Origin IGS: gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatttctttaactctatcctgattcatagttgcattatatactatttgagacaaattttcaaagagatgaggtttgtcaagatatacataaatttggaaatgc Mask Tandem Repeat Region ================================================ gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt Find is-nt database================================================ Query_seq: TDE0303:TDE0304|TDE0303:TDE0304:hypothetical protein:hypothetical protein:->->:333920..334022 103 gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0303:TDE0304|TDE0303:TDE0304:hypothetical protein:hypothetical protein:->->:333920..334022 103 gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0303:TDE0304|TDE0303:TDE0304:hypothetical protein:hypothetical protein:->->:333920..334022 103 gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 11 End: 103 .......... M Y V Y L D K P H L F E N L S Q I V Y N A T M N Q D R V K E I gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt 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: 90 Start: 41 End: 70 ........................................TTTGAAAATTTGTCTCAAATAGTATATAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0303:TDE0304|TDE0303:TDE0304:hypothetical protein:hypothetical protein:->->:333920..334022 103 gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002967_TDE0303_TDE0304|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[333920,334022]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt gcatttccaaatttatgtatatcttgacaaacctcatctctttgaaaatttgtctcaaatagtatataatgcaactatgaatcaggatagagttaaagaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAUUUCCAAAUUUAUGUAUAUCUUGACAAACCUCAUCUCUUUGAAAAUUUGUCUCAAAUAGUAUAUAAUGCAACUAUGAAUCAGGAUAGAGUUAAAGAAAUU .....(((..(((((((........((((((..(((......)))...)))))).......((((...))))...)))))))..)))................ (-12.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUCUUUAACUCUAUCCUGAUUCAUAGUUGCAUUAUAUACUAUUUGAGACAAAUUUUCAAAGAGAUGAGGUUUGUCAAGAUAUACAUAAAUUUGGAAAUGC ................(((.((((.(((((..........)))))....(((((((((.((......)))))))))))............)))).)))..... (-13.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 50 1 111 67 NC_002967:TDE1915|5end_alcohol_dehydrogenase,_iron-containing_1933103..1933333_NEGATIVE 224 49 4 230 185 NC_002967:TDE0368|5end_type_I_restriction-modification_system,_S_subunit,_putative_418245..418475_NEGATIVE 222 59 16 190 149 NC_002967:TDE1342|5end_hypothetical_protein_1378442..1378672_POSITIVE 202 48 1 111 59 NC_002967:TDE0991|5end_ribosomal_protein_L28_1018065..1018295_NEGATIVE 199 43 6 102 63 NC_002967:TDE1203|5end_cell_division_protein_FtsA_1235033..1235263_POSITIVE 191 55 15 220 183 NC_002967:TDE0399|5end_zinc_carboxypeptidase_family_protein_449428..449658_POSITIVE 189 47 1 110 66 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 189 46 7 117 70 NC_002967:TDE0743|5end_thioredoxin_reductase_778718..778948_POSITIVE 182 94 51 72 15 NC_002967:TDE1187|5end_hypothetical_protein_1213588..1213818_POSITIVE 182 47 22 224 196 NC_002967:TDE0750|5end_magnesium_chelatase,_subunit_D/I_family_790135..790365_NEGATIVE 180 88 43 146 104 NC_002967:TDE0659|5end_hypothetical_protein_696202..696432_NEGATIVE 178 40 1 99 38 NC_002967:TDE1349|5end_rod_shape-determining_protein_MreB_1389286..1389516_POSITIVE 176 65 28 47 13 NC_002967:TDE1606|5end_transcriptional_regulator,_TetR_family_1656858..1657088_NEGATIVE 176 45 10 37 3 NC_002967:TDE0063|5end_hypothetical_protein_69714..69944_POSITIVE 175 43 4 46 15 NC_002967:TDE2156|5end_translation_initiation_factor_IF-3_2190719..2190949_NEGATIVE 175 58 16 164 107 NC_002967:TDE1793|5end_hydrolase,_carbon-nitrogen_family_1830844..1831074_NEGATIVE 175 57 23 144 109 NC_002967:TDE1312|5end_hypothetical_protein_1349088..1349318_POSITIVE 173 46 1 219 173 NC_002967:TDE1876|5end_glycosyl_transferase,_WecB/TagA/CpsF_family_1897679..1897909_NEGATIVE 171 46 1 109 50 NC_002967:TDE1501|5end_pyruvate_phosphate_dikinase_1548041..1548271_POSITIVE 171 51 33 115 97 NC_002967:TDE1164|5end_hypothetical_protein_1198166..1198396_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 49 4 119 74 NC_002967:TDE0369|3end_type_I_restriction-modification_system,_M_subunit_418356..418506_NEGATIVE 199 43 6 109 70 NC_002967:TDE1202|3end_cell_division_protein_FtsQ,_putative_1235120..1235270_POSITIVE 196 67 33 86 56 NC_002967:TDE0519|3end_hypothetical_protein_565438..565588_NEGATIVE 194 44 1 145 107 NC_002967:TDE1886|3end_MiaB-like_tRNA_modifying_enzyme_1907082..1907232_NEGATIVE 193 55 23 104 71 NC_002967:TDE0964|3end_hypothetical_protein_990578..990728_POSITIVE 191 55 15 148 111 NC_002967:TDE0398|3end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein_449436..449586_POSITIVE 189 69 29 98 42 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 189 47 1 96 52 NC_002967:TDE1144|3end_hypothetical_protein_1181848..1181998_NEGATIVE 189 55 11 86 36 NC_002967:TDE0525|3end_hypothetical_protein_571163..571313_POSITIVE 180 88 43 69 27 NC_002967:TDE0660|3end_transcriptional_regulator,_putative_696279..696429_NEGATIVE 178 40 1 81 20 NC_002967:TDE1348|3end_TPR_domain_protein_1389348..1389498_POSITIVE 176 90 49 59 24 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 172 56 26 117 86 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 171 51 33 100 82 NC_002967:TDE1165|3end_hypothetical_protein_1198181..1198331_NEGATIVE 171 46 6 142 102 NC_002967:TDE0797|3end_acylphosphatase_821223..821373_POSITIVE 169 65 21 144 93 NC_002967:TDE1004|3end_flagellar_filament_core_protein_1029276..1029426_NEGATIVE 168 26 1 131 108 NC_002967:TDE1010|3end_excinuclease_ABC,_A_subunit_1038171..1038321_POSITIVE 167 36 1 151 105 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 165 100 52 136 95 NC_002967:TDE2660|3end_hypothetical_protein_2697158..2697308_NEGATIVE 164 55 24 86 54 NC_002967:TDE1101|3end_acetyltransferase,_GNAT_family_1134663..1134813_NEGATIVE