Origin IGS: ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacgaattttgatatatcaaattatcttcattatatatttttctatgttttttgtaaatattttttgagtaattt .........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 aaattactcaaaaaatatttacaaaaaacatagaaaaatatataatgaagataatttgatatatcaaaattcgttgatgtagagttttattactagttattgttataatataaatgcatgttgtctatttaaaggggagatgatgaagaaggctatgaaaatcacgctcattccagcatatttagcagatgatgggtgaaagcgttggagaacaaatggaaaggaggaaaaag Mask Tandem Repeat Region ================================================ ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacgaattttgatatatcaaattatcttcattatatatttttctatgttttttgtaaatattttttgagtaattt Find is-nt database================================================ Query_seq: SSA_1474:SSA_1475|SSA_1474:SSA_1475:Lipoprotein, putative:hypothetical protein:<-<-:1479832..1480064 233 ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacgaattttgatatatcaaattatcttcattatatatttttctatgttttttgtaaatattttttgagtaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1474:SSA_1475|SSA_1474:SSA_1475:Lipoprotein, putative:hypothetical protein:<-<-:1479832..1480064 233 ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacgaattttgatatatcaaattatcttcattatatatttttctatgttttttgtaaatattttttgagtaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1474:SSA_1475|SSA_1474:SSA_1475:Lipoprotein, putative:hypothetical protein:<-<-:1479832..1480064 233 ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacgaattttgatatatcaaattatcttcattatatatttttctatgttttttgtaaatattttttgagtaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacgaattttgatatatcaaattatcttcattatatatttttctatgttttttgtaaatattttttgagtaattt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 119 End: 223 ...................................................................................................................... M Y I I T I T S N K T L H Q R I L I Y Q I I F I I Y F S M F F V N I F .......... Protein_Len: 36 Strand: - Start: 38 End: 145 ..................................... G D D A L Y A P I L T I K M A K K M M E G K F L C C A N I N Y C Y S T M ........................................................................................ ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacgaattttgatatatcaaattatcttcattatatatttttctatgttttttgtaaatattttttgagtaattt 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: 87 Start: 188 End: 217 ...........................................................................................................................................................................................ATTTACAAAAAACATAGAAAAATATATAAT................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacgaattttgatatatcaaattatcttcattatatatttttctatgttttttgtaaatattttttgagtaattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1474:SSA_1475|SSA_1474:SSA_1475:Lipoprotein, putative:hypothetical protein:<-<-:1479832..1480064 233 ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacgaattttgatatatcaaattatcttcattatatatttttctatgttttttgtaaatattttttgagtaattt Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_009009_SSA_1474_SSA_1475|Lipoprotein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1479832,1480064]|233 HSP 1 e-value: 2.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacga...................................................................... ctttttcctcctttccatttgttctccaacgctttcacccatcatctgctaaatatgctggaatgagcgtgattttcatagccttcttcatcatctcccctttaaatagacaacatgcatttatattataacaataactagtaataaaactctacatcaacga...................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUUCCUCCUUUCCAUUUGUUCUCCAACGCUUUCACCCAUCAUCUGCUAAAUAUGCUGGAAUGAGCGUGAUUUUCAUAGCCUUCUUCAUCAUCUCCCCUUUAAAUAGACAACAUGCAUUUAUAUUAUAACAAUAACUAGUAAUAAAACUCUACAUCAACGA ..................(((((.....((((((....(((.(((.(.....).))).)))...)))))).....................................................((((((...........))))))............))))) (-12.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUUGAUGUAGAGUUUUAUUACUAGUUAUUGUUAUAAUAUAAAUGCAUGUUGUCUAUUUAAAGGGGAGAUGAUGAAGAAGGCUAUGAAAAUCACGCUCAUUCCAGCAUAUUUAGCAGAUGAUGGGUGAAAGCGUUGGAGAACAAAUGGAAAGGAGGAAAAAG ((.(..((((..((((((.......(((((....))))).......(((.((.(((......))).)).)))......)))))).......((((.((((((...((.......)).))))).).))))..))))..).))...................... (-24.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 950 70 21 161 112 NC_009009:SSA_1474|5end_Lipoprotein,_putative_1479741..1479971_NEGATIVE 344 50 2 145 92 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 329 100 57 60 18 NC_009009:SSA_2185|5end_Adenylosuccinate_synthetase,_putative_2185290..2185520_NEGATIVE 328 100 56 190 146 NC_009009:SSA_1759|5end_hypothetical_protein_1746969..1747199_NEGATIVE 309 98 55 222 170 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 304 101 63 116 71 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 300 59 11 140 84 NC_009009:SSA_1736|5end_L-cysteine_desulfhydrase,_putative_1722619..1722849_NEGATIVE 299 59 26 72 18 NC_009009:SSA_1620|5end_Uridylate_kinase,_putative_1622981..1623211_NEGATIVE 296 79 31 207 148 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 295 104 63 146 107 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 293 90 42 107 66 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 286 48 10 180 141 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 283 90 44 142 101 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 283 49 2 197 147 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 282 59 29 45 15 NC_009009:SSA_0276|5end_Glycosyltransferase,_family_2/glycosyltransferase_family_8,_putative_269718..269948_POSITIVE 281 50 4 94 46 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 276 48 5 151 97 NC_009009:SSA_1146|5end_Phosphotransferase_system_cellobiose-specific_component_IIA,_putative_1176453..1176683_POSITIVE 275 77 31 96 50 NC_009009:SSA_1699|5end_hypothetical_protein_1691096..1691326_NEGATIVE 273 50 9 222 180 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 273 82 46 170 130 NC_009009:SSA_1506|5end_Lipopolysaccharide_biosynthesis_protein,_putative_1511222..1511452_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 50 2 67 14 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 304 101 63 116 71 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 300 59 11 138 82 NC_009009:SSA_1737|3end_Cystathionine_gamma-synthase,_putative_1722621..1722771_NEGATIVE 295 104 63 137 98 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 293 90 42 93 52 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 286 59 15 140 102 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 283 90 44 151 110 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 283 49 2 151 101 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 281 50 4 122 74 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 280 37 1 151 120 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 272 97 57 60 21 NC_009009:SSA_1587|3end_hypothetical_protein_1588238..1588388_NEGATIVE 272 63 32 44 19 NC_009009:SSA_0660|3end_Cell_division_protein_DivIVA,_putative_644672..644822_POSITIVE 270 109 63 47 1 NC_009009:SSA_1760|3end_hypothetical_protein_1747126..1747276_NEGATIVE 268 69 21 148 100 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 265 69 30 127 74 NC_009009:SSA_1428|3end_hypothetical_protein_1435638..1435788_NEGATIVE 265 50 4 143 89 NC_009009:SSA_1119|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1145305..1145455_POSITIVE 262 61 30 119 92 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 261 50 1 130 80 NC_009009:SSA_0796|3end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_779060..779210_POSITIVE 256 59 13 147 96 NC_009009:SSA_2233|3end_hypothetical_protein_2232967..2233117_NEGATIVE 256 71 31 144 106 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE