Origin IGS: ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctaaactataattaattgttgaaaggaggtataaagtgatactaggaccaatagaatttacgtcaggacctttagtatctggaccagatattatattttcaatatttggtattcctattagttccacc Mask Tandem Repeat Region ================================================ ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag Find is-nt database================================================ Query_seq: FN0364:FN0365|FN0364:FN0365:ATP synthase A chain, sodium ion specific:ATP synthase protein I, sodium ion specific:<-<-:994504..994631 128 ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0364:FN0365|FN0364:FN0365:ATP synthase A chain, sodium ion specific:ATP synthase protein I, sodium ion specific:<-<-:994504..994631 128 ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0364:FN0365|FN0364:FN0365:ATP synthase A chain, sodium ion specific:ATP synthase protein I, sodium ion specific:<-<-:994504..994631 128 ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 2 End: 127 . M E L I G I P N I E N I I S G P D T K G P D V N S I G P S I T L Y L L S T I N Y S L . Protein_Len: 38 Strand: - Start: 1 End: 114 T S S I P I G F I S F I I D P G S V L P G S T F E I P G L I V K Y R R E V M .............. ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.7 Tail_Score: -3.27602 Start: 20 End: 45 Full_Region: cctttagtatctgga ccagatatt atattttc aatatttgg tattcctattagttc ...................ccagatattatattttcaatatttgg................................................................................... TransTerm Strand: - Conf: 73 HP_score: -7.7 Tail_Score: -3.75707 Start: 36 End: 56 Full_Region: ttacgtcaggacctt tagtatctg gac cagatatta tattttcaatatttg ...................................tagtatctggaccagatatta........................................................................ TransTerm Strand: - Conf: 73 HP_score: -7.2 Tail_Score: -3.98224 Start: 39 End: 53 Full_Region: cgtcaggacctttag tatctg gac cagata ttatattttcaatat ......................................tatctggaccagata........................................................................... Find igs database================================================ Query_seq: FN0364:FN0365|FN0364:FN0365:ATP synthase A chain, sodium ion specific:ATP synthase protein I, sodium ion specific:<-<-:994504..994631 128 ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_003454_FN0364_FN0365|ATP synthase A chain, sodium ion specific:ATP synthase protein I, sodium ion specific|NEGATIVE:NEGATIVE|[994504,994631]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag ggtggaactaataggaataccaaatattgaaaatataatatctggtccagatactaaaggtcctgacgtaaattctattggtcctagtatcactttatacctcctttcaacaattaattatagtttag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGGAACUAAUAGGAAUACCAAAUAUUGAAAAUAUAAUAUCUGGUCCAGAUACUAAAGGUCCUGACGUAAAUUCUAUUGGUCCUAGUAUCACUUUAUACCUCCUUUCAACAAUUAAUUAUAGUUUAG ((.((........(((...(((.((((((......)))))).)))))).((((((..(((.((................)).)))))))))........)).))........................ (-23.89) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAAACUAUAAUUAAUUGUUGAAAGGAGGUAUAAAGUGAUACUAGGACCAAUAGAAUUUACGUCAGGACCUUUAGUAUCUGGACCAGAUAUUAUAUUUUCAAUAUUUGGUAUUCCUAUUAGUUCCACC ........................((((.((......(((((((((.((....(......)....)).)))..)))))).((((((((((((........)))))))))...)))...)).))))... (-24.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 886 90 41 181 132 NC_003454:FN0364|5end_ATP_synthase_A_chain,_sodium_ion_specific_994413..994643_NEGATIVE 255 109 61 104 50 NC_003454:FN1847|5end_DTDP-4-dehydrorhamnose_3,5-epimerase_336142..336372_POSITIVE 239 76 35 172 131 NC_003454:FN0161|5end_RNA-directed_DNA_polymerase_788763..788993_POSITIVE 235 110 62 108 57 NC_003454:FN1698|5end_dTDP-4-dehydrorhamnose_reductase_194593..194823_NEGATIVE 232 88 47 200 150 NC_003454:FN1591|5end_RNFB-related_protein_103135..103365_NEGATIVE 218 111 73 139 97 NC_003454:FN0938|5end_hypothetical_protein_1591125..1591355_NEGATIVE 217 105 62 135 84 NC_003454:FN2081|5end_ABC_transporter_substrate-binding_protein_592974..593204_NEGATIVE 212 107 64 109 63 NC_003454:FN2115|5end_hypothetical_protein_624843..625073_NEGATIVE 209 119 73 230 189 NC_003454:FN0173|5end_hypothetical_protein_797839..798069_POSITIVE 205 104 76 122 94 NC_003454:FN0343|5end_hypothetical_protein_976653..976883_NEGATIVE 204 110 73 110 68 NC_003454:FN1683|5end_Acetyltransferase_179082..179312_NEGATIVE 202 98 54 96 36 NC_003454:FN0856|5end_glycogen_branching_enzyme_1516524..1516754_NEGATIVE 201 109 63 90 34 NC_003454:FN0435|5end_Purine_nucleoside_phosphorylase_1077016..1077246_POSITIVE 200 106 74 106 74 NC_003454:FN1197|5end_hypothetical_protein_1857676..1857906_NEGATIVE 200 70 34 68 29 NC_003454:FN0226|5end_4-hydroxythreonine-4-phosphate_dehydrogenase_854089..854319_NEGATIVE 199 92 58 62 26 NC_003454:FN1106|5end_L-serine_dehydratase_1750567..1750797_POSITIVE 197 76 45 215 182 NC_003454:FN1236|5end_Choline_transport_protein_1893480..1893710_NEGATIVE 196 90 43 175 126 NC_003454:FN1011|5end_MGPA_protein_1665660..1665890_NEGATIVE 196 106 61 107 62 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 196 65 25 60 23 NC_003454:FN1917|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_413756..413986_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 109 61 107 53 NC_003454:FN1846|3end_hypothetical_protein_336225..336375_POSITIVE 235 110 62 98 47 NC_003454:FN1699|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_194603..194753_NEGATIVE 225 86 49 70 36 NC_003454:FN1442|3end_Transposase_2110155..2110305_NEGATIVE 209 119 73 116 75 NC_003454:FN0172|3end_RNA_binding_protein_797805..797955_POSITIVE 204 110 73 109 67 NC_003454:FN1684|3end_N-acetylneuraminate_synthase_179083..179233_NEGATIVE 202 98 54 67 7 NC_003454:FN0857|3end_Glycogen_phosphorylase_1516553..1516703_NEGATIVE 200 106 74 103 71 NC_003454:FN1198|3end_Transporter_1857679..1857829_NEGATIVE 200 70 34 43 4 NC_003454:FN0227|3end_hypothetical_protein_854114..854264_NEGATIVE 196 65 25 76 39 NC_003454:FN1918|3end_SPO0B-associated_GTP-binding_protein_413740..413890_NEGATIVE 194 111 89 120 94 NC_003454:FN0802|3end_Amino_acid_transport_system_permease_protein_1461426..1461576_NEGATIVE 190 109 64 74 20 NC_003454:FN0415|3end_hypothetical_protein_1053996..1054146_POSITIVE 190 99 67 112 79 NC_003454:FN1644|3end_50S_ribosomal_protein_L4_140017..140167_NEGATIVE 188 119 73 96 44 NC_003454:FN1830|3end_DNA_polymerase_III_subunits_gamma_and_tau_318571..318721_NEGATIVE 187 110 61 140 97 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 185 96 54 60 19 NC_003454:FN1475|3end_N-acetylneuraminate_lyase_2158737..2158887_POSITIVE 185 109 90 113 91 NC_003454:FN0605|3end_aspartate_aminotransferase_1261097..1261247_POSITIVE 185 101 76 150 125 NC_003454:FN0344|3end_Methyltransferase_976622..976772_NEGATIVE 184 116 78 93 64 NC_003454:FN1632|3end_LSU_ribosomal_protein_L5P_135268..135418_NEGATIVE 183 118 74 95 44 NC_003454:FN1483|3end_adenine_phosphoribosyltransferase_2166011..2166161_NEGATIVE 183 104 73 80 46 NC_003454:FN0361|3end_ATP_synthase_delta_chain,_sodium_ion_specific_992381..992531_NEGATIVE