Origin IGS: gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattaaaaaaaatcgttatcgctttctaattattcaaggcagaaaagatctatagaaaaaaatcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 atattacctcttatattaaaatccatgatagcttttttgttgcggaatttcaagataccatatgattataagatttttttctatagatcttttctgccttgaataattagaaagcgataacgattttttttaatgcccttttaagatatggcgagattctttcaaaggagcttatagaatacaccaaggccattgttcataatcttatatcccgcttctttatcgaaaactgggaaccgaaagaatttatagagcactttcaaaaacaaataatgtggatgaagaacgggcttaagagcagggaattaacttc Mask Tandem Repeat Region ================================================ gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattaaaaaaaatcgttatcgctttctaattattcaaggcagaaaagatctatagaaaaaaatcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat Find is-nt database================================================ Query_seq: TDE2775:TDE2776|TDE2775:TDE2776:lipoprotein, putative:proline iminopeptidase:->->:2827191..2827503 313 gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattaaaaaaaatcgttatcgctttctaattattcaaggcagaaaagatctatagaaaaaaatcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2775:TDE2776|TDE2775:TDE2776:lipoprotein, putative:proline iminopeptidase:->->:2827191..2827503 313 gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattaaaaaaaatcgttatcgctttctaattattcaaggcagaaaagatctatagaaaaaaatcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2775:TDE2776|TDE2775:TDE2776:lipoprotein, putative:proline iminopeptidase:->->:2827191..2827503 313 gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattaaaaaaaatcgttatcgctttctaattattcaaggcagaaaagatctatagaaaaaaatcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattaaaaaaaatcgttatcgctttctaattattcaaggcagaaaagatctatagaaaaaaatcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 45 End: 149 ............................................ M F L K V L Y K F F R F P V F D K E A G Y K I M N N G L G V F Y K L L .................................................................................................................................................................... Protein_Len: 33 Strand: - Start: 215 End: 313 ...................................................................................................................................................................................................................... P L F S R Y F F I K Y D Y P I K F N R L L F A I M S K L I L P L M Protein_Len: 60 Strand: - Start: 3 End: 197 .. K L G N K M W M I Q K Q F H E I F E K P E W N E I F F R S I L N H V I A K T Y E I L E K S L I E G Y R L L A N F F I T M .................................................................................................................... gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattaaaaaaaatcgttatcgctttctaattattcaaggcagaaaagatctatagaaaaaaatcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat 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: 84 Start: 260 End: 289 ...................................................................................................................................................................................................................................................................CTTGAAATTCCGCAACAAAAAAGCTATCAT........................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattaaaaaaaatcgttatcgctttctaattattcaaggcagaaaagatctatagaaaaaaatcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2775:TDE2776|TDE2775:TDE2776:lipoprotein, putative:proline iminopeptidase:->->:2827191..2827503 313 gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattaaaaaaaatcgttatcgctttctaattattcaaggcagaaaagatctatagaaaaaaatcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat Intra-Species Hit: Count: 1 Min: 1 Max: 313 Len: 313 Subject: NC_002967_TDE2775_TDE2776|lipoprotein, putative:proline iminopeptidase|POSITIVE:POSITIVE|[2827191,2827503]|313 HSP 1 e-value: 1.0E-150 bit: 531.0 Len: 313 Query Start:1 Query End:313 Subject Strand: POSITIVE Subject Start: 1 Subject End: 313 gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattnnnnnnnntcgttatcgctttctaattattcaaggcagaaaagatctatagnnnnnnntcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat gaagttaattccctgctcttaagcccgttcttcatccacattatttgtttttgaaagtgctctataaattctttcggttcccagttttcgataaagaagcgggatataagattatgaacaatggccttggtgtattctataagctcctttgaaagaatctcgccatatcttaaaagggcattaaaaaaaatcgttatcgctttctaattattcaaggcagaaaagatctatagaaaaaaatcttataatcatatggtatcttgaaattccgcaacaaaaaagctatcatggattttaatataagaggtaatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGUUAAUUCCCUGCUCUUAAGCCCGUUCUUCAUCCACAUUAUUUGUUUUUGAAAGUGCUCUAUAAAUUCUUUCGGUUCCCAGUUUUCGAUAAAGAAGCGGGAUAUAAGAUUAUGAACAAUGGCCUUGGUGUAUUCUAUAAGCUCCUUUGAAAGAAUCUCGCCAUAUCUUAAAAGGGCAUUAAAAAAAAUCGUUAUCGCUUUCUAAUUAUUCAAGGCAGAAAAGAUCUAUAGAAAAAAAUCUUAUAAUCAUAUGGUAUCUUGAAAUUCCGCAACAAAAAAGCUAUCAUGGAUUUUAAUAUAAGAGGUAAUAU ...............((((((.........((((...(((.....)))...)))).....((((((.((..((((((...)).(((((.((((((((((.(.((((...((((......((((.((((((((.(((((..(((...)))....)))))..))))).........))).))))......))))..)))).))))))..))))).))))).))))..)).))))))........(((.((((.(((((((.(((.................))).))))))))))).)))..))))))....... (-52.43) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUACCUCUUAUAUUAAAAUCCAUGAUAGCUUUUUUGUUGCGGAAUUUCAAGAUACCAUAUGAUUAUAAGAUUUUUUUCUAUAGAUCUUUUCUGCCUUGAAUAAUUAGAAAGCGAUAACGAUUUUUUUUAAUGCCCUUUUAAGAUAUGGCGAGAUUCUUUCAAAGGAGCUUAUAGAAUACACCAAGGCCAUUGUUCAUAAUCUUAUAUCCCGCUUCUUUAUCGAAAACUGGGAACCGAAAGAAUUUAUAGAGCACUUUCAAAAACAAAUAAUGUGGAUGAAGAACGGGCUUAAGAGCAGGGAAUUAACUUC .....................(((.((..((((((((((....((((((((......(((((.((....(((((((........))))))).))...((((((..((((((((.((....))....)))))))).....)))))).))))).))))))))..))))))))))....(((((..(....)....)))))....(((((...((((.(((((((((..............(((((..((....))...)))))....(((.....))).)))))))))))))..))))).)).)))......... (-58.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 170 121 82 26 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 314 49 9 44 1 NC_002967:TDE0524|5end_hypothetical_protein_570017..570247_POSITIVE 311 90 41 172 107 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 281 154 115 160 119 NC_002967:TDE0591|5end_acetyl-CoA_carboxylase,_biotin_carboxylase_631352..631582_NEGATIVE 280 170 121 189 136 NC_002967:TDE2154|5end_50S_ribosomal_protein_L20_2189934..2190164_NEGATIVE 275 158 118 214 169 NC_002967:TDE1262|5end_hypothetical_protein_1297332..1297562_NEGATIVE 271 58 11 200 147 NC_002967:TDE1304|5end_hypothetical_protein_1339716..1339946_POSITIVE 270 47 11 228 188 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 263 34 9 118 94 NC_002967:TDE0654|5end_peptidase,_M20/M25/M40_family_689606..689836_POSITIVE 262 114 71 62 16 NC_002967:TDE1119|5end_hypothetical_protein_1151327..1151557_POSITIVE 262 60 12 116 51 NC_002967:TDE0351|5end_L-lactate_dehydrogenase_395998..396228_NEGATIVE 260 287 241 129 77 NC_002967:TDE2717|5end_phosphatidate_cytidylyltransferase,_putative_2774547..2774777_NEGATIVE 258 60 11 206 157 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 258 291 251 157 116 NC_002967:TDE0844|5end_pyruvate_phosphate_dikinase,_putative_864886..865116_POSITIVE 257 100 51 169 124 NC_002967:TDE2354|5end_hypothetical_protein_2390395..2390625_POSITIVE 256 34 5 134 97 NC_002967:TDE0777|5end_50S_ribosomal_protein_L14_811109..811339_POSITIVE 254 42 4 122 77 NC_002967:TDE1292|5end_TldD/PmbA_family_protein_1330621..1330851_NEGATIVE 254 91 58 36 6 NC_002967:TDE1158|5end_phage_terminase,_small_subunit,_putative_1194024..1194254_NEGATIVE 252 67 26 122 83 NC_002967:TDE2095|5end_hypothetical_protein_2121749..2121979_POSITIVE 250 110 71 159 119 NC_002967:TDE1864|5end_crossover_junction_endodeoxyribonuclease_RuvC_1889108..1889338_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 102 62 125 75 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 281 154 115 149 108 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 277 164 121 151 105 NC_002967:TDE2155|3end_50S_ribosomal_protein_L35_2189965..2190115_NEGATIVE 263 34 9 106 82 NC_002967:TDE0653|3end_hypothetical_protein_689674..689824_POSITIVE 260 287 241 124 72 NC_002967:TDE2718|3end_magnesium_transporter_2774552..2774702_NEGATIVE 260 104 71 133 88 NC_002967:TDE0248|3end_hypothetical_protein_282516..282666_POSITIVE 258 291 251 146 105 NC_002967:TDE0843|3end_hypothetical_protein_864955..865105_POSITIVE 257 100 51 150 105 NC_002967:TDE2353|3end_flagellar_hook-associated_protein_2390456..2390606_POSITIVE 257 163 123 74 34 NC_002967:TDE2088|3end_C4_zinc_finger_domain_protein,_DksA/TraR_family_2116183..2116333_POSITIVE 256 34 5 115 78 NC_002967:TDE0776|3end_ribosomal_protein_S17_811170..811320_POSITIVE 254 90 45 64 17 NC_002967:TDE2482|3end_hypothetical_protein_2505822..2505972_POSITIVE 254 42 4 122 77 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 254 91 58 32 2 NC_002967:TDE1159|3end_hypothetical_protein_1194028..1194178_NEGATIVE 251 102 65 149 108 NC_002967:TDE2380|3end_hypothetical_protein_2411062..2411212_POSITIVE 250 110 71 126 86 NC_002967:TDE1865|3end_peptidase,_M16_family_1889141..1889291_NEGATIVE 247 59 14 142 86 NC_002967:TDE1864|3end_crossover_junction_endodeoxyribonuclease_RuvC_1888572..1888722_NEGATIVE 247 179 144 114 74 NC_002967:TDE0515|3end_hypothetical_protein_562770..562920_NEGATIVE 246 37 8 117 83 NC_002967:TDE0475|3end_ABC_transporter,_ATP-binding_protein_531153..531303_NEGATIVE 246 60 13 75 17 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 244 57 14 108 69 NC_002967:TDE2357|3end_iron_compound_ABC_transporter,_permease_protein_2393101..2393251_POSITIVE