Origin IGS: acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggtttttttgacatgatgggagaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctctcccatcatgtcaaaaaaaccgggtctcgtcccggttttttgatgtttgattcttgtcaatgttagcagcaaaccacttaccgcccaaaatctaccacttactgaacacaagccttgtttctcgggagtttcttgttataataaagataagcagatggaaaggagagcgt Mask Tandem Repeat Region ================================================ acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggtttttttgacatgatgggagaga Find is-nt database================================================ Query_seq: SSA_1982:SSA_1984|SSA_1982:SSA_1984:Transcriptional regulator, LytR/AlgR family, putative:Cell surface SD repeat antigen precursor, putative:<-<-:1975964..1976137 174 acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggtttttttgacatgatgggagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1982:SSA_1984|SSA_1982:SSA_1984:Transcriptional regulator, LytR/AlgR family, putative:Cell surface SD repeat antigen precursor, putative:<-<-:1975964..1976137 174 acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggtttttttgacatgatgggagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1982:SSA_1984|SSA_1982:SSA_1984:Transcriptional regulator, LytR/AlgR family, putative:Cell surface SD repeat antigen precursor, putative:<-<-:1975964..1976137 174 acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggtttttttgacatgatgggagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggtttttttgacatgatgggagaga Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 60 End: 173 ........................................................... M C S V S G R F W A V S G L L L T L T R I K H Q K T G T R P G F F D M M G E . Protein_Len: 41 Strand: - Start: 2 End: 124 . A R R E M Q K D K N Y C S V G S F C P K H E T L P L N Q A T L P K S S V N V L I M .................................................. Protein_Len: 39 Strand: - Start: 1 End: 117 R E G K W R S I K I I V L F E R S V L S T N L L H Y I K P P L H N A A L M S M ......................................................... acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggtttttttgacatgatgggagaga 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================================================ acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggtttttttgacatgatgggagaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -7.5 Tail_Score: -5.44721 Start: 136 End: 151 Full_Region: TCAAACATCAAAAAA CCGGG ACGAGA CCCGG TTTTTTTGACATGAT .......................................................................................................................................CCGGGACGAGACCCGG....................... Find igs database================================================ Query_seq: SSA_1982:SSA_1984|SSA_1982:SSA_1984:Transcriptional regulator, LytR/AlgR family, putative:Cell surface SD repeat antigen precursor, putative:<-<-:1975964..1976137 174 acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggtttttttgacatgatgggagaga Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_009009_SSA_1982_SSA_1984|Transcriptional regulator, LytR/AlgR family, putative:Cell surface SD repeat antigen precursor, putative|NEGATIVE:NEGATIVE|[1975964,1976137]|174 HSP 1 e-value: 1.0E-81 bit: 303.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggnnnnnnngacatgatgggagaga acgctctcctttccatctgcttatctttattataacaagaaactcccgagaaacaaggcttgtgttcagtaagtggtagattttgggcggtaagtggtttgctgctaacattgacaagaatcaaacatcaaaaaaccgggacgagacccggtttttttgacatgatgggagaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGCUCUCCUUUCCAUCUGCUUAUCUUUAUUAUAACAAGAAACUCCCGAGAAACAAGGCUUGUGUUCAGUAAGUGGUAGAUUUUGGGCGGUAAGUGGUUUGCUGCUAACAUUGACAAGAAUCAAACAUCAAAAAACCGGGACGAGACCCGGUUUUUUUGACAUGAUGGGAGAGA ...(((((((.((.(((((((...(((.......(((((...((...........)).))))).......))).)))))))....(((((((((...)))))))))....((((......))))...(((((((((((((......))))).))))))))...)).))))))). (-48.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCUCCCAUCAUGUCAAAAAAACCGGGUCUCGUCCCGGUUUUUUGAUGUUUGAUUCUUGUCAAUGUUAGCAGCAAACCACUUACCGCCCAAAAUCUACCACUUACUGAACACAAGCCUUGUUUCUCGGGAGUUUCUUGUUAUAAUAAAGAUAAGCAGAUGGAAAGGAGAGCGU (((((.(((((..(((((((((.(((((......))))))))))))))........((((((..(((((..(((((...((((.(((....................(((.(((.....)))))).)))))))...))))).)))))..))))))..)))))...))))).... (-44.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 957 90 41 181 132 NC_009009:SSA_1982|5end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975873..1976103_NEGATIVE 345 94 51 192 144 NC_009009:SSA_1662|5end_NADH-dependent_oxidoreductase,_putative_1659422..1659652_NEGATIVE 340 105 69 231 179 NC_009009:SSA_1779|5end_Segregation_and_condensation_protein_A,_putative_1766414..1766644_NEGATIVE 318 98 51 198 152 NC_009009:SSA_0728|5end_Protease,_putative_713688..713918_POSITIVE 314 90 44 230 191 NC_009009:SSA_2332|5end_D-alanyl_carrier_protein,_putative_2335196..2335426_NEGATIVE 312 129 81 205 157 NC_009009:SSA_0554|5end_hypothetical_protein_549265..549495_POSITIVE 302 90 43 78 34 NC_009009:SSA_1990|5end_Zn-porter_lipoprotein,_putative_1986319..1986549_NEGATIVE 294 106 63 32 1 NC_009009:SSA_2303|5end_hypothetical_protein_2305177..2305407_NEGATIVE 292 90 42 185 146 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 288 77 35 177 137 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 286 100 57 186 126 NC_009009:SSA_2331|5end_D-alanine_transfer_protein,_putative_2334964..2335194_NEGATIVE 285 160 115 175 126 NC_009009:SSA_0841|5end_hypothetical_protein_826935..827165_POSITIVE 284 116 77 65 29 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 284 116 77 222 186 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 282 127 89 103 56 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 282 107 66 90 39 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 279 88 43 205 152 NC_009009:SSA_2011|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012856..2013086_NEGATIVE 279 98 65 204 171 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 277 105 63 194 150 NC_009009:SSA_2008|5end_Molecular_chaperone_GrpE_(HSP-70_cofactor),_putative_2010062..2010292_NEGATIVE 275 50 3 151 95 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 160 121 89 47 NC_009009:SSA_1664|3end_Phosphatidylethanolamine_N-methyltransferase,_putative_1664449..1664599_NEGATIVE 319 89 49 126 80 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 318 98 51 69 23 NC_009009:SSA_0727|3end_Metal-dependent_membrane_protease,_putative_713639..713789_POSITIVE 302 90 43 57 13 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 288 77 35 83 43 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 282 107 66 80 29 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 280 158 119 80 27 NC_009009:SSA_2135|3end_Transcriptional_repressor,_DeoR_family_(possibly_truncated),_putative_2137474..2137624_POSITIVE 273 106 61 134 82 NC_009009:SSA_1440|3end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444407..1444557_NEGATIVE 270 48 1 120 76 NC_009009:SSA_2106|3end_Flavin_monoxygenase,_putative_2108015..2108165_NEGATIVE 269 158 130 83 56 NC_009009:SSA_1521|3end_Phosphoenolpyruvate_carboxylase,_putative_1527837..1527987_NEGATIVE 267 165 127 62 30 NC_009009:SSA_2327|3end_hypothetical_protein_2331400..2331550_POSITIVE 266 157 137 92 72 NC_009009:SSA_1955|3end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1951340..1951490_NEGATIVE 266 111 74 107 75 NC_009009:SSA_1629|3end_Peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type,_putative_1631236..1631386_POSITIVE 266 48 7 65 21 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 265 60 14 91 55 NC_009009:SSA_1494|3end_Conserved_uncharacterized_protein_1499514..1499664_NEGATIVE 263 48 1 126 78 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 260 114 72 100 56 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 259 105 74 49 15 NC_009009:SSA_1891|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888146..1888296_NEGATIVE 259 79 46 44 7 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 259 170 123 104 56 NC_009009:SSA_0861|3end_hypothetical_protein_851742..851892_NEGATIVE