Origin IGS: agctggatttctagctttttttcttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttttcctccaaaagttttcctacctattttatcacaaaagatagggaaattcatctatatttggctataaagtaagaaaaaaagctagaaatccagct Mask Tandem Repeat Region ================================================ agctggatttctagctttttttcttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac Find is-nt database================================================ Query_seq: SSA_1528:SSA_1529|SSA_1528:SSA_1529:Phosphoglycerate mutase, putative:Lysyl-tRNA synthetase, putative:->->:1535911..1536010 100 agctggatttctagctttttttcttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1528:SSA_1529|SSA_1528:SSA_1529:Phosphoglycerate mutase, putative:Lysyl-tRNA synthetase, putative:->->:1535911..1536010 100 agctggatttctagctttttttcttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1528:SSA_1529|SSA_1528:SSA_1529:Phosphoglycerate mutase, putative:Lysyl-tRNA synthetase, putative:->->:1535911..1536010 100 agctggatttctagctttttttcttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctggatttctagctttttttcttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac Predict ORF larger than 30AA ================================================ agctggatttctagctttttttcttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac 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================================================ agctggatttctagctttttttcttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1528:SSA_1529|SSA_1528:SSA_1529:Phosphoglycerate mutase, putative:Lysyl-tRNA synthetase, putative:->->:1535911..1536010 100 agctggatttctagctttttttcttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_009009_SSA_1528_SSA_1529|Phosphoglycerate mutase, putative:Lysyl-tRNA synthetase, putative|POSITIVE:POSITIVE|[1535911,1536010]|100 HSP 1 e-value: 8.0E-38 bit: 157.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 agctggatttctagcnnnnnnncttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac agctggatttctagctttttttcttactttatagccaaatatagatgaatttccctatcttttgtgataaaataggtaggaaaacttttggaggaaaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGGAUUUCUAGCUUUUUUUCUUACUUUAUAGCCAAAUAUAGAUGAAUUUCCCUAUCUUUUGUGAUAAAAUAGGUAGGAAAACUUUUGGAGGAAAAAC ((((((....))))))(((((((((..((((((......))))))........((((((((((......))).)))))))..........))))))))). (-22.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUCCUCCAAAAGUUUUCCUACCUAUUUUAUCACAAAAGAUAGGGAAAUUCAUCUAUAUUUGGCUAUAAAGUAAGAAAAAAAGCUAGAAAUCCAGCU .((((((.......((((((((((.((.............)).))))))))))......(((((.......))))).)))))).((((.(....).)))) (-13.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 80 50 129 98 NC_009009:SSA_1155|5end_Serine_hydroxymethyltransferase,_putative_1183298..1183528_POSITIVE 257 38 1 184 132 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 249 54 11 134 91 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 246 37 1 90 48 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 243 80 49 69 39 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 240 45 2 177 132 NC_009009:SSA_2012|5end_hypothetical_protein_2013470..2013700_NEGATIVE 238 36 4 179 149 NC_009009:SSA_1601|5end_VacB-like_protein,_putative_1607059..1607289_NEGATIVE 237 96 51 127 81 NC_009009:SSA_1503|5end_Ferredoxin,_putative_1506209..1506439_POSITIVE 234 86 41 134 90 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 224 80 34 65 18 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 221 97 53 211 163 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 218 38 4 101 68 NC_009009:SSA_1644|5end_hypothetical_protein_1645617..1645847_NEGATIVE 218 93 62 44 7 NC_009009:SSA_1588|5end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1591905..1592135_NEGATIVE 217 81 41 190 141 NC_009009:SSA_0190|5end_hypothetical_protein_191481..191711_POSITIVE 215 91 58 210 177 NC_009009:SSA_1166|5end_hypothetical_protein_1191929..1192159_POSITIVE 213 56 11 142 93 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 213 48 1 178 129 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 209 37 1 118 75 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 208 37 1 54 23 NC_009009:SSA_2008|5end_Molecular_chaperone_GrpE_(HSP-70_cofactor),_putative_2010062..2010292_NEGATIVE 208 36 1 149 114 NC_009009:SSA_0577|5end_Ancient_RNA-binding_IF3-C_fold_(CRS1/YhbY_domain),_putative_571253..571483_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 80 50 82 51 NC_009009:SSA_1154|3end_hypothetical_protein_1183331..1183481_POSITIVE 249 54 11 147 104 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 248 37 1 151 100 NC_009009:SSA_0590|3end_hypothetical_protein_582817..582967_POSITIVE 243 80 49 72 42 NC_009009:SSA_0852|3end_ATP-dependent_DNA_helicase,_putative_841418..841568_POSITIVE 224 80 34 72 25 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 222 38 1 111 69 NC_009009:SSA_1990|3end_Zn-porter_lipoprotein,_putative_1985402..1985552_NEGATIVE 218 38 4 117 84 NC_009009:SSA_1645|3end_hypothetical_protein_1645601..1645751_NEGATIVE 218 93 62 42 5 NC_009009:SSA_1589|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1591907..1592057_NEGATIVE 215 91 58 66 33 NC_009009:SSA_1165|3end_Transcriptional_regulator,_GntR_family,_putative_1191865..1192015_POSITIVE 213 56 11 50 1 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 213 60 14 121 79 NC_009009:SSA_0189|3end_Competence_protein_ComGF,_putative_191523..191673_POSITIVE 211 47 2 75 29 NC_009009:SSA_0738|3end_Ornithine_carbamoyltransferase,_catabolic,_putative_721000..721150_POSITIVE 210 30 1 106 75 NC_009009:SSA_1528|3end_Phosphoglycerate_mutase,_putative_1535850..1536000_POSITIVE 209 37 1 125 82 NC_009009:SSA_0709|3end_hypothetical_protein_695632..695782_NEGATIVE 208 36 1 41 6 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 208 36 1 102 60 NC_009009:SSA_0247|3end_hypothetical_protein_241455..241605_POSITIVE 208 49 1 113 68 NC_009009:SSA_0207|3end_hypothetical_protein_204944..205094_POSITIVE 206 39 1 117 74 NC_009009:SSA_1611|3end_Era-like_GTP-binding_protein,_putative_1615133..1615283_NEGATIVE 206 46 3 146 106 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 205 60 11 131 91 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE