Origin IGS: atcttatattttcggcctttttttaaaaaaaatcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgtttttttccttaaaataaggaggatatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 catatcctccttattttaaggaaaaaaacaccctgtaggtctaatcttaagtatataatatcacaattttaatgttttatccatagtagcgggctcatattgctaaaaagaaccaaggttacccggtgtctatatagaagagaaaccgtatcgggctcttgattttttttaaaaaaaggccgaaaatataagat Mask Tandem Repeat Region ================================================ atcttatattttcggcctttttttaaaaaaaatcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgtttttttccttaaaataaggaggatatg Find is-nt database================================================ Query_seq: TDE1245:TDE1246|TDE1245:TDE1246:hypothetical protein:lipoprotein, putative:<-->:1278985..1279178 194 atcttatattttcggcctttttttaaaaaaaatcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgtttttttccttaaaataaggaggatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1245:TDE1246|TDE1245:TDE1246:hypothetical protein:lipoprotein, putative:<-->:1278985..1279178 194 atcttatattttcggcctttttttaaaaaaaatcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgtttttttccttaaaataaggaggatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1245:TDE1246|TDE1245:TDE1246:hypothetical protein:lipoprotein, putative:<-->:1278985..1279178 194 atcttatattttcggcctttttttaaaaaaaatcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgtttttttccttaaaataaggaggatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcttatattttcggcctttttttaaaaaaaatcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgtttttttccttaaaataaggaggatatg Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 1 End: 123 M L Y F R P F F K K N Q E P D T V S L L Y R H R V T L V L F S N M S P L L W I K H ....................................................................... atcttatattttcggcctttttttaaaaaaaatcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgtttttttccttaaaataaggaggatatg 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: 81 Start: 111 End: 140 ..............................................................................................................ATGGATAAAACATTAAAATTGTGATATTAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcttatattttcggcctttttttaaaaaaaatcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgtttttttccttaaaataaggaggatatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1245:TDE1246|TDE1245:TDE1246:hypothetical protein:lipoprotein, putative:<-->:1278985..1279178 194 atcttatattttcggcctttttttaaaaaaaatcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgtttttttccttaaaataaggaggatatg Intra-Species Hit: Count: 1 Min: 33 Max: 194 Len: 162 Subject: NC_002967_TDE1245_TDE1246|hypothetical protein:lipoprotein, putative|NEGATIVE:POSITIVE|[1278985,1279178]|194 HSP 1 e-value: 2.0E-74 bit: 280.0 Len: 162 Query Start:33 Query End:194 Subject Strand: POSITIVE Subject Start: 33 Subject End: 194 ................................tcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgnnnnnnnccttaaaataaggaggatatg ................................tcaagagcccgatacggtttctcttctatatagacaccgggtaaccttggttctttttagcaatatgagcccgctactatggataaaacattaaaattgtgatattatatacttaagattagacctacagggtgtttttttccttaaaataaggaggatatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAGAGCCCGAUACGGUUUCUCUUCUAUAUAGACACCGGGUAACCUUGGUUCUUUUUAGCAAUAUGAGCCCGCUACUAUGGAUAAAACAUUAAAAUUGUGAUAUUAUAUACUUAAGAUUAGACCUACAGGGUGUUUUUUUCCUUAAAAUAAGGAGGAUAUG ......((((..((.(((((.(((((((...(((.((((((....)))))))))...)))..((((((...(((....(((.......))).......)))...))))))....))))..)))))))..))))....(((((((((...))))))))).... (-32.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAUCCUCCUUAUUUUAAGGAAAAAAACACCCUGUAGGUCUAAUCUUAAGUAUAUAAUAUCACAAUUUUAAUGUUUUAUCCAUAGUAGCGGGCUCAUAUUGCUAAAAAGAACCAAGGUUACCCGGUGUCUAUAUAGAAGAGAAACCGUAUCGGGCUCUUGA .......((((((...))))))........(((.((((((....((((...(((((((((((........................((((((.......)))))).....(((....)))....))))).)))))).))))...))).))).)))....... (-27.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 968 50 1 173 124 NC_002967:TDE1245|5end_hypothetical_protein_1278894..1279124_NEGATIVE 528 88 41 117 69 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 308 47 4 206 162 NC_002967:TDE2511|5end_ABC_transporter,_ATP-binding/permease_protein_2535917..2536147_POSITIVE 304 46 7 148 104 NC_002967:TDE0547|5end_hypothetical_protein_586882..587112_NEGATIVE 299 78 36 165 122 NC_002967:TDE0085|5end_ATP-dependent_DNA_helicase,_UvrD/Rep_family_101015..101245_NEGATIVE 290 71 34 199 156 NC_002967:TDE1952|5end_hypothetical_protein_1969046..1969276_NEGATIVE 290 50 1 206 153 NC_002967:TDE0839|5end_rhodanese-like_domain_protein_859341..859571_NEGATIVE 283 46 2 222 172 NC_002967:TDE2553|5end_lysyl-tRNA_synthetase_2580633..2580863_NEGATIVE 282 80 31 76 20 NC_002967:TDE0685|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_722620..722850_NEGATIVE 276 48 7 208 159 NC_002967:TDE1463|5end_hypothetical_protein_1513072..1513302_NEGATIVE 276 75 32 139 95 NC_002967:TDE1084|5end_folylpolyglutamate_synthetase,_putative_1116286..1116516_NEGATIVE 266 71 35 47 19 NC_002967:TDE1382|5end_transcriptional_regulator,_ArsR_family_1422000..1422230_POSITIVE 265 79 38 105 67 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 264 50 6 188 124 NC_002967:TDE1159|5end_hypothetical_protein_1194420..1194650_NEGATIVE 260 75 39 52 14 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 255 46 5 162 121 NC_002967:TDE2534|5end_endonuclease_III_2560144..2560374_POSITIVE 251 75 36 123 81 NC_002967:TDE0777|5end_50S_ribosomal_protein_L14_811109..811339_POSITIVE 250 49 3 71 22 NC_002967:TDE0138|5end_alkyldihydroxyacetonephosphate_synthase,_putative_158221..158451_POSITIVE 249 60 11 222 166 NC_002967:TDE1721|5end_radical_SAM_domain_protein_1775140..1775370_POSITIVE 247 75 32 142 102 NC_002967:TDE2393|5end_hypothetical_protein_2422398..2422628_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 46 7 148 104 NC_002967:TDE0548|3end_hypothetical_protein_586882..587032_NEGATIVE 299 78 36 141 98 NC_002967:TDE0086|3end_hypothetical_protein_101039..101189_NEGATIVE 290 75 38 82 50 NC_002967:TDE2317|3end_hemolysin_III_2354118..2354268_NEGATIVE 290 50 1 128 75 NC_002967:TDE0840|3end_hypothetical_protein_859419..859569_NEGATIVE 277 77 31 120 74 NC_002967:TDE0626|3end_hypothetical_protein_659684..659834_POSITIVE 251 75 36 104 62 NC_002967:TDE0776|3end_ribosomal_protein_S17_811170..811320_POSITIVE 247 46 6 62 22 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 245 43 10 113 80 NC_002967:TDE1743|3end_chromate_transport_protein_1797940..1798090_NEGATIVE 245 48 3 148 103 NC_002967:TDE0050|3end_RNA_methyltransferase,_TrmH_family_59283..59433_NEGATIVE 242 57 15 75 42 NC_002967:TDE0607|3end_ParA_family_ATPase_644125..644275_NEGATIVE 241 49 4 49 1 NC_002967:TDE0137|3end_carbohydrate_kinase,_FGGY_family_158279..158429_POSITIVE 240 48 4 126 76 NC_002967:TDE2218|3end_hypothetical_protein_2259002..2259152_POSITIVE 238 50 7 139 95 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 237 52 14 35 3 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 236 47 4 141 85 NC_002967:TDE1051|3end_hypothetical_protein_1078212..1078362_NEGATIVE 235 50 6 71 28 NC_002967:TDE2372|3end_hypothetical_protein_2405199..2405349_POSITIVE 235 60 14 140 95 NC_002967:TDE2066|3end_exodeoxyribonuclease_VII,_small_subunit_2092222..2092372_POSITIVE 235 76 32 146 105 NC_002967:TDE1331|3end_anaerobic_ribonucleoside_triphosphate_reductase_1368074..1368224_POSITIVE 230 86 50 142 103 NC_002967:TDE0410|3end_peptidase,_M48_family_462999..463149_POSITIVE 230 50 4 124 64 NC_002967:TDE0293|3end_MATE_efflux_family_protein_322018..322168_NEGATIVE