Origin IGS: tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagttaaaaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttttttaactacactcacaatcttaattaaaggtttgagtgtagttttttatcttgataaaatttattttaaatgttaaaatctattaatatatattaaacttaggggaggattttca Mask Tandem Repeat Region ================================================ tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagttaaaaaaat Find is-nt database================================================ Query_seq: FN0288:FN0289|FN0288:FN0289:Hypoxanthine-guanine phosphoribosyltransferase:hypothetical protein:<-<-:915856..915975 120 tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagttaaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0288:FN0289|FN0288:FN0289:Hypoxanthine-guanine phosphoribosyltransferase:hypothetical protein:<-<-:915856..915975 120 tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagttaaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0288:FN0289|FN0288:FN0289:Hypoxanthine-guanine phosphoribosyltransferase:hypothetical protein:<-<-:915856..915975 120 tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagttaaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagttaaaaaaat Predict ORF larger than 30AA ================================================ tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagttaaaaaaat 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: 37 End: 66 ....................................CTTGATAAAATTTATTTTAAATGTTAAAAT...................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 56 End: 85 .......................................................TTTGAGTGTAGTTTTTTATCTTGATAAAAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagttaaaaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0288:FN0289|FN0288:FN0289:Hypoxanthine-guanine phosphoribosyltransferase:hypothetical protein:<-<-:915856..915975 120 tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagttaaaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_003454_FN0288_FN0289|Hypoxanthine-guanine phosphoribosyltransferase:hypothetical protein|NEGATIVE:NEGATIVE|[915856,915975]|120 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagtt........ tgaaaatcctcccctaagtttaatatatattaatagattttaacatttaaaataaattttatcaagataaaaaactacactcaaacctttaattaagattgtgagtgtagtt........ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAUCCUCCCCUAAGUUUAAUAUAUAUUAAUAGAUUUUAACAUUUAAAAUAAAUUUUAUCAAGAUAAAAAACUACACUCAAACCUUUAAUUAAGAUUGUGAGUGUAGUU ...............(((((((.((.....)).)))))))................((((((....)))))).((((((((((...(((.....)))....)))))))))). (-16.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUACACUCACAAUCUUAAUUAAAGGUUUGAGUGUAGUUUUUUAUCUUGAUAAAAUUUAUUUUAAAUGUUAAAAUCUAUUAAUAUAUAUUAAACUUAGGGGAGGAUUUUCA (((((((((((.((((((.....))))))))))))))))).....((((..(.((.((((...((.(((((((......))))))).)).)))).)).)..))))....... (-21.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 731 110 61 201 152 NC_003454:FN0288|5end_Hypoxanthine-guanine_phosphoribosyltransferase_915765..915995_NEGATIVE 198 109 71 214 172 NC_003454:FN1929|5end_Competence-damage_protein_cinA_429733..429963_NEGATIVE 191 110 73 70 31 NC_003454:FN0839|5end_hypothetical_protein_1501426..1501656_NEGATIVE 190 27 5 80 60 NC_003454:FN1255|5end_NagD_protein_1911892..1912122_NEGATIVE 187 29 1 33 11 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 181 16 3 120 107 NC_003454:FN0018|5end_hypothetical_protein_656448..656678_NEGATIVE 179 50 1 128 82 NC_003454:FN0564|5end_hypothetical_protein_1217017..1217247_NEGATIVE 178 110 69 136 93 NC_003454:FN1443|5end_Transposase_2111518..2111748_NEGATIVE 178 110 69 136 93 NC_003454:FN0786|5end_Transposase_1442465..1442695_POSITIVE 178 110 69 136 93 NC_003454:FN0135|5end_Transposase_770238..770468_POSITIVE 178 48 8 159 103 NC_003454:FN1797|5end_Spermidine/putrescine_transport_ATP-binding_protein_potA_278821..279051_POSITIVE 164 60 13 156 101 NC_003454:FN1231|5end_Inosine-5'-monophosphate_dehydrogenase_1888906..1889136_NEGATIVE 163 110 73 200 161 NC_003454:FN1444|5end_GMP_synthase_[glutamine-hydrolyzing]_2111585..2111815_POSITIVE 160 47 5 142 95 NC_003454:FN0022|5end_hypothetical_protein_660790..661020_POSITIVE 159 46 5 137 98 NC_003454:FN0635|5end_tRNA_pseudouridine_synthase_B_1294993..1295223_NEGATIVE 159 42 7 138 99 NC_003454:FN0257|5end_Transporter_882516..882746_POSITIVE 158 41 7 128 96 NC_003454:FN1957|5end_hypothetical_protein_460827..461057_NEGATIVE 157 50 5 145 97 NC_003454:FN0819|5end_Tetratricopeptide_repeat_family_protein_1477248..1477478_POSITIVE 155 23 7 111 95 NC_003454:FN1306|5end_Methyltransferase_1961674..1961904_POSITIVE 155 18 4 107 92 NC_003454:FN0829|5end_hypothetical_protein_1489873..1490103_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 110 64 76 31 NC_003454:FN1498|3end_Integral_membrane_protein_3542..3692_POSITIVE 249 110 64 78 31 NC_003454:FN1719|3end_hypothetical_protein_218747..218897_POSITIVE 198 110 71 66 26 NC_003454:FN0177|3end_Cell_division_inhibitor_MinE_802336..802486_POSITIVE 191 110 73 42 3 NC_003454:FN1019|3end_3-hydroxybutyryl-CoA_dehydrogenase_1672945..1673095_NEGATIVE 190 27 5 52 32 NC_003454:FN1256|3end_C4-dicarboxylate_transporter_large_subunit_1911920..1912070_NEGATIVE 185 110 68 87 39 NC_003454:FN1904|3end_Transcriptional_regulator,_MarR_family_393633..393783_POSITIVE 181 110 62 78 23 NC_003454:FN1499|3end_Cell_surface_protein_5166..5316_POSITIVE 179 50 1 94 48 NC_003454:FN0565|3end_hypothetical_protein_1217051..1217201_NEGATIVE 179 32 10 60 38 NC_003454:FN0173|3end_hypothetical_protein_799304..799454_POSITIVE 178 110 69 68 26 NC_003454:FN0178|3end_UNC-44_ankyrins_802390..802540_NEGATIVE 171 110 64 69 25 NC_003454:FN0435|3end_Purine_nucleoside_phosphorylase_1077821..1077971_POSITIVE 171 110 64 82 37 NC_003454:FN1545|3end_Ferredoxin_like_protein_59497..59647_POSITIVE 169 110 90 29 8 NC_003454:FN1798|3end_Spermidine/putrescine_transport_system_permease_protein_potB_280872..281022_POSITIVE 164 60 13 62 7 NC_003454:FN1232|3end_Transcriptional_regulator,_MarR_family_1889000..1889150_NEGATIVE 164 110 63 75 21 NC_003454:FN1546|3end_translation_elongation_factor_EF-G_59529..59679_NEGATIVE 160 47 5 126 79 NC_003454:FN0021|3end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_660854..661004_POSITIVE 159 110 73 80 41 NC_003454:FN1463|3end_pyridoxine_biosynthesis_protein_2145924..2146074_POSITIVE 155 29 7 52 29 NC_003454:FN0950|3end_Precorrin-6X_reductase_1606975..1607125_NEGATIVE 155 63 28 69 33 NC_003454:FN1796|3end_hypothetical_protein_278795..278945_POSITIVE 153 45 7 139 97 NC_003454:FN0479|3end_RNA_polymerase_sigma-E_factor_1127532..1127682_POSITIVE