Multiple sequence alignment - TraesCS6B01G217000

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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 TraesCS6B01G217000 chr6B 100.000 3006 0 0 1 3006 298488952 298485947 0.000000e+00 5552.0
1 TraesCS6B01G217000 chr6A 90.610 2098 81 39 550 2574 223978845 223980899 0.000000e+00 2676.0
2 TraesCS6B01G217000 chr6A 93.049 446 20 6 2570 3006 223980976 223981419 2.530000e-180 641.0
3 TraesCS6B01G217000 chr6D 91.121 1802 80 33 380 2131 187206238 187204467 0.000000e+00 2368.0
4 TraesCS6B01G217000 chr6D 95.082 427 21 0 2580 3006 187204069 187203643 0.000000e+00 673.0
5 TraesCS6B01G217000 chr6D 89.668 271 15 5 2219 2489 187204478 187204221 1.730000e-87 333.0
6 TraesCS6B01G217000 chr3D 86.081 273 29 6 57 326 78011044 78010778 4.900000e-73 285.0
7 TraesCS6B01G217000 chr3D 85.393 267 33 4 57 322 78104200 78103939 3.820000e-69 272.0
8 TraesCS6B01G217000 chr7A 79.706 340 42 8 57 382 181019958 181019632 1.400000e-53 220.0
9 TraesCS6B01G217000 chr7A 83.951 81 12 1 137 216 491889062 491888982 3.210000e-10 76.8
10 TraesCS6B01G217000 chr3B 83.889 180 22 3 102 274 786785508 786785329 6.670000e-37 165.0


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 TraesCS6B01G217000 chr6B 298485947 298488952 3005 True 5552.000000 5552 100.0000 1 3006 1 chr6B.!!$R1 3005
1 TraesCS6B01G217000 chr6A 223978845 223981419 2574 False 1658.500000 2676 91.8295 550 3006 2 chr6A.!!$F1 2456
2 TraesCS6B01G217000 chr6D 187203643 187206238 2595 True 1124.666667 2368 91.9570 380 3006 3 chr6D.!!$R1 2626

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
703 707 0.038435 CCCAATGATTTGTGCGCACA 60.038 50.0 37.86 37.86 39.98 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2172 0.033011 TCAGGAGGGGAGTAGAGTGC 60.033 60.0 0.0 0.0 0.0 4.4 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 3.271014 AGCCATGAAGCAGCAACG 58.729 55.556 0.00 0.00 34.23 4.10
18 19 2.505557 GCCATGAAGCAGCAACGC 60.506 61.111 0.00 0.00 0.00 4.84
19 20 2.956194 CCATGAAGCAGCAACGCA 59.044 55.556 0.00 0.00 0.00 5.24
20 21 1.286570 CCATGAAGCAGCAACGCAA 59.713 52.632 0.00 0.00 0.00 4.85
21 22 1.005294 CCATGAAGCAGCAACGCAAC 61.005 55.000 0.00 0.00 0.00 4.17
22 23 1.081906 ATGAAGCAGCAACGCAACG 60.082 52.632 0.00 0.00 0.00 4.10
23 24 2.427410 GAAGCAGCAACGCAACGG 60.427 61.111 0.00 0.00 0.00 4.44
24 25 3.879351 GAAGCAGCAACGCAACGGG 62.879 63.158 0.00 0.00 0.00 5.28
57 58 4.181010 CGGAGGGGTGGAGCATGG 62.181 72.222 0.00 0.00 0.00 3.66
58 59 2.692368 GGAGGGGTGGAGCATGGA 60.692 66.667 0.00 0.00 0.00 3.41
59 60 2.750657 GGAGGGGTGGAGCATGGAG 61.751 68.421 0.00 0.00 0.00 3.86
60 61 2.693864 AGGGGTGGAGCATGGAGG 60.694 66.667 0.00 0.00 0.00 4.30
61 62 3.017581 GGGGTGGAGCATGGAGGT 61.018 66.667 0.00 0.00 0.00 3.85
62 63 2.273449 GGGTGGAGCATGGAGGTG 59.727 66.667 0.00 0.00 0.00 4.00
63 64 2.300967 GGGTGGAGCATGGAGGTGA 61.301 63.158 0.00 0.00 0.00 4.02
64 65 1.685224 GGTGGAGCATGGAGGTGAA 59.315 57.895 0.00 0.00 0.00 3.18
65 66 0.393537 GGTGGAGCATGGAGGTGAAG 60.394 60.000 0.00 0.00 0.00 3.02
66 67 0.393537 GTGGAGCATGGAGGTGAAGG 60.394 60.000 0.00 0.00 0.00 3.46
67 68 1.225704 GGAGCATGGAGGTGAAGGG 59.774 63.158 0.00 0.00 0.00 3.95
68 69 1.274703 GGAGCATGGAGGTGAAGGGA 61.275 60.000 0.00 0.00 0.00 4.20
69 70 0.842635 GAGCATGGAGGTGAAGGGAT 59.157 55.000 0.00 0.00 0.00 3.85
70 71 0.549950 AGCATGGAGGTGAAGGGATG 59.450 55.000 0.00 0.00 0.00 3.51
71 72 0.466922 GCATGGAGGTGAAGGGATGG 60.467 60.000 0.00 0.00 0.00 3.51
72 73 0.184451 CATGGAGGTGAAGGGATGGG 59.816 60.000 0.00 0.00 0.00 4.00
73 74 0.995675 ATGGAGGTGAAGGGATGGGG 60.996 60.000 0.00 0.00 0.00 4.96
74 75 2.386935 GGAGGTGAAGGGATGGGGG 61.387 68.421 0.00 0.00 0.00 5.40
88 89 3.961414 GGGGGTGAGCCGTTTCCA 61.961 66.667 0.00 0.00 34.97 3.53
89 90 2.359975 GGGGTGAGCCGTTTCCAG 60.360 66.667 0.00 0.00 34.97 3.86
90 91 2.430367 GGGTGAGCCGTTTCCAGT 59.570 61.111 0.00 0.00 34.97 4.00
91 92 1.228154 GGGTGAGCCGTTTCCAGTT 60.228 57.895 0.00 0.00 34.97 3.16
92 93 1.515521 GGGTGAGCCGTTTCCAGTTG 61.516 60.000 0.00 0.00 34.97 3.16
93 94 1.282875 GTGAGCCGTTTCCAGTTGC 59.717 57.895 0.00 0.00 0.00 4.17
94 95 1.148273 TGAGCCGTTTCCAGTTGCT 59.852 52.632 0.00 0.00 34.40 3.91
95 96 1.165907 TGAGCCGTTTCCAGTTGCTG 61.166 55.000 0.00 0.00 31.23 4.41
104 105 3.993535 CAGTTGCTGGAGAAGGGC 58.006 61.111 0.00 0.00 0.00 5.19
105 106 2.037136 CAGTTGCTGGAGAAGGGCG 61.037 63.158 0.00 0.00 0.00 6.13
106 107 2.747855 GTTGCTGGAGAAGGGCGG 60.748 66.667 0.00 0.00 0.00 6.13
107 108 2.927856 TTGCTGGAGAAGGGCGGA 60.928 61.111 0.00 0.00 0.00 5.54
108 109 2.959484 TTGCTGGAGAAGGGCGGAG 61.959 63.158 0.00 0.00 0.00 4.63
121 122 2.278857 CGGAGCATTCGACGGAGG 60.279 66.667 0.00 0.00 42.19 4.30
122 123 2.771639 CGGAGCATTCGACGGAGGA 61.772 63.158 0.00 0.00 42.19 3.71
123 124 1.066587 GGAGCATTCGACGGAGGAG 59.933 63.158 0.00 0.00 0.00 3.69
124 125 1.066587 GAGCATTCGACGGAGGAGG 59.933 63.158 0.00 0.00 0.00 4.30
125 126 2.107141 GCATTCGACGGAGGAGGG 59.893 66.667 0.00 0.00 0.00 4.30
126 127 2.107141 CATTCGACGGAGGAGGGC 59.893 66.667 0.00 0.00 0.00 5.19
127 128 3.528370 ATTCGACGGAGGAGGGCG 61.528 66.667 0.00 0.00 0.00 6.13
143 144 3.326210 CGGAGCGCTCGATCTTGC 61.326 66.667 29.81 13.85 0.00 4.01
144 145 2.964389 GGAGCGCTCGATCTTGCC 60.964 66.667 29.81 11.58 0.00 4.52
145 146 3.326210 GAGCGCTCGATCTTGCCG 61.326 66.667 23.61 0.00 0.00 5.69
169 170 2.279784 CCTCTCATTCGCGAGGCC 60.280 66.667 9.59 0.00 40.27 5.19
170 171 2.656651 CTCTCATTCGCGAGGCCG 60.657 66.667 9.59 0.00 39.16 6.13
171 172 3.126074 CTCTCATTCGCGAGGCCGA 62.126 63.158 9.59 4.52 38.22 5.54
172 173 2.656651 CTCATTCGCGAGGCCGAG 60.657 66.667 9.59 10.11 38.60 4.63
173 174 4.873129 TCATTCGCGAGGCCGAGC 62.873 66.667 9.59 14.35 38.60 5.03
181 182 4.821589 GAGGCCGAGCGACAAGGG 62.822 72.222 0.00 0.00 0.00 3.95
183 184 4.699522 GGCCGAGCGACAAGGGTT 62.700 66.667 0.00 0.00 0.00 4.11
184 185 2.668550 GCCGAGCGACAAGGGTTT 60.669 61.111 0.00 0.00 0.00 3.27
185 186 2.677979 GCCGAGCGACAAGGGTTTC 61.678 63.158 0.00 0.00 0.00 2.78
186 187 2.033194 CCGAGCGACAAGGGTTTCC 61.033 63.158 0.00 0.00 0.00 3.13
188 189 1.014564 CGAGCGACAAGGGTTTCCTC 61.015 60.000 0.00 0.00 44.07 3.71
189 190 0.673956 GAGCGACAAGGGTTTCCTCC 60.674 60.000 0.00 0.00 44.07 4.30
190 191 1.674651 GCGACAAGGGTTTCCTCCC 60.675 63.158 0.00 0.00 44.07 4.30
196 197 4.068257 GGGTTTCCTCCCCGATCT 57.932 61.111 0.00 0.00 41.54 2.75
197 198 1.830836 GGGTTTCCTCCCCGATCTC 59.169 63.158 0.00 0.00 41.54 2.75
198 199 0.981277 GGGTTTCCTCCCCGATCTCA 60.981 60.000 0.00 0.00 41.54 3.27
199 200 1.132500 GGTTTCCTCCCCGATCTCAT 58.868 55.000 0.00 0.00 0.00 2.90
200 201 1.070914 GGTTTCCTCCCCGATCTCATC 59.929 57.143 0.00 0.00 0.00 2.92
201 202 1.762957 GTTTCCTCCCCGATCTCATCA 59.237 52.381 0.00 0.00 0.00 3.07
202 203 1.709578 TTCCTCCCCGATCTCATCAG 58.290 55.000 0.00 0.00 0.00 2.90
203 204 0.178950 TCCTCCCCGATCTCATCAGG 60.179 60.000 0.00 0.00 0.00 3.86
204 205 1.670590 CTCCCCGATCTCATCAGGC 59.329 63.158 0.00 0.00 0.00 4.85
205 206 2.152297 CTCCCCGATCTCATCAGGCG 62.152 65.000 0.00 0.00 0.00 5.52
206 207 2.502492 CCCCGATCTCATCAGGCGT 61.502 63.158 0.00 0.00 0.00 5.68
207 208 1.300465 CCCGATCTCATCAGGCGTG 60.300 63.158 0.00 0.00 0.00 5.34
208 209 1.300465 CCGATCTCATCAGGCGTGG 60.300 63.158 6.56 0.00 0.00 4.94
209 210 1.735973 CGATCTCATCAGGCGTGGA 59.264 57.895 6.56 0.00 0.00 4.02
210 211 0.103026 CGATCTCATCAGGCGTGGAA 59.897 55.000 6.56 0.00 0.00 3.53
211 212 1.863267 GATCTCATCAGGCGTGGAAG 58.137 55.000 6.56 2.29 0.00 3.46
212 213 1.137872 GATCTCATCAGGCGTGGAAGT 59.862 52.381 6.56 0.00 0.00 3.01
213 214 0.532573 TCTCATCAGGCGTGGAAGTC 59.467 55.000 6.56 0.00 0.00 3.01
214 215 0.534412 CTCATCAGGCGTGGAAGTCT 59.466 55.000 6.56 0.00 0.00 3.24
215 216 0.532573 TCATCAGGCGTGGAAGTCTC 59.467 55.000 6.56 0.00 0.00 3.36
216 217 0.803768 CATCAGGCGTGGAAGTCTCG 60.804 60.000 6.56 0.00 0.00 4.04
220 221 4.373116 GCGTGGAAGTCTCGCCCA 62.373 66.667 9.13 0.00 43.41 5.36
221 222 2.125912 CGTGGAAGTCTCGCCCAG 60.126 66.667 0.00 0.00 0.00 4.45
222 223 2.266055 GTGGAAGTCTCGCCCAGG 59.734 66.667 0.00 0.00 0.00 4.45
223 224 3.003173 TGGAAGTCTCGCCCAGGG 61.003 66.667 0.00 0.00 0.00 4.45
224 225 2.683933 GGAAGTCTCGCCCAGGGA 60.684 66.667 10.89 0.00 0.00 4.20
225 226 2.066999 GGAAGTCTCGCCCAGGGAT 61.067 63.158 10.89 0.00 0.00 3.85
226 227 0.759436 GGAAGTCTCGCCCAGGGATA 60.759 60.000 10.89 0.00 0.00 2.59
227 228 0.676736 GAAGTCTCGCCCAGGGATAG 59.323 60.000 10.89 5.30 0.00 2.08
228 229 0.760945 AAGTCTCGCCCAGGGATAGG 60.761 60.000 10.89 0.00 0.00 2.57
229 230 2.524394 TCTCGCCCAGGGATAGGC 60.524 66.667 10.89 0.00 0.00 3.93
230 231 3.631046 CTCGCCCAGGGATAGGCC 61.631 72.222 10.89 0.00 0.00 5.19
236 237 3.642078 CAGGGATAGGCCGTGGAA 58.358 61.111 0.00 0.00 46.38 3.53
237 238 1.912220 CAGGGATAGGCCGTGGAAA 59.088 57.895 0.00 0.00 46.38 3.13
238 239 0.179045 CAGGGATAGGCCGTGGAAAG 60.179 60.000 0.00 0.00 46.38 2.62
239 240 1.148498 GGGATAGGCCGTGGAAAGG 59.852 63.158 0.00 0.00 39.09 3.11
240 241 1.148498 GGATAGGCCGTGGAAAGGG 59.852 63.158 0.00 0.00 35.32 3.95
247 248 4.351054 CGTGGAAAGGGCAGGGCT 62.351 66.667 0.00 0.00 0.00 5.19
248 249 2.677875 GTGGAAAGGGCAGGGCTG 60.678 66.667 0.00 0.00 0.00 4.85
263 264 4.722700 CTGCCCCGGTCTTGTGGG 62.723 72.222 0.00 0.00 45.58 4.61
277 278 4.629958 TGGGCCCCCAAATGCGTT 62.630 61.111 22.27 0.00 44.12 4.84
278 279 4.081185 GGGCCCCCAAATGCGTTG 62.081 66.667 12.23 0.00 36.94 4.10
296 297 2.904866 GCGCATTGCCCGGGATAA 60.905 61.111 29.31 19.36 37.76 1.75
297 298 2.485795 GCGCATTGCCCGGGATAAA 61.486 57.895 29.31 15.86 37.76 1.40
298 299 2.010582 GCGCATTGCCCGGGATAAAA 62.011 55.000 29.31 12.99 37.76 1.52
299 300 0.673437 CGCATTGCCCGGGATAAAAT 59.327 50.000 29.31 14.85 0.00 1.82
300 301 1.068434 CGCATTGCCCGGGATAAAATT 59.932 47.619 29.31 0.14 0.00 1.82
301 302 2.294791 CGCATTGCCCGGGATAAAATTA 59.705 45.455 29.31 0.00 0.00 1.40
302 303 3.056891 CGCATTGCCCGGGATAAAATTAT 60.057 43.478 29.31 0.00 0.00 1.28
303 304 4.494484 GCATTGCCCGGGATAAAATTATC 58.506 43.478 29.31 1.80 39.01 1.75
315 316 6.656003 GGATAAAATTATCCGTGGTTTCTCG 58.344 40.000 14.66 0.00 46.87 4.04
316 317 6.293244 GGATAAAATTATCCGTGGTTTCTCGG 60.293 42.308 14.66 0.00 46.87 4.63
317 318 1.949465 ATTATCCGTGGTTTCTCGGC 58.051 50.000 0.00 0.00 46.21 5.54
318 319 0.108041 TTATCCGTGGTTTCTCGGCC 60.108 55.000 0.00 0.00 46.21 6.13
319 320 0.974010 TATCCGTGGTTTCTCGGCCT 60.974 55.000 0.00 0.00 46.21 5.19
320 321 2.521958 ATCCGTGGTTTCTCGGCCTG 62.522 60.000 0.00 0.00 46.21 4.85
321 322 2.742372 CGTGGTTTCTCGGCCTGG 60.742 66.667 0.00 0.00 0.00 4.45
322 323 2.359975 GTGGTTTCTCGGCCTGGG 60.360 66.667 0.00 0.00 0.00 4.45
323 324 3.646715 TGGTTTCTCGGCCTGGGG 61.647 66.667 0.00 0.00 0.00 4.96
324 325 3.327404 GGTTTCTCGGCCTGGGGA 61.327 66.667 0.00 0.00 0.00 4.81
325 326 2.754375 GTTTCTCGGCCTGGGGAA 59.246 61.111 0.00 0.00 0.00 3.97
326 327 1.377333 GTTTCTCGGCCTGGGGAAG 60.377 63.158 0.00 0.00 0.00 3.46
336 337 4.626745 TGGGGAAGGCCAGGGGAA 62.627 66.667 5.01 0.00 35.15 3.97
337 338 3.744155 GGGGAAGGCCAGGGGAAG 61.744 72.222 5.01 0.00 35.15 3.46
338 339 2.614013 GGGAAGGCCAGGGGAAGA 60.614 66.667 5.01 0.00 35.15 2.87
339 340 2.684499 GGGAAGGCCAGGGGAAGAG 61.684 68.421 5.01 0.00 35.15 2.85
340 341 2.684499 GGAAGGCCAGGGGAAGAGG 61.684 68.421 5.01 0.00 0.00 3.69
345 346 3.415087 CCAGGGGAAGAGGCAGGG 61.415 72.222 0.00 0.00 0.00 4.45
346 347 2.285668 CAGGGGAAGAGGCAGGGA 60.286 66.667 0.00 0.00 0.00 4.20
347 348 1.695597 CAGGGGAAGAGGCAGGGAT 60.696 63.158 0.00 0.00 0.00 3.85
348 349 1.385206 AGGGGAAGAGGCAGGGATC 60.385 63.158 0.00 0.00 0.00 3.36
349 350 2.456443 GGGGAAGAGGCAGGGATCC 61.456 68.421 1.92 1.92 0.00 3.36
350 351 2.456443 GGGAAGAGGCAGGGATCCC 61.456 68.421 24.59 24.59 42.74 3.85
351 352 2.812619 GGAAGAGGCAGGGATCCCG 61.813 68.421 25.48 20.00 41.95 5.14
352 353 2.041265 AAGAGGCAGGGATCCCGT 59.959 61.111 25.48 11.34 41.95 5.28
353 354 2.317149 GAAGAGGCAGGGATCCCGTG 62.317 65.000 25.48 22.36 41.71 4.94
354 355 3.866582 GAGGCAGGGATCCCGTGG 61.867 72.222 25.48 18.96 39.49 4.94
364 365 4.470764 TCCCGTGGGATCATGTGA 57.529 55.556 2.72 0.00 39.76 3.58
365 366 2.690367 TCCCGTGGGATCATGTGAA 58.310 52.632 2.72 0.00 39.76 3.18
366 367 0.988063 TCCCGTGGGATCATGTGAAA 59.012 50.000 2.72 0.00 39.76 2.69
367 368 1.094785 CCCGTGGGATCATGTGAAAC 58.905 55.000 0.00 0.00 37.50 2.78
368 369 1.094785 CCGTGGGATCATGTGAAACC 58.905 55.000 0.00 0.00 34.36 3.27
369 370 1.612991 CCGTGGGATCATGTGAAACCA 60.613 52.381 0.00 5.30 34.36 3.67
370 371 2.158559 CGTGGGATCATGTGAAACCAA 58.841 47.619 9.64 0.00 36.25 3.67
371 372 2.556189 CGTGGGATCATGTGAAACCAAA 59.444 45.455 9.64 0.00 36.25 3.28
372 373 3.193267 CGTGGGATCATGTGAAACCAAAT 59.807 43.478 9.64 0.00 36.25 2.32
373 374 4.497300 GTGGGATCATGTGAAACCAAATG 58.503 43.478 9.64 0.00 36.25 2.32
374 375 4.220382 GTGGGATCATGTGAAACCAAATGA 59.780 41.667 9.64 1.27 41.20 2.57
375 376 4.463539 TGGGATCATGTGAAACCAAATGAG 59.536 41.667 4.81 0.00 40.52 2.90
376 377 4.706476 GGGATCATGTGAAACCAAATGAGA 59.294 41.667 4.81 0.00 40.52 3.27
377 378 5.393461 GGGATCATGTGAAACCAAATGAGAC 60.393 44.000 4.81 2.31 40.52 3.36
378 379 5.393461 GGATCATGTGAAACCAAATGAGACC 60.393 44.000 4.81 6.63 40.52 3.85
384 385 5.163141 TGTGAAACCAAATGAGACCTTAGGA 60.163 40.000 4.77 0.00 34.36 2.94
394 395 4.296056 TGAGACCTTAGGATTTAGGGACC 58.704 47.826 4.77 0.00 35.79 4.46
419 420 2.487428 CCTCGAGTGTGAGAGGCG 59.513 66.667 12.31 0.00 46.23 5.52
429 430 1.347707 TGTGAGAGGCGGTCAGATTTT 59.652 47.619 0.00 0.00 0.00 1.82
430 431 2.565391 TGTGAGAGGCGGTCAGATTTTA 59.435 45.455 0.00 0.00 0.00 1.52
434 435 2.027192 AGAGGCGGTCAGATTTTAAGCA 60.027 45.455 0.00 0.00 0.00 3.91
440 441 3.125316 CGGTCAGATTTTAAGCACTCACC 59.875 47.826 0.00 0.00 0.00 4.02
442 443 4.518970 GGTCAGATTTTAAGCACTCACCAA 59.481 41.667 0.00 0.00 0.00 3.67
454 455 5.957798 AGCACTCACCAAATCATATTGTTG 58.042 37.500 0.00 0.00 0.00 3.33
493 494 3.799137 TTAGATGAAAACAACGTCCGC 57.201 42.857 0.00 0.00 0.00 5.54
502 503 1.091197 ACAACGTCCGCGAAACCTTT 61.091 50.000 8.23 0.00 42.00 3.11
512 513 2.127251 GCGAAACCTTTTGCCTTTCTG 58.873 47.619 0.00 0.00 40.83 3.02
515 516 2.602257 AACCTTTTGCCTTTCTGTGC 57.398 45.000 0.00 0.00 0.00 4.57
543 544 0.663153 GCAGAAGTCACCGCAAAAGT 59.337 50.000 0.00 0.00 0.00 2.66
545 546 2.719798 CAGAAGTCACCGCAAAAGTTG 58.280 47.619 0.00 0.00 0.00 3.16
587 588 2.247637 GTTCGATTAAAAAGCACGGGC 58.752 47.619 0.00 0.00 41.61 6.13
636 640 1.471287 GGTTGTTTTCCGCCCTATGAC 59.529 52.381 0.00 0.00 0.00 3.06
663 667 3.301771 GCACACGCAGACAAATCAAAAAC 60.302 43.478 0.00 0.00 38.36 2.43
703 707 0.038435 CCCAATGATTTGTGCGCACA 60.038 50.000 37.86 37.86 39.98 4.57
788 795 2.949451 ATGAACCGAGCTCACACTAG 57.051 50.000 15.40 0.00 0.00 2.57
802 815 1.065926 ACACTAGCAGCAGCAGCAATA 60.066 47.619 12.92 0.00 45.49 1.90
846 859 6.312672 GGAAACTGAGAGAGAAAGCTATCAAC 59.687 42.308 0.00 0.00 35.88 3.18
893 906 6.765989 GTCTGCTACAATCCAAACCATATACA 59.234 38.462 0.00 0.00 0.00 2.29
894 907 6.765989 TCTGCTACAATCCAAACCATATACAC 59.234 38.462 0.00 0.00 0.00 2.90
896 909 6.542005 TGCTACAATCCAAACCATATACACTG 59.458 38.462 0.00 0.00 0.00 3.66
897 910 6.542370 GCTACAATCCAAACCATATACACTGT 59.458 38.462 0.00 0.00 0.00 3.55
898 911 7.713507 GCTACAATCCAAACCATATACACTGTA 59.286 37.037 0.00 0.00 0.00 2.74
899 912 9.261180 CTACAATCCAAACCATATACACTGTAG 57.739 37.037 0.00 0.00 0.00 2.74
931 952 1.098712 ACCGTTCCGTGCAACATGTT 61.099 50.000 4.92 4.92 35.74 2.71
936 957 2.015627 CCGTGCAACATGTTTGGCG 61.016 57.895 8.77 12.58 35.74 5.69
952 973 4.079090 CGGAGCTGATCGACACAC 57.921 61.111 0.00 0.00 0.00 3.82
957 981 1.741770 GCTGATCGACACACACCCC 60.742 63.158 0.00 0.00 0.00 4.95
960 984 1.079127 GATCGACACACACCCCCAG 60.079 63.158 0.00 0.00 0.00 4.45
1013 1037 4.488136 CGCCACCAGCCAGCCATA 62.488 66.667 0.00 0.00 38.78 2.74
1082 1106 3.296709 AACACGTAGGCAGAGCGGG 62.297 63.158 0.00 0.00 34.89 6.13
1234 1261 2.930562 AGCACCACCTCCCTGTCC 60.931 66.667 0.00 0.00 0.00 4.02
1364 1409 2.879233 AAGCCTTTCTCCGACGGCA 61.879 57.895 9.66 0.00 44.85 5.69
1663 1714 4.147449 TGGTGATGAGCCGGCGAG 62.147 66.667 23.20 0.00 0.00 5.03
1736 1791 4.025563 CAGCTGAGCTAGTACAGTAGTACG 60.026 50.000 8.42 0.00 45.57 3.67
1737 1792 6.420030 CAGCTGAGCTAGTACAGTAGTACGT 61.420 48.000 8.42 0.00 45.57 3.57
1738 1793 7.173949 CAGCTGAGCTAGTACAGTAGTACGTA 61.174 46.154 8.42 0.00 45.57 3.57
1789 1846 2.441410 CCCTTCTGCTTCCTCCTTTTC 58.559 52.381 0.00 0.00 0.00 2.29
1820 1877 9.219603 CATCTTCTTGTAGTAGGATTTTTGACA 57.780 33.333 0.00 0.00 0.00 3.58
1821 1878 9.793259 ATCTTCTTGTAGTAGGATTTTTGACAA 57.207 29.630 0.00 0.00 0.00 3.18
1838 1896 8.700722 TTTTGACAATATTTGATGTGGCATAC 57.299 30.769 0.00 0.00 0.00 2.39
1839 1897 7.401955 TTGACAATATTTGATGTGGCATACA 57.598 32.000 0.00 0.00 44.87 2.29
1925 1987 6.413783 TCTCTGTGTTGTCCTTGTACATAA 57.586 37.500 0.00 0.00 0.00 1.90
1951 2013 3.459598 TCCTTTCCTCCCCTTGTATCATG 59.540 47.826 0.00 0.00 0.00 3.07
2099 2161 4.084287 ACTGACTCCACCGATGTTTACTA 58.916 43.478 0.00 0.00 0.00 1.82
2110 2172 3.486108 CGATGTTTACTAAGGCTACGCTG 59.514 47.826 0.00 0.00 0.00 5.18
2117 2179 1.676529 CTAAGGCTACGCTGCACTCTA 59.323 52.381 0.00 0.00 34.04 2.43
2136 2198 4.699994 TCTACTCCCCTCCTGATTTTTCT 58.300 43.478 0.00 0.00 0.00 2.52
2138 2200 4.039603 ACTCCCCTCCTGATTTTTCTTG 57.960 45.455 0.00 0.00 0.00 3.02
2142 2208 4.588528 TCCCCTCCTGATTTTTCTTGTTTG 59.411 41.667 0.00 0.00 0.00 2.93
2152 2218 5.771602 TTTTTCTTGTTTGAGCCGAAAAC 57.228 34.783 0.00 0.76 37.90 2.43
2157 2223 2.286872 TGTTTGAGCCGAAAACCGTAA 58.713 42.857 4.58 0.00 36.82 3.18
2168 2234 5.458126 GCCGAAAACCGTAAAACAATTGTTA 59.542 36.000 23.53 6.97 35.14 2.41
2221 2309 1.000283 CTGAAGCCAGCTACCTATCCG 60.000 57.143 0.00 0.00 33.07 4.18
2229 2317 1.076350 AGCTACCTATCCGCTCCTGAT 59.924 52.381 0.00 0.00 0.00 2.90
2231 2319 2.685897 GCTACCTATCCGCTCCTGATAG 59.314 54.545 0.00 0.00 40.80 2.08
2235 2323 2.494073 CCTATCCGCTCCTGATAGAACC 59.506 54.545 8.48 0.00 42.77 3.62
2272 2360 3.823304 AGATGAAACACCAAAGAGGAAGC 59.177 43.478 0.00 0.00 41.22 3.86
2282 2370 3.490078 CCAAAGAGGAAGCTCGCTAGTAG 60.490 52.174 0.00 0.00 41.22 2.57
2317 2405 4.084066 TGAAATGCTAGTACAAGTGTTGCG 60.084 41.667 0.00 0.00 0.00 4.85
2319 2407 3.100658 TGCTAGTACAAGTGTTGCGAA 57.899 42.857 0.00 0.00 0.00 4.70
2369 2460 3.779444 TCCGGATTCTCTATGGCTATGT 58.221 45.455 0.00 0.00 0.00 2.29
2371 2462 3.118956 CCGGATTCTCTATGGCTATGTCC 60.119 52.174 0.00 0.00 0.00 4.02
2372 2463 3.766591 CGGATTCTCTATGGCTATGTCCT 59.233 47.826 0.00 0.00 0.00 3.85
2373 2464 4.381398 CGGATTCTCTATGGCTATGTCCTG 60.381 50.000 0.00 0.00 0.00 3.86
2374 2465 4.774726 GGATTCTCTATGGCTATGTCCTGA 59.225 45.833 0.00 0.00 0.00 3.86
2375 2466 5.424895 GGATTCTCTATGGCTATGTCCTGAT 59.575 44.000 0.00 0.00 0.00 2.90
2376 2467 6.070309 GGATTCTCTATGGCTATGTCCTGATT 60.070 42.308 0.00 0.00 0.00 2.57
2377 2468 5.991933 TCTCTATGGCTATGTCCTGATTC 57.008 43.478 0.00 0.00 0.00 2.52
2378 2469 4.774726 TCTCTATGGCTATGTCCTGATTCC 59.225 45.833 0.00 0.00 0.00 3.01
2463 2554 1.892391 GAACCATTCGGCGGGATCC 60.892 63.158 7.21 1.92 34.57 3.36
2502 2593 7.149569 TCTCTTGCGAATGATTTCTTGATTT 57.850 32.000 0.00 0.00 0.00 2.17
2533 2624 1.172812 AAGGGCAGCTGAAACGAACC 61.173 55.000 20.43 6.83 0.00 3.62
2534 2625 1.896660 GGGCAGCTGAAACGAACCA 60.897 57.895 20.43 0.00 0.00 3.67
2535 2626 1.452145 GGGCAGCTGAAACGAACCAA 61.452 55.000 20.43 0.00 0.00 3.67
2557 2648 3.282021 CCAATTCCAGGACGAATCATGT 58.718 45.455 0.00 0.00 34.74 3.21
2574 2665 9.698309 CGAATCATGTACTCTGTTCCTAAATAT 57.302 33.333 0.00 0.00 0.00 1.28
2695 2879 4.673968 ACTCCAGTACAGGTGTGATTCTA 58.326 43.478 10.81 0.00 34.33 2.10
2786 2970 1.069049 CAAGCCCACACAGAAAAAGGG 59.931 52.381 0.00 0.00 42.55 3.95
2795 2979 1.533033 AGAAAAAGGGGGTTGGGCG 60.533 57.895 0.00 0.00 0.00 6.13
2824 3008 2.486982 GTGATTGCTCAGTTGACATGCT 59.513 45.455 0.00 0.00 30.18 3.79
2947 3131 2.334838 CTGCCTTTTGCTGATTGCTTC 58.665 47.619 0.00 0.00 41.11 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.986306 GCGTTGCTGCTTCATGGCT 61.986 57.895 0.00 0.00 0.00 4.75
1 2 2.505557 GCGTTGCTGCTTCATGGC 60.506 61.111 0.00 0.00 0.00 4.40
2 3 1.005294 GTTGCGTTGCTGCTTCATGG 61.005 55.000 0.00 0.00 35.36 3.66
3 4 1.332180 CGTTGCGTTGCTGCTTCATG 61.332 55.000 0.00 0.00 35.36 3.07
4 5 1.081906 CGTTGCGTTGCTGCTTCAT 60.082 52.632 0.00 0.00 35.36 2.57
5 6 2.327592 CGTTGCGTTGCTGCTTCA 59.672 55.556 0.00 0.00 35.36 3.02
6 7 2.427410 CCGTTGCGTTGCTGCTTC 60.427 61.111 0.00 0.00 35.36 3.86
7 8 3.964875 CCCGTTGCGTTGCTGCTT 61.965 61.111 0.00 0.00 35.36 3.91
39 40 4.181010 CATGCTCCACCCCTCCGG 62.181 72.222 0.00 0.00 37.81 5.14
40 41 4.181010 CCATGCTCCACCCCTCCG 62.181 72.222 0.00 0.00 0.00 4.63
41 42 2.692368 TCCATGCTCCACCCCTCC 60.692 66.667 0.00 0.00 0.00 4.30
42 43 2.750657 CCTCCATGCTCCACCCCTC 61.751 68.421 0.00 0.00 0.00 4.30
43 44 2.693864 CCTCCATGCTCCACCCCT 60.694 66.667 0.00 0.00 0.00 4.79
44 45 3.017581 ACCTCCATGCTCCACCCC 61.018 66.667 0.00 0.00 0.00 4.95
45 46 1.852157 TTCACCTCCATGCTCCACCC 61.852 60.000 0.00 0.00 0.00 4.61
46 47 0.393537 CTTCACCTCCATGCTCCACC 60.394 60.000 0.00 0.00 0.00 4.61
47 48 0.393537 CCTTCACCTCCATGCTCCAC 60.394 60.000 0.00 0.00 0.00 4.02
48 49 1.565390 CCCTTCACCTCCATGCTCCA 61.565 60.000 0.00 0.00 0.00 3.86
49 50 1.225704 CCCTTCACCTCCATGCTCC 59.774 63.158 0.00 0.00 0.00 4.70
50 51 0.842635 ATCCCTTCACCTCCATGCTC 59.157 55.000 0.00 0.00 0.00 4.26
51 52 0.549950 CATCCCTTCACCTCCATGCT 59.450 55.000 0.00 0.00 0.00 3.79
52 53 0.466922 CCATCCCTTCACCTCCATGC 60.467 60.000 0.00 0.00 0.00 4.06
53 54 0.184451 CCCATCCCTTCACCTCCATG 59.816 60.000 0.00 0.00 0.00 3.66
54 55 0.995675 CCCCATCCCTTCACCTCCAT 60.996 60.000 0.00 0.00 0.00 3.41
55 56 1.619363 CCCCATCCCTTCACCTCCA 60.619 63.158 0.00 0.00 0.00 3.86
56 57 2.386935 CCCCCATCCCTTCACCTCC 61.387 68.421 0.00 0.00 0.00 4.30
57 58 3.335711 CCCCCATCCCTTCACCTC 58.664 66.667 0.00 0.00 0.00 3.85
71 72 3.920093 CTGGAAACGGCTCACCCCC 62.920 68.421 0.00 0.00 0.00 5.40
72 73 2.359975 CTGGAAACGGCTCACCCC 60.360 66.667 0.00 0.00 0.00 4.95
73 74 1.228154 AACTGGAAACGGCTCACCC 60.228 57.895 0.00 0.00 41.93 4.61
74 75 1.949257 CAACTGGAAACGGCTCACC 59.051 57.895 0.00 0.00 41.93 4.02
75 76 1.166531 AGCAACTGGAAACGGCTCAC 61.167 55.000 0.00 0.00 41.93 3.51
76 77 1.148273 AGCAACTGGAAACGGCTCA 59.852 52.632 0.00 0.00 41.93 4.26
77 78 1.576421 CAGCAACTGGAAACGGCTC 59.424 57.895 0.00 0.00 41.93 4.70
78 79 3.749981 CAGCAACTGGAAACGGCT 58.250 55.556 0.00 0.00 41.93 5.52
87 88 2.037136 CGCCCTTCTCCAGCAACTG 61.037 63.158 0.00 0.00 0.00 3.16
88 89 2.348998 CGCCCTTCTCCAGCAACT 59.651 61.111 0.00 0.00 0.00 3.16
89 90 2.747855 CCGCCCTTCTCCAGCAAC 60.748 66.667 0.00 0.00 0.00 4.17
90 91 2.927856 TCCGCCCTTCTCCAGCAA 60.928 61.111 0.00 0.00 0.00 3.91
91 92 3.393970 CTCCGCCCTTCTCCAGCA 61.394 66.667 0.00 0.00 0.00 4.41
92 93 4.847444 GCTCCGCCCTTCTCCAGC 62.847 72.222 0.00 0.00 0.00 4.85
93 94 2.262774 AATGCTCCGCCCTTCTCCAG 62.263 60.000 0.00 0.00 0.00 3.86
94 95 2.257409 GAATGCTCCGCCCTTCTCCA 62.257 60.000 0.00 0.00 0.00 3.86
95 96 1.524849 GAATGCTCCGCCCTTCTCC 60.525 63.158 0.00 0.00 0.00 3.71
96 97 1.884926 CGAATGCTCCGCCCTTCTC 60.885 63.158 0.00 0.00 0.00 2.87
97 98 2.187946 CGAATGCTCCGCCCTTCT 59.812 61.111 0.00 0.00 0.00 2.85
98 99 2.174319 GTCGAATGCTCCGCCCTTC 61.174 63.158 0.00 0.00 0.00 3.46
99 100 2.125106 GTCGAATGCTCCGCCCTT 60.125 61.111 0.00 0.00 0.00 3.95
100 101 4.514577 CGTCGAATGCTCCGCCCT 62.515 66.667 0.00 0.00 0.00 5.19
102 103 4.508128 TCCGTCGAATGCTCCGCC 62.508 66.667 0.00 0.00 0.00 6.13
103 104 2.956964 CTCCGTCGAATGCTCCGC 60.957 66.667 0.00 0.00 0.00 5.54
104 105 2.278857 CCTCCGTCGAATGCTCCG 60.279 66.667 0.00 0.00 0.00 4.63
105 106 1.066587 CTCCTCCGTCGAATGCTCC 59.933 63.158 0.00 0.00 0.00 4.70
106 107 1.066587 CCTCCTCCGTCGAATGCTC 59.933 63.158 0.00 0.00 0.00 4.26
107 108 2.427245 CCCTCCTCCGTCGAATGCT 61.427 63.158 0.00 0.00 0.00 3.79
108 109 2.107141 CCCTCCTCCGTCGAATGC 59.893 66.667 0.00 0.00 0.00 3.56
109 110 2.107141 GCCCTCCTCCGTCGAATG 59.893 66.667 0.00 0.00 0.00 2.67
110 111 3.528370 CGCCCTCCTCCGTCGAAT 61.528 66.667 0.00 0.00 0.00 3.34
126 127 3.326210 GCAAGATCGAGCGCTCCG 61.326 66.667 30.66 24.12 0.00 4.63
127 128 2.964389 GGCAAGATCGAGCGCTCC 60.964 66.667 30.66 17.35 0.00 4.70
128 129 3.326210 CGGCAAGATCGAGCGCTC 61.326 66.667 27.64 27.64 0.00 5.03
153 154 2.656651 CGGCCTCGCGAATGAGAG 60.657 66.667 11.33 0.00 41.22 3.20
154 155 3.126074 CTCGGCCTCGCGAATGAGA 62.126 63.158 11.33 7.04 38.28 3.27
155 156 2.656651 CTCGGCCTCGCGAATGAG 60.657 66.667 11.33 10.96 36.13 2.90
156 157 4.873129 GCTCGGCCTCGCGAATGA 62.873 66.667 11.33 4.66 36.13 2.57
164 165 4.821589 CCCTTGTCGCTCGGCCTC 62.822 72.222 0.00 0.00 0.00 4.70
166 167 4.699522 AACCCTTGTCGCTCGGCC 62.700 66.667 0.00 0.00 0.00 6.13
167 168 2.668550 AAACCCTTGTCGCTCGGC 60.669 61.111 0.00 0.00 0.00 5.54
168 169 2.033194 GGAAACCCTTGTCGCTCGG 61.033 63.158 0.00 0.00 0.00 4.63
169 170 1.004918 AGGAAACCCTTGTCGCTCG 60.005 57.895 0.00 0.00 0.00 5.03
170 171 0.673956 GGAGGAAACCCTTGTCGCTC 60.674 60.000 0.00 0.00 33.25 5.03
171 172 1.375326 GGAGGAAACCCTTGTCGCT 59.625 57.895 0.00 0.00 33.25 4.93
172 173 1.674651 GGGAGGAAACCCTTGTCGC 60.675 63.158 0.00 0.00 45.90 5.19
173 174 4.716003 GGGAGGAAACCCTTGTCG 57.284 61.111 0.00 0.00 45.90 4.35
180 181 1.070914 GATGAGATCGGGGAGGAAACC 59.929 57.143 0.00 0.00 0.00 3.27
181 182 1.762957 TGATGAGATCGGGGAGGAAAC 59.237 52.381 0.00 0.00 0.00 2.78
182 183 2.042464 CTGATGAGATCGGGGAGGAAA 58.958 52.381 0.00 0.00 31.92 3.13
183 184 1.709578 CTGATGAGATCGGGGAGGAA 58.290 55.000 0.00 0.00 31.92 3.36
184 185 3.446658 CTGATGAGATCGGGGAGGA 57.553 57.895 0.00 0.00 31.92 3.71
190 191 1.300465 CCACGCCTGATGAGATCGG 60.300 63.158 0.00 0.00 35.39 4.18
191 192 0.103026 TTCCACGCCTGATGAGATCG 59.897 55.000 0.00 0.00 0.00 3.69
192 193 1.137872 ACTTCCACGCCTGATGAGATC 59.862 52.381 0.00 0.00 0.00 2.75
193 194 1.137872 GACTTCCACGCCTGATGAGAT 59.862 52.381 0.00 0.00 0.00 2.75
194 195 0.532573 GACTTCCACGCCTGATGAGA 59.467 55.000 0.00 0.00 0.00 3.27
195 196 0.534412 AGACTTCCACGCCTGATGAG 59.466 55.000 0.00 0.00 0.00 2.90
196 197 0.532573 GAGACTTCCACGCCTGATGA 59.467 55.000 0.00 0.00 0.00 2.92
197 198 0.803768 CGAGACTTCCACGCCTGATG 60.804 60.000 0.00 0.00 0.00 3.07
198 199 1.513158 CGAGACTTCCACGCCTGAT 59.487 57.895 0.00 0.00 0.00 2.90
199 200 2.962569 CGAGACTTCCACGCCTGA 59.037 61.111 0.00 0.00 0.00 3.86
200 201 2.811317 GCGAGACTTCCACGCCTG 60.811 66.667 0.00 0.00 45.35 4.85
204 205 2.125912 CTGGGCGAGACTTCCACG 60.126 66.667 0.00 0.00 0.00 4.94
205 206 2.266055 CCTGGGCGAGACTTCCAC 59.734 66.667 0.00 0.00 0.00 4.02
206 207 2.822643 ATCCCTGGGCGAGACTTCCA 62.823 60.000 8.22 0.00 0.00 3.53
207 208 0.759436 TATCCCTGGGCGAGACTTCC 60.759 60.000 8.22 0.00 0.00 3.46
208 209 0.676736 CTATCCCTGGGCGAGACTTC 59.323 60.000 8.22 0.00 0.00 3.01
209 210 0.760945 CCTATCCCTGGGCGAGACTT 60.761 60.000 8.22 0.00 0.00 3.01
210 211 1.152440 CCTATCCCTGGGCGAGACT 60.152 63.158 8.22 0.00 0.00 3.24
211 212 2.873525 GCCTATCCCTGGGCGAGAC 61.874 68.421 8.22 0.00 39.45 3.36
212 213 2.524394 GCCTATCCCTGGGCGAGA 60.524 66.667 8.22 0.00 39.45 4.04
217 218 3.560251 CCACGGCCTATCCCTGGG 61.560 72.222 6.33 6.33 37.37 4.45
218 219 1.632018 TTTCCACGGCCTATCCCTGG 61.632 60.000 0.00 0.00 40.97 4.45
219 220 0.179045 CTTTCCACGGCCTATCCCTG 60.179 60.000 0.00 0.00 0.00 4.45
220 221 1.345715 CCTTTCCACGGCCTATCCCT 61.346 60.000 0.00 0.00 0.00 4.20
221 222 1.148498 CCTTTCCACGGCCTATCCC 59.852 63.158 0.00 0.00 0.00 3.85
222 223 1.148498 CCCTTTCCACGGCCTATCC 59.852 63.158 0.00 0.00 0.00 2.59
223 224 1.526225 GCCCTTTCCACGGCCTATC 60.526 63.158 0.00 0.00 39.39 2.08
224 225 2.270874 CTGCCCTTTCCACGGCCTAT 62.271 60.000 0.00 0.00 45.07 2.57
225 226 2.931105 TGCCCTTTCCACGGCCTA 60.931 61.111 0.00 0.00 45.07 3.93
226 227 4.351054 CTGCCCTTTCCACGGCCT 62.351 66.667 0.00 0.00 45.07 5.19
230 231 4.351054 AGCCCTGCCCTTTCCACG 62.351 66.667 0.00 0.00 0.00 4.94
231 232 2.677875 CAGCCCTGCCCTTTCCAC 60.678 66.667 0.00 0.00 0.00 4.02
246 247 4.722700 CCCACAAGACCGGGGCAG 62.723 72.222 6.32 0.00 38.95 4.85
260 261 4.629958 AACGCATTTGGGGGCCCA 62.630 61.111 26.86 7.88 45.63 5.36
261 262 4.081185 CAACGCATTTGGGGGCCC 62.081 66.667 15.76 15.76 0.00 5.80
279 280 2.010582 TTTTATCCCGGGCAATGCGC 62.011 55.000 18.49 12.54 41.28 6.09
280 281 0.673437 ATTTTATCCCGGGCAATGCG 59.327 50.000 18.49 0.00 0.00 4.73
281 282 2.908688 AATTTTATCCCGGGCAATGC 57.091 45.000 18.49 0.00 0.00 3.56
304 305 2.742372 CCAGGCCGAGAAACCACG 60.742 66.667 0.00 0.00 0.00 4.94
305 306 2.359975 CCCAGGCCGAGAAACCAC 60.360 66.667 0.00 0.00 0.00 4.16
306 307 3.646715 CCCCAGGCCGAGAAACCA 61.647 66.667 0.00 0.00 0.00 3.67
307 308 2.821679 CTTCCCCAGGCCGAGAAACC 62.822 65.000 0.00 0.00 0.00 3.27
308 309 1.377333 CTTCCCCAGGCCGAGAAAC 60.377 63.158 0.00 0.00 0.00 2.78
309 310 2.602676 CCTTCCCCAGGCCGAGAAA 61.603 63.158 0.00 0.00 35.13 2.52
310 311 3.009115 CCTTCCCCAGGCCGAGAA 61.009 66.667 0.00 0.00 35.13 2.87
319 320 4.626745 TTCCCCTGGCCTTCCCCA 62.627 66.667 3.32 0.00 0.00 4.96
320 321 3.744155 CTTCCCCTGGCCTTCCCC 61.744 72.222 3.32 0.00 0.00 4.81
321 322 2.614013 TCTTCCCCTGGCCTTCCC 60.614 66.667 3.32 0.00 0.00 3.97
322 323 2.684499 CCTCTTCCCCTGGCCTTCC 61.684 68.421 3.32 0.00 0.00 3.46
323 324 3.002371 CCTCTTCCCCTGGCCTTC 58.998 66.667 3.32 0.00 0.00 3.46
324 325 3.342477 GCCTCTTCCCCTGGCCTT 61.342 66.667 3.32 0.00 40.71 4.35
325 326 4.682714 TGCCTCTTCCCCTGGCCT 62.683 66.667 3.32 0.00 45.56 5.19
326 327 4.120755 CTGCCTCTTCCCCTGGCC 62.121 72.222 0.00 0.00 45.56 5.36
327 328 4.120755 CCTGCCTCTTCCCCTGGC 62.121 72.222 0.00 0.00 46.26 4.85
328 329 3.415087 CCCTGCCTCTTCCCCTGG 61.415 72.222 0.00 0.00 0.00 4.45
329 330 1.695597 ATCCCTGCCTCTTCCCCTG 60.696 63.158 0.00 0.00 0.00 4.45
330 331 1.385206 GATCCCTGCCTCTTCCCCT 60.385 63.158 0.00 0.00 0.00 4.79
331 332 2.456443 GGATCCCTGCCTCTTCCCC 61.456 68.421 0.00 0.00 0.00 4.81
332 333 2.456443 GGGATCCCTGCCTCTTCCC 61.456 68.421 24.69 0.00 39.35 3.97
333 334 2.812619 CGGGATCCCTGCCTCTTCC 61.813 68.421 28.42 0.00 0.00 3.46
334 335 2.066999 ACGGGATCCCTGCCTCTTC 61.067 63.158 28.42 0.00 32.02 2.87
335 336 2.041265 ACGGGATCCCTGCCTCTT 59.959 61.111 28.42 3.32 32.02 2.85
336 337 2.765807 CACGGGATCCCTGCCTCT 60.766 66.667 28.42 3.68 32.02 3.69
337 338 3.866582 CCACGGGATCCCTGCCTC 61.867 72.222 28.42 0.93 32.02 4.70
348 349 1.094785 GTTTCACATGATCCCACGGG 58.905 55.000 0.00 0.00 0.00 5.28
349 350 1.094785 GGTTTCACATGATCCCACGG 58.905 55.000 0.00 0.00 0.00 4.94
350 351 1.819928 TGGTTTCACATGATCCCACG 58.180 50.000 0.00 0.00 0.00 4.94
351 352 4.220382 TCATTTGGTTTCACATGATCCCAC 59.780 41.667 0.00 0.00 35.77 4.61
352 353 4.414677 TCATTTGGTTTCACATGATCCCA 58.585 39.130 0.00 0.00 35.77 4.37
353 354 4.706476 TCTCATTTGGTTTCACATGATCCC 59.294 41.667 0.00 0.00 38.79 3.85
354 355 5.393461 GGTCTCATTTGGTTTCACATGATCC 60.393 44.000 0.00 0.00 38.79 3.36
355 356 5.416952 AGGTCTCATTTGGTTTCACATGATC 59.583 40.000 0.00 0.00 38.79 2.92
356 357 5.327732 AGGTCTCATTTGGTTTCACATGAT 58.672 37.500 0.00 0.00 38.79 2.45
357 358 4.728772 AGGTCTCATTTGGTTTCACATGA 58.271 39.130 0.00 0.00 37.64 3.07
358 359 5.458041 AAGGTCTCATTTGGTTTCACATG 57.542 39.130 0.00 0.00 33.58 3.21
359 360 5.711976 CCTAAGGTCTCATTTGGTTTCACAT 59.288 40.000 0.00 0.00 0.00 3.21
360 361 5.070001 CCTAAGGTCTCATTTGGTTTCACA 58.930 41.667 0.00 0.00 0.00 3.58
361 362 5.313712 TCCTAAGGTCTCATTTGGTTTCAC 58.686 41.667 0.00 0.00 0.00 3.18
362 363 5.576563 TCCTAAGGTCTCATTTGGTTTCA 57.423 39.130 0.00 0.00 0.00 2.69
363 364 7.468141 AAATCCTAAGGTCTCATTTGGTTTC 57.532 36.000 0.00 0.00 0.00 2.78
364 365 7.615757 CCTAAATCCTAAGGTCTCATTTGGTTT 59.384 37.037 0.00 0.00 0.00 3.27
365 366 7.119387 CCTAAATCCTAAGGTCTCATTTGGTT 58.881 38.462 0.00 0.00 0.00 3.67
366 367 6.353951 CCCTAAATCCTAAGGTCTCATTTGGT 60.354 42.308 0.00 0.00 0.00 3.67
367 368 6.064717 CCCTAAATCCTAAGGTCTCATTTGG 58.935 44.000 0.00 0.00 0.00 3.28
368 369 6.768381 GTCCCTAAATCCTAAGGTCTCATTTG 59.232 42.308 0.00 0.00 0.00 2.32
369 370 6.126449 GGTCCCTAAATCCTAAGGTCTCATTT 60.126 42.308 0.00 0.00 0.00 2.32
370 371 5.369993 GGTCCCTAAATCCTAAGGTCTCATT 59.630 44.000 0.00 0.00 0.00 2.57
371 372 4.908481 GGTCCCTAAATCCTAAGGTCTCAT 59.092 45.833 0.00 0.00 0.00 2.90
372 373 4.296056 GGTCCCTAAATCCTAAGGTCTCA 58.704 47.826 0.00 0.00 0.00 3.27
373 374 3.321396 CGGTCCCTAAATCCTAAGGTCTC 59.679 52.174 0.00 0.00 0.00 3.36
374 375 3.306613 CGGTCCCTAAATCCTAAGGTCT 58.693 50.000 0.00 0.00 0.00 3.85
375 376 3.036819 ACGGTCCCTAAATCCTAAGGTC 58.963 50.000 0.00 0.00 0.00 3.85
376 377 3.126323 ACGGTCCCTAAATCCTAAGGT 57.874 47.619 0.00 0.00 0.00 3.50
377 378 5.619132 TTTACGGTCCCTAAATCCTAAGG 57.381 43.478 0.00 0.00 0.00 2.69
378 379 5.819379 GGTTTTACGGTCCCTAAATCCTAAG 59.181 44.000 10.81 0.00 0.00 2.18
394 395 2.030540 TCTCACACTCGAGGGTTTTACG 60.031 50.000 20.03 6.68 33.59 3.18
404 405 2.282251 ACCGCCTCTCACACTCGA 60.282 61.111 0.00 0.00 0.00 4.04
405 406 2.179517 GACCGCCTCTCACACTCG 59.820 66.667 0.00 0.00 0.00 4.18
417 418 2.742053 TGAGTGCTTAAAATCTGACCGC 59.258 45.455 0.00 0.00 0.00 5.68
418 419 3.125316 GGTGAGTGCTTAAAATCTGACCG 59.875 47.826 0.00 0.00 0.00 4.79
419 420 4.072131 TGGTGAGTGCTTAAAATCTGACC 58.928 43.478 0.00 0.00 35.39 4.02
429 430 7.392953 TCAACAATATGATTTGGTGAGTGCTTA 59.607 33.333 0.99 0.00 45.80 3.09
430 431 6.209192 TCAACAATATGATTTGGTGAGTGCTT 59.791 34.615 0.99 0.00 45.80 3.91
440 441 7.148540 CCAAACCTGCTTCAACAATATGATTTG 60.149 37.037 0.00 0.00 0.00 2.32
442 443 6.400568 CCAAACCTGCTTCAACAATATGATT 58.599 36.000 0.00 0.00 0.00 2.57
454 455 6.207691 TCTAAAATATGCCAAACCTGCTTC 57.792 37.500 0.00 0.00 0.00 3.86
493 494 3.115554 CACAGAAAGGCAAAAGGTTTCG 58.884 45.455 0.00 0.00 35.70 3.46
502 503 4.559300 GCTTTCAATAGCACAGAAAGGCAA 60.559 41.667 17.02 0.00 45.09 4.52
512 513 4.378874 GGTGACTTCTGCTTTCAATAGCAC 60.379 45.833 0.00 0.00 45.72 4.40
515 516 3.181516 GCGGTGACTTCTGCTTTCAATAG 60.182 47.826 0.00 0.00 36.83 1.73
545 546 1.143183 CAGGATGGCAGGCAAATGC 59.857 57.895 0.00 0.00 45.74 3.56
548 549 1.980232 CAGCAGGATGGCAGGCAAA 60.980 57.895 0.00 0.00 35.86 3.68
551 552 3.951769 AACCAGCAGGATGGCAGGC 62.952 63.158 0.35 0.00 43.62 4.85
587 588 0.320374 TAGGGGTTTCTGCAGACGTG 59.680 55.000 18.03 0.00 0.00 4.49
663 667 1.743252 GCCCAAGAGAAGCGTGAGG 60.743 63.158 0.00 0.00 0.00 3.86
735 739 0.955905 TTCTTTTGGCCTAACGCACC 59.044 50.000 3.32 0.00 40.31 5.01
788 795 2.406401 CGGTATTGCTGCTGCTGC 59.594 61.111 22.51 22.51 40.48 5.25
893 906 1.215647 GCACGCTGCTACCTACAGT 59.784 57.895 0.00 0.00 40.96 3.55
894 907 1.078759 GTGCACGCTGCTACCTACAG 61.079 60.000 0.00 0.00 45.31 2.74
896 909 1.810030 GGTGCACGCTGCTACCTAC 60.810 63.158 11.45 6.60 45.31 3.18
897 910 2.577059 GGTGCACGCTGCTACCTA 59.423 61.111 11.45 0.00 45.31 3.08
898 911 4.742201 CGGTGCACGCTGCTACCT 62.742 66.667 11.45 0.00 45.31 3.08
931 952 2.184322 GTCGATCAGCTCCGCCAA 59.816 61.111 0.00 0.00 0.00 4.52
936 957 0.737715 GGTGTGTGTCGATCAGCTCC 60.738 60.000 0.00 0.00 0.00 4.70
941 962 1.826340 CTGGGGGTGTGTGTCGATCA 61.826 60.000 0.00 0.00 0.00 2.92
946 967 3.884774 TGGCTGGGGGTGTGTGTC 61.885 66.667 0.00 0.00 0.00 3.67
951 972 0.783850 ATAAAAGTGGCTGGGGGTGT 59.216 50.000 0.00 0.00 0.00 4.16
952 973 2.818751 TATAAAAGTGGCTGGGGGTG 57.181 50.000 0.00 0.00 0.00 4.61
960 984 5.400066 TGGAGCCTTTTTATAAAAGTGGC 57.600 39.130 29.82 29.82 43.38 5.01
1013 1037 1.004440 GCTCTGGCGTGAGGAACTT 60.004 57.895 8.93 0.00 41.55 2.66
1075 1099 1.841302 TTGGCATCTTGTCCCGCTCT 61.841 55.000 0.00 0.00 0.00 4.09
1082 1106 2.295885 CCTCTCCATTGGCATCTTGTC 58.704 52.381 0.00 0.00 0.00 3.18
1212 1239 2.930562 GGGAGGTGGTGCTCCTGT 60.931 66.667 6.34 0.00 39.58 4.00
1663 1714 1.076485 AGCAACCTGGATGGATGGC 60.076 57.895 0.00 0.00 38.83 4.40
1736 1791 3.743167 CGCGCGCGCTCATACTAC 61.743 66.667 45.97 19.75 39.32 2.73
1789 1846 9.454859 AAAATCCTACTACAAGAAGATGAAAGG 57.545 33.333 0.00 0.00 0.00 3.11
1821 1878 8.882736 CGTACATATGTATGCCACATCAAATAT 58.117 33.333 19.51 0.00 44.99 1.28
1847 1905 4.803426 AGCGCCGCTCACACTAGC 62.803 66.667 5.39 0.00 30.62 3.42
2110 2172 0.033011 TCAGGAGGGGAGTAGAGTGC 60.033 60.000 0.00 0.00 0.00 4.40
2117 2179 3.399305 ACAAGAAAAATCAGGAGGGGAGT 59.601 43.478 0.00 0.00 0.00 3.85
2136 2198 1.096416 ACGGTTTTCGGCTCAAACAA 58.904 45.000 9.70 0.00 44.45 2.83
2138 2200 3.337301 TTTACGGTTTTCGGCTCAAAC 57.663 42.857 0.00 0.95 44.45 2.93
2142 2208 3.337301 TTGTTTTACGGTTTTCGGCTC 57.663 42.857 0.00 0.00 44.45 4.70
2212 2300 4.333690 GTTCTATCAGGAGCGGATAGGTA 58.666 47.826 13.83 4.75 42.80 3.08
2221 2309 1.476891 TGACACGGTTCTATCAGGAGC 59.523 52.381 0.00 0.00 0.00 4.70
2231 2319 3.390135 TCTCAAGAACATGACACGGTTC 58.610 45.455 0.00 11.90 42.82 3.62
2235 2323 5.050159 TGTTTCATCTCAAGAACATGACACG 60.050 40.000 0.00 0.00 32.26 4.49
2272 2360 3.628487 AGCTAACCAACTCTACTAGCGAG 59.372 47.826 7.82 7.82 39.93 5.03
2282 2370 4.938226 ACTAGCATTTCAGCTAACCAACTC 59.062 41.667 0.00 0.00 45.69 3.01
2376 2467 5.688807 GAATGAGAATCCATTCCTTCAGGA 58.311 41.667 11.09 0.00 43.95 3.86
2458 2549 2.270874 AATCCCACAGCACCGGATCC 62.271 60.000 9.46 0.00 35.27 3.36
2463 2554 0.036010 AGAGAAATCCCACAGCACCG 60.036 55.000 0.00 0.00 0.00 4.94
2466 2557 1.538047 GCAAGAGAAATCCCACAGCA 58.462 50.000 0.00 0.00 0.00 4.41
2502 2593 1.152860 TGCCCTTGCAGGAAAACGA 60.153 52.632 0.00 0.00 44.23 3.85
2517 2608 0.317854 GTTGGTTCGTTTCAGCTGCC 60.318 55.000 9.47 2.79 0.00 4.85
2521 2612 2.793278 ATTGGTTGGTTCGTTTCAGC 57.207 45.000 0.00 0.00 0.00 4.26
2533 2624 3.081061 TGATTCGTCCTGGAATTGGTTG 58.919 45.455 0.00 0.00 36.79 3.77
2534 2625 3.433306 TGATTCGTCCTGGAATTGGTT 57.567 42.857 0.00 0.00 36.79 3.67
2535 2626 3.282021 CATGATTCGTCCTGGAATTGGT 58.718 45.455 0.00 0.00 36.79 3.67
2592 2767 2.358957 TCCAGATGATTTGAACTGCCG 58.641 47.619 0.00 0.00 0.00 5.69
2593 2768 7.934855 ATATATCCAGATGATTTGAACTGCC 57.065 36.000 0.00 0.00 34.76 4.85
2642 2823 7.368833 AGTGTACATCGCTATACCACTTTATC 58.631 38.462 0.00 0.00 34.88 1.75
2657 2838 4.156190 ACTGGAGTGAACTAGTGTACATCG 59.844 45.833 0.00 0.00 30.79 3.84
2695 2879 0.318762 GCTCTGAAGAAGTGACGGGT 59.681 55.000 0.00 0.00 0.00 5.28
2786 2970 3.068064 CCCATTCACGCCCAACCC 61.068 66.667 0.00 0.00 0.00 4.11
2795 2979 2.440409 ACTGAGCAATCACCCATTCAC 58.560 47.619 0.00 0.00 0.00 3.18
2824 3008 2.649516 CAAGCGACGATTCAAGCAAAA 58.350 42.857 0.00 0.00 0.00 2.44
2947 3131 1.234615 ACGCTCGTCCCAAATGGTTG 61.235 55.000 0.00 0.00 34.77 3.77


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

AutoCloner maintained by Alex Coulton.