Origin IGS: aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcaaaaaaactcagctaatttagtgattagctgagtttttatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataaaaactcagctaatcactaaattagctgagtttttttgagcggattttaattggatgatgagcggatttcaccctttctggtctagccctctttatcggctttctt Mask Tandem Repeat Region ================================================ aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcaaaaaaactcagctaatttagtgattagctgagtttttatt Find is-nt database================================================ Query_seq: SSA_0405:SSA_0406|SSA_0405:SSA_0406:Transcriptional regulator, XRE family, putative:hypothetical protein:-><-:402176..402285 110 aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcaaaaaaactcagctaatttagtgattagctgagtttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0405:SSA_0406|SSA_0405:SSA_0406:Transcriptional regulator, XRE family, putative:hypothetical protein:-><-:402176..402285 110 aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcaaaaaaactcagctaatttagtgattagctgagtttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0405:SSA_0406|SSA_0405:SSA_0406:Transcriptional regulator, XRE family, putative:hypothetical protein:-><-:402176..402285 110 aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcaaaaaaactcagctaatttagtgattagctgagtttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcaaaaaaactcagctaatttagtgattagctgagtttttatt Predict ORF larger than 30AA ================================================ aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcaaaaaaactcagctaatttagtgattagctgagtttttatt 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================================================ aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcaaaaaaactcagctaatttagtgattagctgagtttttatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0405:SSA_0406|SSA_0405:SSA_0406:Transcriptional regulator, XRE family, putative:hypothetical protein:-><-:402176..402285 110 aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcaaaaaaactcagctaatttagtgattagctgagtttttatt Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_009009_SSA_0405_SSA_0406|Transcriptional regulator, XRE family, putative:hypothetical protein|POSITIVE:NEGATIVE|[402176,402285]|110 HSP 1 e-value: 9.0E-44 bit: 176.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcnnnnnnnctcagctaatttagtgattagctgagtttttatt aagaaagccgataaagagggctagaccagaaagggtgaaatccgctcatcatccaattaaaatccgctcaaaaaaactcagctaatttagtgattagctgagtttttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAAGCCGAUAAAGAGGGCUAGACCAGAAAGGGUGAAAUCCGCUCAUCAUCCAAUUAAAAUCCGCUCAAAAAAACUCAGCUAAUUUAGUGAUUAGCUGAGUUUUUAUU .....(((.(((.....((......)).....((((((..........)))))).......))).)))...((((((((((((((((....))))))))))))))))... (-33.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAAACUCAGCUAAUCACUAAAUUAGCUGAGUUUUUUUGAGCGGAUUUUAAUUGGAUGAUGAGCGGAUUUCACCCUUUCUGGUCUAGCCCUCUUUAUCGGCUUUCUU ...(((((((((((((((......)))))))))))))))..((((.(((.......((.....((.((((..........)))).))...))......))).)))).... (-31.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 58 11 171 110 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 315 47 3 151 103 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 302 56 15 187 152 NC_009009:SSA_0503|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_502231..502461_POSITIVE 297 70 27 149 102 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 295 44 2 53 15 NC_009009:SSA_1719|5end_Conserved_uncharacterized_protein_1706793..1707023_NEGATIVE 294 56 17 143 106 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 294 46 8 224 181 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 291 50 2 148 92 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 290 44 2 148 110 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 285 67 33 41 6 NC_009009:SSA_0871|5end_Cell_division_protein_FtsX,_putative_863621..863851_POSITIVE 283 54 15 97 47 NC_009009:SSA_1851|5end_Guanylate_kinase,_putative_1846682..1846912_NEGATIVE 281 49 6 67 7 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 281 50 6 156 100 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 281 45 8 52 18 NC_009009:SSA_0415|5end_Permease,_putative_410568..410798_POSITIVE 281 50 7 62 11 NC_009009:SSA_0330|5end_hypothetical_protein_323799..324029_POSITIVE 279 55 13 205 158 NC_009009:SSA_0943|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_950846..951076_POSITIVE 278 45 2 57 12 NC_009009:SSA_0086|5end_V-type_sodium_ATPase,_subunit_K,_putative_87839..88069_POSITIVE 277 106 63 142 97 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 274 47 15 187 156 NC_009009:SSA_1484|5end_DNA_ligase,_putative_1492188..1492418_NEGATIVE 272 46 7 207 154 NC_009009:SSA_2256|5end_hypothetical_protein_2250604..2250834_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 48 2 55 14 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 295 110 65 78 29 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 295 44 2 50 12 NC_009009:SSA_1720|3end_Initiation-control_protein,_putative_1706796..1706946_NEGATIVE 291 110 73 90 60 NC_009009:SSA_1895|3end_Ribosome-binding_factor_A,_putative_1890815..1890965_NEGATIVE 290 44 2 148 110 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 285 67 33 48 13 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 280 47 6 74 40 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 277 106 63 67 22 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 275 46 2 89 44 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 274 47 15 81 50 NC_009009:SSA_1485|3end_Citrulline_cluster-linked_gene,_putative_1492294..1492444_NEGATIVE 272 56 19 51 18 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 271 54 13 138 94 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 268 48 8 133 99 NC_009009:SSA_1182|3end_Gid-like_protein,_putative_1209532..1209682_NEGATIVE 267 105 63 139 88 NC_009009:SSA_1906|3end_Diadenosine_tetraphosphate_(Ap4A)_hydrolase_(histidine_triad_protein,_cell-cycle_regulation),_putative_1900516..1900666_POSITIVE 264 43 13 80 39 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 263 45 8 149 105 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE 261 32 6 61 33 NC_009009:SSA_1728|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713424..1713574_NEGATIVE 261 48 7 64 22 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 257 46 2 106 40 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 253 45 2 71 30 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE