Multiple sequence alignment - TraesCS5D01G341400

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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 TraesCS5D01G341400 chr5D 100.000 5987 0 0 1 5987 429708777 429714763 0.000000e+00 11057.0
1 TraesCS5D01G341400 chr5A 92.468 1872 76 36 3742 5571 545563098 545564946 0.000000e+00 2615.0
2 TraesCS5D01G341400 chr5A 94.494 1017 36 10 2730 3738 545562015 545563019 0.000000e+00 1550.0
3 TraesCS5D01G341400 chr5A 87.805 1025 80 25 342 1345 545559607 545560607 0.000000e+00 1158.0
4 TraesCS5D01G341400 chr5A 95.745 611 24 2 2008 2617 545561408 545562017 0.000000e+00 983.0
5 TraesCS5D01G341400 chr5A 93.867 375 14 5 5613 5987 545564938 545565303 1.880000e-154 556.0
6 TraesCS5D01G341400 chr5A 86.837 509 43 17 1346 1841 545560911 545561408 1.130000e-151 547.0
7 TraesCS5D01G341400 chr5B 93.720 1672 71 11 2008 3662 518956270 518957924 0.000000e+00 2475.0
8 TraesCS5D01G341400 chr5B 95.149 1340 49 8 2 1337 518954436 518955763 0.000000e+00 2100.0
9 TraesCS5D01G341400 chr5B 94.951 1327 51 9 3816 5134 518958184 518959502 0.000000e+00 2065.0
10 TraesCS5D01G341400 chr5B 89.978 449 16 9 5559 5987 518959953 518960392 2.440000e-153 553.0
11 TraesCS5D01G341400 chr5B 91.765 340 22 5 1371 1708 518955763 518956098 9.090000e-128 468.0
12 TraesCS5D01G341400 chr5B 80.098 407 36 23 5135 5507 518959558 518959953 1.660000e-65 261.0
13 TraesCS5D01G341400 chr5B 95.833 144 6 0 1705 1848 518956134 518956277 3.610000e-57 233.0
14 TraesCS5D01G341400 chr5B 97.321 112 3 0 3742 3853 518958034 518958145 2.200000e-44 191.0
15 TraesCS5D01G341400 chr5B 100.000 33 0 0 3709 3741 518957925 518957957 1.800000e-05 62.1
16 TraesCS5D01G341400 chr5B 100.000 30 0 0 5177 5206 518959508 518959537 8.380000e-04 56.5
17 TraesCS5D01G341400 chr6B 91.111 90 8 0 3646 3735 188192924 188192835 8.150000e-24 122.0
18 TraesCS5D01G341400 chr6A 92.405 79 5 1 3645 3723 123539086 123539009 1.760000e-20 111.0
19 TraesCS5D01G341400 chr6D 85.586 111 5 6 3624 3724 102470372 102470263 8.210000e-19 106.0
20 TraesCS5D01G341400 chr2B 85.714 91 13 0 3621 3711 416507048 416507138 4.940000e-16 97.1
21 TraesCS5D01G341400 chr4D 83.784 111 3 3 1903 2008 57063339 57063439 2.300000e-14 91.6
22 TraesCS5D01G341400 chr4A 84.314 102 4 6 1903 2004 731251020 731250931 8.260000e-14 89.8
23 TraesCS5D01G341400 chr4B 97.059 34 1 0 3677 3710 413818764 413818797 2.330000e-04 58.4
24 TraesCS5D01G341400 chr3D 100.000 29 0 0 3624 3652 595524321 595524293 3.000000e-03 54.7


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 TraesCS5D01G341400 chr5D 429708777 429714763 5986 False 11057.000000 11057 100.000000 1 5987 1 chr5D.!!$F1 5986
1 TraesCS5D01G341400 chr5A 545559607 545565303 5696 False 1234.833333 2615 91.869333 342 5987 6 chr5A.!!$F1 5645
2 TraesCS5D01G341400 chr5B 518954436 518960392 5956 False 846.460000 2475 93.881500 2 5987 10 chr5B.!!$F1 5985

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
80 81 1.198767 CCATTGCACACACAAACACG 58.801 50.0 0.00 0.0 32.27 4.49 F
1873 2264 0.107703 CGGAGCCAGCATCCTAACAA 60.108 55.0 0.00 0.0 34.45 2.83 F
2004 2395 0.041833 TCCTCAACTAGCTCTGCCCT 59.958 55.0 0.00 0.0 0.00 5.19 F
2007 2398 0.615331 TCAACTAGCTCTGCCCTTGG 59.385 55.0 0.00 0.0 0.00 3.61 F
2854 3255 0.894184 AACTTGAGACGGCGAGGAGA 60.894 55.0 16.62 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2376 0.041833 AGGGCAGAGCTAGTTGAGGA 59.958 55.000 0.00 0.00 0.00 3.71 R
3527 3930 0.245539 AGCAGCCATTCATTGTGCAC 59.754 50.000 10.75 10.75 36.57 4.57 R
4154 4716 7.290061 AGGATAAAATCTAACCAGCAATAGCA 58.710 34.615 0.00 0.00 45.49 3.49 R
4241 4803 2.211250 AGCACTGCTGGAACATGAAT 57.789 45.000 1.67 0.00 37.57 2.57 R
5010 5579 0.044092 TACTGGATGCTCCCCCTCAA 59.956 55.000 0.50 0.00 35.03 3.02 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
43 44 3.463944 CGGTCAGGTGGGTATTATGAAC 58.536 50.000 0.00 0.00 0.00 3.18
71 72 2.798976 ACATTGTGTCCATTGCACAC 57.201 45.000 3.82 3.82 45.20 3.82
77 78 2.192624 GTGTCCATTGCACACACAAAC 58.807 47.619 5.98 0.00 43.20 2.93
80 81 1.198767 CCATTGCACACACAAACACG 58.801 50.000 0.00 0.00 32.27 4.49
133 134 7.175797 AGCCTAGTTGCTACCTTATTTCTTTT 58.824 34.615 0.00 0.00 40.56 2.27
135 136 7.337184 GCCTAGTTGCTACCTTATTTCTTTTCT 59.663 37.037 0.00 0.00 0.00 2.52
136 137 9.232473 CCTAGTTGCTACCTTATTTCTTTTCTT 57.768 33.333 0.00 0.00 0.00 2.52
138 139 8.465273 AGTTGCTACCTTATTTCTTTTCTTGT 57.535 30.769 0.00 0.00 0.00 3.16
139 140 8.914011 AGTTGCTACCTTATTTCTTTTCTTGTT 58.086 29.630 0.00 0.00 0.00 2.83
140 141 9.181805 GTTGCTACCTTATTTCTTTTCTTGTTC 57.818 33.333 0.00 0.00 0.00 3.18
141 142 7.581476 TGCTACCTTATTTCTTTTCTTGTTCG 58.419 34.615 0.00 0.00 0.00 3.95
177 178 6.101734 TCTCATCTCCATTAGCTGGGTTAATT 59.898 38.462 0.00 0.00 45.98 1.40
180 181 5.826643 TCTCCATTAGCTGGGTTAATTTGT 58.173 37.500 0.00 0.00 45.98 2.83
193 194 8.570068 TGGGTTAATTTGTATGTCTAAAGGTC 57.430 34.615 0.00 0.00 0.00 3.85
198 199 7.923414 AATTTGTATGTCTAAAGGTCTGTCC 57.077 36.000 0.00 0.00 0.00 4.02
200 201 4.338012 TGTATGTCTAAAGGTCTGTCCGA 58.662 43.478 0.00 0.00 41.99 4.55
223 224 7.653311 CCGACATCTACATCAATAAATGACAGA 59.347 37.037 0.00 0.00 41.93 3.41
239 240 1.548269 ACAGACAGAGTGCTAGAAGCC 59.452 52.381 0.00 0.00 41.51 4.35
315 316 3.890756 CCCAATGCAATGTATAGAGGCAA 59.109 43.478 0.21 0.00 38.08 4.52
615 619 7.823745 ATGTGTAGTCAGAACAATTTTTCCT 57.176 32.000 0.68 0.00 0.00 3.36
945 993 6.257630 GCACAGTAAAATCATCTTCTCCTCTC 59.742 42.308 0.00 0.00 0.00 3.20
952 1000 5.919348 ATCATCTTCTCCTCTCTCTCTCT 57.081 43.478 0.00 0.00 0.00 3.10
1248 1296 3.329386 TCTCCTTCTTGATTTCTGTGCG 58.671 45.455 0.00 0.00 0.00 5.34
1268 1316 1.473434 GCGAATTTGAGATCCCGACCT 60.473 52.381 0.00 0.00 0.00 3.85
1271 1319 3.678806 CGAATTTGAGATCCCGACCTTGA 60.679 47.826 0.00 0.00 0.00 3.02
1333 1381 1.984026 CCATTGGTGGGCTGGTTCC 60.984 63.158 0.00 0.00 42.11 3.62
1345 1393 3.109928 GGCTGGTTCCTAGGGTTAGTTA 58.890 50.000 9.46 0.00 0.00 2.24
1346 1394 3.134262 GGCTGGTTCCTAGGGTTAGTTAG 59.866 52.174 9.46 0.35 0.00 2.34
1348 1396 4.031611 CTGGTTCCTAGGGTTAGTTAGCT 58.968 47.826 9.46 0.00 0.00 3.32
1349 1397 4.432316 TGGTTCCTAGGGTTAGTTAGCTT 58.568 43.478 9.46 0.00 0.00 3.74
1352 1701 6.501453 TGGTTCCTAGGGTTAGTTAGCTTTTA 59.499 38.462 9.46 0.00 0.00 1.52
1377 1726 6.749036 ACAAATACTAATACCTGAGGAGGG 57.251 41.667 4.99 0.00 44.84 4.30
1388 1737 4.913475 CCTGAGGAGGGTGCAAGGATTG 62.913 59.091 0.00 0.00 41.95 2.67
1407 1756 7.112779 AGGATTGGTGGTTAGTTCTTGATAAG 58.887 38.462 0.00 0.00 0.00 1.73
1418 1767 9.469807 GTTAGTTCTTGATAAGTGATGATCGAT 57.530 33.333 0.00 0.00 0.00 3.59
1437 1786 0.880278 TTTGCGCTCCACTCAGTCAC 60.880 55.000 9.73 0.00 0.00 3.67
1554 1903 4.184079 ACCAACTATCGTGGTTGAGTAC 57.816 45.455 13.11 0.00 44.58 2.73
1608 1957 6.012113 TCATGATTTGGTGTTCTCATTCCTT 58.988 36.000 0.00 0.00 0.00 3.36
1628 1977 4.202050 CCTTGGATGTAGCAGGCAAATAAC 60.202 45.833 0.00 0.00 0.00 1.89
1665 2014 8.166422 TCTAGAAAAACTTAAGCAAGAAAGGG 57.834 34.615 1.29 0.00 35.60 3.95
1686 2035 9.747898 AAAGGGTGAATTGAATACAATACACTA 57.252 29.630 0.00 0.00 44.67 2.74
1706 2055 8.870075 ACACTATATCATATGACTGCTGTAGA 57.130 34.615 7.78 0.00 0.00 2.59
1739 2130 7.176690 TCCTGAAATTTTACCTTCCAAGCTTAG 59.823 37.037 0.00 0.00 0.00 2.18
1766 2157 5.163652 CCATACTTTTTCTTTCACGGGATCC 60.164 44.000 1.92 1.92 0.00 3.36
1811 2202 4.978083 AAATGAAGCAATGACTAGCCAG 57.022 40.909 0.00 0.00 0.00 4.85
1841 2232 9.023962 TCTTGCTTTGATAAATTATTGGACTGT 57.976 29.630 0.00 0.00 0.00 3.55
1842 2233 9.643693 CTTGCTTTGATAAATTATTGGACTGTT 57.356 29.630 0.00 0.00 0.00 3.16
1843 2234 8.984891 TGCTTTGATAAATTATTGGACTGTTG 57.015 30.769 0.00 0.00 0.00 3.33
1844 2235 8.584157 TGCTTTGATAAATTATTGGACTGTTGT 58.416 29.630 0.00 0.00 0.00 3.32
1845 2236 9.423061 GCTTTGATAAATTATTGGACTGTTGTT 57.577 29.630 0.00 0.00 0.00 2.83
1849 2240 9.521841 TGATAAATTATTGGACTGTTGTTACCA 57.478 29.630 0.00 0.00 0.00 3.25
1851 2242 7.833285 AAATTATTGGACTGTTGTTACCAGT 57.167 32.000 0.00 0.00 45.52 4.00
1852 2243 6.817765 ATTATTGGACTGTTGTTACCAGTG 57.182 37.500 0.00 0.00 43.00 3.66
1853 2244 2.631160 TGGACTGTTGTTACCAGTGG 57.369 50.000 7.91 7.91 43.00 4.00
1854 2245 1.235724 GGACTGTTGTTACCAGTGGC 58.764 55.000 9.78 0.00 43.00 5.01
1855 2246 0.865769 GACTGTTGTTACCAGTGGCG 59.134 55.000 9.78 0.00 43.00 5.69
1856 2247 0.534203 ACTGTTGTTACCAGTGGCGG 60.534 55.000 9.78 0.00 41.47 6.13
1857 2248 0.250124 CTGTTGTTACCAGTGGCGGA 60.250 55.000 9.78 0.00 0.00 5.54
1858 2249 0.250124 TGTTGTTACCAGTGGCGGAG 60.250 55.000 9.78 0.00 0.00 4.63
1871 2262 4.445699 CGGAGCCAGCATCCTAAC 57.554 61.111 0.00 0.00 34.45 2.34
1872 2263 1.522092 CGGAGCCAGCATCCTAACA 59.478 57.895 0.00 0.00 34.45 2.41
1873 2264 0.107703 CGGAGCCAGCATCCTAACAA 60.108 55.000 0.00 0.00 34.45 2.83
1874 2265 1.475751 CGGAGCCAGCATCCTAACAAT 60.476 52.381 0.00 0.00 34.45 2.71
1875 2266 1.952296 GGAGCCAGCATCCTAACAATG 59.048 52.381 0.00 0.00 33.77 2.82
1876 2267 1.952296 GAGCCAGCATCCTAACAATGG 59.048 52.381 0.00 0.00 0.00 3.16
1877 2268 1.035139 GCCAGCATCCTAACAATGGG 58.965 55.000 0.00 0.00 0.00 4.00
1878 2269 1.686115 GCCAGCATCCTAACAATGGGT 60.686 52.381 0.00 0.00 0.00 4.51
1879 2270 2.026641 CCAGCATCCTAACAATGGGTG 58.973 52.381 0.00 0.00 38.66 4.61
1880 2271 2.621407 CCAGCATCCTAACAATGGGTGT 60.621 50.000 0.00 0.00 44.64 4.16
1881 2272 3.371487 CCAGCATCCTAACAATGGGTGTA 60.371 47.826 0.00 0.00 40.60 2.90
1882 2273 3.627577 CAGCATCCTAACAATGGGTGTAC 59.372 47.826 0.00 0.00 40.60 2.90
1883 2274 3.265737 AGCATCCTAACAATGGGTGTACA 59.734 43.478 0.00 0.00 40.60 2.90
1884 2275 4.079787 AGCATCCTAACAATGGGTGTACAT 60.080 41.667 0.00 0.00 40.60 2.29
1885 2276 5.131977 AGCATCCTAACAATGGGTGTACATA 59.868 40.000 0.00 0.00 40.60 2.29
1886 2277 5.470098 GCATCCTAACAATGGGTGTACATAG 59.530 44.000 0.00 0.00 40.60 2.23
1887 2278 5.623956 TCCTAACAATGGGTGTACATAGG 57.376 43.478 0.00 3.67 40.60 2.57
1888 2279 5.034200 TCCTAACAATGGGTGTACATAGGT 58.966 41.667 12.43 0.00 40.60 3.08
1889 2280 5.129815 TCCTAACAATGGGTGTACATAGGTC 59.870 44.000 12.43 0.00 40.60 3.85
1890 2281 4.919774 AACAATGGGTGTACATAGGTCA 57.080 40.909 0.00 0.00 40.60 4.02
1891 2282 4.216411 ACAATGGGTGTACATAGGTCAC 57.784 45.455 0.00 0.00 39.29 3.67
1892 2283 3.844211 ACAATGGGTGTACATAGGTCACT 59.156 43.478 0.00 0.00 39.29 3.41
1893 2284 5.027460 ACAATGGGTGTACATAGGTCACTA 58.973 41.667 0.00 0.00 39.29 2.74
1894 2285 5.128827 ACAATGGGTGTACATAGGTCACTAG 59.871 44.000 0.00 0.00 39.29 2.57
1895 2286 4.596354 TGGGTGTACATAGGTCACTAGA 57.404 45.455 0.00 0.00 31.54 2.43
1896 2287 4.938028 TGGGTGTACATAGGTCACTAGAA 58.062 43.478 0.00 0.00 31.54 2.10
1897 2288 5.525484 TGGGTGTACATAGGTCACTAGAAT 58.475 41.667 0.00 0.00 31.54 2.40
1898 2289 5.597182 TGGGTGTACATAGGTCACTAGAATC 59.403 44.000 0.00 0.00 31.54 2.52
1899 2290 5.834204 GGGTGTACATAGGTCACTAGAATCT 59.166 44.000 0.00 0.00 31.54 2.40
1900 2291 6.324254 GGGTGTACATAGGTCACTAGAATCTT 59.676 42.308 0.00 0.00 31.54 2.40
1901 2292 7.504911 GGGTGTACATAGGTCACTAGAATCTTA 59.495 40.741 0.00 0.00 31.54 2.10
1902 2293 8.569641 GGTGTACATAGGTCACTAGAATCTTAG 58.430 40.741 0.00 0.00 31.54 2.18
1903 2294 9.122779 GTGTACATAGGTCACTAGAATCTTAGT 57.877 37.037 0.00 0.00 34.26 2.24
1904 2295 9.696572 TGTACATAGGTCACTAGAATCTTAGTT 57.303 33.333 0.00 0.00 31.64 2.24
1907 2298 9.877178 ACATAGGTCACTAGAATCTTAGTTTTG 57.123 33.333 0.00 0.00 31.64 2.44
1908 2299 9.877178 CATAGGTCACTAGAATCTTAGTTTTGT 57.123 33.333 0.00 0.00 31.64 2.83
1911 2302 9.877178 AGGTCACTAGAATCTTAGTTTTGTATG 57.123 33.333 0.00 0.00 31.64 2.39
1912 2303 9.654663 GGTCACTAGAATCTTAGTTTTGTATGT 57.345 33.333 0.00 0.00 31.64 2.29
1930 2321 9.674068 TTTGTATGTGAATTATACCTTAGCACA 57.326 29.630 0.00 0.00 38.86 4.57
1931 2322 8.657074 TGTATGTGAATTATACCTTAGCACAC 57.343 34.615 0.00 0.00 37.57 3.82
1932 2323 8.261522 TGTATGTGAATTATACCTTAGCACACA 58.738 33.333 0.00 0.00 37.57 3.72
1933 2324 9.104965 GTATGTGAATTATACCTTAGCACACAA 57.895 33.333 0.00 0.00 38.76 3.33
1934 2325 7.609760 TGTGAATTATACCTTAGCACACAAG 57.390 36.000 0.00 0.00 33.82 3.16
1935 2326 7.165485 TGTGAATTATACCTTAGCACACAAGT 58.835 34.615 0.00 0.00 33.82 3.16
1936 2327 7.663905 TGTGAATTATACCTTAGCACACAAGTT 59.336 33.333 0.00 0.00 33.82 2.66
1937 2328 8.512138 GTGAATTATACCTTAGCACACAAGTTT 58.488 33.333 0.00 0.00 0.00 2.66
1938 2329 9.073475 TGAATTATACCTTAGCACACAAGTTTT 57.927 29.630 0.00 0.00 0.00 2.43
1939 2330 9.908152 GAATTATACCTTAGCACACAAGTTTTT 57.092 29.630 0.00 0.00 0.00 1.94
1965 2356 5.930837 CCAAATAATGGGTGTACATTGGT 57.069 39.130 10.97 0.00 46.27 3.67
1966 2357 5.659463 CCAAATAATGGGTGTACATTGGTG 58.341 41.667 10.97 0.00 46.27 4.17
1967 2358 5.186797 CCAAATAATGGGTGTACATTGGTGT 59.813 40.000 10.97 0.00 46.27 4.16
1968 2359 6.378564 CCAAATAATGGGTGTACATTGGTGTA 59.621 38.462 10.97 0.00 46.27 2.90
1988 2379 3.806949 ACAAATGTACACCCATGTCCT 57.193 42.857 0.00 0.00 40.48 3.85
1989 2380 3.686016 ACAAATGTACACCCATGTCCTC 58.314 45.455 0.00 0.00 40.48 3.71
1990 2381 3.073798 ACAAATGTACACCCATGTCCTCA 59.926 43.478 0.00 0.00 40.48 3.86
1991 2382 4.078537 CAAATGTACACCCATGTCCTCAA 58.921 43.478 0.00 0.00 40.48 3.02
1992 2383 2.851263 TGTACACCCATGTCCTCAAC 57.149 50.000 0.00 0.00 40.48 3.18
1993 2384 2.334977 TGTACACCCATGTCCTCAACT 58.665 47.619 0.00 0.00 40.48 3.16
1994 2385 3.512496 TGTACACCCATGTCCTCAACTA 58.488 45.455 0.00 0.00 40.48 2.24
1995 2386 3.513912 TGTACACCCATGTCCTCAACTAG 59.486 47.826 0.00 0.00 40.48 2.57
1996 2387 1.279271 ACACCCATGTCCTCAACTAGC 59.721 52.381 0.00 0.00 31.55 3.42
1997 2388 1.556911 CACCCATGTCCTCAACTAGCT 59.443 52.381 0.00 0.00 0.00 3.32
1998 2389 1.834263 ACCCATGTCCTCAACTAGCTC 59.166 52.381 0.00 0.00 0.00 4.09
1999 2390 2.114616 CCCATGTCCTCAACTAGCTCT 58.885 52.381 0.00 0.00 0.00 4.09
2000 2391 2.158986 CCCATGTCCTCAACTAGCTCTG 60.159 54.545 0.00 0.00 0.00 3.35
2001 2392 2.548875 CATGTCCTCAACTAGCTCTGC 58.451 52.381 0.00 0.00 0.00 4.26
2002 2393 0.898320 TGTCCTCAACTAGCTCTGCC 59.102 55.000 0.00 0.00 0.00 4.85
2003 2394 0.176910 GTCCTCAACTAGCTCTGCCC 59.823 60.000 0.00 0.00 0.00 5.36
2004 2395 0.041833 TCCTCAACTAGCTCTGCCCT 59.958 55.000 0.00 0.00 0.00 5.19
2005 2396 0.908198 CCTCAACTAGCTCTGCCCTT 59.092 55.000 0.00 0.00 0.00 3.95
2006 2397 1.406614 CCTCAACTAGCTCTGCCCTTG 60.407 57.143 0.00 0.00 0.00 3.61
2007 2398 0.615331 TCAACTAGCTCTGCCCTTGG 59.385 55.000 0.00 0.00 0.00 3.61
2077 2468 7.201565 GGAACTTCATGTCTTACTATGCTGTTC 60.202 40.741 0.00 0.00 36.58 3.18
2116 2515 2.241941 TGGGCATTTCCTAGAGCATCAA 59.758 45.455 0.00 0.00 33.66 2.57
2210 2609 3.256631 ACGATGCAAAAGCAGAAGGAAAT 59.743 39.130 0.00 0.00 0.00 2.17
2268 2667 8.974408 CATTATCACAATATGAAATTGCACTGG 58.026 33.333 0.00 0.00 41.93 4.00
2369 2768 3.500680 TGGTAAGACATTTTTCTGGTCGC 59.499 43.478 0.00 0.00 36.68 5.19
2458 2857 1.654105 GAACATGCAGTAGTTCGGTCG 59.346 52.381 11.97 0.00 35.34 4.79
2548 2948 4.895889 TCCATTCCTGATGTACTGTAGGAG 59.104 45.833 10.84 3.75 40.21 3.69
2556 2956 5.965922 TGATGTACTGTAGGAGTGTCATTG 58.034 41.667 0.00 0.00 35.96 2.82
2566 2966 7.847096 TGTAGGAGTGTCATTGCTTTTATCTA 58.153 34.615 0.00 0.00 0.00 1.98
2688 3088 9.826574 TGCGTCCTTATTATTTAGTGTAAGATT 57.173 29.630 0.00 0.00 0.00 2.40
2721 3121 1.284491 TGCATTGGGAATACAGAGGCA 59.716 47.619 0.00 0.00 0.00 4.75
2728 3128 1.065126 GGAATACAGAGGCAGGCAGTT 60.065 52.381 0.00 0.00 0.00 3.16
2729 3129 2.284190 GAATACAGAGGCAGGCAGTTC 58.716 52.381 0.00 0.00 0.00 3.01
2731 3131 1.185618 TACAGAGGCAGGCAGTTCGT 61.186 55.000 0.00 0.00 0.00 3.85
2755 3155 4.201822 CGACAGTAAATGCCTTTAGCTTCC 60.202 45.833 0.00 0.00 44.23 3.46
2773 3174 2.370349 TCCCTCTCTCGTCACATCTTC 58.630 52.381 0.00 0.00 0.00 2.87
2774 3175 2.025793 TCCCTCTCTCGTCACATCTTCT 60.026 50.000 0.00 0.00 0.00 2.85
2775 3176 2.357637 CCCTCTCTCGTCACATCTTCTC 59.642 54.545 0.00 0.00 0.00 2.87
2776 3177 3.013219 CCTCTCTCGTCACATCTTCTCA 58.987 50.000 0.00 0.00 0.00 3.27
2829 3230 1.251251 GCTGGAGCCAACACTCATTT 58.749 50.000 0.00 0.00 38.50 2.32
2854 3255 0.894184 AACTTGAGACGGCGAGGAGA 60.894 55.000 16.62 0.00 0.00 3.71
2885 3286 3.869272 GTGATCGGGCGCTGCAAG 61.869 66.667 7.64 0.00 0.00 4.01
3039 3440 2.367202 TGGATCCGGCTTGTCCCTC 61.367 63.158 7.39 0.00 0.00 4.30
3164 3565 5.820947 ACAACGCTCCTTTTCTTCTTCTTTA 59.179 36.000 0.00 0.00 0.00 1.85
3386 3787 6.170506 AGGTTTTTACTGCACAATCGATCTA 58.829 36.000 0.00 0.00 0.00 1.98
3499 3901 8.072567 GTGATAATGCAATCAATCTGTCCTAAC 58.927 37.037 2.64 0.00 37.61 2.34
3503 3905 4.263462 TGCAATCAATCTGTCCTAACCTGT 60.263 41.667 0.00 0.00 0.00 4.00
3527 3930 7.448161 TGTTGCTAATAGGATGAATAATGGTGG 59.552 37.037 0.00 0.00 0.00 4.61
3622 4032 4.340666 TGAGCTCTTCATGTCAGGATAGAC 59.659 45.833 16.19 0.00 38.99 2.59
3905 4467 7.572759 CCATGTTAATATGTTATGTGGTCGAC 58.427 38.462 7.13 7.13 0.00 4.20
4154 4716 9.582431 CATGAAAAGCTTGAAAACTATGATGAT 57.418 29.630 0.00 0.00 0.00 2.45
4253 4815 8.945481 TTTTTATGCCATTATTCATGTTCCAG 57.055 30.769 0.00 0.00 0.00 3.86
4519 5082 4.843220 AGTAACGTATTGGTCCTATCGG 57.157 45.455 0.00 0.00 0.00 4.18
4585 5148 5.275067 TGCTGGCACAATTTTCTTTAGTT 57.725 34.783 0.00 0.00 38.70 2.24
4958 5523 5.227908 CGTTTCTTTCCAGAAGTAGTAGCA 58.772 41.667 0.00 0.00 40.28 3.49
4959 5524 5.869888 CGTTTCTTTCCAGAAGTAGTAGCAT 59.130 40.000 0.00 0.00 40.28 3.79
4987 5556 6.924060 AGCATAATGAACTATACAGACGAACC 59.076 38.462 0.00 0.00 0.00 3.62
5003 5572 0.188342 AACCTGGCTTGGTGTCCATT 59.812 50.000 3.70 0.00 40.73 3.16
5004 5573 0.540365 ACCTGGCTTGGTGTCCATTG 60.540 55.000 0.00 0.00 39.17 2.82
5005 5574 0.251297 CCTGGCTTGGTGTCCATTGA 60.251 55.000 0.00 0.00 31.53 2.57
5006 5575 1.171308 CTGGCTTGGTGTCCATTGAG 58.829 55.000 0.00 0.00 31.53 3.02
5007 5576 0.251297 TGGCTTGGTGTCCATTGAGG 60.251 55.000 0.00 0.00 39.47 3.86
5008 5577 1.598701 GGCTTGGTGTCCATTGAGGC 61.599 60.000 0.00 0.00 37.29 4.70
5009 5578 1.598701 GCTTGGTGTCCATTGAGGCC 61.599 60.000 0.00 0.00 37.29 5.19
5010 5579 0.038744 CTTGGTGTCCATTGAGGCCT 59.961 55.000 3.86 3.86 37.29 5.19
5022 5591 4.682714 AGGCCTTGAGGGGGAGCA 62.683 66.667 0.00 0.00 35.18 4.26
5043 5612 7.083062 AGCATCCAGTATATCCTTTGAATCA 57.917 36.000 0.00 0.00 0.00 2.57
5057 5629 2.161855 TGAATCATGGTGGCTGTTGAC 58.838 47.619 0.00 0.00 0.00 3.18
5074 5646 6.846283 GCTGTTGACGATAAGTTATGTAATGC 59.154 38.462 0.00 0.00 0.00 3.56
5101 5673 0.788995 CTCTTGCTGTCAGAACGCTG 59.211 55.000 3.32 0.00 43.67 5.18
5145 5772 5.122396 CCGTTCTTGGACTTTATTCTCCTTG 59.878 44.000 0.00 0.00 0.00 3.61
5234 5862 8.221766 CGACTCCTCATTTTTCTTTTGTAGTAC 58.778 37.037 0.00 0.00 0.00 2.73
5277 5916 5.450965 CGAATTGCTTTTATGGCAGATCCTT 60.451 40.000 0.00 0.00 40.90 3.36
5288 5927 2.290960 GGCAGATCCTTACCTGTTGGTT 60.291 50.000 0.00 0.00 46.05 3.67
5298 5937 3.795688 ACCTGTTGGTTCATCTCATGT 57.204 42.857 0.00 0.00 46.05 3.21
5299 5938 3.415212 ACCTGTTGGTTCATCTCATGTG 58.585 45.455 0.00 0.00 46.05 3.21
5300 5939 3.181440 ACCTGTTGGTTCATCTCATGTGT 60.181 43.478 0.00 0.00 46.05 3.72
5323 5962 2.700722 TTTTTGCCCAACAAGGAACC 57.299 45.000 0.00 0.00 40.06 3.62
5325 5964 1.118838 TTTGCCCAACAAGGAACCAG 58.881 50.000 0.00 0.00 40.06 4.00
5328 5967 1.179174 GCCCAACAAGGAACCAGGAC 61.179 60.000 0.00 0.00 41.22 3.85
5329 5968 0.889186 CCCAACAAGGAACCAGGACG 60.889 60.000 0.00 0.00 41.22 4.79
5334 5973 0.107831 CAAGGAACCAGGACGTTGGA 59.892 55.000 13.22 0.00 40.87 3.53
5335 5974 1.064825 AAGGAACCAGGACGTTGGAT 58.935 50.000 13.22 0.63 40.87 3.41
5336 5975 1.064825 AGGAACCAGGACGTTGGATT 58.935 50.000 13.22 3.94 40.87 3.01
5337 5976 1.165270 GGAACCAGGACGTTGGATTG 58.835 55.000 13.22 0.00 40.87 2.67
5338 5977 1.165270 GAACCAGGACGTTGGATTGG 58.835 55.000 13.22 8.01 40.87 3.16
5352 5991 1.549203 GATTGGTTGGCCTGTCACAT 58.451 50.000 3.32 0.00 35.27 3.21
5357 5996 2.235016 GGTTGGCCTGTCACATTGTAA 58.765 47.619 3.32 0.00 0.00 2.41
5364 6003 4.158394 GGCCTGTCACATTGTAAATCATGT 59.842 41.667 0.00 0.00 0.00 3.21
5365 6004 5.335127 GCCTGTCACATTGTAAATCATGTC 58.665 41.667 0.00 0.00 0.00 3.06
5367 6006 6.405065 GCCTGTCACATTGTAAATCATGTCAT 60.405 38.462 0.00 0.00 0.00 3.06
5368 6007 7.541162 CCTGTCACATTGTAAATCATGTCATT 58.459 34.615 0.00 0.00 0.00 2.57
5369 6008 8.030692 CCTGTCACATTGTAAATCATGTCATTT 58.969 33.333 0.00 0.00 0.00 2.32
5371 6010 9.838975 TGTCACATTGTAAATCATGTCATTTAC 57.161 29.630 17.20 17.20 44.49 2.01
5372 6011 8.998989 GTCACATTGTAAATCATGTCATTTACG 58.001 33.333 18.13 10.88 46.07 3.18
5373 6012 8.180920 TCACATTGTAAATCATGTCATTTACGG 58.819 33.333 18.13 14.29 46.07 4.02
5374 6013 8.180920 CACATTGTAAATCATGTCATTTACGGA 58.819 33.333 18.13 12.79 46.07 4.69
5375 6014 8.397906 ACATTGTAAATCATGTCATTTACGGAG 58.602 33.333 18.13 14.05 46.07 4.63
5394 6058 3.858238 GGAGTAGTTTCTATGCACGTGAC 59.142 47.826 22.23 11.46 0.00 3.67
5395 6059 4.380655 GGAGTAGTTTCTATGCACGTGACT 60.381 45.833 22.23 14.14 0.00 3.41
5403 6067 3.349006 GCACGTGACTGCCAGTGG 61.349 66.667 22.23 4.20 35.35 4.00
5425 6089 3.037549 TGGGTTTCAACTTGATGCCTTT 58.962 40.909 10.28 0.00 0.00 3.11
5428 6092 3.809279 GGTTTCAACTTGATGCCTTTTGG 59.191 43.478 0.00 0.00 44.18 3.28
5488 6156 7.734538 AAACGTGACAAACTTTTCATTGTAG 57.265 32.000 0.00 0.00 39.73 2.74
5489 6157 6.431198 ACGTGACAAACTTTTCATTGTAGT 57.569 33.333 0.00 0.00 39.73 2.73
5490 6158 7.542534 ACGTGACAAACTTTTCATTGTAGTA 57.457 32.000 0.00 0.00 39.73 1.82
5513 6181 6.696825 ATCAACGAATATGCAGTTATCTCG 57.303 37.500 0.00 2.11 0.00 4.04
5518 6186 3.577649 ATATGCAGTTATCTCGGTCCG 57.422 47.619 4.39 4.39 0.00 4.79
5569 6237 1.061887 ACACAAATATTCGCCGCGC 59.938 52.632 8.21 0.00 0.00 6.86
5572 6240 4.307908 AAATATTCGCCGCGCCGC 62.308 61.111 3.85 10.88 0.00 6.53
5712 6400 4.511636 GCTACTGCTCAGGTCAGC 57.488 61.111 1.66 3.75 40.13 4.26
5713 6401 1.518133 GCTACTGCTCAGGTCAGCG 60.518 63.158 1.66 0.00 42.92 5.18
5714 6402 1.886585 CTACTGCTCAGGTCAGCGT 59.113 57.895 1.66 0.00 42.92 5.07
5715 6403 0.179150 CTACTGCTCAGGTCAGCGTC 60.179 60.000 1.66 0.00 42.92 5.19
5716 6404 1.923227 TACTGCTCAGGTCAGCGTCG 61.923 60.000 1.66 0.00 42.92 5.12
5717 6405 3.978723 CTGCTCAGGTCAGCGTCGG 62.979 68.421 0.00 0.00 42.92 4.79
5833 6521 2.799371 CAGCGGTCGTAGAGGTCC 59.201 66.667 0.00 0.00 36.95 4.46
5926 6614 4.680237 TTGTCCTCCACGCTGGCG 62.680 66.667 13.56 13.56 46.03 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.049680 CCGCCACATTGATACATAAGTTACC 60.050 44.000 0.00 0.00 0.00 2.85
43 44 6.202379 TGCAATGGACACAATGTTTAATGTTG 59.798 34.615 0.00 0.00 30.07 3.33
98 99 6.894103 AGGTAGCAACTAGGCTTAGTAACTAA 59.106 38.462 9.17 0.00 42.71 2.24
101 102 5.595257 AGGTAGCAACTAGGCTTAGTAAC 57.405 43.478 9.17 4.63 42.71 2.50
133 134 3.231818 AGAGGAGGAAGAACGAACAAGA 58.768 45.455 0.00 0.00 0.00 3.02
135 136 2.963101 TGAGAGGAGGAAGAACGAACAA 59.037 45.455 0.00 0.00 0.00 2.83
136 137 2.594131 TGAGAGGAGGAAGAACGAACA 58.406 47.619 0.00 0.00 0.00 3.18
137 138 3.445805 AGATGAGAGGAGGAAGAACGAAC 59.554 47.826 0.00 0.00 0.00 3.95
138 139 3.697045 GAGATGAGAGGAGGAAGAACGAA 59.303 47.826 0.00 0.00 0.00 3.85
139 140 3.283751 GAGATGAGAGGAGGAAGAACGA 58.716 50.000 0.00 0.00 0.00 3.85
140 141 2.360801 GGAGATGAGAGGAGGAAGAACG 59.639 54.545 0.00 0.00 0.00 3.95
141 142 3.370104 TGGAGATGAGAGGAGGAAGAAC 58.630 50.000 0.00 0.00 0.00 3.01
177 178 4.768448 TCGGACAGACCTTTAGACATACAA 59.232 41.667 0.00 0.00 36.31 2.41
180 181 4.978083 GTCGGACAGACCTTTAGACATA 57.022 45.455 2.62 0.00 43.95 2.29
193 194 7.653311 TCATTTATTGATGTAGATGTCGGACAG 59.347 37.037 16.84 0.00 0.00 3.51
198 199 8.483218 GTCTGTCATTTATTGATGTAGATGTCG 58.517 37.037 0.00 0.00 36.54 4.35
200 201 9.322773 CTGTCTGTCATTTATTGATGTAGATGT 57.677 33.333 0.00 0.00 36.54 3.06
223 224 1.268283 GGGGGCTTCTAGCACTCTGT 61.268 60.000 0.45 0.00 43.33 3.41
257 258 6.150140 GCTTGCCTTATATAATCCTTCACCAG 59.850 42.308 0.00 0.00 0.00 4.00
315 316 3.132111 CCACTTGTGCCAAAAGTAAGGTT 59.868 43.478 0.00 0.00 35.70 3.50
581 585 9.990360 TTGTTCTGACTACACATAGATTTTGTA 57.010 29.630 0.00 0.00 32.23 2.41
656 660 9.594478 TTCTTTCGCTTGAACACTAATCATATA 57.406 29.630 0.00 0.00 0.00 0.86
778 793 7.867909 TGTGTATTTTCTGAGTCTGAGTACTTG 59.132 37.037 0.00 0.00 0.00 3.16
917 965 5.006165 GGAGAAGATGATTTTACTGTGCTCG 59.994 44.000 0.00 0.00 0.00 5.03
1248 1296 0.938008 GGTCGGGATCTCAAATTCGC 59.062 55.000 0.00 0.00 0.00 4.70
1268 1316 7.615365 ACCATATGTCCTAATCAAAGCTTTCAA 59.385 33.333 9.23 0.50 0.00 2.69
1271 1319 6.322201 CCACCATATGTCCTAATCAAAGCTTT 59.678 38.462 5.69 5.69 0.00 3.51
1352 1701 8.017251 ACCCTCCTCAGGTATTAGTATTTGTAT 58.983 37.037 0.00 0.00 38.30 2.29
1367 1716 1.277580 ATCCTTGCACCCTCCTCAGG 61.278 60.000 0.00 0.00 39.98 3.86
1373 1722 0.967380 CCACCAATCCTTGCACCCTC 60.967 60.000 0.00 0.00 0.00 4.30
1377 1726 2.514803 ACTAACCACCAATCCTTGCAC 58.485 47.619 0.00 0.00 0.00 4.57
1388 1737 7.103641 TCATCACTTATCAAGAACTAACCACC 58.896 38.462 0.00 0.00 0.00 4.61
1391 1740 7.921214 TCGATCATCACTTATCAAGAACTAACC 59.079 37.037 0.00 0.00 0.00 2.85
1398 1747 6.074142 CGCAAATCGATCATCACTTATCAAGA 60.074 38.462 0.00 0.00 41.67 3.02
1400 1749 5.558844 GCGCAAATCGATCATCACTTATCAA 60.559 40.000 0.30 0.00 41.67 2.57
1418 1767 0.880278 GTGACTGAGTGGAGCGCAAA 60.880 55.000 11.47 0.00 0.00 3.68
1459 1808 7.610580 AAATCTGAAGGGTCCAACAAAATAA 57.389 32.000 0.00 0.00 0.00 1.40
1460 1809 7.508977 AGAAAATCTGAAGGGTCCAACAAAATA 59.491 33.333 0.00 0.00 0.00 1.40
1461 1810 6.327365 AGAAAATCTGAAGGGTCCAACAAAAT 59.673 34.615 0.00 0.00 0.00 1.82
1462 1811 5.660864 AGAAAATCTGAAGGGTCCAACAAAA 59.339 36.000 0.00 0.00 0.00 2.44
1577 1926 8.408043 TGAGAACACCAAATCATGAAACTAAT 57.592 30.769 0.00 0.00 0.00 1.73
1608 1957 3.287222 GGTTATTTGCCTGCTACATCCA 58.713 45.455 0.00 0.00 0.00 3.41
1628 1977 7.653767 AAGTTTTTCTAGAGTGTATTGTCGG 57.346 36.000 0.00 0.00 0.00 4.79
1656 2005 9.573133 GTATTGTATTCAATTCACCCTTTCTTG 57.427 33.333 2.68 0.00 43.12 3.02
1686 2035 8.646004 ACAAGTTCTACAGCAGTCATATGATAT 58.354 33.333 9.02 0.00 0.00 1.63
1705 2054 7.652105 GGAAGGTAAAATTTCAGGAACAAGTTC 59.348 37.037 4.39 4.39 38.80 3.01
1706 2055 7.125053 TGGAAGGTAAAATTTCAGGAACAAGTT 59.875 33.333 0.00 0.00 0.00 2.66
1739 2130 5.239963 TCCCGTGAAAGAAAAAGTATGGAAC 59.760 40.000 0.00 0.00 0.00 3.62
1853 2244 1.889573 GTTAGGATGCTGGCTCCGC 60.890 63.158 0.00 0.00 37.88 5.54
1854 2245 0.107703 TTGTTAGGATGCTGGCTCCG 60.108 55.000 0.00 0.00 37.88 4.63
1855 2246 1.952296 CATTGTTAGGATGCTGGCTCC 59.048 52.381 0.00 0.00 0.00 4.70
1856 2247 1.952296 CCATTGTTAGGATGCTGGCTC 59.048 52.381 0.00 0.00 0.00 4.70
1857 2248 1.410648 CCCATTGTTAGGATGCTGGCT 60.411 52.381 0.00 0.00 0.00 4.75
1858 2249 1.035139 CCCATTGTTAGGATGCTGGC 58.965 55.000 0.00 0.00 0.00 4.85
1859 2250 2.026641 CACCCATTGTTAGGATGCTGG 58.973 52.381 0.00 0.00 0.00 4.85
1860 2251 2.726821 ACACCCATTGTTAGGATGCTG 58.273 47.619 0.00 0.00 33.09 4.41
1861 2252 3.265737 TGTACACCCATTGTTAGGATGCT 59.734 43.478 0.00 0.00 39.91 3.79
1862 2253 3.616219 TGTACACCCATTGTTAGGATGC 58.384 45.455 0.00 0.00 39.91 3.91
1863 2254 5.997746 CCTATGTACACCCATTGTTAGGATG 59.002 44.000 8.59 0.00 38.03 3.51
1864 2255 5.670361 ACCTATGTACACCCATTGTTAGGAT 59.330 40.000 17.69 4.09 38.03 3.24
1865 2256 5.034200 ACCTATGTACACCCATTGTTAGGA 58.966 41.667 17.69 0.00 38.03 2.94
1866 2257 5.104693 TGACCTATGTACACCCATTGTTAGG 60.105 44.000 11.62 11.62 40.23 2.69
1867 2258 5.815740 GTGACCTATGTACACCCATTGTTAG 59.184 44.000 0.00 0.00 39.91 2.34
1868 2259 5.486063 AGTGACCTATGTACACCCATTGTTA 59.514 40.000 0.00 0.00 39.91 2.41
1869 2260 4.288626 AGTGACCTATGTACACCCATTGTT 59.711 41.667 0.00 0.00 39.91 2.83
1870 2261 3.844211 AGTGACCTATGTACACCCATTGT 59.156 43.478 0.00 0.00 42.84 2.71
1871 2262 4.487714 AGTGACCTATGTACACCCATTG 57.512 45.455 0.00 0.00 35.47 2.82
1872 2263 5.525484 TCTAGTGACCTATGTACACCCATT 58.475 41.667 0.00 0.00 35.47 3.16
1873 2264 5.138758 TCTAGTGACCTATGTACACCCAT 57.861 43.478 0.00 0.00 35.47 4.00
1874 2265 4.596354 TCTAGTGACCTATGTACACCCA 57.404 45.455 0.00 0.00 35.47 4.51
1875 2266 5.834204 AGATTCTAGTGACCTATGTACACCC 59.166 44.000 0.00 0.00 35.47 4.61
1876 2267 6.963083 AGATTCTAGTGACCTATGTACACC 57.037 41.667 0.00 0.00 35.47 4.16
1877 2268 9.122779 ACTAAGATTCTAGTGACCTATGTACAC 57.877 37.037 0.00 0.00 30.76 2.90
1878 2269 9.696572 AACTAAGATTCTAGTGACCTATGTACA 57.303 33.333 0.00 0.00 32.35 2.90
1881 2272 9.877178 CAAAACTAAGATTCTAGTGACCTATGT 57.123 33.333 0.00 0.00 32.35 2.29
1882 2273 9.877178 ACAAAACTAAGATTCTAGTGACCTATG 57.123 33.333 0.00 0.00 32.35 2.23
1885 2276 9.877178 CATACAAAACTAAGATTCTAGTGACCT 57.123 33.333 0.00 0.00 32.35 3.85
1886 2277 9.654663 ACATACAAAACTAAGATTCTAGTGACC 57.345 33.333 0.00 0.00 32.35 4.02
1904 2295 9.674068 TGTGCTAAGGTATAATTCACATACAAA 57.326 29.630 0.00 0.00 31.67 2.83
1905 2296 9.104965 GTGTGCTAAGGTATAATTCACATACAA 57.895 33.333 0.00 0.00 35.75 2.41
1906 2297 8.261522 TGTGTGCTAAGGTATAATTCACATACA 58.738 33.333 0.00 0.00 35.75 2.29
1907 2298 8.657074 TGTGTGCTAAGGTATAATTCACATAC 57.343 34.615 0.00 0.00 35.75 2.39
1908 2299 9.325198 CTTGTGTGCTAAGGTATAATTCACATA 57.675 33.333 0.00 0.00 35.75 2.29
1909 2300 7.829211 ACTTGTGTGCTAAGGTATAATTCACAT 59.171 33.333 0.00 0.00 35.75 3.21
1910 2301 7.165485 ACTTGTGTGCTAAGGTATAATTCACA 58.835 34.615 0.00 0.00 0.00 3.58
1911 2302 7.611213 ACTTGTGTGCTAAGGTATAATTCAC 57.389 36.000 0.00 0.00 0.00 3.18
1912 2303 8.630054 AAACTTGTGTGCTAAGGTATAATTCA 57.370 30.769 0.00 0.00 0.00 2.57
1913 2304 9.908152 AAAAACTTGTGTGCTAAGGTATAATTC 57.092 29.630 0.00 0.00 0.00 2.17
1937 2328 6.174720 TGTACACCCATTATTTGGCAAAAA 57.825 33.333 17.70 12.47 44.97 1.94
1938 2329 5.808366 TGTACACCCATTATTTGGCAAAA 57.192 34.783 17.70 1.21 44.97 2.44
1939 2330 6.169094 CAATGTACACCCATTATTTGGCAAA 58.831 36.000 16.01 16.01 44.97 3.68
1940 2331 5.337894 CCAATGTACACCCATTATTTGGCAA 60.338 40.000 0.00 0.00 44.97 4.52
1941 2332 4.161189 CCAATGTACACCCATTATTTGGCA 59.839 41.667 0.00 0.00 44.97 4.92
1942 2333 4.161377 ACCAATGTACACCCATTATTTGGC 59.839 41.667 16.75 0.00 44.97 4.52
1943 2334 5.186797 ACACCAATGTACACCCATTATTTGG 59.813 40.000 15.70 15.70 40.60 3.28
1944 2335 6.279513 ACACCAATGTACACCCATTATTTG 57.720 37.500 0.00 0.00 37.26 2.32
1967 2358 4.287326 TGAGGACATGGGTGTACATTTGTA 59.713 41.667 0.00 0.00 41.96 2.41
1968 2359 3.073798 TGAGGACATGGGTGTACATTTGT 59.926 43.478 0.00 0.67 41.96 2.83
1969 2360 3.684908 TGAGGACATGGGTGTACATTTG 58.315 45.455 0.00 0.00 41.96 2.32
1970 2361 4.079253 GTTGAGGACATGGGTGTACATTT 58.921 43.478 0.00 0.00 41.96 2.32
1971 2362 3.330701 AGTTGAGGACATGGGTGTACATT 59.669 43.478 0.00 0.00 41.96 2.71
1972 2363 2.912956 AGTTGAGGACATGGGTGTACAT 59.087 45.455 0.00 0.00 41.96 2.29
1973 2364 2.334977 AGTTGAGGACATGGGTGTACA 58.665 47.619 0.00 0.00 41.96 2.90
1974 2365 3.679083 GCTAGTTGAGGACATGGGTGTAC 60.679 52.174 0.00 0.00 39.09 2.90
1975 2366 2.500098 GCTAGTTGAGGACATGGGTGTA 59.500 50.000 0.00 0.00 39.09 2.90
1976 2367 1.279271 GCTAGTTGAGGACATGGGTGT 59.721 52.381 0.00 0.00 42.49 4.16
1977 2368 1.556911 AGCTAGTTGAGGACATGGGTG 59.443 52.381 0.00 0.00 0.00 4.61
1978 2369 1.834263 GAGCTAGTTGAGGACATGGGT 59.166 52.381 0.00 0.00 0.00 4.51
1979 2370 2.114616 AGAGCTAGTTGAGGACATGGG 58.885 52.381 0.00 0.00 0.00 4.00
1980 2371 2.741228 GCAGAGCTAGTTGAGGACATGG 60.741 54.545 0.00 0.00 0.00 3.66
1981 2372 2.548875 GCAGAGCTAGTTGAGGACATG 58.451 52.381 0.00 0.00 0.00 3.21
1982 2373 1.484240 GGCAGAGCTAGTTGAGGACAT 59.516 52.381 0.00 0.00 0.00 3.06
1983 2374 0.898320 GGCAGAGCTAGTTGAGGACA 59.102 55.000 0.00 0.00 0.00 4.02
1984 2375 0.176910 GGGCAGAGCTAGTTGAGGAC 59.823 60.000 0.00 0.00 0.00 3.85
1985 2376 0.041833 AGGGCAGAGCTAGTTGAGGA 59.958 55.000 0.00 0.00 0.00 3.71
1986 2377 0.908198 AAGGGCAGAGCTAGTTGAGG 59.092 55.000 0.00 0.00 0.00 3.86
1987 2378 1.406614 CCAAGGGCAGAGCTAGTTGAG 60.407 57.143 0.00 0.00 0.00 3.02
1988 2379 0.615331 CCAAGGGCAGAGCTAGTTGA 59.385 55.000 0.00 0.00 0.00 3.18
1989 2380 3.165606 CCAAGGGCAGAGCTAGTTG 57.834 57.895 0.00 0.00 0.00 3.16
2001 2392 2.014068 GCAGTTAGTAGCAGCCAAGGG 61.014 57.143 0.00 0.00 0.00 3.95
2002 2393 1.373570 GCAGTTAGTAGCAGCCAAGG 58.626 55.000 0.00 0.00 0.00 3.61
2003 2394 1.373570 GGCAGTTAGTAGCAGCCAAG 58.626 55.000 14.37 0.00 44.59 3.61
2004 2395 3.551259 GGCAGTTAGTAGCAGCCAA 57.449 52.632 14.37 0.00 44.59 4.52
2006 2397 0.827368 AGAGGCAGTTAGTAGCAGCC 59.173 55.000 11.81 11.81 45.54 4.85
2007 2398 3.802948 TTAGAGGCAGTTAGTAGCAGC 57.197 47.619 0.00 0.00 0.00 5.25
2077 2468 2.624838 CCCAGCCCAACATAGCATAAAG 59.375 50.000 0.00 0.00 0.00 1.85
2116 2515 3.633986 CAGGAAGGCAAAACTCTTCAACT 59.366 43.478 0.00 0.00 40.65 3.16
2210 2609 2.229543 CTGTCCAGCTGCAAAATGCTTA 59.770 45.455 8.66 0.00 45.31 3.09
2268 2667 3.648339 TTCCAGTTCAGCAGCAATTTC 57.352 42.857 0.00 0.00 0.00 2.17
2369 2768 2.611518 GATGTCCTCCGAGTTGTCAAG 58.388 52.381 0.00 0.00 0.00 3.02
2508 2908 9.116067 CAGGAATGGATAAACCGTAGATAAAAA 57.884 33.333 0.00 0.00 42.61 1.94
2548 2948 9.846248 ACAGAAAATAGATAAAAGCAATGACAC 57.154 29.630 0.00 0.00 0.00 3.67
2556 2956 9.952188 GGGATTACACAGAAAATAGATAAAAGC 57.048 33.333 0.00 0.00 0.00 3.51
2566 2966 5.687166 TCTACCGGGATTACACAGAAAAT 57.313 39.130 6.32 0.00 0.00 1.82
2581 2981 1.153349 GCTCCCTGCTTTCTACCGG 60.153 63.158 0.00 0.00 38.95 5.28
2634 3034 2.398588 ACGTATCTGGATGGTCCACAT 58.601 47.619 0.00 0.00 42.67 3.21
2653 3053 3.470645 AATAAGGACGCACATCCCTAC 57.529 47.619 0.00 0.00 39.91 3.18
2688 3088 7.658525 ATTCCCAATGCATATTGTTCAGTAA 57.341 32.000 0.00 0.00 41.68 2.24
2692 3092 6.832900 TCTGTATTCCCAATGCATATTGTTCA 59.167 34.615 0.00 0.00 41.68 3.18
2706 3106 0.913934 TGCCTGCCTCTGTATTCCCA 60.914 55.000 0.00 0.00 0.00 4.37
2721 3121 0.956633 TTACTGTCGACGAACTGCCT 59.043 50.000 11.62 0.00 0.00 4.75
2728 3128 2.736144 AAGGCATTTACTGTCGACGA 57.264 45.000 11.62 0.00 33.51 4.20
2729 3129 3.241995 GCTAAAGGCATTTACTGTCGACG 60.242 47.826 11.62 8.41 41.35 5.12
2731 3131 4.202245 AGCTAAAGGCATTTACTGTCGA 57.798 40.909 0.00 0.00 44.79 4.20
2755 3155 3.013219 TGAGAAGATGTGACGAGAGAGG 58.987 50.000 0.00 0.00 0.00 3.69
2773 3174 6.207417 GGTAGGAGAGAGATCAGAGAAATGAG 59.793 46.154 0.00 0.00 31.44 2.90
2774 3175 6.068010 GGTAGGAGAGAGATCAGAGAAATGA 58.932 44.000 0.00 0.00 0.00 2.57
2775 3176 5.048782 CGGTAGGAGAGAGATCAGAGAAATG 60.049 48.000 0.00 0.00 0.00 2.32
2776 3177 5.070001 CGGTAGGAGAGAGATCAGAGAAAT 58.930 45.833 0.00 0.00 0.00 2.17
2826 3227 3.374058 CGCCGTCTCAAGTTGGATAAAAT 59.626 43.478 2.34 0.00 0.00 1.82
2829 3230 1.546923 TCGCCGTCTCAAGTTGGATAA 59.453 47.619 2.34 0.00 0.00 1.75
2882 3283 4.688419 CCACGCGTTGCAGGCTTG 62.688 66.667 10.22 10.22 0.00 4.01
3463 3865 7.878547 TGATTGCATTATCACCACAATAGAA 57.121 32.000 0.00 0.00 31.40 2.10
3478 3880 5.359009 CAGGTTAGGACAGATTGATTGCATT 59.641 40.000 0.00 0.00 0.00 3.56
3499 3901 7.667219 ACCATTATTCATCCTATTAGCAACAGG 59.333 37.037 0.00 0.00 0.00 4.00
3503 3905 7.448161 CACCACCATTATTCATCCTATTAGCAA 59.552 37.037 0.00 0.00 0.00 3.91
3527 3930 0.245539 AGCAGCCATTCATTGTGCAC 59.754 50.000 10.75 10.75 36.57 4.57
4154 4716 7.290061 AGGATAAAATCTAACCAGCAATAGCA 58.710 34.615 0.00 0.00 45.49 3.49
4241 4803 2.211250 AGCACTGCTGGAACATGAAT 57.789 45.000 1.67 0.00 37.57 2.57
4253 4815 6.002062 ACAATACTCAAAACTTAGCACTGC 57.998 37.500 0.00 0.00 0.00 4.40
4448 5011 4.688879 TGAACTACACTGGAAGCATAAACG 59.311 41.667 0.00 0.00 37.60 3.60
4519 5082 3.694734 CCGTGCAACCAAATATCATCAC 58.305 45.455 0.00 0.00 0.00 3.06
4760 5323 0.109342 ACAAGGTCTGAGGGTGCAAG 59.891 55.000 0.00 0.00 0.00 4.01
4761 5324 0.179020 CACAAGGTCTGAGGGTGCAA 60.179 55.000 0.00 0.00 0.00 4.08
4973 5542 3.448686 CAAGCCAGGTTCGTCTGTATAG 58.551 50.000 0.00 0.00 33.14 1.31
4987 5556 1.171308 CTCAATGGACACCAAGCCAG 58.829 55.000 0.00 0.00 36.95 4.85
5003 5572 2.285668 CTCCCCCTCAAGGCCTCA 60.286 66.667 5.23 0.00 0.00 3.86
5004 5573 3.803162 GCTCCCCCTCAAGGCCTC 61.803 72.222 5.23 0.00 0.00 4.70
5005 5574 3.978241 ATGCTCCCCCTCAAGGCCT 62.978 63.158 0.00 0.00 0.00 5.19
5006 5575 3.424105 ATGCTCCCCCTCAAGGCC 61.424 66.667 0.00 0.00 0.00 5.19
5007 5576 2.194326 GATGCTCCCCCTCAAGGC 59.806 66.667 0.00 0.00 0.00 4.35
5008 5577 1.992519 CTGGATGCTCCCCCTCAAGG 61.993 65.000 0.50 0.00 35.03 3.61
5009 5578 1.277580 ACTGGATGCTCCCCCTCAAG 61.278 60.000 0.50 0.00 35.03 3.02
5010 5579 0.044092 TACTGGATGCTCCCCCTCAA 59.956 55.000 0.50 0.00 35.03 3.02
5022 5591 7.886970 CACCATGATTCAAAGGATATACTGGAT 59.113 37.037 13.60 0.00 0.00 3.41
5043 5612 2.027192 ACTTATCGTCAACAGCCACCAT 60.027 45.455 0.00 0.00 0.00 3.55
5089 5661 1.256812 TCAGATCCAGCGTTCTGACA 58.743 50.000 6.79 0.00 42.52 3.58
5101 5673 2.224257 GGTCAGGCTCATCTTCAGATCC 60.224 54.545 0.00 0.00 31.21 3.36
5145 5772 3.308866 GTGTATCATACGTGAAAGCACCC 59.691 47.826 0.00 0.00 42.09 4.61
5214 5842 7.481798 GCATCCGTACTACAAAAGAAAAATGAG 59.518 37.037 0.00 0.00 0.00 2.90
5234 5862 1.854743 CGACAACAGATAGTGCATCCG 59.145 52.381 0.00 0.00 33.75 4.18
5277 5916 4.041567 ACACATGAGATGAACCAACAGGTA 59.958 41.667 0.00 0.00 33.53 3.08
5305 5944 1.484240 CTGGTTCCTTGTTGGGCAAAA 59.516 47.619 0.00 0.00 36.53 2.44
5313 5952 1.675552 CAACGTCCTGGTTCCTTGTT 58.324 50.000 0.00 0.00 0.00 2.83
5323 5962 0.881118 CCAACCAATCCAACGTCCTG 59.119 55.000 0.00 0.00 0.00 3.86
5325 5964 1.584495 GCCAACCAATCCAACGTCC 59.416 57.895 0.00 0.00 0.00 4.79
5328 5967 1.178534 ACAGGCCAACCAATCCAACG 61.179 55.000 5.01 0.00 39.06 4.10
5329 5968 0.603065 GACAGGCCAACCAATCCAAC 59.397 55.000 5.01 0.00 39.06 3.77
5334 5973 1.619827 CAATGTGACAGGCCAACCAAT 59.380 47.619 5.01 0.00 39.06 3.16
5335 5974 1.039068 CAATGTGACAGGCCAACCAA 58.961 50.000 5.01 0.00 39.06 3.67
5336 5975 0.106268 ACAATGTGACAGGCCAACCA 60.106 50.000 5.01 0.00 39.06 3.67
5337 5976 1.904287 TACAATGTGACAGGCCAACC 58.096 50.000 5.01 0.00 0.00 3.77
5338 5977 4.022416 TGATTTACAATGTGACAGGCCAAC 60.022 41.667 5.01 0.00 0.00 3.77
5352 5991 7.915293 ACTCCGTAAATGACATGATTTACAA 57.085 32.000 21.04 12.39 44.14 2.41
5357 5996 8.041323 AGAAACTACTCCGTAAATGACATGATT 58.959 33.333 0.00 0.00 0.00 2.57
5364 6003 6.755141 GTGCATAGAAACTACTCCGTAAATGA 59.245 38.462 0.00 0.00 0.00 2.57
5365 6004 6.291637 CGTGCATAGAAACTACTCCGTAAATG 60.292 42.308 0.00 0.00 0.00 2.32
5367 6006 5.097529 CGTGCATAGAAACTACTCCGTAAA 58.902 41.667 0.00 0.00 0.00 2.01
5368 6007 4.156556 ACGTGCATAGAAACTACTCCGTAA 59.843 41.667 0.00 0.00 0.00 3.18
5369 6008 3.691118 ACGTGCATAGAAACTACTCCGTA 59.309 43.478 0.00 0.00 0.00 4.02
5371 6010 2.852413 CACGTGCATAGAAACTACTCCG 59.148 50.000 0.82 0.00 0.00 4.63
5372 6011 3.858238 GTCACGTGCATAGAAACTACTCC 59.142 47.826 11.67 0.00 0.00 3.85
5373 6012 4.559251 CAGTCACGTGCATAGAAACTACTC 59.441 45.833 11.67 0.00 0.00 2.59
5374 6013 4.486090 CAGTCACGTGCATAGAAACTACT 58.514 43.478 11.67 1.73 0.00 2.57
5375 6014 3.060895 GCAGTCACGTGCATAGAAACTAC 59.939 47.826 11.67 0.00 43.41 2.73
5394 6058 0.754957 TTGAAACCCACCACTGGCAG 60.755 55.000 14.16 14.16 36.00 4.85
5395 6059 1.040339 GTTGAAACCCACCACTGGCA 61.040 55.000 0.00 0.00 36.00 4.92
5403 6067 1.963515 AGGCATCAAGTTGAAACCCAC 59.036 47.619 18.99 5.08 0.00 4.61
5425 6089 7.528307 GCACAAAATTGCATCAAAATATCCAA 58.472 30.769 0.00 0.00 42.49 3.53
5457 6122 2.730382 AGTTTGTCACGTTTTCCCCTT 58.270 42.857 0.00 0.00 0.00 3.95
5488 6156 7.201359 CCGAGATAACTGCATATTCGTTGATAC 60.201 40.741 0.00 0.00 0.00 2.24
5489 6157 6.806739 CCGAGATAACTGCATATTCGTTGATA 59.193 38.462 0.00 0.00 0.00 2.15
5490 6158 5.635280 CCGAGATAACTGCATATTCGTTGAT 59.365 40.000 0.00 0.00 0.00 2.57
5513 6181 0.109226 GCGCCTACTGATATCGGACC 60.109 60.000 18.63 2.65 0.00 4.46
5518 6186 0.994995 CGCATGCGCCTACTGATATC 59.005 55.000 29.09 0.00 33.11 1.63
5549 6217 0.096281 CGCGGCGAATATTTGTGTGT 59.904 50.000 19.16 0.00 0.00 3.72
5550 6218 1.193665 GCGCGGCGAATATTTGTGTG 61.194 55.000 28.54 5.63 0.00 3.82
5551 6219 1.061887 GCGCGGCGAATATTTGTGT 59.938 52.632 28.54 0.00 0.00 3.72
5552 6220 1.654137 GGCGCGGCGAATATTTGTG 60.654 57.895 28.54 0.00 0.00 3.33
5553 6221 2.713154 GGCGCGGCGAATATTTGT 59.287 55.556 28.54 0.00 0.00 2.83
5554 6222 2.425124 CGGCGCGGCGAATATTTG 60.425 61.111 46.73 17.56 0.00 2.32
5569 6237 4.072088 GTTTCAGCCACGACGCGG 62.072 66.667 12.47 0.00 0.00 6.46
5572 6240 1.278637 GTTGGTTTCAGCCACGACG 59.721 57.895 0.00 0.00 38.42 5.12
5651 6338 2.518949 GCTTTGTACATTGCGTGATGG 58.481 47.619 0.00 0.00 0.00 3.51
5700 6388 4.056125 CCGACGCTGACCTGAGCA 62.056 66.667 0.00 0.00 39.07 4.26
5926 6614 4.162690 ATCCTGCCGCCCTTCGTC 62.163 66.667 0.00 0.00 36.19 4.20


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

AutoCloner maintained by Alex Coulton.