Origin IGS: gtaaaatgtcgttagttagcttatttctaaagatgataaaataatatgcgaaaaatataagtgtaagataaaagaaatatgtaaatttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatttatattacaaatgtaattcttattatctttttaagttatagccaacgcacaaatttacatatttcttttatcttacacttatatttttcgcatattattttatcatctttagaaataagctaactaacgacattttac Mask Tandem Repeat Region ================================================ gtaaaatgtcgttagttagcttatttctaaagatgataaaataatatgcgaaaaatataagtgtaagataaaagaaatatgtaaatttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt Find is-nt database================================================ Query_seq: TF3015:TF3016|TF3015:TF3016:hypothetical protein:conserved hypothetical protein:->->:3238744..3238885 142 gtaaaatgtcgttagttagcttatttctaaagatgataaaataatatgcgaaaaatataagtgtaagataaaagaaatatgtaaatttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3015:TF3016|TF3015:TF3016:hypothetical protein:conserved hypothetical protein:->->:3238744..3238885 142 gtaaaatgtcgttagttagcttatttctaaagatgataaaataatatgcgaaaaatataagtgtaagataaaagaaatatgtaaatttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3015:TF3016|TF3015:TF3016:hypothetical protein:conserved hypothetical protein:->->:3238744..3238885 142 gtaaaatgtcgttagttagcttatttctaaagatgataaaataatatgcgaaaaatataagtgtaagataaaagaaatatgtaaatttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaaaatgtcgttagttagcttatttctaaagatgataaaataatatgcgaaaaatataagtgtaagataaaagaaatatgtaaatttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 19 End: 141 .................. S I E L S S L I I H S F Y L H L I F S I H L N T R Q S Y S L F I I L I V N T I Y M . gtaaaatgtcgttagttagcttatttctaaagatgataaaataatatgcgaaaaatataagtgtaagataaaagaaatatgtaaatttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtaaaatgtcgttagttagcttatttctaaagatgataaaataatatgcgaaaaatataagtgtaagataaaagaaatatgtaaatttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3015:TF3016|TF3015:TF3016:hypothetical protein:conserved hypothetical protein:->->:3238744..3238885 142 gtaaaatgtcgttagttagcttatttctaaagatgataaaataatatgcgaaaaatataagtgtaagataaaagaaatatgtaaatttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: tfor_TF3015_TF3016|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3238744,3238885]|142 HSP 1 e-value: 6.0E-24 bit: 111.0 Len: 56 Query Start:87 Query End:142 Subject Strand: POSITIVE Subject Start: 87 Subject End: 142 ......................................................................................ttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt ......................................................................................ttgtgcgttggctataacttaaaaagataataagaattacatttgtaatataaatt HSP 2 e-value: 1.0E-6 bit: 54.0 Len: 27 Query Start:1 Query End:27 Subject Strand: POSITIVE Subject Start: 1 Subject End: 27 gtaaaatgtcgttagttagcttatttc................................................................................................................... gtaaaatgtcgttagttagcttatttc................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAAAUGUCGUUAGUUAGCUUAUUUCUAAAGAUGAUAAAAUAAUAUGCGAAAAAUAUAAGUGUAAGAUAAAAGAAAUAUGUAAAUUUGUGCGUUGGCUAUAACUUAAAAAGAUAAUAAGAAUUACAUUUGUAAUAUAAAUU ........((((..((((..(((((((....)).)))))..))))..))))....(((((((((((......((....(((((......)))))...))....((((.........))))..)))))))))))......... (-18.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUAUAUUACAAAUGUAAUUCUUAUUAUCUUUUUAAGUUAUAGCCAACGCACAAAUUUACAUAUUUCUUUUAUCUUACACUUAUAUUUUUCGCAUAUUAUUUUAUCAUCUUUAGAAAUAAGCUAACUAACGACAUUUUAC (((....(((((....)))))....))).........(((((..((....))...........(((((((..............((((.......))))...............)))))))...)))))............. ( -7.65) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 36 8 129 97 tfor:TF0435|5end_DNA_mismatch_repair_protein_457182..457412_POSITIVE 231 102 74 166 138 tfor:TF0077|5end_hypothetical_protein_84241..84471_POSITIVE 224 98 65 197 157 tfor:TF0281|5end_hypothetical_protein_308909..309139_POSITIVE 224 98 65 95 55 tfor:TF0280|5end_hypothetical_protein_308807..309037_POSITIVE 223 98 54 180 136 tfor:TF0981|5end_possible_hydrolase_1038112..1038342_POSITIVE 204 106 73 186 157 tfor:TF1646|5end_hypothetical_protein_1756900..1757130_POSITIVE 202 117 88 95 61 tfor:TF2458|5end_ribosome-binding_factor_A_2635233..2635463_POSITIVE 194 39 12 181 154 tfor:TF3096|5end_conserved_hypothetical_protein_3327963..3328193_POSITIVE 194 98 60 217 165 tfor:TF0477|5end_dipeptide/tripeptide_permease,_POT_family_(proton-dependent_oligopeptide_transport_family)_495449..495679_POSITIVE 188 98 60 167 122 tfor:TF1963|5end_hypothetical_protein_2113359..2113589_POSITIVE 184 99 61 153 117 tfor:TF1536|5end_hypothetical_protein_1643245..1643475_POSITIVE 180 86 44 132 86 tfor:TF1922|5end_hypothetical_protein_2072018..2072248_POSITIVE 180 104 87 53 35 tfor:TF1042|5end_possible_surface_antigen_with_leucine-rich_repeat_1102957..1103187_POSITIVE 179 106 75 42 14 tfor:TF2535|5end_histidyl-tRNA_synthetase_2717740..2717970_POSITIVE 179 98 78 43 23 tfor:TF2263|5end_transfer_region-related_protein,_TraN_2431901..2432131_POSITIVE 174 124 88 231 185 tfor:TF2805|5end_zinc_protease_2995212..2995442_POSITIVE 174 95 55 153 110 tfor:TF1663|5end_ABC_transporter,_permease_component_1777680..1777910_POSITIVE 173 40 7 121 86 tfor:TF2959|5end_type_I_restriction_enzyme_methyltransferase,_M_protein_3169288..3169518_POSITIVE 173 102 63 224 171 tfor:TF2920|5end_conserved_hypothetical_protein_3115903..3116133_POSITIVE 173 97 60 49 15 tfor:TF0953|5end_conserved_hypothetical_protein;_possible_DNA_binding_protein_997929..998159_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 102 74 121 93 tfor:TF0076|3end_probable_carbohydrate_kinase,_PfkB_family_84276..84426_POSITIVE 223 98 54 110 66 tfor:TF0980|3end_outer_membrane_TonB-dependent_receptor_1038122..1038272_POSITIVE 202 117 88 84 50 tfor:TF2457|3end_ABC_transporter,_permease_component,_zinc-binding_protein_2635302..2635452_POSITIVE 180 86 44 85 39 tfor:TF1921|3end_hypothetical_protein_2072051..2072201_POSITIVE 180 104 87 36 18 tfor:TF1041|3end_dihydroorotate_dehydrogenase,_catalytic_subunit_1103020..1103170_POSITIVE 179 106 75 35 7 tfor:TF2534|3end_conserved_hypothetical_protein_2717813..2717963_POSITIVE 176 99 53 134 87 tfor:TF0474|3end_outer_membrane_efflux_protein_493662..493812_POSITIVE 173 40 7 114 79 tfor:TF2958|3end_type_I_restriction-modification_system_R_subunit_3169361..3169511_POSITIVE 173 97 60 49 15 tfor:TF0952|3end_conserved_hypothetical_protein_998009..998159_POSITIVE 172 115 86 54 31 tfor:TF3019|3end_tRNA_and_rRNA_cytosine-C5-methylase_3243587..3243737_POSITIVE 171 105 79 63 36 tfor:TF3038|3end_conserved_hypothetical_protein_3265799..3265949_POSITIVE 171 38 6 84 48 tfor:TF2795|3end_hypothetical_protein_2980909..2981059_POSITIVE 170 52 13 97 66 tfor:TF0973|3end_conserved_hypothetical_protein_1024101..1024251_POSITIVE 168 34 4 83 51 tfor:TF0120|3end_hexouronate_transporter_132811..132961_POSITIVE 167 100 80 36 15 tfor:TF2382|3end_transposase_2548176..2548326_POSITIVE 167 100 59 110 61 tfor:TF0839|3end_aminopeptidasem_M28_family_891529..891679_POSITIVE 167 106 61 64 13 tfor:TF0285|3end_conserved_hypothetical_protein_315534..315684_POSITIVE 165 105 65 63 22 tfor:TF2634|3end_conserved_hypothetical_protein_2804286..2804436_POSITIVE 164 99 67 111 71 tfor:TF1608|3end_sulfate_transporter_1728463..1728613_POSITIVE 164 98 59 55 10 tfor:TF0794|3end_hypothetical_protein_851960..852110_POSITIVE