Multiple sequence alignment - TraesCS2A01G089600

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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 TraesCS2A01G089600 chr2A 100.000 3476 0 0 1 3476 42722341 42718866 0.000000e+00 6420
1 TraesCS2A01G089600 chr2A 90.406 271 17 1 1147 1408 724517091 724516821 7.140000e-92 348
2 TraesCS2A01G089600 chr2D 91.926 2638 150 25 871 3476 37829741 37827135 0.000000e+00 3633
3 TraesCS2A01G089600 chr2D 84.168 499 44 16 395 875 37830285 37829804 5.290000e-123 451
4 TraesCS2A01G089600 chr2B 91.780 2652 143 36 871 3476 66216149 66213527 0.000000e+00 3620
5 TraesCS2A01G089600 chr2B 83.626 684 64 25 197 875 66216852 66216212 1.790000e-167 599
6 TraesCS2A01G089600 chr4D 86.783 575 71 5 1046 1619 177317672 177317102 1.360000e-178 636
7 TraesCS2A01G089600 chr1A 88.484 521 43 12 2721 3237 564326545 564326038 6.380000e-172 614
8 TraesCS2A01G089600 chr1A 89.219 269 22 4 1147 1408 10501279 10501011 2.590000e-86 329
9 TraesCS2A01G089600 chr6B 87.908 521 46 12 2721 3237 14720697 14720190 6.420000e-167 597
10 TraesCS2A01G089600 chr1D 90.154 325 32 0 1295 1619 412282502 412282826 1.150000e-114 424
11 TraesCS2A01G089600 chr1D 90.840 262 24 0 1147 1408 486449310 486449049 5.520000e-93 351
12 TraesCS2A01G089600 chr7A 90.566 265 22 1 1147 1408 727763607 727763343 7.140000e-92 348
13 TraesCS2A01G089600 chr7A 87.833 263 30 2 1147 1408 5349059 5348798 1.210000e-79 307
14 TraesCS2A01G089600 chr7A 90.798 163 11 3 1 163 33007359 33007201 7.560000e-52 215
15 TraesCS2A01G089600 chr5D 88.550 262 30 0 1147 1408 391158959 391159220 5.600000e-83 318


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 TraesCS2A01G089600 chr2A 42718866 42722341 3475 True 6420.0 6420 100.000 1 3476 1 chr2A.!!$R1 3475
1 TraesCS2A01G089600 chr2D 37827135 37830285 3150 True 2042.0 3633 88.047 395 3476 2 chr2D.!!$R1 3081
2 TraesCS2A01G089600 chr2B 66213527 66216852 3325 True 2109.5 3620 87.703 197 3476 2 chr2B.!!$R1 3279
3 TraesCS2A01G089600 chr4D 177317102 177317672 570 True 636.0 636 86.783 1046 1619 1 chr4D.!!$R1 573
4 TraesCS2A01G089600 chr1A 564326038 564326545 507 True 614.0 614 88.484 2721 3237 1 chr1A.!!$R2 516
5 TraesCS2A01G089600 chr6B 14720190 14720697 507 True 597.0 597 87.908 2721 3237 1 chr6B.!!$R1 516

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
244 246 0.039165 GTTTGCTCCCTTGGCTTTCG 60.039 55.000 0.0 0.0 0.00 3.46 F
250 252 0.611714 TCCCTTGGCTTTCGGTAGTC 59.388 55.000 0.0 0.0 0.00 2.59 F
926 1016 1.144057 CCGGACTGATTCTTCCCCG 59.856 63.158 0.0 0.0 36.98 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 1882 0.107752 GGCTTGAGAGGCTCTTCCAG 60.108 60.0 19.80 15.09 44.59 3.86 R
1881 1980 0.179171 AGCCGAGATCAACGTACACG 60.179 55.0 0.00 0.00 46.33 4.49 R
2497 2596 1.009829 CGAACCCTATCTGCAGCAAC 58.990 55.0 9.47 0.00 0.00 4.17 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
28 29 3.138205 GACACCGAGTCTAGTCATGTG 57.862 52.381 0.00 0.00 44.09 3.21
29 30 1.202582 ACACCGAGTCTAGTCATGTGC 59.797 52.381 0.00 0.00 0.00 4.57
30 31 0.452184 ACCGAGTCTAGTCATGTGCG 59.548 55.000 0.00 0.00 0.00 5.34
31 32 0.452184 CCGAGTCTAGTCATGTGCGT 59.548 55.000 0.00 0.00 0.00 5.24
32 33 1.669265 CCGAGTCTAGTCATGTGCGTA 59.331 52.381 0.00 0.00 0.00 4.42
33 34 2.539142 CCGAGTCTAGTCATGTGCGTAC 60.539 54.545 0.00 0.00 0.00 3.67
34 35 2.352034 CGAGTCTAGTCATGTGCGTACT 59.648 50.000 4.97 0.00 0.00 2.73
35 36 3.554731 CGAGTCTAGTCATGTGCGTACTA 59.445 47.826 4.97 0.00 0.00 1.82
36 37 4.318192 CGAGTCTAGTCATGTGCGTACTAG 60.318 50.000 4.97 10.77 42.60 2.57
37 38 3.312973 AGTCTAGTCATGTGCGTACTAGC 59.687 47.826 11.77 8.36 41.53 3.42
38 39 3.312973 GTCTAGTCATGTGCGTACTAGCT 59.687 47.826 11.77 0.00 41.53 3.32
39 40 2.568696 AGTCATGTGCGTACTAGCTG 57.431 50.000 4.97 0.00 38.13 4.24
40 41 0.924090 GTCATGTGCGTACTAGCTGC 59.076 55.000 4.97 0.00 38.13 5.25
41 42 0.179111 TCATGTGCGTACTAGCTGCC 60.179 55.000 4.97 0.00 38.13 4.85
42 43 1.226974 ATGTGCGTACTAGCTGCCG 60.227 57.895 4.97 0.00 38.13 5.69
43 44 1.945354 ATGTGCGTACTAGCTGCCGT 61.945 55.000 4.97 0.00 38.13 5.68
44 45 2.158959 GTGCGTACTAGCTGCCGTG 61.159 63.158 0.00 0.00 38.13 4.94
45 46 2.582498 GCGTACTAGCTGCCGTGG 60.582 66.667 0.00 0.00 0.00 4.94
46 47 2.582498 CGTACTAGCTGCCGTGGC 60.582 66.667 3.30 3.30 42.35 5.01
57 58 3.094386 GCCGTGGCATATTTCCAGA 57.906 52.632 5.89 0.00 41.49 3.86
58 59 1.609208 GCCGTGGCATATTTCCAGAT 58.391 50.000 5.89 0.00 41.49 2.90
59 60 1.956477 GCCGTGGCATATTTCCAGATT 59.044 47.619 5.89 0.00 41.49 2.40
60 61 2.030805 GCCGTGGCATATTTCCAGATTC 60.031 50.000 5.89 0.00 41.49 2.52
61 62 2.554032 CCGTGGCATATTTCCAGATTCC 59.446 50.000 0.00 0.00 33.63 3.01
62 63 3.213506 CGTGGCATATTTCCAGATTCCA 58.786 45.455 0.00 0.00 33.63 3.53
63 64 3.003689 CGTGGCATATTTCCAGATTCCAC 59.996 47.826 0.00 0.00 39.32 4.02
64 65 3.319122 GTGGCATATTTCCAGATTCCACC 59.681 47.826 0.00 0.00 37.38 4.61
65 66 2.554032 GGCATATTTCCAGATTCCACCG 59.446 50.000 0.00 0.00 0.00 4.94
66 67 3.214328 GCATATTTCCAGATTCCACCGT 58.786 45.455 0.00 0.00 0.00 4.83
67 68 4.385825 GCATATTTCCAGATTCCACCGTA 58.614 43.478 0.00 0.00 0.00 4.02
68 69 5.003804 GCATATTTCCAGATTCCACCGTAT 58.996 41.667 0.00 0.00 0.00 3.06
69 70 6.170506 GCATATTTCCAGATTCCACCGTATA 58.829 40.000 0.00 0.00 0.00 1.47
70 71 6.313905 GCATATTTCCAGATTCCACCGTATAG 59.686 42.308 0.00 0.00 0.00 1.31
71 72 3.746045 TTCCAGATTCCACCGTATAGC 57.254 47.619 0.00 0.00 0.00 2.97
72 73 1.611977 TCCAGATTCCACCGTATAGCG 59.388 52.381 0.00 0.00 40.95 4.26
73 74 1.340248 CCAGATTCCACCGTATAGCGT 59.660 52.381 0.00 0.00 39.32 5.07
74 75 2.555325 CCAGATTCCACCGTATAGCGTA 59.445 50.000 0.00 0.00 39.32 4.42
75 76 3.192844 CCAGATTCCACCGTATAGCGTAT 59.807 47.826 0.00 0.00 39.32 3.06
76 77 4.397103 CCAGATTCCACCGTATAGCGTATA 59.603 45.833 0.00 0.00 39.32 1.47
77 78 5.330295 CAGATTCCACCGTATAGCGTATAC 58.670 45.833 0.00 0.00 39.32 1.47
78 79 5.005740 AGATTCCACCGTATAGCGTATACA 58.994 41.667 3.32 0.00 40.78 2.29
79 80 5.651139 AGATTCCACCGTATAGCGTATACAT 59.349 40.000 3.32 0.00 40.78 2.29
80 81 6.825213 AGATTCCACCGTATAGCGTATACATA 59.175 38.462 3.32 0.00 40.78 2.29
81 82 7.501559 AGATTCCACCGTATAGCGTATACATAT 59.498 37.037 3.32 3.58 40.78 1.78
82 83 6.367686 TCCACCGTATAGCGTATACATATG 57.632 41.667 0.00 0.00 40.78 1.78
83 84 6.114767 TCCACCGTATAGCGTATACATATGA 58.885 40.000 10.38 0.00 40.78 2.15
84 85 6.769341 TCCACCGTATAGCGTATACATATGAT 59.231 38.462 10.38 1.47 40.78 2.45
85 86 7.933033 TCCACCGTATAGCGTATACATATGATA 59.067 37.037 10.38 0.49 40.78 2.15
86 87 8.727910 CCACCGTATAGCGTATACATATGATAT 58.272 37.037 10.38 6.41 40.78 1.63
87 88 9.543018 CACCGTATAGCGTATACATATGATATG 57.457 37.037 10.38 10.75 40.78 1.78
88 89 9.281371 ACCGTATAGCGTATACATATGATATGT 57.719 33.333 20.57 20.57 40.78 2.29
119 120 4.993029 TTTTGACGTGAAATTCTTGGGT 57.007 36.364 0.00 0.00 0.00 4.51
120 121 6.452494 TTTTTGACGTGAAATTCTTGGGTA 57.548 33.333 0.00 0.00 0.00 3.69
121 122 6.642707 TTTTGACGTGAAATTCTTGGGTAT 57.357 33.333 0.00 0.00 0.00 2.73
122 123 6.642707 TTTGACGTGAAATTCTTGGGTATT 57.357 33.333 0.00 0.00 0.00 1.89
123 124 5.873179 TGACGTGAAATTCTTGGGTATTC 57.127 39.130 0.00 0.00 0.00 1.75
124 125 4.698304 TGACGTGAAATTCTTGGGTATTCC 59.302 41.667 0.00 0.00 0.00 3.01
125 126 4.658063 ACGTGAAATTCTTGGGTATTCCA 58.342 39.130 0.00 0.00 45.43 3.53
138 139 6.013554 TGGGTATTCCAAGGAAATCTTAGG 57.986 41.667 5.52 0.00 43.84 2.69
139 140 5.734140 TGGGTATTCCAAGGAAATCTTAGGA 59.266 40.000 5.52 0.00 43.84 2.94
140 141 6.218730 TGGGTATTCCAAGGAAATCTTAGGAA 59.781 38.462 5.52 0.00 43.84 3.36
141 142 7.091537 TGGGTATTCCAAGGAAATCTTAGGAAT 60.092 37.037 5.52 17.60 45.02 3.01
142 143 8.445588 GGGTATTCCAAGGAAATCTTAGGAATA 58.554 37.037 5.52 16.41 43.41 1.75
146 147 7.138054 TCCAAGGAAATCTTAGGAATACTCC 57.862 40.000 0.00 0.00 36.31 3.85
147 148 6.101296 TCCAAGGAAATCTTAGGAATACTCCC 59.899 42.308 0.00 0.00 36.56 4.30
148 149 6.126478 CCAAGGAAATCTTAGGAATACTCCCA 60.126 42.308 0.00 0.00 36.56 4.37
149 150 6.755542 AGGAAATCTTAGGAATACTCCCAG 57.244 41.667 0.00 0.00 43.64 4.45
150 151 5.072464 AGGAAATCTTAGGAATACTCCCAGC 59.928 44.000 0.00 0.00 43.64 4.85
151 152 4.608948 AATCTTAGGAATACTCCCAGCG 57.391 45.455 0.00 0.00 43.64 5.18
152 153 1.687123 TCTTAGGAATACTCCCAGCGC 59.313 52.381 0.00 0.00 43.64 5.92
153 154 0.756903 TTAGGAATACTCCCAGCGCC 59.243 55.000 2.29 0.00 43.64 6.53
154 155 1.461091 TAGGAATACTCCCAGCGCCG 61.461 60.000 2.29 0.00 43.64 6.46
155 156 2.967615 GAATACTCCCAGCGCCGC 60.968 66.667 2.29 0.00 0.00 6.53
156 157 4.547367 AATACTCCCAGCGCCGCC 62.547 66.667 4.98 0.00 0.00 6.13
164 165 4.760047 CAGCGCCGCCACTAGGTT 62.760 66.667 4.98 0.00 37.19 3.50
165 166 4.760047 AGCGCCGCCACTAGGTTG 62.760 66.667 4.98 0.00 37.19 3.77
168 169 3.712907 GCCGCCACTAGGTTGGGA 61.713 66.667 1.83 0.00 37.10 4.37
169 170 3.043999 GCCGCCACTAGGTTGGGAT 62.044 63.158 1.83 0.00 37.10 3.85
170 171 1.692173 GCCGCCACTAGGTTGGGATA 61.692 60.000 1.83 0.00 37.10 2.59
171 172 1.056660 CCGCCACTAGGTTGGGATAT 58.943 55.000 1.83 0.00 37.10 1.63
172 173 1.002087 CCGCCACTAGGTTGGGATATC 59.998 57.143 1.83 0.00 37.10 1.63
173 174 1.691976 CGCCACTAGGTTGGGATATCA 59.308 52.381 4.83 0.00 37.10 2.15
174 175 2.548067 CGCCACTAGGTTGGGATATCAC 60.548 54.545 4.83 0.39 37.10 3.06
175 176 2.706190 GCCACTAGGTTGGGATATCACT 59.294 50.000 6.51 0.00 37.10 3.41
176 177 3.495100 GCCACTAGGTTGGGATATCACTG 60.495 52.174 6.51 0.00 37.10 3.66
177 178 3.711704 CCACTAGGTTGGGATATCACTGT 59.288 47.826 6.51 0.00 32.35 3.55
178 179 4.202264 CCACTAGGTTGGGATATCACTGTC 60.202 50.000 6.51 0.00 32.35 3.51
179 180 3.967987 ACTAGGTTGGGATATCACTGTCC 59.032 47.826 6.51 6.09 32.06 4.02
180 181 3.136641 AGGTTGGGATATCACTGTCCT 57.863 47.619 6.51 8.22 33.34 3.85
181 182 3.464828 AGGTTGGGATATCACTGTCCTT 58.535 45.455 6.51 0.00 33.34 3.36
182 183 3.456277 AGGTTGGGATATCACTGTCCTTC 59.544 47.826 6.51 0.00 33.34 3.46
183 184 3.456277 GGTTGGGATATCACTGTCCTTCT 59.544 47.826 6.51 0.00 33.34 2.85
184 185 4.654262 GGTTGGGATATCACTGTCCTTCTA 59.346 45.833 6.51 0.00 33.34 2.10
185 186 5.130477 GGTTGGGATATCACTGTCCTTCTAA 59.870 44.000 6.51 0.00 33.34 2.10
186 187 5.871396 TGGGATATCACTGTCCTTCTAAC 57.129 43.478 6.51 0.00 33.34 2.34
187 188 4.654262 TGGGATATCACTGTCCTTCTAACC 59.346 45.833 6.51 0.00 33.34 2.85
188 189 4.654262 GGGATATCACTGTCCTTCTAACCA 59.346 45.833 4.83 0.00 33.34 3.67
189 190 5.308237 GGGATATCACTGTCCTTCTAACCAT 59.692 44.000 4.83 0.00 33.34 3.55
190 191 6.226787 GGATATCACTGTCCTTCTAACCATG 58.773 44.000 4.83 0.00 30.28 3.66
191 192 6.183361 GGATATCACTGTCCTTCTAACCATGT 60.183 42.308 4.83 0.00 30.28 3.21
192 193 7.015292 GGATATCACTGTCCTTCTAACCATGTA 59.985 40.741 4.83 0.00 30.28 2.29
193 194 6.814954 ATCACTGTCCTTCTAACCATGTAT 57.185 37.500 0.00 0.00 0.00 2.29
194 195 6.222038 TCACTGTCCTTCTAACCATGTATC 57.778 41.667 0.00 0.00 0.00 2.24
195 196 5.958380 TCACTGTCCTTCTAACCATGTATCT 59.042 40.000 0.00 0.00 0.00 1.98
207 208 5.514500 ACCATGTATCTACAGGTTGGTTT 57.486 39.130 7.86 0.00 41.71 3.27
211 212 5.554437 TGTATCTACAGGTTGGTTTGTCA 57.446 39.130 0.00 0.00 0.00 3.58
212 213 6.121776 TGTATCTACAGGTTGGTTTGTCAT 57.878 37.500 0.00 0.00 0.00 3.06
213 214 7.247456 TGTATCTACAGGTTGGTTTGTCATA 57.753 36.000 0.00 0.00 0.00 2.15
214 215 7.857456 TGTATCTACAGGTTGGTTTGTCATAT 58.143 34.615 0.00 0.00 0.00 1.78
216 217 5.416083 TCTACAGGTTGGTTTGTCATATCG 58.584 41.667 0.00 0.00 0.00 2.92
217 218 3.343617 ACAGGTTGGTTTGTCATATCGG 58.656 45.455 0.00 0.00 0.00 4.18
218 219 3.244770 ACAGGTTGGTTTGTCATATCGGT 60.245 43.478 0.00 0.00 0.00 4.69
219 220 3.374058 CAGGTTGGTTTGTCATATCGGTC 59.626 47.826 0.00 0.00 0.00 4.79
234 236 2.706890 TCGGTCTTAATGTTTGCTCCC 58.293 47.619 0.00 0.00 0.00 4.30
239 241 2.825532 TCTTAATGTTTGCTCCCTTGGC 59.174 45.455 0.00 0.00 0.00 4.52
244 246 0.039165 GTTTGCTCCCTTGGCTTTCG 60.039 55.000 0.00 0.00 0.00 3.46
245 247 1.178534 TTTGCTCCCTTGGCTTTCGG 61.179 55.000 0.00 0.00 0.00 4.30
247 249 1.298667 GCTCCCTTGGCTTTCGGTA 59.701 57.895 0.00 0.00 0.00 4.02
250 252 0.611714 TCCCTTGGCTTTCGGTAGTC 59.388 55.000 0.00 0.00 0.00 2.59
259 261 4.222145 TGGCTTTCGGTAGTCTTAGTCATT 59.778 41.667 0.00 0.00 0.00 2.57
264 266 7.758528 GCTTTCGGTAGTCTTAGTCATTTTCTA 59.241 37.037 0.00 0.00 0.00 2.10
265 267 9.804758 CTTTCGGTAGTCTTAGTCATTTTCTAT 57.195 33.333 0.00 0.00 0.00 1.98
268 270 9.798994 TCGGTAGTCTTAGTCATTTTCTATTTC 57.201 33.333 0.00 0.00 0.00 2.17
305 307 9.476202 TCGTAATTCTGGTATGATGTAAGAATG 57.524 33.333 0.00 0.00 37.58 2.67
310 312 9.988815 ATTCTGGTATGATGTAAGAATGTACTC 57.011 33.333 0.00 0.00 36.49 2.59
311 313 7.952671 TCTGGTATGATGTAAGAATGTACTCC 58.047 38.462 0.00 0.00 0.00 3.85
313 315 9.078990 CTGGTATGATGTAAGAATGTACTCCTA 57.921 37.037 0.00 0.00 0.00 2.94
327 329 8.964476 AATGTACTCCTATTATTTGTGGACAG 57.036 34.615 0.00 0.00 0.00 3.51
329 331 8.598202 TGTACTCCTATTATTTGTGGACAGTA 57.402 34.615 0.00 0.00 0.00 2.74
330 332 8.472413 TGTACTCCTATTATTTGTGGACAGTAC 58.528 37.037 0.00 0.00 34.04 2.73
341 343 4.641396 TGTGGACAGTACAAATGGAAGAG 58.359 43.478 0.00 0.00 0.00 2.85
359 361 2.243221 AGAGCATGCCCCTTTAGTTCAT 59.757 45.455 15.66 0.00 0.00 2.57
466 472 8.756376 CAATTGTTTGCACTTAATTTGTGAAG 57.244 30.769 13.29 0.65 37.60 3.02
483 489 4.125703 GTGAAGGACCAGATCATTGCTAG 58.874 47.826 0.00 0.00 29.49 3.42
486 492 5.069648 TGAAGGACCAGATCATTGCTAGTAG 59.930 44.000 0.00 0.00 29.49 2.57
487 493 4.551671 AGGACCAGATCATTGCTAGTAGT 58.448 43.478 0.00 0.00 0.00 2.73
488 494 5.706447 AGGACCAGATCATTGCTAGTAGTA 58.294 41.667 0.00 0.00 0.00 1.82
496 502 9.973450 CAGATCATTGCTAGTAGTAGTACAAAT 57.027 33.333 10.33 2.30 0.00 2.32
523 529 9.405587 GAGTAAATGAGAGAGATACACATAAGC 57.594 37.037 0.00 0.00 0.00 3.09
527 533 6.384258 TGAGAGAGATACACATAAGCTCAC 57.616 41.667 0.00 0.00 0.00 3.51
529 535 4.586841 AGAGAGATACACATAAGCTCACCC 59.413 45.833 0.00 0.00 0.00 4.61
551 557 6.070078 ACCCCACATTTATTTTCTACGGAGTA 60.070 38.462 0.00 0.00 45.11 2.59
592 604 4.324267 CTTTATTTTCCACCGACTCCACT 58.676 43.478 0.00 0.00 0.00 4.00
593 605 2.951229 ATTTTCCACCGACTCCACTT 57.049 45.000 0.00 0.00 0.00 3.16
594 606 2.721425 TTTTCCACCGACTCCACTTT 57.279 45.000 0.00 0.00 0.00 2.66
595 607 3.842007 TTTTCCACCGACTCCACTTTA 57.158 42.857 0.00 0.00 0.00 1.85
596 608 4.360951 TTTTCCACCGACTCCACTTTAT 57.639 40.909 0.00 0.00 0.00 1.40
700 723 3.362851 CTAACTCCGCGCCGCAAAC 62.363 63.158 10.75 0.00 0.00 2.93
777 800 4.689549 TCCTCCCACCTTCGCCGA 62.690 66.667 0.00 0.00 0.00 5.54
926 1016 1.144057 CCGGACTGATTCTTCCCCG 59.856 63.158 0.00 0.00 36.98 5.73
943 1033 3.749064 GCGAGGCCGTCAGACTCA 61.749 66.667 0.00 0.00 38.24 3.41
957 1047 3.062466 CTCAGACTGGCCGACCGA 61.062 66.667 1.81 0.00 39.70 4.69
977 1067 3.506096 CCGCCGCTAGACTCGTGA 61.506 66.667 0.00 0.00 0.00 4.35
984 1074 1.297012 CTAGACTCGTGAGCGCGAC 60.297 63.158 12.10 2.99 36.80 5.19
1461 1560 1.439858 CGTCGACTTCGTCTTCGCA 60.440 57.895 14.70 0.00 40.80 5.10
1753 1852 3.131577 CACAATTGGGGATCACAAGATGG 59.868 47.826 10.83 0.00 33.72 3.51
1762 1861 1.649321 TCACAAGATGGAGCTCCTGT 58.351 50.000 32.28 24.41 36.82 4.00
1794 1893 1.684386 CGCTGATCCTGGAAGAGCCT 61.684 60.000 19.24 0.00 37.63 4.58
1797 1896 1.688197 CTGATCCTGGAAGAGCCTCTC 59.312 57.143 0.00 0.00 37.63 3.20
1854 1953 3.196685 ACATCAAGTACCTTCCAGAGCTC 59.803 47.826 5.27 5.27 0.00 4.09
2043 2142 1.682344 GGGGGTCACATTGCTTCCC 60.682 63.158 0.00 0.00 37.59 3.97
2100 2199 1.526917 GATCAATGGCGACCCTGGG 60.527 63.158 12.28 12.28 0.00 4.45
2229 2328 1.185618 AGTGGCTGAAGCAGACGGTA 61.186 55.000 4.43 0.00 43.58 4.02
2497 2596 2.635714 TGCTGCCATACACATTCAGAG 58.364 47.619 0.00 0.00 0.00 3.35
2511 2610 2.975732 TCAGAGTTGCTGCAGATAGG 57.024 50.000 20.43 0.00 44.52 2.57
2628 2727 5.749462 AGGGATTTGGTCTATTCTCTGTTG 58.251 41.667 0.00 0.00 0.00 3.33
2629 2728 4.884164 GGGATTTGGTCTATTCTCTGTTGG 59.116 45.833 0.00 0.00 0.00 3.77
2630 2729 5.501156 GGATTTGGTCTATTCTCTGTTGGT 58.499 41.667 0.00 0.00 0.00 3.67
2631 2730 5.946377 GGATTTGGTCTATTCTCTGTTGGTT 59.054 40.000 0.00 0.00 0.00 3.67
2632 2731 7.110155 GGATTTGGTCTATTCTCTGTTGGTTA 58.890 38.462 0.00 0.00 0.00 2.85
2679 2778 8.539117 AAAGAAGATTTGAGGAAAAGAAAGGA 57.461 30.769 0.00 0.00 0.00 3.36
2719 2819 3.129287 CCAGTAAAATTCTGCGGATTGCT 59.871 43.478 0.00 0.00 46.63 3.91
2775 2875 9.740239 AATCAATTTAGATTCATTCGATTGGTG 57.260 29.630 7.42 0.00 33.03 4.17
2776 2876 8.504812 TCAATTTAGATTCATTCGATTGGTGA 57.495 30.769 7.42 0.00 31.09 4.02
2780 2880 9.740239 ATTTAGATTCATTCGATTGGTGAATTG 57.260 29.630 13.50 0.00 41.30 2.32
2807 2908 2.979678 ACTATGTTCACTTCCCCTGTGT 59.020 45.455 0.00 0.00 36.83 3.72
2809 2911 4.595781 ACTATGTTCACTTCCCCTGTGTTA 59.404 41.667 0.00 0.00 36.83 2.41
2816 2918 5.205056 TCACTTCCCCTGTGTTATTTTGTT 58.795 37.500 0.00 0.00 36.83 2.83
2821 2923 5.074115 TCCCCTGTGTTATTTTGTTAGGTG 58.926 41.667 0.00 0.00 0.00 4.00
2835 2937 1.352083 TAGGTGGTTCTTGCAGCTCT 58.648 50.000 0.00 0.00 0.00 4.09
2853 2955 6.510799 GCAGCTCTATTTGTATTACTGCACTG 60.511 42.308 6.77 0.00 46.45 3.66
2879 2982 6.039159 TGTTCATCACATTTGTTTGCTGTAGA 59.961 34.615 0.00 0.00 0.00 2.59
2913 3017 2.109128 TCAGGAATTTTAGGTGTGCCCA 59.891 45.455 0.00 0.00 34.66 5.36
2935 3039 3.878778 ACTCTATGCTGAATGGGTGAAC 58.121 45.455 0.00 0.00 0.00 3.18
2957 3061 2.050442 CCGAAAAGGCGGTTGTGC 60.050 61.111 0.00 0.00 46.07 4.57
2974 3078 1.866601 GTGCATTTTGTGGTGCCTTTC 59.133 47.619 0.00 0.00 40.56 2.62
2996 3105 3.049708 TCTGCCATGACTCTCAACAAG 57.950 47.619 0.00 0.00 0.00 3.16
3000 3109 1.808945 CCATGACTCTCAACAAGCCAC 59.191 52.381 0.00 0.00 0.00 5.01
3001 3110 2.497138 CATGACTCTCAACAAGCCACA 58.503 47.619 0.00 0.00 0.00 4.17
3004 3113 2.092968 TGACTCTCAACAAGCCACAACT 60.093 45.455 0.00 0.00 0.00 3.16
3005 3114 2.289002 GACTCTCAACAAGCCACAACTG 59.711 50.000 0.00 0.00 0.00 3.16
3014 3123 2.908073 GCCACAACTGCCTGGTTCG 61.908 63.158 0.00 0.00 0.00 3.95
3118 3228 5.800296 TGCATTACCTCTGTTTAGCTACAA 58.200 37.500 0.00 0.00 0.00 2.41
3119 3229 5.874810 TGCATTACCTCTGTTTAGCTACAAG 59.125 40.000 0.00 0.00 0.00 3.16
3131 3241 1.139853 AGCTACAAGATGGGCTACTGC 59.860 52.381 0.00 0.00 38.76 4.40
3161 3273 7.277098 TGCAGTAATCGGTTAGTTTATCAAGTC 59.723 37.037 0.00 0.00 0.00 3.01
3176 3288 4.462508 TCAAGTCCACTGATCTGATCAC 57.537 45.455 16.06 6.67 35.06 3.06
3178 3290 4.284234 TCAAGTCCACTGATCTGATCACAA 59.716 41.667 16.06 0.13 35.06 3.33
3179 3291 5.046087 TCAAGTCCACTGATCTGATCACAAT 60.046 40.000 16.06 2.75 35.06 2.71
3212 3326 7.062255 GGTTCAAGTATTTTTCAGTTGCTATGC 59.938 37.037 0.00 0.00 0.00 3.14
3237 3351 1.227943 AGACATGCGTGTGTGCCTT 60.228 52.632 18.17 0.00 39.09 4.35
3283 3397 0.389817 TCCTGCACTGCACACGTATC 60.390 55.000 0.00 0.00 33.79 2.24
3364 3501 6.721571 TGTTTCTAAACATCGTGGAAGATC 57.278 37.500 4.19 0.00 43.45 2.75
3366 3503 5.414789 TTCTAAACATCGTGGAAGATCCA 57.585 39.130 0.00 0.00 45.98 3.41
3424 3561 5.685728 TGGGGTGGTTTTATTTCCTTTTTG 58.314 37.500 0.00 0.00 0.00 2.44
3444 3581 2.739913 TGTTGCCAAAGATAGTACGTGC 59.260 45.455 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.732597 GCACATGACTAGACTCGGTGTC 60.733 54.545 0.00 2.07 45.67 3.67
9 10 1.202582 GCACATGACTAGACTCGGTGT 59.797 52.381 0.00 0.00 0.00 4.16
10 11 1.795525 CGCACATGACTAGACTCGGTG 60.796 57.143 0.00 2.18 0.00 4.94
11 12 0.452184 CGCACATGACTAGACTCGGT 59.548 55.000 0.00 0.00 0.00 4.69
12 13 0.452184 ACGCACATGACTAGACTCGG 59.548 55.000 0.00 0.00 0.00 4.63
13 14 2.352034 AGTACGCACATGACTAGACTCG 59.648 50.000 0.00 0.00 0.00 4.18
14 15 4.553156 GCTAGTACGCACATGACTAGACTC 60.553 50.000 18.09 2.37 43.55 3.36
15 16 3.312973 GCTAGTACGCACATGACTAGACT 59.687 47.826 18.09 9.93 43.55 3.24
16 17 3.312973 AGCTAGTACGCACATGACTAGAC 59.687 47.826 18.09 11.30 43.55 2.59
17 18 3.312697 CAGCTAGTACGCACATGACTAGA 59.687 47.826 18.09 0.00 43.55 2.43
18 19 3.622828 CAGCTAGTACGCACATGACTAG 58.377 50.000 12.13 12.13 43.65 2.57
19 20 2.223502 GCAGCTAGTACGCACATGACTA 60.224 50.000 0.00 0.00 0.00 2.59
20 21 1.469940 GCAGCTAGTACGCACATGACT 60.470 52.381 0.00 0.00 0.00 3.41
21 22 0.924090 GCAGCTAGTACGCACATGAC 59.076 55.000 0.00 0.00 0.00 3.06
22 23 0.179111 GGCAGCTAGTACGCACATGA 60.179 55.000 0.00 0.00 0.00 3.07
23 24 1.482621 CGGCAGCTAGTACGCACATG 61.483 60.000 0.00 0.00 0.00 3.21
24 25 1.226974 CGGCAGCTAGTACGCACAT 60.227 57.895 0.00 0.00 0.00 3.21
25 26 2.180769 CGGCAGCTAGTACGCACA 59.819 61.111 0.00 0.00 0.00 4.57
26 27 2.158959 CACGGCAGCTAGTACGCAC 61.159 63.158 0.00 0.00 0.00 5.34
27 28 2.180769 CACGGCAGCTAGTACGCA 59.819 61.111 0.00 0.00 0.00 5.24
28 29 2.582498 CCACGGCAGCTAGTACGC 60.582 66.667 0.00 0.00 0.00 4.42
29 30 2.582498 GCCACGGCAGCTAGTACG 60.582 66.667 2.36 0.00 41.49 3.67
39 40 1.609208 ATCTGGAAATATGCCACGGC 58.391 50.000 0.00 0.00 42.35 5.68
40 41 2.554032 GGAATCTGGAAATATGCCACGG 59.446 50.000 0.00 0.00 0.00 4.94
41 42 3.003689 GTGGAATCTGGAAATATGCCACG 59.996 47.826 0.00 0.00 35.72 4.94
42 43 3.319122 GGTGGAATCTGGAAATATGCCAC 59.681 47.826 4.16 4.16 42.78 5.01
43 44 3.565307 GGTGGAATCTGGAAATATGCCA 58.435 45.455 0.00 0.00 0.00 4.92
44 45 2.554032 CGGTGGAATCTGGAAATATGCC 59.446 50.000 0.00 0.00 0.00 4.40
45 46 3.214328 ACGGTGGAATCTGGAAATATGC 58.786 45.455 0.00 0.00 0.00 3.14
46 47 6.313905 GCTATACGGTGGAATCTGGAAATATG 59.686 42.308 0.00 0.00 0.00 1.78
47 48 6.407202 GCTATACGGTGGAATCTGGAAATAT 58.593 40.000 0.00 0.00 0.00 1.28
48 49 5.566032 CGCTATACGGTGGAATCTGGAAATA 60.566 44.000 0.00 0.00 38.44 1.40
49 50 4.642429 GCTATACGGTGGAATCTGGAAAT 58.358 43.478 0.00 0.00 0.00 2.17
50 51 3.491964 CGCTATACGGTGGAATCTGGAAA 60.492 47.826 0.00 0.00 38.44 3.13
51 52 2.035449 CGCTATACGGTGGAATCTGGAA 59.965 50.000 0.00 0.00 38.44 3.53
52 53 1.611977 CGCTATACGGTGGAATCTGGA 59.388 52.381 0.00 0.00 38.44 3.86
53 54 2.065993 CGCTATACGGTGGAATCTGG 57.934 55.000 0.00 0.00 38.44 3.86
97 98 5.331876 ACCCAAGAATTTCACGTCAAAAA 57.668 34.783 0.00 0.00 0.00 1.94
98 99 4.993029 ACCCAAGAATTTCACGTCAAAA 57.007 36.364 0.00 0.00 0.00 2.44
99 100 6.294286 GGAATACCCAAGAATTTCACGTCAAA 60.294 38.462 0.00 0.00 34.14 2.69
100 101 5.182380 GGAATACCCAAGAATTTCACGTCAA 59.818 40.000 0.00 0.00 34.14 3.18
101 102 4.698304 GGAATACCCAAGAATTTCACGTCA 59.302 41.667 0.00 0.00 34.14 4.35
102 103 4.698304 TGGAATACCCAAGAATTTCACGTC 59.302 41.667 0.00 0.00 43.29 4.34
103 104 4.658063 TGGAATACCCAAGAATTTCACGT 58.342 39.130 0.00 0.00 43.29 4.49
115 116 5.734140 TCCTAAGATTTCCTTGGAATACCCA 59.266 40.000 2.65 0.00 44.93 4.51
116 117 6.262056 TCCTAAGATTTCCTTGGAATACCC 57.738 41.667 2.65 0.00 35.61 3.69
120 121 8.221251 GGAGTATTCCTAAGATTTCCTTGGAAT 58.779 37.037 17.20 17.20 44.86 3.01
121 122 7.366551 GGGAGTATTCCTAAGATTTCCTTGGAA 60.367 40.741 4.04 0.00 43.49 3.53
122 123 6.101296 GGGAGTATTCCTAAGATTTCCTTGGA 59.899 42.308 4.04 0.00 43.49 3.53
123 124 6.126478 TGGGAGTATTCCTAAGATTTCCTTGG 60.126 42.308 4.04 0.00 43.49 3.61
124 125 6.900194 TGGGAGTATTCCTAAGATTTCCTTG 58.100 40.000 4.04 0.00 43.49 3.61
125 126 6.409810 GCTGGGAGTATTCCTAAGATTTCCTT 60.410 42.308 4.04 0.00 43.49 3.36
126 127 5.072464 GCTGGGAGTATTCCTAAGATTTCCT 59.928 44.000 4.04 0.00 43.49 3.36
127 128 5.309638 GCTGGGAGTATTCCTAAGATTTCC 58.690 45.833 4.04 0.00 43.49 3.13
128 129 4.991687 CGCTGGGAGTATTCCTAAGATTTC 59.008 45.833 4.04 0.00 43.49 2.17
129 130 4.743955 GCGCTGGGAGTATTCCTAAGATTT 60.744 45.833 0.00 0.00 43.49 2.17
130 131 3.244249 GCGCTGGGAGTATTCCTAAGATT 60.244 47.826 0.00 0.00 43.49 2.40
131 132 2.300437 GCGCTGGGAGTATTCCTAAGAT 59.700 50.000 0.00 0.00 43.49 2.40
132 133 1.687123 GCGCTGGGAGTATTCCTAAGA 59.313 52.381 0.00 0.00 43.49 2.10
133 134 1.270358 GGCGCTGGGAGTATTCCTAAG 60.270 57.143 7.64 4.01 43.49 2.18
134 135 0.756903 GGCGCTGGGAGTATTCCTAA 59.243 55.000 7.64 0.00 43.49 2.69
135 136 1.461091 CGGCGCTGGGAGTATTCCTA 61.461 60.000 8.83 0.00 43.49 2.94
136 137 2.797278 CGGCGCTGGGAGTATTCCT 61.797 63.158 8.83 0.00 43.49 3.36
137 138 2.280186 CGGCGCTGGGAGTATTCC 60.280 66.667 8.83 0.00 43.23 3.01
138 139 2.967615 GCGGCGCTGGGAGTATTC 60.968 66.667 26.86 0.00 0.00 1.75
139 140 4.547367 GGCGGCGCTGGGAGTATT 62.547 66.667 32.30 0.00 0.00 1.89
147 148 4.760047 AACCTAGTGGCGGCGCTG 62.760 66.667 32.63 20.21 36.63 5.18
148 149 4.760047 CAACCTAGTGGCGGCGCT 62.760 66.667 32.30 28.68 36.63 5.92
151 152 1.692173 TATCCCAACCTAGTGGCGGC 61.692 60.000 0.00 0.00 37.34 6.53
152 153 1.002087 GATATCCCAACCTAGTGGCGG 59.998 57.143 0.00 0.00 37.34 6.13
153 154 1.691976 TGATATCCCAACCTAGTGGCG 59.308 52.381 0.00 0.00 37.34 5.69
154 155 2.706190 AGTGATATCCCAACCTAGTGGC 59.294 50.000 0.00 0.00 37.34 5.01
155 156 3.711704 ACAGTGATATCCCAACCTAGTGG 59.288 47.826 0.00 0.00 38.51 4.00
156 157 4.202264 GGACAGTGATATCCCAACCTAGTG 60.202 50.000 0.00 0.00 0.00 2.74
157 158 3.967987 GGACAGTGATATCCCAACCTAGT 59.032 47.826 0.00 0.00 0.00 2.57
158 159 4.227197 AGGACAGTGATATCCCAACCTAG 58.773 47.826 0.00 0.00 0.00 3.02
159 160 4.280789 AGGACAGTGATATCCCAACCTA 57.719 45.455 0.00 0.00 0.00 3.08
160 161 3.136641 AGGACAGTGATATCCCAACCT 57.863 47.619 0.00 0.52 0.00 3.50
161 162 3.456277 AGAAGGACAGTGATATCCCAACC 59.544 47.826 0.00 0.00 0.00 3.77
162 163 4.762289 AGAAGGACAGTGATATCCCAAC 57.238 45.455 0.00 0.00 0.00 3.77
163 164 5.130477 GGTTAGAAGGACAGTGATATCCCAA 59.870 44.000 0.00 0.00 0.00 4.12
164 165 4.654262 GGTTAGAAGGACAGTGATATCCCA 59.346 45.833 0.00 0.00 0.00 4.37
165 166 4.654262 TGGTTAGAAGGACAGTGATATCCC 59.346 45.833 0.00 0.00 0.00 3.85
166 167 5.871396 TGGTTAGAAGGACAGTGATATCC 57.129 43.478 0.00 0.00 0.00 2.59
167 168 6.821388 ACATGGTTAGAAGGACAGTGATATC 58.179 40.000 0.00 0.00 0.00 1.63
168 169 6.814954 ACATGGTTAGAAGGACAGTGATAT 57.185 37.500 0.00 0.00 0.00 1.63
169 170 7.785028 AGATACATGGTTAGAAGGACAGTGATA 59.215 37.037 0.00 0.00 0.00 2.15
170 171 6.613271 AGATACATGGTTAGAAGGACAGTGAT 59.387 38.462 0.00 0.00 0.00 3.06
171 172 5.958380 AGATACATGGTTAGAAGGACAGTGA 59.042 40.000 0.00 0.00 0.00 3.41
172 173 6.227298 AGATACATGGTTAGAAGGACAGTG 57.773 41.667 0.00 0.00 0.00 3.66
173 174 6.895756 TGTAGATACATGGTTAGAAGGACAGT 59.104 38.462 0.00 0.00 0.00 3.55
174 175 7.348080 TGTAGATACATGGTTAGAAGGACAG 57.652 40.000 0.00 0.00 0.00 3.51
175 176 6.323996 CCTGTAGATACATGGTTAGAAGGACA 59.676 42.308 0.00 0.00 35.36 4.02
176 177 6.324254 ACCTGTAGATACATGGTTAGAAGGAC 59.676 42.308 0.00 0.00 35.59 3.85
177 178 6.441222 ACCTGTAGATACATGGTTAGAAGGA 58.559 40.000 0.00 0.00 35.59 3.36
178 179 6.732896 ACCTGTAGATACATGGTTAGAAGG 57.267 41.667 0.00 0.00 35.59 3.46
179 180 6.986817 CCAACCTGTAGATACATGGTTAGAAG 59.013 42.308 18.29 11.03 41.42 2.85
180 181 6.442564 ACCAACCTGTAGATACATGGTTAGAA 59.557 38.462 18.29 0.00 41.71 2.10
181 182 5.962031 ACCAACCTGTAGATACATGGTTAGA 59.038 40.000 18.29 0.00 41.71 2.10
182 183 6.235231 ACCAACCTGTAGATACATGGTTAG 57.765 41.667 18.29 15.60 41.71 2.34
183 184 6.630203 AACCAACCTGTAGATACATGGTTA 57.370 37.500 20.29 0.00 46.79 2.85
184 185 5.514500 AACCAACCTGTAGATACATGGTT 57.486 39.130 17.72 17.72 45.26 3.67
185 186 5.222048 ACAAACCAACCTGTAGATACATGGT 60.222 40.000 9.83 9.83 44.57 3.55
186 187 5.253330 ACAAACCAACCTGTAGATACATGG 58.747 41.667 8.80 8.80 38.93 3.66
187 188 5.937540 TGACAAACCAACCTGTAGATACATG 59.062 40.000 0.00 0.00 35.36 3.21
188 189 6.121776 TGACAAACCAACCTGTAGATACAT 57.878 37.500 0.00 0.00 35.36 2.29
189 190 5.554437 TGACAAACCAACCTGTAGATACA 57.446 39.130 0.00 0.00 34.56 2.29
190 191 7.169308 CGATATGACAAACCAACCTGTAGATAC 59.831 40.741 0.00 0.00 0.00 2.24
191 192 7.207383 CGATATGACAAACCAACCTGTAGATA 58.793 38.462 0.00 0.00 0.00 1.98
192 193 6.049149 CGATATGACAAACCAACCTGTAGAT 58.951 40.000 0.00 0.00 0.00 1.98
193 194 5.416083 CGATATGACAAACCAACCTGTAGA 58.584 41.667 0.00 0.00 0.00 2.59
194 195 4.570772 CCGATATGACAAACCAACCTGTAG 59.429 45.833 0.00 0.00 0.00 2.74
195 196 4.020039 ACCGATATGACAAACCAACCTGTA 60.020 41.667 0.00 0.00 0.00 2.74
207 208 6.112734 AGCAAACATTAAGACCGATATGACA 58.887 36.000 0.00 0.00 0.00 3.58
211 212 5.063880 GGGAGCAAACATTAAGACCGATAT 58.936 41.667 0.00 0.00 0.00 1.63
212 213 4.163458 AGGGAGCAAACATTAAGACCGATA 59.837 41.667 0.00 0.00 0.00 2.92
213 214 3.054361 AGGGAGCAAACATTAAGACCGAT 60.054 43.478 0.00 0.00 0.00 4.18
214 215 2.304761 AGGGAGCAAACATTAAGACCGA 59.695 45.455 0.00 0.00 0.00 4.69
216 217 3.193479 CCAAGGGAGCAAACATTAAGACC 59.807 47.826 0.00 0.00 0.00 3.85
217 218 3.367395 GCCAAGGGAGCAAACATTAAGAC 60.367 47.826 0.00 0.00 0.00 3.01
218 219 2.825532 GCCAAGGGAGCAAACATTAAGA 59.174 45.455 0.00 0.00 0.00 2.10
219 220 2.827921 AGCCAAGGGAGCAAACATTAAG 59.172 45.455 0.00 0.00 0.00 1.85
234 236 4.174762 GACTAAGACTACCGAAAGCCAAG 58.825 47.826 0.00 0.00 0.00 3.61
239 241 9.804758 ATAGAAAATGACTAAGACTACCGAAAG 57.195 33.333 0.00 0.00 0.00 2.62
279 281 9.476202 CATTCTTACATCATACCAGAATTACGA 57.524 33.333 0.00 0.00 32.91 3.43
301 303 8.958119 TGTCCACAAATAATAGGAGTACATTC 57.042 34.615 0.00 0.00 0.00 2.67
305 307 8.472413 TGTACTGTCCACAAATAATAGGAGTAC 58.528 37.037 0.00 0.00 34.73 2.73
308 310 8.786826 TTTGTACTGTCCACAAATAATAGGAG 57.213 34.615 5.08 0.00 40.12 3.69
317 319 5.441500 TCTTCCATTTGTACTGTCCACAAA 58.558 37.500 10.35 10.35 46.64 2.83
318 320 5.042463 TCTTCCATTTGTACTGTCCACAA 57.958 39.130 0.00 0.00 34.18 3.33
319 321 4.641396 CTCTTCCATTTGTACTGTCCACA 58.359 43.478 0.00 0.00 0.00 4.17
320 322 3.437049 GCTCTTCCATTTGTACTGTCCAC 59.563 47.826 0.00 0.00 0.00 4.02
321 323 3.072330 TGCTCTTCCATTTGTACTGTCCA 59.928 43.478 0.00 0.00 0.00 4.02
322 324 3.674997 TGCTCTTCCATTTGTACTGTCC 58.325 45.455 0.00 0.00 0.00 4.02
327 329 2.099756 GGGCATGCTCTTCCATTTGTAC 59.900 50.000 18.92 0.00 0.00 2.90
329 331 1.188863 GGGCATGCTCTTCCATTTGT 58.811 50.000 18.92 0.00 0.00 2.83
330 332 0.462789 GGGGCATGCTCTTCCATTTG 59.537 55.000 18.99 0.00 0.00 2.32
333 335 0.337428 AAAGGGGCATGCTCTTCCAT 59.663 50.000 18.99 4.60 0.00 3.41
341 343 3.893326 AAATGAACTAAAGGGGCATGC 57.107 42.857 9.90 9.90 0.00 4.06
381 383 4.221703 ACAATGAATACATCCCCGCAAAAA 59.778 37.500 0.00 0.00 35.50 1.94
384 386 3.011566 ACAATGAATACATCCCCGCAA 57.988 42.857 0.00 0.00 35.50 4.85
386 388 4.385358 AAAACAATGAATACATCCCCGC 57.615 40.909 0.00 0.00 35.50 6.13
450 456 4.518970 TCTGGTCCTTCACAAATTAAGTGC 59.481 41.667 6.17 0.00 36.93 4.40
453 459 7.636150 ATGATCTGGTCCTTCACAAATTAAG 57.364 36.000 0.00 0.00 0.00 1.85
460 466 2.306805 AGCAATGATCTGGTCCTTCACA 59.693 45.455 0.00 0.00 0.00 3.58
466 472 4.946478 ACTACTAGCAATGATCTGGTCC 57.054 45.455 0.00 0.00 0.00 4.46
523 529 5.065988 CCGTAGAAAATAAATGTGGGGTGAG 59.934 44.000 0.00 0.00 0.00 3.51
527 533 5.190677 ACTCCGTAGAAAATAAATGTGGGG 58.809 41.667 0.00 0.00 0.00 4.96
529 535 9.028185 GTACTACTCCGTAGAAAATAAATGTGG 57.972 37.037 7.94 0.00 38.29 4.17
550 556 6.758806 AAAGGTCCTCCAAAAGAAGTACTA 57.241 37.500 0.00 0.00 35.89 1.82
551 557 5.648330 AAAGGTCCTCCAAAAGAAGTACT 57.352 39.130 0.00 0.00 35.89 2.73
552 558 7.997773 AATAAAGGTCCTCCAAAAGAAGTAC 57.002 36.000 0.00 0.00 35.89 2.73
592 604 8.361139 TCTCGGTGCTTCCAAAAATAAAATAAA 58.639 29.630 0.00 0.00 35.57 1.40
593 605 7.887381 TCTCGGTGCTTCCAAAAATAAAATAA 58.113 30.769 0.00 0.00 35.57 1.40
594 606 7.392113 TCTCTCGGTGCTTCCAAAAATAAAATA 59.608 33.333 0.00 0.00 35.57 1.40
595 607 6.208599 TCTCTCGGTGCTTCCAAAAATAAAAT 59.791 34.615 0.00 0.00 35.57 1.82
596 608 5.533154 TCTCTCGGTGCTTCCAAAAATAAAA 59.467 36.000 0.00 0.00 35.57 1.52
656 679 2.116533 GGGGTTGCCCGGAATTACG 61.117 63.158 0.73 2.08 46.66 3.18
845 868 1.077285 GTAATTGGGGACGGTGGGG 60.077 63.158 0.00 0.00 0.00 4.96
901 991 4.373116 AATCAGTCCGGCGTGCGT 62.373 61.111 6.01 0.00 0.00 5.24
902 992 3.554692 GAATCAGTCCGGCGTGCG 61.555 66.667 6.01 0.00 0.00 5.34
909 999 1.521681 GCGGGGAAGAATCAGTCCG 60.522 63.158 0.00 0.00 37.84 4.79
910 1000 1.521681 CGCGGGGAAGAATCAGTCC 60.522 63.158 0.00 0.00 0.00 3.85
912 1002 1.517832 CTCGCGGGGAAGAATCAGT 59.482 57.895 6.13 0.00 0.00 3.41
914 1004 2.900273 CCTCGCGGGGAAGAATCA 59.100 61.111 24.25 0.00 0.00 2.57
926 1016 3.691744 CTGAGTCTGACGGCCTCGC 62.692 68.421 0.00 0.00 40.63 5.03
931 1021 1.214062 CCAGTCTGAGTCTGACGGC 59.786 63.158 20.49 0.00 37.39 5.68
940 1030 3.062466 TCGGTCGGCCAGTCTGAG 61.062 66.667 6.96 0.00 34.09 3.35
984 1074 4.457496 ATGCGGACCTGAGCCACG 62.457 66.667 0.00 0.00 0.00 4.94
1016 1115 2.750350 CCTTCCCGTGCCACTTCT 59.250 61.111 0.00 0.00 0.00 2.85
1435 1534 2.762234 CGAAGTCGACGGAGGAGGG 61.762 68.421 10.46 0.00 43.02 4.30
1539 1638 2.179517 GAGGTGAGCACGACGAGG 59.820 66.667 0.00 0.00 0.00 4.63
1626 1725 2.892425 GGGCAGTTGATCTCGCGG 60.892 66.667 6.13 0.00 0.00 6.46
1722 1821 1.411977 TCCCCAATTGTGCAGTTGTTG 59.588 47.619 4.43 0.00 0.00 3.33
1724 1823 1.895131 GATCCCCAATTGTGCAGTTGT 59.105 47.619 4.43 0.00 0.00 3.32
1770 1869 2.657102 CTTCCAGGATCAGCGGCTCC 62.657 65.000 0.00 0.00 0.00 4.70
1783 1882 0.107752 GGCTTGAGAGGCTCTTCCAG 60.108 60.000 19.80 15.09 44.59 3.86
1784 1883 1.986413 GGCTTGAGAGGCTCTTCCA 59.014 57.895 19.80 10.25 44.59 3.53
1881 1980 0.179171 AGCCGAGATCAACGTACACG 60.179 55.000 0.00 0.00 46.33 4.49
2043 2142 1.524621 CTTGACCCAGGCGGCATAG 60.525 63.158 13.08 0.48 33.26 2.23
2100 2199 1.071542 GCCTTAGCCTCATCCTCCTTC 59.928 57.143 0.00 0.00 0.00 3.46
2160 2259 1.089920 CCTTGCCGGACATCTTCTTG 58.910 55.000 5.05 0.00 33.16 3.02
2187 2286 1.261989 CGAAATCAAATGCCTGCACG 58.738 50.000 0.00 0.00 0.00 5.34
2229 2328 1.384989 CCACGTAGTCCTGCTCCGAT 61.385 60.000 0.00 0.00 41.61 4.18
2497 2596 1.009829 CGAACCCTATCTGCAGCAAC 58.990 55.000 9.47 0.00 0.00 4.17
2511 2610 3.655276 TTTGTCCTCTGTAGTCGAACC 57.345 47.619 0.00 0.00 0.00 3.62
2593 2692 9.851267 ATAGACCAAATCCCTTAATCTCTATCT 57.149 33.333 0.00 0.00 0.00 1.98
2599 2698 8.435982 CAGAGAATAGACCAAATCCCTTAATCT 58.564 37.037 0.00 0.00 0.00 2.40
2612 2711 6.681729 AACTAACCAACAGAGAATAGACCA 57.318 37.500 0.00 0.00 0.00 4.02
2643 2742 9.284968 TCCTCAAATCTTCTTTTAACTACAAGG 57.715 33.333 0.00 0.00 0.00 3.61
2657 2756 6.865726 GCTTCCTTTCTTTTCCTCAAATCTTC 59.134 38.462 0.00 0.00 0.00 2.87
2658 2757 6.515696 CGCTTCCTTTCTTTTCCTCAAATCTT 60.516 38.462 0.00 0.00 0.00 2.40
2679 2778 2.228822 CTGGGAATGCAGTTAAACGCTT 59.771 45.455 0.00 0.00 0.00 4.68
2719 2819 8.856153 TCCTTTGCTCAATAACAGTAACAATA 57.144 30.769 0.00 0.00 0.00 1.90
2770 2870 3.823873 ACATAGTTTCGGCAATTCACCAA 59.176 39.130 0.00 0.00 0.00 3.67
2771 2871 3.417101 ACATAGTTTCGGCAATTCACCA 58.583 40.909 0.00 0.00 0.00 4.17
2772 2872 4.083003 TGAACATAGTTTCGGCAATTCACC 60.083 41.667 0.00 0.00 0.00 4.02
2773 2873 4.851558 GTGAACATAGTTTCGGCAATTCAC 59.148 41.667 0.00 0.00 38.30 3.18
2774 2874 4.759693 AGTGAACATAGTTTCGGCAATTCA 59.240 37.500 0.00 0.00 0.00 2.57
2775 2875 5.296813 AGTGAACATAGTTTCGGCAATTC 57.703 39.130 0.00 0.00 0.00 2.17
2776 2876 5.335661 GGAAGTGAACATAGTTTCGGCAATT 60.336 40.000 0.00 0.00 0.00 2.32
2780 2880 2.418976 GGGAAGTGAACATAGTTTCGGC 59.581 50.000 0.00 0.00 0.00 5.54
2807 2908 6.716934 TGCAAGAACCACCTAACAAAATAA 57.283 33.333 0.00 0.00 0.00 1.40
2809 2911 4.501400 GCTGCAAGAACCACCTAACAAAAT 60.501 41.667 0.00 0.00 34.07 1.82
2816 2918 1.352083 AGAGCTGCAAGAACCACCTA 58.648 50.000 1.02 0.00 34.07 3.08
2821 2923 6.442513 AATACAAATAGAGCTGCAAGAACC 57.557 37.500 1.02 0.00 34.07 3.62
2835 2937 7.971183 TGAACACAGTGCAGTAATACAAATA 57.029 32.000 0.00 0.00 0.00 1.40
2913 3017 4.263462 TGTTCACCCATTCAGCATAGAGTT 60.263 41.667 0.00 0.00 0.00 3.01
2957 3061 4.053295 CAGAAGAAAGGCACCACAAAATG 58.947 43.478 0.00 0.00 0.00 2.32
2974 3078 3.049708 TGTTGAGAGTCATGGCAGAAG 57.950 47.619 0.00 0.00 0.00 2.85
3000 3109 3.343972 CCACGAACCAGGCAGTTG 58.656 61.111 0.00 0.00 0.00 3.16
3014 3123 4.778143 AGGTTCCGCGGATGCCAC 62.778 66.667 35.38 27.84 38.08 5.01
3048 3158 3.539604 CTTGGAGAACAGAGCAATAGGG 58.460 50.000 0.00 0.00 0.00 3.53
3052 3162 1.074405 TGGCTTGGAGAACAGAGCAAT 59.926 47.619 0.00 0.00 35.96 3.56
3118 3228 1.396653 GCAATTGCAGTAGCCCATCT 58.603 50.000 25.36 0.00 41.13 2.90
3119 3229 3.953201 GCAATTGCAGTAGCCCATC 57.047 52.632 25.36 0.00 41.13 3.51
3131 3241 8.394877 TGATAAACTAACCGATTACTGCAATTG 58.605 33.333 0.00 0.00 0.00 2.32
3150 3260 7.010923 GTGATCAGATCAGTGGACTTGATAAAC 59.989 40.741 13.78 0.00 40.53 2.01
3200 3312 2.858622 GCACCAGCATAGCAACTGA 58.141 52.632 0.00 0.00 41.58 3.41
3237 3351 0.245266 TGCTTGGACGATTACAGCGA 59.755 50.000 0.00 0.00 0.00 4.93
3366 3503 4.862641 ACAAATAAGGCCAGACATACCT 57.137 40.909 5.01 0.00 34.45 3.08
3424 3561 2.095372 GGCACGTACTATCTTTGGCAAC 59.905 50.000 0.00 0.00 33.17 4.17
3444 3581 0.545071 ACATTCCAGGGCCAAAAGGG 60.545 55.000 6.18 0.00 40.85 3.95


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

AutoCloner maintained by Alex Coulton.