Origin IGS: aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatattttttttatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attaacccccttaagataagccgatatttaattttactcttattccaaaataaaatcaaggtcgaaaatgtttattcaaatccaagttttttatacacaattcatgatatccctcaccgttttcaaaagaaaagggggtgaaaatccgaggtcaaataaaaaaaatattctcttacaaaattgctgcaagtgtgatataatacaaccaatgaggaaacagtt Mask Tandem Repeat Region ================================================ aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatattttttttatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat Find is-nt database================================================ Query_seq: TDE0948:TDE0949|TDE0948:TDE0949:hypothetical protein:enolase:<-->:971928..972149 222 aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatattttttttatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0948:TDE0949|TDE0948:TDE0949:hypothetical protein:enolase:<-->:971928..972149 222 aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatattttttttatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0948:TDE0949|TDE0948:TDE0949:hypothetical protein:enolase:<-->:971928..972149 222 aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatattttttttatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatattttttttatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 13 End: 129 ............ M G C I I S H L Q Q F C K R I F F L F D L G F S P P F L L K T V R D I M N C V ............................................................................................. Protein_Len: 46 Strand: - Start: 85 End: 222 .................................................................................... G R K K Q F R H P I D H I T Y L F S P N S Y V N E V K I K N Q F L L L I L Y R S I K L P N M Protein_Len: 57 Strand: - Start: 3 End: 173 .. Q K R M P Q I I D C K C C N Q L L I N K K N S R P N E G G K R K F V T L S I M F Q T Y F V Q I Q I F M K S R S K M ................................................. aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatattttttttatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat 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: 83 Start: 22 End: 51 .....................CTTACAAAATTGCTGCAAGTGTGATATAAT........................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 163 End: 192 ..................................................................................................................................................................CTTGATTTTATTTTGGAATAAGAGTAAAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatattttttttatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0948:TDE0949|TDE0948:TDE0949:hypothetical protein:enolase:<-->:971928..972149 222 aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatattttttttatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat Intra-Species Hit: Count: 1 Min: 1 Max: 222 Len: 222 Subject: NC_002967_TDE0948_TDE0949|hypothetical protein:enolase|NEGATIVE:POSITIVE|[971928,972149]|222 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 222 Query Start:1 Query End:222 Subject Strand: POSITIVE Subject Start: 1 Subject End: 222 aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatannnnnnnnatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat aactgtttcctcattggttgtattatatcacacttgcagcaattttgtaagagaatattttttttatttgacctcggattttcacccccttttcttttgaaaacggtgagggatatcatgaattgtgtataaaaaacttggatttgaataaacattttcgaccttgattttattttggaataagagtaaaattaaatatcggcttatcttaagggggttaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUGUUUCCUCAUUGGUUGUAUUAUAUCACACUUGCAGCAAUUUUGUAAGAGAAUAUUUUUUUUAUUUGACCUCGGAUUUUCACCCCCUUUUCUUUUGAAAACGGUGAGGGAUAUCAUGAAUUGUGUAUAAAAAACUUGGAUUUGAAUAAACAUUUUCGACCUUGAUUUUAUUUUGGAAUAAGAGUAAAAUUAAAUAUCGGCUUAUCUUAAGGGGGUUAAU .......(((......((((((............))))))..((..((((((((.....))))))))..))....))).....(((((((((((....))))..((((((.((((......................(((((..((......))..)))))..(((((((((((((......))))))))))))).))))..))))))...))))))).... (-42.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAACCCCCUUAAGAUAAGCCGAUAUUUAAUUUUACUCUUAUUCCAAAAUAAAAUCAAGGUCGAAAAUGUUUAUUCAAAUCCAAGUUUUUUAUACACAAUUCAUGAUAUCCCUCACCGUUUUCAAAAGAAAAGGGGGUGAAAAUCCGAGGUCAAAUAAAAAAAAUAUUCUCUUACAAAAUUGCUGCAAGUGUGAUAUAAUACAACCAAUGAGGAAACAGUU ....((((((((.......(((...((((.(((((...........))))).))))...))).(((((((...............((.......))........(((......))).))))))).......))))))))........((((.................))))..........((((...((((......))))..((.....))...)))). (-29.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 907 120 71 211 162 NC_002967:TDE0948|5end_hypothetical_protein_971837..972067_NEGATIVE 423 53 11 144 102 NC_002967:TDE0975|5end_hypothetical_protein_998921..999151_POSITIVE 407 50 3 141 94 NC_002967:TDE2678|5end_alpha-amylase_family_protein_2719390..2719620_NEGATIVE 382 41 7 131 97 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 295 50 3 139 96 NC_002967:TDE0530|5end_hypothetical_protein_574363..574593_POSITIVE 278 103 72 42 8 NC_002967:TDE1659|5end_alanyl-tRNA_synthetase_1710633..1710863_NEGATIVE 266 117 73 92 42 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 256 125 88 69 33 NC_002967:TDE0462|5end_metallo-beta-lactamase_family_protein_516987..517217_NEGATIVE 255 55 11 141 95 NC_002967:TDE1936|5end_hypothetical_protein_1953086..1953316_POSITIVE 255 55 11 49 3 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 247 112 73 207 166 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 242 113 71 75 35 NC_002967:TDE0760|5end_hypothetical_protein_799436..799666_POSITIVE 242 107 66 74 32 NC_002967:TDE0152|5end_amino_acid_permease_family_protein_174477..174707_NEGATIVE 241 219 173 225 181 NC_002967:TDE1975|5end_hypothetical_protein_1988869..1989099_POSITIVE 240 111 73 42 7 NC_002967:TDE1446|5end_hypothetical_protein_1491970..1492200_POSITIVE 240 118 76 50 7 NC_002967:TDE0885|5end_50S_ribosomal_protein_L19_902945..903175_POSITIVE 239 119 73 123 73 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 238 77 31 154 108 NC_002967:TDE1370|5end_YjeF-related_protein_1413284..1413514_NEGATIVE 236 109 74 121 75 NC_002967:TDE1952|5end_hypothetical_protein_1969046..1969276_NEGATIVE 235 111 71 126 80 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 50 3 77 34 NC_002967:TDE0529|3end_hypothetical_protein_574381..574531_POSITIVE 275 112 85 39 6 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 275 112 85 39 6 NC_002967:TDE0724|3end_hypothetical_protein_763237..763387_POSITIVE 269 78 32 120 66 NC_002967:TDE2142|3end_methyl-accepting_chemotaxis_protein_2177987..2178137_POSITIVE 258 78 40 41 5 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 255 55 11 141 95 NC_002967:TDE1935|3end_hypothetical_protein_1953166..1953316_POSITIVE 242 112 86 59 27 NC_002967:TDE0723|3end_hypothetical_protein_761661..761811_POSITIVE 242 112 86 39 7 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE 242 112 86 39 7 NC_002967:TDE0715|3end_hypothetical_protein_750550..750700_POSITIVE 242 107 66 63 21 NC_002967:TDE0153|3end_coenzyme_A_disulfide_reductase,_putative_174488..174638_NEGATIVE 240 118 71 61 12 NC_002967:TDE1386|3end_methyl-accepting_chemotaxis_protein_1426856..1427006_POSITIVE 240 118 76 57 14 NC_002967:TDE0884|3end_tRNA_(guanine-N(1)-)-methyltransferase_903032..903182_POSITIVE 239 112 74 76 24 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 238 77 31 140 94 NC_002967:TDE1371|3end_RNB-like_family_protein_1413298..1413448_NEGATIVE 236 109 74 137 91 NC_002967:TDE1953|3end_transcriptional_regulator,_TetR_family_1969030..1969180_NEGATIVE 233 119 74 116 63 NC_002967:TDE2650|3end_transcriptional_regulator,_putative_2688666..2688816_NEGATIVE 229 125 87 81 45 NC_002967:TDE0614|3end_precorrin-4_C11-methyltransferase_648816..648966_POSITIVE 228 107 61 123 71 NC_002967:TDE0424|3end_bacteriocin-type_signal_domain_protein_479773..479923_POSITIVE 226 112 84 138 104 NC_002967:TDE2329|3end_hypothetical_protein_2366347..2366497_NEGATIVE 225 107 69 89 50 NC_002967:TDE2170|3end_hypothetical_protein_2201606..2201756_NEGATIVE