01
55 56 3.807631 GATGGATAGCGCGGGTGCA 62.808 63.158 8.83 3.84 42.97 4.57
56 57 3.399105 ATGGATAGCGCGGGTGCAA 62.399 57.895 8.83 0.00 42.97 4.08
57 58 2.591715 GGATAGCGCGGGTGCAAT 60.592 61.111 8.83 0.00 42.97 3.56
58 59 2.186826 GGATAGCGCGGGTGCAATT 61.187 57.895 8.83 0.00 42.97 2.32
59 60 1.009675 GATAGCGCGGGTGCAATTG 60.010 57.895 8.83 0.00 42.97 2.32
60 61 1.714899 GATAGCGCGGGTGCAATTGT 61.715 55.000 8.83 0.00 42.97 2.71
61 62 1.312371 ATAGCGCGGGTGCAATTGTT 61.312 50.000 8.83 0.00 42.97 2.83
62 63 1.917782 TAGCGCGGGTGCAATTGTTC 61.918 55.000 8.83 0.56 42.97 3.18
63 64 2.642129 CGCGGGTGCAATTGTTCA 59.358 55.556 7.40 0.00 42.97 3.18
64 65 1.212490 CGCGGGTGCAATTGTTCAT 59.788 52.632 7.40 0.00 42.97 2.57
65 66 0.449786 CGCGGGTGCAATTGTTCATA 59.550 50.000 7.40 0.00 42.97 2.15
66 67 1.135546 CGCGGGTGCAATTGTTCATAA 60.136 47.619 7.40 0.00 42.97 1.90
67 68 2.669670 CGCGGGTGCAATTGTTCATAAA 60.670 45.455 7.40 0.00 42.97 1.40
68 69 3.321497 GCGGGTGCAATTGTTCATAAAA 58.679 40.909 7.40 0.00 42.15 1.52
69 70 3.367630 GCGGGTGCAATTGTTCATAAAAG 59.632 43.478 7.40 0.00 42.15 2.27
70 71 4.555262 CGGGTGCAATTGTTCATAAAAGT 58.445 39.130 7.40 0.00 0.00 2.66
71 72 4.987912 CGGGTGCAATTGTTCATAAAAGTT 59.012 37.500 7.40 0.00 0.00 2.66
72 73 5.465056 CGGGTGCAATTGTTCATAAAAGTTT 59.535 36.000 7.40 0.00 0.00 2.66
73 74 6.346518 CGGGTGCAATTGTTCATAAAAGTTTC 60.347 38.462 7.40 0.00 0.00 2.78
74 75 6.346518 GGGTGCAATTGTTCATAAAAGTTTCG 60.347 38.462 7.40 0.00 0.00 3.46
75 76 6.064525 GTGCAATTGTTCATAAAAGTTTCGC 58.935 36.000 7.40 0.00 0.00 4.70
76 77 5.108065 TGCAATTGTTCATAAAAGTTTCGCG 60.108 36.000 7.40 0.00 0.00 5.87
77 78 5.297314 CAATTGTTCATAAAAGTTTCGCGC 58.703 37.500 0.00 0.00 0.00 6.86
78 79 3.889196 TGTTCATAAAAGTTTCGCGCT 57.111 38.095 5.56 0.00 0.00 5.92
79 80 3.550561 TGTTCATAAAAGTTTCGCGCTG 58.449 40.909 5.56 0.00 0.00 5.18
80 81 3.002862 TGTTCATAAAAGTTTCGCGCTGT 59.997 39.130 5.56 0.00 0.00 4.40
81 82 4.211584 TGTTCATAAAAGTTTCGCGCTGTA 59.788 37.500 5.56 0.00 0.00 2.74
82 83 4.994220 TCATAAAAGTTTCGCGCTGTAA 57.006 36.364 5.56 0.00 0.00 2.41
83 84 4.704457 TCATAAAAGTTTCGCGCTGTAAC 58.296 39.130 5.56 9.51 0.00 2.50
84 85 4.211584 TCATAAAAGTTTCGCGCTGTAACA 59.788 37.500 18.11 4.31 30.87 2.41
85 86 2.378507 AAAGTTTCGCGCTGTAACAC 57.621 45.000 18.11 3.62 30.87 3.32
86 87 0.231279 AAGTTTCGCGCTGTAACACG 59.769 50.000 18.11 0.00 30.87 4.49
87 88 1.154727 GTTTCGCGCTGTAACACGG 60.155 57.895 5.56 0.00 0.00 4.94
88 89 1.300003 TTTCGCGCTGTAACACGGA 60.300 52.632 5.56 0.00 0.00 4.69
89 90 0.875040 TTTCGCGCTGTAACACGGAA 60.875 50.000 5.56 0.00 0.00 4.30
90 91 1.279527 TTCGCGCTGTAACACGGAAG 61.280 55.000 5.56 0.00 0.00 3.46
91 92 2.474712 GCGCTGTAACACGGAAGC 59.525 61.111 0.00 0.00 0.00 3.86
92 93 2.314647 GCGCTGTAACACGGAAGCA 61.315 57.895 0.00 0.00 35.33 3.91
93 94 1.837538 GCGCTGTAACACGGAAGCAA 61.838 55.000 0.00 0.00 35.33 3.91
94 95 0.796312 CGCTGTAACACGGAAGCAAT 59.204 50.000 0.00 0.00 35.33 3.56
95 96 1.196808 CGCTGTAACACGGAAGCAATT 59.803 47.619 0.00 0.00 35.33 2.32
96 97 2.350388 CGCTGTAACACGGAAGCAATTT 60.350 45.455 0.00 0.00 35.33 1.82
97 98 3.638484 GCTGTAACACGGAAGCAATTTT 58.362 40.909 0.00 0.00 35.69 1.82
98 99 4.048504 GCTGTAACACGGAAGCAATTTTT 58.951 39.130 0.00 0.00 35.69 1.94
130 131 4.463515 TTCGCGCTATATATAGGCTACG 57.536 45.455 19.19 14.80 0.00 3.51
131 132 3.461061 TCGCGCTATATATAGGCTACGT 58.539 45.455 19.19 0.00 0.00 3.57
132 133 3.246936 TCGCGCTATATATAGGCTACGTG 59.753 47.826 19.19 18.34 0.00 4.49
133 134 3.002042 CGCGCTATATATAGGCTACGTGT 59.998 47.826 19.19 0.00 0.00 4.49
134 135 4.495349 CGCGCTATATATAGGCTACGTGTT 60.495 45.833 19.19 0.00 0.00 3.32
135 136 5.338365 GCGCTATATATAGGCTACGTGTTT 58.662 41.667 19.19 0.00 0.00 2.83
136 137 5.454877 GCGCTATATATAGGCTACGTGTTTC 59.545 44.000 19.19 0.14 0.00 2.78
137 138 6.677431 GCGCTATATATAGGCTACGTGTTTCT 60.677 42.308 19.19 0.00 0.00 2.52
138 139 6.687531 CGCTATATATAGGCTACGTGTTTCTG 59.312 42.308 19.19 0.00 0.00 3.02
139 140 6.973474 GCTATATATAGGCTACGTGTTTCTGG 59.027 42.308 19.19 0.00 0.00 3.86
140 141 2.981859 ATAGGCTACGTGTTTCTGGG 57.018 50.000 0.00 0.00 0.00 4.45
141 142 0.248289 TAGGCTACGTGTTTCTGGGC 59.752 55.000 0.00 0.00 0.00 5.36
142 143 2.038837 GGCTACGTGTTTCTGGGCC 61.039 63.158 0.00 0.00 0.00 5.80
143 144 2.388232 GCTACGTGTTTCTGGGCCG 61.388 63.158 0.00 0.00 0.00 6.13
144 145 1.740296 CTACGTGTTTCTGGGCCGG 60.740 63.158 5.83 5.83 0.00 6.13
145 146 3.887335 TACGTGTTTCTGGGCCGGC 62.887 63.158 21.18 21.18 0.00 6.13
161 162 4.814294 GCCCACGAGGTACGCCAG 62.814 72.222 0.00 0.00 46.94 4.85
162 163 3.379445 CCCACGAGGTACGCCAGT 61.379 66.667 0.00 0.00 46.94 4.00
163 164 2.654877 CCACGAGGTACGCCAGTT 59.345 61.111 0.00 0.00 46.94 3.16
164 165 1.445582 CCACGAGGTACGCCAGTTC 60.446 63.158 0.00 0.00 46.94 3.01
165 166 1.445582 CACGAGGTACGCCAGTTCC 60.446 63.158 0.00 0.00 46.94 3.62
166 167 1.904865 ACGAGGTACGCCAGTTCCA 60.905 57.895 0.00 0.00 46.94 3.53
167 168 1.255667 ACGAGGTACGCCAGTTCCAT 61.256 55.000 0.00 0.00 46.94 3.41
168 169 0.742505 CGAGGTACGCCAGTTCCATA 59.257 55.000 0.00 0.00 39.91 2.74
169 170 1.135527 CGAGGTACGCCAGTTCCATAA 59.864 52.381 0.00 0.00 39.91 1.90
170 171 2.417651 CGAGGTACGCCAGTTCCATAAA 60.418 50.000 0.00 0.00 39.91 1.40
171 172 2.934553 GAGGTACGCCAGTTCCATAAAC 59.065 50.000 0.00 0.00 39.91 2.01
172 173 2.011947 GGTACGCCAGTTCCATAAACC 58.988 52.381 0.00 0.00 38.76 3.27
173 174 1.662122 GTACGCCAGTTCCATAAACCG 59.338 52.381 0.00 0.00 38.76 4.44
174 175 0.675522 ACGCCAGTTCCATAAACCGG 60.676 55.000 0.00 0.00 38.31 5.28
176 177 2.094904 CCAGTTCCATAAACCGGCG 58.905 57.895 0.00 0.00 38.76 6.46
177 178 1.427819 CAGTTCCATAAACCGGCGC 59.572 57.895 0.00 0.00 38.76 6.53
178 179 1.003112 AGTTCCATAAACCGGCGCA 60.003 52.632 10.83 0.00 38.76 6.09
179 180 0.393808 AGTTCCATAAACCGGCGCAT 60.394 50.000 10.83 0.00 38.76 4.73
180 181 1.134340 AGTTCCATAAACCGGCGCATA 60.134 47.619 10.83 0.00 38.76 3.14
181 182 1.671845 GTTCCATAAACCGGCGCATAA 59.328 47.619 10.83 0.00 31.20 1.90
182 183 2.039818 TCCATAAACCGGCGCATAAA 57.960 45.000 10.83 0.00 0.00 1.40
183 184 2.366533 TCCATAAACCGGCGCATAAAA 58.633 42.857 10.83 0.00 0.00 1.52
184 185 2.952978 TCCATAAACCGGCGCATAAAAT 59.047 40.909 10.83 0.00 0.00 1.82
185 186 3.049206 CCATAAACCGGCGCATAAAATG 58.951 45.455 10.83 5.32 0.00 2.32
186 187 3.490078 CCATAAACCGGCGCATAAAATGT 60.490 43.478 10.83 0.00 0.00 2.71
187 188 2.271821 AAACCGGCGCATAAAATGTC 57.728 45.000 10.83 0.00 0.00 3.06
188 189 1.169577 AACCGGCGCATAAAATGTCA 58.830 45.000 10.83 0.00 0.00 3.58
189 190 1.169577 ACCGGCGCATAAAATGTCAA 58.830 45.000 10.83 0.00 0.00 3.18
190 191 1.542030 ACCGGCGCATAAAATGTCAAA 59.458 42.857 10.83 0.00 0.00 2.69
191 192 2.029828 ACCGGCGCATAAAATGTCAAAA 60.030 40.909 10.83 0.00 0.00 2.44
192 193 2.598192 CCGGCGCATAAAATGTCAAAAG 59.402 45.455 10.83 0.00 0.00 2.27
193 194 3.497118 CGGCGCATAAAATGTCAAAAGA 58.503 40.909 10.83 0.00 0.00 2.52
194 195 3.917380 CGGCGCATAAAATGTCAAAAGAA 59.083 39.130 10.83 0.00 0.00 2.52
195 196 4.384247 CGGCGCATAAAATGTCAAAAGAAA 59.616 37.500 10.83 0.00 0.00 2.52
196 197 5.107683 CGGCGCATAAAATGTCAAAAGAAAA 60.108 36.000 10.83 0.00 0.00 2.29
197 198 6.298853 GGCGCATAAAATGTCAAAAGAAAAG 58.701 36.000 10.83 0.00 0.00 2.27
198 199 6.145371 GGCGCATAAAATGTCAAAAGAAAAGA 59.855 34.615 10.83 0.00 0.00 2.52
199 200 7.003648 GCGCATAAAATGTCAAAAGAAAAGAC 58.996 34.615 0.30 0.00 0.00 3.01
200 201 7.306515 GCGCATAAAATGTCAAAAGAAAAGACA 60.307 33.333 0.30 0.00 45.26 3.41
201 202 8.538856 CGCATAAAATGTCAAAAGAAAAGACAA 58.461 29.630 0.00 0.00 44.47 3.18
205 206 6.908870 AATGTCAAAAGAAAAGACAAAGGC 57.091 33.333 0.00 0.00 44.47 4.35
206 207 5.398603 TGTCAAAAGAAAAGACAAAGGCA 57.601 34.783 0.00 0.00 39.15 4.75
207 208 5.410067 TGTCAAAAGAAAAGACAAAGGCAG 58.590 37.500 0.00 0.00 39.15 4.85
208 209 5.184864 TGTCAAAAGAAAAGACAAAGGCAGA 59.815 36.000 0.00 0.00 39.15 4.26
209 210 5.745769 GTCAAAAGAAAAGACAAAGGCAGAG 59.254 40.000 0.00 0.00 32.68 3.35
210 211 4.926140 AAAGAAAAGACAAAGGCAGAGG 57.074 40.909 0.00 0.00 0.00 3.69
211 212 3.584733 AGAAAAGACAAAGGCAGAGGT 57.415 42.857 0.00 0.00 0.00 3.85
412 413 1.275291 GTCCATCTCGGTTCAGGTGAA 59.725 52.381 0.00 0.00 35.57 3.18
413 414 1.974957 TCCATCTCGGTTCAGGTGAAA 59.025 47.619 0.00 0.00 35.58 2.69
513 515 1.174712 AGTGCCCAAGTGTGTCATGC 61.175 55.000 0.00 0.00 0.00 4.06
677 681 5.490139 TGCATTACTAGCAAGCATCTTTC 57.510 39.130 0.00 0.00 39.39 2.62
1141 1150 4.202182 GCAGCCATTTACCATCATTGTCAT 60.202 41.667 0.00 0.00 0.00 3.06
1218 1227 4.545706 CAAGAGGGGCGCGGCATA 62.546 66.667 34.30 0.00 0.00 3.14
1245 1254 2.034939 TGCATTGAGAGTTTTGCACCTG 59.965 45.455 0.00 0.00 39.98 4.00
1355 1364 6.000246 TCAGTTAGGAAATCATGGTATGCA 58.000 37.500 0.00 0.00 0.00 3.96
1480 1489 3.115554 CTCGCAAAGGGAAACAAGTTTG 58.884 45.455 2.45 0.00 32.11 2.93
1505 1514 3.788227 ACTTGTGGAGTTGCATAGGAA 57.212 42.857 0.00 0.00 33.92 3.36
1641 1650 5.011329 TGAATTGTCGGTACTTTCTGGTACT 59.989 40.000 0.00 0.00 41.07 2.73
1670 1679 9.212641 TCTGATTAGCTTATATGCAAGATGTTC 57.787 33.333 12.65 1.66 34.99 3.18
2568 2577 3.696051 GCTGGATAGAAATTGGCAGTGAA 59.304 43.478 0.00 0.00 0.00 3.18
2601 2610 7.283127 ACTTTCACAGCAGAAAACAGATCTAAA 59.717 33.333 0.00 0.00 37.09 1.85
2771 2791 1.570813 TAGATCGCCGCAGTCATTTG 58.429 50.000 0.00 0.00 0.00 2.32
2844 2866 3.643763 AGACTTGCGATATGATTCGTCC 58.356 45.455 0.00 0.00 41.16 4.79
2850 2872 2.276540 GCGATATGATTCGTCCGATTCG 59.723 50.000 0.00 0.00 41.16 3.34
2965 2991 8.231837 TCTTATACGCACTTGATGTTTTAAACC 58.768 33.333 5.32 0.00 0.00 3.27
3029 3055 3.829601 TGCGAACCATTTGGGAACTTTAT 59.170 39.130 0.96 0.00 41.15 1.40
3309 3342 4.836125 CCATCATAAAGCATGGTGTACC 57.164 45.455 0.00 0.00 43.27 3.34
3310 3343 3.569701 CCATCATAAAGCATGGTGTACCC 59.430 47.826 0.00 0.00 43.27 3.69
3325 3358 7.726033 TGGTGTACCCAAAATATAAAGCATT 57.274 32.000 0.00 0.00 41.50 3.56
3326 3359 7.551585 TGGTGTACCCAAAATATAAAGCATTG 58.448 34.615 0.00 0.00 41.50 2.82
3327 3360 6.478673 GGTGTACCCAAAATATAAAGCATTGC 59.521 38.462 0.00 0.00 0.00 3.56
3328 3361 7.038659 GTGTACCCAAAATATAAAGCATTGCA 58.961 34.615 11.91 0.00 0.00 4.08
3329 3362 7.222611 GTGTACCCAAAATATAAAGCATTGCAG 59.777 37.037 11.91 0.00 0.00 4.41
3447 3480 8.630054 TTGGTAGACATGCAATAAGTAAAAGT 57.370 30.769 0.00 0.00 0.00 2.66
3448 3481 8.263940 TGGTAGACATGCAATAAGTAAAAGTC 57.736 34.615 0.00 0.00 0.00 3.01
3449 3482 7.335924 TGGTAGACATGCAATAAGTAAAAGTCC 59.664 37.037 0.00 0.00 0.00 3.85
3450 3483 7.553044 GGTAGACATGCAATAAGTAAAAGTCCT 59.447 37.037 0.00 0.00 0.00 3.85
3469 3502 5.070446 AGTCCTAGTCAAAGTTGTGTGATGA 59.930 40.000 0.00 0.00 0.00 2.92
3511 3544 3.630312 GCGCCTTATATTTTGTGAAGGGA 59.370 43.478 0.00 0.00 39.14 4.20
3515 3548 5.891551 GCCTTATATTTTGTGAAGGGAGGAA 59.108 40.000 1.95 0.00 39.14 3.36
3685 3719 5.155278 TGTAAGGCTTCATTCGGTTAGAA 57.845 39.130 1.30 0.00 43.93 2.10
3693 3727 1.280998 CATTCGGTTAGAACCCACCCT 59.719 52.381 5.85 0.00 46.53 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.501261 TCCTACGTGGATACCATCTCG 58.499 52.381 0.00 0.00 40.56 4.04
11 12 0.811616 GCAGCAAGGATCCTACGTGG 60.812 60.000 16.55 5.36 37.10 4.94
12 13 0.176680 AGCAGCAAGGATCCTACGTG 59.823 55.000 16.55 11.31 0.00 4.49
13 14 0.905357 AAGCAGCAAGGATCCTACGT 59.095 50.000 16.55 0.00 0.00 3.57
14 15 1.134699 TCAAGCAGCAAGGATCCTACG 60.135 52.381 16.55 10.81 0.00 3.51
15 16 2.698855 TCAAGCAGCAAGGATCCTAC 57.301 50.000 16.55 10.79 0.00 3.18
16 17 2.158711 CCATCAAGCAGCAAGGATCCTA 60.159 50.000 16.55 0.00 0.00 2.94
17 18 1.409802 CCATCAAGCAGCAAGGATCCT 60.410 52.381 9.02 9.02 0.00 3.24
18 19 1.030457 CCATCAAGCAGCAAGGATCC 58.970 55.000 2.48 2.48 0.00 3.36
19 20 2.048444 TCCATCAAGCAGCAAGGATC 57.952 50.000 0.00 0.00 0.00 3.36
20 21 2.307768 CATCCATCAAGCAGCAAGGAT 58.692 47.619 0.00 0.00 0.00 3.24
21 22 1.683938 CCATCCATCAAGCAGCAAGGA 60.684 52.381 0.00 0.00 0.00 3.36
22 23 0.744874 CCATCCATCAAGCAGCAAGG 59.255 55.000 0.00 0.00 0.00 3.61
23 24 1.758936 TCCATCCATCAAGCAGCAAG 58.241 50.000 0.00 0.00 0.00 4.01
24 25 2.447408 ATCCATCCATCAAGCAGCAA 57.553 45.000 0.00 0.00 0.00 3.91
25 26 2.812983 GCTATCCATCCATCAAGCAGCA 60.813 50.000 0.00 0.00 0.00 4.41
26 27 1.811359 GCTATCCATCCATCAAGCAGC 59.189 52.381 0.00 0.00 0.00 5.25
27 28 2.074576 CGCTATCCATCCATCAAGCAG 58.925 52.381 0.00 0.00 0.00 4.24
28 29 1.879372 GCGCTATCCATCCATCAAGCA 60.879 52.381 0.00 0.00 0.00 3.91
29 30 0.801251 GCGCTATCCATCCATCAAGC 59.199 55.000 0.00 0.00 0.00 4.01
30 31 1.073964 CGCGCTATCCATCCATCAAG 58.926 55.000 5.56 0.00 0.00 3.02
31 32 0.320683 CCGCGCTATCCATCCATCAA 60.321 55.000 5.56 0.00 0.00 2.57
32 33 1.293179 CCGCGCTATCCATCCATCA 59.707 57.895 5.56 0.00 0.00 3.07
33 34 1.448540 CCCGCGCTATCCATCCATC 60.449 63.158 5.56 0.00 0.00 3.51
34 35 2.217038 ACCCGCGCTATCCATCCAT 61.217 57.895 5.56 0.00 0.00 3.41
35 36 2.842462 ACCCGCGCTATCCATCCA 60.842 61.111 5.56 0.00 0.00 3.41
36 37 2.357517 CACCCGCGCTATCCATCC 60.358 66.667 5.56 0.00 0.00 3.51
37 38 3.044305 GCACCCGCGCTATCCATC 61.044 66.667 5.56 0.00 0.00 3.51
38 39 2.680974 ATTGCACCCGCGCTATCCAT 62.681 55.000 5.56 0.00 42.97 3.41
39 40 2.884997 AATTGCACCCGCGCTATCCA 62.885 55.000 5.56 0.00 42.97 3.41
40 41 2.186826 AATTGCACCCGCGCTATCC 61.187 57.895 5.56 0.00 42.97 2.59
41 42 1.009675 CAATTGCACCCGCGCTATC 60.010 57.895 5.56 0.00 42.97 2.08
42 43 1.312371 AACAATTGCACCCGCGCTAT 61.312 50.000 5.56 0.00 42.97 2.97
43 44 1.917782 GAACAATTGCACCCGCGCTA 61.918 55.000 5.56 0.00 42.97 4.26
44 45 3.267597 GAACAATTGCACCCGCGCT 62.268 57.895 5.56 0.00 42.97 5.92
45 46 2.804931 GAACAATTGCACCCGCGC 60.805 61.111 5.05 0.00 42.97 6.86
46 47 0.449786 TATGAACAATTGCACCCGCG 59.550 50.000 5.05 0.00 42.97 6.46
47 48 2.645730 TTATGAACAATTGCACCCGC 57.354 45.000 5.05 0.00 39.24 6.13
48 49 4.555262 ACTTTTATGAACAATTGCACCCG 58.445 39.130 5.05 0.00 0.00 5.28
49 50 6.346518 CGAAACTTTTATGAACAATTGCACCC 60.347 38.462 5.05 0.00 0.00 4.61
50 51 6.580476 CGAAACTTTTATGAACAATTGCACC 58.420 36.000 5.05 0.00 0.00 5.01
51 52 6.064525 GCGAAACTTTTATGAACAATTGCAC 58.935 36.000 5.05 0.23 0.00 4.57
52 53 5.108065 CGCGAAACTTTTATGAACAATTGCA 60.108 36.000 0.00 0.00 0.00 4.08
53 54 5.297314 CGCGAAACTTTTATGAACAATTGC 58.703 37.500 0.00 0.00 0.00 3.56
54 55 5.116983 AGCGCGAAACTTTTATGAACAATTG 59.883 36.000 12.10 3.24 0.00 2.32
55 56 5.116983 CAGCGCGAAACTTTTATGAACAATT 59.883 36.000 12.10 0.00 0.00 2.32
56 57 4.616802 CAGCGCGAAACTTTTATGAACAAT 59.383 37.500 12.10 0.00 0.00 2.71
57 58 3.971871 CAGCGCGAAACTTTTATGAACAA 59.028 39.130 12.10 0.00 0.00 2.83
58 59 3.002862 ACAGCGCGAAACTTTTATGAACA 59.997 39.130 12.10 0.00 0.00 3.18
59 60 3.551551 ACAGCGCGAAACTTTTATGAAC 58.448 40.909 12.10 0.00 0.00 3.18
60 61 3.889196 ACAGCGCGAAACTTTTATGAA 57.111 38.095 12.10 0.00 0.00 2.57
61 62 4.211584 TGTTACAGCGCGAAACTTTTATGA 59.788 37.500 12.10 0.29 0.00 2.15
62 63 4.317291 GTGTTACAGCGCGAAACTTTTATG 59.683 41.667 12.10 4.62 0.00 1.90
63 64 4.460505 GTGTTACAGCGCGAAACTTTTAT 58.539 39.130 12.10 0.00 0.00 1.40
64 65 3.602038 CGTGTTACAGCGCGAAACTTTTA 60.602 43.478 12.10 1.71 44.10 1.52
65 66 2.711885 GTGTTACAGCGCGAAACTTTT 58.288 42.857 12.10 0.00 0.00 2.27
66 67 1.332552 CGTGTTACAGCGCGAAACTTT 60.333 47.619 12.10 0.00 44.10 2.66
67 68 0.231279 CGTGTTACAGCGCGAAACTT 59.769 50.000 12.10 0.00 44.10 2.66
68 69 1.554042 CCGTGTTACAGCGCGAAACT 61.554 55.000 12.10 0.00 44.10 2.66
69 70 1.154727 CCGTGTTACAGCGCGAAAC 60.155 57.895 12.10 8.72 44.10 2.78
70 71 0.875040 TTCCGTGTTACAGCGCGAAA 60.875 50.000 12.10 0.00 44.10 3.46
71 72 1.279527 CTTCCGTGTTACAGCGCGAA 61.280 55.000 12.10 0.00 44.10 4.70
72 73 1.731613 CTTCCGTGTTACAGCGCGA 60.732 57.895 12.10 0.00 44.10 5.87
73 74 2.769617 CTTCCGTGTTACAGCGCG 59.230 61.111 0.00 0.00 41.44 6.86
74 75 1.837538 TTGCTTCCGTGTTACAGCGC 61.838 55.000 0.00 0.00 34.82 5.92
75 76 0.796312 ATTGCTTCCGTGTTACAGCG 59.204 50.000 0.00 0.00 34.82 5.18
76 77 2.989422 AATTGCTTCCGTGTTACAGC 57.011 45.000 0.00 0.00 0.00 4.40
106 107 5.740569 CGTAGCCTATATATAGCGCGAAAAA 59.259 40.000 12.10 0.00 34.15 1.94
107 108 5.163723 ACGTAGCCTATATATAGCGCGAAAA 60.164 40.000 12.10 0.00 34.15 2.29
108 109 4.333649 ACGTAGCCTATATATAGCGCGAAA 59.666 41.667 12.10 0.00 34.15 3.46
109 110 3.873361 ACGTAGCCTATATATAGCGCGAA 59.127 43.478 12.10 15.80 34.15 4.70
110 111 3.246936 CACGTAGCCTATATATAGCGCGA 59.753 47.826 12.10 17.53 34.15 5.87
111 112 3.002042 ACACGTAGCCTATATATAGCGCG 59.998 47.826 13.49 17.19 34.15 6.86
112 113 4.548991 ACACGTAGCCTATATATAGCGC 57.451 45.455 13.49 16.32 0.00 5.92
113 114 6.687531 CAGAAACACGTAGCCTATATATAGCG 59.312 42.308 13.49 13.18 0.00 4.26
114 115 6.973474 CCAGAAACACGTAGCCTATATATAGC 59.027 42.308 13.49 9.43 0.00 2.97
115 116 7.481642 CCCAGAAACACGTAGCCTATATATAG 58.518 42.308 12.18 12.18 0.00 1.31
116 117 6.127535 GCCCAGAAACACGTAGCCTATATATA 60.128 42.308 0.00 0.00 0.00 0.86
117 118 5.337330 GCCCAGAAACACGTAGCCTATATAT 60.337 44.000 0.00 0.00 0.00 0.86
118 119 4.021719 GCCCAGAAACACGTAGCCTATATA 60.022 45.833 0.00 0.00 0.00 0.86
119 120 3.244112 GCCCAGAAACACGTAGCCTATAT 60.244 47.826 0.00 0.00 0.00 0.86
120 121 2.101917 GCCCAGAAACACGTAGCCTATA 59.898 50.000 0.00 0.00 0.00 1.31
121 122 1.134491 GCCCAGAAACACGTAGCCTAT 60.134 52.381 0.00 0.00 0.00 2.57
122 123 0.248289 GCCCAGAAACACGTAGCCTA 59.752 55.000 0.00 0.00 0.00 3.93
123 124 1.003718 GCCCAGAAACACGTAGCCT 60.004 57.895 0.00 0.00 0.00 4.58
124 125 2.038837 GGCCCAGAAACACGTAGCC 61.039 63.158 0.00 0.00 0.00 3.93
125 126 2.388232 CGGCCCAGAAACACGTAGC 61.388 63.158 0.00 0.00 0.00 3.58
126 127 1.740296 CCGGCCCAGAAACACGTAG 60.740 63.158 0.00 0.00 0.00 3.51
127 128 2.344500 CCGGCCCAGAAACACGTA 59.656 61.111 0.00 0.00 0.00 3.57
144 145 4.814294 CTGGCGTACCTCGTGGGC 62.814 72.222 8.63 1.57 42.13 5.36
145 146 2.830704 GAACTGGCGTACCTCGTGGG 62.831 65.000 8.63 2.00 42.13 4.61
146 147 1.445582 GAACTGGCGTACCTCGTGG 60.446 63.158 0.99 0.99 42.13 4.94
147 148 1.445582 GGAACTGGCGTACCTCGTG 60.446 63.158 0.00 0.00 42.13 4.35
148 149 1.255667 ATGGAACTGGCGTACCTCGT 61.256 55.000 0.00 0.00 42.13 4.18
149 150 0.742505 TATGGAACTGGCGTACCTCG 59.257 55.000 0.00 0.00 43.12 4.63
150 151 2.934553 GTTTATGGAACTGGCGTACCTC 59.065 50.000 0.00 0.00 35.31 3.85
151 152 2.355412 GGTTTATGGAACTGGCGTACCT 60.355 50.000 0.00 0.00 38.35 3.08
152 153 2.011947 GGTTTATGGAACTGGCGTACC 58.988 52.381 0.00 0.00 38.35 3.34
153 154 1.662122 CGGTTTATGGAACTGGCGTAC 59.338 52.381 0.00 0.00 40.32 3.67
154 155 2.012937 CGGTTTATGGAACTGGCGTA 57.987 50.000 0.00 0.00 40.32 4.42
155 156 2.849081 CGGTTTATGGAACTGGCGT 58.151 52.632 0.00 0.00 40.32 5.68
159 160 1.302383 TGCGCCGGTTTATGGAACTG 61.302 55.000 4.18 0.00 43.05 3.16
160 161 0.393808 ATGCGCCGGTTTATGGAACT 60.394 50.000 4.18 0.00 38.35 3.01
161 162 1.301423 TATGCGCCGGTTTATGGAAC 58.699 50.000 4.18 0.00 37.53 3.62
162 163 2.039818 TTATGCGCCGGTTTATGGAA 57.960 45.000 4.18 0.00 0.00 3.53
163 164 2.039818 TTTATGCGCCGGTTTATGGA 57.960 45.000 4.18 0.00 0.00 3.41
164 165 2.853731 TTTTATGCGCCGGTTTATGG 57.146 45.000 4.18 0.00 0.00 2.74
165 166 3.701241 ACATTTTATGCGCCGGTTTATG 58.299 40.909 4.18 4.46 0.00 1.90
166 167 3.378742 TGACATTTTATGCGCCGGTTTAT 59.621 39.130 4.18 0.00 0.00 1.40
167 168 2.747989 TGACATTTTATGCGCCGGTTTA 59.252 40.909 4.18 0.00 0.00 2.01
168 169 1.542030 TGACATTTTATGCGCCGGTTT 59.458 42.857 4.18 0.00 0.00 3.27
169 170 1.169577 TGACATTTTATGCGCCGGTT 58.830 45.000 4.18 0.00 0.00 4.44
170 171 1.169577 TTGACATTTTATGCGCCGGT 58.830 45.000 4.18 0.00 0.00 5.28
171 172 2.270275 TTTGACATTTTATGCGCCGG 57.730 45.000 4.18 0.00 0.00 6.13
172 173 3.497118 TCTTTTGACATTTTATGCGCCG 58.503 40.909 4.18 0.00 0.00 6.46
173 174 5.837586 TTTCTTTTGACATTTTATGCGCC 57.162 34.783 4.18 0.00 0.00 6.53
174 175 7.003648 GTCTTTTCTTTTGACATTTTATGCGC 58.996 34.615 0.00 0.00 0.00 6.09
175 176 8.060020 TGTCTTTTCTTTTGACATTTTATGCG 57.940 30.769 0.00 0.00 36.03 4.73
179 180 8.878769 GCCTTTGTCTTTTCTTTTGACATTTTA 58.121 29.630 0.00 0.00 39.92 1.52
180 181 7.390162 TGCCTTTGTCTTTTCTTTTGACATTTT 59.610 29.630 0.00 0.00 39.92 1.82
181 182 6.878389 TGCCTTTGTCTTTTCTTTTGACATTT 59.122 30.769 0.00 0.00 39.92 2.32
182 183 6.405538 TGCCTTTGTCTTTTCTTTTGACATT 58.594 32.000 0.00 0.00 39.92 2.71
183 184 5.976458 TGCCTTTGTCTTTTCTTTTGACAT 58.024 33.333 0.00 0.00 39.92 3.06
184 185 5.184864 TCTGCCTTTGTCTTTTCTTTTGACA 59.815 36.000 0.00 0.00 38.71 3.58
185 186 5.650543 TCTGCCTTTGTCTTTTCTTTTGAC 58.349 37.500 0.00 0.00 0.00 3.18
186 187 5.163519 CCTCTGCCTTTGTCTTTTCTTTTGA 60.164 40.000 0.00 0.00 0.00 2.69
187 188 5.045872 CCTCTGCCTTTGTCTTTTCTTTTG 58.954 41.667 0.00 0.00 0.00 2.44
188 189 4.711846 ACCTCTGCCTTTGTCTTTTCTTTT 59.288 37.500 0.00 0.00 0.00 2.27
189 190 4.281657 ACCTCTGCCTTTGTCTTTTCTTT 58.718 39.130 0.00 0.00 0.00 2.52
190 191 3.903467 ACCTCTGCCTTTGTCTTTTCTT 58.097 40.909 0.00 0.00 0.00 2.52
191 192 3.584733 ACCTCTGCCTTTGTCTTTTCT 57.415 42.857 0.00 0.00 0.00 2.52
192 193 5.703876 CAATACCTCTGCCTTTGTCTTTTC 58.296 41.667 0.00 0.00 0.00 2.29
193 194 4.021981 GCAATACCTCTGCCTTTGTCTTTT 60.022 41.667 0.00 0.00 33.51 2.27
194 195 3.507622 GCAATACCTCTGCCTTTGTCTTT 59.492 43.478 0.00 0.00 33.51 2.52
195 196 3.084786 GCAATACCTCTGCCTTTGTCTT 58.915 45.455 0.00 0.00 33.51 3.01
196 197 2.307098 AGCAATACCTCTGCCTTTGTCT 59.693 45.455 0.00 0.00 40.86 3.41
197 198 2.680339 GAGCAATACCTCTGCCTTTGTC 59.320 50.000 0.00 0.00 40.86 3.18
198 199 2.716217 GAGCAATACCTCTGCCTTTGT 58.284 47.619 0.00 0.00 40.86 2.83
199 200 1.667724 CGAGCAATACCTCTGCCTTTG 59.332 52.381 0.00 0.00 40.86 2.77
200 201 1.279271 ACGAGCAATACCTCTGCCTTT 59.721 47.619 0.00 0.00 40.86 3.11
201 202 0.905357 ACGAGCAATACCTCTGCCTT 59.095 50.000 0.00 0.00 40.86 4.35
202 203 0.905357 AACGAGCAATACCTCTGCCT 59.095 50.000 0.00 0.00 40.86 4.75
203 204 1.739067 AAACGAGCAATACCTCTGCC 58.261 50.000 0.00 0.00 40.86 4.85
204 205 3.003480 AGAAAACGAGCAATACCTCTGC 58.997 45.455 0.00 0.00 40.24 4.26
205 206 4.245660 TCAGAAAACGAGCAATACCTCTG 58.754 43.478 0.00 0.00 0.00 3.35
206 207 4.537135 TCAGAAAACGAGCAATACCTCT 57.463 40.909 0.00 0.00 0.00 3.69
207 208 5.582665 AGAATCAGAAAACGAGCAATACCTC 59.417 40.000 0.00 0.00 0.00 3.85
208 209 5.491982 AGAATCAGAAAACGAGCAATACCT 58.508 37.500 0.00 0.00 0.00 3.08
209 210 5.220681 GGAGAATCAGAAAACGAGCAATACC 60.221 44.000 0.00 0.00 36.25 2.73
210 211 5.220681 GGGAGAATCAGAAAACGAGCAATAC 60.221 44.000 0.00 0.00 36.25 1.89
211 212 4.876107 GGGAGAATCAGAAAACGAGCAATA 59.124 41.667 0.00 0.00 36.25 1.90
325 326 1.225704 GACAGCCTTGGAGATGGGG 59.774 63.158 0.00 0.00 0.00 4.96
513 515 3.558505 CTGTTCAATTCGAGCACCAAAG 58.441 45.455 0.00 0.00 30.79 2.77
675 679 7.775093 AGAATGCTTGCCAGTAATACAATAGAA 59.225 33.333 0.00 0.00 0.00 2.10
677 681 7.308229 GGAGAATGCTTGCCAGTAATACAATAG 60.308 40.741 0.00 0.00 0.00 1.73
987 993 5.181748 CCTAGAAGCATGAACAGCTAAACT 58.818 41.667 0.00 0.00 42.53 2.66
1141 1150 0.666274 GCCACACACAGACGAATCGA 60.666 55.000 10.55 0.00 0.00 3.59
1218 1227 4.021807 TGCAAAACTCTCAATGCATCATGT 60.022 37.500 0.00 0.00 43.32 3.21
1272 1281 3.008485 GGTGATGAGACAAACCTTCCTCT 59.992 47.826 0.00 0.00 0.00 3.69
1355 1364 2.550978 CGAACCGCACTTCTCCATTAT 58.449 47.619 0.00 0.00 0.00 1.28
1480 1489 1.593196 TGCAACTCCACAAGTAGCAC 58.407 50.000 0.00 0.00 37.17 4.40
1641 1650 9.433153 CATCTTGCATATAAGCTAATCAGAGAA 57.567 33.333 1.16 0.00 34.99 2.87
1670 1679 2.008329 GACAAGCATTCTCCAGCTGAG 58.992 52.381 17.39 10.96 41.70 3.35
1818 1827 4.158394 GTGGCAAATGTGATGTCATTAGGT 59.842 41.667 0.00 0.00 37.09 3.08
2568 2577 8.220755 TGTTTTCTGCTGTGAAAGTATAAACT 57.779 30.769 0.00 0.00 37.27 2.66
2601 2610 4.592778 AGGACATTGTTTATTTGGTGGCTT 59.407 37.500 0.00 0.00 0.00 4.35
2844 2866 6.880822 TTGAATACTTTGAGGTACGAATCG 57.119 37.500 0.00 0.00 0.00 3.34
2886 2908 3.071167 GTCAGGTGGGAAAACTCTACTGT 59.929 47.826 0.00 0.00 0.00 3.55
2965 2991 8.732531 GCCTAGTCTAATTACTAGTGTATCCTG 58.267 40.741 5.39 0.00 45.00 3.86
3302 3335 6.478673 GCAATGCTTTATATTTTGGGTACACC 59.521 38.462 0.00 0.00 40.81 4.16
3303 3336 7.038659 TGCAATGCTTTATATTTTGGGTACAC 58.961 34.615 6.82 0.00 0.00 2.90
3304 3337 7.093552 ACTGCAATGCTTTATATTTTGGGTACA 60.094 33.333 6.82 0.00 0.00 2.90
3305 3338 7.264947 ACTGCAATGCTTTATATTTTGGGTAC 58.735 34.615 6.82 0.00 0.00 3.34
3306 3339 7.416964 ACTGCAATGCTTTATATTTTGGGTA 57.583 32.000 6.82 0.00 0.00 3.69
3307 3340 6.298441 ACTGCAATGCTTTATATTTTGGGT 57.702 33.333 6.82 0.00 0.00 4.51
3318 3351 7.864379 GCACTTTGATATATACTGCAATGCTTT 59.136 33.333 6.82 0.00 0.00 3.51
3319 3352 7.013559 TGCACTTTGATATATACTGCAATGCTT 59.986 33.333 6.82 0.00 30.48 3.91
3320 3353 6.487668 TGCACTTTGATATATACTGCAATGCT 59.512 34.615 6.82 0.00 30.48 3.79
3321 3354 6.671190 TGCACTTTGATATATACTGCAATGC 58.329 36.000 0.00 0.00 30.48 3.56
3322 3355 9.687210 AAATGCACTTTGATATATACTGCAATG 57.313 29.630 0.00 0.00 36.78 2.82
3440 3473 7.279313 TCACACAACTTTGACTAGGACTTTTAC 59.721 37.037 0.00 0.00 0.00 2.01
3441 3474 7.332557 TCACACAACTTTGACTAGGACTTTTA 58.667 34.615 0.00 0.00 0.00 1.52
3442 3475 6.177610 TCACACAACTTTGACTAGGACTTTT 58.822 36.000 0.00 0.00 0.00 2.27
3443 3476 5.741011 TCACACAACTTTGACTAGGACTTT 58.259 37.500 0.00 0.00 0.00 2.66
3444 3477 5.353394 TCACACAACTTTGACTAGGACTT 57.647 39.130 0.00 0.00 0.00 3.01
3445 3478 5.070446 TCATCACACAACTTTGACTAGGACT 59.930 40.000 0.00 0.00 0.00 3.85
3446 3479 5.297547 TCATCACACAACTTTGACTAGGAC 58.702 41.667 0.00 0.00 0.00 3.85
3447 3480 5.545063 TCATCACACAACTTTGACTAGGA 57.455 39.130 0.00 0.00 0.00 2.94
3448 3481 5.991606 TCTTCATCACACAACTTTGACTAGG 59.008 40.000 0.00 0.00 0.00 3.02
3449 3482 6.073548 GGTCTTCATCACACAACTTTGACTAG 60.074 42.308 0.00 0.00 0.00 2.57
3450 3483 5.758296 GGTCTTCATCACACAACTTTGACTA 59.242 40.000 0.00 0.00 0.00 2.59
3488 3521 3.548014 CCCTTCACAAAATATAAGGCGCG 60.548 47.826 0.00 0.00 37.71 6.86
3511 3544 8.270744 ACAAGAATGCAACTAAGAGATATTCCT 58.729 33.333 0.00 0.00 0.00 3.36
3515 3548 6.769822 CCCACAAGAATGCAACTAAGAGATAT 59.230 38.462 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.