Origin IGS: aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatgatctccaatcattattttctatatttccttcacttaaaaaggaaaaagaaagagtaaactgagtagaccgagaaggagccagatccagccaaagataaagaataaaagtattttaacaaaagtaaaaatatgaaacatgattttctcctttcctatcagattgctatt Mask Tandem Repeat Region ================================================ aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc Find is-nt database================================================ Query_seq: SSA_0725:SSA_0726|SSA_0725:SSA_0726:hypothetical protein:FmtA-like protein, putative:->->:710873..711044 172 aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0725:SSA_0726|SSA_0725:SSA_0726:hypothetical protein:FmtA-like protein, putative:->->:710873..711044 172 aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0725:SSA_0726|SSA_0725:SSA_0726:hypothetical protein:FmtA-like protein, putative:->->:710873..711044 172 aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 10 End: 132 ......... M I G K E K I M F H I F T F V K I L L F F I F G W I W L L L G L L S L L F L F P F ........................................ Protein_Len: 33 Strand: + Start: 38 End: 136 ..................................... M F L L L L K Y F Y S L S L A G S G S F S V Y S V Y S F F F L F K .................................... Protein_Len: 35 Strand: + Start: 66 End: 170 ................................................................. M L Y L W L D L A P S R S T Q F T L S F S F L S E G N I E N N D W R S .. aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc 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================================================ aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0725:SSA_0726|SSA_0725:SSA_0726:hypothetical protein:FmtA-like protein, putative:->->:710873..711044 172 aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: NC_009009_SSA_0725_SSA_0726|hypothetical protein:FmtA-like protein, putative|POSITIVE:POSITIVE|[710873,711044]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc aatagcaatctgataggaaaggagaaaatcatgtttcatatttttacttttgttaaaatacttttattctttatctttggctggatctggctccttctcggtctactcagtttactctttctttttcctttttaagtgaaggaaatatagaaaataatgattggagatcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGCAAUCUGAUAGGAAAGGAGAAAAUCAUGUUUCAUAUUUUUACUUUUGUUAAAAUACUUUUAUUCUUUAUCUUUGGCUGGAUCUGGCUCCUUCUCGGUCUACUCAGUUUACUCUUUCUUUUUCCUUUUUAAGUGAAGGAAAUAUAGAAAAUAAUGAUUGGAGAUCAUC ...............(..((((((..............((((((.((....)).))))))........((..((((......))))..))))))))..)(((((.(.(((((.....(((((.((((((((......))))))))...))))).....)))))))))))... (-32.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAUCUCCAAUCAUUAUUUUCUAUAUUUCCUUCACUUAAAAAGGAAAAAGAAAGAGUAAACUGAGUAGACCGAGAAGGAGCCAGAUCCAGCCAAAGAUAAAGAAUAAAAGUAUUUUAACAAAAGUAAAAAUAUGAAACAUGAUUUUCUCCUUUCCUAUCAGAUUGCUAUU ((((((.....))))))..(((((...(((((((........))))))).))))).(((((.((((...((..((((((((......))).....................(((((((.((....)).)))))))...........)))))...))...)))).)))))... (-30.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 119 75 64 13 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 335 110 74 204 165 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 331 126 81 80 34 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 323 108 61 203 144 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 310 112 75 74 31 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 309 109 62 168 111 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 303 117 74 184 139 NC_009009:SSA_0072|5end_ABC_sugar_transporter,_MsmK-like_protein,_putative_75922..76152_POSITIVE 299 120 74 67 15 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 298 120 73 80 30 NC_009009:SSA_0324|5end_Conserved_uncharacterized_protein_317019..317249_POSITIVE 293 128 82 206 153 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 293 120 77 202 168 NC_009009:SSA_1339|5end_Pneumococcal_histidine_triad_protein_D_precursor,_putative_1355424..1355654_NEGATIVE 292 119 74 85 32 NC_009009:SSA_1791|5end_Acylphosphatase,_putative_1773676..1773906_POSITIVE 287 102 61 127 92 NC_009009:SSA_2014|5end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014807..2015037_NEGATIVE 287 111 75 80 37 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 284 108 75 55 16 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 284 120 73 187 138 NC_009009:SSA_0055|5end_PTS_system,_IIC_component,_putative_59034..59264_POSITIVE 283 129 89 102 65 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 282 119 74 209 158 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 279 109 73 114 81 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 277 120 79 197 165 NC_009009:SSA_1416|5end_hypothetical_protein_1427317..1427547_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 119 75 77 26 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 331 126 81 83 37 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 318 105 61 149 88 NC_009009:SSA_0212|3end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_209079..209229_POSITIVE 310 112 75 64 21 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 309 109 62 139 82 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 301 129 87 151 110 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 301 129 81 97 53 NC_009009:SSA_0298|3end_Malate_permease,_putative_292447..292597_POSITIVE 299 109 62 151 89 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 287 102 61 140 105 NC_009009:SSA_2015|3end_Phosphoglycerate_mutase,_putative_2014794..2014944_NEGATIVE 287 111 75 87 44 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 287 119 71 99 53 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 284 108 75 44 5 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 283 129 89 109 72 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 279 109 73 104 71 NC_009009:SSA_1502|3end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1505782..1505932_NEGATIVE 277 120 74 52 4 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 275 119 71 99 49 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE 274 110 79 99 67 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 274 104 67 83 42 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 273 109 69 39 2 NC_009009:SSA_2047|3end_hypothetical_protein_2049735..2049885_NEGATIVE 270 130 81 92 24 NC_009009:SSA_2111|3end_30S_ribosomal_protein_S12,_putative_2115599..2115749_NEGATIVE