Multiple sequence alignment - TraesCS3D01G283600

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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 TraesCS3D01G283600 chr3D 100.000 2294 0 0 1 2294 392040173 392042466 0.000000e+00 4237
1 TraesCS3D01G283600 chr3A 88.048 1598 89 41 1 1549 512302404 512303948 0.000000e+00 1799
2 TraesCS3D01G283600 chr3A 81.783 785 55 41 1566 2294 512304013 512304765 5.500000e-161 577
3 TraesCS3D01G283600 chr3B 90.706 1388 50 37 6 1348 511065396 511066749 0.000000e+00 1775
4 TraesCS3D01G283600 chr3B 85.312 960 49 40 1385 2294 511066754 511067671 0.000000e+00 907
5 TraesCS3D01G283600 chr3B 95.161 124 6 0 6 129 511063680 511063803 1.800000e-46 196


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 TraesCS3D01G283600 chr3D 392040173 392042466 2293 False 4237.000000 4237 100.0000 1 2294 1 chr3D.!!$F1 2293
1 TraesCS3D01G283600 chr3A 512302404 512304765 2361 False 1188.000000 1799 84.9155 1 2294 2 chr3A.!!$F1 2293
2 TraesCS3D01G283600 chr3B 511063680 511067671 3991 False 959.333333 1775 90.3930 6 2294 3 chr3B.!!$F1 2288

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
217 1950 0.040514 CTCAGAGCGAGCGATCGAAT 60.041 55.0 29.29 14.62 35.44 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 3914 0.097325 CGTCGTCCTGAGAGTAGTGC 59.903 60.0 0.0 0.0 0.0 4.4 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
86 1798 2.031465 TTCCTCACCGTTTCCCGC 59.969 61.111 0.00 0.00 34.38 6.13
151 1881 7.790027 AGTATAGCAGTGAGTGAAGATCAATT 58.210 34.615 0.00 0.00 0.00 2.32
189 1919 5.300286 GTCCTTTTGATGTTGGCTATGCTAT 59.700 40.000 0.00 0.00 0.00 2.97
217 1950 0.040514 CTCAGAGCGAGCGATCGAAT 60.041 55.000 29.29 14.62 35.44 3.34
229 1962 2.480037 GCGATCGAATACCATGCATGAA 59.520 45.455 28.31 15.61 0.00 2.57
284 2017 4.980805 GCGCGTCCACCCACAGAA 62.981 66.667 8.43 0.00 0.00 3.02
285 2018 2.047274 CGCGTCCACCCACAGAAT 60.047 61.111 0.00 0.00 0.00 2.40
292 2025 1.746615 CACCCACAGAATCTGGCCG 60.747 63.158 15.38 3.41 35.51 6.13
293 2026 1.918293 ACCCACAGAATCTGGCCGA 60.918 57.895 15.38 0.00 35.51 5.54
294 2027 1.153289 CCCACAGAATCTGGCCGAG 60.153 63.158 15.38 0.00 35.51 4.63
295 2028 1.617018 CCCACAGAATCTGGCCGAGA 61.617 60.000 15.38 2.41 35.51 4.04
296 2029 0.179089 CCACAGAATCTGGCCGAGAG 60.179 60.000 15.38 0.00 35.51 3.20
297 2030 0.809241 CACAGAATCTGGCCGAGAGC 60.809 60.000 15.38 0.00 42.60 4.09
298 2031 1.260538 ACAGAATCTGGCCGAGAGCA 61.261 55.000 15.38 0.00 46.50 4.26
299 2032 0.530211 CAGAATCTGGCCGAGAGCAG 60.530 60.000 1.53 0.00 46.50 4.24
300 2033 1.886777 GAATCTGGCCGAGAGCAGC 60.887 63.158 0.00 0.00 46.50 5.25
301 2034 2.584261 GAATCTGGCCGAGAGCAGCA 62.584 60.000 0.00 0.00 46.50 4.41
302 2035 1.980784 AATCTGGCCGAGAGCAGCAT 61.981 55.000 0.00 0.00 46.50 3.79
303 2036 2.661840 ATCTGGCCGAGAGCAGCATG 62.662 60.000 0.00 0.00 46.50 4.06
304 2037 4.478371 TGGCCGAGAGCAGCATGG 62.478 66.667 0.00 0.00 46.50 3.66
307 2040 2.203167 CCGAGAGCAGCATGGCAT 60.203 61.111 0.00 0.00 35.86 4.40
308 2041 2.252346 CCGAGAGCAGCATGGCATC 61.252 63.158 0.00 0.00 35.86 3.91
309 2042 2.252346 CGAGAGCAGCATGGCATCC 61.252 63.158 0.00 0.00 35.86 3.51
310 2043 1.148723 GAGAGCAGCATGGCATCCT 59.851 57.895 0.00 0.00 35.86 3.24
311 2044 0.885596 GAGAGCAGCATGGCATCCTC 60.886 60.000 0.00 1.53 35.86 3.71
335 2068 4.382114 TGCCACGCGTGCAAATCG 62.382 61.111 33.17 19.18 35.40 3.34
397 2130 1.825285 CTGCACGCAGACACACAGAC 61.825 60.000 13.87 0.00 46.30 3.51
420 2153 1.302993 AACACGTGGGGTATGCCAC 60.303 57.895 21.57 0.00 39.12 5.01
448 2181 4.420168 CAACACAACCAATCAAGAAACGT 58.580 39.130 0.00 0.00 0.00 3.99
449 2182 4.027572 ACACAACCAATCAAGAAACGTG 57.972 40.909 0.00 0.00 0.00 4.49
451 2184 2.425312 ACAACCAATCAAGAAACGTGCA 59.575 40.909 0.00 0.00 0.00 4.57
452 2185 2.774439 ACCAATCAAGAAACGTGCAC 57.226 45.000 6.82 6.82 0.00 4.57
496 2243 3.418913 CGCCGCAAATCACGTCCA 61.419 61.111 0.00 0.00 0.00 4.02
514 2261 1.401931 CCAGGTTCATTCAAGCAAGCG 60.402 52.381 0.00 0.00 34.67 4.68
524 2271 1.008538 AAGCAAGCGCCAAAACGAG 60.009 52.632 2.29 0.00 39.83 4.18
781 2544 4.180817 CCGCATACTTATCTGTCACACAA 58.819 43.478 0.00 0.00 0.00 3.33
782 2545 4.811024 CCGCATACTTATCTGTCACACAAT 59.189 41.667 0.00 0.00 0.00 2.71
905 2676 2.064723 TATCTCGGCGAGCTGTCTGC 62.065 60.000 31.01 0.00 43.29 4.26
922 2693 2.654912 GCCTGTCCGTCGTGTTTCG 61.655 63.158 0.00 0.00 41.41 3.46
941 2713 1.160137 GCAAGCTCTCGTCATTGGTT 58.840 50.000 0.00 0.00 0.00 3.67
975 2751 1.099879 TAGCTAGCCCCGAGTTCGTC 61.100 60.000 12.13 0.00 37.74 4.20
978 2754 1.304713 TAGCCCCGAGTTCGTCCTT 60.305 57.895 0.48 0.00 37.74 3.36
979 2755 0.901580 TAGCCCCGAGTTCGTCCTTT 60.902 55.000 0.48 0.00 37.74 3.11
980 2756 2.033194 GCCCCGAGTTCGTCCTTTG 61.033 63.158 0.48 0.00 37.74 2.77
981 2757 2.033194 CCCCGAGTTCGTCCTTTGC 61.033 63.158 0.48 0.00 37.74 3.68
982 2758 1.301401 CCCGAGTTCGTCCTTTGCA 60.301 57.895 0.48 0.00 37.74 4.08
983 2759 1.566018 CCCGAGTTCGTCCTTTGCAC 61.566 60.000 0.48 0.00 37.74 4.57
984 2760 0.878523 CCGAGTTCGTCCTTTGCACA 60.879 55.000 0.48 0.00 37.74 4.57
1324 3112 4.520846 CGCGCCCATCTTGTTCGC 62.521 66.667 0.00 0.00 42.05 4.70
1329 3117 3.864686 CCATCTTGTTCGCGGCCG 61.865 66.667 24.05 24.05 0.00 6.13
1379 3167 2.125147 GCCGGCTGCAGTGATACA 60.125 61.111 22.15 0.00 40.77 2.29
1380 3168 1.524621 GCCGGCTGCAGTGATACAT 60.525 57.895 22.15 0.00 40.77 2.29
1381 3169 1.779025 GCCGGCTGCAGTGATACATG 61.779 60.000 22.15 0.00 40.77 3.21
1382 3170 1.645455 CGGCTGCAGTGATACATGC 59.355 57.895 16.64 0.00 42.86 4.06
1383 3171 0.812811 CGGCTGCAGTGATACATGCT 60.813 55.000 16.64 0.00 42.98 3.79
1388 3176 2.608090 CTGCAGTGATACATGCTGTCTG 59.392 50.000 5.25 0.00 42.98 3.51
1398 3186 2.031163 GCTGTCTGCTTGGGTCGT 59.969 61.111 0.00 0.00 38.95 4.34
1400 3188 1.845809 GCTGTCTGCTTGGGTCGTTG 61.846 60.000 0.00 0.00 38.95 4.10
1401 3189 0.249868 CTGTCTGCTTGGGTCGTTGA 60.250 55.000 0.00 0.00 0.00 3.18
1402 3190 0.396435 TGTCTGCTTGGGTCGTTGAT 59.604 50.000 0.00 0.00 0.00 2.57
1403 3191 1.079503 GTCTGCTTGGGTCGTTGATC 58.920 55.000 0.00 0.00 0.00 2.92
1404 3192 0.036388 TCTGCTTGGGTCGTTGATCC 60.036 55.000 0.00 0.00 32.52 3.36
1405 3193 0.321564 CTGCTTGGGTCGTTGATCCA 60.322 55.000 0.00 0.00 41.61 3.41
1406 3194 0.321564 TGCTTGGGTCGTTGATCCAG 60.322 55.000 0.00 0.00 44.28 3.86
1407 3195 0.321653 GCTTGGGTCGTTGATCCAGT 60.322 55.000 0.00 0.00 44.28 4.00
1408 3196 1.882352 GCTTGGGTCGTTGATCCAGTT 60.882 52.381 0.00 0.00 44.28 3.16
1449 3241 1.112113 ACGGAGCATAGGACGAATGT 58.888 50.000 0.00 0.00 0.00 2.71
1452 3244 1.337071 GGAGCATAGGACGAATGTCGA 59.663 52.381 4.40 0.00 46.49 4.20
1536 3329 9.681692 AAATTTAATCCGTTGGTGTAAACTTAC 57.318 29.630 0.00 0.00 0.00 2.34
1542 3335 4.210537 CCGTTGGTGTAAACTTACTCTGTG 59.789 45.833 1.58 0.00 34.77 3.66
1549 3342 5.973565 GTGTAAACTTACTCTGTGTGTACGT 59.026 40.000 0.00 0.00 34.77 3.57
1551 3344 4.644103 AACTTACTCTGTGTGTACGTGT 57.356 40.909 0.00 0.00 0.00 4.49
1553 3346 3.379372 ACTTACTCTGTGTGTACGTGTGT 59.621 43.478 0.00 0.00 0.00 3.72
1555 3348 1.475280 ACTCTGTGTGTACGTGTGTGT 59.525 47.619 0.00 0.00 0.00 3.72
1560 3355 1.322338 GTGTGTACGTGTGTGTGTGTC 59.678 52.381 0.00 0.00 0.00 3.67
1561 3356 1.067776 TGTGTACGTGTGTGTGTGTCA 60.068 47.619 0.00 0.00 0.00 3.58
1562 3357 2.198406 GTGTACGTGTGTGTGTGTCAT 58.802 47.619 0.00 0.00 0.00 3.06
1563 3358 3.181489 TGTGTACGTGTGTGTGTGTCATA 60.181 43.478 0.00 0.00 0.00 2.15
1564 3359 3.985279 GTGTACGTGTGTGTGTGTCATAT 59.015 43.478 0.00 0.00 0.00 1.78
1566 3361 5.630264 GTGTACGTGTGTGTGTGTCATATAA 59.370 40.000 0.00 0.00 0.00 0.98
1572 3367 9.589111 ACGTGTGTGTGTGTCATATAAATATAA 57.411 29.630 0.00 0.00 0.00 0.98
1610 3455 4.136517 GCAAATGCAATGTGGTTTCTTG 57.863 40.909 0.00 0.00 41.59 3.02
1611 3456 3.808726 GCAAATGCAATGTGGTTTCTTGA 59.191 39.130 0.00 0.00 41.59 3.02
1616 3461 7.701539 AATGCAATGTGGTTTCTTGATACTA 57.298 32.000 0.00 0.00 0.00 1.82
1706 3558 3.622163 GCATCTCTGTGGACTCATTCAAG 59.378 47.826 0.00 0.00 0.00 3.02
1715 3567 4.757149 GTGGACTCATTCAAGCAACTACTT 59.243 41.667 0.00 0.00 0.00 2.24
1725 3577 3.340814 AGCAACTACTTGATCAGGTGG 57.659 47.619 19.92 18.94 29.81 4.61
1726 3578 2.639839 AGCAACTACTTGATCAGGTGGT 59.360 45.455 19.32 19.32 35.44 4.16
1756 3616 4.325030 GGTAACTTCTGGAAATCCCCATGA 60.325 45.833 0.00 0.00 35.33 3.07
1813 3690 5.242171 GGGTAATCAGCTTAGAGAGTCCTAC 59.758 48.000 0.00 0.00 0.00 3.18
1845 3730 5.280011 CCCCATCCACCATGTAATACTACTC 60.280 48.000 0.00 0.00 0.00 2.59
1846 3731 5.544176 CCCATCCACCATGTAATACTACTCT 59.456 44.000 0.00 0.00 0.00 3.24
1847 3732 6.724441 CCCATCCACCATGTAATACTACTCTA 59.276 42.308 0.00 0.00 0.00 2.43
1848 3733 7.309867 CCCATCCACCATGTAATACTACTCTAC 60.310 44.444 0.00 0.00 0.00 2.59
1849 3734 7.451877 CCATCCACCATGTAATACTACTCTACT 59.548 40.741 0.00 0.00 0.00 2.57
1850 3735 9.516546 CATCCACCATGTAATACTACTCTACTA 57.483 37.037 0.00 0.00 0.00 1.82
1851 3736 8.915057 TCCACCATGTAATACTACTCTACTAC 57.085 38.462 0.00 0.00 0.00 2.73
1852 3737 8.721479 TCCACCATGTAATACTACTCTACTACT 58.279 37.037 0.00 0.00 0.00 2.57
1879 3764 9.819754 ACTTAATTCGTACTTATACCCTATCCT 57.180 33.333 0.00 0.00 0.00 3.24
1888 3778 9.237187 GTACTTATACCCTATCCTAAGTACACC 57.763 40.741 19.14 1.43 46.78 4.16
1915 3806 0.253327 CTAGGGGGTCAAGTCAAGCC 59.747 60.000 0.00 0.00 0.00 4.35
1918 3809 4.404691 GGGTCAAGTCAAGCCCAG 57.595 61.111 0.00 0.00 40.76 4.45
1919 3810 1.973812 GGGTCAAGTCAAGCCCAGC 60.974 63.158 0.00 0.00 40.76 4.85
1923 3814 1.408702 GTCAAGTCAAGCCCAGCAAAA 59.591 47.619 0.00 0.00 0.00 2.44
1942 3833 1.693627 AGACGATGCTACGGGAAGAT 58.306 50.000 7.82 0.00 37.61 2.40
1945 3836 1.754803 ACGATGCTACGGGAAGATCAA 59.245 47.619 0.00 0.00 37.61 2.57
1948 3839 3.305676 CGATGCTACGGGAAGATCAAGAT 60.306 47.826 0.00 0.00 0.00 2.40
1999 3899 2.114838 GATGCAGCCCAGGATCCC 59.885 66.667 8.55 0.00 31.00 3.85
2002 3902 4.864334 GCAGCCCAGGATCCCGTG 62.864 72.222 8.55 0.28 0.00 4.94
2003 3903 4.181010 CAGCCCAGGATCCCGTGG 62.181 72.222 8.55 10.75 45.43 4.94
2004 3904 4.741239 AGCCCAGGATCCCGTGGT 62.741 66.667 16.74 5.28 44.61 4.16
2005 3905 2.766651 GCCCAGGATCCCGTGGTA 60.767 66.667 16.74 0.00 44.61 3.25
2006 3906 2.808206 GCCCAGGATCCCGTGGTAG 61.808 68.421 16.74 5.80 44.61 3.18
2007 3907 2.808206 CCCAGGATCCCGTGGTAGC 61.808 68.421 16.74 0.00 44.61 3.58
2008 3908 1.762460 CCAGGATCCCGTGGTAGCT 60.762 63.158 8.55 0.00 41.97 3.32
2009 3909 1.742768 CAGGATCCCGTGGTAGCTC 59.257 63.158 8.55 0.00 0.00 4.09
2010 3910 1.043116 CAGGATCCCGTGGTAGCTCA 61.043 60.000 8.55 0.00 0.00 4.26
2011 3911 0.757188 AGGATCCCGTGGTAGCTCAG 60.757 60.000 8.55 0.00 0.00 3.35
2012 3912 1.742768 GATCCCGTGGTAGCTCAGG 59.257 63.158 0.00 0.00 0.00 3.86
2013 3913 1.001760 ATCCCGTGGTAGCTCAGGT 59.998 57.895 0.00 0.00 0.00 4.00
2014 3914 1.330655 ATCCCGTGGTAGCTCAGGTG 61.331 60.000 0.00 0.00 0.00 4.00
2015 3915 2.125512 CCGTGGTAGCTCAGGTGC 60.126 66.667 0.00 0.00 0.00 5.01
2016 3916 2.656646 CGTGGTAGCTCAGGTGCA 59.343 61.111 0.00 0.00 34.99 4.57
2024 3924 1.181786 AGCTCAGGTGCACTACTCTC 58.818 55.000 17.98 0.00 34.99 3.20
2026 3926 1.135141 GCTCAGGTGCACTACTCTCAG 60.135 57.143 17.98 1.79 0.00 3.35
2038 3938 2.437895 TCTCAGGACGACGGCGAT 60.438 61.111 22.49 0.00 41.64 4.58
2043 3943 2.044555 AGGACGACGGCGATGAAGA 61.045 57.895 22.49 0.00 41.64 2.87
2054 3954 0.094901 CGATGAAGACGACGACGAGT 59.905 55.000 15.32 0.37 42.66 4.18
2066 3966 2.821688 GACGAGTACTCCGGCGAGG 61.822 68.421 17.23 2.51 40.77 4.63
2104 4013 2.282462 CCCAACCGGCAGAAAGCT 60.282 61.111 0.00 0.00 44.79 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.233578 GCTCGTCAAATGATTTTTCGCA 58.766 40.909 6.61 0.00 0.00 5.10
8 9 2.594214 GGCTCGTCAAATGATTTTTCGC 59.406 45.455 6.61 0.00 0.00 4.70
9 10 2.840176 CGGCTCGTCAAATGATTTTTCG 59.160 45.455 5.52 5.52 0.00 3.46
86 1798 0.461516 AGGACGATGCTCACATGCAG 60.462 55.000 0.00 0.00 46.71 4.41
229 1962 2.203523 TTGGCAGTGGCACATGCT 60.204 55.556 28.33 6.65 44.52 3.79
284 2017 2.441675 ATGCTGCTCTCGGCCAGAT 61.442 57.895 2.24 0.00 43.94 2.90
285 2018 3.079478 ATGCTGCTCTCGGCCAGA 61.079 61.111 2.24 4.00 43.94 3.86
292 2025 0.885596 GAGGATGCCATGCTGCTCTC 60.886 60.000 2.44 0.00 0.00 3.20
293 2026 1.148723 GAGGATGCCATGCTGCTCT 59.851 57.895 2.44 0.00 0.00 4.09
294 2027 2.252346 CGAGGATGCCATGCTGCTC 61.252 63.158 2.44 0.00 0.00 4.26
295 2028 2.203167 CGAGGATGCCATGCTGCT 60.203 61.111 2.44 0.00 0.00 4.24
296 2029 3.285215 CCGAGGATGCCATGCTGC 61.285 66.667 2.44 0.00 0.00 5.25
297 2030 3.285215 GCCGAGGATGCCATGCTG 61.285 66.667 2.44 0.00 0.00 4.41
298 2031 4.923942 CGCCGAGGATGCCATGCT 62.924 66.667 0.00 0.00 0.00 3.79
335 2068 2.048503 CACTGACGTCCGGGGAAC 60.049 66.667 14.12 0.00 0.00 3.62
379 2112 1.882625 GTCTGTGTGTCTGCGTGCA 60.883 57.895 0.00 0.00 0.00 4.57
397 2130 1.448985 CATACCCCACGTGTTCTTGG 58.551 55.000 15.65 7.82 33.45 3.61
420 2153 1.955778 TGATTGGTTGTGTTGCCTCTG 59.044 47.619 0.00 0.00 0.00 3.35
422 2155 2.622942 TCTTGATTGGTTGTGTTGCCTC 59.377 45.455 0.00 0.00 0.00 4.70
423 2156 2.665165 TCTTGATTGGTTGTGTTGCCT 58.335 42.857 0.00 0.00 0.00 4.75
424 2157 3.451141 TTCTTGATTGGTTGTGTTGCC 57.549 42.857 0.00 0.00 0.00 4.52
452 2185 3.781926 TTTTGTCGCAGCGTGCACG 62.782 57.895 34.01 34.01 45.36 5.34
454 2187 2.024022 GTTTTGTCGCAGCGTGCA 59.976 55.556 15.93 12.45 45.36 4.57
455 2188 3.085010 CGTTTTGTCGCAGCGTGC 61.085 61.111 15.93 9.83 40.69 5.34
496 2243 0.242017 GCGCTTGCTTGAATGAACCT 59.758 50.000 0.00 0.00 35.07 3.50
514 2261 1.004504 GATCTGATCGCTCGTTTTGGC 60.005 52.381 1.26 0.00 0.00 4.52
524 2271 6.417044 CCTGATTTTGATTTTGATCTGATCGC 59.583 38.462 12.65 1.33 0.00 4.58
737 2499 0.250727 TTGAGCTTTGACGGGAAGGG 60.251 55.000 0.00 0.00 0.00 3.95
781 2544 2.359107 CGTGTGGAGCTGCACCAT 60.359 61.111 32.10 0.00 39.69 3.55
782 2545 4.624364 CCGTGTGGAGCTGCACCA 62.624 66.667 32.10 18.90 37.49 4.17
905 2676 2.654912 GCGAAACACGACGGACAGG 61.655 63.158 0.00 0.00 45.77 4.00
907 2678 1.484227 CTTGCGAAACACGACGGACA 61.484 55.000 0.00 0.00 45.77 4.02
922 2693 1.135859 CAACCAATGACGAGAGCTTGC 60.136 52.381 0.00 0.00 0.00 4.01
941 2713 0.907486 AGCTAGCTGTGAATGAGGCA 59.093 50.000 18.57 0.00 0.00 4.75
970 2746 2.250939 CGGCTGTGCAAAGGACGAA 61.251 57.895 5.91 0.00 32.69 3.85
1314 3102 2.813908 GTCGGCCGCGAACAAGAT 60.814 61.111 23.51 0.00 0.00 2.40
1362 3150 1.524621 ATGTATCACTGCAGCCGGC 60.525 57.895 21.89 21.89 45.13 6.13
1363 3151 1.779025 GCATGTATCACTGCAGCCGG 61.779 60.000 15.27 0.00 38.28 6.13
1364 3152 0.812811 AGCATGTATCACTGCAGCCG 60.813 55.000 15.27 5.38 40.88 5.52
1365 3153 0.661552 CAGCATGTATCACTGCAGCC 59.338 55.000 15.27 0.00 40.88 4.85
1381 3169 1.598130 AACGACCCAAGCAGACAGC 60.598 57.895 0.00 0.00 46.19 4.40
1382 3170 0.249868 TCAACGACCCAAGCAGACAG 60.250 55.000 0.00 0.00 0.00 3.51
1383 3171 0.396435 ATCAACGACCCAAGCAGACA 59.604 50.000 0.00 0.00 0.00 3.41
1388 3176 0.321653 ACTGGATCAACGACCCAAGC 60.322 55.000 0.00 0.00 0.00 4.01
1408 3196 9.565090 TCCGTAGCTATCTTATTTACTCTACAA 57.435 33.333 0.00 0.00 0.00 2.41
1437 3228 6.986817 AGAAAATTCATCGACATTCGTCCTAT 59.013 34.615 0.00 0.00 41.35 2.57
1442 3233 6.480524 TGAAGAAAATTCATCGACATTCGT 57.519 33.333 0.00 0.00 41.35 3.85
1445 3236 6.968904 CCGATTGAAGAAAATTCATCGACATT 59.031 34.615 16.61 0.00 34.53 2.71
1449 3241 5.874810 AGACCGATTGAAGAAAATTCATCGA 59.125 36.000 16.61 0.00 34.53 3.59
1452 3244 7.636150 ATGAGACCGATTGAAGAAAATTCAT 57.364 32.000 0.00 0.00 0.00 2.57
1536 3329 1.852280 CACACACACGTACACACAGAG 59.148 52.381 0.00 0.00 0.00 3.35
1542 3335 1.631284 TGACACACACACACGTACAC 58.369 50.000 0.00 0.00 0.00 2.90
1572 3367 5.813672 GCATTTGCATTTTGACCAGATGTAT 59.186 36.000 0.00 0.00 41.59 2.29
1610 3455 5.630661 ATGTGTAGATGGAGCGTAGTATC 57.369 43.478 0.00 0.00 0.00 2.24
1611 3456 4.154375 CGATGTGTAGATGGAGCGTAGTAT 59.846 45.833 0.00 0.00 0.00 2.12
1616 3461 0.249073 GCGATGTGTAGATGGAGCGT 60.249 55.000 0.00 0.00 0.00 5.07
1706 3558 3.059352 ACCACCTGATCAAGTAGTTGC 57.941 47.619 5.35 0.00 33.23 4.17
1715 3567 2.274542 ACCCATGTAACCACCTGATCA 58.725 47.619 0.00 0.00 0.00 2.92
1725 3577 6.095021 GGATTTCCAGAAGTTACCCATGTAAC 59.905 42.308 7.36 7.36 44.68 2.50
1726 3578 6.184789 GGATTTCCAGAAGTTACCCATGTAA 58.815 40.000 0.00 0.00 33.64 2.41
1756 3616 6.916360 TCCAGCCATTTTTGTCTTATCTTT 57.084 33.333 0.00 0.00 0.00 2.52
1813 3690 5.715439 ACATGGTGGATGGGGTATATATG 57.285 43.478 0.00 0.00 36.23 1.78
1853 3738 9.819754 AGGATAGGGTATAAGTACGAATTAAGT 57.180 33.333 0.00 0.00 0.00 2.24
1869 3754 4.897670 GCTTGGTGTACTTAGGATAGGGTA 59.102 45.833 0.00 0.00 0.00 3.69
1870 3755 3.710165 GCTTGGTGTACTTAGGATAGGGT 59.290 47.826 0.00 0.00 0.00 4.34
1879 3764 3.958798 CCCTAGCTAGCTTGGTGTACTTA 59.041 47.826 33.76 9.90 37.27 2.24
1882 3767 1.413077 CCCCTAGCTAGCTTGGTGTAC 59.587 57.143 33.76 0.00 37.27 2.90
1888 3778 1.139853 CTTGACCCCCTAGCTAGCTTG 59.860 57.143 24.88 21.01 0.00 4.01
1918 3809 0.373716 CCCGTAGCATCGTCTTTTGC 59.626 55.000 0.00 0.00 39.17 3.68
1919 3810 2.004583 TCCCGTAGCATCGTCTTTTG 57.995 50.000 0.00 0.00 0.00 2.44
1923 3814 1.609555 GATCTTCCCGTAGCATCGTCT 59.390 52.381 0.00 0.00 0.00 4.18
1932 3823 5.932619 TTCTTCATCTTGATCTTCCCGTA 57.067 39.130 0.00 0.00 0.00 4.02
1942 3833 5.947566 TGCTTCATGGAATTCTTCATCTTGA 59.052 36.000 5.23 0.00 0.00 3.02
1945 3836 5.589452 GTCTGCTTCATGGAATTCTTCATCT 59.411 40.000 5.23 0.00 0.00 2.90
1948 3839 4.654915 TGTCTGCTTCATGGAATTCTTCA 58.345 39.130 5.23 0.00 0.00 3.02
1999 3899 1.738099 GTGCACCTGAGCTACCACG 60.738 63.158 5.22 0.00 34.99 4.94
2001 3901 0.895530 GTAGTGCACCTGAGCTACCA 59.104 55.000 14.63 0.00 34.99 3.25
2002 3902 1.135333 GAGTAGTGCACCTGAGCTACC 59.865 57.143 14.63 0.00 35.65 3.18
2003 3903 2.096248 AGAGTAGTGCACCTGAGCTAC 58.904 52.381 14.63 8.39 35.37 3.58
2004 3904 2.290960 TGAGAGTAGTGCACCTGAGCTA 60.291 50.000 14.63 0.00 34.99 3.32
2005 3905 1.181786 GAGAGTAGTGCACCTGAGCT 58.818 55.000 14.63 4.82 34.99 4.09
2006 3906 0.891373 TGAGAGTAGTGCACCTGAGC 59.109 55.000 14.63 0.00 0.00 4.26
2007 3907 1.476085 CCTGAGAGTAGTGCACCTGAG 59.524 57.143 14.63 6.78 0.00 3.35
2008 3908 1.075536 TCCTGAGAGTAGTGCACCTGA 59.924 52.381 14.63 0.00 0.00 3.86
2009 3909 1.203523 GTCCTGAGAGTAGTGCACCTG 59.796 57.143 14.63 0.78 0.00 4.00
2010 3910 1.551452 GTCCTGAGAGTAGTGCACCT 58.449 55.000 14.63 3.90 0.00 4.00
2011 3911 0.171455 CGTCCTGAGAGTAGTGCACC 59.829 60.000 14.63 0.00 0.00 5.01
2012 3912 1.135632 GTCGTCCTGAGAGTAGTGCAC 60.136 57.143 9.40 9.40 0.00 4.57
2013 3913 1.166129 GTCGTCCTGAGAGTAGTGCA 58.834 55.000 0.00 0.00 0.00 4.57
2014 3914 0.097325 CGTCGTCCTGAGAGTAGTGC 59.903 60.000 0.00 0.00 0.00 4.40
2015 3915 0.727970 CCGTCGTCCTGAGAGTAGTG 59.272 60.000 0.00 0.00 0.00 2.74
2016 3916 1.025647 GCCGTCGTCCTGAGAGTAGT 61.026 60.000 0.00 0.00 0.00 2.73
2024 3924 1.874019 CTTCATCGCCGTCGTCCTG 60.874 63.158 0.00 0.00 36.96 3.86
2026 3926 1.872679 GTCTTCATCGCCGTCGTCC 60.873 63.158 0.00 0.00 36.96 4.79
2038 3938 1.723542 GAGTACTCGTCGTCGTCTTCA 59.276 52.381 7.22 0.00 38.33 3.02
2043 3943 2.097038 CCGGAGTACTCGTCGTCGT 61.097 63.158 16.56 0.00 38.33 4.34
2045 3945 2.402787 GCCGGAGTACTCGTCGTC 59.597 66.667 16.56 1.89 0.00 4.20
2047 3947 3.152937 CTCGCCGGAGTACTCGTCG 62.153 68.421 16.56 17.47 35.48 5.12
2089 3998 0.954452 AAGAAGCTTTCTGCCGGTTG 59.046 50.000 1.90 0.00 44.23 3.77
2104 4013 0.837272 GGATGTCGATGGGGGAAGAA 59.163 55.000 0.00 0.00 0.00 2.52
2214 4123 3.993234 CGATCATCACGCTGGCGC 61.993 66.667 15.04 0.00 44.19 6.53
2217 4126 2.202919 TGCCGATCATCACGCTGG 60.203 61.111 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.