Origin IGS: taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttctcccattgagccatgtttatattataaatggtatcatatatggtgtcaagatgtaattcattttattatcataaaacataaataatagctgttatataccta Mask Tandem Repeat Region ================================================ taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa Find is-nt database================================================ Query_seq: TDE0988:TDE0989|TDE0988:TDE0989:oligopeptide/dipeptide ABC transporter, peptide-binding protein:hypothetical protein:->->:1017166..1017271 106 taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0988:TDE0989|TDE0988:TDE0989:oligopeptide/dipeptide ABC transporter, peptide-binding protein:hypothetical protein:->->:1017166..1017271 106 taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0988:TDE0989|TDE0988:TDE0989:oligopeptide/dipeptide ABC transporter, peptide-binding protein:hypothetical protein:->->:1017166..1017271 106 taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa Predict ORF larger than 30AA ================================================ taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa 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: 92 Start: 53 End: 82 ....................................................CTTGACACCATATATGATACCATTTATAAT........................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0988:TDE0989|TDE0988:TDE0989:oligopeptide/dipeptide ABC transporter, peptide-binding protein:hypothetical protein:->->:1017166..1017271 106 taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: NC_002967_TDE0988_TDE0989|oligopeptide/dipeptide ABC transporter, peptide-binding protein:hypothetical protein|POSITIVE:POSITIVE|[1017166,1017271]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa taggtatataacagctattatttatgttttatgataataaaatgaattacatcttgacaccatatatgataccatttataatataaacatggctcaatgggagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUAUAUAACAGCUAUUAUUUAUGUUUUAUGAUAAUAAAAUGAAUUACAUCUUGACACCAUAUAUGAUACCAUUUAUAAUAUAAACAUGGCUCAAUGGGAGAAA ............((((((.......(((((((....))))))).....................(((((......)))))........))))))............ ( -8.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCCCAUUGAGCCAUGUUUAUAUUAUAAAUGGUAUCAUAUAUGGUGUCAAGAUGUAAUUCAUUUUAUUAUCAUAAAACAUAAAUAAUAGCUGUUAUAUACCUA ..........((((((((.............))))).)))..(((((((..((((((.....))))))..)))))))........(((((....)))))....... (-14.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 94 51 118 80 NC_002967:TDE2036|5end_ATPase,_AAA_family_2066638..2066868_NEGATIVE 226 68 21 231 181 NC_002967:TDE2589|5end_putative_aminopeptidase_1_2626406..2626636_NEGATIVE 195 94 52 128 83 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 183 100 55 196 145 NC_002967:TDE0420|5end_hypothetical_protein_472218..472448_POSITIVE 182 94 54 185 145 NC_002967:TDE0483|5end_hypothetical_protein_538805..539035_POSITIVE 181 64 28 68 27 NC_002967:TDE1133|5end_hypothetical_protein_1165058..1165288_NEGATIVE 177 46 2 153 111 NC_002967:TDE1438|5end_glycosyl_transferase,_group_1_family_protein_1483240..1483470_POSITIVE 171 44 1 230 182 NC_002967:TDE2269|5end_hypothetical_protein_2305920..2306150_NEGATIVE 162 99 69 123 90 NC_002967:TDE2350|5end_lipoprotein,_putative_2386661..2386891_NEGATIVE 161 74 49 203 166 NC_002967:TDE2029|5end_hydrolase,_TatD_family_2058002..2058232_NEGATIVE 161 95 72 27 5 NC_002967:TDE0752|5end_hypothetical_protein_791353..791583_POSITIVE 159 63 39 49 25 NC_002967:TDE2104|5end_hypothetical_protein_2131083..2131313_NEGATIVE 157 87 50 148 111 NC_002967:TDE0700|5end_hypothetical_protein_736398..736628_NEGATIVE 153 96 72 212 176 NC_002967:TDE2363|5end_high-affinity_branched_chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398179..2398409_NEGATIVE 151 35 14 101 81 NC_002967:TDE2080|5end_cytidylate_kinase/ribosomal_protein_S1_2111484..2111714_NEGATIVE 149 95 51 150 96 NC_002967:TDE1417|5end_ABC_transporter,_ATP-binding_protein_1460656..1460886_POSITIVE 147 64 25 231 195 NC_002967:TDE0375|5end_ABC_transporter,_ATP-binding_protein_430147..430377_NEGATIVE 145 94 73 227 206 NC_002967:TDE0336|5end_hypothetical_protein_376311..376541_NEGATIVE 144 89 53 100 70 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 143 94 64 32 8 NC_002967:TDE2747|5end_type_I_restriction-modification_system,_R_subunit_2804942..2805172_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 94 51 109 71 NC_002967:TDE2037|3end_ATP:guanido_phosphotransferase_domain_protein_2066647..2066797_NEGATIVE 195 94 52 116 71 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 181 64 28 64 23 NC_002967:TDE1134|3end_hypothetical_protein_1165062..1165212_NEGATIVE 177 46 2 119 77 NC_002967:TDE1437|3end_capsular_polysaccharide_biosynthesis_protein_1483286..1483436_POSITIVE 149 95 51 141 87 NC_002967:TDE1416|3end_ABC_transporter,_permease_protein_1460727..1460877_POSITIVE 145 94 51 88 38 NC_002967:TDE0497|3end_hypothetical_protein_551374..551524_NEGATIVE 142 77 34 96 55 NC_002967:TDE2215|3end_galactoside_ABC_transporter,_permease_protein,_putative_2253441..2253591_NEGATIVE 141 40 12 54 28 NC_002967:TDE2739|3end_hypothetical_protein_2795169..2795319_POSITIVE 141 95 51 89 40 NC_002967:TDE0424|3end_bacteriocin-type_signal_domain_protein_479773..479923_POSITIVE 140 67 21 106 65 NC_002967:TDE2676|3end_threonine_synthase_2715678..2715828_POSITIVE 139 80 50 81 52 NC_002967:TDE1644|3end_methionyl-tRNA_formyltransferase_1694578..1694728_NEGATIVE 138 87 65 27 1 NC_002967:TDE0701|3end_hypothetical_protein_736519..736669_NEGATIVE 138 75 31 49 6 NC_002967:TDE0633|3end_D-alanyl-D-alanine_carboxypeptidase,_putative_668658..668808_POSITIVE 137 35 2 110 79 NC_002967:TDE2489|3end_peptide_chain_release_factor_1_2511391..2511541_NEGATIVE 134 100 52 140 90 NC_002967:TDE2623|3end_hypothetical_protein_2663584..2663734_NEGATIVE 134 95 52 77 31 NC_002967:TDE0259|3end_transcriptional_regulator,_MarR_family_293789..293939_POSITIVE 133 87 58 50 24 NC_002967:TDE0567|3end_hypothetical_protein_598916..599066_POSITIVE 132 54 13 136 77 NC_002967:TDE1822|3end_hypothetical_protein_1855479..1855629_NEGATIVE 132 96 58 68 27 NC_002967:TDE0234|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_268944..269094_POSITIVE 131 70 43 128 99 NC_002967:TDE2638|3end_hypothetical_protein_2678199..2678349_POSITIVE