Origin IGS: aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtacataaaataaaaatatgataaaattaaaaatagattttttagcaggaatacatactgcaaaaaaaaggagatagt .........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 actatctccttttttttgcagtatgtattcctgctaaaaaatctatttttaattttatcatatttttattttatgtactagatgttaaaaacttacttttcttatactcttgacttttatcccttttattgatataatccacaatctttaatgtgtattgtccttaacaggattgtattgaaatctttgagcggggtttcccgctctataatataaggagtctagttt Mask Tandem Repeat Region ================================================ aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtacataaaataaaaatatgataaaattaaaaatagattttttagcaggaatacatactgcaaaaaaaaggagatagt Find is-nt database================================================ Query_seq: TDE2400:TDE2401|TDE2400:TDE2401:50S ribosomal protein L34:hypothetical protein:<-->:2426418..2426645 228 aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtacataaaataaaaatatgataaaattaaaaatagattttttagcaggaatacatactgcaaaaaaaaggagatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2400:TDE2401|TDE2400:TDE2401:50S ribosomal protein L34:hypothetical protein:<-->:2426418..2426645 228 aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtacataaaataaaaatatgataaaattaaaaatagattttttagcaggaatacatactgcaaaaaaaaggagatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2400:TDE2401|TDE2400:TDE2401:50S ribosomal protein L34:hypothetical protein:<-->:2426418..2426645 228 aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtacataaaataaaaatatgataaaattaaaaatagattttttagcaggaatacatactgcaaaaaaaaggagatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtacataaaataaaaatatgataaaattaaaaatagattttttagcaggaatacatactgcaaaaaaaaggagatagt Predict ORF larger than 30AA ================================================ aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtacataaaataaaaatatgataaaattaaaaatagattttttagcaggaatacatactgcaaaaaaaaggagatagt 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: 92 Start: 91 End: 120 ..........................................................................................CTTGACTTTTATCCCTTTTATTGATATAAT............................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtacataaaataaaaatatgataaaattaaaaatagattttttagcaggaatacatactgcaaaaaaaaggagatagt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -12.7 Tail_Score: -2.8547 Start: 23 End: 40 Full_Region: tgtattgaaatcttt gagcggg gttt cccgctc tataatataaggagt ......................gagcggggtttcccgctc............................................................................................................................................................................................ TransTerm Strand: - Conf: 77 HP_score: -9.5 Tail_Score: -2.97747 Start: 25 End: 38 Full_Region: tattgaaatctttga gcggg gttt cccgc tctataatataagga ........................gcggggtttcccgc.............................................................................................................................................................................................. Find igs database================================================ Query_seq: TDE2400:TDE2401|TDE2400:TDE2401:50S ribosomal protein L34:hypothetical protein:<-->:2426418..2426645 228 aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtacataaaataaaaatatgataaaattaaaaatagattttttagcaggaatacatactgcaaaaaaaaggagatagt Intra-Species Hit: Count: 1 Min: 1 Max: 154 Len: 154 Subject: NC_002967_TDE2400_TDE2401|50S ribosomal protein L34:hypothetical protein|NEGATIVE:POSITIVE|[2426418,2426645]|228 HSP 1 e-value: 3.0E-82 bit: 305.0 Len: 154 Query Start:1 Query End:154 Subject Strand: POSITIVE Subject Start: 1 Subject End: 154 aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtac.......................................................................... aaactagactccttatattatagagcgggaaaccccgctcaaagatttcaatacaatcctgttaaggacaatacacattaaagattgtggattatatcaataaaagggataaaagtcaagagtataagaaaagtaagtttttaacatctagtac.......................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUAGACUCCUUAUAUUAUAGAGCGGGAAACCCCGCUCAAAGAUUUCAAUACAAUCCUGUUAAGGACAAUACACAUUAAAGAUUGUGGAUUAUAUCAAUAAAAGGGAUAAAAGUCAAGAGUAUAAGAAAAGUAAGUUUUUAACAUCUAGUAC ..((((((...((((((((...(((((((....)))))))....((..(.......((((....)))).....((((........))))................)..))..........))))))))........((.....)).)))))).. (-35.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUACUAGAUGUUAAAAACUUACUUUUCUUAUACUCUUGACUUUUAUCCCUUUUAUUGAUAUAAUCCACAAUCUUUAAUGUGUAUUGUCCUUAACAGGAUUGUAUUGAAAUCUUUGAGCGGGGUUUCCCGCUCUAUAAUAUAAGGAGUCUAGUUU ..(((((((...............((((((((......................(..(((((((((((((((........).)))))........)))))))))..).......(((((((....))))))).....))))))))))))))).. (-35.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 922 70 21 161 112 NC_002967:TDE2400|5end_50S_ribosomal_protein_L34_2426327..2426557_NEGATIVE 308 58 22 229 190 NC_002967:TDE2007|5end_ABC_transporter,_ATP-binding/permease_protein_2026819..2027049_POSITIVE 290 69 23 177 128 NC_002967:TDE0723|5end_hypothetical_protein_760304..760534_POSITIVE 285 68 25 67 18 NC_002967:TDE0593|5end_internalin-related_protein_633936..634166_NEGATIVE 283 60 22 166 132 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 274 37 9 136 102 NC_002967:TDE1140|5end_hypothetical_protein_1169845..1170075_NEGATIVE 271 67 24 140 93 NC_002967:TDE1638|5end_dephospho-CoA_kinase,_putative_1688882..1689112_POSITIVE 257 50 9 230 191 NC_002967:TDE1144|5end_hypothetical_protein_1182855..1183085_NEGATIVE 252 67 23 202 162 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 242 52 26 34 1 NC_002967:TDE0670|5end_ATP-dependent_protease_La_707938..708168_POSITIVE 240 63 26 138 102 NC_002967:TDE0881|5end_ribosomal_protein_S16_901167..901397_POSITIVE 238 68 22 188 145 NC_002967:TDE1613|5end_hypothetical_protein_1661625..1661855_POSITIVE 237 62 24 175 122 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 231 41 10 116 81 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 231 69 23 110 50 NC_002967:TDE1971|5end_DNA_polymerase_III_domain_protein_1987030..1987260_NEGATIVE 231 66 24 95 50 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 230 50 5 90 40 NC_002967:TDE1919|5end_hypothetical_protein_1939890..1940120_NEGATIVE 229 70 26 110 59 NC_002967:TDE1629|5end_dihydrolipoamide_dehydrogenase_1678514..1678744_NEGATIVE 226 38 10 139 109 NC_002967:TDE1106|5end_translation_initiation_factor_IF-2_1140882..1141112_NEGATIVE 226 40 1 55 11 NC_002967:TDE0612|5end_hypothetical_protein_647471..647701_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 130 86 83 33 NC_002967:TDE2750|3end_GTP-binding_protein_HflX,_truncation_2807288..2807438_POSITIVE 283 60 22 92 58 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 274 37 9 121 87 NC_002967:TDE1141|3end_tail_fiber_domain_protein_1169860..1170010_NEGATIVE 271 67 24 140 93 NC_002967:TDE1637|3end_DNA_polymerase_I_1688962..1689112_POSITIVE 264 69 22 66 25 NC_002967:TDE1062|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1090387..1090537_POSITIVE 247 55 22 55 15 NC_002967:TDE2117|3end_hypothetical_protein_2149175..2149325_POSITIVE 235 58 20 92 48 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 231 41 10 119 84 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 231 66 24 89 44 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 230 50 5 62 12 NC_002967:TDE1920|3end_lipoprotein,_putative_1939918..1940068_NEGATIVE 226 38 22 147 130 NC_002967:TDE1612|3end_phosphoribosyl_transferase_domain_protein_1661690..1661840_POSITIVE 226 38 10 131 101 NC_002967:TDE1107|3end_transcription_elongation_factor_NusA_1140890..1141040_NEGATIVE 223 56 23 57 19 NC_002967:TDE1540|3end_hypothetical_protein_1584948..1585098_POSITIVE 220 69 22 75 27 NC_002967:TDE1513|3end_hypothetical_protein_1560698..1560848_POSITIVE 219 50 8 130 93 NC_002967:TDE1454|3end_sugar_transporter_1502882..1503032_POSITIVE 218 70 23 48 5 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE 216 49 21 136 111 NC_002967:TDE2237|3end_hypothetical_protein_2276298..2276448_NEGATIVE 215 67 22 89 41 NC_002967:TDE2762|3end_flagellar_motor_switch_protein_FliY_2816563..2816713_NEGATIVE 213 49 2 61 7 NC_002967:TDE2558|3end_ABC_transporter,_ATP-binding/permease_protein_2583729..2583879_NEGATIVE 212 39 20 23 1 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE