Origin IGS: aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagtttttttgtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accgaacccccggtttcatatatgcaataaaattttttactaaatttaatatactagtaatatatttcatttttgttacaaaaaaactactttgtatttctaaatgatacaaatagattaacttgaataataaaataactcaatatagtgattttttctgaaaattttatagttttcaagaaaatgctaattttataagaaagtcaggagggttcaacctgacaacttgaaaacactggcttttttaaatctagcttccttacttatacaaaaataaacttggataatctaaggtttatagatgactgaaataaaactgtaacacaatctgagtgaacatcttttagacatgagttaaaggaagcaaaatgaaaaggacttagccctgtccaatgcagaactaaatccttttactggttatttatctaacttttgggaataatttaagtttcctctggtt Mask Tandem Repeat Region ================================================ aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagtttttttgtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt Find is-nt database================================================ Query_seq: SSA_0611:SSA_0612|SSA_0611:SSA_0612:HtpX protease, putative:Rgg protein, putative:->->:600576..601035 460 aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagtttttttgtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0611:SSA_0612|SSA_0611:SSA_0612:HtpX protease, putative:Rgg protein, putative:->->:600576..601035 460 aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagtttttttgtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0611:SSA_0612|SSA_0611:SSA_0612:HtpX protease, putative:Rgg protein, putative:->->:600576..601035 460 aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagtttttttgtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagtttttttgtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 63 End: 194 .............................................................. M H W T G L S P F H F A S F N S C L K D V H S D C V T V L F Q S S I N L R L S K F I F V .......................................................................................................................................................................................................................................................................... Protein_Len: 34 Strand: + Start: 270 End: 371 ............................................................................................................................................................................................................................................................................. M S I F L K T I K F S E K I T I L S Y F I I Q V N L F V S F R N T K ......................................................................................... Protein_Len: 45 Strand: + Start: 325 End: 459 .................................................................................................................................................................................................................................................................................................................................... M L L F K L I Y L Y H L E I Q S S F F V T K M K Y I T S I L N L V K N F I A Y M K P G V R . aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagtttttttgtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt 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: 82 Start: 281 End: 310 ........................................................................................................................................................................................................................................................................................CTTGAAAACTATAAAATTTTCAGAAAAAAT...................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagtttttttgtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 68 HP_score: -7.2 Tail_Score: -3.30638 Start: 48 End: 90 Full_Region: TAGATAAATAACCAG TAAAAGGATTTAGTTCTG CATTGGA CAGGGCTAAGTCCTTTTC ATTTTGCTTCCTTTA ...............................................TAAAAGGATTTAGTTCTGCATTGGACAGGGCTAAGTCCTTTTC.................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 78 HP_score: -7.1 Tail_Score: -4.72729 Start: 53 End: 85 Full_Region: AAATAACCAGTAAAA GGATTTAGTTCTG CATTGGA CAGGGCTAAGTCC TTTTCATTTTGCTTC ....................................................GGATTTAGTTCTGCATTGGACAGGGCTAAGTCC....................................................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0611:SSA_0612|SSA_0611:SSA_0612:HtpX protease, putative:Rgg protein, putative:->->:600576..601035 460 aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagtttttttgtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt Intra-Species Hit: Count: 1 Min: 1 Max: 460 Len: 460 Subject: NC_009009_SSA_0611_SSA_0612|HtpX protease, putative:Rgg protein, putative|POSITIVE:POSITIVE|[600576,601035]|460 HSP 1 e-value: 0.0 bit: 870.0 Len: 460 Query Start:1 Query End:460 Subject Strand: POSITIVE Subject Start: 1 Subject End: 460 aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagnnnnnnngtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt aaccagaggaaacttaaattattcccaaaagttagataaataaccagtaaaaggatttagttctgcattggacagggctaagtccttttcattttgcttcctttaactcatgtctaaaagatgttcactcagattgtgttacagttttatttcagtcatctataaaccttagattatccaagtttatttttgtataagtaaggaagctagatttaaaaaagccagtgttttcaagttgtcaggttgaaccctcctgactttcttataaaattagcattttcttgaaaactataaaattttcagaaaaaatcactatattgagttattttattattcaagttaatctatttgtatcatttagaaatacaaagtagtttttttgtaacaaaaatgaaatatattactagtatattaaatttagtaaaaaattttattgcatatatgaaaccgggggttcggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCAGAGGAAACUUAAAUUAUUCCCAAAAGUUAGAUAAAUAACCAGUAAAAGGAUUUAGUUCUGCAUUGGACAGGGCUAAGUCCUUUUCAUUUUGCUUCCUUUAACUCAUGUCUAAAAGAUGUUCACUCAGAUUGUGUUACAGUUUUAUUUCAGUCAUCUAUAAACCUUAGAUUAUCCAAGUUUAUUUUUGUAUAAGUAAGGAAGCUAGAUUUAAAAAAGCCAGUGUUUUCAAGUUGUCAGGUUGAACCCUCCUGACUUUCUUAUAAAAUUAGCAUUUUCUUGAAAACUAUAAAAUUUUCAGAAAAAAUCACUAUAUUGAGUUAUUUUAUUAUUCAAGUUAAUCUAUUUGUAUCAUUUAGAAAUACAAAGUAGUUUUUUUGUAACAAAAAUGAAAUAUAUUACUAGUAUAUUAAAUUUAGUAAAAAAUUUUAUUGCAUAUAUGAAACCGGGGGUUCGGU .(((.(((....))).....((((((......(((((...((((..(.((((((((((((((((((....).)))))))))))))))))).....((((((((..(((.(((....(((((((..(.....(((((...((......))...))))).((((.......))))........)..))))))).))).)))))))))))..((..(((((.(((((((((....(((..((((((.........))))))...)))............((((((.(((((........))))))))))).......)))))).))).)))))....))..)))))))))...((.((((.((....(((((((......))))))).....((((((((.(.(((((((..........))))))).).))))))))...)).)))).)).))))))..))) (-96.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGAACCCCCGGUUUCAUAUAUGCAAUAAAAUUUUUUACUAAAUUUAAUAUACUAGUAAUAUAUUUCAUUUUUGUUACAAAAAAACUACUUUGUAUUUCUAAAUGAUACAAAUAGAUUAACUUGAAUAAUAAAAUAACUCAAUAUAGUGAUUUUUUCUGAAAAUUUUAUAGUUUUCAAGAAAAUGCUAAUUUUAUAAGAAAGUCAGGAGGGUUCAACCUGACAACUUGAAAACACUGGCUUUUUUAAAUCUAGCUUCCUUACUUAUACAAAAAUAAACUUGGAUAAUCUAAGGUUUAUAGAUGACUGAAAUAAAACUGUAACACAAUCUGAGUGAACAUCUUUUAGACAUGAGUUAAAGGAAGCAAAAUGAAAAGGACUUAGCCCUGUCCAAUGCAGAACUAAAUCCUUUUACUGGUUAUUUAUCUAACUUUUGGGAAUAAUUUAAGUUUCCUCUGGUU ((((......))))......................((((((............))))))......((((((....((((((........)))))).....))))))......((((..(((((((((....(((((((.((...((((.(((((((.((((((((....)))))))))))))))))))......((((((((((((..(..(((((.........)))))..).))))))))))))......(((((((((((((............(((((.....)))))(((((.(((((......(((....)))..(((.......)))..)))))..))))).)))))..))))))))......(((((((.((((..((((.....))))..)))).)))))))..))))))))).(((........)))...)))))))))...))))... (-95.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 255 220 229 185 NC_009009:SSA_0700|5end_hypothetical_protein_682496..682726_POSITIVE 323 110 61 147 83 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 314 100 51 219 161 NC_009009:SSA_1693|5end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1686811..1687041_NEGATIVE 302 127 83 121 75 NC_009009:SSA_0064|5end_hypothetical_protein_66330..66560_POSITIVE 300 116 73 125 86 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 300 98 60 162 126 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 291 147 107 157 118 NC_009009:SSA_1130|5end_Iron-dependent_peroxidase,_putative_1155802..1156032_POSITIVE 290 106 61 196 150 NC_009009:SSA_2177|5end_hypothetical_protein_2176215..2176445_NEGATIVE 290 85 44 78 29 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 288 126 86 222 186 NC_009009:SSA_0762|5end_hypothetical_protein_744187..744417_POSITIVE 283 100 53 172 125 NC_009009:SSA_2308|5end_hypothetical_protein_2310474..2310704_NEGATIVE 282 105 69 103 59 NC_009009:SSA_1493|5end_hypothetical_protein_1499480..1499710_NEGATIVE 281 259 218 64 23 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 278 250 201 214 160 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 270 94 56 175 130 NC_009009:SSA_2203|5end_30S_ribosomal_protein_S2,_putative_2204205..2204435_NEGATIVE 268 100 58 231 180 NC_009009:SSA_1808|5end_hypothetical_protein_1792209..1792439_NEGATIVE 268 138 91 156 115 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 265 99 57 200 157 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 265 259 212 175 125 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 264 105 62 174 143 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 498 89 50 136 97 NC_009009:SSA_1362|3end_ORFB,_transposon_ISSsa2_1378599..1378749_POSITIVE 498 89 50 136 97 NC_009009:SSA_0266|3end_ORFB,_transposon_ISSsa1_260822..260972_POSITIVE 403 89 49 42 2 NC_009009:SSA_0611|3end_HtpX_protease,_putative_600515..600665_POSITIVE 317 89 50 54 14 NC_009009:SSA_1829|3end_RNA_methyltransferase,_putative_1818959..1819109_NEGATIVE 312 99 52 90 27 NC_009009:SSA_0004|3end_Lipoprotein,_putative_3213..3363_NEGATIVE 302 127 83 124 78 NC_009009:SSA_0063|3end_Holliday_junction_DNA_helicase_ruvB,_putative_66413..66563_POSITIVE 300 116 73 122 83 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 290 106 61 123 77 NC_009009:SSA_2178|3end_hypothetical_protein_2176288..2176438_NEGATIVE 288 126 86 124 88 NC_009009:SSA_0761|3end_Transcriptional_regulator,_XRE_family,_putative_744169..744319_POSITIVE 287 238 198 80 32 NC_009009:SSA_1010|3end_UDP-glucose_4-epimerase,_putative_1013862..1014012_POSITIVE 282 105 69 69 25 NC_009009:SSA_1494|3end_Conserved_uncharacterized_protein_1499514..1499664_NEGATIVE 282 146 107 151 113 NC_009009:SSA_1129|3end_Periplasmic_iron_transport_lipoprotein,_putative_1155877..1156027_POSITIVE 281 259 218 46 5 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 281 87 61 47 22 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 276 79 34 84 41 NC_009009:SSA_2235|3end_Conserved_uncharacterized_protein_2234971..2235121_NEGATIVE 265 99 57 92 49 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 263 106 62 131 80 NC_009009:SSA_2084|3end_Phosphotransferase_system_(PTS),_galactitol-specific_IIC_component,_putative_2087973..2088123_NEGATIVE 257 104 64 90 38 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 257 99 52 64 14 NC_009009:SSA_0634|3end_Anthranilate_phosphoribosyltransferase,_putative_624471..624621_POSITIVE 256 109 62 122 63 NC_009009:SSA_2042|3end_hypothetical_protein_2046669..2046819_NEGATIVE