Multiple sequence alignment - TraesCS2D01G321300

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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 TraesCS2D01G321300 chr2D 100.000 2565 0 0 1 2565 412831409 412833973 0.000000e+00 4737
1 TraesCS2D01G321300 chr2A 88.295 1777 77 53 1 1709 579970891 579972604 0.000000e+00 2008
2 TraesCS2D01G321300 chr2A 95.522 670 18 4 1898 2565 580017754 580018413 0.000000e+00 1061
3 TraesCS2D01G321300 chr2A 92.500 80 3 2 1817 1895 580017699 580017776 7.500000e-21 111
4 TraesCS2D01G321300 chr2B 86.559 1860 82 66 1 1780 486116087 486117858 0.000000e+00 1895
5 TraesCS2D01G321300 chr2B 94.690 678 10 10 1898 2565 486191030 486191691 0.000000e+00 1029
6 TraesCS2D01G321300 chr2B 87.083 240 15 4 145 384 526383156 526382933 9.110000e-65 257
7 TraesCS2D01G321300 chr2B 88.350 103 10 1 1 103 526383319 526383219 3.470000e-24 122
8 TraesCS2D01G321300 chr2B 98.214 56 1 0 1837 1892 486190994 486191049 5.840000e-17 99


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 TraesCS2D01G321300 chr2D 412831409 412833973 2564 False 4737 4737 100.000 1 2565 1 chr2D.!!$F1 2564
1 TraesCS2D01G321300 chr2A 579970891 579972604 1713 False 2008 2008 88.295 1 1709 1 chr2A.!!$F1 1708
2 TraesCS2D01G321300 chr2A 580017699 580018413 714 False 586 1061 94.011 1817 2565 2 chr2A.!!$F2 748
3 TraesCS2D01G321300 chr2B 486116087 486117858 1771 False 1895 1895 86.559 1 1780 1 chr2B.!!$F1 1779
4 TraesCS2D01G321300 chr2B 486190994 486191691 697 False 564 1029 96.452 1837 2565 2 chr2B.!!$F2 728

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
951 1051 0.381089 CTAGCTTCCCTCACGTACGG 59.619 60.0 21.06 8.79 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1947 0.312102 AAAGCAAAACTCTGCCGAGC 59.688 50.0 4.89 0.0 43.73 5.03 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
104 105 1.526225 GTTCATAGCCCCCTTCCGC 60.526 63.158 0.00 0.00 0.00 5.54
127 144 1.205064 CACGAAGGCTTGAACTGCG 59.795 57.895 3.46 2.97 42.68 5.18
143 160 2.189342 CTGCGCAGTAGTTCTTAGCTC 58.811 52.381 29.24 0.00 34.87 4.09
205 226 5.237344 CGAACTCAACCTAATTCCATCCATC 59.763 44.000 0.00 0.00 0.00 3.51
206 227 5.715439 ACTCAACCTAATTCCATCCATCA 57.285 39.130 0.00 0.00 0.00 3.07
207 228 5.688807 ACTCAACCTAATTCCATCCATCAG 58.311 41.667 0.00 0.00 0.00 2.90
208 229 5.429762 ACTCAACCTAATTCCATCCATCAGA 59.570 40.000 0.00 0.00 0.00 3.27
209 230 5.933617 TCAACCTAATTCCATCCATCAGAG 58.066 41.667 0.00 0.00 0.00 3.35
210 231 5.429762 TCAACCTAATTCCATCCATCAGAGT 59.570 40.000 0.00 0.00 0.00 3.24
244 265 4.614306 CGATGCACATGAAACAAGTGTCAT 60.614 41.667 0.00 0.00 35.79 3.06
250 271 0.951558 GAAACAAGTGTCATGGCCGT 59.048 50.000 0.00 0.00 0.00 5.68
251 272 0.667993 AAACAAGTGTCATGGCCGTG 59.332 50.000 19.62 19.62 0.00 4.94
252 273 0.465460 AACAAGTGTCATGGCCGTGT 60.465 50.000 24.24 2.05 0.00 4.49
253 274 0.884704 ACAAGTGTCATGGCCGTGTC 60.885 55.000 24.24 19.23 0.00 3.67
254 275 0.884259 CAAGTGTCATGGCCGTGTCA 60.884 55.000 24.24 21.67 0.00 3.58
255 276 0.603707 AAGTGTCATGGCCGTGTCAG 60.604 55.000 22.91 0.00 0.00 3.51
256 277 1.005037 GTGTCATGGCCGTGTCAGA 60.005 57.895 22.91 2.44 0.00 3.27
257 278 1.005037 TGTCATGGCCGTGTCAGAC 60.005 57.895 24.24 15.29 0.00 3.51
266 287 3.702555 GTGTCAGACGCACGCCAC 61.703 66.667 9.36 0.00 0.00 5.01
267 288 4.214327 TGTCAGACGCACGCCACA 62.214 61.111 0.00 0.00 0.00 4.17
268 289 2.964925 GTCAGACGCACGCCACAA 60.965 61.111 0.00 0.00 0.00 3.33
269 290 2.202946 TCAGACGCACGCCACAAA 60.203 55.556 0.00 0.00 0.00 2.83
270 291 2.243957 TCAGACGCACGCCACAAAG 61.244 57.895 0.00 0.00 0.00 2.77
271 292 2.108157 AGACGCACGCCACAAAGA 59.892 55.556 0.00 0.00 0.00 2.52
272 293 1.956170 AGACGCACGCCACAAAGAG 60.956 57.895 0.00 0.00 0.00 2.85
273 294 3.579626 GACGCACGCCACAAAGAGC 62.580 63.158 0.00 0.00 0.00 4.09
274 295 3.349006 CGCACGCCACAAAGAGCT 61.349 61.111 0.00 0.00 0.00 4.09
320 366 3.896133 GCAGCCGGTCCATGCATG 61.896 66.667 20.19 20.19 39.75 4.06
321 367 3.896133 CAGCCGGTCCATGCATGC 61.896 66.667 21.69 11.82 0.00 4.06
322 368 4.429522 AGCCGGTCCATGCATGCA 62.430 61.111 25.04 25.04 0.00 3.96
693 747 1.459592 GCATAAATACGTAGCGGGCAG 59.540 52.381 0.08 0.00 0.00 4.85
703 757 2.130073 TAGCGGGCAGTCGATCGATG 62.130 60.000 22.50 19.51 0.00 3.84
818 904 5.527214 TCCACTGTTATTTATGATCGCTTGG 59.473 40.000 0.00 0.00 0.00 3.61
857 951 0.958876 TCCTCTCTGAAGCGTGCGTA 60.959 55.000 0.00 0.00 0.00 4.42
946 1046 0.383949 GCTCTCTAGCTTCCCTCACG 59.616 60.000 0.00 0.00 45.85 4.35
947 1047 1.757682 CTCTCTAGCTTCCCTCACGT 58.242 55.000 0.00 0.00 0.00 4.49
948 1048 2.920524 CTCTCTAGCTTCCCTCACGTA 58.079 52.381 0.00 0.00 0.00 3.57
949 1049 2.614983 CTCTCTAGCTTCCCTCACGTAC 59.385 54.545 0.00 0.00 0.00 3.67
950 1050 1.331138 CTCTAGCTTCCCTCACGTACG 59.669 57.143 15.01 15.01 0.00 3.67
951 1051 0.381089 CTAGCTTCCCTCACGTACGG 59.619 60.000 21.06 8.79 0.00 4.02
952 1052 1.033746 TAGCTTCCCTCACGTACGGG 61.034 60.000 21.06 17.09 42.05 5.28
953 1053 2.643232 GCTTCCCTCACGTACGGGT 61.643 63.158 18.57 0.00 41.40 5.28
1089 1210 3.589654 CTCGTGCGTGACCCATGGT 62.590 63.158 11.73 0.00 39.44 3.55
1123 1244 0.037232 AAGTAAGCCAGCCAGTCGAC 60.037 55.000 7.70 7.70 0.00 4.20
1173 1294 2.094700 TGCGTAGGACTCTTGCTACTTG 60.095 50.000 2.44 0.00 42.92 3.16
1238 1359 0.750182 TTATGCAGGTTTAGGCGCCC 60.750 55.000 26.15 7.48 0.00 6.13
1239 1360 2.933878 TATGCAGGTTTAGGCGCCCG 62.934 60.000 26.15 4.00 0.00 6.13
1372 1493 2.647949 GGGGGAGAGGGAGGAGGAA 61.648 68.421 0.00 0.00 0.00 3.36
1383 1504 1.210722 GGAGGAGGAACAAGGGATGAC 59.789 57.143 0.00 0.00 0.00 3.06
1622 1761 5.290400 CACTACTTTTACCGTTTAGCTAGCC 59.710 44.000 12.13 0.00 0.00 3.93
1670 1809 1.921243 CGTGATGCTTGTGGATCGTA 58.079 50.000 0.00 0.00 42.88 3.43
1671 1810 1.854743 CGTGATGCTTGTGGATCGTAG 59.145 52.381 0.00 0.00 42.88 3.51
1720 1862 2.543848 AGTTAATGTGCCGCGACATATG 59.456 45.455 8.23 0.00 35.43 1.78
1722 1864 1.662517 AATGTGCCGCGACATATGAA 58.337 45.000 8.23 0.00 35.43 2.57
1776 1924 1.588139 GATCACGGGTTAGCGGTCG 60.588 63.158 0.00 0.00 0.00 4.79
1777 1925 1.996786 GATCACGGGTTAGCGGTCGA 61.997 60.000 0.00 0.00 0.00 4.20
1778 1926 1.389609 ATCACGGGTTAGCGGTCGAT 61.390 55.000 0.00 0.00 0.00 3.59
1779 1927 0.747644 TCACGGGTTAGCGGTCGATA 60.748 55.000 0.00 0.00 0.00 2.92
1780 1928 0.317603 CACGGGTTAGCGGTCGATAG 60.318 60.000 0.00 0.00 0.00 2.08
1796 1944 3.357166 GATAGAATAGCTATCGGCCGG 57.643 52.381 27.83 10.87 44.32 6.13
1797 1945 2.211250 TAGAATAGCTATCGGCCGGT 57.789 50.000 27.83 23.47 43.05 5.28
1798 1946 2.211250 AGAATAGCTATCGGCCGGTA 57.789 50.000 27.83 23.29 43.05 4.02
1799 1947 2.093106 AGAATAGCTATCGGCCGGTAG 58.907 52.381 36.06 36.06 43.05 3.18
1803 1951 2.561885 CTATCGGCCGGTAGCTCG 59.438 66.667 31.22 10.34 43.05 5.03
1810 1958 3.141488 CCGGTAGCTCGGCAGAGT 61.141 66.667 15.48 5.13 46.03 3.24
1811 1959 2.711922 CCGGTAGCTCGGCAGAGTT 61.712 63.158 15.48 11.99 46.03 3.01
1812 1960 1.215647 CGGTAGCTCGGCAGAGTTT 59.784 57.895 15.48 6.95 46.03 2.66
1813 1961 0.389948 CGGTAGCTCGGCAGAGTTTT 60.390 55.000 15.48 4.58 46.03 2.43
1814 1962 1.079503 GGTAGCTCGGCAGAGTTTTG 58.920 55.000 15.48 0.00 46.03 2.44
1815 1963 0.444260 GTAGCTCGGCAGAGTTTTGC 59.556 55.000 15.48 1.26 46.03 3.68
1819 1967 1.535462 GCTCGGCAGAGTTTTGCTTTA 59.465 47.619 15.48 0.00 46.03 1.85
1890 2039 5.575606 AGTGCACGTACAAGTACAATACATC 59.424 40.000 12.01 0.00 35.87 3.06
1891 2040 5.346551 GTGCACGTACAAGTACAATACATCA 59.653 40.000 0.00 0.00 35.87 3.07
1892 2041 5.575218 TGCACGTACAAGTACAATACATCAG 59.425 40.000 10.63 0.00 35.87 2.90
1893 2042 5.005394 GCACGTACAAGTACAATACATCAGG 59.995 44.000 10.63 0.00 35.87 3.86
1894 2043 6.327154 CACGTACAAGTACAATACATCAGGA 58.673 40.000 10.63 0.00 35.87 3.86
1895 2044 6.978659 CACGTACAAGTACAATACATCAGGAT 59.021 38.462 10.63 0.00 35.87 3.24
1896 2045 7.491372 CACGTACAAGTACAATACATCAGGATT 59.509 37.037 10.63 0.00 35.87 3.01
1897 2046 7.705325 ACGTACAAGTACAATACATCAGGATTC 59.295 37.037 10.63 0.00 35.87 2.52
1898 2047 7.096599 CGTACAAGTACAATACATCAGGATTCG 60.097 40.741 10.63 0.00 35.87 3.34
1899 2048 6.640518 ACAAGTACAATACATCAGGATTCGT 58.359 36.000 0.00 0.00 0.00 3.85
1900 2049 7.778083 ACAAGTACAATACATCAGGATTCGTA 58.222 34.615 0.00 0.00 0.00 3.43
1901 2050 7.705325 ACAAGTACAATACATCAGGATTCGTAC 59.295 37.037 0.00 0.00 0.00 3.67
1902 2051 7.342769 AGTACAATACATCAGGATTCGTACA 57.657 36.000 0.00 0.00 31.38 2.90
1903 2052 7.778083 AGTACAATACATCAGGATTCGTACAA 58.222 34.615 0.00 0.00 31.38 2.41
1904 2053 7.921214 AGTACAATACATCAGGATTCGTACAAG 59.079 37.037 0.00 0.00 31.38 3.16
1905 2054 6.640518 ACAATACATCAGGATTCGTACAAGT 58.359 36.000 0.00 0.00 0.00 3.16
1906 2055 7.778083 ACAATACATCAGGATTCGTACAAGTA 58.222 34.615 0.00 0.00 0.00 2.24
1907 2056 7.705325 ACAATACATCAGGATTCGTACAAGTAC 59.295 37.037 0.29 0.29 0.00 2.73
1908 2057 5.654603 ACATCAGGATTCGTACAAGTACA 57.345 39.130 10.63 0.00 35.87 2.90
1909 2058 6.032956 ACATCAGGATTCGTACAAGTACAA 57.967 37.500 10.63 4.90 35.87 2.41
1910 2059 6.640518 ACATCAGGATTCGTACAAGTACAAT 58.359 36.000 10.63 8.75 35.87 2.71
1911 2060 7.778083 ACATCAGGATTCGTACAAGTACAATA 58.222 34.615 10.63 0.00 35.87 1.90
1912 2061 7.705325 ACATCAGGATTCGTACAAGTACAATAC 59.295 37.037 10.63 9.35 35.87 1.89
1913 2062 7.160547 TCAGGATTCGTACAAGTACAATACA 57.839 36.000 10.63 0.00 35.87 2.29
1914 2063 7.778083 TCAGGATTCGTACAAGTACAATACAT 58.222 34.615 10.63 0.00 35.87 2.29
1915 2064 7.919091 TCAGGATTCGTACAAGTACAATACATC 59.081 37.037 10.63 4.27 35.87 3.06
1916 2065 7.704899 CAGGATTCGTACAAGTACAATACATCA 59.295 37.037 10.63 0.00 35.87 3.07
1917 2066 7.921214 AGGATTCGTACAAGTACAATACATCAG 59.079 37.037 10.63 0.00 35.87 2.90
1918 2067 7.169308 GGATTCGTACAAGTACAATACATCAGG 59.831 40.741 10.63 0.00 35.87 3.86
1919 2068 6.762702 TCGTACAAGTACAATACATCAGGA 57.237 37.500 10.63 0.00 35.87 3.86
1920 2069 7.342769 TCGTACAAGTACAATACATCAGGAT 57.657 36.000 10.63 0.00 35.87 3.24
1921 2070 7.778083 TCGTACAAGTACAATACATCAGGATT 58.222 34.615 10.63 0.00 35.87 3.01
2076 2225 8.076178 TGTACAAAAGAGAGCTAAAAATTCTGC 58.924 33.333 0.00 0.00 0.00 4.26
2085 2234 3.611530 GCTAAAAATTCTGCAACGAGGCA 60.612 43.478 5.71 5.71 42.53 4.75
2157 2308 2.652095 TTGTTACCTCGGGCCGGAG 61.652 63.158 28.76 28.76 0.00 4.63
2548 2706 0.620556 ACATCACACATGGGAGGGAC 59.379 55.000 0.00 0.00 32.80 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.032549 CAGTTCAAGCCTTCGTGTCAAG 60.033 50.000 0.00 0.00 0.00 3.02
127 144 4.347813 CTCTTCGAGCTAAGAACTACTGC 58.652 47.826 0.79 0.00 35.14 4.40
143 160 3.068732 TGGATGAGTGAATAGGCTCTTCG 59.931 47.826 7.95 0.00 37.01 3.79
205 226 2.544694 GCATCGTGGGTCTGATACTCTG 60.545 54.545 0.00 0.00 0.00 3.35
206 227 1.683917 GCATCGTGGGTCTGATACTCT 59.316 52.381 0.00 0.00 0.00 3.24
207 228 1.409064 TGCATCGTGGGTCTGATACTC 59.591 52.381 0.00 0.00 0.00 2.59
208 229 1.137086 GTGCATCGTGGGTCTGATACT 59.863 52.381 0.00 0.00 0.00 2.12
209 230 1.134818 TGTGCATCGTGGGTCTGATAC 60.135 52.381 0.00 0.00 0.00 2.24
210 231 1.190643 TGTGCATCGTGGGTCTGATA 58.809 50.000 0.00 0.00 0.00 2.15
250 271 3.724914 TTGTGGCGTGCGTCTGACA 62.725 57.895 8.73 0.00 0.00 3.58
251 272 2.430080 CTTTGTGGCGTGCGTCTGAC 62.430 60.000 0.00 0.00 0.00 3.51
252 273 2.202946 TTTGTGGCGTGCGTCTGA 60.203 55.556 0.00 0.00 0.00 3.27
253 274 2.162921 CTCTTTGTGGCGTGCGTCTG 62.163 60.000 0.00 0.00 0.00 3.51
254 275 1.956170 CTCTTTGTGGCGTGCGTCT 60.956 57.895 0.00 0.00 0.00 4.18
255 276 2.551270 CTCTTTGTGGCGTGCGTC 59.449 61.111 0.00 0.00 0.00 5.19
256 277 3.649986 GCTCTTTGTGGCGTGCGT 61.650 61.111 0.00 0.00 0.00 5.24
257 278 2.896801 AAGCTCTTTGTGGCGTGCG 61.897 57.895 0.00 0.00 0.00 5.34
258 279 1.370900 CAAGCTCTTTGTGGCGTGC 60.371 57.895 0.00 0.00 32.23 5.34
259 280 1.283793 CCAAGCTCTTTGTGGCGTG 59.716 57.895 0.00 0.00 37.60 5.34
260 281 3.749981 CCAAGCTCTTTGTGGCGT 58.250 55.556 0.00 0.00 34.87 5.68
263 284 1.288127 GCTGCCAAGCTCTTTGTGG 59.712 57.895 0.00 0.00 46.60 4.17
264 285 4.959446 GCTGCCAAGCTCTTTGTG 57.041 55.556 0.00 0.00 46.60 3.33
272 293 2.666190 TGTCTGACGCTGCCAAGC 60.666 61.111 2.98 0.00 46.66 4.01
273 294 2.661566 CGTGTCTGACGCTGCCAAG 61.662 63.158 18.17 0.00 42.21 3.61
274 295 2.661537 CGTGTCTGACGCTGCCAA 60.662 61.111 18.17 0.00 42.21 4.52
449 496 4.498850 CGTGTATATTCTGCTCTGCTCTGT 60.499 45.833 0.00 0.00 0.00 3.41
599 650 3.795041 CAGAGGAGCAGCTGGGGG 61.795 72.222 17.12 0.00 0.00 5.40
693 747 1.413382 GATGTGCCTCATCGATCGAC 58.587 55.000 22.06 7.90 42.57 4.20
703 757 2.034053 CGAGGAGAAGTAGATGTGCCTC 59.966 54.545 0.00 0.00 37.63 4.70
717 799 1.893544 ACACGAAGAAGACGAGGAGA 58.106 50.000 0.00 0.00 34.70 3.71
857 951 4.857588 GCGCTTGCTTATATAGATACACGT 59.142 41.667 0.00 0.00 35.07 4.49
946 1046 0.748005 TGGTAGAGCCGTACCCGTAC 60.748 60.000 9.16 0.00 41.79 3.67
947 1047 0.183492 ATGGTAGAGCCGTACCCGTA 59.817 55.000 9.16 0.00 41.79 4.02
948 1048 0.183492 TATGGTAGAGCCGTACCCGT 59.817 55.000 9.16 2.23 41.79 5.28
949 1049 1.000938 GTTATGGTAGAGCCGTACCCG 60.001 57.143 9.16 0.00 41.79 5.28
950 1050 1.000938 CGTTATGGTAGAGCCGTACCC 60.001 57.143 9.16 0.00 41.79 3.69
951 1051 1.678101 ACGTTATGGTAGAGCCGTACC 59.322 52.381 5.32 5.32 42.68 3.34
952 1052 2.724349 CACGTTATGGTAGAGCCGTAC 58.276 52.381 0.00 0.00 38.40 3.67
953 1053 1.066002 GCACGTTATGGTAGAGCCGTA 59.934 52.381 0.00 0.00 41.21 4.02
1055 1170 4.471908 AGCACGATGCCGATGCCA 62.472 61.111 6.39 0.00 46.52 4.92
1056 1171 3.643978 GAGCACGATGCCGATGCC 61.644 66.667 6.39 0.00 46.52 4.40
1057 1172 3.993234 CGAGCACGATGCCGATGC 61.993 66.667 0.00 0.00 46.52 3.91
1058 1173 2.583319 ACGAGCACGATGCCGATG 60.583 61.111 11.40 7.07 46.52 3.84
1059 1174 2.583319 CACGAGCACGATGCCGAT 60.583 61.111 11.40 7.98 46.52 4.18
1089 1210 0.840617 TACTTGGTGTGGTTCTGGCA 59.159 50.000 0.00 0.00 0.00 4.92
1173 1294 3.823330 GCCATGTCAGCTGCTGGC 61.823 66.667 27.69 27.69 46.54 4.85
1295 1416 4.477975 CTGCCCTCCGTCGTCGTC 62.478 72.222 0.71 0.00 35.01 4.20
1319 1440 1.264749 TTCTCCTGATGGGACGGTGG 61.265 60.000 0.00 0.00 39.58 4.61
1355 1476 1.383386 GTTCCTCCTCCCTCTCCCC 60.383 68.421 0.00 0.00 0.00 4.81
1361 1482 0.423544 ATCCCTTGTTCCTCCTCCCT 59.576 55.000 0.00 0.00 0.00 4.20
1372 1493 1.215647 GAGCGTCGTCATCCCTTGT 59.784 57.895 0.00 0.00 0.00 3.16
1622 1761 5.005971 CACCAAACAAGAGCAAAATCACAAG 59.994 40.000 0.00 0.00 0.00 3.16
1670 1809 2.963782 ACTTACAACACTCGAGGAACCT 59.036 45.455 18.41 0.00 0.00 3.50
1671 1810 3.382048 ACTTACAACACTCGAGGAACC 57.618 47.619 18.41 0.00 0.00 3.62
1710 1852 5.896922 AAAGAAGAGATTCATATGTCGCG 57.103 39.130 0.00 0.00 0.00 5.87
1720 1862 8.401709 ACTTGTTGTCTTCAAAAGAAGAGATTC 58.598 33.333 8.09 5.15 41.31 2.52
1722 1864 7.872113 ACTTGTTGTCTTCAAAAGAAGAGAT 57.128 32.000 8.09 0.00 41.31 2.75
1739 1881 5.287274 GTGATCAGTCATCGTCTACTTGTTG 59.713 44.000 0.00 0.00 36.60 3.33
1776 1924 2.688958 ACCGGCCGATAGCTATTCTATC 59.311 50.000 30.73 0.00 46.53 2.08
1777 1925 2.736347 ACCGGCCGATAGCTATTCTAT 58.264 47.619 30.73 0.00 43.05 1.98
1778 1926 2.211250 ACCGGCCGATAGCTATTCTA 57.789 50.000 30.73 0.00 43.05 2.10
1779 1927 2.093106 CTACCGGCCGATAGCTATTCT 58.907 52.381 30.73 0.00 43.05 2.40
1780 1928 1.469423 GCTACCGGCCGATAGCTATTC 60.469 57.143 38.95 14.47 40.59 1.75
1781 1929 0.531200 GCTACCGGCCGATAGCTATT 59.469 55.000 38.95 10.43 40.59 1.73
1782 1930 2.190756 GCTACCGGCCGATAGCTAT 58.809 57.895 38.95 5.76 40.59 2.97
1783 1931 3.677527 GCTACCGGCCGATAGCTA 58.322 61.111 38.95 13.91 40.59 3.32
1785 1933 2.258897 GAGCTACCGGCCGATAGC 59.741 66.667 39.40 39.40 43.49 2.97
1786 1934 2.561885 CGAGCTACCGGCCGATAG 59.438 66.667 30.73 26.68 43.05 2.08
1787 1935 2.981909 CCGAGCTACCGGCCGATA 60.982 66.667 30.73 14.83 43.25 2.92
1794 1942 0.389948 AAAACTCTGCCGAGCTACCG 60.390 55.000 4.89 0.00 41.09 4.02
1795 1943 1.079503 CAAAACTCTGCCGAGCTACC 58.920 55.000 4.89 0.00 41.09 3.18
1796 1944 0.444260 GCAAAACTCTGCCGAGCTAC 59.556 55.000 4.89 0.00 41.09 3.58
1797 1945 0.321671 AGCAAAACTCTGCCGAGCTA 59.678 50.000 4.89 0.00 43.73 3.32
1798 1946 0.536006 AAGCAAAACTCTGCCGAGCT 60.536 50.000 4.89 0.00 43.73 4.09
1799 1947 0.312102 AAAGCAAAACTCTGCCGAGC 59.688 50.000 4.89 0.00 43.73 5.03
1800 1948 2.808543 AGTAAAGCAAAACTCTGCCGAG 59.191 45.455 3.27 3.27 43.73 4.63
1801 1949 2.846193 AGTAAAGCAAAACTCTGCCGA 58.154 42.857 0.00 0.00 43.73 5.54
1802 1950 3.746492 AGTAGTAAAGCAAAACTCTGCCG 59.254 43.478 0.00 0.00 43.73 5.69
1803 1951 5.932883 AGTAGTAGTAAAGCAAAACTCTGCC 59.067 40.000 0.00 0.00 43.73 4.85
1804 1952 8.530269 TTAGTAGTAGTAAAGCAAAACTCTGC 57.470 34.615 0.00 0.00 42.97 4.26
1834 1982 3.270877 CGTGCTAAGGCTAAATCCTTGT 58.729 45.455 5.38 0.00 45.51 3.16
1835 1983 2.614057 CCGTGCTAAGGCTAAATCCTTG 59.386 50.000 5.38 0.00 45.51 3.61
1890 2039 7.704899 TGATGTATTGTACTTGTACGAATCCTG 59.295 37.037 5.12 0.00 0.00 3.86
1891 2040 7.778083 TGATGTATTGTACTTGTACGAATCCT 58.222 34.615 5.12 0.00 0.00 3.24
1892 2041 7.169308 CCTGATGTATTGTACTTGTACGAATCC 59.831 40.741 5.12 0.58 0.00 3.01
1893 2042 7.919091 TCCTGATGTATTGTACTTGTACGAATC 59.081 37.037 5.12 5.16 0.00 2.52
1894 2043 7.778083 TCCTGATGTATTGTACTTGTACGAAT 58.222 34.615 5.12 8.56 0.00 3.34
1895 2044 7.160547 TCCTGATGTATTGTACTTGTACGAA 57.839 36.000 5.12 2.72 0.00 3.85
1896 2045 6.762702 TCCTGATGTATTGTACTTGTACGA 57.237 37.500 3.63 3.63 0.00 3.43
1897 2046 7.704899 TGAATCCTGATGTATTGTACTTGTACG 59.295 37.037 6.46 0.00 0.00 3.67
1898 2047 8.942338 TGAATCCTGATGTATTGTACTTGTAC 57.058 34.615 4.14 4.14 0.00 2.90
1899 2048 8.204160 CCTGAATCCTGATGTATTGTACTTGTA 58.796 37.037 0.00 0.00 0.00 2.41
1900 2049 7.050377 CCTGAATCCTGATGTATTGTACTTGT 58.950 38.462 0.00 0.00 0.00 3.16
1901 2050 7.275183 TCCTGAATCCTGATGTATTGTACTTG 58.725 38.462 0.00 0.00 0.00 3.16
1902 2051 7.126421 ACTCCTGAATCCTGATGTATTGTACTT 59.874 37.037 0.00 0.00 0.00 2.24
1903 2052 6.613271 ACTCCTGAATCCTGATGTATTGTACT 59.387 38.462 0.00 0.00 0.00 2.73
1904 2053 6.821388 ACTCCTGAATCCTGATGTATTGTAC 58.179 40.000 0.00 0.00 0.00 2.90
1905 2054 7.255977 GCTACTCCTGAATCCTGATGTATTGTA 60.256 40.741 0.00 0.00 0.00 2.41
1906 2055 5.965033 ACTCCTGAATCCTGATGTATTGT 57.035 39.130 0.00 0.00 0.00 2.71
1907 2056 5.931146 GCTACTCCTGAATCCTGATGTATTG 59.069 44.000 0.00 0.00 0.00 1.90
1908 2057 5.604231 TGCTACTCCTGAATCCTGATGTATT 59.396 40.000 0.00 0.00 0.00 1.89
1909 2058 5.150715 TGCTACTCCTGAATCCTGATGTAT 58.849 41.667 0.00 0.00 0.00 2.29
1910 2059 4.546674 TGCTACTCCTGAATCCTGATGTA 58.453 43.478 0.00 0.00 0.00 2.29
1911 2060 3.378512 TGCTACTCCTGAATCCTGATGT 58.621 45.455 0.00 0.00 0.00 3.06
1912 2061 4.620589 ATGCTACTCCTGAATCCTGATG 57.379 45.455 0.00 0.00 0.00 3.07
1913 2062 5.279910 GCTAATGCTACTCCTGAATCCTGAT 60.280 44.000 0.00 0.00 36.03 2.90
1914 2063 4.039730 GCTAATGCTACTCCTGAATCCTGA 59.960 45.833 0.00 0.00 36.03 3.86
1915 2064 4.314121 GCTAATGCTACTCCTGAATCCTG 58.686 47.826 0.00 0.00 36.03 3.86
1916 2065 3.326297 GGCTAATGCTACTCCTGAATCCT 59.674 47.826 0.00 0.00 39.59 3.24
1917 2066 3.071602 TGGCTAATGCTACTCCTGAATCC 59.928 47.826 0.00 0.00 39.59 3.01
1918 2067 4.061596 GTGGCTAATGCTACTCCTGAATC 58.938 47.826 0.00 0.00 45.51 2.52
1919 2068 4.078639 GTGGCTAATGCTACTCCTGAAT 57.921 45.455 0.00 0.00 45.51 2.57
1920 2069 3.543680 GTGGCTAATGCTACTCCTGAA 57.456 47.619 0.00 0.00 45.51 3.02
2076 2225 3.347411 GGCTAGTAGTGCCTCGTTG 57.653 57.895 0.00 0.00 46.38 4.10
2107 2256 4.932146 AGAACAAAACAAAATGGTCCTCG 58.068 39.130 0.00 0.00 33.68 4.63
2141 2292 2.757099 TCTCCGGCCCGAGGTAAC 60.757 66.667 19.35 0.00 0.00 2.50
2142 2293 2.441532 CTCTCCGGCCCGAGGTAA 60.442 66.667 19.35 1.53 0.00 2.85


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

AutoCloner maintained by Alex Coulton.