Origin IGS: aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcccgaacatccttttaacatgtacatataaaagattatacaatttatttgcttgtttgtcattaggaattgaaaagtttttaagggataggataatttttccgataaaagggtgtt Mask Tandem Repeat Region ================================================ aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct Find is-nt database================================================ Query_seq: TDE1495:TDE1496|TDE1495:TDE1496:hypothetical protein:chromosome partition protein SmC, putative:<-->:1540307..1540424 118 aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1495:TDE1496|TDE1495:TDE1496:hypothetical protein:chromosome partition protein SmC, putative:<-->:1540307..1540424 118 aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1495:TDE1496|TDE1495:TDE1496:hypothetical protein:chromosome partition protein SmC, putative:<-->:1540307..1540424 118 aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 12 End: 116 ........... M G K I I L S L K N F S I P N D K Q A N K L Y N L L Y V H V K R M F G .. Protein_Len: 36 Strand: - Start: 2 End: 109 . C G K I P F I I R D R L F K E I G L S L C A F L N Y L R K Y T C T L L M ......... aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct 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: 88 Start: 54 End: 83 .....................................................AATGACAAACAAGCAAATAAATTGTATAAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1495:TDE1496|TDE1495:TDE1496:hypothetical protein:chromosome partition protein SmC, putative:<-->:1540307..1540424 118 aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_002967_TDE1495_TDE1496|hypothetical protein:chromosome partition protein SmC, putative|NEGATIVE:POSITIVE|[1540307,1540424]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct aacacccttttatcggaaaaattatcctatcccttaaaaacttttcaattcctaatgacaaacaagcaaataaattgtataatcttttatatgtacatgttaaaaggatgttcgggct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACACCCUUUUAUCGGAAAAAUUAUCCUAUCCCUUAAAAACUUUUCAAUUCCUAAUGACAAACAAGCAAAUAAAUUGUAUAAUCUUUUAUAUGUACAUGUUAAAAGGAUGUUCGGGCU ....(((.......(((.......)))......................((((..(((((.....(((.(((((...........))))).)))...)))))..)))).....))).. (-14.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCCGAACAUCCUUUUAACAUGUACAUAUAAAAGAUUAUACAAUUUAUUUGCUUGUUUGUCAUUAGGAAUUGAAAAGUUUUUAAGGGAUAGGAUAAUUUUUCCGAUAAAAGGGUGUU ......((((((((((((......(((..(((((((((....))))).))))..))).((((.(((((((((....)))))))))..))))(((.......)))..)))))))))))) (-24.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 735 60 11 151 102 NC_002967:TDE1495|5end_hypothetical_protein_1540216..1540446_NEGATIVE 242 32 8 218 193 NC_002967:TDE2001|5end_oligoendopeptidase_F,_putative_2021568..2021798_NEGATIVE 233 35 2 105 66 NC_002967:TDE2297|5end_TPR_domain_protein_2337019..2337249_NEGATIVE 222 35 5 106 69 NC_002967:TDE1858|5end_transcriptional_regulator,_PadR_family_1884632..1884862_POSITIVE 221 60 13 59 6 NC_002967:TDE1707|5end_hypothetical_protein_1763191..1763421_NEGATIVE 219 34 6 100 66 NC_002967:TDE2085|5end_uridylate_kinase_2114182..2114412_POSITIVE 206 55 28 150 118 NC_002967:TDE0619|5end_methyl-accepting_chemotaxis_protein_650318..650548_POSITIVE 201 56 23 128 91 NC_002967:TDE2267|5end_HRDC_domain_protein_2304464..2304694_NEGATIVE 199 33 2 63 32 NC_002967:TDE0614|5end_precorrin-4_C11-methyltransferase_647987..648217_POSITIVE 195 38 5 190 151 NC_002967:TDE1631|5end_citrate_lyase,_alpha_subunit_1681556..1681786_NEGATIVE 195 45 7 38 9 NC_002967:TDE0060|5end_hypothetical_protein_67838..68068_NEGATIVE 193 53 11 230 189 NC_002967:TDE0909|5end_type_II_DNA_modification_methyltransferase_M.TdeIII_927166..927396_POSITIVE 192 46 2 194 150 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 191 58 21 122 87 NC_002967:TDE0317|5end_hypothetical_protein_350656..350886_POSITIVE 190 46 7 46 4 NC_002967:TDE2453|5end_hypothetical_protein_2481437..2481667_POSITIVE 186 47 4 104 53 NC_002967:TDE1896|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1917505..1917735_NEGATIVE 185 85 42 59 21 NC_002967:TDE1889|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_1910888..1911118_NEGATIVE 183 38 7 71 40 NC_002967:TDE1370|5end_YjeF-related_protein_1413284..1413514_NEGATIVE 182 59 13 110 48 NC_002967:TDE0099|5end_adenine-specific_DNA_modification_methyltransferase_115648..115878_POSITIVE 180 46 5 230 193 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 221 60 13 62 9 NC_002967:TDE1708|3end_apolipoprotein_N-acyltransferase_1763188..1763338_NEGATIVE 219 34 6 67 33 NC_002967:TDE2084|3end_RNA_methyltransferase,_TrmH_family_2114229..2114379_POSITIVE 214 70 27 139 91 NC_002967:TDE0568|3end_hypothetical_protein_599228..599378_POSITIVE 203 46 2 143 93 NC_002967:TDE1965|3end_sodium/hydrogen_exchanger_family_protein_1978895..1979045_NEGATIVE 193 53 11 69 28 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 191 34 5 151 130 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 186 47 4 84 33 NC_002967:TDE1897|3end_phosphoribosylglycinamide_formyltransferase_1917525..1917675_NEGATIVE 183 38 7 57 26 NC_002967:TDE1371|3end_RNB-like_family_protein_1413298..1413448_NEGATIVE 178 35 7 107 75 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 177 48 8 76 32 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 177 46 5 80 34 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 176 67 25 125 80 NC_002967:TDE2338|3end_hypothetical_protein_2374624..2374774_NEGATIVE 176 48 5 94 49 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 176 56 23 109 74 NC_002967:TDE0254|3end_hypothetical_protein_289312..289462_POSITIVE 175 79 31 59 3 NC_002967:TDE1612|3end_phosphoribosyl_transferase_domain_protein_1661690..1661840_POSITIVE 172 43 5 114 80 NC_002967:TDE1192|3end_hypothetical_protein_1219573..1219723_POSITIVE 169 48 7 61 19 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 168 46 2 149 105 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 168 50 4 106 55 NC_002967:TDE1660|3end_leucine_Rich_Repeat_domain_protein_1710710..1710860_NEGATIVE 167 47 8 119 74 NC_002967:TDE2297|3end_TPR_domain_protein_2336339..2336489_NEGATIVE