Multiple sequence alignment - TraesCS2A01G156800

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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 TraesCS2A01G156800 chr2A 100.000 2561 0 0 1 2561 103356374 103353814 0.000000e+00 4730
1 TraesCS2A01G156800 chr2B 90.333 1500 75 29 440 1901 157285359 157283892 0.000000e+00 1903
2 TraesCS2A01G156800 chr2B 87.029 239 13 5 2302 2534 157282981 157282755 1.180000e-63 254
3 TraesCS2A01G156800 chr2B 90.345 145 6 2 1937 2073 157283891 157283747 1.570000e-42 183
4 TraesCS2A01G156800 chr2D 88.531 1491 81 35 439 1886 106971980 106970537 0.000000e+00 1724
5 TraesCS2A01G156800 chr2D 94.373 391 16 3 1919 2304 106970535 106970146 1.700000e-166 595
6 TraesCS2A01G156800 chr2D 94.231 260 13 1 2302 2561 106970077 106969820 1.850000e-106 396
7 TraesCS2A01G156800 chr6D 87.879 363 36 5 1787 2149 208836401 208836755 1.100000e-113 420
8 TraesCS2A01G156800 chr6D 86.076 316 21 8 1416 1730 208809191 208809484 4.110000e-83 318


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 TraesCS2A01G156800 chr2A 103353814 103356374 2560 True 4730 4730 100.000000 1 2561 1 chr2A.!!$R1 2560
1 TraesCS2A01G156800 chr2B 157282755 157285359 2604 True 780 1903 89.235667 440 2534 3 chr2B.!!$R1 2094
2 TraesCS2A01G156800 chr2D 106969820 106971980 2160 True 905 1724 92.378333 439 2561 3 chr2D.!!$R1 2122

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
610 621 0.109597 CTGCTTCCACAACATTCCGC 60.11 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 1922 0.243095 GTTCGTCCTGAAGCTACCGT 59.757 55.0 0.0 0.0 37.23 4.83 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
39 40 9.467796 TGATATACTACATATTAGCTCTGCTGT 57.532 33.333 1.96 0.00 40.10 4.40
44 45 8.183104 ACTACATATTAGCTCTGCTGTTATCA 57.817 34.615 1.96 0.00 40.10 2.15
45 46 8.642432 ACTACATATTAGCTCTGCTGTTATCAA 58.358 33.333 1.96 0.00 40.10 2.57
46 47 9.481340 CTACATATTAGCTCTGCTGTTATCAAA 57.519 33.333 1.96 0.00 40.10 2.69
47 48 8.147642 ACATATTAGCTCTGCTGTTATCAAAC 57.852 34.615 1.96 0.00 40.10 2.93
48 49 7.770433 ACATATTAGCTCTGCTGTTATCAAACA 59.230 33.333 1.96 0.00 43.32 2.83
49 50 8.781196 CATATTAGCTCTGCTGTTATCAAACAT 58.219 33.333 1.96 0.00 44.43 2.71
50 51 4.959596 AGCTCTGCTGTTATCAAACATG 57.040 40.909 0.00 0.00 44.43 3.21
51 52 4.582869 AGCTCTGCTGTTATCAAACATGA 58.417 39.130 0.00 0.00 44.43 3.07
52 53 5.005740 AGCTCTGCTGTTATCAAACATGAA 58.994 37.500 0.00 0.00 44.43 2.57
53 54 5.651139 AGCTCTGCTGTTATCAAACATGAAT 59.349 36.000 0.00 0.00 44.43 2.57
54 55 5.742453 GCTCTGCTGTTATCAAACATGAATG 59.258 40.000 0.00 0.00 44.43 2.67
55 56 6.403964 GCTCTGCTGTTATCAAACATGAATGA 60.404 38.462 0.00 3.47 44.43 2.57
56 57 7.634671 TCTGCTGTTATCAAACATGAATGAT 57.365 32.000 17.64 17.64 44.43 2.45
57 58 7.700505 TCTGCTGTTATCAAACATGAATGATC 58.299 34.615 17.23 8.42 44.43 2.92
58 59 7.337436 TCTGCTGTTATCAAACATGAATGATCA 59.663 33.333 17.23 0.00 44.43 2.92
60 61 8.132995 TGCTGTTATCAAACATGAATGATCATC 58.867 33.333 9.06 3.57 44.53 2.92
61 62 7.322938 GCTGTTATCAAACATGAATGATCATCG 59.677 37.037 9.06 0.94 44.53 3.84
62 63 8.212317 TGTTATCAAACATGAATGATCATCGT 57.788 30.769 9.06 1.58 44.53 3.73
63 64 8.676401 TGTTATCAAACATGAATGATCATCGTT 58.324 29.630 9.06 7.67 44.53 3.85
64 65 9.162793 GTTATCAAACATGAATGATCATCGTTC 57.837 33.333 9.06 12.14 44.53 3.95
65 66 6.990341 TCAAACATGAATGATCATCGTTCT 57.010 33.333 18.53 4.01 44.53 3.01
66 67 8.667076 ATCAAACATGAATGATCATCGTTCTA 57.333 30.769 18.53 7.46 44.53 2.10
67 68 8.134905 TCAAACATGAATGATCATCGTTCTAG 57.865 34.615 18.53 13.42 44.53 2.43
68 69 7.765819 TCAAACATGAATGATCATCGTTCTAGT 59.234 33.333 18.53 13.95 44.53 2.57
69 70 7.474398 AACATGAATGATCATCGTTCTAGTG 57.526 36.000 18.53 15.84 44.53 2.74
70 71 5.464722 ACATGAATGATCATCGTTCTAGTGC 59.535 40.000 18.53 0.00 44.53 4.40
71 72 5.268118 TGAATGATCATCGTTCTAGTGCT 57.732 39.130 18.53 0.00 41.66 4.40
72 73 5.664457 TGAATGATCATCGTTCTAGTGCTT 58.336 37.500 18.53 0.00 41.66 3.91
73 74 5.521372 TGAATGATCATCGTTCTAGTGCTTG 59.479 40.000 18.53 0.00 41.66 4.01
74 75 4.456280 TGATCATCGTTCTAGTGCTTGT 57.544 40.909 0.00 0.00 0.00 3.16
75 76 4.424626 TGATCATCGTTCTAGTGCTTGTC 58.575 43.478 0.00 0.00 0.00 3.18
76 77 3.232213 TCATCGTTCTAGTGCTTGTCC 57.768 47.619 0.00 0.00 0.00 4.02
77 78 2.560981 TCATCGTTCTAGTGCTTGTCCA 59.439 45.455 0.00 0.00 0.00 4.02
78 79 2.433868 TCGTTCTAGTGCTTGTCCAC 57.566 50.000 0.00 0.00 35.98 4.02
79 80 1.684450 TCGTTCTAGTGCTTGTCCACA 59.316 47.619 0.00 0.00 38.18 4.17
80 81 1.792949 CGTTCTAGTGCTTGTCCACAC 59.207 52.381 0.00 0.00 38.18 3.82
81 82 2.801699 CGTTCTAGTGCTTGTCCACACA 60.802 50.000 0.00 0.00 39.30 3.72
82 83 3.202906 GTTCTAGTGCTTGTCCACACAA 58.797 45.455 0.00 0.00 40.40 3.33
90 91 2.719531 TTGTCCACACAAGCCTACAA 57.280 45.000 0.00 0.00 37.61 2.41
91 92 2.949177 TGTCCACACAAGCCTACAAT 57.051 45.000 0.00 0.00 0.00 2.71
92 93 2.503331 TGTCCACACAAGCCTACAATG 58.497 47.619 0.00 0.00 0.00 2.82
93 94 1.812571 GTCCACACAAGCCTACAATGG 59.187 52.381 0.00 0.00 0.00 3.16
94 95 1.176527 CCACACAAGCCTACAATGGG 58.823 55.000 0.00 0.00 0.00 4.00
95 96 1.176527 CACACAAGCCTACAATGGGG 58.823 55.000 0.00 0.00 0.00 4.96
96 97 1.072266 ACACAAGCCTACAATGGGGA 58.928 50.000 0.00 0.00 0.00 4.81
97 98 1.004745 ACACAAGCCTACAATGGGGAG 59.995 52.381 0.00 0.00 0.00 4.30
98 99 0.625849 ACAAGCCTACAATGGGGAGG 59.374 55.000 0.00 0.00 0.00 4.30
99 100 0.625849 CAAGCCTACAATGGGGAGGT 59.374 55.000 0.00 0.00 32.53 3.85
100 101 0.919710 AAGCCTACAATGGGGAGGTC 59.080 55.000 0.00 0.00 32.53 3.85
101 102 1.146263 GCCTACAATGGGGAGGTCG 59.854 63.158 0.00 0.00 32.53 4.79
102 103 1.146263 CCTACAATGGGGAGGTCGC 59.854 63.158 0.00 0.00 0.00 5.19
103 104 1.338136 CCTACAATGGGGAGGTCGCT 61.338 60.000 0.00 0.00 0.00 4.93
104 105 0.179073 CTACAATGGGGAGGTCGCTG 60.179 60.000 0.00 0.00 0.00 5.18
105 106 1.622607 TACAATGGGGAGGTCGCTGG 61.623 60.000 0.00 0.00 0.00 4.85
106 107 2.610859 AATGGGGAGGTCGCTGGT 60.611 61.111 0.00 0.00 0.00 4.00
107 108 2.231380 AATGGGGAGGTCGCTGGTT 61.231 57.895 0.00 0.00 0.00 3.67
108 109 2.198304 AATGGGGAGGTCGCTGGTTC 62.198 60.000 0.00 0.00 0.00 3.62
109 110 4.452733 GGGGAGGTCGCTGGTTCG 62.453 72.222 0.00 0.00 0.00 3.95
110 111 3.379445 GGGAGGTCGCTGGTTCGA 61.379 66.667 0.00 0.00 35.95 3.71
111 112 2.654877 GGAGGTCGCTGGTTCGAA 59.345 61.111 0.00 0.00 40.43 3.71
112 113 1.737008 GGAGGTCGCTGGTTCGAAC 60.737 63.158 20.14 20.14 45.80 3.95
113 114 1.737008 GAGGTCGCTGGTTCGAACC 60.737 63.158 35.49 35.49 46.56 3.62
131 132 3.191182 CCCCCTACCATCAGTTTGC 57.809 57.895 0.00 0.00 0.00 3.68
132 133 0.625849 CCCCCTACCATCAGTTTGCT 59.374 55.000 0.00 0.00 0.00 3.91
133 134 1.005924 CCCCCTACCATCAGTTTGCTT 59.994 52.381 0.00 0.00 0.00 3.91
134 135 2.557452 CCCCCTACCATCAGTTTGCTTT 60.557 50.000 0.00 0.00 0.00 3.51
135 136 3.165071 CCCCTACCATCAGTTTGCTTTT 58.835 45.455 0.00 0.00 0.00 2.27
136 137 3.578282 CCCCTACCATCAGTTTGCTTTTT 59.422 43.478 0.00 0.00 0.00 1.94
137 138 4.770010 CCCCTACCATCAGTTTGCTTTTTA 59.230 41.667 0.00 0.00 0.00 1.52
138 139 5.422012 CCCCTACCATCAGTTTGCTTTTTAT 59.578 40.000 0.00 0.00 0.00 1.40
139 140 6.405842 CCCCTACCATCAGTTTGCTTTTTATC 60.406 42.308 0.00 0.00 0.00 1.75
140 141 6.152661 CCCTACCATCAGTTTGCTTTTTATCA 59.847 38.462 0.00 0.00 0.00 2.15
141 142 7.147846 CCCTACCATCAGTTTGCTTTTTATCAT 60.148 37.037 0.00 0.00 0.00 2.45
142 143 8.253113 CCTACCATCAGTTTGCTTTTTATCATT 58.747 33.333 0.00 0.00 0.00 2.57
143 144 9.643693 CTACCATCAGTTTGCTTTTTATCATTT 57.356 29.630 0.00 0.00 0.00 2.32
144 145 8.907222 ACCATCAGTTTGCTTTTTATCATTTT 57.093 26.923 0.00 0.00 0.00 1.82
145 146 9.995003 ACCATCAGTTTGCTTTTTATCATTTTA 57.005 25.926 0.00 0.00 0.00 1.52
196 197 6.874278 AAGGCAAGGGCTTTTCTATAAAAT 57.126 33.333 0.00 0.00 46.16 1.82
197 198 6.471233 AGGCAAGGGCTTTTCTATAAAATC 57.529 37.500 0.00 0.00 40.87 2.17
198 199 5.363868 AGGCAAGGGCTTTTCTATAAAATCC 59.636 40.000 0.00 0.00 39.24 3.01
199 200 5.281727 GCAAGGGCTTTTCTATAAAATCCG 58.718 41.667 1.50 0.00 40.34 4.18
200 201 5.281727 CAAGGGCTTTTCTATAAAATCCGC 58.718 41.667 1.50 0.00 40.34 5.54
201 202 3.889538 AGGGCTTTTCTATAAAATCCGCC 59.110 43.478 6.55 6.55 40.34 6.13
202 203 3.304458 GGGCTTTTCTATAAAATCCGCCG 60.304 47.826 8.19 0.00 41.19 6.46
203 204 3.314357 GGCTTTTCTATAAAATCCGCCGT 59.686 43.478 1.10 0.00 35.19 5.68
204 205 4.279659 GCTTTTCTATAAAATCCGCCGTG 58.720 43.478 0.00 0.00 34.18 4.94
205 206 3.955771 TTTCTATAAAATCCGCCGTGC 57.044 42.857 0.00 0.00 0.00 5.34
206 207 3.242478 TTTTCTATAAAATCCGCCGTGCG 60.242 43.478 10.75 10.75 39.49 5.34
207 208 5.445761 TTTTCTATAAAATCCGCCGTGCGA 61.446 41.667 17.96 6.42 40.92 5.10
208 209 7.413510 TTTTCTATAAAATCCGCCGTGCGAC 62.414 44.000 17.96 0.00 40.92 5.19
223 224 4.537433 GACAGCGGCAGGCCCTAG 62.537 72.222 0.00 0.00 45.17 3.02
255 256 3.074594 CCATGTAGGCAACGGGTAC 57.925 57.895 0.00 0.00 46.39 3.34
256 257 0.250793 CCATGTAGGCAACGGGTACA 59.749 55.000 0.00 0.00 46.39 2.90
257 258 1.134220 CCATGTAGGCAACGGGTACAT 60.134 52.381 0.00 0.00 46.39 2.29
258 259 2.210116 CATGTAGGCAACGGGTACATC 58.790 52.381 0.00 0.00 46.39 3.06
259 260 0.538118 TGTAGGCAACGGGTACATCC 59.462 55.000 0.00 0.00 46.39 3.51
267 268 3.906660 CGGGTACATCCGCATACAT 57.093 52.632 0.00 0.00 43.71 2.29
268 269 1.428448 CGGGTACATCCGCATACATG 58.572 55.000 0.00 0.00 43.71 3.21
269 270 1.000394 CGGGTACATCCGCATACATGA 60.000 52.381 0.00 0.00 43.71 3.07
270 271 2.547007 CGGGTACATCCGCATACATGAA 60.547 50.000 0.00 0.00 43.71 2.57
271 272 3.472652 GGGTACATCCGCATACATGAAA 58.527 45.455 0.00 0.00 37.00 2.69
272 273 4.072131 GGGTACATCCGCATACATGAAAT 58.928 43.478 0.00 0.00 37.00 2.17
273 274 4.083324 GGGTACATCCGCATACATGAAATG 60.083 45.833 0.00 4.01 43.71 2.32
291 292 9.616634 CATGAAATGTAACTGTATATGAATGCC 57.383 33.333 0.00 0.00 40.20 4.40
292 293 8.165239 TGAAATGTAACTGTATATGAATGCCC 57.835 34.615 0.00 0.00 0.00 5.36
293 294 7.777440 TGAAATGTAACTGTATATGAATGCCCA 59.223 33.333 0.00 0.00 0.00 5.36
294 295 8.710749 AAATGTAACTGTATATGAATGCCCAT 57.289 30.769 0.00 0.00 0.00 4.00
295 296 7.692460 ATGTAACTGTATATGAATGCCCATG 57.308 36.000 0.00 0.00 0.00 3.66
296 297 5.473162 TGTAACTGTATATGAATGCCCATGC 59.527 40.000 0.00 0.00 38.26 4.06
308 309 2.523245 TGCCCATGCAAGTTTGATACA 58.477 42.857 0.00 0.00 46.66 2.29
309 310 2.896044 TGCCCATGCAAGTTTGATACAA 59.104 40.909 0.00 0.00 46.66 2.41
310 311 3.056678 TGCCCATGCAAGTTTGATACAAG 60.057 43.478 0.00 0.00 46.66 3.16
311 312 3.056607 GCCCATGCAAGTTTGATACAAGT 60.057 43.478 0.00 0.00 37.47 3.16
312 313 4.561326 GCCCATGCAAGTTTGATACAAGTT 60.561 41.667 0.00 0.00 37.47 2.66
313 314 5.540911 CCCATGCAAGTTTGATACAAGTTT 58.459 37.500 0.00 0.00 0.00 2.66
314 315 6.686630 CCCATGCAAGTTTGATACAAGTTTA 58.313 36.000 0.00 0.00 0.00 2.01
315 316 7.322664 CCCATGCAAGTTTGATACAAGTTTAT 58.677 34.615 0.00 0.00 0.00 1.40
316 317 7.276218 CCCATGCAAGTTTGATACAAGTTTATG 59.724 37.037 0.00 0.00 0.00 1.90
317 318 7.814107 CCATGCAAGTTTGATACAAGTTTATGT 59.186 33.333 0.00 0.00 37.32 2.29
318 319 9.838975 CATGCAAGTTTGATACAAGTTTATGTA 57.161 29.630 0.00 0.00 39.91 2.29
330 331 7.129109 ACAAGTTTATGTATCAAACTGACCG 57.871 36.000 1.54 0.00 43.62 4.79
331 332 6.708949 ACAAGTTTATGTATCAAACTGACCGT 59.291 34.615 1.54 0.00 43.62 4.83
332 333 6.963049 AGTTTATGTATCAAACTGACCGTC 57.037 37.500 0.00 0.00 42.98 4.79
333 334 5.575606 AGTTTATGTATCAAACTGACCGTCG 59.424 40.000 0.00 0.00 42.98 5.12
334 335 3.587797 ATGTATCAAACTGACCGTCGT 57.412 42.857 0.00 0.00 0.00 4.34
335 336 4.707030 ATGTATCAAACTGACCGTCGTA 57.293 40.909 0.00 0.00 0.00 3.43
336 337 4.707030 TGTATCAAACTGACCGTCGTAT 57.293 40.909 0.00 0.00 0.00 3.06
337 338 5.816449 TGTATCAAACTGACCGTCGTATA 57.184 39.130 0.00 0.00 0.00 1.47
338 339 6.381481 TGTATCAAACTGACCGTCGTATAT 57.619 37.500 0.00 0.00 0.00 0.86
339 340 7.495135 TGTATCAAACTGACCGTCGTATATA 57.505 36.000 0.00 0.00 0.00 0.86
340 341 7.929159 TGTATCAAACTGACCGTCGTATATAA 58.071 34.615 0.00 0.00 0.00 0.98
341 342 8.071967 TGTATCAAACTGACCGTCGTATATAAG 58.928 37.037 0.00 0.00 0.00 1.73
342 343 6.441093 TCAAACTGACCGTCGTATATAAGT 57.559 37.500 0.00 0.00 0.00 2.24
343 344 6.855836 TCAAACTGACCGTCGTATATAAGTT 58.144 36.000 0.00 0.00 0.00 2.66
344 345 7.984391 TCAAACTGACCGTCGTATATAAGTTA 58.016 34.615 0.00 0.00 0.00 2.24
345 346 8.623903 TCAAACTGACCGTCGTATATAAGTTAT 58.376 33.333 0.17 0.17 0.00 1.89
346 347 9.882996 CAAACTGACCGTCGTATATAAGTTATA 57.117 33.333 5.08 5.08 0.00 0.98
349 350 9.440773 ACTGACCGTCGTATATAAGTTATATGA 57.559 33.333 20.98 10.83 33.60 2.15
350 351 9.699985 CTGACCGTCGTATATAAGTTATATGAC 57.300 37.037 20.98 18.42 40.44 3.06
351 352 9.440773 TGACCGTCGTATATAAGTTATATGACT 57.559 33.333 20.98 9.11 41.11 3.41
393 394 4.391405 AAAAACTGTCCAGGAGCTTTTG 57.609 40.909 0.00 0.00 0.00 2.44
394 395 1.986882 AACTGTCCAGGAGCTTTTGG 58.013 50.000 10.38 10.38 35.74 3.28
395 396 1.140312 ACTGTCCAGGAGCTTTTGGA 58.860 50.000 14.25 14.25 41.06 3.53
396 397 1.494721 ACTGTCCAGGAGCTTTTGGAA 59.505 47.619 18.48 10.25 44.61 3.53
397 398 2.157738 CTGTCCAGGAGCTTTTGGAAG 58.842 52.381 18.48 14.38 44.61 3.46
410 411 1.410882 TTTGGAAGCTTCCCAAAACCG 59.589 47.619 36.75 0.00 46.99 4.44
411 412 1.964448 GGAAGCTTCCCAAAACCGG 59.036 57.895 31.91 0.00 41.62 5.28
412 413 1.289066 GAAGCTTCCCAAAACCGGC 59.711 57.895 15.97 0.00 0.00 6.13
413 414 1.456705 AAGCTTCCCAAAACCGGCA 60.457 52.632 0.00 0.00 0.00 5.69
414 415 0.831711 AAGCTTCCCAAAACCGGCAT 60.832 50.000 0.00 0.00 0.00 4.40
415 416 1.079888 GCTTCCCAAAACCGGCATG 60.080 57.895 0.00 0.00 0.00 4.06
416 417 1.591183 CTTCCCAAAACCGGCATGG 59.409 57.895 0.00 7.67 46.41 3.66
419 420 3.784573 CCAAAACCGGCATGGGAA 58.215 55.556 0.00 0.00 44.64 3.97
420 421 1.591183 CCAAAACCGGCATGGGAAG 59.409 57.895 0.00 0.00 44.64 3.46
421 422 1.591183 CAAAACCGGCATGGGAAGG 59.409 57.895 0.00 0.00 44.64 3.46
422 423 1.155155 AAAACCGGCATGGGAAGGT 59.845 52.632 0.00 0.00 44.64 3.50
423 424 2.851045 AACCGGCATGGGAAGGTT 59.149 55.556 0.00 0.00 44.64 3.50
424 425 1.155155 AACCGGCATGGGAAGGTTT 59.845 52.632 0.00 0.00 43.72 3.27
425 426 0.471022 AACCGGCATGGGAAGGTTTT 60.471 50.000 0.00 0.00 43.72 2.43
426 427 1.184970 ACCGGCATGGGAAGGTTTTG 61.185 55.000 0.00 0.00 44.64 2.44
427 428 1.591183 CGGCATGGGAAGGTTTTGG 59.409 57.895 0.00 0.00 0.00 3.28
428 429 1.887344 CGGCATGGGAAGGTTTTGGG 61.887 60.000 0.00 0.00 0.00 4.12
429 430 0.544120 GGCATGGGAAGGTTTTGGGA 60.544 55.000 0.00 0.00 0.00 4.37
430 431 0.897621 GCATGGGAAGGTTTTGGGAG 59.102 55.000 0.00 0.00 0.00 4.30
431 432 0.897621 CATGGGAAGGTTTTGGGAGC 59.102 55.000 0.00 0.00 0.00 4.70
432 433 0.786435 ATGGGAAGGTTTTGGGAGCT 59.214 50.000 0.00 0.00 0.00 4.09
433 434 0.560688 TGGGAAGGTTTTGGGAGCTT 59.439 50.000 0.00 0.00 39.85 3.74
437 438 1.807142 GAAGGTTTTGGGAGCTTCTCG 59.193 52.381 8.98 0.00 45.81 4.04
438 439 0.765510 AGGTTTTGGGAGCTTCTCGT 59.234 50.000 0.00 0.00 0.00 4.18
439 440 1.975680 AGGTTTTGGGAGCTTCTCGTA 59.024 47.619 0.00 0.00 0.00 3.43
440 441 2.370849 AGGTTTTGGGAGCTTCTCGTAA 59.629 45.455 0.00 0.00 0.00 3.18
441 442 2.483106 GGTTTTGGGAGCTTCTCGTAAC 59.517 50.000 0.00 0.00 0.00 2.50
442 443 2.467566 TTTGGGAGCTTCTCGTAACC 57.532 50.000 0.00 0.00 0.00 2.85
443 444 0.245539 TTGGGAGCTTCTCGTAACCG 59.754 55.000 0.00 0.00 0.00 4.44
444 445 1.141234 GGGAGCTTCTCGTAACCGG 59.859 63.158 0.00 0.00 33.95 5.28
446 447 1.318158 GGAGCTTCTCGTAACCGGGA 61.318 60.000 6.32 0.00 43.18 5.14
453 454 0.175073 CTCGTAACCGGGAAAGAGGG 59.825 60.000 6.32 0.00 36.35 4.30
460 461 1.623542 CCGGGAAAGAGGGGATTCGT 61.624 60.000 0.00 0.00 0.00 3.85
467 468 1.153349 GAGGGGATTCGTCTGGTGC 60.153 63.158 0.00 0.00 0.00 5.01
481 482 0.256177 TGGTGCGTTAATATGGGCCA 59.744 50.000 9.61 9.61 0.00 5.36
499 504 2.947243 GCCAGCCCAATTTGATGAGAGA 60.947 50.000 0.00 0.00 0.00 3.10
610 621 0.109597 CTGCTTCCACAACATTCCGC 60.110 55.000 0.00 0.00 0.00 5.54
631 642 1.227943 ACATGCCGAACAGTGCAGT 60.228 52.632 0.00 0.00 41.46 4.40
739 750 2.983791 GATTCCAACCCGACCCGA 59.016 61.111 0.00 0.00 0.00 5.14
740 751 1.449070 GATTCCAACCCGACCCGAC 60.449 63.158 0.00 0.00 0.00 4.79
741 752 2.864378 GATTCCAACCCGACCCGACC 62.864 65.000 0.00 0.00 0.00 4.79
742 753 4.938074 TCCAACCCGACCCGACCA 62.938 66.667 0.00 0.00 0.00 4.02
743 754 4.692475 CCAACCCGACCCGACCAC 62.692 72.222 0.00 0.00 0.00 4.16
762 773 0.390735 CGGTTTAACGTCCTCCCCAG 60.391 60.000 0.00 0.00 0.00 4.45
800 811 4.408821 GCCACCACGCCATCAGGA 62.409 66.667 0.00 0.00 36.89 3.86
804 815 1.176527 CACCACGCCATCAGGAAAAT 58.823 50.000 0.00 0.00 36.89 1.82
806 817 1.545582 ACCACGCCATCAGGAAAATTG 59.454 47.619 0.00 0.00 36.89 2.32
890 901 1.744014 GCCCTCCGCCGTCTTATAA 59.256 57.895 0.00 0.00 0.00 0.98
914 925 1.373570 CTCCTGTTCCAAATCCGCTC 58.626 55.000 0.00 0.00 0.00 5.03
950 961 2.507992 CAGAGAACTCGCCGGCAG 60.508 66.667 28.98 23.74 34.09 4.85
952 963 2.202676 GAGAACTCGCCGGCAGAG 60.203 66.667 32.51 32.51 41.27 3.35
978 1000 1.391157 CCTCTTCTCCCCTCTCGCTG 61.391 65.000 0.00 0.00 0.00 5.18
987 1009 4.200283 CTCTCGCTGTCGGCTCCC 62.200 72.222 1.37 0.00 39.13 4.30
1009 1031 2.044352 TCGCTCCCATGGACTCGA 60.044 61.111 15.22 15.08 32.13 4.04
1135 1157 1.293924 GGTGCATCACTTCATCCTCG 58.706 55.000 0.00 0.00 34.40 4.63
1220 1251 2.993853 GCTGAAGGAGGTCCAGGG 59.006 66.667 0.00 0.00 38.89 4.45
1398 1435 4.475135 GAGCTCCCCAAGGCGGAC 62.475 72.222 0.87 0.00 36.56 4.79
1540 1580 0.250081 GGAGGAGCCGATCAACATCC 60.250 60.000 0.00 0.00 0.00 3.51
1599 1639 2.194201 ATTGGTTCCGATTGGTTCGT 57.806 45.000 0.00 0.00 46.65 3.85
1604 1644 2.291190 GGTTCCGATTGGTTCGTTTCAA 59.709 45.455 0.00 0.00 46.65 2.69
1679 1723 5.326069 ACTAGTAGTTGCTGAAGAGGAGAA 58.674 41.667 0.00 0.00 0.00 2.87
1701 1747 3.011369 AGAGGAGGAATTGGGGGTAAAAC 59.989 47.826 0.00 0.00 0.00 2.43
1750 1796 3.253921 TGCTGTGATGTCAATGAAACTGG 59.746 43.478 0.00 0.00 0.00 4.00
1785 1831 2.159393 TCAGACAAAGCACTGTGTTTGC 60.159 45.455 23.33 18.54 37.19 3.68
1851 1908 4.985413 TCGCAATGATCTTGTCAAATTCC 58.015 39.130 0.00 0.00 40.97 3.01
1863 1920 7.035004 TCTTGTCAAATTCCTTGTTGTTTCTG 58.965 34.615 0.00 0.00 36.34 3.02
1865 1922 5.108517 GTCAAATTCCTTGTTGTTTCTGCA 58.891 37.500 0.00 0.00 36.34 4.41
1890 1948 1.002087 AGCTTCAGGACGAACGGATTT 59.998 47.619 0.00 0.00 0.00 2.17
1898 1956 0.802494 ACGAACGGATTTGTGCATCC 59.198 50.000 0.00 0.00 39.69 3.51
1901 1959 1.750778 GAACGGATTTGTGCATCCCAT 59.249 47.619 0.00 0.00 39.92 4.00
1903 1961 0.308684 CGGATTTGTGCATCCCATCG 59.691 55.000 0.00 0.00 39.92 3.84
1904 1962 1.392589 GGATTTGTGCATCCCATCGT 58.607 50.000 0.00 0.00 37.36 3.73
1905 1963 1.750778 GGATTTGTGCATCCCATCGTT 59.249 47.619 0.00 0.00 37.36 3.85
1906 1964 2.480073 GGATTTGTGCATCCCATCGTTG 60.480 50.000 0.00 0.00 37.36 4.10
1907 1965 0.887247 TTTGTGCATCCCATCGTTGG 59.113 50.000 5.47 5.47 43.23 3.77
1908 1966 0.251121 TTGTGCATCCCATCGTTGGT 60.251 50.000 11.51 0.00 41.91 3.67
1909 1967 0.251121 TGTGCATCCCATCGTTGGTT 60.251 50.000 11.51 0.00 41.91 3.67
1910 1968 0.887933 GTGCATCCCATCGTTGGTTT 59.112 50.000 11.51 0.00 41.91 3.27
1911 1969 1.135402 GTGCATCCCATCGTTGGTTTC 60.135 52.381 11.51 0.00 41.91 2.78
1912 1970 0.098728 GCATCCCATCGTTGGTTTCG 59.901 55.000 11.51 0.00 41.91 3.46
1913 1971 0.732571 CATCCCATCGTTGGTTTCGG 59.267 55.000 11.51 0.00 41.91 4.30
1914 1972 0.326927 ATCCCATCGTTGGTTTCGGT 59.673 50.000 11.51 0.00 41.91 4.69
1915 1973 0.975135 TCCCATCGTTGGTTTCGGTA 59.025 50.000 11.51 0.00 41.91 4.02
1916 1974 1.066716 TCCCATCGTTGGTTTCGGTAG 60.067 52.381 11.51 0.00 41.91 3.18
1917 1975 1.365699 CCATCGTTGGTTTCGGTAGG 58.634 55.000 4.23 0.00 38.30 3.18
1960 2018 1.464608 GTGCTGTGTATGCGTCAACAT 59.535 47.619 0.00 0.00 0.00 2.71
1981 2039 2.930562 GACTGGAGGGGTGTGGCT 60.931 66.667 0.00 0.00 0.00 4.75
2000 2066 0.599060 TGGTCGCGTAACATCTGTCA 59.401 50.000 5.77 0.00 0.00 3.58
2089 2155 0.877213 AAACGACGGACCGTGAAAGG 60.877 55.000 27.26 10.42 41.37 3.11
2096 2162 1.199097 CGGACCGTGAAAGGAAAATGG 59.801 52.381 5.48 0.00 34.73 3.16
2144 2678 0.106669 GCTGGGGACTGGGGTTTATC 60.107 60.000 0.00 0.00 0.00 1.75
2150 2684 3.465966 GGGGACTGGGGTTTATCCTTATT 59.534 47.826 0.00 0.00 36.25 1.40
2258 2792 0.625980 TGGCATCTAACCCATCCCCA 60.626 55.000 0.00 0.00 0.00 4.96
2277 2811 8.585018 CATCCCCAAAACTTAACTCTTAACAAT 58.415 33.333 0.00 0.00 0.00 2.71
2278 2812 8.541899 TCCCCAAAACTTAACTCTTAACAATT 57.458 30.769 0.00 0.00 0.00 2.32
2280 2814 9.607988 CCCCAAAACTTAACTCTTAACAATTTT 57.392 29.630 0.00 0.00 0.00 1.82
2313 2957 8.992835 ATTTCTGCATTCCTTTAGAAACATTC 57.007 30.769 0.00 0.00 40.65 2.67
2381 3025 7.820872 AGGGTTCAAATGAAAGCAAATATTCTG 59.179 33.333 0.00 0.00 35.58 3.02
2392 3036 9.577110 GAAAGCAAATATTCTGAATGAACATGA 57.423 29.630 13.01 0.00 37.52 3.07
2500 3149 2.484062 CCCATGAGATTGCCGGTGC 61.484 63.158 1.90 0.00 38.26 5.01
2529 3178 8.498054 TCTCTTTAATGATCAAAGTCATGGTC 57.502 34.615 0.00 0.00 38.76 4.02
2539 3188 0.044702 AGTCATGGTCATCTCCCCCA 59.955 55.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.467796 ACAGCAGAGCTAATATGTAGTATATCA 57.532 33.333 0.00 0.00 36.40 2.15
18 19 9.297037 TGATAACAGCAGAGCTAATATGTAGTA 57.703 33.333 0.00 0.00 36.40 1.82
19 20 8.183104 TGATAACAGCAGAGCTAATATGTAGT 57.817 34.615 0.00 0.00 36.40 2.73
20 21 9.481340 TTTGATAACAGCAGAGCTAATATGTAG 57.519 33.333 0.00 0.00 36.40 2.74
21 22 9.261180 GTTTGATAACAGCAGAGCTAATATGTA 57.739 33.333 0.00 0.00 36.40 2.29
22 23 7.770433 TGTTTGATAACAGCAGAGCTAATATGT 59.230 33.333 0.00 0.00 39.29 2.29
23 24 8.146479 TGTTTGATAACAGCAGAGCTAATATG 57.854 34.615 0.00 0.00 39.29 1.78
24 25 8.781196 CATGTTTGATAACAGCAGAGCTAATAT 58.219 33.333 0.00 0.00 46.71 1.28
25 26 7.986889 TCATGTTTGATAACAGCAGAGCTAATA 59.013 33.333 0.00 0.00 46.71 0.98
26 27 6.825213 TCATGTTTGATAACAGCAGAGCTAAT 59.175 34.615 0.00 0.00 46.71 1.73
27 28 6.172630 TCATGTTTGATAACAGCAGAGCTAA 58.827 36.000 0.00 0.00 46.71 3.09
28 29 5.733676 TCATGTTTGATAACAGCAGAGCTA 58.266 37.500 0.00 0.00 46.71 3.32
29 30 4.582869 TCATGTTTGATAACAGCAGAGCT 58.417 39.130 0.00 0.00 46.71 4.09
30 31 4.952262 TCATGTTTGATAACAGCAGAGC 57.048 40.909 0.00 0.00 46.71 4.09
31 32 7.080353 TCATTCATGTTTGATAACAGCAGAG 57.920 36.000 0.00 0.00 46.71 3.35
32 33 7.337436 TGATCATTCATGTTTGATAACAGCAGA 59.663 33.333 11.42 0.00 46.71 4.26
33 34 7.477494 TGATCATTCATGTTTGATAACAGCAG 58.523 34.615 11.42 0.00 46.71 4.24
34 35 7.393841 TGATCATTCATGTTTGATAACAGCA 57.606 32.000 11.42 4.81 46.71 4.41
35 36 7.322938 CGATGATCATTCATGTTTGATAACAGC 59.677 37.037 10.14 9.01 46.71 4.40
36 37 8.340443 ACGATGATCATTCATGTTTGATAACAG 58.660 33.333 10.14 6.57 46.71 3.16
38 39 9.162793 GAACGATGATCATTCATGTTTGATAAC 57.837 33.333 10.14 3.92 42.73 1.89
39 40 9.112725 AGAACGATGATCATTCATGTTTGATAA 57.887 29.630 10.14 6.63 42.73 1.75
40 41 8.667076 AGAACGATGATCATTCATGTTTGATA 57.333 30.769 10.14 4.02 42.73 2.15
41 42 7.563888 AGAACGATGATCATTCATGTTTGAT 57.436 32.000 10.14 11.30 42.73 2.57
42 43 6.990341 AGAACGATGATCATTCATGTTTGA 57.010 33.333 10.14 0.00 42.73 2.69
43 44 7.849515 CACTAGAACGATGATCATTCATGTTTG 59.150 37.037 10.14 9.23 42.73 2.93
44 45 7.466455 GCACTAGAACGATGATCATTCATGTTT 60.466 37.037 10.14 6.76 42.73 2.83
45 46 6.018425 GCACTAGAACGATGATCATTCATGTT 60.018 38.462 10.14 12.04 42.73 2.71
46 47 5.464722 GCACTAGAACGATGATCATTCATGT 59.535 40.000 10.14 4.00 42.73 3.21
47 48 5.695363 AGCACTAGAACGATGATCATTCATG 59.305 40.000 10.14 6.01 42.73 3.07
48 49 5.851720 AGCACTAGAACGATGATCATTCAT 58.148 37.500 10.14 0.00 45.39 2.57
49 50 5.268118 AGCACTAGAACGATGATCATTCA 57.732 39.130 10.14 0.00 36.00 2.57
50 51 5.521735 ACAAGCACTAGAACGATGATCATTC 59.478 40.000 10.14 4.50 0.00 2.67
51 52 5.423015 ACAAGCACTAGAACGATGATCATT 58.577 37.500 10.14 0.00 0.00 2.57
52 53 5.016051 ACAAGCACTAGAACGATGATCAT 57.984 39.130 8.25 8.25 0.00 2.45
53 54 4.424626 GACAAGCACTAGAACGATGATCA 58.575 43.478 0.00 0.00 0.00 2.92
54 55 3.799420 GGACAAGCACTAGAACGATGATC 59.201 47.826 0.00 0.00 0.00 2.92
55 56 3.195610 TGGACAAGCACTAGAACGATGAT 59.804 43.478 0.00 0.00 0.00 2.45
56 57 2.560981 TGGACAAGCACTAGAACGATGA 59.439 45.455 0.00 0.00 0.00 2.92
57 58 2.668457 GTGGACAAGCACTAGAACGATG 59.332 50.000 0.00 0.00 0.00 3.84
58 59 2.299013 TGTGGACAAGCACTAGAACGAT 59.701 45.455 0.00 0.00 0.00 3.73
59 60 1.684450 TGTGGACAAGCACTAGAACGA 59.316 47.619 0.00 0.00 0.00 3.85
60 61 1.792949 GTGTGGACAAGCACTAGAACG 59.207 52.381 0.00 0.00 33.22 3.95
61 62 2.833794 TGTGTGGACAAGCACTAGAAC 58.166 47.619 0.00 0.00 36.63 3.01
62 63 3.552132 TTGTGTGGACAAGCACTAGAA 57.448 42.857 0.00 0.00 37.15 2.10
71 72 2.719531 TTGTAGGCTTGTGTGGACAA 57.280 45.000 0.00 0.00 39.88 3.18
72 73 2.503331 CATTGTAGGCTTGTGTGGACA 58.497 47.619 0.00 0.00 0.00 4.02
73 74 1.812571 CCATTGTAGGCTTGTGTGGAC 59.187 52.381 0.00 0.00 0.00 4.02
74 75 1.271871 CCCATTGTAGGCTTGTGTGGA 60.272 52.381 0.00 0.00 0.00 4.02
75 76 1.176527 CCCATTGTAGGCTTGTGTGG 58.823 55.000 0.00 0.00 0.00 4.17
76 77 1.176527 CCCCATTGTAGGCTTGTGTG 58.823 55.000 0.00 0.00 0.00 3.82
77 78 1.004745 CTCCCCATTGTAGGCTTGTGT 59.995 52.381 0.00 0.00 0.00 3.72
78 79 1.683011 CCTCCCCATTGTAGGCTTGTG 60.683 57.143 0.00 0.00 0.00 3.33
79 80 0.625849 CCTCCCCATTGTAGGCTTGT 59.374 55.000 0.00 0.00 0.00 3.16
80 81 0.625849 ACCTCCCCATTGTAGGCTTG 59.374 55.000 0.00 0.00 33.42 4.01
81 82 0.919710 GACCTCCCCATTGTAGGCTT 59.080 55.000 0.00 0.00 33.42 4.35
82 83 1.338136 CGACCTCCCCATTGTAGGCT 61.338 60.000 0.00 0.00 33.42 4.58
83 84 1.146263 CGACCTCCCCATTGTAGGC 59.854 63.158 0.00 0.00 33.42 3.93
84 85 1.146263 GCGACCTCCCCATTGTAGG 59.854 63.158 0.00 0.00 36.42 3.18
85 86 0.179073 CAGCGACCTCCCCATTGTAG 60.179 60.000 0.00 0.00 0.00 2.74
86 87 1.622607 CCAGCGACCTCCCCATTGTA 61.623 60.000 0.00 0.00 0.00 2.41
87 88 2.671070 CAGCGACCTCCCCATTGT 59.329 61.111 0.00 0.00 0.00 2.71
88 89 2.124570 CCAGCGACCTCCCCATTG 60.125 66.667 0.00 0.00 0.00 2.82
89 90 2.198304 GAACCAGCGACCTCCCCATT 62.198 60.000 0.00 0.00 0.00 3.16
90 91 2.610859 AACCAGCGACCTCCCCAT 60.611 61.111 0.00 0.00 0.00 4.00
91 92 3.319198 GAACCAGCGACCTCCCCA 61.319 66.667 0.00 0.00 0.00 4.96
92 93 4.452733 CGAACCAGCGACCTCCCC 62.453 72.222 0.00 0.00 0.00 4.81
93 94 2.939261 TTCGAACCAGCGACCTCCC 61.939 63.158 0.00 0.00 40.42 4.30
94 95 1.737008 GTTCGAACCAGCGACCTCC 60.737 63.158 17.68 0.00 40.42 4.30
95 96 3.857909 GTTCGAACCAGCGACCTC 58.142 61.111 17.68 0.00 40.42 3.85
113 114 0.625849 AGCAAACTGATGGTAGGGGG 59.374 55.000 0.00 0.00 0.00 5.40
114 115 2.514458 AAGCAAACTGATGGTAGGGG 57.486 50.000 0.00 0.00 0.00 4.79
115 116 4.871933 AAAAAGCAAACTGATGGTAGGG 57.128 40.909 0.00 0.00 0.00 3.53
116 117 7.156876 TGATAAAAAGCAAACTGATGGTAGG 57.843 36.000 0.00 0.00 0.00 3.18
117 118 9.643693 AAATGATAAAAAGCAAACTGATGGTAG 57.356 29.630 0.00 0.00 0.00 3.18
118 119 9.995003 AAAATGATAAAAAGCAAACTGATGGTA 57.005 25.926 0.00 0.00 0.00 3.25
119 120 8.907222 AAAATGATAAAAAGCAAACTGATGGT 57.093 26.923 0.00 0.00 0.00 3.55
170 171 6.680148 TTATAGAAAAGCCCTTGCCTTTTT 57.320 33.333 0.00 0.00 38.69 1.94
171 172 6.680148 TTTATAGAAAAGCCCTTGCCTTTT 57.320 33.333 0.00 0.00 38.69 2.27
172 173 6.680148 TTTTATAGAAAAGCCCTTGCCTTT 57.320 33.333 0.00 0.00 38.69 3.11
173 174 6.874278 ATTTTATAGAAAAGCCCTTGCCTT 57.126 33.333 1.35 0.00 37.94 4.35
174 175 6.471233 GATTTTATAGAAAAGCCCTTGCCT 57.529 37.500 0.00 0.00 37.94 4.75
182 183 4.279659 CACGGCGGATTTTATAGAAAAGC 58.720 43.478 13.24 2.26 39.68 3.51
183 184 4.279659 GCACGGCGGATTTTATAGAAAAG 58.720 43.478 13.24 0.00 37.94 2.27
184 185 4.281525 GCACGGCGGATTTTATAGAAAA 57.718 40.909 13.24 0.00 38.87 2.29
185 186 3.955771 GCACGGCGGATTTTATAGAAA 57.044 42.857 13.24 0.00 0.00 2.52
206 207 4.537433 CTAGGGCCTGCCGCTGTC 62.537 72.222 18.53 0.00 37.31 3.51
237 238 0.250793 TGTACCCGTTGCCTACATGG 59.749 55.000 0.00 0.00 39.35 3.66
238 239 2.210116 GATGTACCCGTTGCCTACATG 58.790 52.381 0.00 0.00 32.41 3.21
239 240 1.140252 GGATGTACCCGTTGCCTACAT 59.860 52.381 0.00 0.00 34.47 2.29
240 241 0.538118 GGATGTACCCGTTGCCTACA 59.462 55.000 0.00 0.00 0.00 2.74
241 242 0.529119 CGGATGTACCCGTTGCCTAC 60.529 60.000 2.68 0.00 44.23 3.18
242 243 1.817881 CGGATGTACCCGTTGCCTA 59.182 57.895 2.68 0.00 44.23 3.93
243 244 2.582436 CGGATGTACCCGTTGCCT 59.418 61.111 2.68 0.00 44.23 4.75
250 251 2.831685 TCATGTATGCGGATGTACCC 57.168 50.000 0.00 0.00 34.64 3.69
251 252 4.515191 ACATTTCATGTATGCGGATGTACC 59.485 41.667 0.00 0.00 42.78 3.34
252 253 5.673337 ACATTTCATGTATGCGGATGTAC 57.327 39.130 0.00 0.00 42.78 2.90
253 254 6.989759 AGTTACATTTCATGTATGCGGATGTA 59.010 34.615 0.00 8.99 44.51 2.29
254 255 5.822519 AGTTACATTTCATGTATGCGGATGT 59.177 36.000 0.00 10.26 44.51 3.06
255 256 6.138088 CAGTTACATTTCATGTATGCGGATG 58.862 40.000 0.00 0.00 44.51 3.51
256 257 5.822519 ACAGTTACATTTCATGTATGCGGAT 59.177 36.000 0.00 0.00 44.51 4.18
257 258 5.182487 ACAGTTACATTTCATGTATGCGGA 58.818 37.500 9.49 0.00 44.51 5.54
258 259 5.484173 ACAGTTACATTTCATGTATGCGG 57.516 39.130 9.49 0.00 44.51 5.69
259 260 9.745323 CATATACAGTTACATTTCATGTATGCG 57.255 33.333 9.49 0.00 44.51 4.73
265 266 9.616634 GGCATTCATATACAGTTACATTTCATG 57.383 33.333 0.00 0.00 0.00 3.07
266 267 8.796475 GGGCATTCATATACAGTTACATTTCAT 58.204 33.333 0.00 0.00 0.00 2.57
267 268 7.777440 TGGGCATTCATATACAGTTACATTTCA 59.223 33.333 0.00 0.00 0.00 2.69
268 269 8.165239 TGGGCATTCATATACAGTTACATTTC 57.835 34.615 0.00 0.00 0.00 2.17
269 270 8.579006 CATGGGCATTCATATACAGTTACATTT 58.421 33.333 0.00 0.00 0.00 2.32
270 271 7.309377 GCATGGGCATTCATATACAGTTACATT 60.309 37.037 0.00 0.00 40.72 2.71
271 272 6.151648 GCATGGGCATTCATATACAGTTACAT 59.848 38.462 0.00 0.00 40.72 2.29
272 273 5.473162 GCATGGGCATTCATATACAGTTACA 59.527 40.000 0.00 0.00 40.72 2.41
273 274 5.942872 GCATGGGCATTCATATACAGTTAC 58.057 41.667 0.00 0.00 40.72 2.50
289 290 3.056607 ACTTGTATCAAACTTGCATGGGC 60.057 43.478 4.44 0.00 41.68 5.36
290 291 4.789012 ACTTGTATCAAACTTGCATGGG 57.211 40.909 4.44 0.00 0.00 4.00
291 292 7.814107 ACATAAACTTGTATCAAACTTGCATGG 59.186 33.333 4.44 0.00 0.00 3.66
292 293 8.746922 ACATAAACTTGTATCAAACTTGCATG 57.253 30.769 0.00 0.00 0.00 4.06
304 305 8.879759 CGGTCAGTTTGATACATAAACTTGTAT 58.120 33.333 0.00 0.00 43.71 2.29
305 306 7.874016 ACGGTCAGTTTGATACATAAACTTGTA 59.126 33.333 0.00 0.00 43.71 2.41
306 307 6.708949 ACGGTCAGTTTGATACATAAACTTGT 59.291 34.615 0.00 0.00 43.71 3.16
307 308 7.129109 ACGGTCAGTTTGATACATAAACTTG 57.871 36.000 0.00 0.00 43.71 3.16
308 309 6.090358 CGACGGTCAGTTTGATACATAAACTT 59.910 38.462 9.10 0.00 43.71 2.66
309 310 5.575606 CGACGGTCAGTTTGATACATAAACT 59.424 40.000 9.10 0.00 46.23 2.66
310 311 5.346822 ACGACGGTCAGTTTGATACATAAAC 59.653 40.000 9.10 0.00 38.09 2.01
311 312 5.472148 ACGACGGTCAGTTTGATACATAAA 58.528 37.500 9.10 0.00 0.00 1.40
312 313 5.063180 ACGACGGTCAGTTTGATACATAA 57.937 39.130 9.10 0.00 0.00 1.90
313 314 4.707030 ACGACGGTCAGTTTGATACATA 57.293 40.909 9.10 0.00 0.00 2.29
314 315 3.587797 ACGACGGTCAGTTTGATACAT 57.412 42.857 9.10 0.00 0.00 2.29
315 316 4.707030 ATACGACGGTCAGTTTGATACA 57.293 40.909 9.10 0.00 0.00 2.29
316 317 8.072567 ACTTATATACGACGGTCAGTTTGATAC 58.927 37.037 9.10 0.00 0.00 2.24
317 318 8.158169 ACTTATATACGACGGTCAGTTTGATA 57.842 34.615 9.10 3.55 0.00 2.15
318 319 7.035840 ACTTATATACGACGGTCAGTTTGAT 57.964 36.000 9.10 1.63 0.00 2.57
319 320 6.441093 ACTTATATACGACGGTCAGTTTGA 57.559 37.500 9.10 0.00 0.00 2.69
320 321 8.792831 ATAACTTATATACGACGGTCAGTTTG 57.207 34.615 9.10 0.00 0.00 2.93
323 324 9.440773 TCATATAACTTATATACGACGGTCAGT 57.559 33.333 9.10 9.49 30.48 3.41
324 325 9.699985 GTCATATAACTTATATACGACGGTCAG 57.300 37.037 9.10 3.87 30.48 3.51
325 326 9.440773 AGTCATATAACTTATATACGACGGTCA 57.559 33.333 9.10 0.00 33.07 4.02
372 373 3.132824 CCAAAAGCTCCTGGACAGTTTTT 59.867 43.478 8.09 0.00 35.40 1.94
373 374 2.695147 CCAAAAGCTCCTGGACAGTTTT 59.305 45.455 8.09 0.00 34.35 2.43
374 375 2.091885 TCCAAAAGCTCCTGGACAGTTT 60.092 45.455 11.75 0.00 36.79 2.66
375 376 1.494721 TCCAAAAGCTCCTGGACAGTT 59.505 47.619 11.75 0.00 36.79 3.16
376 377 1.140312 TCCAAAAGCTCCTGGACAGT 58.860 50.000 11.75 0.00 36.79 3.55
377 378 2.157738 CTTCCAAAAGCTCCTGGACAG 58.842 52.381 14.72 11.73 41.49 3.51
378 379 2.276732 CTTCCAAAAGCTCCTGGACA 57.723 50.000 14.72 7.24 41.49 4.02
393 394 1.964448 CCGGTTTTGGGAAGCTTCC 59.036 57.895 33.67 33.67 46.82 3.46
394 395 1.289066 GCCGGTTTTGGGAAGCTTC 59.711 57.895 18.54 18.54 0.00 3.86
395 396 0.831711 ATGCCGGTTTTGGGAAGCTT 60.832 50.000 1.90 0.00 31.01 3.74
396 397 1.228862 ATGCCGGTTTTGGGAAGCT 60.229 52.632 1.90 0.00 31.01 3.74
397 398 1.079888 CATGCCGGTTTTGGGAAGC 60.080 57.895 1.90 0.00 31.01 3.86
398 399 1.591183 CCATGCCGGTTTTGGGAAG 59.409 57.895 1.90 0.00 31.01 3.46
399 400 3.784573 CCATGCCGGTTTTGGGAA 58.215 55.556 1.90 0.00 31.01 3.97
402 403 1.591183 CTTCCCATGCCGGTTTTGG 59.409 57.895 1.90 7.92 0.00 3.28
403 404 1.184970 ACCTTCCCATGCCGGTTTTG 61.185 55.000 1.90 0.00 0.00 2.44
404 405 0.471022 AACCTTCCCATGCCGGTTTT 60.471 50.000 1.90 0.00 36.39 2.43
405 406 0.471022 AAACCTTCCCATGCCGGTTT 60.471 50.000 1.90 10.98 43.00 3.27
406 407 0.471022 AAAACCTTCCCATGCCGGTT 60.471 50.000 1.90 0.00 41.25 4.44
407 408 1.155155 AAAACCTTCCCATGCCGGT 59.845 52.632 1.90 0.00 0.00 5.28
408 409 1.591183 CAAAACCTTCCCATGCCGG 59.409 57.895 0.00 0.00 0.00 6.13
409 410 1.591183 CCAAAACCTTCCCATGCCG 59.409 57.895 0.00 0.00 0.00 5.69
410 411 0.544120 TCCCAAAACCTTCCCATGCC 60.544 55.000 0.00 0.00 0.00 4.40
411 412 0.897621 CTCCCAAAACCTTCCCATGC 59.102 55.000 0.00 0.00 0.00 4.06
412 413 0.897621 GCTCCCAAAACCTTCCCATG 59.102 55.000 0.00 0.00 0.00 3.66
413 414 0.786435 AGCTCCCAAAACCTTCCCAT 59.214 50.000 0.00 0.00 0.00 4.00
414 415 0.560688 AAGCTCCCAAAACCTTCCCA 59.439 50.000 0.00 0.00 0.00 4.37
415 416 1.203063 AGAAGCTCCCAAAACCTTCCC 60.203 52.381 0.00 0.00 35.47 3.97
416 417 2.163509 GAGAAGCTCCCAAAACCTTCC 58.836 52.381 0.00 0.00 35.47 3.46
417 418 1.807142 CGAGAAGCTCCCAAAACCTTC 59.193 52.381 0.00 0.00 35.19 3.46
418 419 1.143073 ACGAGAAGCTCCCAAAACCTT 59.857 47.619 0.00 0.00 0.00 3.50
419 420 0.765510 ACGAGAAGCTCCCAAAACCT 59.234 50.000 0.00 0.00 0.00 3.50
420 421 2.467566 TACGAGAAGCTCCCAAAACC 57.532 50.000 0.00 0.00 0.00 3.27
421 422 2.483106 GGTTACGAGAAGCTCCCAAAAC 59.517 50.000 0.00 0.00 0.00 2.43
422 423 2.774687 GGTTACGAGAAGCTCCCAAAA 58.225 47.619 0.00 0.00 0.00 2.44
423 424 1.337447 CGGTTACGAGAAGCTCCCAAA 60.337 52.381 0.00 0.00 44.60 3.28
424 425 0.245539 CGGTTACGAGAAGCTCCCAA 59.754 55.000 0.00 0.00 44.60 4.12
425 426 1.601419 CCGGTTACGAGAAGCTCCCA 61.601 60.000 0.00 0.00 44.60 4.37
426 427 1.141234 CCGGTTACGAGAAGCTCCC 59.859 63.158 0.00 0.00 44.60 4.30
427 428 1.141234 CCCGGTTACGAGAAGCTCC 59.859 63.158 0.00 0.00 44.60 4.70
428 429 0.529378 TTCCCGGTTACGAGAAGCTC 59.471 55.000 0.00 0.00 44.60 4.09
429 430 0.971386 TTTCCCGGTTACGAGAAGCT 59.029 50.000 0.00 0.00 44.60 3.74
430 431 1.067354 TCTTTCCCGGTTACGAGAAGC 60.067 52.381 0.00 0.00 44.60 3.86
431 432 2.416972 CCTCTTTCCCGGTTACGAGAAG 60.417 54.545 0.00 0.00 44.60 2.85
432 433 1.547372 CCTCTTTCCCGGTTACGAGAA 59.453 52.381 0.00 0.00 44.60 2.87
433 434 1.180029 CCTCTTTCCCGGTTACGAGA 58.820 55.000 0.00 0.00 44.60 4.04
434 435 0.175073 CCCTCTTTCCCGGTTACGAG 59.825 60.000 0.00 0.70 44.60 4.18
435 436 1.259840 CCCCTCTTTCCCGGTTACGA 61.260 60.000 0.00 0.00 44.60 3.43
436 437 1.219935 CCCCTCTTTCCCGGTTACG 59.780 63.158 0.00 0.00 40.55 3.18
437 438 1.210538 ATCCCCTCTTTCCCGGTTAC 58.789 55.000 0.00 0.00 0.00 2.50
438 439 1.841919 GAATCCCCTCTTTCCCGGTTA 59.158 52.381 0.00 0.00 0.00 2.85
439 440 0.624254 GAATCCCCTCTTTCCCGGTT 59.376 55.000 0.00 0.00 0.00 4.44
440 441 1.623542 CGAATCCCCTCTTTCCCGGT 61.624 60.000 0.00 0.00 0.00 5.28
441 442 1.146263 CGAATCCCCTCTTTCCCGG 59.854 63.158 0.00 0.00 0.00 5.73
442 443 0.179081 GACGAATCCCCTCTTTCCCG 60.179 60.000 0.00 0.00 0.00 5.14
443 444 1.134371 CAGACGAATCCCCTCTTTCCC 60.134 57.143 0.00 0.00 0.00 3.97
444 445 1.134371 CCAGACGAATCCCCTCTTTCC 60.134 57.143 0.00 0.00 0.00 3.13
446 447 1.279271 CACCAGACGAATCCCCTCTTT 59.721 52.381 0.00 0.00 0.00 2.52
451 452 2.511600 CGCACCAGACGAATCCCC 60.512 66.667 0.00 0.00 0.00 4.81
453 454 1.717194 TTAACGCACCAGACGAATCC 58.283 50.000 0.00 0.00 0.00 3.01
460 461 1.476110 GGCCCATATTAACGCACCAGA 60.476 52.381 0.00 0.00 0.00 3.86
481 482 2.025605 TGCTCTCTCATCAAATTGGGCT 60.026 45.455 0.00 0.00 0.00 5.19
499 504 1.153745 TTTTTGCAAACGCCGTGCT 60.154 47.368 12.39 0.00 42.69 4.40
610 621 1.229975 TGCACTGTTCGGCATGTGAG 61.230 55.000 0.00 0.00 34.58 3.51
631 642 1.074090 TGGTGGGGTCAACTGAGGA 60.074 57.895 0.00 0.00 0.00 3.71
712 723 1.248101 GGTTGGAATCGGTTGGGTGG 61.248 60.000 0.00 0.00 0.00 4.61
713 724 1.248101 GGGTTGGAATCGGTTGGGTG 61.248 60.000 0.00 0.00 0.00 4.61
714 725 1.076014 GGGTTGGAATCGGTTGGGT 59.924 57.895 0.00 0.00 0.00 4.51
715 726 2.043980 CGGGTTGGAATCGGTTGGG 61.044 63.158 0.00 0.00 0.00 4.12
739 750 0.033920 GGAGGACGTTAAACCGTGGT 59.966 55.000 0.00 0.00 41.98 4.16
740 751 0.671472 GGGAGGACGTTAAACCGTGG 60.671 60.000 0.00 0.00 41.98 4.94
741 752 0.671472 GGGGAGGACGTTAAACCGTG 60.671 60.000 0.00 0.00 41.98 4.94
742 753 1.120795 TGGGGAGGACGTTAAACCGT 61.121 55.000 0.00 0.00 45.18 4.83
743 754 0.390735 CTGGGGAGGACGTTAAACCG 60.391 60.000 0.00 0.00 0.00 4.44
744 755 0.689055 ACTGGGGAGGACGTTAAACC 59.311 55.000 0.00 0.00 0.00 3.27
745 756 1.338484 GGACTGGGGAGGACGTTAAAC 60.338 57.143 0.00 0.00 0.00 2.01
746 757 0.978907 GGACTGGGGAGGACGTTAAA 59.021 55.000 0.00 0.00 0.00 1.52
783 794 3.918253 TTCCTGATGGCGTGGTGGC 62.918 63.158 0.00 0.00 45.12 5.01
800 811 1.152052 AGCTGTGGGCCCCAATTTT 60.152 52.632 22.27 0.00 43.05 1.82
804 815 3.970410 CTGAGCTGTGGGCCCCAA 61.970 66.667 22.27 6.28 43.05 4.12
806 817 4.106925 CTCTGAGCTGTGGGCCCC 62.107 72.222 22.27 11.72 43.05 5.80
890 901 1.077169 GGATTTGGAACAGGAGGGGTT 59.923 52.381 0.00 0.00 42.39 4.11
914 925 5.463392 TCTCTGTTTTTCTCGTGAGATGTTG 59.537 40.000 0.00 0.00 40.84 3.33
952 963 1.764454 GGGGAGAAGAGGAGGAGCC 60.764 68.421 0.00 0.00 0.00 4.70
987 1009 2.444706 TCCATGGGAGCGAGGGAG 60.445 66.667 13.02 0.00 0.00 4.30
994 1016 1.945354 TTCGTCGAGTCCATGGGAGC 61.945 60.000 13.02 2.72 29.39 4.70
1009 1031 2.314647 CCATGTTGTCGCCGTTCGT 61.315 57.895 0.00 0.00 39.67 3.85
1135 1157 4.516195 GGAGAAGAGGTCGCCGCC 62.516 72.222 0.00 0.00 36.38 6.13
1517 1557 2.127869 TTGATCGGCTCCTCCCTCG 61.128 63.158 0.00 0.00 0.00 4.63
1540 1580 0.949397 TAATCCACGTCCTCGATCCG 59.051 55.000 0.00 0.00 40.62 4.18
1616 1656 6.955963 CGAAGATGATGAAGAAAAGTAAACCG 59.044 38.462 0.00 0.00 0.00 4.44
1617 1657 7.807680 ACGAAGATGATGAAGAAAAGTAAACC 58.192 34.615 0.00 0.00 0.00 3.27
1618 1658 9.107367 CAACGAAGATGATGAAGAAAAGTAAAC 57.893 33.333 0.00 0.00 29.10 2.01
1619 1659 8.836413 ACAACGAAGATGATGAAGAAAAGTAAA 58.164 29.630 0.00 0.00 33.32 2.01
1620 1660 8.378172 ACAACGAAGATGATGAAGAAAAGTAA 57.622 30.769 0.00 0.00 33.32 2.24
1622 1662 6.867662 ACAACGAAGATGATGAAGAAAAGT 57.132 33.333 0.00 0.00 33.32 2.66
1623 1663 7.796838 TGTACAACGAAGATGATGAAGAAAAG 58.203 34.615 0.00 0.00 33.32 2.27
1679 1723 2.680439 TTACCCCCAATTCCTCCTCT 57.320 50.000 0.00 0.00 0.00 3.69
1701 1747 5.049828 TCCGCATCTGAATTATGTACACAG 58.950 41.667 0.00 0.31 0.00 3.66
1757 1803 2.050144 AGTGCTTTGTCTGAAGGGAGA 58.950 47.619 0.00 0.00 0.00 3.71
1760 1806 1.605710 CACAGTGCTTTGTCTGAAGGG 59.394 52.381 0.00 0.00 35.84 3.95
1851 1908 2.602217 GCTACCGTGCAGAAACAACAAG 60.602 50.000 0.00 0.00 0.00 3.16
1863 1920 1.805945 CGTCCTGAAGCTACCGTGC 60.806 63.158 0.00 0.00 0.00 5.34
1865 1922 0.243095 GTTCGTCCTGAAGCTACCGT 59.757 55.000 0.00 0.00 37.23 4.83
1890 1948 4.317359 CCAACGATGGGATGCACA 57.683 55.556 3.28 0.00 43.51 4.57
1901 1959 0.600782 GCACCTACCGAAACCAACGA 60.601 55.000 0.00 0.00 0.00 3.85
1903 1961 0.872388 CAGCACCTACCGAAACCAAC 59.128 55.000 0.00 0.00 0.00 3.77
1904 1962 0.887387 GCAGCACCTACCGAAACCAA 60.887 55.000 0.00 0.00 0.00 3.67
1905 1963 1.302192 GCAGCACCTACCGAAACCA 60.302 57.895 0.00 0.00 0.00 3.67
1906 1964 2.388232 CGCAGCACCTACCGAAACC 61.388 63.158 0.00 0.00 0.00 3.27
1907 1965 3.165498 CGCAGCACCTACCGAAAC 58.835 61.111 0.00 0.00 0.00 2.78
1929 1987 3.292936 ACAGCACCAGCAAGCAGC 61.293 61.111 0.00 0.00 45.49 5.25
1960 2018 1.606601 CACACCCCTCCAGTCTCGA 60.607 63.158 0.00 0.00 0.00 4.04
1981 2039 0.599060 TGACAGATGTTACGCGACCA 59.401 50.000 15.93 6.32 0.00 4.02
2000 2066 2.699954 GTCTCGATCACCAACCACATT 58.300 47.619 0.00 0.00 0.00 2.71
2089 2155 3.829886 TTCAGATGTGTCGCCATTTTC 57.170 42.857 0.00 0.00 0.00 2.29
2096 2162 3.165058 TGGAGTATTCAGATGTGTCGC 57.835 47.619 0.00 0.00 0.00 5.19
2144 2678 2.423538 CTGCACCCGGAAAAGAATAAGG 59.576 50.000 0.73 0.00 0.00 2.69
2150 2684 2.569853 TCTTATCTGCACCCGGAAAAGA 59.430 45.455 0.73 0.03 0.00 2.52
2313 2957 9.947669 TTGAATTATTGAAAACAATTGCTTTGG 57.052 25.926 11.41 0.00 39.80 3.28
2381 3025 9.639601 ATCATCATATTTGCATCATGTTCATTC 57.360 29.630 0.00 0.00 0.00 2.67
2411 3055 8.423906 ACATATATTGGACCGTAGATCTTTCT 57.576 34.615 0.00 0.00 35.90 2.52


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

AutoCloner maintained by Alex Coulton.