Origin IGS: attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatgaacggtgagaaagtataaaataaaatagtttattgacatgaaaactaaattatcttatatttgtattataaatggtacaaattatactttaaagatggattatccaaaaggaaaat Mask Tandem Repeat Region ================================================ attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc Find is-nt database================================================ Query_seq: TDE0700:TDE0701|TDE0700:TDE0701:hypothetical protein:hypothetical protein:<-<-:736489..736608 120 attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0700:TDE0701|TDE0700:TDE0701:hypothetical protein:hypothetical protein:<-<-:736489..736608 120 attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0700:TDE0701|TDE0700:TDE0701:hypothetical protein:hypothetical protein:<-<-:736489..736608 120 attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc Predict ORF larger than 30AA ================================================ attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc 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: 88 Start: 56 End: 85 .......................................................ATTGACATGAAAACTAAATTATCTTATATT................................... PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 23 End: 52 ......................CTTTAAAGTATAATTTGTACCATTTATAAT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0700:TDE0701|TDE0700:TDE0701:hypothetical protein:hypothetical protein:<-<-:736489..736608 120 attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: NC_002967_TDE0700_TDE0701|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[736489,736608]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc attttccttttggataatccatctttaaagtataatttgtaccatttataatacaaatataagataatttagttttcatgtcaataaactattttattttatactttctcaccgttcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCCUUUUGGAUAAUCCAUCUUUAAAGUAUAAUUUGUACCAUUUAUAAUACAAAUAUAAGAUAAUUUAGUUUUCAUGUCAAUAAACUAUUUUAUUUUAUACUUUCUCACCGUUCAUC ....(((....)))............((((((..(((((((..........))))))).((((((((..((((((..........))))))..))))))))))))))............. (-15.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAACGGUGAGAAAGUAUAAAAUAAAAUAGUUUAUUGACAUGAAAACUAAAUUAUCUUAUAUUUGUAUUAUAAAUGGUACAAAUUAUACUUUAAAGAUGGAUUAUCCAAAAGGAAAAU (((((.(.((...(((((((((.((((.((((((((((........)).)))))))).))))..((((((((....)))))))).)))))))))....)).).)))))............ (-19.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 706 120 71 211 162 NC_002967:TDE0700|5end_hypothetical_protein_736398..736628_NEGATIVE 329 50 1 133 70 NC_002967:TDE0703|5end_transcriptional_regulator,_AbrB_family_738190..738420_NEGATIVE 261 114 73 221 183 NC_002967:TDE0383|5end_hypothetical_protein_434609..434839_POSITIVE 236 47 4 137 98 NC_002967:TDE1561|5end_hypothetical_protein_1614834..1615064_POSITIVE 231 117 71 154 104 NC_002967:TDE2241|5end_glycosyl_transferase,_group_2_family_protein_2279651..2279881_NEGATIVE 224 117 71 111 69 NC_002967:TDE0818|5end_ABC_transporter,_ATP-binding/permease_protein_841647..841877_NEGATIVE 204 114 71 201 159 NC_002967:TDE1252|5end_lipoprotein,_putative_1286400..1286630_POSITIVE 201 119 72 231 187 NC_002967:TDE1174|5end_hypothetical_protein_1203400..1203630_NEGATIVE 199 114 72 186 142 NC_002967:TDE2739|5end_hypothetical_protein_2794673..2794903_POSITIVE 183 80 36 229 183 NC_002967:TDE0517|5end_hypothetical_protein_564605..564835_NEGATIVE 183 120 73 126 78 NC_002967:TDE0154|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_178286..178516_NEGATIVE 182 43 2 174 118 NC_002967:TDE1947|5end_ABC_transporter,_permease_protein_1963449..1963679_NEGATIVE 181 120 102 155 140 NC_002967:TDE2630|5end_peptide_ABC_transporter,_permease_protein,_putative_2670879..2671109_POSITIVE 181 114 72 123 79 NC_002967:TDE0783|5end_ribosomal_protein_L18_813520..813750_POSITIVE 178 115 96 68 49 NC_002967:TDE0967|5end_hypothetical_protein_992201..992431_POSITIVE 172 40 4 140 105 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 172 47 1 135 95 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 172 49 6 221 179 NC_002967:TDE1166|5end_hypothetical_protein_1198717..1198947_NEGATIVE 172 47 3 149 98 NC_002967:TDE0521|5end_carboxylesterase_family_protein_568252..568482_NEGATIVE 171 50 2 92 42 NC_002967:TDE1852|5end_ABC_transporter,_ATP-binding_protein_1881866..1882096_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 236 47 4 133 94 NC_002967:TDE1560|3end_YD_repeat_protein_1614910..1615060_POSITIVE 224 117 71 109 67 NC_002967:TDE0819|3end_ABC_transporter,_ATP-binding/permease_protein_841649..841799_NEGATIVE 201 119 72 114 70 NC_002967:TDE1175|3end_chaperonin_GroEL_1203517..1203667_NEGATIVE 187 37 1 71 34 NC_002967:TDE0215|3end_hypothetical_protein_251263..251413_NEGATIVE 183 80 36 131 85 NC_002967:TDE0518|3end_hypothetical_protein_564703..564853_NEGATIVE 183 119 71 124 78 NC_002967:TDE0418|3end_lipoprotein,_putative_470893..471043_POSITIVE 183 120 73 129 81 NC_002967:TDE0155|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_178283..178433_NEGATIVE 181 114 72 112 68 NC_002967:TDE0782|3end_50S_ribosomal_protein_L6_813589..813739_POSITIVE 179 40 7 134 105 NC_002967:TDE0527|3end_hypothetical_protein_573161..573311_POSITIVE 175 111 72 151 116 NC_002967:TDE0749|3end_cobalamin_biosynthesis_protein_CobN,_putative_784473..784623_NEGATIVE 172 40 4 45 10 NC_002967:TDE1891|3end_hypothetical_protein_1912050..1912200_POSITIVE 172 47 1 42 2 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 170 100 58 123 80 NC_002967:TDE1951|3end_ribonuclease_Z_1967403..1967553_NEGATIVE 169 120 88 105 76 NC_002967:TDE1695|3end_CoA-substrate-specific_enzyme_activase_domain_protein_1749498..1749648_NEGATIVE 169 58 13 143 99 NC_002967:TDE1536|3end_TPR_domain_protein_1579944..1580094_NEGATIVE 167 49 2 132 86 NC_002967:TDE0800|3end_acetyltransferase,_GNAT_family_823454..823604_NEGATIVE 167 118 73 109 66 NC_002967:TDE0432|3end_TPR_domain_protein,_truncation_487720..487870_NEGATIVE 163 120 72 95 38 NC_002967:TDE1978|3end_hypothetical_protein_1991501..1991651_NEGATIVE 163 118 89 107 65 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 162 110 68 106 57 NC_002967:TDE1397|3end_flagellar_synthesis_regulator_FleN,_putative_1437260..1437410_POSITIVE