Origin IGS: aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacaaaaaaatgagtctggaataatttccagactcattttgtatttct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaaatacaaaatgagtctggaaattattccagactcatttttttgtgtttacagcaattaaacaatctaatataaaaataaagataaaaacttccgatttaaattgtcggaagtttttgatatgcatattagttt Mask Tandem Repeat Region ================================================ aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacaaaaaaatgagtctggaataatttccagactcattttgtatttct Find is-nt database================================================ Query_seq: SSA_1300:SSA_1301|SSA_1300:SSA_1301:Maltose ABC transporter, permease protein, putative:Conserved uncharacterized protein, possible surface protein:-><-:1318964..1319099 136 aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacaaaaaaatgagtctggaataatttccagactcattttgtatttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1300:SSA_1301|SSA_1300:SSA_1301:Maltose ABC transporter, permease protein, putative:Conserved uncharacterized protein, possible surface protein:-><-:1318964..1319099 136 aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacaaaaaaatgagtctggaataatttccagactcattttgtatttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1300:SSA_1301|SSA_1300:SSA_1301:Maltose ABC transporter, permease protein, putative:Conserved uncharacterized protein, possible surface protein:-><-:1318964..1319099 136 aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacaaaaaaatgagtctggaataatttccagactcattttgtatttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacaaaaaaatgagtctggaataatttccagactcattttgtatttct Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 9 End: 98 ........ M H I K N F R Q F K S E V F I F I F I L D C L I A V N T K K ...................................... Protein_Len: 30 Strand: - Start: 2 End: 91 . V L I C I L F K R C N L D S T K I K I K I N S Q K I A T F M ............................................. aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacaaaaaaatgagtctggaataatttccagactcattttgtatttct 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================================================ aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacaaaaaaatgagtctggaataatttccagactcattttgtatttct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -5.6 Tail_Score: -4.81551 Start: 23 End: 45 Full_Region: aaataaagataaaaa cttccgat ttaaatt gtcggaag tttttgatatgcata ......................cttccgatttaaattgtcggaag........................................................................................... Find igs database================================================ Query_seq: SSA_1300:SSA_1301|SSA_1300:SSA_1301:Maltose ABC transporter, permease protein, putative:Conserved uncharacterized protein, possible surface protein:-><-:1318964..1319099 136 aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacaaaaaaatgagtctggaataatttccagactcattttgtatttct Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_009009_SSA_1300_SSA_1301|Maltose ABC transporter, permease protein, putative:Conserved uncharacterized protein, possible surface protein|POSITIVE:NEGATIVE|[1318964,1319099]|136 HSP 1 e-value: 4.0E-59 bit: 228.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacnnnnnnntgagtctggaataatttccagactcattttgtatttct aaactaatatgcatatcaaaaacttccgacaatttaaatcggaagtttttatctttatttttatattagattgtttaattgctgtaaacacaaaaaaatgagtctggaataatttccagactcattttgtatttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUAAUAUGCAUAUCAAAAACUUCCGACAAUUUAAAUCGGAAGUUUUUAUCUUUAUUUUUAUAUUAGAUUGUUUAAUUGCUGUAAACACAAAAAAAUGAGUCUGGAAUAAUUUCCAGACUCAUUUUGUAUUUCU ...((((((((.(((..((((((((((((.........)))))))))))).....)))...))))))))..((((((.......))))))....(((((((((((((((....)))))))))))))))........ (-41.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAUACAAAAUGAGUCUGGAAAUUAUUCCAGACUCAUUUUUUUGUGUUUACAGCAAUUAAACAAUCUAAUAUAAAAAUAAAGAUAAAAACUUCCGAUUUAAAUUGUCGGAAGUUUUUGAUAUGCAUAUUAGUUU ..(((((((((((((((((((((....))))))))))))...)))))))))................(((((((....(((....((((((((((((((.......)))))))))))))).)))..)))))))... (-44.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 127 82 231 193 NC_009009:SSA_1128|5end_Voltage_gated_chloride_channel_EriC,_putative_1153250..1153480_POSITIVE 264 130 90 204 160 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 248 49 4 136 96 NC_009009:SSA_1820|5end_hypothetical_protein_1809822..1810052_NEGATIVE 226 50 7 45 9 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 214 63 23 72 34 NC_009009:SSA_0431|5end_hypothetical_protein_433275..433505_NEGATIVE 211 84 51 126 97 NC_009009:SSA_1629|5end_Peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type,_putative_1630338..1630568_POSITIVE 204 85 43 209 153 NC_009009:SSA_1802|5end_Snf2_family_protein,_putative_1786470..1786700_NEGATIVE 198 67 23 103 52 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 196 57 18 187 151 NC_009009:SSA_0173|5end_23S_rRNA_m1G745_methyltransferase,_putative_170535..170765_NEGATIVE 194 80 33 228 187 NC_009009:SSA_2112|5end_hypothetical_protein_2116091..2116321_NEGATIVE 194 48 7 159 118 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 194 45 15 65 36 NC_009009:SSA_0053|5end_Beta-galactosidase,_putative_56748..56978_POSITIVE 193 119 73 51 8 NC_009009:SSA_1482|5end_Pullulanase,_putative_1489246..1489476_NEGATIVE 191 56 11 95 49 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 190 85 41 224 175 NC_009009:SSA_0276|5end_Glycosyltransferase,_family_2/glycosyltransferase_family_8,_putative_269718..269948_POSITIVE 189 90 41 90 44 NC_009009:SSA_1475|5end_hypothetical_protein_1480121..1480351_NEGATIVE 187 128 99 75 42 NC_009009:SSA_1487|5end_Conserved_uncharacterized_protein_1494190..1494420_NEGATIVE 186 56 22 227 184 NC_009009:SSA_0851|5end_Cation_efflux_family_protein,_putative_838900..839130_NEGATIVE 181 62 24 95 60 NC_009009:SSA_0303|5end_surface_protein_C_296451..296681_POSITIVE 180 61 24 158 112 NC_009009:SSA_2168|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2167461..2167691_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 120 71 77 28 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 328 128 82 89 50 NC_009009:SSA_1127|3end_H2O-forming_NADH_dehydrogenase,_putative_1153187..1153337_POSITIVE 275 50 18 73 41 NC_009009:SSA_1300|3end_Maltose_ABC_transporter,_permease_protein,_putative_1318903..1319053_POSITIVE 268 119 78 67 31 NC_009009:SSA_1434|3end_Conserved_uncharacterized_Firmicutes_protein_1441100..1441250_POSITIVE 264 120 78 60 18 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 264 130 90 91 47 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 252 128 99 91 55 NC_009009:SSA_1762|3end_Permease,_putative_1748928..1749078_NEGATIVE 252 128 90 92 57 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 242 129 89 84 55 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 226 50 7 58 22 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 218 130 90 102 60 NC_009009:SSA_0799|3end_hypothetical_protein_781713..781863_NEGATIVE 218 60 11 96 50 NC_009009:SSA_0177|3end_DNA-directed_RNA_polymerase_I,_beta_chain_(160_kDa_subunit),_putative_182132..182282_POSITIVE 214 128 95 87 53 NC_009009:SSA_1535|3end_hypothetical_protein_1542457..1542607_NEGATIVE 214 63 23 59 21 NC_009009:SSA_0432|3end_Formate--tetrahydrofolate_ligase,_putative_433288..433438_NEGATIVE 211 84 51 71 42 NC_009009:SSA_1628|3end_MutT/nudix_family_protein,_putative_1630363..1630513_POSITIVE 204 130 82 55 3 NC_009009:SSA_1964|3end_conserved_uncharacterized_protein_1960996..1961146_NEGATIVE 204 85 43 80 24 NC_009009:SSA_1803|3end_GTP-binding_protein,_putative_1786599..1786749_NEGATIVE 201 129 91 78 47 NC_009009:SSA_1533|3end_Glutathione_reductase,_putative_1542212..1542362_POSITIVE 201 130 91 53 17 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 199 84 45 99 60 NC_009009:SSA_2113|3end_hypothetical_protein_2116228..2116378_NEGATIVE