Origin IGS: caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caacacggaaatgatggattgaaatacggtatatgcattcgtaagggcgagataaaatgttttttattgcttgaaaaacttgatatcttggtatatcatattagtaggtctaatatgcgttatgctcacacgctattggcgtgttttttataaggaggtttttg Mask Tandem Repeat Region ================================================ caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg Find is-nt database================================================ Query_seq: TDE0281:TDE0282|TDE0281:TDE0282:hypothetical protein:ABC transporter, ATP-binding protein:<-<-:310581..310744 164 caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0281:TDE0282|TDE0281:TDE0282:hypothetical protein:ABC transporter, ATP-binding protein:<-<-:310581..310744 164 caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0281:TDE0282|TDE0281:TDE0282:hypothetical protein:ABC transporter, ATP-binding protein:<-<-:310581..310744 164 caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 71 End: 163 ...................................................................... M P R Y Q V F Q A I K N I L S R P Y E C I Y R I S I H H F R V . Protein_Len: 44 Strand: - Start: 15 End: 146 .............. L F C A L L T H A Y R M N S R S I H Y V L I D L K E L L L F C K I E G K R I C I G Y K M .................. Protein_Len: 31 Strand: - Start: 2 End: 94 . F V E K Y F V R W Y R T L M V C I L G V L I I Y W S I L N K M ...................................................................... caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg 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: 66 End: 95 .................................................................CTTGAAAAACTTGATATCTTGGTATATCAT..................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 49 End: 78 ................................................CTTGGTATATCATATTAGTAGGTCTAATAT...................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 89 HP_score: -7.8 Tail_Score: -5.24129 Start: 22 End: 36 Full_Region: tatgcgttatgctca cacgct att ggcgtg ttttttataaggagg .....................cacgctattggcgtg................................................................................................................................ TransTerm Strand: - Conf: 43 HP_score: -3.5 Tail_Score: -2.64099 Start: 47 End: 69 Full_Region: tgatatcttggtata tcatattag taggt ctaatatgc gttatgctcacacgc ..............................................tcatattagtaggtctaatatgc............................................................................................... TransTerm Strand: + Conf: 45 HP_score: -3.8 Tail_Score: -2.62396 Start: 50 End: 66 Full_Region: TGTGAGCATAACGCA TATTAG ACCTA CTAATA TGATATACCAAGATA .................................................TATTAGACCTACTAATA.................................................................................................. TransTerm Strand: - Conf: 45 HP_score: -3.8 Tail_Score: -2.61548 Start: 50 End: 66 Full_Region: tatcttggtatatca tattag taggt ctaata tgcgttatgctcaca .................................................tattagtaggtctaata.................................................................................................. TransTerm Strand: + Conf: 41 HP_score: -2.8 Tail_Score: -2.60211 Start: 67 End: 84 Full_Region: TTAGACCTACTAATA TGATAT ACCAAG ATATCA AGTTTTTCAAGCAAT ..................................................................TGATATACCAAGATATCA................................................................................ TransTerm Strand: - Conf: 45 HP_score: -2.8 Tail_Score: -3.16492 Start: 67 End: 84 Full_Region: attgcttgaaaaact tgatat cttggt atatca tattagtaggtctaa ..................................................................tgatatcttggtatatca................................................................................ Find igs database================================================ Query_seq: TDE0281:TDE0282|TDE0281:TDE0282:hypothetical protein:ABC transporter, ATP-binding protein:<-<-:310581..310744 164 caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: NC_002967_TDE0281_TDE0282|hypothetical protein:ABC transporter, ATP-binding protein|NEGATIVE:NEGATIVE|[310581,310744]|164 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg caaaaacctccttataaaaaacacgccaatagcgtgtgagcataacgcatattagacctactaatatgatataccaagatatcaagtttttcaagcaataaaaaacattttatctcgcccttacgaatgcatataccgtatttcaatccatcatttccgtgttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAAACCUCCUUAUAAAAAACACGCCAAUAGCGUGUGAGCAUAACGCAUAUUAGACCUACUAAUAUGAUAUACCAAGAUAUCAAGUUUUUCAAGCAAUAAAAAACAUUUUAUCUCGCCCUUACGAAUGCAUAUACCGUAUUUCAAUCCAUCAUUUCCGUGUUG ...................((((((........(.(((((.((((..((((((((.....)))))))).................((((((.........))))))...))))))))).)....((((((.......))))))..............)))))). (-23.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACACGGAAAUGAUGGAUUGAAAUACGGUAUAUGCAUUCGUAAGGGCGAGAUAAAAUGUUUUUUAUUGCUUGAAAAACUUGAUAUCUUGGUAUAUCAUAUUAGUAGGUCUAAUAUGCGUUAUGCUCACACGCUAUUGGCGUGUUUUUUAUAAGGAGGUUUUUG .....(((((((..((((((..((((.(((((((....((....)).(((((((....((((((((.....))))))))....)))))))))))))).))))....)))))).....(.(((((...((((((.....))))))....))))).)..))))))) (-35.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 900 70 21 161 112 NC_002967:TDE0281|5end_hypothetical_protein_310490..310720_NEGATIVE 443 59 22 141 104 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 304 49 7 43 2 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 285 48 6 87 42 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 276 160 116 96 47 NC_002967:TDE0519|5end_hypothetical_protein_565989..566219_NEGATIVE 266 70 23 76 15 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 259 75 31 204 158 NC_002967:TDE2757|5end_nucleotidyltransferase_family_protein_2813673..2813903_POSITIVE 257 158 112 175 122 NC_002967:TDE2683|5end_sigma_factor_WhiG_2724155..2724385_NEGATIVE 254 158 117 231 199 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 252 48 25 225 201 NC_002967:TDE1766|5end_hypothetical_protein_1812733..1812963_NEGATIVE 247 50 7 66 19 NC_002967:TDE0035|5end_acetyltransferase,_GNAT_family_42020..42250_NEGATIVE 243 160 114 57 17 NC_002967:TDE2298|5end_galactokinase,_putative_2338267..2338497_NEGATIVE 239 62 25 106 66 NC_002967:TDE1396|5end_hypothetical_protein_1435661..1435891_POSITIVE 236 140 94 58 8 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 235 50 4 225 170 NC_002967:TDE2748|5end_acetyltransferase,_GNAT_family_2805108..2805338_POSITIVE 234 160 113 124 71 NC_002967:TDE0350|5end_MATE_efflux_family_protein_393572..393802_POSITIVE 233 42 7 44 7 NC_002967:TDE1461|5end_septum_formation_initiator_family_protein_1511181..1511411_POSITIVE 233 95 51 174 130 NC_002967:TDE0034|5end_hypothetical_protein_41450..41680_NEGATIVE 228 159 112 102 69 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 228 45 7 66 18 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 160 118 143 97 NC_002967:TDE2165|3end_hydrogenase_accessory_protein_HypB_2197053..2197203_NEGATIVE 269 149 102 45 3 NC_002967:TDE2230|3end_hypothetical_protein_2269453..2269603_POSITIVE 257 158 112 150 97 NC_002967:TDE2684|3end_hypothetical_protein_2724180..2724330_NEGATIVE 252 48 25 32 8 NC_002967:TDE1767|3end_hypothetical_protein_1812926..1813076_NEGATIVE 239 62 25 43 3 NC_002967:TDE1395|3end_glycosyl_hydrolase,_family_57_1435678..1435828_POSITIVE 234 160 113 122 69 NC_002967:TDE0349|3end_phosphoenolpyruvate_synthase,_putative_393650..393800_POSITIVE 232 49 7 52 7 NC_002967:TDE2308|3end_hypothetical_protein_2346313..2346463_POSITIVE 228 66 25 61 23 NC_002967:TDE1325|3end_hypothetical_protein_1361620..1361770_NEGATIVE 227 79 31 130 82 NC_002967:TDE0161|3end_hypothetical_protein_187725..187875_NEGATIVE 224 144 111 111 70 NC_002967:TDE1449|3end_GTPase_YjeQ_1495379..1495529_POSITIVE 224 56 20 90 55 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 223 61 24 73 38 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 223 78 31 113 66 NC_002967:TDE0293|3end_MATE_efflux_family_protein_322018..322168_NEGATIVE 221 130 90 38 3 NC_002967:TDE1746|3end_hypothetical_protein_1799474..1799624_NEGATIVE 220 95 52 44 1 NC_002967:TDE0035|3end_acetyltransferase,_GNAT_family_41580..41730_NEGATIVE 219 72 33 76 32 NC_002967:TDE1961|3end_PIN_domain_protein_1974550..1974700_NEGATIVE 219 138 110 48 20 NC_002967:TDE0473|3end_heavy_metal_translocating_P-type_ATPase_530800..530950_POSITIVE 217 41 8 147 110 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 216 50 8 65 26 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 215 69 31 82 43 NC_002967:TDE2235|3end_methylaspartate_ammonia-lyase_2273350..2273500_NEGATIVE