Origin IGS: gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaaatgatggatagacgggaatcctcctgtctgtcttttttactatctttttgttataatggtcagagtgaaaatctagaaatatccaagggagattatc Mask Tandem Repeat Region ================================================ gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg Find is-nt database================================================ Query_seq: SSA_1182:SSA_1183|SSA_1182:SSA_1183:Gid-like protein, putative:hypothetical protein:<-<-:1210957..1211057 101 gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1182:SSA_1183|SSA_1182:SSA_1183:Gid-like protein, putative:hypothetical protein:<-<-:1210957..1211057 101 gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1182:SSA_1183|SSA_1182:SSA_1183:Gid-like protein, putative:hypothetical protein:<-<-:1210957..1211057 101 gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 2 End: 97 . Y D G K S I E L N E S Q G N Y C F S L L F S L C S S E R R D M M .... gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg 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================================================ gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1182:SSA_1183|SSA_1182:SSA_1183:Gid-like protein, putative:hypothetical protein:<-<-:1210957..1211057 101 gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_009009_SSA_1182_SSA_1183|Gid-like protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1210957,1211057]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg gataatctcccttggatatttctagattttcactctgaccattataacaaaaagatagtaaaaaagacagacaggaggattcccgtctatccatcattttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAAUCUCCCUUGGAUAUUUCUAGAUUUUCACUCUGACCAUUAUAACAAAAAGAUAGUAAAAAAGACAGACAGGAGGAUUCCCGUCUAUCCAUCAUUUUG ((.(((((.....(((....)))))))).))................(((((.(((.........((.((((.((......)).)))).)).))).))))) (-12.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAAUGAUGGAUAGACGGGAAUCCUCCUGUCUGUCUUUUUUACUAUCUUUUUGUUAUAAUGGUCAGAGUGAAAAUCUAGAAAUAUCCAAGGGAGAUUAUC .((((....((((((((((((....)))))))))))).))))...((((((((...(((....(((((.......))).))..)))...)))))))).... (-23.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 833 100 51 191 142 NC_009009:SSA_1182|5end_Gid-like_protein,_putative_1210866..1211096_NEGATIVE 268 46 1 58 2 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 249 78 32 230 180 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 249 44 1 68 15 NC_009009:SSA_0866|5end_Cation-transporting_ATPase,_E1-E_2_family,_putative_856983..857213_POSITIVE 243 94 53 91 43 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 239 44 6 57 8 NC_009009:SSA_1491|5end_Methionine_aminopeptidase_A,_putative_1497637..1497867_NEGATIVE 231 80 31 185 134 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 229 44 6 164 130 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 222 99 51 198 147 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 221 57 16 126 71 NC_009009:SSA_1818|5end_Very_short_patch_repair_endonuclease,_putative_1806110..1806340_NEGATIVE 221 80 31 194 146 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 219 96 65 198 157 NC_009009:SSA_2300|5end_hypothetical_protein_2302508..2302738_NEGATIVE 219 98 68 160 124 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 218 79 33 218 175 NC_009009:SSA_1986|5end_Acetyltransferase,_GNAT_family,_putative_1982531..1982761_NEGATIVE 218 97 53 183 127 NC_009009:SSA_0503|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_502231..502461_POSITIVE 217 57 19 146 104 NC_009009:SSA_1126|5end_Thiamine_biosynthesis_lipoprotein,_putative_1151522..1151752_NEGATIVE 217 35 9 89 62 NC_009009:SSA_0792|5end_hypothetical_protein_774618..774848_POSITIVE 216 88 49 168 134 NC_009009:SSA_0154|5end_hypothetical_protein_149836..150066_POSITIVE 215 93 72 196 170 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 214 99 54 198 147 NC_009009:SSA_1584|5end_Ring-cleavage_extradiol_dioxygenase,_putative_1587030..1587260_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 88 52 78 42 NC_009009:SSA_0773|3end_PTS_enzyme_I,_putative_754416..754566_POSITIVE 243 94 53 75 27 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 217 35 9 96 69 NC_009009:SSA_0791|3end_UDP-N-acetylglucosamine-like_protein,_putative_774705..774855_POSITIVE 217 87 49 69 21 NC_009009:SSA_0102|3end_Kinase,_putative_104627..104777_POSITIVE 215 96 68 37 3 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 213 48 4 116 69 NC_009009:SSA_2097|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_2102154..2102304_NEGATIVE 213 92 57 76 49 NC_009009:SSA_1980|3end_50S_ribosomal_protein_L28,_putative_1974444..1974594_NEGATIVE 212 70 22 89 48 NC_009009:SSA_2243|3end_Conserved_uncharacterized_protein_2238769..2238919_NEGATIVE 212 88 54 74 41 NC_009009:SSA_0138|3end_Metal-binding_(Zn)_permease,_putative_134115..134265_POSITIVE 211 45 1 122 83 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 211 87 69 23 1 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 210 96 51 88 28 NC_009009:SSA_0020|3end_Ribose-phosphate_pyrophosphokinase_1,_putative_26609..26759_POSITIVE 209 52 18 45 12 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 209 98 63 107 71 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 206 57 29 41 12 NC_009009:SSA_1819|3end_Valyl-tRNA_synthetase,_putative_1806195..1806345_NEGATIVE 205 43 4 119 75 NC_009009:SSA_2194|3end_Nicotinamide_mononucleotide_transporter,_putative_2194848..2194998_NEGATIVE 203 88 52 83 51 NC_009009:SSA_0027|3end_Acyl_carrier_protein,_putative_31802..31952_POSITIVE 202 42 8 83 40 NC_009009:SSA_1843|3end_Histidine_kinase,_putative_1836472..1836622_NEGATIVE 198 95 72 114 92 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 198 100 65 100 69 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE