Origin IGS: gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatcgtaaattattgcataagaaaggagaaagctatgttaagaatttttatccgaatggtatacagaagtatcgcctatgcgattgttgaagctaaatagaaaggaaatatc Mask Tandem Repeat Region ================================================ gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat Find is-nt database================================================ Query_seq: SSA_1371:SSA_1372|SSA_1371:SSA_1372:FmtA-like protein, putative:hypothetical protein:<-<-:1388923..1389035 113 gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1371:SSA_1372|SSA_1371:SSA_1372:FmtA-like protein, putative:hypothetical protein:<-<-:1388923..1389035 113 gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1371:SSA_1372|SSA_1371:SSA_1372:FmtA-like protein, putative:hypothetical protein:<-<-:1388923..1389035 113 gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 16 End: 111 ............... K A E V I A Y A I S R Y V M R I F I R L M A K E K R I C Y N V M .. gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat 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================================================ gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1371:SSA_1372|SSA_1371:SSA_1372:FmtA-like protein, putative:hypothetical protein:<-<-:1388923..1389035 113 gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_009009_SSA_1371_SSA_1372|FmtA-like protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1388923,1389035]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat gatatttcctttctatttagcttcaacaatcgcataggcgatacttctgtataccattcggataaaaattcttaacatagctttctcctttcttatgcaataatttacgatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUUUCCUUUCUAUUUAGCUUCAACAAUCGCAUAGGCGAUACUUCUGUAUACCAUUCGGAUAAAAAUUCUUAACAUAGCUUUCUCCUUUCUUAUGCAAUAAUUUACGAUAU ...............................(((((((..((((....)))).......(((.(((...............))).)))...)))))))............... (-10.96) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUCGUAAAUUAUUGCAUAAGAAAGGAGAAAGCUAUGUUAAGAAUUUUUAUCCGAAUGGUAUACAGAAGUAUCGCCUAUGCGAUUGUUGAAGCUAAAUAGAAAGGAAAUAUC .....((.(((.((((((((.....(((((((.((......))...)))).)))....(((((((....)))).))))))))))).)))...))................... (-14.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 863 60 11 151 102 NC_009009:SSA_1371|5end_FmtA-like_protein,_putative_1388832..1389062_NEGATIVE 293 47 6 64 23 NC_009009:SSA_0200|5end_Bifunctional_folate_synthesis_protein,_putative_198918..199148_POSITIVE 271 65 22 52 11 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 266 42 5 67 26 NC_009009:SSA_1586|5end_hypothetical_protein_1588182..1588412_NEGATIVE 260 90 44 102 53 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 254 90 42 87 46 NC_009009:SSA_2286|5end_Dihydroxy-acid_dehydratase,_putative_2289596..2289826_NEGATIVE 254 42 5 196 160 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 252 50 1 43 4 NC_009009:SSA_1583|5end_6-O-methylguanine-DNA_methyltransferase,_putative_1586026..1586256_NEGATIVE 245 90 41 102 48 NC_009009:SSA_1824|5end_hypothetical_protein_1812746..1812976_NEGATIVE 244 49 13 66 22 NC_009009:SSA_1541|5end_Peptidase,_U32_family,_putative_1546600..1546830_NEGATIVE 243 88 44 101 53 NC_009009:SSA_1535|5end_hypothetical_protein_1543188..1543418_NEGATIVE 240 50 4 220 162 NC_009009:SSA_1932|5end_Biotin_carboxylase,_putative_1920874..1921104_NEGATIVE 235 88 44 58 13 NC_009009:SSA_2072|5end_Phosphatidate_cytidylyltransferase,_putative_2075603..2075833_NEGATIVE 235 50 8 50 10 NC_009009:SSA_0152|5end_hypothetical_protein_145799..146029_POSITIVE 234 60 12 211 163 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 232 59 20 93 55 NC_009009:SSA_1472|5end_hypothetical_protein_1478655..1478885_NEGATIVE 232 50 15 37 1 NC_009009:SSA_0852|5end_ATP-dependent_DNA_helicase,_putative_839050..839280_POSITIVE 231 58 22 151 108 NC_009009:SSA_0900|5end_Tetratricopeptide_repeat_(TPR)_family_protein_891068..891298_POSITIVE 231 61 28 171 141 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 226 90 45 104 53 NC_009009:SSA_1571|5end_Threonyl-tRNA_synthetase,_putative_1575154..1575384_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 90 44 57 8 NC_009009:SSA_2054|3end_hypothetical_protein_2057792..2057942_NEGATIVE 243 60 16 42 6 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 242 58 11 148 109 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 235 50 8 42 2 NC_009009:SSA_0151|3end_hypothetical_protein_145871..146021_POSITIVE 232 48 3 136 92 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 226 90 45 111 60 NC_009009:SSA_1572|3end_hypothetical_protein_1575147..1575297_NEGATIVE 225 98 56 102 52 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 224 50 3 132 96 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 223 95 57 76 36 NC_009009:SSA_1735|3end_UreX,_putative_1720461..1720611_NEGATIVE 223 93 54 107 63 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 222 56 13 55 13 NC_009009:SSA_0112|3end_50S_ribosomal_protein_L22,_putative_111389..111539_POSITIVE 218 48 16 44 10 NC_009009:SSA_0156|3end_ATPase_with_chaperone_activity,_ATP-binding_subunit,_putative_153322..153472_POSITIVE 216 43 2 127 76 NC_009009:SSA_1139|3end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1167934..1168084_POSITIVE 214 59 17 151 107 NC_009009:SSA_2314|3end_hypothetical_protein_2315886..2316036_NEGATIVE 212 49 11 55 5 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE 211 70 25 57 4 NC_009009:SSA_0073|3end_hypothetical_protein_77611..77761_POSITIVE 208 50 1 126 80 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE 208 39 5 140 110 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 206 66 29 39 1 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 205 64 31 139 104 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE