Origin IGS: ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataataaaaaaatgataaaatacgccctacaaagataggattattggaggtatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatacctccaataatcctatctttgtagggcgtattttatcatttttttattatagttacaagcagtatcaattttttaaaaagcttgacattcctccaatacttgtataaattatgcttttaaggaattattgaa Mask Tandem Repeat Region ================================================ ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataataaaaaaatgataaaatacgccctacaaagataggattattggaggtatat Find is-nt database================================================ Query_seq: TDE0471:TDE0472|TDE0471:TDE0472:BNR domain protein:hypothetical protein:<-->:528379..528515 137 ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataataaaaaaatgataaaatacgccctacaaagataggattattggaggtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0471:TDE0472|TDE0471:TDE0472:BNR domain protein:hypothetical protein:<-->:528379..528515 137 ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataataaaaaaatgataaaatacgccctacaaagataggattattggaggtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0471:TDE0472|TDE0471:TDE0472:BNR domain protein:hypothetical protein:<-->:528379..528515 137 ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataataaaaaaatgataaaatacgccctacaaagataggattattggaggtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataataaaaaaatgataaaatacgccctacaaagataggattattggaggtatat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 29 End: 118 ............................ V L I P P I D L K K F F Q Y Q K Y S Y Y F F S L I R G V F M ................... ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataataaaaaaatgataaaatacgccctacaaagataggattattggaggtatat 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: 84 Start: 23 End: 52 ......................CTTGACATTCCTCCAATACTTGTATAAATT..................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 74 End: 103 .........................................................................CTTGTAACTATAATAAAAAAATGATAAAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataataaaaaaatgataaaatacgccctacaaagataggattattggaggtatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0471:TDE0472|TDE0471:TDE0472:BNR domain protein:hypothetical protein:<-->:528379..528515 137 ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataataaaaaaatgataaaatacgccctacaaagataggattattggaggtatat Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_002967_TDE0471_TDE0472|BNR domain protein:hypothetical protein|NEGATIVE:POSITIVE|[528379,528515]|137 HSP 1 e-value: 9.0E-60 bit: 230.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataatnnnnnnntgataaaatacgccctacaaagataggattattggaggtatat ttcaataattccttaaaagcataatttatacaagtattggaggaatgtcaagctttttaaaaaattgatactgcttgtaactataataaaaaaatgataaaatacgccctacaaagataggattattggaggtatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAUAAUUCCUUAAAAGCAUAAUUUAUACAAGUAUUGGAGGAAUGUCAAGCUUUUUAAAAAAUUGAUACUGCUUGUAACUAUAAUAAAAAAAUGAUAAAAUACGCCCUACAAAGAUAGGAUUAUUGGAGGUAUAU ((((((((((((((....((.((.(((((.....(((((.((......(((((...((((....))))....)))))...)).)))))........))))).)).))......)))...)))))))))))....... (-18.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUACCUCCAAUAAUCCUAUCUUUGUAGGGCGUAUUUUAUCAUUUUUUUAUUAUAGUUACAAGCAGUAUCAAUUUUUUAAAAAGCUUGACAUUCCUCCAAUACUUGUAUAAAUUAUGCUUUUAAGGAAUUAUUGAA .........(((((((....((((((.((((((((.(((((((.............((..(((((...................)))))))..............)).))))).))))))))))))))))))))).. (-20.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 753 80 31 171 122 NC_002967:TDE0471|5end_BNR_domain_protein_528288..528518_NEGATIVE 262 52 11 154 117 NC_002967:TDE0457|5end_hypothetical_protein_513525..513755_POSITIVE 255 46 2 165 123 NC_002967:TDE0022|5end_hypothetical_protein_27872..28102_POSITIVE 238 76 36 199 154 NC_002967:TDE0938|5end_hypothetical_protein_962174..962404_NEGATIVE 231 58 16 229 185 NC_002967:TDE0333|5end_MATE_efflux_family_protein_371648..371878_POSITIVE 214 108 71 172 133 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 211 79 33 58 16 NC_002967:TDE1358|5end_hypothetical_protein_1397732..1397962_POSITIVE 210 80 38 187 145 NC_002967:TDE1226|5end_zinc_ABC_transporter,_periplasmic_zinc-binding_protein_1260483..1260713_NEGATIVE 207 54 36 219 200 NC_002967:TDE0468|5end_hypothetical_protein_521273..521503_NEGATIVE 205 77 39 208 169 NC_002967:TDE2168|5end_hypothetical_protein_2201003..2201233_NEGATIVE 204 122 87 134 106 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 203 64 32 139 108 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 202 47 5 50 6 NC_002967:TDE0584|5end_permease,_putative_623134..623364_NEGATIVE 200 80 41 54 17 NC_002967:TDE2527|5end_hypothetical_protein_2556219..2556449_NEGATIVE 198 70 33 149 119 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 198 82 47 151 123 NC_002967:TDE1499|5end_adenylosuccinate_lyase,_putative_1545266..1545496_POSITIVE 198 129 104 88 60 NC_002967:TDE0849|5end_hypothetical_protein_871599..871829_POSITIVE 197 130 99 137 111 NC_002967:TDE1238|5end_translocase_1270815..1271045_POSITIVE 196 50 1 226 178 NC_002967:TDE1564|5end_hypothetical_protein_1616502..1616732_POSITIVE 194 57 11 209 151 NC_002967:TDE0122|5end_dihydrouridine_synthase,_putative_141539..141769_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 46 2 108 66 NC_002967:TDE0021|3end_CDP-alcohol_phosphatidyltransferase_family_protein_27895..28045_POSITIVE 231 58 16 147 103 NC_002967:TDE0332|3end_transcriptional_regulator,_TetR_family_371646..371796_POSITIVE 217 59 31 104 72 NC_002967:TDE2243|3end_CutC_family_protein_2282214..2282364_NEGATIVE 211 79 33 76 34 NC_002967:TDE1357|3end_aldose_1-epimerase_1397830..1397980_POSITIVE 207 78 33 106 67 NC_002967:TDE1015|3end_hypothetical_protein_1045599..1045749_POSITIVE 203 64 32 34 3 NC_002967:TDE2235|3end_methylaspartate_ammonia-lyase_2273350..2273500_NEGATIVE 202 47 5 46 2 NC_002967:TDE0585|3end_hypothetical_protein_623138..623288_NEGATIVE 200 80 41 53 16 NC_002967:TDE2528|3end_hypothetical_protein_2556220..2556370_NEGATIVE 198 82 47 59 31 NC_002967:TDE1498|3end_hypothetical_protein_1545254..1545404_POSITIVE 197 130 99 58 32 NC_002967:TDE1237|3end_hypothetical_protein_1270816..1270966_POSITIVE 195 45 1 151 109 NC_002967:TDE1563|3end_hypothetical_protein_1616513..1616663_POSITIVE 190 37 8 128 100 NC_002967:TDE0195|3end_acetyltransferase,_GNAT_family_231942..232092_NEGATIVE 188 120 73 106 53 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 184 75 39 81 40 NC_002967:TDE1904|3end_hypothetical_protein_1923197..1923347_NEGATIVE 184 59 33 139 114 NC_002967:TDE1358|3end_hypothetical_protein_1397910..1398060_POSITIVE 184 52 11 81 43 NC_002967:TDE0114|3end_iron-dependent_transcriptional_regulator_133581..133731_NEGATIVE 182 61 32 59 28 NC_002967:TDE0492|3end_sensor_histidine_kinase/response_regulator_548657..548807_POSITIVE 181 45 19 32 4 NC_002967:TDE1172|3end_hypothetical_protein_1201280..1201430_POSITIVE 178 54 20 92 44 NC_002967:TDE1874|3end_hypothetical_protein_1895640..1895790_NEGATIVE 178 60 16 94 52 NC_002967:TDE0117|3end_lipoprotein,_putative_136607..136757_POSITIVE