Multiple sequence alignment - TraesCS2A01G035100

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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 TraesCS2A01G035100 chr2A 100.000 1783 0 0 1 1783 15268988 15270770 0.000000e+00 3293.0
1 TraesCS2A01G035100 chr2A 100.000 257 0 0 2125 2381 15271112 15271368 2.140000e-130 475.0
2 TraesCS2A01G035100 chr2B 93.895 1425 71 12 350 1765 23877454 23878871 0.000000e+00 2135.0
3 TraesCS2A01G035100 chr2B 85.656 244 26 6 2125 2363 23878909 23879148 5.080000e-62 248.0
4 TraesCS2A01G035100 chr2D 92.926 1442 77 14 350 1775 13227999 13229431 0.000000e+00 2074.0
5 TraesCS2A01G035100 chr2D 88.672 256 25 2 2125 2379 13229498 13229750 2.300000e-80 309.0
6 TraesCS2A01G035100 chr2D 85.417 144 21 0 132 275 502573637 502573780 1.470000e-32 150.0
7 TraesCS2A01G035100 chr3D 96.615 325 11 0 1 325 584164832 584165156 7.490000e-150 540.0
8 TraesCS2A01G035100 chr5D 95.692 325 14 0 1 325 439207851 439207527 7.540000e-145 523.0
9 TraesCS2A01G035100 chr5D 95.077 325 16 0 1 325 320451019 320450695 1.630000e-141 512.0
10 TraesCS2A01G035100 chrUn 93.538 325 21 0 1 325 287942760 287942436 3.560000e-133 484.0
11 TraesCS2A01G035100 chrUn 93.538 325 21 0 1 325 287948829 287948505 3.560000e-133 484.0
12 TraesCS2A01G035100 chrUn 87.500 256 21 3 82 326 93791041 93791296 3.870000e-73 285.0
13 TraesCS2A01G035100 chr7D 84.188 234 22 7 104 325 72718488 72718258 1.850000e-51 213.0
14 TraesCS2A01G035100 chr4D 81.783 258 36 10 1141 1391 323354816 323354563 3.100000e-49 206.0
15 TraesCS2A01G035100 chr4B 81.526 249 36 9 1141 1383 403624662 403624418 1.870000e-46 196.0
16 TraesCS2A01G035100 chr4A 80.769 260 38 11 1141 1392 148757869 148758124 2.420000e-45 193.0
17 TraesCS2A01G035100 chr1A 84.483 174 18 8 158 325 63059149 63058979 1.890000e-36 163.0
18 TraesCS2A01G035100 chr1B 97.143 35 1 0 103 137 566691043 566691009 2.560000e-05 60.2


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 TraesCS2A01G035100 chr2A 15268988 15271368 2380 False 1884.0 3293 100.0000 1 2381 2 chr2A.!!$F1 2380
1 TraesCS2A01G035100 chr2B 23877454 23879148 1694 False 1191.5 2135 89.7755 350 2363 2 chr2B.!!$F1 2013
2 TraesCS2A01G035100 chr2D 13227999 13229750 1751 False 1191.5 2074 90.7990 350 2379 2 chr2D.!!$F2 2029

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
136 137 0.026803 GATCAGATCAACAACGCCGC 59.973 55.0 5.44 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1411 0.250209 CCATCCGCCATCCAGAAGAG 60.25 60.0 0.0 0.0 0.0 2.85 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 2.203070 CCCATAGGCCAGCACGAC 60.203 66.667 5.01 0.00 0.00 4.34
18 19 2.586079 CCATAGGCCAGCACGACG 60.586 66.667 5.01 0.00 0.00 5.12
19 20 3.264897 CATAGGCCAGCACGACGC 61.265 66.667 5.01 0.00 42.91 5.19
20 21 4.530857 ATAGGCCAGCACGACGCC 62.531 66.667 5.01 0.00 44.04 5.68
25 26 4.680237 CCAGCACGACGCCAAGGA 62.680 66.667 0.00 0.00 44.04 3.36
26 27 3.114616 CAGCACGACGCCAAGGAG 61.115 66.667 0.00 0.00 44.04 3.69
27 28 3.303135 AGCACGACGCCAAGGAGA 61.303 61.111 0.00 0.00 44.04 3.71
28 29 3.112709 GCACGACGCCAAGGAGAC 61.113 66.667 0.00 0.00 32.94 3.36
29 30 2.805353 CACGACGCCAAGGAGACG 60.805 66.667 12.20 12.20 38.64 4.18
30 31 4.719369 ACGACGCCAAGGAGACGC 62.719 66.667 13.44 0.00 36.75 5.19
31 32 4.421479 CGACGCCAAGGAGACGCT 62.421 66.667 1.91 0.00 0.00 5.07
32 33 2.811317 GACGCCAAGGAGACGCTG 60.811 66.667 0.00 0.00 0.00 5.18
33 34 3.575351 GACGCCAAGGAGACGCTGT 62.575 63.158 0.00 0.00 0.00 4.40
34 35 2.811317 CGCCAAGGAGACGCTGTC 60.811 66.667 0.00 1.15 0.00 3.51
35 36 2.811317 GCCAAGGAGACGCTGTCG 60.811 66.667 0.00 0.00 37.67 4.35
55 56 3.612251 GCCATGCCAGCAGAATGT 58.388 55.556 0.00 0.00 39.31 2.71
56 57 1.436336 GCCATGCCAGCAGAATGTC 59.564 57.895 0.00 0.00 39.31 3.06
57 58 1.317431 GCCATGCCAGCAGAATGTCA 61.317 55.000 0.00 0.00 39.31 3.58
58 59 0.454600 CCATGCCAGCAGAATGTCAC 59.545 55.000 0.00 0.00 39.31 3.67
59 60 0.098200 CATGCCAGCAGAATGTCACG 59.902 55.000 0.00 0.00 39.31 4.35
60 61 1.651240 ATGCCAGCAGAATGTCACGC 61.651 55.000 0.00 0.00 39.31 5.34
61 62 2.037136 GCCAGCAGAATGTCACGCT 61.037 57.895 0.00 0.00 39.31 5.07
62 63 1.975363 GCCAGCAGAATGTCACGCTC 61.975 60.000 0.00 0.00 39.31 5.03
63 64 0.671472 CCAGCAGAATGTCACGCTCA 60.671 55.000 0.00 0.00 39.31 4.26
64 65 1.150827 CAGCAGAATGTCACGCTCAA 58.849 50.000 0.00 0.00 39.31 3.02
65 66 1.128136 CAGCAGAATGTCACGCTCAAG 59.872 52.381 0.00 0.00 39.31 3.02
66 67 0.179205 GCAGAATGTCACGCTCAAGC 60.179 55.000 0.00 0.00 39.31 4.01
67 68 1.150827 CAGAATGTCACGCTCAAGCA 58.849 50.000 2.50 0.00 42.21 3.91
68 69 1.136141 CAGAATGTCACGCTCAAGCAC 60.136 52.381 2.50 0.00 42.21 4.40
69 70 0.867746 GAATGTCACGCTCAAGCACA 59.132 50.000 2.50 0.00 42.21 4.57
70 71 0.870393 AATGTCACGCTCAAGCACAG 59.130 50.000 2.50 0.00 42.21 3.66
71 72 0.033920 ATGTCACGCTCAAGCACAGA 59.966 50.000 2.50 0.00 42.21 3.41
72 73 0.033920 TGTCACGCTCAAGCACAGAT 59.966 50.000 2.50 0.00 42.21 2.90
73 74 0.441533 GTCACGCTCAAGCACAGATG 59.558 55.000 2.50 0.00 42.21 2.90
74 75 0.671472 TCACGCTCAAGCACAGATGG 60.671 55.000 2.50 0.00 42.21 3.51
75 76 2.037136 ACGCTCAAGCACAGATGGC 61.037 57.895 2.50 0.00 42.21 4.40
76 77 2.758089 CGCTCAAGCACAGATGGCC 61.758 63.158 0.00 0.00 42.21 5.36
77 78 1.676635 GCTCAAGCACAGATGGCCA 60.677 57.895 8.56 8.56 41.59 5.36
78 79 1.930908 GCTCAAGCACAGATGGCCAC 61.931 60.000 8.16 1.58 41.59 5.01
79 80 1.642037 CTCAAGCACAGATGGCCACG 61.642 60.000 8.16 1.38 0.00 4.94
80 81 3.058160 AAGCACAGATGGCCACGC 61.058 61.111 8.16 6.16 0.00 5.34
98 99 4.170062 CGGCGATGCAGCAACCTG 62.170 66.667 0.00 0.00 42.13 4.00
99 100 3.058160 GGCGATGCAGCAACCTGT 61.058 61.111 1.53 0.00 41.26 4.00
100 101 2.482374 GCGATGCAGCAACCTGTC 59.518 61.111 1.53 0.00 41.26 3.51
101 102 2.780643 CGATGCAGCAACCTGTCG 59.219 61.111 1.53 0.00 41.26 4.35
102 103 2.743752 CGATGCAGCAACCTGTCGG 61.744 63.158 1.53 0.00 41.26 4.79
103 104 1.375908 GATGCAGCAACCTGTCGGA 60.376 57.895 0.00 0.00 41.26 4.55
104 105 1.364626 GATGCAGCAACCTGTCGGAG 61.365 60.000 0.00 0.00 41.26 4.63
105 106 3.426568 GCAGCAACCTGTCGGAGC 61.427 66.667 0.00 0.00 41.26 4.70
106 107 2.743928 CAGCAACCTGTCGGAGCC 60.744 66.667 0.00 0.00 36.15 4.70
107 108 4.379243 AGCAACCTGTCGGAGCCG 62.379 66.667 1.74 1.74 36.15 5.52
108 109 4.681978 GCAACCTGTCGGAGCCGT 62.682 66.667 8.96 0.00 40.74 5.68
109 110 2.432628 CAACCTGTCGGAGCCGTC 60.433 66.667 8.96 3.93 40.74 4.79
110 111 3.692406 AACCTGTCGGAGCCGTCC 61.692 66.667 8.96 1.92 40.74 4.79
111 112 4.988716 ACCTGTCGGAGCCGTCCA 62.989 66.667 8.96 6.37 44.18 4.02
112 113 3.691342 CCTGTCGGAGCCGTCCAA 61.691 66.667 8.96 0.00 44.18 3.53
113 114 2.125912 CTGTCGGAGCCGTCCAAG 60.126 66.667 8.96 0.00 44.18 3.61
114 115 4.373116 TGTCGGAGCCGTCCAAGC 62.373 66.667 8.96 0.00 44.18 4.01
126 127 2.914908 TCCAAGCCGGATCAGATCA 58.085 52.632 5.05 0.00 39.64 2.92
127 128 1.203237 TCCAAGCCGGATCAGATCAA 58.797 50.000 5.05 0.00 39.64 2.57
128 129 1.134401 TCCAAGCCGGATCAGATCAAC 60.134 52.381 5.05 1.00 39.64 3.18
129 130 1.407299 CCAAGCCGGATCAGATCAACA 60.407 52.381 5.05 0.00 36.56 3.33
130 131 2.358957 CAAGCCGGATCAGATCAACAA 58.641 47.619 5.05 0.00 0.00 2.83
131 132 2.029838 AGCCGGATCAGATCAACAAC 57.970 50.000 5.05 0.00 0.00 3.32
132 133 0.652592 GCCGGATCAGATCAACAACG 59.347 55.000 5.05 5.96 0.00 4.10
133 134 0.652592 CCGGATCAGATCAACAACGC 59.347 55.000 12.66 0.00 0.00 4.84
134 135 0.652592 CGGATCAGATCAACAACGCC 59.347 55.000 12.66 0.00 0.00 5.68
135 136 0.652592 GGATCAGATCAACAACGCCG 59.347 55.000 12.66 0.00 0.00 6.46
136 137 0.026803 GATCAGATCAACAACGCCGC 59.973 55.000 5.44 0.00 0.00 6.53
137 138 0.391661 ATCAGATCAACAACGCCGCT 60.392 50.000 0.00 0.00 0.00 5.52
138 139 1.133253 CAGATCAACAACGCCGCTG 59.867 57.895 0.00 0.00 0.00 5.18
139 140 2.202349 GATCAACAACGCCGCTGC 60.202 61.111 0.00 0.00 0.00 5.25
140 141 2.669569 ATCAACAACGCCGCTGCT 60.670 55.556 0.00 0.00 34.43 4.24
141 142 2.568935 GATCAACAACGCCGCTGCTC 62.569 60.000 0.00 0.00 34.43 4.26
142 143 3.349006 CAACAACGCCGCTGCTCT 61.349 61.111 0.00 0.00 34.43 4.09
143 144 3.349006 AACAACGCCGCTGCTCTG 61.349 61.111 0.00 0.00 34.43 3.35
152 153 3.552839 GCTGCTCTGCGCGAGAAG 61.553 66.667 26.02 25.14 46.73 2.85
153 154 3.552839 CTGCTCTGCGCGAGAAGC 61.553 66.667 26.02 20.19 38.58 3.86
154 155 3.986030 CTGCTCTGCGCGAGAAGCT 62.986 63.158 26.02 0.00 38.58 3.74
155 156 3.253930 GCTCTGCGCGAGAAGCTC 61.254 66.667 26.02 9.67 45.59 4.09
175 176 4.680237 CGCCGTGCCTGAGAACCA 62.680 66.667 0.00 0.00 0.00 3.67
176 177 3.050275 GCCGTGCCTGAGAACCAC 61.050 66.667 0.00 0.00 0.00 4.16
177 178 2.358737 CCGTGCCTGAGAACCACC 60.359 66.667 0.00 0.00 0.00 4.61
178 179 2.358737 CGTGCCTGAGAACCACCC 60.359 66.667 0.00 0.00 0.00 4.61
179 180 2.836154 GTGCCTGAGAACCACCCA 59.164 61.111 0.00 0.00 0.00 4.51
180 181 1.600916 GTGCCTGAGAACCACCCAC 60.601 63.158 0.00 0.00 0.00 4.61
181 182 2.358737 GCCTGAGAACCACCCACG 60.359 66.667 0.00 0.00 0.00 4.94
182 183 2.358737 CCTGAGAACCACCCACGC 60.359 66.667 0.00 0.00 0.00 5.34
183 184 2.358737 CTGAGAACCACCCACGCC 60.359 66.667 0.00 0.00 0.00 5.68
184 185 4.308458 TGAGAACCACCCACGCCG 62.308 66.667 0.00 0.00 0.00 6.46
202 203 4.796231 CGAGCAAGGTCCCCGTCG 62.796 72.222 0.00 0.00 0.00 5.12
262 263 4.214327 GCGGCGGAGAGGAGGAAG 62.214 72.222 9.78 0.00 0.00 3.46
263 264 3.532155 CGGCGGAGAGGAGGAAGG 61.532 72.222 0.00 0.00 0.00 3.46
264 265 3.157949 GGCGGAGAGGAGGAAGGG 61.158 72.222 0.00 0.00 0.00 3.95
265 266 2.042843 GCGGAGAGGAGGAAGGGA 60.043 66.667 0.00 0.00 0.00 4.20
266 267 1.686110 GCGGAGAGGAGGAAGGGAA 60.686 63.158 0.00 0.00 0.00 3.97
267 268 1.681486 GCGGAGAGGAGGAAGGGAAG 61.681 65.000 0.00 0.00 0.00 3.46
268 269 0.033011 CGGAGAGGAGGAAGGGAAGA 60.033 60.000 0.00 0.00 0.00 2.87
269 270 1.412361 CGGAGAGGAGGAAGGGAAGAT 60.412 57.143 0.00 0.00 0.00 2.40
270 271 2.770447 GGAGAGGAGGAAGGGAAGATT 58.230 52.381 0.00 0.00 0.00 2.40
271 272 3.119319 GGAGAGGAGGAAGGGAAGATTT 58.881 50.000 0.00 0.00 0.00 2.17
272 273 3.118075 GGAGAGGAGGAAGGGAAGATTTG 60.118 52.174 0.00 0.00 0.00 2.32
273 274 3.521531 GAGAGGAGGAAGGGAAGATTTGT 59.478 47.826 0.00 0.00 0.00 2.83
274 275 3.265479 AGAGGAGGAAGGGAAGATTTGTG 59.735 47.826 0.00 0.00 0.00 3.33
275 276 2.989571 AGGAGGAAGGGAAGATTTGTGT 59.010 45.455 0.00 0.00 0.00 3.72
276 277 3.084786 GGAGGAAGGGAAGATTTGTGTG 58.915 50.000 0.00 0.00 0.00 3.82
277 278 3.084786 GAGGAAGGGAAGATTTGTGTGG 58.915 50.000 0.00 0.00 0.00 4.17
278 279 1.546029 GGAAGGGAAGATTTGTGTGGC 59.454 52.381 0.00 0.00 0.00 5.01
279 280 1.200020 GAAGGGAAGATTTGTGTGGCG 59.800 52.381 0.00 0.00 0.00 5.69
280 281 0.609131 AGGGAAGATTTGTGTGGCGG 60.609 55.000 0.00 0.00 0.00 6.13
281 282 1.212751 GGAAGATTTGTGTGGCGGC 59.787 57.895 0.00 0.00 0.00 6.53
282 283 1.154225 GAAGATTTGTGTGGCGGCG 60.154 57.895 0.51 0.51 0.00 6.46
283 284 2.527547 GAAGATTTGTGTGGCGGCGG 62.528 60.000 9.78 0.00 0.00 6.13
284 285 4.776647 GATTTGTGTGGCGGCGGC 62.777 66.667 27.76 27.76 38.90 6.53
286 287 3.910914 ATTTGTGTGGCGGCGGCTA 62.911 57.895 33.21 19.85 39.81 3.93
297 298 4.091939 GCGGCTAGGGTTCGGGTT 62.092 66.667 0.00 0.00 0.00 4.11
298 299 2.125269 CGGCTAGGGTTCGGGTTG 60.125 66.667 0.00 0.00 0.00 3.77
299 300 2.437895 GGCTAGGGTTCGGGTTGC 60.438 66.667 0.00 0.00 0.00 4.17
300 301 2.437895 GCTAGGGTTCGGGTTGCC 60.438 66.667 0.00 0.00 0.00 4.52
301 302 3.074281 CTAGGGTTCGGGTTGCCA 58.926 61.111 0.00 0.00 0.00 4.92
302 303 1.376812 CTAGGGTTCGGGTTGCCAC 60.377 63.158 0.00 0.00 0.00 5.01
303 304 2.814913 CTAGGGTTCGGGTTGCCACC 62.815 65.000 0.00 0.00 43.37 4.61
329 330 4.446413 CCACACGGGAGCGGTACC 62.446 72.222 5.55 5.55 40.01 3.34
330 331 4.446413 CACACGGGAGCGGTACCC 62.446 72.222 11.07 10.97 43.57 3.69
334 335 4.157120 CGGGAGCGGTACCCCAAG 62.157 72.222 11.07 0.00 44.09 3.61
335 336 3.007323 GGGAGCGGTACCCCAAGT 61.007 66.667 3.85 0.00 42.24 3.16
336 337 1.686800 GGGAGCGGTACCCCAAGTA 60.687 63.158 3.85 0.00 42.24 2.24
337 338 1.683418 GGGAGCGGTACCCCAAGTAG 61.683 65.000 3.85 0.00 42.24 2.57
338 339 0.685458 GGAGCGGTACCCCAAGTAGA 60.685 60.000 6.25 0.00 0.00 2.59
339 340 1.411041 GAGCGGTACCCCAAGTAGAT 58.589 55.000 6.25 0.00 0.00 1.98
340 341 1.340568 GAGCGGTACCCCAAGTAGATC 59.659 57.143 6.25 0.00 0.00 2.75
341 342 1.063114 AGCGGTACCCCAAGTAGATCT 60.063 52.381 6.25 0.00 0.00 2.75
342 343 1.761198 GCGGTACCCCAAGTAGATCTT 59.239 52.381 6.25 0.00 36.75 2.40
343 344 2.223994 GCGGTACCCCAAGTAGATCTTC 60.224 54.545 6.25 0.00 33.63 2.87
344 345 3.028850 CGGTACCCCAAGTAGATCTTCA 58.971 50.000 6.25 0.00 33.63 3.02
345 346 3.181478 CGGTACCCCAAGTAGATCTTCAC 60.181 52.174 6.25 0.00 33.63 3.18
346 347 3.181478 GGTACCCCAAGTAGATCTTCACG 60.181 52.174 0.00 0.00 33.63 4.35
347 348 1.207329 ACCCCAAGTAGATCTTCACGC 59.793 52.381 0.00 0.00 33.63 5.34
348 349 1.482593 CCCCAAGTAGATCTTCACGCT 59.517 52.381 0.00 0.00 33.63 5.07
366 367 7.400599 TCACGCTCTTAGATAGAAGGTTTTA 57.599 36.000 0.00 0.00 30.91 1.52
369 370 8.756864 CACGCTCTTAGATAGAAGGTTTTATTC 58.243 37.037 0.00 0.00 30.91 1.75
387 388 0.605319 TCGGCACTCGCTTGGAAATT 60.605 50.000 0.00 0.00 39.05 1.82
394 395 1.062587 CTCGCTTGGAAATTGGCTACG 59.937 52.381 0.00 0.00 0.00 3.51
405 406 2.163818 TTGGCTACGAACTGACTTGG 57.836 50.000 0.00 0.00 0.00 3.61
450 459 0.043940 ATCTTGGGACCTCTGCTCCT 59.956 55.000 0.00 0.00 0.00 3.69
453 462 1.194781 TTGGGACCTCTGCTCCTCAC 61.195 60.000 0.00 0.00 0.00 3.51
454 463 1.305718 GGGACCTCTGCTCCTCACT 60.306 63.158 0.00 0.00 0.00 3.41
455 464 1.326951 GGGACCTCTGCTCCTCACTC 61.327 65.000 0.00 0.00 0.00 3.51
456 465 1.326951 GGACCTCTGCTCCTCACTCC 61.327 65.000 0.00 0.00 0.00 3.85
457 466 0.324275 GACCTCTGCTCCTCACTCCT 60.324 60.000 0.00 0.00 0.00 3.69
458 467 0.324275 ACCTCTGCTCCTCACTCCTC 60.324 60.000 0.00 0.00 0.00 3.71
459 468 0.324183 CCTCTGCTCCTCACTCCTCA 60.324 60.000 0.00 0.00 0.00 3.86
460 469 1.105457 CTCTGCTCCTCACTCCTCAG 58.895 60.000 0.00 0.00 0.00 3.35
461 470 0.969917 TCTGCTCCTCACTCCTCAGC 60.970 60.000 0.00 0.00 0.00 4.26
462 471 1.228988 TGCTCCTCACTCCTCAGCA 60.229 57.895 0.00 0.00 37.76 4.41
463 472 0.616964 TGCTCCTCACTCCTCAGCAT 60.617 55.000 0.00 0.00 35.17 3.79
464 473 1.342374 TGCTCCTCACTCCTCAGCATA 60.342 52.381 0.00 0.00 35.17 3.14
480 489 7.394641 TCCTCAGCATATCTAAGTATCATTCGT 59.605 37.037 0.00 0.00 0.00 3.85
510 519 5.254901 ACCGATACCAGATGTAGGAGATAC 58.745 45.833 0.00 0.00 31.61 2.24
517 526 4.279671 CCAGATGTAGGAGATACACCAGAC 59.720 50.000 0.00 0.00 47.00 3.51
554 563 1.543802 TCAAACCACATCCAATTCGCC 59.456 47.619 0.00 0.00 0.00 5.54
555 564 1.271934 CAAACCACATCCAATTCGCCA 59.728 47.619 0.00 0.00 0.00 5.69
556 565 1.626686 AACCACATCCAATTCGCCAA 58.373 45.000 0.00 0.00 0.00 4.52
557 566 1.626686 ACCACATCCAATTCGCCAAA 58.373 45.000 0.00 0.00 0.00 3.28
558 567 1.272212 ACCACATCCAATTCGCCAAAC 59.728 47.619 0.00 0.00 0.00 2.93
559 568 1.404047 CCACATCCAATTCGCCAAACC 60.404 52.381 0.00 0.00 0.00 3.27
561 570 2.094078 CACATCCAATTCGCCAAACCAT 60.094 45.455 0.00 0.00 0.00 3.55
562 571 2.566724 ACATCCAATTCGCCAAACCATT 59.433 40.909 0.00 0.00 0.00 3.16
658 671 1.591158 GAACGCGTTCACAAAGACAGA 59.409 47.619 39.21 0.00 39.31 3.41
690 704 6.471841 TGTCAAAATGAAAATCACACACTTCG 59.528 34.615 0.00 0.00 0.00 3.79
711 725 1.599047 CTCCTCCTGCCAATCGTGT 59.401 57.895 0.00 0.00 0.00 4.49
735 750 5.725362 ACAAGTAGAAAAGATCTTCCTCCG 58.275 41.667 8.78 2.40 39.71 4.63
745 760 3.708220 CTTCCTCCGACGCTCCAGC 62.708 68.421 0.00 0.00 37.78 4.85
771 786 6.070653 TGCTTGCCTGAAAAATATCTCCAATT 60.071 34.615 0.00 0.00 0.00 2.32
789 804 0.952497 TTAGACGAGACGACGTGGCT 60.952 55.000 4.58 0.34 46.52 4.75
841 856 0.948678 GGTGCACGTAAAAGCTTCCA 59.051 50.000 11.45 0.00 0.00 3.53
936 952 6.259387 AGCTATAAATACAAACCTTACCGCAC 59.741 38.462 0.00 0.00 0.00 5.34
963 979 2.095718 GCAGCAACTTGTTACAGCCTAC 60.096 50.000 0.00 0.00 0.00 3.18
1323 1339 3.382832 AAGGACTCCGACCCGCTG 61.383 66.667 0.00 0.00 0.00 5.18
1405 1421 4.261238 CGTACGTGCTAATCTCTTCTGGAT 60.261 45.833 7.22 0.00 0.00 3.41
1413 1429 0.755079 TCTCTTCTGGATGGCGGATG 59.245 55.000 0.00 0.00 0.00 3.51
1442 1458 1.557443 GACGTGGTGTTCTTGGCTCG 61.557 60.000 0.00 0.00 0.00 5.03
1516 1533 4.807304 CGGGATGTATGTAGTAAAAACGCT 59.193 41.667 0.00 0.00 0.00 5.07
1531 1548 5.738619 AAAACGCTCCAAATATTTTCCCT 57.261 34.783 0.00 0.00 0.00 4.20
1606 1623 1.401761 TTATGGATGTGTGCATGGGC 58.598 50.000 0.00 0.00 36.99 5.36
1622 1639 0.601311 GGGCATGATGTAGAGGCGAC 60.601 60.000 0.00 0.00 0.00 5.19
1624 1641 1.473257 GGCATGATGTAGAGGCGACAA 60.473 52.381 0.00 0.00 0.00 3.18
1647 1664 4.918588 TCTGGTCCTCCTTTTCCATTAAC 58.081 43.478 0.00 0.00 34.23 2.01
1775 1794 1.728971 CGCCAGACTTTGAGATGTGTC 59.271 52.381 0.00 0.00 0.00 3.67
1776 1795 2.771089 GCCAGACTTTGAGATGTGTCA 58.229 47.619 0.00 0.00 32.41 3.58
1777 1796 3.341823 GCCAGACTTTGAGATGTGTCAT 58.658 45.455 0.00 0.00 32.41 3.06
1778 1797 3.373439 GCCAGACTTTGAGATGTGTCATC 59.627 47.826 1.98 1.98 32.41 2.92
1779 1798 3.937706 CCAGACTTTGAGATGTGTCATCC 59.062 47.826 6.18 0.35 32.41 3.51
2142 2161 2.125673 CAACCCGCGGATTCGACT 60.126 61.111 30.73 0.00 39.00 4.18
2146 2165 1.008767 CCCGCGGATTCGACTAGTC 60.009 63.158 30.73 13.18 39.00 2.59
2147 2166 1.721664 CCCGCGGATTCGACTAGTCA 61.722 60.000 30.73 4.49 39.00 3.41
2148 2167 0.099968 CCGCGGATTCGACTAGTCAA 59.900 55.000 24.07 15.11 39.00 3.18
2201 2221 2.676121 CCATTTGTGCTCCCGCCA 60.676 61.111 0.00 0.00 34.43 5.69
2224 2244 3.936203 GCACCGACCCACCTGTCA 61.936 66.667 0.00 0.00 34.88 3.58
2226 2246 2.200370 ACCGACCCACCTGTCAGA 59.800 61.111 0.00 0.00 34.88 3.27
2227 2247 1.229209 ACCGACCCACCTGTCAGAT 60.229 57.895 0.00 0.00 34.88 2.90
2303 2324 2.583441 CCACCCCTCTGTCTTGCGA 61.583 63.158 0.00 0.00 0.00 5.10
2321 2345 2.741228 GCGAAATGATGAGAGGCTCTGT 60.741 50.000 24.21 10.44 0.00 3.41
2349 2373 1.079127 CGGTTTCCTCGCCATGTCT 60.079 57.895 0.00 0.00 0.00 3.41
2379 2403 1.153429 GTCGTGCCTCCATACCCAC 60.153 63.158 0.00 0.00 0.00 4.61
2380 2404 2.189521 CGTGCCTCCATACCCACC 59.810 66.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.203070 GTCGTGCTGGCCTATGGG 60.203 66.667 3.32 0.00 0.00 4.00
1 2 2.586079 CGTCGTGCTGGCCTATGG 60.586 66.667 3.32 0.00 0.00 2.74
2 3 3.264897 GCGTCGTGCTGGCCTATG 61.265 66.667 3.32 0.00 41.73 2.23
3 4 4.530857 GGCGTCGTGCTGGCCTAT 62.531 66.667 3.32 0.00 45.43 2.57
8 9 4.680237 TCCTTGGCGTCGTGCTGG 62.680 66.667 0.00 3.74 45.43 4.85
9 10 3.114616 CTCCTTGGCGTCGTGCTG 61.115 66.667 0.00 0.00 45.43 4.41
10 11 3.303135 TCTCCTTGGCGTCGTGCT 61.303 61.111 0.00 0.00 45.43 4.40
11 12 3.112709 GTCTCCTTGGCGTCGTGC 61.113 66.667 0.00 0.00 45.38 5.34
12 13 2.805353 CGTCTCCTTGGCGTCGTG 60.805 66.667 0.00 0.00 39.21 4.35
13 14 4.719369 GCGTCTCCTTGGCGTCGT 62.719 66.667 0.00 0.00 46.81 4.34
14 15 4.421479 AGCGTCTCCTTGGCGTCG 62.421 66.667 0.00 0.00 46.81 5.12
15 16 2.811317 CAGCGTCTCCTTGGCGTC 60.811 66.667 0.00 0.00 46.81 5.19
16 17 3.575351 GACAGCGTCTCCTTGGCGT 62.575 63.158 2.10 0.00 46.81 5.68
18 19 2.811317 CGACAGCGTCTCCTTGGC 60.811 66.667 7.03 0.00 0.00 4.52
38 39 1.317431 TGACATTCTGCTGGCATGGC 61.317 55.000 13.29 13.29 0.00 4.40
39 40 0.454600 GTGACATTCTGCTGGCATGG 59.545 55.000 0.00 0.00 36.33 3.66
40 41 0.098200 CGTGACATTCTGCTGGCATG 59.902 55.000 0.00 0.00 36.33 4.06
41 42 1.651240 GCGTGACATTCTGCTGGCAT 61.651 55.000 0.00 0.00 36.33 4.40
42 43 2.327343 GCGTGACATTCTGCTGGCA 61.327 57.895 0.00 0.00 0.00 4.92
43 44 1.975363 GAGCGTGACATTCTGCTGGC 61.975 60.000 0.00 0.00 37.91 4.85
44 45 0.671472 TGAGCGTGACATTCTGCTGG 60.671 55.000 0.00 0.00 37.91 4.85
45 46 1.128136 CTTGAGCGTGACATTCTGCTG 59.872 52.381 0.00 0.00 37.91 4.41
46 47 1.436600 CTTGAGCGTGACATTCTGCT 58.563 50.000 0.00 0.00 41.11 4.24
47 48 0.179205 GCTTGAGCGTGACATTCTGC 60.179 55.000 0.00 0.00 0.00 4.26
48 49 1.136141 GTGCTTGAGCGTGACATTCTG 60.136 52.381 0.00 0.00 45.83 3.02
49 50 1.151668 GTGCTTGAGCGTGACATTCT 58.848 50.000 0.00 0.00 45.83 2.40
50 51 0.867746 TGTGCTTGAGCGTGACATTC 59.132 50.000 0.00 0.00 45.83 2.67
51 52 0.870393 CTGTGCTTGAGCGTGACATT 59.130 50.000 0.00 0.00 45.83 2.71
52 53 0.033920 TCTGTGCTTGAGCGTGACAT 59.966 50.000 0.00 0.00 45.83 3.06
53 54 0.033920 ATCTGTGCTTGAGCGTGACA 59.966 50.000 0.00 0.00 45.83 3.58
54 55 0.441533 CATCTGTGCTTGAGCGTGAC 59.558 55.000 0.00 0.00 45.83 3.67
55 56 0.671472 CCATCTGTGCTTGAGCGTGA 60.671 55.000 0.00 0.00 45.83 4.35
56 57 1.792301 CCATCTGTGCTTGAGCGTG 59.208 57.895 0.00 0.00 45.83 5.34
57 58 2.037136 GCCATCTGTGCTTGAGCGT 61.037 57.895 0.00 0.00 45.83 5.07
58 59 2.758089 GGCCATCTGTGCTTGAGCG 61.758 63.158 0.00 0.00 45.83 5.03
59 60 1.676635 TGGCCATCTGTGCTTGAGC 60.677 57.895 0.00 0.00 42.50 4.26
60 61 1.642037 CGTGGCCATCTGTGCTTGAG 61.642 60.000 9.72 0.00 0.00 3.02
61 62 1.672030 CGTGGCCATCTGTGCTTGA 60.672 57.895 9.72 0.00 0.00 3.02
62 63 2.872557 CGTGGCCATCTGTGCTTG 59.127 61.111 9.72 0.00 0.00 4.01
63 64 3.058160 GCGTGGCCATCTGTGCTT 61.058 61.111 9.72 0.00 0.00 3.91
81 82 4.170062 CAGGTTGCTGCATCGCCG 62.170 66.667 1.84 0.38 0.00 6.46
82 83 3.044059 GACAGGTTGCTGCATCGCC 62.044 63.158 1.84 6.73 0.00 5.54
83 84 2.482374 GACAGGTTGCTGCATCGC 59.518 61.111 1.84 0.00 0.00 4.58
84 85 2.743752 CCGACAGGTTGCTGCATCG 61.744 63.158 13.87 13.87 0.00 3.84
85 86 1.364626 CTCCGACAGGTTGCTGCATC 61.365 60.000 1.84 1.98 39.05 3.91
86 87 1.376424 CTCCGACAGGTTGCTGCAT 60.376 57.895 1.84 0.00 39.05 3.96
87 88 2.031012 CTCCGACAGGTTGCTGCA 59.969 61.111 0.00 0.00 39.05 4.41
88 89 3.426568 GCTCCGACAGGTTGCTGC 61.427 66.667 0.00 0.00 39.05 5.25
89 90 2.743928 GGCTCCGACAGGTTGCTG 60.744 66.667 0.00 0.00 37.86 4.41
90 91 4.379243 CGGCTCCGACAGGTTGCT 62.379 66.667 1.35 0.00 42.83 3.91
91 92 4.681978 ACGGCTCCGACAGGTTGC 62.682 66.667 15.95 0.00 42.83 4.17
92 93 2.432628 GACGGCTCCGACAGGTTG 60.433 66.667 15.95 0.00 42.83 3.77
93 94 3.692406 GGACGGCTCCGACAGGTT 61.692 66.667 15.95 0.00 42.83 3.50
94 95 4.988716 TGGACGGCTCCGACAGGT 62.989 66.667 15.95 0.00 39.88 4.00
95 96 3.649277 CTTGGACGGCTCCGACAGG 62.649 68.421 15.95 9.86 39.88 4.00
96 97 2.125912 CTTGGACGGCTCCGACAG 60.126 66.667 15.95 0.00 39.88 3.51
97 98 4.373116 GCTTGGACGGCTCCGACA 62.373 66.667 15.95 10.43 39.88 4.35
109 110 1.303309 GTTGATCTGATCCGGCTTGG 58.697 55.000 14.71 0.00 40.09 3.61
110 111 2.028420 TGTTGATCTGATCCGGCTTG 57.972 50.000 14.71 0.00 0.00 4.01
111 112 2.359900 GTTGTTGATCTGATCCGGCTT 58.640 47.619 14.71 0.00 0.00 4.35
112 113 1.740380 CGTTGTTGATCTGATCCGGCT 60.740 52.381 14.71 0.00 0.00 5.52
113 114 0.652592 CGTTGTTGATCTGATCCGGC 59.347 55.000 14.71 5.87 0.00 6.13
114 115 0.652592 GCGTTGTTGATCTGATCCGG 59.347 55.000 14.71 0.00 0.00 5.14
115 116 0.652592 GGCGTTGTTGATCTGATCCG 59.347 55.000 14.71 11.15 0.00 4.18
116 117 0.652592 CGGCGTTGTTGATCTGATCC 59.347 55.000 14.71 1.44 0.00 3.36
117 118 0.026803 GCGGCGTTGTTGATCTGATC 59.973 55.000 9.37 10.72 0.00 2.92
118 119 0.391661 AGCGGCGTTGTTGATCTGAT 60.392 50.000 9.37 0.00 0.00 2.90
119 120 1.005037 AGCGGCGTTGTTGATCTGA 60.005 52.632 9.37 0.00 0.00 3.27
120 121 1.133253 CAGCGGCGTTGTTGATCTG 59.867 57.895 15.94 4.04 0.00 2.90
121 122 2.680913 GCAGCGGCGTTGTTGATCT 61.681 57.895 24.20 0.00 0.00 2.75
122 123 2.202349 GCAGCGGCGTTGTTGATC 60.202 61.111 24.20 4.11 0.00 2.92
138 139 3.253930 GAGCTTCTCGCGCAGAGC 61.254 66.667 19.83 15.94 46.44 4.09
139 140 2.948648 CGAGCTTCTCGCGCAGAG 60.949 66.667 18.94 18.94 46.75 3.35
158 159 4.680237 TGGTTCTCAGGCACGGCG 62.680 66.667 4.80 4.80 0.00 6.46
159 160 3.050275 GTGGTTCTCAGGCACGGC 61.050 66.667 0.00 0.00 0.00 5.68
160 161 2.358737 GGTGGTTCTCAGGCACGG 60.359 66.667 0.00 0.00 0.00 4.94
161 162 2.358737 GGGTGGTTCTCAGGCACG 60.359 66.667 0.00 0.00 0.00 5.34
162 163 1.600916 GTGGGTGGTTCTCAGGCAC 60.601 63.158 0.00 0.00 0.00 5.01
163 164 2.836154 GTGGGTGGTTCTCAGGCA 59.164 61.111 0.00 0.00 0.00 4.75
164 165 2.358737 CGTGGGTGGTTCTCAGGC 60.359 66.667 0.00 0.00 0.00 4.85
165 166 2.358737 GCGTGGGTGGTTCTCAGG 60.359 66.667 0.00 0.00 35.72 3.86
166 167 2.358737 GGCGTGGGTGGTTCTCAG 60.359 66.667 0.00 0.00 0.00 3.35
167 168 4.308458 CGGCGTGGGTGGTTCTCA 62.308 66.667 0.00 0.00 0.00 3.27
226 227 4.436998 GTCGGAGGACGCCACAGG 62.437 72.222 0.00 0.00 43.86 4.00
245 246 4.214327 CTTCCTCCTCTCCGCCGC 62.214 72.222 0.00 0.00 0.00 6.53
246 247 3.532155 CCTTCCTCCTCTCCGCCG 61.532 72.222 0.00 0.00 0.00 6.46
247 248 3.157949 CCCTTCCTCCTCTCCGCC 61.158 72.222 0.00 0.00 0.00 6.13
248 249 1.681486 CTTCCCTTCCTCCTCTCCGC 61.681 65.000 0.00 0.00 0.00 5.54
249 250 0.033011 TCTTCCCTTCCTCCTCTCCG 60.033 60.000 0.00 0.00 0.00 4.63
250 251 2.487746 ATCTTCCCTTCCTCCTCTCC 57.512 55.000 0.00 0.00 0.00 3.71
251 252 3.521531 ACAAATCTTCCCTTCCTCCTCTC 59.478 47.826 0.00 0.00 0.00 3.20
252 253 3.265479 CACAAATCTTCCCTTCCTCCTCT 59.735 47.826 0.00 0.00 0.00 3.69
253 254 3.009584 ACACAAATCTTCCCTTCCTCCTC 59.990 47.826 0.00 0.00 0.00 3.71
254 255 2.989571 ACACAAATCTTCCCTTCCTCCT 59.010 45.455 0.00 0.00 0.00 3.69
255 256 3.084786 CACACAAATCTTCCCTTCCTCC 58.915 50.000 0.00 0.00 0.00 4.30
256 257 3.084786 CCACACAAATCTTCCCTTCCTC 58.915 50.000 0.00 0.00 0.00 3.71
257 258 2.819348 GCCACACAAATCTTCCCTTCCT 60.819 50.000 0.00 0.00 0.00 3.36
258 259 1.546029 GCCACACAAATCTTCCCTTCC 59.454 52.381 0.00 0.00 0.00 3.46
259 260 1.200020 CGCCACACAAATCTTCCCTTC 59.800 52.381 0.00 0.00 0.00 3.46
260 261 1.247567 CGCCACACAAATCTTCCCTT 58.752 50.000 0.00 0.00 0.00 3.95
261 262 0.609131 CCGCCACACAAATCTTCCCT 60.609 55.000 0.00 0.00 0.00 4.20
262 263 1.883021 CCGCCACACAAATCTTCCC 59.117 57.895 0.00 0.00 0.00 3.97
263 264 1.212751 GCCGCCACACAAATCTTCC 59.787 57.895 0.00 0.00 0.00 3.46
264 265 1.154225 CGCCGCCACACAAATCTTC 60.154 57.895 0.00 0.00 0.00 2.87
265 266 2.625823 CCGCCGCCACACAAATCTT 61.626 57.895 0.00 0.00 0.00 2.40
266 267 3.055719 CCGCCGCCACACAAATCT 61.056 61.111 0.00 0.00 0.00 2.40
267 268 4.776647 GCCGCCGCCACACAAATC 62.777 66.667 0.00 0.00 0.00 2.17
268 269 3.910914 TAGCCGCCGCCACACAAAT 62.911 57.895 0.00 0.00 34.57 2.32
269 270 4.627801 TAGCCGCCGCCACACAAA 62.628 61.111 0.00 0.00 34.57 2.83
280 281 4.091939 AACCCGAACCCTAGCCGC 62.092 66.667 0.00 0.00 0.00 6.53
281 282 2.125269 CAACCCGAACCCTAGCCG 60.125 66.667 0.00 0.00 0.00 5.52
282 283 2.437895 GCAACCCGAACCCTAGCC 60.438 66.667 0.00 0.00 0.00 3.93
283 284 2.437895 GGCAACCCGAACCCTAGC 60.438 66.667 0.00 0.00 0.00 3.42
284 285 1.376812 GTGGCAACCCGAACCCTAG 60.377 63.158 0.00 0.00 0.00 3.02
285 286 2.751688 GTGGCAACCCGAACCCTA 59.248 61.111 0.00 0.00 0.00 3.53
286 287 4.280019 GGTGGCAACCCGAACCCT 62.280 66.667 0.00 0.00 41.04 4.34
312 313 4.446413 GGTACCGCTCCCGTGTGG 62.446 72.222 0.00 0.00 42.85 4.17
313 314 4.446413 GGGTACCGCTCCCGTGTG 62.446 72.222 5.65 0.00 40.86 3.82
320 321 6.291477 GAAGATCTACTTGGGGTACCGCTC 62.291 54.167 27.34 15.53 45.08 5.03
321 322 4.505701 GAAGATCTACTTGGGGTACCGCT 61.506 52.174 27.34 11.93 45.08 5.52
322 323 2.223994 GAAGATCTACTTGGGGTACCGC 60.224 54.545 21.62 21.62 45.08 5.68
323 324 3.028850 TGAAGATCTACTTGGGGTACCG 58.971 50.000 5.65 0.00 45.08 4.02
324 325 3.181478 CGTGAAGATCTACTTGGGGTACC 60.181 52.174 2.17 2.17 43.92 3.34
325 326 3.737355 GCGTGAAGATCTACTTGGGGTAC 60.737 52.174 0.00 0.00 39.13 3.34
326 327 2.429610 GCGTGAAGATCTACTTGGGGTA 59.570 50.000 0.00 0.00 39.13 3.69
327 328 1.207329 GCGTGAAGATCTACTTGGGGT 59.793 52.381 0.00 0.00 39.13 4.95
328 329 1.482593 AGCGTGAAGATCTACTTGGGG 59.517 52.381 0.00 0.00 39.13 4.96
329 330 2.428890 AGAGCGTGAAGATCTACTTGGG 59.571 50.000 0.00 0.00 44.93 4.12
330 331 3.791973 AGAGCGTGAAGATCTACTTGG 57.208 47.619 0.00 0.00 44.93 3.61
331 332 6.125327 TCTAAGAGCGTGAAGATCTACTTG 57.875 41.667 0.00 0.00 46.24 3.16
332 333 6.952773 ATCTAAGAGCGTGAAGATCTACTT 57.047 37.500 0.00 0.00 46.24 2.24
333 334 7.446769 TCTATCTAAGAGCGTGAAGATCTACT 58.553 38.462 0.00 0.00 46.24 2.57
334 335 7.661127 TCTATCTAAGAGCGTGAAGATCTAC 57.339 40.000 0.00 0.00 46.24 2.59
335 336 7.389330 CCTTCTATCTAAGAGCGTGAAGATCTA 59.611 40.741 0.00 0.00 46.24 1.98
337 338 6.016610 ACCTTCTATCTAAGAGCGTGAAGATC 60.017 42.308 0.00 0.00 35.05 2.75
338 339 5.830991 ACCTTCTATCTAAGAGCGTGAAGAT 59.169 40.000 0.00 0.00 35.05 2.40
339 340 5.194432 ACCTTCTATCTAAGAGCGTGAAGA 58.806 41.667 0.00 0.00 35.05 2.87
340 341 5.508200 ACCTTCTATCTAAGAGCGTGAAG 57.492 43.478 0.00 0.00 35.05 3.02
341 342 5.916661 AACCTTCTATCTAAGAGCGTGAA 57.083 39.130 0.00 0.00 35.05 3.18
342 343 5.916661 AAACCTTCTATCTAAGAGCGTGA 57.083 39.130 0.00 0.00 35.05 4.35
343 344 8.649973 AATAAAACCTTCTATCTAAGAGCGTG 57.350 34.615 0.00 0.00 35.05 5.34
344 345 7.648510 CGAATAAAACCTTCTATCTAAGAGCGT 59.351 37.037 0.00 0.00 35.05 5.07
345 346 7.115095 CCGAATAAAACCTTCTATCTAAGAGCG 59.885 40.741 0.00 0.00 35.05 5.03
346 347 7.095565 GCCGAATAAAACCTTCTATCTAAGAGC 60.096 40.741 0.00 0.00 35.05 4.09
347 348 7.926555 TGCCGAATAAAACCTTCTATCTAAGAG 59.073 37.037 0.00 0.00 35.05 2.85
348 349 7.709613 GTGCCGAATAAAACCTTCTATCTAAGA 59.290 37.037 0.00 0.00 0.00 2.10
366 367 0.605319 TTTCCAAGCGAGTGCCGAAT 60.605 50.000 0.00 0.00 44.31 3.34
369 370 0.454957 CAATTTCCAAGCGAGTGCCG 60.455 55.000 0.00 0.00 44.31 5.69
387 388 1.334160 TCCAAGTCAGTTCGTAGCCA 58.666 50.000 0.00 0.00 0.00 4.75
405 406 3.691609 GGACCATGTCACTGGAGAAATTC 59.308 47.826 7.93 0.00 39.73 2.17
450 459 7.234355 TGATACTTAGATATGCTGAGGAGTGA 58.766 38.462 0.00 0.00 34.68 3.41
453 462 7.914871 CGAATGATACTTAGATATGCTGAGGAG 59.085 40.741 0.00 0.00 34.68 3.69
454 463 7.394641 ACGAATGATACTTAGATATGCTGAGGA 59.605 37.037 0.00 0.00 34.68 3.71
455 464 7.487509 CACGAATGATACTTAGATATGCTGAGG 59.512 40.741 0.00 0.00 34.68 3.86
456 465 7.487509 CCACGAATGATACTTAGATATGCTGAG 59.512 40.741 0.00 0.00 36.37 3.35
457 466 7.315890 CCACGAATGATACTTAGATATGCTGA 58.684 38.462 0.00 0.00 0.00 4.26
458 467 6.533012 CCCACGAATGATACTTAGATATGCTG 59.467 42.308 0.00 0.00 0.00 4.41
459 468 6.634805 CCCACGAATGATACTTAGATATGCT 58.365 40.000 0.00 0.00 0.00 3.79
460 469 5.292101 GCCCACGAATGATACTTAGATATGC 59.708 44.000 0.00 0.00 0.00 3.14
461 470 6.634805 AGCCCACGAATGATACTTAGATATG 58.365 40.000 0.00 0.00 0.00 1.78
462 471 6.859112 AGCCCACGAATGATACTTAGATAT 57.141 37.500 0.00 0.00 0.00 1.63
463 472 6.665992 AAGCCCACGAATGATACTTAGATA 57.334 37.500 0.00 0.00 0.00 1.98
464 473 5.552870 AAGCCCACGAATGATACTTAGAT 57.447 39.130 0.00 0.00 0.00 1.98
480 489 1.691976 CATCTGGTATCGGTAAGCCCA 59.308 52.381 0.00 0.00 0.00 5.36
510 519 9.551734 TGAAAAATATCTGAGATATGTCTGGTG 57.448 33.333 15.21 0.00 33.97 4.17
554 563 5.163513 GTGCCAGAGAACAATAATGGTTTG 58.836 41.667 0.00 0.00 33.42 2.93
555 564 4.832266 TGTGCCAGAGAACAATAATGGTTT 59.168 37.500 0.00 0.00 33.42 3.27
556 565 4.406456 TGTGCCAGAGAACAATAATGGTT 58.594 39.130 0.00 0.00 33.42 3.67
557 566 4.032960 TGTGCCAGAGAACAATAATGGT 57.967 40.909 0.00 0.00 33.42 3.55
558 567 4.218200 TGTTGTGCCAGAGAACAATAATGG 59.782 41.667 0.00 0.00 38.47 3.16
559 568 5.375417 TGTTGTGCCAGAGAACAATAATG 57.625 39.130 0.00 0.00 38.47 1.90
561 570 5.069318 TCATGTTGTGCCAGAGAACAATAA 58.931 37.500 0.00 0.00 40.94 1.40
562 571 4.650734 TCATGTTGTGCCAGAGAACAATA 58.349 39.130 0.00 0.00 40.94 1.90
658 671 8.327429 GTGTGATTTTCATTTTGACACGAAAAT 58.673 29.630 8.29 8.29 45.80 1.82
690 704 1.144936 CGATTGGCAGGAGGAGGAC 59.855 63.158 0.00 0.00 0.00 3.85
711 725 6.662234 TCGGAGGAAGATCTTTTCTACTTGTA 59.338 38.462 9.87 0.00 33.05 2.41
745 760 4.400251 TGGAGATATTTTTCAGGCAAGCAG 59.600 41.667 0.00 0.00 0.00 4.24
771 786 1.357258 GAGCCACGTCGTCTCGTCTA 61.357 60.000 0.00 0.00 42.27 2.59
789 804 0.036388 GTCTGGGCCAATCGTTCTGA 60.036 55.000 8.04 0.00 0.00 3.27
841 856 0.396556 AAGTTTGGGCGTTTGGGAGT 60.397 50.000 0.00 0.00 0.00 3.85
936 952 2.116366 GTAACAAGTTGCTGCGTTTGG 58.884 47.619 1.81 0.00 0.00 3.28
963 979 3.173668 TCGACGGAGATTTTATGTGGG 57.826 47.619 0.00 0.00 0.00 4.61
1323 1339 3.591023 GTTCTCCTTGCAGTAGTTCTCC 58.409 50.000 0.00 0.00 0.00 3.71
1395 1411 0.250209 CCATCCGCCATCCAGAAGAG 60.250 60.000 0.00 0.00 0.00 2.85
1397 1413 0.816825 CACCATCCGCCATCCAGAAG 60.817 60.000 0.00 0.00 0.00 2.85
1405 1421 2.350895 CACCTTCACCATCCGCCA 59.649 61.111 0.00 0.00 0.00 5.69
1413 1429 1.597027 CACCACGTCCACCTTCACC 60.597 63.158 0.00 0.00 0.00 4.02
1442 1458 2.046217 GGTTTCTCGGGCTCCCAC 60.046 66.667 5.70 0.00 35.37 4.61
1516 1533 4.683766 TGTCCCAGGGAAAATATTTGGA 57.316 40.909 10.89 0.08 31.38 3.53
1531 1548 4.650131 TGTATATCAACCACGTATGTCCCA 59.350 41.667 0.00 0.00 0.00 4.37
1606 1623 3.739810 CAGATTGTCGCCTCTACATCATG 59.260 47.826 0.00 0.00 0.00 3.07
1610 1627 2.101582 GACCAGATTGTCGCCTCTACAT 59.898 50.000 0.00 0.00 0.00 2.29
1622 1639 3.439857 TGGAAAAGGAGGACCAGATTG 57.560 47.619 0.00 0.00 38.94 2.67
1624 1641 5.015178 TGTTAATGGAAAAGGAGGACCAGAT 59.985 40.000 0.00 0.00 38.94 2.90
1647 1664 6.642540 GTCAGGTTTTTAGAGCTTCCATTTTG 59.357 38.462 0.00 0.00 0.00 2.44
1732 1751 6.036083 GCGTGTCTATCAGATTGCTTTTAGAA 59.964 38.462 0.00 0.00 0.00 2.10
1752 1771 1.070758 ACATCTCAAAGTCTGGCGTGT 59.929 47.619 0.00 0.00 0.00 4.49
2142 2161 2.159421 GCCAGTTCGTCGAGATTGACTA 60.159 50.000 0.00 0.00 36.71 2.59
2146 2165 1.391485 CAAGCCAGTTCGTCGAGATTG 59.609 52.381 0.00 0.00 0.00 2.67
2147 2166 1.272490 TCAAGCCAGTTCGTCGAGATT 59.728 47.619 0.00 0.00 0.00 2.40
2148 2167 0.888619 TCAAGCCAGTTCGTCGAGAT 59.111 50.000 0.00 0.00 0.00 2.75
2214 2234 0.391661 CGGAACATCTGACAGGTGGG 60.392 60.000 19.74 2.73 0.00 4.61
2224 2244 2.490217 CCTCGTCGCGGAACATCT 59.510 61.111 6.13 0.00 0.00 2.90
2226 2246 3.379445 ACCCTCGTCGCGGAACAT 61.379 61.111 6.13 0.00 0.00 2.71
2227 2247 4.351938 CACCCTCGTCGCGGAACA 62.352 66.667 6.13 0.00 0.00 3.18
2303 2324 2.026542 TGCACAGAGCCTCTCATCATTT 60.027 45.455 0.00 0.00 44.83 2.32
2332 2356 0.804989 CAAGACATGGCGAGGAAACC 59.195 55.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.