Origin IGS: tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcaaaaaaactttttggaggtgtttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaacacctccaaaaagtttttttgattgatatgcctcaattttaatcgattttgcttaaaataaaagtgccgaaagtcattttttatagggaaaatagta Mask Tandem Repeat Region ================================================ tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcaaaaaaactttttggaggtgtttt Find is-nt database================================================ Query_seq: TDE2377:TDE2378|TDE2377:TDE2378:hypothetical protein:ABC transporter, ATP-binding protein, putative:<-->:2407758..2407858 101 tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcaaaaaaactttttggaggtgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2377:TDE2378|TDE2377:TDE2378:hypothetical protein:ABC transporter, ATP-binding protein, putative:<-->:2407758..2407858 101 tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcaaaaaaactttttggaggtgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2377:TDE2378|TDE2377:TDE2378:hypothetical protein:ABC transporter, ATP-binding protein, putative:<-->:2407758..2407858 101 tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcaaaaaaactttttggaggtgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcaaaaaaactttttggaggtgtttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 5 End: 100 .... M F P I K N D F R H F Y F K Q N R L K L R H I N Q K N F L E V F . tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcaaaaaaactttttggaggtgtttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcaaaaaaactttttggaggtgtttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2377:TDE2378|TDE2377:TDE2378:hypothetical protein:ABC transporter, ATP-binding protein, putative:<-->:2407758..2407858 101 tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcaaaaaaactttttggaggtgtttt Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_002967_TDE2377_TDE2378|hypothetical protein:ABC transporter, ATP-binding protein, putative|NEGATIVE:POSITIVE|[2407758,2407858]|101 HSP 1 e-value: 2.0E-38 bit: 159.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcnnnnnnnctttttggaggtgtttt tactattttccctataaaaaatgactttcggcacttttattttaagcaaaatcgattaaaattgaggcatatcaatcaaaaaaactttttggaggtgtttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUAUUUUCCCUAUAAAAAAUGACUUUCGGCACUUUUAUUUUAAGCAAAAUCGAUUAAAAUUGAGGCAUAUCAAUCAAAAAAACUUUUUGGAGGUGUUUU .............................((((((..........((....(((((....))))).)).......((((((.....)))))).)))))).. (-10.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACACCUCCAAAAAGUUUUUUUGAUUGAUAUGCCUCAAUUUUAAUCGAUUUUGCUUAAAAUAAAAGUGCCGAAAGUCAUUUUUUAUAGGGAAAAUAGUA ........(((...((((....((((((((.((......)).))))))))....)))).....(((((((.(....).))))))).....)))........ (-17.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 761 70 21 161 112 NC_002967:TDE2377|5end_hypothetical_protein_2407667..2407897_NEGATIVE 303 68 25 77 25 NC_002967:TDE0832|5end_hypothetical_protein_852549..852779_POSITIVE 264 85 44 58 9 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 215 68 22 165 108 NC_002967:TDE1082|5end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_1113135..1113365_POSITIVE 211 55 11 146 101 NC_002967:TDE0237|5end_HDIG_domain_protein_271190..271420_NEGATIVE 210 100 52 214 161 NC_002967:TDE1087|5end_cytidylate_kinase_1118670..1118900_POSITIVE 208 68 22 179 141 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 205 68 26 167 122 NC_002967:TDE1165|5end_hypothetical_protein_1198390..1198620_NEGATIVE 199 68 28 77 27 NC_002967:TDE2262|5end_peptidase,_U32_family_2299277..2299507_NEGATIVE 197 94 64 146 105 NC_002967:TDE1297|5end_LysM_domain/M23/M37_peptidase_domain_protein_1334782..1335012_NEGATIVE 197 70 36 129 87 NC_002967:TDE0406|5end_hypothetical_protein_457230..457460_POSITIVE 195 70 24 170 139 NC_002967:TDE0988|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1015082..1015312_POSITIVE 194 65 25 207 164 NC_002967:TDE2407|5end_amidophosphoribosyltransferase_2435107..2435337_NEGATIVE 193 56 11 70 33 NC_002967:TDE0151|5end_integral_membrane_protein,_YeeE/YedE_family_173101..173331_NEGATIVE 193 49 6 141 104 NC_002967:TDE0082|5end_transcriptional_regulator,_MerR_family_94251..94481_NEGATIVE 190 69 31 44 3 NC_002967:TDE2662|5end_lipoprotein,_putative_2698650..2698880_NEGATIVE 190 95 51 110 59 NC_002967:TDE0648|5end_protein-glutamate_methylesterase_682800..683030_POSITIVE 187 79 31 72 16 NC_002967:TDE2456|5end_hypothetical_protein_2484573..2484803_NEGATIVE 185 69 21 198 153 NC_002967:TDE1550|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_1592747..1592977_POSITIVE 185 47 2 231 182 NC_002967:TDE0927|5end_phosphonate_ABC_transporter,_permease_protein,_putative_950873..951103_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 213 64 21 99 56 NC_002967:TDE1569|3end_hypothetical_protein_1619975..1620125_POSITIVE 206 69 29 78 33 NC_002967:TDE2663|3end_isoleucyl-tRNA_synthetase_2698616..2698766_NEGATIVE 199 68 28 77 27 NC_002967:TDE2263|3end_acetyl_hydrolase,_putative_2299277..2299427_NEGATIVE 197 94 64 146 105 NC_002967:TDE1298|3end_cyclic_nucleotide_binding_domain_protein_1334782..1334932_NEGATIVE 195 70 24 85 54 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 194 65 25 97 54 NC_002967:TDE2408|3end_hypothetical_protein_2435217..2435367_NEGATIVE 193 56 11 49 12 NC_002967:TDE0152|3end_amino_acid_permease_family_protein_173122..173272_NEGATIVE 193 49 6 138 101 NC_002967:TDE0083|3end_GTP-binding_protein_EngA_94254..94404_NEGATIVE 192 54 26 142 118 NC_002967:TDE1166|3end_hypothetical_protein_1198394..1198544_NEGATIVE 190 70 25 149 103 NC_002967:TDE1665|3end_hypothetical_protein_1718908..1719058_NEGATIVE 190 95 51 69 18 NC_002967:TDE0647|3end_chemotaxis_protein_methyltransferase_682839..682989_POSITIVE 186 69 34 112 83 NC_002967:TDE2717|3end_phosphatidate_cytidylyltransferase,_putative_2773921..2774071_NEGATIVE 185 50 8 43 1 NC_002967:TDE2095|3end_hypothetical_protein_2123283..2123433_POSITIVE 183 57 11 58 7 NC_002967:TDE2359|3end_DAK2_domain_protein_2394153..2394303_NEGATIVE 181 54 23 142 115 NC_002967:TDE1331|3end_anaerobic_ribonucleoside_triphosphate_reductase_1368074..1368224_POSITIVE 180 48 8 139 99 NC_002967:TDE2577|3end_hypothetical_protein_2602490..2602640_NEGATIVE 179 67 29 136 94 NC_002967:TDE2437|3end_cyclic_nucleotide_binding_domain_protein_2467418..2467568_NEGATIVE 179 33 3 145 115 NC_002967:TDE1981|3end_hypothetical_protein_1992437..1992587_POSITIVE 179 99 62 105 67 NC_002967:TDE1320|3end_ComEC/Rec2-related_protein_1359418..1359568_POSITIVE 174 33 3 104 75 NC_002967:TDE1407|3end_hypothetical_protein_1449433..1449583_NEGATIVE