Multiple sequence alignment - TraesCS2B01G403600

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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 TraesCS2B01G403600 chr2B 100.000 2576 0 0 1 2576 572077859 572080434 0.000000e+00 4758.0
1 TraesCS2B01G403600 chr2B 79.384 422 75 12 2050 2465 653808489 653808904 1.170000e-73 287.0
2 TraesCS2B01G403600 chr2B 89.024 82 8 1 290 371 98678295 98678215 1.630000e-17 100.0
3 TraesCS2B01G403600 chr2B 81.188 101 14 5 275 372 383333778 383333876 2.750000e-10 76.8
4 TraesCS2B01G403600 chr2B 80.198 101 15 5 275 372 244785684 244785782 1.280000e-08 71.3
5 TraesCS2B01G403600 chr2B 80.000 100 15 5 276 372 699218573 699218670 4.600000e-08 69.4
6 TraesCS2B01G403600 chr2D 93.430 2207 92 23 368 2538 487314355 487316544 0.000000e+00 3223.0
7 TraesCS2B01G403600 chr2D 76.649 561 103 22 1925 2465 547559495 547560047 4.200000e-73 285.0
8 TraesCS2B01G403600 chr2D 76.960 421 87 9 2050 2465 547574744 547575159 5.540000e-57 231.0
9 TraesCS2B01G403600 chr2A 92.575 2155 101 18 421 2547 632389207 632391330 0.000000e+00 3038.0
10 TraesCS2B01G403600 chr2A 78.622 421 80 10 2050 2465 691391850 691391435 1.170000e-68 270.0
11 TraesCS2B01G403600 chr2A 83.186 113 15 4 262 372 480058810 480058700 1.630000e-17 100.0
12 TraesCS2B01G403600 chr6D 87.500 144 12 2 230 373 108695544 108695407 7.380000e-36 161.0
13 TraesCS2B01G403600 chr6D 84.158 101 11 5 277 375 233689277 233689374 2.730000e-15 93.5
14 TraesCS2B01G403600 chr6D 80.769 104 9 9 283 381 220273039 220273136 1.280000e-08 71.3
15 TraesCS2B01G403600 chr7B 83.761 117 12 6 260 372 727574863 727574750 1.260000e-18 104.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G403600 chr2B 572077859 572080434 2575 False 4758 4758 100.000 1 2576 1 chr2B.!!$F3 2575
1 TraesCS2B01G403600 chr2D 487314355 487316544 2189 False 3223 3223 93.430 368 2538 1 chr2D.!!$F1 2170
2 TraesCS2B01G403600 chr2D 547559495 547560047 552 False 285 285 76.649 1925 2465 1 chr2D.!!$F2 540
3 TraesCS2B01G403600 chr2A 632389207 632391330 2123 False 3038 3038 92.575 421 2547 1 chr2A.!!$F1 2126

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
84 85 0.034896 AGGAACACTAACCCTGTGCG 59.965 55.0 0.0 0.0 38.86 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 1969 0.391661 GACATGGTGATCTGCGGTGT 60.392 55.0 0.0 0.0 0.0 4.16 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
18 19 2.894858 AGCTCGAAGGGAAGAGAGG 58.105 57.895 0.00 0.00 36.65 3.69
19 20 0.686112 AGCTCGAAGGGAAGAGAGGG 60.686 60.000 0.00 0.00 36.65 4.30
20 21 0.684805 GCTCGAAGGGAAGAGAGGGA 60.685 60.000 0.00 0.00 36.65 4.20
21 22 1.107945 CTCGAAGGGAAGAGAGGGAC 58.892 60.000 0.00 0.00 36.65 4.46
22 23 0.408309 TCGAAGGGAAGAGAGGGACA 59.592 55.000 0.00 0.00 0.00 4.02
23 24 1.203137 TCGAAGGGAAGAGAGGGACAA 60.203 52.381 0.00 0.00 0.00 3.18
24 25 1.205893 CGAAGGGAAGAGAGGGACAAG 59.794 57.143 0.00 0.00 0.00 3.16
25 26 1.557371 GAAGGGAAGAGAGGGACAAGG 59.443 57.143 0.00 0.00 0.00 3.61
26 27 0.912006 AGGGAAGAGAGGGACAAGGC 60.912 60.000 0.00 0.00 0.00 4.35
27 28 1.201429 GGGAAGAGAGGGACAAGGCA 61.201 60.000 0.00 0.00 0.00 4.75
28 29 0.251634 GGAAGAGAGGGACAAGGCAG 59.748 60.000 0.00 0.00 0.00 4.85
29 30 0.392327 GAAGAGAGGGACAAGGCAGC 60.392 60.000 0.00 0.00 0.00 5.25
30 31 1.130054 AAGAGAGGGACAAGGCAGCA 61.130 55.000 0.00 0.00 0.00 4.41
31 32 1.078567 GAGAGGGACAAGGCAGCAG 60.079 63.158 0.00 0.00 0.00 4.24
32 33 2.045536 GAGGGACAAGGCAGCAGG 60.046 66.667 0.00 0.00 0.00 4.85
33 34 2.530151 AGGGACAAGGCAGCAGGA 60.530 61.111 0.00 0.00 0.00 3.86
34 35 2.045536 GGGACAAGGCAGCAGGAG 60.046 66.667 0.00 0.00 0.00 3.69
35 36 2.045536 GGACAAGGCAGCAGGAGG 60.046 66.667 0.00 0.00 0.00 4.30
36 37 2.753029 GACAAGGCAGCAGGAGGT 59.247 61.111 0.00 0.00 0.00 3.85
37 38 1.673665 GACAAGGCAGCAGGAGGTG 60.674 63.158 0.00 0.00 45.83 4.00
38 39 2.360852 CAAGGCAGCAGGAGGTGG 60.361 66.667 0.00 0.00 43.34 4.61
39 40 2.856000 AAGGCAGCAGGAGGTGGT 60.856 61.111 0.00 0.00 43.34 4.16
40 41 2.900106 AAGGCAGCAGGAGGTGGTC 61.900 63.158 0.00 0.00 43.34 4.02
41 42 4.767255 GGCAGCAGGAGGTGGTCG 62.767 72.222 0.00 0.00 43.34 4.79
42 43 3.695606 GCAGCAGGAGGTGGTCGA 61.696 66.667 0.00 0.00 43.34 4.20
43 44 2.575993 CAGCAGGAGGTGGTCGAG 59.424 66.667 0.00 0.00 39.53 4.04
44 45 2.681778 AGCAGGAGGTGGTCGAGG 60.682 66.667 0.00 0.00 27.31 4.63
45 46 2.680352 GCAGGAGGTGGTCGAGGA 60.680 66.667 0.00 0.00 0.00 3.71
46 47 2.716017 GCAGGAGGTGGTCGAGGAG 61.716 68.421 0.00 0.00 0.00 3.69
47 48 2.363147 AGGAGGTGGTCGAGGAGC 60.363 66.667 0.00 0.00 0.00 4.70
48 49 3.827898 GGAGGTGGTCGAGGAGCG 61.828 72.222 0.00 0.00 42.69 5.03
49 50 4.500116 GAGGTGGTCGAGGAGCGC 62.500 72.222 0.00 0.00 40.61 5.92
72 73 4.025401 CGGCGGCACAAGGAACAC 62.025 66.667 10.53 0.00 0.00 3.32
73 74 2.594592 GGCGGCACAAGGAACACT 60.595 61.111 3.07 0.00 0.00 3.55
74 75 1.302192 GGCGGCACAAGGAACACTA 60.302 57.895 3.07 0.00 0.00 2.74
75 76 0.887387 GGCGGCACAAGGAACACTAA 60.887 55.000 3.07 0.00 0.00 2.24
76 77 0.237498 GCGGCACAAGGAACACTAAC 59.763 55.000 0.00 0.00 0.00 2.34
77 78 0.872388 CGGCACAAGGAACACTAACC 59.128 55.000 0.00 0.00 0.00 2.85
78 79 1.244816 GGCACAAGGAACACTAACCC 58.755 55.000 0.00 0.00 0.00 4.11
79 80 1.202891 GGCACAAGGAACACTAACCCT 60.203 52.381 0.00 0.00 0.00 4.34
80 81 1.880027 GCACAAGGAACACTAACCCTG 59.120 52.381 0.00 0.00 0.00 4.45
81 82 2.748465 GCACAAGGAACACTAACCCTGT 60.748 50.000 0.00 0.00 0.00 4.00
82 83 2.878406 CACAAGGAACACTAACCCTGTG 59.122 50.000 0.00 0.00 40.87 3.66
83 84 1.880027 CAAGGAACACTAACCCTGTGC 59.120 52.381 0.00 0.00 38.86 4.57
84 85 0.034896 AGGAACACTAACCCTGTGCG 59.965 55.000 0.00 0.00 38.86 5.34
85 86 0.953960 GGAACACTAACCCTGTGCGG 60.954 60.000 0.00 0.00 38.86 5.69
86 87 0.250166 GAACACTAACCCTGTGCGGT 60.250 55.000 0.00 0.00 38.86 5.68
87 88 0.534203 AACACTAACCCTGTGCGGTG 60.534 55.000 0.00 0.00 38.86 4.94
88 89 1.369692 CACTAACCCTGTGCGGTGA 59.630 57.895 0.00 0.00 35.83 4.02
89 90 0.670546 CACTAACCCTGTGCGGTGAG 60.671 60.000 0.00 0.00 40.00 3.51
90 91 1.079127 CTAACCCTGTGCGGTGAGG 60.079 63.158 0.00 0.00 35.83 3.86
91 92 1.534476 TAACCCTGTGCGGTGAGGA 60.534 57.895 0.00 0.00 35.83 3.71
92 93 1.541310 TAACCCTGTGCGGTGAGGAG 61.541 60.000 0.00 0.00 35.83 3.69
93 94 4.767255 CCCTGTGCGGTGAGGAGC 62.767 72.222 0.00 0.00 0.00 4.70
128 129 0.770008 CGAAGCGTTTTCTTTTGCGG 59.230 50.000 0.00 0.00 0.00 5.69
129 130 1.128513 GAAGCGTTTTCTTTTGCGGG 58.871 50.000 0.00 0.00 0.00 6.13
130 131 0.741915 AAGCGTTTTCTTTTGCGGGA 59.258 45.000 0.00 0.00 0.00 5.14
131 132 0.310854 AGCGTTTTCTTTTGCGGGAG 59.689 50.000 0.00 0.00 0.00 4.30
132 133 0.663269 GCGTTTTCTTTTGCGGGAGG 60.663 55.000 0.00 0.00 0.00 4.30
133 134 0.948678 CGTTTTCTTTTGCGGGAGGA 59.051 50.000 0.00 0.00 0.00 3.71
134 135 1.069227 CGTTTTCTTTTGCGGGAGGAG 60.069 52.381 0.00 0.00 0.00 3.69
135 136 2.227194 GTTTTCTTTTGCGGGAGGAGA 58.773 47.619 0.00 0.00 0.00 3.71
136 137 2.820197 GTTTTCTTTTGCGGGAGGAGAT 59.180 45.455 0.00 0.00 0.00 2.75
137 138 2.879103 TTCTTTTGCGGGAGGAGATT 57.121 45.000 0.00 0.00 0.00 2.40
138 139 2.113860 TCTTTTGCGGGAGGAGATTG 57.886 50.000 0.00 0.00 0.00 2.67
139 140 1.351017 TCTTTTGCGGGAGGAGATTGT 59.649 47.619 0.00 0.00 0.00 2.71
140 141 2.162681 CTTTTGCGGGAGGAGATTGTT 58.837 47.619 0.00 0.00 0.00 2.83
141 142 1.533625 TTTGCGGGAGGAGATTGTTG 58.466 50.000 0.00 0.00 0.00 3.33
142 143 0.322456 TTGCGGGAGGAGATTGTTGG 60.322 55.000 0.00 0.00 0.00 3.77
143 144 1.299976 GCGGGAGGAGATTGTTGGT 59.700 57.895 0.00 0.00 0.00 3.67
144 145 0.322546 GCGGGAGGAGATTGTTGGTT 60.323 55.000 0.00 0.00 0.00 3.67
145 146 1.886655 GCGGGAGGAGATTGTTGGTTT 60.887 52.381 0.00 0.00 0.00 3.27
146 147 2.514803 CGGGAGGAGATTGTTGGTTTT 58.485 47.619 0.00 0.00 0.00 2.43
147 148 2.890945 CGGGAGGAGATTGTTGGTTTTT 59.109 45.455 0.00 0.00 0.00 1.94
208 209 2.427232 TTTTTCTCGATCGACCGTGT 57.573 45.000 15.15 0.00 0.00 4.49
209 210 3.557577 TTTTTCTCGATCGACCGTGTA 57.442 42.857 15.15 0.00 0.00 2.90
210 211 2.819422 TTTCTCGATCGACCGTGTAG 57.181 50.000 15.15 2.55 0.00 2.74
212 213 0.176449 TCTCGATCGACCGTGTAGGA 59.824 55.000 15.15 4.43 45.00 2.94
213 214 1.012086 CTCGATCGACCGTGTAGGAA 58.988 55.000 15.15 0.00 45.00 3.36
214 215 0.729116 TCGATCGACCGTGTAGGAAC 59.271 55.000 15.15 0.00 45.00 3.62
215 216 0.248377 CGATCGACCGTGTAGGAACC 60.248 60.000 10.26 0.00 45.00 3.62
216 217 1.101331 GATCGACCGTGTAGGAACCT 58.899 55.000 0.00 0.00 45.00 3.50
217 218 1.065251 GATCGACCGTGTAGGAACCTC 59.935 57.143 0.00 0.00 45.00 3.85
218 219 1.136147 CGACCGTGTAGGAACCTCG 59.864 63.158 0.00 0.00 45.00 4.63
219 220 1.580845 CGACCGTGTAGGAACCTCGT 61.581 60.000 0.00 0.00 45.00 4.18
220 221 0.109412 GACCGTGTAGGAACCTCGTG 60.109 60.000 0.00 0.00 45.00 4.35
221 222 0.825010 ACCGTGTAGGAACCTCGTGT 60.825 55.000 0.00 0.00 45.00 4.49
222 223 0.388134 CCGTGTAGGAACCTCGTGTG 60.388 60.000 0.00 0.00 45.00 3.82
223 224 0.388134 CGTGTAGGAACCTCGTGTGG 60.388 60.000 0.00 0.00 0.00 4.17
224 225 0.037605 GTGTAGGAACCTCGTGTGGG 60.038 60.000 0.00 0.00 0.00 4.61
225 226 1.079336 GTAGGAACCTCGTGTGGGC 60.079 63.158 0.00 0.00 0.00 5.36
226 227 1.534476 TAGGAACCTCGTGTGGGCA 60.534 57.895 0.00 0.00 0.00 5.36
227 228 0.907704 TAGGAACCTCGTGTGGGCAT 60.908 55.000 0.00 0.00 0.00 4.40
228 229 1.303317 GGAACCTCGTGTGGGCATT 60.303 57.895 0.00 0.00 0.00 3.56
229 230 0.893727 GGAACCTCGTGTGGGCATTT 60.894 55.000 0.00 0.00 0.00 2.32
230 231 0.958822 GAACCTCGTGTGGGCATTTT 59.041 50.000 0.00 0.00 0.00 1.82
231 232 1.339929 GAACCTCGTGTGGGCATTTTT 59.660 47.619 0.00 0.00 0.00 1.94
248 249 2.725008 TTTTTGGTTCGGCGCTGG 59.275 55.556 17.88 4.31 0.00 4.85
249 250 1.824329 TTTTTGGTTCGGCGCTGGA 60.824 52.632 17.88 4.05 0.00 3.86
250 251 1.384989 TTTTTGGTTCGGCGCTGGAA 61.385 50.000 17.88 13.22 0.00 3.53
251 252 2.065906 TTTTGGTTCGGCGCTGGAAC 62.066 55.000 26.12 26.12 42.32 3.62
252 253 2.951475 TTTGGTTCGGCGCTGGAACT 62.951 55.000 29.77 0.00 42.58 3.01
253 254 2.102109 TTGGTTCGGCGCTGGAACTA 62.102 55.000 29.77 25.40 42.58 2.24
254 255 1.810030 GGTTCGGCGCTGGAACTAG 60.810 63.158 29.77 7.32 42.58 2.57
255 256 1.810030 GTTCGGCGCTGGAACTAGG 60.810 63.158 26.52 2.01 40.41 3.02
256 257 3.014085 TTCGGCGCTGGAACTAGGG 62.014 63.158 17.88 0.00 0.00 3.53
260 261 2.187946 CGCTGGAACTAGGGCAGG 59.812 66.667 0.00 0.00 0.00 4.85
261 262 2.359169 CGCTGGAACTAGGGCAGGA 61.359 63.158 0.00 0.00 0.00 3.86
262 263 1.690219 CGCTGGAACTAGGGCAGGAT 61.690 60.000 0.00 0.00 0.00 3.24
263 264 0.107643 GCTGGAACTAGGGCAGGATC 59.892 60.000 0.00 0.00 0.00 3.36
264 265 0.390860 CTGGAACTAGGGCAGGATCG 59.609 60.000 0.00 0.00 0.00 3.69
265 266 1.069935 GGAACTAGGGCAGGATCGC 59.930 63.158 0.00 0.00 0.00 4.58
266 267 1.403687 GGAACTAGGGCAGGATCGCT 61.404 60.000 0.00 0.00 0.00 4.93
267 268 0.249657 GAACTAGGGCAGGATCGCTG 60.250 60.000 6.79 6.79 0.00 5.18
268 269 0.687757 AACTAGGGCAGGATCGCTGA 60.688 55.000 13.48 0.00 0.00 4.26
269 270 0.470833 ACTAGGGCAGGATCGCTGAT 60.471 55.000 13.48 3.52 0.00 2.90
270 271 1.203063 ACTAGGGCAGGATCGCTGATA 60.203 52.381 13.48 4.27 0.00 2.15
271 272 1.203523 CTAGGGCAGGATCGCTGATAC 59.796 57.143 13.48 4.68 0.00 2.24
272 273 1.373497 GGGCAGGATCGCTGATACG 60.373 63.158 13.48 0.00 0.00 3.06
273 274 1.364171 GGCAGGATCGCTGATACGT 59.636 57.895 13.48 0.00 0.00 3.57
274 275 0.941463 GGCAGGATCGCTGATACGTG 60.941 60.000 13.48 0.00 0.00 4.49
275 276 0.941463 GCAGGATCGCTGATACGTGG 60.941 60.000 13.48 0.00 0.00 4.94
276 277 0.319040 CAGGATCGCTGATACGTGGG 60.319 60.000 0.00 0.00 0.00 4.61
277 278 0.467474 AGGATCGCTGATACGTGGGA 60.467 55.000 0.00 0.00 0.00 4.37
278 279 0.039074 GGATCGCTGATACGTGGGAG 60.039 60.000 0.00 0.00 0.00 4.30
279 280 0.039074 GATCGCTGATACGTGGGAGG 60.039 60.000 0.00 0.00 0.00 4.30
280 281 0.755698 ATCGCTGATACGTGGGAGGT 60.756 55.000 0.00 0.00 0.00 3.85
281 282 1.226974 CGCTGATACGTGGGAGGTG 60.227 63.158 0.00 0.00 0.00 4.00
282 283 1.144057 GCTGATACGTGGGAGGTGG 59.856 63.158 0.00 0.00 0.00 4.61
283 284 1.823295 CTGATACGTGGGAGGTGGG 59.177 63.158 0.00 0.00 0.00 4.61
284 285 0.686441 CTGATACGTGGGAGGTGGGA 60.686 60.000 0.00 0.00 0.00 4.37
285 286 0.252330 TGATACGTGGGAGGTGGGAA 60.252 55.000 0.00 0.00 0.00 3.97
286 287 1.129058 GATACGTGGGAGGTGGGAAT 58.871 55.000 0.00 0.00 0.00 3.01
287 288 0.837272 ATACGTGGGAGGTGGGAATG 59.163 55.000 0.00 0.00 0.00 2.67
288 289 0.252330 TACGTGGGAGGTGGGAATGA 60.252 55.000 0.00 0.00 0.00 2.57
289 290 1.221840 CGTGGGAGGTGGGAATGAG 59.778 63.158 0.00 0.00 0.00 2.90
290 291 1.609783 GTGGGAGGTGGGAATGAGG 59.390 63.158 0.00 0.00 0.00 3.86
291 292 0.914417 GTGGGAGGTGGGAATGAGGA 60.914 60.000 0.00 0.00 0.00 3.71
292 293 0.914417 TGGGAGGTGGGAATGAGGAC 60.914 60.000 0.00 0.00 0.00 3.85
293 294 1.522569 GGAGGTGGGAATGAGGACG 59.477 63.158 0.00 0.00 0.00 4.79
294 295 0.976073 GGAGGTGGGAATGAGGACGA 60.976 60.000 0.00 0.00 0.00 4.20
295 296 0.902531 GAGGTGGGAATGAGGACGAA 59.097 55.000 0.00 0.00 0.00 3.85
296 297 1.278127 GAGGTGGGAATGAGGACGAAA 59.722 52.381 0.00 0.00 0.00 3.46
297 298 1.702957 AGGTGGGAATGAGGACGAAAA 59.297 47.619 0.00 0.00 0.00 2.29
298 299 2.107552 AGGTGGGAATGAGGACGAAAAA 59.892 45.455 0.00 0.00 0.00 1.94
334 335 6.687081 TGGGACAAAATATAACCGATGAAC 57.313 37.500 0.00 0.00 31.92 3.18
335 336 5.294799 TGGGACAAAATATAACCGATGAACG 59.705 40.000 0.00 0.00 37.24 3.95
336 337 5.524646 GGGACAAAATATAACCGATGAACGA 59.475 40.000 0.00 0.00 45.77 3.85
337 338 6.037391 GGGACAAAATATAACCGATGAACGAA 59.963 38.462 0.00 0.00 45.77 3.85
338 339 7.123830 GGACAAAATATAACCGATGAACGAAG 58.876 38.462 0.00 0.00 45.77 3.79
339 340 7.010738 GGACAAAATATAACCGATGAACGAAGA 59.989 37.037 0.00 0.00 45.77 2.87
340 341 7.681903 ACAAAATATAACCGATGAACGAAGAC 58.318 34.615 0.00 0.00 45.77 3.01
341 342 7.548075 ACAAAATATAACCGATGAACGAAGACT 59.452 33.333 0.00 0.00 45.77 3.24
342 343 9.027129 CAAAATATAACCGATGAACGAAGACTA 57.973 33.333 0.00 0.00 45.77 2.59
343 344 9.590451 AAAATATAACCGATGAACGAAGACTAA 57.410 29.630 0.00 0.00 45.77 2.24
344 345 8.571461 AATATAACCGATGAACGAAGACTAAC 57.429 34.615 0.00 0.00 45.77 2.34
345 346 3.928727 ACCGATGAACGAAGACTAACA 57.071 42.857 0.00 0.00 45.77 2.41
346 347 4.247267 ACCGATGAACGAAGACTAACAA 57.753 40.909 0.00 0.00 45.77 2.83
347 348 3.985925 ACCGATGAACGAAGACTAACAAC 59.014 43.478 0.00 0.00 45.77 3.32
348 349 4.235360 CCGATGAACGAAGACTAACAACT 58.765 43.478 0.00 0.00 45.77 3.16
349 350 4.090066 CCGATGAACGAAGACTAACAACTG 59.910 45.833 0.00 0.00 45.77 3.16
350 351 4.915667 CGATGAACGAAGACTAACAACTGA 59.084 41.667 0.00 0.00 45.77 3.41
351 352 5.059832 CGATGAACGAAGACTAACAACTGAG 59.940 44.000 0.00 0.00 45.77 3.35
352 353 5.509716 TGAACGAAGACTAACAACTGAGA 57.490 39.130 0.00 0.00 0.00 3.27
353 354 5.279384 TGAACGAAGACTAACAACTGAGAC 58.721 41.667 0.00 0.00 0.00 3.36
354 355 4.913335 ACGAAGACTAACAACTGAGACA 57.087 40.909 0.00 0.00 0.00 3.41
355 356 5.455056 ACGAAGACTAACAACTGAGACAT 57.545 39.130 0.00 0.00 0.00 3.06
356 357 5.844004 ACGAAGACTAACAACTGAGACATT 58.156 37.500 0.00 0.00 0.00 2.71
357 358 6.978338 ACGAAGACTAACAACTGAGACATTA 58.022 36.000 0.00 0.00 0.00 1.90
358 359 7.085116 ACGAAGACTAACAACTGAGACATTAG 58.915 38.462 0.00 0.00 0.00 1.73
359 360 6.528423 CGAAGACTAACAACTGAGACATTAGG 59.472 42.308 0.00 0.00 0.00 2.69
360 361 7.540474 AAGACTAACAACTGAGACATTAGGA 57.460 36.000 0.00 0.00 0.00 2.94
361 362 7.164230 AGACTAACAACTGAGACATTAGGAG 57.836 40.000 0.00 0.00 0.00 3.69
362 363 6.722129 AGACTAACAACTGAGACATTAGGAGT 59.278 38.462 0.00 0.00 0.00 3.85
363 364 7.889073 AGACTAACAACTGAGACATTAGGAGTA 59.111 37.037 0.00 0.00 0.00 2.59
364 365 8.057536 ACTAACAACTGAGACATTAGGAGTAG 57.942 38.462 0.00 0.00 0.00 2.57
365 366 7.889073 ACTAACAACTGAGACATTAGGAGTAGA 59.111 37.037 0.00 0.00 0.00 2.59
366 367 6.767524 ACAACTGAGACATTAGGAGTAGAG 57.232 41.667 0.00 0.00 0.00 2.43
386 387 9.087871 AGTAGAGATATTCATGCTAACAGTCAT 57.912 33.333 0.00 0.00 0.00 3.06
615 626 2.862347 GAATTGCCGTGCAGCTGCTC 62.862 60.000 36.61 31.59 40.61 4.26
713 732 2.787994 CATTTGCTCCTCTGGTCAAGT 58.212 47.619 0.00 0.00 0.00 3.16
789 808 0.681243 GATTCCCTGGTGGCTTGGAC 60.681 60.000 0.00 0.00 0.00 4.02
803 822 2.673043 GCTTGGACACAAAGATGGCATG 60.673 50.000 3.81 0.00 35.89 4.06
881 903 2.699846 AGCTAATCAGGCTGAAGAGAGG 59.300 50.000 22.84 9.64 38.73 3.69
890 912 1.937108 GCTGAAGAGAGGTTGACACGG 60.937 57.143 0.00 0.00 0.00 4.94
942 967 1.378911 GCTGGTCCATCCATGCACA 60.379 57.895 0.00 0.00 46.12 4.57
963 988 0.827368 GCACTACCCTCCCTCTCAAG 59.173 60.000 0.00 0.00 0.00 3.02
973 998 3.067461 CCTCCCTCTCAAGTCTCAATACG 59.933 52.174 0.00 0.00 0.00 3.06
988 1016 2.403252 ATACGACCAAGCTTTCTGGG 57.597 50.000 7.81 3.54 39.46 4.45
1020 1048 0.107643 TGGCGAACACAAGGATGACA 59.892 50.000 0.00 0.00 0.00 3.58
1021 1049 1.271325 TGGCGAACACAAGGATGACAT 60.271 47.619 0.00 0.00 0.00 3.06
1044 1072 3.541996 CACATGTGCTACCTCACCATA 57.458 47.619 13.94 0.00 36.17 2.74
1104 1132 3.285215 AGCGACACTGACGACGGT 61.285 61.111 5.05 0.00 35.84 4.83
1106 1134 1.511464 GCGACACTGACGACGGTAG 60.511 63.158 5.05 0.00 33.89 3.18
1311 1339 0.109873 CGTCGCTGTTCTACTTCGGT 60.110 55.000 0.00 0.00 0.00 4.69
1322 1350 6.192234 GTTCTACTTCGGTGAGAACATAGA 57.808 41.667 8.70 0.00 45.49 1.98
1323 1351 6.618811 GTTCTACTTCGGTGAGAACATAGAA 58.381 40.000 8.70 0.00 45.49 2.10
1335 1363 2.514458 ACATAGAAGTGGGCAAAGGG 57.486 50.000 0.00 0.00 0.00 3.95
1500 1528 0.747644 TCGGGTGCGGTAAGATCGTA 60.748 55.000 0.00 0.00 0.00 3.43
1582 1618 2.280119 GGCCATACTGATCGCGCA 60.280 61.111 8.75 0.00 0.00 6.09
1590 1626 2.356433 TGATCGCGCACCGTTGAA 60.356 55.556 8.75 0.00 38.35 2.69
1602 1638 1.296867 CGTTGAATGATCACGCCGC 60.297 57.895 0.00 0.00 34.61 6.53
1617 1653 1.208870 CCGCGCATGCAAGTTAACA 59.791 52.632 19.57 0.00 42.97 2.41
1634 1670 4.101448 AGCATCCCTCCACGTGGC 62.101 66.667 30.25 15.83 34.44 5.01
1695 1731 6.869421 ACTTGTAATTCGCAAATTGTATGC 57.131 33.333 0.00 0.00 40.41 3.14
1703 1739 6.834959 TTCGCAAATTGTATGCTTCAAAAA 57.165 29.167 0.00 0.00 41.64 1.94
1736 1772 7.425577 TTCACATTTTCATCACTGACAGTAG 57.574 36.000 8.02 3.36 0.00 2.57
1737 1773 6.524734 TCACATTTTCATCACTGACAGTAGT 58.475 36.000 8.02 0.00 0.00 2.73
1738 1774 7.666623 TCACATTTTCATCACTGACAGTAGTA 58.333 34.615 8.02 0.00 0.00 1.82
1739 1775 8.314021 TCACATTTTCATCACTGACAGTAGTAT 58.686 33.333 8.02 0.00 0.00 2.12
1783 1833 5.705441 TGAACGCTTCAAATTAACTCTCCAT 59.295 36.000 0.00 0.00 36.59 3.41
1856 1906 2.514013 GCATACGAGAACCCGCACG 61.514 63.158 0.00 0.00 0.00 5.34
1896 1946 7.072454 TCCTATATAATGACTGCACTTCCCTTT 59.928 37.037 0.00 0.00 0.00 3.11
1918 1968 2.293399 GCAAACTTCACCAAATCGACCT 59.707 45.455 0.00 0.00 0.00 3.85
1919 1969 3.500680 GCAAACTTCACCAAATCGACCTA 59.499 43.478 0.00 0.00 0.00 3.08
1954 2004 2.048222 TCTCCTTTCGCCTGCGTG 60.048 61.111 11.68 3.57 40.74 5.34
2473 2538 1.068741 CCGCCCTACTGATTCTGTACC 59.931 57.143 0.00 0.00 0.00 3.34
2474 2541 1.068741 CGCCCTACTGATTCTGTACCC 59.931 57.143 0.00 0.00 0.00 3.69
2475 2542 2.116238 GCCCTACTGATTCTGTACCCA 58.884 52.381 0.00 0.00 0.00 4.51
2485 2552 3.756933 TTCTGTACCCAAAGCTAACGT 57.243 42.857 0.00 0.00 0.00 3.99
2547 2614 4.273480 CCATAGTTCATAACAAAGCGGGAG 59.727 45.833 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.686112 CCCTCTCTTCCCTTCGAGCT 60.686 60.000 0.00 0.00 0.00 4.09
1 2 0.684805 TCCCTCTCTTCCCTTCGAGC 60.685 60.000 0.00 0.00 0.00 5.03
2 3 1.107945 GTCCCTCTCTTCCCTTCGAG 58.892 60.000 0.00 0.00 0.00 4.04
3 4 0.408309 TGTCCCTCTCTTCCCTTCGA 59.592 55.000 0.00 0.00 0.00 3.71
4 5 1.205893 CTTGTCCCTCTCTTCCCTTCG 59.794 57.143 0.00 0.00 0.00 3.79
5 6 1.557371 CCTTGTCCCTCTCTTCCCTTC 59.443 57.143 0.00 0.00 0.00 3.46
6 7 1.662686 CCTTGTCCCTCTCTTCCCTT 58.337 55.000 0.00 0.00 0.00 3.95
7 8 0.912006 GCCTTGTCCCTCTCTTCCCT 60.912 60.000 0.00 0.00 0.00 4.20
8 9 1.201429 TGCCTTGTCCCTCTCTTCCC 61.201 60.000 0.00 0.00 0.00 3.97
9 10 0.251634 CTGCCTTGTCCCTCTCTTCC 59.748 60.000 0.00 0.00 0.00 3.46
10 11 0.392327 GCTGCCTTGTCCCTCTCTTC 60.392 60.000 0.00 0.00 0.00 2.87
11 12 1.130054 TGCTGCCTTGTCCCTCTCTT 61.130 55.000 0.00 0.00 0.00 2.85
12 13 1.537397 TGCTGCCTTGTCCCTCTCT 60.537 57.895 0.00 0.00 0.00 3.10
13 14 1.078567 CTGCTGCCTTGTCCCTCTC 60.079 63.158 0.00 0.00 0.00 3.20
14 15 2.600729 CCTGCTGCCTTGTCCCTCT 61.601 63.158 0.00 0.00 0.00 3.69
15 16 2.045536 CCTGCTGCCTTGTCCCTC 60.046 66.667 0.00 0.00 0.00 4.30
16 17 2.530151 TCCTGCTGCCTTGTCCCT 60.530 61.111 0.00 0.00 0.00 4.20
17 18 2.045536 CTCCTGCTGCCTTGTCCC 60.046 66.667 0.00 0.00 0.00 4.46
18 19 2.045536 CCTCCTGCTGCCTTGTCC 60.046 66.667 0.00 0.00 0.00 4.02
19 20 1.673665 CACCTCCTGCTGCCTTGTC 60.674 63.158 0.00 0.00 0.00 3.18
20 21 2.433446 CACCTCCTGCTGCCTTGT 59.567 61.111 0.00 0.00 0.00 3.16
21 22 2.360852 CCACCTCCTGCTGCCTTG 60.361 66.667 0.00 0.00 0.00 3.61
22 23 2.856000 ACCACCTCCTGCTGCCTT 60.856 61.111 0.00 0.00 0.00 4.35
23 24 3.325753 GACCACCTCCTGCTGCCT 61.326 66.667 0.00 0.00 0.00 4.75
24 25 4.767255 CGACCACCTCCTGCTGCC 62.767 72.222 0.00 0.00 0.00 4.85
25 26 3.655810 CTCGACCACCTCCTGCTGC 62.656 68.421 0.00 0.00 0.00 5.25
26 27 2.575993 CTCGACCACCTCCTGCTG 59.424 66.667 0.00 0.00 0.00 4.41
27 28 2.681778 CCTCGACCACCTCCTGCT 60.682 66.667 0.00 0.00 0.00 4.24
28 29 2.680352 TCCTCGACCACCTCCTGC 60.680 66.667 0.00 0.00 0.00 4.85
29 30 2.716017 GCTCCTCGACCACCTCCTG 61.716 68.421 0.00 0.00 0.00 3.86
30 31 2.363147 GCTCCTCGACCACCTCCT 60.363 66.667 0.00 0.00 0.00 3.69
31 32 3.827898 CGCTCCTCGACCACCTCC 61.828 72.222 0.00 0.00 41.67 4.30
32 33 4.500116 GCGCTCCTCGACCACCTC 62.500 72.222 0.00 0.00 41.67 3.85
55 56 4.025401 GTGTTCCTTGTGCCGCCG 62.025 66.667 0.00 0.00 0.00 6.46
56 57 0.887387 TTAGTGTTCCTTGTGCCGCC 60.887 55.000 0.00 0.00 0.00 6.13
57 58 0.237498 GTTAGTGTTCCTTGTGCCGC 59.763 55.000 0.00 0.00 0.00 6.53
58 59 0.872388 GGTTAGTGTTCCTTGTGCCG 59.128 55.000 0.00 0.00 0.00 5.69
59 60 1.202891 AGGGTTAGTGTTCCTTGTGCC 60.203 52.381 0.00 0.00 0.00 5.01
60 61 1.880027 CAGGGTTAGTGTTCCTTGTGC 59.120 52.381 0.00 0.00 0.00 4.57
61 62 3.208747 ACAGGGTTAGTGTTCCTTGTG 57.791 47.619 0.00 0.00 41.34 3.33
62 63 2.748465 GCACAGGGTTAGTGTTCCTTGT 60.748 50.000 0.00 0.00 43.15 3.16
63 64 1.880027 GCACAGGGTTAGTGTTCCTTG 59.120 52.381 0.00 0.00 39.17 3.61
64 65 1.542547 CGCACAGGGTTAGTGTTCCTT 60.543 52.381 0.00 0.00 39.17 3.36
65 66 0.034896 CGCACAGGGTTAGTGTTCCT 59.965 55.000 0.00 0.00 39.17 3.36
66 67 0.953960 CCGCACAGGGTTAGTGTTCC 60.954 60.000 0.00 0.00 39.17 3.62
67 68 0.250166 ACCGCACAGGGTTAGTGTTC 60.250 55.000 0.00 0.00 46.96 3.18
68 69 0.534203 CACCGCACAGGGTTAGTGTT 60.534 55.000 0.00 0.00 46.96 3.32
69 70 1.070786 CACCGCACAGGGTTAGTGT 59.929 57.895 0.00 0.00 46.96 3.55
70 71 0.670546 CTCACCGCACAGGGTTAGTG 60.671 60.000 0.00 0.00 46.96 2.74
71 72 1.671742 CTCACCGCACAGGGTTAGT 59.328 57.895 0.00 0.00 46.96 2.24
72 73 1.079127 CCTCACCGCACAGGGTTAG 60.079 63.158 0.00 0.00 46.96 2.34
73 74 1.534476 TCCTCACCGCACAGGGTTA 60.534 57.895 0.00 0.00 46.96 2.85
74 75 2.847234 TCCTCACCGCACAGGGTT 60.847 61.111 0.00 0.00 46.96 4.11
75 76 3.314331 CTCCTCACCGCACAGGGT 61.314 66.667 0.00 0.00 46.96 4.34
76 77 4.767255 GCTCCTCACCGCACAGGG 62.767 72.222 0.00 0.00 46.96 4.45
101 102 0.722799 GAAAACGCTTCGCACAGAGC 60.723 55.000 0.00 0.00 40.87 4.09
102 103 0.861837 AGAAAACGCTTCGCACAGAG 59.138 50.000 0.00 0.00 0.00 3.35
103 104 1.295792 AAGAAAACGCTTCGCACAGA 58.704 45.000 0.00 0.00 0.00 3.41
104 105 2.105323 AAAGAAAACGCTTCGCACAG 57.895 45.000 0.00 0.00 0.00 3.66
105 106 2.181205 CAAAAGAAAACGCTTCGCACA 58.819 42.857 0.00 0.00 0.00 4.57
106 107 1.072154 GCAAAAGAAAACGCTTCGCAC 60.072 47.619 0.00 0.00 0.00 5.34
107 108 1.196200 GCAAAAGAAAACGCTTCGCA 58.804 45.000 0.00 0.00 0.00 5.10
108 109 0.156651 CGCAAAAGAAAACGCTTCGC 59.843 50.000 0.00 0.00 0.00 4.70
109 110 0.770008 CCGCAAAAGAAAACGCTTCG 59.230 50.000 0.00 0.00 0.00 3.79
110 111 1.128513 CCCGCAAAAGAAAACGCTTC 58.871 50.000 0.00 0.00 0.00 3.86
111 112 0.741915 TCCCGCAAAAGAAAACGCTT 59.258 45.000 0.00 0.00 0.00 4.68
112 113 0.310854 CTCCCGCAAAAGAAAACGCT 59.689 50.000 0.00 0.00 0.00 5.07
113 114 0.663269 CCTCCCGCAAAAGAAAACGC 60.663 55.000 0.00 0.00 0.00 4.84
114 115 0.948678 TCCTCCCGCAAAAGAAAACG 59.051 50.000 0.00 0.00 0.00 3.60
115 116 2.227194 TCTCCTCCCGCAAAAGAAAAC 58.773 47.619 0.00 0.00 0.00 2.43
116 117 2.649531 TCTCCTCCCGCAAAAGAAAA 57.350 45.000 0.00 0.00 0.00 2.29
117 118 2.819608 CAATCTCCTCCCGCAAAAGAAA 59.180 45.455 0.00 0.00 0.00 2.52
118 119 2.224769 ACAATCTCCTCCCGCAAAAGAA 60.225 45.455 0.00 0.00 0.00 2.52
119 120 1.351017 ACAATCTCCTCCCGCAAAAGA 59.649 47.619 0.00 0.00 0.00 2.52
120 121 1.826385 ACAATCTCCTCCCGCAAAAG 58.174 50.000 0.00 0.00 0.00 2.27
121 122 1.885887 CAACAATCTCCTCCCGCAAAA 59.114 47.619 0.00 0.00 0.00 2.44
122 123 1.533625 CAACAATCTCCTCCCGCAAA 58.466 50.000 0.00 0.00 0.00 3.68
123 124 0.322456 CCAACAATCTCCTCCCGCAA 60.322 55.000 0.00 0.00 0.00 4.85
124 125 1.299648 CCAACAATCTCCTCCCGCA 59.700 57.895 0.00 0.00 0.00 5.69
125 126 0.322546 AACCAACAATCTCCTCCCGC 60.323 55.000 0.00 0.00 0.00 6.13
126 127 2.200373 AAACCAACAATCTCCTCCCG 57.800 50.000 0.00 0.00 0.00 5.14
189 190 2.427232 ACACGGTCGATCGAGAAAAA 57.573 45.000 27.34 0.00 0.00 1.94
190 191 2.159476 CCTACACGGTCGATCGAGAAAA 60.159 50.000 27.34 7.39 0.00 2.29
191 192 1.399440 CCTACACGGTCGATCGAGAAA 59.601 52.381 27.34 9.91 0.00 2.52
192 193 1.012086 CCTACACGGTCGATCGAGAA 58.988 55.000 27.34 7.94 0.00 2.87
193 194 0.176449 TCCTACACGGTCGATCGAGA 59.824 55.000 27.34 10.02 0.00 4.04
194 195 1.012086 TTCCTACACGGTCGATCGAG 58.988 55.000 27.34 20.40 0.00 4.04
195 196 0.729116 GTTCCTACACGGTCGATCGA 59.271 55.000 27.34 15.15 0.00 3.59
196 197 0.248377 GGTTCCTACACGGTCGATCG 60.248 60.000 18.18 18.18 0.00 3.69
197 198 1.065251 GAGGTTCCTACACGGTCGATC 59.935 57.143 0.00 0.00 0.00 3.69
198 199 1.101331 GAGGTTCCTACACGGTCGAT 58.899 55.000 0.00 0.00 0.00 3.59
199 200 1.300971 CGAGGTTCCTACACGGTCGA 61.301 60.000 0.00 0.00 0.00 4.20
200 201 1.136147 CGAGGTTCCTACACGGTCG 59.864 63.158 0.00 0.00 0.00 4.79
201 202 0.109412 CACGAGGTTCCTACACGGTC 60.109 60.000 0.00 0.00 32.65 4.79
202 203 0.825010 ACACGAGGTTCCTACACGGT 60.825 55.000 0.00 0.00 32.65 4.83
203 204 0.388134 CACACGAGGTTCCTACACGG 60.388 60.000 0.00 0.00 32.65 4.94
204 205 0.388134 CCACACGAGGTTCCTACACG 60.388 60.000 0.00 0.00 33.87 4.49
205 206 0.037605 CCCACACGAGGTTCCTACAC 60.038 60.000 0.00 0.00 0.00 2.90
206 207 1.823169 GCCCACACGAGGTTCCTACA 61.823 60.000 0.00 0.00 0.00 2.74
207 208 1.079336 GCCCACACGAGGTTCCTAC 60.079 63.158 0.00 0.00 0.00 3.18
208 209 0.907704 ATGCCCACACGAGGTTCCTA 60.908 55.000 0.00 0.00 0.00 2.94
209 210 1.779061 AATGCCCACACGAGGTTCCT 61.779 55.000 0.00 0.00 0.00 3.36
210 211 0.893727 AAATGCCCACACGAGGTTCC 60.894 55.000 0.00 0.00 0.00 3.62
211 212 0.958822 AAAATGCCCACACGAGGTTC 59.041 50.000 0.00 0.00 0.00 3.62
212 213 1.408969 AAAAATGCCCACACGAGGTT 58.591 45.000 0.00 0.00 0.00 3.50
213 214 3.125520 AAAAATGCCCACACGAGGT 57.874 47.368 0.00 0.00 0.00 3.85
231 232 1.384989 TTCCAGCGCCGAACCAAAAA 61.385 50.000 2.29 0.00 0.00 1.94
232 233 1.824329 TTCCAGCGCCGAACCAAAA 60.824 52.632 2.29 0.00 0.00 2.44
233 234 2.203224 TTCCAGCGCCGAACCAAA 60.203 55.556 2.29 0.00 0.00 3.28
234 235 2.102109 TAGTTCCAGCGCCGAACCAA 62.102 55.000 25.96 16.25 40.43 3.67
235 236 2.501223 CTAGTTCCAGCGCCGAACCA 62.501 60.000 25.96 16.57 40.43 3.67
236 237 1.810030 CTAGTTCCAGCGCCGAACC 60.810 63.158 25.96 13.62 40.43 3.62
237 238 1.810030 CCTAGTTCCAGCGCCGAAC 60.810 63.158 23.57 23.57 39.96 3.95
238 239 2.577059 CCTAGTTCCAGCGCCGAA 59.423 61.111 2.29 3.05 0.00 4.30
239 240 3.458163 CCCTAGTTCCAGCGCCGA 61.458 66.667 2.29 0.00 0.00 5.54
241 242 4.096003 TGCCCTAGTTCCAGCGCC 62.096 66.667 2.29 0.00 0.00 6.53
242 243 2.512515 CTGCCCTAGTTCCAGCGC 60.513 66.667 0.00 0.00 0.00 5.92
243 244 1.690219 ATCCTGCCCTAGTTCCAGCG 61.690 60.000 0.00 0.00 0.00 5.18
244 245 0.107643 GATCCTGCCCTAGTTCCAGC 59.892 60.000 0.00 0.00 0.00 4.85
245 246 0.390860 CGATCCTGCCCTAGTTCCAG 59.609 60.000 0.00 0.00 0.00 3.86
246 247 1.686325 GCGATCCTGCCCTAGTTCCA 61.686 60.000 0.00 0.00 0.00 3.53
247 248 1.069935 GCGATCCTGCCCTAGTTCC 59.930 63.158 0.00 0.00 0.00 3.62
248 249 0.249657 CAGCGATCCTGCCCTAGTTC 60.250 60.000 0.00 0.00 34.21 3.01
249 250 0.687757 TCAGCGATCCTGCCCTAGTT 60.688 55.000 6.38 0.00 41.50 2.24
250 251 0.470833 ATCAGCGATCCTGCCCTAGT 60.471 55.000 6.38 0.00 41.50 2.57
251 252 1.203523 GTATCAGCGATCCTGCCCTAG 59.796 57.143 6.38 0.00 41.50 3.02
252 253 1.257743 GTATCAGCGATCCTGCCCTA 58.742 55.000 6.38 0.00 41.50 3.53
253 254 1.810606 CGTATCAGCGATCCTGCCCT 61.811 60.000 6.38 0.00 41.50 5.19
254 255 1.373497 CGTATCAGCGATCCTGCCC 60.373 63.158 6.38 0.00 41.50 5.36
255 256 0.941463 CACGTATCAGCGATCCTGCC 60.941 60.000 6.38 0.00 41.50 4.85
256 257 0.941463 CCACGTATCAGCGATCCTGC 60.941 60.000 6.38 0.00 41.50 4.85
257 258 0.319040 CCCACGTATCAGCGATCCTG 60.319 60.000 5.18 5.18 43.17 3.86
258 259 0.467474 TCCCACGTATCAGCGATCCT 60.467 55.000 0.00 0.00 35.59 3.24
259 260 0.039074 CTCCCACGTATCAGCGATCC 60.039 60.000 0.00 0.00 35.59 3.36
260 261 0.039074 CCTCCCACGTATCAGCGATC 60.039 60.000 0.00 0.00 35.59 3.69
261 262 0.755698 ACCTCCCACGTATCAGCGAT 60.756 55.000 0.00 0.00 35.59 4.58
262 263 1.379443 ACCTCCCACGTATCAGCGA 60.379 57.895 0.00 0.00 35.59 4.93
263 264 1.226974 CACCTCCCACGTATCAGCG 60.227 63.158 0.00 0.00 37.94 5.18
264 265 1.144057 CCACCTCCCACGTATCAGC 59.856 63.158 0.00 0.00 0.00 4.26
265 266 0.686441 TCCCACCTCCCACGTATCAG 60.686 60.000 0.00 0.00 0.00 2.90
266 267 0.252330 TTCCCACCTCCCACGTATCA 60.252 55.000 0.00 0.00 0.00 2.15
267 268 1.129058 ATTCCCACCTCCCACGTATC 58.871 55.000 0.00 0.00 0.00 2.24
268 269 0.837272 CATTCCCACCTCCCACGTAT 59.163 55.000 0.00 0.00 0.00 3.06
269 270 0.252330 TCATTCCCACCTCCCACGTA 60.252 55.000 0.00 0.00 0.00 3.57
270 271 1.537889 TCATTCCCACCTCCCACGT 60.538 57.895 0.00 0.00 0.00 4.49
271 272 1.221840 CTCATTCCCACCTCCCACG 59.778 63.158 0.00 0.00 0.00 4.94
272 273 0.914417 TCCTCATTCCCACCTCCCAC 60.914 60.000 0.00 0.00 0.00 4.61
273 274 0.914417 GTCCTCATTCCCACCTCCCA 60.914 60.000 0.00 0.00 0.00 4.37
274 275 1.915983 GTCCTCATTCCCACCTCCC 59.084 63.158 0.00 0.00 0.00 4.30
275 276 0.976073 TCGTCCTCATTCCCACCTCC 60.976 60.000 0.00 0.00 0.00 4.30
276 277 0.902531 TTCGTCCTCATTCCCACCTC 59.097 55.000 0.00 0.00 0.00 3.85
277 278 1.358152 TTTCGTCCTCATTCCCACCT 58.642 50.000 0.00 0.00 0.00 4.00
278 279 2.194201 TTTTCGTCCTCATTCCCACC 57.806 50.000 0.00 0.00 0.00 4.61
296 297 5.885449 TTGTCCCATCAAACCTGATTTTT 57.115 34.783 0.00 0.00 40.49 1.94
297 298 5.885449 TTTGTCCCATCAAACCTGATTTT 57.115 34.783 0.00 0.00 40.49 1.82
298 299 5.885449 TTTTGTCCCATCAAACCTGATTT 57.115 34.783 0.00 0.00 40.49 2.17
299 300 7.738437 ATATTTTGTCCCATCAAACCTGATT 57.262 32.000 0.00 0.00 40.49 2.57
300 301 8.695456 GTTATATTTTGTCCCATCAAACCTGAT 58.305 33.333 0.00 0.00 43.40 2.90
301 302 7.123547 GGTTATATTTTGTCCCATCAAACCTGA 59.876 37.037 0.00 0.00 37.10 3.86
302 303 7.264947 GGTTATATTTTGTCCCATCAAACCTG 58.735 38.462 0.00 0.00 37.10 4.00
303 304 6.096282 CGGTTATATTTTGTCCCATCAAACCT 59.904 38.462 0.00 0.00 37.10 3.50
304 305 6.095720 TCGGTTATATTTTGTCCCATCAAACC 59.904 38.462 0.00 0.00 37.10 3.27
305 306 7.090953 TCGGTTATATTTTGTCCCATCAAAC 57.909 36.000 0.00 0.00 37.10 2.93
306 307 7.558081 TCATCGGTTATATTTTGTCCCATCAAA 59.442 33.333 0.00 0.00 35.83 2.69
307 308 7.057264 TCATCGGTTATATTTTGTCCCATCAA 58.943 34.615 0.00 0.00 0.00 2.57
308 309 6.596621 TCATCGGTTATATTTTGTCCCATCA 58.403 36.000 0.00 0.00 0.00 3.07
309 310 7.360361 GTTCATCGGTTATATTTTGTCCCATC 58.640 38.462 0.00 0.00 0.00 3.51
310 311 6.017440 CGTTCATCGGTTATATTTTGTCCCAT 60.017 38.462 0.00 0.00 35.71 4.00
311 312 5.294799 CGTTCATCGGTTATATTTTGTCCCA 59.705 40.000 0.00 0.00 35.71 4.37
312 313 5.524646 TCGTTCATCGGTTATATTTTGTCCC 59.475 40.000 0.00 0.00 40.32 4.46
313 314 6.592798 TCGTTCATCGGTTATATTTTGTCC 57.407 37.500 0.00 0.00 40.32 4.02
314 315 7.844653 GTCTTCGTTCATCGGTTATATTTTGTC 59.155 37.037 0.00 0.00 40.32 3.18
315 316 7.548075 AGTCTTCGTTCATCGGTTATATTTTGT 59.452 33.333 0.00 0.00 40.32 2.83
316 317 7.906160 AGTCTTCGTTCATCGGTTATATTTTG 58.094 34.615 0.00 0.00 40.32 2.44
317 318 9.590451 TTAGTCTTCGTTCATCGGTTATATTTT 57.410 29.630 0.00 0.00 40.32 1.82
318 319 9.028185 GTTAGTCTTCGTTCATCGGTTATATTT 57.972 33.333 0.00 0.00 40.32 1.40
319 320 8.192774 TGTTAGTCTTCGTTCATCGGTTATATT 58.807 33.333 0.00 0.00 40.32 1.28
320 321 7.709947 TGTTAGTCTTCGTTCATCGGTTATAT 58.290 34.615 0.00 0.00 40.32 0.86
321 322 7.087409 TGTTAGTCTTCGTTCATCGGTTATA 57.913 36.000 0.00 0.00 40.32 0.98
322 323 5.957798 TGTTAGTCTTCGTTCATCGGTTAT 58.042 37.500 0.00 0.00 40.32 1.89
323 324 5.375417 TGTTAGTCTTCGTTCATCGGTTA 57.625 39.130 0.00 0.00 40.32 2.85
324 325 4.247267 TGTTAGTCTTCGTTCATCGGTT 57.753 40.909 0.00 0.00 40.32 4.44
325 326 3.928727 TGTTAGTCTTCGTTCATCGGT 57.071 42.857 0.00 0.00 40.32 4.69
326 327 4.090066 CAGTTGTTAGTCTTCGTTCATCGG 59.910 45.833 0.00 0.00 40.32 4.18
327 328 4.915667 TCAGTTGTTAGTCTTCGTTCATCG 59.084 41.667 0.00 0.00 41.41 3.84
328 329 6.088350 GTCTCAGTTGTTAGTCTTCGTTCATC 59.912 42.308 0.00 0.00 0.00 2.92
329 330 5.921408 GTCTCAGTTGTTAGTCTTCGTTCAT 59.079 40.000 0.00 0.00 0.00 2.57
330 331 5.163591 TGTCTCAGTTGTTAGTCTTCGTTCA 60.164 40.000 0.00 0.00 0.00 3.18
331 332 5.279384 TGTCTCAGTTGTTAGTCTTCGTTC 58.721 41.667 0.00 0.00 0.00 3.95
332 333 5.258456 TGTCTCAGTTGTTAGTCTTCGTT 57.742 39.130 0.00 0.00 0.00 3.85
333 334 4.913335 TGTCTCAGTTGTTAGTCTTCGT 57.087 40.909 0.00 0.00 0.00 3.85
334 335 6.528423 CCTAATGTCTCAGTTGTTAGTCTTCG 59.472 42.308 0.00 0.00 0.00 3.79
335 336 7.603651 TCCTAATGTCTCAGTTGTTAGTCTTC 58.396 38.462 0.00 0.00 0.00 2.87
336 337 7.233757 ACTCCTAATGTCTCAGTTGTTAGTCTT 59.766 37.037 0.00 0.00 0.00 3.01
337 338 6.722129 ACTCCTAATGTCTCAGTTGTTAGTCT 59.278 38.462 0.00 0.00 0.00 3.24
338 339 6.926313 ACTCCTAATGTCTCAGTTGTTAGTC 58.074 40.000 0.00 0.00 0.00 2.59
339 340 6.919775 ACTCCTAATGTCTCAGTTGTTAGT 57.080 37.500 0.00 0.00 0.00 2.24
340 341 8.282455 TCTACTCCTAATGTCTCAGTTGTTAG 57.718 38.462 0.00 0.00 0.00 2.34
341 342 8.107729 TCTCTACTCCTAATGTCTCAGTTGTTA 58.892 37.037 0.00 0.00 0.00 2.41
342 343 6.948886 TCTCTACTCCTAATGTCTCAGTTGTT 59.051 38.462 0.00 0.00 0.00 2.83
343 344 6.486056 TCTCTACTCCTAATGTCTCAGTTGT 58.514 40.000 0.00 0.00 0.00 3.32
344 345 7.581213 ATCTCTACTCCTAATGTCTCAGTTG 57.419 40.000 0.00 0.00 0.00 3.16
345 346 9.875708 AATATCTCTACTCCTAATGTCTCAGTT 57.124 33.333 0.00 0.00 0.00 3.16
346 347 9.515226 GAATATCTCTACTCCTAATGTCTCAGT 57.485 37.037 0.00 0.00 0.00 3.41
347 348 9.513906 TGAATATCTCTACTCCTAATGTCTCAG 57.486 37.037 0.00 0.00 0.00 3.35
350 351 8.748412 GCATGAATATCTCTACTCCTAATGTCT 58.252 37.037 0.00 0.00 0.00 3.41
351 352 8.748412 AGCATGAATATCTCTACTCCTAATGTC 58.252 37.037 0.00 0.00 0.00 3.06
352 353 8.663209 AGCATGAATATCTCTACTCCTAATGT 57.337 34.615 0.00 0.00 0.00 2.71
355 356 9.588096 TGTTAGCATGAATATCTCTACTCCTAA 57.412 33.333 0.00 0.00 0.00 2.69
356 357 9.237187 CTGTTAGCATGAATATCTCTACTCCTA 57.763 37.037 0.00 0.00 0.00 2.94
357 358 7.728083 ACTGTTAGCATGAATATCTCTACTCCT 59.272 37.037 0.00 0.00 0.00 3.69
358 359 7.891561 ACTGTTAGCATGAATATCTCTACTCC 58.108 38.462 0.00 0.00 0.00 3.85
359 360 8.572185 TGACTGTTAGCATGAATATCTCTACTC 58.428 37.037 0.00 0.00 0.00 2.59
360 361 8.470657 TGACTGTTAGCATGAATATCTCTACT 57.529 34.615 0.00 0.00 0.00 2.57
361 362 9.138062 CATGACTGTTAGCATGAATATCTCTAC 57.862 37.037 0.00 0.00 43.43 2.59
362 363 8.309656 CCATGACTGTTAGCATGAATATCTCTA 58.690 37.037 8.94 0.00 43.43 2.43
363 364 7.015974 TCCATGACTGTTAGCATGAATATCTCT 59.984 37.037 8.94 0.00 43.43 3.10
364 365 7.157347 TCCATGACTGTTAGCATGAATATCTC 58.843 38.462 8.94 0.00 43.43 2.75
365 366 7.071069 TCCATGACTGTTAGCATGAATATCT 57.929 36.000 8.94 0.00 43.43 1.98
366 367 7.443575 ACTTCCATGACTGTTAGCATGAATATC 59.556 37.037 8.94 0.00 43.43 1.63
386 387 2.575532 CTGAGCCAAGTCAAACTTCCA 58.424 47.619 0.00 0.00 36.03 3.53
411 412 7.120579 ACGATGAGCTATTTGGTATCACAAAAA 59.879 33.333 0.00 0.00 42.91 1.94
416 417 5.050490 ACACGATGAGCTATTTGGTATCAC 58.950 41.667 0.00 0.00 0.00 3.06
615 626 7.626028 GCAAGAGAAGATTAAGGAAGAAGCAAG 60.626 40.741 0.00 0.00 0.00 4.01
713 732 3.505680 GGCACAAACAAGATGATGGTGTA 59.494 43.478 0.00 0.00 0.00 2.90
776 795 0.670162 CTTTGTGTCCAAGCCACCAG 59.330 55.000 0.00 0.00 31.71 4.00
803 822 2.732597 CGTTAGTGTGCTCTAGCTGGTC 60.733 54.545 0.00 0.00 42.66 4.02
881 903 1.788886 GGTAGAACGTTCCGTGTCAAC 59.211 52.381 24.22 10.88 39.99 3.18
890 912 6.655078 TGGTTATATAGGGGTAGAACGTTC 57.345 41.667 20.71 20.71 28.95 3.95
942 967 0.339859 TGAGAGGGAGGGTAGTGCAT 59.660 55.000 0.00 0.00 0.00 3.96
946 971 2.004589 AGACTTGAGAGGGAGGGTAGT 58.995 52.381 0.00 0.00 0.00 2.73
948 973 2.000803 TGAGACTTGAGAGGGAGGGTA 58.999 52.381 0.00 0.00 0.00 3.69
949 974 0.787084 TGAGACTTGAGAGGGAGGGT 59.213 55.000 0.00 0.00 0.00 4.34
952 977 3.948473 TCGTATTGAGACTTGAGAGGGAG 59.052 47.826 0.00 0.00 0.00 4.30
963 988 4.092091 CAGAAAGCTTGGTCGTATTGAGAC 59.908 45.833 0.00 0.00 37.86 3.36
973 998 1.248486 GGTTCCCAGAAAGCTTGGTC 58.752 55.000 0.00 0.00 0.00 4.02
1044 1072 4.380867 GCCAGTAATGCAAGCAGTAACAAT 60.381 41.667 3.61 0.00 0.00 2.71
1226 1254 2.989824 CGTATCCCGCGATCCCCT 60.990 66.667 8.23 0.00 0.00 4.79
1299 1327 6.192234 TCTATGTTCTCACCGAAGTAGAAC 57.808 41.667 7.35 7.35 45.99 3.01
1311 1339 4.326826 CTTTGCCCACTTCTATGTTCTCA 58.673 43.478 0.00 0.00 0.00 3.27
1318 1346 0.394352 CGCCCTTTGCCCACTTCTAT 60.394 55.000 0.00 0.00 36.24 1.98
1322 1350 2.597510 GACGCCCTTTGCCCACTT 60.598 61.111 0.00 0.00 36.24 3.16
1500 1528 4.796231 GTGTCGCCGGAGTCGCAT 62.796 66.667 5.05 0.00 34.56 4.73
1582 1618 1.358725 CGGCGTGATCATTCAACGGT 61.359 55.000 0.00 0.00 32.48 4.83
1602 1638 2.179589 GATGCTGTTAACTTGCATGCG 58.820 47.619 29.90 1.59 45.90 4.73
1617 1653 4.101448 GCCACGTGGAGGGATGCT 62.101 66.667 38.30 0.00 37.39 3.79
1634 1670 6.043327 TCGATGGTAAATAACTTTGATGCG 57.957 37.500 0.00 0.00 0.00 4.73
1728 1764 9.433153 CGAGTAATGGAGTATATACTACTGTCA 57.567 37.037 22.91 13.17 38.02 3.58
1736 1772 8.194433 TCATCGTCGAGTAATGGAGTATATAC 57.806 38.462 4.60 4.60 0.00 1.47
1737 1773 8.663025 GTTCATCGTCGAGTAATGGAGTATATA 58.337 37.037 0.00 0.00 0.00 0.86
1738 1774 7.528307 GTTCATCGTCGAGTAATGGAGTATAT 58.472 38.462 0.00 0.00 0.00 0.86
1739 1775 6.347160 CGTTCATCGTCGAGTAATGGAGTATA 60.347 42.308 0.00 0.00 34.52 1.47
1741 1777 4.260497 CGTTCATCGTCGAGTAATGGAGTA 60.260 45.833 0.00 0.00 34.52 2.59
1742 1778 3.487042 CGTTCATCGTCGAGTAATGGAGT 60.487 47.826 0.00 0.00 34.52 3.85
1743 1779 3.036633 CGTTCATCGTCGAGTAATGGAG 58.963 50.000 0.00 0.00 34.52 3.86
1896 1946 2.034053 GGTCGATTTGGTGAAGTTTGCA 59.966 45.455 0.00 0.00 0.00 4.08
1918 1968 0.901827 ACATGGTGATCTGCGGTGTA 59.098 50.000 0.00 0.00 0.00 2.90
1919 1969 0.391661 GACATGGTGATCTGCGGTGT 60.392 55.000 0.00 0.00 0.00 4.16
2308 2373 3.727258 CATGTCTTCCCCGGGGCA 61.727 66.667 36.68 26.85 34.68 5.36
2473 2538 0.669318 TCTCGCCACGTTAGCTTTGG 60.669 55.000 0.00 0.00 0.00 3.28
2474 2541 1.359848 ATCTCGCCACGTTAGCTTTG 58.640 50.000 0.00 0.00 0.00 2.77
2475 2542 2.953466 TATCTCGCCACGTTAGCTTT 57.047 45.000 0.00 0.00 0.00 3.51
2485 2552 6.932400 ACGTTATTTCCAAATATATCTCGCCA 59.068 34.615 0.00 0.00 31.47 5.69
2551 2618 7.706100 GTTATGAACTATGGTACCCCAAAAA 57.294 36.000 10.07 0.00 46.04 1.94


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

AutoCloner maintained by Alex Coulton.