Multiple sequence alignment - TraesCS2B01G051300

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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 TraesCS2B01G051300 chr2B 100.000 3260 0 0 1 3260 25074382 25071123 0.000000e+00 6021.0
1 TraesCS2B01G051300 chr2D 92.366 2515 124 28 786 3260 13774683 13772197 0.000000e+00 3518.0
2 TraesCS2B01G051300 chr2D 91.667 168 5 4 6 170 13775862 13775701 1.180000e-54 224.0
3 TraesCS2B01G051300 chr2D 80.065 306 31 9 375 668 13775159 13774872 1.980000e-47 200.0
4 TraesCS2B01G051300 chr2A 92.199 2474 112 21 833 3260 15964216 15961778 0.000000e+00 3424.0
5 TraesCS2B01G051300 chr2A 91.429 210 14 2 1 210 15968443 15968238 5.320000e-73 285.0
6 TraesCS2B01G051300 chr3B 88.462 52 3 3 618 668 485535990 485536039 3.510000e-05 60.2
7 TraesCS2B01G051300 chr7A 77.273 110 15 9 575 682 388727419 388727520 4.540000e-04 56.5
8 TraesCS2B01G051300 chr6A 78.351 97 14 6 575 668 140147970 140148062 4.540000e-04 56.5


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 TraesCS2B01G051300 chr2B 25071123 25074382 3259 True 6021 6021 100.000000 1 3260 1 chr2B.!!$R1 3259
1 TraesCS2B01G051300 chr2D 13772197 13775862 3665 True 1314 3518 88.032667 6 3260 3 chr2D.!!$R1 3254
2 TraesCS2B01G051300 chr2A 15961778 15964216 2438 True 3424 3424 92.199000 833 3260 1 chr2A.!!$R1 2427

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
211 215 0.173481 CGGTGGCTGATCGAGAAAGA 59.827 55.0 0.0 0.0 0.0 2.52 F
372 376 0.250081 GATGATCTCGGAAGTGGGCC 60.250 60.0 0.0 0.0 0.0 5.80 F
1257 1808 0.383231 CGCCCAAGCTCCAATCATTC 59.617 55.0 0.0 0.0 36.6 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 1840 0.038618 AGTGCAAGCGACACGTATCA 60.039 50.0 0.0 0.00 42.94 2.15 R
1291 1843 0.311477 TACAGTGCAAGCGACACGTA 59.689 50.0 0.0 4.96 42.94 3.57 R
2739 3318 0.411452 ACTGAGGAGGCTGAAGAGGA 59.589 55.0 0.0 0.00 0.00 3.71 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
64 65 4.949121 AGTGTGGTCCTAGGTAGAGAAAT 58.051 43.478 9.08 0.00 0.00 2.17
68 69 2.973406 GGTCCTAGGTAGAGAAATGGGG 59.027 54.545 9.08 0.00 0.00 4.96
69 70 3.632906 GGTCCTAGGTAGAGAAATGGGGT 60.633 52.174 9.08 0.00 0.00 4.95
70 71 3.388350 GTCCTAGGTAGAGAAATGGGGTG 59.612 52.174 9.08 0.00 0.00 4.61
71 72 2.104963 CCTAGGTAGAGAAATGGGGTGC 59.895 54.545 0.00 0.00 0.00 5.01
72 73 1.972588 AGGTAGAGAAATGGGGTGCT 58.027 50.000 0.00 0.00 0.00 4.40
73 74 3.130734 AGGTAGAGAAATGGGGTGCTA 57.869 47.619 0.00 0.00 0.00 3.49
74 75 3.460825 AGGTAGAGAAATGGGGTGCTAA 58.539 45.455 0.00 0.00 0.00 3.09
77 78 1.918957 AGAGAAATGGGGTGCTAAGCT 59.081 47.619 0.00 0.00 0.00 3.74
80 81 3.879892 GAGAAATGGGGTGCTAAGCTAAG 59.120 47.826 0.00 0.00 0.00 2.18
82 83 0.183731 ATGGGGTGCTAAGCTAAGCC 59.816 55.000 0.00 0.00 42.05 4.35
103 104 0.998928 AGCCCATCATTACACCCACA 59.001 50.000 0.00 0.00 0.00 4.17
106 107 2.368439 CCCATCATTACACCCACACTG 58.632 52.381 0.00 0.00 0.00 3.66
185 189 0.316204 CCTGGCTTTTGGCTGTTCAG 59.684 55.000 0.00 0.00 46.20 3.02
200 204 1.723608 TTCAGTTTGTGCGGTGGCTG 61.724 55.000 0.00 0.00 40.82 4.85
201 205 2.186160 CAGTTTGTGCGGTGGCTGA 61.186 57.895 0.00 0.00 40.82 4.26
202 206 1.228245 AGTTTGTGCGGTGGCTGAT 60.228 52.632 0.00 0.00 40.82 2.90
203 207 1.210155 GTTTGTGCGGTGGCTGATC 59.790 57.895 0.00 0.00 40.82 2.92
204 208 2.324330 TTTGTGCGGTGGCTGATCG 61.324 57.895 0.00 0.00 40.82 3.69
205 209 2.723586 TTTGTGCGGTGGCTGATCGA 62.724 55.000 0.00 0.00 40.82 3.59
206 210 2.887568 GTGCGGTGGCTGATCGAG 60.888 66.667 0.00 0.00 40.82 4.04
210 214 1.424493 GCGGTGGCTGATCGAGAAAG 61.424 60.000 0.00 0.00 35.83 2.62
211 215 0.173481 CGGTGGCTGATCGAGAAAGA 59.827 55.000 0.00 0.00 0.00 2.52
212 216 1.646189 GGTGGCTGATCGAGAAAGAC 58.354 55.000 0.00 0.00 0.00 3.01
213 217 1.646189 GTGGCTGATCGAGAAAGACC 58.354 55.000 0.00 0.00 0.00 3.85
214 218 1.205893 GTGGCTGATCGAGAAAGACCT 59.794 52.381 0.00 0.00 0.00 3.85
215 219 1.205655 TGGCTGATCGAGAAAGACCTG 59.794 52.381 0.00 0.00 0.00 4.00
216 220 1.478510 GGCTGATCGAGAAAGACCTGA 59.521 52.381 0.00 0.00 0.00 3.86
217 221 2.093973 GGCTGATCGAGAAAGACCTGAA 60.094 50.000 0.00 0.00 0.00 3.02
218 222 2.926838 GCTGATCGAGAAAGACCTGAAC 59.073 50.000 0.00 0.00 0.00 3.18
219 223 3.615110 GCTGATCGAGAAAGACCTGAACA 60.615 47.826 0.00 0.00 0.00 3.18
220 224 4.560128 CTGATCGAGAAAGACCTGAACAA 58.440 43.478 0.00 0.00 0.00 2.83
221 225 4.560128 TGATCGAGAAAGACCTGAACAAG 58.440 43.478 0.00 0.00 0.00 3.16
229 233 2.846532 CCTGAACAAGGGTGGGCT 59.153 61.111 0.00 0.00 43.15 5.19
230 234 1.604593 CCTGAACAAGGGTGGGCTG 60.605 63.158 0.00 0.00 43.15 4.85
231 235 1.604593 CTGAACAAGGGTGGGCTGG 60.605 63.158 0.00 0.00 0.00 4.85
232 236 2.991540 GAACAAGGGTGGGCTGGC 60.992 66.667 0.00 0.00 0.00 4.85
233 237 3.511610 AACAAGGGTGGGCTGGCT 61.512 61.111 0.00 0.00 0.00 4.75
234 238 3.815407 AACAAGGGTGGGCTGGCTG 62.815 63.158 0.00 0.00 0.00 4.85
249 253 4.711949 CTGCAAGCTCCCGCACCT 62.712 66.667 1.57 0.00 39.10 4.00
250 254 4.269523 TGCAAGCTCCCGCACCTT 62.270 61.111 1.57 0.00 39.10 3.50
251 255 3.741476 GCAAGCTCCCGCACCTTG 61.741 66.667 0.00 0.00 39.08 3.61
252 256 2.281761 CAAGCTCCCGCACCTTGT 60.282 61.111 0.00 0.00 39.10 3.16
253 257 2.032681 AAGCTCCCGCACCTTGTC 59.967 61.111 0.00 0.00 39.10 3.18
254 258 2.818169 AAGCTCCCGCACCTTGTCA 61.818 57.895 0.00 0.00 39.10 3.58
255 259 2.281484 GCTCCCGCACCTTGTCAA 60.281 61.111 0.00 0.00 35.78 3.18
256 260 2.617274 GCTCCCGCACCTTGTCAAC 61.617 63.158 0.00 0.00 35.78 3.18
257 261 1.071471 CTCCCGCACCTTGTCAACT 59.929 57.895 0.00 0.00 0.00 3.16
258 262 1.227823 TCCCGCACCTTGTCAACTG 60.228 57.895 0.00 0.00 0.00 3.16
259 263 1.227823 CCCGCACCTTGTCAACTGA 60.228 57.895 0.00 0.00 0.00 3.41
260 264 1.230635 CCCGCACCTTGTCAACTGAG 61.231 60.000 0.00 0.00 0.00 3.35
261 265 0.532862 CCGCACCTTGTCAACTGAGT 60.533 55.000 0.00 0.00 0.00 3.41
262 266 1.299541 CGCACCTTGTCAACTGAGTT 58.700 50.000 0.00 0.00 0.00 3.01
263 267 2.479837 CGCACCTTGTCAACTGAGTTA 58.520 47.619 0.00 0.00 0.00 2.24
264 268 2.221055 CGCACCTTGTCAACTGAGTTAC 59.779 50.000 0.00 0.00 0.00 2.50
265 269 2.221055 GCACCTTGTCAACTGAGTTACG 59.779 50.000 0.00 0.00 0.00 3.18
266 270 2.221055 CACCTTGTCAACTGAGTTACGC 59.779 50.000 0.00 0.00 0.00 4.42
267 271 2.102588 ACCTTGTCAACTGAGTTACGCT 59.897 45.455 0.00 0.00 0.00 5.07
268 272 2.731976 CCTTGTCAACTGAGTTACGCTC 59.268 50.000 0.00 0.00 44.36 5.03
269 273 3.553096 CCTTGTCAACTGAGTTACGCTCT 60.553 47.826 0.00 0.00 44.41 4.09
270 274 3.013276 TGTCAACTGAGTTACGCTCTG 57.987 47.619 0.00 0.00 44.41 3.35
277 281 4.167554 CTGAGTTACGCTCTGTTCTTCT 57.832 45.455 0.00 0.00 44.41 2.85
278 282 3.902150 TGAGTTACGCTCTGTTCTTCTG 58.098 45.455 0.00 0.00 44.41 3.02
279 283 3.568430 TGAGTTACGCTCTGTTCTTCTGA 59.432 43.478 0.00 0.00 44.41 3.27
280 284 4.218635 TGAGTTACGCTCTGTTCTTCTGAT 59.781 41.667 0.00 0.00 44.41 2.90
281 285 4.739195 AGTTACGCTCTGTTCTTCTGATC 58.261 43.478 0.00 0.00 0.00 2.92
282 286 2.270275 ACGCTCTGTTCTTCTGATCG 57.730 50.000 0.00 0.00 38.75 3.69
283 287 1.813178 ACGCTCTGTTCTTCTGATCGA 59.187 47.619 0.00 0.00 37.19 3.59
284 288 2.159448 ACGCTCTGTTCTTCTGATCGAG 60.159 50.000 0.00 0.00 37.19 4.04
285 289 2.096657 CGCTCTGTTCTTCTGATCGAGA 59.903 50.000 0.00 0.00 36.33 4.04
286 290 3.426829 CGCTCTGTTCTTCTGATCGAGAA 60.427 47.826 0.00 7.20 38.45 2.87
287 291 4.489810 GCTCTGTTCTTCTGATCGAGAAA 58.510 43.478 7.35 0.00 40.33 2.52
288 292 4.926238 GCTCTGTTCTTCTGATCGAGAAAA 59.074 41.667 7.35 2.92 40.33 2.29
289 293 5.406780 GCTCTGTTCTTCTGATCGAGAAAAA 59.593 40.000 7.35 0.32 40.33 1.94
290 294 6.091986 GCTCTGTTCTTCTGATCGAGAAAAAT 59.908 38.462 7.35 0.00 40.33 1.82
291 295 7.276658 GCTCTGTTCTTCTGATCGAGAAAAATA 59.723 37.037 7.35 1.02 40.33 1.40
292 296 9.144747 CTCTGTTCTTCTGATCGAGAAAAATAA 57.855 33.333 7.35 0.56 40.33 1.40
293 297 9.489084 TCTGTTCTTCTGATCGAGAAAAATAAA 57.511 29.630 7.35 0.00 40.33 1.40
333 337 1.507141 CGTGGTCTGGGTTGCTTGTC 61.507 60.000 0.00 0.00 0.00 3.18
352 356 1.412710 TCAAGCCGAGAGTGAGTGTTT 59.587 47.619 0.00 0.00 0.00 2.83
354 358 1.040646 AGCCGAGAGTGAGTGTTTGA 58.959 50.000 0.00 0.00 0.00 2.69
355 359 1.620819 AGCCGAGAGTGAGTGTTTGAT 59.379 47.619 0.00 0.00 0.00 2.57
356 360 1.728971 GCCGAGAGTGAGTGTTTGATG 59.271 52.381 0.00 0.00 0.00 3.07
357 361 2.610479 GCCGAGAGTGAGTGTTTGATGA 60.610 50.000 0.00 0.00 0.00 2.92
358 362 3.854666 CCGAGAGTGAGTGTTTGATGAT 58.145 45.455 0.00 0.00 0.00 2.45
359 363 3.862267 CCGAGAGTGAGTGTTTGATGATC 59.138 47.826 0.00 0.00 0.00 2.92
360 364 4.381398 CCGAGAGTGAGTGTTTGATGATCT 60.381 45.833 0.00 0.00 0.00 2.75
361 365 4.797868 CGAGAGTGAGTGTTTGATGATCTC 59.202 45.833 0.00 0.00 0.00 2.75
362 366 4.742417 AGAGTGAGTGTTTGATGATCTCG 58.258 43.478 0.00 0.00 0.00 4.04
363 367 3.854666 AGTGAGTGTTTGATGATCTCGG 58.145 45.455 0.00 0.00 0.00 4.63
364 368 3.511540 AGTGAGTGTTTGATGATCTCGGA 59.488 43.478 0.00 0.00 0.00 4.55
366 370 4.328440 GTGAGTGTTTGATGATCTCGGAAG 59.672 45.833 0.00 0.00 0.00 3.46
367 371 4.021104 TGAGTGTTTGATGATCTCGGAAGT 60.021 41.667 0.00 0.00 0.00 3.01
368 372 4.248859 AGTGTTTGATGATCTCGGAAGTG 58.751 43.478 0.00 0.00 0.00 3.16
369 373 3.372206 GTGTTTGATGATCTCGGAAGTGG 59.628 47.826 0.00 0.00 0.00 4.00
370 374 2.939103 GTTTGATGATCTCGGAAGTGGG 59.061 50.000 0.00 0.00 0.00 4.61
372 376 0.250081 GATGATCTCGGAAGTGGGCC 60.250 60.000 0.00 0.00 0.00 5.80
373 377 1.700042 ATGATCTCGGAAGTGGGCCC 61.700 60.000 17.59 17.59 0.00 5.80
378 810 2.365105 CGGAAGTGGGCCCCTCTA 60.365 66.667 22.27 0.00 0.00 2.43
411 843 1.202879 TCTCGGAAGTGGCAAATGGTT 60.203 47.619 0.00 0.00 0.00 3.67
433 865 4.993705 TGTGTTGAGGATTAAGGAAGGT 57.006 40.909 0.00 0.00 0.00 3.50
434 866 4.651778 TGTGTTGAGGATTAAGGAAGGTG 58.348 43.478 0.00 0.00 0.00 4.00
435 867 4.104102 TGTGTTGAGGATTAAGGAAGGTGT 59.896 41.667 0.00 0.00 0.00 4.16
459 891 2.351726 GTGTGATGCAAGTTATCGGTCC 59.648 50.000 0.00 0.00 0.00 4.46
466 898 3.380954 TGCAAGTTATCGGTCCGTATGTA 59.619 43.478 11.88 0.00 0.00 2.29
467 899 4.142204 TGCAAGTTATCGGTCCGTATGTAA 60.142 41.667 11.88 4.40 0.00 2.41
468 900 4.805192 GCAAGTTATCGGTCCGTATGTAAA 59.195 41.667 11.88 0.00 0.00 2.01
469 901 5.291614 GCAAGTTATCGGTCCGTATGTAAAA 59.708 40.000 11.88 0.00 0.00 1.52
470 902 6.699063 CAAGTTATCGGTCCGTATGTAAAAC 58.301 40.000 11.88 6.58 0.00 2.43
471 903 5.036737 AGTTATCGGTCCGTATGTAAAACG 58.963 41.667 11.88 0.00 40.01 3.60
472 904 3.781079 ATCGGTCCGTATGTAAAACGA 57.219 42.857 11.88 0.00 42.90 3.85
473 905 3.567576 TCGGTCCGTATGTAAAACGAA 57.432 42.857 11.88 0.00 42.90 3.85
474 906 3.906998 TCGGTCCGTATGTAAAACGAAA 58.093 40.909 11.88 0.00 42.90 3.46
475 907 4.302455 TCGGTCCGTATGTAAAACGAAAA 58.698 39.130 11.88 0.00 42.90 2.29
476 908 4.928615 TCGGTCCGTATGTAAAACGAAAAT 59.071 37.500 11.88 0.00 42.90 1.82
477 909 5.016985 CGGTCCGTATGTAAAACGAAAATG 58.983 41.667 2.08 0.00 42.90 2.32
478 910 5.389725 CGGTCCGTATGTAAAACGAAAATGT 60.390 40.000 2.08 0.00 42.90 2.71
479 911 5.791480 GGTCCGTATGTAAAACGAAAATGTG 59.209 40.000 0.00 0.00 42.90 3.21
480 912 6.365050 GTCCGTATGTAAAACGAAAATGTGT 58.635 36.000 0.00 0.00 42.90 3.72
481 913 6.517374 GTCCGTATGTAAAACGAAAATGTGTC 59.483 38.462 0.00 0.00 42.90 3.67
482 914 5.791480 CCGTATGTAAAACGAAAATGTGTCC 59.209 40.000 0.00 0.00 42.90 4.02
489 921 2.557317 ACGAAAATGTGTCCGACTTGT 58.443 42.857 0.00 0.00 0.00 3.16
496 928 6.627395 AAATGTGTCCGACTTGTATTTTCA 57.373 33.333 0.00 0.00 0.00 2.69
510 942 7.712264 TTGTATTTTCAAGTGGCTGAAATTG 57.288 32.000 1.81 0.00 43.12 2.32
513 945 3.815856 TTCAAGTGGCTGAAATTGCAA 57.184 38.095 0.00 0.00 32.39 4.08
519 951 5.275067 AGTGGCTGAAATTGCAAGTTTTA 57.725 34.783 14.04 5.56 0.00 1.52
521 953 5.754890 AGTGGCTGAAATTGCAAGTTTTAAG 59.245 36.000 14.04 12.39 0.00 1.85
522 954 4.511082 TGGCTGAAATTGCAAGTTTTAAGC 59.489 37.500 23.38 23.38 32.37 3.09
523 955 4.083855 GGCTGAAATTGCAAGTTTTAAGCC 60.084 41.667 29.40 29.40 39.42 4.35
524 956 4.511082 GCTGAAATTGCAAGTTTTAAGCCA 59.489 37.500 22.01 11.80 0.00 4.75
527 959 7.565323 TGAAATTGCAAGTTTTAAGCCAAAT 57.435 28.000 14.04 0.00 0.00 2.32
530 962 7.806409 AATTGCAAGTTTTAAGCCAAATCTT 57.194 28.000 4.94 0.93 36.86 2.40
536 968 5.482006 AGTTTTAAGCCAAATCTTGCCATC 58.518 37.500 0.00 0.00 0.00 3.51
552 985 3.244146 TGCCATCACAATGAAAAAGGGTG 60.244 43.478 0.00 0.00 34.61 4.61
568 1011 2.472695 GGTGACCACAGCTGTTCATA 57.527 50.000 21.03 5.66 40.78 2.15
569 1012 2.778299 GGTGACCACAGCTGTTCATAA 58.222 47.619 21.03 3.59 40.78 1.90
572 1015 4.562757 GGTGACCACAGCTGTTCATAACTA 60.563 45.833 21.03 0.00 40.78 2.24
593 1036 6.010219 ACTAAAACCAAACATATGAGTGGCT 58.990 36.000 21.80 12.22 34.27 4.75
608 1051 6.061022 TGAGTGGCTATCTTCAACCATTAA 57.939 37.500 0.00 0.00 34.04 1.40
616 1059 7.446625 GGCTATCTTCAACCATTAACATCTCAT 59.553 37.037 0.00 0.00 0.00 2.90
626 1069 7.378181 ACCATTAACATCTCATTCAACCAAAC 58.622 34.615 0.00 0.00 0.00 2.93
641 1085 6.825610 TCAACCAAACAGAAAAATGGCTATT 58.174 32.000 0.00 0.00 36.37 1.73
645 1089 6.101997 CCAAACAGAAAAATGGCTATTCCTC 58.898 40.000 0.00 0.00 35.26 3.71
646 1090 6.295236 CCAAACAGAAAAATGGCTATTCCTCA 60.295 38.462 0.00 0.00 35.26 3.86
659 1103 1.067295 TTCCTCATCAGCTGGTTGGT 58.933 50.000 15.13 0.00 0.00 3.67
668 1112 1.064463 CAGCTGGTTGGTGATACCCAT 60.064 52.381 5.57 0.00 46.27 4.00
669 1113 1.064463 AGCTGGTTGGTGATACCCATG 60.064 52.381 0.00 0.00 37.50 3.66
670 1114 1.064758 GCTGGTTGGTGATACCCATGA 60.065 52.381 0.00 0.00 37.50 3.07
671 1115 2.643551 CTGGTTGGTGATACCCATGAC 58.356 52.381 0.00 0.00 37.50 3.06
677 1121 1.143684 GGTGATACCCATGACCAGCAT 59.856 52.381 0.00 0.00 38.25 3.79
678 1122 2.498167 GTGATACCCATGACCAGCATC 58.502 52.381 0.00 0.00 34.15 3.91
680 1124 2.509131 TGATACCCATGACCAGCATCAA 59.491 45.455 0.00 0.00 34.15 2.57
681 1125 3.053768 TGATACCCATGACCAGCATCAAA 60.054 43.478 0.00 0.00 34.15 2.69
682 1126 2.307496 ACCCATGACCAGCATCAAAA 57.693 45.000 0.00 0.00 34.15 2.44
684 1128 2.564062 ACCCATGACCAGCATCAAAAAG 59.436 45.455 0.00 0.00 34.15 2.27
687 1131 3.444742 CCATGACCAGCATCAAAAAGCTA 59.555 43.478 0.00 0.00 39.50 3.32
688 1132 4.082081 CCATGACCAGCATCAAAAAGCTAA 60.082 41.667 0.00 0.00 39.50 3.09
690 1134 3.888323 TGACCAGCATCAAAAAGCTAACA 59.112 39.130 0.00 0.00 39.50 2.41
691 1135 4.229876 GACCAGCATCAAAAAGCTAACAC 58.770 43.478 0.00 0.00 39.50 3.32
693 1137 4.281688 ACCAGCATCAAAAAGCTAACACAT 59.718 37.500 0.00 0.00 39.50 3.21
694 1138 4.624024 CCAGCATCAAAAAGCTAACACATG 59.376 41.667 0.00 0.00 39.50 3.21
696 1140 6.097356 CAGCATCAAAAAGCTAACACATGAT 58.903 36.000 0.00 0.00 39.50 2.45
697 1141 6.588756 CAGCATCAAAAAGCTAACACATGATT 59.411 34.615 0.00 0.00 39.50 2.57
699 1143 7.658575 AGCATCAAAAAGCTAACACATGATTTT 59.341 29.630 0.00 0.00 39.78 1.82
755 1251 4.764940 GCATGTGCATGTTTTTCTTCAAC 58.235 39.130 12.96 0.00 40.80 3.18
763 1259 6.417635 TGCATGTTTTTCTTCAACGAAATCTC 59.582 34.615 0.00 0.00 33.33 2.75
784 1280 9.515226 AATCTCAAAGCAAAAACTGTAGGTATA 57.485 29.630 0.00 0.00 0.00 1.47
830 1346 9.643693 CCTAAATCAAAGCTTAACACATGATTT 57.356 29.630 25.96 25.96 44.83 2.17
833 1349 8.752766 AATCAAAGCTTAACACATGATTTGAG 57.247 30.769 13.54 0.00 44.72 3.02
834 1350 7.275888 TCAAAGCTTAACACATGATTTGAGT 57.724 32.000 0.00 0.00 40.02 3.41
843 1359 5.258841 ACACATGATTTGAGTCATCCACAT 58.741 37.500 0.00 0.00 36.72 3.21
847 1363 4.264253 TGATTTGAGTCATCCACATCACC 58.736 43.478 0.00 0.00 29.01 4.02
876 1392 7.275888 GGAAATTGAAAATCCCAAAGCTTTT 57.724 32.000 9.53 0.00 0.00 2.27
879 1395 8.978874 AAATTGAAAATCCCAAAGCTTTTACT 57.021 26.923 9.53 0.00 0.00 2.24
882 1398 7.118496 TGAAAATCCCAAAGCTTTTACTGAA 57.882 32.000 9.53 0.00 0.00 3.02
902 1418 4.638421 TGAATCCCAACGCTATAAAACCAG 59.362 41.667 0.00 0.00 0.00 4.00
903 1419 2.361789 TCCCAACGCTATAAAACCAGC 58.638 47.619 0.00 0.00 0.00 4.85
904 1420 2.088423 CCCAACGCTATAAAACCAGCA 58.912 47.619 0.00 0.00 37.66 4.41
943 1459 2.203640 ACACACCCTCTCCGCTCA 60.204 61.111 0.00 0.00 0.00 4.26
953 1474 2.362247 TCCGCTCAGCTCAGCTCT 60.362 61.111 8.35 0.00 36.40 4.09
958 1479 1.077645 GCTCAGCTCAGCTCTCAACG 61.078 60.000 0.67 0.00 36.40 4.10
1100 1642 4.047125 CCCCCAAGACGGCCACAT 62.047 66.667 2.24 0.00 0.00 3.21
1126 1677 4.293648 CGGTGTCCTCGTGGTGCA 62.294 66.667 2.99 1.72 34.23 4.57
1237 1788 1.954382 GGGTAAGCGAAAATCCCATCC 59.046 52.381 0.00 0.00 38.15 3.51
1242 1793 2.193536 CGAAAATCCCATCCCGCCC 61.194 63.158 0.00 0.00 0.00 6.13
1243 1794 1.076339 GAAAATCCCATCCCGCCCA 60.076 57.895 0.00 0.00 0.00 5.36
1244 1795 0.686112 GAAAATCCCATCCCGCCCAA 60.686 55.000 0.00 0.00 0.00 4.12
1253 1804 2.631012 ATCCCGCCCAAGCTCCAATC 62.631 60.000 0.00 0.00 36.60 2.67
1257 1808 0.383231 CGCCCAAGCTCCAATCATTC 59.617 55.000 0.00 0.00 36.60 2.67
1258 1809 1.477553 GCCCAAGCTCCAATCATTCA 58.522 50.000 0.00 0.00 35.50 2.57
1259 1810 2.037144 GCCCAAGCTCCAATCATTCAT 58.963 47.619 0.00 0.00 35.50 2.57
1260 1811 2.433239 GCCCAAGCTCCAATCATTCATT 59.567 45.455 0.00 0.00 35.50 2.57
1261 1812 3.740141 GCCCAAGCTCCAATCATTCATTG 60.740 47.826 0.00 0.00 37.88 2.82
1271 1823 3.536956 ATCATTCATTGGCCTTTGCTG 57.463 42.857 3.32 3.29 37.74 4.41
1272 1824 1.066716 TCATTCATTGGCCTTTGCTGC 60.067 47.619 3.32 0.00 37.74 5.25
1291 1843 4.457496 CGCTGGGCTGACGGTGAT 62.457 66.667 0.00 0.00 0.00 3.06
1292 1844 2.900273 GCTGGGCTGACGGTGATA 59.100 61.111 0.00 0.00 0.00 2.15
1293 1845 1.521681 GCTGGGCTGACGGTGATAC 60.522 63.158 0.00 0.00 0.00 2.24
1294 1846 1.226974 CTGGGCTGACGGTGATACG 60.227 63.158 0.00 0.00 40.31 3.06
1307 1859 0.038618 TGATACGTGTCGCTTGCACT 60.039 50.000 7.84 0.00 34.91 4.40
1437 1989 4.796231 ACACGGTCAGATCGGCGC 62.796 66.667 8.24 0.00 0.00 6.53
1438 1990 4.498520 CACGGTCAGATCGGCGCT 62.499 66.667 7.64 0.00 0.00 5.92
1645 2197 3.251004 CCTTCGCCCATTTACTAGAATGC 59.749 47.826 0.00 0.00 36.04 3.56
1646 2198 3.838244 TCGCCCATTTACTAGAATGCT 57.162 42.857 0.00 0.00 36.04 3.79
1647 2199 4.948341 TCGCCCATTTACTAGAATGCTA 57.052 40.909 0.00 0.00 36.04 3.49
1656 2208 6.422776 TTTACTAGAATGCTACTTGCTTGC 57.577 37.500 0.00 0.00 43.37 4.01
1677 2229 6.072112 TGCTTTCAGAACTTTTGGTACATC 57.928 37.500 0.00 0.00 39.30 3.06
1679 2231 6.096141 TGCTTTCAGAACTTTTGGTACATCAA 59.904 34.615 0.00 0.00 39.30 2.57
1699 2251 8.819974 ACATCAATGAAATGTGTTTGAAGAAAC 58.180 29.630 0.00 0.00 41.72 2.78
1733 2288 8.131100 TGCTATTTTTGCTACATAAATCAGCTC 58.869 33.333 16.04 3.04 36.26 4.09
1763 2342 4.933505 TTCATGATTGACAAAAGTGGCA 57.066 36.364 0.00 0.00 42.77 4.92
1767 2346 4.241590 TGATTGACAAAAGTGGCATGTC 57.758 40.909 11.14 11.14 44.33 3.06
1893 2472 1.307355 TTACCGGAGTCGTGATCGCA 61.307 55.000 9.46 0.00 36.96 5.10
1941 2520 1.860676 TCGTGACCAGGAACGAAAAG 58.139 50.000 16.60 0.00 45.14 2.27
1968 2547 2.738521 CTGGGCGAACCGACAGTG 60.739 66.667 0.00 0.00 44.64 3.66
1977 2556 4.704833 CCGACAGTGCCCACCCTG 62.705 72.222 0.00 0.00 34.82 4.45
1986 2565 4.715130 CCCACCCTGGAGGACGGA 62.715 72.222 0.69 0.00 40.96 4.69
2086 2665 3.499737 GGCAGCGGTGGATGTTCG 61.500 66.667 17.54 0.00 0.00 3.95
2097 2676 4.814294 ATGTTCGTCGGGGCGCTC 62.814 66.667 7.64 1.18 0.00 5.03
2378 2957 4.377226 GCGCTGTTTACGTGTAATTAACCA 60.377 41.667 0.00 0.00 0.00 3.67
2383 2962 7.288317 TGTTTACGTGTAATTAACCATACCG 57.712 36.000 0.00 0.00 0.00 4.02
2399 2978 5.221382 ACCATACCGACTGTAACATGTATCC 60.221 44.000 0.00 0.00 31.94 2.59
2400 2979 5.010719 CCATACCGACTGTAACATGTATCCT 59.989 44.000 0.00 0.00 31.94 3.24
2510 3089 5.243426 TCTTACTGCCAACTTTGTGTTTC 57.757 39.130 0.00 0.00 36.63 2.78
2566 3145 1.152777 TGGACTGCCAAACCAGGTG 60.153 57.895 0.00 0.00 42.49 4.00
2598 3177 0.468771 GCCATCCCCAGATTTCCCAG 60.469 60.000 0.00 0.00 0.00 4.45
2739 3318 0.449388 GACGACAACGACCTCGGTAT 59.551 55.000 0.00 0.00 44.95 2.73
2813 3392 2.867624 AGCTCTTCATTCACCTTGCAA 58.132 42.857 0.00 0.00 0.00 4.08
2816 3395 2.555325 CTCTTCATTCACCTTGCAAGCA 59.445 45.455 21.43 3.89 0.00 3.91
2830 3409 3.403624 AGCATCCTCGGCTTTGGA 58.596 55.556 0.00 0.00 38.81 3.53
2833 3412 4.567318 ATCCTCGGCTTTGGATGC 57.433 55.556 4.58 0.00 41.13 3.91
2840 3419 2.272146 GCTTTGGATGCCGAGGGA 59.728 61.111 0.00 0.00 0.00 4.20
2852 3431 1.686325 CCGAGGGATCGACCAATGGT 61.686 60.000 3.74 3.74 41.20 3.55
2918 3497 1.971167 GGATTCAACGGGTGCAGCA 60.971 57.895 19.06 0.00 0.00 4.41
2927 3506 2.337532 GGTGCAGCAACAGCCTTG 59.662 61.111 11.86 0.00 31.85 3.61
3007 3586 1.486726 GCTAGCACAGGAACCCATAGT 59.513 52.381 10.63 0.00 0.00 2.12
3099 3678 1.376812 GAACGCGGGGAAGAATGGT 60.377 57.895 12.47 0.00 0.00 3.55
3140 3719 2.439880 AGGAGGAAGGGCTATTTGTAGC 59.560 50.000 0.00 0.00 42.12 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.204786 TGGCTTAGCTTAGCACCCCA 61.205 55.000 24.76 11.55 43.02 4.96
68 69 0.735471 GGCTTGGCTTAGCTTAGCAC 59.265 55.000 24.76 14.91 43.02 4.40
69 70 0.394352 GGGCTTGGCTTAGCTTAGCA 60.394 55.000 24.76 9.51 43.02 3.49
70 71 0.394352 TGGGCTTGGCTTAGCTTAGC 60.394 55.000 16.30 16.30 40.99 3.09
71 72 2.225467 GATGGGCTTGGCTTAGCTTAG 58.775 52.381 3.59 0.00 40.99 2.18
72 73 1.563879 TGATGGGCTTGGCTTAGCTTA 59.436 47.619 3.59 0.00 40.99 3.09
73 74 0.332632 TGATGGGCTTGGCTTAGCTT 59.667 50.000 3.59 0.00 40.99 3.74
74 75 0.554792 ATGATGGGCTTGGCTTAGCT 59.445 50.000 3.59 0.00 40.99 3.32
77 78 3.287222 GTGTAATGATGGGCTTGGCTTA 58.713 45.455 0.00 0.00 0.00 3.09
80 81 0.746659 GGTGTAATGATGGGCTTGGC 59.253 55.000 0.00 0.00 0.00 4.52
82 83 1.750778 GTGGGTGTAATGATGGGCTTG 59.249 52.381 0.00 0.00 0.00 4.01
170 174 2.604462 CACAAACTGAACAGCCAAAAGC 59.396 45.455 1.46 0.00 44.25 3.51
171 175 2.604462 GCACAAACTGAACAGCCAAAAG 59.396 45.455 1.46 0.00 0.00 2.27
172 176 2.615869 GCACAAACTGAACAGCCAAAA 58.384 42.857 1.46 0.00 0.00 2.44
173 177 1.468908 CGCACAAACTGAACAGCCAAA 60.469 47.619 1.46 0.00 0.00 3.28
174 178 0.100325 CGCACAAACTGAACAGCCAA 59.900 50.000 1.46 0.00 0.00 4.52
175 179 1.723608 CCGCACAAACTGAACAGCCA 61.724 55.000 1.46 0.00 0.00 4.75
176 180 1.008538 CCGCACAAACTGAACAGCC 60.009 57.895 1.46 0.00 0.00 4.85
177 181 0.592247 CACCGCACAAACTGAACAGC 60.592 55.000 1.46 0.00 0.00 4.40
178 182 0.029300 CCACCGCACAAACTGAACAG 59.971 55.000 0.00 0.00 0.00 3.16
179 183 1.999071 GCCACCGCACAAACTGAACA 61.999 55.000 0.00 0.00 34.03 3.18
180 184 1.299089 GCCACCGCACAAACTGAAC 60.299 57.895 0.00 0.00 34.03 3.18
185 189 1.210155 GATCAGCCACCGCACAAAC 59.790 57.895 0.00 0.00 37.52 2.93
200 204 3.929610 CCTTGTTCAGGTCTTTCTCGATC 59.070 47.826 0.00 0.00 37.99 3.69
201 205 3.307059 CCCTTGTTCAGGTCTTTCTCGAT 60.307 47.826 0.00 0.00 42.02 3.59
202 206 2.037251 CCCTTGTTCAGGTCTTTCTCGA 59.963 50.000 0.00 0.00 42.02 4.04
203 207 2.224305 ACCCTTGTTCAGGTCTTTCTCG 60.224 50.000 0.00 0.00 42.02 4.04
204 208 3.142174 CACCCTTGTTCAGGTCTTTCTC 58.858 50.000 0.00 0.00 42.02 2.87
205 209 2.158608 CCACCCTTGTTCAGGTCTTTCT 60.159 50.000 0.00 0.00 42.02 2.52
206 210 2.230660 CCACCCTTGTTCAGGTCTTTC 58.769 52.381 0.00 0.00 42.02 2.62
210 214 1.603739 GCCCACCCTTGTTCAGGTC 60.604 63.158 0.00 0.00 42.02 3.85
211 215 2.084930 AGCCCACCCTTGTTCAGGT 61.085 57.895 0.00 0.00 42.02 4.00
212 216 1.604593 CAGCCCACCCTTGTTCAGG 60.605 63.158 0.00 0.00 43.49 3.86
213 217 1.604593 CCAGCCCACCCTTGTTCAG 60.605 63.158 0.00 0.00 0.00 3.02
214 218 2.520458 CCAGCCCACCCTTGTTCA 59.480 61.111 0.00 0.00 0.00 3.18
215 219 2.991540 GCCAGCCCACCCTTGTTC 60.992 66.667 0.00 0.00 0.00 3.18
216 220 3.511610 AGCCAGCCCACCCTTGTT 61.512 61.111 0.00 0.00 0.00 2.83
217 221 4.290622 CAGCCAGCCCACCCTTGT 62.291 66.667 0.00 0.00 0.00 3.16
239 243 1.071471 AGTTGACAAGGTGCGGGAG 59.929 57.895 0.00 0.00 0.00 4.30
240 244 1.227823 CAGTTGACAAGGTGCGGGA 60.228 57.895 0.00 0.00 0.00 5.14
241 245 1.227823 TCAGTTGACAAGGTGCGGG 60.228 57.895 0.00 0.00 0.00 6.13
242 246 0.532862 ACTCAGTTGACAAGGTGCGG 60.533 55.000 0.00 0.00 0.00 5.69
243 247 1.299541 AACTCAGTTGACAAGGTGCG 58.700 50.000 0.00 0.00 0.00 5.34
244 248 2.221055 CGTAACTCAGTTGACAAGGTGC 59.779 50.000 0.00 0.00 0.00 5.01
245 249 2.221055 GCGTAACTCAGTTGACAAGGTG 59.779 50.000 0.00 0.00 0.00 4.00
246 250 2.102588 AGCGTAACTCAGTTGACAAGGT 59.897 45.455 0.00 0.00 0.00 3.50
247 251 2.731976 GAGCGTAACTCAGTTGACAAGG 59.268 50.000 0.00 0.00 45.49 3.61
258 262 4.162096 TCAGAAGAACAGAGCGTAACTC 57.838 45.455 0.00 0.00 46.66 3.01
259 263 4.673061 CGATCAGAAGAACAGAGCGTAACT 60.673 45.833 0.00 0.00 38.66 2.24
260 264 3.544285 CGATCAGAAGAACAGAGCGTAAC 59.456 47.826 0.00 0.00 38.66 2.50
261 265 3.439129 TCGATCAGAAGAACAGAGCGTAA 59.561 43.478 0.00 0.00 42.68 3.18
262 266 3.007635 TCGATCAGAAGAACAGAGCGTA 58.992 45.455 0.00 0.00 42.68 4.42
263 267 1.813178 TCGATCAGAAGAACAGAGCGT 59.187 47.619 0.00 0.00 42.68 5.07
264 268 2.096657 TCTCGATCAGAAGAACAGAGCG 59.903 50.000 0.00 0.00 43.27 5.03
265 269 3.773860 TCTCGATCAGAAGAACAGAGC 57.226 47.619 0.00 0.00 0.00 4.09
266 270 7.593875 ATTTTTCTCGATCAGAAGAACAGAG 57.406 36.000 10.75 0.00 42.37 3.35
267 271 9.489084 TTTATTTTTCTCGATCAGAAGAACAGA 57.511 29.630 10.75 0.00 42.37 3.41
314 318 1.507141 GACAAGCAACCCAGACCACG 61.507 60.000 0.00 0.00 0.00 4.94
333 337 1.528586 CAAACACTCACTCTCGGCTTG 59.471 52.381 0.00 0.00 0.00 4.01
352 356 0.465705 GCCCACTTCCGAGATCATCA 59.534 55.000 0.00 0.00 0.00 3.07
354 358 1.700042 GGGCCCACTTCCGAGATCAT 61.700 60.000 19.95 0.00 0.00 2.45
355 359 2.367202 GGGCCCACTTCCGAGATCA 61.367 63.158 19.95 0.00 0.00 2.92
356 360 2.506472 GGGCCCACTTCCGAGATC 59.494 66.667 19.95 0.00 0.00 2.75
357 361 3.090532 GGGGCCCACTTCCGAGAT 61.091 66.667 26.86 0.00 0.00 2.75
358 362 4.332543 AGGGGCCCACTTCCGAGA 62.333 66.667 27.72 0.00 0.00 4.04
359 363 2.873557 TAGAGGGGCCCACTTCCGAG 62.874 65.000 27.98 0.00 0.00 4.63
360 364 2.873557 CTAGAGGGGCCCACTTCCGA 62.874 65.000 27.98 8.94 0.00 4.55
361 365 2.365105 TAGAGGGGCCCACTTCCG 60.365 66.667 27.98 0.00 0.00 4.30
362 366 0.400670 ATCTAGAGGGGCCCACTTCC 60.401 60.000 27.98 5.28 0.00 3.46
363 367 1.512735 AATCTAGAGGGGCCCACTTC 58.487 55.000 27.98 17.81 0.00 3.01
364 368 1.847088 GAAATCTAGAGGGGCCCACTT 59.153 52.381 27.98 9.49 0.00 3.16
366 370 1.141858 CAGAAATCTAGAGGGGCCCAC 59.858 57.143 27.72 20.26 0.00 4.61
367 371 1.274416 ACAGAAATCTAGAGGGGCCCA 60.274 52.381 27.72 2.92 0.00 5.36
368 372 1.418264 GACAGAAATCTAGAGGGGCCC 59.582 57.143 17.12 17.12 0.00 5.80
369 373 1.069358 CGACAGAAATCTAGAGGGGCC 59.931 57.143 0.00 0.00 0.00 5.80
370 374 2.032620 TCGACAGAAATCTAGAGGGGC 58.967 52.381 0.00 0.00 0.00 5.80
372 376 4.083537 CGAGATCGACAGAAATCTAGAGGG 60.084 50.000 0.00 0.00 43.02 4.30
373 377 4.083537 CCGAGATCGACAGAAATCTAGAGG 60.084 50.000 3.31 0.00 43.02 3.69
378 810 3.697045 ACTTCCGAGATCGACAGAAATCT 59.303 43.478 3.31 0.00 43.02 2.40
411 843 5.070001 CACCTTCCTTAATCCTCAACACAA 58.930 41.667 0.00 0.00 0.00 3.33
433 865 3.186205 CGATAACTTGCATCACACACACA 59.814 43.478 0.00 0.00 0.00 3.72
434 866 3.424829 CCGATAACTTGCATCACACACAC 60.425 47.826 0.00 0.00 0.00 3.82
435 867 2.741517 CCGATAACTTGCATCACACACA 59.258 45.455 0.00 0.00 0.00 3.72
459 891 5.502004 CGGACACATTTTCGTTTTACATACG 59.498 40.000 0.00 0.00 40.23 3.06
466 898 4.142556 ACAAGTCGGACACATTTTCGTTTT 60.143 37.500 11.27 0.00 0.00 2.43
467 899 3.375922 ACAAGTCGGACACATTTTCGTTT 59.624 39.130 11.27 0.00 0.00 3.60
468 900 2.940410 ACAAGTCGGACACATTTTCGTT 59.060 40.909 11.27 0.00 0.00 3.85
469 901 2.557317 ACAAGTCGGACACATTTTCGT 58.443 42.857 11.27 0.00 0.00 3.85
470 902 4.921470 ATACAAGTCGGACACATTTTCG 57.079 40.909 11.27 0.00 0.00 3.46
471 903 7.136119 TGAAAATACAAGTCGGACACATTTTC 58.864 34.615 24.12 24.12 39.56 2.29
472 904 7.033530 TGAAAATACAAGTCGGACACATTTT 57.966 32.000 11.27 14.01 0.00 1.82
473 905 6.627395 TGAAAATACAAGTCGGACACATTT 57.373 33.333 11.27 7.08 0.00 2.32
474 906 6.627395 TTGAAAATACAAGTCGGACACATT 57.373 33.333 11.27 1.38 0.00 2.71
475 907 6.241207 CTTGAAAATACAAGTCGGACACAT 57.759 37.500 11.27 0.00 41.32 3.21
476 908 5.666969 CTTGAAAATACAAGTCGGACACA 57.333 39.130 11.27 0.00 41.32 3.72
489 921 5.851720 TGCAATTTCAGCCACTTGAAAATA 58.148 33.333 5.41 0.00 46.63 1.40
496 928 3.825143 AACTTGCAATTTCAGCCACTT 57.175 38.095 0.00 0.00 0.00 3.16
502 934 6.601741 TTGGCTTAAAACTTGCAATTTCAG 57.398 33.333 0.00 0.96 0.00 3.02
505 937 7.806409 AGATTTGGCTTAAAACTTGCAATTT 57.194 28.000 0.00 0.89 28.09 1.82
506 938 7.641760 CAAGATTTGGCTTAAAACTTGCAATT 58.358 30.769 17.06 0.00 45.72 2.32
522 954 4.459390 TCATTGTGATGGCAAGATTTGG 57.541 40.909 0.00 0.00 33.93 3.28
523 955 6.788684 TTTTCATTGTGATGGCAAGATTTG 57.211 33.333 0.00 0.00 33.93 2.32
524 956 6.428771 CCTTTTTCATTGTGATGGCAAGATTT 59.571 34.615 0.00 0.00 33.93 2.17
527 959 4.262549 CCCTTTTTCATTGTGATGGCAAGA 60.263 41.667 0.00 0.00 33.93 3.02
530 962 2.971330 ACCCTTTTTCATTGTGATGGCA 59.029 40.909 0.00 0.00 33.93 4.92
536 968 3.131933 TGTGGTCACCCTTTTTCATTGTG 59.868 43.478 0.00 0.00 0.00 3.33
552 985 6.371389 GTTTTAGTTATGAACAGCTGTGGTC 58.629 40.000 22.49 15.91 41.28 4.02
568 1011 6.493458 AGCCACTCATATGTTTGGTTTTAGTT 59.507 34.615 19.93 3.17 0.00 2.24
569 1012 6.010219 AGCCACTCATATGTTTGGTTTTAGT 58.990 36.000 19.93 5.09 0.00 2.24
572 1015 6.891908 AGATAGCCACTCATATGTTTGGTTTT 59.108 34.615 19.93 12.83 0.00 2.43
589 1032 6.662755 AGATGTTAATGGTTGAAGATAGCCA 58.337 36.000 0.00 0.00 35.33 4.75
593 1036 9.904198 TGAATGAGATGTTAATGGTTGAAGATA 57.096 29.630 0.00 0.00 0.00 1.98
608 1051 6.713762 TTTCTGTTTGGTTGAATGAGATGT 57.286 33.333 0.00 0.00 0.00 3.06
616 1059 5.096443 AGCCATTTTTCTGTTTGGTTGAA 57.904 34.783 0.00 0.00 0.00 2.69
626 1069 6.704289 TGATGAGGAATAGCCATTTTTCTG 57.296 37.500 0.00 0.00 40.02 3.02
641 1085 0.325933 CACCAACCAGCTGATGAGGA 59.674 55.000 17.39 0.00 0.00 3.71
645 1089 2.292267 GGTATCACCAACCAGCTGATG 58.708 52.381 17.39 13.68 38.42 3.07
646 1090 1.212935 GGGTATCACCAACCAGCTGAT 59.787 52.381 17.39 0.00 41.02 2.90
659 1103 2.126057 TGATGCTGGTCATGGGTATCA 58.874 47.619 0.00 0.00 35.05 2.15
668 1112 3.888323 TGTTAGCTTTTTGATGCTGGTCA 59.112 39.130 0.00 0.00 40.08 4.02
669 1113 4.229876 GTGTTAGCTTTTTGATGCTGGTC 58.770 43.478 0.00 0.00 40.08 4.02
670 1114 3.636300 TGTGTTAGCTTTTTGATGCTGGT 59.364 39.130 0.00 0.00 40.08 4.00
671 1115 4.241590 TGTGTTAGCTTTTTGATGCTGG 57.758 40.909 0.00 0.00 40.08 4.85
674 1118 6.956299 AATCATGTGTTAGCTTTTTGATGC 57.044 33.333 0.00 0.00 0.00 3.91
677 1121 9.598517 AAGAAAAATCATGTGTTAGCTTTTTGA 57.401 25.926 0.00 0.00 0.00 2.69
714 1210 8.441608 GCACATGCAAATAAACACATGAAAATA 58.558 29.630 0.00 0.00 41.59 1.40
716 1212 6.656945 GCACATGCAAATAAACACATGAAAA 58.343 32.000 0.00 0.00 41.59 2.29
717 1213 6.225703 GCACATGCAAATAAACACATGAAA 57.774 33.333 0.00 0.00 41.59 2.69
733 1229 4.606673 CGTTGAAGAAAAACATGCACATGC 60.607 41.667 10.50 0.00 42.39 4.06
741 1237 8.925161 TTTGAGATTTCGTTGAAGAAAAACAT 57.075 26.923 0.00 0.00 42.52 2.71
743 1239 7.009174 TGCTTTGAGATTTCGTTGAAGAAAAAC 59.991 33.333 0.00 0.00 42.52 2.43
755 1251 6.360681 CCTACAGTTTTTGCTTTGAGATTTCG 59.639 38.462 0.00 0.00 0.00 3.46
784 1280 4.559726 AGGCCCCATTTTGATGTTGATAT 58.440 39.130 0.00 0.00 0.00 1.63
788 1284 4.550076 TTTAGGCCCCATTTTGATGTTG 57.450 40.909 0.00 0.00 0.00 3.33
830 1346 2.026915 CCTTGGTGATGTGGATGACTCA 60.027 50.000 0.00 0.00 0.00 3.41
831 1347 2.636830 CCTTGGTGATGTGGATGACTC 58.363 52.381 0.00 0.00 0.00 3.36
832 1348 1.283029 CCCTTGGTGATGTGGATGACT 59.717 52.381 0.00 0.00 0.00 3.41
833 1349 1.683011 CCCCTTGGTGATGTGGATGAC 60.683 57.143 0.00 0.00 0.00 3.06
834 1350 0.625316 CCCCTTGGTGATGTGGATGA 59.375 55.000 0.00 0.00 0.00 2.92
843 1359 4.285775 GGATTTTCAATTTCCCCTTGGTGA 59.714 41.667 0.00 0.00 0.00 4.02
876 1392 5.818857 GGTTTTATAGCGTTGGGATTCAGTA 59.181 40.000 0.00 0.00 0.00 2.74
879 1395 4.590918 TGGTTTTATAGCGTTGGGATTCA 58.409 39.130 0.00 0.00 0.00 2.57
882 1398 2.949644 GCTGGTTTTATAGCGTTGGGAT 59.050 45.455 0.00 0.00 0.00 3.85
943 1459 2.126149 CGCGTTGAGAGCTGAGCT 60.126 61.111 6.69 6.69 43.88 4.09
1053 1595 1.611491 GCGAGGTAGAAGAGGATGGAG 59.389 57.143 0.00 0.00 0.00 3.86
1237 1788 1.039233 AATGATTGGAGCTTGGGCGG 61.039 55.000 0.00 0.00 44.37 6.13
1253 1804 1.365699 GCAGCAAAGGCCAATGAATG 58.634 50.000 5.01 7.24 42.56 2.67
1274 1826 3.076258 TATCACCGTCAGCCCAGCG 62.076 63.158 0.00 0.00 0.00 5.18
1276 1828 1.226974 CGTATCACCGTCAGCCCAG 60.227 63.158 0.00 0.00 0.00 4.45
1277 1829 1.980232 ACGTATCACCGTCAGCCCA 60.980 57.895 0.00 0.00 35.95 5.36
1279 1831 0.801067 GACACGTATCACCGTCAGCC 60.801 60.000 0.00 0.00 39.45 4.85
1280 1832 1.132199 CGACACGTATCACCGTCAGC 61.132 60.000 0.00 0.00 39.45 4.26
1281 1833 1.132199 GCGACACGTATCACCGTCAG 61.132 60.000 0.00 0.00 39.45 3.51
1282 1834 1.154169 GCGACACGTATCACCGTCA 60.154 57.895 0.00 0.00 39.45 4.35
1283 1835 0.455633 AAGCGACACGTATCACCGTC 60.456 55.000 0.00 0.00 39.45 4.79
1284 1836 0.731514 CAAGCGACACGTATCACCGT 60.732 55.000 0.00 0.00 42.87 4.83
1285 1837 1.988409 CAAGCGACACGTATCACCG 59.012 57.895 0.00 0.00 0.00 4.94
1286 1838 1.011968 TGCAAGCGACACGTATCACC 61.012 55.000 0.00 0.00 0.00 4.02
1287 1839 0.093026 GTGCAAGCGACACGTATCAC 59.907 55.000 0.00 0.00 0.00 3.06
1288 1840 0.038618 AGTGCAAGCGACACGTATCA 60.039 50.000 0.00 0.00 42.94 2.15
1289 1841 0.366871 CAGTGCAAGCGACACGTATC 59.633 55.000 0.00 0.00 42.94 2.24
1290 1842 0.319555 ACAGTGCAAGCGACACGTAT 60.320 50.000 0.00 0.00 42.94 3.06
1291 1843 0.311477 TACAGTGCAAGCGACACGTA 59.689 50.000 0.00 4.96 42.94 3.57
1292 1844 1.066752 TACAGTGCAAGCGACACGT 59.933 52.632 0.00 0.00 42.94 4.49
1293 1845 1.487231 GTACAGTGCAAGCGACACG 59.513 57.895 0.00 0.00 42.94 4.49
1294 1846 0.600255 AGGTACAGTGCAAGCGACAC 60.600 55.000 0.00 0.00 38.35 3.67
1295 1847 0.599991 CAGGTACAGTGCAAGCGACA 60.600 55.000 0.00 0.00 0.00 4.35
1307 1859 2.222213 CGCATTTCGTCAAACAGGTACA 59.778 45.455 0.00 0.00 0.00 2.90
1470 2022 0.944311 AAGTAGTTGTGCGTCAGCCG 60.944 55.000 0.00 0.00 44.33 5.52
1519 2071 3.003763 AGAACCGCCAGTCCTCCC 61.004 66.667 0.00 0.00 0.00 4.30
1645 2197 5.429957 AAGTTCTGAAAGCAAGCAAGTAG 57.570 39.130 0.00 0.00 0.00 2.57
1646 2198 5.835113 AAAGTTCTGAAAGCAAGCAAGTA 57.165 34.783 0.00 0.00 0.00 2.24
1647 2199 4.725790 AAAGTTCTGAAAGCAAGCAAGT 57.274 36.364 0.00 0.00 0.00 3.16
1656 2208 8.352201 TCATTGATGTACCAAAAGTTCTGAAAG 58.648 33.333 0.00 0.00 0.00 2.62
1699 2251 3.308438 AGCAAAAATAGCAGCAAGGTG 57.692 42.857 0.00 0.00 0.00 4.00
1703 2255 8.249638 TGATTTATGTAGCAAAAATAGCAGCAA 58.750 29.630 0.00 0.00 0.00 3.91
1733 2288 4.598406 TGTCAATCATGAATTTCGACCG 57.402 40.909 0.00 0.00 37.30 4.79
1763 2342 1.074405 ACACCTGCATCCAACAGACAT 59.926 47.619 0.00 0.00 37.32 3.06
1767 2346 2.030540 CAGAAACACCTGCATCCAACAG 60.031 50.000 0.00 0.00 34.82 3.16
1977 2556 3.391382 CCCCACAGTCCGTCCTCC 61.391 72.222 0.00 0.00 0.00 4.30
1986 2565 3.379445 CGCGAGTACCCCCACAGT 61.379 66.667 0.00 0.00 0.00 3.55
2010 2589 1.414527 GCTGCTCGCCGAAGTAGTTC 61.415 60.000 0.00 0.00 32.21 3.01
2097 2676 1.499056 GAGGCACATGCTGTTGACG 59.501 57.895 3.48 0.00 41.70 4.35
2378 2957 6.016192 CAGAGGATACATGTTACAGTCGGTAT 60.016 42.308 2.30 0.00 41.41 2.73
2383 2962 6.920758 GTGATCAGAGGATACATGTTACAGTC 59.079 42.308 2.30 0.18 41.41 3.51
2399 2978 6.808008 ACACAAATTAACAGGTGATCAGAG 57.192 37.500 0.00 0.00 35.33 3.35
2400 2979 7.552687 GGATACACAAATTAACAGGTGATCAGA 59.447 37.037 0.00 0.00 35.33 3.27
2510 3089 6.114089 ACTTCAATGTCATGATTCTCAGAGG 58.886 40.000 0.00 0.00 0.00 3.69
2566 3145 1.405933 GGGATGGCCAAAATGCAACTC 60.406 52.381 10.96 0.00 35.15 3.01
2598 3177 2.076863 AGACCTTGCTGCGTTAACATC 58.923 47.619 6.39 0.00 0.00 3.06
2739 3318 0.411452 ACTGAGGAGGCTGAAGAGGA 59.589 55.000 0.00 0.00 0.00 3.71
2782 3361 1.860641 TGAAGAGCTTATCCCCGTGA 58.139 50.000 0.00 0.00 0.00 4.35
2784 3363 2.771943 TGAATGAAGAGCTTATCCCCGT 59.228 45.455 0.00 0.00 0.00 5.28
2813 3392 1.918253 ATCCAAAGCCGAGGATGCT 59.082 52.632 1.00 0.00 42.86 3.79
2816 3395 1.152881 GGCATCCAAAGCCGAGGAT 60.153 57.895 0.00 0.00 45.30 3.24
2833 3412 1.069765 CCATTGGTCGATCCCTCGG 59.930 63.158 0.00 0.00 45.10 4.63
2840 3419 1.812571 GTTGAAGCACCATTGGTCGAT 59.187 47.619 5.04 0.00 31.02 3.59
2852 3431 0.468226 AGGTCCTTGTCGTTGAAGCA 59.532 50.000 0.00 0.00 0.00 3.91
2902 3481 1.106351 TGTTGCTGCACCCGTTGAAT 61.106 50.000 0.00 0.00 0.00 2.57
2906 3485 3.595758 GCTGTTGCTGCACCCGTT 61.596 61.111 0.00 0.00 36.03 4.44
2918 3497 2.520968 GTCACCCCCAAGGCTGTT 59.479 61.111 0.00 0.00 40.58 3.16
2927 3506 4.796495 GACATGCCGGTCACCCCC 62.796 72.222 1.90 0.00 37.73 5.40
2986 3565 1.486310 CTATGGGTTCCTGTGCTAGCA 59.514 52.381 14.93 14.93 0.00 3.49
3007 3586 3.840102 GCCGGAGCAATCCATAACGGA 62.840 57.143 5.05 0.00 43.96 4.69
3140 3719 4.553323 CAACAAATTTCCTTGCTCCTCTG 58.447 43.478 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.