Multiple sequence alignment - TraesCS1A01G106600

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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 TraesCS1A01G106600 chr1A 100.000 3645 0 0 1 3645 104376811 104380455 0.000000e+00 6732
1 TraesCS1A01G106600 chr1A 89.340 394 39 3 3254 3645 104437742 104438134 3.270000e-135 492
2 TraesCS1A01G106600 chr1D 90.405 1209 70 21 397 1582 101096463 101095278 0.000000e+00 1548
3 TraesCS1A01G106600 chr1D 91.369 1147 64 15 1938 3067 101094586 101093458 0.000000e+00 1537
4 TraesCS1A01G106600 chr1D 92.397 605 23 14 3064 3645 101092934 101092330 0.000000e+00 841
5 TraesCS1A01G106600 chr1D 89.196 398 36 5 3254 3645 100898781 100898385 1.180000e-134 490
6 TraesCS1A01G106600 chr1B 92.561 941 45 12 1994 2912 150663416 150664353 0.000000e+00 1327
7 TraesCS1A01G106600 chr1B 90.368 924 42 17 698 1582 150662181 150663096 0.000000e+00 1170
8 TraesCS1A01G106600 chr1B 92.005 738 34 9 2917 3645 150664412 150665133 0.000000e+00 1013
9 TraesCS1A01G106600 chr1B 89.196 398 36 5 3254 3645 150801071 150801467 1.180000e-134 490
10 TraesCS1A01G106600 chr4A 92.954 369 21 5 5 372 629300255 629299891 1.930000e-147 532
11 TraesCS1A01G106600 chr4A 84.755 387 43 9 5 384 743381421 743381044 1.240000e-99 374
12 TraesCS1A01G106600 chr7A 92.244 361 21 5 13 372 76126025 76126379 4.200000e-139 505
13 TraesCS1A01G106600 chr7A 90.811 370 26 4 5 374 689262656 689262295 4.230000e-134 488
14 TraesCS1A01G106600 chr3A 90.642 374 24 7 5 375 171346705 171346340 1.520000e-133 486
15 TraesCS1A01G106600 chr2D 87.634 372 37 8 5 372 83534586 83534220 1.210000e-114 424
16 TraesCS1A01G106600 chr4D 86.863 373 40 8 5 372 351454025 351453657 3.390000e-110 409
17 TraesCS1A01G106600 chr4D 88.276 290 28 5 87 372 481181087 481181374 3.490000e-90 342
18 TraesCS1A01G106600 chr3D 85.255 373 39 9 5 374 72042468 72042109 1.600000e-98 370


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 TraesCS1A01G106600 chr1A 104376811 104380455 3644 False 6732.000000 6732 100.000000 1 3645 1 chr1A.!!$F1 3644
1 TraesCS1A01G106600 chr1D 101092330 101096463 4133 True 1308.666667 1548 91.390333 397 3645 3 chr1D.!!$R2 3248
2 TraesCS1A01G106600 chr1B 150662181 150665133 2952 False 1170.000000 1327 91.644667 698 3645 3 chr1B.!!$F2 2947

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
337 338 0.106519 GCCACATGGGATAGCTGGTT 60.107 55.0 0.00 0.0 40.01 3.67 F
1755 1843 0.179089 TGTTGGCGCTTGCAAATTGT 60.179 45.0 7.64 0.0 41.71 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1899 0.108329 CTATTGGCGGACAGAACGGT 60.108 55.0 0.0 0.0 0.00 4.83 R
3220 4247 0.401356 TGATGGGCGATGGCATATGT 59.599 50.0 0.0 0.0 42.47 2.29 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
35 36 3.502237 GGTTACGCCGTTTGAGAGA 57.498 52.632 0.00 0.00 0.00 3.10
36 37 1.787012 GGTTACGCCGTTTGAGAGAA 58.213 50.000 0.00 0.00 0.00 2.87
37 38 2.137523 GGTTACGCCGTTTGAGAGAAA 58.862 47.619 0.00 0.00 0.00 2.52
38 39 2.157085 GGTTACGCCGTTTGAGAGAAAG 59.843 50.000 0.00 0.00 0.00 2.62
39 40 2.798847 GTTACGCCGTTTGAGAGAAAGT 59.201 45.455 0.00 0.00 0.00 2.66
40 41 1.949465 ACGCCGTTTGAGAGAAAGTT 58.051 45.000 0.00 0.00 0.00 2.66
41 42 1.597663 ACGCCGTTTGAGAGAAAGTTG 59.402 47.619 0.00 0.00 0.00 3.16
42 43 1.597663 CGCCGTTTGAGAGAAAGTTGT 59.402 47.619 0.00 0.00 0.00 3.32
43 44 2.798283 CGCCGTTTGAGAGAAAGTTGTA 59.202 45.455 0.00 0.00 0.00 2.41
44 45 3.432252 CGCCGTTTGAGAGAAAGTTGTAT 59.568 43.478 0.00 0.00 0.00 2.29
45 46 4.666655 CGCCGTTTGAGAGAAAGTTGTATG 60.667 45.833 0.00 0.00 0.00 2.39
46 47 4.712763 CCGTTTGAGAGAAAGTTGTATGC 58.287 43.478 0.00 0.00 0.00 3.14
47 48 4.213270 CCGTTTGAGAGAAAGTTGTATGCA 59.787 41.667 0.00 0.00 0.00 3.96
48 49 5.106555 CCGTTTGAGAGAAAGTTGTATGCAT 60.107 40.000 3.79 3.79 0.00 3.96
49 50 6.092122 CCGTTTGAGAGAAAGTTGTATGCATA 59.908 38.462 1.16 1.16 0.00 3.14
50 51 7.201644 CCGTTTGAGAGAAAGTTGTATGCATAT 60.202 37.037 10.16 0.00 0.00 1.78
51 52 8.177663 CGTTTGAGAGAAAGTTGTATGCATATT 58.822 33.333 10.16 0.00 0.00 1.28
52 53 9.846248 GTTTGAGAGAAAGTTGTATGCATATTT 57.154 29.630 10.16 6.22 0.00 1.40
55 56 9.453572 TGAGAGAAAGTTGTATGCATATTTTCT 57.546 29.630 23.59 23.59 34.56 2.52
91 92 9.712305 ATAATACATAAAGTCCTTGGATCTTCG 57.288 33.333 0.00 0.00 0.00 3.79
92 93 4.192317 ACATAAAGTCCTTGGATCTTCGC 58.808 43.478 0.00 0.00 0.00 4.70
93 94 2.115343 AAAGTCCTTGGATCTTCGCC 57.885 50.000 0.00 0.00 0.00 5.54
94 95 1.280457 AAGTCCTTGGATCTTCGCCT 58.720 50.000 0.00 0.00 0.00 5.52
95 96 0.827368 AGTCCTTGGATCTTCGCCTC 59.173 55.000 0.00 0.00 0.00 4.70
96 97 0.827368 GTCCTTGGATCTTCGCCTCT 59.173 55.000 0.00 0.00 0.00 3.69
97 98 0.826715 TCCTTGGATCTTCGCCTCTG 59.173 55.000 0.00 0.00 0.00 3.35
98 99 0.539051 CCTTGGATCTTCGCCTCTGT 59.461 55.000 0.00 0.00 0.00 3.41
99 100 1.472376 CCTTGGATCTTCGCCTCTGTC 60.472 57.143 0.00 0.00 0.00 3.51
100 101 1.480137 CTTGGATCTTCGCCTCTGTCT 59.520 52.381 0.00 0.00 0.00 3.41
101 102 0.820226 TGGATCTTCGCCTCTGTCTG 59.180 55.000 0.00 0.00 0.00 3.51
102 103 1.107114 GGATCTTCGCCTCTGTCTGA 58.893 55.000 0.00 0.00 0.00 3.27
103 104 1.478510 GGATCTTCGCCTCTGTCTGAA 59.521 52.381 0.00 0.00 0.00 3.02
104 105 2.093973 GGATCTTCGCCTCTGTCTGAAA 60.094 50.000 0.00 0.00 0.00 2.69
105 106 3.589988 GATCTTCGCCTCTGTCTGAAAA 58.410 45.455 0.00 0.00 0.00 2.29
106 107 3.469008 TCTTCGCCTCTGTCTGAAAAA 57.531 42.857 0.00 0.00 0.00 1.94
107 108 4.008074 TCTTCGCCTCTGTCTGAAAAAT 57.992 40.909 0.00 0.00 0.00 1.82
108 109 5.147330 TCTTCGCCTCTGTCTGAAAAATA 57.853 39.130 0.00 0.00 0.00 1.40
109 110 5.734720 TCTTCGCCTCTGTCTGAAAAATAT 58.265 37.500 0.00 0.00 0.00 1.28
110 111 6.173339 TCTTCGCCTCTGTCTGAAAAATATT 58.827 36.000 0.00 0.00 0.00 1.28
111 112 6.655003 TCTTCGCCTCTGTCTGAAAAATATTT 59.345 34.615 0.00 0.00 0.00 1.40
112 113 7.822334 TCTTCGCCTCTGTCTGAAAAATATTTA 59.178 33.333 0.01 0.00 0.00 1.40
113 114 7.915293 TCGCCTCTGTCTGAAAAATATTTAA 57.085 32.000 0.01 0.00 0.00 1.52
114 115 8.330466 TCGCCTCTGTCTGAAAAATATTTAAA 57.670 30.769 0.01 0.00 0.00 1.52
115 116 8.788806 TCGCCTCTGTCTGAAAAATATTTAAAA 58.211 29.630 0.01 0.00 0.00 1.52
116 117 9.405587 CGCCTCTGTCTGAAAAATATTTAAAAA 57.594 29.630 0.01 0.00 0.00 1.94
177 178 5.649782 AAAAATCCACAACAGCCTATCAG 57.350 39.130 0.00 0.00 0.00 2.90
178 179 2.338577 ATCCACAACAGCCTATCAGC 57.661 50.000 0.00 0.00 0.00 4.26
179 180 0.108186 TCCACAACAGCCTATCAGCG 60.108 55.000 0.00 0.00 38.01 5.18
180 181 0.108186 CCACAACAGCCTATCAGCGA 60.108 55.000 0.00 0.00 38.01 4.93
181 182 1.284657 CACAACAGCCTATCAGCGAG 58.715 55.000 0.00 0.00 38.01 5.03
182 183 0.898320 ACAACAGCCTATCAGCGAGT 59.102 50.000 0.00 0.00 38.01 4.18
183 184 1.284657 CAACAGCCTATCAGCGAGTG 58.715 55.000 0.00 0.00 38.01 3.51
184 185 0.460987 AACAGCCTATCAGCGAGTGC 60.461 55.000 0.00 0.00 43.24 4.40
185 186 1.593750 CAGCCTATCAGCGAGTGCC 60.594 63.158 0.00 0.00 44.31 5.01
186 187 2.060383 AGCCTATCAGCGAGTGCCA 61.060 57.895 0.00 0.00 44.31 4.92
187 188 1.884926 GCCTATCAGCGAGTGCCAC 60.885 63.158 0.00 0.00 44.31 5.01
188 189 1.819229 CCTATCAGCGAGTGCCACT 59.181 57.895 0.00 0.00 44.31 4.00
189 190 0.176680 CCTATCAGCGAGTGCCACTT 59.823 55.000 0.00 0.00 44.31 3.16
190 191 1.406069 CCTATCAGCGAGTGCCACTTT 60.406 52.381 0.00 0.00 44.31 2.66
191 192 1.662629 CTATCAGCGAGTGCCACTTTG 59.337 52.381 0.00 0.00 44.31 2.77
192 193 1.580845 ATCAGCGAGTGCCACTTTGC 61.581 55.000 13.31 13.31 44.31 3.68
193 194 2.203195 AGCGAGTGCCACTTTGCA 60.203 55.556 20.52 0.41 44.31 4.08
194 195 1.601759 AGCGAGTGCCACTTTGCAT 60.602 52.632 20.52 7.23 44.30 3.96
195 196 0.321564 AGCGAGTGCCACTTTGCATA 60.322 50.000 20.52 0.00 44.30 3.14
196 197 0.521291 GCGAGTGCCACTTTGCATAA 59.479 50.000 15.52 0.00 44.30 1.90
197 198 1.729149 GCGAGTGCCACTTTGCATAAC 60.729 52.381 15.52 0.00 44.30 1.89
198 199 1.135689 CGAGTGCCACTTTGCATAACC 60.136 52.381 0.00 0.00 44.30 2.85
199 200 1.202348 GAGTGCCACTTTGCATAACCC 59.798 52.381 0.00 0.00 44.30 4.11
200 201 1.203050 AGTGCCACTTTGCATAACCCT 60.203 47.619 0.00 0.00 44.30 4.34
201 202 1.618343 GTGCCACTTTGCATAACCCTT 59.382 47.619 0.00 0.00 44.30 3.95
202 203 1.892474 TGCCACTTTGCATAACCCTTC 59.108 47.619 0.00 0.00 36.04 3.46
203 204 1.892474 GCCACTTTGCATAACCCTTCA 59.108 47.619 0.00 0.00 0.00 3.02
204 205 2.497273 GCCACTTTGCATAACCCTTCAT 59.503 45.455 0.00 0.00 0.00 2.57
205 206 3.055891 GCCACTTTGCATAACCCTTCATT 60.056 43.478 0.00 0.00 0.00 2.57
206 207 4.563374 GCCACTTTGCATAACCCTTCATTT 60.563 41.667 0.00 0.00 0.00 2.32
207 208 5.337169 GCCACTTTGCATAACCCTTCATTTA 60.337 40.000 0.00 0.00 0.00 1.40
208 209 6.696411 CCACTTTGCATAACCCTTCATTTAA 58.304 36.000 0.00 0.00 0.00 1.52
209 210 7.158021 CCACTTTGCATAACCCTTCATTTAAA 58.842 34.615 0.00 0.00 0.00 1.52
210 211 7.659390 CCACTTTGCATAACCCTTCATTTAAAA 59.341 33.333 0.00 0.00 0.00 1.52
211 212 9.050601 CACTTTGCATAACCCTTCATTTAAAAA 57.949 29.630 0.00 0.00 0.00 1.94
271 272 9.829507 ACATTTGAAAAATAATCCACACTTTCA 57.170 25.926 0.00 0.00 32.51 2.69
302 303 7.637709 AAAATAACAAAAGATTTCTCACCGC 57.362 32.000 0.00 0.00 0.00 5.68
303 304 2.969443 ACAAAAGATTTCTCACCGCG 57.031 45.000 0.00 0.00 0.00 6.46
304 305 1.535462 ACAAAAGATTTCTCACCGCGG 59.465 47.619 26.86 26.86 0.00 6.46
305 306 0.521735 AAAAGATTTCTCACCGCGGC 59.478 50.000 28.58 5.95 0.00 6.53
306 307 1.305930 AAAGATTTCTCACCGCGGCC 61.306 55.000 28.58 4.16 0.00 6.13
307 308 2.435938 GATTTCTCACCGCGGCCA 60.436 61.111 28.58 11.32 0.00 5.36
308 309 2.033448 ATTTCTCACCGCGGCCAA 59.967 55.556 28.58 11.39 0.00 4.52
309 310 2.253414 GATTTCTCACCGCGGCCAAC 62.253 60.000 28.58 5.00 0.00 3.77
322 323 4.347453 CCAACCAGCTTGCGCCAC 62.347 66.667 4.18 0.00 36.60 5.01
323 324 3.594775 CAACCAGCTTGCGCCACA 61.595 61.111 4.18 0.00 36.60 4.17
324 325 2.598394 AACCAGCTTGCGCCACAT 60.598 55.556 4.18 0.00 36.60 3.21
325 326 2.922950 AACCAGCTTGCGCCACATG 61.923 57.895 4.18 0.00 36.60 3.21
326 327 4.124351 CCAGCTTGCGCCACATGG 62.124 66.667 4.18 4.49 36.60 3.66
327 328 4.124351 CAGCTTGCGCCACATGGG 62.124 66.667 4.18 0.00 40.85 4.00
328 329 4.349503 AGCTTGCGCCACATGGGA 62.350 61.111 4.18 0.00 40.01 4.37
329 330 3.142838 GCTTGCGCCACATGGGAT 61.143 61.111 4.18 0.00 40.01 3.85
330 331 1.823470 GCTTGCGCCACATGGGATA 60.823 57.895 4.18 0.00 40.01 2.59
331 332 1.789078 GCTTGCGCCACATGGGATAG 61.789 60.000 4.18 0.00 40.01 2.08
332 333 1.789078 CTTGCGCCACATGGGATAGC 61.789 60.000 4.18 0.00 40.01 2.97
333 334 2.111878 GCGCCACATGGGATAGCT 59.888 61.111 0.00 0.00 40.01 3.32
334 335 2.256591 GCGCCACATGGGATAGCTG 61.257 63.158 0.00 0.00 40.01 4.24
335 336 1.598962 CGCCACATGGGATAGCTGG 60.599 63.158 0.00 0.00 40.01 4.85
336 337 1.533711 GCCACATGGGATAGCTGGT 59.466 57.895 0.00 0.00 40.01 4.00
337 338 0.106519 GCCACATGGGATAGCTGGTT 60.107 55.000 0.00 0.00 40.01 3.67
338 339 1.683943 CCACATGGGATAGCTGGTTG 58.316 55.000 0.00 0.00 40.01 3.77
339 340 1.683943 CACATGGGATAGCTGGTTGG 58.316 55.000 0.00 0.00 0.00 3.77
340 341 0.106519 ACATGGGATAGCTGGTTGGC 60.107 55.000 0.00 0.00 0.00 4.52
341 342 0.825010 CATGGGATAGCTGGTTGGCC 60.825 60.000 0.00 0.00 0.00 5.36
342 343 2.203209 GGGATAGCTGGTTGGCCG 60.203 66.667 0.00 0.00 37.67 6.13
343 344 2.902343 GGATAGCTGGTTGGCCGC 60.902 66.667 0.00 0.00 37.67 6.53
344 345 2.902343 GATAGCTGGTTGGCCGCC 60.902 66.667 1.04 1.04 37.67 6.13
345 346 4.506255 ATAGCTGGTTGGCCGCCC 62.506 66.667 7.03 8.51 37.67 6.13
349 350 4.659172 CTGGTTGGCCGCCCTTCA 62.659 66.667 7.03 1.26 37.67 3.02
350 351 3.944250 CTGGTTGGCCGCCCTTCAT 62.944 63.158 7.03 0.00 37.67 2.57
351 352 3.451894 GGTTGGCCGCCCTTCATG 61.452 66.667 7.03 0.00 0.00 3.07
352 353 3.451894 GTTGGCCGCCCTTCATGG 61.452 66.667 7.03 0.00 0.00 3.66
367 368 6.966534 CCTTCATGGGTAGCTTAATGATTT 57.033 37.500 0.00 0.00 0.00 2.17
368 369 7.352079 CCTTCATGGGTAGCTTAATGATTTT 57.648 36.000 0.00 0.00 0.00 1.82
369 370 8.463930 CCTTCATGGGTAGCTTAATGATTTTA 57.536 34.615 0.00 0.00 0.00 1.52
370 371 8.912988 CCTTCATGGGTAGCTTAATGATTTTAA 58.087 33.333 0.00 0.00 0.00 1.52
388 389 9.610705 TGATTTTAATTTGATGGAGAGAGAGAG 57.389 33.333 0.00 0.00 0.00 3.20
389 390 9.829507 GATTTTAATTTGATGGAGAGAGAGAGA 57.170 33.333 0.00 0.00 0.00 3.10
390 391 9.835389 ATTTTAATTTGATGGAGAGAGAGAGAG 57.165 33.333 0.00 0.00 0.00 3.20
391 392 4.942761 ATTTGATGGAGAGAGAGAGAGC 57.057 45.455 0.00 0.00 0.00 4.09
392 393 1.965935 TGATGGAGAGAGAGAGAGCG 58.034 55.000 0.00 0.00 0.00 5.03
393 394 0.593128 GATGGAGAGAGAGAGAGCGC 59.407 60.000 0.00 0.00 0.00 5.92
394 395 1.165907 ATGGAGAGAGAGAGAGCGCG 61.166 60.000 0.00 0.00 0.00 6.86
395 396 1.817941 GGAGAGAGAGAGAGCGCGT 60.818 63.158 8.43 0.00 0.00 6.01
396 397 1.351707 GAGAGAGAGAGAGCGCGTG 59.648 63.158 8.43 0.00 0.00 5.34
397 398 2.047151 GAGAGAGAGAGAGCGCGTGG 62.047 65.000 8.43 0.00 0.00 4.94
398 399 2.045829 AGAGAGAGAGCGCGTGGA 60.046 61.111 8.43 0.00 0.00 4.02
399 400 2.047151 GAGAGAGAGAGCGCGTGGAG 62.047 65.000 8.43 0.00 0.00 3.86
400 401 2.360600 AGAGAGAGCGCGTGGAGT 60.361 61.111 8.43 0.00 0.00 3.85
401 402 2.101380 GAGAGAGCGCGTGGAGTC 59.899 66.667 8.43 0.00 0.00 3.36
402 403 3.404141 GAGAGAGCGCGTGGAGTCC 62.404 68.421 8.43 0.73 0.00 3.85
403 404 3.749064 GAGAGCGCGTGGAGTCCA 61.749 66.667 8.12 8.12 0.00 4.02
419 420 1.096416 TCCACACCACCGTTTCAAAC 58.904 50.000 0.00 0.00 0.00 2.93
448 449 6.347160 GCTTTGATGAATTGGCAGAAAGAAAC 60.347 38.462 0.00 0.00 0.00 2.78
476 477 0.606604 TGTAGAACCTTCAGCCGGAC 59.393 55.000 5.05 0.00 0.00 4.79
498 499 3.570912 TTTCGTCAGAGGGGAACTTTT 57.429 42.857 0.00 0.00 0.00 2.27
506 507 3.753797 CAGAGGGGAACTTTTAGTTGCTC 59.246 47.826 10.24 6.90 45.97 4.26
513 514 6.231951 GGGAACTTTTAGTTGCTCTAGAACT 58.768 40.000 10.24 0.00 44.59 3.01
540 541 8.487176 GGCAACAAAAATACAGTAATTCAAGTG 58.513 33.333 0.00 0.00 0.00 3.16
553 554 8.135529 CAGTAATTCAAGTGTCGAGTATGGATA 58.864 37.037 0.00 0.00 0.00 2.59
558 559 8.420374 TTCAAGTGTCGAGTATGGATATTTTC 57.580 34.615 0.00 0.00 0.00 2.29
604 606 4.688879 CCTTTTCTTTTGCGGGTTAAATCC 59.311 41.667 0.00 0.00 0.00 3.01
656 658 5.355071 TGTCCATGCAGAAATCATCTTGTAC 59.645 40.000 0.00 0.00 35.73 2.90
657 659 5.587844 GTCCATGCAGAAATCATCTTGTACT 59.412 40.000 0.00 0.00 35.73 2.73
658 660 6.763135 GTCCATGCAGAAATCATCTTGTACTA 59.237 38.462 0.00 0.00 35.73 1.82
659 661 7.443575 GTCCATGCAGAAATCATCTTGTACTAT 59.556 37.037 0.00 0.00 35.73 2.12
660 662 8.650490 TCCATGCAGAAATCATCTTGTACTATA 58.350 33.333 0.00 0.00 35.73 1.31
661 663 8.715998 CCATGCAGAAATCATCTTGTACTATAC 58.284 37.037 0.00 0.00 35.73 1.47
674 676 8.092521 TCTTGTACTATACTAGATTACACGCC 57.907 38.462 0.00 0.00 36.02 5.68
684 686 4.380841 AGATTACACGCCGAAATCTGTA 57.619 40.909 11.30 0.00 38.28 2.74
687 689 6.509656 AGATTACACGCCGAAATCTGTAATA 58.490 36.000 9.22 0.00 39.05 0.98
688 690 6.982141 AGATTACACGCCGAAATCTGTAATAA 59.018 34.615 9.22 0.00 39.05 1.40
689 691 7.656137 AGATTACACGCCGAAATCTGTAATAAT 59.344 33.333 9.22 1.46 39.05 1.28
742 745 5.705441 AGATTGCGAACAAACATTAGGAGAA 59.295 36.000 0.00 0.00 39.77 2.87
926 942 0.400213 AATTGTTCCTGCGTCTCCCA 59.600 50.000 0.00 0.00 0.00 4.37
989 1016 1.658686 GCCGAGCGAGGAGAAGAGAA 61.659 60.000 4.64 0.00 0.00 2.87
994 1021 3.214328 GAGCGAGGAGAAGAGAAGAGAT 58.786 50.000 0.00 0.00 0.00 2.75
995 1022 3.214328 AGCGAGGAGAAGAGAAGAGATC 58.786 50.000 0.00 0.00 0.00 2.75
996 1023 2.032030 GCGAGGAGAAGAGAAGAGATCG 60.032 54.545 0.00 0.00 0.00 3.69
1096 1128 4.379243 CGGACAACCTGCTCCGCT 62.379 66.667 0.00 0.00 42.86 5.52
1202 1234 0.233848 CGTGCGTACCAACCAAACTC 59.766 55.000 0.00 0.00 0.00 3.01
1203 1235 0.589708 GTGCGTACCAACCAAACTCC 59.410 55.000 0.00 0.00 0.00 3.85
1204 1236 0.470766 TGCGTACCAACCAAACTCCT 59.529 50.000 0.00 0.00 0.00 3.69
1205 1237 1.134037 TGCGTACCAACCAAACTCCTT 60.134 47.619 0.00 0.00 0.00 3.36
1232 1267 1.289530 CTTCCTCCCTAGTCCTCCTGT 59.710 57.143 0.00 0.00 0.00 4.00
1253 1288 1.076332 CTTGCTACTGTACCGCAACC 58.924 55.000 9.59 0.00 38.59 3.77
1297 1336 3.533606 TGCTGCTCCTGATCTTAGTTC 57.466 47.619 0.00 0.00 0.00 3.01
1385 1424 2.112815 GGGTAGCGGTTGCCATGAC 61.113 63.158 9.55 0.00 44.31 3.06
1407 1446 4.157817 ACGCGTATGTTCGTGGTC 57.842 55.556 11.67 0.00 44.13 4.02
1458 1498 5.659440 TGGAATTAATTGGTCTGCCTTTC 57.341 39.130 5.17 0.00 35.27 2.62
1473 1513 0.460284 CTTTCGCTGTACCGGAGCAT 60.460 55.000 9.46 0.00 36.12 3.79
1475 1515 0.818938 TTCGCTGTACCGGAGCATAA 59.181 50.000 9.46 1.06 36.12 1.90
1478 1518 1.287425 GCTGTACCGGAGCATAACAC 58.713 55.000 9.46 0.00 36.40 3.32
1642 1730 0.818040 GGTTTGCCGAACTGACCACT 60.818 55.000 0.00 0.00 38.35 4.00
1648 1736 0.811915 CCGAACTGACCACTCGATCT 59.188 55.000 0.00 0.00 34.52 2.75
1649 1737 2.014857 CCGAACTGACCACTCGATCTA 58.985 52.381 0.00 0.00 34.52 1.98
1682 1770 9.004717 GGATCTAACCATTTCTTATTAAGCTCC 57.995 37.037 0.00 0.00 0.00 4.70
1704 1792 3.713288 GGGTCTAACCTGTTTGTTTTGC 58.287 45.455 0.00 0.00 38.64 3.68
1740 1828 8.522830 ACCTGGATGAACAATAGTAATTTGTTG 58.477 33.333 0.00 0.00 44.90 3.33
1754 1842 0.935898 TTGTTGGCGCTTGCAAATTG 59.064 45.000 7.64 0.00 41.71 2.32
1755 1843 0.179089 TGTTGGCGCTTGCAAATTGT 60.179 45.000 7.64 0.00 41.71 2.71
1757 1845 2.131183 GTTGGCGCTTGCAAATTGTAA 58.869 42.857 7.64 0.00 41.71 2.41
1759 1847 2.335752 TGGCGCTTGCAAATTGTAATG 58.664 42.857 7.64 0.00 41.71 1.90
1792 1880 5.703130 GGGATCATAGGATTTGCTACACTTC 59.297 44.000 0.00 0.00 32.67 3.01
1811 1899 6.772716 ACACTTCCAATTTAAGCTTCAGAGAA 59.227 34.615 0.00 0.00 0.00 2.87
1820 1908 1.689273 AGCTTCAGAGAACCGTTCTGT 59.311 47.619 18.59 11.81 42.11 3.41
1822 1910 2.678324 CTTCAGAGAACCGTTCTGTCC 58.322 52.381 18.59 4.55 42.11 4.02
1834 1922 2.433436 GTTCTGTCCGCCAATAGGTTT 58.567 47.619 0.00 0.00 37.19 3.27
1835 1923 2.396590 TCTGTCCGCCAATAGGTTTC 57.603 50.000 0.00 0.00 37.19 2.78
1868 2225 6.488344 TCTTAATGCACAACAGTTATGTTCCA 59.512 34.615 0.00 0.00 46.90 3.53
1869 2226 5.528043 AATGCACAACAGTTATGTTCCAA 57.472 34.783 0.00 0.00 46.90 3.53
1878 2235 8.137437 ACAACAGTTATGTTCCAAAGAATCAAG 58.863 33.333 0.00 0.00 46.90 3.02
1898 2255 6.393171 TCAAGATACTCTATCCATCATTGCG 58.607 40.000 0.00 0.00 35.79 4.85
1899 2256 5.336150 AGATACTCTATCCATCATTGCGG 57.664 43.478 0.00 0.00 35.79 5.69
1901 2258 1.696336 ACTCTATCCATCATTGCGGCT 59.304 47.619 0.00 0.00 0.00 5.52
1907 2281 3.213206 TCCATCATTGCGGCTTAGATT 57.787 42.857 0.00 0.00 0.00 2.40
1917 2291 6.935741 TTGCGGCTTAGATTATGTTACATT 57.064 33.333 2.23 0.00 0.00 2.71
1919 2293 7.328277 TGCGGCTTAGATTATGTTACATTTT 57.672 32.000 2.23 0.00 0.00 1.82
1920 2294 7.767261 TGCGGCTTAGATTATGTTACATTTTT 58.233 30.769 2.23 0.00 0.00 1.94
1958 2354 6.472680 CGATAAATATGGACGCATCAATGAG 58.527 40.000 0.00 0.00 0.00 2.90
1959 2355 6.091305 CGATAAATATGGACGCATCAATGAGT 59.909 38.462 0.00 0.00 43.51 3.41
1960 2356 7.275560 CGATAAATATGGACGCATCAATGAGTA 59.724 37.037 0.00 0.00 40.91 2.59
1973 2373 8.276325 CGCATCAATGAGTAAACTAGTTATTCC 58.724 37.037 8.92 0.14 29.47 3.01
2041 2441 5.278414 CCTTGTTCATGCAGTTTACATGTGA 60.278 40.000 9.11 0.00 44.26 3.58
2052 2452 6.595716 GCAGTTTACATGTGAAAGATCCTAGT 59.404 38.462 9.11 0.00 0.00 2.57
2053 2453 7.413438 GCAGTTTACATGTGAAAGATCCTAGTG 60.413 40.741 9.11 0.00 0.00 2.74
2072 2472 3.483808 TGTGCTCACACCTTGTATCAA 57.516 42.857 0.00 0.00 46.86 2.57
2073 2473 3.138304 TGTGCTCACACCTTGTATCAAC 58.862 45.455 0.00 0.00 46.86 3.18
2074 2474 2.157668 GTGCTCACACCTTGTATCAACG 59.842 50.000 0.00 0.00 41.21 4.10
2274 2682 5.608437 ACCACTCCAGACCATAATGTATCAT 59.392 40.000 0.00 0.00 0.00 2.45
2278 2686 8.534496 CACTCCAGACCATAATGTATCATCATA 58.466 37.037 0.00 0.00 0.00 2.15
2279 2687 8.535335 ACTCCAGACCATAATGTATCATCATAC 58.465 37.037 0.00 0.00 36.18 2.39
2300 2708 4.437239 ACATGATCTCCTCGACACATTTC 58.563 43.478 0.00 0.00 0.00 2.17
2307 2715 4.466370 TCTCCTCGACACATTTCCTGTAAT 59.534 41.667 0.00 0.00 35.91 1.89
2310 2718 6.703319 TCCTCGACACATTTCCTGTAATAAA 58.297 36.000 0.00 0.00 35.91 1.40
2328 2736 8.428536 TGTAATAAAATTCCGCGTTTTCATTTG 58.571 29.630 4.92 0.00 31.71 2.32
2332 2740 1.218763 TCCGCGTTTTCATTTGTCGA 58.781 45.000 4.92 0.00 0.00 4.20
2338 2746 3.541711 CGTTTTCATTTGTCGACAGGTC 58.458 45.455 19.11 4.32 0.00 3.85
2339 2747 3.247648 CGTTTTCATTTGTCGACAGGTCT 59.752 43.478 19.11 1.96 0.00 3.85
2350 2758 0.391597 GACAGGTCTCCGTGGTTTCA 59.608 55.000 0.00 0.00 0.00 2.69
2484 2893 2.325082 CGGCCAAACGACCTCCAAG 61.325 63.158 2.24 0.00 35.47 3.61
2493 2902 1.968493 ACGACCTCCAAGCTGTTCTTA 59.032 47.619 0.00 0.00 32.74 2.10
2541 2950 9.053840 CATCATAATAGAGTGCTGATCTTTTGT 57.946 33.333 0.00 0.00 0.00 2.83
2608 3017 4.684134 AACAATGCCGCCTGCCCT 62.684 61.111 0.00 0.00 40.16 5.19
2652 3061 3.713248 AGTAACCATGCCTGATCTCATCA 59.287 43.478 0.00 0.00 37.76 3.07
2664 3073 3.811497 TGATCTCATCATCGCAAATGTCC 59.189 43.478 0.00 0.00 33.59 4.02
2684 3093 3.701542 TCCACATGTGTTTTAGTTTGCCA 59.298 39.130 23.79 0.00 0.00 4.92
2778 3187 1.409241 CCTGTGGATGATTCCCAGGTG 60.409 57.143 15.73 0.20 45.83 4.00
2847 3256 8.981659 TGCTTATCTTCAGCCTAGCTTTTGCT 62.982 42.308 0.00 0.00 46.89 3.91
2888 3310 4.111198 TGCTGTTTGTTGCATACAGTTTG 58.889 39.130 16.65 0.00 42.46 2.93
2984 3460 3.622612 TCACATTACGGTTGCATCTGATG 59.377 43.478 13.26 13.26 0.00 3.07
3013 3490 7.046652 CAGTGGATCATGATGATAATCCTACC 58.953 42.308 14.30 4.38 37.20 3.18
3091 4095 1.670674 GCCACAAACACATGCATCCAG 60.671 52.381 0.00 0.00 0.00 3.86
3106 4110 6.942532 TGCATCCAGGTTAAAAGTGATATC 57.057 37.500 0.00 0.00 0.00 1.63
3179 4183 5.645056 TGGAGCTAAATCCCATTGTCATA 57.355 39.130 0.00 0.00 38.72 2.15
3192 4196 4.517285 CATTGTCATAACACCCTACAGCT 58.483 43.478 0.00 0.00 34.35 4.24
3220 4247 0.028770 CTGCGAAAAGTCACGGCAAA 59.971 50.000 0.00 0.00 0.00 3.68
3224 4259 2.350007 GCGAAAAGTCACGGCAAACATA 60.350 45.455 0.00 0.00 0.00 2.29
3273 4308 1.134098 CATCCACCACCACCAGGATAC 60.134 57.143 0.00 0.00 38.77 2.24
3291 4326 2.969821 ACCAAAATGTACAGCAGGGA 57.030 45.000 0.33 0.00 0.00 4.20
3454 4489 2.131972 CGAGTGGTCGTTCATGAACAA 58.868 47.619 32.06 16.85 41.57 2.83
3521 4556 2.932614 CGACAGGAAGATGCTTTCGATT 59.067 45.455 1.87 0.00 39.79 3.34
3602 4637 0.400525 CCCCCTTCATAGGCCTCTGA 60.401 60.000 16.47 16.47 40.50 3.27
3635 4670 2.649531 ATGTGACCGGGAAAAGAACA 57.350 45.000 6.32 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.787012 TTCTCTCAAACGGCGTAACC 58.213 50.000 15.20 0.00 0.00 2.85
18 19 2.798847 ACTTTCTCTCAAACGGCGTAAC 59.201 45.455 15.20 0.00 0.00 2.50
19 20 3.102052 ACTTTCTCTCAAACGGCGTAA 57.898 42.857 15.20 0.00 0.00 3.18
20 21 2.798283 CAACTTTCTCTCAAACGGCGTA 59.202 45.455 15.20 0.00 0.00 4.42
21 22 1.597663 CAACTTTCTCTCAAACGGCGT 59.402 47.619 6.77 6.77 0.00 5.68
22 23 1.597663 ACAACTTTCTCTCAAACGGCG 59.402 47.619 4.80 4.80 0.00 6.46
23 24 4.712763 CATACAACTTTCTCTCAAACGGC 58.287 43.478 0.00 0.00 0.00 5.68
24 25 4.213270 TGCATACAACTTTCTCTCAAACGG 59.787 41.667 0.00 0.00 0.00 4.44
25 26 5.342806 TGCATACAACTTTCTCTCAAACG 57.657 39.130 0.00 0.00 0.00 3.60
26 27 9.846248 AAATATGCATACAACTTTCTCTCAAAC 57.154 29.630 8.99 0.00 0.00 2.93
29 30 9.453572 AGAAAATATGCATACAACTTTCTCTCA 57.546 29.630 19.41 0.00 31.54 3.27
65 66 9.712305 CGAAGATCCAAGGACTTTATGTATTAT 57.288 33.333 0.00 0.00 0.00 1.28
66 67 7.656137 GCGAAGATCCAAGGACTTTATGTATTA 59.344 37.037 0.00 0.00 0.00 0.98
67 68 6.483640 GCGAAGATCCAAGGACTTTATGTATT 59.516 38.462 0.00 0.00 0.00 1.89
68 69 5.992217 GCGAAGATCCAAGGACTTTATGTAT 59.008 40.000 0.00 0.00 0.00 2.29
69 70 5.357257 GCGAAGATCCAAGGACTTTATGTA 58.643 41.667 0.00 0.00 0.00 2.29
70 71 4.192317 GCGAAGATCCAAGGACTTTATGT 58.808 43.478 0.00 0.00 0.00 2.29
71 72 3.561725 GGCGAAGATCCAAGGACTTTATG 59.438 47.826 0.00 0.00 0.00 1.90
72 73 3.456277 AGGCGAAGATCCAAGGACTTTAT 59.544 43.478 0.00 0.00 0.00 1.40
73 74 2.838202 AGGCGAAGATCCAAGGACTTTA 59.162 45.455 0.00 0.00 0.00 1.85
74 75 1.630878 AGGCGAAGATCCAAGGACTTT 59.369 47.619 0.00 0.00 0.00 2.66
75 76 1.208293 GAGGCGAAGATCCAAGGACTT 59.792 52.381 0.00 0.00 0.00 3.01
76 77 0.827368 GAGGCGAAGATCCAAGGACT 59.173 55.000 0.00 0.00 0.00 3.85
77 78 0.827368 AGAGGCGAAGATCCAAGGAC 59.173 55.000 0.00 0.00 0.00 3.85
78 79 0.826715 CAGAGGCGAAGATCCAAGGA 59.173 55.000 0.00 0.00 0.00 3.36
79 80 0.539051 ACAGAGGCGAAGATCCAAGG 59.461 55.000 0.00 0.00 0.00 3.61
80 81 1.480137 AGACAGAGGCGAAGATCCAAG 59.520 52.381 0.00 0.00 0.00 3.61
81 82 1.205655 CAGACAGAGGCGAAGATCCAA 59.794 52.381 0.00 0.00 0.00 3.53
82 83 0.820226 CAGACAGAGGCGAAGATCCA 59.180 55.000 0.00 0.00 0.00 3.41
83 84 1.107114 TCAGACAGAGGCGAAGATCC 58.893 55.000 0.00 0.00 0.00 3.36
84 85 2.949451 TTCAGACAGAGGCGAAGATC 57.051 50.000 0.00 0.00 0.00 2.75
85 86 3.685139 TTTTCAGACAGAGGCGAAGAT 57.315 42.857 0.00 0.00 0.00 2.40
86 87 3.469008 TTTTTCAGACAGAGGCGAAGA 57.531 42.857 0.00 0.00 0.00 2.87
87 88 6.428385 AATATTTTTCAGACAGAGGCGAAG 57.572 37.500 0.00 0.00 0.00 3.79
88 89 6.817765 AAATATTTTTCAGACAGAGGCGAA 57.182 33.333 0.00 0.00 0.00 4.70
89 90 7.915293 TTAAATATTTTTCAGACAGAGGCGA 57.085 32.000 5.91 0.00 0.00 5.54
90 91 8.964420 TTTTAAATATTTTTCAGACAGAGGCG 57.036 30.769 5.91 0.00 0.00 5.52
155 156 4.082026 GCTGATAGGCTGTTGTGGATTTTT 60.082 41.667 0.00 0.00 0.00 1.94
156 157 3.445096 GCTGATAGGCTGTTGTGGATTTT 59.555 43.478 0.00 0.00 0.00 1.82
157 158 3.019564 GCTGATAGGCTGTTGTGGATTT 58.980 45.455 0.00 0.00 0.00 2.17
158 159 2.648059 GCTGATAGGCTGTTGTGGATT 58.352 47.619 0.00 0.00 0.00 3.01
159 160 1.473965 CGCTGATAGGCTGTTGTGGAT 60.474 52.381 0.00 0.00 0.00 3.41
160 161 0.108186 CGCTGATAGGCTGTTGTGGA 60.108 55.000 0.00 0.00 0.00 4.02
161 162 0.108186 TCGCTGATAGGCTGTTGTGG 60.108 55.000 0.00 0.00 0.00 4.17
162 163 1.284657 CTCGCTGATAGGCTGTTGTG 58.715 55.000 0.00 0.00 0.00 3.33
163 164 0.898320 ACTCGCTGATAGGCTGTTGT 59.102 50.000 0.00 0.00 0.00 3.32
164 165 1.284657 CACTCGCTGATAGGCTGTTG 58.715 55.000 0.00 0.00 0.00 3.33
165 166 0.460987 GCACTCGCTGATAGGCTGTT 60.461 55.000 0.00 0.00 34.30 3.16
166 167 1.142748 GCACTCGCTGATAGGCTGT 59.857 57.895 0.00 0.00 34.30 4.40
167 168 1.593750 GGCACTCGCTGATAGGCTG 60.594 63.158 0.00 0.00 38.60 4.85
168 169 2.060383 TGGCACTCGCTGATAGGCT 61.060 57.895 0.00 0.00 38.60 4.58
169 170 1.884926 GTGGCACTCGCTGATAGGC 60.885 63.158 11.13 0.00 38.60 3.93
170 171 0.176680 AAGTGGCACTCGCTGATAGG 59.823 55.000 22.31 0.00 38.60 2.57
171 172 1.662629 CAAAGTGGCACTCGCTGATAG 59.337 52.381 22.31 1.23 38.60 2.08
172 173 1.725641 CAAAGTGGCACTCGCTGATA 58.274 50.000 22.31 0.00 38.60 2.15
173 174 1.580845 GCAAAGTGGCACTCGCTGAT 61.581 55.000 26.14 7.93 38.60 2.90
174 175 2.253758 GCAAAGTGGCACTCGCTGA 61.254 57.895 26.14 0.00 38.60 4.26
175 176 2.253452 GCAAAGTGGCACTCGCTG 59.747 61.111 26.14 21.11 38.60 5.18
176 177 2.203195 TGCAAAGTGGCACTCGCT 60.203 55.556 30.33 12.89 39.25 4.93
183 184 1.892474 TGAAGGGTTATGCAAAGTGGC 59.108 47.619 0.00 0.00 0.00 5.01
184 185 4.806640 AATGAAGGGTTATGCAAAGTGG 57.193 40.909 0.00 0.00 0.00 4.00
185 186 8.600449 TTTTAAATGAAGGGTTATGCAAAGTG 57.400 30.769 0.00 0.00 0.00 3.16
245 246 9.829507 TGAAAGTGTGGATTATTTTTCAAATGT 57.170 25.926 0.00 0.00 33.20 2.71
277 278 7.096230 CGCGGTGAGAAATCTTTTGTTATTTTT 60.096 33.333 0.00 0.00 0.00 1.94
278 279 6.362283 CGCGGTGAGAAATCTTTTGTTATTTT 59.638 34.615 0.00 0.00 0.00 1.82
279 280 5.856455 CGCGGTGAGAAATCTTTTGTTATTT 59.144 36.000 0.00 0.00 0.00 1.40
280 281 5.390613 CGCGGTGAGAAATCTTTTGTTATT 58.609 37.500 0.00 0.00 0.00 1.40
281 282 4.142687 CCGCGGTGAGAAATCTTTTGTTAT 60.143 41.667 19.50 0.00 0.00 1.89
282 283 3.187637 CCGCGGTGAGAAATCTTTTGTTA 59.812 43.478 19.50 0.00 0.00 2.41
283 284 2.031157 CCGCGGTGAGAAATCTTTTGTT 60.031 45.455 19.50 0.00 0.00 2.83
284 285 1.535462 CCGCGGTGAGAAATCTTTTGT 59.465 47.619 19.50 0.00 0.00 2.83
285 286 1.729149 GCCGCGGTGAGAAATCTTTTG 60.729 52.381 28.70 0.00 0.00 2.44
286 287 0.521735 GCCGCGGTGAGAAATCTTTT 59.478 50.000 28.70 0.00 0.00 2.27
287 288 1.305930 GGCCGCGGTGAGAAATCTTT 61.306 55.000 28.70 0.00 0.00 2.52
288 289 1.745489 GGCCGCGGTGAGAAATCTT 60.745 57.895 28.70 0.00 0.00 2.40
289 290 2.125106 GGCCGCGGTGAGAAATCT 60.125 61.111 28.70 0.00 0.00 2.40
290 291 2.038269 TTGGCCGCGGTGAGAAATC 61.038 57.895 28.70 6.82 0.00 2.17
291 292 2.033448 TTGGCCGCGGTGAGAAAT 59.967 55.556 28.70 0.00 0.00 2.17
292 293 2.975799 GTTGGCCGCGGTGAGAAA 60.976 61.111 28.70 11.29 0.00 2.52
313 314 1.789078 GCTATCCCATGTGGCGCAAG 61.789 60.000 10.83 0.00 43.44 4.01
314 315 1.823470 GCTATCCCATGTGGCGCAA 60.823 57.895 10.83 0.00 0.00 4.85
315 316 2.203195 GCTATCCCATGTGGCGCA 60.203 61.111 10.83 1.92 0.00 6.09
316 317 2.111878 AGCTATCCCATGTGGCGC 59.888 61.111 0.00 0.00 0.00 6.53
317 318 1.598962 CCAGCTATCCCATGTGGCG 60.599 63.158 0.00 0.00 0.00 5.69
318 319 0.106519 AACCAGCTATCCCATGTGGC 60.107 55.000 0.00 0.00 0.00 5.01
319 320 1.683943 CAACCAGCTATCCCATGTGG 58.316 55.000 0.00 0.00 0.00 4.17
320 321 1.683943 CCAACCAGCTATCCCATGTG 58.316 55.000 0.00 0.00 0.00 3.21
321 322 0.106519 GCCAACCAGCTATCCCATGT 60.107 55.000 0.00 0.00 0.00 3.21
322 323 0.825010 GGCCAACCAGCTATCCCATG 60.825 60.000 0.00 0.00 35.26 3.66
323 324 1.538666 GGCCAACCAGCTATCCCAT 59.461 57.895 0.00 0.00 35.26 4.00
324 325 3.006677 GGCCAACCAGCTATCCCA 58.993 61.111 0.00 0.00 35.26 4.37
325 326 2.203209 CGGCCAACCAGCTATCCC 60.203 66.667 2.24 0.00 34.57 3.85
326 327 2.902343 GCGGCCAACCAGCTATCC 60.902 66.667 2.24 0.00 34.11 2.59
327 328 2.902343 GGCGGCCAACCAGCTATC 60.902 66.667 15.62 0.00 36.24 2.08
328 329 4.506255 GGGCGGCCAACCAGCTAT 62.506 66.667 25.33 0.00 36.24 2.97
332 333 3.944250 ATGAAGGGCGGCCAACCAG 62.944 63.158 31.59 0.00 34.57 4.00
333 334 3.978193 ATGAAGGGCGGCCAACCA 61.978 61.111 31.59 23.10 34.57 3.67
334 335 3.451894 CATGAAGGGCGGCCAACC 61.452 66.667 31.59 18.16 0.00 3.77
335 336 3.451894 CCATGAAGGGCGGCCAAC 61.452 66.667 31.59 22.46 0.00 3.77
344 345 6.966534 AAATCATTAAGCTACCCATGAAGG 57.033 37.500 0.00 0.00 37.03 3.46
362 363 9.610705 CTCTCTCTCTCCATCAAATTAAAATCA 57.389 33.333 0.00 0.00 0.00 2.57
363 364 9.829507 TCTCTCTCTCTCCATCAAATTAAAATC 57.170 33.333 0.00 0.00 0.00 2.17
364 365 9.835389 CTCTCTCTCTCTCCATCAAATTAAAAT 57.165 33.333 0.00 0.00 0.00 1.82
365 366 7.768120 GCTCTCTCTCTCTCCATCAAATTAAAA 59.232 37.037 0.00 0.00 0.00 1.52
366 367 7.271511 GCTCTCTCTCTCTCCATCAAATTAAA 58.728 38.462 0.00 0.00 0.00 1.52
367 368 6.460814 CGCTCTCTCTCTCTCCATCAAATTAA 60.461 42.308 0.00 0.00 0.00 1.40
368 369 5.009510 CGCTCTCTCTCTCTCCATCAAATTA 59.990 44.000 0.00 0.00 0.00 1.40
369 370 4.202141 CGCTCTCTCTCTCTCCATCAAATT 60.202 45.833 0.00 0.00 0.00 1.82
370 371 3.318839 CGCTCTCTCTCTCTCCATCAAAT 59.681 47.826 0.00 0.00 0.00 2.32
371 372 2.687425 CGCTCTCTCTCTCTCCATCAAA 59.313 50.000 0.00 0.00 0.00 2.69
372 373 2.296792 CGCTCTCTCTCTCTCCATCAA 58.703 52.381 0.00 0.00 0.00 2.57
373 374 1.965935 CGCTCTCTCTCTCTCCATCA 58.034 55.000 0.00 0.00 0.00 3.07
374 375 0.593128 GCGCTCTCTCTCTCTCCATC 59.407 60.000 0.00 0.00 0.00 3.51
375 376 1.165907 CGCGCTCTCTCTCTCTCCAT 61.166 60.000 5.56 0.00 0.00 3.41
376 377 1.817520 CGCGCTCTCTCTCTCTCCA 60.818 63.158 5.56 0.00 0.00 3.86
377 378 1.817941 ACGCGCTCTCTCTCTCTCC 60.818 63.158 5.73 0.00 0.00 3.71
378 379 1.351707 CACGCGCTCTCTCTCTCTC 59.648 63.158 5.73 0.00 0.00 3.20
379 380 2.112198 CCACGCGCTCTCTCTCTCT 61.112 63.158 5.73 0.00 0.00 3.10
380 381 2.047151 CTCCACGCGCTCTCTCTCTC 62.047 65.000 5.73 0.00 0.00 3.20
381 382 2.045829 TCCACGCGCTCTCTCTCT 60.046 61.111 5.73 0.00 0.00 3.10
382 383 2.317685 GACTCCACGCGCTCTCTCTC 62.318 65.000 5.73 0.00 0.00 3.20
383 384 2.360600 ACTCCACGCGCTCTCTCT 60.361 61.111 5.73 0.00 0.00 3.10
384 385 2.101380 GACTCCACGCGCTCTCTC 59.899 66.667 5.73 0.00 0.00 3.20
385 386 3.444805 GGACTCCACGCGCTCTCT 61.445 66.667 5.73 0.00 0.00 3.10
386 387 3.749064 TGGACTCCACGCGCTCTC 61.749 66.667 5.73 0.00 0.00 3.20
387 388 4.057428 GTGGACTCCACGCGCTCT 62.057 66.667 12.59 0.00 44.95 4.09
395 396 1.628238 AAACGGTGGTGTGGACTCCA 61.628 55.000 0.00 0.00 37.19 3.86
396 397 0.883370 GAAACGGTGGTGTGGACTCC 60.883 60.000 0.00 0.00 0.00 3.85
397 398 0.179067 TGAAACGGTGGTGTGGACTC 60.179 55.000 0.00 0.00 0.00 3.36
398 399 0.253610 TTGAAACGGTGGTGTGGACT 59.746 50.000 0.00 0.00 0.00 3.85
399 400 1.096416 TTTGAAACGGTGGTGTGGAC 58.904 50.000 0.00 0.00 0.00 4.02
400 401 1.096416 GTTTGAAACGGTGGTGTGGA 58.904 50.000 0.00 0.00 0.00 4.02
401 402 1.099689 AGTTTGAAACGGTGGTGTGG 58.900 50.000 1.97 0.00 36.23 4.17
402 403 2.525055 CAAGTTTGAAACGGTGGTGTG 58.475 47.619 1.97 0.00 36.23 3.82
403 404 1.474879 CCAAGTTTGAAACGGTGGTGT 59.525 47.619 19.43 0.00 36.96 4.16
404 405 1.801025 GCCAAGTTTGAAACGGTGGTG 60.801 52.381 24.73 11.40 41.06 4.17
405 406 0.458260 GCCAAGTTTGAAACGGTGGT 59.542 50.000 24.73 0.00 41.06 4.16
406 407 0.744281 AGCCAAGTTTGAAACGGTGG 59.256 50.000 21.91 21.91 41.56 4.61
419 420 3.056393 TCTGCCAATTCATCAAAGCCAAG 60.056 43.478 0.00 0.00 0.00 3.61
448 449 4.688413 GCTGAAGGTTCTACAAGAGACAAG 59.312 45.833 0.00 0.00 32.31 3.16
476 477 2.841442 AGTTCCCCTCTGACGAAAAG 57.159 50.000 0.00 0.00 0.00 2.27
506 507 6.970484 ACTGTATTTTTGTTGCCAGTTCTAG 58.030 36.000 0.00 0.00 29.32 2.43
513 514 8.200792 ACTTGAATTACTGTATTTTTGTTGCCA 58.799 29.630 0.00 0.00 0.00 4.92
529 530 9.477484 AATATCCATACTCGACACTTGAATTAC 57.523 33.333 0.00 0.00 0.00 1.89
533 534 8.420374 GAAAATATCCATACTCGACACTTGAA 57.580 34.615 0.00 0.00 0.00 2.69
574 576 6.109156 ACCCGCAAAAGAAAAGGAATTATT 57.891 33.333 0.00 0.00 0.00 1.40
587 589 6.478673 GGAATTATGGATTTAACCCGCAAAAG 59.521 38.462 0.00 0.00 0.00 2.27
604 606 3.555966 GTGACTCCTTGGGGGAATTATG 58.444 50.000 0.00 0.00 44.58 1.90
623 625 2.349590 TCTGCATGGACAGATTTCGTG 58.650 47.619 0.00 0.00 41.72 4.35
625 627 4.095334 TGATTTCTGCATGGACAGATTTCG 59.905 41.667 4.16 0.00 45.75 3.46
656 658 7.482113 CAGATTTCGGCGTGTAATCTAGTATAG 59.518 40.741 23.25 13.01 41.23 1.31
657 659 7.040892 ACAGATTTCGGCGTGTAATCTAGTATA 60.041 37.037 23.25 0.00 41.23 1.47
658 660 6.150318 CAGATTTCGGCGTGTAATCTAGTAT 58.850 40.000 23.25 8.57 41.23 2.12
659 661 5.066893 ACAGATTTCGGCGTGTAATCTAGTA 59.933 40.000 23.25 0.00 41.23 1.82
660 662 4.142227 ACAGATTTCGGCGTGTAATCTAGT 60.142 41.667 23.25 20.49 41.23 2.57
661 663 4.360563 ACAGATTTCGGCGTGTAATCTAG 58.639 43.478 23.25 20.10 41.23 2.43
671 673 6.523201 GGCAATTATTATTACAGATTTCGGCG 59.477 38.462 0.00 0.00 0.00 6.46
674 676 7.881142 TGGGGCAATTATTATTACAGATTTCG 58.119 34.615 0.00 0.00 0.00 3.46
684 686 7.732222 TCAGAAACTTGGGGCAATTATTATT 57.268 32.000 0.00 0.00 0.00 1.40
687 689 6.432403 TTTCAGAAACTTGGGGCAATTATT 57.568 33.333 0.00 0.00 0.00 1.40
688 690 6.625532 ATTTCAGAAACTTGGGGCAATTAT 57.374 33.333 0.00 0.00 0.00 1.28
689 691 7.732222 ATATTTCAGAAACTTGGGGCAATTA 57.268 32.000 0.00 0.00 0.00 1.40
742 745 3.087781 GCCTCCTGCAAAGATTCTTCTT 58.912 45.455 0.00 0.00 44.20 2.52
926 942 2.100749 CCGCTGTTTGGAAGGAAAAGTT 59.899 45.455 0.00 0.00 0.00 2.66
989 1016 2.827423 CAGCCATGGCCGATCTCT 59.173 61.111 33.14 10.12 43.17 3.10
1096 1128 4.373116 GAGCAGGTTGTCGCCGGA 62.373 66.667 5.05 0.00 0.00 5.14
1202 1234 0.341609 AGGGAGGAAGAGGAGGAAGG 59.658 60.000 0.00 0.00 0.00 3.46
1203 1235 2.246327 ACTAGGGAGGAAGAGGAGGAAG 59.754 54.545 0.00 0.00 0.00 3.46
1204 1236 2.245287 GACTAGGGAGGAAGAGGAGGAA 59.755 54.545 0.00 0.00 0.00 3.36
1205 1237 1.854280 GACTAGGGAGGAAGAGGAGGA 59.146 57.143 0.00 0.00 0.00 3.71
1232 1267 2.823924 TTGCGGTACAGTAGCAAGAA 57.176 45.000 10.37 0.00 44.66 2.52
1253 1288 1.070758 AGGCTGACAGGTACACAACTG 59.929 52.381 4.26 0.00 40.48 3.16
1285 1324 2.854777 CGCGACAAGGAACTAAGATCAG 59.145 50.000 0.00 0.00 38.49 2.90
1324 1363 2.034685 CAGATCGGAATCTTAGCACGGA 59.965 50.000 0.00 0.00 40.38 4.69
1331 1370 3.252701 GGCTCGTACAGATCGGAATCTTA 59.747 47.826 0.00 0.00 40.38 2.10
1374 1413 3.747976 GTGCGGGTCATGGCAACC 61.748 66.667 0.00 0.00 41.46 3.77
1385 1424 3.908951 CGAACATACGCGTGCGGG 61.909 66.667 24.59 10.81 44.69 6.13
1407 1446 2.430465 AGCAAGTAGGCAACAGACATG 58.570 47.619 0.00 0.00 41.41 3.21
1458 1498 0.179121 TGTTATGCTCCGGTACAGCG 60.179 55.000 0.00 0.00 40.01 5.18
1642 1730 6.127101 TGGTTAGATCCAGAGTTTAGATCGA 58.873 40.000 0.00 0.00 41.06 3.59
1649 1737 9.981460 AATAAGAAATGGTTAGATCCAGAGTTT 57.019 29.630 0.00 0.00 41.05 2.66
1682 1770 3.794138 GCAAAACAAACAGGTTAGACCCG 60.794 47.826 0.00 0.00 39.75 5.28
1714 1802 8.522830 CAACAAATTACTATTGTTCATCCAGGT 58.477 33.333 1.92 0.00 45.27 4.00
1740 1828 2.345341 GTCATTACAATTTGCAAGCGCC 59.655 45.455 2.29 0.00 37.32 6.53
1754 1842 6.493802 TCCTATGATCCCTGTGTAGTCATTAC 59.506 42.308 0.00 0.00 32.31 1.89
1755 1843 6.620429 TCCTATGATCCCTGTGTAGTCATTA 58.380 40.000 0.00 0.00 32.31 1.90
1757 1845 5.079998 TCCTATGATCCCTGTGTAGTCAT 57.920 43.478 0.00 0.00 34.26 3.06
1759 1847 6.226787 CAAATCCTATGATCCCTGTGTAGTC 58.773 44.000 0.00 0.00 0.00 2.59
1792 1880 4.455877 ACGGTTCTCTGAAGCTTAAATTGG 59.544 41.667 0.00 0.00 0.00 3.16
1811 1899 0.108329 CTATTGGCGGACAGAACGGT 60.108 55.000 0.00 0.00 0.00 4.83
1841 1929 7.865385 GGAACATAACTGTTGTGCATTAAGAAA 59.135 33.333 15.91 0.00 45.57 2.52
1842 1930 7.013750 TGGAACATAACTGTTGTGCATTAAGAA 59.986 33.333 15.91 0.00 45.57 2.52
1844 1932 6.676950 TGGAACATAACTGTTGTGCATTAAG 58.323 36.000 15.91 0.00 45.57 1.85
1845 1933 6.641169 TGGAACATAACTGTTGTGCATTAA 57.359 33.333 15.91 0.00 45.57 1.40
1847 1935 5.528043 TTGGAACATAACTGTTGTGCATT 57.472 34.783 15.91 5.23 45.57 3.56
1848 1936 5.301551 TCTTTGGAACATAACTGTTGTGCAT 59.698 36.000 15.91 6.55 45.57 3.96
1849 1937 4.642437 TCTTTGGAACATAACTGTTGTGCA 59.358 37.500 15.91 4.89 45.57 4.57
1850 1938 5.181690 TCTTTGGAACATAACTGTTGTGC 57.818 39.130 15.91 0.00 45.57 4.57
1852 1940 7.581213 TGATTCTTTGGAACATAACTGTTGT 57.419 32.000 2.69 0.00 45.57 3.32
1853 1941 8.352201 TCTTGATTCTTTGGAACATAACTGTTG 58.648 33.333 2.69 0.00 45.57 3.33
1855 1943 8.641498 ATCTTGATTCTTTGGAACATAACTGT 57.359 30.769 0.00 0.00 39.30 3.55
1878 2235 3.868077 GCCGCAATGATGGATAGAGTATC 59.132 47.826 0.00 0.00 34.42 2.24
1884 2241 3.930336 TCTAAGCCGCAATGATGGATAG 58.070 45.455 0.00 0.00 0.00 2.08
1894 2251 6.935741 AATGTAACATAATCTAAGCCGCAA 57.064 33.333 0.00 0.00 0.00 4.85
1895 2252 6.935741 AAATGTAACATAATCTAAGCCGCA 57.064 33.333 0.00 0.00 0.00 5.69
1917 2291 5.798015 TTATCGCTGCCGTACATTAAAAA 57.202 34.783 0.00 0.00 35.54 1.94
1919 2293 5.994887 ATTTATCGCTGCCGTACATTAAA 57.005 34.783 0.00 0.00 35.54 1.52
1920 2294 6.091577 CCATATTTATCGCTGCCGTACATTAA 59.908 38.462 0.00 0.00 35.54 1.40
1922 2296 4.391830 CCATATTTATCGCTGCCGTACATT 59.608 41.667 0.00 0.00 35.54 2.71
1927 2301 2.413837 GTCCATATTTATCGCTGCCGT 58.586 47.619 0.00 0.00 35.54 5.68
1929 2303 1.128692 GCGTCCATATTTATCGCTGCC 59.871 52.381 0.00 0.00 42.88 4.85
1930 2304 1.798223 TGCGTCCATATTTATCGCTGC 59.202 47.619 9.08 0.00 45.69 5.25
1934 2330 6.091305 ACTCATTGATGCGTCCATATTTATCG 59.909 38.462 2.83 0.00 0.00 2.92
1936 2332 8.846943 TTACTCATTGATGCGTCCATATTTAT 57.153 30.769 2.83 0.00 0.00 1.40
1960 2356 9.477484 CGCTATATGAACAGGAATAACTAGTTT 57.523 33.333 14.49 0.00 0.00 2.66
1973 2373 8.773645 TCATGGTTAAATTCGCTATATGAACAG 58.226 33.333 0.00 0.00 0.00 3.16
2005 2405 5.476254 TGCATGAACAAGGAATATCACACAA 59.524 36.000 0.00 0.00 0.00 3.33
2052 2452 3.138304 GTTGATACAAGGTGTGAGCACA 58.862 45.455 0.00 0.00 46.95 4.57
2053 2453 2.157668 CGTTGATACAAGGTGTGAGCAC 59.842 50.000 0.00 0.00 44.53 4.40
2068 2468 4.732355 GCCACAGTTGTAAAACACGTTGAT 60.732 41.667 0.00 0.00 0.00 2.57
2070 2470 2.849473 GCCACAGTTGTAAAACACGTTG 59.151 45.455 0.00 0.00 0.00 4.10
2071 2471 2.159352 GGCCACAGTTGTAAAACACGTT 60.159 45.455 0.00 0.00 0.00 3.99
2072 2472 1.402613 GGCCACAGTTGTAAAACACGT 59.597 47.619 0.00 0.00 0.00 4.49
2073 2473 1.673920 AGGCCACAGTTGTAAAACACG 59.326 47.619 5.01 0.00 0.00 4.49
2074 2474 3.881089 AGTAGGCCACAGTTGTAAAACAC 59.119 43.478 5.01 0.00 0.00 3.32
2274 2682 4.207165 TGTGTCGAGGAGATCATGTATGA 58.793 43.478 0.00 0.00 41.70 2.15
2278 2686 4.437239 GAAATGTGTCGAGGAGATCATGT 58.563 43.478 0.00 0.00 0.00 3.21
2279 2687 3.806521 GGAAATGTGTCGAGGAGATCATG 59.193 47.826 0.00 0.00 0.00 3.07
2280 2688 3.708631 AGGAAATGTGTCGAGGAGATCAT 59.291 43.478 0.00 0.00 0.00 2.45
2290 2698 7.428183 CGGAATTTTATTACAGGAAATGTGTCG 59.572 37.037 0.00 0.00 43.80 4.35
2300 2708 6.087522 TGAAAACGCGGAATTTTATTACAGG 58.912 36.000 12.47 0.00 29.44 4.00
2307 2715 5.115773 CGACAAATGAAAACGCGGAATTTTA 59.884 36.000 12.47 6.15 29.44 1.52
2310 2718 2.977169 CGACAAATGAAAACGCGGAATT 59.023 40.909 12.47 1.27 0.00 2.17
2328 2736 1.803366 AACCACGGAGACCTGTCGAC 61.803 60.000 9.11 9.11 34.09 4.20
2332 2740 0.834612 TTGAAACCACGGAGACCTGT 59.165 50.000 0.00 0.00 0.00 4.00
2338 2746 2.290641 CAGGACTTTTGAAACCACGGAG 59.709 50.000 0.00 0.00 0.00 4.63
2339 2747 2.294074 CAGGACTTTTGAAACCACGGA 58.706 47.619 0.00 0.00 0.00 4.69
2350 2758 3.500471 GGGGATCTCCAAACAGGACTTTT 60.500 47.826 6.79 0.00 43.07 2.27
2468 2876 1.600916 AGCTTGGAGGTCGTTTGGC 60.601 57.895 0.00 0.00 0.00 4.52
2484 2893 3.004734 ACACAATGTGGCTTAAGAACAGC 59.995 43.478 18.37 0.00 37.94 4.40
2541 2950 1.208052 GCACCCTGCAGTTCAGAGATA 59.792 52.381 13.81 0.00 45.72 1.98
2608 3017 0.813610 CTGGCTTGACAACGGTGACA 60.814 55.000 7.88 3.73 0.00 3.58
2652 3061 2.161855 ACACATGTGGACATTTGCGAT 58.838 42.857 28.64 0.98 37.50 4.58
2664 3073 4.930963 TCTGGCAAACTAAAACACATGTG 58.069 39.130 24.25 24.25 0.00 3.21
2684 3093 5.026790 GGCCAACTGGATATATAGGACTCT 58.973 45.833 0.00 0.00 37.39 3.24
2778 3187 3.120199 GGACACATGCACAGATTACACAC 60.120 47.826 0.00 0.00 0.00 3.82
2847 3256 0.900182 AGCACGGACTGACTCATGGA 60.900 55.000 0.00 0.00 0.00 3.41
2888 3310 8.555361 GCAGAATCCATTTTATTCAGACTCTAC 58.445 37.037 0.00 0.00 36.09 2.59
2984 3460 2.336945 TCATCATGATCCACTGTGGC 57.663 50.000 22.02 9.61 37.47 5.01
3013 3490 5.177374 GCTTAAAGCAAATACAAACGCTG 57.823 39.130 0.00 0.00 41.89 5.18
3091 4095 7.302524 TGCGTTTGAAGATATCACTTTTAACC 58.697 34.615 5.32 0.00 37.92 2.85
3106 4110 1.221466 TGACGAGCCTGCGTTTGAAG 61.221 55.000 0.00 0.00 45.72 3.02
3179 4183 1.073763 TGATGCAAGCTGTAGGGTGTT 59.926 47.619 0.00 0.00 0.00 3.32
3220 4247 0.401356 TGATGGGCGATGGCATATGT 59.599 50.000 0.00 0.00 42.47 2.29
3224 4259 1.076850 TTGTGATGGGCGATGGCAT 60.077 52.632 0.00 0.00 42.47 4.40
3233 4268 2.361757 TGAACTTTGCTGTTGTGATGGG 59.638 45.455 0.00 0.00 0.00 4.00
3273 4308 1.818674 GGTCCCTGCTGTACATTTTGG 59.181 52.381 0.00 0.00 0.00 3.28
3291 4326 1.568504 TCGGAGATGCTAAACCTGGT 58.431 50.000 0.00 0.00 0.00 4.00
3521 4556 1.004745 GTCTTCCTCAAATCTGGGCCA 59.995 52.381 5.85 5.85 0.00 5.36
3602 4637 2.430465 GTCACATTCACCTGCATCACT 58.570 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.