Origin IGS: ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttatcccgaattataaaaaccagtatagcatattaggatatttaatgtaaatataaaaagccgccctaaacattaaagtttaagacggctttaagaatttactttttaataaatttataaaccttaattcggtctaaaa Mask Tandem Repeat Region ================================================ ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa Find is-nt database================================================ Query_seq: TDE0654:TDE0655|TDE0654:TDE0655:peptidase, M20/M25/M40 family:response regulator:->->:690919..691060 142 ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0654:TDE0655|TDE0654:TDE0655:peptidase, M20/M25/M40 family:response regulator:->->:690919..691060 142 ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0654:TDE0655|TDE0654:TDE0655:peptidase, M20/M25/M40 family:response regulator:->->:690919..691060 142 ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa Predict ORF larger than 30AA ================================================ ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa 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================================================ ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.8 Tail_Score: -5.20783 Start: 51 End: 80 Full_Region: AAGTAAATTCTTAAA GCCGTCTTAAAC TTTAAT GTTTAGGGCGGC TTTTTATATTTACAT ..................................................GCCGTCTTAAACTTTAATGTTTAGGGCGGC.............................................................. TransTerm Strand: - Conf: 66 HP_score: -6.4 Tail_Score: -3.65084 Start: 51 End: 80 Full_Region: atgtaaatataaaaa gccgccctaaac attaaa gtttaagacggc tttaagaatttactt ..................................................gccgccctaaacattaaagtttaagacggc.............................................................. Find igs database================================================ Query_seq: TDE0654:TDE0655|TDE0654:TDE0655:peptidase, M20/M25/M40 family:response regulator:->->:690919..691060 142 ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_002967_TDE0654_TDE0655|peptidase, M20/M25/M40 family:response regulator|POSITIVE:POSITIVE|[690919,691060]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa ttttagaccgaattaaggtttataaatttattaaaaagtaaattcttaaagccgtcttaaactttaatgtttagggcggctttttatatttacattaaatatcctaatatgctatactggtttttataattcgggataaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAGACCGAAUUAAGGUUUAUAAAUUUAUUAAAAAGUAAAUUCUUAAAGCCGUCUUAAACUUUAAUGUUUAGGGCGGCUUUUUAUAUUUACAUUAAAUAUCCUAAUAUGCUAUACUGGUUUUUAUAAUUCGGGAUAAAAA (((((..((((((((......................((((((....(((((((((((((((......)))))))))))))))....))))))..((((...((..............))..))))))))))))..))))). (-40.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAUCCCGAAUUAUAAAAACCAGUAUAGCAUAUUAGGAUAUUUAAUGUAAAUAUAAAAAGCCGCCCUAAACAUUAAAGUUUAAGACGGCUUUAAGAAUUUACUUUUUAAUAAAUUUAUAAACCUUAAUUCGGUCUAAAA .(((((..((((((((......(((((((...))))).))....((((.((((((....(((((((.(.(((((......))))).).)))))))....))))))...))))...............))))))))..))))) (-29.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 80 36 147 95 NC_002967:TDE1024|5end_conserved_hypothetical_protein_TIGR01319_1055575..1055805_POSITIVE 274 80 31 119 64 NC_002967:TDE1876|5end_glycosyl_transferase,_WecB/TagA/CpsF_family_1897679..1897909_NEGATIVE 264 85 43 224 187 NC_002967:TDE2139|5end_hypothetical_protein_2172032..2172262_POSITIVE 250 79 42 140 104 NC_002967:TDE2216|5end_galactoside_ABC_transporter,_ATP-binding_protein_2256653..2256883_NEGATIVE 240 87 45 70 18 NC_002967:TDE1895|5end_GTP-binding_protein_Era_1914963..1915193_POSITIVE 239 81 48 213 172 NC_002967:TDE1930|5end_hypothetical_protein_1948556..1948786_NEGATIVE 239 80 45 69 24 NC_002967:TDE0473|5end_heavy_metal_translocating_P-type_ATPase_528621..528851_POSITIVE 237 90 46 132 78 NC_002967:TDE1990|5end_ATP-dependent_helicase,_DinG_family_2008496..2008726_NEGATIVE 235 90 42 134 69 NC_002967:TDE2613|5end_hypothetical_protein_2655372..2655602_POSITIVE 234 82 50 146 125 NC_002967:TDE1193|5end_hypothetical_protein_1219657..1219887_NEGATIVE 234 82 50 146 125 NC_002967:TDE0579|5end_hypothetical_protein_610029..610259_NEGATIVE 233 88 44 171 122 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 229 82 48 166 132 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 224 79 50 165 127 NC_002967:TDE0469|5end_hypothetical_protein_523987..524217_NEGATIVE 220 118 74 141 102 NC_002967:TDE1356|5end_lipoprotein,_putative_1396669..1396899_NEGATIVE 220 80 43 49 12 NC_002967:TDE1279|5end_phosphoribosylformylglycinamidine_synthase_II_1315115..1315345_NEGATIVE 216 81 49 50 19 NC_002967:TDE1278|5end_conserved_hypothetical_protein_TIGR01440_1312788..1313018_NEGATIVE 215 86 53 41 1 NC_002967:TDE0763|5end_hypothetical_protein_804338..804568_NEGATIVE 214 79 51 215 187 NC_002967:TDE0860|5end_ribosomal_small_subunit_pseudouridine_synthase_A_881023..881253_POSITIVE 213 80 43 114 80 NC_002967:TDE0963|5end_DNA_polymerase_IV_985895..986125_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 83 48 43 8 NC_002967:TDE0654|3end_peptidase,_M20/M25/M40_family_690858..691008_POSITIVE 278 80 36 114 62 NC_002967:TDE1023|3end_methylaspartate_mutase_subunit_S_1055622..1055772_POSITIVE 276 79 45 115 72 NC_002967:TDE1569|3end_hypothetical_protein_1619975..1620125_POSITIVE 275 86 50 65 30 NC_002967:TDE2665|3end_inositol-5-monophosphate_dehydrogenase_2703611..2703761_POSITIVE 274 80 31 138 83 NC_002967:TDE1877|3end_conserved_hypothetical_protein_TIGR00046_1897660..1897810_NEGATIVE 255 90 50 76 40 NC_002967:TDE2666|3end_hydrolase,_carbon-nitrogen_family_2703663..2703813_NEGATIVE 248 84 50 145 105 NC_002967:TDE1624|3end_glycine_dehydrogenase_subunit_2_1672071..1672221_NEGATIVE 248 86 52 145 104 NC_002967:TDE0763|3end_hypothetical_protein_804234..804384_NEGATIVE 241 85 48 41 6 NC_002967:TDE0406|3end_hypothetical_protein_458929..459079_POSITIVE 240 87 45 68 16 NC_002967:TDE1894|3end_ferredoxin_1915041..1915191_POSITIVE 239 85 45 63 21 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 238 80 52 42 8 NC_002967:TDE0472|3end_hypothetical_protein_528674..528824_POSITIVE 235 90 42 141 76 NC_002967:TDE2612|3end_hypothetical_protein_2655459..2655609_POSITIVE 234 79 43 115 71 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 234 84 51 147 121 NC_002967:TDE1278|3end_conserved_hypothetical_protein_TIGR01440_1312228..1312378_NEGATIVE 234 85 48 87 52 NC_002967:TDE1012|3end_tex_protein,_putative_1043926..1044076_POSITIVE 232 80 49 129 98 NC_002967:TDE0146|3end_amidohydrolase_family_protein_167435..167585_NEGATIVE 228 84 50 118 81 NC_002967:TDE2717|3end_phosphatidate_cytidylyltransferase,_putative_2773921..2774071_NEGATIVE 223 85 48 76 42 NC_002967:TDE2694|3end_hypothetical_protein_2734079..2734229_NEGATIVE 221 85 48 47 13 NC_002967:TDE2693|3end_ankyrin_repeat_protein_2734014..2734164_POSITIVE