Origin IGS: tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcaaattcgactcttctctaattcaagcgggaaaaggtcgctgtaatgttctgcaattaaatcgtatacattcatagtttttccttatgatacccctgaaaaccttaagaatactacaaaagcactaaaaaagcaatgcttttaataaaaga Mask Tandem Repeat Region ================================================ tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag Find is-nt database================================================ Query_seq: TDE1602:TDE1603|TDE1602:TDE1603:hypothetical protein:ABC transporter, ATP-binding protein:<-<-:1653348..1653500 153 tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1602:TDE1603|TDE1602:TDE1603:hypothetical protein:ABC transporter, ATP-binding protein:<-<-:1653348..1653500 153 tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1602:TDE1603|TDE1602:TDE1603:hypothetical protein:ABC transporter, ATP-binding protein:<-<-:1653348..1653500 153 tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag Predict ORF larger than 30AA ================================================ tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag 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================================================ tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1602:TDE1603|TDE1602:TDE1603:hypothetical protein:ABC transporter, ATP-binding protein:<-<-:1653348..1653500 153 tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_002967_TDE1602_TDE1603|hypothetical protein:ABC transporter, ATP-binding protein|NEGATIVE:NEGATIVE|[1653348,1653500]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag tcttttattaaaagcattgcttttttagtgcttttgtagtattcttaaggttttcaggggtatcataaggaaaaactatgaatgtatacgatttaattgcagaacattacagcgaccttttcccgcttgaattagagaagagtcgaatttgag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUAUUAAAAGCAUUGCUUUUUUAGUGCUUUUGUAGUAUUCUUAAGGUUUUCAGGGGUAUCAUAAGGAAAAACUAUGAAUGUAUACGAUUUAAUUGCAGAACAUUACAGCGACCUUUUCCCGCUUGAAUUAGAGAAGAGUCGAAUUUGAG .........((((((((((......))))))))))(((((.((((...((((.......((((((((.(......))))))...))).......))))..)))).)))))..((((((((((............)))))).))))........ (-26.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAAAUUCGACUCUUCUCUAAUUCAAGCGGGAAAAGGUCGCUGUAAUGUUCUGCAAUUAAAUCGUAUACAUUCAUAGUUUUUCCUUAUGAUACCCCUGAAAACCUUAAGAAUACUACAAAAGCACUAAAAAAGCAAUGCUUUUAAUAAAAGA ........(((((.(((((..........)))))..))))).((((.((((((.........(((.......((((((.......))))))......)))........)))))).))))..........((((((...))))))......... (-20.45) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 857 130 81 221 172 NC_002967:TDE1602|5end_hypothetical_protein_1653257..1653487_NEGATIVE 749 60 11 163 114 NC_002967:TDE1607|5end_MutT/nudix_family_protein_1657531..1657761_NEGATIVE 297 127 84 105 52 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 288 42 11 225 194 NC_002967:TDE1575|5end_lipoyl_synthase_1621903..1622133_POSITIVE 288 42 11 122 91 NC_002967:TDE1574|5end_hypothetical_protein_1621800..1622030_POSITIVE 274 60 12 181 134 NC_002967:TDE1258|5end_grdX_protein_1292183..1292413_NEGATIVE 269 59 13 202 160 NC_002967:TDE1068|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1096686..1096916_NEGATIVE 263 129 85 66 19 NC_002967:TDE1112|5end_adenylate_kinase_1146918..1147148_POSITIVE 252 128 89 142 97 NC_002967:TDE1978|5end_hypothetical_protein_1991758..1991988_NEGATIVE 252 60 12 136 86 NC_002967:TDE1005|5end_hypothetical_protein_1030206..1030436_POSITIVE 251 70 36 160 122 NC_002967:TDE1179|5end_iron_compound_ABC_transporter,_permease_protein_1208906..1209136_NEGATIVE 248 78 37 206 158 NC_002967:TDE1305|5end_DNA-binding_protein_1340100..1340330_POSITIVE 248 59 11 220 168 NC_002967:TDE1213|5end_flagellar_basal_body_rod_protein_1245817..1246047_POSITIVE 245 142 114 141 117 NC_002967:TDE1070|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1098725..1098955_NEGATIVE 242 131 98 69 36 NC_002967:TDE0292|5end_hypothetical_protein_322014..322244_NEGATIVE 240 126 86 40 1 NC_002967:TDE0982|5end_dihydroorotate_dehydrogenase/oxidoreductase,_FAD-binding_1006477..1006707_POSITIVE 240 86 44 206 164 NC_002967:TDE0954|5end_branched-chain_amino_acid_ABC_transporter,_permease_protein_977924..978154_POSITIVE 236 44 4 171 125 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 236 145 108 56 14 NC_002967:TDE0909|5end_type_II_DNA_modification_methyltransferase_M.TdeIII_927166..927396_POSITIVE 235 148 110 224 190 NC_002967:TDE2408|5end_hypothetical_protein_2435387..2435617_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 127 84 70 17 NC_002967:TDE1213|3end_flagellar_basal_body_rod_protein_1246352..1246502_POSITIVE 274 60 12 118 71 NC_002967:TDE1259|3end_amino_acid_carrier_family_protein_1292246..1292396_NEGATIVE 252 128 89 145 100 NC_002967:TDE1979|3end_hypothetical_protein_1991755..1991905_NEGATIVE 251 70 36 147 109 NC_002967:TDE1180|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein_1208919..1209069_NEGATIVE 248 90 48 70 15 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 245 142 114 53 29 NC_002967:TDE1071|3end_peptide_ABC_transporter,_peptide-binding_protein_OppA_1098813..1098963_NEGATIVE 242 131 98 65 32 NC_002967:TDE0293|3end_MATE_efflux_family_protein_322018..322168_NEGATIVE 237 129 84 55 7 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 237 138 97 88 42 NC_002967:TDE1084|3end_folylpolyglutamate_synthetase,_putative_1114934..1115084_NEGATIVE 235 148 110 126 92 NC_002967:TDE2409|3end_hypothetical_protein_2435485..2435635_NEGATIVE 234 86 48 84 51 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 232 63 29 128 92 NC_002967:TDE2080|3end_cytidylate_kinase/ribosomal_protein_S1_2109049..2109199_NEGATIVE 230 140 111 28 2 NC_002967:TDE0218|3end_hypothetical_protein_253367..253517_POSITIVE 226 147 106 63 22 NC_002967:TDE1386|3end_methyl-accepting_chemotaxis_protein_1426856..1427006_POSITIVE 226 60 19 66 24 NC_002967:TDE0104|3end_3-dehydroquinate_synthase_123683..123833_NEGATIVE 225 146 111 140 107 NC_002967:TDE0339|3end_transcriptional_regulator,_TetR_family_378568..378718_POSITIVE 224 65 28 38 4 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 223 125 92 148 118 NC_002967:TDE0718|3end_hypothetical_protein_753498..753648_POSITIVE 222 53 13 89 44 NC_002967:TDE0862|3end_hypothetical_protein_884126..884276_POSITIVE 221 100 56 116 71 NC_002967:TDE0991|3end_ribosomal_protein_L28_1017874..1018024_NEGATIVE