Multiple sequence alignment - TraesCS5B01G101400

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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 TraesCS5B01G101400 chr5B 100.000 3353 0 0 1 3353 134449661 134446309 0.000000e+00 6192
1 TraesCS5B01G101400 chr5B 85.393 534 68 8 2752 3283 215845902 215846427 2.270000e-151 545
2 TraesCS5B01G101400 chr5A 94.900 3059 99 24 323 3353 132597160 132594131 0.000000e+00 4732
3 TraesCS5B01G101400 chr5D 96.093 2508 74 11 323 2815 121175118 121172620 0.000000e+00 4067
4 TraesCS5B01G101400 chr5D 94.812 559 21 6 2797 3353 121172606 121172054 0.000000e+00 865
5 TraesCS5B01G101400 chr5D 85.047 321 38 8 1 317 125452597 125452911 5.400000e-83 318
6 TraesCS5B01G101400 chr3D 89.079 1053 103 7 1316 2364 17792237 17793281 0.000000e+00 1297
7 TraesCS5B01G101400 chr3D 88.696 575 59 3 1752 2326 17807509 17808077 0.000000e+00 697
8 TraesCS5B01G101400 chr3D 87.478 575 61 5 1754 2326 17793682 17794247 0.000000e+00 652
9 TraesCS5B01G101400 chr3D 88.889 522 58 0 1753 2274 17796382 17796903 0.000000e+00 643
10 TraesCS5B01G101400 chr3D 92.287 376 29 0 1899 2274 17834713 17835088 4.920000e-148 534
11 TraesCS5B01G101400 chrUn 90.353 539 45 5 1826 2364 37157942 37157411 0.000000e+00 701
12 TraesCS5B01G101400 chrUn 86.612 605 69 10 2752 3353 244072314 244072909 0.000000e+00 658
13 TraesCS5B01G101400 chrUn 86.612 605 69 10 2752 3353 256066503 256065908 0.000000e+00 658
14 TraesCS5B01G101400 chrUn 86.612 605 69 10 2752 3353 268677061 268676466 0.000000e+00 658
15 TraesCS5B01G101400 chrUn 84.921 378 30 11 1421 1798 37158287 37157937 1.140000e-94 357
16 TraesCS5B01G101400 chrUn 82.490 257 37 6 65 319 24502032 24502282 5.630000e-53 219
17 TraesCS5B01G101400 chr7A 86.230 610 69 12 2752 3353 727513180 727513782 0.000000e+00 647
18 TraesCS5B01G101400 chr2A 85.785 605 73 10 2752 3353 394800919 394800325 2.200000e-176 628
19 TraesCS5B01G101400 chr2A 85.785 605 73 10 2752 3353 406408614 406409208 2.200000e-176 628
20 TraesCS5B01G101400 chr2A 84.564 447 69 0 1150 1596 133671044 133671490 8.540000e-121 444
21 TraesCS5B01G101400 chr2A 80.380 474 59 25 1602 2055 133671627 133672086 2.490000e-86 329
22 TraesCS5B01G101400 chr2B 85.011 447 67 0 1150 1596 180558787 180559233 3.940000e-124 455
23 TraesCS5B01G101400 chr2B 81.366 483 51 30 1594 2055 180559327 180559791 1.140000e-94 357
24 TraesCS5B01G101400 chr2D 84.787 447 68 0 1150 1596 126968383 126968829 1.830000e-122 449
25 TraesCS5B01G101400 chr2D 80.462 476 71 18 1594 2055 126968941 126969408 8.910000e-91 344
26 TraesCS5B01G101400 chr7D 85.758 330 33 10 1 325 473862154 473861834 1.490000e-88 337
27 TraesCS5B01G101400 chr6D 84.247 292 34 8 32 319 261703357 261703640 1.190000e-69 274
28 TraesCS5B01G101400 chr6D 76.104 385 72 16 1161 1535 454231330 454231704 2.050000e-42 183
29 TraesCS5B01G101400 chr1B 82.353 323 45 9 1 317 132297831 132298147 1.530000e-68 270
30 TraesCS5B01G101400 chr6B 83.444 302 36 11 25 319 462645916 462645622 5.510000e-68 268
31 TraesCS5B01G101400 chr6B 75.328 381 75 15 1161 1533 690560723 690560354 7.440000e-37 165
32 TraesCS5B01G101400 chr4A 83.051 295 35 9 16 306 458288927 458288644 1.540000e-63 254
33 TraesCS5B01G101400 chr4A 82.474 291 36 9 20 306 458013944 458013665 1.200000e-59 241
34 TraesCS5B01G101400 chr4B 79.930 284 50 4 25 306 421853601 421853323 5.670000e-48 202
35 TraesCS5B01G101400 chr6A 75.584 385 74 18 1161 1535 600404314 600404688 4.450000e-39 172


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 TraesCS5B01G101400 chr5B 134446309 134449661 3352 True 6192.0 6192 100.0000 1 3353 1 chr5B.!!$R1 3352
1 TraesCS5B01G101400 chr5B 215845902 215846427 525 False 545.0 545 85.3930 2752 3283 1 chr5B.!!$F1 531
2 TraesCS5B01G101400 chr5A 132594131 132597160 3029 True 4732.0 4732 94.9000 323 3353 1 chr5A.!!$R1 3030
3 TraesCS5B01G101400 chr5D 121172054 121175118 3064 True 2466.0 4067 95.4525 323 3353 2 chr5D.!!$R1 3030
4 TraesCS5B01G101400 chr3D 17792237 17796903 4666 False 864.0 1297 88.4820 1316 2364 3 chr3D.!!$F3 1048
5 TraesCS5B01G101400 chr3D 17807509 17808077 568 False 697.0 697 88.6960 1752 2326 1 chr3D.!!$F1 574
6 TraesCS5B01G101400 chrUn 244072314 244072909 595 False 658.0 658 86.6120 2752 3353 1 chrUn.!!$F2 601
7 TraesCS5B01G101400 chrUn 256065908 256066503 595 True 658.0 658 86.6120 2752 3353 1 chrUn.!!$R1 601
8 TraesCS5B01G101400 chrUn 268676466 268677061 595 True 658.0 658 86.6120 2752 3353 1 chrUn.!!$R2 601
9 TraesCS5B01G101400 chrUn 37157411 37158287 876 True 529.0 701 87.6370 1421 2364 2 chrUn.!!$R3 943
10 TraesCS5B01G101400 chr7A 727513180 727513782 602 False 647.0 647 86.2300 2752 3353 1 chr7A.!!$F1 601
11 TraesCS5B01G101400 chr2A 394800325 394800919 594 True 628.0 628 85.7850 2752 3353 1 chr2A.!!$R1 601
12 TraesCS5B01G101400 chr2A 406408614 406409208 594 False 628.0 628 85.7850 2752 3353 1 chr2A.!!$F1 601
13 TraesCS5B01G101400 chr2A 133671044 133672086 1042 False 386.5 444 82.4720 1150 2055 2 chr2A.!!$F2 905
14 TraesCS5B01G101400 chr2B 180558787 180559791 1004 False 406.0 455 83.1885 1150 2055 2 chr2B.!!$F1 905
15 TraesCS5B01G101400 chr2D 126968383 126969408 1025 False 396.5 449 82.6245 1150 2055 2 chr2D.!!$F1 905

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
318 319 0.179119 GCGCAACGGTCCACTAGTAT 60.179 55.0 0.3 0.0 0.0 2.12 F
909 922 0.337428 ATTGCCTGCCATTTCCTCCT 59.663 50.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2368 0.322008 CCTGGCTGAAGGTGAAGGTC 60.322 60.0 0.00 0.0 32.17 3.85 R
2777 4379 1.093972 TGGTTGGCATGCTAACATCG 58.906 50.0 37.38 0.0 38.84 3.84 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
74 75 7.420184 AAACAAAAGCCTATGTATGTTTTGC 57.580 32.000 5.90 0.00 40.28 3.68
75 76 6.345096 ACAAAAGCCTATGTATGTTTTGCT 57.655 33.333 5.90 0.00 40.28 3.91
76 77 6.389906 ACAAAAGCCTATGTATGTTTTGCTC 58.610 36.000 5.90 0.00 40.28 4.26
77 78 6.015519 ACAAAAGCCTATGTATGTTTTGCTCA 60.016 34.615 5.90 0.00 40.28 4.26
78 79 6.588719 AAAGCCTATGTATGTTTTGCTCAA 57.411 33.333 0.00 0.00 0.00 3.02
79 80 6.588719 AAGCCTATGTATGTTTTGCTCAAA 57.411 33.333 0.00 0.00 0.00 2.69
80 81 5.954335 AGCCTATGTATGTTTTGCTCAAAC 58.046 37.500 5.42 5.42 44.64 2.93
88 89 2.601804 GTTTTGCTCAAACACAACCGT 58.398 42.857 7.08 0.00 43.93 4.83
89 90 2.990514 GTTTTGCTCAAACACAACCGTT 59.009 40.909 7.08 0.00 43.93 4.44
90 91 2.270275 TTGCTCAAACACAACCGTTG 57.730 45.000 9.80 9.80 0.00 4.10
91 92 1.454201 TGCTCAAACACAACCGTTGA 58.546 45.000 18.19 0.00 0.00 3.18
92 93 1.813178 TGCTCAAACACAACCGTTGAA 59.187 42.857 18.19 0.00 0.00 2.69
93 94 2.229062 TGCTCAAACACAACCGTTGAAA 59.771 40.909 18.19 0.00 0.00 2.69
94 95 3.246619 GCTCAAACACAACCGTTGAAAA 58.753 40.909 18.19 0.00 0.00 2.29
95 96 3.303229 GCTCAAACACAACCGTTGAAAAG 59.697 43.478 18.19 7.14 0.00 2.27
96 97 4.481463 CTCAAACACAACCGTTGAAAAGT 58.519 39.130 18.19 7.71 0.00 2.66
97 98 4.230657 TCAAACACAACCGTTGAAAAGTG 58.769 39.130 18.19 7.65 0.00 3.16
98 99 2.931512 ACACAACCGTTGAAAAGTGG 57.068 45.000 18.19 1.48 0.00 4.00
99 100 2.438411 ACACAACCGTTGAAAAGTGGA 58.562 42.857 18.19 0.00 0.00 4.02
100 101 2.820787 ACACAACCGTTGAAAAGTGGAA 59.179 40.909 18.19 0.00 0.00 3.53
101 102 3.256136 ACACAACCGTTGAAAAGTGGAAA 59.744 39.130 18.19 0.00 0.00 3.13
102 103 4.081917 ACACAACCGTTGAAAAGTGGAAAT 60.082 37.500 18.19 0.00 0.00 2.17
103 104 5.125739 ACACAACCGTTGAAAAGTGGAAATA 59.874 36.000 18.19 0.00 0.00 1.40
104 105 6.183360 ACACAACCGTTGAAAAGTGGAAATAT 60.183 34.615 18.19 0.00 0.00 1.28
105 106 6.699642 CACAACCGTTGAAAAGTGGAAATATT 59.300 34.615 18.19 0.00 0.00 1.28
106 107 7.223777 CACAACCGTTGAAAAGTGGAAATATTT 59.776 33.333 18.19 0.00 0.00 1.40
107 108 7.766738 ACAACCGTTGAAAAGTGGAAATATTTT 59.233 29.630 18.19 0.00 0.00 1.82
108 109 8.608317 CAACCGTTGAAAAGTGGAAATATTTTT 58.392 29.630 5.23 0.00 0.00 1.94
109 110 9.819267 AACCGTTGAAAAGTGGAAATATTTTTA 57.181 25.926 1.43 0.00 0.00 1.52
110 111 9.819267 ACCGTTGAAAAGTGGAAATATTTTTAA 57.181 25.926 1.43 0.00 0.00 1.52
121 122 9.824534 GTGGAAATATTTTTAATGCAAACTTGG 57.175 29.630 1.43 0.00 0.00 3.61
122 123 9.566432 TGGAAATATTTTTAATGCAAACTTGGT 57.434 25.926 1.43 0.00 0.00 3.67
129 130 8.956617 TTTTTAATGCAAACTTGGTTTCAAAC 57.043 26.923 0.00 0.00 33.10 2.93
130 131 4.856115 AATGCAAACTTGGTTTCAAACG 57.144 36.364 0.00 0.00 33.10 3.60
131 132 2.611518 TGCAAACTTGGTTTCAAACGG 58.388 42.857 0.00 0.00 33.10 4.44
132 133 1.930503 GCAAACTTGGTTTCAAACGGG 59.069 47.619 0.00 0.00 33.10 5.28
133 134 2.675603 GCAAACTTGGTTTCAAACGGGT 60.676 45.455 0.00 0.00 33.10 5.28
134 135 3.183754 CAAACTTGGTTTCAAACGGGTC 58.816 45.455 0.00 0.00 33.10 4.46
135 136 2.430248 ACTTGGTTTCAAACGGGTCT 57.570 45.000 0.00 0.00 31.77 3.85
136 137 2.294979 ACTTGGTTTCAAACGGGTCTC 58.705 47.619 0.00 0.00 31.77 3.36
137 138 2.092592 ACTTGGTTTCAAACGGGTCTCT 60.093 45.455 0.00 0.00 31.77 3.10
138 139 1.961793 TGGTTTCAAACGGGTCTCTG 58.038 50.000 0.00 0.00 0.00 3.35
139 140 1.210967 TGGTTTCAAACGGGTCTCTGT 59.789 47.619 0.00 0.00 0.00 3.41
140 141 1.602377 GGTTTCAAACGGGTCTCTGTG 59.398 52.381 0.00 0.00 31.84 3.66
141 142 2.557317 GTTTCAAACGGGTCTCTGTGA 58.443 47.619 0.00 0.00 31.84 3.58
142 143 2.940410 GTTTCAAACGGGTCTCTGTGAA 59.060 45.455 0.00 0.00 31.84 3.18
143 144 2.234300 TCAAACGGGTCTCTGTGAAC 57.766 50.000 0.00 0.00 31.84 3.18
144 145 0.859232 CAAACGGGTCTCTGTGAACG 59.141 55.000 0.00 4.30 31.85 3.95
145 146 0.462789 AAACGGGTCTCTGTGAACGT 59.537 50.000 5.32 5.32 40.57 3.99
146 147 0.249322 AACGGGTCTCTGTGAACGTG 60.249 55.000 10.15 0.00 39.40 4.49
147 148 1.372997 CGGGTCTCTGTGAACGTGG 60.373 63.158 0.00 0.00 31.85 4.94
148 149 1.746517 GGGTCTCTGTGAACGTGGT 59.253 57.895 0.00 0.00 31.85 4.16
149 150 0.963962 GGGTCTCTGTGAACGTGGTA 59.036 55.000 0.00 0.00 31.85 3.25
150 151 1.067776 GGGTCTCTGTGAACGTGGTAG 60.068 57.143 0.00 0.00 31.85 3.18
151 152 1.669211 GGTCTCTGTGAACGTGGTAGC 60.669 57.143 0.00 0.00 0.00 3.58
152 153 1.000607 GTCTCTGTGAACGTGGTAGCA 60.001 52.381 0.00 0.00 0.00 3.49
153 154 1.684450 TCTCTGTGAACGTGGTAGCAA 59.316 47.619 0.00 0.00 0.00 3.91
154 155 2.101750 TCTCTGTGAACGTGGTAGCAAA 59.898 45.455 0.00 0.00 0.00 3.68
155 156 3.067106 CTCTGTGAACGTGGTAGCAAAT 58.933 45.455 0.00 0.00 0.00 2.32
156 157 4.021807 TCTCTGTGAACGTGGTAGCAAATA 60.022 41.667 0.00 0.00 0.00 1.40
157 158 4.827692 TCTGTGAACGTGGTAGCAAATAT 58.172 39.130 0.00 0.00 0.00 1.28
158 159 5.242434 TCTGTGAACGTGGTAGCAAATATT 58.758 37.500 0.00 0.00 0.00 1.28
159 160 5.121611 TCTGTGAACGTGGTAGCAAATATTG 59.878 40.000 0.00 0.00 0.00 1.90
160 161 4.757657 TGTGAACGTGGTAGCAAATATTGT 59.242 37.500 0.00 0.00 0.00 2.71
161 162 5.086058 GTGAACGTGGTAGCAAATATTGTG 58.914 41.667 0.00 0.00 0.00 3.33
162 163 4.757657 TGAACGTGGTAGCAAATATTGTGT 59.242 37.500 0.00 0.00 0.00 3.72
163 164 4.678509 ACGTGGTAGCAAATATTGTGTG 57.321 40.909 0.00 0.00 0.00 3.82
164 165 4.069304 ACGTGGTAGCAAATATTGTGTGT 58.931 39.130 0.00 0.00 0.00 3.72
165 166 4.517453 ACGTGGTAGCAAATATTGTGTGTT 59.483 37.500 0.00 0.00 0.00 3.32
166 167 5.701750 ACGTGGTAGCAAATATTGTGTGTTA 59.298 36.000 0.00 0.00 0.00 2.41
167 168 6.019152 CGTGGTAGCAAATATTGTGTGTTAC 58.981 40.000 0.00 4.79 0.00 2.50
168 169 6.319399 GTGGTAGCAAATATTGTGTGTTACC 58.681 40.000 18.00 18.00 44.75 2.85
169 170 6.503589 GGTAGCAAATATTGTGTGTTACCA 57.496 37.500 19.13 0.00 44.23 3.25
170 171 6.915349 GGTAGCAAATATTGTGTGTTACCAA 58.085 36.000 19.13 0.00 44.23 3.67
171 172 7.371936 GGTAGCAAATATTGTGTGTTACCAAA 58.628 34.615 19.13 0.00 44.23 3.28
172 173 8.032451 GGTAGCAAATATTGTGTGTTACCAAAT 58.968 33.333 19.13 0.00 44.23 2.32
173 174 9.418045 GTAGCAAATATTGTGTGTTACCAAATT 57.582 29.630 0.00 0.00 0.00 1.82
175 176 9.988815 AGCAAATATTGTGTGTTACCAAATTAA 57.011 25.926 0.00 0.00 0.00 1.40
182 183 9.606631 ATTGTGTGTTACCAAATTAAAATGTGT 57.393 25.926 0.00 0.00 0.00 3.72
183 184 9.436957 TTGTGTGTTACCAAATTAAAATGTGTT 57.563 25.926 0.00 0.00 0.00 3.32
184 185 9.436957 TGTGTGTTACCAAATTAAAATGTGTTT 57.563 25.926 0.00 0.00 0.00 2.83
204 205 9.936759 TGTGTTTTATACATCTCATTGTAGACA 57.063 29.630 0.00 0.00 39.39 3.41
218 219 5.856126 TTGTAGACAACAATCAATCGACC 57.144 39.130 0.00 0.00 43.22 4.79
219 220 4.888917 TGTAGACAACAATCAATCGACCA 58.111 39.130 0.00 0.00 34.29 4.02
220 221 5.487433 TGTAGACAACAATCAATCGACCAT 58.513 37.500 0.00 0.00 34.29 3.55
221 222 4.952262 AGACAACAATCAATCGACCATG 57.048 40.909 0.00 0.00 0.00 3.66
222 223 4.326826 AGACAACAATCAATCGACCATGT 58.673 39.130 0.00 0.00 0.00 3.21
223 224 4.761739 AGACAACAATCAATCGACCATGTT 59.238 37.500 0.00 0.00 0.00 2.71
224 225 5.241506 AGACAACAATCAATCGACCATGTTT 59.758 36.000 0.00 0.00 0.00 2.83
225 226 5.460646 ACAACAATCAATCGACCATGTTTC 58.539 37.500 0.00 0.00 0.00 2.78
226 227 4.701956 ACAATCAATCGACCATGTTTCC 57.298 40.909 0.00 0.00 0.00 3.13
227 228 4.335416 ACAATCAATCGACCATGTTTCCT 58.665 39.130 0.00 0.00 0.00 3.36
228 229 5.496556 ACAATCAATCGACCATGTTTCCTA 58.503 37.500 0.00 0.00 0.00 2.94
229 230 6.122277 ACAATCAATCGACCATGTTTCCTAT 58.878 36.000 0.00 0.00 0.00 2.57
230 231 6.603201 ACAATCAATCGACCATGTTTCCTATT 59.397 34.615 0.00 0.00 0.00 1.73
231 232 7.773224 ACAATCAATCGACCATGTTTCCTATTA 59.227 33.333 0.00 0.00 0.00 0.98
232 233 8.620416 CAATCAATCGACCATGTTTCCTATTAA 58.380 33.333 0.00 0.00 0.00 1.40
233 234 8.746052 ATCAATCGACCATGTTTCCTATTAAA 57.254 30.769 0.00 0.00 0.00 1.52
234 235 8.208718 TCAATCGACCATGTTTCCTATTAAAG 57.791 34.615 0.00 0.00 0.00 1.85
236 237 5.433526 TCGACCATGTTTCCTATTAAAGGG 58.566 41.667 0.00 0.00 46.55 3.95
237 238 5.190132 TCGACCATGTTTCCTATTAAAGGGA 59.810 40.000 0.00 0.94 46.55 4.20
238 239 6.062095 CGACCATGTTTCCTATTAAAGGGAT 58.938 40.000 0.00 0.00 46.55 3.85
239 240 6.546034 CGACCATGTTTCCTATTAAAGGGATT 59.454 38.462 0.00 0.00 46.55 3.01
240 241 7.717875 CGACCATGTTTCCTATTAAAGGGATTA 59.282 37.037 0.00 0.00 46.55 1.75
241 242 9.416284 GACCATGTTTCCTATTAAAGGGATTAA 57.584 33.333 0.00 0.00 46.55 1.40
242 243 9.777008 ACCATGTTTCCTATTAAAGGGATTAAA 57.223 29.630 0.00 0.00 46.55 1.52
276 277 4.517952 TTTTTCATCGCACACATGGATT 57.482 36.364 0.00 0.00 0.00 3.01
277 278 4.517952 TTTTCATCGCACACATGGATTT 57.482 36.364 0.00 0.00 0.00 2.17
278 279 5.635417 TTTTCATCGCACACATGGATTTA 57.365 34.783 0.00 0.00 0.00 1.40
279 280 4.880886 TTCATCGCACACATGGATTTAG 57.119 40.909 0.00 0.00 0.00 1.85
280 281 2.613595 TCATCGCACACATGGATTTAGC 59.386 45.455 0.00 0.00 0.00 3.09
281 282 1.006086 TCGCACACATGGATTTAGCG 58.994 50.000 0.00 4.34 44.45 4.26
282 283 0.726827 CGCACACATGGATTTAGCGT 59.273 50.000 0.00 0.00 38.98 5.07
283 284 1.529622 CGCACACATGGATTTAGCGTG 60.530 52.381 0.00 0.00 38.98 5.34
284 285 1.795162 GCACACATGGATTTAGCGTGC 60.795 52.381 0.00 0.00 41.12 5.34
285 286 1.094785 ACACATGGATTTAGCGTGCC 58.905 50.000 0.00 0.00 0.00 5.01
286 287 1.340017 ACACATGGATTTAGCGTGCCT 60.340 47.619 0.00 0.00 0.00 4.75
287 288 1.331756 CACATGGATTTAGCGTGCCTC 59.668 52.381 0.00 0.00 0.00 4.70
288 289 1.210478 ACATGGATTTAGCGTGCCTCT 59.790 47.619 0.00 0.00 0.00 3.69
289 290 1.600957 CATGGATTTAGCGTGCCTCTG 59.399 52.381 0.00 0.00 0.00 3.35
290 291 0.613260 TGGATTTAGCGTGCCTCTGT 59.387 50.000 0.00 0.00 0.00 3.41
291 292 1.009829 GGATTTAGCGTGCCTCTGTG 58.990 55.000 0.00 0.00 0.00 3.66
292 293 0.375106 GATTTAGCGTGCCTCTGTGC 59.625 55.000 0.00 0.00 0.00 4.57
293 294 1.026718 ATTTAGCGTGCCTCTGTGCC 61.027 55.000 0.00 0.00 0.00 5.01
294 295 2.390306 TTTAGCGTGCCTCTGTGCCA 62.390 55.000 0.00 0.00 0.00 4.92
295 296 2.184020 TTAGCGTGCCTCTGTGCCAT 62.184 55.000 0.00 0.00 0.00 4.40
296 297 2.184020 TAGCGTGCCTCTGTGCCATT 62.184 55.000 0.00 0.00 0.00 3.16
297 298 2.629656 GCGTGCCTCTGTGCCATTT 61.630 57.895 0.00 0.00 0.00 2.32
298 299 1.210931 CGTGCCTCTGTGCCATTTG 59.789 57.895 0.00 0.00 0.00 2.32
299 300 1.588082 GTGCCTCTGTGCCATTTGG 59.412 57.895 0.00 0.00 38.53 3.28
309 310 2.126502 CCATTTGGCGCAACGGTC 60.127 61.111 10.83 0.00 0.00 4.79
310 311 2.126502 CATTTGGCGCAACGGTCC 60.127 61.111 10.83 0.00 0.00 4.46
311 312 2.596046 ATTTGGCGCAACGGTCCA 60.596 55.556 10.83 0.00 0.00 4.02
312 313 2.914908 ATTTGGCGCAACGGTCCAC 61.915 57.895 10.83 0.00 0.00 4.02
313 314 4.555709 TTGGCGCAACGGTCCACT 62.556 61.111 10.83 0.00 0.00 4.00
314 315 2.661840 TTTGGCGCAACGGTCCACTA 62.662 55.000 10.83 0.00 0.00 2.74
315 316 2.813908 GGCGCAACGGTCCACTAG 60.814 66.667 10.83 0.00 0.00 2.57
316 317 2.048503 GCGCAACGGTCCACTAGT 60.049 61.111 0.30 0.00 0.00 2.57
317 318 1.213537 GCGCAACGGTCCACTAGTA 59.786 57.895 0.30 0.00 0.00 1.82
318 319 0.179119 GCGCAACGGTCCACTAGTAT 60.179 55.000 0.30 0.00 0.00 2.12
319 320 1.738030 GCGCAACGGTCCACTAGTATT 60.738 52.381 0.30 0.00 0.00 1.89
320 321 1.924524 CGCAACGGTCCACTAGTATTG 59.075 52.381 0.00 0.00 0.00 1.90
321 322 2.673043 CGCAACGGTCCACTAGTATTGT 60.673 50.000 0.00 0.00 0.00 2.71
333 334 7.387948 GTCCACTAGTATTGTATAATGGGCAAG 59.612 40.741 0.00 0.00 0.00 4.01
347 348 1.017387 GGCAAGGTAGCAAATCCGAG 58.983 55.000 0.00 0.00 35.83 4.63
391 392 8.936070 AGTTTAATGATGTGTAAGCGTGTATA 57.064 30.769 0.00 0.00 0.00 1.47
432 439 9.284968 GTACATATTTAATGATTGCAGTAGGGT 57.715 33.333 0.00 0.00 0.00 4.34
447 454 6.212791 TGCAGTAGGGTTTGTCTAAGATACTT 59.787 38.462 0.00 0.00 0.00 2.24
448 455 7.398047 TGCAGTAGGGTTTGTCTAAGATACTTA 59.602 37.037 0.00 0.00 0.00 2.24
476 489 4.685169 AGTAAATGAAAGATGGCGTGTG 57.315 40.909 0.00 0.00 0.00 3.82
499 512 0.663568 GTCCACCGTCGTTGTCAGAG 60.664 60.000 0.00 0.00 0.00 3.35
518 531 3.964031 AGAGGAAGTAAGCCGAGATGATT 59.036 43.478 0.00 0.00 0.00 2.57
526 539 1.089481 GCCGAGATGATTCCGTTGCA 61.089 55.000 0.00 0.00 0.00 4.08
547 560 1.679977 GGCCCATCAGCTTTGAGCA 60.680 57.895 2.47 0.00 45.56 4.26
738 751 5.941948 ATGTGTACATCGATCGATCACTA 57.058 39.130 31.56 23.47 31.94 2.74
853 866 5.297547 TCGTTGTTGATGCTTCTTCTTACT 58.702 37.500 0.88 0.00 0.00 2.24
876 889 7.088905 ACTACTGTATTATTATTCTTCGCCGG 58.911 38.462 0.00 0.00 0.00 6.13
909 922 0.337428 ATTGCCTGCCATTTCCTCCT 59.663 50.000 0.00 0.00 0.00 3.69
912 925 0.548510 GCCTGCCATTTCCTCCTAGT 59.451 55.000 0.00 0.00 0.00 2.57
935 948 3.383620 GATCAGCTCGATCCATCACTT 57.616 47.619 12.51 0.00 44.25 3.16
936 949 2.591571 TCAGCTCGATCCATCACTTG 57.408 50.000 0.00 0.00 0.00 3.16
937 950 1.827344 TCAGCTCGATCCATCACTTGT 59.173 47.619 0.00 0.00 0.00 3.16
938 951 1.931841 CAGCTCGATCCATCACTTGTG 59.068 52.381 0.00 0.00 0.00 3.33
939 952 0.654683 GCTCGATCCATCACTTGTGC 59.345 55.000 0.00 0.00 0.00 4.57
940 953 1.741732 GCTCGATCCATCACTTGTGCT 60.742 52.381 0.00 0.00 0.00 4.40
952 967 4.211125 TCACTTGTGCTCTAGCTAGCTAT 58.789 43.478 24.36 3.01 43.19 2.97
960 975 5.472137 GTGCTCTAGCTAGCTATCTTACTGT 59.528 44.000 24.36 0.00 43.19 3.55
963 978 5.377478 TCTAGCTAGCTATCTTACTGTGCA 58.623 41.667 24.36 0.00 0.00 4.57
999 1014 0.392998 ATTAGCAGGGGAGTGCAACG 60.393 55.000 0.00 0.00 46.60 4.10
1033 1048 1.815003 GCAAGTCTATGCTTGTGGCTT 59.185 47.619 7.51 0.00 45.47 4.35
1059 1074 4.681978 GCGGTCACCTGCTCCGTT 62.682 66.667 3.69 0.00 45.11 4.44
2013 2212 1.374560 CCAACCTCAACAACGTCACA 58.625 50.000 0.00 0.00 0.00 3.58
2169 2368 0.249447 TCATGCGCAAGGACGATAGG 60.249 55.000 17.11 0.00 44.26 2.57
2493 3690 2.047844 CTGAGTGGTCCGTGCAGG 60.048 66.667 0.00 0.00 42.97 4.85
2750 4350 7.851508 TCAAAGTTTCTTCATAACTTGTCTCG 58.148 34.615 0.00 0.00 43.14 4.04
2808 4442 0.663153 GCCAACCAACTCACTGACAC 59.337 55.000 0.00 0.00 0.00 3.67
2810 4444 1.670811 CCAACCAACTCACTGACACAC 59.329 52.381 0.00 0.00 0.00 3.82
2816 4450 0.806102 ACTCACTGACACACGCACAC 60.806 55.000 0.00 0.00 0.00 3.82
2827 4462 3.064820 ACACACGCACACTAAGGAAAAAG 59.935 43.478 0.00 0.00 0.00 2.27
2862 4497 0.673333 TGCTACAACATCTGCCCACG 60.673 55.000 0.00 0.00 0.00 4.94
2873 4508 0.321564 CTGCCCACGTCCATGAAAGA 60.322 55.000 0.00 0.00 0.00 2.52
2874 4509 0.327924 TGCCCACGTCCATGAAAGAT 59.672 50.000 0.00 0.00 0.00 2.40
2875 4510 1.017387 GCCCACGTCCATGAAAGATC 58.983 55.000 0.00 0.00 0.00 2.75
2876 4511 1.678728 GCCCACGTCCATGAAAGATCA 60.679 52.381 0.00 0.00 40.57 2.92
2901 4536 6.969993 ACCTGAAGGCAATTGTACTAAAAA 57.030 33.333 7.40 0.00 39.32 1.94
2902 4537 7.539034 ACCTGAAGGCAATTGTACTAAAAAT 57.461 32.000 7.40 0.00 39.32 1.82
2903 4538 8.644374 ACCTGAAGGCAATTGTACTAAAAATA 57.356 30.769 7.40 0.00 39.32 1.40
2904 4539 9.084533 ACCTGAAGGCAATTGTACTAAAAATAA 57.915 29.630 7.40 0.00 39.32 1.40
2944 4846 5.655090 TGATTGACTTGATTGAGCCATGAAT 59.345 36.000 0.00 0.00 0.00 2.57
3102 5623 5.862811 GTGATGACACAGAGAAATTGCTAC 58.137 41.667 0.00 0.00 45.32 3.58
3286 6071 6.389091 CCATGCATGTTAATACAACAACACT 58.611 36.000 24.58 0.00 37.47 3.55
3316 6101 7.001674 ACTACATTAACATCCAACAGGAACAA 58.998 34.615 0.00 0.00 34.49 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 8.983724 GCAAAACATACATAGGCTTTTGTTTAA 58.016 29.630 7.91 0.00 36.56 1.52
49 50 8.364142 AGCAAAACATACATAGGCTTTTGTTTA 58.636 29.630 7.91 0.00 36.56 2.01
50 51 7.216494 AGCAAAACATACATAGGCTTTTGTTT 58.784 30.769 7.91 4.69 38.53 2.83
51 52 6.758254 AGCAAAACATACATAGGCTTTTGTT 58.242 32.000 7.91 0.00 35.28 2.83
52 53 6.015519 TGAGCAAAACATACATAGGCTTTTGT 60.016 34.615 0.00 0.00 35.28 2.83
53 54 6.389091 TGAGCAAAACATACATAGGCTTTTG 58.611 36.000 0.00 0.00 35.72 2.44
54 55 6.588719 TGAGCAAAACATACATAGGCTTTT 57.411 33.333 0.00 0.00 0.00 2.27
55 56 6.588719 TTGAGCAAAACATACATAGGCTTT 57.411 33.333 0.00 0.00 0.00 3.51
56 57 6.389906 GTTTGAGCAAAACATACATAGGCTT 58.610 36.000 9.45 0.00 46.30 4.35
57 58 5.954335 GTTTGAGCAAAACATACATAGGCT 58.046 37.500 9.45 0.00 46.30 4.58
69 70 2.989840 CAACGGTTGTGTTTGAGCAAAA 59.010 40.909 12.66 0.00 31.33 2.44
70 71 2.229062 TCAACGGTTGTGTTTGAGCAAA 59.771 40.909 19.47 0.00 0.00 3.68
71 72 1.813178 TCAACGGTTGTGTTTGAGCAA 59.187 42.857 19.47 0.00 0.00 3.91
72 73 1.454201 TCAACGGTTGTGTTTGAGCA 58.546 45.000 19.47 0.00 0.00 4.26
73 74 2.553079 TTCAACGGTTGTGTTTGAGC 57.447 45.000 19.47 0.00 0.00 4.26
74 75 4.323336 CACTTTTCAACGGTTGTGTTTGAG 59.677 41.667 19.47 12.22 0.00 3.02
75 76 4.230657 CACTTTTCAACGGTTGTGTTTGA 58.769 39.130 19.47 0.00 0.00 2.69
76 77 3.366422 CCACTTTTCAACGGTTGTGTTTG 59.634 43.478 19.47 11.46 0.00 2.93
77 78 3.256136 TCCACTTTTCAACGGTTGTGTTT 59.744 39.130 19.47 0.68 0.00 2.83
78 79 2.820787 TCCACTTTTCAACGGTTGTGTT 59.179 40.909 19.47 0.02 0.00 3.32
79 80 2.438411 TCCACTTTTCAACGGTTGTGT 58.562 42.857 19.47 11.73 0.00 3.72
80 81 3.495670 TTCCACTTTTCAACGGTTGTG 57.504 42.857 19.47 10.45 0.00 3.33
81 82 4.729227 ATTTCCACTTTTCAACGGTTGT 57.271 36.364 19.47 0.00 0.00 3.32
82 83 7.707774 AAATATTTCCACTTTTCAACGGTTG 57.292 32.000 14.62 14.62 0.00 3.77
83 84 8.725405 AAAAATATTTCCACTTTTCAACGGTT 57.275 26.923 0.10 0.00 0.00 4.44
84 85 9.819267 TTAAAAATATTTCCACTTTTCAACGGT 57.181 25.926 0.10 0.00 0.00 4.83
95 96 9.824534 CCAAGTTTGCATTAAAAATATTTCCAC 57.175 29.630 0.10 0.00 0.00 4.02
96 97 9.566432 ACCAAGTTTGCATTAAAAATATTTCCA 57.434 25.926 0.10 0.00 0.00 3.53
103 104 9.566530 GTTTGAAACCAAGTTTGCATTAAAAAT 57.433 25.926 0.00 0.00 35.77 1.82
104 105 7.746475 CGTTTGAAACCAAGTTTGCATTAAAAA 59.254 29.630 2.00 0.00 35.77 1.94
105 106 7.237173 CGTTTGAAACCAAGTTTGCATTAAAA 58.763 30.769 2.00 0.00 35.77 1.52
106 107 6.183360 CCGTTTGAAACCAAGTTTGCATTAAA 60.183 34.615 2.00 0.00 35.77 1.52
107 108 5.292101 CCGTTTGAAACCAAGTTTGCATTAA 59.708 36.000 2.00 0.00 35.77 1.40
108 109 4.806247 CCGTTTGAAACCAAGTTTGCATTA 59.194 37.500 2.00 0.00 35.77 1.90
109 110 3.620821 CCGTTTGAAACCAAGTTTGCATT 59.379 39.130 2.00 0.00 35.77 3.56
110 111 3.194062 CCGTTTGAAACCAAGTTTGCAT 58.806 40.909 2.00 0.00 35.77 3.96
111 112 2.611518 CCGTTTGAAACCAAGTTTGCA 58.388 42.857 2.00 0.00 35.77 4.08
112 113 1.930503 CCCGTTTGAAACCAAGTTTGC 59.069 47.619 2.00 0.00 35.77 3.68
113 114 3.119280 AGACCCGTTTGAAACCAAGTTTG 60.119 43.478 2.00 0.00 35.77 2.93
114 115 3.093814 AGACCCGTTTGAAACCAAGTTT 58.906 40.909 2.00 0.00 38.54 2.66
115 116 2.686405 GAGACCCGTTTGAAACCAAGTT 59.314 45.455 2.00 0.00 0.00 2.66
116 117 2.092592 AGAGACCCGTTTGAAACCAAGT 60.093 45.455 2.00 0.00 0.00 3.16
117 118 2.290641 CAGAGACCCGTTTGAAACCAAG 59.709 50.000 2.00 0.00 0.00 3.61
118 119 2.294074 CAGAGACCCGTTTGAAACCAA 58.706 47.619 2.00 0.00 0.00 3.67
119 120 1.210967 ACAGAGACCCGTTTGAAACCA 59.789 47.619 2.00 0.00 0.00 3.67
120 121 1.602377 CACAGAGACCCGTTTGAAACC 59.398 52.381 2.00 0.00 0.00 3.27
121 122 2.557317 TCACAGAGACCCGTTTGAAAC 58.443 47.619 0.00 0.00 0.00 2.78
122 123 2.940410 GTTCACAGAGACCCGTTTGAAA 59.060 45.455 0.00 0.00 0.00 2.69
123 124 2.557317 GTTCACAGAGACCCGTTTGAA 58.443 47.619 0.00 0.00 0.00 2.69
124 125 1.537348 CGTTCACAGAGACCCGTTTGA 60.537 52.381 0.00 0.00 0.00 2.69
125 126 0.859232 CGTTCACAGAGACCCGTTTG 59.141 55.000 0.00 0.00 0.00 2.93
126 127 0.462789 ACGTTCACAGAGACCCGTTT 59.537 50.000 0.00 0.00 32.05 3.60
127 128 0.249322 CACGTTCACAGAGACCCGTT 60.249 55.000 0.00 0.00 33.30 4.44
128 129 1.362717 CACGTTCACAGAGACCCGT 59.637 57.895 0.00 0.00 35.23 5.28
129 130 1.372997 CCACGTTCACAGAGACCCG 60.373 63.158 0.00 0.00 0.00 5.28
130 131 0.963962 TACCACGTTCACAGAGACCC 59.036 55.000 0.00 0.00 0.00 4.46
131 132 1.669211 GCTACCACGTTCACAGAGACC 60.669 57.143 0.00 0.00 0.00 3.85
132 133 1.000607 TGCTACCACGTTCACAGAGAC 60.001 52.381 0.00 0.00 0.00 3.36
133 134 1.324383 TGCTACCACGTTCACAGAGA 58.676 50.000 0.00 0.00 0.00 3.10
134 135 2.148916 TTGCTACCACGTTCACAGAG 57.851 50.000 0.00 0.00 0.00 3.35
135 136 2.605837 TTTGCTACCACGTTCACAGA 57.394 45.000 0.00 0.00 0.00 3.41
136 137 5.106712 ACAATATTTGCTACCACGTTCACAG 60.107 40.000 0.00 0.00 0.00 3.66
137 138 4.757657 ACAATATTTGCTACCACGTTCACA 59.242 37.500 0.00 0.00 0.00 3.58
138 139 5.086058 CACAATATTTGCTACCACGTTCAC 58.914 41.667 0.00 0.00 0.00 3.18
139 140 4.757657 ACACAATATTTGCTACCACGTTCA 59.242 37.500 0.00 0.00 0.00 3.18
140 141 5.086058 CACACAATATTTGCTACCACGTTC 58.914 41.667 0.00 0.00 0.00 3.95
141 142 4.517453 ACACACAATATTTGCTACCACGTT 59.483 37.500 0.00 0.00 0.00 3.99
142 143 4.069304 ACACACAATATTTGCTACCACGT 58.931 39.130 0.00 0.00 0.00 4.49
143 144 4.678509 ACACACAATATTTGCTACCACG 57.321 40.909 0.00 0.00 0.00 4.94
144 145 6.072397 TGGTAACACACAATATTTGCTACCAC 60.072 38.462 13.38 0.00 46.17 4.16
145 146 6.004574 TGGTAACACACAATATTTGCTACCA 58.995 36.000 13.38 13.38 46.17 3.25
146 147 6.503589 TGGTAACACACAATATTTGCTACC 57.496 37.500 9.75 9.75 46.17 3.18
178 179 9.936759 TGTCTACAATGAGATGTATAAAACACA 57.063 29.630 0.00 0.00 42.09 3.72
197 198 4.888917 TGGTCGATTGATTGTTGTCTACA 58.111 39.130 0.00 0.00 34.12 2.74
198 199 5.351465 ACATGGTCGATTGATTGTTGTCTAC 59.649 40.000 0.00 0.00 0.00 2.59
199 200 5.487433 ACATGGTCGATTGATTGTTGTCTA 58.513 37.500 0.00 0.00 0.00 2.59
200 201 4.326826 ACATGGTCGATTGATTGTTGTCT 58.673 39.130 0.00 0.00 0.00 3.41
201 202 4.685169 ACATGGTCGATTGATTGTTGTC 57.315 40.909 0.00 0.00 0.00 3.18
202 203 5.452078 AAACATGGTCGATTGATTGTTGT 57.548 34.783 0.00 0.00 30.15 3.32
203 204 4.858692 GGAAACATGGTCGATTGATTGTTG 59.141 41.667 0.00 0.00 30.15 3.33
204 205 4.766891 AGGAAACATGGTCGATTGATTGTT 59.233 37.500 0.00 4.07 0.00 2.83
205 206 4.335416 AGGAAACATGGTCGATTGATTGT 58.665 39.130 0.00 0.00 0.00 2.71
206 207 4.970662 AGGAAACATGGTCGATTGATTG 57.029 40.909 0.00 0.00 0.00 2.67
207 208 8.746052 TTAATAGGAAACATGGTCGATTGATT 57.254 30.769 0.00 0.00 0.00 2.57
208 209 8.746052 TTTAATAGGAAACATGGTCGATTGAT 57.254 30.769 0.00 0.00 0.00 2.57
209 210 8.208718 CTTTAATAGGAAACATGGTCGATTGA 57.791 34.615 0.00 0.00 0.00 2.57
255 256 4.517952 AATCCATGTGTGCGATGAAAAA 57.482 36.364 0.00 0.00 0.00 1.94
256 257 4.517952 AAATCCATGTGTGCGATGAAAA 57.482 36.364 0.00 0.00 0.00 2.29
257 258 4.438608 GCTAAATCCATGTGTGCGATGAAA 60.439 41.667 0.00 0.00 0.00 2.69
258 259 3.065233 GCTAAATCCATGTGTGCGATGAA 59.935 43.478 0.00 0.00 0.00 2.57
259 260 2.613595 GCTAAATCCATGTGTGCGATGA 59.386 45.455 0.00 0.00 0.00 2.92
260 261 2.600556 CGCTAAATCCATGTGTGCGATG 60.601 50.000 0.00 0.00 43.81 3.84
261 262 1.599071 CGCTAAATCCATGTGTGCGAT 59.401 47.619 0.00 0.00 43.81 4.58
262 263 1.006086 CGCTAAATCCATGTGTGCGA 58.994 50.000 0.00 0.00 43.81 5.10
263 264 0.726827 ACGCTAAATCCATGTGTGCG 59.273 50.000 0.00 0.00 46.02 5.34
264 265 2.178474 CACGCTAAATCCATGTGTGC 57.822 50.000 0.00 0.00 35.83 4.57
265 266 1.202177 GGCACGCTAAATCCATGTGTG 60.202 52.381 0.00 0.00 42.83 3.82
266 267 1.094785 GGCACGCTAAATCCATGTGT 58.905 50.000 0.00 0.00 33.23 3.72
267 268 1.331756 GAGGCACGCTAAATCCATGTG 59.668 52.381 0.00 0.00 0.00 3.21
268 269 1.210478 AGAGGCACGCTAAATCCATGT 59.790 47.619 0.00 0.00 36.12 3.21
269 270 1.600957 CAGAGGCACGCTAAATCCATG 59.399 52.381 0.00 0.00 35.27 3.66
270 271 1.210478 ACAGAGGCACGCTAAATCCAT 59.790 47.619 0.00 0.00 35.27 3.41
271 272 0.613260 ACAGAGGCACGCTAAATCCA 59.387 50.000 0.00 0.00 35.27 3.41
272 273 1.009829 CACAGAGGCACGCTAAATCC 58.990 55.000 0.00 0.00 35.27 3.01
273 274 0.375106 GCACAGAGGCACGCTAAATC 59.625 55.000 0.00 0.00 35.27 2.17
274 275 1.026718 GGCACAGAGGCACGCTAAAT 61.027 55.000 0.00 0.00 35.27 1.40
275 276 1.671054 GGCACAGAGGCACGCTAAA 60.671 57.895 0.00 0.00 35.27 1.85
276 277 2.047274 GGCACAGAGGCACGCTAA 60.047 61.111 0.00 0.00 35.27 3.09
292 293 2.126502 GACCGTTGCGCCAAATGG 60.127 61.111 15.25 15.25 41.30 3.16
293 294 2.126502 GGACCGTTGCGCCAAATG 60.127 61.111 4.18 0.00 0.00 2.32
294 295 2.596046 TGGACCGTTGCGCCAAAT 60.596 55.556 4.18 0.00 0.00 2.32
295 296 2.661840 TAGTGGACCGTTGCGCCAAA 62.662 55.000 4.18 0.00 32.68 3.28
296 297 3.166490 TAGTGGACCGTTGCGCCAA 62.166 57.895 4.18 0.00 32.68 4.52
297 298 3.583276 CTAGTGGACCGTTGCGCCA 62.583 63.158 4.18 0.00 0.00 5.69
298 299 2.216750 TACTAGTGGACCGTTGCGCC 62.217 60.000 4.18 0.00 0.00 6.53
299 300 0.179119 ATACTAGTGGACCGTTGCGC 60.179 55.000 5.39 0.00 0.00 6.09
300 301 1.924524 CAATACTAGTGGACCGTTGCG 59.075 52.381 5.39 0.00 0.00 4.85
301 302 2.968675 ACAATACTAGTGGACCGTTGC 58.031 47.619 5.39 0.00 0.00 4.17
302 303 7.384115 CCATTATACAATACTAGTGGACCGTTG 59.616 40.741 5.39 3.94 28.82 4.10
303 304 7.439381 CCATTATACAATACTAGTGGACCGTT 58.561 38.462 5.39 0.00 28.82 4.44
304 305 6.014840 CCCATTATACAATACTAGTGGACCGT 60.015 42.308 5.39 0.00 28.82 4.83
305 306 6.395629 CCCATTATACAATACTAGTGGACCG 58.604 44.000 5.39 0.00 28.82 4.79
306 307 6.171213 GCCCATTATACAATACTAGTGGACC 58.829 44.000 5.39 0.00 28.82 4.46
307 308 6.765403 TGCCCATTATACAATACTAGTGGAC 58.235 40.000 5.39 0.00 28.82 4.02
308 309 7.381789 TTGCCCATTATACAATACTAGTGGA 57.618 36.000 5.39 0.00 28.82 4.02
309 310 6.655003 CCTTGCCCATTATACAATACTAGTGG 59.345 42.308 5.39 0.00 0.00 4.00
310 311 7.224297 ACCTTGCCCATTATACAATACTAGTG 58.776 38.462 5.39 0.00 0.00 2.74
311 312 7.388638 ACCTTGCCCATTATACAATACTAGT 57.611 36.000 0.00 0.00 0.00 2.57
312 313 7.549488 GCTACCTTGCCCATTATACAATACTAG 59.451 40.741 0.00 0.00 0.00 2.57
313 314 7.016760 TGCTACCTTGCCCATTATACAATACTA 59.983 37.037 0.00 0.00 0.00 1.82
314 315 6.183361 TGCTACCTTGCCCATTATACAATACT 60.183 38.462 0.00 0.00 0.00 2.12
315 316 6.001460 TGCTACCTTGCCCATTATACAATAC 58.999 40.000 0.00 0.00 0.00 1.89
316 317 6.194285 TGCTACCTTGCCCATTATACAATA 57.806 37.500 0.00 0.00 0.00 1.90
317 318 5.060427 TGCTACCTTGCCCATTATACAAT 57.940 39.130 0.00 0.00 0.00 2.71
318 319 4.511786 TGCTACCTTGCCCATTATACAA 57.488 40.909 0.00 0.00 0.00 2.41
319 320 4.511786 TTGCTACCTTGCCCATTATACA 57.488 40.909 0.00 0.00 0.00 2.29
320 321 5.048013 GGATTTGCTACCTTGCCCATTATAC 60.048 44.000 0.00 0.00 0.00 1.47
321 322 5.076873 GGATTTGCTACCTTGCCCATTATA 58.923 41.667 0.00 0.00 0.00 0.98
333 334 2.957006 TCTACTCCTCGGATTTGCTACC 59.043 50.000 0.00 0.00 0.00 3.18
347 348 6.593268 AAACTTGGTCTAGACTTCTACTCC 57.407 41.667 21.88 3.90 0.00 3.85
448 455 9.424319 CACGCCATCTTTCATTTACTAGTATAT 57.576 33.333 2.79 1.46 0.00 0.86
450 457 7.224753 CACACGCCATCTTTCATTTACTAGTAT 59.775 37.037 2.79 0.00 0.00 2.12
451 458 6.533723 CACACGCCATCTTTCATTTACTAGTA 59.466 38.462 0.00 0.00 0.00 1.82
452 459 5.351465 CACACGCCATCTTTCATTTACTAGT 59.649 40.000 0.00 0.00 0.00 2.57
453 460 5.220662 CCACACGCCATCTTTCATTTACTAG 60.221 44.000 0.00 0.00 0.00 2.57
499 512 3.394719 GGAATCATCTCGGCTTACTTCC 58.605 50.000 0.00 0.00 0.00 3.46
518 531 2.037049 ATGGGCCATTGCAACGGA 59.963 55.556 17.32 0.00 40.13 4.69
526 539 1.481871 CTCAAAGCTGATGGGCCATT 58.518 50.000 22.20 1.14 0.00 3.16
547 560 0.684805 AAAGGACGCGGGAGATCTCT 60.685 55.000 21.81 1.63 0.00 3.10
738 751 3.644606 CAGCACCACCTCCCTGCT 61.645 66.667 0.00 0.00 42.08 4.24
853 866 6.864685 CACCGGCGAAGAATAATAATACAGTA 59.135 38.462 9.30 0.00 0.00 2.74
876 889 0.735978 GGCAATTAAAGGCCGTGCAC 60.736 55.000 6.82 6.82 40.93 4.57
932 945 4.469657 AGATAGCTAGCTAGAGCACAAGT 58.530 43.478 27.42 9.31 45.43 3.16
933 946 5.452078 AAGATAGCTAGCTAGAGCACAAG 57.548 43.478 27.42 0.00 45.43 3.16
935 948 5.471797 CAGTAAGATAGCTAGCTAGAGCACA 59.528 44.000 27.42 7.09 45.43 4.57
936 949 5.472137 ACAGTAAGATAGCTAGCTAGAGCAC 59.528 44.000 27.42 20.88 45.43 4.40
937 950 5.471797 CACAGTAAGATAGCTAGCTAGAGCA 59.528 44.000 27.42 8.61 45.43 4.26
938 951 5.619086 GCACAGTAAGATAGCTAGCTAGAGC 60.619 48.000 27.42 17.86 43.19 4.09
939 952 5.471797 TGCACAGTAAGATAGCTAGCTAGAG 59.528 44.000 27.42 12.80 31.45 2.43
940 953 5.239744 GTGCACAGTAAGATAGCTAGCTAGA 59.760 44.000 27.42 10.17 31.45 2.43
952 967 2.872245 GCAAGAACAGTGCACAGTAAGA 59.128 45.455 21.04 0.00 41.80 2.10
1059 1074 1.148273 GGGATCATAGGCAACCGCA 59.852 57.895 0.00 0.00 41.24 5.69
2013 2212 2.022718 ACTGGAAGCTGAAGACCTCT 57.977 50.000 0.00 0.00 37.60 3.69
2139 2338 2.107750 CGCATGAGCACCTCCGAT 59.892 61.111 0.00 0.00 42.27 4.18
2169 2368 0.322008 CCTGGCTGAAGGTGAAGGTC 60.322 60.000 0.00 0.00 32.17 3.85
2202 2401 2.607187 CCGTTGAAGTAGATCTTGCGT 58.393 47.619 0.00 0.00 36.40 5.24
2342 3538 2.575279 GGATAGATGGATCATGCCACCT 59.425 50.000 0.00 0.00 41.56 4.00
2343 3539 2.306805 TGGATAGATGGATCATGCCACC 59.693 50.000 0.00 0.00 41.56 4.61
2493 3690 1.714899 AATATGTTGCCGGAGCGCAC 61.715 55.000 11.47 1.97 44.31 5.34
2642 4242 9.525826 AAGAGATGAACTACATGAAAAAGGATT 57.474 29.630 0.00 0.00 39.56 3.01
2652 4252 9.591792 TTACTCAATGAAGAGATGAACTACATG 57.408 33.333 0.00 0.00 39.56 3.21
2750 4350 1.373497 CGTGCGGGGATCATCTAGC 60.373 63.158 0.00 0.00 0.00 3.42
2777 4379 1.093972 TGGTTGGCATGCTAACATCG 58.906 50.000 37.38 0.00 38.84 3.84
2780 4382 1.885887 GAGTTGGTTGGCATGCTAACA 59.114 47.619 37.38 24.90 38.84 2.41
2808 4442 4.024048 ACATCTTTTTCCTTAGTGTGCGTG 60.024 41.667 0.00 0.00 0.00 5.34
2810 4444 4.749245 ACATCTTTTTCCTTAGTGTGCG 57.251 40.909 0.00 0.00 0.00 5.34
2816 4450 8.616076 CCACATAGCTAACATCTTTTTCCTTAG 58.384 37.037 0.00 0.00 0.00 2.18
2827 4462 4.693283 TGTAGCACCACATAGCTAACATC 58.307 43.478 0.00 0.00 44.18 3.06
2862 4497 5.105997 CCTTCAGGTTTGATCTTTCATGGAC 60.106 44.000 0.00 0.00 32.27 4.02
2873 4508 5.079643 AGTACAATTGCCTTCAGGTTTGAT 58.920 37.500 5.05 0.00 37.57 2.57
2874 4509 4.469657 AGTACAATTGCCTTCAGGTTTGA 58.530 39.130 5.05 0.00 37.57 2.69
2875 4510 4.853924 AGTACAATTGCCTTCAGGTTTG 57.146 40.909 5.05 0.13 37.57 2.93
2876 4511 6.969993 TTTAGTACAATTGCCTTCAGGTTT 57.030 33.333 5.05 0.00 37.57 3.27
3102 5623 5.247507 AGATTTCAGTCAGAGATCGAGTG 57.752 43.478 0.00 0.00 41.47 3.51
3286 6071 9.575868 TCCTGTTGGATGTTAATGTAGTTTAAA 57.424 29.630 0.00 0.00 37.46 1.52
3316 6101 6.541641 GTCCTTTGATGATTCTTCTGCACTAT 59.458 38.462 1.76 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.