Origin IGS: atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag .........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 ctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacaaagggtattaaagccgactgcaaccaccttatgagaacaacatacccctatgcttgcgtcggggttgttgatttttctataaaatactgttatttctttttataaaatacttgtaaattacctcaattgttgatatattgtattttgtaaattttggttgactcatagtaaggagttttgat Mask Tandem Repeat Region ================================================ atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag Find is-nt database================================================ Query_seq: TDE2498:TDE2499|TDE2498:TDE2499:metallo-beta-lactamase family protein:hypothetical protein:<-<-:2523052..2523280 229 atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2498:TDE2499|TDE2498:TDE2499:metallo-beta-lactamase family protein:hypothetical protein:<-<-:2523052..2523280 229 atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2498:TDE2499|TDE2498:TDE2499:metallo-beta-lactamase family protein:hypothetical protein:<-<-:2523052..2523280 229 atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 90 End: 224 ......................................................................................... M T V F Y R K I N N P D A S I G V C C S H K V V A V G F N T L C Y D A S V G V L N P P H E * ..... Protein_Len: 32 Strand: - Start: 81 End: 176 ................................................................................ L F F Y C Y K I S F D V V G V C A Y P Y T T R M L H N C D A K M ..................................................... atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag 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: 85 Start: 44 End: 73 ...........................................CTTGTAAATTACCTCAATTGTTGATATATT............................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -4.3 Tail_Score: -4.9792 Start: 112 End: 146 Full_Region: aaccaccttatgaga acaacatacccctatg cttg cgtcggggttgttga tttttctataaaata ...............................................................................................................acaacatacccctatgcttgcgtcggggttgttga................................................................................... TransTerm Strand: - Conf: 71 HP_score: -7.8 Tail_Score: -3.58029 Start: 113 End: 145 Full_Region: accaccttatgagaa caacatacccctatg cttg cgtcggggttgttg atttttctataaaat ................................................................................................................caacatacccctatgcttgcgtcggggttgttg.................................................................................... Find igs database================================================ Query_seq: TDE2498:TDE2499|TDE2498:TDE2499:metallo-beta-lactamase family protein:hypothetical protein:<-<-:2523052..2523280 229 atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag Intra-Species Hit: Count: 2 Min: 1 Max: 229 Len: 229 Subject: NC_002967_TDE2498_TDE2499|metallo-beta-lactamase family protein:hypothetical protein|NEGATIVE:NEGATIVE|[2523052,2523280]|229 HSP 1 e-value: 1.0E-127 bit: 454.0 Len: 229 Query Start:1 Query End:229 Subject Strand: POSITIVE Subject Start: 1 Subject End: 229 atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag atcaaaactccttactatgagtcaaccaaaatttacaaaatacaatatatcaacaattgaggtaatttacaagtattttataaaaagaaataacagtattttatagaaaaatcaacaaccccgacgcaagcataggggtatgttgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag Subject: NC_002967_TDE0333_TDE0334|MATE efflux family protein:hypothetical protein|POSITIVE:NEGATIVE|[373144,373385]|242 HSP 1 e-value: 3.0E-39 bit: 163.0 Len: 86 Query Start:144 Query End:229 Subject Strand: NEGATIVE Subject Start: 25 Subject End: 110 ...............................................................................................................................................tgttctcataaggtggttgcagtcggctttaataccctttgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag ...............................................................................................................................................tgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag HSP 2 e-value: 5.0E-7 bit: 56.0 Len: 32 Query Start:109 Query End:140 Subject Strand: NEGATIVE Subject Start: 135 Subject End: 166 ............................................................................................................aaatcaacaaccccgacgcaagcataggggta......................................................................................... ............................................................................................................aaatcaacaaccccgacgcaagcatcggggta......................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAAACUCCUUACUAUGAGUCAACCAAAAUUUACAAAAUACAAUAUAUCAACAAUUGAGGUAAUUUACAAGUAUUUUAUAAAAAGAAAUAACAGUAUUUUAUAGAAAAAUCAACAACCCCGACGCAAGCAUAGGGGUAUGUUGUUCUCAUAAGGUGGUUGCAGUCGGCUUUAAUACCCUUUGUUACGACGCAAGCGUCGGGGUAUUAAACCCUCCGCACGAAUAAAG .((..(((((((...((((((..........((((.(((((((..(((.(((.....))).))).........((((((.......))))))...))))))).)))).....((((((((((..(....)....))))).)))))..))))))))).))))((.(..((.((((((((((.......(((((....)))))))))))))))))..).))..))...... (-55.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAUUCGUGCGGAGGGUUUAAUACCCCGACGCUUGCGUCGUAACAAAGGGUAUUAAAGCCGACUGCAACCACCUUAUGAGAACAACAUACCCCUAUGCUUGCGUCGGGGUUGUUGAUUUUUCUAUAAAAUACUGUUAUUUCUUUUUAUAAAAUACUUGUAAAUUACCUCAAUUGUUGAUAUAUUGUAUUUUGUAAAUUUUGGUUGACUCAUAGUAAGGAGUUUUGAU .........(((((.((.(((((((((((((((....))))).......)))))))))).))..)))))....((((((((((((((((.(((((.(((....))).))))))))))..)))))...........((((...((.((((((((((((..(((.((((.(......).)))).))).))))))))))))....)).)))).....))))))......... (-66.51) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 962 200 151 230 181 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 876 200 151 218 168 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 875 170 121 218 168 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 854 140 91 231 182 NC_002967:TDE2498|5end_metallo-beta-lactamase_family_protein_2522961..2523191_NEGATIVE 851 210 161 187 137 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 850 169 121 145 97 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 610 220 176 169 132 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 560 220 188 178 145 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 391 145 101 83 42 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 388 145 118 156 129 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 386 145 115 175 145 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 356 218 179 69 27 NC_002967:TDE0071|5end_peptidase,_U32_family_78602..78832_POSITIVE 334 220 189 166 125 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 331 207 161 227 178 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 326 219 182 231 194 NC_002967:TDE0237|5end_HDIG_domain_protein_271190..271420_NEGATIVE 324 210 161 60 13 NC_002967:TDE1856|5end_radical_SAM_domain_protein_1883133..1883363_POSITIVE 324 172 134 51 6 NC_002967:TDE0997|5end_glutamate_dehydrogenase_1025283..1025513_NEGATIVE 322 199 155 224 181 NC_002967:TDE2404|5end_RNA_polymerase_sigma-54_factor,_putative_2430704..2430934_NEGATIVE 317 170 126 206 158 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 316 145 101 228 186 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 975 170 121 54 5 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 963 220 171 57 8 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 858 220 174 47 1 NC_002967:TDE2140|3end_protease_II_2173083..2173233_NEGATIVE 851 210 161 117 67 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 851 220 171 139 90 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 850 169 121 75 27 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 709 220 187 34 1 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 693 220 188 50 18 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 560 220 188 41 8 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 467 220 172 63 6 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 393 205 161 74 37 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 388 145 118 88 61 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 386 145 115 135 105 NC_002967:TDE0510|3end_hypothetical_protein_560413..560563_NEGATIVE 345 200 155 46 6 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 342 220 171 105 55 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 340 149 101 64 15 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE 333 131 105 75 47 NC_002967:TDE1939|3end_hypothetical_protein_1955435..1955585_POSITIVE 326 145 101 132 91 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 324 210 161 60 13 NC_002967:TDE1855|3end_hypothetical_protein_1883213..1883363_POSITIVE 317 170 126 95 47 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE