Multiple sequence alignment - TraesCS1A01G072200

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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 TraesCS1A01G072200 chr1A 100.000 3924 0 0 1 3924 54464175 54460252 0.000000e+00 7247
1 TraesCS1A01G072200 chr1A 92.712 1276 53 10 2658 3922 56371944 56370698 0.000000e+00 1805
2 TraesCS1A01G072200 chr1A 94.693 848 37 5 3082 3922 56339597 56338751 0.000000e+00 1310
3 TraesCS1A01G072200 chr1A 91.995 787 63 0 2297 3083 56341094 56340308 0.000000e+00 1105
4 TraesCS1A01G072200 chr1A 89.720 214 22 0 452 665 56452534 56452747 1.390000e-69 274
5 TraesCS1A01G072200 chr1A 89.623 212 22 0 452 663 56483000 56483211 1.800000e-68 270
6 TraesCS1A01G072200 chr1A 88.479 217 25 0 452 668 54687534 54687318 3.010000e-66 263
7 TraesCS1A01G072200 chr1A 88.732 213 24 0 452 664 54691483 54691271 1.080000e-65 261
8 TraesCS1A01G072200 chr1A 88.095 210 22 2 455 662 56481395 56481603 3.030000e-61 246
9 TraesCS1A01G072200 chr1D 96.374 1765 61 2 2160 3922 56426890 56428653 0.000000e+00 2902
10 TraesCS1A01G072200 chr1D 93.618 1708 65 21 453 2131 56425216 56426908 0.000000e+00 2510
11 TraesCS1A01G072200 chr1D 91.964 1319 68 12 2619 3900 56528262 56529579 0.000000e+00 1814
12 TraesCS1A01G072200 chr1D 94.082 980 54 1 2943 3922 56872915 56873890 0.000000e+00 1485
13 TraesCS1A01G072200 chr1D 91.332 946 51 2 2977 3922 56608161 56609075 0.000000e+00 1264
14 TraesCS1A01G072200 chr1D 92.944 411 27 2 2287 2696 56868618 56869027 7.260000e-167 597
15 TraesCS1A01G072200 chr1D 88.121 463 42 7 2 453 39659570 39660030 4.460000e-149 538
16 TraesCS1A01G072200 chr1D 86.609 463 49 6 2 453 117218126 117218586 2.110000e-137 499
17 TraesCS1A01G072200 chr1D 86.481 466 35 11 8 453 287220055 287219598 1.640000e-133 486
18 TraesCS1A01G072200 chr1D 93.609 266 17 0 2653 2918 56607886 56608151 7.900000e-107 398
19 TraesCS1A01G072200 chr1D 91.589 214 16 2 452 663 56290444 56290657 1.070000e-75 294
20 TraesCS1A01G072200 chr1D 90.610 213 19 1 452 663 56102699 56102911 8.300000e-72 281
21 TraesCS1A01G072200 chr1D 96.203 158 6 0 2785 2942 56869385 56869542 3.890000e-65 259
22 TraesCS1A01G072200 chr1D 88.372 215 23 2 452 664 56104340 56104554 1.400000e-64 257
23 TraesCS1A01G072200 chr1B 93.792 1643 84 6 2297 3922 91879200 91880841 0.000000e+00 2453
24 TraesCS1A01G072200 chr1B 94.070 1231 60 3 783 2004 91877629 91878855 0.000000e+00 1857
25 TraesCS1A01G072200 chr5A 88.627 466 39 4 2 453 72909871 72910336 4.430000e-154 555
26 TraesCS1A01G072200 chr2A 88.009 467 43 5 2 457 54277061 54277525 1.240000e-149 540
27 TraesCS1A01G072200 chr2D 87.069 464 48 5 2 454 28100983 28100521 7.520000e-142 514
28 TraesCS1A01G072200 chr2D 87.174 460 44 7 8 453 596072762 596073220 3.500000e-140 508
29 TraesCS1A01G072200 chr7D 86.412 471 45 9 2 456 443539033 443538566 7.570000e-137 497
30 TraesCS1A01G072200 chr7D 86.771 446 51 6 2 444 555834428 555833988 1.270000e-134 490
31 TraesCS1A01G072200 chr3B 86.177 463 52 5 2 453 662383149 662382688 1.270000e-134 490


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 TraesCS1A01G072200 chr1A 54460252 54464175 3923 True 7247.000000 7247 100.000000 1 3924 1 chr1A.!!$R1 3923
1 TraesCS1A01G072200 chr1A 56370698 56371944 1246 True 1805.000000 1805 92.712000 2658 3922 1 chr1A.!!$R2 1264
2 TraesCS1A01G072200 chr1A 56338751 56341094 2343 True 1207.500000 1310 93.344000 2297 3922 2 chr1A.!!$R4 1625
3 TraesCS1A01G072200 chr1A 54687318 54691483 4165 True 262.000000 263 88.605500 452 668 2 chr1A.!!$R3 216
4 TraesCS1A01G072200 chr1A 56481395 56483211 1816 False 258.000000 270 88.859000 452 663 2 chr1A.!!$F2 211
5 TraesCS1A01G072200 chr1D 56425216 56428653 3437 False 2706.000000 2902 94.996000 453 3922 2 chr1D.!!$F6 3469
6 TraesCS1A01G072200 chr1D 56528262 56529579 1317 False 1814.000000 1814 91.964000 2619 3900 1 chr1D.!!$F3 1281
7 TraesCS1A01G072200 chr1D 56607886 56609075 1189 False 831.000000 1264 92.470500 2653 3922 2 chr1D.!!$F7 1269
8 TraesCS1A01G072200 chr1D 56868618 56873890 5272 False 780.333333 1485 94.409667 2287 3922 3 chr1D.!!$F8 1635
9 TraesCS1A01G072200 chr1D 56102699 56104554 1855 False 269.000000 281 89.491000 452 664 2 chr1D.!!$F5 212
10 TraesCS1A01G072200 chr1B 91877629 91880841 3212 False 2155.000000 2453 93.931000 783 3922 2 chr1B.!!$F1 3139

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
173 174 0.107263 TGGCGCACCATACATCACAT 60.107 50.0 10.83 0.0 42.67 3.21 F
396 397 0.250234 AGTGATAGTGGCGCACATGT 59.750 50.0 10.83 0.0 36.74 3.21 F
1517 2705 0.169230 CACACGGTCTCTCCTTCTCG 59.831 60.0 0.00 0.0 0.00 4.04 F
1518 2706 0.250814 ACACGGTCTCTCCTTCTCGT 60.251 55.0 0.00 0.0 0.00 4.18 F
2158 3491 0.517316 AGAACGAAGACGCCAAATGC 59.483 50.0 0.00 0.0 43.96 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 2631 0.107643 TTGCGGACATTGTGGAGTGA 59.892 50.0 0.00 0.00 0.00 3.41 R
2158 3491 0.179056 AATACATTCCCTGCCGGACG 60.179 55.0 5.05 0.00 41.83 4.79 R
2379 3716 0.746063 ACCACATTGCACCTGTGTTG 59.254 50.0 21.16 12.73 41.93 3.33 R
2524 3862 0.810031 CACCGTAGTGTATGGCTGCC 60.810 60.0 12.87 12.87 39.30 4.85 R
3733 11552 0.106819 CATCCTCCAAGGGAAGCTGG 60.107 60.0 0.00 0.00 39.02 4.85 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
26 27 9.658799 CCGGAGACTAATATGATGAATTGTATT 57.341 33.333 0.00 0.00 0.00 1.89
64 65 9.880064 CTTCTATTGTATTTGATGAATCTGCTG 57.120 33.333 0.00 0.00 0.00 4.41
65 66 8.969260 TCTATTGTATTTGATGAATCTGCTGT 57.031 30.769 0.00 0.00 0.00 4.40
66 67 9.399797 TCTATTGTATTTGATGAATCTGCTGTT 57.600 29.630 0.00 0.00 0.00 3.16
75 76 9.791820 TTTGATGAATCTGCTGTTTATATGTTG 57.208 29.630 0.00 0.00 0.00 3.33
76 77 8.510243 TGATGAATCTGCTGTTTATATGTTGT 57.490 30.769 0.00 0.00 0.00 3.32
77 78 8.400186 TGATGAATCTGCTGTTTATATGTTGTG 58.600 33.333 0.00 0.00 0.00 3.33
79 80 8.510243 TGAATCTGCTGTTTATATGTTGTGAT 57.490 30.769 0.00 0.00 0.00 3.06
81 82 7.870509 ATCTGCTGTTTATATGTTGTGATGT 57.129 32.000 0.00 0.00 0.00 3.06
82 83 7.307493 TCTGCTGTTTATATGTTGTGATGTC 57.693 36.000 0.00 0.00 0.00 3.06
83 84 7.105588 TCTGCTGTTTATATGTTGTGATGTCT 58.894 34.615 0.00 0.00 0.00 3.41
84 85 8.257306 TCTGCTGTTTATATGTTGTGATGTCTA 58.743 33.333 0.00 0.00 0.00 2.59
85 86 8.962884 TGCTGTTTATATGTTGTGATGTCTAT 57.037 30.769 0.00 0.00 0.00 1.98
94 95 6.908870 TGTTGTGATGTCTATATTCTGTGC 57.091 37.500 0.00 0.00 0.00 4.57
98 99 7.346751 TGTGATGTCTATATTCTGTGCAGTA 57.653 36.000 0.00 0.00 0.00 2.74
99 100 7.781056 TGTGATGTCTATATTCTGTGCAGTAA 58.219 34.615 0.00 0.00 0.00 2.24
100 101 8.424133 TGTGATGTCTATATTCTGTGCAGTAAT 58.576 33.333 0.00 0.00 0.00 1.89
101 102 9.914131 GTGATGTCTATATTCTGTGCAGTAATA 57.086 33.333 0.00 0.00 0.00 0.98
114 115 9.899661 TCTGTGCAGTAATATATTTTGTAACCT 57.100 29.630 2.68 0.00 0.00 3.50
115 116 9.935682 CTGTGCAGTAATATATTTTGTAACCTG 57.064 33.333 2.68 1.34 0.00 4.00
116 117 9.456147 TGTGCAGTAATATATTTTGTAACCTGT 57.544 29.630 2.68 0.00 0.00 4.00
117 118 9.716507 GTGCAGTAATATATTTTGTAACCTGTG 57.283 33.333 2.68 0.00 0.00 3.66
118 119 9.456147 TGCAGTAATATATTTTGTAACCTGTGT 57.544 29.630 2.68 0.00 0.00 3.72
158 159 8.827177 TTTTCCTAATATTCATACTAGTGGCG 57.173 34.615 5.39 0.00 0.00 5.69
159 160 5.962433 TCCTAATATTCATACTAGTGGCGC 58.038 41.667 5.39 0.00 0.00 6.53
160 161 5.479027 TCCTAATATTCATACTAGTGGCGCA 59.521 40.000 10.83 0.00 0.00 6.09
162 163 2.240493 ATTCATACTAGTGGCGCACC 57.760 50.000 10.83 0.00 34.49 5.01
163 164 0.899019 TTCATACTAGTGGCGCACCA 59.101 50.000 10.83 0.00 46.51 4.17
171 172 4.217035 TGGCGCACCATACATCAC 57.783 55.556 10.83 0.00 42.67 3.06
172 173 1.298014 TGGCGCACCATACATCACA 59.702 52.632 10.83 0.00 42.67 3.58
173 174 0.107263 TGGCGCACCATACATCACAT 60.107 50.000 10.83 0.00 42.67 3.21
176 177 2.224079 GGCGCACCATACATCACATTAG 59.776 50.000 10.83 0.00 35.26 1.73
177 178 2.872245 GCGCACCATACATCACATTAGT 59.128 45.455 0.30 0.00 0.00 2.24
178 179 6.314908 GGCGCACCATACATCACATTAGTG 62.315 50.000 10.83 0.00 40.75 2.74
179 180 3.248363 CGCACCATACATCACATTAGTGG 59.752 47.826 0.00 0.00 45.91 4.00
180 181 3.003689 GCACCATACATCACATTAGTGGC 59.996 47.826 0.00 0.00 45.91 5.01
181 182 3.248363 CACCATACATCACATTAGTGGCG 59.752 47.826 0.00 0.00 45.91 5.69
182 183 2.224079 CCATACATCACATTAGTGGCGC 59.776 50.000 0.00 0.00 45.91 6.53
183 184 2.682155 TACATCACATTAGTGGCGCA 57.318 45.000 10.83 0.00 45.91 6.09
184 185 1.086696 ACATCACATTAGTGGCGCAC 58.913 50.000 10.83 5.73 45.91 5.34
186 187 1.063027 CATCACATTAGTGGCGCACTG 59.937 52.381 18.70 8.70 45.01 3.66
187 188 1.135315 CACATTAGTGGCGCACTGC 59.865 57.895 18.70 2.75 45.01 4.40
199 200 3.405170 GCGCACTGCAATAAACATACT 57.595 42.857 0.30 0.00 45.45 2.12
201 202 4.518217 GCGCACTGCAATAAACATACTAG 58.482 43.478 0.30 0.00 45.45 2.57
202 203 4.034048 GCGCACTGCAATAAACATACTAGT 59.966 41.667 0.30 0.00 45.45 2.57
203 204 5.492854 CGCACTGCAATAAACATACTAGTG 58.507 41.667 5.39 0.00 37.82 2.74
205 206 6.478588 GCACTGCAATAAACATACTAGTGAC 58.521 40.000 5.39 0.00 37.15 3.67
207 208 7.456253 CACTGCAATAAACATACTAGTGACAC 58.544 38.462 5.39 0.00 37.15 3.67
209 210 7.824289 ACTGCAATAAACATACTAGTGACACAT 59.176 33.333 5.39 0.00 0.00 3.21
210 211 8.560355 TGCAATAAACATACTAGTGACACATT 57.440 30.769 5.39 0.00 0.00 2.71
224 225 5.639506 AGTGACACATTATCAGTTAGTGTGC 59.360 40.000 8.59 7.42 46.84 4.57
225 226 4.935205 TGACACATTATCAGTTAGTGTGCC 59.065 41.667 12.02 4.47 46.84 5.01
226 227 4.905429 ACACATTATCAGTTAGTGTGCCA 58.095 39.130 12.02 0.00 46.84 4.92
227 228 5.500234 ACACATTATCAGTTAGTGTGCCAT 58.500 37.500 12.02 0.00 46.84 4.40
230 231 7.280876 ACACATTATCAGTTAGTGTGCCATTAG 59.719 37.037 12.02 0.00 46.84 1.73
233 234 9.325198 CATTATCAGTTAGTGTGCCATTAGTAA 57.675 33.333 0.00 0.00 0.00 2.24
234 235 8.712285 TTATCAGTTAGTGTGCCATTAGTAAC 57.288 34.615 0.00 0.00 34.46 2.50
236 237 4.634443 CAGTTAGTGTGCCATTAGTAACCC 59.366 45.833 0.00 0.00 34.68 4.11
237 238 4.287585 AGTTAGTGTGCCATTAGTAACCCA 59.712 41.667 0.00 0.00 34.68 4.51
238 239 3.350219 AGTGTGCCATTAGTAACCCAG 57.650 47.619 0.00 0.00 0.00 4.45
239 240 2.910319 AGTGTGCCATTAGTAACCCAGA 59.090 45.455 0.00 0.00 0.00 3.86
240 241 3.055094 AGTGTGCCATTAGTAACCCAGAG 60.055 47.826 0.00 0.00 0.00 3.35
241 242 2.289565 GTGCCATTAGTAACCCAGAGC 58.710 52.381 0.00 0.00 0.00 4.09
243 244 2.289565 GCCATTAGTAACCCAGAGCAC 58.710 52.381 0.00 0.00 0.00 4.40
244 245 2.355716 GCCATTAGTAACCCAGAGCACA 60.356 50.000 0.00 0.00 0.00 4.57
245 246 3.872240 GCCATTAGTAACCCAGAGCACAA 60.872 47.826 0.00 0.00 0.00 3.33
246 247 3.941483 CCATTAGTAACCCAGAGCACAAG 59.059 47.826 0.00 0.00 0.00 3.16
247 248 4.323485 CCATTAGTAACCCAGAGCACAAGA 60.323 45.833 0.00 0.00 0.00 3.02
249 250 6.408092 CCATTAGTAACCCAGAGCACAAGATA 60.408 42.308 0.00 0.00 0.00 1.98
251 252 5.499004 AGTAACCCAGAGCACAAGATAAA 57.501 39.130 0.00 0.00 0.00 1.40
255 256 6.949352 AACCCAGAGCACAAGATAAATATG 57.051 37.500 0.00 0.00 0.00 1.78
257 258 4.217118 CCCAGAGCACAAGATAAATATGGC 59.783 45.833 0.00 0.00 0.00 4.40
258 259 4.217118 CCAGAGCACAAGATAAATATGGCC 59.783 45.833 0.00 0.00 0.00 5.36
261 262 4.401925 AGCACAAGATAAATATGGCCCTC 58.598 43.478 0.00 0.00 0.00 4.30
262 263 4.105377 AGCACAAGATAAATATGGCCCTCT 59.895 41.667 0.00 0.00 0.00 3.69
263 264 4.217118 GCACAAGATAAATATGGCCCTCTG 59.783 45.833 0.00 0.00 0.00 3.35
264 265 4.763793 CACAAGATAAATATGGCCCTCTGG 59.236 45.833 0.00 0.00 0.00 3.86
279 280 2.304180 CCTCTGGGAGGCATACTAATGG 59.696 54.545 0.34 0.00 43.29 3.16
280 281 2.975489 CTCTGGGAGGCATACTAATGGT 59.025 50.000 0.00 0.00 33.38 3.55
281 282 2.705658 TCTGGGAGGCATACTAATGGTG 59.294 50.000 0.00 0.00 33.38 4.17
282 283 1.142870 TGGGAGGCATACTAATGGTGC 59.857 52.381 0.00 0.00 38.12 5.01
284 285 2.222027 GGAGGCATACTAATGGTGCAC 58.778 52.381 8.80 8.80 40.53 4.57
285 286 2.421388 GGAGGCATACTAATGGTGCACA 60.421 50.000 20.43 5.24 40.53 4.57
286 287 2.874701 GAGGCATACTAATGGTGCACAG 59.125 50.000 20.43 9.85 40.53 3.66
289 290 3.009723 GCATACTAATGGTGCACAGTGT 58.990 45.455 20.43 8.80 38.68 3.55
290 291 3.181507 GCATACTAATGGTGCACAGTGTG 60.182 47.826 20.43 19.27 38.68 3.82
291 292 2.928801 ACTAATGGTGCACAGTGTGA 57.071 45.000 27.37 9.25 35.23 3.58
292 293 2.494059 ACTAATGGTGCACAGTGTGAC 58.506 47.619 27.37 19.50 35.23 3.67
293 294 2.104792 ACTAATGGTGCACAGTGTGACT 59.895 45.455 27.37 8.83 35.23 3.41
294 295 2.057137 AATGGTGCACAGTGTGACTT 57.943 45.000 27.37 10.82 35.23 3.01
296 297 1.948104 TGGTGCACAGTGTGACTTAC 58.052 50.000 27.37 17.18 35.23 2.34
297 298 1.484653 TGGTGCACAGTGTGACTTACT 59.515 47.619 27.37 0.00 35.23 2.24
299 300 3.133183 TGGTGCACAGTGTGACTTACTAA 59.867 43.478 27.37 9.07 35.23 2.24
300 301 3.493503 GGTGCACAGTGTGACTTACTAAC 59.506 47.826 27.37 10.31 35.23 2.34
301 302 3.181774 GTGCACAGTGTGACTTACTAACG 59.818 47.826 27.37 0.00 35.23 3.18
302 303 2.729882 GCACAGTGTGACTTACTAACGG 59.270 50.000 27.37 0.00 35.23 4.44
303 304 2.729882 CACAGTGTGACTTACTAACGGC 59.270 50.000 18.83 0.00 35.23 5.68
304 305 1.983605 CAGTGTGACTTACTAACGGCG 59.016 52.381 4.80 4.80 0.00 6.46
305 306 0.712222 GTGTGACTTACTAACGGCGC 59.288 55.000 6.90 0.00 0.00 6.53
306 307 0.314618 TGTGACTTACTAACGGCGCA 59.685 50.000 10.83 0.00 0.00 6.09
307 308 0.712222 GTGACTTACTAACGGCGCAC 59.288 55.000 10.83 0.00 0.00 5.34
308 309 0.599558 TGACTTACTAACGGCGCACT 59.400 50.000 10.83 0.00 0.00 4.40
310 311 1.012486 ACTTACTAACGGCGCACTGC 61.012 55.000 10.83 0.00 45.38 4.40
328 329 2.918712 GCCTCATGCACCACTATAGT 57.081 50.000 0.00 0.00 40.77 2.12
329 330 2.760374 GCCTCATGCACCACTATAGTC 58.240 52.381 1.26 0.00 40.77 2.59
330 331 2.366916 GCCTCATGCACCACTATAGTCT 59.633 50.000 1.26 0.00 40.77 3.24
331 332 3.801638 GCCTCATGCACCACTATAGTCTG 60.802 52.174 1.26 2.66 40.77 3.51
332 333 3.244009 CCTCATGCACCACTATAGTCTGG 60.244 52.174 1.26 5.10 0.00 3.86
334 335 4.542697 TCATGCACCACTATAGTCTGGTA 58.457 43.478 13.24 2.06 32.72 3.25
335 336 5.147767 TCATGCACCACTATAGTCTGGTAT 58.852 41.667 13.24 4.04 32.72 2.73
337 338 6.208797 TCATGCACCACTATAGTCTGGTATAC 59.791 42.308 13.24 8.01 32.72 1.47
338 339 5.702266 TGCACCACTATAGTCTGGTATACT 58.298 41.667 13.24 0.00 32.72 2.12
339 340 6.844829 TGCACCACTATAGTCTGGTATACTA 58.155 40.000 13.24 0.00 34.11 1.82
340 341 7.292319 TGCACCACTATAGTCTGGTATACTAA 58.708 38.462 13.24 0.00 33.36 2.24
341 342 7.948447 TGCACCACTATAGTCTGGTATACTAAT 59.052 37.037 13.24 0.00 33.36 1.73
342 343 8.244802 GCACCACTATAGTCTGGTATACTAATG 58.755 40.741 13.24 2.61 33.36 1.90
343 344 8.740906 CACCACTATAGTCTGGTATACTAATGG 58.259 40.741 13.24 5.06 37.21 3.16
344 345 7.396623 ACCACTATAGTCTGGTATACTAATGGC 59.603 40.741 12.24 0.00 35.97 4.40
346 347 3.662247 AGTCTGGTATACTAATGGCGC 57.338 47.619 0.00 0.00 0.00 6.53
347 348 2.963101 AGTCTGGTATACTAATGGCGCA 59.037 45.455 10.83 0.00 0.00 6.09
348 349 3.057734 GTCTGGTATACTAATGGCGCAC 58.942 50.000 10.83 0.00 0.00 5.34
349 350 2.036733 TCTGGTATACTAATGGCGCACC 59.963 50.000 10.83 5.12 0.00 5.01
372 373 1.722011 GGCGCGCCATTAGTATATGT 58.278 50.000 43.55 0.00 35.81 2.29
373 374 2.073816 GGCGCGCCATTAGTATATGTT 58.926 47.619 43.55 0.00 35.81 2.71
374 375 3.255725 GGCGCGCCATTAGTATATGTTA 58.744 45.455 43.55 0.00 35.81 2.41
375 376 3.061697 GGCGCGCCATTAGTATATGTTAC 59.938 47.826 43.55 10.95 35.81 2.50
377 378 5.097529 GCGCGCCATTAGTATATGTTACTA 58.902 41.667 23.24 0.00 0.00 1.82
378 379 5.229469 GCGCGCCATTAGTATATGTTACTAG 59.771 44.000 23.24 0.00 32.35 2.57
380 381 6.250739 CGCGCCATTAGTATATGTTACTAGTG 59.749 42.308 5.39 10.64 37.44 2.74
382 383 7.974501 GCGCCATTAGTATATGTTACTAGTGAT 59.025 37.037 5.39 0.00 38.94 3.06
389 390 8.041829 AGTATATGTTACTAGTGATAGTGGCG 57.958 38.462 5.39 0.00 0.00 5.69
390 391 3.431922 TGTTACTAGTGATAGTGGCGC 57.568 47.619 5.39 0.00 0.00 6.53
393 394 1.182667 ACTAGTGATAGTGGCGCACA 58.817 50.000 10.83 1.22 36.74 4.57
394 395 1.757118 ACTAGTGATAGTGGCGCACAT 59.243 47.619 10.83 0.00 36.74 3.21
395 396 2.130395 CTAGTGATAGTGGCGCACATG 58.870 52.381 10.83 0.00 36.74 3.21
396 397 0.250234 AGTGATAGTGGCGCACATGT 59.750 50.000 10.83 0.00 36.74 3.21
397 398 1.480545 AGTGATAGTGGCGCACATGTA 59.519 47.619 10.83 1.84 36.74 2.29
398 399 2.103094 AGTGATAGTGGCGCACATGTAT 59.897 45.455 10.83 6.58 36.74 2.29
399 400 2.872245 GTGATAGTGGCGCACATGTATT 59.128 45.455 10.83 0.00 36.74 1.89
400 401 2.871633 TGATAGTGGCGCACATGTATTG 59.128 45.455 10.83 0.00 36.74 1.90
401 402 1.013596 TAGTGGCGCACATGTATTGC 58.986 50.000 10.83 2.53 36.74 3.56
411 412 5.794650 GCACATGTATTGCGTCATTAATG 57.205 39.130 9.29 9.29 0.00 1.90
414 415 3.980646 TGTATTGCGTCATTAATGGCC 57.019 42.857 14.27 7.85 0.00 5.36
415 416 3.282885 TGTATTGCGTCATTAATGGCCA 58.717 40.909 8.56 8.56 0.00 5.36
416 417 3.696548 TGTATTGCGTCATTAATGGCCAA 59.303 39.130 10.96 19.44 30.99 4.52
417 418 3.883830 ATTGCGTCATTAATGGCCAAA 57.116 38.095 20.42 13.49 30.51 3.28
418 419 3.667497 TTGCGTCATTAATGGCCAAAA 57.333 38.095 10.96 8.13 0.00 2.44
419 420 2.953020 TGCGTCATTAATGGCCAAAAC 58.047 42.857 10.96 3.84 0.00 2.43
420 421 2.297315 TGCGTCATTAATGGCCAAAACA 59.703 40.909 10.96 2.91 0.00 2.83
421 422 2.923020 GCGTCATTAATGGCCAAAACAG 59.077 45.455 10.96 4.40 0.00 3.16
423 424 4.677779 GCGTCATTAATGGCCAAAACAGAT 60.678 41.667 10.96 0.00 0.00 2.90
424 425 5.449862 GCGTCATTAATGGCCAAAACAGATA 60.450 40.000 10.96 0.00 0.00 1.98
425 426 5.971202 CGTCATTAATGGCCAAAACAGATAC 59.029 40.000 10.96 0.71 0.00 2.24
426 427 5.971202 GTCATTAATGGCCAAAACAGATACG 59.029 40.000 10.96 0.00 0.00 3.06
427 428 5.650266 TCATTAATGGCCAAAACAGATACGT 59.350 36.000 10.96 0.00 0.00 3.57
428 429 5.554822 TTAATGGCCAAAACAGATACGTC 57.445 39.130 10.96 0.00 0.00 4.34
429 430 2.552599 TGGCCAAAACAGATACGTCA 57.447 45.000 0.61 0.00 0.00 4.35
430 431 2.147958 TGGCCAAAACAGATACGTCAC 58.852 47.619 0.61 0.00 0.00 3.67
431 432 2.224426 TGGCCAAAACAGATACGTCACT 60.224 45.455 0.61 0.00 0.00 3.41
433 434 3.998341 GGCCAAAACAGATACGTCACTAA 59.002 43.478 0.00 0.00 0.00 2.24
434 435 4.634443 GGCCAAAACAGATACGTCACTAAT 59.366 41.667 0.00 0.00 0.00 1.73
435 436 5.813672 GGCCAAAACAGATACGTCACTAATA 59.186 40.000 0.00 0.00 0.00 0.98
436 437 6.314400 GGCCAAAACAGATACGTCACTAATAA 59.686 38.462 0.00 0.00 0.00 1.40
437 438 7.148373 GGCCAAAACAGATACGTCACTAATAAA 60.148 37.037 0.00 0.00 0.00 1.40
438 439 8.395633 GCCAAAACAGATACGTCACTAATAAAT 58.604 33.333 0.00 0.00 0.00 1.40
439 440 9.916397 CCAAAACAGATACGTCACTAATAAATC 57.084 33.333 0.00 0.00 0.00 2.17
472 1627 1.329599 GTAGTAAGCCGCCATTTTCCG 59.670 52.381 0.00 0.00 0.00 4.30
480 1635 1.473257 CCGCCATTTTCCGATCTCTGA 60.473 52.381 0.00 0.00 0.00 3.27
533 1688 8.723311 ACGGTTAAACTAAATGAATGAATCGAA 58.277 29.630 0.00 0.00 0.00 3.71
582 1737 9.915629 ATAAGAAATGTATCACTCCGAGAATAC 57.084 33.333 1.33 9.86 0.00 1.89
596 1751 1.478510 AGAATACCAGAGCACGGACAG 59.521 52.381 0.00 0.00 0.00 3.51
685 1845 8.615878 AAAGGCTAAACTTTGTGTTTTCTTTT 57.384 26.923 0.00 0.34 45.69 2.27
693 1853 7.346208 ACTTTGTGTTTTCTTTTTCCTTTCG 57.654 32.000 0.00 0.00 0.00 3.46
704 1864 6.503524 TCTTTTTCCTTTCGTTTTCAGGATG 58.496 36.000 0.00 0.00 36.56 3.51
742 1902 0.320374 CTCACACCAACCGGCTAGAA 59.680 55.000 0.00 0.00 34.57 2.10
764 1924 2.158900 ACATCGTGGAATTCAGCTAGGG 60.159 50.000 7.93 0.00 0.00 3.53
765 1925 1.568504 TCGTGGAATTCAGCTAGGGT 58.431 50.000 7.93 0.00 0.00 4.34
766 1926 1.906574 TCGTGGAATTCAGCTAGGGTT 59.093 47.619 7.93 0.00 0.00 4.11
767 1927 2.009774 CGTGGAATTCAGCTAGGGTTG 58.990 52.381 7.93 0.00 0.00 3.77
778 1938 2.104111 AGCTAGGGTTGCACGCATATAA 59.896 45.455 0.00 0.00 32.95 0.98
858 2020 2.170036 CGCACGCGGTAGTTGTTG 59.830 61.111 12.47 0.00 35.56 3.33
914 2079 4.023707 CAGAAAGCGTGACCAGATTTTTCT 60.024 41.667 0.00 0.00 34.70 2.52
916 2081 4.918810 AAGCGTGACCAGATTTTTCTTT 57.081 36.364 0.00 0.00 0.00 2.52
917 2082 4.918810 AGCGTGACCAGATTTTTCTTTT 57.081 36.364 0.00 0.00 0.00 2.27
972 2139 1.900545 CTCCGAAACCCCTCCACTCC 61.901 65.000 0.00 0.00 0.00 3.85
973 2140 2.669240 CGAAACCCCTCCACTCCC 59.331 66.667 0.00 0.00 0.00 4.30
1266 2442 1.405463 TGCAAGCTCTACGACATCGAT 59.595 47.619 8.54 0.00 43.02 3.59
1272 2448 1.099295 TCTACGACATCGATGGGCGT 61.099 55.000 34.37 34.37 42.49 5.68
1281 2457 0.968901 TCGATGGGCGTGAGTACCTT 60.969 55.000 0.00 0.00 41.80 3.50
1435 2611 3.672503 GCTCCCCACCAACCCCAT 61.673 66.667 0.00 0.00 0.00 4.00
1443 2631 0.178935 CACCAACCCCATCCCAAACT 60.179 55.000 0.00 0.00 0.00 2.66
1446 2634 1.256812 CAACCCCATCCCAAACTCAC 58.743 55.000 0.00 0.00 0.00 3.51
1458 2646 2.554032 CCAAACTCACTCCACAATGTCC 59.446 50.000 0.00 0.00 0.00 4.02
1485 2673 1.891919 TTCGACGCTTTGCTTGCCT 60.892 52.632 0.00 0.00 0.00 4.75
1489 2677 2.075426 GACGCTTTGCTTGCCTGGTT 62.075 55.000 0.00 0.00 0.00 3.67
1490 2678 0.821711 ACGCTTTGCTTGCCTGGTTA 60.822 50.000 0.00 0.00 0.00 2.85
1517 2705 0.169230 CACACGGTCTCTCCTTCTCG 59.831 60.000 0.00 0.00 0.00 4.04
1518 2706 0.250814 ACACGGTCTCTCCTTCTCGT 60.251 55.000 0.00 0.00 0.00 4.18
1524 2712 2.428491 GTCTCTCCTTCTCGTCTGACA 58.572 52.381 8.73 0.00 0.00 3.58
1534 2722 4.808414 TCTCGTCTGACATCCATTTCTT 57.192 40.909 8.73 0.00 0.00 2.52
1781 2969 1.068352 ACAGGGAGCCCTTTGAACCT 61.068 55.000 5.03 0.00 45.70 3.50
1913 3101 0.598065 GGATTCACAGTGCCACCAAC 59.402 55.000 0.00 0.00 0.00 3.77
1998 3186 6.374417 AGGTATGACACAACTTACCTTCAT 57.626 37.500 0.00 0.00 43.55 2.57
2022 3347 9.737427 CATTAATAGTTGTCTCTGTAGTCGATT 57.263 33.333 0.00 0.00 0.00 3.34
2023 3348 9.737427 ATTAATAGTTGTCTCTGTAGTCGATTG 57.263 33.333 0.00 0.00 0.00 2.67
2031 3356 6.127730 TGTCTCTGTAGTCGATTGCATAGAAA 60.128 38.462 13.65 7.66 0.00 2.52
2042 3367 8.774586 GTCGATTGCATAGAAATAATTAGTGGT 58.225 33.333 0.00 0.00 0.00 4.16
2156 3489 5.427036 TTTTTAGAACGAAGACGCCAAAT 57.573 34.783 0.00 0.00 43.96 2.32
2158 3491 0.517316 AGAACGAAGACGCCAAATGC 59.483 50.000 0.00 0.00 43.96 3.56
2353 3690 7.814264 AGTTCAACTTCTGTCAATTTGAGAT 57.186 32.000 0.00 0.00 0.00 2.75
2376 3713 7.667575 ATGTGGAGACATCTAATCTACTGTT 57.332 36.000 0.00 0.00 46.14 3.16
2379 3716 6.256757 GTGGAGACATCTAATCTACTGTTTGC 59.743 42.308 0.00 0.00 46.14 3.68
2425 3762 1.299976 CACAGGTTACCTCTGGGCC 59.700 63.158 0.00 0.00 36.62 5.80
2444 3781 3.436470 GGCCCATGAGGTTTATGGTGTAT 60.436 47.826 0.00 0.00 42.85 2.29
2497 3835 1.606313 CAACGGCCTTCCCATTGGT 60.606 57.895 0.00 0.00 0.00 3.67
2512 3850 2.597510 GGTGTGGCCTTGGTCACC 60.598 66.667 20.04 15.44 42.40 4.02
2534 3872 1.595093 AAAGGTTGCGGCAGCCATAC 61.595 55.000 32.83 15.04 44.33 2.39
2551 3889 1.927487 TACACTACGGTGACCATGGT 58.073 50.000 19.89 19.89 45.61 3.55
2737 4136 0.744414 CCGGTCTCATCGTTGGCATT 60.744 55.000 0.00 0.00 0.00 3.56
2795 5827 1.200948 GCTTGGATGCTGGTGTCTTTC 59.799 52.381 0.00 0.00 0.00 2.62
3602 11421 2.643272 GTCGTGACGTCCTGCAGA 59.357 61.111 17.39 0.00 0.00 4.26
3677 11496 0.943835 CGTCACCATGCTGAACGACA 60.944 55.000 7.00 0.00 0.00 4.35
3768 11587 0.179037 GATGAGCTGCAGTATGGCCA 60.179 55.000 16.64 8.56 35.86 5.36
3923 11981 2.025441 CCGCCAACGTTGTTGGTG 59.975 61.111 27.19 27.19 46.64 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.658799 AATACAATTCATCATATTAGTCTCCGG 57.341 33.333 0.00 0.00 0.00 5.14
37 38 9.842775 AGCAGATTCATCAAATACAATAGAAGA 57.157 29.630 0.00 0.00 0.00 2.87
38 39 9.880064 CAGCAGATTCATCAAATACAATAGAAG 57.120 33.333 0.00 0.00 0.00 2.85
40 41 8.969260 ACAGCAGATTCATCAAATACAATAGA 57.031 30.769 0.00 0.00 0.00 1.98
50 51 8.959548 ACAACATATAAACAGCAGATTCATCAA 58.040 29.630 0.00 0.00 0.00 2.57
52 53 8.615211 TCACAACATATAAACAGCAGATTCATC 58.385 33.333 0.00 0.00 0.00 2.92
53 54 8.510243 TCACAACATATAAACAGCAGATTCAT 57.490 30.769 0.00 0.00 0.00 2.57
55 56 8.400947 ACATCACAACATATAAACAGCAGATTC 58.599 33.333 0.00 0.00 0.00 2.52
56 57 8.284945 ACATCACAACATATAAACAGCAGATT 57.715 30.769 0.00 0.00 0.00 2.40
57 58 7.772292 AGACATCACAACATATAAACAGCAGAT 59.228 33.333 0.00 0.00 0.00 2.90
58 59 7.105588 AGACATCACAACATATAAACAGCAGA 58.894 34.615 0.00 0.00 0.00 4.26
59 60 7.312657 AGACATCACAACATATAAACAGCAG 57.687 36.000 0.00 0.00 0.00 4.24
68 69 9.212641 GCACAGAATATAGACATCACAACATAT 57.787 33.333 0.00 0.00 0.00 1.78
69 70 8.203485 TGCACAGAATATAGACATCACAACATA 58.797 33.333 0.00 0.00 0.00 2.29
71 72 6.405538 TGCACAGAATATAGACATCACAACA 58.594 36.000 0.00 0.00 0.00 3.33
72 73 6.536582 ACTGCACAGAATATAGACATCACAAC 59.463 38.462 4.31 0.00 0.00 3.32
73 74 6.643388 ACTGCACAGAATATAGACATCACAA 58.357 36.000 4.31 0.00 0.00 3.33
74 75 6.225981 ACTGCACAGAATATAGACATCACA 57.774 37.500 4.31 0.00 0.00 3.58
75 76 8.824159 ATTACTGCACAGAATATAGACATCAC 57.176 34.615 4.31 0.00 0.00 3.06
88 89 9.899661 AGGTTACAAAATATATTACTGCACAGA 57.100 29.630 4.31 0.00 0.00 3.41
91 92 9.716507 CACAGGTTACAAAATATATTACTGCAC 57.283 33.333 0.00 1.40 0.00 4.57
132 133 9.268268 CGCCACTAGTATGAATATTAGGAAAAA 57.732 33.333 0.00 0.00 29.74 1.94
133 134 7.386848 GCGCCACTAGTATGAATATTAGGAAAA 59.613 37.037 0.00 0.00 29.74 2.29
134 135 6.872020 GCGCCACTAGTATGAATATTAGGAAA 59.128 38.462 0.00 0.00 29.74 3.13
135 136 6.014925 TGCGCCACTAGTATGAATATTAGGAA 60.015 38.462 4.18 0.00 29.74 3.36
136 137 5.479027 TGCGCCACTAGTATGAATATTAGGA 59.521 40.000 4.18 0.00 29.74 2.94
138 139 5.577164 GGTGCGCCACTAGTATGAATATTAG 59.423 44.000 12.58 0.00 34.40 1.73
139 140 5.011227 TGGTGCGCCACTAGTATGAATATTA 59.989 40.000 16.89 0.00 40.46 0.98
141 142 3.323691 TGGTGCGCCACTAGTATGAATAT 59.676 43.478 16.89 0.00 40.46 1.28
142 143 2.696187 TGGTGCGCCACTAGTATGAATA 59.304 45.455 16.89 0.00 40.46 1.75
144 145 0.899019 TGGTGCGCCACTAGTATGAA 59.101 50.000 16.89 0.00 40.46 2.57
145 146 2.585876 TGGTGCGCCACTAGTATGA 58.414 52.632 16.89 0.00 40.46 2.15
155 156 1.024271 AATGTGATGTATGGTGCGCC 58.976 50.000 10.11 10.11 0.00 6.53
156 157 2.872245 ACTAATGTGATGTATGGTGCGC 59.128 45.455 0.00 0.00 0.00 6.09
157 158 3.248363 CCACTAATGTGATGTATGGTGCG 59.752 47.826 0.00 0.00 46.55 5.34
158 159 3.003689 GCCACTAATGTGATGTATGGTGC 59.996 47.826 0.00 0.00 46.55 5.01
159 160 3.248363 CGCCACTAATGTGATGTATGGTG 59.752 47.826 0.00 0.00 46.55 4.17
160 161 3.466836 CGCCACTAATGTGATGTATGGT 58.533 45.455 0.00 0.00 46.55 3.55
162 163 2.871633 TGCGCCACTAATGTGATGTATG 59.128 45.455 4.18 0.00 46.55 2.39
163 164 2.872245 GTGCGCCACTAATGTGATGTAT 59.128 45.455 4.18 0.00 46.55 2.29
164 165 2.093711 AGTGCGCCACTAATGTGATGTA 60.094 45.455 4.18 0.00 43.46 2.29
166 167 1.063027 CAGTGCGCCACTAATGTGATG 59.937 52.381 4.18 0.00 43.43 3.07
167 168 1.372582 CAGTGCGCCACTAATGTGAT 58.627 50.000 4.18 0.00 43.43 3.06
169 170 1.135315 GCAGTGCGCCACTAATGTG 59.865 57.895 4.18 0.00 43.43 3.21
170 171 0.888736 TTGCAGTGCGCCACTAATGT 60.889 50.000 11.20 0.00 43.43 2.71
171 172 0.452987 ATTGCAGTGCGCCACTAATG 59.547 50.000 11.20 0.00 43.43 1.90
172 173 2.036958 TATTGCAGTGCGCCACTAAT 57.963 45.000 11.20 8.73 43.43 1.73
173 174 1.814793 TTATTGCAGTGCGCCACTAA 58.185 45.000 11.20 1.43 43.43 2.24
176 177 0.039617 TGTTTATTGCAGTGCGCCAC 60.040 50.000 11.20 3.02 41.33 5.01
177 178 0.887247 ATGTTTATTGCAGTGCGCCA 59.113 45.000 11.20 0.00 41.33 5.69
178 179 2.097466 AGTATGTTTATTGCAGTGCGCC 59.903 45.455 11.20 0.00 41.33 6.53
179 180 3.405170 AGTATGTTTATTGCAGTGCGC 57.595 42.857 11.20 0.00 42.89 6.09
180 181 5.290885 TCACTAGTATGTTTATTGCAGTGCG 59.709 40.000 11.20 0.00 33.77 5.34
181 182 6.092122 TGTCACTAGTATGTTTATTGCAGTGC 59.908 38.462 8.58 8.58 33.77 4.40
182 183 7.117667 TGTGTCACTAGTATGTTTATTGCAGTG 59.882 37.037 4.27 0.00 34.78 3.66
183 184 7.158697 TGTGTCACTAGTATGTTTATTGCAGT 58.841 34.615 4.27 0.00 0.00 4.40
184 185 7.595311 TGTGTCACTAGTATGTTTATTGCAG 57.405 36.000 4.27 0.00 0.00 4.41
185 186 8.560355 AATGTGTCACTAGTATGTTTATTGCA 57.440 30.769 4.27 0.00 0.00 4.08
191 192 9.944376 AACTGATAATGTGTCACTAGTATGTTT 57.056 29.630 4.27 0.00 0.00 2.83
197 198 8.029522 CACACTAACTGATAATGTGTCACTAGT 58.970 37.037 4.27 0.00 39.46 2.57
198 199 7.009631 GCACACTAACTGATAATGTGTCACTAG 59.990 40.741 8.05 0.00 42.13 2.57
199 200 6.811665 GCACACTAACTGATAATGTGTCACTA 59.188 38.462 8.05 0.00 42.13 2.74
201 202 5.163854 GGCACACTAACTGATAATGTGTCAC 60.164 44.000 6.31 0.00 43.66 3.67
202 203 4.935205 GGCACACTAACTGATAATGTGTCA 59.065 41.667 6.31 0.00 43.66 3.58
203 204 4.935205 TGGCACACTAACTGATAATGTGTC 59.065 41.667 4.50 4.50 44.29 3.67
221 222 2.289565 GCTCTGGGTTACTAATGGCAC 58.710 52.381 0.00 0.00 0.00 5.01
223 224 2.289565 GTGCTCTGGGTTACTAATGGC 58.710 52.381 0.00 0.00 0.00 4.40
224 225 3.627395 TGTGCTCTGGGTTACTAATGG 57.373 47.619 0.00 0.00 0.00 3.16
225 226 4.832248 TCTTGTGCTCTGGGTTACTAATG 58.168 43.478 0.00 0.00 0.00 1.90
226 227 5.700402 ATCTTGTGCTCTGGGTTACTAAT 57.300 39.130 0.00 0.00 0.00 1.73
227 228 6.614694 TTATCTTGTGCTCTGGGTTACTAA 57.385 37.500 0.00 0.00 0.00 2.24
230 231 7.041098 CCATATTTATCTTGTGCTCTGGGTTAC 60.041 40.741 0.00 0.00 0.00 2.50
233 234 5.380043 CCATATTTATCTTGTGCTCTGGGT 58.620 41.667 0.00 0.00 0.00 4.51
234 235 4.217118 GCCATATTTATCTTGTGCTCTGGG 59.783 45.833 0.00 0.00 0.00 4.45
236 237 4.217118 GGGCCATATTTATCTTGTGCTCTG 59.783 45.833 4.39 0.00 0.00 3.35
237 238 4.105377 AGGGCCATATTTATCTTGTGCTCT 59.895 41.667 6.18 0.00 0.00 4.09
238 239 4.401925 AGGGCCATATTTATCTTGTGCTC 58.598 43.478 6.18 0.00 0.00 4.26
239 240 4.105377 AGAGGGCCATATTTATCTTGTGCT 59.895 41.667 6.18 0.00 0.00 4.40
240 241 4.217118 CAGAGGGCCATATTTATCTTGTGC 59.783 45.833 6.18 0.00 0.00 4.57
241 242 4.763793 CCAGAGGGCCATATTTATCTTGTG 59.236 45.833 6.18 0.00 0.00 3.33
243 244 4.043310 TCCCAGAGGGCCATATTTATCTTG 59.957 45.833 6.18 0.00 43.94 3.02
244 245 4.251169 TCCCAGAGGGCCATATTTATCTT 58.749 43.478 6.18 0.00 43.94 2.40
245 246 3.848975 CTCCCAGAGGGCCATATTTATCT 59.151 47.826 6.18 0.00 43.94 1.98
246 247 3.054065 CCTCCCAGAGGGCCATATTTATC 60.054 52.174 6.18 0.00 45.43 1.75
247 248 2.922283 CCTCCCAGAGGGCCATATTTAT 59.078 50.000 6.18 0.00 45.43 1.40
249 250 1.152649 CCTCCCAGAGGGCCATATTT 58.847 55.000 6.18 0.00 45.43 1.40
251 252 4.677378 CCTCCCAGAGGGCCATAT 57.323 61.111 6.18 0.00 45.43 1.78
261 262 2.811873 GCACCATTAGTATGCCTCCCAG 60.812 54.545 0.00 0.00 33.06 4.45
262 263 1.142870 GCACCATTAGTATGCCTCCCA 59.857 52.381 0.00 0.00 33.06 4.37
263 264 1.142870 TGCACCATTAGTATGCCTCCC 59.857 52.381 0.00 0.00 38.63 4.30
264 265 2.222027 GTGCACCATTAGTATGCCTCC 58.778 52.381 5.22 0.00 38.63 4.30
265 266 2.874701 CTGTGCACCATTAGTATGCCTC 59.125 50.000 15.69 0.00 38.63 4.70
266 267 2.239654 ACTGTGCACCATTAGTATGCCT 59.760 45.455 15.69 0.00 38.63 4.75
267 268 2.355756 CACTGTGCACCATTAGTATGCC 59.644 50.000 15.69 0.00 38.63 4.40
268 269 3.009723 ACACTGTGCACCATTAGTATGC 58.990 45.455 15.69 0.00 39.88 3.14
269 270 4.093408 GTCACACTGTGCACCATTAGTATG 59.907 45.833 15.69 10.58 32.98 2.39
271 272 3.323691 AGTCACACTGTGCACCATTAGTA 59.676 43.478 15.69 0.00 32.98 1.82
273 274 2.771089 AGTCACACTGTGCACCATTAG 58.229 47.619 15.69 7.42 32.98 1.73
274 275 2.928801 AGTCACACTGTGCACCATTA 57.071 45.000 15.69 0.00 32.98 1.90
275 276 2.057137 AAGTCACACTGTGCACCATT 57.943 45.000 15.69 0.00 32.98 3.16
279 280 3.181774 CGTTAGTAAGTCACACTGTGCAC 59.818 47.826 10.75 10.75 32.98 4.57
280 281 3.377439 CGTTAGTAAGTCACACTGTGCA 58.623 45.455 7.90 0.00 32.98 4.57
281 282 2.729882 CCGTTAGTAAGTCACACTGTGC 59.270 50.000 7.90 0.33 32.98 4.57
282 283 2.729882 GCCGTTAGTAAGTCACACTGTG 59.270 50.000 6.19 6.19 34.45 3.66
284 285 1.983605 CGCCGTTAGTAAGTCACACTG 59.016 52.381 0.00 0.00 0.00 3.66
285 286 1.668047 GCGCCGTTAGTAAGTCACACT 60.668 52.381 0.00 0.00 0.00 3.55
286 287 0.712222 GCGCCGTTAGTAAGTCACAC 59.288 55.000 0.00 0.00 0.00 3.82
289 290 0.599558 AGTGCGCCGTTAGTAAGTCA 59.400 50.000 4.18 0.00 0.00 3.41
290 291 0.989890 CAGTGCGCCGTTAGTAAGTC 59.010 55.000 4.18 0.00 0.00 3.01
291 292 1.012486 GCAGTGCGCCGTTAGTAAGT 61.012 55.000 4.18 0.00 32.94 2.24
292 293 1.708027 GCAGTGCGCCGTTAGTAAG 59.292 57.895 4.18 0.00 32.94 2.34
293 294 3.864944 GCAGTGCGCCGTTAGTAA 58.135 55.556 4.18 0.00 32.94 2.24
310 311 3.244009 CCAGACTATAGTGGTGCATGAGG 60.244 52.174 10.90 0.00 0.00 3.86
311 312 3.386078 ACCAGACTATAGTGGTGCATGAG 59.614 47.826 10.90 0.00 45.72 2.90
312 313 3.374764 ACCAGACTATAGTGGTGCATGA 58.625 45.455 10.90 0.00 45.72 3.07
313 314 3.827008 ACCAGACTATAGTGGTGCATG 57.173 47.619 10.90 0.00 45.72 4.06
314 315 6.315714 AGTATACCAGACTATAGTGGTGCAT 58.684 40.000 20.23 11.89 46.87 3.96
316 317 7.756395 TTAGTATACCAGACTATAGTGGTGC 57.244 40.000 20.23 12.39 46.87 5.01
317 318 8.740906 CCATTAGTATACCAGACTATAGTGGTG 58.259 40.741 20.23 13.00 46.87 4.17
320 321 7.473366 CGCCATTAGTATACCAGACTATAGTG 58.527 42.308 10.90 0.00 29.68 2.74
321 322 6.095160 GCGCCATTAGTATACCAGACTATAGT 59.905 42.308 4.68 4.68 29.68 2.12
322 323 6.095021 TGCGCCATTAGTATACCAGACTATAG 59.905 42.308 4.18 0.00 29.68 1.31
323 324 5.947566 TGCGCCATTAGTATACCAGACTATA 59.052 40.000 4.18 0.00 29.68 1.31
324 325 4.770531 TGCGCCATTAGTATACCAGACTAT 59.229 41.667 4.18 0.00 29.68 2.12
325 326 4.022589 GTGCGCCATTAGTATACCAGACTA 60.023 45.833 4.18 0.00 0.00 2.59
326 327 2.963101 TGCGCCATTAGTATACCAGACT 59.037 45.455 4.18 0.00 0.00 3.24
327 328 3.057734 GTGCGCCATTAGTATACCAGAC 58.942 50.000 4.18 0.00 0.00 3.51
328 329 2.036733 GGTGCGCCATTAGTATACCAGA 59.963 50.000 12.58 0.00 34.09 3.86
329 330 2.224185 TGGTGCGCCATTAGTATACCAG 60.224 50.000 16.89 0.00 40.46 4.00
330 331 1.763545 TGGTGCGCCATTAGTATACCA 59.236 47.619 16.89 5.52 40.46 3.25
331 332 2.036733 TCTGGTGCGCCATTAGTATACC 59.963 50.000 21.54 2.32 45.05 2.73
332 333 3.318017 CTCTGGTGCGCCATTAGTATAC 58.682 50.000 21.54 0.00 45.05 1.47
334 335 1.070758 CCTCTGGTGCGCCATTAGTAT 59.929 52.381 21.54 0.00 45.05 2.12
335 336 0.464036 CCTCTGGTGCGCCATTAGTA 59.536 55.000 21.54 2.44 45.05 1.82
337 338 2.182842 GCCTCTGGTGCGCCATTAG 61.183 63.158 21.54 19.23 45.05 1.73
338 339 2.124736 GCCTCTGGTGCGCCATTA 60.125 61.111 21.54 10.41 45.05 1.90
347 348 3.740128 CTAATGGCGCGCCTCTGGT 62.740 63.158 45.79 28.69 36.94 4.00
348 349 2.363711 TACTAATGGCGCGCCTCTGG 62.364 60.000 45.79 34.74 36.94 3.86
349 350 0.319900 ATACTAATGGCGCGCCTCTG 60.320 55.000 45.79 33.22 36.94 3.35
350 351 1.254026 TATACTAATGGCGCGCCTCT 58.746 50.000 45.79 34.48 36.94 3.69
351 352 1.927174 CATATACTAATGGCGCGCCTC 59.073 52.381 45.79 25.26 36.94 4.70
353 354 1.722011 ACATATACTAATGGCGCGCC 58.278 50.000 42.35 42.35 0.00 6.53
354 355 3.924686 AGTAACATATACTAATGGCGCGC 59.075 43.478 25.94 25.94 0.00 6.86
355 356 6.250739 CACTAGTAACATATACTAATGGCGCG 59.749 42.308 0.00 0.00 30.55 6.86
356 357 7.310664 TCACTAGTAACATATACTAATGGCGC 58.689 38.462 0.00 0.00 30.75 6.53
363 364 9.159364 CGCCACTATCACTAGTAACATATACTA 57.841 37.037 0.00 0.00 35.99 1.82
364 365 7.361885 GCGCCACTATCACTAGTAACATATACT 60.362 40.741 0.00 0.00 35.99 2.12
365 366 6.746364 GCGCCACTATCACTAGTAACATATAC 59.254 42.308 0.00 0.00 35.99 1.47
366 367 6.431852 TGCGCCACTATCACTAGTAACATATA 59.568 38.462 4.18 0.00 35.99 0.86
369 370 3.383505 TGCGCCACTATCACTAGTAACAT 59.616 43.478 4.18 0.00 35.99 2.71
370 371 2.756207 TGCGCCACTATCACTAGTAACA 59.244 45.455 4.18 0.00 35.99 2.41
371 372 3.114065 GTGCGCCACTATCACTAGTAAC 58.886 50.000 4.18 0.00 35.99 2.50
372 373 2.756207 TGTGCGCCACTATCACTAGTAA 59.244 45.455 4.18 0.00 35.99 2.24
373 374 2.371306 TGTGCGCCACTATCACTAGTA 58.629 47.619 4.18 0.00 35.99 1.82
374 375 1.182667 TGTGCGCCACTATCACTAGT 58.817 50.000 4.18 0.00 38.79 2.57
375 376 2.130395 CATGTGCGCCACTATCACTAG 58.870 52.381 4.18 0.00 35.11 2.57
377 378 0.250234 ACATGTGCGCCACTATCACT 59.750 50.000 4.18 0.00 35.11 3.41
378 379 1.934589 TACATGTGCGCCACTATCAC 58.065 50.000 9.11 0.00 35.11 3.06
380 381 2.349817 GCAATACATGTGCGCCACTATC 60.350 50.000 9.11 0.00 35.11 2.08
382 383 1.013596 GCAATACATGTGCGCCACTA 58.986 50.000 9.11 0.00 35.11 2.74
383 384 1.802636 GCAATACATGTGCGCCACT 59.197 52.632 9.11 0.00 35.11 4.00
384 385 4.382728 GCAATACATGTGCGCCAC 57.617 55.556 9.11 3.72 34.56 5.01
389 390 4.676471 CCATTAATGACGCAATACATGTGC 59.324 41.667 17.23 2.24 43.55 4.57
390 391 4.676471 GCCATTAATGACGCAATACATGTG 59.324 41.667 17.23 0.00 45.28 3.21
393 394 3.888323 TGGCCATTAATGACGCAATACAT 59.112 39.130 17.23 0.00 0.00 2.29
394 395 3.282885 TGGCCATTAATGACGCAATACA 58.717 40.909 17.23 3.66 0.00 2.29
395 396 3.980646 TGGCCATTAATGACGCAATAC 57.019 42.857 17.23 1.25 0.00 1.89
396 397 4.991153 TTTGGCCATTAATGACGCAATA 57.009 36.364 17.23 0.00 0.00 1.90
397 398 3.883830 TTTGGCCATTAATGACGCAAT 57.116 38.095 17.23 0.00 0.00 3.56
398 399 3.243873 TGTTTTGGCCATTAATGACGCAA 60.244 39.130 17.23 8.89 0.00 4.85
399 400 2.297315 TGTTTTGGCCATTAATGACGCA 59.703 40.909 17.23 3.20 0.00 5.24
400 401 2.923020 CTGTTTTGGCCATTAATGACGC 59.077 45.455 17.23 12.01 0.00 5.19
401 402 4.433186 TCTGTTTTGGCCATTAATGACG 57.567 40.909 17.23 2.24 0.00 4.35
404 405 5.890334 ACGTATCTGTTTTGGCCATTAATG 58.110 37.500 6.09 8.58 0.00 1.90
405 406 5.650266 TGACGTATCTGTTTTGGCCATTAAT 59.350 36.000 6.09 0.00 0.00 1.40
408 409 3.190535 GTGACGTATCTGTTTTGGCCATT 59.809 43.478 6.09 0.00 0.00 3.16
409 410 2.747446 GTGACGTATCTGTTTTGGCCAT 59.253 45.455 6.09 0.00 0.00 4.40
410 411 2.147958 GTGACGTATCTGTTTTGGCCA 58.852 47.619 0.00 0.00 0.00 5.36
411 412 2.423577 AGTGACGTATCTGTTTTGGCC 58.576 47.619 0.00 0.00 0.00 5.36
442 443 4.220382 TGGCGGCTTACTACACTACTAAAA 59.780 41.667 11.43 0.00 0.00 1.52
444 445 3.355378 TGGCGGCTTACTACACTACTAA 58.645 45.455 11.43 0.00 0.00 2.24
445 446 3.003394 TGGCGGCTTACTACACTACTA 57.997 47.619 11.43 0.00 0.00 1.82
446 447 1.843368 TGGCGGCTTACTACACTACT 58.157 50.000 11.43 0.00 0.00 2.57
447 448 2.884894 ATGGCGGCTTACTACACTAC 57.115 50.000 11.43 0.00 0.00 2.73
448 449 3.899052 AAATGGCGGCTTACTACACTA 57.101 42.857 11.43 0.00 0.00 2.74
449 450 2.781681 AAATGGCGGCTTACTACACT 57.218 45.000 11.43 0.00 0.00 3.55
582 1737 2.898729 ATATTCTGTCCGTGCTCTGG 57.101 50.000 0.00 0.00 0.00 3.86
704 1864 3.066203 TGAGAACACGGGCTTTTCTTTTC 59.934 43.478 0.00 0.00 29.54 2.29
705 1865 3.020984 TGAGAACACGGGCTTTTCTTTT 58.979 40.909 0.00 0.00 29.54 2.27
706 1866 2.357952 GTGAGAACACGGGCTTTTCTTT 59.642 45.455 0.00 0.00 37.28 2.52
707 1867 1.947456 GTGAGAACACGGGCTTTTCTT 59.053 47.619 0.00 0.00 37.28 2.52
708 1868 1.594331 GTGAGAACACGGGCTTTTCT 58.406 50.000 0.00 0.00 37.28 2.52
734 1894 2.004583 TTCCACGATGTTTCTAGCCG 57.995 50.000 0.00 0.00 0.00 5.52
742 1902 3.535561 CCTAGCTGAATTCCACGATGTT 58.464 45.455 2.27 0.00 0.00 2.71
764 1924 5.006261 TGTCACTGTATTATATGCGTGCAAC 59.994 40.000 0.00 0.00 0.00 4.17
765 1925 5.112686 TGTCACTGTATTATATGCGTGCAA 58.887 37.500 0.00 0.00 0.00 4.08
766 1926 4.688021 TGTCACTGTATTATATGCGTGCA 58.312 39.130 0.00 0.00 0.00 4.57
767 1927 4.982295 TCTGTCACTGTATTATATGCGTGC 59.018 41.667 0.00 0.00 0.00 5.34
778 1938 6.543831 ACTTCTTTTGCTTTCTGTCACTGTAT 59.456 34.615 0.00 0.00 0.00 2.29
856 2018 4.803088 GCTACTGTTTTTGTTGTGCATCAA 59.197 37.500 0.00 0.00 0.00 2.57
857 2019 4.358851 GCTACTGTTTTTGTTGTGCATCA 58.641 39.130 0.00 0.00 0.00 3.07
858 2020 3.735746 GGCTACTGTTTTTGTTGTGCATC 59.264 43.478 0.00 0.00 0.00 3.91
914 2079 3.822167 GTCGGGGTTGGATGAAGTTAAAA 59.178 43.478 0.00 0.00 0.00 1.52
916 2081 2.290450 GGTCGGGGTTGGATGAAGTTAA 60.290 50.000 0.00 0.00 0.00 2.01
917 2082 1.279846 GGTCGGGGTTGGATGAAGTTA 59.720 52.381 0.00 0.00 0.00 2.24
973 2140 3.447025 GATTCGGGGTGGGCGAGAG 62.447 68.421 0.00 0.00 0.00 3.20
1266 2442 1.116536 TGTCAAGGTACTCACGCCCA 61.117 55.000 0.00 0.00 38.49 5.36
1272 2448 0.249120 CGGCCATGTCAAGGTACTCA 59.751 55.000 2.24 0.00 38.49 3.41
1435 2611 2.174639 ACATTGTGGAGTGAGTTTGGGA 59.825 45.455 0.00 0.00 0.00 4.37
1443 2631 0.107643 TTGCGGACATTGTGGAGTGA 59.892 50.000 0.00 0.00 0.00 3.41
1446 2634 1.227999 ACGTTGCGGACATTGTGGAG 61.228 55.000 0.00 0.00 0.00 3.86
1485 2673 1.700739 ACCGTGTGGGAAGATTAACCA 59.299 47.619 0.00 0.00 40.75 3.67
1489 2677 2.758979 GAGAGACCGTGTGGGAAGATTA 59.241 50.000 0.00 0.00 40.75 1.75
1490 2678 1.550976 GAGAGACCGTGTGGGAAGATT 59.449 52.381 0.00 0.00 40.75 2.40
1517 2705 4.670221 GCGTTCAAGAAATGGATGTCAGAC 60.670 45.833 0.00 0.00 0.00 3.51
1518 2706 3.436704 GCGTTCAAGAAATGGATGTCAGA 59.563 43.478 0.00 0.00 0.00 3.27
1524 2712 1.131126 CTGCGCGTTCAAGAAATGGAT 59.869 47.619 8.43 0.00 0.00 3.41
1748 2936 0.613260 CCCTGTACTGCACCTTGCTA 59.387 55.000 0.00 0.00 45.31 3.49
1781 2969 2.359850 GTTGAGCCGGGCATGACA 60.360 61.111 23.09 12.44 0.00 3.58
1913 3101 2.832931 CAGTCCCTGCAAGAACTCG 58.167 57.895 0.00 0.00 34.07 4.18
1998 3186 7.701078 GCAATCGACTACAGAGACAACTATTAA 59.299 37.037 0.00 0.00 0.00 1.40
2004 3192 3.575630 TGCAATCGACTACAGAGACAAC 58.424 45.455 0.00 0.00 0.00 3.32
2007 3332 5.425577 TCTATGCAATCGACTACAGAGAC 57.574 43.478 0.00 0.00 0.00 3.36
2015 3340 8.993121 CCACTAATTATTTCTATGCAATCGACT 58.007 33.333 0.00 0.00 0.00 4.18
2088 3413 5.485620 CACTGATGAATCTCCAGAACAGAA 58.514 41.667 0.00 0.00 0.00 3.02
2134 3467 4.879104 TTTGGCGTCTTCGTTCTAAAAA 57.121 36.364 0.00 0.00 39.49 1.94
2140 3473 3.001576 GCATTTGGCGTCTTCGTTC 57.998 52.632 0.00 0.00 39.49 3.95
2158 3491 0.179056 AATACATTCCCTGCCGGACG 60.179 55.000 5.05 0.00 41.83 4.79
2169 3502 8.870075 ATTAGGAAGCAATAGGGAATACATTC 57.130 34.615 0.00 0.00 36.08 2.67
2171 3504 8.673251 AGAATTAGGAAGCAATAGGGAATACAT 58.327 33.333 0.00 0.00 0.00 2.29
2173 3506 7.391833 CCAGAATTAGGAAGCAATAGGGAATAC 59.608 40.741 0.00 0.00 0.00 1.89
2175 3508 6.310149 CCAGAATTAGGAAGCAATAGGGAAT 58.690 40.000 0.00 0.00 0.00 3.01
2205 3538 3.753272 ACAATGATCAGAAAGTTGTCCCG 59.247 43.478 0.09 0.00 0.00 5.14
2353 3690 7.323420 CAAACAGTAGATTAGATGTCTCCACA 58.677 38.462 0.00 0.00 36.78 4.17
2379 3716 0.746063 ACCACATTGCACCTGTGTTG 59.254 50.000 21.16 12.73 41.93 3.33
2444 3781 4.523083 GCCAAGGTCATTATGTCAGGTAA 58.477 43.478 0.00 0.00 0.00 2.85
2482 3820 2.035626 ACACCAATGGGAAGGCCG 59.964 61.111 3.55 0.00 38.05 6.13
2497 3835 2.272230 TTTCGGTGACCAAGGCCACA 62.272 55.000 5.01 0.00 35.13 4.17
2512 3850 2.429069 GCTGCCGCAACCTTTTCG 60.429 61.111 0.00 0.00 35.78 3.46
2524 3862 0.810031 CACCGTAGTGTATGGCTGCC 60.810 60.000 12.87 12.87 39.30 4.85
2534 3872 1.134907 GGTACCATGGTCACCGTAGTG 60.135 57.143 23.76 0.00 46.00 2.74
2551 3889 2.897207 CCTCCGCCGAATGTGGTA 59.103 61.111 0.00 0.00 45.41 3.25
2795 5827 4.697756 TTTCCCGGCCGTCAGCAG 62.698 66.667 26.12 7.18 46.50 4.24
3564 11383 0.525668 GCGATGTTCGTCCTCGTCAT 60.526 55.000 0.00 0.00 42.81 3.06
3602 11421 0.916358 ACCTGCAGCCCTGGTCTAAT 60.916 55.000 8.66 0.00 41.44 1.73
3733 11552 0.106819 CATCCTCCAAGGGAAGCTGG 60.107 60.000 0.00 0.00 39.02 4.85
3768 11587 5.128499 AGCTTCAGTAACTGATGACTATGCT 59.872 40.000 0.00 0.00 40.39 3.79


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

AutoCloner maintained by Alex Coulton.