Multiple sequence alignment - TraesCS7D01G228100

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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 TraesCS7D01G228100 chr7D 100.000 2922 0 0 1 2922 188320234 188317313 0.000000e+00 5397.0
1 TraesCS7D01G228100 chr7D 98.155 542 5 5 2383 2922 188310819 188310281 0.000000e+00 941.0
2 TraesCS7D01G228100 chr7D 96.324 544 15 5 2383 2922 97345456 97344914 0.000000e+00 889.0
3 TraesCS7D01G228100 chr7D 96.330 545 13 5 2383 2922 552945199 552944657 0.000000e+00 889.0
4 TraesCS7D01G228100 chr7D 98.113 265 5 0 13 277 384952518 384952254 2.050000e-126 462.0
5 TraesCS7D01G228100 chr7D 98.113 265 5 0 13 277 470431178 470430914 2.050000e-126 462.0
6 TraesCS7D01G228100 chr7D 97.736 265 6 0 13 277 470423312 470423048 9.540000e-125 457.0
7 TraesCS7D01G228100 chr7D 96.604 265 9 0 13 277 384960386 384960122 9.610000e-120 440.0
8 TraesCS7D01G228100 chr7D 89.238 223 24 0 980 1202 188361495 188361273 2.220000e-71 279.0
9 TraesCS7D01G228100 chr7D 84.091 88 9 4 267 353 127077694 127077777 2.410000e-11 80.5
10 TraesCS7D01G228100 chr7A 88.462 1430 121 16 976 2387 195567893 195569296 0.000000e+00 1687.0
11 TraesCS7D01G228100 chr7A 91.343 901 45 12 1494 2387 195734774 195735648 0.000000e+00 1201.0
12 TraesCS7D01G228100 chr7A 85.899 695 58 19 278 950 195567231 195567907 0.000000e+00 704.0
13 TraesCS7D01G228100 chr7A 93.293 328 9 6 976 1302 195733836 195734151 3.410000e-129 472.0
14 TraesCS7D01G228100 chr7A 87.649 251 28 1 1293 1543 195734615 195734862 3.680000e-74 289.0
15 TraesCS7D01G228100 chr7A 87.383 214 27 0 980 1193 195550094 195550307 2.250000e-61 246.0
16 TraesCS7D01G228100 chr7A 94.904 157 7 1 794 950 195733695 195733850 8.090000e-61 244.0
17 TraesCS7D01G228100 chr7A 90.625 96 6 2 635 727 195733462 195733557 1.100000e-24 124.0
18 TraesCS7D01G228100 chr7B 91.944 1142 78 8 976 2104 332172836 332171696 0.000000e+00 1587.0
19 TraesCS7D01G228100 chr7B 89.900 1099 94 7 1302 2387 332242691 332241597 0.000000e+00 1399.0
20 TraesCS7D01G228100 chr7B 86.275 408 39 2 288 678 332245695 332245288 7.480000e-116 427.0
21 TraesCS7D01G228100 chr7B 92.708 288 11 3 667 954 332243378 332243101 9.750000e-110 407.0
22 TraesCS7D01G228100 chr7B 94.872 234 10 1 976 1207 332243119 332242886 5.950000e-97 364.0
23 TraesCS7D01G228100 chr7B 87.234 282 35 1 2106 2387 332171482 332171202 1.310000e-83 320.0
24 TraesCS7D01G228100 chr7B 88.341 223 26 0 980 1202 332256131 332255909 4.800000e-68 268.0
25 TraesCS7D01G228100 chr7B 93.671 158 9 1 796 953 332172975 332172819 4.870000e-58 235.0
26 TraesCS7D01G228100 chr6D 96.673 541 15 3 2383 2922 82499230 82498692 0.000000e+00 896.0
27 TraesCS7D01G228100 chr3D 96.488 541 13 5 2383 2922 133567391 133566856 0.000000e+00 889.0
28 TraesCS7D01G228100 chr3D 96.475 539 15 4 2386 2922 49633168 49632632 0.000000e+00 887.0
29 TraesCS7D01G228100 chr3D 96.303 541 18 2 2383 2922 316516367 316515828 0.000000e+00 887.0
30 TraesCS7D01G228100 chr3D 96.310 542 16 4 2385 2922 577004921 577004380 0.000000e+00 887.0
31 TraesCS7D01G228100 chr3D 95.668 554 19 5 2370 2922 66918911 66918362 0.000000e+00 885.0
32 TraesCS7D01G228100 chr3D 93.208 265 18 0 13 277 546008679 546008943 9.820000e-105 390.0
33 TraesCS7D01G228100 chr3D 76.471 136 30 2 297 431 61185104 61184970 4.040000e-09 73.1
34 TraesCS7D01G228100 chr3D 76.230 122 29 0 297 418 451377096 451376975 6.760000e-07 65.8
35 TraesCS7D01G228100 chr2D 97.736 265 6 0 13 277 198284635 198284899 9.540000e-125 457.0
36 TraesCS7D01G228100 chr2D 95.849 265 11 0 13 277 198296383 198296647 2.080000e-116 429.0
37 TraesCS7D01G228100 chr2D 93.893 262 14 2 13 273 477158397 477158137 7.590000e-106 394.0
38 TraesCS7D01G228100 chr2D 93.233 266 16 2 13 277 477150445 477150181 9.820000e-105 390.0
39 TraesCS7D01G228100 chr2D 88.000 75 7 2 281 354 198276442 198276515 1.440000e-13 87.9
40 TraesCS7D01G228100 chr3B 89.189 74 6 2 281 353 208757028 208756956 1.120000e-14 91.6
41 TraesCS7D01G228100 chr4B 88.000 75 7 2 281 354 64374679 64374752 1.440000e-13 87.9
42 TraesCS7D01G228100 chr5A 87.500 72 7 2 281 351 154452260 154452330 6.710000e-12 82.4
43 TraesCS7D01G228100 chr5D 86.301 73 10 0 281 353 487645779 487645707 2.410000e-11 80.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G228100 chr7D 188317313 188320234 2921 True 5397.00 5397 100.000000 1 2922 1 chr7D.!!$R3 2921
1 TraesCS7D01G228100 chr7D 188310281 188310819 538 True 941.00 941 98.155000 2383 2922 1 chr7D.!!$R2 539
2 TraesCS7D01G228100 chr7D 97344914 97345456 542 True 889.00 889 96.324000 2383 2922 1 chr7D.!!$R1 539
3 TraesCS7D01G228100 chr7D 552944657 552945199 542 True 889.00 889 96.330000 2383 2922 1 chr7D.!!$R9 539
4 TraesCS7D01G228100 chr7A 195567231 195569296 2065 False 1195.50 1687 87.180500 278 2387 2 chr7A.!!$F2 2109
5 TraesCS7D01G228100 chr7A 195733462 195735648 2186 False 466.00 1201 91.562800 635 2387 5 chr7A.!!$F3 1752
6 TraesCS7D01G228100 chr7B 332171202 332172975 1773 True 714.00 1587 90.949667 796 2387 3 chr7B.!!$R2 1591
7 TraesCS7D01G228100 chr7B 332241597 332245695 4098 True 649.25 1399 90.938750 288 2387 4 chr7B.!!$R3 2099
8 TraesCS7D01G228100 chr6D 82498692 82499230 538 True 896.00 896 96.673000 2383 2922 1 chr6D.!!$R1 539
9 TraesCS7D01G228100 chr3D 133566856 133567391 535 True 889.00 889 96.488000 2383 2922 1 chr3D.!!$R4 539
10 TraesCS7D01G228100 chr3D 49632632 49633168 536 True 887.00 887 96.475000 2386 2922 1 chr3D.!!$R1 536
11 TraesCS7D01G228100 chr3D 316515828 316516367 539 True 887.00 887 96.303000 2383 2922 1 chr3D.!!$R5 539
12 TraesCS7D01G228100 chr3D 577004380 577004921 541 True 887.00 887 96.310000 2385 2922 1 chr3D.!!$R7 537
13 TraesCS7D01G228100 chr3D 66918362 66918911 549 True 885.00 885 95.668000 2370 2922 1 chr3D.!!$R3 552

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
273 274 0.108585 AGCATGATTATCCGGGCGTT 59.891 50.0 0.0 0.0 0.00 4.84 F
399 400 0.179121 CGGCATGAATGTGCAGCAAT 60.179 50.0 0.0 0.0 46.81 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 4301 0.108041 CGTAACCACGCCCATAACCT 60.108 55.0 0.0 0.0 42.05 3.50 R
2247 5168 0.249398 GGCGGTAGTTGATGGAGTGT 59.751 55.0 0.0 0.0 0.00 3.55 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.752961 TTTTACTGTTTTAATTCAACTTAGGGC 57.247 29.630 0.00 0.00 0.00 5.19
51 52 6.969993 ACTGTTTTAATTCAACTTAGGGCA 57.030 33.333 2.94 0.00 0.00 5.36
52 53 7.539034 ACTGTTTTAATTCAACTTAGGGCAT 57.461 32.000 2.94 0.00 0.00 4.40
53 54 7.962441 ACTGTTTTAATTCAACTTAGGGCATT 58.038 30.769 2.94 0.00 0.00 3.56
54 55 8.428852 ACTGTTTTAATTCAACTTAGGGCATTT 58.571 29.630 2.94 0.00 0.00 2.32
55 56 9.921637 CTGTTTTAATTCAACTTAGGGCATTTA 57.078 29.630 2.94 0.00 0.00 1.40
112 113 7.633193 AATTACCTTTGTAATATTCGGCACA 57.367 32.000 0.00 0.00 44.89 4.57
113 114 7.633193 ATTACCTTTGTAATATTCGGCACAA 57.367 32.000 0.00 0.00 44.05 3.33
114 115 5.968528 ACCTTTGTAATATTCGGCACAAA 57.031 34.783 11.76 11.76 36.29 2.83
115 116 5.705902 ACCTTTGTAATATTCGGCACAAAC 58.294 37.500 9.25 0.00 36.29 2.93
116 117 5.099575 CCTTTGTAATATTCGGCACAAACC 58.900 41.667 9.25 0.00 36.29 3.27
127 128 3.584095 GGCACAAACCGAACATTTTTG 57.416 42.857 0.00 0.00 36.49 2.44
128 129 2.933260 GGCACAAACCGAACATTTTTGT 59.067 40.909 0.00 0.00 42.76 2.83
129 130 3.372514 GGCACAAACCGAACATTTTTGTT 59.627 39.130 0.00 0.00 40.62 2.83
130 131 4.142795 GGCACAAACCGAACATTTTTGTTT 60.143 37.500 0.00 0.00 40.62 2.83
131 132 5.018869 GCACAAACCGAACATTTTTGTTTC 58.981 37.500 0.00 0.00 40.62 2.78
132 133 5.389935 GCACAAACCGAACATTTTTGTTTCA 60.390 36.000 0.00 0.00 40.62 2.69
133 134 6.593978 CACAAACCGAACATTTTTGTTTCAA 58.406 32.000 0.00 0.00 40.62 2.69
134 135 7.239972 CACAAACCGAACATTTTTGTTTCAAT 58.760 30.769 0.00 0.00 40.62 2.57
135 136 7.215942 CACAAACCGAACATTTTTGTTTCAATG 59.784 33.333 0.00 0.00 40.62 2.82
136 137 6.976636 AACCGAACATTTTTGTTTCAATGT 57.023 29.167 0.00 0.00 43.94 2.71
144 145 9.824534 AACATTTTTGTTTCAATGTTTGAAGAC 57.175 25.926 4.75 5.87 46.70 3.01
154 155 8.545229 TTCAATGTTTGAAGACATTTGTTTGT 57.455 26.923 0.81 0.00 45.38 2.83
155 156 8.545229 TCAATGTTTGAAGACATTTGTTTGTT 57.455 26.923 0.81 0.00 45.38 2.83
156 157 8.997323 TCAATGTTTGAAGACATTTGTTTGTTT 58.003 25.926 0.81 0.00 45.38 2.83
157 158 9.053135 CAATGTTTGAAGACATTTGTTTGTTTG 57.947 29.630 0.81 0.00 45.38 2.93
158 159 6.597614 TGTTTGAAGACATTTGTTTGTTTGC 58.402 32.000 0.00 0.00 0.00 3.68
159 160 5.793026 TTGAAGACATTTGTTTGTTTGCC 57.207 34.783 0.00 0.00 0.00 4.52
160 161 4.825422 TGAAGACATTTGTTTGTTTGCCA 58.175 34.783 0.00 0.00 0.00 4.92
161 162 5.426504 TGAAGACATTTGTTTGTTTGCCAT 58.573 33.333 0.00 0.00 0.00 4.40
162 163 6.577103 TGAAGACATTTGTTTGTTTGCCATA 58.423 32.000 0.00 0.00 0.00 2.74
163 164 7.215789 TGAAGACATTTGTTTGTTTGCCATAT 58.784 30.769 0.00 0.00 0.00 1.78
164 165 7.714377 TGAAGACATTTGTTTGTTTGCCATATT 59.286 29.630 0.00 0.00 0.00 1.28
165 166 8.449251 AAGACATTTGTTTGTTTGCCATATTT 57.551 26.923 0.00 0.00 0.00 1.40
166 167 8.449251 AGACATTTGTTTGTTTGCCATATTTT 57.551 26.923 0.00 0.00 0.00 1.82
167 168 8.344098 AGACATTTGTTTGTTTGCCATATTTTG 58.656 29.630 0.00 0.00 0.00 2.44
168 169 8.218338 ACATTTGTTTGTTTGCCATATTTTGA 57.782 26.923 0.00 0.00 0.00 2.69
169 170 8.680903 ACATTTGTTTGTTTGCCATATTTTGAA 58.319 25.926 0.00 0.00 0.00 2.69
170 171 9.680315 CATTTGTTTGTTTGCCATATTTTGAAT 57.320 25.926 0.00 0.00 0.00 2.57
172 173 9.512435 TTTGTTTGTTTGCCATATTTTGAATTG 57.488 25.926 0.00 0.00 0.00 2.32
173 174 8.442632 TGTTTGTTTGCCATATTTTGAATTGA 57.557 26.923 0.00 0.00 0.00 2.57
174 175 9.064706 TGTTTGTTTGCCATATTTTGAATTGAT 57.935 25.926 0.00 0.00 0.00 2.57
175 176 9.896263 GTTTGTTTGCCATATTTTGAATTGATT 57.104 25.926 0.00 0.00 0.00 2.57
199 200 9.796120 ATTTTTGAATCAGTTTTGAACTAACGA 57.204 25.926 0.00 0.00 40.46 3.85
200 201 9.627395 TTTTTGAATCAGTTTTGAACTAACGAA 57.373 25.926 0.00 0.00 40.46 3.85
201 202 9.627395 TTTTGAATCAGTTTTGAACTAACGAAA 57.373 25.926 0.00 0.00 40.46 3.46
202 203 8.835467 TTGAATCAGTTTTGAACTAACGAAAG 57.165 30.769 0.00 0.00 40.46 2.62
203 204 7.981142 TGAATCAGTTTTGAACTAACGAAAGT 58.019 30.769 0.00 0.00 44.02 2.66
204 205 8.455682 TGAATCAGTTTTGAACTAACGAAAGTT 58.544 29.630 6.83 6.83 46.62 2.66
205 206 9.285770 GAATCAGTTTTGAACTAACGAAAGTTT 57.714 29.630 8.22 0.00 46.68 2.66
207 208 9.931210 ATCAGTTTTGAACTAACGAAAGTTTAG 57.069 29.630 8.22 0.00 46.68 1.85
218 219 5.074430 ACGAAAGTTTAGCAACAGTAACG 57.926 39.130 0.00 0.00 46.40 3.18
219 220 4.805192 ACGAAAGTTTAGCAACAGTAACGA 59.195 37.500 0.00 0.00 46.40 3.85
220 221 5.291614 ACGAAAGTTTAGCAACAGTAACGAA 59.708 36.000 0.00 0.00 46.40 3.85
221 222 5.839239 CGAAAGTTTAGCAACAGTAACGAAG 59.161 40.000 0.00 0.00 35.05 3.79
222 223 5.668558 AAGTTTAGCAACAGTAACGAAGG 57.331 39.130 0.00 0.00 35.05 3.46
223 224 4.700700 AGTTTAGCAACAGTAACGAAGGT 58.299 39.130 0.00 0.00 35.05 3.50
224 225 4.510340 AGTTTAGCAACAGTAACGAAGGTG 59.490 41.667 0.00 0.00 35.05 4.00
225 226 2.902705 AGCAACAGTAACGAAGGTGA 57.097 45.000 0.00 0.00 0.00 4.02
226 227 2.480845 AGCAACAGTAACGAAGGTGAC 58.519 47.619 0.00 0.00 0.00 3.67
227 228 1.191647 GCAACAGTAACGAAGGTGACG 59.808 52.381 0.00 0.00 32.28 4.35
228 229 2.466846 CAACAGTAACGAAGGTGACGT 58.533 47.619 0.00 0.00 45.89 4.34
229 230 2.129823 ACAGTAACGAAGGTGACGTG 57.870 50.000 0.00 0.00 43.16 4.49
230 231 1.269413 ACAGTAACGAAGGTGACGTGG 60.269 52.381 0.00 0.00 43.16 4.94
231 232 0.319297 AGTAACGAAGGTGACGTGGC 60.319 55.000 0.00 0.00 43.16 5.01
232 233 0.598158 GTAACGAAGGTGACGTGGCA 60.598 55.000 0.00 0.00 43.16 4.92
233 234 0.319083 TAACGAAGGTGACGTGGCAT 59.681 50.000 0.00 0.00 43.16 4.40
234 235 0.949105 AACGAAGGTGACGTGGCATC 60.949 55.000 0.00 0.00 43.16 3.91
235 236 1.374125 CGAAGGTGACGTGGCATCA 60.374 57.895 0.00 0.00 0.00 3.07
236 237 0.740868 CGAAGGTGACGTGGCATCAT 60.741 55.000 0.00 0.00 0.00 2.45
237 238 1.453155 GAAGGTGACGTGGCATCATT 58.547 50.000 0.00 0.00 0.00 2.57
238 239 2.627945 GAAGGTGACGTGGCATCATTA 58.372 47.619 0.00 0.00 0.00 1.90
239 240 2.315925 AGGTGACGTGGCATCATTAG 57.684 50.000 0.00 0.00 0.00 1.73
240 241 0.657840 GGTGACGTGGCATCATTAGC 59.342 55.000 0.00 0.00 0.00 3.09
241 242 1.368641 GTGACGTGGCATCATTAGCA 58.631 50.000 0.00 0.00 0.00 3.49
242 243 1.942657 GTGACGTGGCATCATTAGCAT 59.057 47.619 0.00 0.00 0.00 3.79
243 244 1.941975 TGACGTGGCATCATTAGCATG 59.058 47.619 0.00 0.00 0.00 4.06
244 245 1.265095 GACGTGGCATCATTAGCATGG 59.735 52.381 0.00 0.00 0.00 3.66
245 246 0.594602 CGTGGCATCATTAGCATGGG 59.405 55.000 0.00 0.00 0.00 4.00
246 247 1.815021 CGTGGCATCATTAGCATGGGA 60.815 52.381 0.00 0.00 0.00 4.37
247 248 2.522185 GTGGCATCATTAGCATGGGAT 58.478 47.619 0.00 0.00 0.00 3.85
248 249 2.895404 GTGGCATCATTAGCATGGGATT 59.105 45.455 0.00 0.00 0.00 3.01
249 250 4.081406 GTGGCATCATTAGCATGGGATTA 58.919 43.478 0.00 0.00 0.00 1.75
250 251 4.081406 TGGCATCATTAGCATGGGATTAC 58.919 43.478 0.00 0.00 0.00 1.89
251 252 4.202599 TGGCATCATTAGCATGGGATTACT 60.203 41.667 0.00 0.00 0.00 2.24
252 253 4.157289 GGCATCATTAGCATGGGATTACTG 59.843 45.833 0.00 0.00 0.00 2.74
253 254 4.763793 GCATCATTAGCATGGGATTACTGT 59.236 41.667 0.00 0.00 0.00 3.55
254 255 5.939883 GCATCATTAGCATGGGATTACTGTA 59.060 40.000 0.00 0.00 0.00 2.74
255 256 6.093219 GCATCATTAGCATGGGATTACTGTAG 59.907 42.308 0.00 0.00 0.00 2.74
256 257 5.551233 TCATTAGCATGGGATTACTGTAGC 58.449 41.667 0.00 0.00 0.00 3.58
257 258 5.071653 TCATTAGCATGGGATTACTGTAGCA 59.928 40.000 0.00 0.00 0.00 3.49
258 259 5.567037 TTAGCATGGGATTACTGTAGCAT 57.433 39.130 0.00 0.00 0.00 3.79
259 260 3.748083 AGCATGGGATTACTGTAGCATG 58.252 45.455 0.00 0.00 0.00 4.06
260 261 3.392285 AGCATGGGATTACTGTAGCATGA 59.608 43.478 0.00 0.00 0.00 3.07
261 262 4.042560 AGCATGGGATTACTGTAGCATGAT 59.957 41.667 0.00 0.00 0.00 2.45
262 263 4.763793 GCATGGGATTACTGTAGCATGATT 59.236 41.667 0.00 0.00 0.00 2.57
263 264 5.939883 GCATGGGATTACTGTAGCATGATTA 59.060 40.000 0.00 0.00 0.00 1.75
264 265 6.600822 GCATGGGATTACTGTAGCATGATTAT 59.399 38.462 0.00 0.00 0.00 1.28
265 266 7.201679 GCATGGGATTACTGTAGCATGATTATC 60.202 40.741 0.00 0.00 0.00 1.75
266 267 6.711277 TGGGATTACTGTAGCATGATTATCC 58.289 40.000 0.00 0.00 0.00 2.59
267 268 5.812642 GGGATTACTGTAGCATGATTATCCG 59.187 44.000 0.00 0.00 31.87 4.18
268 269 5.812642 GGATTACTGTAGCATGATTATCCGG 59.187 44.000 0.00 0.00 0.00 5.14
269 270 3.685139 ACTGTAGCATGATTATCCGGG 57.315 47.619 0.00 0.00 0.00 5.73
270 271 2.289694 ACTGTAGCATGATTATCCGGGC 60.290 50.000 0.00 0.00 0.00 6.13
271 272 1.337728 TGTAGCATGATTATCCGGGCG 60.338 52.381 0.00 0.00 0.00 6.13
272 273 0.973632 TAGCATGATTATCCGGGCGT 59.026 50.000 0.00 0.00 0.00 5.68
273 274 0.108585 AGCATGATTATCCGGGCGTT 59.891 50.000 0.00 0.00 0.00 4.84
274 275 1.346395 AGCATGATTATCCGGGCGTTA 59.654 47.619 0.00 0.00 0.00 3.18
275 276 1.463444 GCATGATTATCCGGGCGTTAC 59.537 52.381 0.00 0.00 0.00 2.50
276 277 2.761559 CATGATTATCCGGGCGTTACA 58.238 47.619 0.00 0.00 0.00 2.41
330 331 0.251386 TCCAGTGAGAGGTCGCTTCT 60.251 55.000 0.00 0.00 40.90 2.85
341 342 2.884685 CGCTTCTGCTCTGAGCCG 60.885 66.667 25.61 19.81 41.51 5.52
370 371 1.594310 GAAGAAGGCGCTCTGGAGT 59.406 57.895 7.64 0.00 0.00 3.85
378 379 1.301244 CGCTCTGGAGTTGTGCTGT 60.301 57.895 0.00 0.00 0.00 4.40
399 400 0.179121 CGGCATGAATGTGCAGCAAT 60.179 50.000 0.00 0.00 46.81 3.56
401 402 1.663643 GGCATGAATGTGCAGCAATTG 59.336 47.619 0.00 0.00 46.81 2.32
420 421 1.004560 CTTCGTGCAGGAGAGGCAA 60.005 57.895 9.34 0.00 43.91 4.52
445 446 1.792118 GCGGGCTCGGTTTTTGAGTT 61.792 55.000 8.71 0.00 35.85 3.01
523 534 8.598075 GCGTCTAGTTTTTAGAATTTCGGATAA 58.402 33.333 0.00 0.00 0.00 1.75
541 552 5.602628 GGATAACCCAACTGATCTACAGAC 58.397 45.833 0.00 0.00 40.90 3.51
555 566 6.598457 TGATCTACAGACTAATAGGATACCGC 59.402 42.308 0.00 0.00 37.17 5.68
623 655 5.424757 GTCCATATGCCTTTACACTGTACA 58.575 41.667 0.00 0.00 0.00 2.90
789 2862 4.767255 GTCAGTGCCCCGCTCTGG 62.767 72.222 13.86 0.00 46.15 3.86
865 2938 6.352222 CCCGGTTTGATCATATCCTAGCTAAT 60.352 42.308 0.00 0.00 0.00 1.73
903 2976 3.873910 ACATGGAGTTATCGAAGGTTGG 58.126 45.455 0.00 0.00 0.00 3.77
909 2982 5.001874 GGAGTTATCGAAGGTTGGAACTTT 58.998 41.667 0.00 0.00 0.00 2.66
923 2996 7.985184 AGGTTGGAACTTTTTAAAATTGGAGAC 59.015 33.333 0.55 0.00 0.00 3.36
924 2997 7.225931 GGTTGGAACTTTTTAAAATTGGAGACC 59.774 37.037 0.55 6.48 0.00 3.85
982 3055 8.557592 TTATTATTTTTGAACCAATGCATGCA 57.442 26.923 25.04 25.04 0.00 3.96
983 3056 7.633193 ATTATTTTTGAACCAATGCATGCAT 57.367 28.000 27.46 27.46 38.46 3.96
984 3057 8.734218 ATTATTTTTGAACCAATGCATGCATA 57.266 26.923 32.36 13.94 35.31 3.14
985 3058 5.859521 TTTTTGAACCAATGCATGCATAC 57.140 34.783 32.36 20.03 35.31 2.39
986 3059 4.532314 TTTGAACCAATGCATGCATACA 57.468 36.364 32.36 22.01 35.31 2.29
987 3060 4.739587 TTGAACCAATGCATGCATACAT 57.260 36.364 32.36 18.82 35.31 2.29
1047 3120 6.039270 AGCGATATCATCTCATCCTAAGCTAC 59.961 42.308 3.12 0.00 0.00 3.58
1142 3215 1.140804 GCTCCTGCTTCTCTCCGAC 59.859 63.158 0.00 0.00 36.03 4.79
1401 4075 2.979678 TGCCTAAGAAAGAGAAGTGGGT 59.020 45.455 0.00 0.00 0.00 4.51
1407 4081 3.858135 AGAAAGAGAAGTGGGTAGGTGA 58.142 45.455 0.00 0.00 0.00 4.02
1422 4096 4.458989 GGTAGGTGAAAACAAGCATGATGA 59.541 41.667 0.00 0.00 0.00 2.92
1429 4103 7.417116 GGTGAAAACAAGCATGATGAAGGATAT 60.417 37.037 0.00 0.00 0.00 1.63
1460 4152 1.832998 GAGGGTATGGAAACGGTGGTA 59.167 52.381 0.00 0.00 0.00 3.25
1485 4177 1.426751 GGTAACGGTGGGGGATATGA 58.573 55.000 0.00 0.00 0.00 2.15
1491 4183 2.041891 ACGGTGGGGGATATGAAAACAA 59.958 45.455 0.00 0.00 0.00 2.83
1497 4189 3.387699 GGGGGATATGAAAACAATGGTGG 59.612 47.826 0.00 0.00 0.00 4.61
1501 4193 4.202151 GGATATGAAAACAATGGTGGAGGC 60.202 45.833 0.00 0.00 0.00 4.70
1544 4236 1.024271 CAATGGTGGAGGTTATGGCG 58.976 55.000 0.00 0.00 0.00 5.69
1557 4249 3.244422 GGTTATGGCGATGGAGGTTATGA 60.244 47.826 0.00 0.00 0.00 2.15
1558 4250 2.847327 ATGGCGATGGAGGTTATGAG 57.153 50.000 0.00 0.00 0.00 2.90
1570 4262 3.356290 AGGTTATGAGAACAATGGTGGC 58.644 45.455 0.00 0.00 0.00 5.01
1572 4264 1.378531 TATGAGAACAATGGTGGCGC 58.621 50.000 0.00 0.00 0.00 6.53
1591 4283 1.325355 CGTATGGTGGAGGATACGGT 58.675 55.000 0.00 0.00 42.32 4.83
1593 4285 2.486982 CGTATGGTGGAGGATACGGTAG 59.513 54.545 0.00 0.00 42.32 3.18
1600 4292 2.242965 TGGAGGATACGGTAGTTCTGGA 59.757 50.000 0.00 0.00 46.39 3.86
1609 4301 0.963962 GTAGTTCTGGACACGGTGGA 59.036 55.000 13.48 0.00 0.00 4.02
1645 4337 4.256180 GGCGGTGGAGGCTATGGG 62.256 72.222 0.00 0.00 0.00 4.00
1726 4418 1.085796 TGGGGGATATGGTGGTGGT 59.914 57.895 0.00 0.00 0.00 4.16
1743 4435 1.598130 GTGGCGGATATGGTGGAGC 60.598 63.158 0.00 0.00 0.00 4.70
1863 4562 7.656948 CACAATGGTTGGAACTATGAAAACAAT 59.343 33.333 0.00 0.00 30.01 2.71
1864 4563 7.656948 ACAATGGTTGGAACTATGAAAACAATG 59.343 33.333 0.00 0.00 30.01 2.82
1969 4670 5.067413 CGTTATAGGAGCAAGGTCTGTAAGA 59.933 44.000 0.00 0.00 43.69 2.10
2247 5168 0.884259 CACTCACGGCAATGGTCACA 60.884 55.000 0.00 0.00 0.00 3.58
2266 5189 0.249398 ACACTCCATCAACTACCGCC 59.751 55.000 0.00 0.00 0.00 6.13
2310 5233 3.138798 GACACGCCGGCTCCTCTA 61.139 66.667 26.68 0.00 0.00 2.43
2343 5266 3.410631 TTGTAGCGAGGAAATCACCAA 57.589 42.857 0.00 0.00 0.00 3.67
2344 5267 3.627395 TGTAGCGAGGAAATCACCAAT 57.373 42.857 0.00 0.00 0.00 3.16
2346 5269 2.496899 AGCGAGGAAATCACCAATGT 57.503 45.000 0.00 0.00 0.00 2.71
2661 5586 2.169561 GGAAGGAGAGGTTGATGGAGAC 59.830 54.545 0.00 0.00 0.00 3.36
2812 5738 0.916809 CCCCTTTATATAGGCCCCCG 59.083 60.000 0.00 0.00 33.73 5.73
2815 5741 1.556238 CCTTTATATAGGCCCCCGGGA 60.556 57.143 26.32 0.00 37.50 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.752961 GCCCTAAGTTGAATTAAAACAGTAAAA 57.247 29.630 6.33 0.00 0.00 1.52
25 26 8.915036 TGCCCTAAGTTGAATTAAAACAGTAAA 58.085 29.630 6.33 0.00 0.00 2.01
26 27 8.466617 TGCCCTAAGTTGAATTAAAACAGTAA 57.533 30.769 6.33 0.00 0.00 2.24
27 28 8.644374 ATGCCCTAAGTTGAATTAAAACAGTA 57.356 30.769 6.33 0.00 0.00 2.74
28 29 6.969993 TGCCCTAAGTTGAATTAAAACAGT 57.030 33.333 6.33 0.00 0.00 3.55
29 30 8.831715 AAATGCCCTAAGTTGAATTAAAACAG 57.168 30.769 6.33 0.00 0.00 3.16
86 87 9.344772 TGTGCCGAATATTACAAAGGTAATTAT 57.655 29.630 5.52 0.00 45.62 1.28
87 88 8.734218 TGTGCCGAATATTACAAAGGTAATTA 57.266 30.769 5.52 0.00 45.62 1.40
88 89 7.633193 TGTGCCGAATATTACAAAGGTAATT 57.367 32.000 5.52 0.00 45.62 1.40
90 91 7.306953 GTTTGTGCCGAATATTACAAAGGTAA 58.693 34.615 12.42 0.00 41.87 2.85
91 92 6.127952 GGTTTGTGCCGAATATTACAAAGGTA 60.128 38.462 12.42 0.00 41.87 3.08
92 93 5.336134 GGTTTGTGCCGAATATTACAAAGGT 60.336 40.000 12.42 0.00 41.87 3.50
93 94 5.099575 GGTTTGTGCCGAATATTACAAAGG 58.900 41.667 12.42 2.92 41.87 3.11
107 108 2.933260 ACAAAAATGTTCGGTTTGTGCC 59.067 40.909 0.51 0.00 42.36 5.01
108 109 4.591998 AACAAAAATGTTCGGTTTGTGC 57.408 36.364 2.08 0.00 42.96 4.57
109 110 6.158175 TGAAACAAAAATGTTCGGTTTGTG 57.842 33.333 2.08 0.00 42.96 3.33
110 111 6.787085 TTGAAACAAAAATGTTCGGTTTGT 57.213 29.167 3.76 0.00 45.04 2.83
111 112 7.239972 ACATTGAAACAAAAATGTTCGGTTTG 58.760 30.769 3.76 0.00 42.85 2.93
112 113 7.371126 ACATTGAAACAAAAATGTTCGGTTT 57.629 28.000 0.00 0.00 42.85 3.27
113 114 6.976636 ACATTGAAACAAAAATGTTCGGTT 57.023 29.167 0.00 0.00 42.85 4.44
123 124 9.823098 CAAATGTCTTCAAACATTGAAACAAAA 57.177 25.926 16.80 2.23 46.49 2.44
124 125 8.997323 ACAAATGTCTTCAAACATTGAAACAAA 58.003 25.926 16.80 2.77 46.49 2.83
125 126 8.545229 ACAAATGTCTTCAAACATTGAAACAA 57.455 26.923 16.80 0.00 46.49 2.83
126 127 8.545229 AACAAATGTCTTCAAACATTGAAACA 57.455 26.923 15.94 15.94 46.49 2.83
127 128 9.264782 CAAACAAATGTCTTCAAACATTGAAAC 57.735 29.630 6.93 8.35 46.49 2.78
128 129 8.997323 ACAAACAAATGTCTTCAAACATTGAAA 58.003 25.926 6.93 0.00 46.49 2.69
129 130 8.545229 ACAAACAAATGTCTTCAAACATTGAA 57.455 26.923 5.50 5.50 46.49 2.69
130 131 8.545229 AACAAACAAATGTCTTCAAACATTGA 57.455 26.923 3.25 0.00 46.49 2.57
131 132 9.053135 CAAACAAACAAATGTCTTCAAACATTG 57.947 29.630 3.25 1.77 46.49 2.82
133 134 7.242783 GCAAACAAACAAATGTCTTCAAACAT 58.757 30.769 0.00 0.00 41.60 2.71
134 135 6.348050 GGCAAACAAACAAATGTCTTCAAACA 60.348 34.615 0.00 0.00 31.81 2.83
135 136 6.020984 GGCAAACAAACAAATGTCTTCAAAC 58.979 36.000 0.00 0.00 31.81 2.93
136 137 5.702670 TGGCAAACAAACAAATGTCTTCAAA 59.297 32.000 0.00 0.00 31.81 2.69
137 138 5.240891 TGGCAAACAAACAAATGTCTTCAA 58.759 33.333 0.00 0.00 31.81 2.69
138 139 4.825422 TGGCAAACAAACAAATGTCTTCA 58.175 34.783 0.00 0.00 31.81 3.02
139 140 5.989551 ATGGCAAACAAACAAATGTCTTC 57.010 34.783 0.00 0.00 31.81 2.87
140 141 8.449251 AAATATGGCAAACAAACAAATGTCTT 57.551 26.923 0.00 0.00 31.81 3.01
141 142 8.344098 CAAAATATGGCAAACAAACAAATGTCT 58.656 29.630 0.00 0.00 31.81 3.41
142 143 8.341173 TCAAAATATGGCAAACAAACAAATGTC 58.659 29.630 0.00 0.00 31.81 3.06
143 144 8.218338 TCAAAATATGGCAAACAAACAAATGT 57.782 26.923 0.00 0.00 34.24 2.71
144 145 9.680315 ATTCAAAATATGGCAAACAAACAAATG 57.320 25.926 0.00 0.00 0.00 2.32
146 147 9.512435 CAATTCAAAATATGGCAAACAAACAAA 57.488 25.926 0.00 0.00 0.00 2.83
147 148 8.896744 TCAATTCAAAATATGGCAAACAAACAA 58.103 25.926 0.00 0.00 0.00 2.83
148 149 8.442632 TCAATTCAAAATATGGCAAACAAACA 57.557 26.923 0.00 0.00 0.00 2.83
149 150 9.896263 AATCAATTCAAAATATGGCAAACAAAC 57.104 25.926 0.00 0.00 0.00 2.93
173 174 9.796120 TCGTTAGTTCAAAACTGATTCAAAAAT 57.204 25.926 2.65 0.00 42.84 1.82
174 175 9.627395 TTCGTTAGTTCAAAACTGATTCAAAAA 57.373 25.926 2.65 0.00 42.84 1.94
175 176 9.627395 TTTCGTTAGTTCAAAACTGATTCAAAA 57.373 25.926 2.65 0.00 42.84 2.44
176 177 9.284594 CTTTCGTTAGTTCAAAACTGATTCAAA 57.715 29.630 2.65 0.00 42.84 2.69
177 178 8.455682 ACTTTCGTTAGTTCAAAACTGATTCAA 58.544 29.630 2.65 0.00 42.84 2.69
178 179 7.981142 ACTTTCGTTAGTTCAAAACTGATTCA 58.019 30.769 2.65 0.00 42.84 2.57
179 180 8.836959 AACTTTCGTTAGTTCAAAACTGATTC 57.163 30.769 2.65 0.00 42.84 2.52
181 182 9.931210 CTAAACTTTCGTTAGTTCAAAACTGAT 57.069 29.630 2.65 0.00 42.84 2.90
182 183 7.906527 GCTAAACTTTCGTTAGTTCAAAACTGA 59.093 33.333 2.65 0.00 42.84 3.41
183 184 7.694784 TGCTAAACTTTCGTTAGTTCAAAACTG 59.305 33.333 2.65 0.00 42.84 3.16
184 185 7.754625 TGCTAAACTTTCGTTAGTTCAAAACT 58.245 30.769 5.61 0.00 45.40 2.66
185 186 7.958112 TGCTAAACTTTCGTTAGTTCAAAAC 57.042 32.000 5.61 0.00 37.37 2.43
186 187 8.021973 TGTTGCTAAACTTTCGTTAGTTCAAAA 58.978 29.630 5.61 0.60 37.37 2.44
187 188 7.528307 TGTTGCTAAACTTTCGTTAGTTCAAA 58.472 30.769 5.61 0.00 37.37 2.69
188 189 7.074507 TGTTGCTAAACTTTCGTTAGTTCAA 57.925 32.000 5.61 4.16 37.37 2.69
189 190 6.314400 ACTGTTGCTAAACTTTCGTTAGTTCA 59.686 34.615 5.61 0.00 37.37 3.18
190 191 6.712549 ACTGTTGCTAAACTTTCGTTAGTTC 58.287 36.000 5.61 0.00 37.37 3.01
191 192 6.673154 ACTGTTGCTAAACTTTCGTTAGTT 57.327 33.333 0.18 0.18 39.97 2.24
192 193 7.515684 CGTTACTGTTGCTAAACTTTCGTTAGT 60.516 37.037 0.00 0.00 37.19 2.24
193 194 6.784227 CGTTACTGTTGCTAAACTTTCGTTAG 59.216 38.462 0.00 0.00 37.19 2.34
194 195 6.475076 TCGTTACTGTTGCTAAACTTTCGTTA 59.525 34.615 0.00 0.00 37.19 3.18
195 196 5.291614 TCGTTACTGTTGCTAAACTTTCGTT 59.708 36.000 0.00 0.00 37.19 3.85
196 197 4.805192 TCGTTACTGTTGCTAAACTTTCGT 59.195 37.500 0.00 0.00 37.19 3.85
197 198 5.319232 TCGTTACTGTTGCTAAACTTTCG 57.681 39.130 0.00 0.00 37.19 3.46
198 199 6.134061 CCTTCGTTACTGTTGCTAAACTTTC 58.866 40.000 0.00 0.00 37.19 2.62
199 200 5.587443 ACCTTCGTTACTGTTGCTAAACTTT 59.413 36.000 0.00 0.00 37.19 2.66
200 201 5.007332 CACCTTCGTTACTGTTGCTAAACTT 59.993 40.000 0.00 0.00 37.19 2.66
201 202 4.510340 CACCTTCGTTACTGTTGCTAAACT 59.490 41.667 0.00 0.00 37.19 2.66
202 203 4.508861 TCACCTTCGTTACTGTTGCTAAAC 59.491 41.667 0.00 0.00 36.78 2.01
203 204 4.508861 GTCACCTTCGTTACTGTTGCTAAA 59.491 41.667 0.00 0.00 0.00 1.85
204 205 4.053295 GTCACCTTCGTTACTGTTGCTAA 58.947 43.478 0.00 0.00 0.00 3.09
205 206 3.645884 GTCACCTTCGTTACTGTTGCTA 58.354 45.455 0.00 0.00 0.00 3.49
206 207 2.480845 GTCACCTTCGTTACTGTTGCT 58.519 47.619 0.00 0.00 0.00 3.91
207 208 1.191647 CGTCACCTTCGTTACTGTTGC 59.808 52.381 0.00 0.00 0.00 4.17
208 209 2.217847 CACGTCACCTTCGTTACTGTTG 59.782 50.000 0.00 0.00 39.55 3.33
209 210 2.466846 CACGTCACCTTCGTTACTGTT 58.533 47.619 0.00 0.00 39.55 3.16
210 211 1.269413 CCACGTCACCTTCGTTACTGT 60.269 52.381 0.00 0.00 39.55 3.55
211 212 1.415374 CCACGTCACCTTCGTTACTG 58.585 55.000 0.00 0.00 39.55 2.74
212 213 0.319297 GCCACGTCACCTTCGTTACT 60.319 55.000 0.00 0.00 39.55 2.24
213 214 0.598158 TGCCACGTCACCTTCGTTAC 60.598 55.000 0.00 0.00 39.55 2.50
214 215 0.319083 ATGCCACGTCACCTTCGTTA 59.681 50.000 0.00 0.00 39.55 3.18
215 216 0.949105 GATGCCACGTCACCTTCGTT 60.949 55.000 0.00 0.00 39.55 3.85
216 217 1.374252 GATGCCACGTCACCTTCGT 60.374 57.895 0.00 0.00 42.33 3.85
217 218 0.740868 ATGATGCCACGTCACCTTCG 60.741 55.000 0.00 0.00 0.00 3.79
218 219 1.453155 AATGATGCCACGTCACCTTC 58.547 50.000 0.00 0.00 0.00 3.46
219 220 2.632377 CTAATGATGCCACGTCACCTT 58.368 47.619 0.00 0.00 0.00 3.50
220 221 1.743772 GCTAATGATGCCACGTCACCT 60.744 52.381 0.00 0.00 0.00 4.00
221 222 0.657840 GCTAATGATGCCACGTCACC 59.342 55.000 0.00 0.00 0.00 4.02
222 223 1.368641 TGCTAATGATGCCACGTCAC 58.631 50.000 0.00 0.00 0.00 3.67
223 224 1.941975 CATGCTAATGATGCCACGTCA 59.058 47.619 0.00 0.00 35.67 4.35
224 225 1.265095 CCATGCTAATGATGCCACGTC 59.735 52.381 0.00 0.00 35.67 4.34
225 226 1.311859 CCATGCTAATGATGCCACGT 58.688 50.000 0.00 0.00 35.67 4.49
226 227 0.594602 CCCATGCTAATGATGCCACG 59.405 55.000 0.00 0.00 35.67 4.94
227 228 1.985473 TCCCATGCTAATGATGCCAC 58.015 50.000 0.00 0.00 35.67 5.01
228 229 2.984435 ATCCCATGCTAATGATGCCA 57.016 45.000 0.00 0.00 35.67 4.92
229 230 4.157289 CAGTAATCCCATGCTAATGATGCC 59.843 45.833 0.00 0.00 35.67 4.40
230 231 4.763793 ACAGTAATCCCATGCTAATGATGC 59.236 41.667 0.00 0.00 35.67 3.91
231 232 6.093219 GCTACAGTAATCCCATGCTAATGATG 59.907 42.308 0.00 0.00 35.67 3.07
232 233 6.176183 GCTACAGTAATCCCATGCTAATGAT 58.824 40.000 0.00 0.00 35.67 2.45
233 234 5.071653 TGCTACAGTAATCCCATGCTAATGA 59.928 40.000 0.00 0.00 35.67 2.57
234 235 5.308014 TGCTACAGTAATCCCATGCTAATG 58.692 41.667 0.00 0.00 0.00 1.90
235 236 5.567037 TGCTACAGTAATCCCATGCTAAT 57.433 39.130 0.00 0.00 0.00 1.73
236 237 5.071653 TCATGCTACAGTAATCCCATGCTAA 59.928 40.000 0.00 0.00 32.36 3.09
237 238 4.592778 TCATGCTACAGTAATCCCATGCTA 59.407 41.667 0.00 0.00 32.36 3.49
238 239 3.392285 TCATGCTACAGTAATCCCATGCT 59.608 43.478 0.00 0.00 32.36 3.79
239 240 3.743521 TCATGCTACAGTAATCCCATGC 58.256 45.455 0.00 0.00 32.36 4.06
240 241 7.281774 GGATAATCATGCTACAGTAATCCCATG 59.718 40.741 0.00 0.00 33.29 3.66
241 242 7.341805 GGATAATCATGCTACAGTAATCCCAT 58.658 38.462 0.00 0.00 0.00 4.00
242 243 6.574269 CGGATAATCATGCTACAGTAATCCCA 60.574 42.308 0.00 0.00 0.00 4.37
243 244 5.812642 CGGATAATCATGCTACAGTAATCCC 59.187 44.000 0.00 0.00 0.00 3.85
244 245 5.812642 CCGGATAATCATGCTACAGTAATCC 59.187 44.000 0.00 0.00 0.00 3.01
245 246 5.812642 CCCGGATAATCATGCTACAGTAATC 59.187 44.000 0.73 0.00 0.00 1.75
246 247 5.734720 CCCGGATAATCATGCTACAGTAAT 58.265 41.667 0.73 0.00 0.00 1.89
247 248 4.562757 GCCCGGATAATCATGCTACAGTAA 60.563 45.833 0.73 0.00 0.00 2.24
248 249 3.056107 GCCCGGATAATCATGCTACAGTA 60.056 47.826 0.73 0.00 0.00 2.74
249 250 2.289694 GCCCGGATAATCATGCTACAGT 60.290 50.000 0.73 0.00 0.00 3.55
250 251 2.350522 GCCCGGATAATCATGCTACAG 58.649 52.381 0.73 0.00 0.00 2.74
251 252 1.337728 CGCCCGGATAATCATGCTACA 60.338 52.381 0.73 0.00 0.00 2.74
252 253 1.337823 ACGCCCGGATAATCATGCTAC 60.338 52.381 0.73 0.00 0.00 3.58
253 254 0.973632 ACGCCCGGATAATCATGCTA 59.026 50.000 0.73 0.00 0.00 3.49
254 255 0.108585 AACGCCCGGATAATCATGCT 59.891 50.000 0.73 0.00 0.00 3.79
255 256 1.463444 GTAACGCCCGGATAATCATGC 59.537 52.381 0.73 0.00 0.00 4.06
256 257 2.761559 TGTAACGCCCGGATAATCATG 58.238 47.619 0.73 0.00 0.00 3.07
257 258 3.596214 GATGTAACGCCCGGATAATCAT 58.404 45.455 0.73 0.00 0.00 2.45
258 259 2.289195 GGATGTAACGCCCGGATAATCA 60.289 50.000 0.73 0.00 0.00 2.57
259 260 2.344025 GGATGTAACGCCCGGATAATC 58.656 52.381 0.73 0.00 0.00 1.75
260 261 1.002773 GGGATGTAACGCCCGGATAAT 59.997 52.381 0.73 0.00 34.00 1.28
261 262 0.393820 GGGATGTAACGCCCGGATAA 59.606 55.000 0.73 0.00 34.00 1.75
262 263 2.051941 GGGATGTAACGCCCGGATA 58.948 57.895 0.73 0.00 34.00 2.59
263 264 2.826702 GGGATGTAACGCCCGGAT 59.173 61.111 0.73 0.00 34.00 4.18
267 268 1.095807 GCAAGAGGGATGTAACGCCC 61.096 60.000 0.00 0.00 45.04 6.13
268 269 1.095807 GGCAAGAGGGATGTAACGCC 61.096 60.000 0.00 0.00 0.00 5.68
269 270 1.095807 GGGCAAGAGGGATGTAACGC 61.096 60.000 0.00 0.00 0.00 4.84
270 271 0.810031 CGGGCAAGAGGGATGTAACG 60.810 60.000 0.00 0.00 0.00 3.18
271 272 0.463833 CCGGGCAAGAGGGATGTAAC 60.464 60.000 0.00 0.00 0.00 2.50
272 273 1.912220 CCGGGCAAGAGGGATGTAA 59.088 57.895 0.00 0.00 0.00 2.41
273 274 2.742116 GCCGGGCAAGAGGGATGTA 61.742 63.158 15.62 0.00 0.00 2.29
274 275 4.115199 GCCGGGCAAGAGGGATGT 62.115 66.667 15.62 0.00 0.00 3.06
275 276 3.426309 ATGCCGGGCAAGAGGGATG 62.426 63.158 27.70 0.00 43.62 3.51
276 277 3.099170 ATGCCGGGCAAGAGGGAT 61.099 61.111 27.70 4.18 43.62 3.85
330 331 0.181114 ATTAATGCCGGCTCAGAGCA 59.819 50.000 29.70 5.17 44.75 4.26
378 379 2.409055 GCTGCACATTCATGCCGGA 61.409 57.895 5.05 0.00 45.50 5.14
401 402 2.817396 GCCTCTCCTGCACGAAGC 60.817 66.667 0.00 0.00 45.96 3.86
445 446 2.123208 TGTCCGACACCCAGACCA 60.123 61.111 0.00 0.00 0.00 4.02
523 534 6.551601 CCTATTAGTCTGTAGATCAGTTGGGT 59.448 42.308 0.00 0.00 43.97 4.51
541 552 3.928727 TCCAACGCGGTATCCTATTAG 57.071 47.619 12.47 0.00 35.57 1.73
549 560 0.804544 CGTGTCATCCAACGCGGTAT 60.805 55.000 12.47 0.00 46.48 2.73
555 566 2.476051 GCAGCGTGTCATCCAACG 59.524 61.111 0.00 0.00 0.00 4.10
604 629 7.279615 TGCTAATGTACAGTGTAAAGGCATAT 58.720 34.615 5.98 0.00 0.00 1.78
623 655 4.356405 TGATTCGACCCATCATGCTAAT 57.644 40.909 0.00 0.00 0.00 1.73
789 2862 0.696485 TGATTAGCTACCCCCACCCC 60.696 60.000 0.00 0.00 0.00 4.95
903 2976 5.404366 GCCGGTCTCCAATTTTAAAAAGTTC 59.596 40.000 1.90 0.00 0.00 3.01
909 2982 4.642885 CCTATGCCGGTCTCCAATTTTAAA 59.357 41.667 1.90 0.00 0.00 1.52
923 2996 3.653009 CATGCACGCCTATGCCGG 61.653 66.667 0.00 0.00 45.50 6.13
924 2997 4.318021 GCATGCACGCCTATGCCG 62.318 66.667 14.21 0.00 45.50 5.69
956 3029 9.175312 TGCATGCATTGGTTCAAAAATAATAAT 57.825 25.926 18.46 0.00 0.00 1.28
957 3030 8.557592 TGCATGCATTGGTTCAAAAATAATAA 57.442 26.923 18.46 0.00 0.00 1.40
958 3031 8.734218 ATGCATGCATTGGTTCAAAAATAATA 57.266 26.923 27.46 0.00 31.82 0.98
959 3032 7.633193 ATGCATGCATTGGTTCAAAAATAAT 57.367 28.000 27.46 0.00 31.82 1.28
960 3033 7.605309 TGTATGCATGCATTGGTTCAAAAATAA 59.395 29.630 36.23 11.97 37.82 1.40
961 3034 7.101700 TGTATGCATGCATTGGTTCAAAAATA 58.898 30.769 36.23 12.43 37.82 1.40
962 3035 5.938710 TGTATGCATGCATTGGTTCAAAAAT 59.061 32.000 36.23 12.44 37.82 1.82
963 3036 5.303165 TGTATGCATGCATTGGTTCAAAAA 58.697 33.333 36.23 13.17 37.82 1.94
964 3037 4.891260 TGTATGCATGCATTGGTTCAAAA 58.109 34.783 36.23 13.93 37.82 2.44
965 3038 4.532314 TGTATGCATGCATTGGTTCAAA 57.468 36.364 36.23 14.69 37.82 2.69
966 3039 4.434520 CATGTATGCATGCATTGGTTCAA 58.565 39.130 36.23 15.46 44.87 2.69
967 3040 4.048241 CATGTATGCATGCATTGGTTCA 57.952 40.909 36.23 24.78 44.87 3.18
978 3051 3.572632 AGAGGCAAGACATGTATGCAT 57.427 42.857 27.69 23.90 41.80 3.96
979 3052 3.054875 AGAAGAGGCAAGACATGTATGCA 60.055 43.478 27.69 0.00 41.80 3.96
980 3053 3.539604 AGAAGAGGCAAGACATGTATGC 58.460 45.455 21.90 21.90 39.33 3.14
981 3054 8.147058 ACTTATAGAAGAGGCAAGACATGTATG 58.853 37.037 3.65 2.15 36.45 2.39
982 3055 8.256356 ACTTATAGAAGAGGCAAGACATGTAT 57.744 34.615 3.65 0.00 36.45 2.29
983 3056 7.661536 ACTTATAGAAGAGGCAAGACATGTA 57.338 36.000 3.65 0.00 36.45 2.29
984 3057 6.552445 ACTTATAGAAGAGGCAAGACATGT 57.448 37.500 3.65 0.00 36.45 3.21
985 3058 6.638873 CGTACTTATAGAAGAGGCAAGACATG 59.361 42.308 3.65 0.00 36.45 3.21
986 3059 6.239064 CCGTACTTATAGAAGAGGCAAGACAT 60.239 42.308 3.65 0.00 36.45 3.06
987 3060 5.067413 CCGTACTTATAGAAGAGGCAAGACA 59.933 44.000 3.65 0.00 36.45 3.41
988 3061 5.521544 CCGTACTTATAGAAGAGGCAAGAC 58.478 45.833 3.65 0.00 36.45 3.01
989 3062 4.037684 GCCGTACTTATAGAAGAGGCAAGA 59.962 45.833 21.60 0.00 43.71 3.02
1234 3434 7.380870 CGTGCATATATAGGATGAAGTATGAGC 59.619 40.741 0.00 0.00 0.00 4.26
1373 4047 1.452108 CTTTCTTAGGCAGGCCCGG 60.452 63.158 6.70 0.00 39.21 5.73
1388 4062 5.131067 GTTTTCACCTACCCACTTCTCTTT 58.869 41.667 0.00 0.00 0.00 2.52
1401 4075 5.183713 CCTTCATCATGCTTGTTTTCACCTA 59.816 40.000 0.00 0.00 0.00 3.08
1407 4081 6.608405 TCCATATCCTTCATCATGCTTGTTTT 59.392 34.615 0.00 0.00 0.00 2.43
1422 4096 2.172717 CCTCCACCGTTTCCATATCCTT 59.827 50.000 0.00 0.00 0.00 3.36
1429 4103 0.616371 CATACCCTCCACCGTTTCCA 59.384 55.000 0.00 0.00 0.00 3.53
1460 4152 1.044790 CCCCCACCGTTACCGTATCT 61.045 60.000 0.00 0.00 0.00 1.98
1485 4177 3.099141 CCATAGCCTCCACCATTGTTTT 58.901 45.455 0.00 0.00 0.00 2.43
1491 4183 1.134098 CGTTTCCATAGCCTCCACCAT 60.134 52.381 0.00 0.00 0.00 3.55
1497 4189 0.539986 TCCACCGTTTCCATAGCCTC 59.460 55.000 0.00 0.00 0.00 4.70
1501 4193 2.547218 CCCGTATCCACCGTTTCCATAG 60.547 54.545 0.00 0.00 0.00 2.23
1544 4236 5.297776 CACCATTGTTCTCATAACCTCCATC 59.702 44.000 0.00 0.00 0.00 3.51
1557 4249 0.392461 ATACGCGCCACCATTGTTCT 60.392 50.000 5.73 0.00 0.00 3.01
1558 4250 0.248054 CATACGCGCCACCATTGTTC 60.248 55.000 5.73 0.00 0.00 3.18
1570 4262 0.386858 CGTATCCTCCACCATACGCG 60.387 60.000 3.53 3.53 40.89 6.01
1572 4264 1.325355 ACCGTATCCTCCACCATACG 58.675 55.000 4.81 4.81 44.88 3.06
1591 4283 1.254026 CTCCACCGTGTCCAGAACTA 58.746 55.000 0.00 0.00 0.00 2.24
1593 4285 1.004918 CCTCCACCGTGTCCAGAAC 60.005 63.158 0.00 0.00 0.00 3.01
1600 4292 1.988015 CCCATAACCTCCACCGTGT 59.012 57.895 0.00 0.00 0.00 4.49
1609 4301 0.108041 CGTAACCACGCCCATAACCT 60.108 55.000 0.00 0.00 42.05 3.50
1645 4337 2.281761 CCGCCACCATATCCAGGC 60.282 66.667 0.00 0.00 43.61 4.85
1726 4418 1.766059 AGCTCCACCATATCCGCCA 60.766 57.895 0.00 0.00 0.00 5.69
1743 4435 2.417516 CGCCACCGTATCCTCCAG 59.582 66.667 0.00 0.00 0.00 3.86
1776 4468 2.037251 CCATATCCTCCACCGTAACCTG 59.963 54.545 0.00 0.00 0.00 4.00
1935 4635 3.512680 GCTCCTATAACGCGAGCATAAT 58.487 45.455 15.93 0.00 46.63 1.28
1969 4670 0.610174 TGCTCGCCTGACTTCTCAAT 59.390 50.000 0.00 0.00 0.00 2.57
2242 5163 3.326747 GGTAGTTGATGGAGTGTGTGAC 58.673 50.000 0.00 0.00 0.00 3.67
2247 5168 0.249398 GGCGGTAGTTGATGGAGTGT 59.751 55.000 0.00 0.00 0.00 3.55
2266 5189 0.608640 ACACCTCTTTGCTCCCTACG 59.391 55.000 0.00 0.00 0.00 3.51
2310 5233 1.068333 CGCTACAATGCACTTGGCTTT 60.068 47.619 11.76 0.00 45.15 3.51
2343 5266 3.354678 GCAAGGGCGTCAACACAT 58.645 55.556 0.00 0.00 0.00 3.21
2507 5431 3.007940 ACTCCATCAACCTCGTTCATTGA 59.992 43.478 0.00 0.00 36.81 2.57


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

AutoCloner maintained by Alex Coulton.