Origin IGS: tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggataacattatgttcaaatttttaaagacagggtatatggttttataccttgccttgcagcccctttccactgcgttggaagtaggagtttcgtatgta Mask Tandem Repeat Region ================================================ tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt Find is-nt database================================================ Query_seq: TDE2552:TDE2553|TDE2552:TDE2553:ABC transporter, ATP-binding/permease protein:lysyl-tRNA synthetase:<-<-:2579035..2579136 102 tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2552:TDE2553|TDE2552:TDE2553:ABC transporter, ATP-binding/permease protein:lysyl-tRNA synthetase:<-<-:2579035..2579136 102 tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2552:TDE2553|TDE2552:TDE2553:ABC transporter, ATP-binding/permease protein:lysyl-tRNA synthetase:<-<-:2579035..2579136 102 tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 1 End: 93 V Y S V G V E L A T S L P Q L A L Y L V M Y G T K L F K F M M ......... tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt 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================================================ tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -4.9 Tail_Score: -3.63968 Start: 46 End: 73 Full_Region: GGAAAGGGGCTGCAA GGCAAGGTATA AAACCA TATACCCTGTC TTTAAAAATTTGAAC .............................................GGCAAGGTATAAAACCATATACCCTGTC............................. Find igs database================================================ Query_seq: TDE2552:TDE2553|TDE2552:TDE2553:ABC transporter, ATP-binding/permease protein:lysyl-tRNA synthetase:<-<-:2579035..2579136 102 tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: NC_002967_TDE2552_TDE2553|ABC transporter, ATP-binding/permease protein:lysyl-tRNA synthetase|NEGATIVE:NEGATIVE|[2579035,2579136]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt tacatacgaaactcctacttccaacgcagtggaaaggggctgcaaggcaaggtataaaaccatataccctgtctttaaaaatttgaacataatgttatcctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAUACGAAACUCCUACUUCCAACGCAGUGGAAAGGGGCUGCAAGGCAAGGUAUAAAACCAUAUACCCUGUCUUUAAAAAUUUGAACAUAAUGUUAUCCUU .((((......(((((..(((((......))))))))))....((((((.((((((......)))))).))))))................))))....... (-22.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGAUAACAUUAUGUUCAAAUUUUUAAAGACAGGGUAUAUGGUUUUAUACCUUGCCUUGCAGCCCCUUUCCACUGCGUUGGAAGUAGGAGUUUCGUAUGUA .......((((.(((............(((.(((((((((......))))))))).)))..(((.((((((((......)))))..))).))).))))))). (-22.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 993 50 1 141 92 NC_002967:TDE2552|5end_ABC_transporter,_ATP-binding/permease_protein_2578944..2579174_NEGATIVE 348 59 11 69 9 NC_002967:TDE2739|5end_hypothetical_protein_2794673..2794903_POSITIVE 328 65 21 103 57 NC_002967:TDE2280|5end_transglycosylase,_SLT_family_2317358..2317588_NEGATIVE 317 43 12 135 98 NC_002967:TDE0474|5end_hypothetical_protein_530740..530970_POSITIVE 300 50 7 98 46 NC_002967:TDE2494|5end_hypothetical_protein_2518497..2518727_POSITIVE 300 52 14 93 48 NC_002967:TDE1964|5end_Na/Pi_cotransporter_family_protein_1978780..1979010_NEGATIVE 300 46 5 213 166 NC_002967:TDE0756|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_796859..797089_NEGATIVE 299 76 31 108 56 NC_002967:TDE2383|5end_cobalamin_5'-phosphate_synthase_2412826..2413056_POSITIVE 298 57 12 48 1 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 297 44 5 161 128 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 294 80 31 202 157 NC_002967:TDE1743|5end_chromate_transport_protein_1798503..1798733_NEGATIVE 288 63 25 50 8 NC_002967:TDE1905|5end_hypothetical_protein_1923877..1924107_NEGATIVE 285 52 11 126 66 NC_002967:TDE1885|5end_hypothetical_protein_1906857..1907087_POSITIVE 285 55 26 167 128 NC_002967:TDE0917|5end_hypothetical_protein_935327..935557_NEGATIVE 284 67 28 194 154 NC_002967:TDE1730|5end_glycosyl_hydrolase,_family_2_1785545..1785775_NEGATIVE 283 43 4 204 168 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 282 77 31 90 23 NC_002967:TDE1245|5end_hypothetical_protein_1278894..1279124_NEGATIVE 280 44 7 50 20 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 277 48 1 115 68 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 273 52 12 229 181 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 43 12 115 78 NC_002967:TDE0473|3end_heavy_metal_translocating_P-type_ATPase_530800..530950_POSITIVE 299 76 31 111 59 NC_002967:TDE2382|3end_cobinamide_kinase/cobinamide_phosphate_guanyltransferase_2412909..2413059_POSITIVE 298 73 31 141 97 NC_002967:TDE1343|3end_trypsin_domain/PDZ_domain_protein_1382236..1382386_POSITIVE 285 48 1 80 29 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 283 43 4 72 36 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 278 76 31 65 14 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 270 50 8 143 106 NC_002967:TDE0834|3end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854291..854441_NEGATIVE 266 49 12 123 82 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 263 60 17 149 102 NC_002967:TDE2484|3end_hypothetical_protein_2506653..2506803_NEGATIVE 261 48 4 56 13 NC_002967:TDE2163|3end_hypothetical_protein_2195533..2195683_NEGATIVE 259 70 31 105 53 NC_002967:TDE1017|3end_exodeoxyribonuclease_VII,_large_subunit_1049211..1049361_POSITIVE 258 55 17 76 32 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 256 69 26 77 24 NC_002967:TDE2142|3end_methyl-accepting_chemotaxis_protein_2177987..2178137_POSITIVE 255 45 3 63 15 NC_002967:TDE2700|3end_citrate_carrier_protein,_CCS_family_2745768..2745918_POSITIVE 254 54 11 75 23 NC_002967:TDE2716|3end_HAD-superfamily_hydrolase,_subfamily_IA_2773931..2774081_POSITIVE 250 54 15 50 16 NC_002967:TDE0399|3end_zinc_carboxypeptidase_family_protein_450845..450995_POSITIVE 249 65 31 41 3 NC_002967:TDE2281|3end_LysM_domain_protein_2317420..2317570_NEGATIVE 249 76 31 151 88 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 249 48 7 105 50 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 248 48 13 131 89 NC_002967:TDE2685|3end_flagellar_synthesis_regulator_FleN_2724896..2725046_NEGATIVE