Origin IGS: acagcctcccttatttattacagttttacttatatataagtatatcacaaaaaataaaaaacaacaatcggaatataaaaaaaatgaaattattttcttcttgaaattttattttttttgttgtatggtgattataaggcgggagggatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatccctcccgccttataatcaccatacaacaaaaaaaataaaatttcaagaagaaaataatttcattttttttatattccgattgttgttttttattttttgtgatatacttatatataagtaaaactgtaataaataagggaggctgt Mask Tandem Repeat Region ================================================ acagcctcccttatttattacagttttacttatatataagtatatcacaaaaaataaaaaacaacaatcggaatataaaaaaaatgaaattattttcttcttgaaattttattttttttgttgtatggtgattataaggcgggagggatt Find is-nt database================================================ Query_seq: TDE1328:TDE1329|TDE1328:TDE1329:hypothetical protein:ATPase, AAA family:<-->:1363493..1363642 150 acagcctcccttatttattacagttttacttatatataagtatatcacaaaaaataaaaaacaacaatcggaatataaaaaaaatgaaattattttcttcttgaaattttattttttttgttgtatggtgattataaggcgggagggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1328:TDE1329|TDE1328:TDE1329:hypothetical protein:ATPase, AAA family:<-->:1363493..1363642 150 acagcctcccttatttattacagttttacttatatataagtatatcacaaaaaataaaaaacaacaatcggaatataaaaaaaatgaaattattttcttcttgaaattttattttttttgttgtatggtgattataaggcgggagggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1328:TDE1329|TDE1328:TDE1329:hypothetical protein:ATPase, AAA family:<-->:1363493..1363642 150 acagcctcccttatttattacagttttacttatatataagtatatcacaaaaaataaaaaacaacaatcggaatataaaaaaaatgaaattattttcttcttgaaattttattttttttgttgtatggtgattataaggcgggagggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acagcctcccttatttattacagttttacttatatataagtatatcacaaaaaataaaaaacaacaatcggaatataaaaaaaatgaaattattttcttcttgaaattttattttttttgttgtatggtgattataaggcgggagggatt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 17 End: 148 ................ M T V L L I Y K Y I T K N K K Q Q S E Y K K N E I I F F L K F Y F F C C M V I I R R E G .. Protein_Len: 31 Strand: - Start: 1 End: 93 C G G K N I V T K S I Y L Y I V F F L F C C D S Y L F F S I M ......................................................... acagcctcccttatttattacagttttacttatatataagtatatcacaaaaaataaaaaacaacaatcggaatataaaaaaaatgaaattattttcttcttgaaattttattttttttgttgtatggtgattataaggcgggagggatt 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: 85 Start: 100 End: 129 ...................................................................................................CTTGAAATTTTATTTTTTTTGTTGTATGGT..................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 39 End: 68 ......................................ATTGTTGTTTTTTATTTTTTGTGATATACT.................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acagcctcccttatttattacagttttacttatatataagtatatcacaaaaaataaaaaacaacaatcggaatataaaaaaaatgaaattattttcttcttgaaattttattttttttgttgtatggtgattataaggcgggagggatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1328:TDE1329|TDE1328:TDE1329:hypothetical protein:ATPase, AAA family:<-->:1363493..1363642 150 acagcctcccttatttattacagttttacttatatataagtatatcacaaaaaataaaaaacaacaatcggaatataaaaaaaatgaaattattttcttcttgaaattttattttttttgttgtatggtgattataaggcgggagggatt Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_002967_TDE1328_TDE1329|hypothetical protein:ATPase, AAA family|NEGATIVE:POSITIVE|[1363493,1363642]|150 HSP 1 e-value: 4.0E-19 bit: 95.6 Len: 48 Query Start:1 Query End:48 Subject Strand: POSITIVE Subject Start: 1 Subject End: 48 acagcctcccttatttattacagttttacttatatataagtatatcac...................................................................................................... acagcctcccttatttattacagttttacttatatataagtatatcac...................................................................................................... HSP 2 e-value: 6.0E-12 bit: 71.9 Len: 60 Query Start:91 Query End:150 Subject Strand: POSITIVE Subject Start: 91 Subject End: 150 ..........................................................................................tattttcttcttgaaattttannnnnnnngttgtatggtgattataaggcgggagggatt ..........................................................................................tattttcttcttgaaattttattttttttgttgtatggtgattataaggcgggagggatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGCCUCCCUUAUUUAUUACAGUUUUACUUAUAUAUAAGUAUAUCACAAAAAAUAAAAAACAACAAUCGGAAUAUAAAAAAAAUGAAAUUAUUUUCUUCUUGAAAUUUUAUUUUUUUUGUUGUAUGGUGAUUAUAAGGCGGGAGGGAUU ....((((((((((..(((((.(...((((((....))))))...)..............(((((((...........(((((((((((((....((.....))))))))))))))))))))))...))))).))))...)))))).... (-29.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCCCUCCCGCCUUAUAAUCACCAUACAACAAAAAAAAUAAAAUUUCAAGAAGAAAAUAAUUUCAUUUUUUUUAUAUUCCGAUUGUUGUUUUUUAUUUUUUGUGAUAUACUUAUAUAUAAGUAAAACUGUAAUAAAUAAGGGAGGCUGU ....((((((...................((((((((...(((((..(((...(((.((((...........)))).)))...)))..)))))...))))))))....((((((....))))))................)))))).... (-26.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 732 50 1 141 92 NC_002967:TDE1328|5end_hypothetical_protein_1363402..1363632_NEGATIVE 263 148 118 195 170 NC_002967:TDE2080|5end_cytidylate_kinase/ribosomal_protein_S1_2111484..2111714_NEGATIVE 246 149 105 60 11 NC_002967:TDE0858|5end_hypothetical_protein_879518..879748_POSITIVE 238 146 102 140 96 NC_002967:TDE0905|5end_hypothetical_protein_922432..922662_POSITIVE 235 148 120 146 116 NC_002967:TDE2216|5end_galactoside_ABC_transporter,_ATP-binding_protein_2256653..2256883_NEGATIVE 232 106 69 39 5 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 228 145 107 148 111 NC_002967:TDE0116|5end_hypothetical_protein_134709..134939_POSITIVE 224 146 101 146 94 NC_002967:TDE1497|5end_hypothetical_protein_1543208..1543438_POSITIVE 221 145 117 144 119 NC_002967:TDE0915|5end_hypothetical_protein_933320..933550_NEGATIVE 216 149 112 39 5 NC_002967:TDE0577|5end_glutamyl-tRNA(Gln)_amidotransferase,_C_subunit_609509..609739_NEGATIVE 215 140 100 205 165 NC_002967:TDE2355|5end_carbon_storage_regulator_2390838..2391068_POSITIVE 211 150 123 70 36 NC_002967:TDE0792|5end_ribosomal_protein_L17_818387..818617_POSITIVE 210 148 103 213 167 NC_002967:TDE1273|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1308624..1308854_NEGATIVE 208 144 112 107 78 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 207 147 111 190 143 NC_002967:TDE2476|5end_carbamate_kinase_2499450..2499680_NEGATIVE 207 146 118 70 43 NC_002967:TDE1434|5end_hypothetical_protein_1478462..1478692_NEGATIVE 207 148 106 72 29 NC_002967:TDE1412|5end_sodium/hydrogen_exchanger_family_protein_1453462..1453692_POSITIVE 207 147 101 72 26 NC_002967:TDE0271|5end_hypothetical_protein_301976..302206_POSITIVE 206 147 119 211 185 NC_002967:TDE0180|5end_hypothetical_protein_213018..213248_NEGATIVE 201 148 107 170 132 NC_002967:TDE0469|5end_hypothetical_protein_523987..524217_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 149 105 60 11 NC_002967:TDE0857|3end_lipoprotein,_putative_879598..879748_POSITIVE 235 148 120 35 5 NC_002967:TDE2217|3end_galactose/glucose-binding_lipoprotein_2256764..2256914_NEGATIVE 228 145 107 140 103 NC_002967:TDE0115|3end_hypothetical_protein_134781..134931_POSITIVE 216 147 121 146 116 NC_002967:TDE2227|3end_hypothetical_protein_2267134..2267284_POSITIVE 211 150 123 80 46 NC_002967:TDE0791|3end_DNA-directed_RNA_polymerase_alpha_subunit_818477..818627_POSITIVE 208 144 112 102 73 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 204 150 104 62 25 NC_002967:TDE2759|3end_hypothetical_protein_2815101..2815251_POSITIVE 203 147 126 56 39 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 197 47 3 61 25 NC_002967:TDE1251|3end_batB_protein,_putative_1286496..1286646_POSITIVE 195 150 117 114 78 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 195 142 112 100 67 NC_002967:TDE0677|3end_hypothetical_protein_716051..716201_POSITIVE 192 143 102 101 56 NC_002967:TDE0319|3end_hypothetical_protein_352547..352697_POSITIVE 191 148 117 132 99 NC_002967:TDE2491|3end_DNA_polymerase_domain_protein_2514705..2514855_NEGATIVE 191 146 122 26 1 NC_002967:TDE0897|3end_ABC_transporter,_ATP-binding/permease_protein_915938..916088_POSITIVE 190 148 113 49 2 NC_002967:TDE0926|3end_phosphonate_ABC_transporter,_permease_protein,_putative_949192..949342_NEGATIVE 189 149 107 131 82 NC_002967:TDE2618|3end_PHP_domain_protein_2660347..2660497_POSITIVE 189 40 1 124 82 NC_002967:TDE2366|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399959..2400109_NEGATIVE 189 148 134 49 36 NC_002967:TDE2163|3end_hypothetical_protein_2195533..2195683_NEGATIVE 188 141 101 113 72 NC_002967:TDE2353|3end_flagellar_hook-associated_protein_2390456..2390606_POSITIVE 187 147 117 137 107 NC_002967:TDE2713|3end_RNA_methyltransferase,_TrmH_family_2769557..2769707_NEGATIVE