Multiple sequence alignment - TraesCS3B01G325000

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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 TraesCS3B01G325000 chr3B 100.000 2270 0 0 1 2270 525834255 525831986 0.000000e+00 4193.0
1 TraesCS3B01G325000 chr3B 86.047 1075 144 4 229 1298 222250264 222249191 0.000000e+00 1149.0
2 TraesCS3B01G325000 chr3B 88.889 207 19 2 1 203 792276367 792276573 3.740000e-63 252.0
3 TraesCS3B01G325000 chr3B 88.889 207 19 2 1 203 792362762 792362968 3.740000e-63 252.0
4 TraesCS3B01G325000 chr3B 90.909 55 5 0 1538 1592 187352153 187352207 8.700000e-10 75.0
5 TraesCS3B01G325000 chr3A 95.577 814 18 7 1296 2093 519210446 519209635 0.000000e+00 1288.0
6 TraesCS3B01G325000 chr3A 87.208 1071 135 2 229 1298 496599482 496598413 0.000000e+00 1218.0
7 TraesCS3B01G325000 chr3A 89.091 55 6 0 1538 1592 142896670 142896724 4.050000e-08 69.4
8 TraesCS3B01G325000 chr3D 93.356 888 21 13 1305 2175 400277666 400276800 0.000000e+00 1279.0
9 TraesCS3B01G325000 chr3D 89.091 55 6 0 1538 1592 130933092 130933146 4.050000e-08 69.4
10 TraesCS3B01G325000 chr4B 88.208 1060 124 1 229 1287 65529278 65528219 0.000000e+00 1264.0
11 TraesCS3B01G325000 chr4B 86.884 1075 130 7 232 1303 65144856 65143790 0.000000e+00 1194.0
12 TraesCS3B01G325000 chr6B 87.302 1071 135 1 229 1298 683422309 683421239 0.000000e+00 1223.0
13 TraesCS3B01G325000 chr1B 86.778 1074 139 3 229 1301 419276422 419275351 0.000000e+00 1194.0
14 TraesCS3B01G325000 chr1B 85.768 1061 149 2 229 1288 14989263 14988204 0.000000e+00 1122.0
15 TraesCS3B01G325000 chr1B 85.261 1072 155 3 229 1299 301295011 301296080 0.000000e+00 1101.0
16 TraesCS3B01G325000 chr1B 75.432 521 98 27 1440 1940 580631820 580632330 2.270000e-55 226.0
17 TraesCS3B01G325000 chrUn 85.849 1060 150 0 229 1288 2466328 2465269 0.000000e+00 1127.0
18 TraesCS3B01G325000 chrUn 89.216 204 18 2 4 203 155018149 155017946 3.740000e-63 252.0
19 TraesCS3B01G325000 chrUn 88.889 207 19 2 1 203 399496993 399497199 3.740000e-63 252.0
20 TraesCS3B01G325000 chrUn 88.889 207 19 2 1 203 463429234 463429440 3.740000e-63 252.0
21 TraesCS3B01G325000 chr6D 89.372 207 18 2 1 203 99798776 99798982 8.050000e-65 257.0
22 TraesCS3B01G325000 chr2B 89.372 207 18 2 1 203 745704329 745704123 8.050000e-65 257.0
23 TraesCS3B01G325000 chr2B 89.372 207 16 4 3 203 68216499 68216293 2.890000e-64 255.0
24 TraesCS3B01G325000 chr7D 88.426 216 20 3 1 212 32071046 32070832 2.890000e-64 255.0
25 TraesCS3B01G325000 chr1A 89.583 144 14 1 1798 1940 527175253 527175396 4.980000e-42 182.0
26 TraesCS3B01G325000 chr1A 96.875 64 2 0 1529 1592 527174608 527174671 8.570000e-20 108.0
27 TraesCS3B01G325000 chr1A 95.238 42 2 0 1681 1722 527175126 527175167 1.460000e-07 67.6
28 TraesCS3B01G325000 chr1D 88.971 136 15 0 1805 1940 429696895 429697030 3.880000e-38 169.0
29 TraesCS3B01G325000 chr1D 78.713 202 28 15 1529 1721 429696443 429696638 1.100000e-23 121.0


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 TraesCS3B01G325000 chr3B 525831986 525834255 2269 True 4193 4193 100.000 1 2270 1 chr3B.!!$R2 2269
1 TraesCS3B01G325000 chr3B 222249191 222250264 1073 True 1149 1149 86.047 229 1298 1 chr3B.!!$R1 1069
2 TraesCS3B01G325000 chr3A 519209635 519210446 811 True 1288 1288 95.577 1296 2093 1 chr3A.!!$R2 797
3 TraesCS3B01G325000 chr3A 496598413 496599482 1069 True 1218 1218 87.208 229 1298 1 chr3A.!!$R1 1069
4 TraesCS3B01G325000 chr3D 400276800 400277666 866 True 1279 1279 93.356 1305 2175 1 chr3D.!!$R1 870
5 TraesCS3B01G325000 chr4B 65528219 65529278 1059 True 1264 1264 88.208 229 1287 1 chr4B.!!$R2 1058
6 TraesCS3B01G325000 chr4B 65143790 65144856 1066 True 1194 1194 86.884 232 1303 1 chr4B.!!$R1 1071
7 TraesCS3B01G325000 chr6B 683421239 683422309 1070 True 1223 1223 87.302 229 1298 1 chr6B.!!$R1 1069
8 TraesCS3B01G325000 chr1B 419275351 419276422 1071 True 1194 1194 86.778 229 1301 1 chr1B.!!$R2 1072
9 TraesCS3B01G325000 chr1B 14988204 14989263 1059 True 1122 1122 85.768 229 1288 1 chr1B.!!$R1 1059
10 TraesCS3B01G325000 chr1B 301295011 301296080 1069 False 1101 1101 85.261 229 1299 1 chr1B.!!$F1 1070
11 TraesCS3B01G325000 chr1B 580631820 580632330 510 False 226 226 75.432 1440 1940 1 chr1B.!!$F2 500
12 TraesCS3B01G325000 chrUn 2465269 2466328 1059 True 1127 1127 85.849 229 1288 1 chrUn.!!$R1 1059

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
117 118 0.033366 TGCGCACAGTCTCTTTGCTA 59.967 50.0 5.66 0.0 33.9 3.49 F
582 583 0.101219 GGGCCGAAGACATCATTTGC 59.899 55.0 0.00 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1182 1.040646 TCCAGCTTTCTGTCACGTCT 58.959 50.0 0.0 0.0 38.66 4.18 R
2148 2217 0.738389 CCAAAGTGTGCCGTGTCTTT 59.262 50.0 0.0 0.0 0.00 2.52 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
61 62 9.935241 ATTACATACAAACAAAATTATGGTGCA 57.065 25.926 0.00 0.00 0.00 4.57
62 63 9.764363 TTACATACAAACAAAATTATGGTGCAA 57.236 25.926 0.00 0.00 0.00 4.08
63 64 8.845413 ACATACAAACAAAATTATGGTGCAAT 57.155 26.923 0.00 0.00 0.00 3.56
64 65 9.935241 ACATACAAACAAAATTATGGTGCAATA 57.065 25.926 0.00 0.00 0.00 1.90
103 104 5.425577 TTTTTATGAACAGTAACTGCGCA 57.574 34.783 10.98 10.98 34.37 6.09
104 105 4.398549 TTTATGAACAGTAACTGCGCAC 57.601 40.909 5.66 0.00 34.37 5.34
105 106 1.877637 ATGAACAGTAACTGCGCACA 58.122 45.000 5.66 0.00 34.37 4.57
115 116 1.206072 CTGCGCACAGTCTCTTTGC 59.794 57.895 5.66 0.00 39.22 3.68
116 117 1.226686 CTGCGCACAGTCTCTTTGCT 61.227 55.000 5.66 0.00 39.22 3.91
117 118 0.033366 TGCGCACAGTCTCTTTGCTA 59.967 50.000 5.66 0.00 33.90 3.49
118 119 0.440371 GCGCACAGTCTCTTTGCTAC 59.560 55.000 0.30 0.00 33.90 3.58
119 120 1.783284 CGCACAGTCTCTTTGCTACA 58.217 50.000 6.38 0.00 33.90 2.74
120 121 1.723542 CGCACAGTCTCTTTGCTACAG 59.276 52.381 6.38 0.00 33.90 2.74
121 122 2.760374 GCACAGTCTCTTTGCTACAGT 58.240 47.619 1.37 0.00 33.26 3.55
122 123 2.478134 GCACAGTCTCTTTGCTACAGTG 59.522 50.000 1.37 0.00 34.76 3.66
123 124 3.722147 CACAGTCTCTTTGCTACAGTGT 58.278 45.455 0.00 0.00 0.00 3.55
124 125 3.738282 CACAGTCTCTTTGCTACAGTGTC 59.262 47.826 0.00 0.00 0.00 3.67
125 126 3.639094 ACAGTCTCTTTGCTACAGTGTCT 59.361 43.478 0.00 0.00 0.00 3.41
126 127 3.986572 CAGTCTCTTTGCTACAGTGTCTG 59.013 47.826 0.00 0.00 37.52 3.51
128 129 3.738282 GTCTCTTTGCTACAGTGTCTGTG 59.262 47.826 11.92 4.43 45.01 3.66
129 130 3.636764 TCTCTTTGCTACAGTGTCTGTGA 59.363 43.478 11.92 0.26 45.01 3.58
130 131 4.281941 TCTCTTTGCTACAGTGTCTGTGAT 59.718 41.667 11.92 0.00 45.01 3.06
131 132 5.476945 TCTCTTTGCTACAGTGTCTGTGATA 59.523 40.000 11.92 0.00 45.01 2.15
132 133 6.153510 TCTCTTTGCTACAGTGTCTGTGATAT 59.846 38.462 11.92 0.00 45.01 1.63
133 134 6.701340 TCTTTGCTACAGTGTCTGTGATATT 58.299 36.000 11.92 0.00 45.01 1.28
134 135 6.813649 TCTTTGCTACAGTGTCTGTGATATTC 59.186 38.462 11.92 0.00 45.01 1.75
135 136 5.921962 TGCTACAGTGTCTGTGATATTCT 57.078 39.130 11.92 0.00 45.01 2.40
136 137 6.286240 TGCTACAGTGTCTGTGATATTCTT 57.714 37.500 11.92 0.00 45.01 2.52
137 138 6.701340 TGCTACAGTGTCTGTGATATTCTTT 58.299 36.000 11.92 0.00 45.01 2.52
138 139 6.813649 TGCTACAGTGTCTGTGATATTCTTTC 59.186 38.462 11.92 0.00 45.01 2.62
139 140 7.038659 GCTACAGTGTCTGTGATATTCTTTCT 58.961 38.462 11.92 0.00 45.01 2.52
140 141 7.547370 GCTACAGTGTCTGTGATATTCTTTCTT 59.453 37.037 11.92 0.00 45.01 2.52
141 142 7.897575 ACAGTGTCTGTGATATTCTTTCTTC 57.102 36.000 1.44 0.00 43.63 2.87
142 143 7.445121 ACAGTGTCTGTGATATTCTTTCTTCA 58.555 34.615 1.44 0.00 43.63 3.02
143 144 8.099537 ACAGTGTCTGTGATATTCTTTCTTCAT 58.900 33.333 1.44 0.00 43.63 2.57
144 145 8.944029 CAGTGTCTGTGATATTCTTTCTTCATT 58.056 33.333 0.00 0.00 0.00 2.57
145 146 9.512588 AGTGTCTGTGATATTCTTTCTTCATTT 57.487 29.630 0.00 0.00 0.00 2.32
148 149 9.070149 GTCTGTGATATTCTTTCTTCATTTTGC 57.930 33.333 0.00 0.00 0.00 3.68
149 150 8.795513 TCTGTGATATTCTTTCTTCATTTTGCA 58.204 29.630 0.00 0.00 0.00 4.08
150 151 8.746922 TGTGATATTCTTTCTTCATTTTGCAC 57.253 30.769 0.00 0.00 0.00 4.57
151 152 8.579006 TGTGATATTCTTTCTTCATTTTGCACT 58.421 29.630 0.00 0.00 0.00 4.40
152 153 8.857216 GTGATATTCTTTCTTCATTTTGCACTG 58.143 33.333 0.00 0.00 0.00 3.66
153 154 8.795513 TGATATTCTTTCTTCATTTTGCACTGA 58.204 29.630 0.00 0.00 0.00 3.41
154 155 8.976986 ATATTCTTTCTTCATTTTGCACTGAC 57.023 30.769 0.00 0.00 0.00 3.51
155 156 5.833406 TCTTTCTTCATTTTGCACTGACA 57.167 34.783 0.00 0.00 0.00 3.58
156 157 6.395426 TCTTTCTTCATTTTGCACTGACAT 57.605 33.333 0.00 0.00 0.00 3.06
157 158 6.808829 TCTTTCTTCATTTTGCACTGACATT 58.191 32.000 0.00 0.00 0.00 2.71
158 159 6.698329 TCTTTCTTCATTTTGCACTGACATTG 59.302 34.615 0.00 0.00 0.00 2.82
159 160 4.300803 TCTTCATTTTGCACTGACATTGC 58.699 39.130 10.65 10.65 40.63 3.56
164 165 3.099002 TGCACTGACATTGCACTGT 57.901 47.368 15.76 9.76 45.06 3.55
165 166 2.252976 TGCACTGACATTGCACTGTA 57.747 45.000 15.76 0.00 45.06 2.74
166 167 2.570135 TGCACTGACATTGCACTGTAA 58.430 42.857 15.76 1.44 45.06 2.41
167 168 2.290367 TGCACTGACATTGCACTGTAAC 59.710 45.455 15.76 0.00 45.06 2.50
168 169 2.549754 GCACTGACATTGCACTGTAACT 59.450 45.455 9.97 0.00 39.93 2.24
169 170 3.003689 GCACTGACATTGCACTGTAACTT 59.996 43.478 9.97 0.00 39.93 2.66
170 171 4.776743 CACTGACATTGCACTGTAACTTC 58.223 43.478 9.97 0.00 0.00 3.01
171 172 3.494626 ACTGACATTGCACTGTAACTTCG 59.505 43.478 9.97 0.00 0.00 3.79
172 173 3.462982 TGACATTGCACTGTAACTTCGT 58.537 40.909 9.97 0.00 0.00 3.85
173 174 3.247411 TGACATTGCACTGTAACTTCGTG 59.753 43.478 9.97 0.00 0.00 4.35
174 175 3.462982 ACATTGCACTGTAACTTCGTGA 58.537 40.909 8.09 0.00 0.00 4.35
175 176 3.247648 ACATTGCACTGTAACTTCGTGAC 59.752 43.478 8.09 0.00 0.00 3.67
176 177 2.588027 TGCACTGTAACTTCGTGACA 57.412 45.000 0.00 0.00 0.00 3.58
177 178 3.106242 TGCACTGTAACTTCGTGACAT 57.894 42.857 0.00 0.00 0.00 3.06
178 179 3.057019 TGCACTGTAACTTCGTGACATC 58.943 45.455 0.00 0.00 0.00 3.06
179 180 2.412089 GCACTGTAACTTCGTGACATCC 59.588 50.000 0.00 0.00 0.00 3.51
180 181 3.861131 GCACTGTAACTTCGTGACATCCT 60.861 47.826 0.00 0.00 0.00 3.24
181 182 4.307432 CACTGTAACTTCGTGACATCCTT 58.693 43.478 0.00 0.00 0.00 3.36
182 183 4.750098 CACTGTAACTTCGTGACATCCTTT 59.250 41.667 0.00 0.00 0.00 3.11
183 184 5.236478 CACTGTAACTTCGTGACATCCTTTT 59.764 40.000 0.00 0.00 0.00 2.27
184 185 6.422701 CACTGTAACTTCGTGACATCCTTTTA 59.577 38.462 0.00 0.00 0.00 1.52
185 186 7.117812 CACTGTAACTTCGTGACATCCTTTTAT 59.882 37.037 0.00 0.00 0.00 1.40
186 187 7.117812 ACTGTAACTTCGTGACATCCTTTTATG 59.882 37.037 0.00 0.00 0.00 1.90
187 188 7.156000 TGTAACTTCGTGACATCCTTTTATGA 58.844 34.615 0.00 0.00 0.00 2.15
188 189 7.822334 TGTAACTTCGTGACATCCTTTTATGAT 59.178 33.333 0.00 0.00 0.00 2.45
189 190 6.668541 ACTTCGTGACATCCTTTTATGATG 57.331 37.500 0.00 0.00 44.13 3.07
200 201 8.558973 CATCCTTTTATGATGTTAGAGGATCC 57.441 38.462 2.48 2.48 39.77 3.36
201 202 6.759272 TCCTTTTATGATGTTAGAGGATCCG 58.241 40.000 5.98 0.00 33.66 4.18
202 203 6.326583 TCCTTTTATGATGTTAGAGGATCCGT 59.673 38.462 5.98 0.00 33.66 4.69
203 204 7.507956 TCCTTTTATGATGTTAGAGGATCCGTA 59.492 37.037 5.98 0.00 33.66 4.02
204 205 8.148351 CCTTTTATGATGTTAGAGGATCCGTAA 58.852 37.037 5.98 5.81 33.66 3.18
205 206 8.882415 TTTTATGATGTTAGAGGATCCGTAAC 57.118 34.615 23.41 23.41 33.66 2.50
206 207 4.931661 TGATGTTAGAGGATCCGTAACC 57.068 45.455 25.50 16.83 33.66 2.85
207 208 3.640029 TGATGTTAGAGGATCCGTAACCC 59.360 47.826 25.50 20.02 33.66 4.11
208 209 3.393426 TGTTAGAGGATCCGTAACCCT 57.607 47.619 25.50 13.11 33.66 4.34
209 210 3.294214 TGTTAGAGGATCCGTAACCCTC 58.706 50.000 25.50 10.91 45.16 4.30
210 211 3.294214 GTTAGAGGATCCGTAACCCTCA 58.706 50.000 21.17 0.18 46.74 3.86
211 212 2.544844 AGAGGATCCGTAACCCTCAA 57.455 50.000 5.98 0.00 46.74 3.02
212 213 2.829023 AGAGGATCCGTAACCCTCAAA 58.171 47.619 5.98 0.00 46.74 2.69
213 214 2.500504 AGAGGATCCGTAACCCTCAAAC 59.499 50.000 5.98 0.00 46.74 2.93
214 215 2.235402 GAGGATCCGTAACCCTCAAACA 59.765 50.000 5.98 0.00 44.42 2.83
215 216 2.027469 AGGATCCGTAACCCTCAAACAC 60.027 50.000 5.98 0.00 0.00 3.32
216 217 2.027469 GGATCCGTAACCCTCAAACACT 60.027 50.000 0.00 0.00 0.00 3.55
217 218 3.196254 GGATCCGTAACCCTCAAACACTA 59.804 47.826 0.00 0.00 0.00 2.74
218 219 3.947910 TCCGTAACCCTCAAACACTAG 57.052 47.619 0.00 0.00 0.00 2.57
219 220 3.233507 TCCGTAACCCTCAAACACTAGT 58.766 45.455 0.00 0.00 0.00 2.57
220 221 4.406456 TCCGTAACCCTCAAACACTAGTA 58.594 43.478 0.00 0.00 0.00 1.82
221 222 4.218417 TCCGTAACCCTCAAACACTAGTAC 59.782 45.833 0.00 0.00 0.00 2.73
222 223 4.161333 CGTAACCCTCAAACACTAGTACG 58.839 47.826 0.00 0.00 0.00 3.67
223 224 4.320494 CGTAACCCTCAAACACTAGTACGT 60.320 45.833 0.00 0.00 0.00 3.57
224 225 3.930634 ACCCTCAAACACTAGTACGTC 57.069 47.619 0.00 0.00 0.00 4.34
225 226 2.560105 ACCCTCAAACACTAGTACGTCC 59.440 50.000 0.00 0.00 0.00 4.79
226 227 2.094338 CCCTCAAACACTAGTACGTCCC 60.094 54.545 0.00 0.00 0.00 4.46
227 228 2.824341 CCTCAAACACTAGTACGTCCCT 59.176 50.000 0.00 0.00 0.00 4.20
321 322 2.224769 ACAACGGATGTGGAATGACCTT 60.225 45.455 0.00 0.00 41.93 3.50
327 328 3.445096 GGATGTGGAATGACCTTTGGAAG 59.555 47.826 0.00 0.00 39.86 3.46
328 329 2.238521 TGTGGAATGACCTTTGGAAGC 58.761 47.619 0.00 0.00 39.86 3.86
351 352 1.112315 ATGTTTTGCCCAAGGTGCGA 61.112 50.000 0.00 0.00 0.00 5.10
354 355 1.040339 TTTTGCCCAAGGTGCGAGTT 61.040 50.000 0.00 0.00 0.00 3.01
360 361 1.266989 CCCAAGGTGCGAGTTTTCTTC 59.733 52.381 0.00 0.00 0.00 2.87
382 383 0.935366 GCGAGTGCTGCGAGGTATAC 60.935 60.000 0.00 0.00 38.39 1.47
432 433 5.331902 CGGCATATTCGTCAACAAAATCTT 58.668 37.500 0.00 0.00 0.00 2.40
451 452 4.121317 TCTTTGCAAGATTTGTTTGGCTG 58.879 39.130 0.00 0.00 31.20 4.85
466 467 0.107945 GGCTGCACAGGAGAACCTAG 60.108 60.000 0.50 0.00 45.94 3.02
468 469 1.825474 GCTGCACAGGAGAACCTAGTA 59.175 52.381 0.00 0.00 45.94 1.82
495 496 0.689055 TCTTGGAGTGCTCACATGCT 59.311 50.000 2.63 0.00 0.00 3.79
498 499 0.538584 TGGAGTGCTCACATGCTAGG 59.461 55.000 2.63 0.00 0.00 3.02
525 526 1.576421 GGAAGAGGCGCAACAACTG 59.424 57.895 10.83 0.00 0.00 3.16
540 541 2.609459 ACAACTGTTCGACTTCAAGCTG 59.391 45.455 0.00 0.00 0.00 4.24
543 544 0.179059 TGTTCGACTTCAAGCTGCCA 60.179 50.000 0.00 0.00 0.00 4.92
544 545 0.944386 GTTCGACTTCAAGCTGCCAA 59.056 50.000 0.00 0.00 0.00 4.52
561 562 0.325933 CAAGGCTCCATCCTGTGACA 59.674 55.000 0.00 0.00 36.38 3.58
582 583 0.101219 GGGCCGAAGACATCATTTGC 59.899 55.000 0.00 0.00 0.00 3.68
591 592 3.461061 AGACATCATTTGCGATGATCGT 58.539 40.909 16.83 12.23 44.67 3.73
663 664 2.353208 GCACTCGAGGAACAGATTGACT 60.353 50.000 18.41 0.00 0.00 3.41
669 670 2.941720 GAGGAACAGATTGACTCATGGC 59.058 50.000 0.00 0.00 0.00 4.40
690 691 2.429907 GATCAGCTCGATCCGGCG 60.430 66.667 0.00 0.00 44.25 6.46
708 709 1.063951 CGAGTTCAGTACGACGCACC 61.064 60.000 0.00 0.00 0.00 5.01
709 710 0.240411 GAGTTCAGTACGACGCACCT 59.760 55.000 0.00 0.00 0.00 4.00
735 736 2.623889 GGCGCTATCTCTTCTTGAGGTA 59.376 50.000 7.64 0.00 42.86 3.08
738 739 3.004944 CGCTATCTCTTCTTGAGGTACCC 59.995 52.174 8.74 0.32 42.86 3.69
741 742 1.356738 TCTCTTCTTGAGGTACCCCGA 59.643 52.381 8.74 0.00 42.86 5.14
747 748 1.346722 CTTGAGGTACCCCGACAACTT 59.653 52.381 8.74 0.00 35.12 2.66
750 751 2.030958 GGTACCCCGACAACTTGCG 61.031 63.158 0.00 0.00 0.00 4.85
751 752 1.301165 GTACCCCGACAACTTGCGT 60.301 57.895 0.00 0.00 0.00 5.24
813 814 4.351192 GTTTTGTCACCATCAACACTGAC 58.649 43.478 0.00 0.00 33.30 3.51
822 823 1.163420 TCAACACTGACGCGGCAATT 61.163 50.000 19.01 8.19 0.00 2.32
826 827 1.604755 ACACTGACGCGGCAATTAAAA 59.395 42.857 19.01 0.00 0.00 1.52
836 837 3.793492 GCGGCAATTAAAAGAGAAGATGC 59.207 43.478 0.00 0.00 0.00 3.91
872 873 4.247781 CGTAGCCCGGTCCTCTAA 57.752 61.111 0.00 0.00 0.00 2.10
882 883 3.958798 CCCGGTCCTCTAACTCATTTCTA 59.041 47.826 0.00 0.00 0.00 2.10
927 928 4.263243 CCTGGAGTTATGGATCCCTTCATC 60.263 50.000 9.90 2.04 34.47 2.92
928 929 3.652869 TGGAGTTATGGATCCCTTCATCC 59.347 47.826 9.90 11.87 42.68 3.51
962 963 1.890510 TGCGCGACGGAGCTATCTA 60.891 57.895 12.10 0.00 39.95 1.98
993 994 3.324268 TGAGGGGTTTTACACACGTCATA 59.676 43.478 0.00 0.00 46.55 2.15
1050 1051 1.508545 CACTCGCCATGACTCTCGT 59.491 57.895 0.00 0.00 0.00 4.18
1062 1063 1.173444 ACTCTCGTTCAGTCGTGGCT 61.173 55.000 0.00 0.00 0.00 4.75
1083 1084 5.066593 GCTCCTATCCTGTTAGAAATTGGG 58.933 45.833 0.00 0.00 0.00 4.12
1135 1137 7.543756 TGATATTCGGCATATTGTAAGATCGA 58.456 34.615 0.00 0.00 0.00 3.59
1137 1140 3.909430 TCGGCATATTGTAAGATCGACC 58.091 45.455 0.00 0.00 0.00 4.79
1188 1191 4.123497 AGCTTGCATAATAGACGTGACA 57.877 40.909 0.00 0.00 0.00 3.58
1203 1206 2.736719 CGTGACAGAAAGCTGGATCGAT 60.737 50.000 0.00 0.00 46.60 3.59
1205 1208 4.433615 GTGACAGAAAGCTGGATCGATAA 58.566 43.478 0.00 0.00 46.60 1.75
1206 1209 4.268884 GTGACAGAAAGCTGGATCGATAAC 59.731 45.833 0.00 0.00 46.60 1.89
1215 1218 3.570550 GCTGGATCGATAACACTCCTAGT 59.429 47.826 0.00 0.00 0.00 2.57
1221 1224 6.489361 GGATCGATAACACTCCTAGTTTCCTA 59.511 42.308 0.00 0.00 0.00 2.94
1254 1257 2.437359 GCAGACTGCTCGGCCAAT 60.437 61.111 20.41 0.00 40.96 3.16
1281 1284 7.677511 GCCTTTAAGCAATAAAGCTCTCACTAC 60.678 40.741 13.65 0.00 46.10 2.73
1288 1291 2.327325 AAGCTCTCACTACTTCCCCA 57.673 50.000 0.00 0.00 0.00 4.96
1289 1292 2.327325 AGCTCTCACTACTTCCCCAA 57.673 50.000 0.00 0.00 0.00 4.12
1290 1293 2.621070 AGCTCTCACTACTTCCCCAAA 58.379 47.619 0.00 0.00 0.00 3.28
1626 1634 1.153429 CCCGTCCTCCTTTTAGGCG 60.153 63.158 0.00 0.00 36.51 5.52
1642 1659 3.179433 GCGTTTGCCTTTTCCAGTC 57.821 52.632 0.00 0.00 33.98 3.51
1646 1663 2.357637 CGTTTGCCTTTTCCAGTCTTCA 59.642 45.455 0.00 0.00 0.00 3.02
1978 2046 4.201783 GCAATTATGTGGTCCTGTAACGAC 60.202 45.833 0.00 0.00 0.00 4.34
2106 2174 4.842574 TGTTATGCTGGAGTGCTTATTCA 58.157 39.130 0.00 0.00 0.00 2.57
2110 2178 4.551702 TGCTGGAGTGCTTATTCACTTA 57.448 40.909 0.00 0.00 46.40 2.24
2121 2189 9.561069 AGTGCTTATTCACTTATTATGGGTAAG 57.439 33.333 0.00 0.00 44.26 2.34
2122 2190 8.784043 GTGCTTATTCACTTATTATGGGTAAGG 58.216 37.037 0.00 0.00 34.28 2.69
2123 2191 8.499406 TGCTTATTCACTTATTATGGGTAAGGT 58.501 33.333 0.00 0.00 34.28 3.50
2124 2192 8.784043 GCTTATTCACTTATTATGGGTAAGGTG 58.216 37.037 0.00 0.00 34.28 4.00
2148 2217 3.559171 GCTGGAGTGTTGTATTCCTGGAA 60.559 47.826 12.26 12.26 36.22 3.53
2157 2226 3.670625 TGTATTCCTGGAAAAGACACGG 58.329 45.455 14.03 0.00 0.00 4.94
2165 2234 1.404035 GGAAAAGACACGGCACACTTT 59.596 47.619 0.00 0.00 34.67 2.66
2175 2244 2.223711 ACGGCACACTTTGGTCATTTTC 60.224 45.455 0.00 0.00 0.00 2.29
2176 2245 2.034558 CGGCACACTTTGGTCATTTTCT 59.965 45.455 0.00 0.00 0.00 2.52
2177 2246 3.252215 CGGCACACTTTGGTCATTTTCTA 59.748 43.478 0.00 0.00 0.00 2.10
2178 2247 4.082787 CGGCACACTTTGGTCATTTTCTAT 60.083 41.667 0.00 0.00 0.00 1.98
2179 2248 5.123186 CGGCACACTTTGGTCATTTTCTATA 59.877 40.000 0.00 0.00 0.00 1.31
2180 2249 6.555315 GGCACACTTTGGTCATTTTCTATAG 58.445 40.000 0.00 0.00 0.00 1.31
2181 2250 6.151144 GGCACACTTTGGTCATTTTCTATAGT 59.849 38.462 0.00 0.00 0.00 2.12
2182 2251 7.023575 GCACACTTTGGTCATTTTCTATAGTG 58.976 38.462 0.00 0.00 37.19 2.74
2183 2252 7.308589 GCACACTTTGGTCATTTTCTATAGTGT 60.309 37.037 0.00 0.00 42.99 3.55
2184 2253 8.567948 CACACTTTGGTCATTTTCTATAGTGTT 58.432 33.333 0.00 0.00 41.01 3.32
2185 2254 9.131791 ACACTTTGGTCATTTTCTATAGTGTTT 57.868 29.630 0.00 0.00 40.32 2.83
2186 2255 9.612620 CACTTTGGTCATTTTCTATAGTGTTTC 57.387 33.333 0.00 0.00 0.00 2.78
2187 2256 9.349713 ACTTTGGTCATTTTCTATAGTGTTTCA 57.650 29.630 0.00 0.00 0.00 2.69
2188 2257 9.831737 CTTTGGTCATTTTCTATAGTGTTTCAG 57.168 33.333 0.00 0.00 0.00 3.02
2189 2258 9.567776 TTTGGTCATTTTCTATAGTGTTTCAGA 57.432 29.630 0.00 0.00 0.00 3.27
2190 2259 9.567776 TTGGTCATTTTCTATAGTGTTTCAGAA 57.432 29.630 0.00 0.00 0.00 3.02
2191 2260 9.219603 TGGTCATTTTCTATAGTGTTTCAGAAG 57.780 33.333 0.00 0.00 0.00 2.85
2192 2261 9.436957 GGTCATTTTCTATAGTGTTTCAGAAGA 57.563 33.333 0.00 0.00 0.00 2.87
2201 2270 5.876612 AGTGTTTCAGAAGATCATTCAGC 57.123 39.130 0.00 0.00 0.00 4.26
2202 2271 5.558818 AGTGTTTCAGAAGATCATTCAGCT 58.441 37.500 0.00 0.00 0.00 4.24
2203 2272 6.002704 AGTGTTTCAGAAGATCATTCAGCTT 58.997 36.000 0.00 0.00 0.00 3.74
2204 2273 6.489361 AGTGTTTCAGAAGATCATTCAGCTTT 59.511 34.615 0.00 0.00 0.00 3.51
2205 2274 7.014038 AGTGTTTCAGAAGATCATTCAGCTTTT 59.986 33.333 0.00 0.00 0.00 2.27
2206 2275 7.650903 GTGTTTCAGAAGATCATTCAGCTTTTT 59.349 33.333 0.00 0.00 0.00 1.94
2207 2276 7.864379 TGTTTCAGAAGATCATTCAGCTTTTTC 59.136 33.333 0.00 0.00 0.00 2.29
2208 2277 6.506500 TCAGAAGATCATTCAGCTTTTTCC 57.493 37.500 0.00 0.00 0.00 3.13
2209 2278 6.005823 TCAGAAGATCATTCAGCTTTTTCCA 58.994 36.000 0.00 0.00 0.00 3.53
2210 2279 6.072286 TCAGAAGATCATTCAGCTTTTTCCAC 60.072 38.462 0.00 0.00 0.00 4.02
2211 2280 4.691860 AGATCATTCAGCTTTTTCCACG 57.308 40.909 0.00 0.00 0.00 4.94
2212 2281 4.074970 AGATCATTCAGCTTTTTCCACGT 58.925 39.130 0.00 0.00 0.00 4.49
2213 2282 5.245531 AGATCATTCAGCTTTTTCCACGTA 58.754 37.500 0.00 0.00 0.00 3.57
2214 2283 5.352569 AGATCATTCAGCTTTTTCCACGTAG 59.647 40.000 0.00 0.00 0.00 3.51
2215 2284 3.188460 TCATTCAGCTTTTTCCACGTAGC 59.812 43.478 0.00 0.00 0.00 3.58
2216 2285 2.248280 TCAGCTTTTTCCACGTAGCA 57.752 45.000 8.35 0.00 36.11 3.49
2217 2286 2.778299 TCAGCTTTTTCCACGTAGCAT 58.222 42.857 8.35 0.00 36.11 3.79
2218 2287 2.483877 TCAGCTTTTTCCACGTAGCATG 59.516 45.455 8.35 4.32 36.11 4.06
2219 2288 2.226437 CAGCTTTTTCCACGTAGCATGT 59.774 45.455 8.35 0.00 36.11 3.21
2220 2289 2.484264 AGCTTTTTCCACGTAGCATGTC 59.516 45.455 8.35 0.00 36.11 3.06
2221 2290 2.484264 GCTTTTTCCACGTAGCATGTCT 59.516 45.455 0.93 0.00 33.88 3.41
2222 2291 3.058224 GCTTTTTCCACGTAGCATGTCTT 60.058 43.478 0.93 0.00 33.88 3.01
2223 2292 4.466828 CTTTTTCCACGTAGCATGTCTTG 58.533 43.478 0.00 0.00 0.00 3.02
2224 2293 2.831685 TTCCACGTAGCATGTCTTGT 57.168 45.000 0.00 0.00 0.00 3.16
2225 2294 3.945981 TTCCACGTAGCATGTCTTGTA 57.054 42.857 0.00 0.00 0.00 2.41
2226 2295 3.945981 TCCACGTAGCATGTCTTGTAA 57.054 42.857 0.00 0.00 0.00 2.41
2227 2296 4.465632 TCCACGTAGCATGTCTTGTAAT 57.534 40.909 0.00 0.00 0.00 1.89
2228 2297 5.585820 TCCACGTAGCATGTCTTGTAATA 57.414 39.130 0.00 0.00 0.00 0.98
2229 2298 6.156748 TCCACGTAGCATGTCTTGTAATAT 57.843 37.500 0.00 0.00 0.00 1.28
2230 2299 6.578944 TCCACGTAGCATGTCTTGTAATATT 58.421 36.000 0.00 0.00 0.00 1.28
2231 2300 7.045416 TCCACGTAGCATGTCTTGTAATATTT 58.955 34.615 0.00 0.00 0.00 1.40
2232 2301 7.551262 TCCACGTAGCATGTCTTGTAATATTTT 59.449 33.333 0.00 0.00 0.00 1.82
2233 2302 8.181573 CCACGTAGCATGTCTTGTAATATTTTT 58.818 33.333 0.00 0.00 0.00 1.94
2251 2320 4.929819 TTTTACTTTGAAGAAGTGCCCC 57.070 40.909 1.89 0.00 0.00 5.80
2252 2321 3.586470 TTACTTTGAAGAAGTGCCCCA 57.414 42.857 1.89 0.00 0.00 4.96
2253 2322 1.692411 ACTTTGAAGAAGTGCCCCAC 58.308 50.000 0.00 0.00 34.10 4.61
2265 2334 4.489306 AGTGCCCCACTTTACTCTTATC 57.511 45.455 0.00 0.00 42.59 1.75
2266 2335 4.104831 AGTGCCCCACTTTACTCTTATCT 58.895 43.478 0.00 0.00 42.59 1.98
2267 2336 4.080863 AGTGCCCCACTTTACTCTTATCTG 60.081 45.833 0.00 0.00 42.59 2.90
2268 2337 3.199946 TGCCCCACTTTACTCTTATCTGG 59.800 47.826 0.00 0.00 0.00 3.86
2269 2338 3.433740 GCCCCACTTTACTCTTATCTGGG 60.434 52.174 0.00 0.00 37.24 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.935241 TGCACCATAATTTTGTTTGTATGTAAT 57.065 25.926 0.00 0.00 0.00 1.89
36 37 9.764363 TTGCACCATAATTTTGTTTGTATGTAA 57.236 25.926 0.00 0.00 0.00 2.41
37 38 9.935241 ATTGCACCATAATTTTGTTTGTATGTA 57.065 25.926 0.00 0.00 0.00 2.29
38 39 8.845413 ATTGCACCATAATTTTGTTTGTATGT 57.155 26.923 0.00 0.00 0.00 2.29
81 82 5.209240 GTGCGCAGTTACTGTTCATAAAAA 58.791 37.500 12.22 0.00 33.43 1.94
82 83 4.273724 TGTGCGCAGTTACTGTTCATAAAA 59.726 37.500 12.22 0.00 33.43 1.52
83 84 3.810386 TGTGCGCAGTTACTGTTCATAAA 59.190 39.130 12.22 1.00 33.43 1.40
84 85 3.394719 TGTGCGCAGTTACTGTTCATAA 58.605 40.909 12.22 3.10 33.43 1.90
85 86 2.993220 CTGTGCGCAGTTACTGTTCATA 59.007 45.455 19.30 9.16 37.92 2.15
86 87 1.800586 CTGTGCGCAGTTACTGTTCAT 59.199 47.619 19.30 0.00 37.92 2.57
87 88 1.217001 CTGTGCGCAGTTACTGTTCA 58.783 50.000 19.30 9.09 37.92 3.18
98 99 3.333414 GCAAAGAGACTGTGCGCA 58.667 55.556 5.66 5.66 34.87 6.09
101 102 2.478134 CACTGTAGCAAAGAGACTGTGC 59.522 50.000 5.86 5.86 44.43 4.57
102 103 3.722147 ACACTGTAGCAAAGAGACTGTG 58.278 45.455 8.99 8.99 44.18 3.66
103 104 3.639094 AGACACTGTAGCAAAGAGACTGT 59.361 43.478 0.00 0.00 0.00 3.55
104 105 3.986572 CAGACACTGTAGCAAAGAGACTG 59.013 47.826 0.00 0.00 0.00 3.51
105 106 3.639094 ACAGACACTGTAGCAAAGAGACT 59.361 43.478 2.43 0.00 43.46 3.24
106 107 3.738282 CACAGACACTGTAGCAAAGAGAC 59.262 47.826 4.08 0.00 43.43 3.36
107 108 3.636764 TCACAGACACTGTAGCAAAGAGA 59.363 43.478 4.08 0.00 43.43 3.10
108 109 3.982475 TCACAGACACTGTAGCAAAGAG 58.018 45.455 4.08 0.00 43.43 2.85
109 110 4.607293 ATCACAGACACTGTAGCAAAGA 57.393 40.909 4.08 0.00 43.43 2.52
110 111 6.815641 AGAATATCACAGACACTGTAGCAAAG 59.184 38.462 4.08 0.00 43.43 2.77
111 112 6.701340 AGAATATCACAGACACTGTAGCAAA 58.299 36.000 4.08 0.00 43.43 3.68
112 113 6.286240 AGAATATCACAGACACTGTAGCAA 57.714 37.500 4.08 0.00 43.43 3.91
113 114 5.921962 AGAATATCACAGACACTGTAGCA 57.078 39.130 4.08 0.00 43.43 3.49
114 115 7.038659 AGAAAGAATATCACAGACACTGTAGC 58.961 38.462 4.08 0.00 43.43 3.58
115 116 8.994429 AAGAAAGAATATCACAGACACTGTAG 57.006 34.615 4.08 0.74 43.43 2.74
116 117 8.585018 TGAAGAAAGAATATCACAGACACTGTA 58.415 33.333 4.08 0.00 43.43 2.74
117 118 7.445121 TGAAGAAAGAATATCACAGACACTGT 58.555 34.615 0.00 0.00 46.51 3.55
118 119 7.895975 TGAAGAAAGAATATCACAGACACTG 57.104 36.000 0.00 0.00 37.52 3.66
119 120 9.512588 AAATGAAGAAAGAATATCACAGACACT 57.487 29.630 0.00 0.00 0.00 3.55
122 123 9.070149 GCAAAATGAAGAAAGAATATCACAGAC 57.930 33.333 0.00 0.00 0.00 3.51
123 124 8.795513 TGCAAAATGAAGAAAGAATATCACAGA 58.204 29.630 0.00 0.00 0.00 3.41
124 125 8.857216 GTGCAAAATGAAGAAAGAATATCACAG 58.143 33.333 0.00 0.00 0.00 3.66
125 126 8.579006 AGTGCAAAATGAAGAAAGAATATCACA 58.421 29.630 0.00 0.00 0.00 3.58
126 127 8.857216 CAGTGCAAAATGAAGAAAGAATATCAC 58.143 33.333 0.00 0.00 0.00 3.06
127 128 8.795513 TCAGTGCAAAATGAAGAAAGAATATCA 58.204 29.630 0.00 0.00 0.00 2.15
128 129 9.070149 GTCAGTGCAAAATGAAGAAAGAATATC 57.930 33.333 0.00 0.00 0.00 1.63
129 130 8.579006 TGTCAGTGCAAAATGAAGAAAGAATAT 58.421 29.630 0.00 0.00 0.00 1.28
130 131 7.939782 TGTCAGTGCAAAATGAAGAAAGAATA 58.060 30.769 0.00 0.00 0.00 1.75
131 132 6.808829 TGTCAGTGCAAAATGAAGAAAGAAT 58.191 32.000 0.00 0.00 0.00 2.40
132 133 6.206395 TGTCAGTGCAAAATGAAGAAAGAA 57.794 33.333 0.00 0.00 0.00 2.52
133 134 5.833406 TGTCAGTGCAAAATGAAGAAAGA 57.167 34.783 0.00 0.00 0.00 2.52
134 135 6.563381 GCAATGTCAGTGCAAAATGAAGAAAG 60.563 38.462 19.81 0.00 41.80 2.62
135 136 5.234757 GCAATGTCAGTGCAAAATGAAGAAA 59.765 36.000 19.81 0.00 41.80 2.52
136 137 4.746115 GCAATGTCAGTGCAAAATGAAGAA 59.254 37.500 19.81 0.00 41.80 2.52
137 138 4.300803 GCAATGTCAGTGCAAAATGAAGA 58.699 39.130 19.81 0.00 41.80 2.87
138 139 4.640805 GCAATGTCAGTGCAAAATGAAG 57.359 40.909 19.81 0.00 41.80 3.02
147 148 2.549754 AGTTACAGTGCAATGTCAGTGC 59.450 45.455 24.81 18.07 40.20 4.40
148 149 4.609113 CGAAGTTACAGTGCAATGTCAGTG 60.609 45.833 24.81 6.43 41.81 3.66
149 150 3.494626 CGAAGTTACAGTGCAATGTCAGT 59.505 43.478 24.81 13.28 34.56 3.41
150 151 3.494626 ACGAAGTTACAGTGCAATGTCAG 59.505 43.478 24.81 11.72 37.78 3.51
151 152 3.247411 CACGAAGTTACAGTGCAATGTCA 59.753 43.478 24.81 10.54 41.61 3.58
152 153 3.493129 TCACGAAGTTACAGTGCAATGTC 59.507 43.478 24.81 10.60 41.61 3.06
153 154 3.247648 GTCACGAAGTTACAGTGCAATGT 59.752 43.478 24.48 24.48 41.61 2.71
154 155 3.247411 TGTCACGAAGTTACAGTGCAATG 59.753 43.478 13.51 13.51 39.94 2.82
155 156 3.462982 TGTCACGAAGTTACAGTGCAAT 58.537 40.909 0.00 0.00 39.94 3.56
156 157 2.894902 TGTCACGAAGTTACAGTGCAA 58.105 42.857 0.00 0.00 39.94 4.08
157 158 2.588027 TGTCACGAAGTTACAGTGCA 57.412 45.000 0.00 0.00 39.94 4.57
163 164 7.591006 TCATAAAAGGATGTCACGAAGTTAC 57.409 36.000 0.00 0.00 41.61 2.50
164 165 8.196802 CATCATAAAAGGATGTCACGAAGTTA 57.803 34.615 0.00 0.00 36.94 2.24
165 166 7.076842 CATCATAAAAGGATGTCACGAAGTT 57.923 36.000 0.00 0.00 36.94 2.66
166 167 6.668541 CATCATAAAAGGATGTCACGAAGT 57.331 37.500 0.00 0.00 38.56 3.01
175 176 7.332926 CGGATCCTCTAACATCATAAAAGGATG 59.667 40.741 10.75 0.00 45.93 3.51
176 177 7.016661 ACGGATCCTCTAACATCATAAAAGGAT 59.983 37.037 10.75 0.77 43.16 3.24
177 178 6.326583 ACGGATCCTCTAACATCATAAAAGGA 59.673 38.462 10.75 0.00 36.00 3.36
178 179 6.525629 ACGGATCCTCTAACATCATAAAAGG 58.474 40.000 10.75 0.00 0.00 3.11
179 180 8.979574 GTTACGGATCCTCTAACATCATAAAAG 58.020 37.037 18.07 0.00 0.00 2.27
180 181 7.929785 GGTTACGGATCCTCTAACATCATAAAA 59.070 37.037 21.83 0.00 0.00 1.52
181 182 7.439381 GGTTACGGATCCTCTAACATCATAAA 58.561 38.462 21.83 0.00 0.00 1.40
182 183 6.014840 GGGTTACGGATCCTCTAACATCATAA 60.015 42.308 21.83 2.21 0.00 1.90
183 184 5.479375 GGGTTACGGATCCTCTAACATCATA 59.521 44.000 21.83 0.00 0.00 2.15
184 185 4.283722 GGGTTACGGATCCTCTAACATCAT 59.716 45.833 21.83 0.00 0.00 2.45
185 186 3.640029 GGGTTACGGATCCTCTAACATCA 59.360 47.826 21.83 0.00 0.00 3.07
186 187 3.896272 AGGGTTACGGATCCTCTAACATC 59.104 47.826 21.83 15.89 0.00 3.06
187 188 3.896272 GAGGGTTACGGATCCTCTAACAT 59.104 47.826 21.83 14.09 42.70 2.71
188 189 3.294214 GAGGGTTACGGATCCTCTAACA 58.706 50.000 21.83 0.00 42.70 2.41
189 190 3.294214 TGAGGGTTACGGATCCTCTAAC 58.706 50.000 17.87 14.07 45.36 2.34
190 191 3.675348 TGAGGGTTACGGATCCTCTAA 57.325 47.619 17.87 2.45 45.36 2.10
191 192 3.675348 TTGAGGGTTACGGATCCTCTA 57.325 47.619 17.87 10.16 45.36 2.43
192 193 2.500504 GTTTGAGGGTTACGGATCCTCT 59.499 50.000 17.87 4.16 45.36 3.69
193 194 2.235402 TGTTTGAGGGTTACGGATCCTC 59.765 50.000 10.75 12.13 45.36 3.71
194 195 2.027469 GTGTTTGAGGGTTACGGATCCT 60.027 50.000 10.75 0.00 0.00 3.24
195 196 2.027469 AGTGTTTGAGGGTTACGGATCC 60.027 50.000 0.00 0.00 0.00 3.36
196 197 3.329929 AGTGTTTGAGGGTTACGGATC 57.670 47.619 0.00 0.00 0.00 3.36
197 198 3.836562 ACTAGTGTTTGAGGGTTACGGAT 59.163 43.478 0.00 0.00 0.00 4.18
198 199 3.233507 ACTAGTGTTTGAGGGTTACGGA 58.766 45.455 0.00 0.00 0.00 4.69
199 200 3.672767 ACTAGTGTTTGAGGGTTACGG 57.327 47.619 0.00 0.00 0.00 4.02
200 201 4.161333 CGTACTAGTGTTTGAGGGTTACG 58.839 47.826 5.39 0.00 0.00 3.18
201 202 5.126396 ACGTACTAGTGTTTGAGGGTTAC 57.874 43.478 5.39 0.00 0.00 2.50
202 203 4.218417 GGACGTACTAGTGTTTGAGGGTTA 59.782 45.833 5.39 0.00 0.00 2.85
203 204 3.006217 GGACGTACTAGTGTTTGAGGGTT 59.994 47.826 5.39 0.00 0.00 4.11
204 205 2.560105 GGACGTACTAGTGTTTGAGGGT 59.440 50.000 5.39 0.00 0.00 4.34
205 206 2.094338 GGGACGTACTAGTGTTTGAGGG 60.094 54.545 5.39 0.00 0.00 4.30
206 207 2.824341 AGGGACGTACTAGTGTTTGAGG 59.176 50.000 5.39 0.00 0.00 3.86
207 208 3.119566 GGAGGGACGTACTAGTGTTTGAG 60.120 52.174 5.39 0.00 0.00 3.02
208 209 2.821969 GGAGGGACGTACTAGTGTTTGA 59.178 50.000 5.39 0.00 0.00 2.69
209 210 2.415090 CGGAGGGACGTACTAGTGTTTG 60.415 54.545 5.39 0.00 0.00 2.93
210 211 1.815003 CGGAGGGACGTACTAGTGTTT 59.185 52.381 5.39 0.00 0.00 2.83
211 212 1.003580 TCGGAGGGACGTACTAGTGTT 59.996 52.381 5.39 0.00 34.94 3.32
212 213 0.615331 TCGGAGGGACGTACTAGTGT 59.385 55.000 5.39 0.00 34.94 3.55
213 214 1.297664 CTCGGAGGGACGTACTAGTG 58.702 60.000 5.39 0.00 34.94 2.74
214 215 0.463474 GCTCGGAGGGACGTACTAGT 60.463 60.000 7.20 0.00 34.94 2.57
215 216 0.179051 AGCTCGGAGGGACGTACTAG 60.179 60.000 7.20 0.00 34.94 2.57
216 217 0.179062 GAGCTCGGAGGGACGTACTA 60.179 60.000 7.20 0.00 34.94 1.82
217 218 1.451747 GAGCTCGGAGGGACGTACT 60.452 63.158 7.20 0.00 34.94 2.73
218 219 0.179062 TAGAGCTCGGAGGGACGTAC 60.179 60.000 8.37 0.00 34.94 3.67
219 220 0.106335 CTAGAGCTCGGAGGGACGTA 59.894 60.000 8.37 0.00 34.94 3.57
220 221 1.153127 CTAGAGCTCGGAGGGACGT 60.153 63.158 8.37 0.00 34.94 4.34
221 222 1.153127 ACTAGAGCTCGGAGGGACG 60.153 63.158 19.16 2.91 0.00 4.79
222 223 0.107116 TCACTAGAGCTCGGAGGGAC 60.107 60.000 16.95 0.00 0.00 4.46
223 224 0.107116 GTCACTAGAGCTCGGAGGGA 60.107 60.000 16.95 16.95 0.00 4.20
224 225 0.106918 AGTCACTAGAGCTCGGAGGG 60.107 60.000 19.16 16.37 0.00 4.30
225 226 1.305201 GAGTCACTAGAGCTCGGAGG 58.695 60.000 19.16 9.36 0.00 4.30
226 227 0.934496 CGAGTCACTAGAGCTCGGAG 59.066 60.000 18.74 12.33 45.60 4.63
227 228 3.067074 CGAGTCACTAGAGCTCGGA 57.933 57.895 18.74 2.17 45.60 4.55
292 293 3.395639 TCCACATCCGTTGTTTGTCTAC 58.604 45.455 0.00 0.00 36.00 2.59
293 294 3.755112 TCCACATCCGTTGTTTGTCTA 57.245 42.857 0.00 0.00 36.00 2.59
297 298 3.564511 GTCATTCCACATCCGTTGTTTG 58.435 45.455 0.00 0.00 36.00 2.93
321 322 2.224257 GGGCAAAACATTCAGCTTCCAA 60.224 45.455 0.00 0.00 0.00 3.53
327 328 1.070601 ACCTTGGGCAAAACATTCAGC 59.929 47.619 0.00 0.00 0.00 4.26
328 329 2.758009 CACCTTGGGCAAAACATTCAG 58.242 47.619 0.00 0.00 0.00 3.02
351 352 1.202698 AGCACTCGCCAGAAGAAAACT 60.203 47.619 0.00 0.00 39.83 2.66
354 355 1.230635 GCAGCACTCGCCAGAAGAAA 61.231 55.000 0.00 0.00 39.83 2.52
382 383 5.334957 GCATGAGAATGCATTCATCTGGTAG 60.335 44.000 34.59 18.88 46.25 3.18
432 433 2.211806 GCAGCCAAACAAATCTTGCAA 58.788 42.857 0.00 0.00 0.00 4.08
445 446 1.228245 GGTTCTCCTGTGCAGCCAA 60.228 57.895 0.00 0.00 0.00 4.52
451 452 3.786635 CATGTACTAGGTTCTCCTGTGC 58.213 50.000 0.00 0.00 44.81 4.57
495 496 1.271926 GCCTCTTCCCAAAACTGCCTA 60.272 52.381 0.00 0.00 0.00 3.93
498 499 1.581447 CGCCTCTTCCCAAAACTGC 59.419 57.895 0.00 0.00 0.00 4.40
525 526 0.944386 TTGGCAGCTTGAAGTCGAAC 59.056 50.000 0.00 0.00 0.00 3.95
540 541 1.751927 CACAGGATGGAGCCTTGGC 60.752 63.158 2.97 2.97 43.62 4.52
543 544 1.064906 CATGTCACAGGATGGAGCCTT 60.065 52.381 0.00 0.00 43.62 4.35
544 545 0.545171 CATGTCACAGGATGGAGCCT 59.455 55.000 0.00 0.00 43.62 4.58
561 562 2.026641 CAAATGATGTCTTCGGCCCAT 58.973 47.619 0.00 0.00 0.00 4.00
582 583 3.551046 CCCTGGAAGTAAGACGATCATCG 60.551 52.174 5.22 5.22 46.93 3.84
591 592 1.848652 CTCGGTCCCTGGAAGTAAGA 58.151 55.000 0.00 0.00 0.00 2.10
619 620 2.806945 ATGGACCACATGACCGAAAT 57.193 45.000 0.00 0.00 38.70 2.17
663 664 1.744639 GAGCTGATCCTCGCCATGA 59.255 57.895 0.00 0.00 0.00 3.07
690 691 0.240411 AGGTGCGTCGTACTGAACTC 59.760 55.000 13.25 0.00 0.00 3.01
696 697 2.282674 TCCCAGGTGCGTCGTACT 60.283 61.111 13.25 0.00 0.00 2.73
708 709 0.316841 GAAGAGATAGCGCCTCCCAG 59.683 60.000 2.29 0.00 0.00 4.45
709 710 0.105964 AGAAGAGATAGCGCCTCCCA 60.106 55.000 2.29 0.00 0.00 4.37
747 748 1.677300 CCCAGGCATAACCAACGCA 60.677 57.895 0.00 0.00 43.14 5.24
780 781 1.602605 GACAAAACCTGGGTCGGGG 60.603 63.158 0.00 0.00 33.40 5.73
813 814 3.740044 TCTTCTCTTTTAATTGCCGCG 57.260 42.857 0.00 0.00 0.00 6.46
822 823 5.014123 TCCTCCTTTGGCATCTTCTCTTTTA 59.986 40.000 0.00 0.00 0.00 1.52
826 827 2.504996 CTCCTCCTTTGGCATCTTCTCT 59.495 50.000 0.00 0.00 0.00 3.10
836 837 2.679716 CCCCTGCTCCTCCTTTGG 59.320 66.667 0.00 0.00 0.00 3.28
864 865 5.361285 TGCTCCTAGAAATGAGTTAGAGGAC 59.639 44.000 0.00 0.00 30.44 3.85
872 873 3.181456 GCTCCATGCTCCTAGAAATGAGT 60.181 47.826 0.00 0.00 38.95 3.41
882 883 0.333993 ATGGTTTGCTCCATGCTCCT 59.666 50.000 7.60 0.00 45.26 3.69
914 915 1.696965 CCTCTGGGATGAAGGGATCCA 60.697 57.143 15.23 0.00 43.51 3.41
927 928 3.790437 ACTGCCATCGCCTCTGGG 61.790 66.667 0.00 0.00 34.16 4.45
928 929 2.513204 CACTGCCATCGCCTCTGG 60.513 66.667 0.00 0.00 36.81 3.86
956 957 2.546795 CCCCTCAAGCTTGCGTAGATAG 60.547 54.545 21.99 11.42 0.00 2.08
962 963 0.755327 AAAACCCCTCAAGCTTGCGT 60.755 50.000 21.99 11.39 0.00 5.24
967 968 2.583143 GTGTGTAAAACCCCTCAAGCT 58.417 47.619 0.00 0.00 0.00 3.74
993 994 1.326213 CCGAGCAGTCCATCTCCACT 61.326 60.000 0.00 0.00 0.00 4.00
1050 1051 1.112113 GGATAGGAGCCACGACTGAA 58.888 55.000 0.00 0.00 0.00 3.02
1062 1063 5.293643 TCCCCAATTTCTAACAGGATAGGA 58.706 41.667 0.00 0.00 0.00 2.94
1119 1121 4.084537 CCGTTGGTCGATCTTACAATATGC 60.085 45.833 0.00 0.00 42.86 3.14
1135 1137 1.204146 ATATGAGCAGGACCGTTGGT 58.796 50.000 0.00 0.00 39.44 3.67
1137 1140 3.009723 ACAAATATGAGCAGGACCGTTG 58.990 45.455 0.00 0.00 0.00 4.10
1175 1178 4.461431 TCCAGCTTTCTGTCACGTCTATTA 59.539 41.667 0.00 0.00 38.66 0.98
1179 1182 1.040646 TCCAGCTTTCTGTCACGTCT 58.959 50.000 0.00 0.00 38.66 4.18
1188 1191 4.442192 GGAGTGTTATCGATCCAGCTTTCT 60.442 45.833 0.00 0.00 0.00 2.52
1203 1206 9.186837 CTACTGATTAGGAAACTAGGAGTGTTA 57.813 37.037 0.00 0.00 45.45 2.41
1205 1208 6.097129 GCTACTGATTAGGAAACTAGGAGTGT 59.903 42.308 0.00 0.00 45.45 3.55
1206 1209 6.461788 GGCTACTGATTAGGAAACTAGGAGTG 60.462 46.154 0.00 0.00 45.45 3.51
1215 1218 4.705023 GCCAAAAGGCTACTGATTAGGAAA 59.295 41.667 0.00 0.00 0.00 3.13
1221 1224 3.084786 GTCTGCCAAAAGGCTACTGATT 58.915 45.455 8.11 0.00 35.66 2.57
1251 1254 6.335777 AGAGCTTTATTGCTTAAAGGCATTG 58.664 36.000 16.43 0.00 44.69 2.82
1254 1257 5.009631 TGAGAGCTTTATTGCTTAAAGGCA 58.990 37.500 16.43 0.00 44.69 4.75
1257 1260 8.485976 AGTAGTGAGAGCTTTATTGCTTAAAG 57.514 34.615 12.61 12.61 46.45 1.85
1518 1521 3.449018 CCATCGGGATCTATCTACCAAGG 59.551 52.174 0.00 0.00 35.59 3.61
1626 1634 3.381590 AGTGAAGACTGGAAAAGGCAAAC 59.618 43.478 0.00 0.00 35.71 2.93
1646 1663 3.726607 CAGAAAAGTCAGTCAGCAGAGT 58.273 45.455 0.00 0.00 0.00 3.24
1746 1779 1.664873 GGGGACAAGTAATCCGAAGC 58.335 55.000 0.00 0.00 37.08 3.86
1978 2046 1.446907 AGAATGACTTGCTCCAAGCG 58.553 50.000 4.96 0.00 46.26 4.68
2049 2117 8.515695 TGAACAAAATGCATCTAGAGATTCAT 57.484 30.769 0.00 0.00 39.47 2.57
2070 2138 5.634859 CCAGCATAACAAAAGGTGAATGAAC 59.365 40.000 0.00 0.00 32.85 3.18
2106 2174 5.437060 CAGCACACCTTACCCATAATAAGT 58.563 41.667 0.00 0.00 0.00 2.24
2110 2178 2.849943 TCCAGCACACCTTACCCATAAT 59.150 45.455 0.00 0.00 0.00 1.28
2121 2189 2.185004 ATACAACACTCCAGCACACC 57.815 50.000 0.00 0.00 0.00 4.16
2122 2190 2.484264 GGAATACAACACTCCAGCACAC 59.516 50.000 0.00 0.00 0.00 3.82
2123 2191 2.371841 AGGAATACAACACTCCAGCACA 59.628 45.455 0.00 0.00 0.00 4.57
2124 2192 2.744202 CAGGAATACAACACTCCAGCAC 59.256 50.000 0.00 0.00 0.00 4.40
2148 2217 0.738389 CCAAAGTGTGCCGTGTCTTT 59.262 50.000 0.00 0.00 0.00 2.52
2157 2226 7.023575 CACTATAGAAAATGACCAAAGTGTGC 58.976 38.462 6.78 0.00 0.00 4.57
2165 2234 9.219603 CTTCTGAAACACTATAGAAAATGACCA 57.780 33.333 6.78 0.00 0.00 4.02
2175 2244 8.763356 GCTGAATGATCTTCTGAAACACTATAG 58.237 37.037 0.00 0.00 0.00 1.31
2176 2245 8.481314 AGCTGAATGATCTTCTGAAACACTATA 58.519 33.333 12.59 0.00 0.00 1.31
2177 2246 7.337167 AGCTGAATGATCTTCTGAAACACTAT 58.663 34.615 12.59 0.00 0.00 2.12
2178 2247 6.705302 AGCTGAATGATCTTCTGAAACACTA 58.295 36.000 12.59 0.00 0.00 2.74
2179 2248 5.558818 AGCTGAATGATCTTCTGAAACACT 58.441 37.500 12.59 2.17 0.00 3.55
2180 2249 5.876612 AGCTGAATGATCTTCTGAAACAC 57.123 39.130 12.59 0.00 0.00 3.32
2181 2250 6.889301 AAAGCTGAATGATCTTCTGAAACA 57.111 33.333 12.59 0.00 0.00 2.83
2182 2251 7.328005 GGAAAAAGCTGAATGATCTTCTGAAAC 59.672 37.037 12.59 0.00 0.00 2.78
2183 2252 7.014518 TGGAAAAAGCTGAATGATCTTCTGAAA 59.985 33.333 12.59 0.00 0.00 2.69
2184 2253 6.491062 TGGAAAAAGCTGAATGATCTTCTGAA 59.509 34.615 12.59 0.00 0.00 3.02
2185 2254 6.005823 TGGAAAAAGCTGAATGATCTTCTGA 58.994 36.000 12.59 0.00 0.00 3.27
2186 2255 6.091437 GTGGAAAAAGCTGAATGATCTTCTG 58.909 40.000 0.00 1.46 0.00 3.02
2187 2256 5.106396 CGTGGAAAAAGCTGAATGATCTTCT 60.106 40.000 0.00 0.00 0.00 2.85
2188 2257 5.091431 CGTGGAAAAAGCTGAATGATCTTC 58.909 41.667 0.00 0.00 0.00 2.87
2189 2258 4.520492 ACGTGGAAAAAGCTGAATGATCTT 59.480 37.500 0.00 0.00 0.00 2.40
2190 2259 4.074970 ACGTGGAAAAAGCTGAATGATCT 58.925 39.130 0.00 0.00 0.00 2.75
2191 2260 4.425577 ACGTGGAAAAAGCTGAATGATC 57.574 40.909 0.00 0.00 0.00 2.92
2192 2261 4.142600 GCTACGTGGAAAAAGCTGAATGAT 60.143 41.667 1.81 0.00 32.18 2.45
2193 2262 3.188460 GCTACGTGGAAAAAGCTGAATGA 59.812 43.478 1.81 0.00 32.18 2.57
2194 2263 3.058293 TGCTACGTGGAAAAAGCTGAATG 60.058 43.478 1.81 0.00 35.95 2.67
2195 2264 3.146066 TGCTACGTGGAAAAAGCTGAAT 58.854 40.909 1.81 0.00 35.95 2.57
2196 2265 2.566913 TGCTACGTGGAAAAAGCTGAA 58.433 42.857 1.81 0.00 35.95 3.02
2197 2266 2.248280 TGCTACGTGGAAAAAGCTGA 57.752 45.000 1.81 0.00 35.95 4.26
2198 2267 2.226437 ACATGCTACGTGGAAAAAGCTG 59.774 45.455 1.81 3.72 35.95 4.24
2199 2268 2.484264 GACATGCTACGTGGAAAAAGCT 59.516 45.455 1.81 0.00 35.95 3.74
2200 2269 2.484264 AGACATGCTACGTGGAAAAAGC 59.516 45.455 1.81 0.02 35.51 3.51
2201 2270 4.024048 ACAAGACATGCTACGTGGAAAAAG 60.024 41.667 1.81 0.00 0.00 2.27
2202 2271 3.880490 ACAAGACATGCTACGTGGAAAAA 59.120 39.130 1.81 0.00 0.00 1.94
2203 2272 3.472652 ACAAGACATGCTACGTGGAAAA 58.527 40.909 1.81 0.00 0.00 2.29
2204 2273 3.120321 ACAAGACATGCTACGTGGAAA 57.880 42.857 1.81 0.00 0.00 3.13
2205 2274 2.831685 ACAAGACATGCTACGTGGAA 57.168 45.000 1.81 0.00 0.00 3.53
2206 2275 3.945981 TTACAAGACATGCTACGTGGA 57.054 42.857 1.81 0.00 0.00 4.02
2207 2276 6.844696 AATATTACAAGACATGCTACGTGG 57.155 37.500 0.00 0.00 0.00 4.94
2225 2294 8.094548 GGGGCACTTCTTCAAAGTAAAAATATT 58.905 33.333 0.00 0.00 0.00 1.28
2226 2295 7.234577 TGGGGCACTTCTTCAAAGTAAAAATAT 59.765 33.333 0.00 0.00 0.00 1.28
2227 2296 6.551601 TGGGGCACTTCTTCAAAGTAAAAATA 59.448 34.615 0.00 0.00 0.00 1.40
2228 2297 5.365314 TGGGGCACTTCTTCAAAGTAAAAAT 59.635 36.000 0.00 0.00 0.00 1.82
2229 2298 4.712337 TGGGGCACTTCTTCAAAGTAAAAA 59.288 37.500 0.00 0.00 0.00 1.94
2230 2299 4.098807 GTGGGGCACTTCTTCAAAGTAAAA 59.901 41.667 0.00 0.00 0.00 1.52
2231 2300 3.634910 GTGGGGCACTTCTTCAAAGTAAA 59.365 43.478 0.00 0.00 0.00 2.01
2232 2301 3.117663 AGTGGGGCACTTCTTCAAAGTAA 60.118 43.478 0.00 0.00 42.59 2.24
2233 2302 2.441750 AGTGGGGCACTTCTTCAAAGTA 59.558 45.455 0.00 0.00 42.59 2.24
2234 2303 1.215423 AGTGGGGCACTTCTTCAAAGT 59.785 47.619 0.00 0.00 42.59 2.66
2235 2304 1.986882 AGTGGGGCACTTCTTCAAAG 58.013 50.000 0.00 0.00 42.59 2.77
2245 2314 4.192317 CAGATAAGAGTAAAGTGGGGCAC 58.808 47.826 0.00 0.00 34.10 5.01
2246 2315 3.199946 CCAGATAAGAGTAAAGTGGGGCA 59.800 47.826 0.00 0.00 0.00 5.36
2247 2316 3.433740 CCCAGATAAGAGTAAAGTGGGGC 60.434 52.174 0.00 0.00 39.69 5.80
2248 2317 4.423625 CCCAGATAAGAGTAAAGTGGGG 57.576 50.000 0.00 0.00 39.69 4.96


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

AutoCloner maintained by Alex Coulton.