Multiple sequence alignment - TraesCS5B01G067500

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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 TraesCS5B01G067500 chr5B 100.000 3073 0 0 1 3073 75339403 75336331 0.000000e+00 5675.0
1 TraesCS5B01G067500 chr5B 99.612 2580 10 0 494 3073 75743698 75741119 0.000000e+00 4710.0
2 TraesCS5B01G067500 chr5B 91.111 180 13 3 1409 1585 75744125 75743946 1.100000e-59 241.0
3 TraesCS5B01G067500 chr5B 88.235 51 4 2 2428 2476 25255102 25255152 3.310000e-05 60.2
4 TraesCS5B01G067500 chr5D 91.018 1002 68 10 1400 2393 70483597 70482610 0.000000e+00 1332.0
5 TraesCS5B01G067500 chr5D 93.878 49 3 0 3024 3072 70417098 70417050 1.180000e-09 75.0
6 TraesCS5B01G067500 chr5A 91.556 675 39 7 1374 2046 60330982 60330324 0.000000e+00 915.0
7 TraesCS5B01G067500 chr5A 90.489 368 32 3 2027 2393 60315639 60315274 1.660000e-132 483.0
8 TraesCS5B01G067500 chr5A 90.698 86 8 0 1202 1287 60331080 60330995 6.960000e-22 115.0
9 TraesCS5B01G067500 chr1B 93.709 302 15 4 2592 2892 23246510 23246212 1.680000e-122 449.0
10 TraesCS5B01G067500 chr6B 93.421 304 17 3 2592 2894 136158495 136158796 6.040000e-122 448.0
11 TraesCS5B01G067500 chr6B 84.375 64 8 2 2415 2476 629021192 629021129 9.200000e-06 62.1
12 TraesCS5B01G067500 chr2B 93.960 298 13 5 2598 2893 193570550 193570844 2.170000e-121 446.0
13 TraesCS5B01G067500 chr4D 93.092 304 15 5 2594 2894 440510043 440510343 1.010000e-119 440.0
14 TraesCS5B01G067500 chr7B 92.359 301 20 3 2598 2897 745278797 745278499 2.830000e-115 425.0
15 TraesCS5B01G067500 chr7B 86.282 277 24 9 238 512 640375493 640375229 3.880000e-74 289.0
16 TraesCS5B01G067500 chr7B 86.957 253 27 5 349 600 618327616 618327369 2.330000e-71 279.0
17 TraesCS5B01G067500 chr7B 86.719 256 28 5 346 600 618768352 618768602 2.330000e-71 279.0
18 TraesCS5B01G067500 chr7A 92.282 298 16 6 2601 2894 27741509 27741215 1.700000e-112 416.0
19 TraesCS5B01G067500 chr7A 85.372 376 37 13 229 597 669394208 669394572 1.040000e-99 374.0
20 TraesCS5B01G067500 chr2D 92.000 300 17 5 2598 2894 501303674 501303969 6.130000e-112 414.0
21 TraesCS5B01G067500 chr6A 91.362 301 19 7 2598 2894 392126520 392126817 3.690000e-109 405.0
22 TraesCS5B01G067500 chr6A 88.235 51 4 2 2428 2476 540016488 540016438 3.310000e-05 60.2
23 TraesCS5B01G067500 chr6A 88.235 51 4 2 2428 2476 562503112 562503062 3.310000e-05 60.2
24 TraesCS5B01G067500 chrUn 85.791 373 35 13 229 596 352242836 352243195 2.240000e-101 379.0
25 TraesCS5B01G067500 chrUn 86.275 51 5 2 2428 2476 105564878 105564928 2.000000e-03 54.7
26 TraesCS5B01G067500 chr7D 88.235 51 4 2 2428 2476 26518803 26518853 3.310000e-05 60.2
27 TraesCS5B01G067500 chr3A 88.235 51 4 2 2428 2476 99288362 99288412 3.310000e-05 60.2
28 TraesCS5B01G067500 chr2A 88.235 51 4 2 2428 2476 399652678 399652728 3.310000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G067500 chr5B 75336331 75339403 3072 True 5675.0 5675 100.0000 1 3073 1 chr5B.!!$R1 3072
1 TraesCS5B01G067500 chr5B 75741119 75744125 3006 True 2475.5 4710 95.3615 494 3073 2 chr5B.!!$R2 2579
2 TraesCS5B01G067500 chr5D 70482610 70483597 987 True 1332.0 1332 91.0180 1400 2393 1 chr5D.!!$R2 993
3 TraesCS5B01G067500 chr5A 60330324 60331080 756 True 515.0 915 91.1270 1202 2046 2 chr5A.!!$R2 844

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
234 235 0.113972 TGTTTCCATGTCCCATGGCA 59.886 50.0 16.67 5.03 39.01 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2866 2880 5.52887 CCTGTTTGGTTCCAAATAAGTCAC 58.471 41.667 18.11 6.79 38.07 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.071471 AGGTGGTGGTGCTTCTTCG 59.929 57.895 0.00 0.00 0.00 3.79
21 22 3.056328 GGTGGTGCTTCTTCGCCC 61.056 66.667 0.00 0.00 35.81 6.13
22 23 2.032681 GTGGTGCTTCTTCGCCCT 59.967 61.111 0.00 0.00 35.81 5.19
23 24 1.295423 GTGGTGCTTCTTCGCCCTA 59.705 57.895 0.00 0.00 35.81 3.53
24 25 0.741221 GTGGTGCTTCTTCGCCCTAG 60.741 60.000 0.00 0.00 35.81 3.02
25 26 0.902984 TGGTGCTTCTTCGCCCTAGA 60.903 55.000 0.00 0.00 35.81 2.43
27 28 1.687123 GGTGCTTCTTCGCCCTAGATA 59.313 52.381 0.00 0.00 0.00 1.98
28 29 2.288518 GGTGCTTCTTCGCCCTAGATAG 60.289 54.545 0.00 0.00 0.00 2.08
29 30 2.362717 GTGCTTCTTCGCCCTAGATAGT 59.637 50.000 0.00 0.00 0.00 2.12
30 31 2.623889 TGCTTCTTCGCCCTAGATAGTC 59.376 50.000 0.00 0.00 0.00 2.59
31 32 2.888414 GCTTCTTCGCCCTAGATAGTCT 59.112 50.000 0.00 0.00 0.00 3.24
33 34 3.579534 TCTTCGCCCTAGATAGTCTGT 57.420 47.619 0.00 0.00 0.00 3.41
34 35 4.701651 TCTTCGCCCTAGATAGTCTGTA 57.298 45.455 0.00 0.00 0.00 2.74
35 36 5.244189 TCTTCGCCCTAGATAGTCTGTAT 57.756 43.478 0.00 0.00 0.00 2.29
36 37 5.632118 TCTTCGCCCTAGATAGTCTGTATT 58.368 41.667 0.00 0.00 0.00 1.89
37 38 6.776744 TCTTCGCCCTAGATAGTCTGTATTA 58.223 40.000 0.00 0.00 0.00 0.98
41 42 5.587043 CGCCCTAGATAGTCTGTATTAGAGG 59.413 48.000 0.00 0.00 35.70 3.69
43 44 6.376018 GCCCTAGATAGTCTGTATTAGAGGTG 59.624 46.154 0.00 0.00 35.70 4.00
44 45 7.691213 CCCTAGATAGTCTGTATTAGAGGTGA 58.309 42.308 0.00 0.00 35.70 4.02
45 46 8.333235 CCCTAGATAGTCTGTATTAGAGGTGAT 58.667 40.741 0.00 0.00 35.70 3.06
46 47 9.391006 CCTAGATAGTCTGTATTAGAGGTGATC 57.609 40.741 0.00 0.00 35.70 2.92
47 48 9.952030 CTAGATAGTCTGTATTAGAGGTGATCA 57.048 37.037 0.00 0.00 35.70 2.92
48 49 8.630054 AGATAGTCTGTATTAGAGGTGATCAC 57.370 38.462 17.91 17.91 35.70 3.06
49 50 8.221251 AGATAGTCTGTATTAGAGGTGATCACA 58.779 37.037 26.47 6.73 35.70 3.58
51 52 5.596361 AGTCTGTATTAGAGGTGATCACAGG 59.404 44.000 26.47 4.74 35.70 4.00
52 53 5.361285 GTCTGTATTAGAGGTGATCACAGGT 59.639 44.000 26.47 10.99 35.70 4.00
55 56 7.785028 TCTGTATTAGAGGTGATCACAGGTAAT 59.215 37.037 26.47 22.85 34.19 1.89
56 57 9.078990 CTGTATTAGAGGTGATCACAGGTAATA 57.921 37.037 26.47 22.01 0.00 0.98
57 58 9.601810 TGTATTAGAGGTGATCACAGGTAATAT 57.398 33.333 26.47 12.61 0.00 1.28
62 63 8.497910 AGAGGTGATCACAGGTAATATATTGT 57.502 34.615 26.47 0.00 0.00 2.71
63 64 8.589338 AGAGGTGATCACAGGTAATATATTGTC 58.411 37.037 26.47 4.04 0.00 3.18
64 65 8.262601 AGGTGATCACAGGTAATATATTGTCA 57.737 34.615 26.47 0.00 0.00 3.58
66 67 9.507329 GGTGATCACAGGTAATATATTGTCAAT 57.493 33.333 26.47 3.06 0.00 2.57
73 74 7.944000 ACAGGTAATATATTGTCAATCATGGCA 59.056 33.333 8.28 0.00 40.01 4.92
74 75 8.963725 CAGGTAATATATTGTCAATCATGGCAT 58.036 33.333 8.28 0.00 41.66 4.40
124 125 5.842907 AGAACTTATCCAACAAAGTTTGCC 58.157 37.500 15.59 0.00 43.97 4.52
126 127 5.806654 ACTTATCCAACAAAGTTTGCCAT 57.193 34.783 15.59 5.20 32.00 4.40
129 130 1.202627 TCCAACAAAGTTTGCCATGGC 60.203 47.619 30.54 30.54 42.35 4.40
130 131 1.228533 CAACAAAGTTTGCCATGGCC 58.771 50.000 33.44 18.48 41.09 5.36
131 132 0.835941 AACAAAGTTTGCCATGGCCA 59.164 45.000 33.44 21.36 41.09 5.36
132 133 0.835941 ACAAAGTTTGCCATGGCCAA 59.164 45.000 33.44 26.17 41.09 4.52
134 135 1.807742 CAAAGTTTGCCATGGCCAATG 59.192 47.619 33.44 19.43 41.09 2.82
147 148 6.159299 CATGGCCAATGGTAAATATTGTCA 57.841 37.500 10.96 0.00 34.51 3.58
148 149 6.761312 CATGGCCAATGGTAAATATTGTCAT 58.239 36.000 10.96 0.00 34.51 3.06
150 151 4.990426 GGCCAATGGTAAATATTGTCATGC 59.010 41.667 0.00 0.00 34.51 4.06
151 152 5.453057 GGCCAATGGTAAATATTGTCATGCA 60.453 40.000 0.00 0.00 34.51 3.96
152 153 6.225318 GCCAATGGTAAATATTGTCATGCAT 58.775 36.000 0.00 0.00 34.51 3.96
153 154 6.366877 GCCAATGGTAAATATTGTCATGCATC 59.633 38.462 0.00 0.00 34.51 3.91
154 155 7.435305 CCAATGGTAAATATTGTCATGCATCA 58.565 34.615 0.00 0.00 34.51 3.07
155 156 7.927092 CCAATGGTAAATATTGTCATGCATCAA 59.073 33.333 0.00 0.00 34.51 2.57
156 157 8.974408 CAATGGTAAATATTGTCATGCATCAAG 58.026 33.333 0.00 0.00 32.30 3.02
157 158 7.041635 TGGTAAATATTGTCATGCATCAAGG 57.958 36.000 0.00 0.00 0.00 3.61
158 159 6.832900 TGGTAAATATTGTCATGCATCAAGGA 59.167 34.615 0.00 0.00 0.00 3.36
159 160 7.341512 TGGTAAATATTGTCATGCATCAAGGAA 59.658 33.333 0.00 0.00 0.00 3.36
160 161 8.196771 GGTAAATATTGTCATGCATCAAGGAAA 58.803 33.333 0.00 0.00 0.00 3.13
163 164 8.657074 AATATTGTCATGCATCAAGGAAATTG 57.343 30.769 0.00 0.00 40.52 2.32
164 165 5.471556 TTGTCATGCATCAAGGAAATTGT 57.528 34.783 0.00 0.00 40.05 2.71
165 166 6.587206 TTGTCATGCATCAAGGAAATTGTA 57.413 33.333 0.00 0.00 40.05 2.41
167 168 5.711506 TGTCATGCATCAAGGAAATTGTAGT 59.288 36.000 0.00 0.00 40.05 2.73
168 169 6.032094 GTCATGCATCAAGGAAATTGTAGTG 58.968 40.000 0.00 0.00 40.05 2.74
169 170 5.711506 TCATGCATCAAGGAAATTGTAGTGT 59.288 36.000 0.00 0.00 40.05 3.55
170 171 6.883756 TCATGCATCAAGGAAATTGTAGTGTA 59.116 34.615 0.00 0.00 40.05 2.90
173 174 6.095300 TGCATCAAGGAAATTGTAGTGTATGG 59.905 38.462 0.00 0.00 40.05 2.74
174 175 6.318648 GCATCAAGGAAATTGTAGTGTATGGA 59.681 38.462 0.00 0.00 40.05 3.41
175 176 7.013655 GCATCAAGGAAATTGTAGTGTATGGAT 59.986 37.037 0.00 0.00 40.05 3.41
176 177 8.562892 CATCAAGGAAATTGTAGTGTATGGATC 58.437 37.037 0.00 0.00 40.05 3.36
178 179 8.274322 TCAAGGAAATTGTAGTGTATGGATCAT 58.726 33.333 0.00 0.00 40.05 2.45
179 180 8.347771 CAAGGAAATTGTAGTGTATGGATCATG 58.652 37.037 0.00 0.00 33.95 3.07
181 182 6.294176 GGAAATTGTAGTGTATGGATCATGGC 60.294 42.308 0.00 0.00 0.00 4.40
183 184 4.980339 TGTAGTGTATGGATCATGGCAT 57.020 40.909 0.00 0.00 0.00 4.40
186 187 7.019656 TGTAGTGTATGGATCATGGCATATT 57.980 36.000 0.00 0.00 0.00 1.28
187 188 7.460910 TGTAGTGTATGGATCATGGCATATTT 58.539 34.615 0.00 0.00 0.00 1.40
189 190 7.223260 AGTGTATGGATCATGGCATATTTTG 57.777 36.000 0.00 0.00 0.00 2.44
190 191 6.779049 AGTGTATGGATCATGGCATATTTTGT 59.221 34.615 0.00 0.00 0.00 2.83
191 192 7.944000 AGTGTATGGATCATGGCATATTTTGTA 59.056 33.333 0.00 0.00 0.00 2.41
192 193 8.239314 GTGTATGGATCATGGCATATTTTGTAG 58.761 37.037 0.00 0.00 0.00 2.74
193 194 7.944000 TGTATGGATCATGGCATATTTTGTAGT 59.056 33.333 0.00 0.00 0.00 2.73
194 195 6.882610 TGGATCATGGCATATTTTGTAGTC 57.117 37.500 0.00 0.00 0.00 2.59
195 196 6.604171 TGGATCATGGCATATTTTGTAGTCT 58.396 36.000 0.00 0.00 0.00 3.24
196 197 7.744733 TGGATCATGGCATATTTTGTAGTCTA 58.255 34.615 0.00 0.00 0.00 2.59
197 198 8.385491 TGGATCATGGCATATTTTGTAGTCTAT 58.615 33.333 0.00 0.00 0.00 1.98
198 199 8.671921 GGATCATGGCATATTTTGTAGTCTATG 58.328 37.037 0.00 0.00 0.00 2.23
199 200 7.984422 TCATGGCATATTTTGTAGTCTATGG 57.016 36.000 0.00 0.00 0.00 2.74
200 201 7.744733 TCATGGCATATTTTGTAGTCTATGGA 58.255 34.615 0.00 0.00 0.00 3.41
201 202 8.385491 TCATGGCATATTTTGTAGTCTATGGAT 58.615 33.333 0.00 0.00 0.00 3.41
202 203 8.671921 CATGGCATATTTTGTAGTCTATGGATC 58.328 37.037 0.00 0.00 0.00 3.36
203 204 7.744733 TGGCATATTTTGTAGTCTATGGATCA 58.255 34.615 0.00 0.00 0.00 2.92
221 222 6.229733 TGGATCATTTTCCAACAATGTTTCC 58.770 36.000 0.00 0.00 42.82 3.13
222 223 6.183361 TGGATCATTTTCCAACAATGTTTCCA 60.183 34.615 6.36 6.36 42.82 3.53
223 224 6.880529 GGATCATTTTCCAACAATGTTTCCAT 59.119 34.615 0.00 0.00 36.30 3.41
225 226 6.590068 TCATTTTCCAACAATGTTTCCATGT 58.410 32.000 0.00 0.00 33.91 3.21
226 227 6.705381 TCATTTTCCAACAATGTTTCCATGTC 59.295 34.615 0.00 0.00 33.91 3.06
227 228 4.599047 TTCCAACAATGTTTCCATGTCC 57.401 40.909 0.00 0.00 0.00 4.02
229 230 2.632028 CCAACAATGTTTCCATGTCCCA 59.368 45.455 0.00 0.00 0.00 4.37
231 232 4.247258 CAACAATGTTTCCATGTCCCATG 58.753 43.478 0.00 0.00 0.00 3.66
232 233 2.833338 ACAATGTTTCCATGTCCCATGG 59.167 45.455 15.59 15.59 40.48 3.66
233 234 1.488390 ATGTTTCCATGTCCCATGGC 58.512 50.000 16.67 5.61 39.01 4.40
234 235 0.113972 TGTTTCCATGTCCCATGGCA 59.886 50.000 16.67 5.03 39.01 4.92
236 237 1.622811 GTTTCCATGTCCCATGGCAAA 59.377 47.619 16.67 14.28 39.01 3.68
237 238 2.236893 GTTTCCATGTCCCATGGCAAAT 59.763 45.455 16.67 0.00 39.01 2.32
238 239 2.250921 TCCATGTCCCATGGCAAATT 57.749 45.000 16.67 0.00 39.01 1.82
239 240 2.549082 TCCATGTCCCATGGCAAATTT 58.451 42.857 16.67 0.00 39.01 1.82
240 241 2.911636 TCCATGTCCCATGGCAAATTTT 59.088 40.909 16.67 0.00 39.01 1.82
243 244 5.191323 TCCATGTCCCATGGCAAATTTTATT 59.809 36.000 16.67 0.00 39.01 1.40
244 245 6.385176 TCCATGTCCCATGGCAAATTTTATTA 59.615 34.615 16.67 0.00 39.01 0.98
246 247 7.720515 CCATGTCCCATGGCAAATTTTATTATT 59.279 33.333 6.09 0.00 31.75 1.40
247 248 8.776470 CATGTCCCATGGCAAATTTTATTATTC 58.224 33.333 6.09 0.00 0.00 1.75
248 249 7.855375 TGTCCCATGGCAAATTTTATTATTCA 58.145 30.769 6.09 0.00 0.00 2.57
249 250 7.986320 TGTCCCATGGCAAATTTTATTATTCAG 59.014 33.333 6.09 0.00 0.00 3.02
250 251 8.203485 GTCCCATGGCAAATTTTATTATTCAGA 58.797 33.333 6.09 0.00 0.00 3.27
252 253 7.172019 CCCATGGCAAATTTTATTATTCAGAGC 59.828 37.037 6.09 0.00 0.00 4.09
255 256 8.651391 TGGCAAATTTTATTATTCAGAGCATG 57.349 30.769 0.00 0.00 0.00 4.06
256 257 8.476447 TGGCAAATTTTATTATTCAGAGCATGA 58.524 29.630 0.00 0.00 35.62 3.07
257 258 8.758715 GGCAAATTTTATTATTCAGAGCATGAC 58.241 33.333 0.00 0.00 37.77 3.06
275 276 9.503427 GAGCATGACACTTATAATTAAAACACC 57.497 33.333 0.00 0.00 0.00 4.16
276 277 9.019656 AGCATGACACTTATAATTAAAACACCA 57.980 29.630 0.00 0.00 0.00 4.17
277 278 9.801873 GCATGACACTTATAATTAAAACACCAT 57.198 29.630 0.00 0.00 0.00 3.55
280 281 8.247562 TGACACTTATAATTAAAACACCATGGC 58.752 33.333 13.04 0.00 0.00 4.40
281 282 8.128322 ACACTTATAATTAAAACACCATGGCA 57.872 30.769 13.04 0.00 0.00 4.92
282 283 8.589338 ACACTTATAATTAAAACACCATGGCAA 58.411 29.630 13.04 0.00 0.00 4.52
283 284 9.429359 CACTTATAATTAAAACACCATGGCAAA 57.571 29.630 13.04 0.00 0.00 3.68
290 291 9.958234 AATTAAAACACCATGGCAAATTTTAAC 57.042 25.926 23.94 0.00 35.49 2.01
291 292 8.738645 TTAAAACACCATGGCAAATTTTAACT 57.261 26.923 20.74 5.41 30.53 2.24
292 293 7.637631 AAAACACCATGGCAAATTTTAACTT 57.362 28.000 13.04 0.00 0.00 2.66
293 294 6.616774 AACACCATGGCAAATTTTAACTTG 57.383 33.333 13.04 0.00 0.00 3.16
294 295 4.514816 ACACCATGGCAAATTTTAACTTGC 59.485 37.500 13.04 0.34 45.79 4.01
330 331 7.577979 GCCATGGCAATTATGTTCATAATTTG 58.422 34.615 32.08 17.35 41.49 2.32
332 333 8.552865 CCATGGCAATTATGTTCATAATTTGTG 58.447 33.333 21.00 14.99 35.27 3.33
333 334 7.536895 TGGCAATTATGTTCATAATTTGTGC 57.463 32.000 21.00 20.80 35.27 4.57
334 335 7.329499 TGGCAATTATGTTCATAATTTGTGCT 58.671 30.769 24.09 8.71 35.27 4.40
336 337 8.755018 GGCAATTATGTTCATAATTTGTGCTAC 58.245 33.333 24.09 14.22 35.27 3.58
340 341 8.909708 TTATGTTCATAATTTGTGCTACTTGC 57.090 30.769 1.68 0.00 43.25 4.01
342 343 5.476599 TGTTCATAATTTGTGCTACTTGCCT 59.523 36.000 0.00 0.00 42.00 4.75
344 345 6.677781 TCATAATTTGTGCTACTTGCCTAC 57.322 37.500 0.00 0.00 42.00 3.18
345 346 6.414732 TCATAATTTGTGCTACTTGCCTACT 58.585 36.000 0.00 0.00 42.00 2.57
346 347 6.884295 TCATAATTTGTGCTACTTGCCTACTT 59.116 34.615 0.00 0.00 42.00 2.24
347 348 5.629079 AATTTGTGCTACTTGCCTACTTC 57.371 39.130 0.00 0.00 42.00 3.01
348 349 3.762407 TTGTGCTACTTGCCTACTTCA 57.238 42.857 0.00 0.00 42.00 3.02
349 350 3.040147 TGTGCTACTTGCCTACTTCAC 57.960 47.619 0.00 0.00 42.00 3.18
351 352 3.007940 TGTGCTACTTGCCTACTTCACAT 59.992 43.478 0.00 0.00 42.00 3.21
352 353 4.221924 TGTGCTACTTGCCTACTTCACATA 59.778 41.667 0.00 0.00 42.00 2.29
353 354 4.567159 GTGCTACTTGCCTACTTCACATAC 59.433 45.833 0.00 0.00 42.00 2.39
354 355 4.221924 TGCTACTTGCCTACTTCACATACA 59.778 41.667 0.00 0.00 42.00 2.29
355 356 5.104941 TGCTACTTGCCTACTTCACATACAT 60.105 40.000 0.00 0.00 42.00 2.29
356 357 5.235186 GCTACTTGCCTACTTCACATACATG 59.765 44.000 0.00 0.00 35.15 3.21
357 358 4.517285 ACTTGCCTACTTCACATACATGG 58.483 43.478 0.00 0.00 0.00 3.66
358 359 2.917933 TGCCTACTTCACATACATGGC 58.082 47.619 0.00 0.00 39.53 4.40
359 360 2.238395 TGCCTACTTCACATACATGGCA 59.762 45.455 0.00 0.00 45.51 4.92
361 362 3.694072 GCCTACTTCACATACATGGCAAA 59.306 43.478 0.00 0.00 38.99 3.68
363 364 5.163519 GCCTACTTCACATACATGGCAAATT 60.164 40.000 0.00 0.00 38.99 1.82
364 365 6.498304 CCTACTTCACATACATGGCAAATTC 58.502 40.000 0.00 0.00 0.00 2.17
365 366 5.329035 ACTTCACATACATGGCAAATTCC 57.671 39.130 0.00 0.00 0.00 3.01
366 367 5.018809 ACTTCACATACATGGCAAATTCCT 58.981 37.500 0.00 0.00 0.00 3.36
367 368 5.126061 ACTTCACATACATGGCAAATTCCTC 59.874 40.000 0.00 0.00 0.00 3.71
368 369 4.598022 TCACATACATGGCAAATTCCTCA 58.402 39.130 0.00 0.00 0.00 3.86
369 370 4.398988 TCACATACATGGCAAATTCCTCAC 59.601 41.667 0.00 0.00 0.00 3.51
370 371 4.158209 CACATACATGGCAAATTCCTCACA 59.842 41.667 0.00 0.00 0.00 3.58
371 372 4.158394 ACATACATGGCAAATTCCTCACAC 59.842 41.667 0.00 0.00 0.00 3.82
372 373 2.596346 ACATGGCAAATTCCTCACACA 58.404 42.857 0.00 0.00 0.00 3.72
374 375 2.064434 TGGCAAATTCCTCACACACA 57.936 45.000 0.00 0.00 0.00 3.72
376 377 2.762887 TGGCAAATTCCTCACACACAAA 59.237 40.909 0.00 0.00 0.00 2.83
377 378 3.123050 GGCAAATTCCTCACACACAAAC 58.877 45.455 0.00 0.00 0.00 2.93
378 379 3.430098 GGCAAATTCCTCACACACAAACA 60.430 43.478 0.00 0.00 0.00 2.83
379 380 4.370917 GCAAATTCCTCACACACAAACAT 58.629 39.130 0.00 0.00 0.00 2.71
380 381 4.209703 GCAAATTCCTCACACACAAACATG 59.790 41.667 0.00 0.00 0.00 3.21
381 382 5.590145 CAAATTCCTCACACACAAACATGA 58.410 37.500 0.00 0.00 0.00 3.07
382 383 4.836125 ATTCCTCACACACAAACATGAC 57.164 40.909 0.00 0.00 0.00 3.06
383 384 3.274095 TCCTCACACACAAACATGACA 57.726 42.857 0.00 0.00 0.00 3.58
384 385 3.615155 TCCTCACACACAAACATGACAA 58.385 40.909 0.00 0.00 0.00 3.18
385 386 3.376859 TCCTCACACACAAACATGACAAC 59.623 43.478 0.00 0.00 0.00 3.32
387 388 4.142403 CCTCACACACAAACATGACAACTT 60.142 41.667 0.00 0.00 0.00 2.66
389 390 6.404184 CCTCACACACAAACATGACAACTTTA 60.404 38.462 0.00 0.00 0.00 1.85
390 391 7.094508 TCACACACAAACATGACAACTTTAT 57.905 32.000 0.00 0.00 0.00 1.40
391 392 7.542890 TCACACACAAACATGACAACTTTATT 58.457 30.769 0.00 0.00 0.00 1.40
393 394 9.295214 CACACACAAACATGACAACTTTATTTA 57.705 29.630 0.00 0.00 0.00 1.40
394 395 9.862371 ACACACAAACATGACAACTTTATTTAA 57.138 25.926 0.00 0.00 0.00 1.52
468 469 5.401033 TTTTTCACACATGGCAATTTTCG 57.599 34.783 0.00 0.00 0.00 3.46
469 470 2.063156 TCACACATGGCAATTTTCGC 57.937 45.000 0.00 0.00 0.00 4.70
470 471 1.339291 TCACACATGGCAATTTTCGCA 59.661 42.857 0.00 0.00 0.00 5.10
471 472 2.029200 TCACACATGGCAATTTTCGCAT 60.029 40.909 0.00 0.00 0.00 4.73
472 473 3.192212 TCACACATGGCAATTTTCGCATA 59.808 39.130 0.00 0.00 0.00 3.14
473 474 3.304026 CACACATGGCAATTTTCGCATAC 59.696 43.478 0.00 0.00 0.00 2.39
474 475 3.056962 ACACATGGCAATTTTCGCATACA 60.057 39.130 0.00 0.00 0.00 2.29
475 476 4.114073 CACATGGCAATTTTCGCATACAT 58.886 39.130 0.00 0.00 0.00 2.29
476 477 4.567558 CACATGGCAATTTTCGCATACATT 59.432 37.500 0.00 0.00 0.00 2.71
477 478 5.747675 CACATGGCAATTTTCGCATACATTA 59.252 36.000 0.00 0.00 0.00 1.90
478 479 6.421501 CACATGGCAATTTTCGCATACATTAT 59.578 34.615 0.00 0.00 0.00 1.28
479 480 7.594386 CACATGGCAATTTTCGCATACATTATA 59.406 33.333 0.00 0.00 0.00 0.98
480 481 8.306038 ACATGGCAATTTTCGCATACATTATAT 58.694 29.630 0.00 0.00 0.00 0.86
481 482 8.588789 CATGGCAATTTTCGCATACATTATATG 58.411 33.333 0.00 0.00 0.00 1.78
482 483 7.089538 TGGCAATTTTCGCATACATTATATGG 58.910 34.615 0.00 0.00 33.60 2.74
483 484 7.040132 TGGCAATTTTCGCATACATTATATGGA 60.040 33.333 0.00 0.00 33.60 3.41
484 485 7.812191 GGCAATTTTCGCATACATTATATGGAA 59.188 33.333 0.00 0.00 33.60 3.53
485 486 9.190858 GCAATTTTCGCATACATTATATGGAAA 57.809 29.630 0.00 0.00 33.60 3.13
2888 2902 5.068460 TGGTGACTTATTTGGAACCAAACAG 59.932 40.000 19.23 18.64 46.80 3.16
2920 2934 5.414360 TGGACTCAGATGATTTTCTCTTCG 58.586 41.667 0.00 0.00 34.14 3.79
2921 2935 4.269844 GGACTCAGATGATTTTCTCTTCGC 59.730 45.833 0.00 0.00 34.14 4.70
2963 2977 1.067425 TCGAACGTCGACATTCCCAAT 60.067 47.619 17.82 0.00 44.82 3.16
2966 2980 1.722011 ACGTCGACATTCCCAATGAC 58.278 50.000 17.16 0.00 41.46 3.06
2975 2989 4.398319 ACATTCCCAATGACGAGTTCTTT 58.602 39.130 3.24 0.00 41.46 2.52
3036 3050 0.319555 CATGACGAACGACACACCCT 60.320 55.000 0.14 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.071471 CGAAGAAGCACCACCACCT 59.929 57.895 0.00 0.00 0.00 4.00
1 2 2.617274 GCGAAGAAGCACCACCACC 61.617 63.158 0.00 0.00 37.05 4.61
4 5 2.180159 TAGGGCGAAGAAGCACCACC 62.180 60.000 0.00 0.00 42.61 4.61
5 6 0.741221 CTAGGGCGAAGAAGCACCAC 60.741 60.000 0.00 0.00 42.61 4.16
6 7 0.902984 TCTAGGGCGAAGAAGCACCA 60.903 55.000 0.00 0.00 42.61 4.17
7 8 0.466124 ATCTAGGGCGAAGAAGCACC 59.534 55.000 0.00 0.00 42.61 5.01
10 11 2.888414 AGACTATCTAGGGCGAAGAAGC 59.112 50.000 0.00 0.00 0.00 3.86
11 12 3.886505 ACAGACTATCTAGGGCGAAGAAG 59.113 47.826 0.00 0.00 0.00 2.85
12 13 3.899726 ACAGACTATCTAGGGCGAAGAA 58.100 45.455 0.00 0.00 0.00 2.52
14 15 5.968528 AATACAGACTATCTAGGGCGAAG 57.031 43.478 0.00 0.00 0.00 3.79
15 16 6.776744 TCTAATACAGACTATCTAGGGCGAA 58.223 40.000 0.00 0.00 0.00 4.70
16 17 6.370186 TCTAATACAGACTATCTAGGGCGA 57.630 41.667 0.00 0.00 0.00 5.54
17 18 5.587043 CCTCTAATACAGACTATCTAGGGCG 59.413 48.000 0.00 0.00 0.00 6.13
18 19 6.376018 CACCTCTAATACAGACTATCTAGGGC 59.624 46.154 0.00 0.00 0.00 5.19
21 22 9.952030 TGATCACCTCTAATACAGACTATCTAG 57.048 37.037 0.00 0.00 0.00 2.43
22 23 9.727859 GTGATCACCTCTAATACAGACTATCTA 57.272 37.037 15.31 0.00 0.00 1.98
23 24 8.221251 TGTGATCACCTCTAATACAGACTATCT 58.779 37.037 22.85 0.00 0.00 1.98
24 25 8.397575 TGTGATCACCTCTAATACAGACTATC 57.602 38.462 22.85 0.00 0.00 2.08
25 26 7.450014 CCTGTGATCACCTCTAATACAGACTAT 59.550 40.741 22.85 0.00 36.96 2.12
27 28 5.596361 CCTGTGATCACCTCTAATACAGACT 59.404 44.000 22.85 0.00 36.96 3.24
28 29 5.361285 ACCTGTGATCACCTCTAATACAGAC 59.639 44.000 22.85 0.00 36.96 3.51
29 30 5.519808 ACCTGTGATCACCTCTAATACAGA 58.480 41.667 22.85 0.00 36.96 3.41
30 31 5.860941 ACCTGTGATCACCTCTAATACAG 57.139 43.478 22.85 9.90 35.17 2.74
31 32 7.914427 ATTACCTGTGATCACCTCTAATACA 57.086 36.000 22.85 0.04 0.00 2.29
36 37 9.601810 ACAATATATTACCTGTGATCACCTCTA 57.398 33.333 22.85 6.40 0.00 2.43
37 38 8.497910 ACAATATATTACCTGTGATCACCTCT 57.502 34.615 22.85 7.36 0.00 3.69
45 46 9.506018 CCATGATTGACAATATATTACCTGTGA 57.494 33.333 0.00 0.00 0.00 3.58
46 47 8.239314 GCCATGATTGACAATATATTACCTGTG 58.761 37.037 0.00 0.00 0.00 3.66
47 48 7.944000 TGCCATGATTGACAATATATTACCTGT 59.056 33.333 0.00 0.00 0.00 4.00
48 49 8.339344 TGCCATGATTGACAATATATTACCTG 57.661 34.615 0.00 0.00 0.00 4.00
49 50 9.537852 AATGCCATGATTGACAATATATTACCT 57.462 29.630 0.00 0.00 0.00 3.08
98 99 8.736244 GGCAAACTTTGTTGGATAAGTTCTATA 58.264 33.333 3.48 0.00 42.17 1.31
100 101 6.547880 TGGCAAACTTTGTTGGATAAGTTCTA 59.452 34.615 3.48 0.00 42.17 2.10
101 102 5.362430 TGGCAAACTTTGTTGGATAAGTTCT 59.638 36.000 3.48 0.00 42.17 3.01
102 103 5.596845 TGGCAAACTTTGTTGGATAAGTTC 58.403 37.500 3.48 0.00 42.17 3.01
103 104 5.606348 TGGCAAACTTTGTTGGATAAGTT 57.394 34.783 3.48 0.00 44.20 2.66
104 105 5.511202 CCATGGCAAACTTTGTTGGATAAGT 60.511 40.000 0.00 0.00 36.20 2.24
105 106 4.931002 CCATGGCAAACTTTGTTGGATAAG 59.069 41.667 0.00 0.00 32.59 1.73
106 107 4.802248 GCCATGGCAAACTTTGTTGGATAA 60.802 41.667 32.08 0.00 41.49 1.75
107 108 3.306641 GCCATGGCAAACTTTGTTGGATA 60.307 43.478 32.08 0.00 41.49 2.59
108 109 2.550639 GCCATGGCAAACTTTGTTGGAT 60.551 45.455 32.08 0.36 41.49 3.41
109 110 1.202627 GCCATGGCAAACTTTGTTGGA 60.203 47.619 32.08 0.00 41.49 3.53
110 111 1.228533 GCCATGGCAAACTTTGTTGG 58.771 50.000 32.08 12.40 41.49 3.77
111 112 1.228533 GGCCATGGCAAACTTTGTTG 58.771 50.000 36.56 0.00 44.11 3.33
112 113 0.835941 TGGCCATGGCAAACTTTGTT 59.164 45.000 36.56 0.00 44.11 2.83
113 114 0.835941 TTGGCCATGGCAAACTTTGT 59.164 45.000 36.56 0.00 44.79 2.83
114 115 3.702147 TTGGCCATGGCAAACTTTG 57.298 47.368 36.56 0.00 44.79 2.77
124 125 6.159299 TGACAATATTTACCATTGGCCATG 57.841 37.500 6.09 7.26 40.15 3.66
126 127 5.453057 GCATGACAATATTTACCATTGGCCA 60.453 40.000 0.00 0.00 40.15 5.36
129 130 7.435305 TGATGCATGACAATATTTACCATTGG 58.565 34.615 2.46 0.00 37.64 3.16
130 131 8.874744 TTGATGCATGACAATATTTACCATTG 57.125 30.769 2.46 0.00 38.95 2.82
131 132 8.145767 CCTTGATGCATGACAATATTTACCATT 58.854 33.333 2.46 0.00 0.00 3.16
132 133 7.506599 TCCTTGATGCATGACAATATTTACCAT 59.493 33.333 2.46 0.00 0.00 3.55
134 135 7.275888 TCCTTGATGCATGACAATATTTACC 57.724 36.000 2.46 0.00 0.00 2.85
135 136 9.754382 ATTTCCTTGATGCATGACAATATTTAC 57.246 29.630 2.46 0.00 0.00 2.01
137 138 9.104965 CAATTTCCTTGATGCATGACAATATTT 57.895 29.630 2.46 0.00 36.97 1.40
138 139 8.262227 ACAATTTCCTTGATGCATGACAATATT 58.738 29.630 2.46 0.00 38.29 1.28
139 140 7.788026 ACAATTTCCTTGATGCATGACAATAT 58.212 30.769 2.46 0.00 38.29 1.28
140 141 7.172868 ACAATTTCCTTGATGCATGACAATA 57.827 32.000 2.46 0.00 38.29 1.90
142 143 5.471556 ACAATTTCCTTGATGCATGACAA 57.528 34.783 2.46 1.74 38.29 3.18
143 144 5.711506 ACTACAATTTCCTTGATGCATGACA 59.288 36.000 2.46 0.00 38.29 3.58
144 145 6.032094 CACTACAATTTCCTTGATGCATGAC 58.968 40.000 2.46 0.00 38.29 3.06
147 148 7.201848 CCATACACTACAATTTCCTTGATGCAT 60.202 37.037 0.00 0.00 38.29 3.96
148 149 6.095300 CCATACACTACAATTTCCTTGATGCA 59.905 38.462 0.00 0.00 38.29 3.96
150 151 7.864108 TCCATACACTACAATTTCCTTGATG 57.136 36.000 0.00 0.00 38.29 3.07
151 152 8.274322 TGATCCATACACTACAATTTCCTTGAT 58.726 33.333 0.00 0.00 38.29 2.57
152 153 7.629157 TGATCCATACACTACAATTTCCTTGA 58.371 34.615 0.00 0.00 38.29 3.02
153 154 7.864108 TGATCCATACACTACAATTTCCTTG 57.136 36.000 0.00 0.00 40.90 3.61
154 155 7.503566 CCATGATCCATACACTACAATTTCCTT 59.496 37.037 0.00 0.00 0.00 3.36
155 156 7.000472 CCATGATCCATACACTACAATTTCCT 59.000 38.462 0.00 0.00 0.00 3.36
156 157 6.294176 GCCATGATCCATACACTACAATTTCC 60.294 42.308 0.00 0.00 0.00 3.13
157 158 6.262944 TGCCATGATCCATACACTACAATTTC 59.737 38.462 0.00 0.00 0.00 2.17
158 159 6.128486 TGCCATGATCCATACACTACAATTT 58.872 36.000 0.00 0.00 0.00 1.82
159 160 5.693961 TGCCATGATCCATACACTACAATT 58.306 37.500 0.00 0.00 0.00 2.32
160 161 5.308976 TGCCATGATCCATACACTACAAT 57.691 39.130 0.00 0.00 0.00 2.71
162 163 4.980339 ATGCCATGATCCATACACTACA 57.020 40.909 0.00 0.00 0.00 2.74
163 164 7.928307 AAATATGCCATGATCCATACACTAC 57.072 36.000 0.00 0.00 0.00 2.73
164 165 7.944000 ACAAAATATGCCATGATCCATACACTA 59.056 33.333 0.00 0.00 0.00 2.74
165 166 6.779049 ACAAAATATGCCATGATCCATACACT 59.221 34.615 0.00 0.00 0.00 3.55
167 168 7.944000 ACTACAAAATATGCCATGATCCATACA 59.056 33.333 0.00 0.00 0.00 2.29
168 169 8.340618 ACTACAAAATATGCCATGATCCATAC 57.659 34.615 0.00 0.00 0.00 2.39
169 170 8.385491 AGACTACAAAATATGCCATGATCCATA 58.615 33.333 0.00 0.00 0.00 2.74
170 171 7.236529 AGACTACAAAATATGCCATGATCCAT 58.763 34.615 0.00 0.00 0.00 3.41
173 174 8.671921 CCATAGACTACAAAATATGCCATGATC 58.328 37.037 0.00 0.00 0.00 2.92
174 175 8.385491 TCCATAGACTACAAAATATGCCATGAT 58.615 33.333 0.00 0.00 0.00 2.45
175 176 7.744733 TCCATAGACTACAAAATATGCCATGA 58.255 34.615 0.00 0.00 0.00 3.07
176 177 7.984422 TCCATAGACTACAAAATATGCCATG 57.016 36.000 0.00 0.00 0.00 3.66
178 179 7.744733 TGATCCATAGACTACAAAATATGCCA 58.255 34.615 0.00 0.00 0.00 4.92
179 180 8.798859 ATGATCCATAGACTACAAAATATGCC 57.201 34.615 0.00 0.00 0.00 4.40
196 197 7.474507 TGGAAACATTGTTGGAAAATGATCCAT 60.475 33.333 16.80 0.00 42.57 3.41
197 198 6.183361 TGGAAACATTGTTGGAAAATGATCCA 60.183 34.615 16.80 16.80 43.68 3.41
198 199 6.229733 TGGAAACATTGTTGGAAAATGATCC 58.770 36.000 2.13 3.76 40.69 3.36
225 226 8.316497 TCTGAATAATAAAATTTGCCATGGGA 57.684 30.769 15.13 8.24 0.00 4.37
226 227 7.172019 GCTCTGAATAATAAAATTTGCCATGGG 59.828 37.037 15.13 0.00 0.00 4.00
227 228 7.711772 TGCTCTGAATAATAAAATTTGCCATGG 59.288 33.333 7.63 7.63 0.00 3.66
229 230 9.268268 CATGCTCTGAATAATAAAATTTGCCAT 57.732 29.630 0.00 0.00 0.00 4.40
231 232 8.758715 GTCATGCTCTGAATAATAAAATTTGCC 58.241 33.333 0.00 0.00 35.07 4.52
232 233 9.304731 TGTCATGCTCTGAATAATAAAATTTGC 57.695 29.630 0.00 0.00 35.07 3.68
249 250 9.503427 GGTGTTTTAATTATAAGTGTCATGCTC 57.497 33.333 0.00 0.00 0.00 4.26
250 251 9.019656 TGGTGTTTTAATTATAAGTGTCATGCT 57.980 29.630 0.00 0.00 0.00 3.79
255 256 8.247562 TGCCATGGTGTTTTAATTATAAGTGTC 58.752 33.333 14.67 0.00 0.00 3.67
256 257 8.128322 TGCCATGGTGTTTTAATTATAAGTGT 57.872 30.769 14.67 0.00 0.00 3.55
257 258 8.994429 TTGCCATGGTGTTTTAATTATAAGTG 57.006 30.769 14.67 0.00 0.00 3.16
264 265 9.958234 GTTAAAATTTGCCATGGTGTTTTAATT 57.042 25.926 24.36 15.33 35.09 1.40
266 267 8.738645 AGTTAAAATTTGCCATGGTGTTTTAA 57.261 26.923 14.67 19.17 32.07 1.52
269 270 6.459435 GCAAGTTAAAATTTGCCATGGTGTTT 60.459 34.615 14.67 9.12 43.32 2.83
270 271 5.008514 GCAAGTTAAAATTTGCCATGGTGTT 59.991 36.000 14.67 0.00 43.32 3.32
271 272 4.514816 GCAAGTTAAAATTTGCCATGGTGT 59.485 37.500 14.67 0.00 43.32 4.16
273 274 4.712476 TGCAAGTTAAAATTTGCCATGGT 58.288 34.783 14.67 0.00 46.98 3.55
274 275 5.883503 ATGCAAGTTAAAATTTGCCATGG 57.116 34.783 17.04 7.63 46.98 3.66
275 276 8.576936 AAAAATGCAAGTTAAAATTTGCCATG 57.423 26.923 17.04 0.00 46.98 3.66
304 305 6.422344 ATTATGAACATAATTGCCATGGCA 57.578 33.333 35.59 35.59 40.11 4.92
314 315 9.520204 GCAAGTAGCACAAATTATGAACATAAT 57.480 29.630 12.49 12.49 42.83 1.28
315 316 8.909708 GCAAGTAGCACAAATTATGAACATAA 57.090 30.769 9.23 9.23 44.79 1.90
332 333 4.755411 TGTATGTGAAGTAGGCAAGTAGC 58.245 43.478 0.00 0.00 44.65 3.58
333 334 5.755375 CCATGTATGTGAAGTAGGCAAGTAG 59.245 44.000 0.00 0.00 0.00 2.57
334 335 5.670485 CCATGTATGTGAAGTAGGCAAGTA 58.330 41.667 0.00 0.00 0.00 2.24
336 337 3.313526 GCCATGTATGTGAAGTAGGCAAG 59.686 47.826 0.00 0.00 40.50 4.01
340 341 6.455360 AATTTGCCATGTATGTGAAGTAGG 57.545 37.500 0.00 0.00 0.00 3.18
342 343 6.186957 AGGAATTTGCCATGTATGTGAAGTA 58.813 36.000 0.00 0.00 0.00 2.24
344 345 5.125900 TGAGGAATTTGCCATGTATGTGAAG 59.874 40.000 0.00 0.00 0.00 3.02
345 346 5.015515 TGAGGAATTTGCCATGTATGTGAA 58.984 37.500 0.00 0.00 0.00 3.18
346 347 4.398988 GTGAGGAATTTGCCATGTATGTGA 59.601 41.667 0.00 0.00 0.00 3.58
347 348 4.158209 TGTGAGGAATTTGCCATGTATGTG 59.842 41.667 0.00 0.00 0.00 3.21
348 349 4.158394 GTGTGAGGAATTTGCCATGTATGT 59.842 41.667 0.00 0.00 0.00 2.29
349 350 4.158209 TGTGTGAGGAATTTGCCATGTATG 59.842 41.667 0.00 0.00 0.00 2.39
351 352 3.505680 GTGTGTGAGGAATTTGCCATGTA 59.494 43.478 0.00 0.00 0.00 2.29
352 353 2.297033 GTGTGTGAGGAATTTGCCATGT 59.703 45.455 0.00 0.00 0.00 3.21
353 354 2.296752 TGTGTGTGAGGAATTTGCCATG 59.703 45.455 0.00 0.00 0.00 3.66
354 355 2.596346 TGTGTGTGAGGAATTTGCCAT 58.404 42.857 0.00 0.00 0.00 4.40
355 356 2.064434 TGTGTGTGAGGAATTTGCCA 57.936 45.000 0.00 0.00 0.00 4.92
356 357 3.123050 GTTTGTGTGTGAGGAATTTGCC 58.877 45.455 0.00 0.00 0.00 4.52
357 358 3.779759 TGTTTGTGTGTGAGGAATTTGC 58.220 40.909 0.00 0.00 0.00 3.68
358 359 5.459762 GTCATGTTTGTGTGTGAGGAATTTG 59.540 40.000 0.00 0.00 0.00 2.32
359 360 5.126869 TGTCATGTTTGTGTGTGAGGAATTT 59.873 36.000 0.00 0.00 0.00 1.82
361 362 4.206375 TGTCATGTTTGTGTGTGAGGAAT 58.794 39.130 0.00 0.00 0.00 3.01
363 364 3.274095 TGTCATGTTTGTGTGTGAGGA 57.726 42.857 0.00 0.00 0.00 3.71
364 365 3.378112 AGTTGTCATGTTTGTGTGTGAGG 59.622 43.478 0.00 0.00 0.00 3.86
365 366 4.621068 AGTTGTCATGTTTGTGTGTGAG 57.379 40.909 0.00 0.00 0.00 3.51
366 367 5.384063 AAAGTTGTCATGTTTGTGTGTGA 57.616 34.783 0.00 0.00 0.00 3.58
367 368 7.754069 AATAAAGTTGTCATGTTTGTGTGTG 57.246 32.000 0.00 0.00 0.00 3.82
368 369 9.862371 TTAAATAAAGTTGTCATGTTTGTGTGT 57.138 25.926 0.00 0.00 0.00 3.72
446 447 4.260538 GCGAAAATTGCCATGTGTGAAAAA 60.261 37.500 0.00 0.00 0.00 1.94
447 448 3.247173 GCGAAAATTGCCATGTGTGAAAA 59.753 39.130 0.00 0.00 0.00 2.29
448 449 2.799412 GCGAAAATTGCCATGTGTGAAA 59.201 40.909 0.00 0.00 0.00 2.69
449 450 2.223900 TGCGAAAATTGCCATGTGTGAA 60.224 40.909 0.00 0.00 0.00 3.18
450 451 1.339291 TGCGAAAATTGCCATGTGTGA 59.661 42.857 0.00 0.00 0.00 3.58
451 452 1.780806 TGCGAAAATTGCCATGTGTG 58.219 45.000 0.00 0.00 0.00 3.82
452 453 2.747396 ATGCGAAAATTGCCATGTGT 57.253 40.000 0.00 0.00 0.00 3.72
453 454 3.509740 TGTATGCGAAAATTGCCATGTG 58.490 40.909 0.00 0.00 0.00 3.21
454 455 3.865011 TGTATGCGAAAATTGCCATGT 57.135 38.095 0.00 0.00 0.00 3.21
455 456 8.588789 CATATAATGTATGCGAAAATTGCCATG 58.411 33.333 0.00 0.00 0.00 3.66
456 457 7.760794 CCATATAATGTATGCGAAAATTGCCAT 59.239 33.333 0.00 0.00 0.00 4.40
457 458 7.040132 TCCATATAATGTATGCGAAAATTGCCA 60.040 33.333 0.00 0.00 0.00 4.92
458 459 7.312154 TCCATATAATGTATGCGAAAATTGCC 58.688 34.615 0.00 0.00 0.00 4.52
459 460 8.741101 TTCCATATAATGTATGCGAAAATTGC 57.259 30.769 0.00 0.00 0.00 3.56
494 495 9.553064 TCACAGTAAAAATTGCCATGTTATTTT 57.447 25.926 0.00 0.00 34.03 1.82
495 496 9.553064 TTCACAGTAAAAATTGCCATGTTATTT 57.447 25.926 0.00 0.00 0.00 1.40
496 497 9.723601 ATTCACAGTAAAAATTGCCATGTTATT 57.276 25.926 0.00 0.00 0.00 1.40
497 498 9.723601 AATTCACAGTAAAAATTGCCATGTTAT 57.276 25.926 0.00 0.00 0.00 1.89
498 499 9.553064 AAATTCACAGTAAAAATTGCCATGTTA 57.447 25.926 0.00 0.00 0.00 2.41
499 500 8.344098 CAAATTCACAGTAAAAATTGCCATGTT 58.656 29.630 0.00 0.00 0.00 2.71
500 501 7.520292 GCAAATTCACAGTAAAAATTGCCATGT 60.520 33.333 8.50 0.00 0.00 3.21
2866 2880 5.528870 CCTGTTTGGTTCCAAATAAGTCAC 58.471 41.667 18.11 6.79 38.07 3.67
2888 2902 0.842635 ATCTGAGTCCATTCAGGGCC 59.157 55.000 0.00 0.00 45.84 5.80
2920 2934 1.314730 TGGGGAAGAGAAACAAACGC 58.685 50.000 0.00 0.00 0.00 4.84
2921 2935 3.317993 ACAATGGGGAAGAGAAACAAACG 59.682 43.478 0.00 0.00 0.00 3.60
2963 2977 8.148807 TGAAATTGTCATTAAAGAACTCGTCA 57.851 30.769 0.00 0.00 0.00 4.35
2975 2989 7.673673 CGATGTCGGGGATGAAATTGTCATTA 61.674 42.308 0.00 0.00 40.42 1.90
3036 3050 1.680522 GGAGCAGCGGAAGGAGATGA 61.681 60.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.