Origin IGS: tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataaatcctcttttaacatttgatttctactctattcattatagcatatctcttgcagactatttgccaaaaactttccttatgacactcttatagatagacttacgttattagaaaaaacgaacaaatcaacttttgttcgttttctaaattcca Mask Tandem Repeat Region ================================================ tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata Find is-nt database================================================ Query_seq: SSA_0456:SSA_0457|SSA_0456:SSA_0457:Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific, putative:Fructokinase, putative:->->:460646..460802 157 tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0456:SSA_0457|SSA_0456:SSA_0457:Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific, putative:Fructokinase, putative:->->:460646..460802 157 tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0456:SSA_0457|SSA_0456:SSA_0457:Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific, putative:Fructokinase, putative:->->:460646..460802 157 tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 64 End: 156 ............................................................... L L T M L F T K P L Y D A L S I S Y H I S Y F D F T L L P N M . Protein_Len: 36 Strand: - Start: 2 End: 109 . S N L F R V F T S K N T K E L L T L R D I L T D Y P F N K A F L R C S M ................................................ tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata 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================================================ tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0456:SSA_0457|SSA_0456:SSA_0457:Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific, putative:Fructokinase, putative:->->:460646..460802 157 tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_009009_SSA_0456_SSA_0457|Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific, putative:Fructokinase, putative|POSITIVE:POSITIVE|[460646,460802]|157 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata tggaatttagaaaacgaacaaaagttgatttgttcgttttttctaataacgtaagtctatctataagagtgtcataaggaaagtttttggcaaatagtctgcaagagatatgctataatgaatagagtagaaatcaaatgttaaaagaggatttata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAAUUUAGAAAACGAACAAAAGUUGAUUUGUUCGUUUUUUCUAAUAACGUAAGUCUAUCUAUAAGAGUGUCAUAAGGAAAGUUUUUGGCAAAUAGUCUGCAAGAGAUAUGCUAUAAUGAAUAGAGUAGAAAUCAAAUGUUAAAAGAGGAUUUAUA ..((((((.(((((((((((((......)))))))))))))(((..((((((...(((((((((.......((((..((...((((((.(((.......))).))))))...))...))))))))).))))......))))))..)))))))))... (-28.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAUCCUCUUUUAACAUUUGAUUUCUACUCUAUUCAUUAUAGCAUAUCUCUUGCAGACUAUUUGCCAAAAACUUUCCUUAUGACACUCUUAUAGAUAGACUUACGUUAUUAGAAAAAACGAACAAAUCAACUUUUGUUCGUUUUCUAAAUUCCA .........(((..((((.....(..((((.(((((((((...............(((((...)))))..............)))).......)))))))))..)..))))..))).((((((((((((......)))))))))))).......... (-22.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 130 81 61 8 NC_009009:SSA_1573|5end_hypothetical_protein_1576536..1576766_NEGATIVE 260 114 77 194 150 NC_009009:SSA_1470|5end_3-dehydroquinate_dehydratase,_putative_1476984..1477214_NEGATIVE 248 100 53 175 129 NC_009009:SSA_1101|5end_Multidrug_resistance_efflux_pump/hemolysin_secretion_transmembrane_protein,_putative_1121911..1122141_POSITIVE 242 108 61 211 168 NC_009009:SSA_0743|5end_Transcriptional_repressor_(arginine_synthesis),_putative_725759..725989_NEGATIVE 236 90 50 202 153 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 236 130 85 82 43 NC_009009:SSA_1008|5end_Galactokinase,_putative_1009856..1010086_POSITIVE 236 128 82 61 15 NC_009009:SSA_0948|5end_hypothetical_protein_954955..955185_POSITIVE 236 129 82 203 148 NC_009009:SSA_0574|5end_YdjX_protein,_putative_569427..569657_NEGATIVE 233 103 70 178 138 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 232 137 94 75 36 NC_009009:SSA_1725|5end_Branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1711703..1711933_NEGATIVE 229 113 77 181 144 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 228 116 77 58 24 NC_009009:SSA_0105|5end_Uridine_kinase,_putative_106761..106991_POSITIVE 224 102 61 151 111 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 224 63 21 125 75 NC_009009:SSA_1645|5end_hypothetical_protein_1646227..1646457_NEGATIVE 224 107 61 173 130 NC_009009:SSA_1255|5end_hypothetical_protein_1282244..1282474_NEGATIVE 224 114 78 230 195 NC_009009:SSA_1214|5end_Conserved_uncharacterized_Lactobacillales_protein_1237482..1237712_POSITIVE 223 114 82 175 138 NC_009009:SSA_0746|5end_Glucosamine-6-phosphate_deaminase,_putative_727078..727308_POSITIVE 222 99 54 87 41 NC_009009:SSA_2258|5end_hypothetical_protein_2254699..2254929_NEGATIVE 218 109 81 152 127 NC_009009:SSA_1232|5end_Topoisomerase_IV_subunit_B,_putative_1256755..1256985_NEGATIVE 218 110 68 124 83 NC_009009:SSA_0697|5end_hypothetical_protein_680083..680313_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 46 7 84 45 NC_009009:SSA_0456|3end_Phosphotransferase_system_IIC_components,_glucose/maltose/N-acetylglucosamine-specific,_putative_460585..460735_POSITIVE 232 137 94 75 36 NC_009009:SSA_1726|3end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1711703..1711853_NEGATIVE 224 102 61 151 111 NC_009009:SSA_1660|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1656819..1656969_NEGATIVE 224 107 61 60 17 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 223 116 76 107 64 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 222 99 54 59 13 NC_009009:SSA_2259|3end_hypothetical_protein_2254727..2254877_NEGATIVE 218 108 64 64 26 NC_009009:SSA_2193|3end_ADP-ribose_pyrophosphatase,_putative_2194011..2194161_NEGATIVE 217 104 80 26 1 NC_009009:SSA_1502|3end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1505782..1505932_NEGATIVE 214 74 34 130 78 NC_009009:SSA_1236|3end_Mutator_protein,_putative_1261240..1261390_NEGATIVE 213 129 87 55 22 NC_009009:SSA_0741|3end_Acetylornithine_deacetylase/Succinyl-diaminopimelate_desuccinylase,_putative_725190..725340_POSITIVE 210 114 77 38 4 NC_009009:SSA_2011|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012017..2012167_NEGATIVE 209 79 33 45 2 NC_009009:SSA_1207|3end_Phosphate_acetyltransferase,_putative_1231297..1231447_NEGATIVE 209 116 83 32 5 NC_009009:SSA_0104|3end_Queuine_tRNA-ribosyltransferase,_putative_106815..106965_POSITIVE 208 108 66 84 39 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 208 136 91 79 33 NC_009009:SSA_0180|3end_hypothetical_protein_184989..185139_POSITIVE 207 115 86 48 21 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 207 99 53 60 14 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 206 69 34 103 67 NC_009009:SSA_1994|3end_CTP_synthase,_putative_1990861..1991011_NEGATIVE 206 129 85 73 26 NC_009009:SSA_1925|3end_Seryl-tRNA_synthetase,_putative_1914865..1915015_POSITIVE 206 115 74 143 96 NC_009009:SSA_0780|3end_Acid_phosphatase_(PAP2_family),_putative_765328..765478_POSITIVE