Origin IGS: atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagatatagatattagacaagaggaagcga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcgcttcctcttgtctaatatctatatctagtatatcaaaaaaagctagatttctctagctgtgactttttatgttatacttattgcaagagaaaaaacgaggagatggat Mask Tandem Repeat Region ================================================ atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagatatagatattagacaagaggaagcga Find is-nt database================================================ Query_seq: SMT_978:SMT_979|SMT_978:SMT_979:hypothetical protein:K03709 Mn-dependent transcriptional regulator:<-->:926698..926808 111 atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagatatagatattagacaagaggaagcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_978:SMT_979|SMT_978:SMT_979:hypothetical protein:K03709 Mn-dependent transcriptional regulator:<-->:926698..926808 111 atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagatatagatattagacaagaggaagcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_978:SMT_979|SMT_978:SMT_979:hypothetical protein:K03709 Mn-dependent transcriptional regulator:<-->:926698..926808 111 atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagatatagatattagacaagaggaagcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagatatagatattagacaagaggaagcga Predict ORF larger than 30AA ================================================ atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagatatagatattagacaagaggaagcga 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: 81 Start: 53 End: 82 ....................................................CTAGAGAAATCTAGCTTTTTTTGATATACT............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagatatagatattagacaagaggaagcga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -7.6 Tail_Score: -5.59357 Start: 52 End: 67 Full_Region: ACATAAAAAGTCACA GCTAGA GAAA TCTAGC TTTTTTTGATATACT ...................................................GCTAGAGAAATCTAGC............................................ Find igs database================================================ Query_seq: SMT_978:SMT_979|SMT_978:SMT_979:hypothetical protein:K03709 Mn-dependent transcriptional regulator:<-->:926698..926808 111 atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagatatagatattagacaagaggaagcga Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: smit_SMT_978_SMT_979|hypothetical protein:K03709 Mn-dependent transcriptional regulator|NEGATIVE:POSITIVE|[926698,926808]|111 HSP 1 e-value: 2.0E-44 bit: 178.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagcnnnnnnngatatactagatatagatattagacaagaggaagcga atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagatatagatattagacaagaggaagcga Inter-species Hit: Count: 3 Min: 1 Max: 107 Len: 107 Subject: NC_008533_SPD_1449_SPD_1450|hypothetical protein:iron-dependent transcriptional regulator|NEGATIVE:POSITIVE|[1466093,1466203]|111 HSP 1 e-value: 1.0E-39 bit: 163.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagcnnnnnnngatatactagatatagatattagacaagaggaa.... atccatctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagataaagatattagacaagaggaa.... Subject: NC_003098_spr1479_spr1480|hypothetical protein:Metalloregulator|NEGATIVE:POSITIVE|[1458568, 1458672]|105 HSP 1 e-value: 5.0E-36 bit: 151.0 Len: 101 Query Start:7 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 ......ctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagcnnnnnnngatatactagatatagatattagacaagaggaa.... ......ctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagataaagatattagacaagaggaa.... Subject: NC_003028_SP_1637_SP_1638|hypothetical protein:iron-dependent transcriptional regulator|NEGATIVE:POSITIVE|[1537244,1537348]|105 HSP 1 e-value: 5.0E-36 bit: 151.0 Len: 101 Query Start:7 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 ......ctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagcnnnnnnngatatactagatatagatattagacaagaggaa.... ......ctcctcgttttttctcttgcaataagtataacataaaaagtcacagctagagaaatctagctttttttgatatactagataaagatattagacaagaggaa.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCAUCUCCUCGUUUUUUCUCUUGCAAUAAGUAUAACAUAAAAAGUCACAGCUAGAGAAAUCUAGCUUUUUUUGAUAUACUAGAUAUAGAUAUUAGACAAGAGGAA .......(((((((((..(.(((.......((((((.((.((((......(((((((....))))))))))).)).))))))......))).)..))))..))))). (-25.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUCUUGUCUAAUAUCUAUAUCUAGUAUAUCAAAAAAAGCUAGAUUUCUCUAGCUGUGACUUUUUAUGUUAUACUUAUUGCAAGAGAAAAAACGAGGAGAUGGAU .(((((((.((..........(((((((............)))))))((((((.((((((((.......))))))......)).)))))).....)).)))).))). (-25.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 779 50 1 141 92 smit:SMT_978|5end_hypothetical_protein_926607..926837_NEGATIVE 294 67 25 65 21 smit:SMT_1498|5end_transcriptional_regulator,_LytR_family_1481958..1482188_POSITIVE 274 35 3 91 58 smit:SMT_1345|5end_K06198_competence_protein_CoiA_1323770..1324000_NEGATIVE 261 100 62 184 143 smit:SMT_1518|5end_sensor_histidine_kinase_1499009..1499239_NEGATIVE 231 77 42 77 32 smit:SMT_1722|5end_x-prolyl-dipeptidyl_aminopeptidase_1707529..1707759_POSITIVE 225 50 1 100 48 smit:SMT_713|5end_heat_shock_protein_HtpX_620888..621118_NEGATIVE 225 50 1 100 48 smit:SMT_695|5end_heat_shock_protein_HtpX_606883..607113_NEGATIVE 223 26 3 28 1 smit:SMT_1103|5end_hypothetical_protein_1045744..1045974_NEGATIVE 216 88 43 163 121 smit:SMT_1848|5end_K03458_nucleobase:cation_symporter-2,_NCS2_family_1813014..1813244_NEGATIVE 214 46 2 143 96 smit:SMT_92|5end_GTP-binding_protein,_probable_translation_factor_22857..23087_POSITIVE 213 85 43 49 2 smit:SMT_1350|5end_multidrug_resistance_efflux_pump_1329225..1329455_NEGATIVE 206 49 4 166 128 smit:SMT_1376|5end_tetrapyrrole_(corrin/porphyrin)_methylase_family_protein_1355553..1355783_NEGATIVE 203 49 10 150 111 smit:SMT_413|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_356677..356907_POSITIVE 197 49 2 169 120 smit:SMT_358|5end_hypothetical_protein_293947..294177_POSITIVE 194 57 11 144 88 smit:SMT_1495|5end_hypothetical_protein_1480271..1480501_POSITIVE 193 46 3 69 31 smit:SMT_725|5end_hypothetical_protein_630415..630645_NEGATIVE 193 49 1 48 5 smit:SMT_103|5end_adenylosuccinate_synthetase_40766..40996_POSITIVE 191 78 31 231 180 smit:SMT_1359|5end_dihydroorotate_dehydrogenase_electron_transfer_subunit_1338003..1338233_NEGATIVE 189 38 5 215 172 smit:SMT_1827|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1797568..1797798_POSITIVE 189 38 5 55 12 smit:SMT_1826|5end_ATP_synthase_beta_chain_1797408..1797638_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 67 25 57 13 smit:SMT_1497|3end_acetyltransferase,_GNAT_family_1482030..1482180_POSITIVE 258 98 51 95 46 smit:SMT_1716|3end_hypothetical_protein_1703657..1703807_POSITIVE 234 72 31 101 53 smit:SMT_1217|3end_hypothetical_protein_1176166..1176316_NEGATIVE 231 77 42 53 8 smit:SMT_1721|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1707585..1707735_POSITIVE 226 77 53 146 120 smit:SMT_1504|3end_topology_modulation_protein_1487808..1487958_POSITIVE 225 50 1 98 46 smit:SMT_714|3end_hypothetical_protein_predicted_by_Glimmer/Critica_620890..621040_NEGATIVE 225 50 1 98 46 smit:SMT_696|3end_K03744_LemA_protein_606885..607035_NEGATIVE 218 71 38 45 12 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE 214 46 2 58 11 smit:SMT_91|3end_hypothetical_protein_22852..23002_POSITIVE 201 23 6 87 70 smit:SMT_1648|3end_hypothetical_protein_1634883..1635033_POSITIVE 193 46 3 72 34 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 192 86 41 91 44 smit:SMT_1223|3end_pneumococcal_surface_protein_A_1187151..1187301_NEGATIVE 192 80 37 70 29 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 188 83 45 50 12 smit:SMT_1030|3end_alpha-galactosidase_965667..965817_NEGATIVE 188 30 2 62 28 smit:SMT_925|3end_DNA-directed_RNA_polymerase_omega_chain_879969..880119_NEGATIVE 186 84 50 149 117 smit:SMT_1742|3end_sodium-dependent_phosphate_transporter_1724991..1725141_POSITIVE 186 70 24 123 78 smit:SMT_808|3end_hypothetical_protein_predicted_by_Glimmer/Critica_717897..718047_NEGATIVE 185 58 11 70 18 smit:SMT_1541|3end_isopentenyl-diphosphate_delta-isomerase_1525083..1525233_NEGATIVE 184 66 46 135 113 smit:SMT_960|3end_putative_esterase_906126..906276_NEGATIVE 183 98 52 80 32 smit:SMT_1854|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1818952..1819102_POSITIVE