Origin IGS: tagaaaacgagtcggagagatgttctcttgactcgtttttttgtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcctagtcccctctaaaatttctctcatttactaaaatattcgcaaaaagaaagagaaactatctagacaaaaaaacgagtcaagagaacatctctccgactcgttttcta Mask Tandem Repeat Region ================================================ tagaaaacgagtcggagagatgttctcttgactcgtttttttgtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat Find is-nt database================================================ Query_seq: SSA_0748:SSA_0749|SSA_0748:SSA_0749:Sugar:H+ symporter, permease of the major facilitator superfamily, putative:Competence protein, putative:->->:730696..730807 112 tagaaaacgagtcggagagatgttctcttgactcgtttttttgtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0748:SSA_0749|SSA_0748:SSA_0749:Sugar:H+ symporter, permease of the major facilitator superfamily, putative:Competence protein, putative:->->:730696..730807 112 tagaaaacgagtcggagagatgttctcttgactcgtttttttgtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0748:SSA_0749|SSA_0748:SSA_0749:Sugar:H+ symporter, permease of the major facilitator superfamily, putative:Competence protein, putative:->->:730696..730807 112 tagaaaacgagtcggagagatgttctcttgactcgtttttttgtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaaaacgagtcggagagatgttctcttgactcgtttttttgtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat Predict ORF larger than 30AA ================================================ tagaaaacgagtcggagagatgttctcttgactcgtttttttgtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat 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================================================ tagaaaacgagtcggagagatgttctcttgactcgtttttttgtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0748:SSA_0749|SSA_0748:SSA_0749:Sugar:H+ symporter, permease of the major facilitator superfamily, putative:Competence protein, putative:->->:730696..730807 112 tagaaaacgagtcggagagatgttctcttgactcgtttttttgtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_009009_SSA_0748_SSA_0749|Sugar:H+ symporter, permease of the major facilitator superfamily, putative:Competence protein, putative|POSITIVE:POSITIVE|[730696,730807]|112 HSP 1 e-value: 6.0E-45 bit: 180.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 tagaaaacgagtcggagagatgttctcttgactcgnnnnnnngtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat tagaaaacgagtcggagagatgttctcttgactcgtttttttgtctagatagtttctctttctttttgcgaatattttagtaaatgagagaaattttagaggggactaggat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAACGAGUCGGAGAGAUGUUCUCUUGACUCGUUUUUUUGUCUAGAUAGUUUCUCUUUCUUUUUGCGAAUAUUUUAGUAAAUGAGAGAAAUUUUAGAGGGGACUAGGAU .(((((((((((((.((((.....))))))))))))))))).((((....((((((((((....(((((..........))))).)))))))))).......))))...... (-36.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCUAGUCCCCUCUAAAAUUUCUCUCAUUUACUAAAAUAUUCGCAAAAAGAAAGAGAAACUAUCUAGACAAAAAAACGAGUCAAGAGAACAUCUCUCCGACUCGUUUUCUA ......(((..........(((((((..............(((.......)))))))))).......)))...((((((((((.((((.....))))..))))))))))... (-22.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 46 6 100 53 NC_009009:SSA_1863|5end_NH(3)-dependent_NAD(+)_synthetase,_putative_1859413..1859643_NEGATIVE 286 60 11 84 39 NC_009009:SSA_0711|5end_hypothetical_protein_696631..696861_NEGATIVE 280 60 13 84 37 NC_009009:SSA_1128|5end_Voltage_gated_chloride_channel_EriC,_putative_1153250..1153480_POSITIVE 280 67 21 126 70 NC_009009:SSA_0248|5end_hypothetical_protein_241360..241590_POSITIVE 272 46 8 98 59 NC_009009:SSA_2363|5end_Phosphoglycolate_phosphatase,_putative_2365632..2365862_POSITIVE 266 58 14 70 36 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 259 57 23 189 155 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 255 68 26 224 166 NC_009009:SSA_1602|5end_Exoribonuclease,_VacB/Rnb_family,_putative_1609370..1609600_NEGATIVE 249 53 31 75 52 NC_009009:SSA_0393|5end_Bacteriocin_ABC-type_exporter,_ATP_binding/permease_protein,_putative_388766..388996_POSITIVE 248 70 21 223 184 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 247 69 21 85 24 NC_009009:SSA_0315|5end_Transcriptional_regulator,_MarR_family,_putative_310102..310332_POSITIVE 246 50 5 150 112 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 246 57 23 78 45 NC_009009:SSA_0827|5end_Conserved_uncharacterized_cytosolic_protein,_putative_806033..806263_POSITIVE 246 46 9 71 25 NC_009009:SSA_0653|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_636390..636620_POSITIVE 243 68 23 81 41 NC_009009:SSA_1080|5end_Transcriptional_repressor_of_the_fructose_operon,_DeoR_family,_putative_1097538..1097768_POSITIVE 241 52 11 68 12 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 240 69 21 88 30 NC_009009:SSA_0677|5end_rRNA_methylase,_putative_659466..659696_POSITIVE 240 59 13 178 117 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 237 70 21 122 49 NC_009009:SSA_0779|5end_Glycogen_phosphorylase,_putative_762209..762439_POSITIVE 236 70 24 168 113 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 435 50 2 100 50 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 317 66 26 92 52 NC_009009:SSA_0080|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_84194..84344_POSITIVE 299 46 2 96 60 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 297 46 6 103 56 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 292 49 6 136 93 NC_009009:SSA_0022|3end_Surface_protein_cell_wall_anchor,_sortase_B_family,_putative_28428..28578_POSITIVE 288 59 12 45 1 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 280 67 21 141 85 NC_009009:SSA_0247|3end_hypothetical_protein_241455..241605_POSITIVE 272 46 8 46 7 NC_009009:SSA_2362|3end_L-serine_dehydratase_alpha_subunit_2365660..2365810_POSITIVE 261 36 1 85 47 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 259 57 23 150 116 NC_009009:SSA_2233|3end_hypothetical_protein_2232967..2233117_NEGATIVE 252 49 11 109 57 NC_009009:SSA_1625|3end_Lactoylglutathione_lyase,_putative_1626577..1626727_NEGATIVE 251 39 4 84 50 NC_009009:SSA_2374|3end_Inosine-5'-monophosphate_dehydrogenase,_putative_2375534..2375684_NEGATIVE 246 50 5 58 20 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 246 46 9 69 23 NC_009009:SSA_0652|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase,_putative_636468..636618_POSITIVE 241 52 11 65 9 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 240 69 21 95 37 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 240 59 13 138 77 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 236 32 8 31 4 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 235 72 31 140 75 NC_009009:SSA_0189|3end_Competence_protein_ComGF,_putative_191523..191673_POSITIVE 234 56 11 102 62 NC_009009:SSA_0809|3end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791606..791756_POSITIVE