Origin IGS: aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagtattttttgcattggaatttttcttttcttttttttcttctttatgttacaatactagtacgaattatgtattaaataagaatttataaaaaaatttagagggagatata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatatctccctctaaatttttttataaattcttatttaatacataattcgtactagtattgtaacataaagaagaaaaaaaagaaaagaaaaattccaatgcaaaaaatactcctagttctcactaagagtattttctattaattttataatttaatacaatgggagaatctccactt Mask Tandem Repeat Region ================================================ aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagtattttttgcattggaatttttcttttcttttttttcttctttatgttacaatactagtacgaattatgtattaaataagaatttataaaaaaatttagagggagatata Find is-nt database================================================ Query_seq: FN0221:FN0222|FN0221:FN0222:Carbon starvation protein A:Melibiose carrier protein:->->:846774..846951 178 aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagtattttttgcattggaatttttcttttcttttttttcttctttatgttacaatactagtacgaattatgtattaaataagaatttataaaaaaatttagagggagatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0221:FN0222|FN0221:FN0222:Carbon starvation protein A:Melibiose carrier protein:->->:846774..846951 178 aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagtattttttgcattggaatttttcttttcttttttttcttctttatgttacaatactagtacgaattatgtattaaataagaatttataaaaaaatttagagggagatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0221:FN0222|FN0221:FN0222:Carbon starvation protein A:Melibiose carrier protein:->->:846774..846951 178 aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagtattttttgcattggaatttttcttttcttttttttcttctttatgttacaatactagtacgaattatgtattaaataagaatttataaaaaaatttagagggagatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagtattttttgcattggaatttttcttttcttttttttcttctttatgttacaatactagtacgaattatgtattaaataagaatttataaaaaaatttagagggagatata Predict ORF larger than 30AA ================================================ aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagtattttttgcattggaatttttcttttcttttttttcttctttatgttacaatactagtacgaattatgtattaaataagaatttataaaaaaatttagagggagatata 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: 81 Start: 92 End: 121 ...........................................................................................TTTTCTTTTTTTTCTTCTTTATGTTACAAT......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagtattttttgcattggaatttttcttttcttttttttcttctttatgttacaatactagtacgaattatgtattaaataagaatttataaaaaaatttagagggagatata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -9.0 Tail_Score: -5.15969 Start: 47 End: 70 Full_Region: AAAATTAATAGAAAA TACTCTTAGT GAGA ACTAGGAGTA TTTTTTGCATTGGAA ..............................................TACTCTTAGTGAGAACTAGGAGTA............................................................................................................ TransTerm Strand: - Conf: 81 HP_score: -6.8 Tail_Score: -4.77629 Start: 47 End: 70 Full_Region: ttccaatgcaaaaaa tactcctagt tctc actaagagta ttttctattaatttt ..............................................tactcctagttctcactaagagta............................................................................................................ Find igs database================================================ Query_seq: FN0221:FN0222|FN0221:FN0222:Carbon starvation protein A:Melibiose carrier protein:->->:846774..846951 178 aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagtattttttgcattggaatttttcttttcttttttttcttctttatgttacaatactagtacgaattatgtattaaataagaatttataaaaaaatttagagggagatata Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: NC_003454_FN0221_FN0222|Carbon starvation protein A:Melibiose carrier protein|POSITIVE:POSITIVE|[846774,846951]|178 HSP 1 e-value: 4.0E-32 bit: 139.0 Len: 70 Query Start:1 Query End:70 Subject Strand: POSITIVE Subject Start: 1 Subject End: 70 aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagta............................................................................................................ aagtggagattctcccattgtattaaattataaaattaatagaaaatactcttagtgagaactaggagta............................................................................................................ HSP 2 e-value: 7.0E-18 bit: 91.7 Len: 67 Query Start:112 Query End:178 Subject Strand: POSITIVE Subject Start: 112 Subject End: 178 ...............................................................................................................atgttacaatactagtacgaattatgtattaaataagaatttatnnnnnnntttagagggagatata ...............................................................................................................atgttacaatactagtacgaattatgtattaaataagaatttataaaaaaatttagagggagatata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUGGAGAUUCUCCCAUUGUAUUAAAUUAUAAAAUUAAUAGAAAAUACUCUUAGUGAGAACUAGGAGUAUUUUUUGCAUUGGAAUUUUUCUUUUCUUUUUUUUCUUCUUUAUGUUACAAUACUAGUACGAAUUAUGUAUUAAAUAAGAAUUUAUAAAAAAAUUUAGAGGGAGAUAUA (((..((((.....(((.((((....((((......)))).(((((((((((((((....))))))))))))))))))).)))......))))..))).....((((((((............(((((((.....))))))).....((((((......)))))).)))))))).... (-37.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUCUCCCUCUAAAUUUUUUUAUAAAUUCUUAUUUAAUACAUAAUUCGUACUAGUAUUGUAACAUAAAGAAGAAAAAAAAGAAAAGAAAAAUUCCAAUGCAAAAAAUACUCCUAGUUCUCACUAAGAGUAUUUUCUAUUAAUUUUAUAAUUUAAUACAAUGGGAGAAUCUCCACUU ....((((((.....(((...((((((((((((.((((....(((((.(......).)))))....)))).)))))............................(((((((((.((((....)))).)))))))))........)))))))...))).....)))))).......... (-28.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 110 64 223 177 NC_003454:FN1780|5end_hypothetical_protein_261664..261894_NEGATIVE 253 130 81 54 7 NC_003454:FN1432|5end_Leucine-,_isoleucine-,_valine-,_threonine-,_and_alanine-binding_protein_2101580..2101810_NEGATIVE 238 110 61 119 72 NC_003454:FN2085|5end_hypothetical_protein_597045..597275_NEGATIVE 237 108 64 214 171 NC_003454:FN1622|5end_Uridylate_kinase_129640..129870_POSITIVE 231 127 81 47 8 NC_003454:FN1252|5end_34_kDa_membrane_antigen_precursor_1909368..1909598_POSITIVE 226 118 77 76 39 NC_003454:FN1792|5end_hypothetical_protein_273264..273494_NEGATIVE 221 116 72 56 13 NC_003454:FN0244|5end_COP_associated_protein_868115..868345_POSITIVE 215 107 63 114 64 NC_003454:FN1364|5end_LSU_ribosomal_protein_L32P_2015561..2015791_NEGATIVE 215 120 71 93 42 NC_003454:FN0105|5end_Hypothetical_cytosolic_protein_740207..740437_POSITIVE 213 93 53 104 68 NC_003454:FN1704|5end_Serine_protease_199135..199365_POSITIVE 209 107 61 111 66 NC_003454:FN0173|5end_hypothetical_protein_797839..798069_POSITIVE 207 115 74 170 114 NC_003454:FN0309|5end_Iron(III)-transport_system_permease_protein_sfuB_944099..944329_POSITIVE 205 128 84 54 5 NC_003454:FN1652|5end_Oligopeptide-binding_protein_oppA_147540..147770_NEGATIVE 203 113 71 87 37 NC_003454:FN1763|5end_Hypothetical_cytosolic_protein_256562..256792_NEGATIVE 201 106 67 221 182 NC_003454:FN1230|5end_Hypothetical_cytosolic_protein_1887172..1887402_NEGATIVE 201 106 63 55 4 NC_003454:FN2015|5end_ATP-dependent_protease_ATP-binding_subunit_518255..518485_NEGATIVE 199 110 62 164 122 NC_003454:FN0716|5end_Phophatidylinositol-4-phosphate_5-kinase_1373969..1374199_POSITIVE 199 114 72 230 189 NC_003454:FN0245|5end_Copper-exporting_ATPase_868291..868521_POSITIVE 199 107 71 47 3 NC_003454:FN1553|5end_Transporter_68538..68768_NEGATIVE 199 109 67 119 78 NC_003454:FN1527|5end_hypothetical_protein_42572..42802_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 76 32 50 2 NC_003454:FN0221|3end_Carbon_starvation_protein_A_846713..846863_POSITIVE 262 100 54 80 39 NC_003454:FN0861|3end_hypothetical_protein_1521738..1521888_NEGATIVE 237 108 64 149 106 NC_003454:FN1621|3end_elongation_factor_Ts_129655..129805_POSITIVE 221 104 64 151 109 NC_003454:FN1781|3end_LytB_protein_261732..261882_NEGATIVE 217 116 74 101 60 NC_003454:FN2055|3end_hypothetical_protein_564002..564152_NEGATIVE 207 108 63 56 13 NC_003454:FN1236|3end_Choline_transport_protein_1892512..1892662_NEGATIVE 207 115 74 151 95 NC_003454:FN0308|3end_Iron(III)-binding_protein_944160..944310_POSITIVE 203 107 69 131 92 NC_003454:FN0805|3end_hypothetical_protein_1464832..1464982_NEGATIVE 202 117 72 145 78 NC_003454:FN2058|3end_Fusobacterium_outer_membrane_protein_family_565711..565861_NEGATIVE 201 116 72 142 85 NC_003454:FN1478|3end_hypothetical_protein_2160328..2160478_NEGATIVE 199 109 67 103 62 NC_003454:FN1528|3end_hypothetical_protein_42588..42738_NEGATIVE 198 128 90 38 1 NC_003454:FN1021|3end_Calcium-transporting_ATPase_1674916..1675066_POSITIVE 197 122 90 37 8 NC_003454:FN0424|3end_Dihydroorotate_dehydrogenase_1068113..1068263_POSITIVE 196 110 61 85 37 NC_003454:FN0626|3end_Hypothetical_cytosolic_protein_1285535..1285685_NEGATIVE 194 109 69 84 45 NC_003454:FN0862|3end_hypothetical_protein_1522126..1522276_NEGATIVE 193 79 31 65 14 NC_003454:FN0670|3end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1326699..1326849_POSITIVE 190 110 66 98 43 NC_003454:FN0203|3end_Glutaconate_CoA-transferase_subunit_B_829631..829781_POSITIVE 189 70 35 78 45 NC_003454:FN0757|3end_Hypothetical_cytosolic_protein_1415656..1415806_NEGATIVE 188 110 61 59 16 NC_003454:FN0889|3end_Dihydrolipoamide_acyltransferase_1551010..1551160_NEGATIVE 186 91 62 135 104 NC_003454:FN1171|3end_Acetate_kinase_1832365..1832515_NEGATIVE