Origin IGS: catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagtttttttacggtaatatcaataaaaatgca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgcatttttattgatattaccgtaaaaaaactatataaacatacggcaatgcccccaattgtgatataaaagtttatatgttgactttttacatgctattatagtaaactcgcataactttatagttatactaatgaggaacgtaaatg Mask Tandem Repeat Region ================================================ catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagtttttttacggtaatatcaataaaaatgca Find is-nt database================================================ Query_seq: TDE1231:TDE1232|TDE1231:TDE1232:hypothetical protein:hypothetical protein:<-<-:1265294..1265442 149 catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagtttttttacggtaatatcaataaaaatgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1231:TDE1232|TDE1231:TDE1232:hypothetical protein:hypothetical protein:<-<-:1265294..1265442 149 catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagtttttttacggtaatatcaataaaaatgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1231:TDE1232|TDE1231:TDE1232:hypothetical protein:hypothetical protein:<-<-:1265294..1265442 149 catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagtttttttacggtaatatcaataaaaatgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagtttttttacggtaatatcaataaaaatgca Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 15 End: 116 .............. M S I T I K L C E F T I I A C K K S T Y K L L Y H N W G H C R M F I ................................. catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagtttttttacggtaatatcaataaaaatgca 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: 82 Start: 111 End: 140 ..............................................................................................................ATTGATATTACCGTAAAAAAACTATATAAA......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagtttttttacggtaatatcaataaaaatgca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1231:TDE1232|TDE1231:TDE1232:hypothetical protein:hypothetical protein:<-<-:1265294..1265442 149 catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagtttttttacggtaatatcaataaaaatgca Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: NC_002967_TDE1231_TDE1232|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1265294,1265442]|149 HSP 1 e-value: 7.0E-67 bit: 254.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagnnnnnnnacggtaatatcaataaaaatgca catttacgttcctcattagtataactataaagttatgcgagtttactataatagcatgtaaaaagtcaacatataaacttttatatcacaattgggggcattgccgtatgtttatatagtttttttacggtaatatcaataaaaatgca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUUACGUUCCUCAUUAGUAUAACUAUAAAGUUAUGCGAGUUUACUAUAAUAGCAUGUAAAAAGUCAACAUAUAAACUUUUAUAUCACAAUUGGGGGCAUUGCCGUAUGUUUAUAUAGUUUUUUUACGGUAAUAUCAAUAAAAAUGCA (((((..((((((.(((.((((((((....))))))))...............(.((((((((.((..........)))))))))))..))).)))))).((((((((.................)))))))).........))))).. (-27.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAUUUUUAUUGAUAUUACCGUAAAAAAACUAUAUAAACAUACGGCAAUGCCCCCAAUUGUGAUAUAAAAGUUUAUAUGUUGACUUUUUACAUGCUAUUAUAGUAAACUCGCAUAACUUUAUAGUUAUACUAAUGAGGAACGUAAAUG (((.(((((((((........((((((((((.(((((((((((..(((((.......)))))..)))....)))))))))))...))))))).(((((...))))).......((((((....))))))..)))))))))..))).... (-21.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 805 110 61 201 152 NC_002967:TDE1231|5end_hypothetical_protein_1265203..1265433_NEGATIVE 252 130 85 51 2 NC_002967:TDE2107|5end_dihydroorotase,_putative_2132874..2133104_NEGATIVE 251 129 87 124 81 NC_002967:TDE1362|5end_hypothetical_protein_1400992..1401222_POSITIVE 245 127 88 167 121 NC_002967:TDE2346|5end_elongation_factor_Ts_2383429..2383659_NEGATIVE 245 110 80 214 172 NC_002967:TDE0548|5end_hypothetical_protein_586995..587225_NEGATIVE 239 137 96 70 23 NC_002967:TDE1382|5end_transcriptional_regulator,_ArsR_family_1422000..1422230_POSITIVE 237 130 85 124 74 NC_002967:TDE2506|5end_radical_SAM_domain_protein_2530581..2530811_POSITIVE 233 122 93 217 179 NC_002967:TDE0111|5end_hypothetical_protein_131615..131845_POSITIVE 231 130 92 165 113 NC_002967:TDE0836|5end_Na(+)-translocating_NADH-quinone_reductase,_C_subunit_856096..856326_NEGATIVE 226 138 91 221 175 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 226 112 79 210 166 NC_002967:TDE2165|5end_hydrogenase_accessory_protein_HypB_2197715..2197945_NEGATIVE 224 132 95 175 123 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 221 122 88 52 8 NC_002967:TDE0967|5end_hypothetical_protein_992201..992431_POSITIVE 220 114 79 178 136 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 217 130 86 168 128 NC_002967:TDE0986|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1013061..1013291_POSITIVE 216 134 94 110 71 NC_002967:TDE2004|5end_hypothetical_protein_2023622..2023852_POSITIVE 214 132 97 143 114 NC_002967:TDE1661|5end_hypothetical_protein_1715402..1715632_POSITIVE 213 108 64 107 66 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 211 130 86 180 140 NC_002967:TDE0059|5end_hypothetical_protein_67294..67524_POSITIVE 210 132 98 90 54 NC_002967:TDE2476|5end_carbamate_kinase_2499450..2499680_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 133 94 102 62 NC_002967:TDE0194|3end_hypothetical_protein_230739..230889_NEGATIVE 247 134 93 51 15 NC_002967:TDE1363|3end_nitroreductase_family_protein_1404126..1404276_NEGATIVE 245 127 88 93 47 NC_002967:TDE2347|3end_30S_ribosomal_protein_S2_2383503..2383653_NEGATIVE 237 130 85 84 34 NC_002967:TDE2505|3end_hypothetical_protein_2530621..2530771_POSITIVE 229 107 79 146 112 NC_002967:TDE1368|3end_hypothetical_protein_1409427..1409577_NEGATIVE 226 113 87 139 115 NC_002967:TDE1361|3end_hypothetical_protein_1401106..1401256_POSITIVE 221 134 92 50 1 NC_002967:TDE0968|3end_translation_elongation_factor_P_992563..992713_NEGATIVE 220 114 79 145 103 NC_002967:TDE0595|3end_hypothetical_protein_634838..634988_NEGATIVE 217 130 86 81 41 NC_002967:TDE0985|3end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_1013054..1013204_POSITIVE 213 69 29 76 32 NC_002967:TDE1579|3end_fibronectin/fibrinogen-binding_protein,_internal_deletion_1626074..1626224_NEGATIVE 213 124 83 148 96 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 208 131 91 45 4 NC_002967:TDE1515|3end_permease_domain_protein_1563179..1563329_POSITIVE 204 124 90 147 106 NC_002967:TDE0642|3end_hypothetical_protein_678460..678610_NEGATIVE 201 113 77 47 2 NC_002967:TDE2633|3end_hypothetical_protein_2674702..2674852_POSITIVE 201 138 95 67 21 NC_002967:TDE0536|3end_hypothetical_protein_578064..578214_NEGATIVE 200 130 94 81 51 NC_002967:TDE0391|3end_hypothetical_protein_441601..441751_NEGATIVE 199 123 89 65 40 NC_002967:TDE1967|3end_hypothetical_protein_1982533..1982683_POSITIVE 198 137 94 78 31 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 198 99 51 108 59 NC_002967:TDE0494|3end_hypothetical_protein_549559..549709_NEGATIVE 197 133 91 134 93 NC_002967:TDE0281|3end_hypothetical_protein_310293..310443_NEGATIVE