Ortholog Set 1504128

Ortholog Set 1504146

Analysis ID	1504128
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504147

Analysis ID	1504146
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504148

Analysis ID	1504147
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504149

Analysis ID	1504148
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504150

Analysis ID	1504149
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504151

Analysis ID	1504150
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504152

Analysis ID	1504151
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504153

Analysis ID	1504152
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504154

Analysis ID	1504153
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504155

Analysis ID	1504154
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504156

Analysis ID	1504155
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504157

Analysis ID	1504156
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504158

Analysis ID	1504157
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504159

Analysis ID	1504158
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504145

Analysis ID	1504159
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504144

Analysis ID	1504145
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504143

Analysis ID	1504144
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504129

Analysis ID	1504143
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504130

Analysis ID	1504129
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504131

Analysis ID	1504130
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504132

Analysis ID	1504131
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504133

Analysis ID	1504132
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504134

Analysis ID	1504133
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504135

Analysis ID	1504134
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504136

Analysis ID	1504135
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504137

Analysis ID	1504136
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504138

Analysis ID	1504137
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504139

Analysis ID	1504138
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504140

Analysis ID	1504139
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504141

Analysis ID	1504140
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504142

Analysis ID	1504141
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Ortholog Set 1504160

Analysis ID	1504142
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2

Analysis ID	1504160
Cluster ID	349
Ortholuge Class	No Ortholuge class assigned. This is often the case when a suitable outgroup species is available to perform Ortholuge analysis, however an outgroup ortholog is not available for this particular ortholog set. SSD Borderline Similar Non-SSD Divergent Non-SSD RBB
Ratio 1
Ratio 2
Local FDR for Ratio 1
Local FDR for Ratio 2
Analysis Type	Ortholuge

Ingroup 1

Strain	Pseudomonas mendocina ymp
GI	146308652
Locus Tag	Pmen_3637
Description	IS66 Orf2 family protein

StrainPseudomonas mendocina ymp GI146306580 Locus TagPmen_1549 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146308106 Locus TagPmen_3085 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146306083 Locus TagPmen_1049 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146306083 Locus TagPmen_1049 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146306197 Locus TagPmen_1164 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146307017 Locus TagPmen_1989 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146308652 Locus TagPmen_3637 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146307017 Locus TagPmen_1989 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305202 Locus TagPmen_0161 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146308652 Locus TagPmen_3637 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146306580 Locus TagPmen_1549 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146306083 Locus TagPmen_1049 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305474 Locus TagPmen_0435 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305471 Locus TagPmen_0432 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305471 Locus TagPmen_0432 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146308106 Locus TagPmen_3085 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305202 Locus TagPmen_0161 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146308106 Locus TagPmen_3085 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305078 Locus TagPmen_0037 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305474 Locus TagPmen_0435 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146306197 Locus TagPmen_1164 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146307017 Locus TagPmen_1989 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305474 Locus TagPmen_0435 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146309129 Locus TagPmen_4115 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305078 Locus TagPmen_0037 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146306197 Locus TagPmen_1164 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305078 Locus TagPmen_0037 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305471 Locus TagPmen_0432 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146306580 Locus TagPmen_1549 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146305202 Locus TagPmen_0161 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146309129 Locus TagPmen_4115 DescriptionIS66 Orf2 family protein StrainPseudomonas mendocina ymp GI146309129 Locus TagPmen_4115 DescriptionIS66 Orf2 family protein

Ingroup 2

Strain	Pseudomonas putida S16
GI	339486355
Locus Tag	PPS_1428
Description	ISPpu15, transposase Orf1

StrainPseudomonas putida S16 GI339486355 Locus TagPPS_1428 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339486355 Locus TagPPS_1428 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339486355 Locus TagPPS_1428 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339486355 Locus TagPPS_1428 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339486355 Locus TagPPS_1428 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339486355 Locus TagPPS_1428 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339486355 Locus TagPPS_1428 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339486355 Locus TagPPS_1428 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339488963 Locus TagPPS_4072 DescriptionISPpu15, transposase StrainPseudomonas putida S16 GI339486355 Locus TagPPS_1428 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339485992 Locus TagPPS_1065 DescriptionISPpu15, transposase Orf1 StrainPseudomonas putida S16 GI339486355 Locus TagPPS_1428 DescriptionISPpu15, transposase Orf1