Multiple sequence alignment - TraesCS2A01G322900

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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 TraesCS2A01G322900 chr2A 100.000 2323 0 0 1 2323 552495054 552497376 0.000000e+00 4290.0
1 TraesCS2A01G322900 chr2A 98.876 178 2 0 1 178 480738376 480738199 3.720000e-83 318.0
2 TraesCS2A01G322900 chr2D 88.481 1936 96 49 271 2179 434356058 434354223 0.000000e+00 2222.0
3 TraesCS2A01G322900 chr2D 95.349 215 5 4 1 211 434356273 434356060 1.030000e-88 337.0
4 TraesCS2A01G322900 chr2B 89.577 969 59 25 448 1394 513280388 513279440 0.000000e+00 1192.0
5 TraesCS2A01G322900 chr2B 95.694 209 6 3 4 211 513280913 513280707 1.330000e-87 333.0
6 TraesCS2A01G322900 chr2B 93.923 181 10 1 271 450 513280705 513280525 2.940000e-69 272.0
7 TraesCS2A01G322900 chr2B 91.304 138 12 0 2037 2174 513279018 513278881 3.050000e-44 189.0
8 TraesCS2A01G322900 chr2B 82.192 146 13 7 1461 1604 513279438 513279304 1.890000e-21 113.0
9 TraesCS2A01G322900 chr2B 93.443 61 3 1 2259 2319 404162866 404162925 3.180000e-14 89.8
10 TraesCS2A01G322900 chr7A 100.000 178 0 0 1 178 394231183 394231360 1.720000e-86 329.0
11 TraesCS2A01G322900 chr3A 99.438 178 1 0 1 178 563624590 563624767 8.010000e-85 324.0
12 TraesCS2A01G322900 chr1A 99.438 178 1 0 1 178 45934463 45934286 8.010000e-85 324.0
13 TraesCS2A01G322900 chr1A 98.876 178 2 0 1 178 46366938 46366761 3.720000e-83 318.0
14 TraesCS2A01G322900 chr1A 98.876 178 2 0 1 178 74488160 74488337 3.720000e-83 318.0
15 TraesCS2A01G322900 chr5A 98.876 178 2 0 1 178 671469376 671469553 3.720000e-83 318.0
16 TraesCS2A01G322900 chr5D 98.000 50 1 0 2270 2319 320627429 320627380 1.140000e-13 87.9
17 TraesCS2A01G322900 chr7D 97.959 49 1 0 2271 2319 127220713 127220665 4.110000e-13 86.1
18 TraesCS2A01G322900 chr6B 96.154 52 2 0 2272 2323 560706182 560706131 4.110000e-13 86.1
19 TraesCS2A01G322900 chr6B 96.154 52 2 0 2272 2323 560745633 560745582 4.110000e-13 86.1
20 TraesCS2A01G322900 chr4A 96.154 52 2 0 2268 2319 584427876 584427825 4.110000e-13 86.1
21 TraesCS2A01G322900 chr3B 93.103 58 3 1 2263 2319 236510051 236509994 1.480000e-12 84.2
22 TraesCS2A01G322900 chr1D 96.078 51 2 0 2269 2319 13037278 13037328 1.480000e-12 84.2
23 TraesCS2A01G322900 chr1D 92.982 57 3 1 2268 2323 436106949 436107005 5.320000e-12 82.4


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 TraesCS2A01G322900 chr2A 552495054 552497376 2322 False 4290.0 4290 100.000 1 2323 1 chr2A.!!$F1 2322
1 TraesCS2A01G322900 chr2D 434354223 434356273 2050 True 1279.5 2222 91.915 1 2179 2 chr2D.!!$R1 2178
2 TraesCS2A01G322900 chr2B 513278881 513280913 2032 True 419.8 1192 90.538 4 2174 5 chr2B.!!$R1 2170

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
888 1052 0.034186 TTCGCTCCAATGCCCTTGAT 60.034 50.0 0.0 0.0 36.97 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2211 0.037419 TGCAACAGTCGCTGATAGCA 60.037 50.0 12.77 14.17 42.58 3.49 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
30 35 2.370189 AGAGTAGCTACCCAATGATGCC 59.630 50.000 20.31 0.00 0.00 4.40
31 36 1.421646 AGTAGCTACCCAATGATGCCC 59.578 52.381 20.31 0.00 0.00 5.36
45 50 4.166011 GCCCGCGTTCATGAGTGC 62.166 66.667 4.92 10.34 0.00 4.40
79 84 2.483106 GACGACAAGGTAAAGAAAGGCC 59.517 50.000 0.00 0.00 0.00 5.19
211 217 0.108520 TCAGGGTACTTAAAGCGGCG 60.109 55.000 0.51 0.51 0.00 6.46
212 218 0.390735 CAGGGTACTTAAAGCGGCGT 60.391 55.000 9.37 0.00 0.00 5.68
215 221 0.997196 GGTACTTAAAGCGGCGTCAG 59.003 55.000 9.37 0.00 0.00 3.51
216 222 0.369248 GTACTTAAAGCGGCGTCAGC 59.631 55.000 9.37 0.00 44.18 4.26
227 233 2.009888 GCGTCAGCATTCAGTAGGC 58.990 57.895 0.00 0.00 44.35 3.93
228 234 0.740868 GCGTCAGCATTCAGTAGGCA 60.741 55.000 0.00 0.00 44.35 4.75
229 235 1.284657 CGTCAGCATTCAGTAGGCAG 58.715 55.000 0.00 0.00 0.00 4.85
230 236 1.404717 CGTCAGCATTCAGTAGGCAGT 60.405 52.381 0.00 0.00 0.00 4.40
231 237 2.159240 CGTCAGCATTCAGTAGGCAGTA 60.159 50.000 0.00 0.00 0.00 2.74
232 238 3.452474 GTCAGCATTCAGTAGGCAGTAG 58.548 50.000 0.00 0.00 0.00 2.57
233 239 2.159043 TCAGCATTCAGTAGGCAGTAGC 60.159 50.000 0.00 0.00 41.10 3.58
244 250 4.148825 CAGTAGCCGCCGCCTCTT 62.149 66.667 0.00 0.00 34.57 2.85
245 251 3.391382 AGTAGCCGCCGCCTCTTT 61.391 61.111 0.00 0.00 34.57 2.52
246 252 2.436115 GTAGCCGCCGCCTCTTTT 60.436 61.111 0.00 0.00 34.57 2.27
247 253 2.038837 GTAGCCGCCGCCTCTTTTT 61.039 57.895 0.00 0.00 34.57 1.94
248 254 1.743995 TAGCCGCCGCCTCTTTTTC 60.744 57.895 0.00 0.00 34.57 2.29
249 255 4.460873 GCCGCCGCCTCTTTTTCG 62.461 66.667 0.00 0.00 0.00 3.46
250 256 3.799755 CCGCCGCCTCTTTTTCGG 61.800 66.667 0.00 0.00 45.46 4.30
253 259 3.668386 CCGCCTCTTTTTCGGCTT 58.332 55.556 0.00 0.00 44.11 4.35
254 260 2.849081 CCGCCTCTTTTTCGGCTTA 58.151 52.632 0.00 0.00 44.11 3.09
255 261 1.161843 CCGCCTCTTTTTCGGCTTAA 58.838 50.000 0.00 0.00 44.11 1.85
256 262 1.538075 CCGCCTCTTTTTCGGCTTAAA 59.462 47.619 0.00 0.00 44.11 1.52
257 263 2.030628 CCGCCTCTTTTTCGGCTTAAAA 60.031 45.455 0.00 0.00 44.11 1.52
258 264 3.551250 CCGCCTCTTTTTCGGCTTAAAAA 60.551 43.478 8.50 8.50 44.11 1.94
259 265 3.424198 CGCCTCTTTTTCGGCTTAAAAAC 59.576 43.478 0.00 0.00 44.11 2.43
260 266 4.617959 GCCTCTTTTTCGGCTTAAAAACT 58.382 39.130 5.68 0.00 42.98 2.66
261 267 4.444388 GCCTCTTTTTCGGCTTAAAAACTG 59.556 41.667 5.68 3.15 42.98 3.16
262 268 4.444388 CCTCTTTTTCGGCTTAAAAACTGC 59.556 41.667 5.68 0.00 34.31 4.40
263 269 4.364860 TCTTTTTCGGCTTAAAAACTGCC 58.635 39.130 5.68 0.00 42.94 4.85
264 270 2.804697 TTTCGGCTTAAAAACTGCCC 57.195 45.000 0.00 0.00 43.42 5.36
265 271 1.989706 TTCGGCTTAAAAACTGCCCT 58.010 45.000 0.00 0.00 43.42 5.19
266 272 1.243902 TCGGCTTAAAAACTGCCCTG 58.756 50.000 0.00 0.00 43.42 4.45
267 273 1.202830 TCGGCTTAAAAACTGCCCTGA 60.203 47.619 0.00 0.00 43.42 3.86
268 274 1.200020 CGGCTTAAAAACTGCCCTGAG 59.800 52.381 0.00 0.00 43.42 3.35
269 275 1.546029 GGCTTAAAAACTGCCCTGAGG 59.454 52.381 0.00 0.00 40.71 3.86
270 276 2.514803 GCTTAAAAACTGCCCTGAGGA 58.485 47.619 0.00 0.00 33.47 3.71
271 277 2.229062 GCTTAAAAACTGCCCTGAGGAC 59.771 50.000 0.00 0.00 33.47 3.85
272 278 3.486383 CTTAAAAACTGCCCTGAGGACA 58.514 45.455 0.00 0.00 33.47 4.02
330 336 1.046204 TCAACCAATGGCATGCACAA 58.954 45.000 21.36 4.56 0.00 3.33
396 402 6.196918 TGGGAATCTTGAGCAGATGATATT 57.803 37.500 0.00 0.00 41.93 1.28
450 456 5.426504 CATGAGGCTACTGAAGAATCAAGT 58.573 41.667 0.00 0.00 34.49 3.16
452 458 5.482908 TGAGGCTACTGAAGAATCAAGTTC 58.517 41.667 0.00 0.00 34.49 3.01
453 459 5.012046 TGAGGCTACTGAAGAATCAAGTTCA 59.988 40.000 0.00 0.00 39.39 3.18
454 460 5.869579 AGGCTACTGAAGAATCAAGTTCAA 58.130 37.500 0.00 0.00 39.39 2.69
456 462 6.944862 AGGCTACTGAAGAATCAAGTTCAAAT 59.055 34.615 0.00 0.00 39.39 2.32
521 668 4.130286 GTTTCATTCAAAACCACACCCA 57.870 40.909 0.00 0.00 33.86 4.51
857 1015 4.695928 GTGTAAATCTCCTGTCCTTTGACC 59.304 45.833 0.00 0.00 41.01 4.02
871 1035 0.319900 TTGACCTGCGAGCTGTCTTC 60.320 55.000 15.35 4.93 0.00 2.87
888 1052 0.034186 TTCGCTCCAATGCCCTTGAT 60.034 50.000 0.00 0.00 36.97 2.57
906 1070 5.928839 CCTTGATCGGCTATATATATGCACC 59.071 44.000 5.44 3.46 0.00 5.01
907 1071 5.121221 TGATCGGCTATATATATGCACCG 57.879 43.478 19.17 19.17 40.47 4.94
921 1091 3.878160 TGCACCGAACATACATAGACA 57.122 42.857 0.00 0.00 0.00 3.41
1008 1181 1.271543 TGTGGAGAAGGCATGAGGTTG 60.272 52.381 0.00 0.00 0.00 3.77
1013 1186 1.211457 AGAAGGCATGAGGTTGCTAGG 59.789 52.381 0.00 0.00 42.38 3.02
1147 1320 3.052036 AGTGTTGATGTTTGCGATTTGC 58.948 40.909 0.00 0.00 46.70 3.68
1151 1324 2.674954 TGATGTTTGCGATTTGCTTGG 58.325 42.857 0.00 0.00 46.63 3.61
1161 1334 2.485426 CGATTTGCTTGGTGATGAGTGT 59.515 45.455 0.00 0.00 0.00 3.55
1163 1336 0.953727 TTGCTTGGTGATGAGTGTGC 59.046 50.000 0.00 0.00 0.00 4.57
1326 1504 0.961019 GCCCAAGCACAACTGATTCA 59.039 50.000 0.00 0.00 39.53 2.57
1327 1505 1.068055 GCCCAAGCACAACTGATTCAG 60.068 52.381 12.17 12.17 39.53 3.02
1329 1507 1.884579 CCAAGCACAACTGATTCAGCT 59.115 47.619 13.64 2.62 34.37 4.24
1330 1508 3.076621 CCAAGCACAACTGATTCAGCTA 58.923 45.455 13.64 0.00 34.37 3.32
1355 1538 4.119136 GCTAGCTAGAAGAAAGCCTCTTG 58.881 47.826 25.15 0.00 44.82 3.02
1387 1572 2.507992 CTCCTTCAGCAGCGACCG 60.508 66.667 0.00 0.00 0.00 4.79
1402 1587 1.512926 GACCGTCTGCTCAAATGTGT 58.487 50.000 0.00 0.00 0.00 3.72
1403 1588 1.873591 GACCGTCTGCTCAAATGTGTT 59.126 47.619 0.00 0.00 0.00 3.32
1419 1604 0.615331 TGTTAGCAGGGGAAGCTCTG 59.385 55.000 0.00 0.00 42.32 3.35
1433 1618 0.387202 GCTCTGGATTCAGCTAGCGA 59.613 55.000 9.55 7.13 40.69 4.93
1448 1633 1.388547 AGCGATCGAGAAGAAGCTCT 58.611 50.000 21.57 0.00 41.01 4.09
1464 1649 1.761009 GCTCTCAGCTCCCCTAATCCT 60.761 57.143 0.00 0.00 38.45 3.24
1479 1664 6.158871 CCCCTAATCCTCCTTCTTACTTCTTT 59.841 42.308 0.00 0.00 0.00 2.52
1498 1688 9.856488 ACTTCTTTAGTAGTATGTGTGTGTATG 57.144 33.333 0.00 0.00 34.56 2.39
1499 1689 9.856488 CTTCTTTAGTAGTATGTGTGTGTATGT 57.144 33.333 0.00 0.00 0.00 2.29
1653 1856 8.889717 TCTTTCAGTTACACTTTTGTAAGAAGG 58.110 33.333 0.00 1.44 46.63 3.46
1654 1857 8.570068 TTTCAGTTACACTTTTGTAAGAAGGT 57.430 30.769 0.00 0.00 46.63 3.50
1655 1858 9.669887 TTTCAGTTACACTTTTGTAAGAAGGTA 57.330 29.630 0.00 0.00 46.63 3.08
1656 1859 8.652810 TCAGTTACACTTTTGTAAGAAGGTAC 57.347 34.615 0.00 0.00 46.63 3.34
1657 1860 8.480501 TCAGTTACACTTTTGTAAGAAGGTACT 58.519 33.333 0.00 0.00 46.63 2.73
1658 1861 8.548721 CAGTTACACTTTTGTAAGAAGGTACTG 58.451 37.037 0.00 0.00 46.63 2.74
1663 1866 8.917088 ACACTTTTGTAAGAAGGTACTGTAGTA 58.083 33.333 0.00 0.00 33.30 1.82
1686 1889 2.875933 TGTGGATTCGTTTGGTGAAGTC 59.124 45.455 0.00 0.00 0.00 3.01
1711 1914 4.018779 TGGTTATTTCCCCTGTAAGTGAGG 60.019 45.833 0.00 0.00 0.00 3.86
1722 1925 4.118410 CTGTAAGTGAGGAGTGATCATGC 58.882 47.826 0.00 0.00 0.00 4.06
1761 1964 1.135199 TCGTAATGGAACCAGACGAGC 60.135 52.381 21.49 1.96 40.69 5.03
1855 2067 1.218230 GCGCTTCCTCACGATGGATC 61.218 60.000 0.00 0.00 33.09 3.36
1862 2074 2.130395 CCTCACGATGGATCACATTCG 58.870 52.381 0.00 0.00 40.72 3.34
1868 2080 1.003545 GATGGATCACATTCGCCAACG 60.004 52.381 0.00 0.00 40.72 4.10
1869 2081 1.062525 GGATCACATTCGCCAACGC 59.937 57.895 0.00 0.00 39.84 4.84
1870 2082 1.369091 GGATCACATTCGCCAACGCT 61.369 55.000 0.00 0.00 39.84 5.07
1883 2095 0.249447 CAACGCTCTATGGATCGGCA 60.249 55.000 7.25 0.00 35.69 5.69
1884 2096 0.032678 AACGCTCTATGGATCGGCAG 59.967 55.000 7.25 0.00 35.69 4.85
1886 2098 0.032678 CGCTCTATGGATCGGCAGTT 59.967 55.000 0.00 0.00 0.00 3.16
1888 2100 1.869767 GCTCTATGGATCGGCAGTTTG 59.130 52.381 0.00 0.00 0.00 2.93
1889 2101 2.743183 GCTCTATGGATCGGCAGTTTGT 60.743 50.000 0.00 0.00 0.00 2.83
1890 2102 3.492656 GCTCTATGGATCGGCAGTTTGTA 60.493 47.826 0.00 0.00 0.00 2.41
1891 2103 4.693283 CTCTATGGATCGGCAGTTTGTAA 58.307 43.478 0.00 0.00 0.00 2.41
1892 2104 4.439057 TCTATGGATCGGCAGTTTGTAAC 58.561 43.478 0.00 0.00 0.00 2.50
1893 2105 2.851263 TGGATCGGCAGTTTGTAACT 57.149 45.000 0.00 0.00 44.06 2.24
1894 2106 3.965379 TGGATCGGCAGTTTGTAACTA 57.035 42.857 0.00 0.00 40.46 2.24
1897 2109 2.823924 TCGGCAGTTTGTAACTAGCA 57.176 45.000 12.53 0.00 40.46 3.49
1910 2122 4.459685 TGTAACTAGCACCTCTCAGAAGAC 59.540 45.833 0.00 0.00 0.00 3.01
1917 2129 1.203523 ACCTCTCAGAAGACGACATGC 59.796 52.381 0.00 0.00 0.00 4.06
1972 2188 0.776810 TGGTTCTGCCCCAAAGATGA 59.223 50.000 0.00 0.00 36.04 2.92
2003 2219 6.988109 GCAAATGCTAAAGATTGCTATCAG 57.012 37.500 10.78 0.77 43.58 2.90
2008 2224 4.054671 GCTAAAGATTGCTATCAGCGACT 58.945 43.478 10.78 0.00 46.26 4.18
2179 2398 5.187772 TCAGATACAAGAAGCGGCCATATAT 59.812 40.000 2.24 0.00 0.00 0.86
2180 2399 5.877012 CAGATACAAGAAGCGGCCATATATT 59.123 40.000 2.24 0.00 0.00 1.28
2181 2400 6.372659 CAGATACAAGAAGCGGCCATATATTT 59.627 38.462 2.24 0.00 0.00 1.40
2182 2401 4.836125 ACAAGAAGCGGCCATATATTTG 57.164 40.909 2.24 2.38 0.00 2.32
2183 2402 4.207165 ACAAGAAGCGGCCATATATTTGT 58.793 39.130 2.24 3.06 0.00 2.83
2184 2403 4.036734 ACAAGAAGCGGCCATATATTTGTG 59.963 41.667 2.24 0.00 0.00 3.33
2185 2404 2.554032 AGAAGCGGCCATATATTTGTGC 59.446 45.455 2.24 0.00 0.00 4.57
2186 2405 0.874390 AGCGGCCATATATTTGTGCG 59.126 50.000 2.24 0.00 0.00 5.34
2187 2406 0.591170 GCGGCCATATATTTGTGCGT 59.409 50.000 2.24 0.00 0.00 5.24
2188 2407 1.662876 GCGGCCATATATTTGTGCGTG 60.663 52.381 2.24 0.00 0.00 5.34
2189 2408 1.601903 CGGCCATATATTTGTGCGTGT 59.398 47.619 2.24 0.00 0.00 4.49
2190 2409 2.032799 CGGCCATATATTTGTGCGTGTT 59.967 45.455 2.24 0.00 0.00 3.32
2191 2410 3.488384 CGGCCATATATTTGTGCGTGTTT 60.488 43.478 2.24 0.00 0.00 2.83
2192 2411 4.429108 GGCCATATATTTGTGCGTGTTTT 58.571 39.130 0.00 0.00 0.00 2.43
2193 2412 4.867608 GGCCATATATTTGTGCGTGTTTTT 59.132 37.500 0.00 0.00 0.00 1.94
2212 2431 4.652421 TTTTGAAATGCTCAACTGCTCA 57.348 36.364 0.00 0.00 43.90 4.26
2213 2432 3.631145 TTGAAATGCTCAACTGCTCAC 57.369 42.857 0.00 0.00 39.20 3.51
2214 2433 1.532437 TGAAATGCTCAACTGCTCACG 59.468 47.619 0.00 0.00 0.00 4.35
2215 2434 1.800586 GAAATGCTCAACTGCTCACGA 59.199 47.619 0.00 0.00 0.00 4.35
2216 2435 1.436600 AATGCTCAACTGCTCACGAG 58.563 50.000 0.00 0.00 0.00 4.18
2217 2436 0.605083 ATGCTCAACTGCTCACGAGA 59.395 50.000 0.00 0.00 0.00 4.04
2218 2437 0.319040 TGCTCAACTGCTCACGAGAC 60.319 55.000 0.00 0.00 0.00 3.36
2219 2438 0.319040 GCTCAACTGCTCACGAGACA 60.319 55.000 0.00 0.00 0.00 3.41
2220 2439 1.413382 CTCAACTGCTCACGAGACAC 58.587 55.000 0.00 0.00 0.00 3.67
2221 2440 1.000827 CTCAACTGCTCACGAGACACT 60.001 52.381 0.00 0.00 0.00 3.55
2222 2441 1.409064 TCAACTGCTCACGAGACACTT 59.591 47.619 0.00 0.00 0.00 3.16
2223 2442 2.621526 TCAACTGCTCACGAGACACTTA 59.378 45.455 0.00 0.00 0.00 2.24
2224 2443 3.067601 TCAACTGCTCACGAGACACTTAA 59.932 43.478 0.00 0.00 0.00 1.85
2225 2444 3.728076 ACTGCTCACGAGACACTTAAA 57.272 42.857 0.00 0.00 0.00 1.52
2226 2445 4.258702 ACTGCTCACGAGACACTTAAAT 57.741 40.909 0.00 0.00 0.00 1.40
2227 2446 4.632153 ACTGCTCACGAGACACTTAAATT 58.368 39.130 0.00 0.00 0.00 1.82
2228 2447 5.779922 ACTGCTCACGAGACACTTAAATTA 58.220 37.500 0.00 0.00 0.00 1.40
2229 2448 6.220930 ACTGCTCACGAGACACTTAAATTAA 58.779 36.000 0.00 0.00 0.00 1.40
2230 2449 6.704493 ACTGCTCACGAGACACTTAAATTAAA 59.296 34.615 0.00 0.00 0.00 1.52
2231 2450 7.095607 ACTGCTCACGAGACACTTAAATTAAAG 60.096 37.037 0.00 0.00 0.00 1.85
2232 2451 6.147164 TGCTCACGAGACACTTAAATTAAAGG 59.853 38.462 0.00 0.00 0.00 3.11
2233 2452 6.147328 GCTCACGAGACACTTAAATTAAAGGT 59.853 38.462 0.00 0.00 0.00 3.50
2234 2453 7.621633 GCTCACGAGACACTTAAATTAAAGGTC 60.622 40.741 0.00 7.82 31.88 3.85
2235 2454 7.439381 TCACGAGACACTTAAATTAAAGGTCT 58.561 34.615 14.72 14.72 38.55 3.85
2236 2455 7.929785 TCACGAGACACTTAAATTAAAGGTCTT 59.070 33.333 15.48 3.95 37.25 3.01
2237 2456 8.221766 CACGAGACACTTAAATTAAAGGTCTTC 58.778 37.037 15.48 10.34 37.25 2.87
2238 2457 7.929785 ACGAGACACTTAAATTAAAGGTCTTCA 59.070 33.333 15.48 0.00 37.25 3.02
2239 2458 8.936864 CGAGACACTTAAATTAAAGGTCTTCAT 58.063 33.333 15.48 0.68 37.25 2.57
2242 2461 9.989869 GACACTTAAATTAAAGGTCTTCATAGC 57.010 33.333 8.37 0.00 0.00 2.97
2243 2462 9.740710 ACACTTAAATTAAAGGTCTTCATAGCT 57.259 29.630 0.00 0.00 0.00 3.32
2247 2466 9.614792 TTAAATTAAAGGTCTTCATAGCTCTCC 57.385 33.333 0.00 0.00 0.00 3.71
2248 2467 7.444703 AATTAAAGGTCTTCATAGCTCTCCT 57.555 36.000 0.00 0.00 0.00 3.69
2249 2468 6.472686 TTAAAGGTCTTCATAGCTCTCCTC 57.527 41.667 0.00 0.00 0.00 3.71
2250 2469 3.971468 AGGTCTTCATAGCTCTCCTCT 57.029 47.619 0.00 0.00 0.00 3.69
2251 2470 5.396057 AAGGTCTTCATAGCTCTCCTCTA 57.604 43.478 0.00 0.00 0.00 2.43
2252 2471 4.725490 AGGTCTTCATAGCTCTCCTCTAC 58.275 47.826 0.00 0.00 0.00 2.59
2253 2472 4.167113 AGGTCTTCATAGCTCTCCTCTACA 59.833 45.833 0.00 0.00 0.00 2.74
2254 2473 4.277423 GGTCTTCATAGCTCTCCTCTACAC 59.723 50.000 0.00 0.00 0.00 2.90
2255 2474 4.277423 GTCTTCATAGCTCTCCTCTACACC 59.723 50.000 0.00 0.00 0.00 4.16
2256 2475 3.231207 TCATAGCTCTCCTCTACACCC 57.769 52.381 0.00 0.00 0.00 4.61
2257 2476 2.786445 TCATAGCTCTCCTCTACACCCT 59.214 50.000 0.00 0.00 0.00 4.34
2258 2477 3.981375 TCATAGCTCTCCTCTACACCCTA 59.019 47.826 0.00 0.00 0.00 3.53
2259 2478 4.604050 TCATAGCTCTCCTCTACACCCTAT 59.396 45.833 0.00 0.00 0.00 2.57
2260 2479 3.518992 AGCTCTCCTCTACACCCTATC 57.481 52.381 0.00 0.00 0.00 2.08
2261 2480 2.786445 AGCTCTCCTCTACACCCTATCA 59.214 50.000 0.00 0.00 0.00 2.15
2262 2481 3.153919 GCTCTCCTCTACACCCTATCAG 58.846 54.545 0.00 0.00 0.00 2.90
2263 2482 3.435890 GCTCTCCTCTACACCCTATCAGT 60.436 52.174 0.00 0.00 0.00 3.41
2264 2483 4.202482 GCTCTCCTCTACACCCTATCAGTA 60.202 50.000 0.00 0.00 0.00 2.74
2265 2484 5.515886 GCTCTCCTCTACACCCTATCAGTAT 60.516 48.000 0.00 0.00 0.00 2.12
2266 2485 6.129414 TCTCCTCTACACCCTATCAGTATC 57.871 45.833 0.00 0.00 0.00 2.24
2267 2486 5.611408 TCTCCTCTACACCCTATCAGTATCA 59.389 44.000 0.00 0.00 0.00 2.15
2268 2487 6.102762 TCTCCTCTACACCCTATCAGTATCAA 59.897 42.308 0.00 0.00 0.00 2.57
2269 2488 6.864421 TCCTCTACACCCTATCAGTATCAAT 58.136 40.000 0.00 0.00 0.00 2.57
2270 2489 7.996788 TCCTCTACACCCTATCAGTATCAATA 58.003 38.462 0.00 0.00 0.00 1.90
2271 2490 8.624670 TCCTCTACACCCTATCAGTATCAATAT 58.375 37.037 0.00 0.00 0.00 1.28
2272 2491 9.922477 CCTCTACACCCTATCAGTATCAATATA 57.078 37.037 0.00 0.00 0.00 0.86
2276 2495 8.596781 ACACCCTATCAGTATCAATATACTCC 57.403 38.462 0.00 0.00 44.05 3.85
2277 2496 7.620094 ACACCCTATCAGTATCAATATACTCCC 59.380 40.741 0.00 0.00 44.05 4.30
2278 2497 7.841729 CACCCTATCAGTATCAATATACTCCCT 59.158 40.741 0.00 0.00 44.05 4.20
2279 2498 8.062536 ACCCTATCAGTATCAATATACTCCCTC 58.937 40.741 0.00 0.00 44.05 4.30
2280 2499 7.507616 CCCTATCAGTATCAATATACTCCCTCC 59.492 44.444 0.00 0.00 44.05 4.30
2281 2500 7.229707 CCTATCAGTATCAATATACTCCCTCCG 59.770 44.444 0.00 0.00 44.05 4.63
2282 2501 5.888901 TCAGTATCAATATACTCCCTCCGT 58.111 41.667 0.00 0.00 44.05 4.69
2283 2502 5.944599 TCAGTATCAATATACTCCCTCCGTC 59.055 44.000 0.00 0.00 44.05 4.79
2284 2503 5.125739 CAGTATCAATATACTCCCTCCGTCC 59.874 48.000 0.00 0.00 44.05 4.79
2285 2504 3.605726 TCAATATACTCCCTCCGTCCA 57.394 47.619 0.00 0.00 0.00 4.02
2286 2505 3.918566 TCAATATACTCCCTCCGTCCAA 58.081 45.455 0.00 0.00 0.00 3.53
2287 2506 4.489737 TCAATATACTCCCTCCGTCCAAT 58.510 43.478 0.00 0.00 0.00 3.16
2288 2507 5.647230 TCAATATACTCCCTCCGTCCAATA 58.353 41.667 0.00 0.00 0.00 1.90
2289 2508 6.079336 TCAATATACTCCCTCCGTCCAATAA 58.921 40.000 0.00 0.00 0.00 1.40
2290 2509 6.729100 TCAATATACTCCCTCCGTCCAATAAT 59.271 38.462 0.00 0.00 0.00 1.28
2291 2510 7.897030 TCAATATACTCCCTCCGTCCAATAATA 59.103 37.037 0.00 0.00 0.00 0.98
2292 2511 8.705594 CAATATACTCCCTCCGTCCAATAATAT 58.294 37.037 0.00 0.00 0.00 1.28
2293 2512 9.947189 AATATACTCCCTCCGTCCAATAATATA 57.053 33.333 0.00 0.00 0.00 0.86
2294 2513 9.947189 ATATACTCCCTCCGTCCAATAATATAA 57.053 33.333 0.00 0.00 0.00 0.98
2295 2514 8.674925 ATACTCCCTCCGTCCAATAATATAAA 57.325 34.615 0.00 0.00 0.00 1.40
2296 2515 7.383156 ACTCCCTCCGTCCAATAATATAAAA 57.617 36.000 0.00 0.00 0.00 1.52
2297 2516 7.808218 ACTCCCTCCGTCCAATAATATAAAAA 58.192 34.615 0.00 0.00 0.00 1.94
2298 2517 7.718314 ACTCCCTCCGTCCAATAATATAAAAAC 59.282 37.037 0.00 0.00 0.00 2.43
2299 2518 6.707161 TCCCTCCGTCCAATAATATAAAAACG 59.293 38.462 0.00 0.00 0.00 3.60
2300 2519 6.484308 CCCTCCGTCCAATAATATAAAAACGT 59.516 38.462 0.00 0.00 0.00 3.99
2301 2520 7.012610 CCCTCCGTCCAATAATATAAAAACGTT 59.987 37.037 0.00 0.00 0.00 3.99
2302 2521 8.400186 CCTCCGTCCAATAATATAAAAACGTTT 58.600 33.333 7.96 7.96 0.00 3.60
2303 2522 9.777575 CTCCGTCCAATAATATAAAAACGTTTT 57.222 29.630 20.26 20.26 0.00 2.43
2317 2536 9.925268 ATAAAAACGTTTTTGACACTACACTAG 57.075 29.630 36.92 0.00 40.33 2.57
2318 2537 6.973229 AAACGTTTTTGACACTACACTAGT 57.027 33.333 7.96 0.00 40.28 2.57
2319 2538 8.477984 AAAACGTTTTTGACACTACACTAGTA 57.522 30.769 20.26 0.00 37.23 1.82
2320 2539 7.455331 AACGTTTTTGACACTACACTAGTAC 57.545 36.000 0.00 0.00 37.23 2.73
2321 2540 5.979517 ACGTTTTTGACACTACACTAGTACC 59.020 40.000 0.00 0.00 37.23 3.34
2322 2541 5.978919 CGTTTTTGACACTACACTAGTACCA 59.021 40.000 0.00 0.00 37.23 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.556004 GGCATCATTGGGTAGCTACTCTC 60.556 52.174 23.96 13.76 0.00 3.20
30 35 2.108514 ATGGCACTCATGAACGCGG 61.109 57.895 12.47 0.00 34.22 6.46
31 36 3.489731 ATGGCACTCATGAACGCG 58.510 55.556 3.53 3.53 34.22 6.01
45 50 0.460109 TGTCGTCAAGATCGGCATGG 60.460 55.000 0.00 0.00 37.98 3.66
79 84 4.429854 TTTTGGGGATTTGGTTTCCTTG 57.570 40.909 0.00 0.00 33.53 3.61
134 139 5.762179 AGATTGACAGTGATGGTTAGGAA 57.238 39.130 0.00 0.00 0.00 3.36
211 217 2.393271 ACTGCCTACTGAATGCTGAC 57.607 50.000 0.00 0.00 0.00 3.51
212 218 2.159043 GCTACTGCCTACTGAATGCTGA 60.159 50.000 0.00 0.00 0.00 4.26
227 233 3.665675 AAAGAGGCGGCGGCTACTG 62.666 63.158 36.29 0.00 38.98 2.74
228 234 2.465055 AAAAAGAGGCGGCGGCTACT 62.465 55.000 36.29 28.20 38.98 2.57
229 235 1.978712 GAAAAAGAGGCGGCGGCTAC 61.979 60.000 36.29 26.55 38.98 3.58
230 236 1.743995 GAAAAAGAGGCGGCGGCTA 60.744 57.895 36.29 0.00 38.98 3.93
231 237 3.056328 GAAAAAGAGGCGGCGGCT 61.056 61.111 36.82 36.82 42.48 5.52
232 238 4.460873 CGAAAAAGAGGCGGCGGC 62.461 66.667 27.24 27.24 38.90 6.53
233 239 3.799755 CCGAAAAAGAGGCGGCGG 61.800 66.667 9.78 0.00 38.46 6.13
239 245 4.444388 GCAGTTTTTAAGCCGAAAAAGAGG 59.556 41.667 6.39 2.21 38.59 3.69
240 246 4.444388 GGCAGTTTTTAAGCCGAAAAAGAG 59.556 41.667 6.39 4.38 38.59 2.85
241 247 4.364860 GGCAGTTTTTAAGCCGAAAAAGA 58.635 39.130 6.39 0.00 38.59 2.52
242 248 4.708868 GGCAGTTTTTAAGCCGAAAAAG 57.291 40.909 6.39 0.00 38.59 2.27
250 256 2.229062 GTCCTCAGGGCAGTTTTTAAGC 59.771 50.000 0.00 0.00 0.00 3.09
251 257 3.253432 GTGTCCTCAGGGCAGTTTTTAAG 59.747 47.826 0.00 0.00 0.00 1.85
252 258 3.219281 GTGTCCTCAGGGCAGTTTTTAA 58.781 45.455 0.00 0.00 0.00 1.52
253 259 2.488347 GGTGTCCTCAGGGCAGTTTTTA 60.488 50.000 0.00 0.00 0.00 1.52
254 260 1.692411 GTGTCCTCAGGGCAGTTTTT 58.308 50.000 0.00 0.00 0.00 1.94
255 261 0.178990 GGTGTCCTCAGGGCAGTTTT 60.179 55.000 0.00 0.00 0.00 2.43
256 262 1.456287 GGTGTCCTCAGGGCAGTTT 59.544 57.895 0.00 0.00 0.00 2.66
257 263 2.529744 GGGTGTCCTCAGGGCAGTT 61.530 63.158 0.00 0.00 0.00 3.16
258 264 2.930562 GGGTGTCCTCAGGGCAGT 60.931 66.667 0.00 0.00 0.00 4.40
259 265 1.856539 ATTGGGTGTCCTCAGGGCAG 61.857 60.000 0.00 0.00 0.00 4.85
260 266 1.852157 ATTGGGTGTCCTCAGGGCA 60.852 57.895 0.00 0.00 0.00 5.36
261 267 1.077429 GATTGGGTGTCCTCAGGGC 60.077 63.158 0.00 0.00 0.00 5.19
262 268 1.609783 GGATTGGGTGTCCTCAGGG 59.390 63.158 0.00 0.00 32.85 4.45
263 269 1.207488 TGGGATTGGGTGTCCTCAGG 61.207 60.000 0.00 0.00 36.00 3.86
264 270 0.921896 ATGGGATTGGGTGTCCTCAG 59.078 55.000 0.00 0.00 36.00 3.35
265 271 0.625316 CATGGGATTGGGTGTCCTCA 59.375 55.000 0.00 0.00 36.00 3.86
266 272 0.918983 TCATGGGATTGGGTGTCCTC 59.081 55.000 0.00 0.00 36.00 3.71
267 273 0.921896 CTCATGGGATTGGGTGTCCT 59.078 55.000 0.00 0.00 36.00 3.85
268 274 0.106519 CCTCATGGGATTGGGTGTCC 60.107 60.000 0.00 0.00 37.23 4.02
269 275 0.753111 GCCTCATGGGATTGGGTGTC 60.753 60.000 0.00 0.00 37.23 3.67
270 276 1.217057 AGCCTCATGGGATTGGGTGT 61.217 55.000 0.00 0.00 37.23 4.16
271 277 0.846015 TAGCCTCATGGGATTGGGTG 59.154 55.000 0.00 0.00 37.23 4.61
272 278 1.496429 CTTAGCCTCATGGGATTGGGT 59.504 52.381 0.00 0.00 37.23 4.51
297 303 1.535028 TGGTTGATTGCTGTGCTAACG 59.465 47.619 0.00 0.00 0.00 3.18
330 336 5.470777 CACTGGGATTTGAAATTGCATTTGT 59.529 36.000 0.00 0.00 31.47 2.83
450 456 9.738832 GGTTTTGTTTAGTTAGCACTATTTGAA 57.261 29.630 0.00 0.00 35.32 2.69
452 458 8.138712 TGGGTTTTGTTTAGTTAGCACTATTTG 58.861 33.333 0.00 0.00 35.32 2.32
453 459 8.240267 TGGGTTTTGTTTAGTTAGCACTATTT 57.760 30.769 0.00 0.00 35.32 1.40
454 460 7.826918 TGGGTTTTGTTTAGTTAGCACTATT 57.173 32.000 0.00 0.00 35.32 1.73
456 462 6.294286 GCATGGGTTTTGTTTAGTTAGCACTA 60.294 38.462 0.00 0.00 34.06 2.74
521 668 2.327325 ACATGGAGTAGTGGAGTGGT 57.673 50.000 0.00 0.00 0.00 4.16
551 706 8.562892 GCGATTAACTAGTGATTGGTACTACTA 58.437 37.037 0.00 0.00 0.00 1.82
552 707 7.424001 GCGATTAACTAGTGATTGGTACTACT 58.576 38.462 0.00 0.00 0.00 2.57
553 708 6.359087 CGCGATTAACTAGTGATTGGTACTAC 59.641 42.308 0.00 0.00 0.00 2.73
554 709 6.432936 CGCGATTAACTAGTGATTGGTACTA 58.567 40.000 0.00 0.00 0.00 1.82
555 710 5.279384 CGCGATTAACTAGTGATTGGTACT 58.721 41.667 0.00 0.00 0.00 2.73
556 711 4.443394 CCGCGATTAACTAGTGATTGGTAC 59.557 45.833 8.23 0.00 0.00 3.34
557 712 4.613944 CCGCGATTAACTAGTGATTGGTA 58.386 43.478 8.23 0.00 0.00 3.25
558 713 3.454375 CCGCGATTAACTAGTGATTGGT 58.546 45.455 8.23 0.00 0.00 3.67
559 714 2.221055 GCCGCGATTAACTAGTGATTGG 59.779 50.000 8.23 0.00 0.00 3.16
560 715 3.123804 AGCCGCGATTAACTAGTGATTG 58.876 45.455 8.23 0.00 0.00 2.67
871 1035 1.779025 CGATCAAGGGCATTGGAGCG 61.779 60.000 12.41 9.45 39.54 5.03
888 1052 4.399934 TGTTCGGTGCATATATATAGCCGA 59.600 41.667 20.86 20.86 43.90 5.54
906 1070 5.037385 CACCTGAGTGTCTATGTATGTTCG 58.963 45.833 0.00 0.00 39.30 3.95
907 1071 4.806247 GCACCTGAGTGTCTATGTATGTTC 59.194 45.833 0.00 0.00 46.35 3.18
908 1072 4.222810 TGCACCTGAGTGTCTATGTATGTT 59.777 41.667 0.00 0.00 46.35 2.71
918 1088 1.670406 CCTGCTGCACCTGAGTGTC 60.670 63.158 0.00 0.00 46.35 3.67
921 1091 0.322975 CTAACCTGCTGCACCTGAGT 59.677 55.000 0.00 0.00 0.00 3.41
960 1133 1.889454 CGCTCTGCTCCTCTCAACT 59.111 57.895 0.00 0.00 0.00 3.16
980 1153 1.966451 CCTTCTCCACACCCGTTGC 60.966 63.158 0.00 0.00 0.00 4.17
981 1154 1.966451 GCCTTCTCCACACCCGTTG 60.966 63.158 0.00 0.00 0.00 4.10
988 1161 1.067295 AACCTCATGCCTTCTCCACA 58.933 50.000 0.00 0.00 0.00 4.17
1008 1181 0.464554 GCCTCACAATCCCACCTAGC 60.465 60.000 0.00 0.00 0.00 3.42
1013 1186 1.270550 CAACAAGCCTCACAATCCCAC 59.729 52.381 0.00 0.00 0.00 4.61
1080 1253 3.260884 TGACAGATGACTTACCAACTCCC 59.739 47.826 0.00 0.00 0.00 4.30
1147 1320 2.074576 CAGAGCACACTCATCACCAAG 58.925 52.381 0.00 0.00 46.09 3.61
1151 1324 3.397482 AGTTTCAGAGCACACTCATCAC 58.603 45.455 0.00 0.00 46.09 3.06
1161 1334 5.643379 AGAACAAAACAAGTTTCAGAGCA 57.357 34.783 0.00 0.00 31.45 4.26
1163 1336 6.308766 CCACAAGAACAAAACAAGTTTCAGAG 59.691 38.462 0.00 0.00 31.45 3.35
1327 1505 8.710980 AGAGGCTTTCTTCTAGCTAGCTATAGC 61.711 44.444 24.36 21.41 43.46 2.97
1329 1507 6.548321 AGAGGCTTTCTTCTAGCTAGCTATA 58.452 40.000 24.36 15.07 38.67 1.31
1330 1508 5.393866 AGAGGCTTTCTTCTAGCTAGCTAT 58.606 41.667 24.36 5.91 38.67 2.97
1354 1537 4.704103 AGCCAGAGCCCGGAGACA 62.704 66.667 0.73 0.00 41.25 3.41
1355 1538 3.844090 GAGCCAGAGCCCGGAGAC 61.844 72.222 0.73 0.00 41.25 3.36
1394 1579 2.094545 GCTTCCCCTGCTAACACATTTG 60.095 50.000 0.00 0.00 0.00 2.32
1402 1587 0.252696 TCCAGAGCTTCCCCTGCTAA 60.253 55.000 0.00 0.00 41.30 3.09
1403 1588 0.030705 ATCCAGAGCTTCCCCTGCTA 60.031 55.000 0.00 0.00 41.30 3.49
1419 1604 1.537638 TCTCGATCGCTAGCTGAATCC 59.462 52.381 13.93 5.35 0.00 3.01
1433 1618 2.869233 GCTGAGAGCTTCTTCTCGAT 57.131 50.000 0.00 0.00 45.26 3.59
1448 1633 0.944999 AGGAGGATTAGGGGAGCTGA 59.055 55.000 0.00 0.00 0.00 4.26
1455 1640 6.816616 AAGAAGTAAGAAGGAGGATTAGGG 57.183 41.667 0.00 0.00 0.00 3.53
1456 1641 8.983789 ACTAAAGAAGTAAGAAGGAGGATTAGG 58.016 37.037 0.00 0.00 36.36 2.69
1479 1664 7.012610 ACGCATACATACACACACATACTACTA 59.987 37.037 0.00 0.00 0.00 1.82
1492 1682 1.545614 CGCCGGACGCATACATACAC 61.546 60.000 5.05 0.00 37.30 2.90
1653 1856 7.201496 CCAAACGAATCCACATTACTACAGTAC 60.201 40.741 0.00 0.00 0.00 2.73
1654 1857 6.814644 CCAAACGAATCCACATTACTACAGTA 59.185 38.462 0.00 0.00 0.00 2.74
1655 1858 5.642063 CCAAACGAATCCACATTACTACAGT 59.358 40.000 0.00 0.00 0.00 3.55
1656 1859 5.642063 ACCAAACGAATCCACATTACTACAG 59.358 40.000 0.00 0.00 0.00 2.74
1657 1860 5.410132 CACCAAACGAATCCACATTACTACA 59.590 40.000 0.00 0.00 0.00 2.74
1658 1861 5.640357 TCACCAAACGAATCCACATTACTAC 59.360 40.000 0.00 0.00 0.00 2.73
1663 1866 3.888930 ACTTCACCAAACGAATCCACATT 59.111 39.130 0.00 0.00 0.00 2.71
1686 1889 4.018779 TCACTTACAGGGGAAATAACCAGG 60.019 45.833 0.00 0.00 0.00 4.45
1711 1914 5.410924 TGTTACAGTAGTGCATGATCACTC 58.589 41.667 8.99 0.00 45.32 3.51
1722 1925 8.746751 CATTACGATTGAGATGTTACAGTAGTG 58.253 37.037 0.00 0.00 0.00 2.74
1727 1930 7.254455 GGTTCCATTACGATTGAGATGTTACAG 60.254 40.741 0.00 0.00 0.00 2.74
1761 1964 2.048444 AACATATGCTGCTCAGTGGG 57.952 50.000 1.58 0.00 0.00 4.61
1795 1998 1.754803 TCGAACGGCCATAGAGACAAT 59.245 47.619 2.24 0.00 0.00 2.71
1798 2001 2.128035 CAATCGAACGGCCATAGAGAC 58.872 52.381 2.24 0.00 0.00 3.36
1842 2047 2.130395 CGAATGTGATCCATCGTGAGG 58.870 52.381 0.00 0.00 31.75 3.86
1855 2067 1.004610 CATAGAGCGTTGGCGAATGTG 60.005 52.381 2.48 0.00 46.35 3.21
1862 2074 2.522060 CGATCCATAGAGCGTTGGC 58.478 57.895 0.00 0.00 46.56 4.52
1868 2080 1.869767 CAAACTGCCGATCCATAGAGC 59.130 52.381 0.00 0.00 0.00 4.09
1869 2081 3.185246 ACAAACTGCCGATCCATAGAG 57.815 47.619 0.00 0.00 0.00 2.43
1870 2082 4.161565 AGTTACAAACTGCCGATCCATAGA 59.838 41.667 0.00 0.00 41.01 1.98
1883 2095 4.833380 TCTGAGAGGTGCTAGTTACAAACT 59.167 41.667 0.00 0.00 45.40 2.66
1884 2096 5.135508 TCTGAGAGGTGCTAGTTACAAAC 57.864 43.478 0.00 0.00 0.00 2.93
1886 2098 5.047943 GTCTTCTGAGAGGTGCTAGTTACAA 60.048 44.000 0.00 0.00 31.07 2.41
1888 2100 4.437659 CGTCTTCTGAGAGGTGCTAGTTAC 60.438 50.000 0.00 0.00 34.02 2.50
1889 2101 3.690139 CGTCTTCTGAGAGGTGCTAGTTA 59.310 47.826 0.00 0.00 34.02 2.24
1890 2102 2.490115 CGTCTTCTGAGAGGTGCTAGTT 59.510 50.000 0.00 0.00 34.02 2.24
1891 2103 2.088423 CGTCTTCTGAGAGGTGCTAGT 58.912 52.381 0.00 0.00 34.02 2.57
1892 2104 2.096819 GTCGTCTTCTGAGAGGTGCTAG 59.903 54.545 0.00 0.00 38.58 3.42
1893 2105 2.085320 GTCGTCTTCTGAGAGGTGCTA 58.915 52.381 0.00 0.00 38.58 3.49
1894 2106 0.885196 GTCGTCTTCTGAGAGGTGCT 59.115 55.000 0.00 0.00 38.58 4.40
1897 2109 1.203523 GCATGTCGTCTTCTGAGAGGT 59.796 52.381 0.00 0.00 38.58 3.85
1910 2122 1.213275 TGCATTTGCCTGCATGTCG 59.787 52.632 0.00 0.00 46.76 4.35
1917 2129 2.129607 GTCAAACAGTGCATTTGCCTG 58.870 47.619 15.17 15.17 41.71 4.85
1995 2211 0.037419 TGCAACAGTCGCTGATAGCA 60.037 50.000 12.77 14.17 42.58 3.49
1998 2214 1.398041 GCAATGCAACAGTCGCTGATA 59.602 47.619 12.77 0.00 35.18 2.15
2003 2219 2.502510 CCGCAATGCAACAGTCGC 60.503 61.111 5.91 0.00 0.00 5.19
2008 2224 1.175654 ATCATCACCGCAATGCAACA 58.824 45.000 5.91 0.00 0.00 3.33
2190 2409 4.805192 GTGAGCAGTTGAGCATTTCAAAAA 59.195 37.500 0.00 0.00 46.85 1.94
2191 2410 4.362279 GTGAGCAGTTGAGCATTTCAAAA 58.638 39.130 0.00 0.00 46.85 2.44
2192 2411 3.548616 CGTGAGCAGTTGAGCATTTCAAA 60.549 43.478 0.00 0.00 46.85 2.69
2193 2412 2.031769 CGTGAGCAGTTGAGCATTTCAA 60.032 45.455 0.00 0.00 43.40 2.69
2194 2413 1.532437 CGTGAGCAGTTGAGCATTTCA 59.468 47.619 0.00 0.00 36.85 2.69
2195 2414 1.800586 TCGTGAGCAGTTGAGCATTTC 59.199 47.619 0.00 0.00 36.85 2.17
2196 2415 1.802960 CTCGTGAGCAGTTGAGCATTT 59.197 47.619 0.00 0.00 36.85 2.32
2197 2416 1.001293 TCTCGTGAGCAGTTGAGCATT 59.999 47.619 0.00 0.00 36.85 3.56
2198 2417 0.605083 TCTCGTGAGCAGTTGAGCAT 59.395 50.000 0.00 0.00 36.85 3.79
2199 2418 0.319040 GTCTCGTGAGCAGTTGAGCA 60.319 55.000 0.00 0.00 36.85 4.26
2200 2419 0.319040 TGTCTCGTGAGCAGTTGAGC 60.319 55.000 0.00 0.00 0.00 4.26
2201 2420 1.000827 AGTGTCTCGTGAGCAGTTGAG 60.001 52.381 0.00 0.00 0.00 3.02
2202 2421 1.032794 AGTGTCTCGTGAGCAGTTGA 58.967 50.000 0.00 0.00 0.00 3.18
2203 2422 1.858091 AAGTGTCTCGTGAGCAGTTG 58.142 50.000 11.15 0.00 31.67 3.16
2204 2423 3.728076 TTAAGTGTCTCGTGAGCAGTT 57.272 42.857 14.38 14.38 34.71 3.16
2205 2424 3.728076 TTTAAGTGTCTCGTGAGCAGT 57.272 42.857 0.00 0.00 0.00 4.40
2206 2425 6.706055 TTAATTTAAGTGTCTCGTGAGCAG 57.294 37.500 0.00 0.00 0.00 4.24
2207 2426 6.147164 CCTTTAATTTAAGTGTCTCGTGAGCA 59.853 38.462 3.70 0.00 0.00 4.26
2208 2427 6.147328 ACCTTTAATTTAAGTGTCTCGTGAGC 59.853 38.462 3.70 0.00 0.00 4.26
2209 2428 7.599245 AGACCTTTAATTTAAGTGTCTCGTGAG 59.401 37.037 16.15 0.00 33.91 3.51
2210 2429 7.439381 AGACCTTTAATTTAAGTGTCTCGTGA 58.561 34.615 16.15 0.00 33.91 4.35
2211 2430 7.653767 AGACCTTTAATTTAAGTGTCTCGTG 57.346 36.000 16.15 0.00 33.91 4.35
2212 2431 7.929785 TGAAGACCTTTAATTTAAGTGTCTCGT 59.070 33.333 19.47 11.15 36.00 4.18
2213 2432 8.306680 TGAAGACCTTTAATTTAAGTGTCTCG 57.693 34.615 19.47 3.06 36.00 4.04
2216 2435 9.989869 GCTATGAAGACCTTTAATTTAAGTGTC 57.010 33.333 13.44 13.44 0.00 3.67
2217 2436 9.740710 AGCTATGAAGACCTTTAATTTAAGTGT 57.259 29.630 3.70 1.70 0.00 3.55
2221 2440 9.614792 GGAGAGCTATGAAGACCTTTAATTTAA 57.385 33.333 0.00 0.00 0.00 1.52
2222 2441 8.993424 AGGAGAGCTATGAAGACCTTTAATTTA 58.007 33.333 0.00 0.00 0.00 1.40
2223 2442 7.866870 AGGAGAGCTATGAAGACCTTTAATTT 58.133 34.615 0.00 0.00 0.00 1.82
2224 2443 7.346960 AGAGGAGAGCTATGAAGACCTTTAATT 59.653 37.037 0.00 0.00 0.00 1.40
2225 2444 6.843861 AGAGGAGAGCTATGAAGACCTTTAAT 59.156 38.462 0.00 0.00 0.00 1.40
2226 2445 6.198639 AGAGGAGAGCTATGAAGACCTTTAA 58.801 40.000 0.00 0.00 0.00 1.52
2227 2446 5.772004 AGAGGAGAGCTATGAAGACCTTTA 58.228 41.667 0.00 0.00 0.00 1.85
2228 2447 4.619679 AGAGGAGAGCTATGAAGACCTTT 58.380 43.478 0.00 0.00 0.00 3.11
2229 2448 4.264373 AGAGGAGAGCTATGAAGACCTT 57.736 45.455 0.00 0.00 0.00 3.50
2230 2449 3.971468 AGAGGAGAGCTATGAAGACCT 57.029 47.619 0.00 0.00 0.00 3.85
2231 2450 4.277423 GTGTAGAGGAGAGCTATGAAGACC 59.723 50.000 0.00 0.00 0.00 3.85
2232 2451 4.277423 GGTGTAGAGGAGAGCTATGAAGAC 59.723 50.000 0.00 0.00 0.00 3.01
2233 2452 4.465886 GGTGTAGAGGAGAGCTATGAAGA 58.534 47.826 0.00 0.00 0.00 2.87
2234 2453 3.572255 GGGTGTAGAGGAGAGCTATGAAG 59.428 52.174 0.00 0.00 0.00 3.02
2235 2454 3.205507 AGGGTGTAGAGGAGAGCTATGAA 59.794 47.826 0.00 0.00 0.00 2.57
2236 2455 2.786445 AGGGTGTAGAGGAGAGCTATGA 59.214 50.000 0.00 0.00 0.00 2.15
2237 2456 3.237268 AGGGTGTAGAGGAGAGCTATG 57.763 52.381 0.00 0.00 0.00 2.23
2238 2457 4.604050 TGATAGGGTGTAGAGGAGAGCTAT 59.396 45.833 0.00 0.00 0.00 2.97
2239 2458 3.981375 TGATAGGGTGTAGAGGAGAGCTA 59.019 47.826 0.00 0.00 0.00 3.32
2240 2459 2.786445 TGATAGGGTGTAGAGGAGAGCT 59.214 50.000 0.00 0.00 0.00 4.09
2241 2460 3.153919 CTGATAGGGTGTAGAGGAGAGC 58.846 54.545 0.00 0.00 0.00 4.09
2242 2461 4.447138 ACTGATAGGGTGTAGAGGAGAG 57.553 50.000 0.00 0.00 0.00 3.20
2243 2462 5.611408 TGATACTGATAGGGTGTAGAGGAGA 59.389 44.000 0.00 0.00 0.00 3.71
2244 2463 5.882040 TGATACTGATAGGGTGTAGAGGAG 58.118 45.833 0.00 0.00 0.00 3.69
2245 2464 5.924769 TGATACTGATAGGGTGTAGAGGA 57.075 43.478 0.00 0.00 0.00 3.71
2246 2465 8.830915 ATATTGATACTGATAGGGTGTAGAGG 57.169 38.462 0.00 0.00 0.00 3.69
2250 2469 9.696572 GGAGTATATTGATACTGATAGGGTGTA 57.303 37.037 2.40 0.00 46.83 2.90
2251 2470 7.620094 GGGAGTATATTGATACTGATAGGGTGT 59.380 40.741 2.40 0.00 46.83 4.16
2252 2471 7.841729 AGGGAGTATATTGATACTGATAGGGTG 59.158 40.741 2.40 0.00 46.83 4.61
2253 2472 7.956357 AGGGAGTATATTGATACTGATAGGGT 58.044 38.462 2.40 0.00 46.83 4.34
2254 2473 7.507616 GGAGGGAGTATATTGATACTGATAGGG 59.492 44.444 2.40 0.00 46.83 3.53
2255 2474 7.229707 CGGAGGGAGTATATTGATACTGATAGG 59.770 44.444 2.40 0.00 46.83 2.57
2256 2475 7.776030 ACGGAGGGAGTATATTGATACTGATAG 59.224 40.741 2.40 0.00 46.83 2.08
2257 2476 7.640313 ACGGAGGGAGTATATTGATACTGATA 58.360 38.462 2.40 0.00 46.83 2.15
2258 2477 6.494952 ACGGAGGGAGTATATTGATACTGAT 58.505 40.000 2.40 0.00 46.83 2.90
2259 2478 5.888901 ACGGAGGGAGTATATTGATACTGA 58.111 41.667 2.40 0.00 46.83 3.41
2260 2479 5.125739 GGACGGAGGGAGTATATTGATACTG 59.874 48.000 2.40 0.00 46.83 2.74
2262 2481 5.014858 TGGACGGAGGGAGTATATTGATAC 58.985 45.833 0.00 0.00 38.63 2.24
2263 2482 5.265290 TGGACGGAGGGAGTATATTGATA 57.735 43.478 0.00 0.00 0.00 2.15
2264 2483 4.127918 TGGACGGAGGGAGTATATTGAT 57.872 45.455 0.00 0.00 0.00 2.57
2265 2484 3.605726 TGGACGGAGGGAGTATATTGA 57.394 47.619 0.00 0.00 0.00 2.57
2266 2485 4.891992 ATTGGACGGAGGGAGTATATTG 57.108 45.455 0.00 0.00 0.00 1.90
2267 2486 8.855804 ATATTATTGGACGGAGGGAGTATATT 57.144 34.615 0.00 0.00 0.00 1.28
2268 2487 9.947189 TTATATTATTGGACGGAGGGAGTATAT 57.053 33.333 0.00 0.00 0.00 0.86
2269 2488 9.772605 TTTATATTATTGGACGGAGGGAGTATA 57.227 33.333 0.00 0.00 0.00 1.47
2270 2489 8.674925 TTTATATTATTGGACGGAGGGAGTAT 57.325 34.615 0.00 0.00 0.00 2.12
2271 2490 8.495160 TTTTATATTATTGGACGGAGGGAGTA 57.505 34.615 0.00 0.00 0.00 2.59
2272 2491 7.383156 TTTTATATTATTGGACGGAGGGAGT 57.617 36.000 0.00 0.00 0.00 3.85
2273 2492 7.095355 CGTTTTTATATTATTGGACGGAGGGAG 60.095 40.741 0.00 0.00 0.00 4.30
2274 2493 6.707161 CGTTTTTATATTATTGGACGGAGGGA 59.293 38.462 0.00 0.00 0.00 4.20
2275 2494 6.484308 ACGTTTTTATATTATTGGACGGAGGG 59.516 38.462 0.00 0.00 33.95 4.30
2276 2495 7.486802 ACGTTTTTATATTATTGGACGGAGG 57.513 36.000 0.00 0.00 33.95 4.30
2277 2496 9.777575 AAAACGTTTTTATATTATTGGACGGAG 57.222 29.630 20.26 0.00 33.95 4.63
2291 2510 9.925268 CTAGTGTAGTGTCAAAAACGTTTTTAT 57.075 29.630 32.12 19.76 38.23 1.40
2292 2511 8.934825 ACTAGTGTAGTGTCAAAAACGTTTTTA 58.065 29.630 32.12 18.43 36.61 1.52
2293 2512 7.809665 ACTAGTGTAGTGTCAAAAACGTTTTT 58.190 30.769 28.62 28.62 37.99 1.94
2294 2513 7.368480 ACTAGTGTAGTGTCAAAAACGTTTT 57.632 32.000 20.26 20.26 37.69 2.43
2295 2514 6.973229 ACTAGTGTAGTGTCAAAAACGTTT 57.027 33.333 7.96 7.96 37.69 3.60
2296 2515 6.476706 GGTACTAGTGTAGTGTCAAAAACGTT 59.523 38.462 5.39 0.00 39.81 3.99
2297 2516 5.979517 GGTACTAGTGTAGTGTCAAAAACGT 59.020 40.000 5.39 0.00 39.81 3.99
2298 2517 5.978919 TGGTACTAGTGTAGTGTCAAAAACG 59.021 40.000 5.39 0.00 39.81 3.60


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

AutoCloner maintained by Alex Coulton.