Origin IGS: tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagtctctcctaaattcttcattatgaaaatacattacatcttttatattcttatagtgtaacatagtcggactcaagttccaatgaaaaacaggatacttcagcataatcatgaatatacaaaaaagacacgaaactaatcgtatcttttgttca Mask Tandem Repeat Region ================================================ tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg Find is-nt database================================================ Query_seq: SSA_0946:SSA_0947|SSA_0946:SSA_0947:Phosphate transport system regulatory protein, putative:hypothetical protein:->->:954187..954342 156 tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0946:SSA_0947|SSA_0946:SSA_0947:Phosphate transport system regulatory protein, putative:hypothetical protein:->->:954187..954342 156 tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0946:SSA_0947|SSA_0946:SSA_0947:Phosphate transport system regulatory protein, putative:hypothetical protein:->->:954187..954342 156 tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 11 End: 154 .......... M R L V S C L F C I F M I M L K Y P V F H W N L S P T M L H Y K N I K D V M Y F H N E E F R R D .. tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 72 End: 101 .......................................................................ATTGGAACTTGAGTCCGACTATGTTACACT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0946:SSA_0947|SSA_0946:SSA_0947:Phosphate transport system regulatory protein, putative:hypothetical protein:->->:954187..954342 156 tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_009009_SSA_0946_SSA_0947|Phosphate transport system regulatory protein, putative:hypothetical protein|POSITIVE:POSITIVE|[954187,954342]|156 HSP 1 e-value: 1.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg tgaacaaaagatacgattagtttcgtgtcttttttgtatattcatgattatgctgaagtatcctgtttttcattggaacttgagtccgactatgttacactataagaatataaaagatgtaatgtattttcataatgaagaatttaggagagactg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAACAAAAGAUACGAUUAGUUUCGUGUCUUUUUUGUAUAUUCAUGAUUAUGCUGAAGUAUCCUGUUUUUCAUUGGAACUUGAGUCCGACUAUGUUACACUAUAAGAAUAUAAAAGAUGUAAUGUAUUUUCAUAAUGAAGAAUUUAGGAGAGACUG .....(((((((((((......)))))))))))..(((((........)))))...(((.(((((((((((((((((.(....))))...(((((((((((.............)).))))))))).......))))))))))..))))...))). (-35.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUCUCUCCUAAAUUCUUCAUUAUGAAAAUACAUUACAUCUUUUAUAUUCUUAUAGUGUAACAUAGUCGGACUCAAGUUCCAAUGAAAAACAGGAUACUUCAGCAUAAUCAUGAAUAUACAAAAAAGACACGAAACUAAUCGUAUCUUUUGUUCA .((((.(..(((.......((((((((.((((..............)))).)))))))).....)))..))))).(((((((...........))).))))...........((((((......(((((.((((......)))).))))))))))) (-20.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 100 51 211 170 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 276 89 51 133 91 NC_009009:SSA_1782|5end_hypothetical_protein_1768123..1768353_NEGATIVE 262 58 13 80 33 NC_009009:SSA_0745|5end_hypothetical_protein_727035..727265_NEGATIVE 257 97 52 63 9 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 255 110 61 130 77 NC_009009:SSA_2167|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2167371..2167601_NEGATIVE 254 80 41 126 87 NC_009009:SSA_0780|5end_Acid_phosphatase_(PAP2_family),_putative_764748..764978_POSITIVE 251 96 51 188 143 NC_009009:SSA_1392|5end_hypothetical_protein_1408423..1408653_NEGATIVE 248 97 51 225 177 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 241 69 21 226 173 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 239 88 41 55 12 NC_009009:SSA_1640|5end_hypothetical_protein_1642530..1642760_NEGATIVE 238 70 23 71 21 NC_009009:SSA_0077|5end_Oxidoreductase,_putative_80738..80968_POSITIVE 235 69 21 146 86 NC_009009:SSA_0770|5end_Ribonucleoside-diphosphate_reductase,_putative_751411..751641_NEGATIVE 234 44 5 206 158 NC_009009:SSA_0837|5end_Glucosyltransferase,_putative_823902..824132_POSITIVE 233 89 44 202 152 NC_009009:SSA_0795|5end_hypothetical_protein_776620..776850_POSITIVE 227 73 31 91 44 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 225 92 51 224 184 NC_009009:SSA_1641|5end_MutT/nudix_family_protein,_putative_1643094..1643324_NEGATIVE 224 99 51 214 141 NC_009009:SSA_2346|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2348546..2348776_NEGATIVE 224 98 51 57 3 NC_009009:SSA_0327|5end_Glycosyltransferase,_putative_319979..320209_POSITIVE 224 89 52 211 164 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 222 99 52 160 118 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 95 51 148 102 NC_009009:SSA_0714|3end_hypothetical_protein_700649..700799_POSITIVE 262 89 52 122 76 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 256 90 46 132 89 NC_009009:SSA_1316|3end_Nicotinamide_mononucleotide_transporter,_putative_1332157..1332307_NEGATIVE 237 85 51 133 104 NC_009009:SSA_0085|3end_V-type_sodium_ATPase,_subunit_I,_putative_87785..87935_POSITIVE 235 49 6 98 58 NC_009009:SSA_0946|3end_Phosphate_transport_system_regulatory_protein,_putative_954126..954276_POSITIVE 227 73 31 87 40 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 224 99 51 113 40 NC_009009:SSA_2347|3end_Coenzyme_F390_synthetase,_putative_2348647..2348797_NEGATIVE 222 99 52 95 53 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 222 76 37 46 1 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 221 89 45 133 82 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE 221 78 41 98 56 NC_009009:SSA_1293|3end_hypothetical_protein_1311554..1311704_NEGATIVE 221 88 42 68 25 NC_009009:SSA_0692|3end_D-Ala-D-Ala_adding_enzyme,_putative_677820..677970_POSITIVE 220 94 53 49 15 NC_009009:SSA_1641|3end_MutT/nudix_family_protein,_putative_1642543..1642693_NEGATIVE 217 35 8 104 72 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 215 87 41 68 25 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 211 93 51 110 78 NC_009009:SSA_1149|3end_Glycosyl_hydrolase,_family_1,_putative_1179876..1180026_POSITIVE 211 96 52 59 11 NC_009009:SSA_0580|3end_Isochorismatase_family_protein,_putative_573399..573549_POSITIVE 211 92 55 59 24 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 210 88 42 150 104 NC_009009:SSA_1878|3end_Conserved_uncharacterized_protein_1871943..1872093_NEGATIVE 207 70 23 151 86 NC_009009:SSA_1415|3end_Oxidoreductase,_putative_1425414..1425564_NEGATIVE