Origin IGS: caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttaataatatgtgttaaatttgctaatttgtcaaccggtacagcggttcatggagcaaaaaataagttgagcaaaaaataacggtctgtaccaagtccggcatagaccattattcaaagctttttaacctg Mask Tandem Repeat Region ================================================ caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac Find is-nt database================================================ Query_seq: TDE0062:TDE0063|TDE0062:TDE0063:PTS system, IIA component:hypothetical protein:->->:69722..69853 132 caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0062:TDE0063|TDE0062:TDE0063:PTS system, IIA component:hypothetical protein:->->:69722..69853 132 caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0062:TDE0063|TDE0062:TDE0063:PTS system, IIA component:hypothetical protein:->->:69722..69853 132 caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac Predict ORF larger than 30AA ================================================ caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 97 End: 126 ................................................................................................GTTGACAAATTAGCAAATTTAACACATATT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0062:TDE0063|TDE0062:TDE0063:PTS system, IIA component:hypothetical protein:->->:69722..69853 132 caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_002967_TDE0062_TDE0063|PTS system, IIA component:hypothetical protein|POSITIVE:POSITIVE|[69722,69853]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac caggttaaaaagctttgaataatggtctatgccggacttggtacagaccgttattttttgctcaacttattttttgctccatgaaccgctgtaccggttgacaaattagcaaatttaacacatattattaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGGUUAAAAAGCUUUGAAUAAUGGUCUAUGCCGGACUUGGUACAGACCGUUAUUUUUUGCUCAACUUAUUUUUUGCUCCAUGAACCGCUGUACCGGUUGACAAAUUAGCAAAUUUAACACAUAUUAUUAAC ...((((((.(((...((((((((((((.(((((....))))).))))))))))))...)))..........((((((...(.(((((......))))).)......))))))))))))............. (-34.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAAUAAUAUGUGUUAAAUUUGCUAAUUUGUCAACCGGUACAGCGGUUCAUGGAGCAAAAAAUAAGUUGAGCAAAAAAUAACGGUCUGUACCAAGUCCGGCAUAGACCAUUAUUCAAAGCUUUUUAACCUG (((((..............((((((...(..(.(((((......))))).)..))))))).........((((....(((((.(((((((.((......)).))))))).)))))....)))).)))))... (-30.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 64 21 90 41 NC_002967:TDE0096|5end_NADH_oxidase_112723..112953_POSITIVE 298 99 59 50 9 NC_002967:TDE2346|5end_elongation_factor_Ts_2383429..2383659_NEGATIVE 293 60 11 86 35 NC_002967:TDE2554|5end_chaperonin,_33_kDa_family_2580745..2580975_POSITIVE 285 50 9 210 164 NC_002967:TDE1907|5end_holo-(acyl-carrier-protein)_synthase_1925097..1925327_NEGATIVE 280 80 31 101 54 NC_002967:TDE0013|5end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_18639..18869_NEGATIVE 276 51 22 183 153 NC_002967:TDE2630|5end_peptide_ABC_transporter,_permease_protein,_putative_2670879..2671109_POSITIVE 275 112 76 143 117 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 274 70 30 105 61 NC_002967:TDE0588|5end_histidine_ammonia-lyase_626450..626680_POSITIVE 273 107 76 48 19 NC_002967:TDE2289|5end_phosphoribulokinase/uridine_kinase_family_protein_2325764..2325994_POSITIVE 271 97 56 194 149 NC_002967:TDE0909|5end_type_II_DNA_modification_methyltransferase_M.TdeIII_927166..927396_POSITIVE 268 80 31 196 137 NC_002967:TDE1566|5end_hypothetical_protein_1617822..1618052_POSITIVE 267 49 24 174 144 NC_002967:TDE2320|5end_RNA_polymerase_sigma-24_factor,_putative_2356951..2357181_NEGATIVE 266 63 23 208 155 NC_002967:TDE0787|5end_preprotein_translocase_SecY_815068..815298_POSITIVE 265 99 53 174 135 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 265 79 32 226 181 NC_002967:TDE2607|5end_hypothetical_protein_2648586..2648816_POSITIVE 261 83 45 155 120 NC_002967:TDE1436|5end_inner_membrane_protein_1479460..1479690_POSITIVE 260 63 24 189 153 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 259 90 44 101 51 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 258 51 14 136 103 NC_002967:TDE1738|5end_M23/M37_peptidase_domain_protein_1790536..1790766_POSITIVE 256 104 66 181 143 NC_002967:TDE0644|5end_ABC_transporter,_ATP-binding_protein_680576..680806_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 55 11 73 29 NC_002967:TDE0062|3end_PTS_system,_IIA_component_69661..69811_POSITIVE 275 112 76 146 120 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 275 100 70 40 3 NC_002967:TDE0812|3end_ABC_transporter,_ATP-binding/permease_protein_834137..834287_POSITIVE 274 70 30 72 28 NC_002967:TDE0587|3end_hypothetical_protein_626497..626647_POSITIVE 265 59 33 134 108 NC_002967:TDE2691|3end_hypothetical_protein_2729346..2729496_POSITIVE 265 79 32 111 66 NC_002967:TDE2606|3end_urocanate_hydratase_2648551..2648701_POSITIVE 258 51 14 149 116 NC_002967:TDE1737|3end_hypothetical_protein_1790629..1790779_POSITIVE 255 55 11 129 85 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 250 64 23 124 86 NC_002967:TDE1958|3end_surface_protein,_putative_1972309..1972459_NEGATIVE 249 97 61 110 66 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 247 32 4 53 25 NC_002967:TDE1651|3end_BioY_family_protein_1698121..1698271_NEGATIVE 246 61 22 36 1 NC_002967:TDE0834|3end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854291..854441_NEGATIVE 244 60 23 130 87 NC_002967:TDE0599|3end_PIN_domain_protein_638191..638341_NEGATIVE 243 45 9 149 117 NC_002967:TDE0967|3end_hypothetical_protein_992529..992679_POSITIVE 243 59 13 79 29 NC_002967:TDE0473|3end_heavy_metal_translocating_P-type_ATPase_530800..530950_POSITIVE 242 77 31 45 5 NC_002967:TDE2490|3end_primosomal_protein_N'_2512703..2512853_NEGATIVE 241 59 22 105 65 NC_002967:TDE2542|3end_antigen,_putative_2569441..2569591_NEGATIVE 241 80 32 118 52 NC_002967:TDE2304|3end_hypothetical_protein_2343735..2343885_POSITIVE 241 56 12 78 27 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 240 100 60 146 96 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE