Multiple sequence alignment - TraesCS5A01G491600

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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 TraesCS5A01G491600 chr5A 100.000 3677 0 0 1 3677 660444148 660440472 0.000000e+00 6791.0
1 TraesCS5A01G491600 chr5A 83.083 266 36 7 3240 3501 112090722 112090982 2.210000e-57 233.0
2 TraesCS5A01G491600 chr5A 82.558 258 38 5 3243 3497 661659458 661659711 1.720000e-53 220.0
3 TraesCS5A01G491600 chr5A 96.875 32 0 1 3019 3049 168127642 168127673 7.000000e-03 52.8
4 TraesCS5A01G491600 chr4D 89.661 2921 119 73 153 2960 482157440 482160290 0.000000e+00 3552.0
5 TraesCS5A01G491600 chr4D 87.259 518 48 4 3154 3667 482161375 482161878 3.180000e-160 575.0
6 TraesCS5A01G491600 chr4B 88.612 2248 98 55 74 2215 611852247 611854442 0.000000e+00 2588.0
7 TraesCS5A01G491600 chr4B 91.966 697 40 12 2354 3036 611854628 611855322 0.000000e+00 963.0
8 TraesCS5A01G491600 chr4B 89.374 527 38 4 3153 3675 611855793 611856305 0.000000e+00 647.0
9 TraesCS5A01G491600 chr2D 84.586 266 35 5 3240 3501 485982593 485982856 3.640000e-65 259.0
10 TraesCS5A01G491600 chr2D 83.395 271 38 7 3244 3509 56643662 56643394 1.020000e-60 244.0
11 TraesCS5A01G491600 chr7B 83.582 268 39 4 3244 3510 322488456 322488719 2.840000e-61 246.0
12 TraesCS5A01G491600 chr7D 82.657 271 41 6 3244 3510 363048663 363048931 6.140000e-58 235.0
13 TraesCS5A01G491600 chr5D 82.331 266 38 7 3240 3501 108339107 108339367 4.780000e-54 222.0
14 TraesCS5A01G491600 chr1B 82.857 245 24 10 1094 1335 348862312 348862541 1.730000e-48 204.0
15 TraesCS5A01G491600 chr1B 89.431 123 13 0 1486 1608 348862632 348862754 4.920000e-34 156.0
16 TraesCS5A01G491600 chr1B 90.217 92 9 0 1722 1813 348862893 348862984 1.790000e-23 121.0
17 TraesCS5A01G491600 chr1A 82.661 248 19 10 1094 1335 337150716 337150945 8.050000e-47 198.0
18 TraesCS5A01G491600 chr1A 87.755 147 17 1 1486 1631 337151038 337151184 1.760000e-38 171.0
19 TraesCS5A01G491600 chr1A 91.304 92 8 0 1722 1813 337151304 337151395 3.850000e-25 126.0
20 TraesCS5A01G491600 chr1D 87.075 147 18 1 1486 1631 263072786 263072932 8.170000e-37 165.0
21 TraesCS5A01G491600 chr1D 90.217 92 9 0 1722 1813 263073046 263073137 1.790000e-23 121.0


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 TraesCS5A01G491600 chr5A 660440472 660444148 3676 True 6791.000000 6791 100.000 1 3677 1 chr5A.!!$R1 3676
1 TraesCS5A01G491600 chr4D 482157440 482161878 4438 False 2063.500000 3552 88.460 153 3667 2 chr4D.!!$F1 3514
2 TraesCS5A01G491600 chr4B 611852247 611856305 4058 False 1399.333333 2588 89.984 74 3675 3 chr4B.!!$F1 3601

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
44 45 0.107361 ACCGCTTATTTCTTCCCGGG 60.107 55.0 16.85 16.85 39.96 5.73 F
1341 1424 0.166814 GCGTCAAGAGGTACGTACGT 59.833 55.0 25.98 25.98 41.10 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1936 0.111266 GTTGTACGCACGACAAGCAG 60.111 55.0 0.98 0.0 38.72 4.24 R
2838 3109 0.838122 AAGTACAGGCAGGGCTCACT 60.838 55.0 0.00 0.0 0.00 3.41 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
33 34 5.678132 AAAACGTGTTTTCTACCGCTTAT 57.322 34.783 4.93 0.00 38.27 1.73
34 35 5.678132 AAACGTGTTTTCTACCGCTTATT 57.322 34.783 0.00 0.00 0.00 1.40
35 36 5.678132 AACGTGTTTTCTACCGCTTATTT 57.322 34.783 0.00 0.00 0.00 1.40
36 37 5.273523 ACGTGTTTTCTACCGCTTATTTC 57.726 39.130 0.00 0.00 0.00 2.17
37 38 4.992951 ACGTGTTTTCTACCGCTTATTTCT 59.007 37.500 0.00 0.00 0.00 2.52
38 39 5.467735 ACGTGTTTTCTACCGCTTATTTCTT 59.532 36.000 0.00 0.00 0.00 2.52
39 40 6.013689 CGTGTTTTCTACCGCTTATTTCTTC 58.986 40.000 0.00 0.00 0.00 2.87
40 41 6.312487 GTGTTTTCTACCGCTTATTTCTTCC 58.688 40.000 0.00 0.00 0.00 3.46
41 42 5.413523 TGTTTTCTACCGCTTATTTCTTCCC 59.586 40.000 0.00 0.00 0.00 3.97
42 43 3.447918 TCTACCGCTTATTTCTTCCCG 57.552 47.619 0.00 0.00 0.00 5.14
43 44 2.101917 TCTACCGCTTATTTCTTCCCGG 59.898 50.000 0.00 0.00 41.31 5.73
44 45 0.107361 ACCGCTTATTTCTTCCCGGG 60.107 55.000 16.85 16.85 39.96 5.73
45 46 0.818040 CCGCTTATTTCTTCCCGGGG 60.818 60.000 23.50 6.77 32.58 5.73
46 47 0.818040 CGCTTATTTCTTCCCGGGGG 60.818 60.000 23.50 14.50 0.00 5.40
70 71 3.706373 GACGAGGCCCAGCTGGAA 61.706 66.667 34.91 0.00 37.39 3.53
71 72 3.011517 ACGAGGCCCAGCTGGAAT 61.012 61.111 34.91 18.79 37.39 3.01
72 73 2.515523 CGAGGCCCAGCTGGAATG 60.516 66.667 34.91 18.56 37.39 2.67
79 80 2.401766 CCAGCTGGAATGGACACGC 61.402 63.158 29.88 0.00 40.51 5.34
104 105 2.124320 GCCCGCTTGCATCCCTAA 60.124 61.111 0.00 0.00 0.00 2.69
106 107 1.224592 CCCGCTTGCATCCCTAACT 59.775 57.895 0.00 0.00 0.00 2.24
118 119 0.966920 CCCTAACTGAGGTGACACGT 59.033 55.000 0.00 0.00 45.03 4.49
120 121 1.336887 CCTAACTGAGGTGACACGTGG 60.337 57.143 21.57 1.23 40.98 4.94
134 135 2.694065 CGTGGCACATGGTCCATAG 58.306 57.895 19.09 1.47 44.52 2.23
138 139 1.136828 GGCACATGGTCCATAGGGTA 58.863 55.000 3.38 0.00 34.93 3.69
227 228 3.353836 GGAAGTTTCCGCTGCGCA 61.354 61.111 18.00 10.98 37.65 6.09
229 230 1.441016 GAAGTTTCCGCTGCGCAAG 60.441 57.895 18.00 8.72 43.44 4.01
289 291 1.021390 AGCAGTACACTGAATGCCGC 61.021 55.000 13.50 0.00 46.59 6.53
349 351 4.999939 GCGGTGCAAAAGTGGCGG 63.000 66.667 0.00 0.00 0.00 6.13
506 527 3.319198 GTCTCCCACCGCTCCCAA 61.319 66.667 0.00 0.00 0.00 4.12
583 609 1.575922 CGCTGCTTGCTTTGCACTA 59.424 52.632 0.00 0.00 38.71 2.74
587 613 2.413371 GCTGCTTGCTTTGCACTACTAC 60.413 50.000 0.00 0.00 38.71 2.73
1182 1262 1.674651 GGGGAGGTTCAACTTCGCC 60.675 63.158 18.42 18.42 46.69 5.54
1338 1421 1.135315 GCGCGTCAAGAGGTACGTA 59.865 57.895 8.43 0.00 41.10 3.57
1339 1422 1.130458 GCGCGTCAAGAGGTACGTAC 61.130 60.000 17.56 17.56 41.10 3.67
1340 1423 0.854853 CGCGTCAAGAGGTACGTACG 60.855 60.000 18.98 15.01 41.10 3.67
1341 1424 0.166814 GCGTCAAGAGGTACGTACGT 59.833 55.000 25.98 25.98 41.10 3.57
1356 1439 3.353524 CGTACGTCGTAATCCATTCGAA 58.646 45.455 6.68 0.00 35.44 3.71
1368 1451 1.062587 CCATTCGAACATCGCCTCAAC 59.937 52.381 0.00 0.00 40.21 3.18
1444 1527 2.253603 CGATTGCTGCTTGCCTAAAAC 58.746 47.619 0.00 0.00 42.00 2.43
1458 1541 3.425758 GCCTAAAACGTGCTGTGGATTAC 60.426 47.826 0.00 0.00 0.00 1.89
1636 1721 1.556911 CCTGCAGGTACACCATCTTCT 59.443 52.381 25.53 0.00 38.89 2.85
1675 1764 5.126869 TCGTGCAACATCCATCCATTTTTAT 59.873 36.000 0.00 0.00 35.74 1.40
1676 1765 5.459762 CGTGCAACATCCATCCATTTTTATC 59.540 40.000 0.00 0.00 35.74 1.75
1677 1766 6.576185 GTGCAACATCCATCCATTTTTATCT 58.424 36.000 0.00 0.00 36.32 1.98
1678 1767 6.698766 GTGCAACATCCATCCATTTTTATCTC 59.301 38.462 0.00 0.00 36.32 2.75
1684 1778 8.636213 ACATCCATCCATTTTTATCTCATTGAC 58.364 33.333 0.00 0.00 0.00 3.18
1822 1916 3.711842 CGATGGTGCGTTGCGTGT 61.712 61.111 0.00 0.00 0.00 4.49
1823 1917 2.173382 GATGGTGCGTTGCGTGTC 59.827 61.111 0.00 0.00 0.00 3.67
1828 1922 4.980805 TGCGTTGCGTGTCCCCTC 62.981 66.667 0.00 0.00 0.00 4.30
1829 1923 4.681978 GCGTTGCGTGTCCCCTCT 62.682 66.667 0.00 0.00 0.00 3.69
1830 1924 2.432628 CGTTGCGTGTCCCCTCTC 60.433 66.667 0.00 0.00 0.00 3.20
1831 1925 2.932234 CGTTGCGTGTCCCCTCTCT 61.932 63.158 0.00 0.00 0.00 3.10
1832 1926 1.079750 GTTGCGTGTCCCCTCTCTC 60.080 63.158 0.00 0.00 0.00 3.20
1833 1927 1.228894 TTGCGTGTCCCCTCTCTCT 60.229 57.895 0.00 0.00 0.00 3.10
1834 1928 1.251527 TTGCGTGTCCCCTCTCTCTC 61.252 60.000 0.00 0.00 0.00 3.20
1835 1929 2.419739 GCGTGTCCCCTCTCTCTCC 61.420 68.421 0.00 0.00 0.00 3.71
1836 1930 1.755008 CGTGTCCCCTCTCTCTCCC 60.755 68.421 0.00 0.00 0.00 4.30
1837 1931 1.388531 GTGTCCCCTCTCTCTCCCA 59.611 63.158 0.00 0.00 0.00 4.37
1838 1932 0.973496 GTGTCCCCTCTCTCTCCCAC 60.973 65.000 0.00 0.00 0.00 4.61
1839 1933 1.388531 GTCCCCTCTCTCTCCCACA 59.611 63.158 0.00 0.00 0.00 4.17
1840 1934 0.973496 GTCCCCTCTCTCTCCCACAC 60.973 65.000 0.00 0.00 0.00 3.82
1841 1935 1.687493 CCCCTCTCTCTCCCACACC 60.687 68.421 0.00 0.00 0.00 4.16
1842 1936 1.687493 CCCTCTCTCTCCCACACCC 60.687 68.421 0.00 0.00 0.00 4.61
1843 1937 1.390125 CCTCTCTCTCCCACACCCT 59.610 63.158 0.00 0.00 0.00 4.34
1844 1938 0.975040 CCTCTCTCTCCCACACCCTG 60.975 65.000 0.00 0.00 0.00 4.45
1857 1951 2.048597 CCCTGCTTGTCGTGCGTA 60.049 61.111 0.00 0.00 0.00 4.42
1859 1953 1.663388 CCTGCTTGTCGTGCGTACA 60.663 57.895 4.09 0.00 0.00 2.90
1860 1954 1.218875 CCTGCTTGTCGTGCGTACAA 61.219 55.000 4.09 0.00 35.61 2.41
1861 1955 0.111266 CTGCTTGTCGTGCGTACAAC 60.111 55.000 4.09 0.00 33.45 3.32
1865 1959 1.126113 CTTGTCGTGCGTACAACATCC 59.874 52.381 0.00 0.00 33.45 3.51
1881 1975 4.695231 CCGCTCGTCAACGTCCGT 62.695 66.667 2.09 0.00 40.80 4.69
1885 1979 3.245948 CTCGTCAACGTCCGTCCGT 62.246 63.158 2.09 0.00 44.23 4.69
1902 1996 0.319900 CGTCCGATCCATCCATCCAC 60.320 60.000 0.00 0.00 0.00 4.02
1903 1997 1.051812 GTCCGATCCATCCATCCACT 58.948 55.000 0.00 0.00 0.00 4.00
1904 1998 1.001406 GTCCGATCCATCCATCCACTC 59.999 57.143 0.00 0.00 0.00 3.51
1905 1999 1.051008 CCGATCCATCCATCCACTCA 58.949 55.000 0.00 0.00 0.00 3.41
1906 2000 1.627329 CCGATCCATCCATCCACTCAT 59.373 52.381 0.00 0.00 0.00 2.90
1907 2001 2.354503 CCGATCCATCCATCCACTCATC 60.355 54.545 0.00 0.00 0.00 2.92
1908 2002 2.354503 CGATCCATCCATCCACTCATCC 60.355 54.545 0.00 0.00 0.00 3.51
1909 2003 2.195153 TCCATCCATCCACTCATCCA 57.805 50.000 0.00 0.00 0.00 3.41
1910 2004 2.709966 TCCATCCATCCACTCATCCAT 58.290 47.619 0.00 0.00 0.00 3.41
1911 2005 2.641321 TCCATCCATCCACTCATCCATC 59.359 50.000 0.00 0.00 0.00 3.51
1912 2006 2.290768 CCATCCATCCACTCATCCATCC 60.291 54.545 0.00 0.00 0.00 3.51
1913 2007 2.195153 TCCATCCACTCATCCATCCA 57.805 50.000 0.00 0.00 0.00 3.41
1995 2089 4.436050 CCTGACGTTGACATGTTTATCTGC 60.436 45.833 0.00 0.00 0.00 4.26
2075 2179 1.449353 GCAGGTAGCTCCCTCCATG 59.551 63.158 0.00 0.00 41.15 3.66
2096 2200 1.556564 CGGTAGTCGTTGGCATGTAG 58.443 55.000 0.00 0.00 0.00 2.74
2099 2203 2.165845 GGTAGTCGTTGGCATGTAGTCT 59.834 50.000 0.00 0.00 0.00 3.24
2101 2205 3.784701 AGTCGTTGGCATGTAGTCTAG 57.215 47.619 0.00 0.00 0.00 2.43
2102 2206 2.159226 AGTCGTTGGCATGTAGTCTAGC 60.159 50.000 0.00 0.00 0.00 3.42
2103 2207 1.200483 CGTTGGCATGTAGTCTAGCG 58.800 55.000 0.00 0.00 0.00 4.26
2104 2208 1.469251 CGTTGGCATGTAGTCTAGCGT 60.469 52.381 0.00 0.00 0.00 5.07
2105 2209 2.194271 GTTGGCATGTAGTCTAGCGTC 58.806 52.381 0.00 0.00 0.00 5.19
2106 2210 1.763968 TGGCATGTAGTCTAGCGTCT 58.236 50.000 0.00 0.00 0.00 4.18
2107 2211 2.927028 TGGCATGTAGTCTAGCGTCTA 58.073 47.619 0.00 0.00 0.00 2.59
2108 2212 3.284617 TGGCATGTAGTCTAGCGTCTAA 58.715 45.455 0.00 0.00 0.00 2.10
2176 2306 5.288804 GCACCAAGATTTGCTTCTGTTTTA 58.711 37.500 0.00 0.00 33.60 1.52
2188 2318 9.651913 TTTGCTTCTGTTTTAAAATTGACTCTT 57.348 25.926 3.52 0.00 0.00 2.85
2215 2345 8.784994 CAGATAAAATATGCTGCTTTCTCTCAT 58.215 33.333 0.00 0.00 0.00 2.90
2216 2346 9.001542 AGATAAAATATGCTGCTTTCTCTCATC 57.998 33.333 0.00 0.00 0.00 2.92
2220 2350 3.345508 TGCTGCTTTCTCTCATCATGT 57.654 42.857 0.00 0.00 0.00 3.21
2224 2354 4.082895 GCTGCTTTCTCTCATCATGTTGTT 60.083 41.667 3.76 0.00 0.00 2.83
2225 2355 5.122869 GCTGCTTTCTCTCATCATGTTGTTA 59.877 40.000 3.76 0.00 0.00 2.41
2226 2356 6.675002 GCTGCTTTCTCTCATCATGTTGTTAG 60.675 42.308 3.76 3.48 0.00 2.34
2227 2357 6.233434 TGCTTTCTCTCATCATGTTGTTAGT 58.767 36.000 3.76 0.00 0.00 2.24
2229 2359 7.020010 GCTTTCTCTCATCATGTTGTTAGTTG 58.980 38.462 3.76 1.14 0.00 3.16
2230 2360 6.486253 TTCTCTCATCATGTTGTTAGTTGC 57.514 37.500 3.76 0.00 0.00 4.17
2231 2361 5.798132 TCTCTCATCATGTTGTTAGTTGCT 58.202 37.500 3.76 0.00 0.00 3.91
2232 2362 6.935167 TCTCTCATCATGTTGTTAGTTGCTA 58.065 36.000 3.76 0.00 0.00 3.49
2233 2363 6.813649 TCTCTCATCATGTTGTTAGTTGCTAC 59.186 38.462 3.76 0.00 0.00 3.58
2234 2364 5.874810 TCTCATCATGTTGTTAGTTGCTACC 59.125 40.000 3.76 0.00 0.00 3.18
2235 2365 5.555966 TCATCATGTTGTTAGTTGCTACCA 58.444 37.500 3.76 0.00 0.00 3.25
2236 2366 6.179756 TCATCATGTTGTTAGTTGCTACCAT 58.820 36.000 3.76 0.00 0.00 3.55
2237 2367 5.878332 TCATGTTGTTAGTTGCTACCATG 57.122 39.130 6.62 6.62 0.00 3.66
2240 2370 4.323417 TGTTGTTAGTTGCTACCATGGAG 58.677 43.478 21.47 12.61 0.00 3.86
2241 2371 4.202419 TGTTGTTAGTTGCTACCATGGAGT 60.202 41.667 21.47 0.00 0.00 3.85
2242 2372 5.012251 TGTTGTTAGTTGCTACCATGGAGTA 59.988 40.000 21.47 8.31 0.00 2.59
2243 2373 5.339008 TGTTAGTTGCTACCATGGAGTAG 57.661 43.478 21.47 11.97 42.25 2.57
2245 2375 5.127194 TGTTAGTTGCTACCATGGAGTAGAG 59.873 44.000 21.47 8.26 41.98 2.43
2246 2376 3.714144 AGTTGCTACCATGGAGTAGAGT 58.286 45.455 21.47 1.16 41.98 3.24
2247 2377 4.868268 AGTTGCTACCATGGAGTAGAGTA 58.132 43.478 21.47 4.02 41.98 2.59
2248 2378 4.890581 AGTTGCTACCATGGAGTAGAGTAG 59.109 45.833 21.47 8.85 41.98 2.57
2263 2528 9.418045 GGAGTAGAGTAGAATAGATTGATTTGC 57.582 37.037 0.00 0.00 0.00 3.68
2278 2543 3.071457 TGATTTGCACTCCAGAGTCTTCA 59.929 43.478 0.00 0.00 40.20 3.02
2282 2547 2.266554 GCACTCCAGAGTCTTCATTCG 58.733 52.381 0.00 0.00 40.20 3.34
2283 2548 2.353208 GCACTCCAGAGTCTTCATTCGT 60.353 50.000 0.00 0.00 40.20 3.85
2284 2549 3.119459 GCACTCCAGAGTCTTCATTCGTA 60.119 47.826 0.00 0.00 40.20 3.43
2285 2550 4.416620 CACTCCAGAGTCTTCATTCGTAC 58.583 47.826 0.00 0.00 40.20 3.67
2286 2551 4.156922 CACTCCAGAGTCTTCATTCGTACT 59.843 45.833 0.00 0.00 40.20 2.73
2287 2552 4.396790 ACTCCAGAGTCTTCATTCGTACTC 59.603 45.833 0.00 0.00 36.92 2.59
2296 2561 8.480643 AGTCTTCATTCGTACTCTAATTTTGG 57.519 34.615 0.00 0.00 0.00 3.28
2345 2610 0.458716 GTGCTGGCTTAGTCCGAGTC 60.459 60.000 0.00 0.00 0.00 3.36
2363 2628 2.240160 AGTCCACGTATCTCCAGAGTCT 59.760 50.000 0.00 0.00 0.00 3.24
2372 2637 5.919707 CGTATCTCCAGAGTCTTCATTCATG 59.080 44.000 0.00 0.00 0.00 3.07
2392 2657 7.846644 TCATGATTTTGCAAGTGTTTCTTTT 57.153 28.000 0.00 0.00 33.63 2.27
2407 2672 8.190784 AGTGTTTCTTTTAAACTCATGGTTCTG 58.809 33.333 0.00 0.00 37.12 3.02
2415 2680 5.954296 AAACTCATGGTTCTGACATTCAG 57.046 39.130 0.00 0.00 45.59 3.02
2431 2696 4.818546 ACATTCAGTTCTTCTCCTTGTGTG 59.181 41.667 0.00 0.00 0.00 3.82
2491 2756 2.184322 GCCTCAAGATCGCGACCA 59.816 61.111 12.93 0.00 0.00 4.02
2493 2758 1.218230 GCCTCAAGATCGCGACCATC 61.218 60.000 12.93 5.29 0.00 3.51
2562 2827 2.606308 GCACAACCTCATGTTTCAGCAG 60.606 50.000 0.00 0.00 34.00 4.24
2619 2887 2.643272 CAGCTGCAGCACCAACAG 59.357 61.111 38.24 15.70 45.16 3.16
2625 2893 2.643272 CAGCACCAACAGCAGCAG 59.357 61.111 0.00 0.00 0.00 4.24
2687 2955 2.801111 CAAGAGAGTGATGGCGATGATG 59.199 50.000 0.00 0.00 0.00 3.07
2748 3017 1.408969 TGCAGACCCAAAGGAAAACC 58.591 50.000 0.00 0.00 36.73 3.27
2777 3046 7.805071 GGTTTAGAGTTGAACTGTGAATTCATG 59.195 37.037 12.12 10.29 36.02 3.07
2826 3095 6.636666 ATGTCGTCGTTAATAATCGTTGTT 57.363 33.333 0.00 0.00 0.00 2.83
2827 3096 5.834951 TGTCGTCGTTAATAATCGTTGTTG 58.165 37.500 0.00 0.00 0.00 3.33
2838 3109 1.464734 TCGTTGTTGTTTTCCAGGCA 58.535 45.000 0.00 0.00 0.00 4.75
2866 3139 4.145052 CCCTGCCTGTACTTTCTTTTTCT 58.855 43.478 0.00 0.00 0.00 2.52
2991 3584 6.524101 TCTATTTGTTGGGTATTTTCTGCC 57.476 37.500 0.00 0.00 0.00 4.85
2992 3585 6.252995 TCTATTTGTTGGGTATTTTCTGCCT 58.747 36.000 0.00 0.00 0.00 4.75
3004 3597 0.388649 TTCTGCCTCTTCGTCGCTTC 60.389 55.000 0.00 0.00 0.00 3.86
3007 3600 2.875485 CCTCTTCGTCGCTTCGGA 59.125 61.111 0.00 0.00 0.00 4.55
3016 3609 1.064505 CGTCGCTTCGGAATACACCTA 59.935 52.381 0.00 0.00 0.00 3.08
3023 3616 4.745620 GCTTCGGAATACACCTAACATCTC 59.254 45.833 0.00 0.00 0.00 2.75
3036 3629 8.258708 ACACCTAACATCTCTGTTCCTAAATAC 58.741 37.037 0.00 0.00 44.43 1.89
3050 3646 6.524101 TCCTAAATACAAGATGTTTTGGCC 57.476 37.500 0.00 0.00 35.31 5.36
3051 3647 6.252995 TCCTAAATACAAGATGTTTTGGCCT 58.747 36.000 3.32 0.00 35.31 5.19
3052 3648 7.406916 TCCTAAATACAAGATGTTTTGGCCTA 58.593 34.615 3.32 0.00 35.31 3.93
3054 3650 9.349713 CCTAAATACAAGATGTTTTGGCCTATA 57.650 33.333 3.32 0.00 30.13 1.31
3058 3654 6.515272 ACAAGATGTTTTGGCCTATAAGTG 57.485 37.500 3.32 0.00 32.32 3.16
3059 3655 6.245408 ACAAGATGTTTTGGCCTATAAGTGA 58.755 36.000 3.32 0.00 32.32 3.41
3061 3657 7.397192 ACAAGATGTTTTGGCCTATAAGTGAAT 59.603 33.333 3.32 0.00 32.32 2.57
3063 3659 8.682936 AGATGTTTTGGCCTATAAGTGAATAG 57.317 34.615 3.32 0.00 0.00 1.73
3064 3660 6.693315 TGTTTTGGCCTATAAGTGAATAGC 57.307 37.500 3.32 0.00 0.00 2.97
3066 3662 4.682778 TTGGCCTATAAGTGAATAGCGT 57.317 40.909 3.32 0.00 0.00 5.07
3067 3663 3.990092 TGGCCTATAAGTGAATAGCGTG 58.010 45.455 3.32 0.00 0.00 5.34
3068 3664 2.737252 GGCCTATAAGTGAATAGCGTGC 59.263 50.000 0.00 0.00 0.00 5.34
3069 3665 2.408704 GCCTATAAGTGAATAGCGTGCG 59.591 50.000 0.00 0.00 0.00 5.34
3071 3667 4.486090 CCTATAAGTGAATAGCGTGCGAT 58.514 43.478 0.00 0.00 0.00 4.58
3072 3668 4.923871 CCTATAAGTGAATAGCGTGCGATT 59.076 41.667 0.00 0.00 0.00 3.34
3073 3669 5.405571 CCTATAAGTGAATAGCGTGCGATTT 59.594 40.000 1.77 0.00 0.00 2.17
3074 3670 3.658351 AAGTGAATAGCGTGCGATTTC 57.342 42.857 1.77 0.65 0.00 2.17
3075 3671 2.616960 AGTGAATAGCGTGCGATTTCA 58.383 42.857 1.77 3.03 0.00 2.69
3076 3672 3.000041 AGTGAATAGCGTGCGATTTCAA 59.000 40.909 1.77 0.00 0.00 2.69
3077 3673 3.435327 AGTGAATAGCGTGCGATTTCAAA 59.565 39.130 1.77 0.00 0.00 2.69
3079 3675 4.615121 GTGAATAGCGTGCGATTTCAAAAA 59.385 37.500 1.77 0.00 0.00 1.94
3102 3698 4.348863 AAAAATGCCATGCTTTACCACA 57.651 36.364 0.00 0.00 0.00 4.17
3103 3699 4.556592 AAAATGCCATGCTTTACCACAT 57.443 36.364 0.00 0.00 0.00 3.21
3104 3700 4.556592 AAATGCCATGCTTTACCACATT 57.443 36.364 0.00 0.00 0.00 2.71
3105 3701 3.806625 ATGCCATGCTTTACCACATTC 57.193 42.857 0.00 0.00 0.00 2.67
3106 3702 2.806434 TGCCATGCTTTACCACATTCT 58.194 42.857 0.00 0.00 0.00 2.40
3107 3703 3.164268 TGCCATGCTTTACCACATTCTT 58.836 40.909 0.00 0.00 0.00 2.52
3108 3704 4.339748 TGCCATGCTTTACCACATTCTTA 58.660 39.130 0.00 0.00 0.00 2.10
3109 3705 4.955450 TGCCATGCTTTACCACATTCTTAT 59.045 37.500 0.00 0.00 0.00 1.73
3110 3706 5.421693 TGCCATGCTTTACCACATTCTTATT 59.578 36.000 0.00 0.00 0.00 1.40
3111 3707 6.070881 TGCCATGCTTTACCACATTCTTATTT 60.071 34.615 0.00 0.00 0.00 1.40
3112 3708 7.123397 TGCCATGCTTTACCACATTCTTATTTA 59.877 33.333 0.00 0.00 0.00 1.40
3113 3709 7.649306 GCCATGCTTTACCACATTCTTATTTAG 59.351 37.037 0.00 0.00 0.00 1.85
3217 4419 7.877097 TCCGACTCCTACAGTTATACTATCTTC 59.123 40.741 0.00 0.00 34.41 2.87
3271 4477 6.600427 TCCCTCCGTTTTTATTTACTCCAATC 59.400 38.462 0.00 0.00 0.00 2.67
3275 4481 6.657541 TCCGTTTTTATTTACTCCAATCAGCT 59.342 34.615 0.00 0.00 0.00 4.24
3359 4565 8.664211 TGACAATAATAAACGTATATGGTGCA 57.336 30.769 0.00 0.00 0.00 4.57
3497 4703 7.546250 TGCAAAGTAAATAAAAATGGAGGGA 57.454 32.000 0.00 0.00 0.00 4.20
3538 4744 6.455360 ACTGGAGTAATAACAATTGCCATG 57.545 37.500 5.05 0.00 0.00 3.66
3552 4758 8.088463 ACAATTGCCATGATATTCCCTTTTAA 57.912 30.769 5.05 0.00 0.00 1.52
3556 4762 8.551682 TTGCCATGATATTCCCTTTTAAGAAT 57.448 30.769 0.00 0.00 36.67 2.40
3557 4763 8.181904 TGCCATGATATTCCCTTTTAAGAATC 57.818 34.615 0.00 0.00 34.60 2.52
3571 4777 8.893727 CCTTTTAAGAATCCATAGAACGAATGT 58.106 33.333 0.00 0.00 0.00 2.71
3639 4845 8.254508 AGATTGGACTAGTGATACAAAGAAGTC 58.745 37.037 0.00 0.00 32.92 3.01
3667 4873 5.948162 AGCACAAGGAGACACAATGATAAAT 59.052 36.000 0.00 0.00 0.00 1.40
3669 4875 6.032094 CACAAGGAGACACAATGATAAATGC 58.968 40.000 0.00 0.00 0.00 3.56
3675 4881 7.994911 AGGAGACACAATGATAAATGCTCATAA 59.005 33.333 0.00 0.00 33.08 1.90
3676 4882 8.623903 GGAGACACAATGATAAATGCTCATAAA 58.376 33.333 0.00 0.00 33.08 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.678132 ATAAGCGGTAGAAAACACGTTTT 57.322 34.783 7.59 7.59 44.59 2.43
12 13 5.678132 AATAAGCGGTAGAAAACACGTTT 57.322 34.783 0.00 0.00 32.85 3.60
13 14 5.467735 AGAAATAAGCGGTAGAAAACACGTT 59.532 36.000 0.00 0.00 0.00 3.99
14 15 4.992951 AGAAATAAGCGGTAGAAAACACGT 59.007 37.500 0.00 0.00 0.00 4.49
15 16 5.526010 AGAAATAAGCGGTAGAAAACACG 57.474 39.130 0.00 0.00 0.00 4.49
16 17 6.312487 GGAAGAAATAAGCGGTAGAAAACAC 58.688 40.000 0.00 0.00 0.00 3.32
17 18 5.413523 GGGAAGAAATAAGCGGTAGAAAACA 59.586 40.000 0.00 0.00 0.00 2.83
18 19 5.446875 CGGGAAGAAATAAGCGGTAGAAAAC 60.447 44.000 0.00 0.00 0.00 2.43
19 20 4.632688 CGGGAAGAAATAAGCGGTAGAAAA 59.367 41.667 0.00 0.00 0.00 2.29
20 21 4.186159 CGGGAAGAAATAAGCGGTAGAAA 58.814 43.478 0.00 0.00 0.00 2.52
21 22 3.431207 CCGGGAAGAAATAAGCGGTAGAA 60.431 47.826 0.00 0.00 0.00 2.10
22 23 2.101917 CCGGGAAGAAATAAGCGGTAGA 59.898 50.000 0.00 0.00 0.00 2.59
23 24 2.480845 CCGGGAAGAAATAAGCGGTAG 58.519 52.381 0.00 0.00 0.00 3.18
24 25 1.139455 CCCGGGAAGAAATAAGCGGTA 59.861 52.381 18.48 0.00 0.00 4.02
25 26 0.107361 CCCGGGAAGAAATAAGCGGT 60.107 55.000 18.48 0.00 0.00 5.68
26 27 0.818040 CCCCGGGAAGAAATAAGCGG 60.818 60.000 26.32 0.00 0.00 5.52
27 28 0.818040 CCCCCGGGAAGAAATAAGCG 60.818 60.000 26.32 0.00 37.50 4.68
28 29 3.111405 CCCCCGGGAAGAAATAAGC 57.889 57.895 26.32 0.00 37.50 3.09
53 54 3.036429 ATTCCAGCTGGGCCTCGTC 62.036 63.158 32.23 0.00 36.21 4.20
54 55 3.011517 ATTCCAGCTGGGCCTCGT 61.012 61.111 32.23 9.50 36.21 4.18
55 56 2.515523 CATTCCAGCTGGGCCTCG 60.516 66.667 32.23 12.90 36.21 4.63
56 57 2.123982 CCATTCCAGCTGGGCCTC 60.124 66.667 32.23 0.00 36.21 4.70
57 58 2.614969 TCCATTCCAGCTGGGCCT 60.615 61.111 32.23 14.40 36.21 5.19
58 59 2.440980 GTCCATTCCAGCTGGGCC 60.441 66.667 32.23 10.26 31.99 5.80
59 60 2.048603 GTGTCCATTCCAGCTGGGC 61.049 63.158 32.23 9.99 38.91 5.36
60 61 1.746615 CGTGTCCATTCCAGCTGGG 60.747 63.158 32.23 16.40 34.36 4.45
61 62 2.401766 GCGTGTCCATTCCAGCTGG 61.402 63.158 27.87 27.87 34.93 4.85
62 63 2.743752 CGCGTGTCCATTCCAGCTG 61.744 63.158 6.78 6.78 0.00 4.24
63 64 2.434884 CGCGTGTCCATTCCAGCT 60.435 61.111 0.00 0.00 0.00 4.24
64 65 3.499737 CCGCGTGTCCATTCCAGC 61.500 66.667 4.92 0.00 0.00 4.85
65 66 2.100631 GTCCGCGTGTCCATTCCAG 61.101 63.158 4.92 0.00 0.00 3.86
66 67 2.047655 GTCCGCGTGTCCATTCCA 60.048 61.111 4.92 0.00 0.00 3.53
67 68 3.186047 CGTCCGCGTGTCCATTCC 61.186 66.667 4.92 0.00 0.00 3.01
68 69 3.849953 GCGTCCGCGTGTCCATTC 61.850 66.667 4.92 0.00 40.81 2.67
104 105 2.421739 GCCACGTGTCACCTCAGT 59.578 61.111 15.65 0.00 0.00 3.41
106 107 2.038814 ATGTGCCACGTGTCACCTCA 62.039 55.000 25.26 8.96 32.51 3.86
118 119 0.918799 ACCCTATGGACCATGTGCCA 60.919 55.000 17.73 6.27 38.78 4.92
120 121 2.851195 CTTACCCTATGGACCATGTGC 58.149 52.381 17.73 0.00 34.81 4.57
138 139 0.180406 CTATGTTACCTGCGGGGCTT 59.820 55.000 18.00 6.60 39.10 4.35
145 146 1.209504 TCCAGCACCTATGTTACCTGC 59.790 52.381 0.00 0.00 0.00 4.85
208 209 2.863153 CGCAGCGGAAACTTCCTG 59.137 61.111 7.00 0.79 45.33 3.86
572 598 1.606994 CCGTGGTAGTAGTGCAAAGCA 60.607 52.381 0.00 0.00 35.60 3.91
614 640 2.182842 CGCTCCATGCTTACCTGCC 61.183 63.158 0.00 0.00 40.11 4.85
972 1040 3.318017 CAGGTTCAGGTACGAGTTGAAG 58.682 50.000 0.00 0.00 32.00 3.02
977 1045 1.546961 CTCCAGGTTCAGGTACGAGT 58.453 55.000 0.00 0.00 0.00 4.18
1171 1251 2.754375 GGGGGAGGCGAAGTTGAA 59.246 61.111 0.00 0.00 0.00 2.69
1257 1337 2.898729 TGATCTTCTTCATCTCGGCC 57.101 50.000 0.00 0.00 0.00 6.13
1338 1421 3.220507 TGTTCGAATGGATTACGACGT 57.779 42.857 5.52 5.52 35.82 4.34
1339 1422 3.121795 CGATGTTCGAATGGATTACGACG 60.122 47.826 0.00 0.00 43.74 5.12
1340 1423 3.361724 GCGATGTTCGAATGGATTACGAC 60.362 47.826 0.00 0.00 43.74 4.34
1341 1424 2.792674 GCGATGTTCGAATGGATTACGA 59.207 45.455 0.00 0.00 43.74 3.43
1356 1439 2.198827 TTGATTGGTTGAGGCGATGT 57.801 45.000 0.00 0.00 0.00 3.06
1368 1451 3.422732 CGCGATCTTGATCGATTGATTGG 60.423 47.826 29.67 9.17 46.12 3.16
1444 1527 0.719465 GTTCCGTAATCCACAGCACG 59.281 55.000 0.00 0.00 0.00 5.34
1458 1541 2.094700 TCCAAACTCGATCTCAGTTCCG 60.095 50.000 7.24 3.38 32.71 4.30
1627 1712 2.024846 TCGAGAGGAGGAAGAAGATGGT 60.025 50.000 0.00 0.00 0.00 3.55
1628 1713 2.360801 GTCGAGAGGAGGAAGAAGATGG 59.639 54.545 0.00 0.00 0.00 3.51
1636 1721 0.677098 CACGAGGTCGAGAGGAGGAA 60.677 60.000 6.35 0.00 43.02 3.36
1675 1764 6.994496 AGTCAACTCAATTTCAGTCAATGAGA 59.006 34.615 7.98 0.00 39.68 3.27
1676 1765 7.041576 TCAGTCAACTCAATTTCAGTCAATGAG 60.042 37.037 0.00 0.00 39.68 2.90
1677 1766 6.767423 TCAGTCAACTCAATTTCAGTCAATGA 59.233 34.615 0.00 0.00 35.62 2.57
1678 1767 6.962686 TCAGTCAACTCAATTTCAGTCAATG 58.037 36.000 0.00 0.00 0.00 2.82
1684 1778 5.954296 ACCATCAGTCAACTCAATTTCAG 57.046 39.130 0.00 0.00 0.00 3.02
1692 1786 4.201628 CGAATTCGAACCATCAGTCAACTC 60.202 45.833 23.29 0.00 43.02 3.01
1812 1906 4.681978 AGAGGGGACACGCAACGC 62.682 66.667 0.00 0.00 0.00 4.84
1821 1915 0.973496 GTGTGGGAGAGAGAGGGGAC 60.973 65.000 0.00 0.00 0.00 4.46
1822 1916 1.388531 GTGTGGGAGAGAGAGGGGA 59.611 63.158 0.00 0.00 0.00 4.81
1823 1917 1.687493 GGTGTGGGAGAGAGAGGGG 60.687 68.421 0.00 0.00 0.00 4.79
1826 1920 1.612395 GCAGGGTGTGGGAGAGAGAG 61.612 65.000 0.00 0.00 0.00 3.20
1827 1921 1.610673 GCAGGGTGTGGGAGAGAGA 60.611 63.158 0.00 0.00 0.00 3.10
1828 1922 1.197430 AAGCAGGGTGTGGGAGAGAG 61.197 60.000 0.00 0.00 0.00 3.20
1829 1923 1.152030 AAGCAGGGTGTGGGAGAGA 60.152 57.895 0.00 0.00 0.00 3.10
1830 1924 1.002868 CAAGCAGGGTGTGGGAGAG 60.003 63.158 0.00 0.00 0.00 3.20
1831 1925 1.768684 GACAAGCAGGGTGTGGGAGA 61.769 60.000 0.00 0.00 0.00 3.71
1832 1926 1.302832 GACAAGCAGGGTGTGGGAG 60.303 63.158 0.00 0.00 0.00 4.30
1833 1927 2.836154 GACAAGCAGGGTGTGGGA 59.164 61.111 0.00 0.00 0.00 4.37
1834 1928 2.669569 CGACAAGCAGGGTGTGGG 60.670 66.667 0.00 0.00 0.00 4.61
1835 1929 2.111043 ACGACAAGCAGGGTGTGG 59.889 61.111 0.00 0.00 0.00 4.17
1836 1930 2.896801 GCACGACAAGCAGGGTGTG 61.897 63.158 0.00 0.00 33.09 3.82
1837 1931 2.591715 GCACGACAAGCAGGGTGT 60.592 61.111 0.00 0.00 33.09 4.16
1838 1932 3.716006 CGCACGACAAGCAGGGTG 61.716 66.667 0.00 0.00 0.00 4.61
1839 1933 2.863346 TACGCACGACAAGCAGGGT 61.863 57.895 0.00 0.00 0.00 4.34
1840 1934 2.048597 TACGCACGACAAGCAGGG 60.049 61.111 0.00 0.00 0.00 4.45
1841 1935 1.218875 TTGTACGCACGACAAGCAGG 61.219 55.000 0.00 0.00 33.03 4.85
1842 1936 0.111266 GTTGTACGCACGACAAGCAG 60.111 55.000 0.98 0.00 38.72 4.24
1843 1937 0.806492 TGTTGTACGCACGACAAGCA 60.806 50.000 6.37 0.43 44.48 3.91
1844 1938 1.928653 TGTTGTACGCACGACAAGC 59.071 52.632 6.37 0.00 44.48 4.01
1857 1951 1.282248 CGTTGACGAGCGGATGTTGT 61.282 55.000 0.00 0.00 43.02 3.32
1859 1953 1.006571 ACGTTGACGAGCGGATGTT 60.007 52.632 10.87 0.00 43.02 2.71
1860 1954 1.443872 GACGTTGACGAGCGGATGT 60.444 57.895 10.87 0.00 43.02 3.06
1861 1955 2.158959 GGACGTTGACGAGCGGATG 61.159 63.158 10.87 0.00 43.02 3.51
1865 1959 3.164011 GACGGACGTTGACGAGCG 61.164 66.667 10.87 0.00 43.02 5.03
1881 1975 1.185618 GGATGGATGGATCGGACGGA 61.186 60.000 0.00 0.00 0.00 4.69
1885 1979 1.342074 GAGTGGATGGATGGATCGGA 58.658 55.000 0.00 0.00 0.00 4.55
1909 2003 1.750399 GCCAAGCACATCGGTGGAT 60.750 57.895 0.00 0.00 45.38 3.41
1910 2004 2.359850 GCCAAGCACATCGGTGGA 60.360 61.111 0.00 0.00 45.38 4.02
1911 2005 2.672651 TGCCAAGCACATCGGTGG 60.673 61.111 0.00 0.00 45.38 4.61
1995 2089 0.792640 ACACGTACGACTAGGACACG 59.207 55.000 24.41 0.82 38.52 4.49
2067 2166 2.822399 GACTACCGGCATGGAGGG 59.178 66.667 0.00 0.00 42.00 4.30
2068 2167 1.956629 AACGACTACCGGCATGGAGG 61.957 60.000 0.00 0.00 43.93 4.30
2075 2179 2.125269 ATGCCAACGACTACCGGC 60.125 61.111 0.00 0.00 45.11 6.13
2096 2200 6.857777 TGGATTAGTACTTAGACGCTAGAC 57.142 41.667 0.00 0.00 0.00 2.59
2099 2203 7.095060 CCGTAATGGATTAGTACTTAGACGCTA 60.095 40.741 0.00 0.00 42.00 4.26
2101 2205 5.855395 CCGTAATGGATTAGTACTTAGACGC 59.145 44.000 0.00 0.00 42.00 5.19
2102 2206 7.194607 TCCGTAATGGATTAGTACTTAGACG 57.805 40.000 0.00 0.70 43.74 4.18
2154 2284 7.769272 TTTAAAACAGAAGCAAATCTTGGTG 57.231 32.000 0.00 0.00 41.89 4.17
2188 2318 7.989170 TGAGAGAAAGCAGCATATTTTATCTGA 59.011 33.333 6.70 0.00 33.84 3.27
2200 2330 3.345508 ACATGATGAGAGAAAGCAGCA 57.654 42.857 0.00 0.00 34.68 4.41
2202 2332 5.624344 AACAACATGATGAGAGAAAGCAG 57.376 39.130 10.29 0.00 0.00 4.24
2215 2345 4.699735 CCATGGTAGCAACTAACAACATGA 59.300 41.667 2.57 0.00 37.20 3.07
2216 2346 4.699735 TCCATGGTAGCAACTAACAACATG 59.300 41.667 12.58 0.00 37.20 3.21
2220 2350 4.634012 ACTCCATGGTAGCAACTAACAA 57.366 40.909 12.58 0.00 37.20 2.83
2224 2354 4.868268 ACTCTACTCCATGGTAGCAACTA 58.132 43.478 12.58 0.00 39.05 2.24
2225 2355 3.714144 ACTCTACTCCATGGTAGCAACT 58.286 45.455 12.58 0.00 39.05 3.16
2226 2356 4.888239 TCTACTCTACTCCATGGTAGCAAC 59.112 45.833 12.58 0.00 39.05 4.17
2227 2357 5.125367 TCTACTCTACTCCATGGTAGCAA 57.875 43.478 12.58 0.00 39.05 3.91
2229 2359 7.169591 TCTATTCTACTCTACTCCATGGTAGC 58.830 42.308 12.58 0.00 39.05 3.58
2230 2360 9.747898 AATCTATTCTACTCTACTCCATGGTAG 57.252 37.037 12.58 10.43 40.15 3.18
2231 2361 9.521841 CAATCTATTCTACTCTACTCCATGGTA 57.478 37.037 12.58 0.00 0.00 3.25
2232 2362 8.228206 TCAATCTATTCTACTCTACTCCATGGT 58.772 37.037 12.58 0.00 0.00 3.55
2233 2363 8.642935 TCAATCTATTCTACTCTACTCCATGG 57.357 38.462 4.97 4.97 0.00 3.66
2237 2367 9.418045 GCAAATCAATCTATTCTACTCTACTCC 57.582 37.037 0.00 0.00 0.00 3.85
2240 2370 9.757227 AGTGCAAATCAATCTATTCTACTCTAC 57.243 33.333 0.00 0.00 0.00 2.59
2241 2371 9.973450 GAGTGCAAATCAATCTATTCTACTCTA 57.027 33.333 0.00 0.00 36.88 2.43
2242 2372 7.930865 GGAGTGCAAATCAATCTATTCTACTCT 59.069 37.037 0.00 0.00 39.56 3.24
2243 2373 7.712639 TGGAGTGCAAATCAATCTATTCTACTC 59.287 37.037 0.00 0.00 39.56 2.59
2245 2375 7.712639 TCTGGAGTGCAAATCAATCTATTCTAC 59.287 37.037 0.00 0.00 39.56 2.59
2246 2376 7.795047 TCTGGAGTGCAAATCAATCTATTCTA 58.205 34.615 0.00 0.00 39.56 2.10
2247 2377 6.656902 TCTGGAGTGCAAATCAATCTATTCT 58.343 36.000 0.00 0.00 39.56 2.40
2248 2378 6.541641 ACTCTGGAGTGCAAATCAATCTATTC 59.458 38.462 2.15 0.00 40.75 1.75
2263 2528 3.584406 ACGAATGAAGACTCTGGAGTG 57.416 47.619 8.06 0.00 42.66 3.51
2278 2543 8.617290 AACACTTCCAAAATTAGAGTACGAAT 57.383 30.769 0.00 0.00 0.00 3.34
2287 2552 8.964150 CGGTTAAAGAAACACTTCCAAAATTAG 58.036 33.333 0.00 0.00 40.08 1.73
2296 2561 3.363673 CCGAGCGGTTAAAGAAACACTTC 60.364 47.826 0.00 0.00 40.08 3.01
2345 2610 3.017442 TGAAGACTCTGGAGATACGTGG 58.983 50.000 0.00 0.00 0.00 4.94
2363 2628 7.711772 AGAAACACTTGCAAAATCATGAATGAA 59.288 29.630 0.00 0.00 40.69 2.57
2372 2637 9.689075 GAGTTTAAAAGAAACACTTGCAAAATC 57.311 29.630 0.00 0.00 38.98 2.17
2407 2672 5.049818 CACACAAGGAGAAGAACTGAATGTC 60.050 44.000 0.00 0.00 0.00 3.06
2415 2680 3.206150 TCAAGCACACAAGGAGAAGAAC 58.794 45.455 0.00 0.00 0.00 3.01
2488 2753 2.419198 GATGCCGAGCTCGATGGT 59.581 61.111 36.59 18.95 43.02 3.55
2490 2755 2.732468 CCGATGCCGAGCTCGATG 60.732 66.667 36.59 21.81 43.02 3.84
2491 2756 4.654412 GCCGATGCCGAGCTCGAT 62.654 66.667 36.59 23.08 43.02 3.59
2573 2838 1.271127 TATGGGTGTAGCCTGCTGCA 61.271 55.000 5.79 5.79 44.83 4.41
2654 2922 3.688185 TCACTCTCTTGATTCATGCTTGC 59.312 43.478 0.00 0.00 0.00 4.01
2687 2955 2.494870 AGTCCAATCAAATGCTTCTGCC 59.505 45.455 0.00 0.00 38.71 4.85
2693 2961 6.305272 TCTTCTCTAGTCCAATCAAATGCT 57.695 37.500 0.00 0.00 0.00 3.79
2748 3017 6.677781 TTCACAGTTCAACTCTAAACCAAG 57.322 37.500 0.00 0.00 0.00 3.61
2826 3095 2.719376 GCTCACTGCCTGGAAAACA 58.281 52.632 0.00 0.00 35.15 2.83
2838 3109 0.838122 AAGTACAGGCAGGGCTCACT 60.838 55.000 0.00 0.00 0.00 3.41
2885 3158 6.879458 ACTGAAAGGTAACATATCCACAGAAC 59.121 38.462 0.00 0.00 39.30 3.01
2991 3584 2.110226 GTATTCCGAAGCGACGAAGAG 58.890 52.381 0.00 0.00 35.09 2.85
2992 3585 1.469703 TGTATTCCGAAGCGACGAAGA 59.530 47.619 0.00 0.00 35.09 2.87
3004 3597 5.263968 ACAGAGATGTTAGGTGTATTCCG 57.736 43.478 0.00 0.00 0.00 4.30
3007 3600 6.875972 AGGAACAGAGATGTTAGGTGTATT 57.124 37.500 0.00 0.00 31.35 1.89
3016 3609 9.388506 CATCTTGTATTTAGGAACAGAGATGTT 57.611 33.333 13.48 0.00 37.01 2.71
3023 3616 7.542130 GCCAAAACATCTTGTATTTAGGAACAG 59.458 37.037 0.00 0.00 0.00 3.16
3036 3629 6.757897 TCACTTATAGGCCAAAACATCTTG 57.242 37.500 5.01 0.00 0.00 3.02
3041 3637 5.295787 CGCTATTCACTTATAGGCCAAAACA 59.704 40.000 5.01 0.00 0.00 2.83
3050 3646 6.143919 TGAAATCGCACGCTATTCACTTATAG 59.856 38.462 0.00 0.00 0.00 1.31
3051 3647 5.980715 TGAAATCGCACGCTATTCACTTATA 59.019 36.000 0.00 0.00 0.00 0.98
3052 3648 4.808895 TGAAATCGCACGCTATTCACTTAT 59.191 37.500 0.00 0.00 0.00 1.73
3054 3650 3.000041 TGAAATCGCACGCTATTCACTT 59.000 40.909 0.00 0.00 0.00 3.16
3056 3652 3.383546 TTGAAATCGCACGCTATTCAC 57.616 42.857 5.06 0.00 30.34 3.18
3081 3677 4.348863 TGTGGTAAAGCATGGCATTTTT 57.651 36.364 0.00 4.62 0.00 1.94
3082 3678 4.556592 ATGTGGTAAAGCATGGCATTTT 57.443 36.364 0.00 0.00 0.00 1.82
3083 3679 4.223477 AGAATGTGGTAAAGCATGGCATTT 59.777 37.500 0.00 0.00 0.00 2.32
3085 3681 3.368248 AGAATGTGGTAAAGCATGGCAT 58.632 40.909 0.00 0.00 0.00 4.40
3086 3682 2.806434 AGAATGTGGTAAAGCATGGCA 58.194 42.857 0.00 0.00 0.00 4.92
3087 3683 3.874392 AAGAATGTGGTAAAGCATGGC 57.126 42.857 0.00 0.00 0.00 4.40
3088 3684 8.902806 TCTAAATAAGAATGTGGTAAAGCATGG 58.097 33.333 0.00 0.00 0.00 3.66
3091 3687 8.856153 TGTCTAAATAAGAATGTGGTAAAGCA 57.144 30.769 0.00 0.00 35.47 3.91
3105 3701 9.950680 ACCGCATTCATATTTTGTCTAAATAAG 57.049 29.630 4.00 0.88 40.94 1.73
3108 3704 9.950680 CTTACCGCATTCATATTTTGTCTAAAT 57.049 29.630 0.00 0.00 39.69 1.40
3109 3705 7.913297 GCTTACCGCATTCATATTTTGTCTAAA 59.087 33.333 0.00 0.00 38.92 1.85
3110 3706 7.066404 TGCTTACCGCATTCATATTTTGTCTAA 59.934 33.333 0.00 0.00 45.47 2.10
3111 3707 6.540551 TGCTTACCGCATTCATATTTTGTCTA 59.459 34.615 0.00 0.00 45.47 2.59
3112 3708 5.356751 TGCTTACCGCATTCATATTTTGTCT 59.643 36.000 0.00 0.00 45.47 3.41
3113 3709 5.577835 TGCTTACCGCATTCATATTTTGTC 58.422 37.500 0.00 0.00 45.47 3.18
3194 4396 9.781633 TCTGAAGATAGTATAACTGTAGGAGTC 57.218 37.037 0.00 0.00 31.73 3.36
3196 4398 9.562408 TGTCTGAAGATAGTATAACTGTAGGAG 57.438 37.037 0.00 0.00 0.00 3.69
3285 4491 9.366216 ACTTGATTAAACTCCAAAAAGTTTGAC 57.634 29.630 11.26 4.66 46.28 3.18
3335 4541 9.938670 TTTGCACCATATACGTTTATTATTGTC 57.061 29.630 0.00 0.00 0.00 3.18
3374 4580 8.906867 CACCAAATCAATACCATTAGATTCACT 58.093 33.333 0.00 0.00 30.87 3.41
3375 4581 8.137437 CCACCAAATCAATACCATTAGATTCAC 58.863 37.037 0.00 0.00 30.87 3.18
3448 4654 9.683069 CATGTTAGCTTTTGTCTAAAGTCAATT 57.317 29.630 8.29 0.00 44.21 2.32
3449 4655 7.809806 GCATGTTAGCTTTTGTCTAAAGTCAAT 59.190 33.333 8.29 0.00 44.21 2.57
3471 4677 8.040132 TCCCTCCATTTTTATTTACTTTGCATG 58.960 33.333 0.00 0.00 0.00 4.06
3552 4758 5.994054 CCATGACATTCGTTCTATGGATTCT 59.006 40.000 0.00 0.00 35.25 2.40
3556 4762 3.118445 TGCCATGACATTCGTTCTATGGA 60.118 43.478 0.00 0.00 35.25 3.41
3557 4763 3.205338 TGCCATGACATTCGTTCTATGG 58.795 45.455 0.00 0.00 35.84 2.74
3595 4801 9.606631 GTCCAATCTGAAATATCTAGTTCTTGT 57.393 33.333 0.00 0.00 32.06 3.16
3639 4845 2.245159 TGTGTCTCCTTGTGCTTCTG 57.755 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.