Origin IGS: ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt .........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 aactcctccttcaccatctattcaaaaataactcactataaagcacccaagtgcttttaaaacacagaaaagagcgcgcaaatgcacgctttaatacaaatattataacaaaaatatgaagtagggtaaaggtcatttcagacttttttctgcttatcatcagcctcataaatgactgtcagcagcaaacttcctgaaagcagactagcaattgttttaattgcatgacttatatagaaaaacaaacctagttttcactaggttcgtcatttcttatctgcaagaaggtctgaatttaagagtaattcaagctctgccctaacatttcagacttgcaactttgcagtccatttgataaactcaaaccaa Mask Tandem Repeat Region ================================================ ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt Find is-nt database================================================ Query_seq: SSA_1106:SSA_1107|SSA_1106:SSA_1107:IgA-specific metalloendopeptidase:Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein, putative:->->:1131739..1132107 369 ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1106:SSA_1107|SSA_1106:SSA_1107:IgA-specific metalloendopeptidase:Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein, putative:->->:1131739..1132107 369 ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1106:SSA_1107|SSA_1106:SSA_1107:IgA-specific metalloendopeptidase:Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein, putative:->->:1131739..1132107 369 ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 125 End: 229 ............................................................................................................................ M F F Y I S H A I K T I A S L L S G S L L L T V I Y E A D D K Q K K V ............................................................................................................................................ Protein_Len: 52 Strand: + Start: 201 End: 356 ........................................................................................................................................................................................................ M R L M I S R K K S E M T F T L L H I F V I I F V L K R A F A R S F L C F K S T W V L Y S E L F L N R W ............. Protein_Len: 33 Strand: - Start: 51 End: 149 .................................................. P L A Q I V R L N L G E Q L Y S I V F R T F V L N T K R Y L D H M ............................................................................................................................................................................................................................ ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt 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: 89 Start: 239 End: 268 ..............................................................................................................................................................................................................................................CTTTACCCTACTTCATATTTTTGTTATAAT..................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.4 Tail_Score: -5.04597 Start: 104 End: 127 Full_Region: GCAGATAAGAAATGA CGAACCTAGT GAAA ACTAGGTTTG TTTTTCTATATAAGT .......................................................................................................CGAACCTAGTGAAAACTAGGTTTG.................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 70 HP_score: -8.2 Tail_Score: -3.17195 Start: 104 End: 127 Full_Region: acttatatagaaaaa caaacctagt tttc actaggttcg tcatttcttatctgc .......................................................................................................caaacctagttttcactaggttcg.................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 51 HP_score: -5.2 Tail_Score: -2.7314 Start: 146 End: 162 Full_Region: TTCTATATAAGTCAT GCAATT AAAAC AATTGC TAGTCTGCTTTCAGG .................................................................................................................................................GCAATTAAAACAATTGC............................................................................................................................................................................................................... TransTerm Strand: - Conf: 40 HP_score: -2.4 Tail_Score: -2.64416 Start: 218 End: 231 Full_Region: gggtaaaggtcattt caga cttttt tctg cttatcatcagcctc .........................................................................................................................................................................................................................cagacttttttctg.......................................................................................................................................... TransTerm Strand: + Conf: 74 HP_score: -5.6 Tail_Score: -4.78933 Start: 279 End: 298 Full_Region: ATAATATTTGTATTA AAGCGTGC ATTT GCGCGCTC TTTTCTGTGTTTTAA ......................................................................................................................................................................................................................................................................................AAGCGTGCATTTGCGCGCTC....................................................................... TransTerm Strand: + Conf: 79 HP_score: -8.2 Tail_Score: -3.9872 Start: 281 End: 296 Full_Region: AATATTTGTATTAAA GCGTGC ATTT GCGCGC TCTTTTCTGTGTTTT ........................................................................................................................................................................................................................................................................................GCGTGCATTTGCGCGC......................................................................... Find igs database================================================ Query_seq: SSA_1106:SSA_1107|SSA_1106:SSA_1107:IgA-specific metalloendopeptidase:Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein, putative:->->:1131739..1132107 369 ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt Intra-Species Hit: Count: 1 Min: 1 Max: 369 Len: 369 Subject: NC_009009_SSA_1106_SSA_1107|IgA-specific metalloendopeptidase:Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein, putative|POSITIVE:POSITIVE|[1131739,1132107]|369 HSP 1 e-value: 0.0 bit: 731.0 Len: 369 Query Start:1 Query End:369 Subject Strand: POSITIVE Subject Start: 1 Subject End: 369 ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt ttggtttgagtttatcaaatggactgcaaagttgcaagtctgaaatgttagggcagagcttgaattactcttaaattcagaccttcttgcagataagaaatgacgaacctagtgaaaactaggtttgtttttctatataagtcatgcaattaaaacaattgctagtctgctttcaggaagtttgctgctgacagtcatttatgaggctgatgataagcagaaaaaagtctgaaatgacctttaccctacttcatatttttgttataatatttgtattaaagcgtgcatttgcgcgctcttttctgtgttttaaaagcacttgggtgctttatagtgagttatttttgaatagatggtgaaggaggagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGGUUUGAGUUUAUCAAAUGGACUGCAAAGUUGCAAGUCUGAAAUGUUAGGGCAGAGCUUGAAUUACUCUUAAAUUCAGACCUUCUUGCAGAUAAGAAAUGACGAACCUAGUGAAAACUAGGUUUGUUUUUCUAUAUAAGUCAUGCAAUUAAAACAAUUGCUAGUCUGCUUUCAGGAAGUUUGCUGCUGACAGUCAUUUAUGAGGCUGAUGAUAAGCAGAAAAAAGUCUGAAAUGACCUUUACCCUACUUCAUAUUUUUGUUAUAAUAUUUGUAUUAAAGCGUGCAUUUGCGCGCUCUUUUCUGUGUUUUAAAAGCACUUGGGUGCUUUAUAGUGAGUUAUUUUUGAAUAGAUGGUGAAGGAGGAGUU ..((((((((((((......((((((((....))).)))))......(((((......)))))........)))))))))))).....((((((.(((((.((((((((((((....)))))))))))))))))...........((((((.....))))))..)))))).((((((...(((.(((((..(((((........)))))......))))).)))...))))))....(((((((((((.((((....((..(((((.............(((((((....)))))))................((((((....)))))))))))..)).......)))))))..))))))))....... (-111.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUCCUCCUUCACCAUCUAUUCAAAAAUAACUCACUAUAAAGCACCCAAGUGCUUUUAAAACACAGAAAAGAGCGCGCAAAUGCACGCUUUAAUACAAAUAUUAUAACAAAAAUAUGAAGUAGGGUAAAGGUCAUUUCAGACUUUUUUCUGCUUAUCAUCAGCCUCAUAAAUGACUGUCAGCAGCAAACUUCCUGAAAGCAGACUAGCAAUUGUUUUAAUUGCAUGACUUAUAUAGAAAAACAAACCUAGUUUUCACUAGGUUCGUCAUUUCUUAUCUGCAAGAAGGUCUGAAUUUAAGAGUAAUUCAAGCUCUGCCCUAACAUUUCAGACUUGCAACUUUGCAGUCCAUUUGAUAAACUCAAACCAA .((.(((.(((((..........................(((((((....))))))).............((((((.((....)).))))))........................))))).)))))...(((...((((((((((((.(((((.((..(((..........)))..)).)))))..............(((((...(((((((...)))))))...........(((((.((.((((((((....)))))))).))..)))))..))))).)))))))))))).....((((...(((((...((......)).....((((.(((....)))))))..)))))...))))..))).. (-85.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 209 161 182 146 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 336 208 161 197 145 NC_009009:SSA_1571|5end_Threonyl-tRNA_synthetase,_putative_1575154..1575384_NEGATIVE 334 55 20 50 20 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 326 218 173 213 169 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 325 210 164 221 171 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 322 210 165 199 152 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 316 91 51 163 114 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 307 60 15 226 173 NC_009009:SSA_1692|5end_Phospho-B-galactosidase_LacG,_putative_1685006..1685236_NEGATIVE 307 210 166 87 34 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 306 60 11 71 26 NC_009009:SSA_2081|5end_hypothetical_protein_2085309..2085539_POSITIVE 303 208 161 151 93 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 301 204 161 217 171 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 299 194 161 207 167 NC_009009:SSA_2263|5end_Ribonucleotide_reductase_(NrdI_family_protein),_putative_2261176..2261406_NEGATIVE 299 329 282 133 85 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 298 208 162 99 46 NC_009009:SSA_2041|5end_Leucine-rich_protein,_putative_2046682..2046912_NEGATIVE 297 338 292 194 150 NC_009009:SSA_2240|5end_Holliday_junction_resolvase,_putative_2237677..2237907_NEGATIVE 297 207 161 76 24 NC_009009:SSA_1587|5end_hypothetical_protein_1589086..1589316_NEGATIVE 295 207 161 68 9 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 295 194 161 58 32 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 293 213 171 66 25 NC_009009:SSA_0144|5end_Transcriptional_regulator,_TetR_family,_putative_138565..138795_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 209 161 126 90 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 334 55 20 53 23 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 326 330 281 113 53 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 322 210 165 114 67 NC_009009:SSA_1368|3end_hypothetical_protein_1383748..1383898_NEGATIVE 316 329 285 52 1 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 307 60 15 127 74 NC_009009:SSA_1693|3end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1685105..1685255_NEGATIVE 307 210 166 100 47 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 304 207 169 49 5 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 303 208 161 148 90 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 299 194 161 144 104 NC_009009:SSA_2264|3end_hypothetical_protein_2261239..2261389_NEGATIVE 299 329 282 123 75 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 298 208 162 112 59 NC_009009:SSA_2042|3end_hypothetical_protein_2046669..2046819_NEGATIVE 295 207 161 67 8 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 289 328 294 38 6 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 289 210 161 55 17 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 287 58 23 65 15 NC_009009:SSA_1726|3end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1711703..1711853_NEGATIVE 284 210 161 130 86 NC_009009:SSA_1433|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1439933..1440083_NEGATIVE 283 129 87 92 42 NC_009009:SSA_1480|3end_hypothetical_protein_1483960..1484110_NEGATIVE 281 210 166 148 101 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 281 192 159 30 2 NC_009009:SSA_0336|3end_Isopentenyl-diphosphate_delta-isomerase,_putative_330879..331029_POSITIVE