Origin IGS: gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttttcactcccttcaagtccaaaatctatataatcataccacatatagaaaagagtgtcaagtattttctgtaagtataatgtagctcctttttattatacaaacaagaagaccaactgctctgctgcagctggtcttcttttgc Mask Tandem Repeat Region ================================================ gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa Find is-nt database================================================ Query_seq: SSA_0819:SSA_0820|SSA_0819:SSA_0820:hypothetical protein:Ribosomal protein S21, putative:->->:801242..801388 147 gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0819:SSA_0820|SSA_0819:SSA_0820:hypothetical protein:Ribosomal protein S21, putative:->->:801242..801388 147 gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0819:SSA_0820|SSA_0819:SSA_0820:hypothetical protein:Ribosomal protein S21, putative:->->:801242..801388 147 gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 16 End: 117 ............... M Q Q S S W S S C L Y N K K E L H Y T Y R K Y L T L F S I C G M I I .............................. Protein_Len: 30 Strand: - Start: 2 End: 91 . L L L G A A A S C N T K K N T Y Y F P A V N Y K C F I S S M ........................................................ gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa 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: 91 Start: 84 End: 113 ...................................................................................CTTGACACTCTTTTCTATATGTGGTATGAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0819:SSA_0820|SSA_0819:SSA_0820:hypothetical protein:Ribosomal protein S21, putative:->->:801242..801388 147 gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: NC_009009_SSA_0819_SSA_0820|hypothetical protein:Ribosomal protein S21, putative|POSITIVE:POSITIVE|[801242,801388]|147 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa gcaaaagaagaccagctgcagcagagcagttggtcttcttgtttgtataataaaaaggagctacattatacttacagaaaatacttgacactcttttctatatgtggtatgattatatagattttggacttgaagggagtgaaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAAAGAAGACCAGCUGCAGCAGAGCAGUUGGUCUUCUUGUUUGUAUAAUAAAAAGGAGCUACAUUAUACUUACAGAAAAUACUUGACACUCUUUUCUAUAUGUGGUAUGAUUAUAUAGAUUUUGGACUUGAAGGGAGUGAAAAAA ....(((((((((((((((......)))))))))))))))((..(((((((.............)))))))..)).............((((((((((..((((((((...))))))))............))))))))))...... (-43.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUCACUCCCUUCAAGUCCAAAAUCUAUAUAAUCAUACCACAUAUAGAAAAGAGUGUCAAGUAUUUUCUGUAAGUAUAAUGUAGCUCCUUUUUAUUAUACAAACAAGAAGACCAACUGCUCUGCUGCAGCUGGUCUUCUUUUGC ......(((((.(.....).......(((((((...........)))))))...))))).................((((((((...........))))))))....((((((((((.((((......)))).)))))))))).... (-32.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 50 1 153 105 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 337 59 14 58 5 NC_009009:SSA_0672|5end_hypothetical_protein_655191..655421_POSITIVE 331 47 3 81 36 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 330 45 11 71 36 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 328 50 4 156 108 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 323 43 6 165 128 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 308 36 13 65 38 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 302 47 4 164 125 NC_009009:SSA_2089|5end_L-xylulose-5-phosphate_3-epimerase,_putative_2094339..2094569_NEGATIVE 302 42 4 145 108 NC_009009:SSA_0583|5end_Nucleotidyltransferase,_putative_574505..574735_POSITIVE 301 44 3 217 173 NC_009009:SSA_0150|5end_hypothetical_protein_143936..144166_POSITIVE 300 45 4 206 162 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 296 60 14 164 111 NC_009009:SSA_0729|5end_hypothetical_protein_714397..714627_POSITIVE 294 40 1 149 111 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 290 45 1 190 143 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 284 43 13 86 52 NC_009009:SSA_0941|5end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_949157..949387_POSITIVE 283 47 11 46 3 NC_009009:SSA_1356|5end_Helicase_subunit_of_the_DNA_excision_repair_complex,_subunit_B,_putative_1371915..1372145_NEGATIVE 282 49 3 87 43 NC_009009:SSA_0590|5end_hypothetical_protein_582144..582374_POSITIVE 281 60 12 82 24 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 279 44 14 87 51 NC_009009:SSA_1734|5end_Cation_(Mg/Ni_uptake)_transport_ATPase,_putative_1720303..1720533_NEGATIVE 277 46 13 203 161 NC_009009:SSA_1899|5end_hypothetical_protein_1894739..1894969_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 473 44 5 92 51 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 400 50 1 96 48 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 338 43 1 66 23 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 337 59 14 61 8 NC_009009:SSA_0671|3end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_655274..655424_POSITIVE 330 45 11 84 49 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 329 46 12 40 1 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE 328 50 4 101 53 NC_009009:SSA_0354|3end_Uncharacterized_membrane_protein_346872..347022_POSITIVE 323 43 6 80 43 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 308 36 13 62 35 NC_009009:SSA_2278|3end_Ukp_protein,_putative_2280410..2280560_NEGATIVE 302 42 4 143 106 NC_009009:SSA_0582|3end_Methylase,_putative_574583..574733_POSITIVE 296 60 11 63 18 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE 295 46 1 88 49 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 294 40 1 59 21 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 288 38 4 150 121 NC_009009:SSA_2090|3end_Hexulose-6-phosphate_synthase,_putative_2094343..2094493_NEGATIVE 285 60 13 115 75 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 282 49 3 70 26 NC_009009:SSA_0589|3end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_582207..582357_POSITIVE 281 60 12 98 40 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 277 47 15 118 75 NC_009009:SSA_1104|3end_50S_ribosomal_protein_L10,_putative_1125323..1125473_POSITIVE 271 38 8 39 5 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 269 32 1 84 49 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE