Origin IGS: tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcagtttaggcttaccaattactttcagctttacatttcctattgcctgtggcgatgttattttaattacagccattctttattctttctttttgaattcaaaatgatca Mask Tandem Repeat Region ================================================ tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt Find is-nt database================================================ Query_seq: PI1612:PI1613|PI1612:PI1613:hypothetical protein:hypothetical protein:->->:1540006..1540117 112 tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1612:PI1613|PI1612:PI1613:hypothetical protein:hypothetical protein:->->:1540006..1540117 112 tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1612:PI1613|PI1612:PI1613:hypothetical protein:hypothetical protein:->->:1540006..1540117 112 tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 7 End: 111 ...... K S N L F F S Y L I A T I L I V D G C A I P F T F S F T I P L G L S M . tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1612:PI1613|PI1612:PI1613:hypothetical protein:hypothetical protein:->->:1540006..1540117 112 tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: pint_PI1612_PI1613|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1540006,1540117]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt tgatcattttgaattcaaaaagaaagaataaagaatggctgtaattaaaataacatcgccacaggcaataggaaatgtaaagctgaaagtaattggtaagcctaaactgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCAUUUUGAAUUCAAAAAGAAAGAAUAAAGAAUGGCUGUAAUUAAAAUAACAUCGCCACAGGCAAUAGGAAAUGUAAAGCUGAAAGUAAUUGGUAAGCCUAAACUGAUU ...((.(((((....))))).)).............((((............((((..((..........))..))))...((..(......)..)).)))).......... (-14.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCAGUUUAGGCUUACCAAUUACUUUCAGCUUUACAUUUCCUAUUGCCUGUGGCGAUGUUAUUUUAAUUACAGCCAUUCUUUAUUCUUUCUUUUUGAAUUCAAAAUGAUCA ..........((((....(((((......(.....)......(((((((...)))))))......)))))..)))).............((.(((((....))))).))... (-12.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 87 45 161 106 pint:PI0101|5end_lauroyl/myristoyl_acyltransferase_96729..96959_POSITIVE 287 99 52 124 62 pint:PI0189|5end_integrase_179623..179853_POSITIVE 280 96 54 169 135 pint:PI1157|5end_hypothetical_protein_1081704..1081934_POSITIVE 251 98 58 225 181 pint:PI0418|5end_hypothetical_protein_386666..386896_POSITIVE 251 98 58 110 66 pint:PI0420|5end_hypothetical_protein_386551..386781_POSITIVE 251 98 58 96 52 pint:PI0417|5end_hypothetical_protein_386537..386767_POSITIVE 250 98 58 204 156 pint:PI0310|5end_outer_membrane_protein_291657..291887_POSITIVE 250 98 58 50 2 pint:PI0309|5end_hypothetical_protein_291503..291733_POSITIVE 248 58 11 88 43 pint:PI0012|5end_conserved_hypothetical_protein_13406..13636_POSITIVE 244 103 63 111 73 pint:PI2172|5end_hypothetical_protein_2113819..2114049_POSITIVE 244 103 63 87 49 pint:PI2173|5end_hypothetical_protein_2113795..2114025_POSITIVE 241 99 54 120 67 pint:PI1476|5end_acyl-CoA_synthase/O-succinylbenzoic_acid-CoA_ligase_1397699..1397929_POSITIVE 235 110 61 218 175 pint:PI0941|5end_hypothetical_protein_874443..874673_POSITIVE 232 98 56 202 162 pint:PI1744|5end_chromosome_partitioning_protein_1665635..1665865_POSITIVE 228 91 52 72 39 pint:PI1812|5end_possible_alpha-amylase_1750759..1750989_POSITIVE 228 98 57 47 11 pint:PI0958|5end_G:T/U_mismatch-specific_DNA_glycosylase_889911..890141_POSITIVE 227 84 58 208 183 pint:PI0799|5end_alpha-amylase_family_protein_737083..737313_POSITIVE 227 97 56 120 72 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 225 97 51 80 43 pint:PI1831|5end_conserved_hypothetical_protein_1770298..1770528_POSITIVE 222 100 58 223 176 pint:PI1835|5end_L-asparaginase_I_1776144..1776374_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 87 45 78 23 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 287 99 52 91 29 pint:PI0188|3end_phosphomethylpyrimidine_kinase_179670..179820_POSITIVE 250 98 58 69 21 pint:PI0308|3end_conserved_hypothetical_protein_291602..291752_POSITIVE 244 103 63 43 5 pint:PI2171|3end_conserved_hypothetical_protein_2113831..2113981_POSITIVE 240 100 58 140 93 pint:PI0692|3end_iron_compound_ABC_transporter,_permease_protein_628269..628419_POSITIVE 235 110 61 124 81 pint:PI0940|3end_ribonuclease_G_874429..874579_POSITIVE 228 98 57 43 7 pint:PI0957|3end_conserved_hypothetical_protein_889987..890137_POSITIVE 227 97 56 60 12 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 225 97 51 63 26 pint:PI1830|3end_conserved_hypothetical_protein_1770361..1770511_POSITIVE 221 100 58 151 103 pint:PI1414|3end_conserved_hypothetical_protein_1334436..1334586_POSITIVE 218 100 53 82 21 pint:PI0739|3end_conserved_hypothetical_protein_672161..672311_POSITIVE 217 97 63 58 21 pint:PI1391|3end_hypothetical_protein_1311694..1311844_POSITIVE 216 109 61 131 94 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 215 98 53 121 72 pint:PI1442|3end_radical-activating_enzyme_(pyruvate-formate_lyase-activating_enzyme)_1364649..1364799_POSITIVE 214 65 22 151 102 pint:PI0059|3end_peptide_chain_release_factor_RF-2_58171..58321_POSITIVE 213 95 56 88 54 pint:PI0782|3end_beta-lactamase_induction_signal_transducer,_AmpG_protein_721927..722077_POSITIVE 208 100 56 61 23 pint:PI0784|3end_possible_amidase_enhancer_precursor_723303..723453_POSITIVE 208 81 53 142 115 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE 205 74 37 75 39 pint:PI1170|3end_possible_response_regulator_1091398..1091548_POSITIVE 204 97 54 71 20 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE