Origin IGS: agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttaaaaaaatgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatttttagacaatataaaatgggcgttggtgaacgcttatgggtttaagaataatccattaacgctcctcaacgcccacatttttttaaccataaattgaaaggaaaagagaaaatggctgtatcaattgaagatataaagaagctacgcgct Mask Tandem Repeat Region ================================================ agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttaaaaaaatgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta Find is-nt database================================================ Query_seq: PI1798:PI1799|PI1798:PI1799: elongation factor Ts:30S ribosomal protein S2:->->:1732885..1733039 155 agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttaaaaaaatgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1798:PI1799|PI1798:PI1799: elongation factor Ts:30S ribosomal protein S2:->->:1732885..1733039 155 agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttaaaaaaatgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1798:PI1799|PI1798:PI1799: elongation factor Ts:30S ribosomal protein S2:->->:1732885..1733039 155 agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttaaaaaaatgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttaaaaaaatgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 1 End: 96 A R L K K I D E I S V A M K E K G K L K H N F F H P R Q P A N M ........................................................... agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttaaaaaaatgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta 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================================================ agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttaaaaaaatgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.8 Tail_Score: -4.76963 Start: 76 End: 134 Full_Region: ATGGTTAAAAAAATG TGGGCGTTGAGGAGCGTTAATGGATT ATTCTTA AACCCATAAGCGTTCACCAACGCCCA TTTTATATTGTCTAA ...........................................................................TGGGCGTTGAGGAGCGTTAATGGATTATTCTTAAACCCATAAGCGTTCACCAACGCCCA..................... TransTerm Strand: - Conf: 82 HP_score: -11.8 Tail_Score: -2.90056 Start: 76 End: 134 Full_Region: ttagacaatataaaa tgggcgttggtgaacgcttatgggtt taagaat aatccattaacgctcctcaacgccca catttttttaaccat ...........................................................................tgggcgttggtgaacgcttatgggtttaagaataatccattaacgctcctcaacgccca..................... Find igs database================================================ Query_seq: PI1798:PI1799|PI1798:PI1799: elongation factor Ts:30S ribosomal protein S2:->->:1732885..1733039 155 agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttaaaaaaatgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 155 Len: 155 Subject: pint_PI1798_PI1799| elongation factor Ts:30S ribosomal protein S2|POSITIVE:POSITIVE|[1732885,1733039]|155 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 1 Subject End: 155 agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttnnnnnnntgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta agcgcgtagcttctttatatcttcaattgatacagccattttctcttttcctttcaatttatggttaaaaaaatgtgggcgttgaggagcgttaatggattattcttaaacccataagcgttcaccaacgcccattttatattgtctaaaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGCGUAGCUUCUUUAUAUCUUCAAUUGAUACAGCCAUUUUCUCUUUUCCUUUCAAUUUAUGGUUAAAAAAAUGUGGGCGUUGAGGAGCGUUAAUGGAUUAUUCUUAAACCCAUAAGCGUUCACCAACGCCCAUUUUAUAUUGUCUAAAAAUUA (((.....))).................((((.((((((.....................))))))........((((((((((..(((((((.((((.............)))).)))))))..)))))))))).......))))......... (-39.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUUUAGACAAUAUAAAAUGGGCGUUGGUGAACGCUUAUGGGUUUAAGAAUAAUCCAUUAACGCUCCUCAACGCCCACAUUUUUUUAACCAUAAAUUGAAAGGAAAAGAGAAAAUGGCUGUAUCAAUUGAAGAUAUAAAGAAGCUACGCGCU ..((((((((...(((((...((((((((((.((.((...(((((((.......)))))))...)).)).))))))))))(((((((((..((...........))....)))))))))..)))))...)))))))).......(((.....))) (-37.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 50 1 120 58 pint:PI0040|5end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41010..41240_POSITIVE 278 120 71 96 53 pint:PI0727|5end_integrase_659261..659491_POSITIVE 274 100 75 146 115 pint:PI0243|5end_hypothetical_protein_240506..240736_POSITIVE 273 119 74 57 14 pint:PI0034|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_37151..37381_POSITIVE 271 119 75 213 165 pint:PI2034|5end_conserved_hypothetical_protein_1987573..1987803_POSITIVE 263 120 73 160 104 pint:PI0985|5end_aspartyl-tRNA_synthetase_910174..910404_POSITIVE 250 64 26 168 123 pint:PI0818|5end_alpha-amylase_758185..758415_POSITIVE 249 43 1 55 6 pint:PI0321|5end_conserved_hypothetical_protein_302598..302828_POSITIVE 246 102 74 136 103 pint:PI1565|5end_conserved_hypothetical_protein;_possible_surface_antigen_1485460..1485690_POSITIVE 246 99 76 217 193 pint:PI1133|5end_GrpE_protein_1059662..1059892_POSITIVE 244 120 75 64 16 pint:PI0733|5end_membrane_protein;_predicted_exporter_664389..664619_POSITIVE 239 135 96 47 8 pint:PI0210|5end_hypothetical_protein_202966..203196_POSITIVE 238 130 81 44 5 pint:PI2006|5end_potassium_uptake_system_protein_1964480..1964710_POSITIVE 237 108 71 155 110 pint:PI1728|5end_ATP-dependent_Clp_protease,_proteolytic_subunit_1646916..1647146_POSITIVE 236 120 73 77 36 pint:PI2042|5end_cation-transporting_ATPase_1994175..1994405_POSITIVE 236 120 73 63 22 pint:PI2041|5end_conserved_hypothetical_protein_1994161..1994391_POSITIVE 236 133 94 196 160 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 235 119 72 48 5 pint:PI1532|5end_uridylate_kinase_1451644..1451874_POSITIVE 235 50 1 133 83 pint:PI0916|5end_hypothetical_protein_845617..845847_POSITIVE 234 38 4 90 57 pint:PI1961|5end_hypothetical_protein_1918947..1919177_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 50 1 107 45 pint:PI0039|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_41077..41227_POSITIVE 250 64 26 112 67 pint:PI0817|3end_glycosyl_transferase,_group_1_family_protein_758209..758359_POSITIVE 248 80 35 132 93 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 246 102 74 68 35 pint:PI1564|3end_surface_antigen_BspA_1485472..1485622_POSITIVE 246 99 76 143 119 pint:PI1132|3end_DnaJ_heat_shock_protein_(Hsp40)_1059668..1059818_POSITIVE 243 50 1 122 69 pint:PI1025|3end_tRNA_modification_GTPase_942232..942382_POSITIVE 241 80 34 98 50 pint:PI0726|3end_hypothetical_protein_659253..659403_POSITIVE 240 44 1 113 62 pint:PI2005|3end_potassium_uptake_protein_1964367..1964517_POSITIVE 237 108 71 148 103 pint:PI1727|3end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1646989..1647139_POSITIVE 235 119 72 58 15 pint:PI1531|3end_biotin--acetyl-CoA-carboxylase_ligase_1451734..1451884_POSITIVE 235 130 85 44 1 pint:PI0025|3end_two_component_system_sensor_histidine_kinase_29823..29973_POSITIVE 234 38 4 46 13 pint:PI1960|3end_hypothetical_protein_1918983..1919133_POSITIVE 234 133 110 141 123 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 234 37 1 72 36 pint:PI0115|3end_hypothetical_protein_108669..108819_POSITIVE 232 130 89 47 10 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 231 56 24 143 110 pint:PI2091|3end_DNA_processing_protein_2049226..2049376_POSITIVE 231 119 73 143 97 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 230 109 72 44 2 pint:PI0477|3end_30S_ribosomal_protein_S5_440981..441131_POSITIVE 229 120 73 136 101 pint:PI1973|3end_conserved_hypothetical_protein_1931171..1931321_POSITIVE 229 120 74 112 51 pint:PI0300|3end_transposase_285761..285911_POSITIVE