Multiple sequence alignment - TraesCS1B01G398900

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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 TraesCS1B01G398900 chr1B 100.000 3435 0 0 1 3435 630059487 630062921 0.000000e+00 6344.0
1 TraesCS1B01G398900 chr1D 89.497 3161 159 70 348 3435 458675545 458678605 0.000000e+00 3838.0
2 TraesCS1B01G398900 chr1A 90.803 1979 97 38 1505 3435 551049698 551051639 0.000000e+00 2567.0
3 TraesCS1B01G398900 chr1A 87.297 984 55 38 462 1405 551048604 551049557 0.000000e+00 1061.0
4 TraesCS1B01G398900 chr5B 88.871 620 30 9 1041 1635 668600746 668600141 0.000000e+00 726.0
5 TraesCS1B01G398900 chr3B 88.710 620 31 9 1041 1635 36492396 36493001 0.000000e+00 721.0
6 TraesCS1B01G398900 chr3B 83.333 84 14 0 1167 1250 8130919 8131002 1.020000e-10 78.7
7 TraesCS1B01G398900 chr7B 88.339 626 34 9 1035 1635 253370762 253371373 0.000000e+00 715.0
8 TraesCS1B01G398900 chr3A 84.962 266 35 5 9 270 73932445 73932709 7.310000e-67 265.0
9 TraesCS1B01G398900 chr3A 82.955 88 14 1 1167 1253 13520481 13520394 1.020000e-10 78.7
10 TraesCS1B01G398900 chr3D 80.682 88 17 0 1167 1254 6727475 6727562 6.150000e-08 69.4


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 TraesCS1B01G398900 chr1B 630059487 630062921 3434 False 6344 6344 100.000 1 3435 1 chr1B.!!$F1 3434
1 TraesCS1B01G398900 chr1D 458675545 458678605 3060 False 3838 3838 89.497 348 3435 1 chr1D.!!$F1 3087
2 TraesCS1B01G398900 chr1A 551048604 551051639 3035 False 1814 2567 89.050 462 3435 2 chr1A.!!$F1 2973
3 TraesCS1B01G398900 chr5B 668600141 668600746 605 True 726 726 88.871 1041 1635 1 chr5B.!!$R1 594
4 TraesCS1B01G398900 chr3B 36492396 36493001 605 False 721 721 88.710 1041 1635 1 chr3B.!!$F2 594
5 TraesCS1B01G398900 chr7B 253370762 253371373 611 False 715 715 88.339 1035 1635 1 chr7B.!!$F1 600

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
20 21 0.108662 CATGCCACAGTAGCTGTCGA 60.109 55.0 0.0 0.0 43.43 4.2 F
867 935 0.123266 TCCATTCCCTTCCCTTCCCT 59.877 55.0 0.0 0.0 0.00 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 1977 0.170561 GCATCAGCTGAGGTTGCAAG 59.829 55.0 27.8 10.51 37.91 4.01 R
2512 2673 0.392706 TGTGAAGCGAGTGTCCATGT 59.607 50.0 0.0 0.00 0.00 3.21 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.772739 CCATGCCACAGTAGCTGTC 58.227 57.895 0.00 0.00 43.43 3.51
19 20 1.086067 CCATGCCACAGTAGCTGTCG 61.086 60.000 0.00 0.00 43.43 4.35
20 21 0.108662 CATGCCACAGTAGCTGTCGA 60.109 55.000 0.00 0.00 43.43 4.20
21 22 0.174389 ATGCCACAGTAGCTGTCGAG 59.826 55.000 0.00 0.00 43.43 4.04
22 23 1.153745 GCCACAGTAGCTGTCGAGG 60.154 63.158 0.00 0.00 43.43 4.63
23 24 1.153745 CCACAGTAGCTGTCGAGGC 60.154 63.158 0.00 2.46 43.43 4.70
24 25 1.515088 CACAGTAGCTGTCGAGGCG 60.515 63.158 0.00 0.00 43.43 5.52
25 26 2.103143 CAGTAGCTGTCGAGGCGG 59.897 66.667 0.00 0.00 34.52 6.13
26 27 3.827898 AGTAGCTGTCGAGGCGGC 61.828 66.667 0.00 0.00 40.86 6.53
27 28 4.129737 GTAGCTGTCGAGGCGGCA 62.130 66.667 13.08 0.00 42.87 5.69
28 29 4.129737 TAGCTGTCGAGGCGGCAC 62.130 66.667 13.08 3.38 42.87 5.01
42 43 4.699522 GCACCACTGGACGGGGAC 62.700 72.222 0.71 0.00 0.00 4.46
43 44 3.238497 CACCACTGGACGGGGACA 61.238 66.667 0.71 0.00 0.00 4.02
44 45 2.446994 ACCACTGGACGGGGACAA 60.447 61.111 0.71 0.00 0.00 3.18
45 46 2.347490 CCACTGGACGGGGACAAG 59.653 66.667 0.00 0.00 0.00 3.16
46 47 2.358737 CACTGGACGGGGACAAGC 60.359 66.667 0.00 0.00 0.00 4.01
47 48 3.637273 ACTGGACGGGGACAAGCC 61.637 66.667 0.00 0.00 0.00 4.35
56 57 2.034221 GGACAAGCCCTCCACCAC 59.966 66.667 0.00 0.00 0.00 4.16
57 58 2.829384 GGACAAGCCCTCCACCACA 61.829 63.158 0.00 0.00 0.00 4.17
58 59 1.600916 GACAAGCCCTCCACCACAC 60.601 63.158 0.00 0.00 0.00 3.82
59 60 2.282462 CAAGCCCTCCACCACACC 60.282 66.667 0.00 0.00 0.00 4.16
60 61 2.776526 AAGCCCTCCACCACACCA 60.777 61.111 0.00 0.00 0.00 4.17
61 62 3.133365 AAGCCCTCCACCACACCAC 62.133 63.158 0.00 0.00 0.00 4.16
62 63 3.884774 GCCCTCCACCACACCACA 61.885 66.667 0.00 0.00 0.00 4.17
63 64 2.431683 CCCTCCACCACACCACAG 59.568 66.667 0.00 0.00 0.00 3.66
64 65 2.146724 CCCTCCACCACACCACAGA 61.147 63.158 0.00 0.00 0.00 3.41
65 66 1.372683 CCTCCACCACACCACAGAG 59.627 63.158 0.00 0.00 0.00 3.35
66 67 1.302033 CTCCACCACACCACAGAGC 60.302 63.158 0.00 0.00 0.00 4.09
67 68 2.666190 CCACCACACCACAGAGCG 60.666 66.667 0.00 0.00 0.00 5.03
68 69 2.421314 CACCACACCACAGAGCGA 59.579 61.111 0.00 0.00 0.00 4.93
69 70 1.665916 CACCACACCACAGAGCGAG 60.666 63.158 0.00 0.00 0.00 5.03
70 71 2.740055 CCACACCACAGAGCGAGC 60.740 66.667 0.00 0.00 0.00 5.03
71 72 2.341543 CACACCACAGAGCGAGCT 59.658 61.111 0.00 0.00 0.00 4.09
72 73 2.025969 CACACCACAGAGCGAGCTG 61.026 63.158 0.84 3.74 41.63 4.24
73 74 3.117171 CACCACAGAGCGAGCTGC 61.117 66.667 0.84 0.00 46.98 5.25
93 94 4.821589 CCGGAGCTTCGAGGCACC 62.822 72.222 23.16 23.16 39.10 5.01
114 115 3.579302 CCACCAAGCCCACCAGGA 61.579 66.667 0.00 0.00 38.24 3.86
115 116 2.520458 CACCAAGCCCACCAGGAA 59.480 61.111 0.00 0.00 38.24 3.36
116 117 1.903404 CACCAAGCCCACCAGGAAC 60.903 63.158 0.00 0.00 38.24 3.62
117 118 2.672996 CCAAGCCCACCAGGAACG 60.673 66.667 0.00 0.00 38.24 3.95
118 119 2.113139 CAAGCCCACCAGGAACGT 59.887 61.111 0.00 0.00 38.24 3.99
119 120 1.966451 CAAGCCCACCAGGAACGTC 60.966 63.158 0.00 0.00 38.24 4.34
120 121 2.147387 AAGCCCACCAGGAACGTCT 61.147 57.895 0.00 0.00 38.24 4.18
121 122 2.358737 GCCCACCAGGAACGTCTG 60.359 66.667 0.00 0.00 38.24 3.51
122 123 2.358737 CCCACCAGGAACGTCTGC 60.359 66.667 0.00 0.00 38.24 4.26
123 124 2.738521 CCACCAGGAACGTCTGCG 60.739 66.667 0.00 0.00 40.00 5.18
124 125 3.414700 CACCAGGAACGTCTGCGC 61.415 66.667 0.00 0.00 42.83 6.09
125 126 4.681978 ACCAGGAACGTCTGCGCC 62.682 66.667 4.18 0.00 42.83 6.53
147 148 3.916061 CGCGAGGAAGAAGAGAGAG 57.084 57.895 0.00 0.00 0.00 3.20
148 149 1.091537 CGCGAGGAAGAAGAGAGAGT 58.908 55.000 0.00 0.00 0.00 3.24
149 150 1.063469 CGCGAGGAAGAAGAGAGAGTC 59.937 57.143 0.00 0.00 0.00 3.36
150 151 1.063469 GCGAGGAAGAAGAGAGAGTCG 59.937 57.143 0.00 0.00 0.00 4.18
151 152 2.352388 CGAGGAAGAAGAGAGAGTCGT 58.648 52.381 0.00 0.00 0.00 4.34
152 153 2.095213 CGAGGAAGAAGAGAGAGTCGTG 59.905 54.545 0.00 0.00 0.00 4.35
153 154 1.816224 AGGAAGAAGAGAGAGTCGTGC 59.184 52.381 0.00 0.00 0.00 5.34
154 155 1.135228 GGAAGAAGAGAGAGTCGTGCC 60.135 57.143 0.00 0.00 0.00 5.01
155 156 1.542030 GAAGAAGAGAGAGTCGTGCCA 59.458 52.381 0.00 0.00 0.00 4.92
156 157 1.173043 AGAAGAGAGAGTCGTGCCAG 58.827 55.000 0.00 0.00 0.00 4.85
157 158 0.172352 GAAGAGAGAGTCGTGCCAGG 59.828 60.000 0.00 0.00 0.00 4.45
158 159 1.254284 AAGAGAGAGTCGTGCCAGGG 61.254 60.000 0.00 0.00 0.00 4.45
159 160 1.679305 GAGAGAGTCGTGCCAGGGA 60.679 63.158 0.00 0.00 0.00 4.20
160 161 1.662438 GAGAGAGTCGTGCCAGGGAG 61.662 65.000 0.00 0.00 0.00 4.30
161 162 1.679305 GAGAGTCGTGCCAGGGAGA 60.679 63.158 0.00 0.00 0.00 3.71
162 163 1.228894 AGAGTCGTGCCAGGGAGAA 60.229 57.895 0.00 0.00 0.00 2.87
163 164 1.216710 GAGTCGTGCCAGGGAGAAG 59.783 63.158 0.00 0.00 0.00 2.85
164 165 2.435059 GTCGTGCCAGGGAGAAGC 60.435 66.667 0.00 0.00 0.00 3.86
165 166 3.706373 TCGTGCCAGGGAGAAGCC 61.706 66.667 0.00 0.00 0.00 4.35
193 194 4.404098 CGGCACTACCCGGGCTTT 62.404 66.667 24.08 3.13 44.46 3.51
194 195 2.750237 GGCACTACCCGGGCTTTG 60.750 66.667 24.08 16.16 0.00 2.77
195 196 3.440415 GCACTACCCGGGCTTTGC 61.440 66.667 24.08 22.37 0.00 3.68
205 206 2.750237 GGCTTTGCCCGGTAGTGG 60.750 66.667 0.00 0.00 44.06 4.00
233 234 2.840102 CGGCGAGGAGGAGGGAAT 60.840 66.667 0.00 0.00 0.00 3.01
234 235 2.825264 GGCGAGGAGGAGGGAATG 59.175 66.667 0.00 0.00 0.00 2.67
235 236 2.812619 GGCGAGGAGGAGGGAATGG 61.813 68.421 0.00 0.00 0.00 3.16
236 237 2.066999 GCGAGGAGGAGGGAATGGT 61.067 63.158 0.00 0.00 0.00 3.55
237 238 1.826024 CGAGGAGGAGGGAATGGTG 59.174 63.158 0.00 0.00 0.00 4.17
238 239 1.690219 CGAGGAGGAGGGAATGGTGG 61.690 65.000 0.00 0.00 0.00 4.61
239 240 0.326618 GAGGAGGAGGGAATGGTGGA 60.327 60.000 0.00 0.00 0.00 4.02
240 241 0.327000 AGGAGGAGGGAATGGTGGAG 60.327 60.000 0.00 0.00 0.00 3.86
241 242 1.348775 GGAGGAGGGAATGGTGGAGG 61.349 65.000 0.00 0.00 0.00 4.30
242 243 0.326618 GAGGAGGGAATGGTGGAGGA 60.327 60.000 0.00 0.00 0.00 3.71
243 244 0.327000 AGGAGGGAATGGTGGAGGAG 60.327 60.000 0.00 0.00 0.00 3.69
244 245 1.348775 GGAGGGAATGGTGGAGGAGG 61.349 65.000 0.00 0.00 0.00 4.30
245 246 1.308216 AGGGAATGGTGGAGGAGGG 60.308 63.158 0.00 0.00 0.00 4.30
246 247 2.597903 GGAATGGTGGAGGAGGGC 59.402 66.667 0.00 0.00 0.00 5.19
247 248 2.597903 GAATGGTGGAGGAGGGCC 59.402 66.667 0.00 0.00 0.00 5.80
248 249 3.406595 GAATGGTGGAGGAGGGCCG 62.407 68.421 0.00 0.00 39.96 6.13
273 274 3.162154 GGGGGCTAGGGTTCTCCG 61.162 72.222 0.00 0.00 41.52 4.63
274 275 2.365237 GGGGCTAGGGTTCTCCGT 60.365 66.667 0.00 0.00 41.52 4.69
275 276 2.732619 GGGGCTAGGGTTCTCCGTG 61.733 68.421 0.00 0.00 41.52 4.94
276 277 1.988406 GGGCTAGGGTTCTCCGTGT 60.988 63.158 0.00 0.00 41.52 4.49
277 278 1.516423 GGCTAGGGTTCTCCGTGTC 59.484 63.158 0.00 0.00 41.52 3.67
278 279 1.139095 GCTAGGGTTCTCCGTGTCG 59.861 63.158 0.00 0.00 41.52 4.35
279 280 1.139095 CTAGGGTTCTCCGTGTCGC 59.861 63.158 0.00 0.00 41.52 5.19
280 281 1.303888 TAGGGTTCTCCGTGTCGCT 60.304 57.895 0.00 0.00 41.52 4.93
281 282 0.896940 TAGGGTTCTCCGTGTCGCTT 60.897 55.000 0.00 0.00 41.52 4.68
282 283 1.737008 GGGTTCTCCGTGTCGCTTC 60.737 63.158 0.00 0.00 33.83 3.86
283 284 2.087009 GGTTCTCCGTGTCGCTTCG 61.087 63.158 0.00 0.00 0.00 3.79
284 285 2.087009 GTTCTCCGTGTCGCTTCGG 61.087 63.158 5.82 5.82 46.93 4.30
289 290 2.202492 CGTGTCGCTTCGGAGAGG 60.202 66.667 0.00 0.00 38.43 3.69
290 291 2.182030 GTGTCGCTTCGGAGAGGG 59.818 66.667 0.00 0.00 38.43 4.30
291 292 2.035155 TGTCGCTTCGGAGAGGGA 59.965 61.111 0.00 0.00 38.43 4.20
292 293 2.341101 TGTCGCTTCGGAGAGGGAC 61.341 63.158 20.11 20.11 42.77 4.46
293 294 2.766306 TGTCGCTTCGGAGAGGGACT 62.766 60.000 23.70 0.00 42.84 3.85
294 295 1.304217 TCGCTTCGGAGAGGGACTT 60.304 57.895 0.00 0.00 41.55 3.01
295 296 1.153745 CGCTTCGGAGAGGGACTTG 60.154 63.158 0.00 0.00 41.55 3.16
296 297 1.219393 GCTTCGGAGAGGGACTTGG 59.781 63.158 0.00 0.00 41.55 3.61
297 298 1.901085 CTTCGGAGAGGGACTTGGG 59.099 63.158 0.00 0.00 41.55 4.12
298 299 1.612442 TTCGGAGAGGGACTTGGGG 60.612 63.158 0.00 0.00 41.55 4.96
299 300 3.083997 CGGAGAGGGACTTGGGGG 61.084 72.222 0.00 0.00 41.55 5.40
300 301 2.454941 GGAGAGGGACTTGGGGGA 59.545 66.667 0.00 0.00 41.55 4.81
301 302 1.996187 GGAGAGGGACTTGGGGGAC 60.996 68.421 0.00 0.00 41.55 4.46
302 303 2.284699 AGAGGGACTTGGGGGACG 60.285 66.667 0.00 0.00 41.55 4.79
303 304 3.400054 GAGGGACTTGGGGGACGG 61.400 72.222 0.00 0.00 41.55 4.79
306 307 4.029809 GGACTTGGGGGACGGGTG 62.030 72.222 0.00 0.00 0.00 4.61
307 308 4.029809 GACTTGGGGGACGGGTGG 62.030 72.222 0.00 0.00 0.00 4.61
314 315 4.817909 GGGACGGGTGGGGATCCT 62.818 72.222 12.58 0.00 0.00 3.24
315 316 3.162154 GGACGGGTGGGGATCCTC 61.162 72.222 12.58 8.60 0.00 3.71
316 317 3.162154 GACGGGTGGGGATCCTCC 61.162 72.222 9.81 10.72 44.03 4.30
318 319 4.853142 CGGGTGGGGATCCTCCGA 62.853 72.222 22.45 0.00 45.87 4.55
319 320 2.844839 GGGTGGGGATCCTCCGAG 60.845 72.222 9.81 0.00 45.32 4.63
320 321 2.282446 GGTGGGGATCCTCCGAGA 59.718 66.667 9.81 0.00 37.43 4.04
321 322 1.834822 GGTGGGGATCCTCCGAGAG 60.835 68.421 9.81 0.00 37.43 3.20
337 338 3.305398 GAGAGGTCTCGAAAGCTTGAA 57.695 47.619 0.00 0.00 32.78 2.69
338 339 3.855858 GAGAGGTCTCGAAAGCTTGAAT 58.144 45.455 0.00 0.00 32.78 2.57
339 340 5.000012 GAGAGGTCTCGAAAGCTTGAATA 58.000 43.478 0.00 0.00 32.78 1.75
340 341 5.596845 GAGAGGTCTCGAAAGCTTGAATAT 58.403 41.667 0.00 0.00 32.78 1.28
341 342 5.983540 AGAGGTCTCGAAAGCTTGAATATT 58.016 37.500 0.00 0.00 34.09 1.28
342 343 5.814705 AGAGGTCTCGAAAGCTTGAATATTG 59.185 40.000 0.00 0.00 34.09 1.90
343 344 4.878397 AGGTCTCGAAAGCTTGAATATTGG 59.122 41.667 0.00 0.00 0.00 3.16
344 345 4.035675 GGTCTCGAAAGCTTGAATATTGGG 59.964 45.833 0.00 0.00 0.00 4.12
345 346 4.876107 GTCTCGAAAGCTTGAATATTGGGA 59.124 41.667 0.00 0.00 0.00 4.37
346 347 5.007136 GTCTCGAAAGCTTGAATATTGGGAG 59.993 44.000 0.00 0.00 0.00 4.30
358 359 4.755266 ATATTGGGAGACAGCTTACGTT 57.245 40.909 0.00 0.00 0.00 3.99
360 361 2.922740 TGGGAGACAGCTTACGTTTT 57.077 45.000 0.00 0.00 0.00 2.43
361 362 3.202829 TGGGAGACAGCTTACGTTTTT 57.797 42.857 0.00 0.00 0.00 1.94
380 381 5.564048 TTTTTAATATACAAGCGGCCGTT 57.436 34.783 28.70 20.13 0.00 4.44
405 406 4.747108 CGCCGAGAGATTCTTCACATTAAT 59.253 41.667 0.00 0.00 0.00 1.40
406 407 5.920840 CGCCGAGAGATTCTTCACATTAATA 59.079 40.000 0.00 0.00 0.00 0.98
407 408 6.420903 CGCCGAGAGATTCTTCACATTAATAA 59.579 38.462 0.00 0.00 0.00 1.40
408 409 7.116948 CGCCGAGAGATTCTTCACATTAATAAT 59.883 37.037 0.00 0.00 0.00 1.28
436 443 5.820947 AGGAACAAGACAAAGAAACGTGTAT 59.179 36.000 0.00 0.00 0.00 2.29
484 491 1.620822 GATGTTCCCAACAGCCAAGT 58.379 50.000 0.00 0.00 45.95 3.16
511 526 0.618458 AGCCGCCTCATCCAAAACTA 59.382 50.000 0.00 0.00 0.00 2.24
515 530 3.489229 GCCGCCTCATCCAAAACTAAATC 60.489 47.826 0.00 0.00 0.00 2.17
536 551 0.886490 CCAACAGCTCCACCTGTCAC 60.886 60.000 0.00 0.00 44.86 3.67
541 563 2.960688 GCTCCACCTGTCACCCTCC 61.961 68.421 0.00 0.00 0.00 4.30
566 588 3.191371 CACTCCAAGATTAAAGCACACCC 59.809 47.826 0.00 0.00 0.00 4.61
569 591 2.231235 CCAAGATTAAAGCACACCCCAC 59.769 50.000 0.00 0.00 0.00 4.61
570 592 2.890311 CAAGATTAAAGCACACCCCACA 59.110 45.455 0.00 0.00 0.00 4.17
660 686 8.590719 AGATATGATATGACAATGATCGATGC 57.409 34.615 0.54 0.00 0.00 3.91
661 687 8.422566 AGATATGATATGACAATGATCGATGCT 58.577 33.333 0.54 0.00 0.00 3.79
662 688 9.688592 GATATGATATGACAATGATCGATGCTA 57.311 33.333 0.54 0.00 0.00 3.49
663 689 7.767745 ATGATATGACAATGATCGATGCTAC 57.232 36.000 0.54 0.00 0.00 3.58
664 690 6.928520 TGATATGACAATGATCGATGCTACT 58.071 36.000 0.54 0.00 0.00 2.57
665 691 8.055279 TGATATGACAATGATCGATGCTACTA 57.945 34.615 0.54 0.00 0.00 1.82
707 735 8.695456 TCATTATAAGTATTCTCACAGACTGCA 58.305 33.333 1.25 0.00 0.00 4.41
713 741 6.940739 AGTATTCTCACAGACTGCAATAGTT 58.059 36.000 1.25 0.00 40.53 2.24
714 742 7.038659 AGTATTCTCACAGACTGCAATAGTTC 58.961 38.462 1.25 0.00 40.53 3.01
717 745 5.955488 TCTCACAGACTGCAATAGTTCTAC 58.045 41.667 1.25 0.00 40.53 2.59
740 790 0.537188 TTCGTCTCAGAATCCAGCCC 59.463 55.000 0.00 0.00 0.00 5.19
805 860 0.178068 GCTTCTTCAGATACCCGGCA 59.822 55.000 0.00 0.00 0.00 5.69
863 931 1.773541 ACCTTCCATTCCCTTCCCTT 58.226 50.000 0.00 0.00 0.00 3.95
864 932 1.641192 ACCTTCCATTCCCTTCCCTTC 59.359 52.381 0.00 0.00 0.00 3.46
865 933 1.063642 CCTTCCATTCCCTTCCCTTCC 60.064 57.143 0.00 0.00 0.00 3.46
866 934 1.007607 TTCCATTCCCTTCCCTTCCC 58.992 55.000 0.00 0.00 0.00 3.97
867 935 0.123266 TCCATTCCCTTCCCTTCCCT 59.877 55.000 0.00 0.00 0.00 4.20
887 955 1.651240 CCTGACCTTGCTTGGCATCG 61.651 60.000 0.00 0.00 38.76 3.84
980 1048 4.393074 GACGTACGCTAGCTATATGTGAC 58.607 47.826 16.72 7.78 0.00 3.67
1267 1336 6.673154 AGGTAAAAACGTCTTGGCATATAC 57.327 37.500 0.00 0.00 0.00 1.47
1268 1337 6.412214 AGGTAAAAACGTCTTGGCATATACT 58.588 36.000 0.00 0.00 0.00 2.12
1269 1338 6.315393 AGGTAAAAACGTCTTGGCATATACTG 59.685 38.462 0.00 0.00 0.00 2.74
1270 1339 6.093082 GGTAAAAACGTCTTGGCATATACTGT 59.907 38.462 0.00 0.00 0.00 3.55
1271 1340 7.278424 GGTAAAAACGTCTTGGCATATACTGTA 59.722 37.037 0.00 0.00 0.00 2.74
1272 1341 6.657836 AAAACGTCTTGGCATATACTGTAC 57.342 37.500 0.00 0.00 0.00 2.90
1273 1342 3.961182 ACGTCTTGGCATATACTGTACG 58.039 45.455 0.00 0.00 0.00 3.67
1274 1343 3.379372 ACGTCTTGGCATATACTGTACGT 59.621 43.478 0.00 0.00 36.34 3.57
1275 1344 4.576053 ACGTCTTGGCATATACTGTACGTA 59.424 41.667 0.00 0.00 39.05 3.57
1317 1386 2.184385 GCAGTGGCTGAATTGAATCG 57.816 50.000 0.00 0.00 36.96 3.34
1322 1391 1.811965 TGGCTGAATTGAATCGGTGTG 59.188 47.619 0.00 0.00 0.00 3.82
1405 1474 4.694760 ATGTGAGATATGCTTGCAGGTA 57.305 40.909 0.87 0.00 0.00 3.08
1409 1490 5.887598 TGTGAGATATGCTTGCAGGTAAAAT 59.112 36.000 0.87 0.00 0.00 1.82
1458 1544 5.709164 GCATGGCTGACTAATGGAGAATATT 59.291 40.000 0.00 0.00 0.00 1.28
1506 1596 4.141642 TGGATAACTGATGTCATCCACTGG 60.142 45.833 10.36 0.00 41.52 4.00
1510 1626 4.207891 ACTGATGTCATCCACTGGTAAC 57.792 45.455 10.36 0.00 0.00 2.50
1544 1660 2.441750 ACCAAACTACAAGGCTCCTTCA 59.558 45.455 0.00 0.00 33.42 3.02
1595 1713 5.422214 TCTTCTTCAGGTACCAATCTTCC 57.578 43.478 15.94 0.00 0.00 3.46
1656 1774 6.699366 TGGATCATCTAATGCTCTTCTCATC 58.301 40.000 0.00 0.00 0.00 2.92
1740 1858 0.254178 ATGATCGCCAAGCTTCCACT 59.746 50.000 0.00 0.00 0.00 4.00
1817 1936 4.637276 ACATACAGACATCCGTTGTTTCA 58.363 39.130 0.00 0.00 39.18 2.69
1829 1948 2.711964 CGTTGTTTCATTCGACGGTTTG 59.288 45.455 0.00 0.00 38.54 2.93
1830 1949 2.392933 TGTTTCATTCGACGGTTTGC 57.607 45.000 0.00 0.00 0.00 3.68
1831 1950 1.671328 TGTTTCATTCGACGGTTTGCA 59.329 42.857 0.00 0.00 0.00 4.08
1832 1951 2.097629 TGTTTCATTCGACGGTTTGCAA 59.902 40.909 0.00 0.00 0.00 4.08
1833 1952 3.243234 TGTTTCATTCGACGGTTTGCAAT 60.243 39.130 0.00 0.00 0.00 3.56
1834 1953 2.610219 TCATTCGACGGTTTGCAATG 57.390 45.000 0.00 0.00 0.00 2.82
1858 1977 8.364129 TGAAAAATTAACAGCCTGAAACATTC 57.636 30.769 0.00 0.13 0.00 2.67
1921 2040 2.046023 TCGGTCTACCTCGGCGAA 60.046 61.111 12.13 0.00 0.00 4.70
1966 2085 3.285371 ACCGTAAGTGAGGCTCCG 58.715 61.111 12.86 7.59 0.00 4.63
2003 2125 1.345415 TCCACACGTTTTCCCTAGACC 59.655 52.381 0.00 0.00 0.00 3.85
2013 2135 5.625150 GTTTTCCCTAGACCAGATGCATAT 58.375 41.667 0.00 0.00 0.00 1.78
2040 2162 2.969821 ACCCAGCAAATGTAACCTGA 57.030 45.000 0.00 0.00 0.00 3.86
2180 2302 4.521256 GTGGCAGGTTTGTAAAACCATCTA 59.479 41.667 20.82 9.18 42.69 1.98
2181 2303 4.764823 TGGCAGGTTTGTAAAACCATCTAG 59.235 41.667 20.82 8.55 42.69 2.43
2182 2304 4.765339 GGCAGGTTTGTAAAACCATCTAGT 59.235 41.667 20.82 0.00 42.69 2.57
2183 2305 5.941647 GGCAGGTTTGTAAAACCATCTAGTA 59.058 40.000 20.82 0.00 42.69 1.82
2223 2345 6.317789 TGTTTATGAAGTTTCTGGCTGAAG 57.682 37.500 6.91 0.00 35.89 3.02
2265 2393 1.331756 GCTATGCATGGTCAGGTTTCG 59.668 52.381 10.16 0.00 0.00 3.46
2355 2483 0.472925 TCCAGTAGTGCACCAAGGGA 60.473 55.000 14.63 13.25 0.00 4.20
2464 2625 4.503007 GTGAGTTGTGGCTGTACGTATATG 59.497 45.833 0.00 0.00 0.00 1.78
2471 2632 4.852104 GTGGCTGTACGTATATGATCTTCG 59.148 45.833 0.00 0.00 0.00 3.79
2530 2691 2.363788 TACATGGACACTCGCTTCAC 57.636 50.000 0.00 0.00 0.00 3.18
2551 2712 6.101997 TCACAAGCTATGAAGATGTAGTGTG 58.898 40.000 0.00 0.00 0.00 3.82
2555 2716 4.054671 GCTATGAAGATGTAGTGTGCCTC 58.945 47.826 0.00 0.00 0.00 4.70
2563 2724 2.536066 TGTAGTGTGCCTCCTGTACAT 58.464 47.619 0.00 0.00 41.79 2.29
2567 2728 1.001974 GTGTGCCTCCTGTACATGACA 59.998 52.381 0.00 0.00 41.79 3.58
2583 2744 4.021894 ACATGACAAGAGACAGGAGTACAC 60.022 45.833 0.00 0.00 0.00 2.90
2584 2745 2.552743 TGACAAGAGACAGGAGTACACG 59.447 50.000 0.00 0.00 0.00 4.49
2585 2746 2.812591 GACAAGAGACAGGAGTACACGA 59.187 50.000 0.00 0.00 0.00 4.35
2586 2747 3.422796 ACAAGAGACAGGAGTACACGAT 58.577 45.455 0.00 0.00 0.00 3.73
2607 2771 9.529325 CACGATGATGTAGGAATTTTAGACTTA 57.471 33.333 0.00 0.00 0.00 2.24
2627 2791 5.296531 ACTTATGCAATGTACATTCGATGCA 59.703 36.000 26.70 26.70 32.86 3.96
2659 2823 2.417379 GCAGAAATCACTCTGTCGCCTA 60.417 50.000 2.81 0.00 44.04 3.93
2662 2826 3.449018 AGAAATCACTCTGTCGCCTACAT 59.551 43.478 0.00 0.00 37.50 2.29
2663 2827 3.895232 AATCACTCTGTCGCCTACATT 57.105 42.857 0.00 0.00 37.50 2.71
2664 2828 2.654749 TCACTCTGTCGCCTACATTG 57.345 50.000 0.00 0.00 37.50 2.82
2708 2872 2.627699 ACAATTCGCCAGTTCCAAATGT 59.372 40.909 0.00 0.00 0.00 2.71
2758 2922 0.389817 GCACTACCATGCTGTCGTCA 60.390 55.000 0.00 0.00 42.62 4.35
2800 2964 6.486056 ACCATAGACAGAGTACATCCGATAT 58.514 40.000 0.00 0.00 0.00 1.63
2829 2993 6.228258 TCGCAAGACTTAAGGATTAACACTT 58.772 36.000 7.53 0.00 45.01 3.16
2844 3011 7.094933 GGATTAACACTTAGTTCAATTCACGGT 60.095 37.037 0.00 0.00 41.64 4.83
2855 3023 3.257873 TCAATTCACGGTTCAAATGGCAT 59.742 39.130 0.00 0.00 0.00 4.40
2871 3039 4.233632 TGGCATCAACAGTTCATCCATA 57.766 40.909 0.00 0.00 0.00 2.74
2955 3124 3.441572 GTGCAAGTTAGGTCATCATGCTT 59.558 43.478 0.00 0.00 33.66 3.91
2956 3125 3.691118 TGCAAGTTAGGTCATCATGCTTC 59.309 43.478 0.00 0.00 33.66 3.86
2957 3126 3.944015 GCAAGTTAGGTCATCATGCTTCT 59.056 43.478 0.00 0.00 0.00 2.85
2958 3127 4.034975 GCAAGTTAGGTCATCATGCTTCTC 59.965 45.833 0.00 0.00 0.00 2.87
2959 3128 5.426504 CAAGTTAGGTCATCATGCTTCTCT 58.573 41.667 0.00 0.00 0.00 3.10
2960 3129 6.577103 CAAGTTAGGTCATCATGCTTCTCTA 58.423 40.000 0.00 0.00 0.00 2.43
2961 3130 6.798427 AGTTAGGTCATCATGCTTCTCTAA 57.202 37.500 0.00 0.00 0.00 2.10
2962 3131 6.815089 AGTTAGGTCATCATGCTTCTCTAAG 58.185 40.000 0.00 0.00 35.68 2.18
2963 3132 6.382570 AGTTAGGTCATCATGCTTCTCTAAGT 59.617 38.462 0.00 0.00 34.99 2.24
2964 3133 5.690464 AGGTCATCATGCTTCTCTAAGTT 57.310 39.130 0.00 0.00 34.99 2.66
2965 3134 6.059787 AGGTCATCATGCTTCTCTAAGTTT 57.940 37.500 0.00 0.00 34.99 2.66
2966 3135 6.479884 AGGTCATCATGCTTCTCTAAGTTTT 58.520 36.000 0.00 0.00 34.99 2.43
2967 3136 6.944862 AGGTCATCATGCTTCTCTAAGTTTTT 59.055 34.615 0.00 0.00 34.99 1.94
2968 3137 7.120432 AGGTCATCATGCTTCTCTAAGTTTTTC 59.880 37.037 0.00 0.00 34.99 2.29
2969 3138 7.094634 GGTCATCATGCTTCTCTAAGTTTTTCA 60.095 37.037 0.00 0.00 34.99 2.69
3001 3185 4.997395 TGACAGCTCTAACACTGGATTTTC 59.003 41.667 0.00 0.00 38.25 2.29
3002 3186 4.973168 ACAGCTCTAACACTGGATTTTCA 58.027 39.130 0.00 0.00 38.25 2.69
3188 3378 3.233684 TGAATTCCGTATACGCACACA 57.766 42.857 19.86 11.86 38.18 3.72
3193 3383 1.134936 TCCGTATACGCACACAGCAAT 60.135 47.619 19.86 0.00 46.13 3.56
3219 3409 9.573166 TGAATGATATCCTACCAACCTAAAATG 57.427 33.333 0.00 0.00 0.00 2.32
3323 3513 1.255882 CCCAAATGTACAGCTGGCAA 58.744 50.000 19.93 2.49 0.00 4.52
3349 3539 2.123982 CCCAGGGCAGCTCCAATC 60.124 66.667 0.00 0.00 36.21 2.67
3387 3577 1.743321 GAGGAGGAGGCATCGTCAGG 61.743 65.000 21.04 0.00 41.21 3.86
3407 3597 4.715523 GTGCCGCCCCTACTTGCA 62.716 66.667 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.086067 CGACAGCTACTGTGGCATGG 61.086 60.000 18.51 9.52 45.44 3.66
1 2 0.108662 TCGACAGCTACTGTGGCATG 60.109 55.000 18.51 14.57 45.44 4.06
2 3 0.174389 CTCGACAGCTACTGTGGCAT 59.826 55.000 18.51 5.79 45.44 4.40
3 4 1.586541 CTCGACAGCTACTGTGGCA 59.413 57.895 18.51 0.00 45.44 4.92
4 5 1.153745 CCTCGACAGCTACTGTGGC 60.154 63.158 8.20 8.20 45.44 5.01
5 6 1.153745 GCCTCGACAGCTACTGTGG 60.154 63.158 4.71 4.11 45.44 4.17
6 7 1.515088 CGCCTCGACAGCTACTGTG 60.515 63.158 4.71 0.00 45.44 3.66
8 9 2.103143 CCGCCTCGACAGCTACTG 59.897 66.667 0.00 0.00 37.52 2.74
9 10 3.827898 GCCGCCTCGACAGCTACT 61.828 66.667 0.00 0.00 0.00 2.57
10 11 4.129737 TGCCGCCTCGACAGCTAC 62.130 66.667 0.00 0.00 0.00 3.58
11 12 4.129737 GTGCCGCCTCGACAGCTA 62.130 66.667 0.00 0.00 0.00 3.32
25 26 4.699522 GTCCCCGTCCAGTGGTGC 62.700 72.222 9.54 2.72 0.00 5.01
26 27 2.731691 CTTGTCCCCGTCCAGTGGTG 62.732 65.000 9.54 3.00 0.00 4.17
27 28 2.446994 TTGTCCCCGTCCAGTGGT 60.447 61.111 9.54 0.00 0.00 4.16
28 29 2.347490 CTTGTCCCCGTCCAGTGG 59.653 66.667 1.40 1.40 0.00 4.00
29 30 2.358737 GCTTGTCCCCGTCCAGTG 60.359 66.667 0.00 0.00 0.00 3.66
30 31 3.637273 GGCTTGTCCCCGTCCAGT 61.637 66.667 0.00 0.00 0.00 4.00
39 40 2.034221 GTGGTGGAGGGCTTGTCC 59.966 66.667 0.00 0.00 34.31 4.02
40 41 1.600916 GTGTGGTGGAGGGCTTGTC 60.601 63.158 0.00 0.00 0.00 3.18
41 42 2.515901 GTGTGGTGGAGGGCTTGT 59.484 61.111 0.00 0.00 0.00 3.16
42 43 2.282462 GGTGTGGTGGAGGGCTTG 60.282 66.667 0.00 0.00 0.00 4.01
43 44 2.776526 TGGTGTGGTGGAGGGCTT 60.777 61.111 0.00 0.00 0.00 4.35
44 45 3.570212 GTGGTGTGGTGGAGGGCT 61.570 66.667 0.00 0.00 0.00 5.19
45 46 3.850098 CTGTGGTGTGGTGGAGGGC 62.850 68.421 0.00 0.00 0.00 5.19
46 47 2.116983 CTCTGTGGTGTGGTGGAGGG 62.117 65.000 0.00 0.00 0.00 4.30
47 48 1.372683 CTCTGTGGTGTGGTGGAGG 59.627 63.158 0.00 0.00 0.00 4.30
48 49 1.302033 GCTCTGTGGTGTGGTGGAG 60.302 63.158 0.00 0.00 0.00 3.86
49 50 2.828868 GCTCTGTGGTGTGGTGGA 59.171 61.111 0.00 0.00 0.00 4.02
50 51 2.666190 CGCTCTGTGGTGTGGTGG 60.666 66.667 0.00 0.00 0.00 4.61
51 52 1.665916 CTCGCTCTGTGGTGTGGTG 60.666 63.158 0.00 0.00 0.00 4.17
52 53 2.737180 CTCGCTCTGTGGTGTGGT 59.263 61.111 0.00 0.00 0.00 4.16
53 54 2.740055 GCTCGCTCTGTGGTGTGG 60.740 66.667 0.00 0.00 0.00 4.17
54 55 2.025969 CAGCTCGCTCTGTGGTGTG 61.026 63.158 0.00 0.00 35.44 3.82
55 56 2.341543 CAGCTCGCTCTGTGGTGT 59.658 61.111 0.00 0.00 35.44 4.16
56 57 3.117171 GCAGCTCGCTCTGTGGTG 61.117 66.667 5.80 0.00 41.30 4.17
57 58 4.385405 GGCAGCTCGCTCTGTGGT 62.385 66.667 7.85 0.00 41.91 4.16
76 77 4.821589 GGTGCCTCGAAGCTCCGG 62.822 72.222 11.10 0.00 36.74 5.14
97 98 3.145473 TTCCTGGTGGGCTTGGTGG 62.145 63.158 0.00 0.00 34.39 4.61
98 99 1.903404 GTTCCTGGTGGGCTTGGTG 60.903 63.158 0.00 0.00 34.39 4.17
99 100 2.520968 GTTCCTGGTGGGCTTGGT 59.479 61.111 0.00 0.00 34.39 3.67
100 101 2.672996 CGTTCCTGGTGGGCTTGG 60.673 66.667 0.00 0.00 34.39 3.61
101 102 1.966451 GACGTTCCTGGTGGGCTTG 60.966 63.158 0.00 0.00 34.39 4.01
102 103 2.147387 AGACGTTCCTGGTGGGCTT 61.147 57.895 0.00 0.00 34.39 4.35
103 104 2.526873 AGACGTTCCTGGTGGGCT 60.527 61.111 0.00 0.00 34.39 5.19
104 105 2.358737 CAGACGTTCCTGGTGGGC 60.359 66.667 0.00 0.00 34.39 5.36
105 106 2.358737 GCAGACGTTCCTGGTGGG 60.359 66.667 6.41 0.00 34.82 4.61
106 107 2.738521 CGCAGACGTTCCTGGTGG 60.739 66.667 6.41 0.00 34.82 4.61
107 108 3.414700 GCGCAGACGTTCCTGGTG 61.415 66.667 0.30 0.00 42.83 4.17
108 109 4.681978 GGCGCAGACGTTCCTGGT 62.682 66.667 10.83 0.00 42.83 4.00
125 126 4.129737 TCTTCTTCCTCGCGGGCG 62.130 66.667 6.13 6.74 41.35 6.13
126 127 2.202810 CTCTTCTTCCTCGCGGGC 60.203 66.667 6.13 0.00 34.39 6.13
127 128 1.032657 TCTCTCTTCTTCCTCGCGGG 61.033 60.000 6.13 0.59 0.00 6.13
128 129 0.380378 CTCTCTCTTCTTCCTCGCGG 59.620 60.000 6.13 0.00 0.00 6.46
129 130 1.063469 GACTCTCTCTTCTTCCTCGCG 59.937 57.143 0.00 0.00 0.00 5.87
130 131 1.063469 CGACTCTCTCTTCTTCCTCGC 59.937 57.143 0.00 0.00 0.00 5.03
131 132 2.095213 CACGACTCTCTCTTCTTCCTCG 59.905 54.545 0.00 0.00 0.00 4.63
132 133 2.159435 GCACGACTCTCTCTTCTTCCTC 60.159 54.545 0.00 0.00 0.00 3.71
133 134 1.816224 GCACGACTCTCTCTTCTTCCT 59.184 52.381 0.00 0.00 0.00 3.36
134 135 1.135228 GGCACGACTCTCTCTTCTTCC 60.135 57.143 0.00 0.00 0.00 3.46
135 136 1.542030 TGGCACGACTCTCTCTTCTTC 59.458 52.381 0.00 0.00 0.00 2.87
136 137 1.543802 CTGGCACGACTCTCTCTTCTT 59.456 52.381 0.00 0.00 0.00 2.52
137 138 1.173043 CTGGCACGACTCTCTCTTCT 58.827 55.000 0.00 0.00 0.00 2.85
138 139 0.172352 CCTGGCACGACTCTCTCTTC 59.828 60.000 0.00 0.00 0.00 2.87
139 140 1.254284 CCCTGGCACGACTCTCTCTT 61.254 60.000 0.00 0.00 0.00 2.85
140 141 1.680651 CCCTGGCACGACTCTCTCT 60.681 63.158 0.00 0.00 0.00 3.10
141 142 1.662438 CTCCCTGGCACGACTCTCTC 61.662 65.000 0.00 0.00 0.00 3.20
142 143 1.680651 CTCCCTGGCACGACTCTCT 60.681 63.158 0.00 0.00 0.00 3.10
143 144 1.251527 TTCTCCCTGGCACGACTCTC 61.252 60.000 0.00 0.00 0.00 3.20
144 145 1.228894 TTCTCCCTGGCACGACTCT 60.229 57.895 0.00 0.00 0.00 3.24
145 146 1.216710 CTTCTCCCTGGCACGACTC 59.783 63.158 0.00 0.00 0.00 3.36
146 147 2.948720 GCTTCTCCCTGGCACGACT 61.949 63.158 0.00 0.00 0.00 4.18
147 148 2.435059 GCTTCTCCCTGGCACGAC 60.435 66.667 0.00 0.00 0.00 4.34
148 149 3.706373 GGCTTCTCCCTGGCACGA 61.706 66.667 0.00 0.00 0.00 4.35
176 177 4.404098 AAAGCCCGGGTAGTGCCG 62.404 66.667 24.63 0.00 38.44 5.69
177 178 2.750237 CAAAGCCCGGGTAGTGCC 60.750 66.667 24.63 3.42 0.00 5.01
178 179 3.440415 GCAAAGCCCGGGTAGTGC 61.440 66.667 24.63 23.58 0.00 4.40
179 180 2.750237 GGCAAAGCCCGGGTAGTG 60.750 66.667 24.63 17.95 44.06 2.74
216 217 2.840102 ATTCCCTCCTCCTCGCCG 60.840 66.667 0.00 0.00 0.00 6.46
217 218 2.812619 CCATTCCCTCCTCCTCGCC 61.813 68.421 0.00 0.00 0.00 5.54
218 219 2.066999 ACCATTCCCTCCTCCTCGC 61.067 63.158 0.00 0.00 0.00 5.03
219 220 1.690219 CCACCATTCCCTCCTCCTCG 61.690 65.000 0.00 0.00 0.00 4.63
220 221 0.326618 TCCACCATTCCCTCCTCCTC 60.327 60.000 0.00 0.00 0.00 3.71
221 222 0.327000 CTCCACCATTCCCTCCTCCT 60.327 60.000 0.00 0.00 0.00 3.69
222 223 1.348775 CCTCCACCATTCCCTCCTCC 61.349 65.000 0.00 0.00 0.00 4.30
223 224 0.326618 TCCTCCACCATTCCCTCCTC 60.327 60.000 0.00 0.00 0.00 3.71
224 225 0.327000 CTCCTCCACCATTCCCTCCT 60.327 60.000 0.00 0.00 0.00 3.69
225 226 1.348775 CCTCCTCCACCATTCCCTCC 61.349 65.000 0.00 0.00 0.00 4.30
226 227 1.348775 CCCTCCTCCACCATTCCCTC 61.349 65.000 0.00 0.00 0.00 4.30
227 228 1.308216 CCCTCCTCCACCATTCCCT 60.308 63.158 0.00 0.00 0.00 4.20
228 229 3.061905 GCCCTCCTCCACCATTCCC 62.062 68.421 0.00 0.00 0.00 3.97
229 230 2.597903 GCCCTCCTCCACCATTCC 59.402 66.667 0.00 0.00 0.00 3.01
230 231 2.597903 GGCCCTCCTCCACCATTC 59.402 66.667 0.00 0.00 0.00 2.67
231 232 3.411517 CGGCCCTCCTCCACCATT 61.412 66.667 0.00 0.00 0.00 3.16
256 257 3.162154 CGGAGAACCCTAGCCCCC 61.162 72.222 0.00 0.00 0.00 5.40
257 258 2.365237 ACGGAGAACCCTAGCCCC 60.365 66.667 0.00 0.00 0.00 5.80
258 259 1.957765 GACACGGAGAACCCTAGCCC 61.958 65.000 0.00 0.00 0.00 5.19
259 260 1.516423 GACACGGAGAACCCTAGCC 59.484 63.158 0.00 0.00 0.00 3.93
260 261 1.139095 CGACACGGAGAACCCTAGC 59.861 63.158 0.00 0.00 0.00 3.42
261 262 1.139095 GCGACACGGAGAACCCTAG 59.861 63.158 0.00 0.00 0.00 3.02
262 263 0.896940 AAGCGACACGGAGAACCCTA 60.897 55.000 0.00 0.00 0.00 3.53
263 264 2.156051 GAAGCGACACGGAGAACCCT 62.156 60.000 0.00 0.00 0.00 4.34
264 265 1.737008 GAAGCGACACGGAGAACCC 60.737 63.158 0.00 0.00 0.00 4.11
265 266 2.087009 CGAAGCGACACGGAGAACC 61.087 63.158 0.00 0.00 0.00 3.62
266 267 3.449042 CGAAGCGACACGGAGAAC 58.551 61.111 0.00 0.00 0.00 3.01
272 273 2.202492 CCTCTCCGAAGCGACACG 60.202 66.667 0.00 0.00 0.00 4.49
273 274 2.182030 CCCTCTCCGAAGCGACAC 59.818 66.667 0.00 0.00 0.00 3.67
274 275 2.035155 TCCCTCTCCGAAGCGACA 59.965 61.111 0.00 0.00 0.00 4.35
275 276 1.596895 AAGTCCCTCTCCGAAGCGAC 61.597 60.000 0.00 0.00 0.00 5.19
276 277 1.304217 AAGTCCCTCTCCGAAGCGA 60.304 57.895 0.00 0.00 0.00 4.93
277 278 1.153745 CAAGTCCCTCTCCGAAGCG 60.154 63.158 0.00 0.00 0.00 4.68
278 279 1.219393 CCAAGTCCCTCTCCGAAGC 59.781 63.158 0.00 0.00 0.00 3.86
279 280 1.617947 CCCCAAGTCCCTCTCCGAAG 61.618 65.000 0.00 0.00 0.00 3.79
280 281 1.612442 CCCCAAGTCCCTCTCCGAA 60.612 63.158 0.00 0.00 0.00 4.30
281 282 2.038975 CCCCAAGTCCCTCTCCGA 59.961 66.667 0.00 0.00 0.00 4.55
282 283 3.083997 CCCCCAAGTCCCTCTCCG 61.084 72.222 0.00 0.00 0.00 4.63
283 284 1.996187 GTCCCCCAAGTCCCTCTCC 60.996 68.421 0.00 0.00 0.00 3.71
284 285 2.359967 CGTCCCCCAAGTCCCTCTC 61.360 68.421 0.00 0.00 0.00 3.20
285 286 2.284699 CGTCCCCCAAGTCCCTCT 60.285 66.667 0.00 0.00 0.00 3.69
286 287 3.400054 CCGTCCCCCAAGTCCCTC 61.400 72.222 0.00 0.00 0.00 4.30
289 290 4.029809 CACCCGTCCCCCAAGTCC 62.030 72.222 0.00 0.00 0.00 3.85
290 291 4.029809 CCACCCGTCCCCCAAGTC 62.030 72.222 0.00 0.00 0.00 3.01
297 298 4.817909 AGGATCCCCACCCGTCCC 62.818 72.222 8.55 0.00 33.88 4.46
298 299 3.162154 GAGGATCCCCACCCGTCC 61.162 72.222 8.55 0.00 33.88 4.79
317 318 3.305398 TTCAAGCTTTCGAGACCTCTC 57.695 47.619 0.00 0.00 39.55 3.20
318 319 3.971245 ATTCAAGCTTTCGAGACCTCT 57.029 42.857 0.00 0.00 0.00 3.69
319 320 5.007136 CCAATATTCAAGCTTTCGAGACCTC 59.993 44.000 0.00 0.00 0.00 3.85
320 321 4.878397 CCAATATTCAAGCTTTCGAGACCT 59.122 41.667 0.00 0.00 0.00 3.85
321 322 4.035675 CCCAATATTCAAGCTTTCGAGACC 59.964 45.833 0.00 0.00 0.00 3.85
322 323 4.876107 TCCCAATATTCAAGCTTTCGAGAC 59.124 41.667 0.00 0.00 0.00 3.36
323 324 5.097742 TCCCAATATTCAAGCTTTCGAGA 57.902 39.130 0.00 0.00 0.00 4.04
324 325 5.007136 GTCTCCCAATATTCAAGCTTTCGAG 59.993 44.000 0.00 0.00 0.00 4.04
325 326 4.876107 GTCTCCCAATATTCAAGCTTTCGA 59.124 41.667 0.00 0.00 0.00 3.71
326 327 4.635765 TGTCTCCCAATATTCAAGCTTTCG 59.364 41.667 0.00 0.00 0.00 3.46
327 328 5.449725 GCTGTCTCCCAATATTCAAGCTTTC 60.450 44.000 0.00 0.00 0.00 2.62
328 329 4.400567 GCTGTCTCCCAATATTCAAGCTTT 59.599 41.667 0.00 0.00 0.00 3.51
329 330 3.950395 GCTGTCTCCCAATATTCAAGCTT 59.050 43.478 0.00 0.00 0.00 3.74
330 331 3.201708 AGCTGTCTCCCAATATTCAAGCT 59.798 43.478 0.00 0.00 0.00 3.74
331 332 3.549794 AGCTGTCTCCCAATATTCAAGC 58.450 45.455 0.00 0.00 0.00 4.01
332 333 5.235186 CGTAAGCTGTCTCCCAATATTCAAG 59.765 44.000 0.00 0.00 0.00 3.02
333 334 5.116180 CGTAAGCTGTCTCCCAATATTCAA 58.884 41.667 0.00 0.00 0.00 2.69
334 335 4.161565 ACGTAAGCTGTCTCCCAATATTCA 59.838 41.667 0.00 0.00 45.62 2.57
335 336 4.694339 ACGTAAGCTGTCTCCCAATATTC 58.306 43.478 0.00 0.00 45.62 1.75
336 337 4.755266 ACGTAAGCTGTCTCCCAATATT 57.245 40.909 0.00 0.00 45.62 1.28
337 338 4.755266 AACGTAAGCTGTCTCCCAATAT 57.245 40.909 0.00 0.00 45.62 1.28
338 339 4.546829 AAACGTAAGCTGTCTCCCAATA 57.453 40.909 0.00 0.00 45.62 1.90
339 340 3.418684 AAACGTAAGCTGTCTCCCAAT 57.581 42.857 0.00 0.00 45.62 3.16
340 341 2.922740 AAACGTAAGCTGTCTCCCAA 57.077 45.000 0.00 0.00 45.62 4.12
341 342 2.922740 AAAACGTAAGCTGTCTCCCA 57.077 45.000 0.00 0.00 45.62 4.37
358 359 5.564048 AACGGCCGCTTGTATATTAAAAA 57.436 34.783 28.58 0.00 0.00 1.94
360 361 4.260294 CGAAACGGCCGCTTGTATATTAAA 60.260 41.667 28.58 0.00 0.00 1.52
361 362 3.245754 CGAAACGGCCGCTTGTATATTAA 59.754 43.478 28.58 0.00 0.00 1.40
362 363 2.796031 CGAAACGGCCGCTTGTATATTA 59.204 45.455 28.58 0.00 0.00 0.98
363 364 1.595794 CGAAACGGCCGCTTGTATATT 59.404 47.619 28.58 6.25 0.00 1.28
366 367 3.481661 CGAAACGGCCGCTTGTAT 58.518 55.556 28.58 0.00 0.00 2.29
380 381 1.544246 TGTGAAGAATCTCTCGGCGAA 59.456 47.619 12.13 0.00 0.00 4.70
406 407 9.063615 ACGTTTCTTTGTCTTGTTCCTATAATT 57.936 29.630 0.00 0.00 0.00 1.40
407 408 8.504005 CACGTTTCTTTGTCTTGTTCCTATAAT 58.496 33.333 0.00 0.00 0.00 1.28
408 409 7.496591 ACACGTTTCTTTGTCTTGTTCCTATAA 59.503 33.333 0.00 0.00 0.00 0.98
410 411 5.820947 ACACGTTTCTTTGTCTTGTTCCTAT 59.179 36.000 0.00 0.00 0.00 2.57
414 421 6.711579 TCATACACGTTTCTTTGTCTTGTTC 58.288 36.000 0.00 0.00 0.00 3.18
436 443 2.114616 GAATCTCTCCTGCCTCCTTCA 58.885 52.381 0.00 0.00 0.00 3.02
484 491 0.464373 GATGAGGCGGCTTTCCATGA 60.464 55.000 14.76 0.00 0.00 3.07
511 526 1.707427 AGGTGGAGCTGTTGGAGATTT 59.293 47.619 0.00 0.00 0.00 2.17
515 530 0.321122 GACAGGTGGAGCTGTTGGAG 60.321 60.000 12.50 0.00 33.50 3.86
536 551 0.921256 AATCTTGGAGTGGGGGAGGG 60.921 60.000 0.00 0.00 0.00 4.30
541 563 2.755103 GTGCTTTAATCTTGGAGTGGGG 59.245 50.000 0.00 0.00 0.00 4.96
566 588 1.868498 CTTGCTTGCATTGGTTTGTGG 59.132 47.619 0.00 0.00 0.00 4.17
569 591 4.121317 TCTTTCTTGCTTGCATTGGTTTG 58.879 39.130 0.00 0.00 0.00 2.93
570 592 4.405116 TCTTTCTTGCTTGCATTGGTTT 57.595 36.364 0.00 0.00 0.00 3.27
691 719 7.175347 AGAACTATTGCAGTCTGTGAGAATA 57.825 36.000 0.93 0.00 36.04 1.75
697 725 6.857956 AGTAGTAGAACTATTGCAGTCTGTG 58.142 40.000 0.93 0.00 36.04 3.66
757 812 1.065564 AGAAGCAAGAGATGGAGTGGC 60.066 52.381 0.00 0.00 0.00 5.01
805 860 3.017581 AGGCCGGGGCTTTGATCT 61.018 61.111 18.71 0.00 41.60 2.75
863 931 1.492133 CCAAGCAAGGTCAGGAGGGA 61.492 60.000 0.00 0.00 0.00 4.20
864 932 1.001641 CCAAGCAAGGTCAGGAGGG 60.002 63.158 0.00 0.00 0.00 4.30
865 933 1.676967 GCCAAGCAAGGTCAGGAGG 60.677 63.158 0.00 0.00 0.00 4.30
866 934 0.323178 ATGCCAAGCAAGGTCAGGAG 60.323 55.000 0.00 0.00 43.62 3.69
867 935 0.322816 GATGCCAAGCAAGGTCAGGA 60.323 55.000 0.00 0.00 43.62 3.86
951 1019 3.780267 CTAGCGTACGTCGGCCGAC 62.780 68.421 41.75 41.75 40.70 4.79
998 1066 1.636340 GCGAAATGGTCCGTCATCG 59.364 57.895 12.62 12.62 0.00 3.84
1003 1071 2.515996 ATCACCGCGAAATGGTCCGT 62.516 55.000 8.23 0.00 37.72 4.69
1204 1273 4.765970 AGGGGCCTCCATGCAGGA 62.766 66.667 6.94 2.01 46.75 3.86
1240 1309 3.314080 TGCCAAGACGTTTTTACCTTCAG 59.686 43.478 0.00 0.00 0.00 3.02
1270 1339 4.154737 AGACAAGAGCAATGTACGTACGTA 59.845 41.667 23.60 23.60 0.00 3.57
1271 1340 3.057736 AGACAAGAGCAATGTACGTACGT 60.058 43.478 25.98 25.98 0.00 3.57
1272 1341 3.300853 CAGACAAGAGCAATGTACGTACG 59.699 47.826 20.18 15.01 0.00 3.67
1273 1342 4.482386 TCAGACAAGAGCAATGTACGTAC 58.518 43.478 18.90 18.90 0.00 3.67
1274 1343 4.776795 TCAGACAAGAGCAATGTACGTA 57.223 40.909 0.00 0.00 0.00 3.57
1275 1344 3.660501 TCAGACAAGAGCAATGTACGT 57.339 42.857 0.00 0.00 0.00 3.57
1317 1386 3.433615 GTGAGCATACTGAAAGACACACC 59.566 47.826 0.00 0.00 37.43 4.16
1322 1391 2.094182 TCCGGTGAGCATACTGAAAGAC 60.094 50.000 0.00 0.00 37.43 3.01
1506 1596 3.980646 TGGTGTGAATTGCTGTGTTAC 57.019 42.857 0.00 0.00 0.00 2.50
1510 1626 3.441496 AGTTTGGTGTGAATTGCTGTG 57.559 42.857 0.00 0.00 0.00 3.66
1595 1713 3.713858 TGTTTGACAGGTGAAGCATTG 57.286 42.857 0.00 0.00 0.00 2.82
1671 1789 0.749454 GGGCCTGTGCTTGGATGTAG 60.749 60.000 0.84 0.00 37.74 2.74
1740 1858 3.255642 GGCAACAGATTACAGCTTTTGGA 59.744 43.478 0.00 0.00 0.00 3.53
1817 1936 3.634568 TTTCATTGCAAACCGTCGAAT 57.365 38.095 1.71 0.00 0.00 3.34
1826 1945 6.765036 TCAGGCTGTTAATTTTTCATTGCAAA 59.235 30.769 15.27 0.00 0.00 3.68
1829 1948 6.783892 TTCAGGCTGTTAATTTTTCATTGC 57.216 33.333 15.27 0.00 0.00 3.56
1830 1949 8.140677 TGTTTCAGGCTGTTAATTTTTCATTG 57.859 30.769 15.27 0.00 0.00 2.82
1831 1950 8.907222 ATGTTTCAGGCTGTTAATTTTTCATT 57.093 26.923 15.27 0.00 0.00 2.57
1832 1951 8.907222 AATGTTTCAGGCTGTTAATTTTTCAT 57.093 26.923 15.27 6.82 0.00 2.57
1833 1952 8.203485 AGAATGTTTCAGGCTGTTAATTTTTCA 58.797 29.630 15.27 4.93 0.00 2.69
1834 1953 8.593492 AGAATGTTTCAGGCTGTTAATTTTTC 57.407 30.769 15.27 12.77 0.00 2.29
1858 1977 0.170561 GCATCAGCTGAGGTTGCAAG 59.829 55.000 27.80 10.51 37.91 4.01
1921 2040 1.288127 GACGGTGTAGACGCCTTGT 59.712 57.895 10.40 1.96 44.11 3.16
1986 2105 2.322658 TCTGGTCTAGGGAAAACGTGT 58.677 47.619 0.00 0.00 0.00 4.49
1995 2114 6.784473 TCCATATATATGCATCTGGTCTAGGG 59.216 42.308 16.08 0.00 32.40 3.53
2003 2125 5.530171 GCTGGGTTCCATATATATGCATCTG 59.470 44.000 16.08 3.84 30.82 2.90
2013 2135 5.830991 GGTTACATTTGCTGGGTTCCATATA 59.169 40.000 0.00 0.00 30.82 0.86
2040 2162 6.072286 TCCACAAAACAAAATTTTGCACACAT 60.072 30.769 26.94 7.17 41.66 3.21
2193 2315 7.014615 AGCCAGAAACTTCATAAACATTTCAGT 59.985 33.333 0.00 0.00 32.78 3.41
2195 2317 7.014134 TCAGCCAGAAACTTCATAAACATTTCA 59.986 33.333 0.00 0.00 32.78 2.69
2216 2338 1.200020 CGTTCCATTTCCACTTCAGCC 59.800 52.381 0.00 0.00 0.00 4.85
2223 2345 1.336702 TGCATTGCGTTCCATTTCCAC 60.337 47.619 3.84 0.00 0.00 4.02
2265 2393 2.747855 CCTGCGGCTTCTGGTTCC 60.748 66.667 0.00 0.00 0.00 3.62
2355 2483 3.745480 CGCATCCAGGTCCATATCTGTTT 60.745 47.826 0.00 0.00 31.30 2.83
2464 2625 6.967767 CGATATACACAGGTATTCCGAAGATC 59.032 42.308 0.00 0.00 40.61 2.75
2471 2632 8.882415 TTTCTTTCGATATACACAGGTATTCC 57.118 34.615 0.00 0.00 40.61 3.01
2506 2667 4.099419 TGAAGCGAGTGTCCATGTATGTAT 59.901 41.667 0.00 0.00 0.00 2.29
2512 2673 0.392706 TGTGAAGCGAGTGTCCATGT 59.607 50.000 0.00 0.00 0.00 3.21
2530 2691 4.272018 GGCACACTACATCTTCATAGCTTG 59.728 45.833 0.00 0.00 0.00 4.01
2535 2696 4.100035 CAGGAGGCACACTACATCTTCATA 59.900 45.833 0.00 0.00 29.75 2.15
2545 2706 2.496070 GTCATGTACAGGAGGCACACTA 59.504 50.000 11.08 0.00 0.00 2.74
2555 2716 3.854666 CCTGTCTCTTGTCATGTACAGG 58.145 50.000 19.08 19.08 45.64 4.00
2563 2724 2.552743 CGTGTACTCCTGTCTCTTGTCA 59.447 50.000 0.00 0.00 0.00 3.58
2567 2728 3.687125 TCATCGTGTACTCCTGTCTCTT 58.313 45.455 0.00 0.00 0.00 2.85
2585 2746 9.851686 TGCATAAGTCTAAAATTCCTACATCAT 57.148 29.630 0.00 0.00 0.00 2.45
2586 2747 9.679661 TTGCATAAGTCTAAAATTCCTACATCA 57.320 29.630 0.00 0.00 0.00 3.07
2607 2771 3.956233 GTGCATCGAATGTACATTGCAT 58.044 40.909 27.05 16.10 44.02 3.96
2627 2791 6.002704 AGAGTGATTTCTGCATTTTCTCTGT 58.997 36.000 0.00 0.00 0.00 3.41
2642 2806 3.895232 ATGTAGGCGACAGAGTGATTT 57.105 42.857 6.59 0.00 42.79 2.17
2659 2823 6.593382 AGCAACAATAACAACAACAACAATGT 59.407 30.769 0.00 0.00 43.14 2.71
2662 2826 5.287274 CGAGCAACAATAACAACAACAACAA 59.713 36.000 0.00 0.00 0.00 2.83
2663 2827 4.795795 CGAGCAACAATAACAACAACAACA 59.204 37.500 0.00 0.00 0.00 3.33
2664 2828 5.031578 TCGAGCAACAATAACAACAACAAC 58.968 37.500 0.00 0.00 0.00 3.32
2708 2872 5.104527 AGGCTGATATACCTTACACAAGCAA 60.105 40.000 0.00 0.00 29.74 3.91
2758 2922 5.643379 ATGGTATCGAAATTTGTGCTGTT 57.357 34.783 0.00 0.00 0.00 3.16
2829 2993 5.563867 GCCATTTGAACCGTGAATTGAACTA 60.564 40.000 0.00 0.00 0.00 2.24
2844 3011 4.933505 TGAACTGTTGATGCCATTTGAA 57.066 36.364 0.00 0.00 0.00 2.69
2855 3023 4.080413 TGCTGGATATGGATGAACTGTTGA 60.080 41.667 0.00 0.00 0.00 3.18
2871 3039 4.232188 AGTTGTGATCTGATTGCTGGAT 57.768 40.909 0.00 0.00 0.00 3.41
2987 3171 5.412594 GCTCACAGATGAAAATCCAGTGTTA 59.587 40.000 0.00 0.00 33.30 2.41
2992 3176 5.426504 AGTAGCTCACAGATGAAAATCCAG 58.573 41.667 0.00 0.00 33.30 3.86
3001 3185 5.330455 TCTTGGTAAGTAGCTCACAGATG 57.670 43.478 0.00 0.00 0.00 2.90
3002 3186 6.552445 AATCTTGGTAAGTAGCTCACAGAT 57.448 37.500 0.00 0.00 0.00 2.90
3188 3378 6.006449 GGTTGGTAGGATATCATTCATTGCT 58.994 40.000 4.83 0.00 27.62 3.91
3193 3383 9.573166 CATTTTAGGTTGGTAGGATATCATTCA 57.427 33.333 4.83 0.00 27.62 2.57
3323 3513 3.797507 CTGCCCTGGGTGTTGCAGT 62.798 63.158 15.56 0.00 44.69 4.40
3349 3539 1.376424 ACATGCTGCAAGAGTCCCG 60.376 57.895 12.28 0.00 34.07 5.14
3387 3577 1.745489 CAAGTAGGGGCGGCACTTC 60.745 63.158 22.71 15.79 30.20 3.01
3407 3597 2.045047 TGGAGTCTCTTCAAGGGAGGAT 59.955 50.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.