Origin IGS: taaatattgaccgaccattaaaaaaacaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctatacagtctttcttggcgtaaagatagccaatattgtgataatcaagtaaaaagacagataggttttaactacaattatgattagaagaatgctttattgtttttttaatggtcggtcaatattta Mask Tandem Repeat Region ================================================ taaatattgaccgaccattaaaaaaacaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag Find is-nt database================================================ Query_seq: PI2141:PI2142|PI2141:PI2142:hypothetical protein:conserved hypothetical protein:->->:2087618..2087745 128 taaatattgaccgaccattaaaaaaacaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2141:PI2142|PI2141:PI2142:hypothetical protein:conserved hypothetical protein:->->:2087618..2087745 128 taaatattgaccgaccattaaaaaaacaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2141:PI2142|PI2141:PI2142:hypothetical protein:conserved hypothetical protein:->->:2087618..2087745 128 taaatattgaccgaccattaaaaaaacaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatattgaccgaccattaaaaaaacaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 36 End: 125 ................................... M L L I I I V V K T Y L S F Y L I I T I L A I F T P R K T V * ... taaatattgaccgaccattaaaaaaacaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag 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================================================ taaatattgaccgaccattaaaaaaacaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2141:PI2142|PI2141:PI2142:hypothetical protein:conserved hypothetical protein:->->:2087618..2087745 128 taaatattgaccgaccattaaaaaaacaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: pint_PI2141_PI2142|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2087618,2087745]|128 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 taaatattgaccgaccattnnnnnnncaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag taaatattgaccgaccattaaaaaaacaataaagcattcttctaatcataattgtagttaaaacctatctgtctttttacttgattatcacaatattggctatctttacgccaagaaagactgtatag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAUUGACCGACCAUUAAAAAAACAAUAAAGCAUUCUUCUAAUCAUAAUUGUAGUUAAAACCUAUCUGUCUUUUUACUUGAUUAUCACAAUAUUGGCUAUCUUUACGCCAAGAAAGACUGUAUAG ....(((((.................)))))..(((.((((.((((((.....((((..((.((......)).)).)))).))))))........(((((((....)).)))))..)))).))).... (-12.33) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUACAGUCUUUCUUGGCGUAAAGAUAGCCAAUAUUGUGAUAAUCAAGUAAAAAGACAGAUAGGUUUUAACUACAAUUAUGAUUAGAAGAAUGCUUUAUUGUUUUUUUAAUGGUCGGUCAAUAUUUA ((((...((((((.(((((.........)))))..(((.......)))....))))))..))))...............((.(((((((((((........))))))))))).))............. (-19.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 240 110 64 53 4 pint:PI1652|5end_hypothetical_protein_1564655..1564885_POSITIVE 218 100 68 129 101 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 215 72 33 76 37 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 210 117 80 54 5 pint:PI0910|5end_possible_sodium_hydrogen_antiporter_(Na+/H+_antiporter)_838085..838315_POSITIVE 208 117 71 86 42 pint:PI1172|5end_sensor_histidine_kinase_1091850..1092080_POSITIVE 208 117 94 210 186 pint:PI0343|5end_hypothetical_protein_317505..317735_POSITIVE 208 106 70 231 188 pint:PI0098|5end_conserved_hypothetical_protein_(possible_glycosyl/glycerophosphate_transferase)_94622..94852_POSITIVE 205 39 7 117 80 pint:PI0281|5end_conserved_hypothetical_protein_266309..266539_POSITIVE 200 120 79 66 10 pint:PI0434|5end_possible_beta-lactamase_405692..405922_POSITIVE 194 112 79 28 1 pint:PI0576|5end_helicase,_UvrD/Rep_520226..520456_POSITIVE 189 115 81 190 141 pint:PI0955|5end_conserved_hypothetical_protein_884736..884966_POSITIVE 188 113 88 224 198 pint:PI1510|5end_cell_division_protein_1428412..1428642_POSITIVE 188 113 86 88 61 pint:PI0185|5end_conserved_hypothetical_protein_176992..177222_POSITIVE 184 113 78 90 60 pint:PI2113|5end_hypothetical_protein_2063794..2064024_POSITIVE 184 113 78 31 1 pint:PI2114|5end_conserved_hypothetical_protein_2063735..2063965_POSITIVE 184 113 79 156 117 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 184 60 11 200 155 pint:PI0283|5end_Zn-dependent_peptidase_267554..267784_POSITIVE 180 69 29 182 147 pint:PI1226|5end_hypothetical_protein_1147884..1148114_POSITIVE 180 69 29 56 21 pint:PI1225|5end_hypothetical_protein_1147758..1147988_POSITIVE 180 110 64 214 165 pint:PI0838|5end_DNA_replication_and_repair_protein_772699..772929_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 218 100 68 123 95 pint:PI0336|3end_hypothetical_protein_314806..314956_POSITIVE 205 39 7 102 65 pint:PI0280|3end_conserved_hypothetical_protein_266374..266524_POSITIVE 196 110 61 144 99 pint:PI0438|3end_elongation_factor_Tu_410304..410454_POSITIVE 194 112 81 149 115 pint:PI1791|3end_conserved_hypothetical_protein_1724241..1724391_POSITIVE 192 115 81 43 9 pint:PI0286|3end_ISPg3-related_transposase_272065..272215_POSITIVE 189 115 81 149 100 pint:PI0952|3end_conserved_hypothetical_protein_884775..884925_POSITIVE 188 106 64 134 87 pint:PI1021|3end_conserved_hypothetical_protein;_possible_methyltransferase_939634..939784_POSITIVE 186 120 81 132 91 pint:PI1800|3end_hypothetical_protein_1733901..1734051_POSITIVE 186 120 81 50 9 pint:PI1799|3end_30S_ribosomal_protein_S2_1733819..1733969_POSITIVE 184 113 79 143 104 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 180 69 29 151 116 pint:PI1225|3end_hypothetical_protein_1147933..1148083_POSITIVE 180 110 64 116 67 pint:PI0837|3end_conserved_hypothetical_protein_772681..772831_POSITIVE 180 110 63 141 90 pint:PI0473|3end_30S_ribosomal_protein_S14_439013..439163_POSITIVE 178 112 73 134 84 pint:PI1210|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_(SAICAR_synthetase)_1129959..1130109_POSITIVE 177 108 65 81 28 pint:PI0611|3end_hypothetical_protein_559901..560051_POSITIVE 172 115 71 115 71 pint:PI0802|3end_hypothetical_protein_739827..739977_POSITIVE 171 115 94 54 29 pint:PI2035|3end_Holliday_junction_DNA_helicase_ruvB_1989323..1989473_POSITIVE 171 114 84 37 7 pint:PI1428|3end_quinolinate_synthetase_A_1347695..1347845_POSITIVE 170 120 80 69 25 pint:PI1134|3end_ABC_transporter,_ATP-binding_protein_1062073..1062223_POSITIVE 167 77 33 133 95 pint:PI1001|3end_hypothetical_protein_923922..924072_POSITIVE