Origin IGS: attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt .........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 aaagtgtgaaggactactcttcattataatgaaggatgcacatccgtgtacaccgcggctgatatagactatgctctacgactggcgaaggttataatctacatccggcatagattaggatctttgtctgccggtttatataagacagtttatatcccttttgaattgatagtgaaataat Mask Tandem Repeat Region ================================================ attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt Find is-nt database================================================ Query_seq: TDE0546:TDE0547|TDE0546:TDE0547:hypothetical protein:hypothetical protein:-><-:585880..586060 181 attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0546:TDE0547|TDE0546:TDE0547:hypothetical protein:hypothetical protein:-><-:585880..586060 181 attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0546:TDE0547|TDE0546:TDE0547:hypothetical protein:hypothetical protein:-><-:585880..586060 181 attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: - Start: 5 End: 136 .... * K V I L E F P I Y V T K Y L G A S L S G L R H R I Y I I V K A L R L A Y D I D A A T Y M ............................................. attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt 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================================================ attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0546:TDE0547|TDE0546:TDE0547:hypothetical protein:hypothetical protein:-><-:585880..586060 181 attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_002967_TDE0546_TDE0547|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[585880,586060]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt attatttcactatcaattcaaaagggatataaactgtcttatataaaccggcagacaaagatcctaatctatgccggatgtagattataaccttcgccagtcgtagagcatagtctatatcagccgcggtgtacacggatgtgcatccttcattataatgaagagtagtccttcacacttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUUCACUAUCAAUUCAAAAGGGAUAUAAACUGUCUUAUAUAAACCGGCAGACAAAGAUCCUAAUCUAUGCCGGAUGUAGAUUAUAACCUUCGCCAGUCGUAGAGCAUAGUCUAUAUCAGCCGCGGUGUACACGGAUGUGCAUCCUUCAUUAUAAUGAAGAGUAGUCCUUCACACUUU ........(((((...((((...((((((.....)))))).(((((..((((.(.((.((((....)))).)).).((((((((((((...(((..(.....)..))).)))))))))))).)))).((((((((....)))))))).....))))).))))..)))))............ (-40.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUGUGAAGGACUACUCUUCAUUAUAAUGAAGGAUGCACAUCCGUGUACACCGCGGCUGAUAUAGACUAUGCUCUACGACUGGCGAAGGUUAUAAUCUACAUCCGGCAUAGAUUAGGAUCUUUGUCUGCCGGUUUAUAUAAGACAGUUUAUAUCCCUUUUGAAUUGAUAGUGAAAUAAU ...(((((..(((.((..((((((....))))))..))....)))...)))))...((..((((((((((...((....((((((((((((((.(((((((.........))))))).)))))))....)))))))......))..))))))))))))....................... (-43.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 144 102 61 1 NC_002967:TDE0978|5end_hypothetical_protein_1001868..1002098_POSITIVE 343 138 91 186 126 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 341 139 91 54 6 NC_002967:TDE0189|5end_hypothetical_protein_226460..226690_NEGATIVE 313 138 92 171 124 NC_002967:TDE1516|5end_ABC_transporter,_ATP-binding_protein,_putative_1563127..1563357_POSITIVE 306 131 92 62 22 NC_002967:TDE0464|5end_NifU_domain_protein_518175..518405_NEGATIVE 305 150 102 86 29 NC_002967:TDE2009|5end_hypothetical_protein_2030382..2030612_POSITIVE 304 139 91 83 27 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 304 135 95 51 8 NC_002967:TDE0353|5end_lipase/acylhydrolase,_GDSL_family_398338..398568_NEGATIVE 300 110 63 219 169 NC_002967:TDE0350|5end_MATE_efflux_family_protein_393572..393802_POSITIVE 299 149 104 44 5 NC_002967:TDE2425|5end_50S_ribosomal_protein_L11_2455150..2455380_NEGATIVE 298 143 102 185 152 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 297 138 91 221 165 NC_002967:TDE1350|5end_rod_shape-determining_protein_MreC_1390327..1390557_POSITIVE 296 131 91 66 11 NC_002967:TDE2572|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_2598738..2598968_NEGATIVE 294 138 92 130 79 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 293 159 123 82 45 NC_002967:TDE0096|5end_NADH_oxidase_112723..112953_POSITIVE 290 138 92 122 79 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 289 152 112 83 37 NC_002967:TDE1544|5end_mannosyltransferase,_putative_1587154..1587384_POSITIVE 289 105 66 167 125 NC_002967:TDE1086|5end_conserved_hypothetical_protein_TIGR00255_1117786..1118016_POSITIVE 285 170 121 203 152 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 285 129 87 124 67 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 130 82 134 88 NC_002967:TDE1844|3end_DNA_integrase_1873197..1873347_NEGATIVE 313 138 92 143 96 NC_002967:TDE1515|3end_permease_domain_protein_1563179..1563329_POSITIVE 297 129 90 42 8 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 295 130 82 77 31 NC_002967:TDE0272|3end_hypothetical_protein_302256..302406_NEGATIVE 293 148 114 126 90 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 293 150 104 76 34 NC_002967:TDE0578|3end_hypothetical_protein_609677..609827_POSITIVE 289 105 66 151 109 NC_002967:TDE1085|3end_UDP-N-acetylmuramate--L-alanine_ligase_1117850..1118000_POSITIVE 288 129 92 134 97 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 285 170 121 92 41 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 284 132 95 36 2 NC_002967:TDE0760|3end_hypothetical_protein_800013..800163_POSITIVE 283 127 93 143 107 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 283 129 92 134 97 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 280 164 123 67 22 NC_002967:TDE0452|3end_hypothetical_protein_509949..510099_NEGATIVE 278 139 95 72 4 NC_002967:TDE0847|3end_hypothetical_protein_871342..871492_POSITIVE 277 138 96 97 49 NC_002967:TDE2199|3end_racemase,_Asp/Glu/Hydantoin_family_2236476..2236626_NEGATIVE 274 127 87 146 97 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 273 88 45 54 20 NC_002967:TDE2248|3end_HesA/MoeB/ThiF_family_protein_2286756..2286906_NEGATIVE 271 138 91 128 90 NC_002967:TDE1079|3end_DNA-binding_protein/PTS_system,_IIA_component_1111805..1111955_POSITIVE 270 138 91 146 88 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 270 108 62 47 6 NC_002967:TDE0500|3end_hypothetical_protein_553564..553714_NEGATIVE