Origin IGS: tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt .........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 aaaactatgttatgttgatttaaagtagcgcaaagttaagactttttagagtataaacaaaattcttggcttttaaatcttgctaaaacttgaaatttatgcgttttttatgtgatatttaacacttagaacgctatttgagctatttgcattccttctttcgtttcagcgaaatatcta Mask Tandem Repeat Region ================================================ tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt Find is-nt database================================================ Query_seq: PI1586:PI1587|PI1586:PI1587:possible HesA/MoeB/ThiF family protein:conserved hypothetical protein; possible permease:->->:1515244..1515423 180 tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1586:PI1587|PI1586:PI1587:possible HesA/MoeB/ThiF family protein:conserved hypothetical protein; possible permease:->->:1515244..1515423 180 tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1586:PI1587|PI1586:PI1587:possible HesA/MoeB/ThiF family protein:conserved hypothetical protein; possible permease:->->:1515244..1515423 180 tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt Predict ORF larger than 30AA ================================================ tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt 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================================================ tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1586:PI1587|PI1586:PI1587:possible HesA/MoeB/ThiF family protein:conserved hypothetical protein; possible permease:->->:1515244..1515423 180 tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: pint_PI1586_PI1587|possible HesA/MoeB/ThiF family protein:conserved hypothetical protein; possible permease|POSITIVE:POSITIVE|[1515244,1515423]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt tagatatttcgctgaaacgaaagaaggaatgcaaatagctcaaatagcgttctaagtgttaaatatcacataaaaaacgcataaatttcaagttttagcaagatttaaaagccaagaattttgtttatactctaaaaagtcttaactttgcgctactttaaatcaacataacatagtttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUAUUUCGCUGAAACGAAAGAAGGAAUGCAAAUAGCUCAAAUAGCGUUCUAAGUGUUAAAUAUCACAUAAAAAACGCAUAAAUUUCAAGUUUUAGCAAGAUUUAAAAGCCAAGAAUUUUGUUUAUACUCUAAAAAGUCUUAACUUUGCGCUACUUUAAAUCAACAUAACAUAGUUUU ..........((((((((....((((..((((.....(((.....))).......(((........))).........))))...))))..))))))))..(((((((((((((((......(((...(((......)))...))))))).)))..))))))))................ (-30.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACUAUGUUAUGUUGAUUUAAAGUAGCGCAAAGUUAAGACUUUUUAGAGUAUAAACAAAAUUCUUGGCUUUUAAAUCUUGCUAAAACUUGAAAUUUAUGCGUUUUUUAUGUGAUAUUUAACACUUAGAACGCUAUUUGAGCUAUUUGCAUUCCUUCUUUCGUUUCAGCGAAAUAUCUA ........(..((((.......(((((((.((((.(((((((((....)))).............(((((...........)))))..))))).......(((((((....(((........)))..)))))))..)))).)))))))))))..)...((((((....))))))...... (-30.31) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 60 11 54 2 pint:PI2169|5end_hypothetical_protein_2111706..2111936_POSITIVE 269 50 9 156 121 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 252 51 11 107 67 pint:PI0628|5end_phosphoribosylglycinamide_formyltransferase_576027..576257_POSITIVE 236 159 120 136 96 pint:PI0632|5end_NusB_family_protein_(N_utilization_substance_protein_B)_578476..578706_POSITIVE 231 153 111 229 191 pint:PI1082|5end_polypeptide_deformylase_1001282..1001512_POSITIVE 229 60 11 122 79 pint:PI1006|5end_conserved_hypothetical_protein_926604..926834_POSITIVE 223 53 11 225 192 pint:PI2109|5end_surface_antigen_BspA_2060553..2060783_POSITIVE 223 48 1 189 138 pint:PI1201|5end_peptidyl-arginine_deiminase_1116598..1116828_POSITIVE 223 118 79 72 32 pint:PI1032|5end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_948463..948693_POSITIVE 222 47 7 101 55 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 220 58 19 51 6 pint:PI1574|5end_conserved_hypothetical_protein_1500325..1500555_POSITIVE 220 60 22 201 161 pint:PI0777|5end_predicted_TPR-repeat-containing_protein_713285..713515_POSITIVE 219 49 6 183 143 pint:PI0198|5end_hypothetical_protein_190719..190949_POSITIVE 216 58 11 148 102 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 216 53 11 229 175 pint:PI0025|5end_two_component_system_sensor_histidine_kinase_28682..28912_POSITIVE 215 154 111 195 157 pint:PI0246|5end_conserved_hypothetical_protein_244166..244396_POSITIVE 214 70 30 55 14 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 214 49 6 65 20 pint:PI2027|5end_arginine_decarboxylase_1980161..1980391_POSITIVE 214 50 7 200 151 pint:PI1898|5end_S-adenosyl-methyltransferase_1841288..1841518_POSITIVE 213 53 11 136 90 pint:PI2146|5end_prolipoprotein_diacylglyceryl_transferase_2092402..2092632_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 49 11 150 107 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 252 51 11 81 41 pint:PI0627|3end_conserved_hypothetical_protein_576081..576231_POSITIVE 242 59 22 121 90 pint:PI1695|3end_hypothetical_protein_1610310..1610460_POSITIVE 225 166 121 67 20 pint:PI0429|3end_hypothetical_protein_399602..399752_POSITIVE 223 48 1 113 62 pint:PI1200|3end_carbon-nitrogen_hydrolase/beta-alanine_synthase_1116602..1116752_POSITIVE 218 49 5 57 13 pint:PI0594|3end_possible_rare_lipoprotein_A_545157..545307_POSITIVE 217 48 5 140 110 pint:PI0776|3end_predicted_TPR-repeat-containing_protein_713323..713473_POSITIVE 216 118 89 36 10 pint:PI1031|3end_hypothetical_protein_948507..948657_POSITIVE 216 58 11 139 93 pint:PI0929|3end_copper_homeostasis_protein_861048..861198_POSITIVE 214 50 7 67 18 pint:PI1897|3end_conserved_hypothetical_protein_1841235..1841385_POSITIVE 208 59 22 117 84 pint:PI0914|3end_ATPase,_AAA_family_844992..845142_POSITIVE 205 44 1 144 103 pint:PI0727|3end_integrase_660492..660642_POSITIVE 204 60 12 59 8 pint:PI1827|3end_peptidase,_M23/M37_family,_N-terminal_1768602..1768752_POSITIVE 204 59 13 41 2 pint:PI0894|3end_2-oxoglutarate_oxidoreductase,_gamma_subunit_(2-oxoglutarate-ferredoxin_oxidoreductase)_826350..826500_POSITIVE 203 70 25 128 86 pint:PI1284|3end_ATP_synthase,_delta_subunit_1200323..1200473_POSITIVE 203 50 10 79 29 pint:PI0107|3end_2-methylthioadenine_synthetase_104652..104802_POSITIVE 202 46 2 115 68 pint:PI0782|3end_beta-lactamase_induction_signal_transducer,_AmpG_protein_721927..722077_POSITIVE 201 168 121 135 84 pint:PI1165|3end_hypothetical_protein_1089636..1089786_POSITIVE 200 39 10 61 33 pint:PI1465|3end_conserved_hypothetical_protein_1392017..1392167_POSITIVE 200 49 11 90 58 pint:PI0553|3end_recombination_protein_504383..504533_POSITIVE