Origin IGS: atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacactacctccggttatagtataattctaagccagccctaagattttgtcaagcctacgaaaataaatctgacaaaaatacgatcaaaaaagttatccctagaataattttatattgacttttaatacgtaataatatatacttaatacgtatggaggtaaat Mask Tandem Repeat Region ================================================ atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt Find is-nt database================================================ Query_seq: TDE0888:TDE0889|TDE0888:TDE0889:hypothetical protein:hypothetical protein:<-->:905066..905229 164 atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0888:TDE0889|TDE0888:TDE0889:hypothetical protein:hypothetical protein:<-->:905066..905229 164 atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0888:TDE0889|TDE0888:TDE0889:hypothetical protein:hypothetical protein:<-->:905066..905229 164 atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 11 End: 106 .......... M R I K Y I L L R I K S Q Y K I I L G I T F L I V F L S D L F S .......................................................... atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt 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: 91 Start: 111 End: 140 ..............................................................................................................CTTGACAAAATCTTAGGGCTGGCTTAGAAT........................ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 21 End: 50 ....................ATTGACTTTTAATACGTAATAATATATACT.................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0888:TDE0889|TDE0888:TDE0889:hypothetical protein:hypothetical protein:<-->:905066..905229 164 atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: NC_002967_TDE0888_TDE0889|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[905066,905229]|164 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt atttacctccatacgtattaagtatatattattacgtattaaaagtcaatataaaattattctagggataacttttttgatcgtatttttgtcagatttattttcgtaggcttgacaaaatcttagggctggcttagaattatactataaccggaggtagtgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUACCUCCAUACGUAUUAAGUAUAUAUUAUUACGUAUUAAAAGUCAAUAUAAAAUUAUUCUAGGGAUAACUUUUUUGAUCGUAUUUUUGUCAGAUUUAUUUUCGUAGGCUUGACAAAAUCUUAGGGCUGGCUUAGAAUUAUACUAUAACCGGAGGUAGUGUU ..((((((((.((((((.(((.......))).))))))...........((((.....((((((((..((.((((...(((......((((((((.(((((....))))).)))))))))))..)))).)).)))))))).....))))...)))))))).... (-36.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACACUACCUCCGGUUAUAGUAUAAUUCUAAGCCAGCCCUAAGAUUUUGUCAAGCCUACGAAAAUAAAUCUGACAAAAAUACGAUCAAAAAAGUUAUCCCUAGAAUAAUUUUAUAUUGACUUUUAAUACGUAAUAAUAUAUACUUAAUACGUAUGGAGGUAAAU .....(((((((((((.(((.......)))))))..........((((((((..................))))))))..........((((((((....((((.....))))...)))))))).(((((((.(((.......))).))))))))))))))... (-28.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 854 140 91 231 182 NC_002967:TDE0888|5end_hypothetical_protein_904975..905205_NEGATIVE 261 145 102 222 178 NC_002967:TDE1687|5end_hypothetical_protein_1744042..1744272_NEGATIVE 257 115 75 76 21 NC_002967:TDE2531|5end_hypothetical_protein_2558241..2558471_POSITIVE 254 140 91 194 139 NC_002967:TDE2765|5end_flagellar_motor_protein_2820093..2820323_NEGATIVE 250 129 83 205 169 NC_002967:TDE1205|5end_integrase/recombinase_XerD_1237689..1237919_POSITIVE 250 110 64 94 50 NC_002967:TDE0720|5end_bacteriocin_ABC_transporter,_bacteriocin-binding_protein,_putative_755612..755842_POSITIVE 249 136 104 169 128 NC_002967:TDE2275|5end_tRNA_pseudouridine_synthase_A_2311076..2311306_POSITIVE 249 136 108 29 1 NC_002967:TDE0377|5end_hypothetical_protein_431977..432207_NEGATIVE 249 136 97 217 182 NC_002967:TDE0376|5end_ABC_transporter,_permease_protein,_putative_431789..432019_NEGATIVE 246 160 116 223 167 NC_002967:TDE0421|5end_lipoprotein,_putative_473416..473646_POSITIVE 246 160 116 223 167 NC_002967:TDE0413|5end_lipoprotein,_putative_466338..466568_POSITIVE 243 155 119 137 94 NC_002967:TDE2333|5end_sanA_protein,_putative_2368551..2368781_NEGATIVE 242 107 67 113 68 NC_002967:TDE2510|5end_ABC_transporter,_ATP-binding/permease_protein_2534182..2534412_POSITIVE 242 139 91 45 11 NC_002967:TDE1269|5end_hypothetical_protein_1304522..1304752_NEGATIVE 241 139 91 210 167 NC_002967:TDE1741|5end_penicillin-binding_protein_1792792..1793022_POSITIVE 241 39 6 165 126 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 240 138 94 181 142 NC_002967:TDE1291|5end_HD_domain_protein_1329213..1329443_NEGATIVE 237 140 94 227 191 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 237 133 91 37 2 NC_002967:TDE0143|5end_thiamine_ABC_transporter,_thiamine-binding_protein_164013..164243_POSITIVE 232 149 101 222 176 NC_002967:TDE0593|5end_internalin-related_protein_633936..634166_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 129 83 102 66 NC_002967:TDE1204|3end_cell_division_protein_FtsZ_1237666..1237816_POSITIVE 250 110 64 97 53 NC_002967:TDE0719|3end_bacteriocin_ABC_transporter,_ATP-binding/permease_protein,_putative_755695..755845_POSITIVE 249 136 97 121 86 NC_002967:TDE0377|3end_hypothetical_protein_431885..432035_NEGATIVE 246 156 111 143 98 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 240 138 94 80 41 NC_002967:TDE1292|3end_TldD/PmbA_family_protein_1329314..1329464_NEGATIVE 239 140 105 66 31 NC_002967:TDE1133|3end_hypothetical_protein_1164753..1164903_NEGATIVE 232 149 101 147 101 NC_002967:TDE0594|3end_cysteine_protease_domain,_YopT-type_634011..634161_NEGATIVE 227 116 72 103 62 NC_002967:TDE0736|3end_hypothetical_protein_775000..775150_NEGATIVE 226 145 109 70 37 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 226 156 119 99 59 NC_002967:TDE0827|3end_hypothetical_protein_847877..848027_NEGATIVE 224 130 89 121 70 NC_002967:TDE0577|3end_glutamyl-tRNA(Gln)_amidotransferase,_C_subunit_609198..609348_NEGATIVE 223 50 6 60 8 NC_002967:TDE1024|3end_conserved_hypothetical_protein_TIGR01319_1057034..1057184_POSITIVE 221 130 86 121 69 NC_002967:TDE1646|3end_hypothetical_protein_1696049..1696199_NEGATIVE 220 116 71 121 73 NC_002967:TDE2533|3end_hypothetical_protein_2560240..2560390_POSITIVE 219 47 7 54 14 NC_002967:TDE0656|3end_sensor_histidine_kinase,_putative_692750..692900_POSITIVE 218 158 122 86 47 NC_002967:TDE2542|3end_antigen,_putative_2569441..2569591_NEGATIVE 218 159 125 87 47 NC_002967:TDE1749|3end_50S_ribosomal_protein_L27_1803158..1803308_NEGATIVE 216 158 124 110 72 NC_002967:TDE0797|3end_acylphosphatase_821223..821373_POSITIVE 216 113 76 106 77 NC_002967:TDE0040|3end_AMP-binding_protein_45776..45926_NEGATIVE 214 135 105 79 52 NC_002967:TDE0837|3end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_856093..856243_NEGATIVE