Multiple sequence alignment - TraesCS5A01G224700

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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 TraesCS5A01G224700 chr5A 100.000 2664 0 0 610 3273 439826768 439824105 0.000000e+00 4920.0
1 TraesCS5A01G224700 chr5A 100.000 363 0 0 1 363 439827377 439827015 0.000000e+00 671.0
2 TraesCS5A01G224700 chr5A 86.703 549 67 4 1526 2068 439773389 439772841 3.610000e-169 604.0
3 TraesCS5A01G224700 chr5A 79.084 808 132 24 1526 2320 439854688 439853905 3.740000e-144 521.0
4 TraesCS5A01G224700 chr5D 93.673 2450 83 33 866 3273 339087158 339084739 0.000000e+00 3600.0
5 TraesCS5A01G224700 chr5D 87.455 550 61 7 1526 2068 339067460 339066912 7.710000e-176 627.0
6 TraesCS5A01G224700 chr5D 91.209 364 31 1 1 363 339090250 339089887 8.160000e-136 494.0
7 TraesCS5A01G224700 chr5D 78.505 749 116 25 1582 2320 339092284 339091571 1.790000e-122 449.0
8 TraesCS5A01G224700 chr5B 94.369 1332 52 7 791 2100 398060449 398059119 0.000000e+00 2023.0
9 TraesCS5A01G224700 chr5B 88.293 615 42 16 2104 2703 398059026 398058427 0.000000e+00 710.0
10 TraesCS5A01G224700 chr5B 85.643 599 76 8 1526 2116 397966172 397965576 3.590000e-174 621.0
11 TraesCS5A01G224700 chr5B 79.890 726 114 21 1582 2297 398064107 398063404 1.360000e-138 503.0
12 TraesCS5A01G224700 chr5B 94.709 189 10 0 3085 3273 398058426 398058238 8.880000e-76 294.0
13 TraesCS5A01G224700 chr5B 85.443 158 8 3 617 762 398060984 398060830 2.030000e-32 150.0
14 TraesCS5A01G224700 chr2A 78.166 687 114 22 1664 2336 236918916 236918252 3.930000e-109 405.0
15 TraesCS5A01G224700 chr2B 79.661 118 13 6 1745 1857 752395509 752395398 1.260000e-09 75.0
16 TraesCS5A01G224700 chr2D 71.658 374 73 23 1745 2105 616923646 616923293 4.530000e-09 73.1


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 TraesCS5A01G224700 chr5A 439824105 439827377 3272 True 2795.500000 4920 100.000000 1 3273 2 chr5A.!!$R3 3272
1 TraesCS5A01G224700 chr5A 439772841 439773389 548 True 604.000000 604 86.703000 1526 2068 1 chr5A.!!$R1 542
2 TraesCS5A01G224700 chr5A 439853905 439854688 783 True 521.000000 521 79.084000 1526 2320 1 chr5A.!!$R2 794
3 TraesCS5A01G224700 chr5D 339084739 339092284 7545 True 1514.333333 3600 87.795667 1 3273 3 chr5D.!!$R2 3272
4 TraesCS5A01G224700 chr5D 339066912 339067460 548 True 627.000000 627 87.455000 1526 2068 1 chr5D.!!$R1 542
5 TraesCS5A01G224700 chr5B 398058238 398064107 5869 True 736.000000 2023 88.540800 617 3273 5 chr5B.!!$R2 2656
6 TraesCS5A01G224700 chr5B 397965576 397966172 596 True 621.000000 621 85.643000 1526 2116 1 chr5B.!!$R1 590
7 TraesCS5A01G224700 chr2A 236918252 236918916 664 True 405.000000 405 78.166000 1664 2336 1 chr2A.!!$R1 672

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
88 89 0.105593 GATCATGAGCGGCTGGAGAA 59.894 55.0 7.50 0.0 0.00 2.87 F
89 90 0.106335 ATCATGAGCGGCTGGAGAAG 59.894 55.0 7.50 0.0 0.00 2.85 F
169 170 0.190815 AAACAATGGTGAAGGGGCCT 59.809 50.0 0.84 0.0 0.00 5.19 F
332 333 0.191064 ACAAGTCAGGGGAGAGTGGA 59.809 55.0 0.00 0.0 0.00 4.02 F
354 355 0.241749 ACGGCGTGATGAAACTACGA 59.758 50.0 13.76 0.0 40.01 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 6927 0.397675 ACGGAGATCTGCTGGGATCA 60.398 55.0 12.78 0.0 43.11 2.92 R
1863 7455 0.625849 AATAGGGGCACTCCACCTTG 59.374 55.0 0.00 0.0 35.98 3.61 R
1879 7480 1.164411 CAGAACACCCGCTTGCAATA 58.836 50.0 0.00 0.0 0.00 1.90 R
2181 7887 0.247185 CCCGCACCTGCAAATCAAAT 59.753 50.0 0.00 0.0 42.21 2.32 R
2351 8072 0.728542 CAATACCGCCCAACCGTTAC 59.271 55.0 0.00 0.0 0.00 2.50 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
21 22 4.701956 GGTGAACATTGTACCATCTTGG 57.298 45.455 4.21 0.00 45.02 3.61
23 24 3.088532 TGAACATTGTACCATCTTGGGC 58.911 45.455 0.00 0.00 43.37 5.36
24 25 3.245229 TGAACATTGTACCATCTTGGGCT 60.245 43.478 0.00 0.00 43.37 5.19
25 26 3.004752 ACATTGTACCATCTTGGGCTC 57.995 47.619 0.00 0.00 43.37 4.70
26 27 2.578021 ACATTGTACCATCTTGGGCTCT 59.422 45.455 0.00 0.00 43.37 4.09
27 28 3.010584 ACATTGTACCATCTTGGGCTCTT 59.989 43.478 0.00 0.00 43.37 2.85
28 29 2.787473 TGTACCATCTTGGGCTCTTG 57.213 50.000 0.00 0.00 43.37 3.02
29 30 2.265367 TGTACCATCTTGGGCTCTTGA 58.735 47.619 0.00 0.00 43.37 3.02
30 31 2.846206 TGTACCATCTTGGGCTCTTGAT 59.154 45.455 0.00 0.00 43.37 2.57
32 33 1.030457 CCATCTTGGGCTCTTGATGC 58.970 55.000 12.04 0.00 36.08 3.91
41 42 3.338250 TCTTGATGCCCGGCCCTT 61.338 61.111 7.03 0.00 0.00 3.95
42 43 2.362889 CTTGATGCCCGGCCCTTT 60.363 61.111 7.03 0.00 0.00 3.11
43 44 1.984026 CTTGATGCCCGGCCCTTTT 60.984 57.895 7.03 0.00 0.00 2.27
44 45 2.229690 CTTGATGCCCGGCCCTTTTG 62.230 60.000 7.03 0.00 0.00 2.44
47 48 3.826265 ATGCCCGGCCCTTTTGTGT 62.826 57.895 7.03 0.00 0.00 3.72
48 49 3.680786 GCCCGGCCCTTTTGTGTC 61.681 66.667 0.00 0.00 0.00 3.67
49 50 2.203422 CCCGGCCCTTTTGTGTCA 60.203 61.111 0.00 0.00 0.00 3.58
50 51 1.606313 CCCGGCCCTTTTGTGTCAT 60.606 57.895 0.00 0.00 0.00 3.06
52 53 1.080569 CGGCCCTTTTGTGTCATGC 60.081 57.895 0.00 0.00 0.00 4.06
54 55 0.392336 GGCCCTTTTGTGTCATGCAA 59.608 50.000 0.00 0.00 0.00 4.08
55 56 1.501169 GCCCTTTTGTGTCATGCAAC 58.499 50.000 0.00 0.00 0.00 4.17
56 57 1.873486 GCCCTTTTGTGTCATGCAACC 60.873 52.381 0.00 0.00 0.00 3.77
57 58 1.411977 CCCTTTTGTGTCATGCAACCA 59.588 47.619 0.00 0.00 0.00 3.67
58 59 2.472816 CCTTTTGTGTCATGCAACCAC 58.527 47.619 0.00 0.00 0.00 4.16
60 61 2.575694 TTTGTGTCATGCAACCACAC 57.424 45.000 15.71 15.71 38.71 3.82
63 64 0.874390 GTGTCATGCAACCACACGAT 59.126 50.000 9.61 0.00 31.67 3.73
64 65 0.873721 TGTCATGCAACCACACGATG 59.126 50.000 0.00 0.00 0.00 3.84
66 67 1.535028 GTCATGCAACCACACGATGAA 59.465 47.619 0.00 0.00 0.00 2.57
67 68 2.031245 GTCATGCAACCACACGATGAAA 60.031 45.455 0.00 0.00 0.00 2.69
68 69 2.226200 TCATGCAACCACACGATGAAAG 59.774 45.455 0.00 0.00 0.00 2.62
70 71 1.234821 GCAACCACACGATGAAAGGA 58.765 50.000 0.00 0.00 0.00 3.36
72 73 2.159517 GCAACCACACGATGAAAGGATC 60.160 50.000 0.00 0.00 0.00 3.36
73 74 3.073678 CAACCACACGATGAAAGGATCA 58.926 45.455 0.00 0.00 43.67 2.92
81 82 3.085208 TGAAAGGATCATGAGCGGC 57.915 52.632 4.63 0.00 31.50 6.53
84 85 0.465097 AAAGGATCATGAGCGGCTGG 60.465 55.000 7.50 0.00 0.00 4.85
85 86 1.340399 AAGGATCATGAGCGGCTGGA 61.340 55.000 7.50 2.25 0.00 3.86
86 87 1.301558 GGATCATGAGCGGCTGGAG 60.302 63.158 7.50 0.00 0.00 3.86
87 88 1.744639 GATCATGAGCGGCTGGAGA 59.255 57.895 7.50 1.88 0.00 3.71
88 89 0.105593 GATCATGAGCGGCTGGAGAA 59.894 55.000 7.50 0.00 0.00 2.87
89 90 0.106335 ATCATGAGCGGCTGGAGAAG 59.894 55.000 7.50 0.00 0.00 2.85
90 91 1.523258 CATGAGCGGCTGGAGAAGG 60.523 63.158 7.50 0.00 0.00 3.46
91 92 1.687146 ATGAGCGGCTGGAGAAGGA 60.687 57.895 7.50 0.00 0.00 3.36
93 94 2.604686 AGCGGCTGGAGAAGGACA 60.605 61.111 0.00 0.00 0.00 4.02
94 95 2.435059 GCGGCTGGAGAAGGACAC 60.435 66.667 0.00 0.00 0.00 3.67
95 96 3.059982 CGGCTGGAGAAGGACACA 58.940 61.111 0.00 0.00 0.00 3.72
96 97 1.599047 CGGCTGGAGAAGGACACAT 59.401 57.895 0.00 0.00 0.00 3.21
99 100 1.271597 GGCTGGAGAAGGACACATTGT 60.272 52.381 0.00 0.00 0.00 2.71
101 102 3.003480 GCTGGAGAAGGACACATTGTAC 58.997 50.000 0.00 0.00 0.00 2.90
102 103 3.307059 GCTGGAGAAGGACACATTGTACT 60.307 47.826 0.00 0.00 45.16 2.73
130 131 8.804743 TGATTATAAGAAAGTTTAGACTTCGCG 58.195 33.333 0.00 0.00 45.18 5.87
132 133 3.655276 AGAAAGTTTAGACTTCGCGGA 57.345 42.857 6.13 0.00 45.18 5.54
133 134 3.986277 AGAAAGTTTAGACTTCGCGGAA 58.014 40.909 6.13 0.00 45.18 4.30
134 135 4.566987 AGAAAGTTTAGACTTCGCGGAAT 58.433 39.130 6.13 0.00 45.18 3.01
135 136 4.389077 AGAAAGTTTAGACTTCGCGGAATG 59.611 41.667 6.13 0.00 45.18 2.67
136 137 3.314541 AGTTTAGACTTCGCGGAATGT 57.685 42.857 6.13 0.00 29.87 2.71
137 138 4.445452 AGTTTAGACTTCGCGGAATGTA 57.555 40.909 6.13 0.00 29.87 2.29
138 139 4.813027 AGTTTAGACTTCGCGGAATGTAA 58.187 39.130 6.13 0.00 29.87 2.41
140 141 5.697633 AGTTTAGACTTCGCGGAATGTAAAA 59.302 36.000 6.13 0.00 29.87 1.52
141 142 6.370718 AGTTTAGACTTCGCGGAATGTAAAAT 59.629 34.615 6.13 0.00 29.87 1.82
142 143 4.600012 AGACTTCGCGGAATGTAAAATG 57.400 40.909 6.13 0.00 0.00 2.32
145 146 1.080298 TCGCGGAATGTAAAATGCGT 58.920 45.000 6.13 0.00 45.23 5.24
146 147 2.269172 TCGCGGAATGTAAAATGCGTA 58.731 42.857 6.13 0.00 45.23 4.42
147 148 2.029486 TCGCGGAATGTAAAATGCGTAC 59.971 45.455 6.13 0.00 45.23 3.67
149 150 2.353579 GCGGAATGTAAAATGCGTACCT 59.646 45.455 0.00 0.00 32.62 3.08
150 151 3.556775 GCGGAATGTAAAATGCGTACCTA 59.443 43.478 0.00 0.00 32.62 3.08
151 152 4.034279 GCGGAATGTAAAATGCGTACCTAA 59.966 41.667 0.00 0.00 32.62 2.69
152 153 5.447548 GCGGAATGTAAAATGCGTACCTAAA 60.448 40.000 0.00 0.00 32.62 1.85
153 154 5.961263 CGGAATGTAAAATGCGTACCTAAAC 59.039 40.000 0.00 0.00 0.00 2.01
154 155 6.402334 CGGAATGTAAAATGCGTACCTAAACA 60.402 38.462 0.00 0.00 0.00 2.83
155 156 7.306953 GGAATGTAAAATGCGTACCTAAACAA 58.693 34.615 0.00 0.00 0.00 2.83
156 157 7.971722 GGAATGTAAAATGCGTACCTAAACAAT 59.028 33.333 0.00 0.00 0.00 2.71
157 158 8.682128 AATGTAAAATGCGTACCTAAACAATG 57.318 30.769 0.00 0.00 0.00 2.82
158 159 6.613233 TGTAAAATGCGTACCTAAACAATGG 58.387 36.000 0.00 0.00 0.00 3.16
159 160 5.715434 AAAATGCGTACCTAAACAATGGT 57.285 34.783 0.00 0.00 40.12 3.55
160 161 4.695217 AATGCGTACCTAAACAATGGTG 57.305 40.909 0.00 0.00 37.74 4.17
161 162 3.404224 TGCGTACCTAAACAATGGTGA 57.596 42.857 0.00 0.00 37.74 4.02
162 163 3.741249 TGCGTACCTAAACAATGGTGAA 58.259 40.909 0.00 0.00 37.74 3.18
163 164 3.749088 TGCGTACCTAAACAATGGTGAAG 59.251 43.478 0.00 0.00 37.74 3.02
167 168 1.824852 CCTAAACAATGGTGAAGGGGC 59.175 52.381 0.00 0.00 0.00 5.80
169 170 0.190815 AAACAATGGTGAAGGGGCCT 59.809 50.000 0.84 0.00 0.00 5.19
170 171 0.542702 AACAATGGTGAAGGGGCCTG 60.543 55.000 0.84 0.00 0.00 4.85
172 173 2.855770 AATGGTGAAGGGGCCTGCA 61.856 57.895 0.84 0.00 0.00 4.41
175 176 4.284550 GTGAAGGGGCCTGCACCA 62.285 66.667 13.87 0.00 44.76 4.17
176 177 3.970410 TGAAGGGGCCTGCACCAG 61.970 66.667 13.87 0.00 43.35 4.00
177 178 3.650950 GAAGGGGCCTGCACCAGA 61.651 66.667 13.87 0.00 43.35 3.86
178 179 3.185203 AAGGGGCCTGCACCAGAA 61.185 61.111 13.87 0.00 43.35 3.02
181 182 4.666253 GGGCCTGCACCAGAAGCA 62.666 66.667 0.84 0.00 40.19 3.91
186 187 4.481195 TGCACCAGAAGCAGTTCC 57.519 55.556 0.00 0.00 37.02 3.62
187 188 1.531259 TGCACCAGAAGCAGTTCCA 59.469 52.632 0.00 0.00 37.02 3.53
188 189 0.535780 TGCACCAGAAGCAGTTCCAG 60.536 55.000 0.00 0.00 37.02 3.86
189 190 0.250467 GCACCAGAAGCAGTTCCAGA 60.250 55.000 0.00 0.00 32.48 3.86
190 191 1.612726 GCACCAGAAGCAGTTCCAGAT 60.613 52.381 0.00 0.00 32.48 2.90
193 194 2.290577 ACCAGAAGCAGTTCCAGATTCC 60.291 50.000 0.00 0.00 32.09 3.01
194 195 2.005451 CAGAAGCAGTTCCAGATTCCG 58.995 52.381 0.00 0.00 32.09 4.30
195 196 1.902508 AGAAGCAGTTCCAGATTCCGA 59.097 47.619 0.00 0.00 32.09 4.55
197 198 1.561643 AGCAGTTCCAGATTCCGAGA 58.438 50.000 0.00 0.00 0.00 4.04
198 199 1.205893 AGCAGTTCCAGATTCCGAGAC 59.794 52.381 0.00 0.00 0.00 3.36
199 200 1.205893 GCAGTTCCAGATTCCGAGACT 59.794 52.381 0.00 0.00 0.00 3.24
200 201 2.737039 GCAGTTCCAGATTCCGAGACTC 60.737 54.545 0.00 0.00 0.00 3.36
201 202 1.746220 AGTTCCAGATTCCGAGACTCG 59.254 52.381 18.08 18.08 40.07 4.18
202 203 0.456221 TTCCAGATTCCGAGACTCGC 59.544 55.000 19.55 5.74 38.82 5.03
205 206 0.869454 CAGATTCCGAGACTCGCAGC 60.869 60.000 19.55 10.53 38.82 5.25
206 207 1.590259 GATTCCGAGACTCGCAGCC 60.590 63.158 19.55 4.76 38.82 4.85
207 208 3.417275 ATTCCGAGACTCGCAGCCG 62.417 63.158 19.55 5.56 38.82 5.52
221 222 4.078516 GCCGCGGTGGTCCTACTT 62.079 66.667 28.70 0.00 41.21 2.24
222 223 2.660802 CCGCGGTGGTCCTACTTT 59.339 61.111 19.50 0.00 0.00 2.66
224 225 1.005394 CGCGGTGGTCCTACTTTGT 60.005 57.895 0.00 0.00 0.00 2.83
225 226 0.244450 CGCGGTGGTCCTACTTTGTA 59.756 55.000 0.00 0.00 0.00 2.41
226 227 1.734707 CGCGGTGGTCCTACTTTGTAG 60.735 57.143 0.00 0.00 0.00 2.74
227 228 2.005560 GCGGTGGTCCTACTTTGTAGC 61.006 57.143 0.00 0.00 0.00 3.58
228 229 1.274167 CGGTGGTCCTACTTTGTAGCA 59.726 52.381 0.00 0.00 0.00 3.49
229 230 2.696506 GGTGGTCCTACTTTGTAGCAC 58.303 52.381 0.00 0.00 39.11 4.40
230 231 2.334838 GTGGTCCTACTTTGTAGCACG 58.665 52.381 0.00 0.00 31.57 5.34
233 234 2.028748 GGTCCTACTTTGTAGCACGGAA 60.029 50.000 0.00 0.00 0.00 4.30
234 235 2.991866 GTCCTACTTTGTAGCACGGAAC 59.008 50.000 0.00 0.00 0.00 3.62
263 264 5.557891 GCTTCATGCATCCCTATAATGAC 57.442 43.478 0.00 0.00 42.31 3.06
264 265 5.005740 GCTTCATGCATCCCTATAATGACA 58.994 41.667 0.00 0.00 42.31 3.58
266 267 5.830799 TCATGCATCCCTATAATGACAGT 57.169 39.130 0.00 0.00 0.00 3.55
268 269 5.072193 TCATGCATCCCTATAATGACAGTGT 59.928 40.000 0.00 0.00 0.00 3.55
271 272 4.516698 GCATCCCTATAATGACAGTGTTGG 59.483 45.833 0.00 0.00 0.00 3.77
273 274 5.353394 TCCCTATAATGACAGTGTTGGTC 57.647 43.478 0.00 0.00 35.83 4.02
274 275 5.030147 TCCCTATAATGACAGTGTTGGTCT 58.970 41.667 0.00 0.00 36.26 3.85
275 276 5.128827 TCCCTATAATGACAGTGTTGGTCTC 59.871 44.000 0.00 0.00 36.26 3.36
276 277 5.129485 CCCTATAATGACAGTGTTGGTCTCT 59.871 44.000 0.00 0.00 36.26 3.10
278 279 2.175878 ATGACAGTGTTGGTCTCTGC 57.824 50.000 0.00 0.00 40.16 4.26
279 280 1.123077 TGACAGTGTTGGTCTCTGCT 58.877 50.000 0.00 0.00 40.16 4.24
280 281 1.069204 TGACAGTGTTGGTCTCTGCTC 59.931 52.381 0.00 0.00 40.16 4.26
281 282 1.069204 GACAGTGTTGGTCTCTGCTCA 59.931 52.381 0.00 0.00 40.16 4.26
282 283 1.696336 ACAGTGTTGGTCTCTGCTCAT 59.304 47.619 0.00 0.00 40.16 2.90
283 284 2.899900 ACAGTGTTGGTCTCTGCTCATA 59.100 45.455 0.00 0.00 40.16 2.15
284 285 3.056250 ACAGTGTTGGTCTCTGCTCATAG 60.056 47.826 0.00 0.00 40.16 2.23
285 286 2.093764 AGTGTTGGTCTCTGCTCATAGC 60.094 50.000 0.00 0.00 42.82 2.97
295 296 1.884926 GCTCATAGCAGCGACACCC 60.885 63.158 0.00 0.00 41.89 4.61
296 297 1.227380 CTCATAGCAGCGACACCCC 60.227 63.158 0.00 0.00 0.00 4.95
297 298 1.960040 CTCATAGCAGCGACACCCCA 61.960 60.000 0.00 0.00 0.00 4.96
298 299 1.815421 CATAGCAGCGACACCCCAC 60.815 63.158 0.00 0.00 0.00 4.61
299 300 2.290287 ATAGCAGCGACACCCCACA 61.290 57.895 0.00 0.00 0.00 4.17
301 302 4.927782 GCAGCGACACCCCACACA 62.928 66.667 0.00 0.00 0.00 3.72
302 303 2.972505 CAGCGACACCCCACACAC 60.973 66.667 0.00 0.00 0.00 3.82
303 304 3.475494 AGCGACACCCCACACACA 61.475 61.111 0.00 0.00 0.00 3.72
304 305 2.281484 GCGACACCCCACACACAT 60.281 61.111 0.00 0.00 0.00 3.21
305 306 2.616330 GCGACACCCCACACACATG 61.616 63.158 0.00 0.00 0.00 3.21
319 320 2.838736 ACACATGGTGAGACACAAGTC 58.161 47.619 2.98 0.00 39.84 3.01
320 321 2.170397 ACACATGGTGAGACACAAGTCA 59.830 45.455 2.98 0.00 40.96 3.41
321 322 3.742327 ACACATGGTGAGACACAAGTCAG 60.742 47.826 2.98 0.00 40.96 3.51
322 323 6.782558 ACACATGGTGAGACACAAGTCAGG 62.783 50.000 2.98 0.00 40.96 3.86
329 330 1.343069 GACACAAGTCAGGGGAGAGT 58.657 55.000 0.00 0.00 44.34 3.24
331 332 0.322975 CACAAGTCAGGGGAGAGTGG 59.677 60.000 0.00 0.00 0.00 4.00
332 333 0.191064 ACAAGTCAGGGGAGAGTGGA 59.809 55.000 0.00 0.00 0.00 4.02
333 334 0.610687 CAAGTCAGGGGAGAGTGGAC 59.389 60.000 0.00 0.00 0.00 4.02
334 335 0.900647 AAGTCAGGGGAGAGTGGACG 60.901 60.000 0.00 0.00 33.84 4.79
338 339 3.450115 GGGGAGAGTGGACGACGG 61.450 72.222 0.00 0.00 0.00 4.79
350 351 3.856508 CGACGGCGTGATGAAACT 58.143 55.556 21.19 0.00 0.00 2.66
351 352 3.024423 CGACGGCGTGATGAAACTA 57.976 52.632 21.19 0.00 0.00 2.24
352 353 0.638746 CGACGGCGTGATGAAACTAC 59.361 55.000 21.19 0.00 0.00 2.73
353 354 0.638746 GACGGCGTGATGAAACTACG 59.361 55.000 21.19 0.00 40.52 3.51
354 355 0.241749 ACGGCGTGATGAAACTACGA 59.758 50.000 13.76 0.00 40.01 3.43
355 356 1.336148 ACGGCGTGATGAAACTACGAA 60.336 47.619 13.76 0.00 40.01 3.85
356 357 1.320555 CGGCGTGATGAAACTACGAAG 59.679 52.381 0.00 0.00 40.01 3.79
359 360 2.092211 GCGTGATGAAACTACGAAGGTG 59.908 50.000 0.00 0.00 40.01 4.00
360 361 3.571571 CGTGATGAAACTACGAAGGTGA 58.428 45.455 0.00 0.00 40.01 4.02
361 362 3.985279 CGTGATGAAACTACGAAGGTGAA 59.015 43.478 0.00 0.00 40.01 3.18
362 363 4.143389 CGTGATGAAACTACGAAGGTGAAC 60.143 45.833 0.00 0.00 40.01 3.18
637 3393 1.001887 AACGAGACGAGGAGAGGCT 60.002 57.895 0.00 0.00 0.00 4.58
657 3413 1.915489 TGCATGGGGTTCACTAGACAT 59.085 47.619 0.00 0.00 0.00 3.06
687 3443 3.090765 CAAGGGGGCTTAGGCAGT 58.909 61.111 8.32 0.00 40.87 4.40
758 3757 6.575162 AAAAAGGAGCATCGTTACAAGAAT 57.425 33.333 0.00 0.00 43.22 2.40
833 4196 1.067142 ACTTTTACGAGCCGATGAGCA 60.067 47.619 1.50 0.00 34.23 4.26
837 4200 2.936829 TACGAGCCGATGAGCAAGCG 62.937 60.000 1.50 0.00 34.23 4.68
891 6459 1.349357 TCCGATTCACCACATCCAACA 59.651 47.619 0.00 0.00 0.00 3.33
909 6485 1.229496 AAAAATCCAGCCCCCACCC 60.229 57.895 0.00 0.00 0.00 4.61
1315 6901 1.002502 AAGGGGAGGCGCAAACTAC 60.003 57.895 10.83 0.00 0.00 2.73
1317 6903 2.818274 GGGAGGCGCAAACTACGG 60.818 66.667 10.83 0.00 0.00 4.02
1341 6927 1.531602 GCTGCCCCTGTTTCCTGTT 60.532 57.895 0.00 0.00 0.00 3.16
1345 6931 1.177401 GCCCCTGTTTCCTGTTGATC 58.823 55.000 0.00 0.00 0.00 2.92
1377 6963 2.430244 TCGAAACCAGAGACGCGC 60.430 61.111 5.73 0.00 0.00 6.86
1522 7108 2.669569 GCTCCAACAGCGCCAAGA 60.670 61.111 2.29 0.00 38.76 3.02
1523 7109 2.260869 GCTCCAACAGCGCCAAGAA 61.261 57.895 2.29 0.00 38.76 2.52
1524 7110 1.795170 GCTCCAACAGCGCCAAGAAA 61.795 55.000 2.29 0.00 38.76 2.52
1684 7270 4.020617 CTGACCCGGGCTGCAAGA 62.021 66.667 24.08 0.00 34.07 3.02
1879 7480 3.260100 CCAAGGTGGAGTGCCCCT 61.260 66.667 0.00 0.00 40.96 4.79
2177 7883 9.260002 CAAAGTGCAAACTAATTATTGTTTCCT 57.740 29.630 0.00 0.00 34.60 3.36
2178 7884 9.476202 AAAGTGCAAACTAATTATTGTTTCCTC 57.524 29.630 0.00 0.00 34.60 3.71
2179 7885 8.409358 AGTGCAAACTAATTATTGTTTCCTCT 57.591 30.769 0.00 0.00 34.60 3.69
2180 7886 8.299570 AGTGCAAACTAATTATTGTTTCCTCTG 58.700 33.333 0.00 0.00 34.60 3.35
2181 7887 8.296713 GTGCAAACTAATTATTGTTTCCTCTGA 58.703 33.333 0.00 0.00 34.60 3.27
2342 8063 9.982651 AAGTAATTATGCAGATATTGACTACGT 57.017 29.630 0.00 0.00 0.00 3.57
2360 8081 6.489675 ACTACGTATATCTGTGTAACGGTTG 58.510 40.000 3.07 0.00 45.64 3.77
2370 8091 0.728542 GTAACGGTTGGGCGGTATTG 59.271 55.000 3.07 0.00 0.00 1.90
2373 8094 1.238625 ACGGTTGGGCGGTATTGTTG 61.239 55.000 0.00 0.00 0.00 3.33
2379 8100 4.822896 GGTTGGGCGGTATTGTTGATATTA 59.177 41.667 0.00 0.00 0.00 0.98
2384 8105 6.261381 TGGGCGGTATTGTTGATATTAACTTC 59.739 38.462 11.24 0.79 0.00 3.01
2472 8194 1.304464 GGAGCTGGTTTCCTTGGGG 60.304 63.158 0.00 0.00 0.00 4.96
2480 8202 1.133606 GGTTTCCTTGGGGTCTTGTGA 60.134 52.381 0.00 0.00 0.00 3.58
2510 8235 2.595750 TTTGAACAATCACCGGGGAT 57.404 45.000 15.27 15.27 34.61 3.85
2528 8253 1.907936 GATGGAGGAGGAGGATGGATG 59.092 57.143 0.00 0.00 0.00 3.51
2529 8254 0.104777 TGGAGGAGGAGGATGGATGG 60.105 60.000 0.00 0.00 0.00 3.51
2530 8255 0.192064 GGAGGAGGAGGATGGATGGA 59.808 60.000 0.00 0.00 0.00 3.41
2531 8256 1.203415 GGAGGAGGAGGATGGATGGAT 60.203 57.143 0.00 0.00 0.00 3.41
2549 8274 6.259608 GGATGGATCCTCGCTTGAATATATTG 59.740 42.308 14.23 0.00 43.73 1.90
2551 8281 4.333926 GGATCCTCGCTTGAATATATTGCC 59.666 45.833 3.84 0.00 0.00 4.52
2627 8359 2.561569 GTATTGCCGCCAAGACATAGT 58.438 47.619 0.00 0.00 41.56 2.12
2659 8391 7.202047 CCTCTAATCAGGTTCCTTGTAGCTAAT 60.202 40.741 0.00 0.00 0.00 1.73
2778 8539 1.970917 GATGTTGAAGCCGAGGTGCG 61.971 60.000 0.00 0.00 40.47 5.34
2858 8619 1.379843 CATACTTGGGGCGGCCTTT 60.380 57.895 28.80 11.86 0.00 3.11
2908 8669 2.422597 TGGAAGCAACATCGTACCTTG 58.577 47.619 0.00 0.00 0.00 3.61
2934 8695 4.527564 CAAAAACTGTTCTCCGTGATGTC 58.472 43.478 0.00 0.00 0.00 3.06
2970 8731 2.165845 TGTCTTTAGAGCTTAGCCGGTC 59.834 50.000 1.90 0.00 0.00 4.79
2985 8746 1.896465 CCGGTCTTTGAAGAGGAGTCT 59.104 52.381 0.00 0.00 35.32 3.24
3067 8828 2.612212 GTCGTCTTTTGAGGTGAGCAAA 59.388 45.455 0.00 0.00 35.92 3.68
3068 8829 2.612212 TCGTCTTTTGAGGTGAGCAAAC 59.388 45.455 0.00 0.00 35.20 2.93
3114 8875 4.142293 TGAAGTCTGATGAGTGAGGAATCG 60.142 45.833 0.00 0.00 0.00 3.34
3137 8898 5.745294 CGTTCATCATTGGATCCATTTGTTC 59.255 40.000 17.06 7.69 0.00 3.18
3139 8900 7.201723 CGTTCATCATTGGATCCATTTGTTCTA 60.202 37.037 17.06 0.00 0.00 2.10
3229 8990 9.726232 CTTATAACAGACCATCAAACATGATTG 57.274 33.333 9.31 9.31 0.00 2.67
3252 9013 3.522759 TGGGACTAGGATTGTGGTGTTA 58.477 45.455 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.209410 CATCAAGAGCCCAAGATGGTAC 58.791 50.000 0.00 0.00 35.17 3.34
11 12 2.421952 GCATCAAGAGCCCAAGATGGTA 60.422 50.000 0.00 0.00 38.57 3.25
12 13 1.684248 GCATCAAGAGCCCAAGATGGT 60.684 52.381 0.00 0.00 38.57 3.55
13 14 1.030457 GCATCAAGAGCCCAAGATGG 58.970 55.000 0.00 0.00 38.57 3.51
15 16 3.509517 GGCATCAAGAGCCCAAGAT 57.490 52.632 0.00 0.00 46.50 2.40
23 24 2.843912 AAAGGGCCGGGCATCAAGAG 62.844 60.000 30.95 0.00 0.00 2.85
24 25 2.439553 AAAAGGGCCGGGCATCAAGA 62.440 55.000 30.95 0.00 0.00 3.02
25 26 1.984026 AAAAGGGCCGGGCATCAAG 60.984 57.895 30.95 0.00 0.00 3.02
26 27 2.119391 AAAAGGGCCGGGCATCAA 59.881 55.556 30.95 0.00 0.00 2.57
27 28 2.679642 CAAAAGGGCCGGGCATCA 60.680 61.111 30.95 0.00 0.00 3.07
28 29 2.679996 ACAAAAGGGCCGGGCATC 60.680 61.111 30.95 13.65 0.00 3.91
29 30 2.996734 CACAAAAGGGCCGGGCAT 60.997 61.111 30.95 22.14 0.00 4.40
30 31 4.531426 ACACAAAAGGGCCGGGCA 62.531 61.111 30.95 0.00 0.00 5.36
32 33 1.606313 ATGACACAAAAGGGCCGGG 60.606 57.895 2.18 0.00 0.00 5.73
33 34 1.586028 CATGACACAAAAGGGCCGG 59.414 57.895 0.00 0.00 0.00 6.13
34 35 1.080569 GCATGACACAAAAGGGCCG 60.081 57.895 0.00 0.00 0.00 6.13
38 39 2.159128 TGTGGTTGCATGACACAAAAGG 60.159 45.455 13.96 0.00 41.65 3.11
39 40 2.859538 GTGTGGTTGCATGACACAAAAG 59.140 45.455 16.85 0.00 45.53 2.27
41 42 1.202234 CGTGTGGTTGCATGACACAAA 60.202 47.619 16.85 0.00 45.53 2.83
42 43 0.380024 CGTGTGGTTGCATGACACAA 59.620 50.000 16.85 0.00 45.53 3.33
43 44 0.462759 TCGTGTGGTTGCATGACACA 60.463 50.000 18.25 15.72 42.29 3.72
44 45 0.874390 ATCGTGTGGTTGCATGACAC 59.126 50.000 11.51 11.51 37.24 3.67
47 48 1.889545 TTCATCGTGTGGTTGCATGA 58.110 45.000 0.00 0.00 38.56 3.07
48 49 2.587956 CTTTCATCGTGTGGTTGCATG 58.412 47.619 0.00 0.00 0.00 4.06
49 50 1.541147 CCTTTCATCGTGTGGTTGCAT 59.459 47.619 0.00 0.00 0.00 3.96
50 51 0.950836 CCTTTCATCGTGTGGTTGCA 59.049 50.000 0.00 0.00 0.00 4.08
52 53 3.073678 TGATCCTTTCATCGTGTGGTTG 58.926 45.455 0.00 0.00 0.00 3.77
54 55 3.055167 TCATGATCCTTTCATCGTGTGGT 60.055 43.478 0.00 0.00 43.40 4.16
55 56 3.534554 TCATGATCCTTTCATCGTGTGG 58.465 45.455 0.00 0.00 43.40 4.17
56 57 3.002042 GCTCATGATCCTTTCATCGTGTG 59.998 47.826 0.00 2.56 43.40 3.82
57 58 3.201290 GCTCATGATCCTTTCATCGTGT 58.799 45.455 0.00 0.00 43.40 4.49
58 59 2.220363 CGCTCATGATCCTTTCATCGTG 59.780 50.000 0.00 0.00 43.40 4.35
60 61 1.797046 CCGCTCATGATCCTTTCATCG 59.203 52.381 0.00 0.00 43.40 3.84
63 64 0.543277 AGCCGCTCATGATCCTTTCA 59.457 50.000 0.00 0.00 39.12 2.69
64 65 0.942962 CAGCCGCTCATGATCCTTTC 59.057 55.000 0.00 0.00 0.00 2.62
66 67 1.147824 CCAGCCGCTCATGATCCTT 59.852 57.895 0.00 0.00 0.00 3.36
67 68 1.756408 CTCCAGCCGCTCATGATCCT 61.756 60.000 0.00 0.00 0.00 3.24
68 69 1.301558 CTCCAGCCGCTCATGATCC 60.302 63.158 0.00 0.00 0.00 3.36
70 71 0.106335 CTTCTCCAGCCGCTCATGAT 59.894 55.000 0.00 0.00 0.00 2.45
72 73 1.523258 CCTTCTCCAGCCGCTCATG 60.523 63.158 0.00 0.00 0.00 3.07
73 74 1.687146 TCCTTCTCCAGCCGCTCAT 60.687 57.895 0.00 0.00 0.00 2.90
74 75 2.283894 TCCTTCTCCAGCCGCTCA 60.284 61.111 0.00 0.00 0.00 4.26
75 76 2.185608 GTCCTTCTCCAGCCGCTC 59.814 66.667 0.00 0.00 0.00 5.03
77 78 2.435059 GTGTCCTTCTCCAGCCGC 60.435 66.667 0.00 0.00 0.00 6.53
79 80 1.271597 ACAATGTGTCCTTCTCCAGCC 60.272 52.381 0.00 0.00 0.00 4.85
81 82 4.543590 AGTACAATGTGTCCTTCTCCAG 57.456 45.455 0.00 0.00 0.00 3.86
84 85 7.440523 AATCAAAGTACAATGTGTCCTTCTC 57.559 36.000 0.00 0.00 25.97 2.87
104 105 8.804743 CGCGAAGTCTAAACTTTCTTATAATCA 58.195 33.333 0.00 0.00 45.80 2.57
105 106 8.267367 CCGCGAAGTCTAAACTTTCTTATAATC 58.733 37.037 8.23 0.00 45.80 1.75
106 107 7.977853 TCCGCGAAGTCTAAACTTTCTTATAAT 59.022 33.333 8.23 0.00 45.80 1.28
107 108 7.315142 TCCGCGAAGTCTAAACTTTCTTATAA 58.685 34.615 8.23 0.00 45.80 0.98
108 109 6.855836 TCCGCGAAGTCTAAACTTTCTTATA 58.144 36.000 8.23 0.00 45.80 0.98
110 111 5.125100 TCCGCGAAGTCTAAACTTTCTTA 57.875 39.130 8.23 0.00 45.80 2.10
111 112 3.986277 TCCGCGAAGTCTAAACTTTCTT 58.014 40.909 8.23 0.00 45.80 2.52
112 113 3.655276 TCCGCGAAGTCTAAACTTTCT 57.345 42.857 8.23 0.00 45.80 2.52
113 114 4.151867 ACATTCCGCGAAGTCTAAACTTTC 59.848 41.667 8.23 0.00 45.80 2.62
114 115 4.062991 ACATTCCGCGAAGTCTAAACTTT 58.937 39.130 8.23 0.00 45.80 2.66
118 119 6.539324 CATTTTACATTCCGCGAAGTCTAAA 58.461 36.000 8.23 0.78 0.00 1.85
119 120 5.446741 GCATTTTACATTCCGCGAAGTCTAA 60.447 40.000 8.23 0.00 0.00 2.10
120 121 4.033587 GCATTTTACATTCCGCGAAGTCTA 59.966 41.667 8.23 0.00 0.00 2.59
121 122 3.181510 GCATTTTACATTCCGCGAAGTCT 60.182 43.478 8.23 0.00 0.00 3.24
122 123 3.098636 GCATTTTACATTCCGCGAAGTC 58.901 45.455 8.23 0.00 0.00 3.01
123 124 2.475519 CGCATTTTACATTCCGCGAAGT 60.476 45.455 8.23 2.47 45.17 3.01
124 125 2.101125 CGCATTTTACATTCCGCGAAG 58.899 47.619 8.23 0.00 45.17 3.79
125 126 1.465387 ACGCATTTTACATTCCGCGAA 59.535 42.857 8.23 0.00 45.17 4.70
126 127 1.080298 ACGCATTTTACATTCCGCGA 58.920 45.000 8.23 0.00 45.17 5.87
130 131 6.844254 TGTTTAGGTACGCATTTTACATTCC 58.156 36.000 0.00 0.00 0.00 3.01
132 133 7.757624 CCATTGTTTAGGTACGCATTTTACATT 59.242 33.333 0.00 0.00 0.00 2.71
133 134 7.094118 ACCATTGTTTAGGTACGCATTTTACAT 60.094 33.333 0.00 0.00 36.07 2.29
134 135 6.207025 ACCATTGTTTAGGTACGCATTTTACA 59.793 34.615 0.00 0.00 36.07 2.41
135 136 6.525280 CACCATTGTTTAGGTACGCATTTTAC 59.475 38.462 0.00 0.00 36.07 2.01
136 137 6.430308 TCACCATTGTTTAGGTACGCATTTTA 59.570 34.615 0.00 0.00 36.07 1.52
137 138 5.241949 TCACCATTGTTTAGGTACGCATTTT 59.758 36.000 0.00 0.00 36.07 1.82
138 139 4.762765 TCACCATTGTTTAGGTACGCATTT 59.237 37.500 0.00 0.00 36.07 2.32
140 141 3.945346 TCACCATTGTTTAGGTACGCAT 58.055 40.909 0.00 0.00 36.07 4.73
141 142 3.404224 TCACCATTGTTTAGGTACGCA 57.596 42.857 0.00 0.00 36.07 5.24
142 143 3.126343 CCTTCACCATTGTTTAGGTACGC 59.874 47.826 0.00 0.00 36.07 4.42
145 146 3.562609 GCCCCTTCACCATTGTTTAGGTA 60.563 47.826 0.00 0.00 36.07 3.08
146 147 2.821625 GCCCCTTCACCATTGTTTAGGT 60.822 50.000 0.00 0.00 39.10 3.08
147 148 1.824852 GCCCCTTCACCATTGTTTAGG 59.175 52.381 0.00 0.00 0.00 2.69
149 150 1.431243 AGGCCCCTTCACCATTGTTTA 59.569 47.619 0.00 0.00 0.00 2.01
150 151 0.190815 AGGCCCCTTCACCATTGTTT 59.809 50.000 0.00 0.00 0.00 2.83
151 152 0.542702 CAGGCCCCTTCACCATTGTT 60.543 55.000 0.00 0.00 0.00 2.83
152 153 1.077265 CAGGCCCCTTCACCATTGT 59.923 57.895 0.00 0.00 0.00 2.71
153 154 2.353610 GCAGGCCCCTTCACCATTG 61.354 63.158 0.00 0.00 0.00 2.82
154 155 2.037847 GCAGGCCCCTTCACCATT 59.962 61.111 0.00 0.00 0.00 3.16
155 156 3.267233 TGCAGGCCCCTTCACCAT 61.267 61.111 0.00 0.00 0.00 3.55
156 157 4.284550 GTGCAGGCCCCTTCACCA 62.285 66.667 0.00 0.00 34.87 4.17
158 159 4.284550 TGGTGCAGGCCCCTTCAC 62.285 66.667 8.35 8.35 39.00 3.18
159 160 3.970410 CTGGTGCAGGCCCCTTCA 61.970 66.667 0.00 0.00 0.00 3.02
160 161 3.210012 TTCTGGTGCAGGCCCCTTC 62.210 63.158 0.00 0.00 31.51 3.46
161 162 3.185203 TTCTGGTGCAGGCCCCTT 61.185 61.111 0.00 0.00 31.51 3.95
162 163 3.655211 CTTCTGGTGCAGGCCCCT 61.655 66.667 0.00 0.00 31.51 4.79
169 170 0.535780 CTGGAACTGCTTCTGGTGCA 60.536 55.000 0.00 0.00 38.81 4.57
170 171 0.250467 TCTGGAACTGCTTCTGGTGC 60.250 55.000 0.00 0.00 0.00 5.01
172 173 2.290577 GGAATCTGGAACTGCTTCTGGT 60.291 50.000 0.00 0.00 33.86 4.00
174 175 2.005451 CGGAATCTGGAACTGCTTCTG 58.995 52.381 0.00 0.00 33.86 3.02
175 176 1.902508 TCGGAATCTGGAACTGCTTCT 59.097 47.619 0.00 0.00 33.86 2.85
176 177 2.093973 TCTCGGAATCTGGAACTGCTTC 60.094 50.000 0.00 0.00 32.86 3.86
177 178 1.902508 TCTCGGAATCTGGAACTGCTT 59.097 47.619 0.00 0.00 0.00 3.91
178 179 1.205893 GTCTCGGAATCTGGAACTGCT 59.794 52.381 0.00 0.00 0.00 4.24
181 182 1.746220 CGAGTCTCGGAATCTGGAACT 59.254 52.381 14.68 0.00 36.00 3.01
182 183 1.799548 GCGAGTCTCGGAATCTGGAAC 60.800 57.143 23.09 0.00 40.84 3.62
183 184 0.456221 GCGAGTCTCGGAATCTGGAA 59.544 55.000 23.09 0.00 40.84 3.53
184 185 0.679960 TGCGAGTCTCGGAATCTGGA 60.680 55.000 23.09 0.00 37.25 3.86
185 186 0.248825 CTGCGAGTCTCGGAATCTGG 60.249 60.000 23.09 5.04 40.32 3.86
186 187 0.869454 GCTGCGAGTCTCGGAATCTG 60.869 60.000 23.09 10.03 40.32 2.90
187 188 1.435515 GCTGCGAGTCTCGGAATCT 59.564 57.895 23.09 0.00 40.32 2.40
188 189 1.590259 GGCTGCGAGTCTCGGAATC 60.590 63.158 23.09 14.25 40.32 2.52
189 190 2.496817 GGCTGCGAGTCTCGGAAT 59.503 61.111 23.09 0.00 40.32 3.01
190 191 4.116328 CGGCTGCGAGTCTCGGAA 62.116 66.667 23.09 0.00 40.32 4.30
202 203 4.814294 GTAGGACCACCGCGGCTG 62.814 72.222 28.58 21.81 41.83 4.85
205 206 1.740296 CAAAGTAGGACCACCGCGG 60.740 63.158 26.86 26.86 41.83 6.46
206 207 0.244450 TACAAAGTAGGACCACCGCG 59.756 55.000 0.00 0.00 41.83 6.46
207 208 2.005560 GCTACAAAGTAGGACCACCGC 61.006 57.143 6.34 0.00 41.83 5.68
208 209 1.274167 TGCTACAAAGTAGGACCACCG 59.726 52.381 6.34 0.00 41.83 4.94
209 210 2.696506 GTGCTACAAAGTAGGACCACC 58.303 52.381 15.28 0.00 30.94 4.61
210 211 2.334838 CGTGCTACAAAGTAGGACCAC 58.665 52.381 18.81 11.31 33.14 4.16
213 214 2.991866 GTTCCGTGCTACAAAGTAGGAC 59.008 50.000 15.95 15.95 33.36 3.85
214 215 2.352030 CGTTCCGTGCTACAAAGTAGGA 60.352 50.000 6.34 0.48 0.00 2.94
218 219 1.068127 AGACGTTCCGTGCTACAAAGT 59.932 47.619 0.00 0.00 41.37 2.66
220 221 3.247442 CATAGACGTTCCGTGCTACAAA 58.753 45.455 0.00 0.00 41.37 2.83
221 222 2.871133 CATAGACGTTCCGTGCTACAA 58.129 47.619 0.00 0.00 41.37 2.41
222 223 1.468565 GCATAGACGTTCCGTGCTACA 60.469 52.381 0.00 0.00 41.37 2.74
224 225 1.100510 AGCATAGACGTTCCGTGCTA 58.899 50.000 14.31 0.16 41.37 3.49
225 226 0.246635 AAGCATAGACGTTCCGTGCT 59.753 50.000 11.31 11.31 41.37 4.40
226 227 0.645868 GAAGCATAGACGTTCCGTGC 59.354 55.000 7.73 7.73 41.37 5.34
227 228 1.990799 TGAAGCATAGACGTTCCGTG 58.009 50.000 0.00 0.00 41.37 4.94
228 229 2.540515 CATGAAGCATAGACGTTCCGT 58.459 47.619 0.00 0.00 45.10 4.69
229 230 1.258982 GCATGAAGCATAGACGTTCCG 59.741 52.381 0.00 0.00 44.79 4.30
242 243 6.148976 CACTGTCATTATAGGGATGCATGAAG 59.851 42.308 2.46 0.00 0.00 3.02
243 244 5.999600 CACTGTCATTATAGGGATGCATGAA 59.000 40.000 2.46 0.00 0.00 2.57
244 245 5.072193 ACACTGTCATTATAGGGATGCATGA 59.928 40.000 2.46 0.00 0.00 3.07
245 246 5.311265 ACACTGTCATTATAGGGATGCATG 58.689 41.667 2.46 0.00 0.00 4.06
246 247 5.573380 ACACTGTCATTATAGGGATGCAT 57.427 39.130 0.00 0.00 0.00 3.96
247 248 5.125356 CAACACTGTCATTATAGGGATGCA 58.875 41.667 0.00 0.00 0.00 3.96
248 249 4.516698 CCAACACTGTCATTATAGGGATGC 59.483 45.833 0.00 0.00 0.00 3.91
250 251 5.667626 AGACCAACACTGTCATTATAGGGAT 59.332 40.000 0.00 0.00 35.15 3.85
251 252 5.030147 AGACCAACACTGTCATTATAGGGA 58.970 41.667 0.00 0.00 35.15 4.20
254 255 5.521735 GCAGAGACCAACACTGTCATTATAG 59.478 44.000 0.00 0.00 38.96 1.31
255 256 5.187772 AGCAGAGACCAACACTGTCATTATA 59.812 40.000 0.00 0.00 38.96 0.98
256 257 4.019860 AGCAGAGACCAACACTGTCATTAT 60.020 41.667 0.00 0.00 38.96 1.28
257 258 3.324846 AGCAGAGACCAACACTGTCATTA 59.675 43.478 0.00 0.00 38.96 1.90
258 259 2.105477 AGCAGAGACCAACACTGTCATT 59.895 45.455 0.00 0.00 38.96 2.57
259 260 1.696336 AGCAGAGACCAACACTGTCAT 59.304 47.619 0.00 0.00 38.96 3.06
260 261 1.069204 GAGCAGAGACCAACACTGTCA 59.931 52.381 0.00 0.00 38.96 3.58
262 263 1.123077 TGAGCAGAGACCAACACTGT 58.877 50.000 0.00 0.00 38.96 3.55
263 264 2.469274 ATGAGCAGAGACCAACACTG 57.531 50.000 0.00 0.00 39.55 3.66
264 265 2.093764 GCTATGAGCAGAGACCAACACT 60.094 50.000 0.00 0.00 41.89 3.55
266 267 2.680312 GCTATGAGCAGAGACCAACA 57.320 50.000 0.00 0.00 41.89 3.33
278 279 1.227380 GGGGTGTCGCTGCTATGAG 60.227 63.158 0.00 0.00 0.00 2.90
279 280 1.987306 TGGGGTGTCGCTGCTATGA 60.987 57.895 0.00 0.00 0.00 2.15
280 281 1.815421 GTGGGGTGTCGCTGCTATG 60.815 63.158 0.00 0.00 0.00 2.23
281 282 2.290287 TGTGGGGTGTCGCTGCTAT 61.290 57.895 0.00 0.00 0.00 2.97
282 283 2.920384 TGTGGGGTGTCGCTGCTA 60.920 61.111 0.00 0.00 0.00 3.49
283 284 4.626081 GTGTGGGGTGTCGCTGCT 62.626 66.667 0.00 0.00 0.00 4.24
284 285 4.927782 TGTGTGGGGTGTCGCTGC 62.928 66.667 0.00 0.00 0.00 5.25
285 286 2.972505 GTGTGTGGGGTGTCGCTG 60.973 66.667 0.00 0.00 0.00 5.18
286 287 2.818169 ATGTGTGTGGGGTGTCGCT 61.818 57.895 0.00 0.00 0.00 4.93
289 290 1.150536 ACCATGTGTGTGGGGTGTC 59.849 57.895 0.00 0.00 43.77 3.67
290 291 1.152777 CACCATGTGTGTGGGGTGT 60.153 57.895 0.00 0.00 44.47 4.16
292 293 1.059584 TCTCACCATGTGTGTGGGGT 61.060 55.000 12.26 0.00 43.41 4.95
293 294 0.606401 GTCTCACCATGTGTGTGGGG 60.606 60.000 12.26 0.00 45.61 4.96
295 296 1.229428 GTGTCTCACCATGTGTGTGG 58.771 55.000 12.26 8.17 45.61 4.17
296 297 1.952193 TGTGTCTCACCATGTGTGTG 58.048 50.000 12.26 10.57 45.61 3.82
297 298 2.092968 ACTTGTGTCTCACCATGTGTGT 60.093 45.455 12.26 0.00 45.61 3.72
298 299 2.545526 GACTTGTGTCTCACCATGTGTG 59.454 50.000 7.72 7.72 39.94 3.82
299 300 2.170397 TGACTTGTGTCTCACCATGTGT 59.830 45.455 0.00 0.00 43.29 3.72
301 302 2.224378 CCTGACTTGTGTCTCACCATGT 60.224 50.000 0.00 0.00 43.29 3.21
302 303 2.420642 CCTGACTTGTGTCTCACCATG 58.579 52.381 0.00 0.00 43.29 3.66
303 304 1.349026 CCCTGACTTGTGTCTCACCAT 59.651 52.381 0.00 0.00 43.29 3.55
304 305 0.758734 CCCTGACTTGTGTCTCACCA 59.241 55.000 0.00 0.00 43.29 4.17
305 306 0.035458 CCCCTGACTTGTGTCTCACC 59.965 60.000 0.00 0.00 43.29 4.02
308 309 1.548269 CTCTCCCCTGACTTGTGTCTC 59.452 57.143 0.00 0.00 43.29 3.36
309 310 1.133009 ACTCTCCCCTGACTTGTGTCT 60.133 52.381 0.00 0.00 43.29 3.41
310 311 1.001406 CACTCTCCCCTGACTTGTGTC 59.999 57.143 0.00 0.00 43.20 3.67
311 312 1.051812 CACTCTCCCCTGACTTGTGT 58.948 55.000 0.00 0.00 0.00 3.72
313 314 0.191064 TCCACTCTCCCCTGACTTGT 59.809 55.000 0.00 0.00 0.00 3.16
315 316 0.900647 CGTCCACTCTCCCCTGACTT 60.901 60.000 0.00 0.00 0.00 3.01
316 317 1.304547 CGTCCACTCTCCCCTGACT 60.305 63.158 0.00 0.00 0.00 3.41
317 318 1.304217 TCGTCCACTCTCCCCTGAC 60.304 63.158 0.00 0.00 0.00 3.51
318 319 1.304217 GTCGTCCACTCTCCCCTGA 60.304 63.158 0.00 0.00 0.00 3.86
319 320 2.701780 CGTCGTCCACTCTCCCCTG 61.702 68.421 0.00 0.00 0.00 4.45
320 321 2.361357 CGTCGTCCACTCTCCCCT 60.361 66.667 0.00 0.00 0.00 4.79
321 322 3.450115 CCGTCGTCCACTCTCCCC 61.450 72.222 0.00 0.00 0.00 4.81
322 323 4.131088 GCCGTCGTCCACTCTCCC 62.131 72.222 0.00 0.00 0.00 4.30
323 324 4.477975 CGCCGTCGTCCACTCTCC 62.478 72.222 0.00 0.00 0.00 3.71
333 334 0.638746 GTAGTTTCATCACGCCGTCG 59.361 55.000 0.00 0.00 42.43 5.12
334 335 0.638746 CGTAGTTTCATCACGCCGTC 59.361 55.000 0.00 0.00 0.00 4.79
338 339 2.092211 CACCTTCGTAGTTTCATCACGC 59.908 50.000 0.00 0.00 35.70 5.34
609 610 3.119602 TCCTCGTCTCGTTCTTATGGTTG 60.120 47.826 0.00 0.00 0.00 3.77
610 611 3.087031 TCCTCGTCTCGTTCTTATGGTT 58.913 45.455 0.00 0.00 0.00 3.67
611 612 2.683867 CTCCTCGTCTCGTTCTTATGGT 59.316 50.000 0.00 0.00 0.00 3.55
612 613 2.943690 TCTCCTCGTCTCGTTCTTATGG 59.056 50.000 0.00 0.00 0.00 2.74
614 615 3.207778 CCTCTCCTCGTCTCGTTCTTAT 58.792 50.000 0.00 0.00 0.00 1.73
615 616 2.630158 CCTCTCCTCGTCTCGTTCTTA 58.370 52.381 0.00 0.00 0.00 2.10
616 617 1.455248 CCTCTCCTCGTCTCGTTCTT 58.545 55.000 0.00 0.00 0.00 2.52
617 618 1.027792 GCCTCTCCTCGTCTCGTTCT 61.028 60.000 0.00 0.00 0.00 3.01
618 619 1.027792 AGCCTCTCCTCGTCTCGTTC 61.028 60.000 0.00 0.00 0.00 3.95
619 620 1.001887 AGCCTCTCCTCGTCTCGTT 60.002 57.895 0.00 0.00 0.00 3.85
620 621 1.747367 CAGCCTCTCCTCGTCTCGT 60.747 63.158 0.00 0.00 0.00 4.18
637 3393 1.357137 TGTCTAGTGAACCCCATGCA 58.643 50.000 0.00 0.00 0.00 3.96
657 3413 3.057548 CCTTGCTCATGCGCCACA 61.058 61.111 4.18 0.00 43.34 4.17
687 3443 5.092554 TGGTAAATGATTCTAACCGAGCA 57.907 39.130 0.00 0.00 32.69 4.26
779 4142 6.716934 ACACTCTCAGTTTCTCTTCTTGTA 57.283 37.500 0.00 0.00 0.00 2.41
780 4143 5.606348 ACACTCTCAGTTTCTCTTCTTGT 57.394 39.130 0.00 0.00 0.00 3.16
781 4144 6.238320 CCAAACACTCTCAGTTTCTCTTCTTG 60.238 42.308 0.00 0.00 37.10 3.02
782 4145 5.819901 CCAAACACTCTCAGTTTCTCTTCTT 59.180 40.000 0.00 0.00 37.10 2.52
789 4152 2.221981 CGAGCCAAACACTCTCAGTTTC 59.778 50.000 0.00 0.00 37.10 2.78
833 4196 1.004277 CTCAAACGTCGCTCTCGCTT 61.004 55.000 0.00 0.00 35.26 4.68
837 4200 3.587403 AAAAACTCAAACGTCGCTCTC 57.413 42.857 0.00 0.00 0.00 3.20
872 6440 1.819928 TGTTGGATGTGGTGAATCGG 58.180 50.000 0.00 0.00 0.00 4.18
891 6459 1.229496 GGGTGGGGGCTGGATTTTT 60.229 57.895 0.00 0.00 0.00 1.94
909 6485 1.679139 ACTGATGCGAGAGAGAGAGG 58.321 55.000 0.00 0.00 0.00 3.69
1099 6685 0.988145 TCGATGGGGCAGAAGGGATT 60.988 55.000 0.00 0.00 0.00 3.01
1100 6686 1.384502 TCGATGGGGCAGAAGGGAT 60.385 57.895 0.00 0.00 0.00 3.85
1143 6729 0.472734 AGGAGCCAAGGACTGTCACT 60.473 55.000 10.38 1.67 0.00 3.41
1317 6903 3.553095 AAACAGGGGCAGCTCCGAC 62.553 63.158 5.37 0.00 34.94 4.79
1341 6927 0.397675 ACGGAGATCTGCTGGGATCA 60.398 55.000 12.78 0.00 43.11 2.92
1345 6931 1.667154 TTCGACGGAGATCTGCTGGG 61.667 60.000 12.78 0.00 0.00 4.45
1668 7254 3.565214 TTCTTGCAGCCCGGGTCA 61.565 61.111 24.63 15.12 0.00 4.02
1863 7455 0.625849 AATAGGGGCACTCCACCTTG 59.374 55.000 0.00 0.00 35.98 3.61
1879 7480 1.164411 CAGAACACCCGCTTGCAATA 58.836 50.000 0.00 0.00 0.00 1.90
2100 7708 1.478510 GGAGCGAAGGAGATTCAGTGA 59.521 52.381 0.00 0.00 37.83 3.41
2177 7883 2.095110 CGCACCTGCAAATCAAATCAGA 60.095 45.455 0.00 0.00 42.21 3.27
2178 7884 2.256174 CGCACCTGCAAATCAAATCAG 58.744 47.619 0.00 0.00 42.21 2.90
2179 7885 1.067706 CCGCACCTGCAAATCAAATCA 60.068 47.619 0.00 0.00 42.21 2.57
2180 7886 1.632422 CCGCACCTGCAAATCAAATC 58.368 50.000 0.00 0.00 42.21 2.17
2181 7887 0.247185 CCCGCACCTGCAAATCAAAT 59.753 50.000 0.00 0.00 42.21 2.32
2340 8061 4.046462 CCCAACCGTTACACAGATATACG 58.954 47.826 0.00 0.00 0.00 3.06
2341 8062 3.805971 GCCCAACCGTTACACAGATATAC 59.194 47.826 0.00 0.00 0.00 1.47
2342 8063 3.491276 CGCCCAACCGTTACACAGATATA 60.491 47.826 0.00 0.00 0.00 0.86
2343 8064 2.740580 CGCCCAACCGTTACACAGATAT 60.741 50.000 0.00 0.00 0.00 1.63
2351 8072 0.728542 CAATACCGCCCAACCGTTAC 59.271 55.000 0.00 0.00 0.00 2.50
2355 8076 0.956410 TCAACAATACCGCCCAACCG 60.956 55.000 0.00 0.00 0.00 4.44
2360 8081 6.261381 TGAAGTTAATATCAACAATACCGCCC 59.739 38.462 0.00 0.00 0.00 6.13
2370 8091 7.761409 TGATGCCAACTGAAGTTAATATCAAC 58.239 34.615 10.49 0.00 36.32 3.18
2379 8100 4.768968 AGCTAAATGATGCCAACTGAAGTT 59.231 37.500 0.00 0.00 39.12 2.66
2384 8105 2.679837 ACGAGCTAAATGATGCCAACTG 59.320 45.455 0.00 0.00 0.00 3.16
2510 8235 0.104777 CCATCCATCCTCCTCCTCCA 60.105 60.000 0.00 0.00 0.00 3.86
2528 8253 4.333926 GGCAATATATTCAAGCGAGGATCC 59.666 45.833 2.48 2.48 0.00 3.36
2529 8254 4.033358 CGGCAATATATTCAAGCGAGGATC 59.967 45.833 0.00 0.00 0.00 3.36
2530 8255 3.935203 CGGCAATATATTCAAGCGAGGAT 59.065 43.478 0.00 0.00 0.00 3.24
2531 8256 3.006430 TCGGCAATATATTCAAGCGAGGA 59.994 43.478 0.00 0.00 0.00 3.71
2538 8263 9.114952 TGTTGATACTTTCGGCAATATATTCAA 57.885 29.630 0.00 0.00 0.00 2.69
2549 8274 4.024387 TGTCAACTTGTTGATACTTTCGGC 60.024 41.667 17.56 4.32 33.02 5.54
2551 8281 6.628856 CACTTGTCAACTTGTTGATACTTTCG 59.371 38.462 17.56 6.82 33.02 3.46
2580 8310 1.661821 GCCCGCTAGCACATCTACG 60.662 63.158 16.45 0.00 0.00 3.51
2627 8359 2.758979 GGAACCTGATTAGAGGTCGTCA 59.241 50.000 0.00 0.00 46.29 4.35
2659 8391 8.645814 TCATTTCCAACTTACTGTCTAGACTA 57.354 34.615 23.01 6.11 0.00 2.59
2699 8431 2.420687 GGATTCAAGGAATGGCGAGTCT 60.421 50.000 0.00 0.00 31.89 3.24
2700 8432 1.943340 GGATTCAAGGAATGGCGAGTC 59.057 52.381 0.00 0.00 31.89 3.36
2702 8434 2.338577 AGGATTCAAGGAATGGCGAG 57.661 50.000 0.00 0.00 31.89 5.03
2703 8435 3.924114 TTAGGATTCAAGGAATGGCGA 57.076 42.857 0.00 0.00 31.89 5.54
2704 8436 5.520376 AATTTAGGATTCAAGGAATGGCG 57.480 39.130 0.00 0.00 31.89 5.69
2757 8518 1.742761 CACCTCGGCTTCAACATCAT 58.257 50.000 0.00 0.00 0.00 2.45
2778 8539 2.125106 GGGACATGGACACCTCGC 60.125 66.667 0.00 0.00 0.00 5.03
2858 8619 2.673775 ACACAATTCATCCACCACCA 57.326 45.000 0.00 0.00 0.00 4.17
2908 8669 0.313987 CGGAGAACAGTTTTTGCCCC 59.686 55.000 0.00 0.00 0.00 5.80
2934 8695 1.479709 AGACAATCTCTCCCACGAGG 58.520 55.000 0.00 0.00 36.70 4.63
2985 8746 7.598493 GTGCCAACAAAGCTCAAAATCTTTATA 59.402 33.333 0.00 0.00 31.89 0.98
3031 8792 3.466836 AGACGACAAAGACTTCAATGCA 58.533 40.909 0.00 0.00 0.00 3.96
3067 8828 8.143193 TCATTTTTGTCAATGAAAGCATACAGT 58.857 29.630 0.00 0.00 39.69 3.55
3068 8829 8.523523 TCATTTTTGTCAATGAAAGCATACAG 57.476 30.769 0.00 0.00 39.69 2.74
3114 8875 6.870769 AGAACAAATGGATCCAATGATGAAC 58.129 36.000 28.31 17.83 0.00 3.18
3137 8898 4.433186 TGTCATTGTTGCGGGATTTTAG 57.567 40.909 0.00 0.00 0.00 1.85
3139 8900 3.742433 TTGTCATTGTTGCGGGATTTT 57.258 38.095 0.00 0.00 0.00 1.82
3229 8990 2.039879 ACACCACAATCCTAGTCCCAAC 59.960 50.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.