Origin IGS: tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcccagtttgtagaactaacaacttaataaaaattaccacaggaacagtaaatcaaaaaaggtttactgtttttctttactcaaaattagaaagggaggaaacgagaaa Mask Tandem Repeat Region ================================================ tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat Find is-nt database================================================ Query_seq: TDE2173:TDE2174|TDE2173:TDE2174:hypothetical protein:hypothetical protein:<-<-:2203079..2203188 110 tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2173:TDE2174|TDE2173:TDE2174:hypothetical protein:hypothetical protein:<-<-:2203079..2203188 110 tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2173:TDE2174|TDE2173:TDE2174:hypothetical protein:hypothetical protein:<-<-:2203079..2203188 110 tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 3 End: 110 .. R T E E R E L K S Y L F V T F R K Q N V T G T T I K I L N N T R C V P M tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat 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================================================ tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -6.1 Tail_Score: -5.33405 Start: 41 End: 64 Full_Region: aaattaccacaggaa cagtaaatc aaaaaa ggtttactg tttttctttactcaa ........................................cagtaaatcaaaaaaggtttactg.............................................. Find igs database================================================ Query_seq: TDE2173:TDE2174|TDE2173:TDE2174:hypothetical protein:hypothetical protein:<-<-:2203079..2203188 110 tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002967_TDE2173_TDE2174|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2203079,2203188]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat tttctcgtttcctccctttctaattttgagtaaagaaaaacagtaaaccttttttgatttactgttcctgtggtaatttttattaagttgttagttctacaaactgggat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCGUUUCCUCCCUUUCUAAUUUUGAGUAAAGAAAAACAGUAAACCUUUUUUGAUUUACUGUUCCUGUGGUAAUUUUUAUUAAGUUGUUAGUUCUACAAACUGGGAU ............((((......................(((((((((.(......).)))))))))..(((((.((((..((......))..)))))))))....)))). (-19.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCCAGUUUGUAGAACUAACAACUUAAUAAAAAUUACCACAGGAACAGUAAAUCAAAAAAGGUUUACUGUUUUUCUUUACUCAAAAUUAGAAAGGGAGGAAACGAGAAA .((((.(((.(.....).)))....................((((((((((((((......))))))))))))))...................))))(....)...... (-21.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 779 110 61 201 152 NC_002967:TDE2173|5end_hypothetical_protein_2202988..2203218_NEGATIVE 279 49 1 179 137 NC_002967:TDE1222|5end_iron-dependent_transcriptional_regulator_1256709..1256939_NEGATIVE 217 65 27 140 101 NC_002967:TDE2279|5end_HD_domain_protein_2313731..2313961_POSITIVE 215 57 11 43 5 NC_002967:TDE1363|5end_nitroreductase_family_protein_1404635..1404865_NEGATIVE 214 90 42 146 94 NC_002967:TDE2700|5end_citrate_carrier_protein,_CCS_family_2744396..2744626_POSITIVE 210 98 51 75 33 NC_002967:TDE1150|5end_hypothetical_protein_1188243..1188473_NEGATIVE 210 53 12 137 98 NC_002967:TDE0832|5end_hypothetical_protein_852549..852779_POSITIVE 206 55 11 149 99 NC_002967:TDE2015|5end_lipoprotein,_putative_2037532..2037762_NEGATIVE 202 46 9 97 49 NC_002967:TDE2780|5end_hypothetical_protein_2830621..2830851_NEGATIVE 202 98 51 215 166 NC_002967:TDE1471|5end_hypothetical_protein_1518747..1518977_NEGATIVE 201 79 37 189 153 NC_002967:TDE2416|5end_hypothetical_protein_2442799..2443029_NEGATIVE 200 15 1 213 199 NC_002967:TDE0415|5end_lipoprotein,_putative_467667..467897_POSITIVE 199 75 37 53 6 NC_002967:TDE0078|5end_glycine_reductase_complex_selenoprotein_GrdB1_90076..90306_NEGATIVE 197 74 48 125 101 NC_002967:TDE0644|5end_ABC_transporter,_ATP-binding_protein_680576..680806_NEGATIVE 196 77 40 46 6 NC_002967:TDE2643|5end_oxidoreductase,_FAD-dependent_2682185..2682415_POSITIVE 196 79 49 104 64 NC_002967:TDE1469|5end_conserved_hypothetical_protein_TIGR00150_1517764..1517994_NEGATIVE 194 99 58 51 17 NC_002967:TDE1979|5end_hypothetical_protein_1991985..1992215_NEGATIVE 193 108 62 147 97 NC_002967:TDE2541|5end_hypothetical_protein_2568165..2568395_POSITIVE 192 79 31 118 62 NC_002967:TDE2652|5end_hypothetical_protein_2690135..2690365_POSITIVE 192 59 11 202 159 NC_002967:TDE2407|5end_amidophosphoribosyltransferase_2435107..2435337_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 89 46 131 76 NC_002967:TDE2261|3end_hypothetical_protein_2297915..2298065_NEGATIVE 220 47 1 151 111 NC_002967:TDE1223|3end_zinc_ABC_transporter,_permease_protein_1256735..1256885_NEGATIVE 214 90 42 133 81 NC_002967:TDE2699|3end_antigen,_putative_2744463..2744613_POSITIVE 212 97 56 131 96 NC_002967:TDE0880|3end_nicotinate-nucleotide-dimethylbenzimidazole_phosphoribosyltransferase_901136..901286_POSITIVE 210 98 51 50 8 NC_002967:TDE1151|3end_hypothetical_protein_1188268..1188418_NEGATIVE 208 99 56 71 19 NC_002967:TDE0022|3end_hypothetical_protein_28521..28671_POSITIVE 205 70 27 129 79 NC_002967:TDE0198|3end_hypothetical_protein_234224..234374_POSITIVE 202 46 9 79 31 NC_002967:TDE2781|3end_ABC_transporter,_ATP-binding/permease_protein_2830639..2830789_NEGATIVE 200 15 1 108 94 NC_002967:TDE0414|3end_hypothetical_protein_467642..467792_POSITIVE 197 74 48 132 108 NC_002967:TDE0645|3end_hypothetical_protein_680569..680719_NEGATIVE 196 79 49 102 62 NC_002967:TDE1470|3end_hypothetical_protein_1517766..1517916_NEGATIVE 194 99 58 76 42 NC_002967:TDE1980|3end_hypothetical_protein_1991960..1992110_NEGATIVE 192 79 31 121 65 NC_002967:TDE2651|3end_ABC_transporter,_ATP-binding_protein_2690218..2690368_POSITIVE 192 59 11 92 49 NC_002967:TDE2408|3end_hypothetical_protein_2435217..2435367_NEGATIVE 192 43 5 43 3 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 189 50 9 133 96 NC_002967:TDE0712|3end_hypothetical_protein_746181..746331_NEGATIVE 185 88 65 128 103 NC_002967:TDE2090|3end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2117563..2117713_NEGATIVE 185 21 1 113 95 NC_002967:TDE1526|3end_hypothetical_protein_1570887..1571037_POSITIVE 185 28 1 99 74 NC_002967:TDE1243|3end_hemolysin_C_1275891..1276041_POSITIVE 185 105 62 91 46 NC_002967:TDE0357|3end_hypothetical_protein_400108..400258_NEGATIVE