Multiple sequence alignment - TraesCS5D01G225500

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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 TraesCS5D01G225500 chr5D 100.000 2375 0 0 1 2375 333382253 333384627 0.000000e+00 4386.0
1 TraesCS5D01G225500 chr5D 81.250 96 18 0 1088 1183 88520309 88520404 7.040000e-11 78.7
2 TraesCS5D01G225500 chr5A 95.677 1966 47 13 443 2375 435040650 435042610 0.000000e+00 3125.0
3 TraesCS5D01G225500 chr5A 85.009 567 61 12 815 1380 686506677 686506134 2.670000e-154 555.0
4 TraesCS5D01G225500 chr5A 81.250 96 18 0 1088 1183 82306838 82306933 7.040000e-11 78.7
5 TraesCS5D01G225500 chr5B 95.487 1950 56 11 446 2375 389820454 389822391 0.000000e+00 3085.0
6 TraesCS5D01G225500 chr5B 86.301 73 10 0 1111 1183 94092999 94093071 1.960000e-11 80.5
7 TraesCS5D01G225500 chr4D 81.862 419 33 22 57 435 131266625 131266210 1.770000e-81 313.0
8 TraesCS5D01G225500 chr1B 81.679 131 21 3 312 441 567187464 567187336 3.230000e-19 106.0
9 TraesCS5D01G225500 chr6B 80.597 134 23 3 312 445 30413579 30413449 1.500000e-17 100.0
10 TraesCS5D01G225500 chr1A 88.312 77 7 2 2255 2330 14027775 14027700 9.040000e-15 91.6


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 TraesCS5D01G225500 chr5D 333382253 333384627 2374 False 4386 4386 100.000 1 2375 1 chr5D.!!$F2 2374
1 TraesCS5D01G225500 chr5A 435040650 435042610 1960 False 3125 3125 95.677 443 2375 1 chr5A.!!$F2 1932
2 TraesCS5D01G225500 chr5A 686506134 686506677 543 True 555 555 85.009 815 1380 1 chr5A.!!$R1 565
3 TraesCS5D01G225500 chr5B 389820454 389822391 1937 False 3085 3085 95.487 446 2375 1 chr5B.!!$F2 1929

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
308 309 0.17902 CGAGGGGATTGGCATGCTAA 60.179 55.0 19.4 19.4 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 2311 0.570734 CACGTTAATACTCGGCAGCG 59.429 55.0 0.0 0.0 0.0 5.18 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
25 26 8.854614 AAGGTATGAGAAAATATGGCATACTC 57.145 34.615 9.83 11.94 40.48 2.59
26 27 7.398024 AGGTATGAGAAAATATGGCATACTCC 58.602 38.462 9.83 0.50 40.48 3.85
27 28 6.313905 GGTATGAGAAAATATGGCATACTCCG 59.686 42.308 9.83 0.00 40.48 4.63
28 29 5.290493 TGAGAAAATATGGCATACTCCGT 57.710 39.130 9.83 0.00 0.00 4.69
29 30 5.680619 TGAGAAAATATGGCATACTCCGTT 58.319 37.500 9.83 0.00 0.00 4.44
30 31 5.527214 TGAGAAAATATGGCATACTCCGTTG 59.473 40.000 9.83 0.00 0.00 4.10
31 32 4.821805 AGAAAATATGGCATACTCCGTTGG 59.178 41.667 9.83 0.00 0.00 3.77
32 33 2.185004 ATATGGCATACTCCGTTGGC 57.815 50.000 9.83 0.00 38.77 4.52
33 34 0.249699 TATGGCATACTCCGTTGGCG 60.250 55.000 2.32 0.00 41.00 5.69
43 44 3.790177 CGTTGGCGGCTACTTACC 58.210 61.111 20.05 0.00 0.00 2.85
44 45 1.217244 CGTTGGCGGCTACTTACCT 59.783 57.895 20.05 0.00 0.00 3.08
45 46 1.082117 CGTTGGCGGCTACTTACCTG 61.082 60.000 20.05 1.18 0.00 4.00
46 47 1.078708 TTGGCGGCTACTTACCTGC 60.079 57.895 11.43 0.00 0.00 4.85
47 48 2.203029 GGCGGCTACTTACCTGCC 60.203 66.667 0.00 0.00 42.94 4.85
48 49 2.732619 GGCGGCTACTTACCTGCCT 61.733 63.158 0.00 0.00 44.09 4.75
49 50 1.397390 GGCGGCTACTTACCTGCCTA 61.397 60.000 0.00 0.00 44.09 3.93
50 51 0.680061 GCGGCTACTTACCTGCCTAT 59.320 55.000 0.00 0.00 44.09 2.57
51 52 1.605712 GCGGCTACTTACCTGCCTATG 60.606 57.143 0.00 0.00 44.09 2.23
52 53 1.000955 CGGCTACTTACCTGCCTATGG 59.999 57.143 0.00 0.00 44.09 2.74
53 54 2.326428 GGCTACTTACCTGCCTATGGA 58.674 52.381 0.00 0.00 43.05 3.41
54 55 2.037381 GGCTACTTACCTGCCTATGGAC 59.963 54.545 0.00 0.00 43.05 4.02
55 56 2.966516 GCTACTTACCTGCCTATGGACT 59.033 50.000 0.00 0.00 0.00 3.85
56 57 3.243907 GCTACTTACCTGCCTATGGACTG 60.244 52.174 0.00 0.00 0.00 3.51
57 58 2.119495 ACTTACCTGCCTATGGACTGG 58.881 52.381 0.00 0.00 0.00 4.00
58 59 1.417890 CTTACCTGCCTATGGACTGGG 59.582 57.143 0.00 0.00 0.00 4.45
63 64 2.512896 CCTATGGACTGGGCAGCC 59.487 66.667 1.26 1.26 0.00 4.85
64 65 2.109799 CTATGGACTGGGCAGCCG 59.890 66.667 5.00 0.00 0.00 5.52
65 66 3.466791 CTATGGACTGGGCAGCCGG 62.467 68.421 5.00 0.00 0.00 6.13
81 82 3.499737 GGCGTTGATGGCCGTCAG 61.500 66.667 26.16 17.44 41.39 3.51
82 83 4.166011 GCGTTGATGGCCGTCAGC 62.166 66.667 27.07 27.07 42.60 4.26
83 84 2.741985 CGTTGATGGCCGTCAGCA 60.742 61.111 32.94 17.31 46.50 4.41
84 85 2.743752 CGTTGATGGCCGTCAGCAG 61.744 63.158 32.94 23.74 43.16 4.24
85 86 1.672356 GTTGATGGCCGTCAGCAGT 60.672 57.895 30.54 0.00 43.16 4.40
86 87 1.073025 TTGATGGCCGTCAGCAGTT 59.927 52.632 26.16 0.00 43.16 3.16
87 88 1.236616 TTGATGGCCGTCAGCAGTTG 61.237 55.000 26.16 0.00 43.16 3.16
88 89 1.375908 GATGGCCGTCAGCAGTTGA 60.376 57.895 20.55 0.00 46.50 3.18
89 90 0.745845 GATGGCCGTCAGCAGTTGAT 60.746 55.000 20.55 0.00 46.50 2.57
90 91 0.745845 ATGGCCGTCAGCAGTTGATC 60.746 55.000 0.00 0.00 46.50 2.92
91 92 2.109126 GGCCGTCAGCAGTTGATCC 61.109 63.158 0.00 0.00 46.50 3.36
92 93 1.375908 GCCGTCAGCAGTTGATCCA 60.376 57.895 0.00 0.00 42.97 3.41
93 94 1.364626 GCCGTCAGCAGTTGATCCAG 61.365 60.000 0.00 0.00 42.97 3.86
94 95 0.247460 CCGTCAGCAGTTGATCCAGA 59.753 55.000 0.00 0.00 38.29 3.86
95 96 1.638133 CGTCAGCAGTTGATCCAGAG 58.362 55.000 0.00 0.00 38.29 3.35
96 97 1.203287 CGTCAGCAGTTGATCCAGAGA 59.797 52.381 0.00 0.00 38.29 3.10
97 98 2.734809 CGTCAGCAGTTGATCCAGAGAG 60.735 54.545 0.00 0.00 38.29 3.20
98 99 1.829849 TCAGCAGTTGATCCAGAGAGG 59.170 52.381 0.00 0.00 39.47 3.69
106 107 2.757508 TCCAGAGAGGAGGCGCTG 60.758 66.667 7.64 0.00 43.07 5.18
107 108 4.527583 CCAGAGAGGAGGCGCTGC 62.528 72.222 7.64 0.00 41.22 5.25
108 109 3.459965 CAGAGAGGAGGCGCTGCT 61.460 66.667 7.64 3.64 34.11 4.24
109 110 3.459965 AGAGAGGAGGCGCTGCTG 61.460 66.667 7.64 0.00 30.82 4.41
110 111 3.768922 GAGAGGAGGCGCTGCTGT 61.769 66.667 7.64 2.17 30.82 4.40
111 112 4.079850 AGAGGAGGCGCTGCTGTG 62.080 66.667 7.64 0.00 30.82 3.66
121 122 3.314331 CTGCTGTGGGGACGACCT 61.314 66.667 3.44 0.00 40.03 3.85
122 123 3.596066 CTGCTGTGGGGACGACCTG 62.596 68.421 3.44 0.00 40.03 4.00
124 125 3.314331 CTGTGGGGACGACCTGCT 61.314 66.667 3.44 0.00 40.03 4.24
125 126 3.302347 CTGTGGGGACGACCTGCTC 62.302 68.421 3.44 0.00 40.03 4.26
127 128 4.671590 TGGGGACGACCTGCTCGA 62.672 66.667 3.44 0.00 46.14 4.04
128 129 4.131088 GGGGACGACCTGCTCGAC 62.131 72.222 3.44 0.00 46.14 4.20
129 130 4.477975 GGGACGACCTGCTCGACG 62.478 72.222 3.44 0.00 46.14 5.12
130 131 4.477975 GGACGACCTGCTCGACGG 62.478 72.222 0.37 0.00 46.14 4.79
131 132 3.735029 GACGACCTGCTCGACGGT 61.735 66.667 0.37 0.00 46.14 4.83
132 133 3.664223 GACGACCTGCTCGACGGTC 62.664 68.421 11.81 11.81 46.14 4.79
141 142 3.872728 TCGACGGTCGAGGCGATG 61.873 66.667 27.66 0.00 44.82 3.84
143 144 4.194720 GACGGTCGAGGCGATGCT 62.195 66.667 0.00 0.00 38.42 3.79
144 145 4.498520 ACGGTCGAGGCGATGCTG 62.499 66.667 0.00 0.00 38.42 4.41
146 147 4.899239 GGTCGAGGCGATGCTGGG 62.899 72.222 0.00 0.00 38.42 4.45
147 148 4.899239 GTCGAGGCGATGCTGGGG 62.899 72.222 0.00 0.00 38.42 4.96
166 167 4.106925 GGTGGGGCAGCAGAGGAG 62.107 72.222 0.00 0.00 0.00 3.69
167 168 3.005539 GTGGGGCAGCAGAGGAGA 61.006 66.667 0.00 0.00 0.00 3.71
168 169 2.686470 TGGGGCAGCAGAGGAGAG 60.686 66.667 0.00 0.00 0.00 3.20
169 170 4.173924 GGGGCAGCAGAGGAGAGC 62.174 72.222 0.00 0.00 0.00 4.09
170 171 3.397439 GGGCAGCAGAGGAGAGCA 61.397 66.667 0.00 0.00 0.00 4.26
171 172 2.187424 GGCAGCAGAGGAGAGCAG 59.813 66.667 0.00 0.00 0.00 4.24
172 173 2.187424 GCAGCAGAGGAGAGCAGG 59.813 66.667 0.00 0.00 0.00 4.85
173 174 2.187424 CAGCAGAGGAGAGCAGGC 59.813 66.667 0.00 0.00 0.00 4.85
174 175 3.459965 AGCAGAGGAGAGCAGGCG 61.460 66.667 0.00 0.00 0.00 5.52
175 176 4.527583 GCAGAGGAGAGCAGGCGG 62.528 72.222 0.00 0.00 0.00 6.13
176 177 3.073735 CAGAGGAGAGCAGGCGGT 61.074 66.667 0.00 0.00 0.00 5.68
177 178 3.073735 AGAGGAGAGCAGGCGGTG 61.074 66.667 0.00 0.00 0.00 4.94
178 179 4.154347 GAGGAGAGCAGGCGGTGG 62.154 72.222 0.00 0.00 0.00 4.61
224 225 4.803426 GGCACGAGCGACAGGAGG 62.803 72.222 0.00 0.00 43.41 4.30
225 226 4.803426 GCACGAGCGACAGGAGGG 62.803 72.222 0.00 0.00 0.00 4.30
226 227 3.062466 CACGAGCGACAGGAGGGA 61.062 66.667 0.00 0.00 0.00 4.20
227 228 3.063084 ACGAGCGACAGGAGGGAC 61.063 66.667 0.00 0.00 0.00 4.46
228 229 4.180946 CGAGCGACAGGAGGGACG 62.181 72.222 0.00 0.00 0.00 4.79
229 230 3.827898 GAGCGACAGGAGGGACGG 61.828 72.222 0.00 0.00 0.00 4.79
259 260 4.056125 TGCGAGGCACTGACGAGG 62.056 66.667 0.00 0.00 41.55 4.63
261 262 4.056125 CGAGGCACTGACGAGGCA 62.056 66.667 0.00 0.00 41.55 4.75
262 263 2.125753 GAGGCACTGACGAGGCAG 60.126 66.667 4.09 4.09 41.55 4.85
263 264 2.601666 AGGCACTGACGAGGCAGA 60.602 61.111 13.60 0.00 37.18 4.26
264 265 1.954362 GAGGCACTGACGAGGCAGAT 61.954 60.000 13.60 0.00 41.55 2.90
265 266 1.812922 GGCACTGACGAGGCAGATG 60.813 63.158 13.60 8.34 39.20 2.90
266 267 1.216444 GCACTGACGAGGCAGATGA 59.784 57.895 13.60 0.00 39.20 2.92
267 268 0.805322 GCACTGACGAGGCAGATGAG 60.805 60.000 13.60 1.02 39.20 2.90
268 269 0.813821 CACTGACGAGGCAGATGAGA 59.186 55.000 13.60 0.00 39.20 3.27
269 270 1.203287 CACTGACGAGGCAGATGAGAA 59.797 52.381 13.60 0.00 39.20 2.87
270 271 1.476085 ACTGACGAGGCAGATGAGAAG 59.524 52.381 13.60 0.00 39.20 2.85
271 272 1.747924 CTGACGAGGCAGATGAGAAGA 59.252 52.381 0.00 0.00 38.14 2.87
272 273 1.747924 TGACGAGGCAGATGAGAAGAG 59.252 52.381 0.00 0.00 0.00 2.85
273 274 2.020720 GACGAGGCAGATGAGAAGAGA 58.979 52.381 0.00 0.00 0.00 3.10
274 275 2.425312 GACGAGGCAGATGAGAAGAGAA 59.575 50.000 0.00 0.00 0.00 2.87
275 276 2.165437 ACGAGGCAGATGAGAAGAGAAC 59.835 50.000 0.00 0.00 0.00 3.01
276 277 2.794282 CGAGGCAGATGAGAAGAGAACG 60.794 54.545 0.00 0.00 0.00 3.95
277 278 2.425312 GAGGCAGATGAGAAGAGAACGA 59.575 50.000 0.00 0.00 0.00 3.85
278 279 3.030291 AGGCAGATGAGAAGAGAACGAT 58.970 45.455 0.00 0.00 0.00 3.73
279 280 3.068024 AGGCAGATGAGAAGAGAACGATC 59.932 47.826 0.00 0.00 0.00 3.69
280 281 3.181482 GGCAGATGAGAAGAGAACGATCA 60.181 47.826 0.00 0.00 0.00 2.92
281 282 4.428209 GCAGATGAGAAGAGAACGATCAA 58.572 43.478 0.00 0.00 0.00 2.57
282 283 4.503734 GCAGATGAGAAGAGAACGATCAAG 59.496 45.833 0.00 0.00 0.00 3.02
283 284 5.042593 CAGATGAGAAGAGAACGATCAAGG 58.957 45.833 0.00 0.00 0.00 3.61
284 285 4.952957 AGATGAGAAGAGAACGATCAAGGA 59.047 41.667 0.00 0.00 0.00 3.36
285 286 4.442375 TGAGAAGAGAACGATCAAGGAC 57.558 45.455 0.00 0.00 0.00 3.85
286 287 3.119814 TGAGAAGAGAACGATCAAGGACG 60.120 47.826 0.00 0.00 0.00 4.79
287 288 2.820787 AGAAGAGAACGATCAAGGACGT 59.179 45.455 0.00 0.00 44.57 4.34
288 289 2.638556 AGAGAACGATCAAGGACGTG 57.361 50.000 0.00 0.00 42.43 4.49
289 290 0.992802 GAGAACGATCAAGGACGTGC 59.007 55.000 0.00 0.00 42.43 5.34
290 291 0.732880 AGAACGATCAAGGACGTGCG 60.733 55.000 0.00 0.00 42.13 5.34
291 292 0.731514 GAACGATCAAGGACGTGCGA 60.732 55.000 0.00 0.00 42.43 5.10
292 293 0.732880 AACGATCAAGGACGTGCGAG 60.733 55.000 0.00 0.00 42.43 5.03
293 294 1.874019 CGATCAAGGACGTGCGAGG 60.874 63.158 0.00 0.00 0.00 4.63
294 295 1.519455 GATCAAGGACGTGCGAGGG 60.519 63.158 0.00 0.00 0.00 4.30
295 296 2.907897 GATCAAGGACGTGCGAGGGG 62.908 65.000 0.00 0.00 0.00 4.79
296 297 3.691342 CAAGGACGTGCGAGGGGA 61.691 66.667 0.00 0.00 0.00 4.81
297 298 2.683933 AAGGACGTGCGAGGGGAT 60.684 61.111 0.00 0.00 0.00 3.85
298 299 2.291043 AAGGACGTGCGAGGGGATT 61.291 57.895 0.00 0.00 0.00 3.01
299 300 2.511600 GGACGTGCGAGGGGATTG 60.512 66.667 0.00 0.00 0.00 2.67
300 301 2.511600 GACGTGCGAGGGGATTGG 60.512 66.667 0.00 0.00 0.00 3.16
301 302 4.778143 ACGTGCGAGGGGATTGGC 62.778 66.667 0.00 0.00 0.00 4.52
302 303 4.776322 CGTGCGAGGGGATTGGCA 62.776 66.667 0.00 0.00 0.00 4.92
303 304 2.124151 GTGCGAGGGGATTGGCAT 60.124 61.111 0.00 0.00 37.77 4.40
304 305 2.124193 TGCGAGGGGATTGGCATG 60.124 61.111 0.00 0.00 0.00 4.06
305 306 3.599704 GCGAGGGGATTGGCATGC 61.600 66.667 9.90 9.90 0.00 4.06
306 307 2.194056 CGAGGGGATTGGCATGCT 59.806 61.111 18.92 0.00 0.00 3.79
307 308 1.451504 CGAGGGGATTGGCATGCTA 59.548 57.895 18.92 9.16 0.00 3.49
308 309 0.179020 CGAGGGGATTGGCATGCTAA 60.179 55.000 19.40 19.40 0.00 3.09
309 310 1.546323 CGAGGGGATTGGCATGCTAAT 60.546 52.381 27.10 27.10 0.00 1.73
310 311 2.601905 GAGGGGATTGGCATGCTAATT 58.398 47.619 27.38 13.75 0.00 1.40
311 312 2.967887 GAGGGGATTGGCATGCTAATTT 59.032 45.455 27.38 14.95 0.00 1.82
312 313 4.151883 GAGGGGATTGGCATGCTAATTTA 58.848 43.478 27.38 3.01 0.00 1.40
313 314 3.897505 AGGGGATTGGCATGCTAATTTAC 59.102 43.478 27.38 20.00 0.00 2.01
314 315 3.897505 GGGGATTGGCATGCTAATTTACT 59.102 43.478 27.38 8.59 0.00 2.24
315 316 5.076873 GGGGATTGGCATGCTAATTTACTA 58.923 41.667 27.38 1.05 0.00 1.82
316 317 5.048013 GGGGATTGGCATGCTAATTTACTAC 60.048 44.000 27.38 14.77 0.00 2.73
317 318 5.770162 GGGATTGGCATGCTAATTTACTACT 59.230 40.000 27.38 6.36 0.00 2.57
318 319 6.294176 GGGATTGGCATGCTAATTTACTACTG 60.294 42.308 27.38 0.00 0.00 2.74
319 320 6.263168 GGATTGGCATGCTAATTTACTACTGT 59.737 38.462 27.38 4.89 0.00 3.55
320 321 7.444183 GGATTGGCATGCTAATTTACTACTGTA 59.556 37.037 27.38 0.00 0.00 2.74
321 322 7.548196 TTGGCATGCTAATTTACTACTGTAC 57.452 36.000 18.92 0.00 0.00 2.90
322 323 6.053005 TGGCATGCTAATTTACTACTGTACC 58.947 40.000 18.92 0.00 0.00 3.34
323 324 5.469084 GGCATGCTAATTTACTACTGTACCC 59.531 44.000 18.92 0.00 0.00 3.69
324 325 6.289064 GCATGCTAATTTACTACTGTACCCT 58.711 40.000 11.37 0.00 0.00 4.34
325 326 6.766467 GCATGCTAATTTACTACTGTACCCTT 59.234 38.462 11.37 0.00 0.00 3.95
326 327 7.282450 GCATGCTAATTTACTACTGTACCCTTT 59.718 37.037 11.37 0.00 0.00 3.11
327 328 8.827677 CATGCTAATTTACTACTGTACCCTTTC 58.172 37.037 0.00 0.00 0.00 2.62
328 329 8.142485 TGCTAATTTACTACTGTACCCTTTCT 57.858 34.615 0.00 0.00 0.00 2.52
329 330 9.258629 TGCTAATTTACTACTGTACCCTTTCTA 57.741 33.333 0.00 0.00 0.00 2.10
330 331 9.526713 GCTAATTTACTACTGTACCCTTTCTAC 57.473 37.037 0.00 0.00 0.00 2.59
333 334 7.838079 TTTACTACTGTACCCTTTCTACACA 57.162 36.000 0.00 0.00 0.00 3.72
334 335 7.838079 TTACTACTGTACCCTTTCTACACAA 57.162 36.000 0.00 0.00 0.00 3.33
335 336 6.736110 ACTACTGTACCCTTTCTACACAAA 57.264 37.500 0.00 0.00 0.00 2.83
336 337 7.128234 ACTACTGTACCCTTTCTACACAAAA 57.872 36.000 0.00 0.00 0.00 2.44
337 338 7.567458 ACTACTGTACCCTTTCTACACAAAAA 58.433 34.615 0.00 0.00 0.00 1.94
338 339 8.215736 ACTACTGTACCCTTTCTACACAAAAAT 58.784 33.333 0.00 0.00 0.00 1.82
339 340 9.715121 CTACTGTACCCTTTCTACACAAAAATA 57.285 33.333 0.00 0.00 0.00 1.40
340 341 8.983702 ACTGTACCCTTTCTACACAAAAATAA 57.016 30.769 0.00 0.00 0.00 1.40
341 342 9.411189 ACTGTACCCTTTCTACACAAAAATAAA 57.589 29.630 0.00 0.00 0.00 1.40
342 343 9.673454 CTGTACCCTTTCTACACAAAAATAAAC 57.327 33.333 0.00 0.00 0.00 2.01
343 344 9.186837 TGTACCCTTTCTACACAAAAATAAACA 57.813 29.630 0.00 0.00 0.00 2.83
387 388 9.521503 GATTTAATGGTTAGGAAAAATCAGAGC 57.478 33.333 0.00 0.00 34.82 4.09
388 389 8.650143 TTTAATGGTTAGGAAAAATCAGAGCT 57.350 30.769 0.00 0.00 0.00 4.09
389 390 6.521151 AATGGTTAGGAAAAATCAGAGCTG 57.479 37.500 0.00 0.00 0.00 4.24
390 391 4.335416 TGGTTAGGAAAAATCAGAGCTGG 58.665 43.478 0.00 0.00 0.00 4.85
391 392 4.042809 TGGTTAGGAAAAATCAGAGCTGGA 59.957 41.667 0.00 0.00 0.00 3.86
392 393 4.637977 GGTTAGGAAAAATCAGAGCTGGAG 59.362 45.833 0.00 0.00 0.00 3.86
393 394 5.249420 GTTAGGAAAAATCAGAGCTGGAGT 58.751 41.667 0.00 0.00 0.00 3.85
394 395 4.379302 AGGAAAAATCAGAGCTGGAGTT 57.621 40.909 0.00 0.00 0.00 3.01
395 396 5.505181 AGGAAAAATCAGAGCTGGAGTTA 57.495 39.130 0.00 0.00 0.00 2.24
396 397 5.249420 AGGAAAAATCAGAGCTGGAGTTAC 58.751 41.667 0.00 0.00 0.00 2.50
397 398 5.003804 GGAAAAATCAGAGCTGGAGTTACA 58.996 41.667 0.00 0.00 0.00 2.41
398 399 5.649831 GGAAAAATCAGAGCTGGAGTTACAT 59.350 40.000 0.00 0.00 0.00 2.29
399 400 6.404074 GGAAAAATCAGAGCTGGAGTTACATG 60.404 42.308 0.00 0.00 0.00 3.21
400 401 5.426689 AAATCAGAGCTGGAGTTACATGA 57.573 39.130 0.00 0.00 0.00 3.07
401 402 5.426689 AATCAGAGCTGGAGTTACATGAA 57.573 39.130 0.00 0.00 0.00 2.57
402 403 4.890158 TCAGAGCTGGAGTTACATGAAA 57.110 40.909 0.00 0.00 0.00 2.69
403 404 5.426689 TCAGAGCTGGAGTTACATGAAAT 57.573 39.130 0.00 0.00 0.00 2.17
404 405 5.809001 TCAGAGCTGGAGTTACATGAAATT 58.191 37.500 0.00 0.00 0.00 1.82
405 406 6.946340 TCAGAGCTGGAGTTACATGAAATTA 58.054 36.000 0.00 0.00 0.00 1.40
406 407 6.818644 TCAGAGCTGGAGTTACATGAAATTAC 59.181 38.462 0.00 0.00 0.00 1.89
407 408 6.595326 CAGAGCTGGAGTTACATGAAATTACA 59.405 38.462 0.00 0.00 0.00 2.41
408 409 7.119699 CAGAGCTGGAGTTACATGAAATTACAA 59.880 37.037 0.00 0.00 0.00 2.41
409 410 7.665559 AGAGCTGGAGTTACATGAAATTACAAA 59.334 33.333 0.00 0.00 0.00 2.83
410 411 8.353423 AGCTGGAGTTACATGAAATTACAAAT 57.647 30.769 0.00 0.00 0.00 2.32
411 412 8.806146 AGCTGGAGTTACATGAAATTACAAATT 58.194 29.630 0.00 0.00 0.00 1.82
412 413 8.863049 GCTGGAGTTACATGAAATTACAAATTG 58.137 33.333 0.00 0.00 0.00 2.32
413 414 9.912634 CTGGAGTTACATGAAATTACAAATTGT 57.087 29.630 3.43 3.43 0.00 2.71
430 431 7.424227 CAAATTGTAATTTGCCAATCACTGT 57.576 32.000 14.85 0.00 45.86 3.55
431 432 8.531622 CAAATTGTAATTTGCCAATCACTGTA 57.468 30.769 14.85 0.00 45.86 2.74
432 433 8.986847 CAAATTGTAATTTGCCAATCACTGTAA 58.013 29.630 14.85 0.00 45.86 2.41
433 434 9.553064 AAATTGTAATTTGCCAATCACTGTAAA 57.447 25.926 2.01 0.00 37.24 2.01
434 435 9.553064 AATTGTAATTTGCCAATCACTGTAAAA 57.447 25.926 0.00 0.00 31.15 1.52
435 436 7.938563 TGTAATTTGCCAATCACTGTAAAAC 57.061 32.000 0.00 0.00 0.00 2.43
436 437 7.492524 TGTAATTTGCCAATCACTGTAAAACA 58.507 30.769 0.00 0.00 0.00 2.83
528 529 8.233868 TGTACAATTCTCACGTGAAAATATTGG 58.766 33.333 27.15 17.53 0.00 3.16
688 696 2.388735 TCGTCTACTGGCTGATCCATT 58.611 47.619 0.00 0.00 45.50 3.16
701 709 5.069516 GGCTGATCCATTGGTACATGAAATT 59.930 40.000 0.00 0.00 33.77 1.82
943 955 1.625818 AGCTAGCTAGTTTGCACCTGT 59.374 47.619 17.69 0.00 34.99 4.00
971 983 2.829206 CGTTCGCACCACCTTTGCA 61.829 57.895 0.00 0.00 40.20 4.08
1383 1395 6.605194 TGTCTCTCAAGCTCTGATATTACTGT 59.395 38.462 0.00 0.00 32.14 3.55
1384 1396 6.917477 GTCTCTCAAGCTCTGATATTACTGTG 59.083 42.308 0.00 0.00 32.14 3.66
1518 1530 2.292828 TCTCCCTTTCCTTTTGCTGG 57.707 50.000 0.00 0.00 0.00 4.85
1520 1532 0.188342 TCCCTTTCCTTTTGCTGGCT 59.812 50.000 0.00 0.00 0.00 4.75
1657 1678 3.012518 CTGCCCAAGTTACAAGGATGAG 58.987 50.000 0.00 0.00 0.00 2.90
1658 1679 1.745653 GCCCAAGTTACAAGGATGAGC 59.254 52.381 0.00 0.00 0.00 4.26
1660 1681 3.624777 CCCAAGTTACAAGGATGAGCAT 58.375 45.455 0.00 0.00 0.00 3.79
1662 1683 5.380043 CCCAAGTTACAAGGATGAGCATAT 58.620 41.667 0.00 0.00 0.00 1.78
1663 1684 6.533730 CCCAAGTTACAAGGATGAGCATATA 58.466 40.000 0.00 0.00 0.00 0.86
2012 2050 4.680440 GCTTGTGGAAAAGGAAAAAGCAGA 60.680 41.667 0.00 0.00 0.00 4.26
2058 2096 3.140325 TCTTGGACACAGAATCCCAAC 57.860 47.619 0.00 0.00 35.14 3.77
2075 2113 4.026052 CCCAACAAATTCTTCCCTATGCT 58.974 43.478 0.00 0.00 0.00 3.79
2165 2203 2.588439 GAGGTTTACCCCGGCCTC 59.412 66.667 7.66 7.66 40.39 4.70
2166 2205 3.381333 GAGGTTTACCCCGGCCTCG 62.381 68.421 7.66 0.00 38.22 4.63
2272 2311 3.563808 TGTGCACTACAGGAAAATCACAC 59.436 43.478 19.41 0.00 33.42 3.82
2304 2343 2.336554 TAACGTGTAAGCCGAGTGTC 57.663 50.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.885399 GGAGTATGCCATATTTTCTCATACCTT 59.115 37.037 0.00 0.00 39.92 3.50
2 3 6.313905 CGGAGTATGCCATATTTTCTCATACC 59.686 42.308 0.00 0.00 39.92 2.73
3 4 6.874134 ACGGAGTATGCCATATTTTCTCATAC 59.126 38.462 0.00 0.00 41.94 2.39
5 6 5.869579 ACGGAGTATGCCATATTTTCTCAT 58.130 37.500 3.39 0.00 41.94 2.90
6 7 5.290493 ACGGAGTATGCCATATTTTCTCA 57.710 39.130 3.39 0.00 41.94 3.27
7 8 5.049405 CCAACGGAGTATGCCATATTTTCTC 60.049 44.000 0.00 0.00 45.00 2.87
8 9 4.821805 CCAACGGAGTATGCCATATTTTCT 59.178 41.667 0.00 0.00 45.00 2.52
9 10 4.556699 GCCAACGGAGTATGCCATATTTTC 60.557 45.833 0.00 0.00 45.00 2.29
10 11 3.317993 GCCAACGGAGTATGCCATATTTT 59.682 43.478 0.00 0.00 45.00 1.82
11 12 2.884639 GCCAACGGAGTATGCCATATTT 59.115 45.455 0.00 0.00 45.00 1.40
12 13 2.504367 GCCAACGGAGTATGCCATATT 58.496 47.619 0.00 0.00 45.00 1.28
13 14 1.608025 CGCCAACGGAGTATGCCATAT 60.608 52.381 0.00 0.00 45.00 1.78
14 15 0.249699 CGCCAACGGAGTATGCCATA 60.250 55.000 0.00 0.00 45.00 2.74
15 16 1.523711 CGCCAACGGAGTATGCCAT 60.524 57.895 0.00 0.00 45.00 4.40
16 17 2.125310 CGCCAACGGAGTATGCCA 60.125 61.111 0.00 0.00 45.00 4.92
26 27 1.082117 CAGGTAAGTAGCCGCCAACG 61.082 60.000 0.00 0.00 39.67 4.10
27 28 1.366854 GCAGGTAAGTAGCCGCCAAC 61.367 60.000 0.00 0.00 0.00 3.77
28 29 1.078708 GCAGGTAAGTAGCCGCCAA 60.079 57.895 0.00 0.00 0.00 4.52
29 30 2.582436 GCAGGTAAGTAGCCGCCA 59.418 61.111 0.00 0.00 0.00 5.69
30 31 2.203029 GGCAGGTAAGTAGCCGCC 60.203 66.667 0.00 0.00 38.86 6.13
34 35 2.966516 AGTCCATAGGCAGGTAAGTAGC 59.033 50.000 0.00 0.00 0.00 3.58
35 36 3.322254 CCAGTCCATAGGCAGGTAAGTAG 59.678 52.174 0.00 0.00 0.00 2.57
36 37 3.305720 CCAGTCCATAGGCAGGTAAGTA 58.694 50.000 0.00 0.00 0.00 2.24
37 38 2.119495 CCAGTCCATAGGCAGGTAAGT 58.881 52.381 0.00 0.00 0.00 2.24
38 39 1.417890 CCCAGTCCATAGGCAGGTAAG 59.582 57.143 0.00 0.00 0.00 2.34
39 40 1.507140 CCCAGTCCATAGGCAGGTAA 58.493 55.000 0.00 0.00 0.00 2.85
40 41 1.054406 GCCCAGTCCATAGGCAGGTA 61.054 60.000 0.00 0.00 46.34 3.08
41 42 2.378634 GCCCAGTCCATAGGCAGGT 61.379 63.158 0.00 0.00 46.34 4.00
42 43 2.512896 GCCCAGTCCATAGGCAGG 59.487 66.667 0.00 0.00 46.34 4.85
46 47 2.512896 GGCTGCCCAGTCCATAGG 59.487 66.667 7.66 0.00 0.00 2.57
47 48 2.109799 CGGCTGCCCAGTCCATAG 59.890 66.667 14.12 0.00 0.00 2.23
48 49 3.479203 CCGGCTGCCCAGTCCATA 61.479 66.667 14.12 0.00 0.00 2.74
64 65 3.499737 CTGACGGCCATCAACGCC 61.500 66.667 1.82 0.00 43.38 5.68
65 66 4.166011 GCTGACGGCCATCAACGC 62.166 66.667 1.82 0.00 34.27 4.84
66 67 2.741985 TGCTGACGGCCATCAACG 60.742 61.111 1.82 0.00 40.92 4.10
67 68 1.237285 AACTGCTGACGGCCATCAAC 61.237 55.000 1.82 0.00 40.92 3.18
68 69 1.073025 AACTGCTGACGGCCATCAA 59.927 52.632 1.82 0.00 40.92 2.57
69 70 1.672030 CAACTGCTGACGGCCATCA 60.672 57.895 0.00 0.00 40.92 3.07
70 71 0.745845 ATCAACTGCTGACGGCCATC 60.746 55.000 2.24 0.00 40.92 3.51
71 72 0.745845 GATCAACTGCTGACGGCCAT 60.746 55.000 2.24 0.00 40.92 4.40
72 73 1.375908 GATCAACTGCTGACGGCCA 60.376 57.895 2.24 0.00 40.92 5.36
73 74 2.109126 GGATCAACTGCTGACGGCC 61.109 63.158 3.22 0.00 40.92 6.13
74 75 1.364626 CTGGATCAACTGCTGACGGC 61.365 60.000 0.00 0.00 36.69 5.68
75 76 0.247460 TCTGGATCAACTGCTGACGG 59.753 55.000 0.00 0.00 36.69 4.79
76 77 1.203287 TCTCTGGATCAACTGCTGACG 59.797 52.381 0.00 0.00 36.69 4.35
77 78 2.418471 CCTCTCTGGATCAACTGCTGAC 60.418 54.545 0.00 0.00 36.69 3.51
78 79 1.829849 CCTCTCTGGATCAACTGCTGA 59.170 52.381 0.00 0.00 38.35 4.26
79 80 1.829849 TCCTCTCTGGATCAACTGCTG 59.170 52.381 0.00 0.00 40.56 4.41
80 81 2.109774 CTCCTCTCTGGATCAACTGCT 58.890 52.381 0.00 0.00 45.16 4.24
81 82 1.138661 CCTCCTCTCTGGATCAACTGC 59.861 57.143 0.00 0.00 45.16 4.40
82 83 1.138661 GCCTCCTCTCTGGATCAACTG 59.861 57.143 0.00 0.00 45.16 3.16
83 84 1.494960 GCCTCCTCTCTGGATCAACT 58.505 55.000 0.00 0.00 45.16 3.16
84 85 0.103937 CGCCTCCTCTCTGGATCAAC 59.896 60.000 0.00 0.00 45.16 3.18
85 86 1.680522 GCGCCTCCTCTCTGGATCAA 61.681 60.000 0.00 0.00 45.16 2.57
86 87 2.130426 GCGCCTCCTCTCTGGATCA 61.130 63.158 0.00 0.00 45.16 2.92
87 88 1.832167 AGCGCCTCCTCTCTGGATC 60.832 63.158 2.29 0.00 45.16 3.36
88 89 2.132996 CAGCGCCTCCTCTCTGGAT 61.133 63.158 2.29 0.00 45.16 3.41
89 90 2.757508 CAGCGCCTCCTCTCTGGA 60.758 66.667 2.29 0.00 43.86 3.86
90 91 4.527583 GCAGCGCCTCCTCTCTGG 62.528 72.222 2.29 0.00 37.10 3.86
91 92 3.459965 AGCAGCGCCTCCTCTCTG 61.460 66.667 2.29 0.00 0.00 3.35
92 93 3.459965 CAGCAGCGCCTCCTCTCT 61.460 66.667 2.29 0.00 0.00 3.10
93 94 3.768922 ACAGCAGCGCCTCCTCTC 61.769 66.667 2.29 0.00 0.00 3.20
94 95 4.079850 CACAGCAGCGCCTCCTCT 62.080 66.667 2.29 0.00 0.00 3.69
104 105 3.314331 AGGTCGTCCCCACAGCAG 61.314 66.667 0.00 0.00 0.00 4.24
105 106 3.625897 CAGGTCGTCCCCACAGCA 61.626 66.667 0.00 0.00 0.00 4.41
107 108 3.302347 GAGCAGGTCGTCCCCACAG 62.302 68.421 0.00 0.00 0.00 3.66
108 109 3.311110 GAGCAGGTCGTCCCCACA 61.311 66.667 0.00 0.00 0.00 4.17
109 110 4.436998 CGAGCAGGTCGTCCCCAC 62.437 72.222 14.02 0.00 44.20 4.61
117 118 3.429141 TCGACCGTCGAGCAGGTC 61.429 66.667 19.51 19.24 44.82 3.85
126 127 4.194720 AGCATCGCCTCGACCGTC 62.195 66.667 1.28 0.00 39.18 4.79
127 128 4.498520 CAGCATCGCCTCGACCGT 62.499 66.667 1.28 0.00 39.18 4.83
129 130 4.899239 CCCAGCATCGCCTCGACC 62.899 72.222 0.00 0.00 39.18 4.79
130 131 4.899239 CCCCAGCATCGCCTCGAC 62.899 72.222 0.00 0.00 39.18 4.20
149 150 4.106925 CTCCTCTGCTGCCCCACC 62.107 72.222 0.00 0.00 0.00 4.61
150 151 3.005539 TCTCCTCTGCTGCCCCAC 61.006 66.667 0.00 0.00 0.00 4.61
151 152 2.686470 CTCTCCTCTGCTGCCCCA 60.686 66.667 0.00 0.00 0.00 4.96
152 153 4.173924 GCTCTCCTCTGCTGCCCC 62.174 72.222 0.00 0.00 0.00 5.80
153 154 3.388703 CTGCTCTCCTCTGCTGCCC 62.389 68.421 0.00 0.00 0.00 5.36
154 155 2.187424 CTGCTCTCCTCTGCTGCC 59.813 66.667 0.00 0.00 0.00 4.85
155 156 2.187424 CCTGCTCTCCTCTGCTGC 59.813 66.667 0.00 0.00 0.00 5.25
156 157 2.187424 GCCTGCTCTCCTCTGCTG 59.813 66.667 0.00 0.00 0.00 4.41
157 158 3.459965 CGCCTGCTCTCCTCTGCT 61.460 66.667 0.00 0.00 0.00 4.24
158 159 4.527583 CCGCCTGCTCTCCTCTGC 62.528 72.222 0.00 0.00 0.00 4.26
159 160 3.073735 ACCGCCTGCTCTCCTCTG 61.074 66.667 0.00 0.00 0.00 3.35
160 161 3.073735 CACCGCCTGCTCTCCTCT 61.074 66.667 0.00 0.00 0.00 3.69
161 162 4.154347 CCACCGCCTGCTCTCCTC 62.154 72.222 0.00 0.00 0.00 3.71
207 208 4.803426 CCTCCTGTCGCTCGTGCC 62.803 72.222 3.52 0.00 35.36 5.01
208 209 4.803426 CCCTCCTGTCGCTCGTGC 62.803 72.222 0.00 0.00 0.00 5.34
209 210 3.062466 TCCCTCCTGTCGCTCGTG 61.062 66.667 0.00 0.00 0.00 4.35
210 211 3.063084 GTCCCTCCTGTCGCTCGT 61.063 66.667 0.00 0.00 0.00 4.18
211 212 4.180946 CGTCCCTCCTGTCGCTCG 62.181 72.222 0.00 0.00 0.00 5.03
212 213 3.827898 CCGTCCCTCCTGTCGCTC 61.828 72.222 0.00 0.00 0.00 5.03
242 243 4.056125 CCTCGTCAGTGCCTCGCA 62.056 66.667 0.00 0.00 35.60 5.10
244 245 3.978723 CTGCCTCGTCAGTGCCTCG 62.979 68.421 0.00 0.00 0.00 4.63
245 246 1.954362 ATCTGCCTCGTCAGTGCCTC 61.954 60.000 0.00 0.00 35.63 4.70
246 247 1.986757 ATCTGCCTCGTCAGTGCCT 60.987 57.895 0.00 0.00 35.63 4.75
247 248 1.812922 CATCTGCCTCGTCAGTGCC 60.813 63.158 0.00 0.00 35.63 5.01
248 249 0.805322 CTCATCTGCCTCGTCAGTGC 60.805 60.000 0.00 0.00 35.63 4.40
249 250 0.813821 TCTCATCTGCCTCGTCAGTG 59.186 55.000 0.00 0.00 35.63 3.66
250 251 1.476085 CTTCTCATCTGCCTCGTCAGT 59.524 52.381 0.00 0.00 35.63 3.41
251 252 1.747924 TCTTCTCATCTGCCTCGTCAG 59.252 52.381 0.00 0.00 35.46 3.51
252 253 1.747924 CTCTTCTCATCTGCCTCGTCA 59.252 52.381 0.00 0.00 0.00 4.35
253 254 2.020720 TCTCTTCTCATCTGCCTCGTC 58.979 52.381 0.00 0.00 0.00 4.20
254 255 2.136298 TCTCTTCTCATCTGCCTCGT 57.864 50.000 0.00 0.00 0.00 4.18
255 256 2.794282 CGTTCTCTTCTCATCTGCCTCG 60.794 54.545 0.00 0.00 0.00 4.63
256 257 2.425312 TCGTTCTCTTCTCATCTGCCTC 59.575 50.000 0.00 0.00 0.00 4.70
257 258 2.451490 TCGTTCTCTTCTCATCTGCCT 58.549 47.619 0.00 0.00 0.00 4.75
258 259 2.949451 TCGTTCTCTTCTCATCTGCC 57.051 50.000 0.00 0.00 0.00 4.85
259 260 4.039151 TGATCGTTCTCTTCTCATCTGC 57.961 45.455 0.00 0.00 0.00 4.26
260 261 5.042593 CCTTGATCGTTCTCTTCTCATCTG 58.957 45.833 0.00 0.00 0.00 2.90
261 262 4.952957 TCCTTGATCGTTCTCTTCTCATCT 59.047 41.667 0.00 0.00 0.00 2.90
262 263 5.040635 GTCCTTGATCGTTCTCTTCTCATC 58.959 45.833 0.00 0.00 0.00 2.92
263 264 4.439426 CGTCCTTGATCGTTCTCTTCTCAT 60.439 45.833 0.00 0.00 0.00 2.90
264 265 3.119814 CGTCCTTGATCGTTCTCTTCTCA 60.120 47.826 0.00 0.00 0.00 3.27
265 266 3.119779 ACGTCCTTGATCGTTCTCTTCTC 60.120 47.826 0.00 0.00 36.93 2.87
266 267 2.820787 ACGTCCTTGATCGTTCTCTTCT 59.179 45.455 0.00 0.00 36.93 2.85
267 268 2.917971 CACGTCCTTGATCGTTCTCTTC 59.082 50.000 0.00 0.00 38.23 2.87
268 269 2.927014 GCACGTCCTTGATCGTTCTCTT 60.927 50.000 0.00 0.00 38.23 2.85
269 270 1.402984 GCACGTCCTTGATCGTTCTCT 60.403 52.381 0.00 0.00 38.23 3.10
270 271 0.992802 GCACGTCCTTGATCGTTCTC 59.007 55.000 0.00 0.00 38.23 2.87
271 272 0.732880 CGCACGTCCTTGATCGTTCT 60.733 55.000 0.00 0.00 38.23 3.01
272 273 0.731514 TCGCACGTCCTTGATCGTTC 60.732 55.000 0.00 0.00 38.23 3.95
273 274 0.732880 CTCGCACGTCCTTGATCGTT 60.733 55.000 0.00 0.00 38.23 3.85
274 275 1.154016 CTCGCACGTCCTTGATCGT 60.154 57.895 0.00 0.00 40.99 3.73
275 276 1.874019 CCTCGCACGTCCTTGATCG 60.874 63.158 0.00 0.00 0.00 3.69
276 277 1.519455 CCCTCGCACGTCCTTGATC 60.519 63.158 0.00 0.00 0.00 2.92
277 278 2.579201 CCCTCGCACGTCCTTGAT 59.421 61.111 0.00 0.00 0.00 2.57
278 279 3.691342 CCCCTCGCACGTCCTTGA 61.691 66.667 0.00 0.00 0.00 3.02
279 280 2.521958 AATCCCCTCGCACGTCCTTG 62.522 60.000 0.00 0.00 0.00 3.61
280 281 2.291043 AATCCCCTCGCACGTCCTT 61.291 57.895 0.00 0.00 0.00 3.36
281 282 2.683933 AATCCCCTCGCACGTCCT 60.684 61.111 0.00 0.00 0.00 3.85
282 283 2.511600 CAATCCCCTCGCACGTCC 60.512 66.667 0.00 0.00 0.00 4.79
283 284 2.511600 CCAATCCCCTCGCACGTC 60.512 66.667 0.00 0.00 0.00 4.34
284 285 4.778143 GCCAATCCCCTCGCACGT 62.778 66.667 0.00 0.00 0.00 4.49
285 286 4.776322 TGCCAATCCCCTCGCACG 62.776 66.667 0.00 0.00 0.00 5.34
286 287 2.124151 ATGCCAATCCCCTCGCAC 60.124 61.111 0.00 0.00 33.31 5.34
287 288 2.124193 CATGCCAATCCCCTCGCA 60.124 61.111 0.00 0.00 35.35 5.10
288 289 2.680974 TAGCATGCCAATCCCCTCGC 62.681 60.000 15.66 0.00 0.00 5.03
289 290 0.179020 TTAGCATGCCAATCCCCTCG 60.179 55.000 15.66 0.00 0.00 4.63
290 291 2.299326 ATTAGCATGCCAATCCCCTC 57.701 50.000 15.66 0.00 0.00 4.30
291 292 2.781403 AATTAGCATGCCAATCCCCT 57.219 45.000 15.66 0.00 0.00 4.79
292 293 3.897505 AGTAAATTAGCATGCCAATCCCC 59.102 43.478 15.66 3.98 0.00 4.81
293 294 5.770162 AGTAGTAAATTAGCATGCCAATCCC 59.230 40.000 15.66 4.33 0.00 3.85
294 295 6.263168 ACAGTAGTAAATTAGCATGCCAATCC 59.737 38.462 15.66 4.69 0.00 3.01
295 296 7.264373 ACAGTAGTAAATTAGCATGCCAATC 57.736 36.000 15.66 0.80 0.00 2.67
296 297 7.228706 GGTACAGTAGTAAATTAGCATGCCAAT 59.771 37.037 15.66 10.24 30.67 3.16
297 298 6.540914 GGTACAGTAGTAAATTAGCATGCCAA 59.459 38.462 15.66 7.75 30.67 4.52
298 299 6.053005 GGTACAGTAGTAAATTAGCATGCCA 58.947 40.000 15.66 0.00 30.67 4.92
299 300 5.469084 GGGTACAGTAGTAAATTAGCATGCC 59.531 44.000 15.66 0.00 30.67 4.40
300 301 6.289064 AGGGTACAGTAGTAAATTAGCATGC 58.711 40.000 10.51 10.51 30.67 4.06
301 302 8.732746 AAAGGGTACAGTAGTAAATTAGCATG 57.267 34.615 0.00 0.00 30.67 4.06
302 303 8.769359 AGAAAGGGTACAGTAGTAAATTAGCAT 58.231 33.333 0.00 0.00 30.67 3.79
303 304 8.142485 AGAAAGGGTACAGTAGTAAATTAGCA 57.858 34.615 0.00 0.00 30.67 3.49
304 305 9.526713 GTAGAAAGGGTACAGTAGTAAATTAGC 57.473 37.037 0.00 0.00 30.67 3.09
307 308 8.873144 TGTGTAGAAAGGGTACAGTAGTAAATT 58.127 33.333 0.00 0.00 31.00 1.82
308 309 8.426569 TGTGTAGAAAGGGTACAGTAGTAAAT 57.573 34.615 0.00 0.00 31.00 1.40
309 310 7.838079 TGTGTAGAAAGGGTACAGTAGTAAA 57.162 36.000 0.00 0.00 31.00 2.01
310 311 7.838079 TTGTGTAGAAAGGGTACAGTAGTAA 57.162 36.000 0.00 0.00 31.00 2.24
311 312 7.838079 TTTGTGTAGAAAGGGTACAGTAGTA 57.162 36.000 0.00 0.00 31.00 1.82
312 313 6.736110 TTTGTGTAGAAAGGGTACAGTAGT 57.264 37.500 0.00 0.00 31.00 2.73
313 314 8.617290 ATTTTTGTGTAGAAAGGGTACAGTAG 57.383 34.615 0.00 0.00 31.00 2.57
315 316 8.983702 TTATTTTTGTGTAGAAAGGGTACAGT 57.016 30.769 0.00 0.00 31.00 3.55
316 317 9.673454 GTTTATTTTTGTGTAGAAAGGGTACAG 57.327 33.333 0.00 0.00 31.00 2.74
317 318 9.186837 TGTTTATTTTTGTGTAGAAAGGGTACA 57.813 29.630 0.00 0.00 0.00 2.90
361 362 9.521503 GCTCTGATTTTTCCTAACCATTAAATC 57.478 33.333 0.00 0.00 34.32 2.17
362 363 9.259832 AGCTCTGATTTTTCCTAACCATTAAAT 57.740 29.630 0.00 0.00 0.00 1.40
363 364 8.522830 CAGCTCTGATTTTTCCTAACCATTAAA 58.477 33.333 0.00 0.00 0.00 1.52
364 365 7.122650 CCAGCTCTGATTTTTCCTAACCATTAA 59.877 37.037 0.00 0.00 0.00 1.40
365 366 6.603201 CCAGCTCTGATTTTTCCTAACCATTA 59.397 38.462 0.00 0.00 0.00 1.90
366 367 5.420104 CCAGCTCTGATTTTTCCTAACCATT 59.580 40.000 0.00 0.00 0.00 3.16
367 368 4.952335 CCAGCTCTGATTTTTCCTAACCAT 59.048 41.667 0.00 0.00 0.00 3.55
368 369 4.042809 TCCAGCTCTGATTTTTCCTAACCA 59.957 41.667 0.00 0.00 0.00 3.67
369 370 4.589908 TCCAGCTCTGATTTTTCCTAACC 58.410 43.478 0.00 0.00 0.00 2.85
370 371 5.249420 ACTCCAGCTCTGATTTTTCCTAAC 58.751 41.667 0.00 0.00 0.00 2.34
371 372 5.505181 ACTCCAGCTCTGATTTTTCCTAA 57.495 39.130 0.00 0.00 0.00 2.69
372 373 5.505181 AACTCCAGCTCTGATTTTTCCTA 57.495 39.130 0.00 0.00 0.00 2.94
373 374 4.379302 AACTCCAGCTCTGATTTTTCCT 57.621 40.909 0.00 0.00 0.00 3.36
374 375 5.003804 TGTAACTCCAGCTCTGATTTTTCC 58.996 41.667 0.00 0.00 0.00 3.13
375 376 6.372659 TCATGTAACTCCAGCTCTGATTTTTC 59.627 38.462 0.00 0.00 0.00 2.29
376 377 6.240894 TCATGTAACTCCAGCTCTGATTTTT 58.759 36.000 0.00 0.00 0.00 1.94
377 378 5.809001 TCATGTAACTCCAGCTCTGATTTT 58.191 37.500 0.00 0.00 0.00 1.82
378 379 5.426689 TCATGTAACTCCAGCTCTGATTT 57.573 39.130 0.00 0.00 0.00 2.17
379 380 5.426689 TTCATGTAACTCCAGCTCTGATT 57.573 39.130 0.00 0.00 0.00 2.57
380 381 5.426689 TTTCATGTAACTCCAGCTCTGAT 57.573 39.130 0.00 0.00 0.00 2.90
381 382 4.890158 TTTCATGTAACTCCAGCTCTGA 57.110 40.909 0.00 0.00 0.00 3.27
382 383 6.595326 TGTAATTTCATGTAACTCCAGCTCTG 59.405 38.462 0.00 0.00 0.00 3.35
383 384 6.711277 TGTAATTTCATGTAACTCCAGCTCT 58.289 36.000 0.00 0.00 0.00 4.09
384 385 6.985188 TGTAATTTCATGTAACTCCAGCTC 57.015 37.500 0.00 0.00 0.00 4.09
385 386 7.759489 TTTGTAATTTCATGTAACTCCAGCT 57.241 32.000 0.00 0.00 0.00 4.24
386 387 8.863049 CAATTTGTAATTTCATGTAACTCCAGC 58.137 33.333 0.00 0.00 0.00 4.85
387 388 9.912634 ACAATTTGTAATTTCATGTAACTCCAG 57.087 29.630 0.00 0.00 0.00 3.86
407 408 9.553064 TTTACAGTGATTGGCAAATTACAATTT 57.447 25.926 11.05 0.00 37.43 1.82
408 409 9.553064 TTTTACAGTGATTGGCAAATTACAATT 57.447 25.926 11.05 0.00 37.43 2.32
409 410 8.987890 GTTTTACAGTGATTGGCAAATTACAAT 58.012 29.630 11.05 1.55 39.81 2.71
410 411 7.981789 TGTTTTACAGTGATTGGCAAATTACAA 59.018 29.630 11.05 0.00 35.32 2.41
411 412 7.492524 TGTTTTACAGTGATTGGCAAATTACA 58.507 30.769 11.05 0.00 35.32 2.41
412 413 7.938563 TGTTTTACAGTGATTGGCAAATTAC 57.061 32.000 3.01 0.40 33.55 1.89
428 429 8.357402 GGAAAAGAAAATAGGAGCTGTTTTACA 58.643 33.333 0.00 0.00 35.53 2.41
429 430 8.577296 AGGAAAAGAAAATAGGAGCTGTTTTAC 58.423 33.333 0.00 0.00 35.53 2.01
430 431 8.706322 AGGAAAAGAAAATAGGAGCTGTTTTA 57.294 30.769 0.00 0.00 35.53 1.52
431 432 7.603180 AGGAAAAGAAAATAGGAGCTGTTTT 57.397 32.000 0.00 0.00 37.46 2.43
432 433 7.603180 AAGGAAAAGAAAATAGGAGCTGTTT 57.397 32.000 0.00 0.00 0.00 2.83
433 434 7.603180 AAAGGAAAAGAAAATAGGAGCTGTT 57.397 32.000 0.00 0.00 0.00 3.16
434 435 8.577296 GTTAAAGGAAAAGAAAATAGGAGCTGT 58.423 33.333 0.00 0.00 0.00 4.40
435 436 8.029522 GGTTAAAGGAAAAGAAAATAGGAGCTG 58.970 37.037 0.00 0.00 0.00 4.24
436 437 7.728532 TGGTTAAAGGAAAAGAAAATAGGAGCT 59.271 33.333 0.00 0.00 0.00 4.09
437 438 7.892609 TGGTTAAAGGAAAAGAAAATAGGAGC 58.107 34.615 0.00 0.00 0.00 4.70
528 529 1.808133 CGGAGCTTGCTCAAGTATCCC 60.808 57.143 21.97 4.16 40.35 3.85
688 696 7.595819 AAAGGACAAGAAATTTCATGTACCA 57.404 32.000 27.17 0.00 39.82 3.25
701 709 5.592688 AGGAAAACGATGAAAAGGACAAGAA 59.407 36.000 0.00 0.00 0.00 2.52
892 904 8.687242 TGTGTATTCTAGTTGTCTAGGAGAATG 58.313 37.037 5.84 0.00 42.66 2.67
943 955 3.235481 TGCGAACGGGGGTCTCAA 61.235 61.111 0.00 0.00 0.00 3.02
1383 1395 1.538204 GCAGTGACAAGAACCTCGACA 60.538 52.381 0.00 0.00 0.00 4.35
1384 1396 1.140816 GCAGTGACAAGAACCTCGAC 58.859 55.000 0.00 0.00 0.00 4.20
1562 1583 6.238484 CCATAGTATGTCTTTGCCTTGCTTAC 60.238 42.308 9.28 0.00 0.00 2.34
2165 2203 4.541482 GTGCACCGCATGATGCCG 62.541 66.667 12.40 8.09 41.91 5.69
2166 2205 3.442167 TGTGCACCGCATGATGCC 61.442 61.111 15.69 0.00 41.91 4.40
2244 2283 6.488344 TGATTTTCCTGTAGTGCACAATACAA 59.512 34.615 21.04 4.97 40.68 2.41
2272 2311 0.570734 CACGTTAATACTCGGCAGCG 59.429 55.000 0.00 0.00 0.00 5.18
2304 2343 1.164041 AGCCGAGAACCCGTGTTTTG 61.164 55.000 0.00 0.00 33.97 2.44


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

AutoCloner maintained by Alex Coulton.