Origin IGS: gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta .........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 taaactcaacatcagtattgttgttgattaattctttcggaaacgctaaactatgttaataataattaatatcaatgctttcacgctgttatgcgtttcgtacctaataaaaaatgagtaattttgcagaccgattatttcgagggtgagcttagatccctcagcacgttgtgtgttaatagtgttgcttttggccgagcagc Mask Tandem Repeat Region ================================================ gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta Find is-nt database================================================ Query_seq: PI1802:PI1803|PI1802:PI1803:50S ribosomal protein L13:conserved hypothetical protein:->->:1735018..1735220 203 gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1802:PI1803|PI1802:PI1803:50S ribosomal protein L13:conserved hypothetical protein:->->:1735018..1735220 203 gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1802:PI1803|PI1802:PI1803:50S ribosomal protein L13:conserved hypothetical protein:->->:1735018..1735220 203 gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 24 End: 155 ....................... M N T Q R A E G S K L T L E I I G L Q N Y S F F I R Y E T H N S V K A L I L I I I N I V ................................................ gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta 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: 152 End: 181 .......................................................................................................................................................GTTGATTAATTCTTTCGGAAACGCTAAACT...................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 144 End: 173 ...............................................................................................................................................ATTAACATAGTTTAGCGTTTCCGAAAGAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1802:PI1803|PI1802:PI1803:50S ribosomal protein L13:conserved hypothetical protein:->->:1735018..1735220 203 gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: pint_PI1802_PI1803|50S ribosomal protein L13:conserved hypothetical protein|POSITIVE:POSITIVE|[1735018,1735220]|203 HSP 1 e-value: 1.0E-111 bit: 402.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta gctgctcggccaaaagcaacactattaacacacaacgtgctgagggatctaagctcaccctcgaaataatcggtctgcaaaattactcattttttattaggtacgaaacgcataacagcgtgaaagcattgatattaattattattaacatagtttagcgtttccgaaagaattaatcaacaacaatactgatgttgagttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUGCUCGGCCAAAAGCAACACUAUUAACACACAACGUGCUGAGGGAUCUAAGCUCACCCUCGAAAUAAUCGGUCUGCAAAAUUACUCAUUUUUUAUUAGGUACGAAACGCAUAACAGCGUGAAAGCAUUGAUAUUAAUUAUUAUUAACAUAGUUUAGCGUUUCCGAAAGAAUUAAUCAACAACAAUACUGAUGUUGAGUUUA ..(((..((((.................(((.....)))..(((((...........))))).........)))).))).....(((((.....((((((....(((((((..(((.((......)).((((((........))))))....)))..)))))))(....)..................)))))).)))))... (-40.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACUCAACAUCAGUAUUGUUGUUGAUUAAUUCUUUCGGAAACGCUAAACUAUGUUAAUAAUAAUUAAUAUCAAUGCUUUCACGCUGUUAUGCGUUUCGUACCUAAUAAAAAAUGAGUAAUUUUGCAGACCGAUUAUUUCGAGGGUGAGCUUAGAUCCCUCAGCACGUUGUGUGUUAAUAGUGUUGCUUUUGGCCGAGCAGC ...(((((.....(((((((.(((((((((.......((....))......(((....))).))))))))).)))))))...((((......))))..................)))))....((((.(.((((.......(((((...........))))).(((((((((......)))))).)))..)))).)..)))). (-43.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 80 31 75 19 pint:PI0189|5end_integrase_179623..179853_POSITIVE 319 79 31 71 13 pint:PI0749|5end_hypothetical_protein_677234..677464_POSITIVE 279 80 36 127 68 pint:PI0790|5end_hypothetical_protein_728953..729183_POSITIVE 268 80 32 60 6 pint:PI0813|5end_conserved_hypothetical_protein_751095..751325_POSITIVE 268 48 2 51 5 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 265 80 34 134 79 pint:PI0213|5end_conserved_hypothetical_protein_207065..207295_POSITIVE 264 80 31 173 124 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 262 80 36 76 32 pint:PI0056|5end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_54967..55197_POSITIVE 260 50 1 166 116 pint:PI1806|5end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1740777..1741007_POSITIVE 260 119 71 191 140 pint:PI0126|5end_conserved_hypothetical_protein_117925..118155_POSITIVE 259 47 1 84 31 pint:PI1382|5end_hypothetical_protein_1303608..1303838_POSITIVE 258 78 38 220 183 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 258 78 35 63 26 pint:PI0578|5end_methyltransferase_522646..522876_POSITIVE 258 78 33 47 1 pint:PI0221|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_212356..212586_POSITIVE 251 74 35 96 63 pint:PI0439|5end_conserved_hypothetical_protein;_possible_preprotein_translocase_subunit_SecE_410319..410549_POSITIVE 248 95 52 61 9 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 246 78 35 158 113 pint:PI1545|5end_conserved_hypothetical_protein_1463587..1463817_POSITIVE 246 78 35 78 33 pint:PI1544|5end_hypothetical_protein_1463507..1463737_POSITIVE 245 120 71 200 147 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 244 46 1 195 121 pint:PI0785|5end_hypothetical_protein_723744..723974_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 80 40 42 1 pint:PI0188|3end_phosphomethylpyrimidine_kinase_179670..179820_POSITIVE 262 80 36 73 29 pint:PI0055|3end_hypothetical_protein_55044..55194_POSITIVE 260 119 71 76 25 pint:PI0125|3end_undecaprenyl_pyrophosphate_synthase_117890..118040_POSITIVE 259 47 1 72 19 pint:PI1381|3end_conserved_hypothetical_protein_1303676..1303826_POSITIVE 252 75 31 146 96 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 251 80 32 80 38 pint:PI1736|3end_topoisomerase_IV,_subunit_A_1657090..1657240_POSITIVE 246 95 60 45 5 pint:PI2098|3end_hypothetical_protein_2052473..2052623_POSITIVE 244 79 33 86 34 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 243 48 1 123 61 pint:PI1818|3end_hypothetical_protein_1757270..1757420_POSITIVE 242 136 99 129 87 pint:PI1644|3end_hypothetical_protein_1561030..1561180_POSITIVE 242 78 36 37 1 pint:PI0577|3end_conserved_hypothetical_protein_522700..522850_POSITIVE 241 78 31 75 30 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 241 132 100 54 17 pint:PI0625|3end_possible_membrane_transport_protein_574353..574503_POSITIVE 241 78 35 86 36 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 239 46 1 69 17 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 238 63 21 85 46 pint:PI1726|3end_ATP-dependent_DNA_helicase_1645542..1645692_POSITIVE 237 80 32 69 28 pint:PI0901|3end_hypothetical_protein_832207..832357_POSITIVE 236 78 36 151 109 pint:PI0053|3end_hypothetical_protein_55124..55274_POSITIVE 235 80 32 47 5 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 232 73 31 128 77 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE