Multiple sequence alignment - TraesCS7A01G099700

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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 TraesCS7A01G099700 chr7A 100.000 3158 0 0 1 3158 60643574 60640417 0.000000e+00 5832.0
1 TraesCS7A01G099700 chr7A 88.543 1318 101 26 1750 3054 2816791 2818071 0.000000e+00 1552.0
2 TraesCS7A01G099700 chr7A 85.275 781 62 19 424 1202 2815299 2816028 0.000000e+00 756.0
3 TraesCS7A01G099700 chr7A 86.452 310 16 14 1204 1492 2816491 2816795 1.830000e-82 316.0
4 TraesCS7A01G099700 chr7A 89.362 94 10 0 424 517 727871322 727871415 5.530000e-23 119.0
5 TraesCS7A01G099700 chr3A 99.011 2628 22 4 428 3054 739168353 739165729 0.000000e+00 4706.0
6 TraesCS7A01G099700 chr3A 86.957 69 5 4 2989 3054 55486062 55485995 1.210000e-09 75.0
7 TraesCS7A01G099700 chr2D 88.081 2668 192 42 425 3054 429115978 429118557 0.000000e+00 3049.0
8 TraesCS7A01G099700 chr2D 97.368 38 0 1 3022 3058 14977626 14977589 2.630000e-06 63.9
9 TraesCS7A01G099700 chr6D 90.822 2190 161 23 893 3054 258192452 258190275 0.000000e+00 2894.0
10 TraesCS7A01G099700 chr6D 91.259 286 24 1 421 706 258298387 258298103 3.820000e-104 388.0
11 TraesCS7A01G099700 chr6D 91.270 126 11 0 704 829 258194424 258194299 4.190000e-39 172.0
12 TraesCS7A01G099700 chr6D 90.000 60 6 0 2996 3055 12823711 12823652 9.390000e-11 78.7
13 TraesCS7A01G099700 chr2B 86.814 1805 123 55 785 2525 61257393 61259146 0.000000e+00 1908.0
14 TraesCS7A01G099700 chr2B 86.601 306 32 6 425 722 61257062 61257366 2.350000e-86 329.0
15 TraesCS7A01G099700 chr3D 86.689 1773 127 41 427 2167 229480856 229482551 0.000000e+00 1866.0
16 TraesCS7A01G099700 chr6A 86.003 1286 120 21 419 1690 394728642 394727403 0.000000e+00 1323.0
17 TraesCS7A01G099700 chr6A 87.968 1122 80 18 1272 2359 488077528 488076428 0.000000e+00 1273.0
18 TraesCS7A01G099700 chr6A 87.897 975 90 16 2090 3054 394725141 394724185 0.000000e+00 1122.0
19 TraesCS7A01G099700 chr6A 88.525 427 25 5 1686 2095 394725706 394725287 2.190000e-136 496.0
20 TraesCS7A01G099700 chr6A 89.773 88 9 0 427 514 4823023 4823110 2.570000e-21 113.0
21 TraesCS7A01G099700 chrUn 87.191 648 59 10 1635 2265 71281160 71281800 0.000000e+00 715.0
22 TraesCS7A01G099700 chrUn 89.474 247 21 4 2716 2960 413295491 413295248 1.100000e-79 307.0
23 TraesCS7A01G099700 chr7D 92.603 365 8 9 77 429 56237386 56237029 1.010000e-139 507.0
24 TraesCS7A01G099700 chr7D 89.623 106 7 2 3054 3158 56237029 56236927 7.110000e-27 132.0
25 TraesCS7A01G099700 chr7D 93.023 86 6 0 426 511 38995521 38995606 3.310000e-25 126.0
26 TraesCS7A01G099700 chr1A 89.333 75 3 4 2985 3058 504715496 504715426 4.340000e-14 89.8


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 TraesCS7A01G099700 chr7A 60640417 60643574 3157 True 5832.000000 5832 100.000000 1 3158 1 chr7A.!!$R1 3157
1 TraesCS7A01G099700 chr7A 2815299 2818071 2772 False 874.666667 1552 86.756667 424 3054 3 chr7A.!!$F2 2630
2 TraesCS7A01G099700 chr3A 739165729 739168353 2624 True 4706.000000 4706 99.011000 428 3054 1 chr3A.!!$R2 2626
3 TraesCS7A01G099700 chr2D 429115978 429118557 2579 False 3049.000000 3049 88.081000 425 3054 1 chr2D.!!$F1 2629
4 TraesCS7A01G099700 chr6D 258190275 258194424 4149 True 1533.000000 2894 91.046000 704 3054 2 chr6D.!!$R3 2350
5 TraesCS7A01G099700 chr2B 61257062 61259146 2084 False 1118.500000 1908 86.707500 425 2525 2 chr2B.!!$F1 2100
6 TraesCS7A01G099700 chr3D 229480856 229482551 1695 False 1866.000000 1866 86.689000 427 2167 1 chr3D.!!$F1 1740
7 TraesCS7A01G099700 chr6A 488076428 488077528 1100 True 1273.000000 1273 87.968000 1272 2359 1 chr6A.!!$R1 1087
8 TraesCS7A01G099700 chr6A 394724185 394728642 4457 True 980.333333 1323 87.475000 419 3054 3 chr6A.!!$R2 2635
9 TraesCS7A01G099700 chrUn 71281160 71281800 640 False 715.000000 715 87.191000 1635 2265 1 chrUn.!!$F1 630

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
242 243 0.11319 CCCAGCTGAAAAAGGGACCT 59.887 55.0 17.39 0.0 44.3 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2890 7149 4.583073 AGGTTAGCTTGTCGGTTTCAAAAT 59.417 37.5 0.0 0.0 0.0 1.82 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
17 18 3.177600 CTTCCCACAATCGCCACG 58.822 61.111 0.00 0.00 0.00 4.94
18 19 3.039202 CTTCCCACAATCGCCACGC 62.039 63.158 0.00 0.00 0.00 5.34
29 30 4.585526 GCCACGCGGGATCGATCA 62.586 66.667 25.93 0.00 40.01 2.92
30 31 2.340078 CCACGCGGGATCGATCAT 59.660 61.111 25.93 3.87 40.01 2.45
31 32 1.300931 CCACGCGGGATCGATCATT 60.301 57.895 25.93 2.96 40.01 2.57
32 33 1.284982 CCACGCGGGATCGATCATTC 61.285 60.000 25.93 13.76 40.01 2.67
33 34 1.006102 ACGCGGGATCGATCATTCC 60.006 57.895 25.93 16.80 39.00 3.01
34 35 1.738099 CGCGGGATCGATCATTCCC 60.738 63.158 25.93 18.54 46.96 3.97
41 42 5.948992 GGGATCGATCATTCCCTTTTTAG 57.051 43.478 25.93 0.00 46.91 1.85
42 43 4.762251 GGGATCGATCATTCCCTTTTTAGG 59.238 45.833 25.93 0.00 46.91 2.69
43 44 4.216472 GGATCGATCATTCCCTTTTTAGGC 59.784 45.833 25.93 0.00 0.00 3.93
44 45 4.503714 TCGATCATTCCCTTTTTAGGCT 57.496 40.909 0.00 0.00 0.00 4.58
45 46 4.855340 TCGATCATTCCCTTTTTAGGCTT 58.145 39.130 0.00 0.00 0.00 4.35
46 47 5.261216 TCGATCATTCCCTTTTTAGGCTTT 58.739 37.500 0.00 0.00 0.00 3.51
47 48 5.357032 TCGATCATTCCCTTTTTAGGCTTTC 59.643 40.000 0.00 0.00 0.00 2.62
48 49 5.358160 CGATCATTCCCTTTTTAGGCTTTCT 59.642 40.000 0.00 0.00 0.00 2.52
49 50 6.127619 CGATCATTCCCTTTTTAGGCTTTCTT 60.128 38.462 0.00 0.00 0.00 2.52
50 51 6.994421 TCATTCCCTTTTTAGGCTTTCTTT 57.006 33.333 0.00 0.00 0.00 2.52
51 52 7.373617 TCATTCCCTTTTTAGGCTTTCTTTT 57.626 32.000 0.00 0.00 0.00 2.27
52 53 8.485578 TCATTCCCTTTTTAGGCTTTCTTTTA 57.514 30.769 0.00 0.00 0.00 1.52
53 54 8.585018 TCATTCCCTTTTTAGGCTTTCTTTTAG 58.415 33.333 0.00 0.00 0.00 1.85
54 55 7.907841 TTCCCTTTTTAGGCTTTCTTTTAGT 57.092 32.000 0.00 0.00 0.00 2.24
55 56 7.520451 TCCCTTTTTAGGCTTTCTTTTAGTC 57.480 36.000 0.00 0.00 0.00 2.59
56 57 7.295340 TCCCTTTTTAGGCTTTCTTTTAGTCT 58.705 34.615 0.00 0.00 0.00 3.24
57 58 7.783119 TCCCTTTTTAGGCTTTCTTTTAGTCTT 59.217 33.333 0.00 0.00 0.00 3.01
58 59 8.421784 CCCTTTTTAGGCTTTCTTTTAGTCTTT 58.578 33.333 0.00 0.00 0.00 2.52
59 60 9.464714 CCTTTTTAGGCTTTCTTTTAGTCTTTC 57.535 33.333 0.00 0.00 0.00 2.62
62 63 9.628500 TTTTAGGCTTTCTTTTAGTCTTTCTCT 57.372 29.630 0.00 0.00 0.00 3.10
63 64 9.628500 TTTAGGCTTTCTTTTAGTCTTTCTCTT 57.372 29.630 0.00 0.00 0.00 2.85
64 65 7.737972 AGGCTTTCTTTTAGTCTTTCTCTTC 57.262 36.000 0.00 0.00 0.00 2.87
65 66 7.513856 AGGCTTTCTTTTAGTCTTTCTCTTCT 58.486 34.615 0.00 0.00 0.00 2.85
66 67 7.996066 AGGCTTTCTTTTAGTCTTTCTCTTCTT 59.004 33.333 0.00 0.00 0.00 2.52
67 68 8.625651 GGCTTTCTTTTAGTCTTTCTCTTCTTT 58.374 33.333 0.00 0.00 0.00 2.52
93 94 9.758651 TTTTAAAACTCCTCTTTATTTCAAGGC 57.241 29.630 0.00 0.00 0.00 4.35
94 95 6.976934 AAAACTCCTCTTTATTTCAAGGCA 57.023 33.333 0.00 0.00 0.00 4.75
95 96 6.976934 AAACTCCTCTTTATTTCAAGGCAA 57.023 33.333 0.00 0.00 0.00 4.52
96 97 6.581171 AACTCCTCTTTATTTCAAGGCAAG 57.419 37.500 0.00 0.00 0.00 4.01
97 98 4.460731 ACTCCTCTTTATTTCAAGGCAAGC 59.539 41.667 0.00 0.00 0.00 4.01
98 99 4.406456 TCCTCTTTATTTCAAGGCAAGCA 58.594 39.130 0.00 0.00 0.00 3.91
99 100 5.018809 TCCTCTTTATTTCAAGGCAAGCAT 58.981 37.500 0.00 0.00 0.00 3.79
100 101 5.105635 TCCTCTTTATTTCAAGGCAAGCATG 60.106 40.000 0.00 0.00 0.00 4.06
101 102 5.105635 CCTCTTTATTTCAAGGCAAGCATGA 60.106 40.000 0.00 0.00 0.00 3.07
102 103 6.406624 CCTCTTTATTTCAAGGCAAGCATGAT 60.407 38.462 0.00 0.00 0.00 2.45
103 104 6.567050 TCTTTATTTCAAGGCAAGCATGATC 58.433 36.000 0.00 0.00 0.00 2.92
104 105 2.925578 TTTCAAGGCAAGCATGATCG 57.074 45.000 0.00 0.00 0.00 3.69
105 106 2.112380 TTCAAGGCAAGCATGATCGA 57.888 45.000 0.00 0.00 0.00 3.59
106 107 2.336945 TCAAGGCAAGCATGATCGAT 57.663 45.000 0.00 0.00 0.00 3.59
107 108 2.216046 TCAAGGCAAGCATGATCGATC 58.784 47.619 18.72 18.72 0.00 3.69
108 109 1.070108 CAAGGCAAGCATGATCGATCG 60.070 52.381 20.03 9.36 0.00 3.69
109 110 0.390492 AGGCAAGCATGATCGATCGA 59.610 50.000 21.86 21.86 0.00 3.59
110 111 1.001746 AGGCAAGCATGATCGATCGAT 59.998 47.619 29.76 29.76 37.59 3.59
121 122 4.497473 GATCGATCGATCTTTCCTGACT 57.503 45.455 38.45 14.09 45.42 3.41
122 123 4.865776 GATCGATCGATCTTTCCTGACTT 58.134 43.478 38.45 13.89 45.42 3.01
123 124 4.720649 TCGATCGATCTTTCCTGACTTT 57.279 40.909 22.43 0.00 0.00 2.66
124 125 5.073311 TCGATCGATCTTTCCTGACTTTT 57.927 39.130 22.43 0.00 0.00 2.27
125 126 5.479306 TCGATCGATCTTTCCTGACTTTTT 58.521 37.500 22.43 0.00 0.00 1.94
149 150 8.746052 TTTTTGAGACAATCTTTCCTGACTAA 57.254 30.769 0.00 0.00 0.00 2.24
150 151 8.746052 TTTTGAGACAATCTTTCCTGACTAAA 57.254 30.769 0.00 0.00 0.00 1.85
151 152 7.969536 TTGAGACAATCTTTCCTGACTAAAG 57.030 36.000 0.00 0.00 35.66 1.85
152 153 7.067496 TGAGACAATCTTTCCTGACTAAAGT 57.933 36.000 0.00 0.00 35.79 2.66
153 154 7.155328 TGAGACAATCTTTCCTGACTAAAGTC 58.845 38.462 3.08 3.08 44.97 3.01
167 168 2.281345 AGTCGTCCGTGACTCCGT 60.281 61.111 3.15 0.00 45.97 4.69
168 169 2.126965 GTCGTCCGTGACTCCGTG 60.127 66.667 3.15 0.00 35.95 4.94
169 170 2.592574 TCGTCCGTGACTCCGTGT 60.593 61.111 3.15 0.00 0.00 4.49
170 171 1.301637 TCGTCCGTGACTCCGTGTA 60.302 57.895 3.15 0.00 0.00 2.90
171 172 1.154338 CGTCCGTGACTCCGTGTAC 60.154 63.158 3.15 0.00 0.00 2.90
172 173 1.211190 GTCCGTGACTCCGTGTACC 59.789 63.158 0.00 0.00 0.00 3.34
173 174 2.177531 CCGTGACTCCGTGTACCG 59.822 66.667 0.00 0.00 0.00 4.02
174 175 2.327343 CCGTGACTCCGTGTACCGA 61.327 63.158 5.46 0.00 39.56 4.69
175 176 1.575922 CGTGACTCCGTGTACCGAA 59.424 57.895 5.46 0.00 39.56 4.30
176 177 0.453950 CGTGACTCCGTGTACCGAAG 60.454 60.000 5.46 0.00 39.56 3.79
177 178 0.731855 GTGACTCCGTGTACCGAAGC 60.732 60.000 5.46 0.00 39.56 3.86
178 179 1.153881 GACTCCGTGTACCGAAGCC 60.154 63.158 5.46 0.00 39.56 4.35
179 180 1.593296 GACTCCGTGTACCGAAGCCT 61.593 60.000 5.46 0.00 39.56 4.58
180 181 1.153823 CTCCGTGTACCGAAGCCTG 60.154 63.158 5.46 0.00 39.56 4.85
181 182 2.125673 CCGTGTACCGAAGCCTGG 60.126 66.667 5.46 0.00 39.56 4.45
182 183 2.813908 CGTGTACCGAAGCCTGGC 60.814 66.667 11.65 11.65 39.56 4.85
183 184 2.436115 GTGTACCGAAGCCTGGCC 60.436 66.667 16.57 0.00 0.00 5.36
184 185 4.077184 TGTACCGAAGCCTGGCCG 62.077 66.667 16.57 12.78 0.00 6.13
185 186 3.766691 GTACCGAAGCCTGGCCGA 61.767 66.667 16.57 0.00 0.00 5.54
186 187 2.998480 TACCGAAGCCTGGCCGAA 60.998 61.111 16.57 1.85 0.00 4.30
187 188 2.363975 TACCGAAGCCTGGCCGAAT 61.364 57.895 16.57 7.12 0.00 3.34
188 189 1.906105 TACCGAAGCCTGGCCGAATT 61.906 55.000 16.57 2.25 0.00 2.17
189 190 1.153249 CCGAAGCCTGGCCGAATTA 60.153 57.895 16.57 0.00 0.00 1.40
190 191 0.535102 CCGAAGCCTGGCCGAATTAT 60.535 55.000 16.57 0.00 0.00 1.28
191 192 1.270625 CCGAAGCCTGGCCGAATTATA 60.271 52.381 16.57 0.00 0.00 0.98
192 193 1.798813 CGAAGCCTGGCCGAATTATAC 59.201 52.381 16.57 0.00 0.00 1.47
193 194 2.548067 CGAAGCCTGGCCGAATTATACT 60.548 50.000 16.57 0.00 0.00 2.12
194 195 2.550830 AGCCTGGCCGAATTATACTG 57.449 50.000 16.57 0.00 0.00 2.74
195 196 1.072331 AGCCTGGCCGAATTATACTGG 59.928 52.381 16.57 0.00 0.00 4.00
196 197 1.523758 CCTGGCCGAATTATACTGGC 58.476 55.000 0.00 0.00 46.82 4.85
199 200 3.717842 GCCGAATTATACTGGCCCA 57.282 52.632 0.00 0.00 41.70 5.36
200 201 1.235724 GCCGAATTATACTGGCCCAC 58.764 55.000 0.00 0.00 41.70 4.61
201 202 1.892209 CCGAATTATACTGGCCCACC 58.108 55.000 0.00 0.00 0.00 4.61
202 203 1.544759 CCGAATTATACTGGCCCACCC 60.545 57.143 0.00 0.00 33.59 4.61
203 204 1.142060 CGAATTATACTGGCCCACCCA 59.858 52.381 0.00 0.00 42.79 4.51
210 211 3.897122 TGGCCCACCCAGTCCAAC 61.897 66.667 0.00 0.00 39.18 3.77
212 213 3.948719 GCCCACCCAGTCCAACGA 61.949 66.667 0.00 0.00 0.00 3.85
213 214 2.833227 CCCACCCAGTCCAACGAA 59.167 61.111 0.00 0.00 0.00 3.85
214 215 1.302511 CCCACCCAGTCCAACGAAG 60.303 63.158 0.00 0.00 0.00 3.79
215 216 1.966451 CCACCCAGTCCAACGAAGC 60.966 63.158 0.00 0.00 0.00 3.86
216 217 1.966451 CACCCAGTCCAACGAAGCC 60.966 63.158 0.00 0.00 0.00 4.35
217 218 2.147387 ACCCAGTCCAACGAAGCCT 61.147 57.895 0.00 0.00 0.00 4.58
218 219 1.376037 CCCAGTCCAACGAAGCCTC 60.376 63.158 0.00 0.00 0.00 4.70
219 220 1.371183 CCAGTCCAACGAAGCCTCA 59.629 57.895 0.00 0.00 0.00 3.86
220 221 0.951040 CCAGTCCAACGAAGCCTCAC 60.951 60.000 0.00 0.00 0.00 3.51
221 222 1.006102 AGTCCAACGAAGCCTCACG 60.006 57.895 0.00 0.00 0.00 4.35
222 223 2.027625 GTCCAACGAAGCCTCACGG 61.028 63.158 0.00 0.00 0.00 4.94
232 233 4.020617 CCTCACGGCCCAGCTGAA 62.021 66.667 17.39 0.00 38.46 3.02
233 234 2.032528 CTCACGGCCCAGCTGAAA 59.967 61.111 17.39 0.00 38.46 2.69
234 235 1.600636 CTCACGGCCCAGCTGAAAA 60.601 57.895 17.39 0.00 38.46 2.29
235 236 1.152860 TCACGGCCCAGCTGAAAAA 60.153 52.632 17.39 0.00 38.46 1.94
236 237 1.172180 TCACGGCCCAGCTGAAAAAG 61.172 55.000 17.39 4.96 38.46 2.27
237 238 1.903404 ACGGCCCAGCTGAAAAAGG 60.903 57.895 17.39 8.58 38.46 3.11
238 239 2.639327 CGGCCCAGCTGAAAAAGGG 61.639 63.158 17.39 7.87 44.37 3.95
239 240 1.228862 GGCCCAGCTGAAAAAGGGA 60.229 57.895 17.39 0.00 44.30 4.20
240 241 1.536073 GGCCCAGCTGAAAAAGGGAC 61.536 60.000 17.39 4.62 44.30 4.46
241 242 1.536073 GCCCAGCTGAAAAAGGGACC 61.536 60.000 17.39 0.00 44.30 4.46
242 243 0.113190 CCCAGCTGAAAAAGGGACCT 59.887 55.000 17.39 0.00 44.30 3.85
243 244 1.539157 CCAGCTGAAAAAGGGACCTC 58.461 55.000 17.39 0.00 0.00 3.85
244 245 1.202927 CCAGCTGAAAAAGGGACCTCA 60.203 52.381 17.39 0.00 0.00 3.86
245 246 2.586425 CAGCTGAAAAAGGGACCTCAA 58.414 47.619 8.42 0.00 0.00 3.02
246 247 3.160269 CAGCTGAAAAAGGGACCTCAAT 58.840 45.455 8.42 0.00 0.00 2.57
247 248 3.192212 CAGCTGAAAAAGGGACCTCAATC 59.808 47.826 8.42 0.00 0.00 2.67
248 249 2.493675 GCTGAAAAAGGGACCTCAATCC 59.506 50.000 0.00 0.00 38.13 3.01
249 250 3.815757 GCTGAAAAAGGGACCTCAATCCT 60.816 47.826 0.00 0.00 38.95 3.24
250 251 4.013050 CTGAAAAAGGGACCTCAATCCTC 58.987 47.826 0.00 0.00 38.95 3.71
251 252 3.245264 TGAAAAAGGGACCTCAATCCTCC 60.245 47.826 0.00 0.00 38.95 4.30
252 253 2.059756 AAAGGGACCTCAATCCTCCA 57.940 50.000 0.00 0.00 38.95 3.86
253 254 2.293598 AAGGGACCTCAATCCTCCAT 57.706 50.000 0.00 0.00 38.95 3.41
254 255 1.813102 AGGGACCTCAATCCTCCATC 58.187 55.000 0.00 0.00 38.95 3.51
255 256 0.394565 GGGACCTCAATCCTCCATCG 59.605 60.000 0.00 0.00 38.95 3.84
256 257 1.414158 GGACCTCAATCCTCCATCGA 58.586 55.000 0.00 0.00 35.68 3.59
257 258 1.974236 GGACCTCAATCCTCCATCGAT 59.026 52.381 0.00 0.00 35.68 3.59
258 259 3.165875 GGACCTCAATCCTCCATCGATA 58.834 50.000 0.00 0.00 35.68 2.92
259 260 3.056465 GGACCTCAATCCTCCATCGATAC 60.056 52.174 0.00 0.00 35.68 2.24
260 261 2.558795 ACCTCAATCCTCCATCGATACG 59.441 50.000 0.00 0.00 0.00 3.06
261 262 2.094494 CCTCAATCCTCCATCGATACGG 60.094 54.545 0.00 0.00 0.00 4.02
262 263 1.272490 TCAATCCTCCATCGATACGGC 59.728 52.381 0.00 0.00 0.00 5.68
263 264 0.608640 AATCCTCCATCGATACGGCC 59.391 55.000 0.00 0.00 0.00 6.13
264 265 1.258445 ATCCTCCATCGATACGGCCC 61.258 60.000 0.00 0.00 0.00 5.80
265 266 2.207229 CCTCCATCGATACGGCCCA 61.207 63.158 0.00 0.00 0.00 5.36
266 267 1.290324 CTCCATCGATACGGCCCAG 59.710 63.158 0.00 0.00 0.00 4.45
267 268 2.357517 CCATCGATACGGCCCAGC 60.358 66.667 0.00 0.00 0.00 4.85
268 269 2.737180 CATCGATACGGCCCAGCT 59.263 61.111 0.00 0.00 0.00 4.24
269 270 1.665916 CATCGATACGGCCCAGCTG 60.666 63.158 6.78 6.78 41.29 4.24
270 271 1.832608 ATCGATACGGCCCAGCTGA 60.833 57.895 17.39 0.00 38.46 4.26
271 272 1.399744 ATCGATACGGCCCAGCTGAA 61.400 55.000 17.39 0.00 38.46 3.02
272 273 1.153449 CGATACGGCCCAGCTGAAA 60.153 57.895 17.39 0.00 38.46 2.69
273 274 0.742990 CGATACGGCCCAGCTGAAAA 60.743 55.000 17.39 0.00 38.46 2.29
274 275 1.459450 GATACGGCCCAGCTGAAAAA 58.541 50.000 17.39 0.00 38.46 1.94
365 366 9.420118 ACAATATTTTTACATCCTATGCTTGGA 57.580 29.630 0.00 0.00 38.06 3.53
422 423 9.797556 AGACTTTTTAGTGTTTAACATGGAAAC 57.202 29.630 15.12 15.12 37.32 2.78
758 769 7.991084 ATACCTTCGCACTATACATAGTACA 57.009 36.000 1.64 0.00 41.44 2.90
2461 6717 7.283329 AGTCAAGAACTGGTATTTTTCAGTCT 58.717 34.615 0.00 0.00 42.67 3.24
2890 7149 9.048446 GTTCACTACTTTGGTACTATGAAAACA 57.952 33.333 0.00 0.00 0.00 2.83
3054 7313 1.171308 GCGCGGGGTATCATCTAGTA 58.829 55.000 8.83 0.00 0.00 1.82
3055 7314 1.542915 GCGCGGGGTATCATCTAGTAA 59.457 52.381 8.83 0.00 0.00 2.24
3056 7315 2.165845 GCGCGGGGTATCATCTAGTAAT 59.834 50.000 8.83 0.00 0.00 1.89
3057 7316 3.734293 GCGCGGGGTATCATCTAGTAATC 60.734 52.174 8.83 0.00 0.00 1.75
3058 7317 3.695060 CGCGGGGTATCATCTAGTAATCT 59.305 47.826 0.00 0.00 0.00 2.40
3059 7318 4.201930 CGCGGGGTATCATCTAGTAATCTC 60.202 50.000 0.00 0.00 0.00 2.75
3060 7319 4.098196 GCGGGGTATCATCTAGTAATCTCC 59.902 50.000 0.00 0.00 0.00 3.71
3061 7320 5.262009 CGGGGTATCATCTAGTAATCTCCA 58.738 45.833 0.00 0.00 0.00 3.86
3062 7321 5.715279 CGGGGTATCATCTAGTAATCTCCAA 59.285 44.000 0.00 0.00 0.00 3.53
3063 7322 6.210784 CGGGGTATCATCTAGTAATCTCCAAA 59.789 42.308 0.00 0.00 0.00 3.28
3064 7323 7.093289 CGGGGTATCATCTAGTAATCTCCAAAT 60.093 40.741 0.00 0.00 0.00 2.32
3065 7324 8.606830 GGGGTATCATCTAGTAATCTCCAAATT 58.393 37.037 0.00 0.00 0.00 1.82
3073 7332 9.920946 ATCTAGTAATCTCCAAATTTTTAGGCA 57.079 29.630 0.00 0.00 0.00 4.75
3074 7333 9.747898 TCTAGTAATCTCCAAATTTTTAGGCAA 57.252 29.630 0.00 0.00 0.00 4.52
3077 7336 9.034800 AGTAATCTCCAAATTTTTAGGCAATCA 57.965 29.630 0.00 0.00 0.00 2.57
3078 7337 9.087424 GTAATCTCCAAATTTTTAGGCAATCAC 57.913 33.333 0.00 0.00 0.00 3.06
3079 7338 6.662865 TCTCCAAATTTTTAGGCAATCACA 57.337 33.333 0.00 0.00 0.00 3.58
3080 7339 7.243604 TCTCCAAATTTTTAGGCAATCACAT 57.756 32.000 0.00 0.00 0.00 3.21
3081 7340 7.678837 TCTCCAAATTTTTAGGCAATCACATT 58.321 30.769 0.00 0.00 0.00 2.71
3082 7341 7.603404 TCTCCAAATTTTTAGGCAATCACATTG 59.397 33.333 0.00 0.00 43.06 2.82
3083 7342 7.222872 TCCAAATTTTTAGGCAATCACATTGT 58.777 30.769 0.00 0.00 42.20 2.71
3084 7343 7.387397 TCCAAATTTTTAGGCAATCACATTGTC 59.613 33.333 0.00 0.00 44.92 3.18
3085 7344 7.172875 CCAAATTTTTAGGCAATCACATTGTCA 59.827 33.333 3.80 0.00 46.90 3.58
3086 7345 8.557864 CAAATTTTTAGGCAATCACATTGTCAA 58.442 29.630 3.80 0.00 46.90 3.18
3087 7346 7.656707 ATTTTTAGGCAATCACATTGTCAAC 57.343 32.000 3.80 0.00 46.90 3.18
3088 7347 5.781210 TTTAGGCAATCACATTGTCAACA 57.219 34.783 3.80 0.00 46.90 3.33
3089 7348 3.648339 AGGCAATCACATTGTCAACAC 57.352 42.857 3.80 0.00 46.90 3.32
3090 7349 3.225104 AGGCAATCACATTGTCAACACT 58.775 40.909 3.80 0.00 46.90 3.55
3091 7350 4.397420 AGGCAATCACATTGTCAACACTA 58.603 39.130 3.80 0.00 46.90 2.74
3092 7351 5.012239 AGGCAATCACATTGTCAACACTAT 58.988 37.500 3.80 0.00 46.90 2.12
3093 7352 5.477984 AGGCAATCACATTGTCAACACTATT 59.522 36.000 3.80 0.00 46.90 1.73
3094 7353 5.574055 GGCAATCACATTGTCAACACTATTG 59.426 40.000 0.00 0.00 44.04 1.90
3095 7354 6.380995 GCAATCACATTGTCAACACTATTGA 58.619 36.000 12.98 0.00 42.20 2.57
3096 7355 6.525628 GCAATCACATTGTCAACACTATTGAG 59.474 38.462 12.98 0.00 42.20 3.02
3097 7356 7.573656 GCAATCACATTGTCAACACTATTGAGA 60.574 37.037 12.98 2.11 42.20 3.27
3098 7357 8.456471 CAATCACATTGTCAACACTATTGAGAT 58.544 33.333 6.67 0.09 35.57 2.75
3099 7358 7.368480 TCACATTGTCAACACTATTGAGATG 57.632 36.000 9.62 9.62 33.22 2.90
3100 7359 6.936335 TCACATTGTCAACACTATTGAGATGT 59.064 34.615 10.50 10.50 37.10 3.06
3101 7360 7.445096 TCACATTGTCAACACTATTGAGATGTT 59.555 33.333 12.42 0.00 35.77 2.71
3102 7361 8.077991 CACATTGTCAACACTATTGAGATGTTT 58.922 33.333 12.42 0.00 35.77 2.83
3103 7362 9.283768 ACATTGTCAACACTATTGAGATGTTTA 57.716 29.630 10.50 0.00 35.04 2.01
3106 7365 8.902540 TGTCAACACTATTGAGATGTTTAAGT 57.097 30.769 0.00 0.00 34.36 2.24
3107 7366 9.337396 TGTCAACACTATTGAGATGTTTAAGTT 57.663 29.630 0.00 0.00 34.36 2.66
3145 7404 1.832402 GCGTCTCGCGATTTTAAAAGC 59.168 47.619 10.36 6.12 44.55 3.51
3146 7405 2.474032 GCGTCTCGCGATTTTAAAAGCT 60.474 45.455 10.36 0.00 44.55 3.74
3147 7406 3.084278 CGTCTCGCGATTTTAAAAGCTG 58.916 45.455 10.36 8.67 44.77 4.24
3148 7407 3.417185 GTCTCGCGATTTTAAAAGCTGG 58.583 45.455 10.36 5.94 0.00 4.85
3149 7408 2.418628 TCTCGCGATTTTAAAAGCTGGG 59.581 45.455 10.36 14.06 0.00 4.45
3150 7409 2.156098 TCGCGATTTTAAAAGCTGGGT 58.844 42.857 3.71 0.00 0.00 4.51
3151 7410 3.336468 TCGCGATTTTAAAAGCTGGGTA 58.664 40.909 3.71 4.70 0.00 3.69
3152 7411 3.942748 TCGCGATTTTAAAAGCTGGGTAT 59.057 39.130 3.71 0.00 0.00 2.73
3153 7412 5.117584 TCGCGATTTTAAAAGCTGGGTATA 58.882 37.500 3.71 0.00 0.00 1.47
3154 7413 5.585445 TCGCGATTTTAAAAGCTGGGTATAA 59.415 36.000 3.71 0.00 0.00 0.98
3155 7414 6.093771 TCGCGATTTTAAAAGCTGGGTATAAA 59.906 34.615 3.71 0.00 0.00 1.40
3156 7415 6.195798 CGCGATTTTAAAAGCTGGGTATAAAC 59.804 38.462 13.81 0.00 0.00 2.01
3157 7416 7.030768 GCGATTTTAAAAGCTGGGTATAAACA 58.969 34.615 13.81 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.039202 GCGTGGCGATTGTGGGAAG 62.039 63.158 0.00 0.00 0.00 3.46
1 2 3.053291 GCGTGGCGATTGTGGGAA 61.053 61.111 0.00 0.00 0.00 3.97
12 13 3.865929 ATGATCGATCCCGCGTGGC 62.866 63.158 22.31 0.00 35.37 5.01
13 14 1.284982 GAATGATCGATCCCGCGTGG 61.285 60.000 22.31 8.42 35.37 4.94
14 15 1.284982 GGAATGATCGATCCCGCGTG 61.285 60.000 22.31 0.00 35.37 5.34
15 16 1.006102 GGAATGATCGATCCCGCGT 60.006 57.895 22.31 3.23 35.37 6.01
16 17 1.738099 GGGAATGATCGATCCCGCG 60.738 63.158 22.31 0.00 45.56 6.46
17 18 4.285851 GGGAATGATCGATCCCGC 57.714 61.111 22.31 14.92 45.56 6.13
20 21 4.216472 GCCTAAAAAGGGAATGATCGATCC 59.784 45.833 22.31 8.63 34.85 3.36
21 22 5.066593 AGCCTAAAAAGGGAATGATCGATC 58.933 41.667 18.72 18.72 0.00 3.69
22 23 5.053978 AGCCTAAAAAGGGAATGATCGAT 57.946 39.130 0.00 0.00 0.00 3.59
23 24 4.503714 AGCCTAAAAAGGGAATGATCGA 57.496 40.909 0.00 0.00 0.00 3.59
24 25 5.358160 AGAAAGCCTAAAAAGGGAATGATCG 59.642 40.000 0.00 0.00 0.00 3.69
25 26 6.782082 AGAAAGCCTAAAAAGGGAATGATC 57.218 37.500 0.00 0.00 0.00 2.92
26 27 7.559335 AAAGAAAGCCTAAAAAGGGAATGAT 57.441 32.000 0.00 0.00 0.00 2.45
27 28 6.994421 AAAGAAAGCCTAAAAAGGGAATGA 57.006 33.333 0.00 0.00 0.00 2.57
28 29 8.367911 ACTAAAAGAAAGCCTAAAAAGGGAATG 58.632 33.333 0.00 0.00 0.00 2.67
29 30 8.492415 ACTAAAAGAAAGCCTAAAAAGGGAAT 57.508 30.769 0.00 0.00 0.00 3.01
30 31 7.783119 AGACTAAAAGAAAGCCTAAAAAGGGAA 59.217 33.333 0.00 0.00 0.00 3.97
31 32 7.295340 AGACTAAAAGAAAGCCTAAAAAGGGA 58.705 34.615 0.00 0.00 0.00 4.20
32 33 7.526142 AGACTAAAAGAAAGCCTAAAAAGGG 57.474 36.000 0.00 0.00 0.00 3.95
33 34 9.464714 GAAAGACTAAAAGAAAGCCTAAAAAGG 57.535 33.333 0.00 0.00 0.00 3.11
36 37 9.628500 AGAGAAAGACTAAAAGAAAGCCTAAAA 57.372 29.630 0.00 0.00 0.00 1.52
37 38 9.628500 AAGAGAAAGACTAAAAGAAAGCCTAAA 57.372 29.630 0.00 0.00 0.00 1.85
38 39 9.274206 GAAGAGAAAGACTAAAAGAAAGCCTAA 57.726 33.333 0.00 0.00 0.00 2.69
39 40 8.652290 AGAAGAGAAAGACTAAAAGAAAGCCTA 58.348 33.333 0.00 0.00 0.00 3.93
40 41 7.513856 AGAAGAGAAAGACTAAAAGAAAGCCT 58.486 34.615 0.00 0.00 0.00 4.58
41 42 7.737972 AGAAGAGAAAGACTAAAAGAAAGCC 57.262 36.000 0.00 0.00 0.00 4.35
67 68 9.758651 GCCTTGAAATAAAGAGGAGTTTTAAAA 57.241 29.630 0.00 0.00 0.00 1.52
68 69 8.919145 TGCCTTGAAATAAAGAGGAGTTTTAAA 58.081 29.630 0.00 0.00 0.00 1.52
69 70 8.472007 TGCCTTGAAATAAAGAGGAGTTTTAA 57.528 30.769 0.00 0.00 0.00 1.52
70 71 8.472007 TTGCCTTGAAATAAAGAGGAGTTTTA 57.528 30.769 0.00 0.00 0.00 1.52
71 72 6.976934 TGCCTTGAAATAAAGAGGAGTTTT 57.023 33.333 0.00 0.00 0.00 2.43
72 73 6.517362 GCTTGCCTTGAAATAAAGAGGAGTTT 60.517 38.462 0.00 0.00 0.00 2.66
73 74 5.047731 GCTTGCCTTGAAATAAAGAGGAGTT 60.048 40.000 0.00 0.00 0.00 3.01
74 75 4.460731 GCTTGCCTTGAAATAAAGAGGAGT 59.539 41.667 0.00 0.00 0.00 3.85
75 76 4.460382 TGCTTGCCTTGAAATAAAGAGGAG 59.540 41.667 0.00 0.00 0.00 3.69
76 77 4.406456 TGCTTGCCTTGAAATAAAGAGGA 58.594 39.130 0.00 0.00 0.00 3.71
77 78 4.789012 TGCTTGCCTTGAAATAAAGAGG 57.211 40.909 0.00 0.00 0.00 3.69
78 79 5.957798 TCATGCTTGCCTTGAAATAAAGAG 58.042 37.500 0.00 0.00 0.00 2.85
79 80 5.981088 TCATGCTTGCCTTGAAATAAAGA 57.019 34.783 0.00 0.00 0.00 2.52
80 81 5.457799 CGATCATGCTTGCCTTGAAATAAAG 59.542 40.000 0.00 0.00 32.17 1.85
81 82 5.125257 TCGATCATGCTTGCCTTGAAATAAA 59.875 36.000 0.00 0.00 32.17 1.40
82 83 4.639755 TCGATCATGCTTGCCTTGAAATAA 59.360 37.500 0.00 0.00 32.17 1.40
83 84 4.198530 TCGATCATGCTTGCCTTGAAATA 58.801 39.130 0.00 0.00 32.17 1.40
84 85 3.018856 TCGATCATGCTTGCCTTGAAAT 58.981 40.909 0.00 0.00 32.17 2.17
85 86 2.435422 TCGATCATGCTTGCCTTGAAA 58.565 42.857 0.00 0.00 32.17 2.69
86 87 2.112380 TCGATCATGCTTGCCTTGAA 57.888 45.000 0.00 0.00 32.17 2.69
87 88 2.216046 GATCGATCATGCTTGCCTTGA 58.784 47.619 20.52 0.00 32.85 3.02
88 89 1.070108 CGATCGATCATGCTTGCCTTG 60.070 52.381 24.40 0.45 0.00 3.61
89 90 1.202568 TCGATCGATCATGCTTGCCTT 60.203 47.619 24.40 0.00 0.00 4.35
90 91 0.390492 TCGATCGATCATGCTTGCCT 59.610 50.000 24.40 0.00 0.00 4.75
91 92 1.436600 ATCGATCGATCATGCTTGCC 58.563 50.000 24.60 0.00 0.00 4.52
101 102 4.927978 AAGTCAGGAAAGATCGATCGAT 57.072 40.909 29.76 29.76 37.59 3.59
102 103 4.720649 AAAGTCAGGAAAGATCGATCGA 57.279 40.909 21.86 21.86 0.00 3.59
103 104 5.786401 AAAAAGTCAGGAAAGATCGATCG 57.214 39.130 19.33 9.36 0.00 3.69
124 125 8.746052 TTAGTCAGGAAAGATTGTCTCAAAAA 57.254 30.769 0.00 0.00 0.00 1.94
125 126 8.746052 TTTAGTCAGGAAAGATTGTCTCAAAA 57.254 30.769 0.00 0.00 0.00 2.44
126 127 7.993183 ACTTTAGTCAGGAAAGATTGTCTCAAA 59.007 33.333 2.31 0.00 37.35 2.69
127 128 7.509546 ACTTTAGTCAGGAAAGATTGTCTCAA 58.490 34.615 2.31 0.00 37.35 3.02
128 129 7.067496 ACTTTAGTCAGGAAAGATTGTCTCA 57.933 36.000 2.31 0.00 37.35 3.27
129 130 6.309251 CGACTTTAGTCAGGAAAGATTGTCTC 59.691 42.308 10.27 0.00 44.99 3.36
130 131 6.159988 CGACTTTAGTCAGGAAAGATTGTCT 58.840 40.000 10.27 0.00 44.99 3.41
131 132 5.927115 ACGACTTTAGTCAGGAAAGATTGTC 59.073 40.000 10.27 0.00 44.99 3.18
132 133 5.855045 ACGACTTTAGTCAGGAAAGATTGT 58.145 37.500 10.27 0.00 44.99 2.71
133 134 5.348997 GGACGACTTTAGTCAGGAAAGATTG 59.651 44.000 10.27 0.00 44.99 2.67
134 135 5.480205 GGACGACTTTAGTCAGGAAAGATT 58.520 41.667 10.27 0.00 44.99 2.40
135 136 4.380655 CGGACGACTTTAGTCAGGAAAGAT 60.381 45.833 10.27 0.00 44.99 2.40
136 137 3.057736 CGGACGACTTTAGTCAGGAAAGA 60.058 47.826 10.27 0.00 44.99 2.52
137 138 3.243336 CGGACGACTTTAGTCAGGAAAG 58.757 50.000 10.27 0.00 44.99 2.62
138 139 2.624838 ACGGACGACTTTAGTCAGGAAA 59.375 45.455 10.27 0.00 44.99 3.13
139 140 2.030540 CACGGACGACTTTAGTCAGGAA 60.031 50.000 10.27 0.00 44.99 3.36
140 141 1.538512 CACGGACGACTTTAGTCAGGA 59.461 52.381 10.27 0.00 44.99 3.86
141 142 1.538512 TCACGGACGACTTTAGTCAGG 59.461 52.381 10.27 0.00 44.99 3.86
142 143 2.225963 AGTCACGGACGACTTTAGTCAG 59.774 50.000 10.27 5.67 43.84 3.51
143 144 2.224606 AGTCACGGACGACTTTAGTCA 58.775 47.619 10.27 0.00 43.84 3.41
144 145 2.413897 GGAGTCACGGACGACTTTAGTC 60.414 54.545 0.00 0.00 46.26 2.59
145 146 1.538950 GGAGTCACGGACGACTTTAGT 59.461 52.381 0.00 0.00 46.26 2.24
146 147 1.465354 CGGAGTCACGGACGACTTTAG 60.465 57.143 0.00 0.00 46.26 1.85
147 148 0.518636 CGGAGTCACGGACGACTTTA 59.481 55.000 0.00 0.00 46.26 1.85
148 149 1.285023 CGGAGTCACGGACGACTTT 59.715 57.895 0.00 0.00 46.26 2.66
149 150 1.895707 ACGGAGTCACGGACGACTT 60.896 57.895 0.00 0.00 46.26 3.01
151 152 1.568612 TACACGGAGTCACGGACGAC 61.569 60.000 0.00 0.00 41.61 4.34
152 153 1.301637 TACACGGAGTCACGGACGA 60.302 57.895 0.00 0.00 41.61 4.20
153 154 1.154338 GTACACGGAGTCACGGACG 60.154 63.158 6.08 0.00 41.61 4.79
154 155 1.211190 GGTACACGGAGTCACGGAC 59.789 63.158 0.00 0.00 41.61 4.79
155 156 2.327343 CGGTACACGGAGTCACGGA 61.327 63.158 0.00 0.00 41.61 4.69
156 157 1.855213 TTCGGTACACGGAGTCACGG 61.855 60.000 0.00 0.00 41.61 4.94
157 158 0.453950 CTTCGGTACACGGAGTCACG 60.454 60.000 0.00 0.00 43.41 4.35
158 159 3.396491 CTTCGGTACACGGAGTCAC 57.604 57.895 0.00 0.00 43.41 3.67
163 164 2.642254 CCAGGCTTCGGTACACGGA 61.642 63.158 0.00 0.00 44.45 4.69
164 165 2.125673 CCAGGCTTCGGTACACGG 60.126 66.667 0.00 0.00 44.45 4.94
165 166 2.813908 GCCAGGCTTCGGTACACG 60.814 66.667 3.29 0.00 46.11 4.49
166 167 2.436115 GGCCAGGCTTCGGTACAC 60.436 66.667 12.43 0.00 0.00 2.90
167 168 4.077184 CGGCCAGGCTTCGGTACA 62.077 66.667 12.43 0.00 0.00 2.90
168 169 2.588856 ATTCGGCCAGGCTTCGGTAC 62.589 60.000 12.43 0.00 0.00 3.34
169 170 1.906105 AATTCGGCCAGGCTTCGGTA 61.906 55.000 12.43 0.05 0.00 4.02
170 171 1.906105 TAATTCGGCCAGGCTTCGGT 61.906 55.000 12.43 0.00 0.00 4.69
171 172 0.535102 ATAATTCGGCCAGGCTTCGG 60.535 55.000 12.43 0.00 0.00 4.30
172 173 1.798813 GTATAATTCGGCCAGGCTTCG 59.201 52.381 12.43 7.66 0.00 3.79
173 174 2.808543 CAGTATAATTCGGCCAGGCTTC 59.191 50.000 12.43 0.00 0.00 3.86
174 175 2.487265 CCAGTATAATTCGGCCAGGCTT 60.487 50.000 12.43 0.00 0.00 4.35
175 176 1.072331 CCAGTATAATTCGGCCAGGCT 59.928 52.381 12.43 0.00 0.00 4.58
176 177 1.523758 CCAGTATAATTCGGCCAGGC 58.476 55.000 1.26 1.26 0.00 4.85
177 178 1.523758 GCCAGTATAATTCGGCCAGG 58.476 55.000 2.24 0.00 38.67 4.45
181 182 1.235724 GTGGGCCAGTATAATTCGGC 58.764 55.000 6.40 0.00 44.10 5.54
182 183 1.544759 GGGTGGGCCAGTATAATTCGG 60.545 57.143 6.40 0.00 36.17 4.30
183 184 1.142060 TGGGTGGGCCAGTATAATTCG 59.858 52.381 6.40 0.00 36.17 3.34
184 185 2.174854 ACTGGGTGGGCCAGTATAATTC 59.825 50.000 6.40 0.00 45.29 2.17
185 186 2.174854 GACTGGGTGGGCCAGTATAATT 59.825 50.000 6.40 0.00 46.81 1.40
186 187 1.774856 GACTGGGTGGGCCAGTATAAT 59.225 52.381 6.40 0.00 46.81 1.28
187 188 1.209621 GACTGGGTGGGCCAGTATAA 58.790 55.000 6.40 0.00 46.81 0.98
188 189 0.693092 GGACTGGGTGGGCCAGTATA 60.693 60.000 6.40 0.00 46.81 1.47
189 190 2.001269 GGACTGGGTGGGCCAGTAT 61.001 63.158 6.40 0.00 46.81 2.12
190 191 2.609610 GGACTGGGTGGGCCAGTA 60.610 66.667 6.40 0.00 46.81 2.74
192 193 3.579302 TTGGACTGGGTGGGCCAG 61.579 66.667 6.40 0.00 40.72 4.85
193 194 3.897122 GTTGGACTGGGTGGGCCA 61.897 66.667 0.00 0.00 36.17 5.36
195 196 3.485346 TTCGTTGGACTGGGTGGGC 62.485 63.158 0.00 0.00 0.00 5.36
196 197 1.302511 CTTCGTTGGACTGGGTGGG 60.303 63.158 0.00 0.00 0.00 4.61
197 198 1.966451 GCTTCGTTGGACTGGGTGG 60.966 63.158 0.00 0.00 0.00 4.61
198 199 1.966451 GGCTTCGTTGGACTGGGTG 60.966 63.158 0.00 0.00 0.00 4.61
199 200 2.113243 GAGGCTTCGTTGGACTGGGT 62.113 60.000 0.00 0.00 0.00 4.51
200 201 1.376037 GAGGCTTCGTTGGACTGGG 60.376 63.158 0.00 0.00 0.00 4.45
201 202 0.951040 GTGAGGCTTCGTTGGACTGG 60.951 60.000 0.00 0.00 0.00 4.00
202 203 1.284982 CGTGAGGCTTCGTTGGACTG 61.285 60.000 0.00 0.00 0.00 3.51
203 204 1.006102 CGTGAGGCTTCGTTGGACT 60.006 57.895 0.00 0.00 0.00 3.85
204 205 3.550656 CGTGAGGCTTCGTTGGAC 58.449 61.111 0.00 0.00 0.00 4.02
216 217 1.172180 TTTTTCAGCTGGGCCGTGAG 61.172 55.000 15.13 0.00 0.00 3.51
217 218 1.152860 TTTTTCAGCTGGGCCGTGA 60.153 52.632 15.13 0.00 0.00 4.35
218 219 1.286880 CTTTTTCAGCTGGGCCGTG 59.713 57.895 15.13 0.00 0.00 4.94
219 220 1.903404 CCTTTTTCAGCTGGGCCGT 60.903 57.895 15.13 0.00 0.00 5.68
220 221 2.639327 CCCTTTTTCAGCTGGGCCG 61.639 63.158 15.13 0.00 32.49 6.13
221 222 1.228862 TCCCTTTTTCAGCTGGGCC 60.229 57.895 15.13 0.00 39.49 5.80
222 223 1.536073 GGTCCCTTTTTCAGCTGGGC 61.536 60.000 15.13 0.00 39.49 5.36
223 224 0.113190 AGGTCCCTTTTTCAGCTGGG 59.887 55.000 15.13 5.98 40.95 4.45
224 225 1.202927 TGAGGTCCCTTTTTCAGCTGG 60.203 52.381 15.13 0.00 0.00 4.85
225 226 2.276732 TGAGGTCCCTTTTTCAGCTG 57.723 50.000 7.63 7.63 0.00 4.24
226 227 3.425659 GATTGAGGTCCCTTTTTCAGCT 58.574 45.455 0.00 0.00 0.00 4.24
227 228 2.493675 GGATTGAGGTCCCTTTTTCAGC 59.506 50.000 0.00 0.00 31.82 4.26
228 229 4.013050 GAGGATTGAGGTCCCTTTTTCAG 58.987 47.826 0.00 0.00 39.17 3.02
229 230 3.245264 GGAGGATTGAGGTCCCTTTTTCA 60.245 47.826 0.00 0.00 39.17 2.69
230 231 3.245264 TGGAGGATTGAGGTCCCTTTTTC 60.245 47.826 0.00 0.00 39.17 2.29
231 232 2.721906 TGGAGGATTGAGGTCCCTTTTT 59.278 45.455 0.00 0.00 39.17 1.94
232 233 2.358258 TGGAGGATTGAGGTCCCTTTT 58.642 47.619 0.00 0.00 39.17 2.27
233 234 2.059756 TGGAGGATTGAGGTCCCTTT 57.940 50.000 0.00 0.00 39.17 3.11
234 235 2.131023 GATGGAGGATTGAGGTCCCTT 58.869 52.381 0.00 0.00 39.17 3.95
235 236 1.813102 GATGGAGGATTGAGGTCCCT 58.187 55.000 0.00 0.00 39.17 4.20
236 237 0.394565 CGATGGAGGATTGAGGTCCC 59.605 60.000 0.00 0.00 39.17 4.46
237 238 1.414158 TCGATGGAGGATTGAGGTCC 58.586 55.000 0.00 0.00 38.62 4.46
238 239 3.366476 CGTATCGATGGAGGATTGAGGTC 60.366 52.174 8.54 0.00 0.00 3.85
239 240 2.558795 CGTATCGATGGAGGATTGAGGT 59.441 50.000 8.54 0.00 0.00 3.85
240 241 2.094494 CCGTATCGATGGAGGATTGAGG 60.094 54.545 8.54 0.00 32.85 3.86
241 242 2.672478 GCCGTATCGATGGAGGATTGAG 60.672 54.545 8.54 0.00 32.85 3.02
242 243 1.272490 GCCGTATCGATGGAGGATTGA 59.728 52.381 8.54 0.00 32.85 2.57
243 244 1.673033 GGCCGTATCGATGGAGGATTG 60.673 57.143 8.54 0.00 32.85 2.67
244 245 0.608640 GGCCGTATCGATGGAGGATT 59.391 55.000 8.54 0.00 32.85 3.01
245 246 1.258445 GGGCCGTATCGATGGAGGAT 61.258 60.000 8.54 0.00 32.85 3.24
246 247 1.906824 GGGCCGTATCGATGGAGGA 60.907 63.158 8.54 0.00 32.85 3.71
247 248 2.159819 CTGGGCCGTATCGATGGAGG 62.160 65.000 8.54 9.55 32.85 4.30
248 249 1.290324 CTGGGCCGTATCGATGGAG 59.710 63.158 8.54 0.00 32.85 3.86
249 250 2.867855 GCTGGGCCGTATCGATGGA 61.868 63.158 8.54 0.00 32.85 3.41
250 251 2.357517 GCTGGGCCGTATCGATGG 60.358 66.667 8.54 2.36 34.45 3.51
251 252 1.665916 CAGCTGGGCCGTATCGATG 60.666 63.158 8.54 0.00 0.00 3.84
252 253 1.399744 TTCAGCTGGGCCGTATCGAT 61.400 55.000 15.13 2.16 0.00 3.59
253 254 1.609635 TTTCAGCTGGGCCGTATCGA 61.610 55.000 15.13 0.00 0.00 3.59
254 255 0.742990 TTTTCAGCTGGGCCGTATCG 60.743 55.000 15.13 0.00 0.00 2.92
255 256 1.459450 TTTTTCAGCTGGGCCGTATC 58.541 50.000 15.13 0.00 0.00 2.24
256 257 3.662290 TTTTTCAGCTGGGCCGTAT 57.338 47.368 15.13 0.00 0.00 3.06
278 279 9.990868 ATGATAAAATGGTACCCTAAAAAGACT 57.009 29.630 10.07 0.00 0.00 3.24
280 281 9.762381 ACATGATAAAATGGTACCCTAAAAAGA 57.238 29.630 10.07 0.00 31.46 2.52
339 340 9.420118 TCCAAGCATAGGATGTAAAAATATTGT 57.580 29.630 0.00 0.00 0.00 2.71
396 397 9.797556 GTTTCCATGTTAAACACTAAAAAGTCT 57.202 29.630 13.30 0.00 36.92 3.24
397 398 9.575783 TGTTTCCATGTTAAACACTAAAAAGTC 57.424 29.630 15.77 0.00 40.83 3.01
407 408 9.522804 GTTAGATTTGTGTTTCCATGTTAAACA 57.477 29.630 15.77 15.77 42.83 2.83
408 409 9.522804 TGTTAGATTTGTGTTTCCATGTTAAAC 57.477 29.630 11.92 11.92 37.35 2.01
411 412 9.906660 GAATGTTAGATTTGTGTTTCCATGTTA 57.093 29.630 0.00 0.00 0.00 2.41
412 413 8.641541 AGAATGTTAGATTTGTGTTTCCATGTT 58.358 29.630 0.00 0.00 0.00 2.71
413 414 8.181904 AGAATGTTAGATTTGTGTTTCCATGT 57.818 30.769 0.00 0.00 0.00 3.21
449 450 6.980577 TGAGAAAATTGGTAATAGTGGGGAT 58.019 36.000 0.00 0.00 0.00 3.85
758 769 1.675641 GGAAGTGCCTTGGTGCGAT 60.676 57.895 0.00 0.00 0.00 4.58
2890 7149 4.583073 AGGTTAGCTTGTCGGTTTCAAAAT 59.417 37.500 0.00 0.00 0.00 1.82
2930 7189 7.170965 TCAAAGAGTTATGAGAGGCTTCAAAT 58.829 34.615 0.00 0.00 0.00 2.32
3054 7313 7.678837 TGTGATTGCCTAAAAATTTGGAGATT 58.321 30.769 0.00 0.00 0.00 2.40
3055 7314 7.243604 TGTGATTGCCTAAAAATTTGGAGAT 57.756 32.000 0.00 0.00 0.00 2.75
3056 7315 6.662865 TGTGATTGCCTAAAAATTTGGAGA 57.337 33.333 0.00 0.00 0.00 3.71
3057 7316 7.388500 ACAATGTGATTGCCTAAAAATTTGGAG 59.612 33.333 0.00 0.00 43.98 3.86
3058 7317 7.222872 ACAATGTGATTGCCTAAAAATTTGGA 58.777 30.769 0.00 0.00 43.98 3.53
3059 7318 7.172875 TGACAATGTGATTGCCTAAAAATTTGG 59.827 33.333 0.00 0.00 43.98 3.28
3060 7319 8.085720 TGACAATGTGATTGCCTAAAAATTTG 57.914 30.769 0.00 0.00 43.98 2.32
3061 7320 8.558700 GTTGACAATGTGATTGCCTAAAAATTT 58.441 29.630 0.00 0.00 43.98 1.82
3062 7321 7.714377 TGTTGACAATGTGATTGCCTAAAAATT 59.286 29.630 0.00 0.00 43.98 1.82
3063 7322 7.171337 GTGTTGACAATGTGATTGCCTAAAAAT 59.829 33.333 0.00 0.00 43.98 1.82
3064 7323 6.478344 GTGTTGACAATGTGATTGCCTAAAAA 59.522 34.615 0.00 0.00 43.98 1.94
3065 7324 5.982516 GTGTTGACAATGTGATTGCCTAAAA 59.017 36.000 0.00 0.00 43.98 1.52
3066 7325 5.301551 AGTGTTGACAATGTGATTGCCTAAA 59.698 36.000 0.00 0.00 43.98 1.85
3067 7326 4.826733 AGTGTTGACAATGTGATTGCCTAA 59.173 37.500 0.00 0.00 43.98 2.69
3068 7327 4.397420 AGTGTTGACAATGTGATTGCCTA 58.603 39.130 0.00 0.00 43.98 3.93
3069 7328 3.225104 AGTGTTGACAATGTGATTGCCT 58.775 40.909 0.00 0.00 43.98 4.75
3070 7329 3.648339 AGTGTTGACAATGTGATTGCC 57.352 42.857 0.00 0.00 43.98 4.52
3071 7330 6.380995 TCAATAGTGTTGACAATGTGATTGC 58.619 36.000 0.00 0.00 43.98 3.56
3072 7331 7.809665 TCTCAATAGTGTTGACAATGTGATTG 58.190 34.615 0.00 1.03 45.59 2.67
3073 7332 7.984422 TCTCAATAGTGTTGACAATGTGATT 57.016 32.000 0.00 0.00 0.00 2.57
3074 7333 7.609146 ACATCTCAATAGTGTTGACAATGTGAT 59.391 33.333 17.84 8.59 32.76 3.06
3075 7334 6.936335 ACATCTCAATAGTGTTGACAATGTGA 59.064 34.615 17.84 7.07 32.76 3.58
3076 7335 7.137490 ACATCTCAATAGTGTTGACAATGTG 57.863 36.000 17.84 8.28 32.76 3.21
3077 7336 7.750229 AACATCTCAATAGTGTTGACAATGT 57.250 32.000 14.94 14.94 34.98 2.71
3080 7339 9.337396 ACTTAAACATCTCAATAGTGTTGACAA 57.663 29.630 0.00 0.00 36.31 3.18
3081 7340 8.902540 ACTTAAACATCTCAATAGTGTTGACA 57.097 30.769 0.00 0.00 36.31 3.58
3126 7385 3.084278 CAGCTTTTAAAATCGCGAGACG 58.916 45.455 16.66 0.00 46.97 4.18
3127 7386 3.417185 CCAGCTTTTAAAATCGCGAGAC 58.583 45.455 16.66 0.00 46.97 3.36
3129 7388 2.161609 ACCCAGCTTTTAAAATCGCGAG 59.838 45.455 16.66 0.00 0.00 5.03
3130 7389 2.156098 ACCCAGCTTTTAAAATCGCGA 58.844 42.857 13.09 13.09 0.00 5.87
3131 7390 2.629639 ACCCAGCTTTTAAAATCGCG 57.370 45.000 0.00 0.00 0.00 5.87
3132 7391 7.030768 TGTTTATACCCAGCTTTTAAAATCGC 58.969 34.615 0.09 2.62 0.00 4.58


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

AutoCloner maintained by Alex Coulton.