Origin IGS: tgtataaataggtaatttaccggaaaaaaacggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataggtgaatcatgtacctgtaaccaaaatacaattaaaacgaacttaacaaaatctcaaatcatcagtgaaaaataagaatggtcataaatctttaccgtttttttccggtaaattacctatttataca Mask Tandem Repeat Region ================================================ tgtataaataggtaatttaccggaaaaaaacggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat Find is-nt database================================================ Query_seq: TDE1455:TDE1456|TDE1455:TDE1456:prevent-host-death family protein:GGDEF domain protein:-><-:1503272..1503401 130 tgtataaataggtaatttaccggaaaaaaacggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1455:TDE1456|TDE1455:TDE1456:prevent-host-death family protein:GGDEF domain protein:-><-:1503272..1503401 130 tgtataaataggtaatttaccggaaaaaaacggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1455:TDE1456|TDE1455:TDE1456:prevent-host-death family protein:GGDEF domain protein:-><-:1503272..1503401 130 tgtataaataggtaatttaccggaaaaaaacggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtataaataggtaatttaccggaaaaaaacggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat Predict ORF larger than 30AA ================================================ tgtataaataggtaatttaccggaaaaaaacggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat 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================================================ tgtataaataggtaatttaccggaaaaaaacggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1455:TDE1456|TDE1455:TDE1456:prevent-host-death family protein:GGDEF domain protein:-><-:1503272..1503401 130 tgtataaataggtaatttaccggaaaaaaacggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_002967_TDE1455_TDE1456|prevent-host-death family protein:GGDEF domain protein|POSITIVE:NEGATIVE|[1503272,1503401]|130 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 tgtataaataggtaatttaccggnnnnnnncggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat tgtataaataggtaatttaccggaaaaaaacggtaaagatttatgaccattcttatttttcactgatgatttgagattttgttaagttcgttttaattgtattttggttacaggtacatgattcacctat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAUAAAUAGGUAAUUUACCGGAAAAAAACGGUAAAGAUUUAUGACCAUUCUUAUUUUUCACUGAUGAUUUGAGAUUUUGUUAAGUUCGUUUUAAUUGUAUUUUGGUUACAGGUACAUGAUUCACCUAU .......((((((..(((((((........)))))))...((((((((....(((((.......))))).(..((((...((((((.....))))))...))))..).....))).)))))...)))))) (-25.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGGUGAAUCAUGUACCUGUAACCAAAAUACAAUUAAAACGAACUUAACAAAAUCUCAAAUCAUCAGUGAAAAAUAAGAAUGGUCAUAAAUCUUUACCGUUUUUUUCCGGUAAAUUACCUAUUUAUACA ((((((((...(((.(((.(((.......))).............................(((....)))...........))))))......((((((........)))))).))))))))....... (-17.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 90 41 79 34 NC_002967:TDE2526|5end_hypothetical_protein_2555034..2555264_NEGATIVE 268 88 43 202 143 NC_002967:TDE1217|5end_flagellar_assembly_protein_1249511..1249741_POSITIVE 250 113 71 151 109 NC_002967:TDE0382|5end_hypothetical_protein_434393..434623_POSITIVE 242 90 44 129 85 NC_002967:TDE1200|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,_6-diaminopimelate--D-alanyl-D-alanyl_ligase_1231618..1231848_POSITIVE 226 118 71 77 16 NC_002967:TDE2246|5end_hypothetical_protein_2286132..2286362_POSITIVE 217 90 44 137 85 NC_002967:TDE2487|5end_acetyltransferase,_GNAT_family_2509807..2510037_POSITIVE 216 128 81 50 13 NC_002967:TDE1079|5end_DNA-binding_protein/PTS_system,_IIA_component_1111120..1111350_POSITIVE 211 101 64 86 40 NC_002967:TDE1733|5end_methionine_aminopeptidase,_type_I_1787853..1788083_POSITIVE 207 77 31 108 69 NC_002967:TDE2638|5end_hypothetical_protein_2677493..2677723_POSITIVE 203 125 84 48 12 NC_002967:TDE0278|5end_hypothetical_protein_308782..309012_NEGATIVE 199 120 71 85 39 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 199 127 86 64 35 NC_002967:TDE1042|5end_deoxyuridine_5'triphosphate_nucleotidohydrolase_1070492..1070722_POSITIVE 199 128 81 188 149 NC_002967:TDE0882|5end_hypothetical_protein_901449..901679_POSITIVE 196 86 43 205 161 NC_002967:TDE1020|5end_dicarboxylate_transporter,_periplasmic_dicarboxylate-binding_protein,_putative_1052593..1052823_NEGATIVE 196 90 46 70 21 NC_002967:TDE0772|5end_50S_ribosomal_protein_L22_809084..809314_POSITIVE 195 46 5 225 183 NC_002967:TDE0242|5end_hypothetical_protein_276024..276254_NEGATIVE 193 110 61 45 7 NC_002967:TDE2659|5end_GAF_domain/HD_domain_protein_2695850..2696080_POSITIVE 191 60 19 71 32 NC_002967:TDE1033|5end_polyA_polymerase_family_protein_1061069..1061299_POSITIVE 190 60 18 101 55 NC_002967:TDE2760|5end_flagellar_biosynthesis_protein_2815881..2816111_NEGATIVE 190 76 31 117 64 NC_002967:TDE2655|5end_hypothetical_protein_2693070..2693300_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 113 71 139 97 NC_002967:TDE0381|3end_hypothetical_protein_434461..434611_POSITIVE 249 108 74 138 104 NC_002967:TDE1878|3end_hydrolase,_haloacid_dehalogenase-like_family_1899960..1900110_NEGATIVE 242 90 44 136 92 NC_002967:TDE1199|3end_cell_division_protein_FtsL,_putative_1231705..1231855_POSITIVE 239 69 21 110 66 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE 239 124 87 138 96 NC_002967:TDE0803|3end_hypothetical_protein_826875..827025_POSITIVE 217 90 44 121 69 NC_002967:TDE2486|3end_hypothetical_protein_2509871..2510021_POSITIVE 212 115 77 73 29 NC_002967:TDE0636|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_670532..670682_NEGATIVE 211 101 64 99 53 NC_002967:TDE1732|3end_hypothetical_protein_1787946..1788096_POSITIVE 209 116 73 48 1 NC_002967:TDE2572|3end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_2598145..2598295_NEGATIVE 199 49 7 60 19 NC_002967:TDE0967|3end_hypothetical_protein_992529..992679_POSITIVE 199 128 81 151 112 NC_002967:TDE0881|3end_ribosomal_protein_S16_901492..901642_POSITIVE 196 90 46 59 10 NC_002967:TDE0771|3end_ribosomal_protein_S19_809153..809303_POSITIVE 193 117 71 117 63 NC_002967:TDE0998|3end_hypothetical_protein_1025494..1025644_POSITIVE 192 120 102 20 1 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 190 60 18 104 58 NC_002967:TDE2761|3end_hypothetical_protein_2815878..2816028_NEGATIVE 190 79 31 151 105 NC_002967:TDE2150|3end_hypothetical_protein_2187254..2187404_NEGATIVE 188 62 31 74 43 NC_002967:TDE1625|3end_glycine_cleavage_system_P_protein,_subunit_1_1673519..1673669_NEGATIVE 187 117 72 144 114 NC_002967:TDE0971|3end_arginyl-tRNA_synthetase_997031..997181_POSITIVE 186 91 53 131 91 NC_002967:TDE2087|3end_translation_initiation_factor_IF-1_2115468..2115618_NEGATIVE 186 55 20 137 106 NC_002967:TDE1070|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1097700..1097850_NEGATIVE