Multiple sequence alignment - TraesCS7A01G290900

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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 TraesCS7A01G290900 chr7A 100.000 3929 0 0 1 3929 352859323 352863251 0.000000e+00 7256
1 TraesCS7A01G290900 chr7A 93.458 321 20 1 1 320 352817213 352817533 3.550000e-130 475
2 TraesCS7A01G290900 chr7A 88.545 323 35 2 1 322 378224711 378225032 1.320000e-104 390
3 TraesCS7A01G290900 chr7D 98.526 3120 33 5 820 3929 342633091 342629975 0.000000e+00 5494
4 TraesCS7A01G290900 chr7D 91.700 506 29 9 323 828 342634021 342633529 0.000000e+00 689
5 TraesCS7A01G290900 chr7D 88.379 327 29 8 1 322 332942063 332942385 6.160000e-103 385
6 TraesCS7A01G290900 chr7D 87.805 328 30 8 1 322 332934552 332934875 3.710000e-100 375
7 TraesCS7A01G290900 chr7B 97.171 3075 49 17 334 3401 281387713 281384670 0.000000e+00 5162
8 TraesCS7A01G290900 chr7B 95.752 306 11 1 3624 3929 281384034 281383731 3.530000e-135 492
9 TraesCS7A01G290900 chr7B 99.099 111 1 0 3403 3513 281384505 281384395 2.390000e-47 200
10 TraesCS7A01G290900 chr7B 96.610 118 4 0 3511 3628 281384272 281384155 3.100000e-46 196
11 TraesCS7A01G290900 chr5A 78.808 1930 354 39 1011 2929 428408418 428410303 0.000000e+00 1247
12 TraesCS7A01G290900 chr5A 87.730 326 32 8 1 323 398859547 398859867 1.330000e-99 374
13 TraesCS7A01G290900 chr5D 79.988 1679 306 25 1263 2929 327992030 327990370 0.000000e+00 1212
14 TraesCS7A01G290900 chr5B 79.893 1676 310 18 1263 2929 381357892 381356235 0.000000e+00 1203
15 TraesCS7A01G290900 chr3D 89.329 328 24 10 1 322 398117624 398117946 6.120000e-108 401
16 TraesCS7A01G290900 chr3D 88.957 326 28 7 1 322 253036307 253035986 2.850000e-106 396
17 TraesCS7A01G290900 chr6D 88.073 327 29 8 1 322 444278586 444278265 2.870000e-101 379
18 TraesCS7A01G290900 chr4A 87.613 331 33 7 1 325 338934458 338934130 1.030000e-100 377


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 TraesCS7A01G290900 chr7A 352859323 352863251 3928 False 7256.0 7256 100.000 1 3929 1 chr7A.!!$F2 3928
1 TraesCS7A01G290900 chr7D 342629975 342634021 4046 True 3091.5 5494 95.113 323 3929 2 chr7D.!!$R1 3606
2 TraesCS7A01G290900 chr7B 281383731 281387713 3982 True 1512.5 5162 97.158 334 3929 4 chr7B.!!$R1 3595
3 TraesCS7A01G290900 chr5A 428408418 428410303 1885 False 1247.0 1247 78.808 1011 2929 1 chr5A.!!$F2 1918
4 TraesCS7A01G290900 chr5D 327990370 327992030 1660 True 1212.0 1212 79.988 1263 2929 1 chr5D.!!$R1 1666
5 TraesCS7A01G290900 chr5B 381356235 381357892 1657 True 1203.0 1203 79.893 1263 2929 1 chr5B.!!$R1 1666

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
288 289 0.035439 GGGATCCGCTCCTTTTGTGA 60.035 55.0 5.45 0.0 44.28 3.58 F
310 311 0.321996 GATCGGCCATCTAGGGTTCC 59.678 60.0 2.24 0.0 38.09 3.62 F
311 312 0.399949 ATCGGCCATCTAGGGTTCCA 60.400 55.0 2.24 0.0 38.09 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2282 2742 0.246635 TAGTTCGAGGCAGGACAAGC 59.753 55.000 0.0 0.0 0.00 4.01 R
2448 2908 2.443255 AGGTGAATCCTTGACCTTGTGT 59.557 45.455 0.0 0.0 45.67 3.72 R
3180 3642 6.238731 GCTATATCAACATGCTACTTGCCAAA 60.239 38.462 0.0 0.0 42.00 3.28 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
27 28 2.750637 TCGAGAGAGACCACGGCC 60.751 66.667 0.00 0.00 34.84 6.13
28 29 3.827898 CGAGAGAGACCACGGCCC 61.828 72.222 0.00 0.00 0.00 5.80
29 30 3.462678 GAGAGAGACCACGGCCCC 61.463 72.222 0.00 0.00 0.00 5.80
30 31 3.966930 GAGAGAGACCACGGCCCCT 62.967 68.421 0.00 0.00 0.00 4.79
31 32 3.462678 GAGAGACCACGGCCCCTC 61.463 72.222 0.00 0.00 0.00 4.30
32 33 3.966930 GAGAGACCACGGCCCCTCT 62.967 68.421 0.00 1.34 38.57 3.69
33 34 3.003763 GAGACCACGGCCCCTCTT 61.004 66.667 0.00 0.00 0.00 2.85
34 35 2.529389 AGACCACGGCCCCTCTTT 60.529 61.111 0.00 0.00 0.00 2.52
35 36 2.359975 GACCACGGCCCCTCTTTG 60.360 66.667 0.00 0.00 0.00 2.77
36 37 3.920093 GACCACGGCCCCTCTTTGG 62.920 68.421 0.00 0.00 0.00 3.28
37 38 3.646715 CCACGGCCCCTCTTTGGA 61.647 66.667 0.00 0.00 38.35 3.53
38 39 2.045926 CACGGCCCCTCTTTGGAG 60.046 66.667 0.00 0.00 38.35 3.86
39 40 2.203938 ACGGCCCCTCTTTGGAGA 60.204 61.111 0.00 0.00 41.86 3.71
40 41 1.846124 ACGGCCCCTCTTTGGAGAA 60.846 57.895 0.00 0.00 41.86 2.87
41 42 1.078143 CGGCCCCTCTTTGGAGAAG 60.078 63.158 0.00 0.00 41.86 2.85
42 43 1.553690 CGGCCCCTCTTTGGAGAAGA 61.554 60.000 0.00 0.00 41.86 2.87
43 44 0.922626 GGCCCCTCTTTGGAGAAGAT 59.077 55.000 0.00 0.00 41.86 2.40
44 45 1.133945 GGCCCCTCTTTGGAGAAGATC 60.134 57.143 0.00 0.00 41.86 2.75
63 64 3.062122 TCCACGTTGGATTTAAGACCC 57.938 47.619 3.02 0.00 42.67 4.46
64 65 2.089201 CCACGTTGGATTTAAGACCCC 58.911 52.381 0.00 0.00 40.96 4.95
65 66 2.089201 CACGTTGGATTTAAGACCCCC 58.911 52.381 0.00 0.00 0.00 5.40
66 67 1.990327 ACGTTGGATTTAAGACCCCCT 59.010 47.619 0.00 0.00 0.00 4.79
67 68 2.026542 ACGTTGGATTTAAGACCCCCTC 60.027 50.000 0.00 0.00 0.00 4.30
68 69 2.238898 CGTTGGATTTAAGACCCCCTCT 59.761 50.000 0.00 0.00 0.00 3.69
69 70 3.681874 CGTTGGATTTAAGACCCCCTCTC 60.682 52.174 0.00 0.00 0.00 3.20
70 71 2.116238 TGGATTTAAGACCCCCTCTCG 58.884 52.381 0.00 0.00 0.00 4.04
71 72 1.416772 GGATTTAAGACCCCCTCTCGG 59.583 57.143 0.00 0.00 0.00 4.63
88 89 2.043953 GGTGGCCCCATCAAGACC 60.044 66.667 0.00 0.00 0.00 3.85
89 90 2.616458 GGTGGCCCCATCAAGACCT 61.616 63.158 0.00 0.00 0.00 3.85
90 91 1.077429 GTGGCCCCATCAAGACCTC 60.077 63.158 0.00 0.00 0.00 3.85
91 92 2.308722 TGGCCCCATCAAGACCTCC 61.309 63.158 0.00 0.00 0.00 4.30
92 93 2.003548 GGCCCCATCAAGACCTCCT 61.004 63.158 0.00 0.00 0.00 3.69
93 94 1.529309 GCCCCATCAAGACCTCCTC 59.471 63.158 0.00 0.00 0.00 3.71
94 95 1.274703 GCCCCATCAAGACCTCCTCA 61.275 60.000 0.00 0.00 0.00 3.86
95 96 1.516110 CCCCATCAAGACCTCCTCAT 58.484 55.000 0.00 0.00 0.00 2.90
96 97 1.142465 CCCCATCAAGACCTCCTCATG 59.858 57.143 0.00 0.00 0.00 3.07
97 98 1.142465 CCCATCAAGACCTCCTCATGG 59.858 57.143 0.00 0.00 0.00 3.66
98 99 2.121948 CCATCAAGACCTCCTCATGGA 58.878 52.381 0.00 0.00 40.69 3.41
109 110 2.907892 TCCTCATGGAGAAGAACCAGT 58.092 47.619 0.00 0.00 40.89 4.00
110 111 3.251484 TCCTCATGGAGAAGAACCAGTT 58.749 45.455 0.00 0.00 40.89 3.16
111 112 4.425772 TCCTCATGGAGAAGAACCAGTTA 58.574 43.478 0.00 0.00 40.89 2.24
112 113 4.223032 TCCTCATGGAGAAGAACCAGTTAC 59.777 45.833 0.00 0.00 40.89 2.50
113 114 4.508662 CTCATGGAGAAGAACCAGTTACC 58.491 47.826 0.00 0.00 40.89 2.85
114 115 3.263425 TCATGGAGAAGAACCAGTTACCC 59.737 47.826 0.00 0.00 40.89 3.69
115 116 2.986050 TGGAGAAGAACCAGTTACCCT 58.014 47.619 0.00 0.00 33.22 4.34
116 117 4.136341 TGGAGAAGAACCAGTTACCCTA 57.864 45.455 0.00 0.00 33.22 3.53
117 118 4.695606 TGGAGAAGAACCAGTTACCCTAT 58.304 43.478 0.00 0.00 33.22 2.57
118 119 5.098663 TGGAGAAGAACCAGTTACCCTATT 58.901 41.667 0.00 0.00 33.22 1.73
119 120 5.550403 TGGAGAAGAACCAGTTACCCTATTT 59.450 40.000 0.00 0.00 33.22 1.40
120 121 6.731919 TGGAGAAGAACCAGTTACCCTATTTA 59.268 38.462 0.00 0.00 33.22 1.40
121 122 7.404980 TGGAGAAGAACCAGTTACCCTATTTAT 59.595 37.037 0.00 0.00 33.22 1.40
122 123 7.932491 GGAGAAGAACCAGTTACCCTATTTATC 59.068 40.741 0.00 0.00 0.00 1.75
123 124 8.388656 AGAAGAACCAGTTACCCTATTTATCA 57.611 34.615 0.00 0.00 0.00 2.15
124 125 9.004231 AGAAGAACCAGTTACCCTATTTATCAT 57.996 33.333 0.00 0.00 0.00 2.45
125 126 9.274206 GAAGAACCAGTTACCCTATTTATCATC 57.726 37.037 0.00 0.00 0.00 2.92
126 127 7.746703 AGAACCAGTTACCCTATTTATCATCC 58.253 38.462 0.00 0.00 0.00 3.51
127 128 6.449830 ACCAGTTACCCTATTTATCATCCC 57.550 41.667 0.00 0.00 0.00 3.85
128 129 6.158260 ACCAGTTACCCTATTTATCATCCCT 58.842 40.000 0.00 0.00 0.00 4.20
129 130 6.624021 ACCAGTTACCCTATTTATCATCCCTT 59.376 38.462 0.00 0.00 0.00 3.95
130 131 6.942576 CCAGTTACCCTATTTATCATCCCTTG 59.057 42.308 0.00 0.00 0.00 3.61
131 132 7.421382 CCAGTTACCCTATTTATCATCCCTTGT 60.421 40.741 0.00 0.00 0.00 3.16
132 133 7.998964 CAGTTACCCTATTTATCATCCCTTGTT 59.001 37.037 0.00 0.00 0.00 2.83
133 134 7.998964 AGTTACCCTATTTATCATCCCTTGTTG 59.001 37.037 0.00 0.00 0.00 3.33
134 135 6.590656 ACCCTATTTATCATCCCTTGTTGA 57.409 37.500 0.00 0.00 0.00 3.18
135 136 6.365520 ACCCTATTTATCATCCCTTGTTGAC 58.634 40.000 0.00 0.00 0.00 3.18
136 137 6.160459 ACCCTATTTATCATCCCTTGTTGACT 59.840 38.462 0.00 0.00 0.00 3.41
137 138 7.062957 CCCTATTTATCATCCCTTGTTGACTT 58.937 38.462 0.00 0.00 0.00 3.01
138 139 7.561356 CCCTATTTATCATCCCTTGTTGACTTT 59.439 37.037 0.00 0.00 0.00 2.66
139 140 8.408601 CCTATTTATCATCCCTTGTTGACTTTG 58.591 37.037 0.00 0.00 0.00 2.77
140 141 6.588719 TTTATCATCCCTTGTTGACTTTGG 57.411 37.500 0.00 0.00 0.00 3.28
141 142 3.874383 TCATCCCTTGTTGACTTTGGA 57.126 42.857 0.00 0.00 0.00 3.53
142 143 4.387026 TCATCCCTTGTTGACTTTGGAT 57.613 40.909 0.00 0.00 32.95 3.41
143 144 4.335416 TCATCCCTTGTTGACTTTGGATC 58.665 43.478 0.00 0.00 30.36 3.36
144 145 2.778299 TCCCTTGTTGACTTTGGATCG 58.222 47.619 0.00 0.00 0.00 3.69
145 146 2.105821 TCCCTTGTTGACTTTGGATCGT 59.894 45.455 0.00 0.00 0.00 3.73
146 147 2.226437 CCCTTGTTGACTTTGGATCGTG 59.774 50.000 0.00 0.00 0.00 4.35
147 148 2.878406 CCTTGTTGACTTTGGATCGTGT 59.122 45.455 0.00 0.00 0.00 4.49
148 149 3.303990 CCTTGTTGACTTTGGATCGTGTG 60.304 47.826 0.00 0.00 0.00 3.82
149 150 3.186702 TGTTGACTTTGGATCGTGTGA 57.813 42.857 0.00 0.00 0.00 3.58
150 151 3.738982 TGTTGACTTTGGATCGTGTGAT 58.261 40.909 0.00 0.00 37.60 3.06
163 164 6.307031 GATCGTGTGATCTCTATGTGTAGT 57.693 41.667 0.00 0.00 46.22 2.73
164 165 5.736486 TCGTGTGATCTCTATGTGTAGTC 57.264 43.478 0.00 0.00 0.00 2.59
165 166 4.270325 TCGTGTGATCTCTATGTGTAGTCG 59.730 45.833 0.00 0.00 0.00 4.18
166 167 4.552961 CGTGTGATCTCTATGTGTAGTCGG 60.553 50.000 0.00 0.00 0.00 4.79
167 168 4.575236 GTGTGATCTCTATGTGTAGTCGGA 59.425 45.833 0.00 0.00 0.00 4.55
168 169 5.239744 GTGTGATCTCTATGTGTAGTCGGAT 59.760 44.000 0.00 0.00 0.00 4.18
169 170 5.470437 TGTGATCTCTATGTGTAGTCGGATC 59.530 44.000 0.00 0.00 34.40 3.36
170 171 5.703592 GTGATCTCTATGTGTAGTCGGATCT 59.296 44.000 0.00 0.00 34.61 2.75
171 172 6.874664 GTGATCTCTATGTGTAGTCGGATCTA 59.125 42.308 0.00 0.00 34.61 1.98
172 173 7.064134 GTGATCTCTATGTGTAGTCGGATCTAG 59.936 44.444 0.00 0.00 34.61 2.43
173 174 5.239351 TCTCTATGTGTAGTCGGATCTAGC 58.761 45.833 0.00 0.00 0.00 3.42
174 175 4.969484 TCTATGTGTAGTCGGATCTAGCA 58.031 43.478 0.00 0.00 0.00 3.49
175 176 5.561679 TCTATGTGTAGTCGGATCTAGCAT 58.438 41.667 0.00 0.00 0.00 3.79
176 177 6.708285 TCTATGTGTAGTCGGATCTAGCATA 58.292 40.000 0.00 0.00 0.00 3.14
177 178 7.339482 TCTATGTGTAGTCGGATCTAGCATAT 58.661 38.462 0.00 0.00 0.00 1.78
178 179 5.629079 TGTGTAGTCGGATCTAGCATATG 57.371 43.478 0.00 0.00 0.00 1.78
179 180 5.070685 TGTGTAGTCGGATCTAGCATATGT 58.929 41.667 4.29 0.00 0.00 2.29
180 181 5.048713 TGTGTAGTCGGATCTAGCATATGTG 60.049 44.000 4.29 0.00 0.00 3.21
181 182 5.048643 GTGTAGTCGGATCTAGCATATGTGT 60.049 44.000 4.29 0.00 0.00 3.72
182 183 4.511617 AGTCGGATCTAGCATATGTGTG 57.488 45.455 4.29 0.00 0.00 3.82
183 184 4.145052 AGTCGGATCTAGCATATGTGTGA 58.855 43.478 4.29 0.73 0.00 3.58
184 185 4.769488 AGTCGGATCTAGCATATGTGTGAT 59.231 41.667 4.29 5.52 0.00 3.06
185 186 5.098893 GTCGGATCTAGCATATGTGTGATC 58.901 45.833 17.61 17.61 32.89 2.92
186 187 4.101235 CGGATCTAGCATATGTGTGATCG 58.899 47.826 18.44 13.54 33.64 3.69
187 188 4.379918 CGGATCTAGCATATGTGTGATCGT 60.380 45.833 18.44 0.00 33.64 3.73
188 189 5.473931 GGATCTAGCATATGTGTGATCGTT 58.526 41.667 18.44 0.00 33.64 3.85
189 190 5.574830 GGATCTAGCATATGTGTGATCGTTC 59.425 44.000 18.44 8.78 33.64 3.95
190 191 5.774498 TCTAGCATATGTGTGATCGTTCT 57.226 39.130 4.29 0.00 0.00 3.01
191 192 6.149129 TCTAGCATATGTGTGATCGTTCTT 57.851 37.500 4.29 0.00 0.00 2.52
192 193 5.979517 TCTAGCATATGTGTGATCGTTCTTG 59.020 40.000 4.29 0.00 0.00 3.02
193 194 4.507710 AGCATATGTGTGATCGTTCTTGT 58.492 39.130 4.29 0.00 0.00 3.16
194 195 4.937620 AGCATATGTGTGATCGTTCTTGTT 59.062 37.500 4.29 0.00 0.00 2.83
195 196 5.023920 GCATATGTGTGATCGTTCTTGTTG 58.976 41.667 4.29 0.00 0.00 3.33
196 197 5.562917 CATATGTGTGATCGTTCTTGTTGG 58.437 41.667 0.00 0.00 0.00 3.77
197 198 2.912771 TGTGTGATCGTTCTTGTTGGT 58.087 42.857 0.00 0.00 0.00 3.67
198 199 3.275143 TGTGTGATCGTTCTTGTTGGTT 58.725 40.909 0.00 0.00 0.00 3.67
199 200 3.692101 TGTGTGATCGTTCTTGTTGGTTT 59.308 39.130 0.00 0.00 0.00 3.27
200 201 4.035017 GTGTGATCGTTCTTGTTGGTTTG 58.965 43.478 0.00 0.00 0.00 2.93
201 202 3.942115 TGTGATCGTTCTTGTTGGTTTGA 59.058 39.130 0.00 0.00 0.00 2.69
202 203 4.035091 TGTGATCGTTCTTGTTGGTTTGAG 59.965 41.667 0.00 0.00 0.00 3.02
203 204 4.035208 GTGATCGTTCTTGTTGGTTTGAGT 59.965 41.667 0.00 0.00 0.00 3.41
204 205 4.035091 TGATCGTTCTTGTTGGTTTGAGTG 59.965 41.667 0.00 0.00 0.00 3.51
205 206 3.601435 TCGTTCTTGTTGGTTTGAGTGA 58.399 40.909 0.00 0.00 0.00 3.41
206 207 4.196193 TCGTTCTTGTTGGTTTGAGTGAT 58.804 39.130 0.00 0.00 0.00 3.06
207 208 4.638421 TCGTTCTTGTTGGTTTGAGTGATT 59.362 37.500 0.00 0.00 0.00 2.57
208 209 4.970003 CGTTCTTGTTGGTTTGAGTGATTC 59.030 41.667 0.00 0.00 0.00 2.52
209 210 5.220854 CGTTCTTGTTGGTTTGAGTGATTCT 60.221 40.000 0.00 0.00 0.00 2.40
210 211 6.202226 GTTCTTGTTGGTTTGAGTGATTCTC 58.798 40.000 0.00 0.00 43.03 2.87
211 212 5.684704 TCTTGTTGGTTTGAGTGATTCTCT 58.315 37.500 0.00 0.00 43.13 3.10
212 213 5.760253 TCTTGTTGGTTTGAGTGATTCTCTC 59.240 40.000 8.48 8.48 43.13 3.20
213 214 4.058124 TGTTGGTTTGAGTGATTCTCTCG 58.942 43.478 10.30 0.00 43.13 4.04
214 215 4.058817 GTTGGTTTGAGTGATTCTCTCGT 58.941 43.478 10.30 0.00 43.13 4.18
215 216 3.653344 TGGTTTGAGTGATTCTCTCGTG 58.347 45.455 10.30 0.00 43.13 4.35
216 217 3.069586 TGGTTTGAGTGATTCTCTCGTGT 59.930 43.478 10.30 0.00 43.13 4.49
217 218 4.058817 GGTTTGAGTGATTCTCTCGTGTT 58.941 43.478 10.30 0.00 43.13 3.32
218 219 4.511826 GGTTTGAGTGATTCTCTCGTGTTT 59.488 41.667 10.30 0.00 43.13 2.83
219 220 5.333416 GGTTTGAGTGATTCTCTCGTGTTTC 60.333 44.000 10.30 0.47 43.13 2.78
220 221 3.914312 TGAGTGATTCTCTCGTGTTTCC 58.086 45.455 10.30 0.00 43.13 3.13
221 222 3.574396 TGAGTGATTCTCTCGTGTTTCCT 59.426 43.478 10.30 0.00 43.13 3.36
222 223 4.170256 GAGTGATTCTCTCGTGTTTCCTC 58.830 47.826 0.32 0.00 39.86 3.71
223 224 3.829601 AGTGATTCTCTCGTGTTTCCTCT 59.170 43.478 0.00 0.00 0.00 3.69
224 225 4.282195 AGTGATTCTCTCGTGTTTCCTCTT 59.718 41.667 0.00 0.00 0.00 2.85
225 226 4.387256 GTGATTCTCTCGTGTTTCCTCTTG 59.613 45.833 0.00 0.00 0.00 3.02
226 227 4.039245 TGATTCTCTCGTGTTTCCTCTTGT 59.961 41.667 0.00 0.00 0.00 3.16
227 228 3.371102 TCTCTCGTGTTTCCTCTTGTG 57.629 47.619 0.00 0.00 0.00 3.33
228 229 2.693591 TCTCTCGTGTTTCCTCTTGTGT 59.306 45.455 0.00 0.00 0.00 3.72
229 230 3.132289 TCTCTCGTGTTTCCTCTTGTGTT 59.868 43.478 0.00 0.00 0.00 3.32
230 231 3.869065 TCTCGTGTTTCCTCTTGTGTTT 58.131 40.909 0.00 0.00 0.00 2.83
231 232 3.869246 TCTCGTGTTTCCTCTTGTGTTTC 59.131 43.478 0.00 0.00 0.00 2.78
232 233 2.940410 TCGTGTTTCCTCTTGTGTTTCC 59.060 45.455 0.00 0.00 0.00 3.13
233 234 2.032924 CGTGTTTCCTCTTGTGTTTCCC 59.967 50.000 0.00 0.00 0.00 3.97
234 235 3.288092 GTGTTTCCTCTTGTGTTTCCCT 58.712 45.455 0.00 0.00 0.00 4.20
235 236 3.699538 GTGTTTCCTCTTGTGTTTCCCTT 59.300 43.478 0.00 0.00 0.00 3.95
236 237 4.159693 GTGTTTCCTCTTGTGTTTCCCTTT 59.840 41.667 0.00 0.00 0.00 3.11
237 238 5.358725 GTGTTTCCTCTTGTGTTTCCCTTTA 59.641 40.000 0.00 0.00 0.00 1.85
238 239 6.040504 GTGTTTCCTCTTGTGTTTCCCTTTAT 59.959 38.462 0.00 0.00 0.00 1.40
239 240 6.040391 TGTTTCCTCTTGTGTTTCCCTTTATG 59.960 38.462 0.00 0.00 0.00 1.90
240 241 5.576563 TCCTCTTGTGTTTCCCTTTATGA 57.423 39.130 0.00 0.00 0.00 2.15
241 242 6.139679 TCCTCTTGTGTTTCCCTTTATGAT 57.860 37.500 0.00 0.00 0.00 2.45
242 243 6.552008 TCCTCTTGTGTTTCCCTTTATGATT 58.448 36.000 0.00 0.00 0.00 2.57
243 244 7.010160 TCCTCTTGTGTTTCCCTTTATGATTT 58.990 34.615 0.00 0.00 0.00 2.17
244 245 7.508977 TCCTCTTGTGTTTCCCTTTATGATTTT 59.491 33.333 0.00 0.00 0.00 1.82
245 246 7.814587 CCTCTTGTGTTTCCCTTTATGATTTTC 59.185 37.037 0.00 0.00 0.00 2.29
246 247 7.666623 TCTTGTGTTTCCCTTTATGATTTTCC 58.333 34.615 0.00 0.00 0.00 3.13
247 248 6.353404 TGTGTTTCCCTTTATGATTTTCCC 57.647 37.500 0.00 0.00 0.00 3.97
248 249 6.081356 TGTGTTTCCCTTTATGATTTTCCCT 58.919 36.000 0.00 0.00 0.00 4.20
249 250 6.556874 TGTGTTTCCCTTTATGATTTTCCCTT 59.443 34.615 0.00 0.00 0.00 3.95
250 251 6.873605 GTGTTTCCCTTTATGATTTTCCCTTG 59.126 38.462 0.00 0.00 0.00 3.61
251 252 6.556874 TGTTTCCCTTTATGATTTTCCCTTGT 59.443 34.615 0.00 0.00 0.00 3.16
252 253 6.603940 TTCCCTTTATGATTTTCCCTTGTG 57.396 37.500 0.00 0.00 0.00 3.33
253 254 5.650283 TCCCTTTATGATTTTCCCTTGTGT 58.350 37.500 0.00 0.00 0.00 3.72
254 255 6.081356 TCCCTTTATGATTTTCCCTTGTGTT 58.919 36.000 0.00 0.00 0.00 3.32
255 256 6.556874 TCCCTTTATGATTTTCCCTTGTGTTT 59.443 34.615 0.00 0.00 0.00 2.83
256 257 6.873605 CCCTTTATGATTTTCCCTTGTGTTTC 59.126 38.462 0.00 0.00 0.00 2.78
257 258 7.256296 CCCTTTATGATTTTCCCTTGTGTTTCT 60.256 37.037 0.00 0.00 0.00 2.52
258 259 7.814587 CCTTTATGATTTTCCCTTGTGTTTCTC 59.185 37.037 0.00 0.00 0.00 2.87
259 260 4.829064 TGATTTTCCCTTGTGTTTCTCG 57.171 40.909 0.00 0.00 0.00 4.04
260 261 4.204012 TGATTTTCCCTTGTGTTTCTCGT 58.796 39.130 0.00 0.00 0.00 4.18
261 262 4.036262 TGATTTTCCCTTGTGTTTCTCGTG 59.964 41.667 0.00 0.00 0.00 4.35
262 263 2.702592 TTCCCTTGTGTTTCTCGTGT 57.297 45.000 0.00 0.00 0.00 4.49
263 264 2.702592 TCCCTTGTGTTTCTCGTGTT 57.297 45.000 0.00 0.00 0.00 3.32
264 265 2.557317 TCCCTTGTGTTTCTCGTGTTC 58.443 47.619 0.00 0.00 0.00 3.18
265 266 2.169769 TCCCTTGTGTTTCTCGTGTTCT 59.830 45.455 0.00 0.00 0.00 3.01
266 267 2.943033 CCCTTGTGTTTCTCGTGTTCTT 59.057 45.455 0.00 0.00 0.00 2.52
267 268 3.242739 CCCTTGTGTTTCTCGTGTTCTTG 60.243 47.826 0.00 0.00 0.00 3.02
268 269 3.354397 CTTGTGTTTCTCGTGTTCTTGC 58.646 45.455 0.00 0.00 0.00 4.01
269 270 1.326245 TGTGTTTCTCGTGTTCTTGCG 59.674 47.619 0.00 0.00 0.00 4.85
270 271 0.934496 TGTTTCTCGTGTTCTTGCGG 59.066 50.000 0.00 0.00 0.00 5.69
271 272 0.234884 GTTTCTCGTGTTCTTGCGGG 59.765 55.000 0.00 0.00 0.00 6.13
272 273 0.105224 TTTCTCGTGTTCTTGCGGGA 59.895 50.000 0.00 0.00 35.65 5.14
273 274 0.320374 TTCTCGTGTTCTTGCGGGAT 59.680 50.000 0.00 0.00 37.45 3.85
274 275 0.108804 TCTCGTGTTCTTGCGGGATC 60.109 55.000 0.00 0.00 32.16 3.36
275 276 1.079405 TCGTGTTCTTGCGGGATCC 60.079 57.895 1.92 1.92 0.00 3.36
285 286 3.813596 CGGGATCCGCTCCTTTTG 58.186 61.111 5.45 0.00 44.28 2.44
286 287 1.078426 CGGGATCCGCTCCTTTTGT 60.078 57.895 5.45 0.00 44.28 2.83
287 288 1.369091 CGGGATCCGCTCCTTTTGTG 61.369 60.000 5.45 0.00 44.28 3.33
288 289 0.035439 GGGATCCGCTCCTTTTGTGA 60.035 55.000 5.45 0.00 44.28 3.58
289 290 1.613255 GGGATCCGCTCCTTTTGTGAA 60.613 52.381 5.45 0.00 44.28 3.18
290 291 2.159382 GGATCCGCTCCTTTTGTGAAA 58.841 47.619 0.00 0.00 41.29 2.69
291 292 2.162408 GGATCCGCTCCTTTTGTGAAAG 59.838 50.000 0.00 0.00 41.29 2.62
292 293 2.631160 TCCGCTCCTTTTGTGAAAGA 57.369 45.000 0.70 0.00 44.03 2.52
293 294 3.140325 TCCGCTCCTTTTGTGAAAGAT 57.860 42.857 0.70 0.00 44.03 2.40
294 295 3.074412 TCCGCTCCTTTTGTGAAAGATC 58.926 45.455 0.70 0.00 44.03 2.75
295 296 2.159653 CCGCTCCTTTTGTGAAAGATCG 60.160 50.000 0.70 1.93 44.03 3.69
296 297 2.159653 CGCTCCTTTTGTGAAAGATCGG 60.160 50.000 0.70 0.00 44.03 4.18
297 298 2.414691 GCTCCTTTTGTGAAAGATCGGC 60.415 50.000 0.70 0.00 44.03 5.54
298 299 2.159382 TCCTTTTGTGAAAGATCGGCC 58.841 47.619 0.00 0.00 44.03 6.13
299 300 1.885887 CCTTTTGTGAAAGATCGGCCA 59.114 47.619 2.24 0.00 44.03 5.36
300 301 2.493278 CCTTTTGTGAAAGATCGGCCAT 59.507 45.455 2.24 0.00 44.03 4.40
301 302 3.428045 CCTTTTGTGAAAGATCGGCCATC 60.428 47.826 2.24 5.26 44.03 3.51
302 303 2.787473 TTGTGAAAGATCGGCCATCT 57.213 45.000 2.24 7.73 44.56 2.90
303 304 3.904800 TTGTGAAAGATCGGCCATCTA 57.095 42.857 15.36 1.49 41.47 1.98
304 305 3.459232 TGTGAAAGATCGGCCATCTAG 57.541 47.619 15.36 0.00 41.47 2.43
305 306 2.103094 TGTGAAAGATCGGCCATCTAGG 59.897 50.000 15.36 0.00 41.47 3.02
306 307 1.694150 TGAAAGATCGGCCATCTAGGG 59.306 52.381 15.36 0.00 41.47 3.53
307 308 1.694696 GAAAGATCGGCCATCTAGGGT 59.305 52.381 15.36 4.91 41.47 4.34
308 309 1.807814 AAGATCGGCCATCTAGGGTT 58.192 50.000 15.36 0.90 41.47 4.11
309 310 1.343069 AGATCGGCCATCTAGGGTTC 58.657 55.000 13.93 0.00 40.41 3.62
310 311 0.321996 GATCGGCCATCTAGGGTTCC 59.678 60.000 2.24 0.00 38.09 3.62
311 312 0.399949 ATCGGCCATCTAGGGTTCCA 60.400 55.000 2.24 0.00 38.09 3.53
312 313 1.146263 CGGCCATCTAGGGTTCCAC 59.854 63.158 2.24 0.00 38.09 4.02
313 314 1.532238 GGCCATCTAGGGTTCCACC 59.468 63.158 0.00 0.00 38.09 4.61
325 326 3.933861 GGTTCCACCCTACATCAGATT 57.066 47.619 0.00 0.00 30.04 2.40
326 327 3.809905 GGTTCCACCCTACATCAGATTC 58.190 50.000 0.00 0.00 30.04 2.52
327 328 3.456277 GGTTCCACCCTACATCAGATTCT 59.544 47.826 0.00 0.00 30.04 2.40
328 329 4.443598 GGTTCCACCCTACATCAGATTCTC 60.444 50.000 0.00 0.00 30.04 2.87
329 330 4.271807 TCCACCCTACATCAGATTCTCT 57.728 45.455 0.00 0.00 0.00 3.10
330 331 4.624913 TCCACCCTACATCAGATTCTCTT 58.375 43.478 0.00 0.00 0.00 2.85
331 332 4.406972 TCCACCCTACATCAGATTCTCTTG 59.593 45.833 0.00 0.00 0.00 3.02
381 382 1.002134 CCTCTTGGGGCATCGTTGT 60.002 57.895 0.00 0.00 0.00 3.32
442 443 1.438651 GTGGTCATTCGTGCTGCTTA 58.561 50.000 0.00 0.00 0.00 3.09
474 475 9.974980 TGGTTAACCAGATTTAGTTTTGATTTC 57.025 29.630 23.69 0.00 42.01 2.17
501 502 2.920724 TGGATGTTCGGTTGAGTTGA 57.079 45.000 0.00 0.00 0.00 3.18
521 522 1.568504 TCATCTGAAGCCGGGTTAGT 58.431 50.000 20.79 0.00 0.00 2.24
552 553 4.705110 TCTTCTTGGATCACCTTGTTCA 57.295 40.909 0.00 0.00 37.04 3.18
563 564 5.147330 TCACCTTGTTCATATTCGACACT 57.853 39.130 0.00 0.00 0.00 3.55
565 566 4.330074 CACCTTGTTCATATTCGACACTCC 59.670 45.833 0.00 0.00 0.00 3.85
566 567 4.223032 ACCTTGTTCATATTCGACACTCCT 59.777 41.667 0.00 0.00 0.00 3.69
567 568 4.806247 CCTTGTTCATATTCGACACTCCTC 59.194 45.833 0.00 0.00 0.00 3.71
568 569 5.394663 CCTTGTTCATATTCGACACTCCTCT 60.395 44.000 0.00 0.00 0.00 3.69
569 570 5.250235 TGTTCATATTCGACACTCCTCTC 57.750 43.478 0.00 0.00 0.00 3.20
570 571 4.950475 TGTTCATATTCGACACTCCTCTCT 59.050 41.667 0.00 0.00 0.00 3.10
574 575 3.644966 ATTCGACACTCCTCTCTCTCT 57.355 47.619 0.00 0.00 0.00 3.10
584 585 4.289672 ACTCCTCTCTCTCTCTCTCTTTGT 59.710 45.833 0.00 0.00 0.00 2.83
601 602 4.904590 TGGGGCGTTGTTGGGTGG 62.905 66.667 0.00 0.00 0.00 4.61
621 622 3.829026 TGGCAACCATACAACAATGCTAA 59.171 39.130 0.00 0.00 34.37 3.09
658 659 2.779430 TGGTTAGATGACCATGGATGCT 59.221 45.455 21.47 12.10 44.53 3.79
670 671 6.043590 TGACCATGGATGCTGAATATCTACTT 59.956 38.462 21.47 0.00 0.00 2.24
674 675 5.773575 TGGATGCTGAATATCTACTTCGTC 58.226 41.667 0.00 0.00 0.00 4.20
675 676 5.164954 GGATGCTGAATATCTACTTCGTCC 58.835 45.833 0.00 0.00 0.00 4.79
679 680 4.083431 GCTGAATATCTACTTCGTCCGCTA 60.083 45.833 0.00 0.00 0.00 4.26
767 768 5.811399 AAATGAATGAAATGCAATGCTGG 57.189 34.783 6.82 0.00 33.83 4.85
1597 2054 3.000819 CCCAGGTGTACGCCTCCA 61.001 66.667 25.28 0.00 36.58 3.86
2282 2742 4.395080 CAATGAGCTTGCGCCATG 57.605 55.556 4.18 0.00 36.60 3.66
3462 4094 5.879223 CCAATCTTGAGTTTCTCTAGTGCAT 59.121 40.000 0.00 0.00 35.49 3.96
3525 4282 5.182001 ACTCTCTTGTACCACATGATTTTGC 59.818 40.000 0.00 0.00 32.80 3.68
3587 4344 8.458573 TTCTCTAATGCACAACTTTTTAAGGA 57.541 30.769 0.00 0.00 0.00 3.36
3726 4608 3.599343 TGGCTGTTGCTATGTTGAGTAG 58.401 45.455 0.00 0.00 39.59 2.57
3769 4651 1.886542 CTTTGTCCTTACAACCTGGGC 59.113 52.381 0.00 0.00 45.18 5.36
3789 4671 1.688197 CATGCCACCAGTTTGAAAGGT 59.312 47.619 0.00 0.00 35.65 3.50
3790 4672 1.859302 TGCCACCAGTTTGAAAGGTT 58.141 45.000 0.00 0.00 32.15 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.557317 GTGGTCTCTCTCGAGGAGTAG 58.443 57.143 22.36 10.63 42.40 2.57
4 5 1.134759 CGTGGTCTCTCTCGAGGAGTA 60.135 57.143 22.36 11.93 42.40 2.59
5 6 0.391927 CGTGGTCTCTCTCGAGGAGT 60.392 60.000 22.36 0.00 42.40 3.85
8 9 2.766400 GCCGTGGTCTCTCTCGAGG 61.766 68.421 13.56 3.44 37.86 4.63
9 10 2.766400 GGCCGTGGTCTCTCTCGAG 61.766 68.421 5.93 5.93 38.67 4.04
10 11 2.750637 GGCCGTGGTCTCTCTCGA 60.751 66.667 0.00 0.00 0.00 4.04
11 12 3.827898 GGGCCGTGGTCTCTCTCG 61.828 72.222 0.00 0.00 0.00 4.04
12 13 3.462678 GGGGCCGTGGTCTCTCTC 61.463 72.222 0.00 0.00 0.00 3.20
13 14 3.966930 GAGGGGCCGTGGTCTCTCT 62.967 68.421 13.19 0.00 43.53 3.10
14 15 3.462678 GAGGGGCCGTGGTCTCTC 61.463 72.222 4.32 4.32 40.36 3.20
15 16 3.547787 AAGAGGGGCCGTGGTCTCT 62.548 63.158 2.05 3.05 38.12 3.10
16 17 2.593956 AAAGAGGGGCCGTGGTCTC 61.594 63.158 2.05 0.21 0.00 3.36
17 18 2.529389 AAAGAGGGGCCGTGGTCT 60.529 61.111 2.05 0.00 0.00 3.85
18 19 2.359975 CAAAGAGGGGCCGTGGTC 60.360 66.667 2.05 0.00 0.00 4.02
19 20 3.966543 CCAAAGAGGGGCCGTGGT 61.967 66.667 2.05 0.00 0.00 4.16
20 21 3.628646 CTCCAAAGAGGGGCCGTGG 62.629 68.421 2.05 2.82 36.39 4.94
21 22 2.045926 CTCCAAAGAGGGGCCGTG 60.046 66.667 2.05 0.00 36.39 4.94
22 23 1.842381 CTTCTCCAAAGAGGGGCCGT 61.842 60.000 0.00 0.00 40.83 5.68
23 24 1.078143 CTTCTCCAAAGAGGGGCCG 60.078 63.158 0.00 0.00 40.83 6.13
24 25 0.922626 ATCTTCTCCAAAGAGGGGCC 59.077 55.000 0.00 0.00 40.83 5.80
25 26 1.133945 GGATCTTCTCCAAAGAGGGGC 60.134 57.143 0.00 0.00 44.26 5.80
44 45 2.089201 GGGGTCTTAAATCCAACGTGG 58.911 52.381 0.00 0.00 39.43 4.94
45 46 2.089201 GGGGGTCTTAAATCCAACGTG 58.911 52.381 0.00 0.00 0.00 4.49
46 47 1.990327 AGGGGGTCTTAAATCCAACGT 59.010 47.619 0.00 0.00 0.00 3.99
47 48 2.238898 AGAGGGGGTCTTAAATCCAACG 59.761 50.000 0.00 0.00 27.07 4.10
48 49 3.681874 CGAGAGGGGGTCTTAAATCCAAC 60.682 52.174 0.00 0.00 34.71 3.77
49 50 2.504175 CGAGAGGGGGTCTTAAATCCAA 59.496 50.000 0.00 0.00 34.71 3.53
50 51 2.116238 CGAGAGGGGGTCTTAAATCCA 58.884 52.381 0.00 0.00 34.71 3.41
51 52 2.912690 CGAGAGGGGGTCTTAAATCC 57.087 55.000 0.00 0.00 34.71 3.01
71 72 2.043953 GGTCTTGATGGGGCCACC 60.044 66.667 0.20 2.19 40.81 4.61
72 73 1.077429 GAGGTCTTGATGGGGCCAC 60.077 63.158 4.39 0.00 0.00 5.01
73 74 2.308722 GGAGGTCTTGATGGGGCCA 61.309 63.158 4.39 0.00 0.00 5.36
74 75 1.988982 GAGGAGGTCTTGATGGGGCC 61.989 65.000 0.00 0.00 0.00 5.80
75 76 1.274703 TGAGGAGGTCTTGATGGGGC 61.275 60.000 0.00 0.00 0.00 5.80
76 77 1.142465 CATGAGGAGGTCTTGATGGGG 59.858 57.143 0.00 0.00 33.05 4.96
77 78 1.142465 CCATGAGGAGGTCTTGATGGG 59.858 57.143 0.00 0.00 34.55 4.00
78 79 2.121948 TCCATGAGGAGGTCTTGATGG 58.878 52.381 1.71 1.71 39.61 3.51
89 90 2.907892 ACTGGTTCTTCTCCATGAGGA 58.092 47.619 0.00 0.00 43.21 3.71
90 91 3.710209 AACTGGTTCTTCTCCATGAGG 57.290 47.619 0.00 0.00 34.26 3.86
91 92 4.508662 GGTAACTGGTTCTTCTCCATGAG 58.491 47.826 0.00 0.00 34.26 2.90
92 93 3.263425 GGGTAACTGGTTCTTCTCCATGA 59.737 47.826 0.00 0.00 34.26 3.07
93 94 3.264450 AGGGTAACTGGTTCTTCTCCATG 59.736 47.826 0.00 0.00 34.26 3.66
94 95 3.532102 AGGGTAACTGGTTCTTCTCCAT 58.468 45.455 0.00 0.00 34.26 3.41
95 96 2.986050 AGGGTAACTGGTTCTTCTCCA 58.014 47.619 0.00 0.00 0.00 3.86
96 97 5.695424 AATAGGGTAACTGGTTCTTCTCC 57.305 43.478 0.00 0.00 0.00 3.71
97 98 8.483758 TGATAAATAGGGTAACTGGTTCTTCTC 58.516 37.037 0.00 0.00 0.00 2.87
98 99 8.388656 TGATAAATAGGGTAACTGGTTCTTCT 57.611 34.615 0.00 0.00 0.00 2.85
99 100 9.274206 GATGATAAATAGGGTAACTGGTTCTTC 57.726 37.037 0.00 0.00 0.00 2.87
100 101 8.218488 GGATGATAAATAGGGTAACTGGTTCTT 58.782 37.037 0.00 0.00 0.00 2.52
101 102 7.202195 GGGATGATAAATAGGGTAACTGGTTCT 60.202 40.741 0.00 0.00 0.00 3.01
102 103 6.940867 GGGATGATAAATAGGGTAACTGGTTC 59.059 42.308 0.00 0.00 0.00 3.62
103 104 6.624021 AGGGATGATAAATAGGGTAACTGGTT 59.376 38.462 0.00 0.00 0.00 3.67
104 105 6.158260 AGGGATGATAAATAGGGTAACTGGT 58.842 40.000 0.00 0.00 0.00 4.00
105 106 6.704056 AGGGATGATAAATAGGGTAACTGG 57.296 41.667 0.00 0.00 0.00 4.00
106 107 7.518188 ACAAGGGATGATAAATAGGGTAACTG 58.482 38.462 0.00 0.00 0.00 3.16
107 108 7.707467 ACAAGGGATGATAAATAGGGTAACT 57.293 36.000 0.00 0.00 0.00 2.24
108 109 7.996644 TCAACAAGGGATGATAAATAGGGTAAC 59.003 37.037 0.00 0.00 0.00 2.50
109 110 7.996644 GTCAACAAGGGATGATAAATAGGGTAA 59.003 37.037 0.00 0.00 0.00 2.85
110 111 7.349859 AGTCAACAAGGGATGATAAATAGGGTA 59.650 37.037 0.00 0.00 0.00 3.69
111 112 6.160459 AGTCAACAAGGGATGATAAATAGGGT 59.840 38.462 0.00 0.00 0.00 4.34
112 113 6.605119 AGTCAACAAGGGATGATAAATAGGG 58.395 40.000 0.00 0.00 0.00 3.53
113 114 8.408601 CAAAGTCAACAAGGGATGATAAATAGG 58.591 37.037 0.00 0.00 0.00 2.57
114 115 8.408601 CCAAAGTCAACAAGGGATGATAAATAG 58.591 37.037 0.00 0.00 0.00 1.73
115 116 8.112822 TCCAAAGTCAACAAGGGATGATAAATA 58.887 33.333 0.00 0.00 0.00 1.40
116 117 6.953520 TCCAAAGTCAACAAGGGATGATAAAT 59.046 34.615 0.00 0.00 0.00 1.40
117 118 6.310941 TCCAAAGTCAACAAGGGATGATAAA 58.689 36.000 0.00 0.00 0.00 1.40
118 119 5.886609 TCCAAAGTCAACAAGGGATGATAA 58.113 37.500 0.00 0.00 0.00 1.75
119 120 5.512942 TCCAAAGTCAACAAGGGATGATA 57.487 39.130 0.00 0.00 0.00 2.15
120 121 4.387026 TCCAAAGTCAACAAGGGATGAT 57.613 40.909 0.00 0.00 0.00 2.45
121 122 3.874383 TCCAAAGTCAACAAGGGATGA 57.126 42.857 0.00 0.00 0.00 2.92
122 123 3.127548 CGATCCAAAGTCAACAAGGGATG 59.872 47.826 0.00 0.00 35.39 3.51
123 124 3.244911 ACGATCCAAAGTCAACAAGGGAT 60.245 43.478 0.00 0.00 37.82 3.85
124 125 2.105821 ACGATCCAAAGTCAACAAGGGA 59.894 45.455 0.00 0.00 0.00 4.20
125 126 2.226437 CACGATCCAAAGTCAACAAGGG 59.774 50.000 0.00 0.00 0.00 3.95
126 127 2.878406 ACACGATCCAAAGTCAACAAGG 59.122 45.455 0.00 0.00 0.00 3.61
127 128 3.559655 TCACACGATCCAAAGTCAACAAG 59.440 43.478 0.00 0.00 0.00 3.16
128 129 3.536570 TCACACGATCCAAAGTCAACAA 58.463 40.909 0.00 0.00 0.00 2.83
129 130 3.186702 TCACACGATCCAAAGTCAACA 57.813 42.857 0.00 0.00 0.00 3.33
130 131 4.327854 GATCACACGATCCAAAGTCAAC 57.672 45.455 0.00 0.00 42.03 3.18
137 138 8.550616 ACTACACATAGAGATCACACGATCCAA 61.551 40.741 0.00 0.00 39.25 3.53
138 139 7.135741 ACTACACATAGAGATCACACGATCCA 61.136 42.308 0.00 0.00 39.25 3.41
139 140 5.239744 ACTACACATAGAGATCACACGATCC 59.760 44.000 0.00 0.00 39.25 3.36
140 141 6.307031 ACTACACATAGAGATCACACGATC 57.693 41.667 0.00 0.00 39.00 3.69
141 142 5.050023 CGACTACACATAGAGATCACACGAT 60.050 44.000 0.00 0.00 32.23 3.73
142 143 4.270325 CGACTACACATAGAGATCACACGA 59.730 45.833 0.00 0.00 32.23 4.35
143 144 4.519147 CGACTACACATAGAGATCACACG 58.481 47.826 0.00 0.00 32.23 4.49
144 145 4.575236 TCCGACTACACATAGAGATCACAC 59.425 45.833 0.00 0.00 32.23 3.82
145 146 4.777463 TCCGACTACACATAGAGATCACA 58.223 43.478 0.00 0.00 32.23 3.58
146 147 5.703592 AGATCCGACTACACATAGAGATCAC 59.296 44.000 0.00 0.00 36.51 3.06
147 148 5.870706 AGATCCGACTACACATAGAGATCA 58.129 41.667 0.00 0.00 36.51 2.92
148 149 6.036735 GCTAGATCCGACTACACATAGAGATC 59.963 46.154 0.00 0.00 35.51 2.75
149 150 5.878116 GCTAGATCCGACTACACATAGAGAT 59.122 44.000 0.00 0.00 32.23 2.75
150 151 5.221661 TGCTAGATCCGACTACACATAGAGA 60.222 44.000 0.00 0.00 32.23 3.10
151 152 4.998033 TGCTAGATCCGACTACACATAGAG 59.002 45.833 0.00 0.00 32.23 2.43
152 153 4.969484 TGCTAGATCCGACTACACATAGA 58.031 43.478 0.00 0.00 32.23 1.98
153 154 5.888691 ATGCTAGATCCGACTACACATAG 57.111 43.478 0.00 0.00 34.25 2.23
154 155 6.884836 ACATATGCTAGATCCGACTACACATA 59.115 38.462 1.58 0.00 0.00 2.29
155 156 5.712446 ACATATGCTAGATCCGACTACACAT 59.288 40.000 1.58 0.00 0.00 3.21
156 157 5.048713 CACATATGCTAGATCCGACTACACA 60.049 44.000 1.58 0.00 0.00 3.72
157 158 5.048643 ACACATATGCTAGATCCGACTACAC 60.049 44.000 1.58 0.00 0.00 2.90
158 159 5.048713 CACACATATGCTAGATCCGACTACA 60.049 44.000 1.58 0.00 0.00 2.74
159 160 5.181433 TCACACATATGCTAGATCCGACTAC 59.819 44.000 1.58 0.00 0.00 2.73
160 161 5.313712 TCACACATATGCTAGATCCGACTA 58.686 41.667 1.58 0.00 0.00 2.59
161 162 4.145052 TCACACATATGCTAGATCCGACT 58.855 43.478 1.58 0.00 0.00 4.18
162 163 4.505313 TCACACATATGCTAGATCCGAC 57.495 45.455 1.58 0.00 0.00 4.79
163 164 4.142600 CGATCACACATATGCTAGATCCGA 60.143 45.833 18.51 2.20 32.45 4.55
164 165 4.101235 CGATCACACATATGCTAGATCCG 58.899 47.826 18.51 13.03 32.45 4.18
165 166 5.065704 ACGATCACACATATGCTAGATCC 57.934 43.478 18.51 7.90 32.45 3.36
166 167 6.385843 AGAACGATCACACATATGCTAGATC 58.614 40.000 16.16 16.16 32.62 2.75
167 168 6.338214 AGAACGATCACACATATGCTAGAT 57.662 37.500 1.58 3.42 0.00 1.98
168 169 5.774498 AGAACGATCACACATATGCTAGA 57.226 39.130 1.58 0.00 0.00 2.43
169 170 5.750547 ACAAGAACGATCACACATATGCTAG 59.249 40.000 1.58 0.00 0.00 3.42
170 171 5.660460 ACAAGAACGATCACACATATGCTA 58.340 37.500 1.58 0.00 0.00 3.49
171 172 4.507710 ACAAGAACGATCACACATATGCT 58.492 39.130 1.58 0.00 0.00 3.79
172 173 4.864916 ACAAGAACGATCACACATATGC 57.135 40.909 1.58 0.00 0.00 3.14
173 174 5.122239 ACCAACAAGAACGATCACACATATG 59.878 40.000 0.00 0.00 0.00 1.78
174 175 5.245531 ACCAACAAGAACGATCACACATAT 58.754 37.500 0.00 0.00 0.00 1.78
175 176 4.637276 ACCAACAAGAACGATCACACATA 58.363 39.130 0.00 0.00 0.00 2.29
176 177 3.476552 ACCAACAAGAACGATCACACAT 58.523 40.909 0.00 0.00 0.00 3.21
177 178 2.912771 ACCAACAAGAACGATCACACA 58.087 42.857 0.00 0.00 0.00 3.72
178 179 3.963383 AACCAACAAGAACGATCACAC 57.037 42.857 0.00 0.00 0.00 3.82
179 180 3.942115 TCAAACCAACAAGAACGATCACA 59.058 39.130 0.00 0.00 0.00 3.58
180 181 4.035208 ACTCAAACCAACAAGAACGATCAC 59.965 41.667 0.00 0.00 0.00 3.06
181 182 4.035091 CACTCAAACCAACAAGAACGATCA 59.965 41.667 0.00 0.00 0.00 2.92
182 183 4.272504 TCACTCAAACCAACAAGAACGATC 59.727 41.667 0.00 0.00 0.00 3.69
183 184 4.196193 TCACTCAAACCAACAAGAACGAT 58.804 39.130 0.00 0.00 0.00 3.73
184 185 3.601435 TCACTCAAACCAACAAGAACGA 58.399 40.909 0.00 0.00 0.00 3.85
185 186 4.552166 ATCACTCAAACCAACAAGAACG 57.448 40.909 0.00 0.00 0.00 3.95
186 187 6.136541 AGAATCACTCAAACCAACAAGAAC 57.863 37.500 0.00 0.00 0.00 3.01
187 188 6.377327 GAGAATCACTCAAACCAACAAGAA 57.623 37.500 0.00 0.00 44.36 2.52
200 201 4.082463 AGAGGAAACACGAGAGAATCACTC 60.082 45.833 0.00 0.00 45.22 3.51
201 202 3.829601 AGAGGAAACACGAGAGAATCACT 59.170 43.478 0.00 0.00 37.82 3.41
202 203 4.181309 AGAGGAAACACGAGAGAATCAC 57.819 45.455 0.00 0.00 37.82 3.06
203 204 4.039245 ACAAGAGGAAACACGAGAGAATCA 59.961 41.667 0.00 0.00 37.82 2.57
204 205 4.387256 CACAAGAGGAAACACGAGAGAATC 59.613 45.833 0.00 0.00 0.00 2.52
205 206 4.202264 ACACAAGAGGAAACACGAGAGAAT 60.202 41.667 0.00 0.00 0.00 2.40
206 207 3.132289 ACACAAGAGGAAACACGAGAGAA 59.868 43.478 0.00 0.00 0.00 2.87
207 208 2.693591 ACACAAGAGGAAACACGAGAGA 59.306 45.455 0.00 0.00 0.00 3.10
208 209 3.099267 ACACAAGAGGAAACACGAGAG 57.901 47.619 0.00 0.00 0.00 3.20
209 210 3.536956 AACACAAGAGGAAACACGAGA 57.463 42.857 0.00 0.00 0.00 4.04
210 211 3.002348 GGAAACACAAGAGGAAACACGAG 59.998 47.826 0.00 0.00 0.00 4.18
211 212 2.940410 GGAAACACAAGAGGAAACACGA 59.060 45.455 0.00 0.00 0.00 4.35
212 213 2.032924 GGGAAACACAAGAGGAAACACG 59.967 50.000 0.00 0.00 0.00 4.49
213 214 3.288092 AGGGAAACACAAGAGGAAACAC 58.712 45.455 0.00 0.00 0.00 3.32
214 215 3.662759 AGGGAAACACAAGAGGAAACA 57.337 42.857 0.00 0.00 0.00 2.83
215 216 6.264518 TCATAAAGGGAAACACAAGAGGAAAC 59.735 38.462 0.00 0.00 0.00 2.78
216 217 6.369629 TCATAAAGGGAAACACAAGAGGAAA 58.630 36.000 0.00 0.00 0.00 3.13
217 218 5.947663 TCATAAAGGGAAACACAAGAGGAA 58.052 37.500 0.00 0.00 0.00 3.36
218 219 5.576563 TCATAAAGGGAAACACAAGAGGA 57.423 39.130 0.00 0.00 0.00 3.71
219 220 6.840780 AATCATAAAGGGAAACACAAGAGG 57.159 37.500 0.00 0.00 0.00 3.69
220 221 7.814587 GGAAAATCATAAAGGGAAACACAAGAG 59.185 37.037 0.00 0.00 0.00 2.85
221 222 7.256154 GGGAAAATCATAAAGGGAAACACAAGA 60.256 37.037 0.00 0.00 0.00 3.02
222 223 6.873605 GGGAAAATCATAAAGGGAAACACAAG 59.126 38.462 0.00 0.00 0.00 3.16
223 224 6.556874 AGGGAAAATCATAAAGGGAAACACAA 59.443 34.615 0.00 0.00 0.00 3.33
224 225 6.081356 AGGGAAAATCATAAAGGGAAACACA 58.919 36.000 0.00 0.00 0.00 3.72
225 226 6.605471 AGGGAAAATCATAAAGGGAAACAC 57.395 37.500 0.00 0.00 0.00 3.32
226 227 6.556874 ACAAGGGAAAATCATAAAGGGAAACA 59.443 34.615 0.00 0.00 0.00 2.83
227 228 6.873605 CACAAGGGAAAATCATAAAGGGAAAC 59.126 38.462 0.00 0.00 0.00 2.78
228 229 6.556874 ACACAAGGGAAAATCATAAAGGGAAA 59.443 34.615 0.00 0.00 0.00 3.13
229 230 6.081356 ACACAAGGGAAAATCATAAAGGGAA 58.919 36.000 0.00 0.00 0.00 3.97
230 231 5.650283 ACACAAGGGAAAATCATAAAGGGA 58.350 37.500 0.00 0.00 0.00 4.20
231 232 6.358974 AACACAAGGGAAAATCATAAAGGG 57.641 37.500 0.00 0.00 0.00 3.95
232 233 7.670364 AGAAACACAAGGGAAAATCATAAAGG 58.330 34.615 0.00 0.00 0.00 3.11
233 234 7.538678 CGAGAAACACAAGGGAAAATCATAAAG 59.461 37.037 0.00 0.00 0.00 1.85
234 235 7.013846 ACGAGAAACACAAGGGAAAATCATAAA 59.986 33.333 0.00 0.00 0.00 1.40
235 236 6.488683 ACGAGAAACACAAGGGAAAATCATAA 59.511 34.615 0.00 0.00 0.00 1.90
236 237 6.001460 ACGAGAAACACAAGGGAAAATCATA 58.999 36.000 0.00 0.00 0.00 2.15
237 238 4.827284 ACGAGAAACACAAGGGAAAATCAT 59.173 37.500 0.00 0.00 0.00 2.45
238 239 4.036262 CACGAGAAACACAAGGGAAAATCA 59.964 41.667 0.00 0.00 0.00 2.57
239 240 4.036380 ACACGAGAAACACAAGGGAAAATC 59.964 41.667 0.00 0.00 0.00 2.17
240 241 3.951680 ACACGAGAAACACAAGGGAAAAT 59.048 39.130 0.00 0.00 0.00 1.82
241 242 3.349022 ACACGAGAAACACAAGGGAAAA 58.651 40.909 0.00 0.00 0.00 2.29
242 243 2.993937 ACACGAGAAACACAAGGGAAA 58.006 42.857 0.00 0.00 0.00 3.13
243 244 2.702592 ACACGAGAAACACAAGGGAA 57.297 45.000 0.00 0.00 0.00 3.97
244 245 2.169769 AGAACACGAGAAACACAAGGGA 59.830 45.455 0.00 0.00 0.00 4.20
245 246 2.561569 AGAACACGAGAAACACAAGGG 58.438 47.619 0.00 0.00 0.00 3.95
246 247 3.788797 GCAAGAACACGAGAAACACAAGG 60.789 47.826 0.00 0.00 0.00 3.61
247 248 3.354397 GCAAGAACACGAGAAACACAAG 58.646 45.455 0.00 0.00 0.00 3.16
248 249 2.222931 CGCAAGAACACGAGAAACACAA 60.223 45.455 0.00 0.00 43.02 3.33
249 250 1.326245 CGCAAGAACACGAGAAACACA 59.674 47.619 0.00 0.00 43.02 3.72
250 251 1.332904 CCGCAAGAACACGAGAAACAC 60.333 52.381 0.00 0.00 43.02 3.32
251 252 0.934496 CCGCAAGAACACGAGAAACA 59.066 50.000 0.00 0.00 43.02 2.83
252 253 0.234884 CCCGCAAGAACACGAGAAAC 59.765 55.000 0.00 0.00 43.02 2.78
253 254 0.105224 TCCCGCAAGAACACGAGAAA 59.895 50.000 0.00 0.00 43.02 2.52
254 255 0.320374 ATCCCGCAAGAACACGAGAA 59.680 50.000 0.00 0.00 43.02 2.87
255 256 0.108804 GATCCCGCAAGAACACGAGA 60.109 55.000 0.00 0.00 43.02 4.04
256 257 1.084370 GGATCCCGCAAGAACACGAG 61.084 60.000 0.00 0.00 43.02 4.18
257 258 1.079405 GGATCCCGCAAGAACACGA 60.079 57.895 0.00 0.00 43.02 4.35
258 259 2.452813 CGGATCCCGCAAGAACACG 61.453 63.158 6.06 0.00 41.17 4.49
259 260 3.486263 CGGATCCCGCAAGAACAC 58.514 61.111 6.06 0.00 41.17 3.32
271 272 3.074412 TCTTTCACAAAAGGAGCGGATC 58.926 45.455 0.00 0.00 41.88 3.36
272 273 3.140325 TCTTTCACAAAAGGAGCGGAT 57.860 42.857 0.00 0.00 41.88 4.18
273 274 2.631160 TCTTTCACAAAAGGAGCGGA 57.369 45.000 0.00 0.00 41.88 5.54
274 275 2.159653 CGATCTTTCACAAAAGGAGCGG 60.160 50.000 0.43 0.00 41.88 5.52
275 276 2.159653 CCGATCTTTCACAAAAGGAGCG 60.160 50.000 1.30 1.30 41.88 5.03
276 277 2.414691 GCCGATCTTTCACAAAAGGAGC 60.415 50.000 0.00 0.00 41.88 4.70
277 278 2.162408 GGCCGATCTTTCACAAAAGGAG 59.838 50.000 0.00 0.00 41.88 3.69
278 279 2.159382 GGCCGATCTTTCACAAAAGGA 58.841 47.619 0.00 0.00 41.88 3.36
279 280 1.885887 TGGCCGATCTTTCACAAAAGG 59.114 47.619 0.00 0.00 41.88 3.11
280 281 3.441572 AGATGGCCGATCTTTCACAAAAG 59.558 43.478 10.78 0.00 38.35 2.27
281 282 3.420893 AGATGGCCGATCTTTCACAAAA 58.579 40.909 10.78 0.00 38.35 2.44
282 283 3.071874 AGATGGCCGATCTTTCACAAA 57.928 42.857 10.78 0.00 38.35 2.83
283 284 2.787473 AGATGGCCGATCTTTCACAA 57.213 45.000 10.78 0.00 38.35 3.33
284 285 2.103094 CCTAGATGGCCGATCTTTCACA 59.897 50.000 18.81 4.46 41.94 3.58
285 286 2.548920 CCCTAGATGGCCGATCTTTCAC 60.549 54.545 18.81 0.00 41.94 3.18
286 287 1.694150 CCCTAGATGGCCGATCTTTCA 59.306 52.381 18.81 5.03 41.94 2.69
287 288 1.694696 ACCCTAGATGGCCGATCTTTC 59.305 52.381 18.81 1.28 41.94 2.62
288 289 1.807814 ACCCTAGATGGCCGATCTTT 58.192 50.000 18.81 3.54 41.94 2.52
289 290 1.694696 GAACCCTAGATGGCCGATCTT 59.305 52.381 18.81 5.00 41.94 2.40
290 291 1.343069 GAACCCTAGATGGCCGATCT 58.657 55.000 18.00 18.00 44.24 2.75
291 292 0.321996 GGAACCCTAGATGGCCGATC 59.678 60.000 0.00 2.42 0.00 3.69
292 293 0.399949 TGGAACCCTAGATGGCCGAT 60.400 55.000 0.00 0.00 0.00 4.18
293 294 1.002403 TGGAACCCTAGATGGCCGA 59.998 57.895 0.00 0.00 0.00 5.54
294 295 1.146263 GTGGAACCCTAGATGGCCG 59.854 63.158 0.00 0.00 0.00 6.13
306 307 4.698575 GAGAATCTGATGTAGGGTGGAAC 58.301 47.826 0.00 0.00 0.00 3.62
322 323 4.020751 TCATCATCCGATCCCAAGAGAATC 60.021 45.833 0.00 0.00 0.00 2.52
323 324 3.906218 TCATCATCCGATCCCAAGAGAAT 59.094 43.478 0.00 0.00 0.00 2.40
324 325 3.308401 TCATCATCCGATCCCAAGAGAA 58.692 45.455 0.00 0.00 0.00 2.87
325 326 2.962859 TCATCATCCGATCCCAAGAGA 58.037 47.619 0.00 0.00 0.00 3.10
326 327 3.597255 CATCATCATCCGATCCCAAGAG 58.403 50.000 0.00 0.00 0.00 2.85
327 328 2.303890 CCATCATCATCCGATCCCAAGA 59.696 50.000 0.00 0.00 0.00 3.02
328 329 2.039480 ACCATCATCATCCGATCCCAAG 59.961 50.000 0.00 0.00 0.00 3.61
329 330 2.057140 ACCATCATCATCCGATCCCAA 58.943 47.619 0.00 0.00 0.00 4.12
330 331 1.348696 CACCATCATCATCCGATCCCA 59.651 52.381 0.00 0.00 0.00 4.37
331 332 1.625315 TCACCATCATCATCCGATCCC 59.375 52.381 0.00 0.00 0.00 3.85
381 382 0.320946 CGGCCGGTAAGAAACTCCAA 60.321 55.000 20.10 0.00 0.00 3.53
442 443 6.128138 ACTAAATCTGGTTAACCAAGCTCT 57.872 37.500 26.90 13.43 46.97 4.09
474 475 1.016627 ACCGAACATCCATTGCATCG 58.983 50.000 0.00 0.00 37.59 3.84
501 502 2.119495 ACTAACCCGGCTTCAGATGAT 58.881 47.619 0.00 0.00 0.00 2.45
521 522 7.461749 AGGTGATCCAAGAAGAATCAAACTTA 58.538 34.615 0.00 0.00 35.89 2.24
552 553 5.071788 AGAGAGAGAGAGGAGTGTCGAATAT 59.928 44.000 0.00 0.00 0.00 1.28
563 564 4.567537 CCACAAAGAGAGAGAGAGAGAGGA 60.568 50.000 0.00 0.00 0.00 3.71
565 566 3.696051 CCCACAAAGAGAGAGAGAGAGAG 59.304 52.174 0.00 0.00 0.00 3.20
566 567 3.563261 CCCCACAAAGAGAGAGAGAGAGA 60.563 52.174 0.00 0.00 0.00 3.10
567 568 2.760092 CCCCACAAAGAGAGAGAGAGAG 59.240 54.545 0.00 0.00 0.00 3.20
568 569 2.813907 CCCCACAAAGAGAGAGAGAGA 58.186 52.381 0.00 0.00 0.00 3.10
569 570 1.206849 GCCCCACAAAGAGAGAGAGAG 59.793 57.143 0.00 0.00 0.00 3.20
570 571 1.270907 GCCCCACAAAGAGAGAGAGA 58.729 55.000 0.00 0.00 0.00 3.10
574 575 0.250295 CAACGCCCCACAAAGAGAGA 60.250 55.000 0.00 0.00 0.00 3.10
584 585 4.904590 CCACCCAACAACGCCCCA 62.905 66.667 0.00 0.00 0.00 4.96
601 602 4.864247 CCTTTAGCATTGTTGTATGGTTGC 59.136 41.667 0.00 0.00 37.43 4.17
621 622 0.396811 ACCAAGCAAGTCGTAGCCTT 59.603 50.000 0.00 0.00 0.00 4.35
670 671 1.320344 ATGCTGGTTCTAGCGGACGA 61.320 55.000 0.00 0.00 46.61 4.20
674 675 2.182842 GGCATGCTGGTTCTAGCGG 61.183 63.158 18.92 0.59 46.61 5.52
675 676 1.153289 AGGCATGCTGGTTCTAGCG 60.153 57.895 18.92 0.00 46.61 4.26
679 680 0.252479 CTCTCAGGCATGCTGGTTCT 59.748 55.000 18.92 2.16 0.00 3.01
804 805 1.227527 CGGTGTGTGCTGAGTCCAA 60.228 57.895 0.00 0.00 0.00 3.53
810 811 4.314440 GGCTCCGGTGTGTGCTGA 62.314 66.667 0.00 0.00 0.00 4.26
2282 2742 0.246635 TAGTTCGAGGCAGGACAAGC 59.753 55.000 0.00 0.00 0.00 4.01
2448 2908 2.443255 AGGTGAATCCTTGACCTTGTGT 59.557 45.455 0.00 0.00 45.67 3.72
3180 3642 6.238731 GCTATATCAACATGCTACTTGCCAAA 60.239 38.462 0.00 0.00 42.00 3.28
3462 4094 8.098286 TCAATTTCTAACACCCGAAAGAAGATA 58.902 33.333 0.00 0.00 33.18 1.98
3587 4344 5.105351 GCTAGGGGTTGCAAATTTCTAACAT 60.105 40.000 0.00 4.70 0.00 2.71
3726 4608 9.683069 AAAGACAAATGATTCACATACTTGAAC 57.317 29.630 0.00 0.00 38.31 3.18
3769 4651 1.688197 ACCTTTCAAACTGGTGGCATG 59.312 47.619 0.00 0.00 32.16 4.06
3790 4672 9.956720 GGATAGCTACGTGAACTAGTAAAATAA 57.043 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.