Origin IGS: acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaatacccaaaaaaaaacgaccataacggtcgtttttttgca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgcaaaaaaacgaccgttatggtcgtttttttttgggtattcaggaatattttttaacatttaagacataccaagcaattgcaaaaatcggaatgacctatttttagagatatctacataatccctttgtcatactctaacattcattgtgcaaaaccacctctaatcctcttctttctctgctctttccttaaagaaatgttaacattttcttaaaactaacttatattaggaatttttaagccgcagtctgtatactttctacaaatcatctaagaaagaggt Mask Tandem Repeat Region ================================================ acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaatacccaaaaaaaaacgaccataacggtcgtttttttgca Find is-nt database================================================ Query_seq: SSA_0425:SSA_0426|SSA_0425:SSA_0426:Glycosyltransferase, putative:hypothetical protein:<-<-:423370..423654 285 acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaatacccaaaaaaaaacgaccataacggtcgtttttttgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0425:SSA_0426|SSA_0425:SSA_0426:Glycosyltransferase, putative:hypothetical protein:<-<-:423370..423654 285 acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaatacccaaaaaaaaacgaccataacggtcgtttttttgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0425:SSA_0426|SSA_0425:SSA_0426:Glycosyltransferase, putative:hypothetical protein:<-<-:423370..423654 285 acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaatacccaaaaaaaaacgaccataacggtcgtttttttgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaatacccaaaaaaaaacgaccataacggtcgtttttttgca Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 73 End: 186 ........................................................................ S F T L M E K L F S C L F F L I L P P K A C H I N S Y S L P I I Y I D R F M ................................................................................................... acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaatacccaaaaaaaaacgaccataacggtcgtttttttgca 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: 84 Start: 56 End: 85 .......................................................GTTAACATTTTCTTAAAACTAACTTATATT........................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaatacccaaaaaaaaacgaccataacggtcgtttttttgca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0425:SSA_0426|SSA_0425:SSA_0426:Glycosyltransferase, putative:hypothetical protein:<-<-:423370..423654 285 acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaatacccaaaaaaaaacgaccataacggtcgtttttttgca Intra-Species Hit: Count: 1 Min: 1 Max: 251 Len: 251 Subject: NC_009009_SSA_0425_SSA_0426|Glycosyltransferase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[423370,423654]|285 HSP 1 e-value: 1.0E-140 bit: 498.0 Len: 251 Query Start:1 Query End:251 Subject Strand: POSITIVE Subject Start: 1 Subject End: 251 acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaataccc.................................. acctctttcttagatgatttgtagaaagtatacagactgcggcttaaaaattcctaatataagttagttttaagaaaatgttaacatttctttaaggaaagagcagagaaagaagaggattagaggtggttttgcacaatgaatgttagagtatgacaaagggattatgtagatatctctaaaaataggtcattccgatttttgcaattgcttggtatgtcttaaatgttaaaaaatattcctgaataccc.................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUCUUUCUUAGAUGAUUUGUAGAAAGUAUACAGACUGCGGCUUAAAAAUUCCUAAUAUAAGUUAGUUUUAAGAAAAUGUUAACAUUUCUUUAAGGAAAGAGCAGAGAAAGAAGAGGAUUAGAGGUGGUUUUGCACAAUGAAUGUUAGAGUAUGACAAAGGGAUUAUGUAGAUAUCUCUAAAAAUAGGUCAUUCCGAUUUUUGCAAUUGCUUGGUAUGUCUUAAAUGUUAAAAAAUAUUCCUGAAUACCC .((((((.(((......((((((.......))))))((((..(((........(((((....))))).(((((..(((((....)))))..)))))..))).))))...))))))))).(((((((((..((((((.(((...(((((.....))))).....))).)))))))))))))))...((((.(((.((((.....((....)))))).))).))))........................... (-48.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUAUUCAGGAAUAUUUUUUAACAUUUAAGACAUACCAAGCAAUUGCAAAAAUCGGAAUGACCUAUUUUUAGAGAUAUCUACAUAAUCCCUUUGUCAUACUCUAACAUUCAUUGUGCAAAACCACCUCUAAUCCUCUUCUUUCUCUGCUCUUUCCUUAAAGAAAUGUUAACAUUUUCUUAAAACUAACUUAUAUUAGGAAUUUUUAAGCCGCAGUCUGUAUACUUUCUACAAAUCAUCUAAGAAAGAGGU .(((((((..((((.((....)).))))..)).)))))......(((((.......(((((........((((((.(((..(((.........))).))))))))))))))....)))))................(((((((((((((.......((((..(((((....)))))..))))..((((......)))).............))))..((((.......)))).........))))))))). (-39.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 854 140 91 231 182 NC_009009:SSA_0425|5end_Glycosyltransferase,_putative_423279..423509_NEGATIVE 347 133 95 85 36 NC_009009:SSA_1049|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064085..1064315_POSITIVE 319 228 181 198 144 NC_009009:SSA_1827|5end_Alpha-glycerophosphate_oxidase,_putative_1816112..1816342_POSITIVE 292 136 93 219 164 NC_009009:SSA_0260|5end_Manganese/Zinc_ABC_transporter_substrate-binding_lipoprotein_precursor,_putative_254585..254815_NEGATIVE 287 124 81 68 12 NC_009009:SSA_0651|5end_hypothetical_protein_634548..634778_POSITIVE 279 223 187 204 164 NC_009009:SSA_2375|5end_Tryptophanyl-tRNA_synthetase,_putative_2378246..2378476_NEGATIVE 275 228 181 183 134 NC_009009:SSA_0851|5end_Cation_efflux_family_protein,_putative_838900..839130_NEGATIVE 269 136 94 198 150 NC_009009:SSA_0388|5end_Mismatch_repair_ATPase_(MutS_family),_putative_382474..382704_POSITIVE 262 135 94 158 112 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 260 130 81 231 183 NC_009009:SSA_1590|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1592702..1592932_POSITIVE 257 143 104 139 92 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 255 126 95 47 15 NC_009009:SSA_0351|5end_Signal_peptidase_I,_putative_344907..345137_NEGATIVE 254 135 104 205 175 NC_009009:SSA_0608|5end_Macrolide-efflux_protein,_putative_598184..598414_NEGATIVE 253 150 101 205 142 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 251 180 132 87 40 NC_009009:SSA_1312|5end_RADC-like_protein,_putative_1329663..1329893_NEGATIVE 250 148 101 190 146 NC_009009:SSA_2066|5end_DNA_polymerase_III_polC-type,_putative_2070137..2070367_NEGATIVE 250 136 96 80 36 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 249 139 91 202 155 NC_009009:SSA_0886|5end_Enolase,_putative_879673..879903_POSITIVE 246 128 87 171 134 NC_009009:SSA_0845|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_830046..830276_NEGATIVE 246 158 111 210 156 NC_009009:SSA_0307|5end_Glutamine_synthetase_type_1,_putative_302987..303217_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 133 95 104 55 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 330 135 102 63 29 NC_009009:SSA_0973|3end_hypothetical_protein_980687..980837_POSITIVE 319 228 181 130 76 NC_009009:SSA_1826|3end_Glycerol_kinase,_putative_1816124..1816274_POSITIVE 291 158 111 84 42 NC_009009:SSA_0658|3end_Conserved_uncharacterized_protein_642805..642955_POSITIVE 271 46 1 51 2 NC_009009:SSA_0549|3end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_545651..545801_POSITIVE 266 150 102 108 53 NC_009009:SSA_1793|3end_Histidine_kinase_(sensor_protein),_putative_1775126..1775276_NEGATIVE 255 126 95 43 11 NC_009009:SSA_0352|3end_Ribonuclease_HIII,_putative_344911..345061_NEGATIVE 254 135 104 142 112 NC_009009:SSA_0609|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_598247..598397_NEGATIVE 254 135 94 87 43 NC_009009:SSA_0098|3end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_100116..100266_POSITIVE 253 150 101 95 32 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 250 136 96 83 39 NC_009009:SSA_1049|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064971..1065121_POSITIVE 248 225 189 94 67 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 246 133 93 105 50 NC_009009:SSA_2076|3end_Conserved_uncharacterized_protein_2079390..2079540_NEGATIVE 241 211 171 138 93 NC_009009:SSA_2073|3end_Undecaprenyl_pyrophosphate_synthetase,_putative_2075622..2075772_NEGATIVE 241 126 90 45 5 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 240 46 2 124 90 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 238 52 12 91 43 NC_009009:SSA_1170|3end_hypothetical_protein_1196933..1197083_NEGATIVE 237 221 187 38 11 NC_009009:SSA_1417|3end_SAM-dependent_methyltransferase,_putative_1427304..1427454_NEGATIVE 234 223 190 143 108 NC_009009:SSA_2044|3end_Cysteinyl-tRNA_synthetase,_putative_2047066..2047216_NEGATIVE 234 129 96 144 114 NC_009009:SSA_1162|3end_Possible_fimbrial_assembly_protein_fimC,_putative_1188489..1188639_NEGATIVE