Origin IGS: tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatagaaaaatcaaagtttgaaggctatgtatctagcagtcaggctttgattttttacagtctgcaatagattttcatcccttatttgtggtataatggaacgatacgatagaaagaata Mask Tandem Repeat Region ================================================ tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc Find is-nt database================================================ Query_seq: SMT_746:SMT_747|SMT_746:SMT_747:LPS biosynthesis protein:transcriptional regulator, LytR family:<-<-:651313..651432 120 tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_746:SMT_747|SMT_746:SMT_747:LPS biosynthesis protein:transcriptional regulator, LytR family:<-<-:651313..651432 120 tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_746:SMT_747|SMT_746:SMT_747:LPS biosynthesis protein:transcriptional regulator, LytR family:<-<-:651313..651432 120 tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc Predict ORF larger than 30AA ================================================ tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc 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================================================ tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_746:SMT_747|SMT_746:SMT_747:LPS biosynthesis protein:transcriptional regulator, LytR family:<-<-:651313..651432 120 tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: smit_SMT_746_SMT_747|LPS biosynthesis protein:transcriptional regulator, LytR family|NEGATIVE:NEGATIVE|[651313,651432]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttctatc Inter-species Hit: Count: 3 Min: 1 Max: 117 Len: 117 Subject: NC_003028_SP_1367_SP_1368|licD3 protein:psr protein|NEGATIVE:NEGATIVE|[1290910,1291187]|278 HSP 1 e-value: 6.0E-39 bit: 161.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttct... tattctttctatcgtatcgtttcattataccacaaacaaggggtgaaaatctattgcagactgtaaaaaatcaaagcctgactgctatccaaatagctatcaaactttgatttttct... Subject: NC_008533_SPD_1201_SPD_1202|phosphotransferase LicD3:Psr protein|NEGATIVE:NEGATIVE|[1231002,1231279]|278 HSP 1 e-value: 2.0E-36 bit: 153.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttct... tattctttctatcgtatcgtttcattataccacaaacaaggggtgaaaatctattgcagactgtaaaaaatcaaagcctgactactatccaaatagctatcaaactttgatttttct... Subject: NC_003098_spr1225_spr1226|LicD1 paralog:hypothetical protein|NEGATIVE:NEGATIVE|[1223471,1223748]|278 HSP 1 e-value: 2.0E-36 bit: 153.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 tattctttctatcgtatcgttccattataccacaaataagggatgaaaatctattgcagactgtaaaaaatcaaagcctgactgctagatacatagccttcaaactttgatttttct... tattctttctatcgtatcgtttcattataccacaaacaaggggtgaaaatctattgcagactgtaaaaaatcaaagcctgactactatccaaatagctatcaaactttgatttttct... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUCUUUCUAUCGUAUCGUUCCAUUAUACCACAAAUAAGGGAUGAAAAUCUAUUGCAGACUGUAAAAAAUCAAAGCCUGACUGCUAGAUACAUAGCCUUCAAACUUUGAUUUUUCU ................(((((((.((((.......)))))))))))...................(((((((((((..(((..((((......))))..)))..))))))))))).. (-24.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAAAUCAAAGUUUGAAGGCUAUGUAUCUAGCAGUCAGGCUUUGAUUUUUUACAGUCUGCAAUAGAUUUUCAUCCCUUAUUUGUGGUAUAAUGGAACGAUACGAUAGAAAGAAUA .(((((((((((((((((..((((......))))..)))))))))))))))))..((((((...)))))).......(((.(((((.((((.........)))).)))))))).... (-31.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 865 100 51 191 142 smit:SMT_746|5end_LPS_biosynthesis_protein_651222..651452_NEGATIVE 276 110 70 50 17 smit:SMT_754|5end_3-dehydroquinate_synthase_659044..659274_NEGATIVE 266 49 3 151 99 smit:SMT_1560|5end_DNA_polymerase_III_alpha_subunit_1548612..1548842_NEGATIVE 264 110 79 140 106 smit:SMT_465|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_protein_403244..403474_POSITIVE 264 110 79 140 106 smit:SMT_417|5end_short_chain_dehydrogenase_360373..360603_POSITIVE 248 50 2 140 95 smit:SMT_1087|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_1024165..1024395_NEGATIVE 245 90 46 168 124 smit:SMT_825|5end_aspartate_aminotransferase_749594..749824_NEGATIVE 241 99 57 178 126 smit:SMT_1773|5end_hypothetical_protein_1749241..1749471_POSITIVE 239 43 3 145 98 smit:SMT_838|5end_cation_efflux_family_protein_782924..783154_POSITIVE 238 60 12 143 88 smit:SMT_485|5end_hypothetical_protein_421401..421631_NEGATIVE 237 110 68 63 3 smit:SMT_618|5end_methionine_aminopeptidase_526697..526927_POSITIVE 236 101 73 37 5 smit:SMT_1292|5end_K02050_sulfonate/nitrate/taurine_transport_system_permease_protein_1254179..1254409_POSITIVE 233 107 75 109 71 smit:SMT_1673|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1659831..1660061_POSITIVE 231 62 22 129 88 smit:SMT_1712|5end_excinuclease_ABC_subunit_A_1700351..1700581_NEGATIVE 228 98 57 94 52 smit:SMT_1709|5end_aminopeptidase_P_1695450..1695680_NEGATIVE 225 43 8 125 91 smit:SMT_1513|5end_hypothetical_protein_1495582..1495812_NEGATIVE 225 110 73 77 46 smit:SMT_1446|5end_pneumococcal_vaccine_antigen_A_1429610..1429840_NEGATIVE 223 110 61 187 127 smit:SMT_1506|5end_Cl-channel,_voltage-gated_family_protein_1489986..1490216_NEGATIVE 217 98 58 45 5 smit:SMT_1080|5end_CAAX_amino_terminal_protease_family_protein_1018490..1018720_NEGATIVE 217 97 56 77 42 smit:SMT_274|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_215221..215451_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 110 75 31 1 smit:SMT_755|3end_shikimate_5-dehydrogenase_659063..659213_NEGATIVE 264 110 79 119 85 smit:SMT_464|3end_ribonuclease_Z_403303..403453_POSITIVE 264 110 79 119 85 smit:SMT_416|3end_ribonuclease_Z_360432..360582_POSITIVE 238 60 12 84 29 smit:SMT_486|3end_hypothetical_protein_421460..421610_NEGATIVE 236 101 73 74 42 smit:SMT_1291|3end_hypothetical_protein_1254296..1254446_POSITIVE 226 48 2 151 108 smit:SMT_1088|3end_hypothetical_protein_1024152..1024302_NEGATIVE 225 109 71 147 101 smit:SMT_2133|3end_hypothetical_protein_2013720..2013870_NEGATIVE 225 110 73 77 46 smit:SMT_1447|3end_hypothetical_protein_1429610..1429760_NEGATIVE 225 109 71 147 101 smit:SMT_872|3end_hypothetical_protein_820331..820481_NEGATIVE 225 109 71 147 101 smit:SMT_385|3end_hypothetical_protein_320262..320412_POSITIVE 221 88 55 64 24 smit:SMT_316|3end_acetyl-CoA_carboxylase_carboxyl_transferase_subunit_alpha_257391..257541_POSITIVE 213 98 52 71 19 smit:SMT_777|3end_hypothetical_protein_686618..686768_NEGATIVE 211 106 85 23 4 smit:SMT_1457|3end_16S_rRNA_m(2)G_1207_methyltransferase_1439829..1439979_NEGATIVE 210 98 61 148 99 smit:SMT_1589|3end_hypothetical_protein_1578606..1578756_POSITIVE 207 108 71 67 32 smit:SMT_1317|3end_glycosyltransferase_1283587..1283737_POSITIVE 205 107 71 92 53 smit:SMT_1483|3end_GTP-binding_protein_1463140..1463290_NEGATIVE 204 101 61 139 96 smit:SMT_424|3end_transcriptional_regulatory_protein_368108..368258_POSITIVE 200 88 48 89 43 smit:SMT_1358|3end_dihydroorotate_dehydrogenase_B_1336254..1336404_NEGATIVE 200 90 49 80 30 smit:SMT_679|3end_LicC_protein_588383..588533_NEGATIVE 199 108 71 74 43 smit:SMT_1161|3end_K05837_rod_shape_determining_protein_RodA_1105185..1105335_NEGATIVE