Origin IGS: atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attattcttccatgtaaaattgatataataaatttttacctattaactaaggtaatattaccgtcctgtacaggatagcatagaaaagcttaatcgtcaacttaaattttaaaaatatcttgcttttttgatgatttcggtatatgattattgtataagtatatttttggaggtatat Mask Tandem Repeat Region ================================================ atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat Find is-nt database================================================ Query_seq: TDE2729:TDE2730|TDE2729:TDE2730:hypothetical protein:hydrolase, TatD family:<-->:2786548..2786725 178 atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2729:TDE2730|TDE2729:TDE2730:hypothetical protein:hydrolase, TatD family:<-->:2786548..2786725 178 atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2729:TDE2730|TDE2729:TDE2730:hypothetical protein:hydrolase, TatD family:<-->:2786548..2786725 178 atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 1 End: 129 M Y L Q K Y T Y T I I I Y R N H Q K S K I F L K F K L T I K L F Y A I L Y R T V I L P ................................................. atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat 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: 87 Start: 78 End: 107 .............................................................................GTTGACGATTAAGCTTTTCTATGCTATCCT....................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 31 End: 60 ..............................CTTGCTTTTTTGATGATTTCGGTATATGAT...................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2729:TDE2730|TDE2729:TDE2730:hypothetical protein:hydrolase, TatD family:<-->:2786548..2786725 178 atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: NC_002967_TDE2729_TDE2730|hypothetical protein:hydrolase, TatD family|NEGATIVE:POSITIVE|[2786548,2786725]|178 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat atatacctccaaaaatatacttatacaataatcatataccgaaatcatcaaaaaagcaagatatttttaaaatttaagttgacgattaagcttttctatgctatcctgtacaggacggtaatattaccttagttaataggtaaaaatttattatatcaattttacatggaagaataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUACCUCCAAAAAUAUACUUAUACAAUAAUCAUAUACCGAAAUCAUCAAAAAAGCAAGAUAUUUUUAAAAUUUAAGUUGACGAUUAAGCUUUUCUAUGCUAUCCUGUACAGGACGGUAAUAUUACCUUAGUUAAUAGGUAAAAAUUUAUUAUAUCAAUUUUACAUGGAAGAAUAAU .(((.(.((((.........................(((((.............(((((((..............(((((........))))).))).)))).((((....)))))))))...((((((........)))))).......................)))).).))).. (-25.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUCUUCCAUGUAAAAUUGAUAUAAUAAAUUUUUACCUAUUAACUAAGGUAAUAUUACCGUCCUGUACAGGAUAGCAUAGAAAAGCUUAAUCGUCAACUUAAAUUUUAAAAAUAUCUUGCUUUUUUGAUGAUUUCGGUAUAUGAUUAUUGUAUAAGUAUAUUUUUGGAGGUAUAU ..(((.((((((.(((......(((((((((....((((((........))))))...(((((((((....))))...(((((((((((................................)))))))).)))....))))).....))))))))).....)))...)))))).))). (-33.55) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 860 130 81 221 172 NC_002967:TDE2729|5end_hypothetical_protein_2786457..2786687_NEGATIVE 306 118 79 181 144 NC_002967:TDE0723|5end_hypothetical_protein_760304..760534_POSITIVE 288 118 77 33 1 NC_002967:TDE0864|5end_phosphohexose_mutase_family_protein_885244..885474_POSITIVE 271 121 82 212 171 NC_002967:TDE2713|5end_RNA_methyltransferase,_TrmH_family_2770324..2770554_NEGATIVE 249 124 87 230 194 NC_002967:TDE1707|5end_hypothetical_protein_1763191..1763421_NEGATIVE 246 120 77 62 13 NC_002967:TDE2584|5end_dipeptidase_2616413..2616643_POSITIVE 245 122 83 208 172 NC_002967:TDE0995|5end_hypothetical_protein_1022576..1022806_NEGATIVE 237 120 83 47 8 NC_002967:TDE1180|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein_1209833..1210063_NEGATIVE 235 123 90 163 122 NC_002967:TDE2631|5end_peptide_ABC_transporter,_permease_protein,_putative_2671829..2672059_POSITIVE 234 118 72 67 20 NC_002967:TDE1029|5end_Hsp20/alpha_crystallin_family_protein_1058574..1058804_POSITIVE 233 126 90 171 128 NC_002967:TDE2400|5end_50S_ribosomal_protein_L34_2426327..2426557_NEGATIVE 232 128 89 62 25 NC_002967:TDE1162|5end_ParB-like_nuclease_domain_protein_1197684..1197914_NEGATIVE 228 120 74 90 36 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 228 121 81 220 180 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 226 140 99 154 117 NC_002967:TDE2258|5end_surface_antigen_BspA,_putative_2296401..2296631_NEGATIVE 226 97 63 146 115 NC_002967:TDE1200|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,_6-diaminopimelate--D-alanyl-D-alanyl_ligase_1231618..1231848_POSITIVE 219 123 93 59 25 NC_002967:TDE0971|5end_arginyl-tRNA_synthetase_995179..995409_POSITIVE 218 121 82 185 146 NC_002967:TDE2633|5end_hypothetical_protein_2674359..2674589_POSITIVE 218 127 88 188 143 NC_002967:TDE1658|5end_basic_membrane_protein,_putative_1708731..1708961_NEGATIVE 217 120 74 47 3 NC_002967:TDE2243|5end_CutC_family_protein_2282954..2283184_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 120 77 69 20 NC_002967:TDE2583|3end_hypothetical_protein_2616500..2616650_POSITIVE 234 118 72 74 27 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE 232 128 89 46 9 NC_002967:TDE1163|3end_hypothetical_protein_1197700..1197850_NEGATIVE 232 115 91 147 125 NC_002967:TDE0894|3end_hypothetical_protein_911239..911389_POSITIVE 224 106 75 130 101 NC_002967:TDE0497|3end_hypothetical_protein_551374..551524_NEGATIVE 218 127 88 88 43 NC_002967:TDE1659|3end_alanyl-tRNA_synthetase_1708831..1708981_NEGATIVE 217 118 71 142 79 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 216 128 85 97 39 NC_002967:TDE2080|3end_cytidylate_kinase/ribosomal_protein_S1_2109049..2109199_NEGATIVE 216 118 83 149 97 NC_002967:TDE0589|3end_acetyl-CoA_carboxylase,_carboxyl_transferase,_alpha_subunit_628127..628277_NEGATIVE 215 119 90 57 27 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 215 119 75 114 75 NC_002967:TDE0938|3end_hypothetical_protein_960963..961113_NEGATIVE 214 116 73 149 98 NC_002967:TDE0542|3end_acetyltransferase,_GNAT_family_583142..583292_POSITIVE 211 134 99 102 63 NC_002967:TDE2543|3end_hypothetical_protein_2570753..2570903_NEGATIVE 210 120 73 127 73 NC_002967:TDE2556|3end_hypothetical_protein_2582316..2582466_NEGATIVE 208 129 85 134 90 NC_002967:TDE1173|3end_site-specific_recombinase,_phage_integrase_family_1201257..1201407_NEGATIVE 208 119 71 141 88 NC_002967:TDE0319|3end_hypothetical_protein_352547..352697_POSITIVE 207 123 85 107 67 NC_002967:TDE1338|3end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_1375823..1375973_POSITIVE 207 136 100 61 23 NC_002967:TDE0967|3end_hypothetical_protein_992529..992679_POSITIVE 207 113 77 46 12 NC_002967:TDE0924|3end_ABC_transporter,_ATP-binding/permease_protein_945751..945901_NEGATIVE 207 120 95 118 90 NC_002967:TDE0515|3end_hypothetical_protein_562770..562920_NEGATIVE