Multiple sequence alignment - TraesCS2D01G371200

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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 TraesCS2D01G371200 chr2D 100.000 4603 0 0 1 4603 475088870 475093472 0.000000e+00 8501
1 TraesCS2D01G371200 chr2A 92.304 4002 177 63 1 3973 617644875 617648774 0.000000e+00 5563
2 TraesCS2D01G371200 chr2A 92.025 790 38 5 1283 2069 595476440 595477207 0.000000e+00 1086
3 TraesCS2D01G371200 chr2A 93.902 410 21 3 4197 4603 617654758 617655166 2.350000e-172 616
4 TraesCS2D01G371200 chr2A 90.805 87 5 2 4085 4169 654916488 654916403 3.760000e-21 113
5 TraesCS2D01G371200 chr2B 94.230 2097 81 14 1886 3973 556199650 556201715 0.000000e+00 3166
6 TraesCS2D01G371200 chr2B 90.881 1645 91 30 250 1858 556197716 556199337 0.000000e+00 2152
7 TraesCS2D01G371200 chr2B 92.512 414 23 3 4197 4603 556202021 556202433 1.850000e-163 586
8 TraesCS2D01G371200 chr2B 98.387 62 1 0 4024 4085 556201841 556201902 4.870000e-20 110
9 TraesCS2D01G371200 chr1B 92.355 811 42 5 1282 2089 85713216 85712423 0.000000e+00 1136
10 TraesCS2D01G371200 chr1B 92.355 811 43 4 1282 2089 124074214 124073420 0.000000e+00 1136
11 TraesCS2D01G371200 chr1B 91.089 101 6 3 4070 4169 453517107 453517009 2.890000e-27 134
12 TraesCS2D01G371200 chr1B 95.000 80 2 1 4085 4162 443529774 443529853 1.740000e-24 124
13 TraesCS2D01G371200 chr4A 92.232 811 44 4 1282 2089 738693187 738693981 0.000000e+00 1131
14 TraesCS2D01G371200 chr4A 91.111 90 5 2 4075 4163 88424478 88424565 8.090000e-23 119
15 TraesCS2D01G371200 chr4B 91.985 811 48 9 1282 2089 564752350 564751554 0.000000e+00 1122
16 TraesCS2D01G371200 chr4B 92.029 276 6 3 1814 2089 672587030 672586771 1.560000e-99 374
17 TraesCS2D01G371200 chr7A 92.025 790 44 4 1283 2069 289953154 289953927 0.000000e+00 1092
18 TraesCS2D01G371200 chr7A 90.805 87 5 2 4087 4173 704270009 704269926 3.760000e-21 113
19 TraesCS2D01G371200 chr5A 92.015 789 44 4 1283 2068 671854615 671855387 0.000000e+00 1090
20 TraesCS2D01G371200 chr7D 93.421 608 24 3 1482 2089 543343003 543342412 0.000000e+00 887
21 TraesCS2D01G371200 chr3D 92.928 608 27 3 1482 2089 98585213 98584622 0.000000e+00 870
22 TraesCS2D01G371200 chr3B 92.754 276 5 2 1814 2089 777670554 777670814 7.220000e-103 385
23 TraesCS2D01G371200 chr3B 89.362 94 4 3 4077 4164 256200749 256200656 3.760000e-21 113
24 TraesCS2D01G371200 chr7B 92.029 276 6 3 1814 2089 113941410 113941151 1.560000e-99 374
25 TraesCS2D01G371200 chr7B 93.902 82 3 1 4083 4162 566635045 566634964 6.250000e-24 122
26 TraesCS2D01G371200 chr4D 94.872 78 2 1 4085 4162 21876059 21876134 2.250000e-23 121
27 TraesCS2D01G371200 chr1A 93.902 82 2 1 4084 4162 238681287 238681368 2.250000e-23 121


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 TraesCS2D01G371200 chr2D 475088870 475093472 4602 False 8501.0 8501 100.0000 1 4603 1 chr2D.!!$F1 4602
1 TraesCS2D01G371200 chr2A 617644875 617648774 3899 False 5563.0 5563 92.3040 1 3973 1 chr2A.!!$F2 3972
2 TraesCS2D01G371200 chr2A 595476440 595477207 767 False 1086.0 1086 92.0250 1283 2069 1 chr2A.!!$F1 786
3 TraesCS2D01G371200 chr2B 556197716 556202433 4717 False 1503.5 3166 94.0025 250 4603 4 chr2B.!!$F1 4353
4 TraesCS2D01G371200 chr1B 85712423 85713216 793 True 1136.0 1136 92.3550 1282 2089 1 chr1B.!!$R1 807
5 TraesCS2D01G371200 chr1B 124073420 124074214 794 True 1136.0 1136 92.3550 1282 2089 1 chr1B.!!$R2 807
6 TraesCS2D01G371200 chr4A 738693187 738693981 794 False 1131.0 1131 92.2320 1282 2089 1 chr4A.!!$F2 807
7 TraesCS2D01G371200 chr4B 564751554 564752350 796 True 1122.0 1122 91.9850 1282 2089 1 chr4B.!!$R1 807
8 TraesCS2D01G371200 chr7A 289953154 289953927 773 False 1092.0 1092 92.0250 1283 2069 1 chr7A.!!$F1 786
9 TraesCS2D01G371200 chr5A 671854615 671855387 772 False 1090.0 1090 92.0150 1283 2068 1 chr5A.!!$F1 785
10 TraesCS2D01G371200 chr7D 543342412 543343003 591 True 887.0 887 93.4210 1482 2089 1 chr7D.!!$R1 607
11 TraesCS2D01G371200 chr3D 98584622 98585213 591 True 870.0 870 92.9280 1482 2089 1 chr3D.!!$R1 607

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
275 284 0.029834 GTCTGCACTGCACAACCAAG 59.970 55.000 0.00 0.0 33.79 3.61 F
427 437 0.179086 TATGCTGCCGCGAATCAAGA 60.179 50.000 8.23 0.0 39.65 3.02 F
1243 1282 0.254178 GGGCAGAAGCAGAAGATGGA 59.746 55.000 0.00 0.0 44.61 3.41 F
1361 1400 0.464735 TTTGGTGGTTCTGTCGTGGG 60.465 55.000 0.00 0.0 0.00 4.61 F
1805 1850 2.033755 CACTCTGCTGCTGTGCCTC 61.034 63.158 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1839 0.322277 ACATGAAGGAGGCACAGCAG 60.322 55.0 0.0 0.0 0.00 4.24 R
2083 2428 0.733150 GCTCATAGGTCCCAAAACGC 59.267 55.0 0.0 0.0 0.00 4.84 R
3038 3392 0.036010 ACTGCCAAGTAAGCATCGCT 60.036 50.0 0.0 0.0 42.56 4.93 R
3278 3633 5.066634 TGAACGACTTTTGGCAGTATCAAAA 59.933 36.0 0.0 0.0 40.46 2.44 R
3794 4149 0.820871 AGCAACAAAACCAAAGGCGA 59.179 45.0 0.0 0.0 0.00 5.54 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
23 24 5.782047 CATACAAATTTGAAAGAGCCCACA 58.218 37.500 24.64 0.00 0.00 4.17
28 29 4.590850 ATTTGAAAGAGCCCACAAACTC 57.409 40.909 0.00 0.00 35.58 3.01
31 32 1.268079 GAAAGAGCCCACAAACTCTGC 59.732 52.381 0.00 0.00 42.41 4.26
32 33 0.183492 AAGAGCCCACAAACTCTGCA 59.817 50.000 0.00 0.00 42.41 4.41
33 34 0.250640 AGAGCCCACAAACTCTGCAG 60.251 55.000 7.63 7.63 41.67 4.41
43 44 0.610232 AACTCTGCAGACATTGGGGC 60.610 55.000 13.74 0.00 0.00 5.80
49 50 2.496871 CTGCAGACATTGGGGCATTTTA 59.503 45.455 8.42 0.00 35.45 1.52
57 61 5.714863 ACATTGGGGCATTTTATGGAGATA 58.285 37.500 0.00 0.00 0.00 1.98
59 63 7.477864 ACATTGGGGCATTTTATGGAGATATA 58.522 34.615 0.00 0.00 0.00 0.86
61 65 6.078456 TGGGGCATTTTATGGAGATATAGG 57.922 41.667 0.00 0.00 0.00 2.57
63 67 6.276806 TGGGGCATTTTATGGAGATATAGGAA 59.723 38.462 0.00 0.00 0.00 3.36
64 68 6.603599 GGGGCATTTTATGGAGATATAGGAAC 59.396 42.308 0.00 0.00 0.00 3.62
65 69 7.406104 GGGCATTTTATGGAGATATAGGAACT 58.594 38.462 0.00 0.00 46.37 3.01
83 87 4.392138 GGAACTGAATCTAGTCGTTTTGGG 59.608 45.833 0.00 0.00 0.00 4.12
84 88 4.884668 ACTGAATCTAGTCGTTTTGGGA 57.115 40.909 0.00 0.00 0.00 4.37
99 103 5.357032 CGTTTTGGGAAAGATATTAGCAGGT 59.643 40.000 0.00 0.00 0.00 4.00
101 105 7.066525 CGTTTTGGGAAAGATATTAGCAGGTTA 59.933 37.037 0.00 0.00 0.00 2.85
102 106 8.914011 GTTTTGGGAAAGATATTAGCAGGTTAT 58.086 33.333 0.00 0.00 0.00 1.89
126 130 1.406205 GCTTGGTAGCTCCTCAGAACC 60.406 57.143 0.00 0.00 44.27 3.62
127 131 1.902508 CTTGGTAGCTCCTCAGAACCA 59.097 52.381 0.00 0.00 36.11 3.67
131 135 0.710588 TAGCTCCTCAGAACCAGGGA 59.289 55.000 0.00 0.00 0.00 4.20
134 138 1.283321 GCTCCTCAGAACCAGGGAATT 59.717 52.381 0.00 0.00 0.00 2.17
138 142 3.716872 TCCTCAGAACCAGGGAATTATCC 59.283 47.826 0.00 0.00 45.77 2.59
156 160 4.957684 ATCCACTAAGCACATACCCTAC 57.042 45.455 0.00 0.00 0.00 3.18
166 170 3.433031 GCACATACCCTACATGGCACTAA 60.433 47.826 0.00 0.00 0.00 2.24
171 175 4.316025 ACCCTACATGGCACTAACATTT 57.684 40.909 0.00 0.00 0.00 2.32
178 182 6.500684 ACATGGCACTAACATTTAAGACTG 57.499 37.500 0.00 0.00 0.00 3.51
183 187 4.201724 GCACTAACATTTAAGACTGCCTCG 60.202 45.833 0.00 0.00 0.00 4.63
216 220 3.627732 ACGCCTAGATGTTCTACGATG 57.372 47.619 0.00 0.00 0.00 3.84
218 222 3.003482 ACGCCTAGATGTTCTACGATGTC 59.997 47.826 0.00 0.00 0.00 3.06
219 223 3.003378 CGCCTAGATGTTCTACGATGTCA 59.997 47.826 0.00 0.00 0.00 3.58
220 224 4.541779 GCCTAGATGTTCTACGATGTCAG 58.458 47.826 0.00 0.00 0.00 3.51
223 227 4.909696 AGATGTTCTACGATGTCAGAGG 57.090 45.455 0.00 0.00 0.00 3.69
230 234 0.603569 ACGATGTCAGAGGTCACCAC 59.396 55.000 0.00 0.00 0.00 4.16
231 235 0.891373 CGATGTCAGAGGTCACCACT 59.109 55.000 0.00 0.00 0.00 4.00
232 236 1.135257 CGATGTCAGAGGTCACCACTC 60.135 57.143 0.00 0.00 35.20 3.51
235 239 0.318762 GTCAGAGGTCACCACTCACC 59.681 60.000 0.00 0.00 37.43 4.02
236 240 0.105709 TCAGAGGTCACCACTCACCA 60.106 55.000 0.00 0.00 37.43 4.17
237 241 0.319728 CAGAGGTCACCACTCACCAG 59.680 60.000 0.00 0.00 37.43 4.00
238 242 0.105453 AGAGGTCACCACTCACCAGT 60.105 55.000 0.00 0.00 37.43 4.00
239 243 0.759346 GAGGTCACCACTCACCAGTT 59.241 55.000 0.00 0.00 34.80 3.16
240 244 1.141053 GAGGTCACCACTCACCAGTTT 59.859 52.381 0.00 0.00 34.80 2.66
241 245 2.367567 GAGGTCACCACTCACCAGTTTA 59.632 50.000 0.00 0.00 34.80 2.01
242 246 2.104281 AGGTCACCACTCACCAGTTTAC 59.896 50.000 0.00 0.00 34.80 2.01
243 247 2.490991 GTCACCACTCACCAGTTTACC 58.509 52.381 0.00 0.00 0.00 2.85
244 248 2.120312 TCACCACTCACCAGTTTACCA 58.880 47.619 0.00 0.00 0.00 3.25
245 249 2.708861 TCACCACTCACCAGTTTACCAT 59.291 45.455 0.00 0.00 0.00 3.55
246 250 3.074412 CACCACTCACCAGTTTACCATC 58.926 50.000 0.00 0.00 0.00 3.51
247 251 2.039879 ACCACTCACCAGTTTACCATCC 59.960 50.000 0.00 0.00 0.00 3.51
261 265 1.279271 ACCATCCAGTACAAGGTCTGC 59.721 52.381 0.00 0.00 0.00 4.26
268 272 0.868406 GTACAAGGTCTGCACTGCAC 59.132 55.000 0.00 0.00 33.79 4.57
274 283 1.383456 GGTCTGCACTGCACAACCAA 61.383 55.000 19.50 0.00 38.44 3.67
275 284 0.029834 GTCTGCACTGCACAACCAAG 59.970 55.000 0.00 0.00 33.79 3.61
278 287 1.002468 CTGCACTGCACAACCAAGTAC 60.002 52.381 0.00 0.00 33.79 2.73
293 302 4.808414 CAAGTACTGGAGAATCACAGGA 57.192 45.455 0.00 0.00 37.61 3.86
310 319 1.978580 AGGAACAATCTCGTCCACCTT 59.021 47.619 0.00 0.00 0.00 3.50
314 323 4.758165 GGAACAATCTCGTCCACCTTAAAA 59.242 41.667 0.00 0.00 0.00 1.52
315 324 5.334646 GGAACAATCTCGTCCACCTTAAAAC 60.335 44.000 0.00 0.00 0.00 2.43
317 326 2.845363 TCTCGTCCACCTTAAAACCC 57.155 50.000 0.00 0.00 0.00 4.11
318 327 1.001181 TCTCGTCCACCTTAAAACCCG 59.999 52.381 0.00 0.00 0.00 5.28
319 328 0.603439 TCGTCCACCTTAAAACCCGC 60.603 55.000 0.00 0.00 0.00 6.13
321 330 1.320507 GTCCACCTTAAAACCCGCAA 58.679 50.000 0.00 0.00 0.00 4.85
322 331 1.001048 GTCCACCTTAAAACCCGCAAC 60.001 52.381 0.00 0.00 0.00 4.17
324 333 1.409427 CCACCTTAAAACCCGCAACAA 59.591 47.619 0.00 0.00 0.00 2.83
325 334 2.036604 CCACCTTAAAACCCGCAACAAT 59.963 45.455 0.00 0.00 0.00 2.71
326 335 3.493524 CCACCTTAAAACCCGCAACAATT 60.494 43.478 0.00 0.00 0.00 2.32
327 336 3.738791 CACCTTAAAACCCGCAACAATTC 59.261 43.478 0.00 0.00 0.00 2.17
328 337 2.983803 CCTTAAAACCCGCAACAATTCG 59.016 45.455 0.00 0.00 0.00 3.34
329 338 3.551250 CCTTAAAACCCGCAACAATTCGT 60.551 43.478 0.00 0.00 0.00 3.85
331 340 3.712091 AAAACCCGCAACAATTCGTAA 57.288 38.095 0.00 0.00 0.00 3.18
332 341 3.926821 AAACCCGCAACAATTCGTAAT 57.073 38.095 0.00 0.00 0.00 1.89
333 342 5.373981 AAAACCCGCAACAATTCGTAATA 57.626 34.783 0.00 0.00 0.00 0.98
334 343 4.345271 AACCCGCAACAATTCGTAATAC 57.655 40.909 0.00 0.00 0.00 1.89
335 344 3.602483 ACCCGCAACAATTCGTAATACT 58.398 40.909 0.00 0.00 0.00 2.12
336 345 4.757594 ACCCGCAACAATTCGTAATACTA 58.242 39.130 0.00 0.00 0.00 1.82
337 346 4.807304 ACCCGCAACAATTCGTAATACTAG 59.193 41.667 0.00 0.00 0.00 2.57
338 347 4.210537 CCCGCAACAATTCGTAATACTAGG 59.789 45.833 0.00 0.00 0.00 3.02
339 348 4.318546 CCGCAACAATTCGTAATACTAGGC 60.319 45.833 0.00 0.00 0.00 3.93
340 349 4.506654 CGCAACAATTCGTAATACTAGGCT 59.493 41.667 0.00 0.00 0.00 4.58
393 403 1.304052 TCCCCAAATCCCAGCAACG 60.304 57.895 0.00 0.00 0.00 4.10
421 431 0.319555 GACCTATATGCTGCCGCGAA 60.320 55.000 8.23 0.00 39.65 4.70
424 434 1.672737 CCTATATGCTGCCGCGAATCA 60.673 52.381 8.23 0.97 39.65 2.57
426 436 0.870393 ATATGCTGCCGCGAATCAAG 59.130 50.000 8.23 0.00 39.65 3.02
427 437 0.179086 TATGCTGCCGCGAATCAAGA 60.179 50.000 8.23 0.00 39.65 3.02
433 443 1.079503 GCCGCGAATCAAGAAGAACT 58.920 50.000 8.23 0.00 0.00 3.01
437 447 3.548268 CCGCGAATCAAGAAGAACTACTC 59.452 47.826 8.23 0.00 0.00 2.59
440 450 5.448768 CGCGAATCAAGAAGAACTACTCCTA 60.449 44.000 0.00 0.00 0.00 2.94
441 451 6.508777 GCGAATCAAGAAGAACTACTCCTAT 58.491 40.000 0.00 0.00 0.00 2.57
443 453 7.592164 GCGAATCAAGAAGAACTACTCCTATAC 59.408 40.741 0.00 0.00 0.00 1.47
444 454 7.799447 CGAATCAAGAAGAACTACTCCTATACG 59.201 40.741 0.00 0.00 0.00 3.06
643 653 0.613012 GGCTCTGTTCTTGGCCCATT 60.613 55.000 0.00 0.00 38.77 3.16
869 879 2.569657 ACGATTCGTGTGCGGCTA 59.430 55.556 11.56 0.00 39.18 3.93
870 880 1.516386 ACGATTCGTGTGCGGCTAG 60.516 57.895 11.56 0.00 39.18 3.42
935 945 1.351707 GCGTTCCAGTGTGTGTGTG 59.648 57.895 0.00 0.00 0.00 3.82
936 946 1.366111 GCGTTCCAGTGTGTGTGTGT 61.366 55.000 0.00 0.00 0.00 3.72
938 948 1.732941 GTTCCAGTGTGTGTGTGTCA 58.267 50.000 0.00 0.00 0.00 3.58
1243 1282 0.254178 GGGCAGAAGCAGAAGATGGA 59.746 55.000 0.00 0.00 44.61 3.41
1319 1358 1.239296 TGCTTGCCTGCTTGCTACTG 61.239 55.000 7.99 0.00 0.00 2.74
1360 1399 0.661020 GTTTGGTGGTTCTGTCGTGG 59.339 55.000 0.00 0.00 0.00 4.94
1361 1400 0.464735 TTTGGTGGTTCTGTCGTGGG 60.465 55.000 0.00 0.00 0.00 4.61
1640 1685 7.928167 CACTGTCTACATTAAGAGCATATCCAA 59.072 37.037 0.00 0.00 0.00 3.53
1789 1834 5.574443 GGCTTGCATAAAGATTTCACTTCAC 59.426 40.000 0.00 0.00 38.24 3.18
1794 1839 6.026513 GCATAAAGATTTCACTTCACTCTGC 58.973 40.000 0.00 0.00 0.00 4.26
1805 1850 2.033755 CACTCTGCTGCTGTGCCTC 61.034 63.158 0.00 0.00 0.00 4.70
1886 2036 6.069088 TGGTATCAAAGGGGATCATTGTACTT 60.069 38.462 0.00 0.00 0.00 2.24
1887 2037 6.833933 GGTATCAAAGGGGATCATTGTACTTT 59.166 38.462 0.00 0.00 0.00 2.66
1888 2038 7.342026 GGTATCAAAGGGGATCATTGTACTTTT 59.658 37.037 0.00 0.00 0.00 2.27
1889 2039 9.403583 GTATCAAAGGGGATCATTGTACTTTTA 57.596 33.333 0.00 0.00 0.00 1.52
1890 2040 8.893563 ATCAAAGGGGATCATTGTACTTTTAA 57.106 30.769 0.00 0.00 0.00 1.52
1891 2041 8.893563 TCAAAGGGGATCATTGTACTTTTAAT 57.106 30.769 0.00 0.00 0.00 1.40
1892 2042 9.983024 TCAAAGGGGATCATTGTACTTTTAATA 57.017 29.630 0.00 0.00 0.00 0.98
2083 2428 3.058160 CTGCCTGGTTTGGGAGCG 61.058 66.667 0.00 0.00 38.66 5.03
2211 2556 4.265073 CACCTTCTATTGGCAGTTTAGCT 58.735 43.478 0.00 0.00 34.17 3.32
2212 2557 5.428253 CACCTTCTATTGGCAGTTTAGCTA 58.572 41.667 0.00 0.00 34.17 3.32
2235 2580 5.072741 ACCATGAGCAAACTAGACATGTTT 58.927 37.500 0.00 0.00 37.29 2.83
2409 2762 3.352554 TTGCTTGTGTGTTATGTGCAG 57.647 42.857 0.00 0.00 0.00 4.41
2466 2820 7.090953 TCGACTGTTTGTTTTCCAATAGTTT 57.909 32.000 0.00 0.00 33.51 2.66
2727 3081 2.351726 GCTACGAACCCTGCTAATGTTG 59.648 50.000 0.00 0.00 0.00 3.33
2796 3150 4.346127 TCCCTGACATGAGAGTATGGAATG 59.654 45.833 0.00 0.00 32.32 2.67
2828 3182 2.445145 TCTGTTGTCCAATCTTTCCCCA 59.555 45.455 0.00 0.00 0.00 4.96
3038 3392 7.459795 TTCTTGTTGGCAATTCATACATACA 57.540 32.000 1.92 0.00 33.65 2.29
3154 3509 8.044060 ACAGTGTCATGATTGATTTTCGTTAT 57.956 30.769 0.00 0.00 33.56 1.89
3156 3511 9.345517 CAGTGTCATGATTGATTTTCGTTATTT 57.654 29.630 0.00 0.00 33.56 1.40
3474 3829 4.039004 CACCAGGAATGTGGATAGAGAGAG 59.961 50.000 0.00 0.00 40.44 3.20
3479 3834 4.261405 GGAATGTGGATAGAGAGAGTGACG 60.261 50.000 0.00 0.00 0.00 4.35
3485 3840 2.873094 TAGAGAGAGTGACGGGAACA 57.127 50.000 0.00 0.00 0.00 3.18
3524 3879 3.680490 TGTTCTATTTCGTGGCATTGGA 58.320 40.909 0.00 0.00 0.00 3.53
3610 3965 2.182827 TCAGCTCTTGTAGATGGCAGT 58.817 47.619 0.00 0.00 42.11 4.40
3618 3973 4.528206 TCTTGTAGATGGCAGTCAGAGAAA 59.472 41.667 0.00 0.00 0.00 2.52
3619 3974 5.188555 TCTTGTAGATGGCAGTCAGAGAAAT 59.811 40.000 0.00 0.00 0.00 2.17
3624 3979 6.244552 AGATGGCAGTCAGAGAAATCATTA 57.755 37.500 0.00 0.00 0.00 1.90
3652 4007 8.356657 TGAAATTCAAACACCTAAACTATGTGG 58.643 33.333 0.00 0.00 34.33 4.17
3653 4008 7.833285 AATTCAAACACCTAAACTATGTGGT 57.167 32.000 0.00 0.00 34.33 4.16
3654 4009 8.927675 AATTCAAACACCTAAACTATGTGGTA 57.072 30.769 0.00 0.00 34.33 3.25
3656 4011 6.232692 TCAAACACCTAAACTATGTGGTACC 58.767 40.000 4.43 4.43 34.33 3.34
3657 4012 6.043474 TCAAACACCTAAACTATGTGGTACCT 59.957 38.462 14.36 0.00 34.33 3.08
3658 4013 6.443995 AACACCTAAACTATGTGGTACCTT 57.556 37.500 14.36 0.00 34.33 3.50
3659 4014 6.443995 ACACCTAAACTATGTGGTACCTTT 57.556 37.500 14.36 6.62 34.33 3.11
3660 4015 6.844829 ACACCTAAACTATGTGGTACCTTTT 58.155 36.000 14.36 5.61 34.33 2.27
3661 4016 7.292319 ACACCTAAACTATGTGGTACCTTTTT 58.708 34.615 14.36 5.94 34.33 1.94
3662 4017 7.446319 ACACCTAAACTATGTGGTACCTTTTTC 59.554 37.037 14.36 0.00 34.33 2.29
3663 4018 6.652062 ACCTAAACTATGTGGTACCTTTTTCG 59.348 38.462 14.36 0.00 0.00 3.46
3664 4019 6.652062 CCTAAACTATGTGGTACCTTTTTCGT 59.348 38.462 14.36 0.61 0.00 3.85
3691 4046 7.310113 CTGAACAACCAGAGAAGAGGTAACTAT 60.310 40.741 0.00 0.00 41.59 2.12
3711 4066 6.756221 ACTATGTGGTAACTTTTTCGTCTCT 58.244 36.000 0.00 0.00 37.61 3.10
3717 4072 5.055144 GGTAACTTTTTCGTCTCTTCCAGT 58.945 41.667 0.00 0.00 0.00 4.00
3732 4087 6.270000 TCTCTTCCAGTCTTAATTGGAGTTGA 59.730 38.462 4.35 4.55 41.78 3.18
3814 4169 1.205893 TCGCCTTTGGTTTTGTTGCTT 59.794 42.857 0.00 0.00 0.00 3.91
3835 4190 8.032952 TGCTTGTGTTGAAGAGATATTAAGTG 57.967 34.615 0.00 0.00 0.00 3.16
3863 4218 9.801873 TTTTATATGGAAAATGCTTAGTTGCTC 57.198 29.630 0.00 0.00 0.00 4.26
3867 4222 2.200373 AAATGCTTAGTTGCTCGGGT 57.800 45.000 0.00 0.00 0.00 5.28
3873 4228 0.675083 TTAGTTGCTCGGGTGAACGA 59.325 50.000 0.00 0.00 41.13 3.85
3877 4232 0.034198 TTGCTCGGGTGAACGATGAA 59.966 50.000 0.00 0.00 42.62 2.57
3878 4233 0.034198 TGCTCGGGTGAACGATGAAA 59.966 50.000 0.00 0.00 42.62 2.69
3879 4234 0.721718 GCTCGGGTGAACGATGAAAG 59.278 55.000 0.00 0.00 42.62 2.62
3880 4235 1.671850 GCTCGGGTGAACGATGAAAGA 60.672 52.381 0.00 0.00 42.62 2.52
3881 4236 1.993370 CTCGGGTGAACGATGAAAGAC 59.007 52.381 0.00 0.00 42.62 3.01
3882 4237 1.341852 TCGGGTGAACGATGAAAGACA 59.658 47.619 0.00 0.00 38.06 3.41
3883 4238 2.139917 CGGGTGAACGATGAAAGACAA 58.860 47.619 0.00 0.00 35.47 3.18
3884 4239 2.096417 CGGGTGAACGATGAAAGACAAC 60.096 50.000 0.00 0.00 35.47 3.32
3885 4240 3.139077 GGGTGAACGATGAAAGACAACT 58.861 45.455 0.00 0.00 0.00 3.16
3886 4241 4.312443 GGGTGAACGATGAAAGACAACTA 58.688 43.478 0.00 0.00 0.00 2.24
3887 4242 4.935808 GGGTGAACGATGAAAGACAACTAT 59.064 41.667 0.00 0.00 0.00 2.12
3888 4243 5.411669 GGGTGAACGATGAAAGACAACTATT 59.588 40.000 0.00 0.00 0.00 1.73
3889 4244 6.307155 GGTGAACGATGAAAGACAACTATTG 58.693 40.000 0.00 0.00 0.00 1.90
3890 4245 6.147164 GGTGAACGATGAAAGACAACTATTGA 59.853 38.462 0.00 0.00 0.00 2.57
3891 4246 7.307751 GGTGAACGATGAAAGACAACTATTGAA 60.308 37.037 0.00 0.00 0.00 2.69
3892 4247 7.742089 GTGAACGATGAAAGACAACTATTGAAG 59.258 37.037 0.00 0.00 0.00 3.02
3893 4248 7.441157 TGAACGATGAAAGACAACTATTGAAGT 59.559 33.333 0.00 0.00 41.49 3.01
3894 4249 7.121974 ACGATGAAAGACAACTATTGAAGTG 57.878 36.000 0.00 0.00 38.88 3.16
3895 4250 6.706270 ACGATGAAAGACAACTATTGAAGTGT 59.294 34.615 0.00 0.00 38.88 3.55
3896 4251 7.095607 ACGATGAAAGACAACTATTGAAGTGTC 60.096 37.037 0.00 0.00 38.88 3.67
3897 4252 6.861065 TGAAAGACAACTATTGAAGTGTCC 57.139 37.500 0.00 0.00 38.88 4.02
3959 4315 2.012937 TAATTTGCAATGCAGCCTGC 57.987 45.000 10.45 10.45 45.29 4.85
3961 4317 0.108329 ATTTGCAATGCAGCCTGCTC 60.108 50.000 18.96 5.17 45.31 4.26
3969 4325 0.686789 TGCAGCCTGCTCTTTGAGTA 59.313 50.000 18.96 0.00 45.31 2.59
3973 4329 3.679917 GCAGCCTGCTCTTTGAGTATACA 60.680 47.826 10.04 0.00 40.96 2.29
3988 4396 6.662755 TGAGTATACAATTTGGAAGATGGCT 58.337 36.000 5.50 0.00 0.00 4.75
3999 4407 0.911769 AAGATGGCTGGTCGATTCCA 59.088 50.000 0.00 0.00 36.00 3.53
4022 4430 8.682710 TCCAATAGCTTTGTTAATCCATTGTAC 58.317 33.333 0.00 0.00 0.00 2.90
4089 4520 2.559231 GCTGGTAGCTATGAGGTACTCC 59.441 54.545 13.76 1.74 46.94 3.85
4090 4521 4.625001 GCTGGTAGCTATGAGGTACTCCC 61.625 56.522 13.76 1.14 46.94 4.30
4091 4522 6.828270 GCTGGTAGCTATGAGGTACTCCCT 62.828 54.167 13.76 0.00 46.94 4.20
4107 4538 9.725206 AGGTACTCCCTCTGTAAAGAAATATAA 57.275 33.333 0.00 0.00 40.71 0.98
4108 4539 9.984190 GGTACTCCCTCTGTAAAGAAATATAAG 57.016 37.037 0.00 0.00 0.00 1.73
4111 4542 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
4112 4543 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
4113 4544 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
4114 4545 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
4132 4563 9.998106 AAGAGTGTTTAGATCACTAAAGCTAAA 57.002 29.630 0.00 0.00 45.42 1.85
4133 4564 9.425577 AGAGTGTTTAGATCACTAAAGCTAAAC 57.574 33.333 14.55 14.55 45.42 2.01
4138 4569 9.425577 GTTTAGATCACTAAAGCTAAACACTCT 57.574 33.333 15.87 0.00 45.85 3.24
4139 4570 9.998106 TTTAGATCACTAAAGCTAAACACTCTT 57.002 29.630 0.00 0.00 41.71 2.85
4157 4588 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
4158 4589 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
4159 4590 9.757227 CACTCTTATATTTCTTTACAGAGGGAG 57.243 37.037 0.00 0.00 32.92 4.30
4160 4591 9.495382 ACTCTTATATTTCTTTACAGAGGGAGT 57.505 33.333 0.00 0.00 32.21 3.85
4171 4602 8.437575 TCTTTACAGAGGGAGTATTGTTTTCTT 58.562 33.333 0.00 0.00 0.00 2.52
4177 4608 2.163613 GGAGTATTGTTTTCTTGGGGCG 59.836 50.000 0.00 0.00 0.00 6.13
4180 4611 0.033366 ATTGTTTTCTTGGGGCGTGC 59.967 50.000 0.00 0.00 0.00 5.34
4182 4613 1.323271 TGTTTTCTTGGGGCGTGCAA 61.323 50.000 0.00 0.00 0.00 4.08
4195 4626 3.472263 GTGCAACGTGTTCCCAATC 57.528 52.632 0.00 0.00 0.00 2.67
4238 4752 0.033781 TGTATATGCGCCGTTACCCC 59.966 55.000 4.18 0.00 0.00 4.95
4262 4776 5.163561 CCTTGGTTGCTGTCTCAAAACTTAA 60.164 40.000 0.00 0.00 0.00 1.85
4287 4801 4.388165 CAGTTCAGAGCTTCTGTATGTGTG 59.612 45.833 11.37 2.10 44.58 3.82
4288 4802 4.281941 AGTTCAGAGCTTCTGTATGTGTGA 59.718 41.667 11.37 0.00 44.58 3.58
4307 4821 7.632721 TGTGTGAAGTAGTTTAAATTTCGTCC 58.367 34.615 0.00 0.00 0.00 4.79
4309 4823 7.797123 GTGTGAAGTAGTTTAAATTTCGTCCTG 59.203 37.037 0.00 0.00 0.00 3.86
4348 4862 4.107622 GCATTGAATGAAAATCTGGACCG 58.892 43.478 9.76 0.00 0.00 4.79
4383 4897 8.757982 AATTTACCACATGAATAAGCTCAGAT 57.242 30.769 0.00 0.00 0.00 2.90
4405 4919 0.536724 GCCCCAAAACTAAGCCATGG 59.463 55.000 7.63 7.63 0.00 3.66
4421 4935 4.228210 AGCCATGGTCAGAAAATCCTAAGA 59.772 41.667 14.67 0.00 0.00 2.10
4494 5012 5.108517 TGGAAAGCTTTTGACAATGTGTTC 58.891 37.500 14.05 0.00 0.00 3.18
4567 5085 5.071653 AGGCCTTTCTAAAATTTGCTTCCAA 59.928 36.000 0.00 0.00 0.00 3.53
4572 5090 8.291740 CCTTTCTAAAATTTGCTTCCAATTTGG 58.708 33.333 9.28 9.28 39.43 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.030540 CCAATGTCTGCAGAGTTTGTGG 60.031 50.000 25.58 20.24 0.00 4.17
21 22 2.233271 CCCAATGTCTGCAGAGTTTGT 58.767 47.619 25.58 8.15 0.00 2.83
23 24 1.915141 CCCCAATGTCTGCAGAGTTT 58.085 50.000 18.89 10.98 0.00 2.66
28 29 0.899720 AAATGCCCCAATGTCTGCAG 59.100 50.000 7.63 7.63 37.12 4.41
31 32 3.705579 TCCATAAAATGCCCCAATGTCTG 59.294 43.478 0.00 0.00 0.00 3.51
32 33 3.962718 CTCCATAAAATGCCCCAATGTCT 59.037 43.478 0.00 0.00 0.00 3.41
33 34 3.960102 TCTCCATAAAATGCCCCAATGTC 59.040 43.478 0.00 0.00 0.00 3.06
49 50 9.474313 GACTAGATTCAGTTCCTATATCTCCAT 57.526 37.037 0.00 0.00 0.00 3.41
57 61 7.042335 CCAAAACGACTAGATTCAGTTCCTAT 58.958 38.462 0.00 0.00 0.00 2.57
59 63 5.238583 CCAAAACGACTAGATTCAGTTCCT 58.761 41.667 0.00 0.00 0.00 3.36
61 65 5.235516 TCCCAAAACGACTAGATTCAGTTC 58.764 41.667 0.00 0.00 0.00 3.01
63 67 4.884668 TCCCAAAACGACTAGATTCAGT 57.115 40.909 0.00 0.00 0.00 3.41
64 68 5.932303 TCTTTCCCAAAACGACTAGATTCAG 59.068 40.000 0.00 0.00 0.00 3.02
65 69 5.860611 TCTTTCCCAAAACGACTAGATTCA 58.139 37.500 0.00 0.00 0.00 2.57
123 127 4.229582 TGCTTAGTGGATAATTCCCTGGTT 59.770 41.667 0.00 0.00 41.83 3.67
126 130 4.780815 TGTGCTTAGTGGATAATTCCCTG 58.219 43.478 0.00 0.00 41.83 4.45
127 131 5.653255 ATGTGCTTAGTGGATAATTCCCT 57.347 39.130 0.00 0.00 41.83 4.20
131 135 6.515512 AGGGTATGTGCTTAGTGGATAATT 57.484 37.500 0.00 0.00 0.00 1.40
134 138 5.460416 TGTAGGGTATGTGCTTAGTGGATA 58.540 41.667 0.00 0.00 0.00 2.59
138 142 4.380531 CCATGTAGGGTATGTGCTTAGTG 58.619 47.826 0.00 0.00 0.00 2.74
142 146 1.563879 TGCCATGTAGGGTATGTGCTT 59.436 47.619 0.00 0.00 38.09 3.91
146 150 3.778075 TGTTAGTGCCATGTAGGGTATGT 59.222 43.478 0.00 0.00 38.09 2.29
156 160 5.335127 GCAGTCTTAAATGTTAGTGCCATG 58.665 41.667 0.00 0.00 33.18 3.66
166 170 4.330074 CGAAATCGAGGCAGTCTTAAATGT 59.670 41.667 0.00 0.00 43.02 2.71
171 175 2.579207 CCGAAATCGAGGCAGTCTTA 57.421 50.000 4.04 0.00 43.02 2.10
183 187 4.690159 GGCGTTCATGCCGAAATC 57.310 55.556 8.53 0.00 46.75 2.17
200 204 5.529430 ACCTCTGACATCGTAGAACATCTAG 59.471 44.000 0.00 0.00 43.58 2.43
209 213 2.092323 TGGTGACCTCTGACATCGTAG 58.908 52.381 2.11 0.00 0.00 3.51
216 220 0.318762 GGTGAGTGGTGACCTCTGAC 59.681 60.000 11.42 12.70 32.15 3.51
218 222 0.319728 CTGGTGAGTGGTGACCTCTG 59.680 60.000 11.42 0.00 32.98 3.35
219 223 0.105453 ACTGGTGAGTGGTGACCTCT 60.105 55.000 5.80 5.80 32.98 3.69
220 224 0.759346 AACTGGTGAGTGGTGACCTC 59.241 55.000 2.11 0.00 32.98 3.85
223 227 2.158871 TGGTAAACTGGTGAGTGGTGAC 60.159 50.000 0.00 0.00 30.61 3.67
230 234 3.703001 ACTGGATGGTAAACTGGTGAG 57.297 47.619 0.00 0.00 0.00 3.51
231 235 3.904965 TGTACTGGATGGTAAACTGGTGA 59.095 43.478 0.00 0.00 0.00 4.02
232 236 4.280436 TGTACTGGATGGTAAACTGGTG 57.720 45.455 0.00 0.00 0.00 4.17
235 239 4.906618 ACCTTGTACTGGATGGTAAACTG 58.093 43.478 11.48 0.00 0.00 3.16
236 240 4.844655 AGACCTTGTACTGGATGGTAAACT 59.155 41.667 11.48 0.00 0.00 2.66
237 241 4.935808 CAGACCTTGTACTGGATGGTAAAC 59.064 45.833 11.48 0.00 0.00 2.01
238 242 4.564821 GCAGACCTTGTACTGGATGGTAAA 60.565 45.833 11.48 0.00 35.05 2.01
239 243 3.055385 GCAGACCTTGTACTGGATGGTAA 60.055 47.826 11.48 0.00 35.05 2.85
240 244 2.500098 GCAGACCTTGTACTGGATGGTA 59.500 50.000 11.48 0.00 35.05 3.25
241 245 1.279271 GCAGACCTTGTACTGGATGGT 59.721 52.381 11.48 1.40 35.05 3.55
242 246 1.278985 TGCAGACCTTGTACTGGATGG 59.721 52.381 11.48 0.00 35.05 3.51
243 247 2.350522 GTGCAGACCTTGTACTGGATG 58.649 52.381 11.48 10.19 39.10 3.51
244 248 2.770164 GTGCAGACCTTGTACTGGAT 57.230 50.000 11.48 0.00 39.10 3.41
261 265 1.603802 CCAGTACTTGGTTGTGCAGTG 59.396 52.381 0.00 0.00 42.41 3.66
274 283 4.160329 TGTTCCTGTGATTCTCCAGTACT 58.840 43.478 0.00 0.00 0.00 2.73
275 284 4.537135 TGTTCCTGTGATTCTCCAGTAC 57.463 45.455 0.00 0.00 0.00 2.73
278 287 4.841422 AGATTGTTCCTGTGATTCTCCAG 58.159 43.478 0.00 0.00 0.00 3.86
293 302 4.517832 GGTTTTAAGGTGGACGAGATTGTT 59.482 41.667 0.00 0.00 0.00 2.83
310 319 4.825546 TTACGAATTGTTGCGGGTTTTA 57.174 36.364 0.00 0.00 0.00 1.52
314 323 3.602483 AGTATTACGAATTGTTGCGGGT 58.398 40.909 0.00 0.00 0.00 5.28
315 324 4.210537 CCTAGTATTACGAATTGTTGCGGG 59.789 45.833 0.00 0.00 0.00 6.13
317 326 4.506654 AGCCTAGTATTACGAATTGTTGCG 59.493 41.667 0.00 0.00 0.00 4.85
318 327 5.986004 AGCCTAGTATTACGAATTGTTGC 57.014 39.130 0.00 0.00 0.00 4.17
319 328 9.395707 CTAGTAGCCTAGTATTACGAATTGTTG 57.604 37.037 0.00 0.00 36.67 3.33
321 330 7.447853 AGCTAGTAGCCTAGTATTACGAATTGT 59.552 37.037 18.65 0.00 43.77 2.71
322 331 7.751348 CAGCTAGTAGCCTAGTATTACGAATTG 59.249 40.741 18.65 0.83 43.77 2.32
324 333 6.127952 GCAGCTAGTAGCCTAGTATTACGAAT 60.128 42.308 18.65 0.00 43.77 3.34
325 334 5.180868 GCAGCTAGTAGCCTAGTATTACGAA 59.819 44.000 18.65 0.00 43.77 3.85
326 335 4.694509 GCAGCTAGTAGCCTAGTATTACGA 59.305 45.833 18.65 0.00 43.77 3.43
327 336 4.972201 GCAGCTAGTAGCCTAGTATTACG 58.028 47.826 18.65 0.00 43.77 3.18
338 347 0.601057 GCTCTAGGGCAGCTAGTAGC 59.399 60.000 14.62 14.62 42.84 3.58
339 348 2.286365 AGCTCTAGGGCAGCTAGTAG 57.714 55.000 18.89 0.00 45.76 2.57
348 357 1.333636 TGGAAGCAGAGCTCTAGGGC 61.334 60.000 17.75 16.13 38.25 5.19
393 403 1.443872 CATATAGGTCGCCCGTCGC 60.444 63.158 0.00 0.00 38.27 5.19
400 410 2.383527 GCGGCAGCATATAGGTCGC 61.384 63.158 3.18 4.11 44.35 5.19
402 412 0.319555 TTCGCGGCAGCATATAGGTC 60.320 55.000 10.08 0.00 45.49 3.85
410 420 1.638388 CTTCTTGATTCGCGGCAGCA 61.638 55.000 10.08 0.00 45.49 4.41
421 431 6.293516 CGCGTATAGGAGTAGTTCTTCTTGAT 60.294 42.308 0.00 0.00 33.40 2.57
424 434 4.275443 CCGCGTATAGGAGTAGTTCTTCTT 59.725 45.833 4.92 0.00 33.40 2.52
426 436 3.608941 GCCGCGTATAGGAGTAGTTCTTC 60.609 52.174 4.92 0.00 0.00 2.87
427 437 2.292845 GCCGCGTATAGGAGTAGTTCTT 59.707 50.000 4.92 0.00 0.00 2.52
433 443 2.620112 GCGGCCGCGTATAGGAGTA 61.620 63.158 37.24 0.00 0.00 2.59
467 477 3.521910 GCGTTCAGCTCGTATTCACGC 62.522 57.143 0.00 0.00 43.95 5.34
643 653 1.375396 CCGCTCAACCAACCATCGA 60.375 57.895 0.00 0.00 0.00 3.59
853 863 2.860628 GCTAGCCGCACACGAATCG 61.861 63.158 2.29 0.00 43.93 3.34
865 875 0.107654 ATGGAAACCTGACGCTAGCC 60.108 55.000 9.66 0.00 0.00 3.93
867 877 1.656652 CCATGGAAACCTGACGCTAG 58.343 55.000 5.56 0.00 0.00 3.42
869 879 1.002134 CCCATGGAAACCTGACGCT 60.002 57.895 15.22 0.00 0.00 5.07
870 880 2.700773 GCCCATGGAAACCTGACGC 61.701 63.158 15.22 0.00 0.00 5.19
871 881 2.046285 GGCCCATGGAAACCTGACG 61.046 63.158 15.22 0.00 0.00 4.35
872 882 2.046285 CGGCCCATGGAAACCTGAC 61.046 63.158 15.22 0.00 0.00 3.51
875 885 4.060667 CCCGGCCCATGGAAACCT 62.061 66.667 15.22 0.00 0.00 3.50
897 907 2.046892 CTGGCCACTCACGAAGGG 60.047 66.667 0.00 0.00 0.00 3.95
935 945 2.728383 CGTCGTGTCGTGGGTGAC 60.728 66.667 0.00 0.00 39.37 3.67
936 946 4.634133 GCGTCGTGTCGTGGGTGA 62.634 66.667 0.00 0.00 0.00 4.02
1319 1358 3.249080 CGAAGGAAGATCTCTACTCGTCC 59.751 52.174 0.00 0.00 40.37 4.79
1360 1399 7.224753 TCGAAGATTTAATCACTAATCACAGCC 59.775 37.037 7.74 0.00 34.06 4.85
1361 1400 8.131455 TCGAAGATTTAATCACTAATCACAGC 57.869 34.615 7.74 0.00 34.06 4.40
1789 1834 2.436292 GGAGGCACAGCAGCAGAG 60.436 66.667 0.00 0.00 35.83 3.35
1794 1839 0.322277 ACATGAAGGAGGCACAGCAG 60.322 55.000 0.00 0.00 0.00 4.24
1805 1850 6.206243 GTCAATCAGGGATGATAACATGAAGG 59.794 42.308 0.00 0.00 36.82 3.46
1893 2043 9.295825 CCCCACTAGTTATTATTATGCAAATCA 57.704 33.333 0.00 0.00 0.00 2.57
1894 2044 9.297037 ACCCCACTAGTTATTATTATGCAAATC 57.703 33.333 0.00 0.00 0.00 2.17
1895 2045 9.654919 AACCCCACTAGTTATTATTATGCAAAT 57.345 29.630 0.00 0.00 0.00 2.32
1896 2046 8.908903 CAACCCCACTAGTTATTATTATGCAAA 58.091 33.333 0.00 0.00 0.00 3.68
1897 2047 8.275758 TCAACCCCACTAGTTATTATTATGCAA 58.724 33.333 0.00 0.00 0.00 4.08
1898 2048 7.807198 TCAACCCCACTAGTTATTATTATGCA 58.193 34.615 0.00 0.00 0.00 3.96
1899 2049 8.154856 TCTCAACCCCACTAGTTATTATTATGC 58.845 37.037 0.00 0.00 0.00 3.14
1918 2263 4.633565 CAGAGCAAAGTAATCCTCTCAACC 59.366 45.833 0.00 0.00 32.65 3.77
2083 2428 0.733150 GCTCATAGGTCCCAAAACGC 59.267 55.000 0.00 0.00 0.00 4.84
2169 2514 4.380867 GGTGCCAACAAGTTGATATCAAGG 60.381 45.833 18.47 15.06 42.93 3.61
2211 2556 5.420725 ACATGTCTAGTTTGCTCATGGTA 57.579 39.130 0.00 0.00 39.76 3.25
2212 2557 4.292186 ACATGTCTAGTTTGCTCATGGT 57.708 40.909 0.00 0.00 39.76 3.55
2235 2580 6.039493 GGATATGACAGAGAAGTCTAACCGAA 59.961 42.308 0.00 0.00 39.27 4.30
2395 2748 3.705604 AGTTTTGCTGCACATAACACAC 58.294 40.909 18.00 2.25 41.21 3.82
2466 2820 8.506437 CATTGTTAGTCAGAAGTTTCATGCTTA 58.494 33.333 0.00 0.00 0.00 3.09
2727 3081 2.673833 CAGTGGAAACGACTCCTGTAC 58.326 52.381 8.63 0.00 36.35 2.90
2796 3150 1.221414 GACAACAGACTGACACTGCC 58.779 55.000 10.08 0.00 38.74 4.85
2828 3182 2.024655 ACCCATCATGTCAGGATGCTTT 60.025 45.455 19.71 5.21 40.60 3.51
3038 3392 0.036010 ACTGCCAAGTAAGCATCGCT 60.036 50.000 0.00 0.00 42.56 4.93
3117 3472 7.623999 ATCATGACACTGTCCCTATCTTTAT 57.376 36.000 6.72 0.00 0.00 1.40
3154 3509 6.780522 AGCAAAGGGTTAGAATAGACCAAAAA 59.219 34.615 0.00 0.00 37.68 1.94
3156 3511 5.887754 AGCAAAGGGTTAGAATAGACCAAA 58.112 37.500 0.00 0.00 37.68 3.28
3278 3633 5.066634 TGAACGACTTTTGGCAGTATCAAAA 59.933 36.000 0.00 0.00 40.46 2.44
3479 3834 2.486191 CCTATCAGCAGGTGATGTTCCC 60.486 54.545 22.95 0.00 46.09 3.97
3524 3879 4.873129 CTGCGCGCCATCCGTAGT 62.873 66.667 30.77 0.00 39.71 2.73
3642 3997 6.204108 CAGACGAAAAAGGTACCACATAGTTT 59.796 38.462 15.94 1.38 0.00 2.66
3643 3998 5.699458 CAGACGAAAAAGGTACCACATAGTT 59.301 40.000 15.94 0.00 0.00 2.24
3645 4000 5.475719 TCAGACGAAAAAGGTACCACATAG 58.524 41.667 15.94 3.25 0.00 2.23
3649 4004 3.872771 TGTTCAGACGAAAAAGGTACCAC 59.127 43.478 15.94 0.00 31.43 4.16
3652 4007 4.333372 TGGTTGTTCAGACGAAAAAGGTAC 59.667 41.667 0.00 0.00 28.64 3.34
3653 4008 4.515361 TGGTTGTTCAGACGAAAAAGGTA 58.485 39.130 0.00 0.00 28.64 3.08
3654 4009 3.349022 TGGTTGTTCAGACGAAAAAGGT 58.651 40.909 0.00 0.00 28.64 3.50
3656 4011 4.570772 TCTCTGGTTGTTCAGACGAAAAAG 59.429 41.667 0.00 0.00 38.70 2.27
3657 4012 4.509616 TCTCTGGTTGTTCAGACGAAAAA 58.490 39.130 0.00 0.00 38.70 1.94
3658 4013 4.131649 TCTCTGGTTGTTCAGACGAAAA 57.868 40.909 0.00 0.00 38.70 2.29
3659 4014 3.812156 TCTCTGGTTGTTCAGACGAAA 57.188 42.857 0.00 0.00 38.70 3.46
3660 4015 3.383505 TCTTCTCTGGTTGTTCAGACGAA 59.616 43.478 0.00 0.00 38.70 3.85
3661 4016 2.956333 TCTTCTCTGGTTGTTCAGACGA 59.044 45.455 0.00 0.00 38.70 4.20
3662 4017 3.312828 CTCTTCTCTGGTTGTTCAGACG 58.687 50.000 0.00 0.00 38.70 4.18
3663 4018 3.070302 ACCTCTTCTCTGGTTGTTCAGAC 59.930 47.826 0.00 0.00 38.70 3.51
3664 4019 3.309296 ACCTCTTCTCTGGTTGTTCAGA 58.691 45.455 0.00 0.00 41.03 3.27
3691 4046 4.812626 GGAAGAGACGAAAAAGTTACCACA 59.187 41.667 0.00 0.00 0.00 4.17
3698 4053 4.674281 AGACTGGAAGAGACGAAAAAGT 57.326 40.909 0.00 0.00 37.43 2.66
3702 4057 5.932303 CCAATTAAGACTGGAAGAGACGAAA 59.068 40.000 0.00 0.00 37.43 3.46
3706 4061 6.043854 ACTCCAATTAAGACTGGAAGAGAC 57.956 41.667 5.51 0.00 41.20 3.36
3711 4066 5.997746 CACTCAACTCCAATTAAGACTGGAA 59.002 40.000 5.51 0.00 41.20 3.53
3732 4087 4.018050 ACCAAAATTCTATCCTGGAGCACT 60.018 41.667 1.52 0.00 0.00 4.40
3794 4149 0.820871 AGCAACAAAACCAAAGGCGA 59.179 45.000 0.00 0.00 0.00 5.54
3853 4208 1.068474 CGTTCACCCGAGCAACTAAG 58.932 55.000 0.00 0.00 0.00 2.18
3863 4218 1.790755 TGTCTTTCATCGTTCACCCG 58.209 50.000 0.00 0.00 0.00 5.28
3867 4222 7.441157 ACTTCAATAGTTGTCTTTCATCGTTCA 59.559 33.333 0.00 0.00 31.29 3.18
3873 4228 6.998074 TGGACACTTCAATAGTTGTCTTTCAT 59.002 34.615 0.00 0.00 36.25 2.57
3877 4232 5.765182 CCTTGGACACTTCAATAGTTGTCTT 59.235 40.000 0.00 0.00 36.25 3.01
3878 4233 5.163195 ACCTTGGACACTTCAATAGTTGTCT 60.163 40.000 0.00 0.00 36.25 3.41
3879 4234 5.063880 ACCTTGGACACTTCAATAGTTGTC 58.936 41.667 0.00 0.00 33.85 3.18
3880 4235 5.048846 ACCTTGGACACTTCAATAGTTGT 57.951 39.130 0.00 0.00 33.85 3.32
3881 4236 7.504924 TTAACCTTGGACACTTCAATAGTTG 57.495 36.000 0.00 0.00 33.85 3.16
3882 4237 8.706322 AATTAACCTTGGACACTTCAATAGTT 57.294 30.769 0.00 0.00 33.85 2.24
3883 4238 8.706322 AAATTAACCTTGGACACTTCAATAGT 57.294 30.769 0.00 0.00 37.68 2.12
3884 4239 9.410556 CAAAATTAACCTTGGACACTTCAATAG 57.589 33.333 0.00 0.00 0.00 1.73
3885 4240 8.364142 CCAAAATTAACCTTGGACACTTCAATA 58.636 33.333 10.62 0.00 44.16 1.90
3886 4241 7.216494 CCAAAATTAACCTTGGACACTTCAAT 58.784 34.615 10.62 0.00 44.16 2.57
3887 4242 6.578023 CCAAAATTAACCTTGGACACTTCAA 58.422 36.000 10.62 0.00 44.16 2.69
3888 4243 5.452636 GCCAAAATTAACCTTGGACACTTCA 60.453 40.000 17.68 0.00 44.16 3.02
3889 4244 4.988540 GCCAAAATTAACCTTGGACACTTC 59.011 41.667 17.68 0.22 44.16 3.01
3890 4245 4.407296 TGCCAAAATTAACCTTGGACACTT 59.593 37.500 17.68 0.00 44.16 3.16
3891 4246 3.964031 TGCCAAAATTAACCTTGGACACT 59.036 39.130 17.68 0.00 44.16 3.55
3892 4247 4.306600 CTGCCAAAATTAACCTTGGACAC 58.693 43.478 17.68 4.76 44.16 3.67
3893 4248 3.244044 GCTGCCAAAATTAACCTTGGACA 60.244 43.478 17.68 13.88 44.16 4.02
3894 4249 3.244044 TGCTGCCAAAATTAACCTTGGAC 60.244 43.478 17.68 11.03 44.16 4.02
3895 4250 2.968574 TGCTGCCAAAATTAACCTTGGA 59.031 40.909 17.68 5.83 44.16 3.53
3896 4251 3.244181 ACTGCTGCCAAAATTAACCTTGG 60.244 43.478 11.48 11.48 44.23 3.61
3897 4252 3.742369 CACTGCTGCCAAAATTAACCTTG 59.258 43.478 0.00 0.00 0.00 3.61
3933 4289 4.107622 GCTGCATTGCAAATTATCGAAGT 58.892 39.130 13.18 0.00 38.41 3.01
3961 4317 7.917505 GCCATCTTCCAAATTGTATACTCAAAG 59.082 37.037 4.17 0.00 0.00 2.77
3969 4325 4.613437 ACCAGCCATCTTCCAAATTGTAT 58.387 39.130 0.00 0.00 0.00 2.29
3973 4329 2.094675 CGACCAGCCATCTTCCAAATT 58.905 47.619 0.00 0.00 0.00 1.82
3988 4396 3.950397 ACAAAGCTATTGGAATCGACCA 58.050 40.909 11.59 0.00 38.24 4.02
4054 4485 3.070159 GCTACCAGCTACAAGATCCATCA 59.930 47.826 0.00 0.00 38.45 3.07
4085 4516 9.495382 ACTCTTATATTTCTTTACAGAGGGAGT 57.505 33.333 0.00 0.00 32.21 3.85
4086 4517 9.757227 CACTCTTATATTTCTTTACAGAGGGAG 57.243 37.037 0.00 0.00 32.92 4.30
4087 4518 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
4088 4519 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
4106 4537 9.998106 TTTAGCTTTAGTGATCTAAACACTCTT 57.002 29.630 0.00 0.00 45.58 2.85
4107 4538 9.425577 GTTTAGCTTTAGTGATCTAAACACTCT 57.574 33.333 14.95 0.00 45.58 3.24
4112 4543 9.425577 AGAGTGTTTAGCTTTAGTGATCTAAAC 57.574 33.333 13.65 13.65 45.25 2.01
4113 4544 9.998106 AAGAGTGTTTAGCTTTAGTGATCTAAA 57.002 29.630 0.00 0.00 41.87 1.85
4131 4562 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
4132 4563 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
4133 4564 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
4134 4565 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
4142 4573 9.588096 AAAACAATACTCCCTCTGTAAAGAAAT 57.412 29.630 0.00 0.00 0.00 2.17
4143 4574 8.990163 AAAACAATACTCCCTCTGTAAAGAAA 57.010 30.769 0.00 0.00 0.00 2.52
4144 4575 8.437575 AGAAAACAATACTCCCTCTGTAAAGAA 58.562 33.333 0.00 0.00 0.00 2.52
4145 4576 7.974504 AGAAAACAATACTCCCTCTGTAAAGA 58.025 34.615 0.00 0.00 0.00 2.52
4146 4577 8.507249 CAAGAAAACAATACTCCCTCTGTAAAG 58.493 37.037 0.00 0.00 0.00 1.85
4147 4578 7.447238 CCAAGAAAACAATACTCCCTCTGTAAA 59.553 37.037 0.00 0.00 0.00 2.01
4148 4579 6.940298 CCAAGAAAACAATACTCCCTCTGTAA 59.060 38.462 0.00 0.00 0.00 2.41
4149 4580 6.472887 CCAAGAAAACAATACTCCCTCTGTA 58.527 40.000 0.00 0.00 0.00 2.74
4150 4581 5.316987 CCAAGAAAACAATACTCCCTCTGT 58.683 41.667 0.00 0.00 0.00 3.41
4151 4582 4.702131 CCCAAGAAAACAATACTCCCTCTG 59.298 45.833 0.00 0.00 0.00 3.35
4152 4583 4.263949 CCCCAAGAAAACAATACTCCCTCT 60.264 45.833 0.00 0.00 0.00 3.69
4153 4584 4.017126 CCCCAAGAAAACAATACTCCCTC 58.983 47.826 0.00 0.00 0.00 4.30
4154 4585 3.817931 GCCCCAAGAAAACAATACTCCCT 60.818 47.826 0.00 0.00 0.00 4.20
4155 4586 2.496070 GCCCCAAGAAAACAATACTCCC 59.504 50.000 0.00 0.00 0.00 4.30
4156 4587 2.163613 CGCCCCAAGAAAACAATACTCC 59.836 50.000 0.00 0.00 0.00 3.85
4157 4588 2.817844 ACGCCCCAAGAAAACAATACTC 59.182 45.455 0.00 0.00 0.00 2.59
4158 4589 2.556622 CACGCCCCAAGAAAACAATACT 59.443 45.455 0.00 0.00 0.00 2.12
4159 4590 2.924880 GCACGCCCCAAGAAAACAATAC 60.925 50.000 0.00 0.00 0.00 1.89
4160 4591 1.271102 GCACGCCCCAAGAAAACAATA 59.729 47.619 0.00 0.00 0.00 1.90
4161 4592 0.033366 GCACGCCCCAAGAAAACAAT 59.967 50.000 0.00 0.00 0.00 2.71
4177 4608 0.665835 TGATTGGGAACACGTTGCAC 59.334 50.000 3.79 0.00 42.67 4.57
4180 4611 2.616376 TCAACTGATTGGGAACACGTTG 59.384 45.455 0.00 0.00 42.67 4.10
4182 4613 2.158813 ACTCAACTGATTGGGAACACGT 60.159 45.455 0.00 0.00 38.77 4.49
4193 4624 9.950496 ATTTTGTCATTAGTCTACTCAACTGAT 57.050 29.630 0.00 0.00 0.00 2.90
4195 4626 8.993121 ACATTTTGTCATTAGTCTACTCAACTG 58.007 33.333 0.00 0.00 0.00 3.16
4238 4752 2.689983 AGTTTTGAGACAGCAACCAAGG 59.310 45.455 0.00 0.00 0.00 3.61
4243 4757 6.322491 ACTGTTTAAGTTTTGAGACAGCAAC 58.678 36.000 0.00 0.00 38.37 4.17
4287 4801 6.148976 AGCCAGGACGAAATTTAAACTACTTC 59.851 38.462 0.00 0.00 0.00 3.01
4288 4802 6.002082 AGCCAGGACGAAATTTAAACTACTT 58.998 36.000 0.00 0.00 0.00 2.24
4304 4818 0.390998 GAGACAGAAGCAGCCAGGAC 60.391 60.000 0.00 0.00 0.00 3.85
4307 4821 1.440708 CTTGAGACAGAAGCAGCCAG 58.559 55.000 0.00 0.00 0.00 4.85
4309 4823 2.169842 GCTTGAGACAGAAGCAGCC 58.830 57.895 0.00 0.00 44.43 4.85
4338 4852 3.495434 TTACCAAACACGGTCCAGATT 57.505 42.857 0.00 0.00 40.67 2.40
4342 4856 5.435820 GTAAATTTACCAAACACGGTCCA 57.564 39.130 16.14 0.00 40.67 4.02
4356 4870 9.679661 TCTGAGCTTATTCATGTGGTAAATTTA 57.320 29.630 0.00 0.00 0.00 1.40
4370 4884 2.234143 GGGGCCAATCTGAGCTTATTC 58.766 52.381 4.39 0.00 0.00 1.75
4375 4889 0.114954 TTTTGGGGCCAATCTGAGCT 59.885 50.000 4.39 0.00 35.70 4.09
4383 4897 2.753319 GGCTTAGTTTTGGGGCCAA 58.247 52.632 4.39 0.00 42.08 4.52
4494 5012 6.656693 ACAGTTAAATCTTCTCTGACAATGGG 59.343 38.462 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.