Multiple sequence alignment - TraesCS3B01G151900

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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 TraesCS3B01G151900 chr3B 100.000 2612 0 0 1 2612 143570347 143572958 0.000000e+00 4824
1 TraesCS3B01G151900 chr3B 86.141 736 89 10 8 734 143557489 143556758 0.000000e+00 782
2 TraesCS3B01G151900 chr3B 80.563 710 83 38 63 751 143585079 143585754 1.810000e-136 496
3 TraesCS3B01G151900 chr3B 81.574 521 87 6 13 529 143506532 143506017 3.110000e-114 422
4 TraesCS3B01G151900 chr3B 87.037 216 27 1 312 526 143568173 143567958 2.600000e-60 243
5 TraesCS3B01G151900 chr3B 83.835 266 30 8 2141 2394 20790492 20790228 9.340000e-60 241
6 TraesCS3B01G151900 chr3B 83.525 261 31 6 2146 2394 716574497 716574237 1.560000e-57 233
7 TraesCS3B01G151900 chr3B 83.133 249 42 0 2146 2394 136487676 136487924 7.270000e-56 228
8 TraesCS3B01G151900 chr3B 91.667 156 13 0 352 507 143523067 143523222 1.570000e-52 217
9 TraesCS3B01G151900 chr3D 93.982 1828 58 12 1 1791 92871521 92869709 0.000000e+00 2719
10 TraesCS3B01G151900 chr3D 87.288 826 57 15 1801 2612 92869736 92868945 0.000000e+00 900
11 TraesCS3B01G151900 chr3D 80.144 695 91 29 43 716 92865427 92864759 2.350000e-130 475
12 TraesCS3B01G151900 chr3D 77.273 638 115 20 997 1613 92857551 92856923 5.350000e-92 348
13 TraesCS3B01G151900 chr3D 89.189 259 19 6 373 628 92891225 92890973 5.430000e-82 315
14 TraesCS3B01G151900 chr3D 84.109 258 28 9 2137 2383 379660116 379660371 1.210000e-58 237
15 TraesCS3B01G151900 chr3A 81.680 726 94 24 8 716 547194639 547193936 3.770000e-158 568
16 TraesCS3B01G151900 chr7A 83.267 251 30 7 2142 2380 1449876 1449626 1.220000e-53 220
17 TraesCS3B01G151900 chr7A 84.444 225 22 6 2142 2354 91928080 91928303 2.630000e-50 209
18 TraesCS3B01G151900 chr2A 81.455 275 35 9 2140 2400 131853852 131853580 7.320000e-51 211
19 TraesCS3B01G151900 chr5B 82.627 236 27 9 2171 2394 648283040 648282807 2.050000e-46 196
20 TraesCS3B01G151900 chr5B 79.283 251 39 10 2145 2394 612558610 612558372 2.080000e-36 163
21 TraesCS3B01G151900 chr5B 85.263 95 14 0 2301 2395 123753613 123753707 5.950000e-17 99
22 TraesCS3B01G151900 chr6B 80.524 267 36 10 2145 2395 161880688 161880422 9.540000e-45 191
23 TraesCS3B01G151900 chr6B 86.441 118 13 3 2146 2260 584057514 584057397 2.730000e-25 126
24 TraesCS3B01G151900 chr1D 82.609 230 25 9 2158 2374 108494171 108494398 3.430000e-44 189
25 TraesCS3B01G151900 chr2D 80.153 262 39 5 2146 2395 52950629 52950369 1.600000e-42 183


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 TraesCS3B01G151900 chr3B 143570347 143572958 2611 False 4824.000000 4824 100.000 1 2612 1 chr3B.!!$F3 2611
1 TraesCS3B01G151900 chr3B 143556758 143557489 731 True 782.000000 782 86.141 8 734 1 chr3B.!!$R3 726
2 TraesCS3B01G151900 chr3B 143585079 143585754 675 False 496.000000 496 80.563 63 751 1 chr3B.!!$F4 688
3 TraesCS3B01G151900 chr3B 143506017 143506532 515 True 422.000000 422 81.574 13 529 1 chr3B.!!$R2 516
4 TraesCS3B01G151900 chr3D 92864759 92871521 6762 True 1364.666667 2719 87.138 1 2612 3 chr3D.!!$R3 2611
5 TraesCS3B01G151900 chr3D 92856923 92857551 628 True 348.000000 348 77.273 997 1613 1 chr3D.!!$R1 616
6 TraesCS3B01G151900 chr3A 547193936 547194639 703 True 568.000000 568 81.680 8 716 1 chr3A.!!$R1 708

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
858 902 0.169672 TCTGAACCGACGTCGATTCC 59.83 55.0 35.41 21.12 41.04 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 2007 0.107456 CCTCCATCACATTCCCTCCG 59.893 60.0 0.0 0.0 0.0 4.63 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
35 36 1.741401 TGTGTAGCACAGCATCGCC 60.741 57.895 0.00 0.00 39.62 5.54
200 207 2.636412 CCGAGAGAGGAACACGCCA 61.636 63.158 0.00 0.00 0.00 5.69
551 579 0.807667 CAAGCAGAAGGATCGTCGGG 60.808 60.000 0.00 0.00 0.00 5.14
699 739 1.576356 CTCGCAGATCTAAAGGCCAC 58.424 55.000 5.01 0.00 33.89 5.01
758 802 6.294564 GGGAGGACTTTGAGGATTAAACAAAC 60.295 42.308 0.00 0.00 31.67 2.93
773 817 1.269621 ACAAACTCGAGTCTGAACCGG 60.270 52.381 25.16 0.00 0.00 5.28
816 860 2.456119 GCGACCGGACTGCAGATTG 61.456 63.158 23.35 8.78 0.00 2.67
858 902 0.169672 TCTGAACCGACGTCGATTCC 59.830 55.000 35.41 21.12 41.04 3.01
866 910 1.812214 GACGTCGATTCCGCATCTGC 61.812 60.000 0.00 0.00 35.37 4.26
895 939 1.762957 CTCGTCTCTCTCCTCTCCTCT 59.237 57.143 0.00 0.00 0.00 3.69
896 940 1.760613 TCGTCTCTCTCCTCTCCTCTC 59.239 57.143 0.00 0.00 0.00 3.20
897 941 1.202651 CGTCTCTCTCCTCTCCTCTCC 60.203 61.905 0.00 0.00 0.00 3.71
898 942 2.127708 GTCTCTCTCCTCTCCTCTCCT 58.872 57.143 0.00 0.00 0.00 3.69
899 943 2.104963 GTCTCTCTCCTCTCCTCTCCTC 59.895 59.091 0.00 0.00 0.00 3.71
1084 1133 1.078143 ATCTTGTTCTCTGCCGGCC 60.078 57.895 26.77 7.71 0.00 6.13
1161 1222 4.503643 CCGGAGAAAAGTTACCACCAAGTA 60.504 45.833 0.00 0.00 0.00 2.24
1262 1350 1.811266 GCGAGATGTGCGTGACCAT 60.811 57.895 0.00 0.00 0.00 3.55
1278 1366 0.179026 CCATCTGGGAGGCTGATGTG 60.179 60.000 10.54 1.15 40.01 3.21
1378 1466 3.164011 CGACGTCGACCGACTTGC 61.164 66.667 33.35 8.11 42.54 4.01
1594 1682 7.757624 CAGAGACTAGTGATACAAGGTTCTTTC 59.242 40.741 0.00 0.00 0.00 2.62
1622 1710 4.280929 TCCAAGAATGTGATCGATCGGTAT 59.719 41.667 20.03 11.21 0.00 2.73
1645 1733 7.937700 ATAGGGTCAGGTTGATATATATGGG 57.062 40.000 0.00 0.00 0.00 4.00
1646 1734 5.927465 AGGGTCAGGTTGATATATATGGGA 58.073 41.667 0.00 0.00 0.00 4.37
1647 1735 6.339220 AGGGTCAGGTTGATATATATGGGAA 58.661 40.000 0.00 0.00 0.00 3.97
1662 1750 1.375268 GGAAGCGCTCTTGCAGACT 60.375 57.895 12.06 0.00 39.99 3.24
1686 1774 9.750125 ACTGATTTCTTTCTTTGTTGGTTAATC 57.250 29.630 0.00 0.00 0.00 1.75
1694 1782 4.837860 TCTTTGTTGGTTAATCATGGCCTT 59.162 37.500 3.32 0.00 0.00 4.35
1695 1783 4.799564 TTGTTGGTTAATCATGGCCTTC 57.200 40.909 3.32 0.00 0.00 3.46
1697 1785 4.415596 TGTTGGTTAATCATGGCCTTCTT 58.584 39.130 3.32 0.00 0.00 2.52
1698 1786 4.837860 TGTTGGTTAATCATGGCCTTCTTT 59.162 37.500 3.32 0.00 0.00 2.52
1699 1787 5.306678 TGTTGGTTAATCATGGCCTTCTTTT 59.693 36.000 3.32 0.00 0.00 2.27
1700 1788 6.183361 TGTTGGTTAATCATGGCCTTCTTTTT 60.183 34.615 3.32 0.00 0.00 1.94
1701 1789 6.036577 TGGTTAATCATGGCCTTCTTTTTC 57.963 37.500 3.32 0.00 0.00 2.29
1702 1790 5.541868 TGGTTAATCATGGCCTTCTTTTTCA 59.458 36.000 3.32 0.00 0.00 2.69
1703 1791 6.213195 TGGTTAATCATGGCCTTCTTTTTCAT 59.787 34.615 3.32 0.00 0.00 2.57
1704 1792 7.105588 GGTTAATCATGGCCTTCTTTTTCATT 58.894 34.615 3.32 0.00 0.00 2.57
1705 1793 7.607607 GGTTAATCATGGCCTTCTTTTTCATTT 59.392 33.333 3.32 0.00 0.00 2.32
1711 1799 4.874966 TGGCCTTCTTTTTCATTTTGTGTG 59.125 37.500 3.32 0.00 0.00 3.82
1724 1812 6.554419 TCATTTTGTGTGACTGTTTTCTCTG 58.446 36.000 0.00 0.00 0.00 3.35
1729 1817 3.689649 GTGTGACTGTTTTCTCTGGTGTT 59.310 43.478 0.00 0.00 0.00 3.32
1736 1824 6.831976 ACTGTTTTCTCTGGTGTTCTCTATT 58.168 36.000 0.00 0.00 0.00 1.73
1746 1834 8.089625 TCTGGTGTTCTCTATTTAATCATGGA 57.910 34.615 0.00 0.00 0.00 3.41
1773 1861 7.227049 TGTGACTGTTCTCTTGTGTCATATA 57.773 36.000 0.00 0.00 39.39 0.86
1774 1862 7.090808 TGTGACTGTTCTCTTGTGTCATATAC 58.909 38.462 0.00 0.00 39.39 1.47
1775 1863 7.039714 TGTGACTGTTCTCTTGTGTCATATACT 60.040 37.037 0.00 0.00 39.39 2.12
1776 1864 7.815068 GTGACTGTTCTCTTGTGTCATATACTT 59.185 37.037 0.00 0.00 39.39 2.24
1777 1865 7.814587 TGACTGTTCTCTTGTGTCATATACTTG 59.185 37.037 0.00 0.00 33.45 3.16
1778 1866 7.671302 ACTGTTCTCTTGTGTCATATACTTGT 58.329 34.615 0.00 0.00 0.00 3.16
1779 1867 7.600375 ACTGTTCTCTTGTGTCATATACTTGTG 59.400 37.037 0.00 0.00 0.00 3.33
1780 1868 7.441836 TGTTCTCTTGTGTCATATACTTGTGT 58.558 34.615 0.00 0.00 0.00 3.72
1781 1869 7.931407 TGTTCTCTTGTGTCATATACTTGTGTT 59.069 33.333 0.00 0.00 0.00 3.32
1782 1870 7.889589 TCTCTTGTGTCATATACTTGTGTTG 57.110 36.000 0.00 0.00 0.00 3.33
1783 1871 7.666623 TCTCTTGTGTCATATACTTGTGTTGA 58.333 34.615 0.00 0.00 0.00 3.18
1784 1872 8.314021 TCTCTTGTGTCATATACTTGTGTTGAT 58.686 33.333 0.00 0.00 0.00 2.57
1785 1873 8.846943 TCTTGTGTCATATACTTGTGTTGATT 57.153 30.769 0.00 0.00 0.00 2.57
1786 1874 9.936759 TCTTGTGTCATATACTTGTGTTGATTA 57.063 29.630 0.00 0.00 0.00 1.75
1789 1877 9.665719 TGTGTCATATACTTGTGTTGATTATGT 57.334 29.630 0.00 0.00 0.00 2.29
1798 1886 8.226543 ACTTGTGTTGATTATGTATTTTTGCG 57.773 30.769 0.00 0.00 0.00 4.85
1799 1887 7.328249 ACTTGTGTTGATTATGTATTTTTGCGG 59.672 33.333 0.00 0.00 0.00 5.69
1800 1888 6.096036 TGTGTTGATTATGTATTTTTGCGGG 58.904 36.000 0.00 0.00 0.00 6.13
1801 1889 6.096695 GTGTTGATTATGTATTTTTGCGGGT 58.903 36.000 0.00 0.00 0.00 5.28
1802 1890 6.034470 GTGTTGATTATGTATTTTTGCGGGTG 59.966 38.462 0.00 0.00 0.00 4.61
1803 1891 4.677584 TGATTATGTATTTTTGCGGGTGC 58.322 39.130 0.00 0.00 43.20 5.01
1834 1922 6.756299 TGTGTTGATGTATGTACATGCATT 57.244 33.333 31.67 19.67 46.20 3.56
1835 1923 7.155655 TGTGTTGATGTATGTACATGCATTT 57.844 32.000 31.67 17.77 46.20 2.32
1875 1963 7.656412 TGTTGTTTAGATTTGTGCACACATAT 58.344 30.769 21.56 18.62 41.52 1.78
1917 2005 1.917273 ATTCGGTCGTATCACCAACG 58.083 50.000 0.00 0.00 41.64 4.10
1919 2007 2.162754 CGGTCGTATCACCAACGGC 61.163 63.158 0.00 0.00 43.94 5.68
1920 2008 2.162754 GGTCGTATCACCAACGGCG 61.163 63.158 4.80 4.80 45.55 6.46
1921 2009 2.162754 GTCGTATCACCAACGGCGG 61.163 63.158 13.24 0.00 40.68 6.13
1922 2010 2.182284 CGTATCACCAACGGCGGA 59.818 61.111 13.24 0.00 36.71 5.54
1928 2016 3.327404 ACCAACGGCGGAGGGAAT 61.327 61.111 21.12 0.94 0.00 3.01
1952 2040 0.928505 TGGAGGGAATGCATCACCAT 59.071 50.000 18.57 14.16 28.52 3.55
1967 2055 0.837272 ACCATAGGGATCACCAACGG 59.163 55.000 0.00 0.00 43.89 4.44
2004 2092 4.210331 CAAAAGATATCCCCCACTCCTTG 58.790 47.826 0.00 0.00 0.00 3.61
2005 2093 2.897823 AGATATCCCCCACTCCTTGT 57.102 50.000 0.00 0.00 0.00 3.16
2006 2094 2.695585 AGATATCCCCCACTCCTTGTC 58.304 52.381 0.00 0.00 0.00 3.18
2007 2095 2.251338 AGATATCCCCCACTCCTTGTCT 59.749 50.000 0.00 0.00 0.00 3.41
2008 2096 3.471306 AGATATCCCCCACTCCTTGTCTA 59.529 47.826 0.00 0.00 0.00 2.59
2009 2097 2.897823 ATCCCCCACTCCTTGTCTAT 57.102 50.000 0.00 0.00 0.00 1.98
2010 2098 2.661176 TCCCCCACTCCTTGTCTATT 57.339 50.000 0.00 0.00 0.00 1.73
2011 2099 2.929301 TCCCCCACTCCTTGTCTATTT 58.071 47.619 0.00 0.00 0.00 1.40
2012 2100 2.576191 TCCCCCACTCCTTGTCTATTTG 59.424 50.000 0.00 0.00 0.00 2.32
2013 2101 2.369394 CCCCACTCCTTGTCTATTTGC 58.631 52.381 0.00 0.00 0.00 3.68
2014 2102 2.369394 CCCACTCCTTGTCTATTTGCC 58.631 52.381 0.00 0.00 0.00 4.52
2015 2103 2.369394 CCACTCCTTGTCTATTTGCCC 58.631 52.381 0.00 0.00 0.00 5.36
2016 2104 2.369394 CACTCCTTGTCTATTTGCCCC 58.631 52.381 0.00 0.00 0.00 5.80
2017 2105 1.992557 ACTCCTTGTCTATTTGCCCCA 59.007 47.619 0.00 0.00 0.00 4.96
2018 2106 2.290960 ACTCCTTGTCTATTTGCCCCAC 60.291 50.000 0.00 0.00 0.00 4.61
2019 2107 1.992557 TCCTTGTCTATTTGCCCCACT 59.007 47.619 0.00 0.00 0.00 4.00
2020 2108 2.026262 TCCTTGTCTATTTGCCCCACTC 60.026 50.000 0.00 0.00 0.00 3.51
2021 2109 2.369394 CTTGTCTATTTGCCCCACTCC 58.631 52.381 0.00 0.00 0.00 3.85
2022 2110 1.668826 TGTCTATTTGCCCCACTCCT 58.331 50.000 0.00 0.00 0.00 3.69
2023 2111 1.992557 TGTCTATTTGCCCCACTCCTT 59.007 47.619 0.00 0.00 0.00 3.36
2024 2112 2.290896 TGTCTATTTGCCCCACTCCTTG 60.291 50.000 0.00 0.00 0.00 3.61
2032 2120 2.026262 TGCCCCACTCCTTGTCTATTTC 60.026 50.000 0.00 0.00 0.00 2.17
2038 2126 4.380233 CCACTCCTTGTCTATTTCGTACGT 60.380 45.833 16.05 0.00 0.00 3.57
2044 2132 0.381801 TCTATTTCGTACGTCGGGCC 59.618 55.000 16.05 0.00 40.32 5.80
2045 2133 0.595825 CTATTTCGTACGTCGGGCCC 60.596 60.000 13.57 13.57 40.32 5.80
2096 2184 1.686587 ACCCTTAACAAGCTTTGGTGC 59.313 47.619 0.00 0.00 34.12 5.01
2098 2186 3.153919 CCCTTAACAAGCTTTGGTGCTA 58.846 45.455 0.00 0.00 43.24 3.49
2104 2192 0.972471 AAGCTTTGGTGCTATGGGCC 60.972 55.000 0.00 0.00 43.24 5.80
2109 2197 2.124151 GGTGCTATGGGCCAGGTG 60.124 66.667 13.78 5.57 40.92 4.00
2112 2200 3.096495 GCTATGGGCCAGGTGGGA 61.096 66.667 13.78 0.00 40.01 4.37
2149 2237 6.669631 CCCCCACCTTCATTAATTAGTACTT 58.330 40.000 0.00 0.00 0.00 2.24
2150 2238 6.771267 CCCCCACCTTCATTAATTAGTACTTC 59.229 42.308 0.00 0.00 0.00 3.01
2151 2239 7.343357 CCCCACCTTCATTAATTAGTACTTCA 58.657 38.462 0.00 0.00 0.00 3.02
2375 2475 7.157347 TCAGCCAAATCTAATATGCAGAGTAG 58.843 38.462 9.46 9.46 0.00 2.57
2376 2476 7.015584 TCAGCCAAATCTAATATGCAGAGTAGA 59.984 37.037 19.50 19.50 0.00 2.59
2390 2490 6.591935 TGCAGAGTAGATAAAAACATAGGGG 58.408 40.000 0.00 0.00 0.00 4.79
2430 2530 9.825109 AGATTTCCTCAGTTACTAAAATAGAGC 57.175 33.333 0.00 0.00 0.00 4.09
2433 2533 8.834004 TTCCTCAGTTACTAAAATAGAGCCTA 57.166 34.615 0.00 0.00 0.00 3.93
2446 2546 8.807948 AAAATAGAGCCTATTTTTAGCACTGA 57.192 30.769 19.12 0.00 34.53 3.41
2531 2631 7.403671 AGGAGGGGTTTATTTAGAGAAAAGAC 58.596 38.462 0.00 0.00 0.00 3.01
2532 2632 7.018249 AGGAGGGGTTTATTTAGAGAAAAGACA 59.982 37.037 0.00 0.00 0.00 3.41
2547 2647 8.616076 AGAGAAAAGACAAATATATTTCAGCCG 58.384 33.333 7.76 0.00 33.53 5.52
2582 2682 7.149202 AGGGCATCCAGTCAGTTATAATTTA 57.851 36.000 0.00 0.00 34.83 1.40
2609 2709 6.268847 AGGAGTATACAGCCTCTTATCCTTTG 59.731 42.308 10.56 0.00 30.54 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 165 0.820226 TGCAGGAGAAGATGGAGTCG 59.180 55.000 0.00 0.00 0.00 4.18
200 207 2.161808 CGACGTGTCCTTGTCTAGTCAT 59.838 50.000 0.00 0.00 32.93 3.06
437 453 0.469331 ACTCGGTCCAGTTGACAGGA 60.469 55.000 0.00 0.00 46.38 3.86
500 528 0.874390 TGTGCCTTTTGCTCGTGATC 59.126 50.000 0.00 0.00 42.00 2.92
551 579 2.708059 GAGCAGCAACGACGACGAC 61.708 63.158 15.32 3.02 42.66 4.34
758 802 0.109689 GTCACCGGTTCAGACTCGAG 60.110 60.000 11.84 11.84 0.00 4.04
773 817 1.451028 GCAGGCAGGGAGATGTCAC 60.451 63.158 0.00 0.00 0.00 3.67
816 860 8.182881 CAGATTTCAGACTCCAATTCAAATCTC 58.817 37.037 0.00 0.00 37.12 2.75
866 910 3.694072 AGGAGAGAGACGAGTTGATCAAG 59.306 47.826 8.80 0.00 0.00 3.02
1027 1076 5.293560 CGGGTATTTGGCTTTCTTGAAAAA 58.706 37.500 0.00 0.00 0.00 1.94
1084 1133 2.932614 CGGACATAAGCAAGAGGAACAG 59.067 50.000 0.00 0.00 0.00 3.16
1161 1222 0.179073 CCTCGATGCCGGTGATTTCT 60.179 55.000 1.90 0.00 36.24 2.52
1260 1348 0.545171 ACACATCAGCCTCCCAGATG 59.455 55.000 0.00 0.00 43.56 2.90
1262 1350 1.556373 CCACACATCAGCCTCCCAGA 61.556 60.000 0.00 0.00 0.00 3.86
1308 1396 1.282157 AGGCATGTCTTGGGGAAGTAC 59.718 52.381 0.00 0.00 0.00 2.73
1378 1466 2.592861 GGCCATGCTTAGCCCGAG 60.593 66.667 0.29 0.00 43.76 4.63
1407 1495 1.376037 CTCGACCTGAAGCAACCCC 60.376 63.158 0.00 0.00 0.00 4.95
1622 1710 7.063801 TCCCATATATATCAACCTGACCCTA 57.936 40.000 0.00 0.00 0.00 3.53
1686 1774 5.528320 ACACAAAATGAAAAAGAAGGCCATG 59.472 36.000 5.01 0.00 0.00 3.66
1694 1782 8.600449 AAAACAGTCACACAAAATGAAAAAGA 57.400 26.923 0.00 0.00 0.00 2.52
1695 1783 8.711457 AGAAAACAGTCACACAAAATGAAAAAG 58.289 29.630 0.00 0.00 0.00 2.27
1697 1785 8.087750 AGAGAAAACAGTCACACAAAATGAAAA 58.912 29.630 0.00 0.00 0.00 2.29
1698 1786 7.541783 CAGAGAAAACAGTCACACAAAATGAAA 59.458 33.333 0.00 0.00 0.00 2.69
1699 1787 7.028962 CAGAGAAAACAGTCACACAAAATGAA 58.971 34.615 0.00 0.00 0.00 2.57
1700 1788 6.404623 CCAGAGAAAACAGTCACACAAAATGA 60.405 38.462 0.00 0.00 0.00 2.57
1701 1789 5.745294 CCAGAGAAAACAGTCACACAAAATG 59.255 40.000 0.00 0.00 0.00 2.32
1702 1790 5.418840 ACCAGAGAAAACAGTCACACAAAAT 59.581 36.000 0.00 0.00 0.00 1.82
1703 1791 4.764823 ACCAGAGAAAACAGTCACACAAAA 59.235 37.500 0.00 0.00 0.00 2.44
1704 1792 4.155826 CACCAGAGAAAACAGTCACACAAA 59.844 41.667 0.00 0.00 0.00 2.83
1705 1793 3.689161 CACCAGAGAAAACAGTCACACAA 59.311 43.478 0.00 0.00 0.00 3.33
1711 1799 4.698575 AGAGAACACCAGAGAAAACAGTC 58.301 43.478 0.00 0.00 0.00 3.51
1724 1812 9.956720 CATTTCCATGATTAAATAGAGAACACC 57.043 33.333 0.00 0.00 31.07 4.16
1736 1824 7.884877 AGAGAACAGTCACATTTCCATGATTAA 59.115 33.333 0.00 0.00 34.11 1.40
1746 1834 5.185454 TGACACAAGAGAACAGTCACATTT 58.815 37.500 0.00 0.00 34.59 2.32
1773 1861 7.328249 CCGCAAAAATACATAATCAACACAAGT 59.672 33.333 0.00 0.00 0.00 3.16
1774 1862 7.201427 CCCGCAAAAATACATAATCAACACAAG 60.201 37.037 0.00 0.00 0.00 3.16
1775 1863 6.587990 CCCGCAAAAATACATAATCAACACAA 59.412 34.615 0.00 0.00 0.00 3.33
1776 1864 6.096036 CCCGCAAAAATACATAATCAACACA 58.904 36.000 0.00 0.00 0.00 3.72
1777 1865 6.034470 CACCCGCAAAAATACATAATCAACAC 59.966 38.462 0.00 0.00 0.00 3.32
1778 1866 6.096036 CACCCGCAAAAATACATAATCAACA 58.904 36.000 0.00 0.00 0.00 3.33
1779 1867 5.005299 GCACCCGCAAAAATACATAATCAAC 59.995 40.000 0.00 0.00 38.36 3.18
1780 1868 5.105752 GCACCCGCAAAAATACATAATCAA 58.894 37.500 0.00 0.00 38.36 2.57
1781 1869 4.677584 GCACCCGCAAAAATACATAATCA 58.322 39.130 0.00 0.00 38.36 2.57
1796 1884 1.663695 ACACAAGTATATGCACCCGC 58.336 50.000 0.00 0.00 39.24 6.13
1797 1885 3.266636 TCAACACAAGTATATGCACCCG 58.733 45.455 0.00 0.00 0.00 5.28
1798 1886 4.640201 ACATCAACACAAGTATATGCACCC 59.360 41.667 0.00 0.00 0.00 4.61
1799 1887 5.818136 ACATCAACACAAGTATATGCACC 57.182 39.130 0.00 0.00 0.00 5.01
1800 1888 7.919690 ACATACATCAACACAAGTATATGCAC 58.080 34.615 0.00 0.00 0.00 4.57
1801 1889 9.040939 GTACATACATCAACACAAGTATATGCA 57.959 33.333 0.00 0.00 0.00 3.96
1802 1890 9.040939 TGTACATACATCAACACAAGTATATGC 57.959 33.333 0.00 0.00 0.00 3.14
1805 1893 9.040939 GCATGTACATACATCAACACAAGTATA 57.959 33.333 8.32 0.00 44.57 1.47
1806 1894 7.552330 TGCATGTACATACATCAACACAAGTAT 59.448 33.333 8.32 0.00 44.57 2.12
1807 1895 6.876257 TGCATGTACATACATCAACACAAGTA 59.124 34.615 8.32 0.00 44.57 2.24
1808 1896 5.704978 TGCATGTACATACATCAACACAAGT 59.295 36.000 8.32 0.00 44.57 3.16
1848 1936 7.032377 TGTGTGCACAAATCTAAACAACATA 57.968 32.000 23.59 0.00 38.56 2.29
1860 1948 8.853126 AGCTCAAATATATATGTGTGCACAAAT 58.147 29.630 28.88 25.36 45.41 2.32
1879 1967 6.374333 ACCGAATAATAGCAAAAGAGCTCAAA 59.626 34.615 17.77 0.00 45.26 2.69
1901 1989 2.162754 GCCGTTGGTGATACGACCG 61.163 63.158 0.00 0.00 41.33 4.79
1902 1990 2.162754 CGCCGTTGGTGATACGACC 61.163 63.158 0.00 0.00 41.33 4.79
1917 2005 1.526917 CCATCACATTCCCTCCGCC 60.527 63.158 0.00 0.00 0.00 6.13
1919 2007 0.107456 CCTCCATCACATTCCCTCCG 59.893 60.000 0.00 0.00 0.00 4.63
1920 2008 0.475906 CCCTCCATCACATTCCCTCC 59.524 60.000 0.00 0.00 0.00 4.30
1921 2009 1.511613 TCCCTCCATCACATTCCCTC 58.488 55.000 0.00 0.00 0.00 4.30
1922 2010 1.985622 TTCCCTCCATCACATTCCCT 58.014 50.000 0.00 0.00 0.00 4.20
1928 2016 1.565288 TGATGCATTCCCTCCATCACA 59.435 47.619 0.00 0.00 40.09 3.58
1952 2040 2.897207 CGCCGTTGGTGATCCCTA 59.103 61.111 0.00 0.00 34.74 3.53
1967 2055 0.383949 TTTTGTCAAAGGGAGTGCGC 59.616 50.000 0.00 0.00 0.00 6.09
2004 2092 2.290960 ACAAGGAGTGGGGCAAATAGAC 60.291 50.000 0.00 0.00 0.00 2.59
2005 2093 1.992557 ACAAGGAGTGGGGCAAATAGA 59.007 47.619 0.00 0.00 0.00 1.98
2006 2094 2.025887 AGACAAGGAGTGGGGCAAATAG 60.026 50.000 0.00 0.00 0.00 1.73
2007 2095 1.992557 AGACAAGGAGTGGGGCAAATA 59.007 47.619 0.00 0.00 0.00 1.40
2008 2096 0.779997 AGACAAGGAGTGGGGCAAAT 59.220 50.000 0.00 0.00 0.00 2.32
2009 2097 1.440618 TAGACAAGGAGTGGGGCAAA 58.559 50.000 0.00 0.00 0.00 3.68
2010 2098 1.668826 ATAGACAAGGAGTGGGGCAA 58.331 50.000 0.00 0.00 0.00 4.52
2011 2099 1.668826 AATAGACAAGGAGTGGGGCA 58.331 50.000 0.00 0.00 0.00 5.36
2012 2100 2.644676 GAAATAGACAAGGAGTGGGGC 58.355 52.381 0.00 0.00 0.00 5.80
2013 2101 2.236395 ACGAAATAGACAAGGAGTGGGG 59.764 50.000 0.00 0.00 0.00 4.96
2014 2102 3.611766 ACGAAATAGACAAGGAGTGGG 57.388 47.619 0.00 0.00 0.00 4.61
2015 2103 4.103357 CGTACGAAATAGACAAGGAGTGG 58.897 47.826 10.44 0.00 0.00 4.00
2016 2104 4.730657 ACGTACGAAATAGACAAGGAGTG 58.269 43.478 24.41 0.00 0.00 3.51
2017 2105 4.436584 CGACGTACGAAATAGACAAGGAGT 60.437 45.833 24.41 0.00 45.77 3.85
2018 2106 4.027065 CGACGTACGAAATAGACAAGGAG 58.973 47.826 24.41 0.00 45.77 3.69
2019 2107 3.181507 CCGACGTACGAAATAGACAAGGA 60.182 47.826 24.41 0.00 45.77 3.36
2020 2108 3.103738 CCGACGTACGAAATAGACAAGG 58.896 50.000 24.41 5.68 45.77 3.61
2021 2109 3.103738 CCCGACGTACGAAATAGACAAG 58.896 50.000 24.41 0.42 45.77 3.16
2022 2110 2.731968 GCCCGACGTACGAAATAGACAA 60.732 50.000 24.41 0.00 45.77 3.18
2023 2111 1.202177 GCCCGACGTACGAAATAGACA 60.202 52.381 24.41 0.00 45.77 3.41
2024 2112 1.470940 GCCCGACGTACGAAATAGAC 58.529 55.000 24.41 0.98 45.77 2.59
2032 2120 4.580551 GATGGGGCCCGACGTACG 62.581 72.222 19.83 15.01 42.18 3.67
2038 2126 1.052124 ATAAGAACGATGGGGCCCGA 61.052 55.000 19.83 13.96 0.00 5.14
2044 2132 9.737427 GATGATAGTGTATATAAGAACGATGGG 57.263 37.037 0.00 0.00 0.00 4.00
2096 2184 0.399949 TACTCCCACCTGGCCCATAG 60.400 60.000 0.00 0.00 0.00 2.23
2098 2186 0.627469 AATACTCCCACCTGGCCCAT 60.627 55.000 0.00 0.00 0.00 4.00
2104 2192 4.143986 GGAGAAGAAATACTCCCACCTG 57.856 50.000 0.00 0.00 44.70 4.00
2126 2214 7.343357 TGAAGTACTAATTAATGAAGGTGGGG 58.657 38.462 0.00 0.00 0.00 4.96
2149 2237 7.033530 ACGCGGATTAAATAAAAATGGATGA 57.966 32.000 12.47 0.00 0.00 2.92
2150 2238 8.964420 ATACGCGGATTAAATAAAAATGGATG 57.036 30.769 12.47 0.00 0.00 3.51
2166 2254 2.159014 TGACCAAAGCTAATACGCGGAT 60.159 45.455 12.47 3.58 34.40 4.18
2346 2446 7.508687 TCTGCATATTAGATTTGGCTGAAGTA 58.491 34.615 0.00 0.00 0.00 2.24
2352 2452 7.308450 TCTACTCTGCATATTAGATTTGGCT 57.692 36.000 0.00 0.00 0.00 4.75
2353 2453 9.658799 TTATCTACTCTGCATATTAGATTTGGC 57.341 33.333 14.49 0.00 34.04 4.52
2388 2488 7.844779 TGAGGAAATCTCTGGTATATATACCCC 59.155 40.741 30.65 22.92 44.22 4.95
2390 2490 9.482175 ACTGAGGAAATCTCTGGTATATATACC 57.518 37.037 28.36 28.36 44.59 2.73
2426 2526 7.796054 TCTTATCAGTGCTAAAAATAGGCTCT 58.204 34.615 0.00 0.00 0.00 4.09
2430 2530 9.606631 AACTCTCTTATCAGTGCTAAAAATAGG 57.393 33.333 0.00 0.00 0.00 2.57
2433 2533 9.678260 ATCAACTCTCTTATCAGTGCTAAAAAT 57.322 29.630 0.00 0.00 0.00 1.82
2494 2594 2.424793 ACCCCTCCTTTCCAAAGTGTA 58.575 47.619 0.00 0.00 34.20 2.90
2531 2631 5.393027 GGGCATACCGGCTGAAATATATTTG 60.393 44.000 15.39 3.55 40.90 2.32
2532 2632 4.705023 GGGCATACCGGCTGAAATATATTT 59.295 41.667 10.51 10.51 40.90 1.40
2536 2636 1.705186 AGGGCATACCGGCTGAAATAT 59.295 47.619 0.00 0.00 46.96 1.28
2541 2641 1.407656 CCTAAGGGCATACCGGCTGA 61.408 60.000 0.00 0.00 46.96 4.26
2582 2682 7.291991 AGGATAAGAGGCTGTATACTCCTAT 57.708 40.000 14.51 10.39 34.27 2.57


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

AutoCloner maintained by Alex Coulton.