Origin IGS: ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagaaaaaaaactctatctttgtagtatggttaagataggcttgcggtctggcag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgccagaccgcaagcctatcttaaccatactacaaagatagagttttttttctgaattatagaattaatattgtaattttgcgaagattatataataatgtatgagcagcgaagaacaaataaagaaagacgactattat Mask Tandem Repeat Region ================================================ ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagaaaaaaaactctatctttgtagtatggttaagataggcttgcggtctggcag Find is-nt database================================================ Query_seq: PI1529:PI1530|PI1529:PI1530:cytosine/adenosine deaminase:conserved hypothetical protein:->->:1450438..1450578 141 ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagaaaaaaaactctatctttgtagtatggttaagataggcttgcggtctggcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1529:PI1530|PI1529:PI1530:cytosine/adenosine deaminase:conserved hypothetical protein:->->:1450438..1450578 141 ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagaaaaaaaactctatctttgtagtatggttaagataggcttgcggtctggcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1529:PI1530|PI1529:PI1530:cytosine/adenosine deaminase:conserved hypothetical protein:->->:1450438..1450578 141 ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagaaaaaaaactctatctttgtagtatggttaagataggcttgcggtctggcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagaaaaaaaactctatctttgtagtatggttaagataggcttgcggtctggcag Predict ORF larger than 30AA ================================================ ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagaaaaaaaactctatctttgtagtatggttaagataggcttgcggtctggcag 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: 83 Start: 42 End: 71 .........................................ATTGTAATTTTGCGAAGATTATATAATAAT...................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 56 End: 85 .......................................................TTCGCAAAATTACAATATTAATTCTATAAT........................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagaaaaaaaactctatctttgtagtatggttaagataggcttgcggtctggcag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1529:PI1530|PI1529:PI1530:cytosine/adenosine deaminase:conserved hypothetical protein:->->:1450438..1450578 141 ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagaaaaaaaactctatctttgtagtatggttaagataggcttgcggtctggcag Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: pint_PI1529_PI1530|cytosine/adenosine deaminase:conserved hypothetical protein|POSITIVE:POSITIVE|[1450438,1450578]|141 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagnnnnnnnnctctatctttgtagtatggttaagataggcttgcggtctggcag ataatagtcgtctttctttatttgttcttcgctgctcatacattattatataatcttcgcaaaattacaatattaattctataattcagaaaaaaaactctatctttgtagtatggttaagataggcttgcggtctggcag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUAGUCGUCUUUCUUUAUUUGUUCUUCGCUGCUCAUACAUUAUUAUAUAAUCUUCGCAAAAUUACAAUAUUAAUUCUAUAAUUCAGAAAAAAAACUCUAUCUUUGUAGUAUGGUUAAGAUAGGCUUGCGGUCUGGCAG ...............................(((((.....(((((...)))))..((((((..............((((.......)))).......((((((((............)))))))).))))))...))))) (-15.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCCAGACCGCAAGCCUAUCUUAACCAUACUACAAAGAUAGAGUUUUUUUUCUGAAUUAUAGAAUUAAUAUUGUAAUUUUGCGAAGAUUAUAUAAUAAUGUAUGAGCAGCGAAGAACAAAUAAAGAAAGACGACUAUUAU .(((......)))...(((((((............))))))).(((.(((((((..((((......)))).((((..((((((.....(((((((....)))))))...)))))).))))....))))))).)))...... (-22.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 140 103 75 36 pint:PI1610|5end_Na+/H+_anti-porter_1536942..1537172_POSITIVE 269 42 7 55 23 pint:PI0837|5end_conserved_hypothetical_protein_772308..772538_POSITIVE 266 133 97 203 173 pint:PI0476|5end_50S_ribosomal_protein_L18_440041..440271_POSITIVE 253 126 85 224 186 pint:PI2038|5end_conserved_hypothetical_protein;_possible_internalin-related_protein_1990463..1990693_POSITIVE 252 138 99 184 145 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 248 139 97 145 102 pint:PI1633|5end_hypothetical_protein_1552504..1552734_POSITIVE 248 139 97 65 22 pint:PI1631|5end_hypothetical_protein_1552424..1552654_POSITIVE 244 140 97 52 7 pint:PI2013|5end_hypothetical_protein_1972329..1972559_POSITIVE 243 140 108 44 6 pint:PI1555|5end_conserved_hypothetical_protein_1470577..1470807_POSITIVE 233 140 98 114 70 pint:PI2107|5end_hypothetical_protein_2059704..2059934_POSITIVE 233 140 98 71 27 pint:PI2108|5end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2059661..2059891_POSITIVE 233 139 97 201 163 pint:PI0560|5end_hypothetical_protein_508600..508830_POSITIVE 232 138 99 46 5 pint:PI0975|5end_glycine_dehydrogenase_[decarboxylating]_subunit_2_900798..901028_POSITIVE 231 139 111 51 16 pint:PI1480|5end_xanthine/uracil_permease_family_protein_1402675..1402905_POSITIVE 229 139 99 210 164 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 228 140 106 41 9 pint:PI1494|5end_conserved_hypothetical_protein_1413046..1413276_POSITIVE 227 35 6 51 22 pint:PI0771|5end_conserved_hypothetical_protein_706524..706754_POSITIVE 225 137 95 63 29 pint:PI0968|5end_hypothetical_protein_895946..896176_POSITIVE 225 140 96 58 6 pint:PI0415|5end_malate_dehydrogenase_385358..385588_POSITIVE 224 140 97 230 175 pint:PI1493|5end_conserved_hypothetical_protein_1412268..1412498_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 42 7 40 8 pint:PI0836|3end_conserved_hypothetical_protein_772373..772523_POSITIVE 253 126 85 50 12 pint:PI2037|3end_TIM-barrel_protein,_NifR3_family_1990369..1990519_POSITIVE 248 139 97 55 12 pint:PI1630|3end_hypothetical_protein_1552494..1552644_POSITIVE 244 140 100 61 30 pint:PI0787|3end_glycosyltransferase_725793..725943_POSITIVE 244 140 105 142 106 pint:PI0541|3end_GTP-binding_protein,_GTP1/OBG_family_495009..495159_POSITIVE 238 140 98 142 103 pint:PI0019|3end_conserved_hypothetical_protein_24454..24604_POSITIVE 236 140 107 104 67 pint:PI0053|3end_hypothetical_protein_55124..55274_POSITIVE 231 139 111 43 8 pint:PI1479|3end_xanthine_phosphoribosyltransferase_1402747..1402897_POSITIVE 227 139 98 123 66 pint:PI0197|3end_acetate_kinase_189827..189977_POSITIVE 225 138 103 151 114 pint:PI1609|3end_Na+/H+_anti-porter_1537100..1537250_POSITIVE 222 140 106 54 23 pint:PI0778|3end_hypothetical_protein_714885..715035_POSITIVE 216 139 98 143 109 pint:PI1915|3end_conserved_hypothetical_protein_1859906..1860056_POSITIVE 216 74 31 118 72 pint:PI1450|3end_hypothetical_protein_1372891..1373041_POSITIVE 216 140 122 50 31 pint:PI0747|3end_possible_mobilization_protein_676702..676852_POSITIVE 216 139 104 125 78 pint:PI0189|3end_integrase_180437..180587_POSITIVE 215 139 98 122 76 pint:PI0955|3end_conserved_hypothetical_protein_886084..886234_POSITIVE 214 36 8 126 100 pint:PI1616|3end_hypothetical_protein_1542669..1542819_POSITIVE 213 37 8 129 95 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 213 140 102 66 30 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 213 140 97 72 27 pint:PI0037|3end_hypothetical_protein_39616..39766_POSITIVE