Multiple sequence alignment - TraesCS4B01G240700

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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 TraesCS4B01G240700 chr4B 100.000 2673 0 0 1 2673 499058904 499061576 0.000000e+00 4937.0
1 TraesCS4B01G240700 chr4B 87.001 1077 88 34 700 1750 470971854 470972904 0.000000e+00 1166.0
2 TraesCS4B01G240700 chr4A 92.824 1282 62 15 507 1786 60343961 60345214 0.000000e+00 1831.0
3 TraesCS4B01G240700 chr4A 96.455 818 23 2 1860 2673 675229209 675228394 0.000000e+00 1345.0
4 TraesCS4B01G240700 chr4A 85.514 1070 86 36 700 1746 65466321 65467344 0.000000e+00 1053.0
5 TraesCS4B01G240700 chr3B 97.314 819 16 2 1858 2672 770735969 770735153 0.000000e+00 1386.0
6 TraesCS4B01G240700 chr3B 97.185 817 16 3 1861 2673 55723013 55723826 0.000000e+00 1375.0
7 TraesCS4B01G240700 chr3B 88.587 368 34 7 1 363 26604084 26604448 8.780000e-120 440.0
8 TraesCS4B01G240700 chr5A 97.195 820 16 3 1858 2673 110288702 110289518 0.000000e+00 1380.0
9 TraesCS4B01G240700 chr6B 97.188 818 16 3 1860 2673 201316351 201317165 0.000000e+00 1376.0
10 TraesCS4B01G240700 chr2B 97.185 817 16 3 1861 2673 97972529 97973342 0.000000e+00 1375.0
11 TraesCS4B01G240700 chr2B 91.045 67 5 1 368 434 26922499 26922564 3.670000e-14 89.8
12 TraesCS4B01G240700 chr7B 97.066 818 17 3 1860 2673 376268395 376267581 0.000000e+00 1371.0
13 TraesCS4B01G240700 chr7B 96.822 818 20 3 1860 2673 677699606 677700421 0.000000e+00 1362.0
14 TraesCS4B01G240700 chr1A 97.260 803 19 2 1871 2673 23289479 23288680 0.000000e+00 1358.0
15 TraesCS4B01G240700 chr4D 85.384 1081 92 38 700 1750 383782810 383783854 0.000000e+00 1061.0
16 TraesCS4B01G240700 chr4D 90.781 781 37 15 364 1132 402970633 402971390 0.000000e+00 1011.0
17 TraesCS4B01G240700 chr4D 91.746 739 40 10 1131 1861 402971415 402972140 0.000000e+00 1007.0
18 TraesCS4B01G240700 chr1D 79.888 716 99 27 995 1692 410482899 410482211 1.440000e-132 483.0
19 TraesCS4B01G240700 chr1D 79.915 702 96 27 995 1678 410472269 410471595 8.660000e-130 473.0
20 TraesCS4B01G240700 chr5D 89.674 368 29 7 1 364 346882008 346882370 6.740000e-126 460.0
21 TraesCS4B01G240700 chr1B 79.190 716 106 32 995 1692 553025253 553024563 8.720000e-125 457.0
22 TraesCS4B01G240700 chr1B 84.167 480 64 6 1216 1692 553135956 553135486 3.140000e-124 455.0
23 TraesCS4B01G240700 chr6D 88.767 365 32 8 1 361 357559830 357559471 3.160000e-119 438.0
24 TraesCS4B01G240700 chr6D 88.122 362 32 10 7 364 49467732 49467378 1.140000e-113 420.0
25 TraesCS4B01G240700 chr3D 88.611 360 31 8 8 364 467979079 467979431 1.900000e-116 429.0
26 TraesCS4B01G240700 chr2A 88.669 353 32 7 18 367 72386505 72386852 8.850000e-115 424.0
27 TraesCS4B01G240700 chrUn 88.056 360 37 5 8 363 48356268 48356625 3.180000e-114 422.0
28 TraesCS4B01G240700 chr3A 87.978 366 31 12 2 363 7121717 7121361 1.140000e-113 420.0
29 TraesCS4B01G240700 chr5B 87.433 374 32 11 1 371 686525146 686525507 1.480000e-112 416.0
30 TraesCS4B01G240700 chr5B 82.432 74 8 5 364 434 38604086 38604015 2.870000e-05 60.2


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 TraesCS4B01G240700 chr4B 499058904 499061576 2672 False 4937 4937 100.0000 1 2673 1 chr4B.!!$F2 2672
1 TraesCS4B01G240700 chr4B 470971854 470972904 1050 False 1166 1166 87.0010 700 1750 1 chr4B.!!$F1 1050
2 TraesCS4B01G240700 chr4A 60343961 60345214 1253 False 1831 1831 92.8240 507 1786 1 chr4A.!!$F1 1279
3 TraesCS4B01G240700 chr4A 675228394 675229209 815 True 1345 1345 96.4550 1860 2673 1 chr4A.!!$R1 813
4 TraesCS4B01G240700 chr4A 65466321 65467344 1023 False 1053 1053 85.5140 700 1746 1 chr4A.!!$F2 1046
5 TraesCS4B01G240700 chr3B 770735153 770735969 816 True 1386 1386 97.3140 1858 2672 1 chr3B.!!$R1 814
6 TraesCS4B01G240700 chr3B 55723013 55723826 813 False 1375 1375 97.1850 1861 2673 1 chr3B.!!$F2 812
7 TraesCS4B01G240700 chr5A 110288702 110289518 816 False 1380 1380 97.1950 1858 2673 1 chr5A.!!$F1 815
8 TraesCS4B01G240700 chr6B 201316351 201317165 814 False 1376 1376 97.1880 1860 2673 1 chr6B.!!$F1 813
9 TraesCS4B01G240700 chr2B 97972529 97973342 813 False 1375 1375 97.1850 1861 2673 1 chr2B.!!$F2 812
10 TraesCS4B01G240700 chr7B 376267581 376268395 814 True 1371 1371 97.0660 1860 2673 1 chr7B.!!$R1 813
11 TraesCS4B01G240700 chr7B 677699606 677700421 815 False 1362 1362 96.8220 1860 2673 1 chr7B.!!$F1 813
12 TraesCS4B01G240700 chr1A 23288680 23289479 799 True 1358 1358 97.2600 1871 2673 1 chr1A.!!$R1 802
13 TraesCS4B01G240700 chr4D 383782810 383783854 1044 False 1061 1061 85.3840 700 1750 1 chr4D.!!$F1 1050
14 TraesCS4B01G240700 chr4D 402970633 402972140 1507 False 1009 1011 91.2635 364 1861 2 chr4D.!!$F2 1497
15 TraesCS4B01G240700 chr1D 410482211 410482899 688 True 483 483 79.8880 995 1692 1 chr1D.!!$R2 697
16 TraesCS4B01G240700 chr1D 410471595 410472269 674 True 473 473 79.9150 995 1678 1 chr1D.!!$R1 683
17 TraesCS4B01G240700 chr1B 553024563 553025253 690 True 457 457 79.1900 995 1692 1 chr1B.!!$R1 697

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
198 199 0.031043 CCAAAACGTCGAAAACCCCC 59.969 55.0 0.00 0.00 0.0 5.40 F
234 235 0.248458 AAAGCTGAAAACACGTGCGG 60.248 50.0 17.22 5.35 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1390 1.227176 CCGAGGGGTTAGCGTTAGC 60.227 63.158 0.0 0.0 45.58 3.09 R
1803 1889 2.094286 ACTCGAAGCTCCAAGACATCAG 60.094 50.000 0.0 0.0 0.00 2.90 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
21 22 3.771798 CGTTTTGTTTTTCCCTTTCCGA 58.228 40.909 0.00 0.00 0.00 4.55
22 23 3.794564 CGTTTTGTTTTTCCCTTTCCGAG 59.205 43.478 0.00 0.00 0.00 4.63
23 24 4.439016 CGTTTTGTTTTTCCCTTTCCGAGA 60.439 41.667 0.00 0.00 0.00 4.04
24 25 4.911514 TTTGTTTTTCCCTTTCCGAGAG 57.088 40.909 0.00 0.00 0.00 3.20
52 53 1.205657 GTGACTCTCGCGAAAACACA 58.794 50.000 21.45 12.20 0.00 3.72
53 54 1.591158 GTGACTCTCGCGAAAACACAA 59.409 47.619 21.45 1.34 0.00 3.33
54 55 1.591158 TGACTCTCGCGAAAACACAAC 59.409 47.619 11.33 0.00 0.00 3.32
55 56 0.935196 ACTCTCGCGAAAACACAACC 59.065 50.000 11.33 0.00 0.00 3.77
56 57 0.111266 CTCTCGCGAAAACACAACCG 60.111 55.000 11.33 0.00 0.00 4.44
57 58 0.806884 TCTCGCGAAAACACAACCGT 60.807 50.000 11.33 0.00 0.00 4.83
66 67 3.414700 CACAACCGTGCCTCTCGC 61.415 66.667 0.00 0.00 36.06 5.03
72 73 2.956964 CGTGCCTCTCGCGGAATC 60.957 66.667 6.13 0.00 44.36 2.52
73 74 2.184322 GTGCCTCTCGCGGAATCA 59.816 61.111 6.13 0.59 42.08 2.57
74 75 1.447838 GTGCCTCTCGCGGAATCAA 60.448 57.895 6.13 0.00 42.08 2.57
75 76 1.019278 GTGCCTCTCGCGGAATCAAA 61.019 55.000 6.13 0.00 42.08 2.69
76 77 0.321210 TGCCTCTCGCGGAATCAAAA 60.321 50.000 6.13 0.00 42.08 2.44
77 78 0.097150 GCCTCTCGCGGAATCAAAAC 59.903 55.000 6.13 0.00 0.00 2.43
78 79 0.727398 CCTCTCGCGGAATCAAAACC 59.273 55.000 6.13 0.00 0.00 3.27
85 86 2.875080 CGGAATCAAAACCGTGACTC 57.125 50.000 0.00 0.00 43.53 3.36
86 87 1.126113 CGGAATCAAAACCGTGACTCG 59.874 52.381 0.00 0.00 43.53 4.18
124 125 3.403033 GAAAATGTGTTTTTCTCGCGC 57.597 42.857 0.00 0.00 46.42 6.86
125 126 2.483583 AAATGTGTTTTTCTCGCGCA 57.516 40.000 8.75 0.00 0.00 6.09
126 127 2.704725 AATGTGTTTTTCTCGCGCAT 57.295 40.000 8.75 0.00 35.21 4.73
127 128 3.822594 AATGTGTTTTTCTCGCGCATA 57.177 38.095 8.75 0.00 33.62 3.14
128 129 3.822594 ATGTGTTTTTCTCGCGCATAA 57.177 38.095 8.75 0.00 32.42 1.90
129 130 3.822594 TGTGTTTTTCTCGCGCATAAT 57.177 38.095 8.75 0.00 0.00 1.28
130 131 4.153958 TGTGTTTTTCTCGCGCATAATT 57.846 36.364 8.75 0.00 0.00 1.40
131 132 4.541779 TGTGTTTTTCTCGCGCATAATTT 58.458 34.783 8.75 0.00 0.00 1.82
132 133 4.979197 TGTGTTTTTCTCGCGCATAATTTT 59.021 33.333 8.75 0.00 0.00 1.82
133 134 5.460419 TGTGTTTTTCTCGCGCATAATTTTT 59.540 32.000 8.75 0.00 0.00 1.94
168 169 8.782533 TTTTTGATCGAAAAGCTAAGAAAGAC 57.217 30.769 15.57 0.00 34.96 3.01
169 170 6.481954 TTGATCGAAAAGCTAAGAAAGACC 57.518 37.500 0.00 0.00 0.00 3.85
170 171 4.625742 TGATCGAAAAGCTAAGAAAGACCG 59.374 41.667 0.00 0.00 0.00 4.79
171 172 4.247267 TCGAAAAGCTAAGAAAGACCGA 57.753 40.909 0.00 0.00 0.00 4.69
172 173 4.235360 TCGAAAAGCTAAGAAAGACCGAG 58.765 43.478 0.00 0.00 0.00 4.63
173 174 3.368236 CGAAAAGCTAAGAAAGACCGAGG 59.632 47.826 0.00 0.00 0.00 4.63
174 175 3.336138 AAAGCTAAGAAAGACCGAGGG 57.664 47.619 0.00 0.00 0.00 4.30
175 176 2.233305 AGCTAAGAAAGACCGAGGGA 57.767 50.000 0.00 0.00 0.00 4.20
176 177 2.537143 AGCTAAGAAAGACCGAGGGAA 58.463 47.619 0.00 0.00 0.00 3.97
177 178 2.904434 AGCTAAGAAAGACCGAGGGAAA 59.096 45.455 0.00 0.00 0.00 3.13
178 179 3.326880 AGCTAAGAAAGACCGAGGGAAAA 59.673 43.478 0.00 0.00 0.00 2.29
179 180 3.436015 GCTAAGAAAGACCGAGGGAAAAC 59.564 47.826 0.00 0.00 0.00 2.43
180 181 2.563261 AGAAAGACCGAGGGAAAACC 57.437 50.000 0.00 0.00 40.67 3.27
181 182 1.772453 AGAAAGACCGAGGGAAAACCA 59.228 47.619 0.00 0.00 43.89 3.67
182 183 2.173996 AGAAAGACCGAGGGAAAACCAA 59.826 45.455 0.00 0.00 43.89 3.67
183 184 2.740506 AAGACCGAGGGAAAACCAAA 57.259 45.000 0.00 0.00 43.89 3.28
184 185 2.740506 AGACCGAGGGAAAACCAAAA 57.259 45.000 0.00 0.00 43.89 2.44
185 186 2.304092 AGACCGAGGGAAAACCAAAAC 58.696 47.619 0.00 0.00 43.89 2.43
186 187 1.002142 GACCGAGGGAAAACCAAAACG 60.002 52.381 0.00 0.00 43.89 3.60
187 188 1.026584 CCGAGGGAAAACCAAAACGT 58.973 50.000 0.00 0.00 43.89 3.99
188 189 1.002142 CCGAGGGAAAACCAAAACGTC 60.002 52.381 0.00 0.00 43.89 4.34
189 190 1.333435 CGAGGGAAAACCAAAACGTCG 60.333 52.381 0.00 0.00 43.89 5.12
190 191 1.941975 GAGGGAAAACCAAAACGTCGA 59.058 47.619 0.00 0.00 43.89 4.20
191 192 2.355444 GAGGGAAAACCAAAACGTCGAA 59.645 45.455 0.00 0.00 43.89 3.71
192 193 2.754002 AGGGAAAACCAAAACGTCGAAA 59.246 40.909 0.00 0.00 43.89 3.46
193 194 3.193056 AGGGAAAACCAAAACGTCGAAAA 59.807 39.130 0.00 0.00 43.89 2.29
194 195 3.304026 GGGAAAACCAAAACGTCGAAAAC 59.696 43.478 0.00 0.00 39.85 2.43
195 196 3.304026 GGAAAACCAAAACGTCGAAAACC 59.696 43.478 0.00 0.00 0.00 3.27
196 197 2.565210 AACCAAAACGTCGAAAACCC 57.435 45.000 0.00 0.00 0.00 4.11
197 198 0.740149 ACCAAAACGTCGAAAACCCC 59.260 50.000 0.00 0.00 0.00 4.95
198 199 0.031043 CCAAAACGTCGAAAACCCCC 59.969 55.000 0.00 0.00 0.00 5.40
228 229 9.619316 AAAAACCATTTTAAAAGCTGAAAACAC 57.381 25.926 6.79 0.00 36.99 3.32
229 230 6.582437 ACCATTTTAAAAGCTGAAAACACG 57.418 33.333 6.79 0.00 0.00 4.49
230 231 6.103330 ACCATTTTAAAAGCTGAAAACACGT 58.897 32.000 6.79 0.00 0.00 4.49
231 232 6.035542 ACCATTTTAAAAGCTGAAAACACGTG 59.964 34.615 15.48 15.48 0.00 4.49
232 233 5.443142 TTTTAAAAGCTGAAAACACGTGC 57.557 34.783 17.22 0.00 0.00 5.34
233 234 1.544686 AAAAGCTGAAAACACGTGCG 58.455 45.000 17.22 0.00 0.00 5.34
234 235 0.248458 AAAGCTGAAAACACGTGCGG 60.248 50.000 17.22 5.35 0.00 5.69
235 236 2.051345 GCTGAAAACACGTGCGGG 60.051 61.111 17.22 1.39 0.00 6.13
236 237 2.539338 GCTGAAAACACGTGCGGGA 61.539 57.895 17.22 0.00 0.00 5.14
237 238 2.018544 CTGAAAACACGTGCGGGAA 58.981 52.632 17.22 0.00 0.00 3.97
238 239 0.378962 CTGAAAACACGTGCGGGAAA 59.621 50.000 17.22 0.00 0.00 3.13
239 240 0.809385 TGAAAACACGTGCGGGAAAA 59.191 45.000 17.22 0.00 0.00 2.29
240 241 1.405821 TGAAAACACGTGCGGGAAAAT 59.594 42.857 17.22 0.00 0.00 1.82
241 242 2.617308 TGAAAACACGTGCGGGAAAATA 59.383 40.909 17.22 0.00 0.00 1.40
242 243 3.066342 TGAAAACACGTGCGGGAAAATAA 59.934 39.130 17.22 0.00 0.00 1.40
243 244 3.712091 AAACACGTGCGGGAAAATAAA 57.288 38.095 17.22 0.00 0.00 1.40
244 245 3.712091 AACACGTGCGGGAAAATAAAA 57.288 38.095 17.22 0.00 0.00 1.52
245 246 3.712091 ACACGTGCGGGAAAATAAAAA 57.288 38.095 17.22 0.00 0.00 1.94
273 274 3.522731 CGGAGGGAGCGTCCAGAG 61.523 72.222 6.41 0.00 38.64 3.35
274 275 3.844090 GGAGGGAGCGTCCAGAGC 61.844 72.222 6.41 0.00 38.64 4.09
275 276 4.200283 GAGGGAGCGTCCAGAGCG 62.200 72.222 6.41 0.00 38.64 5.03
283 284 4.702081 GTCCAGAGCGCGACACGT 62.702 66.667 12.10 0.00 46.11 4.49
284 285 4.700365 TCCAGAGCGCGACACGTG 62.700 66.667 15.48 15.48 46.11 4.49
294 295 2.742372 GACACGTGGCGAATGGCT 60.742 61.111 21.57 0.00 42.94 4.75
295 296 3.027170 GACACGTGGCGAATGGCTG 62.027 63.158 21.57 0.00 42.94 4.85
296 297 2.741985 CACGTGGCGAATGGCTGA 60.742 61.111 7.95 0.00 42.94 4.26
297 298 2.434884 ACGTGGCGAATGGCTGAG 60.435 61.111 0.00 0.00 42.94 3.35
298 299 2.125552 CGTGGCGAATGGCTGAGA 60.126 61.111 0.00 0.00 42.94 3.27
299 300 2.169789 CGTGGCGAATGGCTGAGAG 61.170 63.158 0.00 0.00 42.94 3.20
300 301 2.124983 TGGCGAATGGCTGAGAGC 60.125 61.111 0.00 0.00 42.94 4.09
301 302 3.267860 GGCGAATGGCTGAGAGCG 61.268 66.667 0.00 0.00 43.62 5.03
302 303 3.934684 GCGAATGGCTGAGAGCGC 61.935 66.667 0.00 0.00 43.62 5.92
303 304 3.624300 CGAATGGCTGAGAGCGCG 61.624 66.667 0.00 0.00 43.62 6.86
304 305 2.202797 GAATGGCTGAGAGCGCGA 60.203 61.111 12.10 0.00 43.62 5.87
305 306 2.510238 AATGGCTGAGAGCGCGAC 60.510 61.111 12.10 2.22 43.62 5.19
306 307 3.300934 AATGGCTGAGAGCGCGACA 62.301 57.895 12.10 2.66 43.62 4.35
307 308 2.786539 AATGGCTGAGAGCGCGACAA 62.787 55.000 12.10 0.00 43.62 3.18
308 309 3.184683 GGCTGAGAGCGCGACAAG 61.185 66.667 12.10 6.21 43.62 3.16
309 310 2.431601 GCTGAGAGCGCGACAAGT 60.432 61.111 12.10 0.00 0.00 3.16
310 311 2.724708 GCTGAGAGCGCGACAAGTG 61.725 63.158 12.10 0.00 0.00 3.16
311 312 2.049156 TGAGAGCGCGACAAGTGG 60.049 61.111 12.10 0.00 0.00 4.00
312 313 3.482783 GAGAGCGCGACAAGTGGC 61.483 66.667 12.10 0.00 0.00 5.01
319 320 3.084579 CGACAAGTGGCGCTGATC 58.915 61.111 7.64 1.23 40.91 2.92
320 321 2.792290 CGACAAGTGGCGCTGATCG 61.792 63.158 16.61 16.61 40.91 3.69
321 322 1.738099 GACAAGTGGCGCTGATCGT 60.738 57.895 7.64 0.00 41.07 3.73
322 323 1.291877 GACAAGTGGCGCTGATCGTT 61.292 55.000 7.64 0.00 41.07 3.85
323 324 1.133253 CAAGTGGCGCTGATCGTTG 59.867 57.895 7.64 0.00 41.07 4.10
324 325 2.680913 AAGTGGCGCTGATCGTTGC 61.681 57.895 7.64 0.00 41.07 4.17
337 338 3.479269 GTTGCGACGCTCCCGAAG 61.479 66.667 22.08 0.00 38.29 3.79
350 351 4.470876 CGAAGGAGCGCTCGTTAA 57.529 55.556 36.96 0.00 37.75 2.01
351 352 2.959275 CGAAGGAGCGCTCGTTAAT 58.041 52.632 36.96 21.62 37.75 1.40
352 353 1.278238 CGAAGGAGCGCTCGTTAATT 58.722 50.000 36.96 21.28 37.75 1.40
353 354 2.456989 CGAAGGAGCGCTCGTTAATTA 58.543 47.619 36.96 0.00 37.75 1.40
354 355 2.468040 CGAAGGAGCGCTCGTTAATTAG 59.532 50.000 36.96 23.67 37.75 1.73
355 356 3.445857 GAAGGAGCGCTCGTTAATTAGT 58.554 45.455 36.96 19.55 37.75 2.24
356 357 3.521947 AGGAGCGCTCGTTAATTAGTT 57.478 42.857 29.81 3.47 0.00 2.24
357 358 3.187700 AGGAGCGCTCGTTAATTAGTTG 58.812 45.455 29.81 0.00 0.00 3.16
358 359 2.285660 GGAGCGCTCGTTAATTAGTTGC 60.286 50.000 29.81 8.45 0.00 4.17
359 360 2.603560 GAGCGCTCGTTAATTAGTTGCT 59.396 45.455 23.61 7.90 31.95 3.91
360 361 2.603560 AGCGCTCGTTAATTAGTTGCTC 59.396 45.455 2.64 0.00 0.00 4.26
361 362 2.285660 GCGCTCGTTAATTAGTTGCTCC 60.286 50.000 0.00 0.00 0.00 4.70
362 363 2.284417 CGCTCGTTAATTAGTTGCTCCC 59.716 50.000 0.00 0.00 0.00 4.30
363 364 2.284417 GCTCGTTAATTAGTTGCTCCCG 59.716 50.000 0.00 0.00 0.00 5.14
364 365 2.273557 TCGTTAATTAGTTGCTCCCGC 58.726 47.619 0.00 0.00 0.00 6.13
365 366 2.004017 CGTTAATTAGTTGCTCCCGCA 58.996 47.619 0.00 0.00 46.24 5.69
385 386 1.376543 ACATCTTGGAGCAGCAATCG 58.623 50.000 0.00 0.00 0.00 3.34
395 396 2.372264 AGCAGCAATCGATGGTCAAAT 58.628 42.857 0.00 0.00 32.95 2.32
398 399 4.398988 AGCAGCAATCGATGGTCAAATAAA 59.601 37.500 0.00 0.00 32.95 1.40
399 400 5.101628 GCAGCAATCGATGGTCAAATAAAA 58.898 37.500 0.00 0.00 37.77 1.52
413 414 6.406692 TCAAATAAAATTGACCGACCCAAA 57.593 33.333 0.00 0.00 34.50 3.28
430 431 6.347321 CGACCCAAATTTAAAAATCAGGCAAC 60.347 38.462 0.00 0.00 0.00 4.17
464 465 3.821033 AGGCTGTCATTTAAACACTGGAC 59.179 43.478 0.00 0.00 0.00 4.02
471 472 0.887387 TTAAACACTGGACTGCCGGC 60.887 55.000 22.73 22.73 44.98 6.13
482 483 1.739049 CTGCCGGCAGGAAAACAAA 59.261 52.632 42.81 12.20 41.02 2.83
483 484 0.318955 CTGCCGGCAGGAAAACAAAG 60.319 55.000 42.81 18.94 41.02 2.77
484 485 1.006220 GCCGGCAGGAAAACAAAGG 60.006 57.895 24.80 0.00 41.02 3.11
485 486 1.460273 GCCGGCAGGAAAACAAAGGA 61.460 55.000 24.80 0.00 41.02 3.36
486 487 0.598065 CCGGCAGGAAAACAAAGGAG 59.402 55.000 0.00 0.00 41.02 3.69
487 488 1.318576 CGGCAGGAAAACAAAGGAGT 58.681 50.000 0.00 0.00 0.00 3.85
488 489 1.001378 CGGCAGGAAAACAAAGGAGTG 60.001 52.381 0.00 0.00 0.00 3.51
489 490 2.306847 GGCAGGAAAACAAAGGAGTGA 58.693 47.619 0.00 0.00 0.00 3.41
490 491 2.893489 GGCAGGAAAACAAAGGAGTGAT 59.107 45.455 0.00 0.00 0.00 3.06
491 492 3.321968 GGCAGGAAAACAAAGGAGTGATT 59.678 43.478 0.00 0.00 0.00 2.57
492 493 4.202253 GGCAGGAAAACAAAGGAGTGATTT 60.202 41.667 0.00 0.00 0.00 2.17
493 494 4.984785 GCAGGAAAACAAAGGAGTGATTTC 59.015 41.667 0.00 0.00 38.73 2.17
494 495 5.215160 CAGGAAAACAAAGGAGTGATTTCG 58.785 41.667 0.00 0.00 39.75 3.46
524 526 1.813859 CCCCTTCTCATCGTGCGTA 59.186 57.895 0.00 0.00 0.00 4.42
663 665 4.314440 GTGCTGTGCCGTCCCTGA 62.314 66.667 0.00 0.00 0.00 3.86
811 822 2.715005 GCTGCACGCACAACTTCA 59.285 55.556 0.00 0.00 38.92 3.02
828 839 3.276846 AACACGTTCACGGCTGGC 61.277 61.111 4.07 0.00 44.95 4.85
950 971 1.608055 CACACAGAATCAACAGCCCA 58.392 50.000 0.00 0.00 0.00 5.36
1012 1033 1.277842 TGTGAGTAATGGCGACCATGT 59.722 47.619 11.38 5.77 44.40 3.21
1041 1062 4.335647 CCCTTCACTGGTGCCGCT 62.336 66.667 0.00 0.00 0.00 5.52
1145 1200 3.568538 TCTTTCGTTTACTCCGTACTGC 58.431 45.455 0.00 0.00 0.00 4.40
1255 1311 2.502492 CGCATCGACATCCTCCCCT 61.502 63.158 0.00 0.00 0.00 4.79
1288 1362 4.003788 CCGAGCACGACCCTGGTT 62.004 66.667 4.70 0.00 42.66 3.67
1304 1378 4.912395 TTGCGCCCAAGCCCAAGT 62.912 61.111 4.18 0.00 31.90 3.16
1310 1387 1.607467 CCCAAGCCCAAGTCCAAGG 60.607 63.158 0.00 0.00 0.00 3.61
1314 1391 3.376918 GCCCAAGTCCAAGGCTGC 61.377 66.667 0.00 0.00 43.62 5.25
1315 1392 2.437897 CCCAAGTCCAAGGCTGCT 59.562 61.111 0.00 0.00 0.00 4.24
1316 1393 1.685224 CCCAAGTCCAAGGCTGCTA 59.315 57.895 0.00 0.00 0.00 3.49
1317 1394 0.038166 CCCAAGTCCAAGGCTGCTAA 59.962 55.000 0.00 0.00 0.00 3.09
1318 1395 1.168714 CCAAGTCCAAGGCTGCTAAC 58.831 55.000 0.00 0.00 0.00 2.34
1522 1599 1.180456 TTTCCGTGGCGTCTCTGGTA 61.180 55.000 0.00 0.00 0.00 3.25
1750 1836 2.875094 ACTAGTGGTACGGACTCTGT 57.125 50.000 0.00 0.00 0.00 3.41
1796 1882 7.228590 TCTGTAAGCCTTATAGGTTGTGTTTT 58.771 34.615 8.19 0.00 37.80 2.43
1823 1909 2.538437 CTGATGTCTTGGAGCTTCGAG 58.462 52.381 2.30 2.30 0.00 4.04
1831 1917 0.109272 TGGAGCTTCGAGTTACTGCG 60.109 55.000 0.00 0.00 0.00 5.18
1833 1919 1.734359 GAGCTTCGAGTTACTGCGCG 61.734 60.000 0.00 0.00 0.00 6.86
1834 1920 1.800315 GCTTCGAGTTACTGCGCGA 60.800 57.895 12.10 0.00 38.77 5.87
2348 2438 5.385198 TCTCCCAAGAAATTTGTACAAGCT 58.615 37.500 8.56 2.85 0.00 3.74
2363 2453 2.564947 ACAAGCTCCTCGTCATTCTTCT 59.435 45.455 0.00 0.00 0.00 2.85
2474 2564 3.599343 GACATGCAGATGTAACCTGACA 58.401 45.455 0.00 0.00 43.22 3.58
2667 2757 4.023707 GTCCCACTCTTCATTTGTTCACAG 60.024 45.833 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.771798 TCGGAAAGGGAAAAACAAAACG 58.228 40.909 0.00 0.00 0.00 3.60
1 2 5.001237 TCTCGGAAAGGGAAAAACAAAAC 57.999 39.130 0.00 0.00 0.00 2.43
2 3 4.098807 CCTCTCGGAAAGGGAAAAACAAAA 59.901 41.667 0.00 0.00 0.00 2.44
3 4 3.634910 CCTCTCGGAAAGGGAAAAACAAA 59.365 43.478 0.00 0.00 0.00 2.83
4 5 3.219281 CCTCTCGGAAAGGGAAAAACAA 58.781 45.455 0.00 0.00 0.00 2.83
5 6 2.858745 CCTCTCGGAAAGGGAAAAACA 58.141 47.619 0.00 0.00 0.00 2.83
6 7 1.540267 GCCTCTCGGAAAGGGAAAAAC 59.460 52.381 0.00 0.00 34.26 2.43
7 8 1.144093 TGCCTCTCGGAAAGGGAAAAA 59.856 47.619 0.00 0.00 34.26 1.94
8 9 0.768622 TGCCTCTCGGAAAGGGAAAA 59.231 50.000 0.00 0.00 34.26 2.29
9 10 0.036306 GTGCCTCTCGGAAAGGGAAA 59.964 55.000 0.00 0.00 35.86 3.13
10 11 1.677552 GTGCCTCTCGGAAAGGGAA 59.322 57.895 0.00 0.00 35.86 3.97
11 12 2.646175 CGTGCCTCTCGGAAAGGGA 61.646 63.158 0.00 0.00 34.26 4.20
12 13 2.125512 CGTGCCTCTCGGAAAGGG 60.126 66.667 0.00 0.00 34.26 3.95
29 30 3.909258 TTTCGCGAGAGTCACGGCC 62.909 63.158 9.59 0.00 43.69 6.13
30 31 2.019951 TTTTCGCGAGAGTCACGGC 61.020 57.895 9.59 3.61 43.69 5.68
31 32 0.937699 TGTTTTCGCGAGAGTCACGG 60.938 55.000 9.59 2.55 43.69 4.94
32 33 0.158928 GTGTTTTCGCGAGAGTCACG 59.841 55.000 9.59 5.53 43.69 4.35
33 34 1.205657 TGTGTTTTCGCGAGAGTCAC 58.794 50.000 21.10 21.10 43.69 3.67
34 35 1.591158 GTTGTGTTTTCGCGAGAGTCA 59.409 47.619 9.59 5.72 43.69 3.41
35 36 1.070776 GGTTGTGTTTTCGCGAGAGTC 60.071 52.381 9.59 2.93 43.69 3.36
36 37 0.935196 GGTTGTGTTTTCGCGAGAGT 59.065 50.000 9.59 0.00 43.69 3.24
37 38 0.111266 CGGTTGTGTTTTCGCGAGAG 60.111 55.000 9.59 0.00 43.69 3.20
38 39 0.806884 ACGGTTGTGTTTTCGCGAGA 60.807 50.000 9.59 0.43 39.20 4.04
39 40 0.653323 CACGGTTGTGTTTTCGCGAG 60.653 55.000 9.59 0.00 41.34 5.03
40 41 1.348938 CACGGTTGTGTTTTCGCGA 59.651 52.632 3.71 3.71 41.34 5.87
41 42 3.882668 CACGGTTGTGTTTTCGCG 58.117 55.556 0.00 0.00 41.34 5.87
55 56 2.956964 GATTCCGCGAGAGGCACG 60.957 66.667 8.23 0.00 43.84 5.34
56 57 1.019278 TTTGATTCCGCGAGAGGCAC 61.019 55.000 8.23 0.00 43.84 5.01
57 58 0.321210 TTTTGATTCCGCGAGAGGCA 60.321 50.000 8.23 2.66 43.84 4.75
58 59 0.097150 GTTTTGATTCCGCGAGAGGC 59.903 55.000 8.23 0.00 38.69 4.70
59 60 0.727398 GGTTTTGATTCCGCGAGAGG 59.273 55.000 8.23 0.00 0.00 3.69
60 61 0.370273 CGGTTTTGATTCCGCGAGAG 59.630 55.000 8.23 0.00 40.28 3.20
61 62 2.451693 CGGTTTTGATTCCGCGAGA 58.548 52.632 8.23 0.00 40.28 4.04
67 68 2.875080 CGAGTCACGGTTTTGATTCC 57.125 50.000 0.00 0.00 38.46 3.01
105 106 2.803451 TGCGCGAGAAAAACACATTTT 58.197 38.095 12.10 0.00 43.85 1.82
106 107 2.483583 TGCGCGAGAAAAACACATTT 57.516 40.000 12.10 0.00 0.00 2.32
107 108 2.704725 ATGCGCGAGAAAAACACATT 57.295 40.000 12.10 0.00 0.00 2.71
108 109 3.822594 TTATGCGCGAGAAAAACACAT 57.177 38.095 12.10 2.37 0.00 3.21
109 110 3.822594 ATTATGCGCGAGAAAAACACA 57.177 38.095 12.10 0.00 0.00 3.72
110 111 5.494863 AAAATTATGCGCGAGAAAAACAC 57.505 34.783 12.10 0.00 0.00 3.32
143 144 7.860872 GGTCTTTCTTAGCTTTTCGATCAAAAA 59.139 33.333 0.00 0.00 33.40 1.94
144 145 7.360361 GGTCTTTCTTAGCTTTTCGATCAAAA 58.640 34.615 0.00 0.00 32.77 2.44
145 146 6.347402 CGGTCTTTCTTAGCTTTTCGATCAAA 60.347 38.462 0.00 0.00 0.00 2.69
146 147 5.120208 CGGTCTTTCTTAGCTTTTCGATCAA 59.880 40.000 0.00 0.00 0.00 2.57
147 148 4.625742 CGGTCTTTCTTAGCTTTTCGATCA 59.374 41.667 0.00 0.00 0.00 2.92
148 149 4.863131 TCGGTCTTTCTTAGCTTTTCGATC 59.137 41.667 0.00 0.00 0.00 3.69
149 150 4.817517 TCGGTCTTTCTTAGCTTTTCGAT 58.182 39.130 0.00 0.00 0.00 3.59
150 151 4.235360 CTCGGTCTTTCTTAGCTTTTCGA 58.765 43.478 0.00 0.00 0.00 3.71
151 152 3.368236 CCTCGGTCTTTCTTAGCTTTTCG 59.632 47.826 0.00 0.00 0.00 3.46
152 153 3.685272 CCCTCGGTCTTTCTTAGCTTTTC 59.315 47.826 0.00 0.00 0.00 2.29
153 154 3.326880 TCCCTCGGTCTTTCTTAGCTTTT 59.673 43.478 0.00 0.00 0.00 2.27
154 155 2.904434 TCCCTCGGTCTTTCTTAGCTTT 59.096 45.455 0.00 0.00 0.00 3.51
155 156 2.537143 TCCCTCGGTCTTTCTTAGCTT 58.463 47.619 0.00 0.00 0.00 3.74
156 157 2.233305 TCCCTCGGTCTTTCTTAGCT 57.767 50.000 0.00 0.00 0.00 3.32
157 158 3.329929 TTTCCCTCGGTCTTTCTTAGC 57.670 47.619 0.00 0.00 0.00 3.09
158 159 4.001652 GGTTTTCCCTCGGTCTTTCTTAG 58.998 47.826 0.00 0.00 0.00 2.18
159 160 3.391955 TGGTTTTCCCTCGGTCTTTCTTA 59.608 43.478 0.00 0.00 39.73 2.10
160 161 2.173996 TGGTTTTCCCTCGGTCTTTCTT 59.826 45.455 0.00 0.00 39.73 2.52
161 162 1.772453 TGGTTTTCCCTCGGTCTTTCT 59.228 47.619 0.00 0.00 39.73 2.52
162 163 2.265589 TGGTTTTCCCTCGGTCTTTC 57.734 50.000 0.00 0.00 39.73 2.62
163 164 2.740506 TTGGTTTTCCCTCGGTCTTT 57.259 45.000 0.00 0.00 39.73 2.52
164 165 2.691526 GTTTTGGTTTTCCCTCGGTCTT 59.308 45.455 0.00 0.00 39.73 3.01
165 166 2.304092 GTTTTGGTTTTCCCTCGGTCT 58.696 47.619 0.00 0.00 39.73 3.85
166 167 1.002142 CGTTTTGGTTTTCCCTCGGTC 60.002 52.381 0.00 0.00 39.73 4.79
167 168 1.026584 CGTTTTGGTTTTCCCTCGGT 58.973 50.000 0.00 0.00 39.73 4.69
168 169 1.002142 GACGTTTTGGTTTTCCCTCGG 60.002 52.381 0.00 0.00 39.73 4.63
169 170 1.333435 CGACGTTTTGGTTTTCCCTCG 60.333 52.381 0.00 0.00 39.73 4.63
170 171 1.941975 TCGACGTTTTGGTTTTCCCTC 59.058 47.619 0.00 0.00 39.73 4.30
171 172 2.041251 TCGACGTTTTGGTTTTCCCT 57.959 45.000 0.00 0.00 39.73 4.20
172 173 2.847959 TTCGACGTTTTGGTTTTCCC 57.152 45.000 0.00 0.00 39.73 3.97
173 174 3.304026 GGTTTTCGACGTTTTGGTTTTCC 59.696 43.478 0.00 0.00 41.14 3.13
174 175 3.304026 GGGTTTTCGACGTTTTGGTTTTC 59.696 43.478 0.00 0.00 0.00 2.29
175 176 3.252400 GGGTTTTCGACGTTTTGGTTTT 58.748 40.909 0.00 0.00 0.00 2.43
176 177 2.417107 GGGGTTTTCGACGTTTTGGTTT 60.417 45.455 0.00 0.00 0.00 3.27
177 178 1.134753 GGGGTTTTCGACGTTTTGGTT 59.865 47.619 0.00 0.00 0.00 3.67
178 179 0.740149 GGGGTTTTCGACGTTTTGGT 59.260 50.000 0.00 0.00 0.00 3.67
179 180 0.031043 GGGGGTTTTCGACGTTTTGG 59.969 55.000 0.00 0.00 0.00 3.28
180 181 3.555401 GGGGGTTTTCGACGTTTTG 57.445 52.632 0.00 0.00 0.00 2.44
202 203 9.619316 GTGTTTTCAGCTTTTAAAATGGTTTTT 57.381 25.926 0.09 0.00 38.56 1.94
203 204 7.960195 CGTGTTTTCAGCTTTTAAAATGGTTTT 59.040 29.630 0.09 0.00 36.67 2.43
204 205 7.118535 ACGTGTTTTCAGCTTTTAAAATGGTTT 59.881 29.630 0.09 0.00 0.00 3.27
205 206 6.592220 ACGTGTTTTCAGCTTTTAAAATGGTT 59.408 30.769 0.09 0.00 0.00 3.67
206 207 6.035542 CACGTGTTTTCAGCTTTTAAAATGGT 59.964 34.615 7.58 0.00 0.00 3.55
207 208 6.410038 CACGTGTTTTCAGCTTTTAAAATGG 58.590 36.000 7.58 0.00 0.00 3.16
208 209 5.895889 GCACGTGTTTTCAGCTTTTAAAATG 59.104 36.000 18.38 0.00 0.00 2.32
209 210 5.276161 CGCACGTGTTTTCAGCTTTTAAAAT 60.276 36.000 18.38 0.00 0.00 1.82
210 211 4.030753 CGCACGTGTTTTCAGCTTTTAAAA 59.969 37.500 18.38 0.00 0.00 1.52
211 212 3.544285 CGCACGTGTTTTCAGCTTTTAAA 59.456 39.130 18.38 0.00 0.00 1.52
212 213 3.102276 CGCACGTGTTTTCAGCTTTTAA 58.898 40.909 18.38 0.00 0.00 1.52
213 214 2.539953 CCGCACGTGTTTTCAGCTTTTA 60.540 45.455 18.38 0.00 0.00 1.52
214 215 1.544686 CGCACGTGTTTTCAGCTTTT 58.455 45.000 18.38 0.00 0.00 2.27
215 216 0.248458 CCGCACGTGTTTTCAGCTTT 60.248 50.000 18.38 0.00 0.00 3.51
216 217 1.355210 CCGCACGTGTTTTCAGCTT 59.645 52.632 18.38 0.00 0.00 3.74
217 218 2.542907 CCCGCACGTGTTTTCAGCT 61.543 57.895 18.38 0.00 0.00 4.24
218 219 2.051345 CCCGCACGTGTTTTCAGC 60.051 61.111 18.38 0.00 0.00 4.26
219 220 0.378962 TTTCCCGCACGTGTTTTCAG 59.621 50.000 18.38 0.76 0.00 3.02
220 221 0.809385 TTTTCCCGCACGTGTTTTCA 59.191 45.000 18.38 0.00 0.00 2.69
221 222 2.128367 ATTTTCCCGCACGTGTTTTC 57.872 45.000 18.38 0.00 0.00 2.29
222 223 3.712091 TTATTTTCCCGCACGTGTTTT 57.288 38.095 18.38 0.00 0.00 2.43
223 224 3.712091 TTTATTTTCCCGCACGTGTTT 57.288 38.095 18.38 0.00 0.00 2.83
224 225 3.712091 TTTTATTTTCCCGCACGTGTT 57.288 38.095 18.38 0.00 0.00 3.32
225 226 3.712091 TTTTTATTTTCCCGCACGTGT 57.288 38.095 18.38 0.00 0.00 4.49
244 245 3.380320 CGCTCCCTCCGGATTTTATTTTT 59.620 43.478 3.57 0.00 37.60 1.94
245 246 2.949644 CGCTCCCTCCGGATTTTATTTT 59.050 45.455 3.57 0.00 37.60 1.82
246 247 2.092592 ACGCTCCCTCCGGATTTTATTT 60.093 45.455 3.57 0.00 37.60 1.40
247 248 1.489230 ACGCTCCCTCCGGATTTTATT 59.511 47.619 3.57 0.00 37.60 1.40
248 249 1.070289 GACGCTCCCTCCGGATTTTAT 59.930 52.381 3.57 0.00 37.60 1.40
249 250 0.462789 GACGCTCCCTCCGGATTTTA 59.537 55.000 3.57 0.00 37.60 1.52
250 251 1.221021 GACGCTCCCTCCGGATTTT 59.779 57.895 3.57 0.00 37.60 1.82
251 252 2.732619 GGACGCTCCCTCCGGATTT 61.733 63.158 3.57 0.00 37.60 2.17
252 253 3.155167 GGACGCTCCCTCCGGATT 61.155 66.667 3.57 0.00 37.60 3.01
253 254 4.458829 TGGACGCTCCCTCCGGAT 62.459 66.667 3.57 0.00 37.60 4.18
256 257 3.522731 CTCTGGACGCTCCCTCCG 61.523 72.222 2.23 0.00 35.03 4.63
257 258 3.844090 GCTCTGGACGCTCCCTCC 61.844 72.222 2.23 0.00 35.03 4.30
258 259 4.200283 CGCTCTGGACGCTCCCTC 62.200 72.222 2.23 0.00 35.03 4.30
266 267 4.702081 ACGTGTCGCGCTCTGGAC 62.702 66.667 5.56 5.97 46.11 4.02
267 268 4.700365 CACGTGTCGCGCTCTGGA 62.700 66.667 7.58 0.00 46.11 3.86
275 276 4.147322 CCATTCGCCACGTGTCGC 62.147 66.667 15.09 10.47 0.00 5.19
276 277 4.147322 GCCATTCGCCACGTGTCG 62.147 66.667 13.61 13.61 0.00 4.35
277 278 2.742372 AGCCATTCGCCACGTGTC 60.742 61.111 15.65 0.00 38.78 3.67
278 279 3.049674 CAGCCATTCGCCACGTGT 61.050 61.111 15.65 0.00 38.78 4.49
279 280 2.741985 TCAGCCATTCGCCACGTG 60.742 61.111 9.08 9.08 38.78 4.49
280 281 2.434884 CTCAGCCATTCGCCACGT 60.435 61.111 0.00 0.00 38.78 4.49
281 282 2.125552 TCTCAGCCATTCGCCACG 60.126 61.111 0.00 0.00 38.78 4.94
282 283 2.467826 GCTCTCAGCCATTCGCCAC 61.468 63.158 0.00 0.00 38.78 5.01
283 284 2.124983 GCTCTCAGCCATTCGCCA 60.125 61.111 0.00 0.00 38.78 5.69
284 285 3.267860 CGCTCTCAGCCATTCGCC 61.268 66.667 0.00 0.00 38.18 5.54
285 286 3.934684 GCGCTCTCAGCCATTCGC 61.935 66.667 0.00 0.00 38.18 4.70
286 287 3.624300 CGCGCTCTCAGCCATTCG 61.624 66.667 5.56 0.00 38.18 3.34
287 288 2.202797 TCGCGCTCTCAGCCATTC 60.203 61.111 5.56 0.00 38.18 2.67
288 289 2.510238 GTCGCGCTCTCAGCCATT 60.510 61.111 5.56 0.00 38.18 3.16
289 290 3.300934 TTGTCGCGCTCTCAGCCAT 62.301 57.895 5.56 0.00 38.18 4.40
290 291 3.921767 CTTGTCGCGCTCTCAGCCA 62.922 63.158 5.56 0.00 38.18 4.75
291 292 3.184683 CTTGTCGCGCTCTCAGCC 61.185 66.667 5.56 0.00 38.18 4.85
292 293 2.431601 ACTTGTCGCGCTCTCAGC 60.432 61.111 5.56 0.00 38.02 4.26
293 294 2.091112 CCACTTGTCGCGCTCTCAG 61.091 63.158 5.56 0.00 0.00 3.35
294 295 2.049156 CCACTTGTCGCGCTCTCA 60.049 61.111 5.56 0.00 0.00 3.27
295 296 3.482783 GCCACTTGTCGCGCTCTC 61.483 66.667 5.56 0.00 0.00 3.20
302 303 2.792290 CGATCAGCGCCACTTGTCG 61.792 63.158 2.29 4.51 0.00 4.35
303 304 1.291877 AACGATCAGCGCCACTTGTC 61.292 55.000 2.29 0.00 46.04 3.18
304 305 1.301716 AACGATCAGCGCCACTTGT 60.302 52.632 2.29 0.00 46.04 3.16
305 306 1.133253 CAACGATCAGCGCCACTTG 59.867 57.895 2.29 0.00 46.04 3.16
306 307 2.680913 GCAACGATCAGCGCCACTT 61.681 57.895 2.29 0.00 46.04 3.16
307 308 3.121030 GCAACGATCAGCGCCACT 61.121 61.111 2.29 0.00 46.04 4.00
313 314 3.181967 AGCGTCGCAACGATCAGC 61.182 61.111 21.09 0.30 46.06 4.26
320 321 3.479269 CTTCGGGAGCGTCGCAAC 61.479 66.667 21.09 12.64 0.00 4.17
321 322 4.735132 CCTTCGGGAGCGTCGCAA 62.735 66.667 21.09 3.22 37.25 4.85
331 332 2.552585 TTAACGAGCGCTCCTTCGGG 62.553 60.000 30.66 17.99 0.00 5.14
332 333 0.527817 ATTAACGAGCGCTCCTTCGG 60.528 55.000 30.66 18.71 0.00 4.30
333 334 1.278238 AATTAACGAGCGCTCCTTCG 58.722 50.000 30.66 22.24 0.00 3.79
334 335 3.445857 ACTAATTAACGAGCGCTCCTTC 58.554 45.455 30.66 8.16 0.00 3.46
335 336 3.521947 ACTAATTAACGAGCGCTCCTT 57.478 42.857 30.66 26.03 0.00 3.36
336 337 3.187700 CAACTAATTAACGAGCGCTCCT 58.812 45.455 30.66 20.33 0.00 3.69
337 338 2.285660 GCAACTAATTAACGAGCGCTCC 60.286 50.000 30.66 13.79 0.00 4.70
338 339 2.603560 AGCAACTAATTAACGAGCGCTC 59.396 45.455 27.64 27.64 0.00 5.03
339 340 2.603560 GAGCAACTAATTAACGAGCGCT 59.396 45.455 11.27 11.27 0.00 5.92
340 341 2.285660 GGAGCAACTAATTAACGAGCGC 60.286 50.000 0.00 0.00 0.00 5.92
341 342 2.284417 GGGAGCAACTAATTAACGAGCG 59.716 50.000 0.00 0.00 0.00 5.03
342 343 2.284417 CGGGAGCAACTAATTAACGAGC 59.716 50.000 0.00 0.00 0.00 5.03
358 359 1.372087 GCTCCAAGATGTTGCGGGAG 61.372 60.000 0.00 0.00 46.24 4.30
359 360 1.377202 GCTCCAAGATGTTGCGGGA 60.377 57.895 0.00 0.00 31.64 5.14
360 361 1.651240 CTGCTCCAAGATGTTGCGGG 61.651 60.000 0.00 0.00 31.64 6.13
361 362 1.798735 CTGCTCCAAGATGTTGCGG 59.201 57.895 0.00 0.00 31.64 5.69
362 363 1.136147 GCTGCTCCAAGATGTTGCG 59.864 57.895 0.00 0.00 31.64 4.85
363 364 0.599558 TTGCTGCTCCAAGATGTTGC 59.400 50.000 0.00 0.00 31.64 4.17
364 365 2.477357 CGATTGCTGCTCCAAGATGTTG 60.477 50.000 0.00 0.00 0.00 3.33
365 366 1.741706 CGATTGCTGCTCCAAGATGTT 59.258 47.619 0.00 0.00 0.00 2.71
366 367 1.065926 TCGATTGCTGCTCCAAGATGT 60.066 47.619 0.00 0.00 0.00 3.06
367 368 1.660167 TCGATTGCTGCTCCAAGATG 58.340 50.000 0.00 0.00 0.00 2.90
395 396 9.609346 TTTTTAAATTTGGGTCGGTCAATTTTA 57.391 25.926 0.00 0.00 33.03 1.52
398 399 7.934120 TGATTTTTAAATTTGGGTCGGTCAATT 59.066 29.630 0.00 0.00 0.00 2.32
399 400 7.445945 TGATTTTTAAATTTGGGTCGGTCAAT 58.554 30.769 0.00 0.00 0.00 2.57
405 406 5.233988 TGCCTGATTTTTAAATTTGGGTCG 58.766 37.500 0.00 0.00 0.00 4.79
433 434 9.855021 GTGTTTAAATGACAGCCTACATTTTAT 57.145 29.630 14.46 0.00 41.80 1.40
438 439 5.415701 CCAGTGTTTAAATGACAGCCTACAT 59.584 40.000 0.00 0.00 0.00 2.29
439 440 4.759693 CCAGTGTTTAAATGACAGCCTACA 59.240 41.667 0.00 0.00 0.00 2.74
441 442 5.001232 GTCCAGTGTTTAAATGACAGCCTA 58.999 41.667 0.00 0.00 0.00 3.93
464 465 0.318955 CTTTGTTTTCCTGCCGGCAG 60.319 55.000 43.23 43.23 43.26 4.85
471 472 5.215160 CGAAATCACTCCTTTGTTTTCCTG 58.785 41.667 0.00 0.00 34.03 3.86
474 475 4.976116 CCACGAAATCACTCCTTTGTTTTC 59.024 41.667 0.00 0.00 34.15 2.29
482 483 5.066505 GCAATTATTCCACGAAATCACTCCT 59.933 40.000 0.00 0.00 0.00 3.69
483 484 5.273944 GCAATTATTCCACGAAATCACTCC 58.726 41.667 0.00 0.00 0.00 3.85
484 485 5.273944 GGCAATTATTCCACGAAATCACTC 58.726 41.667 0.00 0.00 0.00 3.51
485 486 4.097892 GGGCAATTATTCCACGAAATCACT 59.902 41.667 0.00 0.00 0.00 3.41
486 487 4.359706 GGGCAATTATTCCACGAAATCAC 58.640 43.478 0.00 0.00 0.00 3.06
487 488 3.383185 GGGGCAATTATTCCACGAAATCA 59.617 43.478 0.00 0.00 0.00 2.57
488 489 3.636764 AGGGGCAATTATTCCACGAAATC 59.363 43.478 0.00 0.00 0.00 2.17
489 490 3.642141 AGGGGCAATTATTCCACGAAAT 58.358 40.909 0.00 0.00 0.00 2.17
490 491 3.094484 AGGGGCAATTATTCCACGAAA 57.906 42.857 0.00 0.00 0.00 3.46
491 492 2.818751 AGGGGCAATTATTCCACGAA 57.181 45.000 0.00 0.00 0.00 3.85
492 493 2.241176 AGAAGGGGCAATTATTCCACGA 59.759 45.455 0.00 0.00 0.00 4.35
493 494 2.618709 GAGAAGGGGCAATTATTCCACG 59.381 50.000 0.00 0.00 0.00 4.94
494 495 3.631250 TGAGAAGGGGCAATTATTCCAC 58.369 45.455 0.00 0.00 0.00 4.02
524 526 1.144057 GCCGGTGATCGAAGTCCAT 59.856 57.895 1.90 0.00 42.43 3.41
553 555 2.493675 AGCAATTAGAGAGACACGCAGA 59.506 45.455 0.00 0.00 0.00 4.26
598 600 4.035208 AGTTTGCGTTTAGGTCTTGTCTTG 59.965 41.667 0.00 0.00 0.00 3.02
602 604 3.311596 GTGAGTTTGCGTTTAGGTCTTGT 59.688 43.478 0.00 0.00 0.00 3.16
651 653 1.227853 AAAGTGTCAGGGACGGCAC 60.228 57.895 0.00 0.00 34.95 5.01
652 654 1.070786 GAAAGTGTCAGGGACGGCA 59.929 57.895 0.00 0.00 34.95 5.69
653 655 1.671379 GGAAAGTGTCAGGGACGGC 60.671 63.158 0.00 0.00 34.95 5.68
654 656 1.374252 CGGAAAGTGTCAGGGACGG 60.374 63.158 0.00 0.00 34.95 4.79
655 657 1.374252 CCGGAAAGTGTCAGGGACG 60.374 63.158 0.00 0.00 37.90 4.79
663 665 1.070289 GTGGAAGACTCCGGAAAGTGT 59.930 52.381 5.23 0.00 45.85 3.55
698 700 1.507141 GGTGGCACAAGTGAACTCCG 61.507 60.000 20.82 0.00 44.16 4.63
811 822 3.276846 GCCAGCCGTGAACGTGTT 61.277 61.111 1.75 0.00 37.74 3.32
881 893 4.493747 GACGCGGGGAAGACGAGG 62.494 72.222 12.47 0.00 35.43 4.63
888 900 1.134729 GTTTATGTAGGACGCGGGGAA 60.135 52.381 12.47 0.00 0.00 3.97
950 971 3.541632 AGATCACACTTGGTTCGTTGTT 58.458 40.909 0.00 0.00 0.00 2.83
1024 1045 4.335647 AGCGGCACCAGTGAAGGG 62.336 66.667 1.45 0.00 0.00 3.95
1145 1200 6.182634 CACACTTAAACTTGAGTTGTACGTG 58.817 40.000 0.00 8.40 38.44 4.49
1209 1265 1.376037 GTCTCCTTGGTTGGCTCGG 60.376 63.158 0.00 0.00 0.00 4.63
1255 1311 3.668142 GGGCTTGGGGTTGGGCTA 61.668 66.667 0.00 0.00 0.00 3.93
1313 1390 1.227176 CCGAGGGGTTAGCGTTAGC 60.227 63.158 0.00 0.00 45.58 3.09
1381 1458 3.849951 CCCACCATAGCGAGCCGT 61.850 66.667 0.00 0.00 0.00 5.68
1522 1599 3.241530 TGTCCCTGAAGCAGCGGT 61.242 61.111 0.00 0.00 0.00 5.68
1655 1732 2.100252 AGTTTCAGACGTTGACGAAGGA 59.900 45.455 10.87 1.61 43.02 3.36
1750 1836 8.289939 ACAGAATCCGTTACAGAATACTCTAA 57.710 34.615 0.00 0.00 0.00 2.10
1796 1882 2.751259 GCTCCAAGACATCAGCATCAAA 59.249 45.455 0.00 0.00 0.00 2.69
1803 1889 2.094286 ACTCGAAGCTCCAAGACATCAG 60.094 50.000 0.00 0.00 0.00 2.90
1808 1894 3.246619 CAGTAACTCGAAGCTCCAAGAC 58.753 50.000 0.00 0.00 0.00 3.01
1823 1909 4.893795 ACTTAATTCATTCGCGCAGTAAC 58.106 39.130 8.75 0.00 0.00 2.50
1831 1917 6.088085 CAGTGGTTTGAACTTAATTCATTCGC 59.912 38.462 0.00 0.00 46.80 4.70
1849 1935 6.618811 CACGTTCTTCTAGTATACAGTGGTT 58.381 40.000 5.50 0.00 0.00 3.67
1850 1936 5.392811 GCACGTTCTTCTAGTATACAGTGGT 60.393 44.000 5.50 0.00 0.00 4.16
1979 2069 9.844257 TTGATCCAAACAAAGGAAACAATTAAT 57.156 25.926 0.00 0.00 38.93 1.40
2138 2228 4.579340 CAGAATAGAGAGCCATGCAAACAT 59.421 41.667 0.00 0.00 36.79 2.71
2139 2229 3.943381 CAGAATAGAGAGCCATGCAAACA 59.057 43.478 0.00 0.00 0.00 2.83
2348 2438 5.414360 CAATCAGAAGAAGAATGACGAGGA 58.586 41.667 0.00 0.00 0.00 3.71
2474 2564 3.010250 GGGACTCCCTAACAAGGTGAAAT 59.990 47.826 6.90 0.00 41.34 2.17


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

AutoCloner maintained by Alex Coulton.