Multiple sequence alignment - TraesCS2A01G288500

Loading Multiple Alignment...

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 TraesCS2A01G288500 chr2A 100.000 2914 0 0 1 2914 496343874 496340961 0.000000e+00 5382.0
1 TraesCS2A01G288500 chr2A 86.408 103 14 0 411 513 705940724 705940622 2.370000e-21 113.0
2 TraesCS2A01G288500 chr4A 91.926 1734 90 17 776 2496 713496461 713498157 0.000000e+00 2381.0
3 TraesCS2A01G288500 chr4A 94.824 425 20 2 2492 2914 713498343 713498767 0.000000e+00 662.0
4 TraesCS2A01G288500 chr4A 94.891 411 20 1 2 412 282091903 282091494 2.450000e-180 641.0
5 TraesCS2A01G288500 chr4A 83.088 408 26 11 399 781 713496045 713496434 6.020000e-87 331.0
6 TraesCS2A01G288500 chr7A 93.631 1209 64 6 776 1974 106821318 106820113 0.000000e+00 1794.0
7 TraesCS2A01G288500 chr7A 94.559 533 22 6 1976 2505 106820006 106819478 0.000000e+00 817.0
8 TraesCS2A01G288500 chr7A 94.159 428 20 3 2492 2914 106819303 106818876 0.000000e+00 647.0
9 TraesCS2A01G288500 chr7A 94.660 412 19 3 2 412 325389265 325388856 1.140000e-178 636.0
10 TraesCS2A01G288500 chr7A 82.368 397 28 16 409 781 106821723 106821345 1.010000e-79 307.0
11 TraesCS2A01G288500 chr7A 87.850 107 13 0 407 513 696838647 696838753 3.050000e-25 126.0
12 TraesCS2A01G288500 chr3D 89.165 683 39 10 1065 1733 264592766 264593427 0.000000e+00 819.0
13 TraesCS2A01G288500 chr2B 85.789 760 50 22 1756 2496 760257500 760256780 0.000000e+00 752.0
14 TraesCS2A01G288500 chr2B 81.313 396 44 13 407 777 760258101 760257711 7.900000e-76 294.0
15 TraesCS2A01G288500 chr2B 82.857 315 40 13 2600 2914 760256193 760255893 1.330000e-68 270.0
16 TraesCS2A01G288500 chr2B 92.241 116 7 2 2492 2605 760256594 760256479 2.320000e-36 163.0
17 TraesCS2A01G288500 chr2B 88.571 105 12 0 409 513 466217460 466217356 8.480000e-26 128.0
18 TraesCS2A01G288500 chr6B 90.206 582 42 10 1908 2483 681355061 681354489 0.000000e+00 745.0
19 TraesCS2A01G288500 chr6B 84.615 143 11 5 1593 1725 42368163 42368304 6.550000e-27 132.0
20 TraesCS2A01G288500 chr6B 83.226 155 15 5 1581 1725 710289909 710289756 6.550000e-27 132.0
21 TraesCS2A01G288500 chr6B 97.143 35 0 1 2773 2806 681354103 681354069 1.130000e-04 58.4
22 TraesCS2A01G288500 chr1A 94.660 412 21 1 2 412 482022530 482022119 3.170000e-179 638.0
23 TraesCS2A01G288500 chr1A 94.647 411 21 1 2 412 473488950 473489359 1.140000e-178 636.0
24 TraesCS2A01G288500 chr1A 84.516 155 13 5 1581 1725 518739338 518739491 3.030000e-30 143.0
25 TraesCS2A01G288500 chr5A 94.647 411 20 1 2 412 513788885 513789293 1.140000e-178 636.0
26 TraesCS2A01G288500 chr5D 94.404 411 23 0 2 412 350195864 350196274 1.470000e-177 632.0
27 TraesCS2A01G288500 chr5D 86.452 155 10 5 1581 1725 531281767 531281920 3.010000e-35 159.0
28 TraesCS2A01G288500 chr5D 85.437 103 15 0 411 513 557599128 557599026 1.100000e-19 108.0
29 TraesCS2A01G288500 chr2D 94.417 412 22 1 2 412 199319519 199319930 1.470000e-177 632.0
30 TraesCS2A01G288500 chr2D 94.404 411 23 0 2 412 347027980 347028390 1.470000e-177 632.0
31 TraesCS2A01G288500 chr2D 94.404 411 22 1 2 412 195672707 195672298 5.300000e-177 630.0
32 TraesCS2A01G288500 chr7B 86.601 306 29 4 1913 2216 685412453 685412158 7.790000e-86 327.0
33 TraesCS2A01G288500 chr7D 88.276 145 16 1 544 688 10102311 10102454 3.860000e-39 172.0
34 TraesCS2A01G288500 chr4D 85.806 155 11 5 1581 1725 477370403 477370556 1.400000e-33 154.0
35 TraesCS2A01G288500 chr4D 85.345 116 11 5 411 523 444286090 444285978 6.600000e-22 115.0
36 TraesCS2A01G288500 chr3B 85.256 156 11 6 1581 1726 793296759 793296912 1.810000e-32 150.0
37 TraesCS2A01G288500 chr3B 86.916 107 13 1 407 513 40623224 40623329 5.100000e-23 119.0
38 TraesCS2A01G288500 chr6D 86.000 100 14 0 410 509 87090713 87090812 1.100000e-19 108.0


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 TraesCS2A01G288500 chr2A 496340961 496343874 2913 True 5382.000000 5382 100.00000 1 2914 1 chr2A.!!$R1 2913
1 TraesCS2A01G288500 chr4A 713496045 713498767 2722 False 1124.666667 2381 89.94600 399 2914 3 chr4A.!!$F1 2515
2 TraesCS2A01G288500 chr7A 106818876 106821723 2847 True 891.250000 1794 91.17925 409 2914 4 chr7A.!!$R2 2505
3 TraesCS2A01G288500 chr3D 264592766 264593427 661 False 819.000000 819 89.16500 1065 1733 1 chr3D.!!$F1 668
4 TraesCS2A01G288500 chr2B 760255893 760258101 2208 True 369.750000 752 85.55000 407 2914 4 chr2B.!!$R2 2507
5 TraesCS2A01G288500 chr6B 681354069 681355061 992 True 401.700000 745 93.67450 1908 2806 2 chr6B.!!$R2 898

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
172 173 0.034089 ACTAATCCAAGGCCCAGTGC 60.034 55.0 0.0 0.0 40.16 4.40 F
173 174 0.034186 CTAATCCAAGGCCCAGTGCA 60.034 55.0 0.0 0.0 43.89 4.57 F
317 318 0.038159 ACGTCAAGAAAGGAGCGAGG 60.038 55.0 0.0 0.0 0.00 4.63 F
1440 1519 0.111253 ACTGGAAGAAGGGTTGCCTG 59.889 55.0 0.0 0.0 37.43 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 1160 0.304705 CGTGAAGCCAACACACTGAC 59.695 55.000 0.00 0.0 38.04 3.51 R
1462 1541 0.333993 ACCCCTCCTCTACGTTGCTA 59.666 55.000 0.00 0.0 0.00 3.49 R
1545 1630 1.173043 CCGTTGCTGCATCCCTTTTA 58.827 50.000 1.84 0.0 0.00 1.52 R
2840 3551 3.698040 ACAATGGCTTCTATGCTTTCCTG 59.302 43.478 0.00 0.0 0.00 3.86 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.049186 TCGAGGACGAGCATAAATTAAGC 58.951 43.478 0.00 0.00 43.81 3.09
28 29 4.051922 CGAGGACGAGCATAAATTAAGCT 58.948 43.478 2.10 2.10 42.66 3.74
29 30 4.508124 CGAGGACGAGCATAAATTAAGCTT 59.492 41.667 3.48 3.48 42.66 3.74
30 31 5.557136 CGAGGACGAGCATAAATTAAGCTTG 60.557 44.000 9.86 13.99 43.74 4.01
31 32 4.576463 AGGACGAGCATAAATTAAGCTTGG 59.424 41.667 18.26 10.23 42.70 3.61
32 33 4.261197 GGACGAGCATAAATTAAGCTTGGG 60.261 45.833 18.26 8.26 42.70 4.12
33 34 3.632145 ACGAGCATAAATTAAGCTTGGGG 59.368 43.478 18.26 6.32 42.70 4.96
34 35 3.882888 CGAGCATAAATTAAGCTTGGGGA 59.117 43.478 9.86 0.00 39.02 4.81
35 36 4.520492 CGAGCATAAATTAAGCTTGGGGAT 59.480 41.667 9.86 0.00 39.02 3.85
36 37 5.563475 CGAGCATAAATTAAGCTTGGGGATG 60.563 44.000 9.86 7.42 39.02 3.51
37 38 4.039609 AGCATAAATTAAGCTTGGGGATGC 59.960 41.667 19.30 19.30 37.91 3.91
38 39 4.039609 GCATAAATTAAGCTTGGGGATGCT 59.960 41.667 9.86 0.00 41.82 3.79
39 40 7.598669 AGCATAAATTAAGCTTGGGGATGCTT 61.599 38.462 21.90 5.56 43.64 3.91
44 45 2.355010 AGCTTGGGGATGCTTGATAC 57.645 50.000 0.00 0.00 35.86 2.24
45 46 0.947244 GCTTGGGGATGCTTGATACG 59.053 55.000 0.00 0.00 0.00 3.06
46 47 1.747206 GCTTGGGGATGCTTGATACGT 60.747 52.381 0.00 0.00 0.00 3.57
47 48 2.213499 CTTGGGGATGCTTGATACGTC 58.787 52.381 0.00 0.00 0.00 4.34
48 49 1.496060 TGGGGATGCTTGATACGTCT 58.504 50.000 0.00 0.00 0.00 4.18
49 50 1.412710 TGGGGATGCTTGATACGTCTC 59.587 52.381 0.00 0.00 0.00 3.36
50 51 1.270358 GGGGATGCTTGATACGTCTCC 60.270 57.143 0.00 0.00 36.55 3.71
51 52 1.412710 GGGATGCTTGATACGTCTCCA 59.587 52.381 0.00 0.00 0.00 3.86
52 53 2.158957 GGGATGCTTGATACGTCTCCAA 60.159 50.000 0.00 0.00 0.00 3.53
53 54 2.866762 GGATGCTTGATACGTCTCCAAC 59.133 50.000 0.00 0.00 0.00 3.77
70 71 9.027129 CGTCTCCAACGTATCTATAATTTTTGA 57.973 33.333 0.00 0.00 46.42 2.69
160 161 9.910267 TTATTTTTGGGACTAACCTACTAATCC 57.090 33.333 0.00 0.00 38.98 3.01
161 162 6.956102 TTTTGGGACTAACCTACTAATCCA 57.044 37.500 0.00 0.00 38.98 3.41
162 163 6.956102 TTTGGGACTAACCTACTAATCCAA 57.044 37.500 0.00 0.00 38.98 3.53
163 164 6.555463 TTGGGACTAACCTACTAATCCAAG 57.445 41.667 0.00 0.00 38.98 3.61
164 165 4.966805 TGGGACTAACCTACTAATCCAAGG 59.033 45.833 0.00 0.00 38.98 3.61
165 166 4.202336 GGGACTAACCTACTAATCCAAGGC 60.202 50.000 0.00 0.00 38.98 4.35
166 167 4.202336 GGACTAACCTACTAATCCAAGGCC 60.202 50.000 0.00 0.00 33.42 5.19
167 168 3.715315 ACTAACCTACTAATCCAAGGCCC 59.285 47.826 0.00 0.00 33.42 5.80
168 169 2.280308 ACCTACTAATCCAAGGCCCA 57.720 50.000 0.00 0.00 33.42 5.36
169 170 2.127708 ACCTACTAATCCAAGGCCCAG 58.872 52.381 0.00 0.00 33.42 4.45
170 171 2.127708 CCTACTAATCCAAGGCCCAGT 58.872 52.381 0.00 0.00 0.00 4.00
171 172 2.158755 CCTACTAATCCAAGGCCCAGTG 60.159 54.545 0.00 0.00 0.00 3.66
172 173 0.034089 ACTAATCCAAGGCCCAGTGC 60.034 55.000 0.00 0.00 40.16 4.40
173 174 0.034186 CTAATCCAAGGCCCAGTGCA 60.034 55.000 0.00 0.00 43.89 4.57
174 175 0.407528 TAATCCAAGGCCCAGTGCAA 59.592 50.000 0.00 0.00 43.89 4.08
175 176 0.471591 AATCCAAGGCCCAGTGCAAA 60.472 50.000 0.00 0.00 43.89 3.68
176 177 0.252375 ATCCAAGGCCCAGTGCAAAT 60.252 50.000 0.00 0.00 43.89 2.32
177 178 0.471591 TCCAAGGCCCAGTGCAAATT 60.472 50.000 0.00 0.00 43.89 1.82
178 179 0.320946 CCAAGGCCCAGTGCAAATTG 60.321 55.000 0.00 0.00 43.89 2.32
179 180 0.952010 CAAGGCCCAGTGCAAATTGC 60.952 55.000 11.58 11.58 45.29 3.56
180 181 2.046988 GGCCCAGTGCAAATTGCC 60.047 61.111 15.98 6.91 44.23 4.52
181 182 2.432972 GCCCAGTGCAAATTGCCG 60.433 61.111 15.98 3.92 44.23 5.69
182 183 3.050339 CCCAGTGCAAATTGCCGT 58.950 55.556 15.98 0.00 44.23 5.68
183 184 1.367102 CCCAGTGCAAATTGCCGTT 59.633 52.632 15.98 0.00 44.23 4.44
184 185 0.249826 CCCAGTGCAAATTGCCGTTT 60.250 50.000 15.98 0.00 44.23 3.60
185 186 1.580815 CCAGTGCAAATTGCCGTTTT 58.419 45.000 15.98 0.00 44.23 2.43
186 187 1.939255 CCAGTGCAAATTGCCGTTTTT 59.061 42.857 15.98 0.00 44.23 1.94
206 207 5.874892 TTTTTGCCGATTTTAGTGTTTCG 57.125 34.783 0.00 0.00 0.00 3.46
207 208 2.604969 TGCCGATTTTAGTGTTTCGC 57.395 45.000 0.00 0.00 0.00 4.70
208 209 1.874231 TGCCGATTTTAGTGTTTCGCA 59.126 42.857 0.00 0.00 0.00 5.10
209 210 2.095969 TGCCGATTTTAGTGTTTCGCAG 60.096 45.455 0.00 0.00 0.00 5.18
210 211 2.158841 GCCGATTTTAGTGTTTCGCAGA 59.841 45.455 0.00 0.00 0.00 4.26
211 212 3.364565 GCCGATTTTAGTGTTTCGCAGAA 60.365 43.478 0.00 0.00 45.90 3.02
212 213 4.778904 CCGATTTTAGTGTTTCGCAGAAA 58.221 39.130 0.55 0.55 45.90 2.52
213 214 5.209240 CCGATTTTAGTGTTTCGCAGAAAA 58.791 37.500 5.51 0.00 45.90 2.29
214 215 5.339611 CCGATTTTAGTGTTTCGCAGAAAAG 59.660 40.000 5.51 0.00 45.90 2.27
215 216 5.339611 CGATTTTAGTGTTTCGCAGAAAAGG 59.660 40.000 5.51 0.00 45.90 3.11
216 217 5.821516 TTTTAGTGTTTCGCAGAAAAGGA 57.178 34.783 5.51 0.00 45.90 3.36
217 218 5.821516 TTTAGTGTTTCGCAGAAAAGGAA 57.178 34.783 5.51 0.00 45.90 3.36
218 219 6.385649 TTTAGTGTTTCGCAGAAAAGGAAT 57.614 33.333 5.51 0.00 45.90 3.01
219 220 7.499321 TTTAGTGTTTCGCAGAAAAGGAATA 57.501 32.000 5.51 0.00 45.90 1.75
220 221 7.681939 TTAGTGTTTCGCAGAAAAGGAATAT 57.318 32.000 5.51 0.00 45.90 1.28
221 222 6.183309 AGTGTTTCGCAGAAAAGGAATATC 57.817 37.500 5.51 0.00 45.90 1.63
222 223 5.705441 AGTGTTTCGCAGAAAAGGAATATCA 59.295 36.000 5.51 0.00 45.90 2.15
223 224 6.206634 AGTGTTTCGCAGAAAAGGAATATCAA 59.793 34.615 5.51 0.00 45.90 2.57
224 225 6.861055 GTGTTTCGCAGAAAAGGAATATCAAA 59.139 34.615 5.51 0.00 45.90 2.69
225 226 7.542130 GTGTTTCGCAGAAAAGGAATATCAAAT 59.458 33.333 5.51 0.00 45.90 2.32
226 227 7.541783 TGTTTCGCAGAAAAGGAATATCAAATG 59.458 33.333 5.51 0.00 45.90 2.32
227 228 6.135290 TCGCAGAAAAGGAATATCAAATGG 57.865 37.500 0.00 0.00 0.00 3.16
228 229 5.885352 TCGCAGAAAAGGAATATCAAATGGA 59.115 36.000 0.00 0.00 0.00 3.41
229 230 6.376864 TCGCAGAAAAGGAATATCAAATGGAA 59.623 34.615 0.00 0.00 0.00 3.53
230 231 7.068593 TCGCAGAAAAGGAATATCAAATGGAAT 59.931 33.333 0.00 0.00 0.00 3.01
231 232 7.380602 CGCAGAAAAGGAATATCAAATGGAATC 59.619 37.037 0.00 0.00 0.00 2.52
232 233 7.380602 GCAGAAAAGGAATATCAAATGGAATCG 59.619 37.037 0.00 0.00 0.00 3.34
233 234 8.623903 CAGAAAAGGAATATCAAATGGAATCGA 58.376 33.333 0.00 0.00 0.00 3.59
234 235 9.189156 AGAAAAGGAATATCAAATGGAATCGAA 57.811 29.630 0.00 0.00 0.00 3.71
235 236 9.801873 GAAAAGGAATATCAAATGGAATCGAAA 57.198 29.630 0.00 0.00 0.00 3.46
236 237 9.586435 AAAAGGAATATCAAATGGAATCGAAAC 57.414 29.630 0.00 0.00 0.00 2.78
237 238 6.959361 AGGAATATCAAATGGAATCGAAACG 58.041 36.000 0.00 0.00 0.00 3.60
238 239 6.017109 AGGAATATCAAATGGAATCGAAACGG 60.017 38.462 0.00 0.00 0.00 4.44
239 240 6.017440 GGAATATCAAATGGAATCGAAACGGA 60.017 38.462 0.00 0.00 0.00 4.69
240 241 6.935741 ATATCAAATGGAATCGAAACGGAA 57.064 33.333 0.00 0.00 0.00 4.30
241 242 5.835113 ATCAAATGGAATCGAAACGGAAT 57.165 34.783 0.00 0.00 0.00 3.01
242 243 4.980590 TCAAATGGAATCGAAACGGAATG 58.019 39.130 0.00 0.00 0.00 2.67
243 244 4.697828 TCAAATGGAATCGAAACGGAATGA 59.302 37.500 0.00 0.00 0.00 2.57
244 245 5.182190 TCAAATGGAATCGAAACGGAATGAA 59.818 36.000 0.00 0.00 0.00 2.57
245 246 5.637006 AATGGAATCGAAACGGAATGAAA 57.363 34.783 0.00 0.00 0.00 2.69
246 247 4.413495 TGGAATCGAAACGGAATGAAAC 57.587 40.909 0.00 0.00 0.00 2.78
247 248 3.189702 TGGAATCGAAACGGAATGAAACC 59.810 43.478 0.00 0.00 0.00 3.27
248 249 3.439129 GGAATCGAAACGGAATGAAACCT 59.561 43.478 0.00 0.00 0.00 3.50
249 250 4.082949 GGAATCGAAACGGAATGAAACCTT 60.083 41.667 0.00 0.00 0.00 3.50
250 251 4.680171 ATCGAAACGGAATGAAACCTTC 57.320 40.909 0.00 0.00 0.00 3.46
251 252 2.477375 TCGAAACGGAATGAAACCTTCG 59.523 45.455 0.00 0.00 36.84 3.79
252 253 2.412325 CGAAACGGAATGAAACCTTCGG 60.412 50.000 0.00 0.00 34.08 4.30
253 254 1.530323 AACGGAATGAAACCTTCGGG 58.470 50.000 0.00 0.00 41.87 5.14
254 255 0.688487 ACGGAATGAAACCTTCGGGA 59.312 50.000 0.00 0.00 38.77 5.14
255 256 1.338769 ACGGAATGAAACCTTCGGGAG 60.339 52.381 0.00 0.00 38.77 4.30
256 257 1.066430 CGGAATGAAACCTTCGGGAGA 60.066 52.381 0.00 0.00 38.77 3.71
257 258 2.633488 GGAATGAAACCTTCGGGAGAG 58.367 52.381 0.00 0.00 41.75 3.20
258 259 2.027100 GGAATGAAACCTTCGGGAGAGT 60.027 50.000 0.00 0.00 41.75 3.24
259 260 3.559384 GGAATGAAACCTTCGGGAGAGTT 60.559 47.826 0.00 0.00 41.75 3.01
260 261 4.323257 GGAATGAAACCTTCGGGAGAGTTA 60.323 45.833 0.00 0.00 41.75 2.24
261 262 5.429130 GAATGAAACCTTCGGGAGAGTTAT 58.571 41.667 0.00 0.00 41.75 1.89
262 263 4.903045 TGAAACCTTCGGGAGAGTTATT 57.097 40.909 0.00 0.00 41.75 1.40
263 264 5.237236 TGAAACCTTCGGGAGAGTTATTT 57.763 39.130 0.00 0.00 41.75 1.40
264 265 5.627135 TGAAACCTTCGGGAGAGTTATTTT 58.373 37.500 0.00 0.00 41.75 1.82
265 266 6.066032 TGAAACCTTCGGGAGAGTTATTTTT 58.934 36.000 0.00 0.00 41.75 1.94
266 267 5.959618 AACCTTCGGGAGAGTTATTTTTG 57.040 39.130 0.00 0.00 41.75 2.44
267 268 4.332828 ACCTTCGGGAGAGTTATTTTTGG 58.667 43.478 0.00 0.00 41.75 3.28
268 269 4.042435 ACCTTCGGGAGAGTTATTTTTGGA 59.958 41.667 0.00 0.00 41.75 3.53
269 270 5.007682 CCTTCGGGAGAGTTATTTTTGGAA 58.992 41.667 0.00 0.00 41.75 3.53
270 271 5.106277 CCTTCGGGAGAGTTATTTTTGGAAC 60.106 44.000 0.00 0.00 41.75 3.62
271 272 4.975631 TCGGGAGAGTTATTTTTGGAACA 58.024 39.130 0.00 0.00 0.00 3.18
272 273 5.828859 TTCGGGAGAGTTATTTTTGGAACAA 59.171 36.000 0.00 0.00 42.84 2.83
273 274 6.321690 TTCGGGAGAGTTATTTTTGGAACAAA 59.678 34.615 0.00 0.00 42.84 2.83
274 275 7.682501 TTCGGGAGAGTTATTTTTGGAACAAAC 60.683 37.037 0.00 0.00 42.84 2.93
284 285 7.733402 ATTTTTGGAACAAACATGATCCAAG 57.267 32.000 16.64 0.00 46.46 3.61
285 286 5.212532 TTTGGAACAAACATGATCCAAGG 57.787 39.130 16.64 0.00 46.46 3.61
286 287 3.164268 TGGAACAAACATGATCCAAGGG 58.836 45.455 0.00 0.00 37.73 3.95
287 288 3.181424 TGGAACAAACATGATCCAAGGGA 60.181 43.478 0.00 0.00 37.73 4.20
288 289 3.193479 GGAACAAACATGATCCAAGGGAC 59.807 47.826 0.00 0.00 32.98 4.46
289 290 7.465463 TGGAACAAACATGATCCAAGGGACT 62.465 44.000 0.00 0.00 37.73 3.85
290 291 8.850028 TGGAACAAACATGATCCAAGGGACTT 62.850 42.308 0.00 0.00 45.15 3.01
302 303 1.836802 AGGGACTTGGAGTAGACGTC 58.163 55.000 7.70 7.70 27.25 4.34
303 304 1.075050 AGGGACTTGGAGTAGACGTCA 59.925 52.381 19.50 0.48 27.25 4.35
304 305 1.891150 GGGACTTGGAGTAGACGTCAA 59.109 52.381 19.50 1.33 0.00 3.18
305 306 2.094649 GGGACTTGGAGTAGACGTCAAG 60.095 54.545 19.50 14.00 41.46 3.02
306 307 2.818432 GGACTTGGAGTAGACGTCAAGA 59.182 50.000 19.50 0.00 38.96 3.02
307 308 3.255149 GGACTTGGAGTAGACGTCAAGAA 59.745 47.826 19.50 0.00 38.96 2.52
308 309 4.261909 GGACTTGGAGTAGACGTCAAGAAA 60.262 45.833 19.50 3.50 38.96 2.52
309 310 4.872664 ACTTGGAGTAGACGTCAAGAAAG 58.127 43.478 19.50 14.61 38.96 2.62
310 311 3.936372 TGGAGTAGACGTCAAGAAAGG 57.064 47.619 19.50 0.00 0.00 3.11
311 312 3.493334 TGGAGTAGACGTCAAGAAAGGA 58.507 45.455 19.50 0.00 0.00 3.36
312 313 3.506455 TGGAGTAGACGTCAAGAAAGGAG 59.494 47.826 19.50 0.00 0.00 3.69
313 314 3.503891 GAGTAGACGTCAAGAAAGGAGC 58.496 50.000 19.50 0.00 0.00 4.70
314 315 2.095161 AGTAGACGTCAAGAAAGGAGCG 60.095 50.000 19.50 0.00 0.00 5.03
315 316 0.959553 AGACGTCAAGAAAGGAGCGA 59.040 50.000 19.50 0.00 0.00 4.93
316 317 1.068194 AGACGTCAAGAAAGGAGCGAG 60.068 52.381 19.50 0.00 0.00 5.03
317 318 0.038159 ACGTCAAGAAAGGAGCGAGG 60.038 55.000 0.00 0.00 0.00 4.63
318 319 0.243907 CGTCAAGAAAGGAGCGAGGA 59.756 55.000 0.00 0.00 0.00 3.71
319 320 1.734047 CGTCAAGAAAGGAGCGAGGAG 60.734 57.143 0.00 0.00 0.00 3.69
320 321 0.898320 TCAAGAAAGGAGCGAGGAGG 59.102 55.000 0.00 0.00 0.00 4.30
321 322 0.742635 CAAGAAAGGAGCGAGGAGGC 60.743 60.000 0.00 0.00 0.00 4.70
322 323 1.904990 AAGAAAGGAGCGAGGAGGCC 61.905 60.000 0.00 0.00 0.00 5.19
323 324 2.607750 AAAGGAGCGAGGAGGCCA 60.608 61.111 5.01 0.00 0.00 5.36
324 325 2.860972 GAAAGGAGCGAGGAGGCCAC 62.861 65.000 5.01 0.00 0.00 5.01
327 328 4.200283 GAGCGAGGAGGCCACGAG 62.200 72.222 5.01 0.00 39.84 4.18
394 395 4.803426 CCTCGCAGCTCCACCGAC 62.803 72.222 0.00 0.00 0.00 4.79
395 396 4.803426 CTCGCAGCTCCACCGACC 62.803 72.222 0.00 0.00 0.00 4.79
397 398 3.449227 CGCAGCTCCACCGACCTA 61.449 66.667 0.00 0.00 0.00 3.08
398 399 2.184579 GCAGCTCCACCGACCTAC 59.815 66.667 0.00 0.00 0.00 3.18
399 400 2.352032 GCAGCTCCACCGACCTACT 61.352 63.158 0.00 0.00 0.00 2.57
400 401 1.889530 GCAGCTCCACCGACCTACTT 61.890 60.000 0.00 0.00 0.00 2.24
401 402 0.173708 CAGCTCCACCGACCTACTTC 59.826 60.000 0.00 0.00 0.00 3.01
402 403 0.251653 AGCTCCACCGACCTACTTCA 60.252 55.000 0.00 0.00 0.00 3.02
403 404 0.824759 GCTCCACCGACCTACTTCAT 59.175 55.000 0.00 0.00 0.00 2.57
404 405 1.202428 GCTCCACCGACCTACTTCATC 60.202 57.143 0.00 0.00 0.00 2.92
405 406 1.409427 CTCCACCGACCTACTTCATCC 59.591 57.143 0.00 0.00 0.00 3.51
406 407 1.006758 TCCACCGACCTACTTCATCCT 59.993 52.381 0.00 0.00 0.00 3.24
407 408 1.409427 CCACCGACCTACTTCATCCTC 59.591 57.143 0.00 0.00 0.00 3.71
451 452 0.820871 CTAAAGCGAGCCCTCTCAGT 59.179 55.000 0.00 0.00 39.30 3.41
509 510 3.139077 GTGTTTCTGGTCGTTGGATCTT 58.861 45.455 0.00 0.00 0.00 2.40
516 517 4.082190 TCTGGTCGTTGGATCTTTGTCTAG 60.082 45.833 0.00 0.00 0.00 2.43
525 526 4.202121 TGGATCTTTGTCTAGTGCGATACC 60.202 45.833 0.00 0.00 0.00 2.73
535 536 1.151221 TGCGATACCGGGCCTACTA 59.849 57.895 6.32 0.00 36.06 1.82
593 618 2.354704 CCATCTAACCAAGCGAGGACAA 60.355 50.000 4.39 0.00 0.00 3.18
632 657 3.114065 GTCTCGCTGGATAACCTAAACG 58.886 50.000 0.00 0.00 37.04 3.60
639 664 2.093553 TGGATAACCTAAACGAACCCCG 60.094 50.000 0.00 0.00 39.68 5.73
657 682 3.406200 CCCCTCCTGACCTGCCTG 61.406 72.222 0.00 0.00 0.00 4.85
659 684 3.007920 CCTCCTGACCTGCCTGCT 61.008 66.667 0.00 0.00 0.00 4.24
660 685 2.583520 CTCCTGACCTGCCTGCTC 59.416 66.667 0.00 0.00 0.00 4.26
661 686 1.988956 CTCCTGACCTGCCTGCTCT 60.989 63.158 0.00 0.00 0.00 4.09
731 756 1.153369 GCGTCAGCTTCCCATGCTA 60.153 57.895 0.00 0.00 38.92 3.49
769 794 2.186903 GGACGCCATCGGTCATGT 59.813 61.111 0.00 0.00 40.69 3.21
836 893 2.434359 GCCCTCGGAAGACAACGG 60.434 66.667 0.00 0.00 35.39 4.44
935 993 2.439883 GACGAGGCGGTCTAGGGT 60.440 66.667 0.00 0.00 34.09 4.34
1101 1160 1.450312 GCATGAACACCTCCTCCGG 60.450 63.158 0.00 0.00 0.00 5.14
1149 1208 2.581354 GCGCCTCCACTCTCATGT 59.419 61.111 0.00 0.00 0.00 3.21
1198 1265 2.582052 CAGTGCAAAGGTAGGTTTGGA 58.418 47.619 0.00 0.00 37.80 3.53
1211 1278 4.657814 AGGTTTGGAGCTTAATTCCTCA 57.342 40.909 7.45 0.00 35.67 3.86
1228 1295 4.104086 TCCTCATATCTTTCCACACTGGT 58.896 43.478 0.00 0.00 39.03 4.00
1235 1302 4.610605 TCTTTCCACACTGGTTTCGATA 57.389 40.909 0.00 0.00 39.03 2.92
1399 1478 6.419710 GTGCTTTTCTACCGTTTAATTTGCTT 59.580 34.615 0.00 0.00 0.00 3.91
1440 1519 0.111253 ACTGGAAGAAGGGTTGCCTG 59.889 55.000 0.00 0.00 37.43 4.85
1492 1574 3.948719 GAGGGGTGTTGCCGTCCA 61.949 66.667 0.00 0.00 38.44 4.02
1612 1697 0.893727 GCCTCCCGTTCCACATGTTT 60.894 55.000 0.00 0.00 0.00 2.83
1617 1702 4.181578 CTCCCGTTCCACATGTTTAGTAG 58.818 47.826 0.00 0.00 0.00 2.57
1737 1823 4.864247 GTGATTTATGCTTTGTTTCGGCAT 59.136 37.500 0.00 0.00 46.49 4.40
1738 1824 4.863689 TGATTTATGCTTTGTTTCGGCATG 59.136 37.500 9.48 0.00 44.83 4.06
1819 1905 6.158598 GCTCCATTTTCTGTTTATTTGCAGA 58.841 36.000 0.00 0.00 39.66 4.26
1875 1961 1.762957 CGGAGGAGATTAAGAAGGGCA 59.237 52.381 0.00 0.00 0.00 5.36
2042 2238 6.112734 TCTATGACAAATCGGTTATGCAGTT 58.887 36.000 0.00 0.00 0.00 3.16
2046 2242 5.703592 TGACAAATCGGTTATGCAGTTAGTT 59.296 36.000 0.00 0.00 0.00 2.24
2209 2411 5.431765 CTGCCACTGGTTATGATAGAACTT 58.568 41.667 0.00 0.00 0.00 2.66
2383 2585 5.831525 TGTCGAAGATATAAGGAGCCAAGTA 59.168 40.000 0.00 0.00 40.67 2.24
2418 2620 7.823745 ACTGTGTCTTTTGGATTACTTGATT 57.176 32.000 0.00 0.00 0.00 2.57
2419 2621 7.651808 ACTGTGTCTTTTGGATTACTTGATTG 58.348 34.615 0.00 0.00 0.00 2.67
2420 2622 7.502226 ACTGTGTCTTTTGGATTACTTGATTGA 59.498 33.333 0.00 0.00 0.00 2.57
2421 2623 8.408043 TGTGTCTTTTGGATTACTTGATTGAT 57.592 30.769 0.00 0.00 0.00 2.57
2549 2955 3.625649 TGCAAACTTCCAAGGCTTTTT 57.374 38.095 0.00 0.00 0.00 1.94
2612 3310 1.207811 GCATGAAATTCCACCCTTGGG 59.792 52.381 3.77 3.77 44.11 4.12
2771 3472 8.978874 ACAAATATTGTCATCACATTAGCCTA 57.021 30.769 0.00 0.00 40.56 3.93
2805 3506 9.871238 ATGTTATTGTAGATTGTTACGTTCTCT 57.129 29.630 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.277538 CCAAGCTTAATTTATGCTCGTCCTC 60.278 44.000 14.94 0.00 38.11 3.71
9 10 4.261197 CCCAAGCTTAATTTATGCTCGTCC 60.261 45.833 14.94 0.00 38.11 4.79
10 11 4.261197 CCCCAAGCTTAATTTATGCTCGTC 60.261 45.833 14.94 0.00 38.11 4.20
11 12 3.632145 CCCCAAGCTTAATTTATGCTCGT 59.368 43.478 14.94 1.23 38.11 4.18
12 13 3.882888 TCCCCAAGCTTAATTTATGCTCG 59.117 43.478 14.94 6.33 38.11 5.03
13 14 5.776744 CATCCCCAAGCTTAATTTATGCTC 58.223 41.667 14.94 0.00 38.11 4.26
14 15 4.039609 GCATCCCCAAGCTTAATTTATGCT 59.960 41.667 18.34 10.20 40.43 3.79
15 16 4.039609 AGCATCCCCAAGCTTAATTTATGC 59.960 41.667 18.11 18.11 38.01 3.14
16 17 5.796424 AGCATCCCCAAGCTTAATTTATG 57.204 39.130 0.00 1.29 38.01 1.90
25 26 1.475751 CGTATCAAGCATCCCCAAGCT 60.476 52.381 0.00 0.00 44.31 3.74
26 27 0.947244 CGTATCAAGCATCCCCAAGC 59.053 55.000 0.00 0.00 0.00 4.01
27 28 2.158900 AGACGTATCAAGCATCCCCAAG 60.159 50.000 0.00 0.00 0.00 3.61
28 29 1.837439 AGACGTATCAAGCATCCCCAA 59.163 47.619 0.00 0.00 0.00 4.12
29 30 1.412710 GAGACGTATCAAGCATCCCCA 59.587 52.381 5.07 0.00 0.00 4.96
30 31 1.270358 GGAGACGTATCAAGCATCCCC 60.270 57.143 12.92 0.00 0.00 4.81
31 32 1.412710 TGGAGACGTATCAAGCATCCC 59.587 52.381 12.92 0.00 0.00 3.85
32 33 2.866762 GTTGGAGACGTATCAAGCATCC 59.133 50.000 12.92 0.00 0.00 3.51
33 34 2.535984 CGTTGGAGACGTATCAAGCATC 59.464 50.000 12.92 0.00 46.49 3.91
34 35 2.540515 CGTTGGAGACGTATCAAGCAT 58.459 47.619 12.92 0.00 46.49 3.79
35 36 1.990799 CGTTGGAGACGTATCAAGCA 58.009 50.000 12.92 0.00 46.49 3.91
134 135 9.910267 GGATTAGTAGGTTAGTCCCAAAAATAA 57.090 33.333 0.00 0.00 36.75 1.40
135 136 9.060137 TGGATTAGTAGGTTAGTCCCAAAAATA 57.940 33.333 0.00 0.00 36.75 1.40
136 137 7.935405 TGGATTAGTAGGTTAGTCCCAAAAAT 58.065 34.615 0.00 0.00 36.75 1.82
137 138 7.332433 TGGATTAGTAGGTTAGTCCCAAAAA 57.668 36.000 0.00 0.00 36.75 1.94
138 139 6.956102 TGGATTAGTAGGTTAGTCCCAAAA 57.044 37.500 0.00 0.00 36.75 2.44
139 140 6.069847 CCTTGGATTAGTAGGTTAGTCCCAAA 60.070 42.308 0.00 0.00 36.75 3.28
140 141 5.427481 CCTTGGATTAGTAGGTTAGTCCCAA 59.573 44.000 0.00 0.00 36.75 4.12
141 142 4.966805 CCTTGGATTAGTAGGTTAGTCCCA 59.033 45.833 0.00 0.00 36.75 4.37
142 143 4.202336 GCCTTGGATTAGTAGGTTAGTCCC 60.202 50.000 0.00 0.00 36.75 4.46
143 144 4.202336 GGCCTTGGATTAGTAGGTTAGTCC 60.202 50.000 0.00 0.00 31.88 3.85
144 145 4.202336 GGGCCTTGGATTAGTAGGTTAGTC 60.202 50.000 0.84 0.00 0.00 2.59
145 146 3.715315 GGGCCTTGGATTAGTAGGTTAGT 59.285 47.826 0.84 0.00 0.00 2.24
146 147 3.714798 TGGGCCTTGGATTAGTAGGTTAG 59.285 47.826 4.53 0.00 0.00 2.34
147 148 3.714798 CTGGGCCTTGGATTAGTAGGTTA 59.285 47.826 4.53 0.00 0.00 2.85
148 149 2.509964 CTGGGCCTTGGATTAGTAGGTT 59.490 50.000 4.53 0.00 0.00 3.50
149 150 2.127708 CTGGGCCTTGGATTAGTAGGT 58.872 52.381 4.53 0.00 0.00 3.08
150 151 2.127708 ACTGGGCCTTGGATTAGTAGG 58.872 52.381 4.53 0.00 0.00 3.18
151 152 2.746472 GCACTGGGCCTTGGATTAGTAG 60.746 54.545 4.53 0.00 36.11 2.57
152 153 1.211949 GCACTGGGCCTTGGATTAGTA 59.788 52.381 4.53 0.00 36.11 1.82
153 154 0.034089 GCACTGGGCCTTGGATTAGT 60.034 55.000 4.53 0.00 36.11 2.24
154 155 0.034186 TGCACTGGGCCTTGGATTAG 60.034 55.000 4.53 0.00 43.89 1.73
155 156 0.407528 TTGCACTGGGCCTTGGATTA 59.592 50.000 4.53 0.00 43.89 1.75
156 157 0.471591 TTTGCACTGGGCCTTGGATT 60.472 50.000 4.53 0.00 43.89 3.01
157 158 0.252375 ATTTGCACTGGGCCTTGGAT 60.252 50.000 4.53 0.00 43.89 3.41
158 159 0.471591 AATTTGCACTGGGCCTTGGA 60.472 50.000 4.53 0.00 43.89 3.53
159 160 0.320946 CAATTTGCACTGGGCCTTGG 60.321 55.000 4.53 0.00 43.89 3.61
160 161 0.952010 GCAATTTGCACTGGGCCTTG 60.952 55.000 16.35 2.84 44.26 3.61
161 162 1.372307 GCAATTTGCACTGGGCCTT 59.628 52.632 16.35 0.00 44.26 4.35
162 163 3.062639 GCAATTTGCACTGGGCCT 58.937 55.556 16.35 0.00 44.26 5.19
184 185 4.207429 GCGAAACACTAAAATCGGCAAAAA 59.793 37.500 0.00 0.00 35.91 1.94
185 186 3.731717 GCGAAACACTAAAATCGGCAAAA 59.268 39.130 0.00 0.00 35.91 2.44
186 187 3.243101 TGCGAAACACTAAAATCGGCAAA 60.243 39.130 0.00 0.00 35.91 3.68
187 188 2.290916 TGCGAAACACTAAAATCGGCAA 59.709 40.909 0.00 0.00 35.91 4.52
188 189 1.874231 TGCGAAACACTAAAATCGGCA 59.126 42.857 0.00 0.00 35.91 5.69
189 190 2.158841 TCTGCGAAACACTAAAATCGGC 59.841 45.455 0.00 0.00 35.91 5.54
190 191 4.398549 TTCTGCGAAACACTAAAATCGG 57.601 40.909 0.00 0.00 35.91 4.18
191 192 5.339611 CCTTTTCTGCGAAACACTAAAATCG 59.660 40.000 3.71 0.00 38.28 3.34
192 193 6.435428 TCCTTTTCTGCGAAACACTAAAATC 58.565 36.000 3.71 0.00 0.00 2.17
193 194 6.385649 TCCTTTTCTGCGAAACACTAAAAT 57.614 33.333 3.71 0.00 0.00 1.82
194 195 5.821516 TCCTTTTCTGCGAAACACTAAAA 57.178 34.783 3.71 0.00 0.00 1.52
195 196 5.821516 TTCCTTTTCTGCGAAACACTAAA 57.178 34.783 3.71 0.00 0.00 1.85
196 197 7.389330 TGATATTCCTTTTCTGCGAAACACTAA 59.611 33.333 3.71 0.00 0.00 2.24
197 198 6.876789 TGATATTCCTTTTCTGCGAAACACTA 59.123 34.615 3.71 0.00 0.00 2.74
198 199 5.705441 TGATATTCCTTTTCTGCGAAACACT 59.295 36.000 3.71 0.00 0.00 3.55
199 200 5.938322 TGATATTCCTTTTCTGCGAAACAC 58.062 37.500 3.71 0.00 0.00 3.32
200 201 6.567687 TTGATATTCCTTTTCTGCGAAACA 57.432 33.333 3.71 0.00 0.00 2.83
201 202 7.009540 CCATTTGATATTCCTTTTCTGCGAAAC 59.990 37.037 3.71 0.00 0.00 2.78
202 203 7.035004 CCATTTGATATTCCTTTTCTGCGAAA 58.965 34.615 0.00 0.55 0.00 3.46
203 204 6.376864 TCCATTTGATATTCCTTTTCTGCGAA 59.623 34.615 0.00 0.00 0.00 4.70
204 205 5.885352 TCCATTTGATATTCCTTTTCTGCGA 59.115 36.000 0.00 0.00 0.00 5.10
205 206 6.135290 TCCATTTGATATTCCTTTTCTGCG 57.865 37.500 0.00 0.00 0.00 5.18
206 207 7.380602 CGATTCCATTTGATATTCCTTTTCTGC 59.619 37.037 0.00 0.00 0.00 4.26
207 208 8.623903 TCGATTCCATTTGATATTCCTTTTCTG 58.376 33.333 0.00 0.00 0.00 3.02
208 209 8.752005 TCGATTCCATTTGATATTCCTTTTCT 57.248 30.769 0.00 0.00 0.00 2.52
209 210 9.801873 TTTCGATTCCATTTGATATTCCTTTTC 57.198 29.630 0.00 0.00 0.00 2.29
210 211 9.586435 GTTTCGATTCCATTTGATATTCCTTTT 57.414 29.630 0.00 0.00 0.00 2.27
211 212 7.915397 CGTTTCGATTCCATTTGATATTCCTTT 59.085 33.333 0.00 0.00 0.00 3.11
212 213 7.417612 CGTTTCGATTCCATTTGATATTCCTT 58.582 34.615 0.00 0.00 0.00 3.36
213 214 6.017109 CCGTTTCGATTCCATTTGATATTCCT 60.017 38.462 0.00 0.00 0.00 3.36
214 215 6.017440 TCCGTTTCGATTCCATTTGATATTCC 60.017 38.462 0.00 0.00 0.00 3.01
215 216 6.954944 TCCGTTTCGATTCCATTTGATATTC 58.045 36.000 0.00 0.00 0.00 1.75
216 217 6.935741 TCCGTTTCGATTCCATTTGATATT 57.064 33.333 0.00 0.00 0.00 1.28
217 218 6.935741 TTCCGTTTCGATTCCATTTGATAT 57.064 33.333 0.00 0.00 0.00 1.63
218 219 6.540551 TCATTCCGTTTCGATTCCATTTGATA 59.459 34.615 0.00 0.00 0.00 2.15
219 220 5.356751 TCATTCCGTTTCGATTCCATTTGAT 59.643 36.000 0.00 0.00 0.00 2.57
220 221 4.697828 TCATTCCGTTTCGATTCCATTTGA 59.302 37.500 0.00 0.00 0.00 2.69
221 222 4.980590 TCATTCCGTTTCGATTCCATTTG 58.019 39.130 0.00 0.00 0.00 2.32
222 223 5.637006 TTCATTCCGTTTCGATTCCATTT 57.363 34.783 0.00 0.00 0.00 2.32
223 224 5.399013 GTTTCATTCCGTTTCGATTCCATT 58.601 37.500 0.00 0.00 0.00 3.16
224 225 4.142469 GGTTTCATTCCGTTTCGATTCCAT 60.142 41.667 0.00 0.00 0.00 3.41
225 226 3.189702 GGTTTCATTCCGTTTCGATTCCA 59.810 43.478 0.00 0.00 0.00 3.53
226 227 3.439129 AGGTTTCATTCCGTTTCGATTCC 59.561 43.478 0.00 0.00 0.00 3.01
227 228 4.680171 AGGTTTCATTCCGTTTCGATTC 57.320 40.909 0.00 0.00 0.00 2.52
228 229 4.378046 CGAAGGTTTCATTCCGTTTCGATT 60.378 41.667 0.00 0.00 35.86 3.34
229 230 3.124636 CGAAGGTTTCATTCCGTTTCGAT 59.875 43.478 0.00 0.00 35.86 3.59
230 231 2.477375 CGAAGGTTTCATTCCGTTTCGA 59.523 45.455 0.00 0.00 35.86 3.71
231 232 2.834689 CGAAGGTTTCATTCCGTTTCG 58.165 47.619 0.00 0.00 0.00 3.46
247 248 5.472137 TGTTCCAAAAATAACTCTCCCGAAG 59.528 40.000 0.00 0.00 0.00 3.79
248 249 5.378332 TGTTCCAAAAATAACTCTCCCGAA 58.622 37.500 0.00 0.00 0.00 4.30
249 250 4.975631 TGTTCCAAAAATAACTCTCCCGA 58.024 39.130 0.00 0.00 0.00 5.14
250 251 5.699097 TTGTTCCAAAAATAACTCTCCCG 57.301 39.130 0.00 0.00 0.00 5.14
251 252 6.811954 TGTTTGTTCCAAAAATAACTCTCCC 58.188 36.000 0.00 0.00 0.00 4.30
252 253 8.141268 TCATGTTTGTTCCAAAAATAACTCTCC 58.859 33.333 0.00 0.00 0.00 3.71
253 254 9.696917 ATCATGTTTGTTCCAAAAATAACTCTC 57.303 29.630 0.00 0.00 0.00 3.20
254 255 9.696917 GATCATGTTTGTTCCAAAAATAACTCT 57.303 29.630 0.00 0.00 0.00 3.24
255 256 8.925700 GGATCATGTTTGTTCCAAAAATAACTC 58.074 33.333 0.00 0.00 40.22 3.01
256 257 8.428063 TGGATCATGTTTGTTCCAAAAATAACT 58.572 29.630 3.82 0.00 44.86 2.24
257 258 8.600449 TGGATCATGTTTGTTCCAAAAATAAC 57.400 30.769 3.82 0.00 44.86 1.89
265 266 3.164268 CCCTTGGATCATGTTTGTTCCA 58.836 45.455 0.00 2.41 45.71 3.53
266 267 3.193479 GTCCCTTGGATCATGTTTGTTCC 59.807 47.826 0.00 0.00 40.69 3.62
267 268 4.082125 AGTCCCTTGGATCATGTTTGTTC 58.918 43.478 0.00 0.00 32.73 3.18
268 269 4.118168 AGTCCCTTGGATCATGTTTGTT 57.882 40.909 0.00 0.00 32.73 2.83
269 270 3.814504 AGTCCCTTGGATCATGTTTGT 57.185 42.857 0.00 0.00 32.73 2.83
270 271 4.445452 CAAGTCCCTTGGATCATGTTTG 57.555 45.455 0.00 0.00 37.77 2.93
281 282 1.893801 ACGTCTACTCCAAGTCCCTTG 59.106 52.381 0.00 0.00 40.75 3.61
282 283 2.169330 GACGTCTACTCCAAGTCCCTT 58.831 52.381 8.70 0.00 0.00 3.95
283 284 1.075050 TGACGTCTACTCCAAGTCCCT 59.925 52.381 17.92 0.00 0.00 4.20
284 285 1.542492 TGACGTCTACTCCAAGTCCC 58.458 55.000 17.92 0.00 0.00 4.46
285 286 2.818432 TCTTGACGTCTACTCCAAGTCC 59.182 50.000 17.92 0.00 37.74 3.85
286 287 4.500603 TTCTTGACGTCTACTCCAAGTC 57.499 45.455 17.92 0.00 37.74 3.01
287 288 4.262079 CCTTTCTTGACGTCTACTCCAAGT 60.262 45.833 17.92 0.00 37.74 3.16
288 289 4.022242 TCCTTTCTTGACGTCTACTCCAAG 60.022 45.833 17.92 11.29 37.82 3.61
289 290 3.893200 TCCTTTCTTGACGTCTACTCCAA 59.107 43.478 17.92 0.75 0.00 3.53
290 291 3.493334 TCCTTTCTTGACGTCTACTCCA 58.507 45.455 17.92 0.00 0.00 3.86
291 292 3.673866 GCTCCTTTCTTGACGTCTACTCC 60.674 52.174 17.92 0.00 0.00 3.85
292 293 3.503891 GCTCCTTTCTTGACGTCTACTC 58.496 50.000 17.92 0.00 0.00 2.59
293 294 2.095161 CGCTCCTTTCTTGACGTCTACT 60.095 50.000 17.92 0.00 0.00 2.57
294 295 2.095364 TCGCTCCTTTCTTGACGTCTAC 60.095 50.000 17.92 0.00 0.00 2.59
295 296 2.156917 TCGCTCCTTTCTTGACGTCTA 58.843 47.619 17.92 8.49 0.00 2.59
296 297 0.959553 TCGCTCCTTTCTTGACGTCT 59.040 50.000 17.92 0.00 0.00 4.18
297 298 1.341606 CTCGCTCCTTTCTTGACGTC 58.658 55.000 9.11 9.11 0.00 4.34
298 299 0.038159 CCTCGCTCCTTTCTTGACGT 60.038 55.000 0.00 0.00 0.00 4.34
299 300 0.243907 TCCTCGCTCCTTTCTTGACG 59.756 55.000 0.00 0.00 0.00 4.35
300 301 1.404851 CCTCCTCGCTCCTTTCTTGAC 60.405 57.143 0.00 0.00 0.00 3.18
301 302 0.898320 CCTCCTCGCTCCTTTCTTGA 59.102 55.000 0.00 0.00 0.00 3.02
302 303 0.742635 GCCTCCTCGCTCCTTTCTTG 60.743 60.000 0.00 0.00 0.00 3.02
303 304 1.599576 GCCTCCTCGCTCCTTTCTT 59.400 57.895 0.00 0.00 0.00 2.52
304 305 2.363172 GGCCTCCTCGCTCCTTTCT 61.363 63.158 0.00 0.00 0.00 2.52
305 306 2.188207 GGCCTCCTCGCTCCTTTC 59.812 66.667 0.00 0.00 0.00 2.62
306 307 2.607750 TGGCCTCCTCGCTCCTTT 60.608 61.111 3.32 0.00 0.00 3.11
307 308 3.394836 GTGGCCTCCTCGCTCCTT 61.395 66.667 3.32 0.00 0.00 3.36
310 311 4.200283 CTCGTGGCCTCCTCGCTC 62.200 72.222 3.32 0.00 39.87 5.03
377 378 4.803426 GTCGGTGGAGCTGCGAGG 62.803 72.222 0.00 0.00 0.00 4.63
378 379 4.803426 GGTCGGTGGAGCTGCGAG 62.803 72.222 0.00 0.00 37.68 5.03
384 385 0.824759 ATGAAGTAGGTCGGTGGAGC 59.175 55.000 0.00 0.00 40.99 4.70
385 386 1.409427 GGATGAAGTAGGTCGGTGGAG 59.591 57.143 0.00 0.00 0.00 3.86
386 387 1.006758 AGGATGAAGTAGGTCGGTGGA 59.993 52.381 0.00 0.00 0.00 4.02
387 388 1.409427 GAGGATGAAGTAGGTCGGTGG 59.591 57.143 0.00 0.00 0.00 4.61
388 389 1.409427 GGAGGATGAAGTAGGTCGGTG 59.591 57.143 0.00 0.00 0.00 4.94
389 390 1.288335 AGGAGGATGAAGTAGGTCGGT 59.712 52.381 0.00 0.00 0.00 4.69
390 391 2.074729 AGGAGGATGAAGTAGGTCGG 57.925 55.000 0.00 0.00 0.00 4.79
391 392 6.071840 CCTTAATAGGAGGATGAAGTAGGTCG 60.072 46.154 0.00 0.00 45.05 4.79
392 393 7.011382 TCCTTAATAGGAGGATGAAGTAGGTC 58.989 42.308 0.00 0.00 45.82 3.85
393 394 6.935036 TCCTTAATAGGAGGATGAAGTAGGT 58.065 40.000 0.00 0.00 45.82 3.08
407 408 5.924825 GTGCGGTTATACTGTCCTTAATAGG 59.075 44.000 0.00 0.00 43.46 2.57
484 485 0.232303 CAACGACCAGAAACACTCGC 59.768 55.000 0.00 0.00 0.00 5.03
509 510 0.742505 CCCGGTATCGCACTAGACAA 59.257 55.000 0.00 0.00 34.56 3.18
516 517 1.174712 TAGTAGGCCCGGTATCGCAC 61.175 60.000 0.00 0.00 34.56 5.34
525 526 1.472662 CCCACAGGATAGTAGGCCCG 61.473 65.000 0.00 0.00 33.47 6.13
764 789 2.268920 GGGAAGGCAGCGACATGA 59.731 61.111 0.00 0.00 0.00 3.07
878 935 3.418913 CGTCGAAACCATGGCGCA 61.419 61.111 13.04 0.00 0.00 6.09
935 993 1.166129 CCTCCTCTCGTCGTCAGAAA 58.834 55.000 0.00 0.00 0.00 2.52
986 1045 2.036731 TCATCCCACCCGTCGTCT 59.963 61.111 0.00 0.00 0.00 4.18
1082 1141 1.450312 CGGAGGAGGTGTTCATGCC 60.450 63.158 0.00 0.00 0.00 4.40
1101 1160 0.304705 CGTGAAGCCAACACACTGAC 59.695 55.000 0.00 0.00 38.04 3.51
1149 1208 1.469251 GCAGAAGAGTAATCACGGCGA 60.469 52.381 16.62 0.00 0.00 5.54
1198 1265 7.500559 GTGTGGAAAGATATGAGGAATTAAGCT 59.499 37.037 0.00 0.00 0.00 3.74
1211 1278 5.160607 TCGAAACCAGTGTGGAAAGATAT 57.839 39.130 0.00 0.00 40.96 1.63
1228 1295 4.759693 ACAACAAACCTGCAGATATCGAAA 59.240 37.500 17.39 0.00 0.00 3.46
1235 1302 5.852282 AAAAGTACAACAAACCTGCAGAT 57.148 34.783 17.39 0.00 0.00 2.90
1299 1368 4.577687 TGAATACTGAAATCGTTCACGC 57.422 40.909 0.00 0.00 38.88 5.34
1399 1478 1.008194 CTCGTTTGTCCACCGACGA 60.008 57.895 0.00 0.00 42.37 4.20
1440 1519 3.256960 TGGCAACCTCCCAGTCCC 61.257 66.667 0.00 0.00 0.00 4.46
1462 1541 0.333993 ACCCCTCCTCTACGTTGCTA 59.666 55.000 0.00 0.00 0.00 3.49
1492 1574 1.340405 GGACAAGCCAGATGATGTGGT 60.340 52.381 10.53 0.00 37.40 4.16
1545 1630 1.173043 CCGTTGCTGCATCCCTTTTA 58.827 50.000 1.84 0.00 0.00 1.52
1694 1780 8.650143 AATCACTAATTTAAAAGGAGCCTGAA 57.350 30.769 0.00 0.00 0.00 3.02
1737 1823 2.284331 TTGACTCTAGGGCGGCCA 60.284 61.111 31.59 15.08 0.00 5.36
1738 1824 1.403687 ATCTTGACTCTAGGGCGGCC 61.404 60.000 22.67 22.67 0.00 6.13
1819 1905 3.446516 GTGTTCCCAAGGTCGAGTAGTAT 59.553 47.826 0.00 0.00 0.00 2.12
1875 1961 3.308705 GTCAGGGACGGAACCGGT 61.309 66.667 17.44 0.00 44.69 5.28
2418 2620 5.483685 ACTCAAAGTTGGCTGTACTATCA 57.516 39.130 0.00 0.00 0.00 2.15
2419 2621 6.603095 CAAACTCAAAGTTGGCTGTACTATC 58.397 40.000 0.00 0.00 38.66 2.08
2420 2622 6.560253 CAAACTCAAAGTTGGCTGTACTAT 57.440 37.500 0.00 0.00 38.66 2.12
2612 3310 7.865706 TTCTAATTTCTTGCCATAGAGGAAC 57.134 36.000 0.00 0.00 41.22 3.62
2840 3551 3.698040 ACAATGGCTTCTATGCTTTCCTG 59.302 43.478 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.