Multiple sequence alignment - TraesCS3A01G205800

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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 TraesCS3A01G205800 chr3A 100.000 4347 0 0 1 4347 362203521 362199175 0.000000e+00 8028.0
1 TraesCS3A01G205800 chr3A 87.160 405 45 5 1341 1743 178987287 178986888 1.840000e-123 453.0
2 TraesCS3A01G205800 chr3A 86.352 403 55 0 1341 1743 68869406 68869004 1.430000e-119 440.0
3 TraesCS3A01G205800 chr3B 89.282 4469 153 106 1 4344 372897918 372893651 0.000000e+00 5299.0
4 TraesCS3A01G205800 chr3B 86.634 404 52 2 1341 1743 95461696 95461294 3.080000e-121 446.0
5 TraesCS3A01G205800 chr3B 92.500 40 3 0 3943 3982 161088445 161088484 1.690000e-04 58.4
6 TraesCS3A01G205800 chr3D 91.050 3687 115 66 514 4117 277221301 277224855 0.000000e+00 4782.0
7 TraesCS3A01G205800 chr3D 87.207 555 18 17 1 526 277220753 277221283 2.250000e-162 582.0
8 TraesCS3A01G205800 chr3D 87.097 403 52 0 1341 1743 59856443 59856041 1.420000e-124 457.0
9 TraesCS3A01G205800 chr3D 89.873 237 6 6 4114 4344 277225037 277225261 5.500000e-74 289.0
10 TraesCS3A01G205800 chr4D 87.532 393 46 1 1352 1744 433393640 433393251 6.630000e-123 451.0
11 TraesCS3A01G205800 chr4B 87.532 393 46 1 1352 1744 531580972 531580583 6.630000e-123 451.0
12 TraesCS3A01G205800 chr4A 87.310 394 45 3 1352 1744 34787845 34787456 3.080000e-121 446.0
13 TraesCS3A01G205800 chr4A 76.821 302 31 20 451 745 624767701 624767432 2.730000e-27 134.0
14 TraesCS3A01G205800 chr1A 76.471 340 41 21 451 783 569343186 569343493 9.740000e-32 148.0
15 TraesCS3A01G205800 chr1B 78.125 256 31 11 536 783 52491192 52490954 5.860000e-29 139.0
16 TraesCS3A01G205800 chr2D 82.550 149 20 6 3753 3896 38627214 38627067 4.560000e-25 126.0
17 TraesCS3A01G205800 chr7D 74.809 262 31 17 3752 3982 604335259 604335002 7.750000e-13 86.1
18 TraesCS3A01G205800 chr7D 95.000 40 2 0 3943 3982 561702610 561702649 3.630000e-06 63.9
19 TraesCS3A01G205800 chr7B 93.023 43 3 0 3943 3985 594898285 594898243 3.630000e-06 63.9


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 TraesCS3A01G205800 chr3A 362199175 362203521 4346 True 8028.000000 8028 100.000000 1 4347 1 chr3A.!!$R3 4346
1 TraesCS3A01G205800 chr3B 372893651 372897918 4267 True 5299.000000 5299 89.282000 1 4344 1 chr3B.!!$R2 4343
2 TraesCS3A01G205800 chr3D 277220753 277225261 4508 False 1884.333333 4782 89.376667 1 4344 3 chr3D.!!$F1 4343

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
852 961 0.033011 TTCTTCCTCCTCCTCCTCCG 60.033 60.0 0.00 0.0 0.0 4.63 F
1133 1245 0.043485 AAACCTCCTCCTCCTCCTCC 59.957 60.0 0.00 0.0 0.0 4.30 F
1874 1996 0.396974 TTCTTGTGCCTTGGCAACCT 60.397 50.0 16.55 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2234 0.104487 CACAGCCGCTCATCTCATCT 59.896 55.0 0.0 0.0 0.00 2.90 R
2143 2301 0.826715 CTCCCAAAGCTCGATCCTCA 59.173 55.0 0.0 0.0 0.00 3.86 R
3474 3677 0.037232 TCACGAGTGCGAGAGAGAGA 60.037 55.0 0.0 0.0 41.64 3.10 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
142 168 8.247666 AGTTTCCACTTCTACTACTGTACTTT 57.752 34.615 0.00 0.00 0.00 2.66
199 229 2.557920 AGGACAGAAGAGTTGCCTTG 57.442 50.000 0.00 0.00 0.00 3.61
203 233 4.042187 AGGACAGAAGAGTTGCCTTGTATT 59.958 41.667 0.00 0.00 0.00 1.89
204 234 4.762251 GGACAGAAGAGTTGCCTTGTATTT 59.238 41.667 0.00 0.00 0.00 1.40
205 235 5.241728 GGACAGAAGAGTTGCCTTGTATTTT 59.758 40.000 0.00 0.00 0.00 1.82
206 236 6.239036 GGACAGAAGAGTTGCCTTGTATTTTT 60.239 38.462 0.00 0.00 0.00 1.94
207 237 7.040686 GGACAGAAGAGTTGCCTTGTATTTTTA 60.041 37.037 0.00 0.00 0.00 1.52
208 238 8.232913 ACAGAAGAGTTGCCTTGTATTTTTAA 57.767 30.769 0.00 0.00 0.00 1.52
265 329 2.094078 GGCCATAGCTAGAGAGAGCATG 60.094 54.545 0.00 0.00 45.43 4.06
266 330 2.824936 GCCATAGCTAGAGAGAGCATGA 59.175 50.000 0.00 0.00 45.43 3.07
267 331 3.257873 GCCATAGCTAGAGAGAGCATGAA 59.742 47.826 0.00 0.00 45.43 2.57
268 332 4.618927 GCCATAGCTAGAGAGAGCATGAAG 60.619 50.000 0.00 0.00 45.43 3.02
269 333 4.082081 CCATAGCTAGAGAGAGCATGAAGG 60.082 50.000 0.00 0.00 45.43 3.46
270 334 2.318908 AGCTAGAGAGAGCATGAAGGG 58.681 52.381 0.00 0.00 45.43 3.95
271 335 2.091389 AGCTAGAGAGAGCATGAAGGGA 60.091 50.000 0.00 0.00 45.43 4.20
272 336 2.697751 GCTAGAGAGAGCATGAAGGGAA 59.302 50.000 0.00 0.00 42.36 3.97
273 337 3.243839 GCTAGAGAGAGCATGAAGGGAAG 60.244 52.174 0.00 0.00 42.36 3.46
274 338 2.117865 AGAGAGAGCATGAAGGGAAGG 58.882 52.381 0.00 0.00 0.00 3.46
380 445 1.176619 GGAGGGGTTTGGTTTGGTCG 61.177 60.000 0.00 0.00 0.00 4.79
387 452 2.099427 GGTTTGGTTTGGTCGTTTGCTA 59.901 45.455 0.00 0.00 0.00 3.49
409 474 1.398234 CTTCTTCTCCCCCTCCCCT 59.602 63.158 0.00 0.00 0.00 4.79
410 475 0.692756 CTTCTTCTCCCCCTCCCCTC 60.693 65.000 0.00 0.00 0.00 4.30
412 477 3.707189 TTCTCCCCCTCCCCTCCC 61.707 72.222 0.00 0.00 0.00 4.30
420 485 4.179599 CTCCCCTCCCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
421 486 4.761304 TCCCCTCCCCCTCCCTCT 62.761 72.222 0.00 0.00 0.00 3.69
422 487 2.708132 CCCCTCCCCCTCCCTCTA 60.708 72.222 0.00 0.00 0.00 2.43
423 488 2.795938 CCCCTCCCCCTCCCTCTAG 61.796 73.684 0.00 0.00 0.00 2.43
479 545 3.083349 CTCTCATGGGGGCCGTCA 61.083 66.667 0.00 0.00 0.00 4.35
612 711 6.871492 CAGGGAAAGAAAGTAGAGAGAGAAAC 59.129 42.308 0.00 0.00 0.00 2.78
730 832 2.486191 CCTCCATCCTTGATACCTGTGC 60.486 54.545 0.00 0.00 0.00 4.57
746 848 0.817229 GTGCTATTCCCTGAGCTGCC 60.817 60.000 0.00 0.00 39.54 4.85
747 849 1.596477 GCTATTCCCTGAGCTGCCG 60.596 63.158 0.00 0.00 35.73 5.69
748 850 1.596477 CTATTCCCTGAGCTGCCGC 60.596 63.158 0.00 0.00 0.00 6.53
749 851 3.106986 TATTCCCTGAGCTGCCGCC 62.107 63.158 0.00 0.00 36.60 6.13
799 908 2.225242 TGGCTCTCTGAACTCTCTCCTT 60.225 50.000 0.00 0.00 0.00 3.36
807 916 4.651503 TCTGAACTCTCTCCTTTTGTCACT 59.348 41.667 0.00 0.00 0.00 3.41
808 917 4.950050 TGAACTCTCTCCTTTTGTCACTC 58.050 43.478 0.00 0.00 0.00 3.51
809 918 4.202264 TGAACTCTCTCCTTTTGTCACTCC 60.202 45.833 0.00 0.00 0.00 3.85
810 919 3.582164 ACTCTCTCCTTTTGTCACTCCT 58.418 45.455 0.00 0.00 0.00 3.69
811 920 3.323403 ACTCTCTCCTTTTGTCACTCCTG 59.677 47.826 0.00 0.00 0.00 3.86
849 958 1.273552 CCTGTTCTTCCTCCTCCTCCT 60.274 57.143 0.00 0.00 0.00 3.69
850 959 2.107366 CTGTTCTTCCTCCTCCTCCTC 58.893 57.143 0.00 0.00 0.00 3.71
851 960 1.273324 TGTTCTTCCTCCTCCTCCTCC 60.273 57.143 0.00 0.00 0.00 4.30
852 961 0.033011 TTCTTCCTCCTCCTCCTCCG 60.033 60.000 0.00 0.00 0.00 4.63
856 965 1.215679 TCCTCCTCCTCCTCCGTTCT 61.216 60.000 0.00 0.00 0.00 3.01
857 966 0.324830 CCTCCTCCTCCTCCGTTCTT 60.325 60.000 0.00 0.00 0.00 2.52
858 967 1.107945 CTCCTCCTCCTCCGTTCTTC 58.892 60.000 0.00 0.00 0.00 2.87
859 968 0.408309 TCCTCCTCCTCCGTTCTTCA 59.592 55.000 0.00 0.00 0.00 3.02
876 985 2.734755 TCATTAATGCCCCCTCTGTG 57.265 50.000 10.76 0.00 0.00 3.66
902 1011 3.118298 GCATCAAATTTATTGCCACCCCT 60.118 43.478 11.58 0.00 0.00 4.79
933 1042 4.320275 GCCTTGGCTAAGTTGTGTTTAGAC 60.320 45.833 9.16 0.00 36.81 2.59
934 1043 5.063880 CCTTGGCTAAGTTGTGTTTAGACT 58.936 41.667 9.16 0.00 37.12 3.24
935 1044 5.531287 CCTTGGCTAAGTTGTGTTTAGACTT 59.469 40.000 9.16 0.00 37.12 3.01
936 1045 6.039382 CCTTGGCTAAGTTGTGTTTAGACTTT 59.961 38.462 9.16 0.00 37.12 2.66
937 1046 7.227910 CCTTGGCTAAGTTGTGTTTAGACTTTA 59.772 37.037 9.16 0.00 37.12 1.85
938 1047 7.724305 TGGCTAAGTTGTGTTTAGACTTTAG 57.276 36.000 0.20 0.00 37.12 1.85
939 1048 7.502696 TGGCTAAGTTGTGTTTAGACTTTAGA 58.497 34.615 0.20 0.00 37.12 2.10
973 1082 6.915786 AGATAACCTAAGGCCTGAATCAAAT 58.084 36.000 5.69 0.00 0.00 2.32
1014 1123 3.753272 GCCGCTTTATGTATCATCACCAT 59.247 43.478 0.00 0.00 0.00 3.55
1131 1243 0.252927 CCAAACCTCCTCCTCCTCCT 60.253 60.000 0.00 0.00 0.00 3.69
1132 1244 1.199615 CAAACCTCCTCCTCCTCCTC 58.800 60.000 0.00 0.00 0.00 3.71
1133 1245 0.043485 AAACCTCCTCCTCCTCCTCC 59.957 60.000 0.00 0.00 0.00 4.30
1134 1246 1.892441 AACCTCCTCCTCCTCCTCCC 61.892 65.000 0.00 0.00 0.00 4.30
1135 1247 2.612251 CTCCTCCTCCTCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
1136 1248 3.036959 TCCTCCTCCTCCTCCCCC 61.037 72.222 0.00 0.00 0.00 5.40
1194 1306 1.298667 CAACCCCGGTAGGTCCTTG 59.701 63.158 2.55 0.00 40.05 3.61
1232 1351 9.657419 ATTTCTTGTTTGTTTTCTCACAATTCT 57.343 25.926 0.00 0.00 36.54 2.40
1235 1354 8.956426 TCTTGTTTGTTTTCTCACAATTCTAGT 58.044 29.630 0.00 0.00 36.54 2.57
1238 1357 8.181573 TGTTTGTTTTCTCACAATTCTAGTGAC 58.818 33.333 0.00 0.00 40.80 3.67
1243 1362 3.501062 TCTCACAATTCTAGTGACGACGT 59.499 43.478 0.00 0.00 40.80 4.34
1331 1453 1.189227 GCGCGTGTTTTTCATGGAAAC 59.811 47.619 8.43 14.74 37.48 2.78
1406 1528 1.068585 GACGAACCGGTTCCTGTGT 59.931 57.895 35.50 28.04 36.27 3.72
1752 1874 3.181474 CGTCTTCTCCAGGTTCTTATCCC 60.181 52.174 0.00 0.00 0.00 3.85
1779 1901 2.432146 TCCAATCTCGATCCACCTCTTG 59.568 50.000 0.00 0.00 0.00 3.02
1785 1907 1.066858 TCGATCCACCTCTTGTGCTTC 60.067 52.381 0.00 0.00 44.01 3.86
1789 1911 2.609747 TCCACCTCTTGTGCTTCTACT 58.390 47.619 0.00 0.00 44.01 2.57
1790 1912 3.774734 TCCACCTCTTGTGCTTCTACTA 58.225 45.455 0.00 0.00 44.01 1.82
1791 1913 4.353777 TCCACCTCTTGTGCTTCTACTAT 58.646 43.478 0.00 0.00 44.01 2.12
1792 1914 4.160439 TCCACCTCTTGTGCTTCTACTATG 59.840 45.833 0.00 0.00 44.01 2.23
1793 1915 3.868077 CACCTCTTGTGCTTCTACTATGC 59.132 47.826 0.00 0.00 38.34 3.14
1794 1916 3.772025 ACCTCTTGTGCTTCTACTATGCT 59.228 43.478 0.00 0.00 0.00 3.79
1799 1921 4.944619 TGTGCTTCTACTATGCTATGCT 57.055 40.909 0.00 0.00 0.00 3.79
1870 1992 5.940617 ACTATATATTCTTGTGCCTTGGCA 58.059 37.500 10.65 10.65 0.00 4.92
1871 1993 6.364701 ACTATATATTCTTGTGCCTTGGCAA 58.635 36.000 16.55 0.00 0.00 4.52
1872 1994 3.874392 ATATTCTTGTGCCTTGGCAAC 57.126 42.857 16.55 10.91 0.00 4.17
1874 1996 0.396974 TTCTTGTGCCTTGGCAACCT 60.397 50.000 16.55 0.00 0.00 3.50
1897 2019 0.526524 CTAGCGAGTGCACTGCCTAC 60.527 60.000 27.27 8.39 46.23 3.18
1907 2029 4.935808 AGTGCACTGCCTACAAATTACTAC 59.064 41.667 20.97 0.00 0.00 2.73
1908 2030 4.935808 GTGCACTGCCTACAAATTACTACT 59.064 41.667 10.32 0.00 0.00 2.57
1909 2031 6.070995 AGTGCACTGCCTACAAATTACTACTA 60.071 38.462 20.97 0.00 0.00 1.82
1935 2057 7.136119 CAGTAGAATTCAAGTAGAGGATCGTC 58.864 42.308 8.44 7.34 42.67 4.20
1980 2114 4.219288 AGGAAGGAACTCATTGTGATTTGC 59.781 41.667 0.00 0.00 38.49 3.68
2002 2137 2.202987 GCGAGTCAGGCCAGATGG 60.203 66.667 5.01 0.00 38.53 3.51
2021 2156 1.493311 GGCAACGAACGCAGAAGAG 59.507 57.895 0.00 0.00 0.00 2.85
2029 2164 0.674895 AACGCAGAAGAGGCATGGAC 60.675 55.000 0.00 0.00 0.00 4.02
2072 2225 4.337274 GGTCCTCTTTCTTTTTGTTTCGGA 59.663 41.667 0.00 0.00 0.00 4.55
2077 2230 5.587289 TCTTTCTTTTTGTTTCGGACATGG 58.413 37.500 0.00 0.00 38.26 3.66
2078 2231 5.358442 TCTTTCTTTTTGTTTCGGACATGGA 59.642 36.000 0.00 0.00 38.26 3.41
2079 2232 5.782893 TTCTTTTTGTTTCGGACATGGAT 57.217 34.783 0.00 0.00 38.26 3.41
2080 2233 5.119931 TCTTTTTGTTTCGGACATGGATG 57.880 39.130 0.00 0.00 38.26 3.51
2081 2234 4.824537 TCTTTTTGTTTCGGACATGGATGA 59.175 37.500 0.00 0.00 38.26 2.92
2121 2279 1.216710 GCTCGTGTGGAAGGAGAGG 59.783 63.158 0.00 0.00 42.34 3.69
2122 2280 1.251527 GCTCGTGTGGAAGGAGAGGA 61.252 60.000 0.00 0.00 42.34 3.71
2123 2281 0.814457 CTCGTGTGGAAGGAGAGGAG 59.186 60.000 0.00 0.00 42.34 3.69
2124 2282 0.404426 TCGTGTGGAAGGAGAGGAGA 59.596 55.000 0.00 0.00 0.00 3.71
2125 2283 0.814457 CGTGTGGAAGGAGAGGAGAG 59.186 60.000 0.00 0.00 0.00 3.20
2143 2301 4.020928 GGAGAGAGATGCTGTGATGATGAT 60.021 45.833 0.00 0.00 0.00 2.45
2144 2302 4.888917 AGAGAGATGCTGTGATGATGATG 58.111 43.478 0.00 0.00 0.00 3.07
2145 2303 4.589374 AGAGAGATGCTGTGATGATGATGA 59.411 41.667 0.00 0.00 0.00 2.92
2229 2387 0.690411 CCATCTCACTCCTCCTGCCT 60.690 60.000 0.00 0.00 0.00 4.75
2263 2421 4.639334 CCTATGCATGCTCACACTATTCT 58.361 43.478 20.33 0.00 0.00 2.40
2364 2526 1.205064 GCGTCGCATGCCATATGAC 59.795 57.895 13.44 12.07 0.00 3.06
2365 2527 1.498043 GCGTCGCATGCCATATGACA 61.498 55.000 13.44 0.00 0.00 3.58
2366 2528 0.936600 CGTCGCATGCCATATGACAA 59.063 50.000 13.15 0.00 0.00 3.18
2367 2529 1.333169 CGTCGCATGCCATATGACAAC 60.333 52.381 13.15 0.00 0.00 3.32
2368 2530 1.670295 GTCGCATGCCATATGACAACA 59.330 47.619 13.15 0.00 0.00 3.33
2369 2531 2.097304 GTCGCATGCCATATGACAACAA 59.903 45.455 13.15 0.00 0.00 2.83
2370 2532 2.751806 TCGCATGCCATATGACAACAAA 59.248 40.909 13.15 0.00 0.00 2.83
2371 2533 3.380954 TCGCATGCCATATGACAACAAAT 59.619 39.130 13.15 0.00 0.00 2.32
2372 2534 3.487942 CGCATGCCATATGACAACAAATG 59.512 43.478 13.15 0.00 0.00 2.32
2373 2535 4.684877 GCATGCCATATGACAACAAATGA 58.315 39.130 6.36 0.00 0.00 2.57
2374 2536 5.110598 GCATGCCATATGACAACAAATGAA 58.889 37.500 6.36 0.00 0.00 2.57
2375 2537 5.005971 GCATGCCATATGACAACAAATGAAC 59.994 40.000 6.36 0.00 0.00 3.18
2376 2538 5.718724 TGCCATATGACAACAAATGAACA 57.281 34.783 3.65 0.00 0.00 3.18
2377 2539 6.094193 TGCCATATGACAACAAATGAACAA 57.906 33.333 3.65 0.00 0.00 2.83
2378 2540 6.519382 TGCCATATGACAACAAATGAACAAA 58.481 32.000 3.65 0.00 0.00 2.83
2379 2541 6.645827 TGCCATATGACAACAAATGAACAAAG 59.354 34.615 3.65 0.00 0.00 2.77
2380 2542 6.867816 GCCATATGACAACAAATGAACAAAGA 59.132 34.615 3.65 0.00 0.00 2.52
2381 2543 7.384660 GCCATATGACAACAAATGAACAAAGAA 59.615 33.333 3.65 0.00 0.00 2.52
2382 2544 9.426837 CCATATGACAACAAATGAACAAAGAAT 57.573 29.630 3.65 0.00 0.00 2.40
2416 2578 4.344978 AGAATCAGGGGAAAGTTTTAGCC 58.655 43.478 0.00 0.00 0.00 3.93
2444 2606 0.898320 TCTCTTGCCCTTCCTTCTCG 59.102 55.000 0.00 0.00 0.00 4.04
2460 2626 2.771089 TCTCGTGCTGCATTTCTTCTT 58.229 42.857 5.27 0.00 0.00 2.52
2461 2627 2.738846 TCTCGTGCTGCATTTCTTCTTC 59.261 45.455 5.27 0.00 0.00 2.87
2686 2867 2.358737 GCGTTCCAGGACCACCAG 60.359 66.667 0.00 0.00 38.94 4.00
2705 2886 1.002990 CACCAGGTCATGCAGCAGA 60.003 57.895 0.00 0.00 0.00 4.26
2847 3028 4.367023 GACGCCTACGCACCACCA 62.367 66.667 0.00 0.00 45.53 4.17
2902 3083 2.510238 GCCACAGCGCTCCTACAG 60.510 66.667 7.13 0.00 0.00 2.74
3247 3428 0.104671 GCAACAACACCAACATGGCT 59.895 50.000 0.00 0.00 42.67 4.75
3417 3608 2.591923 CTGCTACCCTCTAGATCAGCA 58.408 52.381 13.71 13.71 37.46 4.41
3418 3609 2.961741 CTGCTACCCTCTAGATCAGCAA 59.038 50.000 14.72 4.40 38.45 3.91
3452 3648 6.688073 TTGAACTGGGTAATCTCTCTCTTT 57.312 37.500 0.00 0.00 0.00 2.52
3458 3661 6.086011 TGGGTAATCTCTCTCTTTCTCTCT 57.914 41.667 0.00 0.00 0.00 3.10
3460 3663 6.069088 TGGGTAATCTCTCTCTTTCTCTCTCT 60.069 42.308 0.00 0.00 0.00 3.10
3463 3666 7.442666 GGTAATCTCTCTCTTTCTCTCTCTCTC 59.557 44.444 0.00 0.00 0.00 3.20
3464 3667 6.821616 ATCTCTCTCTTTCTCTCTCTCTCT 57.178 41.667 0.00 0.00 0.00 3.10
3465 3668 6.227298 TCTCTCTCTTTCTCTCTCTCTCTC 57.773 45.833 0.00 0.00 0.00 3.20
3466 3669 5.960811 TCTCTCTCTTTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3467 3670 6.097554 TCTCTCTCTTTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
3468 3671 5.960811 TCTCTCTTTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3469 3672 6.097554 TCTCTCTTTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
3470 3673 5.960811 TCTCTTTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3471 3674 6.097554 TCTCTTTCTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
3472 3675 5.960811 TCTTTCTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3473 3676 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
3474 3677 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3475 3678 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3476 3679 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3477 3680 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3478 3681 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3479 3682 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3480 3683 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3481 3684 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3482 3685 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3483 3686 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3484 3687 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
3485 3688 2.362397 TCTCTCTCTCTCTCTCTCTCGC 59.638 54.545 0.00 0.00 0.00 5.03
3486 3689 2.101415 CTCTCTCTCTCTCTCTCTCGCA 59.899 54.545 0.00 0.00 0.00 5.10
3503 3706 0.179205 GCACTCGTGATCTTGCAAGC 60.179 55.000 21.99 9.31 34.97 4.01
3597 3804 6.183360 ACGTGAAAATAATACATGCATCCGTT 60.183 34.615 0.00 0.00 0.00 4.44
3598 3805 6.356977 CGTGAAAATAATACATGCATCCGTTC 59.643 38.462 0.00 0.00 0.00 3.95
3604 3811 2.593346 ACATGCATCCGTTCTCTCTC 57.407 50.000 0.00 0.00 0.00 3.20
3605 3812 2.106566 ACATGCATCCGTTCTCTCTCT 58.893 47.619 0.00 0.00 0.00 3.10
3606 3813 2.100584 ACATGCATCCGTTCTCTCTCTC 59.899 50.000 0.00 0.00 0.00 3.20
3607 3814 2.136298 TGCATCCGTTCTCTCTCTCT 57.864 50.000 0.00 0.00 0.00 3.10
3608 3815 2.020720 TGCATCCGTTCTCTCTCTCTC 58.979 52.381 0.00 0.00 0.00 3.20
3609 3816 2.297701 GCATCCGTTCTCTCTCTCTCT 58.702 52.381 0.00 0.00 0.00 3.10
3610 3817 2.290641 GCATCCGTTCTCTCTCTCTCTC 59.709 54.545 0.00 0.00 0.00 3.20
3611 3818 3.808728 CATCCGTTCTCTCTCTCTCTCT 58.191 50.000 0.00 0.00 0.00 3.10
3612 3819 3.536956 TCCGTTCTCTCTCTCTCTCTC 57.463 52.381 0.00 0.00 0.00 3.20
3613 3820 3.104512 TCCGTTCTCTCTCTCTCTCTCT 58.895 50.000 0.00 0.00 0.00 3.10
3614 3821 3.132289 TCCGTTCTCTCTCTCTCTCTCTC 59.868 52.174 0.00 0.00 0.00 3.20
3615 3822 3.133003 CCGTTCTCTCTCTCTCTCTCTCT 59.867 52.174 0.00 0.00 0.00 3.10
3616 3823 4.363999 CGTTCTCTCTCTCTCTCTCTCTC 58.636 52.174 0.00 0.00 0.00 3.20
3617 3824 4.098654 CGTTCTCTCTCTCTCTCTCTCTCT 59.901 50.000 0.00 0.00 0.00 3.10
3618 3825 5.596845 GTTCTCTCTCTCTCTCTCTCTCTC 58.403 50.000 0.00 0.00 0.00 3.20
3619 3826 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3620 3827 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3621 3828 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3622 3829 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3623 3830 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3624 3831 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3625 3832 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3626 3833 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3650 3859 2.036475 TCTCTCTCTGGCACTCAACAAC 59.964 50.000 0.00 0.00 0.00 3.32
3671 3880 1.709147 GGTCAGCTGCATTGCCTACG 61.709 60.000 9.47 0.00 0.00 3.51
3714 3927 3.479489 TGCTGGGCAATATATCAGTGTG 58.521 45.455 0.00 0.00 34.76 3.82
3719 3932 6.449635 TGGGCAATATATCAGTGTGAAAAC 57.550 37.500 0.00 0.00 0.00 2.43
3762 3983 1.075050 AGAAGTACACACTCCCTCCGA 59.925 52.381 0.00 0.00 32.29 4.55
3775 3996 3.431415 TCCCTCCGATCCATATGTAGTG 58.569 50.000 1.24 0.00 0.00 2.74
3777 3998 2.093973 CCTCCGATCCATATGTAGTGCC 60.094 54.545 1.24 0.00 0.00 5.01
3784 4005 8.002459 TCCGATCCATATGTAGTGCCTATAATA 58.998 37.037 1.24 0.00 0.00 0.98
3814 4035 7.756558 TCAAAAATCAAACCTCGCAAATTTTT 58.243 26.923 0.00 0.00 36.99 1.94
4022 4258 8.936864 ACACACTACAAGTTTTATATTCTCTGC 58.063 33.333 0.00 0.00 0.00 4.26
4029 4265 6.079712 AGTTTTATATTCTCTGCCTTGGGT 57.920 37.500 0.00 0.00 0.00 4.51
4034 4270 8.519799 TTTATATTCTCTGCCTTGGGTAAAAG 57.480 34.615 0.00 0.00 0.00 2.27
4051 4287 9.284968 TGGGTAAAAGAAAGTTTTCTCTATCTG 57.715 33.333 7.52 0.00 46.22 2.90
4066 4302 6.047870 TCTCTATCTGACTAAGGTACACGTC 58.952 44.000 0.00 0.00 0.00 4.34
4164 4584 4.706842 AAGGGAGTACTTTGCTTCTTCA 57.293 40.909 0.00 0.00 0.00 3.02
4209 4638 7.726291 TGTTTGACAATACTATTTTCAAGGGGA 59.274 33.333 9.34 0.00 0.00 4.81
4241 4670 4.819630 GTGTATTTGGGTGAACTGAACTGA 59.180 41.667 0.00 0.00 0.00 3.41
4242 4671 5.298276 GTGTATTTGGGTGAACTGAACTGAA 59.702 40.000 0.00 0.00 0.00 3.02
4243 4672 4.918810 ATTTGGGTGAACTGAACTGAAC 57.081 40.909 0.00 0.00 0.00 3.18
4244 4673 3.644966 TTGGGTGAACTGAACTGAACT 57.355 42.857 0.00 0.00 0.00 3.01
4245 4674 2.917933 TGGGTGAACTGAACTGAACTG 58.082 47.619 0.00 0.00 0.00 3.16
4255 4684 2.291465 TGAACTGAACTGATTGTGCTGC 59.709 45.455 0.00 0.00 0.00 5.25
4277 4706 1.484444 GGTGGTCACTTGGGAGCTCT 61.484 60.000 14.64 0.00 36.30 4.09
4278 4707 0.398318 GTGGTCACTTGGGAGCTCTT 59.602 55.000 14.64 0.00 36.30 2.85
4279 4708 0.397941 TGGTCACTTGGGAGCTCTTG 59.602 55.000 14.64 4.13 36.30 3.02
4280 4709 0.957888 GGTCACTTGGGAGCTCTTGC 60.958 60.000 14.64 0.00 40.05 4.01
4344 4773 7.864686 TCTGTAGTTTATTGATGCATGCATAC 58.135 34.615 32.27 23.97 36.70 2.39
4345 4774 6.657888 TGTAGTTTATTGATGCATGCATACG 58.342 36.000 32.27 0.00 36.70 3.06
4346 4775 5.112220 AGTTTATTGATGCATGCATACGG 57.888 39.130 32.27 0.00 36.70 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 1.172180 ACATTGTGAACCACGCTGGG 61.172 55.000 8.57 0.00 43.37 4.45
113 136 9.786105 GTACAGTAGTAGAAGTGGAAACTATTC 57.214 37.037 0.00 0.00 34.66 1.75
265 329 1.670059 TCTTCCCTTCCCTTCCCTTC 58.330 55.000 0.00 0.00 0.00 3.46
266 330 1.996291 CTTCTTCCCTTCCCTTCCCTT 59.004 52.381 0.00 0.00 0.00 3.95
267 331 1.675007 CTTCTTCCCTTCCCTTCCCT 58.325 55.000 0.00 0.00 0.00 4.20
268 332 0.626382 CCTTCTTCCCTTCCCTTCCC 59.374 60.000 0.00 0.00 0.00 3.97
269 333 0.033991 GCCTTCTTCCCTTCCCTTCC 60.034 60.000 0.00 0.00 0.00 3.46
270 334 0.995803 AGCCTTCTTCCCTTCCCTTC 59.004 55.000 0.00 0.00 0.00 3.46
271 335 0.995803 GAGCCTTCTTCCCTTCCCTT 59.004 55.000 0.00 0.00 0.00 3.95
272 336 0.178861 TGAGCCTTCTTCCCTTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
273 337 0.698818 TTGAGCCTTCTTCCCTTCCC 59.301 55.000 0.00 0.00 0.00 3.97
274 338 1.352687 AGTTGAGCCTTCTTCCCTTCC 59.647 52.381 0.00 0.00 0.00 3.46
315 380 2.897326 GCTTTAGGGGCCAAAAAGAAGA 59.103 45.455 25.52 0.00 33.05 2.87
380 445 2.750166 GGGAGAAGAAGGCTTAGCAAAC 59.250 50.000 6.53 0.00 33.61 2.93
387 452 0.916845 GGAGGGGGAGAAGAAGGCTT 60.917 60.000 0.00 0.00 36.96 4.35
409 474 3.449126 GGGCTAGAGGGAGGGGGA 61.449 72.222 0.00 0.00 0.00 4.81
410 475 4.583442 GGGGCTAGAGGGAGGGGG 62.583 77.778 0.00 0.00 0.00 5.40
412 477 0.252467 CATAGGGGCTAGAGGGAGGG 60.252 65.000 0.00 0.00 0.00 4.30
413 478 0.252467 CCATAGGGGCTAGAGGGAGG 60.252 65.000 0.00 0.00 0.00 4.30
414 479 3.390280 CCATAGGGGCTAGAGGGAG 57.610 63.158 0.00 0.00 0.00 4.30
612 711 4.530161 TCCCTCTTCTCTCCTTTCTTCTTG 59.470 45.833 0.00 0.00 0.00 3.02
730 832 1.596477 GCGGCAGCTCAGGGAATAG 60.596 63.158 0.00 0.00 41.01 1.73
799 908 1.490490 AGGCAAGACAGGAGTGACAAA 59.510 47.619 0.00 0.00 0.00 2.83
807 916 2.436109 GGGCAAGGCAAGACAGGA 59.564 61.111 0.00 0.00 0.00 3.86
808 917 2.677875 GGGGCAAGGCAAGACAGG 60.678 66.667 0.00 0.00 0.00 4.00
809 918 2.677875 GGGGGCAAGGCAAGACAG 60.678 66.667 0.00 0.00 0.00 3.51
810 919 2.786512 GATGGGGGCAAGGCAAGACA 62.787 60.000 0.00 0.00 0.00 3.41
811 920 2.037847 ATGGGGGCAAGGCAAGAC 59.962 61.111 0.00 0.00 0.00 3.01
849 958 2.650322 GGGGCATTAATGAAGAACGGA 58.350 47.619 19.73 0.00 0.00 4.69
850 959 1.681264 GGGGGCATTAATGAAGAACGG 59.319 52.381 19.73 0.00 0.00 4.44
851 960 2.618709 GAGGGGGCATTAATGAAGAACG 59.381 50.000 19.73 0.00 0.00 3.95
852 961 3.633986 CAGAGGGGGCATTAATGAAGAAC 59.366 47.826 19.73 4.79 0.00 3.01
856 965 2.358090 CCACAGAGGGGGCATTAATGAA 60.358 50.000 19.73 0.00 0.00 2.57
857 966 1.215173 CCACAGAGGGGGCATTAATGA 59.785 52.381 19.73 0.00 0.00 2.57
858 967 1.696063 CCACAGAGGGGGCATTAATG 58.304 55.000 11.27 11.27 0.00 1.90
876 985 3.310501 GTGGCAATAAATTTGATGCTGCC 59.689 43.478 21.76 19.40 46.44 4.85
902 1011 0.039618 CTTAGCCAAGGCCCAAGGAA 59.960 55.000 7.62 0.00 43.17 3.36
933 1042 6.610830 AGGTTATCTCTCTCTCCCTCTAAAG 58.389 44.000 0.00 0.00 0.00 1.85
934 1043 6.599986 AGGTTATCTCTCTCTCCCTCTAAA 57.400 41.667 0.00 0.00 0.00 1.85
935 1044 7.202242 CCTTAGGTTATCTCTCTCTCCCTCTAA 60.202 44.444 0.00 0.00 0.00 2.10
936 1045 6.273730 CCTTAGGTTATCTCTCTCTCCCTCTA 59.726 46.154 0.00 0.00 0.00 2.43
937 1046 5.074515 CCTTAGGTTATCTCTCTCTCCCTCT 59.925 48.000 0.00 0.00 0.00 3.69
938 1047 5.321927 CCTTAGGTTATCTCTCTCTCCCTC 58.678 50.000 0.00 0.00 0.00 4.30
939 1048 4.448640 GCCTTAGGTTATCTCTCTCTCCCT 60.449 50.000 0.00 0.00 0.00 4.20
973 1082 2.290071 GGCAAACTTGTAGTGCTAGGGA 60.290 50.000 8.55 0.00 38.36 4.20
1014 1123 1.671379 CTGCTGCTGCTGCTGAAGA 60.671 57.895 27.67 10.07 43.91 2.87
1045 1154 3.267860 CTGATCTGCCGCTTCCGC 61.268 66.667 0.00 0.00 0.00 5.54
1056 1165 2.040939 CTGCTGTCCTGATCCTGATCT 58.959 52.381 8.50 0.00 38.60 2.75
1058 1167 0.469070 GCTGCTGTCCTGATCCTGAT 59.531 55.000 0.00 0.00 0.00 2.90
1059 1168 0.906282 TGCTGCTGTCCTGATCCTGA 60.906 55.000 0.00 0.00 0.00 3.86
1060 1169 0.180642 ATGCTGCTGTCCTGATCCTG 59.819 55.000 0.00 0.00 0.00 3.86
1061 1170 0.180642 CATGCTGCTGTCCTGATCCT 59.819 55.000 0.00 0.00 0.00 3.24
1116 1228 2.329399 GGGAGGAGGAGGAGGAGGT 61.329 68.421 0.00 0.00 0.00 3.85
1136 1248 3.801068 TTGTTGGAGGCCGGGGTTG 62.801 63.158 2.18 0.00 0.00 3.77
1194 1306 6.500910 ACAAACAAGAAATTAAACCGAGGAC 58.499 36.000 0.00 0.00 0.00 3.85
1229 1348 1.335810 AGCAACACGTCGTCACTAGAA 59.664 47.619 0.00 0.00 0.00 2.10
1232 1351 0.318360 CCAGCAACACGTCGTCACTA 60.318 55.000 0.00 0.00 0.00 2.74
1235 1354 1.590525 GTCCAGCAACACGTCGTCA 60.591 57.895 0.00 0.00 0.00 4.35
1238 1357 2.310233 CCAGTCCAGCAACACGTCG 61.310 63.158 0.00 0.00 0.00 5.12
1243 1362 1.059098 ATCAGTCCAGTCCAGCAACA 58.941 50.000 0.00 0.00 0.00 3.33
1331 1453 1.296715 CTCTGGGTCTTGGGTTCCG 59.703 63.158 0.00 0.00 0.00 4.30
1406 1528 2.586245 CCCTTGCCGCAGATCTCA 59.414 61.111 0.00 0.00 0.00 3.27
1752 1874 3.873952 GGTGGATCGAGATTGGAAGAAAG 59.126 47.826 0.00 0.00 0.00 2.62
1779 1901 5.290643 GCATAGCATAGCATAGTAGAAGCAC 59.709 44.000 0.00 0.00 0.00 4.40
1792 1914 8.516313 GAAAGCTTTCATGATGCATAGCATAGC 61.516 40.741 29.93 13.78 41.89 2.97
1793 1915 6.802348 GAAAGCTTTCATGATGCATAGCATAG 59.198 38.462 29.93 6.11 41.89 2.23
1794 1916 6.489022 AGAAAGCTTTCATGATGCATAGCATA 59.511 34.615 34.39 0.00 43.33 3.14
1799 1921 5.068198 GGGAAGAAAGCTTTCATGATGCATA 59.932 40.000 34.39 0.00 39.61 3.14
1863 1985 1.751437 GCTAGGTTAGGTTGCCAAGG 58.249 55.000 0.00 0.00 0.00 3.61
1870 1992 1.067071 GTGCACTCGCTAGGTTAGGTT 60.067 52.381 10.32 0.00 39.64 3.50
1871 1993 0.531200 GTGCACTCGCTAGGTTAGGT 59.469 55.000 10.32 0.00 39.64 3.08
1872 1994 0.818296 AGTGCACTCGCTAGGTTAGG 59.182 55.000 15.25 0.00 39.64 2.69
1874 1996 0.108804 GCAGTGCACTCGCTAGGTTA 60.109 55.000 24.80 0.00 39.64 2.85
1907 2029 8.286800 CGATCCTCTACTTGAATTCTACTGTAG 58.713 40.741 8.55 8.55 0.00 2.74
1908 2030 7.774157 ACGATCCTCTACTTGAATTCTACTGTA 59.226 37.037 7.05 4.14 0.00 2.74
1909 2031 6.603997 ACGATCCTCTACTTGAATTCTACTGT 59.396 38.462 7.05 3.21 0.00 3.55
1997 2132 2.746277 GCGTTCGTTGCCCCATCT 60.746 61.111 0.00 0.00 0.00 2.90
2002 2137 1.901650 CTCTTCTGCGTTCGTTGCCC 61.902 60.000 0.00 0.00 0.00 5.36
2006 2141 0.320771 ATGCCTCTTCTGCGTTCGTT 60.321 50.000 0.00 0.00 0.00 3.85
2007 2142 1.016130 CATGCCTCTTCTGCGTTCGT 61.016 55.000 0.00 0.00 0.00 3.85
2008 2143 1.699656 CCATGCCTCTTCTGCGTTCG 61.700 60.000 0.00 0.00 0.00 3.95
2009 2144 0.391661 TCCATGCCTCTTCTGCGTTC 60.392 55.000 0.00 0.00 0.00 3.95
2029 2164 1.439353 CCCGTCCATCTTTGCATCCG 61.439 60.000 0.00 0.00 0.00 4.18
2072 2225 3.306156 CGCTCATCTCATCTCATCCATGT 60.306 47.826 0.00 0.00 0.00 3.21
2077 2230 1.273048 AGCCGCTCATCTCATCTCATC 59.727 52.381 0.00 0.00 0.00 2.92
2078 2231 1.001068 CAGCCGCTCATCTCATCTCAT 59.999 52.381 0.00 0.00 0.00 2.90
2079 2232 0.388294 CAGCCGCTCATCTCATCTCA 59.612 55.000 0.00 0.00 0.00 3.27
2080 2233 0.388659 ACAGCCGCTCATCTCATCTC 59.611 55.000 0.00 0.00 0.00 2.75
2081 2234 0.104487 CACAGCCGCTCATCTCATCT 59.896 55.000 0.00 0.00 0.00 2.90
2121 2279 4.587584 TCATCATCACAGCATCTCTCTC 57.412 45.455 0.00 0.00 0.00 3.20
2122 2280 4.589374 TCATCATCATCACAGCATCTCTCT 59.411 41.667 0.00 0.00 0.00 3.10
2123 2281 4.884247 TCATCATCATCACAGCATCTCTC 58.116 43.478 0.00 0.00 0.00 3.20
2124 2282 4.262678 CCTCATCATCATCACAGCATCTCT 60.263 45.833 0.00 0.00 0.00 3.10
2125 2283 3.997681 CCTCATCATCATCACAGCATCTC 59.002 47.826 0.00 0.00 0.00 2.75
2143 2301 0.826715 CTCCCAAAGCTCGATCCTCA 59.173 55.000 0.00 0.00 0.00 3.86
2144 2302 1.115467 TCTCCCAAAGCTCGATCCTC 58.885 55.000 0.00 0.00 0.00 3.71
2145 2303 0.827368 GTCTCCCAAAGCTCGATCCT 59.173 55.000 0.00 0.00 0.00 3.24
2253 2411 2.094494 ACAGCACGGAGAGAATAGTGTG 60.094 50.000 0.00 0.00 36.99 3.82
2355 2517 6.867816 TCTTTGTTCATTTGTTGTCATATGGC 59.132 34.615 0.00 0.00 35.04 4.40
2366 2528 9.381033 TGTTCATTTGATTCTTTGTTCATTTGT 57.619 25.926 0.00 0.00 0.00 2.83
2370 2532 9.820725 TCTTTGTTCATTTGATTCTTTGTTCAT 57.179 25.926 0.00 0.00 0.00 2.57
2371 2533 9.650539 TTCTTTGTTCATTTGATTCTTTGTTCA 57.349 25.926 0.00 0.00 0.00 3.18
2374 2536 9.820725 TGATTCTTTGTTCATTTGATTCTTTGT 57.179 25.926 0.00 0.00 0.00 2.83
2376 2538 9.485206 CCTGATTCTTTGTTCATTTGATTCTTT 57.515 29.630 0.00 0.00 0.00 2.52
2377 2539 8.092687 CCCTGATTCTTTGTTCATTTGATTCTT 58.907 33.333 0.00 0.00 0.00 2.52
2378 2540 7.310237 CCCCTGATTCTTTGTTCATTTGATTCT 60.310 37.037 0.00 0.00 0.00 2.40
2379 2541 6.815142 CCCCTGATTCTTTGTTCATTTGATTC 59.185 38.462 0.00 0.00 0.00 2.52
2380 2542 6.497954 TCCCCTGATTCTTTGTTCATTTGATT 59.502 34.615 0.00 0.00 0.00 2.57
2381 2543 6.018469 TCCCCTGATTCTTTGTTCATTTGAT 58.982 36.000 0.00 0.00 0.00 2.57
2382 2544 5.392995 TCCCCTGATTCTTTGTTCATTTGA 58.607 37.500 0.00 0.00 0.00 2.69
2416 2578 3.759086 GGAAGGGCAAGAGAAAAGGTAAG 59.241 47.826 0.00 0.00 0.00 2.34
2444 2606 4.413087 CATCAGAAGAAGAAATGCAGCAC 58.587 43.478 0.00 0.00 0.00 4.40
2460 2626 2.957680 TGCAACAAAGAAAGCCATCAGA 59.042 40.909 0.00 0.00 0.00 3.27
2461 2627 3.054878 GTGCAACAAAGAAAGCCATCAG 58.945 45.455 0.00 0.00 36.32 2.90
2686 2867 2.674033 TGCTGCATGACCTGGTGC 60.674 61.111 2.82 1.76 41.61 5.01
2705 2886 3.253371 CTTCACGTCGAAGTTGCAATT 57.747 42.857 0.59 0.00 45.29 2.32
3247 3428 2.283604 TGTGGCTCGTAGCAGGGA 60.284 61.111 8.71 0.00 44.75 4.20
3292 3479 3.574445 CTGATCTGCTGCTGCGGC 61.574 66.667 25.96 25.96 44.83 6.53
3293 3480 3.574445 GCTGATCTGCTGCTGCGG 61.574 66.667 17.69 17.69 46.48 5.69
3294 3481 2.396157 TTGCTGATCTGCTGCTGCG 61.396 57.895 23.02 6.13 43.34 5.18
3295 3482 1.136984 GTTGCTGATCTGCTGCTGC 59.863 57.895 23.02 8.89 41.53 5.25
3296 3483 1.017701 TCGTTGCTGATCTGCTGCTG 61.018 55.000 23.02 11.74 41.53 4.41
3417 3608 1.613437 CCAGTTCAAAACGCATCCCTT 59.387 47.619 0.00 0.00 36.23 3.95
3418 3609 1.247567 CCAGTTCAAAACGCATCCCT 58.752 50.000 0.00 0.00 36.23 4.20
3452 3648 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3458 3661 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3460 3663 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
3463 3666 3.551863 GCGAGAGAGAGAGAGAGAGAGAG 60.552 56.522 0.00 0.00 0.00 3.20
3464 3667 2.362397 GCGAGAGAGAGAGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
3465 3668 2.101415 TGCGAGAGAGAGAGAGAGAGAG 59.899 54.545 0.00 0.00 0.00 3.20
3466 3669 2.107366 TGCGAGAGAGAGAGAGAGAGA 58.893 52.381 0.00 0.00 0.00 3.10
3467 3670 2.159043 AGTGCGAGAGAGAGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
3468 3671 1.831106 AGTGCGAGAGAGAGAGAGAGA 59.169 52.381 0.00 0.00 0.00 3.10
3469 3672 2.205074 GAGTGCGAGAGAGAGAGAGAG 58.795 57.143 0.00 0.00 0.00 3.20
3470 3673 1.470805 CGAGTGCGAGAGAGAGAGAGA 60.471 57.143 0.00 0.00 40.82 3.10
3471 3674 0.930310 CGAGTGCGAGAGAGAGAGAG 59.070 60.000 0.00 0.00 40.82 3.20
3472 3675 0.248012 ACGAGTGCGAGAGAGAGAGA 59.752 55.000 0.00 0.00 41.64 3.10
3473 3676 0.373370 CACGAGTGCGAGAGAGAGAG 59.627 60.000 0.00 0.00 41.64 3.20
3474 3677 0.037232 TCACGAGTGCGAGAGAGAGA 60.037 55.000 0.00 0.00 41.64 3.10
3475 3678 1.003972 GATCACGAGTGCGAGAGAGAG 60.004 57.143 0.00 0.00 40.30 3.20
3476 3679 1.010580 GATCACGAGTGCGAGAGAGA 58.989 55.000 0.00 0.00 40.30 3.10
3477 3680 1.013596 AGATCACGAGTGCGAGAGAG 58.986 55.000 0.00 0.00 40.30 3.20
3478 3681 1.131315 CAAGATCACGAGTGCGAGAGA 59.869 52.381 0.00 0.00 40.30 3.10
3479 3682 1.543614 CAAGATCACGAGTGCGAGAG 58.456 55.000 0.00 0.00 40.30 3.20
3480 3683 0.456824 GCAAGATCACGAGTGCGAGA 60.457 55.000 0.00 0.00 41.16 4.04
3481 3684 0.733909 TGCAAGATCACGAGTGCGAG 60.734 55.000 0.00 0.00 39.92 5.03
3482 3685 0.319469 TTGCAAGATCACGAGTGCGA 60.319 50.000 0.00 0.00 39.92 5.10
3483 3686 0.094216 CTTGCAAGATCACGAGTGCG 59.906 55.000 22.31 0.00 39.92 5.34
3484 3687 0.179205 GCTTGCAAGATCACGAGTGC 60.179 55.000 30.39 7.45 37.51 4.40
3485 3688 1.436600 AGCTTGCAAGATCACGAGTG 58.563 50.000 30.39 0.22 0.00 3.51
3486 3689 3.257393 CTTAGCTTGCAAGATCACGAGT 58.743 45.455 30.39 5.59 0.00 4.18
3597 3804 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3598 3805 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3604 3811 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3605 3812 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3606 3813 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3607 3814 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3608 3815 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3609 3816 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3610 3817 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3611 3818 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3612 3819 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3613 3820 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3614 3821 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
3615 3822 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
3616 3823 4.039004 CCAGAGAGAGAGAGAGAGAGAGAG 59.961 54.167 0.00 0.00 0.00 3.20
3617 3824 3.963374 CCAGAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
3618 3825 3.494048 GCCAGAGAGAGAGAGAGAGAGAG 60.494 56.522 0.00 0.00 0.00 3.20
3619 3826 2.435805 GCCAGAGAGAGAGAGAGAGAGA 59.564 54.545 0.00 0.00 0.00 3.10
3620 3827 2.171237 TGCCAGAGAGAGAGAGAGAGAG 59.829 54.545 0.00 0.00 0.00 3.20
3621 3828 2.092968 GTGCCAGAGAGAGAGAGAGAGA 60.093 54.545 0.00 0.00 0.00 3.10
3622 3829 2.092753 AGTGCCAGAGAGAGAGAGAGAG 60.093 54.545 0.00 0.00 0.00 3.20
3623 3830 1.915489 AGTGCCAGAGAGAGAGAGAGA 59.085 52.381 0.00 0.00 0.00 3.10
3624 3831 2.292267 GAGTGCCAGAGAGAGAGAGAG 58.708 57.143 0.00 0.00 0.00 3.20
3625 3832 1.632920 TGAGTGCCAGAGAGAGAGAGA 59.367 52.381 0.00 0.00 0.00 3.10
3626 3833 2.127271 TGAGTGCCAGAGAGAGAGAG 57.873 55.000 0.00 0.00 0.00 3.20
3650 3859 0.393402 TAGGCAATGCAGCTGACCAG 60.393 55.000 20.43 5.04 34.17 4.00
3671 3880 5.686397 GCAAACGGAGACAGTAGATATGTAC 59.314 44.000 1.78 1.78 0.00 2.90
3784 4005 6.917217 TGCGAGGTTTGATTTTTGAAAAAT 57.083 29.167 15.10 15.10 0.00 1.82
3790 4011 7.967771 AAAAATTTGCGAGGTTTGATTTTTG 57.032 28.000 0.00 0.00 36.14 2.44
3955 4191 7.934457 ACTCACTCCATTTCATAATGTAATGC 58.066 34.615 2.51 0.00 39.62 3.56
3968 4204 5.745312 TGAGACATGTACTCACTCCATTT 57.255 39.130 18.29 0.00 39.10 2.32
3976 4212 2.093500 GTGGCCATGAGACATGTACTCA 60.093 50.000 22.05 22.05 46.17 3.41
3977 4213 2.093500 TGTGGCCATGAGACATGTACTC 60.093 50.000 9.72 14.67 35.26 2.59
4022 4258 7.348080 AGAGAAAACTTTCTTTTACCCAAGG 57.652 36.000 6.18 0.00 46.84 3.61
4051 4287 2.286067 CCGATCGACGTGTACCTTAGTC 60.286 54.545 18.66 0.00 40.78 2.59
4066 4302 9.245962 GGATTTTCCTTATACATATACCGATCG 57.754 37.037 8.51 8.51 32.53 3.69
4173 4602 6.869421 AGTATTGTCAAACATATTTTGCGC 57.131 33.333 0.00 0.00 0.00 6.09
4209 4638 5.319043 TCACCCAAATACACCTTTCTTCT 57.681 39.130 0.00 0.00 0.00 2.85
4241 4670 1.338973 CACCAAGCAGCACAATCAGTT 59.661 47.619 0.00 0.00 0.00 3.16
4242 4671 0.956633 CACCAAGCAGCACAATCAGT 59.043 50.000 0.00 0.00 0.00 3.41
4243 4672 0.242825 CCACCAAGCAGCACAATCAG 59.757 55.000 0.00 0.00 0.00 2.90
4244 4673 0.467844 ACCACCAAGCAGCACAATCA 60.468 50.000 0.00 0.00 0.00 2.57
4245 4674 0.242017 GACCACCAAGCAGCACAATC 59.758 55.000 0.00 0.00 0.00 2.67
4255 4684 0.890996 GCTCCCAAGTGACCACCAAG 60.891 60.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.