Multiple sequence alignment - TraesCS6A01G341500

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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 TraesCS6A01G341500 chr6A 100.000 2301 0 0 1 2301 574248221 574250521 0.000000e+00 4250
1 TraesCS6A01G341500 chr6A 87.059 425 53 2 1665 2088 292861123 292860700 1.600000e-131 479
2 TraesCS6A01G341500 chr6A 80.402 199 26 8 46 237 292862662 292862470 3.080000e-29 139
3 TraesCS6A01G341500 chr2A 96.555 2090 67 4 1 2088 251254161 251256247 0.000000e+00 3456
4 TraesCS6A01G341500 chr2A 94.829 1083 52 3 525 1605 12657025 12658105 0.000000e+00 1687
5 TraesCS6A01G341500 chr2A 94.274 489 18 3 1601 2089 12659671 12660149 0.000000e+00 739
6 TraesCS6A01G341500 chr2A 93.917 411 16 3 1 407 12636098 12636503 1.510000e-171 612
7 TraesCS6A01G341500 chr2A 75.074 678 130 28 683 1353 768939303 768939948 1.740000e-71 279
8 TraesCS6A01G341500 chr4A 81.533 2139 273 74 1 2088 398096792 398098859 0.000000e+00 1650
9 TraesCS6A01G341500 chr3A 83.189 1505 178 36 622 2088 156351166 156352633 0.000000e+00 1308
10 TraesCS6A01G341500 chr3A 81.165 1391 182 37 1 1375 117457083 117458409 0.000000e+00 1044
11 TraesCS6A01G341500 chr3A 86.416 611 68 10 1483 2088 117458483 117459083 0.000000e+00 654
12 TraesCS6A01G341500 chr3A 91.628 215 17 1 2088 2301 175637538 175637752 1.730000e-76 296
13 TraesCS6A01G341500 chrUn 83.202 887 109 10 1211 2088 38161990 38161135 0.000000e+00 776
14 TraesCS6A01G341500 chrUn 85.340 382 55 1 1708 2088 435670925 435671306 5.960000e-106 394
15 TraesCS6A01G341500 chrUn 92.991 214 15 0 2088 2301 203649400 203649187 1.720000e-81 313
16 TraesCS6A01G341500 chrUn 92.523 214 16 0 2088 2301 143788360 143788573 7.990000e-80 307
17 TraesCS6A01G341500 chr7A 85.864 382 53 1 1708 2088 715059741 715059360 2.750000e-109 405
18 TraesCS6A01G341500 chr7A 75.814 430 68 27 113 520 393446621 393446206 3.900000e-43 185
19 TraesCS6A01G341500 chr7A 84.699 183 22 4 46 227 648204295 648204118 6.530000e-41 178
20 TraesCS6A01G341500 chr1B 81.728 405 54 12 772 1172 121441796 121442184 1.030000e-83 320
21 TraesCS6A01G341500 chr1B 90.187 214 21 0 2088 2301 567972006 567972219 1.740000e-71 279
22 TraesCS6A01G341500 chr5D 92.166 217 16 1 2086 2301 63554289 63554073 2.870000e-79 305
23 TraesCS6A01G341500 chr5D 82.254 355 59 4 1737 2089 42161472 42161824 1.030000e-78 303
24 TraesCS6A01G341500 chr5D 90.233 215 19 2 2088 2301 405212029 405212242 1.740000e-71 279
25 TraesCS6A01G341500 chr2D 92.523 214 14 1 2088 2301 29144680 29144891 2.870000e-79 305
26 TraesCS6A01G341500 chr3B 92.453 212 16 0 2088 2299 84902583 84902794 1.030000e-78 303
27 TraesCS6A01G341500 chr3B 88.710 62 6 1 882 943 742525666 742525606 8.820000e-10 75
28 TraesCS6A01G341500 chr3D 91.509 212 18 0 2088 2299 474652324 474652535 2.240000e-75 292


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 TraesCS6A01G341500 chr6A 574248221 574250521 2300 False 4250 4250 100.0000 1 2301 1 chr6A.!!$F1 2300
1 TraesCS6A01G341500 chr6A 292860700 292862662 1962 True 309 479 83.7305 46 2088 2 chr6A.!!$R1 2042
2 TraesCS6A01G341500 chr2A 251254161 251256247 2086 False 3456 3456 96.5550 1 2088 1 chr2A.!!$F2 2087
3 TraesCS6A01G341500 chr2A 12657025 12660149 3124 False 1213 1687 94.5515 525 2089 2 chr2A.!!$F4 1564
4 TraesCS6A01G341500 chr2A 768939303 768939948 645 False 279 279 75.0740 683 1353 1 chr2A.!!$F3 670
5 TraesCS6A01G341500 chr4A 398096792 398098859 2067 False 1650 1650 81.5330 1 2088 1 chr4A.!!$F1 2087
6 TraesCS6A01G341500 chr3A 156351166 156352633 1467 False 1308 1308 83.1890 622 2088 1 chr3A.!!$F1 1466
7 TraesCS6A01G341500 chr3A 117457083 117459083 2000 False 849 1044 83.7905 1 2088 2 chr3A.!!$F3 2087
8 TraesCS6A01G341500 chrUn 38161135 38161990 855 True 776 776 83.2020 1211 2088 1 chrUn.!!$R1 877

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
659 740 0.250209 CATCCTTCCTCTCATGCCGG 60.25 60.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 3900 0.099082 AACTTTCGCGCCAAAAACGA 59.901 45.0 0.0 0.0 0.0 3.85 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
435 485 1.983119 AACCATCCCACGGATCGCAT 61.983 55.000 0.00 0.00 40.98 4.73
449 499 3.056749 GGATCGCATATCTAAACCGTCCT 60.057 47.826 0.00 0.00 0.00 3.85
455 505 5.221130 GCATATCTAAACCGTCCTGTACTC 58.779 45.833 0.00 0.00 0.00 2.59
581 631 0.465097 ATCCAAATCTCCGCTGCTGG 60.465 55.000 0.00 0.82 0.00 4.85
595 645 3.790437 CTGGACCAGCGCCTCCAT 61.790 66.667 16.99 0.00 35.95 3.41
659 740 0.250209 CATCCTTCCTCTCATGCCGG 60.250 60.000 0.00 0.00 0.00 6.13
1213 1329 1.725169 CCCCACCAGGTTCCCTTTCA 61.725 60.000 0.00 0.00 0.00 2.69
1270 1389 0.030638 GTCAACACGCAGGCAATGTT 59.969 50.000 5.37 5.37 37.02 2.71
1841 3621 2.588877 GCCACGTCGGATCCATGG 60.589 66.667 13.41 13.95 36.56 3.66
1948 3738 5.357032 GTCCATGACGGTTTTAAATGATCCT 59.643 40.000 0.00 0.00 35.57 3.24
2001 3791 7.034416 ACGCGATATACATGACGAATTTTAG 57.966 36.000 15.93 0.00 0.00 1.85
2089 3879 6.374333 TGGATTAACAGAATTCTTGTAGTGGC 59.626 38.462 4.86 0.00 0.00 5.01
2090 3880 5.856126 TTAACAGAATTCTTGTAGTGGCG 57.144 39.130 4.86 0.00 0.00 5.69
2091 3881 2.076863 ACAGAATTCTTGTAGTGGCGC 58.923 47.619 4.86 0.00 0.00 6.53
2092 3882 2.289694 ACAGAATTCTTGTAGTGGCGCT 60.290 45.455 7.64 5.62 0.00 5.92
2093 3883 2.744202 CAGAATTCTTGTAGTGGCGCTT 59.256 45.455 5.61 0.00 0.00 4.68
2094 3884 2.744202 AGAATTCTTGTAGTGGCGCTTG 59.256 45.455 5.61 0.00 0.00 4.01
2095 3885 1.453155 ATTCTTGTAGTGGCGCTTGG 58.547 50.000 5.61 0.00 0.00 3.61
2096 3886 0.605319 TTCTTGTAGTGGCGCTTGGG 60.605 55.000 5.61 0.00 0.00 4.12
2097 3887 2.033448 TTGTAGTGGCGCTTGGGG 59.967 61.111 5.61 0.00 0.00 4.96
2098 3888 3.561120 TTGTAGTGGCGCTTGGGGG 62.561 63.158 5.61 0.00 0.00 5.40
2116 3906 3.795342 CGCCGGCCGAATCGTTTT 61.795 61.111 30.73 0.00 40.02 2.43
2117 3907 2.564458 GCCGGCCGAATCGTTTTT 59.436 55.556 30.73 0.00 0.00 1.94
2118 3908 1.799916 GCCGGCCGAATCGTTTTTG 60.800 57.895 30.73 6.52 0.00 2.44
2119 3909 1.154112 CCGGCCGAATCGTTTTTGG 60.154 57.895 30.73 0.00 0.00 3.28
2120 3910 1.799916 CGGCCGAATCGTTTTTGGC 60.800 57.895 24.07 18.28 44.98 4.52
2121 3911 1.799916 GGCCGAATCGTTTTTGGCG 60.800 57.895 19.21 3.07 46.66 5.69
2122 3912 2.433334 GCCGAATCGTTTTTGGCGC 61.433 57.895 13.77 0.00 35.77 6.53
2123 3913 2.143458 CCGAATCGTTTTTGGCGCG 61.143 57.895 0.00 0.00 0.00 6.86
2124 3914 1.154562 CGAATCGTTTTTGGCGCGA 60.155 52.632 12.10 0.00 39.02 5.87
2125 3915 0.723129 CGAATCGTTTTTGGCGCGAA 60.723 50.000 12.10 0.00 38.17 4.70
2126 3916 1.400550 GAATCGTTTTTGGCGCGAAA 58.599 45.000 13.91 13.91 38.17 3.46
2127 3917 1.382088 GAATCGTTTTTGGCGCGAAAG 59.618 47.619 17.08 6.95 38.17 2.62
2128 3918 0.309612 ATCGTTTTTGGCGCGAAAGT 59.690 45.000 17.08 1.18 38.17 2.66
2129 3919 0.099082 TCGTTTTTGGCGCGAAAGTT 59.901 45.000 17.08 0.00 0.00 2.66
2130 3920 0.225986 CGTTTTTGGCGCGAAAGTTG 59.774 50.000 17.08 7.64 0.00 3.16
2131 3921 0.574922 GTTTTTGGCGCGAAAGTTGG 59.425 50.000 17.08 0.00 0.00 3.77
2132 3922 1.148759 TTTTTGGCGCGAAAGTTGGC 61.149 50.000 17.08 0.00 35.39 4.52
2138 3928 4.103103 GCGAAAGTTGGCGAGCCC 62.103 66.667 12.05 0.00 34.56 5.19
2139 3929 2.358737 CGAAAGTTGGCGAGCCCT 60.359 61.111 12.05 0.00 34.56 5.19
2140 3930 2.391389 CGAAAGTTGGCGAGCCCTC 61.391 63.158 12.05 4.70 34.56 4.30
2141 3931 2.034221 AAAGTTGGCGAGCCCTCC 59.966 61.111 12.05 0.00 34.56 4.30
2142 3932 2.470938 GAAAGTTGGCGAGCCCTCCT 62.471 60.000 12.05 1.70 34.56 3.69
2143 3933 2.069165 AAAGTTGGCGAGCCCTCCTT 62.069 55.000 12.05 7.78 34.56 3.36
2144 3934 2.747855 GTTGGCGAGCCCTCCTTG 60.748 66.667 12.05 0.00 34.56 3.61
2145 3935 4.033776 TTGGCGAGCCCTCCTTGG 62.034 66.667 12.05 0.00 34.56 3.61
2147 3937 3.717294 GGCGAGCCCTCCTTGGAA 61.717 66.667 1.97 0.00 38.35 3.53
2148 3938 2.351276 GCGAGCCCTCCTTGGAAA 59.649 61.111 0.00 0.00 38.35 3.13
2149 3939 1.077429 GCGAGCCCTCCTTGGAAAT 60.077 57.895 0.00 0.00 38.35 2.17
2150 3940 1.379642 GCGAGCCCTCCTTGGAAATG 61.380 60.000 0.00 0.00 38.35 2.32
2151 3941 0.253044 CGAGCCCTCCTTGGAAATGA 59.747 55.000 0.00 0.00 38.35 2.57
2152 3942 1.756430 GAGCCCTCCTTGGAAATGAC 58.244 55.000 0.00 0.00 38.35 3.06
2153 3943 1.283321 GAGCCCTCCTTGGAAATGACT 59.717 52.381 0.00 0.00 38.35 3.41
2154 3944 1.283321 AGCCCTCCTTGGAAATGACTC 59.717 52.381 0.00 0.00 38.35 3.36
2155 3945 2.014068 GCCCTCCTTGGAAATGACTCG 61.014 57.143 0.00 0.00 38.35 4.18
2156 3946 1.407437 CCCTCCTTGGAAATGACTCGG 60.407 57.143 0.00 0.00 38.35 4.63
2157 3947 1.373570 CTCCTTGGAAATGACTCGGC 58.626 55.000 0.00 0.00 0.00 5.54
2158 3948 0.984230 TCCTTGGAAATGACTCGGCT 59.016 50.000 0.00 0.00 0.00 5.52
2159 3949 1.066143 TCCTTGGAAATGACTCGGCTC 60.066 52.381 0.00 0.00 0.00 4.70
2160 3950 1.065854 CCTTGGAAATGACTCGGCTCT 60.066 52.381 0.00 0.00 0.00 4.09
2161 3951 2.616510 CCTTGGAAATGACTCGGCTCTT 60.617 50.000 0.00 0.00 0.00 2.85
2162 3952 2.386661 TGGAAATGACTCGGCTCTTC 57.613 50.000 0.00 0.00 0.00 2.87
2163 3953 1.902508 TGGAAATGACTCGGCTCTTCT 59.097 47.619 0.00 0.00 0.00 2.85
2164 3954 2.093973 TGGAAATGACTCGGCTCTTCTC 60.094 50.000 0.00 0.00 0.00 2.87
2165 3955 2.189342 GAAATGACTCGGCTCTTCTCG 58.811 52.381 0.00 0.00 0.00 4.04
2166 3956 0.179124 AATGACTCGGCTCTTCTCGC 60.179 55.000 0.00 0.00 0.00 5.03
2167 3957 2.010582 ATGACTCGGCTCTTCTCGCC 62.011 60.000 0.00 0.00 44.11 5.54
2172 3962 2.888051 GGCTCTTCTCGCCGCTTC 60.888 66.667 0.00 0.00 37.87 3.86
2173 3963 3.251043 GCTCTTCTCGCCGCTTCG 61.251 66.667 0.00 0.00 0.00 3.79
2174 3964 2.179517 CTCTTCTCGCCGCTTCGT 59.820 61.111 0.00 0.00 0.00 3.85
2175 3965 1.870016 CTCTTCTCGCCGCTTCGTC 60.870 63.158 0.00 0.00 0.00 4.20
2176 3966 3.241059 CTTCTCGCCGCTTCGTCG 61.241 66.667 0.00 0.00 0.00 5.12
2177 3967 3.948086 CTTCTCGCCGCTTCGTCGT 62.948 63.158 0.00 0.00 0.00 4.34
2178 3968 3.940975 TTCTCGCCGCTTCGTCGTC 62.941 63.158 0.00 0.00 0.00 4.20
2182 3972 4.415332 GCCGCTTCGTCGTCCTCA 62.415 66.667 0.00 0.00 0.00 3.86
2183 3973 2.490217 CCGCTTCGTCGTCCTCAT 59.510 61.111 0.00 0.00 0.00 2.90
2184 3974 1.586564 CCGCTTCGTCGTCCTCATC 60.587 63.158 0.00 0.00 0.00 2.92
2185 3975 1.934956 CGCTTCGTCGTCCTCATCG 60.935 63.158 0.00 0.00 0.00 3.84
2186 3976 2.224885 GCTTCGTCGTCCTCATCGC 61.225 63.158 0.00 0.00 0.00 4.58
2187 3977 1.586564 CTTCGTCGTCCTCATCGCC 60.587 63.158 0.00 0.00 0.00 5.54
2188 3978 1.994507 CTTCGTCGTCCTCATCGCCT 61.995 60.000 0.00 0.00 0.00 5.52
2189 3979 1.989966 TTCGTCGTCCTCATCGCCTC 61.990 60.000 0.00 0.00 0.00 4.70
2190 3980 2.761195 CGTCGTCCTCATCGCCTCA 61.761 63.158 0.00 0.00 0.00 3.86
2191 3981 1.064946 GTCGTCCTCATCGCCTCAG 59.935 63.158 0.00 0.00 0.00 3.35
2192 3982 1.378646 TCGTCCTCATCGCCTCAGT 60.379 57.895 0.00 0.00 0.00 3.41
2193 3983 0.965866 TCGTCCTCATCGCCTCAGTT 60.966 55.000 0.00 0.00 0.00 3.16
2194 3984 0.526524 CGTCCTCATCGCCTCAGTTC 60.527 60.000 0.00 0.00 0.00 3.01
2195 3985 0.179097 GTCCTCATCGCCTCAGTTCC 60.179 60.000 0.00 0.00 0.00 3.62
2196 3986 1.144936 CCTCATCGCCTCAGTTCCC 59.855 63.158 0.00 0.00 0.00 3.97
2197 3987 1.227089 CTCATCGCCTCAGTTCCCG 60.227 63.158 0.00 0.00 0.00 5.14
2198 3988 2.892425 CATCGCCTCAGTTCCCGC 60.892 66.667 0.00 0.00 0.00 6.13
2199 3989 4.514577 ATCGCCTCAGTTCCCGCG 62.515 66.667 0.00 0.00 45.76 6.46
2204 3994 4.735132 CTCAGTTCCCGCGGCGAA 62.735 66.667 25.92 21.49 0.00 4.70
2205 3995 4.077184 TCAGTTCCCGCGGCGAAT 62.077 61.111 25.92 11.83 0.00 3.34
2206 3996 3.564027 CAGTTCCCGCGGCGAATC 61.564 66.667 25.92 19.33 0.00 2.52
2207 3997 4.077184 AGTTCCCGCGGCGAATCA 62.077 61.111 25.92 7.22 0.00 2.57
2208 3998 3.122323 GTTCCCGCGGCGAATCAA 61.122 61.111 25.92 7.53 0.00 2.57
2209 3999 2.124901 TTCCCGCGGCGAATCAAT 60.125 55.556 25.92 0.00 0.00 2.57
2210 4000 2.468670 TTCCCGCGGCGAATCAATG 61.469 57.895 25.92 2.11 0.00 2.82
2211 4001 4.612536 CCCGCGGCGAATCAATGC 62.613 66.667 25.92 0.00 0.00 3.56
2218 4008 3.727419 GCGAATCAATGCCAAAGCT 57.273 47.368 0.00 0.00 40.80 3.74
2219 4009 1.274596 GCGAATCAATGCCAAAGCTG 58.725 50.000 0.00 0.00 40.80 4.24
2220 4010 1.403249 GCGAATCAATGCCAAAGCTGT 60.403 47.619 0.00 0.00 40.80 4.40
2221 4011 2.523015 CGAATCAATGCCAAAGCTGTC 58.477 47.619 0.00 0.00 40.80 3.51
2222 4012 2.523015 GAATCAATGCCAAAGCTGTCG 58.477 47.619 0.00 0.00 40.80 4.35
2223 4013 0.171903 ATCAATGCCAAAGCTGTCGC 59.828 50.000 0.00 0.00 40.80 5.19
2224 4014 1.798725 CAATGCCAAAGCTGTCGCG 60.799 57.895 0.00 0.00 42.32 5.87
2225 4015 2.981560 AATGCCAAAGCTGTCGCGG 61.982 57.895 6.13 0.00 42.32 6.46
2242 4032 2.586792 GCGGTCAGCCTCCTTCAT 59.413 61.111 0.00 0.00 40.81 2.57
2243 4033 1.078143 GCGGTCAGCCTCCTTCATT 60.078 57.895 0.00 0.00 40.81 2.57
2244 4034 1.372087 GCGGTCAGCCTCCTTCATTG 61.372 60.000 0.00 0.00 40.81 2.82
2245 4035 0.250234 CGGTCAGCCTCCTTCATTGA 59.750 55.000 0.00 0.00 0.00 2.57
2246 4036 1.134280 CGGTCAGCCTCCTTCATTGAT 60.134 52.381 0.00 0.00 0.00 2.57
2247 4037 2.295885 GGTCAGCCTCCTTCATTGATG 58.704 52.381 0.00 0.00 0.00 3.07
2248 4038 1.674962 GTCAGCCTCCTTCATTGATGC 59.325 52.381 0.00 0.00 0.00 3.91
2249 4039 1.030457 CAGCCTCCTTCATTGATGCC 58.970 55.000 0.00 0.00 0.00 4.40
2250 4040 0.924823 AGCCTCCTTCATTGATGCCT 59.075 50.000 0.00 0.00 0.00 4.75
2251 4041 1.133853 AGCCTCCTTCATTGATGCCTC 60.134 52.381 0.00 0.00 0.00 4.70
2252 4042 1.409241 GCCTCCTTCATTGATGCCTCA 60.409 52.381 0.00 0.00 0.00 3.86
2253 4043 2.752154 GCCTCCTTCATTGATGCCTCAT 60.752 50.000 0.00 0.00 0.00 2.90
2254 4044 2.885266 CCTCCTTCATTGATGCCTCATG 59.115 50.000 0.00 0.00 0.00 3.07
2255 4045 2.885266 CTCCTTCATTGATGCCTCATGG 59.115 50.000 0.00 0.00 0.00 3.66
2256 4046 1.961394 CCTTCATTGATGCCTCATGGG 59.039 52.381 0.00 0.00 38.36 4.00
2275 4065 4.373116 GGCGCAGTGAAGACCGGA 62.373 66.667 9.46 0.00 0.00 5.14
2276 4066 3.112709 GCGCAGTGAAGACCGGAC 61.113 66.667 9.46 0.10 0.00 4.79
2277 4067 2.805353 CGCAGTGAAGACCGGACG 60.805 66.667 9.46 0.00 0.00 4.79
2278 4068 2.649034 GCAGTGAAGACCGGACGA 59.351 61.111 9.46 0.00 0.00 4.20
2279 4069 1.733399 GCAGTGAAGACCGGACGAC 60.733 63.158 9.46 1.68 0.00 4.34
2280 4070 1.442184 CAGTGAAGACCGGACGACG 60.442 63.158 9.46 0.00 43.80 5.12
2281 4071 2.804090 GTGAAGACCGGACGACGC 60.804 66.667 9.46 4.75 42.52 5.19
2282 4072 3.289062 TGAAGACCGGACGACGCA 61.289 61.111 9.46 0.00 42.52 5.24
2283 4073 2.804090 GAAGACCGGACGACGCAC 60.804 66.667 9.46 0.00 42.52 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 79 3.329386 AGTCTGTCACACCATGATTTCG 58.671 45.455 0.00 0.00 40.28 3.46
331 381 3.558418 TCGTTTCCTTGGAGAAAAGAACG 59.442 43.478 12.92 12.92 39.98 3.95
435 485 5.748402 TCAGAGTACAGGACGGTTTAGATA 58.252 41.667 0.00 0.00 0.00 1.98
449 499 2.017782 GCCGTCAGATCTCAGAGTACA 58.982 52.381 0.00 0.00 0.00 2.90
455 505 1.028130 TGCTAGCCGTCAGATCTCAG 58.972 55.000 13.29 0.00 0.00 3.35
659 740 4.489771 ATGGGTACGGCTGGCTGC 62.490 66.667 7.96 7.96 41.94 5.25
762 864 1.144936 GAGAAGAGGACCATGCGGG 59.855 63.158 0.00 0.00 44.81 6.13
844 947 0.932211 ATGTAGGGAGGTAGGACGGT 59.068 55.000 0.00 0.00 0.00 4.83
1213 1329 5.649831 GCCTCAACAAATCCAAAGTAGAGAT 59.350 40.000 0.00 0.00 0.00 2.75
1270 1389 1.066645 AGTCGCATCAACTCATGCTCA 60.067 47.619 4.06 0.00 46.09 4.26
1335 1457 1.065926 TGCATTTCTGGACGCAGATCT 60.066 47.619 0.00 0.00 0.00 2.75
1841 3621 1.080298 GTGCCAGGTCAGCATTTGC 60.080 57.895 0.00 0.00 43.29 3.68
1919 3709 1.544724 AAAACCGTCATGGACCATGG 58.455 50.000 29.97 18.96 41.66 3.66
1948 3738 1.001764 CAGCTGCCCACTCCATGAA 60.002 57.895 0.00 0.00 0.00 2.57
2001 3791 2.483188 GGAAGGGTATGTGTGACGGATC 60.483 54.545 0.00 0.00 0.00 3.36
2099 3889 3.317153 AAAAACGATTCGGCCGGCG 62.317 57.895 27.83 26.79 0.00 6.46
2100 3890 1.799916 CAAAAACGATTCGGCCGGC 60.800 57.895 27.83 21.18 0.00 6.13
2101 3891 1.154112 CCAAAAACGATTCGGCCGG 60.154 57.895 27.83 11.94 0.00 6.13
2102 3892 1.799916 GCCAAAAACGATTCGGCCG 60.800 57.895 22.12 22.12 36.73 6.13
2103 3893 1.799916 CGCCAAAAACGATTCGGCC 60.800 57.895 11.29 0.00 39.69 6.13
2104 3894 2.433334 GCGCCAAAAACGATTCGGC 61.433 57.895 11.29 8.30 39.45 5.54
2105 3895 2.143458 CGCGCCAAAAACGATTCGG 61.143 57.895 11.29 0.00 0.00 4.30
2106 3896 0.723129 TTCGCGCCAAAAACGATTCG 60.723 50.000 0.00 4.14 35.48 3.34
2107 3897 1.382088 CTTTCGCGCCAAAAACGATTC 59.618 47.619 0.00 0.00 35.48 2.52
2108 3898 1.268845 ACTTTCGCGCCAAAAACGATT 60.269 42.857 0.00 0.00 35.48 3.34
2109 3899 0.309612 ACTTTCGCGCCAAAAACGAT 59.690 45.000 0.00 0.00 35.48 3.73
2110 3900 0.099082 AACTTTCGCGCCAAAAACGA 59.901 45.000 0.00 0.00 0.00 3.85
2111 3901 0.225986 CAACTTTCGCGCCAAAAACG 59.774 50.000 0.00 0.00 0.00 3.60
2112 3902 0.574922 CCAACTTTCGCGCCAAAAAC 59.425 50.000 0.00 0.00 0.00 2.43
2113 3903 1.148759 GCCAACTTTCGCGCCAAAAA 61.149 50.000 0.00 0.00 0.00 1.94
2114 3904 1.590259 GCCAACTTTCGCGCCAAAA 60.590 52.632 0.00 1.69 0.00 2.44
2115 3905 2.026879 GCCAACTTTCGCGCCAAA 59.973 55.556 0.00 0.00 0.00 3.28
2116 3906 4.320928 CGCCAACTTTCGCGCCAA 62.321 61.111 0.00 0.00 42.17 4.52
2121 3911 4.103103 GGGCTCGCCAACTTTCGC 62.103 66.667 10.51 0.00 37.98 4.70
2122 3912 2.358737 AGGGCTCGCCAACTTTCG 60.359 61.111 10.51 0.00 37.98 3.46
2123 3913 2.041115 GGAGGGCTCGCCAACTTTC 61.041 63.158 10.51 0.00 37.98 2.62
2124 3914 2.034221 GGAGGGCTCGCCAACTTT 59.966 61.111 10.51 0.00 37.98 2.66
2125 3915 2.529744 AAGGAGGGCTCGCCAACTT 61.530 57.895 9.79 7.60 37.98 2.66
2126 3916 2.930562 AAGGAGGGCTCGCCAACT 60.931 61.111 9.79 0.00 37.98 3.16
2127 3917 2.747855 CAAGGAGGGCTCGCCAAC 60.748 66.667 9.79 2.87 37.98 3.77
2128 3918 4.033776 CCAAGGAGGGCTCGCCAA 62.034 66.667 9.79 0.00 37.98 4.52
2130 3920 2.558380 ATTTCCAAGGAGGGCTCGCC 62.558 60.000 0.00 0.00 38.24 5.54
2131 3921 1.077429 ATTTCCAAGGAGGGCTCGC 60.077 57.895 0.00 0.00 38.24 5.03
2132 3922 0.253044 TCATTTCCAAGGAGGGCTCG 59.747 55.000 0.00 0.00 38.24 5.03
2133 3923 1.283321 AGTCATTTCCAAGGAGGGCTC 59.717 52.381 0.00 0.00 38.24 4.70
2134 3924 1.283321 GAGTCATTTCCAAGGAGGGCT 59.717 52.381 0.00 0.00 38.24 5.19
2135 3925 1.756430 GAGTCATTTCCAAGGAGGGC 58.244 55.000 0.00 0.00 38.24 5.19
2136 3926 1.407437 CCGAGTCATTTCCAAGGAGGG 60.407 57.143 0.00 0.00 38.24 4.30
2137 3927 2.014068 GCCGAGTCATTTCCAAGGAGG 61.014 57.143 0.00 0.00 39.47 4.30
2138 3928 1.065854 AGCCGAGTCATTTCCAAGGAG 60.066 52.381 0.00 0.00 0.00 3.69
2139 3929 0.984230 AGCCGAGTCATTTCCAAGGA 59.016 50.000 0.00 0.00 0.00 3.36
2140 3930 1.065854 AGAGCCGAGTCATTTCCAAGG 60.066 52.381 0.00 0.00 0.00 3.61
2141 3931 2.393271 AGAGCCGAGTCATTTCCAAG 57.607 50.000 0.00 0.00 0.00 3.61
2142 3932 2.303022 AGAAGAGCCGAGTCATTTCCAA 59.697 45.455 0.00 0.00 0.00 3.53
2143 3933 1.902508 AGAAGAGCCGAGTCATTTCCA 59.097 47.619 0.00 0.00 0.00 3.53
2144 3934 2.545731 GAGAAGAGCCGAGTCATTTCC 58.454 52.381 0.00 0.00 0.00 3.13
2145 3935 2.189342 CGAGAAGAGCCGAGTCATTTC 58.811 52.381 0.00 0.00 0.00 2.17
2146 3936 1.737363 GCGAGAAGAGCCGAGTCATTT 60.737 52.381 0.00 0.00 0.00 2.32
2147 3937 0.179124 GCGAGAAGAGCCGAGTCATT 60.179 55.000 0.00 0.00 0.00 2.57
2148 3938 1.435515 GCGAGAAGAGCCGAGTCAT 59.564 57.895 0.00 0.00 0.00 3.06
2149 3939 2.701780 GGCGAGAAGAGCCGAGTCA 61.702 63.158 0.00 0.00 45.58 3.41
2150 3940 2.103340 GGCGAGAAGAGCCGAGTC 59.897 66.667 0.00 0.00 45.58 3.36
2156 3946 3.251043 CGAAGCGGCGAGAAGAGC 61.251 66.667 12.98 0.00 0.00 4.09
2157 3947 1.870016 GACGAAGCGGCGAGAAGAG 60.870 63.158 12.98 0.00 34.83 2.85
2158 3948 2.178521 GACGAAGCGGCGAGAAGA 59.821 61.111 12.98 0.00 34.83 2.87
2165 3955 3.701604 ATGAGGACGACGAAGCGGC 62.702 63.158 0.00 0.00 38.96 6.53
2166 3956 1.586564 GATGAGGACGACGAAGCGG 60.587 63.158 0.00 0.00 35.12 5.52
2167 3957 1.934956 CGATGAGGACGACGAAGCG 60.935 63.158 0.00 0.00 37.29 4.68
2168 3958 2.224885 GCGATGAGGACGACGAAGC 61.225 63.158 0.00 0.00 0.00 3.86
2169 3959 1.586564 GGCGATGAGGACGACGAAG 60.587 63.158 0.00 0.00 0.00 3.79
2170 3960 1.989966 GAGGCGATGAGGACGACGAA 61.990 60.000 0.00 0.00 44.04 3.85
2171 3961 2.437895 AGGCGATGAGGACGACGA 60.438 61.111 0.00 0.00 44.04 4.20
2172 3962 2.024871 GAGGCGATGAGGACGACG 59.975 66.667 0.00 0.00 44.04 5.12
2173 3963 1.064946 CTGAGGCGATGAGGACGAC 59.935 63.158 0.00 0.00 39.24 4.34
2174 3964 0.965866 AACTGAGGCGATGAGGACGA 60.966 55.000 0.00 0.00 0.00 4.20
2175 3965 0.526524 GAACTGAGGCGATGAGGACG 60.527 60.000 0.00 0.00 0.00 4.79
2176 3966 0.179097 GGAACTGAGGCGATGAGGAC 60.179 60.000 0.00 0.00 0.00 3.85
2177 3967 1.330655 GGGAACTGAGGCGATGAGGA 61.331 60.000 0.00 0.00 0.00 3.71
2178 3968 1.144936 GGGAACTGAGGCGATGAGG 59.855 63.158 0.00 0.00 0.00 3.86
2179 3969 1.227089 CGGGAACTGAGGCGATGAG 60.227 63.158 0.00 0.00 36.31 2.90
2180 3970 2.892640 CGGGAACTGAGGCGATGA 59.107 61.111 0.00 0.00 36.31 2.92
2181 3971 2.892425 GCGGGAACTGAGGCGATG 60.892 66.667 0.00 0.00 36.31 3.84
2187 3977 4.735132 TTCGCCGCGGGAACTGAG 62.735 66.667 29.38 0.46 36.31 3.35
2188 3978 4.077184 ATTCGCCGCGGGAACTGA 62.077 61.111 29.38 9.26 37.32 3.41
2189 3979 3.564027 GATTCGCCGCGGGAACTG 61.564 66.667 29.38 6.99 37.32 3.16
2190 3980 2.869503 ATTGATTCGCCGCGGGAACT 62.870 55.000 29.38 16.58 37.32 3.01
2191 3981 2.469516 ATTGATTCGCCGCGGGAAC 61.470 57.895 29.38 19.99 37.32 3.62
2192 3982 2.124901 ATTGATTCGCCGCGGGAA 60.125 55.556 29.38 26.61 38.75 3.97
2193 3983 2.894879 CATTGATTCGCCGCGGGA 60.895 61.111 29.38 19.62 0.00 5.14
2194 3984 4.612536 GCATTGATTCGCCGCGGG 62.613 66.667 29.38 17.41 0.00 6.13
2195 3985 4.612536 GGCATTGATTCGCCGCGG 62.613 66.667 24.05 24.05 38.82 6.46
2200 3990 1.274596 CAGCTTTGGCATTGATTCGC 58.725 50.000 0.00 0.00 41.70 4.70
2201 3991 2.523015 GACAGCTTTGGCATTGATTCG 58.477 47.619 0.00 0.00 41.70 3.34
2202 3992 2.523015 CGACAGCTTTGGCATTGATTC 58.477 47.619 0.00 0.00 41.70 2.52
2203 3993 1.403249 GCGACAGCTTTGGCATTGATT 60.403 47.619 1.60 0.00 41.70 2.57
2204 3994 0.171903 GCGACAGCTTTGGCATTGAT 59.828 50.000 1.60 0.00 41.70 2.57
2205 3995 1.580942 GCGACAGCTTTGGCATTGA 59.419 52.632 1.60 0.00 41.70 2.57
2206 3996 1.798725 CGCGACAGCTTTGGCATTG 60.799 57.895 0.00 0.00 42.32 2.82
2207 3997 2.562912 CGCGACAGCTTTGGCATT 59.437 55.556 0.00 0.00 42.32 3.56
2208 3998 3.434319 CCGCGACAGCTTTGGCAT 61.434 61.111 8.23 0.00 42.32 4.40
2225 4015 1.078143 AATGAAGGAGGCTGACCGC 60.078 57.895 0.00 0.00 42.76 5.68
2226 4016 0.250234 TCAATGAAGGAGGCTGACCG 59.750 55.000 0.00 0.00 42.76 4.79
2227 4017 2.295885 CATCAATGAAGGAGGCTGACC 58.704 52.381 0.00 0.00 0.00 4.02
2228 4018 1.674962 GCATCAATGAAGGAGGCTGAC 59.325 52.381 0.00 0.00 38.88 3.51
2229 4019 1.409241 GGCATCAATGAAGGAGGCTGA 60.409 52.381 0.00 0.00 41.46 4.26
2230 4020 1.030457 GGCATCAATGAAGGAGGCTG 58.970 55.000 0.00 0.00 41.46 4.85
2231 4021 0.924823 AGGCATCAATGAAGGAGGCT 59.075 50.000 0.00 0.00 41.46 4.58
2232 4022 1.316651 GAGGCATCAATGAAGGAGGC 58.683 55.000 0.00 0.00 41.04 4.70
2233 4023 2.723322 TGAGGCATCAATGAAGGAGG 57.277 50.000 0.00 0.00 30.61 4.30
2234 4024 2.885266 CCATGAGGCATCAATGAAGGAG 59.115 50.000 4.62 0.00 39.39 3.69
2235 4025 2.423803 CCCATGAGGCATCAATGAAGGA 60.424 50.000 4.62 0.00 39.39 3.36
2236 4026 1.961394 CCCATGAGGCATCAATGAAGG 59.039 52.381 4.62 2.77 39.39 3.46
2258 4048 4.373116 TCCGGTCTTCACTGCGCC 62.373 66.667 4.18 0.00 0.00 6.53
2259 4049 3.112709 GTCCGGTCTTCACTGCGC 61.113 66.667 0.00 0.00 0.00 6.09
2260 4050 2.805353 CGTCCGGTCTTCACTGCG 60.805 66.667 0.00 0.00 0.00 5.18
2261 4051 1.733399 GTCGTCCGGTCTTCACTGC 60.733 63.158 0.00 0.00 0.00 4.40
2262 4052 1.442184 CGTCGTCCGGTCTTCACTG 60.442 63.158 0.00 0.00 0.00 3.66
2263 4053 2.952245 CGTCGTCCGGTCTTCACT 59.048 61.111 0.00 0.00 0.00 3.41
2264 4054 2.804090 GCGTCGTCCGGTCTTCAC 60.804 66.667 0.00 0.00 36.94 3.18
2265 4055 3.289062 TGCGTCGTCCGGTCTTCA 61.289 61.111 0.00 0.00 36.94 3.02
2266 4056 2.804090 GTGCGTCGTCCGGTCTTC 60.804 66.667 0.00 0.00 36.94 2.87
2267 4057 4.695231 CGTGCGTCGTCCGGTCTT 62.695 66.667 0.00 0.00 36.94 3.01


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

AutoCloner maintained by Alex Coulton.