Multiple sequence alignment - TraesCS3B01G142800

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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 TraesCS3B01G142800 chr3B 100.000 2543 0 0 1 2543 131517624 131515082 0.000000e+00 4697.0
1 TraesCS3B01G142800 chr3B 91.812 1832 109 13 1 1810 132628417 132626605 0.000000e+00 2514.0
2 TraesCS3B01G142800 chr3B 90.613 522 22 11 2030 2543 132626364 132625862 0.000000e+00 667.0
3 TraesCS3B01G142800 chr3A 92.080 1856 109 16 3 1833 100012900 100014742 0.000000e+00 2579.0
4 TraesCS3B01G142800 chr3A 91.714 531 18 6 2030 2543 100014958 100015479 0.000000e+00 713.0
5 TraesCS3B01G142800 chr3D 91.950 1851 113 15 1 1836 83917852 83919681 0.000000e+00 2560.0
6 TraesCS3B01G142800 chr3D 91.667 528 23 8 2033 2543 83919900 83920423 0.000000e+00 712.0
7 TraesCS3B01G142800 chr1B 90.698 129 10 2 2386 2513 585895812 585895685 1.210000e-38 171.0
8 TraesCS3B01G142800 chr2D 81.410 156 24 3 2388 2543 222645433 222645583 3.440000e-24 122.0
9 TraesCS3B01G142800 chr7B 85.294 68 6 3 2477 2543 58724922 58724858 1.630000e-07 67.6


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 TraesCS3B01G142800 chr3B 131515082 131517624 2542 True 4697.0 4697 100.0000 1 2543 1 chr3B.!!$R1 2542
1 TraesCS3B01G142800 chr3B 132625862 132628417 2555 True 1590.5 2514 91.2125 1 2543 2 chr3B.!!$R2 2542
2 TraesCS3B01G142800 chr3A 100012900 100015479 2579 False 1646.0 2579 91.8970 3 2543 2 chr3A.!!$F1 2540
3 TraesCS3B01G142800 chr3D 83917852 83920423 2571 False 1636.0 2560 91.8085 1 2543 2 chr3D.!!$F1 2542

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
796 809 0.033208 TAAGGGAAAGGCAGCCATGG 60.033 55.0 15.8 7.63 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2148 0.521242 CGGCGCTCATGTTTACAAGC 60.521 55.0 7.64 0.0 0.0 4.01 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
130 140 4.700213 GGATGTAAAACCAAGAGCTGCTAA 59.300 41.667 0.15 0.00 0.00 3.09
158 169 7.820648 TCTTTGAAGAATCTTGATTAACTGGC 58.179 34.615 0.00 0.00 30.73 4.85
222 235 3.152341 CAAGGAACAACTCAGGCTGAAT 58.848 45.455 19.29 5.43 0.00 2.57
277 290 2.464682 GCACAGAGAGCCATGTGTC 58.535 57.895 7.12 0.00 46.75 3.67
374 387 2.334977 TCAAGCAAGGAAGAGGTACCA 58.665 47.619 15.94 0.00 0.00 3.25
378 391 1.351350 GCAAGGAAGAGGTACCAGGTT 59.649 52.381 15.94 3.73 0.00 3.50
425 438 4.022242 GCACTGTGAGAGTTTCAGGTACTA 60.022 45.833 12.86 0.00 36.21 1.82
438 451 3.764434 TCAGGTACTAGCCAGAAAGAGTG 59.236 47.826 0.00 0.00 36.02 3.51
459 472 3.724624 AGGAGCAGCCCTCTGAAG 58.275 61.111 2.45 0.00 42.95 3.02
526 539 3.010027 TGCATACAACATTTCCCTGGAGA 59.990 43.478 0.00 0.00 0.00 3.71
573 586 5.984627 TCAACAATGAGTTATGTCAACACG 58.015 37.500 0.00 0.00 38.74 4.49
657 670 4.591072 AGTTACACTGAAAGAGGAAGAGCT 59.409 41.667 0.00 0.00 37.43 4.09
707 720 1.001268 GATCAGAGAGCGGCATCGTAA 60.001 52.381 1.45 0.00 38.89 3.18
729 742 2.110011 CAGGGGAAGGGAAAGAAAGGAA 59.890 50.000 0.00 0.00 0.00 3.36
772 785 6.183361 TGTTGGTACACCTATGAAGTCAAGAA 60.183 38.462 0.00 0.00 39.29 2.52
776 789 7.103641 GGTACACCTATGAAGTCAAGAAATGA 58.896 38.462 0.00 0.00 35.05 2.57
783 796 8.213679 CCTATGAAGTCAAGAAATGATAAGGGA 58.786 37.037 0.00 0.00 40.97 4.20
796 809 0.033208 TAAGGGAAAGGCAGCCATGG 60.033 55.000 15.80 7.63 0.00 3.66
810 823 2.043852 ATGGCCGAGTCCGAGACT 60.044 61.111 0.00 6.29 46.42 3.24
837 850 1.642037 CTCACCATGCAAGCCAGACG 61.642 60.000 0.00 0.00 0.00 4.18
858 871 1.636003 GTCTCATTTCCAAGGACCCCT 59.364 52.381 0.00 0.00 33.87 4.79
879 892 1.379146 GGTTCCACCAAGTCCTCCC 59.621 63.158 0.00 0.00 38.42 4.30
887 900 3.374318 CCACCAAGTCCTCCCTATAGAGT 60.374 52.174 0.00 0.00 31.53 3.24
894 907 1.424302 CCTCCCTATAGAGTGACCGGA 59.576 57.143 9.46 0.00 31.53 5.14
909 922 1.216977 CGGAGTGTACGGAATGCCA 59.783 57.895 0.00 0.00 0.00 4.92
911 924 1.816074 GGAGTGTACGGAATGCCAAA 58.184 50.000 0.00 0.00 0.00 3.28
917 930 2.011947 GTACGGAATGCCAAAGTACCC 58.988 52.381 0.00 0.00 33.57 3.69
925 938 0.690762 GCCAAAGTACCCCACAGAGA 59.309 55.000 0.00 0.00 0.00 3.10
930 943 1.546961 AGTACCCCACAGAGAAGTCG 58.453 55.000 0.00 0.00 0.00 4.18
939 952 2.029828 CACAGAGAAGTCGCTACCAGTT 60.030 50.000 0.00 0.00 0.00 3.16
993 1006 3.058639 GTGTTGCCAGATCAGAAGACAAC 60.059 47.826 0.00 0.00 37.14 3.32
995 1008 0.723981 GCCAGATCAGAAGACAACGC 59.276 55.000 0.00 0.00 0.00 4.84
1099 1115 3.432326 GGCATACCGTTCCTCAGAAGATT 60.432 47.826 0.00 0.00 30.91 2.40
1108 1124 4.842531 TCCTCAGAAGATTACAATGCCA 57.157 40.909 0.00 0.00 0.00 4.92
1114 1130 3.197766 AGAAGATTACAATGCCACCGAGA 59.802 43.478 0.00 0.00 0.00 4.04
1137 1153 1.445410 CGGTTCGGACGATGAGCAA 60.445 57.895 0.00 0.00 0.00 3.91
1161 1180 5.352569 AGAAATTCAAAGCAGAATCGACGAT 59.647 36.000 4.05 4.05 37.24 3.73
1213 1232 6.128472 CGAATGTGTTGATGAGATCACTGAAA 60.128 38.462 0.00 0.00 39.39 2.69
1239 1258 2.099831 AAGATCGTCGACGTCGGC 59.900 61.111 35.05 33.29 41.13 5.54
1402 1421 4.080129 CCAAGATCCTGGGAATGAGAAGAA 60.080 45.833 1.99 0.00 32.32 2.52
1403 1422 5.503927 CAAGATCCTGGGAATGAGAAGAAA 58.496 41.667 0.00 0.00 0.00 2.52
1438 1457 1.613520 GCAGGAAACCTAAGGTGGGTC 60.614 57.143 0.00 0.00 35.34 4.46
1451 1470 2.411504 TGGGTCGCGACGATGATCA 61.412 57.895 30.99 18.44 38.42 2.92
1473 1492 2.814919 CAGATACGGCTACGAGGATTCT 59.185 50.000 0.00 0.00 44.60 2.40
1476 1495 2.048444 ACGGCTACGAGGATTCTGTA 57.952 50.000 0.00 0.00 44.60 2.74
1528 1547 1.068333 GCAAGCAGGCGATCAAGAAAA 60.068 47.619 0.00 0.00 0.00 2.29
1552 1571 3.378427 GGTACACAAATGAGGCAATCTCC 59.622 47.826 0.00 0.00 41.76 3.71
1553 1572 2.450476 ACACAAATGAGGCAATCTCCC 58.550 47.619 0.00 0.00 41.76 4.30
1583 1610 4.753233 TCTTTTCCATGTGGTGTTTGTTG 58.247 39.130 0.00 0.00 36.34 3.33
1608 1635 8.306038 TGCATTTGTCTGAAGTGCTATTATTTT 58.694 29.630 0.00 0.00 36.78 1.82
1632 1659 7.596749 TGTTTCTGTAGCTGAATAAGTTAGC 57.403 36.000 0.00 0.00 37.71 3.09
1702 1732 6.533819 TTTGTGGTTAGTTTAGTGATCACG 57.466 37.500 19.85 0.00 36.20 4.35
1703 1733 5.204409 TGTGGTTAGTTTAGTGATCACGT 57.796 39.130 19.85 11.00 36.20 4.49
1732 1762 2.823196 CACATTCGTGTGTGTGTGTT 57.177 45.000 12.61 0.00 43.43 3.32
1810 1842 4.955811 TGTATGTTTCTGTGAGTGAGGT 57.044 40.909 0.00 0.00 0.00 3.85
1811 1843 5.290493 TGTATGTTTCTGTGAGTGAGGTT 57.710 39.130 0.00 0.00 0.00 3.50
1814 1846 6.704493 TGTATGTTTCTGTGAGTGAGGTTTAC 59.296 38.462 0.00 0.00 0.00 2.01
1815 1847 5.092554 TGTTTCTGTGAGTGAGGTTTACA 57.907 39.130 0.00 0.00 0.00 2.41
1816 1848 5.116180 TGTTTCTGTGAGTGAGGTTTACAG 58.884 41.667 0.00 0.00 39.95 2.74
1818 1850 6.127281 TGTTTCTGTGAGTGAGGTTTACAGTA 60.127 38.462 0.00 0.00 39.66 2.74
1844 1901 8.207545 AGTTTGAAGAACTCTGTCAGTAATCTT 58.792 33.333 13.06 13.06 35.64 2.40
1855 1912 8.463930 TCTGTCAGTAATCTTGGAAACATTTT 57.536 30.769 0.00 0.00 42.32 1.82
1856 1913 8.567948 TCTGTCAGTAATCTTGGAAACATTTTC 58.432 33.333 0.00 0.00 42.32 2.29
1857 1914 8.463930 TGTCAGTAATCTTGGAAACATTTTCT 57.536 30.769 0.00 0.00 42.32 2.52
1858 1915 9.567776 TGTCAGTAATCTTGGAAACATTTTCTA 57.432 29.630 0.00 0.00 42.32 2.10
1867 1924 9.374711 TCTTGGAAACATTTTCTATTTTACCCT 57.625 29.630 0.00 0.00 42.32 4.34
1907 2027 9.273016 TCCTATATTTCATTTCGTTCTTGATCC 57.727 33.333 0.00 0.00 0.00 3.36
1908 2028 8.223769 CCTATATTTCATTTCGTTCTTGATCCG 58.776 37.037 0.00 0.00 0.00 4.18
1909 2029 3.740044 TTCATTTCGTTCTTGATCCGC 57.260 42.857 0.00 0.00 0.00 5.54
1910 2030 2.006888 TCATTTCGTTCTTGATCCGCC 58.993 47.619 0.00 0.00 0.00 6.13
1911 2031 1.006832 ATTTCGTTCTTGATCCGCCG 58.993 50.000 0.00 0.00 0.00 6.46
1912 2032 0.320073 TTTCGTTCTTGATCCGCCGT 60.320 50.000 0.00 0.00 0.00 5.68
1913 2033 0.527113 TTCGTTCTTGATCCGCCGTA 59.473 50.000 0.00 0.00 0.00 4.02
1914 2034 0.179156 TCGTTCTTGATCCGCCGTAC 60.179 55.000 0.00 0.00 0.00 3.67
1915 2035 1.143969 CGTTCTTGATCCGCCGTACC 61.144 60.000 0.00 0.00 0.00 3.34
1916 2036 0.108520 GTTCTTGATCCGCCGTACCA 60.109 55.000 0.00 0.00 0.00 3.25
1917 2037 0.174845 TTCTTGATCCGCCGTACCAG 59.825 55.000 0.00 0.00 0.00 4.00
1918 2038 0.968901 TCTTGATCCGCCGTACCAGT 60.969 55.000 0.00 0.00 0.00 4.00
1919 2039 0.742505 CTTGATCCGCCGTACCAGTA 59.257 55.000 0.00 0.00 0.00 2.74
1920 2040 0.742505 TTGATCCGCCGTACCAGTAG 59.257 55.000 0.00 0.00 0.00 2.57
1921 2041 0.107066 TGATCCGCCGTACCAGTAGA 60.107 55.000 0.00 0.00 0.00 2.59
1922 2042 1.245732 GATCCGCCGTACCAGTAGAT 58.754 55.000 0.00 0.00 0.00 1.98
1923 2043 1.612463 GATCCGCCGTACCAGTAGATT 59.388 52.381 0.00 0.00 0.00 2.40
1924 2044 1.477553 TCCGCCGTACCAGTAGATTT 58.522 50.000 0.00 0.00 0.00 2.17
1925 2045 2.653726 TCCGCCGTACCAGTAGATTTA 58.346 47.619 0.00 0.00 0.00 1.40
1926 2046 2.358898 TCCGCCGTACCAGTAGATTTAC 59.641 50.000 0.00 0.00 0.00 2.01
1927 2047 2.360165 CCGCCGTACCAGTAGATTTACT 59.640 50.000 0.00 0.00 40.79 2.24
1928 2048 3.181483 CCGCCGTACCAGTAGATTTACTT 60.181 47.826 0.00 0.00 38.05 2.24
1929 2049 3.795101 CGCCGTACCAGTAGATTTACTTG 59.205 47.826 0.00 0.00 38.05 3.16
1930 2050 3.554731 GCCGTACCAGTAGATTTACTTGC 59.445 47.826 0.00 0.00 38.05 4.01
1931 2051 4.751060 CCGTACCAGTAGATTTACTTGCA 58.249 43.478 0.00 0.00 38.05 4.08
1932 2052 5.357257 CCGTACCAGTAGATTTACTTGCAT 58.643 41.667 0.00 0.00 38.05 3.96
1933 2053 6.509656 CCGTACCAGTAGATTTACTTGCATA 58.490 40.000 0.00 0.00 38.05 3.14
1934 2054 7.152645 CCGTACCAGTAGATTTACTTGCATAT 58.847 38.462 0.00 0.00 38.05 1.78
1935 2055 7.656137 CCGTACCAGTAGATTTACTTGCATATT 59.344 37.037 0.00 0.00 38.05 1.28
1936 2056 8.700644 CGTACCAGTAGATTTACTTGCATATTC 58.299 37.037 0.00 0.00 38.05 1.75
1937 2057 9.765795 GTACCAGTAGATTTACTTGCATATTCT 57.234 33.333 0.00 0.00 38.05 2.40
1938 2058 8.668510 ACCAGTAGATTTACTTGCATATTCTG 57.331 34.615 0.00 0.00 38.05 3.02
1939 2059 7.227512 ACCAGTAGATTTACTTGCATATTCTGC 59.772 37.037 0.00 0.00 43.59 4.26
1954 2074 6.658831 CATATTCTGCAATACCAACGTAAGG 58.341 40.000 5.48 5.48 46.39 2.69
1955 2075 3.965379 TCTGCAATACCAACGTAAGGA 57.035 42.857 13.37 0.00 46.39 3.36
1956 2076 3.857052 TCTGCAATACCAACGTAAGGAG 58.143 45.455 13.37 0.35 46.39 3.69
1957 2077 3.512329 TCTGCAATACCAACGTAAGGAGA 59.488 43.478 13.37 2.56 46.39 3.71
1958 2078 3.857052 TGCAATACCAACGTAAGGAGAG 58.143 45.455 13.37 2.61 46.39 3.20
1959 2079 3.512329 TGCAATACCAACGTAAGGAGAGA 59.488 43.478 13.37 0.00 46.39 3.10
1960 2080 4.020928 TGCAATACCAACGTAAGGAGAGAA 60.021 41.667 13.37 0.00 46.39 2.87
1961 2081 5.116882 GCAATACCAACGTAAGGAGAGAAT 58.883 41.667 13.37 0.00 46.39 2.40
2010 2130 7.678947 ATTATGTGACCAAAGAGAAACAGAG 57.321 36.000 0.00 0.00 0.00 3.35
2011 2131 4.753516 TGTGACCAAAGAGAAACAGAGA 57.246 40.909 0.00 0.00 0.00 3.10
2014 2134 5.943416 TGTGACCAAAGAGAAACAGAGAAAA 59.057 36.000 0.00 0.00 0.00 2.29
2015 2135 6.094048 TGTGACCAAAGAGAAACAGAGAAAAG 59.906 38.462 0.00 0.00 0.00 2.27
2016 2136 6.094186 GTGACCAAAGAGAAACAGAGAAAAGT 59.906 38.462 0.00 0.00 0.00 2.66
2017 2137 6.094048 TGACCAAAGAGAAACAGAGAAAAGTG 59.906 38.462 0.00 0.00 0.00 3.16
2018 2138 6.180472 ACCAAAGAGAAACAGAGAAAAGTGA 58.820 36.000 0.00 0.00 0.00 3.41
2019 2139 6.317391 ACCAAAGAGAAACAGAGAAAAGTGAG 59.683 38.462 0.00 0.00 0.00 3.51
2020 2140 6.238593 CCAAAGAGAAACAGAGAAAAGTGAGG 60.239 42.308 0.00 0.00 0.00 3.86
2021 2141 5.878406 AGAGAAACAGAGAAAAGTGAGGA 57.122 39.130 0.00 0.00 0.00 3.71
2022 2142 5.852827 AGAGAAACAGAGAAAAGTGAGGAG 58.147 41.667 0.00 0.00 0.00 3.69
2023 2143 5.600484 AGAGAAACAGAGAAAAGTGAGGAGA 59.400 40.000 0.00 0.00 0.00 3.71
2024 2144 6.098982 AGAGAAACAGAGAAAAGTGAGGAGAA 59.901 38.462 0.00 0.00 0.00 2.87
2025 2145 6.653989 AGAAACAGAGAAAAGTGAGGAGAAA 58.346 36.000 0.00 0.00 0.00 2.52
2026 2146 7.112779 AGAAACAGAGAAAAGTGAGGAGAAAA 58.887 34.615 0.00 0.00 0.00 2.29
2027 2147 7.611855 AGAAACAGAGAAAAGTGAGGAGAAAAA 59.388 33.333 0.00 0.00 0.00 1.94
2028 2148 6.934048 ACAGAGAAAAGTGAGGAGAAAAAG 57.066 37.500 0.00 0.00 0.00 2.27
2069 2190 0.813210 GCCGGCTTGAGATTCCTCTG 60.813 60.000 22.15 0.00 40.10 3.35
2209 2331 4.939915 CGATCCTCGCGACGTCGG 62.940 72.222 36.13 25.93 40.23 4.79
2301 2459 4.154347 GAGCCCAGCCTCTCCACG 62.154 72.222 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.604023 ACTTCTCCACTCGCCGACT 60.604 57.895 0.00 0.00 0.00 4.18
46 47 1.074775 CTTGTAGTTGGCCTGGGCA 59.925 57.895 20.19 20.19 44.11 5.36
158 169 3.986572 TGCACCACAATGAAAAATTAGCG 59.013 39.130 0.00 0.00 0.00 4.26
237 250 0.179116 CCAGTCTCGCCATCAGAGTG 60.179 60.000 0.10 0.10 39.96 3.51
270 283 3.124128 CGGTTTCAGATGAGTGACACATG 59.876 47.826 8.59 0.00 30.10 3.21
277 290 2.266554 GAGCTCGGTTTCAGATGAGTG 58.733 52.381 0.00 0.00 0.00 3.51
348 361 4.670765 ACCTCTTCCTTGCTTGATCAATT 58.329 39.130 8.96 0.00 0.00 2.32
374 387 2.571653 TCTGGGATTTCATCGTCAACCT 59.428 45.455 0.00 0.00 0.00 3.50
378 391 2.466846 TCCTCTGGGATTTCATCGTCA 58.533 47.619 0.00 0.00 36.57 4.35
425 438 0.605589 CCTCGACACTCTTTCTGGCT 59.394 55.000 0.00 0.00 0.00 4.75
459 472 0.037447 AGAAAACCCTCAGCTCCTGC 59.963 55.000 0.00 0.00 40.05 4.85
526 539 2.046447 TCCCTTCTCCAATCTCTTCCCT 59.954 50.000 0.00 0.00 0.00 4.20
657 670 5.084519 TGTTCTAGCTTCTCCCTTACTGAA 58.915 41.667 0.00 0.00 0.00 3.02
707 720 1.429299 CCTTTCTTTCCCTTCCCCTGT 59.571 52.381 0.00 0.00 0.00 4.00
729 742 0.615544 CACCCCTTGATGCCATGGTT 60.616 55.000 14.67 0.59 36.24 3.67
762 775 7.629437 GCCTTTCCCTTATCATTTCTTGACTTC 60.629 40.741 0.00 0.00 37.11 3.01
772 785 2.024080 TGGCTGCCTTTCCCTTATCATT 60.024 45.455 21.03 0.00 0.00 2.57
776 789 1.412074 CCATGGCTGCCTTTCCCTTAT 60.412 52.381 21.03 0.00 0.00 1.73
796 809 0.456995 CTTTCAGTCTCGGACTCGGC 60.457 60.000 3.87 0.00 41.37 5.54
797 810 0.171455 CCTTTCAGTCTCGGACTCGG 59.829 60.000 3.87 0.68 41.37 4.63
810 823 2.507484 CTTGCATGGTGAGACCTTTCA 58.493 47.619 0.00 0.00 39.58 2.69
822 835 2.360350 ACCGTCTGGCTTGCATGG 60.360 61.111 1.34 0.00 39.70 3.66
837 850 1.341089 GGGGTCCTTGGAAATGAGACC 60.341 57.143 0.00 0.00 45.15 3.85
879 892 3.493877 CGTACACTCCGGTCACTCTATAG 59.506 52.174 0.00 0.00 0.00 1.31
887 900 0.528924 CATTCCGTACACTCCGGTCA 59.471 55.000 0.00 0.00 45.63 4.02
894 907 2.561478 ACTTTGGCATTCCGTACACT 57.439 45.000 0.00 0.00 34.14 3.55
903 916 1.427368 TCTGTGGGGTACTTTGGCATT 59.573 47.619 0.00 0.00 0.00 3.56
905 918 0.400213 CTCTGTGGGGTACTTTGGCA 59.600 55.000 0.00 0.00 0.00 4.92
909 922 2.299297 CGACTTCTCTGTGGGGTACTTT 59.701 50.000 0.00 0.00 0.00 2.66
911 924 1.546961 CGACTTCTCTGTGGGGTACT 58.453 55.000 0.00 0.00 0.00 2.73
917 930 0.888619 TGGTAGCGACTTCTCTGTGG 59.111 55.000 0.00 0.00 0.00 4.17
925 938 3.139077 CCTTTTGAACTGGTAGCGACTT 58.861 45.455 0.00 0.00 0.00 3.01
930 943 4.943705 TCATCATCCTTTTGAACTGGTAGC 59.056 41.667 0.00 0.00 0.00 3.58
939 952 6.593268 TGAAGCATTTCATCATCCTTTTGA 57.407 33.333 0.00 0.00 38.37 2.69
993 1006 2.159653 GCCTCTGTAGTTCATGTTTGCG 60.160 50.000 0.00 0.00 0.00 4.85
995 1008 4.083110 CCTTGCCTCTGTAGTTCATGTTTG 60.083 45.833 0.00 0.00 0.00 2.93
1053 1066 4.787598 CTTCATTTCCTTCTTGTTGGTCG 58.212 43.478 0.00 0.00 0.00 4.79
1092 1108 3.197766 TCTCGGTGGCATTGTAATCTTCT 59.802 43.478 0.00 0.00 0.00 2.85
1099 1115 2.695359 GTTCTTCTCGGTGGCATTGTA 58.305 47.619 0.00 0.00 0.00 2.41
1114 1130 0.599558 TCATCGTCCGAACCGTTCTT 59.400 50.000 9.55 0.00 0.00 2.52
1137 1153 4.690748 TCGTCGATTCTGCTTTGAATTTCT 59.309 37.500 0.00 0.00 36.86 2.52
1161 1180 0.108472 CATTCCTGCAGCTCTCGTCA 60.108 55.000 8.66 0.00 0.00 4.35
1213 1232 2.662700 GTCGACGATCTTGTCAACACT 58.337 47.619 0.00 0.00 38.84 3.55
1222 1241 2.099831 GCCGACGTCGACGATCTT 59.900 61.111 41.52 21.67 43.02 2.40
1239 1258 0.179150 GAGTAGCAGCACTCTCACCG 60.179 60.000 14.37 0.00 41.49 4.94
1402 1421 0.250209 CTGCCTGCACAGTCTGAGTT 60.250 55.000 6.91 0.00 32.78 3.01
1403 1422 1.370437 CTGCCTGCACAGTCTGAGT 59.630 57.895 6.91 0.00 32.78 3.41
1438 1457 1.972640 GTATCTGTGATCATCGTCGCG 59.027 52.381 0.00 0.00 0.00 5.87
1451 1470 2.273538 ATCCTCGTAGCCGTATCTGT 57.726 50.000 0.00 0.00 35.01 3.41
1473 1492 1.102978 TGCTGCTGCTCGTAGATACA 58.897 50.000 17.00 0.00 40.48 2.29
1476 1495 0.534412 ACTTGCTGCTGCTCGTAGAT 59.466 50.000 17.00 0.00 40.48 1.98
1528 1547 2.264005 TTGCCTCATTTGTGTACCGT 57.736 45.000 0.00 0.00 0.00 4.83
1552 1571 6.158598 CACCACATGGAAAAGAATAAACAGG 58.841 40.000 4.53 0.00 38.94 4.00
1553 1572 6.748132 ACACCACATGGAAAAGAATAAACAG 58.252 36.000 4.53 0.00 38.94 3.16
1583 1610 8.589629 CAAAATAATAGCACTTCAGACAAATGC 58.410 33.333 0.00 0.00 36.52 3.56
1608 1635 6.310467 CGCTAACTTATTCAGCTACAGAAACA 59.690 38.462 0.00 0.00 33.03 2.83
1719 1749 2.157863 TGTACACAAACACACACACACG 59.842 45.455 0.00 0.00 0.00 4.49
1720 1750 3.815337 TGTACACAAACACACACACAC 57.185 42.857 0.00 0.00 0.00 3.82
1721 1751 3.815962 AGTTGTACACAAACACACACACA 59.184 39.130 0.00 0.00 37.63 3.72
1722 1752 4.413495 AGTTGTACACAAACACACACAC 57.587 40.909 0.00 0.00 37.63 3.82
1723 1753 6.745159 AATAGTTGTACACAAACACACACA 57.255 33.333 0.00 0.00 37.63 3.72
1784 1814 7.766278 ACCTCACTCACAGAAACATACATAATC 59.234 37.037 0.00 0.00 0.00 1.75
1810 1842 8.255206 TGACAGAGTTCTTCAAACTACTGTAAA 58.745 33.333 16.03 9.66 38.02 2.01
1811 1843 7.778083 TGACAGAGTTCTTCAAACTACTGTAA 58.222 34.615 16.03 10.53 38.02 2.41
1814 1846 6.276847 ACTGACAGAGTTCTTCAAACTACTG 58.723 40.000 10.08 12.01 34.56 2.74
1815 1847 6.472686 ACTGACAGAGTTCTTCAAACTACT 57.527 37.500 10.08 0.00 0.00 2.57
1816 1848 8.819643 ATTACTGACAGAGTTCTTCAAACTAC 57.180 34.615 10.08 0.00 35.96 2.73
1818 1850 7.731054 AGATTACTGACAGAGTTCTTCAAACT 58.269 34.615 10.08 0.00 35.96 2.66
1879 1936 9.838339 ATCAAGAACGAAATGAAATATAGGAGT 57.162 29.630 0.00 0.00 0.00 3.85
1882 1939 8.223769 CGGATCAAGAACGAAATGAAATATAGG 58.776 37.037 0.00 0.00 0.00 2.57
1883 1940 7.742089 GCGGATCAAGAACGAAATGAAATATAG 59.258 37.037 0.00 0.00 0.00 1.31
1884 1941 7.307751 GGCGGATCAAGAACGAAATGAAATATA 60.308 37.037 0.00 0.00 0.00 0.86
1886 1943 5.220777 GGCGGATCAAGAACGAAATGAAATA 60.221 40.000 0.00 0.00 0.00 1.40
1887 1944 4.438744 GGCGGATCAAGAACGAAATGAAAT 60.439 41.667 0.00 0.00 0.00 2.17
1894 2014 0.527113 TACGGCGGATCAAGAACGAA 59.473 50.000 13.24 0.00 0.00 3.85
1896 2016 1.143969 GGTACGGCGGATCAAGAACG 61.144 60.000 13.24 0.00 0.00 3.95
1907 2027 3.705043 AGTAAATCTACTGGTACGGCG 57.295 47.619 4.80 4.80 36.98 6.46
1908 2028 3.554731 GCAAGTAAATCTACTGGTACGGC 59.445 47.826 0.00 0.00 38.43 5.68
1909 2029 4.751060 TGCAAGTAAATCTACTGGTACGG 58.249 43.478 0.00 0.00 38.43 4.02
1910 2030 8.589335 AATATGCAAGTAAATCTACTGGTACG 57.411 34.615 0.00 0.00 38.43 3.67
1911 2031 9.765795 AGAATATGCAAGTAAATCTACTGGTAC 57.234 33.333 0.00 0.00 38.43 3.34
1912 2032 9.764363 CAGAATATGCAAGTAAATCTACTGGTA 57.236 33.333 0.00 0.00 38.43 3.25
1913 2033 8.668510 CAGAATATGCAAGTAAATCTACTGGT 57.331 34.615 0.00 0.00 38.43 4.00
1930 2050 6.481976 TCCTTACGTTGGTATTGCAGAATATG 59.518 38.462 0.00 0.00 0.00 1.78
1931 2051 6.588204 TCCTTACGTTGGTATTGCAGAATAT 58.412 36.000 0.00 0.00 0.00 1.28
1932 2052 5.979993 TCCTTACGTTGGTATTGCAGAATA 58.020 37.500 0.00 0.00 0.00 1.75
1933 2053 4.839121 TCCTTACGTTGGTATTGCAGAAT 58.161 39.130 0.00 0.00 0.00 2.40
1934 2054 4.020928 TCTCCTTACGTTGGTATTGCAGAA 60.021 41.667 0.00 0.00 0.00 3.02
1935 2055 3.512329 TCTCCTTACGTTGGTATTGCAGA 59.488 43.478 0.00 0.00 0.00 4.26
1936 2056 3.857052 TCTCCTTACGTTGGTATTGCAG 58.143 45.455 0.00 0.00 0.00 4.41
1937 2057 3.512329 TCTCTCCTTACGTTGGTATTGCA 59.488 43.478 0.00 0.00 0.00 4.08
1938 2058 4.119442 TCTCTCCTTACGTTGGTATTGC 57.881 45.455 0.00 0.00 0.00 3.56
1939 2059 5.753921 GGATTCTCTCCTTACGTTGGTATTG 59.246 44.000 0.00 0.00 41.29 1.90
1940 2060 5.424252 TGGATTCTCTCCTTACGTTGGTATT 59.576 40.000 0.00 0.00 45.21 1.89
1941 2061 4.960469 TGGATTCTCTCCTTACGTTGGTAT 59.040 41.667 0.00 0.00 45.21 2.73
1942 2062 4.346730 TGGATTCTCTCCTTACGTTGGTA 58.653 43.478 0.00 0.00 45.21 3.25
1943 2063 3.170717 TGGATTCTCTCCTTACGTTGGT 58.829 45.455 0.00 0.00 45.21 3.67
1944 2064 3.887621 TGGATTCTCTCCTTACGTTGG 57.112 47.619 0.00 0.00 45.21 3.77
1945 2065 6.743575 AATTTGGATTCTCTCCTTACGTTG 57.256 37.500 0.00 0.00 45.21 4.10
1946 2066 7.848128 TCTAATTTGGATTCTCTCCTTACGTT 58.152 34.615 0.00 0.00 45.21 3.99
1947 2067 7.419711 TCTAATTTGGATTCTCTCCTTACGT 57.580 36.000 0.00 0.00 45.21 3.57
1948 2068 8.604890 GTTTCTAATTTGGATTCTCTCCTTACG 58.395 37.037 0.00 0.00 45.21 3.18
1949 2069 9.674068 AGTTTCTAATTTGGATTCTCTCCTTAC 57.326 33.333 0.00 0.00 45.21 2.34
1950 2070 9.672673 CAGTTTCTAATTTGGATTCTCTCCTTA 57.327 33.333 0.00 0.00 45.21 2.69
1951 2071 8.166726 ACAGTTTCTAATTTGGATTCTCTCCTT 58.833 33.333 0.00 0.00 45.21 3.36
1952 2072 7.694093 ACAGTTTCTAATTTGGATTCTCTCCT 58.306 34.615 0.00 0.00 45.21 3.69
1953 2073 7.929941 ACAGTTTCTAATTTGGATTCTCTCC 57.070 36.000 0.00 0.00 45.19 3.71
1984 2104 9.219603 CTCTGTTTCTCTTTGGTCACATAATAA 57.780 33.333 0.00 0.00 0.00 1.40
1987 2107 6.826668 TCTCTGTTTCTCTTTGGTCACATAA 58.173 36.000 0.00 0.00 0.00 1.90
1988 2108 6.419484 TCTCTGTTTCTCTTTGGTCACATA 57.581 37.500 0.00 0.00 0.00 2.29
1989 2109 5.296151 TCTCTGTTTCTCTTTGGTCACAT 57.704 39.130 0.00 0.00 0.00 3.21
1990 2110 4.753516 TCTCTGTTTCTCTTTGGTCACA 57.246 40.909 0.00 0.00 0.00 3.58
1991 2111 6.094186 ACTTTTCTCTGTTTCTCTTTGGTCAC 59.906 38.462 0.00 0.00 0.00 3.67
1992 2112 6.094048 CACTTTTCTCTGTTTCTCTTTGGTCA 59.906 38.462 0.00 0.00 0.00 4.02
1994 2114 6.180472 TCACTTTTCTCTGTTTCTCTTTGGT 58.820 36.000 0.00 0.00 0.00 3.67
1995 2115 6.238593 CCTCACTTTTCTCTGTTTCTCTTTGG 60.239 42.308 0.00 0.00 0.00 3.28
1996 2116 6.540189 TCCTCACTTTTCTCTGTTTCTCTTTG 59.460 38.462 0.00 0.00 0.00 2.77
1998 2118 6.098982 TCTCCTCACTTTTCTCTGTTTCTCTT 59.901 38.462 0.00 0.00 0.00 2.85
2000 2120 5.848406 TCTCCTCACTTTTCTCTGTTTCTC 58.152 41.667 0.00 0.00 0.00 2.87
2002 2122 6.927294 TTTCTCCTCACTTTTCTCTGTTTC 57.073 37.500 0.00 0.00 0.00 2.78
2004 2124 6.183360 GCTTTTTCTCCTCACTTTTCTCTGTT 60.183 38.462 0.00 0.00 0.00 3.16
2005 2125 5.298026 GCTTTTTCTCCTCACTTTTCTCTGT 59.702 40.000 0.00 0.00 0.00 3.41
2006 2126 5.530543 AGCTTTTTCTCCTCACTTTTCTCTG 59.469 40.000 0.00 0.00 0.00 3.35
2010 2130 5.895928 ACAAGCTTTTTCTCCTCACTTTTC 58.104 37.500 0.00 0.00 0.00 2.29
2011 2131 5.921962 ACAAGCTTTTTCTCCTCACTTTT 57.078 34.783 0.00 0.00 0.00 2.27
2014 2134 5.885912 TGTTTACAAGCTTTTTCTCCTCACT 59.114 36.000 0.00 0.00 0.00 3.41
2015 2135 6.131544 TGTTTACAAGCTTTTTCTCCTCAC 57.868 37.500 0.00 0.00 0.00 3.51
2016 2136 6.545666 TCATGTTTACAAGCTTTTTCTCCTCA 59.454 34.615 0.00 0.00 0.00 3.86
2017 2137 6.970484 TCATGTTTACAAGCTTTTTCTCCTC 58.030 36.000 0.00 0.00 0.00 3.71
2018 2138 6.515696 GCTCATGTTTACAAGCTTTTTCTCCT 60.516 38.462 0.00 0.00 29.54 3.69
2019 2139 5.631096 GCTCATGTTTACAAGCTTTTTCTCC 59.369 40.000 0.00 0.00 29.54 3.71
2020 2140 5.340667 CGCTCATGTTTACAAGCTTTTTCTC 59.659 40.000 0.00 0.00 29.84 2.87
2021 2141 5.215160 CGCTCATGTTTACAAGCTTTTTCT 58.785 37.500 0.00 0.00 29.84 2.52
2022 2142 4.143535 GCGCTCATGTTTACAAGCTTTTTC 60.144 41.667 0.00 0.00 29.84 2.29
2023 2143 3.735746 GCGCTCATGTTTACAAGCTTTTT 59.264 39.130 0.00 0.00 29.84 1.94
2024 2144 3.308530 GCGCTCATGTTTACAAGCTTTT 58.691 40.909 0.00 0.00 29.84 2.27
2025 2145 2.351738 GGCGCTCATGTTTACAAGCTTT 60.352 45.455 7.64 0.00 29.84 3.51
2026 2146 1.200020 GGCGCTCATGTTTACAAGCTT 59.800 47.619 7.64 0.00 29.84 3.74
2027 2147 0.804989 GGCGCTCATGTTTACAAGCT 59.195 50.000 7.64 0.00 29.84 3.74
2028 2148 0.521242 CGGCGCTCATGTTTACAAGC 60.521 55.000 7.64 0.00 0.00 4.01
2058 2179 4.344679 AGTCCATGTCATCAGAGGAATCTC 59.655 45.833 0.00 0.00 40.25 2.75
2069 2190 1.026182 TGGCGCAAGTCCATGTCATC 61.026 55.000 10.83 0.00 45.49 2.92
2226 2360 2.281761 CTCTGGTTTGGCTGCGGT 60.282 61.111 0.00 0.00 0.00 5.68
2231 2365 2.980233 GCACGCTCTGGTTTGGCT 60.980 61.111 0.00 0.00 0.00 4.75
2235 2369 1.598130 GTGGAGCACGCTCTGGTTT 60.598 57.895 17.99 0.00 42.38 3.27


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

AutoCloner maintained by Alex Coulton.