Origin IGS: aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttccccagctcctcctaaacccaattctttatctccttttatatcgcattccccctcttgtgtatttaactttgtttatcatagaaaaaatttatttcagtagtt Mask Tandem Repeat Region ================================================ aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa Find is-nt database================================================ Query_seq: SSA_1102:SSA_1103|SSA_1102:SSA_1103:hypothetical protein:hypothetical protein:->->:1123868..1123972 105 aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1102:SSA_1103|SSA_1102:SSA_1103:hypothetical protein:hypothetical protein:->->:1123868..1123972 105 aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1102:SSA_1103|SSA_1102:SSA_1103:hypothetical protein:hypothetical protein:->->:1123868..1123972 105 aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa Predict ORF larger than 30AA ================================================ aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa 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================================================ aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1102:SSA_1103|SSA_1102:SSA_1103:hypothetical protein:hypothetical protein:->->:1123868..1123972 105 aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_009009_SSA_1102_SSA_1103|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1123868,1123972]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa aactactgaaataaattttttctatgataaacaaagttaaatacacaagagggggaatgcgatataaaaggagataaagaattgggtttaggaggagctggggaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUACUGAAAUAAAUUUUUUCUAUGAUAAACAAAGUUAAAUACACAAGAGGGGGAAUGCGAUAUAAAAGGAGAUAAAGAAUUGGGUUUAGGAGGAGCUGGGGAA ..((.(((((...((((((((((............((......(......).......))...........)))..)))))))...))))).))........... ( -7.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCCCAGCUCCUCCUAAACCCAAUUCUUUAUCUCCUUUUAUAUCGCAUUCCCCCUCUUGUGUAUUUAACUUUGUUUAUCAUAGAAAAAAUUUAUUUCAGUAGUU ......((((.((...............................((((..........)))).......((.((.....)).))..............)).)))) ( -2.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 100 58 210 159 NC_009009:SSA_0260|5end_Manganese/Zinc_ABC_transporter_substrate-binding_lipoprotein_precursor,_putative_254585..254815_NEGATIVE 278 98 54 152 107 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 255 98 51 171 119 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 250 100 51 209 161 NC_009009:SSA_1811|5end_6-phosphogluconate_dehydrogenase,_putative_1796830..1797060_NEGATIVE 249 85 47 153 110 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 239 74 45 32 3 NC_009009:SSA_0103|5end_Integral_membrane_protein,_putative_105490..105720_NEGATIVE 236 100 53 73 6 NC_009009:SSA_2333|5end_Integral_membrane_protein,_putative_2336460..2336690_NEGATIVE 233 100 53 229 192 NC_009009:SSA_0252|5end_hypothetical_protein_245839..246069_NEGATIVE 232 89 45 174 123 NC_009009:SSA_1739|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1725540..1725770_POSITIVE 230 85 44 129 89 NC_009009:SSA_1533|5end_Glutathione_reductase,_putative_1540591..1540821_POSITIVE 223 100 59 63 17 NC_009009:SSA_1396|5end_hypothetical_protein_1410374..1410604_NEGATIVE 223 98 51 156 110 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 222 98 66 174 132 NC_009009:SSA_0726|5end_FmtA-like_protein,_putative_710905..711135_POSITIVE 219 96 51 126 69 NC_009009:SSA_1179|5end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1207806..1208036_NEGATIVE 219 96 58 218 172 NC_009009:SSA_0428|5end_Formimidoylglutamase,_putative_428804..429034_NEGATIVE 218 100 51 76 12 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 212 96 54 191 150 NC_009009:SSA_1836|5end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1832236..1832466_NEGATIVE 212 92 51 88 42 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 209 90 44 200 135 NC_009009:SSA_0813|5end_Thioredoxin_reductase,_putative_795406..795636_NEGATIVE 205 99 51 179 141 NC_009009:SSA_0415|5end_Permease,_putative_410568..410798_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 100 59 48 18 NC_009009:SSA_2081|3end_hypothetical_protein_2085490..2085640_POSITIVE 236 100 53 76 9 NC_009009:SSA_2334|3end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2336457..2336607_NEGATIVE 231 99 51 89 25 NC_009009:SSA_0332|3end_hypothetical_protein_326924..327074_POSITIVE 225 100 51 99 43 NC_009009:SSA_2256|3end_hypothetical_protein_2251235..2251385_POSITIVE 223 98 51 151 105 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 219 99 54 81 33 NC_009009:SSA_1203|3end_hypothetical_protein_1227628..1227778_POSITIVE 219 96 51 113 56 NC_009009:SSA_1180|3end_hypothetical_protein_1207819..1207969_NEGATIVE 218 100 51 79 15 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 212 92 51 95 49 NC_009009:SSA_0709|3end_hypothetical_protein_695632..695782_NEGATIVE 211 100 52 54 10 NC_009009:SSA_0704|3end_Isocitrate_dehydrogenase_[NADP],_putative_690550..690700_POSITIVE 211 99 69 29 6 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 209 96 52 39 1 NC_009009:SSA_1744|3end_Iron_compound_ABC_transporter,_permease_protein,_putative_1731999..1732149_POSITIVE 209 90 44 87 22 NC_009009:SSA_0814|3end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_795519..795669_NEGATIVE 205 99 51 100 62 NC_009009:SSA_0414|3end_hypothetical_protein_410569..410719_POSITIVE 200 98 67 62 26 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 198 98 51 63 19 NC_009009:SSA_0066|3end_hypothetical_protein_68095..68245_POSITIVE 194 98 69 147 124 NC_009009:SSA_1329|3end_Conserved_uncharacterized_protein_1345026..1345176_NEGATIVE 192 100 55 60 11 NC_009009:SSA_1743|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1731005..1731155_POSITIVE 191 73 34 49 13 NC_009009:SSA_1325|3end_Ketoacyl_reductase_hetN,_putative_1341573..1341723_NEGATIVE 191 73 46 44 18 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE