Multiple sequence alignment - TraesCS4D01G201900

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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 TraesCS4D01G201900 chr4D 100.000 4946 0 0 1 4946 348803114 348798169 0 9134
1 TraesCS4D01G201900 chr4D 100.000 1047 0 0 5368 6414 348797747 348796701 0 1934
2 TraesCS4D01G201900 chr4A 96.544 4977 128 20 1 4946 116470814 116475777 0 8198
3 TraesCS4D01G201900 chr4A 89.459 1072 62 30 5368 6414 116475821 116476866 0 1306
4 TraesCS4D01G201900 chr4B 93.859 4999 188 44 1 4946 428971766 428966834 0 7420
5 TraesCS4D01G201900 chr4B 89.953 1075 54 25 5368 6414 428966788 428965740 0 1338


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 TraesCS4D01G201900 chr4D 348796701 348803114 6413 True 5534 9134 100.0000 1 6414 2 chr4D.!!$R1 6413
1 TraesCS4D01G201900 chr4A 116470814 116476866 6052 False 4752 8198 93.0015 1 6414 2 chr4A.!!$F1 6413
2 TraesCS4D01G201900 chr4B 428965740 428971766 6026 True 4379 7420 91.9060 1 6414 2 chr4B.!!$R1 6413

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
246 285 0.391130 CGATCTTCCGCTGGGTTTCA 60.391 55.000 0.00 0.00 33.83 2.69 F
682 731 0.463116 GCCGTCGGTCCACCATTTAT 60.463 55.000 13.94 0.00 35.14 1.40 F
1409 1464 0.813210 CAAGCAAGATCCCCTCTCGC 60.813 60.000 0.00 0.00 31.03 5.03 F
2113 2168 1.346062 TCACCAGCTGAGAAGCTTCT 58.654 50.000 28.83 28.83 43.52 2.85 F
2226 2281 1.859302 AGAGCCTGGAGAACCTACAG 58.141 55.000 0.00 0.00 41.81 2.74 F
3227 3282 1.929836 GCCAGTTCAGCAGATCTTACG 59.070 52.381 0.00 0.00 0.00 3.18 F
4175 4234 0.474854 TGGACCCTAGGCTGTTGGAA 60.475 55.000 2.05 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2164 0.588252 CACGCCACAGGTTTCAGAAG 59.412 55.000 0.0 0.0 0.0 2.85 R
2332 2387 0.875059 GCCAGCTTTACCACACACTC 59.125 55.000 0.0 0.0 0.0 3.51 R
2704 2759 1.284297 GGCCACATTTTTGCGAGCAC 61.284 55.000 0.0 0.0 0.0 4.40 R
3821 3880 1.487976 TGCATGAACCTCTCCCATCTC 59.512 52.381 0.0 0.0 0.0 2.75 R
4175 4234 0.179037 CATCATCCATCTGCCCGTGT 60.179 55.000 0.0 0.0 0.0 4.49 R
4578 4637 1.988846 CTCCCCAAACCTCCTTCTCTT 59.011 52.381 0.0 0.0 0.0 2.85 R
5618 5706 0.393267 GCCCTACCAATACCGTGCAA 60.393 55.000 0.0 0.0 0.0 4.08 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
71 78 2.183679 CCACTACTTCTTCTCCAGCCT 58.816 52.381 0.00 0.00 0.00 4.58
84 91 3.714001 AGCCTGCTAGCTGCTGCA 61.714 61.111 25.11 20.12 42.95 4.41
112 119 4.214327 GCGGCCTCTCTTCCGGAG 62.214 72.222 3.34 0.00 45.37 4.63
158 173 7.573968 ACTTTGAAGTGAGCTTGTATTTTCT 57.426 32.000 0.00 0.00 37.98 2.52
188 203 0.529773 TCGGCGGTATGAGATGTTGC 60.530 55.000 7.21 0.00 0.00 4.17
218 257 3.190874 GTGAGTGAGATTGGATTCGTCC 58.809 50.000 0.00 0.00 0.00 4.79
246 285 0.391130 CGATCTTCCGCTGGGTTTCA 60.391 55.000 0.00 0.00 33.83 2.69
281 320 5.108027 CGATTGTTTTCTTTTGCGGGTTAAG 60.108 40.000 0.00 0.00 0.00 1.85
285 326 1.975660 TCTTTTGCGGGTTAAGTGCT 58.024 45.000 0.00 0.00 0.00 4.40
333 377 4.759782 AGATTCGTGAATTCCTAGTGGTG 58.240 43.478 2.27 0.00 34.23 4.17
387 432 3.758931 GCCCGTGTGAATTGCCCC 61.759 66.667 0.00 0.00 0.00 5.80
682 731 0.463116 GCCGTCGGTCCACCATTTAT 60.463 55.000 13.94 0.00 35.14 1.40
712 761 1.244019 ATTTGTCCGTGCCTTCTGCC 61.244 55.000 0.00 0.00 40.16 4.85
765 815 1.527311 GACTTGTCGTGTCTTGGAAGC 59.473 52.381 0.00 0.00 0.00 3.86
807 857 4.211125 TGGTGTTGCAAATAGACAAAGGA 58.789 39.130 0.00 0.00 0.00 3.36
912 967 4.836736 ACTTGTGCCTTTCTGTACCTACTA 59.163 41.667 0.00 0.00 0.00 1.82
984 1039 6.303839 AGAAAACAGGTTATTGTCTGCCTAA 58.696 36.000 0.00 0.00 34.57 2.69
1039 1094 3.071479 GACGAGGTACTTGCAATTTCCA 58.929 45.455 13.67 0.00 45.68 3.53
1040 1095 3.482436 ACGAGGTACTTGCAATTTCCAA 58.518 40.909 13.67 0.00 45.68 3.53
1395 1450 3.009723 GTGCTACTTAATGGCTCAAGCA 58.990 45.455 4.13 0.00 44.36 3.91
1409 1464 0.813210 CAAGCAAGATCCCCTCTCGC 60.813 60.000 0.00 0.00 31.03 5.03
1730 1785 2.945890 GCAGGCTGGCTTTAACATACCT 60.946 50.000 17.64 0.00 0.00 3.08
1839 1894 2.076863 ACAATACTCTGAAACAGCCGC 58.923 47.619 0.00 0.00 0.00 6.53
1916 1971 2.235891 CTTAAACCACCAACCAGACCC 58.764 52.381 0.00 0.00 0.00 4.46
2109 2164 4.194640 TGATAAATCACCAGCTGAGAAGC 58.805 43.478 17.39 1.69 30.20 3.86
2112 2167 2.399916 ATCACCAGCTGAGAAGCTTC 57.600 50.000 19.11 19.11 43.52 3.86
2113 2168 1.346062 TCACCAGCTGAGAAGCTTCT 58.654 50.000 28.83 28.83 43.52 2.85
2143 2198 3.000925 GTGGCGTGTAATGTAAATCCTCG 59.999 47.826 0.00 0.00 0.00 4.63
2147 2202 3.863424 CGTGTAATGTAAATCCTCGCACT 59.137 43.478 0.00 0.00 0.00 4.40
2226 2281 1.859302 AGAGCCTGGAGAACCTACAG 58.141 55.000 0.00 0.00 41.81 2.74
2332 2387 3.446310 AAAAACTGGCAACCTAAACCG 57.554 42.857 0.00 0.00 0.00 4.44
2372 2427 5.596361 TGGCTTTGATTTGTACTCTGGAAAA 59.404 36.000 0.00 0.00 0.00 2.29
2472 2527 2.542411 GGTGTTGCTTGCACTGAGAAAG 60.542 50.000 0.00 0.00 37.07 2.62
2704 2759 5.551760 AAACCAGCAGTTAATCAGATTCG 57.448 39.130 0.00 0.00 37.88 3.34
2931 2986 7.859325 TTGGGTAATAGTCAAATTACTGAGC 57.141 36.000 6.68 0.00 40.60 4.26
3227 3282 1.929836 GCCAGTTCAGCAGATCTTACG 59.070 52.381 0.00 0.00 0.00 3.18
3452 3507 5.487131 AGAAAAGGAAGAGATTGCTAGAGGT 59.513 40.000 0.00 0.00 0.00 3.85
3720 3775 3.773860 TTGTTTTCGCAGTCATGTTGT 57.226 38.095 0.00 0.00 0.00 3.32
3757 3812 3.694734 CTTTGCCCTGTGCGTATTTATG 58.305 45.455 0.00 0.00 45.60 1.90
3799 3854 5.128827 TGACTCTTGTTACAGAAGGTTGTCT 59.871 40.000 0.00 0.00 32.56 3.41
3801 3856 6.415573 ACTCTTGTTACAGAAGGTTGTCTTT 58.584 36.000 2.12 0.00 35.50 2.52
3802 3857 7.562135 ACTCTTGTTACAGAAGGTTGTCTTTA 58.438 34.615 2.12 0.00 35.50 1.85
4175 4234 0.474854 TGGACCCTAGGCTGTTGGAA 60.475 55.000 2.05 0.00 0.00 3.53
4358 4417 0.541764 GGTCCCCTGAAACCATGCAA 60.542 55.000 0.00 0.00 35.53 4.08
4578 4637 0.686789 TGCAGAGGCTGAGCTTACAA 59.313 50.000 3.72 0.00 41.91 2.41
4775 4837 1.997874 AAGGGGCGAGCAGGAAGAT 60.998 57.895 0.00 0.00 0.00 2.40
4799 4861 2.683933 AGGTACCGTGGCCCTCAG 60.684 66.667 6.18 0.00 0.00 3.35
4800 4862 3.782443 GGTACCGTGGCCCTCAGG 61.782 72.222 0.00 0.01 0.00 3.86
5478 5544 1.033746 ATCGGGTGGCTGCATCTTTG 61.034 55.000 0.50 0.00 0.00 2.77
5515 5584 1.021390 GCTGAAGCTAGCAGGCGAAA 61.021 55.000 18.83 0.00 43.17 3.46
5517 5586 1.129437 CTGAAGCTAGCAGGCGAAAAC 59.871 52.381 18.83 0.00 37.29 2.43
5519 5588 1.912371 AAGCTAGCAGGCGAAAACGC 61.912 55.000 18.83 6.05 37.29 4.84
5521 5590 1.912371 GCTAGCAGGCGAAAACGCTT 61.912 55.000 10.63 3.98 35.93 4.68
5526 5595 0.238289 CAGGCGAAAACGCTTGACAT 59.762 50.000 18.69 0.00 43.25 3.06
5529 5598 1.713932 GGCGAAAACGCTTGACATTTC 59.286 47.619 13.81 0.00 34.92 2.17
5602 5690 6.403636 GCAGAAGTGTCTCTTTCTCTCTCTAG 60.404 46.154 0.00 0.00 36.40 2.43
5605 5693 4.943705 AGTGTCTCTTTCTCTCTCTAGCTG 59.056 45.833 0.00 0.00 0.00 4.24
5606 5694 4.096382 GTGTCTCTTTCTCTCTCTAGCTGG 59.904 50.000 0.00 0.00 0.00 4.85
5607 5695 3.632145 GTCTCTTTCTCTCTCTAGCTGGG 59.368 52.174 0.00 0.00 0.00 4.45
5608 5696 2.362077 CTCTTTCTCTCTCTAGCTGGGC 59.638 54.545 0.00 0.00 0.00 5.36
5609 5697 2.024464 TCTTTCTCTCTCTAGCTGGGCT 60.024 50.000 0.00 0.00 43.41 5.19
5610 5698 2.541233 TTCTCTCTCTAGCTGGGCTT 57.459 50.000 0.00 0.00 40.44 4.35
5611 5699 2.541233 TCTCTCTCTAGCTGGGCTTT 57.459 50.000 0.00 0.00 40.44 3.51
5612 5700 3.671740 TCTCTCTCTAGCTGGGCTTTA 57.328 47.619 0.00 0.00 40.44 1.85
5613 5701 3.292460 TCTCTCTCTAGCTGGGCTTTAC 58.708 50.000 0.00 0.00 40.44 2.01
5614 5702 2.364002 CTCTCTCTAGCTGGGCTTTACC 59.636 54.545 0.00 0.00 40.44 2.85
5615 5703 2.023888 TCTCTCTAGCTGGGCTTTACCT 60.024 50.000 0.00 0.00 40.44 3.08
5616 5704 3.204606 TCTCTCTAGCTGGGCTTTACCTA 59.795 47.826 0.00 0.00 40.44 3.08
5617 5705 3.297736 TCTCTAGCTGGGCTTTACCTAC 58.702 50.000 0.00 0.00 40.44 3.18
5618 5706 3.052793 TCTCTAGCTGGGCTTTACCTACT 60.053 47.826 0.00 0.00 40.44 2.57
5652 5740 0.916809 AGGGCGCCCTGTATTAAAGT 59.083 50.000 46.71 19.78 46.22 2.66
5664 5752 6.090898 CCCTGTATTAAAGTGACTTGTCTTCG 59.909 42.308 0.00 0.00 0.00 3.79
5693 5781 1.347707 TGCCTAGTTGTTGGTCTGGAG 59.652 52.381 0.00 0.00 0.00 3.86
5883 5981 4.081476 GGCATTGCCTTTTTCTTATGGAGT 60.081 41.667 20.66 0.00 46.69 3.85
5884 5982 4.866486 GCATTGCCTTTTTCTTATGGAGTG 59.134 41.667 0.00 0.00 0.00 3.51
5886 5984 4.380843 TGCCTTTTTCTTATGGAGTGGA 57.619 40.909 0.00 0.00 0.00 4.02
5887 5985 4.735369 TGCCTTTTTCTTATGGAGTGGAA 58.265 39.130 0.00 0.00 0.00 3.53
5888 5986 5.144100 TGCCTTTTTCTTATGGAGTGGAAA 58.856 37.500 0.00 0.00 0.00 3.13
5890 5988 6.159293 GCCTTTTTCTTATGGAGTGGAAAAG 58.841 40.000 0.00 0.00 38.38 2.27
5891 5989 6.239317 GCCTTTTTCTTATGGAGTGGAAAAGT 60.239 38.462 0.00 0.00 38.38 2.66
5899 6003 2.106511 TGGAGTGGAAAAGTAAGCAGCT 59.893 45.455 0.00 0.00 0.00 4.24
6109 6235 3.564644 TGGATAAGAGTAGACTACGCAGC 59.435 47.826 17.23 1.94 0.00 5.25
6110 6236 3.564644 GGATAAGAGTAGACTACGCAGCA 59.435 47.826 17.23 3.67 0.00 4.41
6111 6237 4.319911 GGATAAGAGTAGACTACGCAGCAG 60.320 50.000 17.23 0.00 0.00 4.24
6112 6238 1.384525 AGAGTAGACTACGCAGCAGG 58.615 55.000 17.23 0.00 0.00 4.85
6124 6250 1.522668 GCAGCAGGACACACAACATA 58.477 50.000 0.00 0.00 0.00 2.29
6256 6382 5.699458 TGGAAATTCTCCTGTTTAAGACGAC 59.301 40.000 0.00 0.00 45.64 4.34
6315 6442 2.056906 ATCTCGGTAGCAATGCCCCC 62.057 60.000 0.00 0.54 0.00 5.40
6330 6457 3.784178 TGCCCCCAAAATTATCTCAACA 58.216 40.909 0.00 0.00 0.00 3.33
6331 6458 3.768757 TGCCCCCAAAATTATCTCAACAG 59.231 43.478 0.00 0.00 0.00 3.16
6332 6459 3.430790 GCCCCCAAAATTATCTCAACAGC 60.431 47.826 0.00 0.00 0.00 4.40
6333 6460 4.026052 CCCCCAAAATTATCTCAACAGCT 58.974 43.478 0.00 0.00 0.00 4.24
6373 6502 5.007136 CCTCAACAGAGTTTCTTCTCAACAC 59.993 44.000 0.00 0.00 36.97 3.32
6374 6503 5.487433 TCAACAGAGTTTCTTCTCAACACA 58.513 37.500 0.00 0.00 36.97 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 107 0.898320 TCAAAGCCTCCGGAAGAGAG 59.102 55.000 5.23 0.00 46.50 3.20
110 117 2.008329 CTGCTGATCACTCAAAGCCTC 58.992 52.381 0.00 0.00 0.00 4.70
111 118 1.339824 CCTGCTGATCACTCAAAGCCT 60.340 52.381 0.00 0.00 0.00 4.58
112 119 1.093159 CCTGCTGATCACTCAAAGCC 58.907 55.000 0.00 0.00 0.00 4.35
113 120 1.818642 ACCTGCTGATCACTCAAAGC 58.181 50.000 0.00 0.00 0.00 3.51
114 121 4.573900 AGTTACCTGCTGATCACTCAAAG 58.426 43.478 0.00 0.00 0.00 2.77
115 122 4.623932 AGTTACCTGCTGATCACTCAAA 57.376 40.909 0.00 0.00 0.00 2.69
116 123 4.623932 AAGTTACCTGCTGATCACTCAA 57.376 40.909 0.00 0.00 0.00 3.02
117 124 4.040339 TCAAAGTTACCTGCTGATCACTCA 59.960 41.667 0.00 0.00 0.00 3.41
144 151 9.479278 GAAATAAGACGAAGAAAATACAAGCTC 57.521 33.333 0.00 0.00 0.00 4.09
158 173 2.937469 TACCGCCGAAATAAGACGAA 57.063 45.000 0.00 0.00 0.00 3.85
188 203 4.576053 TCCAATCTCACTCACAAACAACAG 59.424 41.667 0.00 0.00 0.00 3.16
218 257 3.365868 CCAGCGGAAGATCGATCTAGAAG 60.366 52.174 27.52 18.82 35.76 2.85
246 285 4.062991 AGAAAACAATCGAAGTAACCGCT 58.937 39.130 0.00 0.00 0.00 5.52
281 320 3.991121 GAGAAGAGAACTACCACAAGCAC 59.009 47.826 0.00 0.00 0.00 4.40
285 326 4.040461 CCAAGGAGAAGAGAACTACCACAA 59.960 45.833 0.00 0.00 0.00 3.33
373 418 0.673437 AAACTGGGGCAATTCACACG 59.327 50.000 0.00 0.00 0.00 4.49
387 432 3.746492 CCAAGAGGACTAACCGAAAACTG 59.254 47.826 0.00 0.00 44.74 3.16
420 465 2.876368 GAACTGGGCTGCCACGCTAT 62.876 60.000 22.05 0.50 0.00 2.97
598 647 6.720112 ACTTACTGCAAATCTACCGGTATA 57.280 37.500 16.25 8.72 0.00 1.47
603 652 4.211374 GGCATACTTACTGCAAATCTACCG 59.789 45.833 0.00 0.00 41.47 4.02
682 731 1.202758 ACGGACAAATCTGCCAAGTGA 60.203 47.619 0.00 0.00 34.14 3.41
712 761 1.066573 ACGAGTCAGAGAATTGGCTGG 60.067 52.381 0.00 0.00 32.08 4.85
984 1039 3.119459 CCGACATCTTGCTGTGTAGTAGT 60.119 47.826 0.00 0.00 0.00 2.73
1040 1095 9.643693 CAAGCAACCTAGAATTAACATTCAATT 57.356 29.630 0.00 0.00 41.37 2.32
1409 1464 2.485835 CCCTAGTCTACCACTCTCTCCG 60.486 59.091 0.00 0.00 36.43 4.63
1730 1785 6.824704 TCTGATGCTGAATTGTTGTATGATGA 59.175 34.615 0.00 0.00 0.00 2.92
1834 1889 1.605710 GAAGTTGATATGCATGCGGCT 59.394 47.619 14.09 2.68 45.15 5.52
1836 1891 2.224606 AGGAAGTTGATATGCATGCGG 58.775 47.619 14.09 0.00 0.00 5.69
1839 1894 9.499479 ACTCTTATTAGGAAGTTGATATGCATG 57.501 33.333 10.16 0.00 0.00 4.06
1973 2028 3.868077 GCTCATCTGTGTGATTACCAGAC 59.132 47.826 9.81 0.00 37.13 3.51
2109 2164 0.588252 CACGCCACAGGTTTCAGAAG 59.412 55.000 0.00 0.00 0.00 2.85
2112 2167 1.588674 TTACACGCCACAGGTTTCAG 58.411 50.000 0.00 0.00 0.00 3.02
2113 2168 1.876799 CATTACACGCCACAGGTTTCA 59.123 47.619 0.00 0.00 0.00 2.69
2143 2198 0.958091 TGTTTGTGGCATGGTAGTGC 59.042 50.000 0.00 0.00 44.31 4.40
2147 2202 3.317711 CAGAAACTGTTTGTGGCATGGTA 59.682 43.478 19.38 0.00 30.92 3.25
2226 2281 3.632145 ACATTTTTCTGGATATGTCGCCC 59.368 43.478 0.00 0.00 0.00 6.13
2332 2387 0.875059 GCCAGCTTTACCACACACTC 59.125 55.000 0.00 0.00 0.00 3.51
2372 2427 3.763897 GGACAGCACTACCATTTGGAAAT 59.236 43.478 3.01 0.00 38.94 2.17
2472 2527 4.447724 TGTCACTTCTTCACGCTTGATAAC 59.552 41.667 0.00 0.00 0.00 1.89
2704 2759 1.284297 GGCCACATTTTTGCGAGCAC 61.284 55.000 0.00 0.00 0.00 4.40
2931 2986 6.562270 CGCGGCTCTGTGATTAAGTTATTAAG 60.562 42.308 0.00 0.00 34.44 1.85
3227 3282 4.429854 AGCTCCCAAAATAGGTGATCTC 57.570 45.455 0.00 0.00 0.00 2.75
3452 3507 5.941058 TGGATCGTTTGGCTGTAAATTAGAA 59.059 36.000 0.00 0.00 0.00 2.10
3720 3775 2.300433 CAAAGCCAGCCATGCTACATA 58.700 47.619 0.00 0.00 38.34 2.29
3757 3812 7.511959 AGAGTCAAGGATAAAACCAAGAAAC 57.488 36.000 0.00 0.00 0.00 2.78
3807 3866 5.726308 TCTCCCATCTCTCATTCCTGTAAAA 59.274 40.000 0.00 0.00 0.00 1.52
3821 3880 1.487976 TGCATGAACCTCTCCCATCTC 59.512 52.381 0.00 0.00 0.00 2.75
4175 4234 0.179037 CATCATCCATCTGCCCGTGT 60.179 55.000 0.00 0.00 0.00 4.49
4286 4345 3.743521 TCTTTGACCAGGTGAATGACTG 58.256 45.455 0.00 0.00 34.54 3.51
4358 4417 4.974645 TCTGTTTAGTGGTGGTGATCTT 57.025 40.909 0.00 0.00 0.00 2.40
4578 4637 1.988846 CTCCCCAAACCTCCTTCTCTT 59.011 52.381 0.00 0.00 0.00 2.85
4775 4837 3.065306 CCACGGTACCTGAAGCCA 58.935 61.111 10.90 0.00 0.00 4.75
4865 4930 8.762481 AAGATTCAGATTCATTCATCCATTCA 57.238 30.769 0.00 0.00 0.00 2.57
4867 4932 8.998277 AGAAGATTCAGATTCATTCATCCATT 57.002 30.769 0.00 0.00 0.00 3.16
5478 5544 3.071602 TCAGCTTATACCAAGCAGGATCC 59.928 47.826 2.48 2.48 45.30 3.36
5512 5581 4.608882 CGAGAAGAAATGTCAAGCGTTTTC 59.391 41.667 0.00 0.00 36.51 2.29
5515 5584 2.096218 GCGAGAAGAAATGTCAAGCGTT 60.096 45.455 0.00 0.00 0.00 4.84
5517 5586 1.201965 GGCGAGAAGAAATGTCAAGCG 60.202 52.381 0.00 0.00 0.00 4.68
5519 5588 4.488126 TTTGGCGAGAAGAAATGTCAAG 57.512 40.909 0.00 0.00 0.00 3.02
5521 5590 4.326826 AGATTTGGCGAGAAGAAATGTCA 58.673 39.130 0.00 0.00 0.00 3.58
5526 5595 5.299279 AGTTTGAAGATTTGGCGAGAAGAAA 59.701 36.000 0.00 0.00 0.00 2.52
5529 5598 4.756084 AGTTTGAAGATTTGGCGAGAAG 57.244 40.909 0.00 0.00 0.00 2.85
5602 5690 1.095600 GCAAGTAGGTAAAGCCCAGC 58.904 55.000 0.00 0.00 38.26 4.85
5605 5693 1.084289 CGTGCAAGTAGGTAAAGCCC 58.916 55.000 0.00 0.00 38.26 5.19
5606 5694 1.084289 CCGTGCAAGTAGGTAAAGCC 58.916 55.000 0.00 0.00 37.58 4.35
5607 5695 1.804601 ACCGTGCAAGTAGGTAAAGC 58.195 50.000 0.00 0.00 36.34 3.51
5608 5696 4.331717 CCAATACCGTGCAAGTAGGTAAAG 59.668 45.833 13.30 9.70 42.92 1.85
5609 5697 4.255301 CCAATACCGTGCAAGTAGGTAAA 58.745 43.478 13.30 0.00 42.92 2.01
5610 5698 3.261390 ACCAATACCGTGCAAGTAGGTAA 59.739 43.478 13.30 1.66 42.92 2.85
5611 5699 2.833338 ACCAATACCGTGCAAGTAGGTA 59.167 45.455 12.15 12.15 43.69 3.08
5612 5700 1.626825 ACCAATACCGTGCAAGTAGGT 59.373 47.619 9.00 9.00 41.73 3.08
5613 5701 2.396590 ACCAATACCGTGCAAGTAGG 57.603 50.000 0.00 1.05 0.00 3.18
5614 5702 3.454375 CCTACCAATACCGTGCAAGTAG 58.546 50.000 0.00 0.00 0.00 2.57
5615 5703 2.168936 CCCTACCAATACCGTGCAAGTA 59.831 50.000 0.00 0.00 0.00 2.24
5616 5704 1.065709 CCCTACCAATACCGTGCAAGT 60.066 52.381 0.00 0.00 0.00 3.16
5617 5705 1.663695 CCCTACCAATACCGTGCAAG 58.336 55.000 0.00 0.00 0.00 4.01
5618 5706 0.393267 GCCCTACCAATACCGTGCAA 60.393 55.000 0.00 0.00 0.00 4.08
5652 5740 5.064707 GGCAAATTATAGCGAAGACAAGTCA 59.935 40.000 2.72 0.00 0.00 3.41
5664 5752 6.318900 AGACCAACAACTAGGCAAATTATAGC 59.681 38.462 0.00 0.00 0.00 2.97
5693 5781 2.607282 CGTACCGTATCCCATCTGCTTC 60.607 54.545 0.00 0.00 0.00 3.86
5899 6003 2.097036 CATGAGAAATTCCCAGCAGCA 58.903 47.619 0.00 0.00 0.00 4.41
6051 6169 3.117398 AGAGCTGGGCATAATTTCCATGA 60.117 43.478 0.00 0.00 0.00 3.07
6124 6250 1.176527 CAACGCAGGGGACATCAATT 58.823 50.000 0.00 0.00 0.00 2.32
6176 6302 3.367743 CCGTTGGTCCTCGTCCGA 61.368 66.667 6.36 0.00 0.00 4.55
6256 6382 5.390991 GCACTTGTAGATTTTCTTTCTCGGG 60.391 44.000 0.00 0.00 0.00 5.14
6315 6442 8.119226 GTGTAGCTAGCTGTTGAGATAATTTTG 58.881 37.037 27.68 0.00 0.00 2.44
6330 6457 1.513158 CTGCCGTGTGTAGCTAGCT 59.487 57.895 23.12 23.12 0.00 3.32
6331 6458 4.094684 CTGCCGTGTGTAGCTAGC 57.905 61.111 6.62 6.62 0.00 3.42
6373 6502 0.698238 TGGATGGAAGTTCCCCACTG 59.302 55.000 19.42 0.00 35.12 3.66
6374 6503 0.698818 GTGGATGGAAGTTCCCCACT 59.301 55.000 29.38 11.52 42.25 4.00


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

AutoCloner maintained by Alex Coulton.