"NOTES: column names occur on the third line of this file. Values in the ""include_search"" and ""exclude_search"" columns encode the search parameters with the operator ""&"" representing the binary AND and the ""|"" representing the binary OR. Thus the string ""ndhF & rpl32"" in the include field means ""include all records matching against both 'ndhF' and 'rpl32'"". The ""coverage"" and ""identity"" columns contain the respective values for each parameter used in the corresponding phlawd config file.",,,,,, ,,,,,, gene,genome,include_search,exclude_search,clade,coverage,identity accD,chloroplast,accD,,Streptophytina,0.4,0.4 accD-psaI,chloroplast,accD & psaI,ycf4 | rbcL,Streptophytina,0,0 atp1,mitochondrion,atp1,,Streptophytina,0.4,0.4 atp9,mitochondrion,atp9 | atp synthase subunit 9,rps12,Streptophytina,0.1,0.05 atpA,chloroplast,atpA,,Streptophytina,0.4,0.4 atpA_mt,mitochondrion,atpA | atp1 | atpase alpha subunit & mitochondria | mitochondrion | mitochondrial,chloroplast | trnR | atp6 | atpF | Arabidopsis | plasma membrane,Streptophytina,0.02,0.02 atpB,chloroplast,atpB,,Streptophytina,0.4,0.4 atpB-rbcL,chloroplast,atpB & rbcL,accd | atpe,Streptophytina,0.2,0.2 atpE,chloroplast,atpE,,Streptophytina,0.4,0.4 atpF,chloroplast,atpF,,Streptophytina,0.4,0.4 atpH,chloroplast,atpH,,Streptophytina,0.4,0.4 atpI,chloroplast,atpI,,Streptophytina,0.4,0.4 atpI-atpH,chloroplast,atpI & atpH,rps2 | atpF,Streptophytina,0,0.07 ccsA,chloroplast,ccsA,,Streptophytina,0.4,0.4 cemA,chloroplast,cemA,,Streptophytina,0.4,0.4 clpP,chloroplast,clpP,,Streptophytina,0.4,0.4 cob,mitochondrion,cob,trnL | matK | rbcL | rpl16 | ndhF | trnD | trnH | ribosulation | ribosylation | deoxyhypusine | rps14 | cobi420 | COBRA | Arabidopsis thaliana,Streptophytina,0,0.07 cobi420_mosses,mitochondrion,cob,trnL | matK | rbcL | rpl16 | ndhF | trnD | trnH | ribosulation | deoxyhypusine | rps14,Bryophyta,0,0.07 cox1,mitochondrion,cox1,cox17 | cox2 | coxii | cox3 | coxiii cox19 | cox1i624,Streptophytina,0.1,0.1 cox1i624,mitochondrion,cox1,,Bryophyta,0,0 cox2,mitochondrion,cox2 | coxii | cytochrome oxidase subunit 2 | cytochrome oxidase subunit ii,cox3 | coxiii | nad3 | cox1 | coxi | psba | trnl | transcribed spacer | trnS | chloroplast,Streptophytina,0,0 cox3,mitochondrion,cox2 | coxii | cytochrome oxidase subunit 2 | cytochrome oxidase subunit ii,cox2 | coxii | nad3 | cox1 | coxi | psba | trnl | transcribed spacer | trnS | chloroplast,Streptophytina,0,0 ETS,nuclear,external transcribed spacer | ets,,Streptophytina,0.1,0.1 infA,chloroplast,infA,,Streptophytina,0.4,0.4 ITS,nuclear,its | its2 | 5.8S | internal transcribed spacer,4.5S | 5S | 23S,Streptophytina,0.1,0.1 ITS-23S-5S,nuclear,4.5S | 5S | 23S | internal transcribed spacer | its,18S | 5.8S | 26S,Streptophytina,0.1,0.1 matK,chloroplast,matK,,Streptophytina,0.4,0.4 matR,mitochondrion,matR,,Streptophytina,0.4,0.4 nad2,mitochondrion,nad2,,Streptophytina,0,0 nad5,mitochondrion,nad5,,Streptophytina,0.4,0.4 nad5-nad4,mitochondrion,nad5 & nad4,,Streptophytina,0,0 ndhA,chloroplast,ndhA,,Streptophytina,0.4,0.4 ndhB,chloroplast,ndhB,,Streptophytina,0.4,0.4 ndhC,chloroplast,ndhC,,Streptophytina,0.4,0.4 ndhD,chloroplast,ndhD,,Streptophytina,0.4,0.4 ndhE,chloroplast,ndhE,,Streptophytina,0.4,0.4 ndhF,chloroplast,ndhF,,Streptophytina,0.4,0.4 ndhF-rpl32-trnL,chloroplast,ndhF & rpl32 & trnL,ccsA | ycf1,Streptophytina,0,0 ndhG,chloroplast,ndhG,,Streptophytina,0.4,0.4 ndhH,chloroplast,ndhH,,Streptophytina,0.4,0.4 ndhI,chloroplast,ndhI,,Streptophytina,0.4,0.4 ndhJ,chloroplast,ndhJ,,Streptophytina,0.4,0.4 ndhK,chloroplast,ndhK,,Streptophytina,0.4,0.4 petA,chloroplast,petA,,Streptophytina,0.4,0.4 petA-psbJ,chloroplast,petA & psbJ,cemA | psbL | psbF | psbE,Streptophytina,0,0.7 petB,chloroplast,petB,,Streptophytina,0.4,0.4 petD,chloroplast,petD,,Streptophytina,0.4,0.4 petG,chloroplast,petG,,Streptophytina,0.4,0.4 petL,chloroplast,petL,,Streptophytina,0.4,0.4 petN,chloroplast,petN,,Streptophytina,0.4,0.4 phyA,nuclear,phyA | phytochrome A,Arabidposis thaliana | Pennisetum glaucum,Streptophytina,0.2,0.15 phyB_monocots,nuclear,phyB | phytochrome B,phyB1 | phyB2,Liliopsida,0,0 psaA,chloroplast,psaA,,Streptophytina,0.4,0.4 psaB,chloroplast,psaB,,Streptophytina,0.4,0.4 psaC,chloroplast,psaC,,Streptophytina,0.4,0.4 psaI,chloroplast,psaI,,Streptophytina,0.4,0.4 psaJ,chloroplast,psaJ,,Streptophytina,0.4,0.4 psbA,chloroplast,psbA,,Streptophytina,0.4,0.4 psbA-trnH,chloroplast,trnH,trnK | matK | rpl2 | rpl32,Streptophytina,0.2,0.2 psbA-trnK,chloroplast,psbA & trnK,rps16 | trnH,Streptophytina,0,0 psbB,chloroplast,psbB,,Streptophytina,0.4,0.4 psbC,chloroplast,psbC,,Streptophytina,0.4,0.4 psbD,chloroplast,psbD,,Streptophytina,0.4,0.4 psbE,chloroplast,psbE,,Streptophytina,0.4,0.4 psbE-petL,chloroplast,psbE & petL,psbF | psbL | petG,Streptophytina,0,0 psbF,chloroplast,psbF,,Streptophytina,0.4,0.4 psbH,chloroplast,psbH,,Streptophytina,0.4,0.4 psbI,chloroplast,psbI,,Streptophytina,0.4,0.4 psbJ,chloroplast,psbJ,,Streptophytina,0.4,0.4 psbK,chloroplast,psbK,,Streptophytina,0.4,0.4 psbL,chloroplast,psbL,,Streptophytina,0.4,0.4 psbM,chloroplast,psbM,,Streptophytina,0.4,0.4 psbM-trnD,chloroplast,psbM & trnD,trnY | trnE | petN | ycf6 | trnC,Streptophytina,0.2,0.1 psbN,chloroplast,psbN,,Streptophytina,0.4,0.4 psbT,chloroplast,psbT,,Streptophytina,0.4,0.4 psbT-psbN,chloroplast,psbT & psbN,psbB | psbH | Development of species-specific molecular markers for eight Salix species based on cpDNA polymorphism,Streptophytina,0,0 psbZ,chloroplast,psbZ,,Streptophytina,0.4,0.4 rbcL,chloroplast,rbcL,,Streptophytina,0.4,0.4 rpl14,chloroplast,rpl14,,Streptophytina,0.4,0.4 rpL14-rpS8-rpL36,chloroplast,rpL14 & rpS8 & rpL36,rps3,Streptophytina,0.1,0.1 rpl16,chloroplast,rpl16,,Streptophytina,0.4,0.4 rpl2,chloroplast,rpl2,,Streptophytina,0.4,0.4 rpl20,chloroplast,rpl20,,Streptophytina,0.4,0.4 rpl22,chloroplast,rpl22,,Streptophytina,0.4,0.4 rpl23,chloroplast,rpl23,,Streptophytina,0.4,0.4 rpl32,chloroplast,rpl32,,Streptophytina,0.4,0.4 rpl33,chloroplast,rpl33,,Streptophytina,0.4,0.4 rpl36,chloroplast,rpl36,,Streptophytina,0.4,0.4 rpoA,chloroplast,rpoA,,Streptophytina,0.4,0.4 rpoB,chloroplast,rpoB,,Streptophytina,0.4,0.4 rpoC1,chloroplast,rpoC1,,Streptophytina,0.4,0.4 rpoC2,chloroplast,rpoC2,,Streptophytina,0.4,0.4 rps11,chloroplast,rps11,,Streptophytina,0.4,0.4 rps12,chloroplast,rps12,,Streptophytina,0.4,0.4 rps12-rpl20,chloroplast,rps12 & rpl20,clpP | rps18,Streptophytina,0.1,0.1 rps14,chloroplast,rps14,,Streptophytina,0.4,0.4 rps15,chloroplast,rps15,,Streptophytina,0.4,0.4 rps16,chloroplast,rps16,,Streptophytina,0.4,0.4 rps16-trnK,chloroplast,rps16 & trnK,trnQ | matK | Veronica,Streptophytina,0.05,0.05 rps18,chloroplast,rps18,,Streptophytina,0.4,0.4 rps19,chloroplast,rps19,,Streptophytina,0.4,0.4 rps2,chloroplast,rps2,,Streptophytina,0.4,0.4 rps3,mitochondrion,rps3,,Streptophytina,0.4,0.4 rps4,chloroplast,rps4,,Streptophytina,0.4,0.4 rps4-trnT-trnL,chloroplast,rpS4 & trnT & trnL,trnS | trnF,Streptophytina,0.1,0.1 rps7,chloroplast,rps7,,Streptophytina,0.4,0.4 rps8,chloroplast,rps8,,Streptophytina,0.4,0.4 rrn16,chloroplast,rrn16,,Streptophytina,0.4,0.4 rrn23,chloroplast,rrn23,,Streptophytina,0.4,0.4 rrn4.5,chloroplast,rrn4.5,,Streptophytina,0.4,0.4 rrn5,chloroplast,rrn5,,Streptophytina,0.4,0.4 trnC-rpoB,chloroplast,trnC & rpoB,petN | ycf6 | rpoC1,Streptophytina,0.1,0.1 trnC-ycf6-psbM,chloroplast,ycf6 | petN & psbM,rpoB | trnD,Streptophytina,0,0 trnF-ndhJ,chloroplast,trnF & ndhJ,trnL | ndhK,Streptophytina,0,0 trnG_intron_bryos,chloroplast,trnG,trnR | trnS,Streptophytina,0.1,0.1 trnG_intron_tracheophyta,chloroplast,trnG,trnR | trnS,Tracheophyta,0.1,0.1 trnK_intron,chloroplast,trnK,rps16 | psbA,Streptophytina,0.1,0.1 trnQ-rps16,chloroplast,trnQ & rps16,trnK | psbK,Streptophytina,0.1,0.1 trnS_UGA-trnfM,chloroplast,trnS | tRNA-Ser & trnfM | trnM,rps4 | psbI | psbK | psbC | trnG | trnQ | ycf3 | trnS-GCU | trnR | psbD,Streptophytina,0,0 trnS-rpS4,chloroplast,trnS & rps4,trnT | ycf3,Streptophytina,0,0.2 trnT-psbD,chloroplast,trnT & psbD,psbC | trnE | trnY,Streptophytina,0.1,0.1 trnT-trnL-trnF,chloroplast,trnT | trnL | trnF,trnE | nad7 | rps4 | ndhJ | ndhB | psbM | psbA | trnS | trnfM | trnD,Streptophytina,0.2,0.2 trnV-ndhC,chloroplast,trnV & ndhC,,Streptophytina,0.1,0.1 trnV-trnM,chloroplast,trnV & trnM,,Streptophytina,0.1,0.1 trnY-trnE,chloroplast,trnY & trnE,trnT,Streptophytina,0,0 ycf1,chloroplast,ycf1,,Streptophytina,0.4,0.4 ycf2,chloroplast,ycf2,,Streptophytina,0.4,0.4 ycf3,chloroplast,ycf3,,Streptophytina,0.4,0.4