Origin IGS: agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcatactccaataaaactttatttcccttgtataatgccatatttttacattttgtgcaagtaatgggttttaaaaatactttaagaaaatggtaataaaatttgaaaattgacataatcttattttttcattataatgagccct Mask Tandem Repeat Region ================================================ agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc Find is-nt database================================================ Query_seq: TDE1893:TDE1894|TDE1893:TDE1894:GTP-binding protein LepA:ferredoxin:<-->:1914108..1914252 145 agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1893:TDE1894|TDE1893:TDE1894:GTP-binding protein LepA:ferredoxin:<-->:1914108..1914252 145 agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1893:TDE1894|TDE1893:TDE1894:GTP-binding protein LepA:ferredoxin:<-->:1914108..1914252 145 agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 27 End: 143 .......................... M M S I F K F Y Y H F L K V F L K P I T C T K C K N M A L Y K G N K V L L E Y .. agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc 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: 95 Start: 8 End: 37 .......ATTGACATAATCTTATTTTTTCATTATAAT............................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1893:TDE1894|TDE1893:TDE1894:GTP-binding protein LepA:ferredoxin:<-->:1914108..1914252 145 agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_002967_TDE1893_TDE1894|GTP-binding protein LepA:ferredoxin|NEGATIVE:POSITIVE|[1914108,1914252]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc agggctcattataatgaaaaaataagattatgtcaattttcaaattttattaccattttcttaaagtatttttaaaacccattacttgcacaaaatgtaaaaatatggcattatacaagggaaataaagttttattggagtatgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGCUCAUUAUAAUGAAAAAAUAAGAUUAUGUCAAUUUUCAAAUUUUAUUACCAUUUUCUUAAAGUAUUUUUAAAACCCAUUACUUGCACAAAAUGUAAAAAUAUGGCAUUAUACAAGGGAAAUAAAGUUUUAUUGGAGUAUGC ...((((....((((((((.(((((((((.((........)))))))))))...((((((((...((((.........((((...(((((.....)))))....))))....)))).))))))))....)))))))))))).... (-18.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAUACUCCAAUAAAACUUUAUUUCCCUUGUAUAAUGCCAUAUUUUUACAUUUUGUGCAAGUAAUGGGUUUUAAAAAUACUUUAAGAAAAUGGUAAUAAAAUUUGAAAAUUGACAUAAUCUUAUUUUUUCAUUAUAAUGAGCCCU .....(((...((((((((.(((...(((((((((.................))))))))).))))))))))).........(((((..(((.((((...........)))).)))..)))))...............))).... (-16.63) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 730 120 71 211 162 NC_002967:TDE1893|5end_GTP-binding_protein_LepA_1914017..1914247_NEGATIVE 244 65 30 106 64 NC_002967:TDE1991|5end_hypothetical_protein_2009398..2009628_NEGATIVE 220 80 31 121 65 NC_002967:TDE2196|5end_hypothetical_protein_2232647..2232877_NEGATIVE 200 115 78 53 8 NC_002967:TDE1282|5end_hypothetical_protein_1316801..1317031_POSITIVE 198 34 2 43 10 NC_002967:TDE2037|5end_ATP:guanido_phosphotransferase_domain_protein_2067720..2067950_NEGATIVE 194 129 84 159 98 NC_002967:TDE1336|5end_hypothetical_protein_1372303..1372533_POSITIVE 193 90 44 206 157 NC_002967:TDE0105|5end_MTA/SAH_nucleosidase_125454..125684_NEGATIVE 191 64 30 205 164 NC_002967:TDE2312|5end_hypothetical_protein_2348451..2348681_POSITIVE 190 64 30 164 123 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 185 121 85 50 12 NC_002967:TDE0962|5end_hypothetical_protein_983983..984213_POSITIVE 181 138 105 49 21 NC_002967:TDE2249|5end_phospho-N-acetylmuramoyl-pentapeptide-_transferase_2288556..2288786_NEGATIVE 180 108 78 195 162 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 179 119 78 67 17 NC_002967:TDE0379|5end_hypothetical_protein_432458..432688_POSITIVE 178 37 1 160 124 NC_002967:TDE2473|5end_30S_ribosomal_protein_S21_2496298..2496528_POSITIVE 177 105 81 76 53 NC_002967:TDE1569|5end_hypothetical_protein_1619785..1620015_POSITIVE 177 139 102 44 11 NC_002967:TDE1218|5end_flagellum-specific_ATP_synthase_FliI_1250447..1250677_POSITIVE 173 139 96 172 124 NC_002967:TDE2257|5end_5'-nucleotidase_family_protein_2295104..2295334_NEGATIVE 172 117 77 52 12 NC_002967:TDE1172|5end_hypothetical_protein_1201006..1201236_POSITIVE 171 140 95 230 185 NC_002967:TDE2675|5end_hypothetical_protein_2713374..2713604_POSITIVE 171 73 33 114 66 NC_002967:TDE0885|5end_50S_ribosomal_protein_L19_902945..903175_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 198 34 2 59 26 NC_002967:TDE2038|3end_UVR_domain_protein_2067704..2067854_NEGATIVE 194 129 84 144 83 NC_002967:TDE1335|3end_alginate_O-acetylation_protein,_putative_1372368..1372518_POSITIVE 193 90 44 118 69 NC_002967:TDE0106|3end_hypothetical_protein_125542..125692_NEGATIVE 191 64 30 111 70 NC_002967:TDE2311|3end_hypothetical_protein_2348437..2348587_POSITIVE 186 109 76 68 31 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 184 122 85 124 98 NC_002967:TDE1942|3end_hypothetical_protein_1959438..1959588_POSITIVE 177 105 81 38 15 NC_002967:TDE1568|3end_hypothetical_protein_1619827..1619977_POSITIVE 177 139 102 34 1 NC_002967:TDE1217|3end_flagellar_assembly_protein_1250517..1250667_POSITIVE 171 73 33 121 73 NC_002967:TDE0884|3end_tRNA_(guanine-N(1)-)-methyltransferase_903032..903182_POSITIVE 170 140 119 103 77 NC_002967:TDE2672|3end_TPR_domain_protein_2711630..2711780_POSITIVE 170 79 32 91 47 NC_002967:TDE0627|3end_co-chaperone_protein_GrpE_660668..660818_POSITIVE 169 89 60 65 29 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 168 127 88 47 3 NC_002967:TDE1436|3end_inner_membrane_protein_1482290..1482440_POSITIVE 167 59 31 100 71 NC_002967:TDE2688|3end_hypothetical_protein_2728462..2728612_POSITIVE 167 123 83 68 24 NC_002967:TDE0465|3end_PIN_domain_protein_518268..518418_NEGATIVE 166 91 56 117 76 NC_002967:TDE0639|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_673453..673603_NEGATIVE 165 94 54 105 68 NC_002967:TDE1371|3end_RNB-like_family_protein_1413298..1413448_NEGATIVE 162 139 96 112 69 NC_002967:TDE1921|3end_hypothetical_protein_1940319..1940469_NEGATIVE 162 126 85 80 25 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 161 71 33 113 79 NC_002967:TDE0675|3end_hypothetical_protein_714931..715081_POSITIVE